From 3367a408b25efd4f720dd600e894e10269020013 Mon Sep 17 00:00:00 2001 From: Andrew Schultz Date: Thu, 8 Nov 2018 12:03:24 -0500 Subject: [PATCH 001/469] Add single2 method to Pair that can compute and return the Hessian matrix --- src/pair.cpp | 14 +++++++++++++- src/pair.h | 14 ++++++++++---- src/pair_lj_smooth_linear.cpp | 27 +++++++++++++++++++++++++-- src/pair_lj_smooth_linear.h | 1 + 4 files changed, 49 insertions(+), 7 deletions(-) diff --git a/src/pair.cpp b/src/pair.cpp index 18d561bdb5..f76bb54c36 100644 --- a/src/pair.cpp +++ b/src/pair.cpp @@ -301,7 +301,7 @@ void Pair::init_style() specific pair style can override this function ------------------------------------------------------------------------- */ -void Pair::init_list(int /*which*/, NeighList *ptr) +void Pair::init_list(int which, NeighList *ptr) { list = ptr; } @@ -1740,6 +1740,18 @@ void Pair::init_bitmap(double inner, double outer, int ntablebits, /* ---------------------------------------------------------------------- */ +void Pair::pairTensor(double fforce, double dfac, double delr[3], double phiTensor[6]) { + int m = 0; + for (int k=0; k<3; k++) { + phiTensor[m] = fforce; + for (int l=k; l<3; l++) { + if (l>k) phiTensor[m] = 0; + phiTensor[m++] += delr[k]*delr[l] * dfac; + } + } +} +/* ---------------------------------------------------------------------- */ + double Pair::memory_usage() { double bytes = comm->nthreads*maxeatom * sizeof(double); diff --git a/src/pair.h b/src/pair.h index c1a9e6eef8..a9506480be 100644 --- a/src/pair.h +++ b/src/pair.h @@ -145,6 +145,16 @@ class Pair : protected Pointers { return 0.0; } + void pairTensor(double fforce, double dfac, double delr[3], double phiTensor[6]); + + virtual double single2(int, int, int, int, + double, double[3], double, double, + double& fforce, double d2u[6]) { + fforce = 0.0; + for (int i=0; i<6; i++) d2u[i] = 0; + return 0.0; + } + virtual void settings(int, char **) = 0; virtual void coeff(int, char **) = 0; @@ -207,10 +217,6 @@ class Pair : protected Pointers { typedef union {int i; float f;} union_int_float_t; - // Accessor for the user-intel package to determine virial calc for hybrid - - inline int fdotr_is_set() const { return vflag_fdotr; } - protected: int vflag_fdotr; int maxeatom,maxvatom; diff --git a/src/pair_lj_smooth_linear.cpp b/src/pair_lj_smooth_linear.cpp index 17c789bcee..4cf8d6d3db 100644 --- a/src/pair_lj_smooth_linear.cpp +++ b/src/pair_lj_smooth_linear.cpp @@ -326,9 +326,9 @@ void PairLJSmoothLinear::read_restart_settings(FILE *fp) /* ---------------------------------------------------------------------- */ -double PairLJSmoothLinear::single(int /*i*/, int /*j*/, int itype, int jtype, +double PairLJSmoothLinear::single(int i, int j, int itype, int jtype, double rsq, - double /*factor_coul*/, double factor_lj, + double factor_coul, double factor_lj, double &fforce) { double r2inv,r6inv,forcelj,philj,r,rinv; @@ -347,3 +347,26 @@ double PairLJSmoothLinear::single(int /*i*/, int /*j*/, int itype, int jtype, return factor_lj*philj; } + +double PairLJSmoothLinear::single2(int i, int j, int itype, int jtype, double rsq, + double delr[3], double factor_coul, double factor_lj, + double &fforce, double d2u[6]) +{ + double r2inv,r6inv,forcelj,philj,r,rinv; + + r2inv = 1.0/rsq; + r6inv = r2inv*r2inv*r2inv; + rinv = sqrt(r2inv); + r = sqrt(rsq); + forcelj = r6inv*(lj1[itype][jtype]*r6inv-lj2[itype][jtype]); + forcelj = rinv*forcelj - dljcut[itype][jtype]; + fforce = factor_lj*forcelj*rinv; + + philj = r6inv*(lj3[itype][jtype]*r6inv-lj4[itype][jtype]); + philj = philj - ljcut[itype][jtype] + + (r-cut[itype][jtype])*dljcut[itype][jtype]; + + double d2r = factor_lj * r6inv * (13.0*lj1[itype][jtype]*r6inv - 7.0*lj2[itype][jtype])/rsq; + pairTensor(fforce, -(fforce + d2r) / rsq, delr, d2u); + return factor_lj*philj; +} diff --git a/src/pair_lj_smooth_linear.h b/src/pair_lj_smooth_linear.h index c18c442a18..9cee9f2951 100644 --- a/src/pair_lj_smooth_linear.h +++ b/src/pair_lj_smooth_linear.h @@ -38,6 +38,7 @@ class PairLJSmoothLinear : public Pair { void write_restart_settings(FILE *); void read_restart_settings(FILE *); double single(int, int, int, int, double, double, double, double &); + double single2(int, int, int, int, double, double[3], double, double, double&, double[6]); protected: double cut_global; -- GitLab From 29cd4eb5b6584d62dfc331ad9e58343264334b62 Mon Sep 17 00:00:00 2001 From: Andrew Schultz Date: Thu, 8 Nov 2018 12:03:51 -0500 Subject: [PATCH 002/469] Add HMA compute --- doc/src/compute.txt | 71 +----- doc/src/compute_hma.txt | 147 +++++++++++++ doc/src/computes.txt | 9 +- src/compute_hma.cpp | 470 ++++++++++++++++++++++++++++++++++++++++ src/compute_hma.h | 66 ++++++ 5 files changed, 689 insertions(+), 74 deletions(-) create mode 100644 doc/src/compute_hma.txt create mode 100644 src/compute_hma.cpp create mode 100644 src/compute_hma.h diff --git a/doc/src/compute.txt b/doc/src/compute.txt index 857795ffe5..676c00d7a5 100644 --- a/doc/src/compute.txt +++ b/doc/src/compute.txt @@ -173,65 +173,43 @@ There are also additional accelerated compute styles included in the LAMMPS distribution for faster performance on CPUs, GPUs, and KNLs. The individual style names on the "Commands compute"_Commands_compute.html doc page are followed by one or more of -(g,i,k,o,t) to indicate which accelerated styles exist. +(g,i,k,o,t) to indicate which accerlerated styles exist. -"ackland/atom"_compute_ackland_atom.html - "aggregate/atom"_compute_cluster_atom.html - aggregate ID for each atom -"angle"_compute_angle.html - -"angle/local"_compute_angle_local.html - "angle/local"_compute_bond_local.html - theta and energy of each angle "angmom/chunk"_compute_angmom_chunk.html - angular momentum for each chunk -"basal/atom"_compute_basal_atom.html - "body/local"_compute_body_local.html - attributes of body sub-particles "bond"_compute_bond.html - values computed by a bond style "bond/local"_compute_bond_local.html - distance and energy of each bond "centro/atom"_compute_centro_atom.html - centro-symmetry parameter for each atom "chunk/atom"_compute_chunk_atom.html - assign chunk IDs to each atom -"chunk/spread/atom"_compute_chunk_spread_atom.html - spreads chunk values to each atom in chunk "cluster/atom"_compute_cluster_atom.html - cluster ID for each atom "cna/atom"_compute_cna_atom.html - common neighbor analysis (CNA) for each atom -"cnp/atom"_compute_cnp_atom.html - "com"_compute_com.html - center-of-mass of group of atoms "com/chunk"_compute_com_chunk.html - center-of-mass for each chunk "contact/atom"_compute_contact_atom.html - contact count for each spherical particle "coord/atom"_compute_coord_atom.html - coordination number for each atom "damage/atom"_compute_damage_atom.html - Peridynamic damage for each atom -"dihedral"_compute_dihedral.html - "dihedral/local"_compute_dihedral_local.html - angle of each dihedral "dilatation/atom"_compute_dilatation_atom.html - Peridynamic dilatation for each atom -"dipole/chunk"_compute_dipole_chunk.html - "displace/atom"_compute_displace_atom.html - displacement of each atom -"dpd"_compute_dpd.html - -"dpd/atom"_compute_dpd_atom.html - -"edpd/temp/atom"_compute_edpd_temp_atom.html - -"entropy/atom"_compute_entropy_atom.html - "erotate/asphere"_compute_erotate_asphere.html - rotational energy of aspherical particles "erotate/rigid"_compute_erotate_rigid.html - rotational energy of rigid bodies "erotate/sphere"_compute_erotate_sphere.html - rotational energy of spherical particles "erotate/sphere/atom"_compute_erotate_sphere.html - rotational energy for each spherical particle -"erotate/sphere/atom"_compute_erotate_sphere_atom.html - "event/displace"_compute_event_displace.html - detect event on atom displacement -"fep"_compute_fep.html - -"force/tally"_compute_tally.html - "fragment/atom"_compute_cluster_atom.html - fragment ID for each atom -"global/atom"_compute_global_atom.html - "group/group"_compute_group_group.html - energy/force between two groups of atoms "gyration"_compute_gyration.html - radius of gyration of group of atoms "gyration/chunk"_compute_gyration_chunk.html - radius of gyration for each chunk "heat/flux"_compute_heat_flux.html - heat flux through a group of atoms -"heat/flux/tally"_compute_tally.html - "hexorder/atom"_compute_hexorder_atom.html - bond orientational order parameter q6 -"improper"_compute_improper.html - +"hma"_compute_hma.html - harmonically mapped averaging for atomic crystals "improper/local"_compute_improper_local.html - angle of each improper "inertia/chunk"_compute_inertia_chunk.html - inertia tensor for each chunk "ke"_compute_ke.html - translational kinetic energy "ke/atom"_compute_ke_atom.html - kinetic energy for each atom -"ke/atom/eff"_compute_ke_atom_eff.html - -"ke/eff"_compute_ke_eff.html - "ke/rigid"_compute_ke_rigid.html - translational kinetic energy of rigid bodies -"meso/e/atom"_compute_meso_e_atom.html - -"meso/rho/atom"_compute_meso_rho_atom.html - -"meso/t/atom"_compute_meso_t_atom.html - "msd"_compute_msd.html - mean-squared displacement of group of atoms "msd/chunk"_compute_msd_chunk.html - mean-squared displacement for each chunk "msd/nongauss"_compute_msd_nongauss.html - MSD and non-Gaussian parameter of group of atoms @@ -241,77 +219,36 @@ compute"_Commands_compute.html doc page are followed by one or more of "pair/local"_compute_pair_local.html - distance/energy/force of each pairwise interaction "pe"_compute_pe.html - potential energy "pe/atom"_compute_pe_atom.html - potential energy for each atom -"pe/mol/tally"_compute_tally.html - -"pe/tally"_compute_tally.html - "plasticity/atom"_compute_plasticity_atom.html - Peridynamic plasticity for each atom "pressure"_compute_pressure.html - total pressure and pressure tensor -"pressure/cylinder"_compute_pressure_cylinder.html - -"pressure/uef"_compute_pressure_uef.html - "property/atom"_compute_property_atom.html - convert atom attributes to per-atom vectors/arrays -"property/chunk"_compute_property_chunk.html - extract various per-chunk attributes "property/local"_compute_property_local.html - convert local attributes to localvectors/arrays -"ptm/atom"_compute_ptm_atom.html - +"property/chunk"_compute_property_chunk.html - extract various per-chunk attributes "rdf"_compute_rdf.html - radial distribution function g(r) histogram of group of atoms "reduce"_compute_reduce.html - combine per-atom quantities into a single global value -"reduce/chunk"_compute_reduce_chunk.html - reduce per-atom quantities within each chunk "reduce/region"_compute_reduce.html - same as compute reduce, within a region "rigid/local"_compute_rigid_local.html - extract rigid body attributes -"saed"_compute_saed.html - "slice"_compute_slice.html - extract values from global vector or array -"smd/contact/radius"_compute_smd_contact_radius.html - -"smd/damage"_compute_smd_damage.html - -"smd/hourglass/error"_compute_smd_hourglass_error.html - -"smd/internal/energy"_compute_smd_internal_energy.html - -"smd/plastic/strain"_compute_smd_plastic_strain.html - -"smd/plastic/strain/rate"_compute_smd_plastic_strain_rate.html - -"smd/rho"_compute_smd_rho.html - -"smd/tlsph/defgrad"_compute_smd_tlsph_defgrad.html - -"smd/tlsph/dt"_compute_smd_tlsph_dt.html - -"smd/tlsph/num/neighs"_compute_smd_tlsph_num_neighs.html - -"smd/tlsph/shape"_compute_smd_tlsph_shape.html - -"smd/tlsph/strain"_compute_smd_tlsph_strain.html - -"smd/tlsph/strain/rate"_compute_smd_tlsph_strain_rate.html - -"smd/tlsph/stress"_compute_smd_tlsph_stress.html - -"smd/triangle/vertices"_compute_smd_triangle_vertices.html - -"smd/triangle/vertices"_compute_smd_triangle_vertices.html - -"smd/ulsph/num/neighs"_compute_smd_ulsph_num_neighs.html - -"smd/ulsph/strain"_compute_smd_ulsph_strain.html - -"smd/ulsph/strain/rate"_compute_smd_ulsph_strain_rate.html - -"smd/ulsph/stress"_compute_smd_ulsph_stress.html - -"smd/vol"_compute_smd_vol.html - "sna/atom"_compute_sna_atom.html - calculate bispectrum coefficients for each atom "snad/atom"_compute_sna_atom.html - derivative of bispectrum coefficients for each atom "snav/atom"_compute_sna_atom.html - virial contribution from bispectrum coefficients for each atom -"spin"_compute_spin.html - "stress/atom"_compute_stress_atom.html - stress tensor for each atom -"stress/mop"_compute_stress_mop.html - -"stress/mop/profile"_compute_stress_mop.html - -"stress/tally"_compute_tally.html - -"tdpd/cc/atom"_compute_tdpd_cc_atom.html - "temp"_compute_temp.html - temperature of group of atoms "temp/asphere"_compute_temp_asphere.html - temperature of aspherical particles "temp/body"_compute_temp_body.html - temperature of body particles "temp/chunk"_compute_temp_chunk.html - temperature of each chunk "temp/com"_compute_temp_com.html - temperature after subtracting center-of-mass velocity -"temp/cs"_compute_temp_cs.html - "temp/deform"_compute_temp_deform.html - temperature excluding box deformation velocity -"temp/deform/eff"_compute_temp_deform_eff.html - -"temp/drude"_compute_temp_drude.html - -"temp/eff"_compute_temp_eff.html - "temp/partial"_compute_temp_partial.html - temperature excluding one or more dimensions of velocity "temp/profile"_compute_temp_profile.html - temperature excluding a binned velocity profile "temp/ramp"_compute_temp_ramp.html - temperature excluding ramped velocity component "temp/region"_compute_temp_region.html - temperature of a region of atoms -"temp/region/eff"_compute_temp_region_eff.html - -"temp/rotate"_compute_temp_rotate.html - "temp/sphere"_compute_temp_sphere.html - temperature of spherical particles -"temp/uef"_compute_temp_uef.html - "ti"_compute_ti.html - thermodynamic integration free energy values "torque/chunk"_compute_torque_chunk.html - torque applied on each chunk "vacf"_compute_vacf.html - velocity-autocorrelation function of group of atoms "vcm/chunk"_compute_vcm_chunk.html - velocity of center-of-mass for each chunk -"voronoi/atom"_compute_voronoi_atom.html - Voronoi volume and neighbors for each atom -"xrd"_compute_xrd.html - :ul +"voronoi/atom"_compute_voronoi_atom.html - Voronoi volume and neighbors for each atom :ul [Restrictions:] none diff --git a/doc/src/compute_hma.txt b/doc/src/compute_hma.txt new file mode 100644 index 0000000000..f71ddc9e2e --- /dev/null +++ b/doc/src/compute_hma.txt @@ -0,0 +1,147 @@ +"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c + +:link(lws,http://lammps.sandia.gov) +:link(ld,Manual.html) +:link(lc,Section_commands.html#comm) + +:line + +compute hma command :h3 + +[Syntax:] + +compute ID group-ID hma temp-ID keyword ... :pre + +ID, group-ID are documented in "compute"_compute.html command :l +hma = style name of this compute command :l +temp-ID = ID of fix that specifies the set temperature during canonical simulation :l +keyword = {anharmonic} {u} {p Pharm} {cv} :l + {anharmonic} = compute will return anharmonic property values + {u} = compute will return potential energy + {p} = compute will return pressure. the following keyword must be the difference between the harmonic pressure and lattice pressure as described below + {cv} = compute will return the heat capacity :pre +:ule + +[Examples:] + +compute 2 all hma 1 u +compute 2 all hma 1 anharmonic u p 0.9 +compute 2 all hma 1 u cv :pre + + + +[Description:] + +Define a computation that calculates the properties of a solid (potential +energy, pressure or heat capacity), using the harmonically-mapped averaging +(HMA) method. +This command yields much higher precision than the equivalent compute commands +("compute pe"_compute_pe.html, "compute pressure"_compute_pressure.html, etc.) +commands during a canonical simulation of an atomic crystal. + + +In this method, the analytically known harmonic behavior of a crystal is removed from the traditional ensemble +averages, which leads to an accurate and precise measurement of the anharmonic contributions without contamination +by noise produced by the already-known harmonic behavior. +A detailed description of this method can be found in ("Moustafa"_#hma-Moustafa). The potential energy is computed by the formula: + +\begin\{equation\} +\left< U\right>_\{HMA\} = \frac\{d(N-1)\}\{2\beta\} + \left< U + \frac\{1\}\{2\} F\bullet\Delta r \right> +\end\{equation\} + +where \(N\) is the number of atoms in the system, \(\beta\) is the reciprocal of the thermodynamic temperature, \(d\) is the +dimensionality of the system (2 or 3 for 2d/3d), \(F\bullet\Delta r\) is the sum of dot products of the +atomic force vectors and displacement (from lattice sites) vectors, and \(U\) is the sum of +pair, bond, angle, dihedral, improper, kspace (long-range), and fix energies. + +The pressure is computed by the formula: + +\begin\{equation\} +\left< P\right>_\{HMA\} = \Delta \hat P + \left< P_\{vir\} + \frac\{\beta \Delta \hat P - \rho\}\{d(N-1)\} F\bullet\Delta r \right> +\end\{equation\} + +where \(\rho\) is the number density of the system, \(\Delta \hat P\) is the +difference between theh harmonic and lattice pressure, and \(P_\{vir\}\) is +the virial pressure computed as the sum of pair, bond, angle, dihedral, +improper, kspace (long-range), and fix contributions to the force on each +atom. Although the method will work for any value of \(\Delta \hat P\) +specified (use pressure "units"_units.html), the precision of the resultant +pressure is sensitive to \(\Delta \hat P\); the precision tends to be +best when \(\Delta \hat P\) is the actual the difference between the lattice +pressure and harmonic pressure. + +\begin\{equation\} +\left_\{HMA\} = \frac\{d k_B (N-1)\}\{2\} + \beta \left( \left< +U_\{HMA\}^2 \right> - \left^2 \right)/T + \frac\{1\}\{4 T\} +\left< F\bullet\Delta r + \Delta r \bullet \Phi \bullet \Delta r \right> +\end\{equation\} + +where \(\Phi\) is the Hessian of second derivatives. The compute hma command +computes the full expression for \(C_V\) except for the +\(\left^2\) in the variance term, which can be obtained by +passing the {u} keyword; you must add this extra contribution to the \(C_V\) +value reported by this compute. The variance term can cause significant +roundoff error when computing \(C_V\). To address this, the {anharmonic} +keyword can be passed and/or the output format can be speicified with more +digits. + +thermo_modify format float '%22.15e' :pre + +The {anharmonic} keyword will instruct the compute to return anharmonic +properties rather than the full properties (lattice, harmonic and anharmonic). +When using this keyword, the compute must be first active (it must be included +via a "thermo_style custom"_thermo_style.html command) while the atoms are +still at their lattice sites (before equilibration). + +The temp-ID specified with compute hma command should be same as the fix-ID of Nose-Hoover ("fix nvt"_fix_nh.html) or +Berendsen ("fix temp/berendsen"_fix_temp_berendsen.html) thermostat used for the simulation. While using this command, Langevin thermostat +("fix langevin"_fix_langevin.html) +should be avoided as its extra forces interfere with the HMA implementation. + + + +NOTE: Compute hma command should be used right after the energy minimization, when the atoms are at their lattice sites. +The simulation should not be started before this command has been used in the input script. + + +The following example illustrates the placement of this command in the input script: + + +min_style cg +minimize 1e-35 1e-15 50000 500000 +compute 1 all hma thermostatid u +fix thermostatid all nvt temp 600.0 600.0 100.0 :pre + + + +NOTE: Compute hma should be used when the atoms of the solid do not diffuse. Diffusion will reduce the precision in the potential energy computation. + + +NOTE: The "fix_modify energy yes"_fix_modify.html command must also be specified if a fix is to contribute potential energy to this command. + +:line + +[Output info:] + +This compute calculates a global vector that includes the n properties +requested as arguments to the command (the potential energy, pressure or heat +capacity). The elements of the vector can be accessed by indices 1-n by any +command that uses global vector values as input. See the "Howto +output"_Howto_output.html doc page for an overview of LAMMPS output options. + +The vector values calculated by this compute are "extensive". The +scalar value will be in energy "units"_units.html. + +[Restrictions:] Usage restricted to canonical (NVT) ensemble simulation only. + +[Related commands:] + +"compute pe"_compute_pe.html, "compute pressure"_compute_pressure.html + +[Default:] none + +:line + +:link(hma-Moustafa) +[(Moustafa)] Sabry G. Moustafa, Andrew J. Schultz, and David A. Kofke, {Very fast averaging of thermal properties of crystals by molecular simulation}, +"Phys. Rev. E \[92\], 043303 (2015)"_https://link.aps.org/doi/10.1103/PhysRevE.92.043303 diff --git a/doc/src/computes.txt b/doc/src/computes.txt index 926b8da222..c636633b38 100644 --- a/doc/src/computes.txt +++ b/doc/src/computes.txt @@ -6,7 +6,6 @@ Computes :h1 :maxdepth: 1 compute_ackland_atom - compute_adf compute_angle compute_angle_local compute_angmom_chunk @@ -16,7 +15,6 @@ Computes :h1 compute_bond_local compute_centro_atom compute_chunk_atom - compute_chunk_spread_atom compute_cluster_atom compute_cna_atom compute_cnp_atom @@ -46,6 +44,7 @@ Computes :h1 compute_gyration_chunk compute_heat_flux compute_hexorder_atom + compute_hma compute_improper compute_improper_local compute_inertia_chunk @@ -68,15 +67,12 @@ Computes :h1 compute_pe_atom compute_plasticity_atom compute_pressure - compute_pressure_cylinder compute_pressure_uef compute_property_atom compute_property_chunk compute_property_local - compute_ptm_atom compute_rdf compute_reduce - compute_reduce_chunk compute_rigid_local compute_saed compute_slice @@ -94,7 +90,7 @@ Computes :h1 compute_smd_tlsph_strain compute_smd_tlsph_strain_rate compute_smd_tlsph_stress - compute_smd_triangle_vertices + compute_smd_triangle_mesh_vertices compute_smd_ulsph_num_neighs compute_smd_ulsph_strain compute_smd_ulsph_strain_rate @@ -103,7 +99,6 @@ Computes :h1 compute_sna_atom compute_spin compute_stress_atom - compute_stress_mop compute_tally compute_tdpd_cc_atom compute_temp diff --git a/src/compute_hma.cpp b/src/compute_hma.cpp new file mode 100644 index 0000000000..ac976080ce --- /dev/null +++ b/src/compute_hma.cpp @@ -0,0 +1,470 @@ +/* ---------------------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + http://lammps.sandia.gov, Sandia National Laboratories + Steve Plimpton, sjplimp@sandia.gov + + Copyright (2003) Sandia Corporation. Under the terms of Contract + DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains + certain rights in this software. This software is distributed under + the GNU General Public License. + + See the README file in the top-level LAMMPS directory. +------------------------------------------------------------------------- */ + +#include +#include +#include +#include "compute_hma.h" +#include "atom.h" +#include "update.h" +#include "force.h" +#include "pair.h" +#include "bond.h" +#include "angle.h" +#include "dihedral.h" +#include "improper.h" +#include "kspace.h" +#include "group.h" +#include "domain.h" +#include "modify.h" +#include "fix.h" +#include "fix_store.h" +#include "memory.h" +#include "error.h" +#include "comm.h" +#include "neighbor.h" +#include "neigh_request.h" +#include "neigh_list.h" + +#include + + +using namespace LAMMPS_NS; + +/* ---------------------------------------------------------------------- */ + +ComputeHMA::ComputeHMA(LAMMPS *lmp, int narg, char **arg) : + Compute(lmp, narg, arg), id_temp(NULL), deltaR(NULL) +{ + if (narg < 4) error->all(FLERR,"Illegal compute hma command"); + if (igroup) error->all(FLERR,"Compute hma must use group all"); + if (strcmp(arg[3],"NULL") == 0) {error->all(FLERR,"fix ID specifying the set temperature of canonical simulation is required");} + else { + int n = strlen(arg[3]) + 1; + id_temp = new char[n]; + strcpy(id_temp,arg[3]); + } + + create_attribute = 1; + extscalar = 1; + timeflag = 1; + +// (from compute displace/atom) create a new fix STORE style +// our new fix's id (id_fix)= compute-ID + COMPUTE_STORE +// our new fix's group = same as compute group + + int n = strlen(id) + strlen("_COMPUTE_STORE") + 1; + id_fix = new char[n]; + strcpy(id_fix,id); + strcat(id_fix,"_COMPUTE_STORE"); + + char **newarg = new char*[6]; + newarg[0] = id_fix; + newarg[1] = group->names[igroup]; + newarg[2] = (char *) "STORE"; + newarg[3] = (char *) "peratom"; + newarg[4] = (char *) "1"; + newarg[5] = (char *) "3"; + modify->add_fix(6,newarg); + fix = (FixStore *) modify->fix[modify->nfix-1]; + + delete [] newarg; + + // calculate xu,yu,zu for fix store array + // skip if reset from restart file + + if (fix->restart_reset) fix->restart_reset = 0; + else { + double **xoriginal = fix->astore; + double **x = atom->x; + imageint *image = atom->image; + int nlocal = atom->nlocal; + + for (int i = 0; i < nlocal; i++) + domain->unmap(x[i],image[i],xoriginal[i]); + } + + vector_flag = 1; + extvector = -1; + comm_forward = 0; // 3 if 2nd derivative needed + + computeU = computeP = computeCv = -1; + returnAnharmonic = 0; + std::vector extvec; + for (int iarg=4; iarg narg) error->all(FLERR,"Illegal fix hma command"); + computeP = extvec.size(); + deltaPcap = force->numeric(FLERR, arg[iarg+1]); + extvec.push_back(0); + iarg++; + } + else if (!strcasecmp(arg[iarg], "cv")) { + computeCv = extvec.size(); + comm_forward = 3; + extvec.push_back(1); + } + else if (!strcasecmp(arg[iarg], "anharmonic")) { + returnAnharmonic = -1; + } + else { + error->all(FLERR,"Illegal fix hma command"); + } + } + + if (extvec.size() == 0) { + error->all(FLERR,"Illegal fix hma command"); + } + size_vector = extvec.size(); + memory->create(vector, size_vector, "hma::vector"); + extlist = new int[size_vector]; + for (int i=0; i-1 || computeCv>-1) { + peflag = 1; + } + if (computeP>-1) { + pressflag = 1; + } + + nmax = 0; +} + +/* ---------------------------------------------------------------------- */ + +ComputeHMA::~ComputeHMA() +{ + // check nfix in case all fixes have already been deleted + if (modify->nfix) modify->delete_fix(id_fix); + + delete [] id_fix; + delete [] id_temp; + delete [] extlist; + memory->destroy(vector); + memory->destroy(deltaR); +} + +/* ---------------------------------------------------------------------- */ + +void ComputeHMA::init() { + int irequest = neighbor->request(this,instance_me); + neighbor->requests[irequest]->pair = 0; + neighbor->requests[irequest]->compute = 1; + neighbor->requests[irequest]->occasional = 1; +} + +void ComputeHMA::init_list(int id, NeighList *ptr) { + list = ptr; +} + +void ComputeHMA::setup() +{ + int dummy=0; + int ifix = modify->find_fix(id_temp); + if (ifix < 0) error->all(FLERR,"Could not find compute hma temperature ID"); + double * temperat = (double *) modify->fix[ifix]->extract("t_target",dummy); + if (temperat==NULL) error->all(FLERR,"Could not find compute hma temperature ID"); + finaltemp = * temperat; + + + // set fix which stores original atom coords + + int ifix2 = modify->find_fix(id_fix); + if (ifix2 < 0) error->all(FLERR,"Could not find compute hma ID"); + fix = (FixStore *) modify->fix[ifix2]; +} + +/* ---------------------------------------------------------------------- */ + +void ComputeHMA::compute_vector() +{ + invoked_vector = update->ntimestep; + +// dx,dy,dz = displacement of atom from original position + // original unwrapped position is stored by fix + // for triclinic, need to unwrap current atom coord via h matrix + + // grow deltaR array if necessary + + if (comm_forward>0 && atom->nmax > nmax) { + memory->destroy(deltaR); + nmax = atom->nmax; + memory->create(deltaR,nmax,3,"hma:deltaR"); + } + + double **xoriginal = fix->astore; + double fdr = 0.0; + double **x = atom->x; + double **f = atom->f; + + imageint *image = atom->image; + int nlocal = atom->nlocal; + + double *h = domain->h; + double xprd = domain->xprd; + double yprd = domain->yprd; + double zprd = domain->zprd; + + double u = 0.0; + if (computeU>-1 || computeCv>-1) { + if (force->pair) u += force->pair->eng_vdwl + force->pair->eng_coul; + if (force->bond) u += force->bond->energy; + if (force->angle) u += force->angle->energy; + if (force->dihedral) u += force->dihedral->energy; + if (force->improper) u += force->improper->energy; + } + + int dimension = domain->dimension; + double p = 0, vol = 0; + if (computeP>-1) { + p = virial_compute(dimension); + vol = xprd * yprd; + if (dimension == 3) vol *= zprd; + p *= force->nktv2p / (dimension*vol); + if (returnAnharmonic == -1) { + pLat = p; + } + } + + if (domain->triclinic == 0) { + for (int i = 0; i < nlocal; i++) { + int xbox = (image[i] & IMGMASK) - IMGMAX; + int ybox = (image[i] >> IMGBITS & IMGMASK) - IMGMAX; + int zbox = (image[i] >> IMG2BITS) - IMGMAX; + double dx = x[i][0] + xbox*xprd - xoriginal[i][0]; + double dy = x[i][1] + ybox*yprd - xoriginal[i][1]; + double dz = x[i][2] + zbox*zprd - xoriginal[i][2]; + if (comm_forward>0) { + deltaR[i][0] = dx; + deltaR[i][1] = dy; + deltaR[i][2] = dz; + } + fdr += dx*f[i][0] + dy*f[i][1] + dz*f[i][2]; + } + } + else { + for (int i = 0; i < nlocal; i++) { + int xbox = (image[i] & IMGMASK) - IMGMAX; + int ybox = (image[i] >> IMGBITS & IMGMASK) - IMGMAX; + int zbox = (image[i] >> IMG2BITS) - IMGMAX; + double dx = x[i][0] + h[0]*xbox + h[5]*ybox + h[4]*zbox - xoriginal[i][0]; + double dy = x[i][1] + h[1]*ybox + h[3]*zbox - xoriginal[i][1]; + double dz = x[i][2] + h[2]*zbox - xoriginal[i][2]; + if (comm_forward>0) { + deltaR[i][0] = dx; + deltaR[i][1] = dy; + deltaR[i][2] = dz; + } + fdr += ((dx*f[i][0])+(dy*f[i][1])+(dz*f[i][2])); + } + } + + double phiSum = 0.0; + if (computeCv>-1) { + comm->forward_comm_compute(this); + int *type = atom->type; + double** cutsq = force->pair->cutsq; + if (force->pair) { + double **x = atom->x; + double **f = atom->f; + int *type = atom->type; + int nlocal = atom->nlocal; + double *special_lj = force->special_lj; + double *special_coul = force->special_coul; + int newton_pair = force->newton_pair; + + if (update->firststep == update->ntimestep) neighbor->build_one(list,1); + else neighbor->build_one(list); + int inum = list->inum; + int *ilist = list->ilist; + int *numneigh = list->numneigh; + int **firstneigh = list->firstneigh; + + for (int ii = 0; ii < inum; ii++) { + int i = ilist[ii]; + double fac = (newton_pair || i < nlocal) ? 1.0 : 0.5; + double* ix = x[i]; + int itype = type[i]; + int *jlist = firstneigh[i]; + int jnum = numneigh[i]; + double *idr = deltaR[i]; + for (int jj = 0; jj < jnum; jj++) { + int j = jlist[jj]; + if (!newton_pair && j>=nlocal) fac -= 0.5; + double factor_lj = special_lj[sbmask(j)]; + double factor_coul = special_coul[sbmask(j)]; + j &= NEIGHMASK; + double* jx = x[j]; + double delr[3]; + delr[0] = ix[0] - jx[0]; + delr[1] = ix[1] - jx[1]; + delr[2] = ix[2] - jx[2]; + double rsq = delr[0]*delr[0] + delr[1]*delr[1] + delr[2]*delr[2]; + int jtype = type[j]; + if (rsq < cutsq[itype][jtype]) { + double* jdr = deltaR[j]; + double fforce, d2u[6]; + force->pair->single2(i, j, itype, jtype, rsq, delr, factor_coul, factor_lj, fforce, d2u); + int m = 0; + for (int k=0; k<3; k++) { + double a = fac; + for (int l=k; l<3; l++) { + phiSum += a*(idr[k]*jdr[l]+jdr[k]*idr[l])*d2u[m]; + phiSum -= a*(idr[k]*idr[l]*d2u[m] + jdr[k]*jdr[l]*d2u[m]); + m++; + if (k==l) a *= 2; + } + } + } + } + } + } + } + +//adding PE for this processor + +//adding the energies of all processors + + double fdrTotal; + MPI_Allreduce(&fdr,&fdrTotal,1,MPI_DOUBLE,MPI_SUM,world); + double uTotal; + if (computeU>-1 || computeCv>-1) { + MPI_Allreduce(&u,&uTotal,1,MPI_DOUBLE,MPI_SUM,world); + if (returnAnharmonic == -1) { + uLat = uTotal; + } + if (computeU>-1) { + if (returnAnharmonic) { + vector[computeU] = uTotal - uLat + 0.5*fdrTotal; + } + else { + vector[computeU] = uTotal + 0.5*fdrTotal + 0.5*dimension*(atom->natoms - 1)*force->boltz*finaltemp; + } + } + } + + if (computeP>-1) { + double fv = ((deltaPcap)-(force->boltz*finaltemp*force->nktv2p*atom->natoms/vol))/(force->boltz*finaltemp*dimension*(atom->natoms - 1)); + if (returnAnharmonic) { + vector[computeP] = p - pLat + (fv*fdrTotal); + } + else { + vector[computeP] = p + (fv*fdrTotal) + deltaPcap; + } + } + + if (computeCv>-1) { + if (computeU==-1) MPI_Allreduce(&u,&uTotal,1,MPI_DOUBLE,MPI_SUM,world); + double buTot; + if (returnAnharmonic) { + buTot = (uTotal - uLat + 0.5*fdrTotal)/finaltemp; + } + else { + buTot = (uTotal + 0.5*fdrTotal)/finaltemp + 0.5*dimension*(atom->natoms - 1)*force->boltz; + } + double one = -0.25*(fdr + phiSum)/finaltemp; + double Cv; + MPI_Allreduce(&one,&Cv,1,MPI_DOUBLE,MPI_SUM,world); + vector[computeCv] = Cv + buTot*buTot; + if (!returnAnharmonic) { + vector[computeCv] += 0.5*dimension*(atom->natoms-1); + } + } + if (returnAnharmonic == -1) { + returnAnharmonic = 1; + } +} + +double ComputeHMA::virial_compute(int n) { + double v = 0; + + // sum contributions to virial from forces and fixes + + if (force->pair) v += sumVirial(n, force->pair->virial); + if (force->bond) v += sumVirial(n, force->bond->virial); + if (force->angle) v += sumVirial(n, force->angle->virial); + if (force->dihedral) v += sumVirial(n, force->dihedral->virial); + if (force->improper) v += sumVirial(n, force->improper->virial); + for (int i = 0; i < modify->nfix; i++) + if (modify->fix[i]->thermo_virial) v += sumVirial(n, modify->fix[i]->virial); + + // sum virial across procs + + double virial; + MPI_Allreduce(&v,&virial,1,MPI_DOUBLE,MPI_SUM,world); + + // KSpace virial contribution is already summed across procs + + if (force->kspace) + for (int i = 0; i < n; i++) virial += force->kspace->virial[i]; + return virial; +} + +/* ---------------------------------------------------------------------- */ + +int ComputeHMA::pack_forward_comm(int n, int *list, double *buf, + int pbc_flag, int *pbc) +{ + double **xoriginal = fix->astore; + imageint *image = atom->image; + double **x = atom->x; + double *h = domain->h; + double xprd = domain->xprd; + double yprd = domain->yprd; + double zprd = domain->zprd; + + int m = 0; + for (int ii = 0; ii < n; ii++) { + int i = list[ii]; + buf[m++] = deltaR[i][0]; + buf[m++] = deltaR[i][1]; + buf[m++] = deltaR[i][2]; + } + return m; +} + +/* ---------------------------------------------------------------------- */ + +void ComputeHMA::unpack_forward_comm(int n, int first, double *buf) +{ + double **xoriginal = fix->astore; + int i,m,last; + + m = 0; + last = first + n; + for (i = first; i < last; i++) { + deltaR[i][0] = buf[m++]; + deltaR[i][1] = buf[m++]; + deltaR[i][2] = buf[m++]; + } +} + + +/* ---------------------------------------------------------------------- + initialize one atom's storage values, called when atom is created +------------------------------------------------------------------------- */ + +void ComputeHMA::set_arrays(int i) +{ + double **xoriginal = fix->astore; + double **x = atom->x; + xoriginal[i][0] = x[i][0]; + xoriginal[i][1] = x[i][1]; + xoriginal[i][2] = x[i][2]; +} diff --git a/src/compute_hma.h b/src/compute_hma.h new file mode 100644 index 0000000000..f40103c3c4 --- /dev/null +++ b/src/compute_hma.h @@ -0,0 +1,66 @@ +/* -*- c++ -*- ---------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + http://lammps.sandia.gov, Sandia National Laboratories + Steve Plimpton, sjplimp@sandia.gov + + Copyright (2003) Sandia Corporation. Under the terms of Contract + DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains + certain rights in this software. This software is distributed under + the GNU General Public License. + + See the README file in the top-level LAMMPS directory. +------------------------------------------------------------------------- */ + +#ifdef COMPUTE_CLASS + +ComputeStyle(HMA,ComputeHMA) + +#else + +#ifndef LMP_COMPUTE_HMA_H +#define LMP_COMPUTE_HMA_H + +#include "compute.h" + +namespace LAMMPS_NS { + +class ComputeHMA : public Compute { + public: + ComputeHMA(class LAMMPS *, int, char **); + ~ComputeHMA(); + void setup(); + void init(); + void init_list(int, class NeighList *); + void compute_vector(); + void set_arrays(int); + int pack_forward_comm(int, int *, double *, int, int *); + void unpack_forward_comm(int, int, double *); + + private: + int nmax; + int atomsingroup; + char *id_fix; + char *id_temp; + double finaltemp; + class FixStore *fix; + double boltz, nktv2p, inv_volume; + double deltaPcap; + double virial_compute(int); + static double sumVirial(int n, double* v) { + double x = 0; + for (int i=0; i Date: Fri, 9 Nov 2018 21:28:41 -0500 Subject: [PATCH 003/469] Cleanup, add memory_usage method --- src/compute_hma.cpp | 23 +++++++++++++---------- src/compute_hma.h | 1 + 2 files changed, 14 insertions(+), 10 deletions(-) diff --git a/src/compute_hma.cpp b/src/compute_hma.cpp index ac976080ce..c0a7901640 100644 --- a/src/compute_hma.cpp +++ b/src/compute_hma.cpp @@ -59,9 +59,9 @@ ComputeHMA::ComputeHMA(LAMMPS *lmp, int narg, char **arg) : extscalar = 1; timeflag = 1; -// (from compute displace/atom) create a new fix STORE style -// our new fix's id (id_fix)= compute-ID + COMPUTE_STORE -// our new fix's group = same as compute group + // (from compute displace/atom) create a new fix STORE style + // our new fix's id (id_fix)= compute-ID + COMPUTE_STORE + // our new fix's group = same as compute group int n = strlen(id) + strlen("_COMPUTE_STORE") + 1; id_fix = new char[n]; @@ -169,7 +169,8 @@ void ComputeHMA::init() { neighbor->requests[irequest]->occasional = 1; } -void ComputeHMA::init_list(int id, NeighList *ptr) { +void ComputeHMA::init_list(int id, NeighList *ptr) +{ list = ptr; } @@ -196,12 +197,7 @@ void ComputeHMA::compute_vector() { invoked_vector = update->ntimestep; -// dx,dy,dz = displacement of atom from original position - // original unwrapped position is stored by fix - // for triclinic, need to unwrap current atom coord via h matrix - // grow deltaR array if necessary - if (comm_forward>0 && atom->nmax > nmax) { memory->destroy(deltaR); nmax = atom->nmax; @@ -391,7 +387,8 @@ void ComputeHMA::compute_vector() } } -double ComputeHMA::virial_compute(int n) { +double ComputeHMA::virial_compute(int n) +{ double v = 0; // sum contributions to virial from forces and fixes @@ -468,3 +465,9 @@ void ComputeHMA::set_arrays(int i) xoriginal[i][1] = x[i][1]; xoriginal[i][2] = x[i][2]; } + +double ComputeHMA::memory_usage() +{ + double bytes = nmax * 3 * sizeof(double); + return bytes; +} diff --git a/src/compute_hma.h b/src/compute_hma.h index f40103c3c4..44906b53a1 100644 --- a/src/compute_hma.h +++ b/src/compute_hma.h @@ -35,6 +35,7 @@ class ComputeHMA : public Compute { void set_arrays(int); int pack_forward_comm(int, int *, double *, int, int *); void unpack_forward_comm(int, int, double *); + double memory_usage(); private: int nmax; -- GitLab From 101948ce1e2c0084b1b4e9774446e9e751a98132 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Eugen=20Ro=C5=BEi=C4=87?= Date: Thu, 21 Feb 2019 01:49:04 +0100 Subject: [PATCH 004/469] Added a Morse potential option to 'fix wall/region' --- src/fix_wall_region.cpp | 34 ++++++++++++++++++++++++++++++---- src/fix_wall_region.h | 2 ++ 2 files changed, 32 insertions(+), 4 deletions(-) diff --git a/src/fix_wall_region.cpp b/src/fix_wall_region.cpp index ff147d7446..2b16ec3bf4 100644 --- a/src/fix_wall_region.cpp +++ b/src/fix_wall_region.cpp @@ -31,7 +31,7 @@ using namespace LAMMPS_NS; using namespace FixConst; using namespace MathConst; -enum{LJ93,LJ126,LJ1043,COLLOID,HARMONIC}; +enum{LJ93,LJ126,LJ1043,MORSE,COLLOID,HARMONIC}; /* ---------------------------------------------------------------------- */ @@ -39,7 +39,7 @@ FixWallRegion::FixWallRegion(LAMMPS *lmp, int narg, char **arg) : Fix(lmp, narg, arg), idregion(NULL) { - if (narg != 8) error->all(FLERR,"Illegal fix wall/region command"); + if (narg < 8) error->all(FLERR,"Illegal fix wall/region command"); scalar_flag = 1; vector_flag = 1; @@ -63,6 +63,7 @@ FixWallRegion::FixWallRegion(LAMMPS *lmp, int narg, char **arg) : if (strcmp(arg[4],"lj93") == 0) style = LJ93; else if (strcmp(arg[4],"lj126") == 0) style = LJ126; else if (strcmp(arg[4],"lj1043") == 0) style = LJ1043; + else if (strcmp(arg[4],"morse") == 0) style = MORSE; else if (strcmp(arg[4],"colloid") == 0) style = COLLOID; else if (strcmp(arg[4],"harmonic") == 0) style = HARMONIC; else error->all(FLERR,"Illegal fix wall/region command"); @@ -73,6 +74,14 @@ FixWallRegion::FixWallRegion(LAMMPS *lmp, int narg, char **arg) : sigma = force->numeric(FLERR,arg[6]); cutoff = force->numeric(FLERR,arg[7]); + if (style == MORSE) { + if (narg != 9) + error->all(FLERR,"Illegal fix wall/region command"); + else + alpha = force->numeric(FLERR,arg[8]); + } else if (narg != 8) + error->all(FLERR,"Illegal fix wall/region command"); + if (cutoff <= 0.0) error->all(FLERR,"Fix wall/region cutoff <= 0.0"); eflag = 0; @@ -157,12 +166,15 @@ void FixWallRegion::init() coeff5 = coeff1 * 10.0; coeff6 = coeff2 * 4.0; coeff7 = coeff3 * 3.0; - double rinv = 1.0/cutoff; double r2inv = rinv*rinv; double r4inv = r2inv*r2inv; offset = coeff1*r4inv*r4inv*r2inv - coeff2*r4inv - coeff3*pow(cutoff+coeff4,-3.0); + } else if (style == MORSE) { + coeff1 = 2 * epsilon * alpha; + double alpha_dr = -alpha * (cutoff - sigma); + offset = epsilon * (exp(2.0*alpha_dr) - 2.0*exp(alpha_dr)); } else if (style == COLLOID) { coeff1 = -4.0/315.0 * epsilon * pow(sigma,6.0); coeff2 = -2.0/3.0 * epsilon; @@ -253,6 +265,7 @@ void FixWallRegion::post_force(int vflag) if (style == LJ93) lj93(region->contact[m].r); else if (style == LJ126) lj126(region->contact[m].r); else if (style == LJ1043) lj1043(region->contact[m].r); + else if (style == MORSE) morse(region->contact[m].r); else if (style == COLLOID) colloid(region->contact[m].r,radius[i]); else harmonic(region->contact[m].r); @@ -287,7 +300,7 @@ void FixWallRegion::post_force(int vflag) /* ---------------------------------------------------------------------- */ -void FixWallRegion::post_force_respa(int vflag, int ilevel, int /*iloop*/) +void FixWallRegion::post_force_respa(int vflag, int ilevel, int iloop) { if (ilevel == ilevel_respa) post_force(vflag); } @@ -375,6 +388,19 @@ void FixWallRegion::lj1043(double r) coeff3*pow(r+coeff4,-3.0) - offset; } +/* ---------------------------------------------------------------------- + Morse interaction for particle with wall + compute eng and fwall = magnitude of wall force +------------------------------------------------------------------------- */ + +void FixWallRegion::morse(double r) +{ + double dr = r - sigma; + double dexp = exp(-alpha * dr); + fwall = coeff1 * (dexp*dexp - dexp) / r; + eng = epsilon * (dexp*dexp - 2.0*dexp) - offset; +} + /* ---------------------------------------------------------------------- colloid interaction for finite-size particle of rad with wall compute eng and fwall = magnitude of wall force diff --git a/src/fix_wall_region.h b/src/fix_wall_region.h index e3688c99ee..663a12b257 100644 --- a/src/fix_wall_region.h +++ b/src/fix_wall_region.h @@ -41,6 +41,7 @@ class FixWallRegion : public Fix { private: int style,iregion; double epsilon,sigma,cutoff; + double alpha; int eflag; double ewall[4],ewall_all[4]; int ilevel_respa; @@ -53,6 +54,7 @@ class FixWallRegion : public Fix { void lj93(double); void lj126(double); void lj1043(double); + void morse(double); void colloid(double, double); void harmonic(double); }; -- GitLab From 4ea7d733e8eab688c29948d45e61536f367b4ee2 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Eugen=20Ro=C5=BEi=C4=87?= Date: Thu, 21 Feb 2019 02:17:19 +0100 Subject: [PATCH 005/469] Initial commit... --- src/USER-MISC/pair_cosine_squared.cpp | 473 ++++++++++++++++++++++++++ src/USER-MISC/pair_cosine_squared.h | 95 ++++++ 2 files changed, 568 insertions(+) create mode 100644 src/USER-MISC/pair_cosine_squared.cpp create mode 100644 src/USER-MISC/pair_cosine_squared.h diff --git a/src/USER-MISC/pair_cosine_squared.cpp b/src/USER-MISC/pair_cosine_squared.cpp new file mode 100644 index 0000000000..db3d8a6aa7 --- /dev/null +++ b/src/USER-MISC/pair_cosine_squared.cpp @@ -0,0 +1,473 @@ +/* ---------------------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + http://lammps.sandia.gov, Sandia National Laboratories + Steve Plimpton, sjplimp@sandia.gov + + Copyright (2003) Sandia Corporation. Under the terms of Contract + DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains + certain rights in this software. This software is distributed under + the GNU General Public License. + + See the README file in the top-level LAMMPS directory. +------------------------------------------------------------------------- */ +/* ---------------------------------------------------------------------- + Contributing authors: Eugen Rozic (University College London) +------------------------------------------------------------------------- */ + +#include +#include +#include +#include +#include "pair_cosine_squared.h" +#include "atom.h" +#include "comm.h" +#include "force.h" +#include "neighbor.h" +#include "neigh_list.h" +#include "neigh_request.h" +#include "update.h" +#include "integrate.h" +#include "respa.h" +#include "math_const.h" +#include "memory.h" +#include "error.h" + +using namespace LAMMPS_NS; +using namespace MathConst; + +/* ---------------------------------------------------------------------- */ + +PairCosineSquared::PairCosineSquared(LAMMPS *lmp) : Pair(lmp) +{ + writedata = 1; +} + +/* ---------------------------------------------------------------------- */ + +PairCosineSquared::~PairCosineSquared() +{ + if (allocated) { + memory->destroy(setflag); + memory->destroy(cutsq); + + memory->destroy(epsilon); + memory->destroy(sigma); + memory->destroy(w); + memory->destroy(cut); + memory->destroy(wcaflag); + + memory->destroy(lj12_e); + memory->destroy(lj6_e); + memory->destroy(lj12_f); + memory->destroy(lj6_f); + } +} + +/* ---------------------------------------------------------------------- + allocate all arrays +------------------------------------------------------------------------- */ + +void PairCosineSquared::allocate() +{ + allocated = 1; + int n = atom->ntypes; + memory->create(setflag, n+1, n+1, "pair:setflag"); + memory->create(cutsq, n+1, n+1, "pair:cutsq"); + + memory->create(cut, n+1, n+1, "pair:cut"); + memory->create(epsilon, n+1, n+1, "pair:epsilon"); + memory->create(sigma, n+1, n+1, "pair:sigma"); + memory->create(w, n+1, n+1, "pair:w"); + memory->create(wcaflag, n+1, n+1, "pair:wcaflag"); + + memory->create(lj12_e, n+1, n+1, "pair:lj12_e"); + memory->create(lj6_e, n+1, n+1, "pair:lj6_e"); + memory->create(lj12_f, n+1, n+1, "pair:lj12_f"); + memory->create(lj6_f, n+1, n+1, "pair:lj6_f"); + + for (int i = 1; i <= n; i++) { + for (int j = i; j <= n; j++) { + setflag[i][j] = 0; + wcaflag[i][j] = 0; + } + } +} + +/* ---------------------------------------------------------------------- + global settings +------------------------------------------------------------------------- */ + +void PairCosineSquared::settings(int narg, char **arg) +{ + if (narg != 1) { + error->all(FLERR, "Illegal pair_style command (wrong number of params)"); + } + + cut_global = force->numeric(FLERR, arg[0]); + + // reset cutoffs that have been explicitly set + + if (allocated) { + int i, j; + for (i = 1; i <= atom->ntypes; i++) + for (j = i+1; j <= atom->ntypes; j++) + if (setflag[i][j]) + cut[i][j] = cut_global; + } +} + + +/* ---------------------------------------------------------------------- + set coeffs for one or more type pairs +------------------------------------------------------------------------- */ + +void PairCosineSquared::coeff(int narg, char **arg) +{ + if (narg < 4 || narg > 6) + error->all(FLERR, "Incorrect args for pair coefficients (too few or too many)"); + + if (!allocated) + allocate(); + + int ilo, ihi, jlo, jhi; + force->bounds(FLERR, arg[0], atom->ntypes, ilo, ihi); + force->bounds(FLERR, arg[1], atom->ntypes, jlo, jhi); + + double epsilon_one = force->numeric(FLERR, arg[2]); + double sigma_one = force->numeric(FLERR, arg[3]); + + double cut_one = cut_global; + double wca_one = 0; + if (narg == 6) { + cut_one = force->numeric(FLERR, arg[4]); + if (strcmp(arg[5], "wca") == 0) { + wca_one = 1; + } else { + error->all(FLERR, "Incorrect args for pair coefficients (unknown option)"); + } + } else if (narg == 5) { + if (strcmp(arg[4], "wca") == 0) { + wca_one = 1; + } else { + cut_one = force->numeric(FLERR, arg[4]); + } + } + + if (cut_one <= sigma_one) + error->all(FLERR, "Incorrect args for pair coefficients (cutoff <= sigma)"); + + int count = 0; + for (int i = ilo; i <= ihi; i++) { + for (int j = MAX(jlo,i); j <= jhi; j++) { + epsilon[i][j] = epsilon_one; + sigma[i][j] = sigma_one; + cut[i][j] = cut_one; + wcaflag[i][j] = wca_one; + setflag[i][j] = 1; + count++; + } + } + + if (count == 0) + error->all(FLERR, "Incorrect args for pair coefficients (none set)"); +} + +/* ---------------------------------------------------------------------- + init specific to this pair style (unneccesary) +------------------------------------------------------------------------- */ + +/* +void PairCosineSquared::init_style() +{ + neighbor->request(this,instance_me); +} +*/ + +/* ---------------------------------------------------------------------- + init for one type pair i,j and corresponding j,i +------------------------------------------------------------------------- */ + +double PairCosineSquared::init_one(int i, int j) +{ + if (setflag[i][j] == 0) + error->all(FLERR, "Mixing not supported in pair_style cosine/squared"); + + epsilon[j][i] = epsilon[i][j]; + sigma[j][i] = sigma[i][j]; + cut[j][i] = cut[i][j]; + wcaflag[j][i] = wcaflag[i][j]; + + w[j][i] = w[i][j] = cut[i][j] - sigma[i][j]; + + if (wcaflag[i][j]) { + lj12_e[j][i] = lj12_e[i][j] = epsilon[i][j] * pow(sigma[i][j], 12.0); + lj6_e[j][i] = lj6_e[i][j] = 2.0 * epsilon[i][j] * pow(sigma[i][j], 6.0); + lj12_f[j][i] = lj12_f[i][j] = 12.0 * epsilon[i][j] * pow(sigma[i][j], 12.0); + lj6_f[j][i] = lj6_f[i][j] = 12.0 * epsilon[i][j] * pow(sigma[i][j], 6.0); + } + + // Note: cutsq is set in pair.cpp + + return cut[i][j]; +} + +/* ---------------------------------------------------------------------- + this is here to throw errors & warnings for given options +------------------------------------------------------------------------- */ + +void PairCosineSquared::modify_params(int narg, char **arg) +{ + Pair::modify_params(narg, arg); + + int iarg = 0; + while (iarg < narg) { + if (strcmp(arg[iarg], "mix") == 0) { + error->all(FLERR, "pair_modify mix not supported for pair_style cosine/squared"); + } else if (strcmp(arg[iarg], "shift") == 0) { + error->warning(FLERR, "pair_modify shift is meaningless for pair_style cosine/squared"); + offset_flag = 0; + } else if (strcmp(arg[iarg], "tail") == 0) { + error->warning(FLERR, "pair_modify tail is meaningless for pair_style cosine/squared"); + tail_flag = 0; + } + iarg++; + } +} + +/* ---------------------------------------------------------------------- + proc 0 writes to restart file +------------------------------------------------------------------------- */ + +void PairCosineSquared::write_restart(FILE *fp) +{ + write_restart_settings(fp); + + int i, j; + for (i = 1; i <= atom->ntypes; i++) + for (j = i; j <= atom->ntypes; j++) { + fwrite(&setflag[i][j], sizeof(int), 1, fp); + if (setflag[i][j]) { + fwrite(&epsilon[i][j], sizeof(double), 1, fp); + fwrite(&sigma[i][j], sizeof(double), 1, fp); + fwrite(&cut[i][j], sizeof(double), 1, fp); + fwrite(&wcaflag[i][j], sizeof(int), 1, fp); + } + } +} + +/* ---------------------------------------------------------------------- + proc 0 reads from restart file, bcasts +------------------------------------------------------------------------- */ + +void PairCosineSquared::read_restart(FILE *fp) +{ + read_restart_settings(fp); + allocate(); + + int i,j; + int me = comm->me; + for (i = 1; i <= atom->ntypes; i++) { + for (j = i; j <= atom->ntypes; j++) { + if (me == 0) + fread(&setflag[i][j], sizeof(int), 1, fp); + MPI_Bcast(&setflag[i][j], 1, MPI_INT, 0, world); + if (setflag[i][j]) { + if (me == 0) { + fread(&epsilon[i][j], sizeof(double), 1, fp); + fread(&sigma[i][j], sizeof(double), 1, fp); + fread(&cut[i][j], sizeof(double), 1, fp); + fread(&wcaflag[i][j], sizeof(int), 1, fp); + } + MPI_Bcast(&epsilon[i][j], 1, MPI_DOUBLE, 0, world); + MPI_Bcast(&sigma[i][j], 1, MPI_DOUBLE, 0, world); + MPI_Bcast(&cut[i][j], 1, MPI_DOUBLE, 0, world); + MPI_Bcast(&wcaflag[i][j], 1, MPI_INT, 0, world); + } + } + } +} + +/* ---------------------------------------------------------------------- + proc 0 writes to restart file +------------------------------------------------------------------------- */ + +void PairCosineSquared::write_restart_settings(FILE *fp) +{ + fwrite(&cut_global, sizeof(double), 1, fp); +} + +/* ---------------------------------------------------------------------- + proc 0 reads from restart file, bcasts +------------------------------------------------------------------------- */ + +void PairCosineSquared::read_restart_settings(FILE *fp) +{ + int me = comm->me; + if (me == 0) { + fread(&cut_global, sizeof(double), 1, fp); + } + MPI_Bcast(&cut_global, 1, MPI_DOUBLE, 0, world); +} + +/* ---------------------------------------------------------------------- + proc 0 writes to data file +------------------------------------------------------------------------- */ + +void PairCosineSquared::write_data(FILE *fp) +{ + for (int i = 1; i <= atom->ntypes; i++) + fprintf(fp, "%d %g %g %g %d\n", i, epsilon[i][i], sigma[i][i], + cut[i][i], wcaflag[i][i]); +} + +/* ---------------------------------------------------------------------- + proc 0 writes all pairs to data file +------------------------------------------------------------------------- */ + +void PairCosineSquared::write_data_all(FILE *fp) +{ + for (int i = 1; i <= atom->ntypes; i++) + for (int j = i; j <= atom->ntypes; j++) + fprintf(fp, "%d %d %g %g %g %d\n", i, j, epsilon[i][j], sigma[i][j], + cut[i][j], wcaflag[i][j]); +} + +/* ---------------------------------------------------------------------- */ + +void PairCosineSquared::compute(int eflag, int vflag) +{ + int i, j, ii, jj, inum, jnum, itype, jtype; + int *ilist, *jlist, *numneigh, **firstneigh; + double xtmp, ytmp, ztmp, delx, dely, delz, evdwl, fpair; + double r, rsq, r2inv, r6inv; + double factor_lj, force_lj, force_cos, cosone; + + evdwl = 0.0; + if (eflag || vflag) + ev_setup(eflag, vflag); + else + evflag = vflag_fdotr = 0; + + double **x = atom->x; + double **f = atom->f; + int *type = atom->type; + int nlocal = atom->nlocal; + double *special_lj = force->special_lj; + int newton_pair = force->newton_pair; + + inum = list->inum; + ilist = list->ilist; + numneigh = list->numneigh; + firstneigh = list->firstneigh; + + // loop over neighbors of my atoms + + for (ii = 0; ii < inum; ii++) { + i = ilist[ii]; + xtmp = x[i][0]; + ytmp = x[i][1]; + ztmp = x[i][2]; + itype = type[i]; + jlist = firstneigh[i]; + jnum = numneigh[i]; + + for (jj = 0; jj < jnum; jj++) { + j = jlist[jj]; + factor_lj = special_lj[sbmask(j)]; + j &= NEIGHMASK; + + delx = xtmp - x[j][0]; + dely = ytmp - x[j][1]; + delz = ztmp - x[j][2]; + rsq = delx*delx + dely*dely + delz*delz; + jtype = type[j]; + + if (rsq < cutsq[itype][jtype]) { + + /* + This is exactly what the "single" method does, in fact it could be called + here instead of repeating the code but here energy calculation is optional + so a little bit of calculation is possibly saved + */ + + r = sqrt(rsq); + + if (r <= sigma[itype][jtype]) { + if (wcaflag[itype][jtype]) { + r2inv = 1.0/rsq; + r6inv = r2inv*r2inv*r2inv; + force_lj = r6inv*(lj12_f[itype][jtype]*r6inv - lj6_f[itype][jtype]); + fpair = factor_lj*force_lj*r2inv; + if (eflag) { + evdwl = factor_lj*r6inv * + (lj12_e[itype][jtype]*r6inv - lj6_e[itype][jtype]); + } + } else { + fpair = 0.0; + if (eflag) { + evdwl = -factor_lj*epsilon[itype][jtype]; + } + } + } else { + force_cos = -(MY_PI*epsilon[itype][jtype] / (2.0*w[itype][jtype])) * + sin(MY_PI*(r-sigma[itype][jtype]) / w[itype][jtype]); + fpair = factor_lj*force_cos / r; + if (eflag) { + cosone = cos(MY_PI*(r-sigma[itype][jtype]) / (2.0*w[itype][jtype])); + evdwl = -factor_lj*epsilon[itype][jtype]*cosone*cosone; + } + } + + f[i][0] += delx*fpair; + f[i][1] += dely*fpair; + f[i][2] += delz*fpair; + + if (newton_pair || j < nlocal) { + f[j][0] -= delx*fpair; + f[j][1] -= dely*fpair; + f[j][2] -= delz*fpair; + } + + if (evflag) + ev_tally(i, j, nlocal, newton_pair, evdwl, 0.0, fpair, delx, dely, delz); + } + } + } + + if (vflag_fdotr) + virial_fdotr_compute(); +} + +/* ---------------------------------------------------------------------- + This is used be pair_write; + it is called only if rsq < cutsq[itype][jtype], no need to check that +------------------------------------------------------------------------- */ + +double PairCosineSquared::single(int i, int j, int itype, int jtype, double rsq, + double factor_coul, double factor_lj, + double &fforce) +{ + double r, r2inv, r6inv, cosone, force, energy; + + r = sqrt(rsq); + + if (r <= sigma[itype][jtype]) { + if (wcaflag[itype][jtype]) { + r2inv = 1.0/rsq; + r6inv = r2inv*r2inv*r2inv; + force = r6inv*(lj12_f[itype][jtype]*r6inv - lj6_f[itype][jtype])*r2inv; + energy = r6inv*(lj12_e[itype][jtype]*r6inv - lj6_e[itype][jtype]); + } else { + force = 0.0; + energy = -epsilon[itype][jtype]; + } + } else { + cosone = cos(MY_PI*(r-sigma[itype][jtype]) / (2.0*w[itype][jtype])); + force = -(MY_PI*epsilon[itype][jtype] / (2.0*w[itype][jtype])) * + sin(MY_PI*(r-sigma[itype][jtype]) / w[itype][jtype]) / r; + energy = -epsilon[itype][jtype]*cosone*cosone; + } + fforce = factor_lj*force; + return factor_lj*energy; +} + diff --git a/src/USER-MISC/pair_cosine_squared.h b/src/USER-MISC/pair_cosine_squared.h new file mode 100644 index 0000000000..8c294e0d36 --- /dev/null +++ b/src/USER-MISC/pair_cosine_squared.h @@ -0,0 +1,95 @@ +/* -*- c++ -*- ---------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + http://lammps.sandia.gov, Sandia National Laboratories + Steve Plimpton, sjplimp@sandia.gov + + Copyright (2003) Sandia Corporation. Under the terms of Contract + DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains + certain rights in this software. This software is distributed under + the GNU General Public License. + + See the README file in the top-level LAMMPS directory. +------------------------------------------------------------------------- */ +/* ---------------------------------------------------------------------- + Contributing authors: Eugen Rozic (University College London) +------------------------------------------------------------------------- */ + +#ifdef PAIR_CLASS + +PairStyle(cosine/squared, PairCosineSquared) + +#else + +#ifndef LMP_PAIR_LJ_COS_SQ_H +#define LMP_PAIR_LJ_COS_SQ_H + +#include "pair.h" + +namespace LAMMPS_NS { + +class PairCosineSquared : public Pair { + public: + PairCosineSquared(class LAMMPS *); + virtual ~PairCosineSquared(); + void settings(int, char **); + void coeff(int, char **); + // void init_style(); + double init_one(int, int); + void modify_params(int, char **); + void write_restart(FILE *); + void read_restart(FILE *); + void write_restart_settings(FILE *); + void read_restart_settings(FILE *); + void write_data(FILE *); + void write_data_all(FILE *); + virtual void compute(int, int); + double single(int, int, int, int, double, double, double, double &); + // void *extract(const char *, int &); + +/* RESPA stuff not implemented... + void compute_inner(); + void compute_middle(); + void compute_outer(int, int); +*/ + + protected: + double cut_global; + double **epsilon, **sigma, **w, **cut; + int **wcaflag; + double **lj12_e, **lj6_e, **lj12_f, **lj6_f; + + virtual void allocate(); +}; + +} // namespace LAMMPS_NS + +#endif +#endif + +/* ERROR/WARNING messages: + +E: Illegal ... command + +Self-explanatory. Check the input script syntax and compare to the +documentation for the command. You can use -echo screen as a +command-line option when running LAMMPS to see the offending line. + +E: Incorrect args for pair coefficients + +Self-explanatory. Check the input script or data file. + +E: Mixing not supported in pair_style cosine/squared + +Self-explanatory. All coefficients need to be specified explicitly. + +E: pair_modify mix not supported for pair_style cosine/squared + +Same as above, only when calling "pair_modify" command + +W: pair_modify shift/tail is meaningless for pair_style cosine/squared + +This style by definition gets to zero at cutoff distance, so there is nothing +to shift and there is no tail contribution + +*/ + -- GitLab From 14353c5ea52ff3780873ad93821838dcae46f387 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Eugen=20Ro=C5=BEi=C4=87?= Date: Sun, 3 Mar 2019 01:52:43 +0100 Subject: [PATCH 006/469] Added WCA-only option (sigma == cutoff case with wca) --- src/USER-MISC/pair_cosine_squared.cpp | 25 ++++++++++++++++++++----- 1 file changed, 20 insertions(+), 5 deletions(-) diff --git a/src/USER-MISC/pair_cosine_squared.cpp b/src/USER-MISC/pair_cosine_squared.cpp index db3d8a6aa7..0229af7a08 100644 --- a/src/USER-MISC/pair_cosine_squared.cpp +++ b/src/USER-MISC/pair_cosine_squared.cpp @@ -153,8 +153,15 @@ void PairCosineSquared::coeff(int narg, char **arg) } } - if (cut_one <= sigma_one) - error->all(FLERR, "Incorrect args for pair coefficients (cutoff <= sigma)"); + if (cut_one < sigma_one) { + error->all(FLERR, "Incorrect args for cosine/squared pair coeffs (cutoff < sigma)"); + } else if (cut_one == sigma_one) { + if (wca_one == 0) { + error->all(FLERR, "Incorrect args for cosine/squared pair coeffs (cutoff = sigma w/o wca)") + } else { + error->warning(FLERR, "Cosine/squared set to WCA only (cutoff = sigma)") + } + } int count = 0; for (int i = ilo; i <= ihi; i++) { @@ -224,10 +231,10 @@ void PairCosineSquared::modify_params(int narg, char **arg) if (strcmp(arg[iarg], "mix") == 0) { error->all(FLERR, "pair_modify mix not supported for pair_style cosine/squared"); } else if (strcmp(arg[iarg], "shift") == 0) { - error->warning(FLERR, "pair_modify shift is meaningless for pair_style cosine/squared"); + error->warning(FLERR, "pair_modify shift has no effect on pair_style cosine/squared"); offset_flag = 0; } else if (strcmp(arg[iarg], "tail") == 0) { - error->warning(FLERR, "pair_modify tail is meaningless for pair_style cosine/squared"); + error->warning(FLERR, "pair_modify tail has no effect on pair_style cosine/squared"); tail_flag = 0; } iarg++; @@ -399,8 +406,12 @@ void PairCosineSquared::compute(int eflag, int vflag) force_lj = r6inv*(lj12_f[itype][jtype]*r6inv - lj6_f[itype][jtype]); fpair = factor_lj*force_lj*r2inv; if (eflag) { - evdwl = factor_lj*r6inv * + evdwl = factor_lj*r6inv* (lj12_e[itype][jtype]*r6inv - lj6_e[itype][jtype]); + if (sigma[itype][jtype] == cut[itype][jtype]) { + // this is the WCA-only case (it requires this shift by definition) + evdwl += factor_lj*epsilon[itype][jtype] + } } } else { fpair = 0.0; @@ -457,6 +468,10 @@ double PairCosineSquared::single(int i, int j, int itype, int jtype, double rsq, r6inv = r2inv*r2inv*r2inv; force = r6inv*(lj12_f[itype][jtype]*r6inv - lj6_f[itype][jtype])*r2inv; energy = r6inv*(lj12_e[itype][jtype]*r6inv - lj6_e[itype][jtype]); + if (sigma[itype][jtype] == cut[itype][jtype]) { + // this is the WCA-only case (it requires this shift by definition) + energy += epsilon[itype][jtype] + } } else { force = 0.0; energy = -epsilon[itype][jtype]; -- GitLab From 05f739a5a007d3da97cf7b89b6ec83df3890b7fc Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Eugen=20Ro=C5=BEi=C4=87?= Date: Sun, 3 Mar 2019 01:55:02 +0100 Subject: [PATCH 007/469] Bugfix for WCA-only option (trivial) --- src/USER-MISC/pair_cosine_squared.cpp | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/src/USER-MISC/pair_cosine_squared.cpp b/src/USER-MISC/pair_cosine_squared.cpp index 0229af7a08..67cefd894b 100644 --- a/src/USER-MISC/pair_cosine_squared.cpp +++ b/src/USER-MISC/pair_cosine_squared.cpp @@ -157,9 +157,9 @@ void PairCosineSquared::coeff(int narg, char **arg) error->all(FLERR, "Incorrect args for cosine/squared pair coeffs (cutoff < sigma)"); } else if (cut_one == sigma_one) { if (wca_one == 0) { - error->all(FLERR, "Incorrect args for cosine/squared pair coeffs (cutoff = sigma w/o wca)") + error->all(FLERR, "Incorrect args for cosine/squared pair coeffs (cutoff = sigma w/o wca)"); } else { - error->warning(FLERR, "Cosine/squared set to WCA only (cutoff = sigma)") + error->warning(FLERR, "Cosine/squared set to WCA only (cutoff = sigma)"); } } @@ -410,7 +410,7 @@ void PairCosineSquared::compute(int eflag, int vflag) (lj12_e[itype][jtype]*r6inv - lj6_e[itype][jtype]); if (sigma[itype][jtype] == cut[itype][jtype]) { // this is the WCA-only case (it requires this shift by definition) - evdwl += factor_lj*epsilon[itype][jtype] + evdwl += factor_lj*epsilon[itype][jtype]; } } } else { @@ -470,7 +470,7 @@ double PairCosineSquared::single(int i, int j, int itype, int jtype, double rsq, energy = r6inv*(lj12_e[itype][jtype]*r6inv - lj6_e[itype][jtype]); if (sigma[itype][jtype] == cut[itype][jtype]) { // this is the WCA-only case (it requires this shift by definition) - energy += epsilon[itype][jtype] + energy += epsilon[itype][jtype]; } } else { force = 0.0; -- GitLab From bbec50bef1795ae2737afb9b1cea75cf1bbdb355 Mon Sep 17 00:00:00 2001 From: Andrew Schultz Date: Fri, 29 Mar 2019 15:06:49 -0400 Subject: [PATCH 008/469] Add HMA examples --- examples/USER/hma/README | 22 + examples/USER/hma/hma.in | 36 + examples/USER/hma/log.6Nov18.hma.g++.1 | 10159 +++++++++++++++++++++++ examples/USER/hma/log.6Nov18.hma.g++.4 | 10159 +++++++++++++++++++++++ 4 files changed, 20376 insertions(+) create mode 100644 examples/USER/hma/README create mode 100644 examples/USER/hma/hma.in create mode 100644 examples/USER/hma/log.6Nov18.hma.g++.1 create mode 100644 examples/USER/hma/log.6Nov18.hma.g++.4 diff --git a/examples/USER/hma/README b/examples/USER/hma/README new file mode 100644 index 0000000000..5af6ec15fa --- /dev/null +++ b/examples/USER/hma/README @@ -0,0 +1,22 @@ +The example input script sets up a simple FCC crystal using the Lennard-Jones +potential. The script sets up the HMA compute to calculate the energy, pressure +and heat capacity. The output columns are: + +1: timestep +2: measured temperature +3: potential energy +4: HMA potential energy +5: pressure +6: HMA pressure +7: HMA heat capacity contribution + +Averages of the potential energy (#3 and #4) agree although #4 (HMA) is more precise. + +Averages of the pressure (#5 and #6) agree once the ideal gas +contribution is included; #6 (HMA) is more precise. + +The heat capacity can be computed from colume #3 (convential) as +Cv = Var(#3)/(k T^2) + +With HMA, the heat capacity can be computed from column #4 and #7 as +Cv = #7 + Var(#4)/(k T^2) diff --git a/examples/USER/hma/hma.in b/examples/USER/hma/hma.in new file mode 100644 index 0000000000..50c6dd96fb --- /dev/null +++ b/examples/USER/hma/hma.in @@ -0,0 +1,36 @@ +# Harmonically mapped average example + +units lj +dimension 3 +boundary p p p +atom_style atomic +atom_modify map array +# ---------- Create Atoms ---------------------------- +lattice fcc 1.0 +region box block 0 4 0 4 0 4 units lattice +create_box 1 box +lattice fcc 1.0 orient x 1 0 0 orient y 0 1 0 orient z 0 0 1 +create_atoms 1 region box +# ---------- Define Interatomic Potential --------------------- +pair_style lj/smooth/linear 3 +pair_coeff * * 1.0 1.0 +mass 1 1.0 + +atom_modify sort 0 1 +velocity all create 0.1 45678 dist gaussian + +compute u all pe + +compute p all pressure NULL pair + +compute hma all HMA settemp u p 9.579586686264458 cv + +timestep 0.005 + +fix settemp all nvt temp 1.0 1.0 0.5 +thermo_style custom elapsed temp c_u c_hma[1] c_p c_hma[2] c_hma[3] +thermo_modify format float '%22.15e' +thermo 500 +run 20000 +thermo 20 +run 200000 diff --git a/examples/USER/hma/log.6Nov18.hma.g++.1 b/examples/USER/hma/log.6Nov18.hma.g++.1 new file mode 100644 index 0000000000..fba304d783 --- /dev/null +++ b/examples/USER/hma/log.6Nov18.hma.g++.1 @@ -0,0 +1,10159 @@ +LAMMPS (31 Aug 2018) +# Harmonically mapped average example + +units lj +dimension 3 +boundary p p p +atom_style atomic +atom_modify map array +# ---------- Create Atoms ---------------------------- +lattice fcc 1.0 +Lattice spacing in x,y,z = 1.5874 1.5874 1.5874 +region box block 0 4 0 4 0 4 units lattice +create_box 1 box +Created orthogonal box = (0 0 0) to (6.3496 6.3496 6.3496) + 1 by 1 by 1 MPI processor grid +lattice fcc 1.0 orient x 1 0 0 orient y 0 1 0 orient z 0 0 1 +Lattice spacing in x,y,z = 1.5874 1.5874 1.5874 +create_atoms 1 region box +Created 256 atoms + Time spent = 0.000558853 secs +# ---------- Define Interatomic Potential --------------------- +pair_style lj/smooth/linear 3 +pair_coeff * * 1.0 1.0 +mass 1 1.0 + +atom_modify sort 0 1 +velocity all create 0.1 45678 dist gaussian + +compute u all pe + +compute p all pressure NULL pair + +compute hma all HMA settemp u p 9.579586686264458 cv + +timestep 0.005 + +fix settemp all nvt temp 1.0 1.0 0.5 +thermo_style custom elapsed temp c_u c_hma[1] c_p c_hma[2] c_hma[3] +thermo_modify format float '%22.15e' +thermo 500 +run 20000 +Neighbor list info ... + update every 1 steps, delay 10 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 3.3 + ghost atom cutoff = 3.3 + binsize = 1.65, bins = 4 4 4 + 2 neighbor lists, perpetual/occasional/extra = 1 1 0 + (1) pair lj/smooth/linear, perpetual + attributes: half, newton on + pair build: half/bin/atomonly/newton + stencil: half/bin/3d/newton + bin: standard + (2) compute HMA, occasional, copy from (1) + attributes: half, newton on + pair build: copy + stencil: none + bin: none +Per MPI rank memory allocation (min/avg/max) = 3.425 | 3.425 | 3.425 Mbytes +Elapsed Temp c_u c_hma[1] c_p c_hma[2] c_hma[3] + 0 9.999999999999984e-02 -7.321210550029651e+00 -5.827069925029651e+00 -3.541123363606526e+00 6.038463322657933e+00 8.693908581888376e+03 + 500 2.386148283497847e-01 -7.031289207724356e+00 -5.841955950103862e+00 -1.905706169928171e+00 5.923629444055504e+00 8.738341241696249e+03 + 1000 1.033640532939756e+00 -5.899129588008281e+00 -5.989693420271868e+00 4.270084606318116e+00 4.750053066752854e+00 9.185409687897396e+03 + 1500 9.066678783388608e-01 -6.084949363864708e+00 -6.008077972326689e+00 3.223989663631114e+00 4.665397089651815e+00 9.241882696308397e+03 + 2000 8.653666754537616e-01 -6.040261189331211e+00 -6.030563879284796e+00 3.468617809376976e+00 4.524301264317375e+00 9.311127705836057e+03 + 2500 1.037531298248839e+00 -6.132639377068311e+00 -5.988640354751864e+00 2.977362159634933e+00 4.804226829552658e+00 9.182209655823657e+03 + 3000 1.021622746681649e+00 -5.898542445856487e+00 -6.009151612939077e+00 4.221727087636999e+00 4.586592133535478e+00 9.245164803297535e+03 + 3500 1.106519160715706e+00 -5.970546432235779e+00 -6.015249245376119e+00 3.866123627527625e+00 4.609433156737818e+00 9.263945750662717e+03 + 4000 9.930240066865930e-01 -5.912152557873307e+00 -6.025083715886064e+00 4.138611283233161e+00 4.490143097883684e+00 9.294225198089340e+03 + 4500 9.646555658575586e-01 -6.015677130022131e+00 -6.036721545560821e+00 3.568689708725919e+00 4.447849418089985e+00 9.330138922961722e+03 + 5000 9.434923165946090e-01 -6.027456548570741e+00 -6.014550053270733e+00 3.565441638398635e+00 4.639552731684967e+00 9.261770624752438e+03 + 5500 1.026864240931640e+00 -6.061505823962392e+00 -6.019404988381412e+00 3.401241932620071e+00 4.642991445609312e+00 9.276731237911577e+03 + 6000 9.983312526598234e-01 -5.946349587454857e+00 -5.983050555300542e+00 3.979901469071073e+00 4.769158832244731e+00 9.165087115091061e+03 + 6500 1.006036143286260e+00 -5.945850544079388e+00 -6.071303751273131e+00 3.946077295974201e+00 4.225705566446658e+00 9.437216768355414e+03 + 7000 9.981593359539495e-01 -5.990330698910480e+00 -6.037063892399898e+00 3.663774642188439e+00 4.395425413233882e+00 9.331181435130977e+03 + 7500 9.507280203289744e-01 -5.984730396336532e+00 -5.991644972746507e+00 3.755491186444424e+00 4.715786618671108e+00 9.191404619772287e+03 + 8000 9.048837157594684e-01 -6.079029085917312e+00 -5.964267902838972e+00 3.230203589004437e+00 4.889180061475951e+00 9.107693071292861e+03 + 8500 9.883413333994134e-01 -6.002876846326834e+00 -6.011751334719937e+00 3.642240804100097e+00 4.591282118424260e+00 9.253163154010274e+03 + 9000 1.056758147654552e+00 -6.036760797857792e+00 -6.002535828890329e+00 3.520846457975964e+00 4.717371526083967e+00 9.224856128595033e+03 + 9500 1.035347515567710e+00 -5.969647617813958e+00 -5.990309632036265e+00 3.813299824718261e+00 4.694655341617407e+00 9.187302608800977e+03 + 10000 1.023738343179159e+00 -5.877099589117778e+00 -6.048562900734738e+00 4.344908960531808e+00 4.360340091365503e+00 9.366720846528935e+03 + 10500 1.069815794809561e+00 -5.913367214053245e+00 -6.010777075880958e+00 4.147089675758311e+00 4.587747175016184e+00 9.250158711907829e+03 + 11000 9.776294387160251e-01 -5.925772082085378e+00 -5.989277934483906e+00 4.082344757077178e+00 4.717684325105934e+00 9.184160813848264e+03 + 11500 9.499730095716009e-01 -5.976861040295939e+00 -6.004120411932708e+00 3.808317456317362e+00 4.651789926004906e+00 9.229684845202884e+03 + 12000 9.782073857977380e-01 -6.066220802750934e+00 -6.031270148041170e+00 3.304122260466307e+00 4.504814328406108e+00 9.313293791801259e+03 + 12500 9.552683271823048e-01 -6.108551273751968e+00 -5.979666568626595e+00 3.136478232915417e+00 4.876554154588973e+00 9.154740057331765e+03 + 13000 8.742841944497640e-01 -6.013421944223564e+00 -6.021450865532995e+00 3.577734470946406e+00 4.531631162316097e+00 9.283015239817061e+03 + 13500 1.004344955842980e+00 -5.899309998559693e+00 -6.011273141389537e+00 4.232629792927130e+00 4.589720100557810e+00 9.251678010621874e+03 + 14000 9.987696680587935e-01 -5.929715246484374e+00 -6.008152969607664e+00 4.103967501967555e+00 4.653565957595201e+00 9.242036851405348e+03 + 14500 1.006604156366316e+00 -6.153189106822779e+00 -5.973434451881044e+00 2.841124235115949e+00 4.873303280734345e+00 9.135699098879228e+03 + 15000 9.051321416654020e-01 -6.031733280212374e+00 -5.972657495662279e+00 3.559001586802186e+00 4.898223883636946e+00 9.133297115127007e+03 + 15500 9.682672962081463e-01 -6.067136130017134e+00 -5.966412476549884e+00 3.354912150470541e+00 4.933282955614485e+00 9.114211079881910e+03 + 16000 1.015665897061745e+00 -6.059784334366720e+00 -5.980063616786515e+00 3.369338836061829e+00 4.827107533148539e+00 9.155963314807441e+03 + 16500 1.006968180883997e+00 -5.995526549328130e+00 -5.964005551783969e+00 3.802449041277696e+00 4.983447487034876e+00 9.106875404577086e+03 + 17000 1.042050305358167e+00 -5.919486263379956e+00 -6.013086895161285e+00 4.122119914992582e+00 4.584650602653237e+00 9.257241816102296e+03 + 17500 1.013492134662422e+00 -5.898786232899295e+00 -5.988108507110901e+00 4.246935217818169e+00 4.734032896717861e+00 9.180541556032720e+03 + 18000 1.045293495070465e+00 -6.013155802624135e+00 -6.000945960251793e+00 3.631220305239846e+00 4.701331109608827e+00 9.219959027336774e+03 + 18500 9.134705431704426e-01 -5.943263213107316e+00 -6.036334213909798e+00 4.028889501874485e+00 4.494461412575806e+00 9.328923769735196e+03 + 19000 1.007628738828841e+00 -6.062647924602851e+00 -5.961993496778848e+00 3.347669071096405e+00 4.925642371884200e+00 9.100752827583676e+03 + 19500 1.000237087620137e+00 -5.934759822585448e+00 -6.020766118588664e+00 4.035509558295610e+00 4.541648097213850e+00 9.280908870426259e+03 + 20000 9.615364955745067e-01 -5.859940462234714e+00 -5.981549364677676e+00 4.480555066266412e+00 4.782257929522093e+00 9.160435351560425e+03 +Loop time of 33.5763 on 1 procs for 20000 steps with 256 atoms + +Performance: 257324.049 tau/day, 595.658 timesteps/s +99.9% CPU use with 1 MPI tasks x no OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 30.404 | 30.404 | 30.404 | 0.0 | 90.55 +Neigh | 2.1959 | 2.1959 | 2.1959 | 0.0 | 6.54 +Comm | 0.50746 | 0.50746 | 0.50746 | 0.0 | 1.51 +Output | 0.16503 | 0.16503 | 0.16503 | 0.0 | 0.49 +Modify | 0.237 | 0.237 | 0.237 | 0.0 | 0.71 +Other | | 0.06721 | | | 0.20 + +Nlocal: 256 ave 256 max 256 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 2116 ave 2116 max 2116 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 19135 ave 19135 max 19135 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 19135 +Ave neighs/atom = 74.7461 +Neighbor list builds = 1946 +Dangerous builds = 1902 +thermo 20 +run 200000 +Per MPI rank memory allocation (min/avg/max) = 3.806 | 3.806 | 3.806 Mbytes +Elapsed Temp c_u c_hma[1] c_p c_hma[2] c_hma[3] + 0 9.615364955745067e-01 -5.859940462234714e+00 -5.981549364677676e+00 4.480555066266412e+00 4.782257929522093e+00 9.160435351560425e+03 + 20 1.020600011999315e+00 -5.958432657247554e+00 -5.970407876039725e+00 3.888068459330918e+00 4.819304899867157e+00 9.126408714227488e+03 + 40 9.814651761832457e-01 -5.909251537070915e+00 -5.991660882363840e+00 4.211003703521785e+00 4.737796490044842e+00 9.191407419668969e+03 + 60 1.017977787037964e+00 -5.969196214125930e+00 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-5.981151237033027e+00 3.665707003744082e+00 4.881005328028778e+00 9.159263627748211e+03 + 199300 9.523798101299401e-01 -5.918232667453390e+00 -5.998723135883461e+00 4.163542274049221e+00 4.701353548464017e+00 9.213109595715912e+03 + 199320 1.047474480588589e+00 -6.056307448133158e+00 -5.990589763484913e+00 3.443288105590085e+00 4.820649220619144e+00 9.188171568825132e+03 + 199340 1.052063333482815e+00 -6.061954723129742e+00 -5.995274675364363e+00 3.360298110510838e+00 4.743185263483689e+00 9.202556647255178e+03 + 199360 9.899399315649036e-01 -5.969841175554527e+00 -6.031105574437271e+00 3.837881644118959e+00 4.486091985099155e+00 9.312795952955328e+03 + 199380 1.045345255275729e+00 -6.054903517585581e+00 -6.000275517756035e+00 3.428601172163945e+00 4.742283600840854e+00 9.217917022324442e+03 + 199400 9.780104923920887e-01 -5.958423420917970e+00 -6.016396141193878e+00 3.865736483935700e+00 4.532848152861964e+00 9.267458321744127e+03 + 199420 9.694306975833765e-01 -5.949393899958658e+00 -6.034676514495618e+00 3.942958172837187e+00 4.453252202724016e+00 9.323803532354184e+03 + 199440 1.011138230619257e+00 -6.015121038088004e+00 -6.009321354178946e+00 3.625230601241597e+00 4.658533283745596e+00 9.245682356743368e+03 + 199460 9.823835158722997e-01 -5.976377539506453e+00 -6.001894201937834e+00 3.798620426431028e+00 4.652099802059292e+00 9.222862453835854e+03 + 199480 1.074562355574544e+00 -6.118486926125487e+00 -5.995296473648373e+00 3.016297520865714e+00 4.723676162650218e+00 9.202624643333613e+03 + 199500 9.926831596967829e-01 -6.005199868966562e+00 -6.000357663445108e+00 3.700903545492443e+00 4.728708238925513e+00 9.218133858751144e+03 + 199520 9.528151168241586e-01 -5.959418705000071e+00 -5.963065830859622e+00 3.901076693474031e+00 4.880134332397586e+00 9.104004014073711e+03 + 199540 9.557829809703990e-01 -5.977637161975556e+00 -5.991671870257975e+00 3.799602485859072e+00 4.719013019037336e+00 9.191491214806965e+03 + 199560 9.838846370790553e-01 -6.036655642150919e+00 -6.003509719541851e+00 3.458439215320582e+00 4.648768232256796e+00 9.227830722879620e+03 + 199580 9.843932648042784e-01 -6.058662065699025e+00 -6.020554801397395e+00 3.374629497019970e+00 4.593447305720019e+00 9.280268165956993e+03 + 199600 1.065184573658751e+00 -6.206851690895959e+00 -5.968086425263754e+00 2.610633649932813e+00 4.981660753998377e+00 9.119370099006041e+03 + 199620 9.388817486791809e-01 -6.048259703771625e+00 -6.004812660448888e+00 3.444013103007198e+00 4.693492749174577e+00 9.231822964740768e+03 + 199640 9.473654082682319e-01 -6.087966531003856e+00 -5.979134478052076e+00 3.195402416940680e+00 4.820332906695564e+00 9.153129876030411e+03 + 199660 9.210577256459164e-01 -6.068236326393697e+00 -5.967782053655758e+00 3.335152873111248e+00 4.911976852420958e+00 9.118414230427796e+03 + 199680 9.497229600007705e-01 -6.121910609110069e+00 -5.971990252219380e+00 3.092920192420396e+00 4.953786081786985e+00 9.131271875339731e+03 + 199700 9.516524276659803e-01 -6.127906301058084e+00 -6.000100462469979e+00 2.979286429490728e+00 4.713167332553232e+00 9.217372102518229e+03 + 199720 9.443608833647245e-01 -6.114016019953694e+00 -6.000580190700743e+00 3.091035310234930e+00 4.742401395943221e+00 9.218828712551509e+03 + 199740 8.681959517945045e-01 -5.990991490549361e+00 -5.977120027277696e+00 3.797772807366312e+00 4.877424896074221e+00 9.146908120580996e+03 + 199760 9.625155118642070e-01 -6.110458936060956e+00 -5.978494259332300e+00 3.124357089378134e+00 4.882118684621803e+00 9.151154400341169e+03 + 199780 9.848261985222230e-01 -6.112095588872020e+00 -5.980370944143631e+00 3.096964062230267e+00 4.853347356583562e+00 9.156887038258950e+03 + 199800 9.658504385268453e-01 -6.044741959287682e+00 -5.983150214559801e+00 3.514935168261291e+00 4.868604497780478e+00 9.165405595380049e+03 + 199820 9.830751481829464e-01 -6.030277382849008e+00 -6.003547531492968e+00 3.595906231692601e+00 4.749393174610113e+00 9.227958060577354e+03 + 199840 1.019195363692946e+00 -6.047159382563301e+00 -6.018232273751166e+00 3.484691277977978e+00 4.650795213232877e+00 9.273127872675630e+03 + 199860 1.009814556481902e+00 -6.004451936660288e+00 -6.029796701673096e+00 3.664786858860082e+00 4.519253296066829e+00 9.308739911114350e+03 + 199880 1.004112823631311e+00 -5.975808665464897e+00 -5.994508893678078e+00 3.866906624242725e+00 4.759527019991680e+00 9.200211087352904e+03 + 199900 1.017006687798344e+00 -5.979166475348716e+00 -6.024287631510320e+00 3.884200204963863e+00 4.625107543807584e+00 9.291749564292193e+03 + 199920 1.029645300704506e+00 -5.988407957108219e+00 -6.015604824463416e+00 3.792038397567344e+00 4.635869776512177e+00 9.265017077501841e+03 + 199940 1.016090771897235e+00 -5.963111834339648e+00 -5.964819076856839e+00 3.924983490607407e+00 4.915180239878768e+00 9.109359800541135e+03 + 199960 1.089150523107765e+00 -6.068080542656683e+00 -5.972503306663688e+00 3.396420435709163e+00 4.945239715310409e+00 9.132824214410233e+03 + 199980 9.700833243472550e-01 -5.891585904890412e+00 -6.005450837672986e+00 4.354796401538968e+00 4.700966336960025e+00 9.233789429481529e+03 + 200000 1.036656071639917e+00 -5.992403506639822e+00 -5.993257960485003e+00 3.764547892583718e+00 4.759641486378383e+00 9.196316925648398e+03 +Loop time of 380.886 on 1 procs for 200000 steps with 256 atoms + +Performance: 226839.823 tau/day, 525.092 timesteps/s +99.9% CPU use with 1 MPI tasks x no OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 308.99 | 308.99 | 308.99 | 0.0 | 81.12 +Neigh | 22.559 | 22.559 | 22.559 | 0.0 | 5.92 +Comm | 5.1164 | 5.1164 | 5.1164 | 0.0 | 1.34 +Output | 41.166 | 41.166 | 41.166 | 0.0 | 10.81 +Modify | 2.379 | 2.379 | 2.379 | 0.0 | 0.62 +Other | | 0.6754 | | | 0.18 + +Nlocal: 256 ave 256 max 256 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 2125 ave 2125 max 2125 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 19131 ave 19131 max 19131 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 19131 +Ave neighs/atom = 74.7305 +Neighbor list builds = 19989 +Dangerous builds = 19886 +Total wall time: 0:06:54 diff --git a/examples/USER/hma/log.6Nov18.hma.g++.4 b/examples/USER/hma/log.6Nov18.hma.g++.4 new file mode 100644 index 0000000000..5b25fa5cf5 --- /dev/null +++ b/examples/USER/hma/log.6Nov18.hma.g++.4 @@ -0,0 +1,10159 @@ +LAMMPS (31 Aug 2018) +# Harmonically mapped average example + +units lj +dimension 3 +boundary p p p +atom_style atomic +atom_modify map array +# ---------- Create Atoms ---------------------------- +lattice fcc 1.0 +Lattice spacing in x,y,z = 1.5874 1.5874 1.5874 +region box block 0 4 0 4 0 4 units lattice +create_box 1 box +Created orthogonal box = (0 0 0) to (6.3496 6.3496 6.3496) + 1 by 2 by 2 MPI processor grid +lattice fcc 1.0 orient x 1 0 0 orient y 0 1 0 orient z 0 0 1 +Lattice spacing in x,y,z = 1.5874 1.5874 1.5874 +create_atoms 1 region box +Created 256 atoms + Time spent = 0.000636816 secs +# ---------- Define Interatomic Potential --------------------- +pair_style lj/smooth/linear 3 +pair_coeff * * 1.0 1.0 +mass 1 1.0 + +atom_modify sort 0 1 +velocity all create 0.1 45678 dist gaussian + +compute u all pe + +compute p all pressure NULL pair + +compute hma all HMA settemp u p 9.579586686264458 cv + +timestep 0.005 + +fix settemp all nvt temp 1.0 1.0 0.5 +thermo_style custom elapsed temp c_u c_hma[1] c_p c_hma[2] c_hma[3] +thermo_modify format float '%22.15e' +thermo 500 +run 20000 +Neighbor list info ... + update every 1 steps, delay 10 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 3.3 + ghost atom cutoff = 3.3 + binsize = 1.65, bins = 4 4 4 + 2 neighbor lists, perpetual/occasional/extra = 1 1 0 + (1) pair lj/smooth/linear, perpetual + attributes: half, newton on + pair build: half/bin/atomonly/newton + stencil: half/bin/3d/newton + bin: standard + (2) compute HMA, occasional, copy from (1) + attributes: half, newton on + pair build: copy + stencil: none + bin: none +Per MPI rank memory allocation (min/avg/max) = 3.389 | 3.389 | 3.389 Mbytes +Elapsed Temp c_u c_hma[1] c_p c_hma[2] c_hma[3] + 0 9.999999999999999e-02 -7.321210550030622e+00 -5.827069925030622e+00 -3.541123363606526e+00 6.038463322657932e+00 8.693908581891272e+03 + 500 2.319904532047116e-01 -7.021814067268549e+00 -5.841520703728273e+00 -1.859554996730893e+00 5.917872146525079e+00 8.737041016754241e+03 + 1000 1.104889191155021e+00 -6.005326544560477e+00 -6.005300065747159e+00 3.645694884120414e+00 4.645846929564070e+00 9.233336265503700e+03 + 1500 9.475049376144361e-01 -6.133389836457317e+00 -5.983811791861923e+00 2.980778280706599e+00 4.839678559900945e+00 9.167450093661304e+03 + 2000 9.009354935012601e-01 -6.066361566415782e+00 -5.975649385751911e+00 3.331919983683387e+00 4.852803362719920e+00 9.142450653666589e+03 + 2500 1.002748731362028e+00 -6.037709705055500e+00 -5.998660236350431e+00 3.517524667487255e+00 4.741752759677512e+00 9.212938381713899e+03 + 3000 1.123087652951704e+00 -6.025819107168451e+00 -5.970493239986080e+00 3.598743028856235e+00 4.916432719867683e+00 9.126676463986189e+03 + 3500 1.115128009750835e+00 -6.000529470165528e+00 -5.980015761414576e+00 3.665878335379198e+00 4.783671225513338e+00 9.155782280210480e+03 + 4000 9.904879689205039e-01 -5.990830917252424e+00 -6.007049321999301e+00 3.700324729502504e+00 4.607196139655914e+00 9.238716127101230e+03 + 4500 9.696423790018132e-01 -6.095364960235830e+00 -5.949103254372231e+00 3.188999551316120e+00 5.028856900310743e+00 9.061471896280929e+03 + 5000 1.005681297563624e+00 -6.094938179693363e+00 -6.014945551672039e+00 3.140253069724724e+00 4.599583118642348e+00 9.263005212755274e+03 + 5500 1.067821663160412e+00 -6.055271652935048e+00 -6.039553220002009e+00 3.350955211546091e+00 4.441212885867230e+00 9.338870121131475e+03 + 6000 1.019349023817732e+00 -5.912735006243721e+00 -6.010199997355059e+00 4.160148455119939e+00 4.600489393500003e+00 9.248369562541713e+03 + 6500 1.033977564076081e+00 -5.962511500402099e+00 -5.953097811556573e+00 3.913955620678704e+00 4.968010478793357e+00 9.073605525336026e+03 + 7000 1.035036973336388e+00 -6.011513860495915e+00 -5.988661036457318e+00 3.570585392636366e+00 4.701809844729083e+00 9.182284012600518e+03 + 7500 9.759766417830451e-01 -6.011014245515786e+00 -5.997095489328838e+00 3.659421763886547e+00 4.739345415832561e+00 9.208142257833988e+03 + 8000 9.701274032979823e-01 -6.070706464001116e+00 -5.987899394187518e+00 3.293522632549048e+00 4.769013641771370e+00 9.179944973040452e+03 + 8500 1.002959574283594e+00 -6.000331246180245e+00 -6.022939013616290e+00 3.707537441996905e+00 4.577720142838428e+00 9.287619492673581e+03 + 9000 9.541471061067928e-01 -5.891837375294362e+00 -6.000893913894259e+00 4.214373867383508e+00 4.588154346298096e+00 9.219760426705488e+03 + 9500 1.005476043930556e+00 -6.054397260431607e+00 -5.963822185829731e+00 3.425817325831102e+00 4.945913420642570e+00 9.106317976320150e+03 + 10000 9.834510517532772e-01 -5.979858570968017e+00 -6.007829122692488e+00 3.832487507111145e+00 4.671876270680338e+00 9.241093007564954e+03 + 10500 1.053423257346257e+00 -5.984863687481322e+00 -5.990560458118040e+00 3.742155897948207e+00 4.709444159379769e+00 9.188099433599265e+03 + 11000 1.027766819783240e+00 -5.964303012082833e+00 -5.987340607292543e+00 3.942276092974025e+00 4.809990656223532e+00 9.178213465454402e+03 + 11500 1.030919611642090e+00 -5.996031790431708e+00 -6.010813071174461e+00 3.713452645350145e+00 4.628576243929453e+00 9.250277317464830e+03 + 12000 1.015499044847646e+00 -5.983611533298556e+00 -6.000577066405612e+00 3.747611330243804e+00 4.650192613735324e+00 9.218807640515772e+03 + 12500 9.260784226173562e-01 -5.995616138164384e+00 -6.024603077235440e+00 3.708688522431407e+00 4.542241032571079e+00 9.292727745364478e+03 + 13000 9.581084725650251e-01 -6.095817502268568e+00 -5.989303506622369e+00 3.230806633332333e+00 4.842426479320365e+00 9.184229513868806e+03 + 13500 9.246476920572243e-01 -5.986197290479123e+00 -5.980486024616446e+00 3.778398028002328e+00 4.811193000401358e+00 9.157208321147285e+03 + 14000 9.018834156590910e-01 -5.891981523518482e+00 -5.961281643266227e+00 4.310640039569481e+00 4.912708027819059e+00 9.098571305044385e+03 + 14500 9.458192412990540e-01 -5.924212527125402e+00 -5.974831040418032e+00 4.099524287456710e+00 4.808864950940809e+00 9.139925423823777e+03 + 15000 1.079258475602827e+00 -5.842389291052847e+00 -5.997594135488276e+00 4.542013464261510e+00 4.650803229641226e+00 9.209631946001080e+03 + 15500 1.003773905363782e+00 -5.990536501227417e+00 -5.978949148782005e+00 3.711448614654375e+00 4.777984985532921e+00 9.152543385133793e+03 + 16000 9.589971646383746e-01 -6.022404990638810e+00 -6.013121691584658e+00 3.591520611305744e+00 4.644826751060574e+00 9.257382394405931e+03 + 16500 1.027873542611377e+00 -6.062068879792612e+00 -5.995808570227100e+00 3.344041739290934e+00 4.724518690565871e+00 9.204185610519249e+03 + 17000 9.721883229756479e-01 -6.076377536863534e+00 -5.995495525201934e+00 3.317173564950596e+00 4.781610592362355e+00 9.203227919920830e+03 + 17500 9.870692120707141e-01 -5.965983792560558e+00 -6.036111701999152e+00 3.838886592024325e+00 4.436201283769008e+00 9.328234074356338e+03 + 18000 1.004272604822617e+00 -5.960763698221652e+00 -5.980795290630440e+00 3.950710186832507e+00 4.835685683342340e+00 9.158184493996429e+03 + 18500 9.381056200232580e-01 -5.953631223909241e+00 -6.011057530919335e+00 3.898044457090124e+00 4.568293715545873e+00 9.251034889270257e+03 + 19000 9.369931263537112e-01 -6.012014674095721e+00 -5.987682214265706e+00 3.582518713971043e+00 4.722239463750979e+00 9.179299635700279e+03 + 19500 9.837184187823201e-01 -5.957066902345472e+00 -6.012125787465584e+00 3.937810342708973e+00 4.621653704014352e+00 9.254320960371275e+03 + 20000 1.079101865720838e+00 -6.089503178102808e+00 -5.960131548856806e+00 3.215696838220799e+00 4.958568753546265e+00 9.095068306811330e+03 +Loop time of 4.841 on 4 procs for 20000 steps with 256 atoms + +Performance: 1784755.120 tau/day, 4131.378 timesteps/s +98.7% CPU use with 4 MPI tasks x no OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 2.3889 | 2.6923 | 3.0228 | 14.4 | 55.62 +Neigh | 0.52899 | 0.5489 | 0.57081 | 2.3 | 11.34 +Comm | 1.0419 | 1.3856 | 1.697 | 20.8 | 28.62 +Output | 0.022234 | 0.022308 | 0.022518 | 0.1 | 0.46 +Modify | 0.13626 | 0.14418 | 0.15704 | 2.2 | 2.98 +Other | | 0.04763 | | | 0.98 + +Nlocal: 64 ave 68 max 60 min +Histogram: 1 1 0 0 0 0 0 0 1 1 +Nghost: 1344.25 ave 1352 max 1339 min +Histogram: 1 0 0 2 0 0 0 0 0 1 +Neighs: 4758 ave 5243 max 3935 min +Histogram: 1 0 0 0 0 0 1 0 1 1 + +Total # of neighbors = 19032 +Ave neighs/atom = 74.3438 +Neighbor list builds = 1938 +Dangerous builds = 1898 +thermo 20 +run 200000 +Per MPI rank memory allocation 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-5.968200087682216e+00 3.132786366069281e+00 4.977777659664543e+00 9.119696429693091e+03 + 199920 8.478880513404523e-01 -6.043267344699284e+00 -5.977625330208900e+00 3.500506679661614e+00 4.877433284934312e+00 9.148497479033846e+03 + 199940 8.660608083304254e-01 -6.064289496109857e+00 -6.010313559354831e+00 3.416172307521693e+00 4.726110489118270e+00 9.248739882428541e+03 + 199960 9.304301216794905e-01 -6.139891398497096e+00 -5.977879919520982e+00 3.023079698606037e+00 4.953374682082232e+00 9.149294637624478e+03 + 199980 9.633635787878904e-01 -6.153324116670857e+00 -5.981484082093043e+00 2.878934939218798e+00 4.865667009924017e+00 9.160317920496162e+03 + 200000 9.635163730977483e-01 -6.102203225911095e+00 -5.997212004084306e+00 3.191924486932165e+00 4.794800330000662e+00 9.208486378845661e+03 +Loop time of 56.3641 on 4 procs for 200000 steps with 256 atoms + +Performance: 1532891.800 tau/day, 3548.361 timesteps/s +98.3% CPU use with 4 MPI tasks x no OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 25.291 | 28.255 | 31.464 | 44.1 | 50.13 +Neigh | 5.5169 | 5.6888 | 5.8734 | 6.9 | 10.09 +Comm | 11.506 | 14.839 | 17.828 | 63.0 | 26.33 +Output | 5.5139 | 5.5345 | 5.5859 | 1.3 | 9.82 +Modify | 1.4354 | 1.497 | 1.6066 | 5.6 | 2.66 +Other | | 0.5505 | | | 0.98 + +Nlocal: 64 ave 65 max 63 min +Histogram: 2 0 0 0 0 0 0 0 0 2 +Nghost: 1334.5 ave 1343 max 1328 min +Histogram: 1 0 0 1 1 0 0 0 0 1 +Neighs: 4748.25 ave 5438 max 4111 min +Histogram: 1 0 0 0 1 1 0 0 0 1 + +Total # of neighbors = 18993 +Ave neighs/atom = 74.1914 +Neighbor list builds = 19989 +Dangerous builds = 19885 +Total wall time: 0:01:01 -- GitLab From 02373c4c3b932db416869b07da68207d439ecc9b Mon Sep 17 00:00:00 2001 From: Andrew Schultz Date: Fri, 29 Mar 2019 15:22:44 -0400 Subject: [PATCH 009/469] Move HMA bits into USER-HMA package --- src/USER-HMA/Install.sh | 31 ++++++++++++++++++++++++++++++ src/{ => USER-HMA}/compute_hma.cpp | 0 src/{ => USER-HMA}/compute_hma.h | 0 3 files changed, 31 insertions(+) create mode 100644 src/USER-HMA/Install.sh rename src/{ => USER-HMA}/compute_hma.cpp (100%) rename src/{ => USER-HMA}/compute_hma.h (100%) diff --git a/src/USER-HMA/Install.sh b/src/USER-HMA/Install.sh new file mode 100644 index 0000000000..1f8f418ca2 --- /dev/null +++ b/src/USER-HMA/Install.sh @@ -0,0 +1,31 @@ +# Install/Uninstall package files in LAMMPS +# mode = 0/1/2 for uninstall/install/update + +mode=$1 + +# enforce using portable C locale +LC_ALL=C +export LC_ALL + +# arg1 = file, arg2 = file it depends on + +action () { + if (test $mode = 0) then + rm -f ../$1 + elif (! cmp -s $1 ../$1) then + if (test -z "$2" || test -e ../$2) then + cp $1 .. + if (test $mode = 2) then + echo " updating src/$1" + fi + fi + elif (test -n "$2") then + if (test ! -e ../$2) then + rm -f ../$1 + fi + fi +} + +# package files without dependencies +action compute_hma.h +action compute_hma.cpp diff --git a/src/compute_hma.cpp b/src/USER-HMA/compute_hma.cpp similarity index 100% rename from src/compute_hma.cpp rename to src/USER-HMA/compute_hma.cpp diff --git a/src/compute_hma.h b/src/USER-HMA/compute_hma.h similarity index 100% rename from src/compute_hma.h rename to src/USER-HMA/compute_hma.h -- GitLab From d000c6883b205b92425a61e3a86b23116a1f3795 Mon Sep 17 00:00:00 2001 From: Andrew Schultz Date: Fri, 29 Mar 2019 15:41:15 -0400 Subject: [PATCH 010/469] Mention need to build HMA as USER pacakge --- doc/src/compute_hma.txt | 8 +++++++- 1 file changed, 7 insertions(+), 1 deletion(-) diff --git a/doc/src/compute_hma.txt b/doc/src/compute_hma.txt index f71ddc9e2e..c4ade07ad7 100644 --- a/doc/src/compute_hma.txt +++ b/doc/src/compute_hma.txt @@ -132,7 +132,13 @@ output"_Howto_output.html doc page for an overview of LAMMPS output options. The vector values calculated by this compute are "extensive". The scalar value will be in energy "units"_units.html. -[Restrictions:] Usage restricted to canonical (NVT) ensemble simulation only. +[Restrictions:] + +This compute is distributed as the USER-HMA package. It is only +enabled if LAMMPS was built with that package. See the "Build +package"_Build_package.html doc page for more info. + +Usage restricted to canonical (NVT) ensemble simulation only. [Related commands:] -- GitLab From 62bfd300f0a7ea8ee5efb2324f42affed303c481 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Eugen=20Ro=C5=BEi=C4=87?= Date: Tue, 16 Apr 2019 13:43:02 +0200 Subject: [PATCH 011/469] Gitignore update --- src/.gitignore | 2 ++ 1 file changed, 2 insertions(+) diff --git a/src/.gitignore b/src/.gitignore index 9670d1ca20..00fff20131 100644 --- a/src/.gitignore +++ b/src/.gitignore @@ -760,6 +760,8 @@ /pair_comb3.h /pair_colloid.cpp /pair_colloid.h +/pair_cosine_squared.cpp +/pair_cosine_squared.h /pair_coul_diel.cpp /pair_coul_diel.h /pair_coul_long.cpp -- GitLab From 99430767dfa399dd1b8fd8a0ecf71fdef5544c5d Mon Sep 17 00:00:00 2001 From: "Ryan S. Elliott" Date: Tue, 30 Apr 2019 21:45:21 -0500 Subject: [PATCH 012/469] Start devel of native support for KIM simulator models * CMake change to use KIM-API SimulatorModels branch * Minimal changes to pair_kim to illustrate use of KIM API interface. Only c++ interface is implemented for development. * Added example input: in.kim.simulator-model --- cmake/CMakeLists.txt | 6 +++-- examples/kim/in.kim.simulator-model | 41 +++++++++++++++++++++++++++++ src/KIM/pair_kim.cpp | 21 ++++++++++++++- src/KIM/pair_kim.h | 2 ++ 4 files changed, 67 insertions(+), 3 deletions(-) create mode 100644 examples/kim/in.kim.simulator-model diff --git a/cmake/CMakeLists.txt b/cmake/CMakeLists.txt index dbbbc7f7ac..6acc61576a 100644 --- a/cmake/CMakeLists.txt +++ b/cmake/CMakeLists.txt @@ -738,8 +738,10 @@ if(PKG_KIM) enable_language(Fortran) include(ExternalProject) ExternalProject_Add(kim_build - URL https://s3.openkim.org/kim-api/kim-api-2.0.2.txz - URL_MD5 537d9c0abd30f85b875ebb584f9143fa + GIT_REPOSITORY https://github.com/openkim/kim-api.git + GIT_TAG SimulatorModels + #URL https://s3.openkim.org/kim-api/kim-api-2.0.2.txz + #URL_MD5 537d9c0abd30f85b875ebb584f9143fa BINARY_DIR build CMAKE_ARGS -DCMAKE_C_COMPILER=${CMAKE_C_COMPILER} -DCMAKE_CXX_COMPILER=${CMAKE_CXX_COMPILER} diff --git a/examples/kim/in.kim.simulator-model b/examples/kim/in.kim.simulator-model new file mode 100644 index 0000000000..32baf9d78e --- /dev/null +++ b/examples/kim/in.kim.simulator-model @@ -0,0 +1,41 @@ +# 3d Lennard-Jones melt +# +# This example requires that the example models provided with +# the kim-api package are installed. see the ./lib/kim/README or +# ./lib/kim/Install.py files for details on how to install these +# example models. +# + +variable x index 1 +variable y index 1 +variable z index 1 + +variable xx equal 20*$x +variable yy equal 20*$y +variable zz equal 20*$z + +units metal +atom_style atomic +newton off + +lattice fcc 4.4300 +region box block 0 ${xx} 0 ${yy} 0 ${zz} +create_box 1 box +create_atoms 1 box + +#pair_style lj/cut 8.1500 +#pair_coeff 1 1 0.0104 3.4000 + +pair_style kim ex_sim_model_Si_mod_tersoff +pair_coeff * * Ar + +mass 1 39.95 +velocity all create 200.0 232345 loop geom + +neighbor 0.3 bin +neigh_modify delay 0 every 1 check yes + +fix 1 all nve +#fix 1 all npt temp 1.0 1.0 1.0 iso 1.0 1.0 3.0 + +run 100 diff --git a/src/KIM/pair_kim.cpp b/src/KIM/pair_kim.cpp index a1c13ae81f..01b435194e 100644 --- a/src/KIM/pair_kim.cpp +++ b/src/KIM/pair_kim.cpp @@ -87,6 +87,7 @@ PairKIM::PairKIM(LAMMPS *lmp) : chargeUnit(KIM_CHARGE_UNIT_unused), temperatureUnit(KIM_TEMPERATURE_UNIT_unused), timeUnit(KIM_TIME_UNIT_unused), + simulatorModel(NULL), pkim(NULL), pargs(NULL), kim_model_support_for_energy(KIM_SUPPORT_STATUS_notSupported), @@ -396,8 +397,10 @@ void PairKIM::coeff(int narg, char **arg) // Assume all species arguments are valid // errors will be detected by below + std::string atom_type_sym_list; lmps_num_unique_elements = 0; for (i = 2; i < narg; i++) { + atom_type_sym_list += std::string(" ") + arg[i]; for (j = 0; j < lmps_num_unique_elements; j++) if (strcmp(arg[i],lmps_unique_elements[j]) == 0) break; lmps_map_species_to_unique[i-1] = j; @@ -422,6 +425,15 @@ void PairKIM::coeff(int narg, char **arg) if (count == 0) error->all(FLERR,"Incorrect args for pair coefficients"); + if (simulatorModel) + { + simulatorModel->AddTemplateMap("atom-type-sym-list", atom_type_sym_list); + simulatorModel->CloseTemplateMap(); + + error->all(FLERR,(simulatorModel->ToString()).c_str()); + } + else + { // setup mapping between LAMMPS unique elements and KIM species codes if (kim_particle_codes_ok) { @@ -449,6 +461,7 @@ void PairKIM::coeff(int narg, char **arg) error->all(FLERR, msg.str().c_str()); } } + } return; } @@ -770,7 +783,13 @@ void PairKIM::kim_init() &requestedUnitsAccepted, &pkim); if (kimerror) - error->all(FLERR,"KIM ModelCreate failed"); + { + kimerror = KIM::SimulatorModel::Create(kim_modelname,&simulatorModel); + if (kimerror) + error->all(FLERR,"KIM ModelCreate failed"); + else + return; + } else { if (!requestedUnitsAccepted) { error->all(FLERR,"KIM Model did not accept the requested unit system"); diff --git a/src/KIM/pair_kim.h b/src/KIM/pair_kim.h index 27bab6c687..dcfb4a8af0 100644 --- a/src/KIM/pair_kim.h +++ b/src/KIM/pair_kim.h @@ -68,6 +68,7 @@ class KIM_API_model; extern "C" { #include "KIM_SimulatorHeaders.h" } +#include "KIM_SimulatorModel.hpp" #include @@ -121,6 +122,7 @@ namespace LAMMPS_NS { KIM_TemperatureUnit temperatureUnit; KIM_TimeUnit timeUnit; + KIM::SimulatorModel * simulatorModel; KIM_Model * pkim; KIM_ComputeArguments * pargs; -- GitLab From 11407a165b1b3d26e09e9f6f3a7c0ac96a6080af Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Tue, 7 May 2019 18:21:58 -0400 Subject: [PATCH 013/469] reformat pair style kim to LAMMPS style and add some existing simiulator model code (non-functional) --- src/KIM/pair_kim.cpp | 1465 ++++++++++++++++++++---------------------- src/KIM/pair_kim.h | 201 +++--- 2 files changed, 792 insertions(+), 874 deletions(-) diff --git a/src/KIM/pair_kim.cpp b/src/KIM/pair_kim.cpp index 01b435194e..d75d960355 100644 --- a/src/KIM/pair_kim.cpp +++ b/src/KIM/pair_kim.cpp @@ -55,6 +55,7 @@ #include #include +#include // includes from LAMMPS #include "pair_kim.h" @@ -74,201 +75,187 @@ using namespace LAMMPS_NS; /* ---------------------------------------------------------------------- */ PairKIM::PairKIM(LAMMPS *lmp) : - Pair(lmp), - settings_call_count(0), - init_style_call_count(0), - kim_modelname(NULL), - lmps_map_species_to_unique(NULL), - lmps_unique_elements(NULL), - lmps_num_unique_elements(0), - lmps_units(METAL), - lengthUnit(KIM_LENGTH_UNIT_unused), - energyUnit(KIM_ENERGY_UNIT_unused), - chargeUnit(KIM_CHARGE_UNIT_unused), - temperatureUnit(KIM_TEMPERATURE_UNIT_unused), - timeUnit(KIM_TIME_UNIT_unused), - simulatorModel(NULL), - pkim(NULL), - pargs(NULL), - kim_model_support_for_energy(KIM_SUPPORT_STATUS_notSupported), - kim_model_support_for_forces(KIM_SUPPORT_STATUS_notSupported), - kim_model_support_for_particleEnergy(KIM_SUPPORT_STATUS_notSupported), - kim_model_support_for_particleVirial(KIM_SUPPORT_STATUS_notSupported), - lmps_local_tot_num_atoms(0), - kim_global_influence_distance(0.0), - kim_number_of_neighbor_lists(0), - kim_cutoff_values(NULL), - modelWillNotRequestNeighborsOfNoncontributingParticles(NULL), - neighborLists(NULL), - kim_particle_codes(NULL), - lmps_maxalloc(0), - kim_particleSpecies(NULL), - kim_particleContributing(NULL), - lmps_stripped_neigh_list(NULL), - lmps_stripped_neigh_ptr(NULL) + Pair(lmp), + settings_call_count(0), + init_style_call_count(0), + kim_modelname(NULL), + lmps_map_species_to_unique(NULL), + lmps_unique_elements(NULL), + lmps_num_unique_elements(0), + lmps_units(METAL), + lengthUnit(KIM_LENGTH_UNIT_unused), + energyUnit(KIM_ENERGY_UNIT_unused), + chargeUnit(KIM_CHARGE_UNIT_unused), + temperatureUnit(KIM_TEMPERATURE_UNIT_unused), + timeUnit(KIM_TIME_UNIT_unused), + simulatorModel(NULL), + pkim(NULL), + pargs(NULL), + kim_model_support_for_energy(KIM_SUPPORT_STATUS_notSupported), + kim_model_support_for_forces(KIM_SUPPORT_STATUS_notSupported), + kim_model_support_for_particleEnergy(KIM_SUPPORT_STATUS_notSupported), + kim_model_support_for_particleVirial(KIM_SUPPORT_STATUS_notSupported), + lmps_local_tot_num_atoms(0), + kim_global_influence_distance(0.0), + kim_number_of_neighbor_lists(0), + kim_cutoff_values(NULL), + modelWillNotRequestNeighborsOfNoncontributingParticles(NULL), + neighborLists(NULL), + kim_particle_codes(NULL), + lmps_maxalloc(0), + kim_particleSpecies(NULL), + kim_particleContributing(NULL), + lmps_stripped_neigh_list(NULL), + lmps_stripped_neigh_ptr(NULL), + simulator_class(NULL), + simulator_style(NULL) { - // Initialize Pair data members to appropriate values - single_enable = 0; // We do not provide the Single() function - restartinfo = 0; // We do not write any restart info - one_coeff = 1; // We only allow one coeff * * call - // set to 1, regardless use of fdotr, to avoid ev_set()'s futzing with - // vflag_global - no_virial_fdotr_compute = 1; - - // BEGIN: initial values that determine the KIM state - // (used by kim_free(), etc.) - kim_init_ok = false; - kim_particle_codes_ok = false; - // END - - return; + // Initialize Pair data members to appropriate values + single_enable = 0; // We do not provide the Single() function + restartinfo = 0; // We do not write any restart info + one_coeff = 1; // We only allow one coeff * * call + // set to 1, regardless use of fdotr, to avoid ev_set()'s futzing with + // vflag_global + no_virial_fdotr_compute = 1; + + // BEGIN: initial values that determine the KIM state + // (used by kim_free(), etc.) + kim_init_ok = false; + kim_particle_codes_ok = false; + // END } /* ---------------------------------------------------------------------- */ PairKIM::~PairKIM() { - // clean up kim_modelname - if (kim_modelname != 0) delete [] kim_modelname; + // clean up kim_modelname + if (kim_modelname != 0) delete [] kim_modelname; + + // clean up lammps atom species number to unique particle names mapping + if (lmps_unique_elements) + for (int i = 0; i < lmps_num_unique_elements; i++) + delete [] lmps_unique_elements[i]; + delete [] lmps_unique_elements; + + if (kim_particle_codes_ok) { + delete [] kim_particle_codes; + kim_particle_codes = NULL; + kim_particle_codes_ok = false; + } - // clean up lammps atom species number to unique particle names mapping - if (lmps_unique_elements) - for (int i = 0; i < lmps_num_unique_elements; i++) - delete [] lmps_unique_elements[i]; - delete [] lmps_unique_elements; + // clean up local memory used to support KIM interface + memory->destroy(kim_particleSpecies); + memory->destroy(kim_particleContributing); + memory->destroy(lmps_stripped_neigh_list); + // clean up lmps_stripped_neigh_ptr + if (lmps_stripped_neigh_ptr) { + delete [] lmps_stripped_neigh_ptr; + lmps_stripped_neigh_ptr = 0; + } - if (kim_particle_codes_ok) - { - delete [] kim_particle_codes; - kim_particle_codes = NULL; - kim_particle_codes_ok = false; - } - - // clean up local memory used to support KIM interface - memory->destroy(kim_particleSpecies); - memory->destroy(kim_particleContributing); - memory->destroy(lmps_stripped_neigh_list); - // clean up lmps_stripped_neigh_ptr - if (lmps_stripped_neigh_ptr) - { - delete [] lmps_stripped_neigh_ptr; - lmps_stripped_neigh_ptr = 0; - } - - // clean up allocated memory for standard Pair class usage - // also, we allocate lmps_map_species_to_uniuqe in the allocate() function - if (allocated) { - memory->destroy(setflag); - memory->destroy(cutsq); - delete [] lmps_map_species_to_unique; - } - - // clean up neighborlist pointers - if (neighborLists) - { - delete [] neighborLists; - neighborLists = 0; - } - - // clean up KIM interface (if necessary) - kim_free(); - - return; + // clean up allocated memory for standard Pair class usage + // also, we allocate lmps_map_species_to_uniuqe in the allocate() function + if (allocated) { + memory->destroy(setflag); + memory->destroy(cutsq); + delete [] lmps_map_species_to_unique; + } + + // clean up neighborlist pointers + if (neighborLists) { + delete [] neighborLists; + neighborLists = 0; + } + + // clean up KIM interface (if necessary) + kim_free(); } /* ---------------------------------------------------------------------- */ + void PairKIM::set_contributing() { int const nall = atom->nlocal + atom->nghost; for (int i = 0; i < nall; ++i) - { kim_particleContributing[i] = ( (i < atom->nlocal) ? 1 : 0 ); - } } /* ---------------------------------------------------------------------- */ -void PairKIM::compute(int eflag , int vflag) +void PairKIM::compute(int eflag, int vflag) { - ev_init(eflag,vflag); - - // grow kim_particleSpecies and kim_particleContributing array if necessary - // needs to be atom->nmax in length - if (atom->nmax > lmps_maxalloc) { - memory->destroy(kim_particleSpecies); - memory->destroy(kim_particleContributing); - - lmps_maxalloc = atom->nmax; - memory->create(kim_particleSpecies,lmps_maxalloc, - "pair:kim_particleSpecies"); - int kimerror = KIM_ComputeArguments_SetArgumentPointerInteger(pargs, - KIM_COMPUTE_ARGUMENT_NAME_particleSpeciesCodes, - kim_particleSpecies); - memory->create(kim_particleContributing,lmps_maxalloc, - "pair:kim_particleContributing"); - kimerror = kimerror || KIM_ComputeArguments_SetArgumentPointerInteger( - pargs, - KIM_COMPUTE_ARGUMENT_NAME_particleContributing, - kim_particleContributing); - if (kimerror) - error->all( - FLERR, - "Unable to set KIM particle species codes and/or contributing"); - } - - // kim_particleSpecies = KIM atom species for each LAMMPS atom - - int *species = atom->type; - int nall = atom->nlocal + atom->nghost; - int ielement; - - for (int i = 0; i < nall; i++) { - ielement = lmps_map_species_to_unique[species[i]]; - kim_particleSpecies[i] = kim_particle_codes[ielement]; - } - - // Set kim contributing flags - set_contributing(); - - // pass current atom pointers to KIM - set_argument_pointers(); - - // set number of particles - lmps_local_tot_num_atoms = (int) nall; - - // compute via KIM model - int kimerror = KIM_Model_Compute(pkim, pargs); - if (kimerror) error->all(FLERR,"KIM Compute returned error"); - - // compute virial before reverse comm! - if (vflag_global) - { - virial_fdotr_compute(); - } - - // if newton is off, perform reverse comm - if (!lmps_using_newton) - { - comm->reverse_comm_pair(this); - } - - if ((vflag_atom) && - KIM_SupportStatus_NotEqual(kim_model_support_for_particleVirial, - KIM_SUPPORT_STATUS_notSupported) - ) - { // flip sign and order of virial if KIM is computing it - double tmp; - for (int i = 0; i < nall; ++i) - { - for (int j = 0; j < 3; ++j) vatom[i][j] = -1.0*vatom[i][j]; - tmp = vatom[i][3]; - vatom[i][3] = -vatom[i][5]; - vatom[i][4] = -vatom[i][4]; - vatom[i][5] = -tmp; - } - } + ev_init(eflag,vflag); + + // grow kim_particleSpecies and kim_particleContributing array if necessary + // needs to be atom->nmax in length + if (atom->nmax > lmps_maxalloc) { + memory->destroy(kim_particleSpecies); + memory->destroy(kim_particleContributing); + + lmps_maxalloc = atom->nmax; + memory->create(kim_particleSpecies,lmps_maxalloc, + "pair:kim_particleSpecies"); + int kimerror = KIM_ComputeArguments_SetArgumentPointerInteger(pargs, + KIM_COMPUTE_ARGUMENT_NAME_particleSpeciesCodes, + kim_particleSpecies); + memory->create(kim_particleContributing,lmps_maxalloc, + "pair:kim_particleContributing"); + kimerror = kimerror || KIM_ComputeArguments_SetArgumentPointerInteger( + pargs, + KIM_COMPUTE_ARGUMENT_NAME_particleContributing, + kim_particleContributing); + if (kimerror) + error->all(FLERR, + "Unable to set KIM particle species codes and/or contributing"); + } + + // kim_particleSpecies = KIM atom species for each LAMMPS atom - return; + int *species = atom->type; + int nall = atom->nlocal + atom->nghost; + int ielement; + + for (int i = 0; i < nall; i++) { + ielement = lmps_map_species_to_unique[species[i]]; + kim_particleSpecies[i] = kim_particle_codes[ielement]; + } + + // Set kim contributing flags + set_contributing(); + + // pass current atom pointers to KIM + set_argument_pointers(); + + // set number of particles + lmps_local_tot_num_atoms = (int) nall; + + // compute via KIM model + int kimerror = KIM_Model_Compute(pkim, pargs); + if (kimerror) error->all(FLERR,"KIM Compute returned error"); + + // compute virial before reverse comm! + if (vflag_global) + virial_fdotr_compute(); + + // if newton is off, perform reverse comm + if (!lmps_using_newton) { + comm->reverse_comm_pair(this); + } + + if ((vflag_atom) && + KIM_SupportStatus_NotEqual(kim_model_support_for_particleVirial, + KIM_SUPPORT_STATUS_notSupported)) { + // flip sign and order of virial if KIM is computing it + double tmp; + for (int i = 0; i < nall; ++i) { + for (int j = 0; j < 3; ++j) vatom[i][j] = -1.0*vatom[i][j]; + tmp = vatom[i][3]; + vatom[i][3] = -vatom[i][5]; + vatom[i][4] = -vatom[i][4]; + vatom[i][5] = -tmp; + } + } } /* ---------------------------------------------------------------------- @@ -277,22 +264,20 @@ void PairKIM::compute(int eflag , int vflag) void PairKIM::allocate() { - int n = atom->ntypes; + int n = atom->ntypes; - // allocate standard Pair class arrays - memory->create(setflag,n+1,n+1,"pair:setflag"); - for (int i = 1; i <= n; i++) - for (int j = i; j <= n; j++) - setflag[i][j] = 0; + // allocate standard Pair class arrays + memory->create(setflag,n+1,n+1,"pair:setflag"); + for (int i = 1; i <= n; i++) + for (int j = i; j <= n; j++) + setflag[i][j] = 0; - memory->create(cutsq,n+1,n+1,"pair:cutsq"); + memory->create(cutsq,n+1,n+1,"pair:cutsq"); - // allocate mapping array - lmps_map_species_to_unique = new int[n+1]; + // allocate mapping array + lmps_map_species_to_unique = new int[n+1]; - allocated = 1; - - return; + allocated = 1; } /* ---------------------------------------------------------------------- @@ -301,56 +286,54 @@ void PairKIM::allocate() void PairKIM::settings(int narg, char **arg) { - // This is called when "pair_style kim ..." is read from input - // may be called multiple times - ++settings_call_count; - init_style_call_count = 0; - - if (narg != 1) - { - if ((narg > 0) && ((0 == strcmp("KIMvirial", arg[0])) || - (0 == strcmp("LAMMPSvirial", arg[0])))) - { - error->all(FLERR,"'KIMvirial' or 'LAMMPSvirial' not supported with " - "kim-api."); - } - else - error->all(FLERR,"Illegal pair_style command"); - } - // arg[0] is the KIM Model name - - lmps_using_molecular = (atom->molecular > 0); - - // ensure we are in a clean state for KIM (needed on repeated call) - // first time called will do nothing... - kim_free(); - - // make sure things are allocated - if (allocated != 1) allocate(); - - // clear setflag to ensure coeff() is called after settings() - int n = atom->ntypes; - for (int i = 1; i <= n; i++) - for (int j = i; j <= n; j++) - setflag[i][j] = 0; - - // set lmps_* bool flags - set_lmps_flags(); - - // set KIM Model name - int nmlen = strlen(arg[0]); - if (kim_modelname != 0) - { - delete [] kim_modelname; - kim_modelname = 0; - } - kim_modelname = new char[nmlen+1]; - strcpy(kim_modelname, arg[0]); - - // initialize KIM Model - kim_init(); - - return; + // This is called when "pair_style kim ..." is read from input + // may be called multiple times + ++settings_call_count; + init_style_call_count = 0; + + if (narg != 1) { + if ((narg > 0) && ((0 == strcmp("KIMvirial", arg[0])) || + (0 == strcmp("LAMMPSvirial", arg[0])))) { + error->all(FLERR,"'KIMvirial' or 'LAMMPSvirial' not supported with " + "kim-api."); + } else error->all(FLERR,"Illegal pair_style command"); + } + // arg[0] is the KIM Model name + + lmps_using_molecular = (atom->molecular > 0); + + // ensure we are in a clean state for KIM (needed on repeated call) + // first time called will do nothing... + kim_free(); + + // make sure things are allocated + if (allocated != 1) allocate(); + + // clear setflag to ensure coeff() is called after settings() + int n = atom->ntypes; + for (int i = 1; i <= n; i++) + for (int j = i; j <= n; j++) + setflag[i][j] = 0; + + // set lmps_* bool flags + set_lmps_flags(); + + // set KIM Model name + int nmlen = strlen(arg[0]); + if (kim_modelname != 0) { + delete [] kim_modelname; + kim_modelname = 0; + } + kim_modelname = new char[nmlen+1]; + strcpy(kim_modelname, arg[0]); + + // initialize KIM Model + kim_init(); + + // initialize LAMMPS Simulator model + if (simulatorModel) { + printf("LAMMPS simulator model: %s\n",kim_modelname); + } } /* ---------------------------------------------------------------------- @@ -359,91 +342,85 @@ void PairKIM::settings(int narg, char **arg) void PairKIM::coeff(int narg, char **arg) { - // This is called when "pair_coeff ..." is read from input - // may be called multiple times - - int i,j,n; - - if (!allocated) allocate(); - - if (narg != 2 + atom->ntypes) - error->all(FLERR,"Incorrect args for pair coefficients"); - - // insure I,J args are * * - - if (strcmp(arg[0],"*") != 0 || strcmp(arg[1],"*") != 0) - error->all(FLERR,"Incorrect args for pair coefficients"); - - - int ilo,ihi,jlo,jhi; - force->bounds(FLERR,arg[0],atom->ntypes,ilo,ihi); - force->bounds(FLERR,arg[1],atom->ntypes,jlo,jhi); - - // read args that map atom species to KIM elements - // lmps_map_species_to_unique[i] = - // which element the Ith atom type is - // lmps_num_unique_elements = # of unique elements - // lmps_unique_elements = list of element names - - // if called multiple times: update lmps_unique_elements - if (lmps_unique_elements) { - for (i = 0; i < lmps_num_unique_elements; i++) - delete [] lmps_unique_elements[i]; - delete [] lmps_unique_elements; - } - lmps_unique_elements = new char*[atom->ntypes]; - for (i = 0; i < atom->ntypes; i++) lmps_unique_elements[i] = 0; - - - // Assume all species arguments are valid - // errors will be detected by below - std::string atom_type_sym_list; - lmps_num_unique_elements = 0; - for (i = 2; i < narg; i++) { - atom_type_sym_list += std::string(" ") + arg[i]; - for (j = 0; j < lmps_num_unique_elements; j++) - if (strcmp(arg[i],lmps_unique_elements[j]) == 0) break; - lmps_map_species_to_unique[i-1] = j; - if (j == lmps_num_unique_elements) { - n = strlen(arg[i]) + 1; - lmps_unique_elements[j] = new char[n]; - strcpy(lmps_unique_elements[j],arg[i]); - lmps_num_unique_elements++; - } - } - - int count = 0; - for (int i = ilo; i <= ihi; i++) { - for (int j = MAX(jlo,i); j <= jhi; j++) { - if (lmps_map_species_to_unique[i] >= 0 && - lmps_map_species_to_unique[j] >= 0) { - setflag[i][j] = 1; - count++; - } - } - } - - if (count == 0) error->all(FLERR,"Incorrect args for pair coefficients"); - - if (simulatorModel) - { - simulatorModel->AddTemplateMap("atom-type-sym-list", atom_type_sym_list); - simulatorModel->CloseTemplateMap(); - - error->all(FLERR,(simulatorModel->ToString()).c_str()); - } - else - { - // setup mapping between LAMMPS unique elements and KIM species codes - if (kim_particle_codes_ok) - { - delete [] kim_particle_codes; - kim_particle_codes = NULL; - kim_particle_codes_ok = false; - } - kim_particle_codes = new int[lmps_num_unique_elements]; - kim_particle_codes_ok = true; - for(int i = 0; i < lmps_num_unique_elements; i++){ + // This is called when "pair_coeff ..." is read from input + // may be called multiple times + + int i,j,n; + + if (!allocated) allocate(); + + if (narg != 2 + atom->ntypes) + error->all(FLERR,"Incorrect args for pair coefficients"); + + // insure I,J args are * * + + if (strcmp(arg[0],"*") != 0 || strcmp(arg[1],"*") != 0) + error->all(FLERR,"Incorrect args for pair coefficients"); + + int ilo,ihi,jlo,jhi; + force->bounds(FLERR,arg[0],atom->ntypes,ilo,ihi); + force->bounds(FLERR,arg[1],atom->ntypes,jlo,jhi); + + // read args that map atom species to KIM elements + // lmps_map_species_to_unique[i] = + // which element the Ith atom type is + // lmps_num_unique_elements = # of unique elements + // lmps_unique_elements = list of element names + + // if called multiple times: update lmps_unique_elements + if (lmps_unique_elements) { + for (i = 0; i < lmps_num_unique_elements; i++) + delete [] lmps_unique_elements[i]; + delete [] lmps_unique_elements; + } + lmps_unique_elements = new char*[atom->ntypes]; + for (i = 0; i < atom->ntypes; i++) lmps_unique_elements[i] = 0; + + // Assume all species arguments are valid + // errors will be detected by below + std::string atom_type_sym_list; + lmps_num_unique_elements = 0; + for (i = 2; i < narg; i++) { + atom_type_sym_list += std::string(" ") + arg[i]; + for (j = 0; j < lmps_num_unique_elements; j++) + if (strcmp(arg[i],lmps_unique_elements[j]) == 0) break; + lmps_map_species_to_unique[i-1] = j; + if (j == lmps_num_unique_elements) { + n = strlen(arg[i]) + 1; + lmps_unique_elements[j] = new char[n]; + strcpy(lmps_unique_elements[j],arg[i]); + lmps_num_unique_elements++; + } + } + + int count = 0; + for (int i = ilo; i <= ihi; i++) { + for (int j = MAX(jlo,i); j <= jhi; j++) { + if (lmps_map_species_to_unique[i] >= 0 && + lmps_map_species_to_unique[j] >= 0) { + setflag[i][j] = 1; + count++; + } + } + } + + if (count == 0) error->all(FLERR,"Incorrect args for pair coefficients"); + + if (simulatorModel) { + simulatorModel->AddTemplateMap("atom-type-sym-list", atom_type_sym_list); + simulatorModel->CloseTemplateMap(); + + error->all(FLERR,(simulatorModel->ToString()).c_str()); + } else { + // setup mapping between LAMMPS unique elements and KIM species codes + if (kim_particle_codes_ok) { + delete [] kim_particle_codes; + kim_particle_codes = NULL; + kim_particle_codes_ok = false; + } + kim_particle_codes = new int[lmps_num_unique_elements]; + kim_particle_codes_ok = true; + for(int i = 0; i < lmps_num_unique_elements; i++) { int supported; int code; KIM_Model_GetSpeciesSupportAndCode( @@ -451,19 +428,15 @@ void PairKIM::coeff(int narg, char **arg) KIM_SpeciesName_FromString(lmps_unique_elements[i]), &supported, &code); - if (supported) + if (supported) { kim_particle_codes[i] = code; - else - { - std::stringstream msg; - msg << "create_kim_particle_codes: symbol not found: " - << lmps_unique_elements[i]; - error->all(FLERR, msg.str().c_str()); + } else { + std::string msg("create_kim_particle_codes: symbol not found: "); + msg += lmps_unique_elements[i]; + error->all(FLERR, msg.c_str()); } - } - } - - return; + } + } } /* ---------------------------------------------------------------------- @@ -472,57 +445,48 @@ void PairKIM::coeff(int narg, char **arg) void PairKIM::init_style() { - // This is called for each "run ...", "minimize ...", etc. read from input - ++init_style_call_count; - - if (domain->dimension != 3) - error->all(FLERR,"PairKIM only works with 3D problems"); - - // setup lmps_stripped_neigh_list for neighbors of one atom, if needed - if (lmps_using_molecular) { - memory->destroy(lmps_stripped_neigh_list); - memory->create(lmps_stripped_neigh_list, - kim_number_of_neighbor_lists*neighbor->oneatom, - "pair:lmps_stripped_neigh_list"); - delete [] lmps_stripped_neigh_ptr; - lmps_stripped_neigh_ptr = new int*[kim_number_of_neighbor_lists]; - for (int i = 0; i < kim_number_of_neighbor_lists; ++i) - { - lmps_stripped_neigh_ptr[i] - = &(lmps_stripped_neigh_list[i*(neighbor->oneatom)]); - } + // This is called for each "run ...", "minimize ...", etc. read from input + ++init_style_call_count; + + if (domain->dimension != 3) + error->all(FLERR,"PairKIM only works with 3D problems"); + + // setup lmps_stripped_neigh_list for neighbors of one atom, if needed + if (lmps_using_molecular) { + memory->destroy(lmps_stripped_neigh_list); + memory->create(lmps_stripped_neigh_list, + kim_number_of_neighbor_lists*neighbor->oneatom, + "pair:lmps_stripped_neigh_list"); + delete [] lmps_stripped_neigh_ptr; + lmps_stripped_neigh_ptr = new int*[kim_number_of_neighbor_lists]; + for (int i = 0; i < kim_number_of_neighbor_lists; ++i) + lmps_stripped_neigh_ptr[i] + = &(lmps_stripped_neigh_list[i*(neighbor->oneatom)]); + } + + // make sure comm_reverse expects (at most) 9 values when newton is off + if (!lmps_using_newton) comm_reverse_off = 9; + + // request full neighbor + for (int i = 0; i < kim_number_of_neighbor_lists; ++i) { + int irequest = neighbor->request(this,instance_me); + neighbor->requests[irequest]->id = i; + neighbor->requests[irequest]->half = 0; + neighbor->requests[irequest]->full = 1; + + if (modelWillNotRequestNeighborsOfNoncontributingParticles[i]) + neighbor->requests[irequest]->ghost = 0; + else + neighbor->requests[irequest]->ghost = 1; + + // always want all owned/ghost pairs + neighbor->requests[irequest]->newton = 2; - } - - // make sure comm_reverse expects (at most) 9 values when newton is off - if (!lmps_using_newton) comm_reverse_off = 9; - - // request full neighbor - for (int i = 0; i < kim_number_of_neighbor_lists; ++i) - { - int irequest = neighbor->request(this,instance_me); - neighbor->requests[irequest]->id = i; - neighbor->requests[irequest]->half = 0; - neighbor->requests[irequest]->full = 1; - - if (modelWillNotRequestNeighborsOfNoncontributingParticles[i]) - { - neighbor->requests[irequest]->ghost = 0; - } - else - { - neighbor->requests[irequest]->ghost = 1; - - } - // always want all owned/ghost pairs - neighbor->requests[irequest]->newton = 2; - // set cutoff - neighbor->requests[irequest]->cut = 1; - neighbor->requests[irequest]->cutoff - = kim_cutoff_values[i] + neighbor->skin; - } - - return; + // set cutoff + neighbor->requests[irequest]->cut = 1; + neighbor->requests[irequest]->cutoff + = kim_cutoff_values[i] + neighbor->skin; + } } /* ---------------------------------------------------------------------- @@ -541,154 +505,134 @@ void PairKIM::init_list(int id, NeighList *ptr) double PairKIM::init_one(int i, int j) { - // This is called once of each (unordered) i,j pair for each - // "run ...", "minimize ...", etc. read from input + // This is called once of each (unordered) i,j pair for each + // "run ...", "minimize ...", etc. read from input - if (setflag[i][j] == 0) error->all(FLERR,"All pair coeffs are not set"); + if (setflag[i][j] == 0) error->all(FLERR,"All pair coeffs are not set"); - return kim_global_influence_distance; + return kim_global_influence_distance; } /* ---------------------------------------------------------------------- */ int PairKIM::pack_reverse_comm(int n, int first, double *buf) { - int i,m,last; - double *fp; - fp = &(atom->f[0][0]); - - m = 0; - last = first + n; - if (KIM_SupportStatus_NotEqual(kim_model_support_for_forces, - KIM_SUPPORT_STATUS_notSupported) - && - ((vflag_atom == 0) || - KIM_SupportStatus_Equal(kim_model_support_for_particleVirial, - KIM_SUPPORT_STATUS_notSupported))) - { - for (i = first; i < last; i++) - { - buf[m++] = fp[3*i+0]; - buf[m++] = fp[3*i+1]; - buf[m++] = fp[3*i+2]; - } - return m; - } - else if (KIM_SupportStatus_NotEqual(kim_model_support_for_forces, - KIM_SUPPORT_STATUS_notSupported) && - (vflag_atom == 1) && - KIM_SupportStatus_NotEqual(kim_model_support_for_particleVirial, - KIM_SUPPORT_STATUS_notSupported)) - { - double *va=&(vatom[0][0]); - for (i = first; i < last; i++) - { - buf[m++] = fp[3*i+0]; - buf[m++] = fp[3*i+1]; - buf[m++] = fp[3*i+2]; - - buf[m++] = va[6*i+0]; - buf[m++] = va[6*i+1]; - buf[m++] = va[6*i+2]; - buf[m++] = va[6*i+3]; - buf[m++] = va[6*i+4]; - buf[m++] = va[6*i+5]; - } - return m; - } - else if (KIM_SupportStatus_Equal(kim_model_support_for_forces, - KIM_SUPPORT_STATUS_notSupported) - && - (vflag_atom == 1) && - KIM_SupportStatus_NotEqual(kim_model_support_for_particleVirial, - KIM_SUPPORT_STATUS_notSupported)) - { - double *va=&(vatom[0][0]); - for (i = first; i < last; i++) - { - buf[m++] = va[6*i+0]; - buf[m++] = va[6*i+1]; - buf[m++] = va[6*i+2]; - buf[m++] = va[6*i+3]; - buf[m++] = va[6*i+4]; - buf[m++] = va[6*i+5]; - } - return m; - } - else - return 0; + int i,m,last; + double *fp; + fp = &(atom->f[0][0]); + + m = 0; + last = first + n; + if (KIM_SupportStatus_NotEqual(kim_model_support_for_forces, + KIM_SUPPORT_STATUS_notSupported) + && + ((vflag_atom == 0) || + KIM_SupportStatus_Equal(kim_model_support_for_particleVirial, + KIM_SUPPORT_STATUS_notSupported))) { + for (i = first; i < last; i++) { + buf[m++] = fp[3*i+0]; + buf[m++] = fp[3*i+1]; + buf[m++] = fp[3*i+2]; + } + return m; + } else if (KIM_SupportStatus_NotEqual(kim_model_support_for_forces, + KIM_SUPPORT_STATUS_notSupported) && + (vflag_atom == 1) && + KIM_SupportStatus_NotEqual(kim_model_support_for_particleVirial, + KIM_SUPPORT_STATUS_notSupported)) { + double *va=&(vatom[0][0]); + for (i = first; i < last; i++) { + buf[m++] = fp[3*i+0]; + buf[m++] = fp[3*i+1]; + buf[m++] = fp[3*i+2]; + + buf[m++] = va[6*i+0]; + buf[m++] = va[6*i+1]; + buf[m++] = va[6*i+2]; + buf[m++] = va[6*i+3]; + buf[m++] = va[6*i+4]; + buf[m++] = va[6*i+5]; + } + return m; + } else if (KIM_SupportStatus_Equal(kim_model_support_for_forces, + KIM_SUPPORT_STATUS_notSupported) + && + (vflag_atom == 1) && + KIM_SupportStatus_NotEqual(kim_model_support_for_particleVirial, + KIM_SUPPORT_STATUS_notSupported)) { + double *va=&(vatom[0][0]); + for (i = first; i < last; i++) { + buf[m++] = va[6*i+0]; + buf[m++] = va[6*i+1]; + buf[m++] = va[6*i+2]; + buf[m++] = va[6*i+3]; + buf[m++] = va[6*i+4]; + buf[m++] = va[6*i+5]; + } + return m; + } else return 0; } /* ---------------------------------------------------------------------- */ void PairKIM::unpack_reverse_comm(int n, int *list, double *buf) { - int i,j,m; - double *fp; - fp = &(atom->f[0][0]); - - m = 0; - if (KIM_SupportStatus_NotEqual(kim_model_support_for_forces, - KIM_SUPPORT_STATUS_notSupported) - && - ((vflag_atom == 0) || - KIM_SupportStatus_Equal(kim_model_support_for_particleVirial, - KIM_SUPPORT_STATUS_notSupported))) - { - for (i = 0; i < n; i++) - { - j = list[i]; - fp[3*j+0]+= buf[m++]; - fp[3*j+1]+= buf[m++]; - fp[3*j+2]+= buf[m++]; - } - } - else if (KIM_SupportStatus_NotEqual(kim_model_support_for_forces, - KIM_SUPPORT_STATUS_notSupported) - && - (vflag_atom == 1) && - KIM_SupportStatus_NotEqual(kim_model_support_for_particleVirial, - KIM_SUPPORT_STATUS_notSupported)) - { - double *va=&(vatom[0][0]); - for (i = 0; i < n; i++) - { - j = list[i]; - fp[3*j+0]+= buf[m++]; - fp[3*j+1]+= buf[m++]; - fp[3*j+2]+= buf[m++]; - - va[j*6+0]+=buf[m++]; - va[j*6+1]+=buf[m++]; - va[j*6+2]+=buf[m++]; - va[j*6+3]+=buf[m++]; - va[j*6+4]+=buf[m++]; - va[j*6+5]+=buf[m++]; - } - } - else if (KIM_SupportStatus_Equal(kim_model_support_for_forces, - KIM_SUPPORT_STATUS_notSupported) - && - (vflag_atom == 1) && - KIM_SupportStatus_NotEqual(kim_model_support_for_particleVirial, - KIM_SUPPORT_STATUS_notSupported)) - { - double *va=&(vatom[0][0]); - for (i = 0; i < n; i++) - { - j = list[i]; - va[j*6+0]+=buf[m++]; - va[j*6+1]+=buf[m++]; - va[j*6+2]+=buf[m++]; - va[j*6+3]+=buf[m++]; - va[j*6+4]+=buf[m++]; - va[j*6+5]+=buf[m++]; - } - } else { - ; // do nothing - } - - return; + int i,j,m; + double *fp; + fp = &(atom->f[0][0]); + + m = 0; + if (KIM_SupportStatus_NotEqual(kim_model_support_for_forces, + KIM_SUPPORT_STATUS_notSupported) + && + ((vflag_atom == 0) || + KIM_SupportStatus_Equal(kim_model_support_for_particleVirial, + KIM_SUPPORT_STATUS_notSupported))) { + for (i = 0; i < n; i++) { + j = list[i]; + fp[3*j+0]+= buf[m++]; + fp[3*j+1]+= buf[m++]; + fp[3*j+2]+= buf[m++]; + } + } else if (KIM_SupportStatus_NotEqual(kim_model_support_for_forces, + KIM_SUPPORT_STATUS_notSupported) + && + (vflag_atom == 1) && + KIM_SupportStatus_NotEqual(kim_model_support_for_particleVirial, + KIM_SUPPORT_STATUS_notSupported)) { + double *va=&(vatom[0][0]); + for (i = 0; i < n; i++) { + j = list[i]; + fp[3*j+0]+= buf[m++]; + fp[3*j+1]+= buf[m++]; + fp[3*j+2]+= buf[m++]; + + va[j*6+0]+=buf[m++]; + va[j*6+1]+=buf[m++]; + va[j*6+2]+=buf[m++]; + va[j*6+3]+=buf[m++]; + va[j*6+4]+=buf[m++]; + va[j*6+5]+=buf[m++]; + } + } else if (KIM_SupportStatus_Equal(kim_model_support_for_forces, + KIM_SUPPORT_STATUS_notSupported) + && + (vflag_atom == 1) && + KIM_SupportStatus_NotEqual(kim_model_support_for_particleVirial, + KIM_SUPPORT_STATUS_notSupported)) { + double *va=&(vatom[0][0]); + for (i = 0; i < n; i++) { + j = list[i]; + va[j*6+0]+=buf[m++]; + va[j*6+1]+=buf[m++]; + va[j*6+2]+=buf[m++]; + va[j*6+3]+=buf[m++]; + va[j*6+4]+=buf[m++]; + va[j*6+5]+=buf[m++]; + } + } else { + ; // do nothing + } } /* ---------------------------------------------------------------------- @@ -697,8 +641,34 @@ void PairKIM::unpack_reverse_comm(int n, int *list, double *buf) double PairKIM::memory_usage() { - double bytes = 2 * lmps_maxalloc * sizeof(int); - return bytes; + double bytes = 2 * lmps_maxalloc * sizeof(int); + return bytes; +} + +/* ---------------------------------------------------------------------- + simulator model support functions +------------------------------------------------------------------------- */ + +void PairKIM::simulator_init() +{ + int dummy; + // do not try with suffixes for now. + simulator_class = force->new_pair("lj/cut",1,dummy); + force->store_style(simulator_style,"lj/cut",1); + printf("Simulator model init: %s -> %s\n", kim_modelname, simulator_style); + char **args = new char*[1]; + args[0] = (char *)"8.1500"; + simulator_class->settings(1,args); + delete[] args; +} + +void PairKIM::simulator_free() +{ + printf("Simulator model free: %s -> %s\n", kim_modelname, simulator_style); + delete[] simulator_style; + simulator_style = NULL; + delete simulator_class; + simulator_class = NULL; } /* ---------------------------------------------------------------------- @@ -708,148 +678,128 @@ double PairKIM::memory_usage() int PairKIM::get_neigh(void const * const dataObject, int const numberOfNeighborLists, double const * const cutoffs, - int const neighborListIndex, int const particleNumber, + int const neighborListIndex, + int const particleNumber, int * const numberOfNeighbors, int const ** const neighborsOfParticle) { - PairKIM const * const Model - = reinterpret_cast(dataObject); - - if (numberOfNeighborLists != Model->kim_number_of_neighbor_lists) - return true; - for (int i = 0; i < numberOfNeighborLists; ++i) - { - if (Model->kim_cutoff_values[i] < cutoffs[i]) return true; - } - - // neighborListIndex and particleNumber are validated by KIM API - - // initialize numNeigh - *numberOfNeighbors = 0; - - NeighList * neiobj = Model->neighborLists[neighborListIndex]; - - int *numneigh, **firstneigh; - numneigh = neiobj->numneigh; // # of J neighbors for each I atom - firstneigh = neiobj->firstneigh; // ptr to 1st J int value of each I atom - - *numberOfNeighbors = numneigh[particleNumber]; - - // strip off neighbor mask for molecular systems - if (!Model->lmps_using_molecular) - *neighborsOfParticle = firstneigh[particleNumber]; - else - { - int n = *numberOfNeighbors; - int *ptr = firstneigh[particleNumber]; - int *lmps_stripped_neigh_list - = Model->lmps_stripped_neigh_ptr[neighborListIndex]; - for (int i = 0; i < n; i++) - lmps_stripped_neigh_list[i] = *(ptr++) & NEIGHMASK; - *neighborsOfParticle = lmps_stripped_neigh_list; - } - return false; + PairKIM const * const Model + = reinterpret_cast(dataObject); + + if (numberOfNeighborLists != Model->kim_number_of_neighbor_lists) + return true; + for (int i = 0; i < numberOfNeighborLists; ++i) { + if (Model->kim_cutoff_values[i] < cutoffs[i]) return true; + } + + // neighborListIndex and particleNumber are validated by KIM API + + // initialize numNeigh + *numberOfNeighbors = 0; + + NeighList * neiobj = Model->neighborLists[neighborListIndex]; + + int *numneigh, **firstneigh; + numneigh = neiobj->numneigh; // # of J neighbors for each I atom + firstneigh = neiobj->firstneigh; // ptr to 1st J int value of each I atom + + *numberOfNeighbors = numneigh[particleNumber]; + + // strip off neighbor mask for molecular systems + if (!Model->lmps_using_molecular) + *neighborsOfParticle = firstneigh[particleNumber]; + else { + int n = *numberOfNeighbors; + int *ptr = firstneigh[particleNumber]; + int *lmps_stripped_neigh_list + = Model->lmps_stripped_neigh_ptr[neighborListIndex]; + for (int i = 0; i < n; i++) + lmps_stripped_neigh_list[i] = *(ptr++) & NEIGHMASK; + *neighborsOfParticle = lmps_stripped_neigh_list; + } + return false; } /* ---------------------------------------------------------------------- */ void PairKIM::kim_free() { - if (kim_init_ok) - { - int kimerror = KIM_Model_ComputeArgumentsDestroy(pkim, &pargs); - if (kimerror) - error->all(FLERR,"Unable to destroy Compute Arguments Object"); - - KIM_Model_Destroy(&pkim); - } - kim_init_ok = false; + if (kim_init_ok) { + int kimerror = KIM_Model_ComputeArgumentsDestroy(pkim, &pargs); + if (kimerror) + error->all(FLERR,"Unable to destroy Compute Arguments Object"); - return; + KIM_Model_Destroy(&pkim); + } + kim_init_ok = false; } /* ---------------------------------------------------------------------- */ void PairKIM::kim_init() { - int kimerror; - - // initialize KIM model - int requestedUnitsAccepted; - kimerror = KIM_Model_Create( - KIM_NUMBERING_zeroBased, - lengthUnit, energyUnit, chargeUnit, temperatureUnit, timeUnit, - kim_modelname, - &requestedUnitsAccepted, - &pkim); - if (kimerror) - { - kimerror = KIM::SimulatorModel::Create(kim_modelname,&simulatorModel); - if (kimerror) - error->all(FLERR,"KIM ModelCreate failed"); - else - return; - } - else { - if (!requestedUnitsAccepted) { - error->all(FLERR,"KIM Model did not accept the requested unit system"); - } - - // check that the model does not require unknown capabilities - kimerror = check_for_routine_compatibility(); - if (kimerror) - { - error->all(FLERR, - "KIM Model requires unknown Routines. Unable to proceed."); - } - - kimerror = KIM_Model_ComputeArgumentsCreate(pkim, &pargs); - if (kimerror) - { - KIM_Model_Destroy(&pkim); - error->all(FLERR,"KIM ComputeArgumentsCreate failed"); - } - else - { - kim_init_ok = true; - } - } - - // determine KIM Model capabilities (used in this function below) - set_kim_model_has_flags(); - - KIM_Model_GetInfluenceDistance(pkim, &kim_global_influence_distance); - KIM_Model_GetNeighborListPointers( - pkim, - &kim_number_of_neighbor_lists, - &kim_cutoff_values, - &modelWillNotRequestNeighborsOfNoncontributingParticles); - if (neighborLists) - { - delete [] neighborLists; - neighborLists = 0; - } - neighborLists = new NeighList*[kim_number_of_neighbor_lists]; - - kimerror = KIM_ComputeArguments_SetArgumentPointerInteger(pargs, - KIM_COMPUTE_ARGUMENT_NAME_numberOfParticles, - &lmps_local_tot_num_atoms); - if (KIM_SupportStatus_NotEqual(kim_model_support_for_energy, - KIM_SUPPORT_STATUS_notSupported)) - kimerror = kimerror || KIM_ComputeArguments_SetArgumentPointerDouble(pargs, - KIM_COMPUTE_ARGUMENT_NAME_partialEnergy, - &(eng_vdwl)); - - kimerror = KIM_ComputeArguments_SetCallbackPointer(pargs, - KIM_COMPUTE_CALLBACK_NAME_GetNeighborList, - KIM_LANGUAGE_NAME_cpp, - reinterpret_cast(get_neigh), - reinterpret_cast(this)); - - if (kimerror) - error->all(FLERR,"Unable to register KIM pointers"); - - return; + int kimerror; + + // initialize KIM model + int requestedUnitsAccepted; + kimerror = KIM_Model_Create( + KIM_NUMBERING_zeroBased, + lengthUnit, energyUnit, chargeUnit, temperatureUnit, timeUnit, + kim_modelname, + &requestedUnitsAccepted, + &pkim); + if (kimerror) { + kimerror = KIM::SimulatorModel::Create(kim_modelname,&simulatorModel); + if (kimerror) error->all(FLERR,"KIM ModelCreate failed"); + else return; + } else { + if (!requestedUnitsAccepted) + error->all(FLERR,"KIM Model did not accept the requested unit system"); + + // check that the model does not require unknown capabilities + kimerror = check_for_routine_compatibility(); + if (kimerror) + error->all(FLERR, + "KIM Model requires unknown Routines. Unable to proceed."); + + kimerror = KIM_Model_ComputeArgumentsCreate(pkim, &pargs); + if (kimerror) { + KIM_Model_Destroy(&pkim); + error->all(FLERR,"KIM ComputeArgumentsCreate failed"); + } else kim_init_ok = true; + } + + // determine KIM Model capabilities (used in this function below) + set_kim_model_has_flags(); + + KIM_Model_GetInfluenceDistance(pkim, &kim_global_influence_distance); + KIM_Model_GetNeighborListPointers( + pkim, + &kim_number_of_neighbor_lists, + &kim_cutoff_values, + &modelWillNotRequestNeighborsOfNoncontributingParticles); + if (neighborLists) { + delete [] neighborLists; + neighborLists = 0; + } + neighborLists = new NeighList*[kim_number_of_neighbor_lists]; + + kimerror = KIM_ComputeArguments_SetArgumentPointerInteger(pargs, + KIM_COMPUTE_ARGUMENT_NAME_numberOfParticles, + &lmps_local_tot_num_atoms); + if (KIM_SupportStatus_NotEqual(kim_model_support_for_energy, + KIM_SUPPORT_STATUS_notSupported)) + kimerror = kimerror || KIM_ComputeArguments_SetArgumentPointerDouble(pargs, + KIM_COMPUTE_ARGUMENT_NAME_partialEnergy, + &(eng_vdwl)); + + kimerror = KIM_ComputeArguments_SetCallbackPointer(pargs, + KIM_COMPUTE_CALLBACK_NAME_GetNeighborList, + KIM_LANGUAGE_NAME_cpp, + reinterpret_cast(get_neigh), + reinterpret_cast(this)); + + if (kimerror) error->all(FLERR,"Unable to register KIM pointers"); } /* ---------------------------------------------------------------------- */ @@ -858,16 +808,14 @@ void PairKIM::set_argument_pointers() { int kimerror; kimerror = KIM_ComputeArguments_SetArgumentPointerDouble( - pargs, KIM_COMPUTE_ARGUMENT_NAME_coordinates, &(atom->x[0][0])); + pargs, KIM_COMPUTE_ARGUMENT_NAME_coordinates, &(atom->x[0][0])); // Set KIM pointer appropriately for particalEnergy if (KIM_SupportStatus_Equal(kim_model_support_for_particleEnergy, KIM_SUPPORT_STATUS_required) - && (eflag_atom != 1)) - { + && (eflag_atom != 1)) { // reallocate per-atom energy array if necessary - if (atom->nmax > maxeatom) - { + if (atom->nmax > maxeatom) { maxeatom = atom->nmax; memory->destroy(eatom); memory->create(eatom,comm->nthreads*maxeatom,"pair:eatom"); @@ -875,31 +823,25 @@ void PairKIM::set_argument_pointers() } if (KIM_SupportStatus_Equal(kim_model_support_for_particleEnergy, KIM_SUPPORT_STATUS_optional) - && (eflag_atom != 1)) - { + && (eflag_atom != 1)) { kimerror = kimerror || KIM_ComputeArguments_SetArgumentPointerDouble( - pargs, - KIM_COMPUTE_ARGUMENT_NAME_partialParticleEnergy, - reinterpret_cast(NULL)); - } - else if (KIM_SupportStatus_NotEqual(kim_model_support_for_particleEnergy, - KIM_SUPPORT_STATUS_notSupported)) - { + pargs, + KIM_COMPUTE_ARGUMENT_NAME_partialParticleEnergy, + reinterpret_cast(NULL)); + } else if (KIM_SupportStatus_NotEqual(kim_model_support_for_particleEnergy, + KIM_SUPPORT_STATUS_notSupported)) { kimerror = kimerror || KIM_ComputeArguments_SetArgumentPointerDouble( pargs, KIM_COMPUTE_ARGUMENT_NAME_partialParticleEnergy, eatom); } // Set KIM pointer appropriately for forces if (KIM_SupportStatus_Equal(kim_model_support_for_forces, - KIM_SUPPORT_STATUS_notSupported)) - { + KIM_SUPPORT_STATUS_notSupported)) { kimerror = kimerror || KIM_ComputeArguments_SetArgumentPointerDouble( - pargs, - KIM_COMPUTE_ARGUMENT_NAME_partialForces, - reinterpret_cast(NULL)); - } - else - { + pargs, + KIM_COMPUTE_ARGUMENT_NAME_partialForces, + reinterpret_cast(NULL)); + } else { kimerror = kimerror || KIM_ComputeArguments_SetArgumentPointerDouble( pargs, KIM_COMPUTE_ARGUMENT_NAME_partialForces, &(atom->f[0][0])); } @@ -907,11 +849,9 @@ void PairKIM::set_argument_pointers() // Set KIM pointer appropriately for particleVirial if (KIM_SupportStatus_Equal(kim_model_support_for_particleVirial, KIM_SUPPORT_STATUS_required) - && (vflag_atom != 1)) - { + && (vflag_atom != 1)) { // reallocate per-atom virial array if necessary - if (atom->nmax > maxeatom) - { + if (atom->nmax > maxeatom) { maxvatom = atom->nmax; memory->destroy(vatom); memory->create(vatom,comm->nthreads*maxvatom,6,"pair:vatom"); @@ -919,84 +859,72 @@ void PairKIM::set_argument_pointers() } if (KIM_SupportStatus_Equal(kim_model_support_for_particleVirial, KIM_SUPPORT_STATUS_optional) - && (vflag_atom != 1)) - { + && (vflag_atom != 1)) { kimerror = kimerror || KIM_ComputeArguments_SetArgumentPointerDouble( - pargs, - KIM_COMPUTE_ARGUMENT_NAME_partialParticleVirial, - reinterpret_cast(NULL)); - } - else if (KIM_SupportStatus_NotEqual(kim_model_support_for_particleVirial, - KIM_SUPPORT_STATUS_notSupported)) - { + pargs, + KIM_COMPUTE_ARGUMENT_NAME_partialParticleVirial, + reinterpret_cast(NULL)); + } else if (KIM_SupportStatus_NotEqual(kim_model_support_for_particleVirial, + KIM_SUPPORT_STATUS_notSupported)) { kimerror = kimerror || KIM_ComputeArguments_SetArgumentPointerDouble( - pargs, KIM_COMPUTE_ARGUMENT_NAME_partialParticleEnergy, &(vatom[0][0])); + pargs, KIM_COMPUTE_ARGUMENT_NAME_partialParticleEnergy, &(vatom[0][0])); } - if (kimerror) - { - error->all(FLERR,"Unable to set KIM argument pointers"); - } - - return; + if (kimerror) error->all(FLERR,"Unable to set KIM argument pointers"); } /* ---------------------------------------------------------------------- */ void PairKIM::set_lmps_flags() { - // determint if newton is on or off - lmps_using_newton = (force->newton_pair == 1); - - // determine if running with pair hybrid - if (force->pair_match("hybrid",0)) - { - error->all(FLERR,"pair_kim does not support hybrid"); - } - - // determine unit system and set lmps_units flag - if ((strcmp(update->unit_style,"real")==0)) { - lmps_units = REAL; - lengthUnit = KIM_LENGTH_UNIT_A; - energyUnit = KIM_ENERGY_UNIT_kcal_mol; - chargeUnit = KIM_CHARGE_UNIT_e; - temperatureUnit = KIM_TEMPERATURE_UNIT_K; - timeUnit = KIM_TIME_UNIT_fs; - } else if ((strcmp(update->unit_style,"metal")==0)) { - lmps_units = METAL; - lengthUnit = KIM_LENGTH_UNIT_A; - energyUnit = KIM_ENERGY_UNIT_eV; - chargeUnit = KIM_CHARGE_UNIT_e; - temperatureUnit = KIM_TEMPERATURE_UNIT_K; - timeUnit = KIM_TIME_UNIT_ps; - } else if ((strcmp(update->unit_style,"si")==0)) { - lmps_units = SI; - lengthUnit = KIM_LENGTH_UNIT_m; - energyUnit = KIM_ENERGY_UNIT_J; - chargeUnit = KIM_CHARGE_UNIT_C; - temperatureUnit = KIM_TEMPERATURE_UNIT_K; - timeUnit = KIM_TIME_UNIT_s; - } else if ((strcmp(update->unit_style,"cgs")==0)) { - lmps_units = CGS; - lengthUnit = KIM_LENGTH_UNIT_cm; - energyUnit = KIM_ENERGY_UNIT_erg; - chargeUnit = KIM_CHARGE_UNIT_statC; - temperatureUnit = KIM_TEMPERATURE_UNIT_K; - timeUnit = KIM_TIME_UNIT_s; - } else if ((strcmp(update->unit_style,"electron")==0)) { - lmps_units = ELECTRON; - lengthUnit = KIM_LENGTH_UNIT_Bohr; - energyUnit = KIM_ENERGY_UNIT_Hartree; - chargeUnit = KIM_CHARGE_UNIT_e; - temperatureUnit = KIM_TEMPERATURE_UNIT_K; - timeUnit = KIM_TIME_UNIT_fs; - } else if ((strcmp(update->unit_style,"lj")==0)) { - error->all(FLERR,"LAMMPS unit_style lj not supported by KIM models"); - } else { - error->all(FLERR,"Unknown unit_style"); - } - - return; + // determint if newton is on or off + lmps_using_newton = (force->newton_pair == 1); + + // determine if running with pair hybrid + if (force->pair_match("hybrid",0)) + error->all(FLERR,"pair_kim does not support hybrid"); + + // determine unit system and set lmps_units flag + if ((strcmp(update->unit_style,"real")==0)) { + lmps_units = REAL; + lengthUnit = KIM_LENGTH_UNIT_A; + energyUnit = KIM_ENERGY_UNIT_kcal_mol; + chargeUnit = KIM_CHARGE_UNIT_e; + temperatureUnit = KIM_TEMPERATURE_UNIT_K; + timeUnit = KIM_TIME_UNIT_fs; + } else if ((strcmp(update->unit_style,"metal")==0)) { + lmps_units = METAL; + lengthUnit = KIM_LENGTH_UNIT_A; + energyUnit = KIM_ENERGY_UNIT_eV; + chargeUnit = KIM_CHARGE_UNIT_e; + temperatureUnit = KIM_TEMPERATURE_UNIT_K; + timeUnit = KIM_TIME_UNIT_ps; + } else if ((strcmp(update->unit_style,"si")==0)) { + lmps_units = SI; + lengthUnit = KIM_LENGTH_UNIT_m; + energyUnit = KIM_ENERGY_UNIT_J; + chargeUnit = KIM_CHARGE_UNIT_C; + temperatureUnit = KIM_TEMPERATURE_UNIT_K; + timeUnit = KIM_TIME_UNIT_s; + } else if ((strcmp(update->unit_style,"cgs")==0)) { + lmps_units = CGS; + lengthUnit = KIM_LENGTH_UNIT_cm; + energyUnit = KIM_ENERGY_UNIT_erg; + chargeUnit = KIM_CHARGE_UNIT_statC; + temperatureUnit = KIM_TEMPERATURE_UNIT_K; + timeUnit = KIM_TIME_UNIT_s; + } else if ((strcmp(update->unit_style,"electron")==0)) { + lmps_units = ELECTRON; + lengthUnit = KIM_LENGTH_UNIT_Bohr; + energyUnit = KIM_ENERGY_UNIT_Hartree; + chargeUnit = KIM_CHARGE_UNIT_e; + temperatureUnit = KIM_TEMPERATURE_UNIT_K; + timeUnit = KIM_TIME_UNIT_fs; + } else if ((strcmp(update->unit_style,"lj")==0)) { + error->all(FLERR,"LAMMPS unit_style lj not supported by KIM models"); + } else { + error->all(FLERR,"Unknown unit_style"); + } } /* ---------------------------------------------------------------------- */ @@ -1007,8 +935,7 @@ int PairKIM::check_for_routine_compatibility() int numberOfModelRoutineNames; KIM_MODEL_ROUTINE_NAME_GetNumberOfModelRoutineNames( &numberOfModelRoutineNames); - for (int i = 0; i < numberOfModelRoutineNames; ++i) - { + for (int i = 0; i < numberOfModelRoutineNames; ++i) { KIM_ModelRoutineName modelRoutineName; KIM_MODEL_ROUTINE_NAME_GetModelRoutineName(i, &modelRoutineName); @@ -1016,10 +943,9 @@ int PairKIM::check_for_routine_compatibility() int required; int error = KIM_Model_IsRoutinePresent( pkim, modelRoutineName, &present, &required); - if (error) { return true; } + if (error) return true; - if ((present == true) && (required == true)) - { + if ((present == true) && (required == true)) { if (!(KIM_ModelRoutineName_Equal(modelRoutineName, KIM_MODEL_ROUTINE_NAME_Create) || KIM_ModelRoutineName_Equal( @@ -1033,8 +959,9 @@ int PairKIM::check_for_routine_compatibility() modelRoutineName, KIM_MODEL_ROUTINE_NAME_ComputeArgumentsDestroy) || KIM_ModelRoutineName_Equal(modelRoutineName, - KIM_MODEL_ROUTINE_NAME_Destroy))) - { return true; } + KIM_MODEL_ROUTINE_NAME_Destroy))) { + return true; + } } } @@ -1049,8 +976,7 @@ void PairKIM::set_kim_model_has_flags() int numberOfComputeArgumentNames; KIM_COMPUTE_ARGUMENT_NAME_GetNumberOfComputeArgumentNames( &numberOfComputeArgumentNames); - for (int i = 0; i < numberOfComputeArgumentNames; ++i) - { + for (int i = 0; i < numberOfComputeArgumentNames; ++i) { KIM_ComputeArgumentName computeArgumentName; KIM_COMPUTE_ARGUMENT_NAME_GetComputeArgumentName( i, &computeArgumentName); @@ -1059,32 +985,24 @@ void PairKIM::set_kim_model_has_flags() pargs, computeArgumentName, &supportStatus); if (KIM_ComputeArgumentName_Equal(computeArgumentName, - KIM_COMPUTE_ARGUMENT_NAME_partialEnergy) - ) + KIM_COMPUTE_ARGUMENT_NAME_partialEnergy)) kim_model_support_for_energy = supportStatus; else if (KIM_ComputeArgumentName_Equal( - computeArgumentName, KIM_COMPUTE_ARGUMENT_NAME_partialForces) - ) + computeArgumentName, KIM_COMPUTE_ARGUMENT_NAME_partialForces)) kim_model_support_for_forces = supportStatus; - else if - (KIM_ComputeArgumentName_Equal( - computeArgumentName, - KIM_COMPUTE_ARGUMENT_NAME_partialParticleEnergy)\ - ) + else if (KIM_ComputeArgumentName_Equal( + computeArgumentName, + KIM_COMPUTE_ARGUMENT_NAME_partialParticleEnergy)) kim_model_support_for_particleEnergy = supportStatus; - else if - (KIM_ComputeArgumentName_Equal( - computeArgumentName, - KIM_COMPUTE_ARGUMENT_NAME_partialParticleVirial) - ) + else if (KIM_ComputeArgumentName_Equal( + computeArgumentName, + KIM_COMPUTE_ARGUMENT_NAME_partialParticleVirial)) kim_model_support_for_particleVirial = supportStatus; - else if (KIM_SupportStatus_Equal(supportStatus, KIM_SUPPORT_STATUS_required) - ) - { - std::stringstream msg; - msg << "KIM Model requires unsupported compute argument: " - << KIM_ComputeArgumentName_ToString(computeArgumentName); - error->all(FLERR, msg.str().c_str()); + else if (KIM_SupportStatus_Equal(supportStatus, + KIM_SUPPORT_STATUS_required)) { + std::string msg("KIM Model requires unsupported compute argument: "); + msg += KIM_ComputeArgumentName_ToString(computeArgumentName); + error->all(FLERR, msg.c_str()); } } @@ -1111,20 +1029,15 @@ void PairKIM::set_kim_model_has_flags() int numberOfComputeCallbackNames; KIM_COMPUTE_CALLBACK_NAME_GetNumberOfComputeCallbackNames( &numberOfComputeCallbackNames); - for (int i = 0; i < numberOfComputeCallbackNames; ++i) - { + for (int i = 0; i < numberOfComputeCallbackNames; ++i) { KIM_ComputeCallbackName computeCallbackName; - KIM_COMPUTE_CALLBACK_NAME_GetComputeCallbackName( - i, &computeCallbackName); + KIM_COMPUTE_CALLBACK_NAME_GetComputeCallbackName(i, &computeCallbackName); KIM_SupportStatus supportStatus; - KIM_ComputeArguments_GetCallbackSupportStatus( - pargs, computeCallbackName, &supportStatus); + KIM_ComputeArguments_GetCallbackSupportStatus(pargs, + computeCallbackName, + &supportStatus); if (KIM_SupportStatus_Equal(supportStatus, KIM_SUPPORT_STATUS_required)) - { error->all(FLERR,"KIM Model requires unsupported compute callback"); - } } - - return; } diff --git a/src/KIM/pair_kim.h b/src/KIM/pair_kim.h index dcfb4a8af0..37a6be1e5b 100644 --- a/src/KIM/pair_kim.h +++ b/src/KIM/pair_kim.h @@ -12,7 +12,7 @@ ------------------------------------------------------------------------- */ /* ---------------------------------------------------------------------- - Contributing authors: Ryan S. Elliott (UMinn) + Contributing authors: Ryan S. Elliott (UMinn), Axel Kohlmeyer (Temple U) ------------------------------------------------------------------------- */ /* ---------------------------------------------------------------------- @@ -65,110 +65,115 @@ PairStyle(kim,PairKIM) // includes from KIM & LAMMPS class KIM_API_model; #include "pair.h" + extern "C" { #include "KIM_SimulatorHeaders.h" } #include "KIM_SimulatorModel.hpp" -#include - namespace LAMMPS_NS { - class PairKIM : public Pair { - public: - PairKIM(class LAMMPS*); - ~PairKIM(); - - // LAMMPS Pair class virtual function prototypes - virtual void compute(int, int); - virtual void settings(int, char**); - virtual void coeff(int, char**); - virtual void init_style(); - virtual void init_list(int id, NeighList *ptr); - virtual double init_one(int, int); - virtual int pack_reverse_comm(int, int, double*); - virtual void unpack_reverse_comm(int, int*, double*); - virtual double memory_usage(); - - protected: - // (nearly) all bool flags are not initialized in constructor, but set - // explicitly in the indicated function. All other data members are - // initialized in constructor - int settings_call_count; - int init_style_call_count; - - // values set in settings() - char* kim_modelname; - - // values set in coeff() - - // values set in allocate(), called by coeff() - virtual void allocate(); - int* lmps_map_species_to_unique; - - // values set in coeff(), after calling allocate() - char** lmps_unique_elements; // names of unique elements given - // in pair_coeff command - int lmps_num_unique_elements; - - // values set in set_lmps_flags(), called from init_style() - bool lmps_using_newton; - bool lmps_using_molecular; - enum unit_sys {REAL, METAL, SI, CGS, ELECTRON}; - unit_sys lmps_units; - KIM_LengthUnit lengthUnit; - KIM_EnergyUnit energyUnit; - KIM_ChargeUnit chargeUnit; - KIM_TemperatureUnit temperatureUnit; - KIM_TimeUnit timeUnit; - - KIM::SimulatorModel * simulatorModel; - KIM_Model * pkim; - KIM_ComputeArguments * pargs; - - // values set in set_kim_model_has_flags(), called by kim_init() - KIM_SupportStatus kim_model_support_for_energy; - KIM_SupportStatus kim_model_support_for_forces; - KIM_SupportStatus kim_model_support_for_particleEnergy; - KIM_SupportStatus kim_model_support_for_particleVirial; - - // values set in kim_init() - bool kim_init_ok; - int lmps_local_tot_num_atoms; - double kim_global_influence_distance; // KIM Model cutoff value - int kim_number_of_neighbor_lists; - double const * kim_cutoff_values; - int const * modelWillNotRequestNeighborsOfNoncontributingParticles; - class NeighList ** neighborLists; - - // values set in init_style() - bool kim_particle_codes_ok; - int *kim_particle_codes; - - // values set in compute() - int lmps_maxalloc; // max allocated memory value - int* kim_particleSpecies; // array of KIM particle species - int* kim_particleContributing; // array of KIM particle contributing - int* lmps_stripped_neigh_list; // neighbors of one atom, used when LAMMPS - // is in molecular mode - int** lmps_stripped_neigh_ptr; // pointer into lists - - // KIM specific helper functions - virtual void set_contributing(); - virtual void kim_init(); - virtual void kim_free(); - virtual void set_argument_pointers(); - virtual void set_lmps_flags(); - virtual void set_kim_model_has_flags(); - virtual int check_for_routine_compatibility(); - // static methods used as callbacks from KIM - static int get_neigh( - void const * const dataObject, - int const numberOfCutoffs, double const * const cutoffs, - int const neighborListIndex, int const particleNumber, - int * const numberOfNeighbors, - int const ** const neighborsOfParticle); - }; +class PairKIM : public Pair { + public: + PairKIM(class LAMMPS*); + ~PairKIM(); + + // LAMMPS Pair class virtual function prototypes + virtual void compute(int, int); + virtual void settings(int, char**); + virtual void coeff(int, char**); + virtual void init_style(); + virtual void init_list(int id, NeighList *ptr); + virtual double init_one(int, int); + virtual int pack_reverse_comm(int, int, double*); + virtual void unpack_reverse_comm(int, int*, double*); + virtual double memory_usage(); + + protected: + // (nearly) all bool flags are not initialized in constructor, but set + // explicitly in the indicated function. All other data members are + // initialized in constructor + int settings_call_count; + int init_style_call_count; + + // values set in settings() + char* kim_modelname; + + // values set in coeff() + + // values set in allocate(), called by coeff() + virtual void allocate(); + int* lmps_map_species_to_unique; + + // values set in coeff(), after calling allocate() + char** lmps_unique_elements; // names of unique elements given + // in pair_coeff command + int lmps_num_unique_elements; + + // values set in set_lmps_flags(), called from init_style() + bool lmps_using_newton; + bool lmps_using_molecular; + enum unit_sys {REAL, METAL, SI, CGS, ELECTRON}; + unit_sys lmps_units; + KIM_LengthUnit lengthUnit; + KIM_EnergyUnit energyUnit; + KIM_ChargeUnit chargeUnit; + KIM_TemperatureUnit temperatureUnit; + KIM_TimeUnit timeUnit; + + KIM::SimulatorModel * simulatorModel; + KIM_Model * pkim; + KIM_ComputeArguments * pargs; + + // values set in set_kim_model_has_flags(), called by kim_init() + KIM_SupportStatus kim_model_support_for_energy; + KIM_SupportStatus kim_model_support_for_forces; + KIM_SupportStatus kim_model_support_for_particleEnergy; + KIM_SupportStatus kim_model_support_for_particleVirial; + + // values set in kim_init() + bool kim_init_ok; + int lmps_local_tot_num_atoms; + double kim_global_influence_distance; // KIM Model cutoff value + int kim_number_of_neighbor_lists; + double const * kim_cutoff_values; + int const * modelWillNotRequestNeighborsOfNoncontributingParticles; + class NeighList ** neighborLists; + + // values set in init_style() + bool kim_particle_codes_ok; + int *kim_particle_codes; + + // values set in compute() + int lmps_maxalloc; // max allocated memory value + int* kim_particleSpecies; // array of KIM particle species + int* kim_particleContributing; // array of KIM particle contributing + int* lmps_stripped_neigh_list; // neighbors of one atom, used when LAMMPS + // is in molecular mode + int** lmps_stripped_neigh_ptr; // pointer into lists + + // LAMMPS Simulator model support + Pair *simulator_class; + char *simulator_style; + virtual void simulator_init(); + virtual void simulator_free(); + + // KIM specific helper functions + virtual void set_contributing(); + virtual void kim_init(); + virtual void kim_free(); + virtual void set_argument_pointers(); + virtual void set_lmps_flags(); + virtual void set_kim_model_has_flags(); + virtual int check_for_routine_compatibility(); + // static methods used as callbacks from KIM + static int get_neigh( + void const * const dataObject, + int const numberOfCutoffs, double const * const cutoffs, + int const neighborListIndex, int const particleNumber, + int * const numberOfNeighbors, + int const ** const neighborsOfParticle); +}; } #endif -- GitLab From 32379d2d840a7b5421823ba1f01aed68028d5c6b Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Sat, 18 May 2019 21:07:15 -0400 Subject: [PATCH 014/469] add JSON tokenizer to utils library --- src/utils.cpp | 376 +++++++++++++++++++++++++++++++++++++++++++++++++- src/utils.h | 2 + 2 files changed, 376 insertions(+), 2 deletions(-) diff --git a/src/utils.cpp b/src/utils.cpp index c3c173a73f..77ff8ef749 100644 --- a/src/utils.cpp +++ b/src/utils.cpp @@ -12,6 +12,8 @@ ------------------------------------------------------------------------- */ #include +#include +#include #include "utils.h" #include "error.h" @@ -46,9 +48,68 @@ extern "C" { - /** Match text against a (simplified) regular expression - * (regexp will be compiled automatically). */ +/** Match text against a (simplified) regular expression + * (regexp will be compiled automatically). */ static int re_match(const char *text, const char *pattern); + +/** + * JSON type identifier. Basic types are: + * o Object + * o Array + * o String + * o Other primitive: number, boolean (true/false) or null + */ + typedef enum { + JSMN_UNDEFINED = 0, + JSMN_OBJECT = 1, + JSMN_ARRAY = 2, + JSMN_STRING = 3, + JSMN_PRIMITIVE = 4 + } jsmntype_t; + + enum jsmnerr { + /* Not enough tokens were provided */ + JSMN_ERROR_NOMEM = -1, + /* Invalid character inside JSON string */ + JSMN_ERROR_INVAL = -2, + /* The string is not a full JSON packet, more bytes expected */ + JSMN_ERROR_PART = -3 + }; + +/** + * JSON token description. + * type type (object, array, string etc.) + * start start position in JSON data string + * end end position in JSON data string + */ + typedef struct { + jsmntype_t type; + int start; + int end; + int size; + } jsmntok_t; + +/** + * JSON parser. Contains an array of token blocks available. Also stores + * the string being parsed now and current position in that string + */ + typedef struct { + unsigned int pos; /* offset in the JSON string */ + unsigned int toknext; /* next token to allocate */ + int toksuper; /* superior token node, e.g parent object or array */ + } jsmn_parser; + +/** + * Create JSON parser over an array of tokens + */ + static void jsmn_init(jsmn_parser *parser); + +/** + * Run JSON parser. It parses a JSON data string into and array of tokens, each describing + * a single JSON object. + */ + static int jsmn_parse(jsmn_parser *parser, const char *js, size_t len, + jsmntok_t *tokens, unsigned int num_tokens); } using namespace LAMMPS_NS; @@ -121,6 +182,72 @@ void utils::sfgets(const char *srcname, int srcline, char *s, int size, return; } + + +int utils::kim_simulator_json_parse(int argc, char **argv) +{ + FILE *fp; + jsmn_parser p; + jsmntok_t *tok; + char *buf; + size_t nbytes; + + if (argc != 2) { + printf("usage: %s \n",argv[0]); + return 1; + } + + // open JSON file + + fp = fopen(argv[1],"rb"); + if (!fp) { + perror("Error opening JSON file"); + return 2; + } + + // determine file size and allocate suitable buffer + + fseek(fp,0,SEEK_END); + long int flen = ftell(fp); + rewind(fp); + buf = new char[flen]; + nbytes = fread(buf,1,flen,fp); + fclose(fp); + + // parse once to count number of tokens + + jsmn_init(&p); + int ntok = jsmn_parse(&p,buf,nbytes,NULL,1); + if (ntok < 0) { + printf("failed to parse JSON: %d\n",ntok); + return 3; + } + + // allocate token storage and parse again + + jsmn_init(&p); + tok = new jsmntok_t[ntok]; + int retval = jsmn_parse(&p,buf,nbytes,tok,ntok); + if ((retval < 1) || (tok[0].type != JSMN_OBJECT)) { + printf("failed to parse JSON: no root object\n"); + return 4; + } + + for (int i=1; i < retval; ++i) { + printf("key: %.*s\n",tok[i].end-tok[i].start,buf+tok[i].start); + if (tok[i+1].type == JSMN_ARRAY) { + printf("value is array of size %d\n",tok[i+1].size); + i += tok[i+1].size + 1; + } else { + ++i; + } + } + + delete [] buf; + delete [] tok; + return 0; +} + /* ------------------------------------------------------------------ */ extern "C" { @@ -437,4 +564,249 @@ extern "C" { return 0; } + + +/** + * Allocates a fresh unused token from the token pool. + */ + static jsmntok_t *jsmn_alloc_token(jsmn_parser *parser, + jsmntok_t *tokens, size_t num_tokens) { + jsmntok_t *tok; + if (parser->toknext >= num_tokens) { + return NULL; + } + tok = &tokens[parser->toknext++]; + tok->start = tok->end = -1; + tok->size = 0; + return tok; + } + +/** + * Fills token type and boundaries. + */ + static void jsmn_fill_token(jsmntok_t *token, jsmntype_t type, + int start, int end) { + token->type = type; + token->start = start; + token->end = end; + token->size = 0; + } + +/** + * Fills next available token with JSON primitive. + */ + static int jsmn_parse_primitive(jsmn_parser *parser, const char *js, + size_t len, jsmntok_t *tokens, size_t num_tokens) { + jsmntok_t *token; + int start; + + start = parser->pos; + + for (; parser->pos < len && js[parser->pos] != '\0'; parser->pos++) { + switch (js[parser->pos]) { + case '\t' : case '\r' : case '\n' : case ' ' : + case ',' : case ']' : case '}' : + goto found; + } + if (js[parser->pos] < 32 || js[parser->pos] >= 127) { + parser->pos = start; + return JSMN_ERROR_INVAL; + } + } + + found: + if (tokens == NULL) { + parser->pos--; + return 0; + } + token = jsmn_alloc_token(parser, tokens, num_tokens); + if (token == NULL) { + parser->pos = start; + return JSMN_ERROR_NOMEM; + } + jsmn_fill_token(token, JSMN_PRIMITIVE, start, parser->pos); + parser->pos--; + return 0; + } + +/** + * Fills next token with JSON string. + */ + static int jsmn_parse_string(jsmn_parser *parser, const char *js, + size_t len, jsmntok_t *tokens, size_t num_tokens) { + jsmntok_t *token; + + int start = parser->pos; + + parser->pos++; + + /* Skip starting quote */ + for (; parser->pos < len && js[parser->pos] != '\0'; parser->pos++) { + char c = js[parser->pos]; + + /* Quote: end of string */ + if (c == '\"') { + if (tokens == NULL) { + return 0; + } + token = jsmn_alloc_token(parser, tokens, num_tokens); + if (token == NULL) { + parser->pos = start; + return JSMN_ERROR_NOMEM; + } + jsmn_fill_token(token, JSMN_STRING, start+1, parser->pos); + return 0; + } + + /* Backslash: Quoted symbol expected */ + if (c == '\\' && parser->pos + 1 < len) { + int i; + parser->pos++; + switch (js[parser->pos]) { + /* Allowed escaped symbols */ + case '\"': case '/' : case '\\' : case 'b' : + case 'f' : case 'r' : case 'n' : case 't' : + break; + /* Allows escaped symbol \uXXXX */ + case 'u': + parser->pos++; + for(i = 0; i < 4 && parser->pos < len && js[parser->pos] != '\0'; i++) { + /* If it isn't a hex character we have an error */ + if(!((js[parser->pos] >= 48 && js[parser->pos] <= 57) || /* 0-9 */ + (js[parser->pos] >= 65 && js[parser->pos] <= 70) || /* A-F */ + (js[parser->pos] >= 97 && js[parser->pos] <= 102))) { /* a-f */ + parser->pos = start; + return JSMN_ERROR_INVAL; + } + parser->pos++; + } + parser->pos--; + break; + /* Unexpected symbol */ + default: + parser->pos = start; + return JSMN_ERROR_INVAL; + } + } + } + parser->pos = start; + return JSMN_ERROR_PART; + } + +/** + * Parse JSON string and fill tokens. + */ + int jsmn_parse(jsmn_parser *parser, const char *js, size_t len, + jsmntok_t *tokens, unsigned int num_tokens) { + int r; + int i; + jsmntok_t *token; + int count = parser->toknext; + + for (; parser->pos < len && js[parser->pos] != '\0'; parser->pos++) { + char c; + jsmntype_t type; + + c = js[parser->pos]; + switch (c) { + case '{': case '[': + count++; + if (tokens == NULL) { + break; + } + token = jsmn_alloc_token(parser, tokens, num_tokens); + if (token == NULL) + return JSMN_ERROR_NOMEM; + if (parser->toksuper != -1) { + tokens[parser->toksuper].size++; + } + token->type = (c == '{' ? JSMN_OBJECT : JSMN_ARRAY); + token->start = parser->pos; + parser->toksuper = parser->toknext - 1; + break; + case '}': case ']': + if (tokens == NULL) + break; + type = (c == '}' ? JSMN_OBJECT : JSMN_ARRAY); + for (i = parser->toknext - 1; i >= 0; i--) { + token = &tokens[i]; + if (token->start != -1 && token->end == -1) { + if (token->type != type) { + return JSMN_ERROR_INVAL; + } + parser->toksuper = -1; + token->end = parser->pos + 1; + break; + } + } + /* Error if unmatched closing bracket */ + if (i == -1) return JSMN_ERROR_INVAL; + for (; i >= 0; i--) { + token = &tokens[i]; + if (token->start != -1 && token->end == -1) { + parser->toksuper = i; + break; + } + } + break; + case '\"': + r = jsmn_parse_string(parser, js, len, tokens, num_tokens); + if (r < 0) return r; + count++; + if (parser->toksuper != -1 && tokens != NULL) + tokens[parser->toksuper].size++; + break; + case '\t' : case '\r' : case '\n' : case ' ': + break; + case ':': + parser->toksuper = parser->toknext - 1; + break; + case ',': + if (tokens != NULL && parser->toksuper != -1 && + tokens[parser->toksuper].type != JSMN_ARRAY && + tokens[parser->toksuper].type != JSMN_OBJECT) { + for (i = parser->toknext - 1; i >= 0; i--) { + if (tokens[i].type == JSMN_ARRAY || tokens[i].type == JSMN_OBJECT) { + if (tokens[i].start != -1 && tokens[i].end == -1) { + parser->toksuper = i; + break; + } + } + } + } + break; + /* In non-strict mode every unquoted value is a primitive */ + default: + r = jsmn_parse_primitive(parser, js, len, tokens, num_tokens); + if (r < 0) return r; + count++; + if (parser->toksuper != -1 && tokens != NULL) + tokens[parser->toksuper].size++; + break; + + } + } + + if (tokens != NULL) { + for (i = parser->toknext - 1; i >= 0; i--) { + /* Unmatched opened object or array */ + if (tokens[i].start != -1 && tokens[i].end == -1) { + return JSMN_ERROR_PART; + } + } + } + + return count; + } + +/** + * Creates a new parser based over a given buffer with an array of tokens + * available. + */ + void jsmn_init(jsmn_parser *parser) { + parser->pos = 0; + parser->toknext = 0; + parser->toksuper = -1; + } } + diff --git a/src/utils.h b/src/utils.h index 2596fcd774..e908dcae81 100644 --- a/src/utils.h +++ b/src/utils.h @@ -66,6 +66,8 @@ namespace LAMMPS_NS { */ void sfgets(const char *srcname, int srcline, char *s, int size, FILE *fp, const char *filename, Error *error); + + int kim_simulator_json_parse(int argc, char **argv); } } -- GitLab From b779bf524afaf41e95ad4f9fb4fe7c622022825e Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Sun, 19 May 2019 10:09:25 -0400 Subject: [PATCH 015/469] use KIM-API calls to query simulator model info --- src/KIM/pair_kim.cpp | 45 ++++++++++++++++++++++++++++++++++++++++++-- 1 file changed, 43 insertions(+), 2 deletions(-) diff --git a/src/KIM/pair_kim.cpp b/src/KIM/pair_kim.cpp index d75d960355..fff84a1821 100644 --- a/src/KIM/pair_kim.cpp +++ b/src/KIM/pair_kim.cpp @@ -13,6 +13,7 @@ /* ---------------------------------------------------------------------- Contributing authors: Ryan S. Elliott (UMinn) + Axel Kohlmeyer (Temple U) ------------------------------------------------------------------------- */ /* ---------------------------------------------------------------------- @@ -61,6 +62,7 @@ #include "pair_kim.h" #include "atom.h" #include "comm.h" +#include "universe.h" #include "force.h" #include "neighbor.h" #include "neigh_list.h" @@ -132,6 +134,14 @@ PairKIM::~PairKIM() // clean up kim_modelname if (kim_modelname != 0) delete [] kim_modelname; + if (simulatorModel) { + KIM::SimulatorModel::Destroy(&simulatorModel); + + // clean up KIM interface (if necessary) + kim_free(); + return; + } + // clean up lammps atom species number to unique particle names mapping if (lmps_unique_elements) for (int i = 0; i < lmps_num_unique_elements; i++) @@ -330,9 +340,40 @@ void PairKIM::settings(int narg, char **arg) // initialize KIM Model kim_init(); - // initialize LAMMPS Simulator model + // Set up and initialize LAMMPS Simulator model + if (simulatorModel) { - printf("LAMMPS simulator model: %s\n",kim_modelname); + const std::string *sim_name, *sim_version; + simulatorModel->GetSimulatorName(&sim_name); + simulatorModel->GetSimulatorVersion(&sim_version); + + if (comm->me == 0) { + std::string mesg("Using KIM Simulator Model : "); + mesg += kim_modelname; + mesg += "\n"; + mesg += "For Simulator : "; + mesg += *sim_name + " " + *sim_version + "\n"; + mesg += "Running on : LAMMPS "; + mesg += universe->version; + mesg += "\n"; + + if (screen) fputs(mesg.c_str(),screen); + if (logfile) fputs(mesg.c_str(),logfile); + } + + if (*sim_name != "LAMMPS") + error->all(FLERR,"Incompatible KIM Simulator Model"); + + int sim_fields, sim_lines; + const std::string *sim_field, *sim_value; + simulatorModel->GetNumberOfSimulatorFields(&sim_fields); + printf("sim_fields=%d\n",sim_fields); + for (int i=0; i < sim_fields; ++i) { + simulatorModel->GetSimulatorFieldMetadata(i,&sim_lines,&sim_field); + printf("i=%d: %s (%d)\n",i,sim_field->c_str(),sim_lines); +// for (int j=0; j < +// simulatorModel->GetSimulatorFieldLine(i, + } } } -- GitLab From 56cf97e4970508b42ef4842e6f0de9ecfc1a9618 Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Mon, 20 May 2019 13:53:17 -0400 Subject: [PATCH 016/469] hard code creation of simulator model pair style for now --- src/KIM/pair_kim.cpp | 20 ++++++++++++++++++-- 1 file changed, 18 insertions(+), 2 deletions(-) diff --git a/src/KIM/pair_kim.cpp b/src/KIM/pair_kim.cpp index fff84a1821..87a6d636d2 100644 --- a/src/KIM/pair_kim.cpp +++ b/src/KIM/pair_kim.cpp @@ -371,9 +371,25 @@ void PairKIM::settings(int narg, char **arg) for (int i=0; i < sim_fields; ++i) { simulatorModel->GetSimulatorFieldMetadata(i,&sim_lines,&sim_field); printf("i=%d: %s (%d)\n",i,sim_field->c_str(),sim_lines); -// for (int j=0; j < -// simulatorModel->GetSimulatorFieldLine(i, } + // hard code result for now: + + int dummy; + const char *simulator_style = (const char*)"tersoff/mod"; + simulator_class = force->new_pair(simulator_style,1,dummy); + if (simulator_class) { + if (comm->me == 0) { + std::string mesg("Created simulator pair style: "); + mesg += simulator_style; + mesg += "\n"; + + if (screen) fputs(mesg.c_str(),screen); + if (logfile) fputs(mesg.c_str(),logfile); + } + } else { + error->all(FLERR,"Failure to create simulator model pair style"); + } + simulator_class->settings(0,NULL); } } -- GitLab From 38a8c765f0974799a82cee1a185adff5f3eb06fc Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Mon, 20 May 2019 22:54:20 -0400 Subject: [PATCH 017/469] add support species checking --- examples/kim/in.kim.simulator-model | 6 +-- src/KIM/pair_kim.cpp | 79 +++++++++++++++++++---------- 2 files changed, 54 insertions(+), 31 deletions(-) diff --git a/examples/kim/in.kim.simulator-model b/examples/kim/in.kim.simulator-model index 32baf9d78e..109711fffc 100644 --- a/examples/kim/in.kim.simulator-model +++ b/examples/kim/in.kim.simulator-model @@ -20,16 +20,16 @@ newton off lattice fcc 4.4300 region box block 0 ${xx} 0 ${yy} 0 ${zz} -create_box 1 box +create_box 2 box create_atoms 1 box #pair_style lj/cut 8.1500 #pair_coeff 1 1 0.0104 3.4000 pair_style kim ex_sim_model_Si_mod_tersoff -pair_coeff * * Ar +pair_coeff * * Si Si -mass 1 39.95 +mass * 39.95 velocity all create 200.0 232345 loop geom neighbor 0.3 bin diff --git a/src/KIM/pair_kim.cpp b/src/KIM/pair_kim.cpp index 87a6d636d2..2ed9df0aed 100644 --- a/src/KIM/pair_kim.cpp +++ b/src/KIM/pair_kim.cpp @@ -344,6 +344,8 @@ void PairKIM::settings(int narg, char **arg) if (simulatorModel) { const std::string *sim_name, *sim_version; + std::string atom_type_sym_list; + simulatorModel->GetSimulatorName(&sim_name); simulatorModel->GetSimulatorVersion(&sim_version); @@ -363,33 +365,6 @@ void PairKIM::settings(int narg, char **arg) if (*sim_name != "LAMMPS") error->all(FLERR,"Incompatible KIM Simulator Model"); - - int sim_fields, sim_lines; - const std::string *sim_field, *sim_value; - simulatorModel->GetNumberOfSimulatorFields(&sim_fields); - printf("sim_fields=%d\n",sim_fields); - for (int i=0; i < sim_fields; ++i) { - simulatorModel->GetSimulatorFieldMetadata(i,&sim_lines,&sim_field); - printf("i=%d: %s (%d)\n",i,sim_field->c_str(),sim_lines); - } - // hard code result for now: - - int dummy; - const char *simulator_style = (const char*)"tersoff/mod"; - simulator_class = force->new_pair(simulator_style,1,dummy); - if (simulator_class) { - if (comm->me == 0) { - std::string mesg("Created simulator pair style: "); - mesg += simulator_style; - mesg += "\n"; - - if (screen) fputs(mesg.c_str(),screen); - if (logfile) fputs(mesg.c_str(),logfile); - } - } else { - error->all(FLERR,"Failure to create simulator model pair style"); - } - simulator_class->settings(0,NULL); } } @@ -464,9 +439,57 @@ void PairKIM::coeff(int narg, char **arg) if (count == 0) error->all(FLERR,"Incorrect args for pair coefficients"); if (simulatorModel) { - simulatorModel->AddTemplateMap("atom-type-sym-list", atom_type_sym_list); + simulatorModel->AddTemplateMap("atom-type-sym-list",atom_type_sym_list); simulatorModel->CloseTemplateMap(); + int len = strlen(atom_type_sym_list.c_str())+1; + char *strbuf = new char[len]; + char *strword; + + int sim_num_species; + const std::string *sim_species; + simulatorModel->GetNumberOfSupportedSpecies(&sim_num_species); + for (int i=0; i < sim_num_species; ++i) { + simulatorModel->GetSupportedSpecies(i, &sim_species); + strcpy(strbuf,atom_type_sym_list.c_str()); + strword = strtok(strbuf," \t"); + while (strword) { + if (strcmp(sim_species->c_str(),strword) != 0) + error->all(FLERR,"Species not supported by KIM Simulator Model"); + strword = strtok(NULL," \t"); + } + } + + int sim_fields, sim_lines; + const std::string *sim_field, *sim_value; + simulatorModel->GetNumberOfSimulatorFields(&sim_fields); + if (comm->me==0) printf("sim_fields=%d\n",sim_fields); + for (int i=0; i < sim_fields; ++i) { + simulatorModel->GetSimulatorFieldMetadata(i,&sim_lines,&sim_field); + if (comm->me==0) printf("field[%d]=%s\n",i,sim_field->c_str()); + for (int j=0; j < sim_lines; ++j) { + simulatorModel->GetSimulatorFieldLine(i,j,&sim_value); + if (comm->me==0) printf("line %d: %s\n",j,sim_value->c_str()); + } + } + // hard code result for now: + + int dummy; + const char *simulator_style = (const char*)"tersoff/mod"; + simulator_class = force->new_pair(simulator_style,1,dummy); + if (simulator_class) { + if (comm->me == 0) { + std::string mesg("Created simulator pair style: "); + mesg += simulator_style; + mesg += "\n"; + + if (screen) fputs(mesg.c_str(),screen); + if (logfile) fputs(mesg.c_str(),logfile); + } + } else { + error->all(FLERR,"Failure to create simulator model pair style"); + } + simulator_class->settings(0,NULL); error->all(FLERR,(simulatorModel->ToString()).c_str()); } else { // setup mapping between LAMMPS unique elements and KIM species codes -- GitLab From 92b042552e4de87631b5a6a848209a24945f2cac Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Mon, 20 May 2019 22:54:33 -0400 Subject: [PATCH 018/469] Revert "add JSON tokenizer to utils library" This reverts commit 32379d2d840a7b5421823ba1f01aed68028d5c6b. --- src/utils.cpp | 376 +------------------------------------------------- src/utils.h | 2 - 2 files changed, 2 insertions(+), 376 deletions(-) diff --git a/src/utils.cpp b/src/utils.cpp index 77ff8ef749..c3c173a73f 100644 --- a/src/utils.cpp +++ b/src/utils.cpp @@ -12,8 +12,6 @@ ------------------------------------------------------------------------- */ #include -#include -#include #include "utils.h" #include "error.h" @@ -48,68 +46,9 @@ extern "C" { -/** Match text against a (simplified) regular expression - * (regexp will be compiled automatically). */ + /** Match text against a (simplified) regular expression + * (regexp will be compiled automatically). */ static int re_match(const char *text, const char *pattern); - -/** - * JSON type identifier. Basic types are: - * o Object - * o Array - * o String - * o Other primitive: number, boolean (true/false) or null - */ - typedef enum { - JSMN_UNDEFINED = 0, - JSMN_OBJECT = 1, - JSMN_ARRAY = 2, - JSMN_STRING = 3, - JSMN_PRIMITIVE = 4 - } jsmntype_t; - - enum jsmnerr { - /* Not enough tokens were provided */ - JSMN_ERROR_NOMEM = -1, - /* Invalid character inside JSON string */ - JSMN_ERROR_INVAL = -2, - /* The string is not a full JSON packet, more bytes expected */ - JSMN_ERROR_PART = -3 - }; - -/** - * JSON token description. - * type type (object, array, string etc.) - * start start position in JSON data string - * end end position in JSON data string - */ - typedef struct { - jsmntype_t type; - int start; - int end; - int size; - } jsmntok_t; - -/** - * JSON parser. Contains an array of token blocks available. Also stores - * the string being parsed now and current position in that string - */ - typedef struct { - unsigned int pos; /* offset in the JSON string */ - unsigned int toknext; /* next token to allocate */ - int toksuper; /* superior token node, e.g parent object or array */ - } jsmn_parser; - -/** - * Create JSON parser over an array of tokens - */ - static void jsmn_init(jsmn_parser *parser); - -/** - * Run JSON parser. It parses a JSON data string into and array of tokens, each describing - * a single JSON object. - */ - static int jsmn_parse(jsmn_parser *parser, const char *js, size_t len, - jsmntok_t *tokens, unsigned int num_tokens); } using namespace LAMMPS_NS; @@ -182,72 +121,6 @@ void utils::sfgets(const char *srcname, int srcline, char *s, int size, return; } - - -int utils::kim_simulator_json_parse(int argc, char **argv) -{ - FILE *fp; - jsmn_parser p; - jsmntok_t *tok; - char *buf; - size_t nbytes; - - if (argc != 2) { - printf("usage: %s \n",argv[0]); - return 1; - } - - // open JSON file - - fp = fopen(argv[1],"rb"); - if (!fp) { - perror("Error opening JSON file"); - return 2; - } - - // determine file size and allocate suitable buffer - - fseek(fp,0,SEEK_END); - long int flen = ftell(fp); - rewind(fp); - buf = new char[flen]; - nbytes = fread(buf,1,flen,fp); - fclose(fp); - - // parse once to count number of tokens - - jsmn_init(&p); - int ntok = jsmn_parse(&p,buf,nbytes,NULL,1); - if (ntok < 0) { - printf("failed to parse JSON: %d\n",ntok); - return 3; - } - - // allocate token storage and parse again - - jsmn_init(&p); - tok = new jsmntok_t[ntok]; - int retval = jsmn_parse(&p,buf,nbytes,tok,ntok); - if ((retval < 1) || (tok[0].type != JSMN_OBJECT)) { - printf("failed to parse JSON: no root object\n"); - return 4; - } - - for (int i=1; i < retval; ++i) { - printf("key: %.*s\n",tok[i].end-tok[i].start,buf+tok[i].start); - if (tok[i+1].type == JSMN_ARRAY) { - printf("value is array of size %d\n",tok[i+1].size); - i += tok[i+1].size + 1; - } else { - ++i; - } - } - - delete [] buf; - delete [] tok; - return 0; -} - /* ------------------------------------------------------------------ */ extern "C" { @@ -564,249 +437,4 @@ extern "C" { return 0; } - - -/** - * Allocates a fresh unused token from the token pool. - */ - static jsmntok_t *jsmn_alloc_token(jsmn_parser *parser, - jsmntok_t *tokens, size_t num_tokens) { - jsmntok_t *tok; - if (parser->toknext >= num_tokens) { - return NULL; - } - tok = &tokens[parser->toknext++]; - tok->start = tok->end = -1; - tok->size = 0; - return tok; - } - -/** - * Fills token type and boundaries. - */ - static void jsmn_fill_token(jsmntok_t *token, jsmntype_t type, - int start, int end) { - token->type = type; - token->start = start; - token->end = end; - token->size = 0; - } - -/** - * Fills next available token with JSON primitive. - */ - static int jsmn_parse_primitive(jsmn_parser *parser, const char *js, - size_t len, jsmntok_t *tokens, size_t num_tokens) { - jsmntok_t *token; - int start; - - start = parser->pos; - - for (; parser->pos < len && js[parser->pos] != '\0'; parser->pos++) { - switch (js[parser->pos]) { - case '\t' : case '\r' : case '\n' : case ' ' : - case ',' : case ']' : case '}' : - goto found; - } - if (js[parser->pos] < 32 || js[parser->pos] >= 127) { - parser->pos = start; - return JSMN_ERROR_INVAL; - } - } - - found: - if (tokens == NULL) { - parser->pos--; - return 0; - } - token = jsmn_alloc_token(parser, tokens, num_tokens); - if (token == NULL) { - parser->pos = start; - return JSMN_ERROR_NOMEM; - } - jsmn_fill_token(token, JSMN_PRIMITIVE, start, parser->pos); - parser->pos--; - return 0; - } - -/** - * Fills next token with JSON string. - */ - static int jsmn_parse_string(jsmn_parser *parser, const char *js, - size_t len, jsmntok_t *tokens, size_t num_tokens) { - jsmntok_t *token; - - int start = parser->pos; - - parser->pos++; - - /* Skip starting quote */ - for (; parser->pos < len && js[parser->pos] != '\0'; parser->pos++) { - char c = js[parser->pos]; - - /* Quote: end of string */ - if (c == '\"') { - if (tokens == NULL) { - return 0; - } - token = jsmn_alloc_token(parser, tokens, num_tokens); - if (token == NULL) { - parser->pos = start; - return JSMN_ERROR_NOMEM; - } - jsmn_fill_token(token, JSMN_STRING, start+1, parser->pos); - return 0; - } - - /* Backslash: Quoted symbol expected */ - if (c == '\\' && parser->pos + 1 < len) { - int i; - parser->pos++; - switch (js[parser->pos]) { - /* Allowed escaped symbols */ - case '\"': case '/' : case '\\' : case 'b' : - case 'f' : case 'r' : case 'n' : case 't' : - break; - /* Allows escaped symbol \uXXXX */ - case 'u': - parser->pos++; - for(i = 0; i < 4 && parser->pos < len && js[parser->pos] != '\0'; i++) { - /* If it isn't a hex character we have an error */ - if(!((js[parser->pos] >= 48 && js[parser->pos] <= 57) || /* 0-9 */ - (js[parser->pos] >= 65 && js[parser->pos] <= 70) || /* A-F */ - (js[parser->pos] >= 97 && js[parser->pos] <= 102))) { /* a-f */ - parser->pos = start; - return JSMN_ERROR_INVAL; - } - parser->pos++; - } - parser->pos--; - break; - /* Unexpected symbol */ - default: - parser->pos = start; - return JSMN_ERROR_INVAL; - } - } - } - parser->pos = start; - return JSMN_ERROR_PART; - } - -/** - * Parse JSON string and fill tokens. - */ - int jsmn_parse(jsmn_parser *parser, const char *js, size_t len, - jsmntok_t *tokens, unsigned int num_tokens) { - int r; - int i; - jsmntok_t *token; - int count = parser->toknext; - - for (; parser->pos < len && js[parser->pos] != '\0'; parser->pos++) { - char c; - jsmntype_t type; - - c = js[parser->pos]; - switch (c) { - case '{': case '[': - count++; - if (tokens == NULL) { - break; - } - token = jsmn_alloc_token(parser, tokens, num_tokens); - if (token == NULL) - return JSMN_ERROR_NOMEM; - if (parser->toksuper != -1) { - tokens[parser->toksuper].size++; - } - token->type = (c == '{' ? JSMN_OBJECT : JSMN_ARRAY); - token->start = parser->pos; - parser->toksuper = parser->toknext - 1; - break; - case '}': case ']': - if (tokens == NULL) - break; - type = (c == '}' ? JSMN_OBJECT : JSMN_ARRAY); - for (i = parser->toknext - 1; i >= 0; i--) { - token = &tokens[i]; - if (token->start != -1 && token->end == -1) { - if (token->type != type) { - return JSMN_ERROR_INVAL; - } - parser->toksuper = -1; - token->end = parser->pos + 1; - break; - } - } - /* Error if unmatched closing bracket */ - if (i == -1) return JSMN_ERROR_INVAL; - for (; i >= 0; i--) { - token = &tokens[i]; - if (token->start != -1 && token->end == -1) { - parser->toksuper = i; - break; - } - } - break; - case '\"': - r = jsmn_parse_string(parser, js, len, tokens, num_tokens); - if (r < 0) return r; - count++; - if (parser->toksuper != -1 && tokens != NULL) - tokens[parser->toksuper].size++; - break; - case '\t' : case '\r' : case '\n' : case ' ': - break; - case ':': - parser->toksuper = parser->toknext - 1; - break; - case ',': - if (tokens != NULL && parser->toksuper != -1 && - tokens[parser->toksuper].type != JSMN_ARRAY && - tokens[parser->toksuper].type != JSMN_OBJECT) { - for (i = parser->toknext - 1; i >= 0; i--) { - if (tokens[i].type == JSMN_ARRAY || tokens[i].type == JSMN_OBJECT) { - if (tokens[i].start != -1 && tokens[i].end == -1) { - parser->toksuper = i; - break; - } - } - } - } - break; - /* In non-strict mode every unquoted value is a primitive */ - default: - r = jsmn_parse_primitive(parser, js, len, tokens, num_tokens); - if (r < 0) return r; - count++; - if (parser->toksuper != -1 && tokens != NULL) - tokens[parser->toksuper].size++; - break; - - } - } - - if (tokens != NULL) { - for (i = parser->toknext - 1; i >= 0; i--) { - /* Unmatched opened object or array */ - if (tokens[i].start != -1 && tokens[i].end == -1) { - return JSMN_ERROR_PART; - } - } - } - - return count; - } - -/** - * Creates a new parser based over a given buffer with an array of tokens - * available. - */ - void jsmn_init(jsmn_parser *parser) { - parser->pos = 0; - parser->toknext = 0; - parser->toksuper = -1; - } } - diff --git a/src/utils.h b/src/utils.h index e908dcae81..2596fcd774 100644 --- a/src/utils.h +++ b/src/utils.h @@ -66,8 +66,6 @@ namespace LAMMPS_NS { */ void sfgets(const char *srcname, int srcline, char *s, int size, FILE *fp, const char *filename, Error *error); - - int kim_simulator_json_parse(int argc, char **argv); } } -- GitLab From 1e2ceb88daa631e50d68d79c581193a8bd52bdad Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Tue, 21 May 2019 15:57:14 -0400 Subject: [PATCH 019/469] complete basic simulator model proxy class creation and setup. --- src/KIM/pair_kim.cpp | 118 +++++++++++++++++++++++++++++++++++-------- 1 file changed, 96 insertions(+), 22 deletions(-) diff --git a/src/KIM/pair_kim.cpp b/src/KIM/pair_kim.cpp index 2ed9df0aed..626b7ccb1c 100644 --- a/src/KIM/pair_kim.cpp +++ b/src/KIM/pair_kim.cpp @@ -64,6 +64,7 @@ #include "comm.h" #include "universe.h" #include "force.h" +#include "input.h" #include "neighbor.h" #include "neigh_list.h" #include "neigh_request.h" @@ -71,6 +72,7 @@ #include "memory.h" #include "domain.h" #include "error.h" +#include "utils.h" using namespace LAMMPS_NS; @@ -136,6 +138,7 @@ PairKIM::~PairKIM() if (simulatorModel) { KIM::SimulatorModel::Destroy(&simulatorModel); + delete simulator_class; // clean up KIM interface (if necessary) kim_free(); @@ -446,6 +449,8 @@ void PairKIM::coeff(int narg, char **arg) char *strbuf = new char[len]; char *strword; + // validate species selection + int sim_num_species; const std::string *sim_species; simulatorModel->GetNumberOfSupportedSpecies(&sim_num_species); @@ -454,7 +459,7 @@ void PairKIM::coeff(int narg, char **arg) strcpy(strbuf,atom_type_sym_list.c_str()); strword = strtok(strbuf," \t"); while (strword) { - if (strcmp(sim_species->c_str(),strword) != 0) + if ((strcmp(strword,"NULL") != 0) && (strcmp(sim_species->c_str(),strword) != 0)) error->all(FLERR,"Species not supported by KIM Simulator Model"); strword = strtok(NULL," \t"); } @@ -463,33 +468,102 @@ void PairKIM::coeff(int narg, char **arg) int sim_fields, sim_lines; const std::string *sim_field, *sim_value; simulatorModel->GetNumberOfSimulatorFields(&sim_fields); - if (comm->me==0) printf("sim_fields=%d\n",sim_fields); for (int i=0; i < sim_fields; ++i) { simulatorModel->GetSimulatorFieldMetadata(i,&sim_lines,&sim_field); - if (comm->me==0) printf("field[%d]=%s\n",i,sim_field->c_str()); - for (int j=0; j < sim_lines; ++j) { - simulatorModel->GetSimulatorFieldLine(i,j,&sim_value); - if (comm->me==0) printf("line %d: %s\n",j,sim_value->c_str()); + if (*sim_field == "units") { + simulatorModel->GetSimulatorFieldLine(i,0,&sim_value); + if (*sim_value != update->unit_style) + error->all(FLERR,"Incompatible units for KIM Simulator Model"); + break; + } + } + + for (int i=0; i < sim_fields; ++i) { + simulatorModel->GetSimulatorFieldMetadata(i,&sim_lines,&sim_field); + if (*sim_field == "model-init") { + for (int j=0; j < sim_lines; ++j) { + simulatorModel->GetSimulatorFieldLine(i,j,&sim_value); + input->one(sim_value->c_str()); + } + break; + } + } + + int sim_model_idx=-1; + for (int i=0; i < sim_fields; ++i) { + simulatorModel->GetSimulatorFieldMetadata(i,&sim_lines,&sim_field); + if (*sim_field == "model-defn") { + sim_model_idx = i; + break; } } - // hard code result for now: - - int dummy; - const char *simulator_style = (const char*)"tersoff/mod"; - simulator_class = force->new_pair(simulator_style,1,dummy); - if (simulator_class) { - if (comm->me == 0) { - std::string mesg("Created simulator pair style: "); - mesg += simulator_style; - mesg += "\n"; - - if (screen) fputs(mesg.c_str(),screen); - if (logfile) fputs(mesg.c_str(),logfile); + + if (sim_model_idx < 0) + error->all(FLERR,"KIM Simulator Model has no Model definition"); + else { + for (int j=0; j < sim_lines; ++j) { + simulatorModel->GetSimulatorFieldLine(sim_model_idx,j,&sim_value); + if (utils::strmatch(*sim_value,"^pair_style")) { + char *ptr,*sim_style; + char *style_args[64]; + int style_narg = 0; + int len = strlen(sim_value->c_str())+1; + char *stylecmd = new char[len]; + strcpy(stylecmd,sim_value->c_str()); + + // ignore first word (pair_style) + strtok(stylecmd," \t"); + ptr = sim_style = strtok(NULL," \t"); + while (ptr && (style_narg < 63)) { + ptr = strtok(NULL," \t"); + if (!ptr) break; + style_args[style_narg] = ptr; + ++style_narg; + } + + int dummy; + delete simulator_class; + simulator_class = force->new_pair(sim_style,1,dummy); + if (simulator_class) { + if (comm->me == 0) { + std::string mesg("Created KIM Simulator Model pair style: "); + mesg += sim_style; + mesg += "\n"; + + if (screen) fputs(mesg.c_str(),screen); + if (logfile) fputs(mesg.c_str(),logfile); + } + } else { + error->all(FLERR,"Failure to create simulator model pair style"); + } + simulator_class->settings(style_narg,style_args); + delete[] stylecmd; + } + } + for (int j=0; j < sim_lines; ++j) { + simulatorModel->GetSimulatorFieldLine(sim_model_idx,j,&sim_value); + if (utils::strmatch(*sim_value,"^pair_coeff")) { + char *ptr; + char *coeff_args[64]; + int coeff_narg = 0; + int len = strlen(sim_value->c_str())+1; + char *coeffcmd = new char[len]; + strcpy(coeffcmd,sim_value->c_str()); + + // ignore first word (pair_coeff) + strtok(coeffcmd," \t"); + ptr = strtok(NULL," \t"); + while (ptr && (coeff_narg < 63)) { + coeff_args[coeff_narg] = ptr; + ++coeff_narg; + ptr = strtok(NULL," \t"); + } + + simulator_class->coeff(coeff_narg,coeff_args); + delete[] coeffcmd; + } } - } else { - error->all(FLERR,"Failure to create simulator model pair style"); } - simulator_class->settings(0,NULL); error->all(FLERR,(simulatorModel->ToString()).c_str()); } else { // setup mapping between LAMMPS unique elements and KIM species codes -- GitLab From ce46d52c8a9ab27383d797fc29c9108f4ed59ccd Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Fri, 24 May 2019 10:23:26 -0400 Subject: [PATCH 020/469] add new 'kim_style' command as front end for KIM simulator (and regular) models --- examples/kim/in.kim.simulator-model | 4 +- src/KIM/fix_store_kim.cpp | 127 ++++++++++++ src/KIM/fix_store_kim.h | 98 ++++++++++ src/KIM/kim_query.cpp | 1 - src/KIM/kim_style.cpp | 286 ++++++++++++++++++++++++++++ src/KIM/kim_style.h | 87 +++++++++ src/modify.cpp | 2 +- 7 files changed, 600 insertions(+), 5 deletions(-) create mode 100644 src/KIM/fix_store_kim.cpp create mode 100644 src/KIM/fix_store_kim.h create mode 100644 src/KIM/kim_style.cpp create mode 100644 src/KIM/kim_style.h diff --git a/examples/kim/in.kim.simulator-model b/examples/kim/in.kim.simulator-model index 109711fffc..1e6e9dec89 100644 --- a/examples/kim/in.kim.simulator-model +++ b/examples/kim/in.kim.simulator-model @@ -16,7 +16,6 @@ variable zz equal 20*$z units metal atom_style atomic -newton off lattice fcc 4.4300 region box block 0 ${xx} 0 ${yy} 0 ${zz} @@ -26,8 +25,7 @@ create_atoms 1 box #pair_style lj/cut 8.1500 #pair_coeff 1 1 0.0104 3.4000 -pair_style kim ex_sim_model_Si_mod_tersoff -pair_coeff * * Si Si +kim_style define ex_sim_model_Si_mod_tersoff Si Si mass * 39.95 velocity all create 200.0 232345 loop geom diff --git a/src/KIM/fix_store_kim.cpp b/src/KIM/fix_store_kim.cpp new file mode 100644 index 0000000000..8e9946c20d --- /dev/null +++ b/src/KIM/fix_store_kim.cpp @@ -0,0 +1,127 @@ +/* ---------------------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + http://lammps.sandia.gov, Sandia National Laboratories + Steve Plimpton, sjplimp@sandia.gov + + Copyright (2003) Sandia Corporation. Under the terms of Contract + DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains + certain rights in this software. This software is distributed under + the GNU General Public License. + + See the README file in the top-level LAMMPS directory. +------------------------------------------------------------------------- */ + +/* ---------------------------------------------------------------------- + Contributing authors: Axel Kohlmeyer (Temple U), + Ryan S. Elliott (UMN) +------------------------------------------------------------------------- */ + +/* ---------------------------------------------------------------------- + This program is free software; you can redistribute it and/or modify it + under the terms of the GNU General Public License as published by the Free + Software Foundation; either version 2 of the License, or (at your option) + any later version. + + This program is distributed in the hope that it will be useful, but WITHOUT + ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or + FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for + more details. + + You should have received a copy of the GNU General Public License along with + this program; if not, see . + + Linking LAMMPS statically or dynamically with other modules is making a + combined work based on LAMMPS. Thus, the terms and conditions of the GNU + General Public License cover the whole combination. + + In addition, as a special exception, the copyright holders of LAMMPS give + you permission to combine LAMMPS with free software programs or libraries + that are released under the GNU LGPL and with code included in the standard + release of the "kim-api" under the CDDL (or modified versions of such code, + with unchanged license). You may copy and distribute such a system following + the terms of the GNU GPL for LAMMPS and the licenses of the other code + concerned, provided that you include the source code of that other code + when and as the GNU GPL requires distribution of source code. + + Note that people who make modified versions of LAMMPS are not obligated to + grant this special exception for their modified versions; it is their choice + whether to do so. The GNU General Public License gives permission to release + a modified version without this exception; this exception also makes it + possible to release a modified version which carries forward this exception. +------------------------------------------------------------------------- */ + +/* ---------------------------------------------------------------------- + Designed for use with the kim-api-2.0.2 (and newer) package +------------------------------------------------------------------------- */ + +#include +#include "fix_store_kim.h" +#include "KIM_SimulatorModel.hpp" +#include "error.h" + +using namespace LAMMPS_NS; +using namespace FixConst; + +/* ---------------------------------------------------------------------- */ + +FixStoreKIM::FixStoreKIM(LAMMPS *lmp, int narg, char **arg) + : Fix(lmp, narg, arg), simulator_model(NULL), model_name(NULL) +{ + if (narg != 3) error->all(FLERR,"Illegal fix STORE/KIM command"); +} + +/* ---------------------------------------------------------------------- */ + +FixStoreKIM::~FixStoreKIM() +{ + // free associated storage + + if (simulator_model) { + KIM::SimulatorModel *sm = (KIM::SimulatorModel *)simulator_model; + KIM::SimulatorModel::Destroy(&sm); + simulator_model = NULL; + } + + if (model_name) { + char *mn = (char *)model_name; + delete[] mn; + model_name = NULL; + } +} + +/* ---------------------------------------------------------------------- */ + +int FixStoreKIM::setmask() +{ + int mask = 0; + return mask; +} + + +/* ---------------------------------------------------------------------- */ + +void FixStoreKIM::setptr(const char *name, void *ptr) +{ + if (strcmp(name,"simulator_model") == 0) { + if (simulator_model) { + KIM::SimulatorModel *sm = (KIM::SimulatorModel *)simulator_model; + KIM::SimulatorModel::Destroy(&sm); + } + simulator_model = ptr; + } else if (strcmp(name,"model_name") == 0) { + if (model_name) { + char *mn = (char *)model_name; + delete[] mn; + } + model_name = ptr; + } +} + +/* ---------------------------------------------------------------------- */ + +void *FixStoreKIM::getptr(const char *name) +{ + if (strcmp(name,"simulator_model") == 0) return simulator_model; + else if (strcmp(name,"model_name") == 0) return model_name; + else return NULL; +} diff --git a/src/KIM/fix_store_kim.h b/src/KIM/fix_store_kim.h new file mode 100644 index 0000000000..04081fd6dc --- /dev/null +++ b/src/KIM/fix_store_kim.h @@ -0,0 +1,98 @@ +/* -*- c++ -*- ---------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + http://lammps.sandia.gov, Sandia National Laboratories + Steve Plimpton, sjplimp@sandia.gov + + Copyright (2003) Sandia Corporation. Under the terms of Contract + DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains + certain rights in this software. This software is distributed under + the GNU General Public License. + + See the README file in the top-level LAMMPS directory. +------------------------------------------------------------------------- */ + +/* ---------------------------------------------------------------------- + Contributing authors: Axel Kohlmeyer (Temple U), + Ryan S. Elliott (UMN) +------------------------------------------------------------------------- */ + +/* ---------------------------------------------------------------------- + This program is free software; you can redistribute it and/or modify it + under the terms of the GNU General Public License as published by the Free + Software Foundation; either version 2 of the License, or (at your option) + any later version. + + This program is distributed in the hope that it will be useful, but WITHOUT + ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or + FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for + more details. + + You should have received a copy of the GNU General Public License along with + this program; if not, see . + + Linking LAMMPS statically or dynamically with other modules is making a + combined work based on LAMMPS. Thus, the terms and conditions of the GNU + General Public License cover the whole combination. + + In addition, as a special exception, the copyright holders of LAMMPS give + you permission to combine LAMMPS with free software programs or libraries + that are released under the GNU LGPL and with code included in the standard + release of the "kim-api" under the CDDL (or modified versions of such code, + with unchanged license). You may copy and distribute such a system following + the terms of the GNU GPL for LAMMPS and the licenses of the other code + concerned, provided that you include the source code of that other code + when and as the GNU GPL requires distribution of source code. + + Note that people who make modified versions of LAMMPS are not obligated to + grant this special exception for their modified versions; it is their choice + whether to do so. The GNU General Public License gives permission to release + a modified version without this exception; this exception also makes it + possible to release a modified version which carries forward this exception. +------------------------------------------------------------------------- */ + +/* ---------------------------------------------------------------------- + Designed for use with the kim-api-2.0.2 (and newer) package +------------------------------------------------------------------------- */ + +#ifdef FIX_CLASS + +FixStyle(STORE/KIM,FixStoreKIM) + +#else + +#ifndef LMP_FIX_STORE_KIM_H +#define LMP_FIX_STORE_KIM_H + +#include +#include "fix.h" + +namespace LAMMPS_NS { + +class FixStoreKIM : public Fix { + public: + FixStoreKIM(class LAMMPS *, int, char **); + ~FixStoreKIM(); + int setmask(); + + void setptr(const char *, void *); + void *getptr(const char *); + + private: + void *simulator_model; // pointer to KIM simulator model class + void *model_name; // string of KIM model name +}; + +} + +#endif +#endif + +/* ERROR/WARNING messages: + +E: Illegal ... command + +Self-explanatory. Check the input script syntax and compare to the +documentation for the command. You can use -echo screen as a +command-line option when running LAMMPS to see the offending line. + +*/ diff --git a/src/KIM/kim_query.cpp b/src/KIM/kim_query.cpp index fedc976110..e4818abc94 100644 --- a/src/KIM/kim_query.cpp +++ b/src/KIM/kim_query.cpp @@ -11,7 +11,6 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ - /* ---------------------------------------------------------------------- Contributing authors: Axel Kohlmeyer (Temple U), Ryan S. Elliott (UMN) diff --git a/src/KIM/kim_style.cpp b/src/KIM/kim_style.cpp new file mode 100644 index 0000000000..865f6827ab --- /dev/null +++ b/src/KIM/kim_style.cpp @@ -0,0 +1,286 @@ +/* ---------------------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + http://lammps.sandia.gov, Sandia National Laboratories + Steve Plimpton, sjplimp@sandia.gov + + Copyright (2003) Sandia Corporation. Under the terms of Contract + DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains + certain rights in this software. This software is distributed under + the GNU General Public License. + + See the README file in the top-level LAMMPS directory. +------------------------------------------------------------------------- */ + +/* ---------------------------------------------------------------------- + Contributing authors: Axel Kohlmeyer (Temple U), + Ryan S. Elliott (UMN) +------------------------------------------------------------------------- */ + +/* ---------------------------------------------------------------------- + This program is free software; you can redistribute it and/or modify it + under the terms of the GNU General Public License as published by the Free + Software Foundation; either version 2 of the License, or (at your option) + any later version. + + This program is distributed in the hope that it will be useful, but WITHOUT + ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or + FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for + more details. + + You should have received a copy of the GNU General Public License along with + this program; if not, see . + + Linking LAMMPS statically or dynamically with other modules is making a + combined work based on LAMMPS. Thus, the terms and conditions of the GNU + General Public License cover the whole combination. + + In addition, as a special exception, the copyright holders of LAMMPS give + you permission to combine LAMMPS with free software programs or libraries + that are released under the GNU LGPL and with code included in the standard + release of the "kim-api" under the CDDL (or modified versions of such code, + with unchanged license). You may copy and distribute such a system following + the terms of the GNU GPL for LAMMPS and the licenses of the other code + concerned, provided that you include the source code of that other code + when and as the GNU GPL requires distribution of source code. + + Note that people who make modified versions of LAMMPS are not obligated to + grant this special exception for their modified versions; it is their choice + whether to do so. The GNU General Public License gives permission to release + a modified version without this exception; this exception also makes it + possible to release a modified version which carries forward this exception. +------------------------------------------------------------------------- */ + +/* ---------------------------------------------------------------------- + Designed for use with the kim-api-2.0.2 (and newer) package +------------------------------------------------------------------------- */ + +#include +#include +#include "kim_style.h" +#include "error.h" +#include "atom.h" +#include "comm.h" +#include "domain.h" +#include "modify.h" +#include "update.h" +#include "universe.h" +#include "input.h" +#include "fix_store_kim.h" + +#include "KIM_SimulatorModel.hpp" + + +using namespace LAMMPS_NS; + +/* ---------------------------------------------------------------------- */ + +void KimStyle::command(int narg, char **arg) +{ + if (narg < 2) error->all(FLERR,"Illegal kim_style command"); + + if (strcmp(arg[0],"init") == 0) { + if (narg > 2) error->all(FLERR,"Illegal kim_style init command"); + if (domain->box_exist) + error->all(FLERR,"Must use 'kim_style init' command before " + "simulation box is defined"); + int len = strlen(arg[1])+1; + char *model = new char[len]; + strcpy(model,arg[1]); + do_init(model); + } else if (strcmp(arg[0],"define") == 0) { + if (!domain->box_exist) + error->all(FLERR,"Must use 'kim_style define' command after " + "simulation box is defined"); + do_defn(narg-1,arg+1); + } else error->all(FLERR,"Illegal kim_style command"); +} + + +/* ---------------------------------------------------------------------- */ + +void KimStyle::do_init(char *model) +{ + // create storage proxy fix. delete existing fix, if needed. + + int ifix = modify->find_fix("KIM_MODEL_STORE"); + if (ifix >= 0) modify->delete_fix(ifix); + input->one("fix KIM_MODEL_STORE all STORE/KIM"); + ifix = modify->find_fix("KIM_MODEL_STORE"); + + FixStoreKIM *fix_store = (FixStoreKIM *) modify->fix[ifix]; + fix_store->setptr("model_name", (void *) model); + + int kimerror; + KIM::SimulatorModel * simulatorModel; + kimerror = KIM::SimulatorModel::Create(model,&simulatorModel); + + // not a Kim Simulator Model; nothing else to do here. + if (kimerror) return; + + fix_store->setptr("simulator_model", (void *) simulatorModel); + + // need to call this to have access to (some) simulator model init data. + simulatorModel->CloseTemplateMap(); + + int sim_fields, sim_lines; + const std::string *sim_field, *sim_value; + simulatorModel->GetNumberOfSimulatorFields(&sim_fields); + + // set units + for (int i=0; i < sim_fields; ++i) { + simulatorModel->GetSimulatorFieldMetadata(i,&sim_lines,&sim_field); + if (*sim_field == "units") { + simulatorModel->GetSimulatorFieldLine(i,0,&sim_value); + std::string cmd("units "); + cmd += *sim_value; + input->one(cmd.c_str()); + break; + } + } + + // init model + for (int i=0; i < sim_fields; ++i) { + simulatorModel->GetSimulatorFieldMetadata(i,&sim_lines,&sim_field); + if (*sim_field == "model-init") { + for (int j=0; j < sim_lines; ++j) { + simulatorModel->GetSimulatorFieldLine(i,j,&sim_value); + input->one(sim_value->c_str()); + } + break; + } + } + + // reset template map. + simulatorModel->ClearTemplateMap(); +} + +/* ---------------------------------------------------------------------- */ + +void KimStyle::do_defn(int narg, char **arg) +{ + if (narg != atom->ntypes + 1) + error->all(FLERR,"Incorrect number of arguments for kim_style define command"); + + char *model = arg[0]; + KIM::SimulatorModel *simulatorModel(NULL); + int kimerror; + + // check if we had a kim_style init command by finding fix STORE/KIM + // retrieve model name and pointer to simulator model class instance. + // validate model name if not given as NULL. + // if kim_style init wasn't run try to initialize simulator model now. + + int ifix = modify->find_fix("KIM_MODEL_STORE"); + if (ifix >= 0) { + FixStoreKIM *fix_store = (FixStoreKIM *) modify->fix[ifix]; + if (strcmp(model,"NULL") == 0) + model = (char *)fix_store->getptr("model_name"); + else if (strcmp(model,(const char*)fix_store->getptr("model_name")) != 0) + error->all(FLERR,"Inconsistent KIM model name"); + + simulatorModel = (KIM::SimulatorModel *)fix_store->getptr("simulator_model"); + } else { + + kimerror = KIM::SimulatorModel::Create(model,&simulatorModel); + if (kimerror) simulatorModel = NULL; + } + + if (simulatorModel) { + + const std::string *sim_name, *sim_version; + std::string atom_type_sym_list; + + simulatorModel->GetSimulatorName(&sim_name); + simulatorModel->GetSimulatorVersion(&sim_version); + + if (comm->me == 0) { + std::string mesg("Using KIM Simulator Model : "); + mesg += model; + mesg += "\n"; + mesg += "For Simulator : "; + mesg += *sim_name + " " + *sim_version + "\n"; + mesg += "Running on : LAMMPS "; + mesg += universe->version; + mesg += "\n"; + + if (screen) fputs(mesg.c_str(),screen); + if (logfile) fputs(mesg.c_str(),logfile); + } + + if (*sim_name != "LAMMPS") + error->all(FLERR,"Incompatible KIM Simulator Model"); + + for (int i = 1; i < narg; i++) + atom_type_sym_list += std::string(" ") + arg[i]; + + simulatorModel->AddTemplateMap("atom-type-sym-list",atom_type_sym_list); + simulatorModel->CloseTemplateMap(); + + int len = strlen(atom_type_sym_list.c_str())+1; + char *strbuf = new char[len]; + char *strword; + + // validate species selection + + int sim_num_species; + const std::string *sim_species; + simulatorModel->GetNumberOfSupportedSpecies(&sim_num_species); + for (int i=0; i < sim_num_species; ++i) { + simulatorModel->GetSupportedSpecies(i, &sim_species); + strcpy(strbuf,atom_type_sym_list.c_str()); + strword = strtok(strbuf," \t"); + while (strword) { + if ((strcmp(strword,"NULL") != 0) && (strcmp(sim_species->c_str(),strword) != 0)) + error->all(FLERR,"Species not supported by KIM Simulator Model"); + strword = strtok(NULL," \t"); + } + } + delete[] strbuf; + + int sim_fields, sim_lines; + const std::string *sim_field, *sim_value; + simulatorModel->GetNumberOfSimulatorFields(&sim_fields); + for (int i=0; i < sim_fields; ++i) { + simulatorModel->GetSimulatorFieldMetadata(i,&sim_lines,&sim_field); + if (*sim_field == "units") { + simulatorModel->GetSimulatorFieldLine(i,0,&sim_value); + if (*sim_value != update->unit_style) + error->all(FLERR,"Incompatible units for KIM Simulator Model"); + break; + } + } + + int sim_model_idx=-1; + for (int i=0; i < sim_fields; ++i) { + simulatorModel->GetSimulatorFieldMetadata(i,&sim_lines,&sim_field); + if (*sim_field == "model-defn") { + sim_model_idx = i; + for (int j=0; j < sim_lines; ++j) { + simulatorModel->GetSimulatorFieldLine(sim_model_idx,j,&sim_value); + input->one(sim_value->c_str()); + } + } + } + + if (sim_model_idx < 0) + error->all(FLERR,"KIM Simulator Model has no Model definition"); + + } else { + + // not a simulator model. issue pair_style and pair_coeff commands. + // NOTE: all references to arg must appear before calls to input->one() + // as that will reset the argument vector. + + std::string cmd1("pair_style kim "); + cmd1 += model; + + std::string cmd2("pair_coeff * * "); + for (int i=1; i < narg; ++i) { + cmd2 += arg[i]; + cmd2 += " "; + } + + input->one(cmd1.c_str()); + input->one(cmd2.c_str()); + } +} diff --git a/src/KIM/kim_style.h b/src/KIM/kim_style.h new file mode 100644 index 0000000000..588de6e620 --- /dev/null +++ b/src/KIM/kim_style.h @@ -0,0 +1,87 @@ +/* -*- c++ -*- ---------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + http://lammps.sandia.gov, Sandia National Laboratories + Steve Plimpton, sjplimp@sandia.gov + + Copyright (2003) Sandia Corporation. Under the terms of Contract + DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains + certain rights in this software. This software is distributed under + the GNU General Public License. + + See the README file in the top-level LAMMPS directory. +------------------------------------------------------------------------- */ + +/* ---------------------------------------------------------------------- + Contributing authors: Axel Kohlmeyer (Temple U), + Ryan S. Elliott (UMN) +------------------------------------------------------------------------- */ + +/* ---------------------------------------------------------------------- + This program is free software; you can redistribute it and/or modify it + under the terms of the GNU General Public License as published by the Free + Software Foundation; either version 2 of the License, or (at your option) + any later version. + + This program is distributed in the hope that it will be useful, but WITHOUT + ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or + FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for + more details. + + You should have received a copy of the GNU General Public License along with + this program; if not, see . + + Linking LAMMPS statically or dynamically with other modules is making a + combined work based on LAMMPS. Thus, the terms and conditions of the GNU + General Public License cover the whole combination. + + In addition, as a special exception, the copyright holders of LAMMPS give + you permission to combine LAMMPS with free software programs or libraries + that are released under the GNU LGPL and with code included in the standard + release of the "kim-api" under the CDDL (or modified versions of such code, + with unchanged license). You may copy and distribute such a system following + the terms of the GNU GPL for LAMMPS and the licenses of the other code + concerned, provided that you include the source code of that other code + when and as the GNU GPL requires distribution of source code. + + Note that people who make modified versions of LAMMPS are not obligated to + grant this special exception for their modified versions; it is their choice + whether to do so. The GNU General Public License gives permission to release + a modified version without this exception; this exception also makes it + possible to release a modified version which carries forward this exception. +------------------------------------------------------------------------- */ + +/* ---------------------------------------------------------------------- + Designed for use with the kim-api-2.0.2 (and newer) package +------------------------------------------------------------------------- */ + +#ifdef COMMAND_CLASS + +CommandStyle(kim_style,KimStyle) + +#else + +#ifndef LMP_KIM_STYLE_H +#define LMP_KIM_STYLE_H + +#include "pointers.h" + +namespace LAMMPS_NS { + +class KimStyle : protected Pointers { + public: + KimStyle(class LAMMPS *lmp) : Pointers(lmp) {}; + void command(int, char **); + private: + void do_init(char *); + void do_defn(int, char **); +}; + +} + +#endif +#endif + +/* ERROR/WARNING messages: + + +*/ diff --git a/src/modify.cpp b/src/modify.cpp index 7f43f035d2..9f0457c9d0 100644 --- a/src/modify.cpp +++ b/src/modify.cpp @@ -793,7 +793,7 @@ void Modify::add_fix(int narg, char **arg, int trysuffix) const char *exceptions[] = {"GPU", "OMP", "INTEL", "property/atom", "cmap", "cmap3", "rx", - "deprecated", NULL}; + "deprecated", "STORE/KIM", NULL}; if (domain->box_exist == 0) { int m; -- GitLab From b91b3c18cffff347ca58f2d5cdef7052adf5875b Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Fri, 24 May 2019 11:52:38 -0400 Subject: [PATCH 021/469] remove references to simulator models from pair style kim --- src/KIM/pair_kim.cpp | 269 ++++++------------------------------------- src/KIM/pair_kim.h | 13 +-- 2 files changed, 41 insertions(+), 241 deletions(-) diff --git a/src/KIM/pair_kim.cpp b/src/KIM/pair_kim.cpp index 626b7ccb1c..6251ebb6c7 100644 --- a/src/KIM/pair_kim.cpp +++ b/src/KIM/pair_kim.cpp @@ -92,7 +92,6 @@ PairKIM::PairKIM(LAMMPS *lmp) : chargeUnit(KIM_CHARGE_UNIT_unused), temperatureUnit(KIM_TEMPERATURE_UNIT_unused), timeUnit(KIM_TIME_UNIT_unused), - simulatorModel(NULL), pkim(NULL), pargs(NULL), kim_model_support_for_energy(KIM_SUPPORT_STATUS_notSupported), @@ -110,9 +109,7 @@ PairKIM::PairKIM(LAMMPS *lmp) : kim_particleSpecies(NULL), kim_particleContributing(NULL), lmps_stripped_neigh_list(NULL), - lmps_stripped_neigh_ptr(NULL), - simulator_class(NULL), - simulator_style(NULL) + lmps_stripped_neigh_ptr(NULL) { // Initialize Pair data members to appropriate values single_enable = 0; // We do not provide the Single() function @@ -136,15 +133,6 @@ PairKIM::~PairKIM() // clean up kim_modelname if (kim_modelname != 0) delete [] kim_modelname; - if (simulatorModel) { - KIM::SimulatorModel::Destroy(&simulatorModel); - delete simulator_class; - - // clean up KIM interface (if necessary) - kim_free(); - return; - } - // clean up lammps atom species number to unique particle names mapping if (lmps_unique_elements) for (int i = 0; i < lmps_num_unique_elements; i++) @@ -342,33 +330,6 @@ void PairKIM::settings(int narg, char **arg) // initialize KIM Model kim_init(); - - // Set up and initialize LAMMPS Simulator model - - if (simulatorModel) { - const std::string *sim_name, *sim_version; - std::string atom_type_sym_list; - - simulatorModel->GetSimulatorName(&sim_name); - simulatorModel->GetSimulatorVersion(&sim_version); - - if (comm->me == 0) { - std::string mesg("Using KIM Simulator Model : "); - mesg += kim_modelname; - mesg += "\n"; - mesg += "For Simulator : "; - mesg += *sim_name + " " + *sim_version + "\n"; - mesg += "Running on : LAMMPS "; - mesg += universe->version; - mesg += "\n"; - - if (screen) fputs(mesg.c_str(),screen); - if (logfile) fputs(mesg.c_str(),logfile); - } - - if (*sim_name != "LAMMPS") - error->all(FLERR,"Incompatible KIM Simulator Model"); - } } /* ---------------------------------------------------------------------- @@ -441,154 +402,29 @@ void PairKIM::coeff(int narg, char **arg) if (count == 0) error->all(FLERR,"Incorrect args for pair coefficients"); - if (simulatorModel) { - simulatorModel->AddTemplateMap("atom-type-sym-list",atom_type_sym_list); - simulatorModel->CloseTemplateMap(); - - int len = strlen(atom_type_sym_list.c_str())+1; - char *strbuf = new char[len]; - char *strword; - - // validate species selection - - int sim_num_species; - const std::string *sim_species; - simulatorModel->GetNumberOfSupportedSpecies(&sim_num_species); - for (int i=0; i < sim_num_species; ++i) { - simulatorModel->GetSupportedSpecies(i, &sim_species); - strcpy(strbuf,atom_type_sym_list.c_str()); - strword = strtok(strbuf," \t"); - while (strword) { - if ((strcmp(strword,"NULL") != 0) && (strcmp(sim_species->c_str(),strword) != 0)) - error->all(FLERR,"Species not supported by KIM Simulator Model"); - strword = strtok(NULL," \t"); - } - } - - int sim_fields, sim_lines; - const std::string *sim_field, *sim_value; - simulatorModel->GetNumberOfSimulatorFields(&sim_fields); - for (int i=0; i < sim_fields; ++i) { - simulatorModel->GetSimulatorFieldMetadata(i,&sim_lines,&sim_field); - if (*sim_field == "units") { - simulatorModel->GetSimulatorFieldLine(i,0,&sim_value); - if (*sim_value != update->unit_style) - error->all(FLERR,"Incompatible units for KIM Simulator Model"); - break; - } - } - - for (int i=0; i < sim_fields; ++i) { - simulatorModel->GetSimulatorFieldMetadata(i,&sim_lines,&sim_field); - if (*sim_field == "model-init") { - for (int j=0; j < sim_lines; ++j) { - simulatorModel->GetSimulatorFieldLine(i,j,&sim_value); - input->one(sim_value->c_str()); - } - break; - } - } - - int sim_model_idx=-1; - for (int i=0; i < sim_fields; ++i) { - simulatorModel->GetSimulatorFieldMetadata(i,&sim_lines,&sim_field); - if (*sim_field == "model-defn") { - sim_model_idx = i; - break; - } - } - - if (sim_model_idx < 0) - error->all(FLERR,"KIM Simulator Model has no Model definition"); - else { - for (int j=0; j < sim_lines; ++j) { - simulatorModel->GetSimulatorFieldLine(sim_model_idx,j,&sim_value); - if (utils::strmatch(*sim_value,"^pair_style")) { - char *ptr,*sim_style; - char *style_args[64]; - int style_narg = 0; - int len = strlen(sim_value->c_str())+1; - char *stylecmd = new char[len]; - strcpy(stylecmd,sim_value->c_str()); - - // ignore first word (pair_style) - strtok(stylecmd," \t"); - ptr = sim_style = strtok(NULL," \t"); - while (ptr && (style_narg < 63)) { - ptr = strtok(NULL," \t"); - if (!ptr) break; - style_args[style_narg] = ptr; - ++style_narg; - } - - int dummy; - delete simulator_class; - simulator_class = force->new_pair(sim_style,1,dummy); - if (simulator_class) { - if (comm->me == 0) { - std::string mesg("Created KIM Simulator Model pair style: "); - mesg += sim_style; - mesg += "\n"; - - if (screen) fputs(mesg.c_str(),screen); - if (logfile) fputs(mesg.c_str(),logfile); - } - } else { - error->all(FLERR,"Failure to create simulator model pair style"); - } - simulator_class->settings(style_narg,style_args); - delete[] stylecmd; - } - } - for (int j=0; j < sim_lines; ++j) { - simulatorModel->GetSimulatorFieldLine(sim_model_idx,j,&sim_value); - if (utils::strmatch(*sim_value,"^pair_coeff")) { - char *ptr; - char *coeff_args[64]; - int coeff_narg = 0; - int len = strlen(sim_value->c_str())+1; - char *coeffcmd = new char[len]; - strcpy(coeffcmd,sim_value->c_str()); - - // ignore first word (pair_coeff) - strtok(coeffcmd," \t"); - ptr = strtok(NULL," \t"); - while (ptr && (coeff_narg < 63)) { - coeff_args[coeff_narg] = ptr; - ++coeff_narg; - ptr = strtok(NULL," \t"); - } - - simulator_class->coeff(coeff_narg,coeff_args); - delete[] coeffcmd; - } - } - } - error->all(FLERR,(simulatorModel->ToString()).c_str()); - } else { - // setup mapping between LAMMPS unique elements and KIM species codes - if (kim_particle_codes_ok) { - delete [] kim_particle_codes; - kim_particle_codes = NULL; - kim_particle_codes_ok = false; - } - kim_particle_codes = new int[lmps_num_unique_elements]; - kim_particle_codes_ok = true; - for(int i = 0; i < lmps_num_unique_elements; i++) { - int supported; - int code; - KIM_Model_GetSpeciesSupportAndCode( - pkim, - KIM_SpeciesName_FromString(lmps_unique_elements[i]), - &supported, - &code); - if (supported) { - kim_particle_codes[i] = code; - } else { - std::string msg("create_kim_particle_codes: symbol not found: "); - msg += lmps_unique_elements[i]; - error->all(FLERR, msg.c_str()); - } + // setup mapping between LAMMPS unique elements and KIM species codes + if (kim_particle_codes_ok) { + delete [] kim_particle_codes; + kim_particle_codes = NULL; + kim_particle_codes_ok = false; + } + kim_particle_codes = new int[lmps_num_unique_elements]; + kim_particle_codes_ok = true; + + for(int i = 0; i < lmps_num_unique_elements; i++) { + int supported; + int code; + KIM_Model_GetSpeciesSupportAndCode( + pkim, + KIM_SpeciesName_FromString(lmps_unique_elements[i]), + &supported, + &code); + if (supported) { + kim_particle_codes[i] = code; + } else { + std::string msg("create_kim_particle_codes: symbol not found: "); + msg += lmps_unique_elements[i]; + error->all(FLERR, msg.c_str()); } } } @@ -799,32 +635,6 @@ double PairKIM::memory_usage() return bytes; } -/* ---------------------------------------------------------------------- - simulator model support functions -------------------------------------------------------------------------- */ - -void PairKIM::simulator_init() -{ - int dummy; - // do not try with suffixes for now. - simulator_class = force->new_pair("lj/cut",1,dummy); - force->store_style(simulator_style,"lj/cut",1); - printf("Simulator model init: %s -> %s\n", kim_modelname, simulator_style); - char **args = new char*[1]; - args[0] = (char *)"8.1500"; - simulator_class->settings(1,args); - delete[] args; -} - -void PairKIM::simulator_free() -{ - printf("Simulator model free: %s -> %s\n", kim_modelname, simulator_style); - delete[] simulator_style; - simulator_style = NULL; - delete simulator_class; - simulator_class = NULL; -} - /* ---------------------------------------------------------------------- KIM-specific interface ------------------------------------------------------------------------- */ @@ -902,26 +712,21 @@ void PairKIM::kim_init() kim_modelname, &requestedUnitsAccepted, &pkim); - if (kimerror) { - kimerror = KIM::SimulatorModel::Create(kim_modelname,&simulatorModel); - if (kimerror) error->all(FLERR,"KIM ModelCreate failed"); - else return; - } else { - if (!requestedUnitsAccepted) - error->all(FLERR,"KIM Model did not accept the requested unit system"); + if (kimerror) error->all(FLERR,"KIM ModelCreate failed"); + else if (!requestedUnitsAccepted) + error->all(FLERR,"KIM Model did not accept the requested unit system"); - // check that the model does not require unknown capabilities - kimerror = check_for_routine_compatibility(); - if (kimerror) - error->all(FLERR, - "KIM Model requires unknown Routines. Unable to proceed."); + // check that the model does not require unknown capabilities + kimerror = check_for_routine_compatibility(); + if (kimerror) + error->all(FLERR, + "KIM Model requires unknown Routines. Unable to proceed."); - kimerror = KIM_Model_ComputeArgumentsCreate(pkim, &pargs); - if (kimerror) { - KIM_Model_Destroy(&pkim); - error->all(FLERR,"KIM ComputeArgumentsCreate failed"); - } else kim_init_ok = true; - } + kimerror = KIM_Model_ComputeArgumentsCreate(pkim, &pargs); + if (kimerror) { + KIM_Model_Destroy(&pkim); + error->all(FLERR,"KIM ComputeArgumentsCreate failed"); + } else kim_init_ok = true; // determine KIM Model capabilities (used in this function below) set_kim_model_has_flags(); diff --git a/src/KIM/pair_kim.h b/src/KIM/pair_kim.h index 37a6be1e5b..aa33b9b271 100644 --- a/src/KIM/pair_kim.h +++ b/src/KIM/pair_kim.h @@ -69,7 +69,6 @@ class KIM_API_model; extern "C" { #include "KIM_SimulatorHeaders.h" } -#include "KIM_SimulatorModel.hpp" namespace LAMMPS_NS { @@ -121,7 +120,6 @@ class PairKIM : public Pair { KIM_TemperatureUnit temperatureUnit; KIM_TimeUnit timeUnit; - KIM::SimulatorModel * simulatorModel; KIM_Model * pkim; KIM_ComputeArguments * pargs; @@ -152,12 +150,6 @@ class PairKIM : public Pair { // is in molecular mode int** lmps_stripped_neigh_ptr; // pointer into lists - // LAMMPS Simulator model support - Pair *simulator_class; - char *simulator_style; - virtual void simulator_init(); - virtual void simulator_free(); - // KIM specific helper functions virtual void set_contributing(); virtual void kim_init(); @@ -191,7 +183,10 @@ The KIM model was unable, for some reason, to complete the computation. E: 'KIMvirial' or 'LAMMPSvirial' not supported with kim-api. -"KIMvirial or "LAMMPSvirial" found on the pair_style line. These keys are not supported kim-api. (The virial computation is always performed by LAMMPS.) Please remove these keys, make sure the KIM model you are using supports kim-api, and rerun. +"KIMvirial or "LAMMPSvirial" found on the pair_style line. These keys +are not supported kim-api. (The virial computation is always performed +by LAMMPS.) Please remove these keys, make sure the KIM model you are +using supports kim-api, and rerun. E: Illegal pair_style command -- GitLab From fc8a639d585c7325eb08e2044a274a3b514043d8 Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Fri, 24 May 2019 19:39:15 -0400 Subject: [PATCH 022/469] add documentation for kim_style command. update a few KIM related doc files --- doc/src/Commands_all.txt | 1 + doc/src/Packages_details.txt | 11 +++-- doc/src/commands_list.txt | 1 + doc/src/kim_query.txt | 3 +- doc/src/kim_style.txt | 81 ++++++++++++++++++++++++++++++++++++ doc/src/lammps.book | 1 + doc/src/pair_kim.txt | 3 +- src/KIM/README | 6 +-- 8 files changed, 99 insertions(+), 8 deletions(-) create mode 100644 doc/src/kim_style.txt diff --git a/doc/src/Commands_all.txt b/doc/src/Commands_all.txt index 52c2e67e2e..d76ffac14c 100644 --- a/doc/src/Commands_all.txt +++ b/doc/src/Commands_all.txt @@ -69,6 +69,7 @@ An alphabetic list of all general LAMMPS commands. "include"_include.html, "jump"_jump.html, "kim_query"_kim_query.html, +"kim_style"_kim_style.html, "kspace_modify"_kspace_modify.html, "kspace_style"_kspace_style.html, "label"_label.html, diff --git a/doc/src/Packages_details.txt b/doc/src/Packages_details.txt index 352a38af84..19c7e96fe9 100644 --- a/doc/src/Packages_details.txt +++ b/doc/src/Packages_details.txt @@ -342,7 +342,10 @@ A "pair_style kim"_pair_kim.html command which is a wrapper on the Knowledge Base for Interatomic Models (KIM) repository of interatomic potentials, enabling any of them to be used in LAMMPS simulations. Also a "kim_query"_kim_query.html command, which allows to query -the OpenKIM database for stored properties. +the OpenKIM database for stored properties, and a +"kim_style"_kim_style.html command, which serves as a front end to +generating LAMMPS input on-the-fly for KIM simulator models and native +KIM models. To use this package you must have the KIM library available on your system. @@ -352,8 +355,10 @@ https://openkim.org. The KIM project is led by Ellad Tadmor and Ryan Elliott (U Minnesota). [Authors:] Ryan Elliott (U Minnesota) is the main developer for the KIM -API which the "pair_style kim"_pair_kim.html command uses. He -developed the pair style. +API which the "pair_style kim"_pair_kim.html command uses. He developed +the pair style. Axel Kohlmeyer (Temple U) contributed the +"kim_query"_kim_query.html and "kim_style"_kim_style.html commands in +close collaboration with Ryan. [Install:] diff --git a/doc/src/commands_list.txt b/doc/src/commands_list.txt index cf716df9ac..39d2f7c7d0 100644 --- a/doc/src/commands_list.txt +++ b/doc/src/commands_list.txt @@ -54,6 +54,7 @@ Commands :h1 info jump kim_query + kim_style kspace_modify kspace_style label diff --git a/doc/src/kim_query.txt b/doc/src/kim_query.txt index c581de0ebb..84eca6e676 100644 --- a/doc/src/kim_query.txt +++ b/doc/src/kim_query.txt @@ -43,4 +43,5 @@ See the "Build package"_Build_package.html doc page for more info. [Related commands:] -"pair_style kim"_pair_kim.html, "variable"_variable.html +"pair_style kim"_pair_kim.html, "kim_style"_kim_style.html, +"variable"_variable.html diff --git a/doc/src/kim_style.txt b/doc/src/kim_style.txt new file mode 100644 index 0000000000..ab605c017a --- /dev/null +++ b/doc/src/kim_style.txt @@ -0,0 +1,81 @@ +"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c + +:link(lws,http://lammps.sandia.gov) +:link(ld,Manual.html) +:link(lc,Commands_all.html) + +:line + +kim_style command :h3 + +[Syntax:] + +kim_style mode model args :pre + +mode = {init} or {define} +model = name of the KIM model (potential or simulator model) or NULL +args = atom type to species mapping ({define} option only, one entry per atom type) :ul + +[Examples:] + +kim_style init ex_sim_model_Si_mod_tersoff +kim_style define NULL Si Si +kim_style define LennardJones_Ar Ar :pre + +[Description:] + +The kim_style command is a high-level wrapper around the +"Knowledge Base for Interatomic Models (OpenKIM)"_https://openkim.org +repository of interatomic potentials, so that they can be used by +LAMMPS scripts. It does not implement any computations directly, but +rather will generate LAMMPS input commands based on the information +retrieved from the OpenKIM repository. It is primarily meant to realize +so-called "KIM Simulator Models", which are OpenKIM repository entries +of models using native features of the simulation engine, i.e. LAMMPS +in this case, but it also supports realizing conventional KIM models +via the "pair_style kim"_pair_kim.html command. + +The kim_style command has two modes, {init} and {define}, indicated by +the first argument to the kim_style command. An {init} mode command +must be issued [before] the simulation box is created, while the {define} +mode version may only be used [after] the simulation box exists. The +{init} mode version is only required, if the KIM model requires it. +The second argument to the kim_style command is the KIM model ID. It +can be set to NULL in the kim_style define command, if it was already +set in a kim_style init command. Otherwise, the two model IDs must match. + +Only the kim_style define command allows additional arguments. Those +are used to map the atom types in LAMMPS to the available species in +the KIM model. This is equivalent to the arguments following +"pair_coeff * *" in a "kim"_pair_kim.html pair style. Thus the command + +kim_style define LennardJones_Ar Ar :pre + +will generate the LAMMPS input commands: + +pair_style kim LennardJones_Ar +pair_coeff * * Ar :pre + +For simulator models, the generated input commands may be more complex +and require that LAMMPS is built with the required packages included. +The commands generated by the kim_style command, can be copied to the +screen or log file, through the "echo"_echo.html command. +The kim_style command will also validate, that the selected simulator +model was generated for the LAMMPS MD code and not some other software. +In addition, the version strings for LAMMPS version used for defining +the simulator model and the LAMMPS version being currently run are +printed, so that it can be tracked down, if there are any incompatible +changes to input script or command syntax between the two LAMMPS versions. + +[Restrictions:] + +This command is part of the KIM package. It is only enabled if +LAMMPS was built with that package. Furthermore, its correct +functioning depends on compiling LAMMPS with all required packages +installed that are required by the commands embedded in any KIM +simulator models used. +See the "Build package"_Build_package.html doc page for more info. + +[Related commands:] + +"pair_style kim"_pair_kim.html, "kim_query"_kim_query.html diff --git a/doc/src/lammps.book b/doc/src/lammps.book index 500690597d..cedb6ea709 100644 --- a/doc/src/lammps.book +++ b/doc/src/lammps.book @@ -168,6 +168,7 @@ include.html info.html jump.html kim_query.html +kim_style.html label.html lattice.html log.html diff --git a/doc/src/pair_kim.txt b/doc/src/pair_kim.txt index a415ac606b..523bd89d7c 100644 --- a/doc/src/pair_kim.txt +++ b/doc/src/pair_kim.txt @@ -112,6 +112,7 @@ kim-api package version 2.0.0 and higher. [Related commands:] -"pair_coeff"_pair_coeff.html +"pair_coeff"_pair_coeff.html, "kim_style"_kim_style.html, +"kim_query"_kim_query.html [Default:] none diff --git a/src/KIM/README b/src/KIM/README index a69206596f..4f52d69a67 100644 --- a/src/KIM/README +++ b/src/KIM/README @@ -13,8 +13,8 @@ Using this package requires the KIM library and its models system. The library can be downloaded and built in lib/kim or elsewhere on your system, which must be done before bulding LAMMPS with this package. Details of the download, build, and install -process for KIM are given in the lib/kim/README file, and scripts will -soon be provided to help automate the process. Also see the LAMMPS +process for KIM are given in the lib/kim/README file, and scripts +are provided to help automate the process. Also see the LAMMPS manual for general information on building LAMMPS with external libraries. The settings in the Makefile.lammps file in lib/kim must be correct for LAMMPS to build correctly with this package installed. @@ -24,6 +24,6 @@ Makefile.lammps file usually will not need to be changed. Once you have successfully built LAMMPS with this package and the KIM library you can test it using an input file from the examples dir: -./lmp_serial < lammps/examples/kim/in.kim.lj +./lmp_serial -in lammps/examples/kim/in.kim.lj This pair_style was written by Ryan S. Elliott (U Minn). -- GitLab From ee5fa04732588646047111488bd5f4fec2870772 Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Fri, 24 May 2019 22:41:28 -0400 Subject: [PATCH 023/469] create internal fix via modify->add_fix() so it does not get logged --- src/KIM/kim_style.cpp | 6 +++++- 1 file changed, 5 insertions(+), 1 deletion(-) diff --git a/src/KIM/kim_style.cpp b/src/KIM/kim_style.cpp index 865f6827ab..53bf2958b3 100644 --- a/src/KIM/kim_style.cpp +++ b/src/KIM/kim_style.cpp @@ -104,7 +104,11 @@ void KimStyle::do_init(char *model) int ifix = modify->find_fix("KIM_MODEL_STORE"); if (ifix >= 0) modify->delete_fix(ifix); - input->one("fix KIM_MODEL_STORE all STORE/KIM"); + char *fixarg[3]; + fixarg[0] = (char *)"KIM_MODEL_STORE"; + fixarg[1] = (char *)"all"; + fixarg[2] = (char *)"STORE/KIM"; + modify->add_fix(3,fixarg); ifix = modify->find_fix("KIM_MODEL_STORE"); FixStoreKIM *fix_store = (FixStoreKIM *) modify->fix[ifix]; -- GitLab From 5a929aff6ed77043341a396ecf30b25d14add523 Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Fri, 24 May 2019 22:42:40 -0400 Subject: [PATCH 024/469] error out if kim_style init is required but wasn't called --- src/KIM/kim_style.cpp | 14 ++++++++++++-- 1 file changed, 12 insertions(+), 2 deletions(-) diff --git a/src/KIM/kim_style.cpp b/src/KIM/kim_style.cpp index 53bf2958b3..d906d56041 100644 --- a/src/KIM/kim_style.cpp +++ b/src/KIM/kim_style.cpp @@ -240,17 +240,27 @@ void KimStyle::do_defn(int narg, char **arg) } } delete[] strbuf; - + + // check if units are unchanged, and if kim_style init was required + int sim_fields, sim_lines; const std::string *sim_field, *sim_value; simulatorModel->GetNumberOfSimulatorFields(&sim_fields); for (int i=0; i < sim_fields; ++i) { simulatorModel->GetSimulatorFieldMetadata(i,&sim_lines,&sim_field); + if (*sim_field == "units") { simulatorModel->GetSimulatorFieldLine(i,0,&sim_value); if (*sim_value != update->unit_style) error->all(FLERR,"Incompatible units for KIM Simulator Model"); - break; + } + + if ((ifix < 0) && ( *sim_field == "model-init")) { + for (int j=0; j < sim_lines; ++j) { + simulatorModel->GetSimulatorFieldLine(i,j,&sim_value); + if (*sim_value != "") + error->all(FLERR,"Must use 'kim_style init' with this model"); + } } } -- GitLab From c3897212e2fe7531c6cd37d0165b2c7a419f54da Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Fri, 24 May 2019 22:44:03 -0400 Subject: [PATCH 025/469] must call ClearTemplateMap(), so kim_style define may be called multiple times --- src/KIM/kim_style.cpp | 1 + 1 file changed, 1 insertion(+) diff --git a/src/KIM/kim_style.cpp b/src/KIM/kim_style.cpp index d906d56041..323832fbad 100644 --- a/src/KIM/kim_style.cpp +++ b/src/KIM/kim_style.cpp @@ -279,6 +279,7 @@ void KimStyle::do_defn(int narg, char **arg) if (sim_model_idx < 0) error->all(FLERR,"KIM Simulator Model has no Model definition"); + simulatorModel->ClearTemplateMap(); } else { // not a simulator model. issue pair_style and pair_coeff commands. -- GitLab From 264f6e1630e3d4730953c9ca4b169a5631de3d34 Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Fri, 24 May 2019 22:44:41 -0400 Subject: [PATCH 026/469] whitespace cleanup --- src/KIM/kim_style.cpp | 9 +++++++-- 1 file changed, 7 insertions(+), 2 deletions(-) diff --git a/src/KIM/kim_style.cpp b/src/KIM/kim_style.cpp index 323832fbad..e8aee77b66 100644 --- a/src/KIM/kim_style.cpp +++ b/src/KIM/kim_style.cpp @@ -113,17 +113,19 @@ void KimStyle::do_init(char *model) FixStoreKIM *fix_store = (FixStoreKIM *) modify->fix[ifix]; fix_store->setptr("model_name", (void *) model); - + int kimerror; KIM::SimulatorModel * simulatorModel; kimerror = KIM::SimulatorModel::Create(model,&simulatorModel); // not a Kim Simulator Model; nothing else to do here. + if (kimerror) return; fix_store->setptr("simulator_model", (void *) simulatorModel); // need to call this to have access to (some) simulator model init data. + simulatorModel->CloseTemplateMap(); int sim_fields, sim_lines; @@ -131,6 +133,7 @@ void KimStyle::do_init(char *model) simulatorModel->GetNumberOfSimulatorFields(&sim_fields); // set units + for (int i=0; i < sim_fields; ++i) { simulatorModel->GetSimulatorFieldMetadata(i,&sim_lines,&sim_field); if (*sim_field == "units") { @@ -143,6 +146,7 @@ void KimStyle::do_init(char *model) } // init model + for (int i=0; i < sim_fields; ++i) { simulatorModel->GetSimulatorFieldMetadata(i,&sim_lines,&sim_field); if (*sim_field == "model-init") { @@ -155,6 +159,7 @@ void KimStyle::do_init(char *model) } // reset template map. + simulatorModel->ClearTemplateMap(); } @@ -281,7 +286,7 @@ void KimStyle::do_defn(int narg, char **arg) simulatorModel->ClearTemplateMap(); } else { - + // not a simulator model. issue pair_style and pair_coeff commands. // NOTE: all references to arg must appear before calls to input->one() // as that will reset the argument vector. -- GitLab From 4619018eadc0f9e23bc347d5df53b745a15b60d0 Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Mon, 27 May 2019 23:26:26 -0400 Subject: [PATCH 027/469] provide more simulator model variant input examples --- examples/kim/data.VOH | 118 ++++++++++++++++++ examples/kim/in.kim.VOH.simulator.model | 24 ++++ examples/kim/in.kim.ex_si_1.simulator_model | 69 ++++++++++ examples/kim/in.kim.ex_si_2.simulator_model | 69 ++++++++++ ...ulator-model => in.kim.lj.simulator-model} | 7 +- 5 files changed, 284 insertions(+), 3 deletions(-) create mode 100644 examples/kim/data.VOH create mode 100644 examples/kim/in.kim.VOH.simulator.model create mode 100644 examples/kim/in.kim.ex_si_1.simulator_model create mode 100644 examples/kim/in.kim.ex_si_2.simulator_model rename examples/kim/{in.kim.simulator-model => in.kim.lj.simulator-model} (88%) diff --git a/examples/kim/data.VOH b/examples/kim/data.VOH new file mode 100644 index 0000000000..c093705adc --- /dev/null +++ b/examples/kim/data.VOH @@ -0,0 +1,118 @@ +# VOH example + +100 atoms +4 atom types + +0 25.000 xlo xhi +0 25.000 ylo yhi +0 25.000 zlo zhi + +Masses + +1 1.0080 +2 12.0107 +3 15.9994 +4 50.9415 + +Atoms + + 1 2 0.0 12.35333 12.56112 11.08925 + 2 4 0.0 12.32916 12.62071 13.13099 + 3 3 0.0 14.09425 12.56218 13.76130 + 4 3 0.0 11.42814 11.10330 13.76732 + 5 3 0.0 11.63260 13.89286 13.64097 + 6 1 0.0 10.61647 11.29221 14.30535 + 7 1 0.0 14.38026 13.34626 14.29055 + 8 1 0.0 11.32479 12.58820 10.70253 + 9 1 0.0 12.90918 13.42567 10.69612 + 10 1 0.0 12.84043 11.63643 10.74688 + 11 2 0.0 0.93670 23.74637 24.45218 + 12 4 0.0 2.18151 24.36876 0.94725 + 13 3 0.0 3.93452 24.44779 0.28384 + 14 3 0.0 2.13668 23.10529 2.33362 + 15 3 0.0 1.76108 0.74666 1.48323 + 16 1 0.0 1.82070 23.45305 3.20745 + 17 1 0.0 4.35555 0.34186 0.31083 + 18 1 0.0 24.90472 23.68735 24.82586 + 19 1 0.0 0.97611 24.45631 23.61244 + 20 1 0.0 1.24583 22.75250 24.09589 + 21 2 0.0 2.25730 12.18969 18.74792 + 22 4 0.0 0.67140 13.31162 19.37385 + 23 3 0.0 0.71106 13.43250 21.24545 + 24 3 0.0 24.08603 12.44025 18.87949 + 25 3 0.0 0.70486 14.71920 18.75808 + 26 1 0.0 23.49516 12.95430 18.26686 + 27 1 0.0 0.79723 14.34808 21.60818 + 28 1 0.0 2.24383 12.10285 17.65239 + 29 1 0.0 3.19860 12.66607 19.06030 + 30 1 0.0 2.20214 11.18299 19.18774 + 31 2 0.0 9.32237 8.16220 23.74501 + 32 4 0.0 9.41775 7.26178 21.91463 + 33 3 0.0 8.54752 8.34565 20.65588 + 34 3 0.0 8.50942 5.62151 22.00137 + 35 3 0.0 10.87539 7.02683 21.48455 + 36 1 0.0 9.06507 4.82324 21.80615 + 37 1 0.0 9.11458 8.67119 19.91477 + 38 1 0.0 9.82196 7.53487 24.49616 + 39 1 0.0 9.81855 9.14254 23.70532 + 40 1 0.0 8.27176 8.30387 24.03831 + 41 2 0.0 9.10113 13.98748 23.44281 + 42 4 0.0 8.84954 12.89163 21.73780 + 43 3 0.0 10.01387 13.54293 20.42005 + 44 3 0.0 7.08992 13.11522 21.12954 + 45 3 0.0 9.12937 11.39982 21.99065 + 46 1 0.0 6.55309 12.28287 21.08224 + 47 1 0.0 10.67858 12.89258 20.08249 + 48 1 0.0 8.42108 13.62252 24.22498 + 49 1 0.0 10.13926 13.89766 23.79639 + 50 1 0.0 8.88118 15.04646 23.24289 + 51 2 0.0 17.73225 3.40708 8.28945 + 52 4 0.0 18.49877 5.29835 8.37599 + 53 3 0.0 19.48472 5.62627 6.81505 + 54 3 0.0 19.66498 5.40961 9.84118 + 55 3 0.0 17.38120 6.34466 8.51889 + 56 1 0.0 19.41208 6.07779 10.52927 + 57 1 0.0 19.15960 6.37609 6.25924 + 58 1 0.0 17.15579 3.19557 9.20103 + 59 1 0.0 17.07197 3.31049 7.41454 + 60 1 0.0 18.54903 2.67524 8.20436 + 61 2 0.0 5.18346 20.97409 24.28840 + 62 4 0.0 7.06396 20.17968 24.34847 + 63 3 0.0 7.63220 19.82889 22.59578 + 64 3 0.0 7.00272 18.55243 0.28036 + 65 3 0.0 8.05085 21.13715 0.03620 + 66 1 0.0 7.56109 18.51690 1.09952 + 67 1 0.0 8.44257 20.31624 22.30833 + 68 1 0.0 4.83239 21.17976 0.30904 + 69 1 0.0 5.19182 21.91237 23.71419 + 70 1 0.0 4.49282 20.26573 23.80772 + 71 2 0.0 21.82701 12.79861 20.63056 + 72 4 0.0 21.27646 11.09990 19.63611 + 73 3 0.0 19.52930 10.64327 20.13923 + 74 3 0.0 22.41924 9.70346 20.14638 + 75 3 0.0 21.34556 11.30206 18.11274 + 76 1 0.0 22.94464 9.30084 19.40876 + 77 1 0.0 18.86743 10.62817 19.40629 + 78 1 0.0 22.85378 13.07853 20.35349 + 79 1 0.0 21.14666 13.62206 20.37063 + 80 1 0.0 21.78702 12.62668 21.71522 + 81 2 0.0 4.84801 10.63893 5.85720 + 82 4 0.0 2.99668 11.06158 5.10490 + 83 3 0.0 3.09505 11.09458 3.23258 + 84 3 0.0 2.48053 12.76555 5.69567 + 85 3 0.0 1.96195 10.01780 5.55634 + 86 1 0.0 1.65323 12.78746 6.24245 + 87 1 0.0 2.52753 10.43264 2.76734 + 88 1 0.0 4.80984 10.62196 6.95551 + 89 1 0.0 5.18492 9.65688 5.49273 + 90 1 0.0 5.56737 11.40648 5.53568 + 91 2 0.0 13.58126 9.47098 19.40329 + 92 4 0.0 14.17691 10.17243 21.22692 + 93 3 0.0 14.44428 12.02521 21.10583 + 94 3 0.0 15.81206 9.37183 21.67632 + 95 3 0.0 13.12907 9.86545 22.30960 + 96 1 0.0 15.80034 8.83149 22.50703 + 97 1 0.0 13.87232 12.57457 21.69672 + 98 1 0.0 13.42563 8.38456 19.45392 + 99 1 0.0 12.63978 9.95672 19.10431 + 100 1 0.0 14.35123 9.68789 18.64825 diff --git a/examples/kim/in.kim.VOH.simulator.model b/examples/kim/in.kim.VOH.simulator.model new file mode 100644 index 0000000000..3803ceceba --- /dev/null +++ b/examples/kim/in.kim.VOH.simulator.model @@ -0,0 +1,24 @@ +# REAX potential for VOH system +# ..... + +units real +atom_style charge + +kim_style init Sim_LAMMPS_ReaxFF_ChenowethVanDuinPersson_2008_CHOV__SM_429148913211_000 + +read_data data.VOH + +kim_style define NULL H C O V + +neighbor 2 bin +neigh_modify every 10 delay 0 check no + +fix 1 all nve +fix 2 all qeq/reax 1 0.0 10.0 1e-6 param.qeq +fix 3 all temp/berendsen 500.0 500.0 100.0 + +timestep 0.25 + +#dump 1 all atom 30 dump.reax.voh + +run 300 diff --git a/examples/kim/in.kim.ex_si_1.simulator_model b/examples/kim/in.kim.ex_si_1.simulator_model new file mode 100644 index 0000000000..03f9c25a33 --- /dev/null +++ b/examples/kim/in.kim.ex_si_1.simulator_model @@ -0,0 +1,69 @@ + +units metal +kim_style init ex_sim_model_Si_mod_tersoff + +atom_style atomic +atom_modify map array +boundary p p p + +# temperatures +variable tlo equal 1800.0 +variable thi equal 2400.0 + +# coordination number cutoff + +variable r equal 2.835 + +# minimization parameters + +variable etol equal 1.0e-5 +variable ftol equal 1.0e-5 +variable maxiter equal 100 +variable maxeval equal 100 +variable dmax equal 1.0e-1 + +# diamond unit cell + +variable a equal 5.431 +lattice custom $a & + a1 1.0 0.0 0.0 & + a2 0.0 1.0 0.0 & + a3 0.0 0.0 1.0 & + basis 0.0 0.0 0.0 & + basis 0.0 0.5 0.5 & + basis 0.5 0.0 0.5 & + basis 0.5 0.5 0.0 & + basis 0.25 0.25 0.25 & + basis 0.25 0.75 0.75 & + basis 0.75 0.25 0.75 & + basis 0.75 0.75 0.25 + +region myreg block 0 4 & + 0 4 & + 0 4 +create_box 1 myreg +create_atoms 1 region myreg + +mass 1 28.06 + +group Si type 1 + +velocity all create ${thi} 5287286 mom yes rot yes dist gaussian + +# make a vacancy + +group del id 300 +delete_atoms group del +kim_style define ex_sim_model_Si_mod_tersoff Si + +thermo 10 + +fix 1 all nve +fix 2 all langevin ${thi} ${thi} 0.1 48278 + +timestep 1.0e-3 +neighbor 1.0 bin +neigh_modify every 1 delay 10 check yes + +run 100 + diff --git a/examples/kim/in.kim.ex_si_2.simulator_model b/examples/kim/in.kim.ex_si_2.simulator_model new file mode 100644 index 0000000000..18efd94222 --- /dev/null +++ b/examples/kim/in.kim.ex_si_2.simulator_model @@ -0,0 +1,69 @@ + +units metal +kim_style init ex_sim_model_Si_mod_tersoff + +atom_style atomic +atom_modify map array +boundary p p p + +# temperatures +variable tlo equal 1800.0 +variable thi equal 2400.0 + +# coordination number cutoff + +variable r equal 2.835 + +# minimization parameters + +variable etol equal 1.0e-5 +variable ftol equal 1.0e-5 +variable maxiter equal 100 +variable maxeval equal 100 +variable dmax equal 1.0e-1 + +# diamond unit cell + +variable a equal 5.431 +lattice custom $a & + a1 1.0 0.0 0.0 & + a2 0.0 1.0 0.0 & + a3 0.0 0.0 1.0 & + basis 0.0 0.0 0.0 & + basis 0.0 0.5 0.5 & + basis 0.5 0.0 0.5 & + basis 0.5 0.5 0.0 & + basis 0.25 0.25 0.25 & + basis 0.25 0.75 0.75 & + basis 0.75 0.25 0.75 & + basis 0.75 0.75 0.25 + +region myreg block 0 4 & + 0 4 & + 0 4 +create_box 1 myreg +create_atoms 1 region myreg + +mass 1 28.06 + +group Si type 1 + +velocity all create ${thi} 5287286 mom yes rot yes dist gaussian + +# make a vacancy + +group del id 300 +delete_atoms group del +kim_style define NULL Si + +thermo 10 + +fix 1 all nve +fix 2 all langevin ${thi} ${thi} 0.1 48278 + +timestep 1.0e-3 +neighbor 1.0 bin +neigh_modify every 1 delay 10 check yes + +run 100 + diff --git a/examples/kim/in.kim.simulator-model b/examples/kim/in.kim.lj.simulator-model similarity index 88% rename from examples/kim/in.kim.simulator-model rename to examples/kim/in.kim.lj.simulator-model index 1e6e9dec89..21d60a48d9 100644 --- a/examples/kim/in.kim.simulator-model +++ b/examples/kim/in.kim.lj.simulator-model @@ -16,18 +16,19 @@ variable zz equal 20*$z units metal atom_style atomic +newton on lattice fcc 4.4300 region box block 0 ${xx} 0 ${yy} 0 ${zz} -create_box 2 box +create_box 1 box create_atoms 1 box #pair_style lj/cut 8.1500 #pair_coeff 1 1 0.0104 3.4000 -kim_style define ex_sim_model_Si_mod_tersoff Si Si +kim_style define LennardJones_Ar Ar -mass * 39.95 +mass 1 39.95 velocity all create 200.0 232345 loop geom neighbor 0.3 bin -- GitLab From eb6287d2e8877c3b56af90b89a692c64d9a00036 Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Mon, 27 May 2019 23:26:46 -0400 Subject: [PATCH 028/469] correctly check for supported species --- src/KIM/kim_style.cpp | 25 +++++++++++++++++-------- 1 file changed, 17 insertions(+), 8 deletions(-) diff --git a/src/KIM/kim_style.cpp b/src/KIM/kim_style.cpp index e8aee77b66..eac16f1a8a 100644 --- a/src/KIM/kim_style.cpp +++ b/src/KIM/kim_style.cpp @@ -232,17 +232,26 @@ void KimStyle::do_defn(int narg, char **arg) // validate species selection int sim_num_species; + bool species_is_supported; const std::string *sim_species; simulatorModel->GetNumberOfSupportedSpecies(&sim_num_species); - for (int i=0; i < sim_num_species; ++i) { - simulatorModel->GetSupportedSpecies(i, &sim_species); - strcpy(strbuf,atom_type_sym_list.c_str()); - strword = strtok(strbuf," \t"); - while (strword) { - if ((strcmp(strword,"NULL") != 0) && (strcmp(sim_species->c_str(),strword) != 0)) - error->all(FLERR,"Species not supported by KIM Simulator Model"); - strword = strtok(NULL," \t"); + strcpy(strbuf,atom_type_sym_list.c_str()); + strword = strtok(strbuf," \t"); + while (strword) { + species_is_supported = false; + if (strcmp(strword,"NULL") == 0) continue; + for (int i=0; i < sim_num_species; ++i) { + simulatorModel->GetSupportedSpecies(i, &sim_species); + if (strcmp(sim_species->c_str(),strword) == 0) + species_is_supported = true; } + if (!species_is_supported) { + std::string msg("Species '"); + msg += strword; + msg += "' is not supported by this KIM Simulator Model"; + error->all(FLERR,msg.c_str()); + } + strword = strtok(NULL," \t"); } delete[] strbuf; -- GitLab From b3a01694b7312989554f24817bd94e8ccca2a83d Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Mon, 27 May 2019 23:34:05 -0400 Subject: [PATCH 029/469] remove leftover fix qeq/reax command --- examples/kim/in.kim.VOH.simulator.model | 1 - 1 file changed, 1 deletion(-) diff --git a/examples/kim/in.kim.VOH.simulator.model b/examples/kim/in.kim.VOH.simulator.model index 3803ceceba..a2dd6983c0 100644 --- a/examples/kim/in.kim.VOH.simulator.model +++ b/examples/kim/in.kim.VOH.simulator.model @@ -14,7 +14,6 @@ neighbor 2 bin neigh_modify every 10 delay 0 check no fix 1 all nve -fix 2 all qeq/reax 1 0.0 10.0 1e-6 param.qeq fix 3 all temp/berendsen 500.0 500.0 100.0 timestep 0.25 -- GitLab From 113b8b4be23bdbcfde5031144110a26d178f29a0 Mon Sep 17 00:00:00 2001 From: "Dan S. Bolintineanu" Date: Thu, 30 May 2019 14:21:11 -0600 Subject: [PATCH 030/469] Fixes two bugs in pair granular: 1. User-set cutoffs did not work 2. Restarts not working --- src/GRANULAR/pair_granular.cpp | 7 ++++--- 1 file changed, 4 insertions(+), 3 deletions(-) diff --git a/src/GRANULAR/pair_granular.cpp b/src/GRANULAR/pair_granular.cpp index 903ed303b0..913f6f8b59 100644 --- a/src/GRANULAR/pair_granular.cpp +++ b/src/GRANULAR/pair_granular.cpp @@ -890,6 +890,7 @@ void PairGranular::coeff(int narg, char **arg) if (iarg + 1 >= narg) error->all(FLERR, "Illegal pair_coeff command, not enough parameters"); cutoff_one = force->numeric(FLERR,arg[iarg+1]); + iarg += 2; } else error->all(FLERR, "Illegal pair coeff command"); } @@ -1234,7 +1235,7 @@ void PairGranular::write_restart(FILE *fp) fwrite(&tangential_coeffs[i][j],sizeof(double),3,fp); fwrite(&roll_coeffs[i][j],sizeof(double),3,fp); fwrite(&twist_coeffs[i][j],sizeof(double),3,fp); - fwrite(&cut[i][j],sizeof(double),1,fp); + fwrite(&cutoff_type[i][j],sizeof(double),1,fp); } } } @@ -1264,7 +1265,7 @@ void PairGranular::read_restart(FILE *fp) fread(&tangential_coeffs[i][j],sizeof(double),3,fp); fread(&roll_coeffs[i][j],sizeof(double),3,fp); fread(&twist_coeffs[i][j],sizeof(double),3,fp); - fread(&cut[i][j],sizeof(double),1,fp); + fread(&cutoff_type[i][j],sizeof(double),1,fp); } MPI_Bcast(&normal_model[i][j],1,MPI_INT,0,world); MPI_Bcast(&damping_model[i][j],1,MPI_INT,0,world); @@ -1275,7 +1276,7 @@ void PairGranular::read_restart(FILE *fp) MPI_Bcast(&tangential_coeffs[i][j],3,MPI_DOUBLE,0,world); MPI_Bcast(&roll_coeffs[i][j],3,MPI_DOUBLE,0,world); MPI_Bcast(&twist_coeffs[i][j],3,MPI_DOUBLE,0,world); - MPI_Bcast(&cut[i][j],1,MPI_DOUBLE,0,world); + MPI_Bcast(&cutoff_type[i][j],1,MPI_DOUBLE,0,world); } } } -- GitLab From 24a63f0f31446f5a98a32325248cced2d1c6d21a Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Thu, 30 May 2019 21:51:13 -0400 Subject: [PATCH 031/469] update kim_style command semantics as discussed in PR #1440 this also adds documentation of error messages in the kim_style header --- doc/src/kim_style.txt | 54 ++++++++------- ...lator.model => in.kim.VOH.simulator_model} | 2 +- ...tor_model => in.kim.ex_si.simulator_model} | 2 +- examples/kim/in.kim.ex_si_1.simulator_model | 69 ------------------- ...ulator-model => in.kim.lj.simulator_model} | 4 +- src/KIM/kim_style.cpp | 33 +++------ src/KIM/kim_style.h | 36 ++++++++++ 7 files changed, 81 insertions(+), 119 deletions(-) rename examples/kim/{in.kim.VOH.simulator.model => in.kim.VOH.simulator_model} (92%) rename examples/kim/{in.kim.ex_si_2.simulator_model => in.kim.ex_si.simulator_model} (98%) delete mode 100644 examples/kim/in.kim.ex_si_1.simulator_model rename examples/kim/{in.kim.lj.simulator-model => in.kim.lj.simulator_model} (92%) diff --git a/doc/src/kim_style.txt b/doc/src/kim_style.txt index ab605c017a..dcdfae1cdc 100644 --- a/doc/src/kim_style.txt +++ b/doc/src/kim_style.txt @@ -10,17 +10,18 @@ kim_style command :h3 [Syntax:] -kim_style mode model args :pre +kim_style mode args :pre -mode = {init} or {define} -model = name of the KIM model (potential or simulator model) or NULL -args = atom type to species mapping ({define} option only, one entry per atom type) :ul +mode = {init model} or {define typeargs} +model = name of the KIM model (KIM potential or KIM simulator model) +typeargs = atom type to species mapping (one entry per atom type) :ul [Examples:] kim_style init ex_sim_model_Si_mod_tersoff -kim_style define NULL Si Si -kim_style define LennardJones_Ar Ar :pre +kim_style define Si Si +kim_style init LennardJones_Ar +kim_style define Ar :pre [Description:] @@ -29,27 +30,34 @@ The kim_style command is a high-level wrapper around the repository of interatomic potentials, so that they can be used by LAMMPS scripts. It does not implement any computations directly, but rather will generate LAMMPS input commands based on the information -retrieved from the OpenKIM repository. It is primarily meant to realize -so-called "KIM Simulator Models", which are OpenKIM repository entries -of models using native features of the simulation engine, i.e. LAMMPS +retrieved from the OpenKIM repository. It is able to realize so-called +"KIM Simulator Models", which are OpenKIM repository entries of models +using native features of the simulation engine in use, i.e. LAMMPS in this case, but it also supports realizing conventional KIM models -via the "pair_style kim"_pair_kim.html command. +implicitly via generating a "pair_style kim"_pair_kim.html command +followed by a suitable "pair_coeff"_pair_coeff.html command. The kim_style command has two modes, {init} and {define}, indicated by the first argument to the kim_style command. An {init} mode command must be issued [before] the simulation box is created, while the {define} -mode version may only be used [after] the simulation box exists. The -{init} mode version is only required, if the KIM model requires it. -The second argument to the kim_style command is the KIM model ID. It -can be set to NULL in the kim_style define command, if it was already -set in a kim_style init command. Otherwise, the two model IDs must match. - -Only the kim_style define command allows additional arguments. Those -are used to map the atom types in LAMMPS to the available species in -the KIM model. This is equivalent to the arguments following -"pair_coeff * *" in a "kim"_pair_kim.html pair style. Thus the command - -kim_style define LennardJones_Ar Ar :pre +mode version may only be used [after] the simulation box exists. Both +are required. The {init} mode version sets the model name and may issue +additional commands changing LAMMPS default settings that are required +for using a selected simulator model. If needed, those settings can be +overridden. The second argument to the {kim_style init} command is the +KIM model ID. + +The {kim_style define} command will issue commands that will realize +the selected model (through generating pair_style and pair_coeff commands, +but also other commands, as required). It has to be issued [after] the +the simulation box is defined. The {kim_style define} command allows a +varying numbver of additional arguments. Those are used to map the atom +types in LAMMPS to the available species in the KIM model. This is +equivalent to the arguments following "pair_coeff * *" in a +"kim"_pair_kim.html pair style. Thus the commands: + +kim_style init LennardJones_Ar +kim_style define Ar :pre will generate the LAMMPS input commands: @@ -60,7 +68,7 @@ For simulator models, the generated input commands may be more complex and require that LAMMPS is built with the required packages included. The commands generated by the kim_style command, can be copied to the screen or log file, through the "echo"_echo.html command. -The kim_style command will also validate, that the selected simulator +The kim_style command will also validate, that a selected simulator model was generated for the LAMMPS MD code and not some other software. In addition, the version strings for LAMMPS version used for defining the simulator model and the LAMMPS version being currently run are diff --git a/examples/kim/in.kim.VOH.simulator.model b/examples/kim/in.kim.VOH.simulator_model similarity index 92% rename from examples/kim/in.kim.VOH.simulator.model rename to examples/kim/in.kim.VOH.simulator_model index a2dd6983c0..8696cf265a 100644 --- a/examples/kim/in.kim.VOH.simulator.model +++ b/examples/kim/in.kim.VOH.simulator_model @@ -8,7 +8,7 @@ kim_style init Sim_LAMMPS_ReaxFF_ChenowethVanDuinPersson_2008_CHOV__SM_429148913 read_data data.VOH -kim_style define NULL H C O V +kim_style define H C O V neighbor 2 bin neigh_modify every 10 delay 0 check no diff --git a/examples/kim/in.kim.ex_si_2.simulator_model b/examples/kim/in.kim.ex_si.simulator_model similarity index 98% rename from examples/kim/in.kim.ex_si_2.simulator_model rename to examples/kim/in.kim.ex_si.simulator_model index 18efd94222..2f9e79ef4e 100644 --- a/examples/kim/in.kim.ex_si_2.simulator_model +++ b/examples/kim/in.kim.ex_si.simulator_model @@ -54,7 +54,7 @@ velocity all create ${thi} 5287286 mom yes rot yes dist gaussian group del id 300 delete_atoms group del -kim_style define NULL Si +kim_style define Si thermo 10 diff --git a/examples/kim/in.kim.ex_si_1.simulator_model b/examples/kim/in.kim.ex_si_1.simulator_model deleted file mode 100644 index 03f9c25a33..0000000000 --- a/examples/kim/in.kim.ex_si_1.simulator_model +++ /dev/null @@ -1,69 +0,0 @@ - -units metal -kim_style init ex_sim_model_Si_mod_tersoff - -atom_style atomic -atom_modify map array -boundary p p p - -# temperatures -variable tlo equal 1800.0 -variable thi equal 2400.0 - -# coordination number cutoff - -variable r equal 2.835 - -# minimization parameters - -variable etol equal 1.0e-5 -variable ftol equal 1.0e-5 -variable maxiter equal 100 -variable maxeval equal 100 -variable dmax equal 1.0e-1 - -# diamond unit cell - -variable a equal 5.431 -lattice custom $a & - a1 1.0 0.0 0.0 & - a2 0.0 1.0 0.0 & - a3 0.0 0.0 1.0 & - basis 0.0 0.0 0.0 & - basis 0.0 0.5 0.5 & - basis 0.5 0.0 0.5 & - basis 0.5 0.5 0.0 & - basis 0.25 0.25 0.25 & - basis 0.25 0.75 0.75 & - basis 0.75 0.25 0.75 & - basis 0.75 0.75 0.25 - -region myreg block 0 4 & - 0 4 & - 0 4 -create_box 1 myreg -create_atoms 1 region myreg - -mass 1 28.06 - -group Si type 1 - -velocity all create ${thi} 5287286 mom yes rot yes dist gaussian - -# make a vacancy - -group del id 300 -delete_atoms group del -kim_style define ex_sim_model_Si_mod_tersoff Si - -thermo 10 - -fix 1 all nve -fix 2 all langevin ${thi} ${thi} 0.1 48278 - -timestep 1.0e-3 -neighbor 1.0 bin -neigh_modify every 1 delay 10 check yes - -run 100 - diff --git a/examples/kim/in.kim.lj.simulator-model b/examples/kim/in.kim.lj.simulator_model similarity index 92% rename from examples/kim/in.kim.lj.simulator-model rename to examples/kim/in.kim.lj.simulator_model index 21d60a48d9..15b26c3c64 100644 --- a/examples/kim/in.kim.lj.simulator-model +++ b/examples/kim/in.kim.lj.simulator_model @@ -18,6 +18,8 @@ units metal atom_style atomic newton on +kim_style init LennardJones_Ar + lattice fcc 4.4300 region box block 0 ${xx} 0 ${yy} 0 ${zz} create_box 1 box @@ -26,7 +28,7 @@ create_atoms 1 box #pair_style lj/cut 8.1500 #pair_coeff 1 1 0.0104 3.4000 -kim_style define LennardJones_Ar Ar +kim_style define Ar mass 1 39.95 velocity all create 200.0 232345 loop geom diff --git a/src/KIM/kim_style.cpp b/src/KIM/kim_style.cpp index eac16f1a8a..856fb94c9e 100644 --- a/src/KIM/kim_style.cpp +++ b/src/KIM/kim_style.cpp @@ -79,7 +79,7 @@ void KimStyle::command(int narg, char **arg) if (narg < 2) error->all(FLERR,"Illegal kim_style command"); if (strcmp(arg[0],"init") == 0) { - if (narg > 2) error->all(FLERR,"Illegal kim_style init command"); + if (narg > 2) error->all(FLERR,"Illegal kim_style command"); if (domain->box_exist) error->all(FLERR,"Must use 'kim_style init' command before " "simulation box is defined"); @@ -167,10 +167,10 @@ void KimStyle::do_init(char *model) void KimStyle::do_defn(int narg, char **arg) { - if (narg != atom->ntypes + 1) - error->all(FLERR,"Incorrect number of arguments for kim_style define command"); + if (narg != atom->ntypes) + error->all(FLERR,"Illegal kim_style command"); - char *model = arg[0]; + char *model = NULL; KIM::SimulatorModel *simulatorModel(NULL); int kimerror; @@ -182,17 +182,9 @@ void KimStyle::do_defn(int narg, char **arg) int ifix = modify->find_fix("KIM_MODEL_STORE"); if (ifix >= 0) { FixStoreKIM *fix_store = (FixStoreKIM *) modify->fix[ifix]; - if (strcmp(model,"NULL") == 0) - model = (char *)fix_store->getptr("model_name"); - else if (strcmp(model,(const char*)fix_store->getptr("model_name")) != 0) - error->all(FLERR,"Inconsistent KIM model name"); - + model = (char *)fix_store->getptr("model_name"); simulatorModel = (KIM::SimulatorModel *)fix_store->getptr("simulator_model"); - } else { - - kimerror = KIM::SimulatorModel::Create(model,&simulatorModel); - if (kimerror) simulatorModel = NULL; - } + } else error->all(FLERR,"Must use 'kim_style init' before 'kim_style define'"); if (simulatorModel) { @@ -219,7 +211,7 @@ void KimStyle::do_defn(int narg, char **arg) if (*sim_name != "LAMMPS") error->all(FLERR,"Incompatible KIM Simulator Model"); - for (int i = 1; i < narg; i++) + for (int i = 0; i < narg; i++) atom_type_sym_list += std::string(" ") + arg[i]; simulatorModel->AddTemplateMap("atom-type-sym-list",atom_type_sym_list); @@ -268,14 +260,6 @@ void KimStyle::do_defn(int narg, char **arg) if (*sim_value != update->unit_style) error->all(FLERR,"Incompatible units for KIM Simulator Model"); } - - if ((ifix < 0) && ( *sim_field == "model-init")) { - for (int j=0; j < sim_lines; ++j) { - simulatorModel->GetSimulatorFieldLine(i,j,&sim_value); - if (*sim_value != "") - error->all(FLERR,"Must use 'kim_style init' with this model"); - } - } } int sim_model_idx=-1; @@ -294,6 +278,7 @@ void KimStyle::do_defn(int narg, char **arg) error->all(FLERR,"KIM Simulator Model has no Model definition"); simulatorModel->ClearTemplateMap(); + } else { // not a simulator model. issue pair_style and pair_coeff commands. @@ -304,7 +289,7 @@ void KimStyle::do_defn(int narg, char **arg) cmd1 += model; std::string cmd2("pair_coeff * * "); - for (int i=1; i < narg; ++i) { + for (int i=0; i < narg; ++i) { cmd2 += arg[i]; cmd2 += " "; } diff --git a/src/KIM/kim_style.h b/src/KIM/kim_style.h index 588de6e620..eddc22eebc 100644 --- a/src/KIM/kim_style.h +++ b/src/KIM/kim_style.h @@ -83,5 +83,41 @@ class KimStyle : protected Pointers { /* ERROR/WARNING messages: +E: Illegal kim_style command + +Incorrect number or kind of arguments to kim_style + +E: Must use 'kim_style init' command before simulation box is defined + +Self-explanatory + +E: Must use 'kim_style define' command after simulation box is defined + +Self-explanatory + +E: Must use 'kim_style init' command before 'kim_style define' + +Self-explanatory + +E: Incompatible KIM Simulator Model + +The requested KIM Simulator Model was defined for a different MD code +and thus is not compatible with LAMMPS + +E: Species XXX is not supported by this KIM Simulator Model + +The kim_style define command was referencing a species that is not +present in the requested KIM Simulator Model + +E: Incompatible units for KIM Simulator Model + +The selected unit style is not compatible with the requested KIM +Simulator Model + +E: KIM Simulator Model has no Model definition + +There is no model definition (key: model-defn) in the KIM Simulator +Model. Please contact the OpenKIM database maintainers to verify +and potentially correct this. */ -- GitLab From c9fe5810c1c0029e42fa3ef1d1b4d6b0ea0f1c32 Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Thu, 30 May 2019 21:52:23 -0400 Subject: [PATCH 032/469] add log outputs for updated kim_style command input examples --- ...og.30Apr2019.kim.VOH.simulator_model.g++.1 | 92 ++++++++++++ ....30Apr2019.kim.ex_si.simulator_model.g++.1 | 132 ++++++++++++++++++ ....30Apr2019.kim.ex_si.simulator_model.g++.4 | 132 ++++++++++++++++++ ...log.30Apr2019.kim.lj.simulator_model.g++.1 | 104 ++++++++++++++ ...log.30Apr2019.kim.lj.simulator_model.g++.4 | 104 ++++++++++++++ 5 files changed, 564 insertions(+) create mode 100644 examples/kim/log.30Apr2019.kim.VOH.simulator_model.g++.1 create mode 100644 examples/kim/log.30Apr2019.kim.ex_si.simulator_model.g++.1 create mode 100644 examples/kim/log.30Apr2019.kim.ex_si.simulator_model.g++.4 create mode 100644 examples/kim/log.30Apr2019.kim.lj.simulator_model.g++.1 create mode 100644 examples/kim/log.30Apr2019.kim.lj.simulator_model.g++.4 diff --git a/examples/kim/log.30Apr2019.kim.VOH.simulator_model.g++.1 b/examples/kim/log.30Apr2019.kim.VOH.simulator_model.g++.1 new file mode 100644 index 0000000000..e9d1f17d76 --- /dev/null +++ b/examples/kim/log.30Apr2019.kim.VOH.simulator_model.g++.1 @@ -0,0 +1,92 @@ +LAMMPS (30 Apr 2019) + using 1 OpenMP thread(s) per MPI task +# REAX potential for VOH system +# ..... + +units real +atom_style charge + +kim_style init Sim_LAMMPS_ReaxFF_ChenowethVanDuinPersson_2008_CHOV__SM_429148913211_000 +units real +atom_style charge +neigh_modify one 4000 + +read_data data.VOH + orthogonal box = (0 0 0) to (25 25 25) + 1 by 1 by 1 MPI processor grid + reading atoms ... + 100 atoms + read_data CPU = 0.000217199 secs + +kim_style define H C O V +Using KIM Simulator Model : Sim_LAMMPS_ReaxFF_ChenowethVanDuinPersson_2008_CHOV__SM_429148913211_000 +For Simulator : LAMMPS 28-Feb-2019 +Running on : LAMMPS 30 Apr 2019 +pair_style reax/c /tmp/kim-simulator-model-parameter-file-XXXXXXFRmlac safezone 2.0 mincap 100 +pair_coeff * * /tmp/kim-simulator-model-parameter-file-XXXXXX363kge H C O V +Reading potential file /tmp/kim-simulator-model-parameter-file-XXXXXX363kge with DATE: 2011-02-18 +WARNING: Changed valency_val to valency_boc for X (src/USER-REAXC/reaxc_ffield.cpp:311) +fix reaxqeq all qeq/reax 1 0.0 10.0 1.0e-6 /tmp/kim-simulator-model-parameter-file-XXXXXXzgDl49 + +neighbor 2 bin +neigh_modify every 10 delay 0 check no + +fix 1 all nve +fix 3 all temp/berendsen 500.0 500.0 100.0 + +timestep 0.25 + +#dump 1 all atom 30 dump.reax.voh + +run 300 +Neighbor list info ... + update every 10 steps, delay 0 steps, check no + max neighbors/atom: 4000, page size: 100000 + master list distance cutoff = 12 + ghost atom cutoff = 12 + binsize = 6, bins = 5 5 5 + 2 neighbor lists, perpetual/occasional/extra = 2 0 0 + (1) pair reax/c, perpetual + attributes: half, newton off, ghost + pair build: half/bin/newtoff/ghost + stencil: half/ghost/bin/3d/newtoff + bin: standard + (2) fix qeq/reax, perpetual, copy from (1) + attributes: half, newton off, ghost + pair build: copy + stencil: none + bin: none +Per MPI rank memory allocation (min/avg/max) = 25.97 | 25.97 | 25.97 Mbytes +Step Temp E_pair E_mol TotEng Press + 0 0 -10246.825 0 -10246.825 42.256089 + 300 199.45773 -10218.342 0 -10159.482 -66.730725 +Loop time of 1.06721 on 1 procs for 300 steps with 100 atoms + +Performance: 6.072 ns/day, 3.953 hours/ns, 281.107 timesteps/s +98.8% CPU use with 1 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0.93954 | 0.93954 | 0.93954 | 0.0 | 88.04 +Neigh | 0.029087 | 0.029087 | 0.029087 | 0.0 | 2.73 +Comm | 0.0018935 | 0.0018935 | 0.0018935 | 0.0 | 0.18 +Output | 1.8358e-05 | 1.8358e-05 | 1.8358e-05 | 0.0 | 0.00 +Modify | 0.096112 | 0.096112 | 0.096112 | 0.0 | 9.01 +Other | | 0.0005522 | | | 0.05 + +Nlocal: 100 ave 100 max 100 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 608 ave 608 max 608 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 3441 ave 3441 max 3441 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 3441 +Ave neighs/atom = 34.41 +Neighbor list builds = 30 +Dangerous builds not checked + +Please see the log.cite file for references relevant to this simulation + +Total wall time: 0:00:01 diff --git a/examples/kim/log.30Apr2019.kim.ex_si.simulator_model.g++.1 b/examples/kim/log.30Apr2019.kim.ex_si.simulator_model.g++.1 new file mode 100644 index 0000000000..a6d1c4a955 --- /dev/null +++ b/examples/kim/log.30Apr2019.kim.ex_si.simulator_model.g++.1 @@ -0,0 +1,132 @@ +LAMMPS (30 Apr 2019) + using 1 OpenMP thread(s) per MPI task + +units metal +kim_style init ex_sim_model_Si_mod_tersoff +units metal +newton on + +atom_style atomic +atom_modify map array +boundary p p p + +# temperatures +variable tlo equal 1800.0 +variable thi equal 2400.0 + +# coordination number cutoff + +variable r equal 2.835 + +# minimization parameters + +variable etol equal 1.0e-5 +variable ftol equal 1.0e-5 +variable maxiter equal 100 +variable maxeval equal 100 +variable dmax equal 1.0e-1 + +# diamond unit cell + +variable a equal 5.431 +lattice custom $a a1 1.0 0.0 0.0 a2 0.0 1.0 0.0 a3 0.0 0.0 1.0 basis 0.0 0.0 0.0 basis 0.0 0.5 0.5 basis 0.5 0.0 0.5 basis 0.5 0.5 0.0 basis 0.25 0.25 0.25 basis 0.25 0.75 0.75 basis 0.75 0.25 0.75 basis 0.75 0.75 0.25 +lattice custom 5.431 a1 1.0 0.0 0.0 a2 0.0 1.0 0.0 a3 0.0 0.0 1.0 basis 0.0 0.0 0.0 basis 0.0 0.5 0.5 basis 0.5 0.0 0.5 basis 0.5 0.5 0.0 basis 0.25 0.25 0.25 basis 0.25 0.75 0.75 basis 0.75 0.25 0.75 basis 0.75 0.75 0.25 +Lattice spacing in x,y,z = 5.431 5.431 5.431 + +region myreg block 0 4 0 4 0 4 +create_box 1 myreg +Created orthogonal box = (0 0 0) to (21.724 21.724 21.724) + 1 by 1 by 1 MPI processor grid +create_atoms 1 region myreg +Created 512 atoms + create_atoms CPU = 0.000393867 secs + +mass 1 28.06 + +group Si type 1 +512 atoms in group Si + +velocity all create ${thi} 5287286 mom yes rot yes dist gaussian +velocity all create 2400 5287286 mom yes rot yes dist gaussian + +# make a vacancy + +group del id 300 +1 atoms in group del +delete_atoms group del +Deleted 1 atoms, new total = 511 +kim_style define Si +Using KIM Simulator Model : ex_sim_model_Si_mod_tersoff +For Simulator : LAMMPS 12-Dec-2018 +Running on : LAMMPS 30 Apr 2019 +pair_style tersoff/mod +pair_coeff * * /tmp/kim-simulator-model-parameter-file-XXXXXXVWG8uV Si +Reading potential file /tmp/kim-simulator-model-parameter-file-XXXXXXVWG8uV with DATE: 2013-07-26 + +thermo 10 + +fix 1 all nve +fix 2 all langevin ${thi} ${thi} 0.1 48278 +fix 2 all langevin 2400 ${thi} 0.1 48278 +fix 2 all langevin 2400 2400 0.1 48278 + +timestep 1.0e-3 +neighbor 1.0 bin +neigh_modify every 1 delay 10 check yes + +run 100 +Neighbor list info ... + update every 1 steps, delay 10 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 4.3 + ghost atom cutoff = 4.3 + binsize = 2.15, bins = 11 11 11 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair tersoff/mod, perpetual + attributes: full, newton on + pair build: full/bin/atomonly + stencil: full/bin/3d + bin: standard +Per MPI rank memory allocation (min/avg/max) = 3.11 | 3.11 | 3.11 Mbytes +Step Temp E_pair E_mol TotEng Press + 0 2397.3877 -2363.0694 0 -2205.0272 15086.224 + 10 1328.4035 -2289.1682 0 -2201.5963 29164.666 + 20 1086.1557 -2254.4447 0 -2182.8424 31906.878 + 30 1528.8439 -2270.2968 0 -2169.5113 21610.528 + 40 1345.227 -2250.3915 0 -2161.7105 22146.886 + 50 1300.3329 -2235.8593 0 -2150.1379 23557.875 + 60 1546.1664 -2241.3019 0 -2139.3744 21648.774 + 70 1662.2896 -2236.2369 0 -2126.6543 23958.738 + 80 1631.7284 -2223.45 0 -2115.8821 28842.194 + 90 1795.3629 -2225.2998 0 -2106.9447 29522.37 + 100 1830.156 -2224.3733 0 -2103.7245 28805.09 +Loop time of 0.201725 on 1 procs for 100 steps with 511 atoms + +Performance: 42.831 ns/day, 0.560 hours/ns, 495.724 timesteps/s +99.3% CPU use with 1 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0.19292 | 0.19292 | 0.19292 | 0.0 | 95.63 +Neigh | 0.0037313 | 0.0037313 | 0.0037313 | 0.0 | 1.85 +Comm | 0.00074744 | 0.00074744 | 0.00074744 | 0.0 | 0.37 +Output | 0.00026727 | 0.00026727 | 0.00026727 | 0.0 | 0.13 +Modify | 0.0036564 | 0.0036564 | 0.0036564 | 0.0 | 1.81 +Other | | 0.0004075 | | | 0.20 + +Nlocal: 511 ave 511 max 511 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 970 ave 970 max 970 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 0 ave 0 max 0 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +FullNghs: 9174 ave 9174 max 9174 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 9174 +Ave neighs/atom = 17.953 +Neighbor list builds = 4 +Dangerous builds = 0 + +Total wall time: 0:00:00 diff --git a/examples/kim/log.30Apr2019.kim.ex_si.simulator_model.g++.4 b/examples/kim/log.30Apr2019.kim.ex_si.simulator_model.g++.4 new file mode 100644 index 0000000000..dcb170aeb6 --- /dev/null +++ b/examples/kim/log.30Apr2019.kim.ex_si.simulator_model.g++.4 @@ -0,0 +1,132 @@ +LAMMPS (30 Apr 2019) + using 1 OpenMP thread(s) per MPI task + +units metal +kim_style init ex_sim_model_Si_mod_tersoff +units metal +newton on + +atom_style atomic +atom_modify map array +boundary p p p + +# temperatures +variable tlo equal 1800.0 +variable thi equal 2400.0 + +# coordination number cutoff + +variable r equal 2.835 + +# minimization parameters + +variable etol equal 1.0e-5 +variable ftol equal 1.0e-5 +variable maxiter equal 100 +variable maxeval equal 100 +variable dmax equal 1.0e-1 + +# diamond unit cell + +variable a equal 5.431 +lattice custom $a a1 1.0 0.0 0.0 a2 0.0 1.0 0.0 a3 0.0 0.0 1.0 basis 0.0 0.0 0.0 basis 0.0 0.5 0.5 basis 0.5 0.0 0.5 basis 0.5 0.5 0.0 basis 0.25 0.25 0.25 basis 0.25 0.75 0.75 basis 0.75 0.25 0.75 basis 0.75 0.75 0.25 +lattice custom 5.431 a1 1.0 0.0 0.0 a2 0.0 1.0 0.0 a3 0.0 0.0 1.0 basis 0.0 0.0 0.0 basis 0.0 0.5 0.5 basis 0.5 0.0 0.5 basis 0.5 0.5 0.0 basis 0.25 0.25 0.25 basis 0.25 0.75 0.75 basis 0.75 0.25 0.75 basis 0.75 0.75 0.25 +Lattice spacing in x,y,z = 5.431 5.431 5.431 + +region myreg block 0 4 0 4 0 4 +create_box 1 myreg +Created orthogonal box = (0 0 0) to (21.724 21.724 21.724) + 1 by 2 by 2 MPI processor grid +create_atoms 1 region myreg +Created 512 atoms + create_atoms CPU = 0.102434 secs + +mass 1 28.06 + +group Si type 1 +512 atoms in group Si + +velocity all create ${thi} 5287286 mom yes rot yes dist gaussian +velocity all create 2400 5287286 mom yes rot yes dist gaussian + +# make a vacancy + +group del id 300 +1 atoms in group del +delete_atoms group del +Deleted 1 atoms, new total = 511 +kim_style define Si +Using KIM Simulator Model : ex_sim_model_Si_mod_tersoff +For Simulator : LAMMPS 12-Dec-2018 +Running on : LAMMPS 30 Apr 2019 +pair_style tersoff/mod +pair_coeff * * /tmp/kim-simulator-model-parameter-file-XXXXXXqDlERL Si +Reading potential file /tmp/kim-simulator-model-parameter-file-XXXXXXqDlERL with DATE: 2013-07-26 + +thermo 10 + +fix 1 all nve +fix 2 all langevin ${thi} ${thi} 0.1 48278 +fix 2 all langevin 2400 ${thi} 0.1 48278 +fix 2 all langevin 2400 2400 0.1 48278 + +timestep 1.0e-3 +neighbor 1.0 bin +neigh_modify every 1 delay 10 check yes + +run 100 +Neighbor list info ... + update every 1 steps, delay 10 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 4.3 + ghost atom cutoff = 4.3 + binsize = 2.15, bins = 11 11 11 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair tersoff/mod, perpetual + attributes: full, newton on + pair build: full/bin/atomonly + stencil: full/bin/3d + bin: standard +Per MPI rank memory allocation (min/avg/max) = 3.082 | 3.082 | 3.082 Mbytes +Step Temp E_pair E_mol TotEng Press + 0 2397.5824 -2363.0694 0 -2205.0143 15087.562 + 10 1298.5003 -2292.5456 0 -2206.945 28361.893 + 20 1114.7065 -2260.7006 0 -2187.2161 30574.077 + 30 1504.9472 -2271.8639 0 -2172.6537 20395.651 + 40 1357.5949 -2248.6066 0 -2159.1103 21779.773 + 50 1351.7212 -2235.0803 0 -2145.9713 23404.844 + 60 1582.4191 -2238.3233 0 -2134.006 21711.26 + 70 1654.3988 -2230.0965 0 -2121.0341 24276.504 + 80 1654.9629 -2218.6654 0 -2109.5658 27571.472 + 90 1815.7206 -2219.2065 0 -2099.5093 28475.757 + 100 1901.1544 -2216.5428 0 -2091.2137 28962.04 +Loop time of 4.36959 on 4 procs for 100 steps with 511 atoms + +Performance: 1.977 ns/day, 12.138 hours/ns, 22.885 timesteps/s +47.8% CPU use with 4 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0.051784 | 0.056551 | 0.064825 | 2.1 | 1.29 +Neigh | 0.00093389 | 0.001028 | 0.0011392 | 0.3 | 0.02 +Comm | 2.8964 | 2.9342 | 3.016 | 2.8 | 67.15 +Output | 0.673 | 0.68159 | 0.69707 | 1.1 | 15.60 +Modify | 0.0011303 | 0.0029655 | 0.0081694 | 5.5 | 0.07 +Other | | 0.6933 | | | 15.87 + +Nlocal: 127.75 ave 134 max 123 min +Histogram: 1 0 0 2 0 0 0 0 0 1 +Nghost: 495 ave 498 max 489 min +Histogram: 1 0 0 0 0 0 0 1 1 1 +Neighs: 0 ave 0 max 0 min +Histogram: 4 0 0 0 0 0 0 0 0 0 +FullNghs: 2302 ave 2443 max 2194 min +Histogram: 1 0 0 2 0 0 0 0 0 1 + +Total # of neighbors = 9208 +Ave neighs/atom = 18.0196 +Neighbor list builds = 4 +Dangerous builds = 0 + +Total wall time: 0:00:05 diff --git a/examples/kim/log.30Apr2019.kim.lj.simulator_model.g++.1 b/examples/kim/log.30Apr2019.kim.lj.simulator_model.g++.1 new file mode 100644 index 0000000000..94aaf1aaef --- /dev/null +++ b/examples/kim/log.30Apr2019.kim.lj.simulator_model.g++.1 @@ -0,0 +1,104 @@ +LAMMPS (30 Apr 2019) + using 1 OpenMP thread(s) per MPI task +# 3d Lennard-Jones melt +# +# This example requires that the example models provided with +# the kim-api package are installed. see the ./lib/kim/README or +# ./lib/kim/Install.py files for details on how to install these +# example models. +# + +variable x index 1 +variable y index 1 +variable z index 1 + +variable xx equal 20*$x +variable xx equal 20*1 +variable yy equal 20*$y +variable yy equal 20*1 +variable zz equal 20*$z +variable zz equal 20*1 + +units metal +atom_style atomic +newton on + +kim_style init LennardJones_Ar + +lattice fcc 4.4300 +Lattice spacing in x,y,z = 4.43 4.43 4.43 +region box block 0 ${xx} 0 ${yy} 0 ${zz} +region box block 0 20 0 ${yy} 0 ${zz} +region box block 0 20 0 20 0 ${zz} +region box block 0 20 0 20 0 20 +create_box 1 box +Created orthogonal box = (0 0 0) to (88.6 88.6 88.6) + 1 by 1 by 1 MPI processor grid +create_atoms 1 box +Created 32000 atoms + create_atoms CPU = 0.00314307 secs + +#pair_style lj/cut 8.1500 +#pair_coeff 1 1 0.0104 3.4000 + +kim_style define Ar +pair_style kim LennardJones_Ar +WARNING: KIM Model does not provide `partialParticleEnergy'; energy per atom will be zero (src/KIM/pair_kim.cpp:980) +WARNING: KIM Model does not provide `partialParticleVirial'; virial per atom will be zero (src/KIM/pair_kim.cpp:985) +pair_coeff * * Ar + +mass 1 39.95 +velocity all create 200.0 232345 loop geom + +neighbor 0.3 bin +neigh_modify delay 0 every 1 check yes + +fix 1 all nve +#fix 1 all npt temp 1.0 1.0 1.0 iso 1.0 1.0 3.0 + +run 100 +Neighbor list info ... + update every 1 steps, delay 0 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 8.45 + ghost atom cutoff = 8.45 + binsize = 4.225, bins = 21 21 21 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair kim, perpetual + attributes: full, newton off, cut 8.45 + pair build: full/bin/atomonly + stencil: full/bin/3d + bin: standard +Per MPI rank memory allocation (min/avg/max) = 28.12 | 28.12 | 28.12 Mbytes +Step Temp E_pair E_mol TotEng Press + 0 200 6290.8194 0 7118.0584 129712.25 + 100 95.179725 6718.814 0 7112.496 133346.59 +Loop time of 4.91804 on 1 procs for 100 steps with 32000 atoms + +Performance: 1.757 ns/day, 13.661 hours/ns, 20.333 timesteps/s +99.7% CPU use with 1 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 4.3033 | 4.3033 | 4.3033 | 0.0 | 87.50 +Neigh | 0.53176 | 0.53176 | 0.53176 | 0.0 | 10.81 +Comm | 0.024606 | 0.024606 | 0.024606 | 0.0 | 0.50 +Output | 0.00016403 | 0.00016403 | 0.00016403 | 0.0 | 0.00 +Modify | 0.038671 | 0.038671 | 0.038671 | 0.0 | 0.79 +Other | | 0.01951 | | | 0.40 + +Nlocal: 32000 ave 32000 max 32000 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 19911 ave 19911 max 19911 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 0 ave 0 max 0 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +FullNghs: 4.25375e+06 ave 4.25375e+06 max 4.25375e+06 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 4253750 +Ave neighs/atom = 132.93 +Neighbor list builds = 3 +Dangerous builds = 0 +Total wall time: 0:00:05 diff --git a/examples/kim/log.30Apr2019.kim.lj.simulator_model.g++.4 b/examples/kim/log.30Apr2019.kim.lj.simulator_model.g++.4 new file mode 100644 index 0000000000..3377f22d02 --- /dev/null +++ b/examples/kim/log.30Apr2019.kim.lj.simulator_model.g++.4 @@ -0,0 +1,104 @@ +LAMMPS (30 Apr 2019) + using 1 OpenMP thread(s) per MPI task +# 3d Lennard-Jones melt +# +# This example requires that the example models provided with +# the kim-api package are installed. see the ./lib/kim/README or +# ./lib/kim/Install.py files for details on how to install these +# example models. +# + +variable x index 1 +variable y index 1 +variable z index 1 + +variable xx equal 20*$x +variable xx equal 20*1 +variable yy equal 20*$y +variable yy equal 20*1 +variable zz equal 20*$z +variable zz equal 20*1 + +units metal +atom_style atomic +newton on + +kim_style init LennardJones_Ar + +lattice fcc 4.4300 +Lattice spacing in x,y,z = 4.43 4.43 4.43 +region box block 0 ${xx} 0 ${yy} 0 ${zz} +region box block 0 20 0 ${yy} 0 ${zz} +region box block 0 20 0 20 0 ${zz} +region box block 0 20 0 20 0 20 +create_box 1 box +Created orthogonal box = (0 0 0) to (88.6 88.6 88.6) + 1 by 2 by 2 MPI processor grid +create_atoms 1 box +Created 32000 atoms + create_atoms CPU = 0.0979962 secs + +#pair_style lj/cut 8.1500 +#pair_coeff 1 1 0.0104 3.4000 + +kim_style define Ar +pair_style kim LennardJones_Ar +WARNING: KIM Model does not provide `partialParticleEnergy'; energy per atom will be zero (src/KIM/pair_kim.cpp:980) +WARNING: KIM Model does not provide `partialParticleVirial'; virial per atom will be zero (src/KIM/pair_kim.cpp:985) +pair_coeff * * Ar + +mass 1 39.95 +velocity all create 200.0 232345 loop geom + +neighbor 0.3 bin +neigh_modify delay 0 every 1 check yes + +fix 1 all nve +#fix 1 all npt temp 1.0 1.0 1.0 iso 1.0 1.0 3.0 + +run 100 +Neighbor list info ... + update every 1 steps, delay 0 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 8.45 + ghost atom cutoff = 8.45 + binsize = 4.225, bins = 21 21 21 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair kim, perpetual + attributes: full, newton off, cut 8.45 + pair build: full/bin/atomonly + stencil: full/bin/3d + bin: standard +Per MPI rank memory allocation (min/avg/max) = 9.789 | 9.789 | 9.789 Mbytes +Step Temp E_pair E_mol TotEng Press + 0 200 6290.8194 0 7118.0584 129712.25 + 100 95.179725 6718.814 0 7112.496 133346.59 +Loop time of 6.29539 on 4 procs for 100 steps with 32000 atoms + +Performance: 1.372 ns/day, 17.487 hours/ns, 15.885 timesteps/s +48.4% CPU use with 4 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 1.9399 | 2.079 | 2.2181 | 9.1 | 33.02 +Neigh | 0.25924 | 0.26632 | 0.2692 | 0.8 | 4.23 +Comm | 2.5011 | 2.6605 | 2.751 | 5.9 | 42.26 +Output | 0.069904 | 0.07097 | 0.071545 | 0.3 | 1.13 +Modify | 0.011383 | 0.012206 | 0.01419 | 1.0 | 0.19 +Other | | 1.206 | | | 19.16 + +Nlocal: 8000 ave 8018 max 7967 min +Histogram: 1 0 0 0 0 0 1 0 0 2 +Nghost: 9131 ave 9164 max 9113 min +Histogram: 2 0 0 1 0 0 0 0 0 1 +Neighs: 0 ave 0 max 0 min +Histogram: 4 0 0 0 0 0 0 0 0 0 +FullNghs: 1.06344e+06 ave 1.06594e+06 max 1.05881e+06 min +Histogram: 1 0 0 0 0 0 1 0 0 2 + +Total # of neighbors = 4253750 +Ave neighs/atom = 132.93 +Neighbor list builds = 3 +Dangerous builds = 0 +Total wall time: 0:00:07 -- GitLab From df1308ad922c4fd47bcd90bb5253540902ac2aff Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Thu, 30 May 2019 21:58:18 -0400 Subject: [PATCH 033/469] add kim_style error messages to Errors_messages.txt doc file --- doc/src/Errors_messages.txt | 33 +++++++++++++++++++++++++++++++++ src/KIM/kim_style.h | 14 +++++++------- 2 files changed, 40 insertions(+), 7 deletions(-) diff --git a/doc/src/Errors_messages.txt b/doc/src/Errors_messages.txt index fb5003e602..7f6e80948c 100644 --- a/doc/src/Errors_messages.txt +++ b/doc/src/Errors_messages.txt @@ -5729,6 +5729,16 @@ definitions. :dd The data file header lists improper but no improper types. :dd +{Incompatible KIM Simulator Model} :dt + +The requested KIM Simulator Model was defined for a different MD code +and thus is not compatible with LAMMPS. :dd + +{Incompatible units for KIM Simulator Model} :dt + +The selected unit style is not compatible with the requested KIM +Simulator Model. :dd + {Incomplete use of variables in create_atoms command} :dt The var and set options must be used together. :dd @@ -6988,6 +6998,12 @@ The atom style defined does not have this attribute. :dd The atom style defined does not have these attributes. :dd +{KIM Simulator Model has no Model definition} :dt + +There is no model definition (key: model-defn) in the KIM Simulator +Model. Please contact the OpenKIM database maintainers to verify +and potentially correct this. :dd + {KOKKOS package does not yet support comm_style tiled} :dt Self-explanatory. :dd @@ -7475,6 +7491,18 @@ Self-explanatory. :dd Self-explanatory. :dd +{Must use 'kim_style init' command before simulation box is defined} :dt + +Self-explanatory. :dd + +{Must use 'kim_style define' command after simulation box is defined} :dt + +Self-explanatory. :dd + +{Must use 'kim_style init' command before 'kim_style define'} :dt + +Self-explanatory. :dd + {Must use 'kspace_modify pressure/scalar no' for rRESPA with kspace_style MSM} :dt The kspace scalar pressure option cannot (yet) be used with rRESPA. :dd @@ -9418,6 +9446,11 @@ See the "read_data extra/special/per/atom" command for info on how to leave space in the special bonds list to allow for additional bonds to be formed. :dd +{Species XXX is not supported by this KIM Simulator Model} :dt + +The kim_style define command was referencing a species that is not +present in the requested KIM Simulator Model. :dd + {Specified processors != physical processors} :dt The 3d grid of processors defined by the processors command does not diff --git a/src/KIM/kim_style.h b/src/KIM/kim_style.h index eddc22eebc..f8c0602beb 100644 --- a/src/KIM/kim_style.h +++ b/src/KIM/kim_style.h @@ -85,34 +85,34 @@ class KimStyle : protected Pointers { E: Illegal kim_style command -Incorrect number or kind of arguments to kim_style +Incorrect number or kind of arguments to kim_style. E: Must use 'kim_style init' command before simulation box is defined -Self-explanatory +Self-explanatory. E: Must use 'kim_style define' command after simulation box is defined -Self-explanatory +Self-explanatory. E: Must use 'kim_style init' command before 'kim_style define' -Self-explanatory +Self-explanatory. E: Incompatible KIM Simulator Model The requested KIM Simulator Model was defined for a different MD code -and thus is not compatible with LAMMPS +and thus is not compatible with LAMMPS. E: Species XXX is not supported by this KIM Simulator Model The kim_style define command was referencing a species that is not -present in the requested KIM Simulator Model +present in the requested KIM Simulator Model. E: Incompatible units for KIM Simulator Model The selected unit style is not compatible with the requested KIM -Simulator Model +Simulator Model. E: KIM Simulator Model has no Model definition -- GitLab From edecd2b7601f900e99b6eaeb9c3acb25dfe35edc Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Thu, 30 May 2019 22:19:47 -0400 Subject: [PATCH 034/469] fix typo and update list of false positives for updated docs --- doc/src/kim_style.txt | 2 +- doc/utils/sphinx-config/false_positives.txt | 2 ++ 2 files changed, 3 insertions(+), 1 deletion(-) diff --git a/doc/src/kim_style.txt b/doc/src/kim_style.txt index dcdfae1cdc..afa7a19fab 100644 --- a/doc/src/kim_style.txt +++ b/doc/src/kim_style.txt @@ -51,7 +51,7 @@ The {kim_style define} command will issue commands that will realize the selected model (through generating pair_style and pair_coeff commands, but also other commands, as required). It has to be issued [after] the the simulation box is defined. The {kim_style define} command allows a -varying numbver of additional arguments. Those are used to map the atom +varying number of additional arguments. Those are used to map the atom types in LAMMPS to the available species in the KIM model. This is equivalent to the arguments following "pair_coeff * *" in a "kim"_pair_kim.html pair style. Thus the commands: diff --git a/doc/utils/sphinx-config/false_positives.txt b/doc/utils/sphinx-config/false_positives.txt index 7160800c50..a8bfa8f193 100644 --- a/doc/utils/sphinx-config/false_positives.txt +++ b/doc/utils/sphinx-config/false_positives.txt @@ -521,6 +521,7 @@ decrementing deeppink deepskyblue defgrad +defn deformable del deleteIDs @@ -2792,6 +2793,7 @@ txt typeI typeJ typeN +typeargs Tz Tzou ub -- GitLab From ad8fd4a2a46c004dba1313f9daa7896be8052077 Mon Sep 17 00:00:00 2001 From: Andrew Schultz Date: Mon, 10 Jun 2019 16:13:09 -0400 Subject: [PATCH 035/469] Clean up comments --- src/USER-HMA/compute_hma.cpp | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/src/USER-HMA/compute_hma.cpp b/src/USER-HMA/compute_hma.cpp index c0a7901640..ad86577ba1 100644 --- a/src/USER-HMA/compute_hma.cpp +++ b/src/USER-HMA/compute_hma.cpp @@ -119,6 +119,7 @@ ComputeHMA::ComputeHMA(LAMMPS *lmp, int narg, char **arg) : extvec.push_back(1); } else if (!strcasecmp(arg[iarg], "anharmonic")) { + // the first time we're called, we'll grab lattice pressure and energy returnAnharmonic = -1; } else { @@ -333,9 +334,7 @@ void ComputeHMA::compute_vector() } } -//adding PE for this processor - -//adding the energies of all processors + // compute and sum up properties across processors double fdrTotal; MPI_Allreduce(&fdr,&fdrTotal,1,MPI_DOUBLE,MPI_SUM,world); @@ -383,6 +382,7 @@ void ComputeHMA::compute_vector() } } if (returnAnharmonic == -1) { + // we have our lattice properties returnAnharmonic = 1; } } -- GitLab From 5c9c15025afffecd365bbbf40d5fc9cdc437cd6e Mon Sep 17 00:00:00 2001 From: Andrew Schultz Date: Mon, 10 Jun 2019 16:13:34 -0400 Subject: [PATCH 036/469] Add bits to Packages_details, Packages_user, fix up typos --- doc/src/Packages_details.txt | 20 ++++++++++++++++++++ doc/src/Packages_user.txt | 1 + doc/src/compute_hma.txt | 6 +++--- 3 files changed, 24 insertions(+), 3 deletions(-) diff --git a/doc/src/Packages_details.txt b/doc/src/Packages_details.txt index 0ab1b5e4fd..b5050b8c4b 100644 --- a/doc/src/Packages_details.txt +++ b/doc/src/Packages_details.txt @@ -76,6 +76,7 @@ as contained in the file name. "USER-EFF"_#PKG-USER-EFF, "USER-FEP"_#PKG-USER-FEP, "USER-H5MD"_#PKG-USER-H5MD, +"USER-HMA"_#PKG-USER-HMA, "USER-INTEL"_#PKG-USER-INTEL, "USER-LB"_#PKG-USER-LB, "USER-MANIFOLD"_#PKG-USER-MANIFOLD, @@ -1373,6 +1374,25 @@ lib/h5md/README :line +USER-HMA package :link(PKG-USER-HMA),h4 + +[Contents:] + +Harmonically mapped averaging for efficient calculation of properties of +crystalline solids. The compute hma can specify use of HMA for calculation of +potential energy, pressure and heat capacity. + +[Author:] Apoorva Purohit, Andrew Schultz and David Kofke (University at +Buffalo, NY, USA) + +[Supporting info:] + +examples/USER/hma/README +src/USER-HMA/README +"compute hma"_compute_hma.html :ul + +:line + USER-INTEL package :link(PKG-USER-INTEL),h4 [Contents:] diff --git a/doc/src/Packages_user.txt b/doc/src/Packages_user.txt index 4210f617ef..3ce2a458b6 100644 --- a/doc/src/Packages_user.txt +++ b/doc/src/Packages_user.txt @@ -51,6 +51,7 @@ Package, Description, Doc page, Example, Library "USER-EFF"_Packages_details.html#PKG-USER-EFF, electron force field,"pair_style eff/cut"_pair_eff.html, USER/eff, no "USER-FEP"_Packages_details.html#PKG-USER-FEP, free energy perturbation,"compute fep"_compute_fep.html, USER/fep, no "USER-H5MD"_Packages_details.html#PKG-USER-H5MD, dump output via HDF5,"dump h5md"_dump_h5md.html, n/a, ext +"USER-HMA"_Packages_details.html#PKG-USER-HMA, compute properties via HMA,"compute hma"_compute_hma.html, USER/hma, no "USER-INTEL"_Packages_details.html#PKG-USER-INTEL, optimized Intel CPU and KNL styles,"Speed intel"_Speed_intel.html, "Benchmarks"_http://lammps.sandia.gov/bench.html, no "USER-LB"_Packages_details.html#PKG-USER-LB, Lattice Boltzmann fluid,"fix lb/fluid"_fix_lb_fluid.html, USER/lb, no "USER-MANIFOLD"_Packages_details.html#PKG-USER-MANIFOLD, motion on 2d surfaces,"fix manifoldforce"_fix_manifoldforce.html, USER/manifold, no diff --git a/doc/src/compute_hma.txt b/doc/src/compute_hma.txt index c4ade07ad7..340881bf68 100644 --- a/doc/src/compute_hma.txt +++ b/doc/src/compute_hma.txt @@ -61,7 +61,7 @@ The pressure is computed by the formula: \end\{equation\} where \(\rho\) is the number density of the system, \(\Delta \hat P\) is the -difference between theh harmonic and lattice pressure, and \(P_\{vir\}\) is +difference between the harmonic and lattice pressure, and \(P_\{vir\}\) is the virial pressure computed as the sum of pair, bond, angle, dihedral, improper, kspace (long-range), and fix contributions to the force on each atom. Although the method will work for any value of \(\Delta \hat P\) @@ -76,13 +76,13 @@ U_\{HMA\}^2 \right> - \left^2 \right)/T + \frac\{1\}\{4 T\} \left< F\bullet\Delta r + \Delta r \bullet \Phi \bullet \Delta r \right> \end\{equation\} -where \(\Phi\) is the Hessian of second derivatives. The compute hma command +where \(\Phi\) is the Hessian matrix. The compute hma command computes the full expression for \(C_V\) except for the \(\left^2\) in the variance term, which can be obtained by passing the {u} keyword; you must add this extra contribution to the \(C_V\) value reported by this compute. The variance term can cause significant roundoff error when computing \(C_V\). To address this, the {anharmonic} -keyword can be passed and/or the output format can be speicified with more +keyword can be passed and/or the output format can be specified with more digits. thermo_modify format float '%22.15e' :pre -- GitLab From e438d46ee2c54bdb5cb9927991329f071f5e87c2 Mon Sep 17 00:00:00 2001 From: Andrew Schultz Date: Mon, 10 Jun 2019 16:14:28 -0400 Subject: [PATCH 037/469] Add README in src directory --- src/USER-HMA/README | 30 ++++++++++++++++++++++++++++++ 1 file changed, 30 insertions(+) create mode 100644 src/USER-HMA/README diff --git a/src/USER-HMA/README b/src/USER-HMA/README new file mode 100644 index 0000000000..b27999341b --- /dev/null +++ b/src/USER-HMA/README @@ -0,0 +1,30 @@ +The HMA package implements the compute hma command for LAMMPS, which implements +harmonically-mapped averaging for crystalline solids. The current +implementation handles atomic crystals. + +Computing the heat capacity relies on being able to compute the second +derivative of the energy with respect to atom positions. This capability is +provided by the single2 method in Pair, but is currently only implemented for +the shifted-force LJ potential (lj/smooth/linear). Pair::single2 takes a single +pair and (like Pair::single) returns the energy and sets the force as an out +parameter, but also sets the elements of 6-element double array out parameter, +which are the unique components of the atomic Hessian tensor for the pair. A +helper method exists (Pair::pairTensor), which will compute the tensor from +linear derivatives and the vector between the positions. HMA Heat capacity can +be computed for other models by implementing single2 in those Pair classes. + +More information about HMA is available in these publications: + +A. J. Schultz, D. A. Kofke, “Comprehensive high-precision high-accuracy +equation of state and coexistence properties for classical Lennard-Jones +crystals and low-temperature fluid phases”, J. Chem. Phys. 149, 204508 (2018) +https://dx.doi.org/10.1063/1.5053714 + +S. G. Moustafa, A. J. Schultz, D. A. Kofke, “Harmonically Assisted Methods for +Computing the Free Energy of Classical Crystals by Molecular Simulation: A +Comparative Study”, J. Chem. Theory Comput. 13, 825-834 (2017) +https://dx.doi.org/10.1021/acs.jctc.6b01082 + +S. G. Moustafa, A. J. Schultz, D. A. Kofke, “Very fast averaging of thermal +properties of crystals by molecular simulation”, Phys. Rev. E 92, 043303 (2015) +https://dx.doi.org/10.1103/PhysRevE.92.043303 -- GitLab From b195ccfb27e0037e5e6f1836724d8ae042000ce0 Mon Sep 17 00:00:00 2001 From: Andrew Schultz Date: Mon, 10 Jun 2019 17:08:40 -0400 Subject: [PATCH 038/469] Unbreak compute.txt --- doc/src/compute.txt | 14 ++++++++++++-- 1 file changed, 12 insertions(+), 2 deletions(-) diff --git a/doc/src/compute.txt b/doc/src/compute.txt index c8456fb342..52ae5df0eb 100644 --- a/doc/src/compute.txt +++ b/doc/src/compute.txt @@ -169,7 +169,7 @@ There are also additional accelerated compute styles included in the LAMMPS distribution for faster performance on CPUs, GPUs, and KNLs. The individual style names on the "Commands compute"_Commands_compute.html doc page are followed by one or more of -(g,i,k,o,t) to indicate which accerlerated styles exist. +(g,i,k,o,t) to indicate which accelerated styles exist. "ackland/atom"_compute_ackland_atom.html - "adf"_compute_adf.html - angular distribution function of triples of atoms @@ -184,6 +184,7 @@ compute"_Commands_compute.html doc page are followed by one or more of "bond/local"_compute_bond_local.html - distance and energy of each bond "centro/atom"_compute_centro_atom.html - centro-symmetry parameter for each atom "chunk/atom"_compute_chunk_atom.html - assign chunk IDs to each atom +"chunk/spread/atom"_compute_chunk_spread_atom.html - spreads chunk values to each atom in chunk "cluster/atom"_compute_cluster_atom.html - cluster ID for each atom "cna/atom"_compute_cna_atom.html - common neighbor analysis (CNA) for each atom "cnp/atom"_compute_cnp_atom.html - @@ -223,6 +224,12 @@ compute"_Commands_compute.html doc page are followed by one or more of "inertia/chunk"_compute_inertia_chunk.html - inertia tensor for each chunk "ke"_compute_ke.html - translational kinetic energy "ke/atom"_compute_ke_atom.html - kinetic energy for each atom +"ke/atom/eff"_compute_ke_atom_eff.html - +"ke/eff"_compute_ke_eff.html - +"ke/rigid"_compute_ke_rigid.html - translational kinetic energy of rigid bodies +"meso/e/atom"_compute_meso_e_atom.html - +"meso/rho/atom"_compute_meso_rho_atom.html - +"meso/t/atom"_compute_meso_t_atom.html - "msd"_compute_msd.html - mean-squared displacement of group of atoms "msd/chunk"_compute_msd_chunk.html - mean-squared displacement for each chunk "msd/nongauss"_compute_msd_nongauss.html - MSD and non-Gaussian parameter of group of atoms @@ -239,10 +246,12 @@ compute"_Commands_compute.html doc page are followed by one or more of "pressure/cylinder"_compute_pressure_cylinder.html - "pressure/uef"_compute_pressure_uef.html - "property/atom"_compute_property_atom.html - convert atom attributes to per-atom vectors/arrays +"property/chunk"_compute_property_chunk.html - extract various per-chunk attributes "property/local"_compute_property_local.html - convert local attributes to localvectors/arrays "ptm/atom"_compute_ptm_atom.html - "rdf"_compute_rdf.html - radial distribution function g(r) histogram of group of atoms "reduce"_compute_reduce.html - combine per-atom quantities into a single global value +"reduce/chunk"_compute_reduce_chunk.html - reduce per-atom quantities within each chunk "reduce/region"_compute_reduce.html - same as compute reduce, within a region "rigid/local"_compute_rigid_local.html - extract rigid body attributes "saed"_compute_saed.html - @@ -299,7 +308,8 @@ compute"_Commands_compute.html doc page are followed by one or more of "torque/chunk"_compute_torque_chunk.html - torque applied on each chunk "vacf"_compute_vacf.html - velocity auto-correlation function of group of atoms "vcm/chunk"_compute_vcm_chunk.html - velocity of center-of-mass for each chunk -"voronoi/atom"_compute_voronoi_atom.html - Voronoi volume and neighbors for each atom :ul +"voronoi/atom"_compute_voronoi_atom.html - Voronoi volume and neighbors for each atom +"xrd"_compute_xrd.html - :ul [Restrictions:] none -- GitLab From 2d90bb994795f1a56fda0a4abb5a784c27a925fa Mon Sep 17 00:00:00 2001 From: Andrew Schultz Date: Mon, 10 Jun 2019 17:12:01 -0400 Subject: [PATCH 039/469] Unbreak computes.txt --- doc/src/computes.txt | 8 +++++++- 1 file changed, 7 insertions(+), 1 deletion(-) diff --git a/doc/src/computes.txt b/doc/src/computes.txt index c636633b38..f3a552b740 100644 --- a/doc/src/computes.txt +++ b/doc/src/computes.txt @@ -6,6 +6,7 @@ Computes :h1 :maxdepth: 1 compute_ackland_atom + compute_adf compute_angle compute_angle_local compute_angmom_chunk @@ -15,6 +16,7 @@ Computes :h1 compute_bond_local compute_centro_atom compute_chunk_atom + compute_chunk_spread_atom compute_cluster_atom compute_cna_atom compute_cnp_atom @@ -67,12 +69,15 @@ Computes :h1 compute_pe_atom compute_plasticity_atom compute_pressure + compute_pressure_cylinder compute_pressure_uef compute_property_atom compute_property_chunk compute_property_local + compute_ptm_atom compute_rdf compute_reduce + compute_reduce_chunk compute_rigid_local compute_saed compute_slice @@ -90,7 +95,7 @@ Computes :h1 compute_smd_tlsph_strain compute_smd_tlsph_strain_rate compute_smd_tlsph_stress - compute_smd_triangle_mesh_vertices + compute_smd_triangle_vertices compute_smd_ulsph_num_neighs compute_smd_ulsph_strain compute_smd_ulsph_strain_rate @@ -99,6 +104,7 @@ Computes :h1 compute_sna_atom compute_spin compute_stress_atom + compute_stress_mop compute_tally compute_tdpd_cc_atom compute_temp -- GitLab From 8858846e399a0086d922bbc5bd7c03cb9262a1ca Mon Sep 17 00:00:00 2001 From: Andrew Schultz Date: Mon, 10 Jun 2019 17:13:16 -0400 Subject: [PATCH 040/469] Unbreak pair.h --- src/pair.h | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/src/pair.h b/src/pair.h index 7ebf56173c..3947f4cd81 100644 --- a/src/pair.h +++ b/src/pair.h @@ -221,6 +221,10 @@ class Pair : protected Pointers { typedef union {int i; float f;} union_int_float_t; + // Accessor for the user-intel package to determine virial calc for hybrid + + inline int fdotr_is_set() const { return vflag_fdotr; } + protected: int vflag_fdotr; int maxeatom,maxvatom; -- GitLab From 22fd12b56c803e6e0e5939bb0a950adf080c31a9 Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Mon, 10 Jun 2019 17:14:17 -0400 Subject: [PATCH 041/469] support storing unit conversion variable setting between kim_style calls --- src/KIM/fix_store_kim.cpp | 29 ++++++++++++++++++++++++++++- src/KIM/fix_store_kim.h | 2 ++ 2 files changed, 30 insertions(+), 1 deletion(-) diff --git a/src/KIM/fix_store_kim.cpp b/src/KIM/fix_store_kim.cpp index 8e9946c20d..6423a57e18 100644 --- a/src/KIM/fix_store_kim.cpp +++ b/src/KIM/fix_store_kim.cpp @@ -65,7 +65,8 @@ using namespace FixConst; /* ---------------------------------------------------------------------- */ FixStoreKIM::FixStoreKIM(LAMMPS *lmp, int narg, char **arg) - : Fix(lmp, narg, arg), simulator_model(NULL), model_name(NULL) + : Fix(lmp, narg, arg), simulator_model(NULL), model_name(NULL), + units_from(NULL), units_to(NULL) { if (narg != 3) error->all(FLERR,"Illegal fix STORE/KIM command"); } @@ -87,6 +88,18 @@ FixStoreKIM::~FixStoreKIM() delete[] mn; model_name = NULL; } + + if (units_from) { + char *uf = (char *)units_from; + delete[] uf; + units_from = NULL; + } + + if (units_to) { + char *ut = (char *)units_to; + delete[] ut; + units_to = NULL; + } } /* ---------------------------------------------------------------------- */ @@ -114,6 +127,18 @@ void FixStoreKIM::setptr(const char *name, void *ptr) delete[] mn; } model_name = ptr; + } else if (strcmp(name,"units_from") == 0) { + if (units_from) { + char *uf = (char *)units_from; + delete[] uf; + } + units_from = ptr; + } else if (strcmp(name,"units_to") == 0) { + if (units_to) { + char *ut = (char *)units_to; + delete[] ut; + } + units_to = ptr; } } @@ -123,5 +148,7 @@ void *FixStoreKIM::getptr(const char *name) { if (strcmp(name,"simulator_model") == 0) return simulator_model; else if (strcmp(name,"model_name") == 0) return model_name; + else if (strcmp(name,"units_from") == 0) return units_from; + else if (strcmp(name,"units_to") == 0) return units_to; else return NULL; } diff --git a/src/KIM/fix_store_kim.h b/src/KIM/fix_store_kim.h index 04081fd6dc..5bca2a3dd0 100644 --- a/src/KIM/fix_store_kim.h +++ b/src/KIM/fix_store_kim.h @@ -80,6 +80,8 @@ class FixStoreKIM : public Fix { private: void *simulator_model; // pointer to KIM simulator model class void *model_name; // string of KIM model name + void *units_from; // string of unit conversion origin or NULL + void *units_to; // string of unit conversion target or NULL }; } -- GitLab From 9a428217d9f9d864e7ff66618645dfab4be04341 Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Mon, 10 Jun 2019 17:19:18 -0400 Subject: [PATCH 042/469] prototype implementation of unit conversion variable support --- src/KIM/kim_style.cpp | 161 +++++++++++++++++++++++++++++++++++++++++- src/KIM/kim_style.h | 4 ++ 2 files changed, 162 insertions(+), 3 deletions(-) diff --git a/src/KIM/kim_style.cpp b/src/KIM/kim_style.cpp index 856fb94c9e..814da6b188 100644 --- a/src/KIM/kim_style.cpp +++ b/src/KIM/kim_style.cpp @@ -65,6 +65,7 @@ #include "update.h" #include "universe.h" #include "input.h" +#include "variable.h" #include "fix_store_kim.h" #include "KIM_SimulatorModel.hpp" @@ -78,20 +79,33 @@ void KimStyle::command(int narg, char **arg) { if (narg < 2) error->all(FLERR,"Illegal kim_style command"); + units_from = NULL; + units_to = NULL; + if (strcmp(arg[0],"init") == 0) { - if (narg > 2) error->all(FLERR,"Illegal kim_style command"); if (domain->box_exist) error->all(FLERR,"Must use 'kim_style init' command before " "simulation box is defined"); int len = strlen(arg[1])+1; char *model = new char[len]; strcpy(model,arg[1]); + + int args_done = do_units(narg-2,arg-2); + if (narg > (args_done + 2)) + error->all(FLERR,"Illegal kim_style command"); do_init(model); + do_variables(); } else if (strcmp(arg[0],"define") == 0) { if (!domain->box_exist) error->all(FLERR,"Must use 'kim_style define' command after " "simulation box is defined"); - do_defn(narg-1,arg+1); + int args_done = do_units(narg-1,arg-1); + do_defn(narg - (args_done+1),arg + (args_done+1)); + } else if (strcmp(arg[0],"unit_variables") == 0) { + int args_done = do_units(narg,arg); + if (narg > args_done) + error->all(FLERR,"Illegal kim_style command"); + do_variables(); } else error->all(FLERR,"Illegal kim_style command"); } @@ -113,6 +127,8 @@ void KimStyle::do_init(char *model) FixStoreKIM *fix_store = (FixStoreKIM *) modify->fix[ifix]; fix_store->setptr("model_name", (void *) model); + fix_store->setptr("units_from", (void *) units_from); + fix_store->setptr("units_to", (void *) units_to); int kimerror; KIM::SimulatorModel * simulatorModel; @@ -172,7 +188,6 @@ void KimStyle::do_defn(int narg, char **arg) char *model = NULL; KIM::SimulatorModel *simulatorModel(NULL); - int kimerror; // check if we had a kim_style init command by finding fix STORE/KIM // retrieve model name and pointer to simulator model class instance. @@ -298,3 +313,143 @@ void KimStyle::do_defn(int narg, char **arg) input->one(cmd2.c_str()); } } + +/* ---------------------------------------------------------------------- */ + +int KimStyle::do_units(int narg, char **arg) +{ + // retrieve custom units setting if kim_style had been called before + + int ifix = modify->find_fix("KIM_MODEL_STORE"); + FixStoreKIM *fix_store = NULL; + if (ifix >= 0) { + fix_store = (FixStoreKIM *) modify->fix[ifix]; + units_from = (char *)fix_store->getptr("units_from"); + units_to = (char *)fix_store->getptr("units_to"); + } + + if (narg < 2) return 0; + int iarg=0; + for (iarg = 0; iarg < narg; iarg += 2) { + if (strcmp(arg[iarg],"unit_variables") == 0) { + if (narg > iarg+2) error->all(FLERR,"Illegal kim_style command"); + if (strcmp(arg[iarg+1],"NULL") == 0) { + delete[] units_to; + units_to = NULL; + } else { + int len = strlen(arg[iarg+1])+1; + delete[] units_to; + units_to = new char[len]; + strcpy(units_to,arg[iarg+1]); + } + if (fix_store) fix_store->setptr("units_to",units_to); + } else if (strcmp(arg[iarg],"unit_from") == 0) { + if (narg > iarg+2) error->all(FLERR,"Illegal kim_style command"); + if (strcmp(arg[iarg+1],"NULL") == 0) { + delete[] units_from; + units_from = NULL; + } else { + int len = strlen(arg[iarg+1])+1; + delete[] units_from; + units_from = new char[len]; + strcpy(units_from,arg[iarg+1]); + } + if (fix_store) fix_store->setptr("units_from",units_from); + } else return iarg; + } + return iarg; +} + +/* ---------------------------------------------------------------------- */ + +void KimStyle::do_variables() +{ + char *from, *to; + Variable *variable = input->variable; + + if (units_from) from = units_from; + else from = update->unit_style; + if (units_to) to = units_to; + else to = update->unit_style; + + // refuse convertion from or to reduced units + + if ((strcmp(from,"lj") == 0) || (strcmp(to,"lj") == 0)) + error->all(FLERR,"Cannot set up conversion variables for 'lj' units"); + + // get index to internal style variables. create, if needed. + // default to conversion factor 1.0 for newly created variables + + int v_length, v_mass, v_time; + char *args[3]; + args[1] = (char *)"internal"; + args[2] = (char *)"1.0"; + + args[0] = (char *)"_u_length"; + v_length = variable->find(args[0]); + if (v_length < 0) { + variable->set(3,args); + v_length = variable->find(args[0]); + } + + args[0] = (char *)"_u_mass"; + v_mass = variable->find(args[0]); + if (v_mass < 0) { + variable->set(3,args); + v_mass = variable->find(args[0]); + } + + args[0] = (char *)"_u_time"; + v_time = variable->find(args[0]); + if (v_time < 0) { + variable->set(3,args); + v_time = variable->find(args[0]); + } + + // special case: both unit styles are the same => conversion factor 1.0 + + if (strcmp(from,to) == 0) { + variable->internal_set(v_length,1.0); + variable->internal_set(v_mass,1.0); + variable->internal_set(v_time,1.0); + return; + } + + if (strcmp(from,"real") == 0) { + if (strcmp(to,"metal") == 0) { + variable->internal_set(v_length,1.0); + variable->internal_set(v_mass,1.0); + variable->internal_set(v_time,0.001); + } else { + std::string err("Do not know how to set up conversion variables "); + err += "between '"; + err += from; + err += "' and '"; + err += to; + err += "' units"; + error->all(FLERR,err.c_str()); + } + } else if (strcmp(from,"metal") == 0) { + if (strcmp(to,"real") == 0) { + variable->internal_set(v_length,1.0); + variable->internal_set(v_mass,1.0); + variable->internal_set(v_time,1000.0); + } else { + std::string err("Do not know how to set up conversion variables "); + err += "between '"; + err += from; + err += "' and '"; + err += to; + err += "' units"; + error->all(FLERR,err.c_str()); + } + } else { + std::string err("Do not know how to set up conversion variables "); + err += "between '"; + err += from; + err += "' and '"; + err += to; + err += "' units"; + error->all(FLERR,err.c_str()); + } +} diff --git a/src/KIM/kim_style.h b/src/KIM/kim_style.h index f8c0602beb..36084183ee 100644 --- a/src/KIM/kim_style.h +++ b/src/KIM/kim_style.h @@ -72,8 +72,12 @@ class KimStyle : protected Pointers { KimStyle(class LAMMPS *lmp) : Pointers(lmp) {}; void command(int, char **); private: + char *units_from; + char *units_to; void do_init(char *); void do_defn(int, char **); + int do_units(int, char **); + void do_variables(); }; } -- GitLab From 664b938ed12cafc2fa232a34abccd4d79278a494 Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Mon, 10 Jun 2019 17:45:07 -0400 Subject: [PATCH 043/469] document kim_style changes --- doc/src/kim_style.txt | 26 ++++++++++++++++++++++---- 1 file changed, 22 insertions(+), 4 deletions(-) diff --git a/doc/src/kim_style.txt b/doc/src/kim_style.txt index afa7a19fab..c24cfe8581 100644 --- a/doc/src/kim_style.txt +++ b/doc/src/kim_style.txt @@ -12,15 +12,18 @@ kim_style command :h3 kim_style mode args :pre -mode = {init model} or {define typeargs} +mode = {init model} or {define typeargs} or no mode chosen model = name of the KIM model (KIM potential or KIM simulator model) -typeargs = atom type to species mapping (one entry per atom type) :ul +typeargs = atom type to species mapping (one entry per atom type) +args = {unit_variables unit_style} or {unit_from unit_style} (optional):ul [Examples:] -kim_style init ex_sim_model_Si_mod_tersoff +kim_style init ex_sim_model_Si_mod_tersoff unit_variables metal kim_style define Si Si -kim_style init LennardJones_Ar +kim_style unit_variables real +kim_style init LennardJones_Ar unit_variables metal +kim_style unit_variables real unit_from metal kim_style define Ar :pre [Description:] @@ -47,6 +50,21 @@ for using a selected simulator model. If needed, those settings can be overridden. The second argument to the {kim_style init} command is the KIM model ID. +In both modes, the keywords {unit_variables} and {unit_from} may be +added. They control the values of a set of +"internal style variables"_variable.html that can be used to convert +between different unit styles in LAMMPS. The argument to +each keyword is a LAMMPS unit style or NULL, which means to look up +the unit style from what was set with the "units"_units.html command. +Please note, that KIM simulator models will set their preferred unit style. +By default all conversion variables are set to 1.0. Converting to or +from the "lj" unit style is not supported. The following variables are defined: + +_u_length +_u_mass +_u_time :ul + + The {kim_style define} command will issue commands that will realize the selected model (through generating pair_style and pair_coeff commands, but also other commands, as required). It has to be issued [after] the -- GitLab From 36ebf4d47ab3c6e6263bcdde2a7402089b04e524 Mon Sep 17 00:00:00 2001 From: Andrew Schultz Date: Tue, 11 Jun 2019 10:22:55 -0400 Subject: [PATCH 044/469] Make cmake aware of HMA --- cmake/CMakeLists.txt | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/cmake/CMakeLists.txt b/cmake/CMakeLists.txt index 911b6f0f15..c2356002b2 100644 --- a/cmake/CMakeLists.txt +++ b/cmake/CMakeLists.txt @@ -177,8 +177,8 @@ set(DEFAULT_PACKAGES ASPHERE BODY CLASS2 COLLOID COMPRESS CORESHELL DIPOLE GRANULAR KSPACE LATTE MANYBODY MC MESSAGE MISC MOLECULE PERI POEMS QEQ REPLICA RIGID SHOCK SPIN SNAP SRD KIM PYTHON MSCG MPIIO VORONOI USER-ATC USER-AWPMD USER-BOCS USER-CGDNA USER-MESO USER-CGSDK USER-COLVARS - USER-DIFFRACTION USER-DPD USER-DRUDE USER-EFF USER-FEP USER-H5MD USER-LB - USER-MANIFOLD USER-MEAMC USER-MGPT USER-MISC USER-MOFFF USER-MOLFILE + USER-DIFFRACTION USER-DPD USER-DRUDE USER-EFF USER-FEP USER-H5MD USER-HMA + USER-LB USER-MANIFOLD USER-MEAMC USER-MGPT USER-MISC USER-MOFFF USER-MOLFILE USER-NETCDF USER-PHONON USER-PLUMED USER-PTM USER-QTB USER-REAXC USER-SCAFACOS USER-SDPD USER-SMD USER-SMTBQ USER-SPH USER-TALLY USER-UEF USER-VTK USER-QUIP USER-QMMM USER-YAFF USER-ADIOS) -- GitLab From d9206127fb3bc2309d9260e06644d1025f7545a1 Mon Sep 17 00:00:00 2001 From: Andrew Schultz Date: Wed, 12 Jun 2019 11:40:21 -0400 Subject: [PATCH 045/469] Add hyphen to roundoff, fix false positives --- doc/src/compute_hma.txt | 2 +- doc/utils/sphinx-config/false_positives.txt | 6 ++++++ 2 files changed, 7 insertions(+), 1 deletion(-) diff --git a/doc/src/compute_hma.txt b/doc/src/compute_hma.txt index 340881bf68..c203c281ed 100644 --- a/doc/src/compute_hma.txt +++ b/doc/src/compute_hma.txt @@ -81,7 +81,7 @@ computes the full expression for \(C_V\) except for the \(\left^2\) in the variance term, which can be obtained by passing the {u} keyword; you must add this extra contribution to the \(C_V\) value reported by this compute. The variance term can cause significant -roundoff error when computing \(C_V\). To address this, the {anharmonic} +round-off error when computing \(C_V\). To address this, the {anharmonic} keyword can be passed and/or the output format can be specified with more digits. diff --git a/doc/utils/sphinx-config/false_positives.txt b/doc/utils/sphinx-config/false_positives.txt index 7b7c4d11b2..4d3ea22491 100644 --- a/doc/utils/sphinx-config/false_positives.txt +++ b/doc/utils/sphinx-config/false_positives.txt @@ -98,6 +98,7 @@ antisymmetry anton Antonelli api +Apoorva Appl Apu arccos @@ -1064,6 +1065,7 @@ Hilger histo histogrammed histogramming +hma hmaktulga hoc Hochbruck @@ -1320,6 +1322,7 @@ kmax Kmax Knizhnik knl +Kofke Kohlmeyer Kohn kokkos @@ -1701,6 +1704,7 @@ Morteza Mosayebi Moseler Moskalev +Moustafa mov mpi MPI @@ -2200,6 +2204,7 @@ PTM ptr pu purdue +Purohit pushstore pvar pw @@ -2413,6 +2418,7 @@ Ryckaert Rycroft Rydbergs Rz +Sabry saddlebrown Sadigh saed -- GitLab From 56ae35fb1a4e23aff8238c7baccd747667f3a962 Mon Sep 17 00:00:00 2001 From: Andrew Schultz Date: Wed, 12 Jun 2019 13:09:33 -0400 Subject: [PATCH 046/469] Address feedback on PR #1503 --- src/USER-HMA/compute_hma.cpp | 47 ++++++++++++++++++----------------- src/pair.cpp | 2 +- src/pair_lj_smooth_linear.cpp | 4 +-- 3 files changed, 27 insertions(+), 26 deletions(-) diff --git a/src/USER-HMA/compute_hma.cpp b/src/USER-HMA/compute_hma.cpp index ad86577ba1..8edff5aa59 100644 --- a/src/USER-HMA/compute_hma.cpp +++ b/src/USER-HMA/compute_hma.cpp @@ -11,9 +11,9 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ +#include +#include #include -#include -#include #include "compute_hma.h" #include "atom.h" #include "update.h" @@ -100,25 +100,29 @@ ComputeHMA::ComputeHMA(LAMMPS *lmp, int narg, char **arg) : computeU = computeP = computeCv = -1; returnAnharmonic = 0; - std::vector extvec; + size_vector = 0; + memory->create(extlist, 3, "hma:extlist"); for (int iarg=4; iarg-1) continue; + computeU = size_vector; + extlist[size_vector] = 1; } - else if (!strcasecmp(arg[iarg], "p")) { + else if (!strcmp(arg[iarg], "p")) { if (iarg+2 > narg) error->all(FLERR,"Illegal fix hma command"); - computeP = extvec.size(); + if (computeP>-1) continue; + computeP = size_vector; deltaPcap = force->numeric(FLERR, arg[iarg+1]); - extvec.push_back(0); + extlist[size_vector] = 0; iarg++; } - else if (!strcasecmp(arg[iarg], "cv")) { - computeCv = extvec.size(); + else if (!strcmp(arg[iarg], "cv")) { + if (computeCv>-1) continue; + computeCv = size_vector; comm_forward = 3; - extvec.push_back(1); + extlist[size_vector] = 1; } - else if (!strcasecmp(arg[iarg], "anharmonic")) { + else if (!strcmp(arg[iarg], "anharmonic")) { // the first time we're called, we'll grab lattice pressure and energy returnAnharmonic = -1; } @@ -127,18 +131,16 @@ ComputeHMA::ComputeHMA(LAMMPS *lmp, int narg, char **arg) : } } - if (extvec.size() == 0) { + if (size_vector == 0) { error->all(FLERR,"Illegal fix hma command"); } - size_vector = extvec.size(); - memory->create(vector, size_vector, "hma::vector"); - extlist = new int[size_vector]; - for (int i=0; igrow(extlist, size_vector, "hma:extlist"); } + memory->create(vector, size_vector, "hma:vector"); if (computeU>-1 || computeCv>-1) { - peflag = 1; + peflag = 1; } if (computeP>-1) { pressflag = 1; @@ -156,7 +158,7 @@ ComputeHMA::~ComputeHMA() delete [] id_fix; delete [] id_temp; - delete [] extlist; + memory->destroy(extlist); memory->destroy(vector); memory->destroy(deltaR); } @@ -184,11 +186,10 @@ void ComputeHMA::setup() if (temperat==NULL) error->all(FLERR,"Could not find compute hma temperature ID"); finaltemp = * temperat; - // set fix which stores original atom coords int ifix2 = modify->find_fix(id_fix); - if (ifix2 < 0) error->all(FLERR,"Could not find compute hma ID"); + if (ifix2 < 0) error->all(FLERR,"Could not find hma store fix ID"); fix = (FixStore *) modify->fix[ifix2]; } diff --git a/src/pair.cpp b/src/pair.cpp index c393e7b12b..15efa62c59 100644 --- a/src/pair.cpp +++ b/src/pair.cpp @@ -307,7 +307,7 @@ void Pair::init_style() specific pair style can override this function ------------------------------------------------------------------------- */ -void Pair::init_list(int which, NeighList *ptr) +void Pair::init_list(int /*which*/, NeighList *ptr) { list = ptr; } diff --git a/src/pair_lj_smooth_linear.cpp b/src/pair_lj_smooth_linear.cpp index 370caeddf7..d2bb6a1cc4 100644 --- a/src/pair_lj_smooth_linear.cpp +++ b/src/pair_lj_smooth_linear.cpp @@ -325,7 +325,7 @@ void PairLJSmoothLinear::read_restart_settings(FILE *fp) /* ---------------------------------------------------------------------- */ -double PairLJSmoothLinear::single(int i, int j, int itype, int jtype, +double PairLJSmoothLinear::single(int /*i*/, int /*j*/, int itype, int jtype, double rsq, double factor_coul, double factor_lj, double &fforce) @@ -347,7 +347,7 @@ double PairLJSmoothLinear::single(int i, int j, int itype, int jtype, return factor_lj*philj; } -double PairLJSmoothLinear::single2(int i, int j, int itype, int jtype, double rsq, +double PairLJSmoothLinear::single2(int /*i*/, int /*j*/, int itype, int jtype, double rsq, double delr[3], double factor_coul, double factor_lj, double &fforce, double d2u[6]) { -- GitLab From 053ac654c31f33c97a3648fc2ef0864acff84de2 Mon Sep 17 00:00:00 2001 From: Andrew Schultz Date: Wed, 12 Jun 2019 20:32:22 -0400 Subject: [PATCH 047/469] Install.sh not needed --- src/USER-HMA/Install.sh | 31 ------------------------------- 1 file changed, 31 deletions(-) delete mode 100644 src/USER-HMA/Install.sh diff --git a/src/USER-HMA/Install.sh b/src/USER-HMA/Install.sh deleted file mode 100644 index 1f8f418ca2..0000000000 --- a/src/USER-HMA/Install.sh +++ /dev/null @@ -1,31 +0,0 @@ -# Install/Uninstall package files in LAMMPS -# mode = 0/1/2 for uninstall/install/update - -mode=$1 - -# enforce using portable C locale -LC_ALL=C -export LC_ALL - -# arg1 = file, arg2 = file it depends on - -action () { - if (test $mode = 0) then - rm -f ../$1 - elif (! cmp -s $1 ../$1) then - if (test -z "$2" || test -e ../$2) then - cp $1 .. - if (test $mode = 2) then - echo " updating src/$1" - fi - fi - elif (test -n "$2") then - if (test ! -e ../$2) then - rm -f ../$1 - fi - fi -} - -# package files without dependencies -action compute_hma.h -action compute_hma.cpp -- GitLab From 7fab12c36f847efddd6d6e6c0d1939c0036be0eb Mon Sep 17 00:00:00 2001 From: Julien Devemy Date: Fri, 14 Jun 2019 16:53:26 +0200 Subject: [PATCH 048/469] Add keyword hybridpair for compute_pressure only on a certain pair of a hybrid pair --- src/compute_pressure.cpp | 17 +++++++++++++++++ src/compute_pressure.h | 1 + src/pair_hybrid.h | 1 + 3 files changed, 19 insertions(+) diff --git a/src/compute_pressure.cpp b/src/compute_pressure.cpp index dde02a5aed..8381e04fa8 100644 --- a/src/compute_pressure.cpp +++ b/src/compute_pressure.cpp @@ -22,6 +22,7 @@ #include "fix.h" #include "force.h" #include "pair.h" +#include "pair_hybrid.h" #include "bond.h" #include "angle.h" #include "dihedral.h" @@ -66,6 +67,7 @@ ComputePressure::ComputePressure(LAMMPS *lmp, int narg, char **arg) : // process optional args + hybridpairflag = 0; if (narg == 4) { keflag = 1; pairflag = 1; @@ -79,6 +81,8 @@ ComputePressure::ComputePressure(LAMMPS *lmp, int narg, char **arg) : int iarg = 4; while (iarg < narg) { if (strcmp(arg[iarg],"ke") == 0) keflag = 1; + else if (strcmp(arg[iarg],"hybridpair") == 0) + hybridpairflag = force->inumeric(FLERR, arg[++iarg]); else if (strcmp(arg[iarg],"pair") == 0) pairflag = 1; else if (strcmp(arg[iarg],"bond") == 0) bondflag = 1; else if (strcmp(arg[iarg],"angle") == 0) angleflag = 1; @@ -140,6 +144,12 @@ void ComputePressure::init() nvirial = 0; vptr = NULL; + if (hybridpairflag > 0 && force->pair) { + if (strstr(force->pair_style, "hybrid")) { + PairHybrid *ph = (PairHybrid *) force->pair; + if (hybridpairflag <= ph->nstyles) nvirial++; + } + } if (pairflag && force->pair) nvirial++; if (bondflag && atom->molecular && force->bond) nvirial++; if (angleflag && atom->molecular && force->angle) nvirial++; @@ -152,6 +162,13 @@ void ComputePressure::init() if (nvirial) { vptr = new double*[nvirial]; nvirial = 0; + if (hybridpairflag > 0 && force->pair) { + if (strstr(force->pair_style, "hybrid")) { + PairHybrid *ph = (PairHybrid *) force->pair; + if (hybridpairflag <= ph->nstyles) + vptr[nvirial++] = ph->styles[hybridpairflag-1]->virial; + } + } if (pairflag && force->pair) vptr[nvirial++] = force->pair->virial; if (bondflag && force->bond) vptr[nvirial++] = force->bond->virial; if (angleflag && force->angle) vptr[nvirial++] = force->angle->virial; diff --git a/src/compute_pressure.h b/src/compute_pressure.h index a59a64e634..3259377bd8 100644 --- a/src/compute_pressure.h +++ b/src/compute_pressure.h @@ -41,6 +41,7 @@ class ComputePressure : public Compute { Compute *temperature; char *id_temp; double virial[6]; + int hybridpairflag; int keflag,pairflag,bondflag,angleflag,dihedralflag,improperflag; int fixflag,kspaceflag; diff --git a/src/pair_hybrid.h b/src/pair_hybrid.h index e313e16f18..1e0130ba3d 100644 --- a/src/pair_hybrid.h +++ b/src/pair_hybrid.h @@ -33,6 +33,7 @@ class PairHybrid : public Pair { friend class Respa; friend class Info; friend class PairDeprecated; + friend class ComputePressure; public: PairHybrid(class LAMMPS *); virtual ~PairHybrid(); -- GitLab From db3de8a31bbf16063cf19b6e71939aa933cbeb39 Mon Sep 17 00:00:00 2001 From: Andrew Schultz Date: Fri, 14 Jun 2019 13:48:31 -0400 Subject: [PATCH 049/469] rename Pair::single to single2nd --- src/USER-HMA/compute_hma.cpp | 2 +- src/pair.h | 2 +- src/pair_lj_smooth_linear.cpp | 2 +- src/pair_lj_smooth_linear.h | 2 +- 4 files changed, 4 insertions(+), 4 deletions(-) diff --git a/src/USER-HMA/compute_hma.cpp b/src/USER-HMA/compute_hma.cpp index 8edff5aa59..75ba335879 100644 --- a/src/USER-HMA/compute_hma.cpp +++ b/src/USER-HMA/compute_hma.cpp @@ -318,7 +318,7 @@ void ComputeHMA::compute_vector() if (rsq < cutsq[itype][jtype]) { double* jdr = deltaR[j]; double fforce, d2u[6]; - force->pair->single2(i, j, itype, jtype, rsq, delr, factor_coul, factor_lj, fforce, d2u); + force->pair->single2nd(i, j, itype, jtype, rsq, delr, factor_coul, factor_lj, fforce, d2u); int m = 0; for (int k=0; k<3; k++) { double a = fac; diff --git a/src/pair.h b/src/pair.h index 3947f4cd81..ae5bebf23a 100644 --- a/src/pair.h +++ b/src/pair.h @@ -149,7 +149,7 @@ class Pair : protected Pointers { void pairTensor(double fforce, double dfac, double delr[3], double phiTensor[6]); - virtual double single2(int, int, int, int, + virtual double single2nd(int, int, int, int, double, double[3], double, double, double& fforce, double d2u[6]) { fforce = 0.0; diff --git a/src/pair_lj_smooth_linear.cpp b/src/pair_lj_smooth_linear.cpp index d2bb6a1cc4..57f72dc28e 100644 --- a/src/pair_lj_smooth_linear.cpp +++ b/src/pair_lj_smooth_linear.cpp @@ -347,7 +347,7 @@ double PairLJSmoothLinear::single(int /*i*/, int /*j*/, int itype, int jtype, return factor_lj*philj; } -double PairLJSmoothLinear::single2(int /*i*/, int /*j*/, int itype, int jtype, double rsq, +double PairLJSmoothLinear::single2nd(int /*i*/, int /*j*/, int itype, int jtype, double rsq, double delr[3], double factor_coul, double factor_lj, double &fforce, double d2u[6]) { diff --git a/src/pair_lj_smooth_linear.h b/src/pair_lj_smooth_linear.h index 9cee9f2951..a43cbc23e2 100644 --- a/src/pair_lj_smooth_linear.h +++ b/src/pair_lj_smooth_linear.h @@ -38,7 +38,7 @@ class PairLJSmoothLinear : public Pair { void write_restart_settings(FILE *); void read_restart_settings(FILE *); double single(int, int, int, int, double, double, double, double &); - double single2(int, int, int, int, double, double[3], double, double, double&, double[6]); + double single2nd(int, int, int, int, double, double[3], double, double, double&, double[6]); protected: double cut_global; -- GitLab From 3611cfdaf8c153750ce8cc45ac239c1145eb0a2b Mon Sep 17 00:00:00 2001 From: mkanski Date: Fri, 14 Jun 2019 19:58:31 +0200 Subject: [PATCH 050/469] All styles support setting molecules' orientation --- doc/src/create_atoms.txt | 5 ++--- src/create_atoms.cpp | 10 ++++++---- 2 files changed, 8 insertions(+), 7 deletions(-) diff --git a/doc/src/create_atoms.txt b/doc/src/create_atoms.txt index d80e2d45f1..e673849793 100644 --- a/doc/src/create_atoms.txt +++ b/doc/src/create_atoms.txt @@ -242,9 +242,8 @@ write_dump all atom sinusoid.lammpstrj :pre :c,image(JPG/sinusoid_small.jpg,JPG/sinusoid.jpg) -The {rotate} keyword can only be used with the {single} style and -when adding a single molecule. It allows to specify the orientation -at which the molecule is inserted. The axis of rotation is +The {rotate} keyword allows to specify the orientation +at which molecules are inserted. The axis of rotation is determined by the rotation vector (Rx,Ry,Rz) that goes through the insertion point. The specified {theta} determines the angle of rotation around that axis. Note that the direction of rotation for diff --git a/src/create_atoms.cpp b/src/create_atoms.cpp index 52e4256fca..8869171115 100644 --- a/src/create_atoms.cpp +++ b/src/create_atoms.cpp @@ -176,8 +176,6 @@ void CreateAtoms::command(int narg, char **arg) } else error->all(FLERR,"Illegal create_atoms command"); iarg += 3; } else if (strcmp(arg[iarg],"rotate") == 0) { - if (style != SINGLE) - error->all(FLERR,"Cannot use create_atoms rotate unless single style"); if (iarg+5 > narg) error->all(FLERR,"Illegal create_atoms command"); double thetaone; double axisone[3]; @@ -678,7 +676,9 @@ void CreateAtoms::add_random() coord[1] >= sublo[1] && coord[1] < subhi[1] && coord[2] >= sublo[2] && coord[2] < subhi[2]) { if (mode == ATOM) atom->avec->create_atom(ntype,xone); - else add_molecule(xone); + else if (quatone[0] == 0 && quatone[1] == 0 && quatone[2] == 0) + add_molecule(xone); + else add_molecule(xone, quatone); } } @@ -832,7 +832,9 @@ void CreateAtoms::add_lattice() // add the atom or entire molecule to my list of atoms if (mode == ATOM) atom->avec->create_atom(basistype[m],x); - else add_molecule(x); + else if (quatone[0] == 0 && quatone[1] == 0 && quatone[2] == 0) + add_molecule(x); + else add_molecule(x,quatone); } } } -- GitLab From 343bc728e205f9e33a739aac149c087faec093ee Mon Sep 17 00:00:00 2001 From: Andrew Schultz Date: Fri, 14 Jun 2019 14:11:15 -0400 Subject: [PATCH 051/469] Cleanup: s/fix/compute/ and properly increment size_vector --- src/USER-HMA/compute_hma.cpp | 9 ++++++--- 1 file changed, 6 insertions(+), 3 deletions(-) diff --git a/src/USER-HMA/compute_hma.cpp b/src/USER-HMA/compute_hma.cpp index 75ba335879..9f6a976332 100644 --- a/src/USER-HMA/compute_hma.cpp +++ b/src/USER-HMA/compute_hma.cpp @@ -107,13 +107,15 @@ ComputeHMA::ComputeHMA(LAMMPS *lmp, int narg, char **arg) : if (computeU>-1) continue; computeU = size_vector; extlist[size_vector] = 1; + size_vector++; } else if (!strcmp(arg[iarg], "p")) { - if (iarg+2 > narg) error->all(FLERR,"Illegal fix hma command"); + if (iarg+2 > narg) error->all(FLERR,"Illegal compute hma command"); if (computeP>-1) continue; computeP = size_vector; deltaPcap = force->numeric(FLERR, arg[iarg+1]); extlist[size_vector] = 0; + size_vector++; iarg++; } else if (!strcmp(arg[iarg], "cv")) { @@ -121,18 +123,19 @@ ComputeHMA::ComputeHMA(LAMMPS *lmp, int narg, char **arg) : computeCv = size_vector; comm_forward = 3; extlist[size_vector] = 1; + size_vector++; } else if (!strcmp(arg[iarg], "anharmonic")) { // the first time we're called, we'll grab lattice pressure and energy returnAnharmonic = -1; } else { - error->all(FLERR,"Illegal fix hma command"); + error->all(FLERR,"Illegal compute hma command"); } } if (size_vector == 0) { - error->all(FLERR,"Illegal fix hma command"); + error->all(FLERR,"Illegal compute hma command"); } if (size_vector<3) { memory->grow(extlist, size_vector, "hma:extlist"); -- GitLab From 622cfd571818edc57f1b91443ed38c49f2c24e73 Mon Sep 17 00:00:00 2001 From: Andrew Schultz Date: Fri, 14 Jun 2019 14:12:09 -0400 Subject: [PATCH 052/469] Add single2nd_enable flag for Pair --- src/USER-HMA/compute_hma.cpp | 7 +++++++ src/pair.cpp | 1 + src/pair.h | 1 + src/pair_lj_smooth_linear.cpp | 4 +++- 4 files changed, 12 insertions(+), 1 deletion(-) diff --git a/src/USER-HMA/compute_hma.cpp b/src/USER-HMA/compute_hma.cpp index 9f6a976332..bedcda769d 100644 --- a/src/USER-HMA/compute_hma.cpp +++ b/src/USER-HMA/compute_hma.cpp @@ -169,6 +169,13 @@ ComputeHMA::~ComputeHMA() /* ---------------------------------------------------------------------- */ void ComputeHMA::init() { + if (computeCv>-1) { + if (force->pair == NULL) + error->all(FLERR,"No pair style is defined for compute hma cv"); + if (force->pair->single_enable == 0) + error->all(FLERR,"Pair style does not support compute hma cv"); + } + int irequest = neighbor->request(this,instance_me); neighbor->requests[irequest]->pair = 0; neighbor->requests[irequest]->compute = 1; diff --git a/src/pair.cpp b/src/pair.cpp index 15efa62c59..448df7f511 100644 --- a/src/pair.cpp +++ b/src/pair.cpp @@ -60,6 +60,7 @@ Pair::Pair(LAMMPS *lmp) : Pointers(lmp) comm_forward = comm_reverse = comm_reverse_off = 0; single_enable = 1; + single2nd_enable = 0; restartinfo = 1; respa_enable = 0; one_coeff = 0; diff --git a/src/pair.h b/src/pair.h index ae5bebf23a..d831e3010e 100644 --- a/src/pair.h +++ b/src/pair.h @@ -46,6 +46,7 @@ class Pair : protected Pointers { int comm_reverse_off; // size of reverse comm even if newton off int single_enable; // 1 if single() routine exists + int single2nd_enable; // 1 if single2nd() routine exists int restartinfo; // 1 if pair style writes restart info int respa_enable; // 1 if inner/middle/outer rRESPA routines int one_coeff; // 1 if allows only one coeff * * call diff --git a/src/pair_lj_smooth_linear.cpp b/src/pair_lj_smooth_linear.cpp index 57f72dc28e..0aa19570f2 100644 --- a/src/pair_lj_smooth_linear.cpp +++ b/src/pair_lj_smooth_linear.cpp @@ -30,7 +30,9 @@ using namespace LAMMPS_NS; /* ---------------------------------------------------------------------- */ -PairLJSmoothLinear::PairLJSmoothLinear(LAMMPS *lmp) : Pair(lmp) {} +PairLJSmoothLinear::PairLJSmoothLinear(LAMMPS *lmp) : Pair(lmp) { + single2nd_enable = 1; +} /* ---------------------------------------------------------------------- */ -- GitLab From 959da9de013d29d9e58bb4d2c4b6d8a48308bdc5 Mon Sep 17 00:00:00 2001 From: Rupert Nash Date: Sat, 16 Feb 2019 14:49:44 +0000 Subject: [PATCH 053/469] Create a compute for the momentum of a group of atoms --- src/Makefile.list | 4 +-- src/compute_momentum.cpp | 59 ++++++++++++++++++++++++++++++++++++++++ src/compute_momentum.h | 36 ++++++++++++++++++++++++ 3 files changed, 97 insertions(+), 2 deletions(-) create mode 100644 src/compute_momentum.cpp create mode 100644 src/compute_momentum.h diff --git a/src/Makefile.list b/src/Makefile.list index 65bbebca09..6e4c9726a6 100644 --- a/src/Makefile.list +++ b/src/Makefile.list @@ -7,9 +7,9 @@ SHELL = /bin/sh ROOT = lmp EXE = $(ROOT)_$@ -SRC = angle.cpp angle_charmm.cpp angle_cosine.cpp angle_cosine_delta.cpp angle_cosine_squared.cpp angle_harmonic.cpp angle_hybrid.cpp angle_table.cpp atom.cpp atom_vec.cpp atom_vec_angle.cpp atom_vec_atomic.cpp atom_vec_bond.cpp atom_vec_charge.cpp atom_vec_full.cpp atom_vec_hybrid.cpp atom_vec_molecular.cpp bond.cpp bond_fene.cpp bond_fene_expand.cpp bond_harmonic.cpp bond_hybrid.cpp bond_morse.cpp bond_nonlinear.cpp bond_quartic.cpp bond_table.cpp change_box.cpp comm.cpp compute.cpp compute_angle_local.cpp compute_bond_local.cpp compute_centro_atom.cpp compute_cna_atom.cpp compute_com.cpp compute_com_molecule.cpp compute_coord_atom.cpp compute_dihedral_local.cpp compute_displace_atom.cpp compute_erotate_sphere.cpp compute_group_group.cpp compute_gyration.cpp compute_gyration_molecule.cpp compute_heat_flux.cpp compute_improper_local.cpp compute_ke.cpp compute_ke_atom.cpp compute_msd.cpp compute_msd_molecule.cpp compute_pair_local.cpp compute_pe.cpp compute_pe_atom.cpp compute_pressure.cpp compute_property_atom.cpp compute_property_local.cpp compute_property_molecule.cpp compute_rdf.cpp compute_reduce.cpp compute_reduce_region.cpp compute_stress_atom.cpp compute_temp.cpp compute_temp_com.cpp compute_temp_deform.cpp compute_temp_partial.cpp compute_temp_profile.cpp compute_temp_ramp.cpp compute_temp_region.cpp compute_temp_sphere.cpp create_atoms.cpp create_box.cpp delete_atoms.cpp delete_bonds.cpp dihedral.cpp dihedral_charmm.cpp dihedral_harmonic.cpp dihedral_helix.cpp dihedral_hybrid.cpp dihedral_multi_harmonic.cpp dihedral_opls.cpp displace_atoms.cpp displace_box.cpp domain.cpp dump.cpp dump_atom.cpp dump_cfg.cpp dump_custom.cpp dump_dcd.cpp dump_local.cpp dump_xyz.cpp error.cpp ewald.cpp fft3d.cpp fft3d_wrap.cpp finish.cpp fix.cpp fix_adapt.cpp fix_addforce.cpp fix_ave_atom.cpp fix_ave_correlate.cpp fix_ave_histo.cpp fix_ave_spatial.cpp fix_ave_time.cpp fix_aveforce.cpp fix_bond_break.cpp fix_bond_create.cpp fix_bond_swap.cpp fix_box_relax.cpp fix_deform.cpp fix_deposit.cpp fix_drag.cpp fix_dt_reset.cpp fix_efield.cpp fix_enforce2d.cpp fix_evaporate.cpp fix_gravity.cpp fix_heat.cpp fix_indent.cpp fix_langevin.cpp fix_lineforce.cpp fix_minimize.cpp fix_momentum.cpp fix_move.cpp fix_nh.cpp fix_nh_sphere.cpp fix_nph.cpp fix_nph_sphere.cpp fix_npt.cpp fix_npt_sphere.cpp fix_nve.cpp fix_nve_limit.cpp fix_nve_noforce.cpp fix_nve_sphere.cpp fix_nvt.cpp fix_nvt_sllod.cpp fix_nvt_sphere.cpp fix_orient_fcc.cpp fix_planeforce.cpp fix_press_berendsen.cpp fix_print.cpp fix_qeq_comb.cpp fix_recenter.cpp fix_respa.cpp fix_rigid.cpp fix_rigid_nve.cpp fix_rigid_nvt.cpp fix_setforce.cpp fix_shake.cpp fix_shear_history.cpp fix_spring.cpp fix_spring_rg.cpp fix_spring_self.cpp fix_store_force.cpp fix_store_state.cpp fix_temp_berendsen.cpp fix_temp_rescale.cpp fix_thermal_conductivity.cpp fix_tmd.cpp fix_ttm.cpp fix_viscosity.cpp fix_viscous.cpp fix_wall.cpp fix_wall_harmonic.cpp fix_wall_lj126.cpp fix_wall_lj93.cpp fix_wall_reflect.cpp fix_wall_region.cpp force.cpp group.cpp improper.cpp improper_cvff.cpp improper_harmonic.cpp improper_hybrid.cpp input.cpp integrate.cpp kspace.cpp lammps.cpp lattice.cpp library.cpp main.cpp memory.cpp min.cpp min_cg.cpp min_hftn.cpp min_linesearch.cpp min_sd.cpp minimize.cpp modify.cpp neigh_bond.cpp neigh_derive.cpp neigh_full.cpp neigh_gran.cpp neigh_half_bin.cpp neigh_half_multi.cpp neigh_half_nsq.cpp neigh_list.cpp neigh_request.cpp neigh_respa.cpp neigh_stencil.cpp neighbor.cpp output.cpp pack.cpp pair.cpp pair_airebo.cpp pair_born_coul_long.cpp pair_buck.cpp pair_buck_coul_cut.cpp pair_buck_coul_long.cpp pair_comb.cpp pair_coul_cut.cpp pair_coul_debye.cpp pair_coul_long.cpp pair_dpd.cpp pair_dpd_tstat.cpp pair_eam.cpp pair_eam_alloy.cpp pair_eam_fs.cpp pair_eim.cpp pair_hybrid.cpp pair_hybrid_overlay.cpp pair_lj96_cut.cpp pair_lj_charmm_coul_charmm.cpp pair_lj_charmm_coul_charmm_implicit.cpp pair_lj_charmm_coul_long.cpp pair_lj_cut.cpp pair_lj_cut_coul_cut.cpp pair_lj_cut_coul_debye.cpp pair_lj_cut_coul_long.cpp pair_lj_cut_coul_long_tip4p.cpp pair_lj_expand.cpp pair_lj_gromacs.cpp pair_lj_gromacs_coul_gromacs.cpp pair_lj_smooth.cpp pair_morse.cpp pair_soft.cpp pair_sw.cpp pair_table.cpp pair_tersoff.cpp pair_tersoff_zbl.cpp pair_yukawa.cpp pppm.cpp pppm_tip4p.cpp random_mars.cpp random_park.cpp read_data.cpp read_restart.cpp region.cpp region_block.cpp region_cone.cpp region_cylinder.cpp region_intersect.cpp region_plane.cpp region_prism.cpp region_sphere.cpp region_union.cpp remap.cpp remap_wrap.cpp replicate.cpp respa.cpp run.cpp set.cpp shell.cpp special.cpp temper.cpp thermo.cpp timer.cpp universe.cpp update.cpp variable.cpp velocity.cpp verlet.cpp write_restart.cpp +SRC = angle.cpp angle_charmm.cpp angle_cosine.cpp angle_cosine_delta.cpp angle_cosine_squared.cpp angle_harmonic.cpp angle_hybrid.cpp angle_table.cpp atom.cpp atom_vec.cpp atom_vec_angle.cpp atom_vec_atomic.cpp atom_vec_bond.cpp atom_vec_charge.cpp atom_vec_full.cpp atom_vec_hybrid.cpp atom_vec_molecular.cpp bond.cpp bond_fene.cpp bond_fene_expand.cpp bond_harmonic.cpp bond_hybrid.cpp bond_morse.cpp bond_nonlinear.cpp bond_quartic.cpp bond_table.cpp change_box.cpp comm.cpp compute.cpp compute_angle_local.cpp compute_bond_local.cpp compute_centro_atom.cpp compute_cna_atom.cpp compute_com.cpp compute_com_molecule.cpp compute_coord_atom.cpp compute_dihedral_local.cpp compute_displace_atom.cpp compute_erotate_sphere.cpp compute_group_group.cpp compute_gyration.cpp compute_gyration_molecule.cpp compute_heat_flux.cpp compute_improper_local.cpp compute_ke.cpp compute_ke_atom.cpp compute_momentum.cpp compute_msd.cpp compute_msd_molecule.cpp compute_pair_local.cpp compute_pe.cpp compute_pe_atom.cpp compute_pressure.cpp compute_property_atom.cpp compute_property_local.cpp compute_property_molecule.cpp compute_rdf.cpp compute_reduce.cpp compute_reduce_region.cpp compute_stress_atom.cpp compute_temp.cpp compute_temp_com.cpp compute_temp_deform.cpp compute_temp_partial.cpp compute_temp_profile.cpp compute_temp_ramp.cpp compute_temp_region.cpp compute_temp_sphere.cpp create_atoms.cpp create_box.cpp delete_atoms.cpp delete_bonds.cpp dihedral.cpp dihedral_charmm.cpp dihedral_harmonic.cpp dihedral_helix.cpp dihedral_hybrid.cpp dihedral_multi_harmonic.cpp dihedral_opls.cpp displace_atoms.cpp displace_box.cpp domain.cpp dump.cpp dump_atom.cpp dump_cfg.cpp dump_custom.cpp dump_dcd.cpp dump_local.cpp dump_xyz.cpp error.cpp ewald.cpp fft3d.cpp fft3d_wrap.cpp finish.cpp fix.cpp fix_adapt.cpp fix_addforce.cpp fix_ave_atom.cpp fix_ave_correlate.cpp fix_ave_histo.cpp fix_ave_spatial.cpp fix_ave_time.cpp fix_aveforce.cpp fix_bond_break.cpp fix_bond_create.cpp fix_bond_swap.cpp fix_box_relax.cpp fix_deform.cpp fix_deposit.cpp fix_drag.cpp fix_dt_reset.cpp fix_efield.cpp fix_enforce2d.cpp fix_evaporate.cpp fix_gravity.cpp fix_heat.cpp fix_indent.cpp fix_langevin.cpp fix_lineforce.cpp fix_minimize.cpp fix_momentum.cpp fix_move.cpp fix_nh.cpp fix_nh_sphere.cpp fix_nph.cpp fix_nph_sphere.cpp fix_npt.cpp fix_npt_sphere.cpp fix_nve.cpp fix_nve_limit.cpp fix_nve_noforce.cpp fix_nve_sphere.cpp fix_nvt.cpp fix_nvt_sllod.cpp fix_nvt_sphere.cpp fix_orient_fcc.cpp fix_planeforce.cpp fix_press_berendsen.cpp fix_print.cpp fix_qeq_comb.cpp fix_recenter.cpp fix_respa.cpp fix_rigid.cpp fix_rigid_nve.cpp fix_rigid_nvt.cpp fix_setforce.cpp fix_shake.cpp fix_shear_history.cpp fix_spring.cpp fix_spring_rg.cpp fix_spring_self.cpp fix_store_force.cpp fix_store_state.cpp fix_temp_berendsen.cpp fix_temp_rescale.cpp fix_thermal_conductivity.cpp fix_tmd.cpp fix_ttm.cpp fix_viscosity.cpp fix_viscous.cpp fix_wall.cpp fix_wall_harmonic.cpp fix_wall_lj126.cpp fix_wall_lj93.cpp fix_wall_reflect.cpp fix_wall_region.cpp force.cpp group.cpp improper.cpp improper_cvff.cpp improper_harmonic.cpp improper_hybrid.cpp input.cpp integrate.cpp kspace.cpp lammps.cpp lattice.cpp library.cpp main.cpp memory.cpp min.cpp min_cg.cpp min_hftn.cpp min_linesearch.cpp min_sd.cpp minimize.cpp modify.cpp neigh_bond.cpp neigh_derive.cpp neigh_full.cpp neigh_gran.cpp neigh_half_bin.cpp neigh_half_multi.cpp neigh_half_nsq.cpp neigh_list.cpp neigh_request.cpp neigh_respa.cpp neigh_stencil.cpp neighbor.cpp output.cpp pack.cpp pair.cpp pair_airebo.cpp pair_born_coul_long.cpp pair_buck.cpp pair_buck_coul_cut.cpp pair_buck_coul_long.cpp pair_comb.cpp pair_coul_cut.cpp pair_coul_debye.cpp pair_coul_long.cpp pair_dpd.cpp pair_dpd_tstat.cpp pair_eam.cpp pair_eam_alloy.cpp pair_eam_fs.cpp pair_eim.cpp pair_hybrid.cpp pair_hybrid_overlay.cpp pair_lj96_cut.cpp pair_lj_charmm_coul_charmm.cpp pair_lj_charmm_coul_charmm_implicit.cpp pair_lj_charmm_coul_long.cpp pair_lj_cut.cpp pair_lj_cut_coul_cut.cpp pair_lj_cut_coul_debye.cpp pair_lj_cut_coul_long.cpp pair_lj_cut_coul_long_tip4p.cpp pair_lj_expand.cpp pair_lj_gromacs.cpp pair_lj_gromacs_coul_gromacs.cpp pair_lj_smooth.cpp pair_morse.cpp pair_soft.cpp pair_sw.cpp pair_table.cpp pair_tersoff.cpp pair_tersoff_zbl.cpp pair_yukawa.cpp pppm.cpp pppm_tip4p.cpp random_mars.cpp random_park.cpp read_data.cpp read_restart.cpp region.cpp region_block.cpp region_cone.cpp region_cylinder.cpp region_intersect.cpp region_plane.cpp region_prism.cpp region_sphere.cpp region_union.cpp remap.cpp remap_wrap.cpp replicate.cpp respa.cpp run.cpp set.cpp shell.cpp special.cpp temper.cpp thermo.cpp timer.cpp universe.cpp update.cpp variable.cpp velocity.cpp verlet.cpp write_restart.cpp -INC = angle.h angle_charmm.h angle_cosine.h angle_cosine_delta.h angle_cosine_squared.h angle_harmonic.h angle_hybrid.h angle_table.h atom.h atom_vec.h atom_vec_angle.h atom_vec_atomic.h atom_vec_bond.h atom_vec_charge.h atom_vec_full.h atom_vec_hybrid.h atom_vec_molecular.h bond.h bond_fene.h bond_fene_expand.h bond_harmonic.h bond_hybrid.h bond_morse.h bond_nonlinear.h bond_quartic.h bond_table.h change_box.h comm.h compute.h compute_angle_local.h compute_bond_local.h compute_centro_atom.h compute_cna_atom.h compute_com.h compute_com_molecule.h compute_coord_atom.h compute_dihedral_local.h compute_displace_atom.h compute_erotate_sphere.h compute_group_group.h compute_gyration.h compute_gyration_molecule.h compute_heat_flux.h compute_improper_local.h compute_ke.h compute_ke_atom.h compute_msd.h compute_msd_molecule.h compute_pair_local.h compute_pe.h compute_pe_atom.h compute_pressure.h compute_property_atom.h compute_property_local.h compute_property_molecule.h compute_rdf.h compute_reduce.h compute_reduce_region.h compute_stress_atom.h compute_temp.h compute_temp_com.h compute_temp_deform.h compute_temp_partial.h compute_temp_profile.h compute_temp_ramp.h compute_temp_region.h compute_temp_sphere.h create_atoms.h create_box.h delete_atoms.h delete_bonds.h dihedral.h dihedral_charmm.h dihedral_harmonic.h dihedral_helix.h dihedral_hybrid.h dihedral_multi_harmonic.h dihedral_opls.h displace_atoms.h displace_box.h domain.h dump.h dump_atom.h dump_cfg.h dump_custom.h dump_dcd.h dump_local.h dump_xyz.h error.h ewald.h fft3d.h fft3d_wrap.h finish.h fix.h fix_adapt.h fix_addforce.h fix_ave_atom.h fix_ave_correlate.h fix_ave_histo.h fix_ave_spatial.h fix_ave_time.h fix_aveforce.h fix_bond_break.h fix_bond_create.h fix_bond_swap.h fix_box_relax.h fix_deform.h fix_deposit.h fix_drag.h fix_dt_reset.h fix_efield.h fix_enforce2d.h fix_evaporate.h fix_gravity.h fix_heat.h fix_indent.h fix_langevin.h fix_lineforce.h fix_minimize.h fix_momentum.h fix_move.h fix_nh.h fix_nh_sphere.h fix_nph.h fix_nph_sphere.h fix_npt.h fix_npt_sphere.h fix_nve.h fix_nve_limit.h fix_nve_noforce.h fix_nve_sphere.h fix_nvt.h fix_nvt_sllod.h fix_nvt_sphere.h fix_orient_fcc.h fix_planeforce.h fix_press_berendsen.h fix_print.h fix_qeq_comb.h fix_recenter.h fix_respa.h fix_rigid.h fix_rigid_nve.h fix_rigid_nvt.h fix_setforce.h fix_shake.h fix_shear_history.h fix_spring.h fix_spring_rg.h fix_spring_self.h fix_store_force.h fix_store_state.h fix_temp_berendsen.h fix_temp_rescale.h fix_thermal_conductivity.h fix_tmd.h fix_ttm.h fix_viscosity.h fix_viscous.h fix_wall.h fix_wall_harmonic.h fix_wall_lj126.h fix_wall_lj93.h fix_wall_reflect.h fix_wall_region.h force.h group.h improper.h improper_cvff.h improper_harmonic.h improper_hybrid.h input.h integrate.h kspace.h lammps.h lattice.h library.h math_extra.h memory.h min.h min_cg.h min_hftn.h min_linesearch.h min_sd.h minimize.h modify.h neigh_list.h neigh_request.h neighbor.h output.h pack.h pair.h pair_airebo.h pair_born_coul_long.h pair_buck.h pair_buck_coul_cut.h pair_buck_coul_long.h pair_comb.h pair_coul_cut.h pair_coul_debye.h pair_coul_long.h pair_dpd.h pair_dpd_tstat.h pair_eam.h pair_eam_alloy.h pair_eam_fs.h pair_eim.h pair_hybrid.h pair_hybrid_overlay.h pair_lj96_cut.h pair_lj_charmm_coul_charmm.h pair_lj_charmm_coul_charmm_implicit.h pair_lj_charmm_coul_long.h pair_lj_cut.h pair_lj_cut_coul_cut.h pair_lj_cut_coul_debye.h pair_lj_cut_coul_long.h pair_lj_cut_coul_long_tip4p.h pair_lj_expand.h pair_lj_gromacs.h pair_lj_gromacs_coul_gromacs.h pair_lj_smooth.h pair_morse.h pair_soft.h pair_sw.h pair_table.h pair_tersoff.h pair_tersoff_zbl.h pair_yukawa.h pointers.h pppm.h pppm_tip4p.h random_mars.h random_park.h read_data.h read_restart.h region.h region_block.h region_cone.h region_cylinder.h region_intersect.h region_plane.h region_prism.h region_sphere.h region_union.h remap.h remap_wrap.h replicate.h respa.h run.h set.h shell.h special.h style_angle.h style_atom.h style_bond.h style_command.h style_compute.h style_dihedral.h style_dump.h style_fix.h style_improper.h style_integrate.h style_kspace.h style_minimize.h style_pair.h style_region.h temper.h thermo.h timer.h universe.h update.h variable.h velocity.h verlet.h version.h write_restart.h +INC = angle.h angle_charmm.h angle_cosine.h angle_cosine_delta.h angle_cosine_squared.h angle_harmonic.h angle_hybrid.h angle_table.h atom.h atom_vec.h atom_vec_angle.h atom_vec_atomic.h atom_vec_bond.h atom_vec_charge.h atom_vec_full.h atom_vec_hybrid.h atom_vec_molecular.h bond.h bond_fene.h bond_fene_expand.h bond_harmonic.h bond_hybrid.h bond_morse.h bond_nonlinear.h bond_quartic.h bond_table.h change_box.h comm.h compute.h compute_angle_local.h compute_bond_local.h compute_centro_atom.h compute_cna_atom.h compute_com.h compute_com_molecule.h compute_coord_atom.h compute_dihedral_local.h compute_displace_atom.h compute_erotate_sphere.h compute_group_group.h compute_gyration.h compute_gyration_molecule.h compute_heat_flux.h compute_improper_local.h compute_ke.h compute_ke_atom.h compute_momentum.h compute_msd.h compute_msd_molecule.h compute_pair_local.h compute_pe.h compute_pe_atom.h compute_pressure.h compute_property_atom.h compute_property_local.h compute_property_molecule.h compute_rdf.h compute_reduce.h compute_reduce_region.h compute_stress_atom.h compute_temp.h compute_temp_com.h compute_temp_deform.h compute_temp_partial.h compute_temp_profile.h compute_temp_ramp.h compute_temp_region.h compute_temp_sphere.h create_atoms.h create_box.h delete_atoms.h delete_bonds.h dihedral.h dihedral_charmm.h dihedral_harmonic.h dihedral_helix.h dihedral_hybrid.h dihedral_multi_harmonic.h dihedral_opls.h displace_atoms.h displace_box.h domain.h dump.h dump_atom.h dump_cfg.h dump_custom.h dump_dcd.h dump_local.h dump_xyz.h error.h ewald.h fft3d.h fft3d_wrap.h finish.h fix.h fix_adapt.h fix_addforce.h fix_ave_atom.h fix_ave_correlate.h fix_ave_histo.h fix_ave_spatial.h fix_ave_time.h fix_aveforce.h fix_bond_break.h fix_bond_create.h fix_bond_swap.h fix_box_relax.h fix_deform.h fix_deposit.h fix_drag.h fix_dt_reset.h fix_efield.h fix_enforce2d.h fix_evaporate.h fix_gravity.h fix_heat.h fix_indent.h fix_langevin.h fix_lineforce.h fix_minimize.h fix_momentum.h fix_move.h fix_nh.h fix_nh_sphere.h fix_nph.h fix_nph_sphere.h fix_npt.h fix_npt_sphere.h fix_nve.h fix_nve_limit.h fix_nve_noforce.h fix_nve_sphere.h fix_nvt.h fix_nvt_sllod.h fix_nvt_sphere.h fix_orient_fcc.h fix_planeforce.h fix_press_berendsen.h fix_print.h fix_qeq_comb.h fix_recenter.h fix_respa.h fix_rigid.h fix_rigid_nve.h fix_rigid_nvt.h fix_setforce.h fix_shake.h fix_shear_history.h fix_spring.h fix_spring_rg.h fix_spring_self.h fix_store_force.h fix_store_state.h fix_temp_berendsen.h fix_temp_rescale.h fix_thermal_conductivity.h fix_tmd.h fix_ttm.h fix_viscosity.h fix_viscous.h fix_wall.h fix_wall_harmonic.h fix_wall_lj126.h fix_wall_lj93.h fix_wall_reflect.h fix_wall_region.h force.h group.h improper.h improper_cvff.h improper_harmonic.h improper_hybrid.h input.h integrate.h kspace.h lammps.h lattice.h library.h math_extra.h memory.h min.h min_cg.h min_hftn.h min_linesearch.h min_sd.h minimize.h modify.h neigh_list.h neigh_request.h neighbor.h output.h pack.h pair.h pair_airebo.h pair_born_coul_long.h pair_buck.h pair_buck_coul_cut.h pair_buck_coul_long.h pair_comb.h pair_coul_cut.h pair_coul_debye.h pair_coul_long.h pair_dpd.h pair_dpd_tstat.h pair_eam.h pair_eam_alloy.h pair_eam_fs.h pair_eim.h pair_hybrid.h pair_hybrid_overlay.h pair_lj96_cut.h pair_lj_charmm_coul_charmm.h pair_lj_charmm_coul_charmm_implicit.h pair_lj_charmm_coul_long.h pair_lj_cut.h pair_lj_cut_coul_cut.h pair_lj_cut_coul_debye.h pair_lj_cut_coul_long.h pair_lj_cut_coul_long_tip4p.h pair_lj_expand.h pair_lj_gromacs.h pair_lj_gromacs_coul_gromacs.h pair_lj_smooth.h pair_morse.h pair_soft.h pair_sw.h pair_table.h pair_tersoff.h pair_tersoff_zbl.h pair_yukawa.h pointers.h pppm.h pppm_tip4p.h random_mars.h random_park.h read_data.h read_restart.h region.h region_block.h region_cone.h region_cylinder.h region_intersect.h region_plane.h region_prism.h region_sphere.h region_union.h remap.h remap_wrap.h replicate.h respa.h run.h set.h shell.h special.h style_angle.h style_atom.h style_bond.h style_command.h style_compute.h style_dihedral.h style_dump.h style_fix.h style_improper.h style_integrate.h style_kspace.h style_minimize.h style_pair.h style_region.h temper.h thermo.h timer.h universe.h update.h variable.h velocity.h verlet.h version.h write_restart.h OBJ = $(SRC:.cpp=.o) diff --git a/src/compute_momentum.cpp b/src/compute_momentum.cpp new file mode 100644 index 0000000000..f8fc0ec6ab --- /dev/null +++ b/src/compute_momentum.cpp @@ -0,0 +1,59 @@ + +#include +#include "compute_momentum.h" +#include "atom.h" +#include "update.h" +#include "force.h" +#include "domain.h" +#include "group.h" +#include "error.h" + +using namespace LAMMPS_NS; + +ComputeMomentum::ComputeMomentum(LAMMPS *lmp, int narg, char **arg) : + Compute(lmp, narg, arg) +{ + if (narg != 3) error->all(FLERR,"Illegal compute momentum command"); + + vector_flag = 1; + size_vector = 3; + extvector = 1; + vector = new double[size_vector]; +} + +ComputeMomentum::~ComputeMomentum() { + delete[] vector; +} + +void ComputeMomentum::init() +{ +} + +void ComputeMomentum::compute_vector() +{ + invoked_vector = update->ntimestep; + + double **v = atom->v; + double *rmass = atom->rmass; + double *mass = atom->mass; + int *mask = atom->mask; + int *type = atom->type; + int nlocal = atom->nlocal; + + double mom[3] = {0.0, 0.0, 0.0}; + + if (rmass) { + for (int i = 0; i < nlocal; i++) + if (mask[i] & groupbit) { + for(int j = 0; j < 3; ++j) + mom[j] += rmass[i] * v[i][j]; + } + } else { + for (int i = 0; i < nlocal; i++) + if (mask[i] & groupbit) + for(int j = 0; j < 3; ++j) + mom[j] += mass[type[i]] * v[i][j]; + } + + MPI_Allreduce(&mom, vector, 3, MPI_DOUBLE, MPI_SUM, world); +} diff --git a/src/compute_momentum.h b/src/compute_momentum.h new file mode 100644 index 0000000000..1e0c52c045 --- /dev/null +++ b/src/compute_momentum.h @@ -0,0 +1,36 @@ +#ifdef COMPUTE_CLASS + +ComputeStyle(momentum,ComputeMomentum) + +#else + +#ifndef LMP_COMPUTE_MOMENTUM_H +#define LMP_COMPUTE_MOMENTUM_H + +#include "compute.h" + +namespace LAMMPS_NS { + +class ComputeMomentum : public Compute { + public: + ComputeMomentum(class LAMMPS *, int, char **); + virtual ~ComputeMomentum(); + + virtual void init(); + virtual void compute_vector(); +}; + +} + +#endif +#endif + +/* ERROR/WARNING messages: + +E: Illegal ... command + +Self-explanatory. Check the input script syntax and compare to the +documentation for the command. You can use -echo screen as a +command-line option when running LAMMPS to see the offending line. + +*/ -- GitLab From 26347ec80ce8a33a4162d5d5275d8be52d6666fa Mon Sep 17 00:00:00 2001 From: Rupert Nash Date: Wed, 19 Jun 2019 13:55:10 +0100 Subject: [PATCH 054/469] Add docs for compute momentum --- doc/src/Commands_compute.txt | 1 + doc/src/compute.txt | 1 + doc/src/compute_momentum.txt | 45 ++++++++++++++++++++++++++++++++++++ doc/src/computes.txt | 1 + doc/src/lammps.book | 1 + 5 files changed, 49 insertions(+) create mode 100644 doc/src/compute_momentum.txt diff --git a/doc/src/Commands_compute.txt b/doc/src/Commands_compute.txt index f566702609..0817f44adf 100644 --- a/doc/src/Commands_compute.txt +++ b/doc/src/Commands_compute.txt @@ -80,6 +80,7 @@ KOKKOS, o = USER-OMP, t = OPT. "meso/e/atom"_compute_meso_e_atom.html, "meso/rho/atom"_compute_meso_rho_atom.html, "meso/t/atom"_compute_meso_t_atom.html, +"momentum"_compute_momentum.html, "msd"_compute_msd.html, "msd/chunk"_compute_msd_chunk.html, "msd/nongauss"_compute_msd_nongauss.html, diff --git a/doc/src/compute.txt b/doc/src/compute.txt index 87dbee57d6..12c6b141b7 100644 --- a/doc/src/compute.txt +++ b/doc/src/compute.txt @@ -229,6 +229,7 @@ compute"_Commands_compute.html doc page are followed by one or more of "meso/e/atom"_compute_meso_e_atom.html - "meso/rho/atom"_compute_meso_rho_atom.html - "meso/t/atom"_compute_meso_t_atom.html - +"momentum"_compute_momentum.html - translational momentum "msd"_compute_msd.html - mean-squared displacement of group of atoms "msd/chunk"_compute_msd_chunk.html - mean-squared displacement for each chunk "msd/nongauss"_compute_msd_nongauss.html - MSD and non-Gaussian parameter of group of atoms diff --git a/doc/src/compute_momentum.txt b/doc/src/compute_momentum.txt new file mode 100644 index 0000000000..4db171d42d --- /dev/null +++ b/doc/src/compute_momentum.txt @@ -0,0 +1,45 @@ +"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c + +:link(lws,http://lammps.sandia.gov) +:link(ld,Manual.html) +:link(lc,Commands_all.html) + +:line + +compute momentum command :h3 + +[Syntax:] + +compute ID group-ID momentum :pre + +ID, group-ID are documented in "compute"_compute.html command +momentum = style name of this compute command :ul + +[Examples:] + +compute 1 all momentum :pre + +[Description:] + +Define a computation that calculates the translational momentum +of a group of particles. + +The momentum of each particles is computed as m v, where m and v are +the mass and velocity of the particle. + +[Output info:] + +This compute calculates a global vector (the summed momentum) on +length 3. This value can be used by any command that uses a global +vector value from a compute as input. See the "Howto +output"_Howto_output.html doc page for an overview of LAMMPS output +options. + +The vector value calculated by this compute is "extensive". The vector +value will be in momentum "units"_units.html. + +[Restrictions:] none + +[Related commands:] + +[Default:] none diff --git a/doc/src/computes.txt b/doc/src/computes.txt index 926b8da222..1c914365b1 100644 --- a/doc/src/computes.txt +++ b/doc/src/computes.txt @@ -57,6 +57,7 @@ Computes :h1 compute_meso_e_atom compute_meso_rho_atom compute_meso_t_atom + compute_momentum compute_msd compute_msd_chunk compute_msd_nongauss diff --git a/doc/src/lammps.book b/doc/src/lammps.book index 2738c9b051..816acd3521 100644 --- a/doc/src/lammps.book +++ b/doc/src/lammps.book @@ -468,6 +468,7 @@ compute_ke_rigid.html compute_meso_e_atom.html compute_meso_rho_atom.html compute_meso_t_atom.html +compute_momentum.html compute_msd.html compute_msd_chunk.html compute_msd_nongauss.html -- GitLab From 52a3d825ef32729f101d2fe09703b519e3c06b0a Mon Sep 17 00:00:00 2001 From: Andrew Schultz Date: Wed, 19 Jun 2019 13:35:35 -0400 Subject: [PATCH 055/469] Explain more about advantages of HMA, restrictions, point to examples/hma --- doc/src/compute_hma.txt | 24 +++++++++++++++++++++--- 1 file changed, 21 insertions(+), 3 deletions(-) diff --git a/doc/src/compute_hma.txt b/doc/src/compute_hma.txt index c203c281ed..58934be054 100644 --- a/doc/src/compute_hma.txt +++ b/doc/src/compute_hma.txt @@ -37,8 +37,24 @@ energy, pressure or heat capacity), using the harmonically-mapped averaging (HMA) method. This command yields much higher precision than the equivalent compute commands ("compute pe"_compute_pe.html, "compute pressure"_compute_pressure.html, etc.) -commands during a canonical simulation of an atomic crystal. - +commands during a canonical simulation of an atomic crystal. Specifically, +near melting HMA can yield averages of a given precision an order of magnitude +faster than conventional methods, and this only improves as the temperatures is +lowered. This is particularly important for evaluating the free energy by +thermodynamic integration, where the low-temperature contributions are the +greatest source of statistical uncertainty. Moreover, HMA has other +advantages, including smaller potential-truncation effects, finite-size +effects, smaller timestep inaccuracy, faster equilibration and shorter +decorrelation time. + +HMA should not be used if atoms are expected to diffuse. It is also +restricted to simulations in the NVT ensemble. + +Computation of the heat capacity with this compute is presently restricted to +the "lj_smooth_linear"_lj_smooth_linear.html pair style. Use with other pair +styles requires an additional method (single2nd) to be implemented in the +corresponding Pair class. Computation of the energy and pressure does not +have this restriction. In this method, the analytically known harmonic behavior of a crystal is removed from the traditional ensemble averages, which leads to an accurate and precise measurement of the anharmonic contributions without contamination @@ -119,7 +135,9 @@ NOTE: Compute hma should be used when the atoms of the solid do not diffuse. Dif NOTE: The "fix_modify energy yes"_fix_modify.html command must also be specified if a fix is to contribute potential energy to this command. -:line +An example input script that uses this compute is included in +examples/USER/hma/ along with corresponding LAMMPS output showing that the HMA +properties fluctuate less than the corresponding conventional properties. [Output info:] -- GitLab From 04cfaae54f99e7a6dc4e1cd4e10408a54f551a64 Mon Sep 17 00:00:00 2001 From: Andrew Schultz Date: Wed, 19 Jun 2019 13:37:41 -0400 Subject: [PATCH 056/469] Fold HMA README into source code in preparation for move to MISC --- src/USER-HMA/README | 30 ------------------------------ src/USER-HMA/compute_hma.cpp | 32 ++++++++++++++++++++++++++++++++ 2 files changed, 32 insertions(+), 30 deletions(-) delete mode 100644 src/USER-HMA/README diff --git a/src/USER-HMA/README b/src/USER-HMA/README deleted file mode 100644 index b27999341b..0000000000 --- a/src/USER-HMA/README +++ /dev/null @@ -1,30 +0,0 @@ -The HMA package implements the compute hma command for LAMMPS, which implements -harmonically-mapped averaging for crystalline solids. The current -implementation handles atomic crystals. - -Computing the heat capacity relies on being able to compute the second -derivative of the energy with respect to atom positions. This capability is -provided by the single2 method in Pair, but is currently only implemented for -the shifted-force LJ potential (lj/smooth/linear). Pair::single2 takes a single -pair and (like Pair::single) returns the energy and sets the force as an out -parameter, but also sets the elements of 6-element double array out parameter, -which are the unique components of the atomic Hessian tensor for the pair. A -helper method exists (Pair::pairTensor), which will compute the tensor from -linear derivatives and the vector between the positions. HMA Heat capacity can -be computed for other models by implementing single2 in those Pair classes. - -More information about HMA is available in these publications: - -A. J. Schultz, D. A. Kofke, “Comprehensive high-precision high-accuracy -equation of state and coexistence properties for classical Lennard-Jones -crystals and low-temperature fluid phases”, J. Chem. Phys. 149, 204508 (2018) -https://dx.doi.org/10.1063/1.5053714 - -S. G. Moustafa, A. J. Schultz, D. A. Kofke, “Harmonically Assisted Methods for -Computing the Free Energy of Classical Crystals by Molecular Simulation: A -Comparative Study”, J. Chem. Theory Comput. 13, 825-834 (2017) -https://dx.doi.org/10.1021/acs.jctc.6b01082 - -S. G. Moustafa, A. J. Schultz, D. A. Kofke, “Very fast averaging of thermal -properties of crystals by molecular simulation”, Phys. Rev. E 92, 043303 (2015) -https://dx.doi.org/10.1103/PhysRevE.92.043303 diff --git a/src/USER-HMA/compute_hma.cpp b/src/USER-HMA/compute_hma.cpp index bedcda769d..15cadbdd45 100644 --- a/src/USER-HMA/compute_hma.cpp +++ b/src/USER-HMA/compute_hma.cpp @@ -11,6 +11,38 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ +/* ---------------------------------------------------------------------- +This compute implements harmonically-mapped averaging for crystalline solids. +The current implementation handles atomic crystals. + +Computing the heat capacity relies on being able to compute the second +derivative of the energy with respect to atom positions. This capability is +provided by the single2 method in Pair, but is currently only implemented for +the shifted-force LJ potential (lj/smooth/linear). Pair::single2 takes a single +pair and (like Pair::single) returns the energy and sets the force as an out +parameter, but also sets the elements of 6-element double array out parameter, +which are the unique components of the atomic Hessian tensor for the pair. A +helper method exists (Pair::pairTensor), which will compute the tensor from +linear derivatives and the vector between the positions. HMA Heat capacity can +be computed for other models by implementing single2 in those Pair classes. + +More information about HMA is available in these publications: + +A. J. Schultz, D. A. Kofke, “Comprehensive high-precision high-accuracy +equation of state and coexistence properties for classical Lennard-Jones +crystals and low-temperature fluid phases”, J. Chem. Phys. 149, 204508 (2018) +https://dx.doi.org/10.1063/1.5053714 + +S. G. Moustafa, A. J. Schultz, D. A. Kofke, “Harmonically Assisted Methods for +Computing the Free Energy of Classical Crystals by Molecular Simulation: A +Comparative Study”, J. Chem. Theory Comput. 13, 825-834 (2017) +https://dx.doi.org/10.1021/acs.jctc.6b01082 + +S. G. Moustafa, A. J. Schultz, D. A. Kofke, “Very fast averaging of thermal +properties of crystals by molecular simulation”, Phys. Rev. E 92, 043303 (2015) +https://dx.doi.org/10.1103/PhysRevE.92.043303 +------------------------------------------------------------------------- */ + #include #include #include -- GitLab From 395a9d3739eef12917d172525de3414b6178ee5c Mon Sep 17 00:00:00 2001 From: Andrew Schultz Date: Wed, 19 Jun 2019 16:12:15 -0400 Subject: [PATCH 057/469] Fold hma compute into USER-MISC --- cmake/CMakeLists.txt | 4 ++-- doc/src/Packages_details.txt | 20 ------------------- doc/src/Packages_user.txt | 1 - examples/USER/{ => misc}/hma/README | 0 examples/USER/{ => misc}/hma/hma.in | 0 .../USER/{ => misc}/hma/log.6Nov18.hma.g++.1 | 0 .../USER/{ => misc}/hma/log.6Nov18.hma.g++.4 | 0 src/{USER-HMA => USER-MISC}/compute_hma.cpp | 0 src/{USER-HMA => USER-MISC}/compute_hma.h | 0 9 files changed, 2 insertions(+), 23 deletions(-) rename examples/USER/{ => misc}/hma/README (100%) rename examples/USER/{ => misc}/hma/hma.in (100%) rename examples/USER/{ => misc}/hma/log.6Nov18.hma.g++.1 (100%) rename examples/USER/{ => misc}/hma/log.6Nov18.hma.g++.4 (100%) rename src/{USER-HMA => USER-MISC}/compute_hma.cpp (100%) rename src/{USER-HMA => USER-MISC}/compute_hma.h (100%) diff --git a/cmake/CMakeLists.txt b/cmake/CMakeLists.txt index c2356002b2..911b6f0f15 100644 --- a/cmake/CMakeLists.txt +++ b/cmake/CMakeLists.txt @@ -177,8 +177,8 @@ set(DEFAULT_PACKAGES ASPHERE BODY CLASS2 COLLOID COMPRESS CORESHELL DIPOLE GRANULAR KSPACE LATTE MANYBODY MC MESSAGE MISC MOLECULE PERI POEMS QEQ REPLICA RIGID SHOCK SPIN SNAP SRD KIM PYTHON MSCG MPIIO VORONOI USER-ATC USER-AWPMD USER-BOCS USER-CGDNA USER-MESO USER-CGSDK USER-COLVARS - USER-DIFFRACTION USER-DPD USER-DRUDE USER-EFF USER-FEP USER-H5MD USER-HMA - USER-LB USER-MANIFOLD USER-MEAMC USER-MGPT USER-MISC USER-MOFFF USER-MOLFILE + USER-DIFFRACTION USER-DPD USER-DRUDE USER-EFF USER-FEP USER-H5MD USER-LB + USER-MANIFOLD USER-MEAMC USER-MGPT USER-MISC USER-MOFFF USER-MOLFILE USER-NETCDF USER-PHONON USER-PLUMED USER-PTM USER-QTB USER-REAXC USER-SCAFACOS USER-SDPD USER-SMD USER-SMTBQ USER-SPH USER-TALLY USER-UEF USER-VTK USER-QUIP USER-QMMM USER-YAFF USER-ADIOS) diff --git a/doc/src/Packages_details.txt b/doc/src/Packages_details.txt index 12f63e2e3b..1528adc420 100644 --- a/doc/src/Packages_details.txt +++ b/doc/src/Packages_details.txt @@ -76,7 +76,6 @@ as contained in the file name. "USER-EFF"_#PKG-USER-EFF, "USER-FEP"_#PKG-USER-FEP, "USER-H5MD"_#PKG-USER-H5MD, -"USER-HMA"_#PKG-USER-HMA, "USER-INTEL"_#PKG-USER-INTEL, "USER-LB"_#PKG-USER-LB, "USER-MANIFOLD"_#PKG-USER-MANIFOLD, @@ -1375,25 +1374,6 @@ lib/h5md/README :line -USER-HMA package :link(PKG-USER-HMA),h4 - -[Contents:] - -Harmonically mapped averaging for efficient calculation of properties of -crystalline solids. The compute hma can specify use of HMA for calculation of -potential energy, pressure and heat capacity. - -[Author:] Apoorva Purohit, Andrew Schultz and David Kofke (University at -Buffalo, NY, USA) - -[Supporting info:] - -examples/USER/hma/README -src/USER-HMA/README -"compute hma"_compute_hma.html :ul - -:line - USER-INTEL package :link(PKG-USER-INTEL),h4 [Contents:] diff --git a/doc/src/Packages_user.txt b/doc/src/Packages_user.txt index 3ce2a458b6..4210f617ef 100644 --- a/doc/src/Packages_user.txt +++ b/doc/src/Packages_user.txt @@ -51,7 +51,6 @@ Package, Description, Doc page, Example, Library "USER-EFF"_Packages_details.html#PKG-USER-EFF, electron force field,"pair_style eff/cut"_pair_eff.html, USER/eff, no "USER-FEP"_Packages_details.html#PKG-USER-FEP, free energy perturbation,"compute fep"_compute_fep.html, USER/fep, no "USER-H5MD"_Packages_details.html#PKG-USER-H5MD, dump output via HDF5,"dump h5md"_dump_h5md.html, n/a, ext -"USER-HMA"_Packages_details.html#PKG-USER-HMA, compute properties via HMA,"compute hma"_compute_hma.html, USER/hma, no "USER-INTEL"_Packages_details.html#PKG-USER-INTEL, optimized Intel CPU and KNL styles,"Speed intel"_Speed_intel.html, "Benchmarks"_http://lammps.sandia.gov/bench.html, no "USER-LB"_Packages_details.html#PKG-USER-LB, Lattice Boltzmann fluid,"fix lb/fluid"_fix_lb_fluid.html, USER/lb, no "USER-MANIFOLD"_Packages_details.html#PKG-USER-MANIFOLD, motion on 2d surfaces,"fix manifoldforce"_fix_manifoldforce.html, USER/manifold, no diff --git a/examples/USER/hma/README b/examples/USER/misc/hma/README similarity index 100% rename from examples/USER/hma/README rename to examples/USER/misc/hma/README diff --git a/examples/USER/hma/hma.in b/examples/USER/misc/hma/hma.in similarity index 100% rename from examples/USER/hma/hma.in rename to examples/USER/misc/hma/hma.in diff --git a/examples/USER/hma/log.6Nov18.hma.g++.1 b/examples/USER/misc/hma/log.6Nov18.hma.g++.1 similarity index 100% rename from examples/USER/hma/log.6Nov18.hma.g++.1 rename to examples/USER/misc/hma/log.6Nov18.hma.g++.1 diff --git a/examples/USER/hma/log.6Nov18.hma.g++.4 b/examples/USER/misc/hma/log.6Nov18.hma.g++.4 similarity index 100% rename from examples/USER/hma/log.6Nov18.hma.g++.4 rename to examples/USER/misc/hma/log.6Nov18.hma.g++.4 diff --git a/src/USER-HMA/compute_hma.cpp b/src/USER-MISC/compute_hma.cpp similarity index 100% rename from src/USER-HMA/compute_hma.cpp rename to src/USER-MISC/compute_hma.cpp diff --git a/src/USER-HMA/compute_hma.h b/src/USER-MISC/compute_hma.h similarity index 100% rename from src/USER-HMA/compute_hma.h rename to src/USER-MISC/compute_hma.h -- GitLab From fe5e952319a082deb831be24d27e425b8121aca8 Mon Sep 17 00:00:00 2001 From: Andrew Schultz Date: Wed, 19 Jun 2019 19:17:20 -0400 Subject: [PATCH 058/469] Fix docs issues --- doc/src/compute_hma.txt | 2 +- doc/utils/sphinx-config/false_positives.txt | 1 + 2 files changed, 2 insertions(+), 1 deletion(-) diff --git a/doc/src/compute_hma.txt b/doc/src/compute_hma.txt index 58934be054..581e4afeb4 100644 --- a/doc/src/compute_hma.txt +++ b/doc/src/compute_hma.txt @@ -51,7 +51,7 @@ HMA should not be used if atoms are expected to diffuse. It is also restricted to simulations in the NVT ensemble. Computation of the heat capacity with this compute is presently restricted to -the "lj_smooth_linear"_lj_smooth_linear.html pair style. Use with other pair +the "pair_lj_smooth_linear"_pair_lj_smooth_linear.html pair style. Use with other pair styles requires an additional method (single2nd) to be implemented in the corresponding Pair class. Computation of the energy and pressure does not have this restriction. diff --git a/doc/utils/sphinx-config/false_positives.txt b/doc/utils/sphinx-config/false_positives.txt index 3166544b10..07a0e4eaf0 100644 --- a/doc/utils/sphinx-config/false_positives.txt +++ b/doc/utils/sphinx-config/false_positives.txt @@ -518,6 +518,7 @@ Dcut de dE De +decorrelation debye Debye Decius -- GitLab From 128d021c10c2c0d4fd54bd81d7c49f82bf2dc0a9 Mon Sep 17 00:00:00 2001 From: "Ryan S. Elliott" Date: Thu, 20 Jun 2019 13:13:13 -0500 Subject: [PATCH 059/469] Update to latest prototype for SimulatorModel interface --- src/KIM/kim_style.cpp | 11 ++++++----- 1 file changed, 6 insertions(+), 5 deletions(-) diff --git a/src/KIM/kim_style.cpp b/src/KIM/kim_style.cpp index 814da6b188..b67360ce82 100644 --- a/src/KIM/kim_style.cpp +++ b/src/KIM/kim_style.cpp @@ -68,8 +68,9 @@ #include "variable.h" #include "fix_store_kim.h" +//@@@@@ Need to switch to c-bindings when they are available. #include "KIM_SimulatorModel.hpp" - +//@@@@@ using namespace LAMMPS_NS; @@ -131,6 +132,7 @@ void KimStyle::do_init(char *model) fix_store->setptr("units_to", (void *) units_to); int kimerror; + // @@@@@ switch to c-bindings when they are available KIM::SimulatorModel * simulatorModel; kimerror = KIM::SimulatorModel::Create(model,&simulatorModel); @@ -176,7 +178,7 @@ void KimStyle::do_init(char *model) // reset template map. - simulatorModel->ClearTemplateMap(); + simulatorModel->OpenAndInitializeTemplateMap(); } /* ---------------------------------------------------------------------- */ @@ -206,8 +208,7 @@ void KimStyle::do_defn(int narg, char **arg) const std::string *sim_name, *sim_version; std::string atom_type_sym_list; - simulatorModel->GetSimulatorName(&sim_name); - simulatorModel->GetSimulatorVersion(&sim_version); + simulatorModel->GetSimulatorNameAndVersion(&sim_name, &sim_version); if (comm->me == 0) { std::string mesg("Using KIM Simulator Model : "); @@ -292,7 +293,7 @@ void KimStyle::do_defn(int narg, char **arg) if (sim_model_idx < 0) error->all(FLERR,"KIM Simulator Model has no Model definition"); - simulatorModel->ClearTemplateMap(); + simulatorModel->OpenAndInitializeTemplateMap(); } else { -- GitLab From 0613c10395ab286a0dd7c82e1f0ab092bdacbb5a Mon Sep 17 00:00:00 2001 From: "Ryan S. Elliott" Date: Thu, 20 Jun 2019 16:45:45 -0500 Subject: [PATCH 060/469] Work on kim_style for latest definition prototype --- examples/kim/in.kim.lj.simulator_model | 9 +- src/KIM/kim_style.cpp | 288 ++++++++++++++++--------- src/KIM/kim_style.h | 34 ++- 3 files changed, 218 insertions(+), 113 deletions(-) diff --git a/examples/kim/in.kim.lj.simulator_model b/examples/kim/in.kim.lj.simulator_model index 15b26c3c64..01ee5aa64c 100644 --- a/examples/kim/in.kim.lj.simulator_model +++ b/examples/kim/in.kim.lj.simulator_model @@ -14,12 +14,11 @@ variable xx equal 20*$x variable yy equal 20*$y variable zz equal 20*$z -units metal -atom_style atomic +echo both +#kim_style model LennardJones_Ar metal +kim_style model Sim_LAMMPS_LJcut_AkersonElliott_Alchemy_PbAu real unit_conversion_mode newton on -kim_style init LennardJones_Ar - lattice fcc 4.4300 region box block 0 ${xx} 0 ${yy} 0 ${zz} create_box 1 box @@ -28,7 +27,7 @@ create_atoms 1 box #pair_style lj/cut 8.1500 #pair_coeff 1 1 0.0104 3.4000 -kim_style define Ar +kim_style setup Au mass 1 39.95 velocity all create 200.0 232345 loop geom diff --git a/src/KIM/kim_style.cpp b/src/KIM/kim_style.cpp index b67360ce82..fcc3f33aa2 100644 --- a/src/KIM/kim_style.cpp +++ b/src/KIM/kim_style.cpp @@ -51,7 +51,7 @@ ------------------------------------------------------------------------- */ /* ---------------------------------------------------------------------- - Designed for use with the kim-api-2.0.2 (and newer) package + Designed for use with the kim-api-2.1.0 (and newer) package ------------------------------------------------------------------------- */ #include @@ -68,6 +68,9 @@ #include "variable.h" #include "fix_store_kim.h" +extern "C" { +#include "KIM_SimulatorHeaders.h" +} //@@@@@ Need to switch to c-bindings when they are available. #include "KIM_SimulatorModel.hpp" //@@@@@ @@ -78,42 +81,188 @@ using namespace LAMMPS_NS; void KimStyle::command(int narg, char **arg) { - if (narg < 2) error->all(FLERR,"Illegal kim_style command"); - - units_from = NULL; - units_to = NULL; + if ((narg < 2) || (narg > 4)) error->all(FLERR,"Illegal kim_style command"); - if (strcmp(arg[0],"init") == 0) { + if (strcmp(arg[0],"model") == 0) { if (domain->box_exist) - error->all(FLERR,"Must use 'kim_style init' command before " + error->all(FLERR,"Must use 'kim_style model' command before " "simulation box is defined"); - int len = strlen(arg[1])+1; - char *model = new char[len]; - strcpy(model,arg[1]); - - int args_done = do_units(narg-2,arg-2); - if (narg > (args_done + 2)) - error->all(FLERR,"Illegal kim_style command"); - do_init(model); - do_variables(); - } else if (strcmp(arg[0],"define") == 0) { + int len1 = strlen(arg[1])+1; + int len2 = strlen(arg[2])+1; + char *model_name = new char[len1]; strcpy(model_name,arg[1]); + char *user_units = new char[len2]; strcpy(user_units,arg[2]); + if (narg == 4) { + if (strcmp(arg[3],"unit_conversion_mode")==0) unit_conversion_mode = true; + else { error->all(FLERR,"Illegal kim_style command"); } + } else unit_conversion_mode = false; + + char *model_units; + determine_model_type_and_units(model_name, user_units, &model_units); + + do_init(model_name, user_units, model_units); + if (unit_conversion_mode) do_variables(user_units, model_units); + } else if (strcmp(arg[0],"setup") == 0) { if (!domain->box_exist) - error->all(FLERR,"Must use 'kim_style define' command after " + error->all(FLERR,"Must use 'kim_style setup' command after " "simulation box is defined"); - int args_done = do_units(narg-1,arg-1); - do_defn(narg - (args_done+1),arg + (args_done+1)); - } else if (strcmp(arg[0],"unit_variables") == 0) { - int args_done = do_units(narg,arg); - if (narg > args_done) - error->all(FLERR,"Illegal kim_style command"); - do_variables(); + do_setup(narg-1,++arg); } else error->all(FLERR,"Illegal kim_style command"); } +/* ---------------------------------------------------------------------- */ +namespace { +void get_kim_unit_names( + char const * const system, + KIM_LengthUnit & lengthUnit, + KIM_EnergyUnit & energyUnit, + KIM_ChargeUnit & chargeUnit, + KIM_TemperatureUnit & temperatureUnit, + KIM_TimeUnit & timeUnit, + Error * error) +{ + if ((strcmp(system,"real")==0)) { + lengthUnit = KIM_LENGTH_UNIT_A; + energyUnit = KIM_ENERGY_UNIT_kcal_mol; + chargeUnit = KIM_CHARGE_UNIT_e; + temperatureUnit = KIM_TEMPERATURE_UNIT_K; + timeUnit = KIM_TIME_UNIT_fs; + } else if ((strcmp(system,"metal")==0)) { + lengthUnit = KIM_LENGTH_UNIT_A; + energyUnit = KIM_ENERGY_UNIT_eV; + chargeUnit = KIM_CHARGE_UNIT_e; + temperatureUnit = KIM_TEMPERATURE_UNIT_K; + timeUnit = KIM_TIME_UNIT_ps; + } else if ((strcmp(system,"si")==0)) { + lengthUnit = KIM_LENGTH_UNIT_m; + energyUnit = KIM_ENERGY_UNIT_J; + chargeUnit = KIM_CHARGE_UNIT_C; + temperatureUnit = KIM_TEMPERATURE_UNIT_K; + timeUnit = KIM_TIME_UNIT_s; + } else if ((strcmp(system,"cgs")==0)) { + lengthUnit = KIM_LENGTH_UNIT_cm; + energyUnit = KIM_ENERGY_UNIT_erg; + chargeUnit = KIM_CHARGE_UNIT_statC; + temperatureUnit = KIM_TEMPERATURE_UNIT_K; + timeUnit = KIM_TIME_UNIT_s; + } else if ((strcmp(system,"electron")==0)) { + lengthUnit = KIM_LENGTH_UNIT_Bohr; + energyUnit = KIM_ENERGY_UNIT_Hartree; + chargeUnit = KIM_CHARGE_UNIT_e; + temperatureUnit = KIM_TEMPERATURE_UNIT_K; + timeUnit = KIM_TIME_UNIT_fs; + } else if ((strcmp(system,"lj")==0)) { + error->all(FLERR,"LAMMPS unit_style lj not supported by KIM models"); + } else { + error->all(FLERR,"Unknown unit_style"); + } +} +} // namespace +void KimStyle::determine_model_type_and_units(char * model_name, + char * user_units, + char ** model_units) +{ + KIM_LengthUnit lengthUnit; + KIM_EnergyUnit energyUnit; + KIM_ChargeUnit chargeUnit; + KIM_TemperatureUnit temperatureUnit; + KIM_TimeUnit timeUnit; + int units_accepted; + KIM_Model * kim_MO; + + get_kim_unit_names(user_units, lengthUnit, energyUnit, + chargeUnit, temperatureUnit, timeUnit, error); + int kim_error = KIM_Model_Create(KIM_NUMBERING_zeroBased, + lengthUnit, + energyUnit, + chargeUnit, + temperatureUnit, + timeUnit, + model_name, + &units_accepted, + &kim_MO); + + if (!kim_error) // model is an MO + { + model_type = MO; + KIM_Model_Destroy(&kim_MO); + + if (units_accepted) + { + int len=strlen(user_units); + *model_units = new char[len]; strcpy(*model_units,user_units); + return; + } + else if (unit_conversion_mode) + { + int const num_systems = 5; + char const * const systems[num_systems] + = {"metal", "real", "si", "cgs", "electron"}; + for (int i=0; i < num_systems; ++i) + { + get_kim_unit_names(systems[i], lengthUnit, energyUnit, + chargeUnit, temperatureUnit, timeUnit, error); + kim_error = KIM_Model_Create(KIM_NUMBERING_zeroBased, + lengthUnit, + energyUnit, + chargeUnit, + temperatureUnit, + timeUnit, + model_name, + &units_accepted, + &kim_MO); + KIM_Model_Destroy(&kim_MO); + if (units_accepted) + { + int len=strlen(systems[i]); + *model_units = new char[len]; strcpy(*model_units,systems[i]); + return; + } + } + error->all(FLERR,"KIM Model does not support any lammps unit system"); + } + else + { + error->all(FLERR,"KIM Model does not support the requested unit system"); + } + } + + KIM::SimulatorModel * kim_SM; + kim_error = KIM::SimulatorModel::Create(model_name, &kim_SM); + if (kim_error) + { + error->all(FLERR,"KIM model name not found"); + } + model_type = SM; + + int sim_fields; + int sim_lines; + std::string const * sim_field; + std::string const * sim_value; + kim_SM->GetNumberOfSimulatorFields(&sim_fields); + kim_SM->CloseTemplateMap(); + for (int i=0; i < sim_fields; ++i) { + kim_SM->GetSimulatorFieldMetadata(i,&sim_lines,&sim_field); + + if (*sim_field == "units") { + kim_SM->GetSimulatorFieldLine(i,0,&sim_value); + int len=(*sim_value).length(); + *model_units = new char[len]; strcpy(*model_units,sim_value->c_str()); + break; + } + } + KIM::SimulatorModel::Destroy(&kim_SM); + + if ((! unit_conversion_mode) && (strcmp(*model_units, user_units)!=0)) + { + error->all(FLERR,"Incompatible units for KIM Simulator Model"); + } +} + + /* ---------------------------------------------------------------------- */ -void KimStyle::do_init(char *model) +void KimStyle::do_init(char *model_name, char *user_units, char* model_units) { // create storage proxy fix. delete existing fix, if needed. @@ -127,14 +276,20 @@ void KimStyle::do_init(char *model) ifix = modify->find_fix("KIM_MODEL_STORE"); FixStoreKIM *fix_store = (FixStoreKIM *) modify->fix[ifix]; - fix_store->setptr("model_name", (void *) model); - fix_store->setptr("units_from", (void *) units_from); - fix_store->setptr("units_to", (void *) units_to); + fix_store->setptr("model_name", (void *) model_name); + fix_store->setptr("user_units", (void *) user_units); + fix_store->setptr("model_units", (void *) model_units); + + // set units + + std::string cmd("units "); + cmd += model_units; + input->one(cmd.c_str()); int kimerror; // @@@@@ switch to c-bindings when they are available KIM::SimulatorModel * simulatorModel; - kimerror = KIM::SimulatorModel::Create(model,&simulatorModel); + kimerror = KIM::SimulatorModel::Create(model_name,&simulatorModel); // not a Kim Simulator Model; nothing else to do here. @@ -150,19 +305,6 @@ void KimStyle::do_init(char *model) const std::string *sim_field, *sim_value; simulatorModel->GetNumberOfSimulatorFields(&sim_fields); - // set units - - for (int i=0; i < sim_fields; ++i) { - simulatorModel->GetSimulatorFieldMetadata(i,&sim_lines,&sim_field); - if (*sim_field == "units") { - simulatorModel->GetSimulatorFieldLine(i,0,&sim_value); - std::string cmd("units "); - cmd += *sim_value; - input->one(cmd.c_str()); - break; - } - } - // init model for (int i=0; i < sim_fields; ++i) { @@ -183,7 +325,7 @@ void KimStyle::do_init(char *model) /* ---------------------------------------------------------------------- */ -void KimStyle::do_defn(int narg, char **arg) +void KimStyle::do_setup(int narg, char **arg) { if (narg != atom->ntypes) error->all(FLERR,"Illegal kim_style command"); @@ -201,7 +343,7 @@ void KimStyle::do_defn(int narg, char **arg) FixStoreKIM *fix_store = (FixStoreKIM *) modify->fix[ifix]; model = (char *)fix_store->getptr("model_name"); simulatorModel = (KIM::SimulatorModel *)fix_store->getptr("simulator_model"); - } else error->all(FLERR,"Must use 'kim_style init' before 'kim_style define'"); + } else error->all(FLERR,"Must use 'kim_style model' before 'kim_style setup'"); if (simulatorModel) { @@ -317,62 +459,11 @@ void KimStyle::do_defn(int narg, char **arg) /* ---------------------------------------------------------------------- */ -int KimStyle::do_units(int narg, char **arg) -{ - // retrieve custom units setting if kim_style had been called before - - int ifix = modify->find_fix("KIM_MODEL_STORE"); - FixStoreKIM *fix_store = NULL; - if (ifix >= 0) { - fix_store = (FixStoreKIM *) modify->fix[ifix]; - units_from = (char *)fix_store->getptr("units_from"); - units_to = (char *)fix_store->getptr("units_to"); - } - - if (narg < 2) return 0; - int iarg=0; - for (iarg = 0; iarg < narg; iarg += 2) { - if (strcmp(arg[iarg],"unit_variables") == 0) { - if (narg > iarg+2) error->all(FLERR,"Illegal kim_style command"); - if (strcmp(arg[iarg+1],"NULL") == 0) { - delete[] units_to; - units_to = NULL; - } else { - int len = strlen(arg[iarg+1])+1; - delete[] units_to; - units_to = new char[len]; - strcpy(units_to,arg[iarg+1]); - } - if (fix_store) fix_store->setptr("units_to",units_to); - } else if (strcmp(arg[iarg],"unit_from") == 0) { - if (narg > iarg+2) error->all(FLERR,"Illegal kim_style command"); - if (strcmp(arg[iarg+1],"NULL") == 0) { - delete[] units_from; - units_from = NULL; - } else { - int len = strlen(arg[iarg+1])+1; - delete[] units_from; - units_from = new char[len]; - strcpy(units_from,arg[iarg+1]); - } - if (fix_store) fix_store->setptr("units_from",units_from); - } else return iarg; - } - return iarg; -} - -/* ---------------------------------------------------------------------- */ - -void KimStyle::do_variables() +void KimStyle::do_variables(char *user_units, char *model_units) { - char *from, *to; + char *from = user_units, *to = model_units; Variable *variable = input->variable; - if (units_from) from = units_from; - else from = update->unit_style; - if (units_to) to = units_to; - else to = update->unit_style; - // refuse convertion from or to reduced units if ((strcmp(from,"lj") == 0) || (strcmp(to,"lj") == 0)) @@ -381,6 +472,7 @@ void KimStyle::do_variables() // get index to internal style variables. create, if needed. // default to conversion factor 1.0 for newly created variables + // @@@@@@ below needs to be updated to use Ellad's luc. int v_length, v_mass, v_time; char *args[3]; args[1] = (char *)"internal"; diff --git a/src/KIM/kim_style.h b/src/KIM/kim_style.h index 36084183ee..b7ff47404f 100644 --- a/src/KIM/kim_style.h +++ b/src/KIM/kim_style.h @@ -51,7 +51,7 @@ ------------------------------------------------------------------------- */ /* ---------------------------------------------------------------------- - Designed for use with the kim-api-2.0.2 (and newer) package + Designed for use with the kim-api-2.1.0 (and newer) package ------------------------------------------------------------------------- */ #ifdef COMMAND_CLASS @@ -72,12 +72,14 @@ class KimStyle : protected Pointers { KimStyle(class LAMMPS *lmp) : Pointers(lmp) {}; void command(int, char **); private: - char *units_from; - char *units_to; - void do_init(char *); - void do_defn(int, char **); - int do_units(int, char **); - void do_variables(); + enum model_type_enum {MO, SM}; + model_type_enum model_type; + bool unit_conversion_mode; + + void determine_model_type_and_units(char *, char *, char **); + void do_init(char *, char *, char *); + void do_setup(int, char **); + void do_variables(char*, char*); }; } @@ -91,15 +93,27 @@ E: Illegal kim_style command Incorrect number or kind of arguments to kim_style. -E: Must use 'kim_style init' command before simulation box is defined +E: Must use 'kim_style model' command before simulation box is defined Self-explanatory. -E: Must use 'kim_style define' command after simulation box is defined +E: Must use 'kim_style setup' command after simulation box is defined Self-explanatory. -E: Must use 'kim_style init' command before 'kim_style define' +E: Must use 'kim_style model' command before 'kim_style setup' + +Self-explanatory. + +E: KIM Model does not support the requested unit system + +Self-explanatory. + +E: KIM Model does not support any lammps unit system + +Self-explanatory. + +E: KIM model name not found Self-explanatory. -- GitLab From 1bb18ebde4dec8dab43741b4b9c005f732200214 Mon Sep 17 00:00:00 2001 From: Rupert Nash Date: Fri, 21 Jun 2019 15:50:52 +0100 Subject: [PATCH 061/469] rollback unneeded change to Makefile.list per review --- src/Makefile.list | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/src/Makefile.list b/src/Makefile.list index 6e4c9726a6..65bbebca09 100644 --- a/src/Makefile.list +++ b/src/Makefile.list @@ -7,9 +7,9 @@ SHELL = /bin/sh ROOT = lmp EXE = $(ROOT)_$@ -SRC = angle.cpp angle_charmm.cpp angle_cosine.cpp angle_cosine_delta.cpp angle_cosine_squared.cpp angle_harmonic.cpp angle_hybrid.cpp angle_table.cpp atom.cpp atom_vec.cpp atom_vec_angle.cpp atom_vec_atomic.cpp atom_vec_bond.cpp atom_vec_charge.cpp atom_vec_full.cpp atom_vec_hybrid.cpp atom_vec_molecular.cpp bond.cpp bond_fene.cpp bond_fene_expand.cpp bond_harmonic.cpp bond_hybrid.cpp bond_morse.cpp bond_nonlinear.cpp bond_quartic.cpp bond_table.cpp change_box.cpp comm.cpp compute.cpp compute_angle_local.cpp compute_bond_local.cpp compute_centro_atom.cpp compute_cna_atom.cpp compute_com.cpp compute_com_molecule.cpp compute_coord_atom.cpp compute_dihedral_local.cpp compute_displace_atom.cpp compute_erotate_sphere.cpp compute_group_group.cpp compute_gyration.cpp compute_gyration_molecule.cpp compute_heat_flux.cpp compute_improper_local.cpp compute_ke.cpp compute_ke_atom.cpp compute_momentum.cpp compute_msd.cpp compute_msd_molecule.cpp compute_pair_local.cpp compute_pe.cpp compute_pe_atom.cpp compute_pressure.cpp compute_property_atom.cpp compute_property_local.cpp compute_property_molecule.cpp compute_rdf.cpp compute_reduce.cpp compute_reduce_region.cpp compute_stress_atom.cpp compute_temp.cpp compute_temp_com.cpp compute_temp_deform.cpp compute_temp_partial.cpp compute_temp_profile.cpp compute_temp_ramp.cpp compute_temp_region.cpp compute_temp_sphere.cpp create_atoms.cpp create_box.cpp delete_atoms.cpp delete_bonds.cpp dihedral.cpp dihedral_charmm.cpp dihedral_harmonic.cpp dihedral_helix.cpp dihedral_hybrid.cpp dihedral_multi_harmonic.cpp dihedral_opls.cpp displace_atoms.cpp displace_box.cpp domain.cpp dump.cpp dump_atom.cpp dump_cfg.cpp dump_custom.cpp dump_dcd.cpp dump_local.cpp dump_xyz.cpp error.cpp ewald.cpp fft3d.cpp fft3d_wrap.cpp finish.cpp fix.cpp fix_adapt.cpp fix_addforce.cpp fix_ave_atom.cpp fix_ave_correlate.cpp fix_ave_histo.cpp fix_ave_spatial.cpp fix_ave_time.cpp fix_aveforce.cpp fix_bond_break.cpp fix_bond_create.cpp fix_bond_swap.cpp fix_box_relax.cpp fix_deform.cpp fix_deposit.cpp fix_drag.cpp fix_dt_reset.cpp fix_efield.cpp fix_enforce2d.cpp fix_evaporate.cpp fix_gravity.cpp fix_heat.cpp fix_indent.cpp fix_langevin.cpp fix_lineforce.cpp fix_minimize.cpp fix_momentum.cpp fix_move.cpp fix_nh.cpp fix_nh_sphere.cpp fix_nph.cpp fix_nph_sphere.cpp fix_npt.cpp fix_npt_sphere.cpp fix_nve.cpp fix_nve_limit.cpp fix_nve_noforce.cpp fix_nve_sphere.cpp fix_nvt.cpp fix_nvt_sllod.cpp fix_nvt_sphere.cpp fix_orient_fcc.cpp fix_planeforce.cpp fix_press_berendsen.cpp fix_print.cpp fix_qeq_comb.cpp fix_recenter.cpp fix_respa.cpp fix_rigid.cpp fix_rigid_nve.cpp fix_rigid_nvt.cpp fix_setforce.cpp fix_shake.cpp fix_shear_history.cpp fix_spring.cpp fix_spring_rg.cpp fix_spring_self.cpp fix_store_force.cpp fix_store_state.cpp fix_temp_berendsen.cpp fix_temp_rescale.cpp fix_thermal_conductivity.cpp fix_tmd.cpp fix_ttm.cpp fix_viscosity.cpp fix_viscous.cpp fix_wall.cpp fix_wall_harmonic.cpp fix_wall_lj126.cpp fix_wall_lj93.cpp fix_wall_reflect.cpp fix_wall_region.cpp force.cpp group.cpp improper.cpp improper_cvff.cpp improper_harmonic.cpp improper_hybrid.cpp input.cpp integrate.cpp kspace.cpp lammps.cpp lattice.cpp library.cpp main.cpp memory.cpp min.cpp min_cg.cpp min_hftn.cpp min_linesearch.cpp min_sd.cpp minimize.cpp modify.cpp neigh_bond.cpp neigh_derive.cpp neigh_full.cpp neigh_gran.cpp neigh_half_bin.cpp neigh_half_multi.cpp neigh_half_nsq.cpp neigh_list.cpp neigh_request.cpp neigh_respa.cpp neigh_stencil.cpp neighbor.cpp output.cpp pack.cpp pair.cpp pair_airebo.cpp pair_born_coul_long.cpp pair_buck.cpp pair_buck_coul_cut.cpp pair_buck_coul_long.cpp pair_comb.cpp pair_coul_cut.cpp pair_coul_debye.cpp pair_coul_long.cpp pair_dpd.cpp pair_dpd_tstat.cpp pair_eam.cpp pair_eam_alloy.cpp pair_eam_fs.cpp pair_eim.cpp pair_hybrid.cpp pair_hybrid_overlay.cpp pair_lj96_cut.cpp pair_lj_charmm_coul_charmm.cpp pair_lj_charmm_coul_charmm_implicit.cpp pair_lj_charmm_coul_long.cpp pair_lj_cut.cpp pair_lj_cut_coul_cut.cpp pair_lj_cut_coul_debye.cpp pair_lj_cut_coul_long.cpp pair_lj_cut_coul_long_tip4p.cpp pair_lj_expand.cpp pair_lj_gromacs.cpp pair_lj_gromacs_coul_gromacs.cpp pair_lj_smooth.cpp pair_morse.cpp pair_soft.cpp pair_sw.cpp pair_table.cpp pair_tersoff.cpp pair_tersoff_zbl.cpp pair_yukawa.cpp pppm.cpp pppm_tip4p.cpp random_mars.cpp random_park.cpp read_data.cpp read_restart.cpp region.cpp region_block.cpp region_cone.cpp region_cylinder.cpp region_intersect.cpp region_plane.cpp region_prism.cpp region_sphere.cpp region_union.cpp remap.cpp remap_wrap.cpp replicate.cpp respa.cpp run.cpp set.cpp shell.cpp special.cpp temper.cpp thermo.cpp timer.cpp universe.cpp update.cpp variable.cpp velocity.cpp verlet.cpp write_restart.cpp +SRC = angle.cpp angle_charmm.cpp angle_cosine.cpp angle_cosine_delta.cpp angle_cosine_squared.cpp angle_harmonic.cpp angle_hybrid.cpp angle_table.cpp atom.cpp atom_vec.cpp atom_vec_angle.cpp atom_vec_atomic.cpp atom_vec_bond.cpp atom_vec_charge.cpp atom_vec_full.cpp atom_vec_hybrid.cpp atom_vec_molecular.cpp bond.cpp bond_fene.cpp bond_fene_expand.cpp bond_harmonic.cpp bond_hybrid.cpp bond_morse.cpp bond_nonlinear.cpp bond_quartic.cpp bond_table.cpp change_box.cpp comm.cpp compute.cpp compute_angle_local.cpp compute_bond_local.cpp compute_centro_atom.cpp compute_cna_atom.cpp compute_com.cpp compute_com_molecule.cpp compute_coord_atom.cpp compute_dihedral_local.cpp compute_displace_atom.cpp compute_erotate_sphere.cpp compute_group_group.cpp compute_gyration.cpp compute_gyration_molecule.cpp compute_heat_flux.cpp compute_improper_local.cpp compute_ke.cpp compute_ke_atom.cpp compute_msd.cpp compute_msd_molecule.cpp compute_pair_local.cpp compute_pe.cpp compute_pe_atom.cpp compute_pressure.cpp compute_property_atom.cpp compute_property_local.cpp compute_property_molecule.cpp compute_rdf.cpp compute_reduce.cpp compute_reduce_region.cpp compute_stress_atom.cpp compute_temp.cpp compute_temp_com.cpp compute_temp_deform.cpp compute_temp_partial.cpp compute_temp_profile.cpp compute_temp_ramp.cpp compute_temp_region.cpp compute_temp_sphere.cpp create_atoms.cpp create_box.cpp delete_atoms.cpp delete_bonds.cpp dihedral.cpp dihedral_charmm.cpp dihedral_harmonic.cpp dihedral_helix.cpp dihedral_hybrid.cpp dihedral_multi_harmonic.cpp dihedral_opls.cpp displace_atoms.cpp displace_box.cpp domain.cpp dump.cpp dump_atom.cpp dump_cfg.cpp dump_custom.cpp dump_dcd.cpp dump_local.cpp dump_xyz.cpp error.cpp ewald.cpp fft3d.cpp fft3d_wrap.cpp finish.cpp fix.cpp fix_adapt.cpp fix_addforce.cpp fix_ave_atom.cpp fix_ave_correlate.cpp fix_ave_histo.cpp fix_ave_spatial.cpp fix_ave_time.cpp fix_aveforce.cpp fix_bond_break.cpp fix_bond_create.cpp fix_bond_swap.cpp fix_box_relax.cpp fix_deform.cpp fix_deposit.cpp fix_drag.cpp fix_dt_reset.cpp fix_efield.cpp fix_enforce2d.cpp fix_evaporate.cpp fix_gravity.cpp fix_heat.cpp fix_indent.cpp fix_langevin.cpp fix_lineforce.cpp fix_minimize.cpp fix_momentum.cpp fix_move.cpp fix_nh.cpp fix_nh_sphere.cpp fix_nph.cpp fix_nph_sphere.cpp fix_npt.cpp fix_npt_sphere.cpp fix_nve.cpp fix_nve_limit.cpp fix_nve_noforce.cpp fix_nve_sphere.cpp fix_nvt.cpp fix_nvt_sllod.cpp fix_nvt_sphere.cpp fix_orient_fcc.cpp fix_planeforce.cpp fix_press_berendsen.cpp fix_print.cpp fix_qeq_comb.cpp fix_recenter.cpp fix_respa.cpp fix_rigid.cpp fix_rigid_nve.cpp fix_rigid_nvt.cpp fix_setforce.cpp fix_shake.cpp fix_shear_history.cpp fix_spring.cpp fix_spring_rg.cpp fix_spring_self.cpp fix_store_force.cpp fix_store_state.cpp fix_temp_berendsen.cpp fix_temp_rescale.cpp fix_thermal_conductivity.cpp fix_tmd.cpp fix_ttm.cpp fix_viscosity.cpp fix_viscous.cpp fix_wall.cpp fix_wall_harmonic.cpp fix_wall_lj126.cpp fix_wall_lj93.cpp fix_wall_reflect.cpp fix_wall_region.cpp force.cpp group.cpp improper.cpp improper_cvff.cpp improper_harmonic.cpp improper_hybrid.cpp input.cpp integrate.cpp kspace.cpp lammps.cpp lattice.cpp library.cpp main.cpp memory.cpp min.cpp min_cg.cpp min_hftn.cpp min_linesearch.cpp min_sd.cpp minimize.cpp modify.cpp neigh_bond.cpp neigh_derive.cpp neigh_full.cpp neigh_gran.cpp neigh_half_bin.cpp neigh_half_multi.cpp neigh_half_nsq.cpp neigh_list.cpp neigh_request.cpp neigh_respa.cpp neigh_stencil.cpp neighbor.cpp output.cpp pack.cpp pair.cpp pair_airebo.cpp pair_born_coul_long.cpp pair_buck.cpp pair_buck_coul_cut.cpp pair_buck_coul_long.cpp pair_comb.cpp pair_coul_cut.cpp pair_coul_debye.cpp pair_coul_long.cpp pair_dpd.cpp pair_dpd_tstat.cpp pair_eam.cpp pair_eam_alloy.cpp pair_eam_fs.cpp pair_eim.cpp pair_hybrid.cpp pair_hybrid_overlay.cpp pair_lj96_cut.cpp pair_lj_charmm_coul_charmm.cpp pair_lj_charmm_coul_charmm_implicit.cpp pair_lj_charmm_coul_long.cpp pair_lj_cut.cpp pair_lj_cut_coul_cut.cpp pair_lj_cut_coul_debye.cpp pair_lj_cut_coul_long.cpp pair_lj_cut_coul_long_tip4p.cpp pair_lj_expand.cpp pair_lj_gromacs.cpp pair_lj_gromacs_coul_gromacs.cpp pair_lj_smooth.cpp pair_morse.cpp pair_soft.cpp pair_sw.cpp pair_table.cpp pair_tersoff.cpp pair_tersoff_zbl.cpp pair_yukawa.cpp pppm.cpp pppm_tip4p.cpp random_mars.cpp random_park.cpp read_data.cpp read_restart.cpp region.cpp region_block.cpp region_cone.cpp region_cylinder.cpp region_intersect.cpp region_plane.cpp region_prism.cpp region_sphere.cpp region_union.cpp remap.cpp remap_wrap.cpp replicate.cpp respa.cpp run.cpp set.cpp shell.cpp special.cpp temper.cpp thermo.cpp timer.cpp universe.cpp update.cpp variable.cpp velocity.cpp verlet.cpp write_restart.cpp -INC = angle.h angle_charmm.h angle_cosine.h angle_cosine_delta.h angle_cosine_squared.h angle_harmonic.h angle_hybrid.h angle_table.h atom.h atom_vec.h atom_vec_angle.h atom_vec_atomic.h atom_vec_bond.h atom_vec_charge.h atom_vec_full.h atom_vec_hybrid.h atom_vec_molecular.h bond.h bond_fene.h bond_fene_expand.h bond_harmonic.h bond_hybrid.h bond_morse.h bond_nonlinear.h bond_quartic.h bond_table.h change_box.h comm.h compute.h compute_angle_local.h compute_bond_local.h compute_centro_atom.h compute_cna_atom.h compute_com.h compute_com_molecule.h compute_coord_atom.h compute_dihedral_local.h compute_displace_atom.h compute_erotate_sphere.h compute_group_group.h compute_gyration.h compute_gyration_molecule.h compute_heat_flux.h compute_improper_local.h compute_ke.h compute_ke_atom.h compute_momentum.h compute_msd.h compute_msd_molecule.h compute_pair_local.h compute_pe.h compute_pe_atom.h compute_pressure.h compute_property_atom.h compute_property_local.h compute_property_molecule.h compute_rdf.h compute_reduce.h compute_reduce_region.h compute_stress_atom.h compute_temp.h compute_temp_com.h compute_temp_deform.h compute_temp_partial.h compute_temp_profile.h compute_temp_ramp.h compute_temp_region.h compute_temp_sphere.h create_atoms.h create_box.h delete_atoms.h delete_bonds.h dihedral.h dihedral_charmm.h dihedral_harmonic.h dihedral_helix.h dihedral_hybrid.h dihedral_multi_harmonic.h dihedral_opls.h displace_atoms.h displace_box.h domain.h dump.h dump_atom.h dump_cfg.h dump_custom.h dump_dcd.h dump_local.h dump_xyz.h error.h ewald.h fft3d.h fft3d_wrap.h finish.h fix.h fix_adapt.h fix_addforce.h fix_ave_atom.h fix_ave_correlate.h fix_ave_histo.h fix_ave_spatial.h fix_ave_time.h fix_aveforce.h fix_bond_break.h fix_bond_create.h fix_bond_swap.h fix_box_relax.h fix_deform.h fix_deposit.h fix_drag.h fix_dt_reset.h fix_efield.h fix_enforce2d.h fix_evaporate.h fix_gravity.h fix_heat.h fix_indent.h fix_langevin.h fix_lineforce.h fix_minimize.h fix_momentum.h fix_move.h fix_nh.h fix_nh_sphere.h fix_nph.h fix_nph_sphere.h fix_npt.h fix_npt_sphere.h fix_nve.h fix_nve_limit.h fix_nve_noforce.h fix_nve_sphere.h fix_nvt.h fix_nvt_sllod.h fix_nvt_sphere.h fix_orient_fcc.h fix_planeforce.h fix_press_berendsen.h fix_print.h fix_qeq_comb.h fix_recenter.h fix_respa.h fix_rigid.h fix_rigid_nve.h fix_rigid_nvt.h fix_setforce.h fix_shake.h fix_shear_history.h fix_spring.h fix_spring_rg.h fix_spring_self.h fix_store_force.h fix_store_state.h fix_temp_berendsen.h fix_temp_rescale.h fix_thermal_conductivity.h fix_tmd.h fix_ttm.h fix_viscosity.h fix_viscous.h fix_wall.h fix_wall_harmonic.h fix_wall_lj126.h fix_wall_lj93.h fix_wall_reflect.h fix_wall_region.h force.h group.h improper.h improper_cvff.h improper_harmonic.h improper_hybrid.h input.h integrate.h kspace.h lammps.h lattice.h library.h math_extra.h memory.h min.h min_cg.h min_hftn.h min_linesearch.h min_sd.h minimize.h modify.h neigh_list.h neigh_request.h neighbor.h output.h pack.h pair.h pair_airebo.h pair_born_coul_long.h pair_buck.h pair_buck_coul_cut.h pair_buck_coul_long.h pair_comb.h pair_coul_cut.h pair_coul_debye.h pair_coul_long.h pair_dpd.h pair_dpd_tstat.h pair_eam.h pair_eam_alloy.h pair_eam_fs.h pair_eim.h pair_hybrid.h pair_hybrid_overlay.h pair_lj96_cut.h pair_lj_charmm_coul_charmm.h pair_lj_charmm_coul_charmm_implicit.h pair_lj_charmm_coul_long.h pair_lj_cut.h pair_lj_cut_coul_cut.h pair_lj_cut_coul_debye.h pair_lj_cut_coul_long.h pair_lj_cut_coul_long_tip4p.h pair_lj_expand.h pair_lj_gromacs.h pair_lj_gromacs_coul_gromacs.h pair_lj_smooth.h pair_morse.h pair_soft.h pair_sw.h pair_table.h pair_tersoff.h pair_tersoff_zbl.h pair_yukawa.h pointers.h pppm.h pppm_tip4p.h random_mars.h random_park.h read_data.h read_restart.h region.h region_block.h region_cone.h region_cylinder.h region_intersect.h region_plane.h region_prism.h region_sphere.h region_union.h remap.h remap_wrap.h replicate.h respa.h run.h set.h shell.h special.h style_angle.h style_atom.h style_bond.h style_command.h style_compute.h style_dihedral.h style_dump.h style_fix.h style_improper.h style_integrate.h style_kspace.h style_minimize.h style_pair.h style_region.h temper.h thermo.h timer.h universe.h update.h variable.h velocity.h verlet.h version.h write_restart.h +INC = angle.h angle_charmm.h angle_cosine.h angle_cosine_delta.h angle_cosine_squared.h angle_harmonic.h angle_hybrid.h angle_table.h atom.h atom_vec.h atom_vec_angle.h atom_vec_atomic.h atom_vec_bond.h atom_vec_charge.h atom_vec_full.h atom_vec_hybrid.h atom_vec_molecular.h bond.h bond_fene.h bond_fene_expand.h bond_harmonic.h bond_hybrid.h bond_morse.h bond_nonlinear.h bond_quartic.h bond_table.h change_box.h comm.h compute.h compute_angle_local.h compute_bond_local.h compute_centro_atom.h compute_cna_atom.h compute_com.h compute_com_molecule.h compute_coord_atom.h compute_dihedral_local.h compute_displace_atom.h compute_erotate_sphere.h compute_group_group.h compute_gyration.h compute_gyration_molecule.h compute_heat_flux.h compute_improper_local.h compute_ke.h compute_ke_atom.h compute_msd.h compute_msd_molecule.h compute_pair_local.h compute_pe.h compute_pe_atom.h compute_pressure.h compute_property_atom.h compute_property_local.h compute_property_molecule.h compute_rdf.h compute_reduce.h compute_reduce_region.h compute_stress_atom.h compute_temp.h compute_temp_com.h compute_temp_deform.h compute_temp_partial.h compute_temp_profile.h compute_temp_ramp.h compute_temp_region.h compute_temp_sphere.h create_atoms.h create_box.h delete_atoms.h delete_bonds.h dihedral.h dihedral_charmm.h dihedral_harmonic.h dihedral_helix.h dihedral_hybrid.h dihedral_multi_harmonic.h dihedral_opls.h displace_atoms.h displace_box.h domain.h dump.h dump_atom.h dump_cfg.h dump_custom.h dump_dcd.h dump_local.h dump_xyz.h error.h ewald.h fft3d.h fft3d_wrap.h finish.h fix.h fix_adapt.h fix_addforce.h fix_ave_atom.h fix_ave_correlate.h fix_ave_histo.h fix_ave_spatial.h fix_ave_time.h fix_aveforce.h fix_bond_break.h fix_bond_create.h fix_bond_swap.h fix_box_relax.h fix_deform.h fix_deposit.h fix_drag.h fix_dt_reset.h fix_efield.h fix_enforce2d.h fix_evaporate.h fix_gravity.h fix_heat.h fix_indent.h fix_langevin.h fix_lineforce.h fix_minimize.h fix_momentum.h fix_move.h fix_nh.h fix_nh_sphere.h fix_nph.h fix_nph_sphere.h fix_npt.h fix_npt_sphere.h fix_nve.h fix_nve_limit.h fix_nve_noforce.h fix_nve_sphere.h fix_nvt.h fix_nvt_sllod.h fix_nvt_sphere.h fix_orient_fcc.h fix_planeforce.h fix_press_berendsen.h fix_print.h fix_qeq_comb.h fix_recenter.h fix_respa.h fix_rigid.h fix_rigid_nve.h fix_rigid_nvt.h fix_setforce.h fix_shake.h fix_shear_history.h fix_spring.h fix_spring_rg.h fix_spring_self.h fix_store_force.h fix_store_state.h fix_temp_berendsen.h fix_temp_rescale.h fix_thermal_conductivity.h fix_tmd.h fix_ttm.h fix_viscosity.h fix_viscous.h fix_wall.h fix_wall_harmonic.h fix_wall_lj126.h fix_wall_lj93.h fix_wall_reflect.h fix_wall_region.h force.h group.h improper.h improper_cvff.h improper_harmonic.h improper_hybrid.h input.h integrate.h kspace.h lammps.h lattice.h library.h math_extra.h memory.h min.h min_cg.h min_hftn.h min_linesearch.h min_sd.h minimize.h modify.h neigh_list.h neigh_request.h neighbor.h output.h pack.h pair.h pair_airebo.h pair_born_coul_long.h pair_buck.h pair_buck_coul_cut.h pair_buck_coul_long.h pair_comb.h pair_coul_cut.h pair_coul_debye.h pair_coul_long.h pair_dpd.h pair_dpd_tstat.h pair_eam.h pair_eam_alloy.h pair_eam_fs.h pair_eim.h pair_hybrid.h pair_hybrid_overlay.h pair_lj96_cut.h pair_lj_charmm_coul_charmm.h pair_lj_charmm_coul_charmm_implicit.h pair_lj_charmm_coul_long.h pair_lj_cut.h pair_lj_cut_coul_cut.h pair_lj_cut_coul_debye.h pair_lj_cut_coul_long.h pair_lj_cut_coul_long_tip4p.h pair_lj_expand.h pair_lj_gromacs.h pair_lj_gromacs_coul_gromacs.h pair_lj_smooth.h pair_morse.h pair_soft.h pair_sw.h pair_table.h pair_tersoff.h pair_tersoff_zbl.h pair_yukawa.h pointers.h pppm.h pppm_tip4p.h random_mars.h random_park.h read_data.h read_restart.h region.h region_block.h region_cone.h region_cylinder.h region_intersect.h region_plane.h region_prism.h region_sphere.h region_union.h remap.h remap_wrap.h replicate.h respa.h run.h set.h shell.h special.h style_angle.h style_atom.h style_bond.h style_command.h style_compute.h style_dihedral.h style_dump.h style_fix.h style_improper.h style_integrate.h style_kspace.h style_minimize.h style_pair.h style_region.h temper.h thermo.h timer.h universe.h update.h variable.h velocity.h verlet.h version.h write_restart.h OBJ = $(SRC:.cpp=.o) -- GitLab From 88994d813aeba181736d7c80f2578e74731238df Mon Sep 17 00:00:00 2001 From: "Ellad B. Tadmor" Date: Fri, 21 Jun 2019 18:38:48 -0500 Subject: [PATCH 062/469] Ignore kim.log in examples/kim --- examples/kim/.gitignore | 1 + 1 file changed, 1 insertion(+) create mode 100644 examples/kim/.gitignore diff --git a/examples/kim/.gitignore b/examples/kim/.gitignore new file mode 100644 index 0000000000..63421e4217 --- /dev/null +++ b/examples/kim/.gitignore @@ -0,0 +1 @@ +/kim.log -- GitLab From 08cee18f3207b6cea777dbbd24e17ca1a1f39ded Mon Sep 17 00:00:00 2001 From: "Ellad B. Tadmor" Date: Fri, 21 Jun 2019 18:39:18 -0500 Subject: [PATCH 063/469] Added code to define unit conversion factors --- src/KIM/kim_style.cpp | 219 ++++--- src/KIM/kim_style.h | 2 + src/KIM/kim_units.cpp | 1411 +++++++++++++++++++++++++++++++++++++++++ src/KIM/kim_units.h | 59 ++ 4 files changed, 1596 insertions(+), 95 deletions(-) create mode 100644 src/KIM/kim_units.cpp create mode 100644 src/KIM/kim_units.h diff --git a/src/KIM/kim_style.cpp b/src/KIM/kim_style.cpp index fcc3f33aa2..44d5c411ab 100644 --- a/src/KIM/kim_style.cpp +++ b/src/KIM/kim_style.cpp @@ -56,6 +56,7 @@ #include #include +#include #include "kim_style.h" #include "error.h" #include "atom.h" @@ -67,6 +68,7 @@ #include "input.h" #include "variable.h" #include "fix_store_kim.h" +#include "kim_units.h" extern "C" { #include "KIM_SimulatorHeaders.h" @@ -100,7 +102,6 @@ void KimStyle::command(int narg, char **arg) determine_model_type_and_units(model_name, user_units, &model_units); do_init(model_name, user_units, model_units); - if (unit_conversion_mode) do_variables(user_units, model_units); } else if (strcmp(arg[0],"setup") == 0) { if (!domain->box_exist) error->all(FLERR,"Must use 'kim_style setup' command after " @@ -255,7 +256,10 @@ void KimStyle::determine_model_type_and_units(char * model_name, if ((! unit_conversion_mode) && (strcmp(*model_units, user_units)!=0)) { - error->all(FLERR,"Incompatible units for KIM Simulator Model"); + std::stringstream mesg; + mesg << "Incompatible units for KIM Simulator Model, required units = " + << *model_units; + error->all(FLERR,mesg.str().c_str()); } } @@ -280,17 +284,43 @@ void KimStyle::do_init(char *model_name, char *user_units, char* model_units) fix_store->setptr("user_units", (void *) user_units); fix_store->setptr("model_units", (void *) model_units); + int kimerror; + // @@@@@ switch to c-bindings when they are available + KIM::SimulatorModel * simulatorModel; + kimerror = KIM::SimulatorModel::Create(model_name,&simulatorModel); + + const std::string *sim_name, *sim_version; + simulatorModel->GetSimulatorNameAndVersion(&sim_name, &sim_version); + + if (*sim_name != "LAMMPS") + error->all(FLERR,"Incompatible KIM Simulator Model"); + + // Begin output to log file + kim_style_log_delimiter("begin","model"); + if (comm->me == 0) { + std::string mesg("# Using KIM Simulator Model : "); + mesg += model_name; + mesg += "\n"; + mesg += "# For Simulator : "; + mesg += *sim_name + " " + *sim_version + "\n"; + mesg += "# Running on : LAMMPS "; + mesg += universe->version; + mesg += "\n"; + mesg += "#\n"; + + if (screen) fputs(mesg.c_str(),screen); + if (logfile) fputs(mesg.c_str(),logfile); + } + + // Define unit conversion factor variables and print to log + if (unit_conversion_mode) do_variables(user_units, model_units); + // set units std::string cmd("units "); cmd += model_units; input->one(cmd.c_str()); - int kimerror; - // @@@@@ switch to c-bindings when they are available - KIM::SimulatorModel * simulatorModel; - kimerror = KIM::SimulatorModel::Create(model_name,&simulatorModel); - // not a Kim Simulator Model; nothing else to do here. if (kimerror) return; @@ -318,13 +348,36 @@ void KimStyle::do_init(char *model_name, char *user_units, char* model_units) } } - // reset template map. + // End output to log file + kim_style_log_delimiter("end","model"); + // reset template map. simulatorModel->OpenAndInitializeTemplateMap(); } /* ---------------------------------------------------------------------- */ +void KimStyle::kim_style_log_delimiter(std::string begin_end, + std::string model_setup) +{ + if (comm->me == 0) { + std::string mesg; + if ((begin_end == "begin") && (model_setup == "model")) mesg = + "#=== BEGIN kim-style MODEL ==================================\n"; + else if ((begin_end == "begin") && (model_setup == "setup")) mesg = + "#=== BEGIN kim-style SETUP ==================================\n"; + else if ((begin_end == "end") && (model_setup == "model")) mesg = + "#=== END kim-style MODEL ====================================\n\n"; + else if ((begin_end == "end") && (model_setup == "setup")) mesg = + "#=== END kim-style SETUP ====================================\n\n"; + + if (screen) fputs(mesg.c_str(),screen); + if (logfile) fputs(mesg.c_str(),logfile); + } +} + +/* ---------------------------------------------------------------------- */ + void KimStyle::do_setup(int narg, char **arg) { if (narg != atom->ntypes) @@ -345,30 +398,13 @@ void KimStyle::do_setup(int narg, char **arg) simulatorModel = (KIM::SimulatorModel *)fix_store->getptr("simulator_model"); } else error->all(FLERR,"Must use 'kim_style model' before 'kim_style setup'"); + // Begin output to log file + kim_style_log_delimiter("begin","setup"); + if (simulatorModel) { - const std::string *sim_name, *sim_version; std::string atom_type_sym_list; - simulatorModel->GetSimulatorNameAndVersion(&sim_name, &sim_version); - - if (comm->me == 0) { - std::string mesg("Using KIM Simulator Model : "); - mesg += model; - mesg += "\n"; - mesg += "For Simulator : "; - mesg += *sim_name + " " + *sim_version + "\n"; - mesg += "Running on : LAMMPS "; - mesg += universe->version; - mesg += "\n"; - - if (screen) fputs(mesg.c_str(),screen); - if (logfile) fputs(mesg.c_str(),logfile); - } - - if (*sim_name != "LAMMPS") - error->all(FLERR,"Incompatible KIM Simulator Model"); - for (int i = 0; i < narg; i++) atom_type_sym_list += std::string(" ") + arg[i]; @@ -455,6 +491,10 @@ void KimStyle::do_setup(int narg, char **arg) input->one(cmd1.c_str()); input->one(cmd2.c_str()); } + + // End output to log file + kim_style_log_delimiter("end","setup"); + } /* ---------------------------------------------------------------------- */ @@ -464,85 +504,74 @@ void KimStyle::do_variables(char *user_units, char *model_units) char *from = user_units, *to = model_units; Variable *variable = input->variable; - // refuse convertion from or to reduced units + // refuse conversion from or to reduced units if ((strcmp(from,"lj") == 0) || (strcmp(to,"lj") == 0)) error->all(FLERR,"Cannot set up conversion variables for 'lj' units"); // get index to internal style variables. create, if needed. - // default to conversion factor 1.0 for newly created variables - - // @@@@@@ below needs to be updated to use Ellad's luc. - int v_length, v_mass, v_time; + // set conversion factors for newly created variables. + double conversion_factor; + int ier; char *args[3]; + std::string var_str; args[1] = (char *)"internal"; args[2] = (char *)"1.0"; - - args[0] = (char *)"_u_length"; - v_length = variable->find(args[0]); - if (v_length < 0) { - variable->set(3,args); - v_length = variable->find(args[0]); + int v_unit; + int const nunits = 14; + char *units[nunits] = {(char *)"mass", + (char *)"distance", + (char *)"time", + (char *)"energy", + (char *)"velocity", + (char *)"force", + (char *)"torque", + (char *)"temperature", + (char *)"pressure", + (char *)"viscosity", + (char *)"charge", + (char *)"dipole", + (char *)"efield", + (char *)"density"}; + + if (comm->me == 0) { + std::stringstream mesg; + mesg << "# Conversion factors from " << from << " to " << to + << ":" << std::endl; + if (screen) fputs(mesg.str().c_str(),screen); + if (logfile) fputs(mesg.str().c_str(),logfile); } - args[0] = (char *)"_u_mass"; - v_mass = variable->find(args[0]); - if (v_mass < 0) { - variable->set(3,args); - v_mass = variable->find(args[0]); - } - - args[0] = (char *)"_u_time"; - v_time = variable->find(args[0]); - if (v_time < 0) { - variable->set(3,args); - v_time = variable->find(args[0]); - } - - // special case: both unit styles are the same => conversion factor 1.0 - - if (strcmp(from,to) == 0) { - variable->internal_set(v_length,1.0); - variable->internal_set(v_mass,1.0); - variable->internal_set(v_time,1.0); - return; - } - - if (strcmp(from,"real") == 0) { - if (strcmp(to,"metal") == 0) { - variable->internal_set(v_length,1.0); - variable->internal_set(v_mass,1.0); - variable->internal_set(v_time,0.001); - } else { - std::string err("Do not know how to set up conversion variables "); - err += "between '"; - err += from; - err += "' and '"; - err += to; - err += "' units"; - error->all(FLERR,err.c_str()); + for (int i = 0; i < nunits; i++) + { + var_str = std::string("_u_") + std::string(units[i]); + args[0] = (char *)var_str.c_str(); + v_unit = variable->find(args[0]); + if (v_unit < 0) { + variable->set(3,args); + v_unit = variable->find(args[0]); } - } else if (strcmp(from,"metal") == 0) { - if (strcmp(to,"real") == 0) { - variable->internal_set(v_length,1.0); - variable->internal_set(v_mass,1.0); - variable->internal_set(v_time,1000.0); - } else { - std::string err("Do not know how to set up conversion variables "); - err += "between '"; - err += from; - err += "' and '"; - err += to; - err += "' units"; + ier = lammps_unit_conversion(units[i], + from, + to, + conversion_factor); + if (ier != 0) { + std::string err = std::string("Unable to obtain conversion factor: ") + + "unit = " + units[i] + "; " + "from = " + from + "; " + "to = " + to + "."; error->all(FLERR,err.c_str()); } - } else { - std::string err("Do not know how to set up conversion variables "); - err += "between '"; - err += from; - err += "' and '"; - err += to; - err += "' units"; - error->all(FLERR,err.c_str()); + variable->internal_set(v_unit,conversion_factor); + if (comm->me == 0) { + std::stringstream mesg; + mesg << "# " << var_str << " = " << conversion_factor << std::endl; + if (screen) fputs(mesg.str().c_str(),screen); + if (logfile) fputs(mesg.str().c_str(),logfile); + } + } + if (comm->me == 0) { + if (screen) fputs("#\n",screen); + if (logfile) fputs("#\n",logfile); } } diff --git a/src/KIM/kim_style.h b/src/KIM/kim_style.h index b7ff47404f..b18f6627ea 100644 --- a/src/KIM/kim_style.h +++ b/src/KIM/kim_style.h @@ -80,6 +80,8 @@ class KimStyle : protected Pointers { void do_init(char *, char *, char *); void do_setup(int, char **); void do_variables(char*, char*); + void kim_style_log_delimiter(std::string begin_end, + std::string model_setup); }; } diff --git a/src/KIM/kim_units.cpp b/src/KIM/kim_units.cpp new file mode 100644 index 0000000000..fe90d58e9e --- /dev/null +++ b/src/KIM/kim_units.cpp @@ -0,0 +1,1411 @@ +/* ---------------------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + http://lammps.sandia.gov, Sandia National Laboratories + Steve Plimpton, sjplimp@sandia.gov + + Copyright (2003) Sandia Corporation. Under the terms of Contract + DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains + certain rights in this software. This software is distributed under + the GNU General Public License. + + See the README file in the top-level LAMMPS directory. +------------------------------------------------------------------------- */ + +/* ---------------------------------------------------------------------- + Contributing authors: Ellad B. Tadmor (UMN) +------------------------------------------------------------------------- */ + +/* ---------------------------------------------------------------------- + This program is free software; you can redistribute it and/or modify it + under the terms of the GNU General Public License as published by the Free + Software Foundation; either version 2 of the License, or (at your option) + any later version. + + This program is distributed in the hope that it will be useful, but WITHOUT + ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or + FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for + more details. + + You should have received a copy of the GNU General Public License along with + this program; if not, see . + + Linking LAMMPS statically or dynamically with other modules is making a + combined work based on LAMMPS. Thus, the terms and conditions of the GNU + General Public License cover the whole combination. + + In addition, as a special exception, the copyright holders of LAMMPS give + you permission to combine LAMMPS with free software programs or libraries + that are released under the GNU LGPL and with code included in the standard + release of the "kim-api" under the CDDL (or modified versions of such code, + with unchanged license). You may copy and distribute such a system following + the terms of the GNU GPL for LAMMPS and the licenses of the other code + concerned, provided that you include the source code of that other code + when and as the GNU GPL requires distribution of source code. + + Note that people who make modified versions of LAMMPS are not obligated to + grant this special exception for their modified versions; it is their choice + whether to do so. The GNU General Public License gives permission to release + a modified version without this exception; this exception also makes it + possible to release a modified version which carries forward this exception. +------------------------------------------------------------------------- */ + +/* ---------------------------------------------------------------------- + Designed for use with the kim-api-2.0.2 (and newer) package +------------------------------------------------------------------------- */ + +#include +#include +#include +#include +using namespace std; + +namespace +{ + +// Constants of nature and basic conversion factors +// Source: https://physics.nist.gov/cuu/Constants/Table/allascii.txt +// Working with NIST values even when there are newer values for +// compatibility with LAMMPS + +/*---------------------- + Fundamental constants +------------------------ */ +double const boltz_si = 1.38064852e-23; // [J K^-1] Boltzmann's factor + // (NIST value) +double const Nav = 6.022140857e23; // [unitless] Avogadro's number + // (NIST value) +// double const Nav = 6.02214076e23; // [unitless] Avogadro's number + // (official value May 2019) +double const me = 9.10938356e-31; // [kg] electron rest mass + // (NIST value) +// double me = 9.10938291e-31; // [kg] electron rest mass +double const e_si = 1.6021766208e-19; // [C] elementary charge + // (charge of an electron/proton) + // (NIST value) + +/*---------------------- + Distance units +------------------------ */ +double const bohr_si = 5.2917721067e-11; // [m] Bohr unit (distance between + // nucleus and electron in H) + // (NIST value) +double const angstrom_si = 1e-10; // [m] Angstrom +double const centimeter_si = 1e-2; // [m] centimeter +double const micrometer_si = 1e-6; // [m] micrometer (micron) +double const nanometer_si = 1e-9; // [m] nanometer + +/*---------------------- + Mass units +------------------------ */ +double const gram_per_mole_si = 1e-3/Nav; // [kg] gram per mole +double const amu_si = 1e-3/Nav; // [kg] atomic mass unit (molecular + // weight) For example, the mean + // molecular weight of water + // is 18.015 atomic mass units + // (amu), so one mole of water + // weight 18.015 grams. +double const gram_si = 1e-3; // [kg] gram +double const picogram_si = 1e-15; // [kg] picogram +double const attogram_si = 1e-21; // [kg[ attogram + +/*---------------------- + Time units +------------------------ */ +double const atu_si = 2.418884326509e-17; // [s] atomic time unit + // ( = hbar/E_h where E_h is the + // Hartree energy) (NIST value) +double const atu_electron_si = atu_si*sqrt(amu_si/me); // [s] atomic time unit + // used in electron system (see https://sourceforge.net/p/lammps/mailman/lammps-users/thread/BCA2BDB2-BA03-4280-896F-1E6120EF47B2%40caltech.edu/) +double const microsecond_si = 1e-6; // [s] microsecond +double const nanosecond_si = 1e-9; // [s] nanosecond +double const picosecond_si = 1e-12; // [s] picosecond +double const femtosecond_si = 1e-15; // [s] femtosecond + +/*---------------------- + Density units +------------------------ */ +double const gram_per_centimetercu_si = + gram_si/pow(centimeter_si,3); // [kg/m^3] gram/centimeter^3 +double const amu_per_bohrcu_si = amu_si/pow(bohr_si,3); // [kg/m^3] amu/bohr^3 +double const picogram_per_micrometercu_si = + picogram_si/pow(micrometer_si,3); // [kg/m^3] picogram/micrometer^3 +double const attogram_per_nanometercu_si = + attogram_si/pow(nanometer_si,3); // [kg/m^3] attogram/ + // nanomaterial^3 + +/*---------------------- + Energy/torque units +------------------------ */ +double const kcal_si = 4184.0; // [J] kilocalroie (heat energy + // involved in warming up one + // kilogram of water by one + // degree Kelvin) +double const ev_si = 1.6021766208e-19; // [J] electon volt (amount of + // energy gained or lost by the + // charge of a single electron + // moving across an electric + // potential difference of one + // volt.) (NIST value) +double const hartree_si = 4.359744650e-18; // [J] Hartree (approximately the + // electric potential energy of + // the hydrogen atom in its + // ground state) (NIST value) +double const kcal_per_mole_si = kcal_si/Nav;// [J] kcal/mole +double const erg_si = 1e-7; // [J] erg +double const dyne_centimeter_si = 1e-7; // [J[ dyne*centimeter +double const picogram_micrometersq_per_microsecondsq_si = + picogram_si*pow(micrometer_si,2)/pow(microsecond_si,2); + // [J] pigogram*micrometer^2/ + // micorsecond^2 +double const attogram_nanometersq_per_nanosecondsq_si = + attogram_si*pow(nanometer_si,2)/pow(nanosecond_si,2); + // [J] attogram*nanometer^2/ + // nanosecond^2 + +/*---------------------- + Velocity units +------------------------ */ +double const angstrom_per_femtosecond_si = + angstrom_si/femtosecond_si; // [m/s] Angstrom/femtosecond +double const angstrom_per_picosecond_si = + angstrom_si/picosecond_si; // [m/s] Angstrom/picosecond +double const micrometer_per_microsecond_si = + micrometer_si/microsecond_si; // [m/s] micrometer/microsecond +double const nanometer_per_nanosecond_si = + nanometer_si/nanosecond_si; // [m/s] nanometer/nanosecond +double const centimeter_per_second_si = + centimeter_si; // [m/s] centimeter/second +double const bohr_per_atu_si = + bohr_si/atu_electron_si; // [m/s] bohr/atu + +/*---------------------- + Force units +------------------------ */ +double const kcal_per_mole_angstrom_si = + kcal_per_mole_si/angstrom_si; // [N] kcal/(mole*Angstrom) +double const ev_per_angstrom_si = + ev_si/angstrom_si; // [N] eV/Angstrom +double const dyne_si = + dyne_centimeter_si/centimeter_si; // [N] dyne +double const hartree_per_bohr_si = + hartree_si/bohr_si; // [N] hartree/bohr +double const picogram_micrometer_per_microsecondsq_si = + picogram_si*micrometer_si/pow(microsecond_si,2); + // [N] picogram*micrometer/ + // microsecond^2 +double const attogram_nanometer_per_nanosecondsq_si = + attogram_si*nanometer_si/pow(nanosecond_si,2); + // [N] attogram*nanometer/ + // nanosecond^2 + +/*---------------------- + Pressure units +------------------------ */ +double const atmosphere_si = 101325.0; // [Pa] standard atmosphere (NIST value) +double const bar_si = 1e5; // [Pa] bar +double const dyne_per_centimetersq_si = + dyne_centimeter_si/pow(centimeter_si,3); + // [Pa] dyne/centimeter^2 +double const picogram_per_micrometer_microsecondsq_si = + picogram_si/(micrometer_si*pow(microsecond_si,2)); + // [Pa] picogram/(micrometer* + // microsecond^2) +double const attogram_per_nanometer_nanosecondsq_si = + attogram_si/(nanometer_si*pow(nanosecond_si,2)); + // [Pa] attogram/(nanometer*nanosecond^2) + +/*---------------------- + Viscosity units +------------------------ */ +double const poise_si = 0.1; // [Pa*s] Poise +double const amu_per_bohr_femtosecond_si = + amu_si/(bohr_si*femtosecond_si); // [Pa*s] amu/(bohr*femtosecond) +double const picogram_per_micrometer_microsecond_si = + picogram_si/(micrometer_si*microsecond_si); + // [Pa*s] picogram/(micrometer* + // microsecond) +double const attogram_per_nanometer_nanosecond_si = + attogram_si/(nanometer_si*nanosecond_si); + // [Pa*s] attogram/(nanometer* + // nanosecond) + +/*---------------------- + Charge units +------------------------ */ +double const echarge_si = e_si; // [C] electron charge unit +double const statcoulomb_si = e_si/4.8032044e-10; // [C] Statcoulomb or esu + // (value from LAMMPS units + // documentation) +double const picocoulomb_si = 1e-12; // [C] picocoulomb + +/*---------------------- + Dipole units +------------------------ */ +double const electron_angstrom_si = echarge_si*angstrom_si; + // [C*m] electron*angstrom +double const statcoulomb_centimeter_si = statcoulomb_si*centimeter_si; + // [C*m] statcoulomb*centimeter +double const debye_si = 1e-18*statcoulomb_centimeter_si; + // [C*m] Debye +double const picocoulomb_micrometer_si = picocoulomb_si*micrometer_si; + // [C*m] picocoulomb*micrometer +double const electron_nanometer_si = echarge_si*nanometer_si; + // [C*m] electron*nanometer + +/*---------------------- + Electric field units +------------------------ */ +double const volt_per_angstrom_si = 1.0/angstrom_si;// [V/m] volt/angstrom +double const statvolt_per_centimeter_si = + erg_si/(statcoulomb_si*centimeter_si); // [V/m] statvolt/centimeter +double const volt_per_centimeter_si = + 1.0/centimeter_si; // [V/m] volt/centimeter +double const volt_per_micrometer_si = + 1.0/micrometer_si; // [V/m] volt/micrometer +double const volt_per_nanometer_si = + 1.0/nanometer_si; // [V/m] volt/nanometer + +// Define enumerations +enum sys_type +{ + real = 1, + metal = 2, + si = 3, + cgs = 4, + electron = 5, + micro = 6, + nano = 7 +}; + +enum unit_type +{ + mass = 1, + distance = 2, + time = 3, + energy = 4, + velocity = 5, + force = 6, + torque = 7, + temperature = 8, + pressure = 9, + viscosity = 10, + charge = 11, + dipole = 12, + efield = 13, + density = 14 +}; + +enum units +{ + // mass + gram_per_mole = 101, + kilogram = 102, + gram = 103, + amu = 104, + picogram = 105, + attogram = 106, + // distance + angstrom = 201, + meter = 202, + centimeter = 203, + bohr = 204, + micrometer = 205, + nanometer = 206, + // time + femtosecond = 301, + picosecond = 302, + second = 303, + microsecond = 304, + nanosecond = 305, + // energy + kcal_per_mole = 401, + ev = 402, + joule = 403, + erg = 404, + hartree = 405, + picogram_micrometersq_per_microsecondsq = 406, + attogram_nanometersq_per_nanosecondsq = 407, + // velocity + angstrom_per_femtosecond = 501, + angstrom_per_picosecond = 502, + meter_per_second = 503, + centimeter_per_second = 504, + bohr_per_atu = 505, + micrometer_per_microsecond = 506, + nanometer_per_nanosecond = 507, + // force + kcal_per_mole_angstrom = 601, + ev_per_angstrom = 602, + newton = 603, + dyne = 604, + hartree_per_bohr = 605, + picogram_micrometer_per_microsecondsq = 606, + attogram_nanometer_per_nanosecondsq = 607, + // torque + newton_meter = 701, + dyne_centimeter = 702, + // temperature + kelvin = 801, + // pressure + atmosphere = 901, + bar = 902, + pascal = 903, + dyne_per_centimetersq = 904, + picogram_per_micrometer_microsecondsq = 905, + attogram_per_nanometer_nanosecondsq = 906, + // viscosity + poise = 1001, + pascal_second = 1002, + amu_per_bohr_femtosecond = 1003, // electron system, not in docs, GUESSED + picogram_per_micrometer_microsecond = 1004, + attogram_per_nanometer_nanosecond = 1005, + // charge + echarge = 1101, + coulomb = 1102, + statcoulomb = 1103, + picocoulomb = 1104, + // dipole + electron_angstrom = 1201, + coulomb_meter = 1202, + statcoulomb_centimeter = 1203, + debye = 1204, + picocoulomb_micrometer = 1205, + electron_nanometer = 1206, + // electric field + volt_per_angstrom = 1301, + volt_per_meter = 1302, + statvolt_per_centimeter = 1303, + volt_per_centimeter = 1304, + volt_per_micrometer = 1305, + volt_per_nanometer = 1306, + // density + gram_per_centimetercu = 1401, + kilogram_per_metercu = 1402, + amu_per_bohrcu = 1403, // electron system, not in docs, GUESSED + picogram_per_micrometercu = 1404, + attogram_per_nanometercu = 1405 +}; + +// Define dictionaries +map system_dic; +map unit_dic; +map units_real_dic; +map units_metal_dic; +map units_si_dic; +map units_cgs_dic; +map units_electron_dic; +map units_micro_dic; +map units_nano_dic; + +/* ---------------------------------------------------------------------- */ + +void initialize_dictionaries() +{ + system_dic["real"] = real; + system_dic["metal"] = metal; + system_dic["si"] = si; + system_dic["cgs"] = cgs; + system_dic["electron"] = electron; + system_dic["micro"] = micro; + system_dic["nano"] = nano; + + unit_dic["mass"] = mass; + unit_dic["distance"] = distance; + unit_dic["time"] = time; + unit_dic["energy"] = energy; + unit_dic["velocity"] = velocity; + unit_dic["force"] = force; + unit_dic["torque"] = torque; + unit_dic["temperature"]= temperature; + unit_dic["pressure"] = pressure; + unit_dic["viscosity"] = viscosity; + unit_dic["charge"] = charge; + unit_dic["dipole"] = dipole; + unit_dic["efield"] = efield; + unit_dic["density"] = density; + + units_real_dic[mass] = gram_per_mole; + units_real_dic[distance] = angstrom; + units_real_dic[time] = femtosecond; + units_real_dic[energy] = kcal_per_mole; + units_real_dic[velocity] = angstrom_per_femtosecond; + units_real_dic[force] = kcal_per_mole_angstrom; + units_real_dic[torque] = kcal_per_mole; + units_real_dic[temperature]= kelvin; + units_real_dic[pressure] = atmosphere; + units_real_dic[viscosity] = poise; + units_real_dic[charge] = echarge; + units_real_dic[dipole] = electron_angstrom; + units_real_dic[efield] = volt_per_angstrom; + units_real_dic[density] = gram_per_centimetercu; + + units_metal_dic[mass] = gram_per_mole; + units_metal_dic[distance] = angstrom; + units_metal_dic[time] = picosecond; + units_metal_dic[energy] = ev; + units_metal_dic[velocity] = angstrom_per_picosecond; + units_metal_dic[force] = ev_per_angstrom; + units_metal_dic[torque] = ev; + units_metal_dic[temperature]= kelvin; + units_metal_dic[pressure] = bar; + units_metal_dic[viscosity] = poise; + units_metal_dic[charge] = echarge; + units_metal_dic[dipole] = electron_angstrom; + units_metal_dic[efield] = volt_per_angstrom; + units_metal_dic[density] = gram_per_centimetercu; + + units_si_dic[mass] = kilogram; + units_si_dic[distance] = meter; + units_si_dic[time] = second; + units_si_dic[energy] = joule; + units_si_dic[velocity] = meter_per_second; + units_si_dic[force] = newton; + units_si_dic[torque] = newton_meter; + units_si_dic[temperature]= kelvin; + units_si_dic[pressure] = pascal; + units_si_dic[viscosity] = pascal_second; + units_si_dic[charge] = coulomb; + units_si_dic[dipole] = coulomb_meter; + units_si_dic[efield] = volt_per_meter; + units_si_dic[density] = kilogram_per_metercu; + + units_cgs_dic[mass] = gram; + units_cgs_dic[distance] = centimeter; + units_cgs_dic[time] = second; + units_cgs_dic[energy] = erg; + units_cgs_dic[velocity] = centimeter_per_second; + units_cgs_dic[force] = dyne; + units_cgs_dic[torque] = dyne_centimeter; + units_cgs_dic[temperature]= kelvin; + units_cgs_dic[pressure] = dyne_per_centimetersq; + units_cgs_dic[viscosity] = poise; + units_cgs_dic[charge] = statcoulomb; + units_cgs_dic[dipole] = statcoulomb_centimeter; + units_cgs_dic[efield] = statvolt_per_centimeter; + units_cgs_dic[density] = gram_per_centimetercu; + + units_electron_dic[mass] = amu; + units_electron_dic[distance] = bohr; + units_electron_dic[time] = femtosecond; + units_electron_dic[energy] = hartree; + units_electron_dic[velocity] = bohr_per_atu; + units_electron_dic[force] = hartree_per_bohr; + units_electron_dic[torque] = hartree; // unknown, GUESSED + units_electron_dic[temperature]= kelvin; + units_electron_dic[pressure] = pascal; + units_electron_dic[viscosity] = pascal_second; // unknown, GUESSED + units_electron_dic[charge] = echarge; + units_electron_dic[dipole] = debye; + units_electron_dic[efield] = volt_per_centimeter; + units_electron_dic[density] = amu_per_bohrcu; // unknown, GUESSED + + units_micro_dic[mass] = picogram; + units_micro_dic[distance] = micrometer; + units_micro_dic[time] = microsecond; + units_micro_dic[energy] = picogram_micrometersq_per_microsecondsq; + units_micro_dic[velocity] = micrometer_per_microsecond; + units_micro_dic[force] = picogram_micrometer_per_microsecondsq; + units_micro_dic[torque] = picogram_micrometersq_per_microsecondsq; + units_micro_dic[temperature]= kelvin; + units_micro_dic[pressure] = picogram_per_micrometer_microsecondsq; + units_micro_dic[viscosity] = picogram_per_micrometer_microsecond; + units_micro_dic[charge] = picocoulomb; + units_micro_dic[dipole] = picocoulomb_micrometer; + units_micro_dic[efield] = volt_per_micrometer; + units_micro_dic[density] = picogram_per_micrometercu; + + units_nano_dic[mass] = attogram; + units_nano_dic[distance] = nanometer; + units_nano_dic[time] = nanosecond; + units_nano_dic[energy] = attogram_nanometersq_per_nanosecondsq; + units_nano_dic[velocity] = nanometer_per_nanosecond; + units_nano_dic[force] = attogram_nanometer_per_nanosecondsq; + units_nano_dic[torque] = attogram_nanometersq_per_nanosecondsq; + units_nano_dic[temperature]= kelvin; + units_nano_dic[pressure] = attogram_per_nanometer_nanosecondsq; + units_nano_dic[viscosity] = attogram_per_nanometer_nanosecond; + units_nano_dic[charge] = echarge; + units_nano_dic[dipole] = electron_nanometer; + units_nano_dic[efield] = volt_per_nanometer; + units_nano_dic[density] = attogram_per_nanometercu; + +} + +/* ---------------------------------------------------------------------- */ + +// Get the enumeration for the unit of type `unit_type_enum` +// for LAMMPS system `system_enum`. +units get_lammps_system_unit(sys_type system_enum, unit_type unit_type_enum) +{ + switch(system_enum) { + case real : + return units_real_dic[unit_type_enum]; + case metal : + return units_metal_dic[unit_type_enum]; + case si : + return units_si_dic[unit_type_enum]; + case cgs : + return units_cgs_dic[unit_type_enum]; + case electron : + return units_electron_dic[unit_type_enum]; + case micro : + return units_micro_dic[unit_type_enum]; + case nano : + default : // This is here to a prevent a compiler warning + return units_nano_dic[unit_type_enum]; + } +} + +/* ---------------------------------------------------------------------- */ + +// Mass conversion +double get_mass_conversion_factor(units from_unit_enum, units to_unit_enum) +{ + map > conv; + double to_si; + + conv[kilogram][kilogram] = 1.0; + conv[kilogram][gram_per_mole] = 1.0/gram_per_mole_si; + conv[kilogram][gram] = 1.0/gram_si; + conv[kilogram][amu] = 1.0/amu_si; + conv[kilogram][picogram] = 1.0/picogram_si; + conv[kilogram][attogram] = 1.0/attogram_si; + + to_si = 1.0/conv[kilogram][gram_per_mole]; + conv[gram_per_mole][kilogram] = to_si*conv[kilogram][kilogram]; + conv[gram_per_mole][gram_per_mole] = 1.0; + conv[gram_per_mole][gram] = to_si*conv[kilogram][gram]; + conv[gram_per_mole][amu] = to_si*conv[kilogram][amu]; + conv[gram_per_mole][picogram] = to_si*conv[kilogram][picogram]; + conv[gram_per_mole][attogram] = to_si*conv[kilogram][attogram]; + + to_si = 1.0/conv[kilogram][gram]; + conv[gram][kilogram] = to_si*conv[kilogram][kilogram]; + conv[gram][gram_per_mole] = to_si*conv[kilogram][gram_per_mole]; + conv[gram][gram] = 1.0; + conv[gram][amu] = to_si*conv[kilogram][amu]; + conv[gram][picogram] = to_si*conv[kilogram][picogram]; + conv[gram][attogram] = to_si*conv[kilogram][attogram]; + + to_si = 1.0/conv[kilogram][amu]; + conv[amu][kilogram] = to_si*conv[kilogram][kilogram]; + conv[amu][gram_per_mole] = to_si*conv[kilogram][gram_per_mole]; + conv[amu][gram] = to_si*conv[kilogram][gram]; + conv[amu][amu] = 1.0; + conv[amu][picogram] = to_si*conv[kilogram][picogram]; + conv[amu][attogram] = to_si*conv[kilogram][attogram]; + + to_si = 1.0/conv[kilogram][picogram]; + conv[picogram][kilogram] = to_si*conv[kilogram][kilogram]; + conv[picogram][gram_per_mole] = to_si*conv[kilogram][gram_per_mole]; + conv[picogram][gram] = to_si*conv[kilogram][gram]; + conv[picogram][amu] = to_si*conv[kilogram][amu]; + conv[picogram][picogram] = 1.0; + conv[picogram][attogram] = to_si*conv[kilogram][attogram]; + + to_si = 1.0/conv[kilogram][attogram]; + conv[attogram][kilogram] = to_si*conv[kilogram][kilogram]; + conv[attogram][gram_per_mole] = to_si*conv[kilogram][gram_per_mole]; + conv[attogram][gram] = to_si*conv[kilogram][gram]; + conv[attogram][amu] = to_si*conv[kilogram][amu]; + conv[attogram][picogram] = to_si*conv[kilogram][picogram]; + conv[attogram][attogram] = 1.0; + + return conv[from_unit_enum][to_unit_enum]; +} + +/* ---------------------------------------------------------------------- */ + +// Distance conversion +double get_distance_conversion_factor(units from_unit_enum, units to_unit_enum) +{ + map > conv; + double to_si; + + conv[meter][meter] = 1.0; + conv[meter][angstrom] = 1.0/angstrom_si; + conv[meter][centimeter] = 1.0/centimeter_si; + conv[meter][bohr] = 1.0/bohr_si; + conv[meter][micrometer] = 1.0/micrometer_si; + conv[meter][nanometer] = 1.0/nanometer_si; + + to_si = 1.0/conv[meter][angstrom]; + conv[angstrom][meter] = to_si*conv[meter][meter]; + conv[angstrom][angstrom] = 1.0; + conv[angstrom][centimeter] = to_si*conv[meter][centimeter]; + conv[angstrom][bohr] = to_si*conv[meter][bohr]; + conv[angstrom][micrometer] = to_si*conv[meter][micrometer]; + conv[angstrom][nanometer] = to_si*conv[meter][nanometer]; + + to_si = 1.0/conv[meter][centimeter]; + conv[centimeter][meter] = to_si*conv[meter][meter]; + conv[centimeter][angstrom] = to_si*conv[meter][angstrom]; + conv[centimeter][centimeter] = 1.0; + conv[centimeter][bohr] = to_si*conv[meter][bohr]; + conv[centimeter][micrometer] = to_si*conv[meter][micrometer]; + conv[centimeter][nanometer] = to_si*conv[meter][nanometer]; + + to_si = 1.0/conv[meter][bohr]; + conv[bohr][meter] = to_si*conv[meter][meter]; + conv[bohr][angstrom] = to_si*conv[meter][angstrom]; + conv[bohr][centimeter] = to_si*conv[meter][centimeter]; + conv[bohr][bohr] = 1.0; + conv[bohr][micrometer] = to_si*conv[meter][micrometer]; + conv[bohr][nanometer] = to_si*conv[meter][nanometer]; + + to_si = 1.0/conv[meter][micrometer]; + conv[micrometer][meter] = to_si*conv[meter][meter]; + conv[micrometer][angstrom] = to_si*conv[meter][angstrom]; + conv[micrometer][centimeter] = to_si*conv[meter][centimeter]; + conv[micrometer][bohr] = to_si*conv[meter][bohr]; + conv[micrometer][micrometer] = 1.0; + conv[micrometer][nanometer] = to_si*conv[meter][nanometer]; + + to_si = 1.0/conv[meter][nanometer]; + conv[nanometer][meter] = to_si*conv[meter][meter]; + conv[nanometer][angstrom] = to_si*conv[meter][angstrom]; + conv[nanometer][centimeter] = to_si*conv[meter][centimeter]; + conv[nanometer][bohr] = to_si*conv[meter][bohr]; + conv[nanometer][micrometer] = to_si*conv[meter][micrometer]; + conv[nanometer][nanometer] = 1.0; + + return conv[from_unit_enum][to_unit_enum]; +} + +/* ---------------------------------------------------------------------- */ + +// Time conversion +double get_time_conversion_factor(units from_unit_enum, units to_unit_enum) +{ + map > conv; + double to_si; + + conv[second][second] = 1.0; + conv[second][femtosecond] = 1.0/femtosecond_si; + conv[second][picosecond] = 1.0/picosecond_si; + conv[second][microsecond] = 1.0/microsecond_si; + conv[second][nanosecond] = 1.0/nanosecond_si; + + to_si = 1.0/conv[second][femtosecond]; + conv[femtosecond][second] = to_si*conv[second][second]; + conv[femtosecond][femtosecond] = 1.0; + conv[femtosecond][picosecond] = to_si*conv[second][picosecond]; + conv[femtosecond][microsecond] = to_si*conv[second][microsecond]; + conv[femtosecond][nanosecond] = to_si*conv[second][nanosecond]; + + to_si = 1.0/conv[second][picosecond]; + conv[picosecond][second] = to_si*conv[second][second]; + conv[picosecond][femtosecond] = to_si*conv[second][femtosecond]; + conv[picosecond][picosecond] = 1.0; + conv[picosecond][microsecond] = to_si*conv[second][microsecond]; + conv[picosecond][nanosecond] = to_si*conv[second][nanosecond]; + + to_si = 1.0/conv[second][microsecond]; + conv[microsecond][second] = to_si*conv[second][second]; + conv[microsecond][femtosecond] = to_si*conv[second][femtosecond]; + conv[microsecond][picosecond] = to_si*conv[second][picosecond]; + conv[microsecond][microsecond] = 1.0; + conv[microsecond][nanosecond] = to_si*conv[second][nanosecond]; + + to_si = 1.0/conv[second][nanosecond]; + conv[nanosecond][second] = to_si*conv[second][second]; + conv[nanosecond][femtosecond] = to_si*conv[second][femtosecond]; + conv[nanosecond][picosecond] = to_si*conv[second][picosecond]; + conv[nanosecond][microsecond] = to_si*conv[second][microsecond]; + conv[nanosecond][nanosecond] = 1.0; + + return conv[from_unit_enum][to_unit_enum]; +} + +/* ---------------------------------------------------------------------- */ + +// Energy conversion +double get_energy_conversion_factor(units from_unit_enum, units to_unit_enum) +{ + + map > conv; + double to_si; + + conv[joule][joule] = 1.0; + conv[joule][kcal_per_mole] = 1.0/kcal_per_mole_si; + conv[joule][ev] = 1.0/ev_si; + conv[joule][erg] = 1.0/erg_si; + conv[joule][hartree] = 1.0/hartree_si; + conv[joule][picogram_micrometersq_per_microsecondsq] = 1.0/picogram_micrometersq_per_microsecondsq_si; + conv[joule][attogram_nanometersq_per_nanosecondsq] = 1.0/attogram_nanometersq_per_nanosecondsq_si; + + to_si = 1.0/conv[joule][kcal_per_mole]; + conv[kcal_per_mole][joule] = to_si*conv[joule][joule]; + conv[kcal_per_mole][kcal_per_mole] = 1.0; + conv[kcal_per_mole][ev] = to_si*conv[joule][ev]; + conv[kcal_per_mole][erg] = to_si*conv[joule][erg]; + conv[kcal_per_mole][hartree] = to_si*conv[joule][hartree]; + conv[kcal_per_mole][picogram_micrometersq_per_microsecondsq] = to_si*conv[joule][picogram_micrometersq_per_microsecondsq]; + conv[kcal_per_mole][attogram_nanometersq_per_nanosecondsq] = to_si*conv[joule][attogram_nanometersq_per_nanosecondsq]; + + to_si = 1.0/conv[joule][ev]; + conv[ev][joule] = to_si*conv[joule][joule]; + conv[ev][kcal_per_mole] = to_si*conv[joule][kcal_per_mole]; + conv[ev][ev] = 1.0; + conv[ev][erg] = to_si*conv[joule][erg]; + conv[ev][hartree] = to_si*conv[joule][hartree]; + conv[ev][picogram_micrometersq_per_microsecondsq] = to_si*conv[joule][picogram_micrometersq_per_microsecondsq]; + conv[ev][attogram_nanometersq_per_nanosecondsq] = to_si*conv[joule][attogram_nanometersq_per_nanosecondsq]; + + to_si = 1.0/conv[joule][erg]; + conv[erg][joule] = to_si*conv[joule][joule]; + conv[erg][kcal_per_mole] = to_si*conv[joule][kcal_per_mole]; + conv[erg][ev] = to_si*conv[joule][ev]; + conv[erg][erg] = 1.0; + conv[erg][hartree] = to_si*conv[joule][hartree]; + conv[erg][picogram_micrometersq_per_microsecondsq] = to_si*conv[joule][picogram_micrometersq_per_microsecondsq]; + conv[erg][attogram_nanometersq_per_nanosecondsq] = to_si*conv[joule][attogram_nanometersq_per_nanosecondsq]; + + to_si = 1.0/conv[joule][hartree]; + conv[hartree][joule] = to_si*conv[joule][joule]; + conv[hartree][kcal_per_mole] = to_si*conv[joule][kcal_per_mole]; + conv[hartree][ev] = to_si*conv[joule][ev]; + conv[hartree][erg] = to_si*conv[joule][erg]; + conv[hartree][hartree] = 1.0; + conv[hartree][picogram_micrometersq_per_microsecondsq] = to_si*conv[joule][picogram_micrometersq_per_microsecondsq]; + conv[hartree][attogram_nanometersq_per_nanosecondsq] = to_si*conv[joule][attogram_nanometersq_per_nanosecondsq]; + + to_si = 1.0/conv[joule][picogram_micrometersq_per_microsecondsq]; + conv[picogram_micrometersq_per_microsecondsq][joule] = to_si*conv[joule][joule]; + conv[picogram_micrometersq_per_microsecondsq][kcal_per_mole] = to_si*conv[joule][kcal_per_mole]; + conv[picogram_micrometersq_per_microsecondsq][ev] = to_si*conv[joule][ev]; + conv[picogram_micrometersq_per_microsecondsq][erg] = to_si*conv[joule][erg]; + conv[picogram_micrometersq_per_microsecondsq][hartree] = to_si*conv[joule][hartree]; + conv[picogram_micrometersq_per_microsecondsq][picogram_micrometersq_per_microsecondsq] = 1.0; + conv[picogram_micrometersq_per_microsecondsq][attogram_nanometersq_per_nanosecondsq] = to_si*conv[joule][attogram_nanometersq_per_nanosecondsq]; + + to_si = 1.0/conv[joule][attogram_nanometersq_per_nanosecondsq]; + conv[attogram_nanometersq_per_nanosecondsq][joule] = to_si*conv[joule][joule]; + conv[attogram_nanometersq_per_nanosecondsq][kcal_per_mole] = to_si*conv[joule][kcal_per_mole]; + conv[attogram_nanometersq_per_nanosecondsq][ev] = to_si*conv[joule][ev]; + conv[attogram_nanometersq_per_nanosecondsq][erg] = to_si*conv[joule][erg]; + conv[attogram_nanometersq_per_nanosecondsq][hartree] = to_si*conv[joule][hartree]; + conv[attogram_nanometersq_per_nanosecondsq][picogram_micrometersq_per_microsecondsq] = to_si*conv[joule][picogram_micrometersq_per_microsecondsq]; + conv[attogram_nanometersq_per_nanosecondsq][attogram_nanometersq_per_nanosecondsq] = 1.0; + + return conv[from_unit_enum][to_unit_enum]; +} + +/* ---------------------------------------------------------------------- */ + +// Velocity conversion +double get_velocity_conversion_factor(units from_unit_enum, units to_unit_enum) +{ + map > conv; + double to_si; + + conv[meter_per_second][meter_per_second] = 1.0; + conv[meter_per_second][angstrom_per_femtosecond] = 1.0/angstrom_per_femtosecond_si; + conv[meter_per_second][angstrom_per_picosecond] = 1.0/angstrom_per_picosecond_si; + conv[meter_per_second][centimeter_per_second] = 1.0/centimeter_per_second_si; + conv[meter_per_second][bohr_per_atu] = 1.0/bohr_per_atu_si; + conv[meter_per_second][micrometer_per_microsecond] = 1.0/micrometer_per_microsecond_si; + conv[meter_per_second][nanometer_per_nanosecond] = 1.0/nanometer_per_nanosecond_si; + + to_si = 1.0/conv[meter_per_second][angstrom_per_femtosecond]; + conv[angstrom_per_femtosecond][meter_per_second] = to_si*conv[meter_per_second][meter_per_second]; + conv[angstrom_per_femtosecond][angstrom_per_femtosecond] = 1.0; + conv[angstrom_per_femtosecond][angstrom_per_picosecond] = to_si*conv[meter_per_second][angstrom_per_picosecond]; + conv[angstrom_per_femtosecond][centimeter_per_second] = to_si*conv[meter_per_second][centimeter_per_second]; + conv[angstrom_per_femtosecond][bohr_per_atu] = to_si*conv[meter_per_second][bohr_per_atu]; + conv[angstrom_per_femtosecond][micrometer_per_microsecond] = to_si*conv[meter_per_second][micrometer_per_microsecond]; + conv[angstrom_per_femtosecond][nanometer_per_nanosecond] = to_si*conv[meter_per_second][nanometer_per_nanosecond]; + + to_si = 1.0/conv[meter_per_second][angstrom_per_picosecond]; + conv[angstrom_per_picosecond][meter_per_second] = to_si*conv[meter_per_second][meter_per_second]; + conv[angstrom_per_picosecond][angstrom_per_femtosecond] = to_si*conv[meter_per_second][angstrom_per_femtosecond]; + conv[angstrom_per_picosecond][angstrom_per_picosecond] = 1.0; + conv[angstrom_per_picosecond][centimeter_per_second] = to_si*conv[meter_per_second][centimeter_per_second]; + conv[angstrom_per_picosecond][bohr_per_atu] = to_si*conv[meter_per_second][bohr_per_atu]; + conv[angstrom_per_picosecond][micrometer_per_microsecond] = to_si*conv[meter_per_second][micrometer_per_microsecond]; + conv[angstrom_per_picosecond][nanometer_per_nanosecond] = to_si*conv[meter_per_second][nanometer_per_nanosecond]; + + to_si = 1.0/conv[meter_per_second][centimeter_per_second]; + conv[centimeter_per_second][meter_per_second] = to_si*conv[meter_per_second][meter_per_second]; + conv[centimeter_per_second][angstrom_per_femtosecond] = to_si*conv[meter_per_second][angstrom_per_femtosecond]; + conv[centimeter_per_second][angstrom_per_picosecond] = to_si*conv[meter_per_second][angstrom_per_picosecond]; + conv[centimeter_per_second][centimeter_per_second] = 1.0; + conv[centimeter_per_second][bohr_per_atu] = to_si*conv[meter_per_second][bohr_per_atu]; + conv[centimeter_per_second][micrometer_per_microsecond] = to_si*conv[meter_per_second][micrometer_per_microsecond]; + conv[centimeter_per_second][nanometer_per_nanosecond] = to_si*conv[meter_per_second][nanometer_per_nanosecond]; + + to_si = 1.0/conv[meter_per_second][bohr_per_atu]; + conv[bohr_per_atu][meter_per_second] = to_si*conv[meter_per_second][meter_per_second]; + conv[bohr_per_atu][angstrom_per_femtosecond] = to_si*conv[meter_per_second][angstrom_per_femtosecond]; + conv[bohr_per_atu][angstrom_per_picosecond] = to_si*conv[meter_per_second][angstrom_per_picosecond]; + conv[bohr_per_atu][centimeter_per_second] = to_si*conv[meter_per_second][centimeter_per_second]; + conv[bohr_per_atu][bohr_per_atu] = 1.0; + conv[bohr_per_atu][micrometer_per_microsecond] = to_si*conv[meter_per_second][micrometer_per_microsecond]; + conv[bohr_per_atu][nanometer_per_nanosecond] = to_si*conv[meter_per_second][nanometer_per_nanosecond]; + + to_si = 1.0/conv[meter_per_second][micrometer_per_microsecond]; + conv[micrometer_per_microsecond][meter_per_second] = to_si*conv[meter_per_second][meter_per_second]; + conv[micrometer_per_microsecond][angstrom_per_femtosecond] = to_si*conv[meter_per_second][angstrom_per_femtosecond]; + conv[micrometer_per_microsecond][angstrom_per_picosecond] = to_si*conv[meter_per_second][angstrom_per_picosecond]; + conv[micrometer_per_microsecond][centimeter_per_second] = to_si*conv[meter_per_second][centimeter_per_second]; + conv[micrometer_per_microsecond][bohr_per_atu] = to_si*conv[meter_per_second][bohr_per_atu]; + conv[micrometer_per_microsecond][micrometer_per_microsecond] = 1.0; + conv[micrometer_per_microsecond][nanometer_per_nanosecond] = to_si*conv[meter_per_second][nanometer_per_nanosecond]; + + to_si = 1.0/conv[meter_per_second][nanometer_per_nanosecond]; + conv[nanometer_per_nanosecond][meter_per_second] = to_si*conv[meter_per_second][meter_per_second]; + conv[nanometer_per_nanosecond][angstrom_per_femtosecond] = to_si*conv[meter_per_second][angstrom_per_femtosecond]; + conv[nanometer_per_nanosecond][angstrom_per_picosecond] = to_si*conv[meter_per_second][angstrom_per_picosecond]; + conv[nanometer_per_nanosecond][centimeter_per_second] = to_si*conv[meter_per_second][centimeter_per_second]; + conv[nanometer_per_nanosecond][bohr_per_atu] = to_si*conv[meter_per_second][bohr_per_atu]; + conv[nanometer_per_nanosecond][micrometer_per_microsecond] = to_si*conv[meter_per_second][micrometer_per_microsecond]; + conv[nanometer_per_nanosecond][nanometer_per_nanosecond] = 1.0; + + return conv[from_unit_enum][to_unit_enum]; +} + +/* ---------------------------------------------------------------------- */ + +// Force conversion +double get_force_conversion_factor(units from_unit_enum, units to_unit_enum) +{ + map > conv; + double to_si; + + conv[newton][newton] = 1.0; + conv[newton][kcal_per_mole_angstrom] = 1.0/kcal_per_mole_angstrom_si; + conv[newton][ev_per_angstrom] = 1.0/ev_per_angstrom_si; + conv[newton][dyne] = 1.0/dyne_si; + conv[newton][hartree_per_bohr] = 1.0/hartree_per_bohr_si; + conv[newton][picogram_micrometer_per_microsecondsq] = 1.0/picogram_micrometer_per_microsecondsq_si; + conv[newton][attogram_nanometer_per_nanosecondsq] = 1.0/attogram_nanometer_per_nanosecondsq_si; + + to_si = 1.0/conv[newton][kcal_per_mole_angstrom]; + conv[kcal_per_mole_angstrom][newton] = to_si*conv[newton][newton]; + conv[kcal_per_mole_angstrom][kcal_per_mole_angstrom] = 1.0; + conv[kcal_per_mole_angstrom][ev_per_angstrom] = to_si*conv[newton][ev_per_angstrom]; + conv[kcal_per_mole_angstrom][dyne] = to_si*conv[newton][dyne]; + conv[kcal_per_mole_angstrom][hartree_per_bohr] = to_si*conv[newton][hartree_per_bohr]; + conv[kcal_per_mole_angstrom][picogram_micrometer_per_microsecondsq] = to_si*conv[newton][picogram_micrometer_per_microsecondsq]; + conv[kcal_per_mole_angstrom][attogram_nanometer_per_nanosecondsq] = to_si*conv[newton][attogram_nanometer_per_nanosecondsq]; + + to_si = 1.0/conv[newton][ev_per_angstrom]; + conv[ev_per_angstrom][newton] = to_si*conv[newton][newton]; + conv[ev_per_angstrom][kcal_per_mole_angstrom] = to_si*conv[newton][kcal_per_mole_angstrom]; + conv[ev_per_angstrom][ev_per_angstrom] = 1.0; + conv[ev_per_angstrom][dyne] = to_si*conv[newton][dyne]; + conv[ev_per_angstrom][hartree_per_bohr] = to_si*conv[newton][hartree_per_bohr]; + conv[ev_per_angstrom][picogram_micrometer_per_microsecondsq] = to_si*conv[newton][picogram_micrometer_per_microsecondsq]; + conv[ev_per_angstrom][attogram_nanometer_per_nanosecondsq] = to_si*conv[newton][attogram_nanometer_per_nanosecondsq]; + + to_si = 1.0/conv[newton][dyne]; + conv[dyne][newton] = to_si*conv[newton][newton]; + conv[dyne][kcal_per_mole_angstrom] = to_si*conv[newton][kcal_per_mole_angstrom]; + conv[dyne][ev_per_angstrom] = to_si*conv[newton][ev_per_angstrom]; + conv[dyne][dyne] = 1.0; + conv[dyne][hartree_per_bohr] = to_si*conv[newton][hartree_per_bohr]; + conv[dyne][picogram_micrometer_per_microsecondsq] = to_si*conv[newton][picogram_micrometer_per_microsecondsq]; + conv[dyne][attogram_nanometer_per_nanosecondsq] = to_si*conv[newton][attogram_nanometer_per_nanosecondsq]; + + to_si = 1.0/conv[newton][hartree_per_bohr]; + conv[hartree_per_bohr][newton] = to_si*conv[newton][newton]; + conv[hartree_per_bohr][kcal_per_mole_angstrom] = to_si*conv[newton][kcal_per_mole_angstrom]; + conv[hartree_per_bohr][ev_per_angstrom] = to_si*conv[newton][ev_per_angstrom]; + conv[hartree_per_bohr][dyne] = to_si*conv[newton][dyne]; + conv[hartree_per_bohr][hartree_per_bohr] = 1.0; + conv[hartree_per_bohr][picogram_micrometer_per_microsecondsq] = to_si*conv[newton][picogram_micrometer_per_microsecondsq]; + conv[hartree_per_bohr][attogram_nanometer_per_nanosecondsq] = to_si*conv[newton][attogram_nanometer_per_nanosecondsq]; + + to_si = 1.0/conv[newton][picogram_micrometer_per_microsecondsq]; + conv[picogram_micrometer_per_microsecondsq][newton] = to_si*conv[newton][newton]; + conv[picogram_micrometer_per_microsecondsq][kcal_per_mole_angstrom] = to_si*conv[newton][kcal_per_mole_angstrom]; + conv[picogram_micrometer_per_microsecondsq][ev_per_angstrom] = to_si*conv[newton][ev_per_angstrom]; + conv[picogram_micrometer_per_microsecondsq][dyne] = to_si*conv[newton][dyne]; + conv[picogram_micrometer_per_microsecondsq][hartree_per_bohr] = to_si*conv[newton][hartree_per_bohr]; + conv[picogram_micrometer_per_microsecondsq][picogram_micrometer_per_microsecondsq] = 1.0; + conv[picogram_micrometer_per_microsecondsq][attogram_nanometer_per_nanosecondsq] = to_si*conv[newton][attogram_nanometer_per_nanosecondsq]; + + to_si = 1.0/conv[newton][attogram_nanometer_per_nanosecondsq]; + conv[attogram_nanometer_per_nanosecondsq][newton] = to_si*conv[newton][newton]; + conv[attogram_nanometer_per_nanosecondsq][kcal_per_mole_angstrom] = to_si*conv[newton][kcal_per_mole_angstrom]; + conv[attogram_nanometer_per_nanosecondsq][ev_per_angstrom] = to_si*conv[newton][ev_per_angstrom]; + conv[attogram_nanometer_per_nanosecondsq][dyne] = to_si*conv[newton][dyne]; + conv[attogram_nanometer_per_nanosecondsq][hartree_per_bohr] = to_si*conv[newton][hartree_per_bohr]; + conv[attogram_nanometer_per_nanosecondsq][picogram_micrometer_per_microsecondsq] = to_si*conv[newton][picogram_micrometer_per_microsecondsq]; + conv[attogram_nanometer_per_nanosecondsq][attogram_nanometer_per_nanosecondsq] = 1.0; + + return conv[from_unit_enum][to_unit_enum]; +} + +/* ---------------------------------------------------------------------- */ + +// Torque conversion +double get_torque_conversion_factor(units from_unit_enum, units to_unit_enum) +{ + map > conv; + double to_si; + + conv[newton_meter][newton_meter] = 1.0; + conv[newton_meter][kcal_per_mole] = 1.0/kcal_per_mole_si; + conv[newton_meter][ev] = 1.0/ev_si; + conv[newton_meter][dyne_centimeter] = 1.0/dyne_centimeter_si; + conv[newton_meter][hartree] = 1.0/hartree_si; + conv[newton_meter][picogram_micrometersq_per_microsecondsq] = 1.0/picogram_micrometersq_per_microsecondsq_si; + conv[newton_meter][attogram_nanometersq_per_nanosecondsq] = 1.0/attogram_nanometersq_per_nanosecondsq_si; + + to_si = 1.0/conv[newton_meter][kcal_per_mole]; + conv[kcal_per_mole][newton_meter] = to_si*conv[newton_meter][newton_meter]; + conv[kcal_per_mole][kcal_per_mole] = 1.0; + conv[kcal_per_mole][ev] = to_si*conv[newton_meter][ev]; + conv[kcal_per_mole][dyne_centimeter] = to_si*conv[newton_meter][dyne_centimeter]; + conv[kcal_per_mole][hartree] = to_si*conv[newton_meter][hartree]; + conv[kcal_per_mole][picogram_micrometersq_per_microsecondsq] = to_si*conv[newton_meter][picogram_micrometersq_per_microsecondsq]; + conv[kcal_per_mole][attogram_nanometersq_per_nanosecondsq] = to_si*conv[newton_meter][attogram_nanometersq_per_nanosecondsq]; + + to_si = 1.0/conv[newton_meter][ev]; + conv[ev][newton_meter] = to_si*conv[newton_meter][newton_meter]; + conv[ev][kcal_per_mole] = to_si*conv[newton_meter][kcal_per_mole]; + conv[ev][ev] = 1.0; + conv[ev][dyne_centimeter] = to_si*conv[newton_meter][dyne_centimeter]; + conv[ev][hartree] = to_si*conv[newton_meter][hartree]; + conv[ev][picogram_micrometersq_per_microsecondsq] = to_si*conv[newton_meter][picogram_micrometersq_per_microsecondsq]; + conv[ev][attogram_nanometersq_per_nanosecondsq] = to_si*conv[newton_meter][attogram_nanometersq_per_nanosecondsq]; + + to_si = 1.0/conv[newton_meter][dyne_centimeter]; + conv[dyne_centimeter][newton_meter] = to_si*conv[newton_meter][newton_meter]; + conv[dyne_centimeter][kcal_per_mole] = to_si*conv[newton_meter][kcal_per_mole]; + conv[dyne_centimeter][ev] = to_si*conv[newton_meter][ev]; + conv[dyne_centimeter][dyne_centimeter] = 1.0; + conv[dyne_centimeter][hartree] = to_si*conv[newton_meter][hartree]; + conv[dyne_centimeter][picogram_micrometersq_per_microsecondsq] = to_si*conv[newton_meter][picogram_micrometersq_per_microsecondsq]; + conv[dyne_centimeter][attogram_nanometersq_per_nanosecondsq] = to_si*conv[newton_meter][attogram_nanometersq_per_nanosecondsq]; + + to_si = 1.0/conv[newton_meter][hartree]; + conv[hartree][newton_meter] = to_si*conv[newton_meter][newton_meter]; + conv[hartree][kcal_per_mole] = to_si*conv[newton_meter][kcal_per_mole]; + conv[hartree][ev] = to_si*conv[newton_meter][ev]; + conv[hartree][dyne_centimeter] = to_si*conv[newton_meter][dyne_centimeter]; + conv[hartree][hartree] = 1.0; + conv[hartree][picogram_micrometersq_per_microsecondsq] = to_si*conv[newton_meter][picogram_micrometersq_per_microsecondsq]; + conv[hartree][attogram_nanometersq_per_nanosecondsq] = to_si*conv[newton_meter][attogram_nanometersq_per_nanosecondsq]; + + to_si = 1.0/conv[newton_meter][picogram_micrometersq_per_microsecondsq]; + conv[picogram_micrometersq_per_microsecondsq][newton_meter] = to_si*conv[newton_meter][newton_meter]; + conv[picogram_micrometersq_per_microsecondsq][kcal_per_mole] = to_si*conv[newton_meter][kcal_per_mole]; + conv[picogram_micrometersq_per_microsecondsq][ev] = to_si*conv[newton_meter][ev]; + conv[picogram_micrometersq_per_microsecondsq][dyne_centimeter] = to_si*conv[newton_meter][dyne_centimeter]; + conv[picogram_micrometersq_per_microsecondsq][hartree] = to_si*conv[newton_meter][hartree]; + conv[picogram_micrometersq_per_microsecondsq][picogram_micrometersq_per_microsecondsq] = 1.0; + conv[picogram_micrometersq_per_microsecondsq][attogram_nanometersq_per_nanosecondsq] = to_si*conv[newton_meter][attogram_nanometersq_per_nanosecondsq]; + + to_si = 1.0/conv[newton_meter][attogram_nanometersq_per_nanosecondsq]; + conv[attogram_nanometersq_per_nanosecondsq][newton_meter] = to_si*conv[newton_meter][newton_meter]; + conv[attogram_nanometersq_per_nanosecondsq][kcal_per_mole] = to_si*conv[newton_meter][kcal_per_mole]; + conv[attogram_nanometersq_per_nanosecondsq][ev] = to_si*conv[newton_meter][ev]; + conv[attogram_nanometersq_per_nanosecondsq][dyne_centimeter] = to_si*conv[newton_meter][dyne_centimeter]; + conv[attogram_nanometersq_per_nanosecondsq][hartree] = to_si*conv[newton_meter][hartree]; + conv[attogram_nanometersq_per_nanosecondsq][picogram_micrometersq_per_microsecondsq] = to_si*conv[newton_meter][picogram_micrometersq_per_microsecondsq]; + conv[attogram_nanometersq_per_nanosecondsq][attogram_nanometersq_per_nanosecondsq] = 1.0; + + return conv[from_unit_enum][to_unit_enum]; +} + +/* ---------------------------------------------------------------------- */ + +// Temperature conversion +double get_temperature_conversion_factor(units from_unit_enum, units to_unit_enum) +{ + map > conv; + double to_si; + + conv[kelvin][kelvin] = 1.0; + + return conv[from_unit_enum][to_unit_enum]; +} + +/* ---------------------------------------------------------------------- */ + +// Pressure conversion +double get_pressure_conversion_factor(units from_unit_enum, units to_unit_enum) +{ + map > conv; + double to_si; + + conv[pascal][pascal] = 1.0; + conv[pascal][atmosphere] = 1.0/atmosphere_si; + conv[pascal][bar] = 1.0/bar_si; + conv[pascal][dyne_per_centimetersq] = 1.0/dyne_per_centimetersq_si; + conv[pascal][picogram_per_micrometer_microsecondsq] = 1.0/picogram_per_micrometer_microsecondsq_si; + conv[pascal][attogram_per_nanometer_nanosecondsq] = 1.0/attogram_per_nanometer_nanosecondsq_si; + + to_si = 1.0/conv[pascal][atmosphere]; + conv[atmosphere][pascal] = to_si*conv[pascal][pascal]; + conv[atmosphere][atmosphere] = 1.0; + conv[atmosphere][bar] = to_si*conv[pascal][bar]; + conv[atmosphere][dyne_per_centimetersq] = to_si*conv[pascal][dyne_per_centimetersq]; + conv[atmosphere][picogram_per_micrometer_microsecondsq] = to_si*conv[pascal][picogram_per_micrometer_microsecondsq]; + conv[atmosphere][attogram_per_nanometer_nanosecondsq] = to_si*conv[pascal][attogram_per_nanometer_nanosecondsq]; + + to_si = 1.0/conv[pascal][bar]; + conv[bar][pascal] = to_si*conv[pascal][pascal]; + conv[bar][atmosphere] = to_si*conv[pascal][atmosphere]; + conv[bar][bar] = 1.0; + conv[bar][dyne_per_centimetersq] = to_si*conv[pascal][dyne_per_centimetersq]; + conv[bar][picogram_per_micrometer_microsecondsq] = to_si*conv[pascal][picogram_per_micrometer_microsecondsq]; + conv[bar][attogram_per_nanometer_nanosecondsq] = to_si*conv[pascal][attogram_per_nanometer_nanosecondsq]; + + to_si = 1.0/conv[pascal][dyne_per_centimetersq]; + conv[dyne_per_centimetersq][pascal] = to_si*conv[pascal][pascal]; + conv[dyne_per_centimetersq][atmosphere] = to_si*conv[pascal][atmosphere]; + conv[dyne_per_centimetersq][bar] = to_si*conv[pascal][bar]; + conv[dyne_per_centimetersq][dyne_per_centimetersq] = 1.0; + conv[dyne_per_centimetersq][picogram_per_micrometer_microsecondsq] = to_si*conv[pascal][picogram_per_micrometer_microsecondsq]; + conv[dyne_per_centimetersq][attogram_per_nanometer_nanosecondsq] = to_si*conv[pascal][attogram_per_nanometer_nanosecondsq]; + + to_si = 1.0/conv[pascal][picogram_per_micrometer_microsecondsq]; + conv[picogram_per_micrometer_microsecondsq][pascal] = to_si*conv[pascal][pascal]; + conv[picogram_per_micrometer_microsecondsq][atmosphere] = to_si*conv[pascal][atmosphere]; + conv[picogram_per_micrometer_microsecondsq][bar] = to_si*conv[pascal][bar]; + conv[picogram_per_micrometer_microsecondsq][dyne_per_centimetersq] = to_si*conv[pascal][dyne_per_centimetersq]; + conv[picogram_per_micrometer_microsecondsq][picogram_per_micrometer_microsecondsq] = 1.0; + conv[picogram_per_micrometer_microsecondsq][attogram_per_nanometer_nanosecondsq] = to_si*conv[pascal][attogram_per_nanometer_nanosecondsq]; + + to_si = 1.0/conv[pascal][attogram_per_nanometer_nanosecondsq]; + conv[attogram_per_nanometer_nanosecondsq][pascal] = to_si*conv[pascal][pascal]; + conv[attogram_per_nanometer_nanosecondsq][atmosphere] = to_si*conv[pascal][atmosphere]; + conv[attogram_per_nanometer_nanosecondsq][bar] = to_si*conv[pascal][bar]; + conv[attogram_per_nanometer_nanosecondsq][dyne_per_centimetersq] = to_si*conv[pascal][dyne_per_centimetersq]; + conv[attogram_per_nanometer_nanosecondsq][picogram_per_micrometer_microsecondsq] = to_si*conv[pascal][picogram_per_micrometer_microsecondsq]; + conv[attogram_per_nanometer_nanosecondsq][attogram_per_nanometer_nanosecondsq] = 1.0; + + return conv[from_unit_enum][to_unit_enum]; +} + +/* ---------------------------------------------------------------------- */ + +// Viscosity conversion +double get_viscosity_conversion_factor(units from_unit_enum, units to_unit_enum) +{ + map > conv; + double to_si; + + conv[pascal_second][pascal_second] = 1.0; + conv[pascal_second][poise] = 1.0/poise_si; + conv[pascal_second][amu_per_bohr_femtosecond] = 1.0/amu_per_bohr_femtosecond_si; + conv[pascal_second][picogram_per_micrometer_microsecond] = 1.0/picogram_per_micrometer_microsecond_si; + conv[pascal_second][attogram_per_nanometer_nanosecond] = 1.0/attogram_per_nanometer_nanosecond_si; + + to_si = 1.0/conv[pascal_second][poise]; + conv[poise][pascal_second] = to_si*conv[pascal_second][pascal_second]; + conv[poise][poise] = 1.0; + conv[poise][amu_per_bohr_femtosecond] = to_si*conv[pascal_second][amu_per_bohr_femtosecond]; + conv[poise][picogram_per_micrometer_microsecond] = to_si*conv[pascal_second][picogram_per_micrometer_microsecond]; + conv[poise][attogram_per_nanometer_nanosecond] = to_si*conv[pascal_second][attogram_per_nanometer_nanosecond]; + + to_si = 1.0/conv[pascal_second][amu_per_bohr_femtosecond]; + conv[amu_per_bohr_femtosecond][pascal_second] = to_si*conv[pascal_second][pascal_second]; + conv[amu_per_bohr_femtosecond][poise] = to_si*conv[pascal_second][poise]; + conv[amu_per_bohr_femtosecond][amu_per_bohr_femtosecond] = 1.0; + conv[amu_per_bohr_femtosecond][picogram_per_micrometer_microsecond] = to_si*conv[pascal_second][picogram_per_micrometer_microsecond]; + conv[amu_per_bohr_femtosecond][attogram_per_nanometer_nanosecond] = to_si*conv[pascal_second][attogram_per_nanometer_nanosecond]; + + to_si = 1.0/conv[pascal_second][picogram_per_micrometer_microsecond]; + conv[picogram_per_micrometer_microsecond][pascal_second] = to_si*conv[pascal_second][pascal_second]; + conv[picogram_per_micrometer_microsecond][poise] = to_si*conv[pascal_second][poise]; + conv[picogram_per_micrometer_microsecond][amu_per_bohr_femtosecond] = to_si*conv[pascal_second][amu_per_bohr_femtosecond]; + conv[picogram_per_micrometer_microsecond][picogram_per_micrometer_microsecond] = 1.0; + conv[picogram_per_micrometer_microsecond][attogram_per_nanometer_nanosecond] = to_si*conv[pascal_second][attogram_per_nanometer_nanosecond]; + + to_si = 1.0/conv[pascal_second][attogram_per_nanometer_nanosecond]; + conv[attogram_per_nanometer_nanosecond][pascal_second] = to_si*conv[pascal_second][pascal_second]; + conv[attogram_per_nanometer_nanosecond][poise] = to_si*conv[pascal_second][poise]; + conv[attogram_per_nanometer_nanosecond][amu_per_bohr_femtosecond] = to_si*conv[pascal_second][amu_per_bohr_femtosecond]; + conv[attogram_per_nanometer_nanosecond][picogram_per_micrometer_microsecond] = to_si*conv[pascal_second][picogram_per_micrometer_microsecond]; + conv[attogram_per_nanometer_nanosecond][attogram_per_nanometer_nanosecond] = 1.0; + + return conv[from_unit_enum][to_unit_enum]; +} + +/* ---------------------------------------------------------------------- */ + +// Charge conversion +double get_charge_conversion_factor(units from_unit_enum, units to_unit_enum) +{ + map > conv; + double to_si; + + conv[coulomb][coulomb] = 1.0; + conv[coulomb][echarge] = 1.0/echarge_si; + conv[coulomb][statcoulomb] = 1.0/statcoulomb_si; + conv[coulomb][picocoulomb] = 1.0/picocoulomb_si; + + to_si = 1.0/conv[coulomb][echarge]; + conv[echarge][coulomb] = to_si*conv[coulomb][coulomb]; + conv[echarge][echarge] = 1.0; + conv[echarge][statcoulomb] = to_si*conv[coulomb][statcoulomb]; + conv[echarge][picocoulomb] = to_si*conv[coulomb][picocoulomb]; + + to_si = 1.0/conv[coulomb][statcoulomb]; + conv[statcoulomb][coulomb] = to_si*conv[coulomb][coulomb]; + conv[statcoulomb][echarge] = to_si*conv[coulomb][echarge]; + conv[statcoulomb][statcoulomb] = 1.0; + conv[statcoulomb][picocoulomb] = to_si*conv[coulomb][picocoulomb]; + + to_si = 1.0/conv[coulomb][picocoulomb]; + conv[picocoulomb][coulomb] = to_si*conv[coulomb][coulomb]; + conv[picocoulomb][echarge] = to_si*conv[coulomb][echarge]; + conv[picocoulomb][statcoulomb] = to_si*conv[coulomb][statcoulomb]; + conv[picocoulomb][picocoulomb] = 1.0; + + return conv[from_unit_enum][to_unit_enum]; +} + +/* ---------------------------------------------------------------------- */ + +// Dipole conversion +double get_dipole_conversion_factor(units from_unit_enum, units to_unit_enum) +{ + map > conv; + double to_si; + + conv[coulomb_meter][coulomb_meter] = 1.0; + conv[coulomb_meter][electron_angstrom] = 1.0/electron_angstrom_si; + conv[coulomb_meter][statcoulomb_centimeter] = 1.0/statcoulomb_centimeter_si; + conv[coulomb_meter][debye] = 1.0/debye_si; + conv[coulomb_meter][picocoulomb_micrometer] = 1.0/picocoulomb_micrometer_si; + conv[coulomb_meter][electron_nanometer] = 1.0/electron_nanometer_si; + + to_si = 1.0/conv[coulomb_meter][electron_angstrom]; + conv[electron_angstrom][coulomb_meter] = to_si*conv[coulomb_meter][coulomb_meter]; + conv[electron_angstrom][electron_angstrom] = 1.0; + conv[electron_angstrom][statcoulomb_centimeter] = to_si*conv[coulomb_meter][statcoulomb_centimeter]; + conv[electron_angstrom][debye] = to_si*conv[coulomb_meter][debye]; + conv[electron_angstrom][picocoulomb_micrometer] = to_si*conv[coulomb_meter][picocoulomb_micrometer]; + conv[electron_angstrom][electron_nanometer] = to_si*conv[coulomb_meter][electron_nanometer]; + + to_si = 1.0/conv[coulomb_meter][statcoulomb_centimeter]; + conv[statcoulomb_centimeter][coulomb_meter] = to_si*conv[coulomb_meter][coulomb_meter]; + conv[statcoulomb_centimeter][electron_angstrom] = to_si*conv[coulomb_meter][electron_angstrom]; + conv[statcoulomb_centimeter][statcoulomb_centimeter] = 1.0; + conv[statcoulomb_centimeter][debye] = to_si*conv[coulomb_meter][debye]; + conv[statcoulomb_centimeter][picocoulomb_micrometer] = to_si*conv[coulomb_meter][picocoulomb_micrometer]; + conv[statcoulomb_centimeter][electron_nanometer] = to_si*conv[coulomb_meter][electron_nanometer]; + + to_si = 1.0/conv[coulomb_meter][debye]; + conv[debye][coulomb_meter] = to_si*conv[coulomb_meter][coulomb_meter]; + conv[debye][electron_angstrom] = to_si*conv[coulomb_meter][electron_angstrom]; + conv[debye][statcoulomb_centimeter] = to_si*conv[coulomb_meter][statcoulomb_centimeter]; + conv[debye][debye] = 1.0; + conv[debye][picocoulomb_micrometer] = to_si*conv[coulomb_meter][picocoulomb_micrometer]; + conv[debye][electron_nanometer] = to_si*conv[coulomb_meter][electron_nanometer]; + + to_si = 1.0/conv[coulomb_meter][picocoulomb_micrometer]; + conv[picocoulomb_micrometer][coulomb_meter] = to_si*conv[coulomb_meter][coulomb_meter]; + conv[picocoulomb_micrometer][electron_angstrom] = to_si*conv[coulomb_meter][electron_angstrom]; + conv[picocoulomb_micrometer][statcoulomb_centimeter] = to_si*conv[coulomb_meter][statcoulomb_centimeter]; + conv[picocoulomb_micrometer][debye] = to_si*conv[coulomb_meter][debye]; + conv[picocoulomb_micrometer][picocoulomb_micrometer] = 1.0; + conv[picocoulomb_micrometer][electron_nanometer] = to_si*conv[coulomb_meter][electron_nanometer]; + + to_si = 1.0/conv[coulomb_meter][electron_nanometer]; + conv[electron_nanometer][coulomb_meter] = to_si*conv[coulomb_meter][coulomb_meter]; + conv[electron_nanometer][electron_angstrom] = to_si*conv[coulomb_meter][electron_angstrom]; + conv[electron_nanometer][statcoulomb_centimeter] = to_si*conv[coulomb_meter][statcoulomb_centimeter]; + conv[electron_nanometer][debye] = to_si*conv[coulomb_meter][debye]; + conv[electron_nanometer][picocoulomb_micrometer] = to_si*conv[coulomb_meter][picocoulomb_micrometer]; + conv[electron_nanometer][electron_nanometer] = 1.0; + + return conv[from_unit_enum][to_unit_enum]; +} + +/* ---------------------------------------------------------------------- */ + +// Electric field conversion +double get_efield_conversion_factor(units from_unit_enum, units to_unit_enum) +{ + map > conv; + double to_si; + + conv[volt_per_meter][volt_per_meter] = 1.0; + conv[volt_per_meter][volt_per_angstrom] = 1.0/volt_per_angstrom_si; + conv[volt_per_meter][statvolt_per_centimeter] = 1.0/statvolt_per_centimeter_si; + conv[volt_per_meter][volt_per_centimeter] = 1.0/volt_per_centimeter_si; + conv[volt_per_meter][volt_per_micrometer] = 1.0/volt_per_micrometer_si; + conv[volt_per_meter][volt_per_nanometer] = 1.0/volt_per_nanometer_si; + + to_si = 1.0/conv[volt_per_meter][volt_per_angstrom]; + conv[volt_per_angstrom][volt_per_meter] = to_si*conv[volt_per_meter][volt_per_meter]; + conv[volt_per_angstrom][volt_per_angstrom] = 1.0; + conv[volt_per_angstrom][statvolt_per_centimeter] = to_si*conv[volt_per_meter][statvolt_per_centimeter]; + conv[volt_per_angstrom][volt_per_centimeter] = to_si*conv[volt_per_meter][volt_per_centimeter]; + conv[volt_per_angstrom][volt_per_micrometer] = to_si*conv[volt_per_meter][volt_per_micrometer]; + conv[volt_per_angstrom][volt_per_nanometer] = to_si*conv[volt_per_meter][volt_per_nanometer]; + + to_si = 1.0/conv[volt_per_meter][statvolt_per_centimeter]; + conv[statvolt_per_centimeter][volt_per_meter] = to_si*conv[volt_per_meter][volt_per_meter]; + conv[statvolt_per_centimeter][volt_per_angstrom] = to_si*conv[volt_per_meter][volt_per_angstrom]; + conv[statvolt_per_centimeter][statvolt_per_centimeter] = 1.0; + conv[statvolt_per_centimeter][volt_per_centimeter] = to_si*conv[volt_per_meter][volt_per_centimeter]; + conv[statvolt_per_centimeter][volt_per_micrometer] = to_si*conv[volt_per_meter][volt_per_micrometer]; + conv[statvolt_per_centimeter][volt_per_nanometer] = to_si*conv[volt_per_meter][volt_per_nanometer]; + + to_si = 1.0/conv[volt_per_meter][volt_per_centimeter]; + conv[volt_per_centimeter][volt_per_meter] = to_si*conv[volt_per_meter][volt_per_meter]; + conv[volt_per_centimeter][volt_per_angstrom] = to_si*conv[volt_per_meter][volt_per_angstrom]; + conv[volt_per_centimeter][statvolt_per_centimeter] = to_si*conv[volt_per_meter][statvolt_per_centimeter]; + conv[volt_per_centimeter][volt_per_centimeter] = 1.0; + conv[volt_per_centimeter][volt_per_micrometer] = to_si*conv[volt_per_meter][volt_per_micrometer]; + conv[volt_per_centimeter][volt_per_nanometer] = to_si*conv[volt_per_meter][volt_per_nanometer]; + + to_si = 1.0/conv[volt_per_meter][volt_per_micrometer]; + conv[volt_per_micrometer][volt_per_meter] = to_si*conv[volt_per_meter][volt_per_meter]; + conv[volt_per_micrometer][volt_per_angstrom] = to_si*conv[volt_per_meter][volt_per_angstrom]; + conv[volt_per_micrometer][statvolt_per_centimeter] = to_si*conv[volt_per_meter][statvolt_per_centimeter]; + conv[volt_per_micrometer][volt_per_centimeter] = to_si*conv[volt_per_meter][volt_per_centimeter]; + conv[volt_per_micrometer][volt_per_micrometer] = 1.0; + conv[volt_per_micrometer][volt_per_nanometer] = to_si*conv[volt_per_meter][volt_per_nanometer]; + + to_si = 1.0/conv[volt_per_meter][volt_per_nanometer]; + conv[volt_per_nanometer][volt_per_meter] = to_si*conv[volt_per_meter][volt_per_meter]; + conv[volt_per_nanometer][volt_per_angstrom] = to_si*conv[volt_per_meter][volt_per_angstrom]; + conv[volt_per_nanometer][statvolt_per_centimeter] = to_si*conv[volt_per_meter][statvolt_per_centimeter]; + conv[volt_per_nanometer][volt_per_centimeter] = to_si*conv[volt_per_meter][volt_per_centimeter]; + conv[volt_per_nanometer][volt_per_micrometer] = to_si*conv[volt_per_meter][volt_per_micrometer]; + conv[volt_per_nanometer][volt_per_nanometer] = 1.0; + + return conv[from_unit_enum][to_unit_enum]; +} + +/* ---------------------------------------------------------------------- */ + +// Demsity conversion +double get_density_conversion_factor(units from_unit_enum, units to_unit_enum) +{ + map > conv; + double to_si; + + conv[kilogram_per_metercu][kilogram_per_metercu] = 1.0; + conv[kilogram_per_metercu][gram_per_centimetercu] = 1.0/gram_per_centimetercu_si; + conv[kilogram_per_metercu][amu_per_bohrcu] = 1.0/amu_per_bohrcu_si; + conv[kilogram_per_metercu][picogram_per_micrometercu] = 1.0/picogram_per_micrometercu_si; + conv[kilogram_per_metercu][attogram_per_nanometercu] = 1.0/attogram_per_nanometercu_si; + + to_si = 1.0/conv[kilogram_per_metercu][gram_per_centimetercu]; + conv[gram_per_centimetercu][kilogram_per_metercu] = to_si*conv[kilogram_per_metercu][kilogram_per_metercu]; + conv[gram_per_centimetercu][gram_per_centimetercu] = 1.0; + conv[gram_per_centimetercu][amu_per_bohrcu] = to_si*conv[kilogram_per_metercu][amu_per_bohrcu]; + conv[gram_per_centimetercu][picogram_per_micrometercu] = to_si*conv[kilogram_per_metercu][picogram_per_micrometercu]; + conv[gram_per_centimetercu][attogram_per_nanometercu] = to_si*conv[kilogram_per_metercu][attogram_per_nanometercu]; + + to_si = 1.0/conv[kilogram_per_metercu][amu_per_bohrcu]; + conv[amu_per_bohrcu][kilogram_per_metercu] = to_si*conv[kilogram_per_metercu][kilogram_per_metercu]; + conv[amu_per_bohrcu][gram_per_centimetercu] = to_si*conv[kilogram_per_metercu][gram_per_centimetercu]; + conv[amu_per_bohrcu][amu_per_bohrcu] = 1.0; + conv[amu_per_bohrcu][picogram_per_micrometercu] = to_si*conv[kilogram_per_metercu][picogram_per_micrometercu]; + conv[amu_per_bohrcu][attogram_per_nanometercu] = to_si*conv[kilogram_per_metercu][attogram_per_nanometercu]; + + to_si = 1.0/conv[kilogram_per_metercu][picogram_per_micrometercu]; + conv[picogram_per_micrometercu][kilogram_per_metercu] = to_si*conv[kilogram_per_metercu][kilogram_per_metercu]; + conv[picogram_per_micrometercu][gram_per_centimetercu] = to_si*conv[kilogram_per_metercu][gram_per_centimetercu]; + conv[picogram_per_micrometercu][amu_per_bohrcu] = to_si*conv[kilogram_per_metercu][amu_per_bohrcu]; + conv[picogram_per_micrometercu][picogram_per_micrometercu] = 1.0; + conv[picogram_per_micrometercu][attogram_per_nanometercu] = to_si*conv[kilogram_per_metercu][attogram_per_nanometercu]; + + to_si = 1.0/conv[kilogram_per_metercu][attogram_per_nanometercu]; + conv[attogram_per_nanometercu][kilogram_per_metercu] = to_si*conv[kilogram_per_metercu][kilogram_per_metercu]; + conv[attogram_per_nanometercu][gram_per_centimetercu] = to_si*conv[kilogram_per_metercu][gram_per_centimetercu]; + conv[attogram_per_nanometercu][amu_per_bohrcu] = to_si*conv[kilogram_per_metercu][amu_per_bohrcu]; + conv[attogram_per_nanometercu][picogram_per_micrometercu] = to_si*conv[kilogram_per_metercu][picogram_per_micrometercu]; + conv[attogram_per_nanometercu][attogram_per_nanometercu] = 1.0; + + return conv[from_unit_enum][to_unit_enum]; +} + +/* ---------------------------------------------------------------------- */ + +// This routine returns the unit conversion factor between the +// `from_system_enum` to the `to_system_enum` for the `unit_type_enum`. +double get_unit_conversion_factor(unit_type &unit_type_enum, + sys_type from_system_enum, + sys_type to_system_enum) +{ + units from_unit = get_lammps_system_unit(from_system_enum, unit_type_enum); + units to_unit = get_lammps_system_unit(to_system_enum, unit_type_enum); + switch(unit_type_enum) { + case mass : + return get_mass_conversion_factor(from_unit, to_unit); + case distance : + return get_distance_conversion_factor(from_unit, to_unit); + case time : + return get_time_conversion_factor(from_unit, to_unit); + case energy : + return get_energy_conversion_factor(from_unit, to_unit); + case velocity : + return get_velocity_conversion_factor(from_unit, to_unit); + case force : + return get_force_conversion_factor(from_unit, to_unit); + case torque : + return get_torque_conversion_factor(from_unit, to_unit); + case temperature : + return get_temperature_conversion_factor(from_unit, to_unit); + case pressure : + return get_pressure_conversion_factor(from_unit, to_unit); + case viscosity : + return get_viscosity_conversion_factor(from_unit, to_unit); + case charge : + return get_charge_conversion_factor(from_unit, to_unit); + case dipole : + return get_dipole_conversion_factor(from_unit, to_unit); + case efield : + return get_efield_conversion_factor(from_unit, to_unit); + case density : + default : // This is here to a prevent a compiler warning + return get_density_conversion_factor(from_unit, to_unit); + } +} + +} // end of anonymous name space + +/* ---------------------------------------------------------------------- */ + +// Wrapper to the routine that gets the unit conversion. Translates strings +// to enumerations and then call get_unit_conversion_factor() +int lammps_unit_conversion(string const &unit_type_str, + string const &from_system_str, + string const &to_system_str, + double &conversion_factor) +{ + // initialize + conversion_factor = 0.0; + initialize_dictionaries(); + + // convert input to enumeration + unit_type unit_type_enum; + { + map::const_iterator itr = unit_dic.find(unit_type_str); + if (itr != unit_dic.end()) unit_type_enum = itr->second; + else return 1; // error + } + sys_type from_system_enum; + { + map::const_iterator + itr = system_dic.find(from_system_str); + if (itr != system_dic.end()) from_system_enum = itr->second; + else return 1; // error + } + sys_type to_system_enum; + { + map::const_iterator + itr = system_dic.find(to_system_str); + if (itr != system_dic.end()) to_system_enum = itr->second; + else return 1; + } + + // process unit conversions + conversion_factor = get_unit_conversion_factor(unit_type_enum, + from_system_enum, + to_system_enum); + return 0; +} + + diff --git a/src/KIM/kim_units.h b/src/KIM/kim_units.h new file mode 100644 index 0000000000..97e81a6222 --- /dev/null +++ b/src/KIM/kim_units.h @@ -0,0 +1,59 @@ +/* -*- c++ -*- ---------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + http://lammps.sandia.gov, Sandia National Laboratories + Steve Plimpton, sjplimp@sandia.gov + + Copyright (2003) Sandia Corporation. Under the terms of Contract + DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains + certain rights in this software. This software is distributed under + the GNU General Public License. + + See the README file in the top-level LAMMPS directory. +------------------------------------------------------------------------- */ + +/* ---------------------------------------------------------------------- + Contributing authors: Ellad B. Tadmor (UMN) +------------------------------------------------------------------------- */ + +/* ---------------------------------------------------------------------- + This program is free software; you can redistribute it and/or modify it + under the terms of the GNU General Public License as published by the Free + Software Foundation; either version 2 of the License, or (at your option) + any later version. + + This program is distributed in the hope that it will be useful, but WITHOUT + ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or + FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for + more details. + + You should have received a copy of the GNU General Public License along with + this program; if not, see . + + Linking LAMMPS statically or dynamically with other modules is making a + combined work based on LAMMPS. Thus, the terms and conditions of the GNU + General Public License cover the whole combination. + + In addition, as a special exception, the copyright holders of LAMMPS give + you permission to combine LAMMPS with free software programs or libraries + that are released under the GNU LGPL and with code included in the standard + release of the "kim-api" under the CDDL (or modified versions of such code, + with unchanged license). You may copy and distribute such a system following + the terms of the GNU GPL for LAMMPS and the licenses of the other code + concerned, provided that you include the source code of that other code + when and as the GNU GPL requires distribution of source code. + + Note that people who make modified versions of LAMMPS are not obligated to + grant this special exception for their modified versions; it is their choice + whether to do so. The GNU General Public License gives permission to release + a modified version without this exception; this exception also makes it + possible to release a modified version which carries forward this exception. +------------------------------------------------------------------------- */ + +/* ---------------------------------------------------------------------- + Designed for use with the kim-api-2.0.2 (and newer) package +------------------------------------------------------------------------- */ + +int lammps_unit_conversion(std::string const &unit_type_str, + std::string const &from_system_str, + std::string const &to_system_str, + double &conversion_factor); -- GitLab From dbfd1fd0e739aa9ff263fe5e6d88f73d44d2569d Mon Sep 17 00:00:00 2001 From: "Ryan S. Elliott" Date: Fri, 21 Jun 2019 22:11:58 -0500 Subject: [PATCH 064/469] Added atom-type-num-list mapping to kim_style --- src/KIM/kim_style.cpp | 156 +++++++++++++++++++++++++++++++++++++++--- src/KIM/kim_style.h | 5 +- 2 files changed, 149 insertions(+), 12 deletions(-) diff --git a/src/KIM/kim_style.cpp b/src/KIM/kim_style.cpp index 44d5c411ab..161bc31643 100644 --- a/src/KIM/kim_style.cpp +++ b/src/KIM/kim_style.cpp @@ -77,6 +77,10 @@ extern "C" { #include "KIM_SimulatorModel.hpp" //@@@@@ +#define SNUM(x) \ + static_cast(std::ostringstream() \ + << std::dec << x).str() + using namespace LAMMPS_NS; /* ---------------------------------------------------------------------- */ @@ -257,7 +261,7 @@ void KimStyle::determine_model_type_and_units(char * model_name, if ((! unit_conversion_mode) && (strcmp(*model_units, user_units)!=0)) { std::stringstream mesg; - mesg << "Incompatible units for KIM Simulator Model, required units = " + mesg << "Incompatible units for KIM Simulator Model, required units = " << *model_units; error->all(FLERR,mesg.str().c_str()); } @@ -357,18 +361,18 @@ void KimStyle::do_init(char *model_name, char *user_units, char* model_units) /* ---------------------------------------------------------------------- */ -void KimStyle::kim_style_log_delimiter(std::string begin_end, - std::string model_setup) +void KimStyle::kim_style_log_delimiter(std::string const begin_end, + std::string const model_setup) const { if (comm->me == 0) { std::string mesg; - if ((begin_end == "begin") && (model_setup == "model")) mesg = + if ((begin_end == "begin") && (model_setup == "model")) mesg = "#=== BEGIN kim-style MODEL ==================================\n"; - else if ((begin_end == "begin") && (model_setup == "setup")) mesg = + else if ((begin_end == "begin") && (model_setup == "setup")) mesg = "#=== BEGIN kim-style SETUP ==================================\n"; - else if ((begin_end == "end") && (model_setup == "model")) mesg = + else if ((begin_end == "end") && (model_setup == "model")) mesg = "#=== END kim-style MODEL ====================================\n\n"; - else if ((begin_end == "end") && (model_setup == "setup")) mesg = + else if ((begin_end == "end") && (model_setup == "setup")) mesg = "#=== END kim-style SETUP ====================================\n\n"; if (screen) fputs(mesg.c_str(),screen); @@ -403,12 +407,19 @@ void KimStyle::do_setup(int narg, char **arg) if (simulatorModel) { + std::string delimiter(""); std::string atom_type_sym_list; + std::string atom_type_num_list; for (int i = 0; i < narg; i++) - atom_type_sym_list += std::string(" ") + arg[i]; + { + atom_type_sym_list += delimiter + arg[i]; + atom_type_num_list += delimiter + SNUM(species_to_atomic_no(arg[i])); + delimiter = " "; + } simulatorModel->AddTemplateMap("atom-type-sym-list",atom_type_sym_list); + simulatorModel->AddTemplateMap("atom-type-num-list",atom_type_num_list); simulatorModel->CloseTemplateMap(); int len = strlen(atom_type_sym_list.c_str())+1; @@ -533,10 +544,10 @@ void KimStyle::do_variables(char *user_units, char *model_units) (char *)"dipole", (char *)"efield", (char *)"density"}; - + if (comm->me == 0) { std::stringstream mesg; - mesg << "# Conversion factors from " << from << " to " << to + mesg << "# Conversion factors from " << from << " to " << to << ":" << std::endl; if (screen) fputs(mesg.str().c_str(),screen); if (logfile) fputs(mesg.str().c_str(),logfile); @@ -575,3 +586,128 @@ void KimStyle::do_variables(char *user_units, char *model_units) if (logfile) fputs("#\n",logfile); } } + +/* ---------------------------------------------------------------------- */ + +int KimStyle::species_to_atomic_no(std::string const species) const +{ + if (species == "H") return 1; + else if (species == "He") return 2; + else if (species == "Li") return 3; + else if (species == "Be") return 4; + else if (species == "B") return 5; + else if (species == "C") return 6; + else if (species == "N") return 7; + else if (species == "O") return 8; + else if (species == "F") return 9; + else if (species == "Ne") return 10; + else if (species == "Na") return 11; + else if (species == "Mg") return 12; + else if (species == "Al") return 13; + else if (species == "Si") return 14; + else if (species == "P") return 15; + else if (species == "S") return 16; + else if (species == "Cl") return 17; + else if (species == "Ar") return 18; + else if (species == "K") return 19; + else if (species == "Ca") return 20; + else if (species == "Sc") return 21; + else if (species == "Ti") return 22; + else if (species == "V") return 23; + else if (species == "Cr") return 24; + else if (species == "Mn") return 25; + else if (species == "Fe") return 26; + else if (species == "Co") return 27; + else if (species == "Ni") return 28; + else if (species == "Cu") return 29; + else if (species == "Zn") return 30; + else if (species == "Ga") return 31; + else if (species == "Ge") return 32; + else if (species == "As") return 33; + else if (species == "Se") return 34; + else if (species == "Br") return 35; + else if (species == "Kr") return 36; + else if (species == "Rb") return 37; + else if (species == "Sr") return 38; + else if (species == "Y") return 39; + else if (species == "Zr") return 40; + else if (species == "Nb") return 41; + else if (species == "Mo") return 42; + else if (species == "Tc") return 43; + else if (species == "Ru") return 44; + else if (species == "Rh") return 45; + else if (species == "Pd") return 46; + else if (species == "Ag") return 47; + else if (species == "Cd") return 48; + else if (species == "In") return 49; + else if (species == "Sn") return 50; + else if (species == "Sb") return 51; + else if (species == "Te") return 52; + else if (species == "I") return 53; + else if (species == "Xe") return 54; + else if (species == "Cs") return 55; + else if (species == "Ba") return 56; + else if (species == "La") return 57; + else if (species == "Ce") return 58; + else if (species == "Pr") return 59; + else if (species == "Nd") return 60; + else if (species == "Pm") return 61; + else if (species == "Sm") return 62; + else if (species == "Eu") return 63; + else if (species == "Gd") return 64; + else if (species == "Tb") return 65; + else if (species == "Dy") return 66; + else if (species == "Ho") return 67; + else if (species == "Er") return 68; + else if (species == "Tm") return 69; + else if (species == "Yb") return 70; + else if (species == "Lu") return 71; + else if (species == "Hf") return 72; + else if (species == "Ta") return 73; + else if (species == "W") return 74; + else if (species == "Re") return 75; + else if (species == "Os") return 76; + else if (species == "Ir") return 77; + else if (species == "Pt") return 78; + else if (species == "Au") return 79; + else if (species == "Hg") return 80; + else if (species == "Tl") return 81; + else if (species == "Pb") return 82; + else if (species == "Bi") return 83; + else if (species == "Po") return 84; + else if (species == "At") return 85; + else if (species == "Rn") return 86; + else if (species == "Fr") return 87; + else if (species == "Ra") return 88; + else if (species == "Ac") return 89; + else if (species == "Th") return 90; + else if (species == "Pa") return 91; + else if (species == "U") return 92; + else if (species == "Np") return 93; + else if (species == "Pu") return 94; + else if (species == "Am") return 95; + else if (species == "Cm") return 96; + else if (species == "Bk") return 97; + else if (species == "Cf") return 98; + else if (species == "Es") return 99; + else if (species == "Fm") return 100; + else if (species == "Md") return 101; + else if (species == "No") return 102; + else if (species == "Lr") return 103; + else if (species == "Rf") return 104; + else if (species == "Db") return 105; + else if (species == "Sg") return 106; + else if (species == "Bh") return 107; + else if (species == "Hs") return 108; + else if (species == "Mt") return 109; + else if (species == "Ds") return 110; + else if (species == "Rg") return 111; + else if (species == "Cn") return 112; + else if (species == "Nh") return 113; + else if (species == "Fl") return 114; + else if (species == "Mc") return 115; + else if (species == "Lv") return 116; + else if (species == "Ts") return 117; + else if (species == "Og") return 118; + else return -1; +} diff --git a/src/KIM/kim_style.h b/src/KIM/kim_style.h index b18f6627ea..626f2395bc 100644 --- a/src/KIM/kim_style.h +++ b/src/KIM/kim_style.h @@ -80,8 +80,9 @@ class KimStyle : protected Pointers { void do_init(char *, char *, char *); void do_setup(int, char **); void do_variables(char*, char*); - void kim_style_log_delimiter(std::string begin_end, - std::string model_setup); + int species_to_atomic_no(std::string const species) const; + void kim_style_log_delimiter(std::string const begin_end, + std::string const model_setup) const; }; } -- GitLab From f81c9c5322aa0d8e067f240639528b0292f83bb8 Mon Sep 17 00:00:00 2001 From: Ellad Tadmor Date: Sat, 22 Jun 2019 10:21:05 -0500 Subject: [PATCH 065/469] Changed _u_* output to log to variable commands --- src/KIM/kim_style.cpp | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/src/KIM/kim_style.cpp b/src/KIM/kim_style.cpp index 161bc31643..a583908fc7 100644 --- a/src/KIM/kim_style.cpp +++ b/src/KIM/kim_style.cpp @@ -576,7 +576,8 @@ void KimStyle::do_variables(char *user_units, char *model_units) variable->internal_set(v_unit,conversion_factor); if (comm->me == 0) { std::stringstream mesg; - mesg << "# " << var_str << " = " << conversion_factor << std::endl; + mesg << "variable " << var_str << " internal " << conversion_factor + << std::endl; if (screen) fputs(mesg.str().c_str(),screen); if (logfile) fputs(mesg.str().c_str(),logfile); } -- GitLab From 4a22e3bf70d03dd292319bdab315f2731da41eab Mon Sep 17 00:00:00 2001 From: "Ryan S. Elliott" Date: Sat, 22 Jun 2019 15:21:57 -0500 Subject: [PATCH 066/469] Implement kim_init, kim_interactions & various updates --- src/KIM/README | 27 +- src/KIM/{kim_style.cpp => kim_init.cpp} | 421 +++++------------------- src/KIM/{kim_style.h => kim_init.h} | 35 +- src/KIM/kim_interactions.cpp | 367 +++++++++++++++++++++ src/KIM/kim_interactions.h | 116 +++++++ 5 files changed, 590 insertions(+), 376 deletions(-) rename src/KIM/{kim_style.cpp => kim_init.cpp} (52%) rename src/KIM/{kim_style.h => kim_init.h} (82%) create mode 100644 src/KIM/kim_interactions.cpp create mode 100644 src/KIM/kim_interactions.h diff --git a/src/KIM/README b/src/KIM/README index 4f52d69a67..e61f47426f 100644 --- a/src/KIM/README +++ b/src/KIM/README @@ -1,29 +1,30 @@ -This package provides a pair_style kim command which is a wrapper on -the Knowledge Base for Interatomic Models (KIM) repository of -interatomic potentials, so that they can be used by LAMMPS scripts. +This package provides the kim_init, kim_query, kim_interactions, and +the pair_style kim command which are wrappers on the Knowledgebase of +Interatomic Models (KIM) repository of interatomic potentials, so that +they can be used by LAMMPS scripts. Information about the KIM project can be found at https://openkim.org. -The KIM project is lead by Ellad Tadmor and Ryan Elliott (U Minn) and -James Sethna (Cornell U). Ryan Elliott is the main developer for the -KIM API and he also maintains the code that implements the pair_style -kim command. +The KIM project is lead by Ellad B. Tadmor and Ryan S. Elliott (UMN). +Ryan Elliott is the main developer for the KIM API and he also +maintains the code that implements these commands. -Using this package requires the KIM library and its models +Using this package requires the KIM-API library and its models (interatomic potentials) to be downloaded and installed on your system. The library can be downloaded and built in lib/kim or elsewhere on your system, which must be done before bulding LAMMPS with this package. Details of the download, build, and install -process for KIM are given in the lib/kim/README file, and scripts -are provided to help automate the process. Also see the LAMMPS -manual for general information on building LAMMPS with external +process for the KIM-API are given in the lib/kim/README file, and +scripts are provided to help automate the process. Also see the +LAMMPS manual for general information on building LAMMPS with external libraries. The settings in the Makefile.lammps file in lib/kim must be correct for LAMMPS to build correctly with this package installed. However, the default settings should be correct in most cases and the Makefile.lammps file usually will not need to be changed. Once you have successfully built LAMMPS with this package and the KIM -library you can test it using an input file from the examples dir: +library you can test it using an input files in the examples dir: ./lmp_serial -in lammps/examples/kim/in.kim.lj -This pair_style was written by Ryan S. Elliott (U Minn). +These commands were written by Ryan S. Elliott (UMN), Ellad B. Tadmor +(UMN) and Axel Kohlmeyer (Temple U). diff --git a/src/KIM/kim_style.cpp b/src/KIM/kim_init.cpp similarity index 52% rename from src/KIM/kim_style.cpp rename to src/KIM/kim_init.cpp index a583908fc7..695db0aa0d 100644 --- a/src/KIM/kim_style.cpp +++ b/src/KIM/kim_init.cpp @@ -14,6 +14,7 @@ /* ---------------------------------------------------------------------- Contributing authors: Axel Kohlmeyer (Temple U), Ryan S. Elliott (UMN) + Ellad B. Tadmor (UMN) ------------------------------------------------------------------------- */ /* ---------------------------------------------------------------------- @@ -57,7 +58,8 @@ #include #include #include -#include "kim_style.h" +#include +#include "kim_init.h" #include "error.h" #include "atom.h" #include "comm.h" @@ -85,33 +87,26 @@ using namespace LAMMPS_NS; /* ---------------------------------------------------------------------- */ -void KimStyle::command(int narg, char **arg) +void KimInit::command(int narg, char **arg) { - if ((narg < 2) || (narg > 4)) error->all(FLERR,"Illegal kim_style command"); - - if (strcmp(arg[0],"model") == 0) { - if (domain->box_exist) - error->all(FLERR,"Must use 'kim_style model' command before " - "simulation box is defined"); - int len1 = strlen(arg[1])+1; - int len2 = strlen(arg[2])+1; - char *model_name = new char[len1]; strcpy(model_name,arg[1]); - char *user_units = new char[len2]; strcpy(user_units,arg[2]); - if (narg == 4) { - if (strcmp(arg[3],"unit_conversion_mode")==0) unit_conversion_mode = true; - else { error->all(FLERR,"Illegal kim_style command"); } - } else unit_conversion_mode = false; - - char *model_units; - determine_model_type_and_units(model_name, user_units, &model_units); - - do_init(model_name, user_units, model_units); - } else if (strcmp(arg[0],"setup") == 0) { - if (!domain->box_exist) - error->all(FLERR,"Must use 'kim_style setup' command after " - "simulation box is defined"); - do_setup(narg-1,++arg); - } else error->all(FLERR,"Illegal kim_style command"); + if ((narg < 2) || (narg > 3)) error->all(FLERR,"Illegal kim_init command"); + + if (domain->box_exist) + error->all(FLERR,"Must use 'kim_init' command before " + "simulation box is defined"); + int len0 = strlen(arg[0])+1; + int len1 = strlen(arg[1])+1; + char *model_name = new char[len0]; strcpy(model_name,arg[0]); + char *user_units = new char[len1]; strcpy(user_units,arg[1]); + if (narg == 3) { + if (strcmp(arg[2],"unit_conversion_mode")==0) unit_conversion_mode = true; + else { error->all(FLERR,"Illegal kim_init command"); } + } else unit_conversion_mode = false; + + char *model_units; + determine_model_type_and_units(model_name, user_units, &model_units); + + do_init(model_name, user_units, model_units); } @@ -163,9 +158,9 @@ void get_kim_unit_names( } } } // namespace -void KimStyle::determine_model_type_and_units(char * model_name, - char * user_units, - char ** model_units) +void KimInit::determine_model_type_and_units(char * model_name, + char * user_units, + char ** model_units) { KIM_LengthUnit lengthUnit; KIM_EnergyUnit energyUnit; @@ -270,7 +265,7 @@ void KimStyle::determine_model_type_and_units(char * model_name, /* ---------------------------------------------------------------------- */ -void KimStyle::do_init(char *model_name, char *user_units, char* model_units) +void KimInit::do_init(char *model_name, char *user_units, char* model_units) { // create storage proxy fix. delete existing fix, if needed. @@ -288,229 +283,102 @@ void KimStyle::do_init(char *model_name, char *user_units, char* model_units) fix_store->setptr("user_units", (void *) user_units); fix_store->setptr("model_units", (void *) model_units); + // Begin output to log file + kim_init_log_delimiter("begin"); + int kimerror; // @@@@@ switch to c-bindings when they are available KIM::SimulatorModel * simulatorModel; - kimerror = KIM::SimulatorModel::Create(model_name,&simulatorModel); - - const std::string *sim_name, *sim_version; - simulatorModel->GetSimulatorNameAndVersion(&sim_name, &sim_version); - - if (*sim_name != "LAMMPS") - error->all(FLERR,"Incompatible KIM Simulator Model"); - - // Begin output to log file - kim_style_log_delimiter("begin","model"); - if (comm->me == 0) { - std::string mesg("# Using KIM Simulator Model : "); - mesg += model_name; - mesg += "\n"; - mesg += "# For Simulator : "; - mesg += *sim_name + " " + *sim_version + "\n"; - mesg += "# Running on : LAMMPS "; - mesg += universe->version; - mesg += "\n"; - mesg += "#\n"; - - if (screen) fputs(mesg.c_str(),screen); - if (logfile) fputs(mesg.c_str(),logfile); - } - - // Define unit conversion factor variables and print to log - if (unit_conversion_mode) do_variables(user_units, model_units); - - // set units - - std::string cmd("units "); - cmd += model_units; - input->one(cmd.c_str()); - - // not a Kim Simulator Model; nothing else to do here. - - if (kimerror) return; - - fix_store->setptr("simulator_model", (void *) simulatorModel); - - // need to call this to have access to (some) simulator model init data. - - simulatorModel->CloseTemplateMap(); - - int sim_fields, sim_lines; - const std::string *sim_field, *sim_value; - simulatorModel->GetNumberOfSimulatorFields(&sim_fields); - - // init model - - for (int i=0; i < sim_fields; ++i) { - simulatorModel->GetSimulatorFieldMetadata(i,&sim_lines,&sim_field); - if (*sim_field == "model-init") { - for (int j=0; j < sim_lines; ++j) { - simulatorModel->GetSimulatorFieldLine(i,j,&sim_value); - input->one(sim_value->c_str()); - } - break; - } - } - - // End output to log file - kim_style_log_delimiter("end","model"); + if (model_type == SM) + { + kimerror = KIM::SimulatorModel::Create(model_name,&simulatorModel); - // reset template map. - simulatorModel->OpenAndInitializeTemplateMap(); -} + const std::string *sim_name, *sim_version; + simulatorModel->GetSimulatorNameAndVersion(&sim_name, &sim_version); -/* ---------------------------------------------------------------------- */ + if (*sim_name != "LAMMPS") + error->all(FLERR,"Incompatible KIM Simulator Model"); -void KimStyle::kim_style_log_delimiter(std::string const begin_end, - std::string const model_setup) const -{ if (comm->me == 0) { - std::string mesg; - if ((begin_end == "begin") && (model_setup == "model")) mesg = - "#=== BEGIN kim-style MODEL ==================================\n"; - else if ((begin_end == "begin") && (model_setup == "setup")) mesg = - "#=== BEGIN kim-style SETUP ==================================\n"; - else if ((begin_end == "end") && (model_setup == "model")) mesg = - "#=== END kim-style MODEL ====================================\n\n"; - else if ((begin_end == "end") && (model_setup == "setup")) mesg = - "#=== END kim-style SETUP ====================================\n\n"; + std::string mesg("# Using KIM Simulator Model : "); + mesg += model_name; + mesg += "\n"; + mesg += "# For Simulator : "; + mesg += *sim_name + " " + *sim_version + "\n"; + mesg += "# Running on : LAMMPS "; + mesg += universe->version; + mesg += "\n"; + mesg += "#\n"; if (screen) fputs(mesg.c_str(),screen); if (logfile) fputs(mesg.c_str(),logfile); } -} - -/* ---------------------------------------------------------------------- */ - -void KimStyle::do_setup(int narg, char **arg) -{ - if (narg != atom->ntypes) - error->all(FLERR,"Illegal kim_style command"); - char *model = NULL; - KIM::SimulatorModel *simulatorModel(NULL); + fix_store->setptr("simulator_model", (void *) simulatorModel); - // check if we had a kim_style init command by finding fix STORE/KIM - // retrieve model name and pointer to simulator model class instance. - // validate model name if not given as NULL. - // if kim_style init wasn't run try to initialize simulator model now. + // need to call this to have access to (some) simulator model init data. - int ifix = modify->find_fix("KIM_MODEL_STORE"); - if (ifix >= 0) { - FixStoreKIM *fix_store = (FixStoreKIM *) modify->fix[ifix]; - model = (char *)fix_store->getptr("model_name"); - simulatorModel = (KIM::SimulatorModel *)fix_store->getptr("simulator_model"); - } else error->all(FLERR,"Must use 'kim_style model' before 'kim_style setup'"); - - // Begin output to log file - kim_style_log_delimiter("begin","setup"); - - if (simulatorModel) { - - std::string delimiter(""); - std::string atom_type_sym_list; - std::string atom_type_num_list; - - for (int i = 0; i < narg; i++) - { - atom_type_sym_list += delimiter + arg[i]; - atom_type_num_list += delimiter + SNUM(species_to_atomic_no(arg[i])); - delimiter = " "; - } - - simulatorModel->AddTemplateMap("atom-type-sym-list",atom_type_sym_list); - simulatorModel->AddTemplateMap("atom-type-num-list",atom_type_num_list); simulatorModel->CloseTemplateMap(); + } - int len = strlen(atom_type_sym_list.c_str())+1; - char *strbuf = new char[len]; - char *strword; - - // validate species selection - - int sim_num_species; - bool species_is_supported; - const std::string *sim_species; - simulatorModel->GetNumberOfSupportedSpecies(&sim_num_species); - strcpy(strbuf,atom_type_sym_list.c_str()); - strword = strtok(strbuf," \t"); - while (strword) { - species_is_supported = false; - if (strcmp(strword,"NULL") == 0) continue; - for (int i=0; i < sim_num_species; ++i) { - simulatorModel->GetSupportedSpecies(i, &sim_species); - if (strcmp(sim_species->c_str(),strword) == 0) - species_is_supported = true; - } - if (!species_is_supported) { - std::string msg("Species '"); - msg += strword; - msg += "' is not supported by this KIM Simulator Model"; - error->all(FLERR,msg.c_str()); - } - strword = strtok(NULL," \t"); - } - delete[] strbuf; + // Define unit conversion factor variables and print to log + if (unit_conversion_mode) do_variables(user_units, model_units); - // check if units are unchanged, and if kim_style init was required + // set units + std::string cmd("units "); + cmd += model_units; + input->one(cmd.c_str()); + + if (model_type == SM) + { int sim_fields, sim_lines; const std::string *sim_field, *sim_value; simulatorModel->GetNumberOfSimulatorFields(&sim_fields); - for (int i=0; i < sim_fields; ++i) { - simulatorModel->GetSimulatorFieldMetadata(i,&sim_lines,&sim_field); - if (*sim_field == "units") { - simulatorModel->GetSimulatorFieldLine(i,0,&sim_value); - if (*sim_value != update->unit_style) - error->all(FLERR,"Incompatible units for KIM Simulator Model"); - } - } + // init model - int sim_model_idx=-1; for (int i=0; i < sim_fields; ++i) { simulatorModel->GetSimulatorFieldMetadata(i,&sim_lines,&sim_field); - if (*sim_field == "model-defn") { - sim_model_idx = i; + if (*sim_field == "model-init") { for (int j=0; j < sim_lines; ++j) { - simulatorModel->GetSimulatorFieldLine(sim_model_idx,j,&sim_value); + simulatorModel->GetSimulatorFieldLine(i,j,&sim_value); input->one(sim_value->c_str()); } + break; } } - if (sim_model_idx < 0) - error->all(FLERR,"KIM Simulator Model has no Model definition"); - + // reset template map. simulatorModel->OpenAndInitializeTemplateMap(); + } - } else { + // End output to log file + kim_init_log_delimiter("end"); - // not a simulator model. issue pair_style and pair_coeff commands. - // NOTE: all references to arg must appear before calls to input->one() - // as that will reset the argument vector. +} - std::string cmd1("pair_style kim "); - cmd1 += model; +/* ---------------------------------------------------------------------- */ - std::string cmd2("pair_coeff * * "); - for (int i=0; i < narg; ++i) { - cmd2 += arg[i]; - cmd2 += " "; - } +void KimInit::kim_init_log_delimiter(std::string const begin_end) const +{ + if (comm->me == 0) { + std::string mesg; + if (begin_end == "begin") + mesg = + "#=== BEGIN kim-init ==========================================\n"; + else if (begin_end == "end") + mesg = + "#=== END kim-init ============================================\n\n"; - input->one(cmd1.c_str()); - input->one(cmd2.c_str()); + if (screen) fputs(mesg.c_str(),screen); + if (logfile) fputs(mesg.c_str(),logfile); } - - // End output to log file - kim_style_log_delimiter("end","setup"); - } /* ---------------------------------------------------------------------- */ -void KimStyle::do_variables(char *user_units, char *model_units) +void KimInit::do_variables(char *user_units, char *model_units) { char *from = user_units, *to = model_units; Variable *variable = input->variable; @@ -576,7 +444,9 @@ void KimStyle::do_variables(char *user_units, char *model_units) variable->internal_set(v_unit,conversion_factor); if (comm->me == 0) { std::stringstream mesg; - mesg << "variable " << var_str << " internal " << conversion_factor + mesg << "variable " << std::setw(15) << std::left << var_str + << " internal " + << std::setprecision(12) << std::scientific << conversion_factor << std::endl; if (screen) fputs(mesg.str().c_str(),screen); if (logfile) fputs(mesg.str().c_str(),logfile); @@ -587,128 +457,3 @@ void KimStyle::do_variables(char *user_units, char *model_units) if (logfile) fputs("#\n",logfile); } } - -/* ---------------------------------------------------------------------- */ - -int KimStyle::species_to_atomic_no(std::string const species) const -{ - if (species == "H") return 1; - else if (species == "He") return 2; - else if (species == "Li") return 3; - else if (species == "Be") return 4; - else if (species == "B") return 5; - else if (species == "C") return 6; - else if (species == "N") return 7; - else if (species == "O") return 8; - else if (species == "F") return 9; - else if (species == "Ne") return 10; - else if (species == "Na") return 11; - else if (species == "Mg") return 12; - else if (species == "Al") return 13; - else if (species == "Si") return 14; - else if (species == "P") return 15; - else if (species == "S") return 16; - else if (species == "Cl") return 17; - else if (species == "Ar") return 18; - else if (species == "K") return 19; - else if (species == "Ca") return 20; - else if (species == "Sc") return 21; - else if (species == "Ti") return 22; - else if (species == "V") return 23; - else if (species == "Cr") return 24; - else if (species == "Mn") return 25; - else if (species == "Fe") return 26; - else if (species == "Co") return 27; - else if (species == "Ni") return 28; - else if (species == "Cu") return 29; - else if (species == "Zn") return 30; - else if (species == "Ga") return 31; - else if (species == "Ge") return 32; - else if (species == "As") return 33; - else if (species == "Se") return 34; - else if (species == "Br") return 35; - else if (species == "Kr") return 36; - else if (species == "Rb") return 37; - else if (species == "Sr") return 38; - else if (species == "Y") return 39; - else if (species == "Zr") return 40; - else if (species == "Nb") return 41; - else if (species == "Mo") return 42; - else if (species == "Tc") return 43; - else if (species == "Ru") return 44; - else if (species == "Rh") return 45; - else if (species == "Pd") return 46; - else if (species == "Ag") return 47; - else if (species == "Cd") return 48; - else if (species == "In") return 49; - else if (species == "Sn") return 50; - else if (species == "Sb") return 51; - else if (species == "Te") return 52; - else if (species == "I") return 53; - else if (species == "Xe") return 54; - else if (species == "Cs") return 55; - else if (species == "Ba") return 56; - else if (species == "La") return 57; - else if (species == "Ce") return 58; - else if (species == "Pr") return 59; - else if (species == "Nd") return 60; - else if (species == "Pm") return 61; - else if (species == "Sm") return 62; - else if (species == "Eu") return 63; - else if (species == "Gd") return 64; - else if (species == "Tb") return 65; - else if (species == "Dy") return 66; - else if (species == "Ho") return 67; - else if (species == "Er") return 68; - else if (species == "Tm") return 69; - else if (species == "Yb") return 70; - else if (species == "Lu") return 71; - else if (species == "Hf") return 72; - else if (species == "Ta") return 73; - else if (species == "W") return 74; - else if (species == "Re") return 75; - else if (species == "Os") return 76; - else if (species == "Ir") return 77; - else if (species == "Pt") return 78; - else if (species == "Au") return 79; - else if (species == "Hg") return 80; - else if (species == "Tl") return 81; - else if (species == "Pb") return 82; - else if (species == "Bi") return 83; - else if (species == "Po") return 84; - else if (species == "At") return 85; - else if (species == "Rn") return 86; - else if (species == "Fr") return 87; - else if (species == "Ra") return 88; - else if (species == "Ac") return 89; - else if (species == "Th") return 90; - else if (species == "Pa") return 91; - else if (species == "U") return 92; - else if (species == "Np") return 93; - else if (species == "Pu") return 94; - else if (species == "Am") return 95; - else if (species == "Cm") return 96; - else if (species == "Bk") return 97; - else if (species == "Cf") return 98; - else if (species == "Es") return 99; - else if (species == "Fm") return 100; - else if (species == "Md") return 101; - else if (species == "No") return 102; - else if (species == "Lr") return 103; - else if (species == "Rf") return 104; - else if (species == "Db") return 105; - else if (species == "Sg") return 106; - else if (species == "Bh") return 107; - else if (species == "Hs") return 108; - else if (species == "Mt") return 109; - else if (species == "Ds") return 110; - else if (species == "Rg") return 111; - else if (species == "Cn") return 112; - else if (species == "Nh") return 113; - else if (species == "Fl") return 114; - else if (species == "Mc") return 115; - else if (species == "Lv") return 116; - else if (species == "Ts") return 117; - else if (species == "Og") return 118; - else return -1; -} diff --git a/src/KIM/kim_style.h b/src/KIM/kim_init.h similarity index 82% rename from src/KIM/kim_style.h rename to src/KIM/kim_init.h index 626f2395bc..c22e2be720 100644 --- a/src/KIM/kim_style.h +++ b/src/KIM/kim_init.h @@ -14,6 +14,7 @@ /* ---------------------------------------------------------------------- Contributing authors: Axel Kohlmeyer (Temple U), Ryan S. Elliott (UMN) + Ellad B. Tadmor (UMN) ------------------------------------------------------------------------- */ /* ---------------------------------------------------------------------- @@ -56,20 +57,20 @@ #ifdef COMMAND_CLASS -CommandStyle(kim_style,KimStyle) +CommandStyle(kim_init,KimInit) #else -#ifndef LMP_KIM_STYLE_H -#define LMP_KIM_STYLE_H +#ifndef LMP_KIM_INIT_H +#define LMP_KIM_INIT_H #include "pointers.h" namespace LAMMPS_NS { -class KimStyle : protected Pointers { +class KimInit : protected Pointers { public: - KimStyle(class LAMMPS *lmp) : Pointers(lmp) {}; + KimInit(class LAMMPS *lmp) : Pointers(lmp) {}; void command(int, char **); private: enum model_type_enum {MO, SM}; @@ -78,11 +79,8 @@ class KimStyle : protected Pointers { void determine_model_type_and_units(char *, char *, char **); void do_init(char *, char *, char *); - void do_setup(int, char **); void do_variables(char*, char*); - int species_to_atomic_no(std::string const species) const; - void kim_style_log_delimiter(std::string const begin_end, - std::string const model_setup) const; + void kim_init_log_delimiter(std::string const begin_end) const; }; } @@ -92,19 +90,11 @@ class KimStyle : protected Pointers { /* ERROR/WARNING messages: -E: Illegal kim_style command +E: Illegal kim_init command -Incorrect number or kind of arguments to kim_style. +Incorrect number or kind of arguments to kim_init. -E: Must use 'kim_style model' command before simulation box is defined - -Self-explanatory. - -E: Must use 'kim_style setup' command after simulation box is defined - -Self-explanatory. - -E: Must use 'kim_style model' command before 'kim_style setup' +E: Must use 'kim_init' command before simulation box is defined Self-explanatory. @@ -125,11 +115,6 @@ E: Incompatible KIM Simulator Model The requested KIM Simulator Model was defined for a different MD code and thus is not compatible with LAMMPS. -E: Species XXX is not supported by this KIM Simulator Model - -The kim_style define command was referencing a species that is not -present in the requested KIM Simulator Model. - E: Incompatible units for KIM Simulator Model The selected unit style is not compatible with the requested KIM diff --git a/src/KIM/kim_interactions.cpp b/src/KIM/kim_interactions.cpp new file mode 100644 index 0000000000..491d406ae6 --- /dev/null +++ b/src/KIM/kim_interactions.cpp @@ -0,0 +1,367 @@ +/* ---------------------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + http://lammps.sandia.gov, Sandia National Laboratories + Steve Plimpton, sjplimp@sandia.gov + + Copyright (2003) Sandia Corporation. Under the terms of Contract + DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains + certain rights in this software. This software is distributed under + the GNU General Public License. + + See the README file in the top-level LAMMPS directory. +------------------------------------------------------------------------- */ + +/* ---------------------------------------------------------------------- + Contributing authors: Axel Kohlmeyer (Temple U), + Ryan S. Elliott (UMN) + Ellad B. Tadmor (UMN) +------------------------------------------------------------------------- */ + +/* ---------------------------------------------------------------------- + This program is free software; you can redistribute it and/or modify it + under the terms of the GNU General Public License as published by the Free + Software Foundation; either version 2 of the License, or (at your option) + any later version. + + This program is distributed in the hope that it will be useful, but WITHOUT + ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or + FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for + more details. + + You should have received a copy of the GNU General Public License along with + this program; if not, see . + + Linking LAMMPS statically or dynamically with other modules is making a + combined work based on LAMMPS. Thus, the terms and conditions of the GNU + General Public License cover the whole combination. + + In addition, as a special exception, the copyright holders of LAMMPS give + you permission to combine LAMMPS with free software programs or libraries + that are released under the GNU LGPL and with code included in the standard + release of the "kim-api" under the CDDL (or modified versions of such code, + with unchanged license). You may copy and distribute such a system following + the terms of the GNU GPL for LAMMPS and the licenses of the other code + concerned, provided that you include the source code of that other code + when and as the GNU GPL requires distribution of source code. + + Note that people who make modified versions of LAMMPS are not obligated to + grant this special exception for their modified versions; it is their choice + whether to do so. The GNU General Public License gives permission to release + a modified version without this exception; this exception also makes it + possible to release a modified version which carries forward this exception. +------------------------------------------------------------------------- */ + +/* ---------------------------------------------------------------------- + Designed for use with the kim-api-2.1.0 (and newer) package +------------------------------------------------------------------------- */ + +#include +#include +#include +#include "kim_interactions.h" +#include "error.h" +#include "atom.h" +#include "comm.h" +#include "domain.h" +#include "modify.h" +#include "update.h" +#include "universe.h" +#include "input.h" +#include "variable.h" +#include "fix_store_kim.h" + +extern "C" { +#include "KIM_SimulatorHeaders.h" +} +//@@@@@ Need to switch to c-bindings when they are available. +#include "KIM_SimulatorModel.hpp" +//@@@@@ + +#define SNUM(x) \ + static_cast(std::ostringstream() \ + << std::dec << x).str() + +using namespace LAMMPS_NS; + +/* ---------------------------------------------------------------------- */ + +void KimInteractions::command(int narg, char **arg) +{ + if (narg < 1) error->all(FLERR,"Illegal kim_interactions command"); + + if (!domain->box_exist) + error->all(FLERR,"Must use 'kim_interactions' command after " + "simulation box is defined"); + do_setup(narg,arg); +} + +/* ---------------------------------------------------------------------- */ + +void KimInteractions::kim_interactions_log_delimiter( + std::string const begin_end) const +{ + if (comm->me == 0) { + std::string mesg; + if (begin_end == "begin") + mesg = + "#=== BEGIN kim_interactions ==================================\n"; + else if (begin_end == "end") + mesg = + "#=== END kim_interactions ====================================\n\n"; + + if (screen) fputs(mesg.c_str(),screen); + if (logfile) fputs(mesg.c_str(),logfile); + } +} + +/* ---------------------------------------------------------------------- */ + +void KimInteractions::do_setup(int narg, char **arg) +{ + if (narg != atom->ntypes) + error->all(FLERR,"Illegal kim_interactions command"); + + char *model_name = NULL; + KIM::SimulatorModel *simulatorModel(NULL); + + // check if we had a kim_init command by finding fix STORE/KIM + // retrieve model name and pointer to simulator model class instance. + // validate model name if not given as NULL. + + int ifix = modify->find_fix("KIM_MODEL_STORE"); + if (ifix >= 0) { + FixStoreKIM *fix_store = (FixStoreKIM *) modify->fix[ifix]; + model_name = (char *)fix_store->getptr("model_name"); + simulatorModel = (KIM::SimulatorModel *)fix_store->getptr("simulator_model"); + } else error->all(FLERR,"Must use 'kim_init' before 'kim_interactions'"); + + // Begin output to log file + kim_interactions_log_delimiter("begin"); + + if (simulatorModel) { + + std::string delimiter(""); + std::string atom_type_sym_list; + std::string atom_type_num_list; + + for (int i = 0; i < narg; i++) + { + atom_type_sym_list += delimiter + arg[i]; + atom_type_num_list += delimiter + SNUM(species_to_atomic_no(arg[i])); + delimiter = " "; + } + + simulatorModel->AddTemplateMap("atom-type-sym-list",atom_type_sym_list); + simulatorModel->AddTemplateMap("atom-type-num-list",atom_type_num_list); + simulatorModel->CloseTemplateMap(); + + int len = strlen(atom_type_sym_list.c_str())+1; + char *strbuf = new char[len]; + char *strword; + + // validate species selection + + int sim_num_species; + bool species_is_supported; + const std::string *sim_species; + simulatorModel->GetNumberOfSupportedSpecies(&sim_num_species); + strcpy(strbuf,atom_type_sym_list.c_str()); + strword = strtok(strbuf," \t"); + while (strword) { + species_is_supported = false; + if (strcmp(strword,"NULL") == 0) continue; + for (int i=0; i < sim_num_species; ++i) { + simulatorModel->GetSupportedSpecies(i, &sim_species); + if (strcmp(sim_species->c_str(),strword) == 0) + species_is_supported = true; + } + if (!species_is_supported) { + std::string msg("Species '"); + msg += strword; + msg += "' is not supported by this KIM Simulator Model"; + error->all(FLERR,msg.c_str()); + } + strword = strtok(NULL," \t"); + } + delete[] strbuf; + + // check if units are unchanged + + int sim_fields, sim_lines; + const std::string *sim_field, *sim_value; + simulatorModel->GetNumberOfSimulatorFields(&sim_fields); + for (int i=0; i < sim_fields; ++i) { + simulatorModel->GetSimulatorFieldMetadata(i,&sim_lines,&sim_field); + + if (*sim_field == "units") { + simulatorModel->GetSimulatorFieldLine(i,0,&sim_value); + if (*sim_value != update->unit_style) + error->all(FLERR,"Incompatible units for KIM Simulator Model"); + } + } + + int sim_model_idx=-1; + for (int i=0; i < sim_fields; ++i) { + simulatorModel->GetSimulatorFieldMetadata(i,&sim_lines,&sim_field); + if (*sim_field == "model-defn") { + sim_model_idx = i; + for (int j=0; j < sim_lines; ++j) { + simulatorModel->GetSimulatorFieldLine(sim_model_idx,j,&sim_value); + input->one(sim_value->c_str()); + } + } + } + + if (sim_model_idx < 0) + error->all(FLERR,"KIM Simulator Model has no Model definition"); + + simulatorModel->OpenAndInitializeTemplateMap(); + + } else { + + // not a simulator model. issue pair_style and pair_coeff commands. + // NOTE: all references to arg must appear before calls to input->one() + // as that will reset the argument vector. + + std::string cmd1("pair_style kim "); + cmd1 += model_name; + + std::string cmd2("pair_coeff * * "); + for (int i=0; i < narg; ++i) { + cmd2 += arg[i]; + cmd2 += " "; + } + + input->one(cmd1.c_str()); + input->one(cmd2.c_str()); + } + + // End output to log file + kim_interactions_log_delimiter("end"); + +} + +/* ---------------------------------------------------------------------- */ + +int KimInteractions::species_to_atomic_no(std::string const species) const +{ + if (species == "H") return 1; + else if (species == "He") return 2; + else if (species == "Li") return 3; + else if (species == "Be") return 4; + else if (species == "B") return 5; + else if (species == "C") return 6; + else if (species == "N") return 7; + else if (species == "O") return 8; + else if (species == "F") return 9; + else if (species == "Ne") return 10; + else if (species == "Na") return 11; + else if (species == "Mg") return 12; + else if (species == "Al") return 13; + else if (species == "Si") return 14; + else if (species == "P") return 15; + else if (species == "S") return 16; + else if (species == "Cl") return 17; + else if (species == "Ar") return 18; + else if (species == "K") return 19; + else if (species == "Ca") return 20; + else if (species == "Sc") return 21; + else if (species == "Ti") return 22; + else if (species == "V") return 23; + else if (species == "Cr") return 24; + else if (species == "Mn") return 25; + else if (species == "Fe") return 26; + else if (species == "Co") return 27; + else if (species == "Ni") return 28; + else if (species == "Cu") return 29; + else if (species == "Zn") return 30; + else if (species == "Ga") return 31; + else if (species == "Ge") return 32; + else if (species == "As") return 33; + else if (species == "Se") return 34; + else if (species == "Br") return 35; + else if (species == "Kr") return 36; + else if (species == "Rb") return 37; + else if (species == "Sr") return 38; + else if (species == "Y") return 39; + else if (species == "Zr") return 40; + else if (species == "Nb") return 41; + else if (species == "Mo") return 42; + else if (species == "Tc") return 43; + else if (species == "Ru") return 44; + else if (species == "Rh") return 45; + else if (species == "Pd") return 46; + else if (species == "Ag") return 47; + else if (species == "Cd") return 48; + else if (species == "In") return 49; + else if (species == "Sn") return 50; + else if (species == "Sb") return 51; + else if (species == "Te") return 52; + else if (species == "I") return 53; + else if (species == "Xe") return 54; + else if (species == "Cs") return 55; + else if (species == "Ba") return 56; + else if (species == "La") return 57; + else if (species == "Ce") return 58; + else if (species == "Pr") return 59; + else if (species == "Nd") return 60; + else if (species == "Pm") return 61; + else if (species == "Sm") return 62; + else if (species == "Eu") return 63; + else if (species == "Gd") return 64; + else if (species == "Tb") return 65; + else if (species == "Dy") return 66; + else if (species == "Ho") return 67; + else if (species == "Er") return 68; + else if (species == "Tm") return 69; + else if (species == "Yb") return 70; + else if (species == "Lu") return 71; + else if (species == "Hf") return 72; + else if (species == "Ta") return 73; + else if (species == "W") return 74; + else if (species == "Re") return 75; + else if (species == "Os") return 76; + else if (species == "Ir") return 77; + else if (species == "Pt") return 78; + else if (species == "Au") return 79; + else if (species == "Hg") return 80; + else if (species == "Tl") return 81; + else if (species == "Pb") return 82; + else if (species == "Bi") return 83; + else if (species == "Po") return 84; + else if (species == "At") return 85; + else if (species == "Rn") return 86; + else if (species == "Fr") return 87; + else if (species == "Ra") return 88; + else if (species == "Ac") return 89; + else if (species == "Th") return 90; + else if (species == "Pa") return 91; + else if (species == "U") return 92; + else if (species == "Np") return 93; + else if (species == "Pu") return 94; + else if (species == "Am") return 95; + else if (species == "Cm") return 96; + else if (species == "Bk") return 97; + else if (species == "Cf") return 98; + else if (species == "Es") return 99; + else if (species == "Fm") return 100; + else if (species == "Md") return 101; + else if (species == "No") return 102; + else if (species == "Lr") return 103; + else if (species == "Rf") return 104; + else if (species == "Db") return 105; + else if (species == "Sg") return 106; + else if (species == "Bh") return 107; + else if (species == "Hs") return 108; + else if (species == "Mt") return 109; + else if (species == "Ds") return 110; + else if (species == "Rg") return 111; + else if (species == "Cn") return 112; + else if (species == "Nh") return 113; + else if (species == "Fl") return 114; + else if (species == "Mc") return 115; + else if (species == "Lv") return 116; + else if (species == "Ts") return 117; + else if (species == "Og") return 118; + else return -1; +} diff --git a/src/KIM/kim_interactions.h b/src/KIM/kim_interactions.h new file mode 100644 index 0000000000..6da1880f84 --- /dev/null +++ b/src/KIM/kim_interactions.h @@ -0,0 +1,116 @@ +/* -*- c++ -*- ---------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + http://lammps.sandia.gov, Sandia National Laboratories + Steve Plimpton, sjplimp@sandia.gov + + Copyright (2003) Sandia Corporation. Under the terms of Contract + DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains + certain rights in this software. This software is distributed under + the GNU General Public License. + + See the README file in the top-level LAMMPS directory. +------------------------------------------------------------------------- */ + +/* ---------------------------------------------------------------------- + Contributing authors: Axel Kohlmeyer (Temple U), + Ryan S. Elliott (UMN) + Ellad B. Tadmor (UMN) +------------------------------------------------------------------------- */ + +/* ---------------------------------------------------------------------- + This program is free software; you can redistribute it and/or modify it + under the terms of the GNU General Public License as published by the Free + Software Foundation; either version 2 of the License, or (at your option) + any later version. + + This program is distributed in the hope that it will be useful, but WITHOUT + ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or + FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for + more details. + + You should have received a copy of the GNU General Public License along with + this program; if not, see . + + Linking LAMMPS statically or dynamically with other modules is making a + combined work based on LAMMPS. Thus, the terms and conditions of the GNU + General Public License cover the whole combination. + + In addition, as a special exception, the copyright holders of LAMMPS give + you permission to combine LAMMPS with free software programs or libraries + that are released under the GNU LGPL and with code included in the standard + release of the "kim-api" under the CDDL (or modified versions of such code, + with unchanged license). You may copy and distribute such a system following + the terms of the GNU GPL for LAMMPS and the licenses of the other code + concerned, provided that you include the source code of that other code + when and as the GNU GPL requires distribution of source code. + + Note that people who make modified versions of LAMMPS are not obligated to + grant this special exception for their modified versions; it is their choice + whether to do so. The GNU General Public License gives permission to release + a modified version without this exception; this exception also makes it + possible to release a modified version which carries forward this exception. +------------------------------------------------------------------------- */ + +/* ---------------------------------------------------------------------- + Designed for use with the kim-api-2.1.0 (and newer) package +------------------------------------------------------------------------- */ + +#ifdef COMMAND_CLASS + +CommandStyle(kim_interactions,KimInteractions) + +#else + +#ifndef LMP_KIM_INTERACTIONS_H +#define LMP_KIM_INTERACTIONS_H + +#include "pointers.h" + +namespace LAMMPS_NS { + +class KimInteractions : protected Pointers { + public: + KimInteractions(class LAMMPS *lmp) : Pointers(lmp) {}; + void command(int, char **); + private: + void do_setup(int, char **); + int species_to_atomic_no(std::string const species) const; + void kim_interactions_log_delimiter(std::string const begin_end) const; +}; + +} + +#endif +#endif + +/* ERROR/WARNING messages: + +E: Illegal kim_interactions command + +Incorrect number or kind of arguments to kim_interactions. + +E: Must use 'kim_interactions' command after simulation box is defined + +Self-explanatory. + +E: Must use 'kim_init' command before 'kim_interactions' + +Self-explanatory. + +E: Species XXX is not supported by this KIM Simulator Model + +The kim_interactions command was referencing a species that is not +present in the requested KIM Simulator Model. + +E: Incompatible units for KIM Simulator Model + +The selected unit style is not compatible with the requested KIM +Simulator Model. + +E: KIM Simulator Model has no Model definition + +There is no model definition (key: model-defn) in the KIM Simulator +Model. Please contact the OpenKIM database maintainers to verify +and potentially correct this. + +*/ -- GitLab From 17fa2f787b58cb4c17bc6aa04b1015a9b2778a93 Mon Sep 17 00:00:00 2001 From: Ellad Tadmor Date: Sat, 22 Jun 2019 15:25:21 -0500 Subject: [PATCH 067/469] Added kim_command documentation structure --- doc/src/Commands_all.txt | 5 +- doc/src/commands_list.txt | 3 +- doc/src/kim_commands.txt | 108 ++++++++++++++++++++++++++++++++++++++ 3 files changed, 112 insertions(+), 4 deletions(-) create mode 100644 doc/src/kim_commands.txt diff --git a/doc/src/Commands_all.txt b/doc/src/Commands_all.txt index d76ffac14c..a201fd3f2d 100644 --- a/doc/src/Commands_all.txt +++ b/doc/src/Commands_all.txt @@ -68,8 +68,9 @@ An alphabetic list of all general LAMMPS commands. "improper_style"_improper_style.html, "include"_include.html, "jump"_jump.html, -"kim_query"_kim_query.html, -"kim_style"_kim_style.html, +"kim_init"_kim_commands.html, +"kim_interactions"_kim_commands.html, +"kim_query"_kim_commands.html, "kspace_modify"_kspace_modify.html, "kspace_style"_kspace_style.html, "label"_label.html, diff --git a/doc/src/commands_list.txt b/doc/src/commands_list.txt index 39d2f7c7d0..a5c9b568ed 100644 --- a/doc/src/commands_list.txt +++ b/doc/src/commands_list.txt @@ -53,8 +53,7 @@ Commands :h1 include info jump - kim_query - kim_style + kim_commands kspace_modify kspace_style label diff --git a/doc/src/kim_commands.txt b/doc/src/kim_commands.txt new file mode 100644 index 0000000000..4c53746317 --- /dev/null +++ b/doc/src/kim_commands.txt @@ -0,0 +1,108 @@ +"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c + +:link(lws,http://lammps.sandia.gov) +:link(ld,Manual.html) +:link(lc,Commands_all.html) + +:line + +kim_commands :h3 + +[Syntax:] + +kim_init model user_units :pre +kim_interactions typeargs :pre + +mode = {init model} or {define typeargs} or no mode chosen +model = name of the KIM model (KIM potential or KIM simulator model) +typeargs = atom type to species mapping (one entry per atom type) +args = {unit_variables unit_style} or {unit_from unit_style} (optional):ul + +[Examples:] + +kim_style init ex_sim_model_Si_mod_tersoff unit_variables metal +kim_style define Si Si +kim_style unit_variables real +kim_style init LennardJones_Ar unit_variables metal +kim_style unit_variables real unit_from metal +kim_style define Ar :pre + +[Description:] + +The kim_style command is a high-level wrapper around the +"Knowledge Base for Interatomic Models (OpenKIM)"_https://openkim.org +repository of interatomic potentials, so that they can be used by +LAMMPS scripts. It does not implement any computations directly, but +rather will generate LAMMPS input commands based on the information +retrieved from the OpenKIM repository. It is able to realize so-called +"KIM Simulator Models", which are OpenKIM repository entries of models +using native features of the simulation engine in use, i.e. LAMMPS +in this case, but it also supports realizing conventional KIM models +implicitly via generating a "pair_style kim"_pair_kim.html command +followed by a suitable "pair_coeff"_pair_coeff.html command. + +The kim_style command has two modes, {init} and {define}, indicated by +the first argument to the kim_style command. An {init} mode command +must be issued [before] the simulation box is created, while the {define} +mode version may only be used [after] the simulation box exists. Both +are required. The {init} mode version sets the model name and may issue +additional commands changing LAMMPS default settings that are required +for using a selected simulator model. If needed, those settings can be +overridden. The second argument to the {kim_style init} command is the +KIM model ID. + +In both modes, the keywords {unit_variables} and {unit_from} may be +added. They control the values of a set of +"internal style variables"_variable.html that can be used to convert +between different unit styles in LAMMPS. The argument to +each keyword is a LAMMPS unit style or NULL, which means to look up +the unit style from what was set with the "units"_units.html command. +Please note, that KIM simulator models will set their preferred unit style. +By default all conversion variables are set to 1.0. Converting to or +from the "lj" unit style is not supported. The following variables are defined: + +_u_length +_u_mass +_u_time :ul + + +The {kim_style define} command will issue commands that will realize +the selected model (through generating pair_style and pair_coeff commands, +but also other commands, as required). It has to be issued [after] the +the simulation box is defined. The {kim_style define} command allows a +varying number of additional arguments. Those are used to map the atom +types in LAMMPS to the available species in the KIM model. This is +equivalent to the arguments following "pair_coeff * *" in a +"kim"_pair_kim.html pair style. Thus the commands: + +kim_style init LennardJones_Ar +kim_style define Ar :pre + +will generate the LAMMPS input commands: + +pair_style kim LennardJones_Ar +pair_coeff * * Ar :pre + +For simulator models, the generated input commands may be more complex +and require that LAMMPS is built with the required packages included. +The commands generated by the kim_style command, can be copied to the +screen or log file, through the "echo"_echo.html command. +The kim_style command will also validate, that a selected simulator +model was generated for the LAMMPS MD code and not some other software. +In addition, the version strings for LAMMPS version used for defining +the simulator model and the LAMMPS version being currently run are +printed, so that it can be tracked down, if there are any incompatible +changes to input script or command syntax between the two LAMMPS versions. + +[Restrictions:] + +This command is part of the KIM package. It is only enabled if +LAMMPS was built with that package. Furthermore, its correct +functioning depends on compiling LAMMPS with all required packages +installed that are required by the commands embedded in any KIM +simulator models used. +See the "Build package"_Build_package.html doc page for more info. + +[Related commands:] + +"pair_style kim"_pair_kim.html, "kim_query"_kim_query.html -- GitLab From 33be7f259be9446edf9f75e17309d8bfe7f05e84 Mon Sep 17 00:00:00 2001 From: Ellad Tadmor Date: Sat, 22 Jun 2019 21:49:29 -0500 Subject: [PATCH 068/469] Working on kim_commands documentation --- doc/src/kim_commands.txt | 232 +++++++++++++++++++++++++++++++++++++-- 1 file changed, 221 insertions(+), 11 deletions(-) diff --git a/doc/src/kim_commands.txt b/doc/src/kim_commands.txt index 4c53746317..06ad841240 100644 --- a/doc/src/kim_commands.txt +++ b/doc/src/kim_commands.txt @@ -10,25 +10,235 @@ kim_commands :h3 [Syntax:] -kim_init model user_units :pre -kim_interactions typeargs :pre +kim_init model user_units unitarg +kim_interactions typeargs +kim_query variable query_function web_query_flags :pre -mode = {init model} or {define typeargs} or no mode chosen -model = name of the KIM model (KIM potential or KIM simulator model) +model = designation of the KIM interatomic model (the KIM ID for models archived in OpenKIM) +user_units = the LAMMPS "units"_units.html style assumed in the user input script +unitarg = {unit_conversion_mode} (optional) typeargs = atom type to species mapping (one entry per atom type) -args = {unit_variables unit_style} or {unit_from unit_style} (optional):ul +variable = name of a (string style) variable where the result of the query is stored +query_function = name of the OpenKIM web API query function to be used +web_query_flags = a series of keyword=value pairs that represent the web query; supported keywords depend on query function :ul + [Examples:] -kim_style init ex_sim_model_Si_mod_tersoff unit_variables metal -kim_style define Si Si -kim_style unit_variables real -kim_style init LennardJones_Ar unit_variables metal -kim_style unit_variables real unit_from metal -kim_style define Ar :pre +kim_init SW_StillingerWeber_1985_Si__MO_405512056662_005 metal +kim_interactions Si +kim_init Sim_LAMMPS_ReaxFF_StrachanVanDuinChakraborty_2003_CHNO__SM_107643900657_000 real +kim_init Sim_LAMMPS_ReaxFF_StrachanVanDuinChakraborty_2003_CHNO__SM_107643900657_000 metal unit_conversion_mode +kim_interactions C H O +kim_query NEED EXAMPLES :pre [Description:] +The "Open Knowledgebase for Interatomic Models (OpenKIM)"_https://openkim.org +archives interatomic models (IMs) (potentials and force fields) in a format +that can be directly used with LAMMPS using the commands documented on this +page. + +Benefits of Using OpenKIM IMs :h4 + +Employing OpenKIM IMs provides LAMMPS users with multiple benefits: + +Reliability :h5 + +All content archived in OpenKIM is subject to quality control by the "KIM Editor"_https://openkim.org/governance/. +IMs in OpenKIM are archived with full provenance control. Each is associated with a maintainer responsible for the integrity of the content. All changes are tracked and recorded. +IMs in OpenKIM are exhaustively tested using "KIM Tests"_https://openkim.org/getting-started/kim-tests/ that compute a host of material properties, and "KIM Verification Checks"_https://openkim.org/about-verification-checks/ that provide the user with information on various aspects of the IM behavior and coding correctness. This information is displayed on the IM's page on "OpenKIM"_https://openkim.org. :ul + +Reproducibility :h5 + +Each IM in OpenKIM is issued a unique identifier ("KIM ID"_https://openkim.org/about-kim-ids/), which includes a version number (last three digits). Any changes that can result in different numerical values lead to a version increment in the KIM ID. This makes it possible to reproduce simulations since the specific version of a specific IM used can be retrieved using its KIM ID. +OpenKIM is a member organization of "DataCite"_https://datacite.org/ and issues digitial object identifiers (DOIs) to all IMs archived in OpenKIM. This makes it possible to cite the IM code used in a simulation in a publications to give credit to the developers and further facilitate reproducibility. :ul + +Convenience :h5 + +IMs in OpenKIM are distributed in binary form along with LAMMPS and can be used in a LAMMPS input script simply by providing their KIM ID in the {kim_init} command documented on this page. (For more on using KIM with LAMMPS, see the KIM section of the "Packages details"_Packages_details.html doc page.) +The {kim_query} web query tool provides the ability to use the predictions of IMs for supported material properties (computed via "KIM Tests"https://openkim.org/getting-started/kim-tests/) as part of a LAMMPS input script setup and analysis. +Support is provided for unit conversion between the "units"_units.html system used in the LAMMPS input script and the OpenKIM IM. This makes it possible to use a single input script with IMs using different units without change and minimizes the liklihood of errors due to incompatible units. :ul + +Types of KIM IMs :h4 + +There are two types of IMs archived in OpenKIM: + +The first type is called a {KIM Model}. A KIM Model is an independent computer implemention of an IM written in one of the languages supported by KIM (C, C++, Fortran, Python), which conforms to the KIM Application Programming Interface ("KIM API"_https://openkim.org/kim-api/). A KIM Model will work seamlessly with any simulation code that support the KIM API (including LAMMPS; see "complete list of supported code"_https://openkim.org/projects-using-kim/). +The second type is called a {KIM Simulator Model} (SM). In this case, the IM is implemented natively within the simulation code ({simulator}), i.e. LAMMPS. A separate SM package is archived in OpenKIM for each parameterization of the IM, which includes all of the necessary parameter files, LAMMPS commands, and metadata (supported species, units, etc.) needed to run the IM in LAMMPS. :ol + +With these two IM tpes, OpenKIM can archive and test almost all IMs that +can be used by LAMMPS. (It is easy to contribute new IMs to OpenKIM, see +the "upload instructions"_https://openkim.org/getting-started/adding-content/.) + +OpenKIM IMs are uniquely identified by a +"KIM ID"_https://openkim.org/about-kim-ids/. The extended KIM ID consists of +a human-readable prefix identifying the type of IM, authors, publication year, +and supported species, separated by two underscores from the KIM ID itself, +which begins with an IM code +({MO} for a KIM Model, and {SM} for a KIM Simulator Model) +followed by a unique 12-digit code and a 3-digit version identifier. +By convension SM prefixes begin with {SM} to readily identify them. + +SW_StillingerWeber_1985_Si__MO_405512056662_005 +Sim_LAMMPS_ReaxFF_StrachanVanDuinChakraborty_2003_CHNO__SM_107643900657_000 :pre + +NOTE: It is also possible to locally install IMs not archived in OpenKIM, +in which case their designation does not have to conform to the KIM ID format. + +Using OpenKIM IMs with LAMMPS :h4 + +Two commands are employed when using OpenKIM IMs, one to select the +IM and perform necessary initializations ({kim_init}), and the second +to set up the IM for use by executing any necessary LAMMPS commands +({kim_interactions}). + +OpenKIM IM Initialization :h5 + +The kim_init command must be located at the top of the input script +before any other commands. Input scripts containing a kim_init command +shoud {not} include a "units"_units.html command or an +"atom_style"_atom_style.html command. These are set by the kim_init +command based on its arguments. + +The required arguments of kim_init are the {model} designation of the +IM to be used in the simulation (for an IM archived in OpenKIM this is +its "extended KIM ID"_https://openkim.org/about-kim-ids/), and +the {user_units}, which are the LAMMPS "units"_units.html system used +in the input script. (Any numerical values in the input script and values +read in from files are expected to be in the {user_units} system.) + +Based on the selected model kim_init may modify "atom_style"_atom_style.html. +Some SMs have requirements for this variable. If this is the case, then +atom_style will be set to the required style. Otherwise, the value is left +unchanged (which in the absence of an atom_style command in the input script +is the default LAMMPS value). + +Regarding units, the kim_init command behaves in different ways depending +on whether or not "unit conversion mode" is activated as indicated by the +optional {unitarg} argument. +If unit conversion mode is {not} active, then {user_units} must +either match the required units of the IM or the IM must be able +to adjust its units to match. (The latter is only possible with some KIM Models; +SMs can never adjust their units.) If a match is possible, the LAMMPS +"units"_units.html command is called to set the units to +{user_units}. If the match fails, the simulation is terminated with +an error. + +If unit conversion mode {is} active, then the LAMMPS "units"_units.html +command is called to set the units to the IM's required or preferred units. +Conversion factors between the IM's units and the {user_units} are +defined for all "physical quantities"_units.html (mass, distance, etc.). +These factors are stored as internal "variables"_variable.html with +standard names: + +_u_mass +_u_distance +_u_time +_u_energy +_u_velocity +_u_force +_u_torque +_u_temperature +_u_pressure +_u_viscosity +_u_charge +_u_dipole +_u_efield +_u_density :pre + +If desired, the input script can be designed to work with these conversion +factors so that the script will work without change with any OpenKIM IM. +(This approach is used in the +"OpenKIM Testing Framework"_https://openkim.org/getting-started/kim-tests/.) +For example, the following simple script constructs an fcc lattice with +a lattice parameter defined in meters, computes the total energy, +and prints the cohesive energy in Joules regardless of the units of the IM. + +kim_init EAM_Dynamo_ErcolessiAdams_1994_Al__MO_123629422045_005 si unit_conversion_mode +boundary p p p +lattice fcc 4.032e-10*$\{_u_distance\} +region simbox block 0 1 0 1 0 1 units lattice +create_box 1 simbox +create_atoms 1 box +mass 1 4.480134e-26*$\{_u_mass\} +kim_interactions Al +run 0 +variable Ec_in_J equal (pe/count(all))/$\{_u_energy\} +print "Cohesive Energy = $\{Ec_in_J\} J" :pre + +Note the multiplication by $\{_u_distance\} and $\{_u_mass\} to convert +from SI units (specified in the kim_init command) to whatever units the +IM uses (metal in this case), and the division by $\{_u_energy\} +to convert from the IM's energy units to SI units (Joule). This script +will work correctly for any IM for Al (KIM Model or SM) selected by the +kim_init command. + +Care must be taken to apply unit conversion to dimensional variables read in +from a file. For example if a configuration of atoms is read in from a +dump file using the "read_dump"_read_dump.html command, the following can +be done to convert the box and all atomic positions to the correct units: + +change_box all x scale $\{_u_distance\} y scale $\{_u_distance\} z scale $\{_u_distance\} remap :pre + +NOTE: Unit conversion will only work if the conversion factors are placed in +all appropriate places in the input script. It is up to the user to do this +correctly. + +OpenKIM IM Execution :h5 + +The second and final step in using an OpenKIM IM is to execute the +kim_interaction command. This command must be preceded by a kim_init +command and must follow the "create_box"_create_box.html command, +which defines the number of atom types {N}. +The kim_interaction command has one argument {typeargs}, which contains +a list of {N} chemical species that are mapped to the atom types. + +For example, imagine the OpenKIM IM supports Si and C species. +If the LAMMPS simulation has 4 atom types and you want the first three to be Si, +and the fourth to be C, you would use the following kim_interaction command: + +kim_interaction Si Si Si C :pre + +The kim_interaction command performs all the necessary steps to set up +the OpenKIM IM set in the kim_init command. The specific actions depend +on whether the IM is a KIM Model or a KIM SM. For a KIM Model, +a "pair_style kim"_pair_kim.html command will be executed followed by +the appropriate pair_coeff command. + +For a KIM SM, the set of commands defined in the SM speficiation file +will be executed. For example, consider the ReaxFF SM due to +Strachan et al. (2003) executed by the following commands: + +kim_init Sim_LAMMPS_ReaxFF_StrachanVanDuinChakraborty_2003_CHNO__SM_107643900657_000 real +... +... box specification lines skipped +... +kim_interactions C H N O :pre + +The kim_interactions command executes the following commands defined for this +SM: + +pair_style reax/c lmp_control safezone 2.0 mincap 100 +pair_coeff * * ffield.reax.rdx C H N O +fix reaxqeq all qeq/reax 1 0.0 10.0 1.0e-6 param.qeq :pre + +Note that the files lmp_control, ffield.reax.rdx and param.qeq are specific +to Strachan et al. (2003) ReaxFF parameterization and are archived as part +of the SM package in OpenKIM. Note also that parameters like cutoff radii +and charge tolerances that have an effect on IM predictions are also +included in the SM definition ensuring reproducibility. + +NOTE: Clearly when using using kim_init and kim_interactions to select +and set up an OpenKIM IM, other LAMMPS commands +for the same functions (such as pair_style, pair_coeff, bond_style, +bond_coeff, fixes related to charge equilibration, etc.) should not +appear in the input script. + +Using OpenKIM Web Queries in LAMMPS :h4 + +@@@@@@@@@ + The kim_style command is a high-level wrapper around the "Knowledge Base for Interatomic Models (OpenKIM)"_https://openkim.org repository of interatomic potentials, so that they can be used by -- GitLab From c11caf45095d96aeb2a1477ce78d6e0c03ea7505 Mon Sep 17 00:00:00 2001 From: "Ryan S. Elliott" Date: Sun, 23 Jun 2019 10:34:43 -0500 Subject: [PATCH 069/469] update kim examples to temp. current state of code --- examples/kim/data.VOH | 118 ---------------------- examples/kim/in.kim.VOH.simulator_model | 23 ----- examples/kim/in.kim.ex_si.simulator_model | 69 ------------- examples/kim/in.kim.lj.simulator_model | 10 +- 4 files changed, 2 insertions(+), 218 deletions(-) delete mode 100644 examples/kim/data.VOH delete mode 100644 examples/kim/in.kim.VOH.simulator_model delete mode 100644 examples/kim/in.kim.ex_si.simulator_model diff --git a/examples/kim/data.VOH b/examples/kim/data.VOH deleted file mode 100644 index c093705adc..0000000000 --- a/examples/kim/data.VOH +++ /dev/null @@ -1,118 +0,0 @@ -# VOH example - -100 atoms -4 atom types - -0 25.000 xlo xhi -0 25.000 ylo yhi -0 25.000 zlo zhi - -Masses - -1 1.0080 -2 12.0107 -3 15.9994 -4 50.9415 - -Atoms - - 1 2 0.0 12.35333 12.56112 11.08925 - 2 4 0.0 12.32916 12.62071 13.13099 - 3 3 0.0 14.09425 12.56218 13.76130 - 4 3 0.0 11.42814 11.10330 13.76732 - 5 3 0.0 11.63260 13.89286 13.64097 - 6 1 0.0 10.61647 11.29221 14.30535 - 7 1 0.0 14.38026 13.34626 14.29055 - 8 1 0.0 11.32479 12.58820 10.70253 - 9 1 0.0 12.90918 13.42567 10.69612 - 10 1 0.0 12.84043 11.63643 10.74688 - 11 2 0.0 0.93670 23.74637 24.45218 - 12 4 0.0 2.18151 24.36876 0.94725 - 13 3 0.0 3.93452 24.44779 0.28384 - 14 3 0.0 2.13668 23.10529 2.33362 - 15 3 0.0 1.76108 0.74666 1.48323 - 16 1 0.0 1.82070 23.45305 3.20745 - 17 1 0.0 4.35555 0.34186 0.31083 - 18 1 0.0 24.90472 23.68735 24.82586 - 19 1 0.0 0.97611 24.45631 23.61244 - 20 1 0.0 1.24583 22.75250 24.09589 - 21 2 0.0 2.25730 12.18969 18.74792 - 22 4 0.0 0.67140 13.31162 19.37385 - 23 3 0.0 0.71106 13.43250 21.24545 - 24 3 0.0 24.08603 12.44025 18.87949 - 25 3 0.0 0.70486 14.71920 18.75808 - 26 1 0.0 23.49516 12.95430 18.26686 - 27 1 0.0 0.79723 14.34808 21.60818 - 28 1 0.0 2.24383 12.10285 17.65239 - 29 1 0.0 3.19860 12.66607 19.06030 - 30 1 0.0 2.20214 11.18299 19.18774 - 31 2 0.0 9.32237 8.16220 23.74501 - 32 4 0.0 9.41775 7.26178 21.91463 - 33 3 0.0 8.54752 8.34565 20.65588 - 34 3 0.0 8.50942 5.62151 22.00137 - 35 3 0.0 10.87539 7.02683 21.48455 - 36 1 0.0 9.06507 4.82324 21.80615 - 37 1 0.0 9.11458 8.67119 19.91477 - 38 1 0.0 9.82196 7.53487 24.49616 - 39 1 0.0 9.81855 9.14254 23.70532 - 40 1 0.0 8.27176 8.30387 24.03831 - 41 2 0.0 9.10113 13.98748 23.44281 - 42 4 0.0 8.84954 12.89163 21.73780 - 43 3 0.0 10.01387 13.54293 20.42005 - 44 3 0.0 7.08992 13.11522 21.12954 - 45 3 0.0 9.12937 11.39982 21.99065 - 46 1 0.0 6.55309 12.28287 21.08224 - 47 1 0.0 10.67858 12.89258 20.08249 - 48 1 0.0 8.42108 13.62252 24.22498 - 49 1 0.0 10.13926 13.89766 23.79639 - 50 1 0.0 8.88118 15.04646 23.24289 - 51 2 0.0 17.73225 3.40708 8.28945 - 52 4 0.0 18.49877 5.29835 8.37599 - 53 3 0.0 19.48472 5.62627 6.81505 - 54 3 0.0 19.66498 5.40961 9.84118 - 55 3 0.0 17.38120 6.34466 8.51889 - 56 1 0.0 19.41208 6.07779 10.52927 - 57 1 0.0 19.15960 6.37609 6.25924 - 58 1 0.0 17.15579 3.19557 9.20103 - 59 1 0.0 17.07197 3.31049 7.41454 - 60 1 0.0 18.54903 2.67524 8.20436 - 61 2 0.0 5.18346 20.97409 24.28840 - 62 4 0.0 7.06396 20.17968 24.34847 - 63 3 0.0 7.63220 19.82889 22.59578 - 64 3 0.0 7.00272 18.55243 0.28036 - 65 3 0.0 8.05085 21.13715 0.03620 - 66 1 0.0 7.56109 18.51690 1.09952 - 67 1 0.0 8.44257 20.31624 22.30833 - 68 1 0.0 4.83239 21.17976 0.30904 - 69 1 0.0 5.19182 21.91237 23.71419 - 70 1 0.0 4.49282 20.26573 23.80772 - 71 2 0.0 21.82701 12.79861 20.63056 - 72 4 0.0 21.27646 11.09990 19.63611 - 73 3 0.0 19.52930 10.64327 20.13923 - 74 3 0.0 22.41924 9.70346 20.14638 - 75 3 0.0 21.34556 11.30206 18.11274 - 76 1 0.0 22.94464 9.30084 19.40876 - 77 1 0.0 18.86743 10.62817 19.40629 - 78 1 0.0 22.85378 13.07853 20.35349 - 79 1 0.0 21.14666 13.62206 20.37063 - 80 1 0.0 21.78702 12.62668 21.71522 - 81 2 0.0 4.84801 10.63893 5.85720 - 82 4 0.0 2.99668 11.06158 5.10490 - 83 3 0.0 3.09505 11.09458 3.23258 - 84 3 0.0 2.48053 12.76555 5.69567 - 85 3 0.0 1.96195 10.01780 5.55634 - 86 1 0.0 1.65323 12.78746 6.24245 - 87 1 0.0 2.52753 10.43264 2.76734 - 88 1 0.0 4.80984 10.62196 6.95551 - 89 1 0.0 5.18492 9.65688 5.49273 - 90 1 0.0 5.56737 11.40648 5.53568 - 91 2 0.0 13.58126 9.47098 19.40329 - 92 4 0.0 14.17691 10.17243 21.22692 - 93 3 0.0 14.44428 12.02521 21.10583 - 94 3 0.0 15.81206 9.37183 21.67632 - 95 3 0.0 13.12907 9.86545 22.30960 - 96 1 0.0 15.80034 8.83149 22.50703 - 97 1 0.0 13.87232 12.57457 21.69672 - 98 1 0.0 13.42563 8.38456 19.45392 - 99 1 0.0 12.63978 9.95672 19.10431 - 100 1 0.0 14.35123 9.68789 18.64825 diff --git a/examples/kim/in.kim.VOH.simulator_model b/examples/kim/in.kim.VOH.simulator_model deleted file mode 100644 index 8696cf265a..0000000000 --- a/examples/kim/in.kim.VOH.simulator_model +++ /dev/null @@ -1,23 +0,0 @@ -# REAX potential for VOH system -# ..... - -units real -atom_style charge - -kim_style init Sim_LAMMPS_ReaxFF_ChenowethVanDuinPersson_2008_CHOV__SM_429148913211_000 - -read_data data.VOH - -kim_style define H C O V - -neighbor 2 bin -neigh_modify every 10 delay 0 check no - -fix 1 all nve -fix 3 all temp/berendsen 500.0 500.0 100.0 - -timestep 0.25 - -#dump 1 all atom 30 dump.reax.voh - -run 300 diff --git a/examples/kim/in.kim.ex_si.simulator_model b/examples/kim/in.kim.ex_si.simulator_model deleted file mode 100644 index 2f9e79ef4e..0000000000 --- a/examples/kim/in.kim.ex_si.simulator_model +++ /dev/null @@ -1,69 +0,0 @@ - -units metal -kim_style init ex_sim_model_Si_mod_tersoff - -atom_style atomic -atom_modify map array -boundary p p p - -# temperatures -variable tlo equal 1800.0 -variable thi equal 2400.0 - -# coordination number cutoff - -variable r equal 2.835 - -# minimization parameters - -variable etol equal 1.0e-5 -variable ftol equal 1.0e-5 -variable maxiter equal 100 -variable maxeval equal 100 -variable dmax equal 1.0e-1 - -# diamond unit cell - -variable a equal 5.431 -lattice custom $a & - a1 1.0 0.0 0.0 & - a2 0.0 1.0 0.0 & - a3 0.0 0.0 1.0 & - basis 0.0 0.0 0.0 & - basis 0.0 0.5 0.5 & - basis 0.5 0.0 0.5 & - basis 0.5 0.5 0.0 & - basis 0.25 0.25 0.25 & - basis 0.25 0.75 0.75 & - basis 0.75 0.25 0.75 & - basis 0.75 0.75 0.25 - -region myreg block 0 4 & - 0 4 & - 0 4 -create_box 1 myreg -create_atoms 1 region myreg - -mass 1 28.06 - -group Si type 1 - -velocity all create ${thi} 5287286 mom yes rot yes dist gaussian - -# make a vacancy - -group del id 300 -delete_atoms group del -kim_style define Si - -thermo 10 - -fix 1 all nve -fix 2 all langevin ${thi} ${thi} 0.1 48278 - -timestep 1.0e-3 -neighbor 1.0 bin -neigh_modify every 1 delay 10 check yes - -run 100 - diff --git a/examples/kim/in.kim.lj.simulator_model b/examples/kim/in.kim.lj.simulator_model index 01ee5aa64c..cb7a2e14ed 100644 --- a/examples/kim/in.kim.lj.simulator_model +++ b/examples/kim/in.kim.lj.simulator_model @@ -14,9 +14,7 @@ variable xx equal 20*$x variable yy equal 20*$y variable zz equal 20*$z -echo both -#kim_style model LennardJones_Ar metal -kim_style model Sim_LAMMPS_LJcut_AkersonElliott_Alchemy_PbAu real unit_conversion_mode +kim_init Sim_LAMMPS_LJcut_AkersonElliott_Alchemy_PbAu real unit_conversion_mode newton on lattice fcc 4.4300 @@ -24,10 +22,7 @@ region box block 0 ${xx} 0 ${yy} 0 ${zz} create_box 1 box create_atoms 1 box -#pair_style lj/cut 8.1500 -#pair_coeff 1 1 0.0104 3.4000 - -kim_style setup Au +kim_interactions Au mass 1 39.95 velocity all create 200.0 232345 loop geom @@ -36,6 +31,5 @@ neighbor 0.3 bin neigh_modify delay 0 every 1 check yes fix 1 all nve -#fix 1 all npt temp 1.0 1.0 1.0 iso 1.0 1.0 3.0 run 100 -- GitLab From d08867ce0a05e090056f9dea1e3bbdd2fc4c6afa Mon Sep 17 00:00:00 2001 From: Ellad Tadmor Date: Sun, 23 Jun 2019 11:39:06 -0500 Subject: [PATCH 070/469] Completed first version of kim_commands documentation --- doc/src/kim_commands.txt | 318 +++++++++++++++++++++++---------------- 1 file changed, 189 insertions(+), 129 deletions(-) diff --git a/doc/src/kim_commands.txt b/doc/src/kim_commands.txt index 06ad841240..c3ab799821 100644 --- a/doc/src/kim_commands.txt +++ b/doc/src/kim_commands.txt @@ -12,15 +12,15 @@ kim_commands :h3 kim_init model user_units unitarg kim_interactions typeargs -kim_query variable query_function web_query_flags :pre +kim_query variable query_function queryargs :pre -model = designation of the KIM interatomic model (the KIM ID for models archived in OpenKIM) -user_units = the LAMMPS "units"_units.html style assumed in the user input script +model = name of the KIM interatomic model (the KIM ID for models archived in OpenKIM) +user_units = the LAMMPS "units"_units.html style assumed in the LAMMPS input script unitarg = {unit_conversion_mode} (optional) typeargs = atom type to species mapping (one entry per atom type) variable = name of a (string style) variable where the result of the query is stored query_function = name of the OpenKIM web API query function to be used -web_query_flags = a series of keyword=value pairs that represent the web query; supported keywords depend on query function :ul +queryargs = a series of {keyword=value} pairs that represent the web query; supported keywords depend on the query function :ul [Examples:] @@ -30,14 +30,20 @@ kim_interactions Si kim_init Sim_LAMMPS_ReaxFF_StrachanVanDuinChakraborty_2003_CHNO__SM_107643900657_000 real kim_init Sim_LAMMPS_ReaxFF_StrachanVanDuinChakraborty_2003_CHNO__SM_107643900657_000 metal unit_conversion_mode kim_interactions C H O -kim_query NEED EXAMPLES :pre +kim_query a0 get_lattice_constant_fcc units=\["angstrom"\] :pre + [Description:] -The "Open Knowledgebase for Interatomic Models (OpenKIM)"_https://openkim.org -archives interatomic models (IMs) (potentials and force fields) in a format -that can be directly used with LAMMPS using the commands documented on this -page. +The set of {kim_commands} provide a high-level wrapper around the +"Open Knowledgebase of Interatomic Models (OpenKIM)"_https://openkim.org +repository of interatomic models (IMs) (potentials and force fields), +so that they can be used by LAMMPS scripts. These commands do not implement +any computations directly, but rather generate LAMMPS input commands based +on the information retrieved from the OpenKIM repository to initialize and +activate OpenKIM IMs and query their predictions for use in the LAMMPS script. +All LAMMPS input commands executed by {kim_commands} are echoed to the +LAMMPS log file. Benefits of Using OpenKIM IMs :h4 @@ -52,22 +58,23 @@ IMs in OpenKIM are exhaustively tested using "KIM Tests"_https://openkim.org/get Reproducibility :h5 Each IM in OpenKIM is issued a unique identifier ("KIM ID"_https://openkim.org/about-kim-ids/), which includes a version number (last three digits). Any changes that can result in different numerical values lead to a version increment in the KIM ID. This makes it possible to reproduce simulations since the specific version of a specific IM used can be retrieved using its KIM ID. -OpenKIM is a member organization of "DataCite"_https://datacite.org/ and issues digitial object identifiers (DOIs) to all IMs archived in OpenKIM. This makes it possible to cite the IM code used in a simulation in a publications to give credit to the developers and further facilitate reproducibility. :ul +OpenKIM is a member organization of "DataCite"_https://datacite.org/ and issues digital object identifiers (DOIs) to all IMs archived in OpenKIM. This makes it possible to cite the IM code used in a simulation in a publications to give credit to the developers and further facilitate reproducibility. :ul Convenience :h5 -IMs in OpenKIM are distributed in binary form along with LAMMPS and can be used in a LAMMPS input script simply by providing their KIM ID in the {kim_init} command documented on this page. (For more on using KIM with LAMMPS, see the KIM section of the "Packages details"_Packages_details.html doc page.) +IMs in OpenKIM are distributed in binary form along with LAMMPS and can be used in a LAMMPS input script simply by providing their KIM ID in the {kim_init} command documented on this page. The {kim_query} web query tool provides the ability to use the predictions of IMs for supported material properties (computed via "KIM Tests"https://openkim.org/getting-started/kim-tests/) as part of a LAMMPS input script setup and analysis. -Support is provided for unit conversion between the "units"_units.html system used in the LAMMPS input script and the OpenKIM IM. This makes it possible to use a single input script with IMs using different units without change and minimizes the liklihood of errors due to incompatible units. :ul +Support is provided for unit conversion between the "units style"_units.html used in the LAMMPS input script and the units required by the OpenKIM IM. This makes it possible to use a single input script with IMs using different units without change and minimizes the likelihood of errors due to incompatible units. :ul +:link(IM_types) Types of KIM IMs :h4 There are two types of IMs archived in OpenKIM: -The first type is called a {KIM Model}. A KIM Model is an independent computer implemention of an IM written in one of the languages supported by KIM (C, C++, Fortran, Python), which conforms to the KIM Application Programming Interface ("KIM API"_https://openkim.org/kim-api/). A KIM Model will work seamlessly with any simulation code that support the KIM API (including LAMMPS; see "complete list of supported code"_https://openkim.org/projects-using-kim/). +The first type is called a {KIM Model}. A KIM Model is an independent computer implementation of an IM written in one of the languages supported by KIM (C, C++, Fortran, Python), which conforms to the KIM Application Programming Interface ("KIM API"_https://openkim.org/kim-api/). A KIM Model will work seamlessly with any simulation code that support the KIM API (including LAMMPS; see "complete list of supported code"_https://openkim.org/projects-using-kim/). The second type is called a {KIM Simulator Model} (SM). In this case, the IM is implemented natively within the simulation code ({simulator}), i.e. LAMMPS. A separate SM package is archived in OpenKIM for each parameterization of the IM, which includes all of the necessary parameter files, LAMMPS commands, and metadata (supported species, units, etc.) needed to run the IM in LAMMPS. :ol -With these two IM tpes, OpenKIM can archive and test almost all IMs that +With these two IM types, OpenKIM can archive and test almost all IMs that can be used by LAMMPS. (It is easy to contribute new IMs to OpenKIM, see the "upload instructions"_https://openkim.org/getting-started/adding-content/.) @@ -78,46 +85,59 @@ and supported species, separated by two underscores from the KIM ID itself, which begins with an IM code ({MO} for a KIM Model, and {SM} for a KIM Simulator Model) followed by a unique 12-digit code and a 3-digit version identifier. -By convension SM prefixes begin with {SM} to readily identify them. +By convention SM prefixes begin with {Sim_} to readily identify them. SW_StillingerWeber_1985_Si__MO_405512056662_005 Sim_LAMMPS_ReaxFF_StrachanVanDuinChakraborty_2003_CHNO__SM_107643900657_000 :pre NOTE: It is also possible to locally install IMs not archived in OpenKIM, -in which case their designation does not have to conform to the KIM ID format. +in which case their names do not have to conform to the KIM ID format. Using OpenKIM IMs with LAMMPS :h4 Two commands are employed when using OpenKIM IMs, one to select the IM and perform necessary initializations ({kim_init}), and the second to set up the IM for use by executing any necessary LAMMPS commands -({kim_interactions}). +({kim_interactions}). Both are required. -OpenKIM IM Initialization :h5 +OpenKIM IM Initialization ({kim_init}) :h5 -The kim_init command must be located at the top of the input script -before any other commands. Input scripts containing a kim_init command -shoud {not} include a "units"_units.html command or an -"atom_style"_atom_style.html command. These are set by the kim_init -command based on its arguments. +The {kim_init} mode command must be issued [before] +the simulation box is created (normally at the top of the file). +This command sets the OpenKIM IM that will be used and may issue +additional commands changing LAMMPS default settings that are required +for using the selected IM (such as "units"_units.html or +"atom_style"_atom_style.html). If needed, those settings can be overridden, +however, typically a script containing a {kim_init} command +would not include {units} and {atom_style} commands. -The required arguments of kim_init are the {model} designation of the +The required arguments of {kim_init} are the {model} name of the IM to be used in the simulation (for an IM archived in OpenKIM this is its "extended KIM ID"_https://openkim.org/about-kim-ids/), and -the {user_units}, which are the LAMMPS "units"_units.html system used -in the input script. (Any numerical values in the input script and values -read in from files are expected to be in the {user_units} system.) - -Based on the selected model kim_init may modify "atom_style"_atom_style.html. +the {user_units}, which are the LAMMPS "units style"_units.html used +in the input script. (Any dimensioned numerical values in the input +script and values read in from files are expected to be in the +{user_units} system.) + +The selected IM can be either a "KIM Model or a KIM SM"_#IM_types. +For a KIM SM, the {kim_init} command verifies that the SM is designed +to work with LAMMPS (and not another simulation code). +In addition, the version strings for the LAMMPS version used for defining +the SM and the LAMMPS version being currently run are +printed, to help diagnose any incompatible changes to input script or +command syntax between the two LAMMPS versions. + +Based on the selected model {kim_init} may modify the +"atom_style"_atom_style.html. Some SMs have requirements for this variable. If this is the case, then -atom_style will be set to the required style. Otherwise, the value is left -unchanged (which in the absence of an atom_style command in the input script -is the default LAMMPS value). +{atom_style} will be set to the required style. Otherwise, the value is left +unchanged (which in the absence of an {atom_style} command in the input script +is the "default atom_style value"_atom_style.html). -Regarding units, the kim_init command behaves in different ways depending -on whether or not "unit conversion mode" is activated as indicated by the +Regarding units, the {kim_init} command behaves in different ways depending +on whether or not {unit conversion mode} is activated as indicated by the optional {unitarg} argument. -If unit conversion mode is {not} active, then {user_units} must +If unit conversion mode is [not] active, then {user_units} must either match the required units of the IM or the IM must be able to adjust its units to match. (The latter is only possible with some KIM Models; SMs can never adjust their units.) If a match is possible, the LAMMPS @@ -129,7 +149,8 @@ If unit conversion mode {is} active, then the LAMMPS "units"_units.html command is called to set the units to the IM's required or preferred units. Conversion factors between the IM's units and the {user_units} are defined for all "physical quantities"_units.html (mass, distance, etc.). -These factors are stored as internal "variables"_variable.html with +(Note that converting to or from the "lj" unit style is not supported.) +These factors are stored as "internal style variables"_variable.html with standard names: _u_mass @@ -168,11 +189,11 @@ variable Ec_in_J equal (pe/count(all))/$\{_u_energy\} print "Cohesive Energy = $\{Ec_in_J\} J" :pre Note the multiplication by $\{_u_distance\} and $\{_u_mass\} to convert -from SI units (specified in the kim_init command) to whatever units the +from SI units (specified in the {kim_init} command) to whatever units the IM uses (metal in this case), and the division by $\{_u_energy\} to convert from the IM's energy units to SI units (Joule). This script will work correctly for any IM for Al (KIM Model or SM) selected by the -kim_init command. +{kim_init} command. Care must be taken to apply unit conversion to dimensional variables read in from a file. For example if a configuration of atoms is read in from a @@ -185,30 +206,47 @@ NOTE: Unit conversion will only work if the conversion factors are placed in all appropriate places in the input script. It is up to the user to do this correctly. -OpenKIM IM Execution :h5 +OpenKIM IM Execution ({kim_interactions}) :h5 The second and final step in using an OpenKIM IM is to execute the -kim_interaction command. This command must be preceded by a kim_init -command and must follow the "create_box"_create_box.html command, +{kim_interaction} command. This command must be preceded by a {kim_init} +command and a "create_box"_create_box.html command, which defines the number of atom types {N}. -The kim_interaction command has one argument {typeargs}, which contains -a list of {N} chemical species that are mapped to the atom types. +The {kim_interaction} command has one argument {typeargs}. This argument +contains a list of {N} chemical species, which defines a mapping between +atom types in LAMMPS to the available species in the OpenKIM IM. -For example, imagine the OpenKIM IM supports Si and C species. -If the LAMMPS simulation has 4 atom types and you want the first three to be Si, -and the fourth to be C, you would use the following kim_interaction command: +For example, consider an OpenKIM IM that supports Si and C species. +If the LAMMPS simulation has four atom types, where the first three are Si, +and the fourth is C, the following {kim_interaction} command would be used: kim_interaction Si Si Si C :pre -The kim_interaction command performs all the necessary steps to set up -the OpenKIM IM set in the kim_init command. The specific actions depend +The {kim_interaction} command performs all the necessary steps to set up +the OpenKIM IM selected in the {kim_init} command. The specific actions depend on whether the IM is a KIM Model or a KIM SM. For a KIM Model, -a "pair_style kim"_pair_kim.html command will be executed followed by -the appropriate pair_coeff command. +a "pair_style kim"_pair_kim.html command is executed followed by +the appropriate {pair_coeff} command. For example, for the +Ercolessi and Adams (1994) KIM Model for Al set by the following commands: + +kim_init EAM_Dynamo_ErcolessiAdams_1994_Al__MO_123629422045_005 metal +... +... box specification lines skipped +... +kim_interactions Al :pre + +the {kim_interactions} command executes the following LAMMPS input commands: -For a KIM SM, the set of commands defined in the SM speficiation file -will be executed. For example, consider the ReaxFF SM due to -Strachan et al. (2003) executed by the following commands: +pair_style kim EAM_Dynamo_ErcolessiAdams_1994_Al__MO_123629422045_005 +pair_coeff * * Al :pre + +For a KIM SM, the generated input commands may be more complex +and require that LAMMPS is built with the required packages included +for the type of potential being used. The set of commands to be executed +is defined in the SM specification file, which is part of the SM package +on "OpenKIM"_https://openkim.org. +For example, for the Strachan et al. (2003) ReaxFF SM +set by the following commands: kim_init Sim_LAMMPS_ReaxFF_StrachanVanDuinChakraborty_2003_CHNO__SM_107643900657_000 real ... @@ -216,103 +254,125 @@ kim_init Sim_LAMMPS_ReaxFF_StrachanVanDuinChakraborty_2003_CHNO__SM_107643900657 ... kim_interactions C H N O :pre -The kim_interactions command executes the following commands defined for this -SM: +the {kim_interactions} command executes the following LAMMPS input commands: pair_style reax/c lmp_control safezone 2.0 mincap 100 pair_coeff * * ffield.reax.rdx C H N O fix reaxqeq all qeq/reax 1 0.0 10.0 1.0e-6 param.qeq :pre -Note that the files lmp_control, ffield.reax.rdx and param.qeq are specific -to Strachan et al. (2003) ReaxFF parameterization and are archived as part -of the SM package in OpenKIM. Note also that parameters like cutoff radii -and charge tolerances that have an effect on IM predictions are also -included in the SM definition ensuring reproducibility. +Note that the files {lmp_control}, {ffield.reax.rdx} and {param.qeq} +are specific to the Strachan et al. (2003) ReaxFF parameterization +and are archived as part of the SM package in OpenKIM. +Note also that parameters like cutoff radii and charge tolerances, +which have an effect on IM predictions, are also included in the +SM definition ensuring reproducibility. -NOTE: Clearly when using using kim_init and kim_interactions to select +NOTE: When using using {kim_init} and {kim_interactions} to select and set up an OpenKIM IM, other LAMMPS commands for the same functions (such as pair_style, pair_coeff, bond_style, -bond_coeff, fixes related to charge equilibration, etc.) should not -appear in the input script. - -Using OpenKIM Web Queries in LAMMPS :h4 - -@@@@@@@@@ - -The kim_style command is a high-level wrapper around the -"Knowledge Base for Interatomic Models (OpenKIM)"_https://openkim.org -repository of interatomic potentials, so that they can be used by -LAMMPS scripts. It does not implement any computations directly, but -rather will generate LAMMPS input commands based on the information -retrieved from the OpenKIM repository. It is able to realize so-called -"KIM Simulator Models", which are OpenKIM repository entries of models -using native features of the simulation engine in use, i.e. LAMMPS -in this case, but it also supports realizing conventional KIM models -implicitly via generating a "pair_style kim"_pair_kim.html command -followed by a suitable "pair_coeff"_pair_coeff.html command. - -The kim_style command has two modes, {init} and {define}, indicated by -the first argument to the kim_style command. An {init} mode command -must be issued [before] the simulation box is created, while the {define} -mode version may only be used [after] the simulation box exists. Both -are required. The {init} mode version sets the model name and may issue -additional commands changing LAMMPS default settings that are required -for using a selected simulator model. If needed, those settings can be -overridden. The second argument to the {kim_style init} command is the -KIM model ID. - -In both modes, the keywords {unit_variables} and {unit_from} may be -added. They control the values of a set of -"internal style variables"_variable.html that can be used to convert -between different unit styles in LAMMPS. The argument to -each keyword is a LAMMPS unit style or NULL, which means to look up -the unit style from what was set with the "units"_units.html command. -Please note, that KIM simulator models will set their preferred unit style. -By default all conversion variables are set to 1.0. Converting to or -from the "lj" unit style is not supported. The following variables are defined: - -_u_length -_u_mass -_u_time :ul +bond_coeff, fixes related to charge equilibration, etc.) should normally +not appear in the input script. + +Using OpenKIM Web Queries in LAMMPS ({kim_query}) :h5 +The {kim_query} command performs a web query to retrieve the predictions +of the IM set by {kim_init} for material properties archived in +"OpenKIM"_https://openkim.org. The {kim_query} command must be preceded +by a {kim_init} command. The result of the query is stored in a +"string style variable"_variable.html, the name of which is given as the first +argument of the {kim_query command}. The second required argument +{query_function} is the name of the query function to be called +(e.g. {get_lattice_constant_fcc}). +All following arguments are parameters handed over to the web query +in the format {keyword=value}. The list of supported keywords and +and the type and format of their values depend on the query function +used. -The {kim_style define} command will issue commands that will realize -the selected model (through generating pair_style and pair_coeff commands, -but also other commands, as required). It has to be issued [after] the -the simulation box is defined. The {kim_style define} command allows a -varying number of additional arguments. Those are used to map the atom -types in LAMMPS to the available species in the KIM model. This is -equivalent to the arguments following "pair_coeff * *" in a -"kim"_pair_kim.html pair style. Thus the commands: +NOTE: The current list of supported query functions is available on the OpenKIM +webpage at "https://query.openkim.org"_https://query.openkim.org/ -kim_style init LennardJones_Ar -kim_style define Ar :pre +The data obtained by {kim_query} commands can be used as part of the setup +or analysis phases of LAMMPS simulations. Some examples are given below. -will generate the LAMMPS input commands: +[Define a crystal at its equilibrium lattice constant] -pair_style kim LennardJones_Ar -pair_coeff * * Ar :pre +kim_init EAM_Dynamo_ErcolessiAdams_1994_Al__MO_123629422045_005 metal +boundary p p p +kim_query a0 get_lattice_constant_fcc units=\["angstrom"\] +lattice fcc $\{a0\} +... :pre + +The {kim_query} command retrieves from "OpenKIM"_https://openkim.org +the equilibrium lattice constant predicted by the Ercolessi and Adams (1994) +potential for the face-centered cubic (fcc) structure and places it in +variable {a0}. This variable is then used on the next line to set up the +crystal. By using {kim_query}, the user is saved the trouble and possible +error of tracking this value down, or of having to perform an energy +minimization to find the equilibrium lattice constant. + +[Define a crystal at finite temperature accounting for thermal expansion] + +kim_init EAM_Dynamo_ErcolessiAdams_1994_Al__MO_123629422045_005 metal +boundary p p p +kim_query a0 get_lattice_constant_fcc units=\["angstrom"\] +kim_query alpha get_linear_thermal_expansion_fcc +variable DeltaT equal 300 +lattice fcc $\{a0\}*$\{alpha\}*$\{DeltaT\} +... :pre + +As in the previous example, the equilibrium lattice constant is obtained +for the Ercolessi and Adams (1994) potential. However, in this case the +crystal is scaled to the appropriate lattice constant at 300 K by using +the linear thermal expansion coefficient predicted by the potential. + +[Compute defect formation energy] + +kim_init EAM_Dynamo_ErcolessiAdams_1994_Al__MO_123629422045_005 metal +... +... Build fcc crystal containing some defect and compute the total energy +... which is stored in the variable {Etot} +... +kim_query Ec get_cohesive_energy_fcc units=\["eV"\] +variable Eform equal $\{Etot\} - count(all)*$\{Ec\} +... :pre + +The defect formation energy {Eform} is computed by subtracting from {Etot} the +ideal fcc cohesive energy of the atoms in the system obtained from +"OpenKIM"_https://openkim.org for the Ercolessi and Adams (1994) potential. + +Citation of OpenKIM IMs :h4 + +When publishing results obtained using OpenKIM IMs researchers are requested +to cite the OpenKIM project "(Tadmor)"_#kim-mainpaper and KIM API +"(Elliott)"_#kim-api as well as the specific IM codes used in the simulations. +The citation format for an IM is displayed on its page on +"OpenKIM"_https://openkim.org along with the corresponding BibTex file. + +Citing the codes used in the simulation gives credit +to the researchers who developed them and enables open source efforts like +OpenKIM to function. -For simulator models, the generated input commands may be more complex -and require that LAMMPS is built with the required packages included. -The commands generated by the kim_style command, can be copied to the -screen or log file, through the "echo"_echo.html command. -The kim_style command will also validate, that a selected simulator -model was generated for the LAMMPS MD code and not some other software. -In addition, the version strings for LAMMPS version used for defining -the simulator model and the LAMMPS version being currently run are -printed, so that it can be tracked down, if there are any incompatible -changes to input script or command syntax between the two LAMMPS versions. [Restrictions:] -This command is part of the KIM package. It is only enabled if +The set of {kim_commands} is part of the KIM package. It is only enabled if LAMMPS was built with that package. Furthermore, its correct functioning depends on compiling LAMMPS with all required packages installed that are required by the commands embedded in any KIM -simulator models used. +SM used. See the "Build package"_Build_package.html doc page for more info. [Related commands:] -"pair_style kim"_pair_kim.html, "kim_query"_kim_query.html +"pair_style kim"_pair_kim.html + +:line + +:link(kim-mainpaper) +[(Tadmor)] Tadmor, Elliott, Sethna, Miller and Becker, JOM, 63, 17 (2011). +doi: "https://doi.org/10.1007/s11837-011-0102-6"_https://doi.org/10.1007/s11837-011-0102-6 + +:link(kim-api) +[(Elliott)] Elliott, Tadmor and Bernstein, "https://openkim.org/kim-api"_https://openkim.org/kim-api (2011) +doi: "https://doi.org/10.25950/FF8F563A"_https://doi.org/10.25950/FF8F563A + -- GitLab From a6f6c9bed0c804f039e83943cb9c22a1a66d1429 Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Sun, 23 Jun 2019 12:41:29 -0400 Subject: [PATCH 071/469] fix up links, spelling issues, and inconsistent names in kim commands docs --- doc/src/Build_extras.txt | 2 +- doc/src/Packages_details.txt | 14 ++++----- doc/src/kim_commands.txt | 34 +++++++++++---------- doc/src/pair_kim.txt | 4 +-- doc/utils/sphinx-config/false_positives.txt | 6 ++++ 5 files changed, 34 insertions(+), 26 deletions(-) diff --git a/doc/src/Build_extras.txt b/doc/src/Build_extras.txt index 17d18243f2..220e9420fc 100644 --- a/doc/src/Build_extras.txt +++ b/doc/src/Build_extras.txt @@ -173,7 +173,7 @@ KIM package :h4,link(kim) To build with this package, the KIM library with API v2 must be downloaded and built on your system. It must include the KIM models that you want to -use with LAMMPS. If you want to use the "kim_query"_kim_query.html +use with LAMMPS. If you want to use the "kim_query"_kim_commands.html command, you also need to have libcurl installed with the matching development headers and the curl-config tool. diff --git a/doc/src/Packages_details.txt b/doc/src/Packages_details.txt index 19c7e96fe9..d6e8f8639f 100644 --- a/doc/src/Packages_details.txt +++ b/doc/src/Packages_details.txt @@ -341,11 +341,11 @@ KIM package :link(PKG-KIM),h4 A "pair_style kim"_pair_kim.html command which is a wrapper on the Knowledge Base for Interatomic Models (KIM) repository of interatomic potentials, enabling any of them to be used in LAMMPS simulations. -Also a "kim_query"_kim_query.html command, which allows to query -the OpenKIM database for stored properties, and a -"kim_style"_kim_style.html command, which serves as a front end to -generating LAMMPS input on-the-fly for KIM simulator models and native -KIM models. +Also a "kim_query"_kim_commands.html command, which allows to query +the OpenKIM database for stored properties, and the commands +"kim_init and kim_interactions"_kim_commands.html, which serve as +front end to generating LAMMPS input on-the-fly for KIM simulator +models and native KIM models. To use this package you must have the KIM library available on your system. @@ -357,8 +357,8 @@ Elliott (U Minnesota). [Authors:] Ryan Elliott (U Minnesota) is the main developer for the KIM API which the "pair_style kim"_pair_kim.html command uses. He developed the pair style. Axel Kohlmeyer (Temple U) contributed the -"kim_query"_kim_query.html and "kim_style"_kim_style.html commands in -close collaboration with Ryan. +"kim_query"_kim_commands.html and "kim_init"_kim_commands.html commands +in close collaboration with Ryan. [Install:] diff --git a/doc/src/kim_commands.txt b/doc/src/kim_commands.txt index 06ad841240..7377c0186c 100644 --- a/doc/src/kim_commands.txt +++ b/doc/src/kim_commands.txt @@ -30,7 +30,8 @@ kim_interactions Si kim_init Sim_LAMMPS_ReaxFF_StrachanVanDuinChakraborty_2003_CHNO__SM_107643900657_000 real kim_init Sim_LAMMPS_ReaxFF_StrachanVanDuinChakraborty_2003_CHNO__SM_107643900657_000 metal unit_conversion_mode kim_interactions C H O -kim_query NEED EXAMPLES :pre +kim_query latconst get_test_result test=TE_156715955670 model=MO_800509458712 & + prop=structure-cubic-crystal-npt species=\["Al"\] keys=\["a"\] units=\["angstrom"\] :pre [Description:] @@ -52,22 +53,22 @@ IMs in OpenKIM are exhaustively tested using "KIM Tests"_https://openkim.org/get Reproducibility :h5 Each IM in OpenKIM is issued a unique identifier ("KIM ID"_https://openkim.org/about-kim-ids/), which includes a version number (last three digits). Any changes that can result in different numerical values lead to a version increment in the KIM ID. This makes it possible to reproduce simulations since the specific version of a specific IM used can be retrieved using its KIM ID. -OpenKIM is a member organization of "DataCite"_https://datacite.org/ and issues digitial object identifiers (DOIs) to all IMs archived in OpenKIM. This makes it possible to cite the IM code used in a simulation in a publications to give credit to the developers and further facilitate reproducibility. :ul +OpenKIM is a member organization of "DataCite"_https://datacite.org/ and issues digital object identifiers (DOIs) to all IMs archived in OpenKIM. This makes it possible to cite the IM code used in a simulation in a publications to give credit to the developers and further facilitate reproducibility. :ul Convenience :h5 IMs in OpenKIM are distributed in binary form along with LAMMPS and can be used in a LAMMPS input script simply by providing their KIM ID in the {kim_init} command documented on this page. (For more on using KIM with LAMMPS, see the KIM section of the "Packages details"_Packages_details.html doc page.) The {kim_query} web query tool provides the ability to use the predictions of IMs for supported material properties (computed via "KIM Tests"https://openkim.org/getting-started/kim-tests/) as part of a LAMMPS input script setup and analysis. -Support is provided for unit conversion between the "units"_units.html system used in the LAMMPS input script and the OpenKIM IM. This makes it possible to use a single input script with IMs using different units without change and minimizes the liklihood of errors due to incompatible units. :ul +Support is provided for unit conversion between the "units"_units.html system used in the LAMMPS input script and the OpenKIM IM. This makes it possible to use a single input script with IMs using different units without change and minimizes the likelihood of errors due to incompatible units. :ul Types of KIM IMs :h4 There are two types of IMs archived in OpenKIM: -The first type is called a {KIM Model}. A KIM Model is an independent computer implemention of an IM written in one of the languages supported by KIM (C, C++, Fortran, Python), which conforms to the KIM Application Programming Interface ("KIM API"_https://openkim.org/kim-api/). A KIM Model will work seamlessly with any simulation code that support the KIM API (including LAMMPS; see "complete list of supported code"_https://openkim.org/projects-using-kim/). +The first type is called a {KIM Model}. A KIM Model is an independent computer implementation of an IM written in one of the languages supported by KIM (C, C++, Fortran, Python), which conforms to the KIM Application Programming Interface ("KIM API"_https://openkim.org/kim-api/). A KIM Model will work seamlessly with any simulation code that support the KIM API (including LAMMPS; see "complete list of supported code"_https://openkim.org/projects-using-kim/). The second type is called a {KIM Simulator Model} (SM). In this case, the IM is implemented natively within the simulation code ({simulator}), i.e. LAMMPS. A separate SM package is archived in OpenKIM for each parameterization of the IM, which includes all of the necessary parameter files, LAMMPS commands, and metadata (supported species, units, etc.) needed to run the IM in LAMMPS. :ol -With these two IM tpes, OpenKIM can archive and test almost all IMs that +With these two IM types, OpenKIM can archive and test almost all IMs that can be used by LAMMPS. (It is easy to contribute new IMs to OpenKIM, see the "upload instructions"_https://openkim.org/getting-started/adding-content/.) @@ -78,7 +79,7 @@ and supported species, separated by two underscores from the KIM ID itself, which begins with an IM code ({MO} for a KIM Model, and {SM} for a KIM Simulator Model) followed by a unique 12-digit code and a 3-digit version identifier. -By convension SM prefixes begin with {SM} to readily identify them. +By convention SM prefixes begin with {SM} to readily identify them. SW_StillingerWeber_1985_Si__MO_405512056662_005 Sim_LAMMPS_ReaxFF_StrachanVanDuinChakraborty_2003_CHNO__SM_107643900657_000 :pre @@ -89,7 +90,7 @@ in which case their designation does not have to conform to the KIM ID format. Using OpenKIM IMs with LAMMPS :h4 Two commands are employed when using OpenKIM IMs, one to select the -IM and perform necessary initializations ({kim_init}), and the second +IM and perform necessary initialization ({kim_init}), and the second to set up the IM for use by executing any necessary LAMMPS commands ({kim_interactions}). @@ -97,7 +98,7 @@ OpenKIM IM Initialization :h5 The kim_init command must be located at the top of the input script before any other commands. Input scripts containing a kim_init command -shoud {not} include a "units"_units.html command or an +should {not} include a "units"_units.html command or an "atom_style"_atom_style.html command. These are set by the kim_init command based on its arguments. @@ -188,25 +189,26 @@ correctly. OpenKIM IM Execution :h5 The second and final step in using an OpenKIM IM is to execute the -kim_interaction command. This command must be preceded by a kim_init +kim_interactions command. This command must be preceded by a kim_init command and must follow the "create_box"_create_box.html command, which defines the number of atom types {N}. -The kim_interaction command has one argument {typeargs}, which contains +The kim_interactions command has one argument {typeargs}, which contains a list of {N} chemical species that are mapped to the atom types. For example, imagine the OpenKIM IM supports Si and C species. If the LAMMPS simulation has 4 atom types and you want the first three to be Si, -and the fourth to be C, you would use the following kim_interaction command: +and the fourth to be C, you would use the following kim_interactions command: -kim_interaction Si Si Si C :pre +kim_interactions Si Si Si C +:pre -The kim_interaction command performs all the necessary steps to set up +The kim_interactions command performs all the necessary steps to set up the OpenKIM IM set in the kim_init command. The specific actions depend on whether the IM is a KIM Model or a KIM SM. For a KIM Model, a "pair_style kim"_pair_kim.html command will be executed followed by the appropriate pair_coeff command. -For a KIM SM, the set of commands defined in the SM speficiation file +For a KIM SM, the set of commands defined in the SM specification file will be executed. For example, consider the ReaxFF SM due to Strachan et al. (2003) executed by the following commands: @@ -306,7 +308,7 @@ changes to input script or command syntax between the two LAMMPS versions. [Restrictions:] -This command is part of the KIM package. It is only enabled if +These commands are part of the KIM package. It is only enabled if LAMMPS was built with that package. Furthermore, its correct functioning depends on compiling LAMMPS with all required packages installed that are required by the commands embedded in any KIM @@ -315,4 +317,4 @@ See the "Build package"_Build_package.html doc page for more info. [Related commands:] -"pair_style kim"_pair_kim.html, "kim_query"_kim_query.html +"pair_style kim"_pair_kim.html, "units"_units.html diff --git a/doc/src/pair_kim.txt b/doc/src/pair_kim.txt index 523bd89d7c..7e399b7ce0 100644 --- a/doc/src/pair_kim.txt +++ b/doc/src/pair_kim.txt @@ -112,7 +112,7 @@ kim-api package version 2.0.0 and higher. [Related commands:] -"pair_coeff"_pair_coeff.html, "kim_style"_kim_style.html, -"kim_query"_kim_query.html +"pair_coeff"_pair_coeff.html, "kim_init"_kim_commands.html, +"kim_interactions"_kim_commands, "kim_query"_kim_commands.html [Default:] none diff --git a/doc/utils/sphinx-config/false_positives.txt b/doc/utils/sphinx-config/false_positives.txt index a8bfa8f193..6a75f0555a 100644 --- a/doc/utils/sphinx-config/false_positives.txt +++ b/doc/utils/sphinx-config/false_positives.txt @@ -1606,6 +1606,7 @@ meso mesoparticle mesoscale mesoscopic +metadata metadynamics Metadynamics Methfessel @@ -2271,6 +2272,7 @@ rcutfac rdc rdf RDideal +rdx README realtime reamin @@ -2297,6 +2299,8 @@ Rensselaer reparameterizing repo representable +Reproducibility +reproducibility repuls rescale rescaled @@ -2585,6 +2589,7 @@ Stoll stopstep Stouch Straatsma +Strachan Stratford Strathclyde Straub @@ -2822,6 +2827,7 @@ undump uniaxial uniaxially unimodal +unitarg unitless Universite unix -- GitLab From c9cb6e3658e66f4cf9086e9ed50232e477f7ed3e Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Sun, 23 Jun 2019 13:12:23 -0400 Subject: [PATCH 072/469] remove obsolete files --- doc/src/kim_query.txt | 47 ------------------- doc/src/kim_style.txt | 107 ------------------------------------------ 2 files changed, 154 deletions(-) delete mode 100644 doc/src/kim_query.txt delete mode 100644 doc/src/kim_style.txt diff --git a/doc/src/kim_query.txt b/doc/src/kim_query.txt deleted file mode 100644 index 84eca6e676..0000000000 --- a/doc/src/kim_query.txt +++ /dev/null @@ -1,47 +0,0 @@ -"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c - -:link(lws,http://lammps.sandia.gov) -:link(ld,Manual.html) -:link(lc,Commands_all.html) - -:line - -kim_query command :h3 - -[Syntax:] - -kim_query variable query_function web_query_flags :pre - -variable = name of a (string style) variable where the result of the query is stored -query_function = name of the OpenKIM web API query function to be used -web_query_flags = a series of keyword=value pairs that represent the web query; supported keywords depend on query function :ul - -[Examples:] - -kim_query latconst get_test_result test=TE_156715955670 model=MO_800509458712 & - prop=structure-cubic-crystal-npt species=\["Al"\] keys=\["a"\] units=\["angstrom"\] :pre - -[Description:] - -The kim_query command allows to retrieve properties from the OpenKIM -through a web query. The result is stored in a string style -"variable"_variable.html, the name of which must be given as the first -argument of the kim_query command. The second required argument is the -name of the actual query function (e.g. {get_test_result}). All following -arguments are parameters handed over to the web query in the format -{keyword=value}. The list of supported keywords and the type of how -the value has to be encoded depends on the query function used. This -mirrors the functionality available on the OpenKIM webpage at -"https://query.openkim.org"_https://query.openkim.org/ - -[Restrictions:] - -This command is part of the KIM package. It is only enabled if -LAMMPS was built with that package. Furthermore, its correct -functioning depends on compiling LAMMPS with libcurl support. -See the "Build package"_Build_package.html doc page for more info. - -[Related commands:] - -"pair_style kim"_pair_kim.html, "kim_style"_kim_style.html, -"variable"_variable.html diff --git a/doc/src/kim_style.txt b/doc/src/kim_style.txt deleted file mode 100644 index c24cfe8581..0000000000 --- a/doc/src/kim_style.txt +++ /dev/null @@ -1,107 +0,0 @@ -"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c - -:link(lws,http://lammps.sandia.gov) -:link(ld,Manual.html) -:link(lc,Commands_all.html) - -:line - -kim_style command :h3 - -[Syntax:] - -kim_style mode args :pre - -mode = {init model} or {define typeargs} or no mode chosen -model = name of the KIM model (KIM potential or KIM simulator model) -typeargs = atom type to species mapping (one entry per atom type) -args = {unit_variables unit_style} or {unit_from unit_style} (optional):ul - -[Examples:] - -kim_style init ex_sim_model_Si_mod_tersoff unit_variables metal -kim_style define Si Si -kim_style unit_variables real -kim_style init LennardJones_Ar unit_variables metal -kim_style unit_variables real unit_from metal -kim_style define Ar :pre - -[Description:] - -The kim_style command is a high-level wrapper around the -"Knowledge Base for Interatomic Models (OpenKIM)"_https://openkim.org -repository of interatomic potentials, so that they can be used by -LAMMPS scripts. It does not implement any computations directly, but -rather will generate LAMMPS input commands based on the information -retrieved from the OpenKIM repository. It is able to realize so-called -"KIM Simulator Models", which are OpenKIM repository entries of models -using native features of the simulation engine in use, i.e. LAMMPS -in this case, but it also supports realizing conventional KIM models -implicitly via generating a "pair_style kim"_pair_kim.html command -followed by a suitable "pair_coeff"_pair_coeff.html command. - -The kim_style command has two modes, {init} and {define}, indicated by -the first argument to the kim_style command. An {init} mode command -must be issued [before] the simulation box is created, while the {define} -mode version may only be used [after] the simulation box exists. Both -are required. The {init} mode version sets the model name and may issue -additional commands changing LAMMPS default settings that are required -for using a selected simulator model. If needed, those settings can be -overridden. The second argument to the {kim_style init} command is the -KIM model ID. - -In both modes, the keywords {unit_variables} and {unit_from} may be -added. They control the values of a set of -"internal style variables"_variable.html that can be used to convert -between different unit styles in LAMMPS. The argument to -each keyword is a LAMMPS unit style or NULL, which means to look up -the unit style from what was set with the "units"_units.html command. -Please note, that KIM simulator models will set their preferred unit style. -By default all conversion variables are set to 1.0. Converting to or -from the "lj" unit style is not supported. The following variables are defined: - -_u_length -_u_mass -_u_time :ul - - -The {kim_style define} command will issue commands that will realize -the selected model (through generating pair_style and pair_coeff commands, -but also other commands, as required). It has to be issued [after] the -the simulation box is defined. The {kim_style define} command allows a -varying number of additional arguments. Those are used to map the atom -types in LAMMPS to the available species in the KIM model. This is -equivalent to the arguments following "pair_coeff * *" in a -"kim"_pair_kim.html pair style. Thus the commands: - -kim_style init LennardJones_Ar -kim_style define Ar :pre - -will generate the LAMMPS input commands: - -pair_style kim LennardJones_Ar -pair_coeff * * Ar :pre - -For simulator models, the generated input commands may be more complex -and require that LAMMPS is built with the required packages included. -The commands generated by the kim_style command, can be copied to the -screen or log file, through the "echo"_echo.html command. -The kim_style command will also validate, that a selected simulator -model was generated for the LAMMPS MD code and not some other software. -In addition, the version strings for LAMMPS version used for defining -the simulator model and the LAMMPS version being currently run are -printed, so that it can be tracked down, if there are any incompatible -changes to input script or command syntax between the two LAMMPS versions. - -[Restrictions:] - -This command is part of the KIM package. It is only enabled if -LAMMPS was built with that package. Furthermore, its correct -functioning depends on compiling LAMMPS with all required packages -installed that are required by the commands embedded in any KIM -simulator models used. -See the "Build package"_Build_package.html doc page for more info. - -[Related commands:] - -"pair_style kim"_pair_kim.html, "kim_query"_kim_query.html -- GitLab From ac82aa754b583886e193471bc042635c9c82955c Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Sun, 23 Jun 2019 13:13:05 -0400 Subject: [PATCH 073/469] correct off-by-one error and simplify code by using std::string instead of std::stringstream --- src/KIM/kim_init.cpp | 17 +++++++++-------- 1 file changed, 9 insertions(+), 8 deletions(-) diff --git a/src/KIM/kim_init.cpp b/src/KIM/kim_init.cpp index 695db0aa0d..6339f7397e 100644 --- a/src/KIM/kim_init.cpp +++ b/src/KIM/kim_init.cpp @@ -246,7 +246,7 @@ void KimInit::determine_model_type_and_units(char * model_name, if (*sim_field == "units") { kim_SM->GetSimulatorFieldLine(i,0,&sim_value); - int len=(*sim_value).length(); + int len=(*sim_value).length()+1; *model_units = new char[len]; strcpy(*model_units,sim_value->c_str()); break; } @@ -414,15 +414,16 @@ void KimInit::do_variables(char *user_units, char *model_units) (char *)"density"}; if (comm->me == 0) { - std::stringstream mesg; - mesg << "# Conversion factors from " << from << " to " << to - << ":" << std::endl; - if (screen) fputs(mesg.str().c_str(),screen); - if (logfile) fputs(mesg.str().c_str(),logfile); + std::string mesg("# Conversion factors from "); + mesg += from; + mesg += " to "; + mesg += to; + mesg += ":\n"; + if (screen) fputs(mesg.c_str(),screen); + if (logfile) fputs(mesg.c_str(),logfile); } - for (int i = 0; i < nunits; i++) - { + for (int i = 0; i < nunits; i++) { var_str = std::string("_u_") + std::string(units[i]); args[0] = (char *)var_str.c_str(); v_unit = variable->find(args[0]); -- GitLab From c557c7492b4ce0ab90ca80e2ba6c100b9a83c825 Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Sun, 23 Jun 2019 13:31:12 -0400 Subject: [PATCH 074/469] adapt names of stored properties to code that uses fix STORE/KIM --- src/KIM/fix_store_kim.cpp | 43 ++++++++++++++++++--------------------- src/KIM/fix_store_kim.h | 4 ++-- 2 files changed, 22 insertions(+), 25 deletions(-) diff --git a/src/KIM/fix_store_kim.cpp b/src/KIM/fix_store_kim.cpp index 6423a57e18..8209a6d13e 100644 --- a/src/KIM/fix_store_kim.cpp +++ b/src/KIM/fix_store_kim.cpp @@ -66,7 +66,7 @@ using namespace FixConst; FixStoreKIM::FixStoreKIM(LAMMPS *lmp, int narg, char **arg) : Fix(lmp, narg, arg), simulator_model(NULL), model_name(NULL), - units_from(NULL), units_to(NULL) + model_units(NULL), user_units(NULL) { if (narg != 3) error->all(FLERR,"Illegal fix STORE/KIM command"); } @@ -89,16 +89,15 @@ FixStoreKIM::~FixStoreKIM() model_name = NULL; } - if (units_from) { - char *uf = (char *)units_from; - delete[] uf; - units_from = NULL; + if (model_units) { + char *mu = (char *)model_units; + delete[] mu; + model_units = NULL; } - - if (units_to) { - char *ut = (char *)units_to; - delete[] ut; - units_to = NULL; + if (user_units) { + char *uu = (char *)user_units; + delete[] uu; + user_units = NULL; } } @@ -127,19 +126,17 @@ void FixStoreKIM::setptr(const char *name, void *ptr) delete[] mn; } model_name = ptr; - } else if (strcmp(name,"units_from") == 0) { - if (units_from) { - char *uf = (char *)units_from; - delete[] uf; + } else if (strcmp(name,"model_units") == 0) { + if (model_units) { + char *mu = (char *)model_units; + delete[] mu; } - units_from = ptr; - } else if (strcmp(name,"units_to") == 0) { - if (units_to) { - char *ut = (char *)units_to; - delete[] ut; + } else if (strcmp(name,"user_units") == 0) { + if (user_units) { + char *uu = (char *)user_units; + delete[] uu; } - units_to = ptr; - } + } else error->all(FLERR,"Unknown property in fix STORE/KIM"); } /* ---------------------------------------------------------------------- */ @@ -148,7 +145,7 @@ void *FixStoreKIM::getptr(const char *name) { if (strcmp(name,"simulator_model") == 0) return simulator_model; else if (strcmp(name,"model_name") == 0) return model_name; - else if (strcmp(name,"units_from") == 0) return units_from; - else if (strcmp(name,"units_to") == 0) return units_to; + else if (strcmp(name,"model_units") == 0) return model_units; + else if (strcmp(name,"user_units") == 0) return user_units; else return NULL; } diff --git a/src/KIM/fix_store_kim.h b/src/KIM/fix_store_kim.h index 5bca2a3dd0..655be83ad0 100644 --- a/src/KIM/fix_store_kim.h +++ b/src/KIM/fix_store_kim.h @@ -80,8 +80,8 @@ class FixStoreKIM : public Fix { private: void *simulator_model; // pointer to KIM simulator model class void *model_name; // string of KIM model name - void *units_from; // string of unit conversion origin or NULL - void *units_to; // string of unit conversion target or NULL + void *model_units; // string of unit conversion origin or NULL + void *user_units; // string of unit conversion target or NULL }; } -- GitLab From 065638edba999ab91b078e089b807d58c205b6ae Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Sun, 23 Jun 2019 13:31:43 -0400 Subject: [PATCH 075/469] remove unused macro and reformat to closer match LAMMPS programming style --- src/KIM/kim_init.cpp | 11 ++--------- 1 file changed, 2 insertions(+), 9 deletions(-) diff --git a/src/KIM/kim_init.cpp b/src/KIM/kim_init.cpp index 6339f7397e..0d8849c51c 100644 --- a/src/KIM/kim_init.cpp +++ b/src/KIM/kim_init.cpp @@ -79,10 +79,6 @@ extern "C" { #include "KIM_SimulatorModel.hpp" //@@@@@ -#define SNUM(x) \ - static_cast(std::ostringstream() \ - << std::dec << x).str() - using namespace LAMMPS_NS; /* ---------------------------------------------------------------------- */ @@ -187,14 +183,11 @@ void KimInit::determine_model_type_and_units(char * model_name, model_type = MO; KIM_Model_Destroy(&kim_MO); - if (units_accepted) - { + if (units_accepted) { int len=strlen(user_units); *model_units = new char[len]; strcpy(*model_units,user_units); return; - } - else if (unit_conversion_mode) - { + } else if (unit_conversion_mode) { int const num_systems = 5; char const * const systems[num_systems] = {"metal", "real", "si", "cgs", "electron"}; -- GitLab From 27d1f79fe37e5ba2153590731092997d0bdf9890 Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Sun, 23 Jun 2019 13:39:12 -0400 Subject: [PATCH 076/469] simplify another case of stringstream to use plain std::string --- src/KIM/kim_init.cpp | 11 +++++------ 1 file changed, 5 insertions(+), 6 deletions(-) diff --git a/src/KIM/kim_init.cpp b/src/KIM/kim_init.cpp index 0d8849c51c..1ca55d7adc 100644 --- a/src/KIM/kim_init.cpp +++ b/src/KIM/kim_init.cpp @@ -246,12 +246,11 @@ void KimInit::determine_model_type_and_units(char * model_name, } KIM::SimulatorModel::Destroy(&kim_SM); - if ((! unit_conversion_mode) && (strcmp(*model_units, user_units)!=0)) - { - std::stringstream mesg; - mesg << "Incompatible units for KIM Simulator Model, required units = " - << *model_units; - error->all(FLERR,mesg.str().c_str()); + if ((! unit_conversion_mode) && (strcmp(*model_units, user_units)!=0)) { + std::string mesg("Incompatible units for KIM Simulator Model, " + "required units = "); + mesg += *model_units; + error->all(FLERR,mesg.c_str()); } } -- GitLab From c6d0f807b569bdf6ab6e9ed0665ca81d80f1d3d5 Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Sun, 23 Jun 2019 14:13:24 -0400 Subject: [PATCH 077/469] output messages that would otherwise only show up in logs only when logs are enable for screen or logfile --- src/KIM/kim_init.cpp | 16 ++++++++-------- src/KIM/kim_interactions.cpp | 4 ++-- src/input.h | 6 ++++-- 3 files changed, 14 insertions(+), 12 deletions(-) diff --git a/src/KIM/kim_init.cpp b/src/KIM/kim_init.cpp index 1ca55d7adc..ce1b944792 100644 --- a/src/KIM/kim_init.cpp +++ b/src/KIM/kim_init.cpp @@ -363,8 +363,8 @@ void KimInit::kim_init_log_delimiter(std::string const begin_end) const mesg = "#=== END kim-init ============================================\n\n"; - if (screen) fputs(mesg.c_str(),screen); - if (logfile) fputs(mesg.c_str(),logfile); + if ((screen) && (input->echo_screen)) fputs(mesg.c_str(),screen); + if ((logfile) && (input->echo_log)) fputs(mesg.c_str(),logfile); } } @@ -411,8 +411,8 @@ void KimInit::do_variables(char *user_units, char *model_units) mesg += " to "; mesg += to; mesg += ":\n"; - if (screen) fputs(mesg.c_str(),screen); - if (logfile) fputs(mesg.c_str(),logfile); + if ((screen) && (input->echo_screen)) fputs(mesg.c_str(),screen); + if ((logfile) && (input->echo_log)) fputs(mesg.c_str(),logfile); } for (int i = 0; i < nunits; i++) { @@ -441,12 +441,12 @@ void KimInit::do_variables(char *user_units, char *model_units) << " internal " << std::setprecision(12) << std::scientific << conversion_factor << std::endl; - if (screen) fputs(mesg.str().c_str(),screen); - if (logfile) fputs(mesg.str().c_str(),logfile); + if ((screen) && (input->echo_screen)) fputs(mesg.str().c_str(),screen); + if ((logfile) && (input->echo_log)) fputs(mesg.str().c_str(),logfile); } } if (comm->me == 0) { - if (screen) fputs("#\n",screen); - if (logfile) fputs("#\n",logfile); + if ((screen) && (input->echo_screen)) fputs("#\n",screen); + if ((logfile) && (input->echo_log)) fputs("#\n",logfile); } } diff --git a/src/KIM/kim_interactions.cpp b/src/KIM/kim_interactions.cpp index 491d406ae6..4771272ff8 100644 --- a/src/KIM/kim_interactions.cpp +++ b/src/KIM/kim_interactions.cpp @@ -109,8 +109,8 @@ void KimInteractions::kim_interactions_log_delimiter( mesg = "#=== END kim_interactions ====================================\n\n"; - if (screen) fputs(mesg.c_str(),screen); - if (logfile) fputs(mesg.c_str(),logfile); + if ((screen) && (input->echo_screen)) fputs(mesg.c_str(),screen); + if ((logfile) && (input->echo_log)) fputs(mesg.c_str(),logfile); } } diff --git a/src/input.h b/src/input.h index 47ad7779f1..ebd015619c 100644 --- a/src/input.h +++ b/src/input.h @@ -25,6 +25,8 @@ class Input : protected Pointers { friend class Info; friend class Error; friend class Deprecated; + friend class KimInit; + friend class KimInteractions; public: int narg; // # of command args @@ -42,14 +44,14 @@ class Input : protected Pointers { protected: char *command; // ptr to current command + int echo_screen; // 0 = no, 1 = yes + int echo_log; // 0 = no, 1 = yes private: int me; // proc ID int maxarg; // max # of args in arg char *line,*copy,*work; // input line & copy and work string int maxline,maxcopy,maxwork; // max lengths of char strings - int echo_screen; // 0 = no, 1 = yes - int echo_log; // 0 = no, 1 = yes int nfile,maxfile; // current # and max # of open input files int label_active; // 0 = no label, 1 = looking for label char *labelstr; // label string being looked for -- GitLab From 493269431c354d5177a10acaec2b94c3aed18b67 Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Sun, 23 Jun 2019 14:16:38 -0400 Subject: [PATCH 078/469] add a few more false positives --- doc/utils/sphinx-config/false_positives.txt | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/doc/utils/sphinx-config/false_positives.txt b/doc/utils/sphinx-config/false_positives.txt index 6a75f0555a..5ea7388cd6 100644 --- a/doc/utils/sphinx-config/false_positives.txt +++ b/doc/utils/sphinx-config/false_positives.txt @@ -570,6 +570,7 @@ Dihedrals dihydride Dij dimdim +dimensioned dimensionality dimgray dipolar @@ -599,6 +600,7 @@ Dobson Dodds dodgerblue dof +doi Donadio dotc Doty @@ -749,6 +751,7 @@ equilibrating equilibration Equilibria equilization +Ercolessi eradius erate erc @@ -2243,6 +2246,7 @@ quati quatj quatk quatw +queryargs Queteschiner qw qx -- GitLab From b2ba0550d70d6829fa3b2b40a86025e2faf95a2e Mon Sep 17 00:00:00 2001 From: "Ryan S. Elliott" Date: Sun, 23 Jun 2019 13:18:57 -0500 Subject: [PATCH 079/469] Some minor typo fixes in kim_commands.txt --- doc/src/kim_commands.txt | 7 +++---- 1 file changed, 3 insertions(+), 4 deletions(-) diff --git a/doc/src/kim_commands.txt b/doc/src/kim_commands.txt index 2e94271763..e51aec5dc7 100644 --- a/doc/src/kim_commands.txt +++ b/doc/src/kim_commands.txt @@ -71,7 +71,7 @@ Types of KIM IMs :h4 There are two types of IMs archived in OpenKIM: -The first type is called a {KIM Model}. A KIM Model is an independent computer implementation of an IM written in one of the languages supported by KIM (C, C++, Fortran, Python), which conforms to the KIM Application Programming Interface ("KIM API"_https://openkim.org/kim-api/). A KIM Model will work seamlessly with any simulation code that support the KIM API (including LAMMPS; see "complete list of supported code"_https://openkim.org/projects-using-kim/). +The first type is called a {KIM Model}. A KIM Model is an independent computer implementation of an IM written in one of the languages supported by KIM (C, C++, Fortran), which conforms to the KIM Application Programming Interface ("KIM API"_https://openkim.org/kim-api/). A KIM Model will work seamlessly with any simulation code that supports the KIM API (including LAMMPS; see "complete list of supported code"_https://openkim.org/projects-using-kim/). The second type is called a {KIM Simulator Model} (SM). In this case, the IM is implemented natively within the simulation code ({simulator}), i.e. LAMMPS. A separate SM package is archived in OpenKIM for each parameterization of the IM, which includes all of the necessary parameter files, LAMMPS commands, and metadata (supported species, units, etc.) needed to run the IM in LAMMPS. :ol With these two IM types, OpenKIM can archive and test almost all IMs that @@ -212,13 +212,13 @@ The second and final step in using an OpenKIM IM is to execute the {kim_interactions} command. This command must be preceded by a {kim_init} command and a "create_box"_create_box.html command, which defines the number of atom types {N}. -The {kim_interaction} command has one argument {typeargs}. This argument +The {kim_interactions} command has one argument {typeargs}. This argument contains a list of {N} chemical species, which defines a mapping between atom types in LAMMPS to the available species in the OpenKIM IM. For example, consider an OpenKIM IM that supports Si and C species. If the LAMMPS simulation has four atom types, where the first three are Si, -and the fourth is C, the following {kim_interaction} command would be used: +and the fourth is C, the following {kim_interactions} command would be used: kim_interactions Si Si Si C :pre @@ -376,4 +376,3 @@ doi: "https://doi.org/10.1007/s11837-011-0102-6"_https://doi.org/10.1007/s11837- :link(kim-api) [(Elliott)] Elliott, Tadmor and Bernstein, "https://openkim.org/kim-api"_https://openkim.org/kim-api (2011) doi: "https://doi.org/10.25950/FF8F563A"_https://doi.org/10.25950/FF8F563A - -- GitLab From e42e1e64a894e7b52c3c75a8b830918819cfdafa Mon Sep 17 00:00:00 2001 From: Ellad Tadmor Date: Sun, 23 Jun 2019 14:50:52 -0500 Subject: [PATCH 080/469] Added explanation on Model and SM pages --- doc/src/kim_commands.txt | 18 ++++++++++++++++++ 1 file changed, 18 insertions(+) diff --git a/doc/src/kim_commands.txt b/doc/src/kim_commands.txt index e51aec5dc7..5a50a76879 100644 --- a/doc/src/kim_commands.txt +++ b/doc/src/kim_commands.txt @@ -90,6 +90,24 @@ By convention SM prefixes begin with {Sim_} to readily identify them. SW_StillingerWeber_1985_Si__MO_405512056662_005 Sim_LAMMPS_ReaxFF_StrachanVanDuinChakraborty_2003_CHNO__SM_107643900657_000 :pre +Each OpenKIM IM has a dedicated page on "OpenKIM"_https://openkim.org +providing all the information on the IM including a title, description, +authorship and citation information, test and verification check results, +visualizations of results, a wiki with documentation and user comments, and +access to raw files, and other information. +This is referred to as the "Model Page" or "SM Page". +The URL for such a page is constructed from the +"extended KIM ID"_https://openkim.org/about-kim-ids/ of the IM: + +https://openkim.org/id/extended_KIM_ID +:pre + +For example for the Stillinger-Weber potential +listed above the Model Page is located at: + +"https://openkim.org/id/SW_StillingerWeber_1985_Si__MO_405512056662_005"_https://openkim.org/id/SW_StillingerWeber_1985_Si__MO_405512056662_005 +:pre + NOTE: It is also possible to locally install IMs not archived in OpenKIM, in which case their names do not have to conform to the KIM ID format. -- GitLab From 36649f0534d3b20211953c1dbecedc33e7dd3857 Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Sun, 23 Jun 2019 16:47:12 -0400 Subject: [PATCH 081/469] add workaround for handline include files --- src/input.cpp | 7 +++++++ src/input.h | 1 + 2 files changed, 8 insertions(+) diff --git a/src/input.cpp b/src/input.cpp index f88c8ca0c0..dd445b10f3 100644 --- a/src/input.cpp +++ b/src/input.cpp @@ -77,6 +77,7 @@ Input::Input(LAMMPS *lmp, int argc, char **argv) : Pointers(lmp) echo_screen = 0; echo_log = 1; + eof_return = 0; label_active = 0; labelstr = NULL; @@ -205,6 +206,7 @@ void Input::file() MPI_Bcast(&n,1,MPI_INT,0,world); if (n == 0) { if (label_active) error->all(FLERR,"Label wasn't found in input script"); + if (eof_return) break; if (me == 0) { if (infile != stdin) { fclose(infile); @@ -1051,6 +1053,11 @@ void Input::include() error->one(FLERR,str); } infiles[nfile++] = infile; + eof_return = 1; + file(); + eof_return = 0; + nfile--; + infile = infiles[nfile-1]; } } diff --git a/src/input.h b/src/input.h index ebd015619c..7fb125ffb5 100644 --- a/src/input.h +++ b/src/input.h @@ -46,6 +46,7 @@ class Input : protected Pointers { char *command; // ptr to current command int echo_screen; // 0 = no, 1 = yes int echo_log; // 0 = no, 1 = yes + int eof_return; // if 1: at EOF return from parsing in file() private: int me; // proc ID -- GitLab From bfe6cc29e81b84c6dada9bc9cbd942b3d0a21c93 Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Sun, 23 Jun 2019 17:52:43 -0400 Subject: [PATCH 082/469] fix bug of not storing pointers --- src/KIM/fix_store_kim.cpp | 2 ++ 1 file changed, 2 insertions(+) diff --git a/src/KIM/fix_store_kim.cpp b/src/KIM/fix_store_kim.cpp index 8209a6d13e..c9a99acca9 100644 --- a/src/KIM/fix_store_kim.cpp +++ b/src/KIM/fix_store_kim.cpp @@ -131,11 +131,13 @@ void FixStoreKIM::setptr(const char *name, void *ptr) char *mu = (char *)model_units; delete[] mu; } + model_units = ptr; } else if (strcmp(name,"user_units") == 0) { if (user_units) { char *uu = (char *)user_units; delete[] uu; } + user_units = ptr; } else error->all(FLERR,"Unknown property in fix STORE/KIM"); } -- GitLab From 6d54cf6a07d38d97be5157d4977ea831c10d9f48 Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Sun, 23 Jun 2019 17:53:12 -0400 Subject: [PATCH 083/469] programming style changes --- src/KIM/kim_init.cpp | 39 +++++++++++++++------------------------ 1 file changed, 15 insertions(+), 24 deletions(-) diff --git a/src/KIM/kim_init.cpp b/src/KIM/kim_init.cpp index ce1b944792..080e3dac3f 100644 --- a/src/KIM/kim_init.cpp +++ b/src/KIM/kim_init.cpp @@ -90,10 +90,10 @@ void KimInit::command(int narg, char **arg) if (domain->box_exist) error->all(FLERR,"Must use 'kim_init' command before " "simulation box is defined"); - int len0 = strlen(arg[0])+1; - int len1 = strlen(arg[1])+1; - char *model_name = new char[len0]; strcpy(model_name,arg[0]); - char *user_units = new char[len1]; strcpy(user_units,arg[1]); + char *model_name = new char[strlen(arg[0])+1]; + strcpy(model_name,arg[0]); + char *user_units = new char[strlen(arg[1])+1]; + strcpy(user_units,arg[1]); if (narg == 3) { if (strcmp(arg[2],"unit_conversion_mode")==0) unit_conversion_mode = true; else { error->all(FLERR,"Illegal kim_init command"); } @@ -178,21 +178,19 @@ void KimInit::determine_model_type_and_units(char * model_name, &units_accepted, &kim_MO); - if (!kim_error) // model is an MO - { + if (!kim_error) { // model is an MO model_type = MO; KIM_Model_Destroy(&kim_MO); if (units_accepted) { - int len=strlen(user_units); - *model_units = new char[len]; strcpy(*model_units,user_units); + *model_units = new char[strlen(user_units)+1]; + strcpy(*model_units,user_units); return; } else if (unit_conversion_mode) { int const num_systems = 5; char const * const systems[num_systems] = {"metal", "real", "si", "cgs", "electron"}; - for (int i=0; i < num_systems; ++i) - { + for (int i=0; i < num_systems; ++i) { get_kim_unit_names(systems[i], lengthUnit, energyUnit, chargeUnit, temperatureUnit, timeUnit, error); kim_error = KIM_Model_Create(KIM_NUMBERING_zeroBased, @@ -205,17 +203,13 @@ void KimInit::determine_model_type_and_units(char * model_name, &units_accepted, &kim_MO); KIM_Model_Destroy(&kim_MO); - if (units_accepted) - { - int len=strlen(systems[i]); - *model_units = new char[len]; strcpy(*model_units,systems[i]); + if (units_accepted) { + *model_units = new char[strlen(systems[i])+1]; + strcpy(*model_units,systems[i]); return; } - } - error->all(FLERR,"KIM Model does not support any lammps unit system"); - } - else - { + } error->all(FLERR,"KIM Model does not support any lammps unit system"); + } else { error->all(FLERR,"KIM Model does not support the requested unit system"); } } @@ -223,9 +217,7 @@ void KimInit::determine_model_type_and_units(char * model_name, KIM::SimulatorModel * kim_SM; kim_error = KIM::SimulatorModel::Create(model_name, &kim_SM); if (kim_error) - { error->all(FLERR,"KIM model name not found"); - } model_type = SM; int sim_fields; @@ -257,7 +249,7 @@ void KimInit::determine_model_type_and_units(char * model_name, /* ---------------------------------------------------------------------- */ -void KimInit::do_init(char *model_name, char *user_units, char* model_units) +void KimInit::do_init(char *model_name, char *user_units, char *model_units) { // create storage proxy fix. delete existing fix, if needed. @@ -322,8 +314,7 @@ void KimInit::do_init(char *model_name, char *user_units, char* model_units) cmd += model_units; input->one(cmd.c_str()); - if (model_type == SM) - { + if (model_type == SM) { int sim_fields, sim_lines; const std::string *sim_field, *sim_value; simulatorModel->GetNumberOfSimulatorFields(&sim_fields); -- GitLab From d10fdda6765c6cbe905509bf3eae7888cadb00ad Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Sun, 23 Jun 2019 17:53:52 -0400 Subject: [PATCH 084/469] simplify nested include file handling --- src/input.cpp | 17 ++--------------- src/input.h | 1 - 2 files changed, 2 insertions(+), 16 deletions(-) diff --git a/src/input.cpp b/src/input.cpp index dd445b10f3..268be5b774 100644 --- a/src/input.cpp +++ b/src/input.cpp @@ -77,7 +77,6 @@ Input::Input(LAMMPS *lmp, int argc, char **argv) : Pointers(lmp) echo_screen = 0; echo_log = 1; - eof_return = 0; label_active = 0; labelstr = NULL; @@ -206,18 +205,7 @@ void Input::file() MPI_Bcast(&n,1,MPI_INT,0,world); if (n == 0) { if (label_active) error->all(FLERR,"Label wasn't found in input script"); - if (eof_return) break; - if (me == 0) { - if (infile != stdin) { - fclose(infile); - infile = NULL; - } - nfile--; - } - MPI_Bcast(&nfile,1,MPI_INT,0,world); - if (nfile == 0) break; - if (me == 0) infile = infiles[nfile-1]; - continue; + break; } if (n > maxline) reallocate(line,maxline,n); @@ -1053,9 +1041,8 @@ void Input::include() error->one(FLERR,str); } infiles[nfile++] = infile; - eof_return = 1; file(); - eof_return = 0; + fclose(infile); nfile--; infile = infiles[nfile-1]; } diff --git a/src/input.h b/src/input.h index 7fb125ffb5..ebd015619c 100644 --- a/src/input.h +++ b/src/input.h @@ -46,7 +46,6 @@ class Input : protected Pointers { char *command; // ptr to current command int echo_screen; // 0 = no, 1 = yes int echo_log; // 0 = no, 1 = yes - int eof_return; // if 1: at EOF return from parsing in file() private: int me; // proc ID -- GitLab From b5d4cf4bfdff3b33a76198bcdb070798bbe908ab Mon Sep 17 00:00:00 2001 From: Ellad Tadmor Date: Sun, 23 Jun 2019 17:23:21 -0500 Subject: [PATCH 085/469] Updated KIM package information --- doc/src/Packages_details.txt | 51 ++++++++++++++++++++++-------------- 1 file changed, 31 insertions(+), 20 deletions(-) diff --git a/doc/src/Packages_details.txt b/doc/src/Packages_details.txt index d6e8f8639f..bf71e058f5 100644 --- a/doc/src/Packages_details.txt +++ b/doc/src/Packages_details.txt @@ -338,27 +338,37 @@ KIM package :link(PKG-KIM),h4 [Contents:] -A "pair_style kim"_pair_kim.html command which is a wrapper on the -Knowledge Base for Interatomic Models (KIM) repository of interatomic -potentials, enabling any of them to be used in LAMMPS simulations. -Also a "kim_query"_kim_commands.html command, which allows to query -the OpenKIM database for stored properties, and the commands -"kim_init and kim_interactions"_kim_commands.html, which serve as -front end to generating LAMMPS input on-the-fly for KIM simulator -models and native KIM models. - -To use this package you must have the KIM library available on your -system. +This package contains a set of commands that serve as a wrapper on the +"Open Knowledgebase of Interatomic Models (OpenKIM)"_https://openkim.org +repository of interatomic models (IMs) +enabling compatible ones to be used in LAMMPS simulations. +This includes "kim_init and kim_interactions"_kim_commands.html +commands to select, initialize and instantiate the IM, and a +"kim_query"_kim_commands.html command to perform web queries +for material property predictions of OpenKIM IMs. +Support for KIM IMs that conform to the +"KIM Application Programming Interface (API)"_https://openkim.org/kim-api/ +is provided by the "pair_style kim"_pair_kim.html command. + +NOTE: The command {pair_style kim} is called by {kim_interactions} and +is not recommended to be directly used in input scripts. + +To use this package you must have the KIM API library available on your +system. The KIM API is available for download on the +"OpenKIM website"_https://openkim.org/kim-api/. +When installing LAMMPS from binary, the kim-api package +is a dependency that is automatically downloaded and installed. Information about the KIM project can be found at its website: -https://openkim.org. The KIM project is led by Ellad Tadmor and Ryan -Elliott (U Minnesota). +"https://openkim.org"_https://openkim.org. +The KIM project is led by Ellad Tadmor and Ryan Elliott (U Minnesota) +and is funded by the "National Science Foundation"_https://www.nsf.gov/. [Authors:] Ryan Elliott (U Minnesota) is the main developer for the KIM -API which the "pair_style kim"_pair_kim.html command uses. He developed -the pair style. Axel Kohlmeyer (Temple U) contributed the -"kim_query"_kim_commands.html and "kim_init"_kim_commands.html commands -in close collaboration with Ryan. +API and the {pair_style kim} command. Axel Kohlmeyer (Temple U) and +Ellad Tadmor (U Minnesota) contributed to the "kim_commands"_kim_commands.html +interface in close collaboration with Ryan Elliott. + [Install:] @@ -368,10 +378,11 @@ extras"_Build_extras.html doc page. [Supporting info:] +"kim_commands"_kim_commands.html +"pair_style kim"_pair_kim.html src/KIM: filenames -> commands src/KIM/README lib/kim/README -"pair_style kim"_pair_kim.html examples/kim :ul :line @@ -987,9 +998,9 @@ USER-ADIOS package :link(PKG-USER-ADIOS),h4 [Contents:] -ADIOS is a high-performance I/O library. This package implements the +ADIOS is a high-performance I/O library. This package implements the dump "atom/adios" and dump "custom/adios" commands to write data using -the ADIOS library. +the ADIOS library. [Authors:] Norbert Podhorszki (ORNL) from the ADIOS developer team. -- GitLab From 881f9ff04337c6e743f2fa9a7e0b71af28e85107 Mon Sep 17 00:00:00 2001 From: Ellad Tadmor Date: Sun, 23 Jun 2019 17:36:10 -0500 Subject: [PATCH 086/469] Updated the pair_kim docs --- doc/src/pair_kim.txt | 85 ++++++++++++++++++++------------------------ 1 file changed, 39 insertions(+), 46 deletions(-) diff --git a/doc/src/pair_kim.txt b/doc/src/pair_kim.txt index 7e399b7ce0..86d13808b0 100644 --- a/doc/src/pair_kim.txt +++ b/doc/src/pair_kim.txt @@ -12,76 +12,71 @@ pair_style kim command :h3 pair_style kim model :pre -model = name of KIM model (potential) +model = name of a KIM model (the KIM ID for models archived in OpenKIM) [Examples:] -pair_style kim ex_model_Ar_P_LJ -pair_coeff * * Ar Ar :pre +pair_style kim SW_StillingerWeber_1985_Si__MO_405512056662_005 +pair_coeff * * Si :pre [Description:] -This pair style is a wrapper on the "Knowledge Base for Interatomic +This pair style is a wrapper on the "Open Knowledgebase of Interatomic Models (OpenKIM)"_https://openkim.org repository of interatomic -potentials, so that they can be used by LAMMPS scripts. +potentials to enable their use in LAMMPS scripts. -Note that in LAMMPS lingo, a KIM model driver is a pair style -(e.g. EAM or Tersoff). A KIM model is a pair style for a particular -element or alloy and set of parameters, e.g. EAM for Cu with a -specific EAM potential file. +The preferred interface for using interatomic models archived in +OpenKIM is the "kim_commands interface"_kim_commands.html. That +interface supports both "KIM Models" that conform to the KIM API +and can be used by any KIM-compliant simulation code, and +"KIM Simulator Models" that are natively implemented within a single +simulation code (like LAMMPS) and can only be used with it. +The {pair_style kim} command is limited to KIM Models. It is +used by the "kim_commands interface"_kim_commands.html as needed. -See the current list of "KIM model -drivers"_https://openkim.org/browse/model-drivers/alphabetical. +NOTE: Since {pair_style kim} is called by {kim_interactions} as needed, +is not recommended to be directly used in input scripts. -See the current list of all "KIM -models"_https://openkim.org/browse/models/by-model-drivers - -To use this pair style, you must first download and install the KIM -API library from the "OpenKIM website"_https://openkim.org. The KIM -section of the "Packages details"_Packages_details.html doc page has -instructions on how to do this with a simple make command, when -building LAMMPS. - -See the examples/kim dir for an input script that uses a KIM model -(potential) for Lennard-Jones. - :line The argument {model} is the name of the KIM model for a specific -potential as KIM defines it. In principle, LAMMPS can invoke any KIM -model. You should get an error or warning message from either LAMMPS -or KIM if there is an incompatibility. - -Only a single pair_coeff command is used with the {kim} style which -specifies the mapping of LAMMPS atom types to KIM elements. This is -done by specifying N additional arguments after the * * in the -pair_coeff command, where N is the number of LAMMPS atom types: +potential as KIM defines it. For potentials archived in OpenKIM +this is the extended KIM ID (see "kim_commands"_kim_commands.html +for details). LAMMPS can invoke any KIM Model, however there can +be incompatibilities (for example unit matching issues). +In the event of an incompatibility, the code will terminate with +an error message. Check both the LAMMPS and KIM log files for details. + +Only a single {pair_coeff} command is used with the {kim} style, which +specifies the mapping of LAMMPS atom types to the species supported by +the KIM Model. This is done by specifying {N} additional arguments +after the * * in the {pair_coeff} command, where {N} is the number of +LAMMPS atom types: N element names = mapping of KIM elements to atom types :ul -As an example, imagine the KIM model supports Si and C atoms. If your -LAMMPS simulation has 4 atom types and you want the 1st 3 to be Si, -and the 4th to be C, you would use the following pair_coeff command: +For example, consider a KIM Model that supports Si and C species. +If the LAMMPS simulation has four atom types, where the first three are Si, +and the fourth is C, the following {pair_coeff} command would be used: pair_coeff * * Si Si Si C :pre -The 1st 2 arguments must be * * so as to span all LAMMPS atom types. -The first three Si arguments map LAMMPS atom types 1,2,3 to Si as -defined within KIM. The final C argument maps LAMMPS atom type 4 to C -as defined within KIM. +The first two arguments must be * * so as to span all LAMMPS atom types. +The first three Si arguments map LAMMPS atom types 1, 2, and 3 to Si as +defined within KIM Model. The final C argument maps LAMMPS atom type 4 to C. :line In addition to the usual LAMMPS error messages, the KIM library itself may generate errors, which should be printed to the screen. In this -case it is also useful to check the kim.log file for additional error +case it is also useful to check the {kim.log} file for additional error information. The file kim.log should be generated in the same directory where LAMMPS is running. To download, build, and install the KIM library on your system, see -the lib/kim/README file. Once you have done this and built LAMMPS +the {lib/kim/README} file. Once you have done this and built LAMMPS with the KIM package installed you can run the example input scripts -in examples/kim. +in {examples/kim}. :line @@ -103,16 +98,14 @@ This pair style can only be used via the {pair} keyword of the [Restrictions:] -This pair style is part of the KIM package. It is only enabled if -LAMMPS was built with that package. See the "Build -package"_Build_package.html doc page for more info. +This pair style is part of the KIM package. See details on +restrictions in "kim_commands"_kim_commands.html. This current version of pair_style kim is compatible with the kim-api package version 2.0.0 and higher. [Related commands:] -"pair_coeff"_pair_coeff.html, "kim_init"_kim_commands.html, -"kim_interactions"_kim_commands, "kim_query"_kim_commands.html +"pair_coeff"_pair_coeff.html, "kim_commands"_kim_commands.html [Default:] none -- GitLab From 94e1f87cb81ecd3b6f0d89e457ab94ae82f2641b Mon Sep 17 00:00:00 2001 From: Ellad Tadmor Date: Sun, 23 Jun 2019 17:36:36 -0500 Subject: [PATCH 087/469] Moved some content from pair_kim docs to kim_commands --- doc/src/kim_commands.txt | 24 ++++++++++++++++++------ 1 file changed, 18 insertions(+), 6 deletions(-) diff --git a/doc/src/kim_commands.txt b/doc/src/kim_commands.txt index 5a50a76879..99ed068c44 100644 --- a/doc/src/kim_commands.txt +++ b/doc/src/kim_commands.txt @@ -67,7 +67,7 @@ The {kim_query} web query tool provides the ability to use the predictions of IM Support is provided for unit conversion between the "unit style"_units.html used in the LAMMPS input script and the units required by the OpenKIM IM. This makes it possible to use a single input script with IMs using different units without change and minimizes the likelihood of errors due to incompatible units. :ul :link(IM_types) -Types of KIM IMs :h4 +Types of IMs in OpenKIM :h4 There are two types of IMs archived in OpenKIM: @@ -108,6 +108,10 @@ listed above the Model Page is located at: "https://openkim.org/id/SW_StillingerWeber_1985_Si__MO_405512056662_005"_https://openkim.org/id/SW_StillingerWeber_1985_Si__MO_405512056662_005 :pre +See the "current list of KIM Models and SMs archived in OpenKIM"_https://openkim.org/browse/models/by-species. +This list is sorted by species and can be filtered to display only +IMs for certain species combinations. + NOTE: It is also possible to locally install IMs not archived in OpenKIM, in which case their names do not have to conform to the KIM ID format. @@ -118,6 +122,9 @@ IM and perform necessary initialization ({kim_init}), and the second to set up the IM for use by executing any necessary LAMMPS commands ({kim_interactions}). Both are required. +See the {examples/kim} directory for example input scripts that use KIM Models +and KIM SMs. + OpenKIM IM Initialization ({kim_init}) :h5 The {kim_init} mode command must be issued [before] @@ -375,11 +382,16 @@ OpenKIM to function. [Restrictions:] The set of {kim_commands} is part of the KIM package. It is only enabled if -LAMMPS was built with that package. Furthermore, its correct -functioning depends on compiling LAMMPS with all required packages -installed that are required by the commands embedded in any KIM -SM used. -See the "Build package"_Build_package.html doc page for more info. +LAMMPS is built with that package. A requirement for the KIM package, +is the KIM API library that must be downloaded from the +"OpenKIM website"_https://openkim.org/kim-api/ and installed before +LAMMPS is compiled. When installing LAMMPS from binary, the kim-api package +is a dependency that is automatically downloaded and installed. See the KIM +section of the "Packages details"_Packages_details.html for details. + +Furthermore, when using {kim_commands} to run KIM SMs, any packages required +by the native potential being used or other commands or fixes that it invokes +must be installed. [Related commands:] -- GitLab From d150feb41aa7c13858d56d8dd7ac18212e626492 Mon Sep 17 00:00:00 2001 From: Ellad Tadmor Date: Sun, 23 Jun 2019 17:46:00 -0500 Subject: [PATCH 088/469] Small change to KIM package build --- doc/src/Build_extras.txt | 7 ++++--- 1 file changed, 4 insertions(+), 3 deletions(-) diff --git a/doc/src/Build_extras.txt b/doc/src/Build_extras.txt index 220e9420fc..38d50522bb 100644 --- a/doc/src/Build_extras.txt +++ b/doc/src/Build_extras.txt @@ -177,11 +177,12 @@ use with LAMMPS. If you want to use the "kim_query"_kim_commands.html command, you also need to have libcurl installed with the matching development headers and the curl-config tool. -Note that in LAMMPS lingo, a KIM model driver is a pair style +Note that in LAMMPS jargon, a KIM model driver is a pair style (e.g. EAM or Tersoff). A KIM model is a pair style for a particular element or alloy and set of parameters, e.g. EAM for Cu with a -specific EAM potential file. Also note that downloading and installing -the KIM API library with all its models, may take a long time (10s of +specific EAM potential file. Also note that when downloading and +installing from source +the KIM API library with all its models, may take a long time (tens of minutes to hours) to build. Of course you only need to do that once. See the list of KIM model drivers here: -- GitLab From cf008c163def0bf64d77c8602b092cf4268261ed Mon Sep 17 00:00:00 2001 From: Ellad Tadmor Date: Sun, 23 Jun 2019 18:01:35 -0500 Subject: [PATCH 089/469] Corrected box rescaling --- doc/src/kim_commands.txt | 11 ++++++++++- 1 file changed, 10 insertions(+), 1 deletion(-) diff --git a/doc/src/kim_commands.txt b/doc/src/kim_commands.txt index 99ed068c44..f039202e4e 100644 --- a/doc/src/kim_commands.txt +++ b/doc/src/kim_commands.txt @@ -225,7 +225,16 @@ from a file. For example if a configuration of atoms is read in from a dump file using the "read_dump"_read_dump.html command, the following can be done to convert the box and all atomic positions to the correct units: -change_box all x scale $\{_u_distance\} y scale $\{_u_distance\} z scale $\{_u_distance\} remap :pre +variable xyfinal equal xy*$\{_u_distance\} +variable xzfinal equal xz*$\{_u_distance\} +variable yzfinal equal yz*$\{_u_distance\} +change_box all x scale $\{_u_distance\} & +               y scale $\{_u_distance\} & +               z scale $\{_u_distance\} & +               xy final $\{xyfinal\} & +               xz final $\{xzfinal\} & +               yz final $\{yzfinal\} & +               remap :pre NOTE: Unit conversion will only work if the conversion factors are placed in all appropriate places in the input script. It is up to the user to do this -- GitLab From bfd0c4228d3505da1fad1028cb1629cab68375a6 Mon Sep 17 00:00:00 2001 From: Ellad Tadmor Date: Sun, 23 Jun 2019 18:29:59 -0500 Subject: [PATCH 090/469] Added text that ADP potentials are available in KIM as well as NIST --- doc/src/pair_adp.txt | 16 +++++++++------- 1 file changed, 9 insertions(+), 7 deletions(-) diff --git a/doc/src/pair_adp.txt b/doc/src/pair_adp.txt index fc888ffbff..d5b07e8431 100644 --- a/doc/src/pair_adp.txt +++ b/doc/src/pair_adp.txt @@ -42,16 +42,18 @@ the ADP potential files themselves. Likewise, the ADP potential files list atomic masses; thus you do not need to use the "mass"_mass.html command to specify them. -The NIST WWW site distributes and documents ADP potentials: +[ADP potentials are available from:] -http://www.ctcms.nist.gov/potentials :pre +The NIST WWW site at http://www.ctcms.nist.gov/potentials. +Note that ADP potentials obtained from NIST must be converted +into the extended DYNAMO {setfl} format discussed below. +:l -Note that these must be converted into the extended DYNAMO {setfl} -format discussed below. +The OpenKIM Project at https://openkim.org provides ADP potentials +as Simulator Models that can be used directly in LAMMPS with +the "kim_commands interface"_kim_commands.html. +:l -The NIST site is maintained by Chandler Becker (cbecker at nist.gov) -who is good resource for info on interatomic potentials and file -formats. :line -- GitLab From 7afcfccf48fb06deccf9d185cabc377a5124d437 Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Mon, 24 Jun 2019 13:51:41 -0400 Subject: [PATCH 091/469] follow convention to list all commands in a file as header --- doc/src/kim_commands.txt | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/doc/src/kim_commands.txt b/doc/src/kim_commands.txt index f039202e4e..2aa705b483 100644 --- a/doc/src/kim_commands.txt +++ b/doc/src/kim_commands.txt @@ -6,7 +6,9 @@ :line -kim_commands :h3 +kim_init command :h3 +kim_interactions command :h3 +kim_query command :h3 [Syntax:] -- GitLab From 826a14f54ab8bef2472ef16876706ee2f95897e5 Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Mon, 24 Jun 2019 14:16:00 -0400 Subject: [PATCH 092/469] add workaround for handline include files # Conflicts: # src/input.h --- src/input.cpp | 7 +++++++ 1 file changed, 7 insertions(+) diff --git a/src/input.cpp b/src/input.cpp index 0111cb5738..32b6b697b1 100644 --- a/src/input.cpp +++ b/src/input.cpp @@ -78,6 +78,7 @@ Input::Input(LAMMPS *lmp, int argc, char **argv) : Pointers(lmp) echo_screen = 0; echo_log = 1; + eof_return = 0; label_active = 0; labelstr = NULL; @@ -206,6 +207,7 @@ void Input::file() MPI_Bcast(&n,1,MPI_INT,0,world); if (n == 0) { if (label_active) error->all(FLERR,"Label wasn't found in input script"); + if (eof_return) break; if (me == 0) { if (infile != stdin) { fclose(infile); @@ -1057,6 +1059,11 @@ void Input::include() error->one(FLERR,str); } infiles[nfile++] = infile; + eof_return = 1; + file(); + eof_return = 0; + nfile--; + infile = infiles[nfile-1]; } } -- GitLab From 7f26862f9841ebaab34961288eca4a5ba1187e9c Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Mon, 24 Jun 2019 14:16:51 -0400 Subject: [PATCH 093/469] simplify nested include file handling # Conflicts: # src/input.h --- src/input.cpp | 17 ++--------------- 1 file changed, 2 insertions(+), 15 deletions(-) diff --git a/src/input.cpp b/src/input.cpp index 32b6b697b1..e5fbec6d5a 100644 --- a/src/input.cpp +++ b/src/input.cpp @@ -78,7 +78,6 @@ Input::Input(LAMMPS *lmp, int argc, char **argv) : Pointers(lmp) echo_screen = 0; echo_log = 1; - eof_return = 0; label_active = 0; labelstr = NULL; @@ -207,18 +206,7 @@ void Input::file() MPI_Bcast(&n,1,MPI_INT,0,world); if (n == 0) { if (label_active) error->all(FLERR,"Label wasn't found in input script"); - if (eof_return) break; - if (me == 0) { - if (infile != stdin) { - fclose(infile); - infile = NULL; - } - nfile--; - } - MPI_Bcast(&nfile,1,MPI_INT,0,world); - if (nfile == 0) break; - if (me == 0) infile = infiles[nfile-1]; - continue; + break; } if (n > maxline) reallocate(line,maxline,n); @@ -1059,9 +1047,8 @@ void Input::include() error->one(FLERR,str); } infiles[nfile++] = infile; - eof_return = 1; file(); - eof_return = 0; + fclose(infile); nfile--; infile = infiles[nfile-1]; } -- GitLab From 13237155c8f3d01be9a7b9375672d56bd2e787d5 Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Mon, 24 Jun 2019 14:24:54 -0400 Subject: [PATCH 094/469] make processing of Input::file(const char* filename) more like processing an include file --- src/input.cpp | 31 +++++++++++++++++++++++-------- 1 file changed, 23 insertions(+), 8 deletions(-) diff --git a/src/input.cpp b/src/input.cpp index e5fbec6d5a..644446710f 100644 --- a/src/input.cpp +++ b/src/input.cpp @@ -240,8 +240,8 @@ void Input::file() } /* ---------------------------------------------------------------------- - process all input from filename - called from library interface + process all input from file at filename + mostly called from library interface ------------------------------------------------------------------------- */ void Input::file(const char *filename) @@ -251,21 +251,30 @@ void Input::file(const char *filename) // call to file() will close filename and decrement nfile if (me == 0) { - if (nfile > 1) - error->one(FLERR,"Invalid use of library file() function"); + if (nfile == maxfile) { + maxfile++; + infiles = (FILE **) + memory->srealloc(infiles,maxfile*sizeof(FILE *),"input:infiles"); + } - if (infile && infile != stdin) fclose(infile); infile = fopen(filename,"r"); if (infile == NULL) { char str[128]; snprintf(str,128,"Cannot open input script %s",filename); error->one(FLERR,str); } - infiles[0] = infile; - nfile = 1; + infiles[nfile++] = infile; } + // process contents of file + file(); + + if (me == 0) { + fclose(infile); + nfile--; + infile = infiles[nfile-1]; + } } /* ---------------------------------------------------------------------- @@ -1047,7 +1056,13 @@ void Input::include() error->one(FLERR,str); } infiles[nfile++] = infile; - file(); + } + + // process contents of file + + file(); + + if (me == 0) { fclose(infile); nfile--; infile = infiles[nfile-1]; -- GitLab From f2380a24ef90945f421a90e5d482c58e0bef49b5 Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Mon, 24 Jun 2019 14:27:05 -0400 Subject: [PATCH 095/469] fix parallel processing input include bug --- src/input.cpp | 31 +++++++++++++++++++++++-------- 1 file changed, 23 insertions(+), 8 deletions(-) diff --git a/src/input.cpp b/src/input.cpp index 268be5b774..2f617d2cd0 100644 --- a/src/input.cpp +++ b/src/input.cpp @@ -239,8 +239,8 @@ void Input::file() } /* ---------------------------------------------------------------------- - process all input from filename - called from library interface + process all input from file at filename + mostly called from library interface ------------------------------------------------------------------------- */ void Input::file(const char *filename) @@ -250,21 +250,30 @@ void Input::file(const char *filename) // call to file() will close filename and decrement nfile if (me == 0) { - if (nfile > 1) - error->one(FLERR,"Invalid use of library file() function"); + if (nfile == maxfile) { + maxfile++; + infiles = (FILE **) + memory->srealloc(infiles,maxfile*sizeof(FILE *),"input:infiles"); + } - if (infile && infile != stdin) fclose(infile); infile = fopen(filename,"r"); if (infile == NULL) { char str[128]; snprintf(str,128,"Cannot open input script %s",filename); error->one(FLERR,str); } - infiles[0] = infile; - nfile = 1; + infiles[nfile++] = infile; } + // process contents of file + file(); + + if (me == 0) { + fclose(infile); + nfile--; + infile = infiles[nfile-1]; + } } /* ---------------------------------------------------------------------- @@ -1041,7 +1050,13 @@ void Input::include() error->one(FLERR,str); } infiles[nfile++] = infile; - file(); + } + + // process contents of file + + file(); + + if (me == 0) { fclose(infile); nfile--; infile = infiles[nfile-1]; -- GitLab From 0ddcc023a5074e10b7e5974011e15542a2c5b105 Mon Sep 17 00:00:00 2001 From: Ellad Tadmor Date: Mon, 24 Jun 2019 13:54:55 -0500 Subject: [PATCH 096/469] Improvements and additions to kim_commands doc --- doc/src/kim_commands.txt | 54 +++++++++++++++++++++++++++++++++------- 1 file changed, 45 insertions(+), 9 deletions(-) diff --git a/doc/src/kim_commands.txt b/doc/src/kim_commands.txt index f039202e4e..68306ad6b7 100644 --- a/doc/src/kim_commands.txt +++ b/doc/src/kim_commands.txt @@ -170,10 +170,30 @@ SMs can never adjust their units.) If a match is possible, the LAMMPS {user_units}. If the match fails, the simulation is terminated with an error. -If unit conversion mode {is} active, then the LAMMPS "units"_units.html -command is called to set the units to the IM's required or preferred units. -Conversion factors between the IM's units and the {user_units} are -defined for all "physical quantities"_units.html (mass, distance, etc.). +Here is an example of a LAMMPS script to compute the cohesive energy +of a face-centered cubic (fcc) lattice for the Ercolessi and Adams (1994) +potential for Al: + +kim_init EAM_Dynamo_ErcolessiAdams_1994_Al__MO_123629422045_005 metal +boundary p p p +lattice fcc 4.032 +region simbox block 0 1 0 1 0 1 units lattice +create_box 1 simbox +create_atoms 1 box +mass 1 26.981539 +kim_interactions Al +run 0 +variable Ec equal (pe/count(all))/$\{_u_energy\} +print "Cohesive Energy = $\{EcJ\} eV" +:pre + +The above script will end with an error in the {kim_init} line if the +IM is changed to another potential for Al that does not work with {metal} +units. To address this {kim_init} offers the {unit_conversion_mode}. +If unit conversion mode {is} active, then {kim_init} calls the LAMMPS +"units"_units.html command to set the units to the IM's required or +preferred units. Conversion factors between the IM's units and the {user_units} +are defined for all "physical quantities"_units.html (mass, distance, etc.). (Note that converting to or from the "lj" unit style is not supported.) These factors are stored as "internal style variables"_variable.html with standard names: @@ -197,9 +217,11 @@ If desired, the input script can be designed to work with these conversion factors so that the script will work without change with any OpenKIM IM. (This approach is used in the "OpenKIM Testing Framework"_https://openkim.org/getting-started/kim-tests/.) -For example, the following simple script constructs an fcc lattice with -a lattice parameter defined in meters, computes the total energy, -and prints the cohesive energy in Joules regardless of the units of the IM. +For example, the script given above for the cohesive energy of fcc Al +can be rewritten to work with any IM regardless of units. The following +script constructs an fcc lattice with a lattice parameter defined in +meters, computes the total energy, and prints the cohesive energy in +Joules regardless of the units of the IM. kim_init EAM_Dynamo_ErcolessiAdams_1994_Al__MO_123629422045_005 si unit_conversion_mode boundary p p p @@ -339,18 +361,23 @@ lattice fcc $\{a0\} The {kim_query} command retrieves from "OpenKIM"_https://openkim.org the equilibrium lattice constant predicted by the Ercolessi and Adams (1994) -potential for the face-centered cubic (fcc) structure and places it in +potential for the fcc structure and places it in variable {a0}. This variable is then used on the next line to set up the crystal. By using {kim_query}, the user is saved the trouble and possible error of tracking this value down, or of having to perform an energy minimization to find the equilibrium lattice constant. +Note that in {unit_conversion_mode} the results obtained from a +{kim_query} would need to be converted to the appropriate units system. +For example, in the above script, the lattice command would need to be +changed to: "lattice fcc $\{a0\}*$\{_u_distance\}". + [Define a crystal at finite temperature accounting for thermal expansion] kim_init EAM_Dynamo_ErcolessiAdams_1994_Al__MO_123629422045_005 metal boundary p p p kim_query a0 get_lattice_constant_fcc units=\["angstrom"\] -kim_query alpha get_linear_thermal_expansion_fcc +kim_query alpha get_linear_thermal_expansion_fcc units=\{"1/K"\} variable DeltaT equal 300 lattice fcc $\{a0\}*$\{alpha\}*$\{DeltaT\} ... :pre @@ -375,6 +402,15 @@ The defect formation energy {Eform} is computed by subtracting from {Etot} the ideal fcc cohesive energy of the atoms in the system obtained from "OpenKIM"_https://openkim.org for the Ercolessi and Adams (1994) potential. +NOTE: {kim_query} commands return results archived in +"OpenKIM"_https://openkim.org. These results are obtained +using programs for computing material properties +(KIM Tests and KIM Test Drivers) that were contributed to OpenKIM. +In order to give credit to Test developers, the number of times results +from these programs are queried is tracked. No other information about +the nature of the query or its source is recorded. + + Citation of OpenKIM IMs :h4 When publishing results obtained using OpenKIM IMs researchers are requested -- GitLab From 1047d8f80e10a8c267eb4b022720da8f61f844c0 Mon Sep 17 00:00:00 2001 From: Ellad Tadmor Date: Mon, 24 Jun 2019 14:32:40 -0500 Subject: [PATCH 097/469] Change of terminology to "KIM Portable Model" and streamlining --- doc/src/kim_commands.txt | 55 ++++++++++++++++++++-------------------- 1 file changed, 28 insertions(+), 27 deletions(-) diff --git a/doc/src/kim_commands.txt b/doc/src/kim_commands.txt index d42b509449..9be4a79db5 100644 --- a/doc/src/kim_commands.txt +++ b/doc/src/kim_commands.txt @@ -44,8 +44,8 @@ so that they can be used by LAMMPS scripts. These commands do not implement any computations directly, but rather generate LAMMPS input commands based on the information retrieved from the OpenKIM repository to initialize and activate OpenKIM IMs and query their predictions for use in the LAMMPS script. -All LAMMPS input commands executed by {kim_commands} are echoed to the -LAMMPS log file. +All LAMMPS input commands generated and executed by {kim_commands} are +echoed to the LAMMPS log file. Benefits of Using OpenKIM IMs :h4 @@ -65,7 +65,7 @@ OpenKIM is a member organization of "DataCite"_https://datacite.org/ and issues Convenience :h5 IMs in OpenKIM are distributed in binary form along with LAMMPS and can be used in a LAMMPS input script simply by providing their KIM ID in the {kim_init} command documented on this page. -The {kim_query} web query tool provides the ability to use the predictions of IMs for supported material properties (computed via "KIM Tests"https://openkim.org/getting-started/kim-tests/) as part of a LAMMPS input script setup and analysis. +The {kim_query} web query tool provides the ability to use the predictions of IMs for supported material properties (computed via "KIM Tests"_https://openkim.org/getting-started/kim-tests/) as part of a LAMMPS input script setup and analysis. Support is provided for unit conversion between the "unit style"_units.html used in the LAMMPS input script and the units required by the OpenKIM IM. This makes it possible to use a single input script with IMs using different units without change and minimizes the likelihood of errors due to incompatible units. :ul :link(IM_types) @@ -73,8 +73,8 @@ Types of IMs in OpenKIM :h4 There are two types of IMs archived in OpenKIM: -The first type is called a {KIM Model}. A KIM Model is an independent computer implementation of an IM written in one of the languages supported by KIM (C, C++, Fortran), which conforms to the KIM Application Programming Interface ("KIM API"_https://openkim.org/kim-api/). A KIM Model will work seamlessly with any simulation code that supports the KIM API (including LAMMPS; see "complete list of supported code"_https://openkim.org/projects-using-kim/). -The second type is called a {KIM Simulator Model} (SM). In this case, the IM is implemented natively within the simulation code ({simulator}), i.e. LAMMPS. A separate SM package is archived in OpenKIM for each parameterization of the IM, which includes all of the necessary parameter files, LAMMPS commands, and metadata (supported species, units, etc.) needed to run the IM in LAMMPS. :ol +The first type is called a {KIM Portable Model} (PM). A KIM PM is an independent computer implementation of an IM written in one of the languages supported by KIM (C, C++, Fortran), which conforms to the KIM Application Programming Interface ("KIM API"_https://openkim.org/kim-api/) Portable Model Interface (PMI) standard. A KIM PM will work seamlessly with any simulation code that supports the KIM API/PMI standard (including LAMMPS; see "complete list of supported codes"_https://openkim.org/projects-using-kim/). +The second type is called a {KIM Simulator Model} (SM). A KIM SM is an IM that is implemented natively within a simulation code ({simulator}) that supports the KIM API/SMI (Simulator Model Interface); in this case LAMMPS. A separate SM package is archived in OpenKIM for each parameterization of the IM, which includes all of the necessary parameter files, LAMMPS commands, and metadata (supported species, units, etc.) needed to run the IM in LAMMPS. :ol With these two IM types, OpenKIM can archive and test almost all IMs that can be used by LAMMPS. (It is easy to contribute new IMs to OpenKIM, see @@ -85,7 +85,7 @@ OpenKIM IMs are uniquely identified by a a human-readable prefix identifying the type of IM, authors, publication year, and supported species, separated by two underscores from the KIM ID itself, which begins with an IM code -({MO} for a KIM Model, and {SM} for a KIM Simulator Model) +({MO} for a KIM Portable Model, and {SM} for a KIM Simulator Model) followed by a unique 12-digit code and a 3-digit version identifier. By convention SM prefixes begin with {Sim_} to readily identify them. @@ -97,7 +97,7 @@ providing all the information on the IM including a title, description, authorship and citation information, test and verification check results, visualizations of results, a wiki with documentation and user comments, and access to raw files, and other information. -This is referred to as the "Model Page" or "SM Page". +This is referred to as the "PM Page" or "SM Page". The URL for such a page is constructed from the "extended KIM ID"_https://openkim.org/about-kim-ids/ of the IM: @@ -110,7 +110,7 @@ listed above the Model Page is located at: "https://openkim.org/id/SW_StillingerWeber_1985_Si__MO_405512056662_005"_https://openkim.org/id/SW_StillingerWeber_1985_Si__MO_405512056662_005 :pre -See the "current list of KIM Models and SMs archived in OpenKIM"_https://openkim.org/browse/models/by-species. +See the "current list of KIM PMs and SMs archived in OpenKIM"_https://openkim.org/browse/models/by-species. This list is sorted by species and can be filtered to display only IMs for certain species combinations. @@ -124,7 +124,7 @@ IM and perform necessary initialization ({kim_init}), and the second to set up the IM for use by executing any necessary LAMMPS commands ({kim_interactions}). Both are required. -See the {examples/kim} directory for example input scripts that use KIM Models +See the {examples/kim} directory for example input scripts that use KIM PMs and KIM SMs. OpenKIM IM Initialization ({kim_init}) :h5 @@ -146,17 +146,17 @@ in the input script. (Any dimensioned numerical values in the input script and values read in from files are expected to be in the {user_units} system.) -The selected IM can be either a "KIM Model or a KIM SM"_#IM_types. +The selected IM can be either a "KIM PM or a KIM SM"_#IM_types. For a KIM SM, the {kim_init} command verifies that the SM is designed to work with LAMMPS (and not another simulation code). -In addition, the version strings for the LAMMPS version used for defining +In addition, the LAMMPS version used for defining the SM and the LAMMPS version being currently run are -printed, to help diagnose any incompatible changes to input script or +printed to help diagnose any incompatible changes to input script or command syntax between the two LAMMPS versions. Based on the selected model {kim_init} may modify the "atom_style"_atom_style.html. -Some SMs have requirements for this variable. If this is the case, then +Some SMs have requirements for this setting. If this is the case, then {atom_style} will be set to the required style. Otherwise, the value is left unchanged (which in the absence of an {atom_style} command in the input script is the "default atom_style value"_atom_style.html). @@ -166,7 +166,7 @@ on whether or not {unit conversion mode} is activated as indicated by the optional {unitarg} argument. If unit conversion mode is [not] active, then {user_units} must either match the required units of the IM or the IM must be able -to adjust its units to match. (The latter is only possible with some KIM Models; +to adjust its units to match. (The latter is only possible with some KIM PMs; SMs can never adjust their units.) If a match is possible, the LAMMPS "units"_units.html command is called to set the units to {user_units}. If the match fails, the simulation is terminated with @@ -198,7 +198,7 @@ preferred units. Conversion factors between the IM's units and the {user_units} are defined for all "physical quantities"_units.html (mass, distance, etc.). (Note that converting to or from the "lj" unit style is not supported.) These factors are stored as "internal style variables"_variable.html with -standard names: +the following standard names: _u_mass _u_distance @@ -241,7 +241,7 @@ Note the multiplication by $\{_u_distance\} and $\{_u_mass\} to convert from SI units (specified in the {kim_init} command) to whatever units the IM uses (metal in this case), and the division by $\{_u_energy\} to convert from the IM's energy units to SI units (Joule). This script -will work correctly for any IM for Al (KIM Model or SM) selected by the +will work correctly for any IM for Al (KIM PM or SM) selected by the {kim_init} command. Care must be taken to apply unit conversion to dimensional variables read in @@ -283,10 +283,10 @@ kim_interactions Si Si Si C The {kim_interactions} command performs all the necessary steps to set up the OpenKIM IM selected in the {kim_init} command. The specific actions depend -on whether the IM is a KIM Model or a KIM SM. For a KIM Model, +on whether the IM is a KIM PM or a KIM SM. For a KIM PM, a "pair_style kim"_pair_kim.html command is executed followed by the appropriate {pair_coeff} command. For example, for the -Ercolessi and Adams (1994) KIM Model for Al set by the following commands: +Ercolessi and Adams (1994) KIM PM for Al set by the following commands: kim_init EAM_Dynamo_ErcolessiAdams_1994_Al__MO_123629422045_005 metal ... @@ -302,8 +302,7 @@ pair_coeff * * Al :pre For a KIM SM, the generated input commands may be more complex and require that LAMMPS is built with the required packages included for the type of potential being used. The set of commands to be executed -is defined in the SM specification file, which is part of the SM package -on "OpenKIM"_https://openkim.org. +is defined in the SM specification file, which is part of the SM package. For example, for the Strachan et al. (2003) ReaxFF SM set by the following commands: @@ -416,14 +415,16 @@ the nature of the query or its source is recorded. Citation of OpenKIM IMs :h4 When publishing results obtained using OpenKIM IMs researchers are requested -to cite the OpenKIM project "(Tadmor)"_#kim-mainpaper and KIM API -"(Elliott)"_#kim-api as well as the specific IM codes used in the simulations. +to cite the OpenKIM project "(Tadmor)"_#kim-mainpaper, KIM API +"(Elliott)"_#kim-api, and the specific IM codes used in the simulations, +in addition to the relevant scientific references for the IM. The citation format for an IM is displayed on its page on -"OpenKIM"_https://openkim.org along with the corresponding BibTex file. +"OpenKIM"_https://openkim.org along with the corresponding BibTex file, +and is automatically added to the LAMMPS {log.cite} file. -Citing the codes used in the simulation gives credit -to the researchers who developed them and enables open source efforts like -OpenKIM to function. +Citing the IM software (KIM infrastucture and specific PM or SM codes) +used in the simulation gives credit to the researchers who developed them +and enables open source efforts like OpenKIM to function. [Restrictions:] @@ -442,7 +443,7 @@ must be installed. [Related commands:] -"pair_style kim"_pair_kim.html, "units"_units.html +"pair_style kim"_pair_kim.html :line -- GitLab From b6535367501e4f9c3e85c32ade7cea6ef6cd6f9d Mon Sep 17 00:00:00 2001 From: Ellad Tadmor Date: Mon, 24 Jun 2019 14:38:44 -0500 Subject: [PATCH 098/469] Switched pair_style kim doc to "KIM Portable Model" terminology --- doc/src/pair_kim.txt | 23 ++++++++++++----------- 1 file changed, 12 insertions(+), 11 deletions(-) diff --git a/doc/src/pair_kim.txt b/doc/src/pair_kim.txt index 86d13808b0..41593675ba 100644 --- a/doc/src/pair_kim.txt +++ b/doc/src/pair_kim.txt @@ -27,11 +27,12 @@ potentials to enable their use in LAMMPS scripts. The preferred interface for using interatomic models archived in OpenKIM is the "kim_commands interface"_kim_commands.html. That -interface supports both "KIM Models" that conform to the KIM API -and can be used by any KIM-compliant simulation code, and +interface supports both "KIM Portable Models" (PMs) that conform to the +KIM API Portable Model Interface (PMI) and can be used by any +simulation code that conforms to the KIM API/PMI, and "KIM Simulator Models" that are natively implemented within a single simulation code (like LAMMPS) and can only be used with it. -The {pair_style kim} command is limited to KIM Models. It is +The {pair_style kim} command is limited to KIM PMs. It is used by the "kim_commands interface"_kim_commands.html as needed. NOTE: Since {pair_style kim} is called by {kim_interactions} as needed, @@ -39,23 +40,23 @@ is not recommended to be directly used in input scripts. :line -The argument {model} is the name of the KIM model for a specific -potential as KIM defines it. For potentials archived in OpenKIM +The argument {model} is the name of the KIM PM. +For potentials archived in OpenKIM this is the extended KIM ID (see "kim_commands"_kim_commands.html -for details). LAMMPS can invoke any KIM Model, however there can -be incompatibilities (for example unit matching issues). +for details). LAMMPS can invoke any KIM PM, however there can +be incompatibilities (for example due to unit matching issues). In the event of an incompatibility, the code will terminate with an error message. Check both the LAMMPS and KIM log files for details. Only a single {pair_coeff} command is used with the {kim} style, which specifies the mapping of LAMMPS atom types to the species supported by -the KIM Model. This is done by specifying {N} additional arguments +the KIM PM. This is done by specifying {N} additional arguments after the * * in the {pair_coeff} command, where {N} is the number of LAMMPS atom types: N element names = mapping of KIM elements to atom types :ul -For example, consider a KIM Model that supports Si and C species. +For example, consider a KIM PM that supports Si and C species. If the LAMMPS simulation has four atom types, where the first three are Si, and the fourth is C, the following {pair_coeff} command would be used: @@ -63,14 +64,14 @@ pair_coeff * * Si Si Si C :pre The first two arguments must be * * so as to span all LAMMPS atom types. The first three Si arguments map LAMMPS atom types 1, 2, and 3 to Si as -defined within KIM Model. The final C argument maps LAMMPS atom type 4 to C. +defined within KIM PM. The final C argument maps LAMMPS atom type 4 to C. :line In addition to the usual LAMMPS error messages, the KIM library itself may generate errors, which should be printed to the screen. In this case it is also useful to check the {kim.log} file for additional error -information. The file kim.log should be generated in the same +information. The file {kim.log} should be generated in the same directory where LAMMPS is running. To download, build, and install the KIM library on your system, see -- GitLab From 4284a4fac41a36d0d897ff9a3f079719f57973a0 Mon Sep 17 00:00:00 2001 From: Ellad Tadmor Date: Mon, 24 Jun 2019 14:51:35 -0500 Subject: [PATCH 099/469] Changed me to me_si and fixed some typos in comments --- src/KIM/kim_units.cpp | 18 +++++++++--------- 1 file changed, 9 insertions(+), 9 deletions(-) diff --git a/src/KIM/kim_units.cpp b/src/KIM/kim_units.cpp index fe90d58e9e..40f4917601 100644 --- a/src/KIM/kim_units.cpp +++ b/src/KIM/kim_units.cpp @@ -76,9 +76,9 @@ double const Nav = 6.022140857e23; // [unitless] Avogadro's number // (NIST value) // double const Nav = 6.02214076e23; // [unitless] Avogadro's number // (official value May 2019) -double const me = 9.10938356e-31; // [kg] electron rest mass +double const me_si = 9.10938356e-31; // [kg] electron rest mass // (NIST value) -// double me = 9.10938291e-31; // [kg] electron rest mass +// double me_si = 9.10938291e-31; // [kg] electron rest mass double const e_si = 1.6021766208e-19; // [C] elementary charge // (charge of an electron/proton) // (NIST value) @@ -114,8 +114,9 @@ double const attogram_si = 1e-21; // [kg[ attogram double const atu_si = 2.418884326509e-17; // [s] atomic time unit // ( = hbar/E_h where E_h is the // Hartree energy) (NIST value) -double const atu_electron_si = atu_si*sqrt(amu_si/me); // [s] atomic time unit - // used in electron system (see https://sourceforge.net/p/lammps/mailman/lammps-users/thread/BCA2BDB2-BA03-4280-896F-1E6120EF47B2%40caltech.edu/) +double const atu_electron_si = atu_si*sqrt(amu_si/me_si); + // [s] atomic time unit + // used in electron system (see https://sourceforge.net/p/lammps/mailman/lammps-users/thread/BCA2BDB2-BA03-4280-896F-1E6120EF47B2%40caltech.edu/) double const microsecond_si = 1e-6; // [s] microsecond double const nanosecond_si = 1e-9; // [s] nanosecond double const picosecond_si = 1e-12; // [s] picosecond @@ -130,13 +131,12 @@ double const amu_per_bohrcu_si = amu_si/pow(bohr_si,3); // [kg/m^3] amu/bohr^3 double const picogram_per_micrometercu_si = picogram_si/pow(micrometer_si,3); // [kg/m^3] picogram/micrometer^3 double const attogram_per_nanometercu_si = - attogram_si/pow(nanometer_si,3); // [kg/m^3] attogram/ - // nanomaterial^3 + attogram_si/pow(nanometer_si,3); // [kg/m^3] attogram/nanometer^3 /*---------------------- Energy/torque units ------------------------ */ -double const kcal_si = 4184.0; // [J] kilocalroie (heat energy +double const kcal_si = 4184.0; // [J] kilocalorie (heat energy // involved in warming up one // kilogram of water by one // degree Kelvin) @@ -155,8 +155,8 @@ double const erg_si = 1e-7; // [J] erg double const dyne_centimeter_si = 1e-7; // [J[ dyne*centimeter double const picogram_micrometersq_per_microsecondsq_si = picogram_si*pow(micrometer_si,2)/pow(microsecond_si,2); - // [J] pigogram*micrometer^2/ - // micorsecond^2 + // [J] picogram*micrometer^2/ + // microsecond^2 double const attogram_nanometersq_per_nanosecondsq_si = attogram_si*pow(nanometer_si,2)/pow(nanosecond_si,2); // [J] attogram*nanometer^2/ -- GitLab From 86d878a7eb4b73432eab53538a2c114571be63e0 Mon Sep 17 00:00:00 2001 From: Ellad Tadmor Date: Mon, 24 Jun 2019 15:26:41 -0500 Subject: [PATCH 100/469] Updated language on availability of ADP potentials in OpenKIM --- doc/src/pair_adp.txt | 7 +++---- 1 file changed, 3 insertions(+), 4 deletions(-) diff --git a/doc/src/pair_adp.txt b/doc/src/pair_adp.txt index d5b07e8431..de6717a6c3 100644 --- a/doc/src/pair_adp.txt +++ b/doc/src/pair_adp.txt @@ -49,12 +49,11 @@ Note that ADP potentials obtained from NIST must be converted into the extended DYNAMO {setfl} format discussed below. :l -The OpenKIM Project at https://openkim.org provides ADP potentials -as Simulator Models that can be used directly in LAMMPS with -the "kim_commands interface"_kim_commands.html. +The OpenKIM Project at https://openkim.org/browse/models/by-type provides +ADP potentials that can be used directly in LAMMPS with the "kim_commands +interface"_kim_commands.html. :l - :line Only a single pair_coeff command is used with the {adp} style which -- GitLab From 6a6d08e18ef9f47e679dd79b841bdc1faf05d849 Mon Sep 17 00:00:00 2001 From: Julien Devemy Date: Tue, 25 Jun 2019 12:01:29 +0200 Subject: [PATCH 101/469] Better compute_pressure hybrid and doc --- doc/src/compute_pressure.txt | 8 ++++-- src/compute_pressure.cpp | 50 ++++++++++++++++++++++++++---------- 2 files changed, 42 insertions(+), 16 deletions(-) diff --git a/doc/src/compute_pressure.txt b/doc/src/compute_pressure.txt index bd6e38e392..fd9bfb7aff 100644 --- a/doc/src/compute_pressure.txt +++ b/doc/src/compute_pressure.txt @@ -16,12 +16,13 @@ ID, group-ID are documented in "compute"_compute.html command pressure = style name of this compute command temp-ID = ID of compute that calculates temperature, can be NULL if not needed zero or more keywords may be appended -keyword = {ke} or {pair} or {bond} or {angle} or {dihedral} or {improper} or {kspace} or {fix} or {virial} :ul +keyword = {ke} or {pair} or {bond} or {angle} or {dihedral} or {improper} or {kspace} or {fix} or {virial} or {hybridpair} :ul [Examples:] compute 1 all pressure thermo_temp -compute 1 all pressure NULL pair bond :pre +compute 1 all pressure NULL pair bond +compute 1 all pressure NULL hybridpair lj/cut :pre [Description:] @@ -67,6 +68,9 @@ extra keywords are listed, then only those components are summed to compute temperature or ke and/or the virial. The {virial} keyword means include all terms except the kinetic energy {ke}. +The {hybridpair} keyword means to only include contribution +from a subpair in a {hybrid} or {hybrid/overlay} pair style. + Details of how LAMMPS computes the virial efficiently for the entire system, including for many-body potentials and accounting for the effects of periodic boundary conditions are discussed in diff --git a/src/compute_pressure.cpp b/src/compute_pressure.cpp index 8381e04fa8..96f577219d 100644 --- a/src/compute_pressure.cpp +++ b/src/compute_pressure.cpp @@ -81,8 +81,37 @@ ComputePressure::ComputePressure(LAMMPS *lmp, int narg, char **arg) : int iarg = 4; while (iarg < narg) { if (strcmp(arg[iarg],"ke") == 0) keflag = 1; - else if (strcmp(arg[iarg],"hybridpair") == 0) - hybridpairflag = force->inumeric(FLERR, arg[++iarg]); + else if (strcmp(arg[iarg],"hybridpair") == 0) { + int n = strlen(arg[++iarg]) + 1; + if (lmp->suffix) n += strlen(lmp->suffix) + 1; + pstyle = new char[n]; + strcpy(pstyle,arg[iarg++]); + + nsub = 0; + + if (narg > iarg) { + if (isdigit(arg[iarg][0])) { + nsub = force->inumeric(FLERR,arg[iarg]); + ++iarg; + if (nsub <= 0) + error->all(FLERR,"Illegal compute pressure command"); + } + } + + // check if pair style with and without suffix exists + + hybridpair = (Pair *) force->pair_match(pstyle,1,nsub); + if (!hybridpair && lmp->suffix) { + strcat(pstyle,"/"); + strcat(pstyle,lmp->suffix); + hybridpair = (Pair *) force->pair_match(pstyle,1,nsub); + } + + if (!hybridpair) + error->all(FLERR,"Unrecognized pair style in compute pressure command"); + + hybridpairflag = 1; + } else if (strcmp(arg[iarg],"pair") == 0) pairflag = 1; else if (strcmp(arg[iarg],"bond") == 0) bondflag = 1; else if (strcmp(arg[iarg],"angle") == 0) angleflag = 1; @@ -144,12 +173,7 @@ void ComputePressure::init() nvirial = 0; vptr = NULL; - if (hybridpairflag > 0 && force->pair) { - if (strstr(force->pair_style, "hybrid")) { - PairHybrid *ph = (PairHybrid *) force->pair; - if (hybridpairflag <= ph->nstyles) nvirial++; - } - } + if (hybridpairflag && force->pair) nvirial++; if (pairflag && force->pair) nvirial++; if (bondflag && atom->molecular && force->bond) nvirial++; if (angleflag && atom->molecular && force->angle) nvirial++; @@ -162,12 +186,10 @@ void ComputePressure::init() if (nvirial) { vptr = new double*[nvirial]; nvirial = 0; - if (hybridpairflag > 0 && force->pair) { - if (strstr(force->pair_style, "hybrid")) { - PairHybrid *ph = (PairHybrid *) force->pair; - if (hybridpairflag <= ph->nstyles) - vptr[nvirial++] = ph->styles[hybridpairflag-1]->virial; - } + if (hybridpairflag && force->pair) { + PairHybrid *ph = (PairHybrid *) force->pair; + ph->no_virial_fdotr_compute = 1; + vptr[nvirial++] = hybridpair->virial; } if (pairflag && force->pair) vptr[nvirial++] = force->pair->virial; if (bondflag && force->bond) vptr[nvirial++] = force->bond->virial; -- GitLab From 61ddc98a5a9ef9d53dc7f3227262b755c20fb7f7 Mon Sep 17 00:00:00 2001 From: Julien Devemy Date: Tue, 25 Jun 2019 13:30:41 +0200 Subject: [PATCH 102/469] Missing compute_pressure.h --- src/compute_pressure.h | 5 +++++ 1 file changed, 5 insertions(+) diff --git a/src/compute_pressure.h b/src/compute_pressure.h index 3259377bd8..31983e8e2c 100644 --- a/src/compute_pressure.h +++ b/src/compute_pressure.h @@ -42,10 +42,15 @@ class ComputePressure : public Compute { char *id_temp; double virial[6]; int hybridpairflag; + class Pair *hybridpair; int keflag,pairflag,bondflag,angleflag,dihedralflag,improperflag; int fixflag,kspaceflag; void virial_compute(int, int); + + private: + int nsub; + char *pstyle; }; } -- GitLab From 2fd924562b94c9fb4d1b6a933211416e07b3b869 Mon Sep 17 00:00:00 2001 From: Julien Devemy Date: Tue, 25 Jun 2019 15:15:30 +0200 Subject: [PATCH 103/469] Spell correction --- doc/src/compute_pressure.txt | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/doc/src/compute_pressure.txt b/doc/src/compute_pressure.txt index fd9bfb7aff..070376075e 100644 --- a/doc/src/compute_pressure.txt +++ b/doc/src/compute_pressure.txt @@ -69,7 +69,7 @@ compute temperature or ke and/or the virial. The {virial} keyword means include all terms except the kinetic energy {ke}. The {hybridpair} keyword means to only include contribution -from a subpair in a {hybrid} or {hybrid/overlay} pair style. +from a sub-style in a {hybrid} or {hybrid/overlay} pair style. Details of how LAMMPS computes the virial efficiently for the entire system, including for many-body potentials and accounting for the -- GitLab From e08146c31fa887300dbba54ee01e3f69782440e5 Mon Sep 17 00:00:00 2001 From: "Dan S. Bolintineanu" Date: Tue, 25 Jun 2019 12:06:18 -0600 Subject: [PATCH 104/469] Allow twisting torque to be used without rolling torque in pair granular --- src/GRANULAR/pair_granular.cpp | 39 +++++++++++++++++----------------- 1 file changed, 20 insertions(+), 19 deletions(-) diff --git a/src/GRANULAR/pair_granular.cpp b/src/GRANULAR/pair_granular.cpp index 913f6f8b59..77b1981786 100644 --- a/src/GRANULAR/pair_granular.cpp +++ b/src/GRANULAR/pair_granular.cpp @@ -475,16 +475,12 @@ void PairGranular::compute(int eflag, int vflag) fs3 = -Ft*vtr3; } - //**************************************** - // rolling resistance - //**************************************** - - if (roll_model[itype][jtype] != ROLL_NONE) { + if (roll_model[itype][jtype] != ROLL_NONE || + twist_model[itype][jtype] != TWIST_NONE){ relrot1 = omega[i][0] - omega[j][0]; relrot2 = omega[i][1] - omega[j][1]; relrot3 = omega[i][2] - omega[j][2]; - - // rolling velocity, + // rolling velocity, // see eq. 31 of Wang et al, Particuology v 23, p 49 (2015) // this is different from the Marshall papers, // which use the Bagi/Kuhn formulation @@ -492,7 +488,12 @@ void PairGranular::compute(int eflag, int vflag) // - 0.5*((radj-radi)/radsum)*vtr1; // - 0.5*((radj-radi)/radsum)*vtr2; // - 0.5*((radj-radi)/radsum)*vtr3; + } + //**************************************** + // rolling resistance + //**************************************** + if (roll_model[itype][jtype] != ROLL_NONE) { vrl1 = Reff*(relrot2*nz - relrot3*ny); vrl2 = Reff*(relrot3*nx - relrot1*nz); vrl3 = Reff*(relrot1*ny - relrot2*nx); @@ -1231,10 +1232,10 @@ void PairGranular::write_restart(FILE *fp) fwrite(&tangential_model[i][j],sizeof(int),1,fp); fwrite(&roll_model[i][j],sizeof(int),1,fp); fwrite(&twist_model[i][j],sizeof(int),1,fp); - fwrite(&normal_coeffs[i][j],sizeof(double),4,fp); - fwrite(&tangential_coeffs[i][j],sizeof(double),3,fp); - fwrite(&roll_coeffs[i][j],sizeof(double),3,fp); - fwrite(&twist_coeffs[i][j],sizeof(double),3,fp); + fwrite(normal_coeffs[i][j],sizeof(double),4,fp); + fwrite(tangential_coeffs[i][j],sizeof(double),3,fp); + fwrite(roll_coeffs[i][j],sizeof(double),3,fp); + fwrite(twist_coeffs[i][j],sizeof(double),3,fp); fwrite(&cutoff_type[i][j],sizeof(double),1,fp); } } @@ -1261,10 +1262,10 @@ void PairGranular::read_restart(FILE *fp) fread(&tangential_model[i][j],sizeof(int),1,fp); fread(&roll_model[i][j],sizeof(int),1,fp); fread(&twist_model[i][j],sizeof(int),1,fp); - fread(&normal_coeffs[i][j],sizeof(double),4,fp); - fread(&tangential_coeffs[i][j],sizeof(double),3,fp); - fread(&roll_coeffs[i][j],sizeof(double),3,fp); - fread(&twist_coeffs[i][j],sizeof(double),3,fp); + fread(normal_coeffs[i][j],sizeof(double),4,fp); + fread(tangential_coeffs[i][j],sizeof(double),3,fp); + fread(roll_coeffs[i][j],sizeof(double),3,fp); + fread(twist_coeffs[i][j],sizeof(double),3,fp); fread(&cutoff_type[i][j],sizeof(double),1,fp); } MPI_Bcast(&normal_model[i][j],1,MPI_INT,0,world); @@ -1272,10 +1273,10 @@ void PairGranular::read_restart(FILE *fp) MPI_Bcast(&tangential_model[i][j],1,MPI_INT,0,world); MPI_Bcast(&roll_model[i][j],1,MPI_INT,0,world); MPI_Bcast(&twist_model[i][j],1,MPI_INT,0,world); - MPI_Bcast(&normal_coeffs[i][j],4,MPI_DOUBLE,0,world); - MPI_Bcast(&tangential_coeffs[i][j],3,MPI_DOUBLE,0,world); - MPI_Bcast(&roll_coeffs[i][j],3,MPI_DOUBLE,0,world); - MPI_Bcast(&twist_coeffs[i][j],3,MPI_DOUBLE,0,world); + MPI_Bcast(normal_coeffs[i][j],4,MPI_DOUBLE,0,world); + MPI_Bcast(tangential_coeffs[i][j],3,MPI_DOUBLE,0,world); + MPI_Bcast(roll_coeffs[i][j],3,MPI_DOUBLE,0,world); + MPI_Bcast(twist_coeffs[i][j],3,MPI_DOUBLE,0,world); MPI_Bcast(&cutoff_type[i][j],1,MPI_DOUBLE,0,world); } } -- GitLab From f6319146b04b04e4887fdfe44a47ebc45544d97a Mon Sep 17 00:00:00 2001 From: "Ryan S. Elliott" Date: Tue, 25 Jun 2019 15:03:24 -0500 Subject: [PATCH 105/469] Update kim_query to new interface --- src/KIM/kim_query.cpp | 24 ++++++++++++++++++++---- src/KIM/kim_query.h | 3 +-- 2 files changed, 21 insertions(+), 6 deletions(-) diff --git a/src/KIM/kim_query.cpp b/src/KIM/kim_query.cpp index e4818abc94..2bb404ec26 100644 --- a/src/KIM/kim_query.cpp +++ b/src/KIM/kim_query.cpp @@ -51,7 +51,7 @@ ------------------------------------------------------------------------- */ /* ---------------------------------------------------------------------- - Designed for use with the kim-api-2.0.2 (and newer) package + Designed for use with the kim-api-2.1.0 (and newer) package ------------------------------------------------------------------------- */ #include @@ -61,7 +61,9 @@ #include "comm.h" #include "error.h" #include "input.h" +#include "modify.h" #include "variable.h" +#include "fix_store_kim.h" #if defined(LMP_KIM_CURL) #include @@ -77,7 +79,7 @@ struct WriteBuf { size_t sizeleft; }; -static char *do_query(char *, int, char **, int, MPI_Comm); +static char *do_query(char *, char *, int, char **, int, MPI_Comm); static size_t write_callback(void *, size_t, size_t, void *); #endif @@ -90,12 +92,23 @@ void KimQuery::command(int narg, char **arg) if (narg < 2) error->all(FLERR,"Illegal kim_query command"); + // check if we had a kim_init command by finding fix STORE/KIM + // retrieve model name. + char * model_name; + + int ifix = modify->find_fix("KIM_MODEL_STORE"); + if (ifix >= 0) { + FixStoreKIM *fix_store = (FixStoreKIM *) modify->fix[ifix]; + model_name = (char *)fix_store->getptr("model_name"); + } else error->all(FLERR,"Must use 'kim_init' before 'kim_query'"); + + varname = arg[0]; function = arg[1]; #if defined(LMP_KIM_CURL) - value = do_query(function, narg-2, arg+2, comm->me, world); + value = do_query(function, model_name, narg-2, arg+2, comm->me, world); // check for valid result // on error the content of "value" is a '\0' byte @@ -147,7 +160,8 @@ size_t write_callback(void *data, size_t size, size_t nmemb, void *userp) return 0; // done } -char *do_query(char *qfunction, int narg, char **arg, int rank, MPI_Comm comm) +char *do_query(char *qfunction, char * model_name, int narg, char **arg, + int rank, MPI_Comm comm) { char value[512], *retval; @@ -173,6 +187,8 @@ char *do_query(char *qfunction, int narg, char **arg, int rank, MPI_Comm comm) url += qfunction; std::string query(arg[0]); + query += "&model="; + query += model_name; for (int i=1; i < narg; ++i) { query += '&'; query += arg[i]; diff --git a/src/KIM/kim_query.h b/src/KIM/kim_query.h index 3644e4519b..b5433def79 100644 --- a/src/KIM/kim_query.h +++ b/src/KIM/kim_query.h @@ -51,7 +51,7 @@ ------------------------------------------------------------------------- */ /* ---------------------------------------------------------------------- - Designed for use with the kim-api-2.0.2 (and newer) package + Designed for use with the kim-api-2.1.0 (and newer) package ------------------------------------------------------------------------- */ #ifdef COMMAND_CLASS @@ -71,7 +71,6 @@ class KimQuery : protected Pointers { public: KimQuery(class LAMMPS *lmp) : Pointers(lmp) {}; void command(int, char **); - }; } -- GitLab From f1dfcaf514948935724df4b0b754adecfca3cf04 Mon Sep 17 00:00:00 2001 From: Stan Moore Date: Tue, 25 Jun 2019 14:47:21 -0600 Subject: [PATCH 106/469] WIP --- src/KOKKOS/pair_snap_kokkos.h | 25 +- src/KOKKOS/pair_snap_kokkos_impl.h | 379 ++++--- src/KOKKOS/sna_kokkos.h | 51 +- src/KOKKOS/sna_kokkos_impl.h | 1465 +++++++++++++++++----------- 4 files changed, 1184 insertions(+), 736 deletions(-) diff --git a/src/KOKKOS/pair_snap_kokkos.h b/src/KOKKOS/pair_snap_kokkos.h index b2019879ed..8be0bf9afb 100644 --- a/src/KOKKOS/pair_snap_kokkos.h +++ b/src/KOKKOS/pair_snap_kokkos.h @@ -31,7 +31,10 @@ PairStyle(snap/kk/host,PairSNAPKokkos) namespace LAMMPS_NS { template -struct TagPairSNAP{}; +struct TagPairSNAPCompute{}; + +struct TagPairSNAPBeta{}; +struct TagPairSNAPBispectrum{}; template class PairSNAPKokkos : public PairSNAP { @@ -53,11 +56,17 @@ public: template KOKKOS_INLINE_FUNCTION - void operator() (TagPairSNAP,const typename Kokkos::TeamPolicy >::member_type& team) const; + void operator() (TagPairSNAPCompute,const typename Kokkos::TeamPolicy >::member_type& team) const; template KOKKOS_INLINE_FUNCTION - void operator() (TagPairSNAP,const typename Kokkos::TeamPolicy >::member_type& team, EV_FLOAT&) const; + void operator() (TagPairSNAPCompute,const typename Kokkos::TeamPolicy >::member_type& team, EV_FLOAT&) const; + + KOKKOS_INLINE_FUNCTION + void operator() (TagPairSNAPBeta,const typename Kokkos::TeamPolicy::member_type& team) const; + + KOKKOS_INLINE_FUNCTION + void operator() (TagPairSNAPBispectrum,const typename Kokkos::TeamPolicy::member_type& team) const; template KOKKOS_INLINE_FUNCTION @@ -82,10 +91,14 @@ protected: SNAKokkos snaKK; // How much parallelism to use within an interaction - int vector_length; + int vector_length,team_size; + int team_scratch_size; + int thread_scratch_size; int eflag,vflag; + void compute_beta(); + void compute_bispectrum(); void allocate(); //void read_files(char *, char *); /*template @@ -117,7 +130,9 @@ inline double dist2(double* x,double* y); Kokkos::View d_radelem; // element radii Kokkos::View d_wjelem; // elements weights Kokkos::View d_coeffelem; // element bispectrum coefficients - Kokkos::View d_map; // mapping from atom types to elements + Kokkos::View d_map; // mapping from atom types to elements + Kokkos::View d_beta; // betas for all atoms in list + Kokkos::View d_bispectrum; // bispectrum components for all atoms in list typedef Kokkos::DualView tdual_fparams; tdual_fparams k_cutsq; diff --git a/src/KOKKOS/pair_snap_kokkos_impl.h b/src/KOKKOS/pair_snap_kokkos_impl.h index 0ec4ed0995..687c9dc7cb 100644 --- a/src/KOKKOS/pair_snap_kokkos_impl.h +++ b/src/KOKKOS/pair_snap_kokkos_impl.h @@ -186,31 +186,45 @@ void PairSNAPKokkos::compute(int eflag_in, int vflag_in) snaKK.nmax = max_neighs; - T_INT team_scratch_size = snaKK.size_team_scratch_arrays(); - T_INT thread_scratch_size = snaKK.size_thread_scratch_arrays(); + team_scratch_size = snaKK.size_team_scratch_arrays(); + thread_scratch_size = snaKK.size_thread_scratch_arrays(); //printf("Sizes: %i %i\n",team_scratch_size/1024,thread_scratch_size/1024); int team_size_max = Kokkos::TeamPolicy::team_size_max(*this); - int vector_length = 8; + vector_length = 8; #ifdef KOKKOS_ENABLE_CUDA - int team_size = 32;//max_neighs; + team_size = 32;//max_neighs; if (team_size*vector_length > team_size_max) team_size = team_size_max/vector_length; #else - int team_size = 1; + team_size = 1; #endif + if (beta_max < list->inum) { // TODO: no init + d_beta = Kokkos::View("PairSNAPKokkos:beta", + list->inum,ncoeff); + d_bispectrum = Kokkos::View("PairSNAPKokkos:bispectrum", + list->inum,ncoeff); + beta_max = list->inum; + } + + // compute dE_i/dB_i = beta_i for all i in list + + if (quadraticflag || eflag) + compute_bispectrum(); + compute_beta(); + EV_FLOAT ev; if (eflag) { if (neighflag == HALF) { - typename Kokkos::TeamPolicy > policy(inum,team_size,vector_length); + typename Kokkos::TeamPolicy > policy(inum,team_size,vector_length); Kokkos::parallel_reduce(policy .set_scratch_size(1,Kokkos::PerThread(thread_scratch_size)) .set_scratch_size(1,Kokkos::PerTeam(team_scratch_size)) ,*this,ev); } else if (neighflag == HALFTHREAD) { - typename Kokkos::TeamPolicy > policy(inum,team_size,vector_length); + typename Kokkos::TeamPolicy > policy(inum,team_size,vector_length); Kokkos::parallel_reduce(policy .set_scratch_size(1,Kokkos::PerThread(thread_scratch_size)) .set_scratch_size(1,Kokkos::PerTeam(team_scratch_size)) @@ -218,13 +232,13 @@ void PairSNAPKokkos::compute(int eflag_in, int vflag_in) } } else { if (neighflag == HALF) { - typename Kokkos::TeamPolicy > policy(inum,team_size,vector_length); + typename Kokkos::TeamPolicy > policy(inum,team_size,vector_length); Kokkos::parallel_for(policy .set_scratch_size(1,Kokkos::PerThread(thread_scratch_size)) .set_scratch_size(1,Kokkos::PerTeam(team_scratch_size)) ,*this); } else if (neighflag == HALFTHREAD) { - typename Kokkos::TeamPolicy > policy(inum,team_size,vector_length); + typename Kokkos::TeamPolicy > policy(inum,team_size,vector_length); Kokkos::parallel_for(policy .set_scratch_size(1,Kokkos::PerThread(thread_scratch_size)) .set_scratch_size(1,Kokkos::PerTeam(team_scratch_size)) @@ -232,11 +246,6 @@ void PairSNAPKokkos::compute(int eflag_in, int vflag_in) } } -//static int step =0; -//step++; -//if (step%10==0) -// printf(" %e %e %e %e %e (%e %e): %e\n",t1,t2,t3,t4,t5,t6,t7,t1+t2+t3+t4+t5); - if (need_dup) Kokkos::Experimental::contribute(f, dup_f); @@ -275,6 +284,153 @@ void PairSNAPKokkos::compute(int eflag_in, int vflag_in) } } +/* ---------------------------------------------------------------------- + compute beta +------------------------------------------------------------------------- */ + +template +void PairSNAPKokkos::compute_beta() +{ + // TODO: use RangePolicy instead, or thread over ncoeff? + int inum = list->inum; + typename Kokkos::TeamPolicy policy(inum,team_size,vector_length); + Kokkos::parallel_for(policy + .set_scratch_size(1,Kokkos::PerThread(thread_scratch_size)) + .set_scratch_size(1,Kokkos::PerTeam(team_scratch_size)) + ,*this); +} + +/* ---------------------------------------------------------------------- */ + +template +KOKKOS_INLINE_FUNCTION +void PairSNAPKokkos::operator() (TagPairSNAPBeta,const typename Kokkos::TeamPolicy::member_type& team) const { + + const int ii = team.league_rank(); + const int i = d_ilist[ii]; + const int itype = type[i]; + const int ielem = map[itype]; + Kokkos::View> + d_coeffi(d_coeffelem,ielem,Kokkos::ALL); + + for (int icoeff = 0; icoeff < ncoeff; icoeff++) + d_beta(ii,icoeff) = d_coeffi[icoeff+1]; + + if (quadraticflag) { + int k = ncoeff+1; + for (int icoeff = 0; icoeff < ncoeff; icoeff++) { + double bveci = d_bispectrum(ii,icoeff); + d_beta(ii,icoeff) += d_coeffi[k]*bveci; + k++; + for (int jcoeff = icoeff+1; jcoeff < ncoeff; jcoeff++) { + double bvecj = d_bispectrum(ii,jcoeff); + d_beta(ii,icoeff) += d_coeffi[k]*bvecj; + d_beta(ii,jcoeff) += d_coeffi[k]*bveci; + k++; + } + } + } +} + +/* ---------------------------------------------------------------------- + compute bispectrum +------------------------------------------------------------------------- */ + +template +void PairSNAPKokkos::compute_bispectrum() +{ + int inum = list->inum; + typename Kokkos::TeamPolicy policy(inum,team_size,vector_length); + Kokkos::parallel_for(policy + .set_scratch_size(1,Kokkos::PerThread(thread_scratch_size)) + .set_scratch_size(1,Kokkos::PerTeam(team_scratch_size)) + ,*this); +} + +/* ---------------------------------------------------------------------- */ + +template +KOKKOS_INLINE_FUNCTION +void PairSNAPKokkos::operator() (TagPairSNAPBispectrum,const typename Kokkos::TeamPolicy::member_type& team) const { + + const int ii = team.league_rank(); + const int i = d_ilist[ii]; + SNAKokkos my_sna(snaKK,team); + const double xtmp = x(i,0); + const double ytmp = x(i,1); + const double ztmp = x(i,2); + const int itype = type[i]; + const int ielem = d_map[itype]; + const double radi = d_radelem[ielem]; + + const int num_neighs = d_numneigh[i]; + + // rij[][3] = displacements between atom I and those neighbors + // inside = indices of neighbors of I within cutoff + // wj = weights for neighbors of I within cutoff + // rcutij = cutoffs for neighbors of I within cutoff + // note Rij sign convention => dU/dRij = dU/dRj = -dU/dRi + + int ninside = 0; + Kokkos::parallel_reduce(Kokkos::TeamThreadRange(team,num_neighs), + [&] (const int jj, int& count) { + Kokkos::single(Kokkos::PerThread(team), [&] (){ + T_INT j = d_neighbors(i,jj); + const F_FLOAT dx = x(j,0) - xtmp; + const F_FLOAT dy = x(j,1) - ytmp; + const F_FLOAT dz = x(j,2) - ztmp; + + const int jtype = type(j); + const F_FLOAT rsq = dx*dx + dy*dy + dz*dz; + const int elem_j = d_map[jtype]; + + if ( rsq < rnd_cutsq(itype,jtype) ) + count++; + }); + },ninside); + + if (team.team_rank() == 0) + Kokkos::parallel_scan(Kokkos::ThreadVectorRange(team,num_neighs), + [&] (const int jj, int& offset, bool final) { + //for (int jj = 0; jj < num_neighs; jj++) { + T_INT j = d_neighbors(i,jj); + const F_FLOAT dx = x(j,0) - xtmp; + const F_FLOAT dy = x(j,1) - ytmp; + const F_FLOAT dz = x(j,2) - ztmp; + + const int jtype = type(j); + const F_FLOAT rsq = dx*dx + dy*dy + dz*dz; + const int elem_j = d_map[jtype]; + + if ( rsq < rnd_cutsq(itype,jtype) ) { + if (final) { + my_sna.rij(offset,0) = dx; + my_sna.rij(offset,1) = dy; + my_sna.rij(offset,2) = dz; + my_sna.inside[offset] = j; + my_sna.wj[offset] = d_wjelem[elem_j]; + my_sna.rcutij[offset] = (radi + d_radelem[elem_j])*rcutfac; + } + offset++; + } + }); + team.team_barrier(); + + // compute Ui, Zi, and Bi for atom I + + my_sna.compute_ui(team,ninside); + team.team_barrier(); + + my_sna.compute_zi(team); + team.team_barrier(); + + my_sna.compute_bi(team); + team.team_barrier(); + + for (int icoeff = 0; icoeff < ncoeff; icoeff++) + d_bispectrum(ii,icoeff) = my_sna.blist[icoeff]; +} + /* ---------------------------------------------------------------------- allocate all arrays ------------------------------------------------------------------------- */ @@ -354,7 +510,7 @@ void PairSNAPKokkos::coeff(int narg, char **arg) template template KOKKOS_INLINE_FUNCTION -void PairSNAPKokkos::operator() (TagPairSNAP,const typename Kokkos::TeamPolicy >::member_type& team, EV_FLOAT& ev) const { +void PairSNAPKokkos::operator() (TagPairSNAPCompute,const typename Kokkos::TeamPolicy >::member_type& team, EV_FLOAT& ev) const { // The f array is duplicated for OpenMP, atomic for CUDA, and neither for Serial @@ -364,12 +520,12 @@ void PairSNAPKokkos::operator() (TagPairSNAP,const const int ii = team.league_rank(); const int i = d_ilist[ii]; SNAKokkos my_sna(snaKK,team); - const double x_i = x(i,0); - const double y_i = x(i,1); - const double z_i = x(i,2); - const int type_i = type[i]; - const int elem_i = d_map[type_i]; - const double radi = d_radelem[elem_i]; + const double xtmp = x(i,0); + const double ytmp = x(i,1); + const double ztmp = x(i,2); + const int itype = type[i]; + const int ielem = d_map[itype]; + const double radi = d_radelem[ielem]; const int num_neighs = d_numneigh[i]; @@ -379,41 +535,38 @@ void PairSNAPKokkos::operator() (TagPairSNAP,const // rcutij = cutoffs for neighbors of I within cutoff // note Rij sign convention => dU/dRij = dU/dRj = -dU/dRi - //Kokkos::Timer timer; int ninside = 0; Kokkos::parallel_reduce(Kokkos::TeamThreadRange(team,num_neighs), [&] (const int jj, int& count) { Kokkos::single(Kokkos::PerThread(team), [&] (){ T_INT j = d_neighbors(i,jj); - const F_FLOAT dx = x(j,0) - x_i; - const F_FLOAT dy = x(j,1) - y_i; - const F_FLOAT dz = x(j,2) - z_i; + const F_FLOAT dx = x(j,0) - xtmp; + const F_FLOAT dy = x(j,1) - ytmp; + const F_FLOAT dz = x(j,2) - ztmp; - const int type_j = type(j); + const int jtype = type(j); const F_FLOAT rsq = dx*dx + dy*dy + dz*dz; - const int elem_j = d_map[type_j]; + const int elem_j = d_map[jtype]; - if ( rsq < rnd_cutsq(type_i,type_j) ) + if ( rsq < rnd_cutsq(itype,jtype) ) count++; }); },ninside); - //t1 += timer.seconds(); timer.reset(); - if (team.team_rank() == 0) Kokkos::parallel_scan(Kokkos::ThreadVectorRange(team,num_neighs), - [&] (const int jj, int& offset, bool final){ + [&] (const int jj, int& offset, bool final) { //for (int jj = 0; jj < num_neighs; jj++) { T_INT j = d_neighbors(i,jj); - const F_FLOAT dx = x(j,0) - x_i; - const F_FLOAT dy = x(j,1) - y_i; - const F_FLOAT dz = x(j,2) - z_i; + const F_FLOAT dx = x(j,0) - xtmp; + const F_FLOAT dy = x(j,1) - ytmp; + const F_FLOAT dz = x(j,2) - ztmp; - const int type_j = type(j); + const int jtype = type(j); const F_FLOAT rsq = dx*dx + dy*dy + dz*dz; - const int elem_j = d_map[type_j]; + const int elem_j = d_map[jtype]; - if ( rsq < rnd_cutsq(type_i,type_j) ) { + if ( rsq < rnd_cutsq(itype,jtype) ) { if (final) { my_sna.rij(offset,0) = dx; my_sna.rij(offset,1) = dy; @@ -425,157 +578,85 @@ void PairSNAPKokkos::operator() (TagPairSNAP,const offset++; } }); + team.team_barrier(); - //t2 += timer.seconds(); timer.reset(); + // compute Ui, Yi for atom I - team.team_barrier(); - // compute Ui, Zi, and Bi for atom I my_sna.compute_ui(team,ninside); - //t3 += timer.seconds(); timer.reset(); team.team_barrier(); - my_sna.compute_zi(team); - //t4 += timer.seconds(); timer.reset(); - team.team_barrier(); - - if (quadraticflag) { - my_sna.compute_bi(team); - team.team_barrier(); - my_sna.copy_bi2bvec(team); - team.team_barrier(); - } // for neighbors of I within cutoff: - // compute dUi/drj and dBi/drj - // Fij = dEi/dRj = -dEi/dRi => add to Fi, subtract from Fj + // compute Fij = dEi/dRj = -dEi/dRi + // add to Fi, subtract from Fj + + my_sna.compute_yi(team,d_beta,ii); + team.team_barrier(); Kokkos::View> - d_coeffi(d_coeffelem,elem_i,Kokkos::ALL); + d_coeffi(d_coeffelem,ielem,Kokkos::ALL); Kokkos::parallel_for (Kokkos::TeamThreadRange(team,ninside), [&] (const int jj) { //for (int jj = 0; jj < ninside; jj++) { int j = my_sna.inside[jj]; - //Kokkos::Timer timer2; my_sna.compute_duidrj(team,&my_sna.rij(jj,0), my_sna.wj[jj],my_sna.rcutij[jj]); - //t6 += timer2.seconds(); timer2.reset(); - my_sna.compute_dbidrj(team); - //t7 += timer2.seconds(); timer2.reset(); - my_sna.copy_dbi2dbvec(team); Kokkos::single(Kokkos::PerThread(team), [&] (){ - F_FLOAT fij[3]; - - fij[0] = 0.0; - fij[1] = 0.0; - fij[2] = 0.0; - // linear contributions - - for (int k = 1; k <= ncoeff; k++) { - double bgb = d_coeffi[k]; - fij[0] += bgb*my_sna.dbvec(k-1,0); - fij[1] += bgb*my_sna.dbvec(k-1,1); - fij[2] += bgb*my_sna.dbvec(k-1,2); - } - - if (quadraticflag) { - - int k = ncoeff+1; - for (int icoeff = 0; icoeff < ncoeff; icoeff++) { - double bveci = my_sna.bvec[icoeff]; - double fack = d_coeffi[k]*bveci; - double dbvecix = my_sna.dbvec(icoeff,0); - double dbveciy = my_sna.dbvec(icoeff,1); - double dbveciz = my_sna.dbvec(icoeff,2); - fij[0] += fack*dbvecix; - fij[1] += fack*dbveciy; - fij[2] += fack*dbveciz; - k++; - for (int jcoeff = icoeff+1; jcoeff < ncoeff; jcoeff++) { - double facki = d_coeffi[k]*bveci; - double fackj = d_coeffi[k]*my_sna.bvec[jcoeff]; - fij[0] += facki*my_sna.dbvec(jcoeff,0)+fackj*dbvecix; - fij[1] += facki*my_sna.dbvec(jcoeff,1)+fackj*dbveciy; - fij[2] += facki*my_sna.dbvec(jcoeff,2)+fackj*dbveciz; - k++; + F_FLOAT fij[3]; + my_sna.compute_deidrj(team,fij); + + a_f(i,0) += fij[0]; + a_f(i,1) += fij[1]; + a_f(i,2) += fij[2]; + a_f(j,0) -= fij[0]; + a_f(j,1) -= fij[1]; + a_f(j,2) -= fij[2]; + + // tally global and per-atom virial contribution + + if (EVFLAG) { + if (vflag_either) { + v_tally_xyz(ev,i,j, + fij[0],fij[1],fij[2], + -my_sna.rij(jj,0),-my_sna.rij(jj,1), + -my_sna.rij(jj,2)); } } - } - - // Hard-coded ZBL potential - //const double dx = my_sna.rij(jj,0); - //const double dy = my_sna.rij(jj,1); - //const double dz = my_sna.rij(jj,2); - //const double fdivr = -1.5e6/pow(dx*dx + dy*dy + dz*dz,7.0); - //fij[0] += dx*fdivr; - //fij[1] += dy*fdivr; - //fij[2] += dz*fdivr; - - //OK - //printf("%lf %lf %lf %lf %lf %lf %lf %lf %lf SNAP-COMPARE: FIJ\n" - // ,x(i,0),x(i,1),x(i,2),x(j,0),x(j,1),x(j,2),fij[0],fij[1],fij[2] ); - a_f(i,0) += fij[0]; - a_f(i,1) += fij[1]; - a_f(i,2) += fij[2]; - a_f(j,0) -= fij[0]; - a_f(j,1) -= fij[1]; - a_f(j,2) -= fij[2]; - - // tally global and per-atom virial contribution - - if (EVFLAG) { - if (vflag_either) { - v_tally_xyz(ev,i,j, - fij[0],fij[1],fij[2], - -my_sna.rij(jj,0),-my_sna.rij(jj,1), - -my_sna.rij(jj,2)); - } - } - + }); }); - //t5 += timer.seconds(); timer.reset(); // tally energy contribution if (EVFLAG) { if (eflag_either) { - if (!quadraticflag) { - my_sna.compute_bi(team); - team.team_barrier(); - my_sna.copy_bi2bvec(team); - team.team_barrier(); - } - - // E = beta.B + 0.5*B^t.alpha.B - // coeff[k] = beta[k-1] or - // coeff[k] = alpha_ii or - // coeff[k] = alpha_ij = alpha_ji, j != i - Kokkos::single(Kokkos::PerTeam(team), [&] () { // evdwl = energy of atom I, sum over coeffs_k * Bi_k double evdwl = d_coeffi[0]; - + + // E = beta.B + 0.5*B^t.alpha.B + // linear contributions - // could use thread vector range on this loop - - for (int k = 1; k <= ncoeff; k++) - evdwl += d_coeffi[k]*my_sna.bvec[k-1]; - + + for (int icoeff = 0; icoeff < ncoeff; icoeff++) + evdwl += d_coeffi[icoeff+1]*d_bispectrum(ii,icoeff); + // quadratic contributions - + if (quadraticflag) { int k = ncoeff+1; for (int icoeff = 0; icoeff < ncoeff; icoeff++) { - double bveci = my_sna.bvec[icoeff]; + double bveci = d_bispectrum(ii,icoeff); evdwl += 0.5*d_coeffi[k++]*bveci*bveci; for (int jcoeff = icoeff+1; jcoeff < ncoeff; jcoeff++) { - evdwl += d_coeffi[k++]*bveci*my_sna.bvec[jcoeff]; + double bvecj = d_bispectrum(ii,jcoeff); + evdwl += d_coeffi[k++]*bveci*bvecj; } } } @@ -591,9 +672,9 @@ void PairSNAPKokkos::operator() (TagPairSNAP,const template template KOKKOS_INLINE_FUNCTION -void PairSNAPKokkos::operator() (TagPairSNAP,const typename Kokkos::TeamPolicy >::member_type& team) const { +void PairSNAPKokkos::operator() (TagPairSNAPCompute,const typename Kokkos::TeamPolicy >::member_type& team) const { EV_FLOAT ev; - this->template operator()(TagPairSNAP(), team, ev); + this->template operator()(TagPairSNAPCompute(), team, ev); } /* ---------------------------------------------------------------------- */ diff --git a/src/KOKKOS/sna_kokkos.h b/src/KOKKOS/sna_kokkos.h index 40e5fe0ad4..ff2541dca3 100644 --- a/src/KOKKOS/sna_kokkos.h +++ b/src/KOKKOS/sna_kokkos.h @@ -25,7 +25,11 @@ namespace LAMMPS_NS { -struct SNAKK_LOOPINDICES { +struct SNAKK_ZINDICES { + int j1, j2, j, ma1min, ma2max, mb1min, mb2max, na, nb, jju; +}; + +struct SNAKK_BINDICES { int j1, j2, j; }; @@ -35,9 +39,9 @@ class SNAKokkos { public: typedef Kokkos::View t_sna_1i; typedef Kokkos::View t_sna_1d; + typedef Kokkos::View > t_sna_1d_atomic; typedef Kokkos::View t_sna_2d; typedef Kokkos::View t_sna_3d; - typedef Kokkos::View > t_sna_3d_atomic; typedef Kokkos::View t_sna_4d; typedef Kokkos::View t_sna_3d3; typedef Kokkos::View t_sna_5d; @@ -76,9 +80,10 @@ inline KOKKOS_INLINE_FUNCTION void compute_zi(const typename Kokkos::TeamPolicy::member_type& team); // ForceSNAP KOKKOS_INLINE_FUNCTION - void compute_bi(const typename Kokkos::TeamPolicy::member_type& team); // ForceSNAP + void compute_yi(const typename Kokkos::TeamPolicy::member_type& team, + const Kokkos::View &beta, const int ii); // ForceSNAP KOKKOS_INLINE_FUNCTION - void copy_bi2bvec(const typename Kokkos::TeamPolicy::member_type& team); //ForceSNAP + void compute_bi(const typename Kokkos::TeamPolicy::member_type& team); // ForceSNAP // functions for derivatives @@ -87,7 +92,7 @@ inline KOKKOS_INLINE_FUNCTION void compute_dbidrj(const typename Kokkos::TeamPolicy::member_type& team); //ForceSNAP KOKKOS_INLINE_FUNCTION - void copy_dbi2dbvec(const typename Kokkos::TeamPolicy::member_type& team); //ForceSNAP + void compute_deidrj(const typename Kokkos::TeamPolicy::member_type& team, double *); // ForceSNAP KOKKOS_INLINE_FUNCTION double compute_sfac(double, double); // add_uarraytot, compute_duarray KOKKOS_INLINE_FUNCTION @@ -114,37 +119,41 @@ inline int twojmax, diagonalstyle; // Per InFlight Particle - t_sna_3d barray; - t_sna_3d uarraytot_r, uarraytot_i; - t_sna_3d_atomic uarraytot_r_a, uarraytot_i_a; - t_sna_5d zarray_r, zarray_i; + t_sna_1d blist; + t_sna_1d ulisttot_r, ulisttot_i; + t_sna_1d_atomic ulisttot_r_a, ulisttot_i_a; + t_sna_1d zlist_r, zlist_i; // Per InFlight Interaction - t_sna_3d uarray_r, uarray_i; - - Kokkos::View bvec; + t_sna_1d ulist_r, ulist_i; + t_sna_1d ylist_r, ylist_i; // derivatives of data - Kokkos::View dbvec; - t_sna_4d duarray_r, duarray_i; - t_sna_4d dbarray; + t_sna_2d dulist_r, dulist_i; + t_sna_2d dblist; private: double rmin0, rfac0; //use indexlist instead of loops, constructor generates these - // Same accross all SNAKokkos - Kokkos::View idxj,idxj_full; - int idxj_max,idxj_full_max; + // Same across all SNAKokkos + Kokkos::View idxz; + Kokkos::View idxb; + int idxcg_max, idxu_max, idxz_max, idxb_max; + Kokkos::View idxcg_block; + Kokkos::View idxu_block; + Kokkos::View idxz_block; + Kokkos::View idxb_block; + // data for bispectrum coefficients // Same accross all SNAKokkos - t_sna_5d cgarray; + t_sna_1d cglist; t_sna_2d rootpqarray; - static const int nmaxfactorial = 167; - KOKKOS_INLINE_FUNCTION + static const double nfac_table[]; + inline double factorial(int); KOKKOS_INLINE_FUNCTION diff --git a/src/KOKKOS/sna_kokkos_impl.h b/src/KOKKOS/sna_kokkos_impl.h index c43003af97..4ca8ae4471 100644 --- a/src/KOKKOS/sna_kokkos_impl.h +++ b/src/KOKKOS/sna_kokkos_impl.h @@ -47,13 +47,13 @@ SNAKokkos::SNAKokkos(double rfac0_in, build_indexlist(); - int jdim = twojmax + 1; + int jdimpq = twojmax + 2; + rootpqarray = t_sna_2d("SNAKokkos::rootpqarray",jdimpq,jdimpq); - cgarray = t_sna_5d("SNAKokkos::cgarray",jdim,jdim,jdim,jdim,jdim); - rootpqarray = t_sna_2d("SNAKokkos::rootpqarray",jdim+1,jdim+1); + cglist = t_sna_1d("SNAKokkos::cglist",idxcg_max); if (bzero_flag) { - bzero = Kokkos::View("sna:bzero",jdim); + bzero = Kokkos::View("sna:bzero",twojmax+1); auto h_bzero = Kokkos::create_mirror_view(bzero); double www = wself*wself*wself; @@ -77,11 +77,17 @@ SNAKokkos::SNAKokkos(const SNAKokkos& sna, const typenam ncoeff = sna.ncoeff; nmax = sna.nmax; - idxj = sna.idxj; - idxj_max = sna.idxj_max; - idxj_full = sna.idxj_full; - idxj_full_max = sna.idxj_full_max; - cgarray = sna.cgarray; + idxz = sna.idxz; + idxb = sna.idxb; + idxcg_max = sna.idxcg_max; + idxu_max = sna.idxu_max; + idxz_max = sna.idxz_max; + idxb_max = sna.idxb_max; + idxcg_block = sna.idxcg_block; + idxu_block = sna.idxu_block; + idxz_block = sna.idxz_block; + idxb_block = sna.idxb_block; + cglist = sna.cglist; rootpqarray = sna.rootpqarray; bzero = sna.bzero; create_team_scratch_arrays(team); @@ -100,47 +106,133 @@ template inline void SNAKokkos::build_indexlist() { - int idxj_count = 0; - int idxj_full_count = 0; + // index list for cglist + + int jdim = twojmax + 1; + idxcg_block = Kokkos::View("SNAKokkos::idxcg_block",jdim,jdim,jdim); + auto h_idxcg_block = Kokkos::create_mirror_view(idxcg_block); + int idxcg_count = 0; for(int j1 = 0; j1 <= twojmax; j1++) for(int j2 = 0; j2 <= j1; j2++) - for(int j = abs(j1 - j2); j <= MIN(twojmax, j1 + j2); j += 2) { - if (j >= j1) idxj_count++; - idxj_full_count++; + for(int j = j1 - j2; j <= MIN(twojmax, j1 + j2); j += 2) { + h_idxcg_block(j1,j2,j) = idxcg_count; + for (int m1 = 0; m1 <= j1; m1++) + for (int m2 = 0; m2 <= j2; m2++) + idxcg_count++; } + idxcg_max = idxcg_count; + Kokkos::deep_copy(idxcg_block,h_idxcg_block); + + // index list for uarray + // need to include both halves + + idxu_block = Kokkos::View("SNAKokkos::idxu_block",jdim); + auto h_idxu_block = Kokkos::create_mirror_view(idxu_block); + + int idxu_count = 0; + + for(int j = 0; j <= twojmax; j++) { + h_idxu_block[j] = idxu_count; + for(int mb = 0; mb <= j; mb++) + for(int ma = 0; ma <= j; ma++) + idxu_count++; + } + idxu_max = idxu_count; + Kokkos::deep_copy(idxu_block,h_idxu_block); - // indexList can be changed here + // index list for beta and B - idxj = Kokkos::View("SNAKokkos::idxj",idxj_count); - idxj_full = Kokkos::View("SNAKokkos::idxj_full",idxj_full_count); - auto h_idxj = Kokkos::create_mirror_view(idxj); - auto h_idxj_full = Kokkos::create_mirror_view(idxj_full); + int idxb_count = 0; + for(int j1 = 0; j1 <= twojmax; j1++) + for(int j2 = 0; j2 <= j1; j2++) + for(int j = j1 - j2; j <= MIN(twojmax, j1 + j2); j += 2) + if (j >= j1) idxb_count++; + + idxb_max = idxb_count; + idxb = Kokkos::View("SNAKokkos::idxb",idxb_max); + auto h_idxb = Kokkos::create_mirror_view(idxb); + + idxb_count = 0; + for(int j1 = 0; j1 <= twojmax; j1++) + for(int j2 = 0; j2 <= j1; j2++) + for(int j = j1 - j2; j <= MIN(twojmax, j1 + j2); j += 2) + if (j >= j1) { + h_idxb[idxb_count].j1 = j1; + h_idxb[idxb_count].j2 = j2; + h_idxb[idxb_count].j = j; + idxb_count++; + } + Kokkos::deep_copy(idxb,h_idxb); - idxj_max = idxj_count; - idxj_full_max = idxj_full_count; + // reverse index list for beta and b - idxj_count = 0; - idxj_full_count = 0; + idxb_block = Kokkos::View("SNAKokkos::idxb_block",jdim,jdim,jdim); + auto h_idxb_block = Kokkos::create_mirror_view(idxb_block); + idxb_count = 0; for(int j1 = 0; j1 <= twojmax; j1++) for(int j2 = 0; j2 <= j1; j2++) - for(int j = abs(j1 - j2); j <= MIN(twojmax, j1 + j2); j += 2) { - if (j >= j1) { - h_idxj[idxj_count].j1 = j1; - h_idxj[idxj_count].j2 = j2; - h_idxj[idxj_count].j = j; - idxj_count++; - } - h_idxj_full[idxj_full_count].j1 = j1; - h_idxj_full[idxj_full_count].j2 = j2; - h_idxj_full[idxj_full_count].j = j; - idxj_full_count++; + for(int j = j1 - j2; j <= MIN(twojmax, j1 + j2); j += 2) { + if (j >= j1) { + h_idxb_block(j1,j2,j) = idxb_count; + idxb_count++; + } } - Kokkos::deep_copy(idxj,h_idxj); - Kokkos::deep_copy(idxj_full,h_idxj_full); + Kokkos::deep_copy(idxb_block,h_idxb_block); + + // index list for zlist + int idxz_count = 0; + + for(int j1 = 0; j1 <= twojmax; j1++) + for(int j2 = 0; j2 <= j1; j2++) + for(int j = j1 - j2; j <= MIN(twojmax, j1 + j2); j += 2) + for (int mb = 0; 2*mb <= j; mb++) + for (int ma = 0; ma <= j; ma++) + idxz_count++; + + idxz_max = idxz_count; + idxz = Kokkos::View("SNAKokkos::idxz",idxz_max); + auto h_idxz = Kokkos::create_mirror_view(idxz); + + idxz_block = Kokkos::View("SNAKokkos::idxz_block", jdim,jdim,jdim); + auto h_idxz_block = Kokkos::create_mirror_view(idxz_block); + + idxz_count = 0; + for(int j1 = 0; j1 <= twojmax; j1++) + for(int j2 = 0; j2 <= j1; j2++) + for(int j = j1 - j2; j <= MIN(twojmax, j1 + j2); j += 2) { + h_idxz_block(j1,j2,j) = idxz_count; + + // find right beta(ii,jjb) entry + // multiply and divide by j+1 factors + // account for multiplicity of 1, 2, or 3 + + for (int mb = 0; 2*mb <= j; mb++) + for (int ma = 0; ma <= j; ma++) { + h_idxz[idxz_count].j1 = j1; + h_idxz[idxz_count].j2 = j2; + h_idxz[idxz_count].j = j; + h_idxz[idxz_count].ma1min = MAX(0, (2 * ma - j - j2 + j1) / 2); + h_idxz[idxz_count].ma2max = (2 * ma - j - (2 * h_idxz[idxz_count].ma1min - j1) + j2) / 2; + h_idxz[idxz_count].na = MIN(j1, (2 * ma - j + j2 + j1) / 2) - h_idxz[idxz_count].ma1min + 1; + h_idxz[idxz_count].mb1min = MAX(0, (2 * mb - j - j2 + j1) / 2); + h_idxz[idxz_count].mb2max = (2 * mb - j - (2 * h_idxz[idxz_count].mb1min - j1) + j2) / 2; + h_idxz[idxz_count].nb = MIN(j1, (2 * mb - j + j2 + j1) / 2) - h_idxz[idxz_count].mb1min + 1; + + // apply to z(j1,j2,j,ma,mb) to unique element of y(j) + + const int jju = idxu_block[j] + (j+1)*mb + ma; + h_idxz[idxz_count].jju = jju; + + idxz_count++; + } + } + Kokkos::deep_copy(idxz,h_idxz); + Kokkos::deep_copy(idxz_block,h_idxz_block); } + /* ---------------------------------------------------------------------- */ template @@ -166,6 +258,7 @@ template KOKKOS_INLINE_FUNCTION void SNAKokkos::compute_ui(const typename Kokkos::TeamPolicy::member_type& team, int jnum) { + //printf("jnum %i\n",jnum); double rsq, r, x, y, z, z0, theta0; // utot(j,ma,mb) = 0 for all j,ma,ma @@ -211,93 +304,234 @@ template KOKKOS_INLINE_FUNCTION void SNAKokkos::compute_zi(const typename Kokkos::TeamPolicy::member_type& team) { - // for j1 = 0,...,twojmax - // for j2 = 0,twojmax - // for j = |j1-j2|,Min(twojmax,j1+j2),2 - // for ma = 0,...,j - // for mb = 0,...,jmid - // z(j1,j2,j,ma,mb) = 0 - // for ma1 = Max(0,ma+(j1-j2-j)/2),Min(j1,ma+(j1+j2-j)/2) - // sumb1 = 0 - // ma2 = ma-ma1+(j1+j2-j)/2; - // for mb1 = Max(0,mb+(j1-j2-j)/2),Min(j1,mb+(j1+j2-j)/2) - // mb2 = mb-mb1+(j1+j2-j)/2; - // sumb1 += cg(j1,mb1,j2,mb2,j) * - // u(j1,ma1,mb1) * u(j2,ma2,mb2) - // z(j1,j2,j,ma,mb) += sumb1*cg(j1,ma1,j2,ma2,j) - -#ifdef TIMING_INFO - clock_gettime(CLOCK_REALTIME, &starttime); -#endif - - // compute_dbidrj() requires full j1/j2/j chunk of z elements - // use zarray j1/j2 symmetry - - Kokkos::parallel_for(Kokkos::TeamThreadRange(team,idxj_full_max), - [&] (const int& idx) { - const int j1 = idxj_full(idx).j1; - const int j2 = idxj_full(idx).j2; - const int j = idxj_full(idx).j; + Kokkos::parallel_for(Kokkos::TeamThreadRange(team,idxz_max), + [&] (const int& jjz) { + //for(int jjz = 0; jjz < idxz_max; jjz++) { + const int j1 = idxz[jjz].j1; + const int j2 = idxz[jjz].j2; + const int j = idxz[jjz].j; + const int ma1min = idxz[jjz].ma1min; + const int ma2max = idxz[jjz].ma2max; + const int na = idxz[jjz].na; + const int mb1min = idxz[jjz].mb1min; + const int mb2max = idxz[jjz].mb2max; + const int nb = idxz[jjz].nb; + + const double* cgblock = cglist.data() + idxcg_block(j1,j2,j); + + zlist_r[jjz] = 0.0; + zlist_i[jjz] = 0.0; + + int jju1 = idxu_block[j1] + (j1+1)*mb1min; + int jju2 = idxu_block[j2] + (j2+1)*mb2max; + int icgb = mb1min*(j2+1) + mb2max; + for(int ib = 0; ib < nb; ib++) { + + double suma1_r = 0.0; + double suma1_i = 0.0; + + const double* u1_r = ulisttot_r.data() + jju1; + const double* u1_i = ulisttot_i.data() + jju1; + const double* u2_r = ulisttot_r.data() + jju2; + const double* u2_i = ulisttot_i.data() + jju2; + + int ma1 = ma1min; + int ma2 = ma2max; + int icga = ma1min*(j2+1) + ma2max; + for(int ia = 0; ia < na; ia++) { + suma1_r += cgblock[icga] * (u1_r[ma1] * u2_r[ma2] - u1_i[ma1] * u2_i[ma2]); + suma1_i += cgblock[icga] * (u1_r[ma1] * u2_i[ma2] + u1_i[ma1] * u2_r[ma2]); + ma1++; + ma2--; + icga += j2; + } // end loop over ia + + zlist_r[jjz] += cgblock[icgb] * suma1_r; + zlist_i[jjz] += cgblock[icgb] * suma1_i; + //printf("%i %i %i %g %g\n",j1,j2,j,cgblock[icgb],suma1_r); + jju1 += j1+1; + jju2 -= j2+1; + icgb += j2; + } // end loop over ib + + }); // end loop over jjz +} - const int bound = (j+2)/2; - Kokkos::parallel_for(Kokkos::ThreadVectorRange(team,(j+1)*bound), - [&] (const int mbma ) { - //for(int mb = 0; 2*mb <= j; mb++) - //for(int ma = 0; ma <= j; ma++) { - const int ma = mbma%(j+1); - const int mb = mbma/(j+1); - - //zarray_r(j1,j2,j,ma,mb) = 0.0; - //zarray_i(j1,j2,j,ma,mb) = 0.0; - double z_r = 0.0; - double z_i = 0.0; - - for(int ma1 = MAX(0, (2 * ma - j - j2 + j1) / 2); - ma1 <= MIN(j1, (2 * ma - j + j2 + j1) / 2); ma1++) { - double sumb1_r = 0.0; - double sumb1_i = 0.0; - - const int ma2 = (2 * ma - j - (2 * ma1 - j1) + j2) / 2; - - for(int mb1 = MAX( 0, (2 * mb - j - j2 + j1) / 2); - mb1 <= MIN(j1, (2 * mb - j + j2 + j1) / 2); mb1++) { - - const int mb2 = (2 * mb - j - (2 * mb1 - j1) + j2) / 2; - const double cga = cgarray(j1,j2,j,mb1,mb2); - const double uat1_r = uarraytot_r(j1,ma1,mb1); - const double uat1_i = uarraytot_i(j1,ma1,mb1); - const double uat2_r = uarraytot_r(j2,ma2,mb2); - const double uat2_i = uarraytot_i(j2,ma2,mb2); - sumb1_r += cga * (uat1_r * uat2_r - uat1_i * uat2_i); - sumb1_i += cga * (uat1_r * uat2_i + uat1_i * uat2_r); - /*sumb1_r += cgarray(j1,j2,j,mb1,mb2) * - (uarraytot_r(j1,ma1,mb1) * uarraytot_r(j2,ma2,mb2) - - uarraytot_i(j1,ma1,mb1) * uarraytot_i(j2,ma2,mb2)); - sumb1_i += cgarray(j1,j2,j,mb1,mb2) * - (uarraytot_r(j1,ma1,mb1) * uarraytot_i(j2,ma2,mb2) + - uarraytot_i(j1,ma1,mb1) * uarraytot_r(j2,ma2,mb2));*/ - } // end loop over mb1 - - const double cga = cgarray(j1,j2,j,ma1,ma2); - z_r += sumb1_r * cga;//rray(j1,j2,j,ma1,ma2); - z_i += sumb1_i * cga;//rray(j1,j2,j,ma1,ma2); - } // end loop over ma1 - zarray_r(j1,j2,j,mb,ma) = z_r; - zarray_i(j1,j2,j,mb,ma) = z_i; - }); // end loop over ma, mb - // } - //} - }); - //} // end loop over j - //} // end loop over j1, j2 +/* ---------------------------------------------------------------------- + compute Yi from Ui without storing Zi, looping over zlist indices +------------------------------------------------------------------------- */ + +template +KOKKOS_INLINE_FUNCTION +void SNAKokkos::compute_yi(const typename Kokkos::TeamPolicy::member_type& team, + const Kokkos::View &beta, const int ii) +{ + int j; + int jjz; + int jju; + double betaj; + + { + double* const ptr = ylist_r.data(); + Kokkos::parallel_for(Kokkos::TeamThreadRange(team,ylist_r.span()), + [&] (const int& i) { + ptr[i] = 0.0; + }); + } + { + double* const ptr = ylist_i.data(); + Kokkos::parallel_for(Kokkos::TeamThreadRange(team,ylist_i.span()), + [&] (const int& i) { + ptr[i] = 0.0; + }); + } + + Kokkos::parallel_for(Kokkos::TeamThreadRange(team,idxz_max), + [&] (const int& jjz) { + //for(int jjz = 0; jjz < idxz_max; jjz++) { + const int j1 = idxz[jjz].j1; + const int j2 = idxz[jjz].j2; + const int j = idxz[jjz].j; + const int ma1min = idxz[jjz].ma1min; + const int ma2max = idxz[jjz].ma2max; + const int na = idxz[jjz].na; + const int mb1min = idxz[jjz].mb1min; + const int mb2max = idxz[jjz].mb2max; + const int nb = idxz[jjz].nb; + + const double* cgblock = cglist.data() + idxcg_block(j1,j2,j); + int mb = (2 * (mb1min+mb2max) - j1 - j2 + j) / 2; + int ma = (2 * (ma1min+ma2max) - j1 - j2 + j) / 2; + + double ztmp_r = 0.0; + double ztmp_i = 0.0; + + int jju1 = idxu_block[j1] + (j1+1)*mb1min; + int jju2 = idxu_block[j2] + (j2+1)*mb2max; + int icgb = mb1min*(j2+1) + mb2max; + for(int ib = 0; ib < nb; ib++) { + + double suma1_r = 0.0; + double suma1_i = 0.0; + + const double* u1_r = ulisttot_r.data() + jju1; + const double* u1_i = ulisttot_i.data() + jju1; + const double* u2_r = ulisttot_r.data() + jju2; + const double* u2_i = ulisttot_i.data() + jju2; + + int ma1 = ma1min; + int ma2 = ma2max; + int icga = ma1min*(j2+1) + ma2max; + + for(int ia = 0; ia < na; ia++) { + suma1_r += cgblock[icga] * (u1_r[ma1] * u2_r[ma2] - u1_i[ma1] * u2_i[ma2]); + suma1_i += cgblock[icga] * (u1_r[ma1] * u2_i[ma2] + u1_i[ma1] * u2_r[ma2]); ma1++; + ma2--; + icga += j2; + } // end loop over ia + + ztmp_r += cgblock[icgb] * suma1_r; + ztmp_i += cgblock[icgb] * suma1_i; + jju1 += j1+1; + jju2 -= j2+1; + icgb += j2; + } // end loop over ib + + // apply to z(j1,j2,j,ma,mb) to unique element of y(j) + // find right y_list[jju] and beta(ii,jjb) entries + // multiply and divide by j+1 factors + // account for multiplicity of 1, 2, or 3 + + const int jju = idxz[jjz].jju; + + // pick out right beta value + + if (j >= j1) { + const int jjb = idxb_block(j1,j2,j); + if (j1 == j) { + if (j2 == j) betaj = 3*beta(ii,jjb); + else betaj = 2*beta(ii,jjb); + } else betaj = beta(ii,jjb); + } else if (j >= j2) { + const int jjb = idxb_block(j,j2,j1); + if (j2 == j) betaj = 2*beta(ii,jjb)*(j1+1)/(j+1.0); + else betaj = beta(ii,jjb)*(j1+1)/(j+1.0); + } else { + const int jjb = idxb_block(j2,j,j1); + betaj = beta(ii,jjb)*(j1+1)/(j+1.0); + } + + ylist_r[jju] += betaj*ztmp_r; + ylist_i[jju] += betaj*ztmp_i; + //printf("yi %i %g %g\n",jju,ylist_r[jju],ylist_i[jju]); -#ifdef TIMING_INFO - clock_gettime(CLOCK_REALTIME, &endtime); - timers[1] += (endtime.tv_sec - starttime.tv_sec + 1.0 * - (endtime.tv_nsec - starttime.tv_nsec) / 1000000000); -#endif + }); // end loop over jjz } +/* ---------------------------------------------------------------------- + compute dEidRj +------------------------------------------------------------------------- */ + +template +KOKKOS_INLINE_FUNCTION +void SNAKokkos::compute_deidrj(const typename Kokkos::TeamPolicy::member_type& team, double* dedr) +{ + + for(int k = 0; k < 3; k++) + dedr[k] = 0.0; + + // TODO: which loop is faster to parallelize? + Kokkos::parallel_for(Kokkos::ThreadVectorRange(team,twojmax+1), + [&] (const int& j) { + //for(int j = 0; j <= twojmax; j++) { + int jju = idxu_block[j]; + + for(int mb = 0; 2*mb < j; mb++) + for(int ma = 0; ma <= j; ma++) { + + double jjjmambyarray_r = ylist_r[jju]; + double jjjmambyarray_i = ylist_i[jju]; + + for(int k = 0; k < 3; k++) + dedr[k] += + dulist_r(jju,k) * jjjmambyarray_r + + dulist_i(jju,k) * jjjmambyarray_i; + jju++; + } //end loop over ma mb + + // For j even, handle middle column + + if (j%2 == 0) { + + int mb = j/2; + for(int ma = 0; ma < mb; ma++) { + double jjjmambyarray_r = ylist_r[jju]; + double jjjmambyarray_i = ylist_i[jju]; + + for(int k = 0; k < 3; k++) + dedr[k] += + dulist_r(jju,k) * jjjmambyarray_r + + dulist_i(jju,k) * jjjmambyarray_i; + jju++; + } + + int ma = mb; + double jjjmambyarray_r = ylist_r[jju]; + double jjjmambyarray_i = ylist_i[jju]; + + for(int k = 0; k < 3; k++) + dedr[k] += + (dulist_r(jju,k) * jjjmambyarray_r + + dulist_i(jju,k) * jjjmambyarray_i)*0.5; + } // end if jeven + + }); // end loop over j + + for(int k = 0; k < 3; k++) + dedr[k] *= 2.0; + + //printf("dedr %g %g %g\n",dedr[0],dedr[1],dedr[2]); +} /* ---------------------------------------------------------------------- compute Bi by summing conj(Ui)*Zi @@ -316,31 +550,33 @@ void SNAKokkos::compute_bi(const typename Kokkos::TeamPolicy::compute_bi(const typename Kokkos::TeamPolicy -KOKKOS_INLINE_FUNCTION -void SNAKokkos::copy_bi2bvec(const typename Kokkos::TeamPolicy::member_type& team) -{ - /* int ncount, j1, j2, j; - - ncount = 0; - - for(j1 = 0; j1 <= twojmax; j1++) { - for(j2 = 0; j2 <= j1; j2++) - for(j = abs(j1 - j2); - j <= MIN(twojmax, j1 + j2); j += 2) - if (j >= j1) {*/ - Kokkos::parallel_for(Kokkos::ThreadVectorRange(team,idxj_max), - [&] (const int& JJ) { - //for(int JJ = 0; JJ < idxj_max; JJ++) { - const int j1 = idxj[JJ].j1; - const int j2 = idxj[JJ].j2; - const int j = idxj[JJ].j; - bvec(JJ) = barray(j1,j2,j); - //ncount++; - }); -} - -/* ---------------------------------------------------------------------- - calculate derivative of Ui w.r.t. atom j -------------------------------------------------------------------------- */ - -template -KOKKOS_INLINE_FUNCTION -void SNAKokkos::compute_duidrj(const typename Kokkos::TeamPolicy::member_type& team, - double* rij, double wj, double rcut) -{ - double rsq, r, x, y, z, z0, theta0, cs, sn; - double dz0dr; - - x = rij[0]; - y = rij[1]; - z = rij[2]; - rsq = x * x + y * y + z * z; - r = sqrt(rsq); - double rscale0 = rfac0 * MY_PI / (rcut - rmin0); - theta0 = (r - rmin0) * rscale0; - cs = cos(theta0); - sn = sin(theta0); - z0 = r * cs / sn; - dz0dr = z0 / r - (r*rscale0) * (rsq + z0 * z0) / rsq; - -#ifdef TIMING_INFO - clock_gettime(CLOCK_REALTIME, &starttime); -#endif - - compute_duarray(team, x, y, z, z0, r, dz0dr, wj, rcut); - -#ifdef TIMING_INFO - clock_gettime(CLOCK_REALTIME, &endtime); - timers[3] += (endtime.tv_sec - starttime.tv_sec + 1.0 * - (endtime.tv_nsec - starttime.tv_nsec) / 1000000000); -#endif - } /* ---------------------------------------------------------------------- @@ -478,21 +649,18 @@ void SNAKokkos::compute_dbidrj(const typename Kokkos::TeamPolicy::compute_dbidrj(const typename Kokkos::TeamPolicy dbdr,sumzdu_r; // Sum terms Conj(dudr(j,ma,mb))*z(j1,j2,j,ma,mb) - // use zarray j1/j2 symmetry (optional) - - int j_,j1_,j2_; - if (j1 >= j2) { - //jjjzarray_r = &zarray_r(j1,j2,j); - //jjjzarray_i = &zarray_i(j1,j2,j); - j1_ = j1; - j2_ = j2; - j_ = j; - } else { - j1_ = j2; - j2_ = j1; - j_ = j; - //jjjzarray_r = &zarray_r(j2,j1,j); - //jjjzarray_i = &zarray_i(j2,j1,j); - } + int jjz = idxz_block(j1,j2,j); + int jju = idxu_block[j]; for(int mb = 0; 2*mb < j; mb++) for(int ma = 0; ma <= j; ma++) { - - dudr_r = &duarray_r(j,mb,ma,0); - dudr_i = &duarray_i(j,mb,ma,0); - jjjmambzarray_r = zarray_r(j1_,j2_,j_,mb,ma); - jjjmambzarray_i = zarray_i(j1_,j2_,j_,mb,ma); - sumzdu_r.x += (dudr_r[0] * jjjmambzarray_r + dudr_i[0] * jjjmambzarray_i); - sumzdu_r.y += (dudr_r[1] * jjjmambzarray_r + dudr_i[1] * jjjmambzarray_i); - sumzdu_r.z += (dudr_r[2] * jjjmambzarray_r + dudr_i[2] * jjjmambzarray_i); - + const int jju_index = jju+mb*(j+1)+ma; + const int jjz_index = jjz+mb*(j+1)+ma; + sumzdu_r.x += (dulist_r(jju_index,0) * zlist_r[jjz_index] + dulist_i(jju_index,0) * zlist_i[jjz_index]); + sumzdu_r.y += (dulist_r(jju_index,1) * zlist_r[jjz_index] + dulist_i(jju_index,1) * zlist_i[jjz_index]); + sumzdu_r.z += (dulist_r(jju_index,2) * zlist_r[jjz_index] + dulist_i(jju_index,2) * zlist_i[jjz_index]); } //end loop over ma mb // For j even, handle middle column @@ -535,14 +685,19 @@ void SNAKokkos::compute_dbidrj(const typename Kokkos::TeamPolicy::compute_dbidrj(const typename Kokkos::TeamPolicy= j2) { - j1_ = j; - j2_ = j2; - j_ = j1; - - //jjjzarray_r = zarray_r(j,j2,j1); - //jjjzarray_i = zarray_i(j,j2,j1); - } else { - j1_ = j2; - j2_ = j; - j_ = j1; - //jjjzarray_r = zarray_r(j2,j,j1); - //jjjzarray_i = zarray_i(j2,j,j1); - } - - for(int mb1 = 0; 2*mb1 < j1; mb1++) - for(int ma1 = 0; ma1 <= j1; ma1++) { + sumzdu_r.x = 0.0; sumzdu_r.y = 0.0; sumzdu_r.z = 0.0; - dudr_r = &duarray_r(j1,mb1,ma1,0); - dudr_i = &duarray_i(j1,mb1,ma1,0); - jjjmambzarray_r = zarray_r(j1_,j2_,j_,mb1,ma1); - jjjmambzarray_i = zarray_i(j1_,j2_,j_,mb1,ma1); - sumzdu_r.x += (dudr_r[0] * jjjmambzarray_r + dudr_i[0] * jjjmambzarray_i); - sumzdu_r.y += (dudr_r[1] * jjjmambzarray_r + dudr_i[1] * jjjmambzarray_i); - sumzdu_r.z += (dudr_r[2] * jjjmambzarray_r + dudr_i[2] * jjjmambzarray_i); + for(int mb = 0; 2*mb < j1; mb++) + for(int ma = 0; ma <= j1; ma++) { + const int jju_index = jju+mb*(j1+1)+ma; + const int jjz_index = jjz+mb*(j1+1)+ma; + sumzdu_r.x += (dulist_r(jju_index,0) * zlist_r[jjz_index] + dulist_i(jju_index,0) * zlist_i[jjz_index]); + sumzdu_r.y += (dulist_r(jju_index,1) * zlist_r[jjz_index] + dulist_i(jju_index,1) * zlist_i[jjz_index]); + sumzdu_r.z += (dulist_r(jju_index,2) * zlist_r[jjz_index] + dulist_i(jju_index,2) * zlist_i[jjz_index]); } //end loop over ma1 mb1 // For j1 even, handle middle column if (j1%2 == 0) { - const int mb1 = j1/2; - for(int ma1 = 0; ma1 <= mb1; ma1++) { - dudr_r = &duarray_r(j1,mb1,ma1,0); - dudr_i = &duarray_i(j1,mb1,ma1,0); - const double factor = ma1==mb1?0.5:1.0; - jjjmambzarray_r = zarray_r(j1_,j2_,j_,mb1,ma1) * factor; - jjjmambzarray_i = zarray_i(j1_,j2_,j_,mb1,ma1) * factor; - sumzdu_r.x += (dudr_r[0] * jjjmambzarray_r + dudr_i[0] * jjjmambzarray_i); - sumzdu_r.y += (dudr_r[1] * jjjmambzarray_r + dudr_i[1] * jjjmambzarray_i); - sumzdu_r.z += (dudr_r[2] * jjjmambzarray_r + dudr_i[2] * jjjmambzarray_i); + const int mb = j1/2; + for(int ma = 0; ma <= mb; ma++) { + const int jju_index = jju+(mb-1)*(j1+1)+(j1+1)+ma; + const int jjz_index = jjz+(mb-1)*(j1+1)+(j1+1)+ma; + sumzdu_r.x += (dulist_r(jju_index,0) * zlist_r[jjz_index] + dulist_i(jju_index,0) * zlist_i[jjz_index]); + sumzdu_r.y += (dulist_r(jju_index,1) * zlist_r[jjz_index] + dulist_i(jju_index,1) * zlist_i[jjz_index]); + sumzdu_r.z += (dulist_r(jju_index,2) * zlist_r[jjz_index] + dulist_i(jju_index,2) * zlist_i[jjz_index]); + } + int ma = mb; + const int jju_index = jju+(mb-1)*(j1+1)+(j1+1)+ma; + const int jjz_index = jjz+(mb-1)*(j1+1)+(j1+1)+ma; + for(int k = 0; k < 3; k++) { + sumzdu_r.x += (dulist_r(jju_index,0) * zlist_r[jjz] + dulist_i(jju_index,0) * zlist_i[jjz_index])*0.5; + sumzdu_r.y += (dulist_r(jju_index,1) * zlist_r[jjz] + dulist_i(jju_index,1) * zlist_i[jjz_index])*0.5; + sumzdu_r.z += (dulist_r(jju_index,2) * zlist_r[jjz] + dulist_i(jju_index,2) * zlist_i[jjz_index])*0.5; } } // end if j1even @@ -605,94 +748,74 @@ void SNAKokkos::compute_dbidrj(const typename Kokkos::TeamPolicy= j) { - j1_ = j1; - j2_ = j; - j_ = j2; - //jjjzarray_r = zarray_r(j1,j,j2); - //jjjzarray_i = zarray_i(j1,j,j2); - } else { - j1_ = j; - j2_ = j1; - j_ = j2; - //jjjzarray_r = zarray_r(j,j1,j2); - //jjjzarray_i = zarray_i(j,j1,j2); - } + jjz = idxz_block(j,j1,j2); + jju = idxu_block[j2]; - for(int mb2 = 0; 2*mb2 < j2; mb2++) - for(int ma2 = 0; ma2 <= j2; ma2++) { + sumzdu_r.x = 0.0; sumzdu_r.y = 0.0; sumzdu_r.z = 0.0; - dudr_r = &duarray_r(j2,mb2,ma2,0); - dudr_i = &duarray_i(j2,mb2,ma2,0); - jjjmambzarray_r = zarray_r(j1_,j2_,j_,mb2,ma2); - jjjmambzarray_i = zarray_i(j1_,j2_,j_,mb2,ma2); - sumzdu_r.x += (dudr_r[0] * jjjmambzarray_r + dudr_i[0] * jjjmambzarray_i); - sumzdu_r.y += (dudr_r[1] * jjjmambzarray_r + dudr_i[1] * jjjmambzarray_i); - sumzdu_r.z += (dudr_r[2] * jjjmambzarray_r + dudr_i[2] * jjjmambzarray_i); + for(int mb = 0; 2*mb < j2; mb++) + for(int ma = 0; ma <= j2; ma++) { + const int jju_index = jju+mb*(j2+1)+ma; + const int jjz_index = jjz+mb*(j2+1)+ma; + sumzdu_r.x += (dulist_r(jju_index,0) * zlist_r[jjz_index] + dulist_i(jju_index,0) * zlist_i[jjz_index]); + sumzdu_r.y += (dulist_r(jju_index,1) * zlist_r[jjz_index] + dulist_i(jju_index,1) * zlist_i[jjz_index]); + sumzdu_r.z += (dulist_r(jju_index,2) * zlist_r[jjz_index] + dulist_i(jju_index,2) * zlist_i[jjz_index]); } //end loop over ma2 mb2 // For j2 even, handle middle column if (j2%2 == 0) { - const int mb2 = j2/2; - for(int ma2 = 0; ma2 <= mb2; ma2++) { - dudr_r = &duarray_r(j2,mb2,ma2,0); - dudr_i = &duarray_i(j2,mb2,ma2,0); - const double factor = ma2==mb2?0.5:1.0; - jjjmambzarray_r = zarray_r(j1_,j2_,j_,mb2,ma2) * factor; - jjjmambzarray_i = zarray_i(j1_,j2_,j_,mb2,ma2) * factor; - sumzdu_r.x += (dudr_r[0] * jjjmambzarray_r + dudr_i[0] * jjjmambzarray_i); - sumzdu_r.y += (dudr_r[1] * jjjmambzarray_r + dudr_i[1] * jjjmambzarray_i); - sumzdu_r.z += (dudr_r[2] * jjjmambzarray_r + dudr_i[2] * jjjmambzarray_i); + const int mb = j2/2; + for(int ma = 0; ma <= mb; ma++) { + const int jju_index = jju+(mb-1)*(j2+1)+(j2+1)+ma; + const int jjz_index = jjz+(mb-1)*(j2+1)+(j2+1)+ma; + sumzdu_r.x += (dulist_r(jju_index,0) * zlist_r[jjz_index] + dulist_i(jju_index,0) * zlist_i[jjz_index]); + sumzdu_r.y += (dulist_r(jju_index,1) * zlist_r[jjz_index] + dulist_i(jju_index,1) * zlist_i[jjz_index]); + sumzdu_r.z += (dulist_r(jju_index,2) * zlist_r[jjz_index] + dulist_i(jju_index,2) * zlist_i[jjz_index]); + } + int ma = mb; + const int jju_index = jju+(mb-1)*(j2+1)+(j2+1)+ma; + const int jjz_index = jjz+(mb-1)*(j2+1)+(j2+1)+ma; + for(int k = 0; k < 3; k++) { + sumzdu_r.x += (dulist_r(jju_index,0) * zlist_r[jjz] + dulist_i(jju_index,0) * zlist_i[jjz_index])*0.5; + sumzdu_r.y += (dulist_r(jju_index,1) * zlist_r[jjz] + dulist_i(jju_index,1) * zlist_i[jjz_index])*0.5; + sumzdu_r.z += (dulist_r(jju_index,2) * zlist_r[jjz] + dulist_i(jju_index,2) * zlist_i[jjz_index])*0.5; } } // end if j2even dbdr += 2.0*sumzdu_r*j2fac; - dbarray(j1,j2,j,0) = dbdr.x; - dbarray(j1,j2,j,1) = dbdr.y; - dbarray(j1,j2,j,2) = dbdr.z; - }); //end loop over j1 j2 j - -#ifdef TIMING_INFO - clock_gettime(CLOCK_REALTIME, &endtime); - timers[4] += (endtime.tv_sec - starttime.tv_sec + 1.0 * - (endtime.tv_nsec - starttime.tv_nsec) / 1000000000); -#endif + dblist(jjb,0) = dbdr.x; + dblist(jjb,1) = dbdr.y; + dblist(jjb,2) = dbdr.z; + }); //end loop over j1 j2 j } /* ---------------------------------------------------------------------- - copy Bi derivatives into a vector + calculate derivative of Ui w.r.t. atom j ------------------------------------------------------------------------- */ template KOKKOS_INLINE_FUNCTION -void SNAKokkos::copy_dbi2dbvec(const typename Kokkos::TeamPolicy::member_type& team) +void SNAKokkos::compute_duidrj(const typename Kokkos::TeamPolicy::member_type& team, + double* rij, double wj, double rcut) { - /* int ncount, j1, j2, j; + double rsq, r, x, y, z, z0, theta0, cs, sn; + double dz0dr; - ncount = 0; + x = rij[0]; + y = rij[1]; + z = rij[2]; + rsq = x * x + y * y + z * z; + r = sqrt(rsq); + double rscale0 = rfac0 * MY_PI / (rcut - rmin0); + theta0 = (r - rmin0) * rscale0; + cs = cos(theta0); + sn = sin(theta0); + z0 = r * cs / sn; + dz0dr = z0 / r - (r*rscale0) * (rsq + z0 * z0) / rsq; - for(j1 = 0; j1 <= twojmax; j1++) { - for(j2 = 0; j2 <= j1; j2++) - for(j = abs(j1 - j2); - j <= MIN(twojmax, j1 + j2); j += 2) - if (j >= j1) {*/ - Kokkos::parallel_for(Kokkos::ThreadVectorRange(team,idxj_max), - [&] (const int& JJ) { - //for(int JJ = 0; JJ < idxj_max; JJ++) { - const int j1 = idxj[JJ].j1; - const int j2 = idxj[JJ].j2; - const int j = idxj[JJ].j; - dbvec(JJ,0) = dbarray(j1,j2,j,0); - dbvec(JJ,1) = dbarray(j1,j2,j,1); - dbvec(JJ,2) = dbarray(j1,j2,j,2); - //ncount++; - }); + compute_duarray(team, x, y, z, z0, r, dz0dr, wj, rcut); } /* ---------------------------------------------------------------------- */ @@ -702,15 +825,15 @@ KOKKOS_INLINE_FUNCTION void SNAKokkos::zero_uarraytot(const typename Kokkos::TeamPolicy::member_type& team) { { - double* const ptr = uarraytot_r.data(); - Kokkos::parallel_for(Kokkos::ThreadVectorRange(team,uarraytot_r.span()), + double* const ptr = ulisttot_r.data(); + Kokkos::parallel_for(Kokkos::ThreadVectorRange(team,ulisttot_r.span()), [&] (const int& i) { ptr[i] = 0.0; }); } { - double* const ptr = uarraytot_i.data(); - Kokkos::parallel_for(Kokkos::ThreadVectorRange(team,uarraytot_r.span()), + double* const ptr = ulisttot_i.data(); + Kokkos::parallel_for(Kokkos::ThreadVectorRange(team,ulisttot_i.span()), [&] (const int& i) { ptr[i] = 0.0; }); @@ -723,12 +846,14 @@ template KOKKOS_INLINE_FUNCTION void SNAKokkos::addself_uarraytot(const typename Kokkos::TeamPolicy::member_type& team, double wself_in) { - //for (int j = 0; j <= twojmax; j++) Kokkos::parallel_for(Kokkos::ThreadVectorRange(team,twojmax+1), [&] (const int& j) { + //for (int j = 0; j <= twojmax; j++) + int jju = idxu_block[j]; for (int ma = 0; ma <= j; ma++) { - uarraytot_r(j,ma,ma) = wself_in; - uarraytot_i(j,ma,ma) = 0.0; + ulisttot_r[jju] = wself_in; + ulisttot_i[jju] = 0.0; + jju += j+2; } }); } @@ -743,20 +868,11 @@ void SNAKokkos::add_uarraytot(const typename Kokkos::TeamPolicy::compute_uarray(const typename Kokkos::TeamPolicy::compute_duarray(const typename Kokkos::TeamPolicy::compute_duarray(const typename Kokkos::TeamPolicy KOKKOS_INLINE_FUNCTION void SNAKokkos::create_team_scratch_arrays(const typename Kokkos::TeamPolicy::member_type& team) { - int jdim = twojmax + 1; - uarraytot_r_a = uarraytot_r = t_sna_3d(team.team_scratch(1),jdim,jdim,jdim); - uarraytot_i_a = uarraytot_i = t_sna_3d(team.team_scratch(1),jdim,jdim,jdim); - zarray_r = t_sna_5d(team.team_scratch(1),jdim,jdim,jdim,jdim,jdim); - zarray_i = t_sna_5d(team.team_scratch(1),jdim,jdim,jdim,jdim,jdim); - bvec = Kokkos::View(team.team_scratch(1),ncoeff); - barray = t_sna_3d(team.team_scratch(1),jdim,jdim,jdim); + ulisttot_r_a = ulisttot_r = t_sna_1d(team.team_scratch(1),idxu_max); + ulisttot_i_a = ulisttot_i = t_sna_1d(team.team_scratch(1),idxu_max); + ylist_r = t_sna_1d(team.team_scratch(1),idxu_max); + ylist_i = t_sna_1d(team.team_scratch(1),idxu_max); + zlist_r = t_sna_1d(team.team_scratch(1),idxz_max); + zlist_i = t_sna_1d(team.team_scratch(1),idxz_max); + blist = t_sna_1d(team.team_scratch(1),idxb_max); + dblist = t_sna_2d(team.team_scratch(1),idxb_max,3); rij = t_sna_2d(team.team_scratch(1),nmax,3); rcutij = t_sna_1d(team.team_scratch(1),nmax); @@ -1043,19 +1184,16 @@ void SNAKokkos::create_team_scratch_arrays(const typename Kokkos::Te inside = t_sna_1i(team.team_scratch(1),nmax); } - template inline T_INT SNAKokkos::size_team_scratch_arrays() { T_INT size = 0; - int jdim = twojmax + 1; - size += t_sna_3d::shmem_size(jdim,jdim,jdim); // uarraytot_r_a - size += t_sna_3d::shmem_size(jdim,jdim,jdim); // uarraytot_i_a - size += t_sna_5d::shmem_size(jdim,jdim,jdim,jdim,jdim); // zarray_r - size += t_sna_5d::shmem_size(jdim,jdim,jdim,jdim,jdim); // zarray_i - size += Kokkos::View::shmem_size(ncoeff); // bvec - size += t_sna_3d::shmem_size(jdim,jdim,jdim); // barray + size += t_sna_1d::shmem_size(idxu_max)*2; // ulisttot + size += t_sna_1d::shmem_size(idxu_max)*2; // ylist + size += t_sna_1d::shmem_size(idxz_max)*2; // zlist + size += t_sna_1d::shmem_size(idxb_max); // blist + size += t_sna_2d::shmem_size(idxb_max,3); // dblist size += t_sna_2d::shmem_size(nmax,3); // rij size += t_sna_1d::shmem_size(nmax); // rcutij @@ -1071,53 +1209,225 @@ template KOKKOS_INLINE_FUNCTION void SNAKokkos::create_thread_scratch_arrays(const typename Kokkos::TeamPolicy::member_type& team) { - int jdim = twojmax + 1; - - dbvec = Kokkos::View(team.thread_scratch(1),ncoeff); - dbarray = t_sna_4d(team.thread_scratch(1),jdim,jdim,jdim); + dblist = t_sna_2d(team.thread_scratch(1),idxb_max,3); - uarray_r = t_sna_3d(team.thread_scratch(1),jdim,jdim,jdim); - uarray_i = t_sna_3d(team.thread_scratch(1),jdim,jdim,jdim); - duarray_r = t_sna_4d(team.thread_scratch(1),jdim,jdim,jdim); - duarray_i = t_sna_4d(team.thread_scratch(1),jdim,jdim,jdim); + ulist_r = t_sna_1d(team.thread_scratch(1),idxu_max); + ulist_i = t_sna_1d(team.thread_scratch(1),idxu_max); + dulist_r = t_sna_2d(team.thread_scratch(1),idxu_max,3); + dulist_i = t_sna_2d(team.thread_scratch(1),idxu_max,3); } template inline T_INT SNAKokkos::size_thread_scratch_arrays() { T_INT size = 0; - int jdim = twojmax + 1; - size += Kokkos::View::shmem_size(ncoeff); // dbvec - size += t_sna_4d::shmem_size(jdim,jdim,jdim); // dbarray + size += t_sna_2d::shmem_size(idxb_max,3); // dblist - size += t_sna_3d::shmem_size(jdim,jdim,jdim); // uarray_r - size += t_sna_3d::shmem_size(jdim,jdim,jdim); // uarray_i - size += t_sna_4d::shmem_size(jdim,jdim,jdim); // duarray_r - size += t_sna_4d::shmem_size(jdim,jdim,jdim); // duarray_i + size += t_sna_1d::shmem_size(idxu_max)*2; // ulist + size += t_sna_2d::shmem_size(idxu_max,3)*2; // dulist return size; } /* ---------------------------------------------------------------------- - factorial n + factorial n, wrapper for precomputed table ------------------------------------------------------------------------- */ template -KOKKOS_INLINE_FUNCTION +inline double SNAKokkos::factorial(int n) { - double result = 1.0; - for(int i=1; i<=n; i++) - result *= 1.0*i; - return result; + //if (n < 0 || n > nmaxfactorial) { + // char str[128]; + // sprintf(str, "Invalid argument to factorial %d", n); + // error->all(FLERR, str); + //} + + return nfac_table[n]; } +/* ---------------------------------------------------------------------- + factorial n table, size SNA::nmaxfactorial+1 +------------------------------------------------------------------------- */ + +template +const double SNAKokkos::nfac_table[] = { + 1, + 1, + 2, + 6, + 24, + 120, + 720, + 5040, + 40320, + 362880, + 3628800, + 39916800, + 479001600, + 6227020800, + 87178291200, + 1307674368000, + 20922789888000, + 355687428096000, + 6.402373705728e+15, + 1.21645100408832e+17, + 2.43290200817664e+18, + 5.10909421717094e+19, + 1.12400072777761e+21, + 2.5852016738885e+22, + 6.20448401733239e+23, + 1.5511210043331e+25, + 4.03291461126606e+26, + 1.08888694504184e+28, + 3.04888344611714e+29, + 8.8417619937397e+30, + 2.65252859812191e+32, + 8.22283865417792e+33, + 2.63130836933694e+35, + 8.68331761881189e+36, + 2.95232799039604e+38, + 1.03331479663861e+40, + 3.71993326789901e+41, + 1.37637530912263e+43, + 5.23022617466601e+44, + 2.03978820811974e+46, + 8.15915283247898e+47, + 3.34525266131638e+49, + 1.40500611775288e+51, + 6.04152630633738e+52, + 2.65827157478845e+54, + 1.1962222086548e+56, + 5.50262215981209e+57, + 2.58623241511168e+59, + 1.24139155925361e+61, + 6.08281864034268e+62, + 3.04140932017134e+64, + 1.55111875328738e+66, + 8.06581751709439e+67, + 4.27488328406003e+69, + 2.30843697339241e+71, + 1.26964033536583e+73, + 7.10998587804863e+74, + 4.05269195048772e+76, + 2.35056133128288e+78, + 1.3868311854569e+80, + 8.32098711274139e+81, + 5.07580213877225e+83, + 3.14699732603879e+85, + 1.98260831540444e+87, + 1.26886932185884e+89, + 8.24765059208247e+90, + 5.44344939077443e+92, + 3.64711109181887e+94, + 2.48003554243683e+96, + 1.71122452428141e+98, + 1.19785716699699e+100, + 8.50478588567862e+101, + 6.12344583768861e+103, + 4.47011546151268e+105, + 3.30788544151939e+107, + 2.48091408113954e+109, + 1.88549470166605e+111, + 1.45183092028286e+113, + 1.13242811782063e+115, + 8.94618213078297e+116, + 7.15694570462638e+118, + 5.79712602074737e+120, + 4.75364333701284e+122, + 3.94552396972066e+124, + 3.31424013456535e+126, + 2.81710411438055e+128, + 2.42270953836727e+130, + 2.10775729837953e+132, + 1.85482642257398e+134, + 1.65079551609085e+136, + 1.48571596448176e+138, + 1.3520015276784e+140, + 1.24384140546413e+142, + 1.15677250708164e+144, + 1.08736615665674e+146, + 1.03299784882391e+148, + 9.91677934870949e+149, + 9.61927596824821e+151, + 9.42689044888324e+153, + 9.33262154439441e+155, + 9.33262154439441e+157, + 9.42594775983835e+159, + 9.61446671503512e+161, + 9.90290071648618e+163, + 1.02990167451456e+166, + 1.08139675824029e+168, + 1.14628056373471e+170, + 1.22652020319614e+172, + 1.32464181945183e+174, + 1.44385958320249e+176, + 1.58824554152274e+178, + 1.76295255109024e+180, + 1.97450685722107e+182, + 2.23119274865981e+184, + 2.54355973347219e+186, + 2.92509369349301e+188, + 3.3931086844519e+190, + 3.96993716080872e+192, + 4.68452584975429e+194, + 5.5745857612076e+196, + 6.68950291344912e+198, + 8.09429852527344e+200, + 9.8750442008336e+202, + 1.21463043670253e+205, + 1.50614174151114e+207, + 1.88267717688893e+209, + 2.37217324288005e+211, + 3.01266001845766e+213, + 3.8562048236258e+215, + 4.97450422247729e+217, + 6.46685548922047e+219, + 8.47158069087882e+221, + 1.118248651196e+224, + 1.48727070609069e+226, + 1.99294274616152e+228, + 2.69047270731805e+230, + 3.65904288195255e+232, + 5.01288874827499e+234, + 6.91778647261949e+236, + 9.61572319694109e+238, + 1.34620124757175e+241, + 1.89814375907617e+243, + 2.69536413788816e+245, + 3.85437071718007e+247, + 5.5502938327393e+249, + 8.04792605747199e+251, + 1.17499720439091e+254, + 1.72724589045464e+256, + 2.55632391787286e+258, + 3.80892263763057e+260, + 5.71338395644585e+262, + 8.62720977423323e+264, + 1.31133588568345e+267, + 2.00634390509568e+269, + 3.08976961384735e+271, + 4.78914290146339e+273, + 7.47106292628289e+275, + 1.17295687942641e+278, + 1.85327186949373e+280, + 2.94670227249504e+282, + 4.71472363599206e+284, + 7.59070505394721e+286, + 1.22969421873945e+289, + 2.0044015765453e+291, + 3.28721858553429e+293, + 5.42391066613159e+295, + 9.00369170577843e+297, + 1.503616514865e+300, // nmaxfactorial = 167 +}; + /* ---------------------------------------------------------------------- the function delta given by VMK Eq. 8.2(1) ------------------------------------------------------------------------- */ template -KOKKOS_INLINE_FUNCTION +inline double SNAKokkos::deltacg(int j1, int j2, int j) { double sfaccg = factorial((j1 + j2 + j) / 2 + 1); @@ -1135,33 +1445,39 @@ template inline void SNAKokkos::init_clebsch_gordan() { + auto h_cglist = Kokkos::create_mirror_view(cglist); + double sum,dcg,sfaccg; int m, aa2, bb2, cc2; int ifac; - auto h_cgarray = Kokkos::create_mirror_view(cgarray); - for (int j1 = 0; j1 <= twojmax; j1++) - for (int j2 = 0; j2 <= twojmax; j2++) - for (int j = abs(j1 - j2); j <= MIN(twojmax, j1 + j2); j += 2) - for (int m1 = 0; m1 <= j1; m1 += 1) { + int idxcg_count = 0; + for(int j1 = 0; j1 <= twojmax; j1++) + for(int j2 = 0; j2 <= j1; j2++) + for(int j = j1 - j2; j <= MIN(twojmax, j1 + j2); j += 2) { + for (int m1 = 0; m1 <= j1; m1++) { aa2 = 2 * m1 - j1; - for (int m2 = 0; m2 <= j2; m2 += 1) { + for (int m2 = 0; m2 <= j2; m2++) { // -c <= cc <= c bb2 = 2 * m2 - j2; m = (aa2 + bb2 + j) / 2; - if(m < 0 || m > j) continue; + if(m < 0 || m > j) { + h_cglist[idxcg_count] = 0.0; + idxcg_count++; + continue; + } sum = 0.0; for (int z = MAX(0, MAX(-(j - j2 + aa2) - / 2, -(j - j1 - bb2) / 2)); - z <= MIN((j1 + j2 - j) / 2, - MIN((j1 - aa2) / 2, (j2 + bb2) / 2)); - z++) { + / 2, -(j - j1 - bb2) / 2)); + z <= MIN((j1 + j2 - j) / 2, + MIN((j1 - aa2) / 2, (j2 + bb2) / 2)); + z++) { ifac = z % 2 ? -1 : 1; sum += ifac / (factorial(z) * @@ -1175,18 +1491,19 @@ void SNAKokkos::init_clebsch_gordan() cc2 = 2 * m - j; dcg = deltacg(j1, j2, j); sfaccg = sqrt(factorial((j1 + aa2) / 2) * - factorial((j1 - aa2) / 2) * - factorial((j2 + bb2) / 2) * - factorial((j2 - bb2) / 2) * - factorial((j + cc2) / 2) * - factorial((j - cc2) / 2) * - (j + 1)); - - h_cgarray(j1,j2,j,m1,m2) = sum * dcg * sfaccg; - //printf("SNAP-COMPARE: CG: %i %i %i %i %i %e\n",j1,j2,j,m1,m2,cgarray(j1,j2,j,m1,m2)); + factorial((j1 - aa2) / 2) * + factorial((j2 + bb2) / 2) * + factorial((j2 - bb2) / 2) * + factorial((j + cc2) / 2) * + factorial((j - cc2) / 2) * + (j + 1)); + + h_cglist[idxcg_count] = sum * dcg * sfaccg; + idxcg_count++; } } - Kokkos::deep_copy(cgarray,h_cgarray); + } + Kokkos::deep_copy(cglist,h_cglist); } /* ---------------------------------------------------------------------- @@ -1207,6 +1524,7 @@ void SNAKokkos::init_rootpqarray() /* ---------------------------------------------------------------------- */ + template inline int SNAKokkos::compute_ncoeff() @@ -1217,9 +1535,10 @@ int SNAKokkos::compute_ncoeff() for (int j1 = 0; j1 <= twojmax; j1++) for (int j2 = 0; j2 <= j1; j2++) - for (int j = abs(j1 - j2); - j <= MIN(twojmax, j1 + j2); j += 2) - if (j >= j1) ncount++; + for (int j = j1 - j2; + j <= MIN(twojmax, j1 + j2); j += 2) + if (j >= j1) ncount++; + return ncount; } @@ -1266,15 +1585,39 @@ double SNAKokkos::compute_dsfac(double r, double rcut) template double SNAKokkos::memory_usage() { + int jdimpq = twojmax + 2; int jdim = twojmax + 1; double bytes; - bytes = jdim * jdim * jdim * jdim * jdim * sizeof(double); - bytes += 2 * jdim * jdim * jdim * sizeof(std::complex); - bytes += 2 * jdim * jdim * jdim * sizeof(double); - bytes += jdim * jdim * jdim * 3 * sizeof(std::complex); - bytes += jdim * jdim * jdim * 3 * sizeof(double); - bytes += ncoeff * sizeof(double); - bytes += jdim * jdim * jdim * jdim * jdim * sizeof(std::complex); + + bytes = 0; + + bytes += jdimpq*jdimpq * sizeof(double); // pqarray + bytes += idxcg_max * sizeof(double); // cglist + + bytes += idxu_max * sizeof(double) * 2; // ulist + bytes += idxu_max * sizeof(double) * 2; // ulisttot + bytes += idxu_max * 3 * sizeof(double) * 2; // dulist + + bytes += idxz_max * sizeof(double) * 2; // zlist + bytes += idxb_max * sizeof(double); // blist + bytes += idxb_max * 3 * sizeof(double); // dblist + bytes += idxu_max * sizeof(double) * 2; // ylist + + bytes += jdim * jdim * jdim * sizeof(int); // idxcg_block + bytes += jdim * sizeof(int); // idxu_block + bytes += jdim * jdim * jdim * sizeof(int); // idxz_block + bytes += jdim * jdim * jdim * sizeof(int); // idxb_block + + bytes += idxz_max * sizeof(SNAKK_ZINDICES); // idxz + bytes += idxb_max * sizeof(SNAKK_BINDICES); // idxb + + bytes += jdim * sizeof(double); // bzero + + bytes += nmax * 3 * sizeof(double); // rij + bytes += nmax * sizeof(int); // inside + bytes += nmax * sizeof(double); // wj + bytes += nmax * sizeof(double); // rcutij + return bytes; } -- GitLab From 2be0fd61802b824363308985f415b40e8fb0e38a Mon Sep 17 00:00:00 2001 From: Stan Moore Date: Wed, 26 Jun 2019 16:22:37 -0600 Subject: [PATCH 107/469] Fix GPU issues --- src/KOKKOS/pair_snap_kokkos_impl.h | 9 ++-- src/KOKKOS/sna_kokkos.h | 4 +- src/KOKKOS/sna_kokkos_impl.h | 78 ++++++++++-------------------- 3 files changed, 31 insertions(+), 60 deletions(-) diff --git a/src/KOKKOS/pair_snap_kokkos_impl.h b/src/KOKKOS/pair_snap_kokkos_impl.h index 687c9dc7cb..d56db05d19 100644 --- a/src/KOKKOS/pair_snap_kokkos_impl.h +++ b/src/KOKKOS/pair_snap_kokkos_impl.h @@ -309,7 +309,7 @@ void PairSNAPKokkos::operator() (TagPairSNAPBeta,const typename Kokk const int ii = team.league_rank(); const int i = d_ilist[ii]; const int itype = type[i]; - const int ielem = map[itype]; + const int ielem = d_map[itype]; Kokkos::View> d_coeffi(d_coeffelem,ielem,Kokkos::ALL); @@ -603,11 +603,10 @@ void PairSNAPKokkos::operator() (TagPairSNAPCompute::member_type& team, double, double, double, double, double); // compute_ui - KOKKOS_INLINE_FUNCTION + inline double deltacg(int, int, int); // init_clebsch_gordan inline diff --git a/src/KOKKOS/sna_kokkos_impl.h b/src/KOKKOS/sna_kokkos_impl.h index 4ca8ae4471..e3ce1626d9 100644 --- a/src/KOKKOS/sna_kokkos_impl.h +++ b/src/KOKKOS/sna_kokkos_impl.h @@ -223,7 +223,7 @@ void SNAKokkos::build_indexlist() // apply to z(j1,j2,j,ma,mb) to unique element of y(j) - const int jju = idxu_block[j] + (j+1)*mb + ma; + const int jju = h_idxu_block[j] + (j+1)*mb + ma; h_idxz[idxz_count].jju = jju; idxz_count++; @@ -258,7 +258,6 @@ template KOKKOS_INLINE_FUNCTION void SNAKokkos::compute_ui(const typename Kokkos::TeamPolicy::member_type& team, int jnum) { - //printf("jnum %i\n",jnum); double rsq, r, x, y, z, z0, theta0; // utot(j,ma,mb) = 0 for all j,ma,ma @@ -348,7 +347,7 @@ void SNAKokkos::compute_zi(const typename Kokkos::TeamPolicy::compute_yi(const typename Kokkos::TeamPolicy::member_type& team, const Kokkos::View &beta, const int ii) { - int j; - int jjz; - int jju; double betaj; { @@ -400,8 +396,8 @@ void SNAKokkos::compute_yi(const typename Kokkos::TeamPolicy::compute_yi(const typename Kokkos::TeamPolicy KOKKOS_INLINE_FUNCTION void SNAKokkos::compute_deidrj(const typename Kokkos::TeamPolicy::member_type& team, double* dedr) { - - for(int k = 0; k < 3; k++) - dedr[k] = 0.0; + t_scalar3 sum; // TODO: which loop is faster to parallelize? - Kokkos::parallel_for(Kokkos::ThreadVectorRange(team,twojmax+1), - [&] (const int& j) { + Kokkos::parallel_reduce(Kokkos::ThreadVectorRange(team,twojmax+1), + [&] (const int& j, t_scalar3& sum_tmp) { //for(int j = 0; j <= twojmax; j++) { int jju = idxu_block[j]; for(int mb = 0; 2*mb < j; mb++) for(int ma = 0; ma <= j; ma++) { - - double jjjmambyarray_r = ylist_r[jju]; - double jjjmambyarray_i = ylist_i[jju]; - - for(int k = 0; k < 3; k++) - dedr[k] += - dulist_r(jju,k) * jjjmambyarray_r + - dulist_i(jju,k) * jjjmambyarray_i; + sum_tmp.x += dulist_r(jju,0) * ylist_r[jju] + dulist_i(jju,0) * ylist_i[jju]; + sum_tmp.y += dulist_r(jju,1) * ylist_r[jju] + dulist_i(jju,1) * ylist_i[jju]; + sum_tmp.z += dulist_r(jju,2) * ylist_r[jju] + dulist_i(jju,2) * ylist_i[jju]; jju++; } //end loop over ma mb @@ -505,32 +495,26 @@ void SNAKokkos::compute_deidrj(const typename Kokkos::TeamPolicy::compute_bi(const typename Kokkos::TeamPolicy::compute_bi(const typename Kokkos::TeamPolicy::compute_uarray(const typename Kokkos::TeamPolicy::compute_uarray(const typename Kokkos::TeamPolicy::compute_duarray(const typename Kokkos::TeamPolicy::create_team_scratch_arrays(const typename Kokkos::Te zlist_r = t_sna_1d(team.team_scratch(1),idxz_max); zlist_i = t_sna_1d(team.team_scratch(1),idxz_max); blist = t_sna_1d(team.team_scratch(1),idxb_max); - dblist = t_sna_2d(team.team_scratch(1),idxb_max,3); rij = t_sna_2d(team.team_scratch(1),nmax,3); rcutij = t_sna_1d(team.team_scratch(1),nmax); @@ -1193,7 +1168,6 @@ T_INT SNAKokkos::size_team_scratch_arrays() { size += t_sna_1d::shmem_size(idxu_max)*2; // ylist size += t_sna_1d::shmem_size(idxz_max)*2; // zlist size += t_sna_1d::shmem_size(idxb_max); // blist - size += t_sna_2d::shmem_size(idxb_max,3); // dblist size += t_sna_2d::shmem_size(nmax,3); // rij size += t_sna_1d::shmem_size(nmax); // rcutij @@ -1210,7 +1184,6 @@ KOKKOS_INLINE_FUNCTION void SNAKokkos::create_thread_scratch_arrays(const typename Kokkos::TeamPolicy::member_type& team) { dblist = t_sna_2d(team.thread_scratch(1),idxb_max,3); - ulist_r = t_sna_1d(team.thread_scratch(1),idxu_max); ulist_i = t_sna_1d(team.thread_scratch(1),idxu_max); dulist_r = t_sna_2d(team.thread_scratch(1),idxu_max,3); @@ -1223,7 +1196,6 @@ T_INT SNAKokkos::size_thread_scratch_arrays() { T_INT size = 0; size += t_sna_2d::shmem_size(idxb_max,3); // dblist - size += t_sna_1d::shmem_size(idxu_max)*2; // ulist size += t_sna_2d::shmem_size(idxu_max,3)*2; // dulist return size; -- GitLab From ff36bad09964fecad2b6569fef6992b164e9b56d Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Thu, 27 Jun 2019 00:33:48 -0400 Subject: [PATCH 108/469] cleanup includes in variable.h --- src/variable.h | 3 +-- 1 file changed, 1 insertion(+), 2 deletions(-) diff --git a/src/variable.h b/src/variable.h index 512195bd14..c5f501f266 100644 --- a/src/variable.h +++ b/src/variable.h @@ -14,9 +14,8 @@ #ifndef LMP_VARIABLE_H #define LMP_VARIABLE_H -#include +#include #include "pointers.h" -#include "input.h" namespace LAMMPS_NS { -- GitLab From f7507512b131e2c515db82751b1a793de66aa657 Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Thu, 27 Jun 2019 00:39:47 -0400 Subject: [PATCH 109/469] apply memory alignment settings from my_page.h to my_pool_chunk.h --- src/my_pool_chunk.h | 12 ++++++++++++ 1 file changed, 12 insertions(+) diff --git a/src/my_pool_chunk.h b/src/my_pool_chunk.h index 8bf88d35bb..a313e45f05 100644 --- a/src/my_pool_chunk.h +++ b/src/my_pool_chunk.h @@ -43,6 +43,10 @@ public variables: #ifndef LAMMPS_MY_POOL_CHUNK_H #define LAMMPS_MY_POOL_CHUNK_H +#if defined(LMP_USER_INTEL) && !defined(LAMMPS_MEMALIGN) && !defined(_WIN32) +#define LAMMPS_MEMALIGN 64 +#endif + #include namespace LAMMPS_NS { @@ -190,9 +194,17 @@ class MyPoolChunk { for (int i = oldpage; i < npage; i++) { whichbin[i] = ibin; +#if defined(LAMMPS_MEMALIGN) + void *ptr; + if (posix_memalign(&ptr, LAMMPS_MEMALIGN, + chunkperpage*chunksize[ibin]*sizeof(T))) + errorflag = 2; + pages[i] = (T *) ptr; +#else pages[i] = (T *) malloc(chunkperpage*chunksize[ibin]*sizeof(T)); size += chunkperpage*chunksize[ibin]; if (!pages[i]) errorflag = 2; +#endif } // reset free list for unused chunks on new pages -- GitLab From 17602b4c26fa94e02e204b3e8e85a48cecc65569 Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Thu, 27 Jun 2019 01:02:17 -0400 Subject: [PATCH 110/469] some more include file cleanup. include cstdlib where functions like atoi() are used remove unneeded include statements from headers --- src/PYTHON/python_impl.cpp | 1 + src/USER-MEAMC/meam.h | 1 - src/compute_reduce_chunk.cpp | 3 ++- src/fix_vector.cpp | 1 + src/lammps.cpp | 1 + src/variable.cpp | 1 + 6 files changed, 6 insertions(+), 2 deletions(-) diff --git a/src/PYTHON/python_impl.cpp b/src/PYTHON/python_impl.cpp index aaa4f74c69..9c650330af 100644 --- a/src/PYTHON/python_impl.cpp +++ b/src/PYTHON/python_impl.cpp @@ -15,6 +15,7 @@ Contributing author: Richard Berger and Axel Kohlmeyer (Temple U) ------------------------------------------------------------------------- */ +#include #include #include "lmppython.h" #include "force.h" diff --git a/src/USER-MEAMC/meam.h b/src/USER-MEAMC/meam.h index 42fd722e01..bb40202243 100644 --- a/src/USER-MEAMC/meam.h +++ b/src/USER-MEAMC/meam.h @@ -3,7 +3,6 @@ #include "memory.h" #include -#include #define maxelt 5 diff --git a/src/compute_reduce_chunk.cpp b/src/compute_reduce_chunk.cpp index f31672ef74..5eda71b21b 100644 --- a/src/compute_reduce_chunk.cpp +++ b/src/compute_reduce_chunk.cpp @@ -12,7 +12,8 @@ ------------------------------------------------------------------------- */ #include -#include +#include +#include #include "compute_reduce_chunk.h" #include "atom.h" #include "update.h" diff --git a/src/fix_vector.cpp b/src/fix_vector.cpp index 6387af7676..5657e59ab0 100644 --- a/src/fix_vector.cpp +++ b/src/fix_vector.cpp @@ -11,6 +11,7 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ +#include #include #include "fix_vector.h" #include "update.h" diff --git a/src/lammps.cpp b/src/lammps.cpp index f8d04c9323..320d89ed52 100644 --- a/src/lammps.cpp +++ b/src/lammps.cpp @@ -13,6 +13,7 @@ #include #include +#include #include #include #include diff --git a/src/variable.cpp b/src/variable.cpp index ea7f3044d7..1416754073 100644 --- a/src/variable.cpp +++ b/src/variable.cpp @@ -26,6 +26,7 @@ #include "region.h" #include "modify.h" #include "compute.h" +#include "input.h" #include "fix.h" #include "fix_store.h" #include "force.h" -- GitLab From 08ac695a062079390a47d7115e10428493c5cf75 Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Thu, 27 Jun 2019 01:03:08 -0400 Subject: [PATCH 111/469] move include statements from headers to implementation files where possible in USER-REAXC --- src/USER-OMP/reaxc_multi_body_omp.cpp | 1 + src/USER-REAXC/pair_reaxc.cpp | 1 + src/USER-REAXC/reaxc_control.cpp | 2 ++ src/USER-REAXC/reaxc_ffield.cpp | 2 ++ src/USER-REAXC/reaxc_forces.cpp | 1 + src/USER-REAXC/reaxc_init_md.cpp | 1 + src/USER-REAXC/reaxc_io_tools.cpp | 3 ++- src/USER-REAXC/reaxc_multi_body.cpp | 1 + src/USER-REAXC/reaxc_reset_tools.cpp | 1 + src/USER-REAXC/reaxc_tool_box.cpp | 5 +++++ src/USER-REAXC/reaxc_traj.cpp | 1 + src/USER-REAXC/reaxc_types.h | 10 +--------- 12 files changed, 19 insertions(+), 10 deletions(-) diff --git a/src/USER-OMP/reaxc_multi_body_omp.cpp b/src/USER-OMP/reaxc_multi_body_omp.cpp index 7552e7a733..d791f945a8 100644 --- a/src/USER-OMP/reaxc_multi_body_omp.cpp +++ b/src/USER-OMP/reaxc_multi_body_omp.cpp @@ -26,6 +26,7 @@ . ----------------------------------------------------------------------*/ +#include #include "pair_reaxc_omp.h" #include "thr_data.h" diff --git a/src/USER-REAXC/pair_reaxc.cpp b/src/USER-REAXC/pair_reaxc.cpp index 8f8dcfb8fc..224f3e2568 100644 --- a/src/USER-REAXC/pair_reaxc.cpp +++ b/src/USER-REAXC/pair_reaxc.cpp @@ -20,6 +20,7 @@ Hybrid and hybrid/overlay compatibility added by Ray Shan (Sandia) ------------------------------------------------------------------------- */ +#include #include "pair_reaxc.h" #include "atom.h" #include "update.h" diff --git a/src/USER-REAXC/reaxc_control.cpp b/src/USER-REAXC/reaxc_control.cpp index 535226fff8..060c1a0342 100644 --- a/src/USER-REAXC/reaxc_control.cpp +++ b/src/USER-REAXC/reaxc_control.cpp @@ -24,6 +24,8 @@ . ----------------------------------------------------------------------*/ +#include +#include #include "pair_reaxc.h" #include "reaxc_control.h" #include "reaxc_tool_box.h" diff --git a/src/USER-REAXC/reaxc_ffield.cpp b/src/USER-REAXC/reaxc_ffield.cpp index 9534637645..2160d180cf 100644 --- a/src/USER-REAXC/reaxc_ffield.cpp +++ b/src/USER-REAXC/reaxc_ffield.cpp @@ -24,6 +24,8 @@ . ----------------------------------------------------------------------*/ +#include +#include #include "pair_reaxc.h" #include "error.h" #include "reaxc_ffield.h" diff --git a/src/USER-REAXC/reaxc_forces.cpp b/src/USER-REAXC/reaxc_forces.cpp index 186cde681a..79094ece43 100644 --- a/src/USER-REAXC/reaxc_forces.cpp +++ b/src/USER-REAXC/reaxc_forces.cpp @@ -24,6 +24,7 @@ . ----------------------------------------------------------------------*/ +#include #include "pair_reaxc.h" #include "reaxc_forces.h" #include "reaxc_bond_orders.h" diff --git a/src/USER-REAXC/reaxc_init_md.cpp b/src/USER-REAXC/reaxc_init_md.cpp index df5de49034..a0e15e98f5 100644 --- a/src/USER-REAXC/reaxc_init_md.cpp +++ b/src/USER-REAXC/reaxc_init_md.cpp @@ -24,6 +24,7 @@ . ----------------------------------------------------------------------*/ +#include #include "pair_reaxc.h" #include "reaxc_init_md.h" #include "reaxc_allocate.h" diff --git a/src/USER-REAXC/reaxc_io_tools.cpp b/src/USER-REAXC/reaxc_io_tools.cpp index 51aa8bca0f..f4a1486c48 100644 --- a/src/USER-REAXC/reaxc_io_tools.cpp +++ b/src/USER-REAXC/reaxc_io_tools.cpp @@ -24,6 +24,7 @@ . ----------------------------------------------------------------------*/ +#include #include "pair_reaxc.h" #include "update.h" #include "reaxc_io_tools.h" @@ -85,7 +86,7 @@ int Init_Output_Files( reax_system *system, control_params *control, /************************ close output files ************************/ -int Close_Output_Files( reax_system *system, control_params *control, +int Close_Output_Files( reax_system *system, control_params * /* control */, output_controls *out_control, mpi_datatypes * /*mpi_data*/ ) { if (out_control->write_steps > 0) diff --git a/src/USER-REAXC/reaxc_multi_body.cpp b/src/USER-REAXC/reaxc_multi_body.cpp index f7d72a2678..371b8ed65e 100644 --- a/src/USER-REAXC/reaxc_multi_body.cpp +++ b/src/USER-REAXC/reaxc_multi_body.cpp @@ -24,6 +24,7 @@ . ----------------------------------------------------------------------*/ +#include #include "pair_reaxc.h" #include "reaxc_multi_body.h" #include "reaxc_bond_orders.h" diff --git a/src/USER-REAXC/reaxc_reset_tools.cpp b/src/USER-REAXC/reaxc_reset_tools.cpp index e00656694c..c72ccbadcd 100644 --- a/src/USER-REAXC/reaxc_reset_tools.cpp +++ b/src/USER-REAXC/reaxc_reset_tools.cpp @@ -24,6 +24,7 @@ . ----------------------------------------------------------------------*/ +#include #include "pair_reaxc.h" #include "reaxc_reset_tools.h" #include "reaxc_list.h" diff --git a/src/USER-REAXC/reaxc_tool_box.cpp b/src/USER-REAXC/reaxc_tool_box.cpp index ffe42e37bb..2cf66d8655 100644 --- a/src/USER-REAXC/reaxc_tool_box.cpp +++ b/src/USER-REAXC/reaxc_tool_box.cpp @@ -24,9 +24,14 @@ . ----------------------------------------------------------------------*/ +#include #include "pair_reaxc.h" #include "reaxc_tool_box.h" +#if !defined(_MSC_VER) +#include +#endif + #include "error.h" struct timeval tim; diff --git a/src/USER-REAXC/reaxc_traj.cpp b/src/USER-REAXC/reaxc_traj.cpp index 356d7b6eeb..a536445113 100644 --- a/src/USER-REAXC/reaxc_traj.cpp +++ b/src/USER-REAXC/reaxc_traj.cpp @@ -24,6 +24,7 @@ . ----------------------------------------------------------------------*/ +#include #include "pair_reaxc.h" #include "reaxc_traj.h" #include "reaxc_list.h" diff --git a/src/USER-REAXC/reaxc_types.h b/src/USER-REAXC/reaxc_types.h index 0821c065cc..319c373927 100644 --- a/src/USER-REAXC/reaxc_types.h +++ b/src/USER-REAXC/reaxc_types.h @@ -27,19 +27,11 @@ #ifndef __REAX_TYPES_H_ #define __REAX_TYPES_H_ -#include #include "lmptype.h" - -#include -#include +#include #include -#include -#include -#include -#include #include "accelerator_kokkos.h" - namespace LAMMPS_NS { class Error;} #if defined LMP_USER_OMP -- GitLab From 312a1fa004bbec6f6e11e800f17c6e3038f0ecdc Mon Sep 17 00:00:00 2001 From: Ellad Tadmor Date: Thu, 27 Jun 2019 07:58:32 -0500 Subject: [PATCH 112/469] Added species to kim_queries in docs and some other edits --- doc/src/kim_commands.txt | 16 ++++++++-------- 1 file changed, 8 insertions(+), 8 deletions(-) diff --git a/doc/src/kim_commands.txt b/doc/src/kim_commands.txt index 9be4a79db5..48637ae722 100644 --- a/doc/src/kim_commands.txt +++ b/doc/src/kim_commands.txt @@ -32,7 +32,7 @@ kim_interactions Si kim_init Sim_LAMMPS_ReaxFF_StrachanVanDuinChakraborty_2003_CHNO__SM_107643900657_000 real kim_init Sim_LAMMPS_ReaxFF_StrachanVanDuinChakraborty_2003_CHNO__SM_107643900657_000 metal unit_conversion_mode kim_interactions C H O -kim_query a0 get_lattice_constant_fcc units=\["angstrom"\] :pre +kim_query a0 get_lattice_constant_fcc species=\["Al"] units=\["angstrom"\] :pre [Description:] @@ -53,7 +53,7 @@ Employing OpenKIM IMs provides LAMMPS users with multiple benefits: Reliability :h5 -All content archived in OpenKIM is subject to quality control by the "KIM Editor"_https://openkim.org/governance/. +All content archived in OpenKIM is reviewed by the "KIM Editor"_https://openkim.org/governance/ for quality. IMs in OpenKIM are archived with full provenance control. Each is associated with a maintainer responsible for the integrity of the content. All changes are tracked and recorded. IMs in OpenKIM are exhaustively tested using "KIM Tests"_https://openkim.org/getting-started/kim-tests/ that compute a host of material properties, and "KIM Verification Checks"_https://openkim.org/about-verification-checks/ that provide the user with information on various aspects of the IM behavior and coding correctness. This information is displayed on the IM's page on "OpenKIM"_https://openkim.org. :ul @@ -73,8 +73,8 @@ Types of IMs in OpenKIM :h4 There are two types of IMs archived in OpenKIM: -The first type is called a {KIM Portable Model} (PM). A KIM PM is an independent computer implementation of an IM written in one of the languages supported by KIM (C, C++, Fortran), which conforms to the KIM Application Programming Interface ("KIM API"_https://openkim.org/kim-api/) Portable Model Interface (PMI) standard. A KIM PM will work seamlessly with any simulation code that supports the KIM API/PMI standard (including LAMMPS; see "complete list of supported codes"_https://openkim.org/projects-using-kim/). -The second type is called a {KIM Simulator Model} (SM). A KIM SM is an IM that is implemented natively within a simulation code ({simulator}) that supports the KIM API/SMI (Simulator Model Interface); in this case LAMMPS. A separate SM package is archived in OpenKIM for each parameterization of the IM, which includes all of the necessary parameter files, LAMMPS commands, and metadata (supported species, units, etc.) needed to run the IM in LAMMPS. :ol +The first type is called a {KIM Portable Model} (PM). A KIM PM is an independent computer implementation of an IM written in one of the languages supported by KIM (C, C++, Fortran) that conforms to the KIM Application Programming Interface ("KIM API"_https://openkim.org/kim-api/) Portable Model Interface (PMI) standard. A KIM PM will work seamlessly with any simulation code that supports the KIM API/PMI standard (including LAMMPS; see "complete list of supported codes"_https://openkim.org/projects-using-kim/). +The second type is called a {KIM Simulator Model} (SM). A KIM SM is an IM that is implemented natively within a simulation code ({simulator}) that supports the KIM API Simulator Model Interface (SMI); in this case LAMMPS. A separate SM package is archived in OpenKIM for each parameterization of the IM, which includes all of the necessary parameter files, LAMMPS commands, and metadata (supported species, units, etc.) needed to run the IM in LAMMPS. :ol With these two IM types, OpenKIM can archive and test almost all IMs that can be used by LAMMPS. (It is easy to contribute new IMs to OpenKIM, see @@ -356,7 +356,7 @@ or analysis phases of LAMMPS simulations. Some examples are given below. kim_init EAM_Dynamo_ErcolessiAdams_1994_Al__MO_123629422045_005 metal boundary p p p -kim_query a0 get_lattice_constant_fcc units=\["angstrom"\] +kim_query a0 get_lattice_constant_fcc species=\["Al"\] units=\["angstrom"\] lattice fcc $\{a0\} ... :pre @@ -377,8 +377,8 @@ changed to: "lattice fcc $\{a0\}*$\{_u_distance\}". kim_init EAM_Dynamo_ErcolessiAdams_1994_Al__MO_123629422045_005 metal boundary p p p -kim_query a0 get_lattice_constant_fcc units=\["angstrom"\] -kim_query alpha get_linear_thermal_expansion_fcc units=\{"1/K"\} +kim_query a0 get_lattice_constant_fcc species=\["Al"\] units=\["angstrom"\] +kim_query alpha get_linear_thermal_expansion_fcc species=\["Al"\] units=\{"1/K"\} variable DeltaT equal 300 lattice fcc $\{a0\}*$\{alpha\}*$\{DeltaT\} ... :pre @@ -395,7 +395,7 @@ kim_init EAM_Dynamo_ErcolessiAdams_1994_Al__MO_123629422045_005 metal ... Build fcc crystal containing some defect and compute the total energy ... which is stored in the variable {Etot} ... -kim_query Ec get_cohesive_energy_fcc units=\["eV"\] +kim_query Ec get_cohesive_energy_fcc species=\["Al"\] units=\["eV"\] variable Eform equal $\{Etot\} - count(all)*$\{Ec\} ... :pre -- GitLab From 84e156d380519a7091f657fb89387d4b866280be Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Thu, 27 Jun 2019 09:14:36 -0400 Subject: [PATCH 113/469] first batch of changes suggested by using include-what-you-use tool --- src/angle.cpp | 1 - src/angle.h | 2 +- src/angle_deprecated.cpp | 1 + src/angle_hybrid.cpp | 3 +-- src/angle_zero.cpp | 3 +-- src/bond.h | 2 +- src/compute.h | 2 +- src/dihedral.h | 2 +- src/dump.h | 2 +- src/fix.h | 2 +- src/improper.h | 2 +- src/lmptype.h | 4 ---- src/main.cpp | 3 --- src/pair.h | 2 +- src/pointers.h | 9 +++++++-- 15 files changed, 18 insertions(+), 22 deletions(-) diff --git a/src/angle.cpp b/src/angle.cpp index 2a297990ac..1b9532ea32 100644 --- a/src/angle.cpp +++ b/src/angle.cpp @@ -11,7 +11,6 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include #include "angle.h" #include "atom.h" #include "comm.h" diff --git a/src/angle.h b/src/angle.h index 3d8371242e..6fc8a664c6 100644 --- a/src/angle.h +++ b/src/angle.h @@ -15,7 +15,7 @@ #define LMP_ANGLE_H #include -#include "pointers.h" +#include "pointers.h" // IWYU pragma: export namespace LAMMPS_NS { diff --git a/src/angle_deprecated.cpp b/src/angle_deprecated.cpp index b5af217b7b..73fcccc53a 100644 --- a/src/angle_deprecated.cpp +++ b/src/angle_deprecated.cpp @@ -16,6 +16,7 @@ ------------------------------------------------------------------------- */ #include +#include #include "angle_deprecated.h" #include "angle_hybrid.h" #include "comm.h" diff --git a/src/angle_hybrid.cpp b/src/angle_hybrid.cpp index 6afa7413b2..47baf770a5 100644 --- a/src/angle_hybrid.cpp +++ b/src/angle_hybrid.cpp @@ -11,13 +11,12 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include +#include #include #include #include "angle_hybrid.h" #include "atom.h" #include "neighbor.h" -#include "domain.h" #include "comm.h" #include "force.h" #include "memory.h" diff --git a/src/angle_zero.cpp b/src/angle_zero.cpp index 6eb127fa58..62eab85aee 100644 --- a/src/angle_zero.cpp +++ b/src/angle_zero.cpp @@ -15,8 +15,7 @@ Contributing author: Carsten Svaneborg (SDU) ------------------------------------------------------------------------- */ -#include -#include +#include #include #include "angle_zero.h" #include "atom.h" diff --git a/src/bond.h b/src/bond.h index 8fb7040832..f9fb9384ed 100644 --- a/src/bond.h +++ b/src/bond.h @@ -15,7 +15,7 @@ #define LMP_BOND_H #include -#include "pointers.h" +#include "pointers.h" // IWYU pragma: export namespace LAMMPS_NS { diff --git a/src/compute.h b/src/compute.h index a023834368..38d001db6f 100644 --- a/src/compute.h +++ b/src/compute.h @@ -14,7 +14,7 @@ #ifndef LMP_COMPUTE_H #define LMP_COMPUTE_H -#include "pointers.h" +#include "pointers.h" // IWYU pragma: export namespace LAMMPS_NS { diff --git a/src/dihedral.h b/src/dihedral.h index f1b42008bf..8654132ed5 100644 --- a/src/dihedral.h +++ b/src/dihedral.h @@ -15,7 +15,7 @@ #define LMP_DIHEDRAL_H #include -#include "pointers.h" +#include "pointers.h" // IWYU pragma: export namespace LAMMPS_NS { diff --git a/src/dump.h b/src/dump.h index 1c6a131f76..d42e7f1f39 100644 --- a/src/dump.h +++ b/src/dump.h @@ -16,7 +16,7 @@ #include #include -#include "pointers.h" +#include "pointers.h" // IWYU pragma: export namespace LAMMPS_NS { diff --git a/src/fix.h b/src/fix.h index 7eaff38bd3..7e55e96269 100644 --- a/src/fix.h +++ b/src/fix.h @@ -14,7 +14,7 @@ #ifndef LMP_FIX_H #define LMP_FIX_H -#include "pointers.h" +#include "pointers.h" // IWYU pragma: export namespace LAMMPS_NS { diff --git a/src/improper.h b/src/improper.h index d940b43a13..4af5ad4a35 100644 --- a/src/improper.h +++ b/src/improper.h @@ -15,7 +15,7 @@ #define LMP_IMPROPER_H #include -#include "pointers.h" +#include "pointers.h" // IWYU pragma: export namespace LAMMPS_NS { diff --git a/src/lmptype.h b/src/lmptype.h index 12fa6cc4fb..8a596e9f83 100644 --- a/src/lmptype.h +++ b/src/lmptype.h @@ -48,10 +48,6 @@ namespace LAMMPS_NS { -// enum used for KOKKOS host/device flags - -enum ExecutionSpace{Host,Device}; - // reserve 2 hi bits in molecular system neigh list for special bonds flag // max local + ghost atoms per processor = 2^30 - 1 diff --git a/src/main.cpp b/src/main.cpp index 8eb5e4e543..1be9c253eb 100644 --- a/src/main.cpp +++ b/src/main.cpp @@ -14,9 +14,6 @@ #include #include "lammps.h" #include "input.h" -#include "error.h" -#include -#include #if defined(LAMMPS_TRAP_FPE) && defined(_GNU_SOURCE) #include diff --git a/src/pair.h b/src/pair.h index 7481514dae..501f3af8f8 100644 --- a/src/pair.h +++ b/src/pair.h @@ -14,7 +14,7 @@ #ifndef LMP_PAIR_H #define LMP_PAIR_H -#include "pointers.h" +#include "pointers.h" // IWYU pragma: export namespace LAMMPS_NS { diff --git a/src/pointers.h b/src/pointers.h index 44967f5135..fc359a5667 100644 --- a/src/pointers.h +++ b/src/pointers.h @@ -21,9 +21,10 @@ #ifndef LMP_POINTERS_H #define LMP_POINTERS_H -#include "lmptype.h" +#include "lmptype.h" // IWYU pragma: export #include -#include "lammps.h" +#include +#include "lammps.h" // IWYU pragma: export namespace LAMMPS_NS { @@ -34,6 +35,10 @@ namespace LAMMPS_NS { #define MIN(A,B) ((A) < (B) ? (A) : (B)) #define MAX(A,B) ((A) > (B) ? (A) : (B)) +// enum used for KOKKOS host/device flags + +enum ExecutionSpace{Host,Device}; + class Pointers { public: Pointers(LAMMPS *ptr) : -- GitLab From 333bec0222ed2f68fa84dc208c0b2f738e5e9da2 Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Thu, 27 Jun 2019 10:12:53 -0400 Subject: [PATCH 114/469] headers that directly or indirectly include pointers.h may assume is loaded, too. --- src/angle.h | 1 - src/angle_hybrid.h | 1 - src/angle_zero.h | 1 - src/atom.cpp | 4 ---- src/bond.h | 1 - src/dihedral.h | 1 - src/dump.h | 1 - src/improper.h | 1 - src/pointers.h | 2 +- 9 files changed, 1 insertion(+), 12 deletions(-) diff --git a/src/angle.h b/src/angle.h index 6fc8a664c6..7a008f7ca7 100644 --- a/src/angle.h +++ b/src/angle.h @@ -14,7 +14,6 @@ #ifndef LMP_ANGLE_H #define LMP_ANGLE_H -#include #include "pointers.h" // IWYU pragma: export namespace LAMMPS_NS { diff --git a/src/angle_hybrid.h b/src/angle_hybrid.h index 4fde71e43f..730d55b0e2 100644 --- a/src/angle_hybrid.h +++ b/src/angle_hybrid.h @@ -20,7 +20,6 @@ AngleStyle(hybrid,AngleHybrid) #ifndef LMP_ANGLE_HYBRID_H #define LMP_ANGLE_HYBRID_H -#include #include "angle.h" namespace LAMMPS_NS { diff --git a/src/angle_zero.h b/src/angle_zero.h index b91be5c8d7..bc1ce0725f 100644 --- a/src/angle_zero.h +++ b/src/angle_zero.h @@ -20,7 +20,6 @@ AngleStyle(zero,AngleZero) #ifndef LMP_ANGLE_ZERO_H #define LMP_ANGLE_ZERO_H -#include #include "angle.h" namespace LAMMPS_NS { diff --git a/src/atom.cpp b/src/atom.cpp index 1f5d5a80c4..8176039165 100644 --- a/src/atom.cpp +++ b/src/atom.cpp @@ -12,11 +12,9 @@ ------------------------------------------------------------------------- */ #include -#include #include #include #include -#include #include "atom.h" #include "style_atom.h" #include "atom_vec.h" @@ -28,14 +26,12 @@ #include "fix.h" #include "compute.h" #include "output.h" -#include "thermo.h" #include "update.h" #include "domain.h" #include "group.h" #include "input.h" #include "variable.h" #include "molecule.h" -#include "atom_masks.h" #include "math_const.h" #include "memory.h" #include "error.h" diff --git a/src/bond.h b/src/bond.h index f9fb9384ed..5c3b933083 100644 --- a/src/bond.h +++ b/src/bond.h @@ -14,7 +14,6 @@ #ifndef LMP_BOND_H #define LMP_BOND_H -#include #include "pointers.h" // IWYU pragma: export namespace LAMMPS_NS { diff --git a/src/dihedral.h b/src/dihedral.h index 8654132ed5..ed6c02c5b9 100644 --- a/src/dihedral.h +++ b/src/dihedral.h @@ -14,7 +14,6 @@ #ifndef LMP_DIHEDRAL_H #define LMP_DIHEDRAL_H -#include #include "pointers.h" // IWYU pragma: export namespace LAMMPS_NS { diff --git a/src/dump.h b/src/dump.h index d42e7f1f39..0173aa3112 100644 --- a/src/dump.h +++ b/src/dump.h @@ -15,7 +15,6 @@ #define LMP_DUMP_H #include -#include #include "pointers.h" // IWYU pragma: export namespace LAMMPS_NS { diff --git a/src/improper.h b/src/improper.h index 4af5ad4a35..234dc9cb20 100644 --- a/src/improper.h +++ b/src/improper.h @@ -14,7 +14,6 @@ #ifndef LMP_IMPROPER_H #define LMP_IMPROPER_H -#include #include "pointers.h" // IWYU pragma: export namespace LAMMPS_NS { diff --git a/src/pointers.h b/src/pointers.h index fc359a5667..f9ef229c90 100644 --- a/src/pointers.h +++ b/src/pointers.h @@ -23,7 +23,7 @@ #include "lmptype.h" // IWYU pragma: export #include -#include +#include // IWYU pragma: export #include "lammps.h" // IWYU pragma: export namespace LAMMPS_NS { -- GitLab From 60adaa24cb8f19d9effc6da6f1ea6967c736a947 Mon Sep 17 00:00:00 2001 From: Stan Moore Date: Thu, 27 Jun 2019 08:52:34 -0600 Subject: [PATCH 115/469] Remove redundant computation --- src/KOKKOS/sna_kokkos_impl.h | 22 ---------------------- src/SNAP/sna.cpp | 22 ---------------------- 2 files changed, 44 deletions(-) diff --git a/src/KOKKOS/sna_kokkos_impl.h b/src/KOKKOS/sna_kokkos_impl.h index e3ce1626d9..9b96cb8a16 100644 --- a/src/KOKKOS/sna_kokkos_impl.h +++ b/src/KOKKOS/sna_kokkos_impl.h @@ -1006,11 +1006,9 @@ void SNAKokkos::compute_duarray(const typename Kokkos::TeamPolicy::compute_duarray(const typename Kokkos::TeamPolicy::compute_duarray(const typename Kokkos::TeamPolicy::compute_duarray(const typename Kokkos::TeamPolicy::compute_duarray(const typename Kokkos::TeamPolicy Date: Thu, 27 Jun 2019 08:53:58 -0600 Subject: [PATCH 116/469] Remove no-op --- src/SNAP/sna.cpp | 2 -- 1 file changed, 2 deletions(-) diff --git a/src/SNAP/sna.cpp b/src/SNAP/sna.cpp index 949e0ee071..ada3f528d2 100644 --- a/src/SNAP/sna.cpp +++ b/src/SNAP/sna.cpp @@ -610,8 +610,6 @@ void SNA::compute_bi() sumzu += 0.5*(ulisttot_r[jju]*zlist_r[jjz] + ulisttot_i[jju]*zlist_i[jjz]); - jjz++; - jju++; } // end if jeven blist[jjb] = 2.0*sumzu; -- GitLab From 48220b39b5813b8144a9ca8aa6dd37aa688b238f Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Thu, 27 Jun 2019 10:13:43 -0400 Subject: [PATCH 117/469] include explicitly in .cpp files, though --- src/angle_hybrid.cpp | 1 + src/atom.cpp | 2 +- src/atom_map.cpp | 2 ++ src/atom_vec.cpp | 1 + src/atom_vec.h | 3 +-- src/atom_vec_body.h | 1 - 6 files changed, 6 insertions(+), 4 deletions(-) diff --git a/src/angle_hybrid.cpp b/src/angle_hybrid.cpp index 47baf770a5..48bb241100 100644 --- a/src/angle_hybrid.cpp +++ b/src/angle_hybrid.cpp @@ -12,6 +12,7 @@ ------------------------------------------------------------------------- */ #include +#include #include #include #include "angle_hybrid.h" diff --git a/src/atom.cpp b/src/atom.cpp index 8176039165..b79febfc20 100644 --- a/src/atom.cpp +++ b/src/atom.cpp @@ -12,6 +12,7 @@ ------------------------------------------------------------------------- */ #include +#include #include #include #include @@ -25,7 +26,6 @@ #include "modify.h" #include "fix.h" #include "compute.h" -#include "output.h" #include "update.h" #include "domain.h" #include "group.h" diff --git a/src/atom_map.cpp b/src/atom_map.cpp index e9cd590624..35d7435ae2 100644 --- a/src/atom_map.cpp +++ b/src/atom_map.cpp @@ -11,6 +11,8 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ +#include "lmptype.h" +#include #include #include "atom.h" #include "comm.h" diff --git a/src/atom_vec.cpp b/src/atom_vec.cpp index a7ca6fcb19..91e1980dd0 100644 --- a/src/atom_vec.cpp +++ b/src/atom_vec.cpp @@ -11,6 +11,7 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ +#include #include #include #include "atom_vec.h" diff --git a/src/atom_vec.h b/src/atom_vec.h index 87fb35d9c7..26c181be1e 100644 --- a/src/atom_vec.h +++ b/src/atom_vec.h @@ -14,8 +14,7 @@ #ifndef LMP_ATOM_VEC_H #define LMP_ATOM_VEC_H -#include -#include "pointers.h" +#include "pointers.h" // IWYU pragma: export namespace LAMMPS_NS { diff --git a/src/atom_vec_body.h b/src/atom_vec_body.h index 4d02c4b3e0..09f03caca1 100644 --- a/src/atom_vec_body.h +++ b/src/atom_vec_body.h @@ -112,7 +112,6 @@ class AtomVecBody : public AtomVec { void grow_bonus(); void copy_bonus(int, int); - //void check(int); }; } -- GitLab From 121947e79d33d2d997bf705ec9b656da2c1edae3 Mon Sep 17 00:00:00 2001 From: Ellad Tadmor Date: Thu, 27 Jun 2019 12:52:20 -0500 Subject: [PATCH 118/469] Added hcp query example to kim_commands --- doc/src/kim_commands.txt | 22 +++++++++++++++++++++- 1 file changed, 21 insertions(+), 1 deletion(-) diff --git a/doc/src/kim_commands.txt b/doc/src/kim_commands.txt index 48637ae722..66319d7a08 100644 --- a/doc/src/kim_commands.txt +++ b/doc/src/kim_commands.txt @@ -352,7 +352,7 @@ webpage at "https://query.openkim.org"_https://query.openkim.org/ The data obtained by {kim_query} commands can be used as part of the setup or analysis phases of LAMMPS simulations. Some examples are given below. -[Define a crystal at its equilibrium lattice constant] +[Define an equilibrium fcc crystal] kim_init EAM_Dynamo_ErcolessiAdams_1994_Al__MO_123629422045_005 metal boundary p p p @@ -373,6 +373,26 @@ Note that in {unit_conversion_mode} the results obtained from a For example, in the above script, the lattice command would need to be changed to: "lattice fcc $\{a0\}*$\{_u_distance\}". +[Define an equilibrium hcp crystal] + +kim_init EAM_Dynamo_Mendelev_2007_Zr__MO_848899341753_000 metal +boundary p p p +kim_query latconst get_lattice_constant_hcp species=\["Zr"\] units=\["angstrom"\] +variable a0 equal latconst_1 +variable c0 equal latconst_2 +variable c_to_a equal $\{c0\}/$\{a0\} +lattice custom $\{a0\} a1 0.5 -0.866025 0 a2 0.5 0.866025 0 a3 0 0 $\{c_to_a\} & + basis 0.333333 0.666666 0.25 basis 0.666666 0.333333 0.75 +... :pre + +In this case the {kim_query} returns two arguments (since the hexagonal +close packed (hcp) structure has two independent lattice constants). +In the case where a query returns multiple results, the default behavior +for {kim_query} is to split these into individual variables of the form +{prefix_I}, where {prefix} is set to the the {kim_query} {variable} argument +and {I} ranges from 1 to the number of returned values. The number and order of +the returned values is determined by the type of query performed. + [Define a crystal at finite temperature accounting for thermal expansion] kim_init EAM_Dynamo_ErcolessiAdams_1994_Al__MO_123629422045_005 metal -- GitLab From 03099d6e54e8b5832e945b32b81afcfeb3a3440b Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Thu, 27 Jun 2019 17:11:53 -0400 Subject: [PATCH 119/469] some more include file consistency changes --- src/atom_vec_body.cpp | 3 +-- src/atom_vec_body.h | 1 - src/atom_vec_ellipsoid.cpp | 2 +- src/atom_vec_line.cpp | 1 - src/atom_vec_sphere.cpp | 2 -- src/atom_vec_tri.cpp | 1 - src/balance.cpp | 3 --- src/balance.h | 1 - src/body.cpp | 3 --- src/body.h | 1 - src/bond.cpp | 2 +- src/bond_hybrid.cpp | 4 ++-- src/pointers.h | 5 +++++ 13 files changed, 10 insertions(+), 19 deletions(-) diff --git a/src/atom_vec_body.cpp b/src/atom_vec_body.cpp index d5f286c077..3e9528d6b9 100644 --- a/src/atom_vec_body.cpp +++ b/src/atom_vec_body.cpp @@ -11,17 +11,16 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include #include #include #include "atom_vec_body.h" +#include "my_pool_chunk.h" #include "style_body.h" #include "body.h" #include "atom.h" #include "comm.h" #include "domain.h" #include "modify.h" -#include "force.h" #include "fix.h" #include "memory.h" #include "error.h" diff --git a/src/atom_vec_body.h b/src/atom_vec_body.h index 09f03caca1..38309648fb 100644 --- a/src/atom_vec_body.h +++ b/src/atom_vec_body.h @@ -21,7 +21,6 @@ AtomStyle(body,AtomVecBody) #define LMP_ATOM_VEC_BODY_H #include "atom_vec.h" -#include "my_pool_chunk.h" namespace LAMMPS_NS { diff --git a/src/atom_vec_ellipsoid.cpp b/src/atom_vec_ellipsoid.cpp index 2bf3f683d0..ad167bef79 100644 --- a/src/atom_vec_ellipsoid.cpp +++ b/src/atom_vec_ellipsoid.cpp @@ -16,11 +16,11 @@ ------------------------------------------------------------------------- */ #include +#include #include "atom_vec_ellipsoid.h" #include "math_extra.h" #include "atom.h" #include "comm.h" -#include "force.h" #include "domain.h" #include "modify.h" #include "fix.h" diff --git a/src/atom_vec_line.cpp b/src/atom_vec_line.cpp index 020b622c93..6b197d2663 100644 --- a/src/atom_vec_line.cpp +++ b/src/atom_vec_line.cpp @@ -19,7 +19,6 @@ #include "comm.h" #include "domain.h" #include "modify.h" -#include "force.h" #include "fix.h" #include "math_const.h" #include "memory.h" diff --git a/src/atom_vec_sphere.cpp b/src/atom_vec_sphere.cpp index dec98e5200..b3f4bfe391 100644 --- a/src/atom_vec_sphere.cpp +++ b/src/atom_vec_sphere.cpp @@ -11,7 +11,6 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include #include #include #include "atom_vec_sphere.h" @@ -19,7 +18,6 @@ #include "comm.h" #include "domain.h" #include "modify.h" -#include "force.h" #include "fix.h" #include "fix_adapt.h" #include "math_const.h" diff --git a/src/atom_vec_tri.cpp b/src/atom_vec_tri.cpp index 8fbe0a92dc..b0b6eca19b 100644 --- a/src/atom_vec_tri.cpp +++ b/src/atom_vec_tri.cpp @@ -20,7 +20,6 @@ #include "comm.h" #include "domain.h" #include "modify.h" -#include "force.h" #include "fix.h" #include "math_const.h" #include "memory.h" diff --git a/src/balance.cpp b/src/balance.cpp index 61ac895467..04f342b69b 100644 --- a/src/balance.cpp +++ b/src/balance.cpp @@ -20,7 +20,6 @@ #include #include -#include #include #include "balance.h" #include "atom.h" @@ -30,7 +29,6 @@ #include "domain.h" #include "force.h" #include "update.h" -#include "group.h" #include "modify.h" #include "fix_store.h" #include "imbalance.h" @@ -39,7 +37,6 @@ #include "imbalance_neigh.h" #include "imbalance_store.h" #include "imbalance_var.h" -#include "timer.h" #include "memory.h" #include "error.h" diff --git a/src/balance.h b/src/balance.h index 420031502a..424da33757 100644 --- a/src/balance.h +++ b/src/balance.h @@ -20,7 +20,6 @@ CommandStyle(balance,Balance) #ifndef LMP_BALANCE_H #define LMP_BALANCE_H -#include #include "pointers.h" namespace LAMMPS_NS { diff --git a/src/body.cpp b/src/body.cpp index 78e2f5d71b..10f88bd43b 100644 --- a/src/body.cpp +++ b/src/body.cpp @@ -11,11 +11,8 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include -#include #include #include "body.h" -#include "error.h" using namespace LAMMPS_NS; diff --git a/src/body.h b/src/body.h index 59001620f8..44581b75f6 100644 --- a/src/body.h +++ b/src/body.h @@ -16,7 +16,6 @@ #include "pointers.h" #include "atom_vec_body.h" -#include "my_pool_chunk.h" namespace LAMMPS_NS { diff --git a/src/bond.cpp b/src/bond.cpp index edcd869425..0d50b7e3e5 100644 --- a/src/bond.cpp +++ b/src/bond.cpp @@ -11,7 +11,7 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include +#include #include "bond.h" #include "atom.h" #include "comm.h" diff --git a/src/bond_hybrid.cpp b/src/bond_hybrid.cpp index 65609b4b6e..0fb23a3214 100644 --- a/src/bond_hybrid.cpp +++ b/src/bond_hybrid.cpp @@ -11,13 +11,13 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include +#include +#include #include #include #include "bond_hybrid.h" #include "atom.h" #include "neighbor.h" -#include "domain.h" #include "comm.h" #include "force.h" #include "memory.h" diff --git a/src/pointers.h b/src/pointers.h index f9ef229c90..5df5b72d47 100644 --- a/src/pointers.h +++ b/src/pointers.h @@ -39,6 +39,11 @@ namespace LAMMPS_NS { enum ExecutionSpace{Host,Device}; +// global forward declarations + +template class MyPoolChunk; +template class MyPage; + class Pointers { public: Pointers(LAMMPS *ptr) : -- GitLab From 2c0a66b7f8c21ea580dc7bb893461d3585969559 Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Thu, 27 Jun 2019 20:50:25 -0400 Subject: [PATCH 120/469] increase buffer size of fix tune/kspace. header cleanup. remove use of iostreams --- src/KSPACE/fix_tune_kspace.cpp | 41 +++++++++++++++++----------------- src/KSPACE/fix_tune_kspace.h | 9 ++++---- 2 files changed, 24 insertions(+), 26 deletions(-) diff --git a/src/KSPACE/fix_tune_kspace.cpp b/src/KSPACE/fix_tune_kspace.cpp index 0c726985dc..2b22b44340 100644 --- a/src/KSPACE/fix_tune_kspace.cpp +++ b/src/KSPACE/fix_tune_kspace.cpp @@ -15,13 +15,11 @@ Contributing author: Paul Crozier (SNL) ------------------------------------------------------------------------- */ +#include #include -#include +#include #include "fix_tune_kspace.h" #include "update.h" -#include "domain.h" -#include "atom.h" -#include "comm.h" #include "force.h" #include "kspace.h" #include "pair.h" @@ -31,9 +29,6 @@ #include "neighbor.h" #include "modify.h" #include "compute.h" -#include -#include -#include #define SWAP(a,b) {temp=(a);(a)=(b);(b)=temp;} #define SIGN(a,b) ((b) >= 0.0 ? fabs(a) : -fabs(a)) #define GOLD 1.618034 @@ -101,7 +96,7 @@ void FixTuneKspace::init() double old_acc = force->kspace->accuracy/force->kspace->two_charge_force; char old_acc_str[16]; snprintf(old_acc_str,16,"%g",old_acc); - strcpy(new_acc_str,old_acc_str); + strncpy(new_acc_str,old_acc_str,16); int itmp; double *p_cutoff = (double *) force->pair->extract("cut_coul",itmp); @@ -131,36 +126,37 @@ void FixTuneKspace::pre_exchange() // test Ewald store_old_kspace_settings(); strcpy(new_kspace_style,"ewald"); - sprintf(new_pair_style,"%s/long",base_pair_style); + snprintf(new_pair_style,64,"%s/long",base_pair_style); update_pair_style(new_pair_style,pair_cut_coul); update_kspace_style(new_kspace_style,new_acc_str); } else if (niter == 2) { // test PPPM store_old_kspace_settings(); strcpy(new_kspace_style,"pppm"); - sprintf(new_pair_style,"%s/long",base_pair_style); + snprintf(new_pair_style,64,"%s/long",base_pair_style); update_pair_style(new_pair_style,pair_cut_coul); update_kspace_style(new_kspace_style,new_acc_str); } else if (niter == 3) { // test MSM store_old_kspace_settings(); strcpy(new_kspace_style,"msm"); - sprintf(new_pair_style,"%s/msm",base_pair_style); + snprintf(new_pair_style,64,"%s/msm",base_pair_style); update_pair_style(new_pair_style,pair_cut_coul); update_kspace_style(new_kspace_style,new_acc_str); } else if (niter == 4) { store_old_kspace_settings(); - cout << "ewald_time = " << ewald_time << endl; - cout << "pppm_time = " << pppm_time << endl; - cout << "msm_time = " << msm_time << endl; + if (screen) fprintf(screen,"ewald_time = %g\npppm_time = %g\nmsm_time = %g", + ewald_time, pppm_time, msm_time); + if (logfile) fprintf(logfile,"ewald_time = %g\npppm_time = %g\nmsm_time = %g", + ewald_time, pppm_time, msm_time); // switch to fastest one strcpy(new_kspace_style,"ewald"); - sprintf(new_pair_style,"%s/long",base_pair_style); + snprintf(new_pair_style,64,"%s/long",base_pair_style); if (pppm_time < ewald_time && pppm_time < msm_time) strcpy(new_kspace_style,"pppm"); else if (msm_time < pppm_time && msm_time < ewald_time) { strcpy(new_kspace_style,"msm"); - sprintf(new_pair_style,"%s/msm",base_pair_style); + snprintf(new_pair_style,64,"%s/msm",base_pair_style); } update_pair_style(new_pair_style,pair_cut_coul); update_kspace_style(new_kspace_style,new_acc_str); @@ -243,8 +239,8 @@ void FixTuneKspace::update_pair_style(char *new_pair_style, p_pair_settings_file = tmpfile(); force->pair->write_restart(p_pair_settings_file); rewind(p_pair_settings_file); - - cout << "Creating new pair style: " << new_pair_style << endl; + if (screen) fprintf(screen,"Creating new pair style: %s\n",new_pair_style); + if (logfile) fprintf(logfile,"Creating new pair style: %s\n",new_pair_style); // delete old pair style and create new one force->create_pair(new_pair_style,1); @@ -253,7 +249,8 @@ void FixTuneKspace::update_pair_style(char *new_pair_style, double *pcutoff = (double *) force->pair->extract("cut_coul",itmp); double current_cutoff = *pcutoff; - cout << "Coulomb cutoff for real space: " << current_cutoff << endl; + if (screen) fprintf(screen,"Coulomb cutoff for real space: %g\n", current_cutoff); + if (logfile) fprintf(logfile,"Coulomb cutoff for real space: %g\n", current_cutoff); // close temporary file fclose(p_pair_settings_file); @@ -321,7 +318,8 @@ void FixTuneKspace::adjust_rcut(double time) int itmp; double *p_cutoff = (double *) force->pair->extract("cut_coul",itmp); double current_cutoff = *p_cutoff; - cout << "Old Coulomb cutoff for real space: " << current_cutoff << endl; + if (screen) fprintf(screen,"Old Coulomb cutoff for real space: %g\n",current_cutoff); + if (logfile) fprintf(logfile,"Old Coulomb cutoff for real space: %g\n",current_cutoff); // use Brent's method from Numerical Recipes to find optimal real space cutoff @@ -391,7 +389,8 @@ void FixTuneKspace::adjust_rcut(double time) // report the new cutoff double *new_cutoff = (double *) force->pair->extract("cut_coul",itmp); current_cutoff = *new_cutoff; - cout << "Adjusted Coulomb cutoff for real space: " << current_cutoff << endl; + if (screen) fprintf(screen,"Adjusted Coulomb cutoff for real space: %g\n", current_cutoff); + if (logfile) fprintf(logfile,"Adjusted Coulomb cutoff for real space: %g\n", current_cutoff); store_old_kspace_settings(); update_pair_style(new_pair_style,pair_cut_coul); diff --git a/src/KSPACE/fix_tune_kspace.h b/src/KSPACE/fix_tune_kspace.h index 6f40fc8711..1ccd735317 100644 --- a/src/KSPACE/fix_tune_kspace.h +++ b/src/KSPACE/fix_tune_kspace.h @@ -20,7 +20,6 @@ FixStyle(tune/kspace,FixTuneKspace) #ifndef LMP_FIX_TUNE_KSPACE_H #define LMP_FIX_TUNE_KSPACE_H -#include #include "fix.h" namespace LAMMPS_NS { @@ -52,10 +51,10 @@ class FixTuneKspace : public Fix { double ewald_time,pppm_time,msm_time; double pair_cut_coul; - char new_acc_str[12]; - char new_kspace_style[20]; - char new_pair_style[20]; - char base_pair_style[20]; + char new_acc_str[16]; + char new_kspace_style[64]; + char new_pair_style[64]; + char base_pair_style[64]; int old_differentiation_flag; int old_slabflag; -- GitLab From 932f052cbf0cf4e94a4df52bbe3414dfeca90959 Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Thu, 27 Jun 2019 20:52:23 -0400 Subject: [PATCH 121/469] more header cleanup --- src/GPU/pair_vashishta_gpu.cpp | 1 - src/angle_deprecated.cpp | 1 - src/angle_hybrid.cpp | 1 - src/atom.cpp | 1 - src/atom_map.cpp | 2 +- src/atom_vec.cpp | 1 - src/atom_vec_hybrid.h | 1 - src/bond_zero.cpp | 4 ++-- src/change_box.cpp | 1 - src/citeme.cpp | 3 +-- src/citeme.h | 3 +-- src/comm.cpp | 1 + src/comm_brick.cpp | 8 -------- src/hashlittle.cpp | 2 +- src/lammps.cpp | 1 + 15 files changed, 8 insertions(+), 23 deletions(-) diff --git a/src/GPU/pair_vashishta_gpu.cpp b/src/GPU/pair_vashishta_gpu.cpp index b496359b8a..5539653756 100644 --- a/src/GPU/pair_vashishta_gpu.cpp +++ b/src/GPU/pair_vashishta_gpu.cpp @@ -14,7 +14,6 @@ /* ---------------------------------------------------------------------- Contributing author: Anders Hafreager (UiO) ------------------------------------------------------------------------- */ -#include #include #include #include diff --git a/src/angle_deprecated.cpp b/src/angle_deprecated.cpp index 73fcccc53a..b5af217b7b 100644 --- a/src/angle_deprecated.cpp +++ b/src/angle_deprecated.cpp @@ -16,7 +16,6 @@ ------------------------------------------------------------------------- */ #include -#include #include "angle_deprecated.h" #include "angle_hybrid.h" #include "comm.h" diff --git a/src/angle_hybrid.cpp b/src/angle_hybrid.cpp index 48bb241100..47baf770a5 100644 --- a/src/angle_hybrid.cpp +++ b/src/angle_hybrid.cpp @@ -12,7 +12,6 @@ ------------------------------------------------------------------------- */ #include -#include #include #include #include "angle_hybrid.h" diff --git a/src/atom.cpp b/src/atom.cpp index b79febfc20..eab8a3063d 100644 --- a/src/atom.cpp +++ b/src/atom.cpp @@ -13,7 +13,6 @@ #include #include -#include #include #include #include "atom.h" diff --git a/src/atom_map.cpp b/src/atom_map.cpp index 35d7435ae2..b14ebdba68 100644 --- a/src/atom_map.cpp +++ b/src/atom_map.cpp @@ -11,7 +11,7 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include "lmptype.h" +#include "pointers.h" #include #include #include "atom.h" diff --git a/src/atom_vec.cpp b/src/atom_vec.cpp index 91e1980dd0..a7ca6fcb19 100644 --- a/src/atom_vec.cpp +++ b/src/atom_vec.cpp @@ -11,7 +11,6 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include #include #include #include "atom_vec.h" diff --git a/src/atom_vec_hybrid.h b/src/atom_vec_hybrid.h index a027923a17..8129baccba 100644 --- a/src/atom_vec_hybrid.h +++ b/src/atom_vec_hybrid.h @@ -20,7 +20,6 @@ AtomStyle(hybrid,AtomVecHybrid) #ifndef LMP_ATOM_VEC_HYBRID_H #define LMP_ATOM_VEC_HYBRID_H -#include #include "atom_vec.h" namespace LAMMPS_NS { diff --git a/src/bond_zero.cpp b/src/bond_zero.cpp index 0847cf9e6b..3932846cb4 100644 --- a/src/bond_zero.cpp +++ b/src/bond_zero.cpp @@ -15,8 +15,8 @@ Contributing author: Carsten Svaneborg (SDU) ------------------------------------------------------------------------- */ -#include -#include +#include +#include #include #include "bond_zero.h" #include "atom.h" diff --git a/src/change_box.cpp b/src/change_box.cpp index b7d3cb245f..1fed65b430 100644 --- a/src/change_box.cpp +++ b/src/change_box.cpp @@ -13,7 +13,6 @@ #include #include -#include #include #include "change_box.h" #include "atom.h" diff --git a/src/citeme.cpp b/src/citeme.cpp index d021722671..24896b448c 100644 --- a/src/citeme.cpp +++ b/src/citeme.cpp @@ -11,10 +11,9 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ +#include #include "citeme.h" -#include "version.h" #include "universe.h" -#include "error.h" using namespace LAMMPS_NS; diff --git a/src/citeme.h b/src/citeme.h index 262b284337..c383ec2227 100644 --- a/src/citeme.h +++ b/src/citeme.h @@ -15,7 +15,6 @@ #define LMP_CITEME_H #include "pointers.h" -#include #include namespace LAMMPS_NS { @@ -29,7 +28,7 @@ class CiteMe : protected Pointers { private: FILE *fp; // opaque pointer to log.cite file object typedef std::set citeset; - citeset *cs; // registered set of publications + citeset *cs; // registered set of publications }; } diff --git a/src/comm.cpp b/src/comm.cpp index 052de93793..5f846cf292 100644 --- a/src/comm.cpp +++ b/src/comm.cpp @@ -21,6 +21,7 @@ #include "force.h" #include "pair.h" #include "modify.h" +#include "neighbor.h" #include "fix.h" #include "compute.h" #include "domain.h" diff --git a/src/comm_brick.cpp b/src/comm_brick.cpp index 330551aaed..47f60a3da6 100644 --- a/src/comm_brick.cpp +++ b/src/comm_brick.cpp @@ -19,23 +19,15 @@ #include #include #include -#include #include "comm_brick.h" -#include "comm_tiled.h" -#include "universe.h" #include "atom.h" #include "atom_vec.h" -#include "force.h" #include "pair.h" #include "domain.h" #include "neighbor.h" -#include "group.h" -#include "modify.h" #include "fix.h" #include "compute.h" -#include "output.h" #include "dump.h" -#include "math_extra.h" #include "error.h" #include "memory.h" diff --git a/src/hashlittle.cpp b/src/hashlittle.cpp index f612be9eeb..42109abd24 100644 --- a/src/hashlittle.cpp +++ b/src/hashlittle.cpp @@ -3,7 +3,7 @@ // bob_jenkins@burtleburtle.net #include -#include +#include #include // if the system defines the __BYTE_ORDER__ define, diff --git a/src/lammps.cpp b/src/lammps.cpp index 320d89ed52..83a2f057ee 100644 --- a/src/lammps.cpp +++ b/src/lammps.cpp @@ -12,6 +12,7 @@ ------------------------------------------------------------------------- */ #include +#include #include #include #include -- GitLab From 9c53a5ca3f1c756601b091a97ea5020a7187d2e5 Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Thu, 27 Jun 2019 21:40:28 -0400 Subject: [PATCH 122/469] add first draft of a summary of the rules for include files --- doc/include-file-conventions.md | 125 ++++++++++++++++++++++++++++++++ 1 file changed, 125 insertions(+) create mode 100644 doc/include-file-conventions.md diff --git a/doc/include-file-conventions.md b/doc/include-file-conventions.md new file mode 100644 index 0000000000..5152051ba5 --- /dev/null +++ b/doc/include-file-conventions.md @@ -0,0 +1,125 @@ +# Outline of include file conventions in LAMMPS + +This purpose of this document is to provide a point of reference +for LAMMPS developers and contributors as to what include files +and definitions to put where into LAMMPS source. +Last change 2019-06-27 + +## Table of Contents + + * [Motivation](#motivation) + * [Rules](#rules) + * [Tools](#tools) + * [Legacy Code](#legacy-code) + +## Motivation + +The conventions outlined in this document are supposed to help making +maintenance of the LAMMPS software easier. By trying to achieve +consistency across files contributed by different developers, it will +become easier to modify and adjust files by the code maintainers, and +overall the chance for errors or portability issues will be reduced. +Also the rules employed are supposed to minimize naming conflicts and +simplify dependencies between files (and thus speed up compilation), as +well as make otherwise hidden dependencies visible. + +## Rules + +Below are the various rules that are applied. Not all a enforced +strictly and automatically. If there are no significant side effects, +exceptions may be possible for cases, where a full compliance to the +rules may require a large effort compared to the benefit. + +### Core Files Versus Package Files + +All rules listed below are most strictly observed for core LAMMPS files. +Which are the files that are not part of a package and files of the +packages MOLECULE, MANYBODY, KSPACE, and RIGID. On the other end of +the spectrum are USER packages and legacy packages that predate these +rules and thus may not be fully compliant. Also new contributions +will be checked more closely, while existing code is incrementally +adapted to the rules as time and required effort permits. + +### System Versus Local Header Files + +All system or library provided include files are included with angular +brackets (examples: `#include ` or `#include `) while +include files provided with LAMMPS are included with double quotes +(examples: `#include "pointers.h"` or `#include "compute_temp.h"`). + +For headers declaring functions of the C-library, the corresponding +C++ versions should be included (examples: `#include ` or +`#include `). However, those are limited to those defined +in the C++98 standard. Some files thus must use the older style unless +the minimum C++ standard requirement of LAMMPS is lifted to C++11 or +even beyond (examples: `#include ` versus `#include ` +or `#include ` versus `#include `). + +### C++ Standard Compliance + +LAMMPS core files currently correspond to the C++98 standard. Files +requiring C++11 or later are only permitted in (optional) packages +and particularly packages that are not part of the list of commonly +used packages like MOLECULE, KSPACE, MANYBODY, or RIGID. + +Also, LAMMPS uses the C-style stdio library for I/O instead of iostreams. +Since using both at the same time can cause problems, iostreams should +be avoided where possible. + +### Lean Header Files + +Header files will typically contain the definition of a (single) class. +These header files should have as few include statements as possible. +This is particularly important for classes that implement a "style" and +thus use a macro of the kind `SomeStyle(some/name,SomeName)`. These will +be all included in the auto-generated `"some_style.h"` files which will +result in a high potential for direct or indirect symbol name clashes. + +In the ideal case, the header would only include one file defining the +parent class. That would typically be either `#include "pointers.h"` for +the `Pointers` class, or a header of a class derived from it like +`#include "pair.h"` for the `Pair` class and so on. Referenced to other +classes inside the class should be make through pointers, for which forward +declarations (inside the `LAMMPS_NS` or the new class'es namespace) can +be employed. The full definition will then be included into the corresponding +implementation file. In the given example from above, the header file +would be called `some_name.h` and the implementation `some_name.cpp` (all +lower case with underscores, while the class itself would be in camel case +and no underscores, and the style name with lower case names separated by +a forward slash). + +### Implementation Files + +In the implementation files (typically, those would have the same base name +as the corresponding header with a .cpp extension instead of .h) include +statments should follow the "include what you use" principle. + +### Special Cases and Exceptions + +#### pointers.h + +The `pointer.h` header file also includes `cstdio` and `lmptype.h` +(and throught it `stdint.h`, `intttypes.h`, and `climits`). +This means any header including `pointers.h` can assume that `FILE`, +`NULL`, `INT_MAX` are defined. + +## Tools + +The [Include What You Use tool](https://include-what-you-use.org/) +can be used to provide supporting information about compliance with +the rules listed here. There are some limitations and the IWWU tool +may give incorrect advice. The tools is activated by setting the +CMake variable `CMAKE_CXX_INCLUDE_WHAT_YOU_USE` variable to the +path of the `include-what-you-use` command. When activated, the +tool will be run after each compilation and provide suggestions for +which include files should be added or removed. + +## Legacy Code + +A lot of code predates the application of the rules in this document, +and those rules are a moving target as well. So there is going to be +significant chunks of code, that does not fully comply. This applies +for example to the USER-REAXC, or the USER-ATC package. The LAMMPS +developers are dedicated to make an effort to improve the compliance +and welcome volunteers wanting to help with the process. + -- GitLab From 86a9e4fca24a7cefc832333a3ff75a057763e370 Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Thu, 27 Jun 2019 21:40:50 -0400 Subject: [PATCH 123/469] make body package compile again --- src/BODY/body_nparticle.cpp | 1 + src/BODY/body_rounded_polygon.cpp | 1 + src/BODY/body_rounded_polyhedron.cpp | 1 + 3 files changed, 3 insertions(+) diff --git a/src/BODY/body_nparticle.cpp b/src/BODY/body_nparticle.cpp index 10529ad3af..21070107f5 100644 --- a/src/BODY/body_nparticle.cpp +++ b/src/BODY/body_nparticle.cpp @@ -13,6 +13,7 @@ #include #include "body_nparticle.h" +#include "my_pool_chunk.h" #include "math_extra.h" #include "atom_vec_body.h" #include "atom.h" diff --git a/src/BODY/body_rounded_polygon.cpp b/src/BODY/body_rounded_polygon.cpp index d352c789d7..f7741ada88 100644 --- a/src/BODY/body_rounded_polygon.cpp +++ b/src/BODY/body_rounded_polygon.cpp @@ -17,6 +17,7 @@ #include #include "body_rounded_polygon.h" +#include "my_pool_chunk.h" #include "atom_vec_body.h" #include "atom.h" #include "force.h" diff --git a/src/BODY/body_rounded_polyhedron.cpp b/src/BODY/body_rounded_polyhedron.cpp index 99a380a932..34d918f1f6 100644 --- a/src/BODY/body_rounded_polyhedron.cpp +++ b/src/BODY/body_rounded_polyhedron.cpp @@ -17,6 +17,7 @@ #include #include "body_rounded_polyhedron.h" +#include "my_pool_chunk.h" #include "atom_vec_body.h" #include "atom.h" #include "force.h" -- GitLab From 4ec3a508fc1731e5d6d3708005515ff0addace9f Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Thu, 27 Jun 2019 21:54:07 -0400 Subject: [PATCH 124/469] bulk removal of #include from header files --- src/CLASS2/angle_class2.h | 1 - src/CLASS2/bond_class2.h | 1 - src/CLASS2/dihedral_class2.h | 1 - src/CLASS2/improper_class2.h | 1 - src/GPU/pair_eam_gpu.h | 1 - src/KOKKOS/atom_vec_hybrid_kokkos.h | 1 - src/KOKKOS/pair_eam_alloy_kokkos.h | 1 - src/KOKKOS/pair_eam_fs_kokkos.h | 1 - src/KOKKOS/pair_eam_kokkos.h | 1 - src/KOKKOS/pair_hybrid_kokkos.h | 1 - src/KOKKOS/pair_reaxc_kokkos.h | 1 - src/KOKKOS/pair_tersoff_kokkos.h | 1 - src/KOKKOS/pair_tersoff_mod_kokkos.h | 1 - src/KOKKOS/pair_tersoff_zbl_kokkos.h | 1 - src/MANYBODY/fix_qeq_comb.h | 1 - src/MANYBODY/pair_eam.h | 1 - src/MANYBODY/pair_eim.h | 1 - src/MC/fix_atom_swap.h | 1 - src/MC/fix_gcmc.h | 1 - src/MISC/fix_deposit.h | 1 - src/MOLECULE/angle_charmm.h | 1 - src/MOLECULE/angle_cosine.h | 1 - src/MOLECULE/angle_cosine_delta.h | 1 - src/MOLECULE/angle_cosine_periodic.h | 1 - src/MOLECULE/angle_cosine_squared.h | 1 - src/MOLECULE/angle_harmonic.h | 1 - src/MOLECULE/angle_table.h | 1 - src/MOLECULE/bond_fene.h | 1 - src/MOLECULE/bond_fene_expand.h | 1 - src/MOLECULE/bond_gromos.h | 1 - src/MOLECULE/bond_harmonic.h | 1 - src/MOLECULE/bond_morse.h | 1 - src/MOLECULE/bond_nonlinear.h | 1 - src/MOLECULE/bond_quartic.h | 1 - src/MOLECULE/bond_table.h | 1 - src/MOLECULE/dihedral_charmm.h | 1 - src/MOLECULE/dihedral_charmmfsw.h | 1 - src/MOLECULE/dihedral_harmonic.h | 1 - src/MOLECULE/dihedral_helix.h | 1 - src/MOLECULE/dihedral_multi_harmonic.h | 1 - src/MOLECULE/dihedral_opls.h | 1 - src/MOLECULE/improper_cvff.h | 1 - src/MOLECULE/improper_harmonic.h | 1 - src/MOLECULE/improper_umbrella.h | 1 - src/REPLICA/neb.h | 1 - src/SPIN/neb_spin.h | 1 - src/USER-CGDNA/mf_oxdna.h | 1 - src/USER-CGSDK/angle_sdk.h | 1 - src/USER-DIFFRACTION/fix_saed_vtk.h | 1 - src/USER-INTEL/angle_charmm_intel.h | 1 - src/USER-INTEL/angle_harmonic_intel.h | 1 - src/USER-INTEL/bond_fene_intel.h | 1 - src/USER-INTEL/bond_harmonic_intel.h | 1 - src/USER-INTEL/improper_cvff_intel.h | 1 - src/USER-INTEL/improper_harmonic_intel.h | 1 - src/USER-INTEL/intel_simd.h | 1 - src/USER-INTEL/pair_eam_intel.h | 1 - src/USER-MANIFOLD/manifold_thylakoid.h | 1 - src/USER-MGPT/mgpt_readpot.h | 1 - src/USER-MGPT/pair_mgpt.h | 1 - src/USER-MISC/angle_cosine_shift.h | 1 - src/USER-MISC/angle_cosine_shift_exp.h | 1 - src/USER-MISC/angle_dipole.h | 1 - src/USER-MISC/angle_fourier.h | 1 - src/USER-MISC/angle_fourier_simple.h | 1 - src/USER-MISC/angle_quartic.h | 1 - src/USER-MISC/bond_harmonic_shift.h | 1 - src/USER-MISC/bond_harmonic_shift_cut.h | 1 - src/USER-MISC/dihedral_cosine_shift_exp.h | 1 - src/USER-MISC/dihedral_fourier.h | 1 - src/USER-MISC/dihedral_nharmonic.h | 1 - src/USER-MISC/dihedral_quadratic.h | 1 - src/USER-MISC/dihedral_spherical.h | 1 - src/USER-MISC/fix_ave_correlate_long.h | 1 - src/USER-MISC/fix_srp.h | 1 - src/USER-MISC/improper_cossq.h | 1 - src/USER-MISC/improper_distance.h | 1 - src/USER-MISC/improper_fourier.h | 1 - src/USER-MISC/improper_ring.h | 1 - src/USER-MOFFF/angle_class2_p6.h | 1 - src/USER-MOFFF/angle_cosine_buck6d.h | 1 - src/USER-MOFFF/improper_inversion_harmonic.h | 1 - src/USER-REAXC/fix_reaxc_bonds.h | 1 - src/bond_hybrid.h | 1 - src/bond_zero.h | 1 - src/citeme.cpp | 1 - src/comm_brick.cpp | 1 - src/comm_tiled.cpp | 5 +---- src/comm_tiled.h | 1 + src/compute.cpp | 4 ---- src/compute_adf.h | 1 - src/compute_rdf.h | 1 - src/dihedral_hybrid.h | 1 - src/dihedral_zero.h | 1 - src/fix_ave_atom.h | 1 - src/fix_ave_chunk.h | 1 - src/fix_ave_correlate.h | 1 - src/fix_ave_histo.h | 1 - src/fix_ave_histo_weight.h | 1 - src/fix_ave_time.h | 1 - src/fix_balance.h | 1 - src/fix_halt.h | 1 - src/fix_move.h | 1 - src/fix_print.h | 1 - src/fix_store.h | 1 - src/fix_tmd.h | 1 - src/force.h | 1 - src/group.h | 1 - src/image.h | 1 - src/imbalance.h | 1 - src/improper_hybrid.h | 1 - src/improper_zero.h | 1 - src/input.h | 1 - src/lammps.h | 1 - src/modify.h | 1 - src/pair_hybrid.h | 1 - src/read_data.h | 1 - src/read_dump.h | 1 - src/read_restart.h | 1 - src/universe.h | 1 - src/variable.h | 1 - src/write_coeff.h | 1 - src/write_data.h | 1 - src/write_restart.h | 1 - 124 files changed, 2 insertions(+), 129 deletions(-) diff --git a/src/CLASS2/angle_class2.h b/src/CLASS2/angle_class2.h index 8444ada057..cc155747ac 100644 --- a/src/CLASS2/angle_class2.h +++ b/src/CLASS2/angle_class2.h @@ -20,7 +20,6 @@ AngleStyle(class2,AngleClass2) #ifndef LMP_ANGLE_CLASS2_H #define LMP_ANGLE_CLASS2_H -#include #include "angle.h" namespace LAMMPS_NS { diff --git a/src/CLASS2/bond_class2.h b/src/CLASS2/bond_class2.h index 89d930b548..f0fcc6825e 100644 --- a/src/CLASS2/bond_class2.h +++ b/src/CLASS2/bond_class2.h @@ -20,7 +20,6 @@ BondStyle(class2,BondClass2) #ifndef LMP_BOND_CLASS2_H #define LMP_BOND_CLASS2_H -#include #include "bond.h" namespace LAMMPS_NS { diff --git a/src/CLASS2/dihedral_class2.h b/src/CLASS2/dihedral_class2.h index a4ea9e4bd9..32cd289137 100644 --- a/src/CLASS2/dihedral_class2.h +++ b/src/CLASS2/dihedral_class2.h @@ -20,7 +20,6 @@ DihedralStyle(class2,DihedralClass2) #ifndef LMP_DIHEDRAL_CLASS2_H #define LMP_DIHEDRAL_CLASS2_H -#include #include "dihedral.h" namespace LAMMPS_NS { diff --git a/src/CLASS2/improper_class2.h b/src/CLASS2/improper_class2.h index 1cc3417731..cac805046a 100644 --- a/src/CLASS2/improper_class2.h +++ b/src/CLASS2/improper_class2.h @@ -20,7 +20,6 @@ ImproperStyle(class2,ImproperClass2) #ifndef LMP_IMPROPER_CLASS2_H #define LMP_IMPROPER_CLASS2_H -#include #include "improper.h" namespace LAMMPS_NS { diff --git a/src/GPU/pair_eam_gpu.h b/src/GPU/pair_eam_gpu.h index 099529f3df..e4742a3bef 100644 --- a/src/GPU/pair_eam_gpu.h +++ b/src/GPU/pair_eam_gpu.h @@ -20,7 +20,6 @@ PairStyle(eam/gpu,PairEAMGPU) #ifndef LMP_PAIR_EAM_GPU_H #define LMP_PAIR_EAM_GPU_H -#include #include "pair_eam.h" namespace LAMMPS_NS { diff --git a/src/KOKKOS/atom_vec_hybrid_kokkos.h b/src/KOKKOS/atom_vec_hybrid_kokkos.h index 1bbbd26319..4cfb186b17 100644 --- a/src/KOKKOS/atom_vec_hybrid_kokkos.h +++ b/src/KOKKOS/atom_vec_hybrid_kokkos.h @@ -20,7 +20,6 @@ AtomStyle(hybrid/kk,AtomVecHybridKokkos) #ifndef LMP_ATOM_VEC_HYBRID_KOKKOS_H #define LMP_ATOM_VEC_HYBRID_KOKKOS_H -#include #include "atom_vec_kokkos.h" #include "kokkos_type.h" diff --git a/src/KOKKOS/pair_eam_alloy_kokkos.h b/src/KOKKOS/pair_eam_alloy_kokkos.h index 6593ccae73..e1dd9ab47d 100644 --- a/src/KOKKOS/pair_eam_alloy_kokkos.h +++ b/src/KOKKOS/pair_eam_alloy_kokkos.h @@ -23,7 +23,6 @@ PairStyle(eam/alloy/kk/host,PairEAMAlloyKokkos) #ifndef LMP_PAIR_EAM_ALLOY_KOKKOS_H #define LMP_PAIR_EAM_ALLOY_KOKKOS_H -#include #include "kokkos_base.h" #include "pair_kokkos.h" #include "pair_eam.h" diff --git a/src/KOKKOS/pair_eam_fs_kokkos.h b/src/KOKKOS/pair_eam_fs_kokkos.h index f75605ff6d..e93977869e 100644 --- a/src/KOKKOS/pair_eam_fs_kokkos.h +++ b/src/KOKKOS/pair_eam_fs_kokkos.h @@ -23,7 +23,6 @@ PairStyle(eam/fs/kk/host,PairEAMFSKokkos) #ifndef LMP_PAIR_EAM_FS_KOKKOS_H #define LMP_PAIR_EAM_FS_KOKKOS_H -#include #include "kokkos_base.h" #include "pair_kokkos.h" #include "pair_eam.h" diff --git a/src/KOKKOS/pair_eam_kokkos.h b/src/KOKKOS/pair_eam_kokkos.h index 4040eba858..3bf89c549a 100644 --- a/src/KOKKOS/pair_eam_kokkos.h +++ b/src/KOKKOS/pair_eam_kokkos.h @@ -23,7 +23,6 @@ PairStyle(eam/kk/host,PairEAMKokkos) #ifndef LMP_PAIR_EAM_KOKKOS_H #define LMP_PAIR_EAM_KOKKOS_H -#include #include "kokkos_base.h" #include "pair_kokkos.h" #include "pair_eam.h" diff --git a/src/KOKKOS/pair_hybrid_kokkos.h b/src/KOKKOS/pair_hybrid_kokkos.h index 94e034f875..799354cf01 100644 --- a/src/KOKKOS/pair_hybrid_kokkos.h +++ b/src/KOKKOS/pair_hybrid_kokkos.h @@ -20,7 +20,6 @@ PairStyle(hybrid/kk,PairHybridKokkos) #ifndef LMP_PAIR_HYBRID_KOKKOS_H #define LMP_PAIR_HYBRID_KOKKOS_H -#include #include "pair_hybrid.h" #include "pair_kokkos.h" #include "kokkos_type.h" diff --git a/src/KOKKOS/pair_reaxc_kokkos.h b/src/KOKKOS/pair_reaxc_kokkos.h index 89dfc4d884..783ea33c4e 100644 --- a/src/KOKKOS/pair_reaxc_kokkos.h +++ b/src/KOKKOS/pair_reaxc_kokkos.h @@ -23,7 +23,6 @@ PairStyle(reax/c/kk/host,PairReaxCKokkos) #ifndef LMP_PAIR_REAXC_KOKKOS_H #define LMP_PAIR_REAXC_KOKKOS_H -#include #include "pair_kokkos.h" #include "pair_reaxc.h" #include "neigh_list_kokkos.h" diff --git a/src/KOKKOS/pair_tersoff_kokkos.h b/src/KOKKOS/pair_tersoff_kokkos.h index f73d4fe2d8..7d41fe2346 100644 --- a/src/KOKKOS/pair_tersoff_kokkos.h +++ b/src/KOKKOS/pair_tersoff_kokkos.h @@ -23,7 +23,6 @@ PairStyle(tersoff/kk/host,PairTersoffKokkos) #ifndef LMP_PAIR_TERSOFF_KOKKOS_H #define LMP_PAIR_TERSOFF_KOKKOS_H -#include #include "pair_kokkos.h" #include "pair_tersoff.h" #include "neigh_list_kokkos.h" diff --git a/src/KOKKOS/pair_tersoff_mod_kokkos.h b/src/KOKKOS/pair_tersoff_mod_kokkos.h index d7c94ffc93..889e1eadfa 100644 --- a/src/KOKKOS/pair_tersoff_mod_kokkos.h +++ b/src/KOKKOS/pair_tersoff_mod_kokkos.h @@ -23,7 +23,6 @@ PairStyle(tersoff/mod/kk/host,PairTersoffMODKokkos) #ifndef LMP_PAIR_TERSOFF_MOD_KOKKOS_H #define LMP_PAIR_TERSOFF_MOD_KOKKOS_H -#include #include "pair_kokkos.h" #include "pair_tersoff_mod.h" #include "neigh_list_kokkos.h" diff --git a/src/KOKKOS/pair_tersoff_zbl_kokkos.h b/src/KOKKOS/pair_tersoff_zbl_kokkos.h index 3af4e0d8eb..0c7fa2e963 100644 --- a/src/KOKKOS/pair_tersoff_zbl_kokkos.h +++ b/src/KOKKOS/pair_tersoff_zbl_kokkos.h @@ -23,7 +23,6 @@ PairStyle(tersoff/zbl/kk/host,PairTersoffZBLKokkos) #ifndef LMP_PAIR_TERSOFF_ZBL_KOKKOS_H #define LMP_PAIR_TERSOFF_ZBL_KOKKOS_H -#include #include "pair_kokkos.h" #include "pair_tersoff_zbl.h" #include "neigh_list_kokkos.h" diff --git a/src/MANYBODY/fix_qeq_comb.h b/src/MANYBODY/fix_qeq_comb.h index dd4c9f7290..c3a0ac08f3 100644 --- a/src/MANYBODY/fix_qeq_comb.h +++ b/src/MANYBODY/fix_qeq_comb.h @@ -20,7 +20,6 @@ FixStyle(qeq/comb,FixQEQComb) #ifndef LMP_FIX_QEQ_COMB_H #define LMP_FIX_QEQ_COMB_H -#include #include "fix.h" namespace LAMMPS_NS { diff --git a/src/MANYBODY/pair_eam.h b/src/MANYBODY/pair_eam.h index 234552157b..8bcb44c347 100644 --- a/src/MANYBODY/pair_eam.h +++ b/src/MANYBODY/pair_eam.h @@ -20,7 +20,6 @@ PairStyle(eam,PairEAM) #ifndef LMP_PAIR_EAM_H #define LMP_PAIR_EAM_H -#include #include "pair.h" namespace LAMMPS_NS { diff --git a/src/MANYBODY/pair_eim.h b/src/MANYBODY/pair_eim.h index 50f9934c44..f9fb2d5a77 100644 --- a/src/MANYBODY/pair_eim.h +++ b/src/MANYBODY/pair_eim.h @@ -20,7 +20,6 @@ PairStyle(eim,PairEIM) #ifndef LMP_PAIR_EIM_H #define LMP_PAIR_EIM_H -#include #include "pair.h" namespace LAMMPS_NS { diff --git a/src/MC/fix_atom_swap.h b/src/MC/fix_atom_swap.h index 19895704f1..a5ce89b16b 100644 --- a/src/MC/fix_atom_swap.h +++ b/src/MC/fix_atom_swap.h @@ -20,7 +20,6 @@ FixStyle(atom/swap,FixAtomSwap) #ifndef LMP_FIX_MCSWAP_H #define LMP_FIX_MCSWAP_H -#include #include "fix.h" namespace LAMMPS_NS { diff --git a/src/MC/fix_gcmc.h b/src/MC/fix_gcmc.h index 5d0b7aab8f..da4232d19b 100644 --- a/src/MC/fix_gcmc.h +++ b/src/MC/fix_gcmc.h @@ -20,7 +20,6 @@ FixStyle(gcmc,FixGCMC) #ifndef LMP_FIX_GCMC_H #define LMP_FIX_GCMC_H -#include #include "fix.h" namespace LAMMPS_NS { diff --git a/src/MISC/fix_deposit.h b/src/MISC/fix_deposit.h index 38958b80e7..e3104c890d 100644 --- a/src/MISC/fix_deposit.h +++ b/src/MISC/fix_deposit.h @@ -20,7 +20,6 @@ FixStyle(deposit,FixDeposit) #ifndef LMP_FIX_DEPOSIT_H #define LMP_FIX_DEPOSIT_H -#include #include "fix.h" namespace LAMMPS_NS { diff --git a/src/MOLECULE/angle_charmm.h b/src/MOLECULE/angle_charmm.h index 2228ad8732..444c833d37 100644 --- a/src/MOLECULE/angle_charmm.h +++ b/src/MOLECULE/angle_charmm.h @@ -20,7 +20,6 @@ AngleStyle(charmm,AngleCharmm) #ifndef LMP_ANGLE_CHARMM_H #define LMP_ANGLE_CHARMM_H -#include #include "angle.h" namespace LAMMPS_NS { diff --git a/src/MOLECULE/angle_cosine.h b/src/MOLECULE/angle_cosine.h index f2406bc5dd..ca1f4178f8 100644 --- a/src/MOLECULE/angle_cosine.h +++ b/src/MOLECULE/angle_cosine.h @@ -20,7 +20,6 @@ AngleStyle(cosine,AngleCosine) #ifndef LMP_ANGLE_COSINE_H #define LMP_ANGLE_COSINE_H -#include #include "angle.h" namespace LAMMPS_NS { diff --git a/src/MOLECULE/angle_cosine_delta.h b/src/MOLECULE/angle_cosine_delta.h index 1e19ecaf79..70b574b234 100644 --- a/src/MOLECULE/angle_cosine_delta.h +++ b/src/MOLECULE/angle_cosine_delta.h @@ -20,7 +20,6 @@ AngleStyle(cosine/delta,AngleCosineDelta) #ifndef LMP_ANGLE_COSINE_DELTA_H #define LMP_ANGLE_COSINE_DELTA_H -#include #include "angle_cosine_squared.h" namespace LAMMPS_NS { diff --git a/src/MOLECULE/angle_cosine_periodic.h b/src/MOLECULE/angle_cosine_periodic.h index e131e85101..f0188b6c17 100644 --- a/src/MOLECULE/angle_cosine_periodic.h +++ b/src/MOLECULE/angle_cosine_periodic.h @@ -20,7 +20,6 @@ AngleStyle(cosine/periodic, AngleCosinePeriodic) #ifndef LMP_ANGLE_PERIODIC_H #define LMP_ANGLE_PERIODIC_H -#include #include "angle.h" namespace LAMMPS_NS { diff --git a/src/MOLECULE/angle_cosine_squared.h b/src/MOLECULE/angle_cosine_squared.h index 8e8c84c0f9..a19a923850 100644 --- a/src/MOLECULE/angle_cosine_squared.h +++ b/src/MOLECULE/angle_cosine_squared.h @@ -20,7 +20,6 @@ AngleStyle(cosine/squared,AngleCosineSquared) #ifndef LMP_ANGLE_COSINE_SQUARED_H #define LMP_ANGLE_COSINE_SQUARED_H -#include #include "angle.h" namespace LAMMPS_NS { diff --git a/src/MOLECULE/angle_harmonic.h b/src/MOLECULE/angle_harmonic.h index e0c067653b..f371178d58 100644 --- a/src/MOLECULE/angle_harmonic.h +++ b/src/MOLECULE/angle_harmonic.h @@ -20,7 +20,6 @@ AngleStyle(harmonic,AngleHarmonic) #ifndef LMP_ANGLE_HARMONIC_H #define LMP_ANGLE_HARMONIC_H -#include #include "angle.h" namespace LAMMPS_NS { diff --git a/src/MOLECULE/angle_table.h b/src/MOLECULE/angle_table.h index 0088ace39b..46633d28cc 100644 --- a/src/MOLECULE/angle_table.h +++ b/src/MOLECULE/angle_table.h @@ -20,7 +20,6 @@ AngleStyle(table,AngleTable) #ifndef LMP_ANGLE_TABLE_H #define LMP_ANGLE_TABLE_H -#include #include "angle.h" namespace LAMMPS_NS { diff --git a/src/MOLECULE/bond_fene.h b/src/MOLECULE/bond_fene.h index 58cd6ce289..1963e3ca22 100644 --- a/src/MOLECULE/bond_fene.h +++ b/src/MOLECULE/bond_fene.h @@ -20,7 +20,6 @@ BondStyle(fene,BondFENE) #ifndef LMP_BOND_FENE_H #define LMP_BOND_FENE_H -#include #include "bond.h" namespace LAMMPS_NS { diff --git a/src/MOLECULE/bond_fene_expand.h b/src/MOLECULE/bond_fene_expand.h index cb316ac5f2..8cfc17dc68 100644 --- a/src/MOLECULE/bond_fene_expand.h +++ b/src/MOLECULE/bond_fene_expand.h @@ -20,7 +20,6 @@ BondStyle(fene/expand,BondFENEExpand) #ifndef LMP_BOND_FENE_EXPAND_H #define LMP_BOND_FENE_EXPAND_H -#include #include "bond.h" namespace LAMMPS_NS { diff --git a/src/MOLECULE/bond_gromos.h b/src/MOLECULE/bond_gromos.h index c26ad64b3d..966b914437 100644 --- a/src/MOLECULE/bond_gromos.h +++ b/src/MOLECULE/bond_gromos.h @@ -20,7 +20,6 @@ BondStyle(gromos,BondGromos) #ifndef LMP_BOND_GROMOS_H #define LMP_BOND_GROMOS_H -#include #include "bond.h" namespace LAMMPS_NS { diff --git a/src/MOLECULE/bond_harmonic.h b/src/MOLECULE/bond_harmonic.h index 5c692b2a8e..576e63629b 100644 --- a/src/MOLECULE/bond_harmonic.h +++ b/src/MOLECULE/bond_harmonic.h @@ -20,7 +20,6 @@ BondStyle(harmonic,BondHarmonic) #ifndef LMP_BOND_HARMONIC_H #define LMP_BOND_HARMONIC_H -#include #include "bond.h" namespace LAMMPS_NS { diff --git a/src/MOLECULE/bond_morse.h b/src/MOLECULE/bond_morse.h index c4d60bc217..030a94a8da 100644 --- a/src/MOLECULE/bond_morse.h +++ b/src/MOLECULE/bond_morse.h @@ -20,7 +20,6 @@ BondStyle(morse,BondMorse) #ifndef LMP_BOND_MORSE_H #define LMP_BOND_MORSE_H -#include #include "bond.h" namespace LAMMPS_NS { diff --git a/src/MOLECULE/bond_nonlinear.h b/src/MOLECULE/bond_nonlinear.h index 175421264b..7782b93778 100644 --- a/src/MOLECULE/bond_nonlinear.h +++ b/src/MOLECULE/bond_nonlinear.h @@ -20,7 +20,6 @@ BondStyle(nonlinear,BondNonlinear) #ifndef LMP_BOND_NONLINEAR_H #define LMP_BOND_NONLINEAR_H -#include #include "bond.h" namespace LAMMPS_NS { diff --git a/src/MOLECULE/bond_quartic.h b/src/MOLECULE/bond_quartic.h index 2aaa76e2c3..60ccf307b9 100644 --- a/src/MOLECULE/bond_quartic.h +++ b/src/MOLECULE/bond_quartic.h @@ -20,7 +20,6 @@ BondStyle(quartic,BondQuartic) #ifndef LMP_BOND_QUARTIC_H #define LMP_BOND_QUARTIC_H -#include #include "bond.h" namespace LAMMPS_NS { diff --git a/src/MOLECULE/bond_table.h b/src/MOLECULE/bond_table.h index 5766239167..3db3ade3ab 100644 --- a/src/MOLECULE/bond_table.h +++ b/src/MOLECULE/bond_table.h @@ -20,7 +20,6 @@ BondStyle(table,BondTable) #ifndef LMP_BOND_TABLE_H #define LMP_BOND_TABLE_H -#include #include "bond.h" namespace LAMMPS_NS { diff --git a/src/MOLECULE/dihedral_charmm.h b/src/MOLECULE/dihedral_charmm.h index 8f51b398db..4be3925dad 100644 --- a/src/MOLECULE/dihedral_charmm.h +++ b/src/MOLECULE/dihedral_charmm.h @@ -20,7 +20,6 @@ DihedralStyle(charmm,DihedralCharmm) #ifndef LMP_DIHEDRAL_CHARMM_H #define LMP_DIHEDRAL_CHARMM_H -#include #include "dihedral.h" namespace LAMMPS_NS { diff --git a/src/MOLECULE/dihedral_charmmfsw.h b/src/MOLECULE/dihedral_charmmfsw.h index dd31067a8d..b33250004b 100644 --- a/src/MOLECULE/dihedral_charmmfsw.h +++ b/src/MOLECULE/dihedral_charmmfsw.h @@ -20,7 +20,6 @@ DihedralStyle(charmmfsw,DihedralCharmmfsw) #ifndef LMP_DIHEDRAL_CHARMMFSW_H #define LMP_DIHEDRAL_CHARMMFSW_H -#include #include "dihedral.h" namespace LAMMPS_NS { diff --git a/src/MOLECULE/dihedral_harmonic.h b/src/MOLECULE/dihedral_harmonic.h index 2031261256..938e59918b 100644 --- a/src/MOLECULE/dihedral_harmonic.h +++ b/src/MOLECULE/dihedral_harmonic.h @@ -20,7 +20,6 @@ DihedralStyle(harmonic,DihedralHarmonic) #ifndef LMP_DIHEDRAL_HARMONIC_H #define LMP_DIHEDRAL_HARMONIC_H -#include #include "dihedral.h" namespace LAMMPS_NS { diff --git a/src/MOLECULE/dihedral_helix.h b/src/MOLECULE/dihedral_helix.h index 745ab84115..0213c59e8a 100644 --- a/src/MOLECULE/dihedral_helix.h +++ b/src/MOLECULE/dihedral_helix.h @@ -20,7 +20,6 @@ DihedralStyle(helix,DihedralHelix) #ifndef LMP_DIHEDRAL_HELIX_H #define LMP_DIHEDRAL_HELIX_H -#include #include "dihedral.h" namespace LAMMPS_NS { diff --git a/src/MOLECULE/dihedral_multi_harmonic.h b/src/MOLECULE/dihedral_multi_harmonic.h index 32f17e75ae..bb3d7183f7 100644 --- a/src/MOLECULE/dihedral_multi_harmonic.h +++ b/src/MOLECULE/dihedral_multi_harmonic.h @@ -20,7 +20,6 @@ DihedralStyle(multi/harmonic,DihedralMultiHarmonic) #ifndef LMP_DIHEDRAL_MULTI_HARMONIC_H #define LMP_DIHEDRAL_MULTI_HARMONIC_H -#include #include "dihedral.h" namespace LAMMPS_NS { diff --git a/src/MOLECULE/dihedral_opls.h b/src/MOLECULE/dihedral_opls.h index c1e64ada1e..01878173cd 100644 --- a/src/MOLECULE/dihedral_opls.h +++ b/src/MOLECULE/dihedral_opls.h @@ -20,7 +20,6 @@ DihedralStyle(opls,DihedralOPLS) #ifndef LMP_DIHEDRAL_OPLS_H #define LMP_DIHEDRAL_OPLS_H -#include #include "dihedral.h" namespace LAMMPS_NS { diff --git a/src/MOLECULE/improper_cvff.h b/src/MOLECULE/improper_cvff.h index d4c30cc2ee..055d2ca9b8 100644 --- a/src/MOLECULE/improper_cvff.h +++ b/src/MOLECULE/improper_cvff.h @@ -20,7 +20,6 @@ ImproperStyle(cvff,ImproperCvff) #ifndef LMP_IMPROPER_CVFF_H #define LMP_IMPROPER_CVFF_H -#include #include "improper.h" namespace LAMMPS_NS { diff --git a/src/MOLECULE/improper_harmonic.h b/src/MOLECULE/improper_harmonic.h index fbbb8d33d6..5949c6911e 100644 --- a/src/MOLECULE/improper_harmonic.h +++ b/src/MOLECULE/improper_harmonic.h @@ -20,7 +20,6 @@ ImproperStyle(harmonic,ImproperHarmonic) #ifndef LMP_IMPROPER_HARMONIC_H #define LMP_IMPROPER_HARMONIC_H -#include #include "improper.h" namespace LAMMPS_NS { diff --git a/src/MOLECULE/improper_umbrella.h b/src/MOLECULE/improper_umbrella.h index dc2262d01c..da9d6c8f4b 100644 --- a/src/MOLECULE/improper_umbrella.h +++ b/src/MOLECULE/improper_umbrella.h @@ -20,7 +20,6 @@ ImproperStyle(umbrella,ImproperUmbrella) #ifndef LMP_IMPROPER_UMBRELLA_H #define LMP_IMPROPER_UMBRELLA_H -#include #include "improper.h" namespace LAMMPS_NS { diff --git a/src/REPLICA/neb.h b/src/REPLICA/neb.h index f585a0c8a7..b53992711c 100644 --- a/src/REPLICA/neb.h +++ b/src/REPLICA/neb.h @@ -20,7 +20,6 @@ CommandStyle(neb,NEB) #ifndef LMP_NEB_H #define LMP_NEB_H -#include #include "pointers.h" namespace LAMMPS_NS { diff --git a/src/SPIN/neb_spin.h b/src/SPIN/neb_spin.h index c128eaffa4..568eca0957 100644 --- a/src/SPIN/neb_spin.h +++ b/src/SPIN/neb_spin.h @@ -20,7 +20,6 @@ CommandStyle(neb/spin,NEBSpin) #ifndef LMP_NEB_SPIN_H #define LMP_NEB_SPIN_H -#include #include "pointers.h" namespace LAMMPS_NS { diff --git a/src/USER-CGDNA/mf_oxdna.h b/src/USER-CGDNA/mf_oxdna.h index c63a37cde2..e4ed1bbd03 100644 --- a/src/USER-CGDNA/mf_oxdna.h +++ b/src/USER-CGDNA/mf_oxdna.h @@ -14,7 +14,6 @@ #ifndef MF_OXDNA_H #define MF_OXDNA_H -#include #include "math_extra.h" namespace MFOxdna { diff --git a/src/USER-CGSDK/angle_sdk.h b/src/USER-CGSDK/angle_sdk.h index 293004ad4d..2e94b44470 100644 --- a/src/USER-CGSDK/angle_sdk.h +++ b/src/USER-CGSDK/angle_sdk.h @@ -20,7 +20,6 @@ AngleStyle(sdk,AngleSDK) #ifndef LMP_ANGLE_SDK_H #define LMP_ANGLE_SDK_H -#include #include "angle.h" namespace LAMMPS_NS { diff --git a/src/USER-DIFFRACTION/fix_saed_vtk.h b/src/USER-DIFFRACTION/fix_saed_vtk.h index 2fc09c781c..94abbf0194 100644 --- a/src/USER-DIFFRACTION/fix_saed_vtk.h +++ b/src/USER-DIFFRACTION/fix_saed_vtk.h @@ -20,7 +20,6 @@ FixStyle(saed/vtk,FixSAEDVTK) #ifndef LMP_FIX_SAED_VTK_H #define LMP_FIX_SAED_VTK_H -#include #include "fix.h" namespace LAMMPS_NS { diff --git a/src/USER-INTEL/angle_charmm_intel.h b/src/USER-INTEL/angle_charmm_intel.h index 5d173ee6a9..155ecfaff9 100644 --- a/src/USER-INTEL/angle_charmm_intel.h +++ b/src/USER-INTEL/angle_charmm_intel.h @@ -24,7 +24,6 @@ AngleStyle(charmm/intel,AngleCharmmIntel) #ifndef LMP_ANGLE_CHARMM_INTEL_H #define LMP_ANGLE_CHARMM_INTEL_H -#include #include "angle_charmm.h" #include "fix_intel.h" diff --git a/src/USER-INTEL/angle_harmonic_intel.h b/src/USER-INTEL/angle_harmonic_intel.h index e7768542a1..c00292f7ce 100644 --- a/src/USER-INTEL/angle_harmonic_intel.h +++ b/src/USER-INTEL/angle_harmonic_intel.h @@ -24,7 +24,6 @@ AngleStyle(harmonic/intel,AngleHarmonicIntel) #ifndef LMP_ANGLE_HARMONIC_INTEL_H #define LMP_ANGLE_HARMONIC_INTEL_H -#include #include "angle_harmonic.h" #include "fix_intel.h" diff --git a/src/USER-INTEL/bond_fene_intel.h b/src/USER-INTEL/bond_fene_intel.h index afe3b85470..58fcdb8669 100644 --- a/src/USER-INTEL/bond_fene_intel.h +++ b/src/USER-INTEL/bond_fene_intel.h @@ -24,7 +24,6 @@ BondStyle(fene/intel,BondFENEIntel) #ifndef LMP_BOND_FENE_INTEL_H #define LMP_BOND_FENE_INTEL_H -#include #include "bond_fene.h" #include "fix_intel.h" diff --git a/src/USER-INTEL/bond_harmonic_intel.h b/src/USER-INTEL/bond_harmonic_intel.h index b86a560d6e..3c1d050a3b 100644 --- a/src/USER-INTEL/bond_harmonic_intel.h +++ b/src/USER-INTEL/bond_harmonic_intel.h @@ -24,7 +24,6 @@ BondStyle(harmonic/intel,BondHarmonicIntel) #ifndef LMP_BOND_HARMONIC_INTEL_H #define LMP_BOND_HARMONIC_INTEL_H -#include #include "bond_harmonic.h" #include "fix_intel.h" diff --git a/src/USER-INTEL/improper_cvff_intel.h b/src/USER-INTEL/improper_cvff_intel.h index e815fa75c9..812b49d50c 100644 --- a/src/USER-INTEL/improper_cvff_intel.h +++ b/src/USER-INTEL/improper_cvff_intel.h @@ -24,7 +24,6 @@ ImproperStyle(cvff/intel,ImproperCvffIntel) #ifndef LMP_IMPROPER_CVFF_INTEL_H #define LMP_IMPROPER_CVFF_INTEL_H -#include #include "improper_cvff.h" #include "fix_intel.h" diff --git a/src/USER-INTEL/improper_harmonic_intel.h b/src/USER-INTEL/improper_harmonic_intel.h index ce38e8fc31..6d7c829961 100644 --- a/src/USER-INTEL/improper_harmonic_intel.h +++ b/src/USER-INTEL/improper_harmonic_intel.h @@ -24,7 +24,6 @@ ImproperStyle(harmonic/intel,ImproperHarmonicIntel) #ifndef LMP_IMPROPER_HARMONIC_INTEL_H #define LMP_IMPROPER_HARMONIC_INTEL_H -#include #include "improper_harmonic.h" #include "fix_intel.h" diff --git a/src/USER-INTEL/intel_simd.h b/src/USER-INTEL/intel_simd.h index 75fc9828b9..9022f439c4 100644 --- a/src/USER-INTEL/intel_simd.h +++ b/src/USER-INTEL/intel_simd.h @@ -29,7 +29,6 @@ authors for more details. #ifndef INTEL_SIMD_H #define INTEL_SIMD_H -#include #include "intel_preprocess.h" #include "immintrin.h" diff --git a/src/USER-INTEL/pair_eam_intel.h b/src/USER-INTEL/pair_eam_intel.h index 83b1fbf6a1..a9590f6b3d 100644 --- a/src/USER-INTEL/pair_eam_intel.h +++ b/src/USER-INTEL/pair_eam_intel.h @@ -20,7 +20,6 @@ PairStyle(eam/intel,PairEAMIntel) #ifndef LMP_PAIR_EAM_INTEL_H #define LMP_PAIR_EAM_INTEL_H -#include #include "pair_eam.h" #include "fix_intel.h" diff --git a/src/USER-MANIFOLD/manifold_thylakoid.h b/src/USER-MANIFOLD/manifold_thylakoid.h index 5e5d3b9c41..d8ebe2e94f 100644 --- a/src/USER-MANIFOLD/manifold_thylakoid.h +++ b/src/USER-MANIFOLD/manifold_thylakoid.h @@ -3,7 +3,6 @@ #include "manifold.h" #include -#include #include "manifold_thylakoid_shared.h" diff --git a/src/USER-MGPT/mgpt_readpot.h b/src/USER-MGPT/mgpt_readpot.h index c19ea40774..62f66883b6 100644 --- a/src/USER-MGPT/mgpt_readpot.h +++ b/src/USER-MGPT/mgpt_readpot.h @@ -19,7 +19,6 @@ #ifndef READPOT__ #define READPOT__ -#include #include "mgpt_splinetab.h" diff --git a/src/USER-MGPT/pair_mgpt.h b/src/USER-MGPT/pair_mgpt.h index 94c66fb603..70b36364b1 100644 --- a/src/USER-MGPT/pair_mgpt.h +++ b/src/USER-MGPT/pair_mgpt.h @@ -32,7 +32,6 @@ PairStyle(mgpt,PairMGPT) #include #include -#include #include #include "pair.h" diff --git a/src/USER-MISC/angle_cosine_shift.h b/src/USER-MISC/angle_cosine_shift.h index 030709a0e2..febabcc090 100644 --- a/src/USER-MISC/angle_cosine_shift.h +++ b/src/USER-MISC/angle_cosine_shift.h @@ -20,7 +20,6 @@ AngleStyle(cosine/shift,AngleCosineShift) #ifndef LMP_ANGLE_COSINE_SHIFT_H #define LMP_ANGLE_COSINE_SHIFT_H -#include #include "angle.h" namespace LAMMPS_NS { diff --git a/src/USER-MISC/angle_cosine_shift_exp.h b/src/USER-MISC/angle_cosine_shift_exp.h index 8b8e389380..9614ddcc19 100644 --- a/src/USER-MISC/angle_cosine_shift_exp.h +++ b/src/USER-MISC/angle_cosine_shift_exp.h @@ -18,7 +18,6 @@ AngleStyle(cosine/shift/exp,AngleCosineShiftExp) #ifndef LMP_ANGLE_COSINE_SHIFT_EXP_H #define LMP_ANGLE_COSINE_SHIFT_EXP_H -#include #include "angle.h" namespace LAMMPS_NS { diff --git a/src/USER-MISC/angle_dipole.h b/src/USER-MISC/angle_dipole.h index 6c5dccb803..187822d0d4 100644 --- a/src/USER-MISC/angle_dipole.h +++ b/src/USER-MISC/angle_dipole.h @@ -20,7 +20,6 @@ AngleStyle(dipole,AngleDipole) #ifndef LMP_ANGLE_DIPOLE_H #define LMP_ANGLE_DIPOLE_H -#include #include "angle.h" namespace LAMMPS_NS { diff --git a/src/USER-MISC/angle_fourier.h b/src/USER-MISC/angle_fourier.h index 14b4eedf57..53eeea98da 100644 --- a/src/USER-MISC/angle_fourier.h +++ b/src/USER-MISC/angle_fourier.h @@ -20,7 +20,6 @@ AngleStyle(fourier,AngleFourier) #ifndef ANGLE_FOURIER_H #define ANGLE_FOURIER_H -#include #include "angle.h" namespace LAMMPS_NS { diff --git a/src/USER-MISC/angle_fourier_simple.h b/src/USER-MISC/angle_fourier_simple.h index 3a7bd37750..df2253317f 100644 --- a/src/USER-MISC/angle_fourier_simple.h +++ b/src/USER-MISC/angle_fourier_simple.h @@ -20,7 +20,6 @@ AngleStyle(fourier/simple,AngleFourierSimple) #ifndef ANGLE_FOURIER_SIMPLE_H #define ANGLE_FOURIER_SIMPLE_H -#include #include "angle.h" namespace LAMMPS_NS { diff --git a/src/USER-MISC/angle_quartic.h b/src/USER-MISC/angle_quartic.h index 7043cab064..b916a5f89f 100644 --- a/src/USER-MISC/angle_quartic.h +++ b/src/USER-MISC/angle_quartic.h @@ -20,7 +20,6 @@ AngleStyle(quartic,AngleQuartic) #ifndef LMP_ANGLE_QUARTIC_H #define LMP_ANGLE_QUARTIC_H -#include #include "angle.h" namespace LAMMPS_NS { diff --git a/src/USER-MISC/bond_harmonic_shift.h b/src/USER-MISC/bond_harmonic_shift.h index ff0d358243..b77cefb4af 100644 --- a/src/USER-MISC/bond_harmonic_shift.h +++ b/src/USER-MISC/bond_harmonic_shift.h @@ -20,7 +20,6 @@ BondStyle(harmonic/shift,BondHarmonicShift) #ifndef LMP_BOND_HARMONIC_SHIFT_H #define LMP_BOND_HARMONIC_SHIFT_H -#include #include "bond.h" namespace LAMMPS_NS { diff --git a/src/USER-MISC/bond_harmonic_shift_cut.h b/src/USER-MISC/bond_harmonic_shift_cut.h index 5db76d51aa..ad2bcd61ad 100644 --- a/src/USER-MISC/bond_harmonic_shift_cut.h +++ b/src/USER-MISC/bond_harmonic_shift_cut.h @@ -20,7 +20,6 @@ BondStyle(harmonic/shift/cut,BondHarmonicShiftCut) #ifndef LMP_BOND_HARMONIC_SHIFT_CUT_H #define LMP_BOND_HARMONIC_SHIFT_CUT_H -#include #include "bond.h" namespace LAMMPS_NS { diff --git a/src/USER-MISC/dihedral_cosine_shift_exp.h b/src/USER-MISC/dihedral_cosine_shift_exp.h index fc4be5049b..4d180f42de 100644 --- a/src/USER-MISC/dihedral_cosine_shift_exp.h +++ b/src/USER-MISC/dihedral_cosine_shift_exp.h @@ -20,7 +20,6 @@ DihedralStyle(cosine/shift/exp,DihedralCosineShiftExp) #ifndef LMP_DIHEDRAL_COSINE_SHIFT_EXP_H #define LMP_DIHEDRAL_COSINE_SHIFT_EXP_H -#include #include "dihedral.h" namespace LAMMPS_NS { diff --git a/src/USER-MISC/dihedral_fourier.h b/src/USER-MISC/dihedral_fourier.h index c1ed843c34..8b6291fc4c 100644 --- a/src/USER-MISC/dihedral_fourier.h +++ b/src/USER-MISC/dihedral_fourier.h @@ -20,7 +20,6 @@ DihedralStyle(fourier,DihedralFourier) #ifndef LMP_DIHEDRAL_FOURIER_H #define LMP_DIHEDRAL_FOURIER_H -#include #include "dihedral.h" namespace LAMMPS_NS { diff --git a/src/USER-MISC/dihedral_nharmonic.h b/src/USER-MISC/dihedral_nharmonic.h index 7c6a35b200..6fd1da3b8b 100644 --- a/src/USER-MISC/dihedral_nharmonic.h +++ b/src/USER-MISC/dihedral_nharmonic.h @@ -20,7 +20,6 @@ DihedralStyle(nharmonic,DihedralNHarmonic) #ifndef DIHEDRAL_NHARMONIC_H #define DIHEDRAL_NHARMONIC_H -#include #include "dihedral.h" namespace LAMMPS_NS { diff --git a/src/USER-MISC/dihedral_quadratic.h b/src/USER-MISC/dihedral_quadratic.h index edc29c3cf8..0b99cbc4f7 100644 --- a/src/USER-MISC/dihedral_quadratic.h +++ b/src/USER-MISC/dihedral_quadratic.h @@ -20,7 +20,6 @@ DihedralStyle(quadratic,DihedralQuadratic) #ifndef LMP_DIHEDRAL_QUADRATIC_H #define LMP_DIHEDRAL_QUADRATIC_H -#include #include "dihedral.h" namespace LAMMPS_NS { diff --git a/src/USER-MISC/dihedral_spherical.h b/src/USER-MISC/dihedral_spherical.h index ae0ece189a..472db36f33 100644 --- a/src/USER-MISC/dihedral_spherical.h +++ b/src/USER-MISC/dihedral_spherical.h @@ -20,7 +20,6 @@ DihedralStyle(spherical,DihedralSpherical) #ifndef LMP_DIHEDRAL_SPHERICAL_H #define LMP_DIHEDRAL_SPHERICAL_H -#include #include "dihedral.h" namespace LAMMPS_NS { diff --git a/src/USER-MISC/fix_ave_correlate_long.h b/src/USER-MISC/fix_ave_correlate_long.h index 548a0e7183..a0c5863e99 100644 --- a/src/USER-MISC/fix_ave_correlate_long.h +++ b/src/USER-MISC/fix_ave_correlate_long.h @@ -20,7 +20,6 @@ FixStyle(ave/correlate/long,FixAveCorrelateLong) #ifndef LMP_FIX_AVE_CORRELATE_LONG_H #define LMP_FIX_AVE_CORRELATE_LONG_H -#include #include "fix.h" namespace LAMMPS_NS { diff --git a/src/USER-MISC/fix_srp.h b/src/USER-MISC/fix_srp.h index 7dbf044bda..f8343df8a6 100644 --- a/src/USER-MISC/fix_srp.h +++ b/src/USER-MISC/fix_srp.h @@ -20,7 +20,6 @@ FixStyle(SRP,FixSRP) #ifndef LMP_FIX_SRP_H #define LMP_FIX_SRP_H -#include #include "fix.h" namespace LAMMPS_NS { diff --git a/src/USER-MISC/improper_cossq.h b/src/USER-MISC/improper_cossq.h index ea880adfaf..9e430bfa1a 100644 --- a/src/USER-MISC/improper_cossq.h +++ b/src/USER-MISC/improper_cossq.h @@ -20,7 +20,6 @@ ImproperStyle(cossq,ImproperCossq) #ifndef LMP_IMPROPER_COSSQ_H #define LMP_IMPROPER_COSSQ_H -#include #include "improper.h" namespace LAMMPS_NS { diff --git a/src/USER-MISC/improper_distance.h b/src/USER-MISC/improper_distance.h index 57e4d671e9..d7575c3585 100644 --- a/src/USER-MISC/improper_distance.h +++ b/src/USER-MISC/improper_distance.h @@ -20,7 +20,6 @@ ImproperStyle(distance,ImproperDistance) #ifndef LMP_IMPROPER_DISTANCE_H #define LMP_IMPROPER_DISTANCE_H -#include #include "improper.h" namespace LAMMPS_NS { diff --git a/src/USER-MISC/improper_fourier.h b/src/USER-MISC/improper_fourier.h index 0525c45494..91dfacfd8e 100644 --- a/src/USER-MISC/improper_fourier.h +++ b/src/USER-MISC/improper_fourier.h @@ -20,7 +20,6 @@ ImproperStyle(fourier,ImproperFourier) #ifndef LMP_IMPROPER_FOURIER_H #define LMP_IMPROPER_FOURIER_H -#include #include "improper.h" namespace LAMMPS_NS { diff --git a/src/USER-MISC/improper_ring.h b/src/USER-MISC/improper_ring.h index c31329816f..7c53c6f59f 100644 --- a/src/USER-MISC/improper_ring.h +++ b/src/USER-MISC/improper_ring.h @@ -20,7 +20,6 @@ ImproperStyle(ring,ImproperRing) #ifndef LMP_IMPROPER_RING_H #define LMP_IMPROPER_RING_H -#include #include "improper.h" namespace LAMMPS_NS { diff --git a/src/USER-MOFFF/angle_class2_p6.h b/src/USER-MOFFF/angle_class2_p6.h index b583a45b19..f2f324c0c6 100644 --- a/src/USER-MOFFF/angle_class2_p6.h +++ b/src/USER-MOFFF/angle_class2_p6.h @@ -20,7 +20,6 @@ AngleStyle(class2/p6,AngleClass2P6) #ifndef LMP_ANGLE_CLASS2_P6_H #define LMP_ANGLE_CLASS2_P6_H -#include #include "angle.h" namespace LAMMPS_NS { diff --git a/src/USER-MOFFF/angle_cosine_buck6d.h b/src/USER-MOFFF/angle_cosine_buck6d.h index 689b1634e0..1d0df10228 100644 --- a/src/USER-MOFFF/angle_cosine_buck6d.h +++ b/src/USER-MOFFF/angle_cosine_buck6d.h @@ -20,7 +20,6 @@ AngleStyle(cosine/buck6d, AngleCosineBuck6d) #ifndef LMP_ANGLE_COSINE_BUCK6D_H #define LMP_ANGLE_COSINE_BUCK6D_H -#include #include "angle.h" namespace LAMMPS_NS { diff --git a/src/USER-MOFFF/improper_inversion_harmonic.h b/src/USER-MOFFF/improper_inversion_harmonic.h index 201c9e358d..206b40aebf 100644 --- a/src/USER-MOFFF/improper_inversion_harmonic.h +++ b/src/USER-MOFFF/improper_inversion_harmonic.h @@ -20,7 +20,6 @@ ImproperStyle(inversion/harmonic,ImproperInversionHarmonic) #ifndef LMP_IMPROPER_INVERSION_HARMONIC_H #define LMP_IMPROPER_INVERSION_HARMONIC_H -#include #include "improper.h" namespace LAMMPS_NS { diff --git a/src/USER-REAXC/fix_reaxc_bonds.h b/src/USER-REAXC/fix_reaxc_bonds.h index d72f5446b5..60f41beb02 100644 --- a/src/USER-REAXC/fix_reaxc_bonds.h +++ b/src/USER-REAXC/fix_reaxc_bonds.h @@ -20,7 +20,6 @@ FixStyle(reax/c/bonds,FixReaxCBonds) #ifndef LMP_FIX_REAXC_BONDS_H #define LMP_FIX_REAXC_BONDS_H -#include #include "fix.h" #include "pointers.h" diff --git a/src/bond_hybrid.h b/src/bond_hybrid.h index e51d467ac1..19e4debfed 100644 --- a/src/bond_hybrid.h +++ b/src/bond_hybrid.h @@ -20,7 +20,6 @@ BondStyle(hybrid,BondHybrid) #ifndef LMP_BOND_HYBRID_H #define LMP_BOND_HYBRID_H -#include #include "bond.h" namespace LAMMPS_NS { diff --git a/src/bond_zero.h b/src/bond_zero.h index 9443ff0784..7cbd2b9a96 100644 --- a/src/bond_zero.h +++ b/src/bond_zero.h @@ -20,7 +20,6 @@ BondStyle(zero,BondZero) #ifndef LMP_BOND_ZERO_H #define LMP_BOND_ZERO_H -#include #include "bond.h" namespace LAMMPS_NS { diff --git a/src/citeme.cpp b/src/citeme.cpp index 24896b448c..c8745891cf 100644 --- a/src/citeme.cpp +++ b/src/citeme.cpp @@ -11,7 +11,6 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include #include "citeme.h" #include "universe.h" diff --git a/src/comm_brick.cpp b/src/comm_brick.cpp index 47f60a3da6..dcf30807f5 100644 --- a/src/comm_brick.cpp +++ b/src/comm_brick.cpp @@ -18,7 +18,6 @@ #include #include #include -#include #include "comm_brick.h" #include "atom.h" #include "atom_vec.h" diff --git a/src/comm_tiled.cpp b/src/comm_tiled.cpp index d1d625445a..a85520ed45 100644 --- a/src/comm_tiled.cpp +++ b/src/comm_tiled.cpp @@ -11,19 +11,16 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ +#include #include #include "comm_tiled.h" -#include "comm_brick.h" #include "atom.h" #include "atom_vec.h" #include "domain.h" -#include "force.h" #include "pair.h" #include "neighbor.h" -#include "modify.h" #include "fix.h" #include "compute.h" -#include "output.h" #include "dump.h" #include "memory.h" #include "error.h" diff --git a/src/comm_tiled.h b/src/comm_tiled.h index 13ecbc4b01..5a9beb28f7 100644 --- a/src/comm_tiled.h +++ b/src/comm_tiled.h @@ -14,6 +14,7 @@ #ifndef LMP_COMM_TILED_H #define LMP_COMM_TILED_H +#include #include "comm.h" namespace LAMMPS_NS { diff --git a/src/compute.cpp b/src/compute.cpp index 207f825ec8..8ff8487104 100644 --- a/src/compute.cpp +++ b/src/compute.cpp @@ -11,15 +11,11 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include -#include #include #include #include "compute.h" -#include "atom.h" #include "domain.h" #include "force.h" -#include "comm.h" #include "group.h" #include "modify.h" #include "fix.h" diff --git a/src/compute_adf.h b/src/compute_adf.h index a7983b7173..f768013207 100644 --- a/src/compute_adf.h +++ b/src/compute_adf.h @@ -20,7 +20,6 @@ ComputeStyle(adf,ComputeADF) #ifndef LMP_COMPUTE_ADF_H #define LMP_COMPUTE_ADF_H -#include #include "compute.h" namespace LAMMPS_NS { diff --git a/src/compute_rdf.h b/src/compute_rdf.h index 52a93a38dd..85f6ce6ad2 100644 --- a/src/compute_rdf.h +++ b/src/compute_rdf.h @@ -20,7 +20,6 @@ ComputeStyle(rdf,ComputeRDF) #ifndef LMP_COMPUTE_RDF_H #define LMP_COMPUTE_RDF_H -#include #include "compute.h" namespace LAMMPS_NS { diff --git a/src/dihedral_hybrid.h b/src/dihedral_hybrid.h index 0839fdfc61..2804060af4 100644 --- a/src/dihedral_hybrid.h +++ b/src/dihedral_hybrid.h @@ -20,7 +20,6 @@ DihedralStyle(hybrid,DihedralHybrid) #ifndef LMP_DIHEDRAL_HYBRID_H #define LMP_DIHEDRAL_HYBRID_H -#include #include "dihedral.h" namespace LAMMPS_NS { diff --git a/src/dihedral_zero.h b/src/dihedral_zero.h index e7dbb0d3a5..e97f8f6641 100644 --- a/src/dihedral_zero.h +++ b/src/dihedral_zero.h @@ -24,7 +24,6 @@ DihedralStyle(zero,DihedralZero) #ifndef LMP_DIHEDRAL_ZERO_H #define LMP_DIHEDRAL_ZERO_H -#include #include "dihedral.h" namespace LAMMPS_NS { diff --git a/src/fix_ave_atom.h b/src/fix_ave_atom.h index e4baf6bda1..42aa282d53 100644 --- a/src/fix_ave_atom.h +++ b/src/fix_ave_atom.h @@ -20,7 +20,6 @@ FixStyle(ave/atom,FixAveAtom) #ifndef LMP_FIX_AVE_ATOM_H #define LMP_FIX_AVE_ATOM_H -#include #include "fix.h" namespace LAMMPS_NS { diff --git a/src/fix_ave_chunk.h b/src/fix_ave_chunk.h index 4dc1c1c246..dac5761ae8 100644 --- a/src/fix_ave_chunk.h +++ b/src/fix_ave_chunk.h @@ -20,7 +20,6 @@ FixStyle(ave/chunk,FixAveChunk) #ifndef LMP_FIX_AVE_CHUNK_H #define LMP_FIX_AVE_CHUNK_H -#include #include "fix.h" namespace LAMMPS_NS { diff --git a/src/fix_ave_correlate.h b/src/fix_ave_correlate.h index ff20e8ba94..05fd6b6576 100644 --- a/src/fix_ave_correlate.h +++ b/src/fix_ave_correlate.h @@ -20,7 +20,6 @@ FixStyle(ave/correlate,FixAveCorrelate) #ifndef LMP_FIX_AVE_CORRELATE_H #define LMP_FIX_AVE_CORRELATE_H -#include #include "fix.h" namespace LAMMPS_NS { diff --git a/src/fix_ave_histo.h b/src/fix_ave_histo.h index 3616959c61..35bdfcfa7f 100644 --- a/src/fix_ave_histo.h +++ b/src/fix_ave_histo.h @@ -20,7 +20,6 @@ FixStyle(ave/histo,FixAveHisto) #ifndef LMP_FIX_AVE_HISTO_H #define LMP_FIX_AVE_HISTO_H -#include #include "fix.h" namespace LAMMPS_NS { diff --git a/src/fix_ave_histo_weight.h b/src/fix_ave_histo_weight.h index e5638e1215..6ec3ba5721 100644 --- a/src/fix_ave_histo_weight.h +++ b/src/fix_ave_histo_weight.h @@ -20,7 +20,6 @@ FixStyle(ave/histo/weight,FixAveHistoWeight) #ifndef LMP_FIX_AVE_HISTO_WEIGHT_H #define LMP_FIX_AVE_HISTO_WEIGHT_H -#include #include "fix_ave_histo.h" namespace LAMMPS_NS { diff --git a/src/fix_ave_time.h b/src/fix_ave_time.h index 62dfbad296..01228f9e55 100644 --- a/src/fix_ave_time.h +++ b/src/fix_ave_time.h @@ -20,7 +20,6 @@ FixStyle(ave/time,FixAveTime) #ifndef LMP_FIX_AVE_TIME_H #define LMP_FIX_AVE_TIME_H -#include #include "fix.h" namespace LAMMPS_NS { diff --git a/src/fix_balance.h b/src/fix_balance.h index 64383b5950..76cbea258a 100644 --- a/src/fix_balance.h +++ b/src/fix_balance.h @@ -20,7 +20,6 @@ FixStyle(balance,FixBalance) #ifndef LMP_FIX_BALANCE_H #define LMP_FIX_BALANCE_H -#include #include "fix.h" namespace LAMMPS_NS { diff --git a/src/fix_halt.h b/src/fix_halt.h index 372c915a7f..93c5e95078 100644 --- a/src/fix_halt.h +++ b/src/fix_halt.h @@ -20,7 +20,6 @@ FixStyle(halt,FixHalt) #ifndef LMP_FIX_HALT_H #define LMP_FIX_HALT_H -#include #include "fix.h" namespace LAMMPS_NS { diff --git a/src/fix_move.h b/src/fix_move.h index 5993d7d6e8..740b051be0 100644 --- a/src/fix_move.h +++ b/src/fix_move.h @@ -20,7 +20,6 @@ FixStyle(move,FixMove) #ifndef LMP_FIX_MOVE_H #define LMP_FIX_MOVE_H -#include #include "fix.h" namespace LAMMPS_NS { diff --git a/src/fix_print.h b/src/fix_print.h index 37b6680aee..5644160220 100644 --- a/src/fix_print.h +++ b/src/fix_print.h @@ -20,7 +20,6 @@ FixStyle(print,FixPrint) #ifndef LMP_FIX_PRINT_H #define LMP_FIX_PRINT_H -#include #include "fix.h" namespace LAMMPS_NS { diff --git a/src/fix_store.h b/src/fix_store.h index 5524770a97..437c14f0f7 100644 --- a/src/fix_store.h +++ b/src/fix_store.h @@ -20,7 +20,6 @@ FixStyle(STORE,FixStore) #ifndef LMP_FIX_STORE_H #define LMP_FIX_STORE_H -#include #include "fix.h" namespace LAMMPS_NS { diff --git a/src/fix_tmd.h b/src/fix_tmd.h index b6db41dd5a..f23a64a027 100644 --- a/src/fix_tmd.h +++ b/src/fix_tmd.h @@ -20,7 +20,6 @@ FixStyle(tmd,FixTMD) #ifndef LMP_FIX_TMD_H #define LMP_FIX_TMD_H -#include #include "fix.h" namespace LAMMPS_NS { diff --git a/src/force.h b/src/force.h index 227b9427c0..26a3ecdfb8 100644 --- a/src/force.h +++ b/src/force.h @@ -15,7 +15,6 @@ #define LMP_FORCE_H #include "pointers.h" -#include #include #include diff --git a/src/group.h b/src/group.h index 962d37b32a..ec913f98bc 100644 --- a/src/group.h +++ b/src/group.h @@ -14,7 +14,6 @@ #ifndef LMP_GROUP_H #define LMP_GROUP_H -#include #include "pointers.h" #include diff --git a/src/image.h b/src/image.h index 5672bf85c5..7df81425d9 100644 --- a/src/image.h +++ b/src/image.h @@ -15,7 +15,6 @@ #define LMP_IMAGE_H #include -#include #include "pointers.h" namespace LAMMPS_NS { diff --git a/src/imbalance.h b/src/imbalance.h index d3c3b9a642..5f43c2e51d 100644 --- a/src/imbalance.h +++ b/src/imbalance.h @@ -14,7 +14,6 @@ #ifndef LMP_IMBALANCE_H #define LMP_IMBALANCE_H -#include #include "pointers.h" namespace LAMMPS_NS { diff --git a/src/improper_hybrid.h b/src/improper_hybrid.h index 89595ccfc4..3e5423b173 100644 --- a/src/improper_hybrid.h +++ b/src/improper_hybrid.h @@ -20,7 +20,6 @@ ImproperStyle(hybrid,ImproperHybrid) #ifndef LMP_IMPROPER_HYBRID_H #define LMP_IMPROPER_HYBRID_H -#include #include "improper.h" namespace LAMMPS_NS { diff --git a/src/improper_zero.h b/src/improper_zero.h index 0a2290b6f7..1a70059070 100644 --- a/src/improper_zero.h +++ b/src/improper_zero.h @@ -20,7 +20,6 @@ ImproperStyle(zero,ImproperZero) #ifndef LMP_IMPROPER_ZERO_H #define LMP_IMPROPER_ZERO_H -#include #include "improper.h" namespace LAMMPS_NS { diff --git a/src/input.h b/src/input.h index 33e83bfb06..9573b569bc 100644 --- a/src/input.h +++ b/src/input.h @@ -14,7 +14,6 @@ #ifndef LMP_INPUT_H #define LMP_INPUT_H -#include #include "pointers.h" #include #include diff --git a/src/lammps.h b/src/lammps.h index e02d0c764a..5820f25591 100644 --- a/src/lammps.h +++ b/src/lammps.h @@ -14,7 +14,6 @@ #ifndef LMP_LAMMPS_H #define LMP_LAMMPS_H -#include namespace LAMMPS_NS { diff --git a/src/modify.h b/src/modify.h index 5ff81855fe..b736485196 100644 --- a/src/modify.h +++ b/src/modify.h @@ -14,7 +14,6 @@ #ifndef LMP_MODIFY_H #define LMP_MODIFY_H -#include #include "pointers.h" #include #include diff --git a/src/pair_hybrid.h b/src/pair_hybrid.h index e313e16f18..074517a859 100644 --- a/src/pair_hybrid.h +++ b/src/pair_hybrid.h @@ -20,7 +20,6 @@ PairStyle(hybrid,PairHybrid) #ifndef LMP_PAIR_HYBRID_H #define LMP_PAIR_HYBRID_H -#include #include "pair.h" namespace LAMMPS_NS { diff --git a/src/read_data.h b/src/read_data.h index 26ab6ff381..98de607f6b 100644 --- a/src/read_data.h +++ b/src/read_data.h @@ -20,7 +20,6 @@ CommandStyle(read_data,ReadData) #ifndef LMP_READ_DATA_H #define LMP_READ_DATA_H -#include #include "pointers.h" namespace LAMMPS_NS { diff --git a/src/read_dump.h b/src/read_dump.h index 3ee13f779c..6fb4f11ed1 100644 --- a/src/read_dump.h +++ b/src/read_dump.h @@ -23,7 +23,6 @@ CommandStyle(read_dump,ReadDump) #define LMP_READ_DUMP_H #include -#include #include "pointers.h" namespace LAMMPS_NS { diff --git a/src/read_restart.h b/src/read_restart.h index 23d6ec3fba..63adf37b22 100644 --- a/src/read_restart.h +++ b/src/read_restart.h @@ -20,7 +20,6 @@ CommandStyle(read_restart,ReadRestart) #ifndef LMP_READ_RESTART_H #define LMP_READ_RESTART_H -#include #include "pointers.h" namespace LAMMPS_NS { diff --git a/src/universe.h b/src/universe.h index 3073409b86..fd6655c749 100644 --- a/src/universe.h +++ b/src/universe.h @@ -14,7 +14,6 @@ #ifndef LMP_UNIVERSE_H #define LMP_UNIVERSE_H -#include #include "pointers.h" namespace LAMMPS_NS { diff --git a/src/variable.h b/src/variable.h index c5f501f266..a504da14ec 100644 --- a/src/variable.h +++ b/src/variable.h @@ -14,7 +14,6 @@ #ifndef LMP_VARIABLE_H #define LMP_VARIABLE_H -#include #include "pointers.h" namespace LAMMPS_NS { diff --git a/src/write_coeff.h b/src/write_coeff.h index 569a615e6e..b995e60d63 100644 --- a/src/write_coeff.h +++ b/src/write_coeff.h @@ -20,7 +20,6 @@ CommandStyle(write_coeff,WriteCoeff) #ifndef LMP_WRITE_COEFF_H #define LMP_WRITE_COEFF_H -#include #include "pointers.h" namespace LAMMPS_NS { diff --git a/src/write_data.h b/src/write_data.h index 6f1bb2ec47..1c0f6b2a7c 100644 --- a/src/write_data.h +++ b/src/write_data.h @@ -20,7 +20,6 @@ CommandStyle(write_data,WriteData) #ifndef LMP_WRITE_DATA_H #define LMP_WRITE_DATA_H -#include #include "pointers.h" namespace LAMMPS_NS { diff --git a/src/write_restart.h b/src/write_restart.h index c6202acbfd..e7cdc6a501 100644 --- a/src/write_restart.h +++ b/src/write_restart.h @@ -20,7 +20,6 @@ CommandStyle(write_restart,WriteRestart) #ifndef LMP_WRITE_RESTART_H #define LMP_WRITE_RESTART_H -#include #include "pointers.h" namespace LAMMPS_NS { -- GitLab From 123bd57376066ade0dc92c891bd97de152afd2ad Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Thu, 27 Jun 2019 21:59:05 -0400 Subject: [PATCH 125/469] try to make KOKKOS compile again --- src/KOKKOS/kokkos_type.h | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/KOKKOS/kokkos_type.h b/src/KOKKOS/kokkos_type.h index 942c2af241..e900bbd6d1 100644 --- a/src/KOKKOS/kokkos_type.h +++ b/src/KOKKOS/kokkos_type.h @@ -14,7 +14,7 @@ #ifndef LMP_LMPTYPE_KOKKOS_H #define LMP_LMPTYPE_KOKKOS_H -#include "lmptype.h" +#include "pointers.h" #include #include -- GitLab From 2c119551f7af4eb6dfe1d0424debdec0d6089f80 Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Thu, 27 Jun 2019 22:13:42 -0400 Subject: [PATCH 126/469] add statement about order of include files --- doc/include-file-conventions.md | 8 ++++++++ 1 file changed, 8 insertions(+) diff --git a/doc/include-file-conventions.md b/doc/include-file-conventions.md index 5152051ba5..8d70d6cdec 100644 --- a/doc/include-file-conventions.md +++ b/doc/include-file-conventions.md @@ -94,6 +94,14 @@ In the implementation files (typically, those would have the same base name as the corresponding header with a .cpp extension instead of .h) include statments should follow the "include what you use" principle. +### Order of Include Statements + +Include files should be included in this order: +* lmptype.h (should only be included if `MPI_LMP_XXX` data types are used) +* mpi.h +* system and library headers (anything that is using angular brackets; C-library headers first, then C++) +* LAMMPS local headers (first the header matching the implementation file, the rest in mostly alphabetical order) + ### Special Cases and Exceptions #### pointers.h -- GitLab From a5cb6ddd4a798e4618e2e506ad9d14021f0c4670 Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Thu, 27 Jun 2019 22:14:06 -0400 Subject: [PATCH 127/469] lammps.h must include cstdio and mpi.h --- src/lammps.h | 2 ++ 1 file changed, 2 insertions(+) diff --git a/src/lammps.h b/src/lammps.h index 5820f25591..dc2916f214 100644 --- a/src/lammps.h +++ b/src/lammps.h @@ -14,6 +14,8 @@ #ifndef LMP_LAMMPS_H #define LMP_LAMMPS_H +#include +#include namespace LAMMPS_NS { -- GitLab From 378474c4e642f34614d471953bb3758c04c8754a Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Fri, 28 Jun 2019 02:01:08 -0400 Subject: [PATCH 128/469] more include file cleanup suggested by IWYU --- src/atom_map.cpp | 1 - src/atom_vec_body.cpp | 1 + src/bond_hybrid.cpp | 1 - src/bond_zero.cpp | 1 - src/comm.h | 2 +- src/comm_tiled.cpp | 1 + src/compute_adf.cpp | 3 --- src/compute_aggregate_atom.cpp | 1 + src/compute_angle.cpp | 2 +- src/compute_angmom_chunk.cpp | 1 + src/compute_bond.cpp | 2 +- src/compute_centro_atom.cpp | 1 - src/compute_chunk_atom.cpp | 6 ++++-- src/compute_cluster_atom.cpp | 2 +- src/compute_cna_atom.cpp | 2 +- src/compute_com_chunk.cpp | 1 + src/compute_contact_atom.cpp | 3 --- src/compute_coord_atom.cpp | 1 - src/compute_dihedral.cpp | 2 +- src/compute_dihedral_local.cpp | 2 -- src/compute_dipole_chunk.cpp | 2 ++ src/compute_displace_atom.cpp | 1 - src/compute_erotate_sphere.cpp | 3 --- src/compute_fragment_atom.cpp | 1 + src/compute_global_atom.cpp | 4 ---- src/compute_group_group.cpp | 1 - src/compute_gyration.cpp | 2 +- src/compute_gyration_chunk.cpp | 1 + src/compute_heat_flux.cpp | 3 +-- src/compute_hexorder_atom.cpp | 4 ++-- src/compute_improper.cpp | 2 +- src/compute_improper_local.cpp | 1 - src/compute_inertia_chunk.cpp | 1 + src/compute_ke.cpp | 2 -- src/compute_msd.cpp | 1 + src/compute_msd_chunk.cpp | 1 + src/compute_omega_chunk.cpp | 1 + src/compute_pair_local.cpp | 1 - src/compute_pe_atom.cpp | 1 - src/compute_pressure.cpp | 1 - src/compute_property_chunk.cpp | 1 + src/compute_rdf.cpp | 1 - src/compute_reduce.cpp | 2 -- src/compute_reduce_region.cpp | 3 +-- 44 files changed, 30 insertions(+), 47 deletions(-) diff --git a/src/atom_map.cpp b/src/atom_map.cpp index b14ebdba68..6af3b9c288 100644 --- a/src/atom_map.cpp +++ b/src/atom_map.cpp @@ -11,7 +11,6 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include "pointers.h" #include #include #include "atom.h" diff --git a/src/atom_vec_body.cpp b/src/atom_vec_body.cpp index 3e9528d6b9..fad5b3eae0 100644 --- a/src/atom_vec_body.cpp +++ b/src/atom_vec_body.cpp @@ -13,6 +13,7 @@ #include #include +#include #include "atom_vec_body.h" #include "my_pool_chunk.h" #include "style_body.h" diff --git a/src/bond_hybrid.cpp b/src/bond_hybrid.cpp index 0fb23a3214..9028886758 100644 --- a/src/bond_hybrid.cpp +++ b/src/bond_hybrid.cpp @@ -12,7 +12,6 @@ ------------------------------------------------------------------------- */ #include -#include #include #include #include "bond_hybrid.h" diff --git a/src/bond_zero.cpp b/src/bond_zero.cpp index 3932846cb4..c473abbe4b 100644 --- a/src/bond_zero.cpp +++ b/src/bond_zero.cpp @@ -16,7 +16,6 @@ ------------------------------------------------------------------------- */ #include -#include #include #include "bond_zero.h" #include "atom.h" diff --git a/src/comm.h b/src/comm.h index 30360b1059..6d5592585f 100644 --- a/src/comm.h +++ b/src/comm.h @@ -14,7 +14,7 @@ #ifndef LMP_COMM_H #define LMP_COMM_H -#include "pointers.h" +#include "pointers.h" // IWYU pragma: export namespace LAMMPS_NS { diff --git a/src/comm_tiled.cpp b/src/comm_tiled.cpp index a85520ed45..385b7fdf22 100644 --- a/src/comm_tiled.cpp +++ b/src/comm_tiled.cpp @@ -11,6 +11,7 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ +#include #include #include #include "comm_tiled.h" diff --git a/src/compute_adf.cpp b/src/compute_adf.cpp index e9f9ba2b6f..a17561ff54 100644 --- a/src/compute_adf.cpp +++ b/src/compute_adf.cpp @@ -17,18 +17,15 @@ #include #include -#include #include #include "compute_adf.h" #include "atom.h" #include "update.h" #include "force.h" #include "pair.h" -#include "domain.h" #include "neighbor.h" #include "neigh_request.h" #include "neigh_list.h" -#include "group.h" #include "math_const.h" #include "memory.h" #include "error.h" diff --git a/src/compute_aggregate_atom.cpp b/src/compute_aggregate_atom.cpp index 6c8c8e5d9a..9a797124bd 100644 --- a/src/compute_aggregate_atom.cpp +++ b/src/compute_aggregate_atom.cpp @@ -15,6 +15,7 @@ Contributing author: Axel Kohlmeyer (Temple U) ------------------------------------------------------------------------- */ +#include #include #include #include "compute_aggregate_atom.h" diff --git a/src/compute_angle.cpp b/src/compute_angle.cpp index 59945f5832..c1c02a1cc4 100644 --- a/src/compute_angle.cpp +++ b/src/compute_angle.cpp @@ -12,8 +12,8 @@ ------------------------------------------------------------------------- */ #include -#include #include "compute_angle.h" +#include "angle.h" #include "update.h" #include "force.h" #include "angle_hybrid.h" diff --git a/src/compute_angmom_chunk.cpp b/src/compute_angmom_chunk.cpp index a70eaaf49f..ec42015527 100644 --- a/src/compute_angmom_chunk.cpp +++ b/src/compute_angmom_chunk.cpp @@ -11,6 +11,7 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ +#include #include #include "compute_angmom_chunk.h" #include "atom.h" diff --git a/src/compute_bond.cpp b/src/compute_bond.cpp index 896aaec9bd..4fd3bbef30 100644 --- a/src/compute_bond.cpp +++ b/src/compute_bond.cpp @@ -12,8 +12,8 @@ ------------------------------------------------------------------------- */ #include -#include #include "compute_bond.h" +#include "bond.h" #include "update.h" #include "force.h" #include "bond_hybrid.h" diff --git a/src/compute_centro_atom.cpp b/src/compute_centro_atom.cpp index 5096879b32..7df94271fc 100644 --- a/src/compute_centro_atom.cpp +++ b/src/compute_centro_atom.cpp @@ -16,7 +16,6 @@ ------------------------------------------------------------------------- */ #include -#include #include "compute_centro_atom.h" #include "atom.h" #include "update.h" diff --git a/src/compute_chunk_atom.cpp b/src/compute_chunk_atom.cpp index 61b653b375..fd9204f1cb 100644 --- a/src/compute_chunk_atom.cpp +++ b/src/compute_chunk_atom.cpp @@ -14,8 +14,11 @@ // NOTE: allow for bin center to be variables for sphere/cylinder #include +#include #include #include +#include +#include #include "compute_chunk_atom.h" #include "atom.h" #include "update.h" @@ -24,6 +27,7 @@ #include "region.h" #include "lattice.h" #include "modify.h" +#include "fix.h" #include "fix_store.h" #include "comm.h" #include "group.h" @@ -33,8 +37,6 @@ #include "memory.h" #include "error.h" -#include - using namespace LAMMPS_NS; using namespace MathConst; diff --git a/src/compute_cluster_atom.cpp b/src/compute_cluster_atom.cpp index 0c34b42671..febe0658a0 100644 --- a/src/compute_cluster_atom.cpp +++ b/src/compute_cluster_atom.cpp @@ -11,9 +11,9 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ +#include #include #include -#include #include "compute_cluster_atom.h" #include "atom.h" #include "update.h" diff --git a/src/compute_cna_atom.cpp b/src/compute_cna_atom.cpp index b8ad3f0f64..d764e739b3 100644 --- a/src/compute_cna_atom.cpp +++ b/src/compute_cna_atom.cpp @@ -15,8 +15,8 @@ Contributing author: Wan Liang (Chinese Academy of Sciences) ------------------------------------------------------------------------- */ +#include #include -#include #include #include "compute_cna_atom.h" #include "atom.h" diff --git a/src/compute_com_chunk.cpp b/src/compute_com_chunk.cpp index ec66767245..7b4c960cf4 100644 --- a/src/compute_com_chunk.cpp +++ b/src/compute_com_chunk.cpp @@ -11,6 +11,7 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ +#include #include #include "compute_com_chunk.h" #include "atom.h" diff --git a/src/compute_contact_atom.cpp b/src/compute_contact_atom.cpp index e60a51832a..e4afc1d761 100644 --- a/src/compute_contact_atom.cpp +++ b/src/compute_contact_atom.cpp @@ -11,9 +11,7 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include #include -#include #include "compute_contact_atom.h" #include "atom.h" #include "update.h" @@ -22,7 +20,6 @@ #include "neigh_list.h" #include "neigh_request.h" #include "force.h" -#include "pair.h" #include "comm.h" #include "memory.h" #include "error.h" diff --git a/src/compute_coord_atom.cpp b/src/compute_coord_atom.cpp index 54f4c70c71..8cedcbc027 100644 --- a/src/compute_coord_atom.cpp +++ b/src/compute_coord_atom.cpp @@ -13,7 +13,6 @@ #include #include -#include #include "compute_coord_atom.h" #include "compute_orientorder_atom.h" #include "atom.h" diff --git a/src/compute_dihedral.cpp b/src/compute_dihedral.cpp index 3595b2eda3..16823050da 100644 --- a/src/compute_dihedral.cpp +++ b/src/compute_dihedral.cpp @@ -12,10 +12,10 @@ ------------------------------------------------------------------------- */ #include -#include #include "compute_dihedral.h" #include "update.h" #include "force.h" +#include "dihedral.h" #include "dihedral_hybrid.h" #include "error.h" diff --git a/src/compute_dihedral_local.cpp b/src/compute_dihedral_local.cpp index 9efdd61cb8..784ae9c607 100644 --- a/src/compute_dihedral_local.cpp +++ b/src/compute_dihedral_local.cpp @@ -20,10 +20,8 @@ #include "update.h" #include "domain.h" #include "force.h" -#include "dihedral.h" #include "input.h" #include "variable.h" - #include "math_const.h" #include "memory.h" #include "error.h" diff --git a/src/compute_dipole_chunk.cpp b/src/compute_dipole_chunk.cpp index b0474b6359..090bc5df94 100644 --- a/src/compute_dipole_chunk.cpp +++ b/src/compute_dipole_chunk.cpp @@ -11,6 +11,8 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ +#include +#include #include #include "compute_dipole_chunk.h" #include "atom.h" diff --git a/src/compute_displace_atom.cpp b/src/compute_displace_atom.cpp index d8f279058e..3773159143 100644 --- a/src/compute_displace_atom.cpp +++ b/src/compute_displace_atom.cpp @@ -19,7 +19,6 @@ #include "group.h" #include "domain.h" #include "modify.h" -#include "fix.h" #include "fix_store.h" #include "input.h" #include "variable.h" diff --git a/src/compute_erotate_sphere.cpp b/src/compute_erotate_sphere.cpp index 31ed0aaba5..65bb8a9770 100644 --- a/src/compute_erotate_sphere.cpp +++ b/src/compute_erotate_sphere.cpp @@ -14,11 +14,8 @@ #include #include "compute_erotate_sphere.h" #include "atom.h" -#include "atom_vec.h" #include "update.h" #include "force.h" -#include "domain.h" -#include "group.h" #include "error.h" using namespace LAMMPS_NS; diff --git a/src/compute_fragment_atom.cpp b/src/compute_fragment_atom.cpp index bb273f3bdb..d59b519d09 100644 --- a/src/compute_fragment_atom.cpp +++ b/src/compute_fragment_atom.cpp @@ -15,6 +15,7 @@ Contributing author: Axel Kohlmeyer (Temple U) ------------------------------------------------------------------------- */ +#include #include #include "compute_fragment_atom.h" #include "atom.h" diff --git a/src/compute_global_atom.cpp b/src/compute_global_atom.cpp index dc9ab52f49..6685f746a1 100644 --- a/src/compute_global_atom.cpp +++ b/src/compute_global_atom.cpp @@ -16,12 +16,8 @@ #include "compute_global_atom.h" #include "atom.h" #include "update.h" -#include "domain.h" #include "modify.h" #include "fix.h" -#include "force.h" -#include "comm.h" -#include "group.h" #include "input.h" #include "variable.h" #include "memory.h" diff --git a/src/compute_group_group.cpp b/src/compute_group_group.cpp index e55f679b2e..11e1aac720 100644 --- a/src/compute_group_group.cpp +++ b/src/compute_group_group.cpp @@ -33,7 +33,6 @@ #include "comm.h" #include "domain.h" #include "math_const.h" -#include "utils.h" using namespace LAMMPS_NS; using namespace MathConst; diff --git a/src/compute_gyration.cpp b/src/compute_gyration.cpp index f8d19853e0..3c5656a5af 100644 --- a/src/compute_gyration.cpp +++ b/src/compute_gyration.cpp @@ -11,7 +11,7 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include +#include #include "compute_gyration.h" #include "update.h" #include "atom.h" diff --git a/src/compute_gyration_chunk.cpp b/src/compute_gyration_chunk.cpp index 6a23398aca..f3db37d62f 100644 --- a/src/compute_gyration_chunk.cpp +++ b/src/compute_gyration_chunk.cpp @@ -11,6 +11,7 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ +#include #include #include #include "compute_gyration_chunk.h" diff --git a/src/compute_heat_flux.cpp b/src/compute_heat_flux.cpp index e402da7842..9bd827c713 100644 --- a/src/compute_heat_flux.cpp +++ b/src/compute_heat_flux.cpp @@ -16,14 +16,13 @@ Mario Pinto (Computational Research Lab, Pune, India) ------------------------------------------------------------------------- */ -#include +#include #include #include "compute_heat_flux.h" #include "atom.h" #include "update.h" #include "modify.h" #include "force.h" -#include "group.h" #include "error.h" using namespace LAMMPS_NS; diff --git a/src/compute_hexorder_atom.cpp b/src/compute_hexorder_atom.cpp index 6d17ae15bd..c54f4b1aae 100644 --- a/src/compute_hexorder_atom.cpp +++ b/src/compute_hexorder_atom.cpp @@ -15,9 +15,9 @@ Contributing author: Aidan Thompson (SNL) ------------------------------------------------------------------------- */ -#include +#include #include -#include +#include #include "compute_hexorder_atom.h" #include "atom.h" #include "update.h" diff --git a/src/compute_improper.cpp b/src/compute_improper.cpp index ac2a23e727..2f068dfb74 100644 --- a/src/compute_improper.cpp +++ b/src/compute_improper.cpp @@ -12,10 +12,10 @@ ------------------------------------------------------------------------- */ #include -#include #include "compute_improper.h" #include "update.h" #include "force.h" +#include "improper.h" #include "improper_hybrid.h" #include "error.h" diff --git a/src/compute_improper_local.cpp b/src/compute_improper_local.cpp index 2861850c79..ec1734cd96 100644 --- a/src/compute_improper_local.cpp +++ b/src/compute_improper_local.cpp @@ -20,7 +20,6 @@ #include "update.h" #include "domain.h" #include "force.h" -#include "improper.h" #include "math_const.h" #include "memory.h" #include "error.h" diff --git a/src/compute_inertia_chunk.cpp b/src/compute_inertia_chunk.cpp index a33073c35a..d1a7cb9fc1 100644 --- a/src/compute_inertia_chunk.cpp +++ b/src/compute_inertia_chunk.cpp @@ -11,6 +11,7 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ +#include #include #include "compute_inertia_chunk.h" #include "atom.h" diff --git a/src/compute_ke.cpp b/src/compute_ke.cpp index fb3c5a9695..3418cc678f 100644 --- a/src/compute_ke.cpp +++ b/src/compute_ke.cpp @@ -16,8 +16,6 @@ #include "atom.h" #include "update.h" #include "force.h" -#include "domain.h" -#include "group.h" #include "error.h" using namespace LAMMPS_NS; diff --git a/src/compute_msd.cpp b/src/compute_msd.cpp index fc47b2609a..d2e17eff9e 100644 --- a/src/compute_msd.cpp +++ b/src/compute_msd.cpp @@ -11,6 +11,7 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ +#include #include #include "compute_msd.h" #include "atom.h" diff --git a/src/compute_msd_chunk.cpp b/src/compute_msd_chunk.cpp index 1f974cc06c..8520b36993 100644 --- a/src/compute_msd_chunk.cpp +++ b/src/compute_msd_chunk.cpp @@ -11,6 +11,7 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ +#include #include #include "compute_msd_chunk.h" #include "atom.h" diff --git a/src/compute_omega_chunk.cpp b/src/compute_omega_chunk.cpp index 23447da602..360255e908 100644 --- a/src/compute_omega_chunk.cpp +++ b/src/compute_omega_chunk.cpp @@ -11,6 +11,7 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ +#include #include #include "compute_omega_chunk.h" #include "atom.h" diff --git a/src/compute_pair_local.cpp b/src/compute_pair_local.cpp index c356a08be9..1ab46a0297 100644 --- a/src/compute_pair_local.cpp +++ b/src/compute_pair_local.cpp @@ -22,7 +22,6 @@ #include "neighbor.h" #include "neigh_request.h" #include "neigh_list.h" -#include "group.h" #include "memory.h" #include "error.h" diff --git a/src/compute_pe_atom.cpp b/src/compute_pe_atom.cpp index 2f1dc5650e..b3ace2d419 100644 --- a/src/compute_pe_atom.cpp +++ b/src/compute_pe_atom.cpp @@ -24,7 +24,6 @@ #include "improper.h" #include "kspace.h" #include "modify.h" -#include "fix.h" #include "memory.h" #include "error.h" diff --git a/src/compute_pressure.cpp b/src/compute_pressure.cpp index dde02a5aed..431f039de3 100644 --- a/src/compute_pressure.cpp +++ b/src/compute_pressure.cpp @@ -13,7 +13,6 @@ #include #include -#include #include "compute_pressure.h" #include "atom.h" #include "update.h" diff --git a/src/compute_property_chunk.cpp b/src/compute_property_chunk.cpp index 489890e1cc..089e867598 100644 --- a/src/compute_property_chunk.cpp +++ b/src/compute_property_chunk.cpp @@ -11,6 +11,7 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ +#include #include #include "compute_property_chunk.h" #include "atom.h" diff --git a/src/compute_rdf.cpp b/src/compute_rdf.cpp index d49485b4ea..b1fa8bb2a3 100644 --- a/src/compute_rdf.cpp +++ b/src/compute_rdf.cpp @@ -17,7 +17,6 @@ #include #include -#include #include #include "compute_rdf.h" #include "atom.h" diff --git a/src/compute_reduce.cpp b/src/compute_reduce.cpp index 16dc84628a..e7692b0797 100644 --- a/src/compute_reduce.cpp +++ b/src/compute_reduce.cpp @@ -20,8 +20,6 @@ #include "domain.h" #include "modify.h" #include "fix.h" -#include "force.h" -#include "comm.h" #include "group.h" #include "input.h" #include "variable.h" diff --git a/src/compute_reduce_region.cpp b/src/compute_reduce_region.cpp index 8e91a299e8..30a5c6393f 100644 --- a/src/compute_reduce_region.cpp +++ b/src/compute_reduce_region.cpp @@ -11,8 +11,7 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include -#include +#include #include "compute_reduce_region.h" #include "atom.h" #include "update.h" -- GitLab From df7c56d88160add5ce3492c1f5b9e757b34ebace Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Fri, 28 Jun 2019 05:28:54 -0400 Subject: [PATCH 129/469] use suffix compatible pair style matching when looking for ReaxFF pair style --- src/QEQ/fix_qeq_shielded.cpp | 2 +- src/USER-REAXC/fix_qeq_reax.cpp | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/src/QEQ/fix_qeq_shielded.cpp b/src/QEQ/fix_qeq_shielded.cpp index a74eee7d29..6367feacc5 100644 --- a/src/QEQ/fix_qeq_shielded.cpp +++ b/src/QEQ/fix_qeq_shielded.cpp @@ -80,7 +80,7 @@ void FixQEqShielded::init() void FixQEqShielded::extract_reax() { - Pair *pair = force->pair_match("reax/c",1); + Pair *pair = force->pair_match("^reax/c",0); if (pair == NULL) error->all(FLERR,"No pair reax/c for fix qeq/shielded"); int tmp; chi = (double *) pair->extract("chi",tmp); diff --git a/src/USER-REAXC/fix_qeq_reax.cpp b/src/USER-REAXC/fix_qeq_reax.cpp index b37c8fff83..faa0632608 100644 --- a/src/USER-REAXC/fix_qeq_reax.cpp +++ b/src/USER-REAXC/fix_qeq_reax.cpp @@ -124,7 +124,7 @@ FixQEqReax::FixQEqReax(LAMMPS *lmp, int narg, char **arg) : // register with Atom class reaxc = NULL; - reaxc = (PairReaxC *) force->pair_match("reax/c",0); + reaxc = (PairReaxC *) force->pair_match("^reax/c",0); s_hist = t_hist = NULL; grow_arrays(atom->nmax); -- GitLab From 557a1274e48fdb950a998c28f2e5eba6a996065d Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Fri, 28 Jun 2019 02:12:47 -0400 Subject: [PATCH 130/469] even more include file cleanup --- src/compute_slice.cpp | 2 +- src/compute_stress_atom.cpp | 1 - src/compute_temp.cpp | 2 -- src/compute_temp_chunk.cpp | 1 + src/compute_temp_com.cpp | 3 --- src/compute_temp_partial.cpp | 1 - src/compute_temp_profile.cpp | 2 -- src/compute_temp_ramp.cpp | 2 -- src/compute_temp_sphere.cpp | 2 -- src/compute_torque_chunk.cpp | 1 + src/compute_vacf.cpp | 1 + src/compute_vcm_chunk.cpp | 2 +- src/create_atoms.cpp | 5 +---- src/create_bonds.cpp | 2 +- src/create_box.cpp | 2 -- src/delete_atoms.cpp | 3 ++- src/delete_bonds.cpp | 1 - src/deprecated.cpp | 1 - src/dihedral.cpp | 3 --- 19 files changed, 9 insertions(+), 28 deletions(-) diff --git a/src/compute_slice.cpp b/src/compute_slice.cpp index ac70e7dd15..6e509c24d4 100644 --- a/src/compute_slice.cpp +++ b/src/compute_slice.cpp @@ -11,13 +11,13 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ +#include #include #include #include "compute_slice.h" #include "update.h" #include "modify.h" #include "fix.h" -#include "group.h" #include "input.h" #include "variable.h" #include "memory.h" diff --git a/src/compute_stress_atom.cpp b/src/compute_stress_atom.cpp index 5211f015ab..f84c977bdb 100644 --- a/src/compute_stress_atom.cpp +++ b/src/compute_stress_atom.cpp @@ -11,7 +11,6 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include #include #include "compute_stress_atom.h" #include "atom.h" diff --git a/src/compute_temp.cpp b/src/compute_temp.cpp index f7d3a890ec..c330249a7e 100644 --- a/src/compute_temp.cpp +++ b/src/compute_temp.cpp @@ -12,13 +12,11 @@ ------------------------------------------------------------------------- */ #include -#include #include "compute_temp.h" #include "atom.h" #include "update.h" #include "force.h" #include "domain.h" -#include "comm.h" #include "group.h" #include "error.h" diff --git a/src/compute_temp_chunk.cpp b/src/compute_temp_chunk.cpp index 920515e05c..229e98e258 100644 --- a/src/compute_temp_chunk.cpp +++ b/src/compute_temp_chunk.cpp @@ -11,6 +11,7 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ +#include #include #include "compute_temp_chunk.h" #include "atom.h" diff --git a/src/compute_temp_com.cpp b/src/compute_temp_com.cpp index f2ad40ea43..21814e1940 100644 --- a/src/compute_temp_com.cpp +++ b/src/compute_temp_com.cpp @@ -12,15 +12,12 @@ ------------------------------------------------------------------------- */ #include -#include -#include #include "compute_temp_com.h" #include "atom.h" #include "update.h" #include "force.h" #include "group.h" #include "domain.h" -#include "lattice.h" #include "error.h" using namespace LAMMPS_NS; diff --git a/src/compute_temp_partial.cpp b/src/compute_temp_partial.cpp index 4425aebdda..8d5ff66796 100644 --- a/src/compute_temp_partial.cpp +++ b/src/compute_temp_partial.cpp @@ -12,7 +12,6 @@ ------------------------------------------------------------------------- */ #include -#include #include "compute_temp_partial.h" #include "atom.h" #include "update.h" diff --git a/src/compute_temp_profile.cpp b/src/compute_temp_profile.cpp index c7f0b28a6c..21c87b31a2 100644 --- a/src/compute_temp_profile.cpp +++ b/src/compute_temp_profile.cpp @@ -12,14 +12,12 @@ ------------------------------------------------------------------------- */ #include -#include #include #include "compute_temp_profile.h" #include "atom.h" #include "update.h" #include "force.h" #include "group.h" -#include "fix.h" #include "domain.h" #include "memory.h" #include "error.h" diff --git a/src/compute_temp_ramp.cpp b/src/compute_temp_ramp.cpp index ba572645f3..715d2aa9f4 100644 --- a/src/compute_temp_ramp.cpp +++ b/src/compute_temp_ramp.cpp @@ -12,14 +12,12 @@ ------------------------------------------------------------------------- */ #include -#include #include #include "compute_temp_ramp.h" #include "atom.h" #include "update.h" #include "force.h" #include "group.h" -#include "fix.h" #include "domain.h" #include "lattice.h" #include "memory.h" diff --git a/src/compute_temp_sphere.cpp b/src/compute_temp_sphere.cpp index 651da6dee5..b490a5ec45 100644 --- a/src/compute_temp_sphere.cpp +++ b/src/compute_temp_sphere.cpp @@ -15,12 +15,10 @@ #include #include "compute_temp_sphere.h" #include "atom.h" -#include "atom_vec.h" #include "update.h" #include "force.h" #include "domain.h" #include "modify.h" -#include "comm.h" #include "group.h" #include "error.h" diff --git a/src/compute_torque_chunk.cpp b/src/compute_torque_chunk.cpp index d9de99bcb2..e43155493f 100644 --- a/src/compute_torque_chunk.cpp +++ b/src/compute_torque_chunk.cpp @@ -11,6 +11,7 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ +#include #include #include "compute_torque_chunk.h" #include "atom.h" diff --git a/src/compute_vacf.cpp b/src/compute_vacf.cpp index 3ef3acf0bf..787c2503ca 100644 --- a/src/compute_vacf.cpp +++ b/src/compute_vacf.cpp @@ -11,6 +11,7 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ +#include #include #include "compute_vacf.h" #include "atom.h" diff --git a/src/compute_vcm_chunk.cpp b/src/compute_vcm_chunk.cpp index a6dd796c63..cf30130763 100644 --- a/src/compute_vcm_chunk.cpp +++ b/src/compute_vcm_chunk.cpp @@ -11,13 +11,13 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ +#include #include #include "compute_vcm_chunk.h" #include "atom.h" #include "update.h" #include "modify.h" #include "compute_chunk_atom.h" -#include "domain.h" #include "memory.h" #include "error.h" diff --git a/src/create_atoms.cpp b/src/create_atoms.cpp index 52e4256fca..8504023a70 100644 --- a/src/create_atoms.cpp +++ b/src/create_atoms.cpp @@ -11,8 +11,7 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include -#include +#include #include #include "create_atoms.h" #include "atom.h" @@ -23,8 +22,6 @@ #include "modify.h" #include "force.h" #include "special.h" -#include "fix.h" -#include "compute.h" #include "domain.h" #include "lattice.h" #include "region.h" diff --git a/src/create_bonds.cpp b/src/create_bonds.cpp index e19b565554..e00fe109ca 100644 --- a/src/create_bonds.cpp +++ b/src/create_bonds.cpp @@ -15,7 +15,7 @@ Contributing authors: Mike Salerno (NRL) added single methods ------------------------------------------------------------------------- */ -#include +#include #include #include "create_bonds.h" #include "atom.h" diff --git a/src/create_box.cpp b/src/create_box.cpp index b5e37b759c..5ec960bec4 100644 --- a/src/create_box.cpp +++ b/src/create_box.cpp @@ -11,12 +11,10 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include #include #include "create_box.h" #include "atom.h" #include "atom_vec.h" -#include "force.h" #include "domain.h" #include "region.h" #include "region_prism.h" diff --git a/src/delete_atoms.cpp b/src/delete_atoms.cpp index 41df167f07..ff4b97a3a4 100644 --- a/src/delete_atoms.cpp +++ b/src/delete_atoms.cpp @@ -11,8 +11,9 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include +#include #include +#include #include "delete_atoms.h" #include "atom.h" #include "atom_vec.h" diff --git a/src/delete_bonds.cpp b/src/delete_bonds.cpp index fe32bca879..c4d591543a 100644 --- a/src/delete_bonds.cpp +++ b/src/delete_bonds.cpp @@ -18,7 +18,6 @@ #include "atom.h" #include "atom_vec.h" #include "domain.h" -#include "neighbor.h" #include "comm.h" #include "force.h" #include "group.h" diff --git a/src/deprecated.cpp b/src/deprecated.cpp index b937482669..66ddcfeff4 100644 --- a/src/deprecated.cpp +++ b/src/deprecated.cpp @@ -18,7 +18,6 @@ #include #include "deprecated.h" #include "comm.h" -#include "force.h" #include "error.h" #include "input.h" diff --git a/src/dihedral.cpp b/src/dihedral.cpp index adccf2a490..d2de841dd0 100644 --- a/src/dihedral.cpp +++ b/src/dihedral.cpp @@ -11,13 +11,10 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include #include "dihedral.h" #include "atom.h" #include "comm.h" #include "force.h" -#include "pair.h" -#include "suffix.h" #include "atom_masks.h" #include "memory.h" #include "error.h" -- GitLab From d918432047743f70a0650713ba7a21f0935d5245 Mon Sep 17 00:00:00 2001 From: Stan Moore Date: Fri, 28 Jun 2019 09:54:24 -0600 Subject: [PATCH 131/469] Fix issue with compute_duarray --- src/KOKKOS/pair_snap_kokkos_impl.h | 11 +++++----- src/KOKKOS/sna_kokkos.h | 11 +++++----- src/KOKKOS/sna_kokkos_impl.h | 33 +++++++++++++++++++++++------- src/SNAP/compute_snad_atom.cpp | 2 +- src/SNAP/compute_snav_atom.cpp | 2 +- src/SNAP/pair_snap.cpp | 2 +- src/SNAP/sna.cpp | 27 +++++++++++++++++++----- src/SNAP/sna.h | 7 ++++--- 8 files changed, 67 insertions(+), 28 deletions(-) diff --git a/src/KOKKOS/pair_snap_kokkos_impl.h b/src/KOKKOS/pair_snap_kokkos_impl.h index d56db05d19..d0c7e09e84 100644 --- a/src/KOKKOS/pair_snap_kokkos_impl.h +++ b/src/KOKKOS/pair_snap_kokkos_impl.h @@ -309,7 +309,7 @@ void PairSNAPKokkos::operator() (TagPairSNAPBeta,const typename Kokk const int ii = team.league_rank(); const int i = d_ilist[ii]; const int itype = type[i]; - const int ielem = d_map[itype]; + const int ielem = map[itype]; Kokkos::View> d_coeffi(d_coeffelem,ielem,Kokkos::ALL); @@ -601,12 +601,13 @@ void PairSNAPKokkos::operator() (TagPairSNAPCompute::member_type& team, double*, double, double); //ForceSNAP + void compute_duidrj(const typename Kokkos::TeamPolicy::member_type& team, double*, double, double, int); //ForceSNAP KOKKOS_INLINE_FUNCTION void compute_dbidrj(const typename Kokkos::TeamPolicy::member_type& team); //ForceSNAP KOKKOS_INLINE_FUNCTION @@ -123,10 +123,11 @@ inline t_sna_1d ulisttot_r, ulisttot_i; t_sna_1d_atomic ulisttot_r_a, ulisttot_i_a; t_sna_1d zlist_r, zlist_i; + t_sna_2d ulist_r_ij, ulist_i_ij; // Per InFlight Interaction t_sna_1d ulist_r, ulist_i; - t_sna_1d_atomic ylist_r, ylist_i; + t_sna_1d ylist_r, ylist_i; // derivatives of data t_sna_2d dulist_r, dulist_i; @@ -171,13 +172,13 @@ inline KOKKOS_INLINE_FUNCTION void addself_uarraytot(const typename Kokkos::TeamPolicy::member_type& team, double); // compute_ui KOKKOS_INLINE_FUNCTION - void add_uarraytot(const typename Kokkos::TeamPolicy::member_type& team, double, double, double); // compute_ui + void add_uarraytot(const typename Kokkos::TeamPolicy::member_type& team, double, double, double, int); // compute_ui KOKKOS_INLINE_FUNCTION void compute_uarray(const typename Kokkos::TeamPolicy::member_type& team, double, double, double, double, double); // compute_ui - inline + KOKKOS_INLINE_FUNCTION double deltacg(int, int, int); // init_clebsch_gordan inline @@ -185,7 +186,7 @@ inline KOKKOS_INLINE_FUNCTION void compute_duarray(const typename Kokkos::TeamPolicy::member_type& team, double, double, double, // compute_duidrj - double, double, double, double, double); + double, double, double, double, double, int); // Sets the style for the switching function // 0 = none diff --git a/src/KOKKOS/sna_kokkos_impl.h b/src/KOKKOS/sna_kokkos_impl.h index 9b96cb8a16..8cbb3eb3f6 100644 --- a/src/KOKKOS/sna_kokkos_impl.h +++ b/src/KOKKOS/sna_kokkos_impl.h @@ -289,7 +289,7 @@ void SNAKokkos::compute_ui(const typename Kokkos::TeamPolicy::compute_dbidrj(const typename Kokkos::TeamPolicy KOKKOS_INLINE_FUNCTION void SNAKokkos::compute_duidrj(const typename Kokkos::TeamPolicy::member_type& team, - double* rij, double wj, double rcut) + double* rij, double wj, double rcut, int jj) { double rsq, r, x, y, z, z0, theta0, cs, sn; double dz0dr; @@ -797,7 +797,7 @@ void SNAKokkos::compute_duidrj(const typename Kokkos::TeamPolicy::addself_uarraytot(const typename Kokkos::TeamPolicy< template KOKKOS_INLINE_FUNCTION -void SNAKokkos::add_uarraytot(const typename Kokkos::TeamPolicy::member_type& team, double r, double wj, double rcut) +void SNAKokkos::add_uarraytot(const typename Kokkos::TeamPolicy::member_type& team, + double r, double wj, double rcut, int j) { const double sfac = compute_sfac(r, rcut) * wj; @@ -854,10 +855,19 @@ void SNAKokkos::add_uarraytot(const typename Kokkos::TeamPolicy> + ulist_r_j(ulist_r_ij,j,Kokkos::ALL); + Kokkos::View> + ulist_i_j(ulist_i_ij,j,Kokkos::ALL); + Kokkos::parallel_for(Kokkos::ThreadVectorRange(team,ulisttot_r.span()), [&] (const int& i) { Kokkos::atomic_add(ptrtot_r+i, sfac * ptr_r[i]); Kokkos::atomic_add(ptrtot_i+i, sfac * ptr_i[i]); + + ulist_r_j(i) = ulist_r(i); + ulist_i_j(i) = ulist_i(i); }); } @@ -962,7 +972,7 @@ KOKKOS_INLINE_FUNCTION void SNAKokkos::compute_duarray(const typename Kokkos::TeamPolicy::member_type& team, double x, double y, double z, double z0, double r, double dz0dr, - double wj, double rcut) + double wj, double rcut, int jj) { double r0inv; double a_r, a_i, b_r, b_i; @@ -1006,6 +1016,11 @@ void SNAKokkos::compute_duarray(const typename Kokkos::TeamPolicy> + ulist_r(ulist_r_ij,jj,Kokkos::ALL); + Kokkos::View> + ulist_i(ulist_i_ij,jj,Kokkos::ALL); + dulist_r(0,0) = 0.0; dulist_r(0,1) = 0.0; dulist_r(0,2) = 0.0; @@ -1135,6 +1150,8 @@ void SNAKokkos::create_team_scratch_arrays(const typename Kokkos::Te rcutij = t_sna_1d(team.team_scratch(1),nmax); wj = t_sna_1d(team.team_scratch(1),nmax); inside = t_sna_1i(team.team_scratch(1),nmax); + ulist_r_ij = t_sna_2d(team.team_scratch(1),nmax,idxu_max); + ulist_i_ij = t_sna_2d(team.team_scratch(1),nmax,idxu_max); } template @@ -1151,6 +1168,7 @@ T_INT SNAKokkos::size_team_scratch_arrays() { size += t_sna_1d::shmem_size(nmax); // rcutij size += t_sna_1d::shmem_size(nmax); // wj size += t_sna_1i::shmem_size(nmax); // inside + size += t_sna_2d::shmem_size(nmax,idxu_max)*2; // ulist_ij return size; } @@ -1558,8 +1576,8 @@ double SNAKokkos::memory_usage() bytes += jdim * jdim * jdim * sizeof(int); // idxz_block bytes += jdim * jdim * jdim * sizeof(int); // idxb_block - bytes += idxz_max * sizeof(SNAKK_ZINDICES); // idxz - bytes += idxb_max * sizeof(SNAKK_BINDICES); // idxb + bytes += idxz_max * sizeof(SNAKK_ZINDICES); // idxz + bytes += idxb_max * sizeof(SNAKK_BINDICES); // idxb bytes += jdim * sizeof(double); // bzero @@ -1567,6 +1585,7 @@ double SNAKokkos::memory_usage() bytes += nmax * sizeof(int); // inside bytes += nmax * sizeof(double); // wj bytes += nmax * sizeof(double); // rcutij + bytes += nmax * idxu_max * sizeof(double) * 2; // ulist_ij return bytes; } diff --git a/src/SNAP/compute_snad_atom.cpp b/src/SNAP/compute_snad_atom.cpp index 37587a0aae..0a82cdeb00 100644 --- a/src/SNAP/compute_snad_atom.cpp +++ b/src/SNAP/compute_snad_atom.cpp @@ -263,7 +263,7 @@ void ComputeSNADAtom::compute_peratom() const int j = snaptr->inside[jj]; snaptr->compute_duidrj(snaptr->rij[jj], snaptr->wj[jj], - snaptr->rcutij[jj]); + snaptr->rcutij[jj],jj); snaptr->compute_dbidrj(); // Accumulate -dBi/dRi, -dBi/dRj diff --git a/src/SNAP/compute_snav_atom.cpp b/src/SNAP/compute_snav_atom.cpp index 1f702496ed..374bf32298 100644 --- a/src/SNAP/compute_snav_atom.cpp +++ b/src/SNAP/compute_snav_atom.cpp @@ -258,7 +258,7 @@ void ComputeSNAVAtom::compute_peratom() snaptr->compute_duidrj(snaptr->rij[jj], snaptr->wj[jj], - snaptr->rcutij[jj]); + snaptr->rcutij[jj],jj); snaptr->compute_dbidrj(); // Accumulate -dBi/dRi*Ri, -dBi/dRj*Rj diff --git a/src/SNAP/pair_snap.cpp b/src/SNAP/pair_snap.cpp index f9ba8922a0..4dce39361f 100644 --- a/src/SNAP/pair_snap.cpp +++ b/src/SNAP/pair_snap.cpp @@ -176,7 +176,7 @@ void PairSNAP::compute(int eflag, int vflag) for (int jj = 0; jj < ninside; jj++) { int j = snaptr->inside[jj]; snaptr->compute_duidrj(snaptr->rij[jj], - snaptr->wj[jj],snaptr->rcutij[jj]); + snaptr->wj[jj],snaptr->rcutij[jj],jj); snaptr->compute_deidrj(fij); diff --git a/src/SNAP/sna.cpp b/src/SNAP/sna.cpp index ada3f528d2..f9696e1f12 100644 --- a/src/SNAP/sna.cpp +++ b/src/SNAP/sna.cpp @@ -134,6 +134,8 @@ SNA::SNA(LAMMPS* lmp, double rfac0_in, nmax = 0; idxz = NULL; idxb = NULL; + ulist_r_ij = NULL; + ulist_i_ij = NULL; build_indexlist(); create_twojmax_arrays(); @@ -154,6 +156,8 @@ SNA::~SNA() memory->destroy(inside); memory->destroy(wj); memory->destroy(rcutij); + memory->destroy(ulist_r_ij); + memory->destroy(ulist_i_ij); delete[] idxz; delete[] idxb; destroy_twojmax_arrays(); @@ -299,10 +303,14 @@ void SNA::grow_rij(int newnmax) memory->destroy(inside); memory->destroy(wj); memory->destroy(rcutij); + memory->destroy(ulist_r_ij); + memory->destroy(ulist_i_ij); memory->create(rij, nmax, 3, "pair:rij"); memory->create(inside, nmax, "pair:inside"); memory->create(wj, nmax, "pair:wj"); memory->create(rcutij, nmax, "pair:rcutij"); + memory->create(ulist_r_ij, nmax, idxu_max, "sna:ulist_ij"); + memory->create(ulist_i_ij, nmax, idxu_max, "sna:ulist_ij"); } /* ---------------------------------------------------------------------- @@ -334,7 +342,7 @@ void SNA::compute_ui(int jnum) z0 = r / tan(theta0); compute_uarray(x, y, z, z0, r); - add_uarraytot(r, wj[j], rcutij[j]); + add_uarraytot(r, wj[j], rcutij[j], j); } } @@ -826,7 +834,7 @@ void SNA::compute_dbidrj() calculate derivative of Ui w.r.t. atom j ------------------------------------------------------------------------- */ -void SNA::compute_duidrj(double* rij, double wj, double rcut) +void SNA::compute_duidrj(double* rij, double wj, double rcut, int jj) { double rsq, r, x, y, z, z0, theta0, cs, sn; double dz0dr; @@ -843,7 +851,7 @@ void SNA::compute_duidrj(double* rij, double wj, double rcut) z0 = r * cs / sn; dz0dr = z0 / r - (r*rscale0) * (rsq + z0 * z0) / rsq; - compute_duarray(x, y, z, z0, r, dz0dr, wj, rcut); + compute_duarray(x, y, z, z0, r, dz0dr, wj, rcut, jj); } /* ---------------------------------------------------------------------- */ @@ -879,7 +887,7 @@ void SNA::addself_uarraytot(double wself_in) add Wigner U-functions for one neighbor to the total ------------------------------------------------------------------------- */ -void SNA::add_uarraytot(double r, double wj, double rcut) +void SNA::add_uarraytot(double r, double wj, double rcut, int jj) { double sfac; @@ -887,6 +895,9 @@ void SNA::add_uarraytot(double r, double wj, double rcut) sfac *= wj; + double* ulist_r_j = ulist_r_ij[jj]; + double* ulist_i_j = ulist_i_ij[jj]; + for (int j = 0; j <= twojmax; j++) { int jju = idxu_block[j]; for (int mb = 0; mb <= j; mb++) @@ -895,6 +906,9 @@ void SNA::add_uarraytot(double r, double wj, double rcut) sfac * ulist_r[jju]; ulisttot_i[jju] += sfac * ulist_i[jju]; + + ulist_r_j[jju] = ulist_r[jju]; + ulist_i_j[jju] = ulist_i[jju]; jju++; } } @@ -992,7 +1006,7 @@ void SNA::compute_uarray(double x, double y, double z, void SNA::compute_duarray(double x, double y, double z, double z0, double r, double dz0dr, - double wj, double rcut) + double wj, double rcut, int jj) { double r0inv; double a_r, a_i, b_r, b_i; @@ -1036,6 +1050,9 @@ void SNA::compute_duarray(double x, double y, double z, db_i[0] += -r0inv; db_r[1] += r0inv; + double* ulist_r = ulist_r_ij[jj]; + double* ulist_i = ulist_i_ij[jj]; + dulist_r[0][0] = 0.0; dulist_r[0][1] = 0.0; dulist_r[0][2] = 0.0; diff --git a/src/SNAP/sna.h b/src/SNAP/sna.h index 1e08ef123c..81582cf9e5 100644 --- a/src/SNAP/sna.h +++ b/src/SNAP/sna.h @@ -53,7 +53,7 @@ public: // functions for derivatives - void compute_duidrj(double*, double, double); + void compute_duidrj(double*, double, double, int); void compute_dbidrj(); void compute_deidrj(double*); double compute_sfac(double, double); @@ -86,6 +86,7 @@ private: double* ulisttot_r, * ulisttot_i; double* ulist_r, * ulist_i; + double** ulist_r_ij, ** ulist_i_ij; int* idxu_block; double* zlist_r, * zlist_i; @@ -106,13 +107,13 @@ private: void init_rootpqarray(); void zero_uarraytot(); void addself_uarraytot(double); - void add_uarraytot(double, double, double); + void add_uarraytot(double, double, double, int); void compute_uarray(double, double, double, double, double); double deltacg(int, int, int); int compute_ncoeff(); void compute_duarray(double, double, double, - double, double, double, double, double); + double, double, double, double, double, int); // Sets the style for the switching function // 0 = none -- GitLab From 5eabc820240604ef4ea3859d054e6c03febc3827 Mon Sep 17 00:00:00 2001 From: Stan Moore Date: Fri, 28 Jun 2019 10:17:22 -0600 Subject: [PATCH 132/469] Restore lost changes --- src/KOKKOS/pair_snap_kokkos_impl.h | 9 ++++----- src/KOKKOS/sna_kokkos.h | 4 ++-- 2 files changed, 6 insertions(+), 7 deletions(-) diff --git a/src/KOKKOS/pair_snap_kokkos_impl.h b/src/KOKKOS/pair_snap_kokkos_impl.h index d0c7e09e84..20e04605ce 100644 --- a/src/KOKKOS/pair_snap_kokkos_impl.h +++ b/src/KOKKOS/pair_snap_kokkos_impl.h @@ -309,7 +309,7 @@ void PairSNAPKokkos::operator() (TagPairSNAPBeta,const typename Kokk const int ii = team.league_rank(); const int i = d_ilist[ii]; const int itype = type[i]; - const int ielem = map[itype]; + const int ielem = d_map[itype]; Kokkos::View> d_coeffi(d_coeffelem,ielem,Kokkos::ALL); @@ -603,11 +603,10 @@ void PairSNAPKokkos::operator() (TagPairSNAPCompute::member_type& team, double, double, double, double, double); // compute_ui - KOKKOS_INLINE_FUNCTION + inline double deltacg(int, int, int); // init_clebsch_gordan inline -- GitLab From 5e3a705911e057e2188efca2512394e96a46cc04 Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Fri, 28 Jun 2019 14:28:45 -0400 Subject: [PATCH 133/469] fix bug caused by a parameter shadowing a class variable --- src/thermo.cpp | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/src/thermo.cpp b/src/thermo.cpp index f4ab7b0779..bba867d195 100644 --- a/src/thermo.cpp +++ b/src/thermo.cpp @@ -406,8 +406,9 @@ void Thermo::compute(int flag) call function to compute property ------------------------------------------------------------------------- */ -void Thermo::call_vfunc(int ifield) +void Thermo::call_vfunc(int ifield_in) { + ifield = ifield_in; (this->*vfunc[ifield])(); } -- GitLab From 31cbccda85de0c04dff11eebe97eabc53b57a738 Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Fri, 28 Jun 2019 21:38:19 -0400 Subject: [PATCH 134/469] continue cleaning up include file lists --- src/RIGID/fix_shake.cpp | 4 +--- src/dihedral_hybrid.cpp | 3 +-- src/dihedral_zero.cpp | 3 --- src/displace_atoms.cpp | 2 +- src/domain.cpp | 4 ---- src/domain.h | 2 +- src/dump.cpp | 2 -- src/dump_atom.cpp | 1 - src/dump_cfg.cpp | 8 -------- src/dump_custom.cpp | 1 - src/dump_dcd.cpp | 2 -- src/dump_image.cpp | 4 ++-- src/dump_local.cpp | 1 - src/dump_movie.cpp | 3 --- src/dump_xyz.cpp | 1 - src/error.cpp | 1 - src/finish.cpp | 4 ---- src/fix.cpp | 1 - src/fix_adapt.cpp | 2 -- src/fix_addforce.cpp | 1 + src/fix_ave_atom.cpp | 1 - src/fix_ave_chunk.cpp | 2 ++ src/fix_ave_correlate.cpp | 2 ++ src/fix_ave_histo.cpp | 3 ++- src/fix_ave_histo_weight.cpp | 8 +++----- src/fix_ave_time.cpp | 2 ++ src/fix_aveforce.cpp | 1 - src/fix_balance.cpp | 2 -- src/fix_box_relax.cpp | 1 - src/fix_deform.cpp | 1 - src/fix_drag.cpp | 2 +- src/fix_dt_reset.cpp | 2 +- src/fix_external.cpp | 2 -- src/fix_gravity.cpp | 3 +-- src/fix_halt.cpp | 3 +-- src/fix_heat.cpp | 2 +- src/fix_indent.cpp | 3 +-- src/fix_langevin.cpp | 3 --- src/fix_lineforce.cpp | 1 - src/fix_minimize.cpp | 2 -- src/fix_momentum.cpp | 3 ++- src/fix_move.cpp | 2 -- src/fix_neigh_history.cpp | 4 +--- src/fix_neigh_history.h | 1 - src/fix_nh.cpp | 2 -- src/fix_nh_sphere.cpp | 2 +- src/fix_nve.cpp | 1 - src/fix_nve_limit.cpp | 3 +-- src/fix_nve_noforce.cpp | 1 - src/fix_nve_sphere.cpp | 3 --- src/fix_nvt_sllod.cpp | 1 - src/fix_planeforce.cpp | 1 - src/fix_press_berendsen.cpp | 2 -- src/fix_print.cpp | 2 +- src/fix_property_atom.cpp | 2 -- src/fix_read_restart.cpp | 1 - src/fix_recenter.cpp | 2 +- src/fix_respa.cpp | 1 - src/fix_restrain.cpp | 3 +-- 59 files changed, 32 insertions(+), 101 deletions(-) diff --git a/src/RIGID/fix_shake.cpp b/src/RIGID/fix_shake.cpp index 23ced2d0e7..5c202706af 100644 --- a/src/RIGID/fix_shake.cpp +++ b/src/RIGID/fix_shake.cpp @@ -13,11 +13,9 @@ #include #include -#include +#include #include -#include #include "fix_shake.h" -#include "fix_rattle.h" #include "atom.h" #include "atom_vec.h" #include "molecule.h" diff --git a/src/dihedral_hybrid.cpp b/src/dihedral_hybrid.cpp index f3e4823d53..27fd7084bc 100644 --- a/src/dihedral_hybrid.cpp +++ b/src/dihedral_hybrid.cpp @@ -11,13 +11,12 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include +#include #include #include #include "dihedral_hybrid.h" #include "atom.h" #include "neighbor.h" -#include "domain.h" #include "comm.h" #include "force.h" #include "memory.h" diff --git a/src/dihedral_zero.cpp b/src/dihedral_zero.cpp index 8145d5f32d..0367477267 100644 --- a/src/dihedral_zero.cpp +++ b/src/dihedral_zero.cpp @@ -15,13 +15,10 @@ Contributing author: Carsten Svaneborg (SDU) ------------------------------------------------------------------------- */ -#include -#include #include #include "dihedral_zero.h" #include "atom.h" #include "force.h" -#include "comm.h" #include "memory.h" #include "error.h" diff --git a/src/displace_atoms.cpp b/src/displace_atoms.cpp index 7b29b1d3d5..8bae173a1d 100644 --- a/src/displace_atoms.cpp +++ b/src/displace_atoms.cpp @@ -12,7 +12,7 @@ ------------------------------------------------------------------------- */ #include -#include +#include #include #include "displace_atoms.h" #include "atom.h" diff --git a/src/domain.cpp b/src/domain.cpp index 74d7560c31..197eff514a 100644 --- a/src/domain.cpp +++ b/src/domain.cpp @@ -16,9 +16,7 @@ ------------------------------------------------------------------------- */ #include -#include #include -#include #include #include "domain.h" #include "style_region.h" @@ -37,13 +35,11 @@ #include "output.h" #include "thermo.h" #include "universe.h" -#include "math_const.h" #include "memory.h" #include "error.h" #include "utils.h" using namespace LAMMPS_NS; -using namespace MathConst; #define BIG 1.0e20 #define SMALL 1.0e-4 diff --git a/src/domain.h b/src/domain.h index e131d07a1b..a0bda8ae72 100644 --- a/src/domain.h +++ b/src/domain.h @@ -15,9 +15,9 @@ #define LMP_DOMAIN_H #include -#include "pointers.h" #include #include +#include "pointers.h" namespace LAMMPS_NS { diff --git a/src/dump.cpp b/src/dump.cpp index 8fa07a9cb2..b08a4de2ad 100644 --- a/src/dump.cpp +++ b/src/dump.cpp @@ -12,9 +12,7 @@ ------------------------------------------------------------------------- */ #include -#include #include -#include #include "dump.h" #include "atom.h" #include "irregular.h" diff --git a/src/dump_atom.cpp b/src/dump_atom.cpp index 74583f4013..c95256ac21 100644 --- a/src/dump_atom.cpp +++ b/src/dump_atom.cpp @@ -16,7 +16,6 @@ #include "domain.h" #include "atom.h" #include "update.h" -#include "group.h" #include "memory.h" #include "error.h" diff --git a/src/dump_cfg.cpp b/src/dump_cfg.cpp index ddd662c8a6..eb5329e0d1 100644 --- a/src/dump_cfg.cpp +++ b/src/dump_cfg.cpp @@ -16,18 +16,10 @@ Memory efficiency improved by Ray Shan (Sandia) ------------------------------------------------------------------------- */ -#include -#include #include #include "dump_cfg.h" #include "atom.h" #include "domain.h" -#include "comm.h" -#include "modify.h" -#include "compute.h" -#include "input.h" -#include "fix.h" -#include "variable.h" #include "memory.h" #include "error.h" diff --git a/src/dump_custom.cpp b/src/dump_custom.cpp index 17ad4b89ef..75e4e42bcd 100644 --- a/src/dump_custom.cpp +++ b/src/dump_custom.cpp @@ -11,7 +11,6 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include #include #include #include "dump_custom.h" diff --git a/src/dump_dcd.cpp b/src/dump_dcd.cpp index 384e9089c0..ce669fecfd 100644 --- a/src/dump_dcd.cpp +++ b/src/dump_dcd.cpp @@ -17,8 +17,6 @@ ------------------------------------------------------------------------- */ #include -#include // requires C++-11 -#include #include #include #include "dump_dcd.h" diff --git a/src/dump_image.cpp b/src/dump_image.cpp index 0d63d2e4cb..0b4ca43879 100644 --- a/src/dump_image.cpp +++ b/src/dump_image.cpp @@ -11,20 +11,20 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ +#include #include #include -#include #include #include "dump_image.h" #include "image.h" #include "atom.h" +#include "atom_vec.h" #include "atom_vec_line.h" #include "atom_vec_tri.h" #include "atom_vec_body.h" #include "body.h" #include "molecule.h" #include "domain.h" -#include "group.h" #include "force.h" #include "comm.h" #include "modify.h" diff --git a/src/dump_local.cpp b/src/dump_local.cpp index 8dc0554690..f99b7ac06c 100644 --- a/src/dump_local.cpp +++ b/src/dump_local.cpp @@ -15,7 +15,6 @@ #include #include #include "dump_local.h" -#include "atom.h" #include "modify.h" #include "fix.h" #include "compute.h" diff --git a/src/dump_movie.cpp b/src/dump_movie.cpp index 59dfdc3d6e..37d8a37f4d 100644 --- a/src/dump_movie.cpp +++ b/src/dump_movie.cpp @@ -15,13 +15,10 @@ Contributing author: Axel Kohlmeyer (Temple U) ------------------------------------------------------------------------- */ -#include -#include #include #include "dump_movie.h" #include "comm.h" #include "force.h" -#include "memory.h" #include "error.h" using namespace LAMMPS_NS; diff --git a/src/dump_xyz.cpp b/src/dump_xyz.cpp index fd52671d81..4d50cfc2c8 100644 --- a/src/dump_xyz.cpp +++ b/src/dump_xyz.cpp @@ -14,7 +14,6 @@ #include #include "dump_xyz.h" #include "atom.h" -#include "group.h" #include "error.h" #include "memory.h" #include "update.h" diff --git a/src/error.cpp b/src/error.cpp index cc80dcb4d8..8970145b7c 100644 --- a/src/error.cpp +++ b/src/error.cpp @@ -16,7 +16,6 @@ #include #include "error.h" #include "universe.h" -#include "update.h" #include "output.h" #include "input.h" diff --git a/src/finish.cpp b/src/finish.cpp index 1baa6d6fda..77c959b945 100644 --- a/src/finish.cpp +++ b/src/finish.cpp @@ -15,12 +15,10 @@ #include #include #include -#include #include "finish.h" #include "timer.h" #include "universe.h" #include "accelerator_kokkos.h" -#include "accelerator_omp.h" #include "atom.h" #include "atom_vec.h" #include "molecule.h" @@ -32,10 +30,8 @@ #include "neighbor.h" #include "neigh_list.h" #include "neigh_request.h" -#include "output.h" #include "memory.h" #include "error.h" -#include "utils.h" #ifdef LMP_USER_OMP #include "modify.h" diff --git a/src/fix.cpp b/src/fix.cpp index 634bc2393d..1913ed483e 100644 --- a/src/fix.cpp +++ b/src/fix.cpp @@ -17,7 +17,6 @@ #include "atom.h" #include "group.h" #include "force.h" -#include "comm.h" #include "atom_masks.h" #include "memory.h" #include "error.h" diff --git a/src/fix_adapt.cpp b/src/fix_adapt.cpp index 9a5b528747..7ac6128558 100644 --- a/src/fix_adapt.cpp +++ b/src/fix_adapt.cpp @@ -11,9 +11,7 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include #include -#include #include "fix_adapt.h" #include "atom.h" #include "bond.h" diff --git a/src/fix_addforce.cpp b/src/fix_addforce.cpp index d66457a1f1..e29c4ffe9f 100644 --- a/src/fix_addforce.cpp +++ b/src/fix_addforce.cpp @@ -11,6 +11,7 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ +#include #include #include #include "fix_addforce.h" diff --git a/src/fix_ave_atom.cpp b/src/fix_ave_atom.cpp index c8cbad75c9..e6566632de 100644 --- a/src/fix_ave_atom.cpp +++ b/src/fix_ave_atom.cpp @@ -15,7 +15,6 @@ #include #include "fix_ave_atom.h" #include "atom.h" -#include "domain.h" #include "update.h" #include "modify.h" #include "compute.h" diff --git a/src/fix_ave_chunk.cpp b/src/fix_ave_chunk.cpp index 7aed4dcbe7..1533d1fa4f 100644 --- a/src/fix_ave_chunk.cpp +++ b/src/fix_ave_chunk.cpp @@ -11,6 +11,8 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ +#include +#include // IWYU pragma: keep #include #include #include diff --git a/src/fix_ave_correlate.cpp b/src/fix_ave_correlate.cpp index 5c95f20ec2..555c1ac026 100644 --- a/src/fix_ave_correlate.cpp +++ b/src/fix_ave_correlate.cpp @@ -17,6 +17,8 @@ Reese Jones (Sandia) ------------------------------------------------------------------------- */ +#include +#include // IWYU pragma: keep #include #include #include diff --git a/src/fix_ave_histo.cpp b/src/fix_ave_histo.cpp index 87da5222f0..29fdc21c74 100644 --- a/src/fix_ave_histo.cpp +++ b/src/fix_ave_histo.cpp @@ -11,6 +11,8 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ +#include +#include // IWYU pragma: keep #include #include #include @@ -19,7 +21,6 @@ #include "update.h" #include "modify.h" #include "compute.h" -#include "group.h" #include "input.h" #include "variable.h" #include "memory.h" diff --git a/src/fix_ave_histo_weight.cpp b/src/fix_ave_histo_weight.cpp index c78f4fa1e3..5eeb074472 100644 --- a/src/fix_ave_histo_weight.cpp +++ b/src/fix_ave_histo_weight.cpp @@ -14,21 +14,19 @@ /* ---------------------------------------------------------------------- Contributing author: Shawn Coleman (ARL) ------------------------------------------------------------------------- */ - -#include -#include +#include +#include // IWYU pragma: keep #include +#include "fix.h" #include "fix_ave_histo_weight.h" #include "atom.h" #include "update.h" #include "modify.h" #include "compute.h" -#include "group.h" #include "input.h" #include "variable.h" #include "memory.h" #include "error.h" -#include "force.h" using namespace LAMMPS_NS; using namespace FixConst; diff --git a/src/fix_ave_time.cpp b/src/fix_ave_time.cpp index 50654b6561..4820215f46 100644 --- a/src/fix_ave_time.cpp +++ b/src/fix_ave_time.cpp @@ -15,6 +15,8 @@ Contributing author: Pieter in 't Veld (SNL) ------------------------------------------------------------------------- */ +#include +#include // IWYU pragma: keep #include #include #include diff --git a/src/fix_aveforce.cpp b/src/fix_aveforce.cpp index 1c87ba5785..4791a8b022 100644 --- a/src/fix_aveforce.cpp +++ b/src/fix_aveforce.cpp @@ -13,7 +13,6 @@ #include #include -#include #include "fix_aveforce.h" #include "atom.h" #include "update.h" diff --git a/src/fix_balance.cpp b/src/fix_balance.cpp index ddaf42b49d..f9c32e8df0 100644 --- a/src/fix_balance.cpp +++ b/src/fix_balance.cpp @@ -12,7 +12,6 @@ ------------------------------------------------------------------------- */ #include -#include #include "fix_balance.h" #include "balance.h" #include "update.h" @@ -26,7 +25,6 @@ #include "modify.h" #include "fix_store.h" #include "rcb.h" -#include "timer.h" #include "error.h" using namespace LAMMPS_NS; diff --git a/src/fix_box_relax.cpp b/src/fix_box_relax.cpp index a315330d14..c73c0ade88 100644 --- a/src/fix_box_relax.cpp +++ b/src/fix_box_relax.cpp @@ -17,7 +17,6 @@ #include #include -#include #include "fix_box_relax.h" #include "atom.h" #include "domain.h" diff --git a/src/fix_deform.cpp b/src/fix_deform.cpp index 909ead3e2a..96d7580c39 100644 --- a/src/fix_deform.cpp +++ b/src/fix_deform.cpp @@ -16,7 +16,6 @@ ------------------------------------------------------------------------- */ #include -#include #include #include "fix_deform.h" #include "atom.h" diff --git a/src/fix_drag.cpp b/src/fix_drag.cpp index e4cf12d1ff..006d1c46d0 100644 --- a/src/fix_drag.cpp +++ b/src/fix_drag.cpp @@ -11,8 +11,8 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ +#include #include -#include #include #include "fix_drag.h" #include "atom.h" diff --git a/src/fix_dt_reset.cpp b/src/fix_dt_reset.cpp index 7566094b48..4e6195c4fa 100644 --- a/src/fix_dt_reset.cpp +++ b/src/fix_dt_reset.cpp @@ -11,8 +11,8 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ +#include #include -#include #include #include "fix_dt_reset.h" #include "atom.h" diff --git a/src/fix_external.cpp b/src/fix_external.cpp index b1ffa65e49..2c926e26b5 100644 --- a/src/fix_external.cpp +++ b/src/fix_external.cpp @@ -11,9 +11,7 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include #include -#include #include "fix_external.h" #include "atom.h" #include "update.h" diff --git a/src/fix_gravity.cpp b/src/fix_gravity.cpp index bc10eb2807..8508a92cc4 100644 --- a/src/fix_gravity.cpp +++ b/src/fix_gravity.cpp @@ -11,9 +11,8 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ +#include #include -#include -#include #include #include "fix_gravity.h" #include "atom.h" diff --git a/src/fix_halt.cpp b/src/fix_halt.cpp index 5fda4c30d6..133494fb8e 100644 --- a/src/fix_halt.cpp +++ b/src/fix_halt.cpp @@ -11,13 +11,12 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ +#include #include -#include #include #include "fix_halt.h" #include "update.h" #include "force.h" -#include "update.h" #include "input.h" #include "variable.h" #include "atom.h" diff --git a/src/fix_heat.cpp b/src/fix_heat.cpp index f34845785c..f78a9c0860 100644 --- a/src/fix_heat.cpp +++ b/src/fix_heat.cpp @@ -15,8 +15,8 @@ Contributing author: Paul Crozier (SNL) ------------------------------------------------------------------------- */ +#include #include -#include #include #include "fix_heat.h" #include "atom.h" diff --git a/src/fix_indent.cpp b/src/fix_indent.cpp index b8e07dfd53..6a42cadefd 100644 --- a/src/fix_indent.cpp +++ b/src/fix_indent.cpp @@ -15,9 +15,9 @@ Contributing author: Ravi Agrawal (Northwestern U) ------------------------------------------------------------------------- */ +#include #include #include -#include #include "fix_indent.h" #include "atom.h" #include "input.h" @@ -26,7 +26,6 @@ #include "lattice.h" #include "update.h" #include "modify.h" -#include "output.h" #include "respa.h" #include "error.h" #include "force.h" diff --git a/src/fix_langevin.cpp b/src/fix_langevin.cpp index 36ea47daf6..0f48562048 100644 --- a/src/fix_langevin.cpp +++ b/src/fix_langevin.cpp @@ -19,7 +19,6 @@ #include #include #include -#include #include "fix_langevin.h" #include "math_extra.h" #include "atom.h" @@ -28,8 +27,6 @@ #include "update.h" #include "modify.h" #include "compute.h" -#include "domain.h" -#include "region.h" #include "respa.h" #include "comm.h" #include "input.h" diff --git a/src/fix_lineforce.cpp b/src/fix_lineforce.cpp index aea1a2a25b..61c6341aa6 100644 --- a/src/fix_lineforce.cpp +++ b/src/fix_lineforce.cpp @@ -13,7 +13,6 @@ #include #include -#include #include "fix_lineforce.h" #include "atom.h" #include "update.h" diff --git a/src/fix_minimize.cpp b/src/fix_minimize.cpp index fa39643a1b..df2dfb02a7 100644 --- a/src/fix_minimize.cpp +++ b/src/fix_minimize.cpp @@ -11,12 +11,10 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include #include "fix_minimize.h" #include "atom.h" #include "domain.h" #include "memory.h" -#include "error.h" using namespace LAMMPS_NS; using namespace FixConst; diff --git a/src/fix_momentum.cpp b/src/fix_momentum.cpp index 680251e670..bf94a94362 100644 --- a/src/fix_momentum.cpp +++ b/src/fix_momentum.cpp @@ -11,7 +11,8 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include +#include +#include #include #include "fix_momentum.h" #include "atom.h" diff --git a/src/fix_move.cpp b/src/fix_move.cpp index 0a5f506ab2..646f943ef9 100644 --- a/src/fix_move.cpp +++ b/src/fix_move.cpp @@ -12,11 +12,9 @@ ------------------------------------------------------------------------- */ #include -#include #include #include "fix_move.h" #include "atom.h" -#include "group.h" #include "update.h" #include "modify.h" #include "force.h" diff --git a/src/fix_neigh_history.cpp b/src/fix_neigh_history.cpp index 207c409596..ca593f29df 100644 --- a/src/fix_neigh_history.cpp +++ b/src/fix_neigh_history.cpp @@ -13,16 +13,14 @@ #include #include -#include #include "fix_neigh_history.h" +#include "my_page.h" #include "atom.h" #include "comm.h" #include "neighbor.h" #include "neigh_list.h" #include "force.h" #include "pair.h" -#include "update.h" -#include "modify.h" #include "memory.h" #include "error.h" diff --git a/src/fix_neigh_history.h b/src/fix_neigh_history.h index 601e8a55a2..51d03f5b12 100644 --- a/src/fix_neigh_history.h +++ b/src/fix_neigh_history.h @@ -21,7 +21,6 @@ FixStyle(NEIGH_HISTORY,FixNeighHistory) #define LMP_FIX_NEIGH_HISTORY_H #include "fix.h" -#include "my_page.h" namespace LAMMPS_NS { diff --git a/src/fix_nh.cpp b/src/fix_nh.cpp index deca0ad83d..3ffdff54cf 100644 --- a/src/fix_nh.cpp +++ b/src/fix_nh.cpp @@ -16,10 +16,8 @@ ------------------------------------------------------------------------- */ #include -#include #include #include "fix_nh.h" -#include "math_extra.h" #include "atom.h" #include "force.h" #include "group.h" diff --git a/src/fix_nh_sphere.cpp b/src/fix_nh_sphere.cpp index f176493242..0f1024700a 100644 --- a/src/fix_nh_sphere.cpp +++ b/src/fix_nh_sphere.cpp @@ -16,10 +16,10 @@ ------------------------------------------------------------------------- */ #include +#include #include "fix_nh_sphere.h" #include "atom.h" #include "atom_vec.h" -#include "group.h" #include "error.h" #include "force.h" #include "domain.h" diff --git a/src/fix_nve.cpp b/src/fix_nve.cpp index 959483230e..3396f3ca47 100644 --- a/src/fix_nve.cpp +++ b/src/fix_nve.cpp @@ -11,7 +11,6 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include #include #include "fix_nve.h" #include "atom.h" diff --git a/src/fix_nve_limit.cpp b/src/fix_nve_limit.cpp index 68ff0665a1..49bed2e3dd 100644 --- a/src/fix_nve_limit.cpp +++ b/src/fix_nve_limit.cpp @@ -11,9 +11,8 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ +#include #include -#include -#include #include #include "fix_nve_limit.h" #include "atom.h" diff --git a/src/fix_nve_noforce.cpp b/src/fix_nve_noforce.cpp index d4fca9e676..7b61aac18e 100644 --- a/src/fix_nve_noforce.cpp +++ b/src/fix_nve_noforce.cpp @@ -11,7 +11,6 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include #include #include "fix_nve_noforce.h" #include "atom.h" diff --git a/src/fix_nve_sphere.cpp b/src/fix_nve_sphere.cpp index 0bee8b8685..94e8aa88ac 100644 --- a/src/fix_nve_sphere.cpp +++ b/src/fix_nve_sphere.cpp @@ -12,14 +12,11 @@ ------------------------------------------------------------------------- */ #include -#include #include #include "fix_nve_sphere.h" #include "atom.h" #include "domain.h" #include "atom_vec.h" -#include "update.h" -#include "respa.h" #include "force.h" #include "error.h" #include "math_vector.h" diff --git a/src/fix_nvt_sllod.cpp b/src/fix_nvt_sllod.cpp index c7d23364a7..16e2fb1d3d 100644 --- a/src/fix_nvt_sllod.cpp +++ b/src/fix_nvt_sllod.cpp @@ -15,7 +15,6 @@ Contributing author: Pieter in 't Veld (SNL) ------------------------------------------------------------------------- */ -#include #include #include "fix_nvt_sllod.h" #include "math_extra.h" diff --git a/src/fix_planeforce.cpp b/src/fix_planeforce.cpp index 45dc782fcf..a83d00a506 100644 --- a/src/fix_planeforce.cpp +++ b/src/fix_planeforce.cpp @@ -13,7 +13,6 @@ #include #include -#include #include "fix_planeforce.h" #include "atom.h" #include "update.h" diff --git a/src/fix_press_berendsen.cpp b/src/fix_press_berendsen.cpp index 95db004436..ad3e3d1e1c 100644 --- a/src/fix_press_berendsen.cpp +++ b/src/fix_press_berendsen.cpp @@ -12,7 +12,6 @@ ------------------------------------------------------------------------- */ #include -#include #include #include "fix_press_berendsen.h" #include "atom.h" @@ -23,7 +22,6 @@ #include "compute.h" #include "kspace.h" #include "update.h" -#include "respa.h" #include "domain.h" #include "error.h" diff --git a/src/fix_print.cpp b/src/fix_print.cpp index f6db88114a..da2e2b54f3 100644 --- a/src/fix_print.cpp +++ b/src/fix_print.cpp @@ -11,7 +11,7 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include +#include #include #include "fix_print.h" #include "update.h" diff --git a/src/fix_property_atom.cpp b/src/fix_property_atom.cpp index c89419f850..62c3ec985b 100644 --- a/src/fix_property_atom.cpp +++ b/src/fix_property_atom.cpp @@ -19,8 +19,6 @@ #include "memory.h" #include "error.h" -#include "update.h" - using namespace LAMMPS_NS; using namespace FixConst; diff --git a/src/fix_read_restart.cpp b/src/fix_read_restart.cpp index 3c3178f4af..afedf9c12c 100644 --- a/src/fix_read_restart.cpp +++ b/src/fix_read_restart.cpp @@ -11,7 +11,6 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include #include "fix_read_restart.h" #include "atom.h" #include "memory.h" diff --git a/src/fix_recenter.cpp b/src/fix_recenter.cpp index 75b383d67a..cd50d7dc34 100644 --- a/src/fix_recenter.cpp +++ b/src/fix_recenter.cpp @@ -15,7 +15,7 @@ Contributing author: Naveen Michaud-Agrawal (Johns Hopkins U) ------------------------------------------------------------------------- */ -#include +#include #include #include "fix_recenter.h" #include "atom.h" diff --git a/src/fix_respa.cpp b/src/fix_respa.cpp index 64461ba7ca..ea2eb5050a 100644 --- a/src/fix_respa.cpp +++ b/src/fix_respa.cpp @@ -11,7 +11,6 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include #include #include "fix_respa.h" #include "atom.h" diff --git a/src/fix_restrain.cpp b/src/fix_restrain.cpp index 08485d65b3..3b9980d567 100644 --- a/src/fix_restrain.cpp +++ b/src/fix_restrain.cpp @@ -16,9 +16,9 @@ support for bond and angle restraints by Andres Jaramillo-Botero (Caltech) ------------------------------------------------------------------------- */ +#include #include #include -#include #include "fix_restrain.h" #include "atom.h" #include "force.h" @@ -26,7 +26,6 @@ #include "domain.h" #include "comm.h" #include "respa.h" -#include "input.h" #include "math_const.h" #include "memory.h" #include "error.h" -- GitLab From 96744c49338448068b16c1fe24ad2557460b13b1 Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Sat, 29 Jun 2019 21:30:23 -0400 Subject: [PATCH 135/469] more include file cleanup --- src/BODY/body_nparticle.cpp | 1 + src/BODY/body_rounded_polygon.cpp | 1 + src/BODY/body_rounded_polyhedron.cpp | 1 + src/fix_setforce.cpp | 2 +- src/fix_spring.cpp | 2 -- src/fix_spring_chunk.cpp | 2 -- src/fix_spring_rg.cpp | 2 -- src/fix_spring_self.cpp | 2 +- src/fix_store.cpp | 1 - src/fix_store_force.cpp | 1 - src/fix_temp_berendsen.cpp | 1 - src/fix_temp_csld.cpp | 1 - src/fix_temp_csvr.cpp | 3 +-- src/fix_temp_rescale.cpp | 3 --- src/fix_tmd.cpp | 1 - src/fix_vector.cpp | 1 - src/fix_viscous.cpp | 2 -- src/fix_wall.cpp | 4 +--- src/fix_wall_harmonic.cpp | 1 - src/fix_wall_reflect.cpp | 1 - src/fix_wall_region.cpp | 5 +---- src/force.cpp | 3 --- src/group.cpp | 3 +-- src/hashlittle.cpp | 1 - src/image.cpp | 3 +-- src/imbalance.h | 2 +- src/imbalance_var.cpp | 4 +--- src/improper.cpp | 1 - src/improper_hybrid.cpp | 3 +-- src/improper_zero.cpp | 3 --- src/info.cpp | 12 ++++++------ src/input.cpp | 5 ----- src/integrate.cpp | 1 - src/irregular.cpp | 1 - src/irregular.h | 1 + src/kspace.cpp | 2 ++ src/kspace.h | 1 + src/lammps.cpp | 1 - src/library.cpp | 4 +--- src/library.h | 2 ++ src/math_extra.h | 3 --- src/memory.cpp | 2 -- src/memory.h | 1 - src/min.cpp | 2 +- src/min_cg.cpp | 2 -- src/min_fire.cpp | 2 +- src/min_hftn.cpp | 1 + src/min_linesearch.cpp | 7 ++----- src/min_quickmin.cpp | 1 - src/min_sd.cpp | 2 -- src/minimize.cpp | 1 - src/modify.cpp | 1 - src/molecule.cpp | 6 +++--- src/nbin.cpp | 2 +- src/neigh_list.cpp | 4 +--- src/neigh_list.h | 1 - src/neighbor.cpp | 3 --- src/neighbor.h | 1 - src/npair_copy.cpp | 7 ------- src/npair_full_bin.cpp | 1 - src/npair_full_bin_atomonly.cpp | 2 -- src/procmap.cpp | 1 + 62 files changed, 37 insertions(+), 107 deletions(-) diff --git a/src/BODY/body_nparticle.cpp b/src/BODY/body_nparticle.cpp index 21070107f5..b2d9dbaca3 100644 --- a/src/BODY/body_nparticle.cpp +++ b/src/BODY/body_nparticle.cpp @@ -11,6 +11,7 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ +#include #include #include "body_nparticle.h" #include "my_pool_chunk.h" diff --git a/src/BODY/body_rounded_polygon.cpp b/src/BODY/body_rounded_polygon.cpp index f7741ada88..6e1e49319e 100644 --- a/src/BODY/body_rounded_polygon.cpp +++ b/src/BODY/body_rounded_polygon.cpp @@ -15,6 +15,7 @@ Contributing author: Trung Dac Nguyen (ndactrung@gmail.com) ------------------------------------------------------------------------- */ +#include #include #include "body_rounded_polygon.h" #include "my_pool_chunk.h" diff --git a/src/BODY/body_rounded_polyhedron.cpp b/src/BODY/body_rounded_polyhedron.cpp index 34d918f1f6..4b5208c397 100644 --- a/src/BODY/body_rounded_polyhedron.cpp +++ b/src/BODY/body_rounded_polyhedron.cpp @@ -15,6 +15,7 @@ Contributing author: Trung Dac Nguyen (ndactrung@gmail.com) ------------------------------------------------------------------------- */ +#include #include #include "body_rounded_polyhedron.h" #include "my_pool_chunk.h" diff --git a/src/fix_setforce.cpp b/src/fix_setforce.cpp index fc8b7aeb59..f01008dc10 100644 --- a/src/fix_setforce.cpp +++ b/src/fix_setforce.cpp @@ -11,8 +11,8 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ +#include #include -#include #include "fix_setforce.h" #include "atom.h" #include "update.h" diff --git a/src/fix_spring.cpp b/src/fix_spring.cpp index 328a0eeafd..c87cec2766 100644 --- a/src/fix_spring.cpp +++ b/src/fix_spring.cpp @@ -16,13 +16,11 @@ ------------------------------------------------------------------------- */ #include -#include #include #include "fix_spring.h" #include "atom.h" #include "update.h" #include "respa.h" -#include "domain.h" #include "force.h" #include "group.h" #include "error.h" diff --git a/src/fix_spring_chunk.cpp b/src/fix_spring_chunk.cpp index 5b5d95b111..f6ebadde94 100644 --- a/src/fix_spring_chunk.cpp +++ b/src/fix_spring_chunk.cpp @@ -12,14 +12,12 @@ ------------------------------------------------------------------------- */ #include -#include #include #include "fix_spring_chunk.h" #include "atom.h" #include "update.h" #include "force.h" #include "respa.h" -#include "domain.h" #include "modify.h" #include "compute_chunk_atom.h" #include "compute_com_chunk.h" diff --git a/src/fix_spring_rg.cpp b/src/fix_spring_rg.cpp index 28c8969006..1d5b87c599 100644 --- a/src/fix_spring_rg.cpp +++ b/src/fix_spring_rg.cpp @@ -16,8 +16,6 @@ Paul Crozier (SNL) ------------------------------------------------------------------------- */ -#include -#include #include #include "fix_spring_rg.h" #include "atom.h" diff --git a/src/fix_spring_self.cpp b/src/fix_spring_self.cpp index 670883af41..a5aa600229 100644 --- a/src/fix_spring_self.cpp +++ b/src/fix_spring_self.cpp @@ -15,7 +15,7 @@ Contributing author: Naveen Michaud-Agrawal (Johns Hopkins University) ------------------------------------------------------------------------- */ -#include +#include #include #include "fix_spring_self.h" #include "atom.h" diff --git a/src/fix_store.cpp b/src/fix_store.cpp index 9db65d0987..a370632489 100644 --- a/src/fix_store.cpp +++ b/src/fix_store.cpp @@ -11,7 +11,6 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include #include #include "fix_store.h" #include "atom.h" diff --git a/src/fix_store_force.cpp b/src/fix_store_force.cpp index a841714098..8afd985615 100644 --- a/src/fix_store_force.cpp +++ b/src/fix_store_force.cpp @@ -15,7 +15,6 @@ #include "fix_store_force.h" #include "atom.h" #include "update.h" -#include "group.h" #include "respa.h" #include "memory.h" #include "error.h" diff --git a/src/fix_temp_berendsen.cpp b/src/fix_temp_berendsen.cpp index 55518015c4..b4dd65b0c5 100644 --- a/src/fix_temp_berendsen.cpp +++ b/src/fix_temp_berendsen.cpp @@ -12,7 +12,6 @@ ------------------------------------------------------------------------- */ #include -#include #include #include "fix_temp_berendsen.h" #include "atom.h" diff --git a/src/fix_temp_csld.cpp b/src/fix_temp_csld.cpp index 7bdf776355..57f7104c61 100644 --- a/src/fix_temp_csld.cpp +++ b/src/fix_temp_csld.cpp @@ -16,7 +16,6 @@ ------------------------------------------------------------------------- */ #include -#include #include #include "fix_temp_csld.h" #include "atom.h" diff --git a/src/fix_temp_csvr.cpp b/src/fix_temp_csvr.cpp index 495a155113..9f8135ffc8 100644 --- a/src/fix_temp_csvr.cpp +++ b/src/fix_temp_csvr.cpp @@ -16,13 +16,12 @@ Based on code by Paolo Raiteri (Curtin U) and Giovanni Bussi (SISSA) ------------------------------------------------------------------------- */ +#include #include -#include #include #include "fix_temp_csvr.h" #include "atom.h" #include "force.h" -#include "memory.h" #include "comm.h" #include "input.h" #include "variable.h" diff --git a/src/fix_temp_rescale.cpp b/src/fix_temp_rescale.cpp index 11dfa6a5fc..378997c0c4 100644 --- a/src/fix_temp_rescale.cpp +++ b/src/fix_temp_rescale.cpp @@ -12,15 +12,12 @@ ------------------------------------------------------------------------- */ #include -#include #include #include "fix_temp_rescale.h" #include "atom.h" #include "force.h" #include "group.h" #include "update.h" -#include "domain.h" -#include "region.h" #include "comm.h" #include "input.h" #include "variable.h" diff --git a/src/fix_tmd.cpp b/src/fix_tmd.cpp index 4cbb244bc0..a0425db36c 100644 --- a/src/fix_tmd.cpp +++ b/src/fix_tmd.cpp @@ -18,7 +18,6 @@ #include #include -#include #include #include "fix_tmd.h" #include "atom.h" diff --git a/src/fix_vector.cpp b/src/fix_vector.cpp index 5657e59ab0..b7be472be6 100644 --- a/src/fix_vector.cpp +++ b/src/fix_vector.cpp @@ -18,7 +18,6 @@ #include "force.h" #include "modify.h" #include "compute.h" -#include "group.h" #include "input.h" #include "variable.h" #include "memory.h" diff --git a/src/fix_viscous.cpp b/src/fix_viscous.cpp index e845142322..cc60b1bda4 100644 --- a/src/fix_viscous.cpp +++ b/src/fix_viscous.cpp @@ -11,8 +11,6 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include -#include #include #include "fix_viscous.h" #include "atom.h" diff --git a/src/fix_wall.cpp b/src/fix_wall.cpp index e84d01191d..1046efc2df 100644 --- a/src/fix_wall.cpp +++ b/src/fix_wall.cpp @@ -11,11 +11,9 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include -#include +#include #include #include "fix_wall.h" -#include "atom.h" #include "input.h" #include "variable.h" #include "domain.h" diff --git a/src/fix_wall_harmonic.cpp b/src/fix_wall_harmonic.cpp index 4dc067178a..6c6d5ec402 100644 --- a/src/fix_wall_harmonic.cpp +++ b/src/fix_wall_harmonic.cpp @@ -11,7 +11,6 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include #include "fix_wall_harmonic.h" #include "atom.h" #include "error.h" diff --git a/src/fix_wall_reflect.cpp b/src/fix_wall_reflect.cpp index 8acba72035..edf5c40a5f 100644 --- a/src/fix_wall_reflect.cpp +++ b/src/fix_wall_reflect.cpp @@ -11,7 +11,6 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include #include #include "fix_wall_reflect.h" #include "atom.h" diff --git a/src/fix_wall_region.cpp b/src/fix_wall_region.cpp index ff147d7446..cb1c3c2ab2 100644 --- a/src/fix_wall_region.cpp +++ b/src/fix_wall_region.cpp @@ -11,18 +11,15 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ +#include #include -#include #include #include "fix_wall_region.h" #include "atom.h" -#include "atom_vec.h" #include "domain.h" #include "region.h" #include "force.h" -#include "lattice.h" #include "update.h" -#include "output.h" #include "respa.h" #include "error.h" #include "math_const.h" diff --git a/src/force.cpp b/src/force.cpp index 2648358932..e4939a10e8 100644 --- a/src/force.cpp +++ b/src/force.cpp @@ -21,7 +21,6 @@ #include "style_improper.h" #include "style_pair.h" #include "style_kspace.h" -#include "atom.h" #include "comm.h" #include "pair.h" #include "pair_hybrid.h" @@ -32,8 +31,6 @@ #include "dihedral.h" #include "improper.h" #include "kspace.h" -#include "group.h" -#include "memory.h" #include "error.h" #include "utils.h" diff --git a/src/group.cpp b/src/group.cpp index 256bab7778..a37d209947 100644 --- a/src/group.cpp +++ b/src/group.cpp @@ -13,9 +13,8 @@ #include #include -#include #include -#include +#include #include "group.h" #include "domain.h" #include "atom.h" diff --git a/src/hashlittle.cpp b/src/hashlittle.cpp index 42109abd24..e9340a7e55 100644 --- a/src/hashlittle.cpp +++ b/src/hashlittle.cpp @@ -2,7 +2,6 @@ // from lookup3.c, by Bob Jenkins, May 2006, Public Domain // bob_jenkins@burtleburtle.net -#include #include #include diff --git a/src/image.cpp b/src/image.cpp index 3df167bbf6..ccd6d98d87 100644 --- a/src/image.cpp +++ b/src/image.cpp @@ -18,7 +18,6 @@ #include #include #include -#include #include #include "image.h" #include "math_extra.h" @@ -29,7 +28,7 @@ #include "memory.h" #ifdef LAMMPS_JPEG -#include "jpeglib.h" +#include #endif #ifdef LAMMPS_PNG diff --git a/src/imbalance.h b/src/imbalance.h index 5f43c2e51d..0cc4ac844e 100644 --- a/src/imbalance.h +++ b/src/imbalance.h @@ -14,7 +14,7 @@ #ifndef LMP_IMBALANCE_H #define LMP_IMBALANCE_H -#include "pointers.h" +#include "pointers.h" // IWYU pragma: export namespace LAMMPS_NS { diff --git a/src/imbalance_var.cpp b/src/imbalance_var.cpp index e089b1df0c..ba17c06866 100644 --- a/src/imbalance_var.cpp +++ b/src/imbalance_var.cpp @@ -11,6 +11,7 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ +#include #include #include "imbalance_var.h" #include "atom.h" @@ -20,9 +21,6 @@ #include "memory.h" #include "error.h" -// DEBUG -#include "update.h" - using namespace LAMMPS_NS; /* -------------------------------------------------------------------- */ diff --git a/src/improper.cpp b/src/improper.cpp index 17e2df4e59..eefe3222ee 100644 --- a/src/improper.cpp +++ b/src/improper.cpp @@ -11,7 +11,6 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include #include "improper.h" #include "atom.h" #include "comm.h" diff --git a/src/improper_hybrid.cpp b/src/improper_hybrid.cpp index 5fdcb42a96..af1382d3eb 100644 --- a/src/improper_hybrid.cpp +++ b/src/improper_hybrid.cpp @@ -11,13 +11,12 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include +#include #include #include #include "improper_hybrid.h" #include "atom.h" #include "neighbor.h" -#include "domain.h" #include "comm.h" #include "force.h" #include "memory.h" diff --git a/src/improper_zero.cpp b/src/improper_zero.cpp index 747dd57919..3f36954a0a 100644 --- a/src/improper_zero.cpp +++ b/src/improper_zero.cpp @@ -15,13 +15,10 @@ Contributing author: Carsten Svaneborg (SDU) ------------------------------------------------------------------------- */ -#include -#include #include #include "improper_zero.h" #include "atom.h" #include "force.h" -#include "comm.h" #include "memory.h" #include "error.h" diff --git a/src/info.cpp b/src/info.cpp index 25b9879408..bb2d3c4b45 100644 --- a/src/info.cpp +++ b/src/info.cpp @@ -16,7 +16,13 @@ Richard Berger (Temple U) ------------------------------------------------------------------------- */ +#include +#include #include +#include +#include +#include +#include #include "info.h" #include "accelerator_kokkos.h" #include "atom.h" @@ -44,18 +50,12 @@ #include "error.h" #include "utils.h" -#include -#include -#include -#include - #ifdef _WIN32 #define PSAPI_VERSION 1 #include #include // requires C++-11 #include #else -#include #include #include #endif diff --git a/src/input.cpp b/src/input.cpp index 9e0ad78d9e..cbad1d78bf 100644 --- a/src/input.cpp +++ b/src/input.cpp @@ -12,7 +12,6 @@ ------------------------------------------------------------------------- */ #include -#include #include #include #include @@ -52,10 +51,6 @@ #include "memory.h" #include "utils.h" -#ifdef _OPENMP -#include -#endif - #ifdef _WIN32 #include #endif diff --git a/src/integrate.cpp b/src/integrate.cpp index d6b27e042d..545de849d5 100644 --- a/src/integrate.cpp +++ b/src/integrate.cpp @@ -11,7 +11,6 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include #include "integrate.h" #include "update.h" #include "force.h" diff --git a/src/irregular.cpp b/src/irregular.cpp index 1865f9cbf6..2040d12d0b 100644 --- a/src/irregular.cpp +++ b/src/irregular.cpp @@ -12,7 +12,6 @@ ------------------------------------------------------------------------- */ #include -#include #include #include "irregular.h" #include "atom.h" diff --git a/src/irregular.h b/src/irregular.h index d56bcb253d..3fdfe20b36 100644 --- a/src/irregular.h +++ b/src/irregular.h @@ -14,6 +14,7 @@ #ifndef LMP_IRREGULAR_H #define LMP_IRREGULAR_H +#include #include "pointers.h" namespace LAMMPS_NS { diff --git a/src/kspace.cpp b/src/kspace.cpp index 643cf22113..b51191857d 100644 --- a/src/kspace.cpp +++ b/src/kspace.cpp @@ -11,6 +11,8 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ +#include +#include #include #include #include "kspace.h" diff --git a/src/kspace.h b/src/kspace.h index 69f4ccb433..83ce19cd87 100644 --- a/src/kspace.h +++ b/src/kspace.h @@ -14,6 +14,7 @@ #ifndef LMP_KSPACE_H #define LMP_KSPACE_H +#include #include "pointers.h" #ifdef FFT_SINGLE diff --git a/src/lammps.cpp b/src/lammps.cpp index 83a2f057ee..b73d9f1968 100644 --- a/src/lammps.cpp +++ b/src/lammps.cpp @@ -48,7 +48,6 @@ #include "output.h" #include "citeme.h" #include "accelerator_kokkos.h" -#include "accelerator_omp.h" #include "timer.h" #include "lmppython.h" #include "version.h" diff --git a/src/library.cpp b/src/library.cpp index a653b83adb..033b814865 100644 --- a/src/library.cpp +++ b/src/library.cpp @@ -15,13 +15,11 @@ // customize by adding new LAMMPS-specific functions #include +#include #include #include #include "library.h" -#include "lmptype.h" -#include "lammps.h" #include "universe.h" -#include "input.h" #include "atom_vec.h" #include "atom.h" #include "domain.h" diff --git a/src/library.h b/src/library.h index f6f8d9d75c..8b03bb3621 100644 --- a/src/library.h +++ b/src/library.h @@ -17,7 +17,9 @@ */ #include +#ifdef LAMMPS_BIGBIG #include /* for int64_t */ +#endif /* ifdefs allow this file to be included in a C program */ diff --git a/src/math_extra.h b/src/math_extra.h index 85f57224cf..09b135c641 100644 --- a/src/math_extra.h +++ b/src/math_extra.h @@ -19,9 +19,6 @@ #define LMP_MATH_EXTRA_H #include -#include -#include -#include "error.h" namespace MathExtra { diff --git a/src/memory.cpp b/src/memory.cpp index b2f8a95b17..ca7fd3ea7f 100644 --- a/src/memory.cpp +++ b/src/memory.cpp @@ -11,9 +11,7 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include #include -#include #include "memory.h" #include "error.h" diff --git a/src/memory.h b/src/memory.h index c5eddc7fe7..42c9bf6aba 100644 --- a/src/memory.h +++ b/src/memory.h @@ -14,7 +14,6 @@ #ifndef LMP_MEMORY_H #define LMP_MEMORY_H -#include "lmptype.h" #include "pointers.h" namespace LAMMPS_NS { diff --git a/src/min.cpp b/src/min.cpp index 2a42a444a0..f2e1c982be 100644 --- a/src/min.cpp +++ b/src/min.cpp @@ -19,8 +19,8 @@ JR Shewchuk, http://www-2.cs.cmu.edu/~jrs/jrspapers.html#cg ------------------------------------------------------------------------- */ +#include #include -#include #include #include "min.h" #include "atom.h" diff --git a/src/min_cg.cpp b/src/min_cg.cpp index 20e8cc30dd..eb8831c8f5 100644 --- a/src/min_cg.cpp +++ b/src/min_cg.cpp @@ -13,9 +13,7 @@ #include #include -#include #include "min_cg.h" -#include "atom.h" #include "update.h" #include "output.h" #include "timer.h" diff --git a/src/min_fire.cpp b/src/min_fire.cpp index a50071d562..79346341bb 100644 --- a/src/min_fire.cpp +++ b/src/min_fire.cpp @@ -11,6 +11,7 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ +#include #include #include "min_fire.h" #include "universe.h" @@ -19,7 +20,6 @@ #include "update.h" #include "output.h" #include "timer.h" -#include "error.h" using namespace LAMMPS_NS; diff --git a/src/min_hftn.cpp b/src/min_hftn.cpp index 0c834fbeb4..c2c251c386 100644 --- a/src/min_hftn.cpp +++ b/src/min_hftn.cpp @@ -17,6 +17,7 @@ "Parallel Unconstrained Min", Plantenga, SAND98-8201 ------------------------------------------------------------------------- */ +#include #include #include #include "atom.h" diff --git a/src/min_linesearch.cpp b/src/min_linesearch.cpp index f93a56b09d..33a781ecfe 100644 --- a/src/min_linesearch.cpp +++ b/src/min_linesearch.cpp @@ -21,19 +21,16 @@ JR Shewchuk, http://www-2.cs.cmu.edu/~jrs/jrspapers.html#cg ------------------------------------------------------------------------- */ +#include #include #include "min_linesearch.h" #include "atom.h" -#include "update.h" -#include "neighbor.h" -#include "domain.h" #include "modify.h" +#include "neighbor.h" #include "fix_minimize.h" #include "pair.h" #include "output.h" #include "thermo.h" -#include "timer.h" -#include "error.h" using namespace LAMMPS_NS; diff --git a/src/min_quickmin.cpp b/src/min_quickmin.cpp index 8b48816355..784da82686 100644 --- a/src/min_quickmin.cpp +++ b/src/min_quickmin.cpp @@ -20,7 +20,6 @@ #include "update.h" #include "output.h" #include "timer.h" -#include "error.h" using namespace LAMMPS_NS; diff --git a/src/min_sd.cpp b/src/min_sd.cpp index 5d44437ca0..d66601119b 100644 --- a/src/min_sd.cpp +++ b/src/min_sd.cpp @@ -12,9 +12,7 @@ ------------------------------------------------------------------------- */ #include -#include #include "min_sd.h" -#include "atom.h" #include "update.h" #include "output.h" #include "timer.h" diff --git a/src/minimize.cpp b/src/minimize.cpp index e27fffd74b..e1af924019 100644 --- a/src/minimize.cpp +++ b/src/minimize.cpp @@ -11,7 +11,6 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include #include "minimize.h" #include "domain.h" #include "update.h" diff --git a/src/modify.cpp b/src/modify.cpp index 3f034bf034..61497d86db 100644 --- a/src/modify.cpp +++ b/src/modify.cpp @@ -11,7 +11,6 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include #include #include "modify.h" #include "style_compute.h" diff --git a/src/molecule.cpp b/src/molecule.cpp index 454459084a..4a3790296f 100644 --- a/src/molecule.cpp +++ b/src/molecule.cpp @@ -11,7 +11,9 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include +#include +#include +#include #include #include "molecule.h" #include "atom.h" @@ -21,12 +23,10 @@ #include "comm.h" #include "domain.h" #include "math_extra.h" -#include "math_const.h" #include "memory.h" #include "error.h" using namespace LAMMPS_NS; -using namespace MathConst; #define MAXLINE 256 #define EPSILON 1.0e-7 diff --git a/src/nbin.cpp b/src/nbin.cpp index a30b76cca0..0480c9730d 100644 --- a/src/nbin.cpp +++ b/src/nbin.cpp @@ -11,11 +11,11 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ +#include #include "nbin.h" #include "neighbor.h" #include "neigh_request.h" #include "domain.h" -#include "update.h" #include "memory.h" #include "error.h" diff --git a/src/neigh_list.cpp b/src/neigh_list.cpp index 6bdb9beae6..651b2ed70a 100644 --- a/src/neigh_list.cpp +++ b/src/neigh_list.cpp @@ -12,15 +12,13 @@ ------------------------------------------------------------------------- */ #include "neigh_list.h" +#include "my_page.h" #include "atom.h" #include "comm.h" -#include "update.h" -#include "pair.h" #include "neighbor.h" #include "neigh_request.h" #include "my_page.h" #include "memory.h" -#include "error.h" using namespace LAMMPS_NS; diff --git a/src/neigh_list.h b/src/neigh_list.h index 755a1bf134..aca11cd921 100644 --- a/src/neigh_list.h +++ b/src/neigh_list.h @@ -15,7 +15,6 @@ #define LMP_NEIGH_LIST_H #include "pointers.h" -#include "my_page.h" namespace LAMMPS_NS { diff --git a/src/neighbor.cpp b/src/neighbor.cpp index 0382624198..a2efc5919b 100644 --- a/src/neighbor.cpp +++ b/src/neighbor.cpp @@ -17,7 +17,6 @@ #include #include -#include #include #include "neighbor.h" #include "neigh_list.h" @@ -48,8 +47,6 @@ #include "error.h" #include "utils.h" -#include - using namespace LAMMPS_NS; using namespace NeighConst; diff --git a/src/neighbor.h b/src/neighbor.h index 3466dd426a..50de4b4c98 100644 --- a/src/neighbor.h +++ b/src/neighbor.h @@ -15,7 +15,6 @@ #define LMP_NEIGHBOR_H #include "pointers.h" -#include namespace LAMMPS_NS { diff --git a/src/npair_copy.cpp b/src/npair_copy.cpp index 9426d22ed3..0a522c628d 100644 --- a/src/npair_copy.cpp +++ b/src/npair_copy.cpp @@ -12,14 +12,7 @@ ------------------------------------------------------------------------- */ #include "npair_copy.h" -#include "neighbor.h" #include "neigh_list.h" -#include "atom.h" -#include "atom_vec.h" -#include "molecule.h" -#include "domain.h" -#include "my_page.h" -#include "error.h" using namespace LAMMPS_NS; diff --git a/src/npair_full_bin.cpp b/src/npair_full_bin.cpp index 94a6af129c..464dca9251 100644 --- a/src/npair_full_bin.cpp +++ b/src/npair_full_bin.cpp @@ -12,7 +12,6 @@ ------------------------------------------------------------------------- */ #include "npair_full_bin.h" -#include "neighbor.h" #include "neigh_list.h" #include "atom.h" #include "atom_vec.h" diff --git a/src/npair_full_bin_atomonly.cpp b/src/npair_full_bin_atomonly.cpp index db84733f1c..758fc7e42b 100644 --- a/src/npair_full_bin_atomonly.cpp +++ b/src/npair_full_bin_atomonly.cpp @@ -12,11 +12,9 @@ ------------------------------------------------------------------------- */ #include "npair_full_bin_atomonly.h" -#include "neighbor.h" #include "neigh_list.h" #include "atom.h" #include "atom_vec.h" -#include "domain.h" #include "my_page.h" #include "error.h" diff --git a/src/procmap.cpp b/src/procmap.cpp index 9d1ed83e73..08b60a26af 100644 --- a/src/procmap.cpp +++ b/src/procmap.cpp @@ -15,6 +15,7 @@ Contributing author (NUMA option) : Mike Brown (ORNL) ------------------------------------------------------------------------- */ +#include #include "procmap.h" #include "universe.h" #include "comm.h" -- GitLab From 3e88dacd3f351ad4a373a27b76d6799d7e1558c9 Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Sun, 30 Jun 2019 17:27:29 -0400 Subject: [PATCH 136/469] recover broken compilation of the USER-EFF package --- src/USER-EFF/fix_nvt_sllod_eff.cpp | 1 + 1 file changed, 1 insertion(+) diff --git a/src/USER-EFF/fix_nvt_sllod_eff.cpp b/src/USER-EFF/fix_nvt_sllod_eff.cpp index ed2274dcf9..0ebbf04d64 100644 --- a/src/USER-EFF/fix_nvt_sllod_eff.cpp +++ b/src/USER-EFF/fix_nvt_sllod_eff.cpp @@ -12,6 +12,7 @@ ------------------------------------------------------------------------- */ #include +#include #include #include "fix_nvt_sllod_eff.h" #include "math_extra.h" -- GitLab From e29361523f472a67ca2c7309b7b6da3c9b29aef4 Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Sun, 30 Jun 2019 18:30:59 -0400 Subject: [PATCH 137/469] recover compilation of the USER-PHONON package --- src/USER-PHONON/dynamical_matrix.cpp | 7 +++---- 1 file changed, 3 insertions(+), 4 deletions(-) diff --git a/src/USER-PHONON/dynamical_matrix.cpp b/src/USER-PHONON/dynamical_matrix.cpp index d94bd11a80..559ef4c36f 100644 --- a/src/USER-PHONON/dynamical_matrix.cpp +++ b/src/USER-PHONON/dynamical_matrix.cpp @@ -3,15 +3,15 @@ // #include -#include +#include +#include #include "dynamical_matrix.h" #include "atom.h" -#include "modify.h" #include "domain.h" #include "comm.h" +#include "error.h" #include "group.h" #include "force.h" -#include "math_extra.h" #include "memory.h" #include "bond.h" #include "angle.h" @@ -25,7 +25,6 @@ #include "finish.h" #include - using namespace LAMMPS_NS; enum{REGULAR,ESKM}; -- GitLab From 78af59438101a989c6c1a5708601f7ba4a474f95 Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Sun, 30 Jun 2019 22:45:41 -0400 Subject: [PATCH 138/469] fix typos. restore compilation of LAMMPS class implementation with OpenMP --- doc/include-file-conventions.md | 12 ++++++------ src/lammps.cpp | 1 + 2 files changed, 7 insertions(+), 6 deletions(-) diff --git a/doc/include-file-conventions.md b/doc/include-file-conventions.md index 8d70d6cdec..3f591361f5 100644 --- a/doc/include-file-conventions.md +++ b/doc/include-file-conventions.md @@ -25,7 +25,7 @@ well as make otherwise hidden dependencies visible. ## Rules -Below are the various rules that are applied. Not all a enforced +Below are the various rules that are applied. Not all are enforced strictly and automatically. If there are no significant side effects, exceptions may be possible for cases, where a full compliance to the rules may require a large effort compared to the benefit. @@ -78,9 +78,9 @@ result in a high potential for direct or indirect symbol name clashes. In the ideal case, the header would only include one file defining the parent class. That would typically be either `#include "pointers.h"` for the `Pointers` class, or a header of a class derived from it like -`#include "pair.h"` for the `Pair` class and so on. Referenced to other +`#include "pair.h"` for the `Pair` class and so on. References to other classes inside the class should be make through pointers, for which forward -declarations (inside the `LAMMPS_NS` or the new class'es namespace) can +declarations (inside the `LAMMPS_NS` or the new class' namespace) can be employed. The full definition will then be included into the corresponding implementation file. In the given example from above, the header file would be called `some_name.h` and the implementation `some_name.cpp` (all @@ -92,7 +92,7 @@ a forward slash). In the implementation files (typically, those would have the same base name as the corresponding header with a .cpp extension instead of .h) include -statments should follow the "include what you use" principle. +statements should follow the "include what you use" principle. ### Order of Include Statements @@ -107,7 +107,7 @@ Include files should be included in this order: #### pointers.h The `pointer.h` header file also includes `cstdio` and `lmptype.h` -(and throught it `stdint.h`, `intttypes.h`, and `climits`). +(and through it `stdint.h`, `intttypes.h`, and `climits`). This means any header including `pointers.h` can assume that `FILE`, `NULL`, `INT_MAX` are defined. @@ -115,7 +115,7 @@ This means any header including `pointers.h` can assume that `FILE`, The [Include What You Use tool](https://include-what-you-use.org/) can be used to provide supporting information about compliance with -the rules listed here. There are some limitations and the IWWU tool +the rules listed here. There are some limitations and the IWYU tool may give incorrect advice. The tools is activated by setting the CMake variable `CMAKE_CXX_INCLUDE_WHAT_YOU_USE` variable to the path of the `include-what-you-use` command. When activated, the diff --git a/src/lammps.cpp b/src/lammps.cpp index b73d9f1968..83a2f057ee 100644 --- a/src/lammps.cpp +++ b/src/lammps.cpp @@ -48,6 +48,7 @@ #include "output.h" #include "citeme.h" #include "accelerator_kokkos.h" +#include "accelerator_omp.h" #include "timer.h" #include "lmppython.h" #include "version.h" -- GitLab From e0c04355bb1019ee3ce37242a2cd426dedaef128 Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Sun, 30 Jun 2019 22:59:44 -0400 Subject: [PATCH 139/469] try to recover compiling of USER-OMP with OpenMP enabled --- src/USER-OMP/fix_neigh_history_omp.cpp | 1 + 1 file changed, 1 insertion(+) diff --git a/src/USER-OMP/fix_neigh_history_omp.cpp b/src/USER-OMP/fix_neigh_history_omp.cpp index efa7f5a3f1..be03e1d8f2 100644 --- a/src/USER-OMP/fix_neigh_history_omp.cpp +++ b/src/USER-OMP/fix_neigh_history_omp.cpp @@ -14,6 +14,7 @@ #include #include #include "fix_neigh_history_omp.h" +#include "my_page.h" #include "atom.h" #include "comm.h" #include "neighbor.h" -- GitLab From 44372f52369cb101a3ca6757035d9e1ec2443fb6 Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Sun, 30 Jun 2019 23:12:08 -0400 Subject: [PATCH 140/469] more fixes for USER-OMP --- src/USER-OMP/fix_rigid_nh_omp.cpp | 6 ++++-- src/USER-OMP/fix_rigid_omp.cpp | 6 ++++-- src/USER-OMP/fix_rigid_small_omp.cpp | 4 ++-- src/lammps.cpp | 2 +- 4 files changed, 11 insertions(+), 7 deletions(-) diff --git a/src/USER-OMP/fix_rigid_nh_omp.cpp b/src/USER-OMP/fix_rigid_nh_omp.cpp index 53d0134741..e6a6e065bf 100644 --- a/src/USER-OMP/fix_rigid_nh_omp.cpp +++ b/src/USER-OMP/fix_rigid_nh_omp.cpp @@ -15,6 +15,9 @@ Contributing author: Axel Kohlmeyer (Temple U) ------------------------------------------------------------------------- */ +#include +#include + #include "fix_rigid_nh_omp.h" #include "atom.h" @@ -24,13 +27,12 @@ #include "comm.h" #include "compute.h" #include "domain.h" +#include "error.h" #include "force.h" #include "kspace.h" #include "modify.h" #include "update.h" -#include - #if defined(_OPENMP) #include #endif diff --git a/src/USER-OMP/fix_rigid_omp.cpp b/src/USER-OMP/fix_rigid_omp.cpp index 12c6362ed8..20478b3ca1 100644 --- a/src/USER-OMP/fix_rigid_omp.cpp +++ b/src/USER-OMP/fix_rigid_omp.cpp @@ -15,6 +15,9 @@ Contributing author: Axel Kohlmeyer (Temple U) ------------------------------------------------------------------------- */ +#include +#include + #include "fix_rigid_omp.h" #include "atom.h" @@ -23,8 +26,7 @@ #include "atom_vec_tri.h" #include "comm.h" #include "domain.h" - -#include +#include "error.h" #if defined(_OPENMP) #include diff --git a/src/USER-OMP/fix_rigid_small_omp.cpp b/src/USER-OMP/fix_rigid_small_omp.cpp index a0495b3b93..1f6173497d 100644 --- a/src/USER-OMP/fix_rigid_small_omp.cpp +++ b/src/USER-OMP/fix_rigid_small_omp.cpp @@ -15,6 +15,8 @@ Contributing author: Axel Kohlmeyer (Temple U) ------------------------------------------------------------------------- */ +#include + #include "fix_rigid_small_omp.h" #include "atom.h" @@ -24,8 +26,6 @@ #include "comm.h" #include "domain.h" -#include - #if defined(_OPENMP) #include #endif diff --git a/src/lammps.cpp b/src/lammps.cpp index 83a2f057ee..052d14dfed 100644 --- a/src/lammps.cpp +++ b/src/lammps.cpp @@ -48,7 +48,7 @@ #include "output.h" #include "citeme.h" #include "accelerator_kokkos.h" -#include "accelerator_omp.h" +#include "accelerator_omp.h" // IWYU pragma: keep #include "timer.h" #include "lmppython.h" #include "version.h" -- GitLab From 483b1dbef5ee2d0c7f92885c7de2d8d94600dcbc Mon Sep 17 00:00:00 2001 From: jrgissing Date: Sun, 30 Jun 2019 21:19:04 -0600 Subject: [PATCH 141/469] Update fix_bond_react.txt --- doc/src/fix_bond_react.txt | 48 ++++++++++++++++++++++++-------------- 1 file changed, 31 insertions(+), 17 deletions(-) diff --git a/doc/src/fix_bond_react.txt b/doc/src/fix_bond_react.txt index 34f0e6daf7..7310545e1c 100644 --- a/doc/src/fix_bond_react.txt +++ b/doc/src/fix_bond_react.txt @@ -24,7 +24,7 @@ common_keyword = {stabilization} :l {stabilization} values = {no} or {yes} {group-ID} {xmax} {no} = no reaction site stabilization {yes} = perform reaction site stabilization - {group-ID} = user-assigned prefix for the dynamic group of non-reacting atoms + {group-ID} = user-assigned prefix for the dynamic group of atoms not currently involved in a reaction {xmax} = xmax value that is used by an internally-created "nve/limit"_fix_nve_limit.html integrator :pre react = mandatory argument indicating new reaction specification :l react-ID = user-assigned name for the reaction :l @@ -52,6 +52,8 @@ react = mandatory argument indicating new reaction specification :l [Examples:] +For unabridged example scripts and files, see \examples\USER\misc\bond_react. + molecule mol1 pre_reacted_topology.txt molecule mol2 post_reacted_topology.txt fix 5 all bond/react react myrxn1 all 1 0 3.25 mol1 mol2 map_file.txt :pre @@ -106,6 +108,20 @@ involved in any new reactions. The {xmax} value keyword should typically be set to the maximum distance that non-reacting atoms move during the simulation. +Fix bond/react creates and maintains two important dynamic groups of +atoms when using the {stabilization} keyword. The first group contains +all atoms currently involved in a reaction; this group is +automatically thermostatted by an internally-created +"nve/limit"_fix_nve_limit.html integrator. The second group contains +all atoms currently not involved in a reaction. This group should be +used by a thermostat in order to time integrate the system. The name +of this group of non-reacting atoms is created by appending '_REACT' +to the group-ID argument of the {stabilization} keyword, as shown in +the second example above. + +NOTE: When using reaction stabilization, you should generally not have +a separate thermostat which acts on the 'all' group. + The group-ID set using the {stabilization} keyword can be an existing static group or a previously-unused group-ID. It cannot be specified as 'all'. If the group-ID is previously unused, the fix bond/react @@ -116,20 +132,17 @@ internally-created dynamic group. In both cases, this new dynamic group is named by appending '_REACT' to the group-ID, e.g. nvt_grp_REACT. By specifying an existing group, you may thermostat constant-topology parts of your system separately. The dynamic group -contains only non-reacting atoms at a given timestep, and therefore -should be used by a subsequent system-wide time integrator such as -nvt, npt, or nve, as shown in the second example above. The time -integration command should be placed after the fix bond/react command -due to the internal dynamic grouping performed by fix bond/react. +contains only atoms not involved in a reaction at a given timestep, +and therefore should be used by a subsequent system-wide time +integrator such as nvt, npt, or nve, as shown in the second example +above (full examples can be found at \examples\USER\misc\bond_react). +The time integration command should be placed after the fix bond/react +command due to the internal dynamic grouping performed by fix +bond/react. NOTE: If the group-ID is an existing static group, react-group-IDs should also be specified as this static group, or a subset. -NOTE: If the group-ID is previously unused, the internally-created -group applies to all atoms in the system, i.e. you should generally -not have a separate thermostat which acts on the 'all' group, or any -other group. - The following comments pertain to each {react} argument (in other words, can be customized for each reaction, or reaction step): @@ -352,12 +365,13 @@ an atom that is not deleted. In addition to deleting unwanted reaction by-products, this feature can be used to remove specific topologies, such as small rings, that may be otherwise indistinguishable. -Also, it may be beneficial to ensure reacting atoms are at a certain -temperature before being released to the overall thermostat. For this, -you can use the internally-created dynamic group named -"bond_react_MASTER_group." For example, adding the following command -would thermostat the group of all atoms currently involved in a -reaction: +Optionally, you can enforce additional behaviors on reacting atoms. +For example, it may be beneficial to force reacting atoms to remain at +a certain temperature. For this, you can use the internally-created +dynamic group named "bond_react_MASTER_group", which consists of all +atoms currently involved in a reaction. For example, adding the +following command would add an additional thermostat to the group of +all currently-reacting atoms: fix 1 bond_react_MASTER_group temp/rescale 1 300 300 10 1 :pre -- GitLab From 62bddd47ee99ecbc2f7bee7a5d091e26ba667242 Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Mon, 1 Jul 2019 00:01:00 -0400 Subject: [PATCH 142/469] limit number of nested include file levels to 16 --- src/input.cpp | 22 +++++++++------------- 1 file changed, 9 insertions(+), 13 deletions(-) diff --git a/src/input.cpp b/src/input.cpp index 644446710f..ca9defc66b 100644 --- a/src/input.cpp +++ b/src/input.cpp @@ -85,8 +85,9 @@ Input::Input(LAMMPS *lmp, int argc, char **argv) : Pointers(lmp) ifthenelse_flag = 0; if (me == 0) { - nfile = maxfile = 1; - infiles = (FILE **) memory->smalloc(sizeof(FILE *),"input:infiles"); + nfile = 1; + maxfile = 16; + infiles = new FILE *[maxfile]; infiles[0] = infile; } else infiles = NULL; @@ -138,7 +139,7 @@ Input::~Input() memory->sfree(work); if (labelstr) delete [] labelstr; memory->sfree(arg); - memory->sfree(infiles); + delete [] infiles; delete variable; delete command_map; @@ -251,11 +252,8 @@ void Input::file(const char *filename) // call to file() will close filename and decrement nfile if (me == 0) { - if (nfile == maxfile) { - maxfile++; - infiles = (FILE **) - memory->srealloc(infiles,maxfile*sizeof(FILE *),"input:infiles"); - } + if (nfile == maxfile) + error->one(FLERR,"Too many nested levels of input scripts"); infile = fopen(filename,"r"); if (infile == NULL) { @@ -1044,11 +1042,9 @@ void Input::include() error->all(FLERR,"Cannot use include command within an if command"); if (me == 0) { - if (nfile == maxfile) { - maxfile++; - infiles = (FILE **) - memory->srealloc(infiles,maxfile*sizeof(FILE *),"input:infiles"); - } + if (nfile == maxfile) + error->one(FLERR,"Too many nested levels of input scripts"); + infile = fopen(arg[0],"r"); if (infile == NULL) { char str[128]; -- GitLab From af8103433c63ee4ef6ea9b8ae4ad764d109820f9 Mon Sep 17 00:00:00 2001 From: jrgissing Date: Sun, 30 Jun 2019 22:13:12 -0600 Subject: [PATCH 143/469] add stabilized vs unstabilized examples --- ...in.tiny_nylon => in.tiny_nylon.stabilized} | 2 + .../tiny_nylon/in.tiny_nylon.unstabilized | 48 +++ .../tiny_nylon/log.20Apr18.tiny_nylon.g++.1 | 370 ------------------ .../tiny_nylon/log.20Apr18.tiny_nylon.g++.4 | 370 ------------------ .../log.5Jun19.tiny_nylon.stabilized.g++.1 | 148 +++++++ .../log.5Jun19.tiny_nylon.stabilized.g++.4 | 148 +++++++ .../log.5Jun19.tiny_nylon.unstabilized.g++.1 | 147 +++++++ .../log.5Jun19.tiny_nylon.unstabilized.g++.4 | 147 +++++++ 8 files changed, 640 insertions(+), 740 deletions(-) rename examples/USER/misc/bond_react/tiny_nylon/{in.tiny_nylon => in.tiny_nylon.stabilized} (88%) create mode 100644 examples/USER/misc/bond_react/tiny_nylon/in.tiny_nylon.unstabilized delete mode 100644 examples/USER/misc/bond_react/tiny_nylon/log.20Apr18.tiny_nylon.g++.1 delete mode 100644 examples/USER/misc/bond_react/tiny_nylon/log.20Apr18.tiny_nylon.g++.4 create mode 100644 examples/USER/misc/bond_react/tiny_nylon/log.5Jun19.tiny_nylon.stabilized.g++.1 create mode 100644 examples/USER/misc/bond_react/tiny_nylon/log.5Jun19.tiny_nylon.stabilized.g++.4 create mode 100644 examples/USER/misc/bond_react/tiny_nylon/log.5Jun19.tiny_nylon.unstabilized.g++.1 create mode 100644 examples/USER/misc/bond_react/tiny_nylon/log.5Jun19.tiny_nylon.unstabilized.g++.4 diff --git a/examples/USER/misc/bond_react/tiny_nylon/in.tiny_nylon b/examples/USER/misc/bond_react/tiny_nylon/in.tiny_nylon.stabilized similarity index 88% rename from examples/USER/misc/bond_react/tiny_nylon/in.tiny_nylon rename to examples/USER/misc/bond_react/tiny_nylon/in.tiny_nylon.stabilized index 73cb2eb270..b152dec00a 100644 --- a/examples/USER/misc/bond_react/tiny_nylon/in.tiny_nylon +++ b/examples/USER/misc/bond_react/tiny_nylon/in.tiny_nylon.stabilized @@ -38,6 +38,8 @@ fix myrxns all bond/react stabilization yes statted_grp .03 & fix 1 statted_grp_REACT nvt temp 300 300 100 +# optionally, you can customize behavior of reacting atoms, +# by using the internally-created 'bond_react_MASTER_group', like so: fix 4 bond_react_MASTER_group temp/rescale 1 300 300 10 1 thermo_style custom step temp press density f_myrxns[1] f_myrxns[2] diff --git a/examples/USER/misc/bond_react/tiny_nylon/in.tiny_nylon.unstabilized b/examples/USER/misc/bond_react/tiny_nylon/in.tiny_nylon.unstabilized new file mode 100644 index 0000000000..1e5a493821 --- /dev/null +++ b/examples/USER/misc/bond_react/tiny_nylon/in.tiny_nylon.unstabilized @@ -0,0 +1,48 @@ +# two monomer nylon example +# reaction produces a condensed water molecule + +units real + +boundary p p p + +atom_style full + +kspace_style pppm 1.0e-4 + +pair_style lj/class2/coul/long 8.5 + +angle_style class2 + +bond_style class2 + +dihedral_style class2 + +improper_style class2 + +read_data tiny_nylon.data + +velocity all create 300.0 4928459 dist gaussian + +molecule mol1 rxn1_stp1_unreacted.data_template +molecule mol2 rxn1_stp1_reacted.data_template +molecule mol3 rxn1_stp2_unreacted.data_template +molecule mol4 rxn1_stp2_reacted.data_template + +thermo 50 + +# dump 1 all xyz 1 test_vis.xyz + +fix myrxns all bond/react stabilization no & + react rxn1 all 1 0.0 2.9 mol1 mol2 rxn1_stp1_map & + react rxn2 all 1 0.0 5.0 mol3 mol4 rxn1_stp2_map + +fix 1 all nve/limit .03 + +thermo_style custom step temp press density f_myrxns[1] f_myrxns[2] + +# restart 100 restart1 restart2 + +run 1000 + +# write_restart restart_longrun +# write_data restart_longrun.data diff --git a/examples/USER/misc/bond_react/tiny_nylon/log.20Apr18.tiny_nylon.g++.1 b/examples/USER/misc/bond_react/tiny_nylon/log.20Apr18.tiny_nylon.g++.1 deleted file mode 100644 index 344439f94c..0000000000 --- a/examples/USER/misc/bond_react/tiny_nylon/log.20Apr18.tiny_nylon.g++.1 +++ /dev/null @@ -1,370 +0,0 @@ -LAMMPS (20 Apr 2018) -OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (../comm.cpp:90) - using 1 OpenMP thread(s) per MPI task -# two monomer nylon example -# reaction produces a condensed water molecule - -units real - -boundary p p p - -atom_style full - -kspace_style pppm 1.0e-4 - -pair_style lj/class2/coul/long 8.5 - -angle_style class2 - -bond_style class2 - -dihedral_style class2 - -improper_style class2 - -read_data tiny_nylon.data - orthogonal box = (-25 -25 -25) to (25 25 25) - 1 by 1 by 1 MPI processor grid - reading atoms ... - 44 atoms - reading velocities ... - 44 velocities - scanning bonds ... - 9 = max bonds/atom - scanning angles ... - 21 = max angles/atom - scanning dihedrals ... - 29 = max dihedrals/atom - scanning impropers ... - 29 = max impropers/atom - reading bonds ... - 42 bonds - reading angles ... - 74 angles - reading dihedrals ... - 100 dihedrals - reading impropers ... - 44 impropers - 4 = max # of 1-2 neighbors - 6 = max # of 1-3 neighbors - 12 = max # of 1-4 neighbors - 41 = max # of special neighbors - -velocity all create 300.0 4928459 dist gaussian - -molecule mol1 rxn1_stp1_unreacted.data_template -Read molecule mol1: - 18 atoms with max type 8 - 16 bonds with max type 14 - 25 angles with max type 28 - 23 dihedrals with max type 36 - 14 impropers with max type 11 -molecule mol2 rxn1_stp1_reacted.data_template -Read molecule mol2: - 18 atoms with max type 9 - 17 bonds with max type 13 - 31 angles with max type 27 - 39 dihedrals with max type 33 - 20 impropers with max type 1 -molecule mol3 rxn1_stp2_unreacted.data_template -Read molecule mol3: - 15 atoms with max type 9 - 14 bonds with max type 13 - 25 angles with max type 27 - 30 dihedrals with max type 33 - 16 impropers with max type 1 -molecule mol4 rxn1_stp2_reacted.data_template -Read molecule mol4: - 15 atoms with max type 11 - 13 bonds with max type 15 - 19 angles with max type 29 - 16 dihedrals with max type 32 - 10 impropers with max type 13 - -thermo 50 - -# dump 1 all xyz 1 test_vis.xyz - -fix myrxns all bond/react stabilization yes statted_grp .03 react rxn1 all 1 0.0 2.9 mol1 mol2 rxn1_stp1_map react rxn2 all 1 0.0 5.0 mol3 mol4 rxn1_stp2_map -WARNING: An atom in 'react #1' changes bond connectivity but not atom type (../fix_bond_react.cpp:1489) -WARNING: An atom in 'react #2' changes bond connectivity but not atom type (../fix_bond_react.cpp:1489) -dynamic group bond_react_MASTER_group defined -dynamic group statted_grp defined -dynamic group bond_react_MASTER_group defined -dynamic group statted_grp defined - -fix 1 statted_grp nvt temp 300 300 100 - -fix 4 bond_react_MASTER_group temp/rescale 1 300 300 10 1 - -thermo_style custom step temp press density f_myrxns[1] f_myrxns[2] - -# restart 100 restart1 restart2 - -run 10000 -PPPM initialization ... - using 12-bit tables for long-range coulomb (../kspace.cpp:321) - G vector (1/distance) = 0.0534597 - grid = 2 2 2 - stencil order = 5 - estimated absolute RMS force accuracy = 0.0402256 - estimated relative force accuracy = 0.000121138 - using double precision FFTs - 3d grid and FFT values/proc = 343 8 -Neighbor list info ... - update every 1 steps, delay 10 steps, check yes - max neighbors/atom: 2000, page size: 100000 - master list distance cutoff = 10.5 - ghost atom cutoff = 10.5 - binsize = 5.25, bins = 10 10 10 - 2 neighbor lists, perpetual/occasional/extra = 1 1 0 - (1) pair lj/class2/coul/long, perpetual - attributes: half, newton on - pair build: half/bin/newton - stencil: half/bin/3d/newton - bin: standard - (2) fix bond/react, occasional, copy from (1) - attributes: half, newton on - pair build: copy - stencil: none - bin: none -WARNING: Inconsistent image flags (../domain.cpp:786) -Per MPI rank memory allocation (min/avg/max) = 33.34 | 33.34 | 33.34 Mbytes -Step Temp Press Density f_myrxns[1] f_myrxns[2] - 0 300 346.78165 0.0034851739 0 0 - 50 296.70408 -51.30066 0.0034851739 1 0 - 100 274.25324 46.715512 0.0034851739 1 1 - 150 471.61579 31.321598 0.0034851739 1 1 - 200 362.87766 42.061118 0.0034851739 1 1 - 250 367.58058 65.303109 0.0034851739 1 1 - 300 372.38236 -52.421725 0.0034851739 1 1 - 350 297.69957 17.869945 0.0034851739 1 1 - 400 258.30433 49.19156 0.0034851739 1 1 - 450 253.34384 -5.8162637 0.0034851739 1 1 - 500 269.96465 -43.337517 0.0034851739 1 1 - 550 303.23718 10.180246 0.0034851739 1 1 - 600 329.59579 -48.97461 0.0034851739 1 1 - 650 350.42568 50.983183 0.0034851739 1 1 - 700 342.03272 35.43465 0.0034851739 1 1 - 750 269.23405 -41.873166 0.0034851739 1 1 - 800 245.15025 13.953092 0.0034851739 1 1 - 850 257.85421 -3.1492141 0.0034851739 1 1 - 900 316.15644 7.7798301 0.0034851739 1 1 - 950 299.9124 -15.77014 0.0034851739 1 1 - 1000 302.89968 -17.049693 0.0034851739 1 1 - 1050 308.91651 71.84632 0.0034851739 1 1 - 1100 348.43932 -18.742012 0.0034851739 1 1 - 1150 309.03036 50.536311 0.0034851739 1 1 - 1200 318.9761 -16.905746 0.0034851739 1 1 - 1250 320.42806 -0.057975092 0.0034851739 1 1 - 1300 289.7824 18.200772 0.0034851739 1 1 - 1350 284.79836 -9.1978427 0.0034851739 1 1 - 1400 325.43292 42.082833 0.0034851739 1 1 - 1450 261.5041 -37.823325 0.0034851739 1 1 - 1500 298.88723 -5.1647385 0.0034851739 1 1 - 1550 291.37403 -7.7764201 0.0034851739 1 1 - 1600 293.83475 22.2458 0.0034851739 1 1 - 1650 293.80611 24.202512 0.0034851739 1 1 - 1700 291.70205 -23.397884 0.0034851739 1 1 - 1750 292.32437 -10.671214 0.0034851739 1 1 - 1800 302.01367 -11.671025 0.0034851739 1 1 - 1850 322.1651 24.438331 0.0034851739 1 1 - 1900 310.45076 45.343592 0.0034851739 1 1 - 1950 325.91745 -19.847809 0.0034851739 1 1 - 2000 276.89662 63.387098 0.0034851739 1 1 - 2050 311.33783 -24.683247 0.0034851739 1 1 - 2100 346.2336 -27.526891 0.0034851739 1 1 - 2150 345.30604 -15.722411 0.0034851739 1 1 - 2200 346.7718 -17.857633 0.0034851739 1 1 - 2250 304.28676 -1.9965581 0.0034851739 1 1 - 2300 322.56372 -31.786868 0.0034851739 1 1 - 2350 282.64326 6.1982735 0.0034851739 1 1 - 2400 286.65759 -63.207781 0.0034851739 1 1 - 2450 257.05528 32.931491 0.0034851739 1 1 - 2500 283.64386 26.912373 0.0034851739 1 1 - 2550 299.54005 27.277039 0.0034851739 1 1 - 2600 283.92503 14.660972 0.0034851739 1 1 - 2650 321.93453 -18.977358 0.0034851739 1 1 - 2700 376.7189 31.826935 0.0034851739 1 1 - 2750 372.20075 -32.821697 0.0034851739 1 1 - 2800 361.40604 83.035183 0.0034851739 1 1 - 2850 332.27269 -23.927452 0.0034851739 1 1 - 2900 331.14638 -0.12328446 0.0034851739 1 1 - 2950 303.67489 -24.078857 0.0034851739 1 1 - 3000 311.40462 21.563537 0.0034851739 1 1 - 3050 284.72849 -23.849667 0.0034851739 1 1 - 3100 303.48477 39.347763 0.0034851739 1 1 - 3150 264.2739 -0.22299879 0.0034851739 1 1 - 3200 300.03351 31.545323 0.0034851739 1 1 - 3250 288.56663 5.7225228 0.0034851739 1 1 - 3300 200.13238 -31.239655 0.0034851739 1 1 - 3350 231.32512 16.631728 0.0034851739 1 1 - 3400 260.57402 2.1717992 0.0034851739 1 1 - 3450 301.47128 -42.210623 0.0034851739 1 1 - 3500 321.77414 40.074365 0.0034851739 1 1 - 3550 353.21858 28.387783 0.0034851739 1 1 - 3600 331.45989 -57.800858 0.0034851739 1 1 - 3650 303.88123 44.86596 0.0034851739 1 1 - 3700 329.73833 -0.80615652 0.0034851739 1 1 - 3750 297.55588 -0.49626039 0.0034851739 1 1 - 3800 286.38794 -10.010003 0.0034851739 1 1 - 3850 290.17417 -43.51187 0.0034851739 1 1 - 3900 247.88933 51.23735 0.0034851739 1 1 - 3950 332.31324 -18.194985 0.0034851739 1 1 - 4000 325.56802 18.402825 0.0034851739 1 1 - 4050 338.37593 36.430977 0.0034851739 1 1 - 4100 370.95478 39.290285 0.0034851739 1 1 - 4150 348.47859 -7.0779678 0.0034851739 1 1 - 4200 241.30632 -33.371788 0.0034851739 1 1 - 4250 242.17258 -9.986197 0.0034851739 1 1 - 4300 300.85311 -7.9244294 0.0034851739 1 1 - 4350 273.15684 -21.257283 0.0034851739 1 1 - 4400 305.77463 -5.8720722 0.0034851739 1 1 - 4450 314.97697 45.0373 0.0034851739 1 1 - 4500 310.77723 16.958773 0.0034851739 1 1 - 4550 302.1742 12.156862 0.0034851739 1 1 - 4600 319.74799 6.84889 0.0034851739 1 1 - 4650 270.86805 -13.767905 0.0034851739 1 1 - 4700 249.81731 -31.197487 0.0034851739 1 1 - 4750 285.86481 -9.8916364 0.0034851739 1 1 - 4800 233.98321 7.1338571 0.0034851739 1 1 - 4850 302.60551 49.262889 0.0034851739 1 1 - 4900 316.55056 34.663247 0.0034851739 1 1 - 4950 357.32741 11.583006 0.0034851739 1 1 - 5000 400.21045 -8.1781061 0.0034851739 1 1 - 5050 390.01845 -20.490275 0.0034851739 1 1 - 5100 378.84247 -41.328757 0.0034851739 1 1 - 5150 324.02038 -15.023862 0.0034851739 1 1 - 5200 262.08429 10.937354 0.0034851739 1 1 - 5250 255.75508 16.381455 0.0034851739 1 1 - 5300 277.84989 40.68232 0.0034851739 1 1 - 5350 302.92832 9.1989494 0.0034851739 1 1 - 5400 283.7196 -1.6584671 0.0034851739 1 1 - 5450 300.71266 -4.7030295 0.0034851739 1 1 - 5500 343.5499 -0.30550044 0.0034851739 1 1 - 5550 369.51271 21.691649 0.0034851739 1 1 - 5600 372.69789 -38.67994 0.0034851739 1 1 - 5650 327.41266 11.352137 0.0034851739 1 1 - 5700 278.98614 -23.827304 0.0034851739 1 1 - 5750 308.30054 -20.756187 0.0034851739 1 1 - 5800 341.45594 28.058441 0.0034851739 1 1 - 5850 322.97844 -10.731921 0.0034851739 1 1 - 5900 304.53591 32.825279 0.0034851739 1 1 - 5950 287.1752 -36.780091 0.0034851739 1 1 - 6000 296.52681 18.781896 0.0034851739 1 1 - 6050 314.25442 15.992829 0.0034851739 1 1 - 6100 313.86576 3.4342714 0.0034851739 1 1 - 6150 325.64196 32.392039 0.0034851739 1 1 - 6200 367.42931 -27.160706 0.0034851739 1 1 - 6250 369.30798 39.020934 0.0034851739 1 1 - 6300 328.92285 -23.175157 0.0034851739 1 1 - 6350 305.63077 4.9024453 0.0034851739 1 1 - 6400 241.70341 -13.676629 0.0034851739 1 1 - 6450 265.66717 2.40612 0.0034851739 1 1 - 6500 249.36037 13.420255 0.0034851739 1 1 - 6550 294.53814 10.853462 0.0034851739 1 1 - 6600 308.2025 18.995308 0.0034851739 1 1 - 6650 305.43797 -49.56785 0.0034851739 1 1 - 6700 320.27344 11.336281 0.0034851739 1 1 - 6750 321.78666 -23.463899 0.0034851739 1 1 - 6800 303.40388 7.6224553 0.0034851739 1 1 - 6850 297.18966 51.52256 0.0034851739 1 1 - 6900 284.18909 -8.4947203 0.0034851739 1 1 - 6950 331.03663 13.233655 0.0034851739 1 1 - 7000 311.37928 -43.265479 0.0034851739 1 1 - 7050 286.81661 -14.174683 0.0034851739 1 1 - 7100 302.84119 12.048954 0.0034851739 1 1 - 7150 297.19357 -43.111968 0.0034851739 1 1 - 7200 332.47359 26.048249 0.0034851739 1 1 - 7250 262.70677 41.176242 0.0034851739 1 1 - 7300 250.61405 -23.413982 0.0034851739 1 1 - 7350 296.91117 35.88133 0.0034851739 1 1 - 7400 245.09229 -13.447194 0.0034851739 1 1 - 7450 272.28131 -23.322585 0.0034851739 1 1 - 7500 209.04985 13.871239 0.0034851739 1 1 - 7550 255.00955 4.9325621 0.0034851739 1 1 - 7600 312.30937 -37.368274 0.0034851739 1 1 - 7650 305.65903 55.245496 0.0034851739 1 1 - 7700 325.09504 -18.347711 0.0034851739 1 1 - 7750 363.28282 -22.479686 0.0034851739 1 1 - 7800 350.17429 26.849547 0.0034851739 1 1 - 7850 271.70853 -17.764575 0.0034851739 1 1 - 7900 272.66484 -11.701967 0.0034851739 1 1 - 7950 298.60202 -12.765675 0.0034851739 1 1 - 8000 274.58852 49.641532 0.0034851739 1 1 - 8050 304.72347 -0.55414183 0.0034851739 1 1 - 8100 328.30757 -39.861301 0.0034851739 1 1 - 8150 406.67601 2.8999409 0.0034851739 1 1 - 8200 332.20083 -51.217399 0.0034851739 1 1 - 8250 354.50609 53.128769 0.0034851739 1 1 - 8300 337.2758 20.68562 0.0034851739 1 1 - 8350 361.89708 -54.185869 0.0034851739 1 1 - 8400 305.63496 24.058529 0.0034851739 1 1 - 8450 303.27461 4.304683 0.0034851739 1 1 - 8500 253.53694 -10.909021 0.0034851739 1 1 - 8550 277.03017 23.241479 0.0034851739 1 1 - 8600 291.41844 -22.240665 0.0034851739 1 1 - 8650 307.85368 31.919587 0.0034851739 1 1 - 8700 309.19724 0.53529642 0.0034851739 1 1 - 8750 354.6583 11.565515 0.0034851739 1 1 - 8800 329.78598 19.5996 0.0034851739 1 1 - 8850 240.79198 21.803515 0.0034851739 1 1 - 8900 318.40749 -59.816923 0.0034851739 1 1 - 8950 308.47211 -57.808635 0.0034851739 1 1 - 9000 271.51207 50.943482 0.0034851739 1 1 - 9050 249.4005 6.7529187 0.0034851739 1 1 - 9100 221.8772 47.196092 0.0034851739 1 1 - 9150 297.9351 4.0058184 0.0034851739 1 1 - 9200 274.85051 -24.774393 0.0034851739 1 1 - 9250 336.04757 5.3799028 0.0034851739 1 1 - 9300 380.44956 -22.389381 0.0034851739 1 1 - 9350 336.9824 23.050616 0.0034851739 1 1 - 9400 304.46425 32.530218 0.0034851739 1 1 - 9450 317.55591 -22.265425 0.0034851739 1 1 - 9500 323.70901 -7.0159787 0.0034851739 1 1 - 9550 316.07308 28.062131 0.0034851739 1 1 - 9600 262.74608 -0.78519192 0.0034851739 1 1 - 9650 271.55045 -21.430123 0.0034851739 1 1 - 9700 239.6022 14.483637 0.0034851739 1 1 - 9750 338.1437 -0.72765302 0.0034851739 1 1 - 9800 334.50189 19.495144 0.0034851739 1 1 - 9850 354.87554 19.272719 0.0034851739 1 1 - 9900 334.02141 -22.393457 0.0034851739 1 1 - 9950 293.63651 19.178873 0.0034851739 1 1 - 10000 319.81736 21.904414 0.0034851739 1 1 -Loop time of 1.84987 on 1 procs for 10000 steps with 44 atoms - -Performance: 467.059 ns/day, 0.051 hours/ns, 5405.774 timesteps/s -99.5% CPU use with 1 MPI tasks x 1 OpenMP threads - -MPI task timing breakdown: -Section | min time | avg time | max time |%varavg| %total ---------------------------------------------------------------- -Pair | 0.26152 | 0.26152 | 0.26152 | 0.0 | 14.14 -Bond | 0.74069 | 0.74069 | 0.74069 | 0.0 | 40.04 -Kspace | 0.30505 | 0.30505 | 0.30505 | 0.0 | 16.49 -Neigh | 0.39991 | 0.39991 | 0.39991 | 0.0 | 21.62 -Comm | 0.02261 | 0.02261 | 0.02261 | 0.0 | 1.22 -Output | 0.0034585 | 0.0034585 | 0.0034585 | 0.0 | 0.19 -Modify | 0.099979 | 0.099979 | 0.099979 | 0.0 | 5.40 -Other | | 0.01666 | | | 0.90 - -Nlocal: 44 ave 44 max 44 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Nghost: 44 ave 44 max 44 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Neighs: 823 ave 823 max 823 min -Histogram: 1 0 0 0 0 0 0 0 0 0 - -Total # of neighbors = 823 -Ave neighs/atom = 18.7045 -Ave special neighs/atom = 9.77273 -Neighbor list builds = 10000 -Dangerous builds = 0 - -# write_restart restart_longrun -# write_data restart_longrun.data - -Please see the log.cite file for references relevant to this simulation - -Total wall time: 0:00:01 diff --git a/examples/USER/misc/bond_react/tiny_nylon/log.20Apr18.tiny_nylon.g++.4 b/examples/USER/misc/bond_react/tiny_nylon/log.20Apr18.tiny_nylon.g++.4 deleted file mode 100644 index 377781f48f..0000000000 --- a/examples/USER/misc/bond_react/tiny_nylon/log.20Apr18.tiny_nylon.g++.4 +++ /dev/null @@ -1,370 +0,0 @@ -LAMMPS (20 Apr 2018) -OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (../comm.cpp:90) - using 1 OpenMP thread(s) per MPI task -# two monomer nylon example -# reaction produces a condensed water molecule - -units real - -boundary p p p - -atom_style full - -kspace_style pppm 1.0e-4 - -pair_style lj/class2/coul/long 8.5 - -angle_style class2 - -bond_style class2 - -dihedral_style class2 - -improper_style class2 - -read_data tiny_nylon.data - orthogonal box = (-25 -25 -25) to (25 25 25) - 1 by 2 by 2 MPI processor grid - reading atoms ... - 44 atoms - reading velocities ... - 44 velocities - scanning bonds ... - 9 = max bonds/atom - scanning angles ... - 21 = max angles/atom - scanning dihedrals ... - 29 = max dihedrals/atom - scanning impropers ... - 29 = max impropers/atom - reading bonds ... - 42 bonds - reading angles ... - 74 angles - reading dihedrals ... - 100 dihedrals - reading impropers ... - 44 impropers - 4 = max # of 1-2 neighbors - 6 = max # of 1-3 neighbors - 12 = max # of 1-4 neighbors - 41 = max # of special neighbors - -velocity all create 300.0 4928459 dist gaussian - -molecule mol1 rxn1_stp1_unreacted.data_template -Read molecule mol1: - 18 atoms with max type 8 - 16 bonds with max type 14 - 25 angles with max type 28 - 23 dihedrals with max type 36 - 14 impropers with max type 11 -molecule mol2 rxn1_stp1_reacted.data_template -Read molecule mol2: - 18 atoms with max type 9 - 17 bonds with max type 13 - 31 angles with max type 27 - 39 dihedrals with max type 33 - 20 impropers with max type 1 -molecule mol3 rxn1_stp2_unreacted.data_template -Read molecule mol3: - 15 atoms with max type 9 - 14 bonds with max type 13 - 25 angles with max type 27 - 30 dihedrals with max type 33 - 16 impropers with max type 1 -molecule mol4 rxn1_stp2_reacted.data_template -Read molecule mol4: - 15 atoms with max type 11 - 13 bonds with max type 15 - 19 angles with max type 29 - 16 dihedrals with max type 32 - 10 impropers with max type 13 - -thermo 50 - -# dump 1 all xyz 1 test_vis.xyz - -fix myrxns all bond/react stabilization yes statted_grp .03 react rxn1 all 1 0.0 2.9 mol1 mol2 rxn1_stp1_map react rxn2 all 1 0.0 5.0 mol3 mol4 rxn1_stp2_map -WARNING: An atom in 'react #1' changes bond connectivity but not atom type (../fix_bond_react.cpp:1489) -WARNING: An atom in 'react #2' changes bond connectivity but not atom type (../fix_bond_react.cpp:1489) -dynamic group bond_react_MASTER_group defined -dynamic group statted_grp defined -dynamic group bond_react_MASTER_group defined -dynamic group statted_grp defined - -fix 1 statted_grp nvt temp 300 300 100 - -fix 4 bond_react_MASTER_group temp/rescale 1 300 300 10 1 - -thermo_style custom step temp press density f_myrxns[1] f_myrxns[2] - -# restart 100 restart1 restart2 - -run 10000 -PPPM initialization ... - using 12-bit tables for long-range coulomb (../kspace.cpp:321) - G vector (1/distance) = 0.0534597 - grid = 2 2 2 - stencil order = 5 - estimated absolute RMS force accuracy = 0.0402256 - estimated relative force accuracy = 0.000121138 - using double precision FFTs - 3d grid and FFT values/proc = 252 2 -Neighbor list info ... - update every 1 steps, delay 10 steps, check yes - max neighbors/atom: 2000, page size: 100000 - master list distance cutoff = 10.5 - ghost atom cutoff = 10.5 - binsize = 5.25, bins = 10 10 10 - 2 neighbor lists, perpetual/occasional/extra = 1 1 0 - (1) pair lj/class2/coul/long, perpetual - attributes: half, newton on - pair build: half/bin/newton - stencil: half/bin/3d/newton - bin: standard - (2) fix bond/react, occasional, copy from (1) - attributes: half, newton on - pair build: copy - stencil: none - bin: none -WARNING: Inconsistent image flags (../domain.cpp:786) -Per MPI rank memory allocation (min/avg/max) = 33.34 | 33.69 | 34.37 Mbytes -Step Temp Press Density f_myrxns[1] f_myrxns[2] - 0 300 346.78165 0.0034851739 0 0 - 50 296.70408 -51.30066 0.0034851739 1 0 - 100 274.25324 46.715512 0.0034851739 1 1 - 150 471.61579 31.321598 0.0034851739 1 1 - 200 362.87766 42.061118 0.0034851739 1 1 - 250 367.58058 65.303109 0.0034851739 1 1 - 300 372.38236 -52.421725 0.0034851739 1 1 - 350 297.69957 17.869945 0.0034851739 1 1 - 400 258.30433 49.19156 0.0034851739 1 1 - 450 253.34384 -5.8162637 0.0034851739 1 1 - 500 269.96465 -43.337517 0.0034851739 1 1 - 550 303.23718 10.180246 0.0034851739 1 1 - 600 329.59579 -48.97461 0.0034851739 1 1 - 650 350.42568 50.983183 0.0034851739 1 1 - 700 342.03272 35.43465 0.0034851739 1 1 - 750 269.23405 -41.873166 0.0034851739 1 1 - 800 245.15025 13.953092 0.0034851739 1 1 - 850 257.85421 -3.1492141 0.0034851739 1 1 - 900 316.15644 7.7798301 0.0034851739 1 1 - 950 299.9124 -15.77014 0.0034851739 1 1 - 1000 302.89968 -17.049693 0.0034851739 1 1 - 1050 308.91651 71.84632 0.0034851739 1 1 - 1100 348.43932 -18.742012 0.0034851739 1 1 - 1150 309.03036 50.536311 0.0034851739 1 1 - 1200 318.9761 -16.905746 0.0034851739 1 1 - 1250 320.42806 -0.057975092 0.0034851739 1 1 - 1300 289.7824 18.200772 0.0034851739 1 1 - 1350 284.79836 -9.1978427 0.0034851739 1 1 - 1400 325.43292 42.082833 0.0034851739 1 1 - 1450 261.5041 -37.823325 0.0034851739 1 1 - 1500 298.88723 -5.1647385 0.0034851739 1 1 - 1550 291.37403 -7.7764201 0.0034851739 1 1 - 1600 293.83475 22.2458 0.0034851739 1 1 - 1650 293.80611 24.202512 0.0034851739 1 1 - 1700 291.70205 -23.397884 0.0034851739 1 1 - 1750 292.32437 -10.671214 0.0034851739 1 1 - 1800 302.01367 -11.671025 0.0034851739 1 1 - 1850 322.1651 24.438331 0.0034851739 1 1 - 1900 310.45076 45.343592 0.0034851739 1 1 - 1950 325.91745 -19.847809 0.0034851739 1 1 - 2000 276.89662 63.387098 0.0034851739 1 1 - 2050 311.33783 -24.683247 0.0034851739 1 1 - 2100 346.2336 -27.526891 0.0034851739 1 1 - 2150 345.30604 -15.722411 0.0034851739 1 1 - 2200 346.7718 -17.857633 0.0034851739 1 1 - 2250 304.28676 -1.9965581 0.0034851739 1 1 - 2300 322.56372 -31.786868 0.0034851739 1 1 - 2350 282.64326 6.1982735 0.0034851739 1 1 - 2400 286.65759 -63.207781 0.0034851739 1 1 - 2450 257.05528 32.931491 0.0034851739 1 1 - 2500 283.64386 26.912373 0.0034851739 1 1 - 2550 299.54005 27.277039 0.0034851739 1 1 - 2600 283.92503 14.660972 0.0034851739 1 1 - 2650 321.93453 -18.977358 0.0034851739 1 1 - 2700 376.7189 31.826935 0.0034851739 1 1 - 2750 372.20075 -32.821697 0.0034851739 1 1 - 2800 361.40604 83.035183 0.0034851739 1 1 - 2850 332.27269 -23.927452 0.0034851739 1 1 - 2900 331.14638 -0.12328446 0.0034851739 1 1 - 2950 303.67489 -24.078857 0.0034851739 1 1 - 3000 311.40462 21.563537 0.0034851739 1 1 - 3050 284.72849 -23.849667 0.0034851739 1 1 - 3100 303.48477 39.347763 0.0034851739 1 1 - 3150 264.2739 -0.22299878 0.0034851739 1 1 - 3200 300.03351 31.545323 0.0034851739 1 1 - 3250 288.56663 5.7225229 0.0034851739 1 1 - 3300 200.13238 -31.239655 0.0034851739 1 1 - 3350 231.32512 16.631728 0.0034851739 1 1 - 3400 260.57402 2.1717992 0.0034851739 1 1 - 3450 301.47128 -42.210623 0.0034851739 1 1 - 3500 321.77414 40.074365 0.0034851739 1 1 - 3550 353.21858 28.387783 0.0034851739 1 1 - 3600 331.45989 -57.800858 0.0034851739 1 1 - 3650 303.88123 44.86596 0.0034851739 1 1 - 3700 329.73833 -0.8061567 0.0034851739 1 1 - 3750 297.55588 -0.49626022 0.0034851739 1 1 - 3800 286.38794 -10.010003 0.0034851739 1 1 - 3850 290.17417 -43.51187 0.0034851739 1 1 - 3900 247.88933 51.23735 0.0034851739 1 1 - 3950 332.31324 -18.194985 0.0034851739 1 1 - 4000 325.56802 18.402825 0.0034851739 1 1 - 4050 338.37594 36.430977 0.0034851739 1 1 - 4100 370.95478 39.290285 0.0034851739 1 1 - 4150 348.47859 -7.0779683 0.0034851739 1 1 - 4200 241.30632 -33.371789 0.0034851739 1 1 - 4250 242.17258 -9.9861962 0.0034851739 1 1 - 4300 300.85311 -7.924429 0.0034851739 1 1 - 4350 273.15684 -21.257282 0.0034851739 1 1 - 4400 305.77464 -5.8720712 0.0034851739 1 1 - 4450 314.97697 45.037299 0.0034851739 1 1 - 4500 310.77723 16.958771 0.0034851739 1 1 - 4550 302.17421 12.156862 0.0034851739 1 1 - 4600 319.74799 6.8488914 0.0034851739 1 1 - 4650 270.86805 -13.767907 0.0034851739 1 1 - 4700 249.81731 -31.197484 0.0034851739 1 1 - 4750 285.86481 -9.8916332 0.0034851739 1 1 - 4800 233.98321 7.1338518 0.0034851739 1 1 - 4850 302.60551 49.262886 0.0034851739 1 1 - 4900 316.55055 34.663238 0.0034851739 1 1 - 4950 357.32741 11.583013 0.0034851739 1 1 - 5000 400.21044 -8.1780861 0.0034851739 1 1 - 5050 390.01845 -20.490268 0.0034851739 1 1 - 5100 378.84249 -41.328772 0.0034851739 1 1 - 5150 324.02039 -15.023852 0.0034851739 1 1 - 5200 262.08427 10.937367 0.0034851739 1 1 - 5250 255.75506 16.381495 0.0034851739 1 1 - 5300 277.84991 40.682283 0.0034851739 1 1 - 5350 302.92834 9.1989644 0.0034851739 1 1 - 5400 283.71964 -1.6583895 0.0034851739 1 1 - 5450 300.71261 -4.703054 0.0034851739 1 1 - 5500 343.54987 -0.30546396 0.0034851739 1 1 - 5550 369.51272 21.691639 0.0034851739 1 1 - 5600 372.69786 -38.679919 0.0034851739 1 1 - 5650 327.41256 11.352201 0.0034851739 1 1 - 5700 278.9861 -23.82728 0.0034851739 1 1 - 5750 308.30037 -20.756238 0.0034851739 1 1 - 5800 341.4559 28.058314 0.0034851739 1 1 - 5850 322.9786 -10.731862 0.0034851739 1 1 - 5900 304.53598 32.825105 0.0034851739 1 1 - 5950 287.17515 -36.780057 0.0034851739 1 1 - 6000 296.52688 18.782156 0.0034851739 1 1 - 6050 314.25411 15.99272 0.0034851739 1 1 - 6100 313.86572 3.4344108 0.0034851739 1 1 - 6150 325.64197 32.39212 0.0034851739 1 1 - 6200 367.4298 -27.161154 0.0034851739 1 1 - 6250 369.30937 39.020881 0.0034851739 1 1 - 6300 328.92245 -23.175612 0.0034851739 1 1 - 6350 305.6293 4.9011587 0.0034851739 1 1 - 6400 241.70456 -13.675247 0.0034851739 1 1 - 6450 265.66574 2.4049735 0.0034851739 1 1 - 6500 249.3592 13.420453 0.0034851739 1 1 - 6550 294.5367 10.856753 0.0034851739 1 1 - 6600 308.20246 18.992923 0.0034851739 1 1 - 6650 305.43756 -49.57151 0.0034851739 1 1 - 6700 320.27395 11.339101 0.0034851739 1 1 - 6750 321.7875 -23.463361 0.0034851739 1 1 - 6800 303.40316 7.6256997 0.0034851739 1 1 - 6850 297.18652 51.52186 0.0034851739 1 1 - 6900 284.19084 -8.496294 0.0034851739 1 1 - 6950 331.04173 13.227745 0.0034851739 1 1 - 7000 311.38027 -43.26105 0.0034851739 1 1 - 7050 286.82046 -14.171194 0.0034851739 1 1 - 7100 302.81691 12.058085 0.0034851739 1 1 - 7150 297.18018 -43.110658 0.0034851739 1 1 - 7200 332.46131 26.051496 0.0034851739 1 1 - 7250 262.72288 41.161451 0.0034851739 1 1 - 7300 250.62739 -23.440907 0.0034851739 1 1 - 7350 296.92141 35.869216 0.0034851739 1 1 - 7400 245.06807 -13.467896 0.0034851739 1 1 - 7450 272.2659 -23.292836 0.0034851739 1 1 - 7500 209.05776 13.888665 0.0034851739 1 1 - 7550 255.03716 4.9662624 0.0034851739 1 1 - 7600 312.26011 -37.350427 0.0034851739 1 1 - 7650 305.5823 55.208039 0.0034851739 1 1 - 7700 325.13382 -18.370791 0.0034851739 1 1 - 7750 363.24898 -22.473126 0.0034851739 1 1 - 7800 350.19254 26.792307 0.0034851739 1 1 - 7850 271.76418 -17.843445 0.0034851739 1 1 - 7900 272.70301 -11.709349 0.0034851739 1 1 - 7950 298.5993 -12.736235 0.0034851739 1 1 - 8000 274.52611 49.657345 0.0034851739 1 1 - 8050 304.73711 -0.52485689 0.0034851739 1 1 - 8100 328.29239 -39.901891 0.0034851739 1 1 - 8150 406.52096 2.8669076 0.0034851739 1 1 - 8200 332.17309 -51.168754 0.0034851739 1 1 - 8250 354.68419 53.003157 0.0034851739 1 1 - 8300 337.28934 20.766408 0.0034851739 1 1 - 8350 361.81133 -54.159227 0.0034851739 1 1 - 8400 305.59597 24.011667 0.0034851739 1 1 - 8450 303.25823 4.423341 0.0034851739 1 1 - 8500 253.50747 -11.026949 0.0034851739 1 1 - 8550 277.13504 23.204625 0.0034851739 1 1 - 8600 291.40211 -22.253861 0.0034851739 1 1 - 8650 307.93765 32.14162 0.0034851739 1 1 - 8700 309.1529 0.36279434 0.0034851739 1 1 - 8750 355.10326 11.677219 0.0034851739 1 1 - 8800 330.21328 19.235269 0.0034851739 1 1 - 8850 241.29109 21.707386 0.0034851739 1 1 - 8900 319.15363 -60.010115 0.0034851739 1 1 - 8950 308.88552 -57.637014 0.0034851739 1 1 - 9000 272.22373 51.15837 0.0034851739 1 1 - 9050 248.84947 7.3390565 0.0034851739 1 1 - 9100 221.91564 48.387079 0.0034851739 1 1 - 9150 298.03506 2.9058639 0.0034851739 1 1 - 9200 274.25114 -24.597819 0.0034851739 1 1 - 9250 334.08373 5.1079577 0.0034851739 1 1 - 9300 383.07285 -23.274763 0.0034851739 1 1 - 9350 335.00581 20.94212 0.0034851739 1 1 - 9400 309.23862 34.074744 0.0034851739 1 1 - 9450 312.62262 -28.468057 0.0034851739 1 1 - 9500 324.54274 2.851136 0.0034851739 1 1 - 9550 313.32781 22.468182 0.0034851739 1 1 - 9600 269.04372 4.064934 0.0034851739 1 1 - 9650 270.98476 -21.520127 0.0034851739 1 1 - 9700 236.8736 16.250728 0.0034851739 1 1 - 9750 333.94686 1.6864148 0.0034851739 1 1 - 9800 330.91875 12.150018 0.0034851739 1 1 - 9850 343.8603 25.338853 0.0034851739 1 1 - 9900 330.93364 -28.292992 0.0034851739 1 1 - 9950 291.25518 25.795948 0.0034851739 1 1 - 10000 319.25565 25.323846 0.0034851739 1 1 -Loop time of 3.55353 on 4 procs for 10000 steps with 44 atoms - -Performance: 243.139 ns/day, 0.099 hours/ns, 2814.105 timesteps/s -93.4% CPU use with 4 MPI tasks x 1 OpenMP threads - -MPI task timing breakdown: -Section | min time | avg time | max time |%varavg| %total ---------------------------------------------------------------- -Pair | 0.0030422 | 0.10454 | 0.35211 | 44.8 | 2.94 -Bond | 0.0063896 | 0.29222 | 0.94356 | 71.3 | 8.22 -Kspace | 0.88508 | 1.6486 | 1.979 | 35.1 | 46.39 -Neigh | 0.61154 | 0.62212 | 0.63307 | 1.0 | 17.51 -Comm | 0.18944 | 0.24549 | 0.29196 | 7.9 | 6.91 -Output | 0.0050066 | 0.011804 | 0.032134 | 10.8 | 0.33 -Modify | 0.52282 | 0.60522 | 0.69588 | 7.9 | 17.03 -Other | | 0.02359 | | | 0.66 - -Nlocal: 11 ave 44 max 0 min -Histogram: 3 0 0 0 0 0 0 0 0 1 -Nghost: 33 ave 44 max 0 min -Histogram: 1 0 0 0 0 0 0 0 0 3 -Neighs: 205.75 ave 823 max 0 min -Histogram: 3 0 0 0 0 0 0 0 0 1 - -Total # of neighbors = 823 -Ave neighs/atom = 18.7045 -Ave special neighs/atom = 9.77273 -Neighbor list builds = 10000 -Dangerous builds = 0 - -# write_restart restart_longrun -# write_data restart_longrun.data - -Please see the log.cite file for references relevant to this simulation - -Total wall time: 0:00:03 diff --git a/examples/USER/misc/bond_react/tiny_nylon/log.5Jun19.tiny_nylon.stabilized.g++.1 b/examples/USER/misc/bond_react/tiny_nylon/log.5Jun19.tiny_nylon.stabilized.g++.1 new file mode 100644 index 0000000000..de1167c652 --- /dev/null +++ b/examples/USER/misc/bond_react/tiny_nylon/log.5Jun19.tiny_nylon.stabilized.g++.1 @@ -0,0 +1,148 @@ +LAMMPS (5 Jun 2019) +Reading data file ... + orthogonal box = (-25 -25 -25) to (25 25 25) + 1 by 1 by 1 MPI processor grid + reading atoms ... + 44 atoms + reading velocities ... + 44 velocities + scanning bonds ... + 9 = max bonds/atom + scanning angles ... + 21 = max angles/atom + scanning dihedrals ... + 29 = max dihedrals/atom + scanning impropers ... + 29 = max impropers/atom + reading bonds ... + 42 bonds + reading angles ... + 74 angles + reading dihedrals ... + 100 dihedrals + reading impropers ... + 44 impropers +Finding 1-2 1-3 1-4 neighbors ... + special bond factors lj: 0 0 0 + special bond factors coul: 0 0 0 + 4 = max # of 1-2 neighbors + 6 = max # of 1-3 neighbors + 12 = max # of 1-4 neighbors + 41 = max # of special neighbors + special bonds CPU = 0.000181113 secs + read_data CPU = 0.0251833 secs +Read molecule mol1: + 18 atoms with max type 8 + 16 bonds with max type 14 + 25 angles with max type 28 + 23 dihedrals with max type 36 + 14 impropers with max type 11 +Read molecule mol2: + 18 atoms with max type 9 + 17 bonds with max type 13 + 31 angles with max type 27 + 39 dihedrals with max type 33 + 20 impropers with max type 1 +Read molecule mol3: + 15 atoms with max type 9 + 14 bonds with max type 13 + 25 angles with max type 27 + 30 dihedrals with max type 33 + 16 impropers with max type 1 +Read molecule mol4: + 15 atoms with max type 11 + 13 bonds with max type 15 + 19 angles with max type 29 + 16 dihedrals with max type 32 + 10 impropers with max type 13 +WARNING: Bond/react: Atom affected by reaction rxn1 too close to template edge (../fix_bond_react.cpp:1785) +WARNING: Bond/react: Atom affected by reaction rxn2 too close to template edge (../fix_bond_react.cpp:1785) +dynamic group bond_react_MASTER_group defined +dynamic group statted_grp_REACT defined +PPPM initialization ... + using 12-bit tables for long-range coulomb (../kspace.cpp:319) + G vector (1/distance) = 0.0534597 + grid = 2 2 2 + stencil order = 5 + estimated absolute RMS force accuracy = 0.0402256 + estimated relative force accuracy = 0.000121138 + using double precision FFTs + 3d grid and FFT values/proc = 343 8 +Neighbor list info ... + update every 1 steps, delay 10 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 10.5 + ghost atom cutoff = 10.5 + binsize = 5.25, bins = 10 10 10 + 2 neighbor lists, perpetual/occasional/extra = 1 1 0 + (1) pair lj/class2/coul/long, perpetual + attributes: half, newton on + pair build: half/bin/newton + stencil: half/bin/3d/newton + bin: standard + (2) fix bond/react, occasional, copy from (1) + attributes: half, newton on + pair build: copy + stencil: none + bin: none +Setting up Verlet run ... + Unit style : real + Current step : 0 + Time step : 1 +WARNING: Inconsistent image flags (../domain.cpp:784) +Per MPI rank memory allocation (min/avg/max) = 34.41 | 34.41 | 34.41 Mbytes +Step Temp Press Density f_myrxns[1] f_myrxns[2] + 0 300 346.78165 0.0034851739 0 0 + 50 293.70542 -52.547388 0.0034851739 1 0 + 100 276.36755 54.81826 0.0034851739 1 1 + 150 448.65869 16.874435 0.0034851739 1 1 + 200 379.84257 11.578545 0.0034851739 1 1 + 250 298.21983 90.656585 0.0034851739 1 1 + 300 333.3111 -30.139607 0.0034851739 1 1 + 350 266.57108 6.4505134 0.0034851739 1 1 + 400 264.05476 10.513204 0.0034851739 1 1 + 450 250.70418 -18.635379 0.0034851739 1 1 + 500 261.21632 10.231013 0.0034851739 1 1 + 550 309.89024 -8.8299506 0.0034851739 1 1 + 600 373.45851 30.368993 0.0034851739 1 1 + 650 338.26242 9.0362267 0.0034851739 1 1 + 700 295.67794 -5.6007538 0.0034851739 1 1 + 750 310.86563 -59.228181 0.0034851739 1 1 + 800 286.22678 -9.9022407 0.0034851739 1 1 + 850 218.42135 27.845352 0.0034851739 1 1 + 900 259.62551 24.216336 0.0034851739 1 1 + 950 250.21307 -14.560985 0.0034851739 1 1 + 1000 274.29245 -0.38768626 0.0034851739 1 1 +Loop time of 0.341061 on 1 procs for 1000 steps with 44 atoms + +Performance: 253.327 ns/day, 0.095 hours/ns, 2932.025 timesteps/s +87.9% CPU use with 1 MPI tasks x no OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0.031135 | 0.031135 | 0.031135 | 0.0 | 9.13 +Bond | 0.12623 | 0.12623 | 0.12623 | 0.0 | 37.01 +Kspace | 0.036491 | 0.036491 | 0.036491 | 0.0 | 10.70 +Neigh | 0.046395 | 0.046395 | 0.046395 | 0.0 | 13.60 +Comm | 0.0025396 | 0.0025396 | 0.0025396 | 0.0 | 0.74 +Output | 0.07775 | 0.07775 | 0.07775 | 0.0 | 22.80 +Modify | 0.019219 | 0.019219 | 0.019219 | 0.0 | 5.64 +Other | | 0.001306 | | | 0.38 + +Nlocal: 44 ave 44 max 44 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 2 ave 2 max 2 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 740 ave 740 max 740 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 740 +Ave neighs/atom = 16.8182 +Ave special neighs/atom = 9.77273 +Neighbor list builds = 1000 +Dangerous builds = 0 + +Please see the log.cite file for references relevant to this simulation + +Total wall time: 0:00:00 diff --git a/examples/USER/misc/bond_react/tiny_nylon/log.5Jun19.tiny_nylon.stabilized.g++.4 b/examples/USER/misc/bond_react/tiny_nylon/log.5Jun19.tiny_nylon.stabilized.g++.4 new file mode 100644 index 0000000000..b9c7a3ba15 --- /dev/null +++ b/examples/USER/misc/bond_react/tiny_nylon/log.5Jun19.tiny_nylon.stabilized.g++.4 @@ -0,0 +1,148 @@ +LAMMPS (5 Jun 2019) +Reading data file ... + orthogonal box = (-25 -25 -25) to (25 25 25) + 1 by 2 by 2 MPI processor grid + reading atoms ... + 44 atoms + reading velocities ... + 44 velocities + scanning bonds ... + 9 = max bonds/atom + scanning angles ... + 21 = max angles/atom + scanning dihedrals ... + 29 = max dihedrals/atom + scanning impropers ... + 29 = max impropers/atom + reading bonds ... + 42 bonds + reading angles ... + 74 angles + reading dihedrals ... + 100 dihedrals + reading impropers ... + 44 impropers +Finding 1-2 1-3 1-4 neighbors ... + special bond factors lj: 0 0 0 + special bond factors coul: 0 0 0 + 4 = max # of 1-2 neighbors + 6 = max # of 1-3 neighbors + 12 = max # of 1-4 neighbors + 41 = max # of special neighbors + special bonds CPU = 0.000178751 secs + read_data CPU = 0.0385782 secs +Read molecule mol1: + 18 atoms with max type 8 + 16 bonds with max type 14 + 25 angles with max type 28 + 23 dihedrals with max type 36 + 14 impropers with max type 11 +Read molecule mol2: + 18 atoms with max type 9 + 17 bonds with max type 13 + 31 angles with max type 27 + 39 dihedrals with max type 33 + 20 impropers with max type 1 +Read molecule mol3: + 15 atoms with max type 9 + 14 bonds with max type 13 + 25 angles with max type 27 + 30 dihedrals with max type 33 + 16 impropers with max type 1 +Read molecule mol4: + 15 atoms with max type 11 + 13 bonds with max type 15 + 19 angles with max type 29 + 16 dihedrals with max type 32 + 10 impropers with max type 13 +WARNING: Bond/react: Atom affected by reaction rxn1 too close to template edge (../fix_bond_react.cpp:1785) +WARNING: Bond/react: Atom affected by reaction rxn2 too close to template edge (../fix_bond_react.cpp:1785) +dynamic group bond_react_MASTER_group defined +dynamic group statted_grp_REACT defined +PPPM initialization ... + using 12-bit tables for long-range coulomb (../kspace.cpp:319) + G vector (1/distance) = 0.0534597 + grid = 2 2 2 + stencil order = 5 + estimated absolute RMS force accuracy = 0.0402256 + estimated relative force accuracy = 0.000121138 + using double precision FFTs + 3d grid and FFT values/proc = 252 2 +Neighbor list info ... + update every 1 steps, delay 10 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 10.5 + ghost atom cutoff = 10.5 + binsize = 5.25, bins = 10 10 10 + 2 neighbor lists, perpetual/occasional/extra = 1 1 0 + (1) pair lj/class2/coul/long, perpetual + attributes: half, newton on + pair build: half/bin/newton + stencil: half/bin/3d/newton + bin: standard + (2) fix bond/react, occasional, copy from (1) + attributes: half, newton on + pair build: copy + stencil: none + bin: none +Setting up Verlet run ... + Unit style : real + Current step : 0 + Time step : 1 +WARNING: Inconsistent image flags (../domain.cpp:784) +Per MPI rank memory allocation (min/avg/max) = 34.42 | 34.77 | 35.45 Mbytes +Step Temp Press Density f_myrxns[1] f_myrxns[2] + 0 300 346.78165 0.0034851739 0 0 + 50 293.70542 -52.547388 0.0034851739 1 0 + 100 276.36755 54.81826 0.0034851739 1 1 + 150 448.65869 16.874435 0.0034851739 1 1 + 200 379.84257 11.578545 0.0034851739 1 1 + 250 298.21983 90.656585 0.0034851739 1 1 + 300 333.3111 -30.139607 0.0034851739 1 1 + 350 266.57108 6.4505134 0.0034851739 1 1 + 400 264.05476 10.513204 0.0034851739 1 1 + 450 250.70418 -18.635379 0.0034851739 1 1 + 500 261.21632 10.231013 0.0034851739 1 1 + 550 309.89024 -8.8299506 0.0034851739 1 1 + 600 373.45851 30.368993 0.0034851739 1 1 + 650 338.26242 9.0362267 0.0034851739 1 1 + 700 295.67794 -5.6007538 0.0034851739 1 1 + 750 310.86563 -59.228181 0.0034851739 1 1 + 800 286.22678 -9.9022407 0.0034851739 1 1 + 850 218.42135 27.845352 0.0034851739 1 1 + 900 259.62551 24.216336 0.0034851739 1 1 + 950 250.21307 -14.560985 0.0034851739 1 1 + 1000 274.29245 -0.38768626 0.0034851739 1 1 +Loop time of 0.271242 on 4 procs for 1000 steps with 44 atoms + +Performance: 318.535 ns/day, 0.075 hours/ns, 3686.747 timesteps/s +98.6% CPU use with 4 MPI tasks x no OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0.00023773 | 0.0077322 | 0.016042 | 8.4 | 2.85 +Bond | 0.00073385 | 0.032108 | 0.08446 | 19.4 | 11.84 +Kspace | 0.041659 | 0.098095 | 0.13373 | 12.3 | 36.16 +Neigh | 0.028894 | 0.029247 | 0.029558 | 0.1 | 10.78 +Comm | 0.012367 | 0.013642 | 0.01503 | 0.9 | 5.03 +Output | 0.032475 | 0.040504 | 0.061019 | 5.9 | 14.93 +Modify | 0.032934 | 0.049086 | 0.0577 | 4.3 | 18.10 +Other | | 0.0008281 | | | 0.31 + +Nlocal: 11 ave 21 max 0 min +Histogram: 1 1 0 0 0 0 0 0 0 2 +Nghost: 32.5 ave 43 max 23 min +Histogram: 2 0 0 0 0 0 0 0 0 2 +Neighs: 185 ave 376 max 0 min +Histogram: 2 0 0 0 0 0 0 0 0 2 + +Total # of neighbors = 740 +Ave neighs/atom = 16.8182 +Ave special neighs/atom = 9.77273 +Neighbor list builds = 1000 +Dangerous builds = 0 + +Please see the log.cite file for references relevant to this simulation + +Total wall time: 0:00:00 diff --git a/examples/USER/misc/bond_react/tiny_nylon/log.5Jun19.tiny_nylon.unstabilized.g++.1 b/examples/USER/misc/bond_react/tiny_nylon/log.5Jun19.tiny_nylon.unstabilized.g++.1 new file mode 100644 index 0000000000..14cac1dfad --- /dev/null +++ b/examples/USER/misc/bond_react/tiny_nylon/log.5Jun19.tiny_nylon.unstabilized.g++.1 @@ -0,0 +1,147 @@ +LAMMPS (5 Jun 2019) +Reading data file ... + orthogonal box = (-25 -25 -25) to (25 25 25) + 1 by 1 by 1 MPI processor grid + reading atoms ... + 44 atoms + reading velocities ... + 44 velocities + scanning bonds ... + 9 = max bonds/atom + scanning angles ... + 21 = max angles/atom + scanning dihedrals ... + 29 = max dihedrals/atom + scanning impropers ... + 29 = max impropers/atom + reading bonds ... + 42 bonds + reading angles ... + 74 angles + reading dihedrals ... + 100 dihedrals + reading impropers ... + 44 impropers +Finding 1-2 1-3 1-4 neighbors ... + special bond factors lj: 0 0 0 + special bond factors coul: 0 0 0 + 4 = max # of 1-2 neighbors + 6 = max # of 1-3 neighbors + 12 = max # of 1-4 neighbors + 41 = max # of special neighbors + special bonds CPU = 0.000217102 secs + read_data CPU = 0.00630778 secs +Read molecule mol1: + 18 atoms with max type 8 + 16 bonds with max type 14 + 25 angles with max type 28 + 23 dihedrals with max type 36 + 14 impropers with max type 11 +Read molecule mol2: + 18 atoms with max type 9 + 17 bonds with max type 13 + 31 angles with max type 27 + 39 dihedrals with max type 33 + 20 impropers with max type 1 +Read molecule mol3: + 15 atoms with max type 9 + 14 bonds with max type 13 + 25 angles with max type 27 + 30 dihedrals with max type 33 + 16 impropers with max type 1 +Read molecule mol4: + 15 atoms with max type 11 + 13 bonds with max type 15 + 19 angles with max type 29 + 16 dihedrals with max type 32 + 10 impropers with max type 13 +WARNING: Bond/react: Atom affected by reaction rxn1 too close to template edge (../fix_bond_react.cpp:1785) +WARNING: Bond/react: Atom affected by reaction rxn2 too close to template edge (../fix_bond_react.cpp:1785) +dynamic group bond_react_MASTER_group defined +PPPM initialization ... + using 12-bit tables for long-range coulomb (../kspace.cpp:319) + G vector (1/distance) = 0.0534597 + grid = 2 2 2 + stencil order = 5 + estimated absolute RMS force accuracy = 0.0402256 + estimated relative force accuracy = 0.000121138 + using double precision FFTs + 3d grid and FFT values/proc = 343 8 +Neighbor list info ... + update every 1 steps, delay 10 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 10.5 + ghost atom cutoff = 10.5 + binsize = 5.25, bins = 10 10 10 + 2 neighbor lists, perpetual/occasional/extra = 1 1 0 + (1) pair lj/class2/coul/long, perpetual + attributes: half, newton on + pair build: half/bin/newton + stencil: half/bin/3d/newton + bin: standard + (2) fix bond/react, occasional, copy from (1) + attributes: half, newton on + pair build: copy + stencil: none + bin: none +Setting up Verlet run ... + Unit style : real + Current step : 0 + Time step : 1 +WARNING: Inconsistent image flags (../domain.cpp:784) +Per MPI rank memory allocation (min/avg/max) = 34.35 | 34.35 | 34.35 Mbytes +Step Temp Press Density f_myrxns[1] f_myrxns[2] + 0 300 346.78165 0.0034851739 0 0 + 50 416.49412 -20.293038 0.0034851739 1 0 + 100 746.49323 91.912227 0.0034851739 1 1 + 150 515.15907 -1.4024709 0.0034851739 1 1 + 200 441.14572 -19.333087 0.0034851739 1 1 + 250 376.40996 30.717679 0.0034851739 1 1 + 300 326.15127 -3.0433799 0.0034851739 1 1 + 350 326.21116 6.235391 0.0034851739 1 1 + 400 366.48556 3.9807338 0.0034851739 1 1 + 450 313.79097 7.6674629 0.0034851739 1 1 + 500 278.89836 14.102052 0.0034851739 1 1 + 550 267.50214 18.241417 0.0034851739 1 1 + 600 276.28064 7.4649611 0.0034851739 1 1 + 650 255.26713 -8.5258573 0.0034851739 1 1 + 700 258.59752 -5.3341215 0.0034851739 1 1 + 750 263.71264 33.369869 0.0034851739 1 1 + 800 246.22976 -15.349137 0.0034851739 1 1 + 850 255.93887 16.331669 0.0034851739 1 1 + 900 239.72525 -0.20075789 0.0034851739 1 1 + 950 213.73064 12.17619 0.0034851739 1 1 + 1000 218.25094 -9.0955642 0.0034851739 1 1 +Loop time of 0.348252 on 1 procs for 1000 steps with 44 atoms + +Performance: 248.096 ns/day, 0.097 hours/ns, 2871.483 timesteps/s +91.8% CPU use with 1 MPI tasks x no OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0.031941 | 0.031941 | 0.031941 | 0.0 | 9.17 +Bond | 0.13031 | 0.13031 | 0.13031 | 0.0 | 37.42 +Kspace | 0.037554 | 0.037554 | 0.037554 | 0.0 | 10.78 +Neigh | 0.047397 | 0.047397 | 0.047397 | 0.0 | 13.61 +Comm | 0.0025814 | 0.0025814 | 0.0025814 | 0.0 | 0.74 +Output | 0.083526 | 0.083526 | 0.083526 | 0.0 | 23.98 +Modify | 0.013602 | 0.013602 | 0.013602 | 0.0 | 3.91 +Other | | 0.001336 | | | 0.38 + +Nlocal: 44 ave 44 max 44 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 3 ave 3 max 3 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 818 ave 818 max 818 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 818 +Ave neighs/atom = 18.5909 +Ave special neighs/atom = 9.77273 +Neighbor list builds = 1000 +Dangerous builds = 0 + +Please see the log.cite file for references relevant to this simulation + +Total wall time: 0:00:00 diff --git a/examples/USER/misc/bond_react/tiny_nylon/log.5Jun19.tiny_nylon.unstabilized.g++.4 b/examples/USER/misc/bond_react/tiny_nylon/log.5Jun19.tiny_nylon.unstabilized.g++.4 new file mode 100644 index 0000000000..6b13dd60d3 --- /dev/null +++ b/examples/USER/misc/bond_react/tiny_nylon/log.5Jun19.tiny_nylon.unstabilized.g++.4 @@ -0,0 +1,147 @@ +LAMMPS (5 Jun 2019) +Reading data file ... + orthogonal box = (-25 -25 -25) to (25 25 25) + 1 by 2 by 2 MPI processor grid + reading atoms ... + 44 atoms + reading velocities ... + 44 velocities + scanning bonds ... + 9 = max bonds/atom + scanning angles ... + 21 = max angles/atom + scanning dihedrals ... + 29 = max dihedrals/atom + scanning impropers ... + 29 = max impropers/atom + reading bonds ... + 42 bonds + reading angles ... + 74 angles + reading dihedrals ... + 100 dihedrals + reading impropers ... + 44 impropers +Finding 1-2 1-3 1-4 neighbors ... + special bond factors lj: 0 0 0 + special bond factors coul: 0 0 0 + 4 = max # of 1-2 neighbors + 6 = max # of 1-3 neighbors + 12 = max # of 1-4 neighbors + 41 = max # of special neighbors + special bonds CPU = 0.000163256 secs + read_data CPU = 0.0244579 secs +Read molecule mol1: + 18 atoms with max type 8 + 16 bonds with max type 14 + 25 angles with max type 28 + 23 dihedrals with max type 36 + 14 impropers with max type 11 +Read molecule mol2: + 18 atoms with max type 9 + 17 bonds with max type 13 + 31 angles with max type 27 + 39 dihedrals with max type 33 + 20 impropers with max type 1 +Read molecule mol3: + 15 atoms with max type 9 + 14 bonds with max type 13 + 25 angles with max type 27 + 30 dihedrals with max type 33 + 16 impropers with max type 1 +Read molecule mol4: + 15 atoms with max type 11 + 13 bonds with max type 15 + 19 angles with max type 29 + 16 dihedrals with max type 32 + 10 impropers with max type 13 +WARNING: Bond/react: Atom affected by reaction rxn1 too close to template edge (../fix_bond_react.cpp:1785) +WARNING: Bond/react: Atom affected by reaction rxn2 too close to template edge (../fix_bond_react.cpp:1785) +dynamic group bond_react_MASTER_group defined +PPPM initialization ... + using 12-bit tables for long-range coulomb (../kspace.cpp:319) + G vector (1/distance) = 0.0534597 + grid = 2 2 2 + stencil order = 5 + estimated absolute RMS force accuracy = 0.0402256 + estimated relative force accuracy = 0.000121138 + using double precision FFTs + 3d grid and FFT values/proc = 252 2 +Neighbor list info ... + update every 1 steps, delay 10 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 10.5 + ghost atom cutoff = 10.5 + binsize = 5.25, bins = 10 10 10 + 2 neighbor lists, perpetual/occasional/extra = 1 1 0 + (1) pair lj/class2/coul/long, perpetual + attributes: half, newton on + pair build: half/bin/newton + stencil: half/bin/3d/newton + bin: standard + (2) fix bond/react, occasional, copy from (1) + attributes: half, newton on + pair build: copy + stencil: none + bin: none +Setting up Verlet run ... + Unit style : real + Current step : 0 + Time step : 1 +WARNING: Inconsistent image flags (../domain.cpp:784) +Per MPI rank memory allocation (min/avg/max) = 33.34 | 33.69 | 34.37 Mbytes +Step Temp Press Density f_myrxns[1] f_myrxns[2] + 0 300 346.78165 0.0034851739 0 0 + 50 416.49412 -20.293038 0.0034851739 1 0 + 100 746.49323 91.912227 0.0034851739 1 1 + 150 515.15907 -1.4024709 0.0034851739 1 1 + 200 441.14572 -19.333087 0.0034851739 1 1 + 250 376.40996 30.717679 0.0034851739 1 1 + 300 326.15127 -3.0433799 0.0034851739 1 1 + 350 326.21116 6.235391 0.0034851739 1 1 + 400 366.48556 3.9807338 0.0034851739 1 1 + 450 313.79097 7.6674629 0.0034851739 1 1 + 500 278.89836 14.102052 0.0034851739 1 1 + 550 267.50214 18.241417 0.0034851739 1 1 + 600 276.28064 7.4649611 0.0034851739 1 1 + 650 255.26713 -8.5258573 0.0034851739 1 1 + 700 258.59752 -5.3341215 0.0034851739 1 1 + 750 263.71264 33.369869 0.0034851739 1 1 + 800 246.22976 -15.349137 0.0034851739 1 1 + 850 255.93887 16.331669 0.0034851739 1 1 + 900 239.72525 -0.20075789 0.0034851739 1 1 + 950 213.73064 12.17619 0.0034851739 1 1 + 1000 218.25094 -9.0955642 0.0034851739 1 1 +Loop time of 0.254903 on 4 procs for 1000 steps with 44 atoms + +Performance: 338.952 ns/day, 0.071 hours/ns, 3923.053 timesteps/s +99.8% CPU use with 4 MPI tasks x no OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0.00014252 | 0.0090715 | 0.021332 | 9.6 | 3.56 +Bond | 0.00047028 | 0.037261 | 0.10789 | 22.7 | 14.62 +Kspace | 0.051006 | 0.12756 | 0.1693 | 13.6 | 50.04 +Neigh | 0.035644 | 0.036088 | 0.036523 | 0.2 | 14.16 +Comm | 0.013984 | 0.016074 | 0.018676 | 1.6 | 6.31 +Output | 0.0002816 | 0.00033726 | 0.00044251 | 0.0 | 0.13 +Modify | 0.023697 | 0.027803 | 0.033552 | 2.5 | 10.91 +Other | | 0.0007123 | | | 0.28 + +Nlocal: 11 ave 29 max 0 min +Histogram: 1 1 0 0 1 0 0 0 0 1 +Nghost: 25 ave 31 max 12 min +Histogram: 1 0 0 0 0 0 0 0 2 1 +Neighs: 204.5 ave 443 max 0 min +Histogram: 2 0 0 0 0 0 0 0 1 1 + +Total # of neighbors = 818 +Ave neighs/atom = 18.5909 +Ave special neighs/atom = 9.77273 +Neighbor list builds = 1000 +Dangerous builds = 0 + +Please see the log.cite file for references relevant to this simulation + +Total wall time: 0:00:00 -- GitLab From 39f5b8c734af3e2408656f473638dcf39400babc Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Mon, 1 Jul 2019 04:16:00 -0400 Subject: [PATCH 144/469] transform POEMS library to conform to IWYU conventions --- lib/poems/body.cpp | 14 ++++++++++++-- lib/poems/body.h | 20 +++++++++----------- lib/poems/body23joint.cpp | 16 ++++++++-------- lib/poems/body23joint.h | 6 ++---- lib/poems/colmatmap.h | 3 +++ lib/poems/colmatrix.cpp | 3 +-- lib/poems/colmatrix.h | 3 ++- lib/poems/eulerparameters.cpp | 4 ++++ lib/poems/eulerparameters.h | 6 +++--- lib/poems/fastmatrixops.cpp | 13 +++++++++++-- lib/poems/fastmatrixops.h | 11 ++++++++++- lib/poems/fixedpoint.cpp | 3 +++ lib/poems/fixedpoint.h | 2 ++ lib/poems/freebodyjoint.cpp | 12 ++++++++---- lib/poems/freebodyjoint.h | 3 +++ lib/poems/inertialframe.cpp | 4 +++- lib/poems/inertialframe.h | 3 +++ lib/poems/joint.cpp | 19 +++++++++++++++---- lib/poems/joint.h | 9 +++++++-- lib/poems/mat3x3.cpp | 3 ++- lib/poems/mat3x3.h | 3 +-- lib/poems/mat4x4.cpp | 2 ++ lib/poems/mat4x4.h | 4 +++- lib/poems/mat6x6.cpp | 2 ++ lib/poems/mat6x6.h | 3 ++- lib/poems/matrix.h | 2 ++ lib/poems/matrixfun.cpp | 10 ++++++++-- lib/poems/matrixfun.h | 18 +++++++++++++----- lib/poems/mixedjoint.cpp | 11 ++++++++--- lib/poems/mixedjoint.h | 4 ++++ lib/poems/norm.cpp | 6 ++++++ lib/poems/norm.h | 7 +++++-- lib/poems/onbody.cpp | 7 +++++-- lib/poems/onbody.h | 12 +++++++----- lib/poems/onfunctions.cpp | 9 +++++++-- lib/poems/onfunctions.h | 5 ++++- lib/poems/onsolver.cpp | 14 +++++++++++--- lib/poems/onsolver.h | 4 +++- lib/poems/particle.cpp | 1 - lib/poems/particle.h | 2 ++ lib/poems/poemstreenode.h | 6 ------ lib/poems/point.cpp | 4 +++- lib/poems/prismaticjoint.cpp | 4 ++++ lib/poems/prismaticjoint.h | 4 +++- lib/poems/revolutejoint.cpp | 4 ++++ lib/poems/revolutejoint.h | 5 +++-- lib/poems/rigidbody.cpp | 3 ++- lib/poems/rigidbody.h | 2 ++ lib/poems/rowmatrix.cpp | 2 +- lib/poems/rowmatrix.h | 3 +++ lib/poems/solver.cpp | 3 ++- lib/poems/solver.h | 4 ++-- lib/poems/sphericaljoint.cpp | 10 +++++++--- lib/poems/sphericaljoint.h | 6 ++---- lib/poems/system.cpp | 19 ++++++++++++++++++- lib/poems/system.h | 25 +------------------------ lib/poems/vect3.cpp | 9 +++++++++ lib/poems/vect3.h | 4 ++++ lib/poems/vect4.cpp | 2 ++ lib/poems/vect4.h | 4 +++- lib/poems/vect6.cpp | 2 ++ lib/poems/vect6.h | 3 +++ lib/poems/workspace.cpp | 19 +++++++++++++++---- lib/poems/workspace.h | 9 --------- 64 files changed, 301 insertions(+), 138 deletions(-) diff --git a/lib/poems/body.cpp b/lib/poems/body.cpp index 4ef05dd1e6..487d5e1ab7 100644 --- a/lib/poems/body.cpp +++ b/lib/poems/body.cpp @@ -14,9 +14,19 @@ * 110 8th St. Troy NY 12180 * * CONTACT: anderk5@rpi.edu * *_________________________________________________________________________*/ - -#include "bodies.h" + +#include + +#include "body.h" +#include "inertialframe.h" +#include "mat3x3.h" +#include "particle.h" +#include "poemslist.h" #include "point.h" +#include "rigidbody.h" +#include "vect3.h" + +class Joint; using namespace std; diff --git a/lib/poems/body.h b/lib/poems/body.h index f8e0f6a5a3..06a9c72417 100644 --- a/lib/poems/body.h +++ b/lib/poems/body.h @@ -19,13 +19,11 @@ #ifndef BODY_H #define BODY_H -#include "poemslist.h" #include +#include "poemslist.h" #include "poemsobject.h" - -#include "matrices.h" - - +#include "mat3x3.h" +#include "vect3.h" // emumerated type enum BodyType { @@ -33,16 +31,16 @@ enum BodyType { PARTICLE = 1, RIGIDBODY = 2 }; - + class Point; class Joint; -class CompBody; + class Body : public POEMSObject { public: double mass; Mat3x3 inertia; - + Vect3 r; Vect3 v; Vect3 v_k; @@ -54,13 +52,13 @@ public: Vect3 alpha; Vect3 alpha_t; double KE; - + List joints; List points; Body(); - + bool ReadIn(std::istream& in); void WriteOut(std::ostream& out); bool ReadInPoints(std::istream& in); @@ -68,7 +66,7 @@ public: Point* GetPoint(int p); void AddJoint(Joint* joint); void AddPoint(Point* point); - + virtual bool ReadInBodyData(std::istream& in) = 0; virtual void WriteOutBodyData(std::ostream& out) = 0; virtual ~Body(); diff --git a/lib/poems/body23joint.cpp b/lib/poems/body23joint.cpp index 8cd0a95bca..7aa761fe2a 100644 --- a/lib/poems/body23joint.cpp +++ b/lib/poems/body23joint.cpp @@ -14,18 +14,18 @@ * 110 8th St. Troy NY 12180 * * CONTACT: anderk5@rpi.edu * *_________________________________________________________________________*/ - +#include #include "body23joint.h" -#include "point.h" -#include "matrixfun.h" #include "body.h" -#include "fastmatrixops.h" -#include "norm.h" +#include "colmatrix.h" #include "eulerparameters.h" -#include "matrices.h" -#include - +#include "fastmatrixops.h" +#include "mat3x3.h" +#include "matrixfun.h" +#include "point.h" +#include "vect3.h" +#include "virtualmatrix.h" Body23Joint::Body23Joint(){ DimQandU(4,2); diff --git a/lib/poems/body23joint.h b/lib/poems/body23joint.h index 60253ac8a4..c47cdfb9de 100644 --- a/lib/poems/body23joint.h +++ b/lib/poems/body23joint.h @@ -18,11 +18,9 @@ #ifndef BODY23JOINT_H #define BODY23JOINT_H +#include #include "joint.h" -#include "vect3.h" -#include "mat3x3.h" - - +#include "matrix.h" class Body23Joint : public Joint { Matrix const_sP; diff --git a/lib/poems/colmatmap.h b/lib/poems/colmatmap.h index 3a6267a247..6d84870046 100644 --- a/lib/poems/colmatmap.h +++ b/lib/poems/colmatmap.h @@ -19,7 +19,10 @@ #ifndef COLMATMAP_H #define COLMATMAP_H +#include + #include "virtualcolmatrix.h" +#include "virtualmatrix.h" class ColMatrix; diff --git a/lib/poems/colmatrix.cpp b/lib/poems/colmatrix.cpp index dc6f49be2b..e7ae98a368 100644 --- a/lib/poems/colmatrix.cpp +++ b/lib/poems/colmatrix.cpp @@ -16,9 +16,8 @@ *_________________________________________________________________________*/ #include "colmatrix.h" -#include "rowmatrix.h" + #include -#include #include using namespace std; diff --git a/lib/poems/colmatrix.h b/lib/poems/colmatrix.h index 11fd85a928..70f13356e2 100644 --- a/lib/poems/colmatrix.h +++ b/lib/poems/colmatrix.h @@ -19,8 +19,9 @@ #ifndef COLMATRIX_H #define COLMATRIX_H +#include #include "virtualcolmatrix.h" -#include "colmatmap.h" +#include "virtualmatrix.h" class Matrix; class Vect6; diff --git a/lib/poems/eulerparameters.cpp b/lib/poems/eulerparameters.cpp index 032bc7da82..f698c40b3a 100644 --- a/lib/poems/eulerparameters.cpp +++ b/lib/poems/eulerparameters.cpp @@ -16,8 +16,12 @@ *_________________________________________________________________________*/ #include "eulerparameters.h" + #include +#include "colmatrix.h" +#include "mat3x3.h" + using namespace std; void EP_Derivatives(ColMatrix& q, ColMatrix& u, ColMatrix& qdot){ diff --git a/lib/poems/eulerparameters.h b/lib/poems/eulerparameters.h index 029ade4b78..2e69a85fb9 100644 --- a/lib/poems/eulerparameters.h +++ b/lib/poems/eulerparameters.h @@ -14,12 +14,12 @@ * 110 8th St. Troy NY 12180 * * CONTACT: anderk5@rpi.edu * *_________________________________________________________________________*/ - + #ifndef EULERPARAMETERS_H #define EULERPARAMETERS_H -#include "colmatrix.h" -#include "mat3x3.h" +class ColMatrix; +class Mat3x3; void EP_Derivatives(ColMatrix& q, ColMatrix& u, ColMatrix& qdot); diff --git a/lib/poems/fastmatrixops.cpp b/lib/poems/fastmatrixops.cpp index 782381a706..e6c81f0659 100644 --- a/lib/poems/fastmatrixops.cpp +++ b/lib/poems/fastmatrixops.cpp @@ -15,10 +15,19 @@ * CONTACT: anderk5@rpi.edu * *_________________________________________________________________________*/ -#include -#include "fastmatrixops.h" #include +#include "fastmatrixops.h" +#include "colmatmap.h" +#include "colmatrix.h" +#include "mat3x3.h" +#include "mat4x4.h" +#include "mat6x6.h" +#include "matrix.h" +#include "vect3.h" +#include "vect4.h" +#include "vect6.h" + using namespace std; // diff --git a/lib/poems/fastmatrixops.h b/lib/poems/fastmatrixops.h index e7ccdbd0ca..b2784a6e53 100644 --- a/lib/poems/fastmatrixops.h +++ b/lib/poems/fastmatrixops.h @@ -17,7 +17,16 @@ #ifndef FASTMATRIXOPS_H #define FASTMATRIXOPS_H -#include "matrices.h" + +class ColMatMap; +class ColMatrix; +class Mat3x3; +class Mat4x4; +class Mat6x6; +class Matrix; +class Vect3; +class Vect4; +class Vect6; void FastCross(Vect3& a, Vect3& b, Vect3& c); void FastSimpleRotation(Vect3& v, double q, Mat3x3& C); diff --git a/lib/poems/fixedpoint.cpp b/lib/poems/fixedpoint.cpp index 8600882393..238ddfed70 100644 --- a/lib/poems/fixedpoint.cpp +++ b/lib/poems/fixedpoint.cpp @@ -17,9 +17,12 @@ #include "fixedpoint.h" + #include #include +#include "virtualmatrix.h" + using namespace std; FixedPoint::FixedPoint(){ diff --git a/lib/poems/fixedpoint.h b/lib/poems/fixedpoint.h index b5ecb23906..fb8f23b0ae 100644 --- a/lib/poems/fixedpoint.h +++ b/lib/poems/fixedpoint.h @@ -19,6 +19,8 @@ #ifndef FIXEDPOINT_H #define FIXEDPOINT_H +#include + #include "point.h" #include "vect3.h" diff --git a/lib/poems/freebodyjoint.cpp b/lib/poems/freebodyjoint.cpp index d00f0bdb98..e6c59340f3 100644 --- a/lib/poems/freebodyjoint.cpp +++ b/lib/poems/freebodyjoint.cpp @@ -16,14 +16,18 @@ *_________________________________________________________________________*/ #include "freebodyjoint.h" -#include "point.h" + +#include + #include "matrixfun.h" #include "body.h" #include "fastmatrixops.h" -#include "norm.h" #include "eulerparameters.h" -#include "matrices.h" -#include +#include "colmatrix.h" +#include "mat3x3.h" +#include "mat6x6.h" +#include "vect3.h" +#include "virtualmatrix.h" FreeBodyJoint::FreeBodyJoint(){ diff --git a/lib/poems/freebodyjoint.h b/lib/poems/freebodyjoint.h index 27cacf7dc6..10574847e1 100644 --- a/lib/poems/freebodyjoint.h +++ b/lib/poems/freebodyjoint.h @@ -18,7 +18,10 @@ #ifndef FREEBODYJOINT_H #define FREEBODYJOINT_H +#include + #include "joint.h" +#include "matrix.h" class FreeBodyJoint : public Joint{ diff --git a/lib/poems/inertialframe.cpp b/lib/poems/inertialframe.cpp index 6c97b2f584..98ec820e7f 100644 --- a/lib/poems/inertialframe.cpp +++ b/lib/poems/inertialframe.cpp @@ -16,7 +16,9 @@ *_________________________________________________________________________*/ #include "inertialframe.h" -#include "fixedpoint.h" + +#include "mat3x3.h" +#include "virtualmatrix.h" using namespace std; diff --git a/lib/poems/inertialframe.h b/lib/poems/inertialframe.h index 08d0279a1e..3620641537 100644 --- a/lib/poems/inertialframe.h +++ b/lib/poems/inertialframe.h @@ -19,7 +19,10 @@ #ifndef INERTIALFRAME_H #define INERTIALFRAME_H +#include + #include "body.h" +#include "vect3.h" class InertialFrame : public Body { diff --git a/lib/poems/joint.cpp b/lib/poems/joint.cpp index 3bdd7b5fcd..ff24d5ebf5 100644 --- a/lib/poems/joint.cpp +++ b/lib/poems/joint.cpp @@ -16,13 +16,24 @@ *_________________________________________________________________________*/ -#include "joints.h" +#include +#include +#include + #include "body.h" #include "point.h" -#include -#include "matrixfun.h" #include "fastmatrixops.h" -#include +#include "body23joint.h" +#include "colmatrix.h" +#include "freebodyjoint.h" +#include "joint.h" +#include "mat3x3.h" +#include "matrix.h" +#include "mixedjoint.h" +#include "prismaticjoint.h" +#include "revolutejoint.h" +#include "sphericaljoint.h" +#include "virtualmatrix.h" using namespace std; diff --git a/lib/poems/joint.h b/lib/poems/joint.h index 17122af775..958805c4b5 100644 --- a/lib/poems/joint.h +++ b/lib/poems/joint.h @@ -18,9 +18,14 @@ #ifndef JOINT_H #define JOINT_H -#include "poemsobject.h" #include -#include "matrices.h" +#include "poemsobject.h" +#include "colmatrix.h" +#include "mat3x3.h" +#include "matrix.h" +#include "vect3.h" + +class VirtualMatrix; enum JointType { XYZJOINT = 0, diff --git a/lib/poems/mat3x3.cpp b/lib/poems/mat3x3.cpp index df24d4b108..3d9f1adcca 100644 --- a/lib/poems/mat3x3.cpp +++ b/lib/poems/mat3x3.cpp @@ -16,8 +16,9 @@ *_________________________________________________________________________*/ -#include "mat3x3.h" #include +#include +#include "mat3x3.h" using namespace std; diff --git a/lib/poems/mat3x3.h b/lib/poems/mat3x3.h index 4362b3ad9c..18abeadddc 100644 --- a/lib/poems/mat3x3.h +++ b/lib/poems/mat3x3.h @@ -18,12 +18,11 @@ #ifndef MAT3X3_H #define MAT3X3_H +#include #include "virtualmatrix.h" - class Vect3; class Mat6x6; -class Matrix; class ColMatrix; class Mat3x3 : public VirtualMatrix { diff --git a/lib/poems/mat4x4.cpp b/lib/poems/mat4x4.cpp index 4a611a6796..a6a587bc03 100644 --- a/lib/poems/mat4x4.cpp +++ b/lib/poems/mat4x4.cpp @@ -16,7 +16,9 @@ *_________________________________________________________________________*/ #include "mat4x4.h" + #include +#include using namespace std; diff --git a/lib/poems/mat4x4.h b/lib/poems/mat4x4.h index d7942b248e..c847f6e0d2 100644 --- a/lib/poems/mat4x4.h +++ b/lib/poems/mat4x4.h @@ -18,11 +18,13 @@ #ifndef MAT4X4_H #define MAT4X4_H +#include + #include "virtualmatrix.h" #include "matrix.h" - class Vect4; +class Matrix; class Mat4x4 : public VirtualMatrix { double elements[4][4]; diff --git a/lib/poems/mat6x6.cpp b/lib/poems/mat6x6.cpp index 16bffc5026..fdc917e03d 100644 --- a/lib/poems/mat6x6.cpp +++ b/lib/poems/mat6x6.cpp @@ -16,7 +16,9 @@ *_________________________________________________________________________*/ #include "mat6x6.h" + #include +#include using namespace std; diff --git a/lib/poems/mat6x6.h b/lib/poems/mat6x6.h index 11951b0442..5eaa4f803b 100644 --- a/lib/poems/mat6x6.h +++ b/lib/poems/mat6x6.h @@ -17,8 +17,9 @@ #ifndef MAT6X6_H #define MAT6X6_H -#include "virtualmatrix.h" +#include +#include "virtualmatrix.h" class Matrix; class Mat3x3; diff --git a/lib/poems/matrix.h b/lib/poems/matrix.h index 63699b9835..8bd8110760 100644 --- a/lib/poems/matrix.h +++ b/lib/poems/matrix.h @@ -18,6 +18,8 @@ #ifndef MATRIX_H #define MATRIX_H +#include + #include "virtualmatrix.h" class Mat3x3; diff --git a/lib/poems/matrixfun.cpp b/lib/poems/matrixfun.cpp index d193114679..99fbae4ca1 100644 --- a/lib/poems/matrixfun.cpp +++ b/lib/poems/matrixfun.cpp @@ -16,9 +16,15 @@ *_________________________________________________________________________*/ #include "matrixfun.h" -#include -#include "fastmatrixops.h" + #include +#include + +#include "fastmatrixops.h" +#include "vect4.h" +#include "virtualcolmatrix.h" +#include "virtualmatrix.h" +#include "virtualrowmatrix.h" using namespace std; diff --git a/lib/poems/matrixfun.h b/lib/poems/matrixfun.h index 600b608ad3..e9721eca7b 100644 --- a/lib/poems/matrixfun.h +++ b/lib/poems/matrixfun.h @@ -14,11 +14,22 @@ * 110 8th St. Troy NY 12180 * * CONTACT: anderk5@rpi.edu * *_________________________________________________________________________*/ - + #ifndef MATRIXFUN_H #define MATRIXFUN_H -#include "matrices.h" +#include "colmatrix.h" +#include "mat3x3.h" +#include "mat4x4.h" +#include "mat6x6.h" +#include "matrix.h" +#include "rowmatrix.h" +#include "vect3.h" +#include "vect6.h" + +class VirtualColMatrix; +class VirtualMatrix; +class VirtualRowMatrix; // Create a Matrix VirtualMatrix* NewMatrix(int type); @@ -70,7 +81,4 @@ Matrix HStack(VirtualMatrix& A, VirtualMatrix& B); void Set6DAngularVector(Vect6& v6, Vect3& v3); void Set6DLinearVector(Vect6& v6, Vect3& v3); - - - #endif diff --git a/lib/poems/mixedjoint.cpp b/lib/poems/mixedjoint.cpp index c834ef621e..ef4ccd25df 100644 --- a/lib/poems/mixedjoint.cpp +++ b/lib/poems/mixedjoint.cpp @@ -16,13 +16,18 @@ *_________________________________________________________________________*/ #include "mixedjoint.h" -#include "point.h" + +#include + #include "matrixfun.h" #include "body.h" #include "fastmatrixops.h" -#include "norm.h" #include "eulerparameters.h" -#include "matrices.h" +#include "colmatrix.h" +#include "mat3x3.h" +#include "mat6x6.h" +#include "vect3.h" +#include "virtualmatrix.h" diff --git a/lib/poems/mixedjoint.h b/lib/poems/mixedjoint.h index 5f59b95f09..417f689523 100644 --- a/lib/poems/mixedjoint.h +++ b/lib/poems/mixedjoint.h @@ -18,7 +18,11 @@ #ifndef MIXEDJOINT_H #define MIXEDJOINT_H +#include + #include "joint.h" +#include "matrix.h" +#include "vect6.h" class MixedJoint : public Joint{ diff --git a/lib/poems/norm.cpp b/lib/poems/norm.cpp index 0f918cf968..6b8a56fa29 100644 --- a/lib/poems/norm.cpp +++ b/lib/poems/norm.cpp @@ -16,7 +16,13 @@ *_________________________________________________________________________*/ #include + #include "norm.h" +#include "colmatrix.h" +#include "rowmatrix.h" +#include "vect3.h" +#include "vect4.h" +#include "vect6.h" double Magnitude(ColMatrix& A){ double G; diff --git a/lib/poems/norm.h b/lib/poems/norm.h index 963a2ec5b2..b3ff285dea 100644 --- a/lib/poems/norm.h +++ b/lib/poems/norm.h @@ -18,8 +18,11 @@ #ifndef NORM_H #define NORM_H -#include "matrices.h" - +class ColMatrix; +class RowMatrix; +class Vect3; +class Vect4; +class Vect6; double Magnitude(ColMatrix& A); double Magnitude(RowMatrix& A); diff --git a/lib/poems/onbody.cpp b/lib/poems/onbody.cpp index 102900df8d..bf843be161 100644 --- a/lib/poems/onbody.cpp +++ b/lib/poems/onbody.cpp @@ -16,15 +16,18 @@ *_________________________________________________________________________*/ #include "onbody.h" + +#include +#include + #include "body.h" #include "inertialframe.h" #include "joint.h" #include "onfunctions.h" #include "virtualmatrix.h" #include "matrixfun.h" -#include -#include "norm.h" #include "eulerparameters.h" +#include "colmatrix.h" using namespace std; diff --git a/lib/poems/onbody.h b/lib/poems/onbody.h index d9923773c7..20190dfee8 100644 --- a/lib/poems/onbody.h +++ b/lib/poems/onbody.h @@ -22,6 +22,13 @@ #include "matrix.h" #include "vect6.h" #include "mat6x6.h" +#include "joint.h" +#include "mat3x3.h" +#include "vect3.h" + +class Body; +class ColMatrix; +class InertialFrame; // emumerated type enum Direction { @@ -29,11 +36,6 @@ enum Direction { FORWARD= 1 }; -class Body; -class InertialFrame; -class Joint; -class OnSolver; - class OnBody { Body* system_body; Joint* system_joint; diff --git a/lib/poems/onfunctions.cpp b/lib/poems/onfunctions.cpp index 582ab8cf8b..1d91dbf378 100644 --- a/lib/poems/onfunctions.cpp +++ b/lib/poems/onfunctions.cpp @@ -17,8 +17,13 @@ #include "onfunctions.h" -#include "matrixfun.h" -#include + +#include "mat3x3.h" +#include "mat6x6.h" +#include "vect3.h" +#include "vect6.h" +#include "virtualmatrix.h" + using namespace std; // friend of Vect3 & Vect6 diff --git a/lib/poems/onfunctions.h b/lib/poems/onfunctions.h index 8a69694095..42d0f4ac1c 100644 --- a/lib/poems/onfunctions.h +++ b/lib/poems/onfunctions.h @@ -18,7 +18,10 @@ #ifndef ONFUNCTIONS_H #define ONFUNCTIONS_H -#include "matrices.h" +class Mat3x3; +class Mat6x6; +class Vect3; +class Vect6; void OnPopulateSVect(Vect3& angular, Vect3& linear, Vect6& sV); void OnPopulateSC(Vect3& gamma, Mat3x3& C, Mat6x6& SC); diff --git a/lib/poems/onsolver.cpp b/lib/poems/onsolver.cpp index ad04d7e9e3..dd94c9c7ad 100644 --- a/lib/poems/onsolver.cpp +++ b/lib/poems/onsolver.cpp @@ -16,13 +16,21 @@ *_________________________________________________________________________*/ +#include +#include + #include "onsolver.h" #include "system.h" #include "onbody.h" #include "body.h" -#include "matrixfun.h" -#include - +#include "colmatmap.h" +#include "colmatrix.h" +#include "defines.h" +#include "inertialframe.h" +#include "matrix.h" +#include "poemslist.h" +#include "vect3.h" +#include "virtualmatrix.h" using namespace std; diff --git a/lib/poems/onsolver.h b/lib/poems/onsolver.h index f32b5880a9..b4bbd5e25d 100644 --- a/lib/poems/onsolver.h +++ b/lib/poems/onsolver.h @@ -21,7 +21,9 @@ #include "solver.h" #include "onbody.h" -#include + +class ColMatrix; +class Matrix; diff --git a/lib/poems/particle.cpp b/lib/poems/particle.cpp index 3496bc1906..0d953e00f6 100644 --- a/lib/poems/particle.cpp +++ b/lib/poems/particle.cpp @@ -17,7 +17,6 @@ #include "particle.h" -#include "fixedpoint.h" Particle::Particle(){ } diff --git a/lib/poems/particle.h b/lib/poems/particle.h index 20aa4831ea..0f13252f99 100644 --- a/lib/poems/particle.h +++ b/lib/poems/particle.h @@ -19,6 +19,8 @@ #ifndef PARTICLE_H #define PARTICLE_H +#include + #include "body.h" diff --git a/lib/poems/poemstreenode.h b/lib/poems/poemstreenode.h index b8f46031a5..e22bd9b97d 100644 --- a/lib/poems/poemstreenode.h +++ b/lib/poems/poemstreenode.h @@ -18,12 +18,6 @@ #ifndef TREENODE_H #define TREENODE_H -//#define NULL 0 - - -//Tree depends on TreeNode -class Tree; - // declares a tree node object for a binary tree class TreeNode{ diff --git a/lib/poems/point.cpp b/lib/poems/point.cpp index 4383844736..d7eed94efd 100644 --- a/lib/poems/point.cpp +++ b/lib/poems/point.cpp @@ -16,7 +16,9 @@ *_________________________________________________________________________*/ -#include "points.h" +#include "fixedpoint.h" +#include "point.h" +#include "vect3.h" Point::Point(){ position.Zeros(); diff --git a/lib/poems/prismaticjoint.cpp b/lib/poems/prismaticjoint.cpp index 7c01667a86..c7d4bed568 100644 --- a/lib/poems/prismaticjoint.cpp +++ b/lib/poems/prismaticjoint.cpp @@ -16,10 +16,14 @@ *_________________________________________________________________________*/ #include "prismaticjoint.h" + #include "point.h" #include "matrixfun.h" #include "body.h" #include "fastmatrixops.h" +#include "colmatrix.h" +#include "mat3x3.h" +#include "virtualmatrix.h" PrismaticJoint::PrismaticJoint(){ q.Dim(1); diff --git a/lib/poems/prismaticjoint.h b/lib/poems/prismaticjoint.h index 17cf050a78..c17be350cb 100644 --- a/lib/poems/prismaticjoint.h +++ b/lib/poems/prismaticjoint.h @@ -18,9 +18,11 @@ #ifndef PRISMATICJOINT_H #define PRISMATICJOINT_H +#include + #include "joint.h" #include "vect3.h" -#include "mat3x3.h" +#include "matrix.h" diff --git a/lib/poems/revolutejoint.cpp b/lib/poems/revolutejoint.cpp index ec5b1bec02..955a2f0dea 100644 --- a/lib/poems/revolutejoint.cpp +++ b/lib/poems/revolutejoint.cpp @@ -16,10 +16,14 @@ *_________________________________________________________________________*/ #include "revolutejoint.h" + #include "point.h" #include "matrixfun.h" #include "body.h" #include "fastmatrixops.h" +#include "colmatrix.h" +#include "mat3x3.h" +#include "virtualmatrix.h" RevoluteJoint::RevoluteJoint(){ DimQandU(1); diff --git a/lib/poems/revolutejoint.h b/lib/poems/revolutejoint.h index 478d48dbb9..ac1c06d5c5 100644 --- a/lib/poems/revolutejoint.h +++ b/lib/poems/revolutejoint.h @@ -18,11 +18,12 @@ #ifndef REVOLUTEJOINT_H #define REVOLUTEJOINT_H +#include #include "joint.h" #include "vect3.h" -#include "mat3x3.h" - +#include "matrix.h" +class VirtualMatrix; class RevoluteJoint : public Joint { Vect3 axis_pk; // unit vector in body1 basis diff --git a/lib/poems/rigidbody.cpp b/lib/poems/rigidbody.cpp index 3ac424f9e9..53acfa8bd4 100644 --- a/lib/poems/rigidbody.cpp +++ b/lib/poems/rigidbody.cpp @@ -16,7 +16,8 @@ *_________________________________________________________________________*/ #include "rigidbody.h" -#include "fixedpoint.h" +#include "mat3x3.h" +#include "virtualmatrix.h" using namespace std; diff --git a/lib/poems/rigidbody.h b/lib/poems/rigidbody.h index 0bb2a3ece2..2f4430e264 100644 --- a/lib/poems/rigidbody.h +++ b/lib/poems/rigidbody.h @@ -18,6 +18,8 @@ #ifndef RIGIDBODY_H #define RIGIDBODY_H +#include + #include "body.h" class RigidBody : public Body { diff --git a/lib/poems/rowmatrix.cpp b/lib/poems/rowmatrix.cpp index feb185070e..9fa57e773f 100644 --- a/lib/poems/rowmatrix.cpp +++ b/lib/poems/rowmatrix.cpp @@ -16,7 +16,7 @@ *_________________________________________________________________________*/ #include "rowmatrix.h" -#include "colmatrix.h" + #include #include diff --git a/lib/poems/rowmatrix.h b/lib/poems/rowmatrix.h index b04113e8ed..1dbb3d11e0 100644 --- a/lib/poems/rowmatrix.h +++ b/lib/poems/rowmatrix.h @@ -19,7 +19,10 @@ #ifndef ROWMATRIX_H #define ROWMATRIX_H +#include + #include "virtualrowmatrix.h" +#include "virtualmatrix.h" class RowMatrix : public VirtualRowMatrix { double* elements; diff --git a/lib/poems/solver.cpp b/lib/poems/solver.cpp index 67f5b607e3..9d2245149f 100644 --- a/lib/poems/solver.cpp +++ b/lib/poems/solver.cpp @@ -15,9 +15,10 @@ * CONTACT: anderk5@rpi.edu * *_________________________________________________________________________*/ +#include #include "solver.h" #include "system.h" -#include "matrices.h" +#include "onsolver.h" Solver::Solver(){ diff --git a/lib/poems/solver.h b/lib/poems/solver.h index 45564dd1ef..6a2debf497 100644 --- a/lib/poems/solver.h +++ b/lib/poems/solver.h @@ -17,12 +17,12 @@ #ifndef SOLVER_H #define SOLVER_H -#include + #include "colmatmap.h" -#include "matrices.h" #include "defines.h" class System; +class Matrix; class Solver{ protected: diff --git a/lib/poems/sphericaljoint.cpp b/lib/poems/sphericaljoint.cpp index fb5330db17..cba6d00a6e 100644 --- a/lib/poems/sphericaljoint.cpp +++ b/lib/poems/sphericaljoint.cpp @@ -17,14 +17,18 @@ #include "sphericaljoint.h" + +#include + #include "point.h" #include "matrixfun.h" #include "body.h" #include "fastmatrixops.h" -#include "norm.h" #include "eulerparameters.h" -#include "matrices.h" -#include +#include "colmatrix.h" +#include "mat3x3.h" +#include "vect3.h" +#include "virtualmatrix.h" SphericalJoint::SphericalJoint(){ diff --git a/lib/poems/sphericaljoint.h b/lib/poems/sphericaljoint.h index ef29f8e38e..90f1547873 100644 --- a/lib/poems/sphericaljoint.h +++ b/lib/poems/sphericaljoint.h @@ -18,11 +18,9 @@ #ifndef SPHERICALJOINT_H #define SPHERICALJOINT_H +#include #include "joint.h" -#include "vect3.h" -#include "mat3x3.h" - - +#include "matrix.h" class SphericalJoint : public Joint { Matrix const_sP; diff --git a/lib/poems/system.cpp b/lib/poems/system.cpp index 369213f7d0..1ac9ce1236 100644 --- a/lib/poems/system.cpp +++ b/lib/poems/system.cpp @@ -17,9 +17,26 @@ #include "system.h" + +#include +#include + #include "body.h" #include "joint.h" -#include +#include "colmatrix.h" +#include "eulerparameters.h" +#include "fixedpoint.h" +#include "freebodyjoint.h" +#include "inertialframe.h" +#include "mat3x3.h" +#include "matrix.h" +#include "matrixfun.h" +#include "rigidbody.h" +#include "sphericaljoint.h" +#include "vect3.h" +#include "virtualmatrix.h" + +class Point; System::System(){ diff --git a/lib/poems/system.h b/lib/poems/system.h index 1b59395de7..e5ce27194b 100644 --- a/lib/poems/system.h +++ b/lib/poems/system.h @@ -15,35 +15,12 @@ * CONTACT: anderk5@rpi.edu * *_________________________________________________________________________*/ - + #ifndef SYSTEM_H #define SYSTEM_H - #include -#include -#include -#include -#include - #include "poemslist.h" -#include "matrices.h" -#include "workspace.h" -#include "matrixfun.h" -#include "onsolver.h" -#include "system.h" -#include "inertialframe.h" -#include "rigidbody.h" -#include "revolutejoint.h" -#include "fixedpoint.h" -#include "freebodyjoint.h" -#include "sphericaljoint.h" -#include "body23joint.h" -#include "mixedjoint.h" -#include "eulerparameters.h" -#include "matrices.h" -#include "norm.h" - class Body; class Joint; diff --git a/lib/poems/vect3.cpp b/lib/poems/vect3.cpp index 03c5d7bc00..7ce3230238 100644 --- a/lib/poems/vect3.cpp +++ b/lib/poems/vect3.cpp @@ -16,7 +16,9 @@ *_________________________________________________________________________*/ #include "vect3.h" + #include +#include using namespace std; @@ -141,6 +143,13 @@ Vect3& Vect3::operator+=(const Vect3& A){ return *this; } +Vect3& Vect3::operator-(){ + elements[0] = -elements[0]; + elements[1] = -elements[1]; + elements[2] = -elements[2]; + return *this; +} + Vect3& Vect3::operator-=(const Vect3& A){ elements[0] -= A.elements[0]; elements[1] -= A.elements[1]; diff --git a/lib/poems/vect3.h b/lib/poems/vect3.h index ababe18e51..a28832db6c 100644 --- a/lib/poems/vect3.h +++ b/lib/poems/vect3.h @@ -18,7 +18,10 @@ #ifndef VECT3_H #define VECT3_H +#include + #include "virtualcolmatrix.h" +#include "virtualmatrix.h" class Matrix; class Mat3x3; @@ -52,6 +55,7 @@ public: Vect3& operator*=(double b); Vect3& operator+=(const Vect3& A); Vect3& operator-=(const Vect3& A); + Vect3& operator-(); friend Matrix T(const Vect3& A); // a wasteful transpose friend Mat3x3 CrossMat(Vect3& a); // a wasteful cross matrix implementation diff --git a/lib/poems/vect4.cpp b/lib/poems/vect4.cpp index 3b5afddc50..b045998017 100644 --- a/lib/poems/vect4.cpp +++ b/lib/poems/vect4.cpp @@ -16,7 +16,9 @@ *_________________________________________________________________________*/ #include "vect4.h" + #include +#include using namespace std; diff --git a/lib/poems/vect4.h b/lib/poems/vect4.h index 695f5e158a..0b28994043 100644 --- a/lib/poems/vect4.h +++ b/lib/poems/vect4.h @@ -18,8 +18,10 @@ #ifndef VECT4_H #define VECT4_H -#include "virtualcolmatrix.h" +#include +#include "virtualcolmatrix.h" +#include "virtualmatrix.h" class Matrix; class Mat4x4; diff --git a/lib/poems/vect6.cpp b/lib/poems/vect6.cpp index eb65d24f16..5baadafc34 100644 --- a/lib/poems/vect6.cpp +++ b/lib/poems/vect6.cpp @@ -16,7 +16,9 @@ *_________________________________________________________________________*/ #include "vect6.h" + #include +#include using namespace std; diff --git a/lib/poems/vect6.h b/lib/poems/vect6.h index c346c852ef..8047c1bbf8 100644 --- a/lib/poems/vect6.h +++ b/lib/poems/vect6.h @@ -18,7 +18,10 @@ #ifndef VECT6_H #define VECT6_H +#include + #include "virtualcolmatrix.h" +#include "virtualmatrix.h" class Matrix; class Mat6x6; diff --git a/lib/poems/workspace.cpp b/lib/poems/workspace.cpp index 2b3257b0dd..29a1c95832 100644 --- a/lib/poems/workspace.cpp +++ b/lib/poems/workspace.cpp @@ -15,15 +15,26 @@ * CONTACT: anderk5@rpi.edu * *_________________________________________________________________________*/ +#include +#include // IWYU pragma: keep +#include #include "workspace.h" #include "system.h" #include "solver.h" #include "SystemProcessor.h" -#include -#include -#include -#include +#include "POEMSChain.h" +#include "body.h" +#include "colmatmap.h" +#include "colmatrix.h" +#include "defines.h" +#include "joint.h" +#include "mat3x3.h" +#include "matrix.h" +#include "matrixfun.h" +#include "poemslist.h" +#include "vect3.h" +#include "virtualmatrix.h" using namespace std; diff --git a/lib/poems/workspace.h b/lib/poems/workspace.h index 5faaf904dc..6213815d81 100644 --- a/lib/poems/workspace.h +++ b/lib/poems/workspace.h @@ -19,15 +19,6 @@ #ifndef WORKSPACE_H #define WORKSPACE_H -#include "matrices.h" -#include -#include -#include -#include -#include -#include - - class System; class Solver; -- GitLab From e9e7d995b270fd4abf7041474fd0c667453f4e99 Mon Sep 17 00:00:00 2001 From: Rupert Nash Date: Mon, 1 Jul 2019 11:37:13 +0100 Subject: [PATCH 145/469] move to user-misc --- src/USER-MISC/README | 1 + src/{ => USER-MISC}/compute_momentum.cpp | 0 src/{ => USER-MISC}/compute_momentum.h | 0 3 files changed, 1 insertion(+) rename src/{ => USER-MISC}/compute_momentum.cpp (100%) rename src/{ => USER-MISC}/compute_momentum.h (100%) diff --git a/src/USER-MISC/README b/src/USER-MISC/README index 219e19673d..7c48640e2a 100644 --- a/src/USER-MISC/README +++ b/src/USER-MISC/README @@ -31,6 +31,7 @@ compute basal/atom, Christopher Barrett, cdb333 at cavs.msstate.edu, 3 Mar 2013 compute cnp/atom, Paulo Branicio (USC), branicio at usc.edu, 31 May 2017 compute entropy/atom, Pablo Piaggi (EPFL), pablo.piaggi at epfl.ch, 15 June 2018 compute pressure/cylinder, Cody K. Addington (NCSU), , 2 Oct 2018 +compute momentum, Rupert Nash (University of Edinburgh), r.nash at epcc.ed.ac.uk, 28 June 2019 compute stress/mop, Romain Vermorel (U Pau) & Laurent Joly (U Lyon), romain.vermorel at univ-pau.fr & ljoly.ulyon at gmail.com, 5 Sep 18 compute stress/mop/profile, Romain Vermorel (U Pau) & Laurent Joly (U Lyon), romain.vermorel at univ-pau.fr & ljoly.ulyon at gmail.com, 5 Sep 18 compute temp/rotate, Laurent Joly (U Lyon), ljoly.ulyon at gmail.com, 8 Aug 11 diff --git a/src/compute_momentum.cpp b/src/USER-MISC/compute_momentum.cpp similarity index 100% rename from src/compute_momentum.cpp rename to src/USER-MISC/compute_momentum.cpp diff --git a/src/compute_momentum.h b/src/USER-MISC/compute_momentum.h similarity index 100% rename from src/compute_momentum.h rename to src/USER-MISC/compute_momentum.h -- GitLab From fb5e7e6f3badd73feb79768d6f4dbd0ed0c1c2de Mon Sep 17 00:00:00 2001 From: Rupert Nash Date: Mon, 1 Jul 2019 12:06:40 +0100 Subject: [PATCH 146/469] add note about USER-MISC package --- doc/src/compute_momentum.txt | 8 ++++++-- 1 file changed, 6 insertions(+), 2 deletions(-) diff --git a/doc/src/compute_momentum.txt b/doc/src/compute_momentum.txt index 4db171d42d..fc5243583e 100644 --- a/doc/src/compute_momentum.txt +++ b/doc/src/compute_momentum.txt @@ -36,9 +36,13 @@ output"_Howto_output.html doc page for an overview of LAMMPS output options. The vector value calculated by this compute is "extensive". The vector -value will be in momentum "units"_units.html. +value will be in mass*velocity "units"_units.html. -[Restrictions:] none +[Restrictions:] + +This compute is part of the USER-MISC package. It is only enabled if +LAMMPS was built with that package. See the "Build +package"_Build_package.html doc page for more info. [Related commands:] -- GitLab From 32728375b97714dbbe42e68fc2c14b5a0c770aa8 Mon Sep 17 00:00:00 2001 From: Rupert Nash Date: Mon, 1 Jul 2019 13:39:32 +0100 Subject: [PATCH 147/469] add test script for compute momentum --- examples/USER/misc/momentum/in.momentum | 65 +++++++++++++++++++++++++ 1 file changed, 65 insertions(+) create mode 100644 examples/USER/misc/momentum/in.momentum diff --git a/examples/USER/misc/momentum/in.momentum b/examples/USER/misc/momentum/in.momentum new file mode 100644 index 0000000000..5adcbfeff6 --- /dev/null +++ b/examples/USER/misc/momentum/in.momentum @@ -0,0 +1,65 @@ +# Test compute momentum with by comparing it's output with compute reduce + +# Script will output the two computations of the total momentum as +# thermo vars - they should be identical + +# 3D LJ Poiseuille flow simulation +dimension 3 +boundary p p p + +atom_style atomic +neighbor 0.3 bin +neigh_modify delay 5 + +# create geometry +lattice hcp 0.5 +region box block 0 20 0 10 0 10 +create_box 3 box +create_atoms 1 box + +mass 1 1.0 +mass 2 1.0 +mass 3 1.0 + +# LJ potentials +pair_style lj/cut 1.0 +pair_coeff * * 1.0 1.0 1.0 + +# define groups +region 1 block INF INF INF 1.0 INF INF +group lower region 1 +region 2 block INF INF 9.0 INF INF INF +group upper region 2 +group boundary union lower upper +group liquid subtract all boundary + +set group lower type 2 +set group upper type 3 + +# temperature settings +compute mobile liquid temp +velocity liquid create 1.0 100 temp mobile +fix 1 all nve +fix 2 liquid temp/rescale 200 1.0 2.0 0.02 1.0 +fix_modify 2 temp mobile + +velocity boundary set 0.0 0.0 0.0 +fix 4 lower setforce 0.0 0.0 0.0 +fix 5 upper setforce 0.0 0.0 0.0 +fix 6 liquid addforce 0.1 0.0 0.0 + +# Compute total momentum +compute mom liquid momentum + +# Comparison (momentum variables + compute reduce) +variable mx atom mass*vx +variable my atom mass*vy +variable mz atom mass*vz +compute mom_red liquid reduce sum v_mx v_my v_mz + +# Run +timestep 0.003 +thermo 1000 +thermo_style custom step c_mom_red[*] c_mom[*] + +run 100000 -- GitLab From 2443c8ad13ac452bcea30a3895f55394d89186ca Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Mon, 1 Jul 2019 09:14:22 -0400 Subject: [PATCH 148/469] reduce IWYU warnings for lammps.cpp --- src/lammps.cpp | 28 ++++++++++++++-------------- 1 file changed, 14 insertions(+), 14 deletions(-) diff --git a/src/lammps.cpp b/src/lammps.cpp index 052d14dfed..f8e7dceb89 100644 --- a/src/lammps.cpp +++ b/src/lammps.cpp @@ -19,20 +19,20 @@ #include #include #include "lammps.h" -#include "style_angle.h" -#include "style_atom.h" -#include "style_bond.h" -#include "style_command.h" -#include "style_compute.h" -#include "style_dihedral.h" -#include "style_dump.h" -#include "style_fix.h" -#include "style_improper.h" -#include "style_integrate.h" -#include "style_kspace.h" -#include "style_minimize.h" -#include "style_pair.h" -#include "style_region.h" +#include "style_angle.h" // IWYU pragma: keep +#include "style_atom.h" // IWYU pragma: keep +#include "style_bond.h" // IWYU pragma: keep +#include "style_command.h" // IWYU pragma: keep +#include "style_compute.h" // IWYU pragma: keep +#include "style_dihedral.h" // IWYU pragma: keep +#include "style_dump.h" // IWYU pragma: keep +#include "style_fix.h" // IWYU pragma: keep +#include "style_improper.h" // IWYU pragma: keep +#include "style_integrate.h" // IWYU pragma: keep +#include "style_kspace.h" // IWYU pragma: keep +#include "style_minimize.h" // IWYU pragma: keep +#include "style_pair.h" // IWYU pragma: keep +#include "style_region.h" // IWYU pragma: keep #include "universe.h" #include "input.h" #include "info.h" -- GitLab From e91539d4b52706bd16c5f22e5e3a8b719aa23bae Mon Sep 17 00:00:00 2001 From: Stan Moore Date: Fri, 28 Jun 2019 12:25:48 -0600 Subject: [PATCH 149/469] Cleanup --- src/KOKKOS/pair_snap_kokkos_impl.h | 2 +- src/KOKKOS/sna_kokkos_impl.h | 6 +----- 2 files changed, 2 insertions(+), 6 deletions(-) diff --git a/src/KOKKOS/pair_snap_kokkos_impl.h b/src/KOKKOS/pair_snap_kokkos_impl.h index 20e04605ce..8d72d1fac4 100644 --- a/src/KOKKOS/pair_snap_kokkos_impl.h +++ b/src/KOKKOS/pair_snap_kokkos_impl.h @@ -200,7 +200,7 @@ void PairSNAPKokkos::compute(int eflag_in, int vflag_in) team_size = 1; #endif - if (beta_max < list->inum) { // TODO: no init + if (beta_max < list->inum) { d_beta = Kokkos::View("PairSNAPKokkos:beta", list->inum,ncoeff); d_bispectrum = Kokkos::View("PairSNAPKokkos:bispectrum", diff --git a/src/KOKKOS/sna_kokkos_impl.h b/src/KOKKOS/sna_kokkos_impl.h index 8cbb3eb3f6..f0d45cb5c2 100644 --- a/src/KOKKOS/sna_kokkos_impl.h +++ b/src/KOKKOS/sna_kokkos_impl.h @@ -475,7 +475,6 @@ void SNAKokkos::compute_deidrj(const typename Kokkos::TeamPolicy sum; - // TODO: which loop is faster to parallelize? Kokkos::parallel_reduce(Kokkos::ThreadVectorRange(team,twojmax+1), [&] (const int& j, t_scalar3& sum_tmp) { //for(int j = 0; j <= twojmax; j++) { @@ -632,9 +631,6 @@ void SNAKokkos::compute_dbidrj(const typename Kokkos::TeamPolicy::compute_duarray(const typename Kokkos::TeamPolicy Date: Mon, 1 Jul 2019 08:07:26 -0600 Subject: [PATCH 150/469] Remove temporary ulist variable --- src/SNAP/sna.cpp | 19 ++++++++----------- src/SNAP/sna.h | 3 +-- 2 files changed, 9 insertions(+), 13 deletions(-) diff --git a/src/SNAP/sna.cpp b/src/SNAP/sna.cpp index f9696e1f12..6871bb5573 100644 --- a/src/SNAP/sna.cpp +++ b/src/SNAP/sna.cpp @@ -341,7 +341,7 @@ void SNA::compute_ui(int jnum) // theta0 = (r - rmin0) * rscale0; z0 = r / tan(theta0); - compute_uarray(x, y, z, z0, r); + compute_uarray(x, y, z, z0, r, j); add_uarraytot(r, wj[j], rcutij[j], j); } @@ -895,8 +895,8 @@ void SNA::add_uarraytot(double r, double wj, double rcut, int jj) sfac *= wj; - double* ulist_r_j = ulist_r_ij[jj]; - double* ulist_i_j = ulist_i_ij[jj]; + double* ulist_r = ulist_r_ij[jj]; + double* ulist_i = ulist_i_ij[jj]; for (int j = 0; j <= twojmax; j++) { int jju = idxu_block[j]; @@ -906,9 +906,6 @@ void SNA::add_uarraytot(double r, double wj, double rcut, int jj) sfac * ulist_r[jju]; ulisttot_i[jju] += sfac * ulist_i[jju]; - - ulist_r_j[jju] = ulist_r[jju]; - ulist_i_j[jju] = ulist_i[jju]; jju++; } } @@ -919,7 +916,7 @@ void SNA::add_uarraytot(double r, double wj, double rcut, int jj) ------------------------------------------------------------------------- */ void SNA::compute_uarray(double x, double y, double z, - double z0, double r) + double z0, double r, int jj) { double r0inv; double a_r, b_r, a_i, b_i; @@ -935,6 +932,10 @@ void SNA::compute_uarray(double x, double y, double z, // VMK Section 4.8.2 + + double* ulist_r = ulist_r_ij[jj]; + double* ulist_i = ulist_i_ij[jj]; + ulist_r[0] = 1.0; ulist_i[0] = 0.0; @@ -1208,8 +1209,6 @@ void SNA::create_twojmax_arrays() memory->create(rootpqarray, jdimpq, jdimpq, "sna:rootpqarray"); memory->create(cglist, idxcg_max, "sna:cglist"); - memory->create(ulist_r, idxu_max, "sna:ulist"); - memory->create(ulist_i, idxu_max, "sna:ulist"); memory->create(ulisttot_r, idxu_max, "sna:ulisttot"); memory->create(ulisttot_i, idxu_max, "sna:ulisttot"); memory->create(dulist_r, idxu_max, 3, "sna:dulist"); @@ -1234,8 +1233,6 @@ void SNA::destroy_twojmax_arrays() { memory->destroy(rootpqarray); memory->destroy(cglist); - memory->destroy(ulist_r); - memory->destroy(ulist_i); memory->destroy(ulisttot_r); memory->destroy(ulisttot_i); memory->destroy(dulist_r); diff --git a/src/SNAP/sna.h b/src/SNAP/sna.h index 81582cf9e5..e6bf4e3f9e 100644 --- a/src/SNAP/sna.h +++ b/src/SNAP/sna.h @@ -85,7 +85,6 @@ private: int*** idxcg_block; double* ulisttot_r, * ulisttot_i; - double* ulist_r, * ulist_i; double** ulist_r_ij, ** ulist_i_ij; int* idxu_block; @@ -109,7 +108,7 @@ private: void addself_uarraytot(double); void add_uarraytot(double, double, double, int); void compute_uarray(double, double, double, - double, double); + double, double, int); double deltacg(int, int, int); int compute_ncoeff(); void compute_duarray(double, double, double, -- GitLab From 559c187964622098a5eaa2e79d970e414eb6fa72 Mon Sep 17 00:00:00 2001 From: Stan Moore Date: Mon, 1 Jul 2019 08:20:48 -0600 Subject: [PATCH 151/469] Update SNA::memory_usage() --- src/SNAP/sna.cpp | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/SNAP/sna.cpp b/src/SNAP/sna.cpp index 6871bb5573..985110bdee 100644 --- a/src/SNAP/sna.cpp +++ b/src/SNAP/sna.cpp @@ -1175,7 +1175,7 @@ double SNA::memory_usage() bytes += jdimpq*jdimpq * sizeof(double); // pqarray bytes += idxcg_max * sizeof(double); // cglist - bytes += idxu_max * sizeof(double) * 2; // ulist + bytes += nmax * idxu_max * sizeof(double) * 2; // ulist_ij bytes += idxu_max * sizeof(double) * 2; // ulisttot bytes += idxu_max * 3 * sizeof(double) * 2; // dulist -- GitLab From 42c31227d9635de1da42550c8458aca622195a7a Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Mon, 1 Jul 2019 14:31:41 -0400 Subject: [PATCH 152/469] continuing to clean up include file lists --- lib/poems/mat4x4.h | 2 -- src/KSPACE/pair_buck_coul_long.cpp | 3 +-- src/KSPACE/pair_buck_long_coul_long.cpp | 4 +--- src/MC/fix_bond_swap.cpp | 3 +-- src/MC/fix_bond_swap.h | 1 - src/MC/fix_gcmc.cpp | 7 ++----- src/PYTHON/fix_python_invoke.cpp | 3 --- src/PYTHON/fix_python_move.cpp | 7 ------- src/PYTHON/pair_python.cpp | 2 -- src/PYTHON/python_impl.cpp | 3 ++- src/PYTHON/python_impl.h | 1 + src/RIGID/fix_rigid_nh.cpp | 3 +-- src/RIGID/fix_rigid_nph_small.cpp | 1 - src/RIGID/fix_rigid_npt.cpp | 1 - src/RIGID/fix_rigid_npt_small.cpp | 1 - src/RIGID/fix_rigid_small.cpp | 4 ++-- src/imbalance_store.cpp | 1 - src/imbalance_time.cpp | 1 - src/lmppython.cpp | 4 ++++ src/lmppython.h | 5 ----- src/math_special.cpp | 2 +- src/min_linesearch.cpp | 1 - src/neigh_list.cpp | 2 +- src/npair_full_bin_ghost.cpp | 1 - src/npair_full_multi.cpp | 1 - src/npair_full_nsq.cpp | 1 - src/npair_full_nsq_ghost.cpp | 1 - src/npair_half_bin_atomonly_newton.cpp | 3 --- src/npair_half_bin_newtoff.cpp | 1 - src/npair_half_bin_newtoff_ghost.cpp | 1 - src/npair_half_bin_newton.cpp | 1 - src/npair_half_bin_newton_tri.cpp | 1 - src/npair_half_multi_newtoff.cpp | 1 - src/npair_half_multi_newton.cpp | 1 - src/npair_half_multi_newton_tri.cpp | 1 - src/npair_half_nsq_newtoff.cpp | 1 - src/npair_half_nsq_newtoff_ghost.cpp | 1 - src/npair_half_nsq_newton.cpp | 1 - src/npair_half_respa_bin_newtoff.cpp | 1 - src/npair_half_respa_bin_newton.cpp | 1 - src/npair_half_respa_bin_newton_tri.cpp | 1 - src/npair_half_respa_nsq_newtoff.cpp | 1 - src/npair_half_respa_nsq_newton.cpp | 1 - src/npair_half_size_bin_newtoff.cpp | 2 -- src/npair_half_size_bin_newton.cpp | 2 -- src/npair_half_size_bin_newton_tri.cpp | 2 -- src/npair_half_size_nsq_newtoff.cpp | 2 -- src/npair_half_size_nsq_newton.cpp | 2 -- src/npair_halffull_newtoff.cpp | 4 ---- src/npair_halffull_newton.cpp | 3 --- src/npair_skip.cpp | 3 --- src/pair_buck_coul_cut.cpp | 3 +-- src/pair_coul_cut.cpp | 3 +-- src/pointers.h | 1 + src/variable.cpp | 2 +- 55 files changed, 21 insertions(+), 92 deletions(-) diff --git a/lib/poems/mat4x4.h b/lib/poems/mat4x4.h index c847f6e0d2..a6ae232473 100644 --- a/lib/poems/mat4x4.h +++ b/lib/poems/mat4x4.h @@ -19,9 +19,7 @@ #define MAT4X4_H #include - #include "virtualmatrix.h" -#include "matrix.h" class Vect4; class Matrix; diff --git a/src/KSPACE/pair_buck_coul_long.cpp b/src/KSPACE/pair_buck_coul_long.cpp index 0a1ec88da5..a5427965dc 100644 --- a/src/KSPACE/pair_buck_coul_long.cpp +++ b/src/KSPACE/pair_buck_coul_long.cpp @@ -11,9 +11,8 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ +#include #include -#include -#include #include #include "pair_buck_coul_long.h" #include "atom.h" diff --git a/src/KSPACE/pair_buck_long_coul_long.cpp b/src/KSPACE/pair_buck_long_coul_long.cpp index c7a4a4b2f6..bcd290891e 100644 --- a/src/KSPACE/pair_buck_long_coul_long.cpp +++ b/src/KSPACE/pair_buck_long_coul_long.cpp @@ -15,9 +15,8 @@ Contributing author: Pieter J. in 't Veld (SNL) ------------------------------------------------------------------------- */ +#include #include -#include -#include #include #include "math_vector.h" #include "pair_buck_long_coul_long.h" @@ -29,7 +28,6 @@ #include "force.h" #include "kspace.h" #include "update.h" -#include "integrate.h" #include "respa.h" #include "memory.h" #include "error.h" diff --git a/src/MC/fix_bond_swap.cpp b/src/MC/fix_bond_swap.cpp index 9a72667907..5da2b845d6 100644 --- a/src/MC/fix_bond_swap.cpp +++ b/src/MC/fix_bond_swap.cpp @@ -11,8 +11,8 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ +#include #include -#include #include #include "fix_bond_swap.h" #include "atom.h" @@ -23,7 +23,6 @@ #include "neighbor.h" #include "neigh_list.h" #include "neigh_request.h" -#include "group.h" #include "comm.h" #include "domain.h" #include "modify.h" diff --git a/src/MC/fix_bond_swap.h b/src/MC/fix_bond_swap.h index 0443144c23..d24159d807 100644 --- a/src/MC/fix_bond_swap.h +++ b/src/MC/fix_bond_swap.h @@ -21,7 +21,6 @@ FixStyle(bond/swap,FixBondSwap) #define LMP_FIX_BONDSWAP_H #include "fix.h" -#include "pair.h" namespace LAMMPS_NS { diff --git a/src/MC/fix_gcmc.cpp b/src/MC/fix_gcmc.cpp index 7ab0879335..4e48b71611 100644 --- a/src/MC/fix_gcmc.cpp +++ b/src/MC/fix_gcmc.cpp @@ -15,8 +15,8 @@ Contributing author: Paul Crozier, Aidan Thompson (SNL) ------------------------------------------------------------------------- */ +#include #include -#include #include #include "fix_gcmc.h" #include "atom.h" @@ -43,10 +43,7 @@ #include "math_const.h" #include "memory.h" #include "error.h" -#include "thermo.h" -#include "output.h" #include "neighbor.h" -#include "utils.h" using namespace LAMMPS_NS; using namespace FixConst; @@ -371,7 +368,7 @@ void FixGCMC::options(int narg, char **arg) ngrouptypesmax*sizeof(char *), "fix_gcmc:grouptypestrings"); } - grouptypes[ngrouptypes] = atoi(arg[iarg+1]); + grouptypes[ngrouptypes] = force->inumeric(FLERR,arg[iarg+1]); int n = strlen(arg[iarg+2]) + 1; grouptypestrings[ngrouptypes] = new char[n]; strcpy(grouptypestrings[ngrouptypes],arg[iarg+2]); diff --git a/src/PYTHON/fix_python_invoke.cpp b/src/PYTHON/fix_python_invoke.cpp index 280c2d91e2..f704bd9741 100644 --- a/src/PYTHON/fix_python_invoke.cpp +++ b/src/PYTHON/fix_python_invoke.cpp @@ -16,13 +16,10 @@ ------------------------------------------------------------------------- */ #include -#include #include #include "fix_python_invoke.h" -#include "atom.h" #include "force.h" #include "update.h" -#include "respa.h" #include "error.h" #include "lmppython.h" #include "python_compat.h" diff --git a/src/PYTHON/fix_python_move.cpp b/src/PYTHON/fix_python_move.cpp index ec21dbeadd..56b7768669 100644 --- a/src/PYTHON/fix_python_move.cpp +++ b/src/PYTHON/fix_python_move.cpp @@ -16,15 +16,8 @@ ------------------------------------------------------------------------- */ #include -#include -#include #include #include "fix_python_move.h" -#include "atom.h" -#include "comm.h" -#include "force.h" -#include "memory.h" -#include "neigh_list.h" #include "lmppython.h" #include "error.h" #include "python_compat.h" diff --git a/src/PYTHON/pair_python.cpp b/src/PYTHON/pair_python.cpp index 2148fc67b8..638077da48 100644 --- a/src/PYTHON/pair_python.cpp +++ b/src/PYTHON/pair_python.cpp @@ -16,12 +16,10 @@ ------------------------------------------------------------------------- */ #include -#include #include #include #include "pair_python.h" #include "atom.h" -#include "comm.h" #include "force.h" #include "memory.h" #include "update.h" diff --git a/src/PYTHON/python_impl.cpp b/src/PYTHON/python_impl.cpp index 9c650330af..249d4f7bb1 100644 --- a/src/PYTHON/python_impl.cpp +++ b/src/PYTHON/python_impl.cpp @@ -16,8 +16,9 @@ ------------------------------------------------------------------------- */ #include +#include #include -#include "lmppython.h" +#include "python_impl.h" #include "force.h" #include "input.h" #include "variable.h" diff --git a/src/PYTHON/python_impl.h b/src/PYTHON/python_impl.h index 2ccdda95c9..f890f54f3b 100644 --- a/src/PYTHON/python_impl.h +++ b/src/PYTHON/python_impl.h @@ -15,6 +15,7 @@ #define LMP_PYTHON_IMPL_H #include "pointers.h" +#include "lmppython.h" namespace LAMMPS_NS { diff --git a/src/RIGID/fix_rigid_nh.cpp b/src/RIGID/fix_rigid_nh.cpp index 4dceb1b8b4..4acc8d3411 100644 --- a/src/RIGID/fix_rigid_nh.cpp +++ b/src/RIGID/fix_rigid_nh.cpp @@ -17,8 +17,8 @@ Miller et al., J Chem Phys. 116, 8649-8659 (2002) ------------------------------------------------------------------------- */ +#include #include -#include #include #include "fix_rigid_nh.h" #include "math_extra.h" @@ -32,7 +32,6 @@ #include "comm.h" #include "force.h" #include "kspace.h" -#include "output.h" #include "memory.h" #include "error.h" diff --git a/src/RIGID/fix_rigid_nph_small.cpp b/src/RIGID/fix_rigid_nph_small.cpp index d32e3043f4..9b045eaf13 100644 --- a/src/RIGID/fix_rigid_nph_small.cpp +++ b/src/RIGID/fix_rigid_nph_small.cpp @@ -19,7 +19,6 @@ #include #include "fix_rigid_nph_small.h" -#include "domain.h" #include "modify.h" #include "error.h" diff --git a/src/RIGID/fix_rigid_npt.cpp b/src/RIGID/fix_rigid_npt.cpp index da5d5ffaa5..526fc8f614 100644 --- a/src/RIGID/fix_rigid_npt.cpp +++ b/src/RIGID/fix_rigid_npt.cpp @@ -19,7 +19,6 @@ #include #include "fix_rigid_npt.h" -#include "domain.h" #include "modify.h" #include "error.h" diff --git a/src/RIGID/fix_rigid_npt_small.cpp b/src/RIGID/fix_rigid_npt_small.cpp index f1fd5470da..fff338d687 100644 --- a/src/RIGID/fix_rigid_npt_small.cpp +++ b/src/RIGID/fix_rigid_npt_small.cpp @@ -19,7 +19,6 @@ #include #include "fix_rigid_npt_small.h" -#include "domain.h" #include "modify.h" #include "error.h" diff --git a/src/RIGID/fix_rigid_small.cpp b/src/RIGID/fix_rigid_small.cpp index dedd71c98d..8c2feb6436 100644 --- a/src/RIGID/fix_rigid_small.cpp +++ b/src/RIGID/fix_rigid_small.cpp @@ -11,10 +11,11 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ +#include #include -#include #include #include +#include #include "fix_rigid_small.h" #include "math_extra.h" #include "atom.h" @@ -31,7 +32,6 @@ #include "neighbor.h" #include "force.h" #include "input.h" -#include "output.h" #include "variable.h" #include "random_mars.h" #include "math_const.h" diff --git a/src/imbalance_store.cpp b/src/imbalance_store.cpp index 6b69caf785..c117b60860 100644 --- a/src/imbalance_store.cpp +++ b/src/imbalance_store.cpp @@ -14,7 +14,6 @@ #include #include "imbalance_store.h" #include "atom.h" -#include "input.h" #include "error.h" using namespace LAMMPS_NS; diff --git a/src/imbalance_time.cpp b/src/imbalance_time.cpp index a5fe538b8f..ceb3c08220 100644 --- a/src/imbalance_time.cpp +++ b/src/imbalance_time.cpp @@ -14,7 +14,6 @@ #include #include "imbalance_time.h" #include "atom.h" -#include "comm.h" #include "force.h" #include "timer.h" #include "error.h" diff --git a/src/lmppython.cpp b/src/lmppython.cpp index 7c6a490c24..52abd93f10 100644 --- a/src/lmppython.cpp +++ b/src/lmppython.cpp @@ -12,7 +12,11 @@ ------------------------------------------------------------------------- */ #include "lmppython.h" +#if LMP_PYTHON +#include "python_impl.h" +#else #include "error.h" +#endif using namespace LAMMPS_NS; diff --git a/src/lmppython.h b/src/lmppython.h index afc21037fb..3d55c4827b 100644 --- a/src/lmppython.h +++ b/src/lmppython.h @@ -51,11 +51,6 @@ private: }; } - -#endif - -#if LMP_PYTHON -#include "python_impl.h" #endif /* ERROR/WARNING messages: diff --git a/src/math_special.cpp b/src/math_special.cpp index 31567bdc77..b2f545ddc6 100644 --- a/src/math_special.cpp +++ b/src/math_special.cpp @@ -1,5 +1,5 @@ #include -#include // requires C++-11 +#include // IWYU pragma: keep #include "math_special.h" using namespace LAMMPS_NS; diff --git a/src/min_linesearch.cpp b/src/min_linesearch.cpp index 33a781ecfe..3c0621c602 100644 --- a/src/min_linesearch.cpp +++ b/src/min_linesearch.cpp @@ -26,7 +26,6 @@ #include "min_linesearch.h" #include "atom.h" #include "modify.h" -#include "neighbor.h" #include "fix_minimize.h" #include "pair.h" #include "output.h" diff --git a/src/neigh_list.cpp b/src/neigh_list.cpp index 651b2ed70a..31720cc78c 100644 --- a/src/neigh_list.cpp +++ b/src/neigh_list.cpp @@ -12,7 +12,7 @@ ------------------------------------------------------------------------- */ #include "neigh_list.h" -#include "my_page.h" +#include "my_page.h" // IWYU pragma: keep #include "atom.h" #include "comm.h" #include "neighbor.h" diff --git a/src/npair_full_bin_ghost.cpp b/src/npair_full_bin_ghost.cpp index 2edd03cc9e..61b27dd99d 100644 --- a/src/npair_full_bin_ghost.cpp +++ b/src/npair_full_bin_ghost.cpp @@ -12,7 +12,6 @@ ------------------------------------------------------------------------- */ #include "npair_full_bin_ghost.h" -#include "neighbor.h" #include "neigh_list.h" #include "atom.h" #include "atom_vec.h" diff --git a/src/npair_full_multi.cpp b/src/npair_full_multi.cpp index 9a2490ac5d..40ed2275be 100644 --- a/src/npair_full_multi.cpp +++ b/src/npair_full_multi.cpp @@ -12,7 +12,6 @@ ------------------------------------------------------------------------- */ #include "npair_full_multi.h" -#include "neighbor.h" #include "neigh_list.h" #include "atom.h" #include "atom_vec.h" diff --git a/src/npair_full_nsq.cpp b/src/npair_full_nsq.cpp index 1b404ffc94..76b66fd004 100644 --- a/src/npair_full_nsq.cpp +++ b/src/npair_full_nsq.cpp @@ -12,7 +12,6 @@ ------------------------------------------------------------------------- */ #include "npair_full_nsq.h" -#include "neighbor.h" #include "neigh_list.h" #include "atom.h" #include "atom_vec.h" diff --git a/src/npair_full_nsq_ghost.cpp b/src/npair_full_nsq_ghost.cpp index 1727b2905e..b20fa9b8ce 100644 --- a/src/npair_full_nsq_ghost.cpp +++ b/src/npair_full_nsq_ghost.cpp @@ -12,7 +12,6 @@ ------------------------------------------------------------------------- */ #include "npair_full_nsq_ghost.h" -#include "neighbor.h" #include "neigh_list.h" #include "atom.h" #include "atom_vec.h" diff --git a/src/npair_half_bin_atomonly_newton.cpp b/src/npair_half_bin_atomonly_newton.cpp index 6da44b4a5c..a7fa3985ef 100644 --- a/src/npair_half_bin_atomonly_newton.cpp +++ b/src/npair_half_bin_atomonly_newton.cpp @@ -12,12 +12,9 @@ ------------------------------------------------------------------------- */ #include "npair_half_bin_atomonly_newton.h" -#include "neighbor.h" #include "neigh_list.h" #include "atom.h" #include "atom_vec.h" -#include "molecule.h" -#include "domain.h" #include "my_page.h" #include "error.h" diff --git a/src/npair_half_bin_newtoff.cpp b/src/npair_half_bin_newtoff.cpp index 4c44741ffe..65768918c9 100644 --- a/src/npair_half_bin_newtoff.cpp +++ b/src/npair_half_bin_newtoff.cpp @@ -12,7 +12,6 @@ ------------------------------------------------------------------------- */ #include "npair_half_bin_newtoff.h" -#include "neighbor.h" #include "neigh_list.h" #include "atom.h" #include "atom_vec.h" diff --git a/src/npair_half_bin_newtoff_ghost.cpp b/src/npair_half_bin_newtoff_ghost.cpp index 72ec15e66a..91fbf049cb 100644 --- a/src/npair_half_bin_newtoff_ghost.cpp +++ b/src/npair_half_bin_newtoff_ghost.cpp @@ -12,7 +12,6 @@ ------------------------------------------------------------------------- */ #include "npair_half_bin_newtoff_ghost.h" -#include "neighbor.h" #include "neigh_list.h" #include "atom.h" #include "atom_vec.h" diff --git a/src/npair_half_bin_newton.cpp b/src/npair_half_bin_newton.cpp index 3a387870e3..fe388e1144 100644 --- a/src/npair_half_bin_newton.cpp +++ b/src/npair_half_bin_newton.cpp @@ -12,7 +12,6 @@ ------------------------------------------------------------------------- */ #include "npair_half_bin_newton.h" -#include "neighbor.h" #include "neigh_list.h" #include "atom.h" #include "atom_vec.h" diff --git a/src/npair_half_bin_newton_tri.cpp b/src/npair_half_bin_newton_tri.cpp index 169e710e0e..1f0e3c1187 100644 --- a/src/npair_half_bin_newton_tri.cpp +++ b/src/npair_half_bin_newton_tri.cpp @@ -12,7 +12,6 @@ ------------------------------------------------------------------------- */ #include "npair_half_bin_newton_tri.h" -#include "neighbor.h" #include "neigh_list.h" #include "atom.h" #include "atom_vec.h" diff --git a/src/npair_half_multi_newtoff.cpp b/src/npair_half_multi_newtoff.cpp index 07b5c87a6c..57dcf29cc7 100644 --- a/src/npair_half_multi_newtoff.cpp +++ b/src/npair_half_multi_newtoff.cpp @@ -12,7 +12,6 @@ ------------------------------------------------------------------------- */ #include "npair_half_multi_newtoff.h" -#include "neighbor.h" #include "neigh_list.h" #include "atom.h" #include "atom_vec.h" diff --git a/src/npair_half_multi_newton.cpp b/src/npair_half_multi_newton.cpp index 3d90979329..a9293d3d64 100644 --- a/src/npair_half_multi_newton.cpp +++ b/src/npair_half_multi_newton.cpp @@ -12,7 +12,6 @@ ------------------------------------------------------------------------- */ #include "npair_half_multi_newton.h" -#include "neighbor.h" #include "neigh_list.h" #include "atom.h" #include "atom_vec.h" diff --git a/src/npair_half_multi_newton_tri.cpp b/src/npair_half_multi_newton_tri.cpp index 909c69246b..c1d845cb38 100644 --- a/src/npair_half_multi_newton_tri.cpp +++ b/src/npair_half_multi_newton_tri.cpp @@ -12,7 +12,6 @@ ------------------------------------------------------------------------- */ #include "npair_half_multi_newton_tri.h" -#include "neighbor.h" #include "neigh_list.h" #include "atom.h" #include "atom_vec.h" diff --git a/src/npair_half_nsq_newtoff.cpp b/src/npair_half_nsq_newtoff.cpp index 06e8344332..db369687d0 100644 --- a/src/npair_half_nsq_newtoff.cpp +++ b/src/npair_half_nsq_newtoff.cpp @@ -12,7 +12,6 @@ ------------------------------------------------------------------------- */ #include "npair_half_nsq_newtoff.h" -#include "neighbor.h" #include "neigh_list.h" #include "atom.h" #include "atom_vec.h" diff --git a/src/npair_half_nsq_newtoff_ghost.cpp b/src/npair_half_nsq_newtoff_ghost.cpp index 1865061a8b..0a9b6d0f45 100644 --- a/src/npair_half_nsq_newtoff_ghost.cpp +++ b/src/npair_half_nsq_newtoff_ghost.cpp @@ -12,7 +12,6 @@ ------------------------------------------------------------------------- */ #include "npair_half_nsq_newtoff_ghost.h" -#include "neighbor.h" #include "neigh_list.h" #include "atom.h" #include "atom_vec.h" diff --git a/src/npair_half_nsq_newton.cpp b/src/npair_half_nsq_newton.cpp index 11c71d5609..69489915b2 100644 --- a/src/npair_half_nsq_newton.cpp +++ b/src/npair_half_nsq_newton.cpp @@ -12,7 +12,6 @@ ------------------------------------------------------------------------- */ #include "npair_half_nsq_newton.h" -#include "neighbor.h" #include "neigh_list.h" #include "atom.h" #include "atom_vec.h" diff --git a/src/npair_half_respa_bin_newtoff.cpp b/src/npair_half_respa_bin_newtoff.cpp index 0145771f4a..8c1d8d684f 100644 --- a/src/npair_half_respa_bin_newtoff.cpp +++ b/src/npair_half_respa_bin_newtoff.cpp @@ -12,7 +12,6 @@ ------------------------------------------------------------------------- */ #include "npair_half_respa_bin_newtoff.h" -#include "neighbor.h" #include "neigh_list.h" #include "atom.h" #include "atom_vec.h" diff --git a/src/npair_half_respa_bin_newton.cpp b/src/npair_half_respa_bin_newton.cpp index 72a613204d..d2598fa1a4 100644 --- a/src/npair_half_respa_bin_newton.cpp +++ b/src/npair_half_respa_bin_newton.cpp @@ -12,7 +12,6 @@ ------------------------------------------------------------------------- */ #include "npair_half_respa_bin_newton.h" -#include "neighbor.h" #include "neigh_list.h" #include "atom.h" #include "atom_vec.h" diff --git a/src/npair_half_respa_bin_newton_tri.cpp b/src/npair_half_respa_bin_newton_tri.cpp index add1cf6e5c..efe48d48e1 100644 --- a/src/npair_half_respa_bin_newton_tri.cpp +++ b/src/npair_half_respa_bin_newton_tri.cpp @@ -12,7 +12,6 @@ ------------------------------------------------------------------------- */ #include "npair_half_respa_bin_newton_tri.h" -#include "neighbor.h" #include "neigh_list.h" #include "atom.h" #include "atom_vec.h" diff --git a/src/npair_half_respa_nsq_newtoff.cpp b/src/npair_half_respa_nsq_newtoff.cpp index c0e932f0ae..334ebb5ca8 100644 --- a/src/npair_half_respa_nsq_newtoff.cpp +++ b/src/npair_half_respa_nsq_newtoff.cpp @@ -12,7 +12,6 @@ ------------------------------------------------------------------------- */ #include "npair_half_respa_nsq_newtoff.h" -#include "neighbor.h" #include "neigh_list.h" #include "atom.h" #include "atom_vec.h" diff --git a/src/npair_half_respa_nsq_newton.cpp b/src/npair_half_respa_nsq_newton.cpp index f7d161896d..7ecd02b0c5 100644 --- a/src/npair_half_respa_nsq_newton.cpp +++ b/src/npair_half_respa_nsq_newton.cpp @@ -12,7 +12,6 @@ ------------------------------------------------------------------------- */ #include "npair_half_respa_nsq_newton.h" -#include "neighbor.h" #include "neigh_list.h" #include "atom.h" #include "atom_vec.h" diff --git a/src/npair_half_size_bin_newtoff.cpp b/src/npair_half_size_bin_newtoff.cpp index 021452028b..b9e44675ac 100644 --- a/src/npair_half_size_bin_newtoff.cpp +++ b/src/npair_half_size_bin_newtoff.cpp @@ -11,9 +11,7 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include #include "npair_half_size_bin_newtoff.h" -#include "neighbor.h" #include "neigh_list.h" #include "atom.h" #include "atom_vec.h" diff --git a/src/npair_half_size_bin_newton.cpp b/src/npair_half_size_bin_newton.cpp index 760c09570a..93bcc25373 100644 --- a/src/npair_half_size_bin_newton.cpp +++ b/src/npair_half_size_bin_newton.cpp @@ -11,9 +11,7 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include #include "npair_half_size_bin_newton.h" -#include "neighbor.h" #include "neigh_list.h" #include "atom.h" #include "atom_vec.h" diff --git a/src/npair_half_size_bin_newton_tri.cpp b/src/npair_half_size_bin_newton_tri.cpp index d831982ed6..39068c02bc 100644 --- a/src/npair_half_size_bin_newton_tri.cpp +++ b/src/npair_half_size_bin_newton_tri.cpp @@ -11,9 +11,7 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include #include "npair_half_size_bin_newton_tri.h" -#include "neighbor.h" #include "neigh_list.h" #include "atom.h" #include "atom_vec.h" diff --git a/src/npair_half_size_nsq_newtoff.cpp b/src/npair_half_size_nsq_newtoff.cpp index 1c2fe5f3d5..6f169d0b6c 100644 --- a/src/npair_half_size_nsq_newtoff.cpp +++ b/src/npair_half_size_nsq_newtoff.cpp @@ -11,9 +11,7 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include #include "npair_half_size_nsq_newtoff.h" -#include "neighbor.h" #include "neigh_list.h" #include "atom.h" #include "atom_vec.h" diff --git a/src/npair_half_size_nsq_newton.cpp b/src/npair_half_size_nsq_newton.cpp index ce9f8ec186..d427c14809 100644 --- a/src/npair_half_size_nsq_newton.cpp +++ b/src/npair_half_size_nsq_newton.cpp @@ -11,9 +11,7 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include #include "npair_half_size_nsq_newton.h" -#include "neighbor.h" #include "neigh_list.h" #include "atom.h" #include "atom_vec.h" diff --git a/src/npair_halffull_newtoff.cpp b/src/npair_halffull_newtoff.cpp index 84816f07b2..6ff5433e88 100644 --- a/src/npair_halffull_newtoff.cpp +++ b/src/npair_halffull_newtoff.cpp @@ -12,12 +12,8 @@ ------------------------------------------------------------------------- */ #include "npair_halffull_newtoff.h" -#include "neighbor.h" #include "neigh_list.h" -#include "atom.h" #include "atom_vec.h" -#include "molecule.h" -#include "domain.h" #include "my_page.h" #include "error.h" diff --git a/src/npair_halffull_newton.cpp b/src/npair_halffull_newton.cpp index 371bbd33a8..0912cfe12f 100644 --- a/src/npair_halffull_newton.cpp +++ b/src/npair_halffull_newton.cpp @@ -12,12 +12,9 @@ ------------------------------------------------------------------------- */ #include "npair_halffull_newton.h" -#include "neighbor.h" #include "neigh_list.h" #include "atom.h" #include "atom_vec.h" -#include "molecule.h" -#include "domain.h" #include "my_page.h" #include "error.h" diff --git a/src/npair_skip.cpp b/src/npair_skip.cpp index 1fe202537a..028041a947 100644 --- a/src/npair_skip.cpp +++ b/src/npair_skip.cpp @@ -12,12 +12,9 @@ ------------------------------------------------------------------------- */ #include "npair_skip.h" -#include "neighbor.h" #include "neigh_list.h" #include "atom.h" #include "atom_vec.h" -#include "molecule.h" -#include "domain.h" #include "my_page.h" #include "error.h" diff --git a/src/pair_buck_coul_cut.cpp b/src/pair_buck_coul_cut.cpp index 094797694c..64475166e3 100644 --- a/src/pair_buck_coul_cut.cpp +++ b/src/pair_buck_coul_cut.cpp @@ -15,9 +15,8 @@ Contributing author: Eduardo Bringa (LLNL) ------------------------------------------------------------------------- */ +#include #include -#include -#include #include "pair_buck_coul_cut.h" #include "atom.h" #include "comm.h" diff --git a/src/pair_coul_cut.cpp b/src/pair_coul_cut.cpp index 196e064219..28973026cd 100644 --- a/src/pair_coul_cut.cpp +++ b/src/pair_coul_cut.cpp @@ -11,9 +11,8 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ +#include #include -#include -#include #include #include "pair_coul_cut.h" #include "atom.h" diff --git a/src/pointers.h b/src/pointers.h index 5df5b72d47..1af07d5158 100644 --- a/src/pointers.h +++ b/src/pointers.h @@ -23,6 +23,7 @@ #include "lmptype.h" // IWYU pragma: export #include +#include // IWYU pragme: export #include // IWYU pragma: export #include "lammps.h" // IWYU pragma: export diff --git a/src/variable.cpp b/src/variable.cpp index 1416754073..111fc75a9a 100644 --- a/src/variable.cpp +++ b/src/variable.cpp @@ -11,6 +11,7 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ +#include #include #include #include @@ -34,7 +35,6 @@ #include "thermo.h" #include "random_mars.h" #include "math_const.h" -#include "atom_masks.h" #include "lmppython.h" #include "memory.h" #include "info.h" -- GitLab From 3cd1095dd83aa2b619000f04194e6f211ae2457a Mon Sep 17 00:00:00 2001 From: Andrew Schultz Date: Mon, 1 Jul 2019 16:12:51 -0400 Subject: [PATCH 153/469] Add line for compute hma --- src/USER-MISC/README | 1 + 1 file changed, 1 insertion(+) diff --git a/src/USER-MISC/README b/src/USER-MISC/README index 219e19673d..18a3bfa629 100644 --- a/src/USER-MISC/README +++ b/src/USER-MISC/README @@ -30,6 +30,7 @@ compute ackland/atom, Gerolf Ziegenhain, gerolf at ziegenhain.com, 4 Oct 2007 compute basal/atom, Christopher Barrett, cdb333 at cavs.msstate.edu, 3 Mar 2013 compute cnp/atom, Paulo Branicio (USC), branicio at usc.edu, 31 May 2017 compute entropy/atom, Pablo Piaggi (EPFL), pablo.piaggi at epfl.ch, 15 June 2018 +compute hma, Andrew Schultz & David Kofke (UB), ajs42 at buffalo.edu & kofke at buffalo.edu, 1 Jul 2019 compute pressure/cylinder, Cody K. Addington (NCSU), , 2 Oct 2018 compute stress/mop, Romain Vermorel (U Pau) & Laurent Joly (U Lyon), romain.vermorel at univ-pau.fr & ljoly.ulyon at gmail.com, 5 Sep 18 compute stress/mop/profile, Romain Vermorel (U Pau) & Laurent Joly (U Lyon), romain.vermorel at univ-pau.fr & ljoly.ulyon at gmail.com, 5 Sep 18 -- GitLab From 7547e1dae621f02e14e8e77bffc6ad3c6300e59e Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Mon, 1 Jul 2019 17:10:21 -0400 Subject: [PATCH 154/469] make certain that the vector storage and the size_vector variable are consistent in computes --- src/ASPHERE/compute_temp_asphere.cpp | 2 +- src/BODY/compute_temp_body.cpp | 2 +- src/CORESHELL/compute_temp_cs.cpp | 2 +- src/SPIN/compute_spin.cpp | 2 +- src/USER-BOCS/compute_pressure_bocs.cpp | 6 +++--- src/USER-DRUDE/compute_temp_drude.cpp | 2 +- src/USER-EFF/compute_temp_deform_eff.cpp | 2 +- src/USER-EFF/compute_temp_region_eff.cpp | 2 +- src/USER-FEP/compute_fep.cpp | 2 +- src/USER-MISC/compute_temp_rotate.cpp | 2 +- src/compute_com.cpp | 2 +- src/compute_group_group.cpp | 2 +- src/compute_gyration.cpp | 2 +- src/compute_heat_flux.cpp | 2 +- src/compute_msd.cpp | 2 +- src/compute_pressure.cpp | 2 +- src/compute_temp.cpp | 2 +- src/compute_temp_chunk.cpp | 2 +- src/compute_temp_com.cpp | 2 +- src/compute_temp_deform.cpp | 2 +- src/compute_temp_partial.cpp | 2 +- src/compute_temp_ramp.cpp | 2 +- src/compute_temp_region.cpp | 2 +- src/compute_temp_sphere.cpp | 2 +- src/compute_vacf.cpp | 2 +- 25 files changed, 27 insertions(+), 27 deletions(-) diff --git a/src/ASPHERE/compute_temp_asphere.cpp b/src/ASPHERE/compute_temp_asphere.cpp index 011d8cae80..651c228e41 100644 --- a/src/ASPHERE/compute_temp_asphere.cpp +++ b/src/ASPHERE/compute_temp_asphere.cpp @@ -78,7 +78,7 @@ ComputeTempAsphere::ComputeTempAsphere(LAMMPS *lmp, int narg, char **arg) : if (mode == ROTATE) extra_dof = 0; - vector = new double[6]; + vector = new double[size_vector]; } diff --git a/src/BODY/compute_temp_body.cpp b/src/BODY/compute_temp_body.cpp index 5446fb6d64..b560bdd11d 100644 --- a/src/BODY/compute_temp_body.cpp +++ b/src/BODY/compute_temp_body.cpp @@ -71,7 +71,7 @@ ComputeTempBody::ComputeTempBody(LAMMPS *lmp, int narg, char **arg) : } else error->all(FLERR,"Illegal compute temp/body command"); } - vector = new double[6]; + vector = new double[size_vector]; } diff --git a/src/CORESHELL/compute_temp_cs.cpp b/src/CORESHELL/compute_temp_cs.cpp index 03ebfa154d..dac0d60fce 100644 --- a/src/CORESHELL/compute_temp_cs.cpp +++ b/src/CORESHELL/compute_temp_cs.cpp @@ -101,7 +101,7 @@ ComputeTempCS::ComputeTempCS(LAMMPS *lmp, int narg, char **arg) : // allocate memory - vector = new double[6]; + vector = new double[size_vector]; maxatom = 0; vint = NULL; diff --git a/src/SPIN/compute_spin.cpp b/src/SPIN/compute_spin.cpp index 0a881e1de6..501b708c88 100644 --- a/src/SPIN/compute_spin.cpp +++ b/src/SPIN/compute_spin.cpp @@ -149,6 +149,6 @@ void ComputeSpin::compute_vector() void ComputeSpin::allocate() { - memory->create(vector,6,"compute/spin:vector"); + memory->create(vector,size_vector,"compute/spin:vector"); } diff --git a/src/USER-BOCS/compute_pressure_bocs.cpp b/src/USER-BOCS/compute_pressure_bocs.cpp index fc24efab4c..c43910ec6d 100644 --- a/src/USER-BOCS/compute_pressure_bocs.cpp +++ b/src/USER-BOCS/compute_pressure_bocs.cpp @@ -106,9 +106,9 @@ ComputePressureBocs::ComputePressureBocs(LAMMPS *lmp, int narg, char **arg) : if (keflag && id_temp == NULL) error->all(FLERR,"Compute pressure/bocs requires temperature ID " - "to include kinetic energy"); + "to include kinetic energy"); - vector = new double[6]; + vector = new double[size_vector]; nvirial = 0; vptr = NULL; } @@ -365,7 +365,7 @@ void ComputePressureBocs::compute_vector() if (force->kspace && kspace_virial && force->kspace->scalar_pressure_flag) error->all(FLERR,"Must use 'kspace_modify pressure/scalar no' for " - "tensor components with kspace_style msm"); + "tensor components with kspace_style msm"); // invoke temperature if it hasn't been already diff --git a/src/USER-DRUDE/compute_temp_drude.cpp b/src/USER-DRUDE/compute_temp_drude.cpp index 27b525c07d..4830e950d0 100644 --- a/src/USER-DRUDE/compute_temp_drude.cpp +++ b/src/USER-DRUDE/compute_temp_drude.cpp @@ -46,7 +46,7 @@ ComputeTempDrude::ComputeTempDrude(LAMMPS *lmp, int narg, char **arg) : extlist[2] = extlist[3] = extlist[4] = extlist[5] = 1; tempflag = 0; // because does not compute a single temperature (scalar and vector) - vector = new double[6]; + vector = new double[size_vector]; fix_drude = NULL; id_temp = NULL; temperature = NULL; diff --git a/src/USER-EFF/compute_temp_deform_eff.cpp b/src/USER-EFF/compute_temp_deform_eff.cpp index 23abb4f99d..621eff210f 100644 --- a/src/USER-EFF/compute_temp_deform_eff.cpp +++ b/src/USER-EFF/compute_temp_deform_eff.cpp @@ -54,7 +54,7 @@ ComputeTempDeformEff::ComputeTempDeformEff(LAMMPS *lmp, int narg, char **arg) : maxbias = 0; vbiasall = NULL; - vector = new double[6]; + vector = new double[size_vector]; } /* ---------------------------------------------------------------------- */ diff --git a/src/USER-EFF/compute_temp_region_eff.cpp b/src/USER-EFF/compute_temp_region_eff.cpp index 659bdfca5e..8cab690367 100644 --- a/src/USER-EFF/compute_temp_region_eff.cpp +++ b/src/USER-EFF/compute_temp_region_eff.cpp @@ -58,7 +58,7 @@ ComputeTempRegionEff::ComputeTempRegionEff(LAMMPS *lmp, int narg, char **arg) : maxbias = 0; vbiasall = NULL; - vector = new double[6]; + vector = new double[size_vector]; } /* ---------------------------------------------------------------------- */ diff --git a/src/USER-FEP/compute_fep.cpp b/src/USER-FEP/compute_fep.cpp index 0e5f164f88..dc0b71e71b 100644 --- a/src/USER-FEP/compute_fep.cpp +++ b/src/USER-FEP/compute_fep.cpp @@ -53,7 +53,7 @@ ComputeFEP::ComputeFEP(LAMMPS *lmp, int narg, char **arg) : size_vector = 3; extvector = 0; - vector = new double[3]; + vector = new double[size_vector]; fepinitflag = 0; // avoid init to run entirely when called by write_data diff --git a/src/USER-MISC/compute_temp_rotate.cpp b/src/USER-MISC/compute_temp_rotate.cpp index 66f1b8f5f7..36093bd1e1 100644 --- a/src/USER-MISC/compute_temp_rotate.cpp +++ b/src/USER-MISC/compute_temp_rotate.cpp @@ -46,7 +46,7 @@ ComputeTempRotate::ComputeTempRotate(LAMMPS *lmp, int narg, char **arg) : maxbias = 0; vbiasall = NULL; - vector = new double[6]; + vector = new double[size_vector]; } /* ---------------------------------------------------------------------- */ diff --git a/src/compute_com.cpp b/src/compute_com.cpp index 27606cbc6f..2496aa9446 100644 --- a/src/compute_com.cpp +++ b/src/compute_com.cpp @@ -29,7 +29,7 @@ ComputeCOM::ComputeCOM(LAMMPS *lmp, int narg, char **arg) : size_vector = 3; extvector = 0; - vector = new double[3]; + vector = new double[size_vector]; } /* ---------------------------------------------------------------------- */ diff --git a/src/compute_group_group.cpp b/src/compute_group_group.cpp index e55f679b2e..17e8737350 100644 --- a/src/compute_group_group.cpp +++ b/src/compute_group_group.cpp @@ -105,7 +105,7 @@ ComputeGroupGroup::ComputeGroupGroup(LAMMPS *lmp, int narg, char **arg) : } else error->all(FLERR,"Illegal compute group/group command"); } - vector = new double[3]; + vector = new double[size_vector]; } /* ---------------------------------------------------------------------- */ diff --git a/src/compute_gyration.cpp b/src/compute_gyration.cpp index f8d19853e0..0e29c0d667 100644 --- a/src/compute_gyration.cpp +++ b/src/compute_gyration.cpp @@ -33,7 +33,7 @@ ComputeGyration::ComputeGyration(LAMMPS *lmp, int narg, char **arg) : extscalar = 0; extvector = 0; - vector = new double[6]; + vector = new double[size_vector]; } /* ---------------------------------------------------------------------- */ diff --git a/src/compute_heat_flux.cpp b/src/compute_heat_flux.cpp index e402da7842..0b37865034 100644 --- a/src/compute_heat_flux.cpp +++ b/src/compute_heat_flux.cpp @@ -70,7 +70,7 @@ ComputeHeatFlux::ComputeHeatFlux(LAMMPS *lmp, int narg, char **arg) : error->all(FLERR, "Compute heat/flux compute ID does not compute stress/atom"); - vector = new double[6]; + vector = new double[size_vector]; } /* ---------------------------------------------------------------------- */ diff --git a/src/compute_msd.cpp b/src/compute_msd.cpp index fc47b2609a..608d3e6b33 100644 --- a/src/compute_msd.cpp +++ b/src/compute_msd.cpp @@ -115,7 +115,7 @@ ComputeMSD::ComputeMSD(LAMMPS *lmp, int narg, char **arg) : // displacement vector - vector = new double[4]; + vector = new double[size_vector]; } /* ---------------------------------------------------------------------- */ diff --git a/src/compute_pressure.cpp b/src/compute_pressure.cpp index dde02a5aed..978cad0cad 100644 --- a/src/compute_pressure.cpp +++ b/src/compute_pressure.cpp @@ -101,7 +101,7 @@ ComputePressure::ComputePressure(LAMMPS *lmp, int narg, char **arg) : error->all(FLERR,"Compute pressure requires temperature ID " "to include kinetic energy"); - vector = new double[6]; + vector = new double[size_vector]; nvirial = 0; vptr = NULL; } diff --git a/src/compute_temp.cpp b/src/compute_temp.cpp index f7d3a890ec..70a7734593 100644 --- a/src/compute_temp.cpp +++ b/src/compute_temp.cpp @@ -37,7 +37,7 @@ ComputeTemp::ComputeTemp(LAMMPS *lmp, int narg, char **arg) : extvector = 1; tempflag = 1; - vector = new double[6]; + vector = new double[size_vector]; } /* ---------------------------------------------------------------------- */ diff --git a/src/compute_temp_chunk.cpp b/src/compute_temp_chunk.cpp index 920515e05c..396492e18d 100644 --- a/src/compute_temp_chunk.cpp +++ b/src/compute_temp_chunk.cpp @@ -125,7 +125,7 @@ ComputeTempChunk::ComputeTempChunk(LAMMPS *lmp, int narg, char **arg) : // vector data - vector = new double[6]; + vector = new double[size_vector]; // chunk-based data diff --git a/src/compute_temp_com.cpp b/src/compute_temp_com.cpp index f2ad40ea43..c46a17497f 100644 --- a/src/compute_temp_com.cpp +++ b/src/compute_temp_com.cpp @@ -39,7 +39,7 @@ ComputeTempCOM::ComputeTempCOM(LAMMPS *lmp, int narg, char **arg) : tempflag = 1; tempbias = 1; - vector = new double[6]; + vector = new double[size_vector]; } /* ---------------------------------------------------------------------- */ diff --git a/src/compute_temp_deform.cpp b/src/compute_temp_deform.cpp index 39780b5cf6..280c17dd08 100644 --- a/src/compute_temp_deform.cpp +++ b/src/compute_temp_deform.cpp @@ -48,7 +48,7 @@ ComputeTempDeform::ComputeTempDeform(LAMMPS *lmp, int narg, char **arg) : maxbias = 0; vbiasall = NULL; - vector = new double[6]; + vector = new double[size_vector]; } /* ---------------------------------------------------------------------- */ diff --git a/src/compute_temp_partial.cpp b/src/compute_temp_partial.cpp index 4425aebdda..ee72ba3e74 100644 --- a/src/compute_temp_partial.cpp +++ b/src/compute_temp_partial.cpp @@ -49,7 +49,7 @@ ComputeTempPartial::ComputeTempPartial(LAMMPS *lmp, int narg, char **arg) : maxbias = 0; vbiasall = NULL; - vector = new double[6]; + vector = new double[size_vector]; } /* ---------------------------------------------------------------------- */ diff --git a/src/compute_temp_ramp.cpp b/src/compute_temp_ramp.cpp index ba572645f3..36e7f51ce4 100644 --- a/src/compute_temp_ramp.cpp +++ b/src/compute_temp_ramp.cpp @@ -101,7 +101,7 @@ ComputeTempRamp::ComputeTempRamp(LAMMPS *lmp, int narg, char **arg) : maxbias = 0; vbiasall = NULL; - vector = new double[6]; + vector = new double[size_vector]; } /* ---------------------------------------------------------------------- */ diff --git a/src/compute_temp_region.cpp b/src/compute_temp_region.cpp index 4aa4dac0a1..0c54aeb63c 100644 --- a/src/compute_temp_region.cpp +++ b/src/compute_temp_region.cpp @@ -49,7 +49,7 @@ ComputeTempRegion::ComputeTempRegion(LAMMPS *lmp, int narg, char **arg) : maxbias = 0; vbiasall = NULL; - vector = new double[6]; + vector = new double[size_vector]; } /* ---------------------------------------------------------------------- */ diff --git a/src/compute_temp_sphere.cpp b/src/compute_temp_sphere.cpp index 651da6dee5..23e74634b5 100644 --- a/src/compute_temp_sphere.cpp +++ b/src/compute_temp_sphere.cpp @@ -72,7 +72,7 @@ ComputeTempSphere::ComputeTempSphere(LAMMPS *lmp, int narg, char **arg) : if (mode == ROTATE) extra_dof = 0; - vector = new double[6]; + vector = new double[size_vector]; // error checks diff --git a/src/compute_vacf.cpp b/src/compute_vacf.cpp index 3ef3acf0bf..d46b8b5fa0 100644 --- a/src/compute_vacf.cpp +++ b/src/compute_vacf.cpp @@ -75,7 +75,7 @@ ComputeVACF::ComputeVACF(LAMMPS *lmp, int narg, char **arg) : // displacement vector - vector = new double[4]; + vector = new double[size_vector]; } /* ---------------------------------------------------------------------- */ -- GitLab From ef1b62a42219652cce3750dea3cab3697e8bae26 Mon Sep 17 00:00:00 2001 From: Andrew Schultz Date: Mon, 1 Jul 2019 20:44:03 -0400 Subject: [PATCH 155/469] rename single2nd => single_hessian --- src/USER-MISC/compute_hma.cpp | 2 +- src/pair.cpp | 2 +- src/pair.h | 4 ++-- src/pair_lj_smooth_linear.cpp | 4 ++-- src/pair_lj_smooth_linear.h | 2 +- 5 files changed, 7 insertions(+), 7 deletions(-) diff --git a/src/USER-MISC/compute_hma.cpp b/src/USER-MISC/compute_hma.cpp index 15cadbdd45..a14084b9ca 100644 --- a/src/USER-MISC/compute_hma.cpp +++ b/src/USER-MISC/compute_hma.cpp @@ -360,7 +360,7 @@ void ComputeHMA::compute_vector() if (rsq < cutsq[itype][jtype]) { double* jdr = deltaR[j]; double fforce, d2u[6]; - force->pair->single2nd(i, j, itype, jtype, rsq, delr, factor_coul, factor_lj, fforce, d2u); + force->pair->single_hessian(i, j, itype, jtype, rsq, delr, factor_coul, factor_lj, fforce, d2u); int m = 0; for (int k=0; k<3; k++) { double a = fac; diff --git a/src/pair.cpp b/src/pair.cpp index 61a75dd150..43fc9bc907 100644 --- a/src/pair.cpp +++ b/src/pair.cpp @@ -60,7 +60,7 @@ Pair::Pair(LAMMPS *lmp) : Pointers(lmp) comm_forward = comm_reverse = comm_reverse_off = 0; single_enable = 1; - single2nd_enable = 0; + single_hessian_enable = 0; restartinfo = 1; respa_enable = 0; one_coeff = 0; diff --git a/src/pair.h b/src/pair.h index 8d7362adba..d85b9af0c3 100644 --- a/src/pair.h +++ b/src/pair.h @@ -46,7 +46,7 @@ class Pair : protected Pointers { int comm_reverse_off; // size of reverse comm even if newton off int single_enable; // 1 if single() routine exists - int single2nd_enable; // 1 if single2nd() routine exists + int single_hessian_enable; // 1 if single_hessian() routine exists int restartinfo; // 1 if pair style writes restart info int respa_enable; // 1 if inner/middle/outer rRESPA routines int one_coeff; // 1 if allows only one coeff * * call @@ -151,7 +151,7 @@ class Pair : protected Pointers { void pairTensor(double fforce, double dfac, double delr[3], double phiTensor[6]); - virtual double single2nd(int, int, int, int, + virtual double single_hessian(int, int, int, int, double, double[3], double, double, double& fforce, double d2u[6]) { fforce = 0.0; diff --git a/src/pair_lj_smooth_linear.cpp b/src/pair_lj_smooth_linear.cpp index 0aa19570f2..3ebdda4143 100644 --- a/src/pair_lj_smooth_linear.cpp +++ b/src/pair_lj_smooth_linear.cpp @@ -31,7 +31,7 @@ using namespace LAMMPS_NS; /* ---------------------------------------------------------------------- */ PairLJSmoothLinear::PairLJSmoothLinear(LAMMPS *lmp) : Pair(lmp) { - single2nd_enable = 1; + single_hessian_enable = 1; } /* ---------------------------------------------------------------------- */ @@ -349,7 +349,7 @@ double PairLJSmoothLinear::single(int /*i*/, int /*j*/, int itype, int jtype, return factor_lj*philj; } -double PairLJSmoothLinear::single2nd(int /*i*/, int /*j*/, int itype, int jtype, double rsq, +double PairLJSmoothLinear::single_hessian(int /*i*/, int /*j*/, int itype, int jtype, double rsq, double delr[3], double factor_coul, double factor_lj, double &fforce, double d2u[6]) { diff --git a/src/pair_lj_smooth_linear.h b/src/pair_lj_smooth_linear.h index a43cbc23e2..7e26a7011e 100644 --- a/src/pair_lj_smooth_linear.h +++ b/src/pair_lj_smooth_linear.h @@ -38,7 +38,7 @@ class PairLJSmoothLinear : public Pair { void write_restart_settings(FILE *); void read_restart_settings(FILE *); double single(int, int, int, int, double, double, double, double &); - double single2nd(int, int, int, int, double, double[3], double, double, double&, double[6]); + double single_hessian(int, int, int, int, double, double[3], double, double, double&, double[6]); protected: double cut_global; -- GitLab From 6fc5810bb4d4b0d0042204926bf04d29259db063 Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Tue, 2 Jul 2019 01:30:11 -0400 Subject: [PATCH 156/469] with the refactored include handling we can allow include in if/then/else --- doc/src/if.txt | 3 +-- src/input.cpp | 28 ++++++++-------------------- src/input.h | 1 - 3 files changed, 9 insertions(+), 23 deletions(-) diff --git a/doc/src/if.txt b/doc/src/if.txt index 20caf1a1ef..ceec8f55db 100644 --- a/doc/src/if.txt +++ b/doc/src/if.txt @@ -57,8 +57,7 @@ Boolean expression is FALSE, then no commands are executed. The syntax for Boolean expressions is described below. Each command (t1, f1, e1, etc) can be any valid LAMMPS input script -command, except an "include"_include.html command, which is not -allowed. If the command is more than one word, it must enclosed in +command. If the command is more than one word, it must enclosed in quotes, so it will be treated as a single argument, as in the examples above. diff --git a/src/input.cpp b/src/input.cpp index 9e0ad78d9e..390ca37bf3 100644 --- a/src/input.cpp +++ b/src/input.cpp @@ -82,7 +82,6 @@ Input::Input(LAMMPS *lmp, int argc, char **argv) : Pointers(lmp) label_active = 0; labelstr = NULL; jump_skip = 0; - ifthenelse_flag = 0; if (me == 0) { nfile = maxfile = 1; @@ -962,11 +961,10 @@ void Input::ifthenelse() ncommands++; } - ifthenelse_flag = 1; - for (int i = 0; i < ncommands; i++) one(commands[i]); - ifthenelse_flag = 0; - - for (int i = 0; i < ncommands; i++) delete [] commands[i]; + for (int i = 0; i < ncommands; i++) { + one(commands[i]); + delete [] commands[i]; + } delete [] commands; return; @@ -1018,13 +1016,10 @@ void Input::ifthenelse() // execute the list of commands - ifthenelse_flag = 1; - for (int i = 0; i < ncommands; i++) one(commands[i]); - ifthenelse_flag = 0; - - // clean up - - for (int i = 0; i < ncommands; i++) delete [] commands[i]; + for (int i = 0; i < ncommands; i++) { + one(commands[i]); + delete [] commands[i]; + } delete [] commands; return; @@ -1037,13 +1032,6 @@ void Input::include() { if (narg != 1) error->all(FLERR,"Illegal include command"); - // do not allow include inside an if command - // NOTE: this check will fail if a 2nd if command was inside the if command - // and came before the include - - if (ifthenelse_flag) - error->all(FLERR,"Cannot use include command within an if command"); - if (me == 0) { if (nfile == maxfile) { maxfile++; diff --git a/src/input.h b/src/input.h index 33e83bfb06..7b6e55c2ba 100644 --- a/src/input.h +++ b/src/input.h @@ -54,7 +54,6 @@ class Input : protected Pointers { int label_active; // 0 = no label, 1 = looking for label char *labelstr; // label string being looked for int jump_skip; // 1 if skipping next jump, 0 otherwise - int ifthenelse_flag; // 1 if executing commands inside an if-then-else FILE **infiles; // list of open input files -- GitLab From 968335d4fdc15ec3db520cb780895e5eca151d41 Mon Sep 17 00:00:00 2001 From: Julien Devemy Date: Tue, 2 Jul 2019 10:34:10 +0200 Subject: [PATCH 157/469] Remove useless things --- src/compute_pressure.cpp | 2 +- src/compute_pressure.h | 1 - src/pair_hybrid.h | 1 - 3 files changed, 1 insertion(+), 3 deletions(-) diff --git a/src/compute_pressure.cpp b/src/compute_pressure.cpp index 96f577219d..16e56cb9df 100644 --- a/src/compute_pressure.cpp +++ b/src/compute_pressure.cpp @@ -87,7 +87,7 @@ ComputePressure::ComputePressure(LAMMPS *lmp, int narg, char **arg) : pstyle = new char[n]; strcpy(pstyle,arg[iarg++]); - nsub = 0; + int nsub = 0; if (narg > iarg) { if (isdigit(arg[iarg][0])) { diff --git a/src/compute_pressure.h b/src/compute_pressure.h index 31983e8e2c..2982271390 100644 --- a/src/compute_pressure.h +++ b/src/compute_pressure.h @@ -49,7 +49,6 @@ class ComputePressure : public Compute { void virial_compute(int, int); private: - int nsub; char *pstyle; }; diff --git a/src/pair_hybrid.h b/src/pair_hybrid.h index 1e0130ba3d..e313e16f18 100644 --- a/src/pair_hybrid.h +++ b/src/pair_hybrid.h @@ -33,7 +33,6 @@ class PairHybrid : public Pair { friend class Respa; friend class Info; friend class PairDeprecated; - friend class ComputePressure; public: PairHybrid(class LAMMPS *); virtual ~PairHybrid(); -- GitLab From 0761c4dbb97fbbbe3b61f37fc62b7ca61f74b558 Mon Sep 17 00:00:00 2001 From: Julien Devemy Date: Tue, 2 Jul 2019 10:47:36 +0200 Subject: [PATCH 158/469] Name change hybridpair->pair/hybrid --- doc/src/compute_pressure.txt | 2 +- src/compute_pressure.cpp | 20 ++++++++++---------- src/compute_pressure.h | 4 ++-- 3 files changed, 13 insertions(+), 13 deletions(-) diff --git a/doc/src/compute_pressure.txt b/doc/src/compute_pressure.txt index 070376075e..b8d52b83de 100644 --- a/doc/src/compute_pressure.txt +++ b/doc/src/compute_pressure.txt @@ -22,7 +22,7 @@ keyword = {ke} or {pair} or {bond} or {angle} or {dihedral} or {improper} or {ks compute 1 all pressure thermo_temp compute 1 all pressure NULL pair bond -compute 1 all pressure NULL hybridpair lj/cut :pre +compute 1 all pressure NULL pair/hybrid lj/cut :pre [Description:] diff --git a/src/compute_pressure.cpp b/src/compute_pressure.cpp index 16e56cb9df..d586b7d953 100644 --- a/src/compute_pressure.cpp +++ b/src/compute_pressure.cpp @@ -67,7 +67,7 @@ ComputePressure::ComputePressure(LAMMPS *lmp, int narg, char **arg) : // process optional args - hybridpairflag = 0; + pairhybridflag = 0; if (narg == 4) { keflag = 1; pairflag = 1; @@ -81,7 +81,7 @@ ComputePressure::ComputePressure(LAMMPS *lmp, int narg, char **arg) : int iarg = 4; while (iarg < narg) { if (strcmp(arg[iarg],"ke") == 0) keflag = 1; - else if (strcmp(arg[iarg],"hybridpair") == 0) { + else if (strcmp(arg[iarg],"pair/hybrid") == 0) { int n = strlen(arg[++iarg]) + 1; if (lmp->suffix) n += strlen(lmp->suffix) + 1; pstyle = new char[n]; @@ -100,17 +100,17 @@ ComputePressure::ComputePressure(LAMMPS *lmp, int narg, char **arg) : // check if pair style with and without suffix exists - hybridpair = (Pair *) force->pair_match(pstyle,1,nsub); - if (!hybridpair && lmp->suffix) { + pairhybrid = (Pair *) force->pair_match(pstyle,1,nsub); + if (!pairhybrid && lmp->suffix) { strcat(pstyle,"/"); strcat(pstyle,lmp->suffix); - hybridpair = (Pair *) force->pair_match(pstyle,1,nsub); + pairhybrid = (Pair *) force->pair_match(pstyle,1,nsub); } - if (!hybridpair) + if (!pairhybrid) error->all(FLERR,"Unrecognized pair style in compute pressure command"); - hybridpairflag = 1; + pairhybridflag = 1; } else if (strcmp(arg[iarg],"pair") == 0) pairflag = 1; else if (strcmp(arg[iarg],"bond") == 0) bondflag = 1; @@ -173,7 +173,7 @@ void ComputePressure::init() nvirial = 0; vptr = NULL; - if (hybridpairflag && force->pair) nvirial++; + if (pairhybridflag && force->pair) nvirial++; if (pairflag && force->pair) nvirial++; if (bondflag && atom->molecular && force->bond) nvirial++; if (angleflag && atom->molecular && force->angle) nvirial++; @@ -186,10 +186,10 @@ void ComputePressure::init() if (nvirial) { vptr = new double*[nvirial]; nvirial = 0; - if (hybridpairflag && force->pair) { + if (pairhybridflag && force->pair) { PairHybrid *ph = (PairHybrid *) force->pair; ph->no_virial_fdotr_compute = 1; - vptr[nvirial++] = hybridpair->virial; + vptr[nvirial++] = pairhybrid->virial; } if (pairflag && force->pair) vptr[nvirial++] = force->pair->virial; if (bondflag && force->bond) vptr[nvirial++] = force->bond->virial; diff --git a/src/compute_pressure.h b/src/compute_pressure.h index 2982271390..76a4066179 100644 --- a/src/compute_pressure.h +++ b/src/compute_pressure.h @@ -41,8 +41,8 @@ class ComputePressure : public Compute { Compute *temperature; char *id_temp; double virial[6]; - int hybridpairflag; - class Pair *hybridpair; + int pairhybridflag; + class Pair *pairhybrid; int keflag,pairflag,bondflag,angleflag,dihedralflag,improperflag; int fixflag,kspaceflag; -- GitLab From fc1d8f2cbf03245a376dcb9fd4b1dcaf95e36fe5 Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Tue, 2 Jul 2019 01:12:16 -0400 Subject: [PATCH 159/469] more cleanup of include file handling. starting to work on files in packages --- src/OPT/pair_lj_long_coul_long_opt.cpp | 1 + src/PYTHON/fix_python_invoke.cpp | 2 +- src/PYTHON/fix_python_move.cpp | 2 +- src/PYTHON/pair_python.cpp | 2 +- src/PYTHON/python_impl.cpp | 2 +- src/RIGID/fix_ehex.cpp | 7 +-- src/RIGID/fix_ehex.h | 20 ++++----- src/RIGID/fix_rattle.cpp | 11 ----- src/RIGID/fix_rattle.h | 1 - src/RIGID/fix_rigid.cpp | 3 +- src/RIGID/fix_rigid_nh.cpp | 1 - src/RIGID/fix_rigid_nh_small.cpp | 3 +- src/RIGID/fix_rigid_nph.cpp | 1 - src/SHOCK/fix_append_atoms.cpp | 2 +- src/SHOCK/fix_msst.cpp | 5 +-- src/SHOCK/fix_nphug.cpp | 3 -- src/SHOCK/fix_wall_piston.cpp | 2 - src/SNAP/compute_snav_atom.cpp | 3 +- src/SNAP/pair_snap.cpp | 5 +-- src/SNAP/sna.cpp | 8 +--- src/SPIN/compute_spin.cpp | 8 +--- src/SPIN/fix_langevin_spin.cpp | 22 ++-------- src/SPIN/fix_neb_spin.cpp | 4 -- src/SPIN/fix_nve_spin.cpp | 16 +------ src/SPIN/fix_nve_spin.h | 2 - src/SPIN/fix_precession_spin.cpp | 9 +--- src/SPIN/fix_setforce_spin.cpp | 4 -- src/SPIN/min_spin.cpp | 3 -- src/SPIN/neb_spin.cpp | 8 ---- src/SPIN/pair_spin.cpp | 13 +----- src/SPIN/pair_spin.h | 2 +- src/SPIN/pair_spin_dipole_cut.cpp | 4 +- src/SPIN/pair_spin_dipole_long.cpp | 55 ++++++++++++------------ src/SPIN/pair_spin_dmi.cpp | 8 +--- src/SPIN/pair_spin_exchange.cpp | 8 +--- src/SPIN/pair_spin_magelec.cpp | 8 +--- src/SPIN/pair_spin_neel.cpp | 9 +--- src/SRD/fix_srd.cpp | 3 +- src/SRD/fix_wall_srd.cpp | 4 +- src/USER-EFF/atom_vec_electron.cpp | 2 - src/USER-EFF/compute_ke_atom_eff.cpp | 1 - src/USER-EFF/compute_ke_eff.cpp | 2 - src/USER-EFF/compute_temp_deform_eff.cpp | 1 - src/USER-EFF/compute_temp_eff.cpp | 2 - src/USER-EFF/compute_temp_region_eff.cpp | 2 - src/USER-EFF/fix_langevin_eff.cpp | 6 --- src/USER-EFF/fix_nh_eff.cpp | 2 - src/USER-EFF/fix_nve_eff.cpp | 2 - src/USER-EFF/fix_nvt_eff.cpp | 1 - src/USER-EFF/fix_temp_rescale_eff.cpp | 2 - src/USER-EFF/pair_eff_cut.cpp | 3 +- src/USER-PHONON/fix_phonon.cpp | 5 +-- 52 files changed, 75 insertions(+), 230 deletions(-) diff --git a/src/OPT/pair_lj_long_coul_long_opt.cpp b/src/OPT/pair_lj_long_coul_long_opt.cpp index 243b64391f..03853057f4 100644 --- a/src/OPT/pair_lj_long_coul_long_opt.cpp +++ b/src/OPT/pair_lj_long_coul_long_opt.cpp @@ -16,6 +16,7 @@ ------------------------------------------------------------------------- */ #include +#include #include "pair_lj_long_coul_long_opt.h" #include "atom.h" #include "force.h" diff --git a/src/PYTHON/fix_python_invoke.cpp b/src/PYTHON/fix_python_invoke.cpp index f704bd9741..7fa9861c3f 100644 --- a/src/PYTHON/fix_python_invoke.cpp +++ b/src/PYTHON/fix_python_invoke.cpp @@ -15,7 +15,7 @@ Contributing author: Richard Berger (Temple U) ------------------------------------------------------------------------- */ -#include +#include // IWYU pragma: keep #include #include "fix_python_invoke.h" #include "force.h" diff --git a/src/PYTHON/fix_python_move.cpp b/src/PYTHON/fix_python_move.cpp index 56b7768669..b253df6828 100644 --- a/src/PYTHON/fix_python_move.cpp +++ b/src/PYTHON/fix_python_move.cpp @@ -15,7 +15,7 @@ Contributing author: Richard Berger (Temple U) ------------------------------------------------------------------------- */ -#include +#include // IWYU pragma: keep #include #include "fix_python_move.h" #include "lmppython.h" diff --git a/src/PYTHON/pair_python.cpp b/src/PYTHON/pair_python.cpp index 638077da48..5b8f23400b 100644 --- a/src/PYTHON/pair_python.cpp +++ b/src/PYTHON/pair_python.cpp @@ -15,7 +15,7 @@ Contributing authors: Axel Kohlmeyer and Richard Berger (Temple U) ------------------------------------------------------------------------- */ -#include +#include // IWYU pragma: keep #include #include #include "pair_python.h" diff --git a/src/PYTHON/python_impl.cpp b/src/PYTHON/python_impl.cpp index 249d4f7bb1..7456021675 100644 --- a/src/PYTHON/python_impl.cpp +++ b/src/PYTHON/python_impl.cpp @@ -17,7 +17,7 @@ #include #include -#include +#include // IWYU pragma: keep #include "python_impl.h" #include "force.h" #include "input.h" diff --git a/src/RIGID/fix_ehex.cpp b/src/RIGID/fix_ehex.cpp index 1476c71d3f..0bbdea51c6 100644 --- a/src/RIGID/fix_ehex.cpp +++ b/src/RIGID/fix_ehex.cpp @@ -22,8 +22,8 @@ which implements the heat exchange (HEX) algorithm. ------------------------------------------------------------------------- */ +#include #include -#include #include #include "fix_ehex.h" #include "atom.h" @@ -33,14 +33,9 @@ #include "force.h" #include "update.h" #include "modify.h" -#include "input.h" -#include "variable.h" #include "memory.h" #include "error.h" #include "fix_shake.h" -#include "neighbor.h" -#include "comm.h" -#include "timer.h" using namespace LAMMPS_NS; using namespace FixConst; diff --git a/src/RIGID/fix_ehex.h b/src/RIGID/fix_ehex.h index e29ddac135..860ed3d1f3 100644 --- a/src/RIGID/fix_ehex.h +++ b/src/RIGID/fix_ehex.h @@ -22,8 +22,6 @@ FixStyle(ehex,FixEHEX) #define LMP_FIX_EHEX_H #include "fix.h" -#include "fix_shake.h" -#include "region.h" #define EHEX_DEBUG 0 namespace LAMMPS_NS { @@ -41,9 +39,9 @@ class FixEHEX : public Fix { double memory_usage(); void update_scalingmask(); void com_properties(double *, double *, double *, double*, double *, double*); - bool rescale_atom(int i, Region*region); + bool rescale_atom(int i, class Region *region); virtual void grow_arrays(int nmax); - bool check_cluster(tagint *shake_atom, int n, Region * region); + bool check_cluster(tagint *shake_atom, int n, class Region *region); private: int iregion; @@ -53,14 +51,14 @@ class FixEHEX : public Fix { char *idregion; int me; - double **x; // coordinates - double **f; // forces - double **v; // velocities - double *mass; // masses - double *rmass; // reduced masses - int *type; // atom types + double **x; // coordinates + double **f; // forces + double **v; // velocities + double *mass; // masses + double *rmass; // reduced masses + int *type; // atom types int nlocal; // number of local atoms - FixShake * fshake; // pointer to fix_shake/fix_rattle + class FixShake * fshake; // pointer to fix_shake/fix_rattle int constraints; // constraints (0/1) int cluster; // rescaling entire clusters (0/1) int hex; // HEX mode (0/1) diff --git a/src/RIGID/fix_rattle.cpp b/src/RIGID/fix_rattle.cpp index 403f3091c6..db43b9e82d 100644 --- a/src/RIGID/fix_rattle.cpp +++ b/src/RIGID/fix_rattle.cpp @@ -17,31 +17,20 @@ #include #include -#include #include -#include #include "fix_rattle.h" #include "atom.h" -#include "atom_vec.h" -#include "molecule.h" #include "update.h" -#include "respa.h" #include "modify.h" #include "domain.h" #include "force.h" -#include "bond.h" -#include "angle.h" #include "comm.h" -#include "group.h" -#include "fix_respa.h" -#include "math_const.h" #include "math_extra.h" #include "memory.h" #include "error.h" using namespace LAMMPS_NS; using namespace FixConst; -using namespace MathConst; using namespace MathExtra; // set RATTLE_DEBUG 1 to check constraints at end of timestep diff --git a/src/RIGID/fix_rattle.h b/src/RIGID/fix_rattle.h index 48edaef379..cab148f10c 100644 --- a/src/RIGID/fix_rattle.h +++ b/src/RIGID/fix_rattle.h @@ -20,7 +20,6 @@ FixStyle(rattle,FixRattle) #ifndef LMP_FIX_RATTLE_H #define LMP_FIX_RATTLE_H -#include "fix.h" #include "fix_shake.h" namespace LAMMPS_NS { diff --git a/src/RIGID/fix_rigid.cpp b/src/RIGID/fix_rigid.cpp index abb669bc02..19eb22a7fa 100644 --- a/src/RIGID/fix_rigid.cpp +++ b/src/RIGID/fix_rigid.cpp @@ -11,8 +11,8 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ +#include #include -#include #include #include #include "fix_rigid.h" @@ -31,7 +31,6 @@ #include "force.h" #include "input.h" #include "variable.h" -#include "output.h" #include "math_const.h" #include "memory.h" #include "error.h" diff --git a/src/RIGID/fix_rigid_nh.cpp b/src/RIGID/fix_rigid_nh.cpp index 4acc8d3411..2e1090ec88 100644 --- a/src/RIGID/fix_rigid_nh.cpp +++ b/src/RIGID/fix_rigid_nh.cpp @@ -17,7 +17,6 @@ Miller et al., J Chem Phys. 116, 8649-8659 (2002) ------------------------------------------------------------------------- */ -#include #include #include #include "fix_rigid_nh.h" diff --git a/src/RIGID/fix_rigid_nh_small.cpp b/src/RIGID/fix_rigid_nh_small.cpp index 5016d3f168..8de588bd9b 100644 --- a/src/RIGID/fix_rigid_nh_small.cpp +++ b/src/RIGID/fix_rigid_nh_small.cpp @@ -17,8 +17,8 @@ Miller et al., J Chem Phys. 116, 8649-8659 (2002) ------------------------------------------------------------------------- */ +#include #include -#include #include #include "fix_rigid_nh_small.h" #include "math_extra.h" @@ -32,7 +32,6 @@ #include "comm.h" #include "force.h" #include "kspace.h" -#include "output.h" #include "memory.h" #include "error.h" diff --git a/src/RIGID/fix_rigid_nph.cpp b/src/RIGID/fix_rigid_nph.cpp index 45a4a8d09c..6080fb05af 100644 --- a/src/RIGID/fix_rigid_nph.cpp +++ b/src/RIGID/fix_rigid_nph.cpp @@ -19,7 +19,6 @@ #include #include "fix_rigid_nph.h" -#include "domain.h" #include "modify.h" #include "error.h" diff --git a/src/SHOCK/fix_append_atoms.cpp b/src/SHOCK/fix_append_atoms.cpp index 2e515839c5..5e81b75c0d 100644 --- a/src/SHOCK/fix_append_atoms.cpp +++ b/src/SHOCK/fix_append_atoms.cpp @@ -11,9 +11,9 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ +#include #include #include -#include #include "fix_append_atoms.h" #include "atom.h" #include "atom_vec.h" diff --git a/src/SHOCK/fix_msst.cpp b/src/SHOCK/fix_msst.cpp index c800e8a85d..15ee4d370f 100644 --- a/src/SHOCK/fix_msst.cpp +++ b/src/SHOCK/fix_msst.cpp @@ -17,22 +17,19 @@ see Reed, Fried, Joannopoulos, Phys Rev Lett, 90, 235503 (2003) ------------------------------------------------------------------------- */ +#include #include -#include #include #include "fix_msst.h" #include "atom.h" #include "force.h" #include "comm.h" -#include "output.h" #include "modify.h" #include "fix_external.h" #include "compute.h" #include "kspace.h" #include "update.h" -#include "respa.h" #include "domain.h" -#include "thermo.h" #include "memory.h" #include "error.h" diff --git a/src/SHOCK/fix_nphug.cpp b/src/SHOCK/fix_nphug.cpp index c6df6646cf..5d5a1642c0 100644 --- a/src/SHOCK/fix_nphug.cpp +++ b/src/SHOCK/fix_nphug.cpp @@ -12,7 +12,6 @@ ------------------------------------------------------------------------- */ #include -#include #include #include "fix_nphug.h" #include "modify.h" @@ -22,8 +21,6 @@ #include "force.h" #include "domain.h" #include "group.h" -#include "memory.h" -#include "comm.h" using namespace LAMMPS_NS; using namespace FixConst; diff --git a/src/SHOCK/fix_wall_piston.cpp b/src/SHOCK/fix_wall_piston.cpp index eb89e19517..31f70b4174 100644 --- a/src/SHOCK/fix_wall_piston.cpp +++ b/src/SHOCK/fix_wall_piston.cpp @@ -13,10 +13,8 @@ #include #include -#include #include "fix_wall_piston.h" #include "atom.h" -#include "modify.h" #include "domain.h" #include "lattice.h" #include "update.h" diff --git a/src/SNAP/compute_snav_atom.cpp b/src/SNAP/compute_snav_atom.cpp index 1f702496ed..5faf7a1872 100644 --- a/src/SNAP/compute_snav_atom.cpp +++ b/src/SNAP/compute_snav_atom.cpp @@ -10,10 +10,10 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include "sna.h" #include #include #include "compute_snav_atom.h" +#include "sna.h" #include "atom.h" #include "update.h" #include "modify.h" @@ -21,7 +21,6 @@ #include "neigh_list.h" #include "neigh_request.h" #include "force.h" -#include "pair.h" #include "comm.h" #include "memory.h" #include "error.h" diff --git a/src/SNAP/pair_snap.cpp b/src/SNAP/pair_snap.cpp index f9ba8922a0..f0f3ef72c6 100644 --- a/src/SNAP/pair_snap.cpp +++ b/src/SNAP/pair_snap.cpp @@ -11,24 +11,21 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ +#include #include #include #include #include "pair_snap.h" #include "atom.h" -#include "atom_vec.h" #include "force.h" #include "comm.h" #include "neighbor.h" #include "neigh_list.h" #include "neigh_request.h" #include "sna.h" -#include "domain.h" #include "memory.h" #include "error.h" -#include - using namespace LAMMPS_NS; #define MAXLINE 1024 diff --git a/src/SNAP/sna.cpp b/src/SNAP/sna.cpp index ec545c51b2..d7d9b5163d 100644 --- a/src/SNAP/sna.cpp +++ b/src/SNAP/sna.cpp @@ -15,17 +15,11 @@ Contributing authors: Aidan Thompson, Christian Trott, SNL ------------------------------------------------------------------------- */ -#include "sna.h" #include +#include "sna.h" #include "math_const.h" -#include "math_extra.h" -#include -#include - #include "memory.h" #include "error.h" -#include "comm.h" -#include "atom.h" using namespace std; using namespace LAMMPS_NS; diff --git a/src/SPIN/compute_spin.cpp b/src/SPIN/compute_spin.cpp index 0a881e1de6..ec11bc68f2 100644 --- a/src/SPIN/compute_spin.cpp +++ b/src/SPIN/compute_spin.cpp @@ -22,20 +22,16 @@ ------------------------------------------------------------------------- */ #include -#include -#include "atom.h" +#include #include "compute_spin.h" -#include "domain.h" +#include "atom.h" #include "error.h" #include "force.h" -#include "math_special.h" #include "math_const.h" #include "memory.h" -#include "modify.h" #include "update.h" using namespace LAMMPS_NS; -using namespace MathSpecial; using namespace MathConst; /* ---------------------------------------------------------------------- */ diff --git a/src/SPIN/fix_langevin_spin.cpp b/src/SPIN/fix_langevin_spin.cpp index ec6f719a77..6936c701c6 100644 --- a/src/SPIN/fix_langevin_spin.cpp +++ b/src/SPIN/fix_langevin_spin.cpp @@ -21,31 +21,19 @@ and molecular dynamics. Journal of Computational Physics. ------------------------------------------------------------------------- */ -#include #include #include -#include - -#include "atom.h" -#include "atom_vec_ellipsoid.h" +#include "fix_langevin_spin.h" #include "comm.h" -#include "compute.h" -#include "domain.h" #include "error.h" -#include "fix_langevin_spin.h" #include "force.h" -#include "group.h" -#include "input.h" #include "math_const.h" -#include "math_extra.h" #include "memory.h" #include "modify.h" -#include "random_mars.h" #include "random_park.h" -#include "region.h" #include "respa.h" #include "update.h" -#include "variable.h" +#include "utils.h" using namespace LAMMPS_NS; using namespace FixConst; @@ -142,13 +130,11 @@ void FixLangevinSpin::init() void FixLangevinSpin::setup(int vflag) { - if (strstr(update->integrate_style,"verlet")) - post_force(vflag); - else { + if (utils::strmatch(update->integrate_style,"^respa")) { ((Respa *) update->integrate)->copy_flevel_f(nlevels_respa-1); post_force_respa(vflag,nlevels_respa-1,0); ((Respa *) update->integrate)->copy_f_flevel(nlevels_respa-1); - } + } else post_force(vflag); } /* ---------------------------------------------------------------------- */ diff --git a/src/SPIN/fix_neb_spin.cpp b/src/SPIN/fix_neb_spin.cpp index a8cb0cd2ca..7ed8967a24 100644 --- a/src/SPIN/fix_neb_spin.cpp +++ b/src/SPIN/fix_neb_spin.cpp @@ -23,13 +23,11 @@ #include #include -#include #include #include "fix_neb_spin.h" #include "universe.h" #include "update.h" #include "atom.h" -#include "domain.h" #include "comm.h" #include "modify.h" #include "compute.h" @@ -37,11 +35,9 @@ #include "memory.h" #include "error.h" #include "force.h" -#include "math_const.h" using namespace LAMMPS_NS; using namespace FixConst; -using namespace MathConst; enum{SINGLE_PROC_DIRECT,SINGLE_PROC_MAP,MULTI_PROC}; diff --git a/src/SPIN/fix_nve_spin.cpp b/src/SPIN/fix_nve_spin.cpp index 595ddb0cc2..d35585c7a6 100644 --- a/src/SPIN/fix_nve_spin.cpp +++ b/src/SPIN/fix_nve_spin.cpp @@ -21,38 +21,24 @@ and molecular dynamics. Journal of Computational Physics. ------------------------------------------------------------------------- */ -#include -#include #include - +#include "fix_nve_spin.h" #include "atom.h" -#include "atom_vec.h" #include "citeme.h" #include "comm.h" #include "domain.h" #include "error.h" -#include "fix_nve_spin.h" #include "fix_precession_spin.h" #include "fix_langevin_spin.h" #include "fix_setforce_spin.h" #include "force.h" -#include "math_vector.h" -#include "math_extra.h" -#include "math_const.h" #include "memory.h" #include "modify.h" -#include "neighbor.h" -#include "neigh_list.h" -#include "pair.h" -#include "pair_hybrid.h" #include "pair_spin.h" -#include "respa.h" #include "update.h" using namespace LAMMPS_NS; using namespace FixConst; -using namespace MathConst; -using namespace MathExtra; static const char cite_fix_nve_spin[] = "fix nve/spin command:\n\n" diff --git a/src/SPIN/fix_nve_spin.h b/src/SPIN/fix_nve_spin.h index 4800575c06..1e3b87c1fb 100644 --- a/src/SPIN/fix_nve_spin.h +++ b/src/SPIN/fix_nve_spin.h @@ -21,8 +21,6 @@ FixStyle(nve/spin,FixNVESpin) #define LMP_FIX_NVE_SPIN_H #include "fix.h" -#include "pair.h" -#include "pair_spin.h" namespace LAMMPS_NS { diff --git a/src/SPIN/fix_precession_spin.cpp b/src/SPIN/fix_precession_spin.cpp index 1ea134d367..7764bb0438 100644 --- a/src/SPIN/fix_precession_spin.cpp +++ b/src/SPIN/fix_precession_spin.cpp @@ -21,21 +21,16 @@ and molecular dynamics. Journal of Computational Physics. ------------------------------------------------------------------------- */ +#include #include -#include -#include #include +#include "fix_precession_spin.h" #include "atom.h" #include "error.h" -#include "domain.h" -#include "error.h" -#include "fix_precession_spin.h" #include "force.h" #include "input.h" #include "math_const.h" -#include "memory.h" #include "modify.h" -#include "neigh_list.h" #include "respa.h" #include "update.h" #include "variable.h" diff --git a/src/SPIN/fix_setforce_spin.cpp b/src/SPIN/fix_setforce_spin.cpp index c2807418ec..1ab35c9663 100644 --- a/src/SPIN/fix_setforce_spin.cpp +++ b/src/SPIN/fix_setforce_spin.cpp @@ -21,7 +21,6 @@ and molecular dynamics. Journal of Computational Physics. ------------------------------------------------------------------------- */ -#include #include #include "fix_setforce_spin.h" #include "atom.h" @@ -29,12 +28,9 @@ #include "modify.h" #include "domain.h" #include "region.h" -#include "respa.h" #include "input.h" #include "variable.h" #include "memory.h" -#include "error.h" -#include "force.h" using namespace LAMMPS_NS; using namespace FixConst; diff --git a/src/SPIN/min_spin.cpp b/src/SPIN/min_spin.cpp index 2bddc110e7..3a330f448a 100644 --- a/src/SPIN/min_spin.cpp +++ b/src/SPIN/min_spin.cpp @@ -19,7 +19,6 @@ #include #include -#include #include #include "min_spin.h" #include "universe.h" @@ -29,8 +28,6 @@ #include "output.h" #include "timer.h" #include "error.h" -#include "modify.h" -#include "math_special.h" #include "math_const.h" using namespace LAMMPS_NS; diff --git a/src/SPIN/neb_spin.cpp b/src/SPIN/neb_spin.cpp index 46a0541488..400ce3d363 100644 --- a/src/SPIN/neb_spin.cpp +++ b/src/SPIN/neb_spin.cpp @@ -21,18 +21,12 @@ Computer Physics Communications, 196, 335-347. ------------------------------------------------------------------------- */ -// lmptype.h must be first b/c this file uses MAXBIGINT and includes mpi.h -// due to OpenMPI bug which sets INT64_MAX via its mpi.h -// before lmptype.h can set flags to insure it is done correctly - -#include "lmptype.h" #include #include #include #include #include "neb_spin.h" #include "citeme.h" -#include "compute.h" #include "force.h" #include "universe.h" #include "atom.h" @@ -49,10 +43,8 @@ #include "timer.h" #include "memory.h" #include "error.h" -#include "math_const.h" using namespace LAMMPS_NS; -using namespace MathConst; static const char cite_neb_spin[] = "neb/spin command:\n\n" diff --git a/src/SPIN/pair_spin.cpp b/src/SPIN/pair_spin.cpp index 929b79bef3..93d9a1e127 100644 --- a/src/SPIN/pair_spin.cpp +++ b/src/SPIN/pair_spin.cpp @@ -21,26 +21,15 @@ and molecular dynamics. Journal of Computational Physics. ------------------------------------------------------------------------- */ -#include -#include #include - +#include "pair_spin.h" #include "atom.h" -#include "comm.h" #include "error.h" #include "fix.h" -#include "fix_nve_spin.h" #include "force.h" -#include "neighbor.h" -#include "neigh_list.h" -#include "neigh_request.h" #include "math_const.h" -#include "memory.h" #include "modify.h" #include "pair.h" -#include "pair_hybrid.h" -#include "pair_hybrid_overlay.h" -#include "pair_spin.h" #include "update.h" using namespace LAMMPS_NS; diff --git a/src/SPIN/pair_spin.h b/src/SPIN/pair_spin.h index 1be8550c65..3a909e1d13 100644 --- a/src/SPIN/pair_spin.h +++ b/src/SPIN/pair_spin.h @@ -14,7 +14,7 @@ #ifndef LMP_PAIR_SPIN_H #define LMP_PAIR_SPIN_H -#include "pair.h" +#include "pair.h" // IWYU pragma: export namespace LAMMPS_NS { diff --git a/src/SPIN/pair_spin_dipole_cut.cpp b/src/SPIN/pair_spin_dipole_cut.cpp index 4ff198488a..8d9b5b8f2b 100644 --- a/src/SPIN/pair_spin_dipole_cut.cpp +++ b/src/SPIN/pair_spin_dipole_cut.cpp @@ -21,9 +21,8 @@ and molecular dynamics. Journal of Computational Physics. ------------------------------------------------------------------------- */ +#include #include -#include -#include #include #include "pair_spin_dipole_cut.h" #include "atom.h" @@ -31,6 +30,7 @@ #include "neighbor.h" #include "neigh_list.h" #include "neigh_request.h" +#include "fix.h" #include "fix_nve_spin.h" #include "force.h" #include "math_const.h" diff --git a/src/SPIN/pair_spin_dipole_long.cpp b/src/SPIN/pair_spin_dipole_long.cpp index e3575a6a07..84c55a8c3c 100644 --- a/src/SPIN/pair_spin_dipole_long.cpp +++ b/src/SPIN/pair_spin_dipole_long.cpp @@ -13,20 +13,19 @@ /* ------------------------------------------------------------------------ Contributing authors: Julien Tranchida (SNL) - Stan Moore (SNL) + Stan Moore (SNL) ------------------------------------------------------------------------- */ +#include #include -#include -#include #include - #include "pair_spin_dipole_long.h" #include "atom.h" #include "comm.h" #include "neighbor.h" #include "neigh_list.h" #include "neigh_request.h" +#include "fix.h" #include "fix_nve_spin.h" #include "force.h" #include "kspace.h" @@ -59,12 +58,12 @@ lockfixnvespin(NULL) no_virial_fdotr_compute = 1; lattice_flag = 0; - hbar = force->hplanck/MY_2PI; // eV/(rad.THz) + hbar = force->hplanck/MY_2PI; // eV/(rad.THz) mub = 9.274e-4; // in A.Ang^2 mu_0 = 785.15; // in eV/Ang/A^2 mub2mu0 = mub * mub * mu_0 / (4.0*MY_PI); // in eV.Ang^3 - //mub2mu0 = mub * mub * mu_0 / (4.0*MY_PI); // in eV - mub2mu0hbinv = mub2mu0 / hbar; // in rad.THz + //mub2mu0 = mub * mub * mu_0 / (4.0*MY_PI); // in eV + mub2mu0hbinv = mub2mu0 / hbar; // in rad.THz } @@ -243,7 +242,7 @@ void PairSpinDipoleLong::compute(int eflag, int vflag) double **x = atom->x; double **f = atom->f; double **fm = atom->fm; - double **sp = atom->sp; + double **sp = atom->sp; int *type = atom->type; int nlocal = atom->nlocal; int newton_pair = force->newton_pair; @@ -314,36 +313,36 @@ void PairSpinDipoleLong::compute(int eflag, int vflag) bij[2] = (3.0*bij[1] + pre2*expm2) * r2inv; bij[3] = (5.0*bij[2] + pre3*expm2) * r2inv; - compute_long(i,j,eij,bij,fmi,spi,spj); - compute_long_mech(i,j,eij,bij,fmi,spi,spj); + compute_long(i,j,eij,bij,fmi,spi,spj); + compute_long_mech(i,j,eij,bij,fmi,spi,spj); } // force accumulation - f[i][0] += fi[0]; - f[i][1] += fi[1]; + f[i][0] += fi[0]; + f[i][1] += fi[1]; f[i][2] += fi[2]; - fm[i][0] += fmi[0]; - fm[i][1] += fmi[1]; + fm[i][0] += fmi[0]; + fm[i][1] += fmi[1]; fm[i][2] += fmi[2]; if (newton_pair || j < nlocal) { - f[j][0] -= fi[0]; - f[j][1] -= fi[1]; + f[j][0] -= fi[0]; + f[j][1] -= fi[1]; f[j][2] -= fi[2]; } if (eflag) { - if (rsq <= local_cut2) { - evdwl -= spi[0]*fmi[0] + spi[1]*fmi[1] + - spi[2]*fmi[2]; - evdwl *= hbar; - } + if (rsq <= local_cut2) { + evdwl -= spi[0]*fmi[0] + spi[1]*fmi[1] + + spi[2]*fmi[2]; + evdwl *= hbar; + } } else evdwl = 0.0; if (evflag) ev_tally_xyz(i,j,nlocal,newton_pair, - evdwl,ecoul,fi[0],fi[1],fi[2],rij[0],rij[1],rij[2]); + evdwl,ecoul,fi[0],fi[1],fi[2],rij[0],rij[1],rij[2]); } } @@ -365,7 +364,7 @@ void PairSpinDipoleLong::compute_single_pair(int ii, double fmi[3]) int *type = atom->type; double **x = atom->x; - double **sp = atom->sp; + double **sp = atom->sp; double **fm_long = atom->fm_long; ilist = list->ilist; @@ -550,7 +549,7 @@ void PairSpinDipoleLong::write_restart(FILE *fp) for (j = i; j <= atom->ntypes; j++) { fwrite(&setflag[i][j],sizeof(int),1,fp); if (setflag[i][j]) { - fwrite(&cut_spin_long[i][j],sizeof(int),1,fp); + fwrite(&cut_spin_long[i][j],sizeof(int),1,fp); } } } @@ -573,10 +572,10 @@ void PairSpinDipoleLong::read_restart(FILE *fp) if (me == 0) fread(&setflag[i][j],sizeof(int),1,fp); MPI_Bcast(&setflag[i][j],1,MPI_INT,0,world); if (setflag[i][j]) { - if (me == 0) { - fread(&cut_spin_long[i][j],sizeof(int),1,fp); - } - MPI_Bcast(&cut_spin_long[i][j],1,MPI_INT,0,world); + if (me == 0) { + fread(&cut_spin_long[i][j],sizeof(int),1,fp); + } + MPI_Bcast(&cut_spin_long[i][j],1,MPI_INT,0,world); } } } diff --git a/src/SPIN/pair_spin_dmi.cpp b/src/SPIN/pair_spin_dmi.cpp index 41430d230f..651f4397bd 100644 --- a/src/SPIN/pair_spin_dmi.cpp +++ b/src/SPIN/pair_spin_dmi.cpp @@ -21,28 +21,24 @@ and molecular dynamics. Journal of Computational Physics. ------------------------------------------------------------------------- */ +#include #include -#include #include - +#include "pair_spin_dmi.h" #include "atom.h" #include "comm.h" #include "error.h" #include "force.h" #include "fix.h" #include "fix_nve_spin.h" -#include "pair_hybrid.h" #include "neighbor.h" #include "neigh_list.h" #include "neigh_request.h" -#include "math_const.h" #include "memory.h" #include "modify.h" -#include "pair_spin_dmi.h" #include "update.h" using namespace LAMMPS_NS; -using namespace MathConst; /* ---------------------------------------------------------------------- */ diff --git a/src/SPIN/pair_spin_exchange.cpp b/src/SPIN/pair_spin_exchange.cpp index 93b6d9501e..059a8f5f34 100644 --- a/src/SPIN/pair_spin_exchange.cpp +++ b/src/SPIN/pair_spin_exchange.cpp @@ -21,28 +21,24 @@ and molecular dynamics. Journal of Computational Physics. ------------------------------------------------------------------------- */ +#include #include -#include #include - +#include "pair_spin_exchange.h" #include "atom.h" #include "comm.h" #include "error.h" #include "fix.h" #include "fix_nve_spin.h" #include "force.h" -#include "pair_hybrid.h" #include "neighbor.h" #include "neigh_list.h" #include "neigh_request.h" -#include "math_const.h" #include "memory.h" #include "modify.h" -#include "pair_spin_exchange.h" #include "update.h" using namespace LAMMPS_NS; -using namespace MathConst; /* ---------------------------------------------------------------------- */ diff --git a/src/SPIN/pair_spin_magelec.cpp b/src/SPIN/pair_spin_magelec.cpp index 1f1488b93c..55b96582c8 100644 --- a/src/SPIN/pair_spin_magelec.cpp +++ b/src/SPIN/pair_spin_magelec.cpp @@ -21,28 +21,24 @@ and molecular dynamics. Journal of Computational Physics. ------------------------------------------------------------------------- */ +#include #include -#include #include - +#include "pair_spin_magelec.h" #include "atom.h" #include "comm.h" #include "error.h" #include "fix.h" #include "fix_nve_spin.h" #include "force.h" -#include "pair_hybrid.h" #include "neighbor.h" #include "neigh_list.h" #include "neigh_request.h" -#include "math_const.h" #include "memory.h" #include "modify.h" -#include "pair_spin_magelec.h" #include "update.h" using namespace LAMMPS_NS; -using namespace MathConst; /* ---------------------------------------------------------------------- */ diff --git a/src/SPIN/pair_spin_neel.cpp b/src/SPIN/pair_spin_neel.cpp index 03041da17f..4d68dbdc22 100644 --- a/src/SPIN/pair_spin_neel.cpp +++ b/src/SPIN/pair_spin_neel.cpp @@ -21,29 +21,24 @@ and molecular dynamics. Journal of Computational Physics. ------------------------------------------------------------------------- */ +#include #include -#include #include - +#include "pair_spin_neel.h" #include "atom.h" #include "comm.h" #include "error.h" -#include "force.h" #include "fix.h" #include "fix_nve_spin.h" #include "force.h" -#include "pair_hybrid.h" #include "neighbor.h" #include "neigh_list.h" #include "neigh_request.h" -#include "math_const.h" #include "memory.h" #include "modify.h" -#include "pair_spin_neel.h" #include "update.h" using namespace LAMMPS_NS; -using namespace MathConst; /* ---------------------------------------------------------------------- */ diff --git a/src/SRD/fix_srd.cpp b/src/SRD/fix_srd.cpp index d87d2b5e56..a20ec212fd 100644 --- a/src/SRD/fix_srd.cpp +++ b/src/SRD/fix_srd.cpp @@ -15,9 +15,9 @@ Contributing authors: Jeremy Lechman (SNL), Pieter in 't Veld (BASF) ------------------------------------------------------------------------- */ +#include #include #include -#include #include "fix_srd.h" #include "math_extra.h" #include "atom.h" @@ -27,7 +27,6 @@ #include "group.h" #include "update.h" #include "force.h" -#include "pair.h" #include "domain.h" #include "neighbor.h" #include "comm.h" diff --git a/src/SRD/fix_wall_srd.cpp b/src/SRD/fix_wall_srd.cpp index 24b0c3cec5..cb0f023640 100644 --- a/src/SRD/fix_wall_srd.cpp +++ b/src/SRD/fix_wall_srd.cpp @@ -11,11 +11,9 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include +#include #include #include "fix_wall_srd.h" -#include "atom.h" -#include "modify.h" #include "fix.h" #include "domain.h" #include "lattice.h" diff --git a/src/USER-EFF/atom_vec_electron.cpp b/src/USER-EFF/atom_vec_electron.cpp index 1bc5387c9e..5de78f7510 100644 --- a/src/USER-EFF/atom_vec_electron.cpp +++ b/src/USER-EFF/atom_vec_electron.cpp @@ -15,7 +15,6 @@ Contributing author: Andres Jaramillo-Botero (Caltech) ------------------------------------------------------------------------- */ -#include #include #include #include "atom_vec_electron.h" @@ -23,7 +22,6 @@ #include "comm.h" #include "domain.h" #include "modify.h" -#include "force.h" #include "fix.h" #include "citeme.h" #include "memory.h" diff --git a/src/USER-EFF/compute_ke_atom_eff.cpp b/src/USER-EFF/compute_ke_atom_eff.cpp index b1b87cd3df..c943366f1b 100644 --- a/src/USER-EFF/compute_ke_atom_eff.cpp +++ b/src/USER-EFF/compute_ke_atom_eff.cpp @@ -15,7 +15,6 @@ Contributing author: Andres Jaramillo-Botero ------------------------------------------------------------------------- */ -#include #include #include #include "compute_ke_atom_eff.h" diff --git a/src/USER-EFF/compute_ke_eff.cpp b/src/USER-EFF/compute_ke_eff.cpp index b4f571cb63..3e277fc66c 100644 --- a/src/USER-EFF/compute_ke_eff.cpp +++ b/src/USER-EFF/compute_ke_eff.cpp @@ -16,14 +16,12 @@ ------------------------------------------------------------------------- */ #include -#include #include #include "compute_ke_eff.h" #include "atom.h" #include "update.h" #include "force.h" #include "domain.h" -#include "group.h" #include "error.h" using namespace LAMMPS_NS; diff --git a/src/USER-EFF/compute_temp_deform_eff.cpp b/src/USER-EFF/compute_temp_deform_eff.cpp index 23abb4f99d..7a12a69982 100644 --- a/src/USER-EFF/compute_temp_deform_eff.cpp +++ b/src/USER-EFF/compute_temp_deform_eff.cpp @@ -16,7 +16,6 @@ ------------------------------------------------------------------------- */ #include -#include #include #include #include "compute_temp_deform_eff.h" diff --git a/src/USER-EFF/compute_temp_eff.cpp b/src/USER-EFF/compute_temp_eff.cpp index 956461adf1..d745269ff5 100644 --- a/src/USER-EFF/compute_temp_eff.cpp +++ b/src/USER-EFF/compute_temp_eff.cpp @@ -17,8 +17,6 @@ #include #include -#include -#include #include "compute_temp_eff.h" #include "atom.h" #include "update.h" diff --git a/src/USER-EFF/compute_temp_region_eff.cpp b/src/USER-EFF/compute_temp_region_eff.cpp index 659bdfca5e..cec87b29ab 100644 --- a/src/USER-EFF/compute_temp_region_eff.cpp +++ b/src/USER-EFF/compute_temp_region_eff.cpp @@ -16,14 +16,12 @@ ------------------------------------------------------------------------- */ #include -#include #include #include #include "compute_temp_region_eff.h" #include "atom.h" #include "update.h" #include "force.h" -#include "modify.h" #include "domain.h" #include "region.h" #include "group.h" diff --git a/src/USER-EFF/fix_langevin_eff.cpp b/src/USER-EFF/fix_langevin_eff.cpp index d362113997..5158d7c681 100644 --- a/src/USER-EFF/fix_langevin_eff.cpp +++ b/src/USER-EFF/fix_langevin_eff.cpp @@ -17,19 +17,13 @@ #include #include -#include #include #include "fix_langevin_eff.h" -#include "math_extra.h" #include "atom.h" -#include "force.h" #include "update.h" #include "modify.h" #include "compute.h" #include "domain.h" -#include "region.h" -#include "respa.h" -#include "comm.h" #include "input.h" #include "variable.h" #include "random_mars.h" diff --git a/src/USER-EFF/fix_nh_eff.cpp b/src/USER-EFF/fix_nh_eff.cpp index 3e0a59612c..034233732e 100644 --- a/src/USER-EFF/fix_nh_eff.cpp +++ b/src/USER-EFF/fix_nh_eff.cpp @@ -15,12 +15,10 @@ Contributing author: Andres Jaramillo-Botero (Caltech) ------------------------------------------------------------------------- */ -#include #include #include "fix_nh_eff.h" #include "atom.h" #include "atom_vec.h" -#include "group.h" #include "error.h" #include "domain.h" diff --git a/src/USER-EFF/fix_nve_eff.cpp b/src/USER-EFF/fix_nve_eff.cpp index 699dd9f949..ea719c91c0 100644 --- a/src/USER-EFF/fix_nve_eff.cpp +++ b/src/USER-EFF/fix_nve_eff.cpp @@ -15,8 +15,6 @@ Contributing author: Andres Jaramillo-Botero (Caltech) ------------------------------------------------------------------------- */ -#include -#include #include #include #include "fix_nve_eff.h" diff --git a/src/USER-EFF/fix_nvt_eff.cpp b/src/USER-EFF/fix_nvt_eff.cpp index 9e23ee023b..8516accd31 100644 --- a/src/USER-EFF/fix_nvt_eff.cpp +++ b/src/USER-EFF/fix_nvt_eff.cpp @@ -12,7 +12,6 @@ ------------------------------------------------------------------------- */ #include -#include #include "fix_nvt_eff.h" #include "group.h" #include "modify.h" diff --git a/src/USER-EFF/fix_temp_rescale_eff.cpp b/src/USER-EFF/fix_temp_rescale_eff.cpp index 37f45b3c28..4a8f4b0372 100644 --- a/src/USER-EFF/fix_temp_rescale_eff.cpp +++ b/src/USER-EFF/fix_temp_rescale_eff.cpp @@ -23,8 +23,6 @@ #include "force.h" #include "group.h" #include "update.h" -#include "domain.h" -#include "region.h" #include "comm.h" #include "modify.h" #include "compute.h" diff --git a/src/USER-EFF/pair_eff_cut.cpp b/src/USER-EFF/pair_eff_cut.cpp index f566922ef7..a4c0557620 100644 --- a/src/USER-EFF/pair_eff_cut.cpp +++ b/src/USER-EFF/pair_eff_cut.cpp @@ -15,8 +15,8 @@ Contributing author: Andres Jaramillo-Botero ------------------------------------------------------------------------- */ +#include #include -#include #include #include #include "pair_eff_cut.h" @@ -31,7 +31,6 @@ #include "neigh_list.h" #include "memory.h" #include "error.h" -#include "atom_vec_electron.h" using namespace LAMMPS_NS; diff --git a/src/USER-PHONON/fix_phonon.cpp b/src/USER-PHONON/fix_phonon.cpp index cdbe4068bc..9b663ce383 100644 --- a/src/USER-PHONON/fix_phonon.cpp +++ b/src/USER-PHONON/fix_phonon.cpp @@ -23,8 +23,8 @@ konglt@sjtu.edu.cn; konglt@gmail.com ------------------------------------------------------------------------- */ -#include -#include +#include +#include #include #include "fix_phonon.h" #include "fft3d_wrap.h" @@ -33,7 +33,6 @@ #include "domain.h" #include "force.h" #include "group.h" -#include "lattice.h" #include "modify.h" #include "update.h" #include "citeme.h" -- GitLab From 350d8f581275b43aceb8c2c14d59701ec2c4b3dd Mon Sep 17 00:00:00 2001 From: Julien Devemy Date: Tue, 2 Jul 2019 15:51:52 +0200 Subject: [PATCH 160/469] Missing some hybridpair replacement --- doc/src/compute_pressure.txt | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/doc/src/compute_pressure.txt b/doc/src/compute_pressure.txt index b8d52b83de..9b27413cfc 100644 --- a/doc/src/compute_pressure.txt +++ b/doc/src/compute_pressure.txt @@ -16,7 +16,7 @@ ID, group-ID are documented in "compute"_compute.html command pressure = style name of this compute command temp-ID = ID of compute that calculates temperature, can be NULL if not needed zero or more keywords may be appended -keyword = {ke} or {pair} or {bond} or {angle} or {dihedral} or {improper} or {kspace} or {fix} or {virial} or {hybridpair} :ul +keyword = {ke} or {pair} or {bond} or {angle} or {dihedral} or {improper} or {kspace} or {fix} or {virial} or {pair/hybrid} :ul [Examples:] @@ -68,7 +68,7 @@ extra keywords are listed, then only those components are summed to compute temperature or ke and/or the virial. The {virial} keyword means include all terms except the kinetic energy {ke}. -The {hybridpair} keyword means to only include contribution +The {pair/hybrid} keyword means to only include contribution from a sub-style in a {hybrid} or {hybrid/overlay} pair style. Details of how LAMMPS computes the virial efficiently for the entire -- GitLab From 9984cbc99a371665d933e974bb0c84e66c720846 Mon Sep 17 00:00:00 2001 From: Julien Devemy Date: Tue, 2 Jul 2019 16:13:20 +0200 Subject: [PATCH 161/469] Recheck existence of pair style in init --- src/compute_pressure.cpp | 16 +++++++++++++++- src/compute_pressure.h | 1 + 2 files changed, 16 insertions(+), 1 deletion(-) diff --git a/src/compute_pressure.cpp b/src/compute_pressure.cpp index d586b7d953..2f412c23a0 100644 --- a/src/compute_pressure.cpp +++ b/src/compute_pressure.cpp @@ -87,7 +87,7 @@ ComputePressure::ComputePressure(LAMMPS *lmp, int narg, char **arg) : pstyle = new char[n]; strcpy(pstyle,arg[iarg++]); - int nsub = 0; + nsub = 0; if (narg > iarg) { if (isdigit(arg[iarg][0])) { @@ -166,6 +166,20 @@ void ComputePressure::init() temperature = modify->compute[icompute]; } + // recheck if pair style with and without suffix exists + + if (pairhybridflag) { + pairhybrid = (Pair *) force->pair_match(pstyle,1,nsub); + if (!pairhybrid && lmp->suffix) { + strcat(pstyle,"/"); + strcat(pstyle,lmp->suffix); + pairhybrid = (Pair *) force->pair_match(pstyle,1,nsub); + } + + if (!pairhybrid) + error->all(FLERR,"Unrecognized pair style in compute pressure command"); + } + // detect contributions to virial // vptr points to all virial[6] contributions diff --git a/src/compute_pressure.h b/src/compute_pressure.h index 76a4066179..8d0ec4aa04 100644 --- a/src/compute_pressure.h +++ b/src/compute_pressure.h @@ -50,6 +50,7 @@ class ComputePressure : public Compute { private: char *pstyle; + int nsub; }; } -- GitLab From 11708c8f96aa0f020d8c562a577940578ec4882a Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Tue, 2 Jul 2019 12:07:26 -0400 Subject: [PATCH 162/469] continue cleaning up include files based on IWYU --- src/npair_skip_respa.cpp | 3 --- src/npair_skip_size.cpp | 2 -- src/npair_skip_size_off2on.cpp | 2 -- src/npair_skip_size_off2on_oneside.cpp | 2 -- src/nstencil_full_bin_2d.cpp | 2 -- src/nstencil_full_bin_3d.cpp | 2 -- src/nstencil_full_ghost_bin_2d.cpp | 2 -- src/nstencil_full_ghost_bin_3d.cpp | 2 -- src/nstencil_full_multi_2d.cpp | 2 -- src/nstencil_full_multi_3d.cpp | 2 -- src/nstencil_half_bin_2d_newtoff.cpp | 2 -- src/nstencil_half_bin_2d_newton.cpp | 2 -- src/nstencil_half_bin_2d_newton_tri.cpp | 2 -- src/nstencil_half_bin_3d_newtoff.cpp | 2 -- src/nstencil_half_bin_3d_newton.cpp | 2 -- src/nstencil_half_bin_3d_newton_tri.cpp | 2 -- src/nstencil_half_ghost_bin_2d_newtoff.cpp | 2 -- src/nstencil_half_ghost_bin_3d_newtoff.cpp | 2 -- src/nstencil_half_multi_2d_newtoff.cpp | 2 -- src/nstencil_half_multi_2d_newton.cpp | 2 -- src/nstencil_half_multi_2d_newton_tri.cpp | 2 -- src/nstencil_half_multi_3d_newtoff.cpp | 2 -- src/nstencil_half_multi_3d_newton.cpp | 2 -- src/nstencil_half_multi_3d_newton_tri.cpp | 2 -- src/ntopo.cpp | 2 +- src/output.cpp | 3 --- src/pair.cpp | 10 ++-------- src/pair_beck.cpp | 3 +-- src/pair_born.cpp | 3 +-- src/pair_born_coul_dsf.cpp | 4 +--- src/pair_born_coul_wolf.cpp | 4 +--- src/pair_buck.cpp | 3 +-- src/pair_coul_debye.cpp | 6 +----- src/pair_coul_dsf.cpp | 3 +-- src/pair_coul_streitz.cpp | 4 +--- src/pair_coul_wolf.cpp | 4 +--- src/pair_dpd.cpp | 4 +--- src/pair_dpd_tstat.cpp | 1 + src/pair_gauss.cpp | 4 +--- src/pair_hybrid.cpp | 3 +-- src/pair_hybrid_overlay.cpp | 3 --- src/pair_lj96_cut.cpp | 4 +--- src/pair_lj_cubic.cpp | 5 +---- src/pair_lj_cut.cpp | 4 +--- 44 files changed, 19 insertions(+), 107 deletions(-) diff --git a/src/npair_skip_respa.cpp b/src/npair_skip_respa.cpp index 1d4eda5354..68436654b2 100644 --- a/src/npair_skip_respa.cpp +++ b/src/npair_skip_respa.cpp @@ -12,12 +12,9 @@ ------------------------------------------------------------------------- */ #include "npair_skip_respa.h" -#include "neighbor.h" #include "neigh_list.h" #include "atom.h" #include "atom_vec.h" -#include "molecule.h" -#include "domain.h" #include "my_page.h" #include "error.h" diff --git a/src/npair_skip_size.cpp b/src/npair_skip_size.cpp index 67717ae576..436d21f76f 100644 --- a/src/npair_skip_size.cpp +++ b/src/npair_skip_size.cpp @@ -11,9 +11,7 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include #include "npair_skip_size.h" -#include "neighbor.h" #include "neigh_list.h" #include "atom.h" #include "atom_vec.h" diff --git a/src/npair_skip_size_off2on.cpp b/src/npair_skip_size_off2on.cpp index 74a80e6d3d..cd674ff777 100644 --- a/src/npair_skip_size_off2on.cpp +++ b/src/npair_skip_size_off2on.cpp @@ -11,9 +11,7 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include #include "npair_skip_size_off2on.h" -#include "neighbor.h" #include "neigh_list.h" #include "atom.h" #include "atom_vec.h" diff --git a/src/npair_skip_size_off2on_oneside.cpp b/src/npair_skip_size_off2on_oneside.cpp index a042acd1c6..0540592cba 100644 --- a/src/npair_skip_size_off2on_oneside.cpp +++ b/src/npair_skip_size_off2on_oneside.cpp @@ -11,9 +11,7 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include #include "npair_skip_size_off2on_oneside.h" -#include "neighbor.h" #include "neigh_list.h" #include "atom.h" #include "atom_vec.h" diff --git a/src/nstencil_full_bin_2d.cpp b/src/nstencil_full_bin_2d.cpp index 0986c40dd4..b18d990bba 100644 --- a/src/nstencil_full_bin_2d.cpp +++ b/src/nstencil_full_bin_2d.cpp @@ -12,8 +12,6 @@ ------------------------------------------------------------------------- */ #include "nstencil_full_bin_2d.h" -#include "neighbor.h" -#include "neigh_list.h" using namespace LAMMPS_NS; diff --git a/src/nstencil_full_bin_3d.cpp b/src/nstencil_full_bin_3d.cpp index b6a2198132..46ec073ddd 100644 --- a/src/nstencil_full_bin_3d.cpp +++ b/src/nstencil_full_bin_3d.cpp @@ -12,8 +12,6 @@ ------------------------------------------------------------------------- */ #include "nstencil_full_bin_3d.h" -#include "neighbor.h" -#include "neigh_list.h" using namespace LAMMPS_NS; diff --git a/src/nstencil_full_ghost_bin_2d.cpp b/src/nstencil_full_ghost_bin_2d.cpp index bbbf1a4466..5ac19569c5 100644 --- a/src/nstencil_full_ghost_bin_2d.cpp +++ b/src/nstencil_full_ghost_bin_2d.cpp @@ -12,8 +12,6 @@ ------------------------------------------------------------------------- */ #include "nstencil_full_ghost_bin_2d.h" -#include "neighbor.h" -#include "neigh_list.h" using namespace LAMMPS_NS; diff --git a/src/nstencil_full_ghost_bin_3d.cpp b/src/nstencil_full_ghost_bin_3d.cpp index e9abca2174..6ee56516dc 100644 --- a/src/nstencil_full_ghost_bin_3d.cpp +++ b/src/nstencil_full_ghost_bin_3d.cpp @@ -12,8 +12,6 @@ ------------------------------------------------------------------------- */ #include "nstencil_full_ghost_bin_3d.h" -#include "neighbor.h" -#include "neigh_list.h" using namespace LAMMPS_NS; diff --git a/src/nstencil_full_multi_2d.cpp b/src/nstencil_full_multi_2d.cpp index ed2ffe11dc..c69c53a761 100644 --- a/src/nstencil_full_multi_2d.cpp +++ b/src/nstencil_full_multi_2d.cpp @@ -12,8 +12,6 @@ ------------------------------------------------------------------------- */ #include "nstencil_full_multi_2d.h" -#include "neighbor.h" -#include "neigh_list.h" #include "atom.h" using namespace LAMMPS_NS; diff --git a/src/nstencil_full_multi_3d.cpp b/src/nstencil_full_multi_3d.cpp index c171bfadc5..df47c1e7e9 100644 --- a/src/nstencil_full_multi_3d.cpp +++ b/src/nstencil_full_multi_3d.cpp @@ -12,8 +12,6 @@ ------------------------------------------------------------------------- */ #include "nstencil_full_multi_3d.h" -#include "neighbor.h" -#include "neigh_list.h" #include "atom.h" using namespace LAMMPS_NS; diff --git a/src/nstencil_half_bin_2d_newtoff.cpp b/src/nstencil_half_bin_2d_newtoff.cpp index e51db6fe7a..f3a6c5d08b 100644 --- a/src/nstencil_half_bin_2d_newtoff.cpp +++ b/src/nstencil_half_bin_2d_newtoff.cpp @@ -12,8 +12,6 @@ ------------------------------------------------------------------------- */ #include "nstencil_half_bin_2d_newtoff.h" -#include "neighbor.h" -#include "neigh_list.h" using namespace LAMMPS_NS; diff --git a/src/nstencil_half_bin_2d_newton.cpp b/src/nstencil_half_bin_2d_newton.cpp index 9479bbf0c8..8fdc8f1aa9 100644 --- a/src/nstencil_half_bin_2d_newton.cpp +++ b/src/nstencil_half_bin_2d_newton.cpp @@ -12,8 +12,6 @@ ------------------------------------------------------------------------- */ #include "nstencil_half_bin_2d_newton.h" -#include "neighbor.h" -#include "neigh_list.h" using namespace LAMMPS_NS; diff --git a/src/nstencil_half_bin_2d_newton_tri.cpp b/src/nstencil_half_bin_2d_newton_tri.cpp index 4f89b1c326..30d064fb29 100644 --- a/src/nstencil_half_bin_2d_newton_tri.cpp +++ b/src/nstencil_half_bin_2d_newton_tri.cpp @@ -12,8 +12,6 @@ ------------------------------------------------------------------------- */ #include "nstencil_half_bin_2d_newton_tri.h" -#include "neighbor.h" -#include "neigh_list.h" using namespace LAMMPS_NS; diff --git a/src/nstencil_half_bin_3d_newtoff.cpp b/src/nstencil_half_bin_3d_newtoff.cpp index 433de400c2..e44a93d47d 100644 --- a/src/nstencil_half_bin_3d_newtoff.cpp +++ b/src/nstencil_half_bin_3d_newtoff.cpp @@ -12,8 +12,6 @@ ------------------------------------------------------------------------- */ #include "nstencil_half_bin_3d_newtoff.h" -#include "neighbor.h" -#include "neigh_list.h" using namespace LAMMPS_NS; diff --git a/src/nstencil_half_bin_3d_newton.cpp b/src/nstencil_half_bin_3d_newton.cpp index 24c234c004..998ed28afe 100644 --- a/src/nstencil_half_bin_3d_newton.cpp +++ b/src/nstencil_half_bin_3d_newton.cpp @@ -12,8 +12,6 @@ ------------------------------------------------------------------------- */ #include "nstencil_half_bin_3d_newton.h" -#include "neighbor.h" -#include "neigh_list.h" using namespace LAMMPS_NS; diff --git a/src/nstencil_half_bin_3d_newton_tri.cpp b/src/nstencil_half_bin_3d_newton_tri.cpp index 691ce0bb80..2aae44ceaf 100644 --- a/src/nstencil_half_bin_3d_newton_tri.cpp +++ b/src/nstencil_half_bin_3d_newton_tri.cpp @@ -12,8 +12,6 @@ ------------------------------------------------------------------------- */ #include "nstencil_half_bin_3d_newton_tri.h" -#include "neighbor.h" -#include "neigh_list.h" using namespace LAMMPS_NS; diff --git a/src/nstencil_half_ghost_bin_2d_newtoff.cpp b/src/nstencil_half_ghost_bin_2d_newtoff.cpp index 4bb0ecafe2..6f9a7585fe 100644 --- a/src/nstencil_half_ghost_bin_2d_newtoff.cpp +++ b/src/nstencil_half_ghost_bin_2d_newtoff.cpp @@ -12,8 +12,6 @@ ------------------------------------------------------------------------- */ #include "nstencil_half_ghost_bin_2d_newtoff.h" -#include "neighbor.h" -#include "neigh_list.h" using namespace LAMMPS_NS; diff --git a/src/nstencil_half_ghost_bin_3d_newtoff.cpp b/src/nstencil_half_ghost_bin_3d_newtoff.cpp index 1026b11542..6492fe4a4e 100644 --- a/src/nstencil_half_ghost_bin_3d_newtoff.cpp +++ b/src/nstencil_half_ghost_bin_3d_newtoff.cpp @@ -12,8 +12,6 @@ ------------------------------------------------------------------------- */ #include "nstencil_half_ghost_bin_3d_newtoff.h" -#include "neighbor.h" -#include "neigh_list.h" using namespace LAMMPS_NS; diff --git a/src/nstencil_half_multi_2d_newtoff.cpp b/src/nstencil_half_multi_2d_newtoff.cpp index 567abe2878..63cd3fd524 100644 --- a/src/nstencil_half_multi_2d_newtoff.cpp +++ b/src/nstencil_half_multi_2d_newtoff.cpp @@ -12,8 +12,6 @@ ------------------------------------------------------------------------- */ #include "nstencil_half_multi_2d_newtoff.h" -#include "neighbor.h" -#include "neigh_list.h" #include "atom.h" using namespace LAMMPS_NS; diff --git a/src/nstencil_half_multi_2d_newton.cpp b/src/nstencil_half_multi_2d_newton.cpp index 5dc2c37148..f6f6c488a5 100644 --- a/src/nstencil_half_multi_2d_newton.cpp +++ b/src/nstencil_half_multi_2d_newton.cpp @@ -12,8 +12,6 @@ ------------------------------------------------------------------------- */ #include "nstencil_half_multi_2d_newton.h" -#include "neighbor.h" -#include "neigh_list.h" #include "atom.h" using namespace LAMMPS_NS; diff --git a/src/nstencil_half_multi_2d_newton_tri.cpp b/src/nstencil_half_multi_2d_newton_tri.cpp index 59a5a1d19e..b44ab36ea0 100644 --- a/src/nstencil_half_multi_2d_newton_tri.cpp +++ b/src/nstencil_half_multi_2d_newton_tri.cpp @@ -12,8 +12,6 @@ ------------------------------------------------------------------------- */ #include "nstencil_half_multi_2d_newton_tri.h" -#include "neighbor.h" -#include "neigh_list.h" #include "atom.h" using namespace LAMMPS_NS; diff --git a/src/nstencil_half_multi_3d_newtoff.cpp b/src/nstencil_half_multi_3d_newtoff.cpp index 72b882dddc..5a83c4e002 100644 --- a/src/nstencil_half_multi_3d_newtoff.cpp +++ b/src/nstencil_half_multi_3d_newtoff.cpp @@ -12,8 +12,6 @@ ------------------------------------------------------------------------- */ #include "nstencil_half_multi_3d_newtoff.h" -#include "neighbor.h" -#include "neigh_list.h" #include "atom.h" using namespace LAMMPS_NS; diff --git a/src/nstencil_half_multi_3d_newton.cpp b/src/nstencil_half_multi_3d_newton.cpp index 9a5d5cab65..5b0c7f9f63 100644 --- a/src/nstencil_half_multi_3d_newton.cpp +++ b/src/nstencil_half_multi_3d_newton.cpp @@ -12,8 +12,6 @@ ------------------------------------------------------------------------- */ #include "nstencil_half_multi_3d_newton.h" -#include "neighbor.h" -#include "neigh_list.h" #include "atom.h" using namespace LAMMPS_NS; diff --git a/src/nstencil_half_multi_3d_newton_tri.cpp b/src/nstencil_half_multi_3d_newton_tri.cpp index 953beb3211..b25a0d0bdb 100644 --- a/src/nstencil_half_multi_3d_newton_tri.cpp +++ b/src/nstencil_half_multi_3d_newton_tri.cpp @@ -12,8 +12,6 @@ ------------------------------------------------------------------------- */ #include "nstencil_half_multi_3d_newton_tri.h" -#include "neighbor.h" -#include "neigh_list.h" #include "atom.h" using namespace LAMMPS_NS; diff --git a/src/ntopo.cpp b/src/ntopo.cpp index 8a87a5d6e5..05e287e192 100644 --- a/src/ntopo.cpp +++ b/src/ntopo.cpp @@ -11,7 +11,7 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include +#include #include "ntopo.h" #include "atom.h" #include "neighbor.h" diff --git a/src/output.cpp b/src/output.cpp index 6253d7de37..fb2f9a700d 100644 --- a/src/output.cpp +++ b/src/output.cpp @@ -11,8 +11,6 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include -#include #include #include "output.h" #include "style_dump.h" @@ -26,7 +24,6 @@ #include "domain.h" #include "thermo.h" #include "modify.h" -#include "compute.h" #include "force.h" #include "dump.h" #include "write_restart.h" diff --git a/src/pair.cpp b/src/pair.cpp index 2b4863a54c..3d7bdaa62c 100644 --- a/src/pair.cpp +++ b/src/pair.cpp @@ -16,23 +16,17 @@ ------------------------------------------------------------------------- */ #include -#include -#include -#include +#include // IWYU pragma: keep +#include // IWYU pragma: keep #include -#include -#include #include #include "pair.h" #include "atom.h" #include "neighbor.h" -#include "neigh_list.h" #include "domain.h" #include "comm.h" #include "force.h" #include "kspace.h" -#include "update.h" -#include "modify.h" #include "compute.h" #include "suffix.h" #include "atom_masks.h" diff --git a/src/pair_beck.cpp b/src/pair_beck.cpp index 17731ebf0b..8ba3ef80f2 100644 --- a/src/pair_beck.cpp +++ b/src/pair_beck.cpp @@ -15,9 +15,8 @@ Contributing author: Jonathan Zimmerman (Sandia) ------------------------------------------------------------------------- */ +#include #include -#include -#include #include "pair_beck.h" #include "atom.h" #include "comm.h" diff --git a/src/pair_born.cpp b/src/pair_born.cpp index 78434c91f8..ae7456ddbb 100644 --- a/src/pair_born.cpp +++ b/src/pair_born.cpp @@ -15,9 +15,8 @@ Contributing Author: Sai Jayaraman (Sandia) ------------------------------------------------------------------------- */ +#include #include -#include -#include #include #include "pair_born.h" #include "atom.h" diff --git a/src/pair_born_coul_dsf.cpp b/src/pair_born_coul_dsf.cpp index 2e565897b5..51b9a2677d 100644 --- a/src/pair_born_coul_dsf.cpp +++ b/src/pair_born_coul_dsf.cpp @@ -16,10 +16,8 @@ References: Fennell and Gezelter, JCP 124, 234104 (2006) ------------------------------------------------------------------------- */ +#include #include -#include -#include -#include #include "pair_born_coul_dsf.h" #include "atom.h" #include "comm.h" diff --git a/src/pair_born_coul_wolf.cpp b/src/pair_born_coul_wolf.cpp index 3bb0e39e57..f4ccac80a1 100644 --- a/src/pair_born_coul_wolf.cpp +++ b/src/pair_born_coul_wolf.cpp @@ -15,10 +15,8 @@ Contributing author: Yongfeng Zhang (INL), yongfeng.zhang@inl.gov ------------------------------------------------------------------------- */ +#include #include -#include -#include -#include #include "pair_born_coul_wolf.h" #include "atom.h" #include "comm.h" diff --git a/src/pair_buck.cpp b/src/pair_buck.cpp index a3cf1a38d6..b9795fb0ed 100644 --- a/src/pair_buck.cpp +++ b/src/pair_buck.cpp @@ -11,9 +11,8 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ +#include #include -#include -#include #include #include "pair_buck.h" #include "atom.h" diff --git a/src/pair_coul_debye.cpp b/src/pair_coul_debye.cpp index c8afdabb93..cd23ef1919 100644 --- a/src/pair_coul_debye.cpp +++ b/src/pair_coul_debye.cpp @@ -11,17 +11,13 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ +#include #include -#include -#include -#include #include "pair_coul_debye.h" #include "atom.h" #include "comm.h" #include "force.h" -#include "neighbor.h" #include "neigh_list.h" -#include "memory.h" #include "error.h" using namespace LAMMPS_NS; diff --git a/src/pair_coul_dsf.cpp b/src/pair_coul_dsf.cpp index e487ff171c..4c15b5d330 100644 --- a/src/pair_coul_dsf.cpp +++ b/src/pair_coul_dsf.cpp @@ -16,9 +16,8 @@ References: Fennell and Gezelter, JCP 124, 234104 (2006) ------------------------------------------------------------------------- */ +#include #include -#include -#include #include #include "pair_coul_dsf.h" #include "atom.h" diff --git a/src/pair_coul_streitz.cpp b/src/pair_coul_streitz.cpp index 282c855249..f577564ac1 100644 --- a/src/pair_coul_streitz.cpp +++ b/src/pair_coul_streitz.cpp @@ -15,8 +15,8 @@ Contributing author: Ray Shan (Sandia) ------------------------------------------------------------------------- */ +#include #include -#include #include #include #include "pair_coul_streitz.h" @@ -27,8 +27,6 @@ #include "neighbor.h" #include "neigh_list.h" #include "neigh_request.h" -#include "group.h" -#include "update.h" #include "math_const.h" #include "memory.h" #include "error.h" diff --git a/src/pair_coul_wolf.cpp b/src/pair_coul_wolf.cpp index dbf21b8bee..8c15378de8 100644 --- a/src/pair_coul_wolf.cpp +++ b/src/pair_coul_wolf.cpp @@ -15,10 +15,8 @@ Contributing author: Yongfeng Zhang (INL), yongfeng.zhang@inl.gov ------------------------------------------------------------------------- */ +#include #include -#include -#include -#include #include "pair_coul_wolf.h" #include "atom.h" #include "comm.h" diff --git a/src/pair_dpd.cpp b/src/pair_dpd.cpp index 914b4aee17..e5e6cf7dae 100644 --- a/src/pair_dpd.cpp +++ b/src/pair_dpd.cpp @@ -15,12 +15,10 @@ Contributing author: Kurt Smith (U Pittsburgh) ------------------------------------------------------------------------- */ +#include #include -#include -#include #include "pair_dpd.h" #include "atom.h" -#include "atom_vec.h" #include "comm.h" #include "update.h" #include "force.h" diff --git a/src/pair_dpd_tstat.cpp b/src/pair_dpd_tstat.cpp index 1207c954eb..66c8d91ab1 100644 --- a/src/pair_dpd_tstat.cpp +++ b/src/pair_dpd_tstat.cpp @@ -11,6 +11,7 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ +#include #include #include "pair_dpd_tstat.h" #include "atom.h" diff --git a/src/pair_gauss.cpp b/src/pair_gauss.cpp index 2d157d6cac..7df9a417c3 100644 --- a/src/pair_gauss.cpp +++ b/src/pair_gauss.cpp @@ -15,15 +15,13 @@ Contributing author: Sai Jayaraman (Sandia) ------------------------------------------------------------------------- */ +#include #include -#include -#include #include #include "pair_gauss.h" #include "atom.h" #include "comm.h" #include "force.h" -#include "neighbor.h" #include "neigh_list.h" #include "memory.h" #include "error.h" diff --git a/src/pair_hybrid.cpp b/src/pair_hybrid.cpp index 9aff8a387a..daeee3d2b3 100644 --- a/src/pair_hybrid.cpp +++ b/src/pair_hybrid.cpp @@ -12,8 +12,7 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include -#include +#include #include #include #include "pair_hybrid.h" diff --git a/src/pair_hybrid_overlay.cpp b/src/pair_hybrid_overlay.cpp index 717c0de1d1..496e3d0406 100644 --- a/src/pair_hybrid_overlay.cpp +++ b/src/pair_hybrid_overlay.cpp @@ -11,14 +11,11 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include #include #include #include "pair_hybrid_overlay.h" #include "atom.h" #include "force.h" -#include "neighbor.h" -#include "neigh_request.h" #include "error.h" using namespace LAMMPS_NS; diff --git a/src/pair_lj96_cut.cpp b/src/pair_lj96_cut.cpp index cefe9b87e0..62e645ef2c 100644 --- a/src/pair_lj96_cut.cpp +++ b/src/pair_lj96_cut.cpp @@ -15,9 +15,8 @@ Contributing author: Chuanfu Luo (luochuanfu@gmail.com) ------------------------------------------------------------------------- */ +#include #include -#include -#include #include #include "pair_lj96_cut.h" #include "atom.h" @@ -27,7 +26,6 @@ #include "neigh_list.h" #include "neigh_request.h" #include "update.h" -#include "integrate.h" #include "respa.h" #include "math_const.h" #include "memory.h" diff --git a/src/pair_lj_cubic.cpp b/src/pair_lj_cubic.cpp index fdbfca608f..8b1b4b7627 100644 --- a/src/pair_lj_cubic.cpp +++ b/src/pair_lj_cubic.cpp @@ -16,15 +16,12 @@ Contributing author: Aidan Thompson (SNL) ------------------------------------------------------------------------- */ +#include #include -#include -#include -#include #include "pair_lj_cubic.h" #include "atom.h" #include "comm.h" #include "force.h" -#include "neighbor.h" #include "neigh_list.h" #include "memory.h" #include "error.h" diff --git a/src/pair_lj_cut.cpp b/src/pair_lj_cut.cpp index 2a0fcde3a5..9284923218 100644 --- a/src/pair_lj_cut.cpp +++ b/src/pair_lj_cut.cpp @@ -15,9 +15,8 @@ Contributing author: Paul Crozier (SNL) ------------------------------------------------------------------------- */ +#include #include -#include -#include #include #include "pair_lj_cut.h" #include "atom.h" @@ -27,7 +26,6 @@ #include "neigh_list.h" #include "neigh_request.h" #include "update.h" -#include "integrate.h" #include "respa.h" #include "math_const.h" #include "memory.h" -- GitLab From 0c4af8b820f4d6f559d07086db91a2c1dee67a47 Mon Sep 17 00:00:00 2001 From: jrgissing Date: Tue, 2 Jul 2019 22:13:06 -0600 Subject: [PATCH 163/469] spelling: attempt add file paths to false positives --- doc/utils/sphinx-config/conf.py | 3 +++ doc/utils/sphinx-config/custom_filters.py | 9 +++++++++ 2 files changed, 12 insertions(+) create mode 100644 doc/utils/sphinx-config/custom_filters.py diff --git a/doc/utils/sphinx-config/conf.py b/doc/utils/sphinx-config/conf.py index 29de3af156..646fbd2e94 100644 --- a/doc/utils/sphinx-config/conf.py +++ b/doc/utils/sphinx-config/conf.py @@ -312,3 +312,6 @@ if spelling_spec: spelling_lang='en_US' spelling_word_list_filename='false_positives.txt' + + from custom_filters import PathFilter + spelling_filters = [PathFilter] diff --git a/doc/utils/sphinx-config/custom_filters.py b/doc/utils/sphinx-config/custom_filters.py new file mode 100644 index 0000000000..3df26854e4 --- /dev/null +++ b/doc/utils/sphinx-config/custom_filters.py @@ -0,0 +1,9 @@ +class PathFilter(Filter): + r"""Filter skipping over simple file paths + """ + _DOC_ERRORS = ["zA"] + _pattern = re.compile(r"\/[^\s].*") + def _skip(self,word): + if self._pattern.match(word): + return True + return False -- GitLab From 7967cb11339b3ae52e9de9c671e5c611b1d9b1f2 Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Tue, 2 Jul 2019 22:56:56 -0400 Subject: [PATCH 164/469] put implementation header first to avoid issues with mpi.h and lmptype.h with OpenMPI --- doc/include-file-conventions.md | 4 ++-- src/angle.h | 2 +- src/angle_deprecated.cpp | 5 +++-- src/angle_hybrid.cpp | 2 +- src/angle_zero.cpp | 2 +- src/atom.cpp | 2 +- src/atom_map.cpp | 2 +- src/atom_vec.cpp | 2 +- src/atom_vec_atomic.cpp | 2 +- src/atom_vec_body.cpp | 2 +- src/atom_vec_charge.cpp | 2 +- src/atom_vec_ellipsoid.cpp | 2 +- src/atom_vec_hybrid.cpp | 2 +- src/atom_vec_line.cpp | 2 +- src/atom_vec_sphere.cpp | 2 +- src/atom_vec_tri.cpp | 2 +- src/balance.cpp | 2 +- src/body.cpp | 2 +- src/bond.cpp | 2 +- src/bond_deprecated.cpp | 2 +- src/bond_hybrid.cpp | 2 +- src/bond_zero.cpp | 2 +- src/change_box.cpp | 2 +- src/comm.cpp | 2 +- src/comm_brick.cpp | 2 +- src/comm_tiled.cpp | 2 +- src/compute.cpp | 2 +- src/compute_adf.cpp | 2 +- src/compute_aggregate_atom.cpp | 2 +- src/compute_angle.cpp | 2 +- src/compute_angle_local.cpp | 2 +- src/compute_angmom_chunk.cpp | 2 +- src/compute_bond.cpp | 2 +- src/compute_bond_local.cpp | 2 +- src/compute_centro_atom.cpp | 2 +- src/compute_chunk_atom.cpp | 2 +- src/compute_chunk_spread_atom.cpp | 2 +- src/compute_cluster_atom.cpp | 2 +- src/compute_cna_atom.cpp | 2 +- src/compute_com_chunk.cpp | 2 +- src/compute_contact_atom.cpp | 2 +- src/compute_coord_atom.cpp | 2 +- src/compute_deprecated.cpp | 2 +- src/compute_dihedral.cpp | 2 +- src/compute_dihedral_local.cpp | 2 +- src/compute_dipole_chunk.cpp | 2 +- src/compute_displace_atom.cpp | 2 +- src/compute_erotate_sphere.cpp | 2 +- src/compute_erotate_sphere_atom.cpp | 2 +- src/compute_fragment_atom.cpp | 2 +- src/compute_global_atom.cpp | 2 +- src/compute_group_group.cpp | 2 +- src/compute_gyration.cpp | 2 +- src/compute_gyration_chunk.cpp | 2 +- src/compute_heat_flux.cpp | 2 +- src/compute_hexorder_atom.cpp | 2 +- src/compute_improper.cpp | 2 +- src/compute_improper_local.cpp | 2 +- src/compute_inertia_chunk.cpp | 2 +- src/compute_ke.cpp | 2 +- src/compute_ke_atom.cpp | 2 +- src/compute_msd.cpp | 2 +- src/compute_msd_chunk.cpp | 2 +- src/compute_omega_chunk.cpp | 2 +- src/compute_orientorder_atom.cpp | 2 +- src/compute_pair.cpp | 2 +- src/compute_pair_local.cpp | 2 +- src/compute_pe.cpp | 2 +- src/compute_pe_atom.cpp | 2 +- src/compute_pressure.cpp | 2 +- src/compute_property_atom.cpp | 2 +- src/compute_property_chunk.cpp | 2 +- src/compute_property_local.cpp | 2 +- src/compute_rdf.cpp | 2 +- src/compute_reduce.cpp | 2 +- src/compute_reduce_chunk.cpp | 2 +- src/compute_reduce_region.cpp | 2 +- src/compute_slice.cpp | 2 +- src/compute_stress_atom.cpp | 2 +- src/compute_temp.cpp | 2 +- src/compute_temp_chunk.cpp | 2 +- src/compute_temp_com.cpp | 2 +- src/compute_temp_deform.cpp | 2 +- src/compute_temp_partial.cpp | 2 +- src/compute_temp_profile.cpp | 2 +- src/compute_temp_ramp.cpp | 2 +- src/compute_temp_region.cpp | 2 +- src/compute_temp_sphere.cpp | 2 +- src/compute_torque_chunk.cpp | 2 +- src/compute_vacf.cpp | 2 +- src/compute_vcm_chunk.cpp | 2 +- src/create_atoms.cpp | 2 +- src/create_bonds.cpp | 2 +- src/create_box.cpp | 2 +- src/delete_atoms.cpp | 2 +- src/delete_bonds.cpp | 2 +- src/deprecated.cpp | 2 +- src/dihedral_deprecated.cpp | 2 +- src/dihedral_hybrid.cpp | 2 +- src/dihedral_zero.cpp | 2 +- src/displace_atoms.cpp | 2 +- src/domain.cpp | 2 +- src/dump.cpp | 2 +- src/dump_atom.cpp | 2 +- src/dump_cfg.cpp | 2 +- src/dump_custom.cpp | 2 +- src/dump_dcd.cpp | 2 +- src/dump_deprecated.cpp | 2 +- src/dump_image.cpp | 2 +- src/dump_local.cpp | 2 +- src/dump_movie.cpp | 2 +- src/dump_xyz.cpp | 2 +- src/error.cpp | 2 +- src/finish.cpp | 2 +- src/fix.cpp | 2 +- src/fix_adapt.cpp | 2 +- src/fix_addforce.cpp | 2 +- src/fix_ave_atom.cpp | 2 +- src/fix_ave_chunk.cpp | 3 +-- src/fix_ave_correlate.cpp | 3 +-- src/fix_ave_histo.cpp | 3 +-- src/fix_ave_histo_weight.cpp | 3 +-- src/fix_ave_time.cpp | 3 +-- src/fix_aveforce.cpp | 2 +- src/fix_balance.cpp | 2 +- src/fix_box_relax.cpp | 2 +- src/fix_controller.cpp | 2 +- src/fix_deform.cpp | 2 +- src/fix_deprecated.cpp | 2 +- src/fix_drag.cpp | 2 +- src/fix_dt_reset.cpp | 2 +- src/fix_enforce2d.cpp | 2 +- src/fix_external.cpp | 2 +- src/fix_gravity.cpp | 2 +- src/fix_group.cpp | 2 +- src/fix_halt.cpp | 2 +- src/fix_heat.cpp | 2 +- src/fix_indent.cpp | 2 +- src/fix_langevin.cpp | 2 +- src/fix_lineforce.cpp | 2 +- src/fix_momentum.cpp | 2 +- src/fix_move.cpp | 2 +- src/fix_neigh_history.cpp | 2 +- src/fix_nh.cpp | 2 +- src/fix_nh_sphere.cpp | 2 +- src/fix_nph.cpp | 2 +- src/fix_nph_sphere.cpp | 2 +- src/fix_npt.cpp | 2 +- src/fix_npt_sphere.cpp | 2 +- src/fix_nve.cpp | 2 +- src/fix_nve_limit.cpp | 2 +- src/fix_nve_noforce.cpp | 2 +- src/fix_nve_sphere.cpp | 2 +- src/fix_nvt.cpp | 2 +- src/fix_nvt_sllod.cpp | 2 +- src/fix_nvt_sphere.cpp | 2 +- src/fix_planeforce.cpp | 2 +- src/fix_press_berendsen.cpp | 2 +- src/fix_print.cpp | 2 +- src/fix_property_atom.cpp | 2 +- src/fix_recenter.cpp | 2 +- src/fix_respa.cpp | 2 +- src/fix_restrain.cpp | 2 +- src/fix_setforce.cpp | 2 +- src/fix_spring.cpp | 2 +- src/fix_spring_chunk.cpp | 2 +- src/fix_spring_rg.cpp | 2 +- src/fix_spring_self.cpp | 2 +- src/fix_store.cpp | 2 +- src/fix_store_force.cpp | 2 +- src/fix_store_state.cpp | 2 +- src/fix_temp_berendsen.cpp | 2 +- src/fix_temp_csld.cpp | 2 +- src/fix_temp_csvr.cpp | 2 +- src/fix_temp_rescale.cpp | 2 +- src/fix_tmd.cpp | 2 +- src/fix_vector.cpp | 2 +- src/fix_viscous.cpp | 2 +- src/fix_wall.cpp | 2 +- src/fix_wall_lj1043.cpp | 2 +- src/fix_wall_lj126.cpp | 2 +- src/fix_wall_lj93.cpp | 2 +- src/fix_wall_reflect.cpp | 2 +- src/fix_wall_region.cpp | 2 +- src/force.cpp | 2 +- src/group.cpp | 2 +- src/hashlittle.cpp | 5 ++--- src/hashlittle.h | 11 ++++++++++- src/image.cpp | 2 +- src/output.cpp | 1 + src/pair_lj_cut_coul_cut.cpp | 3 +-- src/pair_lj_cut_coul_debye.cpp | 2 +- src/pair_lj_cut_coul_dsf.cpp | 5 ++--- src/pointers.h | 2 +- 194 files changed, 208 insertions(+), 205 deletions(-) diff --git a/doc/include-file-conventions.md b/doc/include-file-conventions.md index 3f591361f5..1f206c8f88 100644 --- a/doc/include-file-conventions.md +++ b/doc/include-file-conventions.md @@ -97,10 +97,10 @@ statements should follow the "include what you use" principle. ### Order of Include Statements Include files should be included in this order: -* lmptype.h (should only be included if `MPI_LMP_XXX` data types are used) +* the header matching the implementation (`some_class.h` for file `some_class.cpp`) * mpi.h * system and library headers (anything that is using angular brackets; C-library headers first, then C++) -* LAMMPS local headers (first the header matching the implementation file, the rest in mostly alphabetical order) +* LAMMPS local headers (preferably in alphabetical order) ### Special Cases and Exceptions diff --git a/src/angle.h b/src/angle.h index 7a008f7ca7..3e6812c4fd 100644 --- a/src/angle.h +++ b/src/angle.h @@ -14,7 +14,7 @@ #ifndef LMP_ANGLE_H #define LMP_ANGLE_H -#include "pointers.h" // IWYU pragma: export +#include "pointers.h" namespace LAMMPS_NS { diff --git a/src/angle_deprecated.cpp b/src/angle_deprecated.cpp index b5af217b7b..cc29c9978e 100644 --- a/src/angle_deprecated.cpp +++ b/src/angle_deprecated.cpp @@ -15,12 +15,13 @@ Contributing author: Axel Kohlmeyer (Temple U) ------------------------------------------------------------------------- */ -#include #include "angle_deprecated.h" +#include #include "angle_hybrid.h" #include "comm.h" #include "force.h" #include "error.h" +#include "utils.h" using namespace LAMMPS_NS; @@ -43,7 +44,7 @@ void AngleDeprecated::settings(int, char **) // hybrid substyles are created in AngleHybrid::settings(), so when this is // called, our style was just added at the end of the list of substyles - if (strncmp(my_style,"hybrid",6) == 0) { + if (utils::strmatch(my_style,"^hybrid")) { AngleHybrid *hybrid = (AngleHybrid *)force->angle; my_style = hybrid->keywords[hybrid->nstyles]; } diff --git a/src/angle_hybrid.cpp b/src/angle_hybrid.cpp index 47baf770a5..a4729efb38 100644 --- a/src/angle_hybrid.cpp +++ b/src/angle_hybrid.cpp @@ -11,10 +11,10 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ +#include "angle_hybrid.h" #include #include #include -#include "angle_hybrid.h" #include "atom.h" #include "neighbor.h" #include "comm.h" diff --git a/src/angle_zero.cpp b/src/angle_zero.cpp index 62eab85aee..3c92b852b3 100644 --- a/src/angle_zero.cpp +++ b/src/angle_zero.cpp @@ -15,9 +15,9 @@ Contributing author: Carsten Svaneborg (SDU) ------------------------------------------------------------------------- */ +#include "angle_zero.h" #include #include -#include "angle_zero.h" #include "atom.h" #include "force.h" #include "comm.h" diff --git a/src/atom.cpp b/src/atom.cpp index eab8a3063d..1073d9ebbb 100644 --- a/src/atom.cpp +++ b/src/atom.cpp @@ -11,11 +11,11 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ +#include "atom.h" #include #include #include #include -#include "atom.h" #include "style_atom.h" #include "atom_vec.h" #include "atom_vec_ellipsoid.h" diff --git a/src/atom_map.cpp b/src/atom_map.cpp index 6af3b9c288..7949e327a9 100644 --- a/src/atom_map.cpp +++ b/src/atom_map.cpp @@ -11,9 +11,9 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ +#include "atom.h" #include #include -#include "atom.h" #include "comm.h" #include "memory.h" #include "error.h" diff --git a/src/atom_vec.cpp b/src/atom_vec.cpp index a7ca6fcb19..11fe2dba06 100644 --- a/src/atom_vec.cpp +++ b/src/atom_vec.cpp @@ -11,9 +11,9 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ +#include "atom_vec.h" #include #include -#include "atom_vec.h" #include "atom.h" #include "force.h" #include "domain.h" diff --git a/src/atom_vec_atomic.cpp b/src/atom_vec_atomic.cpp index e1c9a1e524..7b452e018f 100644 --- a/src/atom_vec_atomic.cpp +++ b/src/atom_vec_atomic.cpp @@ -11,8 +11,8 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include #include "atom_vec_atomic.h" +#include #include "atom.h" #include "comm.h" #include "domain.h" diff --git a/src/atom_vec_body.cpp b/src/atom_vec_body.cpp index fad5b3eae0..8cc220c8b9 100644 --- a/src/atom_vec_body.cpp +++ b/src/atom_vec_body.cpp @@ -11,10 +11,10 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ +#include "atom_vec_body.h" #include #include #include -#include "atom_vec_body.h" #include "my_pool_chunk.h" #include "style_body.h" #include "body.h" diff --git a/src/atom_vec_charge.cpp b/src/atom_vec_charge.cpp index 440393385d..950fe06488 100644 --- a/src/atom_vec_charge.cpp +++ b/src/atom_vec_charge.cpp @@ -11,8 +11,8 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include #include "atom_vec_charge.h" +#include #include "atom.h" #include "comm.h" #include "domain.h" diff --git a/src/atom_vec_ellipsoid.cpp b/src/atom_vec_ellipsoid.cpp index ad167bef79..a9c36a61f4 100644 --- a/src/atom_vec_ellipsoid.cpp +++ b/src/atom_vec_ellipsoid.cpp @@ -15,9 +15,9 @@ Contributing author: Mike Brown (SNL) ------------------------------------------------------------------------- */ +#include "atom_vec_ellipsoid.h" #include #include -#include "atom_vec_ellipsoid.h" #include "math_extra.h" #include "atom.h" #include "comm.h" diff --git a/src/atom_vec_hybrid.cpp b/src/atom_vec_hybrid.cpp index 7e1fb01e5d..a750b17ac3 100644 --- a/src/atom_vec_hybrid.cpp +++ b/src/atom_vec_hybrid.cpp @@ -11,9 +11,9 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ +#include "atom_vec_hybrid.h" #include #include -#include "atom_vec_hybrid.h" #include "atom.h" #include "domain.h" #include "modify.h" diff --git a/src/atom_vec_line.cpp b/src/atom_vec_line.cpp index 6b197d2663..d694c42043 100644 --- a/src/atom_vec_line.cpp +++ b/src/atom_vec_line.cpp @@ -11,10 +11,10 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ +#include "atom_vec_line.h" #include #include #include -#include "atom_vec_line.h" #include "atom.h" #include "comm.h" #include "domain.h" diff --git a/src/atom_vec_sphere.cpp b/src/atom_vec_sphere.cpp index b3f4bfe391..713fb0d721 100644 --- a/src/atom_vec_sphere.cpp +++ b/src/atom_vec_sphere.cpp @@ -11,9 +11,9 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ +#include "atom_vec_sphere.h" #include #include -#include "atom_vec_sphere.h" #include "atom.h" #include "comm.h" #include "domain.h" diff --git a/src/atom_vec_tri.cpp b/src/atom_vec_tri.cpp index b0b6eca19b..9a6afce02f 100644 --- a/src/atom_vec_tri.cpp +++ b/src/atom_vec_tri.cpp @@ -11,10 +11,10 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ +#include "atom_vec_tri.h" #include #include #include -#include "atom_vec_tri.h" #include "math_extra.h" #include "atom.h" #include "comm.h" diff --git a/src/balance.cpp b/src/balance.cpp index 04f342b69b..c3b6f7d3bf 100644 --- a/src/balance.cpp +++ b/src/balance.cpp @@ -18,10 +18,10 @@ //#define BALANCE_DEBUG 1 +#include "balance.h" #include #include #include -#include "balance.h" #include "atom.h" #include "comm.h" #include "rcb.h" diff --git a/src/body.cpp b/src/body.cpp index 10f88bd43b..c0e58d3f4c 100644 --- a/src/body.cpp +++ b/src/body.cpp @@ -11,8 +11,8 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include #include "body.h" +#include using namespace LAMMPS_NS; diff --git a/src/bond.cpp b/src/bond.cpp index 0d50b7e3e5..bb54306280 100644 --- a/src/bond.cpp +++ b/src/bond.cpp @@ -11,8 +11,8 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include #include "bond.h" +#include #include "atom.h" #include "comm.h" #include "force.h" diff --git a/src/bond_deprecated.cpp b/src/bond_deprecated.cpp index 567b1a4d00..3e20553cac 100644 --- a/src/bond_deprecated.cpp +++ b/src/bond_deprecated.cpp @@ -15,8 +15,8 @@ Contributing author: Axel Kohlmeyer (Temple U) ------------------------------------------------------------------------- */ -#include #include "bond_deprecated.h" +#include #include "bond_hybrid.h" #include "comm.h" #include "force.h" diff --git a/src/bond_hybrid.cpp b/src/bond_hybrid.cpp index 9028886758..0b1c944196 100644 --- a/src/bond_hybrid.cpp +++ b/src/bond_hybrid.cpp @@ -11,10 +11,10 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ +#include "bond_hybrid.h" #include #include #include -#include "bond_hybrid.h" #include "atom.h" #include "neighbor.h" #include "comm.h" diff --git a/src/bond_zero.cpp b/src/bond_zero.cpp index c473abbe4b..9be37c13be 100644 --- a/src/bond_zero.cpp +++ b/src/bond_zero.cpp @@ -15,9 +15,9 @@ Contributing author: Carsten Svaneborg (SDU) ------------------------------------------------------------------------- */ +#include "bond_zero.h" #include #include -#include "bond_zero.h" #include "atom.h" #include "force.h" #include "comm.h" diff --git a/src/change_box.cpp b/src/change_box.cpp index 1fed65b430..98119fb3bf 100644 --- a/src/change_box.cpp +++ b/src/change_box.cpp @@ -11,10 +11,10 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ +#include "change_box.h" #include #include #include -#include "change_box.h" #include "atom.h" #include "modify.h" #include "fix.h" diff --git a/src/comm.cpp b/src/comm.cpp index 5f846cf292..53ec6b990c 100644 --- a/src/comm.cpp +++ b/src/comm.cpp @@ -11,10 +11,10 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ +#include "comm.h" #include #include #include -#include "comm.h" #include "universe.h" #include "atom.h" #include "atom_vec.h" diff --git a/src/comm_brick.cpp b/src/comm_brick.cpp index dcf30807f5..928357d5be 100644 --- a/src/comm_brick.cpp +++ b/src/comm_brick.cpp @@ -15,10 +15,10 @@ Contributing author (triclinic) : Pieter in 't Veld (SNL) ------------------------------------------------------------------------- */ +#include "comm_brick.h" #include #include #include -#include "comm_brick.h" #include "atom.h" #include "atom_vec.h" #include "pair.h" diff --git a/src/comm_tiled.cpp b/src/comm_tiled.cpp index 385b7fdf22..e145f50f75 100644 --- a/src/comm_tiled.cpp +++ b/src/comm_tiled.cpp @@ -11,10 +11,10 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ +#include "comm_tiled.h" #include #include #include -#include "comm_tiled.h" #include "atom.h" #include "atom_vec.h" #include "domain.h" diff --git a/src/compute.cpp b/src/compute.cpp index 8ff8487104..cc92d2b5d3 100644 --- a/src/compute.cpp +++ b/src/compute.cpp @@ -11,9 +11,9 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ +#include "compute.h" #include #include -#include "compute.h" #include "domain.h" #include "force.h" #include "group.h" diff --git a/src/compute_adf.cpp b/src/compute_adf.cpp index a17561ff54..dee5fb214f 100644 --- a/src/compute_adf.cpp +++ b/src/compute_adf.cpp @@ -15,10 +15,10 @@ Contributing authors: Aidan P. Thompson (SNL) ------------------------------------------------------------------------- */ +#include "compute_adf.h" #include #include #include -#include "compute_adf.h" #include "atom.h" #include "update.h" #include "force.h" diff --git a/src/compute_aggregate_atom.cpp b/src/compute_aggregate_atom.cpp index 9a797124bd..e495ac6899 100644 --- a/src/compute_aggregate_atom.cpp +++ b/src/compute_aggregate_atom.cpp @@ -15,10 +15,10 @@ Contributing author: Axel Kohlmeyer (Temple U) ------------------------------------------------------------------------- */ +#include "compute_aggregate_atom.h" #include #include #include -#include "compute_aggregate_atom.h" #include "atom.h" #include "atom_vec.h" #include "update.h" diff --git a/src/compute_angle.cpp b/src/compute_angle.cpp index c1c02a1cc4..fc72a58453 100644 --- a/src/compute_angle.cpp +++ b/src/compute_angle.cpp @@ -11,8 +11,8 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include #include "compute_angle.h" +#include #include "angle.h" #include "update.h" #include "force.h" diff --git a/src/compute_angle_local.cpp b/src/compute_angle_local.cpp index 1196211665..b100824ea9 100644 --- a/src/compute_angle_local.cpp +++ b/src/compute_angle_local.cpp @@ -11,9 +11,9 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ +#include "compute_angle_local.h" #include #include -#include "compute_angle_local.h" #include "atom.h" #include "atom_vec.h" #include "molecule.h" diff --git a/src/compute_angmom_chunk.cpp b/src/compute_angmom_chunk.cpp index ec42015527..05ea963b82 100644 --- a/src/compute_angmom_chunk.cpp +++ b/src/compute_angmom_chunk.cpp @@ -11,9 +11,9 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ +#include "compute_angmom_chunk.h" #include #include -#include "compute_angmom_chunk.h" #include "atom.h" #include "update.h" #include "modify.h" diff --git a/src/compute_bond.cpp b/src/compute_bond.cpp index 4fd3bbef30..5cc947c764 100644 --- a/src/compute_bond.cpp +++ b/src/compute_bond.cpp @@ -11,8 +11,8 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include #include "compute_bond.h" +#include #include "bond.h" #include "update.h" #include "force.h" diff --git a/src/compute_bond_local.cpp b/src/compute_bond_local.cpp index ccdd3ee77c..d579772384 100644 --- a/src/compute_bond_local.cpp +++ b/src/compute_bond_local.cpp @@ -11,9 +11,9 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ +#include "compute_bond_local.h" #include #include -#include "compute_bond_local.h" #include "atom.h" #include "atom_vec.h" #include "molecule.h" diff --git a/src/compute_centro_atom.cpp b/src/compute_centro_atom.cpp index 7df94271fc..18fc31390f 100644 --- a/src/compute_centro_atom.cpp +++ b/src/compute_centro_atom.cpp @@ -15,8 +15,8 @@ Contributing author: Michel Perez (U Lyon) for non-fcc lattices ------------------------------------------------------------------------- */ -#include #include "compute_centro_atom.h" +#include #include "atom.h" #include "update.h" #include "modify.h" diff --git a/src/compute_chunk_atom.cpp b/src/compute_chunk_atom.cpp index fd9204f1cb..92567101de 100644 --- a/src/compute_chunk_atom.cpp +++ b/src/compute_chunk_atom.cpp @@ -13,13 +13,13 @@ // NOTE: allow for bin center to be variables for sphere/cylinder +#include "compute_chunk_atom.h" #include #include #include #include #include #include -#include "compute_chunk_atom.h" #include "atom.h" #include "update.h" #include "force.h" diff --git a/src/compute_chunk_spread_atom.cpp b/src/compute_chunk_spread_atom.cpp index 3d0cea1add..51dad00c25 100644 --- a/src/compute_chunk_spread_atom.cpp +++ b/src/compute_chunk_spread_atom.cpp @@ -11,9 +11,9 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ +#include "compute_chunk_spread_atom.h" #include #include -#include "compute_chunk_spread_atom.h" #include "atom.h" #include "update.h" #include "modify.h" diff --git a/src/compute_cluster_atom.cpp b/src/compute_cluster_atom.cpp index febe0658a0..ff227b3590 100644 --- a/src/compute_cluster_atom.cpp +++ b/src/compute_cluster_atom.cpp @@ -11,10 +11,10 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ +#include "compute_cluster_atom.h" #include #include #include -#include "compute_cluster_atom.h" #include "atom.h" #include "update.h" #include "modify.h" diff --git a/src/compute_cna_atom.cpp b/src/compute_cna_atom.cpp index d764e739b3..054798f637 100644 --- a/src/compute_cna_atom.cpp +++ b/src/compute_cna_atom.cpp @@ -15,10 +15,10 @@ Contributing author: Wan Liang (Chinese Academy of Sciences) ------------------------------------------------------------------------- */ +#include "compute_cna_atom.h" #include #include #include -#include "compute_cna_atom.h" #include "atom.h" #include "update.h" #include "force.h" diff --git a/src/compute_com_chunk.cpp b/src/compute_com_chunk.cpp index 7b4c960cf4..c39911214c 100644 --- a/src/compute_com_chunk.cpp +++ b/src/compute_com_chunk.cpp @@ -11,9 +11,9 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ +#include "compute_com_chunk.h" #include #include -#include "compute_com_chunk.h" #include "atom.h" #include "update.h" #include "modify.h" diff --git a/src/compute_contact_atom.cpp b/src/compute_contact_atom.cpp index e4afc1d761..7a288afb43 100644 --- a/src/compute_contact_atom.cpp +++ b/src/compute_contact_atom.cpp @@ -11,8 +11,8 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include #include "compute_contact_atom.h" +#include #include "atom.h" #include "update.h" #include "modify.h" diff --git a/src/compute_coord_atom.cpp b/src/compute_coord_atom.cpp index 8cedcbc027..30747c1314 100644 --- a/src/compute_coord_atom.cpp +++ b/src/compute_coord_atom.cpp @@ -11,9 +11,9 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ +#include "compute_coord_atom.h" #include #include -#include "compute_coord_atom.h" #include "compute_orientorder_atom.h" #include "atom.h" #include "update.h" diff --git a/src/compute_deprecated.cpp b/src/compute_deprecated.cpp index 069fa73437..1db78b6bdf 100644 --- a/src/compute_deprecated.cpp +++ b/src/compute_deprecated.cpp @@ -11,8 +11,8 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include #include "compute_deprecated.h" +#include #include "comm.h" #include "error.h" diff --git a/src/compute_dihedral.cpp b/src/compute_dihedral.cpp index 16823050da..e50903104a 100644 --- a/src/compute_dihedral.cpp +++ b/src/compute_dihedral.cpp @@ -11,8 +11,8 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include #include "compute_dihedral.h" +#include #include "update.h" #include "force.h" #include "dihedral.h" diff --git a/src/compute_dihedral_local.cpp b/src/compute_dihedral_local.cpp index 784ae9c607..ac2c884c3f 100644 --- a/src/compute_dihedral_local.cpp +++ b/src/compute_dihedral_local.cpp @@ -11,9 +11,9 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ +#include "compute_dihedral_local.h" #include #include -#include "compute_dihedral_local.h" #include "atom.h" #include "atom_vec.h" #include "molecule.h" diff --git a/src/compute_dipole_chunk.cpp b/src/compute_dipole_chunk.cpp index 090bc5df94..3790da2035 100644 --- a/src/compute_dipole_chunk.cpp +++ b/src/compute_dipole_chunk.cpp @@ -11,10 +11,10 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ +#include "compute_dipole_chunk.h" #include #include #include -#include "compute_dipole_chunk.h" #include "atom.h" #include "update.h" #include "modify.h" diff --git a/src/compute_displace_atom.cpp b/src/compute_displace_atom.cpp index 3773159143..41db4db1d6 100644 --- a/src/compute_displace_atom.cpp +++ b/src/compute_displace_atom.cpp @@ -11,9 +11,9 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ +#include "compute_displace_atom.h" #include #include -#include "compute_displace_atom.h" #include "atom.h" #include "update.h" #include "group.h" diff --git a/src/compute_erotate_sphere.cpp b/src/compute_erotate_sphere.cpp index 65bb8a9770..2a8588f061 100644 --- a/src/compute_erotate_sphere.cpp +++ b/src/compute_erotate_sphere.cpp @@ -11,8 +11,8 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include #include "compute_erotate_sphere.h" +#include #include "atom.h" #include "update.h" #include "force.h" diff --git a/src/compute_erotate_sphere_atom.cpp b/src/compute_erotate_sphere_atom.cpp index 999bc062c5..78664a912f 100644 --- a/src/compute_erotate_sphere_atom.cpp +++ b/src/compute_erotate_sphere_atom.cpp @@ -11,8 +11,8 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include #include "compute_erotate_sphere_atom.h" +#include #include "atom.h" #include "update.h" #include "modify.h" diff --git a/src/compute_fragment_atom.cpp b/src/compute_fragment_atom.cpp index d59b519d09..f9b68dd217 100644 --- a/src/compute_fragment_atom.cpp +++ b/src/compute_fragment_atom.cpp @@ -15,9 +15,9 @@ Contributing author: Axel Kohlmeyer (Temple U) ------------------------------------------------------------------------- */ +#include "compute_fragment_atom.h" #include #include -#include "compute_fragment_atom.h" #include "atom.h" #include "atom_vec.h" #include "update.h" diff --git a/src/compute_global_atom.cpp b/src/compute_global_atom.cpp index 6685f746a1..15f8a8f1aa 100644 --- a/src/compute_global_atom.cpp +++ b/src/compute_global_atom.cpp @@ -11,9 +11,9 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ +#include "compute_global_atom.h" #include #include -#include "compute_global_atom.h" #include "atom.h" #include "update.h" #include "modify.h" diff --git a/src/compute_group_group.cpp b/src/compute_group_group.cpp index 11e1aac720..f978b4a228 100644 --- a/src/compute_group_group.cpp +++ b/src/compute_group_group.cpp @@ -16,10 +16,10 @@ K-space terms added by Stan Moore (BYU) ------------------------------------------------------------------------- */ +#include "compute_group_group.h" #include #include #include -#include "compute_group_group.h" #include "atom.h" #include "update.h" #include "force.h" diff --git a/src/compute_gyration.cpp b/src/compute_gyration.cpp index 3c5656a5af..2b1a26cc75 100644 --- a/src/compute_gyration.cpp +++ b/src/compute_gyration.cpp @@ -11,8 +11,8 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include #include "compute_gyration.h" +#include #include "update.h" #include "atom.h" #include "group.h" diff --git a/src/compute_gyration_chunk.cpp b/src/compute_gyration_chunk.cpp index f3db37d62f..5677ce4b6a 100644 --- a/src/compute_gyration_chunk.cpp +++ b/src/compute_gyration_chunk.cpp @@ -11,10 +11,10 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ +#include "compute_gyration_chunk.h" #include #include #include -#include "compute_gyration_chunk.h" #include "atom.h" #include "update.h" #include "modify.h" diff --git a/src/compute_heat_flux.cpp b/src/compute_heat_flux.cpp index 9bd827c713..b717dce04a 100644 --- a/src/compute_heat_flux.cpp +++ b/src/compute_heat_flux.cpp @@ -16,9 +16,9 @@ Mario Pinto (Computational Research Lab, Pune, India) ------------------------------------------------------------------------- */ +#include "compute_heat_flux.h" #include #include -#include "compute_heat_flux.h" #include "atom.h" #include "update.h" #include "modify.h" diff --git a/src/compute_hexorder_atom.cpp b/src/compute_hexorder_atom.cpp index c54f4b1aae..96d4c47678 100644 --- a/src/compute_hexorder_atom.cpp +++ b/src/compute_hexorder_atom.cpp @@ -15,10 +15,10 @@ Contributing author: Aidan Thompson (SNL) ------------------------------------------------------------------------- */ +#include "compute_hexorder_atom.h" #include #include #include -#include "compute_hexorder_atom.h" #include "atom.h" #include "update.h" #include "modify.h" diff --git a/src/compute_improper.cpp b/src/compute_improper.cpp index 2f068dfb74..181771dcfb 100644 --- a/src/compute_improper.cpp +++ b/src/compute_improper.cpp @@ -11,8 +11,8 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include #include "compute_improper.h" +#include #include "update.h" #include "force.h" #include "improper.h" diff --git a/src/compute_improper_local.cpp b/src/compute_improper_local.cpp index ec1734cd96..e363749b67 100644 --- a/src/compute_improper_local.cpp +++ b/src/compute_improper_local.cpp @@ -11,9 +11,9 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ +#include "compute_improper_local.h" #include #include -#include "compute_improper_local.h" #include "atom.h" #include "atom_vec.h" #include "molecule.h" diff --git a/src/compute_inertia_chunk.cpp b/src/compute_inertia_chunk.cpp index d1a7cb9fc1..be980a08ee 100644 --- a/src/compute_inertia_chunk.cpp +++ b/src/compute_inertia_chunk.cpp @@ -11,9 +11,9 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ +#include "compute_inertia_chunk.h" #include #include -#include "compute_inertia_chunk.h" #include "atom.h" #include "update.h" #include "modify.h" diff --git a/src/compute_ke.cpp b/src/compute_ke.cpp index 3418cc678f..c6ba478dcb 100644 --- a/src/compute_ke.cpp +++ b/src/compute_ke.cpp @@ -11,8 +11,8 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include #include "compute_ke.h" +#include #include "atom.h" #include "update.h" #include "force.h" diff --git a/src/compute_ke_atom.cpp b/src/compute_ke_atom.cpp index c5506996da..102d6364ff 100644 --- a/src/compute_ke_atom.cpp +++ b/src/compute_ke_atom.cpp @@ -11,8 +11,8 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include #include "compute_ke_atom.h" +#include #include "atom.h" #include "update.h" #include "modify.h" diff --git a/src/compute_msd.cpp b/src/compute_msd.cpp index d2e17eff9e..b4115d859c 100644 --- a/src/compute_msd.cpp +++ b/src/compute_msd.cpp @@ -11,9 +11,9 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ +#include "compute_msd.h" #include #include -#include "compute_msd.h" #include "atom.h" #include "update.h" #include "group.h" diff --git a/src/compute_msd_chunk.cpp b/src/compute_msd_chunk.cpp index 8520b36993..8039a4fcd5 100644 --- a/src/compute_msd_chunk.cpp +++ b/src/compute_msd_chunk.cpp @@ -11,9 +11,9 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ +#include "compute_msd_chunk.h" #include #include -#include "compute_msd_chunk.h" #include "atom.h" #include "group.h" #include "update.h" diff --git a/src/compute_omega_chunk.cpp b/src/compute_omega_chunk.cpp index 360255e908..327c64493f 100644 --- a/src/compute_omega_chunk.cpp +++ b/src/compute_omega_chunk.cpp @@ -11,9 +11,9 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ +#include "compute_omega_chunk.h" #include #include -#include "compute_omega_chunk.h" #include "atom.h" #include "update.h" #include "modify.h" diff --git a/src/compute_orientorder_atom.cpp b/src/compute_orientorder_atom.cpp index 8a0a525fdc..266df575f9 100644 --- a/src/compute_orientorder_atom.cpp +++ b/src/compute_orientorder_atom.cpp @@ -16,10 +16,10 @@ Axel Kohlmeyer (Temple U) ------------------------------------------------------------------------- */ +#include "compute_orientorder_atom.h" #include #include #include -#include "compute_orientorder_atom.h" #include "atom.h" #include "update.h" #include "modify.h" diff --git a/src/compute_pair.cpp b/src/compute_pair.cpp index df4f3a1ddb..e9a3faf723 100644 --- a/src/compute_pair.cpp +++ b/src/compute_pair.cpp @@ -11,10 +11,10 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ +#include "compute_pair.h" #include #include #include -#include "compute_pair.h" #include "update.h" #include "force.h" #include "pair.h" diff --git a/src/compute_pair_local.cpp b/src/compute_pair_local.cpp index 1ab46a0297..2018d929f3 100644 --- a/src/compute_pair_local.cpp +++ b/src/compute_pair_local.cpp @@ -11,10 +11,10 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ +#include "compute_pair_local.h" #include #include #include -#include "compute_pair_local.h" #include "atom.h" #include "update.h" #include "force.h" diff --git a/src/compute_pe.cpp b/src/compute_pe.cpp index 5839ec2095..fd7b74b43a 100644 --- a/src/compute_pe.cpp +++ b/src/compute_pe.cpp @@ -11,9 +11,9 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ +#include "compute_pe.h" #include #include -#include "compute_pe.h" #include "atom.h" #include "update.h" #include "force.h" diff --git a/src/compute_pe_atom.cpp b/src/compute_pe_atom.cpp index b3ace2d419..274e1b05a6 100644 --- a/src/compute_pe_atom.cpp +++ b/src/compute_pe_atom.cpp @@ -11,8 +11,8 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include #include "compute_pe_atom.h" +#include #include "atom.h" #include "update.h" #include "comm.h" diff --git a/src/compute_pressure.cpp b/src/compute_pressure.cpp index 431f039de3..1782a040ae 100644 --- a/src/compute_pressure.cpp +++ b/src/compute_pressure.cpp @@ -11,9 +11,9 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ +#include "compute_pressure.h" #include #include -#include "compute_pressure.h" #include "atom.h" #include "update.h" #include "domain.h" diff --git a/src/compute_property_atom.cpp b/src/compute_property_atom.cpp index 0b57840696..065e3eeb82 100644 --- a/src/compute_property_atom.cpp +++ b/src/compute_property_atom.cpp @@ -11,9 +11,9 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ +#include "compute_property_atom.h" #include #include -#include "compute_property_atom.h" #include "math_extra.h" #include "atom.h" #include "atom_vec.h" diff --git a/src/compute_property_chunk.cpp b/src/compute_property_chunk.cpp index 089e867598..579c7cae3f 100644 --- a/src/compute_property_chunk.cpp +++ b/src/compute_property_chunk.cpp @@ -11,9 +11,9 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ +#include "compute_property_chunk.h" #include #include -#include "compute_property_chunk.h" #include "atom.h" #include "update.h" #include "modify.h" diff --git a/src/compute_property_local.cpp b/src/compute_property_local.cpp index ddcf5913ca..651e1190b1 100644 --- a/src/compute_property_local.cpp +++ b/src/compute_property_local.cpp @@ -11,8 +11,8 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include #include "compute_property_local.h" +#include #include "atom.h" #include "atom_vec.h" #include "update.h" diff --git a/src/compute_rdf.cpp b/src/compute_rdf.cpp index b1fa8bb2a3..501a506c98 100644 --- a/src/compute_rdf.cpp +++ b/src/compute_rdf.cpp @@ -15,10 +15,10 @@ Contributing authors: Paul Crozier (SNL), Jeff Greathouse (SNL) ------------------------------------------------------------------------- */ +#include "compute_rdf.h" #include #include #include -#include "compute_rdf.h" #include "atom.h" #include "update.h" #include "force.h" diff --git a/src/compute_reduce.cpp b/src/compute_reduce.cpp index e7692b0797..8467554faa 100644 --- a/src/compute_reduce.cpp +++ b/src/compute_reduce.cpp @@ -11,10 +11,10 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ +#include "compute_reduce.h" #include #include #include -#include "compute_reduce.h" #include "atom.h" #include "update.h" #include "domain.h" diff --git a/src/compute_reduce_chunk.cpp b/src/compute_reduce_chunk.cpp index 5eda71b21b..3b68e20fcb 100644 --- a/src/compute_reduce_chunk.cpp +++ b/src/compute_reduce_chunk.cpp @@ -11,10 +11,10 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ +#include "compute_reduce_chunk.h" #include #include #include -#include "compute_reduce_chunk.h" #include "atom.h" #include "update.h" #include "modify.h" diff --git a/src/compute_reduce_region.cpp b/src/compute_reduce_region.cpp index 30a5c6393f..9074124a61 100644 --- a/src/compute_reduce_region.cpp +++ b/src/compute_reduce_region.cpp @@ -11,8 +11,8 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include #include "compute_reduce_region.h" +#include #include "atom.h" #include "update.h" #include "modify.h" diff --git a/src/compute_slice.cpp b/src/compute_slice.cpp index 6e509c24d4..67b60882f6 100644 --- a/src/compute_slice.cpp +++ b/src/compute_slice.cpp @@ -11,10 +11,10 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ +#include "compute_slice.h" #include #include #include -#include "compute_slice.h" #include "update.h" #include "modify.h" #include "fix.h" diff --git a/src/compute_stress_atom.cpp b/src/compute_stress_atom.cpp index f84c977bdb..7c0ed9ef17 100644 --- a/src/compute_stress_atom.cpp +++ b/src/compute_stress_atom.cpp @@ -11,8 +11,8 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include #include "compute_stress_atom.h" +#include #include "atom.h" #include "update.h" #include "comm.h" diff --git a/src/compute_temp.cpp b/src/compute_temp.cpp index c330249a7e..e77531ee28 100644 --- a/src/compute_temp.cpp +++ b/src/compute_temp.cpp @@ -11,8 +11,8 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include #include "compute_temp.h" +#include #include "atom.h" #include "update.h" #include "force.h" diff --git a/src/compute_temp_chunk.cpp b/src/compute_temp_chunk.cpp index 229e98e258..e66aa64a27 100644 --- a/src/compute_temp_chunk.cpp +++ b/src/compute_temp_chunk.cpp @@ -11,9 +11,9 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ +#include "compute_temp_chunk.h" #include #include -#include "compute_temp_chunk.h" #include "atom.h" #include "update.h" #include "force.h" diff --git a/src/compute_temp_com.cpp b/src/compute_temp_com.cpp index 21814e1940..e5b9b3d828 100644 --- a/src/compute_temp_com.cpp +++ b/src/compute_temp_com.cpp @@ -11,8 +11,8 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include #include "compute_temp_com.h" +#include #include "atom.h" #include "update.h" #include "force.h" diff --git a/src/compute_temp_deform.cpp b/src/compute_temp_deform.cpp index 39780b5cf6..ff8909a5c7 100644 --- a/src/compute_temp_deform.cpp +++ b/src/compute_temp_deform.cpp @@ -15,9 +15,9 @@ Contributing author: Pieter in 't Veld (SNL) ------------------------------------------------------------------------- */ +#include "compute_temp_deform.h" #include #include -#include "compute_temp_deform.h" #include "domain.h" #include "atom.h" #include "update.h" diff --git a/src/compute_temp_partial.cpp b/src/compute_temp_partial.cpp index 8d5ff66796..6bffcef374 100644 --- a/src/compute_temp_partial.cpp +++ b/src/compute_temp_partial.cpp @@ -11,8 +11,8 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include #include "compute_temp_partial.h" +#include #include "atom.h" #include "update.h" #include "force.h" diff --git a/src/compute_temp_profile.cpp b/src/compute_temp_profile.cpp index 21c87b31a2..fce145848e 100644 --- a/src/compute_temp_profile.cpp +++ b/src/compute_temp_profile.cpp @@ -11,9 +11,9 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ +#include "compute_temp_profile.h" #include #include -#include "compute_temp_profile.h" #include "atom.h" #include "update.h" #include "force.h" diff --git a/src/compute_temp_ramp.cpp b/src/compute_temp_ramp.cpp index 715d2aa9f4..0899f89fd1 100644 --- a/src/compute_temp_ramp.cpp +++ b/src/compute_temp_ramp.cpp @@ -11,9 +11,9 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ +#include "compute_temp_ramp.h" #include #include -#include "compute_temp_ramp.h" #include "atom.h" #include "update.h" #include "force.h" diff --git a/src/compute_temp_region.cpp b/src/compute_temp_region.cpp index 4aa4dac0a1..a1b1b77648 100644 --- a/src/compute_temp_region.cpp +++ b/src/compute_temp_region.cpp @@ -11,9 +11,9 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ +#include "compute_temp_region.h" #include #include -#include "compute_temp_region.h" #include "atom.h" #include "update.h" #include "force.h" diff --git a/src/compute_temp_sphere.cpp b/src/compute_temp_sphere.cpp index b490a5ec45..d2bfe6db61 100644 --- a/src/compute_temp_sphere.cpp +++ b/src/compute_temp_sphere.cpp @@ -11,9 +11,9 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ +#include "compute_temp_sphere.h" #include #include -#include "compute_temp_sphere.h" #include "atom.h" #include "update.h" #include "force.h" diff --git a/src/compute_torque_chunk.cpp b/src/compute_torque_chunk.cpp index e43155493f..35eef8fe10 100644 --- a/src/compute_torque_chunk.cpp +++ b/src/compute_torque_chunk.cpp @@ -11,9 +11,9 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ +#include "compute_torque_chunk.h" #include #include -#include "compute_torque_chunk.h" #include "atom.h" #include "update.h" #include "modify.h" diff --git a/src/compute_vacf.cpp b/src/compute_vacf.cpp index 787c2503ca..761f827347 100644 --- a/src/compute_vacf.cpp +++ b/src/compute_vacf.cpp @@ -11,9 +11,9 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ +#include "compute_vacf.h" #include #include -#include "compute_vacf.h" #include "atom.h" #include "update.h" #include "group.h" diff --git a/src/compute_vcm_chunk.cpp b/src/compute_vcm_chunk.cpp index cf30130763..b0a8dbeee7 100644 --- a/src/compute_vcm_chunk.cpp +++ b/src/compute_vcm_chunk.cpp @@ -11,9 +11,9 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ +#include "compute_vcm_chunk.h" #include #include -#include "compute_vcm_chunk.h" #include "atom.h" #include "update.h" #include "modify.h" diff --git a/src/create_atoms.cpp b/src/create_atoms.cpp index 8504023a70..f6cff042fe 100644 --- a/src/create_atoms.cpp +++ b/src/create_atoms.cpp @@ -11,9 +11,9 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ +#include "create_atoms.h" #include #include -#include "create_atoms.h" #include "atom.h" #include "atom_vec.h" #include "molecule.h" diff --git a/src/create_bonds.cpp b/src/create_bonds.cpp index e00fe109ca..5b7c354595 100644 --- a/src/create_bonds.cpp +++ b/src/create_bonds.cpp @@ -15,9 +15,9 @@ Contributing authors: Mike Salerno (NRL) added single methods ------------------------------------------------------------------------- */ +#include "create_bonds.h" #include #include -#include "create_bonds.h" #include "atom.h" #include "domain.h" #include "force.h" diff --git a/src/create_box.cpp b/src/create_box.cpp index 5ec960bec4..4a826cb691 100644 --- a/src/create_box.cpp +++ b/src/create_box.cpp @@ -11,8 +11,8 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include #include "create_box.h" +#include #include "atom.h" #include "atom_vec.h" #include "domain.h" diff --git a/src/delete_atoms.cpp b/src/delete_atoms.cpp index ff4b97a3a4..e8d9c5d53b 100644 --- a/src/delete_atoms.cpp +++ b/src/delete_atoms.cpp @@ -11,10 +11,10 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ +#include "delete_atoms.h" #include #include #include -#include "delete_atoms.h" #include "atom.h" #include "atom_vec.h" #include "atom_vec_ellipsoid.h" diff --git a/src/delete_bonds.cpp b/src/delete_bonds.cpp index c4d591543a..c450f77ee7 100644 --- a/src/delete_bonds.cpp +++ b/src/delete_bonds.cpp @@ -11,10 +11,10 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ +#include "delete_bonds.h" #include #include #include -#include "delete_bonds.h" #include "atom.h" #include "atom_vec.h" #include "domain.h" diff --git a/src/deprecated.cpp b/src/deprecated.cpp index 66ddcfeff4..86af54fbfd 100644 --- a/src/deprecated.cpp +++ b/src/deprecated.cpp @@ -15,8 +15,8 @@ Contributing authors: Axel Kohlmeyer (Temple U), ------------------------------------------------------------------------- */ -#include #include "deprecated.h" +#include #include "comm.h" #include "error.h" #include "input.h" diff --git a/src/dihedral_deprecated.cpp b/src/dihedral_deprecated.cpp index 70888ca76d..0205b1b887 100644 --- a/src/dihedral_deprecated.cpp +++ b/src/dihedral_deprecated.cpp @@ -15,8 +15,8 @@ Contributing author: Axel Kohlmeyer (Temple U) ------------------------------------------------------------------------- */ -#include #include "dihedral_deprecated.h" +#include #include "dihedral_hybrid.h" #include "comm.h" #include "force.h" diff --git a/src/dihedral_hybrid.cpp b/src/dihedral_hybrid.cpp index 27fd7084bc..0863be955d 100644 --- a/src/dihedral_hybrid.cpp +++ b/src/dihedral_hybrid.cpp @@ -11,10 +11,10 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ +#include "dihedral_hybrid.h" #include #include #include -#include "dihedral_hybrid.h" #include "atom.h" #include "neighbor.h" #include "comm.h" diff --git a/src/dihedral_zero.cpp b/src/dihedral_zero.cpp index 0367477267..daf46fe79a 100644 --- a/src/dihedral_zero.cpp +++ b/src/dihedral_zero.cpp @@ -15,8 +15,8 @@ Contributing author: Carsten Svaneborg (SDU) ------------------------------------------------------------------------- */ -#include #include "dihedral_zero.h" +#include #include "atom.h" #include "force.h" #include "memory.h" diff --git a/src/displace_atoms.cpp b/src/displace_atoms.cpp index 8bae173a1d..dc94c3ed35 100644 --- a/src/displace_atoms.cpp +++ b/src/displace_atoms.cpp @@ -11,10 +11,10 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ +#include "displace_atoms.h" #include #include #include -#include "displace_atoms.h" #include "atom.h" #include "modify.h" #include "domain.h" diff --git a/src/domain.cpp b/src/domain.cpp index 197eff514a..372b264013 100644 --- a/src/domain.cpp +++ b/src/domain.cpp @@ -15,10 +15,10 @@ Contributing author (triclinic) : Pieter in 't Veld (SNL) ------------------------------------------------------------------------- */ +#include "domain.h" #include #include #include -#include "domain.h" #include "style_region.h" #include "atom.h" #include "atom_vec.h" diff --git a/src/dump.cpp b/src/dump.cpp index b08a4de2ad..57a8decbb0 100644 --- a/src/dump.cpp +++ b/src/dump.cpp @@ -11,9 +11,9 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ +#include "dump.h" #include #include -#include "dump.h" #include "atom.h" #include "irregular.h" #include "update.h" diff --git a/src/dump_atom.cpp b/src/dump_atom.cpp index c95256ac21..e2e77cfb77 100644 --- a/src/dump_atom.cpp +++ b/src/dump_atom.cpp @@ -11,8 +11,8 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include #include "dump_atom.h" +#include #include "domain.h" #include "atom.h" #include "update.h" diff --git a/src/dump_cfg.cpp b/src/dump_cfg.cpp index eb5329e0d1..3430720b8c 100644 --- a/src/dump_cfg.cpp +++ b/src/dump_cfg.cpp @@ -16,8 +16,8 @@ Memory efficiency improved by Ray Shan (Sandia) ------------------------------------------------------------------------- */ -#include #include "dump_cfg.h" +#include #include "atom.h" #include "domain.h" #include "memory.h" diff --git a/src/dump_custom.cpp b/src/dump_custom.cpp index 75e4e42bcd..ce83e442c9 100644 --- a/src/dump_custom.cpp +++ b/src/dump_custom.cpp @@ -11,9 +11,9 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ +#include "dump_custom.h" #include #include -#include "dump_custom.h" #include "atom.h" #include "force.h" #include "domain.h" diff --git a/src/dump_dcd.cpp b/src/dump_dcd.cpp index ce669fecfd..254b371e22 100644 --- a/src/dump_dcd.cpp +++ b/src/dump_dcd.cpp @@ -16,10 +16,10 @@ Axel Kohlmeyer (Temple U), support for groups ------------------------------------------------------------------------- */ +#include "dump_dcd.h" #include #include #include -#include "dump_dcd.h" #include "domain.h" #include "atom.h" #include "update.h" diff --git a/src/dump_deprecated.cpp b/src/dump_deprecated.cpp index f0999f4276..4263b9801f 100644 --- a/src/dump_deprecated.cpp +++ b/src/dump_deprecated.cpp @@ -11,8 +11,8 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include #include "dump_deprecated.h" +#include #include "comm.h" #include "error.h" diff --git a/src/dump_image.cpp b/src/dump_image.cpp index 0b4ca43879..7e6bc0c44c 100644 --- a/src/dump_image.cpp +++ b/src/dump_image.cpp @@ -11,11 +11,11 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ +#include "dump_image.h" #include #include #include #include -#include "dump_image.h" #include "image.h" #include "atom.h" #include "atom_vec.h" diff --git a/src/dump_local.cpp b/src/dump_local.cpp index f99b7ac06c..9f021a7b6a 100644 --- a/src/dump_local.cpp +++ b/src/dump_local.cpp @@ -11,10 +11,10 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ +#include "dump_local.h" #include #include #include -#include "dump_local.h" #include "modify.h" #include "fix.h" #include "compute.h" diff --git a/src/dump_movie.cpp b/src/dump_movie.cpp index 37d8a37f4d..ea67320d4a 100644 --- a/src/dump_movie.cpp +++ b/src/dump_movie.cpp @@ -15,8 +15,8 @@ Contributing author: Axel Kohlmeyer (Temple U) ------------------------------------------------------------------------- */ -#include #include "dump_movie.h" +#include #include "comm.h" #include "force.h" #include "error.h" diff --git a/src/dump_xyz.cpp b/src/dump_xyz.cpp index 4d50cfc2c8..10ba10f995 100644 --- a/src/dump_xyz.cpp +++ b/src/dump_xyz.cpp @@ -11,8 +11,8 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include #include "dump_xyz.h" +#include #include "atom.h" #include "error.h" #include "memory.h" diff --git a/src/error.cpp b/src/error.cpp index 8970145b7c..656c957ee2 100644 --- a/src/error.cpp +++ b/src/error.cpp @@ -11,10 +11,10 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ +#include "error.h" #include #include #include -#include "error.h" #include "universe.h" #include "output.h" #include "input.h" diff --git a/src/finish.cpp b/src/finish.cpp index 77c959b945..bef3ae89eb 100644 --- a/src/finish.cpp +++ b/src/finish.cpp @@ -11,11 +11,11 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ +#include "finish.h" #include #include #include #include -#include "finish.h" #include "timer.h" #include "universe.h" #include "accelerator_kokkos.h" diff --git a/src/fix.cpp b/src/fix.cpp index 1913ed483e..e0cfeca1a9 100644 --- a/src/fix.cpp +++ b/src/fix.cpp @@ -11,9 +11,9 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ +#include "fix.h" #include #include -#include "fix.h" #include "atom.h" #include "group.h" #include "force.h" diff --git a/src/fix_adapt.cpp b/src/fix_adapt.cpp index 7ac6128558..8668690e1d 100644 --- a/src/fix_adapt.cpp +++ b/src/fix_adapt.cpp @@ -11,8 +11,8 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include #include "fix_adapt.h" +#include #include "atom.h" #include "bond.h" #include "update.h" diff --git a/src/fix_addforce.cpp b/src/fix_addforce.cpp index e29c4ffe9f..275ec2c846 100644 --- a/src/fix_addforce.cpp +++ b/src/fix_addforce.cpp @@ -11,10 +11,10 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ +#include "fix_addforce.h" #include #include #include -#include "fix_addforce.h" #include "atom.h" #include "atom_masks.h" #include "update.h" diff --git a/src/fix_ave_atom.cpp b/src/fix_ave_atom.cpp index e6566632de..694df2bcf7 100644 --- a/src/fix_ave_atom.cpp +++ b/src/fix_ave_atom.cpp @@ -11,9 +11,9 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ +#include "fix_ave_atom.h" #include #include -#include "fix_ave_atom.h" #include "atom.h" #include "update.h" #include "modify.h" diff --git a/src/fix_ave_chunk.cpp b/src/fix_ave_chunk.cpp index 1533d1fa4f..45eb38f5c2 100644 --- a/src/fix_ave_chunk.cpp +++ b/src/fix_ave_chunk.cpp @@ -11,12 +11,11 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ +#include "fix_ave_chunk.h" #include -#include // IWYU pragma: keep #include #include #include -#include "fix_ave_chunk.h" #include "atom.h" #include "update.h" #include "force.h" diff --git a/src/fix_ave_correlate.cpp b/src/fix_ave_correlate.cpp index 555c1ac026..f65b53efc8 100644 --- a/src/fix_ave_correlate.cpp +++ b/src/fix_ave_correlate.cpp @@ -17,12 +17,11 @@ Reese Jones (Sandia) ------------------------------------------------------------------------- */ +#include "fix_ave_correlate.h" #include -#include // IWYU pragma: keep #include #include #include -#include "fix_ave_correlate.h" #include "update.h" #include "modify.h" #include "compute.h" diff --git a/src/fix_ave_histo.cpp b/src/fix_ave_histo.cpp index 29fdc21c74..5a5de6d0b6 100644 --- a/src/fix_ave_histo.cpp +++ b/src/fix_ave_histo.cpp @@ -11,12 +11,11 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ +#include "fix_ave_histo.h" #include -#include // IWYU pragma: keep #include #include #include -#include "fix_ave_histo.h" #include "atom.h" #include "update.h" #include "modify.h" diff --git a/src/fix_ave_histo_weight.cpp b/src/fix_ave_histo_weight.cpp index 5eeb074472..1f0d282e5d 100644 --- a/src/fix_ave_histo_weight.cpp +++ b/src/fix_ave_histo_weight.cpp @@ -14,11 +14,10 @@ /* ---------------------------------------------------------------------- Contributing author: Shawn Coleman (ARL) ------------------------------------------------------------------------- */ +#include "fix_ave_histo_weight.h" #include -#include // IWYU pragma: keep #include #include "fix.h" -#include "fix_ave_histo_weight.h" #include "atom.h" #include "update.h" #include "modify.h" diff --git a/src/fix_ave_time.cpp b/src/fix_ave_time.cpp index 4820215f46..05d556d0c8 100644 --- a/src/fix_ave_time.cpp +++ b/src/fix_ave_time.cpp @@ -15,12 +15,11 @@ Contributing author: Pieter in 't Veld (SNL) ------------------------------------------------------------------------- */ +#include "fix_ave_time.h" #include -#include // IWYU pragma: keep #include #include #include -#include "fix_ave_time.h" #include "update.h" #include "force.h" #include "modify.h" diff --git a/src/fix_aveforce.cpp b/src/fix_aveforce.cpp index 4791a8b022..8ad07780a9 100644 --- a/src/fix_aveforce.cpp +++ b/src/fix_aveforce.cpp @@ -11,9 +11,9 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ +#include "fix_aveforce.h" #include #include -#include "fix_aveforce.h" #include "atom.h" #include "update.h" #include "modify.h" diff --git a/src/fix_balance.cpp b/src/fix_balance.cpp index f9c32e8df0..5ca1ec124a 100644 --- a/src/fix_balance.cpp +++ b/src/fix_balance.cpp @@ -11,8 +11,8 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include #include "fix_balance.h" +#include #include "balance.h" #include "update.h" #include "atom.h" diff --git a/src/fix_box_relax.cpp b/src/fix_box_relax.cpp index c73c0ade88..c19ea918b4 100644 --- a/src/fix_box_relax.cpp +++ b/src/fix_box_relax.cpp @@ -15,9 +15,9 @@ Contributing author: Aidan Thompson (SNL) ------------------------------------------------------------------------- */ +#include "fix_box_relax.h" #include #include -#include "fix_box_relax.h" #include "atom.h" #include "domain.h" #include "update.h" diff --git a/src/fix_controller.cpp b/src/fix_controller.cpp index eb7a794962..855869a574 100644 --- a/src/fix_controller.cpp +++ b/src/fix_controller.cpp @@ -11,9 +11,9 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ +#include "fix_controller.h" #include #include -#include "fix_controller.h" #include "force.h" #include "update.h" #include "modify.h" diff --git a/src/fix_deform.cpp b/src/fix_deform.cpp index 96d7580c39..9d84c4bb62 100644 --- a/src/fix_deform.cpp +++ b/src/fix_deform.cpp @@ -15,9 +15,9 @@ Contributing author: Pieter in 't Veld (SNL) ------------------------------------------------------------------------- */ +#include "fix_deform.h" #include #include -#include "fix_deform.h" #include "atom.h" #include "update.h" #include "comm.h" diff --git a/src/fix_deprecated.cpp b/src/fix_deprecated.cpp index 7db27152ba..0c212668b3 100644 --- a/src/fix_deprecated.cpp +++ b/src/fix_deprecated.cpp @@ -11,8 +11,8 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include #include "fix_deprecated.h" +#include #include "comm.h" #include "error.h" diff --git a/src/fix_drag.cpp b/src/fix_drag.cpp index 006d1c46d0..9af5a37675 100644 --- a/src/fix_drag.cpp +++ b/src/fix_drag.cpp @@ -11,10 +11,10 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ +#include "fix_drag.h" #include #include #include -#include "fix_drag.h" #include "atom.h" #include "update.h" #include "respa.h" diff --git a/src/fix_dt_reset.cpp b/src/fix_dt_reset.cpp index 4e6195c4fa..da4bdad827 100644 --- a/src/fix_dt_reset.cpp +++ b/src/fix_dt_reset.cpp @@ -11,10 +11,10 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ +#include "fix_dt_reset.h" #include #include #include -#include "fix_dt_reset.h" #include "atom.h" #include "update.h" #include "integrate.h" diff --git a/src/fix_enforce2d.cpp b/src/fix_enforce2d.cpp index 986ded5d16..3edd24e9af 100644 --- a/src/fix_enforce2d.cpp +++ b/src/fix_enforce2d.cpp @@ -11,8 +11,8 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include #include "fix_enforce2d.h" +#include #include "atom.h" #include "update.h" #include "domain.h" diff --git a/src/fix_external.cpp b/src/fix_external.cpp index 2c926e26b5..afb420df93 100644 --- a/src/fix_external.cpp +++ b/src/fix_external.cpp @@ -11,8 +11,8 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include #include "fix_external.h" +#include #include "atom.h" #include "update.h" #include "memory.h" diff --git a/src/fix_gravity.cpp b/src/fix_gravity.cpp index 8508a92cc4..14ba913c01 100644 --- a/src/fix_gravity.cpp +++ b/src/fix_gravity.cpp @@ -11,10 +11,10 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ +#include "fix_gravity.h" #include #include #include -#include "fix_gravity.h" #include "atom.h" #include "update.h" #include "domain.h" diff --git a/src/fix_group.cpp b/src/fix_group.cpp index 8a332bed95..d2eea9f781 100644 --- a/src/fix_group.cpp +++ b/src/fix_group.cpp @@ -11,8 +11,8 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include #include "fix_group.h" +#include #include "group.h" #include "update.h" #include "atom.h" diff --git a/src/fix_halt.cpp b/src/fix_halt.cpp index 133494fb8e..8ebb39f0e9 100644 --- a/src/fix_halt.cpp +++ b/src/fix_halt.cpp @@ -11,10 +11,10 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ +#include "fix_halt.h" #include #include #include -#include "fix_halt.h" #include "update.h" #include "force.h" #include "input.h" diff --git a/src/fix_heat.cpp b/src/fix_heat.cpp index f78a9c0860..67d445df92 100644 --- a/src/fix_heat.cpp +++ b/src/fix_heat.cpp @@ -15,10 +15,10 @@ Contributing author: Paul Crozier (SNL) ------------------------------------------------------------------------- */ +#include "fix_heat.h" #include #include #include -#include "fix_heat.h" #include "atom.h" #include "domain.h" #include "region.h" diff --git a/src/fix_indent.cpp b/src/fix_indent.cpp index 6a42cadefd..04837ff39b 100644 --- a/src/fix_indent.cpp +++ b/src/fix_indent.cpp @@ -15,10 +15,10 @@ Contributing author: Ravi Agrawal (Northwestern U) ------------------------------------------------------------------------- */ +#include "fix_indent.h" #include #include #include -#include "fix_indent.h" #include "atom.h" #include "input.h" #include "variable.h" diff --git a/src/fix_langevin.cpp b/src/fix_langevin.cpp index 0f48562048..f8fea76c94 100644 --- a/src/fix_langevin.cpp +++ b/src/fix_langevin.cpp @@ -16,10 +16,10 @@ Aidan Thompson (SNL) GJF formulation ------------------------------------------------------------------------- */ +#include "fix_langevin.h" #include #include #include -#include "fix_langevin.h" #include "math_extra.h" #include "atom.h" #include "atom_vec_ellipsoid.h" diff --git a/src/fix_lineforce.cpp b/src/fix_lineforce.cpp index 61c6341aa6..c153ee65dd 100644 --- a/src/fix_lineforce.cpp +++ b/src/fix_lineforce.cpp @@ -11,9 +11,9 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ +#include "fix_lineforce.h" #include #include -#include "fix_lineforce.h" #include "atom.h" #include "update.h" #include "respa.h" diff --git a/src/fix_momentum.cpp b/src/fix_momentum.cpp index bf94a94362..a363cb8eac 100644 --- a/src/fix_momentum.cpp +++ b/src/fix_momentum.cpp @@ -11,10 +11,10 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ +#include "fix_momentum.h" #include #include #include -#include "fix_momentum.h" #include "atom.h" #include "domain.h" #include "group.h" diff --git a/src/fix_move.cpp b/src/fix_move.cpp index 646f943ef9..770c0fca6b 100644 --- a/src/fix_move.cpp +++ b/src/fix_move.cpp @@ -11,9 +11,9 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ +#include "fix_move.h" #include #include -#include "fix_move.h" #include "atom.h" #include "update.h" #include "modify.h" diff --git a/src/fix_neigh_history.cpp b/src/fix_neigh_history.cpp index ca593f29df..5c740ae649 100644 --- a/src/fix_neigh_history.cpp +++ b/src/fix_neigh_history.cpp @@ -11,9 +11,9 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ +#include "fix_neigh_history.h" #include #include -#include "fix_neigh_history.h" #include "my_page.h" #include "atom.h" #include "comm.h" diff --git a/src/fix_nh.cpp b/src/fix_nh.cpp index 3ffdff54cf..bb3fe7559c 100644 --- a/src/fix_nh.cpp +++ b/src/fix_nh.cpp @@ -15,9 +15,9 @@ Contributing authors: Mark Stevens (SNL), Aidan Thompson (SNL) ------------------------------------------------------------------------- */ +#include "fix_nh.h" #include #include -#include "fix_nh.h" #include "atom.h" #include "force.h" #include "group.h" diff --git a/src/fix_nh_sphere.cpp b/src/fix_nh_sphere.cpp index 0f1024700a..1ff3fc2d4d 100644 --- a/src/fix_nh_sphere.cpp +++ b/src/fix_nh_sphere.cpp @@ -15,9 +15,9 @@ Contributing author: Mike Brown (SNL) ------------------------------------------------------------------------- */ +#include "fix_nh_sphere.h" #include #include -#include "fix_nh_sphere.h" #include "atom.h" #include "atom_vec.h" #include "error.h" diff --git a/src/fix_nph.cpp b/src/fix_nph.cpp index 40265ef57c..7148b024de 100644 --- a/src/fix_nph.cpp +++ b/src/fix_nph.cpp @@ -11,8 +11,8 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include #include "fix_nph.h" +#include #include "modify.h" #include "error.h" diff --git a/src/fix_nph_sphere.cpp b/src/fix_nph_sphere.cpp index 3fcbe5e9c6..f64f144f34 100644 --- a/src/fix_nph_sphere.cpp +++ b/src/fix_nph_sphere.cpp @@ -11,8 +11,8 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include #include "fix_nph_sphere.h" +#include #include "modify.h" #include "error.h" diff --git a/src/fix_npt.cpp b/src/fix_npt.cpp index d17577d68d..e856fafe2d 100644 --- a/src/fix_npt.cpp +++ b/src/fix_npt.cpp @@ -11,8 +11,8 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include #include "fix_npt.h" +#include #include "modify.h" #include "error.h" diff --git a/src/fix_npt_sphere.cpp b/src/fix_npt_sphere.cpp index 50ac990daf..9cbb17b0ca 100644 --- a/src/fix_npt_sphere.cpp +++ b/src/fix_npt_sphere.cpp @@ -11,8 +11,8 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include #include "fix_npt_sphere.h" +#include #include "modify.h" #include "error.h" diff --git a/src/fix_nve.cpp b/src/fix_nve.cpp index 3396f3ca47..863ce5404d 100644 --- a/src/fix_nve.cpp +++ b/src/fix_nve.cpp @@ -11,8 +11,8 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include #include "fix_nve.h" +#include #include "atom.h" #include "force.h" #include "update.h" diff --git a/src/fix_nve_limit.cpp b/src/fix_nve_limit.cpp index 49bed2e3dd..d63c736e73 100644 --- a/src/fix_nve_limit.cpp +++ b/src/fix_nve_limit.cpp @@ -11,10 +11,10 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ +#include "fix_nve_limit.h" #include #include #include -#include "fix_nve_limit.h" #include "atom.h" #include "force.h" #include "update.h" diff --git a/src/fix_nve_noforce.cpp b/src/fix_nve_noforce.cpp index 7b61aac18e..022e8abe74 100644 --- a/src/fix_nve_noforce.cpp +++ b/src/fix_nve_noforce.cpp @@ -11,8 +11,8 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include #include "fix_nve_noforce.h" +#include #include "atom.h" #include "update.h" #include "respa.h" diff --git a/src/fix_nve_sphere.cpp b/src/fix_nve_sphere.cpp index 94e8aa88ac..c0fea17c2b 100644 --- a/src/fix_nve_sphere.cpp +++ b/src/fix_nve_sphere.cpp @@ -11,9 +11,9 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ +#include "fix_nve_sphere.h" #include #include -#include "fix_nve_sphere.h" #include "atom.h" #include "domain.h" #include "atom_vec.h" diff --git a/src/fix_nvt.cpp b/src/fix_nvt.cpp index 7247612dd4..6f0d4c6c50 100644 --- a/src/fix_nvt.cpp +++ b/src/fix_nvt.cpp @@ -11,8 +11,8 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include #include "fix_nvt.h" +#include #include "group.h" #include "modify.h" #include "error.h" diff --git a/src/fix_nvt_sllod.cpp b/src/fix_nvt_sllod.cpp index 16e2fb1d3d..138794862a 100644 --- a/src/fix_nvt_sllod.cpp +++ b/src/fix_nvt_sllod.cpp @@ -15,8 +15,8 @@ Contributing author: Pieter in 't Veld (SNL) ------------------------------------------------------------------------- */ -#include #include "fix_nvt_sllod.h" +#include #include "math_extra.h" #include "atom.h" #include "domain.h" diff --git a/src/fix_nvt_sphere.cpp b/src/fix_nvt_sphere.cpp index 44046699ba..fed3799011 100644 --- a/src/fix_nvt_sphere.cpp +++ b/src/fix_nvt_sphere.cpp @@ -11,8 +11,8 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include #include "fix_nvt_sphere.h" +#include #include "group.h" #include "modify.h" #include "error.h" diff --git a/src/fix_planeforce.cpp b/src/fix_planeforce.cpp index a83d00a506..a3f27277bd 100644 --- a/src/fix_planeforce.cpp +++ b/src/fix_planeforce.cpp @@ -11,9 +11,9 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ +#include "fix_planeforce.h" #include #include -#include "fix_planeforce.h" #include "atom.h" #include "update.h" #include "respa.h" diff --git a/src/fix_press_berendsen.cpp b/src/fix_press_berendsen.cpp index ad3e3d1e1c..c090c554e2 100644 --- a/src/fix_press_berendsen.cpp +++ b/src/fix_press_berendsen.cpp @@ -11,9 +11,9 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ +#include "fix_press_berendsen.h" #include #include -#include "fix_press_berendsen.h" #include "atom.h" #include "force.h" #include "comm.h" diff --git a/src/fix_print.cpp b/src/fix_print.cpp index da2e2b54f3..dc76fc39f9 100644 --- a/src/fix_print.cpp +++ b/src/fix_print.cpp @@ -11,9 +11,9 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ +#include "fix_print.h" #include #include -#include "fix_print.h" #include "update.h" #include "input.h" #include "modify.h" diff --git a/src/fix_property_atom.cpp b/src/fix_property_atom.cpp index 62c3ec985b..555114e4f9 100644 --- a/src/fix_property_atom.cpp +++ b/src/fix_property_atom.cpp @@ -11,9 +11,9 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ +#include "fix_property_atom.h" #include #include -#include "fix_property_atom.h" #include "atom.h" #include "comm.h" #include "memory.h" diff --git a/src/fix_recenter.cpp b/src/fix_recenter.cpp index cd50d7dc34..f461e0fa52 100644 --- a/src/fix_recenter.cpp +++ b/src/fix_recenter.cpp @@ -15,9 +15,9 @@ Contributing author: Naveen Michaud-Agrawal (Johns Hopkins U) ------------------------------------------------------------------------- */ +#include "fix_recenter.h" #include #include -#include "fix_recenter.h" #include "atom.h" #include "group.h" #include "update.h" diff --git a/src/fix_respa.cpp b/src/fix_respa.cpp index ea2eb5050a..742dd5c58b 100644 --- a/src/fix_respa.cpp +++ b/src/fix_respa.cpp @@ -11,8 +11,8 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include #include "fix_respa.h" +#include #include "atom.h" #include "force.h" #include "memory.h" diff --git a/src/fix_restrain.cpp b/src/fix_restrain.cpp index 3b9980d567..5a0d4fb662 100644 --- a/src/fix_restrain.cpp +++ b/src/fix_restrain.cpp @@ -16,10 +16,10 @@ support for bond and angle restraints by Andres Jaramillo-Botero (Caltech) ------------------------------------------------------------------------- */ +#include "fix_restrain.h" #include #include #include -#include "fix_restrain.h" #include "atom.h" #include "force.h" #include "update.h" diff --git a/src/fix_setforce.cpp b/src/fix_setforce.cpp index f01008dc10..77c4bfbddc 100644 --- a/src/fix_setforce.cpp +++ b/src/fix_setforce.cpp @@ -11,9 +11,9 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ +#include "fix_setforce.h" #include #include -#include "fix_setforce.h" #include "atom.h" #include "update.h" #include "modify.h" diff --git a/src/fix_spring.cpp b/src/fix_spring.cpp index c87cec2766..510b194ab7 100644 --- a/src/fix_spring.cpp +++ b/src/fix_spring.cpp @@ -15,9 +15,9 @@ Contributing author: Paul Crozier (SNL) ------------------------------------------------------------------------- */ +#include "fix_spring.h" #include #include -#include "fix_spring.h" #include "atom.h" #include "update.h" #include "respa.h" diff --git a/src/fix_spring_chunk.cpp b/src/fix_spring_chunk.cpp index f6ebadde94..e14936a976 100644 --- a/src/fix_spring_chunk.cpp +++ b/src/fix_spring_chunk.cpp @@ -11,9 +11,9 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ +#include "fix_spring_chunk.h" #include #include -#include "fix_spring_chunk.h" #include "atom.h" #include "update.h" #include "force.h" diff --git a/src/fix_spring_rg.cpp b/src/fix_spring_rg.cpp index 1d5b87c599..f1e68bffa4 100644 --- a/src/fix_spring_rg.cpp +++ b/src/fix_spring_rg.cpp @@ -16,8 +16,8 @@ Paul Crozier (SNL) ------------------------------------------------------------------------- */ -#include #include "fix_spring_rg.h" +#include #include "atom.h" #include "update.h" #include "group.h" diff --git a/src/fix_spring_self.cpp b/src/fix_spring_self.cpp index a5aa600229..c94f21b492 100644 --- a/src/fix_spring_self.cpp +++ b/src/fix_spring_self.cpp @@ -15,9 +15,9 @@ Contributing author: Naveen Michaud-Agrawal (Johns Hopkins University) ------------------------------------------------------------------------- */ +#include "fix_spring_self.h" #include #include -#include "fix_spring_self.h" #include "atom.h" #include "update.h" #include "domain.h" diff --git a/src/fix_store.cpp b/src/fix_store.cpp index a370632489..94c62c1850 100644 --- a/src/fix_store.cpp +++ b/src/fix_store.cpp @@ -11,8 +11,8 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include #include "fix_store.h" +#include #include "atom.h" #include "comm.h" #include "force.h" diff --git a/src/fix_store_force.cpp b/src/fix_store_force.cpp index 8afd985615..5c25f0e162 100644 --- a/src/fix_store_force.cpp +++ b/src/fix_store_force.cpp @@ -11,8 +11,8 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include #include "fix_store_force.h" +#include #include "atom.h" #include "update.h" #include "respa.h" diff --git a/src/fix_store_state.cpp b/src/fix_store_state.cpp index da899a173c..18dfa026d9 100644 --- a/src/fix_store_state.cpp +++ b/src/fix_store_state.cpp @@ -11,9 +11,9 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ +#include "fix_store_state.h" #include #include -#include "fix_store_state.h" #include "atom.h" #include "domain.h" #include "update.h" diff --git a/src/fix_temp_berendsen.cpp b/src/fix_temp_berendsen.cpp index b4dd65b0c5..be8922be4e 100644 --- a/src/fix_temp_berendsen.cpp +++ b/src/fix_temp_berendsen.cpp @@ -11,9 +11,9 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ +#include "fix_temp_berendsen.h" #include #include -#include "fix_temp_berendsen.h" #include "atom.h" #include "force.h" #include "comm.h" diff --git a/src/fix_temp_csld.cpp b/src/fix_temp_csld.cpp index 57f7104c61..f827c88f51 100644 --- a/src/fix_temp_csld.cpp +++ b/src/fix_temp_csld.cpp @@ -15,9 +15,9 @@ Contributing author: Axel Kohlmeyer (Temple U) ------------------------------------------------------------------------- */ +#include "fix_temp_csld.h" #include #include -#include "fix_temp_csld.h" #include "atom.h" #include "force.h" #include "memory.h" diff --git a/src/fix_temp_csvr.cpp b/src/fix_temp_csvr.cpp index 9f8135ffc8..55cbb60407 100644 --- a/src/fix_temp_csvr.cpp +++ b/src/fix_temp_csvr.cpp @@ -16,10 +16,10 @@ Based on code by Paolo Raiteri (Curtin U) and Giovanni Bussi (SISSA) ------------------------------------------------------------------------- */ +#include "fix_temp_csvr.h" #include #include #include -#include "fix_temp_csvr.h" #include "atom.h" #include "force.h" #include "comm.h" diff --git a/src/fix_temp_rescale.cpp b/src/fix_temp_rescale.cpp index 378997c0c4..a9d605d5ba 100644 --- a/src/fix_temp_rescale.cpp +++ b/src/fix_temp_rescale.cpp @@ -11,9 +11,9 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ +#include "fix_temp_rescale.h" #include #include -#include "fix_temp_rescale.h" #include "atom.h" #include "force.h" #include "group.h" diff --git a/src/fix_tmd.cpp b/src/fix_tmd.cpp index a0425db36c..ec8cdb859c 100644 --- a/src/fix_tmd.cpp +++ b/src/fix_tmd.cpp @@ -16,10 +16,10 @@ Christian Burisch (Bochum Univeristy, Germany) ------------------------------------------------------------------------- */ +#include "fix_tmd.h" #include #include #include -#include "fix_tmd.h" #include "atom.h" #include "update.h" #include "modify.h" diff --git a/src/fix_vector.cpp b/src/fix_vector.cpp index b7be472be6..53093acbf6 100644 --- a/src/fix_vector.cpp +++ b/src/fix_vector.cpp @@ -11,9 +11,9 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ +#include "fix_vector.h" #include #include -#include "fix_vector.h" #include "update.h" #include "force.h" #include "modify.h" diff --git a/src/fix_viscous.cpp b/src/fix_viscous.cpp index cc60b1bda4..bdd1e19976 100644 --- a/src/fix_viscous.cpp +++ b/src/fix_viscous.cpp @@ -11,8 +11,8 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include #include "fix_viscous.h" +#include #include "atom.h" #include "update.h" #include "respa.h" diff --git a/src/fix_wall.cpp b/src/fix_wall.cpp index 1046efc2df..8ceafb4bfc 100644 --- a/src/fix_wall.cpp +++ b/src/fix_wall.cpp @@ -11,9 +11,9 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ +#include "fix_wall.h" #include #include -#include "fix_wall.h" #include "input.h" #include "variable.h" #include "domain.h" diff --git a/src/fix_wall_lj1043.cpp b/src/fix_wall_lj1043.cpp index a93f4dd699..5656cf113d 100644 --- a/src/fix_wall_lj1043.cpp +++ b/src/fix_wall_lj1043.cpp @@ -15,8 +15,8 @@ Contributing author: Jonathan Lee (Sandia) ------------------------------------------------------------------------- */ -#include #include "fix_wall_lj1043.h" +#include #include "atom.h" #include "math_const.h" diff --git a/src/fix_wall_lj126.cpp b/src/fix_wall_lj126.cpp index 369ef78c97..e748e2ef13 100644 --- a/src/fix_wall_lj126.cpp +++ b/src/fix_wall_lj126.cpp @@ -11,8 +11,8 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include #include "fix_wall_lj126.h" +#include #include "atom.h" #include "error.h" diff --git a/src/fix_wall_lj93.cpp b/src/fix_wall_lj93.cpp index ce5a06c81b..c0e81b60ee 100644 --- a/src/fix_wall_lj93.cpp +++ b/src/fix_wall_lj93.cpp @@ -11,8 +11,8 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include #include "fix_wall_lj93.h" +#include #include "atom.h" #include "error.h" diff --git a/src/fix_wall_reflect.cpp b/src/fix_wall_reflect.cpp index edf5c40a5f..bc3414d650 100644 --- a/src/fix_wall_reflect.cpp +++ b/src/fix_wall_reflect.cpp @@ -11,8 +11,8 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include #include "fix_wall_reflect.h" +#include #include "atom.h" #include "comm.h" #include "update.h" diff --git a/src/fix_wall_region.cpp b/src/fix_wall_region.cpp index cb1c3c2ab2..c1a689d90a 100644 --- a/src/fix_wall_region.cpp +++ b/src/fix_wall_region.cpp @@ -11,10 +11,10 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ +#include "fix_wall_region.h" #include #include #include -#include "fix_wall_region.h" #include "atom.h" #include "domain.h" #include "region.h" diff --git a/src/force.cpp b/src/force.cpp index e4939a10e8..1a826b2843 100644 --- a/src/force.cpp +++ b/src/force.cpp @@ -11,10 +11,10 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ +#include "force.h" #include #include #include -#include "force.h" #include "style_bond.h" #include "style_angle.h" #include "style_dihedral.h" diff --git a/src/group.cpp b/src/group.cpp index a37d209947..d119964ea1 100644 --- a/src/group.cpp +++ b/src/group.cpp @@ -11,11 +11,11 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ +#include "group.h" #include #include #include #include -#include "group.h" #include "domain.h" #include "atom.h" #include "force.h" diff --git a/src/hashlittle.cpp b/src/hashlittle.cpp index e9340a7e55..c3824b71fe 100644 --- a/src/hashlittle.cpp +++ b/src/hashlittle.cpp @@ -2,8 +2,7 @@ // from lookup3.c, by Bob Jenkins, May 2006, Public Domain // bob_jenkins@burtleburtle.net -#include -#include +#include "hashlittle.h" // if the system defines the __BYTE_ORDER__ define, // we use it instead of guessing the platform @@ -141,7 +140,7 @@ acceptable. Do NOT use for cryptographic purposes. ------------------------------------------------------------------------------- */ -uint32_t hashlittle( const void *key, size_t length, uint32_t initval) +uint32_t LAMMPS_NS::hashlittle(const void *key, size_t length, uint32_t initval) { #ifndef PURIFY_HATES_HASHLITTLE diff --git a/src/hashlittle.h b/src/hashlittle.h index 7b57a35c80..75380d366b 100644 --- a/src/hashlittle.h +++ b/src/hashlittle.h @@ -2,4 +2,13 @@ // from lookup3.c, by Bob Jenkins, May 2006, Public Domain // bob_jenkins@burtleburtle.net -uint32_t hashlittle(const void *key, size_t length, uint32_t); +#ifndef LMP_HASHLITTLE_H +#define LMP_HASHLITTLE_H + +#include +#include + +namespace LAMMPS_NS { + uint32_t hashlittle(const void *key, size_t length, uint32_t); +} +#endif diff --git a/src/image.cpp b/src/image.cpp index ccd6d98d87..4a5009b8ed 100644 --- a/src/image.cpp +++ b/src/image.cpp @@ -15,11 +15,11 @@ Contributing author: Nathan Fabian (Sandia) ------------------------------------------------------------------------- */ +#include "image.h" #include #include #include #include -#include "image.h" #include "math_extra.h" #include "random_mars.h" #include "math_const.h" diff --git a/src/output.cpp b/src/output.cpp index fb2f9a700d..be6f66b7aa 100644 --- a/src/output.cpp +++ b/src/output.cpp @@ -11,6 +11,7 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ +#include #include #include "output.h" #include "style_dump.h" diff --git a/src/pair_lj_cut_coul_cut.cpp b/src/pair_lj_cut_coul_cut.cpp index 38a6e2c431..9ffa02156e 100644 --- a/src/pair_lj_cut_coul_cut.cpp +++ b/src/pair_lj_cut_coul_cut.cpp @@ -11,9 +11,8 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ +#include #include -#include -#include #include #include "pair_lj_cut_coul_cut.h" #include "atom.h" diff --git a/src/pair_lj_cut_coul_debye.cpp b/src/pair_lj_cut_coul_debye.cpp index cc6e92b2e3..ab6220bd24 100644 --- a/src/pair_lj_cut_coul_debye.cpp +++ b/src/pair_lj_cut_coul_debye.cpp @@ -11,8 +11,8 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ +#include #include -#include #include "pair_lj_cut_coul_debye.h" #include "atom.h" #include "neigh_list.h" diff --git a/src/pair_lj_cut_coul_dsf.cpp b/src/pair_lj_cut_coul_dsf.cpp index f114a5851f..778f9f2fb4 100644 --- a/src/pair_lj_cut_coul_dsf.cpp +++ b/src/pair_lj_cut_coul_dsf.cpp @@ -16,11 +16,10 @@ References: Fennell and Gezelter, JCP 124, 234104 (2006) ------------------------------------------------------------------------- */ +#include "pair_lj_cut_coul_dsf.h" +#include #include -#include -#include #include -#include "pair_lj_cut_coul_dsf.h" #include "atom.h" #include "comm.h" #include "force.h" diff --git a/src/pointers.h b/src/pointers.h index 1af07d5158..2d528db392 100644 --- a/src/pointers.h +++ b/src/pointers.h @@ -22,7 +22,7 @@ #define LMP_POINTERS_H #include "lmptype.h" // IWYU pragma: export -#include +#include // IWYU pragma: export #include // IWYU pragme: export #include // IWYU pragma: export #include "lammps.h" // IWYU pragma: export -- GitLab From 63dcd999d8c5cbfd07d109836d72355bc138281e Mon Sep 17 00:00:00 2001 From: "Ryan S. Elliott" Date: Wed, 3 Jul 2019 11:49:38 -0500 Subject: [PATCH 165/469] Switch to kim-api c-bindings for SimulatorModel --- src/KIM/fix_store_kim.cpp | 12 +++++--- src/KIM/kim_init.cpp | 60 ++++++++++++++++++------------------ src/KIM/kim_interactions.cpp | 49 +++++++++++++++-------------- 3 files changed, 63 insertions(+), 58 deletions(-) diff --git a/src/KIM/fix_store_kim.cpp b/src/KIM/fix_store_kim.cpp index c9a99acca9..1bd924bcfb 100644 --- a/src/KIM/fix_store_kim.cpp +++ b/src/KIM/fix_store_kim.cpp @@ -56,7 +56,9 @@ #include #include "fix_store_kim.h" -#include "KIM_SimulatorModel.hpp" +extern "C" { +#include "KIM_SimulatorModel.h" +} #include "error.h" using namespace LAMMPS_NS; @@ -78,8 +80,8 @@ FixStoreKIM::~FixStoreKIM() // free associated storage if (simulator_model) { - KIM::SimulatorModel *sm = (KIM::SimulatorModel *)simulator_model; - KIM::SimulatorModel::Destroy(&sm); + KIM_SimulatorModel *sm = (KIM_SimulatorModel *)simulator_model; + KIM_SimulatorModel_Destroy(&sm); simulator_model = NULL; } @@ -116,8 +118,8 @@ void FixStoreKIM::setptr(const char *name, void *ptr) { if (strcmp(name,"simulator_model") == 0) { if (simulator_model) { - KIM::SimulatorModel *sm = (KIM::SimulatorModel *)simulator_model; - KIM::SimulatorModel::Destroy(&sm); + KIM_SimulatorModel *sm = (KIM_SimulatorModel *)simulator_model; + KIM_SimulatorModel_Destroy(&sm); } simulator_model = ptr; } else if (strcmp(name,"model_name") == 0) { diff --git a/src/KIM/kim_init.cpp b/src/KIM/kim_init.cpp index 080e3dac3f..052e63263f 100644 --- a/src/KIM/kim_init.cpp +++ b/src/KIM/kim_init.cpp @@ -75,9 +75,6 @@ extern "C" { #include "KIM_SimulatorHeaders.h" } -//@@@@@ Need to switch to c-bindings when they are available. -#include "KIM_SimulatorModel.hpp" -//@@@@@ using namespace LAMMPS_NS; @@ -214,29 +211,30 @@ void KimInit::determine_model_type_and_units(char * model_name, } } - KIM::SimulatorModel * kim_SM; - kim_error = KIM::SimulatorModel::Create(model_name, &kim_SM); + KIM_SimulatorModel * kim_SM; + kim_error = KIM_SimulatorModel_Create(model_name, &kim_SM); if (kim_error) error->all(FLERR,"KIM model name not found"); model_type = SM; int sim_fields; int sim_lines; - std::string const * sim_field; - std::string const * sim_value; - kim_SM->GetNumberOfSimulatorFields(&sim_fields); - kim_SM->CloseTemplateMap(); + char const * sim_field; + char const * sim_value; + KIM_SimulatorModel_GetNumberOfSimulatorFields(kim_SM, &sim_fields); + KIM_SimulatorModel_CloseTemplateMap(kim_SM); for (int i=0; i < sim_fields; ++i) { - kim_SM->GetSimulatorFieldMetadata(i,&sim_lines,&sim_field); + KIM_SimulatorModel_GetSimulatorFieldMetadata( + kim_SM,i,&sim_lines,&sim_field); - if (*sim_field == "units") { - kim_SM->GetSimulatorFieldLine(i,0,&sim_value); - int len=(*sim_value).length()+1; - *model_units = new char[len]; strcpy(*model_units,sim_value->c_str()); + if (0 == strcmp(sim_field,"units")) { + KIM_SimulatorModel_GetSimulatorFieldLine(kim_SM,i,0,&sim_value); + int len=strlen(sim_value)+1; + *model_units = new char[len]; strcpy(*model_units,sim_value); break; } } - KIM::SimulatorModel::Destroy(&kim_SM); + KIM_SimulatorModel_Destroy(&kim_SM); if ((! unit_conversion_mode) && (strcmp(*model_units, user_units)!=0)) { std::string mesg("Incompatible units for KIM Simulator Model, " @@ -271,16 +269,16 @@ void KimInit::do_init(char *model_name, char *user_units, char *model_units) kim_init_log_delimiter("begin"); int kimerror; - // @@@@@ switch to c-bindings when they are available - KIM::SimulatorModel * simulatorModel; + KIM_SimulatorModel * simulatorModel; if (model_type == SM) { - kimerror = KIM::SimulatorModel::Create(model_name,&simulatorModel); + kimerror = KIM_SimulatorModel_Create(model_name,&simulatorModel); - const std::string *sim_name, *sim_version; - simulatorModel->GetSimulatorNameAndVersion(&sim_name, &sim_version); + char const *sim_name, *sim_version; + KIM_SimulatorModel_GetSimulatorNameAndVersion( + simulatorModel,&sim_name, &sim_version); - if (*sim_name != "LAMMPS") + if (0 != strcmp(sim_name,"LAMMPS")) error->all(FLERR,"Incompatible KIM Simulator Model"); if (comm->me == 0) { @@ -288,7 +286,7 @@ void KimInit::do_init(char *model_name, char *user_units, char *model_units) mesg += model_name; mesg += "\n"; mesg += "# For Simulator : "; - mesg += *sim_name + " " + *sim_version + "\n"; + mesg += std::string(sim_name) + " " + sim_version + "\n"; mesg += "# Running on : LAMMPS "; mesg += universe->version; mesg += "\n"; @@ -302,7 +300,7 @@ void KimInit::do_init(char *model_name, char *user_units, char *model_units) // need to call this to have access to (some) simulator model init data. - simulatorModel->CloseTemplateMap(); + KIM_SimulatorModel_CloseTemplateMap(simulatorModel); } // Define unit conversion factor variables and print to log @@ -316,24 +314,26 @@ void KimInit::do_init(char *model_name, char *user_units, char *model_units) if (model_type == SM) { int sim_fields, sim_lines; - const std::string *sim_field, *sim_value; - simulatorModel->GetNumberOfSimulatorFields(&sim_fields); + char const *sim_field, *sim_value; + KIM_SimulatorModel_GetNumberOfSimulatorFields(simulatorModel, &sim_fields); // init model for (int i=0; i < sim_fields; ++i) { - simulatorModel->GetSimulatorFieldMetadata(i,&sim_lines,&sim_field); - if (*sim_field == "model-init") { + KIM_SimulatorModel_GetSimulatorFieldMetadata( + simulatorModel,i,&sim_lines,&sim_field); + if (0 == strcmp(sim_field,"model-init")) { for (int j=0; j < sim_lines; ++j) { - simulatorModel->GetSimulatorFieldLine(i,j,&sim_value); - input->one(sim_value->c_str()); + KIM_SimulatorModel_GetSimulatorFieldLine( + simulatorModel,i,j,&sim_value); + input->one(sim_value); } break; } } // reset template map. - simulatorModel->OpenAndInitializeTemplateMap(); + KIM_SimulatorModel_OpenAndInitializeTemplateMap(simulatorModel); } // End output to log file diff --git a/src/KIM/kim_interactions.cpp b/src/KIM/kim_interactions.cpp index 4771272ff8..355df9c3be 100644 --- a/src/KIM/kim_interactions.cpp +++ b/src/KIM/kim_interactions.cpp @@ -73,9 +73,6 @@ extern "C" { #include "KIM_SimulatorHeaders.h" } -//@@@@@ Need to switch to c-bindings when they are available. -#include "KIM_SimulatorModel.hpp" -//@@@@@ #define SNUM(x) \ static_cast(std::ostringstream() \ @@ -122,7 +119,7 @@ void KimInteractions::do_setup(int narg, char **arg) error->all(FLERR,"Illegal kim_interactions command"); char *model_name = NULL; - KIM::SimulatorModel *simulatorModel(NULL); + KIM_SimulatorModel *simulatorModel(NULL); // check if we had a kim_init command by finding fix STORE/KIM // retrieve model name and pointer to simulator model class instance. @@ -132,7 +129,7 @@ void KimInteractions::do_setup(int narg, char **arg) if (ifix >= 0) { FixStoreKIM *fix_store = (FixStoreKIM *) modify->fix[ifix]; model_name = (char *)fix_store->getptr("model_name"); - simulatorModel = (KIM::SimulatorModel *)fix_store->getptr("simulator_model"); + simulatorModel = (KIM_SimulatorModel *)fix_store->getptr("simulator_model"); } else error->all(FLERR,"Must use 'kim_init' before 'kim_interactions'"); // Begin output to log file @@ -151,9 +148,11 @@ void KimInteractions::do_setup(int narg, char **arg) delimiter = " "; } - simulatorModel->AddTemplateMap("atom-type-sym-list",atom_type_sym_list); - simulatorModel->AddTemplateMap("atom-type-num-list",atom_type_num_list); - simulatorModel->CloseTemplateMap(); + KIM_SimulatorModel_AddTemplateMap( + simulatorModel,"atom-type-sym-list",atom_type_sym_list.c_str()); + KIM_SimulatorModel_AddTemplateMap( + simulatorModel,"atom-type-num-list",atom_type_num_list.c_str()); + KIM_SimulatorModel_CloseTemplateMap(simulatorModel); int len = strlen(atom_type_sym_list.c_str())+1; char *strbuf = new char[len]; @@ -163,16 +162,17 @@ void KimInteractions::do_setup(int narg, char **arg) int sim_num_species; bool species_is_supported; - const std::string *sim_species; - simulatorModel->GetNumberOfSupportedSpecies(&sim_num_species); + char const *sim_species; + KIM_SimulatorModel_GetNumberOfSupportedSpecies( + simulatorModel,&sim_num_species); strcpy(strbuf,atom_type_sym_list.c_str()); strword = strtok(strbuf," \t"); while (strword) { species_is_supported = false; if (strcmp(strword,"NULL") == 0) continue; for (int i=0; i < sim_num_species; ++i) { - simulatorModel->GetSupportedSpecies(i, &sim_species); - if (strcmp(sim_species->c_str(),strword) == 0) + KIM_SimulatorModel_GetSupportedSpecies(simulatorModel,i,&sim_species); + if (strcmp(sim_species,strword) == 0) species_is_supported = true; } if (!species_is_supported) { @@ -188,26 +188,29 @@ void KimInteractions::do_setup(int narg, char **arg) // check if units are unchanged int sim_fields, sim_lines; - const std::string *sim_field, *sim_value; - simulatorModel->GetNumberOfSimulatorFields(&sim_fields); + const char *sim_field, *sim_value; + KIM_SimulatorModel_GetNumberOfSimulatorFields(simulatorModel, &sim_fields); for (int i=0; i < sim_fields; ++i) { - simulatorModel->GetSimulatorFieldMetadata(i,&sim_lines,&sim_field); + KIM_SimulatorModel_GetSimulatorFieldMetadata( + simulatorModel,i,&sim_lines,&sim_field); - if (*sim_field == "units") { - simulatorModel->GetSimulatorFieldLine(i,0,&sim_value); - if (*sim_value != update->unit_style) + if (0 == strcmp(sim_field,"units")) { + KIM_SimulatorModel_GetSimulatorFieldLine(simulatorModel,i,0,&sim_value); + if (0 != strcmp(sim_value,update->unit_style)) error->all(FLERR,"Incompatible units for KIM Simulator Model"); } } int sim_model_idx=-1; for (int i=0; i < sim_fields; ++i) { - simulatorModel->GetSimulatorFieldMetadata(i,&sim_lines,&sim_field); - if (*sim_field == "model-defn") { + KIM_SimulatorModel_GetSimulatorFieldMetadata( + simulatorModel,i,&sim_lines,&sim_field); + if (0 == strcmp(sim_field,"model-defn")) { sim_model_idx = i; for (int j=0; j < sim_lines; ++j) { - simulatorModel->GetSimulatorFieldLine(sim_model_idx,j,&sim_value); - input->one(sim_value->c_str()); + KIM_SimulatorModel_GetSimulatorFieldLine( + simulatorModel,sim_model_idx,j,&sim_value); + input->one(sim_value); } } } @@ -215,7 +218,7 @@ void KimInteractions::do_setup(int narg, char **arg) if (sim_model_idx < 0) error->all(FLERR,"KIM Simulator Model has no Model definition"); - simulatorModel->OpenAndInitializeTemplateMap(); + KIM_SimulatorModel_OpenAndInitializeTemplateMap(simulatorModel); } else { -- GitLab From 00d820dcf98864fdac0e30a0dbeaafbf57271192 Mon Sep 17 00:00:00 2001 From: "Ryan S. Elliott" Date: Wed, 3 Jul 2019 13:20:55 -0500 Subject: [PATCH 166/469] Added support for log.cite to kim_init --- src/KIM/kim_init.cpp | 52 ++++++++++++++++++++++++++++++++++++++++++++ src/KIM/kim_init.h | 1 + 2 files changed, 53 insertions(+) diff --git a/src/KIM/kim_init.cpp b/src/KIM/kim_init.cpp index 052e63263f..40e0cbaaed 100644 --- a/src/KIM/kim_init.cpp +++ b/src/KIM/kim_init.cpp @@ -69,6 +69,7 @@ #include "universe.h" #include "input.h" #include "variable.h" +#include "citeme.h" #include "fix_store_kim.h" #include "kim_units.h" @@ -99,6 +100,8 @@ void KimInit::command(int narg, char **arg) char *model_units; determine_model_type_and_units(model_name, user_units, &model_units); + write_log_cite(model_name); + do_init(model_name, user_units, model_units); } @@ -441,3 +444,52 @@ void KimInit::do_variables(char *user_units, char *model_units) if ((logfile) && (input->echo_log)) fputs("#\n",logfile); } } + +/* ---------------------------------------------------------------------- */ + +void KimInit::write_log_cite(char * model_name) +{ + KIM_Collections * coll; + int err = KIM_Collections_Create(&coll); + if (err) return; + + int extent; + if (model_type == MO) + { + err = KIM_Collections_CacheListOfItemMetadataFiles( + coll,KIM_COLLECTION_ITEM_TYPE_portableModel,model_name,&extent); + } + else if (model_type == SM) + { + err = KIM_Collections_CacheListOfItemMetadataFiles( + coll,KIM_COLLECTION_ITEM_TYPE_simulatorModel,model_name,&extent); + } + else + { + error->all(FLERR,"Unknown model type."); + } + + if (err) + { + KIM_Collections_Destroy(&coll); + return; + } + + for (int i = 0; i < extent;++i) + { + char const * fileName; + int availableAsString; + char const * fileString; + err = KIM_Collections_GetItemMetadataFile( + coll,i,&fileName,NULL,NULL,&availableAsString,&fileString); + if (err) continue; + + if (0 == strncmp("kimcite-",fileName,8)) + { + if (lmp->citeme) lmp->citeme->add(fileString); + break; + } + } + + KIM_Collections_Destroy(&coll); +} diff --git a/src/KIM/kim_init.h b/src/KIM/kim_init.h index c22e2be720..7c7a24615b 100644 --- a/src/KIM/kim_init.h +++ b/src/KIM/kim_init.h @@ -78,6 +78,7 @@ class KimInit : protected Pointers { bool unit_conversion_mode; void determine_model_type_and_units(char *, char *, char **); + void write_log_cite(char *); void do_init(char *, char *, char *); void do_variables(char*, char*); void kim_init_log_delimiter(std::string const begin_end) const; -- GitLab From bb5a1c5205c281d23633339c7d700ae0569b63ca Mon Sep 17 00:00:00 2001 From: "Ryan S. Elliott" Date: Wed, 3 Jul 2019 13:38:08 -0500 Subject: [PATCH 167/469] Adjust log.cite behavior --- src/KIM/kim_init.cpp | 3 +-- 1 file changed, 1 insertion(+), 2 deletions(-) diff --git a/src/KIM/kim_init.cpp b/src/KIM/kim_init.cpp index 40e0cbaaed..5fb6748427 100644 --- a/src/KIM/kim_init.cpp +++ b/src/KIM/kim_init.cpp @@ -484,10 +484,9 @@ void KimInit::write_log_cite(char * model_name) coll,i,&fileName,NULL,NULL,&availableAsString,&fileString); if (err) continue; - if (0 == strncmp("kimcite-",fileName,8)) + if (0 == strncmp("kimcite",fileName,7)) { if (lmp->citeme) lmp->citeme->add(fileString); - break; } } -- GitLab From 5ef389eaea33ce97355177f91a4478f08f987944 Mon Sep 17 00:00:00 2001 From: Andrew Schultz Date: Wed, 3 Jul 2019 14:45:45 -0400 Subject: [PATCH 168/469] Mention that a smoothly truncated potential works better Add a table of pair styles that implement single_hessian --- doc/src/compute_hma.txt | 19 ++++++++++++------- 1 file changed, 12 insertions(+), 7 deletions(-) diff --git a/doc/src/compute_hma.txt b/doc/src/compute_hma.txt index 581e4afeb4..f62498754c 100644 --- a/doc/src/compute_hma.txt +++ b/doc/src/compute_hma.txt @@ -48,13 +48,18 @@ effects, smaller timestep inaccuracy, faster equilibration and shorter decorrelation time. HMA should not be used if atoms are expected to diffuse. It is also -restricted to simulations in the NVT ensemble. - -Computation of the heat capacity with this compute is presently restricted to -the "pair_lj_smooth_linear"_pair_lj_smooth_linear.html pair style. Use with other pair -styles requires an additional method (single2nd) to be implemented in the -corresponding Pair class. Computation of the energy and pressure does not -have this restriction. +restricted to simulations in the NVT ensemble. While this compute may be +used with any potential in LAMMPS, it may not provide efficiency improvements +for potentials that do not go to 0 smoothly at the truncation distance; +"pair_lj_smooth_linear"_pair_lj_smooth_linear.html and Ewald summation should +work fine, while "pair_lj"_pair_lj.html will perform poorly unless +the cutoff is very large. Furthermore, computation of the heat capacity with +this compute is restricted to those that implement the single_hessian method +in Pair. This is the list of pair styles that currently implement +pair_hessian: + +"lj_smooth_linear"_pair_lj_smooth_linear.html :l +:ule In this method, the analytically known harmonic behavior of a crystal is removed from the traditional ensemble averages, which leads to an accurate and precise measurement of the anharmonic contributions without contamination -- GitLab From 8e9037ac95780facae8a1bb176f1e768fbfd49db Mon Sep 17 00:00:00 2001 From: Andrew Schultz Date: Wed, 3 Jul 2019 16:19:26 -0400 Subject: [PATCH 169/469] Add request to contact if interested in more pair styles --- doc/src/compute_hma.txt | 6 ++++-- 1 file changed, 4 insertions(+), 2 deletions(-) diff --git a/doc/src/compute_hma.txt b/doc/src/compute_hma.txt index f62498754c..35a92664df 100644 --- a/doc/src/compute_hma.txt +++ b/doc/src/compute_hma.txt @@ -55,8 +55,10 @@ for potentials that do not go to 0 smoothly at the truncation distance; work fine, while "pair_lj"_pair_lj.html will perform poorly unless the cutoff is very large. Furthermore, computation of the heat capacity with this compute is restricted to those that implement the single_hessian method -in Pair. This is the list of pair styles that currently implement -pair_hessian: +in Pair. Implementing single_hessian in additional pair styles is simple. +Please contact Andrew Schultz (ajs42 at buffalo.edu) and David Kofke (kofke at +buffalo.edu) if your desired pair style does not have this method. This is +the list of pair styles that currently implement pair_hessian: "lj_smooth_linear"_pair_lj_smooth_linear.html :l :ule -- GitLab From b675edcf5cf658c22f5f5c6f97f906acb3229870 Mon Sep 17 00:00:00 2001 From: Andrew Schultz Date: Wed, 3 Jul 2019 16:28:37 -0400 Subject: [PATCH 170/469] More false positives --- doc/utils/sphinx-config/false_positives.txt | 2 ++ 1 file changed, 2 insertions(+) diff --git a/doc/utils/sphinx-config/false_positives.txt b/doc/utils/sphinx-config/false_positives.txt index 07a0e4eaf0..2d74c5b464 100644 --- a/doc/utils/sphinx-config/false_positives.txt +++ b/doc/utils/sphinx-config/false_positives.txt @@ -44,6 +44,7 @@ Aidan aij airebo Aj +ajs ajaramil akohlmey Aktulga @@ -1324,6 +1325,7 @@ Kmax Knizhnik knl Kofke +kofke Kohlmeyer Kohn kokkos -- GitLab From 256531a29a31d2f80f860504d0653c4013794338 Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Wed, 3 Jul 2019 19:34:13 -0400 Subject: [PATCH 171/469] put implementation header first for all remaining main folder source files --- src/imbalance_neigh.cpp | 2 +- src/imbalance_store.cpp | 2 +- src/imbalance_time.cpp | 2 +- src/imbalance_var.cpp | 2 +- src/improper_deprecated.cpp | 2 +- src/improper_hybrid.cpp | 2 +- src/improper_zero.cpp | 2 +- src/info.cpp | 2 +- src/input.cpp | 2 +- src/irregular.cpp | 2 +- src/kspace.cpp | 2 +- src/kspace_deprecated.cpp | 2 +- src/lammps.cpp | 2 +- src/lattice.cpp | 2 +- src/library.cpp | 2 +- src/main.cpp | 2 +- src/math_extra.cpp | 2 +- src/math_special.cpp | 2 +- src/memory.cpp | 2 +- src/min.cpp | 2 +- src/min_cg.cpp | 2 +- src/min_fire.cpp | 2 +- src/min_hftn.cpp | 2 +- src/min_linesearch.cpp | 2 +- src/min_quickmin.cpp | 2 +- src/min_sd.cpp | 2 +- src/modify.cpp | 2 +- src/molecule.cpp | 2 +- src/nbin.cpp | 2 +- src/neighbor.cpp | 2 +- src/npair.cpp | 2 +- src/ntopo.cpp | 2 +- src/ntopo_angle_all.cpp | 2 +- src/ntopo_angle_partial.cpp | 2 +- src/ntopo_angle_template.cpp | 2 +- src/ntopo_bond_all.cpp | 2 +- src/ntopo_bond_partial.cpp | 2 +- src/ntopo_bond_template.cpp | 2 +- src/ntopo_dihedral_all.cpp | 2 +- src/ntopo_dihedral_partial.cpp | 2 +- src/ntopo_dihedral_template.cpp | 2 +- src/ntopo_improper_all.cpp | 2 +- src/ntopo_improper_partial.cpp | 2 +- src/ntopo_improper_template.cpp | 2 +- src/output.cpp | 2 +- src/pair.cpp | 2 +- src/pair_beck.cpp | 2 +- src/pair_born.cpp | 2 +- src/pair_born_coul_dsf.cpp | 2 +- src/pair_born_coul_wolf.cpp | 2 +- src/pair_buck.cpp | 2 +- src/pair_buck_coul_cut.cpp | 2 +- src/pair_coul_cut.cpp | 2 +- src/pair_coul_debye.cpp | 2 +- src/pair_coul_dsf.cpp | 2 +- src/pair_coul_streitz.cpp | 2 +- src/pair_coul_wolf.cpp | 2 +- src/pair_deprecated.cpp | 2 +- src/pair_dpd.cpp | 2 +- src/pair_dpd_tstat.cpp | 2 +- src/pair_gauss.cpp | 2 +- src/pair_hybrid.cpp | 2 +- src/pair_hybrid_overlay.cpp | 2 +- src/pair_lj96_cut.cpp | 2 +- src/pair_lj_cubic.cpp | 2 +- src/pair_lj_cut.cpp | 2 +- src/pair_lj_cut_coul_cut.cpp | 2 +- src/pair_lj_cut_coul_debye.cpp | 2 +- src/pair_lj_cut_coul_wolf.cpp | 2 +- src/pair_lj_expand.cpp | 2 +- src/pair_lj_gromacs.cpp | 2 +- src/pair_lj_gromacs_coul_gromacs.cpp | 2 +- src/pair_lj_smooth.cpp | 2 +- src/pair_lj_smooth_linear.cpp | 2 +- src/pair_mie_cut.cpp | 2 +- src/pair_morse.cpp | 2 +- src/pair_soft.cpp | 2 +- src/pair_table.cpp | 2 +- src/pair_ufm.cpp | 2 +- src/pair_yukawa.cpp | 2 +- src/pair_zbl.cpp | 2 +- src/pair_zero.cpp | 2 +- src/procmap.cpp | 2 +- src/random_mars.cpp | 2 +- src/random_park.cpp | 2 +- src/rcb.cpp | 2 +- src/read_data.cpp | 2 +- src/read_dump.cpp | 2 +- src/read_restart.cpp | 2 +- src/reader.cpp | 2 +- src/reader_native.cpp | 2 +- src/reader_xyz.cpp | 2 +- src/region.cpp | 2 +- src/region_block.cpp | 2 +- src/region_cone.cpp | 2 +- src/region_cylinder.cpp | 2 +- src/region_deprecated.cpp | 2 +- src/region_intersect.cpp | 2 +- src/region_plane.cpp | 2 +- src/region_prism.cpp | 2 +- src/region_sphere.cpp | 2 +- src/region_union.cpp | 2 +- src/replicate.cpp | 2 +- src/rerun.cpp | 2 +- src/reset_ids.cpp | 2 +- src/respa.cpp | 2 +- src/run.cpp | 2 +- src/set.cpp | 2 +- src/special.cpp | 2 +- src/thermo.cpp | 2 +- src/timer.cpp | 2 +- src/universe.cpp | 2 +- src/update.cpp | 2 +- src/utils.cpp | 2 +- src/variable.cpp | 2 +- src/velocity.cpp | 2 +- src/verlet.cpp | 2 +- src/write_coeff.cpp | 2 +- src/write_data.cpp | 2 +- src/write_dump.cpp | 2 +- src/write_restart.cpp | 2 +- 121 files changed, 121 insertions(+), 121 deletions(-) diff --git a/src/imbalance_neigh.cpp b/src/imbalance_neigh.cpp index 2a55754da8..19f3915a11 100644 --- a/src/imbalance_neigh.cpp +++ b/src/imbalance_neigh.cpp @@ -11,8 +11,8 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include #include "imbalance_neigh.h" +#include #include "atom.h" #include "comm.h" #include "force.h" diff --git a/src/imbalance_store.cpp b/src/imbalance_store.cpp index c117b60860..343d47b189 100644 --- a/src/imbalance_store.cpp +++ b/src/imbalance_store.cpp @@ -11,8 +11,8 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include #include "imbalance_store.h" +#include #include "atom.h" #include "error.h" diff --git a/src/imbalance_time.cpp b/src/imbalance_time.cpp index ceb3c08220..0831713204 100644 --- a/src/imbalance_time.cpp +++ b/src/imbalance_time.cpp @@ -11,8 +11,8 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include #include "imbalance_time.h" +#include #include "atom.h" #include "force.h" #include "timer.h" diff --git a/src/imbalance_var.cpp b/src/imbalance_var.cpp index ba17c06866..ba84ef01ef 100644 --- a/src/imbalance_var.cpp +++ b/src/imbalance_var.cpp @@ -11,9 +11,9 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ +#include "imbalance_var.h" #include #include -#include "imbalance_var.h" #include "atom.h" #include "group.h" #include "input.h" diff --git a/src/improper_deprecated.cpp b/src/improper_deprecated.cpp index 6f4d08764f..62a688527a 100644 --- a/src/improper_deprecated.cpp +++ b/src/improper_deprecated.cpp @@ -15,8 +15,8 @@ Contributing author: Axel Kohlmeyer (Temple U) ------------------------------------------------------------------------- */ -#include #include "improper_deprecated.h" +#include #include "improper_hybrid.h" #include "comm.h" #include "force.h" diff --git a/src/improper_hybrid.cpp b/src/improper_hybrid.cpp index af1382d3eb..f078a73ec0 100644 --- a/src/improper_hybrid.cpp +++ b/src/improper_hybrid.cpp @@ -11,10 +11,10 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ +#include "improper_hybrid.h" #include #include #include -#include "improper_hybrid.h" #include "atom.h" #include "neighbor.h" #include "comm.h" diff --git a/src/improper_zero.cpp b/src/improper_zero.cpp index 3f36954a0a..efa70c8ff5 100644 --- a/src/improper_zero.cpp +++ b/src/improper_zero.cpp @@ -15,8 +15,8 @@ Contributing author: Carsten Svaneborg (SDU) ------------------------------------------------------------------------- */ -#include #include "improper_zero.h" +#include #include "atom.h" #include "force.h" #include "memory.h" diff --git a/src/info.cpp b/src/info.cpp index bb2d3c4b45..8f55fab367 100644 --- a/src/info.cpp +++ b/src/info.cpp @@ -16,6 +16,7 @@ Richard Berger (Temple U) ------------------------------------------------------------------------- */ +#include "info.h" #include #include #include @@ -23,7 +24,6 @@ #include #include #include -#include "info.h" #include "accelerator_kokkos.h" #include "atom.h" #include "comm.h" diff --git a/src/input.cpp b/src/input.cpp index cbad1d78bf..f887bc0245 100644 --- a/src/input.cpp +++ b/src/input.cpp @@ -11,6 +11,7 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ +#include "input.h" #include #include #include @@ -18,7 +19,6 @@ #include #include #include -#include "input.h" #include "style_command.h" #include "universe.h" #include "atom.h" diff --git a/src/irregular.cpp b/src/irregular.cpp index 2040d12d0b..b67214df25 100644 --- a/src/irregular.cpp +++ b/src/irregular.cpp @@ -11,9 +11,9 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ +#include "irregular.h" #include #include -#include "irregular.h" #include "atom.h" #include "atom_vec.h" #include "domain.h" diff --git a/src/kspace.cpp b/src/kspace.cpp index b51191857d..f9020416bf 100644 --- a/src/kspace.cpp +++ b/src/kspace.cpp @@ -11,11 +11,11 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ +#include "kspace.h" #include #include #include #include -#include "kspace.h" #include "atom.h" #include "comm.h" #include "force.h" diff --git a/src/kspace_deprecated.cpp b/src/kspace_deprecated.cpp index 1d62de2692..0b6490b4cf 100644 --- a/src/kspace_deprecated.cpp +++ b/src/kspace_deprecated.cpp @@ -15,8 +15,8 @@ Contributing author: Axel Kohlmeyer (Temple U) ------------------------------------------------------------------------- */ -#include #include "kspace_deprecated.h" +#include #include "comm.h" #include "force.h" #include "error.h" diff --git a/src/lammps.cpp b/src/lammps.cpp index f8e7dceb89..5ddc1600a4 100644 --- a/src/lammps.cpp +++ b/src/lammps.cpp @@ -11,6 +11,7 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ +#include "lammps.h" #include #include #include @@ -18,7 +19,6 @@ #include #include #include -#include "lammps.h" #include "style_angle.h" // IWYU pragma: keep #include "style_atom.h" // IWYU pragma: keep #include "style_bond.h" // IWYU pragma: keep diff --git a/src/lattice.cpp b/src/lattice.cpp index ee2fea2a75..98faf680e8 100644 --- a/src/lattice.cpp +++ b/src/lattice.cpp @@ -11,10 +11,10 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ +#include "lattice.h" #include #include #include -#include "lattice.h" #include "update.h" #include "domain.h" #include "comm.h" diff --git a/src/library.cpp b/src/library.cpp index 033b814865..eabe5fd179 100644 --- a/src/library.cpp +++ b/src/library.cpp @@ -14,11 +14,11 @@ // C or Fortran style library interface to LAMMPS // customize by adding new LAMMPS-specific functions +#include "library.h" #include #include #include #include -#include "library.h" #include "universe.h" #include "atom_vec.h" #include "atom.h" diff --git a/src/main.cpp b/src/main.cpp index 1be9c253eb..b7f6adbdda 100644 --- a/src/main.cpp +++ b/src/main.cpp @@ -11,8 +11,8 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include #include "lammps.h" +#include #include "input.h" #if defined(LAMMPS_TRAP_FPE) && defined(_GNU_SOURCE) diff --git a/src/math_extra.cpp b/src/math_extra.cpp index f7e5bb646b..797d210d0e 100644 --- a/src/math_extra.cpp +++ b/src/math_extra.cpp @@ -15,9 +15,9 @@ Contributing author: Mike Brown (SNL) ------------------------------------------------------------------------- */ +#include "math_extra.h" #include #include -#include "math_extra.h" #define MAXJACOBI 50 diff --git a/src/math_special.cpp b/src/math_special.cpp index b2f545ddc6..bf11a1ad45 100644 --- a/src/math_special.cpp +++ b/src/math_special.cpp @@ -1,6 +1,6 @@ +#include "math_special.h" #include #include // IWYU pragma: keep -#include "math_special.h" using namespace LAMMPS_NS; diff --git a/src/memory.cpp b/src/memory.cpp index ca7fd3ea7f..a513dde6c2 100644 --- a/src/memory.cpp +++ b/src/memory.cpp @@ -11,8 +11,8 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include #include "memory.h" +#include #include "error.h" #if defined(LMP_USER_INTEL) && defined(__INTEL_COMPILER) diff --git a/src/min.cpp b/src/min.cpp index f2e1c982be..408954edb8 100644 --- a/src/min.cpp +++ b/src/min.cpp @@ -19,10 +19,10 @@ JR Shewchuk, http://www-2.cs.cmu.edu/~jrs/jrspapers.html#cg ------------------------------------------------------------------------- */ +#include "min.h" #include #include #include -#include "min.h" #include "atom.h" #include "atom_vec.h" #include "domain.h" diff --git a/src/min_cg.cpp b/src/min_cg.cpp index eb8831c8f5..ff318d23da 100644 --- a/src/min_cg.cpp +++ b/src/min_cg.cpp @@ -11,9 +11,9 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ +#include "min_cg.h" #include #include -#include "min_cg.h" #include "update.h" #include "output.h" #include "timer.h" diff --git a/src/min_fire.cpp b/src/min_fire.cpp index 79346341bb..b7f853afd2 100644 --- a/src/min_fire.cpp +++ b/src/min_fire.cpp @@ -11,9 +11,9 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ +#include "min_fire.h" #include #include -#include "min_fire.h" #include "universe.h" #include "atom.h" #include "force.h" diff --git a/src/min_hftn.cpp b/src/min_hftn.cpp index c2c251c386..dcfed10fef 100644 --- a/src/min_hftn.cpp +++ b/src/min_hftn.cpp @@ -17,12 +17,12 @@ "Parallel Unconstrained Min", Plantenga, SAND98-8201 ------------------------------------------------------------------------- */ +#include "min_hftn.h" #include #include #include #include "atom.h" #include "fix_minimize.h" -#include "min_hftn.h" #include "modify.h" #include "output.h" #include "pair.h" diff --git a/src/min_linesearch.cpp b/src/min_linesearch.cpp index 3c0621c602..a7a10dcd51 100644 --- a/src/min_linesearch.cpp +++ b/src/min_linesearch.cpp @@ -21,9 +21,9 @@ JR Shewchuk, http://www-2.cs.cmu.edu/~jrs/jrspapers.html#cg ------------------------------------------------------------------------- */ +#include "min_linesearch.h" #include #include -#include "min_linesearch.h" #include "atom.h" #include "modify.h" #include "fix_minimize.h" diff --git a/src/min_quickmin.cpp b/src/min_quickmin.cpp index 784da82686..04e72b046d 100644 --- a/src/min_quickmin.cpp +++ b/src/min_quickmin.cpp @@ -11,9 +11,9 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ +#include "min_quickmin.h" #include #include -#include "min_quickmin.h" #include "universe.h" #include "atom.h" #include "force.h" diff --git a/src/min_sd.cpp b/src/min_sd.cpp index d66601119b..e4e159003f 100644 --- a/src/min_sd.cpp +++ b/src/min_sd.cpp @@ -11,8 +11,8 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include #include "min_sd.h" +#include #include "update.h" #include "output.h" #include "timer.h" diff --git a/src/modify.cpp b/src/modify.cpp index 61497d86db..a9b8817aed 100644 --- a/src/modify.cpp +++ b/src/modify.cpp @@ -11,8 +11,8 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include #include "modify.h" +#include #include "style_compute.h" #include "style_fix.h" #include "atom.h" diff --git a/src/molecule.cpp b/src/molecule.cpp index 4a3790296f..38887ebb0c 100644 --- a/src/molecule.cpp +++ b/src/molecule.cpp @@ -11,11 +11,11 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ +#include "molecule.h" #include #include #include #include -#include "molecule.h" #include "atom.h" #include "atom_vec.h" #include "atom_vec_body.h" diff --git a/src/nbin.cpp b/src/nbin.cpp index 0480c9730d..99d41db140 100644 --- a/src/nbin.cpp +++ b/src/nbin.cpp @@ -11,8 +11,8 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include #include "nbin.h" +#include #include "neighbor.h" #include "neigh_request.h" #include "domain.h" diff --git a/src/neighbor.cpp b/src/neighbor.cpp index a2efc5919b..d38aed08c0 100644 --- a/src/neighbor.cpp +++ b/src/neighbor.cpp @@ -15,10 +15,10 @@ Contributing author (triclinic and multi-neigh) : Pieter in 't Veld (SNL) ------------------------------------------------------------------------- */ +#include "neighbor.h" #include #include #include -#include "neighbor.h" #include "neigh_list.h" #include "neigh_request.h" #include "nbin.h" diff --git a/src/npair.cpp b/src/npair.cpp index 24cdc7750a..b63135fad6 100644 --- a/src/npair.cpp +++ b/src/npair.cpp @@ -11,8 +11,8 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include #include "npair.h" +#include #include "neighbor.h" #include "neigh_request.h" #include "nbin.h" diff --git a/src/ntopo.cpp b/src/ntopo.cpp index 05e287e192..ca63b85328 100644 --- a/src/ntopo.cpp +++ b/src/ntopo.cpp @@ -11,8 +11,8 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include #include "ntopo.h" +#include #include "atom.h" #include "neighbor.h" #include "comm.h" diff --git a/src/ntopo_angle_all.cpp b/src/ntopo_angle_all.cpp index 2a358c8ce5..e0c20609a1 100644 --- a/src/ntopo_angle_all.cpp +++ b/src/ntopo_angle_all.cpp @@ -11,8 +11,8 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include #include "ntopo_angle_all.h" +#include #include "atom.h" #include "force.h" #include "domain.h" diff --git a/src/ntopo_angle_partial.cpp b/src/ntopo_angle_partial.cpp index c82110cda5..a6fd900825 100644 --- a/src/ntopo_angle_partial.cpp +++ b/src/ntopo_angle_partial.cpp @@ -11,8 +11,8 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include #include "ntopo_angle_partial.h" +#include #include "atom.h" #include "force.h" #include "domain.h" diff --git a/src/ntopo_angle_template.cpp b/src/ntopo_angle_template.cpp index 15a8b658f3..8cbcf8bcbd 100644 --- a/src/ntopo_angle_template.cpp +++ b/src/ntopo_angle_template.cpp @@ -11,8 +11,8 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include #include "ntopo_angle_template.h" +#include #include "atom.h" #include "atom_vec.h" #include "force.h" diff --git a/src/ntopo_bond_all.cpp b/src/ntopo_bond_all.cpp index 42e9e2303d..5309754554 100644 --- a/src/ntopo_bond_all.cpp +++ b/src/ntopo_bond_all.cpp @@ -11,8 +11,8 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include #include "ntopo_bond_all.h" +#include #include "atom.h" #include "force.h" #include "domain.h" diff --git a/src/ntopo_bond_partial.cpp b/src/ntopo_bond_partial.cpp index 5a1acd9191..1cbf5eed11 100644 --- a/src/ntopo_bond_partial.cpp +++ b/src/ntopo_bond_partial.cpp @@ -11,8 +11,8 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include #include "ntopo_bond_partial.h" +#include #include "atom.h" #include "force.h" #include "domain.h" diff --git a/src/ntopo_bond_template.cpp b/src/ntopo_bond_template.cpp index fa98658ad0..cd7b85aa19 100644 --- a/src/ntopo_bond_template.cpp +++ b/src/ntopo_bond_template.cpp @@ -11,8 +11,8 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include #include "ntopo_bond_template.h" +#include #include "atom.h" #include "atom_vec.h" #include "force.h" diff --git a/src/ntopo_dihedral_all.cpp b/src/ntopo_dihedral_all.cpp index 9c94fb10f9..5af2d526e0 100644 --- a/src/ntopo_dihedral_all.cpp +++ b/src/ntopo_dihedral_all.cpp @@ -11,8 +11,8 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include #include "ntopo_dihedral_all.h" +#include #include "atom.h" #include "force.h" #include "domain.h" diff --git a/src/ntopo_dihedral_partial.cpp b/src/ntopo_dihedral_partial.cpp index 14749e6511..faac57aa51 100644 --- a/src/ntopo_dihedral_partial.cpp +++ b/src/ntopo_dihedral_partial.cpp @@ -11,8 +11,8 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include #include "ntopo_dihedral_partial.h" +#include #include "atom.h" #include "force.h" #include "domain.h" diff --git a/src/ntopo_dihedral_template.cpp b/src/ntopo_dihedral_template.cpp index 8ea860c2e2..bce8ecf4bc 100644 --- a/src/ntopo_dihedral_template.cpp +++ b/src/ntopo_dihedral_template.cpp @@ -11,8 +11,8 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include #include "ntopo_dihedral_template.h" +#include #include "atom.h" #include "atom_vec.h" #include "force.h" diff --git a/src/ntopo_improper_all.cpp b/src/ntopo_improper_all.cpp index 6c478dec52..0cbecbf962 100644 --- a/src/ntopo_improper_all.cpp +++ b/src/ntopo_improper_all.cpp @@ -11,8 +11,8 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include #include "ntopo_improper_all.h" +#include #include "atom.h" #include "force.h" #include "domain.h" diff --git a/src/ntopo_improper_partial.cpp b/src/ntopo_improper_partial.cpp index 2c37668ca8..17e5d4cf62 100644 --- a/src/ntopo_improper_partial.cpp +++ b/src/ntopo_improper_partial.cpp @@ -11,8 +11,8 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include #include "ntopo_improper_partial.h" +#include #include "atom.h" #include "force.h" #include "domain.h" diff --git a/src/ntopo_improper_template.cpp b/src/ntopo_improper_template.cpp index 953e010d89..a80fe60e1d 100644 --- a/src/ntopo_improper_template.cpp +++ b/src/ntopo_improper_template.cpp @@ -11,8 +11,8 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include #include "ntopo_improper_template.h" +#include #include "atom.h" #include "atom_vec.h" #include "force.h" diff --git a/src/output.cpp b/src/output.cpp index be6f66b7aa..193db9ae2a 100644 --- a/src/output.cpp +++ b/src/output.cpp @@ -11,9 +11,9 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ +#include "output.h" #include #include -#include "output.h" #include "style_dump.h" #include "atom.h" #include "neighbor.h" diff --git a/src/pair.cpp b/src/pair.cpp index 3d7bdaa62c..36194aec9b 100644 --- a/src/pair.cpp +++ b/src/pair.cpp @@ -15,12 +15,12 @@ Contributing author: Paul Crozier (SNL) ------------------------------------------------------------------------- */ +#include "pair.h" #include #include // IWYU pragma: keep #include // IWYU pragma: keep #include #include -#include "pair.h" #include "atom.h" #include "neighbor.h" #include "domain.h" diff --git a/src/pair_beck.cpp b/src/pair_beck.cpp index 8ba3ef80f2..b94436b696 100644 --- a/src/pair_beck.cpp +++ b/src/pair_beck.cpp @@ -15,9 +15,9 @@ Contributing author: Jonathan Zimmerman (Sandia) ------------------------------------------------------------------------- */ +#include "pair_beck.h" #include #include -#include "pair_beck.h" #include "atom.h" #include "comm.h" #include "force.h" diff --git a/src/pair_born.cpp b/src/pair_born.cpp index ae7456ddbb..bd993acb56 100644 --- a/src/pair_born.cpp +++ b/src/pair_born.cpp @@ -15,10 +15,10 @@ Contributing Author: Sai Jayaraman (Sandia) ------------------------------------------------------------------------- */ +#include "pair_born.h" #include #include #include -#include "pair_born.h" #include "atom.h" #include "comm.h" #include "force.h" diff --git a/src/pair_born_coul_dsf.cpp b/src/pair_born_coul_dsf.cpp index 51b9a2677d..f7e139c750 100644 --- a/src/pair_born_coul_dsf.cpp +++ b/src/pair_born_coul_dsf.cpp @@ -16,9 +16,9 @@ References: Fennell and Gezelter, JCP 124, 234104 (2006) ------------------------------------------------------------------------- */ +#include "pair_born_coul_dsf.h" #include #include -#include "pair_born_coul_dsf.h" #include "atom.h" #include "comm.h" #include "force.h" diff --git a/src/pair_born_coul_wolf.cpp b/src/pair_born_coul_wolf.cpp index f4ccac80a1..f4d533bdb0 100644 --- a/src/pair_born_coul_wolf.cpp +++ b/src/pair_born_coul_wolf.cpp @@ -15,9 +15,9 @@ Contributing author: Yongfeng Zhang (INL), yongfeng.zhang@inl.gov ------------------------------------------------------------------------- */ +#include "pair_born_coul_wolf.h" #include #include -#include "pair_born_coul_wolf.h" #include "atom.h" #include "comm.h" #include "force.h" diff --git a/src/pair_buck.cpp b/src/pair_buck.cpp index b9795fb0ed..a94ce87891 100644 --- a/src/pair_buck.cpp +++ b/src/pair_buck.cpp @@ -11,10 +11,10 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ +#include "pair_buck.h" #include #include #include -#include "pair_buck.h" #include "atom.h" #include "comm.h" #include "force.h" diff --git a/src/pair_buck_coul_cut.cpp b/src/pair_buck_coul_cut.cpp index 64475166e3..d05c139f71 100644 --- a/src/pair_buck_coul_cut.cpp +++ b/src/pair_buck_coul_cut.cpp @@ -15,9 +15,9 @@ Contributing author: Eduardo Bringa (LLNL) ------------------------------------------------------------------------- */ +#include "pair_buck_coul_cut.h" #include #include -#include "pair_buck_coul_cut.h" #include "atom.h" #include "comm.h" #include "force.h" diff --git a/src/pair_coul_cut.cpp b/src/pair_coul_cut.cpp index 28973026cd..9e6f238eba 100644 --- a/src/pair_coul_cut.cpp +++ b/src/pair_coul_cut.cpp @@ -11,10 +11,10 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ +#include "pair_coul_cut.h" #include #include #include -#include "pair_coul_cut.h" #include "atom.h" #include "comm.h" #include "force.h" diff --git a/src/pair_coul_debye.cpp b/src/pair_coul_debye.cpp index cd23ef1919..1b87a93701 100644 --- a/src/pair_coul_debye.cpp +++ b/src/pair_coul_debye.cpp @@ -11,9 +11,9 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ +#include "pair_coul_debye.h" #include #include -#include "pair_coul_debye.h" #include "atom.h" #include "comm.h" #include "force.h" diff --git a/src/pair_coul_dsf.cpp b/src/pair_coul_dsf.cpp index 4c15b5d330..22230182b0 100644 --- a/src/pair_coul_dsf.cpp +++ b/src/pair_coul_dsf.cpp @@ -16,10 +16,10 @@ References: Fennell and Gezelter, JCP 124, 234104 (2006) ------------------------------------------------------------------------- */ +#include "pair_coul_dsf.h" #include #include #include -#include "pair_coul_dsf.h" #include "atom.h" #include "comm.h" #include "force.h" diff --git a/src/pair_coul_streitz.cpp b/src/pair_coul_streitz.cpp index f577564ac1..628f6a6b36 100644 --- a/src/pair_coul_streitz.cpp +++ b/src/pair_coul_streitz.cpp @@ -15,11 +15,11 @@ Contributing author: Ray Shan (Sandia) ------------------------------------------------------------------------- */ +#include "pair_coul_streitz.h" #include #include #include #include -#include "pair_coul_streitz.h" #include "atom.h" #include "comm.h" #include "force.h" diff --git a/src/pair_coul_wolf.cpp b/src/pair_coul_wolf.cpp index 8c15378de8..15c7839fc6 100644 --- a/src/pair_coul_wolf.cpp +++ b/src/pair_coul_wolf.cpp @@ -15,9 +15,9 @@ Contributing author: Yongfeng Zhang (INL), yongfeng.zhang@inl.gov ------------------------------------------------------------------------- */ +#include "pair_coul_wolf.h" #include #include -#include "pair_coul_wolf.h" #include "atom.h" #include "comm.h" #include "force.h" diff --git a/src/pair_deprecated.cpp b/src/pair_deprecated.cpp index 0b1342fb2d..058809eb80 100644 --- a/src/pair_deprecated.cpp +++ b/src/pair_deprecated.cpp @@ -15,8 +15,8 @@ Contributing author: Axel Kohlmeyer (Temple U) ------------------------------------------------------------------------- */ -#include #include "pair_deprecated.h" +#include #include "pair_hybrid.h" #include "comm.h" #include "force.h" diff --git a/src/pair_dpd.cpp b/src/pair_dpd.cpp index e5e6cf7dae..ec65eaafd6 100644 --- a/src/pair_dpd.cpp +++ b/src/pair_dpd.cpp @@ -15,9 +15,9 @@ Contributing author: Kurt Smith (U Pittsburgh) ------------------------------------------------------------------------- */ +#include "pair_dpd.h" #include #include -#include "pair_dpd.h" #include "atom.h" #include "comm.h" #include "update.h" diff --git a/src/pair_dpd_tstat.cpp b/src/pair_dpd_tstat.cpp index 66c8d91ab1..15d7c90b27 100644 --- a/src/pair_dpd_tstat.cpp +++ b/src/pair_dpd_tstat.cpp @@ -11,9 +11,9 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ +#include "pair_dpd_tstat.h" #include #include -#include "pair_dpd_tstat.h" #include "atom.h" #include "update.h" #include "force.h" diff --git a/src/pair_gauss.cpp b/src/pair_gauss.cpp index 7df9a417c3..7fd3233f4c 100644 --- a/src/pair_gauss.cpp +++ b/src/pair_gauss.cpp @@ -15,10 +15,10 @@ Contributing author: Sai Jayaraman (Sandia) ------------------------------------------------------------------------- */ +#include "pair_gauss.h" #include #include #include -#include "pair_gauss.h" #include "atom.h" #include "comm.h" #include "force.h" diff --git a/src/pair_hybrid.cpp b/src/pair_hybrid.cpp index daeee3d2b3..762b9fe8fc 100644 --- a/src/pair_hybrid.cpp +++ b/src/pair_hybrid.cpp @@ -12,10 +12,10 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ +#include "pair_hybrid.h" #include #include #include -#include "pair_hybrid.h" #include "atom.h" #include "force.h" #include "pair.h" diff --git a/src/pair_hybrid_overlay.cpp b/src/pair_hybrid_overlay.cpp index 496e3d0406..e67cb677af 100644 --- a/src/pair_hybrid_overlay.cpp +++ b/src/pair_hybrid_overlay.cpp @@ -11,9 +11,9 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ +#include "pair_hybrid_overlay.h" #include #include -#include "pair_hybrid_overlay.h" #include "atom.h" #include "force.h" #include "error.h" diff --git a/src/pair_lj96_cut.cpp b/src/pair_lj96_cut.cpp index 62e645ef2c..c27038900d 100644 --- a/src/pair_lj96_cut.cpp +++ b/src/pair_lj96_cut.cpp @@ -15,10 +15,10 @@ Contributing author: Chuanfu Luo (luochuanfu@gmail.com) ------------------------------------------------------------------------- */ +#include "pair_lj96_cut.h" #include #include #include -#include "pair_lj96_cut.h" #include "atom.h" #include "comm.h" #include "force.h" diff --git a/src/pair_lj_cubic.cpp b/src/pair_lj_cubic.cpp index 8b1b4b7627..7990952494 100644 --- a/src/pair_lj_cubic.cpp +++ b/src/pair_lj_cubic.cpp @@ -16,9 +16,9 @@ Contributing author: Aidan Thompson (SNL) ------------------------------------------------------------------------- */ +#include "pair_lj_cubic.h" #include #include -#include "pair_lj_cubic.h" #include "atom.h" #include "comm.h" #include "force.h" diff --git a/src/pair_lj_cut.cpp b/src/pair_lj_cut.cpp index 9284923218..0302858adb 100644 --- a/src/pair_lj_cut.cpp +++ b/src/pair_lj_cut.cpp @@ -15,10 +15,10 @@ Contributing author: Paul Crozier (SNL) ------------------------------------------------------------------------- */ +#include "pair_lj_cut.h" #include #include #include -#include "pair_lj_cut.h" #include "atom.h" #include "comm.h" #include "force.h" diff --git a/src/pair_lj_cut_coul_cut.cpp b/src/pair_lj_cut_coul_cut.cpp index 9ffa02156e..d4640bee3a 100644 --- a/src/pair_lj_cut_coul_cut.cpp +++ b/src/pair_lj_cut_coul_cut.cpp @@ -11,10 +11,10 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ +#include "pair_lj_cut_coul_cut.h" #include #include #include -#include "pair_lj_cut_coul_cut.h" #include "atom.h" #include "comm.h" #include "force.h" diff --git a/src/pair_lj_cut_coul_debye.cpp b/src/pair_lj_cut_coul_debye.cpp index ab6220bd24..4ef533a743 100644 --- a/src/pair_lj_cut_coul_debye.cpp +++ b/src/pair_lj_cut_coul_debye.cpp @@ -11,9 +11,9 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ +#include "pair_lj_cut_coul_debye.h" #include #include -#include "pair_lj_cut_coul_debye.h" #include "atom.h" #include "neigh_list.h" #include "force.h" diff --git a/src/pair_lj_cut_coul_wolf.cpp b/src/pair_lj_cut_coul_wolf.cpp index 55aff0d7c5..fb641f7d24 100644 --- a/src/pair_lj_cut_coul_wolf.cpp +++ b/src/pair_lj_cut_coul_wolf.cpp @@ -15,11 +15,11 @@ Contributing author: Vishal Boddu (FAU) ------------------------------------------------------------------------- */ +#include "pair_lj_cut_coul_wolf.h" #include #include #include #include -#include "pair_lj_cut_coul_wolf.h" #include "atom.h" #include "comm.h" #include "force.h" diff --git a/src/pair_lj_expand.cpp b/src/pair_lj_expand.cpp index d5c0a40f2d..60593fd01d 100644 --- a/src/pair_lj_expand.cpp +++ b/src/pair_lj_expand.cpp @@ -11,11 +11,11 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ +#include "pair_lj_expand.h" #include #include #include #include -#include "pair_lj_expand.h" #include "atom.h" #include "comm.h" #include "force.h" diff --git a/src/pair_lj_gromacs.cpp b/src/pair_lj_gromacs.cpp index 1fdaefebe9..4796c288d7 100644 --- a/src/pair_lj_gromacs.cpp +++ b/src/pair_lj_gromacs.cpp @@ -15,11 +15,11 @@ Contributing author: Mark Stevens (SNL) ------------------------------------------------------------------------- */ +#include "pair_lj_gromacs.h" #include #include #include #include -#include "pair_lj_gromacs.h" #include "atom.h" #include "comm.h" #include "force.h" diff --git a/src/pair_lj_gromacs_coul_gromacs.cpp b/src/pair_lj_gromacs_coul_gromacs.cpp index 28dc8ec79b..45beeb1daf 100644 --- a/src/pair_lj_gromacs_coul_gromacs.cpp +++ b/src/pair_lj_gromacs_coul_gromacs.cpp @@ -15,11 +15,11 @@ Contributing author: Mark Stevens (SNL) ------------------------------------------------------------------------- */ +#include "pair_lj_gromacs_coul_gromacs.h" #include #include #include #include -#include "pair_lj_gromacs_coul_gromacs.h" #include "atom.h" #include "comm.h" #include "force.h" diff --git a/src/pair_lj_smooth.cpp b/src/pair_lj_smooth.cpp index ecacadbffa..d89fee1148 100644 --- a/src/pair_lj_smooth.cpp +++ b/src/pair_lj_smooth.cpp @@ -15,10 +15,10 @@ Contributing author: Craig Maloney (UCSB) ------------------------------------------------------------------------- */ +#include "pair_lj_smooth.h" #include #include #include -#include "pair_lj_smooth.h" #include "atom.h" #include "comm.h" #include "force.h" diff --git a/src/pair_lj_smooth_linear.cpp b/src/pair_lj_smooth_linear.cpp index 265828c4cf..6ed19a452f 100644 --- a/src/pair_lj_smooth_linear.cpp +++ b/src/pair_lj_smooth_linear.cpp @@ -15,10 +15,10 @@ Contributing author: Jonathan Zimmerman (Sandia) ------------------------------------------------------------------------- */ +#include "pair_lj_smooth_linear.h" #include #include #include -#include "pair_lj_smooth_linear.h" #include "atom.h" #include "comm.h" #include "force.h" diff --git a/src/pair_mie_cut.cpp b/src/pair_mie_cut.cpp index 231832dc48..d2b0c20cd5 100644 --- a/src/pair_mie_cut.cpp +++ b/src/pair_mie_cut.cpp @@ -15,11 +15,11 @@ Contributing author: Cassiano Aimoli (aimoli@gmail.com) ------------------------------------------------------------------------- */ +#include "pair_mie_cut.h" #include #include #include #include -#include "pair_mie_cut.h" #include "atom.h" #include "comm.h" #include "force.h" diff --git a/src/pair_morse.cpp b/src/pair_morse.cpp index dca1834c14..47102932db 100644 --- a/src/pair_morse.cpp +++ b/src/pair_morse.cpp @@ -11,11 +11,11 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ +#include "pair_morse.h" #include #include #include #include -#include "pair_morse.h" #include "atom.h" #include "comm.h" #include "force.h" diff --git a/src/pair_soft.cpp b/src/pair_soft.cpp index 7602f7b925..f3d7423b04 100644 --- a/src/pair_soft.cpp +++ b/src/pair_soft.cpp @@ -11,11 +11,11 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ +#include "pair_soft.h" #include #include #include #include -#include "pair_soft.h" #include "atom.h" #include "comm.h" #include "force.h" diff --git a/src/pair_table.cpp b/src/pair_table.cpp index b1b6f45eda..63cda78c67 100644 --- a/src/pair_table.cpp +++ b/src/pair_table.cpp @@ -15,11 +15,11 @@ Contributing author: Paul Crozier (SNL) ------------------------------------------------------------------------- */ +#include "pair_table.h" #include #include #include #include -#include "pair_table.h" #include "atom.h" #include "force.h" #include "comm.h" diff --git a/src/pair_ufm.cpp b/src/pair_ufm.cpp index 226fb6e7d9..40b72136ff 100644 --- a/src/pair_ufm.cpp +++ b/src/pair_ufm.cpp @@ -17,11 +17,11 @@ Maurice de Koning (Unicamp/Brazil) - dekoning@ifi.unicamp.br ------------------------------------------------------------------------- */ +#include "pair_ufm.h" #include #include #include #include -#include "pair_ufm.h" #include "atom.h" #include "comm.h" #include "force.h" diff --git a/src/pair_yukawa.cpp b/src/pair_yukawa.cpp index 913afbd5a1..4a2cf23952 100644 --- a/src/pair_yukawa.cpp +++ b/src/pair_yukawa.cpp @@ -11,9 +11,9 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ +#include "pair_yukawa.h" #include #include -#include "pair_yukawa.h" #include "atom.h" #include "force.h" #include "comm.h" diff --git a/src/pair_zbl.cpp b/src/pair_zbl.cpp index 254a82ea64..b01c301785 100644 --- a/src/pair_zbl.cpp +++ b/src/pair_zbl.cpp @@ -15,11 +15,11 @@ Contributing authors: Stephen Foiles, Aidan Thompson (SNL) ------------------------------------------------------------------------- */ +#include "pair_zbl.h" #include #include #include #include -#include "pair_zbl.h" #include "atom.h" #include "comm.h" #include "force.h" diff --git a/src/pair_zero.cpp b/src/pair_zero.cpp index 143808f598..2692710e20 100644 --- a/src/pair_zero.cpp +++ b/src/pair_zero.cpp @@ -15,11 +15,11 @@ Contributing author: Carsten Svaneborg (SDU) ------------------------------------------------------------------------- */ +#include "pair_zero.h" #include #include #include #include -#include "pair_zero.h" #include "atom.h" #include "comm.h" #include "force.h" diff --git a/src/procmap.cpp b/src/procmap.cpp index 08b60a26af..47afb76da9 100644 --- a/src/procmap.cpp +++ b/src/procmap.cpp @@ -15,8 +15,8 @@ Contributing author (NUMA option) : Mike Brown (ORNL) ------------------------------------------------------------------------- */ -#include #include "procmap.h" +#include #include "universe.h" #include "comm.h" #include "domain.h" diff --git a/src/random_mars.cpp b/src/random_mars.cpp index 464e640eab..9de5290d29 100644 --- a/src/random_mars.cpp +++ b/src/random_mars.cpp @@ -14,8 +14,8 @@ // Marsaglia random number generator // see RANMAR in F James, Comp Phys Comm, 60, 329 (1990) -#include #include "random_mars.h" +#include #include "error.h" using namespace LAMMPS_NS; diff --git a/src/random_park.cpp b/src/random_park.cpp index fc00939bd4..e12e8a3a10 100644 --- a/src/random_park.cpp +++ b/src/random_park.cpp @@ -13,8 +13,8 @@ // Park/Miller RNG -#include #include "random_park.h" +#include #include "error.h" using namespace LAMMPS_NS; diff --git a/src/rcb.cpp b/src/rcb.cpp index 83cdccdf80..b19beae3c5 100644 --- a/src/rcb.cpp +++ b/src/rcb.cpp @@ -11,9 +11,9 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ +#include "rcb.h" #include #include -#include "rcb.h" #include "irregular.h" #include "memory.h" #include "error.h" diff --git a/src/read_data.cpp b/src/read_data.cpp index e70a526c38..a50d41b498 100644 --- a/src/read_data.cpp +++ b/src/read_data.cpp @@ -15,13 +15,13 @@ // due to OpenMPI bug which sets INT64_MAX via its mpi.h // before lmptype.h can set flags to insure it is done correctly +#include "read_data.h" #include "lmptype.h" #include #include #include #include #include -#include "read_data.h" #include "atom.h" #include "atom_vec.h" #include "atom_vec_ellipsoid.h" diff --git a/src/read_dump.cpp b/src/read_dump.cpp index 395f4c8edd..49f96db680 100644 --- a/src/read_dump.cpp +++ b/src/read_dump.cpp @@ -19,11 +19,11 @@ // due to OpenMPI bug which sets INT64_MAX via its mpi.h // before lmptype.h can set flags to insure it is done correctly +#include "read_dump.h" #include "lmptype.h" #include #include #include -#include "read_dump.h" #include "reader.h" #include "style_reader.h" #include "atom.h" diff --git a/src/read_restart.cpp b/src/read_restart.cpp index 6e156da837..17b313bfa2 100644 --- a/src/read_restart.cpp +++ b/src/read_restart.cpp @@ -11,11 +11,11 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ +#include "read_restart.h" #include #include #include #include -#include "read_restart.h" #include "atom.h" #include "atom_vec.h" #include "domain.h" diff --git a/src/reader.cpp b/src/reader.cpp index cf344b37b3..a1fe51f662 100644 --- a/src/reader.cpp +++ b/src/reader.cpp @@ -11,9 +11,9 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ +#include "reader.h" #include #include -#include "reader.h" #include "error.h" using namespace LAMMPS_NS; diff --git a/src/reader_native.cpp b/src/reader_native.cpp index 2c60ffdfd4..9e98a95759 100644 --- a/src/reader_native.cpp +++ b/src/reader_native.cpp @@ -11,9 +11,9 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ +#include "reader_native.h" #include #include -#include "reader_native.h" #include "atom.h" #include "memory.h" #include "error.h" diff --git a/src/reader_xyz.cpp b/src/reader_xyz.cpp index 37d30bd740..fa553dc30f 100644 --- a/src/reader_xyz.cpp +++ b/src/reader_xyz.cpp @@ -15,9 +15,9 @@ Contributing author: Axel Kohlmeyer (Temple U) ------------------------------------------------------------------------- */ +#include "reader_xyz.h" #include #include -#include "reader_xyz.h" #include "atom.h" #include "memory.h" #include "error.h" diff --git a/src/region.cpp b/src/region.cpp index 6b49a2819b..0c4bec16e0 100644 --- a/src/region.cpp +++ b/src/region.cpp @@ -11,10 +11,10 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ +#include "region.h" #include #include #include -#include "region.h" #include "update.h" #include "domain.h" #include "lattice.h" diff --git a/src/region_block.cpp b/src/region_block.cpp index e55c481189..bc52fcd7cf 100644 --- a/src/region_block.cpp +++ b/src/region_block.cpp @@ -11,9 +11,9 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ +#include "region_block.h" #include #include -#include "region_block.h" #include "force.h" #include "domain.h" #include "math_extra.h" diff --git a/src/region_cone.cpp b/src/region_cone.cpp index 72f56a268f..345c9fa8e2 100644 --- a/src/region_cone.cpp +++ b/src/region_cone.cpp @@ -15,10 +15,10 @@ Contributing author: Pim Schravendijk ------------------------------------------------------------------------- */ +#include "region_cone.h" #include #include #include -#include "region_cone.h" #include "domain.h" #include "error.h" #include "force.h" diff --git a/src/region_cylinder.cpp b/src/region_cylinder.cpp index 7709c57aab..968453cf37 100644 --- a/src/region_cylinder.cpp +++ b/src/region_cylinder.cpp @@ -11,10 +11,10 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ +#include "region_cylinder.h" #include #include #include -#include "region_cylinder.h" #include "update.h" #include "domain.h" #include "input.h" diff --git a/src/region_deprecated.cpp b/src/region_deprecated.cpp index 87225959fa..a2e4e88393 100644 --- a/src/region_deprecated.cpp +++ b/src/region_deprecated.cpp @@ -11,8 +11,8 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include #include "region_deprecated.h" +#include #include "comm.h" #include "error.h" diff --git a/src/region_intersect.cpp b/src/region_intersect.cpp index 96d3bed16c..c6c11cf35c 100644 --- a/src/region_intersect.cpp +++ b/src/region_intersect.cpp @@ -11,9 +11,9 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ +#include "region_intersect.h" #include #include -#include "region_intersect.h" #include "domain.h" #include "error.h" #include "force.h" diff --git a/src/region_plane.cpp b/src/region_plane.cpp index e67a2c85bd..950c0a4b53 100644 --- a/src/region_plane.cpp +++ b/src/region_plane.cpp @@ -11,10 +11,10 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ +#include "region_plane.h" #include #include #include -#include "region_plane.h" #include "error.h" #include "force.h" diff --git a/src/region_prism.cpp b/src/region_prism.cpp index 22fc504c37..38fc23da21 100644 --- a/src/region_prism.cpp +++ b/src/region_prism.cpp @@ -15,10 +15,10 @@ Contributing author: Pieter in 't Veld (SNL) ------------------------------------------------------------------------- */ +#include "region_prism.h" #include #include #include -#include "region_prism.h" #include "domain.h" #include "force.h" #include "math_extra.h" diff --git a/src/region_sphere.cpp b/src/region_sphere.cpp index 8080ef5882..9c478960e3 100644 --- a/src/region_sphere.cpp +++ b/src/region_sphere.cpp @@ -11,10 +11,10 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ +#include "region_sphere.h" #include #include #include -#include "region_sphere.h" #include "update.h" #include "input.h" #include "variable.h" diff --git a/src/region_union.cpp b/src/region_union.cpp index 33ac6fedd7..f4e30f5b94 100644 --- a/src/region_union.cpp +++ b/src/region_union.cpp @@ -11,9 +11,9 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ +#include "region_union.h" #include #include -#include "region_union.h" #include "domain.h" #include "error.h" #include "force.h" diff --git a/src/replicate.cpp b/src/replicate.cpp index 3c8f4a8aee..6f8c94238a 100644 --- a/src/replicate.cpp +++ b/src/replicate.cpp @@ -11,9 +11,9 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ +#include "replicate.h" #include #include -#include "replicate.h" #include "atom.h" #include "atom_vec.h" #include "atom_vec_hybrid.h" diff --git a/src/rerun.cpp b/src/rerun.cpp index 063ea882c2..e75779ccc0 100644 --- a/src/rerun.cpp +++ b/src/rerun.cpp @@ -11,9 +11,9 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ +#include "rerun.h" #include #include -#include "rerun.h" #include "read_dump.h" #include "domain.h" #include "update.h" diff --git a/src/reset_ids.cpp b/src/reset_ids.cpp index b2cf7a9bbc..b68b7ca797 100644 --- a/src/reset_ids.cpp +++ b/src/reset_ids.cpp @@ -28,7 +28,7 @@ ResetIDs::ResetIDs(LAMMPS *lmp) : Pointers(lmp) {} /* ---------------------------------------------------------------------- */ -void ResetIDs::command(int narg, char **/*arg*/) +void ResetIDs::command(int narg, char ** /* arg */) { if (domain->box_exist == 0) error->all(FLERR,"Reset_ids command before simulation box is defined"); diff --git a/src/respa.cpp b/src/respa.cpp index 6fa9959d78..867662b3c2 100644 --- a/src/respa.cpp +++ b/src/respa.cpp @@ -15,9 +15,9 @@ Contributing authors: Mark Stevens (SNL), Paul Crozier (SNL) ------------------------------------------------------------------------- */ +#include "respa.h" #include #include -#include "respa.h" #include "neighbor.h" #include "atom.h" #include "atom_vec.h" diff --git a/src/run.cpp b/src/run.cpp index beb71be52c..60861ad3b9 100644 --- a/src/run.cpp +++ b/src/run.cpp @@ -11,9 +11,9 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ +#include "run.h" #include #include -#include "run.h" #include "domain.h" #include "update.h" #include "force.h" diff --git a/src/set.cpp b/src/set.cpp index 00b2d8a9b0..d34aa7753a 100644 --- a/src/set.cpp +++ b/src/set.cpp @@ -11,11 +11,11 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ +#include "set.h" #include #include #include #include -#include "set.h" #include "atom.h" #include "atom_vec.h" #include "atom_vec_ellipsoid.h" diff --git a/src/special.cpp b/src/special.cpp index 903794c0f6..f8661e238c 100644 --- a/src/special.cpp +++ b/src/special.cpp @@ -11,9 +11,9 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ +#include "special.h" #include #include -#include "special.h" #include "atom.h" #include "atom_vec.h" #include "force.h" diff --git a/src/thermo.cpp b/src/thermo.cpp index f4ab7b0779..d267ea260c 100644 --- a/src/thermo.cpp +++ b/src/thermo.cpp @@ -15,12 +15,12 @@ // due to OpenMPI bug which sets INT64_MAX via its mpi.h // before lmptype.h can set flags to insure it is done correctly +#include "thermo.h" #include "lmptype.h" #include #include #include #include -#include "thermo.h" #include "atom.h" #include "update.h" #include "comm.h" diff --git a/src/timer.cpp b/src/timer.cpp index 65cb6ab5d8..0dad8fb756 100644 --- a/src/timer.cpp +++ b/src/timer.cpp @@ -11,10 +11,10 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ +#include "timer.h" #include #include #include -#include "timer.h" #include "comm.h" #include "error.h" #include "force.h" diff --git a/src/universe.cpp b/src/universe.cpp index f078590103..2a7117da51 100644 --- a/src/universe.cpp +++ b/src/universe.cpp @@ -11,12 +11,12 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ +#include "universe.h" #include #include #include #include #include -#include "universe.h" #include "version.h" #include "error.h" #include "force.h" diff --git a/src/update.cpp b/src/update.cpp index f5e706e354..e83f4d9f72 100644 --- a/src/update.cpp +++ b/src/update.cpp @@ -11,9 +11,9 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ +#include "update.h" #include #include -#include "update.h" #include "integrate.h" #include "min.h" #include "style_integrate.h" diff --git a/src/utils.cpp b/src/utils.cpp index 8468b22d8c..ea2ab57f6f 100644 --- a/src/utils.cpp +++ b/src/utils.cpp @@ -11,9 +11,9 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ +#include "utils.h" #include #include -#include "utils.h" #include "lammps.h" #include "error.h" diff --git a/src/variable.cpp b/src/variable.cpp index 111fc75a9a..440fb07f95 100644 --- a/src/variable.cpp +++ b/src/variable.cpp @@ -11,13 +11,13 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ +#include "variable.h" #include #include #include #include #include #include -#include "variable.h" #include "universe.h" #include "atom.h" #include "update.h" diff --git a/src/velocity.cpp b/src/velocity.cpp index 95d820cc22..1a03f71128 100644 --- a/src/velocity.cpp +++ b/src/velocity.cpp @@ -11,12 +11,12 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ +#include "velocity.h" #include #include #include #include #include -#include "velocity.h" #include "atom.h" #include "update.h" #include "domain.h" diff --git a/src/verlet.cpp b/src/verlet.cpp index fcba248d5f..5ccef36259 100644 --- a/src/verlet.cpp +++ b/src/verlet.cpp @@ -11,8 +11,8 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include #include "verlet.h" +#include #include "neighbor.h" #include "domain.h" #include "comm.h" diff --git a/src/write_coeff.cpp b/src/write_coeff.cpp index 9bf54b3c08..08ff964e7c 100644 --- a/src/write_coeff.cpp +++ b/src/write_coeff.cpp @@ -11,10 +11,10 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ +#include "write_coeff.h" #include #include #include -#include "write_coeff.h" #include "pair.h" #include "bond.h" #include "angle.h" diff --git a/src/write_data.cpp b/src/write_data.cpp index decc92ea8c..b78e701d35 100644 --- a/src/write_data.cpp +++ b/src/write_data.cpp @@ -11,9 +11,9 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ +#include "write_data.h" #include #include -#include "write_data.h" #include "atom.h" #include "atom_vec.h" #include "group.h" diff --git a/src/write_dump.cpp b/src/write_dump.cpp index 072680a8a5..903f0e0cdd 100644 --- a/src/write_dump.cpp +++ b/src/write_dump.cpp @@ -15,8 +15,8 @@ Contributing author: Axel Kohlmeyer (Temple U) ------------------------------------------------------------------------- */ -#include #include "write_dump.h" +#include #include "style_dump.h" #include "dump.h" #include "dump_image.h" diff --git a/src/write_restart.cpp b/src/write_restart.cpp index e0e17cd292..5adb39067c 100644 --- a/src/write_restart.cpp +++ b/src/write_restart.cpp @@ -11,9 +11,9 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ +#include "write_restart.h" #include #include -#include "write_restart.h" #include "atom.h" #include "atom_vec.h" #include "atom_vec_hybrid.h" -- GitLab From 5b3a15bd944b0dc6a3b49c0f8d088e6797cfc6db Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Wed, 3 Jul 2019 19:44:58 -0400 Subject: [PATCH 172/469] putting implementation header first in package folder sources --- src/ASPHERE/compute_erotate_asphere.cpp | 2 +- src/ASPHERE/compute_temp_asphere.cpp | 2 +- src/ASPHERE/fix_nh_asphere.cpp | 2 +- src/ASPHERE/fix_nph_asphere.cpp | 2 +- src/ASPHERE/fix_npt_asphere.cpp | 2 +- src/ASPHERE/fix_nve_asphere.cpp | 2 +- src/ASPHERE/fix_nve_asphere_noforce.cpp | 2 +- src/ASPHERE/fix_nve_line.cpp | 2 +- src/ASPHERE/fix_nve_tri.cpp | 2 +- src/ASPHERE/fix_nvt_asphere.cpp | 2 +- src/ASPHERE/pair_gayberne.cpp | 2 +- src/ASPHERE/pair_line_lj.cpp | 2 +- src/ASPHERE/pair_resquared.cpp | 2 +- src/ASPHERE/pair_tri_lj.cpp | 2 +- src/BODY/body_nparticle.cpp | 2 +- src/BODY/body_rounded_polygon.cpp | 2 +- src/BODY/body_rounded_polyhedron.cpp | 2 +- src/BODY/compute_body_local.cpp | 2 +- src/BODY/compute_temp_body.cpp | 2 +- src/BODY/fix_nh_body.cpp | 2 +- src/BODY/fix_nph_body.cpp | 2 +- src/BODY/fix_npt_body.cpp | 2 +- src/BODY/fix_nve_body.cpp | 2 +- src/BODY/fix_nvt_body.cpp | 2 +- src/BODY/fix_wall_body_polygon.cpp | 2 +- src/BODY/fix_wall_body_polyhedron.cpp | 2 +- src/BODY/pair_body_nparticle.cpp | 2 +- src/BODY/pair_body_rounded_polygon.cpp | 2 +- src/BODY/pair_body_rounded_polyhedron.cpp | 2 +- src/CLASS2/angle_class2.cpp | 2 +- src/CLASS2/bond_class2.cpp | 2 +- src/CLASS2/dihedral_class2.cpp | 2 +- src/CLASS2/improper_class2.cpp | 2 +- src/CLASS2/pair_lj_class2.cpp | 2 +- src/CLASS2/pair_lj_class2_coul_cut.cpp | 2 +- src/CLASS2/pair_lj_class2_coul_long.cpp | 2 +- src/COLLOID/fix_wall_colloid.cpp | 2 +- src/COLLOID/pair_brownian.cpp | 2 +- src/COLLOID/pair_brownian_poly.cpp | 2 +- src/COLLOID/pair_colloid.cpp | 2 +- src/COLLOID/pair_lubricate.cpp | 2 +- src/COLLOID/pair_lubricateU.cpp | 2 +- src/COLLOID/pair_lubricateU_poly.cpp | 2 +- src/COLLOID/pair_lubricate_poly.cpp | 2 +- src/COLLOID/pair_yukawa_colloid.cpp | 2 +- src/CORESHELL/compute_temp_cs.cpp | 2 +- src/CORESHELL/pair_born_coul_dsf_cs.cpp | 2 +- src/CORESHELL/pair_born_coul_long_cs.cpp | 2 +- src/CORESHELL/pair_born_coul_wolf_cs.cpp | 2 +- src/CORESHELL/pair_buck_coul_long_cs.cpp | 2 +- src/CORESHELL/pair_coul_long_cs.cpp | 2 +- src/CORESHELL/pair_coul_wolf_cs.cpp | 3 +-- src/CORESHELL/pair_lj_cut_coul_long_cs.cpp | 2 +- src/DIPOLE/atom_vec_dipole.cpp | 2 +- src/DIPOLE/pair_lj_cut_dipole_cut.cpp | 2 +- src/DIPOLE/pair_lj_cut_dipole_long.cpp | 2 +- src/DIPOLE/pair_lj_long_dipole_long.cpp | 2 +- src/GPU/fix_gpu.cpp | 2 +- src/GPU/pair_beck_gpu.cpp | 2 +- src/GPU/pair_born_coul_long_cs_gpu.cpp | 2 +- src/GPU/pair_born_coul_long_gpu.cpp | 2 +- src/GPU/pair_born_coul_wolf_cs_gpu.cpp | 2 +- src/GPU/pair_born_coul_wolf_gpu.cpp | 2 +- src/GPU/pair_born_gpu.cpp | 2 +- src/GPU/pair_buck_coul_cut_gpu.cpp | 2 +- src/GPU/pair_buck_coul_long_gpu.cpp | 2 +- src/GPU/pair_buck_gpu.cpp | 2 +- src/GPU/pair_colloid_gpu.cpp | 2 +- src/GPU/pair_coul_cut_gpu.cpp | 2 +- src/GPU/pair_coul_debye_gpu.cpp | 2 +- src/GPU/pair_coul_dsf_gpu.cpp | 2 +- src/GPU/pair_coul_long_cs_gpu.cpp | 2 +- src/GPU/pair_coul_long_gpu.cpp | 2 +- src/GPU/pair_dpd_gpu.cpp | 2 +- src/GPU/pair_dpd_tstat_gpu.cpp | 2 +- src/GPU/pair_eam_alloy_gpu.cpp | 2 +- src/GPU/pair_eam_fs_gpu.cpp | 2 +- src/GPU/pair_eam_gpu.cpp | 2 +- src/GPU/pair_gauss_gpu.cpp | 2 +- src/GPU/pair_gayberne_gpu.cpp | 2 +- src/GPU/pair_lj96_cut_gpu.cpp | 2 +- src/GPU/pair_lj_charmm_coul_long_gpu.cpp | 2 +- src/GPU/pair_lj_class2_coul_long_gpu.cpp | 2 +- src/GPU/pair_lj_class2_gpu.cpp | 2 +- src/GPU/pair_lj_cubic_gpu.cpp | 2 +- src/GPU/pair_lj_cut_coul_cut_gpu.cpp | 2 +- src/GPU/pair_lj_cut_coul_debye_gpu.cpp | 2 +- src/GPU/pair_lj_cut_coul_dsf_gpu.cpp | 2 +- src/GPU/pair_lj_cut_coul_long_gpu.cpp | 2 +- src/GPU/pair_lj_cut_coul_msm_gpu.cpp | 2 +- src/GPU/pair_lj_cut_dipole_cut_gpu.cpp | 2 +- src/GPU/pair_lj_cut_dipole_long_gpu.cpp | 2 +- src/GPU/pair_lj_cut_gpu.cpp | 2 +- src/GPU/pair_lj_expand_coul_long_gpu.cpp | 2 +- src/GPU/pair_lj_expand_gpu.cpp | 2 +- src/GPU/pair_lj_gromacs_gpu.cpp | 2 +- src/GPU/pair_lj_sdk_coul_long_gpu.cpp | 2 +- src/GPU/pair_lj_sdk_gpu.cpp | 2 +- src/GPU/pair_lj_sf_dipole_sf_gpu.cpp | 2 +- src/GPU/pair_mie_cut_gpu.cpp | 2 +- src/GPU/pair_morse_gpu.cpp | 2 +- src/GPU/pair_resquared_gpu.cpp | 2 +- src/GPU/pair_soft_gpu.cpp | 2 +- src/GPU/pair_sw_gpu.cpp | 2 +- src/GPU/pair_table_gpu.cpp | 2 +- src/GPU/pair_tersoff_gpu.cpp | 2 +- src/GPU/pair_tersoff_mod_gpu.cpp | 2 +- src/GPU/pair_tersoff_zbl_gpu.cpp | 2 +- src/GPU/pair_ufm_gpu.cpp | 2 +- src/GPU/pair_vashishta_gpu.cpp | 3 ++- src/GPU/pair_yukawa_colloid_gpu.cpp | 2 +- src/GPU/pair_yukawa_gpu.cpp | 2 +- src/GPU/pair_zbl_gpu.cpp | 2 +- src/GPU/pppm_gpu.cpp | 2 +- src/GRANULAR/fix_freeze.cpp | 2 +- src/GRANULAR/fix_pour.cpp | 2 +- src/GRANULAR/fix_wall_gran.cpp | 2 +- src/GRANULAR/fix_wall_gran_region.cpp | 2 +- src/GRANULAR/pair_gran_hertz_history.cpp | 2 +- src/GRANULAR/pair_gran_hooke.cpp | 2 +- src/GRANULAR/pair_gran_hooke_history.cpp | 2 +- src/GRANULAR/pair_granular.cpp | 2 +- src/KIM/kim_query.cpp | 2 +- src/KIM/pair_kim.cpp | 4 +--- src/KOKKOS/angle_charmm_kokkos.cpp | 2 +- src/KOKKOS/angle_class2_kokkos.cpp | 2 +- src/KOKKOS/angle_cosine_kokkos.cpp | 2 +- src/KOKKOS/angle_harmonic_kokkos.cpp | 2 +- src/KOKKOS/atom_kokkos.cpp | 2 +- src/KOKKOS/atom_vec_angle_kokkos.cpp | 2 +- src/KOKKOS/atom_vec_atomic_kokkos.cpp | 2 +- src/KOKKOS/atom_vec_bond_kokkos.cpp | 2 +- src/KOKKOS/atom_vec_charge_kokkos.cpp | 2 +- src/KOKKOS/atom_vec_dpd_kokkos.cpp | 2 +- src/KOKKOS/atom_vec_full_kokkos.cpp | 2 +- src/KOKKOS/atom_vec_hybrid_kokkos.cpp | 2 +- src/KOKKOS/atom_vec_molecular_kokkos.cpp | 2 +- src/KOKKOS/atom_vec_sphere_kokkos.cpp | 2 +- src/KOKKOS/bond_class2_kokkos.cpp | 2 +- src/KOKKOS/bond_fene_kokkos.cpp | 2 +- src/KOKKOS/bond_harmonic_kokkos.cpp | 2 +- src/KOKKOS/comm_tiled_kokkos.cpp | 2 +- src/KOKKOS/compute_temp_kokkos.cpp | 2 +- src/KOKKOS/dihedral_charmm_kokkos.cpp | 2 +- src/KOKKOS/dihedral_class2_kokkos.cpp | 2 +- src/KOKKOS/dihedral_opls_kokkos.cpp | 2 +- src/KOKKOS/fix_deform_kokkos.cpp | 2 +- src/KOKKOS/fix_dpd_energy_kokkos.cpp | 2 +- src/KOKKOS/fix_enforce2d_kokkos.cpp | 2 +- src/KOKKOS/fix_eos_table_rx_kokkos.cpp | 2 +- src/KOKKOS/fix_langevin_kokkos.cpp | 2 +- src/KOKKOS/fix_momentum_kokkos.cpp | 2 +- src/KOKKOS/fix_nh_kokkos.cpp | 2 +- src/KOKKOS/fix_nph_kokkos.cpp | 2 +- src/KOKKOS/fix_npt_kokkos.cpp | 2 +- src/KOKKOS/fix_nve_kokkos.cpp | 2 +- src/KOKKOS/fix_nvt_kokkos.cpp | 2 +- src/KOKKOS/fix_property_atom_kokkos.cpp | 2 +- src/KOKKOS/fix_qeq_reax_kokkos.cpp | 2 +- src/KOKKOS/fix_reaxc_bonds_kokkos.cpp | 2 +- src/KOKKOS/fix_reaxc_species_kokkos.cpp | 2 +- src/KOKKOS/fix_rx_kokkos.cpp | 2 +- src/KOKKOS/fix_setforce_kokkos.cpp | 2 +- src/KOKKOS/fix_shardlow_kokkos.cpp | 2 +- src/KOKKOS/fix_wall_lj93_kokkos.cpp | 2 +- src/KOKKOS/fix_wall_reflect_kokkos.cpp | 2 +- src/KOKKOS/gridcomm_kokkos.cpp | 2 +- src/KOKKOS/improper_class2_kokkos.cpp | 2 +- src/KOKKOS/improper_harmonic_kokkos.cpp | 2 +- src/KOKKOS/kokkos.cpp | 2 +- src/KOKKOS/math_special_kokkos.cpp | 2 +- src/KOKKOS/pair_buck_coul_cut_kokkos.cpp | 2 +- src/KOKKOS/pair_buck_coul_long_kokkos.cpp | 2 +- src/KOKKOS/pair_buck_kokkos.cpp | 2 +- src/KOKKOS/pair_coul_cut_kokkos.cpp | 2 +- src/KOKKOS/pair_coul_debye_kokkos.cpp | 2 +- src/KOKKOS/pair_coul_dsf_kokkos.cpp | 2 +- src/KOKKOS/pair_coul_long_kokkos.cpp | 2 +- src/KOKKOS/pair_coul_wolf_kokkos.cpp | 2 +- src/KOKKOS/pair_dpd_fdt_energy_kokkos.cpp | 3 +-- src/KOKKOS/pair_eam_alloy_kokkos.cpp | 2 +- src/KOKKOS/pair_eam_fs_kokkos.cpp | 2 +- src/KOKKOS/pair_eam_kokkos.cpp | 2 +- src/KOKKOS/pair_exp6_rx_kokkos.cpp | 2 +- src/KOKKOS/pair_hybrid_kokkos.cpp | 2 +- src/KOKKOS/pair_hybrid_overlay_kokkos.cpp | 2 +- src/KOKKOS/pair_lj_charmm_coul_charmm_implicit_kokkos.cpp | 2 +- src/KOKKOS/pair_lj_charmm_coul_charmm_kokkos.cpp | 2 +- src/KOKKOS/pair_lj_charmm_coul_long_kokkos.cpp | 2 +- src/KOKKOS/pair_lj_class2_coul_cut_kokkos.cpp | 2 +- src/KOKKOS/pair_lj_class2_coul_long_kokkos.cpp | 2 +- src/KOKKOS/pair_lj_class2_kokkos.cpp | 2 +- src/KOKKOS/pair_lj_cut_coul_cut_kokkos.cpp | 2 +- src/KOKKOS/pair_lj_cut_coul_debye_kokkos.cpp | 2 +- src/KOKKOS/pair_lj_cut_coul_dsf_kokkos.cpp | 2 +- src/KOKKOS/pair_lj_cut_coul_long_kokkos.cpp | 2 +- src/KOKKOS/pair_lj_cut_kokkos.cpp | 2 +- src/KOKKOS/pair_lj_expand_kokkos.cpp | 2 +- src/KOKKOS/pair_lj_gromacs_coul_gromacs_kokkos.cpp | 2 +- src/KOKKOS/pair_lj_gromacs_kokkos.cpp | 2 +- src/KOKKOS/pair_lj_sdk_kokkos.cpp | 2 +- src/KOKKOS/pair_morse_kokkos.cpp | 2 +- src/KOKKOS/pair_multi_lucy_rx_kokkos.cpp | 4 ++-- src/KOKKOS/pair_reaxc_kokkos.cpp | 2 +- src/KOKKOS/pair_sw_kokkos.cpp | 2 +- src/KOKKOS/pair_table_kokkos.cpp | 2 +- src/KOKKOS/pair_table_rx_kokkos.cpp | 2 +- src/KOKKOS/pair_tersoff_kokkos.cpp | 2 +- src/KOKKOS/pair_tersoff_mod_kokkos.cpp | 2 +- src/KOKKOS/pair_tersoff_zbl_kokkos.cpp | 2 +- src/KOKKOS/pair_vashishta_kokkos.cpp | 2 +- src/KOKKOS/pair_yukawa_kokkos.cpp | 3 ++- src/KOKKOS/pair_zbl_kokkos.cpp | 2 +- src/KOKKOS/pppm_kokkos.cpp | 2 +- src/KOKKOS/rand_pool_wrap_kokkos.cpp | 2 +- src/KOKKOS/region_block_kokkos.cpp | 2 +- src/KOKKOS/verlet_kokkos.cpp | 2 +- src/KSPACE/ewald.cpp | 2 +- src/KSPACE/ewald_dipole.cpp | 2 +- src/KSPACE/ewald_dipole_spin.cpp | 2 +- src/KSPACE/ewald_disp.cpp | 2 +- src/KSPACE/fft3d.cpp | 2 +- src/KSPACE/fft3d_wrap.cpp | 2 +- src/KSPACE/fix_tune_kspace.cpp | 2 +- src/KSPACE/gridcomm.cpp | 2 +- src/KSPACE/msm.cpp | 2 +- src/KSPACE/msm_cg.cpp | 2 +- src/KSPACE/pair_born_coul_long.cpp | 2 +- src/KSPACE/pair_born_coul_msm.cpp | 2 +- src/KSPACE/pair_buck_coul_long.cpp | 2 +- src/KSPACE/pair_buck_coul_msm.cpp | 2 +- src/KSPACE/pair_buck_long_coul_long.cpp | 2 +- src/KSPACE/pair_coul_long.cpp | 2 +- src/KSPACE/pair_coul_msm.cpp | 2 +- src/KSPACE/pair_lj_charmm_coul_long.cpp | 2 +- src/KSPACE/pair_lj_charmm_coul_msm.cpp | 2 +- src/KSPACE/pair_lj_charmmfsw_coul_long.cpp | 2 +- src/KSPACE/pair_lj_cut_coul_long.cpp | 2 +- src/KSPACE/pair_lj_cut_coul_msm.cpp | 2 +- src/KSPACE/pair_lj_cut_tip4p_long.cpp | 2 +- src/KSPACE/pair_lj_long_coul_long.cpp | 2 +- src/KSPACE/pair_lj_long_tip4p_long.cpp | 2 +- src/KSPACE/pair_tip4p_long.cpp | 2 +- src/KSPACE/pppm.cpp | 2 +- src/KSPACE/pppm_cg.cpp | 4 +--- src/KSPACE/pppm_dipole.cpp | 2 +- src/KSPACE/pppm_dipole_spin.cpp | 2 +- src/KSPACE/pppm_disp.cpp | 2 +- src/KSPACE/pppm_disp_tip4p.cpp | 2 +- src/KSPACE/pppm_stagger.cpp | 2 +- src/KSPACE/pppm_tip4p.cpp | 2 +- src/KSPACE/remap.cpp | 2 +- src/KSPACE/remap_wrap.cpp | 2 +- 253 files changed, 256 insertions(+), 260 deletions(-) diff --git a/src/ASPHERE/compute_erotate_asphere.cpp b/src/ASPHERE/compute_erotate_asphere.cpp index afec2a9b28..665506acdf 100644 --- a/src/ASPHERE/compute_erotate_asphere.cpp +++ b/src/ASPHERE/compute_erotate_asphere.cpp @@ -11,8 +11,8 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include #include "compute_erotate_asphere.h" +#include #include "math_extra.h" #include "atom.h" #include "atom_vec_ellipsoid.h" diff --git a/src/ASPHERE/compute_temp_asphere.cpp b/src/ASPHERE/compute_temp_asphere.cpp index 011d8cae80..32773b2925 100644 --- a/src/ASPHERE/compute_temp_asphere.cpp +++ b/src/ASPHERE/compute_temp_asphere.cpp @@ -15,9 +15,9 @@ Contributing author: Mike Brown (SNL) ------------------------------------------------------------------------- */ +#include "compute_temp_asphere.h" #include #include -#include "compute_temp_asphere.h" #include "math_extra.h" #include "atom.h" #include "atom_vec_ellipsoid.h" diff --git a/src/ASPHERE/fix_nh_asphere.cpp b/src/ASPHERE/fix_nh_asphere.cpp index 828c064a52..9e8e9d73d9 100644 --- a/src/ASPHERE/fix_nh_asphere.cpp +++ b/src/ASPHERE/fix_nh_asphere.cpp @@ -15,11 +15,11 @@ Contributing author: Mike Brown (SNL) ------------------------------------------------------------------------- */ +#include "fix_nh_asphere.h" #include #include #include #include "math_extra.h" -#include "fix_nh_asphere.h" #include "atom.h" #include "atom_vec_ellipsoid.h" #include "group.h" diff --git a/src/ASPHERE/fix_nph_asphere.cpp b/src/ASPHERE/fix_nph_asphere.cpp index 5f201a8463..70880701ca 100644 --- a/src/ASPHERE/fix_nph_asphere.cpp +++ b/src/ASPHERE/fix_nph_asphere.cpp @@ -11,8 +11,8 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include #include "fix_nph_asphere.h" +#include #include "modify.h" #include "error.h" diff --git a/src/ASPHERE/fix_npt_asphere.cpp b/src/ASPHERE/fix_npt_asphere.cpp index 5d52891169..26d4fff81d 100644 --- a/src/ASPHERE/fix_npt_asphere.cpp +++ b/src/ASPHERE/fix_npt_asphere.cpp @@ -11,8 +11,8 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include #include "fix_npt_asphere.h" +#include #include "modify.h" #include "error.h" diff --git a/src/ASPHERE/fix_nve_asphere.cpp b/src/ASPHERE/fix_nve_asphere.cpp index 61e3c35293..05219e442f 100644 --- a/src/ASPHERE/fix_nve_asphere.cpp +++ b/src/ASPHERE/fix_nve_asphere.cpp @@ -15,10 +15,10 @@ Contributing author: Mike Brown (SNL) ------------------------------------------------------------------------- */ +#include "fix_nve_asphere.h" #include #include #include -#include "fix_nve_asphere.h" #include "math_extra.h" #include "atom.h" #include "atom_vec_ellipsoid.h" diff --git a/src/ASPHERE/fix_nve_asphere_noforce.cpp b/src/ASPHERE/fix_nve_asphere_noforce.cpp index 9cc430592a..015cc8cfb6 100644 --- a/src/ASPHERE/fix_nve_asphere_noforce.cpp +++ b/src/ASPHERE/fix_nve_asphere_noforce.cpp @@ -11,10 +11,10 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ +#include "fix_nve_asphere_noforce.h" #include #include #include -#include "fix_nve_asphere_noforce.h" #include "math_extra.h" #include "atom.h" #include "atom_vec_ellipsoid.h" diff --git a/src/ASPHERE/fix_nve_line.cpp b/src/ASPHERE/fix_nve_line.cpp index 51a502df89..57335f22e0 100644 --- a/src/ASPHERE/fix_nve_line.cpp +++ b/src/ASPHERE/fix_nve_line.cpp @@ -11,10 +11,10 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ +#include "fix_nve_line.h" #include #include #include -#include "fix_nve_line.h" #include "atom.h" #include "atom_vec_line.h" #include "domain.h" diff --git a/src/ASPHERE/fix_nve_tri.cpp b/src/ASPHERE/fix_nve_tri.cpp index fb9bf64c58..b1f7667d06 100644 --- a/src/ASPHERE/fix_nve_tri.cpp +++ b/src/ASPHERE/fix_nve_tri.cpp @@ -11,10 +11,10 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ +#include "fix_nve_tri.h" #include #include #include -#include "fix_nve_tri.h" #include "math_extra.h" #include "atom.h" #include "atom_vec_tri.h" diff --git a/src/ASPHERE/fix_nvt_asphere.cpp b/src/ASPHERE/fix_nvt_asphere.cpp index 5ef91923eb..597fb03514 100644 --- a/src/ASPHERE/fix_nvt_asphere.cpp +++ b/src/ASPHERE/fix_nvt_asphere.cpp @@ -11,8 +11,8 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include #include "fix_nvt_asphere.h" +#include #include "group.h" #include "modify.h" #include "error.h" diff --git a/src/ASPHERE/pair_gayberne.cpp b/src/ASPHERE/pair_gayberne.cpp index 3d4ed3f183..7dbf11c5ea 100644 --- a/src/ASPHERE/pair_gayberne.cpp +++ b/src/ASPHERE/pair_gayberne.cpp @@ -15,11 +15,11 @@ Contributing author: Mike Brown (SNL) ------------------------------------------------------------------------- */ +#include "pair_gayberne.h" #include #include #include #include -#include "pair_gayberne.h" #include "math_extra.h" #include "atom.h" #include "atom_vec_ellipsoid.h" diff --git a/src/ASPHERE/pair_line_lj.cpp b/src/ASPHERE/pair_line_lj.cpp index 4873b44dc4..0cb603c4fa 100644 --- a/src/ASPHERE/pair_line_lj.cpp +++ b/src/ASPHERE/pair_line_lj.cpp @@ -11,11 +11,11 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ +#include "pair_line_lj.h" #include #include #include #include -#include "pair_line_lj.h" #include "atom.h" #include "atom_vec_line.h" #include "force.h" diff --git a/src/ASPHERE/pair_resquared.cpp b/src/ASPHERE/pair_resquared.cpp index b100a5f184..ba73c5ba0c 100644 --- a/src/ASPHERE/pair_resquared.cpp +++ b/src/ASPHERE/pair_resquared.cpp @@ -15,11 +15,11 @@ Contributing author: Mike Brown (SNL) ------------------------------------------------------------------------- */ +#include "pair_resquared.h" #include #include #include #include -#include "pair_resquared.h" #include "math_extra.h" #include "atom.h" #include "atom_vec_ellipsoid.h" diff --git a/src/ASPHERE/pair_tri_lj.cpp b/src/ASPHERE/pair_tri_lj.cpp index cefd73f976..3dde2a4f44 100644 --- a/src/ASPHERE/pair_tri_lj.cpp +++ b/src/ASPHERE/pair_tri_lj.cpp @@ -11,11 +11,11 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ +#include "pair_tri_lj.h" #include #include #include #include -#include "pair_tri_lj.h" #include "math_extra.h" #include "atom.h" #include "atom_vec_tri.h" diff --git a/src/BODY/body_nparticle.cpp b/src/BODY/body_nparticle.cpp index b2d9dbaca3..353ce5550c 100644 --- a/src/BODY/body_nparticle.cpp +++ b/src/BODY/body_nparticle.cpp @@ -11,9 +11,9 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ +#include "body_nparticle.h" #include #include -#include "body_nparticle.h" #include "my_pool_chunk.h" #include "math_extra.h" #include "atom_vec_body.h" diff --git a/src/BODY/body_rounded_polygon.cpp b/src/BODY/body_rounded_polygon.cpp index 6e1e49319e..21f1d7e221 100644 --- a/src/BODY/body_rounded_polygon.cpp +++ b/src/BODY/body_rounded_polygon.cpp @@ -15,9 +15,9 @@ Contributing author: Trung Dac Nguyen (ndactrung@gmail.com) ------------------------------------------------------------------------- */ +#include "body_rounded_polygon.h" #include #include -#include "body_rounded_polygon.h" #include "my_pool_chunk.h" #include "atom_vec_body.h" #include "atom.h" diff --git a/src/BODY/body_rounded_polyhedron.cpp b/src/BODY/body_rounded_polyhedron.cpp index 4b5208c397..15e1871e02 100644 --- a/src/BODY/body_rounded_polyhedron.cpp +++ b/src/BODY/body_rounded_polyhedron.cpp @@ -15,9 +15,9 @@ Contributing author: Trung Dac Nguyen (ndactrung@gmail.com) ------------------------------------------------------------------------- */ +#include "body_rounded_polyhedron.h" #include #include -#include "body_rounded_polyhedron.h" #include "my_pool_chunk.h" #include "atom_vec_body.h" #include "atom.h" diff --git a/src/BODY/compute_body_local.cpp b/src/BODY/compute_body_local.cpp index 20f7d76708..f58b66c2ca 100644 --- a/src/BODY/compute_body_local.cpp +++ b/src/BODY/compute_body_local.cpp @@ -11,9 +11,9 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ +#include "compute_body_local.h" #include #include -#include "compute_body_local.h" #include "atom.h" #include "atom_vec_body.h" #include "body.h" diff --git a/src/BODY/compute_temp_body.cpp b/src/BODY/compute_temp_body.cpp index 5446fb6d64..7beca36df8 100644 --- a/src/BODY/compute_temp_body.cpp +++ b/src/BODY/compute_temp_body.cpp @@ -16,9 +16,9 @@ based on ComputeTempAsphere ------------------------------------------------------------------------- */ +#include "compute_temp_body.h" #include #include -#include "compute_temp_body.h" #include "math_extra.h" #include "atom.h" #include "atom_vec_body.h" diff --git a/src/BODY/fix_nh_body.cpp b/src/BODY/fix_nh_body.cpp index 9739842419..6064f1f9de 100644 --- a/src/BODY/fix_nh_body.cpp +++ b/src/BODY/fix_nh_body.cpp @@ -16,11 +16,11 @@ based on FixNHAsphere ------------------------------------------------------------------------- */ +#include "fix_nh_body.h" #include #include #include #include "math_extra.h" -#include "fix_nh_body.h" #include "atom.h" #include "atom_vec_body.h" #include "group.h" diff --git a/src/BODY/fix_nph_body.cpp b/src/BODY/fix_nph_body.cpp index e647488bce..a65c951c96 100644 --- a/src/BODY/fix_nph_body.cpp +++ b/src/BODY/fix_nph_body.cpp @@ -15,8 +15,8 @@ Contributing author: Trung Dac Nguyen (ndactrung@gmail.com) ------------------------------------------------------------------------- */ -#include #include "fix_nph_body.h" +#include #include "modify.h" #include "error.h" diff --git a/src/BODY/fix_npt_body.cpp b/src/BODY/fix_npt_body.cpp index 3c30e9e4e9..7e8097486e 100644 --- a/src/BODY/fix_npt_body.cpp +++ b/src/BODY/fix_npt_body.cpp @@ -15,8 +15,8 @@ Contributing author: Trung Dac Nguyen (ndactrung@gmail.com) ------------------------------------------------------------------------- */ -#include #include "fix_npt_body.h" +#include #include "modify.h" #include "error.h" diff --git a/src/BODY/fix_nve_body.cpp b/src/BODY/fix_nve_body.cpp index 0c74facf34..3f3bd41cbc 100644 --- a/src/BODY/fix_nve_body.cpp +++ b/src/BODY/fix_nve_body.cpp @@ -11,10 +11,10 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ +#include "fix_nve_body.h" #include #include #include -#include "fix_nve_body.h" #include "math_extra.h" #include "atom.h" #include "atom_vec_body.h" diff --git a/src/BODY/fix_nvt_body.cpp b/src/BODY/fix_nvt_body.cpp index 273b5e7fff..efb05143a1 100644 --- a/src/BODY/fix_nvt_body.cpp +++ b/src/BODY/fix_nvt_body.cpp @@ -15,8 +15,8 @@ Contributing author: Trung Dac Nguyen (ndactrung@gmail.com) ------------------------------------------------------------------------- */ -#include #include "fix_nvt_body.h" +#include #include "group.h" #include "modify.h" #include "error.h" diff --git a/src/BODY/fix_wall_body_polygon.cpp b/src/BODY/fix_wall_body_polygon.cpp index 221937461b..8f27a094cb 100644 --- a/src/BODY/fix_wall_body_polygon.cpp +++ b/src/BODY/fix_wall_body_polygon.cpp @@ -15,10 +15,10 @@ Contributing author: Trung Dac Nguyen (ndactrung@gmail.com) ------------------------------------------------------------------------- */ +#include "fix_wall_body_polygon.h" #include #include #include -#include "fix_wall_body_polygon.h" #include "atom.h" #include "atom_vec_body.h" #include "body_rounded_polygon.h" diff --git a/src/BODY/fix_wall_body_polyhedron.cpp b/src/BODY/fix_wall_body_polyhedron.cpp index 24a9e51dad..37b542803f 100644 --- a/src/BODY/fix_wall_body_polyhedron.cpp +++ b/src/BODY/fix_wall_body_polyhedron.cpp @@ -15,10 +15,10 @@ Contributing author: Trung Dac Nguyen (ndactrung@gmail.com) ------------------------------------------------------------------------- */ +#include "fix_wall_body_polyhedron.h" #include #include #include -#include "fix_wall_body_polyhedron.h" #include "atom.h" #include "atom_vec_body.h" #include "body_rounded_polyhedron.h" diff --git a/src/BODY/pair_body_nparticle.cpp b/src/BODY/pair_body_nparticle.cpp index f2eb2aa520..96a7af6255 100644 --- a/src/BODY/pair_body_nparticle.cpp +++ b/src/BODY/pair_body_nparticle.cpp @@ -11,11 +11,11 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ +#include "pair_body_nparticle.h" #include #include #include #include -#include "pair_body_nparticle.h" #include "math_extra.h" #include "atom.h" #include "atom_vec_body.h" diff --git a/src/BODY/pair_body_rounded_polygon.cpp b/src/BODY/pair_body_rounded_polygon.cpp index 69495ea57f..c818b5a2e6 100644 --- a/src/BODY/pair_body_rounded_polygon.cpp +++ b/src/BODY/pair_body_rounded_polygon.cpp @@ -18,11 +18,11 @@ the contact history for friction forces. ------------------------------------------------------------------------- */ +#include "pair_body_rounded_polygon.h" #include #include #include #include -#include "pair_body_rounded_polygon.h" #include "math_extra.h" #include "atom.h" #include "atom_vec_body.h" diff --git a/src/BODY/pair_body_rounded_polyhedron.cpp b/src/BODY/pair_body_rounded_polyhedron.cpp index 60f6df3582..75caab88bd 100644 --- a/src/BODY/pair_body_rounded_polyhedron.cpp +++ b/src/BODY/pair_body_rounded_polyhedron.cpp @@ -20,11 +20,11 @@ the contact history for friction forces. ------------------------------------------------------------------------- */ +#include "pair_body_rounded_polyhedron.h" #include #include #include #include -#include "pair_body_rounded_polyhedron.h" #include "math_extra.h" #include "atom.h" #include "atom_vec_body.h" diff --git a/src/CLASS2/angle_class2.cpp b/src/CLASS2/angle_class2.cpp index d550767e5e..340152abd4 100644 --- a/src/CLASS2/angle_class2.cpp +++ b/src/CLASS2/angle_class2.cpp @@ -15,10 +15,10 @@ Contributing author: Eric Simon (Cray) ------------------------------------------------------------------------- */ +#include "angle_class2.h" #include #include #include -#include "angle_class2.h" #include "atom.h" #include "neighbor.h" #include "domain.h" diff --git a/src/CLASS2/bond_class2.cpp b/src/CLASS2/bond_class2.cpp index 26c4e63a4d..945555f772 100644 --- a/src/CLASS2/bond_class2.cpp +++ b/src/CLASS2/bond_class2.cpp @@ -15,9 +15,9 @@ Contributing author: Eric Simon (Cray) ------------------------------------------------------------------------- */ +#include "bond_class2.h" #include #include -#include "bond_class2.h" #include "atom.h" #include "neighbor.h" #include "domain.h" diff --git a/src/CLASS2/dihedral_class2.cpp b/src/CLASS2/dihedral_class2.cpp index c471b1f353..c36d976525 100644 --- a/src/CLASS2/dihedral_class2.cpp +++ b/src/CLASS2/dihedral_class2.cpp @@ -15,10 +15,10 @@ Contributing author: Eric Simon (Cray) ------------------------------------------------------------------------- */ +#include "dihedral_class2.h" #include #include #include -#include "dihedral_class2.h" #include "atom.h" #include "neighbor.h" #include "update.h" diff --git a/src/CLASS2/improper_class2.cpp b/src/CLASS2/improper_class2.cpp index ccb81aebd9..aff37df318 100644 --- a/src/CLASS2/improper_class2.cpp +++ b/src/CLASS2/improper_class2.cpp @@ -15,10 +15,10 @@ Contributing author: Eric Simon (Cray) ------------------------------------------------------------------------- */ +#include "improper_class2.h" #include #include #include -#include "improper_class2.h" #include "atom.h" #include "neighbor.h" #include "update.h" diff --git a/src/CLASS2/pair_lj_class2.cpp b/src/CLASS2/pair_lj_class2.cpp index 60b988926a..9a67fafecb 100644 --- a/src/CLASS2/pair_lj_class2.cpp +++ b/src/CLASS2/pair_lj_class2.cpp @@ -9,11 +9,11 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ +#include "pair_lj_class2.h" #include #include #include #include -#include "pair_lj_class2.h" #include "atom.h" #include "comm.h" #include "force.h" diff --git a/src/CLASS2/pair_lj_class2_coul_cut.cpp b/src/CLASS2/pair_lj_class2_coul_cut.cpp index 8dc038b8fc..24620611c6 100644 --- a/src/CLASS2/pair_lj_class2_coul_cut.cpp +++ b/src/CLASS2/pair_lj_class2_coul_cut.cpp @@ -11,11 +11,11 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ +#include "pair_lj_class2_coul_cut.h" #include #include #include #include -#include "pair_lj_class2_coul_cut.h" #include "atom.h" #include "comm.h" #include "force.h" diff --git a/src/CLASS2/pair_lj_class2_coul_long.cpp b/src/CLASS2/pair_lj_class2_coul_long.cpp index c92c7b78f1..cd11294327 100644 --- a/src/CLASS2/pair_lj_class2_coul_long.cpp +++ b/src/CLASS2/pair_lj_class2_coul_long.cpp @@ -11,11 +11,11 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ +#include "pair_lj_class2_coul_long.h" #include #include #include #include -#include "pair_lj_class2_coul_long.h" #include "atom.h" #include "comm.h" #include "force.h" diff --git a/src/COLLOID/fix_wall_colloid.cpp b/src/COLLOID/fix_wall_colloid.cpp index 095d01eef3..f2e895c4f3 100644 --- a/src/COLLOID/fix_wall_colloid.cpp +++ b/src/COLLOID/fix_wall_colloid.cpp @@ -15,9 +15,9 @@ Contributing authors: Jeremy Lechman (SNL) ------------------------------------------------------------------------- */ +#include "fix_wall_colloid.h" #include #include -#include "fix_wall_colloid.h" #include "atom.h" #include "atom_vec.h" #include "update.h" diff --git a/src/COLLOID/pair_brownian.cpp b/src/COLLOID/pair_brownian.cpp index aefa96b1fb..f9185264e0 100644 --- a/src/COLLOID/pair_brownian.cpp +++ b/src/COLLOID/pair_brownian.cpp @@ -15,11 +15,11 @@ Contributing authors: Amit Kumar and Michael Bybee (UIUC) ------------------------------------------------------------------------- */ +#include "pair_brownian.h" #include #include #include #include -#include "pair_brownian.h" #include "atom.h" #include "atom_vec.h" #include "comm.h" diff --git a/src/COLLOID/pair_brownian_poly.cpp b/src/COLLOID/pair_brownian_poly.cpp index 389ae084b7..250dcef1fd 100644 --- a/src/COLLOID/pair_brownian_poly.cpp +++ b/src/COLLOID/pair_brownian_poly.cpp @@ -16,11 +16,11 @@ Dave Heine (Corning), polydispersity ------------------------------------------------------------------------- */ +#include "pair_brownian_poly.h" #include #include #include #include -#include "pair_brownian_poly.h" #include "atom.h" #include "atom_vec.h" #include "comm.h" diff --git a/src/COLLOID/pair_colloid.cpp b/src/COLLOID/pair_colloid.cpp index 04c35a7c00..306cdfebdf 100644 --- a/src/COLLOID/pair_colloid.cpp +++ b/src/COLLOID/pair_colloid.cpp @@ -15,11 +15,11 @@ Contributing author: Pieter in 't Veld (SNL) ------------------------------------------------------------------------- */ +#include "pair_colloid.h" #include #include #include #include -#include "pair_colloid.h" #include "atom.h" #include "comm.h" #include "force.h" diff --git a/src/COLLOID/pair_lubricate.cpp b/src/COLLOID/pair_lubricate.cpp index 4e629bd442..ee55c6cbf5 100644 --- a/src/COLLOID/pair_lubricate.cpp +++ b/src/COLLOID/pair_lubricate.cpp @@ -16,11 +16,11 @@ Amit Kumar and Michael Bybee (UIUC) ------------------------------------------------------------------------- */ +#include "pair_lubricate.h" #include #include #include #include -#include "pair_lubricate.h" #include "atom.h" #include "atom_vec.h" #include "comm.h" diff --git a/src/COLLOID/pair_lubricateU.cpp b/src/COLLOID/pair_lubricateU.cpp index 3ea3d4fe4a..be589167c9 100644 --- a/src/COLLOID/pair_lubricateU.cpp +++ b/src/COLLOID/pair_lubricateU.cpp @@ -15,12 +15,12 @@ Contributing authors: Amit Kumar and Michael Bybee (UIUC) ------------------------------------------------------------------------- */ +#include "pair_lubricateU.h" #include #include #include #include #include -#include "pair_lubricateU.h" #include "atom.h" #include "atom_vec.h" #include "comm.h" diff --git a/src/COLLOID/pair_lubricateU_poly.cpp b/src/COLLOID/pair_lubricateU_poly.cpp index 4fec95dcd8..ebcf939cff 100644 --- a/src/COLLOID/pair_lubricateU_poly.cpp +++ b/src/COLLOID/pair_lubricateU_poly.cpp @@ -17,12 +17,12 @@ Dave Heine (Corning), polydispersity ------------------------------------------------------------------------- */ +#include "pair_lubricateU_poly.h" #include #include #include #include #include -#include "pair_lubricateU_poly.h" #include "atom.h" #include "atom_vec.h" #include "comm.h" diff --git a/src/COLLOID/pair_lubricate_poly.cpp b/src/COLLOID/pair_lubricate_poly.cpp index ffbe7fce3c..f1bfa0c695 100644 --- a/src/COLLOID/pair_lubricate_poly.cpp +++ b/src/COLLOID/pair_lubricate_poly.cpp @@ -17,11 +17,11 @@ Dave Heine (Corning), polydispersity ------------------------------------------------------------------------- */ +#include "pair_lubricate_poly.h" #include #include #include #include -#include "pair_lubricate_poly.h" #include "atom.h" #include "atom_vec.h" #include "comm.h" diff --git a/src/COLLOID/pair_yukawa_colloid.cpp b/src/COLLOID/pair_yukawa_colloid.cpp index ab7d088508..98d0586925 100644 --- a/src/COLLOID/pair_yukawa_colloid.cpp +++ b/src/COLLOID/pair_yukawa_colloid.cpp @@ -15,9 +15,9 @@ Contributing authors: Randy Schunk (Sandia) ------------------------------------------------------------------------- */ +#include "pair_yukawa_colloid.h" #include #include -#include "pair_yukawa_colloid.h" #include "atom.h" #include "atom_vec.h" #include "force.h" diff --git a/src/CORESHELL/compute_temp_cs.cpp b/src/CORESHELL/compute_temp_cs.cpp index 03ebfa154d..4217fe3410 100644 --- a/src/CORESHELL/compute_temp_cs.cpp +++ b/src/CORESHELL/compute_temp_cs.cpp @@ -16,11 +16,11 @@ (hendrik.heenen at mytum.com) ------------------------------------------------------------------------- */ +#include "compute_temp_cs.h" #include #include #include #include -#include "compute_temp_cs.h" #include "atom.h" #include "atom_vec.h" #include "domain.h" diff --git a/src/CORESHELL/pair_born_coul_dsf_cs.cpp b/src/CORESHELL/pair_born_coul_dsf_cs.cpp index f4d7447ade..cd932e560b 100644 --- a/src/CORESHELL/pair_born_coul_dsf_cs.cpp +++ b/src/CORESHELL/pair_born_coul_dsf_cs.cpp @@ -16,11 +16,11 @@ References: Fennell and Gezelter, JCP 124, 234104 (2006) ------------------------------------------------------------------------- */ +#include "pair_born_coul_dsf_cs.h" #include #include #include #include -#include "pair_born_coul_dsf_cs.h" #include "atom.h" #include "comm.h" #include "force.h" diff --git a/src/CORESHELL/pair_born_coul_long_cs.cpp b/src/CORESHELL/pair_born_coul_long_cs.cpp index a19f8c34a8..2ef7fdb273 100644 --- a/src/CORESHELL/pair_born_coul_long_cs.cpp +++ b/src/CORESHELL/pair_born_coul_long_cs.cpp @@ -15,11 +15,11 @@ Contributing author: Hendrik Heenen (hendrik.heenen@mytum.de) ------------------------------------------------------------------------- */ +#include "pair_born_coul_long_cs.h" #include #include #include #include -#include "pair_born_coul_long_cs.h" #include "atom.h" #include "comm.h" #include "force.h" diff --git a/src/CORESHELL/pair_born_coul_wolf_cs.cpp b/src/CORESHELL/pair_born_coul_wolf_cs.cpp index 7b52c28664..c0374e2ddb 100644 --- a/src/CORESHELL/pair_born_coul_wolf_cs.cpp +++ b/src/CORESHELL/pair_born_coul_wolf_cs.cpp @@ -12,11 +12,11 @@ ------------------------------------------------------------------------- */ +#include "pair_born_coul_wolf_cs.h" #include #include #include #include -#include "pair_born_coul_wolf_cs.h" #include "atom.h" #include "comm.h" #include "force.h" diff --git a/src/CORESHELL/pair_buck_coul_long_cs.cpp b/src/CORESHELL/pair_buck_coul_long_cs.cpp index 8df91f39a3..6c897622fa 100644 --- a/src/CORESHELL/pair_buck_coul_long_cs.cpp +++ b/src/CORESHELL/pair_buck_coul_long_cs.cpp @@ -15,11 +15,11 @@ Contributing author: Hendrik Heenen (hendrik.heenen@mytum.de) ------------------------------------------------------------------------- */ +#include "pair_buck_coul_long_cs.h" #include #include #include #include -#include "pair_buck_coul_long_cs.h" #include "atom.h" #include "comm.h" #include "force.h" diff --git a/src/CORESHELL/pair_coul_long_cs.cpp b/src/CORESHELL/pair_coul_long_cs.cpp index c8c8387d6d..6094ae072a 100644 --- a/src/CORESHELL/pair_coul_long_cs.cpp +++ b/src/CORESHELL/pair_coul_long_cs.cpp @@ -15,11 +15,11 @@ Contributing author: Hendrik Heenen (hendrik.heenen@mytum.de) ------------------------------------------------------------------------- */ +#include "pair_coul_long_cs.h" #include #include #include #include -#include "pair_coul_long_cs.h" #include "atom.h" #include "comm.h" #include "force.h" diff --git a/src/CORESHELL/pair_coul_wolf_cs.cpp b/src/CORESHELL/pair_coul_wolf_cs.cpp index 36e037bfc8..40ade7bfe4 100644 --- a/src/CORESHELL/pair_coul_wolf_cs.cpp +++ b/src/CORESHELL/pair_coul_wolf_cs.cpp @@ -11,12 +11,11 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ - +#include "pair_coul_wolf_cs.h" #include #include #include #include -#include "pair_coul_wolf_cs.h" #include "atom.h" #include "comm.h" #include "force.h" diff --git a/src/CORESHELL/pair_lj_cut_coul_long_cs.cpp b/src/CORESHELL/pair_lj_cut_coul_long_cs.cpp index 56c75f0f5d..3f20377cf1 100644 --- a/src/CORESHELL/pair_lj_cut_coul_long_cs.cpp +++ b/src/CORESHELL/pair_lj_cut_coul_long_cs.cpp @@ -15,11 +15,11 @@ Contributing author: Hendrik Heenen (hendrik.heenen@mytum.de) ------------------------------------------------------------------------- */ +#include "pair_lj_cut_coul_long_cs.h" #include #include #include #include -#include "pair_lj_cut_coul_long_cs.h" #include "atom.h" #include "comm.h" #include "force.h" diff --git a/src/DIPOLE/atom_vec_dipole.cpp b/src/DIPOLE/atom_vec_dipole.cpp index c304ae3bc6..67e5aa9e70 100644 --- a/src/DIPOLE/atom_vec_dipole.cpp +++ b/src/DIPOLE/atom_vec_dipole.cpp @@ -11,9 +11,9 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ +#include "atom_vec_dipole.h" #include #include -#include "atom_vec_dipole.h" #include "atom.h" #include "comm.h" #include "domain.h" diff --git a/src/DIPOLE/pair_lj_cut_dipole_cut.cpp b/src/DIPOLE/pair_lj_cut_dipole_cut.cpp index 18b78c55e0..44708edec9 100644 --- a/src/DIPOLE/pair_lj_cut_dipole_cut.cpp +++ b/src/DIPOLE/pair_lj_cut_dipole_cut.cpp @@ -11,10 +11,10 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ +#include "pair_lj_cut_dipole_cut.h" #include #include #include -#include "pair_lj_cut_dipole_cut.h" #include "atom.h" #include "neighbor.h" #include "neigh_list.h" diff --git a/src/DIPOLE/pair_lj_cut_dipole_long.cpp b/src/DIPOLE/pair_lj_cut_dipole_long.cpp index 42446a3777..071dbaeb02 100644 --- a/src/DIPOLE/pair_lj_cut_dipole_long.cpp +++ b/src/DIPOLE/pair_lj_cut_dipole_long.cpp @@ -11,11 +11,11 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ +#include "pair_lj_cut_dipole_long.h" #include #include #include #include -#include "pair_lj_cut_dipole_long.h" #include "atom.h" #include "comm.h" #include "neighbor.h" diff --git a/src/DIPOLE/pair_lj_long_dipole_long.cpp b/src/DIPOLE/pair_lj_long_dipole_long.cpp index fbdc47a15b..1391cc1a1a 100644 --- a/src/DIPOLE/pair_lj_long_dipole_long.cpp +++ b/src/DIPOLE/pair_lj_long_dipole_long.cpp @@ -15,13 +15,13 @@ Contributing author: Pieter J. in 't Veld and Stan Moore (Sandia) ------------------------------------------------------------------------- */ +#include "pair_lj_long_dipole_long.h" #include #include #include #include #include "math_const.h" #include "math_vector.h" -#include "pair_lj_long_dipole_long.h" #include "atom.h" #include "comm.h" #include "neighbor.h" diff --git a/src/GPU/fix_gpu.cpp b/src/GPU/fix_gpu.cpp index f0558e6a02..d4397503dc 100644 --- a/src/GPU/fix_gpu.cpp +++ b/src/GPU/fix_gpu.cpp @@ -11,9 +11,9 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ +#include "fix_gpu.h" #include #include -#include "fix_gpu.h" #include "atom.h" #include "force.h" #include "pair.h" diff --git a/src/GPU/pair_beck_gpu.cpp b/src/GPU/pair_beck_gpu.cpp index 9f76975ef1..d4d36a5837 100644 --- a/src/GPU/pair_beck_gpu.cpp +++ b/src/GPU/pair_beck_gpu.cpp @@ -15,11 +15,11 @@ Contributing author: Trung Dac Nguyen (ORNL) ------------------------------------------------------------------------- */ +#include "pair_beck_gpu.h" #include #include #include #include -#include "pair_beck_gpu.h" #include "atom.h" #include "atom_vec.h" #include "comm.h" diff --git a/src/GPU/pair_born_coul_long_cs_gpu.cpp b/src/GPU/pair_born_coul_long_cs_gpu.cpp index 291ad8ad1f..7314024d71 100644 --- a/src/GPU/pair_born_coul_long_cs_gpu.cpp +++ b/src/GPU/pair_born_coul_long_cs_gpu.cpp @@ -15,11 +15,11 @@ Contributing author: Trung Dac Nguyen (Northwestern) ------------------------------------------------------------------------- */ +#include "pair_born_coul_long_cs_gpu.h" #include #include #include #include -#include "pair_born_coul_long_cs_gpu.h" #include "atom.h" #include "atom_vec.h" #include "comm.h" diff --git a/src/GPU/pair_born_coul_long_gpu.cpp b/src/GPU/pair_born_coul_long_gpu.cpp index eb204691c7..79c0d5f147 100644 --- a/src/GPU/pair_born_coul_long_gpu.cpp +++ b/src/GPU/pair_born_coul_long_gpu.cpp @@ -15,11 +15,11 @@ Contributing author: Trung Dac Nguyen (ORNL) ------------------------------------------------------------------------- */ +#include "pair_born_coul_long_gpu.h" #include #include #include #include -#include "pair_born_coul_long_gpu.h" #include "atom.h" #include "atom_vec.h" #include "comm.h" diff --git a/src/GPU/pair_born_coul_wolf_cs_gpu.cpp b/src/GPU/pair_born_coul_wolf_cs_gpu.cpp index 4877a442b5..5f74d3fc7c 100644 --- a/src/GPU/pair_born_coul_wolf_cs_gpu.cpp +++ b/src/GPU/pair_born_coul_wolf_cs_gpu.cpp @@ -15,11 +15,11 @@ Contributing authors: Trung Dac Nguyen (Northwestern) ------------------------------------------------------------------------- */ +#include "pair_born_coul_wolf_cs_gpu.h" #include #include #include #include -#include "pair_born_coul_wolf_cs_gpu.h" #include "atom.h" #include "atom_vec.h" #include "comm.h" diff --git a/src/GPU/pair_born_coul_wolf_gpu.cpp b/src/GPU/pair_born_coul_wolf_gpu.cpp index 851174988b..693c2abffb 100644 --- a/src/GPU/pair_born_coul_wolf_gpu.cpp +++ b/src/GPU/pair_born_coul_wolf_gpu.cpp @@ -15,11 +15,11 @@ Contributing authors: Trung Dac Nguyen (ORNL) ------------------------------------------------------------------------- */ +#include "pair_born_coul_wolf_gpu.h" #include #include #include #include -#include "pair_born_coul_wolf_gpu.h" #include "atom.h" #include "atom_vec.h" #include "comm.h" diff --git a/src/GPU/pair_born_gpu.cpp b/src/GPU/pair_born_gpu.cpp index 253d2d7282..e9edc4f1c2 100644 --- a/src/GPU/pair_born_gpu.cpp +++ b/src/GPU/pair_born_gpu.cpp @@ -15,11 +15,11 @@ Contributing author: Trung Dac Nguyen (ORNL) ------------------------------------------------------------------------- */ +#include "pair_born_gpu.h" #include #include #include #include -#include "pair_born_gpu.h" #include "atom.h" #include "atom_vec.h" #include "comm.h" diff --git a/src/GPU/pair_buck_coul_cut_gpu.cpp b/src/GPU/pair_buck_coul_cut_gpu.cpp index ed602f9cab..182673fb0d 100644 --- a/src/GPU/pair_buck_coul_cut_gpu.cpp +++ b/src/GPU/pair_buck_coul_cut_gpu.cpp @@ -15,11 +15,11 @@ Contributing authors: Trung Dac Nguyen (ORNL) ------------------------------------------------------------------------- */ +#include "pair_buck_coul_cut_gpu.h" #include #include #include #include -#include "pair_buck_coul_cut_gpu.h" #include "atom.h" #include "atom_vec.h" #include "comm.h" diff --git a/src/GPU/pair_buck_coul_long_gpu.cpp b/src/GPU/pair_buck_coul_long_gpu.cpp index d6b9e53282..75e784fafa 100644 --- a/src/GPU/pair_buck_coul_long_gpu.cpp +++ b/src/GPU/pair_buck_coul_long_gpu.cpp @@ -15,11 +15,11 @@ Contributing author: Trung Dac Nguyen (ORNL) ------------------------------------------------------------------------- */ +#include "pair_buck_coul_long_gpu.h" #include #include #include #include -#include "pair_buck_coul_long_gpu.h" #include "atom.h" #include "atom_vec.h" #include "comm.h" diff --git a/src/GPU/pair_buck_gpu.cpp b/src/GPU/pair_buck_gpu.cpp index 8c85407e6e..1559c45b88 100644 --- a/src/GPU/pair_buck_gpu.cpp +++ b/src/GPU/pair_buck_gpu.cpp @@ -15,11 +15,11 @@ Contributing author: Trung Dac Nguyen (ORNL) ------------------------------------------------------------------------- */ +#include "pair_buck_gpu.h" #include #include #include #include -#include "pair_buck_gpu.h" #include "atom.h" #include "atom_vec.h" #include "comm.h" diff --git a/src/GPU/pair_colloid_gpu.cpp b/src/GPU/pair_colloid_gpu.cpp index 0ee8708b5b..4db18dbc52 100644 --- a/src/GPU/pair_colloid_gpu.cpp +++ b/src/GPU/pair_colloid_gpu.cpp @@ -15,11 +15,11 @@ Contributing author: Trung Dac Nguyen (ORNL) ------------------------------------------------------------------------- */ +#include "pair_colloid_gpu.h" #include #include #include #include -#include "pair_colloid_gpu.h" #include "atom.h" #include "atom_vec.h" #include "comm.h" diff --git a/src/GPU/pair_coul_cut_gpu.cpp b/src/GPU/pair_coul_cut_gpu.cpp index fb50c446b1..8a3eb12f8d 100644 --- a/src/GPU/pair_coul_cut_gpu.cpp +++ b/src/GPU/pair_coul_cut_gpu.cpp @@ -15,11 +15,11 @@ Contributing author: Trung Dac Nguyen ------------------------------------------------------------------------- */ +#include "pair_coul_cut_gpu.h" #include #include #include #include -#include "pair_coul_cut_gpu.h" #include "atom.h" #include "atom_vec.h" #include "comm.h" diff --git a/src/GPU/pair_coul_debye_gpu.cpp b/src/GPU/pair_coul_debye_gpu.cpp index ec771a9935..1fc07f8dac 100644 --- a/src/GPU/pair_coul_debye_gpu.cpp +++ b/src/GPU/pair_coul_debye_gpu.cpp @@ -15,11 +15,11 @@ Contributing author: Trung Dac Nguyen (ndtrung@umich.edu) ------------------------------------------------------------------------- */ +#include "pair_coul_debye_gpu.h" #include #include #include #include -#include "pair_coul_debye_gpu.h" #include "atom.h" #include "atom_vec.h" #include "comm.h" diff --git a/src/GPU/pair_coul_dsf_gpu.cpp b/src/GPU/pair_coul_dsf_gpu.cpp index 1753b8a91c..408be036dd 100644 --- a/src/GPU/pair_coul_dsf_gpu.cpp +++ b/src/GPU/pair_coul_dsf_gpu.cpp @@ -15,11 +15,11 @@ Contributing author: Trung Dac Nguyen (ORNL) ------------------------------------------------------------------------- */ +#include "pair_coul_dsf_gpu.h" #include #include #include #include -#include "pair_coul_dsf_gpu.h" #include "atom.h" #include "atom_vec.h" #include "comm.h" diff --git a/src/GPU/pair_coul_long_cs_gpu.cpp b/src/GPU/pair_coul_long_cs_gpu.cpp index 6ca00d6361..c70424e472 100644 --- a/src/GPU/pair_coul_long_cs_gpu.cpp +++ b/src/GPU/pair_coul_long_cs_gpu.cpp @@ -15,11 +15,11 @@ Contributing author: Trung Nguyen (Northwestern) ------------------------------------------------------------------------- */ +#include "pair_coul_long_cs_gpu.h" #include #include #include #include -#include "pair_coul_long_cs_gpu.h" #include "atom.h" #include "atom_vec.h" #include "comm.h" diff --git a/src/GPU/pair_coul_long_gpu.cpp b/src/GPU/pair_coul_long_gpu.cpp index f75d10b6dd..9623c25f2f 100644 --- a/src/GPU/pair_coul_long_gpu.cpp +++ b/src/GPU/pair_coul_long_gpu.cpp @@ -15,11 +15,11 @@ Contributing author: Axel Kohlmeyer (Temple) ------------------------------------------------------------------------- */ +#include "pair_coul_long_gpu.h" #include #include #include #include -#include "pair_coul_long_gpu.h" #include "atom.h" #include "atom_vec.h" #include "comm.h" diff --git a/src/GPU/pair_dpd_gpu.cpp b/src/GPU/pair_dpd_gpu.cpp index b1e45fbecd..5fcad6a350 100644 --- a/src/GPU/pair_dpd_gpu.cpp +++ b/src/GPU/pair_dpd_gpu.cpp @@ -15,11 +15,11 @@ Contributing author: Trung Dac Nguyen (ORNL) ------------------------------------------------------------------------- */ +#include "pair_dpd_gpu.h" #include #include #include #include -#include "pair_dpd_gpu.h" #include "atom.h" #include "atom_vec.h" #include "comm.h" diff --git a/src/GPU/pair_dpd_tstat_gpu.cpp b/src/GPU/pair_dpd_tstat_gpu.cpp index 0693a27344..2d6798a12d 100644 --- a/src/GPU/pair_dpd_tstat_gpu.cpp +++ b/src/GPU/pair_dpd_tstat_gpu.cpp @@ -15,11 +15,11 @@ Contributing author: Trung Dac Nguyen (ORNL) ------------------------------------------------------------------------- */ +#include "pair_dpd_tstat_gpu.h" #include #include #include #include -#include "pair_dpd_tstat_gpu.h" #include "atom.h" #include "atom_vec.h" #include "comm.h" diff --git a/src/GPU/pair_eam_alloy_gpu.cpp b/src/GPU/pair_eam_alloy_gpu.cpp index 9b3412d3d1..bc55c66676 100644 --- a/src/GPU/pair_eam_alloy_gpu.cpp +++ b/src/GPU/pair_eam_alloy_gpu.cpp @@ -15,10 +15,10 @@ Contributing authors: Trung Dac Nguyen (ORNL), W. Michael Brown (ORNL) ------------------------------------------------------------------------- */ +#include "pair_eam_alloy_gpu.h" #include #include #include -#include "pair_eam_alloy_gpu.h" #include "atom.h" #include "force.h" #include "comm.h" diff --git a/src/GPU/pair_eam_fs_gpu.cpp b/src/GPU/pair_eam_fs_gpu.cpp index 11ef28af3e..ac379a9ce6 100644 --- a/src/GPU/pair_eam_fs_gpu.cpp +++ b/src/GPU/pair_eam_fs_gpu.cpp @@ -15,10 +15,10 @@ Contributing authors: Trung Dac Nguyen (ORNL), W. Michael Brown (ORNL) ------------------------------------------------------------------------- */ +#include "pair_eam_fs_gpu.h" #include #include #include -#include "pair_eam_fs_gpu.h" #include "atom.h" #include "force.h" #include "comm.h" diff --git a/src/GPU/pair_eam_gpu.cpp b/src/GPU/pair_eam_gpu.cpp index 4788a72417..57106f48a4 100644 --- a/src/GPU/pair_eam_gpu.cpp +++ b/src/GPU/pair_eam_gpu.cpp @@ -15,11 +15,11 @@ Contributing authors: Trung Dac Nguyen (ORNL), W. Michael Brown (ORNL) ------------------------------------------------------------------------- */ +#include "pair_eam_gpu.h" #include #include #include #include -#include "pair_eam_gpu.h" #include "atom.h" #include "force.h" #include "comm.h" diff --git a/src/GPU/pair_gauss_gpu.cpp b/src/GPU/pair_gauss_gpu.cpp index c596a9d644..842b84acf2 100644 --- a/src/GPU/pair_gauss_gpu.cpp +++ b/src/GPU/pair_gauss_gpu.cpp @@ -15,11 +15,11 @@ Contributing author: Trung Dac Nguyen (ORNL) ------------------------------------------------------------------------- */ +#include "pair_gauss_gpu.h" #include #include #include #include -#include "pair_gauss_gpu.h" #include "atom.h" #include "atom_vec.h" #include "comm.h" diff --git a/src/GPU/pair_gayberne_gpu.cpp b/src/GPU/pair_gayberne_gpu.cpp index 4ed2750e57..f00accda15 100644 --- a/src/GPU/pair_gayberne_gpu.cpp +++ b/src/GPU/pair_gayberne_gpu.cpp @@ -15,11 +15,11 @@ Contributing author: Mike Brown (SNL) ------------------------------------------------------------------------- */ +#include "pair_gayberne_gpu.h" #include #include #include #include -#include "pair_gayberne_gpu.h" #include "math_extra.h" #include "atom.h" #include "atom_vec.h" diff --git a/src/GPU/pair_lj96_cut_gpu.cpp b/src/GPU/pair_lj96_cut_gpu.cpp index 5bc30c809d..16b6b835c0 100644 --- a/src/GPU/pair_lj96_cut_gpu.cpp +++ b/src/GPU/pair_lj96_cut_gpu.cpp @@ -15,11 +15,11 @@ Contributing author: Mike Brown (SNL) ------------------------------------------------------------------------- */ +#include "pair_lj96_cut_gpu.h" #include #include #include #include -#include "pair_lj96_cut_gpu.h" #include "atom.h" #include "atom_vec.h" #include "comm.h" diff --git a/src/GPU/pair_lj_charmm_coul_long_gpu.cpp b/src/GPU/pair_lj_charmm_coul_long_gpu.cpp index 134295c69f..bacbb400b1 100644 --- a/src/GPU/pair_lj_charmm_coul_long_gpu.cpp +++ b/src/GPU/pair_lj_charmm_coul_long_gpu.cpp @@ -15,11 +15,11 @@ Contributing author: Mike Brown (SNL) ------------------------------------------------------------------------- */ +#include "pair_lj_charmm_coul_long_gpu.h" #include #include #include #include -#include "pair_lj_charmm_coul_long_gpu.h" #include "atom.h" #include "atom_vec.h" #include "comm.h" diff --git a/src/GPU/pair_lj_class2_coul_long_gpu.cpp b/src/GPU/pair_lj_class2_coul_long_gpu.cpp index fdffb06a8d..e34dbb0f99 100644 --- a/src/GPU/pair_lj_class2_coul_long_gpu.cpp +++ b/src/GPU/pair_lj_class2_coul_long_gpu.cpp @@ -15,11 +15,11 @@ Contributing author: Mike Brown (SNL) ------------------------------------------------------------------------- */ +#include "pair_lj_class2_coul_long_gpu.h" #include #include #include #include -#include "pair_lj_class2_coul_long_gpu.h" #include "atom.h" #include "atom_vec.h" #include "comm.h" diff --git a/src/GPU/pair_lj_class2_gpu.cpp b/src/GPU/pair_lj_class2_gpu.cpp index bbb9168169..68f27598f3 100644 --- a/src/GPU/pair_lj_class2_gpu.cpp +++ b/src/GPU/pair_lj_class2_gpu.cpp @@ -15,11 +15,11 @@ Contributing author: Mike Brown (SNL) ------------------------------------------------------------------------- */ +#include "pair_lj_class2_gpu.h" #include #include #include #include -#include "pair_lj_class2_gpu.h" #include "atom.h" #include "atom_vec.h" #include "comm.h" diff --git a/src/GPU/pair_lj_cubic_gpu.cpp b/src/GPU/pair_lj_cubic_gpu.cpp index 95eee6ae8f..542de37840 100644 --- a/src/GPU/pair_lj_cubic_gpu.cpp +++ b/src/GPU/pair_lj_cubic_gpu.cpp @@ -15,11 +15,11 @@ Contributing author: Trung Dac Nguyen (ndactrung@gmail.com) ------------------------------------------------------------------------- */ +#include "pair_lj_cubic_gpu.h" #include #include #include #include -#include "pair_lj_cubic_gpu.h" #include "atom.h" #include "atom_vec.h" #include "comm.h" diff --git a/src/GPU/pair_lj_cut_coul_cut_gpu.cpp b/src/GPU/pair_lj_cut_coul_cut_gpu.cpp index 69fefbcdea..cf3dd711dc 100644 --- a/src/GPU/pair_lj_cut_coul_cut_gpu.cpp +++ b/src/GPU/pair_lj_cut_coul_cut_gpu.cpp @@ -15,11 +15,11 @@ Contributing author: Mike Brown (SNL) ------------------------------------------------------------------------- */ +#include "pair_lj_cut_coul_cut_gpu.h" #include #include #include #include -#include "pair_lj_cut_coul_cut_gpu.h" #include "atom.h" #include "atom_vec.h" #include "comm.h" diff --git a/src/GPU/pair_lj_cut_coul_debye_gpu.cpp b/src/GPU/pair_lj_cut_coul_debye_gpu.cpp index de86c58647..20354e732c 100644 --- a/src/GPU/pair_lj_cut_coul_debye_gpu.cpp +++ b/src/GPU/pair_lj_cut_coul_debye_gpu.cpp @@ -15,11 +15,11 @@ Contributing author: Trung Dac Nguyen (ORNL) ------------------------------------------------------------------------- */ +#include "pair_lj_cut_coul_debye_gpu.h" #include #include #include #include -#include "pair_lj_cut_coul_debye_gpu.h" #include "atom.h" #include "atom_vec.h" #include "comm.h" diff --git a/src/GPU/pair_lj_cut_coul_dsf_gpu.cpp b/src/GPU/pair_lj_cut_coul_dsf_gpu.cpp index 87eac52749..ccaf86efa6 100644 --- a/src/GPU/pair_lj_cut_coul_dsf_gpu.cpp +++ b/src/GPU/pair_lj_cut_coul_dsf_gpu.cpp @@ -15,11 +15,11 @@ Contributing author: Mike Brown (SNL) ------------------------------------------------------------------------- */ +#include "pair_lj_cut_coul_dsf_gpu.h" #include #include #include #include -#include "pair_lj_cut_coul_dsf_gpu.h" #include "atom.h" #include "atom_vec.h" #include "comm.h" diff --git a/src/GPU/pair_lj_cut_coul_long_gpu.cpp b/src/GPU/pair_lj_cut_coul_long_gpu.cpp index c854dab83d..36c72f1143 100644 --- a/src/GPU/pair_lj_cut_coul_long_gpu.cpp +++ b/src/GPU/pair_lj_cut_coul_long_gpu.cpp @@ -15,11 +15,11 @@ Contributing author: Mike Brown (SNL) ------------------------------------------------------------------------- */ +#include "pair_lj_cut_coul_long_gpu.h" #include #include #include #include -#include "pair_lj_cut_coul_long_gpu.h" #include "atom.h" #include "atom_vec.h" #include "comm.h" diff --git a/src/GPU/pair_lj_cut_coul_msm_gpu.cpp b/src/GPU/pair_lj_cut_coul_msm_gpu.cpp index f87dc0ec91..79ca90698a 100644 --- a/src/GPU/pair_lj_cut_coul_msm_gpu.cpp +++ b/src/GPU/pair_lj_cut_coul_msm_gpu.cpp @@ -15,11 +15,11 @@ Contributing author: Trung Dac Nguyen (ORNL) ------------------------------------------------------------------------- */ +#include "pair_lj_cut_coul_msm_gpu.h" #include #include #include #include -#include "pair_lj_cut_coul_msm_gpu.h" #include "atom.h" #include "atom_vec.h" #include "comm.h" diff --git a/src/GPU/pair_lj_cut_dipole_cut_gpu.cpp b/src/GPU/pair_lj_cut_dipole_cut_gpu.cpp index d2c925d950..e2c8b8d686 100644 --- a/src/GPU/pair_lj_cut_dipole_cut_gpu.cpp +++ b/src/GPU/pair_lj_cut_dipole_cut_gpu.cpp @@ -15,11 +15,11 @@ Contributing author: Trung Dac Nguyen (ORNL) ------------------------------------------------------------------------- */ +#include "pair_lj_cut_dipole_cut_gpu.h" #include #include #include #include -#include "pair_lj_cut_dipole_cut_gpu.h" #include "atom.h" #include "atom_vec.h" #include "comm.h" diff --git a/src/GPU/pair_lj_cut_dipole_long_gpu.cpp b/src/GPU/pair_lj_cut_dipole_long_gpu.cpp index 774ff2fae4..fb76376d34 100644 --- a/src/GPU/pair_lj_cut_dipole_long_gpu.cpp +++ b/src/GPU/pair_lj_cut_dipole_long_gpu.cpp @@ -15,11 +15,11 @@ Contributing author: Trung Dac Nguyen (Northwestern) ------------------------------------------------------------------------- */ +#include "pair_lj_cut_dipole_long_gpu.h" #include #include #include #include -#include "pair_lj_cut_dipole_long_gpu.h" #include "atom.h" #include "atom_vec.h" #include "comm.h" diff --git a/src/GPU/pair_lj_cut_gpu.cpp b/src/GPU/pair_lj_cut_gpu.cpp index 6dde9689f7..809e5cf05e 100644 --- a/src/GPU/pair_lj_cut_gpu.cpp +++ b/src/GPU/pair_lj_cut_gpu.cpp @@ -15,11 +15,11 @@ Contributing author: Mike Brown (SNL) ------------------------------------------------------------------------- */ +#include "pair_lj_cut_gpu.h" #include #include #include #include -#include "pair_lj_cut_gpu.h" #include "atom.h" #include "atom_vec.h" #include "comm.h" diff --git a/src/GPU/pair_lj_expand_coul_long_gpu.cpp b/src/GPU/pair_lj_expand_coul_long_gpu.cpp index 31f4fd651c..a530f7ff9a 100644 --- a/src/GPU/pair_lj_expand_coul_long_gpu.cpp +++ b/src/GPU/pair_lj_expand_coul_long_gpu.cpp @@ -15,11 +15,11 @@ Contributing author: Trung Nguyen (Northwestern) ------------------------------------------------------------------------- */ +#include "pair_lj_expand_coul_long_gpu.h" #include #include #include #include -#include "pair_lj_expand_coul_long_gpu.h" #include "atom.h" #include "atom_vec.h" #include "comm.h" diff --git a/src/GPU/pair_lj_expand_gpu.cpp b/src/GPU/pair_lj_expand_gpu.cpp index a2e1cf54e3..86f8a76b52 100644 --- a/src/GPU/pair_lj_expand_gpu.cpp +++ b/src/GPU/pair_lj_expand_gpu.cpp @@ -15,11 +15,11 @@ Contributing author: Inderaj Bains (NVIDIA), ibains@nvidia.com ------------------------------------------------------------------------- */ +#include "pair_lj_expand_gpu.h" #include #include #include #include -#include "pair_lj_expand_gpu.h" #include "atom.h" #include "atom_vec.h" #include "comm.h" diff --git a/src/GPU/pair_lj_gromacs_gpu.cpp b/src/GPU/pair_lj_gromacs_gpu.cpp index e03f4b2e50..78f8b8b461 100644 --- a/src/GPU/pair_lj_gromacs_gpu.cpp +++ b/src/GPU/pair_lj_gromacs_gpu.cpp @@ -15,11 +15,11 @@ Contributing author: Trung Dac Nguyen (ORNL) ------------------------------------------------------------------------- */ +#include "pair_lj_gromacs_gpu.h" #include #include #include #include -#include "pair_lj_gromacs_gpu.h" #include "atom.h" #include "atom_vec.h" #include "comm.h" diff --git a/src/GPU/pair_lj_sdk_coul_long_gpu.cpp b/src/GPU/pair_lj_sdk_coul_long_gpu.cpp index f5029df5dc..24ff8a4f28 100644 --- a/src/GPU/pair_lj_sdk_coul_long_gpu.cpp +++ b/src/GPU/pair_lj_sdk_coul_long_gpu.cpp @@ -15,11 +15,11 @@ Contributing author: Mike Brown (SNL) ------------------------------------------------------------------------- */ +#include "pair_lj_sdk_coul_long_gpu.h" #include #include #include #include -#include "pair_lj_sdk_coul_long_gpu.h" #include "atom.h" #include "atom_vec.h" #include "comm.h" diff --git a/src/GPU/pair_lj_sdk_gpu.cpp b/src/GPU/pair_lj_sdk_gpu.cpp index 4797a34408..2621f49aeb 100644 --- a/src/GPU/pair_lj_sdk_gpu.cpp +++ b/src/GPU/pair_lj_sdk_gpu.cpp @@ -15,11 +15,11 @@ Contributing author: Mike Brown (SNL) ------------------------------------------------------------------------- */ +#include "pair_lj_sdk_gpu.h" #include #include #include #include -#include "pair_lj_sdk_gpu.h" #include "atom.h" #include "atom_vec.h" #include "comm.h" diff --git a/src/GPU/pair_lj_sf_dipole_sf_gpu.cpp b/src/GPU/pair_lj_sf_dipole_sf_gpu.cpp index dd25a70eee..cf26cdf3b4 100644 --- a/src/GPU/pair_lj_sf_dipole_sf_gpu.cpp +++ b/src/GPU/pair_lj_sf_dipole_sf_gpu.cpp @@ -15,11 +15,11 @@ Contributing author: Trung Dac Nguyen (ORNL) ------------------------------------------------------------------------- */ +#include "pair_lj_sf_dipole_sf_gpu.h" #include #include #include #include -#include "pair_lj_sf_dipole_sf_gpu.h" #include "atom.h" #include "atom_vec.h" #include "comm.h" diff --git a/src/GPU/pair_mie_cut_gpu.cpp b/src/GPU/pair_mie_cut_gpu.cpp index 838d28033f..f3a384113f 100644 --- a/src/GPU/pair_mie_cut_gpu.cpp +++ b/src/GPU/pair_mie_cut_gpu.cpp @@ -15,11 +15,11 @@ Contributing author: Trung Dac Nguyen (ORNL) ------------------------------------------------------------------------- */ +#include "pair_mie_cut_gpu.h" #include #include #include #include -#include "pair_mie_cut_gpu.h" #include "atom.h" #include "atom_vec.h" #include "comm.h" diff --git a/src/GPU/pair_morse_gpu.cpp b/src/GPU/pair_morse_gpu.cpp index 1f94643e3a..dcad227045 100644 --- a/src/GPU/pair_morse_gpu.cpp +++ b/src/GPU/pair_morse_gpu.cpp @@ -15,11 +15,11 @@ Contributing author: Mike Brown (SNL) ------------------------------------------------------------------------- */ +#include "pair_morse_gpu.h" #include #include #include #include -#include "pair_morse_gpu.h" #include "atom.h" #include "atom_vec.h" #include "comm.h" diff --git a/src/GPU/pair_resquared_gpu.cpp b/src/GPU/pair_resquared_gpu.cpp index 5e90f788bf..b12a790c81 100644 --- a/src/GPU/pair_resquared_gpu.cpp +++ b/src/GPU/pair_resquared_gpu.cpp @@ -15,11 +15,11 @@ Contributing author: Mike Brown (SNL) ------------------------------------------------------------------------- */ +#include "pair_resquared_gpu.h" #include #include #include #include -#include "pair_resquared_gpu.h" #include "math_extra.h" #include "atom.h" #include "atom_vec.h" diff --git a/src/GPU/pair_soft_gpu.cpp b/src/GPU/pair_soft_gpu.cpp index 42adb02553..0efcb20c8d 100644 --- a/src/GPU/pair_soft_gpu.cpp +++ b/src/GPU/pair_soft_gpu.cpp @@ -15,11 +15,11 @@ Contributing author: Trung Dac Nguyen (ORNL) ------------------------------------------------------------------------- */ +#include "pair_soft_gpu.h" #include #include #include #include -#include "pair_soft_gpu.h" #include "atom.h" #include "atom_vec.h" #include "comm.h" diff --git a/src/GPU/pair_sw_gpu.cpp b/src/GPU/pair_sw_gpu.cpp index 0cc858e57d..8999cb6c47 100644 --- a/src/GPU/pair_sw_gpu.cpp +++ b/src/GPU/pair_sw_gpu.cpp @@ -15,11 +15,11 @@ Contributing author: Mike Brown (ORNL) ------------------------------------------------------------------------- */ +#include "pair_sw_gpu.h" #include #include #include #include -#include "pair_sw_gpu.h" #include "atom.h" #include "neighbor.h" #include "neigh_request.h" diff --git a/src/GPU/pair_table_gpu.cpp b/src/GPU/pair_table_gpu.cpp index a0b6562e5e..4432265874 100644 --- a/src/GPU/pair_table_gpu.cpp +++ b/src/GPU/pair_table_gpu.cpp @@ -15,11 +15,11 @@ Contributing authors: Trung Dac Nguyen (ORNL) ------------------------------------------------------------------------- */ +#include "pair_table_gpu.h" #include #include #include #include -#include "pair_table_gpu.h" #include "atom.h" #include "atom_vec.h" #include "comm.h" diff --git a/src/GPU/pair_tersoff_gpu.cpp b/src/GPU/pair_tersoff_gpu.cpp index cd0c5e6693..e0dc021b57 100644 --- a/src/GPU/pair_tersoff_gpu.cpp +++ b/src/GPU/pair_tersoff_gpu.cpp @@ -15,11 +15,11 @@ Contributing author: Trung Dac Nguyen (ndactrung@gmail.com) ------------------------------------------------------------------------- */ +#include "pair_tersoff_gpu.h" #include #include #include #include -#include "pair_tersoff_gpu.h" #include "atom.h" #include "neighbor.h" #include "neigh_request.h" diff --git a/src/GPU/pair_tersoff_mod_gpu.cpp b/src/GPU/pair_tersoff_mod_gpu.cpp index fd55ddc6e6..a17efb55e8 100644 --- a/src/GPU/pair_tersoff_mod_gpu.cpp +++ b/src/GPU/pair_tersoff_mod_gpu.cpp @@ -15,11 +15,11 @@ Contributing author: Trung Dac Nguyen (ndactrung@gmail.com) ------------------------------------------------------------------------- */ +#include "pair_tersoff_mod_gpu.h" #include #include #include #include -#include "pair_tersoff_mod_gpu.h" #include "atom.h" #include "neighbor.h" #include "neigh_request.h" diff --git a/src/GPU/pair_tersoff_zbl_gpu.cpp b/src/GPU/pair_tersoff_zbl_gpu.cpp index d3828962e2..765d25f8e6 100644 --- a/src/GPU/pair_tersoff_zbl_gpu.cpp +++ b/src/GPU/pair_tersoff_zbl_gpu.cpp @@ -15,11 +15,11 @@ Contributing author: Trung Dac Nguyen (ndactrung@gmail.com) ------------------------------------------------------------------------- */ +#include "pair_tersoff_zbl_gpu.h" #include #include #include #include -#include "pair_tersoff_zbl_gpu.h" #include "atom.h" #include "neighbor.h" #include "neigh_request.h" diff --git a/src/GPU/pair_ufm_gpu.cpp b/src/GPU/pair_ufm_gpu.cpp index 31422b0f4d..97c2eebf24 100644 --- a/src/GPU/pair_ufm_gpu.cpp +++ b/src/GPU/pair_ufm_gpu.cpp @@ -17,11 +17,11 @@ Maurice de Koning (Unicamp/Brazil) - dekoning@ifi.unicamp.br ------------------------------------------------------------------------- */ +#include "pair_ufm_gpu.h" #include #include #include #include -#include "pair_ufm_gpu.h" #include "atom.h" #include "atom_vec.h" #include "comm.h" diff --git a/src/GPU/pair_vashishta_gpu.cpp b/src/GPU/pair_vashishta_gpu.cpp index 5539653756..3b74e5685e 100644 --- a/src/GPU/pair_vashishta_gpu.cpp +++ b/src/GPU/pair_vashishta_gpu.cpp @@ -14,11 +14,12 @@ /* ---------------------------------------------------------------------- Contributing author: Anders Hafreager (UiO) ------------------------------------------------------------------------- */ + +#include "pair_vashishta_gpu.h" #include #include #include #include -#include "pair_vashishta_gpu.h" #include "atom.h" #include "neighbor.h" #include "neigh_request.h" diff --git a/src/GPU/pair_yukawa_colloid_gpu.cpp b/src/GPU/pair_yukawa_colloid_gpu.cpp index 3645f392a2..51c7e683db 100644 --- a/src/GPU/pair_yukawa_colloid_gpu.cpp +++ b/src/GPU/pair_yukawa_colloid_gpu.cpp @@ -15,11 +15,11 @@ Contributing author: Trung Dac Nguyen (ORNL) ------------------------------------------------------------------------- */ +#include "pair_yukawa_colloid_gpu.h" #include #include #include #include -#include "pair_yukawa_colloid_gpu.h" #include "atom.h" #include "atom_vec.h" #include "comm.h" diff --git a/src/GPU/pair_yukawa_gpu.cpp b/src/GPU/pair_yukawa_gpu.cpp index 90317fea34..5dc13c7750 100644 --- a/src/GPU/pair_yukawa_gpu.cpp +++ b/src/GPU/pair_yukawa_gpu.cpp @@ -15,11 +15,11 @@ Contributing author: Trung Dac Nguyen (ORNL) ------------------------------------------------------------------------- */ +#include "pair_yukawa_gpu.h" #include #include #include #include -#include "pair_yukawa_gpu.h" #include "atom.h" #include "atom_vec.h" #include "comm.h" diff --git a/src/GPU/pair_zbl_gpu.cpp b/src/GPU/pair_zbl_gpu.cpp index 99471cbe90..5e24281145 100644 --- a/src/GPU/pair_zbl_gpu.cpp +++ b/src/GPU/pair_zbl_gpu.cpp @@ -15,12 +15,12 @@ Contributing author: Trung Dac Nguyen (ORNL) ------------------------------------------------------------------------- */ +#include "pair_zbl_gpu.h" #include "lmptype.h" #include #include #include #include -#include "pair_zbl_gpu.h" #include "atom.h" #include "atom_vec.h" #include "comm.h" diff --git a/src/GPU/pppm_gpu.cpp b/src/GPU/pppm_gpu.cpp index 1bb1a39703..bbb270ff8e 100644 --- a/src/GPU/pppm_gpu.cpp +++ b/src/GPU/pppm_gpu.cpp @@ -15,12 +15,12 @@ Contributing authors: Mike Brown (ORNL), Axel Kohlmeyer (Temple) ------------------------------------------------------------------------- */ +#include "pppm_gpu.h" #include #include #include #include #include -#include "pppm_gpu.h" #include "atom.h" #include "comm.h" #include "gridcomm.h" diff --git a/src/GRANULAR/fix_freeze.cpp b/src/GRANULAR/fix_freeze.cpp index 73c1c9fc11..e2345bdf19 100644 --- a/src/GRANULAR/fix_freeze.cpp +++ b/src/GRANULAR/fix_freeze.cpp @@ -11,8 +11,8 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include #include "fix_freeze.h" +#include #include "atom.h" #include "update.h" #include "modify.h" diff --git a/src/GRANULAR/fix_pour.cpp b/src/GRANULAR/fix_pour.cpp index 3ffca8db9d..0fe7493127 100644 --- a/src/GRANULAR/fix_pour.cpp +++ b/src/GRANULAR/fix_pour.cpp @@ -11,10 +11,10 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ +#include "fix_pour.h" #include #include #include -#include "fix_pour.h" #include "atom.h" #include "atom_vec.h" #include "force.h" diff --git a/src/GRANULAR/fix_wall_gran.cpp b/src/GRANULAR/fix_wall_gran.cpp index 8513fc702b..b0fbc0c2b8 100644 --- a/src/GRANULAR/fix_wall_gran.cpp +++ b/src/GRANULAR/fix_wall_gran.cpp @@ -16,10 +16,10 @@ Dan Bolintineanu (SNL) ------------------------------------------------------------------------- */ +#include "fix_wall_gran.h" #include #include #include -#include "fix_wall_gran.h" #include "atom.h" #include "domain.h" #include "update.h" diff --git a/src/GRANULAR/fix_wall_gran_region.cpp b/src/GRANULAR/fix_wall_gran_region.cpp index 72798bf7b7..97e889ddcc 100644 --- a/src/GRANULAR/fix_wall_gran_region.cpp +++ b/src/GRANULAR/fix_wall_gran_region.cpp @@ -15,10 +15,10 @@ Contributing authors: Dan Bolintineanu (SNL) ------------------------------------------------------------------------- */ +#include "fix_wall_gran_region.h" #include #include #include -#include "fix_wall_gran_region.h" #include "region.h" #include "atom.h" #include "domain.h" diff --git a/src/GRANULAR/pair_gran_hertz_history.cpp b/src/GRANULAR/pair_gran_hertz_history.cpp index 728491c17a..e303089e56 100644 --- a/src/GRANULAR/pair_gran_hertz_history.cpp +++ b/src/GRANULAR/pair_gran_hertz_history.cpp @@ -15,11 +15,11 @@ Contributing authors: Leo Silbert (SNL), Gary Grest (SNL) ------------------------------------------------------------------------- */ +#include "pair_gran_hertz_history.h" #include #include #include #include -#include "pair_gran_hertz_history.h" #include "atom.h" #include "update.h" #include "force.h" diff --git a/src/GRANULAR/pair_gran_hooke.cpp b/src/GRANULAR/pair_gran_hooke.cpp index cfcc2743ba..a30aa0bb6c 100644 --- a/src/GRANULAR/pair_gran_hooke.cpp +++ b/src/GRANULAR/pair_gran_hooke.cpp @@ -15,10 +15,10 @@ Contributing authors: Leo Silbert (SNL), Gary Grest (SNL) ------------------------------------------------------------------------- */ +#include "pair_gran_hooke.h" #include #include #include -#include "pair_gran_hooke.h" #include "atom.h" #include "force.h" #include "fix.h" diff --git a/src/GRANULAR/pair_gran_hooke_history.cpp b/src/GRANULAR/pair_gran_hooke_history.cpp index 5a78b9d79a..f832fdfac3 100644 --- a/src/GRANULAR/pair_gran_hooke_history.cpp +++ b/src/GRANULAR/pair_gran_hooke_history.cpp @@ -15,11 +15,11 @@ Contributing authors: Leo Silbert (SNL), Gary Grest (SNL) ------------------------------------------------------------------------- */ +#include "pair_gran_hooke_history.h" #include #include #include #include -#include "pair_gran_hooke_history.h" #include "atom.h" #include "atom_vec.h" #include "domain.h" diff --git a/src/GRANULAR/pair_granular.cpp b/src/GRANULAR/pair_granular.cpp index 903ed303b0..942587a676 100644 --- a/src/GRANULAR/pair_granular.cpp +++ b/src/GRANULAR/pair_granular.cpp @@ -16,11 +16,11 @@ See the README file in the top-level LAMMPS directory. Leo Silbert (SNL), Gary Grest (SNL) ----------------------------------------------------------------------- */ +#include "pair_granular.h" #include #include #include #include -#include "pair_granular.h" #include "atom.h" #include "atom_vec.h" #include "domain.h" diff --git a/src/KIM/kim_query.cpp b/src/KIM/kim_query.cpp index fedc976110..dce9c8761a 100644 --- a/src/KIM/kim_query.cpp +++ b/src/KIM/kim_query.cpp @@ -55,10 +55,10 @@ Designed for use with the kim-api-2.0.2 (and newer) package ------------------------------------------------------------------------- */ +#include "kim_query.h" #include #include #include -#include "kim_query.h" #include "comm.h" #include "error.h" #include "input.h" diff --git a/src/KIM/pair_kim.cpp b/src/KIM/pair_kim.cpp index a1c13ae81f..e107e4276f 100644 --- a/src/KIM/pair_kim.cpp +++ b/src/KIM/pair_kim.cpp @@ -53,11 +53,9 @@ Designed for use with the kim-api-2.0.2 (and newer) package ------------------------------------------------------------------------- */ +#include "pair_kim.h" #include #include - -// includes from LAMMPS -#include "pair_kim.h" #include "atom.h" #include "comm.h" #include "force.h" diff --git a/src/KOKKOS/angle_charmm_kokkos.cpp b/src/KOKKOS/angle_charmm_kokkos.cpp index 0f46c958d6..fd9757aab3 100644 --- a/src/KOKKOS/angle_charmm_kokkos.cpp +++ b/src/KOKKOS/angle_charmm_kokkos.cpp @@ -15,9 +15,9 @@ Contributing author: Stan Moore (SNL) ------------------------------------------------------------------------- */ +#include "angle_charmm_kokkos.h" #include #include -#include "angle_charmm_kokkos.h" #include "atom_kokkos.h" #include "neighbor_kokkos.h" #include "domain.h" diff --git a/src/KOKKOS/angle_class2_kokkos.cpp b/src/KOKKOS/angle_class2_kokkos.cpp index 836714764d..809ce7e7dd 100644 --- a/src/KOKKOS/angle_class2_kokkos.cpp +++ b/src/KOKKOS/angle_class2_kokkos.cpp @@ -15,9 +15,9 @@ Contributing author: Ray Shan (Materials Design) ------------------------------------------------------------------------- */ +#include "angle_class2_kokkos.h" #include #include -#include "angle_class2_kokkos.h" #include "atom_kokkos.h" #include "neighbor_kokkos.h" #include "domain.h" diff --git a/src/KOKKOS/angle_cosine_kokkos.cpp b/src/KOKKOS/angle_cosine_kokkos.cpp index 4a4866948f..da0ff398f1 100644 --- a/src/KOKKOS/angle_cosine_kokkos.cpp +++ b/src/KOKKOS/angle_cosine_kokkos.cpp @@ -15,9 +15,9 @@ Contributing author: Stan Moore (SNL) ------------------------------------------------------------------------- */ +#include "angle_cosine_kokkos.h" #include #include -#include "angle_cosine_kokkos.h" #include "atom_kokkos.h" #include "neighbor_kokkos.h" #include "domain.h" diff --git a/src/KOKKOS/angle_harmonic_kokkos.cpp b/src/KOKKOS/angle_harmonic_kokkos.cpp index dbe705800c..fc274bb894 100644 --- a/src/KOKKOS/angle_harmonic_kokkos.cpp +++ b/src/KOKKOS/angle_harmonic_kokkos.cpp @@ -15,9 +15,9 @@ Contributing author: Stan Moore (SNL) ------------------------------------------------------------------------- */ +#include "angle_harmonic_kokkos.h" #include #include -#include "angle_harmonic_kokkos.h" #include "atom_kokkos.h" #include "neighbor_kokkos.h" #include "domain.h" diff --git a/src/KOKKOS/atom_kokkos.cpp b/src/KOKKOS/atom_kokkos.cpp index 813c5ddbf2..4637a9a21c 100644 --- a/src/KOKKOS/atom_kokkos.cpp +++ b/src/KOKKOS/atom_kokkos.cpp @@ -11,8 +11,8 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include #include "atom_kokkos.h" +#include #include "atom_vec.h" #include "atom_vec_kokkos.h" #include "comm_kokkos.h" diff --git a/src/KOKKOS/atom_vec_angle_kokkos.cpp b/src/KOKKOS/atom_vec_angle_kokkos.cpp index e4f27e733a..3e66d813cf 100644 --- a/src/KOKKOS/atom_vec_angle_kokkos.cpp +++ b/src/KOKKOS/atom_vec_angle_kokkos.cpp @@ -11,8 +11,8 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include #include "atom_vec_angle_kokkos.h" +#include #include "atom_kokkos.h" #include "comm_kokkos.h" #include "domain.h" diff --git a/src/KOKKOS/atom_vec_atomic_kokkos.cpp b/src/KOKKOS/atom_vec_atomic_kokkos.cpp index 95e4ddd72b..27aaa96b6d 100644 --- a/src/KOKKOS/atom_vec_atomic_kokkos.cpp +++ b/src/KOKKOS/atom_vec_atomic_kokkos.cpp @@ -11,8 +11,8 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include #include "atom_vec_atomic_kokkos.h" +#include #include "atom_kokkos.h" #include "comm_kokkos.h" #include "domain.h" diff --git a/src/KOKKOS/atom_vec_bond_kokkos.cpp b/src/KOKKOS/atom_vec_bond_kokkos.cpp index 92311d5d09..ad6d5bd486 100644 --- a/src/KOKKOS/atom_vec_bond_kokkos.cpp +++ b/src/KOKKOS/atom_vec_bond_kokkos.cpp @@ -11,8 +11,8 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include #include "atom_vec_bond_kokkos.h" +#include #include "atom_kokkos.h" #include "comm_kokkos.h" #include "domain.h" diff --git a/src/KOKKOS/atom_vec_charge_kokkos.cpp b/src/KOKKOS/atom_vec_charge_kokkos.cpp index 31a690f521..507e8170c5 100644 --- a/src/KOKKOS/atom_vec_charge_kokkos.cpp +++ b/src/KOKKOS/atom_vec_charge_kokkos.cpp @@ -11,8 +11,8 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include #include "atom_vec_charge_kokkos.h" +#include #include "atom_kokkos.h" #include "comm_kokkos.h" #include "domain.h" diff --git a/src/KOKKOS/atom_vec_dpd_kokkos.cpp b/src/KOKKOS/atom_vec_dpd_kokkos.cpp index 4034efee9e..db857909bf 100644 --- a/src/KOKKOS/atom_vec_dpd_kokkos.cpp +++ b/src/KOKKOS/atom_vec_dpd_kokkos.cpp @@ -11,8 +11,8 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include #include "atom_vec_dpd_kokkos.h" +#include #include "atom_kokkos.h" #include "comm_kokkos.h" #include "domain.h" diff --git a/src/KOKKOS/atom_vec_full_kokkos.cpp b/src/KOKKOS/atom_vec_full_kokkos.cpp index 034da88f73..486c4e4c4e 100644 --- a/src/KOKKOS/atom_vec_full_kokkos.cpp +++ b/src/KOKKOS/atom_vec_full_kokkos.cpp @@ -11,8 +11,8 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include #include "atom_vec_full_kokkos.h" +#include #include "atom_kokkos.h" #include "comm_kokkos.h" #include "domain.h" diff --git a/src/KOKKOS/atom_vec_hybrid_kokkos.cpp b/src/KOKKOS/atom_vec_hybrid_kokkos.cpp index 03cbe1ee5e..39d88a0f38 100644 --- a/src/KOKKOS/atom_vec_hybrid_kokkos.cpp +++ b/src/KOKKOS/atom_vec_hybrid_kokkos.cpp @@ -11,9 +11,9 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ +#include "atom_vec_hybrid_kokkos.h" #include #include -#include "atom_vec_hybrid_kokkos.h" #include "atom_kokkos.h" #include "domain.h" #include "modify.h" diff --git a/src/KOKKOS/atom_vec_molecular_kokkos.cpp b/src/KOKKOS/atom_vec_molecular_kokkos.cpp index 9ac8ecd264..49bc7bf3c0 100644 --- a/src/KOKKOS/atom_vec_molecular_kokkos.cpp +++ b/src/KOKKOS/atom_vec_molecular_kokkos.cpp @@ -11,8 +11,8 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include #include "atom_vec_molecular_kokkos.h" +#include #include "atom_kokkos.h" #include "comm_kokkos.h" #include "domain.h" diff --git a/src/KOKKOS/atom_vec_sphere_kokkos.cpp b/src/KOKKOS/atom_vec_sphere_kokkos.cpp index 9e8388488f..b2abbfe8c4 100644 --- a/src/KOKKOS/atom_vec_sphere_kokkos.cpp +++ b/src/KOKKOS/atom_vec_sphere_kokkos.cpp @@ -11,10 +11,10 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ +#include "atom_vec_sphere_kokkos.h" #include #include #include -#include "atom_vec_sphere_kokkos.h" #include "atom_kokkos.h" #include "atom_masks.h" #include "comm_kokkos.h" diff --git a/src/KOKKOS/bond_class2_kokkos.cpp b/src/KOKKOS/bond_class2_kokkos.cpp index 798fb41c92..04281bfdd2 100644 --- a/src/KOKKOS/bond_class2_kokkos.cpp +++ b/src/KOKKOS/bond_class2_kokkos.cpp @@ -15,9 +15,9 @@ Contributing author: Ray Shan (Materials Design) ------------------------------------------------------------------------- */ +#include "bond_class2_kokkos.h" #include #include -#include "bond_class2_kokkos.h" #include "atom_kokkos.h" #include "neighbor_kokkos.h" #include "domain.h" diff --git a/src/KOKKOS/bond_fene_kokkos.cpp b/src/KOKKOS/bond_fene_kokkos.cpp index b5cdc1a05a..361bb61f7e 100644 --- a/src/KOKKOS/bond_fene_kokkos.cpp +++ b/src/KOKKOS/bond_fene_kokkos.cpp @@ -15,9 +15,9 @@ Contributing author: Stan Moore (SNL) ------------------------------------------------------------------------- */ +#include "bond_fene_kokkos.h" #include #include -#include "bond_fene_kokkos.h" #include "atom_kokkos.h" #include "neighbor_kokkos.h" #include "domain.h" diff --git a/src/KOKKOS/bond_harmonic_kokkos.cpp b/src/KOKKOS/bond_harmonic_kokkos.cpp index 51a9fa4389..792d98fe88 100644 --- a/src/KOKKOS/bond_harmonic_kokkos.cpp +++ b/src/KOKKOS/bond_harmonic_kokkos.cpp @@ -15,9 +15,9 @@ Contributing author: Stan Moore (SNL) ------------------------------------------------------------------------- */ +#include "bond_harmonic_kokkos.h" #include #include -#include "bond_harmonic_kokkos.h" #include "atom_kokkos.h" #include "neighbor_kokkos.h" #include "domain.h" diff --git a/src/KOKKOS/comm_tiled_kokkos.cpp b/src/KOKKOS/comm_tiled_kokkos.cpp index 81cf1f0563..fc6de0a0d7 100644 --- a/src/KOKKOS/comm_tiled_kokkos.cpp +++ b/src/KOKKOS/comm_tiled_kokkos.cpp @@ -11,8 +11,8 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include #include "comm_tiled_kokkos.h" +#include #include "comm_brick.h" #include "atom_kokkos.h" #include "atom_vec.h" diff --git a/src/KOKKOS/compute_temp_kokkos.cpp b/src/KOKKOS/compute_temp_kokkos.cpp index 7b76f54f57..a2fcf63125 100644 --- a/src/KOKKOS/compute_temp_kokkos.cpp +++ b/src/KOKKOS/compute_temp_kokkos.cpp @@ -11,9 +11,9 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ +#include "compute_temp_kokkos.h" #include #include -#include "compute_temp_kokkos.h" #include "atom_kokkos.h" #include "update.h" #include "force.h" diff --git a/src/KOKKOS/dihedral_charmm_kokkos.cpp b/src/KOKKOS/dihedral_charmm_kokkos.cpp index 61ddcc425a..94fd0b9bb7 100644 --- a/src/KOKKOS/dihedral_charmm_kokkos.cpp +++ b/src/KOKKOS/dihedral_charmm_kokkos.cpp @@ -15,9 +15,9 @@ Contributing author: Stan Moore (SNL) ------------------------------------------------------------------------- */ +#include "dihedral_charmm_kokkos.h" #include #include -#include "dihedral_charmm_kokkos.h" #include "atom_kokkos.h" #include "comm.h" #include "neighbor_kokkos.h" diff --git a/src/KOKKOS/dihedral_class2_kokkos.cpp b/src/KOKKOS/dihedral_class2_kokkos.cpp index 98436bc696..4b8d171f61 100644 --- a/src/KOKKOS/dihedral_class2_kokkos.cpp +++ b/src/KOKKOS/dihedral_class2_kokkos.cpp @@ -15,9 +15,9 @@ Contributing author: Ray Shan (Materials Design) ------------------------------------------------------------------------- */ +#include "dihedral_class2_kokkos.h" #include #include -#include "dihedral_class2_kokkos.h" #include "atom_kokkos.h" #include "comm.h" #include "neighbor_kokkos.h" diff --git a/src/KOKKOS/dihedral_opls_kokkos.cpp b/src/KOKKOS/dihedral_opls_kokkos.cpp index f50dea2c36..825d106e04 100644 --- a/src/KOKKOS/dihedral_opls_kokkos.cpp +++ b/src/KOKKOS/dihedral_opls_kokkos.cpp @@ -15,9 +15,9 @@ Contributing author: Stan Moore (SNL) ------------------------------------------------------------------------- */ +#include "dihedral_opls_kokkos.h" #include #include -#include "dihedral_opls_kokkos.h" #include "atom_kokkos.h" #include "comm.h" #include "neighbor_kokkos.h" diff --git a/src/KOKKOS/fix_deform_kokkos.cpp b/src/KOKKOS/fix_deform_kokkos.cpp index 7b9336ed3b..05eb1c22f6 100644 --- a/src/KOKKOS/fix_deform_kokkos.cpp +++ b/src/KOKKOS/fix_deform_kokkos.cpp @@ -15,10 +15,10 @@ Contributing author: Pieter in 't Veld (SNL) ------------------------------------------------------------------------- */ +#include "fix_deform_kokkos.h" #include #include #include -#include "fix_deform_kokkos.h" #include "atom_kokkos.h" #include "update.h" #include "comm.h" diff --git a/src/KOKKOS/fix_dpd_energy_kokkos.cpp b/src/KOKKOS/fix_dpd_energy_kokkos.cpp index d092cb4802..debad0407a 100644 --- a/src/KOKKOS/fix_dpd_energy_kokkos.cpp +++ b/src/KOKKOS/fix_dpd_energy_kokkos.cpp @@ -11,9 +11,9 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ +#include "fix_dpd_energy_kokkos.h" #include #include -#include "fix_dpd_energy_kokkos.h" #include "atom_masks.h" #include "atom_kokkos.h" #include "force.h" diff --git a/src/KOKKOS/fix_enforce2d_kokkos.cpp b/src/KOKKOS/fix_enforce2d_kokkos.cpp index 346e440f55..bf2a882539 100644 --- a/src/KOKKOS/fix_enforce2d_kokkos.cpp +++ b/src/KOKKOS/fix_enforce2d_kokkos.cpp @@ -15,11 +15,11 @@ Contributing authors: Stefan Paquay & Matthew Peterson (Brandeis University) ------------------------------------------------------------------------- */ +#include "fix_enforce2d_kokkos.h" #include "atom_masks.h" #include "atom_kokkos.h" #include "comm.h" #include "error.h" -#include "fix_enforce2d_kokkos.h" using namespace LAMMPS_NS; diff --git a/src/KOKKOS/fix_eos_table_rx_kokkos.cpp b/src/KOKKOS/fix_eos_table_rx_kokkos.cpp index 2f730d1193..d0280eeef0 100644 --- a/src/KOKKOS/fix_eos_table_rx_kokkos.cpp +++ b/src/KOKKOS/fix_eos_table_rx_kokkos.cpp @@ -15,9 +15,9 @@ Contributing author: Stan Moore (Sandia) ------------------------------------------------------------------------- */ +#include "fix_eos_table_rx_kokkos.h" #include #include -#include "fix_eos_table_rx_kokkos.h" #include "atom_kokkos.h" #include "error.h" #include "force.h" diff --git a/src/KOKKOS/fix_langevin_kokkos.cpp b/src/KOKKOS/fix_langevin_kokkos.cpp index 0947fee693..23a43b38ef 100644 --- a/src/KOKKOS/fix_langevin_kokkos.cpp +++ b/src/KOKKOS/fix_langevin_kokkos.cpp @@ -11,10 +11,10 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ +#include "fix_langevin_kokkos.h" #include #include #include -#include "fix_langevin_kokkos.h" #include "atom_masks.h" #include "atom_kokkos.h" #include "force.h" diff --git a/src/KOKKOS/fix_momentum_kokkos.cpp b/src/KOKKOS/fix_momentum_kokkos.cpp index 38500531ca..2d4911bfda 100644 --- a/src/KOKKOS/fix_momentum_kokkos.cpp +++ b/src/KOKKOS/fix_momentum_kokkos.cpp @@ -11,9 +11,9 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ +#include "fix_momentum_kokkos.h" #include #include -#include "fix_momentum_kokkos.h" #include "atom_kokkos.h" #include "atom_masks.h" #include "domain.h" diff --git a/src/KOKKOS/fix_nh_kokkos.cpp b/src/KOKKOS/fix_nh_kokkos.cpp index fae9ef8f30..578f2f5c70 100644 --- a/src/KOKKOS/fix_nh_kokkos.cpp +++ b/src/KOKKOS/fix_nh_kokkos.cpp @@ -15,10 +15,10 @@ Contributing author: Stan Moore (SNL) ------------------------------------------------------------------------- */ +#include "fix_nh_kokkos.h" #include #include #include -#include "fix_nh_kokkos.h" #include "math_extra.h" #include "atom.h" #include "force.h" diff --git a/src/KOKKOS/fix_nph_kokkos.cpp b/src/KOKKOS/fix_nph_kokkos.cpp index c5072e6ae9..3830860fd7 100644 --- a/src/KOKKOS/fix_nph_kokkos.cpp +++ b/src/KOKKOS/fix_nph_kokkos.cpp @@ -11,8 +11,8 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include #include "fix_nph_kokkos.h" +#include #include "modify.h" #include "error.h" diff --git a/src/KOKKOS/fix_npt_kokkos.cpp b/src/KOKKOS/fix_npt_kokkos.cpp index c488c8e4f3..5b751c9e4d 100644 --- a/src/KOKKOS/fix_npt_kokkos.cpp +++ b/src/KOKKOS/fix_npt_kokkos.cpp @@ -11,8 +11,8 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include #include "fix_npt_kokkos.h" +#include #include "modify.h" #include "error.h" diff --git a/src/KOKKOS/fix_nve_kokkos.cpp b/src/KOKKOS/fix_nve_kokkos.cpp index 6db8ff8c0f..0ca01c589a 100644 --- a/src/KOKKOS/fix_nve_kokkos.cpp +++ b/src/KOKKOS/fix_nve_kokkos.cpp @@ -11,9 +11,9 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ +#include "fix_nve_kokkos.h" #include #include -#include "fix_nve_kokkos.h" #include "atom_masks.h" #include "atom_kokkos.h" #include "force.h" diff --git a/src/KOKKOS/fix_nvt_kokkos.cpp b/src/KOKKOS/fix_nvt_kokkos.cpp index 4db42a62fb..66165dd7bc 100644 --- a/src/KOKKOS/fix_nvt_kokkos.cpp +++ b/src/KOKKOS/fix_nvt_kokkos.cpp @@ -11,8 +11,8 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include #include "fix_nvt_kokkos.h" +#include #include "group.h" #include "modify.h" #include "error.h" diff --git a/src/KOKKOS/fix_property_atom_kokkos.cpp b/src/KOKKOS/fix_property_atom_kokkos.cpp index 6860676911..ff374b885f 100644 --- a/src/KOKKOS/fix_property_atom_kokkos.cpp +++ b/src/KOKKOS/fix_property_atom_kokkos.cpp @@ -11,9 +11,9 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ +#include "fix_property_atom_kokkos.h" #include #include -#include "fix_property_atom_kokkos.h" #include "atom_kokkos.h" #include "comm.h" #include "memory_kokkos.h" diff --git a/src/KOKKOS/fix_qeq_reax_kokkos.cpp b/src/KOKKOS/fix_qeq_reax_kokkos.cpp index 12369261b3..6f8392ab16 100644 --- a/src/KOKKOS/fix_qeq_reax_kokkos.cpp +++ b/src/KOKKOS/fix_qeq_reax_kokkos.cpp @@ -16,11 +16,11 @@ Kamesh Arumugam (NVIDIA) ------------------------------------------------------------------------- */ +#include "fix_qeq_reax_kokkos.h" #include #include #include #include -#include "fix_qeq_reax_kokkos.h" #include "kokkos.h" #include "atom.h" #include "atom_masks.h" diff --git a/src/KOKKOS/fix_reaxc_bonds_kokkos.cpp b/src/KOKKOS/fix_reaxc_bonds_kokkos.cpp index 9aed0b9ae4..347c477476 100644 --- a/src/KOKKOS/fix_reaxc_bonds_kokkos.cpp +++ b/src/KOKKOS/fix_reaxc_bonds_kokkos.cpp @@ -15,9 +15,9 @@ Contributing author: Stan Moore (Sandia) ------------------------------------------------------------------------- */ +#include "fix_ave_atom.h" #include #include -#include "fix_ave_atom.h" #include "fix_reaxc_bonds_kokkos.h" #include "atom.h" #include "update.h" diff --git a/src/KOKKOS/fix_reaxc_species_kokkos.cpp b/src/KOKKOS/fix_reaxc_species_kokkos.cpp index bd92251960..71aacba68d 100644 --- a/src/KOKKOS/fix_reaxc_species_kokkos.cpp +++ b/src/KOKKOS/fix_reaxc_species_kokkos.cpp @@ -15,12 +15,12 @@ Contributing authors: Stan Moore (Sandia) ------------------------------------------------------------------------- */ +#include "fix_reaxc_species_kokkos.h" #include #include #include "atom.h" #include #include "fix_ave_atom.h" -#include "fix_reaxc_species_kokkos.h" #include "domain.h" #include "update.h" #include "pair_reaxc_kokkos.h" diff --git a/src/KOKKOS/fix_rx_kokkos.cpp b/src/KOKKOS/fix_rx_kokkos.cpp index 80333e1e9b..050dda2400 100644 --- a/src/KOKKOS/fix_rx_kokkos.cpp +++ b/src/KOKKOS/fix_rx_kokkos.cpp @@ -11,9 +11,9 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ +#include "fix_rx_kokkos.h" #include #include -#include "fix_rx_kokkos.h" #include "atom_masks.h" #include "atom_kokkos.h" #include "force.h" diff --git a/src/KOKKOS/fix_setforce_kokkos.cpp b/src/KOKKOS/fix_setforce_kokkos.cpp index 5d15b88d76..03cfd3afb2 100644 --- a/src/KOKKOS/fix_setforce_kokkos.cpp +++ b/src/KOKKOS/fix_setforce_kokkos.cpp @@ -11,9 +11,9 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ +#include "fix_setforce_kokkos.h" #include #include -#include "fix_setforce_kokkos.h" #include "atom_kokkos.h" #include "update.h" #include "modify.h" diff --git a/src/KOKKOS/fix_shardlow_kokkos.cpp b/src/KOKKOS/fix_shardlow_kokkos.cpp index 968f877abd..96f67ccb5e 100644 --- a/src/KOKKOS/fix_shardlow_kokkos.cpp +++ b/src/KOKKOS/fix_shardlow_kokkos.cpp @@ -33,10 +33,10 @@ 135, 204105. ------------------------------------------------------------------------- */ +#include "fix_shardlow_kokkos.h" #include #include #include -#include "fix_shardlow_kokkos.h" #include "atom.h" #include "atom_masks.h" #include "atom_kokkos.h" diff --git a/src/KOKKOS/fix_wall_lj93_kokkos.cpp b/src/KOKKOS/fix_wall_lj93_kokkos.cpp index 5dbb054175..61346144c8 100644 --- a/src/KOKKOS/fix_wall_lj93_kokkos.cpp +++ b/src/KOKKOS/fix_wall_lj93_kokkos.cpp @@ -11,8 +11,8 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include #include "fix_wall_lj93_kokkos.h" +#include #include "atom_kokkos.h" #include "error.h" #include "atom_masks.h" diff --git a/src/KOKKOS/fix_wall_reflect_kokkos.cpp b/src/KOKKOS/fix_wall_reflect_kokkos.cpp index 75a5c1a81e..ba104d19a9 100644 --- a/src/KOKKOS/fix_wall_reflect_kokkos.cpp +++ b/src/KOKKOS/fix_wall_reflect_kokkos.cpp @@ -11,9 +11,9 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ +#include "fix_wall_reflect_kokkos.h" #include #include -#include "fix_wall_reflect_kokkos.h" #include "atom_kokkos.h" #include "comm.h" #include "update.h" diff --git a/src/KOKKOS/gridcomm_kokkos.cpp b/src/KOKKOS/gridcomm_kokkos.cpp index 14b84a5733..1d0371c147 100644 --- a/src/KOKKOS/gridcomm_kokkos.cpp +++ b/src/KOKKOS/gridcomm_kokkos.cpp @@ -11,8 +11,8 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include #include "gridcomm_kokkos.h" +#include #include "comm.h" #include "kspace.h" #include "memory_kokkos.h" diff --git a/src/KOKKOS/improper_class2_kokkos.cpp b/src/KOKKOS/improper_class2_kokkos.cpp index ad32e6da4e..84b721bd2a 100644 --- a/src/KOKKOS/improper_class2_kokkos.cpp +++ b/src/KOKKOS/improper_class2_kokkos.cpp @@ -15,10 +15,10 @@ Contributing author: Ray Shan (Materials Design) ------------------------------------------------------------------------- */ +#include "improper_class2_kokkos.h" #include #include #include -#include "improper_class2_kokkos.h" #include "atom_kokkos.h" #include "comm.h" #include "neighbor_kokkos.h" diff --git a/src/KOKKOS/improper_harmonic_kokkos.cpp b/src/KOKKOS/improper_harmonic_kokkos.cpp index bb397a2c2f..262ffe7700 100644 --- a/src/KOKKOS/improper_harmonic_kokkos.cpp +++ b/src/KOKKOS/improper_harmonic_kokkos.cpp @@ -15,10 +15,10 @@ Contributing author: Stan Moore (SNL) ------------------------------------------------------------------------- */ +#include "improper_harmonic_kokkos.h" #include #include #include -#include "improper_harmonic_kokkos.h" #include "atom_kokkos.h" #include "comm.h" #include "neighbor_kokkos.h" diff --git a/src/KOKKOS/kokkos.cpp b/src/KOKKOS/kokkos.cpp index 3fa84d98b2..c269f69cdd 100644 --- a/src/KOKKOS/kokkos.cpp +++ b/src/KOKKOS/kokkos.cpp @@ -11,6 +11,7 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ +#include "kokkos.h" #include #include #include @@ -18,7 +19,6 @@ #include #include #include -#include "kokkos.h" #include "lammps.h" #include "force.h" #include "neighbor_kokkos.h" diff --git a/src/KOKKOS/math_special_kokkos.cpp b/src/KOKKOS/math_special_kokkos.cpp index 127168ef8b..f5fc725347 100644 --- a/src/KOKKOS/math_special_kokkos.cpp +++ b/src/KOKKOS/math_special_kokkos.cpp @@ -1,7 +1,7 @@ +#include "math_special_kokkos.h" #include #include -#include "math_special_kokkos.h" using namespace LAMMPS_NS; diff --git a/src/KOKKOS/pair_buck_coul_cut_kokkos.cpp b/src/KOKKOS/pair_buck_coul_cut_kokkos.cpp index 57ac3a9c57..e3843262a5 100644 --- a/src/KOKKOS/pair_buck_coul_cut_kokkos.cpp +++ b/src/KOKKOS/pair_buck_coul_cut_kokkos.cpp @@ -15,11 +15,11 @@ Contributing author: Ray Shan (SNL) ------------------------------------------------------------------------- */ +#include "pair_buck_coul_cut_kokkos.h" #include #include #include #include -#include "pair_buck_coul_cut_kokkos.h" #include "kokkos.h" #include "atom_kokkos.h" #include "comm.h" diff --git a/src/KOKKOS/pair_buck_coul_long_kokkos.cpp b/src/KOKKOS/pair_buck_coul_long_kokkos.cpp index 349c4c0601..7457a0988f 100644 --- a/src/KOKKOS/pair_buck_coul_long_kokkos.cpp +++ b/src/KOKKOS/pair_buck_coul_long_kokkos.cpp @@ -15,11 +15,11 @@ Contributing author: Ray Shan (SNL) ------------------------------------------------------------------------- */ +#include "pair_buck_coul_long_kokkos.h" #include #include #include #include -#include "pair_buck_coul_long_kokkos.h" #include "kokkos.h" #include "atom_kokkos.h" #include "comm.h" diff --git a/src/KOKKOS/pair_buck_kokkos.cpp b/src/KOKKOS/pair_buck_kokkos.cpp index 02c02c986e..131622cac5 100644 --- a/src/KOKKOS/pair_buck_kokkos.cpp +++ b/src/KOKKOS/pair_buck_kokkos.cpp @@ -15,11 +15,11 @@ Contributing author: Stan Moore (SNL) ------------------------------------------------------------------------- */ +#include "pair_buck_kokkos.h" #include #include #include #include -#include "pair_buck_kokkos.h" #include "kokkos.h" #include "atom_kokkos.h" #include "comm.h" diff --git a/src/KOKKOS/pair_coul_cut_kokkos.cpp b/src/KOKKOS/pair_coul_cut_kokkos.cpp index 54ba0b63ce..e79f103363 100644 --- a/src/KOKKOS/pair_coul_cut_kokkos.cpp +++ b/src/KOKKOS/pair_coul_cut_kokkos.cpp @@ -11,11 +11,11 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ +#include "pair_coul_cut_kokkos.h" #include #include #include #include -#include "pair_coul_cut_kokkos.h" #include "kokkos.h" #include "atom_kokkos.h" #include "comm.h" diff --git a/src/KOKKOS/pair_coul_debye_kokkos.cpp b/src/KOKKOS/pair_coul_debye_kokkos.cpp index 8966e30394..0fe03af043 100644 --- a/src/KOKKOS/pair_coul_debye_kokkos.cpp +++ b/src/KOKKOS/pair_coul_debye_kokkos.cpp @@ -15,11 +15,11 @@ Contributing author: Ray Shan (SNL) ------------------------------------------------------------------------- */ +#include "pair_coul_debye_kokkos.h" #include #include #include #include -#include "pair_coul_debye_kokkos.h" #include "kokkos.h" #include "atom_kokkos.h" #include "comm.h" diff --git a/src/KOKKOS/pair_coul_dsf_kokkos.cpp b/src/KOKKOS/pair_coul_dsf_kokkos.cpp index 748fed71a7..e94aae4754 100644 --- a/src/KOKKOS/pair_coul_dsf_kokkos.cpp +++ b/src/KOKKOS/pair_coul_dsf_kokkos.cpp @@ -15,11 +15,11 @@ Contributing author: Stan Moore (SNL) ------------------------------------------------------------------------- */ +#include "pair_coul_dsf_kokkos.h" #include #include #include #include -#include "pair_coul_dsf_kokkos.h" #include "kokkos.h" #include "atom_kokkos.h" #include "comm.h" diff --git a/src/KOKKOS/pair_coul_long_kokkos.cpp b/src/KOKKOS/pair_coul_long_kokkos.cpp index a21cb050ff..67132e11f6 100644 --- a/src/KOKKOS/pair_coul_long_kokkos.cpp +++ b/src/KOKKOS/pair_coul_long_kokkos.cpp @@ -15,11 +15,11 @@ Contributing author: Ray Shan (SNL) ------------------------------------------------------------------------- */ +#include "pair_coul_long_kokkos.h" #include #include #include #include -#include "pair_coul_long_kokkos.h" #include "kokkos.h" #include "atom_kokkos.h" #include "comm.h" diff --git a/src/KOKKOS/pair_coul_wolf_kokkos.cpp b/src/KOKKOS/pair_coul_wolf_kokkos.cpp index 20391d9530..dbbb865961 100644 --- a/src/KOKKOS/pair_coul_wolf_kokkos.cpp +++ b/src/KOKKOS/pair_coul_wolf_kokkos.cpp @@ -15,11 +15,11 @@ Contributing author: Stan Moore (SNL) ------------------------------------------------------------------------- */ +#include "pair_coul_wolf_kokkos.h" #include #include #include #include -#include "pair_coul_wolf_kokkos.h" #include "kokkos.h" #include "atom_kokkos.h" #include "comm.h" diff --git a/src/KOKKOS/pair_dpd_fdt_energy_kokkos.cpp b/src/KOKKOS/pair_dpd_fdt_energy_kokkos.cpp index a44ef1790e..7a2fca47a0 100644 --- a/src/KOKKOS/pair_dpd_fdt_energy_kokkos.cpp +++ b/src/KOKKOS/pair_dpd_fdt_energy_kokkos.cpp @@ -15,11 +15,11 @@ Contributing author: Stan Moore (Sandia) ------------------------------------------------------------------------- */ +#include "pair_dpd_fdt_energy_kokkos.h" #include #include #include #include -#include "atom_kokkos.h" #include "atom_vec.h" #include "comm.h" #include "update.h" @@ -30,7 +30,6 @@ #include "neigh_request.h" #include "memory_kokkos.h" #include "modify.h" -#include "pair_dpd_fdt_energy_kokkos.h" #include "error.h" #include "atom_masks.h" #include "kokkos.h" diff --git a/src/KOKKOS/pair_eam_alloy_kokkos.cpp b/src/KOKKOS/pair_eam_alloy_kokkos.cpp index b5442c0d29..aa33d44eee 100644 --- a/src/KOKKOS/pair_eam_alloy_kokkos.cpp +++ b/src/KOKKOS/pair_eam_alloy_kokkos.cpp @@ -15,13 +15,13 @@ Contributing authors: Stan Moore (SNL) ------------------------------------------------------------------------- */ +#include "pair_eam_alloy_kokkos.h" #include #include #include #include #include "kokkos.h" #include "pair_kokkos.h" -#include "pair_eam_alloy_kokkos.h" #include "atom_kokkos.h" #include "force.h" #include "comm.h" diff --git a/src/KOKKOS/pair_eam_fs_kokkos.cpp b/src/KOKKOS/pair_eam_fs_kokkos.cpp index 16701febd6..9832a16a73 100644 --- a/src/KOKKOS/pair_eam_fs_kokkos.cpp +++ b/src/KOKKOS/pair_eam_fs_kokkos.cpp @@ -15,13 +15,13 @@ Contributing authors: Stan Moore (SNL) ------------------------------------------------------------------------- */ +#include "pair_eam_fs_kokkos.h" #include #include #include #include #include "kokkos.h" #include "pair_kokkos.h" -#include "pair_eam_fs_kokkos.h" #include "atom_kokkos.h" #include "force.h" #include "comm.h" diff --git a/src/KOKKOS/pair_eam_kokkos.cpp b/src/KOKKOS/pair_eam_kokkos.cpp index d423f2c927..4c6fadfe92 100644 --- a/src/KOKKOS/pair_eam_kokkos.cpp +++ b/src/KOKKOS/pair_eam_kokkos.cpp @@ -15,13 +15,13 @@ Contributing authors: Stan Moore (SNL), Christian Trott (SNL) ------------------------------------------------------------------------- */ +#include "pair_eam_kokkos.h" #include #include #include #include #include "kokkos.h" #include "pair_kokkos.h" -#include "pair_eam_kokkos.h" #include "atom_kokkos.h" #include "force.h" #include "comm.h" diff --git a/src/KOKKOS/pair_exp6_rx_kokkos.cpp b/src/KOKKOS/pair_exp6_rx_kokkos.cpp index 3a857a6485..31a48fe154 100644 --- a/src/KOKKOS/pair_exp6_rx_kokkos.cpp +++ b/src/KOKKOS/pair_exp6_rx_kokkos.cpp @@ -15,11 +15,11 @@ Contributing author: Stan Moore (Sandia) ------------------------------------------------------------------------- */ +#include "pair_exp6_rx_kokkos.h" #include #include #include #include -#include "pair_exp6_rx_kokkos.h" #include "atom.h" #include "comm.h" #include "force.h" diff --git a/src/KOKKOS/pair_hybrid_kokkos.cpp b/src/KOKKOS/pair_hybrid_kokkos.cpp index 00df4a8f3c..c767d9f470 100644 --- a/src/KOKKOS/pair_hybrid_kokkos.cpp +++ b/src/KOKKOS/pair_hybrid_kokkos.cpp @@ -11,11 +11,11 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ +#include "pair_hybrid_kokkos.h" #include #include #include #include -#include "pair_hybrid_kokkos.h" #include "atom_kokkos.h" #include "force.h" #include "pair.h" diff --git a/src/KOKKOS/pair_hybrid_overlay_kokkos.cpp b/src/KOKKOS/pair_hybrid_overlay_kokkos.cpp index a2c3edab65..cb1389d38e 100644 --- a/src/KOKKOS/pair_hybrid_overlay_kokkos.cpp +++ b/src/KOKKOS/pair_hybrid_overlay_kokkos.cpp @@ -11,10 +11,10 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ +#include "pair_hybrid_overlay_kokkos.h" #include #include #include -#include "pair_hybrid_overlay_kokkos.h" #include "atom.h" #include "force.h" #include "neighbor.h" diff --git a/src/KOKKOS/pair_lj_charmm_coul_charmm_implicit_kokkos.cpp b/src/KOKKOS/pair_lj_charmm_coul_charmm_implicit_kokkos.cpp index 510740112a..b7c3766d5f 100644 --- a/src/KOKKOS/pair_lj_charmm_coul_charmm_implicit_kokkos.cpp +++ b/src/KOKKOS/pair_lj_charmm_coul_charmm_implicit_kokkos.cpp @@ -15,11 +15,11 @@ Contributing author: Ray Shan (SNL) ------------------------------------------------------------------------- */ +#include "pair_lj_charmm_coul_charmm_implicit_kokkos.h" #include #include #include #include -#include "pair_lj_charmm_coul_charmm_implicit_kokkos.h" #include "kokkos.h" #include "atom_kokkos.h" #include "comm.h" diff --git a/src/KOKKOS/pair_lj_charmm_coul_charmm_kokkos.cpp b/src/KOKKOS/pair_lj_charmm_coul_charmm_kokkos.cpp index 51c96354f9..c6a1e3211d 100644 --- a/src/KOKKOS/pair_lj_charmm_coul_charmm_kokkos.cpp +++ b/src/KOKKOS/pair_lj_charmm_coul_charmm_kokkos.cpp @@ -15,11 +15,11 @@ Contributing author: Ray Shan (SNL) ------------------------------------------------------------------------- */ +#include "pair_lj_charmm_coul_charmm_kokkos.h" #include #include #include #include -#include "pair_lj_charmm_coul_charmm_kokkos.h" #include "kokkos.h" #include "atom_kokkos.h" #include "comm.h" diff --git a/src/KOKKOS/pair_lj_charmm_coul_long_kokkos.cpp b/src/KOKKOS/pair_lj_charmm_coul_long_kokkos.cpp index 22faa98935..4ba0651601 100644 --- a/src/KOKKOS/pair_lj_charmm_coul_long_kokkos.cpp +++ b/src/KOKKOS/pair_lj_charmm_coul_long_kokkos.cpp @@ -15,11 +15,11 @@ Contributing author: Ray Shan (SNL) ------------------------------------------------------------------------- */ +#include "pair_lj_charmm_coul_long_kokkos.h" #include #include #include #include -#include "pair_lj_charmm_coul_long_kokkos.h" #include "kokkos.h" #include "atom_kokkos.h" #include "comm.h" diff --git a/src/KOKKOS/pair_lj_class2_coul_cut_kokkos.cpp b/src/KOKKOS/pair_lj_class2_coul_cut_kokkos.cpp index 60d480188b..ef8fe7a128 100644 --- a/src/KOKKOS/pair_lj_class2_coul_cut_kokkos.cpp +++ b/src/KOKKOS/pair_lj_class2_coul_cut_kokkos.cpp @@ -11,11 +11,11 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ +#include "pair_lj_class2_coul_cut_kokkos.h" #include #include #include #include -#include "pair_lj_class2_coul_cut_kokkos.h" #include "kokkos.h" #include "atom_kokkos.h" #include "comm.h" diff --git a/src/KOKKOS/pair_lj_class2_coul_long_kokkos.cpp b/src/KOKKOS/pair_lj_class2_coul_long_kokkos.cpp index 4c8aea8e92..5a25d0250b 100644 --- a/src/KOKKOS/pair_lj_class2_coul_long_kokkos.cpp +++ b/src/KOKKOS/pair_lj_class2_coul_long_kokkos.cpp @@ -11,11 +11,11 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ +#include "pair_lj_class2_coul_long_kokkos.h" #include #include #include #include -#include "pair_lj_class2_coul_long_kokkos.h" #include "kokkos.h" #include "atom_kokkos.h" #include "comm.h" diff --git a/src/KOKKOS/pair_lj_class2_kokkos.cpp b/src/KOKKOS/pair_lj_class2_kokkos.cpp index dd42baa4e0..6d673b2d01 100644 --- a/src/KOKKOS/pair_lj_class2_kokkos.cpp +++ b/src/KOKKOS/pair_lj_class2_kokkos.cpp @@ -15,11 +15,11 @@ Contributing author: Ray Shan (SNL) ------------------------------------------------------------------------- */ +#include "pair_lj_class2_kokkos.h" #include #include #include #include -#include "pair_lj_class2_kokkos.h" #include "kokkos.h" #include "atom_kokkos.h" #include "comm.h" diff --git a/src/KOKKOS/pair_lj_cut_coul_cut_kokkos.cpp b/src/KOKKOS/pair_lj_cut_coul_cut_kokkos.cpp index cb5ab96871..9201a116b5 100644 --- a/src/KOKKOS/pair_lj_cut_coul_cut_kokkos.cpp +++ b/src/KOKKOS/pair_lj_cut_coul_cut_kokkos.cpp @@ -11,11 +11,11 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ +#include "pair_lj_cut_coul_cut_kokkos.h" #include #include #include #include -#include "pair_lj_cut_coul_cut_kokkos.h" #include "kokkos.h" #include "atom_kokkos.h" #include "comm.h" diff --git a/src/KOKKOS/pair_lj_cut_coul_debye_kokkos.cpp b/src/KOKKOS/pair_lj_cut_coul_debye_kokkos.cpp index 800092a09b..8935333c74 100644 --- a/src/KOKKOS/pair_lj_cut_coul_debye_kokkos.cpp +++ b/src/KOKKOS/pair_lj_cut_coul_debye_kokkos.cpp @@ -15,11 +15,11 @@ Contributing author: Ray Shan (SNL) ------------------------------------------------------------------------- */ +#include "pair_lj_cut_coul_debye_kokkos.h" #include #include #include #include -#include "pair_lj_cut_coul_debye_kokkos.h" #include "kokkos.h" #include "atom_kokkos.h" #include "comm.h" diff --git a/src/KOKKOS/pair_lj_cut_coul_dsf_kokkos.cpp b/src/KOKKOS/pair_lj_cut_coul_dsf_kokkos.cpp index f793485b47..aea70faec4 100644 --- a/src/KOKKOS/pair_lj_cut_coul_dsf_kokkos.cpp +++ b/src/KOKKOS/pair_lj_cut_coul_dsf_kokkos.cpp @@ -15,11 +15,11 @@ Contributing author: Ray Shan (SNL) ------------------------------------------------------------------------- */ +#include "pair_lj_cut_coul_dsf_kokkos.h" #include #include #include #include -#include "pair_lj_cut_coul_dsf_kokkos.h" #include "kokkos.h" #include "atom_kokkos.h" #include "comm.h" diff --git a/src/KOKKOS/pair_lj_cut_coul_long_kokkos.cpp b/src/KOKKOS/pair_lj_cut_coul_long_kokkos.cpp index 02150586f4..53d27f2447 100644 --- a/src/KOKKOS/pair_lj_cut_coul_long_kokkos.cpp +++ b/src/KOKKOS/pair_lj_cut_coul_long_kokkos.cpp @@ -11,11 +11,11 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ +#include "pair_lj_cut_coul_long_kokkos.h" #include #include #include #include -#include "pair_lj_cut_coul_long_kokkos.h" #include "kokkos.h" #include "atom_kokkos.h" #include "comm.h" diff --git a/src/KOKKOS/pair_lj_cut_kokkos.cpp b/src/KOKKOS/pair_lj_cut_kokkos.cpp index 4ba8c00f88..ee29e12322 100644 --- a/src/KOKKOS/pair_lj_cut_kokkos.cpp +++ b/src/KOKKOS/pair_lj_cut_kokkos.cpp @@ -11,11 +11,11 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ +#include "pair_lj_cut_kokkos.h" #include #include #include #include -#include "pair_lj_cut_kokkos.h" #include "kokkos.h" #include "atom_kokkos.h" #include "comm.h" diff --git a/src/KOKKOS/pair_lj_expand_kokkos.cpp b/src/KOKKOS/pair_lj_expand_kokkos.cpp index 5ea6c9e438..061fc205fb 100644 --- a/src/KOKKOS/pair_lj_expand_kokkos.cpp +++ b/src/KOKKOS/pair_lj_expand_kokkos.cpp @@ -15,11 +15,11 @@ Contributing author: Ray Shan (SNL) ------------------------------------------------------------------------- */ +#include "pair_lj_expand_kokkos.h" #include #include #include #include -#include "pair_lj_expand_kokkos.h" #include "kokkos.h" #include "atom_kokkos.h" #include "comm.h" diff --git a/src/KOKKOS/pair_lj_gromacs_coul_gromacs_kokkos.cpp b/src/KOKKOS/pair_lj_gromacs_coul_gromacs_kokkos.cpp index 2421d059da..4df9fdea9e 100644 --- a/src/KOKKOS/pair_lj_gromacs_coul_gromacs_kokkos.cpp +++ b/src/KOKKOS/pair_lj_gromacs_coul_gromacs_kokkos.cpp @@ -15,11 +15,11 @@ Contributing author: Ray Shan (SNL) ------------------------------------------------------------------------- */ +#include "pair_lj_gromacs_coul_gromacs_kokkos.h" #include #include #include #include -#include "pair_lj_gromacs_coul_gromacs_kokkos.h" #include "kokkos.h" #include "atom_kokkos.h" #include "comm.h" diff --git a/src/KOKKOS/pair_lj_gromacs_kokkos.cpp b/src/KOKKOS/pair_lj_gromacs_kokkos.cpp index 09a0261ae1..2d395c39d5 100644 --- a/src/KOKKOS/pair_lj_gromacs_kokkos.cpp +++ b/src/KOKKOS/pair_lj_gromacs_kokkos.cpp @@ -15,11 +15,11 @@ Contributing author: Ray Shan (SNL) ------------------------------------------------------------------------- */ +#include "pair_lj_gromacs_kokkos.h" #include #include #include #include -#include "pair_lj_gromacs_kokkos.h" #include "kokkos.h" #include "atom_kokkos.h" #include "comm.h" diff --git a/src/KOKKOS/pair_lj_sdk_kokkos.cpp b/src/KOKKOS/pair_lj_sdk_kokkos.cpp index c2375fa7a8..14c53c38bf 100644 --- a/src/KOKKOS/pair_lj_sdk_kokkos.cpp +++ b/src/KOKKOS/pair_lj_sdk_kokkos.cpp @@ -11,11 +11,11 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ +#include "pair_lj_sdk_kokkos.h" #include #include #include #include -#include "pair_lj_sdk_kokkos.h" #include "kokkos.h" #include "atom_kokkos.h" #include "comm.h" diff --git a/src/KOKKOS/pair_morse_kokkos.cpp b/src/KOKKOS/pair_morse_kokkos.cpp index b308330ead..d679477321 100644 --- a/src/KOKKOS/pair_morse_kokkos.cpp +++ b/src/KOKKOS/pair_morse_kokkos.cpp @@ -15,11 +15,11 @@ Contributing authors: Stefan Paquay (Eindhoven University of Technology) ------------------------------------------------------------------------- */ +#include "pair_morse_kokkos.h" #include #include #include #include -#include "pair_morse_kokkos.h" #include "kokkos.h" #include "atom_kokkos.h" #include "comm.h" diff --git a/src/KOKKOS/pair_multi_lucy_rx_kokkos.cpp b/src/KOKKOS/pair_multi_lucy_rx_kokkos.cpp index 7d17ac3f43..81a4aa7a82 100644 --- a/src/KOKKOS/pair_multi_lucy_rx_kokkos.cpp +++ b/src/KOKKOS/pair_multi_lucy_rx_kokkos.cpp @@ -21,12 +21,12 @@ The Journal of Chemical Physics, 2016, 144, 104501. ------------------------------------------------------------------------------------------- */ +#include "pair_multi_lucy_rx_kokkos.h" #include #include -#include "math_const.h" #include #include -#include "pair_multi_lucy_rx_kokkos.h" +#include "math_const.h" #include "atom_kokkos.h" #include "force.h" #include "comm.h" diff --git a/src/KOKKOS/pair_reaxc_kokkos.cpp b/src/KOKKOS/pair_reaxc_kokkos.cpp index 64651be270..ca897a377c 100644 --- a/src/KOKKOS/pair_reaxc_kokkos.cpp +++ b/src/KOKKOS/pair_reaxc_kokkos.cpp @@ -15,11 +15,11 @@ Contributing author: Ray Shan (SNL), Stan Moore (SNL) ------------------------------------------------------------------------- */ +#include "pair_reaxc_kokkos.h" #include #include #include #include -#include "pair_reaxc_kokkos.h" #include "kokkos.h" #include "atom_kokkos.h" #include "comm.h" diff --git a/src/KOKKOS/pair_sw_kokkos.cpp b/src/KOKKOS/pair_sw_kokkos.cpp index da4737a2c1..dbd45747f0 100644 --- a/src/KOKKOS/pair_sw_kokkos.cpp +++ b/src/KOKKOS/pair_sw_kokkos.cpp @@ -15,11 +15,11 @@ Contributing author: Stan Moore (SNL) ------------------------------------------------------------------------- */ +#include "pair_sw_kokkos.h" #include #include #include #include -#include "pair_sw_kokkos.h" #include "kokkos.h" #include "pair_kokkos.h" #include "atom_kokkos.h" diff --git a/src/KOKKOS/pair_table_kokkos.cpp b/src/KOKKOS/pair_table_kokkos.cpp index 737d600d1e..01966d708a 100644 --- a/src/KOKKOS/pair_table_kokkos.cpp +++ b/src/KOKKOS/pair_table_kokkos.cpp @@ -15,11 +15,11 @@ Contributing author: Christian Trott (SNL) ------------------------------------------------------------------------- */ +#include "pair_table_kokkos.h" #include #include #include #include -#include "pair_table_kokkos.h" #include "kokkos.h" #include "atom.h" #include "force.h" diff --git a/src/KOKKOS/pair_table_rx_kokkos.cpp b/src/KOKKOS/pair_table_rx_kokkos.cpp index ec7a2ffb94..7c2d20c68d 100644 --- a/src/KOKKOS/pair_table_rx_kokkos.cpp +++ b/src/KOKKOS/pair_table_rx_kokkos.cpp @@ -15,11 +15,11 @@ Contributing author: Dan Ibanez (SNL) ------------------------------------------------------------------------- */ +#include "pair_table_rx_kokkos.h" #include #include #include #include -#include "pair_table_rx_kokkos.h" #include "kokkos.h" #include "atom.h" #include "force.h" diff --git a/src/KOKKOS/pair_tersoff_kokkos.cpp b/src/KOKKOS/pair_tersoff_kokkos.cpp index 9252e3de52..b68af84425 100644 --- a/src/KOKKOS/pair_tersoff_kokkos.cpp +++ b/src/KOKKOS/pair_tersoff_kokkos.cpp @@ -15,11 +15,11 @@ Contributing author: Ray Shan (SNL) and Christian Trott (SNL) ------------------------------------------------------------------------- */ +#include "pair_tersoff_kokkos.h" #include #include #include #include -#include "pair_tersoff_kokkos.h" #include "kokkos.h" #include "atom_kokkos.h" #include "comm.h" diff --git a/src/KOKKOS/pair_tersoff_mod_kokkos.cpp b/src/KOKKOS/pair_tersoff_mod_kokkos.cpp index 585074b128..b6921179c0 100644 --- a/src/KOKKOS/pair_tersoff_mod_kokkos.cpp +++ b/src/KOKKOS/pair_tersoff_mod_kokkos.cpp @@ -15,11 +15,11 @@ Contributing author: Ray Shan (SNL) ------------------------------------------------------------------------- */ +#include "pair_tersoff_mod_kokkos.h" #include #include #include #include -#include "pair_tersoff_mod_kokkos.h" #include "kokkos.h" #include "atom_kokkos.h" #include "comm.h" diff --git a/src/KOKKOS/pair_tersoff_zbl_kokkos.cpp b/src/KOKKOS/pair_tersoff_zbl_kokkos.cpp index e1e2211ab5..60ff0a7269 100644 --- a/src/KOKKOS/pair_tersoff_zbl_kokkos.cpp +++ b/src/KOKKOS/pair_tersoff_zbl_kokkos.cpp @@ -15,11 +15,11 @@ Contributing author: Ray Shan (SNL) ------------------------------------------------------------------------- */ +#include "pair_tersoff_zbl_kokkos.h" #include #include #include #include -#include "pair_tersoff_zbl_kokkos.h" #include "kokkos.h" #include "atom_kokkos.h" #include "comm.h" diff --git a/src/KOKKOS/pair_vashishta_kokkos.cpp b/src/KOKKOS/pair_vashishta_kokkos.cpp index 4a1f291b17..febb171c83 100644 --- a/src/KOKKOS/pair_vashishta_kokkos.cpp +++ b/src/KOKKOS/pair_vashishta_kokkos.cpp @@ -15,11 +15,11 @@ Contributing author: Anders Hafreager (UiO), andershaf@gmail.com ------------------------------------------------------------------------- */ +#include "pair_vashishta_kokkos.h" #include #include #include #include -#include "pair_vashishta_kokkos.h" #include "kokkos.h" #include "pair_kokkos.h" #include "atom_kokkos.h" diff --git a/src/KOKKOS/pair_yukawa_kokkos.cpp b/src/KOKKOS/pair_yukawa_kokkos.cpp index 27e18533a2..acfeb2fbdc 100644 --- a/src/KOKKOS/pair_yukawa_kokkos.cpp +++ b/src/KOKKOS/pair_yukawa_kokkos.cpp @@ -14,9 +14,10 @@ /* ---------------------------------------------------------------------- Contributing authors: Stefan Paquay (Brandeis University) ------------------------------------------------------------------------- */ + +#include "pair_yukawa_kokkos.h" #include #include -#include "pair_yukawa_kokkos.h" #include "kokkos.h" #include "atom_kokkos.h" #include "comm.h" diff --git a/src/KOKKOS/pair_zbl_kokkos.cpp b/src/KOKKOS/pair_zbl_kokkos.cpp index 06c84e5189..0f21331266 100644 --- a/src/KOKKOS/pair_zbl_kokkos.cpp +++ b/src/KOKKOS/pair_zbl_kokkos.cpp @@ -15,11 +15,11 @@ Contributing authors: Stan Moore (SNL) ------------------------------------------------------------------------- */ +#include "pair_zbl_kokkos.h" #include #include #include #include -#include "pair_zbl_kokkos.h" #include "atom_kokkos.h" #include "comm.h" #include "force.h" diff --git a/src/KOKKOS/pppm_kokkos.cpp b/src/KOKKOS/pppm_kokkos.cpp index 7c01adc510..1842524e23 100644 --- a/src/KOKKOS/pppm_kokkos.cpp +++ b/src/KOKKOS/pppm_kokkos.cpp @@ -15,12 +15,12 @@ Contributing author: Stan Moore (SNL) ------------------------------------------------------------------------- */ +#include "pppm_kokkos.h" #include #include #include #include #include -#include "pppm_kokkos.h" #include "atom_kokkos.h" #include "comm.h" #include "gridcomm_kokkos.h" diff --git a/src/KOKKOS/rand_pool_wrap_kokkos.cpp b/src/KOKKOS/rand_pool_wrap_kokkos.cpp index 51ebcb154e..2d8865feb0 100644 --- a/src/KOKKOS/rand_pool_wrap_kokkos.cpp +++ b/src/KOKKOS/rand_pool_wrap_kokkos.cpp @@ -11,8 +11,8 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include "comm.h" #include "rand_pool_wrap_kokkos.h" +#include "comm.h" #include "lammps.h" #include "kokkos.h" #include "random_mars.h" diff --git a/src/KOKKOS/region_block_kokkos.cpp b/src/KOKKOS/region_block_kokkos.cpp index 730ef81466..a5734f6ba7 100644 --- a/src/KOKKOS/region_block_kokkos.cpp +++ b/src/KOKKOS/region_block_kokkos.cpp @@ -11,9 +11,9 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ +#include "region_block_kokkos.h" #include #include -#include "region_block_kokkos.h" #include "domain.h" #include "force.h" #include "atom_kokkos.h" diff --git a/src/KOKKOS/verlet_kokkos.cpp b/src/KOKKOS/verlet_kokkos.cpp index b80d5e0646..d555b74d23 100644 --- a/src/KOKKOS/verlet_kokkos.cpp +++ b/src/KOKKOS/verlet_kokkos.cpp @@ -11,8 +11,8 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include #include "verlet_kokkos.h" +#include #include "neighbor.h" #include "domain.h" #include "comm.h" diff --git a/src/KSPACE/ewald.cpp b/src/KSPACE/ewald.cpp index ccbb3ed708..aad0e364d0 100644 --- a/src/KSPACE/ewald.cpp +++ b/src/KSPACE/ewald.cpp @@ -18,12 +18,12 @@ triclinic added by Stan Moore (SNL) ------------------------------------------------------------------------- */ +#include "ewald.h" #include #include #include #include #include -#include "ewald.h" #include "atom.h" #include "comm.h" #include "force.h" diff --git a/src/KSPACE/ewald_dipole.cpp b/src/KSPACE/ewald_dipole.cpp index 89ef7e39a8..53bac0637f 100644 --- a/src/KSPACE/ewald_dipole.cpp +++ b/src/KSPACE/ewald_dipole.cpp @@ -15,12 +15,12 @@ Contributing authors: Julien Tranchida (SNL), Stan Moore (SNL) ------------------------------------------------------------------------- */ +#include "ewald_dipole.h" #include #include #include #include #include -#include "ewald_dipole.h" #include "atom.h" #include "comm.h" #include "force.h" diff --git a/src/KSPACE/ewald_dipole_spin.cpp b/src/KSPACE/ewald_dipole_spin.cpp index 698203c85c..2b6c95f174 100644 --- a/src/KSPACE/ewald_dipole_spin.cpp +++ b/src/KSPACE/ewald_dipole_spin.cpp @@ -15,12 +15,12 @@ Contributing authors: Julien Tranchida (SNL) ------------------------------------------------------------------------- */ +#include "ewald_dipole_spin.h" #include #include #include #include #include -#include "ewald_dipole_spin.h" #include "atom.h" #include "comm.h" #include "force.h" diff --git a/src/KSPACE/ewald_disp.cpp b/src/KSPACE/ewald_disp.cpp index 0603d68eb2..c775056dd8 100644 --- a/src/KSPACE/ewald_disp.cpp +++ b/src/KSPACE/ewald_disp.cpp @@ -15,12 +15,12 @@ Contributing authors: Pieter in 't Veld (SNL), Stan Moore (SNL) ------------------------------------------------------------------------- */ +#include "ewald_disp.h" #include #include #include #include #include -#include "ewald_disp.h" #include "math_vector.h" #include "math_const.h" #include "math_special.h" diff --git a/src/KSPACE/fft3d.cpp b/src/KSPACE/fft3d.cpp index 7d3c8c83f2..e4c38a57f5 100644 --- a/src/KSPACE/fft3d.cpp +++ b/src/KSPACE/fft3d.cpp @@ -19,11 +19,11 @@ Paul Coffman (IBM) added MPI collectives remap ------------------------------------------------------------------------- */ +#include "fft3d.h" #include #include #include #include -#include "fft3d.h" #include "remap.h" #ifdef FFT_KISS diff --git a/src/KSPACE/fft3d_wrap.cpp b/src/KSPACE/fft3d_wrap.cpp index b9a6f0ae46..507b23d27d 100644 --- a/src/KSPACE/fft3d_wrap.cpp +++ b/src/KSPACE/fft3d_wrap.cpp @@ -11,8 +11,8 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include #include "fft3d_wrap.h" +#include #include "error.h" using namespace LAMMPS_NS; diff --git a/src/KSPACE/fix_tune_kspace.cpp b/src/KSPACE/fix_tune_kspace.cpp index 2b22b44340..cfd88609b3 100644 --- a/src/KSPACE/fix_tune_kspace.cpp +++ b/src/KSPACE/fix_tune_kspace.cpp @@ -15,10 +15,10 @@ Contributing author: Paul Crozier (SNL) ------------------------------------------------------------------------- */ +#include "fix_tune_kspace.h" #include #include #include -#include "fix_tune_kspace.h" #include "update.h" #include "force.h" #include "kspace.h" diff --git a/src/KSPACE/gridcomm.cpp b/src/KSPACE/gridcomm.cpp index ba08c9be26..552d80daab 100644 --- a/src/KSPACE/gridcomm.cpp +++ b/src/KSPACE/gridcomm.cpp @@ -11,8 +11,8 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include #include "gridcomm.h" +#include #include "comm.h" #include "kspace.h" #include "memory.h" diff --git a/src/KSPACE/msm.cpp b/src/KSPACE/msm.cpp index d7cc3f6876..bc5360dcd2 100644 --- a/src/KSPACE/msm.cpp +++ b/src/KSPACE/msm.cpp @@ -15,12 +15,12 @@ Contributing authors: Paul Crozier, Stan Moore, Stephen Bond, (all SNL) ------------------------------------------------------------------------- */ +#include "msm.h" #include #include #include #include #include -#include "msm.h" #include "atom.h" #include "comm.h" #include "gridcomm.h" diff --git a/src/KSPACE/msm_cg.cpp b/src/KSPACE/msm_cg.cpp index c7896db50c..22976b8442 100644 --- a/src/KSPACE/msm_cg.cpp +++ b/src/KSPACE/msm_cg.cpp @@ -15,6 +15,7 @@ Contributing authors: Paul Crozier, Stan Moore, Stephen Bond, (all SNL) ------------------------------------------------------------------------- */ +#include "msm_cg.h" #include #include #include @@ -27,7 +28,6 @@ #include "force.h" #include "neighbor.h" #include "memory.h" -#include "msm_cg.h" #include "math_const.h" diff --git a/src/KSPACE/pair_born_coul_long.cpp b/src/KSPACE/pair_born_coul_long.cpp index f12f5779d9..cb8360e401 100644 --- a/src/KSPACE/pair_born_coul_long.cpp +++ b/src/KSPACE/pair_born_coul_long.cpp @@ -15,11 +15,11 @@ Contributing author: Ahmed Ismail (SNL) ------------------------------------------------------------------------- */ +#include "pair_born_coul_long.h" #include #include #include #include -#include "pair_born_coul_long.h" #include "atom.h" #include "comm.h" #include "force.h" diff --git a/src/KSPACE/pair_born_coul_msm.cpp b/src/KSPACE/pair_born_coul_msm.cpp index eaa1c116c1..deaf224334 100644 --- a/src/KSPACE/pair_born_coul_msm.cpp +++ b/src/KSPACE/pair_born_coul_msm.cpp @@ -15,11 +15,11 @@ Contributing author: Stan Moore (SNL), Paul Crozier (SNL) ------------------------------------------------------------------------- */ +#include "pair_born_coul_msm.h" #include #include #include #include -#include "pair_born_coul_msm.h" #include "atom.h" #include "comm.h" #include "force.h" diff --git a/src/KSPACE/pair_buck_coul_long.cpp b/src/KSPACE/pair_buck_coul_long.cpp index a5427965dc..c97856fa3c 100644 --- a/src/KSPACE/pair_buck_coul_long.cpp +++ b/src/KSPACE/pair_buck_coul_long.cpp @@ -11,10 +11,10 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ +#include "pair_buck_coul_long.h" #include #include #include -#include "pair_buck_coul_long.h" #include "atom.h" #include "comm.h" #include "force.h" diff --git a/src/KSPACE/pair_buck_coul_msm.cpp b/src/KSPACE/pair_buck_coul_msm.cpp index 257d1b661f..3d7687df90 100644 --- a/src/KSPACE/pair_buck_coul_msm.cpp +++ b/src/KSPACE/pair_buck_coul_msm.cpp @@ -11,11 +11,11 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ +#include "pair_buck_coul_msm.h" #include #include #include #include -#include "pair_buck_coul_msm.h" #include "atom.h" #include "comm.h" #include "force.h" diff --git a/src/KSPACE/pair_buck_long_coul_long.cpp b/src/KSPACE/pair_buck_long_coul_long.cpp index bcd290891e..8127cbc127 100644 --- a/src/KSPACE/pair_buck_long_coul_long.cpp +++ b/src/KSPACE/pair_buck_long_coul_long.cpp @@ -15,11 +15,11 @@ Contributing author: Pieter J. in 't Veld (SNL) ------------------------------------------------------------------------- */ +#include "pair_buck_long_coul_long.h" #include #include #include #include "math_vector.h" -#include "pair_buck_long_coul_long.h" #include "atom.h" #include "comm.h" #include "neighbor.h" diff --git a/src/KSPACE/pair_coul_long.cpp b/src/KSPACE/pair_coul_long.cpp index ae268b9857..cb45b7a906 100644 --- a/src/KSPACE/pair_coul_long.cpp +++ b/src/KSPACE/pair_coul_long.cpp @@ -15,11 +15,11 @@ Contributing author: Paul Crozier (SNL) ------------------------------------------------------------------------- */ +#include "pair_coul_long.h" #include #include #include #include -#include "pair_coul_long.h" #include "atom.h" #include "comm.h" #include "force.h" diff --git a/src/KSPACE/pair_coul_msm.cpp b/src/KSPACE/pair_coul_msm.cpp index 960505142c..2173171e79 100644 --- a/src/KSPACE/pair_coul_msm.cpp +++ b/src/KSPACE/pair_coul_msm.cpp @@ -15,11 +15,11 @@ Contributing authors: Stan Moore (SNL), Paul Crozier (SNL) ------------------------------------------------------------------------- */ +#include "pair_coul_msm.h" #include #include #include #include -#include "pair_coul_msm.h" #include "atom.h" #include "comm.h" #include "force.h" diff --git a/src/KSPACE/pair_lj_charmm_coul_long.cpp b/src/KSPACE/pair_lj_charmm_coul_long.cpp index b40eab244b..3ad14c8ea7 100644 --- a/src/KSPACE/pair_lj_charmm_coul_long.cpp +++ b/src/KSPACE/pair_lj_charmm_coul_long.cpp @@ -15,11 +15,11 @@ Contributing author: Paul Crozier (SNL) ------------------------------------------------------------------------- */ +#include "pair_lj_charmm_coul_long.h" #include #include #include #include -#include "pair_lj_charmm_coul_long.h" #include "atom.h" #include "comm.h" #include "force.h" diff --git a/src/KSPACE/pair_lj_charmm_coul_msm.cpp b/src/KSPACE/pair_lj_charmm_coul_msm.cpp index 72a8e340bc..2d1775802f 100644 --- a/src/KSPACE/pair_lj_charmm_coul_msm.cpp +++ b/src/KSPACE/pair_lj_charmm_coul_msm.cpp @@ -15,11 +15,11 @@ Contributing authors: Paul Crozier (SNL), Stan Moore (SNL) ------------------------------------------------------------------------- */ +#include "pair_lj_charmm_coul_msm.h" #include #include #include #include -#include "pair_lj_charmm_coul_msm.h" #include "atom.h" #include "comm.h" #include "force.h" diff --git a/src/KSPACE/pair_lj_charmmfsw_coul_long.cpp b/src/KSPACE/pair_lj_charmmfsw_coul_long.cpp index cdde211157..7f32613cba 100644 --- a/src/KSPACE/pair_lj_charmmfsw_coul_long.cpp +++ b/src/KSPACE/pair_lj_charmmfsw_coul_long.cpp @@ -19,11 +19,11 @@ additional assistance from Robert A. Latour, Clemson University ------------------------------------------------------------------------- */ +#include "pair_lj_charmmfsw_coul_long.h" #include #include #include #include -#include "pair_lj_charmmfsw_coul_long.h" #include "atom.h" #include "update.h" #include "comm.h" diff --git a/src/KSPACE/pair_lj_cut_coul_long.cpp b/src/KSPACE/pair_lj_cut_coul_long.cpp index fde7fa8e35..59f4766fa3 100644 --- a/src/KSPACE/pair_lj_cut_coul_long.cpp +++ b/src/KSPACE/pair_lj_cut_coul_long.cpp @@ -15,11 +15,11 @@ Contributing author: Paul Crozier (SNL) ------------------------------------------------------------------------- */ +#include "pair_lj_cut_coul_long.h" #include #include #include #include -#include "pair_lj_cut_coul_long.h" #include "atom.h" #include "comm.h" #include "force.h" diff --git a/src/KSPACE/pair_lj_cut_coul_msm.cpp b/src/KSPACE/pair_lj_cut_coul_msm.cpp index c2e566a117..1305d485da 100644 --- a/src/KSPACE/pair_lj_cut_coul_msm.cpp +++ b/src/KSPACE/pair_lj_cut_coul_msm.cpp @@ -15,11 +15,11 @@ Contributing authors: Stan Moore (SNL), Paul Crozier (SNL) ------------------------------------------------------------------------- */ +#include "pair_lj_cut_coul_msm.h" #include #include #include #include -#include "pair_lj_cut_coul_msm.h" #include "atom.h" #include "comm.h" #include "force.h" diff --git a/src/KSPACE/pair_lj_cut_tip4p_long.cpp b/src/KSPACE/pair_lj_cut_tip4p_long.cpp index f5889fd520..cd9b3c032d 100644 --- a/src/KSPACE/pair_lj_cut_tip4p_long.cpp +++ b/src/KSPACE/pair_lj_cut_tip4p_long.cpp @@ -16,11 +16,11 @@ simpler force assignment added by Rolf Isele-Holder (Aachen University) ------------------------------------------------------------------------- */ +#include "pair_lj_cut_tip4p_long.h" #include #include #include #include -#include "pair_lj_cut_tip4p_long.h" #include "angle.h" #include "atom.h" #include "bond.h" diff --git a/src/KSPACE/pair_lj_long_coul_long.cpp b/src/KSPACE/pair_lj_long_coul_long.cpp index 493866a895..46dbb60a96 100644 --- a/src/KSPACE/pair_lj_long_coul_long.cpp +++ b/src/KSPACE/pair_lj_long_coul_long.cpp @@ -17,12 +17,12 @@ University New Orleans) ------------------------------------------------------------------------- */ +#include "pair_lj_long_coul_long.h" #include #include #include #include #include "math_vector.h" -#include "pair_lj_long_coul_long.h" #include "atom.h" #include "comm.h" #include "neighbor.h" diff --git a/src/KSPACE/pair_lj_long_tip4p_long.cpp b/src/KSPACE/pair_lj_long_tip4p_long.cpp index 3137b9d79a..5a1e347c78 100644 --- a/src/KSPACE/pair_lj_long_tip4p_long.cpp +++ b/src/KSPACE/pair_lj_long_tip4p_long.cpp @@ -16,11 +16,11 @@ Rolf Isele-Holder (Aachen University) ------------------------------------------------------------------------- */ +#include "pair_lj_long_tip4p_long.h" #include #include #include #include -#include "pair_lj_long_tip4p_long.h" #include "angle.h" #include "atom.h" #include "bond.h" diff --git a/src/KSPACE/pair_tip4p_long.cpp b/src/KSPACE/pair_tip4p_long.cpp index 9419fdf196..deb8662a8b 100644 --- a/src/KSPACE/pair_tip4p_long.cpp +++ b/src/KSPACE/pair_tip4p_long.cpp @@ -16,11 +16,11 @@ simpler force assignment added by Rolf Isele-Holder (Aachen University) ------------------------------------------------------------------------- */ +#include "pair_tip4p_long.h" #include #include #include #include -#include "pair_tip4p_long.h" #include "angle.h" #include "atom.h" #include "bond.h" diff --git a/src/KSPACE/pppm.cpp b/src/KSPACE/pppm.cpp index 53c18804a5..ae545c5c27 100644 --- a/src/KSPACE/pppm.cpp +++ b/src/KSPACE/pppm.cpp @@ -18,12 +18,12 @@ triclinic added by Stan Moore (SNL) ------------------------------------------------------------------------- */ +#include "pppm.h" #include #include #include #include #include -#include "pppm.h" #include "atom.h" #include "comm.h" #include "gridcomm.h" diff --git a/src/KSPACE/pppm_cg.cpp b/src/KSPACE/pppm_cg.cpp index 3285dba21c..f9bd7b0cb4 100644 --- a/src/KSPACE/pppm_cg.cpp +++ b/src/KSPACE/pppm_cg.cpp @@ -15,11 +15,11 @@ Contributing author: Axel Kohlmeyer (Temple U) ------------------------------------------------------------------------- */ +#include "pppm_cg.h" #include #include #include #include - #include "atom.h" #include "gridcomm.h" #include "domain.h" @@ -27,8 +27,6 @@ #include "force.h" #include "neighbor.h" #include "memory.h" -#include "pppm_cg.h" - #include "math_const.h" using namespace LAMMPS_NS; diff --git a/src/KSPACE/pppm_dipole.cpp b/src/KSPACE/pppm_dipole.cpp index 21a777dd75..ad03b8205a 100644 --- a/src/KSPACE/pppm_dipole.cpp +++ b/src/KSPACE/pppm_dipole.cpp @@ -15,12 +15,12 @@ Contributing authors: Stan Moore (SNL), Julien Tranchida (SNL) ------------------------------------------------------------------------- */ +#include "pppm_dipole.h" #include #include #include #include #include -#include "pppm_dipole.h" #include "atom.h" #include "comm.h" #include "gridcomm.h" diff --git a/src/KSPACE/pppm_dipole_spin.cpp b/src/KSPACE/pppm_dipole_spin.cpp index 878d40c82e..2c96eadde1 100644 --- a/src/KSPACE/pppm_dipole_spin.cpp +++ b/src/KSPACE/pppm_dipole_spin.cpp @@ -15,12 +15,12 @@ Contributing author: Julien Tranchida (SNL) ------------------------------------------------------------------------- */ +#include "pppm_dipole_spin.h" #include #include #include #include #include -#include "pppm_dipole_spin.h" #include "atom.h" #include "comm.h" #include "gridcomm.h" diff --git a/src/KSPACE/pppm_disp.cpp b/src/KSPACE/pppm_disp.cpp index 45dce0895b..22e570049c 100644 --- a/src/KSPACE/pppm_disp.cpp +++ b/src/KSPACE/pppm_disp.cpp @@ -16,12 +16,12 @@ Paul Crozier (SNL) ------------------------------------------------------------------------- */ +#include "pppm_disp.h" #include #include #include #include #include -#include "pppm_disp.h" #include "math_const.h" #include "atom.h" #include "comm.h" diff --git a/src/KSPACE/pppm_disp_tip4p.cpp b/src/KSPACE/pppm_disp_tip4p.cpp index 2bc63a84bb..36e6159131 100644 --- a/src/KSPACE/pppm_disp_tip4p.cpp +++ b/src/KSPACE/pppm_disp_tip4p.cpp @@ -16,8 +16,8 @@ Rolf Isele-Holder (Aachen University) ------------------------------------------------------------------------- */ -#include #include "pppm_disp_tip4p.h" +#include #include "pppm_disp.h" #include "atom.h" #include "domain.h" diff --git a/src/KSPACE/pppm_stagger.cpp b/src/KSPACE/pppm_stagger.cpp index a5ed6de626..5c2e2a6098 100644 --- a/src/KSPACE/pppm_stagger.cpp +++ b/src/KSPACE/pppm_stagger.cpp @@ -15,12 +15,12 @@ Contributing author: Stan Moore (Sandia) ------------------------------------------------------------------------- */ +#include "pppm_stagger.h" #include #include #include #include #include -#include "pppm_stagger.h" #include "atom.h" #include "gridcomm.h" #include "force.h" diff --git a/src/KSPACE/pppm_tip4p.cpp b/src/KSPACE/pppm_tip4p.cpp index b9fe3e6488..52a1fb3787 100644 --- a/src/KSPACE/pppm_tip4p.cpp +++ b/src/KSPACE/pppm_tip4p.cpp @@ -15,8 +15,8 @@ Contributing authors: Amalie Frischknecht and Ahmed Ismail (SNL) ------------------------------------------------------------------------- */ -#include #include "pppm_tip4p.h" +#include #include "atom.h" #include "domain.h" #include "force.h" diff --git a/src/KSPACE/remap.cpp b/src/KSPACE/remap.cpp index 26541f121e..85fe78c9d7 100644 --- a/src/KSPACE/remap.cpp +++ b/src/KSPACE/remap.cpp @@ -11,9 +11,9 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ +#include "remap.h" #include #include -#include "remap.h" #define PACK_DATA FFT_SCALAR diff --git a/src/KSPACE/remap_wrap.cpp b/src/KSPACE/remap_wrap.cpp index 8ea2918d7f..7929cd053c 100644 --- a/src/KSPACE/remap_wrap.cpp +++ b/src/KSPACE/remap_wrap.cpp @@ -11,8 +11,8 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include #include "remap_wrap.h" +#include #include "error.h" using namespace LAMMPS_NS; -- GitLab From 6cf3bb3e4e5e5176b985fe820876e0d240e1159e Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Wed, 3 Jul 2019 21:56:29 -0400 Subject: [PATCH 173/469] recover compilation of KSPACE package --- src/KSPACE/fft3d.h | 2 ++ 1 file changed, 2 insertions(+) diff --git a/src/KSPACE/fft3d.h b/src/KSPACE/fft3d.h index a51818d986..8c3d2f27ad 100644 --- a/src/KSPACE/fft3d.h +++ b/src/KSPACE/fft3d.h @@ -11,6 +11,8 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ +#include + // User-settable FFT precision // FFT_PRECISION = 1 is single-precision complex (4-byte real, 4-byte imag) -- GitLab From 416911aa7e05a94328bfb9f1d7a580f40a450603 Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Wed, 3 Jul 2019 21:57:39 -0400 Subject: [PATCH 174/469] more rearranging of include file order to put implementation headers first --- src/LATTE/fix_latte.cpp | 2 +- src/MANYBODY/fix_qeq_comb.cpp | 2 +- src/MANYBODY/pair_adp.cpp | 2 +- src/MANYBODY/pair_airebo.cpp | 2 +- src/MANYBODY/pair_atm.cpp | 2 +- src/MANYBODY/pair_bop.cpp | 2 +- src/MANYBODY/pair_comb.cpp | 2 +- src/MANYBODY/pair_comb3.cpp | 2 +- src/MANYBODY/pair_eam.cpp | 2 +- src/MANYBODY/pair_eam_alloy.cpp | 2 +- src/MANYBODY/pair_eam_cd.cpp | 2 +- src/MANYBODY/pair_eam_fs.cpp | 2 +- src/MANYBODY/pair_eim.cpp | 2 +- src/MANYBODY/pair_gw.cpp | 2 +- src/MANYBODY/pair_gw_zbl.cpp | 2 +- src/MANYBODY/pair_lcbop.cpp | 2 +- src/MANYBODY/pair_nb3b_harmonic.cpp | 2 +- src/MANYBODY/pair_polymorphic.cpp | 2 +- src/MANYBODY/pair_sw.cpp | 2 +- src/MANYBODY/pair_tersoff.cpp | 2 +- src/MANYBODY/pair_tersoff_mod.cpp | 2 +- src/MANYBODY/pair_tersoff_mod_c.cpp | 2 +- src/MANYBODY/pair_tersoff_zbl.cpp | 2 +- src/MANYBODY/pair_vashishta.cpp | 2 +- src/MANYBODY/pair_vashishta_table.cpp | 2 +- src/MC/fix_atom_swap.cpp | 2 +- src/MC/fix_bond_break.cpp | 2 +- src/MC/fix_bond_create.cpp | 2 +- src/MC/fix_bond_swap.cpp | 2 +- src/MC/fix_gcmc.cpp | 2 +- src/MC/pair_dsmc.cpp | 2 +- src/MESSAGE/fix_client_md.cpp | 2 +- src/MESSAGE/message.cpp | 2 +- src/MESSAGE/server.cpp | 2 +- src/MESSAGE/server_md.cpp | 2 +- src/MISC/compute_msd_nongauss.cpp | 2 +- src/MISC/compute_ti.cpp | 4 +-- src/MISC/dump_xtc.cpp | 2 +- src/MISC/fix_deposit.cpp | 2 +- src/MISC/fix_efield.cpp | 2 +- src/MISC/fix_evaporate.cpp | 2 +- src/MISC/fix_gld.cpp | 2 +- src/MISC/fix_oneway.cpp | 2 +- src/MISC/fix_orient_bcc.cpp | 2 +- src/MISC/fix_orient_fcc.cpp | 2 +- src/MISC/fix_thermal_conductivity.cpp | 2 +- src/MISC/fix_ttm.cpp | 2 +- src/MISC/fix_viscosity.cpp | 2 +- src/MISC/pair_nm_cut.cpp | 2 +- src/MISC/pair_nm_cut_coul_cut.cpp | 2 +- src/MISC/pair_nm_cut_coul_long.cpp | 2 +- src/MISC/xdr_compat.cpp | 2 +- src/MOLECULE/angle_charmm.cpp | 2 +- src/MOLECULE/angle_cosine.cpp | 2 +- src/MOLECULE/angle_cosine_delta.cpp | 2 +- src/MOLECULE/angle_cosine_periodic.cpp | 2 +- src/MOLECULE/angle_cosine_squared.cpp | 2 +- src/MOLECULE/angle_harmonic.cpp | 2 +- src/MOLECULE/angle_table.cpp | 2 +- src/MOLECULE/atom_vec_angle.cpp | 2 +- src/MOLECULE/atom_vec_bond.cpp | 2 +- src/MOLECULE/atom_vec_full.cpp | 2 +- src/MOLECULE/atom_vec_molecular.cpp | 2 +- src/MOLECULE/atom_vec_template.cpp | 2 +- src/MOLECULE/bond_fene.cpp | 2 +- src/MOLECULE/bond_fene_expand.cpp | 2 +- src/MOLECULE/bond_gromos.cpp | 2 +- src/MOLECULE/bond_harmonic.cpp | 2 +- src/MOLECULE/bond_morse.cpp | 2 +- src/MOLECULE/bond_nonlinear.cpp | 2 +- src/MOLECULE/bond_quartic.cpp | 2 +- src/MOLECULE/bond_table.cpp | 2 +- src/MOLECULE/dihedral_charmm.cpp | 2 +- src/MOLECULE/dihedral_charmmfsw.cpp | 2 +- src/MOLECULE/dihedral_harmonic.cpp | 2 +- src/MOLECULE/dihedral_helix.cpp | 2 +- src/MOLECULE/dihedral_multi_harmonic.cpp | 2 +- src/MOLECULE/dihedral_opls.cpp | 2 +- src/MOLECULE/fix_cmap.cpp | 2 +- src/MOLECULE/improper_cvff.cpp | 2 +- src/MOLECULE/improper_harmonic.cpp | 2 +- src/MOLECULE/improper_umbrella.cpp | 2 +- src/MOLECULE/pair_hbond_dreiding_lj.cpp | 2 +- src/MOLECULE/pair_hbond_dreiding_morse.cpp | 2 +- src/MOLECULE/pair_lj_charmm_coul_charmm.cpp | 2 +- .../pair_lj_charmm_coul_charmm_implicit.cpp | 2 +- .../pair_lj_charmmfsw_coul_charmmfsh.cpp | 2 +- src/MOLECULE/pair_lj_cut_tip4p_cut.cpp | 2 +- src/MOLECULE/pair_tip4p_cut.cpp | 2 +- src/MPIIO/dump_atom_mpiio.cpp | 2 +- src/MPIIO/dump_cfg_mpiio.cpp | 2 +- src/MPIIO/dump_custom_mpiio.cpp | 2 +- src/MPIIO/dump_xyz_mpiio.cpp | 2 +- src/MPIIO/restart_mpiio.cpp | 2 +- src/MSCG/fix_mscg.cpp | 2 +- src/OPT/pair_eam_opt.cpp | 2 +- src/OPT/pair_lj_charmm_coul_long_opt.cpp | 2 +- src/OPT/pair_lj_cut_coul_long_opt.cpp | 2 +- src/OPT/pair_lj_cut_opt.cpp | 2 +- src/OPT/pair_lj_cut_tip4p_long_opt.cpp | 2 +- src/OPT/pair_lj_long_coul_long_opt.cpp | 2 +- src/OPT/pair_morse_opt.cpp | 2 +- src/OPT/pair_ufm_opt.cpp | 2 +- src/PERI/atom_vec_peri.cpp | 2 +- src/PERI/compute_damage_atom.cpp | 2 +- src/PERI/compute_dilatation_atom.cpp | 2 +- src/PERI/compute_plasticity_atom.cpp | 2 +- src/PERI/fix_peri_neigh.cpp | 2 +- src/PERI/pair_peri_eps.cpp | 2 +- src/PERI/pair_peri_lps.cpp | 2 +- src/PERI/pair_peri_pmb.cpp | 2 +- src/PERI/pair_peri_ves.cpp | 2 +- src/POEMS/fix_poems.cpp | 2 +- src/PYTHON/fix_python_invoke.cpp | 2 +- src/PYTHON/fix_python_move.cpp | 2 +- src/PYTHON/pair_python.cpp | 2 +- src/PYTHON/python_impl.cpp | 2 +- src/QEQ/fix_qeq.cpp | 2 +- src/QEQ/fix_qeq_dynamic.cpp | 2 +- src/QEQ/fix_qeq_fire.cpp | 2 +- src/QEQ/fix_qeq_point.cpp | 2 +- src/QEQ/fix_qeq_shielded.cpp | 2 +- src/QEQ/fix_qeq_slater.cpp | 2 +- src/REPLICA/compute_event_displace.cpp | 2 +- src/REPLICA/fix_event.cpp | 2 +- src/REPLICA/fix_event_hyper.cpp | 2 +- src/REPLICA/fix_event_prd.cpp | 2 +- src/REPLICA/fix_event_tad.cpp | 2 +- src/REPLICA/fix_hyper.cpp | 2 +- src/REPLICA/fix_hyper_global.cpp | 2 +- src/REPLICA/fix_hyper_local.cpp | 2 +- src/REPLICA/fix_neb.cpp | 2 +- src/REPLICA/hyper.cpp | 2 +- src/REPLICA/neb.cpp | 2 +- src/REPLICA/prd.cpp | 2 +- src/REPLICA/tad.cpp | 2 +- src/REPLICA/temper.cpp | 2 +- src/REPLICA/verlet_split.cpp | 2 +- src/RIGID/compute_erotate_rigid.cpp | 2 +- src/RIGID/compute_ke_rigid.cpp | 2 +- src/RIGID/compute_rigid_local.cpp | 2 +- src/RIGID/fix_ehex.cpp | 2 +- src/RIGID/fix_rattle.cpp | 2 +- src/RIGID/fix_rigid.cpp | 2 +- src/RIGID/fix_rigid_nh.cpp | 2 +- src/RIGID/fix_rigid_nh_small.cpp | 2 +- src/RIGID/fix_rigid_nph.cpp | 2 +- src/RIGID/fix_rigid_nph_small.cpp | 2 +- src/RIGID/fix_rigid_npt.cpp | 2 +- src/RIGID/fix_rigid_npt_small.cpp | 2 +- src/RIGID/fix_rigid_small.cpp | 2 +- src/RIGID/fix_shake.cpp | 2 +- src/SHOCK/fix_append_atoms.cpp | 2 +- src/SHOCK/fix_msst.cpp | 2 +- src/SHOCK/fix_nphug.cpp | 2 +- src/SHOCK/fix_wall_piston.cpp | 2 +- src/SNAP/compute_sna_atom.cpp | 5 ++-- src/SNAP/compute_snad_atom.cpp | 5 ++-- src/SNAP/compute_snav_atom.cpp | 3 ++- src/SNAP/pair_snap.cpp | 2 +- src/SNAP/sna.cpp | 2 +- src/SPIN/atom_vec_spin.cpp | 2 +- src/SPIN/compute_spin.cpp | 2 +- src/SPIN/fix_langevin_spin.cpp | 2 +- src/SPIN/fix_neb_spin.cpp | 2 +- src/SPIN/fix_nve_spin.cpp | 2 +- src/SPIN/fix_precession_spin.cpp | 2 +- src/SPIN/fix_setforce_spin.cpp | 2 +- src/SPIN/min_spin.cpp | 2 +- src/SPIN/neb_spin.cpp | 2 +- src/SPIN/pair_spin.cpp | 2 +- src/SPIN/pair_spin_dipole_cut.cpp | 2 +- src/SPIN/pair_spin_dipole_long.cpp | 2 +- src/SPIN/pair_spin_dmi.cpp | 2 +- src/SPIN/pair_spin_exchange.cpp | 2 +- src/SPIN/pair_spin_magelec.cpp | 2 +- src/SPIN/pair_spin_neel.cpp | 2 +- src/SRD/fix_srd.cpp | 2 +- src/SRD/fix_wall_srd.cpp | 2 +- src/USER-ADIOS/dump_atom_adios.cpp | 2 +- src/USER-ADIOS/dump_custom_adios.cpp | 4 +-- src/USER-ATC/fix_atc.cpp | 10 +++---- src/USER-AWPMD/atom_vec_wavepacket.cpp | 2 +- src/USER-AWPMD/fix_nve_awpmd.cpp | 2 +- src/USER-AWPMD/pair_awpmd_cut.cpp | 2 +- src/USER-BOCS/compute_pressure_bocs.cpp | 2 +- src/USER-BOCS/fix_bocs.cpp | 2 +- src/USER-CGDNA/bond_oxdna2_fene.cpp | 2 +- src/USER-CGDNA/bond_oxdna_fene.cpp | 2 +- src/USER-CGDNA/fix_nve_dot.cpp | 2 +- src/USER-CGDNA/fix_nve_dotc_langevin.cpp | 2 +- src/USER-CGDNA/pair_oxdna2_coaxstk.cpp | 2 +- src/USER-CGDNA/pair_oxdna2_dh.cpp | 2 +- src/USER-CGDNA/pair_oxdna2_excv.cpp | 2 +- src/USER-CGDNA/pair_oxdna2_stk.cpp | 2 +- src/USER-CGDNA/pair_oxdna_coaxstk.cpp | 2 +- src/USER-CGDNA/pair_oxdna_excv.cpp | 2 +- src/USER-CGDNA/pair_oxdna_hbond.cpp | 2 +- src/USER-CGDNA/pair_oxdna_stk.cpp | 2 +- src/USER-CGDNA/pair_oxdna_xstk.cpp | 2 +- src/USER-CGSDK/angle_sdk.cpp | 2 +- src/USER-CGSDK/pair_lj_sdk.cpp | 2 +- src/USER-CGSDK/pair_lj_sdk_coul_long.cpp | 2 +- src/USER-CGSDK/pair_lj_sdk_coul_msm.cpp | 2 +- src/USER-COLVARS/colvarproxy_lammps.cpp | 26 +++++++++---------- src/USER-COLVARS/fix_colvars.cpp | 2 +- src/USER-COLVARS/group_ndx.cpp | 5 ++-- src/USER-COLVARS/ndx_group.cpp | 7 +++-- 208 files changed, 233 insertions(+), 234 deletions(-) diff --git a/src/LATTE/fix_latte.cpp b/src/LATTE/fix_latte.cpp index 645b298e09..7d4e89272d 100644 --- a/src/LATTE/fix_latte.cpp +++ b/src/LATTE/fix_latte.cpp @@ -15,9 +15,9 @@ Contributing author: Christian Negre (LANL) ------------------------------------------------------------------------- */ +#include "fix_latte.h" #include #include -#include "fix_latte.h" #include "atom.h" #include "comm.h" #include "update.h" diff --git a/src/MANYBODY/fix_qeq_comb.cpp b/src/MANYBODY/fix_qeq_comb.cpp index 5019e7711a..9e9bbcc9d6 100644 --- a/src/MANYBODY/fix_qeq_comb.cpp +++ b/src/MANYBODY/fix_qeq_comb.cpp @@ -15,13 +15,13 @@ Contributing authors: Ray Shan (Sandia, tnshan@sandia.gov) ------------------------------------------------------------------------- */ +#include "fix_qeq_comb.h" #include #include #include #include #include "pair_comb.h" #include "pair_comb3.h" -#include "fix_qeq_comb.h" #include "neighbor.h" #include "neigh_list.h" #include "neigh_request.h" diff --git a/src/MANYBODY/pair_adp.cpp b/src/MANYBODY/pair_adp.cpp index 68511b8709..8051f97634 100644 --- a/src/MANYBODY/pair_adp.cpp +++ b/src/MANYBODY/pair_adp.cpp @@ -16,11 +16,11 @@ Chandra Veer Singh (Cornell) ------------------------------------------------------------------------- */ +#include "pair_adp.h" #include #include #include #include -#include "pair_adp.h" #include "atom.h" #include "force.h" #include "comm.h" diff --git a/src/MANYBODY/pair_airebo.cpp b/src/MANYBODY/pair_airebo.cpp index e3c5a1627b..fd2016b7a7 100644 --- a/src/MANYBODY/pair_airebo.cpp +++ b/src/MANYBODY/pair_airebo.cpp @@ -20,12 +20,12 @@ Thomas C. O'Connor (JHU) 2014 ------------------------------------------------------------------------- */ +#include "pair_airebo.h" #include #include #include #include #include -#include "pair_airebo.h" #include "atom.h" #include "neighbor.h" #include "force.h" diff --git a/src/MANYBODY/pair_atm.cpp b/src/MANYBODY/pair_atm.cpp index c157e0763c..ba68033721 100644 --- a/src/MANYBODY/pair_atm.cpp +++ b/src/MANYBODY/pair_atm.cpp @@ -15,8 +15,8 @@ Contributing author: Sergey Lishchuk ------------------------------------------------------------------------- */ -#include #include "pair_atm.h" +#include #include "atom.h" #include "citeme.h" #include "comm.h" diff --git a/src/MANYBODY/pair_bop.cpp b/src/MANYBODY/pair_bop.cpp index ac157e071c..27c24ce3d7 100644 --- a/src/MANYBODY/pair_bop.cpp +++ b/src/MANYBODY/pair_bop.cpp @@ -32,12 +32,12 @@ Rules"_http://lammps.sandia.gov/open_source.html ------------------------------------------------------------------------- */ +#include "pair_bop.h" #include #include #include #include #include -#include "pair_bop.h" #include "atom.h" #include "neighbor.h" #include "neigh_request.h" diff --git a/src/MANYBODY/pair_comb.cpp b/src/MANYBODY/pair_comb.cpp index 980aa84b2a..b9a17eeb35 100644 --- a/src/MANYBODY/pair_comb.cpp +++ b/src/MANYBODY/pair_comb.cpp @@ -18,11 +18,11 @@ and Aidan Thompson's Tersoff code in LAMMPS ------------------------------------------------------------------------- */ +#include "pair_comb.h" #include #include #include #include -#include "pair_comb.h" #include "atom.h" #include "comm.h" #include "force.h" diff --git a/src/MANYBODY/pair_comb3.cpp b/src/MANYBODY/pair_comb3.cpp index 097f235ff2..846ef7d4b9 100644 --- a/src/MANYBODY/pair_comb3.cpp +++ b/src/MANYBODY/pair_comb3.cpp @@ -17,11 +17,11 @@ Dundar Yilmaz (dundar.yilmaz@zirve.edu.tr) ------------------------------------------------------------------------- */ +#include "pair_comb3.h" #include #include #include #include -#include "pair_comb3.h" #include "atom.h" #include "comm.h" #include "force.h" diff --git a/src/MANYBODY/pair_eam.cpp b/src/MANYBODY/pair_eam.cpp index b7957349b6..e6476b78c5 100644 --- a/src/MANYBODY/pair_eam.cpp +++ b/src/MANYBODY/pair_eam.cpp @@ -15,11 +15,11 @@ Contributing authors: Stephen Foiles (SNL), Murray Daw (SNL) ------------------------------------------------------------------------- */ +#include "pair_eam.h" #include #include #include #include -#include "pair_eam.h" #include "atom.h" #include "force.h" #include "comm.h" diff --git a/src/MANYBODY/pair_eam_alloy.cpp b/src/MANYBODY/pair_eam_alloy.cpp index c004030240..7aae786720 100644 --- a/src/MANYBODY/pair_eam_alloy.cpp +++ b/src/MANYBODY/pair_eam_alloy.cpp @@ -15,10 +15,10 @@ Contributing authors: Stephen Foiles (SNL), Murray Daw (SNL) ------------------------------------------------------------------------- */ +#include "pair_eam_alloy.h" #include #include #include -#include "pair_eam_alloy.h" #include "atom.h" #include "comm.h" #include "force.h" diff --git a/src/MANYBODY/pair_eam_cd.cpp b/src/MANYBODY/pair_eam_cd.cpp index c111c6d950..55ad597cce 100644 --- a/src/MANYBODY/pair_eam_cd.cpp +++ b/src/MANYBODY/pair_eam_cd.cpp @@ -17,11 +17,11 @@ Germany Department of Materials Science ------------------------------------------------------------------------- */ +#include "pair_eam_cd.h" #include #include #include #include -#include "pair_eam_cd.h" #include "atom.h" #include "force.h" #include "comm.h" diff --git a/src/MANYBODY/pair_eam_fs.cpp b/src/MANYBODY/pair_eam_fs.cpp index bbda84fdf1..7b13988d0c 100644 --- a/src/MANYBODY/pair_eam_fs.cpp +++ b/src/MANYBODY/pair_eam_fs.cpp @@ -15,10 +15,10 @@ Contributing authors: Tim Lau (MIT) ------------------------------------------------------------------------- */ +#include "pair_eam_fs.h" #include #include #include -#include "pair_eam_fs.h" #include "atom.h" #include "comm.h" #include "force.h" diff --git a/src/MANYBODY/pair_eim.cpp b/src/MANYBODY/pair_eim.cpp index f1c028ef38..58cb1fd2e0 100644 --- a/src/MANYBODY/pair_eim.cpp +++ b/src/MANYBODY/pair_eim.cpp @@ -15,11 +15,11 @@ Contributing author: Xiaowang Zhou (SNL) ------------------------------------------------------------------------- */ +#include "pair_eim.h" #include #include #include #include -#include "pair_eim.h" #include "atom.h" #include "force.h" #include "comm.h" diff --git a/src/MANYBODY/pair_gw.cpp b/src/MANYBODY/pair_gw.cpp index e4b74f7a29..07e9201f94 100644 --- a/src/MANYBODY/pair_gw.cpp +++ b/src/MANYBODY/pair_gw.cpp @@ -16,11 +16,11 @@ based on PairTersoff by Aidan Thompson (SNL) ------------------------------------------------------------------------- */ +#include "pair_gw.h" #include #include #include #include -#include "pair_gw.h" #include "atom.h" #include "neighbor.h" #include "neigh_list.h" diff --git a/src/MANYBODY/pair_gw_zbl.cpp b/src/MANYBODY/pair_gw_zbl.cpp index f3dd1bc04b..cd83727ed3 100644 --- a/src/MANYBODY/pair_gw_zbl.cpp +++ b/src/MANYBODY/pair_gw_zbl.cpp @@ -16,11 +16,11 @@ Based on PairTersoffZBL by Aidan Thompson (SNL) and David Farrell (NWU) ------------------------------------------------------------------------- */ +#include "pair_gw_zbl.h" #include #include #include #include -#include "pair_gw_zbl.h" #include "atom.h" #include "update.h" #include "neighbor.h" diff --git a/src/MANYBODY/pair_lcbop.cpp b/src/MANYBODY/pair_lcbop.cpp index 05cdea8055..b0240978a9 100644 --- a/src/MANYBODY/pair_lcbop.cpp +++ b/src/MANYBODY/pair_lcbop.cpp @@ -16,12 +16,12 @@ based on pair_airebo by Ase Henry (MIT) ------------------------------------------------------------------------- */ +#include "pair_lcbop.h" #include #include #include #include #include -#include "pair_lcbop.h" #include "atom.h" #include "neighbor.h" #include "neigh_request.h" diff --git a/src/MANYBODY/pair_nb3b_harmonic.cpp b/src/MANYBODY/pair_nb3b_harmonic.cpp index a61b403459..ac20c3e61f 100644 --- a/src/MANYBODY/pair_nb3b_harmonic.cpp +++ b/src/MANYBODY/pair_nb3b_harmonic.cpp @@ -16,11 +16,11 @@ (based on Stillinger-Weber pair style) ------------------------------------------------------------------------- */ +#include "pair_nb3b_harmonic.h" #include #include #include #include -#include "pair_nb3b_harmonic.h" #include "atom.h" #include "neighbor.h" #include "neigh_request.h" diff --git a/src/MANYBODY/pair_polymorphic.cpp b/src/MANYBODY/pair_polymorphic.cpp index d3aca4e889..0cca50823d 100644 --- a/src/MANYBODY/pair_polymorphic.cpp +++ b/src/MANYBODY/pair_polymorphic.cpp @@ -16,11 +16,11 @@ This modifies from pair_tersoff.cpp by Aidan Thompson (SNL) ------------------------------------------------------------------------- */ +#include "pair_polymorphic.h" #include #include #include #include -#include "pair_polymorphic.h" #include "atom.h" #include "neighbor.h" #include "neigh_list.h" diff --git a/src/MANYBODY/pair_sw.cpp b/src/MANYBODY/pair_sw.cpp index 5a148fb152..ea47fc97c3 100644 --- a/src/MANYBODY/pair_sw.cpp +++ b/src/MANYBODY/pair_sw.cpp @@ -15,11 +15,11 @@ Contributing author: Aidan Thompson (SNL) ------------------------------------------------------------------------- */ +#include "pair_sw.h" #include #include #include #include -#include "pair_sw.h" #include "atom.h" #include "neighbor.h" #include "neigh_request.h" diff --git a/src/MANYBODY/pair_tersoff.cpp b/src/MANYBODY/pair_tersoff.cpp index 213b1037bb..9d7f804f9a 100644 --- a/src/MANYBODY/pair_tersoff.cpp +++ b/src/MANYBODY/pair_tersoff.cpp @@ -15,11 +15,11 @@ Contributing author: Aidan Thompson (SNL) ------------------------------------------------------------------------- */ +#include "pair_tersoff.h" #include #include #include #include -#include "pair_tersoff.h" #include "atom.h" #include "neighbor.h" #include "neigh_list.h" diff --git a/src/MANYBODY/pair_tersoff_mod.cpp b/src/MANYBODY/pair_tersoff_mod.cpp index e8fdecfe01..df3c41fc33 100644 --- a/src/MANYBODY/pair_tersoff_mod.cpp +++ b/src/MANYBODY/pair_tersoff_mod.cpp @@ -16,11 +16,11 @@ Vitaly Dozhdikov (JIHT of RAS) - MOD addition ------------------------------------------------------------------------- */ +#include "pair_tersoff_mod.h" #include #include #include #include -#include "pair_tersoff_mod.h" #include "atom.h" #include "neighbor.h" #include "neigh_list.h" diff --git a/src/MANYBODY/pair_tersoff_mod_c.cpp b/src/MANYBODY/pair_tersoff_mod_c.cpp index 4a5904c106..d34291f6cd 100644 --- a/src/MANYBODY/pair_tersoff_mod_c.cpp +++ b/src/MANYBODY/pair_tersoff_mod_c.cpp @@ -15,11 +15,11 @@ Contributing author: Ganga P Purja Pun (George Mason University, Fairfax) ------------------------------------------------------------------------- */ +#include "pair_tersoff_mod_c.h" #include #include #include #include -#include "pair_tersoff_mod_c.h" #include "atom.h" #include "neighbor.h" #include "neigh_list.h" diff --git a/src/MANYBODY/pair_tersoff_zbl.cpp b/src/MANYBODY/pair_tersoff_zbl.cpp index 353e3d2264..6a8aa40782 100644 --- a/src/MANYBODY/pair_tersoff_zbl.cpp +++ b/src/MANYBODY/pair_tersoff_zbl.cpp @@ -16,11 +16,11 @@ David Farrell (NWU) - ZBL addition ------------------------------------------------------------------------- */ +#include "pair_tersoff_zbl.h" #include #include #include #include -#include "pair_tersoff_zbl.h" #include "atom.h" #include "update.h" #include "neighbor.h" diff --git a/src/MANYBODY/pair_vashishta.cpp b/src/MANYBODY/pair_vashishta.cpp index 3d4b1d900e..5055dadfaf 100644 --- a/src/MANYBODY/pair_vashishta.cpp +++ b/src/MANYBODY/pair_vashishta.cpp @@ -16,11 +16,11 @@ Aidan Thompson (SNL) ------------------------------------------------------------------------- */ +#include "pair_vashishta.h" #include #include #include #include -#include "pair_vashishta.h" #include "atom.h" #include "neighbor.h" #include "neigh_request.h" diff --git a/src/MANYBODY/pair_vashishta_table.cpp b/src/MANYBODY/pair_vashishta_table.cpp index d4eaa59f1a..726e0f83f1 100644 --- a/src/MANYBODY/pair_vashishta_table.cpp +++ b/src/MANYBODY/pair_vashishta_table.cpp @@ -15,11 +15,11 @@ Contributing author: Anders Hafreager (UiO), andershaf@gmail.com ------------------------------------------------------------------------- */ +#include "pair_vashishta_table.h" #include #include #include #include -#include "pair_vashishta_table.h" #include "atom.h" #include "neighbor.h" #include "neigh_request.h" diff --git a/src/MC/fix_atom_swap.cpp b/src/MC/fix_atom_swap.cpp index 7d817ffbb1..c14efcca46 100644 --- a/src/MC/fix_atom_swap.cpp +++ b/src/MC/fix_atom_swap.cpp @@ -16,11 +16,11 @@ Alexander Stukowski ------------------------------------------------------------------------- */ +#include "fix_atom_swap.h" #include #include #include #include -#include "fix_atom_swap.h" #include "atom.h" #include "atom_vec.h" #include "atom_vec_hybrid.h" diff --git a/src/MC/fix_bond_break.cpp b/src/MC/fix_bond_break.cpp index 05edc0509e..1b07395f1e 100644 --- a/src/MC/fix_bond_break.cpp +++ b/src/MC/fix_bond_break.cpp @@ -11,11 +11,11 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ +#include "fix_bond_break.h" #include #include #include #include -#include "fix_bond_break.h" #include "update.h" #include "respa.h" #include "atom.h" diff --git a/src/MC/fix_bond_create.cpp b/src/MC/fix_bond_create.cpp index e1dd18cb5b..d2d93b67f6 100644 --- a/src/MC/fix_bond_create.cpp +++ b/src/MC/fix_bond_create.cpp @@ -11,11 +11,11 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ +#include "fix_bond_create.h" #include #include #include #include -#include "fix_bond_create.h" #include "update.h" #include "respa.h" #include "atom.h" diff --git a/src/MC/fix_bond_swap.cpp b/src/MC/fix_bond_swap.cpp index 5da2b845d6..187c552416 100644 --- a/src/MC/fix_bond_swap.cpp +++ b/src/MC/fix_bond_swap.cpp @@ -11,10 +11,10 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ +#include "fix_bond_swap.h" #include #include #include -#include "fix_bond_swap.h" #include "atom.h" #include "force.h" #include "pair.h" diff --git a/src/MC/fix_gcmc.cpp b/src/MC/fix_gcmc.cpp index 4e48b71611..8fe6042c2e 100644 --- a/src/MC/fix_gcmc.cpp +++ b/src/MC/fix_gcmc.cpp @@ -15,10 +15,10 @@ Contributing author: Paul Crozier, Aidan Thompson (SNL) ------------------------------------------------------------------------- */ +#include "fix_gcmc.h" #include #include #include -#include "fix_gcmc.h" #include "atom.h" #include "atom_vec.h" #include "atom_vec_hybrid.h" diff --git a/src/MC/pair_dsmc.cpp b/src/MC/pair_dsmc.cpp index c71eaa2295..cf48706133 100644 --- a/src/MC/pair_dsmc.cpp +++ b/src/MC/pair_dsmc.cpp @@ -15,12 +15,12 @@ Contributing authors: Paul Crozier (SNL) ------------------------------------------------------------------------- */ +#include "pair_dsmc.h" #include #include #include #include #include -#include "pair_dsmc.h" #include "atom.h" #include "comm.h" #include "force.h" diff --git a/src/MESSAGE/fix_client_md.cpp b/src/MESSAGE/fix_client_md.cpp index 727481dcc0..7d4ae13f0f 100644 --- a/src/MESSAGE/fix_client_md.cpp +++ b/src/MESSAGE/fix_client_md.cpp @@ -11,9 +11,9 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ +#include "fix_client_md.h" #include #include -#include "fix_client_md.h" #include "update.h" #include "atom.h" #include "comm.h" diff --git a/src/MESSAGE/message.cpp b/src/MESSAGE/message.cpp index 61221ca26e..f8fc349746 100644 --- a/src/MESSAGE/message.cpp +++ b/src/MESSAGE/message.cpp @@ -11,8 +11,8 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include #include "message.h" +#include #include "error.h" // CSlib interface diff --git a/src/MESSAGE/server.cpp b/src/MESSAGE/server.cpp index f587fb76df..dbcec08488 100644 --- a/src/MESSAGE/server.cpp +++ b/src/MESSAGE/server.cpp @@ -11,8 +11,8 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include #include "server.h" +#include #include "error.h" // customize by adding a new server protocol include and enum diff --git a/src/MESSAGE/server_md.cpp b/src/MESSAGE/server_md.cpp index bef327616e..e16095ad4c 100644 --- a/src/MESSAGE/server_md.cpp +++ b/src/MESSAGE/server_md.cpp @@ -11,9 +11,9 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ +#include "server_md.h" #include #include -#include "server_md.h" #include "atom.h" #include "atom_vec.h" #include "update.h" diff --git a/src/MISC/compute_msd_nongauss.cpp b/src/MISC/compute_msd_nongauss.cpp index f6291f4204..e02dd633cb 100644 --- a/src/MISC/compute_msd_nongauss.cpp +++ b/src/MISC/compute_msd_nongauss.cpp @@ -15,8 +15,8 @@ Contributing authors: Rob Hoy ------------------------------------------------------------------------- */ -#include #include "compute_msd_nongauss.h" +#include #include "atom.h" #include "update.h" #include "group.h" diff --git a/src/MISC/compute_ti.cpp b/src/MISC/compute_ti.cpp index d2e43a9f69..266263785f 100644 --- a/src/MISC/compute_ti.cpp +++ b/src/MISC/compute_ti.cpp @@ -15,10 +15,10 @@ Contributing author: Sai Jayaraman (University of Notre Dame) ------------------------------------------------------------------------- */ +#include "compute_ti.h" #include -#include "atom.h" #include -#include "compute_ti.h" +#include "atom.h" #include "update.h" #include "modify.h" #include "domain.h" diff --git a/src/MISC/dump_xtc.cpp b/src/MISC/dump_xtc.cpp index a82cba20bd..7abe4c4093 100644 --- a/src/MISC/dump_xtc.cpp +++ b/src/MISC/dump_xtc.cpp @@ -22,12 +22,12 @@ support for groups ------------------------------------------------------------------------- */ +#include "dump_xtc.h" #include #include #include #include #include -#include "dump_xtc.h" #include "domain.h" #include "atom.h" #include "update.h" diff --git a/src/MISC/fix_deposit.cpp b/src/MISC/fix_deposit.cpp index 66aed34846..22a144da60 100644 --- a/src/MISC/fix_deposit.cpp +++ b/src/MISC/fix_deposit.cpp @@ -11,10 +11,10 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ +#include "fix_deposit.h" #include #include #include -#include "fix_deposit.h" #include "atom.h" #include "atom_vec.h" #include "molecule.h" diff --git a/src/MISC/fix_efield.cpp b/src/MISC/fix_efield.cpp index 004c8ad7bc..87ece82f57 100644 --- a/src/MISC/fix_efield.cpp +++ b/src/MISC/fix_efield.cpp @@ -16,10 +16,10 @@ Stan Moore (Sandia) for dipole terms ------------------------------------------------------------------------- */ +#include "fix_efield.h" #include #include #include -#include "fix_efield.h" #include "atom.h" #include "update.h" #include "domain.h" diff --git a/src/MISC/fix_evaporate.cpp b/src/MISC/fix_evaporate.cpp index 1bf7a15f1f..e2c7844853 100644 --- a/src/MISC/fix_evaporate.cpp +++ b/src/MISC/fix_evaporate.cpp @@ -11,10 +11,10 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ +#include "fix_evaporate.h" #include #include #include -#include "fix_evaporate.h" #include "atom.h" #include "atom_vec.h" #include "molecule.h" diff --git a/src/MISC/fix_gld.cpp b/src/MISC/fix_gld.cpp index 2bf02889a5..265ee4fb09 100644 --- a/src/MISC/fix_gld.cpp +++ b/src/MISC/fix_gld.cpp @@ -16,10 +16,10 @@ Andrew Baczewski (Michigan State/SNL) ------------------------------------------------------------------------- */ +#include "fix_gld.h" #include #include #include -#include "fix_gld.h" #include "math_extra.h" #include "atom.h" #include "force.h" diff --git a/src/MISC/fix_oneway.cpp b/src/MISC/fix_oneway.cpp index 73853775a3..fcf5a7a0bd 100644 --- a/src/MISC/fix_oneway.cpp +++ b/src/MISC/fix_oneway.cpp @@ -15,8 +15,8 @@ Contributing author: Axel Kohlmeyer (ICTP, Italy) ------------------------------------------------------------------------- */ -#include #include "fix_oneway.h" +#include #include "atom.h" #include "domain.h" #include "error.h" diff --git a/src/MISC/fix_orient_bcc.cpp b/src/MISC/fix_orient_bcc.cpp index 02cce5a014..a300631658 100644 --- a/src/MISC/fix_orient_bcc.cpp +++ b/src/MISC/fix_orient_bcc.cpp @@ -18,11 +18,11 @@ (https://dx.doi.org/10.6084/m9.figshare.1488628.v1 ------------------------------------------------------------------------- */ +#include "fix_orient_bcc.h" #include #include #include #include -#include "fix_orient_bcc.h" #include "atom.h" #include "update.h" #include "respa.h" diff --git a/src/MISC/fix_orient_fcc.cpp b/src/MISC/fix_orient_fcc.cpp index fc827ceb8f..d898f95d2c 100644 --- a/src/MISC/fix_orient_fcc.cpp +++ b/src/MISC/fix_orient_fcc.cpp @@ -15,11 +15,11 @@ Contributing authors: Koenraad Janssens and David Olmsted (SNL) ------------------------------------------------------------------------- */ +#include "fix_orient_fcc.h" #include #include #include #include -#include "fix_orient_fcc.h" #include "atom.h" #include "update.h" #include "respa.h" diff --git a/src/MISC/fix_thermal_conductivity.cpp b/src/MISC/fix_thermal_conductivity.cpp index f1aec3ff69..8da303c8ab 100644 --- a/src/MISC/fix_thermal_conductivity.cpp +++ b/src/MISC/fix_thermal_conductivity.cpp @@ -16,11 +16,11 @@ for swapping atoms of different masses ------------------------------------------------------------------------- */ +#include "fix_thermal_conductivity.h" #include #include #include #include -#include "fix_thermal_conductivity.h" #include "atom.h" #include "force.h" #include "domain.h" diff --git a/src/MISC/fix_ttm.cpp b/src/MISC/fix_ttm.cpp index 170103b0d0..06de732de6 100644 --- a/src/MISC/fix_ttm.cpp +++ b/src/MISC/fix_ttm.cpp @@ -16,11 +16,11 @@ Carolyn Phillips (University of Michigan) ------------------------------------------------------------------------- */ +#include "fix_ttm.h" #include #include #include #include -#include "fix_ttm.h" #include "atom.h" #include "force.h" #include "update.h" diff --git a/src/MISC/fix_viscosity.cpp b/src/MISC/fix_viscosity.cpp index 8e33c1c614..52107954c2 100644 --- a/src/MISC/fix_viscosity.cpp +++ b/src/MISC/fix_viscosity.cpp @@ -16,11 +16,11 @@ for swapping atoms of different masses ------------------------------------------------------------------------- */ +#include "fix_viscosity.h" #include #include #include #include -#include "fix_viscosity.h" #include "atom.h" #include "domain.h" #include "modify.h" diff --git a/src/MISC/pair_nm_cut.cpp b/src/MISC/pair_nm_cut.cpp index 124832b63e..9b8c36da3a 100644 --- a/src/MISC/pair_nm_cut.cpp +++ b/src/MISC/pair_nm_cut.cpp @@ -15,11 +15,11 @@ Contributing Author: Julien Devemy (ICCF) ------------------------------------------------------------------------- */ +#include "pair_nm_cut.h" #include #include #include #include -#include "pair_nm_cut.h" #include "atom.h" #include "comm.h" #include "force.h" diff --git a/src/MISC/pair_nm_cut_coul_cut.cpp b/src/MISC/pair_nm_cut_coul_cut.cpp index a8428ab980..069c363817 100644 --- a/src/MISC/pair_nm_cut_coul_cut.cpp +++ b/src/MISC/pair_nm_cut_coul_cut.cpp @@ -15,11 +15,11 @@ Contributing Author: Julien Devemy (ICCF) ------------------------------------------------------------------------- */ +#include "pair_nm_cut_coul_cut.h" #include #include #include #include -#include "pair_nm_cut_coul_cut.h" #include "atom.h" #include "comm.h" #include "force.h" diff --git a/src/MISC/pair_nm_cut_coul_long.cpp b/src/MISC/pair_nm_cut_coul_long.cpp index af21f02881..b3d42b05f8 100644 --- a/src/MISC/pair_nm_cut_coul_long.cpp +++ b/src/MISC/pair_nm_cut_coul_long.cpp @@ -15,11 +15,11 @@ Contributing Author: Julien Devemy (ICCF) ------------------------------------------------------------------------- */ +#include "pair_nm_cut_coul_long.h" #include #include #include #include -#include "pair_nm_cut_coul_long.h" #include "atom.h" #include "comm.h" #include "force.h" diff --git a/src/MISC/xdr_compat.cpp b/src/MISC/xdr_compat.cpp index 2d8d0ce7e5..e124d52d7b 100644 --- a/src/MISC/xdr_compat.cpp +++ b/src/MISC/xdr_compat.cpp @@ -1,7 +1,7 @@ +#include "xdr_compat.h" #include #include #include -#include "xdr_compat.h" /* This file is needed for systems, that do not provide XDR support * in their system libraries. It was written for windows, but will diff --git a/src/MOLECULE/angle_charmm.cpp b/src/MOLECULE/angle_charmm.cpp index efd1c682f7..fb0afd78c3 100644 --- a/src/MOLECULE/angle_charmm.cpp +++ b/src/MOLECULE/angle_charmm.cpp @@ -15,9 +15,9 @@ Contributing author: Paul Crozier (SNL) ------------------------------------------------------------------------- */ +#include "angle_charmm.h" #include #include -#include "angle_charmm.h" #include "atom.h" #include "neighbor.h" #include "domain.h" diff --git a/src/MOLECULE/angle_cosine.cpp b/src/MOLECULE/angle_cosine.cpp index 6e1b9fa2fb..aff5130323 100644 --- a/src/MOLECULE/angle_cosine.cpp +++ b/src/MOLECULE/angle_cosine.cpp @@ -11,9 +11,9 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ +#include "angle_cosine.h" #include #include -#include "angle_cosine.h" #include "atom.h" #include "neighbor.h" #include "domain.h" diff --git a/src/MOLECULE/angle_cosine_delta.cpp b/src/MOLECULE/angle_cosine_delta.cpp index eca10970f2..13ed00b327 100644 --- a/src/MOLECULE/angle_cosine_delta.cpp +++ b/src/MOLECULE/angle_cosine_delta.cpp @@ -15,9 +15,9 @@ Contributing author: Axel Kohlmeyer (Temple U), akohlmey at gmail.com ------------------------------------------------------------------------- */ +#include "angle_cosine_delta.h" #include #include -#include "angle_cosine_delta.h" #include "atom.h" #include "neighbor.h" #include "domain.h" diff --git a/src/MOLECULE/angle_cosine_periodic.cpp b/src/MOLECULE/angle_cosine_periodic.cpp index cb0a26871a..9f7c02cabc 100644 --- a/src/MOLECULE/angle_cosine_periodic.cpp +++ b/src/MOLECULE/angle_cosine_periodic.cpp @@ -15,9 +15,9 @@ Contributing author: Tod A Pascal (Caltech) ------------------------------------------------------------------------- */ +#include "angle_cosine_periodic.h" #include #include -#include "angle_cosine_periodic.h" #include "atom.h" #include "neighbor.h" #include "domain.h" diff --git a/src/MOLECULE/angle_cosine_squared.cpp b/src/MOLECULE/angle_cosine_squared.cpp index 28d63344a4..789a536c98 100644 --- a/src/MOLECULE/angle_cosine_squared.cpp +++ b/src/MOLECULE/angle_cosine_squared.cpp @@ -15,9 +15,9 @@ Contributing author: Naveen Michaud-Agrawal (Johns Hopkins U) ------------------------------------------------------------------------- */ +#include "angle_cosine_squared.h" #include #include -#include "angle_cosine_squared.h" #include "atom.h" #include "neighbor.h" #include "domain.h" diff --git a/src/MOLECULE/angle_harmonic.cpp b/src/MOLECULE/angle_harmonic.cpp index 48b493d9b2..b626bdfae5 100644 --- a/src/MOLECULE/angle_harmonic.cpp +++ b/src/MOLECULE/angle_harmonic.cpp @@ -11,9 +11,9 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ +#include "angle_harmonic.h" #include #include -#include "angle_harmonic.h" #include "atom.h" #include "neighbor.h" #include "domain.h" diff --git a/src/MOLECULE/angle_table.cpp b/src/MOLECULE/angle_table.cpp index c18b4c43b0..ce7fcdcaf2 100644 --- a/src/MOLECULE/angle_table.cpp +++ b/src/MOLECULE/angle_table.cpp @@ -15,10 +15,10 @@ Contributing author: Chuanfu Luo (luochuanfu@gmail.com) ------------------------------------------------------------------------- */ +#include "angle_table.h" #include #include #include -#include "angle_table.h" #include "atom.h" #include "neighbor.h" #include "domain.h" diff --git a/src/MOLECULE/atom_vec_angle.cpp b/src/MOLECULE/atom_vec_angle.cpp index 6eb5b50fd2..f3c48aa87a 100644 --- a/src/MOLECULE/atom_vec_angle.cpp +++ b/src/MOLECULE/atom_vec_angle.cpp @@ -11,8 +11,8 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include #include "atom_vec_angle.h" +#include #include "atom.h" #include "comm.h" #include "domain.h" diff --git a/src/MOLECULE/atom_vec_bond.cpp b/src/MOLECULE/atom_vec_bond.cpp index 6a7b3585b4..b0f76adc45 100644 --- a/src/MOLECULE/atom_vec_bond.cpp +++ b/src/MOLECULE/atom_vec_bond.cpp @@ -11,8 +11,8 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include #include "atom_vec_bond.h" +#include #include "atom.h" #include "comm.h" #include "domain.h" diff --git a/src/MOLECULE/atom_vec_full.cpp b/src/MOLECULE/atom_vec_full.cpp index d682abf799..c9b2402062 100644 --- a/src/MOLECULE/atom_vec_full.cpp +++ b/src/MOLECULE/atom_vec_full.cpp @@ -11,8 +11,8 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include #include "atom_vec_full.h" +#include #include "atom.h" #include "comm.h" #include "domain.h" diff --git a/src/MOLECULE/atom_vec_molecular.cpp b/src/MOLECULE/atom_vec_molecular.cpp index cdd3f02505..524f7bcb0d 100644 --- a/src/MOLECULE/atom_vec_molecular.cpp +++ b/src/MOLECULE/atom_vec_molecular.cpp @@ -11,8 +11,8 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include #include "atom_vec_molecular.h" +#include #include "atom.h" #include "comm.h" #include "domain.h" diff --git a/src/MOLECULE/atom_vec_template.cpp b/src/MOLECULE/atom_vec_template.cpp index 3172804b95..6a12027b7b 100644 --- a/src/MOLECULE/atom_vec_template.cpp +++ b/src/MOLECULE/atom_vec_template.cpp @@ -11,9 +11,9 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ +#include "atom_vec_template.h" #include #include -#include "atom_vec_template.h" #include "atom.h" #include "molecule.h" #include "comm.h" diff --git a/src/MOLECULE/bond_fene.cpp b/src/MOLECULE/bond_fene.cpp index c023a7e81e..d4f2a4010e 100644 --- a/src/MOLECULE/bond_fene.cpp +++ b/src/MOLECULE/bond_fene.cpp @@ -11,9 +11,9 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ +#include "bond_fene.h" #include #include -#include "bond_fene.h" #include "atom.h" #include "neighbor.h" #include "domain.h" diff --git a/src/MOLECULE/bond_fene_expand.cpp b/src/MOLECULE/bond_fene_expand.cpp index b1bfdc6a1b..3e4ceab42c 100644 --- a/src/MOLECULE/bond_fene_expand.cpp +++ b/src/MOLECULE/bond_fene_expand.cpp @@ -11,9 +11,9 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ +#include "bond_fene_expand.h" #include #include -#include "bond_fene_expand.h" #include "atom.h" #include "neighbor.h" #include "domain.h" diff --git a/src/MOLECULE/bond_gromos.cpp b/src/MOLECULE/bond_gromos.cpp index f65adeb2cb..44e99d8fe0 100644 --- a/src/MOLECULE/bond_gromos.cpp +++ b/src/MOLECULE/bond_gromos.cpp @@ -15,10 +15,10 @@ Contributing author: Axel Kohlmeyer (Temple U) ------------------------------------------------------------------------- */ +#include "bond_gromos.h" #include #include #include -#include "bond_gromos.h" #include "atom.h" #include "neighbor.h" #include "domain.h" diff --git a/src/MOLECULE/bond_harmonic.cpp b/src/MOLECULE/bond_harmonic.cpp index cb8434ce6e..bbbad4102d 100644 --- a/src/MOLECULE/bond_harmonic.cpp +++ b/src/MOLECULE/bond_harmonic.cpp @@ -11,10 +11,10 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ +#include "bond_harmonic.h" #include #include #include -#include "bond_harmonic.h" #include "atom.h" #include "neighbor.h" #include "domain.h" diff --git a/src/MOLECULE/bond_morse.cpp b/src/MOLECULE/bond_morse.cpp index 91dd2dbc49..af476d6fe8 100644 --- a/src/MOLECULE/bond_morse.cpp +++ b/src/MOLECULE/bond_morse.cpp @@ -15,9 +15,9 @@ Contributing author: Jeff Greathouse (SNL) ------------------------------------------------------------------------- */ +#include "bond_morse.h" #include #include -#include "bond_morse.h" #include "atom.h" #include "neighbor.h" #include "domain.h" diff --git a/src/MOLECULE/bond_nonlinear.cpp b/src/MOLECULE/bond_nonlinear.cpp index 9999ead47f..89ddb7b118 100644 --- a/src/MOLECULE/bond_nonlinear.cpp +++ b/src/MOLECULE/bond_nonlinear.cpp @@ -11,9 +11,9 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ +#include "bond_nonlinear.h" #include #include -#include "bond_nonlinear.h" #include "atom.h" #include "neighbor.h" #include "domain.h" diff --git a/src/MOLECULE/bond_quartic.cpp b/src/MOLECULE/bond_quartic.cpp index 895202ff00..34b3ad8288 100644 --- a/src/MOLECULE/bond_quartic.cpp +++ b/src/MOLECULE/bond_quartic.cpp @@ -15,9 +15,9 @@ Contributing authors: Chris Lorenz and Mark Stevens (SNL) ------------------------------------------------------------------------- */ +#include "bond_quartic.h" #include #include -#include "bond_quartic.h" #include "atom.h" #include "neighbor.h" #include "domain.h" diff --git a/src/MOLECULE/bond_table.cpp b/src/MOLECULE/bond_table.cpp index 10851774d7..e80baee6e8 100644 --- a/src/MOLECULE/bond_table.cpp +++ b/src/MOLECULE/bond_table.cpp @@ -15,10 +15,10 @@ Contributing author: Chuanfu Luo (luochuanfu@gmail.com) ------------------------------------------------------------------------- */ +#include "bond_table.h" #include #include #include -#include "bond_table.h" #include "atom.h" #include "neighbor.h" #include "domain.h" diff --git a/src/MOLECULE/dihedral_charmm.cpp b/src/MOLECULE/dihedral_charmm.cpp index 68c62eb4fd..1905c14358 100644 --- a/src/MOLECULE/dihedral_charmm.cpp +++ b/src/MOLECULE/dihedral_charmm.cpp @@ -15,11 +15,11 @@ Contributing author: Paul Crozier (SNL) ------------------------------------------------------------------------- */ +#include "dihedral_charmm.h" #include #include #include #include -#include "dihedral_charmm.h" #include "atom.h" #include "comm.h" #include "neighbor.h" diff --git a/src/MOLECULE/dihedral_charmmfsw.cpp b/src/MOLECULE/dihedral_charmmfsw.cpp index f65d01e9ed..9b02b908d6 100644 --- a/src/MOLECULE/dihedral_charmmfsw.cpp +++ b/src/MOLECULE/dihedral_charmmfsw.cpp @@ -18,11 +18,11 @@ with additional assistance from Robert A. Latour, Clemson University ------------------------------------------------------------------------- */ +#include "dihedral_charmmfsw.h" #include #include #include #include -#include "dihedral_charmmfsw.h" #include "atom.h" #include "comm.h" #include "neighbor.h" diff --git a/src/MOLECULE/dihedral_harmonic.cpp b/src/MOLECULE/dihedral_harmonic.cpp index ddb94dc571..159636ecd5 100644 --- a/src/MOLECULE/dihedral_harmonic.cpp +++ b/src/MOLECULE/dihedral_harmonic.cpp @@ -15,10 +15,10 @@ Contributing author: Paul Crozier (SNL) ------------------------------------------------------------------------- */ +#include "dihedral_harmonic.h" #include #include #include -#include "dihedral_harmonic.h" #include "atom.h" #include "comm.h" #include "neighbor.h" diff --git a/src/MOLECULE/dihedral_helix.cpp b/src/MOLECULE/dihedral_helix.cpp index d19731c097..a7d2aba1d6 100644 --- a/src/MOLECULE/dihedral_helix.cpp +++ b/src/MOLECULE/dihedral_helix.cpp @@ -16,10 +16,10 @@ Mark Stevens (Sandia) ------------------------------------------------------------------------- */ +#include "dihedral_helix.h" #include #include #include -#include "dihedral_helix.h" #include "atom.h" #include "neighbor.h" #include "domain.h" diff --git a/src/MOLECULE/dihedral_multi_harmonic.cpp b/src/MOLECULE/dihedral_multi_harmonic.cpp index 04e7bbb627..ba98cf6ddf 100644 --- a/src/MOLECULE/dihedral_multi_harmonic.cpp +++ b/src/MOLECULE/dihedral_multi_harmonic.cpp @@ -15,9 +15,9 @@ Contributing author: Mathias Puetz (SNL) and friends ------------------------------------------------------------------------- */ +#include "dihedral_multi_harmonic.h" #include #include -#include "dihedral_multi_harmonic.h" #include "atom.h" #include "neighbor.h" #include "domain.h" diff --git a/src/MOLECULE/dihedral_opls.cpp b/src/MOLECULE/dihedral_opls.cpp index 293245e411..d68eba0bec 100644 --- a/src/MOLECULE/dihedral_opls.cpp +++ b/src/MOLECULE/dihedral_opls.cpp @@ -15,9 +15,9 @@ Contributing author: Mark Stevens (SNL) ------------------------------------------------------------------------- */ +#include "dihedral_opls.h" #include #include -#include "dihedral_opls.h" #include "atom.h" #include "comm.h" #include "neighbor.h" diff --git a/src/MOLECULE/fix_cmap.cpp b/src/MOLECULE/fix_cmap.cpp index 3395c7ef14..3d5bf90bdc 100644 --- a/src/MOLECULE/fix_cmap.cpp +++ b/src/MOLECULE/fix_cmap.cpp @@ -27,12 +27,12 @@ - MacKerell et al., J. Comput. Chem. 25(2004):1400-1415. ------------------------------------------------------------------------- */ +#include "fix_cmap.h" #include #include #include #include #include -#include "fix_cmap.h" #include "atom.h" #include "atom_vec.h" #include "update.h" diff --git a/src/MOLECULE/improper_cvff.cpp b/src/MOLECULE/improper_cvff.cpp index 01e9729e80..fd24ab69c3 100644 --- a/src/MOLECULE/improper_cvff.cpp +++ b/src/MOLECULE/improper_cvff.cpp @@ -11,10 +11,10 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ +#include "improper_cvff.h" #include #include #include -#include "improper_cvff.h" #include "atom.h" #include "comm.h" #include "neighbor.h" diff --git a/src/MOLECULE/improper_harmonic.cpp b/src/MOLECULE/improper_harmonic.cpp index c5421fffdb..936c22e94a 100644 --- a/src/MOLECULE/improper_harmonic.cpp +++ b/src/MOLECULE/improper_harmonic.cpp @@ -11,10 +11,10 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ +#include "improper_harmonic.h" #include #include #include -#include "improper_harmonic.h" #include "atom.h" #include "comm.h" #include "neighbor.h" diff --git a/src/MOLECULE/improper_umbrella.cpp b/src/MOLECULE/improper_umbrella.cpp index 3de46df0f3..2e41ac6493 100644 --- a/src/MOLECULE/improper_umbrella.cpp +++ b/src/MOLECULE/improper_umbrella.cpp @@ -15,10 +15,10 @@ Contributing author: Tod A Pascal (Caltech) ------------------------------------------------------------------------- */ +#include "improper_umbrella.h" #include #include #include -#include "improper_umbrella.h" #include "atom.h" #include "comm.h" #include "neighbor.h" diff --git a/src/MOLECULE/pair_hbond_dreiding_lj.cpp b/src/MOLECULE/pair_hbond_dreiding_lj.cpp index ddc1110081..58666f27d1 100644 --- a/src/MOLECULE/pair_hbond_dreiding_lj.cpp +++ b/src/MOLECULE/pair_hbond_dreiding_lj.cpp @@ -15,11 +15,11 @@ Contributing author: Tod A Pascal (Caltech) ------------------------------------------------------------------------- */ +#include "pair_hbond_dreiding_lj.h" #include #include #include #include -#include "pair_hbond_dreiding_lj.h" #include "atom.h" #include "atom_vec.h" #include "molecule.h" diff --git a/src/MOLECULE/pair_hbond_dreiding_morse.cpp b/src/MOLECULE/pair_hbond_dreiding_morse.cpp index 055f0ed46b..120a2d8d55 100644 --- a/src/MOLECULE/pair_hbond_dreiding_morse.cpp +++ b/src/MOLECULE/pair_hbond_dreiding_morse.cpp @@ -15,11 +15,11 @@ Contributing author: Tod A Pascal (Caltech) ------------------------------------------------------------------------- */ +#include "pair_hbond_dreiding_morse.h" #include #include #include #include -#include "pair_hbond_dreiding_morse.h" #include "atom.h" #include "atom_vec.h" #include "molecule.h" diff --git a/src/MOLECULE/pair_lj_charmm_coul_charmm.cpp b/src/MOLECULE/pair_lj_charmm_coul_charmm.cpp index af4611e014..c9becb75c3 100644 --- a/src/MOLECULE/pair_lj_charmm_coul_charmm.cpp +++ b/src/MOLECULE/pair_lj_charmm_coul_charmm.cpp @@ -15,11 +15,11 @@ Contributing author: Paul Crozier (SNL) ------------------------------------------------------------------------- */ +#include "pair_lj_charmm_coul_charmm.h" #include #include #include #include -#include "pair_lj_charmm_coul_charmm.h" #include "atom.h" #include "comm.h" #include "force.h" diff --git a/src/MOLECULE/pair_lj_charmm_coul_charmm_implicit.cpp b/src/MOLECULE/pair_lj_charmm_coul_charmm_implicit.cpp index d68d5e8f6d..a2be2936b2 100644 --- a/src/MOLECULE/pair_lj_charmm_coul_charmm_implicit.cpp +++ b/src/MOLECULE/pair_lj_charmm_coul_charmm_implicit.cpp @@ -11,9 +11,9 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ +#include "pair_lj_charmm_coul_charmm_implicit.h" #include #include -#include "pair_lj_charmm_coul_charmm_implicit.h" #include "atom.h" #include "force.h" #include "neigh_list.h" diff --git a/src/MOLECULE/pair_lj_charmmfsw_coul_charmmfsh.cpp b/src/MOLECULE/pair_lj_charmmfsw_coul_charmmfsh.cpp index 0e1cbd85a5..f2f16c88ce 100644 --- a/src/MOLECULE/pair_lj_charmmfsw_coul_charmmfsh.cpp +++ b/src/MOLECULE/pair_lj_charmmfsw_coul_charmmfsh.cpp @@ -19,11 +19,11 @@ with additional assistance from Robert A. Latour, Clemson University ------------------------------------------------------------------------- */ +#include "pair_lj_charmmfsw_coul_charmmfsh.h" #include #include #include #include -#include "pair_lj_charmmfsw_coul_charmmfsh.h" #include "atom.h" #include "update.h" #include "comm.h" diff --git a/src/MOLECULE/pair_lj_cut_tip4p_cut.cpp b/src/MOLECULE/pair_lj_cut_tip4p_cut.cpp index 2b3d2c60f5..5bb82d7635 100644 --- a/src/MOLECULE/pair_lj_cut_tip4p_cut.cpp +++ b/src/MOLECULE/pair_lj_cut_tip4p_cut.cpp @@ -15,10 +15,10 @@ Contributing author: Pavel Elkind (Gothenburg University) ------------------------------------------------------------------------- */ +#include "pair_lj_cut_tip4p_cut.h" #include #include #include -#include "pair_lj_cut_tip4p_cut.h" #include "atom.h" #include "force.h" #include "neighbor.h" diff --git a/src/MOLECULE/pair_tip4p_cut.cpp b/src/MOLECULE/pair_tip4p_cut.cpp index e6fb9aab99..1511c09384 100644 --- a/src/MOLECULE/pair_tip4p_cut.cpp +++ b/src/MOLECULE/pair_tip4p_cut.cpp @@ -15,9 +15,9 @@ Contributing author: Pavel Elkind (Gothenburg University) ------------------------------------------------------------------------- */ +#include "pair_tip4p_cut.h" #include #include -#include "pair_tip4p_cut.h" #include "atom.h" #include "force.h" #include "neighbor.h" diff --git a/src/MPIIO/dump_atom_mpiio.cpp b/src/MPIIO/dump_atom_mpiio.cpp index f2f2991442..cde5b6258b 100644 --- a/src/MPIIO/dump_atom_mpiio.cpp +++ b/src/MPIIO/dump_atom_mpiio.cpp @@ -15,8 +15,8 @@ Contributing author: Paul Coffman (IBM) ------------------------------------------------------------------------- */ -#include #include "dump_atom_mpiio.h" +#include #include "domain.h" #include "atom.h" #include "update.h" diff --git a/src/MPIIO/dump_cfg_mpiio.cpp b/src/MPIIO/dump_cfg_mpiio.cpp index c580d2e7af..90f92d094d 100644 --- a/src/MPIIO/dump_cfg_mpiio.cpp +++ b/src/MPIIO/dump_cfg_mpiio.cpp @@ -15,10 +15,10 @@ Contributing author: Paul Coffman (IBM) ------------------------------------------------------------------------- */ +#include "dump_cfg_mpiio.h" #include #include #include -#include "dump_cfg_mpiio.h" #include "atom.h" #include "domain.h" #include "comm.h" diff --git a/src/MPIIO/dump_custom_mpiio.cpp b/src/MPIIO/dump_custom_mpiio.cpp index 3650ca994e..5838c61124 100644 --- a/src/MPIIO/dump_custom_mpiio.cpp +++ b/src/MPIIO/dump_custom_mpiio.cpp @@ -15,10 +15,10 @@ Contributing author: Paul Coffman (IBM) ------------------------------------------------------------------------- */ +#include "dump_custom_mpiio.h" #include #include #include -#include "dump_custom_mpiio.h" #include "atom.h" #include "force.h" #include "domain.h" diff --git a/src/MPIIO/dump_xyz_mpiio.cpp b/src/MPIIO/dump_xyz_mpiio.cpp index f15d340cd1..7b647561bf 100644 --- a/src/MPIIO/dump_xyz_mpiio.cpp +++ b/src/MPIIO/dump_xyz_mpiio.cpp @@ -15,10 +15,10 @@ Contributing author: Paul Coffman (IBM) ------------------------------------------------------------------------- */ +#include "dump_xyz_mpiio.h" #include #include #include -#include "dump_xyz_mpiio.h" #include "atom.h" #include "force.h" #include "domain.h" diff --git a/src/MPIIO/restart_mpiio.cpp b/src/MPIIO/restart_mpiio.cpp index 804df211dc..e8ef5c6c4e 100644 --- a/src/MPIIO/restart_mpiio.cpp +++ b/src/MPIIO/restart_mpiio.cpp @@ -15,9 +15,9 @@ Contributing author: Paul Coffman (IBM) ------------------------------------------------------------------------- */ +#include "restart_mpiio.h" #include #include -#include "restart_mpiio.h" #include "error.h" using namespace LAMMPS_NS; diff --git a/src/MSCG/fix_mscg.cpp b/src/MSCG/fix_mscg.cpp index b282595240..caa9a528a7 100644 --- a/src/MSCG/fix_mscg.cpp +++ b/src/MSCG/fix_mscg.cpp @@ -15,10 +15,10 @@ Contributing authors: Lauren Abbott (Sandia) ------------------------------------------------------------------------- */ +#include "fix_mscg.h" #include #include #include -#include "fix_mscg.h" #include "mscg.h" #include "atom.h" #include "comm.h" diff --git a/src/OPT/pair_eam_opt.cpp b/src/OPT/pair_eam_opt.cpp index fc2b6731ee..ad24aaee63 100644 --- a/src/OPT/pair_eam_opt.cpp +++ b/src/OPT/pair_eam_opt.cpp @@ -19,9 +19,9 @@ Vincent Natoli, Stone Ridge Technology ------------------------------------------------------------------------- */ +#include "pair_eam_opt.h" #include #include -#include "pair_eam_opt.h" #include "atom.h" #include "comm.h" #include "force.h" diff --git a/src/OPT/pair_lj_charmm_coul_long_opt.cpp b/src/OPT/pair_lj_charmm_coul_long_opt.cpp index d80d3d1ec4..3dc6bdb6b4 100644 --- a/src/OPT/pair_lj_charmm_coul_long_opt.cpp +++ b/src/OPT/pair_lj_charmm_coul_long_opt.cpp @@ -18,9 +18,9 @@ Vincent Natoli, Stone Ridge Technology ------------------------------------------------------------------------- */ +#include "pair_lj_charmm_coul_long_opt.h" #include #include -#include "pair_lj_charmm_coul_long_opt.h" #include "atom.h" #include "force.h" #include "neigh_list.h" diff --git a/src/OPT/pair_lj_cut_coul_long_opt.cpp b/src/OPT/pair_lj_cut_coul_long_opt.cpp index a25010cf1f..a1f97aaae9 100644 --- a/src/OPT/pair_lj_cut_coul_long_opt.cpp +++ b/src/OPT/pair_lj_cut_coul_long_opt.cpp @@ -11,8 +11,8 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include #include "pair_lj_cut_coul_long_opt.h" +#include #include "atom.h" #include "force.h" #include "neigh_list.h" diff --git a/src/OPT/pair_lj_cut_opt.cpp b/src/OPT/pair_lj_cut_opt.cpp index c6684461be..3b3a19a9e8 100644 --- a/src/OPT/pair_lj_cut_opt.cpp +++ b/src/OPT/pair_lj_cut_opt.cpp @@ -18,8 +18,8 @@ Vincent Natoli, Stone Ridge Technology ------------------------------------------------------------------------- */ -#include #include "pair_lj_cut_opt.h" +#include #include "atom.h" #include "force.h" #include "neigh_list.h" diff --git a/src/OPT/pair_lj_cut_tip4p_long_opt.cpp b/src/OPT/pair_lj_cut_tip4p_long_opt.cpp index 92facca43e..f8181d69a6 100644 --- a/src/OPT/pair_lj_cut_tip4p_long_opt.cpp +++ b/src/OPT/pair_lj_cut_tip4p_long_opt.cpp @@ -15,8 +15,8 @@ OPT version: Axel Kohlmeyer (Temple U) ------------------------------------------------------------------------- */ -#include #include "pair_lj_cut_tip4p_long_opt.h" +#include #include "atom.h" #include "domain.h" #include "force.h" diff --git a/src/OPT/pair_lj_long_coul_long_opt.cpp b/src/OPT/pair_lj_long_coul_long_opt.cpp index 03853057f4..c323d078c4 100644 --- a/src/OPT/pair_lj_long_coul_long_opt.cpp +++ b/src/OPT/pair_lj_long_coul_long_opt.cpp @@ -15,9 +15,9 @@ OPT version: Wayne Mitchell (Loyola University New Orleans) ------------------------------------------------------------------------- */ +#include "pair_lj_long_coul_long_opt.h" #include #include -#include "pair_lj_long_coul_long_opt.h" #include "atom.h" #include "force.h" #include "neigh_list.h" diff --git a/src/OPT/pair_morse_opt.cpp b/src/OPT/pair_morse_opt.cpp index c9c6bba355..1d2e226777 100644 --- a/src/OPT/pair_morse_opt.cpp +++ b/src/OPT/pair_morse_opt.cpp @@ -18,9 +18,9 @@ Vincent Natoli, Stone Ridge Technology ------------------------------------------------------------------------- */ +#include "pair_morse_opt.h" #include #include -#include "pair_morse_opt.h" #include "atom.h" #include "force.h" #include "neigh_list.h" diff --git a/src/OPT/pair_ufm_opt.cpp b/src/OPT/pair_ufm_opt.cpp index f463dac3f1..eabb093b18 100644 --- a/src/OPT/pair_ufm_opt.cpp +++ b/src/OPT/pair_ufm_opt.cpp @@ -17,9 +17,9 @@ Maurice de Koning (Unicamp/Brazil) - dekoning@ifi.unicamp.br ------------------------------------------------------------------------- */ +#include "pair_ufm_opt.h" #include #include -#include "pair_ufm_opt.h" #include "atom.h" #include "force.h" #include "neigh_list.h" diff --git a/src/PERI/atom_vec_peri.cpp b/src/PERI/atom_vec_peri.cpp index d78fe27c94..f677b24eb2 100644 --- a/src/PERI/atom_vec_peri.cpp +++ b/src/PERI/atom_vec_peri.cpp @@ -15,10 +15,10 @@ Contributing author: Mike Parks (SNL) ------------------------------------------------------------------------- */ +#include "atom_vec_peri.h" #include #include #include -#include "atom_vec_peri.h" #include "atom.h" #include "comm.h" #include "domain.h" diff --git a/src/PERI/compute_damage_atom.cpp b/src/PERI/compute_damage_atom.cpp index 4bf8fa17a5..f5a532cd0b 100644 --- a/src/PERI/compute_damage_atom.cpp +++ b/src/PERI/compute_damage_atom.cpp @@ -15,8 +15,8 @@ Contributing author: Mike Parks (SNL) ------------------------------------------------------------------------- */ -#include #include "compute_damage_atom.h" +#include #include "atom.h" #include "update.h" #include "modify.h" diff --git a/src/PERI/compute_dilatation_atom.cpp b/src/PERI/compute_dilatation_atom.cpp index 990731a227..7a6607d65c 100644 --- a/src/PERI/compute_dilatation_atom.cpp +++ b/src/PERI/compute_dilatation_atom.cpp @@ -15,8 +15,8 @@ Contributing author: Rezwanur Rahman, John Foster (UTSA) ------------------------------------------------------------------------- */ -#include #include "compute_dilatation_atom.h" +#include #include "atom.h" #include "update.h" #include "modify.h" diff --git a/src/PERI/compute_plasticity_atom.cpp b/src/PERI/compute_plasticity_atom.cpp index d08fb98e07..0b20bc5075 100644 --- a/src/PERI/compute_plasticity_atom.cpp +++ b/src/PERI/compute_plasticity_atom.cpp @@ -15,8 +15,8 @@ Contributing author: Rezwanur Rahman, John Foster (UTSA) ------------------------------------------------------------------------- */ -#include #include "compute_plasticity_atom.h" +#include #include "atom.h" #include "update.h" #include "modify.h" diff --git a/src/PERI/fix_peri_neigh.cpp b/src/PERI/fix_peri_neigh.cpp index 66137e6a01..297936577f 100644 --- a/src/PERI/fix_peri_neigh.cpp +++ b/src/PERI/fix_peri_neigh.cpp @@ -15,8 +15,8 @@ Contributing authors: Mike Parks (SNL), Ezwanur Rahman, J.T. Foster (UTSA) ------------------------------------------------------------------------- */ -#include #include "fix_peri_neigh.h" +#include #include "pair_peri_pmb.h" #include "pair_peri_lps.h" #include "pair_peri_ves.h" diff --git a/src/PERI/pair_peri_eps.cpp b/src/PERI/pair_peri_eps.cpp index c00495ba4d..07314081da 100644 --- a/src/PERI/pair_peri_eps.cpp +++ b/src/PERI/pair_peri_eps.cpp @@ -15,10 +15,10 @@ Contributing author: Rezwanur Rahman, John Foster (UTSA) ------------------------------------------------------------------------- */ +#include "pair_peri_eps.h" #include #include #include -#include "pair_peri_eps.h" #include "atom.h" #include "domain.h" #include "lattice.h" diff --git a/src/PERI/pair_peri_lps.cpp b/src/PERI/pair_peri_lps.cpp index f0418c8c8d..660209f3f5 100644 --- a/src/PERI/pair_peri_lps.cpp +++ b/src/PERI/pair_peri_lps.cpp @@ -15,10 +15,10 @@ Contributing author: Mike Parks (SNL) ------------------------------------------------------------------------- */ +#include "pair_peri_lps.h" #include #include #include -#include "pair_peri_lps.h" #include "atom.h" #include "domain.h" #include "lattice.h" diff --git a/src/PERI/pair_peri_pmb.cpp b/src/PERI/pair_peri_pmb.cpp index ad2f3fb7c7..fa53efc344 100644 --- a/src/PERI/pair_peri_pmb.cpp +++ b/src/PERI/pair_peri_pmb.cpp @@ -15,11 +15,11 @@ Contributing author: Mike Parks (SNL) ------------------------------------------------------------------------- */ +#include "pair_peri_pmb.h" #include #include #include #include -#include "pair_peri_pmb.h" #include "atom.h" #include "domain.h" #include "lattice.h" diff --git a/src/PERI/pair_peri_ves.cpp b/src/PERI/pair_peri_ves.cpp index 24a9f92a97..1687bed35d 100644 --- a/src/PERI/pair_peri_ves.cpp +++ b/src/PERI/pair_peri_ves.cpp @@ -15,10 +15,10 @@ Contributing authors: Rezwanur Rahman, J.T. Foster (UTSA) ------------------------------------------------------------------------- */ +#include "pair_peri_ves.h" #include #include #include -#include "pair_peri_ves.h" #include "atom.h" #include "domain.h" #include "lattice.h" diff --git a/src/POEMS/fix_poems.cpp b/src/POEMS/fix_poems.cpp index 41cfcede34..6d943a79db 100644 --- a/src/POEMS/fix_poems.cpp +++ b/src/POEMS/fix_poems.cpp @@ -17,13 +17,13 @@ Kurt Anderson (anderk5@rpi.edu) ------------------------------------------------------------------------- */ +#include "fix_poems.h" #include #include #include #include #include #include "workspace.h" -#include "fix_poems.h" #include "atom.h" #include "domain.h" #include "update.h" diff --git a/src/PYTHON/fix_python_invoke.cpp b/src/PYTHON/fix_python_invoke.cpp index 7fa9861c3f..57ea2e9148 100644 --- a/src/PYTHON/fix_python_invoke.cpp +++ b/src/PYTHON/fix_python_invoke.cpp @@ -15,9 +15,9 @@ Contributing author: Richard Berger (Temple U) ------------------------------------------------------------------------- */ +#include "fix_python_invoke.h" #include // IWYU pragma: keep #include -#include "fix_python_invoke.h" #include "force.h" #include "update.h" #include "error.h" diff --git a/src/PYTHON/fix_python_move.cpp b/src/PYTHON/fix_python_move.cpp index b253df6828..be63b851a2 100644 --- a/src/PYTHON/fix_python_move.cpp +++ b/src/PYTHON/fix_python_move.cpp @@ -15,9 +15,9 @@ Contributing author: Richard Berger (Temple U) ------------------------------------------------------------------------- */ +#include "fix_python_move.h" #include // IWYU pragma: keep #include -#include "fix_python_move.h" #include "lmppython.h" #include "error.h" #include "python_compat.h" diff --git a/src/PYTHON/pair_python.cpp b/src/PYTHON/pair_python.cpp index 5b8f23400b..0d79a31946 100644 --- a/src/PYTHON/pair_python.cpp +++ b/src/PYTHON/pair_python.cpp @@ -15,10 +15,10 @@ Contributing authors: Axel Kohlmeyer and Richard Berger (Temple U) ------------------------------------------------------------------------- */ +#include "pair_python.h" #include // IWYU pragma: keep #include #include -#include "pair_python.h" #include "atom.h" #include "force.h" #include "memory.h" diff --git a/src/PYTHON/python_impl.cpp b/src/PYTHON/python_impl.cpp index 7456021675..1188942e75 100644 --- a/src/PYTHON/python_impl.cpp +++ b/src/PYTHON/python_impl.cpp @@ -15,10 +15,10 @@ Contributing author: Richard Berger and Axel Kohlmeyer (Temple U) ------------------------------------------------------------------------- */ +#include "python_impl.h" #include #include #include // IWYU pragma: keep -#include "python_impl.h" #include "force.h" #include "input.h" #include "variable.h" diff --git a/src/QEQ/fix_qeq.cpp b/src/QEQ/fix_qeq.cpp index 0ab010b7bb..2e0b7edbe5 100644 --- a/src/QEQ/fix_qeq.cpp +++ b/src/QEQ/fix_qeq.cpp @@ -16,11 +16,11 @@ Based on fix qeq/reax by H. Metin Aktulga ------------------------------------------------------------------------- */ +#include "fix_qeq.h" #include #include #include #include -#include "fix_qeq.h" #include "atom.h" #include "comm.h" #include "domain.h" diff --git a/src/QEQ/fix_qeq_dynamic.cpp b/src/QEQ/fix_qeq_dynamic.cpp index ba88f4f1c3..fb5fd2ddac 100644 --- a/src/QEQ/fix_qeq_dynamic.cpp +++ b/src/QEQ/fix_qeq_dynamic.cpp @@ -15,11 +15,11 @@ Contributing author: Ray Shan (Sandia) ------------------------------------------------------------------------- */ +#include "fix_qeq_dynamic.h" #include #include #include #include -#include "fix_qeq_dynamic.h" #include "atom.h" #include "comm.h" #include "domain.h" diff --git a/src/QEQ/fix_qeq_fire.cpp b/src/QEQ/fix_qeq_fire.cpp index 1e3686f99c..561a82b714 100644 --- a/src/QEQ/fix_qeq_fire.cpp +++ b/src/QEQ/fix_qeq_fire.cpp @@ -15,11 +15,11 @@ Contributing author: Ray Shan (Sandia) ------------------------------------------------------------------------- */ +#include "fix_qeq_fire.h" #include #include #include #include -#include "fix_qeq_fire.h" #include "atom.h" #include "comm.h" #include "domain.h" diff --git a/src/QEQ/fix_qeq_point.cpp b/src/QEQ/fix_qeq_point.cpp index 9517343974..bb3ce835fc 100644 --- a/src/QEQ/fix_qeq_point.cpp +++ b/src/QEQ/fix_qeq_point.cpp @@ -15,11 +15,11 @@ Contributing author: Ray Shan (Sandia) ------------------------------------------------------------------------- */ +#include "fix_qeq_point.h" #include #include #include #include -#include "fix_qeq_point.h" #include "atom.h" #include "comm.h" #include "domain.h" diff --git a/src/QEQ/fix_qeq_shielded.cpp b/src/QEQ/fix_qeq_shielded.cpp index a74eee7d29..60ff62ca07 100644 --- a/src/QEQ/fix_qeq_shielded.cpp +++ b/src/QEQ/fix_qeq_shielded.cpp @@ -15,11 +15,11 @@ Contributing author: Ray Shan (Sandia) ------------------------------------------------------------------------- */ +#include "fix_qeq_shielded.h" #include #include #include #include -#include "fix_qeq_shielded.h" #include "atom.h" #include "comm.h" #include "domain.h" diff --git a/src/QEQ/fix_qeq_slater.cpp b/src/QEQ/fix_qeq_slater.cpp index 3443a519a2..95105b5ef2 100644 --- a/src/QEQ/fix_qeq_slater.cpp +++ b/src/QEQ/fix_qeq_slater.cpp @@ -15,11 +15,11 @@ Contributing author: Ray Shan (Sandia) ------------------------------------------------------------------------- */ +#include "fix_qeq_slater.h" #include #include #include #include -#include "fix_qeq_slater.h" #include "atom.h" #include "comm.h" #include "domain.h" diff --git a/src/REPLICA/compute_event_displace.cpp b/src/REPLICA/compute_event_displace.cpp index df14221586..4c8d022d70 100644 --- a/src/REPLICA/compute_event_displace.cpp +++ b/src/REPLICA/compute_event_displace.cpp @@ -15,11 +15,11 @@ Contributing author: Mike Brown (SNL) ------------------------------------------------------------------------- */ +#include "compute_event_displace.h" #include #include #include #include -#include "compute_event_displace.h" #include "atom.h" #include "domain.h" #include "modify.h" diff --git a/src/REPLICA/fix_event.cpp b/src/REPLICA/fix_event.cpp index 8fc5de6b16..8cf1acba94 100644 --- a/src/REPLICA/fix_event.cpp +++ b/src/REPLICA/fix_event.cpp @@ -15,9 +15,9 @@ Contributing author: Mike Brown (SNL), Aidan Thompson (SNL) ------------------------------------------------------------------------- */ +#include "fix_event.h" #include #include -#include "fix_event.h" #include "atom.h" #include "update.h" #include "domain.h" diff --git a/src/REPLICA/fix_event_hyper.cpp b/src/REPLICA/fix_event_hyper.cpp index eae1ad021d..3dd1a03eb9 100644 --- a/src/REPLICA/fix_event_hyper.cpp +++ b/src/REPLICA/fix_event_hyper.cpp @@ -11,9 +11,9 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ +#include "fix_event_hyper.h" #include #include -#include "fix_event_hyper.h" #include "atom.h" #include "update.h" #include "domain.h" diff --git a/src/REPLICA/fix_event_prd.cpp b/src/REPLICA/fix_event_prd.cpp index a311a6444a..63c9c2718b 100644 --- a/src/REPLICA/fix_event_prd.cpp +++ b/src/REPLICA/fix_event_prd.cpp @@ -15,9 +15,9 @@ Contributing author: Mike Brown (SNL) ------------------------------------------------------------------------- */ +#include "fix_event_prd.h" #include #include -#include "fix_event_prd.h" #include "atom.h" #include "update.h" #include "domain.h" diff --git a/src/REPLICA/fix_event_tad.cpp b/src/REPLICA/fix_event_tad.cpp index 0916fdf493..b92bc1fd73 100644 --- a/src/REPLICA/fix_event_tad.cpp +++ b/src/REPLICA/fix_event_tad.cpp @@ -15,9 +15,9 @@ Contributing author: Mike Brown (SNL) ------------------------------------------------------------------------- */ +#include "fix_event_tad.h" #include #include -#include "fix_event_tad.h" #include "atom.h" #include "update.h" #include "domain.h" diff --git a/src/REPLICA/fix_hyper.cpp b/src/REPLICA/fix_hyper.cpp index c86c00ad45..21a4fde04d 100644 --- a/src/REPLICA/fix_hyper.cpp +++ b/src/REPLICA/fix_hyper.cpp @@ -11,8 +11,8 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include #include "fix_hyper.h" +#include using namespace LAMMPS_NS; diff --git a/src/REPLICA/fix_hyper_global.cpp b/src/REPLICA/fix_hyper_global.cpp index 0c76b29911..a58798a63e 100644 --- a/src/REPLICA/fix_hyper_global.cpp +++ b/src/REPLICA/fix_hyper_global.cpp @@ -11,11 +11,11 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ +#include "fix_hyper_global.h" #include #include #include #include -#include "fix_hyper_global.h" #include "atom.h" #include "update.h" #include "force.h" diff --git a/src/REPLICA/fix_hyper_local.cpp b/src/REPLICA/fix_hyper_local.cpp index a6db4419f0..555c5234f6 100644 --- a/src/REPLICA/fix_hyper_local.cpp +++ b/src/REPLICA/fix_hyper_local.cpp @@ -11,11 +11,11 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ +#include "fix_hyper_local.h" #include #include #include #include -#include "fix_hyper_local.h" #include "atom.h" #include "update.h" #include "force.h" diff --git a/src/REPLICA/fix_neb.cpp b/src/REPLICA/fix_neb.cpp index e1b1e46a53..2803c37b23 100644 --- a/src/REPLICA/fix_neb.cpp +++ b/src/REPLICA/fix_neb.cpp @@ -16,11 +16,11 @@ new options for inter-replica forces, first/last replica treatment ------------------------------------------------------------------------- */ +#include "fix_neb.h" #include #include #include #include -#include "fix_neb.h" #include "universe.h" #include "update.h" #include "atom.h" diff --git a/src/REPLICA/hyper.cpp b/src/REPLICA/hyper.cpp index 00b91684e9..c400ae097d 100644 --- a/src/REPLICA/hyper.cpp +++ b/src/REPLICA/hyper.cpp @@ -11,10 +11,10 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ +#include "hyper.h" #include #include #include -#include "hyper.h" #include "update.h" #include "atom.h" #include "domain.h" diff --git a/src/REPLICA/neb.cpp b/src/REPLICA/neb.cpp index 6b68c52dbb..b670f3d8f1 100644 --- a/src/REPLICA/neb.cpp +++ b/src/REPLICA/neb.cpp @@ -15,12 +15,12 @@ // due to OpenMPI bug which sets INT64_MAX via its mpi.h // before lmptype.h can set flags to insure it is done correctly +#include "neb.h" #include "lmptype.h" #include #include #include #include -#include "neb.h" #include "universe.h" #include "atom.h" #include "update.h" diff --git a/src/REPLICA/prd.cpp b/src/REPLICA/prd.cpp index 6d450f48e3..19a12ddbbb 100644 --- a/src/REPLICA/prd.cpp +++ b/src/REPLICA/prd.cpp @@ -19,12 +19,12 @@ // due to OpenMPI bug which sets INT64_MAX via its mpi.h // before lmptype.h can set flags to insure it is done correctly +#include "prd.h" #include "lmptype.h" #include #include #include #include -#include "prd.h" #include "universe.h" #include "update.h" #include "atom.h" diff --git a/src/REPLICA/tad.cpp b/src/REPLICA/tad.cpp index da42ba6fae..90667b8865 100644 --- a/src/REPLICA/tad.cpp +++ b/src/REPLICA/tad.cpp @@ -19,12 +19,12 @@ // due to OpenMPI bug which sets INT64_MAX via its mpi.h // before lmptype.h can set flags to insure it is done correctly +#include "tad.h" #include "lmptype.h" #include #include #include #include -#include "tad.h" #include "universe.h" #include "update.h" #include "atom.h" diff --git a/src/REPLICA/temper.cpp b/src/REPLICA/temper.cpp index fe3e3fb993..6eb50c8d9f 100644 --- a/src/REPLICA/temper.cpp +++ b/src/REPLICA/temper.cpp @@ -15,10 +15,10 @@ Contributing author: Mark Sears (SNL) ------------------------------------------------------------------------- */ +#include "temper.h" #include #include #include -#include "temper.h" #include "universe.h" #include "domain.h" #include "atom.h" diff --git a/src/REPLICA/verlet_split.cpp b/src/REPLICA/verlet_split.cpp index 7042fc6993..f268afe7f8 100644 --- a/src/REPLICA/verlet_split.cpp +++ b/src/REPLICA/verlet_split.cpp @@ -15,8 +15,8 @@ Contributing authors: Yuxing Peng and Chris Knight (U Chicago) ------------------------------------------------------------------------- */ -#include #include "verlet_split.h" +#include #include "universe.h" #include "neighbor.h" #include "domain.h" diff --git a/src/RIGID/compute_erotate_rigid.cpp b/src/RIGID/compute_erotate_rigid.cpp index a3ddffd9ab..1a7236e263 100644 --- a/src/RIGID/compute_erotate_rigid.cpp +++ b/src/RIGID/compute_erotate_rigid.cpp @@ -11,9 +11,9 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ +#include "compute_erotate_rigid.h" #include #include -#include "compute_erotate_rigid.h" #include "update.h" #include "force.h" #include "modify.h" diff --git a/src/RIGID/compute_ke_rigid.cpp b/src/RIGID/compute_ke_rigid.cpp index 4de13532b2..66b7a92566 100644 --- a/src/RIGID/compute_ke_rigid.cpp +++ b/src/RIGID/compute_ke_rigid.cpp @@ -11,9 +11,9 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ +#include "compute_ke_rigid.h" #include #include -#include "compute_ke_rigid.h" #include "update.h" #include "force.h" #include "modify.h" diff --git a/src/RIGID/compute_rigid_local.cpp b/src/RIGID/compute_rigid_local.cpp index ec2799b6bc..75334bb759 100644 --- a/src/RIGID/compute_rigid_local.cpp +++ b/src/RIGID/compute_rigid_local.cpp @@ -11,9 +11,9 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ +#include "compute_rigid_local.h" #include #include -#include "compute_rigid_local.h" #include "atom.h" #include "update.h" #include "domain.h" diff --git a/src/RIGID/fix_ehex.cpp b/src/RIGID/fix_ehex.cpp index 0bbdea51c6..a5efc22d11 100644 --- a/src/RIGID/fix_ehex.cpp +++ b/src/RIGID/fix_ehex.cpp @@ -22,10 +22,10 @@ which implements the heat exchange (HEX) algorithm. ------------------------------------------------------------------------- */ +#include "fix_ehex.h" #include #include #include -#include "fix_ehex.h" #include "atom.h" #include "domain.h" #include "region.h" diff --git a/src/RIGID/fix_rattle.cpp b/src/RIGID/fix_rattle.cpp index db43b9e82d..93bf610e94 100644 --- a/src/RIGID/fix_rattle.cpp +++ b/src/RIGID/fix_rattle.cpp @@ -15,10 +15,10 @@ Contributing author: Peter Wirnsberger (University of Cambridge) ------------------------------------------------------------------------- */ +#include "fix_rattle.h" #include #include #include -#include "fix_rattle.h" #include "atom.h" #include "update.h" #include "modify.h" diff --git a/src/RIGID/fix_rigid.cpp b/src/RIGID/fix_rigid.cpp index 19eb22a7fa..912f529403 100644 --- a/src/RIGID/fix_rigid.cpp +++ b/src/RIGID/fix_rigid.cpp @@ -11,11 +11,11 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ +#include "fix_rigid.h" #include #include #include #include -#include "fix_rigid.h" #include "math_extra.h" #include "atom.h" #include "atom_vec_ellipsoid.h" diff --git a/src/RIGID/fix_rigid_nh.cpp b/src/RIGID/fix_rigid_nh.cpp index 2e1090ec88..4738e253f6 100644 --- a/src/RIGID/fix_rigid_nh.cpp +++ b/src/RIGID/fix_rigid_nh.cpp @@ -17,9 +17,9 @@ Miller et al., J Chem Phys. 116, 8649-8659 (2002) ------------------------------------------------------------------------- */ +#include "fix_rigid_nh.h" #include #include -#include "fix_rigid_nh.h" #include "math_extra.h" #include "atom.h" #include "compute.h" diff --git a/src/RIGID/fix_rigid_nh_small.cpp b/src/RIGID/fix_rigid_nh_small.cpp index 8de588bd9b..1545e913c0 100644 --- a/src/RIGID/fix_rigid_nh_small.cpp +++ b/src/RIGID/fix_rigid_nh_small.cpp @@ -17,10 +17,10 @@ Miller et al., J Chem Phys. 116, 8649-8659 (2002) ------------------------------------------------------------------------- */ +#include "fix_rigid_nh_small.h" #include #include #include -#include "fix_rigid_nh_small.h" #include "math_extra.h" #include "atom.h" #include "compute.h" diff --git a/src/RIGID/fix_rigid_nph.cpp b/src/RIGID/fix_rigid_nph.cpp index 6080fb05af..706e08ec12 100644 --- a/src/RIGID/fix_rigid_nph.cpp +++ b/src/RIGID/fix_rigid_nph.cpp @@ -17,8 +17,8 @@ Miller et al., J Chem Phys. 116, 8649-8659 (2002) ------------------------------------------------------------------------- */ -#include #include "fix_rigid_nph.h" +#include #include "modify.h" #include "error.h" diff --git a/src/RIGID/fix_rigid_nph_small.cpp b/src/RIGID/fix_rigid_nph_small.cpp index 9b045eaf13..32ac58220d 100644 --- a/src/RIGID/fix_rigid_nph_small.cpp +++ b/src/RIGID/fix_rigid_nph_small.cpp @@ -17,8 +17,8 @@ Miller et al., J Chem Phys. 116, 8649-8659 (2002) ------------------------------------------------------------------------- */ -#include #include "fix_rigid_nph_small.h" +#include #include "modify.h" #include "error.h" diff --git a/src/RIGID/fix_rigid_npt.cpp b/src/RIGID/fix_rigid_npt.cpp index 526fc8f614..1f19fb4ec7 100644 --- a/src/RIGID/fix_rigid_npt.cpp +++ b/src/RIGID/fix_rigid_npt.cpp @@ -17,8 +17,8 @@ Miller et al., J Chem Phys. 116, 8649-8659 (2002) ------------------------------------------------------------------------- */ -#include #include "fix_rigid_npt.h" +#include #include "modify.h" #include "error.h" diff --git a/src/RIGID/fix_rigid_npt_small.cpp b/src/RIGID/fix_rigid_npt_small.cpp index fff338d687..e8924be79f 100644 --- a/src/RIGID/fix_rigid_npt_small.cpp +++ b/src/RIGID/fix_rigid_npt_small.cpp @@ -17,8 +17,8 @@ Miller et al., J Chem Phys. 116, 8649-8659 (2002) ------------------------------------------------------------------------- */ -#include #include "fix_rigid_npt_small.h" +#include #include "modify.h" #include "error.h" diff --git a/src/RIGID/fix_rigid_small.cpp b/src/RIGID/fix_rigid_small.cpp index 8c2feb6436..14e230ab9c 100644 --- a/src/RIGID/fix_rigid_small.cpp +++ b/src/RIGID/fix_rigid_small.cpp @@ -11,12 +11,12 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ +#include "fix_rigid_small.h" #include #include #include #include #include -#include "fix_rigid_small.h" #include "math_extra.h" #include "atom.h" #include "atom_vec_ellipsoid.h" diff --git a/src/RIGID/fix_shake.cpp b/src/RIGID/fix_shake.cpp index 5c202706af..48a08118c5 100644 --- a/src/RIGID/fix_shake.cpp +++ b/src/RIGID/fix_shake.cpp @@ -11,11 +11,11 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ +#include "fix_shake.h" #include #include #include #include -#include "fix_shake.h" #include "atom.h" #include "atom_vec.h" #include "molecule.h" diff --git a/src/SHOCK/fix_append_atoms.cpp b/src/SHOCK/fix_append_atoms.cpp index 5e81b75c0d..5e85b39076 100644 --- a/src/SHOCK/fix_append_atoms.cpp +++ b/src/SHOCK/fix_append_atoms.cpp @@ -11,10 +11,10 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ +#include "fix_append_atoms.h" #include #include #include -#include "fix_append_atoms.h" #include "atom.h" #include "atom_vec.h" #include "comm.h" diff --git a/src/SHOCK/fix_msst.cpp b/src/SHOCK/fix_msst.cpp index 15ee4d370f..2e9f751824 100644 --- a/src/SHOCK/fix_msst.cpp +++ b/src/SHOCK/fix_msst.cpp @@ -17,10 +17,10 @@ see Reed, Fried, Joannopoulos, Phys Rev Lett, 90, 235503 (2003) ------------------------------------------------------------------------- */ +#include "fix_msst.h" #include #include #include -#include "fix_msst.h" #include "atom.h" #include "force.h" #include "comm.h" diff --git a/src/SHOCK/fix_nphug.cpp b/src/SHOCK/fix_nphug.cpp index 5d5a1642c0..8ad787d759 100644 --- a/src/SHOCK/fix_nphug.cpp +++ b/src/SHOCK/fix_nphug.cpp @@ -11,9 +11,9 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ +#include "fix_nphug.h" #include #include -#include "fix_nphug.h" #include "modify.h" #include "error.h" #include "update.h" diff --git a/src/SHOCK/fix_wall_piston.cpp b/src/SHOCK/fix_wall_piston.cpp index 31f70b4174..5a359d9f6f 100644 --- a/src/SHOCK/fix_wall_piston.cpp +++ b/src/SHOCK/fix_wall_piston.cpp @@ -11,9 +11,9 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ +#include "fix_wall_piston.h" #include #include -#include "fix_wall_piston.h" #include "atom.h" #include "domain.h" #include "lattice.h" diff --git a/src/SNAP/compute_sna_atom.cpp b/src/SNAP/compute_sna_atom.cpp index cc7a84281e..7ca9d52467 100644 --- a/src/SNAP/compute_sna_atom.cpp +++ b/src/SNAP/compute_sna_atom.cpp @@ -10,10 +10,11 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include "sna.h" + +#include "compute_sna_atom.h" #include #include -#include "compute_sna_atom.h" +#include "sna.h" #include "atom.h" #include "update.h" #include "modify.h" diff --git a/src/SNAP/compute_snad_atom.cpp b/src/SNAP/compute_snad_atom.cpp index 37587a0aae..7e71e4a556 100644 --- a/src/SNAP/compute_snad_atom.cpp +++ b/src/SNAP/compute_snad_atom.cpp @@ -10,10 +10,11 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include "sna.h" + +#include "compute_snad_atom.h" #include #include -#include "compute_snad_atom.h" +#include "sna.h" #include "atom.h" #include "update.h" #include "modify.h" diff --git a/src/SNAP/compute_snav_atom.cpp b/src/SNAP/compute_snav_atom.cpp index 5faf7a1872..28c018b1cc 100644 --- a/src/SNAP/compute_snav_atom.cpp +++ b/src/SNAP/compute_snav_atom.cpp @@ -10,9 +10,10 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ + +#include "compute_snav_atom.h" #include #include -#include "compute_snav_atom.h" #include "sna.h" #include "atom.h" #include "update.h" diff --git a/src/SNAP/pair_snap.cpp b/src/SNAP/pair_snap.cpp index f0f3ef72c6..56f59c7fcc 100644 --- a/src/SNAP/pair_snap.cpp +++ b/src/SNAP/pair_snap.cpp @@ -11,11 +11,11 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ +#include "pair_snap.h" #include #include #include #include -#include "pair_snap.h" #include "atom.h" #include "force.h" #include "comm.h" diff --git a/src/SNAP/sna.cpp b/src/SNAP/sna.cpp index d7d9b5163d..9194e44c21 100644 --- a/src/SNAP/sna.cpp +++ b/src/SNAP/sna.cpp @@ -15,8 +15,8 @@ Contributing authors: Aidan Thompson, Christian Trott, SNL ------------------------------------------------------------------------- */ -#include #include "sna.h" +#include #include "math_const.h" #include "memory.h" #include "error.h" diff --git a/src/SPIN/atom_vec_spin.cpp b/src/SPIN/atom_vec_spin.cpp index 37d6fb1e59..5810ecf85b 100644 --- a/src/SPIN/atom_vec_spin.cpp +++ b/src/SPIN/atom_vec_spin.cpp @@ -23,11 +23,11 @@ and molecular dynamics. Journal of Computational Physics. ------------------------------------------------------------------------- */ +#include "atom_vec_spin.h" #include #include #include #include "atom.h" -#include "atom_vec_spin.h" #include "comm.h" #include "domain.h" #include "error.h" diff --git a/src/SPIN/compute_spin.cpp b/src/SPIN/compute_spin.cpp index ec11bc68f2..8dad128994 100644 --- a/src/SPIN/compute_spin.cpp +++ b/src/SPIN/compute_spin.cpp @@ -21,9 +21,9 @@ and molecular dynamics. Journal of Computational Physics. ------------------------------------------------------------------------- */ +#include "compute_spin.h" #include #include -#include "compute_spin.h" #include "atom.h" #include "error.h" #include "force.h" diff --git a/src/SPIN/fix_langevin_spin.cpp b/src/SPIN/fix_langevin_spin.cpp index 6936c701c6..ec9c98c4f8 100644 --- a/src/SPIN/fix_langevin_spin.cpp +++ b/src/SPIN/fix_langevin_spin.cpp @@ -21,9 +21,9 @@ and molecular dynamics. Journal of Computational Physics. ------------------------------------------------------------------------- */ +#include "fix_langevin_spin.h" #include #include -#include "fix_langevin_spin.h" #include "comm.h" #include "error.h" #include "force.h" diff --git a/src/SPIN/fix_neb_spin.cpp b/src/SPIN/fix_neb_spin.cpp index 7ed8967a24..5acbbf59e8 100644 --- a/src/SPIN/fix_neb_spin.cpp +++ b/src/SPIN/fix_neb_spin.cpp @@ -21,10 +21,10 @@ Computer Physics Communications, 196, 335-347. ------------------------------------------------------------------------- */ +#include "fix_neb_spin.h" #include #include #include -#include "fix_neb_spin.h" #include "universe.h" #include "update.h" #include "atom.h" diff --git a/src/SPIN/fix_nve_spin.cpp b/src/SPIN/fix_nve_spin.cpp index d35585c7a6..1165048723 100644 --- a/src/SPIN/fix_nve_spin.cpp +++ b/src/SPIN/fix_nve_spin.cpp @@ -21,8 +21,8 @@ and molecular dynamics. Journal of Computational Physics. ------------------------------------------------------------------------- */ -#include #include "fix_nve_spin.h" +#include #include "atom.h" #include "citeme.h" #include "comm.h" diff --git a/src/SPIN/fix_precession_spin.cpp b/src/SPIN/fix_precession_spin.cpp index 7764bb0438..3296b28228 100644 --- a/src/SPIN/fix_precession_spin.cpp +++ b/src/SPIN/fix_precession_spin.cpp @@ -21,10 +21,10 @@ and molecular dynamics. Journal of Computational Physics. ------------------------------------------------------------------------- */ +#include "fix_precession_spin.h" #include #include #include -#include "fix_precession_spin.h" #include "atom.h" #include "error.h" #include "force.h" diff --git a/src/SPIN/fix_setforce_spin.cpp b/src/SPIN/fix_setforce_spin.cpp index 1ab35c9663..15e5aacfb6 100644 --- a/src/SPIN/fix_setforce_spin.cpp +++ b/src/SPIN/fix_setforce_spin.cpp @@ -21,8 +21,8 @@ and molecular dynamics. Journal of Computational Physics. ------------------------------------------------------------------------- */ -#include #include "fix_setforce_spin.h" +#include #include "atom.h" #include "update.h" #include "modify.h" diff --git a/src/SPIN/min_spin.cpp b/src/SPIN/min_spin.cpp index 3a330f448a..2514645325 100644 --- a/src/SPIN/min_spin.cpp +++ b/src/SPIN/min_spin.cpp @@ -17,10 +17,10 @@ Please cite the related publication: ------------------------------------------------------------------------- */ +#include "min_spin.h" #include #include #include -#include "min_spin.h" #include "universe.h" #include "atom.h" #include "force.h" diff --git a/src/SPIN/neb_spin.cpp b/src/SPIN/neb_spin.cpp index 400ce3d363..2bcfe6573a 100644 --- a/src/SPIN/neb_spin.cpp +++ b/src/SPIN/neb_spin.cpp @@ -21,11 +21,11 @@ Computer Physics Communications, 196, 335-347. ------------------------------------------------------------------------- */ +#include "neb_spin.h" #include #include #include #include -#include "neb_spin.h" #include "citeme.h" #include "force.h" #include "universe.h" diff --git a/src/SPIN/pair_spin.cpp b/src/SPIN/pair_spin.cpp index 93d9a1e127..fef247c09b 100644 --- a/src/SPIN/pair_spin.cpp +++ b/src/SPIN/pair_spin.cpp @@ -21,8 +21,8 @@ and molecular dynamics. Journal of Computational Physics. ------------------------------------------------------------------------- */ -#include #include "pair_spin.h" +#include #include "atom.h" #include "error.h" #include "fix.h" diff --git a/src/SPIN/pair_spin_dipole_cut.cpp b/src/SPIN/pair_spin_dipole_cut.cpp index 8d9b5b8f2b..fb0ec8bb20 100644 --- a/src/SPIN/pair_spin_dipole_cut.cpp +++ b/src/SPIN/pair_spin_dipole_cut.cpp @@ -21,10 +21,10 @@ and molecular dynamics. Journal of Computational Physics. ------------------------------------------------------------------------- */ +#include "pair_spin_dipole_cut.h" #include #include #include -#include "pair_spin_dipole_cut.h" #include "atom.h" #include "comm.h" #include "neighbor.h" diff --git a/src/SPIN/pair_spin_dipole_long.cpp b/src/SPIN/pair_spin_dipole_long.cpp index 84c55a8c3c..670fccfce2 100644 --- a/src/SPIN/pair_spin_dipole_long.cpp +++ b/src/SPIN/pair_spin_dipole_long.cpp @@ -16,10 +16,10 @@ Stan Moore (SNL) ------------------------------------------------------------------------- */ +#include "pair_spin_dipole_long.h" #include #include #include -#include "pair_spin_dipole_long.h" #include "atom.h" #include "comm.h" #include "neighbor.h" diff --git a/src/SPIN/pair_spin_dmi.cpp b/src/SPIN/pair_spin_dmi.cpp index 651f4397bd..afd2deaa6a 100644 --- a/src/SPIN/pair_spin_dmi.cpp +++ b/src/SPIN/pair_spin_dmi.cpp @@ -21,10 +21,10 @@ and molecular dynamics. Journal of Computational Physics. ------------------------------------------------------------------------- */ +#include "pair_spin_dmi.h" #include #include #include -#include "pair_spin_dmi.h" #include "atom.h" #include "comm.h" #include "error.h" diff --git a/src/SPIN/pair_spin_exchange.cpp b/src/SPIN/pair_spin_exchange.cpp index 059a8f5f34..cc28018ad0 100644 --- a/src/SPIN/pair_spin_exchange.cpp +++ b/src/SPIN/pair_spin_exchange.cpp @@ -21,10 +21,10 @@ and molecular dynamics. Journal of Computational Physics. ------------------------------------------------------------------------- */ +#include "pair_spin_exchange.h" #include #include #include -#include "pair_spin_exchange.h" #include "atom.h" #include "comm.h" #include "error.h" diff --git a/src/SPIN/pair_spin_magelec.cpp b/src/SPIN/pair_spin_magelec.cpp index 55b96582c8..6756ebc3cc 100644 --- a/src/SPIN/pair_spin_magelec.cpp +++ b/src/SPIN/pair_spin_magelec.cpp @@ -21,10 +21,10 @@ and molecular dynamics. Journal of Computational Physics. ------------------------------------------------------------------------- */ +#include "pair_spin_magelec.h" #include #include #include -#include "pair_spin_magelec.h" #include "atom.h" #include "comm.h" #include "error.h" diff --git a/src/SPIN/pair_spin_neel.cpp b/src/SPIN/pair_spin_neel.cpp index 4d68dbdc22..355ba20f39 100644 --- a/src/SPIN/pair_spin_neel.cpp +++ b/src/SPIN/pair_spin_neel.cpp @@ -21,10 +21,10 @@ and molecular dynamics. Journal of Computational Physics. ------------------------------------------------------------------------- */ +#include "pair_spin_neel.h" #include #include #include -#include "pair_spin_neel.h" #include "atom.h" #include "comm.h" #include "error.h" diff --git a/src/SRD/fix_srd.cpp b/src/SRD/fix_srd.cpp index a20ec212fd..d5eec91f50 100644 --- a/src/SRD/fix_srd.cpp +++ b/src/SRD/fix_srd.cpp @@ -15,10 +15,10 @@ Contributing authors: Jeremy Lechman (SNL), Pieter in 't Veld (BASF) ------------------------------------------------------------------------- */ +#include "fix_srd.h" #include #include #include -#include "fix_srd.h" #include "math_extra.h" #include "atom.h" #include "atom_vec_ellipsoid.h" diff --git a/src/SRD/fix_wall_srd.cpp b/src/SRD/fix_wall_srd.cpp index cb0f023640..ab113df28a 100644 --- a/src/SRD/fix_wall_srd.cpp +++ b/src/SRD/fix_wall_srd.cpp @@ -11,9 +11,9 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ +#include "fix_wall_srd.h" #include #include -#include "fix_wall_srd.h" #include "fix.h" #include "domain.h" #include "lattice.h" diff --git a/src/USER-ADIOS/dump_atom_adios.cpp b/src/USER-ADIOS/dump_atom_adios.cpp index 55d6c5fbf9..e711b8a583 100644 --- a/src/USER-ADIOS/dump_atom_adios.cpp +++ b/src/USER-ADIOS/dump_atom_adios.cpp @@ -16,6 +16,7 @@ ------------------------------------------------------------------------- */ #include "dump_atom_adios.h" +#include #include "atom.h" #include "domain.h" #include "error.h" @@ -23,7 +24,6 @@ #include "memory.h" #include "universe.h" #include "update.h" -#include #include "adios2.h" diff --git a/src/USER-ADIOS/dump_custom_adios.cpp b/src/USER-ADIOS/dump_custom_adios.cpp index 67f3deeb64..ee6d7d7e49 100644 --- a/src/USER-ADIOS/dump_custom_adios.cpp +++ b/src/USER-ADIOS/dump_custom_adios.cpp @@ -16,6 +16,8 @@ ------------------------------------------------------------------------- */ #include "dump_custom_adios.h" +#include +#include #include "atom.h" #include "compute.h" #include "domain.h" @@ -30,8 +32,6 @@ #include "universe.h" #include "update.h" #include "variable.h" -#include -#include #include "adios2.h" diff --git a/src/USER-ATC/fix_atc.cpp b/src/USER-ATC/fix_atc.cpp index f53343ced1..e2a1768f55 100644 --- a/src/USER-ATC/fix_atc.cpp +++ b/src/USER-ATC/fix_atc.cpp @@ -11,8 +11,10 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -// LAMMPS #include "fix_atc.h" +#include +#include +#include #include "fix_nve.h" #include "atom.h" #include "force.h" @@ -24,7 +26,7 @@ #include "pointers.h" #include "comm.h" #include "group.h" -// ATC + #include "ATC_Method.h" #include "ATC_Transfer.h" #include "ATC_TransferKernel.h" @@ -34,10 +36,6 @@ #include "ATC_CouplingMass.h" #include "ATC_CouplingMomentumEnergy.h" #include "LammpsInterface.h" -// other -#include -#include -#include using namespace LAMMPS_NS; using namespace FixConst; diff --git a/src/USER-AWPMD/atom_vec_wavepacket.cpp b/src/USER-AWPMD/atom_vec_wavepacket.cpp index 7556dd2c8e..bc70c0dbc2 100644 --- a/src/USER-AWPMD/atom_vec_wavepacket.cpp +++ b/src/USER-AWPMD/atom_vec_wavepacket.cpp @@ -15,10 +15,10 @@ Contributing author: Ilya Valuev (JIHT, Moscow, Russia) ------------------------------------------------------------------------- */ +#include "atom_vec_wavepacket.h" #include #include #include -#include "atom_vec_wavepacket.h" #include "atom.h" #include "comm.h" #include "domain.h" diff --git a/src/USER-AWPMD/fix_nve_awpmd.cpp b/src/USER-AWPMD/fix_nve_awpmd.cpp index 7722c93121..57ad17f3e6 100644 --- a/src/USER-AWPMD/fix_nve_awpmd.cpp +++ b/src/USER-AWPMD/fix_nve_awpmd.cpp @@ -15,10 +15,10 @@ Contributing author: Ilya Valuev (JIHT, Moscow, Russia) ------------------------------------------------------------------------- */ +#include "fix_nve_awpmd.h" #include #include #include -#include "fix_nve_awpmd.h" #include "atom.h" #include "force.h" #include "update.h" diff --git a/src/USER-AWPMD/pair_awpmd_cut.cpp b/src/USER-AWPMD/pair_awpmd_cut.cpp index 1b7bf35c28..ae2fbc59fa 100644 --- a/src/USER-AWPMD/pair_awpmd_cut.cpp +++ b/src/USER-AWPMD/pair_awpmd_cut.cpp @@ -15,11 +15,11 @@ Contributing author: Ilya Valuev (JIHT, Moscow, Russia) ------------------------------------------------------------------------- */ +#include "pair_awpmd_cut.h" #include #include #include #include -#include "pair_awpmd_cut.h" #include "atom.h" #include "update.h" #include "min.h" diff --git a/src/USER-BOCS/compute_pressure_bocs.cpp b/src/USER-BOCS/compute_pressure_bocs.cpp index fc24efab4c..33163f7aff 100644 --- a/src/USER-BOCS/compute_pressure_bocs.cpp +++ b/src/USER-BOCS/compute_pressure_bocs.cpp @@ -14,10 +14,10 @@ from The Pennsylvania State University ------------------------------------------------------------------------- */ +#include "compute_pressure_bocs.h" #include #include #include -#include "compute_pressure_bocs.h" #include "atom.h" #include "update.h" #include "domain.h" diff --git a/src/USER-BOCS/fix_bocs.cpp b/src/USER-BOCS/fix_bocs.cpp index 7bdb8933e3..e0952086dd 100644 --- a/src/USER-BOCS/fix_bocs.cpp +++ b/src/USER-BOCS/fix_bocs.cpp @@ -14,10 +14,10 @@ from The Pennsylvania State University ------------------------------------------------------------------------- */ +#include "fix_bocs.h" #include #include #include -#include "fix_bocs.h" #include "math_extra.h" #include "atom.h" #include "force.h" diff --git a/src/USER-CGDNA/bond_oxdna2_fene.cpp b/src/USER-CGDNA/bond_oxdna2_fene.cpp index 39cbb04f88..2cd7883600 100644 --- a/src/USER-CGDNA/bond_oxdna2_fene.cpp +++ b/src/USER-CGDNA/bond_oxdna2_fene.cpp @@ -14,9 +14,9 @@ Contributing author: Oliver Henrich (University of Strathclyde, Glasgow) ------------------------------------------------------------------------- */ +#include "bond_oxdna2_fene.h" #include #include -#include "bond_oxdna2_fene.h" using namespace LAMMPS_NS; diff --git a/src/USER-CGDNA/bond_oxdna_fene.cpp b/src/USER-CGDNA/bond_oxdna_fene.cpp index 8271668e3f..8b94fd6a5a 100644 --- a/src/USER-CGDNA/bond_oxdna_fene.cpp +++ b/src/USER-CGDNA/bond_oxdna_fene.cpp @@ -14,9 +14,9 @@ Contributing author: Oliver Henrich (University of Strathclyde, Glasgow) ------------------------------------------------------------------------- */ +#include "bond_oxdna_fene.h" #include #include -#include "bond_oxdna_fene.h" #include "atom.h" #include "neighbor.h" #include "domain.h" diff --git a/src/USER-CGDNA/fix_nve_dot.cpp b/src/USER-CGDNA/fix_nve_dot.cpp index 72b3388793..3bf6757df7 100644 --- a/src/USER-CGDNA/fix_nve_dot.cpp +++ b/src/USER-CGDNA/fix_nve_dot.cpp @@ -14,10 +14,10 @@ Contributing author: Oliver Henrich (University of Strathclyde, Glasgow) ------------------------------------------------------------------------- */ +#include "fix_nve_dot.h" #include #include #include -#include "fix_nve_dot.h" #include "math_extra.h" #include "atom.h" #include "atom_vec_ellipsoid.h" diff --git a/src/USER-CGDNA/fix_nve_dotc_langevin.cpp b/src/USER-CGDNA/fix_nve_dotc_langevin.cpp index c73801c97a..61e3552f11 100644 --- a/src/USER-CGDNA/fix_nve_dotc_langevin.cpp +++ b/src/USER-CGDNA/fix_nve_dotc_langevin.cpp @@ -15,10 +15,10 @@ Contributing author: Oliver Henrich (University of Strathclyde, Glasgow) ------------------------------------------------------------------------- */ +#include "fix_nve_dotc_langevin.h" #include #include #include -#include "fix_nve_dotc_langevin.h" #include "math_extra.h" #include "atom.h" #include "atom_vec_ellipsoid.h" diff --git a/src/USER-CGDNA/pair_oxdna2_coaxstk.cpp b/src/USER-CGDNA/pair_oxdna2_coaxstk.cpp index dfea97f0bf..1d0a2eb494 100644 --- a/src/USER-CGDNA/pair_oxdna2_coaxstk.cpp +++ b/src/USER-CGDNA/pair_oxdna2_coaxstk.cpp @@ -14,11 +14,11 @@ Contributing author: Oliver Henrich (University of Strathclyde, Glasgow) ------------------------------------------------------------------------- */ +#include "pair_oxdna2_coaxstk.h" #include #include #include #include -#include "pair_oxdna2_coaxstk.h" #include "mf_oxdna.h" #include "atom.h" #include "comm.h" diff --git a/src/USER-CGDNA/pair_oxdna2_dh.cpp b/src/USER-CGDNA/pair_oxdna2_dh.cpp index b4afad12db..22fc79dae4 100644 --- a/src/USER-CGDNA/pair_oxdna2_dh.cpp +++ b/src/USER-CGDNA/pair_oxdna2_dh.cpp @@ -14,11 +14,11 @@ Contributing author: Oliver Henrich (University of Strathclyde, Glasgow) ------------------------------------------------------------------------- */ +#include "pair_oxdna2_dh.h" #include #include #include #include -#include "pair_oxdna2_dh.h" #include "mf_oxdna.h" #include "atom.h" #include "comm.h" diff --git a/src/USER-CGDNA/pair_oxdna2_excv.cpp b/src/USER-CGDNA/pair_oxdna2_excv.cpp index 4329fbe071..de4f8319b9 100644 --- a/src/USER-CGDNA/pair_oxdna2_excv.cpp +++ b/src/USER-CGDNA/pair_oxdna2_excv.cpp @@ -14,11 +14,11 @@ Contributing author: Oliver Henrich (University of Strathclyde, Glasgow) ------------------------------------------------------------------------- */ +#include "pair_oxdna2_excv.h" #include #include #include #include -#include "pair_oxdna2_excv.h" using namespace LAMMPS_NS; diff --git a/src/USER-CGDNA/pair_oxdna2_stk.cpp b/src/USER-CGDNA/pair_oxdna2_stk.cpp index f479572aa6..3b9480bff6 100644 --- a/src/USER-CGDNA/pair_oxdna2_stk.cpp +++ b/src/USER-CGDNA/pair_oxdna2_stk.cpp @@ -14,11 +14,11 @@ Contributing author: Oliver Henrich (University of Strathclyde, Glasgow) ------------------------------------------------------------------------- */ +#include "pair_oxdna2_stk.h" #include #include #include #include -#include "pair_oxdna2_stk.h" using namespace LAMMPS_NS; diff --git a/src/USER-CGDNA/pair_oxdna_coaxstk.cpp b/src/USER-CGDNA/pair_oxdna_coaxstk.cpp index 6f3fa4fa4e..7310f60ec3 100644 --- a/src/USER-CGDNA/pair_oxdna_coaxstk.cpp +++ b/src/USER-CGDNA/pair_oxdna_coaxstk.cpp @@ -14,11 +14,11 @@ Contributing author: Oliver Henrich (University of Strathclyde, Glasgow) ------------------------------------------------------------------------- */ +#include "pair_oxdna_coaxstk.h" #include #include #include #include -#include "pair_oxdna_coaxstk.h" #include "mf_oxdna.h" #include "atom.h" #include "comm.h" diff --git a/src/USER-CGDNA/pair_oxdna_excv.cpp b/src/USER-CGDNA/pair_oxdna_excv.cpp index 82af5ed1c7..68091f4190 100644 --- a/src/USER-CGDNA/pair_oxdna_excv.cpp +++ b/src/USER-CGDNA/pair_oxdna_excv.cpp @@ -14,11 +14,11 @@ Contributing author: Oliver Henrich (University of Strathclyde, Glasgow) ------------------------------------------------------------------------- */ +#include "pair_oxdna_excv.h" #include #include #include #include -#include "pair_oxdna_excv.h" #include "mf_oxdna.h" #include "atom.h" #include "comm.h" diff --git a/src/USER-CGDNA/pair_oxdna_hbond.cpp b/src/USER-CGDNA/pair_oxdna_hbond.cpp index 8cd28f10c8..2de05e66ae 100644 --- a/src/USER-CGDNA/pair_oxdna_hbond.cpp +++ b/src/USER-CGDNA/pair_oxdna_hbond.cpp @@ -14,11 +14,11 @@ Contributing author: Oliver Henrich (University of Strathclyde, Glasgow) ------------------------------------------------------------------------- */ +#include "pair_oxdna_hbond.h" #include #include #include #include -#include "pair_oxdna_hbond.h" #include "mf_oxdna.h" #include "atom.h" #include "comm.h" diff --git a/src/USER-CGDNA/pair_oxdna_stk.cpp b/src/USER-CGDNA/pair_oxdna_stk.cpp index 93c65979ac..aaa25039ef 100644 --- a/src/USER-CGDNA/pair_oxdna_stk.cpp +++ b/src/USER-CGDNA/pair_oxdna_stk.cpp @@ -14,11 +14,11 @@ Contributing author: Oliver Henrich (University of Strathclyde, Glasgow) ------------------------------------------------------------------------- */ +#include "pair_oxdna_stk.h" #include #include #include #include -#include "pair_oxdna_stk.h" #include "mf_oxdna.h" #include "atom.h" #include "comm.h" diff --git a/src/USER-CGDNA/pair_oxdna_xstk.cpp b/src/USER-CGDNA/pair_oxdna_xstk.cpp index 1365d0d2b2..806f8a42c6 100644 --- a/src/USER-CGDNA/pair_oxdna_xstk.cpp +++ b/src/USER-CGDNA/pair_oxdna_xstk.cpp @@ -14,11 +14,11 @@ Contributing author: Oliver Henrich (University of Strathclyde, Glasgow) ------------------------------------------------------------------------- */ +#include "pair_oxdna_xstk.h" #include #include #include #include -#include "pair_oxdna_xstk.h" #include "mf_oxdna.h" #include "atom.h" #include "comm.h" diff --git a/src/USER-CGSDK/angle_sdk.cpp b/src/USER-CGSDK/angle_sdk.cpp index 823c725e07..575b0fae69 100644 --- a/src/USER-CGSDK/angle_sdk.cpp +++ b/src/USER-CGSDK/angle_sdk.cpp @@ -18,9 +18,9 @@ lj/sdk potential for coarse grained MD simulations. ------------------------------------------------------------------------- */ +#include "angle_sdk.h" #include #include -#include "angle_sdk.h" #include "atom.h" #include "neighbor.h" #include "pair.h" diff --git a/src/USER-CGSDK/pair_lj_sdk.cpp b/src/USER-CGSDK/pair_lj_sdk.cpp index 7dd6c04436..b22469566e 100644 --- a/src/USER-CGSDK/pair_lj_sdk.cpp +++ b/src/USER-CGSDK/pair_lj_sdk.cpp @@ -16,11 +16,11 @@ This style is a simplified re-implementation of the CG/CMM pair style ------------------------------------------------------------------------- */ +#include "pair_lj_sdk.h" #include #include #include #include -#include "pair_lj_sdk.h" #include "atom.h" #include "comm.h" #include "force.h" diff --git a/src/USER-CGSDK/pair_lj_sdk_coul_long.cpp b/src/USER-CGSDK/pair_lj_sdk_coul_long.cpp index 33a1659df9..5fba8cde66 100644 --- a/src/USER-CGSDK/pair_lj_sdk_coul_long.cpp +++ b/src/USER-CGSDK/pair_lj_sdk_coul_long.cpp @@ -16,11 +16,11 @@ This style is a simplified re-implementation of the CG/CMM pair style ------------------------------------------------------------------------- */ +#include "pair_lj_sdk_coul_long.h" #include #include #include #include -#include "pair_lj_sdk_coul_long.h" #include "atom.h" #include "comm.h" #include "force.h" diff --git a/src/USER-CGSDK/pair_lj_sdk_coul_msm.cpp b/src/USER-CGSDK/pair_lj_sdk_coul_msm.cpp index d26f8efcdc..b61ed5528f 100644 --- a/src/USER-CGSDK/pair_lj_sdk_coul_msm.cpp +++ b/src/USER-CGSDK/pair_lj_sdk_coul_msm.cpp @@ -16,11 +16,11 @@ This style is a simplified re-implementation of the CG/CMM pair style ------------------------------------------------------------------------- */ +#include "pair_lj_sdk_coul_msm.h" #include #include #include #include -#include "pair_lj_sdk_coul_msm.h" #include "atom.h" #include "comm.h" #include "force.h" diff --git a/src/USER-COLVARS/colvarproxy_lammps.cpp b/src/USER-COLVARS/colvarproxy_lammps.cpp index 651999f79c..685c698ab6 100644 --- a/src/USER-COLVARS/colvarproxy_lammps.cpp +++ b/src/USER-COLVARS/colvarproxy_lammps.cpp @@ -8,7 +8,20 @@ // Colvars repository at GitHub. +#include "colvarproxy_lammps.h" #include +#include +#include +#include + +#include +#include +#include + +#include +#include +#include + #include "lammps.h" #include "atom.h" #include "error.h" @@ -22,19 +35,6 @@ #include "colvarbias.h" #include "colvaratoms.h" #include "colvarproxy.h" -#include "colvarproxy_lammps.h" - -#include -#include -#include - -#include -#include -#include - -#include -#include -#include #define HASH_FAIL -1 diff --git a/src/USER-COLVARS/fix_colvars.cpp b/src/USER-COLVARS/fix_colvars.cpp index ff0e8fb334..9331fe7abb 100644 --- a/src/USER-COLVARS/fix_colvars.cpp +++ b/src/USER-COLVARS/fix_colvars.cpp @@ -24,13 +24,13 @@ Contributing author: Axel Kohlmeyer (Temple U) ------------------------------------------------------------------------- */ +#include "fix_colvars.h" #include #include #include #include #include -#include "fix_colvars.h" #include "atom.h" #include "comm.h" #include "domain.h" diff --git a/src/USER-COLVARS/group_ndx.cpp b/src/USER-COLVARS/group_ndx.cpp index 858336c9d5..7350712c40 100644 --- a/src/USER-COLVARS/group_ndx.cpp +++ b/src/USER-COLVARS/group_ndx.cpp @@ -17,15 +17,14 @@ ------------------------------------------------------------------------- */ #include "group_ndx.h" +#include +#include #include "atom.h" #include "comm.h" #include "group.h" #include "memory.h" #include "error.h" -#include -#include - using namespace LAMMPS_NS; /* ---------------------------------------------------------------------- diff --git a/src/USER-COLVARS/ndx_group.cpp b/src/USER-COLVARS/ndx_group.cpp index 7b46364f18..5436ba7b6b 100644 --- a/src/USER-COLVARS/ndx_group.cpp +++ b/src/USER-COLVARS/ndx_group.cpp @@ -17,6 +17,9 @@ ------------------------------------------------------------------------- */ #include "ndx_group.h" +#include +#include +#include #include "atom.h" #include "comm.h" #include "group.h" @@ -24,10 +27,6 @@ #include "force.h" #include "error.h" -#include -#include -#include - using namespace LAMMPS_NS; #define BUFLEN 4096 #define DELTA 16384 -- GitLab From 95cb995336e4c20211bd354067bdb199baadee07 Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Wed, 3 Jul 2019 22:18:41 -0400 Subject: [PATCH 175/469] recover compilation of MANYBODY package --- src/MANYBODY/pair_polymorphic.h | 1 + 1 file changed, 1 insertion(+) diff --git a/src/MANYBODY/pair_polymorphic.h b/src/MANYBODY/pair_polymorphic.h index 32f1c5414a..e7c3cd0d26 100644 --- a/src/MANYBODY/pair_polymorphic.h +++ b/src/MANYBODY/pair_polymorphic.h @@ -22,6 +22,7 @@ PairStyle(polymorphic,PairPolymorphic) #include "pair.h" #include +#include namespace LAMMPS_NS { -- GitLab From e63fe1fe84e51c734c2170b4f6eb324d01abb58e Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Thu, 4 Jul 2019 00:09:01 -0400 Subject: [PATCH 176/469] please POEMS library in namespace POEMS and remove "using namespace" from headers --- lib/poems/POEMSChain.h | 99 +++--- lib/poems/SystemProcessor.h | 439 +++++++++++------------ lib/poems/body.cpp | 5 +- lib/poems/body.h | 3 +- lib/poems/body23joint.cpp | 3 + lib/poems/body23joint.h | 3 +- lib/poems/colmatmap.cpp | 2 + lib/poems/colmatmap.h | 3 +- lib/poems/colmatrix.cpp | 2 + lib/poems/colmatrix.h | 42 +-- lib/poems/defines.h | 7 +- lib/poems/eulerparameters.cpp | 42 +-- lib/poems/eulerparameters.h | 3 +- lib/poems/fastmatrixops.cpp | 130 +++---- lib/poems/fastmatrixops.h | 3 +- lib/poems/fixedpoint.cpp | 2 + lib/poems/fixedpoint.h | 3 +- lib/poems/freebodyjoint.cpp | 124 +++---- lib/poems/freebodyjoint.h | 8 +- lib/poems/inertialframe.cpp | 2 + lib/poems/inertialframe.h | 4 +- lib/poems/joint.cpp | 4 +- lib/poems/joint.h | 3 +- lib/poems/mat3x3.cpp | 2 + lib/poems/mat3x3.h | 14 +- lib/poems/mat4x4.cpp | 2 + lib/poems/mat4x4.h | 11 +- lib/poems/mat6x6.cpp | 2 + lib/poems/mat6x6.h | 3 +- lib/poems/matrices.h | 13 +- lib/poems/matrix.cpp | 2 + lib/poems/matrix.h | 8 +- lib/poems/matrixfun.cpp | 48 +-- lib/poems/matrixfun.h | 17 +- lib/poems/mixedjoint.cpp | 130 +++---- lib/poems/mixedjoint.h | 12 +- lib/poems/norm.cpp | 2 + lib/poems/norm.h | 7 +- lib/poems/onbody.cpp | 2 + lib/poems/onbody.h | 106 +++--- lib/poems/onfunctions.cpp | 40 ++- lib/poems/onfunctions.h | 3 +- lib/poems/onsolver.cpp | 2 + lib/poems/onsolver.h | 49 ++- lib/poems/particle.cpp | 2 + lib/poems/particle.h | 10 +- lib/poems/poemslist.h | 74 ++-- lib/poems/poemsnodelib.h | 11 +- lib/poems/poemsobject.cpp | 2 + lib/poems/poemsobject.h | 4 +- lib/poems/poemstree.h | 4 +- lib/poems/poemstreenode.cpp | 2 + lib/poems/poemstreenode.h | 39 ++- lib/poems/point.cpp | 4 +- lib/poems/point.h | 18 +- lib/poems/prismaticjoint.cpp | 2 + lib/poems/prismaticjoint.h | 5 +- lib/poems/revolutejoint.cpp | 2 + lib/poems/revolutejoint.h | 3 +- lib/poems/rigidbody.cpp | 2 + lib/poems/rigidbody.h | 3 +- lib/poems/rowmatrix.cpp | 2 + lib/poems/rowmatrix.h | 3 +- lib/poems/solver.cpp | 2 + lib/poems/solver.h | 19 +- lib/poems/sphericaljoint.cpp | 196 +++++------ lib/poems/sphericaljoint.h | 3 +- lib/poems/system.cpp | 615 +++++++++++++++++---------------- lib/poems/system.h | 33 +- lib/poems/vect3.cpp | 2 + lib/poems/vect3.h | 8 +- lib/poems/vect4.cpp | 2 + lib/poems/vect4.h | 9 +- lib/poems/vect6.cpp | 2 + lib/poems/vect6.h | 3 +- lib/poems/virtualcolmatrix.cpp | 2 + lib/poems/virtualcolmatrix.h | 40 +-- lib/poems/virtualmatrix.cpp | 6 +- lib/poems/virtualmatrix.h | 3 +- lib/poems/virtualrowmatrix.cpp | 2 + lib/poems/virtualrowmatrix.h | 11 +- lib/poems/workspace.cpp | 2 + lib/poems/workspace.h | 69 ++-- src/POEMS/fix_poems.cpp | 4 +- src/POEMS/fix_poems.h | 3 +- 85 files changed, 1365 insertions(+), 1274 deletions(-) diff --git a/lib/poems/POEMSChain.h b/lib/poems/POEMSChain.h index 9f0db59333..8baa293dbd 100644 --- a/lib/poems/POEMSChain.h +++ b/lib/poems/POEMSChain.h @@ -3,7 +3,7 @@ * POEMS: PARALLELIZABLE OPEN SOURCE EFFICIENT MULTIBODY SOFTWARE * * DESCRIPTION: SEE READ-ME * * FILE NAME: PoemsChain.h * - * AUTHORS: See Author List * + * AUTHORS: See Author List * * GRANTS: See Grants List * * COPYRIGHT: (C) 2005 by Authors as listed in Author's List * * LICENSE: Please see License Agreement * @@ -11,7 +11,7 @@ * ADMINISTRATOR: Prof. Kurt Anderson * * Computational Dynamics Lab * * Rensselaer Polytechnic Institute * - * 110 8th St. Troy NY 12180 * + * 110 8th St. Troy NY 12180 * * CONTACT: anderk5@rpi.edu * *_________________________________________________________________________*/ @@ -19,56 +19,59 @@ #define POEMSCHAIN_H_ #include "poemslist.h" +#include +namespace POEMS { struct ChildRingData { - List * childRing; - int entranceNodeId; + List * childRing; + int entranceNodeId; }; struct POEMSChain{ - ~POEMSChain(){ - for(int i = 0; i < childChains.GetNumElements(); i++) - { - delete childChains(i); - } - listOfNodes.DeleteValues(); - } - //void printTreeStructure(int tabs); - //void getTreeAsList(List * temp); - List listOfNodes; - List childChains; - POEMSChain * parentChain; - List childRings; - - - void printTreeStructure(int tabs){ - for(int i = 0; i < tabs; i++) - { - cout << "\t"; - } - cout << "Chain: "; - for(int i = 0; i < listOfNodes.GetNumElements(); i++) - { - cout << *(listOfNodes(i)) << " "; - } - cout << endl; - for(int i = 0; i < childChains.GetNumElements(); i++) - { - childChains(i)->printTreeStructure(tabs + 1); - } - } - void getTreeAsList(List * temp) - { - for(int i = 0; i < listOfNodes.GetNumElements(); i++) - { - int * integer = new int; - *integer = *(listOfNodes(i)); - temp->Append(integer); - } - for(int i = 0; i < childChains.GetNumElements(); i++) - { - childChains(i)->getTreeAsList(temp); - } - } + ~POEMSChain(){ + for(int i = 0; i < childChains.GetNumElements(); i++) + { + delete childChains(i); + } + listOfNodes.DeleteValues(); + } + //void printTreeStructure(int tabs); + //void getTreeAsList(List * temp); + List listOfNodes; + List childChains; + POEMSChain * parentChain; + List childRings; + + + void printTreeStructure(int tabs){ + for(int i = 0; i < tabs; i++) + { + std::cout << "\t"; + } + std::cout << "Chain: "; + for(int i = 0; i < listOfNodes.GetNumElements(); i++) + { + std::cout << *(listOfNodes(i)) << " "; + } + std::cout << std::endl; + for(int i = 0; i < childChains.GetNumElements(); i++) + { + childChains(i)->printTreeStructure(tabs + 1); + } + } + void getTreeAsList(List * temp) + { + for(int i = 0; i < listOfNodes.GetNumElements(); i++) + { + int * integer = new int; + *integer = *(listOfNodes(i)); + temp->Append(integer); + } + for(int i = 0; i < childChains.GetNumElements(); i++) + { + childChains(i)->getTreeAsList(temp); + } + } }; +} #endif diff --git a/lib/poems/SystemProcessor.h b/lib/poems/SystemProcessor.h index 3be168c34d..a6001d96d0 100644 --- a/lib/poems/SystemProcessor.h +++ b/lib/poems/SystemProcessor.h @@ -3,7 +3,7 @@ * POEMS: PARALLELIZABLE OPEN SOURCE EFFICIENT MULTIBODY SOFTWARE * * DESCRIPTION: SEE READ-ME * * FILE NAME: SystemProcessor.h * - * AUTHORS: See Author List * + * AUTHORS: See Author List * * GRANTS: See Grants List * * COPYRIGHT: (C) 2005 by Authors as listed in Author's List * * LICENSE: Please see License Agreement * @@ -11,59 +11,61 @@ * ADMINISTRATOR: Prof. Kurt Anderson * * Computational Dynamics Lab * * Rensselaer Polytechnic Institute * - * 110 8th St. Troy NY 12180 * + * 110 8th St. Troy NY 12180 * * CONTACT: anderk5@rpi.edu * *_________________________________________________________________________*/ #ifndef _SYS_PROCESSOR_H_ #define _SYS_PROCESSOR_H_ +#include #include "poemslist.h" #include "poemstree.h" #include "POEMSChain.h" +namespace POEMS { struct POEMSNode { - List links; - List taken; - int idNumber; - bool visited; - - ~POEMSNode(){ - for(int i = 0; i < taken.GetNumElements(); i++) - { - delete taken(i); - } - }; + List links; + List taken; + int idNumber; + bool visited; + + ~POEMSNode(){ + for(int i = 0; i < taken.GetNumElements(); i++) + { + delete taken(i); + } + }; }; class SystemProcessor{ private: - Tree nodes; - static void POEMSNodeDelete_cb(void *node) { - delete (POEMSNode *) node; - } - List headsOfSystems; - List > ringsInSystem; - POEMSNode * findSingleLink(TreeNode * aNode); - POEMSChain * AddNewChain(POEMSNode * currentNode); - bool setLinkVisited(POEMSNode * firstNode, POEMSNode * secondNode); + Tree nodes; + static void POEMSNodeDelete_cb(void *node) { + delete (POEMSNode *) node; + } + List headsOfSystems; + List > ringsInSystem; + POEMSNode * findSingleLink(TreeNode * aNode); + POEMSChain * AddNewChain(POEMSNode * currentNode); + bool setLinkVisited(POEMSNode * firstNode, POEMSNode * secondNode); public: - SystemProcessor(void); - - ~SystemProcessor(void) { - headsOfSystems.DeleteValues(); - for(int i = 0; i < ringsInSystem.GetNumElements(); i++) - { - for(int k = 0; k < ringsInSystem(i)->GetNumElements(); i++) - { - delete (*ringsInSystem(i))(k); - } - } - }; - void processArray(int** links, int numLinks); - List * getSystemData(); - int getNumberOfHeadChains(); + SystemProcessor(void); + + ~SystemProcessor(void) { + headsOfSystems.DeleteValues(); + for(int i = 0; i < ringsInSystem.GetNumElements(); i++) + { + for(int k = 0; k < ringsInSystem(i)->GetNumElements(); i++) + { + delete (*ringsInSystem(i))(k); + } + } + }; + void processArray(int** links, int numLinks); + List * getSystemData(); + int getNumberOfHeadChains(); }; SystemProcessor::SystemProcessor(void){ @@ -73,145 +75,145 @@ SystemProcessor::SystemProcessor(void){ void SystemProcessor::processArray(int** links, int numLinks) { - bool * false_var; //holds the value false; needed because a constant cannot be put into a list; the list requires a - //reference. - for(int i = 0; i < numLinks; i++) //go through all the links in the input array - { - if(!nodes.Find(links[i][0])) //if the first node in the pair is not found in the storage tree - { - POEMSNode * newNode = new POEMSNode; //make a new node -// forDeletion.Append(newNode); - newNode->idNumber = links[i][0]; //set its ID to the value - newNode->visited = false; //set it to be unvisited - nodes.Insert(links[i][0], links[i][0], (void *) newNode); //and add it to the tree storage structure - } - if(!nodes.Find(links[i][1])) //repeat process for the other half of each link - { - POEMSNode * newNode = new POEMSNode; -// forDeletion.Append(newNode); - newNode->idNumber = links[i][1]; - newNode->visited = false; - nodes.Insert(links[i][1], links[i][1], (void *) newNode); - } - POEMSNode * firstNode = (POEMSNode *)nodes.Find(links[i][0]); //now that we are sure both nodes exist, - POEMSNode * secondNode = (POEMSNode *)nodes.Find(links[i][1]); //we can get both of them out of the tree - firstNode->links.Append(secondNode); //and add the link from the first to the second... - false_var = new bool; - *false_var = false; //make a new false boolean to note that the link between these two - firstNode->taken.Append(false_var); //has not already been taken, and append it to the taken list - secondNode->links.Append(firstNode); //repeat process for link from second node to first - false_var = new bool; - *false_var = false; - secondNode->taken.Append(false_var); - } - - TreeNode * temp = nodes.GetRoot(); //get the root node of the node storage tree - POEMSNode * currentNode; - do - { - currentNode = findSingleLink(temp); //find the start of the next available chain - if(currentNode != NULL) - { - headsOfSystems.Append(AddNewChain(currentNode)); //and add it to the headsOfSystems list of chains - } - } - while(currentNode != NULL); //repeat this until all chains have been added + bool * false_var; //holds the value false; needed because a constant cannot be put into a list; the list requires a + //reference. + for(int i = 0; i < numLinks; i++) //go through all the links in the input array + { + if(!nodes.Find(links[i][0])) //if the first node in the pair is not found in the storage tree + { + POEMSNode * newNode = new POEMSNode; //make a new node +// forDeletion.Append(newNode); + newNode->idNumber = links[i][0]; //set its ID to the value + newNode->visited = false; //set it to be unvisited + nodes.Insert(links[i][0], links[i][0], (void *) newNode); //and add it to the tree storage structure + } + if(!nodes.Find(links[i][1])) //repeat process for the other half of each link + { + POEMSNode * newNode = new POEMSNode; +// forDeletion.Append(newNode); + newNode->idNumber = links[i][1]; + newNode->visited = false; + nodes.Insert(links[i][1], links[i][1], (void *) newNode); + } + POEMSNode * firstNode = (POEMSNode *)nodes.Find(links[i][0]); //now that we are sure both nodes exist, + POEMSNode * secondNode = (POEMSNode *)nodes.Find(links[i][1]); //we can get both of them out of the tree + firstNode->links.Append(secondNode); //and add the link from the first to the second... + false_var = new bool; + *false_var = false; //make a new false boolean to note that the link between these two + firstNode->taken.Append(false_var); //has not already been taken, and append it to the taken list + secondNode->links.Append(firstNode); //repeat process for link from second node to first + false_var = new bool; + *false_var = false; + secondNode->taken.Append(false_var); + } + + TreeNode * temp = nodes.GetRoot(); //get the root node of the node storage tree + POEMSNode * currentNode; + do + { + currentNode = findSingleLink(temp); //find the start of the next available chain + if(currentNode != NULL) + { + headsOfSystems.Append(AddNewChain(currentNode)); //and add it to the headsOfSystems list of chains + } + } + while(currentNode != NULL); //repeat this until all chains have been added } POEMSChain * SystemProcessor::AddNewChain(POEMSNode * currentNode){ - if(currentNode == NULL) //Termination condition; if the currentNode is null, then return null - { - return NULL; - } - int * tmp; - POEMSNode * nextNode = NULL; //nextNode stores the proposed next node to add to the chain. this will be checked to make sure no backtracking is occuring before being assigned as the current node. - POEMSChain * newChain = new POEMSChain; //make a new POEMSChain object. This will be the object returned + if(currentNode == NULL) //Termination condition; if the currentNode is null, then return null + { + return NULL; + } + int * tmp; + POEMSNode * nextNode = NULL; //nextNode stores the proposed next node to add to the chain. this will be checked to make sure no backtracking is occuring before being assigned as the current node. + POEMSChain * newChain = new POEMSChain; //make a new POEMSChain object. This will be the object returned - if(currentNode->links.GetNumElements() == 0) //if we have no links from this node, then the whole chain is only one node. Add this node to the chain and return it; mark node as visited for future reference - { - currentNode->visited = true; - tmp = new int; - *tmp = currentNode->idNumber; - newChain->listOfNodes.Append(tmp); - return newChain; - } - while(currentNode->links.GetNumElements() <= 2) //we go until we get to a node that branches, or both branches have already been taken both branches can already be taken if a loop with no spurs is found in the input data - { - currentNode->visited = true; - tmp = new int; - *tmp = currentNode->idNumber; - newChain->listOfNodes.Append(tmp); //append the current node to the chain & mark as visited - //cout << "Appending node " << currentNode->idNumber << " to chain" << endl; - nextNode = currentNode->links.GetHeadElement()->value; //the next node is the first or second value stored in the links array - //of the current node. We get the first value... - if(!setLinkVisited(currentNode, nextNode)) //...and see if it points back to where we came from. If it does... - { //either way, we set this link as visited - if(currentNode->links.GetNumElements() == 1) //if it does, then if that is the only link to this node, we're done with the chain, so append the chain to the list and return the newly created chain - { -// headsOfSystems.Append(newChain); - return newChain; - } - nextNode = currentNode->links.GetHeadElement()->next->value;//follow the other link if there is one, so we go down the chain - if(!setLinkVisited(currentNode, nextNode)) //mark link as followed, so we know not to backtrack - { - // headsOfSystems.Append(newChain); - return newChain; //This condition, where no branches have occurred but both links have already - //been taken can only occur in a loop with no spurs; add this loop to the - //system (currently added as a chain for consistency), and return. - } - } - currentNode = nextNode; //set the current node to be the next node in the chain - } - currentNode->visited = true; - tmp = new int; - *tmp = currentNode->idNumber; - newChain->listOfNodes.Append(tmp); //append the last node before branch (node shared jointly with branch chains) - //re-mark as visited, just to make sure - ListElement * tempNode = currentNode->links.GetHeadElement(); //go through all of the links, one at a time that branch - POEMSChain * tempChain = NULL; //temporary variable to hold data - while(tempNode != NULL) //when we have followed all links, stop - { - if(setLinkVisited(tempNode->value, currentNode)) //dont backtrack, or create closed loops - { - tempChain = AddNewChain(tempNode->value); //Add a new chain created out of the next node down that link - tempChain->parentChain = newChain; //set the parent to be this chain - newChain->childChains.Append(tempChain); //append the chain to this chain's list of child chains - } - tempNode = tempNode->next; //go to process the next chain - } - //headsOfSystems.Append(newChain); //append this chain to the system list - return newChain; + if(currentNode->links.GetNumElements() == 0) //if we have no links from this node, then the whole chain is only one node. Add this node to the chain and return it; mark node as visited for future reference + { + currentNode->visited = true; + tmp = new int; + *tmp = currentNode->idNumber; + newChain->listOfNodes.Append(tmp); + return newChain; + } + while(currentNode->links.GetNumElements() <= 2) //we go until we get to a node that branches, or both branches have already been taken both branches can already be taken if a loop with no spurs is found in the input data + { + currentNode->visited = true; + tmp = new int; + *tmp = currentNode->idNumber; + newChain->listOfNodes.Append(tmp); //append the current node to the chain & mark as visited + //std::cout << "Appending node " << currentNode->idNumber << " to chain" << std::endl; + nextNode = currentNode->links.GetHeadElement()->value; //the next node is the first or second value stored in the links array + //of the current node. We get the first value... + if(!setLinkVisited(currentNode, nextNode)) //...and see if it points back to where we came from. If it does... + { //either way, we set this link as visited + if(currentNode->links.GetNumElements() == 1) //if it does, then if that is the only link to this node, we're done with the chain, so append the chain to the list and return the newly created chain + { +// headsOfSystems.Append(newChain); + return newChain; + } + nextNode = currentNode->links.GetHeadElement()->next->value;//follow the other link if there is one, so we go down the chain + if(!setLinkVisited(currentNode, nextNode)) //mark link as followed, so we know not to backtrack + { + // headsOfSystems.Append(newChain); + return newChain; //This condition, where no branches have occurred but both links have already + //been taken can only occur in a loop with no spurs; add this loop to the + //system (currently added as a chain for consistency), and return. + } + } + currentNode = nextNode; //set the current node to be the next node in the chain + } + currentNode->visited = true; + tmp = new int; + *tmp = currentNode->idNumber; + newChain->listOfNodes.Append(tmp); //append the last node before branch (node shared jointly with branch chains) + //re-mark as visited, just to make sure + ListElement * tempNode = currentNode->links.GetHeadElement(); //go through all of the links, one at a time that branch + POEMSChain * tempChain = NULL; //temporary variable to hold data + while(tempNode != NULL) //when we have followed all links, stop + { + if(setLinkVisited(tempNode->value, currentNode)) //dont backtrack, or create closed loops + { + tempChain = AddNewChain(tempNode->value); //Add a new chain created out of the next node down that link + tempChain->parentChain = newChain; //set the parent to be this chain + newChain->childChains.Append(tempChain); //append the chain to this chain's list of child chains + } + tempNode = tempNode->next; //go to process the next chain + } + //headsOfSystems.Append(newChain); //append this chain to the system list + return newChain; } POEMSNode * SystemProcessor::findSingleLink(TreeNode * aNode) //This function takes the root of a search tree containing POEMSNodes and returns a POEMSNode corresponding to the start of a chain in the //system. It finds a node that has not been visited before, and only has one link; this node will be used as the head of the chain. { - if(aNode == NULL) - { - return NULL; - } - POEMSNode * returnVal = (POEMSNode *)aNode->GetAuxData(); //get the poemsnode data out of the treenode - POEMSNode * detectLoneLoops = NULL; //is used to handle a loop that has no protruding chains - if(returnVal->visited == false) - { - detectLoneLoops = returnVal; //if we find any node that has not been visited yet, save it - } - if(returnVal->links.GetNumElements() == 1 && returnVal->visited == false) //see if it has one element and hasnt been visited already - { - return returnVal; //return the node is it meets this criteria - } - returnVal = findSingleLink(aNode->Left()); //otherwise, check the left subtree - if(returnVal == NULL) //and if we find nothing... - { - returnVal = findSingleLink(aNode->Right()); //check the right subtree - } - if(returnVal == NULL) //if we could not find any chains - { - returnVal = detectLoneLoops; //see if we found any nodes at all that havent been processed - } - return returnVal; //return what we find (will be NULL if no new chains are - //found) + if(aNode == NULL) + { + return NULL; + } + POEMSNode * returnVal = (POEMSNode *)aNode->GetAuxData(); //get the poemsnode data out of the treenode + POEMSNode * detectLoneLoops = NULL; //is used to handle a loop that has no protruding chains + if(returnVal->visited == false) + { + detectLoneLoops = returnVal; //if we find any node that has not been visited yet, save it + } + if(returnVal->links.GetNumElements() == 1 && returnVal->visited == false) //see if it has one element and hasnt been visited already + { + return returnVal; //return the node is it meets this criteria + } + returnVal = findSingleLink(aNode->Left()); //otherwise, check the left subtree + if(returnVal == NULL) //and if we find nothing... + { + returnVal = findSingleLink(aNode->Right()); //check the right subtree + } + if(returnVal == NULL) //if we could not find any chains + { + returnVal = detectLoneLoops; //see if we found any nodes at all that havent been processed + } + return returnVal; //return what we find (will be NULL if no new chains are + //found) } bool SystemProcessor::setLinkVisited(POEMSNode * firstNode, POEMSNode * secondNode) @@ -223,65 +225,66 @@ bool SystemProcessor::setLinkVisited(POEMSNode * firstNode, POEMSNode * secondNo //value for that particular link. Because each link is represented twice, (once at each node in the link), both of the boolean values need //to be set in the event that the link has to be set as visited. { - //cout << "Checking link between nodes " << firstNode->idNumber << " and " << secondNode->idNumber << "... "; - ListElement * tmp = firstNode->links.GetHeadElement(); //get the head element of the list of pointers for node 1 - ListElement * tmp2 = firstNode->taken.GetHeadElement(); //get the head element of the list of bool isVisited flags for node 1 - while(tmp->value != NULL || tmp2->value != NULL) //go through untill we reach the end of the lists - { - if(tmp->value == secondNode) //if we find the link to the other node - { - if(*(tmp2->value) == true) //if the link has already been visited - { - //cout << "visited already" << endl; - return false; //return false to indicate that the link has been visited before this attempt - } - else //otherwise, visit it - { - *tmp2->value = true; - } - break; - } - tmp = tmp->next; //go check next link - tmp2 = tmp2->next; - } + //std::cout << "Checking link between nodes " << firstNode->idNumber << " and " << secondNode->idNumber << "... "; + ListElement * tmp = firstNode->links.GetHeadElement(); //get the head element of the list of pointers for node 1 + ListElement * tmp2 = firstNode->taken.GetHeadElement(); //get the head element of the list of bool isVisited flags for node 1 + while(tmp->value != NULL || tmp2->value != NULL) //go through untill we reach the end of the lists + { + if(tmp->value == secondNode) //if we find the link to the other node + { + if(*(tmp2->value) == true) //if the link has already been visited + { + //std::cout << "visited already" << std::endl; + return false; //return false to indicate that the link has been visited before this attempt + } + else //otherwise, visit it + { + *tmp2->value = true; + } + break; + } + tmp = tmp->next; //go check next link + tmp2 = tmp2->next; + } - tmp = secondNode->links.GetHeadElement(); //now, if the link was unvisited, we need to go set the other node's list such that - //it also knows this link is being visited - tmp2 = secondNode->taken.GetHeadElement(); - while(tmp->value != NULL || tmp2->value != NULL) //go through the list - { - if(tmp->value == firstNode) //if we find the link - { - if(*(tmp2->value) == true) //and it has already been visited, then signal an error; this shouldnt ever happen - { - cout << "Error in parsing structure! Should never reach this condition! \n" << - "Record of visited links out of synch between two adjacent nodes.\n"; - return false; - } - else - { - *tmp2->value = true; //set the appropriate value to true to indicate this link has been visited - } - break; - } - tmp = tmp->next; - tmp2 = tmp2->next; - } - //cout << "not visited" << endl; - return true; //return true to indicate that this is the first time the link has been visited + tmp = secondNode->links.GetHeadElement(); //now, if the link was unvisited, we need to go set the other node's list such that + //it also knows this link is being visited + tmp2 = secondNode->taken.GetHeadElement(); + while(tmp->value != NULL || tmp2->value != NULL) //go through the list + { + if(tmp->value == firstNode) //if we find the link + { + if(*(tmp2->value) == true) //and it has already been visited, then signal an error; this shouldnt ever happen + { + std::cout << "Error in parsing structure! Should never reach this condition! \n" << + "Record of visited links out of synch between two adjacent nodes.\n"; + return false; + } + else + { + *tmp2->value = true; //set the appropriate value to true to indicate this link has been visited + } + break; + } + tmp = tmp->next; + tmp2 = tmp2->next; + } + //std::cout << "not visited" << std::endl; + return true; //return true to indicate that this is the first time the link has been visited } -List * SystemProcessor::getSystemData(void) //Gets the list of POEMSChains that comprise the system. Might eventually only - //return chains linked to the reference plane, but currently returns every chain - //in the system. +List * SystemProcessor::getSystemData(void) //Gets the list of POEMSChains that comprise the system. Might eventually only + //return chains linked to the reference plane, but currently returns every chain + //in the system. { - return &headsOfSystems; + return &headsOfSystems; } int SystemProcessor::getNumberOfHeadChains(void) //This function isnt implemented yet, and might be taken out entirely; this was a holdover - //from when I intended to return an array of chain pointers, rather than a list of chains - //It will probably be deleted once I finish figuring out exactly what needs to be returned + //from when I intended to return an array of chain pointers, rather than a list of chains + //It will probably be deleted once I finish figuring out exactly what needs to be returned { - return 0; + return 0; +} } #endif diff --git a/lib/poems/body.cpp b/lib/poems/body.cpp index 487d5e1ab7..6825941b93 100644 --- a/lib/poems/body.cpp +++ b/lib/poems/body.cpp @@ -26,9 +26,8 @@ #include "rigidbody.h" #include "vect3.h" -class Joint; - using namespace std; +using namespace POEMS; Body::Body() { @@ -132,7 +131,7 @@ void Body::AddPoint(Point* point){ // global body functions // -Body* NewBody(int type){ +Body* POEMS::NewBody(int type){ switch( BodyType(type) ) { case INERTIALFRAME : // The inertial reference frame diff --git a/lib/poems/body.h b/lib/poems/body.h index 06a9c72417..e2394b40aa 100644 --- a/lib/poems/body.h +++ b/lib/poems/body.h @@ -25,6 +25,7 @@ #include "mat3x3.h" #include "vect3.h" +namespace POEMS { // emumerated type enum BodyType { INERTIALFRAME = 0, @@ -75,5 +76,5 @@ public: // global body functions Body* NewBody(int type); - +} #endif diff --git a/lib/poems/body23joint.cpp b/lib/poems/body23joint.cpp index 7aa761fe2a..e3ef32b2a9 100644 --- a/lib/poems/body23joint.cpp +++ b/lib/poems/body23joint.cpp @@ -27,6 +27,9 @@ #include "vect3.h" #include "virtualmatrix.h" +using namespace std; +using namespace POEMS; + Body23Joint::Body23Joint(){ DimQandU(4,2); } diff --git a/lib/poems/body23joint.h b/lib/poems/body23joint.h index c47cdfb9de..43a727c815 100644 --- a/lib/poems/body23joint.h +++ b/lib/poems/body23joint.h @@ -22,6 +22,7 @@ #include "joint.h" #include "matrix.h" +namespace POEMS { class Body23Joint : public Joint { Matrix const_sP; public: @@ -38,5 +39,5 @@ public: void ForwardKinematics(); void BackwardKinematics(); }; - +} #endif diff --git a/lib/poems/colmatmap.cpp b/lib/poems/colmatmap.cpp index 1954e7ff15..34a95feb03 100644 --- a/lib/poems/colmatmap.cpp +++ b/lib/poems/colmatmap.cpp @@ -21,6 +21,8 @@ #include using namespace std; +using namespace POEMS; + ColMatMap::ColMatMap(){ numrows = 0; diff --git a/lib/poems/colmatmap.h b/lib/poems/colmatmap.h index 6d84870046..5a12cf487f 100644 --- a/lib/poems/colmatmap.h +++ b/lib/poems/colmatmap.h @@ -24,6 +24,7 @@ #include "virtualcolmatrix.h" #include "virtualmatrix.h" +namespace POEMS { class ColMatrix; class ColMatMap : public VirtualColMatrix { @@ -64,5 +65,5 @@ public: friend void FastCKRK5(ColMatMap& X, ColMatrix& Xi, ColMatrix* f, double* c, double dt); friend void FastFRK5(ColMatMap& X, ColMatrix& Xi, ColMatrix* f, double* c, double dt); }; - +} #endif diff --git a/lib/poems/colmatrix.cpp b/lib/poems/colmatrix.cpp index e7ae98a368..0cc666645a 100644 --- a/lib/poems/colmatrix.cpp +++ b/lib/poems/colmatrix.cpp @@ -21,6 +21,8 @@ #include using namespace std; +using namespace POEMS; + ColMatrix::ColMatrix(){ numrows = 0; diff --git a/lib/poems/colmatrix.h b/lib/poems/colmatrix.h index 70f13356e2..bcfa86843a 100644 --- a/lib/poems/colmatrix.h +++ b/lib/poems/colmatrix.h @@ -23,12 +23,14 @@ #include "virtualcolmatrix.h" #include "virtualmatrix.h" +namespace POEMS { class Matrix; class Vect6; class Mat3x3; class Vect3; class ColMatrix : public VirtualColMatrix { +protected: double* elements; public: ColMatrix(); @@ -58,28 +60,28 @@ public: ColMatrix& operator=(const VirtualMatrix& A); // overloaded = ColMatrix& operator*=(double b); - void Abs(); - void BasicMax(double& value, int& index); - void BasicMin(double& value, int& index); + void Abs(); + void BasicMax(double& value, int& index); + void BasicMin(double& value, int& index); // fast matrix operations - friend void FastQuaternions(ColMatrix& q, Mat3x3& C); - friend void FastInvQuaternions(Mat3x3& C, ColMatrix& q); - friend void FastQuaternionDerivatives(ColMatrix& q, ColMatrix& omega, ColMatrix& qdot); - friend void FastTMult(Matrix& A, Vect6& B, ColMatrix& C); - friend void FastMult(Matrix& A, ColMatrix& B, Vect6& C); - friend void FastAssign(ColMatrix& A, ColMatrix& C); + friend void FastQuaternions(ColMatrix& q, Mat3x3& C); + friend void FastInvQuaternions(Mat3x3& C, ColMatrix& q); + friend void FastQuaternionDerivatives(ColMatrix& q, ColMatrix& omega, ColMatrix& qdot); + friend void FastTMult(Matrix& A, Vect6& B, ColMatrix& C); + friend void FastMult(Matrix& A, ColMatrix& B, Vect6& C); + friend void FastAssign(ColMatrix& A, ColMatrix& C); - friend void FastMult(Mat3x3& A, ColMatrix& B, Vect3& C); - friend void FastMult(Mat3x3& A, Vect3& B, ColMatrix& C); - friend void FastAssign(ColMatrix&A, Vect3& C); - - friend void EP_Derivatives(ColMatrix& q, ColMatrix& u, ColMatrix& qdot); - friend void EP_Transformation(ColMatrix& q, Mat3x3& C); - friend void EP_FromTransformation(ColMatrix& q, Mat3x3& C); - friend void EP_Normalize(ColMatrix& q); - friend void EPdotdot_udot(ColMatrix& Audot, ColMatrix& Aqdot, ColMatrix& Aq,ColMatrix& Aqddot); - friend void qdot_to_u(ColMatrix& q, ColMatrix& u, ColMatrix& qdot); -}; + friend void FastMult(Mat3x3& A, ColMatrix& B, Vect3& C); + friend void FastMult(Mat3x3& A, Vect3& B, ColMatrix& C); + friend void FastAssign(ColMatrix&A, Vect3& C); + friend void EP_Derivatives(ColMatrix& q, ColMatrix& u, ColMatrix& qdot); + friend void EP_Transformation(ColMatrix& q, Mat3x3& C); + friend void EP_FromTransformation(ColMatrix& q, Mat3x3& C); + friend void EP_Normalize(ColMatrix& q); + friend void EPdotdot_udot(ColMatrix& Audot, ColMatrix& Aqdot, ColMatrix& Aq,ColMatrix& Aqddot); + friend void qdot_to_u(ColMatrix& q, ColMatrix& u, ColMatrix& qdot); +}; +} #endif diff --git a/lib/poems/defines.h b/lib/poems/defines.h index 455bc298d5..877bc0fa0b 100644 --- a/lib/poems/defines.h +++ b/lib/poems/defines.h @@ -15,13 +15,14 @@ * CONTACT: anderk5@rpi.edu * *_________________________________________________________________________*/ -#ifndef _DEFINES_H_ -#define _DEFINES_H_ +#ifndef POEMS_DEFINES_H +#define POEMS_DEFINES_H +namespace POEMS { enum SolverType { ONSOLVER = 0, PARTICLESOLVER = 1 }; - +} #endif diff --git a/lib/poems/eulerparameters.cpp b/lib/poems/eulerparameters.cpp index f698c40b3a..bb8d676796 100644 --- a/lib/poems/eulerparameters.cpp +++ b/lib/poems/eulerparameters.cpp @@ -3,7 +3,7 @@ * POEMS: PARALLELIZABLE OPEN SOURCE EFFICIENT MULTIBODY SOFTWARE * * DESCRIPTION: SEE READ-ME * * FILE NAME: eulerparameters.cpp * - * AUTHORS: See Author List * + * AUTHORS: See Author List * * GRANTS: See Grants List * * COPYRIGHT: (C) 2005 by Authors as listed in Author's List * * LICENSE: Please see License Agreement * @@ -11,7 +11,7 @@ * ADMINISTRATOR: Prof. Kurt Anderson * * Computational Dynamics Lab * * Rensselaer Polytechnic Institute * - * 110 8th St. Troy NY 12180 * + * 110 8th St. Troy NY 12180 * * CONTACT: anderk5@rpi.edu * *_________________________________________________________________________*/ @@ -23,8 +23,10 @@ #include "mat3x3.h" using namespace std; +using namespace POEMS; -void EP_Derivatives(ColMatrix& q, ColMatrix& u, ColMatrix& qdot){ + +void POEMS::EP_Derivatives(ColMatrix& q, ColMatrix& u, ColMatrix& qdot){ EP_Normalize(q); int num=u.GetNumRows(); if (3 @@ -28,10 +28,12 @@ #include "mat6x6.h" #include "vect3.h" #include "virtualmatrix.h" - + +using namespace POEMS; + FreeBodyJoint::FreeBodyJoint(){ - DimQandU(7,6); + DimQandU(7,6); } FreeBodyJoint::~FreeBodyJoint(){ @@ -49,112 +51,112 @@ void FreeBodyJoint::WriteOutJointData(std::ostream& out){ } void FreeBodyJoint::ComputeLocalTransform(){ - Mat3x3 ko_C_k; - EP_Transformation(q, ko_C_k); - FastMult(pk_C_ko,ko_C_k,pk_C_k); + Mat3x3 ko_C_k; + EP_Transformation(q, ko_C_k); + FastMult(pk_C_ko,ko_C_k,pk_C_k); } Matrix FreeBodyJoint::GetForward_sP(){ Mat6x6 sP; - //sP.Identity(); - - sP.Zeros(); + //sP.Identity(); + + sP.Zeros(); Mat3x3 temp0=T(pk_C_k); for(int i=1;i<4;i++){ sP(i,i)=1.0; for(int j=1;j<4;j++){ sP(3+i,3+j)=temp0(i,j); } - } - return sP; + } + return sP; } Matrix FreeBodyJoint::GetBackward_sP(){ Mat6x6 sP; - sP.Identity(); + sP.Identity(); sP =-1.0*sP; - cout<<"Did I come here in "<r); - - //COMMENT STEP3: CALCULATE QDOT + + FastAssign(r12,body2->r); + + //COMMENT STEP3: CALCULATE QDOT qdot_to_u(q, u, qdot); - - + + Vect3 WN; WN.BasicSet(0,u.BasicGet(0)); WN.BasicSet(1,u.BasicGet(1)); WN.BasicSet(2,u.BasicGet(2)); - - Vect3 VN; + + Vect3 VN; VN.BasicSet(0,u.BasicGet(3)); VN.BasicSet(1,u.BasicGet(4)); - VN.BasicSet(2,u.BasicGet(5)); - - FastAssign(WN,body2->omega_k); - + VN.BasicSet(2,u.BasicGet(5)); + + FastAssign(WN,body2->omega_k); + Vect3 pk_w_k; - FastMult(body2->n_C_k,WN,pk_w_k); + FastMult(body2->n_C_k,WN,pk_w_k); FastAssign(pk_w_k,body2->omega); - - - - //COMMENT STEP5: CALCULATE VELOCITES - FastAssign(VN,body2->v); - FastTMult(body2->n_C_k,body2->v,body2->v_k); - - - //CALCULATE KE - + + + + //COMMENT STEP5: CALCULATE VELOCITES + FastAssign(VN,body2->v); + FastTMult(body2->n_C_k,body2->v,body2->v_k); + + + //CALCULATE KE + Matrix tempke; - tempke = T(body2->v)*(body2->v); + tempke = T(body2->v)*(body2->v); double ke = 0.0; - ke = body2->mass*tempke(1,1); + ke = body2->mass*tempke(1,1); FastMult(body2->inertia,body2->omega_k,result1); - tempke= T(body2->omega_k)*result1; + tempke= T(body2->omega_k)*result1; ke = 0.5*ke + 0.5*tempke(1,1); body2->KE=ke; - - + + //COMMENT STEP6: CALCULATE STATE EXPLICIT ANGULAR ACCELERATIONS body2->alpha_t.Zeros(); - - + + //COMMENT STEP7: CALCULATE STATE EXPLICIT ACCELERATIONS - body2->a_t.Zeros(); - + body2->a_t.Zeros(); + } void FreeBodyJoint::BackwardKinematics(){ -cout<<"Did I come here "< #include "virtualmatrix.h" +namespace POEMS { class Vect3; class Mat6x6; class ColMatrix; @@ -67,16 +68,15 @@ public: friend void FastMult(Mat3x3& A, Mat3x3& B, Mat3x3& C); friend void FastMultT(Mat3x3& A, Mat3x3& B, Mat3x3& C); friend void FastAssignT(Mat3x3& A, Mat3x3& C); - friend void FastMult(Mat3x3& A, Vect3& B, ColMatrix& C); - + friend void FastMult(Mat3x3& A, Vect3& B, ColMatrix& C); + friend void OnPopulateSC(Vect3& gamma, Mat3x3& C, Mat6x6& SC); friend void OnPopulateSI(Mat3x3& inertia, double mass, Mat6x6& sI); friend void FastMult(Mat3x3& A, ColMatrix& B, Vect3& C); - + friend void EP_Transformation(ColMatrix& q, Mat3x3& C); friend void EP_FromTransformation(ColMatrix& q, Mat3x3& C); - }; - +} #endif diff --git a/lib/poems/mat4x4.cpp b/lib/poems/mat4x4.cpp index a6a587bc03..9a0e7b8d56 100644 --- a/lib/poems/mat4x4.cpp +++ b/lib/poems/mat4x4.cpp @@ -21,6 +21,8 @@ #include using namespace std; +using namespace POEMS; + Mat4x4::Mat4x4(){ numrows = numcols = 4; diff --git a/lib/poems/mat4x4.h b/lib/poems/mat4x4.h index a6ae232473..3f6d97ba15 100644 --- a/lib/poems/mat4x4.h +++ b/lib/poems/mat4x4.h @@ -3,7 +3,7 @@ * POEMS: PARALLELIZABLE OPEN SOURCE EFFICIENT MULTIBODY SOFTWARE * * DESCRIPTION: SEE READ-ME * * FILE NAME: mat4x4.h * - * AUTHORS: See Author List * + * AUTHORS: See Author List * * GRANTS: See Grants List * * COPYRIGHT: (C) 2005 by Authors as listed in Author's List * * LICENSE: Please see License Agreement * @@ -11,7 +11,7 @@ * ADMINISTRATOR: Prof. Kurt Anderson * * Computational Dynamics Lab * * Rensselaer Polytechnic Institute * - * 110 8th St. Troy NY 12180 * + * 110 8th St. Troy NY 12180 * * CONTACT: anderk5@rpi.edu * *_________________________________________________________________________*/ @@ -21,17 +21,18 @@ #include #include "virtualmatrix.h" +namespace POEMS { class Vect4; class Matrix; class Mat4x4 : public VirtualMatrix { double elements[4][4]; -public: +public: Mat4x4(); ~Mat4x4(); Mat4x4(const Mat4x4& A); // copy constructor Mat4x4(const VirtualMatrix& A); // copy constructor - + double& operator_2int (int i, int j); // array access double Get_2int(int i, int j) const; void Set_2int(int i, int j, double value); @@ -64,5 +65,5 @@ public: friend void FastMultT(Mat4x4& A, Mat4x4& B, Mat4x4& C); friend void FastAssignT(Mat4x4& A, Mat4x4& C); }; - +} #endif diff --git a/lib/poems/mat6x6.cpp b/lib/poems/mat6x6.cpp index fdc917e03d..e9dde2fe87 100644 --- a/lib/poems/mat6x6.cpp +++ b/lib/poems/mat6x6.cpp @@ -21,6 +21,8 @@ #include using namespace std; +using namespace POEMS; + Mat6x6::Mat6x6(){ numrows = numcols = 6; diff --git a/lib/poems/mat6x6.h b/lib/poems/mat6x6.h index 5eaa4f803b..a611bc8283 100644 --- a/lib/poems/mat6x6.h +++ b/lib/poems/mat6x6.h @@ -21,6 +21,7 @@ #include "virtualmatrix.h" +namespace POEMS { class Matrix; class Mat3x3; class Vect6; @@ -73,5 +74,5 @@ public: friend void OnPopulateSC(Vect3& gamma, Mat3x3& C, Mat6x6& SC); friend void OnPopulateSI(Mat3x3& inertia, double mass, Mat6x6& sI); }; - +} #endif diff --git a/lib/poems/matrices.h b/lib/poems/matrices.h index 7a7e2c4b58..15f0d3ad23 100644 --- a/lib/poems/matrices.h +++ b/lib/poems/matrices.h @@ -3,7 +3,7 @@ * POEMS: PARALLELIZABLE OPEN SOURCE EFFICIENT MULTIBODY SOFTWARE * * DESCRIPTION: SEE READ-ME * * FILE NAME: matrices.h * - * AUTHORS: See Author List * + * AUTHORS: See Author List * * GRANTS: See Grants List * * COPYRIGHT: (C) 2005 by Authors as listed in Author's List * * LICENSE: Please see License Agreement * @@ -11,7 +11,7 @@ * ADMINISTRATOR: Prof. Kurt Anderson * * Computational Dynamics Lab * * Rensselaer Polytechnic Institute * - * 110 8th St. Troy NY 12180 * + * 110 8th St. Troy NY 12180 * * CONTACT: anderk5@rpi.edu * *_________________________________________________________________________*/ @@ -20,23 +20,14 @@ #define MATRICES_H #include "matrix.h" - #include "colmatrix.h" - #include "rowmatrix.h" - #include "mat3x3.h" - #include "vect3.h" - #include "mat4x4.h" - #include "vect4.h" - #include "mat6x6.h" - #include "vect6.h" - #include "colmatmap.h" #endif diff --git a/lib/poems/matrix.cpp b/lib/poems/matrix.cpp index f05d6f815c..f7b0c631f2 100644 --- a/lib/poems/matrix.cpp +++ b/lib/poems/matrix.cpp @@ -21,6 +21,8 @@ #include using namespace std; +using namespace POEMS; + Matrix::Matrix(){ numrows = numcols = 0; diff --git a/lib/poems/matrix.h b/lib/poems/matrix.h index 8bd8110760..c2ed92873c 100644 --- a/lib/poems/matrix.h +++ b/lib/poems/matrix.h @@ -3,7 +3,7 @@ * POEMS: PARALLELIZABLE OPEN SOURCE EFFICIENT MULTIBODY SOFTWARE * * DESCRIPTION: SEE READ-ME * * FILE NAME: matrix.h * - * AUTHORS: See Author List * + * AUTHORS: See Author List * * GRANTS: See Grants List * * COPYRIGHT: (C) 2005 by Authors as listed in Author's List * * LICENSE: Please see License Agreement * @@ -11,7 +11,7 @@ * ADMINISTRATOR: Prof. Kurt Anderson * * Computational Dynamics Lab * * Rensselaer Polytechnic Institute * - * 110 8th St. Troy NY 12180 * + * 110 8th St. Troy NY 12180 * * CONTACT: anderk5@rpi.edu * *_________________________________________________________________________*/ @@ -22,6 +22,7 @@ #include "virtualmatrix.h" +namespace POEMS { class Mat3x3; class Mat4x4; class Mat6x6; @@ -73,7 +74,6 @@ public: friend void FastMult(Mat6x6& A, Matrix& B, Matrix& C); friend void FastMult(Matrix& A, ColMatrix& B, Vect6& C); friend void FastMultT(Matrix& A, Matrix& B, Mat6x6& C); - }; - +} #endif diff --git a/lib/poems/matrixfun.cpp b/lib/poems/matrixfun.cpp index 99fbae4ca1..037e986a99 100644 --- a/lib/poems/matrixfun.cpp +++ b/lib/poems/matrixfun.cpp @@ -27,12 +27,14 @@ #include "virtualrowmatrix.h" using namespace std; +using namespace POEMS; + // // Create a new matrix // -VirtualMatrix* NewMatrix(int type){ +VirtualMatrix* POEMS::NewMatrix(int type){ switch( MatrixType(type) ) { case MATRIX : return new Matrix; @@ -50,7 +52,7 @@ VirtualMatrix* NewMatrix(int type){ // Transpose // -Matrix T(const VirtualMatrix& A){ +Matrix POEMS::T(const VirtualMatrix& A){ int numrows = A.GetNumRows(); int numcols = A.GetNumCols(); Matrix C(numcols,numrows); @@ -60,8 +62,8 @@ Matrix T(const VirtualMatrix& A){ return C; } -Mat3x3 T(const Mat3x3& A){ - Mat3x3 C; +Mat3x3 POEMS::T(const Mat3x3& A){ + Mat3x3 C; C.elements[0][0] = A.elements[0][0]; C.elements[1][1] = A.elements[1][1]; C.elements[2][2] = A.elements[2][2]; @@ -76,7 +78,7 @@ Mat3x3 T(const Mat3x3& A){ return C; } -Mat6x6 T(const Mat6x6& A){ +Mat6x6 POEMS::T(const Mat6x6& A){ Mat6x6 C; int i,j; for(i=0;i<6;i++) @@ -86,7 +88,7 @@ Mat6x6 T(const Mat6x6& A){ return C; } -Matrix T(const Vect3& A){ +Matrix POEMS::T(const Vect3& A){ Matrix C(1,3); C.BasicSet(0,0,A.elements[0]); C.BasicSet(0,1,A.elements[1]); @@ -95,7 +97,7 @@ Matrix T(const Vect3& A){ return C; } -Matrix T(const Vect6& A){ +Matrix POEMS::T(const Vect6& A){ Matrix C(1,6); C.BasicSet(0,0,A.elements[0]); C.BasicSet(0,1,A.elements[1]); @@ -107,7 +109,7 @@ Matrix T(const Vect6& A){ return C; } -RowMatrix T(const VirtualColMatrix &A){ +RowMatrix POEMS::T(const VirtualColMatrix &A){ int numele = A.GetNumRows(); RowMatrix C(numele); for(int i=0;i @@ -29,9 +29,11 @@ #include "vect3.h" #include "virtualmatrix.h" - +using namespace POEMS; +using namespace std; + -MixedJoint::MixedJoint(){ +MixedJoint::MixedJoint(){ } MixedJoint::~MixedJoint(){ @@ -54,23 +56,23 @@ void MixedJoint::SetsP(Matrix& sPr, Vect6& temp_dofs, int i, int j){ numrots = i; numtrans = j; if (numrots < 2) - DimQandU(numrots+numtrans,numrots+numtrans); - else - DimQandU((4+numtrans),(numrots+numtrans)); + DimQandU(numrots+numtrans,numrots+numtrans); + else + DimQandU((4+numtrans),(numrots+numtrans)); cout<<"Check "<<4+numtrans<<" "< 1) EP_Normalize(q); // COMMENT STEP1: CALCULATE ORIENTATIONS - ComputeForwardTransforms(); - - + ComputeForwardTransforms(); + + //COMMENT STEP2: CALCULATE POSITION VECTORS - Vect3 result1, result2, result3, result4; + Vect3 result1, result2, result3, result4; result1.Zeros(); for (int k=0; k<3; k++){ if( dofs(3+k) != 0.0 ){ @@ -116,32 +118,32 @@ void MixedJoint::ForwardKinematics(){ result1.BasicSet(k,q.BasicGet(4 + k)); else result1.BasicSet(k,q.BasicGet(numrots + k)); - } + } } - - - - FastAssign(result1,r12); // r12 in parents basis i.e. Newtonian - FastNegMult(k_C_pk,r12,r21); // r21 in body basis - - FastAssign(r12,body2->r); // This is right - - //COMMENT STEP3: CALCULATE QDOT + + + + FastAssign(result1,r12); // r12 in parents basis i.e. Newtonian + FastNegMult(k_C_pk,r12,r21); // r21 in body basis + + FastAssign(r12,body2->r); // This is right + + //COMMENT STEP3: CALCULATE QDOT int pp = 0; if (numrots > 1){ ColMatrix temp_u(3+numtrans); qdot_to_u(q,temp_u,qdot); for (int k=1;k<=6;k++){ if(dofs(k) != 0.0){ - u.BasicSet(pp,temp_u.BasicGet(k-1)); + u.BasicSet(pp,temp_u.BasicGet(k-1)); pp = pp+1; - } + } } } else u = qdot; - - + + Vect3 WN; WN.Zeros(); int p = 0; for (int k=0;k<3;k++){ @@ -151,51 +153,51 @@ void MixedJoint::ForwardKinematics(){ } }// WN is in body basis - - Vect3 VN; VN.Zeros(); + + Vect3 VN; VN.Zeros(); for (int k=0;k<3;k++){ if( dofs(3+k+1) != 0.0 ) { VN.BasicSet(k,u.BasicGet(p)); p=p+1; } }// VN is the vector of translational velocities in Newtonian basis - - FastAssign(WN,body2->omega_k); - // cout<<"Angular Velocity "<omega_k); + + // cout<<"Angular Velocity "<n_C_k,WN,pk_w_k); + FastMult(body2->n_C_k,WN,pk_w_k); FastAssign(pk_w_k,body2->omega); - - - - //COMMENT STEP5: CALCULATE VELOCITES - FastAssign(VN,body2->v); - FastTMult(body2->n_C_k,body2->v,body2->v_k); - - - //CALCULATE KE - + + + + //COMMENT STEP5: CALCULATE VELOCITES + FastAssign(VN,body2->v); + FastTMult(body2->n_C_k,body2->v,body2->v_k); + + + //CALCULATE KE + Matrix tempke; - tempke = T(body2->v)*(body2->v); + tempke = T(body2->v)*(body2->v); double ke = 0.0; - ke = body2->mass*tempke(1,1); + ke = body2->mass*tempke(1,1); FastMult(body2->inertia,body2->omega_k,result1); - tempke= T(body2->omega_k)*result1; + tempke= T(body2->omega_k)*result1; ke = 0.5*ke + 0.5*tempke(1,1); body2->KE=ke; - - + + //COMMENT STEP6: CALCULATE STATE EXPLICIT ANGULAR ACCELERATIONS body2->alpha_t.Zeros(); - - + + //COMMENT STEP7: CALCULATE STATE EXPLICIT ACCELERATIONS - body2->a_t.Zeros(); - + body2->a_t.Zeros(); + } void MixedJoint::BackwardKinematics(){ cout<<"Did I come here "< children; + Body* system_body; + Joint* system_joint; + OnBody* parent; + List children; - Direction joint_dir; - void (Joint::*kinfun)(); // kinematics function - void (Joint::*updatesP)(Matrix&); // sP update function - Vect3* gamma; // pointer to gamma vector - Mat3x3* pk_C_k; // pointer to transformation + Direction joint_dir; + void (Joint::*kinfun)(); // kinematics function + void (Joint::*updatesP)(Matrix&); // sP update function + Vect3* gamma; // pointer to gamma vector + Mat3x3* pk_C_k; // pointer to transformation - - Mat6x6 sI; // spatial inertias - Mat6x6 sIhat; // recursive spatial inertias - Mat6x6 sSC; // spatial shift - Mat6x6 sT; // spatial triangularization - Vect6 sF; // spatial forces - Vect6 sFhat; // recursive spatial forces - Vect6 sAhat; // recursive spatial acceleration + Mat6x6 sI; // spatial inertias + Mat6x6 sIhat; // recursive spatial inertias + Mat6x6 sSC; // spatial shift + Mat6x6 sT; // spatial triangularization - Matrix sP; // spatial partial velocities - Matrix sM; // triangularized mass matrix diagonal elements - Matrix sMinv; // inverse of sM - Matrix sPsMinv; - Matrix sIhatsP; + Vect6 sF; // spatial forces + Vect6 sFhat; // recursive spatial forces + Vect6 sAhat; // recursive spatial acceleration - // states and state derivatives - ColMatrix* q; - ColMatrix* u; - ColMatrix* qdot; - ColMatrix* udot; - ColMatrix* qdotdot; - - ColMatrix* r; - ColMatrix* acc; - ColMatrix* ang; + Matrix sP; // spatial partial velocities + Matrix sM; // triangularized mass matrix diagonal elements + Matrix sMinv; // inverse of sM + Matrix sPsMinv; + Matrix sIhatsP; + + // states and state derivatives + ColMatrix* q; + ColMatrix* u; + ColMatrix* qdot; + ColMatrix* udot; + ColMatrix* qdotdot; + + ColMatrix* r; + ColMatrix* acc; + ColMatrix* ang; // friend classes friend class OnSolver; - -public: - OnBody(); - ~OnBody(); - int RecursiveSetup(InertialFrame* basebody); - int RecursiveSetup(int ID, OnBody* parentbody, Joint* sys_joint); - void RecursiveKinematics(); - void RecursiveTriangularization(); - void RecursiveForwardSubstitution(); - Mat3x3 GetN_C_K(); - Vect3 LocalCart(); - int GetBodyID(); - void CalculateAcceleration(); - void Setup(); - void SetupInertialFrame(); - void LocalKinematics(); - void LocalTriangularization(Vect3& Torque, Vect3& Force); - void LocalForwardSubstitution(); +public: + OnBody(); + ~OnBody(); + int RecursiveSetup(InertialFrame* basebody); + int RecursiveSetup(int ID, OnBody* parentbody, Joint* sys_joint); + void RecursiveKinematics(); + void RecursiveTriangularization(); + void RecursiveForwardSubstitution(); + Mat3x3 GetN_C_K(); + Vect3 LocalCart(); + int GetBodyID(); + void CalculateAcceleration(); + void Setup(); + void SetupInertialFrame(); + void LocalKinematics(); + void LocalTriangularization(Vect3& Torque, Vect3& Force); + void LocalForwardSubstitution(); }; - +} #endif diff --git a/lib/poems/onfunctions.cpp b/lib/poems/onfunctions.cpp index 1d91dbf378..cfc0c60936 100644 --- a/lib/poems/onfunctions.cpp +++ b/lib/poems/onfunctions.cpp @@ -3,7 +3,7 @@ * POEMS: PARALLELIZABLE OPEN SOURCE EFFICIENT MULTIBODY SOFTWARE * * DESCRIPTION: SEE READ-ME * * FILE NAME: onfunction.cpp * - * AUTHORS: See Author List * + * AUTHORS: See Author List * * GRANTS: See Grants List * * COPYRIGHT: (C) 2005 by Authors as listed in Author's List * * LICENSE: Please see License Agreement * @@ -11,10 +11,10 @@ * ADMINISTRATOR: Prof. Kurt Anderson * * Computational Dynamics Lab * * Rensselaer Polytechnic Institute * - * 110 8th St. Troy NY 12180 * + * 110 8th St. Troy NY 12180 * * CONTACT: anderk5@rpi.edu * *_________________________________________________________________________*/ - + #include "onfunctions.h" @@ -25,9 +25,11 @@ #include "virtualmatrix.h" using namespace std; +using namespace POEMS; + // friend of Vect3 & Vect6 -void OnPopulateSVect(Vect3& angular, Vect3& linear, Vect6& sV){ +void POEMS::OnPopulateSVect(Vect3& angular, Vect3& linear, Vect6& sV){ sV.elements[0] = angular.elements[0]; sV.elements[1] = angular.elements[1]; sV.elements[2] = angular.elements[2]; @@ -37,38 +39,38 @@ void OnPopulateSVect(Vect3& angular, Vect3& linear, Vect6& sV){ } // friend of Vect3, Mat3x3, & Mat6x6 -void OnPopulateSC(Vect3& gamma, Mat3x3& C, Mat6x6& SC){ +void POEMS::OnPopulateSC(Vect3& gamma, Mat3x3& C, Mat6x6& SC){ // the block diagonals - + // the gamma cross with transform Mat3x3 temp; Mat3x3 temp2; SC.Zeros(); - temp.Zeros(); + temp.Zeros(); temp2.Zeros(); - //FastTMult(C,gamma,temp); + //FastTMult(C,gamma,temp); temp(1,2)= -gamma(3); temp(1,3)= gamma(2); temp(2,1)= gamma(3); - temp(2,3)= -gamma(1); temp(3,1)= -gamma(2); temp(3,2)= gamma(1); + temp(2,3)= -gamma(1); temp(3,1)= -gamma(2); temp(3,2)= gamma(1); FastMult(temp,C,temp2); - + SC(1,4)=temp2(1,1); SC(2,4)=temp2(2,1); SC(3,4)=temp2(3,1); SC(1,5)=temp2(1,2); SC(2,5)=temp2(2,2); SC(3,5)=temp2(3,2); SC(1,6)=temp2(1,3); SC(2,6)=temp2(2,3); SC(3,6)=temp2(3,3); - + SC(1,1)=C(1,1); SC(2,1)=C(2,1); SC(3,1)=C(3,1); SC(1,2)=C(1,2); SC(2,2)=C(2,2); SC(3,2)=C(3,2); SC(1,3)=C(1,3); SC(2,3)=C(2,3); SC(3,3)=C(3,3); SC(4,4)=C(1,1); SC(5,4)=C(2,1); SC(6,4)=C(3,1); SC(4,5)=C(1,2); SC(5,5)=C(2,2); SC(6,5)=C(3,2); - SC(4,6)=C(1,3); SC(5,6)=C(2,3); SC(6,6)=C(3,3); - + SC(4,6)=C(1,3); SC(5,6)=C(2,3); SC(6,6)=C(3,3); + } // friend of Mat3x3 & Mat6x6 -void OnPopulateSI(Mat3x3& inertia, double mass, Mat6x6& sI){ - - sI(4,4)=mass; sI(5,5)=mass; sI(6,6)=mass; - sI(1,1)=inertia(1,1); sI(1,2)=inertia(1,2); sI(1,3)=inertia(1,3); - sI(2,1)=inertia(2,1); sI(2,2)=inertia(2,2); sI(2,3)=inertia(2,3); - sI(3,1)=inertia(3,1); sI(3,2)=inertia(3,2); sI(3,3)=inertia(3,3); +void POEMS::OnPopulateSI(Mat3x3& inertia, double mass, Mat6x6& sI){ + + sI(4,4)=mass; sI(5,5)=mass; sI(6,6)=mass; + sI(1,1)=inertia(1,1); sI(1,2)=inertia(1,2); sI(1,3)=inertia(1,3); + sI(2,1)=inertia(2,1); sI(2,2)=inertia(2,2); sI(2,3)=inertia(2,3); + sI(3,1)=inertia(3,1); sI(3,2)=inertia(3,2); sI(3,3)=inertia(3,3); } diff --git a/lib/poems/onfunctions.h b/lib/poems/onfunctions.h index 42d0f4ac1c..bb07425b85 100644 --- a/lib/poems/onfunctions.h +++ b/lib/poems/onfunctions.h @@ -18,6 +18,7 @@ #ifndef ONFUNCTIONS_H #define ONFUNCTIONS_H +namespace POEMS { class Mat3x3; class Mat6x6; class Vect3; @@ -30,5 +31,5 @@ void OnPopulateSI(Mat3x3& inertia, double mass, Mat6x6& sI); void Create_Map(int MM); int ICELL(int IX,int IY,int IZ, int MM); - +} #endif diff --git a/lib/poems/onsolver.cpp b/lib/poems/onsolver.cpp index dd94c9c7ad..609ef32613 100644 --- a/lib/poems/onsolver.cpp +++ b/lib/poems/onsolver.cpp @@ -33,6 +33,8 @@ #include "virtualmatrix.h" using namespace std; +using namespace POEMS; + OnSolver::OnSolver(){ numbodies = 0; diff --git a/lib/poems/onsolver.h b/lib/poems/onsolver.h index b4bbd5e25d..1e850b8fc1 100644 --- a/lib/poems/onsolver.h +++ b/lib/poems/onsolver.h @@ -3,7 +3,7 @@ * POEMS: PARALLELIZABLE OPEN SOURCE EFFICIENT MULTIBODY SOFTWARE * * DESCRIPTION: SEE READ-ME * * FILE NAME: onsolver.h * - * AUTHORS: See Author List * + * AUTHORS: See Author List * * GRANTS: See Grants List * * COPYRIGHT: (C) 2005 by Authors as listed in Author's List * * LICENSE: Please see License Agreement * @@ -11,7 +11,7 @@ * ADMINISTRATOR: Prof. Kurt Anderson * * Computational Dynamics Lab * * Rensselaer Polytechnic Institute * - * 110 8th St. Troy NY 12180 * + * 110 8th St. Troy NY 12180 * * CONTACT: anderk5@rpi.edu * *_________________________________________________________________________*/ @@ -22,32 +22,31 @@ #include "solver.h" #include "onbody.h" +namespace POEMS { class ColMatrix; class Matrix; - - class OnSolver : public Solver { - OnBody inertialframe; - int numbodies; - OnBody** bodyarray; - ColMatrix** q; - ColMatrix** qdot; - ColMatrix** qdotdot; - ColMatrix** u; - ColMatrix** udot; - - - - void DeleteModel(); - int CreateTopologyArray(int i, OnBody* body); - void CreateStateMatrixMaps(); - void GetType(); -public: - OnSolver(); - ~OnSolver(); - void CreateModel(); - void Solve(double time, Matrix& FF); -}; + OnBody inertialframe; + int numbodies; + OnBody** bodyarray; + ColMatrix** q; + ColMatrix** qdot; + ColMatrix** qdotdot; + ColMatrix** u; + ColMatrix** udot; + + + void DeleteModel(); + int CreateTopologyArray(int i, OnBody* body); + void CreateStateMatrixMaps(); + void GetType(); +public: + OnSolver(); + ~OnSolver(); + void CreateModel(); + void Solve(double time, Matrix& FF); +}; +} #endif diff --git a/lib/poems/particle.cpp b/lib/poems/particle.cpp index 0d953e00f6..37ec790666 100644 --- a/lib/poems/particle.cpp +++ b/lib/poems/particle.cpp @@ -18,6 +18,8 @@ #include "particle.h" +using namespace POEMS; + Particle::Particle(){ } diff --git a/lib/poems/particle.h b/lib/poems/particle.h index 0f13252f99..8a7a521451 100644 --- a/lib/poems/particle.h +++ b/lib/poems/particle.h @@ -3,7 +3,7 @@ * POEMS: PARALLELIZABLE OPEN SOURCE EFFICIENT MULTIBODY SOFTWARE * * DESCRIPTION: SEE READ-ME * * FILE NAME: particle.h * - * AUTHORS: See Author List * + * AUTHORS: See Author List * * GRANTS: See Grants List * * COPYRIGHT: (C) 2005 by Authors as listed in Author's List * * LICENSE: Please see License Agreement * @@ -11,7 +11,7 @@ * ADMINISTRATOR: Prof. Kurt Anderson * * Computational Dynamics Lab * * Rensselaer Polytechnic Institute * - * 110 8th St. Troy NY 12180 * + * 110 8th St. Troy NY 12180 * * CONTACT: anderk5@rpi.edu * *_________________________________________________________________________*/ @@ -23,14 +23,14 @@ #include "body.h" - +namespace POEMS { class Particle : public Body { -public: +public: Particle(); ~Particle(); BodyType GetType(); bool ReadInBodyData(std::istream& in); void WriteOutBodyData(std::ostream& out); }; - +} #endif diff --git a/lib/poems/poemslist.h b/lib/poems/poemslist.h index 9882af013a..bd0c1456b4 100644 --- a/lib/poems/poemslist.h +++ b/lib/poems/poemslist.h @@ -3,7 +3,7 @@ * POEMS: PARALLELIZABLE OPEN SOURCE EFFICIENT MULTIBODY SOFTWARE * * DESCRIPTION: SEE READ-ME * * FILE NAME: poemslist.h * - * AUTHORS: See Author List * + * AUTHORS: See Author List * * GRANTS: See Grants List * * COPYRIGHT: (C) 2005 by Authors as listed in Author's List * * LICENSE: Please see License Agreement * @@ -11,7 +11,7 @@ * ADMINISTRATOR: Prof. Kurt Anderson * * Computational Dynamics Lab * * Rensselaer Polytechnic Institute * - * 110 8th St. Troy NY 12180 * + * 110 8th St. Troy NY 12180 * * CONTACT: anderk5@rpi.edu * *_________________________________________________________________________*/ @@ -21,8 +21,7 @@ #include #include -using namespace std; - +namespace POEMS { template class ListElement{ public: ListElement* prev; @@ -51,7 +50,7 @@ public: S* operator()(int id); void Append(List * listToAppend); void DeleteValues(); - void RemoveElementAndDeleteValue(ListElement* ele); + void RemoveElementAndDeleteValue(ListElement* ele); void PrintList(); }; @@ -90,9 +89,9 @@ template List::~List(){ template void List::Append(List * listToAppend) { - tail->next = listToAppend->head; - listToAppend->head->prev = tail; - tail = listToAppend->tail; + tail->next = listToAppend->head; + listToAppend->head->prev = tail; + tail = listToAppend->tail; } template int List::GetNumElements(){ @@ -104,17 +103,17 @@ template ListElement* List::GetHeadElement(){ } template ListElement* List::GetTailElement(){ - return tail; + return tail; } template void List::Remove(ListElement* ele){ if(!ele){ - cerr << "ERROR: ListElement to be removed not defined" << endl; + std::cerr << "ERROR: ListElement to be removed not defined" << std::endl; exit(0); } if(!numelements){ - cerr << "ERROR: List is empty" << endl; + std::cerr << "ERROR: List is empty" << std::endl; exit(0); } @@ -135,7 +134,7 @@ template void List::Remove(ListElement* ele){ template ListElement* List::Append(S* v){ if(!v){ - cerr << "ERROR: cannot add null Body to list" << endl; + std::cerr << "ERROR: cannot add null Body to list" << std::endl; exit(0); } @@ -145,22 +144,22 @@ template ListElement* List::Append(S* v){ if(numelements==1) head = tail = ele; else{ - /* + /* tail->next = ele; ele->prev = tail; - tail = ele;*/ - - ele->prev = tail; - tail = ele; - ele->prev->next = ele; - - } + tail = ele;*/ + + ele->prev = tail; + tail = ele; + ele->prev->next = ele; + + } return ele; } template ListElement* List::Prepend(S* v){ if(!v){ - cerr << "ERROR: cannot add null Body to list" << endl; + std::cerr << "ERROR: cannot add null Body to list" << std::endl; exit(0); } @@ -170,9 +169,9 @@ template ListElement* List::Prepend(S* v){ if(numelements==1) head = tail = ele; else{ - ele->next = head; - head = ele; - ele->next->prev = ele; + ele->next = head; + head = ele; + ele->next->prev = ele; } return ele; } @@ -190,15 +189,15 @@ template S** List::CreateArray(){ template S* List::operator()(int id){ if(id >= numelements){ - cerr << "ERROR: subscript out of bounds" << endl; + std::cerr << "ERROR: subscript out of bounds" << std::endl; exit(0); } - + ListElement* ele = head; for(int i=0;inext; } - + return ele->value; } @@ -214,16 +213,15 @@ template void List::RemoveElementAndDeleteValue(ListElement* ele) } template void List::PrintList(){ - cout<<"Printing List "<* ele = head; - cout<<*(ele->value)<<" "; - ele = ele->next; - for(int k =2; kvalue)<<" "; - ele = ele->next; - } - cout<<*(ele->value)<* ele = head; + std::cout << *(ele->value) << " "; + ele = ele->next; + for(int k =2; kvalue) << " "; + ele = ele->next; + } + std::cout << *(ele->value) << std::endl; +} } - - #endif diff --git a/lib/poems/poemsnodelib.h b/lib/poems/poemsnodelib.h index 06cf4530d2..d323b701b0 100644 --- a/lib/poems/poemsnodelib.h +++ b/lib/poems/poemsnodelib.h @@ -20,9 +20,7 @@ #include -using namespace std; - - +namespace POEMS { TreeNode *GetTreeNode(int item,TreeNode *lptr = NULL,TreeNode *rptr =NULL); void FreeTreeNode(TreeNode *p); @@ -81,7 +79,7 @@ TreeNode *GetTreeNode(int item,TreeNode *lptr,TreeNode *rptr) // if insufficient memory, terminatewith an error message if (p == NULL) { - cerr << "Memory allocation failure!\n"; + std::cerr << "Memory allocation failure!\n"; exit(1); } @@ -140,7 +138,7 @@ void IndentBlanks(int num) // const int indentblock = 6; for(int i = 0; i < num; i++) - cout << " "; + std::cout << " "; } void PrintTree (TreeNode *t, int level) @@ -153,10 +151,11 @@ void PrintTree (TreeNode *t, int level) PrintTree(t->Right(),level + 1); // indent to current level; output node data IndentBlanks(indentUnit*level); - cout << t->GetData() << endl; + std::cout << t->GetData() << std::endl; // print left branch of tree t PrintTree(t->Left(),level + 1); } } +} #endif diff --git a/lib/poems/poemsobject.cpp b/lib/poems/poemsobject.cpp index 7c3f1ca872..dfdd95953e 100644 --- a/lib/poems/poemsobject.cpp +++ b/lib/poems/poemsobject.cpp @@ -19,6 +19,8 @@ #include "poemsobject.h" #include +using namespace POEMS; + POEMSObject::POEMSObject(){ name = 0; ChangeName((const char*)"unnamed"); diff --git a/lib/poems/poemsobject.h b/lib/poems/poemsobject.h index 63b2915638..173d9da7ab 100644 --- a/lib/poems/poemsobject.h +++ b/lib/poems/poemsobject.h @@ -19,7 +19,7 @@ #ifndef POEMSOBJECT_H #define POEMSOBJECT_H - +namespace POEMS { class POEMSObject { char* name; int ID; @@ -31,5 +31,5 @@ public: int GetID(); void SetID(int id); }; - +} #endif diff --git a/lib/poems/poemstree.h b/lib/poems/poemstree.h index 8f8e80ab66..d49a0d0a88 100644 --- a/lib/poems/poemstree.h +++ b/lib/poems/poemstree.h @@ -21,7 +21,7 @@ #include "poemstreenode.h" #include "poemsnodelib.h" - +namespace POEMS { // constants to indicate the balance factor of a node const int leftheavy = -1; const int balanced = 0; @@ -609,5 +609,5 @@ void Tree::ClearList(void) delete current; size = 0; } - +} #endif diff --git a/lib/poems/poemstreenode.cpp b/lib/poems/poemstreenode.cpp index 051e13d6e0..ca4307f69f 100644 --- a/lib/poems/poemstreenode.cpp +++ b/lib/poems/poemstreenode.cpp @@ -17,6 +17,8 @@ #include "poemstreenode.h" +using namespace POEMS; + // constructor; initialize the data and pointer fields // The pointer value NULL assigns a empty subtree TreeNode::TreeNode (const int & item, TreeNode *lptr,TreeNode *rptr, diff --git a/lib/poems/poemstreenode.h b/lib/poems/poemstreenode.h index e22bd9b97d..69f3caf958 100644 --- a/lib/poems/poemstreenode.h +++ b/lib/poems/poemstreenode.h @@ -3,7 +3,7 @@ * POEMS: PARALLELIZABLE OPEN SOURCE EFFICIENT MULTIBODY SOFTWARE * * DESCRIPTION: SEE READ-ME * * FILE NAME: poemstreenode.h * - * AUTHORS: See Author List * + * AUTHORS: See Author List * * GRANTS: See Grants List * * COPYRIGHT: (C) 2005 by Authors as listed in Author's List * * LICENSE: Please see License Agreement * @@ -11,36 +11,37 @@ * ADMINISTRATOR: Prof. Kurt Anderson * * Computational Dynamics Lab * * Rensselaer Polytechnic Institute * - * 110 8th St. Troy NY 12180 * + * 110 8th St. Troy NY 12180 * * CONTACT: anderk5@rpi.edu * *_________________________________________________________________________*/ #ifndef TREENODE_H #define TREENODE_H +namespace POEMS { // declares a tree node object for a binary tree class TreeNode{ private: // points to the left and right children of the node - TreeNode *left; - TreeNode *right; + TreeNode *left; + TreeNode *right; - int balanceFactor; - int data; - void * aux_data; -public: - // make Tree a friend because it needs access to left and right pointer fields of a node - friend class Tree; - TreeNode * Left(); - TreeNode * Right(); - int GetData(); - void * GetAuxData() {return aux_data;}; - void SetAuxData(void * AuxData) {aux_data = AuxData;}; - int GetBalanceFactor(); - TreeNode(const int &item, TreeNode *lptr, TreeNode *rptr, int balfac = 0); - //friend class DCASolver; + int balanceFactor; + int data; + void * aux_data; +public: + // make Tree a friend because it needs access to left and right pointer fields of a node + friend class Tree; + TreeNode * Left(); + TreeNode * Right(); + int GetData(); + void * GetAuxData() {return aux_data;}; + void SetAuxData(void * AuxData) {aux_data = AuxData;}; + int GetBalanceFactor(); + TreeNode(const int &item, TreeNode *lptr, TreeNode *rptr, int balfac = 0); + //friend class DCASolver; }; - +} #endif diff --git a/lib/poems/point.cpp b/lib/poems/point.cpp index d7eed94efd..f648b58d3d 100644 --- a/lib/poems/point.cpp +++ b/lib/poems/point.cpp @@ -20,6 +20,8 @@ #include "point.h" #include "vect3.h" +using namespace POEMS; + Point::Point(){ position.Zeros(); } @@ -35,7 +37,7 @@ void Point::WriteOut(std::ostream& out){ WriteOutPointData(out); } -Point* NewPoint(int type){ +Point* POEMS::NewPoint(int type){ switch( PointType(type) ) { case FIXEDPOINT : // A Fixed Point diff --git a/lib/poems/point.h b/lib/poems/point.h index 746a527cd7..c08e92db0d 100644 --- a/lib/poems/point.h +++ b/lib/poems/point.h @@ -3,7 +3,7 @@ * POEMS: PARALLELIZABLE OPEN SOURCE EFFICIENT MULTIBODY SOFTWARE * * DESCRIPTION: SEE READ-ME * * FILE NAME: point.h * - * AUTHORS: See Author List * + * AUTHORS: See Author List * * GRANTS: See Grants List * * COPYRIGHT: (C) 2005 by Authors as listed in Author's List * * LICENSE: Please see License Agreement * @@ -11,7 +11,7 @@ * ADMINISTRATOR: Prof. Kurt Anderson * * Computational Dynamics Lab * * Rensselaer Polytechnic Institute * - * 110 8th St. Troy NY 12180 * + * 110 8th St. Troy NY 12180 * * CONTACT: anderk5@rpi.edu * *_________________________________________________________________________*/ @@ -22,21 +22,21 @@ #include "poemsobject.h" #include "vect3.h" - +namespace POEMS { // emumerated type enum PointType { FIXEDPOINT = 0 }; class Point : public POEMSObject { -public: +public: Vect3 position; - Point(); - bool ReadIn(std::istream& in); + Point(); + bool ReadIn(std::istream& in); void WriteOut(std::ostream& out); - - virtual ~Point(); + + virtual ~Point(); virtual PointType GetType() = 0; virtual Vect3 GetPoint() = 0; virtual bool ReadInPointData(std::istream& in) = 0; @@ -45,5 +45,5 @@ public: // global point functions Point* NewPoint(int type); - +} #endif diff --git a/lib/poems/prismaticjoint.cpp b/lib/poems/prismaticjoint.cpp index c7d4bed568..3e649f0d22 100644 --- a/lib/poems/prismaticjoint.cpp +++ b/lib/poems/prismaticjoint.cpp @@ -25,6 +25,8 @@ #include "mat3x3.h" #include "virtualmatrix.h" +using namespace POEMS; + PrismaticJoint::PrismaticJoint(){ q.Dim(1); qdot.Dim(1); diff --git a/lib/poems/prismaticjoint.h b/lib/poems/prismaticjoint.h index c17be350cb..df3ab3195c 100644 --- a/lib/poems/prismaticjoint.h +++ b/lib/poems/prismaticjoint.h @@ -24,8 +24,7 @@ #include "vect3.h" #include "matrix.h" - - +namespace POEMS { class PrismaticJoint : public Joint { Vect3 axis_pk; // unit vector in body1 basis Vect3 axis_k; // unit vector in body2 basis @@ -45,5 +44,5 @@ public: void ForwardKinematics(); void BackwardKinematics(); }; - +} #endif diff --git a/lib/poems/revolutejoint.cpp b/lib/poems/revolutejoint.cpp index 955a2f0dea..6b11acbf0f 100644 --- a/lib/poems/revolutejoint.cpp +++ b/lib/poems/revolutejoint.cpp @@ -25,6 +25,8 @@ #include "mat3x3.h" #include "virtualmatrix.h" +using namespace POEMS; + RevoluteJoint::RevoluteJoint(){ DimQandU(1); Vect3 axis; diff --git a/lib/poems/revolutejoint.h b/lib/poems/revolutejoint.h index ac1c06d5c5..10a38114df 100644 --- a/lib/poems/revolutejoint.h +++ b/lib/poems/revolutejoint.h @@ -23,6 +23,7 @@ #include "vect3.h" #include "matrix.h" +namespace POEMS { class VirtualMatrix; class RevoluteJoint : public Joint { @@ -44,5 +45,5 @@ public: void ForwardKinematics(); void BackwardKinematics(); }; - +} #endif diff --git a/lib/poems/rigidbody.cpp b/lib/poems/rigidbody.cpp index 53acfa8bd4..a7d4f9f19f 100644 --- a/lib/poems/rigidbody.cpp +++ b/lib/poems/rigidbody.cpp @@ -20,6 +20,8 @@ #include "virtualmatrix.h" using namespace std; +using namespace POEMS; + RigidBody::RigidBody(){ } diff --git a/lib/poems/rigidbody.h b/lib/poems/rigidbody.h index 2f4430e264..d4be92ebcf 100644 --- a/lib/poems/rigidbody.h +++ b/lib/poems/rigidbody.h @@ -22,6 +22,7 @@ #include "body.h" +namespace POEMS { class RigidBody : public Body { public: RigidBody(); @@ -30,5 +31,5 @@ public: bool ReadInBodyData(std::istream& in); void WriteOutBodyData(std::ostream& out); }; - +} #endif diff --git a/lib/poems/rowmatrix.cpp b/lib/poems/rowmatrix.cpp index 9fa57e773f..eac8fbef5d 100644 --- a/lib/poems/rowmatrix.cpp +++ b/lib/poems/rowmatrix.cpp @@ -21,6 +21,8 @@ #include using namespace std; +using namespace POEMS; + RowMatrix::RowMatrix(){ numcols = 0; diff --git a/lib/poems/rowmatrix.h b/lib/poems/rowmatrix.h index 1dbb3d11e0..8e8d7b5f99 100644 --- a/lib/poems/rowmatrix.h +++ b/lib/poems/rowmatrix.h @@ -24,6 +24,7 @@ #include "virtualrowmatrix.h" #include "virtualmatrix.h" +namespace POEMS { class RowMatrix : public VirtualRowMatrix { double* elements; public: @@ -52,5 +53,5 @@ public: RowMatrix& operator=(const VirtualMatrix& A); // overloaded = RowMatrix& operator*=(double b); }; - +} #endif diff --git a/lib/poems/solver.cpp b/lib/poems/solver.cpp index 9d2245149f..04afb27945 100644 --- a/lib/poems/solver.cpp +++ b/lib/poems/solver.cpp @@ -20,6 +20,8 @@ #include "system.h" #include "onsolver.h" +using namespace POEMS; + Solver::Solver(){ } diff --git a/lib/poems/solver.h b/lib/poems/solver.h index 6a2debf497..489e6d41f1 100644 --- a/lib/poems/solver.h +++ b/lib/poems/solver.h @@ -3,7 +3,7 @@ * POEMS: PARALLELIZABLE OPEN SOURCE EFFICIENT MULTIBODY SOFTWARE * * DESCRIPTION: SEE READ-ME * * FILE NAME: solver.h * - * AUTHORS: See Author List * + * AUTHORS: See Author List * * GRANTS: See Grants List * * COPYRIGHT: (C) 2005 by Authors as listed in Author's List * * LICENSE: Please see License Agreement * @@ -11,7 +11,7 @@ * ADMINISTRATOR: Prof. Kurt Anderson * * Computational Dynamics Lab * * Rensselaer Polytechnic Institute * - * 110 8th St. Troy NY 12180 * + * 110 8th St. Troy NY 12180 * * CONTACT: anderk5@rpi.edu * *_________________________________________________________________________*/ @@ -21,6 +21,7 @@ #include "colmatmap.h" #include "defines.h" +namespace POEMS { class System; class Matrix; @@ -28,11 +29,11 @@ class Solver{ protected: System* system; - + double time; ColMatMap state; ColMatMap statedot; - ColMatMap statedoubledot; + ColMatMap statedoubledot; SolverType type; @@ -47,13 +48,13 @@ public: virtual void DeleteModel() = 0; virtual void CreateModel() = 0; - virtual void Solve(double time, Matrix& FF) = 0; - - - + virtual void Solve(double time, Matrix& FF) = 0; + + + ColMatMap* GetState(); ColMatMap* GetStateDerivative(); ColMatMap* GetStateDerivativeDerivative(); }; - +} #endif diff --git a/lib/poems/sphericaljoint.cpp b/lib/poems/sphericaljoint.cpp index cba6d00a6e..996bb5a887 100644 --- a/lib/poems/sphericaljoint.cpp +++ b/lib/poems/sphericaljoint.cpp @@ -3,7 +3,7 @@ * POEMS: PARALLELIZABLE OPEN SOURCE EFFICIENT MULTIBODY SOFTWARE * * DESCRIPTION: SEE READ-ME * * FILE NAME: sphericaljoint.cpp * - * AUTHORS: See Author List * + * AUTHORS: See Author List * * GRANTS: See Grants List * * COPYRIGHT: (C) 2005 by Authors as listed in Author's List * * LICENSE: Please see License Agreement * @@ -11,10 +11,10 @@ * ADMINISTRATOR: Prof. Kurt Anderson * * Computational Dynamics Lab * * Rensselaer Polytechnic Institute * - * 110 8th St. Troy NY 12180 * + * 110 8th St. Troy NY 12180 * * CONTACT: anderk5@rpi.edu * *_________________________________________________________________________*/ - + #include "sphericaljoint.h" @@ -30,6 +30,8 @@ #include "vect3.h" #include "virtualmatrix.h" +using namespace std; +using namespace POEMS; SphericalJoint::SphericalJoint(){ DimQandU(4,3); @@ -48,24 +50,24 @@ bool SphericalJoint::ReadInJointData(std::istream& in){ void SphericalJoint::WriteOutJointData(std::ostream& out){ } -Matrix SphericalJoint::GetForward_sP(){ +Matrix SphericalJoint::GetForward_sP(){ Mat3x3 sPa,sPl; Matrix sP(6,3); - sPa.Identity(); + sPa.Identity(); sPl.Zeros(); - Vect3 temp = -(point2->position); - + Vect3 temp = -(point2->position); + sPl(1,2) = temp(3); sPl(1,3) = -temp(2); - + sPl(2,1) = -temp(3); sPl(2,3) = temp(1); - - sPl(3,1) = temp(2); + + sPl(3,1) = temp(2); sPl(3,2) = -temp(1); - - sP=Stack(sPa,sPl); - return sP; + + sP=Stack(sPa,sPl); + return sP; } void SphericalJoint::UpdateForward_sP( Matrix& sP){ @@ -79,15 +81,15 @@ Matrix SphericalJoint::GetBackward_sP(){ cout<<" -----------"<position(1)); - sPl(2,3)=-(point2->position(1)); + sPa.Identity(); + sPl.Zeros(); + sPl(3,2)=(point2->position(1)); + sPl(2,3)=-(point2->position(1)); sP=Stack(sPa,sPl); - return sP; + return sP; } -void SphericalJoint::UpdateBackward_sP( Matrix& sP){ +void SphericalJoint::UpdateBackward_sP( Matrix& sP){ // sP is constant, do nothing. } @@ -96,106 +98,106 @@ void SphericalJoint::ComputeLocalTransform(){ // Obtain the transformation matrix from euler parameters EP_Transformation(q, ko_C_k); FastMult(pk_C_ko,ko_C_k,pk_C_k); - } + } void SphericalJoint::ForwardKinematics(){ Vect3 result1,result2,result3,result4,result5; Vect3 pk_w_k; - + //cout<<"Check in spherical "<position,result1); // parents basis - FastAdd(result1,point1->position,r12); - - // compute position vector r21 - FastNegMult(k_C_pk,r12,r21); - - - + // COMPUTE POSITION VECTOR R12 aka GAMMA + + FastNegMult(pk_C_k,point2->position,result1); // parents basis + FastAdd(result1,point1->position,r12); + + // compute position vector r21 + FastNegMult(k_C_pk,r12,r21); + + + //----------------------------------// - // COMPUTE GLOBAL LOCATION - FastMult(body1->n_C_k,(body1->GetPoint(2))->position,result1); - FastAdd(result1,body1->r,result1); - FastNegMult(body2->n_C_k,(body2->GetPoint(1))->position,result2); - FastAdd(result1,result2,body2->r); - - qdot_to_u(q, u, qdot); - - - //----------------------------------- - // angular velocities - + // COMPUTE GLOBAL LOCATION + FastMult(body1->n_C_k,(body1->GetPoint(2))->position,result1); + FastAdd(result1,body1->r,result1); + FastNegMult(body2->n_C_k,(body2->GetPoint(1))->position,result2); + FastAdd(result1,result2,body2->r); + + qdot_to_u(q, u, qdot); + + + //----------------------------------- + // angular velocities + FastAssign(u,pk_w_k); - FastTMult(pk_C_k,body1->omega_k,result1); + FastTMult(pk_C_k,body1->omega_k,result1); FastAdd(result1,pk_w_k,body2->omega_k); - FastMult(body2->n_C_k,body2->omega_k,body2->omega); - - - - //----------------------------------- - - // compute velocities - FastCross(body1->omega_k,(body1->GetPoint(2))->position,result1); + FastMult(body2->n_C_k,body2->omega_k,body2->omega); + + + + //----------------------------------- + + // compute velocities + FastCross(body1->omega_k,(body1->GetPoint(2))->position,result1); FastAdd(body1->v_k,result1,result2); - FastTMult(pk_C_k,result2,result1); // In body basis - - FastCross((body2->GetPoint(1))->position,body2->omega_k,result2); - FastAdd(result1,result2,body2->v_k); // In body basis - FastMult(body2->n_C_k,body2->v_k,body2->v); - - + FastTMult(pk_C_k,result2,result1); // In body basis + + FastCross((body2->GetPoint(1))->position,body2->omega_k,result2); + FastAdd(result1,result2,body2->v_k); // In body basis + FastMult(body2->n_C_k,body2->v_k,body2->v); + + //------------------------------------------ - //Compute the KE + //Compute the KE Matrix tempke; - tempke = T(body2->v)*(body2->v); + tempke = T(body2->v)*(body2->v); double ke = 0.0; - ke = body2->mass*tempke(1,1); + ke = body2->mass*tempke(1,1); FastMult(body2->inertia,body2->omega_k,result1); - tempke= T(body2->omega_k)*result1; + tempke= T(body2->omega_k)*result1; ke = 0.5*ke + 0.5*tempke(1,1); body2->KE=ke; - //----------------------------------- - // compute state explicit angular acceleration // Has to be in body basis - FastTMult(pk_C_k,body1->alpha_t,result2); + //----------------------------------- + // compute state explicit angular acceleration // Has to be in body basis + FastTMult(pk_C_k,body1->alpha_t,result2); FastCross(body2->omega_k,pk_w_k,result1); - FastAdd(result1,result2,body2->alpha_t); - - //----------------------------------- - // compute state explicit acceleration - // NEED TO DO THIS COMPLETELY IN BODY BASIS - + FastAdd(result1,result2,body2->alpha_t); + + //----------------------------------- + // compute state explicit acceleration + // NEED TO DO THIS COMPLETELY IN BODY BASIS + FastCross(body1->omega_k,(body1->GetPoint(2))->position,result1); - FastCross(body1->omega_k,result1,result2); - FastTMult(pk_C_k,result2,result1); - - //FastCross(body2->omega_k,-(body2->GetPoint(1))->position,result3); - FastCross((body2->GetPoint(1))->position,body2->omega_k,result3); - FastCross(body2->omega_k,result3,result2); - FastAdd(result1,result2,result3); //wxwxr in body basis - - FastCross(body1->alpha_t,(body1->GetPoint(2))->position,result4); - FastTMult(pk_C_k,result4,result5); + FastCross(body1->omega_k,result1,result2); + FastTMult(pk_C_k,result2,result1); + + //FastCross(body2->omega_k,-(body2->GetPoint(1))->position,result3); + FastCross((body2->GetPoint(1))->position,body2->omega_k,result3); + FastCross(body2->omega_k,result3,result2); + FastAdd(result1,result2,result3); //wxwxr in body basis + + FastCross(body1->alpha_t,(body1->GetPoint(2))->position,result4); + FastTMult(pk_C_k,result4,result5); FastAssign(result5,result4); - - FastCross((body2->GetPoint(1))->position,body2->alpha_t,result2); - FastAdd(result2,result4,result1); //alphaxr in body basis - + + FastCross((body2->GetPoint(1))->position,body2->alpha_t,result2); + FastAdd(result2,result4,result1); //alphaxr in body basis + FastTMult(pk_C_k,body1->a_t,result2); - FastTripleSum(result3,result1,result2,body2->a_t); // in body basis - - - //----------------------------------- + FastTripleSum(result3,result1,result2,body2->a_t); // in body basis + + + //----------------------------------- } // NOTE: NOT USING BACKWARDKINEMATICS AT PRESENT @@ -206,13 +208,13 @@ void SphericalJoint::BackwardKinematics(){ // orientations ComputeBackwardTransforms(); - + // compute position vector r21 //r21 = point2->position - k_C_pk * point1->position; FastMult(k_C_pk,point1->position,result1); FastSubt(point2->position,result1,r21); - + // compute position vector r21 FastNegMult(pk_C_k,r21,r12); @@ -231,7 +233,7 @@ void SphericalJoint::BackwardKinematics(){ EP_Derivatives(q,u,qdot); // angular velocities - + FastMult(body2->n_C_k,u,result2); FastAdd(body2->omega,result2,body1->omega); FastAssign(u,k_w_pk); @@ -251,7 +253,7 @@ void SphericalJoint::BackwardKinematics(){ FastCross(body1->omega_k,k_w_pk,result1); FastMult(pk_C_k,body2->alpha_t,result2); FastAdd(result1,result2,body1->alpha_t); - + // compute state explicit acceleration FastCross(body2->alpha_t,point2->position,result1); FastCross(body2->omega_k,point2->position,result2); @@ -264,5 +266,5 @@ void SphericalJoint::BackwardKinematics(){ FastCross(body1->omega_k,result2,result3); FastTripleSum(result5,result1,result3,body1->a_t); - + } diff --git a/lib/poems/sphericaljoint.h b/lib/poems/sphericaljoint.h index 90f1547873..db048e5544 100644 --- a/lib/poems/sphericaljoint.h +++ b/lib/poems/sphericaljoint.h @@ -22,6 +22,7 @@ #include "joint.h" #include "matrix.h" +namespace POEMS { class SphericalJoint : public Joint { Matrix const_sP; public: @@ -38,5 +39,5 @@ public: void ForwardKinematics(); void BackwardKinematics(); }; - +} #endif diff --git a/lib/poems/system.cpp b/lib/poems/system.cpp index 1ac9ce1236..8515588424 100644 --- a/lib/poems/system.cpp +++ b/lib/poems/system.cpp @@ -3,7 +3,7 @@ * POEMS: PARALLELIZABLE OPEN SOURCE EFFICIENT MULTIBODY SOFTWARE * * DESCRIPTION: SEE READ-ME * * FILE NAME: system.cpp * - * AUTHORS: See Author List * + * AUTHORS: See Author List * * GRANTS: See Grants List * * COPYRIGHT: (C) 2005 by Authors as listed in Author's List * * LICENSE: Please see License Agreement * @@ -11,7 +11,7 @@ * ADMINISTRATOR: Prof. Kurt Anderson * * Computational Dynamics Lab * * Rensselaer Polytechnic Institute * - * 110 8th St. Troy NY 12180 * + * 110 8th St. Troy NY 12180 * * CONTACT: anderk5@rpi.edu * *_________________________________________________________________________*/ @@ -36,11 +36,12 @@ #include "vect3.h" #include "virtualmatrix.h" -class Point; - +namespace POEMS { class Point; } +using namespace std; +using namespace POEMS; System::System(){ - mappings = NULL; + mappings = NULL; } System::~System(){ @@ -59,7 +60,7 @@ int System::GetNumBodies(){ int * System::GetMappings() { - return mappings; + return mappings; } void System::AddBody(Body* body){ @@ -78,16 +79,16 @@ double System::GetTime(){ return time; } -void System::ComputeForces(){ - // NOT DOING ANYTHING AT THIS TIME - } - +void System::ComputeForces(){ + // NOT DOING ANYTHING AT THIS TIME + } + bool System::ReadIn(istream& in){ int numbodies; Body* body; int bodytype; char bodyname[256]; - int index; + int index; // get number of bodies in >> numbodies; @@ -165,12 +166,12 @@ bool System::ReadIn(istream& in){ delete [] bodyarray; return false; } - + joint->SetBodies(bodyarray[body1], bodyarray[body2]); bodyarray[body1]->AddJoint(joint); bodyarray[body2]->AddJoint(joint); - + in >> point1 >> point2; joint->SetPoints(bodyarray[body1]->GetPoint(point1),bodyarray[body2]->GetPoint(point2)); @@ -203,7 +204,7 @@ void System::WriteOut(ostream& out){ // set the body ID for later identification body->SetID(i); - + // write out the data body->WriteOut(out); @@ -211,7 +212,7 @@ void System::WriteOut(ostream& out){ } // number of joints - out << joints.GetNumElements() << endl; + out << joints.GetNumElements() << endl; // joints loop i = 0; @@ -226,7 +227,7 @@ void System::WriteOut(ostream& out){ // write out the data joint->WriteOut(out); - + i++; j_ele = j_ele->next; } } @@ -252,68 +253,68 @@ void System::ClearJointIDs(){ void System::Create_DegenerateSystem(int& nfree, int*freelist, double *&masstotal, double **&inertia, double **&xcm, double **&vcm, double **&omega, double **&ex_space, double **&ey_space, double **&ez_space){ - //-------------------------------------------------------------------------// - // Declaring Temporary Entities - //-------------------------------------------------------------------------// + //-------------------------------------------------------------------------// + // Declaring Temporary Entities + //-------------------------------------------------------------------------// Body* body = NULL; Body* prev; Body* Inertial; Point* origin; Joint* joint; - Point* point_CM; - Point* point_p; - Point* point_k; + Point* point_CM; + Point* point_p; + Point* point_k; Point* point_ch = NULL; - Vect3 r1,r2,r3,v1,v2,v3; + Vect3 r1,r2,r3,v1,v2,v3; Mat3x3 IM, N, PKCK,PKCN ; ColMatrix qo, uo, q, qdot,w; - - mappings = new int[nfree]; - for(int i = 0; i < nfree; i++) - { - mappings[i] = freelist[i]; - } + + mappings = new int[nfree]; + for(int i = 0; i < nfree; i++) + { + mappings[i] = freelist[i]; + } qo.Dim(4); uo.Dim(3); q.Dim(4); - qdot.Dim(4); + qdot.Dim(4); PKCN.Identity(); PKCK.Identity(); w.Dim(3); - -//-------------------------------------------------------------------------// - // Setting up Inertial Frame, gravity and Origin + +//-------------------------------------------------------------------------// + // Setting up Inertial Frame, gravity and Origin //-------------------------------------------------------------------------// - Inertial= new InertialFrame; + Inertial= new InertialFrame; AddBody(Inertial); - - Vect3 temp1; - temp1.Zeros(); - ((InertialFrame*) Inertial)->SetGravity(temp1); + + Vect3 temp1; + temp1.Zeros(); + ((InertialFrame*) Inertial)->SetGravity(temp1); origin= new FixedPoint(temp1); - Inertial->AddPoint(origin); + Inertial->AddPoint(origin); +//-------------------------------------------------------------------------// + double ** xh1 = new double*[nfree]; + double ** xh2 = new double*[nfree]; + + for (int i=0; imass=masstotal[mappings[i]-1]; IM(1,1)=inertia[mappings[i]-1][0]; IM(2,2)=inertia[mappings[i]-1][1]; @@ -324,49 +325,49 @@ void System::Create_DegenerateSystem(int& nfree, int*freelist, double *&masstota IM(2,1)=IM(1,2); IM(3,1)=IM(1,3); IM(3,2)=IM(2,3); - body->inertia = IM; - -//-------------------------------------------------------// - - - for (int k=0;k<3;k++){ - r1(k+1)=xh1[i][k]-xcm[mappings[i]-1][k]; - r3(k+1) = xcm[mappings[i]-1][k]; - r3(k+1)=xh2[i][k]-xcm[mappings[i]-1][k]; - } - - r2.Zeros(); - - for (int k=1;k<=3;k++){ - N(k,1)=ex_space[mappings[i]-1][k-1]; - N(k,2)=ey_space[mappings[i]-1][k-1]; - N(k,3)=ez_space[mappings[i]-1][k-1]; - } - + body->inertia = IM; + +//-------------------------------------------------------// + + + for (int k=0;k<3;k++){ + r1(k+1)=xh1[i][k]-xcm[mappings[i]-1][k]; + r3(k+1) = xcm[mappings[i]-1][k]; + r3(k+1)=xh2[i][k]-xcm[mappings[i]-1][k]; + } + + r2.Zeros(); + + for (int k=1;k<=3;k++){ + N(k,1)=ex_space[mappings[i]-1][k-1]; + N(k,2)=ey_space[mappings[i]-1][k-1]; + N(k,3)=ez_space[mappings[i]-1][k-1]; + } + PKCK=T(N); PKCN=T(N); - - q.Zeros(); + + q.Zeros(); EP_FromTransformation(q,N); - + r1=PKCN*r1; r3=PKCN*r3; - + for (int k=1;k<=3;k++){ - w(k)=omega[mappings[i]-1][k-1]; - } - + w(k)=omega[mappings[i]-1][k-1]; + } + Vect3 cart_r, cart_v; for (int k=1;k<=3;k++){ - cart_r(k)=xcm[mappings[i]-1][k-1]; - cart_v(k)=vcm[mappings[i]-1][k-1]; - } - - w=PKCN*w; - EP_Derivatives(q,w,qdot); - - -//-------------------------------------------------------------------------// + cart_r(k)=xcm[mappings[i]-1][k-1]; + cart_v(k)=vcm[mappings[i]-1][k-1]; + } + + w=PKCN*w; + EP_Derivatives(q,w,qdot); + + +//-------------------------------------------------------------------------// // Create bodies and joints with associated properties for POEMS //-------------------------------------------------------------------------// @@ -376,12 +377,12 @@ void System::Create_DegenerateSystem(int& nfree, int*freelist, double *&masstota body->AddPoint(point_CM); body->AddPoint(point_k); body->AddPoint(point_ch); - AddBody(body); - + AddBody(body); + Mat3x3 One; - One.Identity(); - ColMatrix qq=Stack(q,cart_r); - ColMatrix vv=Stack(qdot,cart_v); + One.Identity(); + ColMatrix qq=Stack(q,cart_r); + ColMatrix vv=Stack(qdot,cart_v); joint=new FreeBodyJoint; AddJoint(joint); joint->SetBodies(prev,body); @@ -391,225 +392,225 @@ void System::Create_DegenerateSystem(int& nfree, int*freelist, double *&masstota joint->SetZeroOrientation(One); joint->DimQandU(7,6); joint->SetInitialState(qq,vv); - joint->ForwardKinematics(); + joint->ForwardKinematics(); } for(int i = 0; i < nfree; i++) { - delete [] xh1[i]; - delete [] xh2[i]; + delete [] xh1[i]; + delete [] xh2[i]; } delete [] xh1; - delete [] xh2; + delete [] xh2; } void System::Create_System_LAMMPS(int numbodies, double *mass,double **inertia, double ** xcm, double ** xjoint,double **vcm,double **omega,double **ex_space, double **ey_space, double **ez_space, int b, int * mapping, int count){ - //-------------------------------------------------------------------------// - // Declaring Temporary Entities - //-------------------------------------------------------------------------// - - Body* body = NULL; - Body* prev; - Body* Inertial; - Point* origin; - Joint* joint; - Point* point_CM; - Point* point_p; - Point* point_k; - Point* point_ch = NULL; - Vect3 r1,r2,r3,v1,v2,v3; - Mat3x3 IM, N, PKCK,PKCN ; - ColMatrix qo, uo, q, qdot,w; - Vect3 cart_r, cart_v; - mappings = new int[b]; - for(int i = 0; i < b; i++){ - mappings[i] = mapping[i]; - } - - - qo.Dim(4); - uo.Dim(3); - q.Dim(4); - qdot.Dim(4); - PKCN.Identity(); - PKCK.Identity(); - w.Dim(3); - - //-------------------------------------------------------------------------// - // Setting up Inertial Frame, gravity and Origin - //-------------------------------------------------------------------------// - Inertial= new InertialFrame; - AddBody(Inertial); - - Vect3 temp1; - temp1.Zeros(); - ((InertialFrame*) Inertial)->SetGravity(temp1); - origin= new FixedPoint(temp1); - Inertial->AddPoint(origin); - //-------------------------------------------------------------------------// - - double ** xh1; - double ** xh2; - - xh1 = new double*[b]; - xh2 = new double*[b]; - - - for (int i=0; iSetGravity(temp1); + origin= new FixedPoint(temp1); + Inertial->AddPoint(origin); + //-------------------------------------------------------------------------// + + double ** xh1; + double ** xh2; + + xh1 = new double*[b]; + xh2 = new double*[b]; + + + for (int i=0; imass=mass[mapping[i]-1]; - IM(1,1)=inertia[mapping[i]-1][0]; - IM(2,2)=inertia[mapping[i]-1][1]; - IM(3,3)=inertia[mapping[i]-1][2]; - IM(1,2)=0.0; - IM(1,3)=0.0; - IM(2,3)=0.0; - IM(2,1)=IM(1,2); - IM(3,1)=IM(1,3); - IM(3,2)=IM(2,3); - body->inertia = IM; - - //-------------------------------------------------------// - - for (int k=0;k<3;k++){ - r1(k+1)=xh1[i][k]-xcm[mapping[i]-1][k]; - r3(k+1)=xh2[i][k]-xcm[mapping[i]-1][k]; - } - r2.Zeros(); - - for (int k=1;k<=3;k++){ - N(k,1)=ex_space[mapping[i]-1][k-1]; - N(k,2)=ey_space[mapping[i]-1][k-1]; - N(k,3)=ez_space[mapping[i]-1][k-1]; - } - - - if (i==0){ - PKCK=T(N); - PKCN=T(N); - - q.Zeros(); - EP_FromTransformation(q,N); - - r1=PKCN*r1; - r3=PKCN*r3; - - for (int k=1;k<=3;k++){ - w(k)=omega[mappings[i]-1][k-1]; - } - - for (int k=1;k<=3;k++){ - cart_r(k)=xcm[mappings[i]-1][k-1]; - cart_v(k)=vcm[mappings[i]-1][k-1]; - } - w=PKCN*w; - EP_Derivatives(q,w,qdot); - - } - else{ - PKCK=PKCN*N; - PKCN=T(N); - - q.Zeros(); - EP_FromTransformation(q,PKCK); - - r1=PKCN*r1; - r3=PKCN*r3; - - for (int k=1;k<=3;k++){ - w(k)=omega[mapping[i]-1][k-1]-omega[mapping[i-1]-1][k-1]; - } - - w=PKCN*w; - EP_Derivatives(q, w, qdot); - } - - - //-------------------------------------------------------------------------// + //-------------------------------------------------------------------------// + for(int i=0;imass=mass[mapping[i]-1]; + IM(1,1)=inertia[mapping[i]-1][0]; + IM(2,2)=inertia[mapping[i]-1][1]; + IM(3,3)=inertia[mapping[i]-1][2]; + IM(1,2)=0.0; + IM(1,3)=0.0; + IM(2,3)=0.0; + IM(2,1)=IM(1,2); + IM(3,1)=IM(1,3); + IM(3,2)=IM(2,3); + body->inertia = IM; + + //-------------------------------------------------------// + + for (int k=0;k<3;k++){ + r1(k+1)=xh1[i][k]-xcm[mapping[i]-1][k]; + r3(k+1)=xh2[i][k]-xcm[mapping[i]-1][k]; + } + r2.Zeros(); + + for (int k=1;k<=3;k++){ + N(k,1)=ex_space[mapping[i]-1][k-1]; + N(k,2)=ey_space[mapping[i]-1][k-1]; + N(k,3)=ez_space[mapping[i]-1][k-1]; + } + + + if (i==0){ + PKCK=T(N); + PKCN=T(N); + + q.Zeros(); + EP_FromTransformation(q,N); + + r1=PKCN*r1; + r3=PKCN*r3; + + for (int k=1;k<=3;k++){ + w(k)=omega[mappings[i]-1][k-1]; + } + + for (int k=1;k<=3;k++){ + cart_r(k)=xcm[mappings[i]-1][k-1]; + cart_v(k)=vcm[mappings[i]-1][k-1]; + } + w=PKCN*w; + EP_Derivatives(q,w,qdot); + + } + else{ + PKCK=PKCN*N; + PKCN=T(N); + + q.Zeros(); + EP_FromTransformation(q,PKCK); + + r1=PKCN*r1; + r3=PKCN*r3; + + for (int k=1;k<=3;k++){ + w(k)=omega[mapping[i]-1][k-1]-omega[mapping[i-1]-1][k-1]; + } + + w=PKCN*w; + EP_Derivatives(q, w, qdot); + } + + + //-------------------------------------------------------------------------// // Create bodies and joints with associated properties for POEMS - //-------------------------------------------------------------------------// - - point_CM = new FixedPoint(r2); - point_k = new FixedPoint(r1); - point_ch = new FixedPoint(r3); - body->AddPoint(point_CM); - body->AddPoint(point_k); - body->AddPoint(point_ch); - AddBody(body); - - Mat3x3 One; - One.Identity(); - if (i==0){ - ColMatrix qq=Stack(q,cart_r); - ColMatrix vv=Stack(qdot,cart_v); - joint=new FreeBodyJoint; - AddJoint(joint); - joint->SetBodies(prev,body); - body->AddJoint(joint); - prev->AddJoint(joint); - joint->SetPoints(point_p,point_k); - joint->SetZeroOrientation(One); - joint->DimQandU(7,6); - joint->SetInitialState(qq,vv); - joint->ForwardKinematics(); - } - else{ - joint= new SphericalJoint; - AddJoint(joint); - joint->SetBodies(prev,body); - body->AddJoint(joint); - prev->AddJoint(joint); - joint->SetPoints(point_p,point_k); - joint->SetZeroOrientation(One); - joint->DimQandU(4,3); - joint->SetInitialState(q,qdot); - joint->ForwardKinematics(); - } - } - for(int i = 0; i < b; i++) - { - delete [] xh1[i]; - delete [] xh2[i]; - } - delete [] xh1; - delete [] xh2; - + //-------------------------------------------------------------------------// + + point_CM = new FixedPoint(r2); + point_k = new FixedPoint(r1); + point_ch = new FixedPoint(r3); + body->AddPoint(point_CM); + body->AddPoint(point_k); + body->AddPoint(point_ch); + AddBody(body); + + Mat3x3 One; + One.Identity(); + if (i==0){ + ColMatrix qq=Stack(q,cart_r); + ColMatrix vv=Stack(qdot,cart_v); + joint=new FreeBodyJoint; + AddJoint(joint); + joint->SetBodies(prev,body); + body->AddJoint(joint); + prev->AddJoint(joint); + joint->SetPoints(point_p,point_k); + joint->SetZeroOrientation(One); + joint->DimQandU(7,6); + joint->SetInitialState(qq,vv); + joint->ForwardKinematics(); + } + else{ + joint= new SphericalJoint; + AddJoint(joint); + joint->SetBodies(prev,body); + body->AddJoint(joint); + prev->AddJoint(joint); + joint->SetPoints(point_p,point_k); + joint->SetZeroOrientation(One); + joint->DimQandU(4,3); + joint->SetInitialState(q,qdot); + joint->ForwardKinematics(); + } + } + for(int i = 0; i < b; i++) + { + delete [] xh1[i]; + delete [] xh2[i]; + } + delete [] xh1; + delete [] xh2; + } diff --git a/lib/poems/system.h b/lib/poems/system.h index e5ce27194b..2402e5852f 100644 --- a/lib/poems/system.h +++ b/lib/poems/system.h @@ -3,7 +3,7 @@ * POEMS: PARALLELIZABLE OPEN SOURCE EFFICIENT MULTIBODY SOFTWARE * * DESCRIPTION: SEE READ-ME * * FILE NAME: system.h * - * AUTHORS: See Author List * + * AUTHORS: See Author List * * GRANTS: See Grants List * * COPYRIGHT: (C) 2005 by Authors as listed in Author's List * * LICENSE: Please see License Agreement * @@ -11,7 +11,7 @@ * ADMINISTRATOR: Prof. Kurt Anderson * * Computational Dynamics Lab * * Rensselaer Polytechnic Institute * - * 110 8th St. Troy NY 12180 * + * 110 8th St. Troy NY 12180 * * CONTACT: anderk5@rpi.edu * *_________________________________________________________________________*/ @@ -22,6 +22,7 @@ #include #include "poemslist.h" +namespace POEMS { class Body; class Joint; @@ -33,37 +34,37 @@ double time; List bodies; List joints; - + System(); ~System(); void Delete(); - + int GetNumBodies(); - + int * GetMappings(); void AddBody(Body* body); - + void AddJoint(Joint* joint); - + void SetTime(double t); - + double GetTime(); - + void ComputeForces(); - + bool ReadIn(std::istream& in); - + void WriteOut(std::ostream& out); - + void ClearBodyIDs(); - - void ClearJointIDs(); + + void ClearJointIDs(); void Create_System_LAMMPS(int numbodies, double *mass,double **inertia, double ** xcm, double ** xjoint,double **vh1,double **omega,double **ex_space, double **ey_space, double **ez_space, int b, int * mapping, int count); - + void Create_DegenerateSystem(int& nfree, int*freelist, double *&masstotal, double **&inertia, double **&xcm, double **&vcm, double **&omega, double **&ex_space, double **&ey_space, double **&ez_space); }; - +} #endif diff --git a/lib/poems/vect3.cpp b/lib/poems/vect3.cpp index 7ce3230238..66c2f902d5 100644 --- a/lib/poems/vect3.cpp +++ b/lib/poems/vect3.cpp @@ -21,6 +21,8 @@ #include using namespace std; +using namespace POEMS; + Vect3::Vect3(){ numrows = 3; numcols = 1; diff --git a/lib/poems/vect3.h b/lib/poems/vect3.h index a28832db6c..6b0efc371a 100644 --- a/lib/poems/vect3.h +++ b/lib/poems/vect3.h @@ -3,7 +3,7 @@ * POEMS: PARALLELIZABLE OPEN SOURCE EFFICIENT MULTIBODY SOFTWARE * * DESCRIPTION: SEE READ-ME * * FILE NAME: vect3.h * - * AUTHORS: See Author List * + * AUTHORS: See Author List * * GRANTS: See Grants List * * COPYRIGHT: (C) 2005 by Authors as listed in Author's List * * LICENSE: Please see License Agreement * @@ -11,7 +11,7 @@ * ADMINISTRATOR: Prof. Kurt Anderson * * Computational Dynamics Lab * * Rensselaer Polytechnic Institute * - * 110 8th St. Troy NY 12180 * + * 110 8th St. Troy NY 12180 * * CONTACT: anderk5@rpi.edu * *_________________________________________________________________________*/ @@ -23,6 +23,7 @@ #include "virtualcolmatrix.h" #include "virtualmatrix.h" +namespace POEMS { class Matrix; class Mat3x3; class Mat6x6; @@ -82,7 +83,6 @@ public: friend void FastMult(Mat3x3& A, ColMatrix& B, Vect3& C); friend void FastAssign(ColMatrix&A, Vect3& C); friend void FastMult(Mat3x3& A, Vect3& B, ColMatrix& C); - }; - +} #endif diff --git a/lib/poems/vect4.cpp b/lib/poems/vect4.cpp index b045998017..8e903d57bd 100644 --- a/lib/poems/vect4.cpp +++ b/lib/poems/vect4.cpp @@ -21,6 +21,8 @@ #include using namespace std; +using namespace POEMS; + Vect4::Vect4(){ numrows = 4; numcols = 1; diff --git a/lib/poems/vect4.h b/lib/poems/vect4.h index 0b28994043..754706f10a 100644 --- a/lib/poems/vect4.h +++ b/lib/poems/vect4.h @@ -3,7 +3,7 @@ * POEMS: PARALLELIZABLE OPEN SOURCE EFFICIENT MULTIBODY SOFTWARE * * DESCRIPTION: SEE READ-ME * * FILE NAME: vect4.h * - * AUTHORS: See Author List * + * AUTHORS: See Author List * * GRANTS: See Grants List * * COPYRIGHT: (C) 2005 by Authors as listed in Author's List * * LICENSE: Please see License Agreement * @@ -11,7 +11,7 @@ * ADMINISTRATOR: Prof. Kurt Anderson * * Computational Dynamics Lab * * Rensselaer Polytechnic Institute * - * 110 8th St. Troy NY 12180 * + * 110 8th St. Troy NY 12180 * * CONTACT: anderk5@rpi.edu * *_________________________________________________________________________*/ @@ -23,6 +23,7 @@ #include "virtualcolmatrix.h" #include "virtualmatrix.h" +namespace POEMS { class Matrix; class Mat4x4; @@ -41,7 +42,7 @@ public: void BasicSet_1int(int i, double value); void BasicIncrement_1int(int i, double value); - + void Const(double value); MatrixType GetType() const; std::ostream& WriteData(std::ostream& c) const; @@ -69,5 +70,5 @@ public: friend void FastAdd(Vect4& A, Vect4& B, Vect4& C); friend void FastSubt(Vect4& A, Vect4& B, Vect4& C); }; - +} #endif diff --git a/lib/poems/vect6.cpp b/lib/poems/vect6.cpp index 5baadafc34..5aabe520e1 100644 --- a/lib/poems/vect6.cpp +++ b/lib/poems/vect6.cpp @@ -21,6 +21,8 @@ #include using namespace std; +using namespace POEMS; + Vect6::Vect6(){ numrows = 6; numcols = 1; diff --git a/lib/poems/vect6.h b/lib/poems/vect6.h index 8047c1bbf8..5def4c6b1b 100644 --- a/lib/poems/vect6.h +++ b/lib/poems/vect6.h @@ -23,6 +23,7 @@ #include "virtualcolmatrix.h" #include "virtualmatrix.h" +namespace POEMS { class Matrix; class Mat6x6; class ColMatrix; @@ -69,5 +70,5 @@ public: friend void OnPopulateSVect(Vect3& angular, Vect3& linear, Vect6& sV); }; - +} #endif diff --git a/lib/poems/virtualcolmatrix.cpp b/lib/poems/virtualcolmatrix.cpp index 3a6c6e22cd..fa430b81f7 100644 --- a/lib/poems/virtualcolmatrix.cpp +++ b/lib/poems/virtualcolmatrix.cpp @@ -20,6 +20,8 @@ #include using namespace std; +using namespace POEMS; + VirtualColMatrix::VirtualColMatrix(){ numcols = 1; diff --git a/lib/poems/virtualcolmatrix.h b/lib/poems/virtualcolmatrix.h index 1548794ca0..040fce051e 100644 --- a/lib/poems/virtualcolmatrix.h +++ b/lib/poems/virtualcolmatrix.h @@ -3,7 +3,7 @@ * POEMS: PARALLELIZABLE OPEN SOURCE EFFICIENT MULTIBODY SOFTWARE * * DESCRIPTION: SEE READ-ME * * FILE NAME: virtualcolmatrix.h * - * AUTHORS: See Author List * + * AUTHORS: See Author List * * GRANTS: See Grants List * * COPYRIGHT: (C) 2005 by Authors as listed in Author's List * * LICENSE: Please see License Agreement * @@ -11,7 +11,7 @@ * ADMINISTRATOR: Prof. Kurt Anderson * * Computational Dynamics Lab * * Rensselaer Polytechnic Institute * - * 110 8th St. Troy NY 12180 * + * 110 8th St. Troy NY 12180 * * CONTACT: anderk5@rpi.edu * *_________________________________________________________________________*/ @@ -21,25 +21,25 @@ #include "virtualmatrix.h" - +namespace POEMS { class VirtualColMatrix : public VirtualMatrix { -public: - VirtualColMatrix(); - ~VirtualColMatrix(); - double& operator_2int (int i, int j); // array access - double Get_2int (int i, int j) const; - void Set_2int (int i, int j, double value); - double BasicGet_2int(int i, int j) const; - void BasicSet_2int(int i, int j, double value); - void BasicIncrement_2int(int i, int j, double value); - - virtual double& operator_1int (int i) = 0; // array access - virtual double Get_1int(int i) const = 0; - virtual void Set_1int(int i, double value) = 0; - virtual double BasicGet_1int(int i) const = 0; - virtual void BasicSet_1int(int i, double value) = 0; - virtual void BasicIncrement_1int(int i, double value) = 0; +public: + VirtualColMatrix(); + ~VirtualColMatrix(); + double& operator_2int (int i, int j); // array access + double Get_2int (int i, int j) const; + void Set_2int (int i, int j, double value); + double BasicGet_2int(int i, int j) const; + void BasicSet_2int(int i, int j, double value); + void BasicIncrement_2int(int i, int j, double value); + + virtual double& operator_1int (int i) = 0; // array access + virtual double Get_1int(int i) const = 0; + virtual void Set_1int(int i, double value) = 0; + virtual double BasicGet_1int(int i) const = 0; + virtual void BasicSet_1int(int i, double value) = 0; + virtual void BasicIncrement_1int(int i, double value) = 0; }; - +} #endif diff --git a/lib/poems/virtualmatrix.cpp b/lib/poems/virtualmatrix.cpp index 19d5946961..bfffeb3d74 100644 --- a/lib/poems/virtualmatrix.cpp +++ b/lib/poems/virtualmatrix.cpp @@ -21,6 +21,8 @@ #include using namespace std; +using namespace POEMS; + VirtualMatrix::VirtualMatrix(){ numrows = numcols = 0; @@ -140,14 +142,14 @@ istream& VirtualMatrix::ReadData(istream& c){ // operators and functions // -ostream& operator<< (ostream& c, const VirtualMatrix& A){ //output +ostream& POEMS::operator<< (ostream& c, const VirtualMatrix& A){ //output c << A.GetType() << ' '; A.WriteData(c); c << endl; return c; } -istream& operator>> (istream& c, VirtualMatrix& A){ //input +istream& POEMS::operator>> (istream& c, VirtualMatrix& A){ //input VirtualMatrix* vm; int matrixtype; c >> matrixtype; diff --git a/lib/poems/virtualmatrix.h b/lib/poems/virtualmatrix.h index a27c7de047..706b943d66 100644 --- a/lib/poems/virtualmatrix.h +++ b/lib/poems/virtualmatrix.h @@ -20,6 +20,7 @@ #define VIRTUALMATRIX_H #include +namespace POEMS { enum MatrixType { MATRIX = 0, COLMATRIX = 1, @@ -83,5 +84,5 @@ protected: // overloaded operators std::ostream& operator<< (std::ostream& c, const VirtualMatrix& A); // output std::istream& operator>> (std::istream& c, VirtualMatrix& A); // input - +} #endif diff --git a/lib/poems/virtualrowmatrix.cpp b/lib/poems/virtualrowmatrix.cpp index 1a12cfbfd9..740c747407 100644 --- a/lib/poems/virtualrowmatrix.cpp +++ b/lib/poems/virtualrowmatrix.cpp @@ -21,6 +21,8 @@ #include using namespace std; +using namespace POEMS; + VirtualRowMatrix::VirtualRowMatrix(){ numrows = 1; diff --git a/lib/poems/virtualrowmatrix.h b/lib/poems/virtualrowmatrix.h index 68b39f137d..0a3c877f64 100644 --- a/lib/poems/virtualrowmatrix.h +++ b/lib/poems/virtualrowmatrix.h @@ -3,7 +3,7 @@ * POEMS: PARALLELIZABLE OPEN SOURCE EFFICIENT MULTIBODY SOFTWARE * * DESCRIPTION: SEE READ-ME * * FILE NAME: virtualrowmatrix.h * - * AUTHORS: See Author List * + * AUTHORS: See Author List * * GRANTS: See Grants List * * COPYRIGHT: (C) 2005 by Authors as listed in Author's List * * LICENSE: Please see License Agreement * @@ -11,7 +11,7 @@ * ADMINISTRATOR: Prof. Kurt Anderson * * Computational Dynamics Lab * * Rensselaer Polytechnic Institute * - * 110 8th St. Troy NY 12180 * + * 110 8th St. Troy NY 12180 * * CONTACT: anderk5@rpi.edu * *_________________________________________________________________________*/ @@ -21,8 +21,9 @@ #include "virtualmatrix.h" +namespace POEMS { class VirtualRowMatrix : public VirtualMatrix { -public: +public: VirtualRowMatrix(); ~VirtualRowMatrix(); double& operator_2int (int i, int j); // array access @@ -31,7 +32,7 @@ public: double BasicGet_2int(int i, int j) const; void BasicSet_2int(int i, int j, double value); void BasicIncrement_2int(int i, int j, double value); - + virtual double& operator_1int (int i) = 0; // array access virtual double Get_1int(int i) const = 0; virtual void Set_1int(int i, double value) = 0; @@ -39,5 +40,5 @@ public: virtual void BasicSet_1int(int i, double value) = 0; virtual void BasicIncrement_1int(int i, double value) = 0; }; - +} #endif diff --git a/lib/poems/workspace.cpp b/lib/poems/workspace.cpp index 29a1c95832..03f18a7895 100644 --- a/lib/poems/workspace.cpp +++ b/lib/poems/workspace.cpp @@ -38,6 +38,8 @@ using namespace std; +using namespace POEMS; + void Workspace::allocateNewSystem() { currentIndex++; diff --git a/lib/poems/workspace.h b/lib/poems/workspace.h index 6213815d81..2510b2fc3a 100644 --- a/lib/poems/workspace.h +++ b/lib/poems/workspace.h @@ -3,7 +3,7 @@ * POEMS: PARALLELIZABLE OPEN SOURCE EFFICIENT MULTIBODY SOFTWARE * * DESCRIPTION: SEE READ-ME * * FILE NAME: workspace.h * - * AUTHORS: See Author List * + * AUTHORS: See Author List * * GRANTS: See Grants List * * COPYRIGHT: (C) 2005 by Authors as listed in Author's List * * LICENSE: Please see License Agreement * @@ -11,7 +11,7 @@ * ADMINISTRATOR: Prof. Kurt Anderson * * Computational Dynamics Lab * * Rensselaer Polytechnic Institute * - * 110 8th St. Troy NY 12180 * + * 110 8th St. Troy NY 12180 * * CONTACT: anderk5@rpi.edu * *_________________________________________________________________________*/ @@ -19,61 +19,62 @@ #ifndef WORKSPACE_H #define WORKSPACE_H +namespace POEMS { class System; class Solver; struct SysData{ - System * system; - int solver; - int integrator; + System * system; + int solver; + int integrator; }; class Workspace { - SysData * system; // the multibody systems data - int currentIndex; - int maxAlloc; - + SysData * system; // the multibody systems data + int currentIndex; + int maxAlloc; + public: Workspace(); ~Workspace(); - + double Thalf; double Tfull; double ConFac; double KE_val; - int FirstTime; - + int FirstTime; + bool LoadFile(char* filename); - + bool SaveFile(char* filename, int index = -1); System* GetSystem(int index = -1); - - void AddSolver(Solver* s, int index = -1); - - - void LobattoOne(double **&xcm, double **&vcm,double **&omega,double **&torque, double **&fcm, double **&ex_space, double **&ey_space, double **&ez_space); - - void LobattoTwo(double **&vcm,double **&omega,double **&torque, double **&fcm); - - + + void AddSolver(Solver* s, int index = -1); + + + void LobattoOne(double **&xcm, double **&vcm,double **&omega,double **&torque, double **&fcm, double **&ex_space, double **&ey_space, double **&ez_space); + + void LobattoTwo(double **&vcm,double **&omega,double **&torque, double **&fcm); + + bool MakeSystem(int& nbody, double *&masstotal, double **&inertia, double **&xcm, double **&vcm, double **&omega, double **&ex_space, double **&ey_space, double **&ez_space, int &njoint, int **&jointbody, double **&xjoint, int& nfree, int*freelist, double dthalf, double dtv, double tempcon, double KE); - - - bool SaveSystem(int& nbody, double *&masstotal, double **&inertia, double **&xcm, double **&xjoint, double **&vcm, double **&omega, double **&ex_space, double **&ey_space, double **&ez_space, double **&acm, double **&alpha, double **&torque, double **&fcm, int **&jointbody, int &njoint); - - bool MakeDegenerateSystem(int& nfree, int*freelist, double *&masstotal, double **&inertia, double **&xcm, double **&vcm, double **&omega, double **&ex_space, double **&ey_space, double **&ez_space); + + + bool SaveSystem(int& nbody, double *&masstotal, double **&inertia, double **&xcm, double **&xjoint, double **&vcm, double **&omega, double **&ex_space, double **&ey_space, double **&ez_space, double **&acm, double **&alpha, double **&torque, double **&fcm, int **&jointbody, int &njoint); + + bool MakeDegenerateSystem(int& nfree, int*freelist, double *&masstotal, double **&inertia, double **&xcm, double **&vcm, double **&omega, double **&ex_space, double **&ey_space, double **&ez_space); int getNumberOfSystems(); - + void SetLammpsValues(double dtv, double dthalf, double tempcon); void SetKE(int temp, double SysKE); - - void RKStep(double **&xcm, double **&vcm,double **&omega,double **&torque, double **&fcm, double **&ex_space, double **&ey_space, double **&ez_space); - - void WriteFile(char* filename); + + void RKStep(double **&xcm, double **&vcm,double **&omega,double **&torque, double **&fcm, double **&ex_space, double **&ey_space, double **&ez_space); + + void WriteFile(char* filename); private: - void allocateNewSystem(); //helper function to handle vector resizing and such for the array of system pointers + void allocateNewSystem(); //helper function to handle vector resizing and such for the array of system pointers }; - +} #endif diff --git a/src/POEMS/fix_poems.cpp b/src/POEMS/fix_poems.cpp index 6d943a79db..21c12f700b 100644 --- a/src/POEMS/fix_poems.cpp +++ b/src/POEMS/fix_poems.cpp @@ -20,7 +20,6 @@ #include "fix_poems.h" #include #include -#include #include #include #include "workspace.h" @@ -30,7 +29,6 @@ #include "respa.h" #include "modify.h" #include "force.h" -#include "output.h" #include "group.h" #include "comm.h" #include "citeme.h" @@ -265,7 +263,7 @@ FixPOEMS::FixPOEMS(LAMMPS *lmp, int narg, char **arg) : // create POEMS instance - poems = new Workspace; + poems = new POEMS::Workspace; // compute per body forces and torques inside final_integrate() by default diff --git a/src/POEMS/fix_poems.h b/src/POEMS/fix_poems.h index 7b2c77a1bd..87f9557ac0 100644 --- a/src/POEMS/fix_poems.h +++ b/src/POEMS/fix_poems.h @@ -22,6 +22,7 @@ FixStyle(poems,FixPOEMS) #include "fix.h" +namespace POEMS { class Workspace; } namespace LAMMPS_NS { class FixPOEMS : public Fix { @@ -94,7 +95,7 @@ class FixPOEMS : public Fix { // POEMS object - class Workspace *poems; + POEMS::Workspace *poems; // internal class functions -- GitLab From fa15bf5edd552cafcfb5cfd28edc2ad327015921 Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Thu, 4 Jul 2019 00:25:33 -0400 Subject: [PATCH 177/469] recover compilation of USER-COLVARS package --- src/USER-COLVARS/colvarproxy_lammps.h | 10 ++++++++-- 1 file changed, 8 insertions(+), 2 deletions(-) diff --git a/src/USER-COLVARS/colvarproxy_lammps.h b/src/USER-COLVARS/colvarproxy_lammps.h index c3d9dbb35f..3243a14fbd 100644 --- a/src/USER-COLVARS/colvarproxy_lammps.h +++ b/src/USER-COLVARS/colvarproxy_lammps.h @@ -38,6 +38,12 @@ inline std::ostream & operator<< (std::ostream &out, const commdata &cd) return out; } +// forward declarations +namespace LAMMPS_NS { + class LAMMPS; + class RanPark; +} + /// \brief Communication between colvars and LAMMPS /// (implementation of \link colvarproxy \endlink) class colvarproxy_lammps : public colvarproxy { @@ -46,8 +52,8 @@ class colvarproxy_lammps : public colvarproxy { protected: // pointers to LAMMPS class instances - class LAMMPS_NS::LAMMPS *_lmp; - class LAMMPS_NS::RanPark *_random; + LAMMPS_NS::LAMMPS *_lmp; + LAMMPS_NS::RanPark *_random; // state of LAMMPS properties double t_target, my_timestep, my_boltzmann, my_angstrom; -- GitLab From 49f27573a7b1e2efade8be7ef7a7d9c101ab7c5c Mon Sep 17 00:00:00 2001 From: Trung Nguyen Date: Wed, 3 Jul 2019 23:44:33 -0500 Subject: [PATCH 178/469] Fixed a bug in lj96 involving missing the special_lj factor --- lib/gpu/lal_lj96.cu | 1 + 1 file changed, 1 insertion(+) diff --git a/lib/gpu/lal_lj96.cu b/lib/gpu/lal_lj96.cu index 3bb7750022..8dd63ef920 100644 --- a/lib/gpu/lal_lj96.cu +++ b/lib/gpu/lal_lj96.cu @@ -174,6 +174,7 @@ __kernel void k_lj96_fast(const __global numtyp4 *restrict x_, numtyp r6inv = r2inv*r2inv*r2inv; numtyp r3inv = ucl_sqrt(r6inv); numtyp force = r2inv*r6inv*(lj1[mtype].x*r3inv-lj1[mtype].y); + force*=factor_lj; f.x+=delx*force; f.y+=dely*force; -- GitLab From 732bd937e0416d46be708778bd234cd3e0c9ba97 Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Thu, 4 Jul 2019 01:16:56 -0400 Subject: [PATCH 179/469] clean up includes in USER-COLVARS package --- src/USER-COLVARS/colvarproxy_lammps.cpp | 13 +-------- src/USER-COLVARS/colvarproxy_lammps.h | 39 +++++++------------------ src/USER-COLVARS/fix_colvars.cpp | 25 ++++++++++++---- src/USER-COLVARS/fix_colvars.h | 5 ++-- src/USER-COLVARS/group_ndx.cpp | 3 +- src/USER-COLVARS/ndx_group.cpp | 4 +-- 6 files changed, 36 insertions(+), 53 deletions(-) diff --git a/src/USER-COLVARS/colvarproxy_lammps.cpp b/src/USER-COLVARS/colvarproxy_lammps.cpp index 685c698ab6..2c43a3fb26 100644 --- a/src/USER-COLVARS/colvarproxy_lammps.cpp +++ b/src/USER-COLVARS/colvarproxy_lammps.cpp @@ -10,30 +10,19 @@ #include "colvarproxy_lammps.h" #include -#include #include -#include - #include -#include #include - #include -#include +#include #include #include "lammps.h" -#include "atom.h" #include "error.h" #include "output.h" #include "random_park.h" -#include "fix_colvars.h" - #include "colvarmodule.h" -#include "colvar.h" -#include "colvarbias.h" -#include "colvaratoms.h" #include "colvarproxy.h" #define HASH_FAIL -1 diff --git a/src/USER-COLVARS/colvarproxy_lammps.h b/src/USER-COLVARS/colvarproxy_lammps.h index 3243a14fbd..8ed03309a3 100644 --- a/src/USER-COLVARS/colvarproxy_lammps.h +++ b/src/USER-COLVARS/colvarproxy_lammps.h @@ -10,39 +10,22 @@ #ifndef COLVARPROXY_LAMMPS_H #define COLVARPROXY_LAMMPS_H -#include "colvarproxy_lammps_version.h" - -#include "colvarmodule.h" -#include "colvarproxy.h" -#include "colvarvalue.h" - -#include "lammps.h" -#include "domain.h" -#include "force.h" -#include "update.h" +#include "colvarproxy_lammps_version.h" // IWYU pragma: export +#include +#include #include #include -#include -/* struct for packed data communication of coordinates and forces. */ -struct commdata { - int tag,type; - double x,y,z,m,q; -}; +#include "colvarmodule.h" +#include "colvarproxy.h" +#include "colvartypes.h" -inline std::ostream & operator<< (std::ostream &out, const commdata &cd) -{ - out << " (" << cd.tag << "/" << cd.type << ": " - << cd.x << ", " << cd.y << ", " << cd.z << ") "; - return out; -} - -// forward declarations -namespace LAMMPS_NS { - class LAMMPS; - class RanPark; -} +#include "random_park.h" +#include "lammps.h" // IWYU pragma: keep +#include "domain.h" // IWYU pragma: keep +#include "force.h" // IWYU pragma: keep +#include "update.h" // IWYU pragma: keep /// \brief Communication between colvars and LAMMPS /// (implementation of \link colvarproxy \endlink) diff --git a/src/USER-COLVARS/fix_colvars.cpp b/src/USER-COLVARS/fix_colvars.cpp index 9331fe7abb..4a57e59fbd 100644 --- a/src/USER-COLVARS/fix_colvars.cpp +++ b/src/USER-COLVARS/fix_colvars.cpp @@ -25,26 +25,28 @@ ------------------------------------------------------------------------- */ #include "fix_colvars.h" -#include -#include +#include #include #include -#include +#include +#include +#include +#include #include "atom.h" #include "comm.h" #include "domain.h" #include "error.h" -#include "group.h" +#include "force.h" #include "memory.h" #include "modify.h" -#include "random_park.h" #include "respa.h" #include "universe.h" #include "update.h" #include "citeme.h" #include "colvarproxy_lammps.h" +#include "colvarmodule.h" static const char colvars_pub[] = "fix colvars command:\n\n" @@ -57,6 +59,19 @@ static const char colvars_pub[] = " note = {doi: 10.1080/00268976.2013.813594}\n" "}\n\n"; +/* struct for packed data communication of coordinates and forces. */ +struct LAMMPS_NS::commdata { + int tag,type; + double x,y,z,m,q; +}; + +inline std::ostream & operator<< (std::ostream &out, const LAMMPS_NS::commdata &cd) +{ + out << " (" << cd.tag << "/" << cd.type << ": " + << cd.x << ", " << cd.y << ", " << cd.z << ") "; + return out; +} + /* re-usable integer hash table code with static linkage. */ /** hash table top level data structure */ diff --git a/src/USER-COLVARS/fix_colvars.h b/src/USER-COLVARS/fix_colvars.h index a0c197fca4..985457e746 100644 --- a/src/USER-COLVARS/fix_colvars.h +++ b/src/USER-COLVARS/fix_colvars.h @@ -34,10 +34,9 @@ FixStyle(colvars,FixColvars) #define LMP_FIX_COLVARS_H #include "fix.h" +#include -// forward declaration class colvarproxy_lammps; -struct commdata; namespace LAMMPS_NS { @@ -64,7 +63,7 @@ class FixColvars : public Fix { virtual void restart(char *); protected: - class colvarproxy_lammps *proxy; // pointer to the colvars proxy class + colvarproxy_lammps *proxy; // pointer to the colvars proxy class char *conf_file; // name of colvars config file char *inp_name; // name/prefix of colvars restart file char *out_name; // prefix string for all output files diff --git a/src/USER-COLVARS/group_ndx.cpp b/src/USER-COLVARS/group_ndx.cpp index 7350712c40..1e37e2de9c 100644 --- a/src/USER-COLVARS/group_ndx.cpp +++ b/src/USER-COLVARS/group_ndx.cpp @@ -17,12 +17,11 @@ ------------------------------------------------------------------------- */ #include "group_ndx.h" -#include +#include #include #include "atom.h" #include "comm.h" #include "group.h" -#include "memory.h" #include "error.h" using namespace LAMMPS_NS; diff --git a/src/USER-COLVARS/ndx_group.cpp b/src/USER-COLVARS/ndx_group.cpp index 5436ba7b6b..a1369df2fb 100644 --- a/src/USER-COLVARS/ndx_group.cpp +++ b/src/USER-COLVARS/ndx_group.cpp @@ -17,14 +17,12 @@ ------------------------------------------------------------------------- */ #include "ndx_group.h" -#include +#include #include #include #include "atom.h" #include "comm.h" #include "group.h" -#include "memory.h" -#include "force.h" #include "error.h" using namespace LAMMPS_NS; -- GitLab From b4cf4b1ed7d976dba74536659bd59c1887f1f546 Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Thu, 4 Jul 2019 06:51:52 -0400 Subject: [PATCH 180/469] recover compilation of KOKKOS package --- src/KOKKOS/pair_dpd_fdt_energy_kokkos.cpp | 1 + 1 file changed, 1 insertion(+) diff --git a/src/KOKKOS/pair_dpd_fdt_energy_kokkos.cpp b/src/KOKKOS/pair_dpd_fdt_energy_kokkos.cpp index 7a2fca47a0..27a7a59c2a 100644 --- a/src/KOKKOS/pair_dpd_fdt_energy_kokkos.cpp +++ b/src/KOKKOS/pair_dpd_fdt_energy_kokkos.cpp @@ -20,6 +20,7 @@ #include #include #include +#include "atom_kokkos.h" #include "atom_vec.h" #include "comm.h" #include "update.h" -- GitLab From ce6fa0118ab69fd09fa19410f6bbfec3608f0f73 Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Thu, 4 Jul 2019 07:23:01 -0400 Subject: [PATCH 181/469] continuing to clean up include file lists --- src/pair_lj_cut_coul_wolf.cpp | 7 +------ src/pair_lj_expand.cpp | 3 +-- src/pair_lj_gromacs.cpp | 5 +---- src/pair_lj_gromacs_coul_gromacs.cpp | 4 +--- src/pair_lj_smooth.cpp | 3 +-- src/pair_lj_smooth_linear.cpp | 3 +-- src/pair_mie_cut.cpp | 4 +--- src/pair_morse.cpp | 3 +-- src/pair_soft.cpp | 4 +--- src/pair_table.cpp | 1 + src/pair_ufm.cpp | 10 +--------- src/pair_yukawa.cpp | 2 +- src/pair_zbl.cpp | 10 ---------- src/pair_zero.cpp | 4 +--- src/procmap.cpp | 8 +++++--- src/rcb.cpp | 1 - src/read_data.cpp | 4 ---- src/read_dump.cpp | 8 +------- src/read_restart.cpp | 2 -- src/reader.cpp | 1 - src/reader_xyz.cpp | 2 -- src/region.cpp | 1 - src/region_block.cpp | 1 - src/region_cone.cpp | 1 - src/region_cylinder.cpp | 1 - src/region_intersect.cpp | 1 - src/region_plane.cpp | 2 -- src/region_prism.cpp | 2 -- src/region_sphere.cpp | 1 - src/region_union.cpp | 1 - src/replicate.cpp | 3 +-- src/rerun.cpp | 1 - src/reset_ids.cpp | 1 + src/respa.cpp | 4 +--- src/run.cpp | 1 - src/set.cpp | 4 +--- src/special.cpp | 2 -- src/thermo.cpp | 5 ----- src/thermo.h | 3 --- 39 files changed, 23 insertions(+), 101 deletions(-) diff --git a/src/pair_lj_cut_coul_wolf.cpp b/src/pair_lj_cut_coul_wolf.cpp index fb641f7d24..00a5832529 100644 --- a/src/pair_lj_cut_coul_wolf.cpp +++ b/src/pair_lj_cut_coul_wolf.cpp @@ -16,18 +16,13 @@ ------------------------------------------------------------------------- */ #include "pair_lj_cut_coul_wolf.h" +#include #include -#include -#include -#include #include "atom.h" #include "comm.h" #include "force.h" #include "neighbor.h" #include "neigh_list.h" -#include "neigh_request.h" -#include "update.h" -#include "integrate.h" #include "math_const.h" #include "memory.h" #include "error.h" diff --git a/src/pair_lj_expand.cpp b/src/pair_lj_expand.cpp index 60593fd01d..a5184bc2f5 100644 --- a/src/pair_lj_expand.cpp +++ b/src/pair_lj_expand.cpp @@ -12,9 +12,8 @@ ------------------------------------------------------------------------- */ #include "pair_lj_expand.h" +#include #include -#include -#include #include #include "atom.h" #include "comm.h" diff --git a/src/pair_lj_gromacs.cpp b/src/pair_lj_gromacs.cpp index 4796c288d7..baef482ef9 100644 --- a/src/pair_lj_gromacs.cpp +++ b/src/pair_lj_gromacs.cpp @@ -16,14 +16,11 @@ ------------------------------------------------------------------------- */ #include "pair_lj_gromacs.h" +#include #include -#include -#include -#include #include "atom.h" #include "comm.h" #include "force.h" -#include "neighbor.h" #include "neigh_list.h" #include "memory.h" #include "error.h" diff --git a/src/pair_lj_gromacs_coul_gromacs.cpp b/src/pair_lj_gromacs_coul_gromacs.cpp index 45beeb1daf..c62944b6a1 100644 --- a/src/pair_lj_gromacs_coul_gromacs.cpp +++ b/src/pair_lj_gromacs_coul_gromacs.cpp @@ -16,10 +16,8 @@ ------------------------------------------------------------------------- */ #include "pair_lj_gromacs_coul_gromacs.h" +#include #include -#include -#include -#include #include "atom.h" #include "comm.h" #include "force.h" diff --git a/src/pair_lj_smooth.cpp b/src/pair_lj_smooth.cpp index d89fee1148..7c7eb51b53 100644 --- a/src/pair_lj_smooth.cpp +++ b/src/pair_lj_smooth.cpp @@ -16,9 +16,8 @@ ------------------------------------------------------------------------- */ #include "pair_lj_smooth.h" +#include #include -#include -#include #include "atom.h" #include "comm.h" #include "force.h" diff --git a/src/pair_lj_smooth_linear.cpp b/src/pair_lj_smooth_linear.cpp index 6ed19a452f..a3e4aed2fe 100644 --- a/src/pair_lj_smooth_linear.cpp +++ b/src/pair_lj_smooth_linear.cpp @@ -16,9 +16,8 @@ ------------------------------------------------------------------------- */ #include "pair_lj_smooth_linear.h" +#include #include -#include -#include #include "atom.h" #include "comm.h" #include "force.h" diff --git a/src/pair_mie_cut.cpp b/src/pair_mie_cut.cpp index d2b0c20cd5..46657687f6 100644 --- a/src/pair_mie_cut.cpp +++ b/src/pair_mie_cut.cpp @@ -16,9 +16,8 @@ ------------------------------------------------------------------------- */ #include "pair_mie_cut.h" +#include #include -#include -#include #include #include "atom.h" #include "comm.h" @@ -27,7 +26,6 @@ #include "neigh_list.h" #include "neigh_request.h" #include "update.h" -#include "integrate.h" #include "respa.h" #include "math_const.h" #include "memory.h" diff --git a/src/pair_morse.cpp b/src/pair_morse.cpp index 47102932db..d088f98bf4 100644 --- a/src/pair_morse.cpp +++ b/src/pair_morse.cpp @@ -12,9 +12,8 @@ ------------------------------------------------------------------------- */ #include "pair_morse.h" +#include #include -#include -#include #include #include "atom.h" #include "comm.h" diff --git a/src/pair_soft.cpp b/src/pair_soft.cpp index f3d7423b04..6f821e684b 100644 --- a/src/pair_soft.cpp +++ b/src/pair_soft.cpp @@ -12,14 +12,12 @@ ------------------------------------------------------------------------- */ #include "pair_soft.h" +#include #include -#include -#include #include #include "atom.h" #include "comm.h" #include "force.h" -#include "update.h" #include "neigh_list.h" #include "math_const.h" #include "memory.h" diff --git a/src/pair_table.cpp b/src/pair_table.cpp index 63cda78c67..9fcbc3ee9f 100644 --- a/src/pair_table.cpp +++ b/src/pair_table.cpp @@ -20,6 +20,7 @@ #include #include #include +#include #include "atom.h" #include "force.h" #include "comm.h" diff --git a/src/pair_ufm.cpp b/src/pair_ufm.cpp index 40b72136ff..8cc4d2796f 100644 --- a/src/pair_ufm.cpp +++ b/src/pair_ufm.cpp @@ -18,25 +18,17 @@ ------------------------------------------------------------------------- */ #include "pair_ufm.h" +#include #include -#include -#include #include #include "atom.h" #include "comm.h" #include "force.h" -#include "neighbor.h" #include "neigh_list.h" -#include "neigh_request.h" -#include "update.h" -#include "integrate.h" -#include "respa.h" -#include "math_const.h" #include "memory.h" #include "error.h" using namespace LAMMPS_NS; -using namespace MathConst; /* ---------------------------------------------------------------------- */ diff --git a/src/pair_yukawa.cpp b/src/pair_yukawa.cpp index 4a2cf23952..e8775c9668 100644 --- a/src/pair_yukawa.cpp +++ b/src/pair_yukawa.cpp @@ -12,8 +12,8 @@ ------------------------------------------------------------------------- */ #include "pair_yukawa.h" +#include #include -#include #include "atom.h" #include "force.h" #include "comm.h" diff --git a/src/pair_zbl.cpp b/src/pair_zbl.cpp index b01c301785..199e4f0907 100644 --- a/src/pair_zbl.cpp +++ b/src/pair_zbl.cpp @@ -17,19 +17,10 @@ #include "pair_zbl.h" #include -#include -#include -#include #include "atom.h" -#include "comm.h" #include "force.h" #include "neighbor.h" #include "neigh_list.h" -#include "neigh_request.h" -#include "update.h" -#include "integrate.h" -#include "respa.h" -#include "math_const.h" #include "memory.h" #include "error.h" @@ -37,7 +28,6 @@ // "The Stopping and Range of Ions in Matter" volume 1, Pergamon, 1985. using namespace LAMMPS_NS; -using namespace MathConst; using namespace PairZBLConstants; /* ---------------------------------------------------------------------- */ diff --git a/src/pair_zero.cpp b/src/pair_zero.cpp index 2692710e20..403bd73944 100644 --- a/src/pair_zero.cpp +++ b/src/pair_zero.cpp @@ -16,9 +16,7 @@ ------------------------------------------------------------------------- */ #include "pair_zero.h" -#include -#include -#include +#include #include #include "atom.h" #include "comm.h" diff --git a/src/procmap.cpp b/src/procmap.cpp index 47afb76da9..69585aa453 100644 --- a/src/procmap.cpp +++ b/src/procmap.cpp @@ -16,7 +16,12 @@ ------------------------------------------------------------------------- */ #include "procmap.h" +#include +#include #include +#include +#include +#include #include "universe.h" #include "comm.h" #include "domain.h" @@ -24,9 +29,6 @@ #include "memory.h" #include "error.h" -#include -#include - using namespace LAMMPS_NS; #define MAXLINE 128 diff --git a/src/rcb.cpp b/src/rcb.cpp index b19beae3c5..f1a6377046 100644 --- a/src/rcb.cpp +++ b/src/rcb.cpp @@ -16,7 +16,6 @@ #include #include "irregular.h" #include "memory.h" -#include "error.h" using namespace LAMMPS_NS; diff --git a/src/read_data.cpp b/src/read_data.cpp index a50d41b498..dad48110f7 100644 --- a/src/read_data.cpp +++ b/src/read_data.cpp @@ -16,18 +16,14 @@ // before lmptype.h can set flags to insure it is done correctly #include "read_data.h" -#include "lmptype.h" #include -#include #include -#include #include #include "atom.h" #include "atom_vec.h" #include "atom_vec_ellipsoid.h" #include "atom_vec_line.h" #include "atom_vec_tri.h" -#include "force.h" #include "molecule.h" #include "group.h" #include "comm.h" diff --git a/src/read_dump.cpp b/src/read_dump.cpp index 49f96db680..d83a96f0fa 100644 --- a/src/read_dump.cpp +++ b/src/read_dump.cpp @@ -20,24 +20,18 @@ // before lmptype.h can set flags to insure it is done correctly #include "read_dump.h" -#include "lmptype.h" #include #include -#include +#include #include "reader.h" #include "style_reader.h" #include "atom.h" #include "atom_vec.h" #include "update.h" -#include "modify.h" -#include "fix.h" -#include "compute.h" #include "domain.h" #include "comm.h" #include "force.h" #include "irregular.h" -#include "input.h" -#include "variable.h" #include "error.h" #include "memory.h" #include "utils.h" diff --git a/src/read_restart.cpp b/src/read_restart.cpp index 17b313bfa2..3d2e2b6592 100644 --- a/src/read_restart.cpp +++ b/src/read_restart.cpp @@ -14,7 +14,6 @@ #include "read_restart.h" #include #include -#include #include #include "atom.h" #include "atom_vec.h" @@ -23,7 +22,6 @@ #include "irregular.h" #include "update.h" #include "modify.h" -#include "fix.h" #include "fix_read_restart.h" #include "group.h" #include "force.h" diff --git a/src/reader.cpp b/src/reader.cpp index a1fe51f662..b2751662e2 100644 --- a/src/reader.cpp +++ b/src/reader.cpp @@ -12,7 +12,6 @@ ------------------------------------------------------------------------- */ #include "reader.h" -#include #include #include "error.h" diff --git a/src/reader_xyz.cpp b/src/reader_xyz.cpp index fa553dc30f..81aaba77bc 100644 --- a/src/reader_xyz.cpp +++ b/src/reader_xyz.cpp @@ -16,9 +16,7 @@ ------------------------------------------------------------------------- */ #include "reader_xyz.h" -#include #include -#include "atom.h" #include "memory.h" #include "error.h" #include "force.h" diff --git a/src/region.cpp b/src/region.cpp index 0c4bec16e0..7a676de1af 100644 --- a/src/region.cpp +++ b/src/region.cpp @@ -13,7 +13,6 @@ #include "region.h" #include -#include #include #include "update.h" #include "domain.h" diff --git a/src/region_block.cpp b/src/region_block.cpp index bc52fcd7cf..8ea8b3f202 100644 --- a/src/region_block.cpp +++ b/src/region_block.cpp @@ -12,7 +12,6 @@ ------------------------------------------------------------------------- */ #include "region_block.h" -#include #include #include "force.h" #include "domain.h" diff --git a/src/region_cone.cpp b/src/region_cone.cpp index 345c9fa8e2..3c7d0a29d8 100644 --- a/src/region_cone.cpp +++ b/src/region_cone.cpp @@ -17,7 +17,6 @@ #include "region_cone.h" #include -#include #include #include "domain.h" #include "error.h" diff --git a/src/region_cylinder.cpp b/src/region_cylinder.cpp index 968453cf37..b2c06270d0 100644 --- a/src/region_cylinder.cpp +++ b/src/region_cylinder.cpp @@ -13,7 +13,6 @@ #include "region_cylinder.h" #include -#include #include #include "update.h" #include "domain.h" diff --git a/src/region_intersect.cpp b/src/region_intersect.cpp index c6c11cf35c..fe074a6b4c 100644 --- a/src/region_intersect.cpp +++ b/src/region_intersect.cpp @@ -12,7 +12,6 @@ ------------------------------------------------------------------------- */ #include "region_intersect.h" -#include #include #include "domain.h" #include "error.h" diff --git a/src/region_plane.cpp b/src/region_plane.cpp index 950c0a4b53..85671357ef 100644 --- a/src/region_plane.cpp +++ b/src/region_plane.cpp @@ -13,8 +13,6 @@ #include "region_plane.h" #include -#include -#include #include "error.h" #include "force.h" diff --git a/src/region_prism.cpp b/src/region_prism.cpp index 38fc23da21..b6c54c2fb9 100644 --- a/src/region_prism.cpp +++ b/src/region_prism.cpp @@ -16,8 +16,6 @@ ------------------------------------------------------------------------- */ #include "region_prism.h" -#include -#include #include #include "domain.h" #include "force.h" diff --git a/src/region_sphere.cpp b/src/region_sphere.cpp index 9c478960e3..bf874ad311 100644 --- a/src/region_sphere.cpp +++ b/src/region_sphere.cpp @@ -13,7 +13,6 @@ #include "region_sphere.h" #include -#include #include #include "update.h" #include "input.h" diff --git a/src/region_union.cpp b/src/region_union.cpp index f4e30f5b94..be1fe6eeff 100644 --- a/src/region_union.cpp +++ b/src/region_union.cpp @@ -12,7 +12,6 @@ ------------------------------------------------------------------------- */ #include "region_union.h" -#include #include #include "domain.h" #include "error.h" diff --git a/src/replicate.cpp b/src/replicate.cpp index 6f8c94238a..1617ab0313 100644 --- a/src/replicate.cpp +++ b/src/replicate.cpp @@ -12,11 +12,10 @@ ------------------------------------------------------------------------- */ #include "replicate.h" -#include +#include #include #include "atom.h" #include "atom_vec.h" -#include "atom_vec_hybrid.h" #include "force.h" #include "domain.h" #include "comm.h" diff --git a/src/rerun.cpp b/src/rerun.cpp index e75779ccc0..3cd1c53628 100644 --- a/src/rerun.cpp +++ b/src/rerun.cpp @@ -12,7 +12,6 @@ ------------------------------------------------------------------------- */ #include "rerun.h" -#include #include #include "read_dump.h" #include "domain.h" diff --git a/src/reset_ids.cpp b/src/reset_ids.cpp index b68b7ca797..857738e841 100644 --- a/src/reset_ids.cpp +++ b/src/reset_ids.cpp @@ -12,6 +12,7 @@ ------------------------------------------------------------------------- */ #include "reset_ids.h" +#include #include "atom.h" #include "atom_vec.h" #include "domain.h" diff --git a/src/respa.cpp b/src/respa.cpp index 867662b3c2..a184756335 100644 --- a/src/respa.cpp +++ b/src/respa.cpp @@ -16,13 +16,13 @@ ------------------------------------------------------------------------- */ #include "respa.h" -#include #include #include "neighbor.h" #include "atom.h" #include "atom_vec.h" #include "domain.h" #include "comm.h" +#include "fix.h" #include "force.h" #include "pair.h" #include "bond.h" @@ -33,10 +33,8 @@ #include "output.h" #include "update.h" #include "modify.h" -#include "compute.h" #include "fix_respa.h" #include "timer.h" -#include "memory.h" #include "error.h" #include "utils.h" #include "pair_hybrid.h" diff --git a/src/run.cpp b/src/run.cpp index 60861ad3b9..2c2f00a7a8 100644 --- a/src/run.cpp +++ b/src/run.cpp @@ -12,7 +12,6 @@ ------------------------------------------------------------------------- */ #include "run.h" -#include #include #include "domain.h" #include "update.h" diff --git a/src/set.cpp b/src/set.cpp index d34aa7753a..3bf00063c5 100644 --- a/src/set.cpp +++ b/src/set.cpp @@ -14,8 +14,8 @@ #include "set.h" #include #include -#include #include +#include #include "atom.h" #include "atom_vec.h" #include "atom_vec_ellipsoid.h" @@ -26,9 +26,7 @@ #include "region.h" #include "group.h" #include "comm.h" -#include "neighbor.h" #include "force.h" -#include "pair.h" #include "input.h" #include "variable.h" #include "random_park.h" diff --git a/src/special.cpp b/src/special.cpp index f8661e238c..b64aa96e2b 100644 --- a/src/special.cpp +++ b/src/special.cpp @@ -13,7 +13,6 @@ #include "special.h" #include -#include #include "atom.h" #include "atom_vec.h" #include "force.h" @@ -23,7 +22,6 @@ #include "accelerator_kokkos.h" #include "atom_masks.h" #include "memory.h" -#include "error.h" using namespace LAMMPS_NS; diff --git a/src/thermo.cpp b/src/thermo.cpp index d267ea260c..be725d907b 100644 --- a/src/thermo.cpp +++ b/src/thermo.cpp @@ -16,10 +16,8 @@ // before lmptype.h can set flags to insure it is done correctly #include "thermo.h" -#include "lmptype.h" #include #include -#include #include #include "atom.h" #include "update.h" @@ -43,11 +41,8 @@ #include "kspace.h" #include "output.h" #include "timer.h" -#include "math_const.h" #include "memory.h" #include "error.h" -#include "universe.h" - #include "math_const.h" using namespace LAMMPS_NS; diff --git a/src/thermo.h b/src/thermo.h index 8c32f24d3c..f2384e0ac3 100644 --- a/src/thermo.h +++ b/src/thermo.h @@ -18,9 +18,6 @@ namespace LAMMPS_NS { -class DumpNetCDF; -class DumpNetCDFMPIIO; - class Thermo : protected Pointers { friend class MinCG; // accesses compute_pe friend class DumpNetCDF; // accesses thermo properties -- GitLab From 2f72b9f1203e6506da83aabfad7d9de6b9d56250 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Sebastian=20H=C3=BCtter?= Date: Thu, 28 Mar 2019 16:13:02 +0100 Subject: [PATCH 182/469] Factor out embedding function, make sure documented logic for emb_lin_neg is obeyed --- src/USER-MEAMC/meam.h | 1 + src/USER-MEAMC/meam_dens_final.cpp | 37 +++++++----------------------- src/USER-MEAMC/meam_funcs.cpp | 22 ++++++++++++++++++ src/USER-MEAMC/meam_setup_done.cpp | 22 ++++-------------- 4 files changed, 36 insertions(+), 46 deletions(-) diff --git a/src/USER-MEAMC/meam.h b/src/USER-MEAMC/meam.h index 42fd722e01..7ca849c983 100644 --- a/src/USER-MEAMC/meam.h +++ b/src/USER-MEAMC/meam.h @@ -187,6 +187,7 @@ protected: double G_gam(const double gamma, const int ibar, int &errorflag) const; double dG_gam(const double gamma, const int ibar, double &dG) const; static double zbl(const double r, const int z1, const int z2); + double embedding(const double A, const double Ec, const double rhobar, double& dF) const; static double erose(const double r, const double re, const double alpha, const double Ec, const double repuls, const double attrac, const int form); static void get_shpfcn(const lattice_t latt, double (&s)[3]); diff --git a/src/USER-MEAMC/meam_dens_final.cpp b/src/USER-MEAMC/meam_dens_final.cpp index 2be215c282..b7d191d812 100644 --- a/src/USER-MEAMC/meam_dens_final.cpp +++ b/src/USER-MEAMC/meam_dens_final.cpp @@ -10,7 +10,7 @@ MEAM::meam_dens_final(int nlocal, int eflag_either, int eflag_global, int eflag_ int i, elti; int m; double rhob, G, dG, Gbar, dGbar, gam, shp[3], Z; - double B, denom, rho_bkgd; + double denom, rho_bkgd, Fl; // Complete the calculation of density @@ -111,35 +111,14 @@ MEAM::meam_dens_final(int nlocal, int eflag_either, int eflag_global, int eflag_ dgamma3[i] = 0.0; } - B = this->A_meam[elti] * this->Ec_meam[elti][elti]; - - if (!iszero(rhob)) { - if (this->emb_lin_neg == 1 && rhob <= 0) { - frhop[i] = -B; - } else { - frhop[i] = B * (log(rhob) + 1.0); - } - if (eflag_either != 0) { - if (eflag_global != 0) { - if (this->emb_lin_neg == 1 && rhob <= 0) { - *eng_vdwl = *eng_vdwl - B * rhob; - } else { - *eng_vdwl = *eng_vdwl + B * rhob * log(rhob); - } - } - if (eflag_atom != 0) { - if (this->emb_lin_neg == 1 && rhob <= 0) { - eatom[i] = eatom[i] - B * rhob; - } else { - eatom[i] = eatom[i] + B * rhob * log(rhob); - } - } + Fl = embedding(this->A_meam[elti], this->Ec_meam[elti][elti], rhob, frhop[i]); + + if (eflag_either != 0) { + if (eflag_global != 0) { + *eng_vdwl = *eng_vdwl + Fl; } - } else { - if (this->emb_lin_neg == 1) { - frhop[i] = -B; - } else { - frhop[i] = B; + if (eflag_atom != 0) { + eatom[i] = eatom[i] + Fl; } } } diff --git a/src/USER-MEAMC/meam_funcs.cpp b/src/USER-MEAMC/meam_funcs.cpp index 1d47dcc1f6..50cabd101c 100644 --- a/src/USER-MEAMC/meam_funcs.cpp +++ b/src/USER-MEAMC/meam_funcs.cpp @@ -143,6 +143,28 @@ MEAM::zbl(const double r, const int z1, const int z2) return result; } +//----------------------------------------------------------------------------- +// Compute embedding function F(rhobar) and derivative F'(rhobar), eqn I.5 +// +double +MEAM::embedding(const double A, const double Ec, const double rhobar, double& dF) const +{ + const double AEc = A * Ec; + + if (rhobar > 0.0) { + dF = AEc * (1.0 + log(rhobar)); + return AEc * rhobar * log(rhobar); + } else { + if (this->emb_lin_neg == 0) { + dF = 0.0; + return 0.0; + } else { + dF = - AEc; + return - AEc * rhobar; + } + } +} + //----------------------------------------------------------------------------- // Compute Rose energy function, I.16 // diff --git a/src/USER-MEAMC/meam_setup_done.cpp b/src/USER-MEAMC/meam_setup_done.cpp index e18a391378..3cd9510cf3 100644 --- a/src/USER-MEAMC/meam_setup_done.cpp +++ b/src/USER-MEAMC/meam_setup_done.cpp @@ -319,7 +319,7 @@ MEAM::phi_meam(double r, int a, int b) double t11av, t21av, t31av, t12av, t22av, t32av; double G1, G2, s1[3], s2[3], rho0_1, rho0_2; double Gam1, Gam2, Z1, Z2; - double rhobar1, rhobar2, F1, F2; + double rhobar1, rhobar2, F1, F2, dF; double rho01, rho11, rho21, rho31; double rho02, rho12, rho22, rho32; double scalfac, phiaa, phibb; @@ -447,22 +447,10 @@ MEAM::phi_meam(double r, int a, int b) } // compute embedding functions, eqn I.5 - if (iszero(rhobar1)) - F1 = 0.0; - else { - if (this->emb_lin_neg == 1 && rhobar1 <= 0) - F1 = -this->A_meam[a] * this->Ec_meam[a][a] * rhobar1; - else - F1 = this->A_meam[a] * this->Ec_meam[a][a] * rhobar1 * log(rhobar1); - } - if (iszero(rhobar2)) - F2 = 0.0; - else { - if (this->emb_lin_neg == 1 && rhobar2 <= 0) - F2 = -this->A_meam[b] * this->Ec_meam[b][b] * rhobar2; - else - F2 = this->A_meam[b] * this->Ec_meam[b][b] * rhobar2 * log(rhobar2); - } + + F1 = embedding(this->A_meam[a], this->Ec_meam[a][a], rhobar1, dF); + F2 = embedding(this->A_meam[b], this->Ec_meam[b][b], rhobar2, dF); + // compute Rose function, I.16 Eu = erose(r, this->re_meam[a][b], this->alpha_meam[a][b], this->Ec_meam[a][b], this->repuls_meam[a][b], -- GitLab From 8dcb42d49c738f96d5feb3b8f3e559e114886183 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Sebastian=20H=C3=BCtter?= Date: Thu, 28 Mar 2019 16:19:29 +0100 Subject: [PATCH 183/469] Check MEAM parameters for t0=1.0, mention this fact in documentation --- doc/src/pair_meamc.txt | 3 ++- src/USER-MEAMC/pair_meamc.cpp | 3 +++ 2 files changed, 5 insertions(+), 1 deletion(-) diff --git a/doc/src/pair_meamc.txt b/doc/src/pair_meamc.txt index 80f69b1a46..7c42e9d2f2 100644 --- a/doc/src/pair_meamc.txt +++ b/doc/src/pair_meamc.txt @@ -147,7 +147,8 @@ asub = "A" parameter for MEAM (see e.g. "(Baskes)"_#Baskes) :pre The alpha, b0, b1, b2, b3, t0, t1, t2, t3 parameters correspond to the standard MEAM parameters in the literature "(Baskes)"_#Baskes (the b -parameters are the standard beta parameters). The rozero parameter is +parameters are the standard beta parameters). Note that only parameters +normalized to t0 = 1.0 are supported. The rozero parameter is an element-dependent density scaling that weights the reference background density (see e.g. equation 4.5 in "(Gullet)"_#Gullet) and is typically 1.0 for single-element systems. The ibar parameter diff --git a/src/USER-MEAMC/pair_meamc.cpp b/src/USER-MEAMC/pair_meamc.cpp index a70fb77aae..7c96fadb44 100644 --- a/src/USER-MEAMC/pair_meamc.cpp +++ b/src/USER-MEAMC/pair_meamc.cpp @@ -460,6 +460,9 @@ void PairMEAMC::read_files(char *globalfile, char *userfile) rozero[i] = atof(words[17]); ibar[i] = atoi(words[18]); + if (!iszero(t0[i]-1.0)) + error->all(FLERR,"Unsupported parameter in MEAM potential file"); + nset++; } -- GitLab From 0d4bb8618325021a263f8705b3a8dcd4a443eee2 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Sebastian=20H=C3=BCtter?= Date: Wed, 10 Apr 2019 17:12:19 +0200 Subject: [PATCH 184/469] MEAM/C: code commenting --- src/USER-MEAMC/meam.h | 6 ++++-- 1 file changed, 4 insertions(+), 2 deletions(-) diff --git a/src/USER-MEAMC/meam.h b/src/USER-MEAMC/meam.h index 7ca849c983..ff9027dfb3 100644 --- a/src/USER-MEAMC/meam.h +++ b/src/USER-MEAMC/meam.h @@ -93,8 +93,9 @@ private: int augt1, ialloy, mix_ref_t, erose_form; int emb_lin_neg, bkgd_dyn; double gsmooth_factor; - int vind2D[3][3], vind3D[3][3][3]; - int v2D[6], v3D[10]; + + int vind2D[3][3], vind3D[3][3][3]; // x-y-z to Voigt-like index + int v2D[6], v3D[10]; // multiplicity of Voigt index (i.e. [1] -> xy+yx = 2 int nr, nrar; double dr, rdrar; @@ -121,6 +122,7 @@ protected: else if (xi <= 0.0) return 0.0; else { + // ( 1.d0 - (1.d0 - xi)**4 )**2, but with better codegen a = 1.0 - xi; a *= a; a *= a; a = 1.0 - a; -- GitLab From 7efb42f0d3926b5e25c29239f1422e8a1a632673 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Sebastian=20H=C3=BCtter?= Date: Mon, 13 May 2019 10:43:21 +0200 Subject: [PATCH 185/469] MEAM/C: code optimization for faster codegen --- src/USER-MEAMC/meam_dens_final.cpp | 2 +- src/USER-MEAMC/meam_dens_init.cpp | 158 ++++++++++++++--------------- src/USER-MEAMC/meam_funcs.cpp | 7 +- src/USER-MEAMC/meam_setup_done.cpp | 2 +- 4 files changed, 85 insertions(+), 84 deletions(-) diff --git a/src/USER-MEAMC/meam_dens_final.cpp b/src/USER-MEAMC/meam_dens_final.cpp index b7d191d812..c55b1b45c4 100644 --- a/src/USER-MEAMC/meam_dens_final.cpp +++ b/src/USER-MEAMC/meam_dens_final.cpp @@ -112,7 +112,7 @@ MEAM::meam_dens_final(int nlocal, int eflag_either, int eflag_global, int eflag_ } Fl = embedding(this->A_meam[elti], this->Ec_meam[elti][elti], rhob, frhop[i]); - + if (eflag_either != 0) { if (eflag_global != 0) { *eng_vdwl = *eng_vdwl + Fl; diff --git a/src/USER-MEAMC/meam_dens_init.cpp b/src/USER-MEAMC/meam_dens_init.cpp index 0aa71125c8..3bb9328142 100644 --- a/src/USER-MEAMC/meam_dens_init.cpp +++ b/src/USER-MEAMC/meam_dens_init.cpp @@ -127,72 +127,20 @@ MEAM::getscreen(int i, double* scrfcn, double* dscrfcn, double* fcpair, double** delyij = yjtmp - yitmp; delzij = zjtmp - zitmp; rij2 = delxij * delxij + delyij * delyij + delzij * delzij; - rij = sqrt(rij2); - const double rbound = this->ebound_meam[elti][eltj] * rij2; - if (rij > this->rc_meam) { - fcij = 0.0; - dfcij = 0.0; - sij = 0.0; - } else { - rnorm = (this->rc_meam - rij) * drinv; - sij = 1.0; - - // if rjk2 > ebound*rijsq, atom k is definitely outside the ellipse - for (kn = 0; kn < numneigh_full; kn++) { - k = firstneigh_full[kn]; - eltk = fmap[type[k]]; - if (eltk < 0) continue; - if (k == j) continue; - - delxjk = x[k][0] - xjtmp; - delyjk = x[k][1] - yjtmp; - delzjk = x[k][2] - zjtmp; - rjk2 = delxjk * delxjk + delyjk * delyjk + delzjk * delzjk; - if (rjk2 > rbound) continue; - - delxik = x[k][0] - xitmp; - delyik = x[k][1] - yitmp; - delzik = x[k][2] - zitmp; - rik2 = delxik * delxik + delyik * delyik + delzik * delzik; - if (rik2 > rbound) continue; - - xik = rik2 / rij2; - xjk = rjk2 / rij2; - a = 1 - (xik - xjk) * (xik - xjk); - // if a < 0, then ellipse equation doesn't describe this case and - // atom k can't possibly screen i-j - if (a <= 0.0) continue; - - cikj = (2.0 * (xik + xjk) + a - 2.0) / a; - Cmax = this->Cmax_meam[elti][eltj][eltk]; - Cmin = this->Cmin_meam[elti][eltj][eltk]; - if (cikj >= Cmax) continue; - // note that cikj may be slightly negative (within numerical - // tolerance) if atoms are colinear, so don't reject that case here - // (other negative cikj cases were handled by the test on "a" above) - else if (cikj <= Cmin) { - sij = 0.0; - break; - } else { - delc = Cmax - Cmin; - cikj = (cikj - Cmin) / delc; - sikj = fcut(cikj); - } - sij *= sikj; - } - - fc = dfcut(rnorm, dfc); - fcij = fc; - dfcij = dfc * drinv; + if (rij2 > this->cutforcesq) { + dscrfcn[jn] = 0.0; + scrfcn[jn] = 0.0; + fcpair[jn] = 0.0; + continue; } - // Now compute derivatives - dscrfcn[jn] = 0.0; - sfcij = sij * fcij; - if (iszero(sfcij) || iszero(sfcij - 1.0)) - goto LABEL_100; + const double rbound = this->ebound_meam[elti][eltj] * rij2; + rij = sqrt(rij2); + rnorm = (this->cutforce - rij) * drinv; + sij = 1.0; + // if rjk2 > ebound*rijsq, atom k is definitely outside the ellipse for (kn = 0; kn < numneigh_full; kn++) { k = firstneigh_full[kn]; if (k == j) continue; @@ -202,6 +150,7 @@ MEAM::getscreen(int i, double* scrfcn, double* dscrfcn, double* fcpair, double** xktmp = x[k][0]; yktmp = x[k][1]; zktmp = x[k][2]; + delxjk = xktmp - xjtmp; delyjk = yktmp - yjtmp; delzjk = zktmp - zjtmp; @@ -224,29 +173,80 @@ MEAM::getscreen(int i, double* scrfcn, double* dscrfcn, double* fcpair, double** cikj = (2.0 * (xik + xjk) + a - 2.0) / a; Cmax = this->Cmax_meam[elti][eltj][eltk]; Cmin = this->Cmin_meam[elti][eltj][eltk]; - if (cikj >= Cmax) { - continue; - // Note that cikj may be slightly negative (within numerical - // tolerance) if atoms are colinear, so don't reject that case - // here - // (other negative cikj cases were handled by the test on "a" - // above) - // Note that we never have 0= Cmax) continue; + // note that cikj may be slightly negative (within numerical + // tolerance) if atoms are colinear, so don't reject that case here + // (other negative cikj cases were handled by the test on "a" above) + else if (cikj <= Cmin) { + sij = 0.0; + break; } else { delc = Cmax - Cmin; cikj = (cikj - Cmin) / delc; - sikj = dfcut(cikj, dfikj); - coef1 = dfikj / (delc * sikj); - dCikj = dCfunc(rij2, rik2, rjk2); - dscrfcn[jn] = dscrfcn[jn] + coef1 * dCikj; + sikj = fcut(cikj); + } + sij *= sikj; + } + + fc = dfcut(rnorm, dfc); + fcij = fc; + dfcij = dfc * drinv; + + // Now compute derivatives + dscrfcn[jn] = 0.0; + sfcij = sij * fcij; + if (!iszero(sfcij) && !iszero(sfcij - 1.0)) { + for (kn = 0; kn < numneigh_full; kn++) { + k = firstneigh_full[kn]; + if (k == j) continue; + eltk = fmap[type[k]]; + if (eltk < 0) continue; + + delxjk = x[k][0] - xjtmp; + delyjk = x[k][1] - yjtmp; + delzjk = x[k][2] - zjtmp; + rjk2 = delxjk * delxjk + delyjk * delyjk + delzjk * delzjk; + if (rjk2 > rbound) continue; + + delxik = x[k][0] - xitmp; + delyik = x[k][1] - yitmp; + delzik = x[k][2] - zitmp; + rik2 = delxik * delxik + delyik * delyik + delzik * delzik; + if (rik2 > rbound) continue; + + xik = rik2 / rij2; + xjk = rjk2 / rij2; + a = 1 - (xik - xjk) * (xik - xjk); + // if a < 0, then ellipse equation doesn't describe this case and + // atom k can't possibly screen i-j + if (a <= 0.0) continue; + + cikj = (2.0 * (xik + xjk) + a - 2.0) / a; + Cmax = this->Cmax_meam[elti][eltj][eltk]; + Cmin = this->Cmin_meam[elti][eltj][eltk]; + if (cikj >= Cmax) { + continue; + // Note that cikj may be slightly negative (within numerical + // tolerance) if atoms are colinear, so don't reject that case + // here + // (other negative cikj cases were handled by the test on "a" + // above) + // Note that we never have 0= 0) { return sqrt(1.0 + gamma); @@ -152,8 +152,9 @@ MEAM::embedding(const double A, const double Ec, const double rhobar, double& dF const double AEc = A * Ec; if (rhobar > 0.0) { - dF = AEc * (1.0 + log(rhobar)); - return AEc * rhobar * log(rhobar); + const double lrb = log(rhobar); + dF = AEc * (1.0 + lrb); + return AEc * rhobar * lrb; } else { if (this->emb_lin_neg == 0) { dF = 0.0; diff --git a/src/USER-MEAMC/meam_setup_done.cpp b/src/USER-MEAMC/meam_setup_done.cpp index 3cd9510cf3..2a762d1204 100644 --- a/src/USER-MEAMC/meam_setup_done.cpp +++ b/src/USER-MEAMC/meam_setup_done.cpp @@ -697,7 +697,7 @@ MEAM::get_densref(double r, int a, int b, double* rho01, double* rho11, double* get_sijk(C, a, a, b, &s112); get_sijk(C, b, b, a, &s221); S11 = s111 * s111 * s112 * s112; - S22 = pow(s221, 4); + S22 = s221 * s221 * s221 * s221; *rho01 = *rho01 + 6 * S11 * rhoa01nn; *rho02 = *rho02 + 6 * S22 * rhoa02nn; -- GitLab From d07a49aeea8a13cb83eb1da6096877d0e6b53ea5 Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Fri, 5 Jul 2019 11:37:21 -0400 Subject: [PATCH 186/469] add missing prototypes --- lib/poems/fastmatrixops.h | 3 +++ 1 file changed, 3 insertions(+) diff --git a/lib/poems/fastmatrixops.h b/lib/poems/fastmatrixops.h index 4c3c1353bd..45573c3eab 100644 --- a/lib/poems/fastmatrixops.h +++ b/lib/poems/fastmatrixops.h @@ -32,6 +32,7 @@ class Vect6; void FastCross(Vect3& a, Vect3& b, Vect3& c); void FastSimpleRotation(Vect3& v, double q, Mat3x3& C); void FastQuaternions(ColMatrix& q, Mat3x3& C); +void FastInvQuaternions(Mat3x3& C, ColMatrix& q); void FastQuaternionDerivatives(ColMatrix& q, ColMatrix& omega, ColMatrix& qdot); void FastLDLT(Matrix& A, Matrix& LD); // C is the LDL^T decomposition of A (SPD) void FastLDLT(Mat6x6& A, Mat6x6& LD); // C is the LDL^T decomposition of A (SPD) @@ -54,6 +55,7 @@ void FastTripleSumPPM(Vect3& a, Vect3& b, Vect3& c, Vect3& d); // d = a+b-c void FastMult(Matrix& A, Matrix& B, Matrix& C); // C = A*B void FastTMult(Matrix& A, Matrix& B, Matrix& C); // C = A^T*B +void FastTMult(Mat3x3& A, Vect3& B, Vect3& C); void FastMult(Mat3x3& A, Vect3& B, Vect3& C); // C = A*B void FastMult(Mat3x3& A, ColMatrix& B, Vect3& C); // C = A*B @@ -90,6 +92,7 @@ void FastAdd(Vect3& A, Vect3& B, Vect3& C); // C = A+B void FastAdd(Vect4& A, Vect4& B, Vect3& C); // C = A+B void FastAdd(Mat6x6& A, Mat6x6& B, Mat6x6& C); // C = A+B void FastAdd(Vect6& A, Vect6& B, Vect6& C); // C = A+B +void FastAdd(Vect4& A, Vect4& B, Vect4& C); void FastSubt(Vect3& A, Vect3& B, Vect3& C); // C = A-B void FastSubt(Vect4& A, Vect4& B, Vect4& C); // C = A-B -- GitLab From 46a9772a6d36504587338602b7adfbb2e50c1fa1 Mon Sep 17 00:00:00 2001 From: Trung Nguyen Date: Fri, 5 Jul 2019 12:12:29 -0500 Subject: [PATCH 187/469] Minor clean-up --- lib/gpu/lal_tersoff.cu | 40 ++++++----------------------------- lib/gpu/lal_tersoff_mod.cu | 37 ++++++-------------------------- lib/gpu/lal_tersoff_zbl.cu | 37 ++++++-------------------------- lib/gpu/lal_yukawa_colloid.cu | 12 +++++------ lib/gpu/lal_zbl.cu | 39 ++++++++++++++-------------------- 5 files changed, 41 insertions(+), 124 deletions(-) diff --git a/lib/gpu/lal_tersoff.cu b/lib/gpu/lal_tersoff.cu index 836f05660d..2e29ca721b 100644 --- a/lib/gpu/lal_tersoff.cu +++ b/lib/gpu/lal_tersoff.cu @@ -308,8 +308,6 @@ __kernel void k_tersoff_zeta(const __global numtyp4 *restrict x_, delr1.z = jx.z-ix.z; numtyp rsq1 = delr1.x*delr1.x+delr1.y*delr1.y+delr1.z*delr1.z; -// if (rsq1 > cutsq[ijparam]) continue; - // compute zeta_ij z = (acctyp)0; @@ -355,13 +353,9 @@ __kernel void k_tersoff_zeta(const __global numtyp4 *restrict x_, rsq1, rsq2, delr1, delr2); } - //int jj = (nbor_j-offset_j-2*nbor_pitch)/n_stride; - //int idx = jj*n_stride + i*t_per_atom + offset_j; - //idx to zetaij is shifted by n_stride relative to nbor_j in dev_short_nbor + // idx to zetaij is shifted by n_stride relative to nbor_j in dev_short_nbor int idx = nbor_j; if (dev_packed==dev_nbor) idx -= n_stride; -// zeta_idx(dev_nbor,dev_packed, nbor_pitch, n_stride, t_per_atom, -// i, nbor_j, offset_j, idx); acc_zeta(z, tid, t_per_atom, offset_k); numtyp4 ts1_ijparam = ts1[ijparam]; //fetch4(ts1_ijparam,ijparam,ts1_tex); @@ -585,14 +579,9 @@ __kernel void k_tersoff_three_center(const __global numtyp4 *restrict x_, numtyp r1inv = ucl_rsqrt(rsq1); // look up for zeta_ij - - //int jj = (nbor_j-offset_j-2*nbor_pitch) / n_stride; - //int idx = jj*n_stride + i*t_per_atom + offset_j; - //idx to zetaij is shifted by n_stride relative to nbor_j in dev_short_nbor + // idx to zetaij is shifted by n_stride relative to nbor_j in dev_short_nbor int idx = nbor_j; if (dev_packed==dev_nbor) idx -= n_stride; -// zeta_idx(dev_nbor,dev_packed, nbor_pitch, n_stride, t_per_atom, -// i, nbor_j, offset_j, idx); acctyp4 zeta_ij = zetaij[idx]; // fetch(zeta_ij,idx,zeta_tex); numtyp force = zeta_ij.x*tpainv; numtyp prefactor = zeta_ij.y; @@ -823,13 +812,9 @@ __kernel void k_tersoff_three_end(const __global numtyp4 *restrict x_, offset_kf = red_acc[2*m+1]; } - //int iix = (ijnum - offset_kf - 2*nbor_pitch) / n_stride; - //int idx = iix*n_stride + j*t_per_atom + offset_kf; - //idx to zetaij is shifted by n_stride relative to ijnum in dev_short_nbor + // idx to zetaij is shifted by n_stride relative to ijnum in dev_short_nbor int idx = ijnum; if (dev_packed==dev_nbor) idx -= n_stride; -// zeta_idx(dev_nbor,dev_packed, nbor_pitch, n_stride, t_per_atom, -// j, ijnum, offset_kf, idx); acctyp4 zeta_ji = zetaij[idx]; // fetch(zeta_ji,idx,zeta_tex); numtyp force = zeta_ji.x*tpainv; numtyp prefactor_ji = zeta_ji.y; @@ -891,13 +876,10 @@ __kernel void k_tersoff_three_end(const __global numtyp4 *restrict x_, f.y += fi[1]; f.z += fi[2]; - //int kk = (nbor_k - offset_k - 2*nbor_pitch) / n_stride; - //int idx = kk*n_stride + j*t_per_atom + offset_k; - //idx to zetaij is shifted by n_stride relative to nbor_k in dev_short_nbor + // idx to zetaij is shifted by n_stride relative to nbor_k in dev_short_nbor int idx = nbor_k; if (dev_packed==dev_nbor) idx -= n_stride; -// zeta_idx(dev_nbor,dev_packed, nbor_pitch, n_stride, t_per_atom, -// j, nbor_k, offset_k, idx); + acctyp4 zeta_jk = zetaij[idx]; // fetch(zeta_jk,idx,zeta_tex); numtyp prefactor_jk = zeta_jk.y; int jkiparam=elem2param[jtype*nelements*nelements+ktype*nelements+itype]; @@ -1068,13 +1050,9 @@ __kernel void k_tersoff_three_end_vatom(const __global numtyp4 *restrict x_, offset_kf = red_acc[2*m+1]; } - //int iix = (ijnum - offset_kf - 2*nbor_pitch) / n_stride; - //int idx = iix*n_stride + j*t_per_atom + offset_kf; - //idx to zetaij is shifted by n_stride relative to ijnum in dev_short_nbor + // idx to zetaij is shifted by n_stride relative to ijnum in dev_short_nbor int idx = ijnum; if (dev_packed==dev_nbor) idx -= n_stride; -// zeta_idx(dev_nbor,dev_packed, nbor_pitch, n_stride, t_per_atom, -// j, ijnum, offset_kf, idx); acctyp4 zeta_ji = zetaij[idx]; // fetch(zeta_ji,idx,zeta_tex); numtyp force = zeta_ji.x*tpainv; numtyp prefactor_ji = zeta_ji.y; @@ -1143,13 +1121,9 @@ __kernel void k_tersoff_three_end_vatom(const __global numtyp4 *restrict x_, virial[4] += TWOTHIRD*(mdelr1[0]*fj[2] + delr2[0]*fk[2]); virial[5] += TWOTHIRD*(mdelr1[1]*fj[2] + delr2[1]*fk[2]); - //int kk = (nbor_k - offset_k - 2*nbor_pitch) / n_stride; - //int idx = kk*n_stride + j*t_per_atom + offset_k; - //idx to zetaij is shifted by n_stride relative to nbor_k in dev_short_nbor + // idx to zetaij is shifted by n_stride relative to nbor_k in dev_short_nbor int idx = nbor_k; if (dev_packed==dev_nbor) idx -= n_stride; -// zeta_idx(dev_nbor,dev_packed, nbor_pitch, n_stride, t_per_atom, -// j, nbor_k, offset_k, idx); acctyp4 zeta_jk = zetaij[idx]; // fetch(zeta_jk,idx,zeta_tex); numtyp prefactor_jk = zeta_jk.y; diff --git a/lib/gpu/lal_tersoff_mod.cu b/lib/gpu/lal_tersoff_mod.cu index dfb94c4145..c85f5e08ca 100644 --- a/lib/gpu/lal_tersoff_mod.cu +++ b/lib/gpu/lal_tersoff_mod.cu @@ -356,13 +356,9 @@ __kernel void k_tersoff_mod_zeta(const __global numtyp4 *restrict x_, ijkparam_c5, rsq1, rsq2, delr1, delr2); } - //int jj = (nbor_j-offset_j-2*nbor_pitch)/n_stride; - //int idx = jj*n_stride + i*t_per_atom + offset_j; - //idx to zetaij is shifted by n_stride relative to nbor_j in dev_short_nbor + // idx to zetaij is shifted by n_stride relative to nbor_j in dev_short_nbor int idx = nbor_j; if (dev_packed==dev_nbor) idx -= n_stride; -// zeta_idx(dev_nbor,dev_packed, nbor_pitch, n_stride, t_per_atom, -// i, nbor_j, offset_j, idx); acc_zeta(z, tid, t_per_atom, offset_k); numtyp4 ts1_ijparam = ts1[ijparam]; //fetch4(ts1_ijparam,ijparam,ts1_tex); @@ -587,14 +583,9 @@ __kernel void k_tersoff_mod_three_center(const __global numtyp4 *restrict x_, numtyp r1inv = ucl_rsqrt(rsq1); // look up for zeta_ij - - //int jj = (nbor_j-offset_j-2*nbor_pitch) / n_stride; - //int idx = jj*n_stride + i*t_per_atom + offset_j; - //idx to zetaij is shifted by n_stride relative to nbor_j in dev_short_nbor + // idx to zetaij is shifted by n_stride relative to nbor_j in dev_short_nbor int idx = nbor_j; if (dev_packed==dev_nbor) idx -= n_stride; -// zeta_idx(dev_nbor,dev_packed, nbor_pitch, n_stride, t_per_atom, -// i, nbor_j, offset_j, idx); acctyp4 zeta_ij = zetaij[idx]; // fetch(zeta_ij,idx,zeta_tex); numtyp force = zeta_ij.x*tpainv; numtyp prefactor = zeta_ij.y; @@ -831,13 +822,9 @@ __kernel void k_tersoff_mod_three_end(const __global numtyp4 *restrict x_, offset_kf = red_acc[2*m+1]; } - //int iix = (ijnum - offset_kf - 2*nbor_pitch) / n_stride; - //int idx = iix*n_stride + j*t_per_atom + offset_kf; - //idx to zetaij is shifted by n_stride relative to ijnum in dev_short_nbor + // idx to zetaij is shifted by n_stride relative to ijnum in dev_short_nbor int idx = ijnum; if (dev_packed==dev_nbor) idx -= n_stride; -// zeta_idx(dev_nbor,dev_packed, nbor_pitch, n_stride, t_per_atom, -// j, ijnum, offset_kf, idx); acctyp4 zeta_ji = zetaij[idx]; // fetch(zeta_ji,idx,zeta_tex); numtyp force = zeta_ji.x*tpainv; numtyp prefactor_ji = zeta_ji.y; @@ -902,13 +889,9 @@ __kernel void k_tersoff_mod_three_end(const __global numtyp4 *restrict x_, f.y += fi[1]; f.z += fi[2]; - //int kk = (nbor_k - offset_k - 2*nbor_pitch) / n_stride; - //int idx = kk*n_stride + j*t_per_atom + offset_k; - //idx to zetaij is shifted by n_stride relative to nbor_k in dev_short_nbor + // idx to zetaij is shifted by n_stride relative to nbor_k in dev_short_nbor int idx = nbor_k; if (dev_packed==dev_nbor) idx -= n_stride; -// zeta_idx(dev_nbor,dev_packed, nbor_pitch, n_stride, t_per_atom, -// j, nbor_k, offset_k, idx); acctyp4 zeta_jk = zetaij[idx]; // fetch(zeta_jk,idx,zeta_tex); numtyp prefactor_jk = zeta_jk.y; int jkiparam=elem2param[jtype*nelements*nelements+ktype*nelements+itype]; @@ -1085,13 +1068,9 @@ __kernel void k_tersoff_mod_three_end_vatom(const __global numtyp4 *restrict x_, offset_kf = red_acc[2*m+1]; } - //int iix = (ijnum - offset_kf - 2*nbor_pitch) / n_stride; - //int idx = iix*n_stride + j*t_per_atom + offset_kf; - //idx to zetaij is shifted by n_stride relative to ijnum in dev_short_nbor + // idx to zetaij is shifted by n_stride relative to ijnum in dev_short_nbor int idx = ijnum; if (dev_packed==dev_nbor) idx -= n_stride; -// zeta_idx(dev_nbor,dev_packed, nbor_pitch, n_stride, t_per_atom, -// j, ijnum, offset_kf, idx); acctyp4 zeta_ji = zetaij[idx]; // fetch(zeta_ji,idx,zeta_tex); numtyp force = zeta_ji.x*tpainv; numtyp prefactor_ji = zeta_ji.y; @@ -1163,13 +1142,9 @@ __kernel void k_tersoff_mod_three_end_vatom(const __global numtyp4 *restrict x_, virial[4] += TWOTHIRD*(mdelr1[0]*fj[2] + delr2[0]*fk[2]); virial[5] += TWOTHIRD*(mdelr1[1]*fj[2] + delr2[1]*fk[2]); - //int kk = (nbor_k - offset_k - 2*nbor_pitch) / n_stride; - //int idx = kk*n_stride + j*t_per_atom + offset_k; - //idx to zetaij is shifted by n_stride relative to nbor_k in dev_short_nbor + // idx to zetaij is shifted by n_stride relative to nbor_k in dev_short_nbor int idx = nbor_k; if (dev_packed==dev_nbor) idx -= n_stride; -// zeta_idx(dev_nbor,dev_packed, nbor_pitch, n_stride, t_per_atom, -// j, nbor_k, offset_k, idx); acctyp4 zeta_jk = zetaij[idx]; // fetch(zeta_jk,idx,zeta_tex); numtyp prefactor_jk = zeta_jk.y; diff --git a/lib/gpu/lal_tersoff_zbl.cu b/lib/gpu/lal_tersoff_zbl.cu index 73ff51c704..b574a529c0 100644 --- a/lib/gpu/lal_tersoff_zbl.cu +++ b/lib/gpu/lal_tersoff_zbl.cu @@ -359,13 +359,9 @@ __kernel void k_tersoff_zbl_zeta(const __global numtyp4 *restrict x_, rsq1, rsq2, delr1, delr2); } - //int jj = (nbor_j-offset_j-2*nbor_pitch)/n_stride; - //int idx = jj*n_stride + i*t_per_atom + offset_j; - //idx to zetaij is shifted by n_stride relative to nbor_j in dev_short_nbor + // idx to zetaij is shifted by n_stride relative to nbor_j in dev_short_nbor int idx = nbor_j; if (dev_packed==dev_nbor) idx -= n_stride; -// zeta_idx(dev_nbor,dev_packed, nbor_pitch, n_stride, t_per_atom, -// i, nbor_j, offset_j, idx); acc_zeta(z, tid, t_per_atom, offset_k); numtyp4 ts1_ijparam = ts1[ijparam]; //fetch4(ts1_ijparam,ijparam,ts1_tex); @@ -603,14 +599,9 @@ __kernel void k_tersoff_zbl_three_center(const __global numtyp4 *restrict x_, numtyp r1inv = ucl_rsqrt(rsq1); // look up for zeta_ij - - //int jj = (nbor_j-offset_j-2*nbor_pitch) / n_stride; - //int idx = jj*n_stride + i*t_per_atom + offset_j; - //idx to zetaij is shifted by n_stride relative to nbor_j in dev_short_nbor + // idx to zetaij is shifted by n_stride relative to nbor_j in dev_short_nbor int idx = nbor_j; if (dev_packed==dev_nbor) idx -= n_stride; -// zeta_idx(dev_nbor,dev_packed, nbor_pitch, n_stride, t_per_atom, -// i, nbor_j, offset_j, idx); acctyp4 zeta_ij = zetaij[idx]; // fetch(zeta_ij,idx,zeta_tex); numtyp force = zeta_ij.x*tpainv; numtyp prefactor = zeta_ij.y; @@ -841,13 +832,9 @@ __kernel void k_tersoff_zbl_three_end(const __global numtyp4 *restrict x_, offset_kf = red_acc[2*m+1]; } - //int iix = (ijnum - offset_kf - 2*nbor_pitch) / n_stride; - //int idx = iix*n_stride + j*t_per_atom + offset_kf; - //idx to zetaij is shifted by n_stride relative to ijnum in dev_short_nbor + // idx to zetaij is shifted by n_stride relative to ijnum in dev_short_nbor int idx = ijnum; if (dev_packed==dev_nbor) idx -= n_stride; -// zeta_idx(dev_nbor,dev_packed, nbor_pitch, n_stride, t_per_atom, -// j, ijnum, offset_kf, idx); acctyp4 zeta_ji = zetaij[idx]; // fetch(zeta_ji,idx,zeta_tex); numtyp force = zeta_ji.x*tpainv; numtyp prefactor_ji = zeta_ji.y; @@ -909,13 +896,9 @@ __kernel void k_tersoff_zbl_three_end(const __global numtyp4 *restrict x_, f.y += fi[1]; f.z += fi[2]; - //int kk = (nbor_k - offset_k - 2*nbor_pitch) / n_stride; - //int idx = kk*n_stride + j*t_per_atom + offset_k; - //idx to zetaij is shifted by n_stride relative to nbor_k in dev_short_nbor + // idx to zetaij is shifted by n_stride relative to nbor_k in dev_short_nbor int idx = nbor_k; if (dev_packed==dev_nbor) idx -= n_stride; -// zeta_idx(dev_nbor,dev_packed, nbor_pitch, n_stride, t_per_atom, -// j, nbor_k, offset_k, idx); acctyp4 zeta_jk = zetaij[idx]; // fetch(zeta_jk,idx,zeta_tex); numtyp prefactor_jk = zeta_jk.y; int jkiparam=elem2param[jtype*nelements*nelements+ktype*nelements+itype]; @@ -1086,13 +1069,9 @@ __kernel void k_tersoff_zbl_three_end_vatom(const __global numtyp4 *restrict x_, offset_kf = red_acc[2*m+1]; } - //int iix = (ijnum - offset_kf - 2*nbor_pitch) / n_stride; - //int idx = iix*n_stride + j*t_per_atom + offset_kf; - //idx to zetaij is shifted by n_stride relative to ijnum in dev_short_nbor + // idx to zetaij is shifted by n_stride relative to ijnum in dev_short_nbor int idx = ijnum; if (dev_packed==dev_nbor) idx -= n_stride; -// zeta_idx(dev_nbor,dev_packed, nbor_pitch, n_stride, t_per_atom, -// j, ijnum, offset_kf, idx); acctyp4 zeta_ji = zetaij[idx]; // fetch(zeta_ji,idx,zeta_tex); numtyp force = zeta_ji.x*tpainv; numtyp prefactor_ji = zeta_ji.y; @@ -1161,13 +1140,9 @@ __kernel void k_tersoff_zbl_three_end_vatom(const __global numtyp4 *restrict x_, virial[4] += TWOTHIRD*(mdelr1[0]*fj[2] + delr2[0]*fk[2]); virial[5] += TWOTHIRD*(mdelr1[1]*fj[2] + delr2[1]*fk[2]); - //int kk = (nbor_k - offset_k - 2*nbor_pitch) / n_stride; - //int idx = kk*n_stride + j*t_per_atom + offset_k; - //idx to zetaij is shifted by n_stride relative to nbor_k in dev_short_nbor + // idx to zetaij is shifted by n_stride relative to nbor_k in dev_short_nbor int idx = nbor_k; if (dev_packed==dev_nbor) idx -= n_stride; -// zeta_idx(dev_nbor,dev_packed, nbor_pitch, n_stride, t_per_atom, -// j, nbor_k, offset_k, idx); acctyp4 zeta_jk = zetaij[idx]; // fetch(zeta_jk,idx,zeta_tex); numtyp prefactor_jk = zeta_jk.y; diff --git a/lib/gpu/lal_yukawa_colloid.cu b/lib/gpu/lal_yukawa_colloid.cu index 48ab47bc94..a3cbbbc11c 100644 --- a/lib/gpu/lal_yukawa_colloid.cu +++ b/lib/gpu/lal_yukawa_colloid.cu @@ -89,10 +89,10 @@ __kernel void k_yukawa_colloid(const __global numtyp4 *restrict x_, if (rsqcut_innersq) { - t = r - cut_inner; - force = t*t * (coeff1[mtype].x + coeff1[mtype].y*t); - } - + if (rsq>cut_innersq) { + t = r - cut_inner; + force = t*t * (coeff1[mtype].x + coeff1[mtype].y*t); + } force *= (numtyp)-1.0*ucl_recip(r); f.x+=delx*force; @@ -148,11 +145,10 @@ __kernel void k_zbl(const __global numtyp4 *restrict x_, if (eflag>0) { numtyp e=e_zbl(r, coeff2[mtype].x, coeff2[mtype].y, coeff2[mtype].z, coeff2[mtype].w, coeff1[mtype].z); - e += coeff3[mtype].z; - if (rsq > cut_innersq) { - e += t*t*t * (coeff3[mtype].x + coeff3[mtype].y*t); - } - + e += coeff3[mtype].z; + if (rsq > cut_innersq) { + e += t*t*t * (coeff3[mtype].x + coeff3[mtype].y*t); + } energy+=e; } if (vflag>0) { @@ -232,15 +228,13 @@ __kernel void k_zbl_fast(const __global numtyp4 *restrict x_, if (rsqcut_innersq) { - t = r - cut_inner; - force += t*t * (coeff1[mtype].x + coeff1[mtype].y*t); - } + if (rsq>cut_innersq) { + t = r - cut_inner; + force += t*t * (coeff1[mtype].x + coeff1[mtype].y*t); + } force *= (numtyp)-1.0*ucl_recip(r); @@ -251,11 +245,10 @@ __kernel void k_zbl_fast(const __global numtyp4 *restrict x_, if (eflag>0) { numtyp e=e_zbl(r, coeff2[mtype].x, coeff2[mtype].y, coeff2[mtype].z, coeff2[mtype].w, coeff1[mtype].z); - e += coeff3[mtype].z; - if (rsq > cut_innersq) { - e += t*t*t * (coeff3[mtype].x + coeff3[mtype].y*t); - } - + e += coeff3[mtype].z; + if (rsq > cut_innersq) { + e += t*t*t * (coeff3[mtype].x + coeff3[mtype].y*t); + } energy+=e; } if (vflag>0) { -- GitLab From 5fffccb076fd350cf0bf6c80374bccee87c210a1 Mon Sep 17 00:00:00 2001 From: Anne Gunn Date: Fri, 5 Jul 2019 12:08:57 -0600 Subject: [PATCH 188/469] Apply minor line editing to new documentation file. --- doc/include-file-conventions.md | 44 ++++++++++++++++----------------- 1 file changed, 22 insertions(+), 22 deletions(-) diff --git a/doc/include-file-conventions.md b/doc/include-file-conventions.md index 1f206c8f88..c9f8bd5cb1 100644 --- a/doc/include-file-conventions.md +++ b/doc/include-file-conventions.md @@ -3,7 +3,7 @@ This purpose of this document is to provide a point of reference for LAMMPS developers and contributors as to what include files and definitions to put where into LAMMPS source. -Last change 2019-06-27 +Last change 2019-07-05 ## Table of Contents @@ -14,43 +14,43 @@ Last change 2019-06-27 ## Motivation -The conventions outlined in this document are supposed to help making +The conventions outlined in this document are supposed to help make maintenance of the LAMMPS software easier. By trying to achieve consistency across files contributed by different developers, it will -become easier to modify and adjust files by the code maintainers, and -overall the chance for errors or portability issues will be reduced. -Also the rules employed are supposed to minimize naming conflicts and -simplify dependencies between files (and thus speed up compilation), as -well as make otherwise hidden dependencies visible. +become easier for the code maintainers to modify and adjust files and, +overall, the chance for errors or portability issues will be reduced. +The rules employed are supposed to minimize naming conflicts and +simplify dependencies between files and thus speed up compilation. They +may, as well, make otherwise hidden dependencies visible. ## Rules Below are the various rules that are applied. Not all are enforced strictly and automatically. If there are no significant side effects, -exceptions may be possible for cases, where a full compliance to the +exceptions may be possible for cases where a full compliance to the rules may require a large effort compared to the benefit. ### Core Files Versus Package Files -All rules listed below are most strictly observed for core LAMMPS files. -Which are the files that are not part of a package and files of the +All rules listed below are most strictly observed for core LAMMPS files, +which are the files that are not part of a package, and the files of the packages MOLECULE, MANYBODY, KSPACE, and RIGID. On the other end of the spectrum are USER packages and legacy packages that predate these -rules and thus may not be fully compliant. Also new contributions -will be checked more closely, while existing code is incrementally +rules and thus may not be fully compliant. Also, new contributions +will be checked more closely, while existing code will be incrementally adapted to the rules as time and required effort permits. ### System Versus Local Header Files -All system or library provided include files are included with angular +All system- or library-provided include files are included with angular brackets (examples: `#include ` or `#include `) while include files provided with LAMMPS are included with double quotes (examples: `#include "pointers.h"` or `#include "compute_temp.h"`). For headers declaring functions of the C-library, the corresponding C++ versions should be included (examples: `#include ` or -`#include `). However, those are limited to those defined -in the C++98 standard. Some files thus must use the older style unless +`#include `). However, these includes are limited to those defined +in the C++98 standard. Some files thus must use the older style until the minimum C++ standard requirement of LAMMPS is lifted to C++11 or even beyond (examples: `#include ` versus `#include ` or `#include ` versus `#include `). @@ -60,7 +60,7 @@ or `#include ` versus `#include `). LAMMPS core files currently correspond to the C++98 standard. Files requiring C++11 or later are only permitted in (optional) packages and particularly packages that are not part of the list of commonly -used packages like MOLECULE, KSPACE, MANYBODY, or RIGID. +used packages such as MOLECULE, KSPACE, MANYBODY, or RIGID. Also, LAMMPS uses the C-style stdio library for I/O instead of iostreams. Since using both at the same time can cause problems, iostreams should @@ -72,8 +72,8 @@ Header files will typically contain the definition of a (single) class. These header files should have as few include statements as possible. This is particularly important for classes that implement a "style" and thus use a macro of the kind `SomeStyle(some/name,SomeName)`. These will -be all included in the auto-generated `"some_style.h"` files which will -result in a high potential for direct or indirect symbol name clashes. +all be included in the auto-generated `"some_style.h"` files which +results in a high potential for direct or indirect symbol name clashes. In the ideal case, the header would only include one file defining the parent class. That would typically be either `#include "pointers.h"` for @@ -85,7 +85,7 @@ be employed. The full definition will then be included into the corresponding implementation file. In the given example from above, the header file would be called `some_name.h` and the implementation `some_name.cpp` (all lower case with underscores, while the class itself would be in camel case -and no underscores, and the style name with lower case names separated by +and no underscores `SomeName`, and the style name with lower case names separated by a forward slash). ### Implementation Files @@ -124,9 +124,9 @@ which include files should be added or removed. ## Legacy Code -A lot of code predates the application of the rules in this document, -and those rules are a moving target as well. So there is going to be -significant chunks of code, that does not fully comply. This applies +A lot of code predates the application of the rules in this document +and the rules themselves are a moving target. So there are going to be +significant chunks of code that do not fully comply. This applies for example to the USER-REAXC, or the USER-ATC package. The LAMMPS developers are dedicated to make an effort to improve the compliance and welcome volunteers wanting to help with the process. -- GitLab From 5d4016c285a1ff930a1e2dfaea055a0bc9f6e74b Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Fri, 5 Jul 2019 14:42:46 -0400 Subject: [PATCH 189/469] cleaning up includes of ASPHERE package --- src/ASPHERE/compute_erotate_asphere.cpp | 1 - src/ASPHERE/compute_temp_asphere.cpp | 1 - src/ASPHERE/fix_nh_asphere.cpp | 5 ----- src/ASPHERE/fix_nve_asphere.cpp | 6 ------ src/ASPHERE/fix_nve_asphere_noforce.cpp | 6 ------ src/ASPHERE/fix_nve_line.cpp | 3 --- src/ASPHERE/fix_nve_tri.cpp | 3 --- src/ASPHERE/pair_gayberne.cpp | 5 +---- 8 files changed, 1 insertion(+), 29 deletions(-) diff --git a/src/ASPHERE/compute_erotate_asphere.cpp b/src/ASPHERE/compute_erotate_asphere.cpp index 665506acdf..3cf23b87eb 100644 --- a/src/ASPHERE/compute_erotate_asphere.cpp +++ b/src/ASPHERE/compute_erotate_asphere.cpp @@ -20,7 +20,6 @@ #include "atom_vec_tri.h" #include "update.h" #include "force.h" -#include "memory.h" #include "error.h" using namespace LAMMPS_NS; diff --git a/src/ASPHERE/compute_temp_asphere.cpp b/src/ASPHERE/compute_temp_asphere.cpp index 32773b2925..d591e2ca81 100644 --- a/src/ASPHERE/compute_temp_asphere.cpp +++ b/src/ASPHERE/compute_temp_asphere.cpp @@ -26,7 +26,6 @@ #include "domain.h" #include "modify.h" #include "group.h" -#include "memory.h" #include "error.h" using namespace LAMMPS_NS; diff --git a/src/ASPHERE/fix_nh_asphere.cpp b/src/ASPHERE/fix_nh_asphere.cpp index 9e8e9d73d9..2f8f11978e 100644 --- a/src/ASPHERE/fix_nh_asphere.cpp +++ b/src/ASPHERE/fix_nh_asphere.cpp @@ -16,14 +16,9 @@ ------------------------------------------------------------------------- */ #include "fix_nh_asphere.h" -#include -#include -#include #include "math_extra.h" #include "atom.h" #include "atom_vec_ellipsoid.h" -#include "group.h" -#include "memory.h" #include "error.h" using namespace LAMMPS_NS; diff --git a/src/ASPHERE/fix_nve_asphere.cpp b/src/ASPHERE/fix_nve_asphere.cpp index 05219e442f..93ccf008f4 100644 --- a/src/ASPHERE/fix_nve_asphere.cpp +++ b/src/ASPHERE/fix_nve_asphere.cpp @@ -16,15 +16,9 @@ ------------------------------------------------------------------------- */ #include "fix_nve_asphere.h" -#include -#include -#include #include "math_extra.h" #include "atom.h" #include "atom_vec_ellipsoid.h" -#include "force.h" -#include "update.h" -#include "memory.h" #include "error.h" using namespace LAMMPS_NS; diff --git a/src/ASPHERE/fix_nve_asphere_noforce.cpp b/src/ASPHERE/fix_nve_asphere_noforce.cpp index 015cc8cfb6..3a7d7e86e9 100644 --- a/src/ASPHERE/fix_nve_asphere_noforce.cpp +++ b/src/ASPHERE/fix_nve_asphere_noforce.cpp @@ -12,15 +12,9 @@ ------------------------------------------------------------------------- */ #include "fix_nve_asphere_noforce.h" -#include -#include -#include #include "math_extra.h" #include "atom.h" #include "atom_vec_ellipsoid.h" -#include "group.h" -#include "update.h" -#include "memory.h" #include "error.h" using namespace LAMMPS_NS; diff --git a/src/ASPHERE/fix_nve_line.cpp b/src/ASPHERE/fix_nve_line.cpp index 57335f22e0..5e17cb355f 100644 --- a/src/ASPHERE/fix_nve_line.cpp +++ b/src/ASPHERE/fix_nve_line.cpp @@ -12,9 +12,6 @@ ------------------------------------------------------------------------- */ #include "fix_nve_line.h" -#include -#include -#include #include "atom.h" #include "atom_vec_line.h" #include "domain.h" diff --git a/src/ASPHERE/fix_nve_tri.cpp b/src/ASPHERE/fix_nve_tri.cpp index b1f7667d06..797fea1c5b 100644 --- a/src/ASPHERE/fix_nve_tri.cpp +++ b/src/ASPHERE/fix_nve_tri.cpp @@ -12,9 +12,6 @@ ------------------------------------------------------------------------- */ #include "fix_nve_tri.h" -#include -#include -#include #include "math_extra.h" #include "atom.h" #include "atom_vec_tri.h" diff --git a/src/ASPHERE/pair_gayberne.cpp b/src/ASPHERE/pair_gayberne.cpp index 7dbf11c5ea..93b164c503 100644 --- a/src/ASPHERE/pair_gayberne.cpp +++ b/src/ASPHERE/pair_gayberne.cpp @@ -16,10 +16,8 @@ ------------------------------------------------------------------------- */ #include "pair_gayberne.h" +#include #include -#include -#include -#include #include "math_extra.h" #include "atom.h" #include "atom_vec_ellipsoid.h" @@ -27,7 +25,6 @@ #include "force.h" #include "neighbor.h" #include "neigh_list.h" -#include "integrate.h" #include "citeme.h" #include "memory.h" #include "error.h" -- GitLab From 2c0eeeb976075e6df3fc5362d2e06566cc20821c Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Fri, 5 Jul 2019 14:43:20 -0400 Subject: [PATCH 190/469] one more chunk of files in src folder to be cleaned up --- src/universe.cpp | 1 - src/update.cpp | 5 ----- src/utils.cpp | 1 - src/velocity.cpp | 4 ---- src/verlet.cpp | 3 --- src/write_coeff.cpp | 1 + src/write_data.cpp | 1 - src/write_dump.cpp | 4 +--- 8 files changed, 2 insertions(+), 18 deletions(-) diff --git a/src/universe.cpp b/src/universe.cpp index 2a7117da51..a36b67d115 100644 --- a/src/universe.cpp +++ b/src/universe.cpp @@ -16,7 +16,6 @@ #include #include #include -#include #include "version.h" #include "error.h" #include "force.h" diff --git a/src/update.cpp b/src/update.cpp index e83f4d9f72..8a3e6f0d1d 100644 --- a/src/update.cpp +++ b/src/update.cpp @@ -13,21 +13,16 @@ #include "update.h" #include -#include #include "integrate.h" #include "min.h" #include "style_integrate.h" #include "style_minimize.h" #include "neighbor.h" -#include "neigh_list.h" #include "force.h" #include "modify.h" #include "fix.h" -#include "domain.h" -#include "region.h" #include "compute.h" #include "output.h" -#include "memory.h" #include "error.h" using namespace LAMMPS_NS; diff --git a/src/utils.cpp b/src/utils.cpp index ea2ab57f6f..f45a834bec 100644 --- a/src/utils.cpp +++ b/src/utils.cpp @@ -12,7 +12,6 @@ ------------------------------------------------------------------------- */ #include "utils.h" -#include #include #include "lammps.h" #include "error.h" diff --git a/src/velocity.cpp b/src/velocity.cpp index 1a03f71128..e5985884f8 100644 --- a/src/velocity.cpp +++ b/src/velocity.cpp @@ -12,13 +12,9 @@ ------------------------------------------------------------------------- */ #include "velocity.h" -#include #include -#include -#include #include #include "atom.h" -#include "update.h" #include "domain.h" #include "lattice.h" #include "input.h" diff --git a/src/verlet.cpp b/src/verlet.cpp index 5ccef36259..8cd6fe940d 100644 --- a/src/verlet.cpp +++ b/src/verlet.cpp @@ -28,10 +28,7 @@ #include "output.h" #include "update.h" #include "modify.h" -#include "compute.h" -#include "fix.h" #include "timer.h" -#include "memory.h" #include "error.h" using namespace LAMMPS_NS; diff --git a/src/write_coeff.cpp b/src/write_coeff.cpp index 08ff964e7c..8e5b4fcb71 100644 --- a/src/write_coeff.cpp +++ b/src/write_coeff.cpp @@ -14,6 +14,7 @@ #include "write_coeff.h" #include #include +#include #include #include "pair.h" #include "bond.h" diff --git a/src/write_data.cpp b/src/write_data.cpp index b78e701d35..3d788b9665 100644 --- a/src/write_data.cpp +++ b/src/write_data.cpp @@ -16,7 +16,6 @@ #include #include "atom.h" #include "atom_vec.h" -#include "group.h" #include "force.h" #include "pair.h" #include "bond.h" diff --git a/src/write_dump.cpp b/src/write_dump.cpp index 903f0e0cdd..31ceb4cbbf 100644 --- a/src/write_dump.cpp +++ b/src/write_dump.cpp @@ -17,13 +17,11 @@ #include "write_dump.h" #include +#include #include "style_dump.h" #include "dump.h" #include "dump_image.h" -#include "atom.h" #include "comm.h" -#include "group.h" -#include "input.h" #include "update.h" #include "error.h" #include "utils.h" -- GitLab From 4db483339504396f084bf269db6b06862f2025cb Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Fri, 5 Jul 2019 21:11:06 -0400 Subject: [PATCH 191/469] fix up includes for BODY package --- src/BODY/body_rounded_polygon.cpp | 2 +- src/BODY/body_rounded_polyhedron.cpp | 2 +- src/BODY/compute_body_local.cpp | 4 +--- src/BODY/compute_temp_body.cpp | 1 - src/BODY/fix_nh_body.cpp | 5 ----- src/BODY/fix_nve_body.cpp | 6 ------ src/BODY/fix_wall_body_polygon.cpp | 4 ---- src/BODY/fix_wall_body_polyhedron.cpp | 4 ---- src/BODY/pair_body_nparticle.cpp | 2 -- src/BODY/pair_body_rounded_polygon.cpp | 3 +-- src/BODY/pair_body_rounded_polyhedron.cpp | 5 +---- 11 files changed, 5 insertions(+), 33 deletions(-) diff --git a/src/BODY/body_rounded_polygon.cpp b/src/BODY/body_rounded_polygon.cpp index 21f1d7e221..caf7e4bb8c 100644 --- a/src/BODY/body_rounded_polygon.cpp +++ b/src/BODY/body_rounded_polygon.cpp @@ -16,8 +16,8 @@ ------------------------------------------------------------------------- */ #include "body_rounded_polygon.h" +#include #include -#include #include "my_pool_chunk.h" #include "atom_vec_body.h" #include "atom.h" diff --git a/src/BODY/body_rounded_polyhedron.cpp b/src/BODY/body_rounded_polyhedron.cpp index 15e1871e02..98f7913859 100644 --- a/src/BODY/body_rounded_polyhedron.cpp +++ b/src/BODY/body_rounded_polyhedron.cpp @@ -16,13 +16,13 @@ ------------------------------------------------------------------------- */ #include "body_rounded_polyhedron.h" +#include #include #include #include "my_pool_chunk.h" #include "atom_vec_body.h" #include "atom.h" #include "force.h" -#include "domain.h" #include "math_extra.h" #include "memory.h" #include "error.h" diff --git a/src/BODY/compute_body_local.cpp b/src/BODY/compute_body_local.cpp index f58b66c2ca..c12502df42 100644 --- a/src/BODY/compute_body_local.cpp +++ b/src/BODY/compute_body_local.cpp @@ -12,15 +12,13 @@ ------------------------------------------------------------------------- */ #include "compute_body_local.h" -#include +#include #include #include "atom.h" #include "atom_vec_body.h" #include "body.h" #include "update.h" -#include "domain.h" #include "force.h" -#include "bond.h" #include "memory.h" #include "error.h" diff --git a/src/BODY/compute_temp_body.cpp b/src/BODY/compute_temp_body.cpp index 7beca36df8..d9007f573d 100644 --- a/src/BODY/compute_temp_body.cpp +++ b/src/BODY/compute_temp_body.cpp @@ -27,7 +27,6 @@ #include "domain.h" #include "modify.h" #include "group.h" -#include "memory.h" #include "error.h" using namespace LAMMPS_NS; diff --git a/src/BODY/fix_nh_body.cpp b/src/BODY/fix_nh_body.cpp index 6064f1f9de..b9a0c81e15 100644 --- a/src/BODY/fix_nh_body.cpp +++ b/src/BODY/fix_nh_body.cpp @@ -17,14 +17,9 @@ ------------------------------------------------------------------------- */ #include "fix_nh_body.h" -#include -#include -#include #include "math_extra.h" #include "atom.h" #include "atom_vec_body.h" -#include "group.h" -#include "memory.h" #include "error.h" using namespace LAMMPS_NS; diff --git a/src/BODY/fix_nve_body.cpp b/src/BODY/fix_nve_body.cpp index 3f3bd41cbc..185e397540 100644 --- a/src/BODY/fix_nve_body.cpp +++ b/src/BODY/fix_nve_body.cpp @@ -12,15 +12,9 @@ ------------------------------------------------------------------------- */ #include "fix_nve_body.h" -#include -#include -#include #include "math_extra.h" #include "atom.h" #include "atom_vec_body.h" -#include "force.h" -#include "update.h" -#include "memory.h" #include "error.h" using namespace LAMMPS_NS; diff --git a/src/BODY/fix_wall_body_polygon.cpp b/src/BODY/fix_wall_body_polygon.cpp index 8f27a094cb..e51476de60 100644 --- a/src/BODY/fix_wall_body_polygon.cpp +++ b/src/BODY/fix_wall_body_polygon.cpp @@ -17,7 +17,6 @@ #include "fix_wall_body_polygon.h" #include -#include #include #include "atom.h" #include "atom_vec_body.h" @@ -25,9 +24,6 @@ #include "domain.h" #include "update.h" #include "force.h" -#include "pair.h" -#include "modify.h" -#include "respa.h" #include "math_const.h" #include "math_extra.h" #include "memory.h" diff --git a/src/BODY/fix_wall_body_polyhedron.cpp b/src/BODY/fix_wall_body_polyhedron.cpp index 37b542803f..42c62de436 100644 --- a/src/BODY/fix_wall_body_polyhedron.cpp +++ b/src/BODY/fix_wall_body_polyhedron.cpp @@ -17,7 +17,6 @@ #include "fix_wall_body_polyhedron.h" #include -#include #include #include "atom.h" #include "atom_vec_body.h" @@ -25,9 +24,6 @@ #include "domain.h" #include "update.h" #include "force.h" -#include "pair.h" -#include "modify.h" -#include "respa.h" #include "math_const.h" #include "math_extra.h" #include "memory.h" diff --git a/src/BODY/pair_body_nparticle.cpp b/src/BODY/pair_body_nparticle.cpp index 96a7af6255..bd7aba5455 100644 --- a/src/BODY/pair_body_nparticle.cpp +++ b/src/BODY/pair_body_nparticle.cpp @@ -13,8 +13,6 @@ #include "pair_body_nparticle.h" #include -#include -#include #include #include "math_extra.h" #include "atom.h" diff --git a/src/BODY/pair_body_rounded_polygon.cpp b/src/BODY/pair_body_rounded_polygon.cpp index c818b5a2e6..f5e18e9d89 100644 --- a/src/BODY/pair_body_rounded_polygon.cpp +++ b/src/BODY/pair_body_rounded_polygon.cpp @@ -19,9 +19,8 @@ ------------------------------------------------------------------------- */ #include "pair_body_rounded_polygon.h" +#include #include -#include -#include #include #include "math_extra.h" #include "atom.h" diff --git a/src/BODY/pair_body_rounded_polyhedron.cpp b/src/BODY/pair_body_rounded_polyhedron.cpp index 75caab88bd..2df58d45cd 100644 --- a/src/BODY/pair_body_rounded_polyhedron.cpp +++ b/src/BODY/pair_body_rounded_polyhedron.cpp @@ -21,11 +21,9 @@ ------------------------------------------------------------------------- */ #include "pair_body_rounded_polyhedron.h" +#include #include -#include -#include #include -#include "math_extra.h" #include "atom.h" #include "atom_vec_body.h" #include "body_rounded_polyhedron.h" @@ -41,7 +39,6 @@ #include "math_const.h" using namespace LAMMPS_NS; -using namespace MathExtra; using namespace MathConst; #define DELTA 10000 -- GitLab From a00d38572e425f7734cfd651959b760b36eb6b12 Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Sat, 6 Jul 2019 06:29:22 -0400 Subject: [PATCH 192/469] clean up includes in packages CLASS2, COLLOID, COMPRESS, and CORESHELL --- src/CLASS2/angle_class2.cpp | 2 +- src/CLASS2/bond_class2.cpp | 3 +-- src/CLASS2/dihedral_class2.cpp | 3 +-- src/CLASS2/improper_class2.cpp | 3 +-- src/CLASS2/pair_lj_class2.cpp | 4 +--- src/CLASS2/pair_lj_class2_coul_cut.cpp | 3 +-- src/CLASS2/pair_lj_class2_coul_long.cpp | 4 +--- src/COLLOID/fix_wall_colloid.cpp | 4 +--- src/COLLOID/pair_brownian.cpp | 6 +----- src/COLLOID/pair_brownian_poly.cpp | 7 +------ src/COLLOID/pair_colloid.cpp | 5 +---- src/COLLOID/pair_lubricate.cpp | 6 +----- src/COLLOID/pair_lubricateU.cpp | 5 ----- src/COLLOID/pair_lubricateU_poly.cpp | 5 ----- src/COLLOID/pair_lubricate_poly.cpp | 6 +----- src/COLLOID/pair_yukawa_colloid.cpp | 3 --- src/COMPRESS/dump_xyz_gz.cpp | 1 - src/CORESHELL/compute_temp_cs.cpp | 3 --- src/CORESHELL/pair_born_coul_dsf_cs.cpp | 6 ------ src/CORESHELL/pair_born_coul_long_cs.cpp | 9 --------- src/CORESHELL/pair_born_coul_wolf_cs.cpp | 8 -------- src/CORESHELL/pair_buck_coul_long_cs.cpp | 10 ---------- src/CORESHELL/pair_coul_long_cs.cpp | 11 ----------- src/CORESHELL/pair_coul_wolf_cs.cpp | 8 -------- src/CORESHELL/pair_lj_cut_coul_long_cs.cpp | 14 -------------- 25 files changed, 13 insertions(+), 126 deletions(-) diff --git a/src/CLASS2/angle_class2.cpp b/src/CLASS2/angle_class2.cpp index 340152abd4..99e1b39c9d 100644 --- a/src/CLASS2/angle_class2.cpp +++ b/src/CLASS2/angle_class2.cpp @@ -16,9 +16,9 @@ ------------------------------------------------------------------------- */ #include "angle_class2.h" +#include #include #include -#include #include "atom.h" #include "neighbor.h" #include "domain.h" diff --git a/src/CLASS2/bond_class2.cpp b/src/CLASS2/bond_class2.cpp index 945555f772..cfc1a93bde 100644 --- a/src/CLASS2/bond_class2.cpp +++ b/src/CLASS2/bond_class2.cpp @@ -16,11 +16,10 @@ ------------------------------------------------------------------------- */ #include "bond_class2.h" +#include #include -#include #include "atom.h" #include "neighbor.h" -#include "domain.h" #include "comm.h" #include "force.h" #include "memory.h" diff --git a/src/CLASS2/dihedral_class2.cpp b/src/CLASS2/dihedral_class2.cpp index c36d976525..725228666e 100644 --- a/src/CLASS2/dihedral_class2.cpp +++ b/src/CLASS2/dihedral_class2.cpp @@ -16,13 +16,12 @@ ------------------------------------------------------------------------- */ #include "dihedral_class2.h" +#include #include #include -#include #include "atom.h" #include "neighbor.h" #include "update.h" -#include "domain.h" #include "comm.h" #include "force.h" #include "math_const.h" diff --git a/src/CLASS2/improper_class2.cpp b/src/CLASS2/improper_class2.cpp index aff37df318..ca7ac95239 100644 --- a/src/CLASS2/improper_class2.cpp +++ b/src/CLASS2/improper_class2.cpp @@ -16,13 +16,12 @@ ------------------------------------------------------------------------- */ #include "improper_class2.h" +#include #include #include -#include #include "atom.h" #include "neighbor.h" #include "update.h" -#include "domain.h" #include "comm.h" #include "force.h" #include "math_const.h" diff --git a/src/CLASS2/pair_lj_class2.cpp b/src/CLASS2/pair_lj_class2.cpp index 9a67fafecb..a0088e52b7 100644 --- a/src/CLASS2/pair_lj_class2.cpp +++ b/src/CLASS2/pair_lj_class2.cpp @@ -10,9 +10,8 @@ ------------------------------------------------------------------------- */ #include "pair_lj_class2.h" +#include #include -#include -#include #include #include "atom.h" #include "comm.h" @@ -21,7 +20,6 @@ #include "neigh_list.h" #include "neigh_request.h" #include "update.h" -#include "integrate.h" #include "respa.h" #include "math_const.h" #include "memory.h" diff --git a/src/CLASS2/pair_lj_class2_coul_cut.cpp b/src/CLASS2/pair_lj_class2_coul_cut.cpp index 24620611c6..e999a3682e 100644 --- a/src/CLASS2/pair_lj_class2_coul_cut.cpp +++ b/src/CLASS2/pair_lj_class2_coul_cut.cpp @@ -12,9 +12,8 @@ ------------------------------------------------------------------------- */ #include "pair_lj_class2_coul_cut.h" +#include #include -#include -#include #include #include "atom.h" #include "comm.h" diff --git a/src/CLASS2/pair_lj_class2_coul_long.cpp b/src/CLASS2/pair_lj_class2_coul_long.cpp index cd11294327..b56c076996 100644 --- a/src/CLASS2/pair_lj_class2_coul_long.cpp +++ b/src/CLASS2/pair_lj_class2_coul_long.cpp @@ -12,16 +12,14 @@ ------------------------------------------------------------------------- */ #include "pair_lj_class2_coul_long.h" +#include #include -#include -#include #include #include "atom.h" #include "comm.h" #include "force.h" #include "kspace.h" #include "update.h" -#include "integrate.h" #include "respa.h" #include "neighbor.h" #include "neigh_list.h" diff --git a/src/COLLOID/fix_wall_colloid.cpp b/src/COLLOID/fix_wall_colloid.cpp index f2e895c4f3..58593a99b1 100644 --- a/src/COLLOID/fix_wall_colloid.cpp +++ b/src/COLLOID/fix_wall_colloid.cpp @@ -16,12 +16,10 @@ ------------------------------------------------------------------------- */ #include "fix_wall_colloid.h" +#include #include -#include #include "atom.h" #include "atom_vec.h" -#include "update.h" -#include "respa.h" #include "error.h" using namespace LAMMPS_NS; diff --git a/src/COLLOID/pair_brownian.cpp b/src/COLLOID/pair_brownian.cpp index f9185264e0..71a5f8c056 100644 --- a/src/COLLOID/pair_brownian.cpp +++ b/src/COLLOID/pair_brownian.cpp @@ -16,22 +16,18 @@ ------------------------------------------------------------------------- */ #include "pair_brownian.h" +#include #include -#include -#include #include #include "atom.h" -#include "atom_vec.h" #include "comm.h" #include "force.h" #include "neighbor.h" #include "neigh_list.h" -#include "neigh_request.h" #include "domain.h" #include "update.h" #include "modify.h" #include "fix.h" -#include "fix_deform.h" #include "fix_wall.h" #include "input.h" #include "variable.h" diff --git a/src/COLLOID/pair_brownian_poly.cpp b/src/COLLOID/pair_brownian_poly.cpp index 250dcef1fd..c3eb4f28a5 100644 --- a/src/COLLOID/pair_brownian_poly.cpp +++ b/src/COLLOID/pair_brownian_poly.cpp @@ -17,13 +17,10 @@ ------------------------------------------------------------------------- */ #include "pair_brownian_poly.h" +#include #include -#include -#include #include #include "atom.h" -#include "atom_vec.h" -#include "comm.h" #include "force.h" #include "neighbor.h" #include "neigh_list.h" @@ -32,14 +29,12 @@ #include "update.h" #include "modify.h" #include "fix.h" -#include "fix_deform.h" #include "fix_wall.h" #include "input.h" #include "variable.h" #include "random_mars.h" #include "math_const.h" #include "math_special.h" -#include "memory.h" #include "error.h" using namespace LAMMPS_NS; diff --git a/src/COLLOID/pair_colloid.cpp b/src/COLLOID/pair_colloid.cpp index 306cdfebdf..ad25184181 100644 --- a/src/COLLOID/pair_colloid.cpp +++ b/src/COLLOID/pair_colloid.cpp @@ -16,14 +16,11 @@ ------------------------------------------------------------------------- */ #include "pair_colloid.h" +#include #include -#include -#include -#include #include "atom.h" #include "comm.h" #include "force.h" -#include "neighbor.h" #include "neigh_list.h" #include "math_special.h" #include "memory.h" diff --git a/src/COLLOID/pair_lubricate.cpp b/src/COLLOID/pair_lubricate.cpp index ee55c6cbf5..4492de3cbb 100644 --- a/src/COLLOID/pair_lubricate.cpp +++ b/src/COLLOID/pair_lubricate.cpp @@ -17,17 +17,14 @@ ------------------------------------------------------------------------- */ #include "pair_lubricate.h" +#include #include -#include -#include #include #include "atom.h" -#include "atom_vec.h" #include "comm.h" #include "force.h" #include "neighbor.h" #include "neigh_list.h" -#include "neigh_request.h" #include "domain.h" #include "modify.h" #include "fix.h" @@ -35,7 +32,6 @@ #include "fix_wall.h" #include "input.h" #include "variable.h" -#include "random_mars.h" #include "math_const.h" #include "memory.h" #include "error.h" diff --git a/src/COLLOID/pair_lubricateU.cpp b/src/COLLOID/pair_lubricateU.cpp index be589167c9..4f7e3917e8 100644 --- a/src/COLLOID/pair_lubricateU.cpp +++ b/src/COLLOID/pair_lubricateU.cpp @@ -18,22 +18,17 @@ #include "pair_lubricateU.h" #include #include -#include -#include #include #include "atom.h" -#include "atom_vec.h" #include "comm.h" #include "force.h" #include "neighbor.h" #include "neigh_list.h" -#include "neigh_request.h" #include "domain.h" #include "update.h" #include "math_const.h" #include "modify.h" #include "fix.h" -#include "fix_deform.h" #include "fix_wall.h" #include "input.h" #include "variable.h" diff --git a/src/COLLOID/pair_lubricateU_poly.cpp b/src/COLLOID/pair_lubricateU_poly.cpp index ebcf939cff..0f16d94300 100644 --- a/src/COLLOID/pair_lubricateU_poly.cpp +++ b/src/COLLOID/pair_lubricateU_poly.cpp @@ -20,21 +20,16 @@ #include "pair_lubricateU_poly.h" #include #include -#include -#include #include #include "atom.h" -#include "atom_vec.h" #include "comm.h" #include "force.h" #include "neighbor.h" #include "neigh_list.h" #include "neigh_request.h" #include "domain.h" -#include "update.h" #include "modify.h" #include "fix.h" -#include "fix_deform.h" #include "fix_wall.h" #include "input.h" #include "variable.h" diff --git a/src/COLLOID/pair_lubricate_poly.cpp b/src/COLLOID/pair_lubricate_poly.cpp index f1bfa0c695..e347441cf4 100644 --- a/src/COLLOID/pair_lubricate_poly.cpp +++ b/src/COLLOID/pair_lubricate_poly.cpp @@ -18,12 +18,10 @@ ------------------------------------------------------------------------- */ #include "pair_lubricate_poly.h" +#include #include -#include -#include #include #include "atom.h" -#include "atom_vec.h" #include "comm.h" #include "force.h" #include "neighbor.h" @@ -33,8 +31,6 @@ #include "modify.h" #include "fix.h" #include "fix_deform.h" -#include "memory.h" -#include "random_mars.h" #include "fix_wall.h" #include "input.h" #include "variable.h" diff --git a/src/COLLOID/pair_yukawa_colloid.cpp b/src/COLLOID/pair_yukawa_colloid.cpp index 98d0586925..1866fa60b5 100644 --- a/src/COLLOID/pair_yukawa_colloid.cpp +++ b/src/COLLOID/pair_yukawa_colloid.cpp @@ -17,14 +17,11 @@ #include "pair_yukawa_colloid.h" #include -#include #include "atom.h" #include "atom_vec.h" #include "force.h" -#include "comm.h" #include "neighbor.h" #include "neigh_list.h" -#include "memory.h" #include "error.h" using namespace LAMMPS_NS; diff --git a/src/COMPRESS/dump_xyz_gz.cpp b/src/COMPRESS/dump_xyz_gz.cpp index 7be1a10fe2..c76b7afa17 100644 --- a/src/COMPRESS/dump_xyz_gz.cpp +++ b/src/COMPRESS/dump_xyz_gz.cpp @@ -12,7 +12,6 @@ ------------------------------------------------------------------------- */ #include "dump_xyz_gz.h" -#include "domain.h" #include "error.h" #include "update.h" diff --git a/src/CORESHELL/compute_temp_cs.cpp b/src/CORESHELL/compute_temp_cs.cpp index 4217fe3410..cccccaf254 100644 --- a/src/CORESHELL/compute_temp_cs.cpp +++ b/src/CORESHELL/compute_temp_cs.cpp @@ -18,9 +18,7 @@ #include "compute_temp_cs.h" #include -#include #include -#include #include "atom.h" #include "atom_vec.h" #include "domain.h" @@ -28,7 +26,6 @@ #include "force.h" #include "group.h" #include "modify.h" -#include "fix.h" #include "fix_store.h" #include "comm.h" #include "memory.h" diff --git a/src/CORESHELL/pair_born_coul_dsf_cs.cpp b/src/CORESHELL/pair_born_coul_dsf_cs.cpp index cd932e560b..9440bca109 100644 --- a/src/CORESHELL/pair_born_coul_dsf_cs.cpp +++ b/src/CORESHELL/pair_born_coul_dsf_cs.cpp @@ -18,17 +18,11 @@ #include "pair_born_coul_dsf_cs.h" #include -#include -#include -#include #include "atom.h" #include "comm.h" #include "force.h" -#include "neighbor.h" #include "neigh_list.h" #include "math_const.h" -#include "memory.h" -#include "error.h" #include "math_special.h" using namespace LAMMPS_NS; diff --git a/src/CORESHELL/pair_born_coul_long_cs.cpp b/src/CORESHELL/pair_born_coul_long_cs.cpp index 2ef7fdb273..f6262fa9e7 100644 --- a/src/CORESHELL/pair_born_coul_long_cs.cpp +++ b/src/CORESHELL/pair_born_coul_long_cs.cpp @@ -17,21 +17,12 @@ #include "pair_born_coul_long_cs.h" #include -#include -#include #include #include "atom.h" -#include "comm.h" #include "force.h" -#include "kspace.h" -#include "neighbor.h" #include "neigh_list.h" -#include "math_const.h" -#include "memory.h" -#include "error.h" using namespace LAMMPS_NS; -using namespace MathConst; #define EWALD_F 1.12837917 #define EWALD_P 9.95473818e-1 diff --git a/src/CORESHELL/pair_born_coul_wolf_cs.cpp b/src/CORESHELL/pair_born_coul_wolf_cs.cpp index c0374e2ddb..398c2ba1ee 100644 --- a/src/CORESHELL/pair_born_coul_wolf_cs.cpp +++ b/src/CORESHELL/pair_born_coul_wolf_cs.cpp @@ -14,22 +14,14 @@ #include "pair_born_coul_wolf_cs.h" #include -#include -#include -#include #include "atom.h" #include "comm.h" #include "force.h" -#include "neighbor.h" #include "neigh_list.h" #include "math_const.h" -#include "math_special.h" -#include "memory.h" -#include "error.h" using namespace LAMMPS_NS; using namespace MathConst; -using namespace MathSpecial; #define EPSILON 1.0e-20 diff --git a/src/CORESHELL/pair_buck_coul_long_cs.cpp b/src/CORESHELL/pair_buck_coul_long_cs.cpp index 6c897622fa..1392ec1880 100644 --- a/src/CORESHELL/pair_buck_coul_long_cs.cpp +++ b/src/CORESHELL/pair_buck_coul_long_cs.cpp @@ -17,21 +17,11 @@ #include "pair_buck_coul_long_cs.h" #include -#include -#include -#include #include "atom.h" -#include "comm.h" #include "force.h" -#include "kspace.h" -#include "neighbor.h" #include "neigh_list.h" -#include "math_const.h" -#include "memory.h" -#include "error.h" using namespace LAMMPS_NS; -using namespace MathConst; #define EWALD_F 1.12837917 #define EWALD_P 9.95473818e-1 diff --git a/src/CORESHELL/pair_coul_long_cs.cpp b/src/CORESHELL/pair_coul_long_cs.cpp index 6094ae072a..8280799389 100644 --- a/src/CORESHELL/pair_coul_long_cs.cpp +++ b/src/CORESHELL/pair_coul_long_cs.cpp @@ -17,20 +17,9 @@ #include "pair_coul_long_cs.h" #include -#include -#include -#include #include "atom.h" -#include "comm.h" #include "force.h" -#include "kspace.h" -#include "neighbor.h" #include "neigh_list.h" -#include "update.h" -#include "integrate.h" -#include "respa.h" -#include "memory.h" -#include "error.h" using namespace LAMMPS_NS; diff --git a/src/CORESHELL/pair_coul_wolf_cs.cpp b/src/CORESHELL/pair_coul_wolf_cs.cpp index 40ade7bfe4..20b7339480 100644 --- a/src/CORESHELL/pair_coul_wolf_cs.cpp +++ b/src/CORESHELL/pair_coul_wolf_cs.cpp @@ -13,22 +13,14 @@ #include "pair_coul_wolf_cs.h" #include -#include -#include -#include #include "atom.h" #include "comm.h" #include "force.h" -#include "neighbor.h" #include "neigh_list.h" #include "math_const.h" -#include "math_special.h" -#include "memory.h" -#include "error.h" using namespace LAMMPS_NS; using namespace MathConst; -using namespace MathSpecial; #define EPSILON 1.0e-20 diff --git a/src/CORESHELL/pair_lj_cut_coul_long_cs.cpp b/src/CORESHELL/pair_lj_cut_coul_long_cs.cpp index 3f20377cf1..7ad544051a 100644 --- a/src/CORESHELL/pair_lj_cut_coul_long_cs.cpp +++ b/src/CORESHELL/pair_lj_cut_coul_long_cs.cpp @@ -17,25 +17,11 @@ #include "pair_lj_cut_coul_long_cs.h" #include -#include -#include -#include #include "atom.h" -#include "comm.h" #include "force.h" -#include "kspace.h" -#include "update.h" -#include "integrate.h" -#include "respa.h" -#include "neighbor.h" #include "neigh_list.h" -#include "neigh_request.h" -#include "math_const.h" -#include "memory.h" -#include "error.h" using namespace LAMMPS_NS; -using namespace MathConst; #define EWALD_F 1.12837917 #define EWALD_P 9.95473818e-1 -- GitLab From 316554297c15d1a5dc62f7d0649c6c5d8a6e9bae Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Sat, 6 Jul 2019 10:00:24 -0400 Subject: [PATCH 193/469] clean up includes in packages DIPOLE and GRANULAR --- src/DIPOLE/pair_lj_cut_dipole_cut.cpp | 2 +- src/DIPOLE/pair_lj_cut_dipole_long.cpp | 3 +-- src/DIPOLE/pair_lj_long_dipole_long.cpp | 6 +----- src/GRANULAR/fix_freeze.cpp | 2 +- src/GRANULAR/fix_pour.cpp | 2 +- src/GRANULAR/fix_wall_gran.cpp | 2 -- src/GRANULAR/fix_wall_gran_region.cpp | 7 ------- src/GRANULAR/pair_gran_hertz_history.cpp | 2 -- src/GRANULAR/pair_gran_hooke.cpp | 2 -- src/GRANULAR/pair_gran_hooke_history.cpp | 5 +---- src/GRANULAR/pair_granular.cpp | 5 +---- 11 files changed, 7 insertions(+), 31 deletions(-) diff --git a/src/DIPOLE/pair_lj_cut_dipole_cut.cpp b/src/DIPOLE/pair_lj_cut_dipole_cut.cpp index 44708edec9..14c511c100 100644 --- a/src/DIPOLE/pair_lj_cut_dipole_cut.cpp +++ b/src/DIPOLE/pair_lj_cut_dipole_cut.cpp @@ -12,8 +12,8 @@ ------------------------------------------------------------------------- */ #include "pair_lj_cut_dipole_cut.h" +#include #include -#include #include #include "atom.h" #include "neighbor.h" diff --git a/src/DIPOLE/pair_lj_cut_dipole_long.cpp b/src/DIPOLE/pair_lj_cut_dipole_long.cpp index 071dbaeb02..fe020ed2e6 100644 --- a/src/DIPOLE/pair_lj_cut_dipole_long.cpp +++ b/src/DIPOLE/pair_lj_cut_dipole_long.cpp @@ -12,9 +12,8 @@ ------------------------------------------------------------------------- */ #include "pair_lj_cut_dipole_long.h" +#include #include -#include -#include #include #include "atom.h" #include "comm.h" diff --git a/src/DIPOLE/pair_lj_long_dipole_long.cpp b/src/DIPOLE/pair_lj_long_dipole_long.cpp index 1391cc1a1a..5e7819c2f4 100644 --- a/src/DIPOLE/pair_lj_long_dipole_long.cpp +++ b/src/DIPOLE/pair_lj_long_dipole_long.cpp @@ -16,9 +16,8 @@ ------------------------------------------------------------------------- */ #include "pair_lj_long_dipole_long.h" +#include #include -#include -#include #include #include "math_const.h" #include "math_vector.h" @@ -26,12 +25,9 @@ #include "comm.h" #include "neighbor.h" #include "neigh_list.h" -#include "neigh_request.h" #include "force.h" #include "kspace.h" #include "update.h" -#include "integrate.h" -#include "respa.h" #include "memory.h" #include "error.h" diff --git a/src/GRANULAR/fix_freeze.cpp b/src/GRANULAR/fix_freeze.cpp index e2345bdf19..1df5c9d0a8 100644 --- a/src/GRANULAR/fix_freeze.cpp +++ b/src/GRANULAR/fix_freeze.cpp @@ -12,11 +12,11 @@ ------------------------------------------------------------------------- */ #include "fix_freeze.h" +#include #include #include "atom.h" #include "update.h" #include "modify.h" -#include "comm.h" #include "respa.h" #include "error.h" diff --git a/src/GRANULAR/fix_pour.cpp b/src/GRANULAR/fix_pour.cpp index 0fe7493127..3b1bbcef35 100644 --- a/src/GRANULAR/fix_pour.cpp +++ b/src/GRANULAR/fix_pour.cpp @@ -12,8 +12,8 @@ ------------------------------------------------------------------------- */ #include "fix_pour.h" +#include #include -#include #include #include "atom.h" #include "atom_vec.h" diff --git a/src/GRANULAR/fix_wall_gran.cpp b/src/GRANULAR/fix_wall_gran.cpp index b0fbc0c2b8..e7464a78a9 100644 --- a/src/GRANULAR/fix_wall_gran.cpp +++ b/src/GRANULAR/fix_wall_gran.cpp @@ -18,13 +18,11 @@ #include "fix_wall_gran.h" #include -#include #include #include "atom.h" #include "domain.h" #include "update.h" #include "force.h" -#include "pair.h" #include "modify.h" #include "respa.h" #include "math_const.h" diff --git a/src/GRANULAR/fix_wall_gran_region.cpp b/src/GRANULAR/fix_wall_gran_region.cpp index 97e889ddcc..a4b798d6aa 100644 --- a/src/GRANULAR/fix_wall_gran_region.cpp +++ b/src/GRANULAR/fix_wall_gran_region.cpp @@ -16,18 +16,12 @@ ------------------------------------------------------------------------- */ #include "fix_wall_gran_region.h" -#include -#include #include #include "region.h" #include "atom.h" #include "domain.h" #include "update.h" -#include "force.h" #include "pair.h" -#include "modify.h" -#include "respa.h" -#include "math_const.h" #include "memory.h" #include "error.h" #include "comm.h" @@ -35,7 +29,6 @@ using namespace LAMMPS_NS; using namespace FixConst; -using namespace MathConst; // same as FixWallGran diff --git a/src/GRANULAR/pair_gran_hertz_history.cpp b/src/GRANULAR/pair_gran_hertz_history.cpp index e303089e56..4a362c0928 100644 --- a/src/GRANULAR/pair_gran_hertz_history.cpp +++ b/src/GRANULAR/pair_gran_hertz_history.cpp @@ -17,8 +17,6 @@ #include "pair_gran_hertz_history.h" #include -#include -#include #include #include "atom.h" #include "update.h" diff --git a/src/GRANULAR/pair_gran_hooke.cpp b/src/GRANULAR/pair_gran_hooke.cpp index a30aa0bb6c..d4be320554 100644 --- a/src/GRANULAR/pair_gran_hooke.cpp +++ b/src/GRANULAR/pair_gran_hooke.cpp @@ -17,8 +17,6 @@ #include "pair_gran_hooke.h" #include -#include -#include #include "atom.h" #include "force.h" #include "fix.h" diff --git a/src/GRANULAR/pair_gran_hooke_history.cpp b/src/GRANULAR/pair_gran_hooke_history.cpp index f832fdfac3..771a5566df 100644 --- a/src/GRANULAR/pair_gran_hooke_history.cpp +++ b/src/GRANULAR/pair_gran_hooke_history.cpp @@ -16,13 +16,10 @@ ------------------------------------------------------------------------- */ #include "pair_gran_hooke_history.h" +#include #include -#include -#include #include #include "atom.h" -#include "atom_vec.h" -#include "domain.h" #include "force.h" #include "update.h" #include "modify.h" diff --git a/src/GRANULAR/pair_granular.cpp b/src/GRANULAR/pair_granular.cpp index 942587a676..e7b4c01f5e 100644 --- a/src/GRANULAR/pair_granular.cpp +++ b/src/GRANULAR/pair_granular.cpp @@ -17,13 +17,10 @@ See the README file in the top-level LAMMPS directory. ----------------------------------------------------------------------- */ #include "pair_granular.h" +#include #include -#include -#include #include #include "atom.h" -#include "atom_vec.h" -#include "domain.h" #include "force.h" #include "update.h" #include "modify.h" -- GitLab From 61ed3b65b75c3781bce511cc00ff298b023965ab Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Sat, 6 Jul 2019 10:20:13 -0400 Subject: [PATCH 194/469] clean up includes in KSPACE package --- src/KSPACE/ewald.cpp | 3 --- src/KSPACE/ewald_dipole.cpp | 5 ----- src/KSPACE/ewald_dipole_spin.cpp | 7 ------- src/KSPACE/ewald_disp.cpp | 2 -- src/KSPACE/gridcomm.cpp | 2 -- src/KSPACE/msm.cpp | 2 -- src/KSPACE/msm_cg.cpp | 5 ----- src/KSPACE/pair_born_coul_long.cpp | 2 -- src/KSPACE/pair_born_coul_msm.cpp | 6 ------ src/KSPACE/pair_coul_long.cpp | 6 +----- src/KSPACE/pair_coul_msm.cpp | 7 ------- src/KSPACE/pair_lj_charmm_coul_long.cpp | 3 --- src/KSPACE/pair_lj_charmm_coul_msm.cpp | 7 ------- src/KSPACE/pair_lj_charmmfsw_coul_long.cpp | 4 ---- src/KSPACE/pair_lj_cut_coul_long.cpp | 3 --- src/KSPACE/pair_lj_cut_coul_msm.cpp | 9 --------- src/KSPACE/pair_lj_cut_tip4p_long.cpp | 7 +------ src/KSPACE/pair_lj_long_coul_long.cpp | 4 +--- src/KSPACE/pair_lj_long_tip4p_long.cpp | 7 +------ src/KSPACE/pair_tip4p_long.cpp | 7 +------ src/KSPACE/pppm.cpp | 2 -- src/KSPACE/pppm_cg.cpp | 2 +- src/KSPACE/pppm_dipole.cpp | 5 ----- src/KSPACE/pppm_dipole_spin.cpp | 10 ---------- src/KSPACE/pppm_disp.cpp | 2 -- src/KSPACE/pppm_disp_tip4p.cpp | 1 - src/KSPACE/pppm_stagger.cpp | 3 --- src/KSPACE/pppm_tip4p.cpp | 2 +- src/KSPACE/remap.cpp | 1 + 29 files changed, 8 insertions(+), 118 deletions(-) diff --git a/src/KSPACE/ewald.cpp b/src/KSPACE/ewald.cpp index aad0e364d0..d74d90b0d6 100644 --- a/src/KSPACE/ewald.cpp +++ b/src/KSPACE/ewald.cpp @@ -20,9 +20,6 @@ #include "ewald.h" #include -#include -#include -#include #include #include "atom.h" #include "comm.h" diff --git a/src/KSPACE/ewald_dipole.cpp b/src/KSPACE/ewald_dipole.cpp index 53bac0637f..c3442beef5 100644 --- a/src/KSPACE/ewald_dipole.cpp +++ b/src/KSPACE/ewald_dipole.cpp @@ -17,8 +17,6 @@ #include "ewald_dipole.h" #include -#include -#include #include #include #include "atom.h" @@ -32,9 +30,6 @@ #include "error.h" #include "update.h" -#include "math_const.h" -#include "math_special.h" - using namespace LAMMPS_NS; using namespace MathConst; using namespace MathSpecial; diff --git a/src/KSPACE/ewald_dipole_spin.cpp b/src/KSPACE/ewald_dipole_spin.cpp index 2b6c95f174..e7d67680a1 100644 --- a/src/KSPACE/ewald_dipole_spin.cpp +++ b/src/KSPACE/ewald_dipole_spin.cpp @@ -17,8 +17,6 @@ #include "ewald_dipole_spin.h" #include -#include -#include #include #include #include "atom.h" @@ -27,17 +25,12 @@ #include "pair.h" #include "domain.h" #include "math_const.h" -#include "math_special.h" #include "memory.h" #include "error.h" #include "update.h" -#include "math_const.h" -#include "math_special.h" - using namespace LAMMPS_NS; using namespace MathConst; -using namespace MathSpecial; #define SMALL 0.00001 diff --git a/src/KSPACE/ewald_disp.cpp b/src/KSPACE/ewald_disp.cpp index c775056dd8..a7ac66fdd3 100644 --- a/src/KSPACE/ewald_disp.cpp +++ b/src/KSPACE/ewald_disp.cpp @@ -18,8 +18,6 @@ #include "ewald_disp.h" #include #include -#include -#include #include #include "math_vector.h" #include "math_const.h" diff --git a/src/KSPACE/gridcomm.cpp b/src/KSPACE/gridcomm.cpp index 552d80daab..368e7370fe 100644 --- a/src/KSPACE/gridcomm.cpp +++ b/src/KSPACE/gridcomm.cpp @@ -13,10 +13,8 @@ #include "gridcomm.h" #include -#include "comm.h" #include "kspace.h" #include "memory.h" -#include "error.h" using namespace LAMMPS_NS; diff --git a/src/KSPACE/msm.cpp b/src/KSPACE/msm.cpp index bc5360dcd2..81dbabdbbd 100644 --- a/src/KSPACE/msm.cpp +++ b/src/KSPACE/msm.cpp @@ -18,8 +18,6 @@ #include "msm.h" #include #include -#include -#include #include #include "atom.h" #include "comm.h" diff --git a/src/KSPACE/msm_cg.cpp b/src/KSPACE/msm_cg.cpp index 22976b8442..9119d51878 100644 --- a/src/KSPACE/msm_cg.cpp +++ b/src/KSPACE/msm_cg.cpp @@ -18,8 +18,6 @@ #include "msm_cg.h" #include #include -#include -#include #include #include "atom.h" #include "gridcomm.h" @@ -29,10 +27,7 @@ #include "neighbor.h" #include "memory.h" -#include "math_const.h" - using namespace LAMMPS_NS; -using namespace MathConst; #define OFFSET 16384 #define SMALLQ 0.00001 diff --git a/src/KSPACE/pair_born_coul_long.cpp b/src/KSPACE/pair_born_coul_long.cpp index cb8360e401..e248a24ef7 100644 --- a/src/KSPACE/pair_born_coul_long.cpp +++ b/src/KSPACE/pair_born_coul_long.cpp @@ -17,8 +17,6 @@ #include "pair_born_coul_long.h" #include -#include -#include #include #include "atom.h" #include "comm.h" diff --git a/src/KSPACE/pair_born_coul_msm.cpp b/src/KSPACE/pair_born_coul_msm.cpp index deaf224334..7300cd92e0 100644 --- a/src/KSPACE/pair_born_coul_msm.cpp +++ b/src/KSPACE/pair_born_coul_msm.cpp @@ -17,21 +17,15 @@ #include "pair_born_coul_msm.h" #include -#include -#include #include #include "atom.h" -#include "comm.h" #include "force.h" #include "kspace.h" -#include "neighbor.h" #include "neigh_list.h" -#include "math_const.h" #include "memory.h" #include "error.h" using namespace LAMMPS_NS; -using namespace MathConst; /* ---------------------------------------------------------------------- */ diff --git a/src/KSPACE/pair_coul_long.cpp b/src/KSPACE/pair_coul_long.cpp index cb45b7a906..7cedf3d003 100644 --- a/src/KSPACE/pair_coul_long.cpp +++ b/src/KSPACE/pair_coul_long.cpp @@ -16,9 +16,8 @@ ------------------------------------------------------------------------- */ #include "pair_coul_long.h" +#include #include -#include -#include #include #include "atom.h" #include "comm.h" @@ -26,9 +25,6 @@ #include "kspace.h" #include "neighbor.h" #include "neigh_list.h" -#include "update.h" -#include "integrate.h" -#include "respa.h" #include "memory.h" #include "error.h" diff --git a/src/KSPACE/pair_coul_msm.cpp b/src/KSPACE/pair_coul_msm.cpp index 2173171e79..0917bb9275 100644 --- a/src/KSPACE/pair_coul_msm.cpp +++ b/src/KSPACE/pair_coul_msm.cpp @@ -17,18 +17,11 @@ #include "pair_coul_msm.h" #include -#include -#include #include #include "atom.h" -#include "comm.h" #include "force.h" #include "kspace.h" -#include "neighbor.h" #include "neigh_list.h" -#include "update.h" -#include "integrate.h" -#include "respa.h" #include "memory.h" #include "error.h" diff --git a/src/KSPACE/pair_lj_charmm_coul_long.cpp b/src/KSPACE/pair_lj_charmm_coul_long.cpp index 3ad14c8ea7..751ee77388 100644 --- a/src/KSPACE/pair_lj_charmm_coul_long.cpp +++ b/src/KSPACE/pair_lj_charmm_coul_long.cpp @@ -17,15 +17,12 @@ #include "pair_lj_charmm_coul_long.h" #include -#include -#include #include #include "atom.h" #include "comm.h" #include "force.h" #include "kspace.h" #include "update.h" -#include "integrate.h" #include "respa.h" #include "neighbor.h" #include "neigh_list.h" diff --git a/src/KSPACE/pair_lj_charmm_coul_msm.cpp b/src/KSPACE/pair_lj_charmm_coul_msm.cpp index 2d1775802f..804ae5919d 100644 --- a/src/KSPACE/pair_lj_charmm_coul_msm.cpp +++ b/src/KSPACE/pair_lj_charmm_coul_msm.cpp @@ -17,19 +17,12 @@ #include "pair_lj_charmm_coul_msm.h" #include -#include -#include #include #include "atom.h" -#include "comm.h" #include "force.h" #include "kspace.h" -#include "update.h" -#include "integrate.h" -#include "respa.h" #include "neighbor.h" #include "neigh_list.h" -#include "neigh_request.h" #include "memory.h" #include "error.h" diff --git a/src/KSPACE/pair_lj_charmmfsw_coul_long.cpp b/src/KSPACE/pair_lj_charmmfsw_coul_long.cpp index 7f32613cba..494a349768 100644 --- a/src/KSPACE/pair_lj_charmmfsw_coul_long.cpp +++ b/src/KSPACE/pair_lj_charmmfsw_coul_long.cpp @@ -21,16 +21,12 @@ #include "pair_lj_charmmfsw_coul_long.h" #include -#include -#include #include #include "atom.h" -#include "update.h" #include "comm.h" #include "force.h" #include "kspace.h" #include "update.h" -#include "integrate.h" #include "respa.h" #include "neighbor.h" #include "neigh_list.h" diff --git a/src/KSPACE/pair_lj_cut_coul_long.cpp b/src/KSPACE/pair_lj_cut_coul_long.cpp index 59f4766fa3..7921c814c3 100644 --- a/src/KSPACE/pair_lj_cut_coul_long.cpp +++ b/src/KSPACE/pair_lj_cut_coul_long.cpp @@ -17,15 +17,12 @@ #include "pair_lj_cut_coul_long.h" #include -#include -#include #include #include "atom.h" #include "comm.h" #include "force.h" #include "kspace.h" #include "update.h" -#include "integrate.h" #include "respa.h" #include "neighbor.h" #include "neigh_list.h" diff --git a/src/KSPACE/pair_lj_cut_coul_msm.cpp b/src/KSPACE/pair_lj_cut_coul_msm.cpp index 1305d485da..f8021cc180 100644 --- a/src/KSPACE/pair_lj_cut_coul_msm.cpp +++ b/src/KSPACE/pair_lj_cut_coul_msm.cpp @@ -17,25 +17,16 @@ #include "pair_lj_cut_coul_msm.h" #include -#include -#include #include #include "atom.h" -#include "comm.h" #include "force.h" #include "kspace.h" #include "update.h" -#include "integrate.h" -#include "respa.h" -#include "neighbor.h" #include "neigh_list.h" -#include "neigh_request.h" -#include "math_const.h" #include "memory.h" #include "error.h" using namespace LAMMPS_NS; -using namespace MathConst; /* ---------------------------------------------------------------------- */ diff --git a/src/KSPACE/pair_lj_cut_tip4p_long.cpp b/src/KSPACE/pair_lj_cut_tip4p_long.cpp index cd9b3c032d..c98092f19b 100644 --- a/src/KSPACE/pair_lj_cut_tip4p_long.cpp +++ b/src/KSPACE/pair_lj_cut_tip4p_long.cpp @@ -17,9 +17,8 @@ ------------------------------------------------------------------------- */ #include "pair_lj_cut_tip4p_long.h" +#include #include -#include -#include #include #include "angle.h" #include "atom.h" @@ -27,12 +26,8 @@ #include "comm.h" #include "domain.h" #include "force.h" -#include "kspace.h" -#include "update.h" -#include "respa.h" #include "neighbor.h" #include "neigh_list.h" -#include "neigh_request.h" #include "memory.h" #include "error.h" diff --git a/src/KSPACE/pair_lj_long_coul_long.cpp b/src/KSPACE/pair_lj_long_coul_long.cpp index 46dbb60a96..610fc4e89b 100644 --- a/src/KSPACE/pair_lj_long_coul_long.cpp +++ b/src/KSPACE/pair_lj_long_coul_long.cpp @@ -18,9 +18,8 @@ ------------------------------------------------------------------------- */ #include "pair_lj_long_coul_long.h" +#include #include -#include -#include #include #include "math_vector.h" #include "atom.h" @@ -31,7 +30,6 @@ #include "force.h" #include "kspace.h" #include "update.h" -#include "integrate.h" #include "respa.h" #include "memory.h" #include "error.h" diff --git a/src/KSPACE/pair_lj_long_tip4p_long.cpp b/src/KSPACE/pair_lj_long_tip4p_long.cpp index 5a1e347c78..08409dce72 100644 --- a/src/KSPACE/pair_lj_long_tip4p_long.cpp +++ b/src/KSPACE/pair_lj_long_tip4p_long.cpp @@ -17,9 +17,8 @@ ------------------------------------------------------------------------- */ #include "pair_lj_long_tip4p_long.h" +#include #include -#include -#include #include #include "angle.h" #include "atom.h" @@ -27,12 +26,8 @@ #include "comm.h" #include "domain.h" #include "force.h" -#include "kspace.h" -#include "update.h" -#include "respa.h" #include "neighbor.h" #include "neigh_list.h" -#include "neigh_request.h" #include "memory.h" #include "error.h" diff --git a/src/KSPACE/pair_tip4p_long.cpp b/src/KSPACE/pair_tip4p_long.cpp index deb8662a8b..2c47f42beb 100644 --- a/src/KSPACE/pair_tip4p_long.cpp +++ b/src/KSPACE/pair_tip4p_long.cpp @@ -17,9 +17,8 @@ ------------------------------------------------------------------------- */ #include "pair_tip4p_long.h" +#include #include -#include -#include #include #include "angle.h" #include "atom.h" @@ -27,12 +26,8 @@ #include "comm.h" #include "domain.h" #include "force.h" -#include "kspace.h" -#include "update.h" -#include "respa.h" #include "neighbor.h" #include "neigh_list.h" -#include "neigh_request.h" #include "memory.h" #include "error.h" diff --git a/src/KSPACE/pppm.cpp b/src/KSPACE/pppm.cpp index ae545c5c27..90db943750 100644 --- a/src/KSPACE/pppm.cpp +++ b/src/KSPACE/pppm.cpp @@ -21,8 +21,6 @@ #include "pppm.h" #include #include -#include -#include #include #include "atom.h" #include "comm.h" diff --git a/src/KSPACE/pppm_cg.cpp b/src/KSPACE/pppm_cg.cpp index f9bd7b0cb4..bd23dedef1 100644 --- a/src/KSPACE/pppm_cg.cpp +++ b/src/KSPACE/pppm_cg.cpp @@ -18,7 +18,6 @@ #include "pppm_cg.h" #include #include -#include #include #include "atom.h" #include "gridcomm.h" @@ -28,6 +27,7 @@ #include "neighbor.h" #include "memory.h" #include "math_const.h" +#include "remap.h" using namespace LAMMPS_NS; using namespace MathConst; diff --git a/src/KSPACE/pppm_dipole.cpp b/src/KSPACE/pppm_dipole.cpp index ad03b8205a..0eb761d9be 100644 --- a/src/KSPACE/pppm_dipole.cpp +++ b/src/KSPACE/pppm_dipole.cpp @@ -18,17 +18,12 @@ #include "pppm_dipole.h" #include #include -#include -#include #include #include "atom.h" #include "comm.h" #include "gridcomm.h" -#include "neighbor.h" #include "force.h" #include "pair.h" -#include "bond.h" -#include "angle.h" #include "domain.h" #include "fft3d_wrap.h" #include "remap_wrap.h" diff --git a/src/KSPACE/pppm_dipole_spin.cpp b/src/KSPACE/pppm_dipole_spin.cpp index 2c96eadde1..9e9f07322c 100644 --- a/src/KSPACE/pppm_dipole_spin.cpp +++ b/src/KSPACE/pppm_dipole_spin.cpp @@ -18,30 +18,20 @@ #include "pppm_dipole_spin.h" #include #include -#include -#include -#include #include "atom.h" #include "comm.h" #include "gridcomm.h" -#include "neighbor.h" #include "force.h" #include "pair.h" -#include "bond.h" -#include "angle.h" #include "domain.h" -#include "fft3d_wrap.h" -#include "remap_wrap.h" #include "memory.h" #include "error.h" #include "update.h" #include "math_const.h" -#include "math_special.h" using namespace LAMMPS_NS; using namespace MathConst; -using namespace MathSpecial; #define MAXORDER 7 #define OFFSET 16384 diff --git a/src/KSPACE/pppm_disp.cpp b/src/KSPACE/pppm_disp.cpp index 22e570049c..d936025d04 100644 --- a/src/KSPACE/pppm_disp.cpp +++ b/src/KSPACE/pppm_disp.cpp @@ -19,8 +19,6 @@ #include "pppm_disp.h" #include #include -#include -#include #include #include "math_const.h" #include "atom.h" diff --git a/src/KSPACE/pppm_disp_tip4p.cpp b/src/KSPACE/pppm_disp_tip4p.cpp index 36e6159131..bc46152e2b 100644 --- a/src/KSPACE/pppm_disp_tip4p.cpp +++ b/src/KSPACE/pppm_disp_tip4p.cpp @@ -22,7 +22,6 @@ #include "atom.h" #include "domain.h" #include "force.h" -#include "memory.h" #include "error.h" #include "math_const.h" diff --git a/src/KSPACE/pppm_stagger.cpp b/src/KSPACE/pppm_stagger.cpp index 5c2e2a6098..7b708d0355 100644 --- a/src/KSPACE/pppm_stagger.cpp +++ b/src/KSPACE/pppm_stagger.cpp @@ -18,12 +18,9 @@ #include "pppm_stagger.h" #include #include -#include -#include #include #include "atom.h" #include "gridcomm.h" -#include "force.h" #include "domain.h" #include "memory.h" #include "error.h" diff --git a/src/KSPACE/pppm_tip4p.cpp b/src/KSPACE/pppm_tip4p.cpp index 52a1fb3787..f664a0dca3 100644 --- a/src/KSPACE/pppm_tip4p.cpp +++ b/src/KSPACE/pppm_tip4p.cpp @@ -16,11 +16,11 @@ ------------------------------------------------------------------------- */ #include "pppm_tip4p.h" +#include #include #include "atom.h" #include "domain.h" #include "force.h" -#include "memory.h" #include "error.h" #include "math_const.h" diff --git a/src/KSPACE/remap.cpp b/src/KSPACE/remap.cpp index 85fe78c9d7..d4cfdea2b0 100644 --- a/src/KSPACE/remap.cpp +++ b/src/KSPACE/remap.cpp @@ -12,6 +12,7 @@ ------------------------------------------------------------------------- */ #include "remap.h" +#include #include #include -- GitLab From 35e2401099f2332e1a65d3a26c23fe685e1b06e5 Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Sun, 7 Jul 2019 03:56:44 -0400 Subject: [PATCH 195/469] clean up includes in MANYBODY package --- src/MANYBODY/fix_qeq_comb.cpp | 3 - src/MANYBODY/pair_adp.cpp | 2 +- src/MANYBODY/pair_airebo.cpp | 5 -- src/MANYBODY/pair_airebo.h | 1 - src/MANYBODY/pair_airebo_morse.cpp | 2 - src/MANYBODY/pair_atm.cpp | 1 + src/MANYBODY/pair_bop.cpp | 7 +- src/MANYBODY/pair_bop.h | 104 +++++++++++--------------- src/MANYBODY/pair_comb.cpp | 3 +- src/MANYBODY/pair_comb.h | 1 - src/MANYBODY/pair_comb3.cpp | 4 +- src/MANYBODY/pair_comb3.h | 1 - src/MANYBODY/pair_eam.cpp | 2 +- src/MANYBODY/pair_eam_alloy.cpp | 3 +- src/MANYBODY/pair_eam_cd.cpp | 3 +- src/MANYBODY/pair_eam_fs.cpp | 3 +- src/MANYBODY/pair_eim.cpp | 3 +- src/MANYBODY/pair_gw.cpp | 2 +- src/MANYBODY/pair_gw_zbl.cpp | 5 +- src/MANYBODY/pair_lcbop.cpp | 21 +----- src/MANYBODY/pair_lcbop.h | 1 - src/MANYBODY/pair_nb3b_harmonic.cpp | 4 +- src/MANYBODY/pair_polymorphic.cpp | 5 +- src/MANYBODY/pair_rebo.cpp | 2 +- src/MANYBODY/pair_sw.cpp | 10 +-- src/MANYBODY/pair_tersoff.cpp | 2 +- src/MANYBODY/pair_tersoff_mod.cpp | 8 +- src/MANYBODY/pair_tersoff_mod_c.cpp | 8 +- src/MANYBODY/pair_tersoff_zbl.cpp | 7 +- src/MANYBODY/pair_vashishta.cpp | 10 +-- src/MANYBODY/pair_vashishta_table.cpp | 9 +-- 31 files changed, 77 insertions(+), 165 deletions(-) diff --git a/src/MANYBODY/fix_qeq_comb.cpp b/src/MANYBODY/fix_qeq_comb.cpp index 9e9bbcc9d6..2f324bf097 100644 --- a/src/MANYBODY/fix_qeq_comb.cpp +++ b/src/MANYBODY/fix_qeq_comb.cpp @@ -18,13 +18,10 @@ #include "fix_qeq_comb.h" #include #include -#include #include #include "pair_comb.h" #include "pair_comb3.h" -#include "neighbor.h" #include "neigh_list.h" -#include "neigh_request.h" #include "atom.h" #include "comm.h" #include "force.h" diff --git a/src/MANYBODY/pair_adp.cpp b/src/MANYBODY/pair_adp.cpp index 8051f97634..64c778659c 100644 --- a/src/MANYBODY/pair_adp.cpp +++ b/src/MANYBODY/pair_adp.cpp @@ -17,8 +17,8 @@ ------------------------------------------------------------------------- */ #include "pair_adp.h" +#include #include -#include #include #include #include "atom.h" diff --git a/src/MANYBODY/pair_airebo.cpp b/src/MANYBODY/pair_airebo.cpp index fd2016b7a7..818663222f 100644 --- a/src/MANYBODY/pair_airebo.cpp +++ b/src/MANYBODY/pair_airebo.cpp @@ -22,26 +22,21 @@ #include "pair_airebo.h" #include -#include -#include #include #include #include "atom.h" #include "neighbor.h" #include "force.h" #include "comm.h" -#include "neighbor.h" #include "neigh_list.h" #include "neigh_request.h" #include "my_page.h" -#include "math_const.h" #include "math_special.h" #include "memory.h" #include "error.h" #include "utils.h" using namespace LAMMPS_NS; -using namespace MathConst; using namespace MathSpecial; #define MAXLINE 1024 diff --git a/src/MANYBODY/pair_airebo.h b/src/MANYBODY/pair_airebo.h index 8e92807afb..04d3fc399f 100644 --- a/src/MANYBODY/pair_airebo.h +++ b/src/MANYBODY/pair_airebo.h @@ -21,7 +21,6 @@ PairStyle(airebo,PairAIREBO) #define LMP_PAIR_AIREBO_H #include "pair.h" -#include "my_page.h" #include #include "math_const.h" diff --git a/src/MANYBODY/pair_airebo_morse.cpp b/src/MANYBODY/pair_airebo_morse.cpp index a39f7df82e..121f9557fd 100644 --- a/src/MANYBODY/pair_airebo_morse.cpp +++ b/src/MANYBODY/pair_airebo_morse.cpp @@ -12,8 +12,6 @@ ------------------------------------------------------------------------- */ #include "pair_airebo_morse.h" -#include "force.h" -#include "error.h" using namespace LAMMPS_NS; diff --git a/src/MANYBODY/pair_atm.cpp b/src/MANYBODY/pair_atm.cpp index ba68033721..e604f44003 100644 --- a/src/MANYBODY/pair_atm.cpp +++ b/src/MANYBODY/pair_atm.cpp @@ -16,6 +16,7 @@ ------------------------------------------------------------------------- */ #include "pair_atm.h" +#include #include #include "atom.h" #include "citeme.h" diff --git a/src/MANYBODY/pair_bop.cpp b/src/MANYBODY/pair_bop.cpp index 27c24ce3d7..38c33e5963 100644 --- a/src/MANYBODY/pair_bop.cpp +++ b/src/MANYBODY/pair_bop.cpp @@ -34,22 +34,17 @@ #include "pair_bop.h" #include -#include -#include #include +#include #include #include "atom.h" #include "neighbor.h" #include "neigh_request.h" #include "force.h" #include "comm.h" -#include "domain.h" -#include "neighbor.h" #include "neigh_list.h" -#include "neigh_request.h" #include "memory.h" #include "error.h" -#include using namespace LAMMPS_NS; diff --git a/src/MANYBODY/pair_bop.h b/src/MANYBODY/pair_bop.h index 3bd9b8cea9..eca0ec52b8 100644 --- a/src/MANYBODY/pair_bop.h +++ b/src/MANYBODY/pair_bop.h @@ -26,8 +26,6 @@ PairStyle(bop,PairBOP) #define LMP_PAIR_BOP_H #include "pair.h" -#include -#include "update.h" namespace LAMMPS_NS { @@ -44,20 +42,20 @@ class PairBOP : public Pair { private: int me; - int maxneigh; // maximum size of neighbor list on this processor - int maxneigh3; // maximum size of neighbor list on this processor - int update_list; // check for changing maximum size of neighbor list - int maxbopn; // maximum size of bop neighbor list for allocation - int maxnall; // maximum size of bop neighbor list for allocation - int *map; // mapping from atom types to elements - int nelements; // # of unique elments - int nr; // increments for the BOP pair potential - int ntheta; // increments for the angle function - int npower; // power of the angular function - int nBOt; // second BO increments - int bop_types; // number of elments in potential - int npairs; // number of element pairs - char **elements; // names of unique elements + int maxneigh; // maximum size of neighbor list on this processor + int maxneigh3; // maximum size of neighbor list on this processor + int update_list; // check for changing maximum size of neighbor list + int maxbopn; // maximum size of bop neighbor list for allocation + int maxnall; // maximum size of bop neighbor list for allocation + int *map; // mapping from atom types to elements + int nelements; // # of unique elments + int nr; // increments for the BOP pair potential + int ntheta; // increments for the angle function + int npower; // power of the angular function + int nBOt; // second BO increments + int bop_types; // number of elments in potential + int npairs; // number of element pairs + char **elements; // names of unique elements int ***elem2param; int nparams; int bop_step; @@ -66,23 +64,22 @@ class PairBOP : public Pair { int allocate_neigh; int nb_pi,nb_sg; int ago1; -// int cnt1; - - int *BOP_index; // index for neighbor list position - int *BOP_total; // index for neighbor list position - int *BOP_index3; // index for neighbor list position - int *BOP_total3; // index for neighbor list position - int *neigh_index; // index for neighbor list position - int *neigh_index3; // index for neighbor list position - int neigh_total; // total number of neighbors stored - int neigh_total3; // total number of neighbors stored - int *cos_index; // index for neighbor cosine if not using on the fly - int *neigh_flag; // index for neighbor cosine if not using on the fly - int *neigh_flag3; // index for neighbor cosine if not using on the fly - int cos_total; // number of cosines stored if not using on the fly - int neigh_ct; // limit for large arrays - -/*Parameters variables*/ + + int *BOP_index; // index for neighbor list position + int *BOP_total; // index for neighbor list position + int *BOP_index3; // index for neighbor list position + int *BOP_total3; // index for neighbor list position + int *neigh_index; // index for neighbor list position + int *neigh_index3; // index for neighbor list position + int neigh_total; // total number of neighbors stored + int neigh_total3; // total number of neighbors stored + int *cos_index; // index for neighbor cosine if not using on the fly + int *neigh_flag; // index for neighbor cosine if not using on the fly + int *neigh_flag3; // index for neighbor cosine if not using on the fly + int cos_total; // number of cosines stored if not using on the fly + int neigh_ct; // limit for large arrays + + // Parameters variables int ncutoff,nfunc; int a_flag; @@ -98,51 +95,50 @@ class PairBOP : public Pair { double beta3,rsmall,rbig,rcore; char **words; - double cutmax; //max cutoff for all elements - int otfly; //Defines whether to do on the fly - //calculations of angles and distances - //on the fly will slow down calculations - //but requires less memory on = 1, off=0 + double cutmax; // max cutoff for all elements + int otfly; // Defines whether to do on the fly + // calculations of angles and distances + // on the fly will slow down calculations + // but requires less memory on = 1, off=0 -/* Neigh variables */ + // Neigh variables double *rcut,*rcut3,*dr,*rdr,*dr3,*rdr3; double *rcutsq,*rcutsq3; double **disij,*rij; double rcutall,rctroot; -/*Triple variables */ + // Triple variables double *cosAng,***dcosAng,***dcAng; -/*Double variables */ + // Double variables double *betaS,*dBetaS,*betaP; double *dBetaP,*repul,*dRepul; -/*Sigma variables */ + // Sigma variables int *itypeSigBk,nSigBk; double sigB,sigB_0; double sigB1; - -/*Pi variables */ + // Pi variables int *itypePiBk,nPiBk; double piB,piB_0; -/*Grids1 variables */ + // Grids1 variables double **pBetaS,**pBetaS1,**pBetaS2,**pBetaS3; double **pBetaS4,**pBetaS5,**pBetaS6; -/*Grids2 variables */ + // Grids2 variables double **pBetaP,**pBetaP1,**pBetaP2,**pBetaP3; double **pBetaP4,**pBetaP5,**pBetaP6; -/*Grids3 variables */ + // Grids3 variables double **pRepul,**pRepul1,**pRepul2,**pRepul3; double **pRepul4,**pRepul5,**pRepul6; @@ -155,13 +151,13 @@ class PairBOP : public Pair { double ****gfunc4,****gfunc5,****gfunc6; double dtheta,rdtheta; -/*Grids4 variables */ + // Grids4 variables double **FsigBO,**FsigBO1,**FsigBO2,**FsigBO3; double **FsigBO4,**FsigBO5,**FsigBO6; double dBO,rdBO; -/* End of BOP variables */ + // End of BOP variables double **rcmin,**rcmax,**rcmaxp; struct B_PI{ @@ -211,14 +207,6 @@ class PairBOP : public Pair { void memory_theta_destroy(); void memory_theta_grow(); double cutoff(double, double, int, double); -/* - double betaSfunc(int, double); - double dBetaSfunc(int, double, double, double); - double betaPfunc(int, double); - double dBetaPfunc(int, double, double, double); - double repulfunc(int, double); - double dRepulfunc(int, double, double, double); -*/ void read_table(char *); void allocate(); @@ -229,9 +217,7 @@ class PairBOP : public Pair { void grow_pi(int,int); void grow_sigma(int,int); }; - } - #endif #endif diff --git a/src/MANYBODY/pair_comb.cpp b/src/MANYBODY/pair_comb.cpp index b9a17eeb35..2fc4caec7b 100644 --- a/src/MANYBODY/pair_comb.cpp +++ b/src/MANYBODY/pair_comb.cpp @@ -19,8 +19,8 @@ ------------------------------------------------------------------------- */ #include "pair_comb.h" +#include #include -#include #include #include #include "atom.h" @@ -30,7 +30,6 @@ #include "neigh_list.h" #include "neigh_request.h" #include "group.h" -#include "update.h" #include "my_page.h" #include "math_const.h" #include "memory.h" diff --git a/src/MANYBODY/pair_comb.h b/src/MANYBODY/pair_comb.h index c798d5f347..19788dfab1 100644 --- a/src/MANYBODY/pair_comb.h +++ b/src/MANYBODY/pair_comb.h @@ -21,7 +21,6 @@ PairStyle(comb,PairComb) #define LMP_PAIR_COMB_H #include "pair.h" -#include "my_page.h" namespace LAMMPS_NS { diff --git a/src/MANYBODY/pair_comb3.cpp b/src/MANYBODY/pair_comb3.cpp index 846ef7d4b9..6f1732dbb7 100644 --- a/src/MANYBODY/pair_comb3.cpp +++ b/src/MANYBODY/pair_comb3.cpp @@ -18,18 +18,18 @@ ------------------------------------------------------------------------- */ #include "pair_comb3.h" +#include #include -#include #include #include #include "atom.h" #include "comm.h" #include "force.h" +#include "my_page.h" #include "neighbor.h" #include "neigh_list.h" #include "neigh_request.h" #include "group.h" -#include "update.h" #include "math_const.h" #include "memory.h" #include "error.h" diff --git a/src/MANYBODY/pair_comb3.h b/src/MANYBODY/pair_comb3.h index 5d7e5d6beb..210f843139 100644 --- a/src/MANYBODY/pair_comb3.h +++ b/src/MANYBODY/pair_comb3.h @@ -21,7 +21,6 @@ PairStyle(comb3,PairComb3) #define LMP_PAIR_COMB3_H #include "pair.h" -#include "my_page.h" namespace LAMMPS_NS { diff --git a/src/MANYBODY/pair_eam.cpp b/src/MANYBODY/pair_eam.cpp index e6476b78c5..acb0e654d8 100644 --- a/src/MANYBODY/pair_eam.cpp +++ b/src/MANYBODY/pair_eam.cpp @@ -16,8 +16,8 @@ ------------------------------------------------------------------------- */ #include "pair_eam.h" +#include #include -#include #include #include #include "atom.h" diff --git a/src/MANYBODY/pair_eam_alloy.cpp b/src/MANYBODY/pair_eam_alloy.cpp index 7aae786720..5b7f9877d7 100644 --- a/src/MANYBODY/pair_eam_alloy.cpp +++ b/src/MANYBODY/pair_eam_alloy.cpp @@ -16,8 +16,7 @@ ------------------------------------------------------------------------- */ #include "pair_eam_alloy.h" -#include -#include +#include #include #include "atom.h" #include "comm.h" diff --git a/src/MANYBODY/pair_eam_cd.cpp b/src/MANYBODY/pair_eam_cd.cpp index 55ad597cce..28004eae7f 100644 --- a/src/MANYBODY/pair_eam_cd.cpp +++ b/src/MANYBODY/pair_eam_cd.cpp @@ -18,14 +18,13 @@ ------------------------------------------------------------------------- */ #include "pair_eam_cd.h" +#include #include -#include #include #include #include "atom.h" #include "force.h" #include "comm.h" -#include "neighbor.h" #include "neigh_list.h" #include "memory.h" #include "error.h" diff --git a/src/MANYBODY/pair_eam_fs.cpp b/src/MANYBODY/pair_eam_fs.cpp index 7b13988d0c..7e00783922 100644 --- a/src/MANYBODY/pair_eam_fs.cpp +++ b/src/MANYBODY/pair_eam_fs.cpp @@ -16,8 +16,7 @@ ------------------------------------------------------------------------- */ #include "pair_eam_fs.h" -#include -#include +#include #include #include "atom.h" #include "comm.h" diff --git a/src/MANYBODY/pair_eim.cpp b/src/MANYBODY/pair_eim.cpp index 58cb1fd2e0..dd65d92cdd 100644 --- a/src/MANYBODY/pair_eim.cpp +++ b/src/MANYBODY/pair_eim.cpp @@ -16,9 +16,8 @@ ------------------------------------------------------------------------- */ #include "pair_eim.h" +#include #include -#include -#include #include #include "atom.h" #include "force.h" diff --git a/src/MANYBODY/pair_gw.cpp b/src/MANYBODY/pair_gw.cpp index 07e9201f94..667311812b 100644 --- a/src/MANYBODY/pair_gw.cpp +++ b/src/MANYBODY/pair_gw.cpp @@ -17,8 +17,8 @@ ------------------------------------------------------------------------- */ #include "pair_gw.h" +#include #include -#include #include #include #include "atom.h" diff --git a/src/MANYBODY/pair_gw_zbl.cpp b/src/MANYBODY/pair_gw_zbl.cpp index cd83727ed3..d39bf53b99 100644 --- a/src/MANYBODY/pair_gw_zbl.cpp +++ b/src/MANYBODY/pair_gw_zbl.cpp @@ -17,15 +17,12 @@ ------------------------------------------------------------------------- */ #include "pair_gw_zbl.h" +#include #include -#include #include #include #include "atom.h" #include "update.h" -#include "neighbor.h" -#include "neigh_list.h" -#include "neigh_request.h" #include "force.h" #include "comm.h" #include "memory.h" diff --git a/src/MANYBODY/pair_lcbop.cpp b/src/MANYBODY/pair_lcbop.cpp index b0240978a9..873a675cd9 100644 --- a/src/MANYBODY/pair_lcbop.cpp +++ b/src/MANYBODY/pair_lcbop.cpp @@ -17,26 +17,20 @@ ------------------------------------------------------------------------- */ #include "pair_lcbop.h" +#include #include -#include -#include #include -#include #include "atom.h" -#include "neighbor.h" -#include "neigh_request.h" #include "force.h" #include "comm.h" #include "neighbor.h" #include "neigh_list.h" #include "neigh_request.h" #include "my_page.h" -#include "math_const.h" #include "memory.h" #include "error.h" using namespace LAMMPS_NS; -using namespace MathConst; #define MAXLINE 1024 #define TOL 1.0e-9 @@ -1099,19 +1093,6 @@ void PairLCBOP::read_file(char *filename) init coefficients for TF_conj ------------------------------------------------------------------------- */ -#include -#include -#include -template< class function > void print_function( double x_0, double x_1, size_t n, function f, std::ostream &stream ) { - double dx = (x_1-x_0)/n; - for( double x=x_0; x<=x_1+0.0001; x+=dx ) { - double f_val, df; - f_val = f(x, &df); - stream << x << " " << f_val << " " << df << std::endl; - } - stream << std::endl; -} - void PairLCBOP::spline_init() { for( size_t N_conj_ij=0; N_conj_ij<2; N_conj_ij++ ) // N_conj_ij for( size_t N_ij=0; N_ij<4-1; N_ij++ ) diff --git a/src/MANYBODY/pair_lcbop.h b/src/MANYBODY/pair_lcbop.h index 0d7c7a51b1..c7a7fab46d 100644 --- a/src/MANYBODY/pair_lcbop.h +++ b/src/MANYBODY/pair_lcbop.h @@ -21,7 +21,6 @@ PairStyle(lcbop,PairLCBOP) #define LMP_PAIR_LCBOP_H #include "pair.h" -#include "my_page.h" #include #include "math_const.h" diff --git a/src/MANYBODY/pair_nb3b_harmonic.cpp b/src/MANYBODY/pair_nb3b_harmonic.cpp index ac20c3e61f..92456790cc 100644 --- a/src/MANYBODY/pair_nb3b_harmonic.cpp +++ b/src/MANYBODY/pair_nb3b_harmonic.cpp @@ -17,8 +17,8 @@ ------------------------------------------------------------------------- */ #include "pair_nb3b_harmonic.h" +#include #include -#include #include #include #include "atom.h" @@ -26,8 +26,6 @@ #include "neigh_request.h" #include "force.h" #include "comm.h" -#include "memory.h" -#include "neighbor.h" #include "neigh_list.h" #include "memory.h" #include "error.h" diff --git a/src/MANYBODY/pair_polymorphic.cpp b/src/MANYBODY/pair_polymorphic.cpp index 0cca50823d..d3964b292c 100644 --- a/src/MANYBODY/pair_polymorphic.cpp +++ b/src/MANYBODY/pair_polymorphic.cpp @@ -17,8 +17,8 @@ ------------------------------------------------------------------------- */ #include "pair_polymorphic.h" +#include #include -#include #include #include #include "atom.h" @@ -30,10 +30,7 @@ #include "memory.h" #include "error.h" -#include "math_const.h" - using namespace LAMMPS_NS; -using namespace MathConst; #define MAXLINE 1024 #define DELTA 4 diff --git a/src/MANYBODY/pair_rebo.cpp b/src/MANYBODY/pair_rebo.cpp index e07a1b3495..06357d8368 100644 --- a/src/MANYBODY/pair_rebo.cpp +++ b/src/MANYBODY/pair_rebo.cpp @@ -26,7 +26,7 @@ PairREBO::PairREBO(LAMMPS *lmp) : PairAIREBO(lmp) { global settings ------------------------------------------------------------------------- */ -void PairREBO::settings(int narg, char **/*arg*/) +void PairREBO::settings(int narg, char ** /* arg */) { if (narg != 0) error->all(FLERR,"Illegal pair_style command"); diff --git a/src/MANYBODY/pair_sw.cpp b/src/MANYBODY/pair_sw.cpp index ea47fc97c3..f1d1a6fa9f 100644 --- a/src/MANYBODY/pair_sw.cpp +++ b/src/MANYBODY/pair_sw.cpp @@ -16,20 +16,18 @@ ------------------------------------------------------------------------- */ #include "pair_sw.h" +#include #include -#include #include #include #include "atom.h" -#include "neighbor.h" -#include "neigh_request.h" -#include "force.h" #include "comm.h" +#include "error.h" +#include "force.h" #include "memory.h" #include "neighbor.h" #include "neigh_list.h" -#include "memory.h" -#include "error.h" +#include "neigh_request.h" using namespace LAMMPS_NS; diff --git a/src/MANYBODY/pair_tersoff.cpp b/src/MANYBODY/pair_tersoff.cpp index 9d7f804f9a..62c74576e0 100644 --- a/src/MANYBODY/pair_tersoff.cpp +++ b/src/MANYBODY/pair_tersoff.cpp @@ -16,8 +16,8 @@ ------------------------------------------------------------------------- */ #include "pair_tersoff.h" +#include #include -#include #include #include #include "atom.h" diff --git a/src/MANYBODY/pair_tersoff_mod.cpp b/src/MANYBODY/pair_tersoff_mod.cpp index df3c41fc33..698dd8fa03 100644 --- a/src/MANYBODY/pair_tersoff_mod.cpp +++ b/src/MANYBODY/pair_tersoff_mod.cpp @@ -17,21 +17,17 @@ ------------------------------------------------------------------------- */ #include "pair_tersoff_mod.h" +#include #include -#include #include #include #include "atom.h" -#include "neighbor.h" -#include "neigh_list.h" -#include "neigh_request.h" #include "force.h" #include "comm.h" +#include "math_const.h" #include "memory.h" #include "error.h" -#include "math_const.h" - using namespace LAMMPS_NS; using namespace MathConst; diff --git a/src/MANYBODY/pair_tersoff_mod_c.cpp b/src/MANYBODY/pair_tersoff_mod_c.cpp index d34291f6cd..6c2c4f4e7a 100644 --- a/src/MANYBODY/pair_tersoff_mod_c.cpp +++ b/src/MANYBODY/pair_tersoff_mod_c.cpp @@ -16,23 +16,17 @@ ------------------------------------------------------------------------- */ #include "pair_tersoff_mod_c.h" +#include #include -#include #include #include #include "atom.h" -#include "neighbor.h" -#include "neigh_list.h" -#include "neigh_request.h" #include "force.h" #include "comm.h" #include "memory.h" #include "error.h" -#include "math_const.h" - using namespace LAMMPS_NS; -using namespace MathConst; #define MAXLINE 1024 #define DELTA 4 diff --git a/src/MANYBODY/pair_tersoff_zbl.cpp b/src/MANYBODY/pair_tersoff_zbl.cpp index 6a8aa40782..ab06e6ec31 100644 --- a/src/MANYBODY/pair_tersoff_zbl.cpp +++ b/src/MANYBODY/pair_tersoff_zbl.cpp @@ -17,21 +17,18 @@ ------------------------------------------------------------------------- */ #include "pair_tersoff_zbl.h" +#include #include -#include #include #include #include "atom.h" #include "update.h" -#include "neighbor.h" -#include "neigh_list.h" -#include "neigh_request.h" #include "force.h" #include "comm.h" #include "memory.h" #include "error.h" - #include "math_const.h" + using namespace LAMMPS_NS; using namespace MathConst; diff --git a/src/MANYBODY/pair_vashishta.cpp b/src/MANYBODY/pair_vashishta.cpp index 5055dadfaf..13b44c58a4 100644 --- a/src/MANYBODY/pair_vashishta.cpp +++ b/src/MANYBODY/pair_vashishta.cpp @@ -17,20 +17,18 @@ ------------------------------------------------------------------------- */ #include "pair_vashishta.h" +#include #include -#include #include #include #include "atom.h" -#include "neighbor.h" -#include "neigh_request.h" -#include "force.h" #include "comm.h" +#include "error.h" +#include "force.h" #include "memory.h" #include "neighbor.h" #include "neigh_list.h" -#include "memory.h" -#include "error.h" +#include "neigh_request.h" using namespace LAMMPS_NS; diff --git a/src/MANYBODY/pair_vashishta_table.cpp b/src/MANYBODY/pair_vashishta_table.cpp index 726e0f83f1..bf39183b9d 100644 --- a/src/MANYBODY/pair_vashishta_table.cpp +++ b/src/MANYBODY/pair_vashishta_table.cpp @@ -16,20 +16,13 @@ ------------------------------------------------------------------------- */ #include "pair_vashishta_table.h" -#include #include -#include -#include #include "atom.h" -#include "neighbor.h" -#include "neigh_request.h" +#include "error.h" #include "force.h" #include "comm.h" #include "memory.h" -#include "neighbor.h" #include "neigh_list.h" -#include "memory.h" -#include "error.h" using namespace LAMMPS_NS; -- GitLab From e5af9db84c7aee6f86e8cb1598fd99e65c4689d0 Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Sun, 7 Jul 2019 11:49:13 -0400 Subject: [PATCH 196/469] clean up includes in MC and MISC package --- src/MC/fix_atom_swap.cpp | 11 ++--------- src/MC/fix_bond_break.cpp | 4 ---- src/MC/fix_bond_create.cpp | 3 --- src/MC/fix_gcmc.cpp | 1 - src/MC/fix_tfmc.cpp | 1 - src/MC/pair_dsmc.cpp | 4 +--- src/MISC/compute_msd_nongauss.cpp | 3 +-- src/MISC/compute_ti.cpp | 1 - src/MISC/dump_xtc.cpp | 1 - src/MISC/fix_deposit.cpp | 2 +- src/MISC/fix_efield.cpp | 3 +-- src/MISC/fix_evaporate.cpp | 4 +--- src/MISC/fix_gld.cpp | 5 +---- src/MISC/fix_oneway.cpp | 1 - src/MISC/fix_orient_bcc.cpp | 1 - src/MISC/fix_orient_fcc.cpp | 1 - src/MISC/fix_thermal_conductivity.cpp | 2 -- src/MISC/fix_ttm.cpp | 2 -- src/MISC/fix_viscosity.cpp | 3 +-- src/MISC/pair_nm_cut.cpp | 3 +-- src/MISC/pair_nm_cut_coul_cut.cpp | 3 +-- src/MISC/pair_nm_cut_coul_long.cpp | 6 +----- src/MISC/xdr_compat.cpp | 1 - src/MISC/xdr_compat.h | 1 - 24 files changed, 12 insertions(+), 55 deletions(-) diff --git a/src/MC/fix_atom_swap.cpp b/src/MC/fix_atom_swap.cpp index c14efcca46..9a4a0b6a7f 100644 --- a/src/MC/fix_atom_swap.cpp +++ b/src/MC/fix_atom_swap.cpp @@ -17,13 +17,12 @@ ------------------------------------------------------------------------- */ #include "fix_atom_swap.h" +#include #include +#include #include -#include #include #include "atom.h" -#include "atom_vec.h" -#include "atom_vec_hybrid.h" #include "update.h" #include "modify.h" #include "fix.h" @@ -40,18 +39,12 @@ #include "dihedral.h" #include "improper.h" #include "kspace.h" -#include "math_const.h" #include "memory.h" #include "error.h" -#include "thermo.h" -#include "output.h" #include "neighbor.h" -#include -using namespace std; using namespace LAMMPS_NS; using namespace FixConst; -using namespace MathConst; /* ---------------------------------------------------------------------- */ diff --git a/src/MC/fix_bond_break.cpp b/src/MC/fix_bond_break.cpp index 1b07395f1e..2ff0e4126f 100644 --- a/src/MC/fix_bond_break.cpp +++ b/src/MC/fix_bond_break.cpp @@ -12,18 +12,14 @@ ------------------------------------------------------------------------- */ #include "fix_bond_break.h" -#include #include #include -#include #include "update.h" #include "respa.h" #include "atom.h" -#include "atom_vec.h" #include "force.h" #include "comm.h" #include "neighbor.h" -#include "domain.h" #include "random_mars.h" #include "memory.h" #include "error.h" diff --git a/src/MC/fix_bond_create.cpp b/src/MC/fix_bond_create.cpp index d2d93b67f6..3f63a22d60 100644 --- a/src/MC/fix_bond_create.cpp +++ b/src/MC/fix_bond_create.cpp @@ -12,14 +12,11 @@ ------------------------------------------------------------------------- */ #include "fix_bond_create.h" -#include #include #include -#include #include "update.h" #include "respa.h" #include "atom.h" -#include "atom_vec.h" #include "force.h" #include "pair.h" #include "comm.h" diff --git a/src/MC/fix_gcmc.cpp b/src/MC/fix_gcmc.cpp index 8fe6042c2e..1050fd4712 100644 --- a/src/MC/fix_gcmc.cpp +++ b/src/MC/fix_gcmc.cpp @@ -21,7 +21,6 @@ #include #include "atom.h" #include "atom_vec.h" -#include "atom_vec_hybrid.h" #include "molecule.h" #include "update.h" #include "modify.h" diff --git a/src/MC/fix_tfmc.cpp b/src/MC/fix_tfmc.cpp index 46c5e592ae..e57f1cdf4a 100644 --- a/src/MC/fix_tfmc.cpp +++ b/src/MC/fix_tfmc.cpp @@ -22,7 +22,6 @@ #include #include "atom.h" #include "force.h" -#include "update.h" #include "group.h" #include "random_mars.h" #include "comm.h" diff --git a/src/MC/pair_dsmc.cpp b/src/MC/pair_dsmc.cpp index cf48706133..43bffa7e8d 100644 --- a/src/MC/pair_dsmc.cpp +++ b/src/MC/pair_dsmc.cpp @@ -16,10 +16,8 @@ ------------------------------------------------------------------------- */ #include "pair_dsmc.h" +#include #include -#include -#include -#include #include #include "atom.h" #include "comm.h" diff --git a/src/MISC/compute_msd_nongauss.cpp b/src/MISC/compute_msd_nongauss.cpp index e02dd633cb..6123bf49af 100644 --- a/src/MISC/compute_msd_nongauss.cpp +++ b/src/MISC/compute_msd_nongauss.cpp @@ -16,13 +16,12 @@ ------------------------------------------------------------------------- */ #include "compute_msd_nongauss.h" -#include +#include #include "atom.h" #include "update.h" #include "group.h" #include "domain.h" #include "fix_store.h" -#include "error.h" using namespace LAMMPS_NS; diff --git a/src/MISC/compute_ti.cpp b/src/MISC/compute_ti.cpp index 266263785f..06188de238 100644 --- a/src/MISC/compute_ti.cpp +++ b/src/MISC/compute_ti.cpp @@ -20,7 +20,6 @@ #include #include "atom.h" #include "update.h" -#include "modify.h" #include "domain.h" #include "force.h" #include "pair.h" diff --git a/src/MISC/dump_xtc.cpp b/src/MISC/dump_xtc.cpp index 7abe4c4093..1a2b71ab6d 100644 --- a/src/MISC/dump_xtc.cpp +++ b/src/MISC/dump_xtc.cpp @@ -24,7 +24,6 @@ #include "dump_xtc.h" #include -#include #include #include #include diff --git a/src/MISC/fix_deposit.cpp b/src/MISC/fix_deposit.cpp index 22a144da60..c9d4958594 100644 --- a/src/MISC/fix_deposit.cpp +++ b/src/MISC/fix_deposit.cpp @@ -12,8 +12,8 @@ ------------------------------------------------------------------------- */ #include "fix_deposit.h" +#include #include -#include #include #include "atom.h" #include "atom_vec.h" diff --git a/src/MISC/fix_efield.cpp b/src/MISC/fix_efield.cpp index 87ece82f57..5a13b93b91 100644 --- a/src/MISC/fix_efield.cpp +++ b/src/MISC/fix_efield.cpp @@ -17,9 +17,8 @@ ------------------------------------------------------------------------- */ #include "fix_efield.h" -#include +#include #include -#include #include "atom.h" #include "update.h" #include "domain.h" diff --git a/src/MISC/fix_evaporate.cpp b/src/MISC/fix_evaporate.cpp index e2c7844853..d868254c50 100644 --- a/src/MISC/fix_evaporate.cpp +++ b/src/MISC/fix_evaporate.cpp @@ -12,8 +12,7 @@ ------------------------------------------------------------------------- */ #include "fix_evaporate.h" -#include -#include +#include #include #include "atom.h" #include "atom_vec.h" @@ -25,7 +24,6 @@ #include "force.h" #include "group.h" #include "random_park.h" -#include "random_mars.h" #include "memory.h" #include "error.h" diff --git a/src/MISC/fix_gld.cpp b/src/MISC/fix_gld.cpp index 265ee4fb09..380c038e4a 100644 --- a/src/MISC/fix_gld.cpp +++ b/src/MISC/fix_gld.cpp @@ -17,17 +17,14 @@ ------------------------------------------------------------------------- */ #include "fix_gld.h" +#include #include -#include #include -#include "math_extra.h" #include "atom.h" #include "force.h" #include "update.h" #include "respa.h" #include "comm.h" -#include "input.h" -#include "variable.h" #include "random_mars.h" #include "memory.h" #include "error.h" diff --git a/src/MISC/fix_oneway.cpp b/src/MISC/fix_oneway.cpp index fcf5a7a0bd..68a27b68be 100644 --- a/src/MISC/fix_oneway.cpp +++ b/src/MISC/fix_oneway.cpp @@ -22,7 +22,6 @@ #include "error.h" #include "force.h" #include "region.h" -#include "error.h" using namespace LAMMPS_NS; using namespace FixConst; diff --git a/src/MISC/fix_orient_bcc.cpp b/src/MISC/fix_orient_bcc.cpp index a300631658..1453ceb317 100644 --- a/src/MISC/fix_orient_bcc.cpp +++ b/src/MISC/fix_orient_bcc.cpp @@ -30,7 +30,6 @@ #include "neigh_list.h" #include "neigh_request.h" #include "comm.h" -#include "output.h" #include "force.h" #include "math_const.h" #include "citeme.h" diff --git a/src/MISC/fix_orient_fcc.cpp b/src/MISC/fix_orient_fcc.cpp index d898f95d2c..082ecaf459 100644 --- a/src/MISC/fix_orient_fcc.cpp +++ b/src/MISC/fix_orient_fcc.cpp @@ -27,7 +27,6 @@ #include "neigh_list.h" #include "neigh_request.h" #include "comm.h" -#include "output.h" #include "force.h" #include "math_const.h" #include "citeme.h" diff --git a/src/MISC/fix_thermal_conductivity.cpp b/src/MISC/fix_thermal_conductivity.cpp index 8da303c8ab..d0add6fecb 100644 --- a/src/MISC/fix_thermal_conductivity.cpp +++ b/src/MISC/fix_thermal_conductivity.cpp @@ -17,10 +17,8 @@ ------------------------------------------------------------------------- */ #include "fix_thermal_conductivity.h" -#include #include #include -#include #include "atom.h" #include "force.h" #include "domain.h" diff --git a/src/MISC/fix_ttm.cpp b/src/MISC/fix_ttm.cpp index 06de732de6..eb9eb2620d 100644 --- a/src/MISC/fix_ttm.cpp +++ b/src/MISC/fix_ttm.cpp @@ -20,12 +20,10 @@ #include #include #include -#include #include "atom.h" #include "force.h" #include "update.h" #include "domain.h" -#include "region.h" #include "respa.h" #include "comm.h" #include "random_mars.h" diff --git a/src/MISC/fix_viscosity.cpp b/src/MISC/fix_viscosity.cpp index 52107954c2..d5a97cd4b0 100644 --- a/src/MISC/fix_viscosity.cpp +++ b/src/MISC/fix_viscosity.cpp @@ -17,10 +17,9 @@ ------------------------------------------------------------------------- */ #include "fix_viscosity.h" -#include #include +#include #include -#include #include "atom.h" #include "domain.h" #include "modify.h" diff --git a/src/MISC/pair_nm_cut.cpp b/src/MISC/pair_nm_cut.cpp index 9b8c36da3a..a084491a78 100644 --- a/src/MISC/pair_nm_cut.cpp +++ b/src/MISC/pair_nm_cut.cpp @@ -16,9 +16,8 @@ ------------------------------------------------------------------------- */ #include "pair_nm_cut.h" +#include #include -#include -#include #include #include "atom.h" #include "comm.h" diff --git a/src/MISC/pair_nm_cut_coul_cut.cpp b/src/MISC/pair_nm_cut_coul_cut.cpp index 069c363817..df8a34062a 100644 --- a/src/MISC/pair_nm_cut_coul_cut.cpp +++ b/src/MISC/pair_nm_cut_coul_cut.cpp @@ -16,9 +16,8 @@ ------------------------------------------------------------------------- */ #include "pair_nm_cut_coul_cut.h" +#include #include -#include -#include #include #include "atom.h" #include "comm.h" diff --git a/src/MISC/pair_nm_cut_coul_long.cpp b/src/MISC/pair_nm_cut_coul_long.cpp index b3d42b05f8..4109fb0d9e 100644 --- a/src/MISC/pair_nm_cut_coul_long.cpp +++ b/src/MISC/pair_nm_cut_coul_long.cpp @@ -16,19 +16,15 @@ ------------------------------------------------------------------------- */ #include "pair_nm_cut_coul_long.h" +#include #include -#include -#include #include #include "atom.h" #include "comm.h" #include "force.h" #include "kspace.h" -#include "update.h" -#include "integrate.h" #include "neighbor.h" #include "neigh_list.h" -#include "neigh_request.h" #include "math_const.h" #include "memory.h" #include "error.h" diff --git a/src/MISC/xdr_compat.cpp b/src/MISC/xdr_compat.cpp index e124d52d7b..9806b0bbd2 100644 --- a/src/MISC/xdr_compat.cpp +++ b/src/MISC/xdr_compat.cpp @@ -1,6 +1,5 @@ #include "xdr_compat.h" #include -#include #include /* This file is needed for systems, that do not provide XDR support diff --git a/src/MISC/xdr_compat.h b/src/MISC/xdr_compat.h index 3062235080..5dfa01e0e8 100644 --- a/src/MISC/xdr_compat.h +++ b/src/MISC/xdr_compat.h @@ -3,7 +3,6 @@ #include #include -#include #ifdef __cplusplus extern "C" { -- GitLab From 57a558854908efe838e9da312389b49080149862 Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Sun, 7 Jul 2019 15:46:34 -0400 Subject: [PATCH 197/469] cleaning up include file handling in packages MOLECULE and PERI --- src/MOLECULE/angle_charmm.cpp | 2 +- src/MOLECULE/angle_cosine.cpp | 2 +- src/MOLECULE/angle_cosine_delta.cpp | 4 ---- src/MOLECULE/angle_cosine_periodic.cpp | 2 +- src/MOLECULE/angle_cosine_squared.cpp | 2 +- src/MOLECULE/angle_harmonic.cpp | 2 +- src/MOLECULE/angle_table.cpp | 1 + src/MOLECULE/atom_vec_template.cpp | 1 - src/MOLECULE/bond_fene.cpp | 3 +-- src/MOLECULE/bond_fene_expand.cpp | 3 +-- src/MOLECULE/bond_gromos.cpp | 4 +--- src/MOLECULE/bond_harmonic.cpp | 3 +-- src/MOLECULE/bond_morse.cpp | 3 +-- src/MOLECULE/bond_nonlinear.cpp | 3 +-- src/MOLECULE/bond_quartic.cpp | 4 +--- src/MOLECULE/bond_table.cpp | 2 +- src/MOLECULE/dihedral_charmm.cpp | 2 -- src/MOLECULE/dihedral_charmmfsw.cpp | 2 -- src/MOLECULE/dihedral_harmonic.cpp | 2 -- src/MOLECULE/dihedral_helix.cpp | 2 -- src/MOLECULE/dihedral_multi_harmonic.cpp | 3 +-- src/MOLECULE/dihedral_opls.cpp | 3 +-- src/MOLECULE/fix_cmap.cpp | 4 ---- src/MOLECULE/improper_cvff.cpp | 2 -- src/MOLECULE/improper_harmonic.cpp | 2 -- src/MOLECULE/improper_umbrella.cpp | 2 -- src/MOLECULE/pair_hbond_dreiding_lj.cpp | 3 --- src/MOLECULE/pair_hbond_dreiding_morse.cpp | 3 --- src/MOLECULE/pair_lj_charmm_coul_charmm.cpp | 3 +-- .../pair_lj_charmm_coul_charmm_implicit.cpp | 2 -- .../pair_lj_charmmfsw_coul_charmmfsh.cpp | 3 +-- src/MOLECULE/pair_lj_cut_tip4p_cut.cpp | 2 +- src/MOLECULE/pair_tip4p_cut.cpp | 4 +--- src/PERI/compute_damage_atom.cpp | 2 -- src/PERI/compute_dilatation_atom.cpp | 4 +--- src/PERI/compute_plasticity_atom.cpp | 3 +-- src/PERI/fix_peri_neigh.cpp | 3 +-- src/PERI/pair_peri_eps.cpp | 16 +++++++--------- src/PERI/pair_peri_lps.cpp | 4 +--- src/PERI/pair_peri_pmb.cpp | 4 +--- src/PERI/pair_peri_ves.cpp | 16 ++++++++-------- 41 files changed, 40 insertions(+), 97 deletions(-) diff --git a/src/MOLECULE/angle_charmm.cpp b/src/MOLECULE/angle_charmm.cpp index fb0afd78c3..8a45f29368 100644 --- a/src/MOLECULE/angle_charmm.cpp +++ b/src/MOLECULE/angle_charmm.cpp @@ -16,8 +16,8 @@ ------------------------------------------------------------------------- */ #include "angle_charmm.h" +#include #include -#include #include "atom.h" #include "neighbor.h" #include "domain.h" diff --git a/src/MOLECULE/angle_cosine.cpp b/src/MOLECULE/angle_cosine.cpp index aff5130323..645cf66ff2 100644 --- a/src/MOLECULE/angle_cosine.cpp +++ b/src/MOLECULE/angle_cosine.cpp @@ -12,8 +12,8 @@ ------------------------------------------------------------------------- */ #include "angle_cosine.h" +#include #include -#include #include "atom.h" #include "neighbor.h" #include "domain.h" diff --git a/src/MOLECULE/angle_cosine_delta.cpp b/src/MOLECULE/angle_cosine_delta.cpp index 13ed00b327..679a8deb0e 100644 --- a/src/MOLECULE/angle_cosine_delta.cpp +++ b/src/MOLECULE/angle_cosine_delta.cpp @@ -17,14 +17,10 @@ #include "angle_cosine_delta.h" #include -#include #include "atom.h" #include "neighbor.h" #include "domain.h" -#include "comm.h" #include "force.h" -#include "memory.h" -#include "error.h" using namespace LAMMPS_NS; diff --git a/src/MOLECULE/angle_cosine_periodic.cpp b/src/MOLECULE/angle_cosine_periodic.cpp index 9f7c02cabc..22c2f7ce8b 100644 --- a/src/MOLECULE/angle_cosine_periodic.cpp +++ b/src/MOLECULE/angle_cosine_periodic.cpp @@ -16,8 +16,8 @@ ------------------------------------------------------------------------- */ #include "angle_cosine_periodic.h" +#include #include -#include #include "atom.h" #include "neighbor.h" #include "domain.h" diff --git a/src/MOLECULE/angle_cosine_squared.cpp b/src/MOLECULE/angle_cosine_squared.cpp index 789a536c98..56b3ee58cf 100644 --- a/src/MOLECULE/angle_cosine_squared.cpp +++ b/src/MOLECULE/angle_cosine_squared.cpp @@ -16,8 +16,8 @@ ------------------------------------------------------------------------- */ #include "angle_cosine_squared.h" +#include #include -#include #include "atom.h" #include "neighbor.h" #include "domain.h" diff --git a/src/MOLECULE/angle_harmonic.cpp b/src/MOLECULE/angle_harmonic.cpp index b626bdfae5..2e96884c9d 100644 --- a/src/MOLECULE/angle_harmonic.cpp +++ b/src/MOLECULE/angle_harmonic.cpp @@ -12,8 +12,8 @@ ------------------------------------------------------------------------- */ #include "angle_harmonic.h" +#include #include -#include #include "atom.h" #include "neighbor.h" #include "domain.h" diff --git a/src/MOLECULE/angle_table.cpp b/src/MOLECULE/angle_table.cpp index ce7fcdcaf2..f05a8c6a4e 100644 --- a/src/MOLECULE/angle_table.cpp +++ b/src/MOLECULE/angle_table.cpp @@ -16,6 +16,7 @@ ------------------------------------------------------------------------- */ #include "angle_table.h" +#include #include #include #include diff --git a/src/MOLECULE/atom_vec_template.cpp b/src/MOLECULE/atom_vec_template.cpp index 6a12027b7b..4c5f576943 100644 --- a/src/MOLECULE/atom_vec_template.cpp +++ b/src/MOLECULE/atom_vec_template.cpp @@ -12,7 +12,6 @@ ------------------------------------------------------------------------- */ #include "atom_vec_template.h" -#include #include #include "atom.h" #include "molecule.h" diff --git a/src/MOLECULE/bond_fene.cpp b/src/MOLECULE/bond_fene.cpp index d4f2a4010e..776291701b 100644 --- a/src/MOLECULE/bond_fene.cpp +++ b/src/MOLECULE/bond_fene.cpp @@ -12,11 +12,10 @@ ------------------------------------------------------------------------- */ #include "bond_fene.h" +#include #include -#include #include "atom.h" #include "neighbor.h" -#include "domain.h" #include "comm.h" #include "update.h" #include "force.h" diff --git a/src/MOLECULE/bond_fene_expand.cpp b/src/MOLECULE/bond_fene_expand.cpp index 3e4ceab42c..d03dfd9125 100644 --- a/src/MOLECULE/bond_fene_expand.cpp +++ b/src/MOLECULE/bond_fene_expand.cpp @@ -12,11 +12,10 @@ ------------------------------------------------------------------------- */ #include "bond_fene_expand.h" +#include #include -#include #include "atom.h" #include "neighbor.h" -#include "domain.h" #include "comm.h" #include "update.h" #include "force.h" diff --git a/src/MOLECULE/bond_gromos.cpp b/src/MOLECULE/bond_gromos.cpp index 44e99d8fe0..284c9202fd 100644 --- a/src/MOLECULE/bond_gromos.cpp +++ b/src/MOLECULE/bond_gromos.cpp @@ -16,12 +16,10 @@ ------------------------------------------------------------------------- */ #include "bond_gromos.h" -#include -#include +#include #include #include "atom.h" #include "neighbor.h" -#include "domain.h" #include "comm.h" #include "force.h" #include "memory.h" diff --git a/src/MOLECULE/bond_harmonic.cpp b/src/MOLECULE/bond_harmonic.cpp index bbbad4102d..7b19034629 100644 --- a/src/MOLECULE/bond_harmonic.cpp +++ b/src/MOLECULE/bond_harmonic.cpp @@ -12,12 +12,11 @@ ------------------------------------------------------------------------- */ #include "bond_harmonic.h" +#include #include -#include #include #include "atom.h" #include "neighbor.h" -#include "domain.h" #include "comm.h" #include "force.h" #include "memory.h" diff --git a/src/MOLECULE/bond_morse.cpp b/src/MOLECULE/bond_morse.cpp index af476d6fe8..6e16070cae 100644 --- a/src/MOLECULE/bond_morse.cpp +++ b/src/MOLECULE/bond_morse.cpp @@ -16,11 +16,10 @@ ------------------------------------------------------------------------- */ #include "bond_morse.h" +#include #include -#include #include "atom.h" #include "neighbor.h" -#include "domain.h" #include "comm.h" #include "force.h" #include "memory.h" diff --git a/src/MOLECULE/bond_nonlinear.cpp b/src/MOLECULE/bond_nonlinear.cpp index 89ddb7b118..e06b1b9aac 100644 --- a/src/MOLECULE/bond_nonlinear.cpp +++ b/src/MOLECULE/bond_nonlinear.cpp @@ -12,11 +12,10 @@ ------------------------------------------------------------------------- */ #include "bond_nonlinear.h" +#include #include -#include #include "atom.h" #include "neighbor.h" -#include "domain.h" #include "comm.h" #include "force.h" #include "memory.h" diff --git a/src/MOLECULE/bond_quartic.cpp b/src/MOLECULE/bond_quartic.cpp index 34b3ad8288..352b642bbe 100644 --- a/src/MOLECULE/bond_quartic.cpp +++ b/src/MOLECULE/bond_quartic.cpp @@ -16,13 +16,11 @@ ------------------------------------------------------------------------- */ #include "bond_quartic.h" +#include #include -#include #include "atom.h" #include "neighbor.h" -#include "domain.h" #include "comm.h" -#include "update.h" #include "force.h" #include "pair.h" #include "memory.h" diff --git a/src/MOLECULE/bond_table.cpp b/src/MOLECULE/bond_table.cpp index e80baee6e8..137690d002 100644 --- a/src/MOLECULE/bond_table.cpp +++ b/src/MOLECULE/bond_table.cpp @@ -16,12 +16,12 @@ ------------------------------------------------------------------------- */ #include "bond_table.h" +#include #include #include #include #include "atom.h" #include "neighbor.h" -#include "domain.h" #include "comm.h" #include "force.h" #include "memory.h" diff --git a/src/MOLECULE/dihedral_charmm.cpp b/src/MOLECULE/dihedral_charmm.cpp index 1905c14358..8cc0713024 100644 --- a/src/MOLECULE/dihedral_charmm.cpp +++ b/src/MOLECULE/dihedral_charmm.cpp @@ -18,12 +18,10 @@ #include "dihedral_charmm.h" #include #include -#include #include #include "atom.h" #include "comm.h" #include "neighbor.h" -#include "domain.h" #include "force.h" #include "pair.h" #include "update.h" diff --git a/src/MOLECULE/dihedral_charmmfsw.cpp b/src/MOLECULE/dihedral_charmmfsw.cpp index 9b02b908d6..f384c4cd36 100644 --- a/src/MOLECULE/dihedral_charmmfsw.cpp +++ b/src/MOLECULE/dihedral_charmmfsw.cpp @@ -21,12 +21,10 @@ #include "dihedral_charmmfsw.h" #include #include -#include #include #include "atom.h" #include "comm.h" #include "neighbor.h" -#include "domain.h" #include "force.h" #include "pair.h" #include "update.h" diff --git a/src/MOLECULE/dihedral_harmonic.cpp b/src/MOLECULE/dihedral_harmonic.cpp index 159636ecd5..f1e5811a84 100644 --- a/src/MOLECULE/dihedral_harmonic.cpp +++ b/src/MOLECULE/dihedral_harmonic.cpp @@ -18,11 +18,9 @@ #include "dihedral_harmonic.h" #include #include -#include #include "atom.h" #include "comm.h" #include "neighbor.h" -#include "domain.h" #include "force.h" #include "update.h" #include "memory.h" diff --git a/src/MOLECULE/dihedral_helix.cpp b/src/MOLECULE/dihedral_helix.cpp index a7d2aba1d6..56f7a3b5e8 100644 --- a/src/MOLECULE/dihedral_helix.cpp +++ b/src/MOLECULE/dihedral_helix.cpp @@ -19,10 +19,8 @@ #include "dihedral_helix.h" #include #include -#include #include "atom.h" #include "neighbor.h" -#include "domain.h" #include "comm.h" #include "force.h" #include "update.h" diff --git a/src/MOLECULE/dihedral_multi_harmonic.cpp b/src/MOLECULE/dihedral_multi_harmonic.cpp index ba98cf6ddf..eda7cede3e 100644 --- a/src/MOLECULE/dihedral_multi_harmonic.cpp +++ b/src/MOLECULE/dihedral_multi_harmonic.cpp @@ -16,11 +16,10 @@ ------------------------------------------------------------------------- */ #include "dihedral_multi_harmonic.h" +#include #include -#include #include "atom.h" #include "neighbor.h" -#include "domain.h" #include "comm.h" #include "force.h" #include "update.h" diff --git a/src/MOLECULE/dihedral_opls.cpp b/src/MOLECULE/dihedral_opls.cpp index d68eba0bec..556efd850a 100644 --- a/src/MOLECULE/dihedral_opls.cpp +++ b/src/MOLECULE/dihedral_opls.cpp @@ -16,12 +16,11 @@ ------------------------------------------------------------------------- */ #include "dihedral_opls.h" +#include #include -#include #include "atom.h" #include "comm.h" #include "neighbor.h" -#include "domain.h" #include "force.h" #include "update.h" #include "memory.h" diff --git a/src/MOLECULE/fix_cmap.cpp b/src/MOLECULE/fix_cmap.cpp index 3d5bf90bdc..fb0a550898 100644 --- a/src/MOLECULE/fix_cmap.cpp +++ b/src/MOLECULE/fix_cmap.cpp @@ -32,15 +32,11 @@ #include #include #include -#include #include "atom.h" -#include "atom_vec.h" #include "update.h" #include "respa.h" -#include "modify.h" #include "domain.h" #include "force.h" -#include "group.h" #include "comm.h" #include "math_const.h" #include "memory.h" diff --git a/src/MOLECULE/improper_cvff.cpp b/src/MOLECULE/improper_cvff.cpp index fd24ab69c3..abd2d4e11e 100644 --- a/src/MOLECULE/improper_cvff.cpp +++ b/src/MOLECULE/improper_cvff.cpp @@ -14,11 +14,9 @@ #include "improper_cvff.h" #include #include -#include #include "atom.h" #include "comm.h" #include "neighbor.h" -#include "domain.h" #include "force.h" #include "update.h" #include "memory.h" diff --git a/src/MOLECULE/improper_harmonic.cpp b/src/MOLECULE/improper_harmonic.cpp index 936c22e94a..778fe646e1 100644 --- a/src/MOLECULE/improper_harmonic.cpp +++ b/src/MOLECULE/improper_harmonic.cpp @@ -14,11 +14,9 @@ #include "improper_harmonic.h" #include #include -#include #include "atom.h" #include "comm.h" #include "neighbor.h" -#include "domain.h" #include "force.h" #include "update.h" #include "math_const.h" diff --git a/src/MOLECULE/improper_umbrella.cpp b/src/MOLECULE/improper_umbrella.cpp index 2e41ac6493..d3adf19993 100644 --- a/src/MOLECULE/improper_umbrella.cpp +++ b/src/MOLECULE/improper_umbrella.cpp @@ -18,11 +18,9 @@ #include "improper_umbrella.h" #include #include -#include #include "atom.h" #include "comm.h" #include "neighbor.h" -#include "domain.h" #include "force.h" #include "update.h" #include "math_const.h" diff --git a/src/MOLECULE/pair_hbond_dreiding_lj.cpp b/src/MOLECULE/pair_hbond_dreiding_lj.cpp index 58666f27d1..53c3101708 100644 --- a/src/MOLECULE/pair_hbond_dreiding_lj.cpp +++ b/src/MOLECULE/pair_hbond_dreiding_lj.cpp @@ -17,13 +17,10 @@ #include "pair_hbond_dreiding_lj.h" #include -#include -#include #include #include "atom.h" #include "atom_vec.h" #include "molecule.h" -#include "comm.h" #include "force.h" #include "neighbor.h" #include "neigh_request.h" diff --git a/src/MOLECULE/pair_hbond_dreiding_morse.cpp b/src/MOLECULE/pair_hbond_dreiding_morse.cpp index 120a2d8d55..3039a662e6 100644 --- a/src/MOLECULE/pair_hbond_dreiding_morse.cpp +++ b/src/MOLECULE/pair_hbond_dreiding_morse.cpp @@ -17,13 +17,10 @@ #include "pair_hbond_dreiding_morse.h" #include -#include -#include #include #include "atom.h" #include "atom_vec.h" #include "molecule.h" -#include "comm.h" #include "force.h" #include "neighbor.h" #include "neigh_request.h" diff --git a/src/MOLECULE/pair_lj_charmm_coul_charmm.cpp b/src/MOLECULE/pair_lj_charmm_coul_charmm.cpp index c9becb75c3..5ebfe0a110 100644 --- a/src/MOLECULE/pair_lj_charmm_coul_charmm.cpp +++ b/src/MOLECULE/pair_lj_charmm_coul_charmm.cpp @@ -16,9 +16,8 @@ ------------------------------------------------------------------------- */ #include "pair_lj_charmm_coul_charmm.h" +#include #include -#include -#include #include #include "atom.h" #include "comm.h" diff --git a/src/MOLECULE/pair_lj_charmm_coul_charmm_implicit.cpp b/src/MOLECULE/pair_lj_charmm_coul_charmm_implicit.cpp index a2be2936b2..ff7dbb290b 100644 --- a/src/MOLECULE/pair_lj_charmm_coul_charmm_implicit.cpp +++ b/src/MOLECULE/pair_lj_charmm_coul_charmm_implicit.cpp @@ -12,8 +12,6 @@ ------------------------------------------------------------------------- */ #include "pair_lj_charmm_coul_charmm_implicit.h" -#include -#include #include "atom.h" #include "force.h" #include "neigh_list.h" diff --git a/src/MOLECULE/pair_lj_charmmfsw_coul_charmmfsh.cpp b/src/MOLECULE/pair_lj_charmmfsw_coul_charmmfsh.cpp index f2f16c88ce..4fb7cc5229 100644 --- a/src/MOLECULE/pair_lj_charmmfsw_coul_charmmfsh.cpp +++ b/src/MOLECULE/pair_lj_charmmfsw_coul_charmmfsh.cpp @@ -20,9 +20,8 @@ ------------------------------------------------------------------------- */ #include "pair_lj_charmmfsw_coul_charmmfsh.h" +#include #include -#include -#include #include #include "atom.h" #include "update.h" diff --git a/src/MOLECULE/pair_lj_cut_tip4p_cut.cpp b/src/MOLECULE/pair_lj_cut_tip4p_cut.cpp index 5bb82d7635..e5f25a511b 100644 --- a/src/MOLECULE/pair_lj_cut_tip4p_cut.cpp +++ b/src/MOLECULE/pair_lj_cut_tip4p_cut.cpp @@ -16,8 +16,8 @@ ------------------------------------------------------------------------- */ #include "pair_lj_cut_tip4p_cut.h" +#include #include -#include #include #include "atom.h" #include "force.h" diff --git a/src/MOLECULE/pair_tip4p_cut.cpp b/src/MOLECULE/pair_tip4p_cut.cpp index 1511c09384..3a6702c9b2 100644 --- a/src/MOLECULE/pair_tip4p_cut.cpp +++ b/src/MOLECULE/pair_tip4p_cut.cpp @@ -16,8 +16,8 @@ ------------------------------------------------------------------------- */ #include "pair_tip4p_cut.h" +#include #include -#include #include "atom.h" #include "force.h" #include "neighbor.h" @@ -26,12 +26,10 @@ #include "angle.h" #include "bond.h" #include "comm.h" -#include "math_const.h" #include "memory.h" #include "error.h" using namespace LAMMPS_NS; -using namespace MathConst; /* ---------------------------------------------------------------------- */ diff --git a/src/PERI/compute_damage_atom.cpp b/src/PERI/compute_damage_atom.cpp index f5a532cd0b..230b766725 100644 --- a/src/PERI/compute_damage_atom.cpp +++ b/src/PERI/compute_damage_atom.cpp @@ -21,8 +21,6 @@ #include "update.h" #include "modify.h" #include "comm.h" -#include "force.h" -#include "pair_peri_pmb.h" #include "fix_peri_neigh.h" #include "memory.h" #include "error.h" diff --git a/src/PERI/compute_dilatation_atom.cpp b/src/PERI/compute_dilatation_atom.cpp index 7a6607d65c..095f619838 100644 --- a/src/PERI/compute_dilatation_atom.cpp +++ b/src/PERI/compute_dilatation_atom.cpp @@ -21,13 +21,11 @@ #include "update.h" #include "modify.h" #include "comm.h" +#include "fix.h" #include "force.h" -#include "pair.h" #include "pair_peri_lps.h" -#include "pair_peri_pmb.h" #include "pair_peri_ves.h" #include "pair_peri_eps.h" -#include "fix_peri_neigh.h" #include "memory.h" #include "error.h" diff --git a/src/PERI/compute_plasticity_atom.cpp b/src/PERI/compute_plasticity_atom.cpp index 0b20bc5075..e312630b62 100644 --- a/src/PERI/compute_plasticity_atom.cpp +++ b/src/PERI/compute_plasticity_atom.cpp @@ -21,9 +21,8 @@ #include "update.h" #include "modify.h" #include "comm.h" -#include "force.h" -#include "pair_peri_pmb.h" #include "fix_peri_neigh.h" +#include "force.h" #include "memory.h" #include "error.h" diff --git a/src/PERI/fix_peri_neigh.cpp b/src/PERI/fix_peri_neigh.cpp index 297936577f..70f46dcdc1 100644 --- a/src/PERI/fix_peri_neigh.cpp +++ b/src/PERI/fix_peri_neigh.cpp @@ -16,8 +16,8 @@ ------------------------------------------------------------------------- */ #include "fix_peri_neigh.h" +#include #include -#include "pair_peri_pmb.h" #include "pair_peri_lps.h" #include "pair_peri_ves.h" #include "pair_peri_eps.h" @@ -25,7 +25,6 @@ #include "domain.h" #include "force.h" #include "comm.h" -#include "update.h" #include "neighbor.h" #include "neigh_list.h" #include "neigh_request.h" diff --git a/src/PERI/pair_peri_eps.cpp b/src/PERI/pair_peri_eps.cpp index 07314081da..2579a9b75a 100644 --- a/src/PERI/pair_peri_eps.cpp +++ b/src/PERI/pair_peri_eps.cpp @@ -16,14 +16,13 @@ ------------------------------------------------------------------------- */ #include "pair_peri_eps.h" +#include #include -#include #include #include "atom.h" #include "domain.h" #include "lattice.h" #include "force.h" -#include "update.h" #include "modify.h" #include "fix.h" #include "fix_peri_neigh.h" @@ -32,7 +31,6 @@ #include "neigh_list.h" #include "memory.h" #include "error.h" -#include "update.h" using namespace LAMMPS_NS; @@ -451,12 +449,12 @@ void PairPeriEPS::coeff(int narg, char **arg) force->bounds(FLERR,arg[0],atom->ntypes,ilo,ihi); force->bounds(FLERR,arg[1],atom->ntypes,jlo,jhi); - double bulkmodulus_one = atof(arg[2]); - double shearmodulus_one = atof(arg[3]); - double cut_one = atof(arg[4]); - double s00_one = atof(arg[5]); - double alpha_one = atof(arg[6]); - double myieldstress_one = atof(arg[7]); + double bulkmodulus_one = force->numeric(FLERR,arg[2]); + double shearmodulus_one = force->numeric(FLERR,arg[3]); + double cut_one = force->numeric(FLERR,arg[4]); + double s00_one = force->numeric(FLERR,arg[5]); + double alpha_one = force->numeric(FLERR,arg[6]); + double myieldstress_one = force->numeric(FLERR,arg[7]); int count = 0; for (int i = ilo; i <= ihi; i++) { diff --git a/src/PERI/pair_peri_lps.cpp b/src/PERI/pair_peri_lps.cpp index 660209f3f5..f32ce5fb1c 100644 --- a/src/PERI/pair_peri_lps.cpp +++ b/src/PERI/pair_peri_lps.cpp @@ -16,14 +16,13 @@ ------------------------------------------------------------------------- */ #include "pair_peri_lps.h" +#include #include -#include #include #include "atom.h" #include "domain.h" #include "lattice.h" #include "force.h" -#include "update.h" #include "modify.h" #include "fix.h" #include "fix_peri_neigh.h" @@ -32,7 +31,6 @@ #include "neigh_list.h" #include "memory.h" #include "error.h" -#include "update.h" #include "math_const.h" using namespace LAMMPS_NS; diff --git a/src/PERI/pair_peri_pmb.cpp b/src/PERI/pair_peri_pmb.cpp index fa53efc344..ceab40d88d 100644 --- a/src/PERI/pair_peri_pmb.cpp +++ b/src/PERI/pair_peri_pmb.cpp @@ -16,22 +16,20 @@ ------------------------------------------------------------------------- */ #include "pair_peri_pmb.h" +#include #include #include -#include #include #include "atom.h" #include "domain.h" #include "lattice.h" #include "force.h" -#include "update.h" #include "modify.h" #include "fix.h" #include "fix_peri_neigh.h" #include "comm.h" #include "neighbor.h" #include "neigh_list.h" -#include "neigh_request.h" #include "memory.h" #include "error.h" diff --git a/src/PERI/pair_peri_ves.cpp b/src/PERI/pair_peri_ves.cpp index 1687bed35d..930ecc6812 100644 --- a/src/PERI/pair_peri_ves.cpp +++ b/src/PERI/pair_peri_ves.cpp @@ -16,6 +16,7 @@ ------------------------------------------------------------------------- */ #include "pair_peri_ves.h" +#include #include #include #include @@ -23,7 +24,6 @@ #include "domain.h" #include "lattice.h" #include "force.h" -#include "update.h" #include "modify.h" #include "fix.h" #include "fix_peri_neigh.h" @@ -428,13 +428,13 @@ void PairPeriVES::coeff(int narg, char **arg) force->bounds(FLERR,arg[0],atom->ntypes,ilo,ihi); force->bounds(FLERR,arg[1],atom->ntypes,jlo,jhi); - double bulkmodulus_one = atof(arg[2]); - double shearmodulus_one = atof(arg[3]); - double cut_one = atof(arg[4]); - double s00_one = atof(arg[5]); - double alpha_one = atof(arg[6]); - double mlambdai_one = atof(arg[7]); - double mtaui_one = atof(arg[8]); + double bulkmodulus_one = force->numeric(FLERR,arg[2]); + double shearmodulus_one = force->numeric(FLERR,arg[3]); + double cut_one = force->numeric(FLERR,arg[4]); + double s00_one = force->numeric(FLERR,arg[5]); + double alpha_one = force->numeric(FLERR,arg[6]); + double mlambdai_one = force->numeric(FLERR,arg[7]); + double mtaui_one = force->numeric(FLERR,arg[8]); int count = 0; for (int i = ilo; i <= ihi; i++) { -- GitLab From 15e1b39531f6d7f17d748b1e1358f5839ffba641 Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Sun, 7 Jul 2019 15:52:21 -0400 Subject: [PATCH 198/469] validate more numbers read from data files through using force->numeric()/force->inumeric() instead of atof()/atoi() --- src/DIPOLE/atom_vec_dipole.cpp | 18 ++++---- src/KOKKOS/atom_vec_angle_kokkos.cpp | 8 ++-- src/KOKKOS/atom_vec_atomic_kokkos.cpp | 4 +- src/KOKKOS/atom_vec_bond_kokkos.cpp | 8 ++-- src/KOKKOS/atom_vec_charge_kokkos.cpp | 8 ++-- src/KOKKOS/atom_vec_dpd_kokkos.cpp | 6 +-- src/KOKKOS/atom_vec_full_kokkos.cpp | 12 ++--- src/KOKKOS/atom_vec_hybrid_kokkos.cpp | 8 ++-- src/KOKKOS/atom_vec_molecular_kokkos.cpp | 8 ++-- src/KOKKOS/atom_vec_sphere_kokkos.cpp | 28 ++++++------ src/MOLECULE/atom_vec_angle.cpp | 2 +- src/MOLECULE/atom_vec_bond.cpp | 2 +- src/MOLECULE/atom_vec_full.cpp | 6 +-- src/MOLECULE/atom_vec_molecular.cpp | 2 +- src/MOLECULE/atom_vec_template.cpp | 10 ++-- src/PERI/atom_vec_peri.cpp | 10 ++-- src/SPIN/atom_vec_spin.cpp | 18 ++++---- src/USER-AWPMD/atom_vec_wavepacket.cpp | 36 +++++++-------- src/USER-DPD/atom_vec_dpd.cpp | 6 +-- src/USER-EFF/atom_vec_electron.cpp | 24 +++++----- src/USER-MESO/atom_vec_edpd.cpp | 6 +-- src/USER-MESO/atom_vec_mdpd.cpp | 6 +-- src/USER-MESO/atom_vec_tdpd.cpp | 2 +- src/USER-SMD/atom_vec_smd.cpp | 28 ++++++------ src/USER-SPH/atom_vec_meso.cpp | 14 +++--- src/atom_vec.cpp | 6 +-- src/atom_vec_atomic.cpp | 2 +- src/atom_vec_body.cpp | 28 ++++++------ src/atom_vec_charge.cpp | 6 +-- src/atom_vec_ellipsoid.cpp | 42 ++++++++--------- src/atom_vec_hybrid.cpp | 8 ++-- src/atom_vec_line.cpp | 36 +++++++-------- src/atom_vec_sphere.cpp | 28 ++++++------ src/atom_vec_tri.cpp | 58 ++++++++++++------------ 34 files changed, 247 insertions(+), 247 deletions(-) diff --git a/src/DIPOLE/atom_vec_dipole.cpp b/src/DIPOLE/atom_vec_dipole.cpp index c304ae3bc6..c6f8fbb432 100644 --- a/src/DIPOLE/atom_vec_dipole.cpp +++ b/src/DIPOLE/atom_vec_dipole.cpp @@ -780,19 +780,19 @@ void AtomVecDipole::data_atom(double *coord, imageint imagetmp, char **values) if (nlocal == nmax) grow(0); tag[nlocal] = ATOTAGINT(values[0]); - type[nlocal] = atoi(values[1]); + type[nlocal] = force->inumeric(FLERR,values[1]); if (type[nlocal] <= 0 || type[nlocal] > atom->ntypes) error->one(FLERR,"Invalid atom type in Atoms section of data file"); - q[nlocal] = atof(values[2]); + q[nlocal] = force->numeric(FLERR,values[2]); x[nlocal][0] = coord[0]; x[nlocal][1] = coord[1]; x[nlocal][2] = coord[2]; - mu[nlocal][0] = atof(values[6]); - mu[nlocal][1] = atof(values[7]); - mu[nlocal][2] = atof(values[8]); + mu[nlocal][0] = force->numeric(FLERR,values[6]); + mu[nlocal][1] = force->numeric(FLERR,values[7]); + mu[nlocal][2] = force->numeric(FLERR,values[8]); mu[nlocal][3] = sqrt(mu[nlocal][0]*mu[nlocal][0] + mu[nlocal][1]*mu[nlocal][1] + mu[nlocal][2]*mu[nlocal][2]); @@ -814,10 +814,10 @@ void AtomVecDipole::data_atom(double *coord, imageint imagetmp, char **values) int AtomVecDipole::data_atom_hybrid(int nlocal, char **values) { - q[nlocal] = atof(values[0]); - mu[nlocal][0] = atof(values[1]); - mu[nlocal][1] = atof(values[2]); - mu[nlocal][2] = atof(values[3]); + q[nlocal] = force->numeric(FLERR,values[0]); + mu[nlocal][0] = force->numeric(FLERR,values[1]); + mu[nlocal][1] = force->numeric(FLERR,values[2]); + mu[nlocal][2] = force->numeric(FLERR,values[3]); mu[nlocal][3] = sqrt(mu[nlocal][0]*mu[nlocal][0] + mu[nlocal][1]*mu[nlocal][1] + mu[nlocal][2]*mu[nlocal][2]); diff --git a/src/KOKKOS/atom_vec_angle_kokkos.cpp b/src/KOKKOS/atom_vec_angle_kokkos.cpp index e4f27e733a..36fa47c712 100644 --- a/src/KOKKOS/atom_vec_angle_kokkos.cpp +++ b/src/KOKKOS/atom_vec_angle_kokkos.cpp @@ -1632,9 +1632,9 @@ void AtomVecAngleKokkos::data_atom(double *coord, imageint imagetmp, if (nlocal == nmax) grow(0); atomKK->modified(Host,ALL_MASK); - h_tag(nlocal) = atoi(values[0]); - h_molecule(nlocal) = atoi(values[1]); - h_type(nlocal) = atoi(values[2]); + h_tag(nlocal) = force->inumeric(FLERR,values[0]); + h_molecule(nlocal) = force->inumeric(FLERR,values[1]); + h_type(nlocal) = force->inumeric(FLERR,values[2]); if (h_type(nlocal) <= 0 || h_type(nlocal) > atom->ntypes) error->one(FLERR,"Invalid atom type in Atoms section of data file"); @@ -1661,7 +1661,7 @@ void AtomVecAngleKokkos::data_atom(double *coord, imageint imagetmp, int AtomVecAngleKokkos::data_atom_hybrid(int nlocal, char **values) { - h_molecule(nlocal) = atoi(values[0]); + h_molecule(nlocal) = force->inumeric(FLERR,values[0]); h_num_bond(nlocal) = 0; h_num_angle(nlocal) = 0; return 1; diff --git a/src/KOKKOS/atom_vec_atomic_kokkos.cpp b/src/KOKKOS/atom_vec_atomic_kokkos.cpp index 95e4ddd72b..61703d1cc8 100644 --- a/src/KOKKOS/atom_vec_atomic_kokkos.cpp +++ b/src/KOKKOS/atom_vec_atomic_kokkos.cpp @@ -823,8 +823,8 @@ void AtomVecAtomicKokkos::data_atom(double *coord, tagint imagetmp, int nlocal = atom->nlocal; if (nlocal == nmax) grow(0); - h_tag[nlocal] = atoi(values[0]); - h_type[nlocal] = atoi(values[1]); + h_tag[nlocal] = force->inumeric(FLERR,values[0]); + h_type[nlocal] = force->inumeric(FLERR,values[1]); if (type[nlocal] <= 0 || type[nlocal] > atom->ntypes) error->one(FLERR,"Invalid atom type in Atoms section of data file"); diff --git a/src/KOKKOS/atom_vec_bond_kokkos.cpp b/src/KOKKOS/atom_vec_bond_kokkos.cpp index 92311d5d09..bbf9f58b58 100644 --- a/src/KOKKOS/atom_vec_bond_kokkos.cpp +++ b/src/KOKKOS/atom_vec_bond_kokkos.cpp @@ -1058,9 +1058,9 @@ void AtomVecBondKokkos::data_atom(double *coord, imageint imagetmp, if (nlocal == nmax) grow(0); atomKK->modified(Host,ALL_MASK); - h_tag(nlocal) = atoi(values[0]); - h_molecule(nlocal) = atoi(values[1]); - h_type(nlocal) = atoi(values[2]); + h_tag(nlocal) = force->inumeric(FLERR,values[0]); + h_molecule(nlocal) = force->inumeric(FLERR,values[1]); + h_type(nlocal) = force->inumeric(FLERR,values[2]); if (h_type(nlocal) <= 0 || h_type(nlocal) > atom->ntypes) error->one(FLERR,"Invalid atom type in Atoms section of data file"); @@ -1086,7 +1086,7 @@ void AtomVecBondKokkos::data_atom(double *coord, imageint imagetmp, int AtomVecBondKokkos::data_atom_hybrid(int nlocal, char **values) { - h_molecule(nlocal) = atoi(values[0]); + h_molecule(nlocal) = force->inumeric(FLERR,values[0]); h_num_bond(nlocal) = 0; return 1; } diff --git a/src/KOKKOS/atom_vec_charge_kokkos.cpp b/src/KOKKOS/atom_vec_charge_kokkos.cpp index 31a690f521..be267d8b16 100644 --- a/src/KOKKOS/atom_vec_charge_kokkos.cpp +++ b/src/KOKKOS/atom_vec_charge_kokkos.cpp @@ -959,12 +959,12 @@ void AtomVecChargeKokkos::data_atom(double *coord, imageint imagetmp, int nlocal = atom->nlocal; if (nlocal == nmax) grow(0); - h_tag[nlocal] = atoi(values[0]); - h_type[nlocal] = atoi(values[1]); + h_tag[nlocal] = force->inumeric(FLERR,values[0]); + h_type[nlocal] = force->inumeric(FLERR,values[1]); if (type[nlocal] <= 0 || type[nlocal] > atom->ntypes) error->one(FLERR,"Invalid atom type in Atoms section of data file"); - h_q[nlocal] = atof(values[2]); + h_q[nlocal] = force->numeric(FLERR,values[2]); h_x(nlocal,0) = coord[0]; h_x(nlocal,1) = coord[1]; @@ -988,7 +988,7 @@ void AtomVecChargeKokkos::data_atom(double *coord, imageint imagetmp, int AtomVecChargeKokkos::data_atom_hybrid(int nlocal, char **values) { - h_q[nlocal] = atof(values[0]); + h_q[nlocal] = force->numeric(FLERR,values[0]); return 1; } diff --git a/src/KOKKOS/atom_vec_dpd_kokkos.cpp b/src/KOKKOS/atom_vec_dpd_kokkos.cpp index 4034efee9e..ffbfc75a93 100644 --- a/src/KOKKOS/atom_vec_dpd_kokkos.cpp +++ b/src/KOKKOS/atom_vec_dpd_kokkos.cpp @@ -1723,11 +1723,11 @@ void AtomVecDPDKokkos::data_atom(double *coord, tagint imagetmp, if (nlocal == nmax) grow(0); h_tag[nlocal] = ATOTAGINT(values[0]); - h_type[nlocal] = atoi(values[1]); + h_type[nlocal] = force->inumeric(FLERR,values[1]); if (type[nlocal] <= 0 || type[nlocal] > atom->ntypes) error->one(FLERR,"Invalid atom type in Atoms section of data file"); - h_dpdTheta[nlocal] = atof(values[2]); + h_dpdTheta[nlocal] = force->numeric(FLERR,values[2]); if (h_dpdTheta[nlocal] <= 0) error->one(FLERR,"Internal temperature in Atoms section of date file must be > zero"); @@ -1761,7 +1761,7 @@ void AtomVecDPDKokkos::data_atom(double *coord, tagint imagetmp, int AtomVecDPDKokkos::data_atom_hybrid(int nlocal, char **values) { - h_dpdTheta(nlocal) = atof(values[0]); + h_dpdTheta(nlocal) = force->numeric(FLERR,values[0]); atomKK->modified(Host,DPDTHETA_MASK); diff --git a/src/KOKKOS/atom_vec_full_kokkos.cpp b/src/KOKKOS/atom_vec_full_kokkos.cpp index 034da88f73..1974c12ebb 100644 --- a/src/KOKKOS/atom_vec_full_kokkos.cpp +++ b/src/KOKKOS/atom_vec_full_kokkos.cpp @@ -1487,13 +1487,13 @@ void AtomVecFullKokkos::data_atom(double *coord, imageint imagetmp, if (nlocal == nmax) grow(0); atomKK->modified(Host,ALL_MASK); - h_tag(nlocal) = atoi(values[0]); - h_molecule(nlocal) = atoi(values[1]); - h_type(nlocal) = atoi(values[2]); + h_tag(nlocal) = force->inumeric(FLERR,values[0]); + h_molecule(nlocal) = force->inumeric(FLERR,values[1]); + h_type(nlocal) = force->inumeric(FLERR,values[2]); if (h_type(nlocal) <= 0 || h_type(nlocal) > atom->ntypes) error->one(FLERR,"Invalid atom type in Atoms section of data file"); - h_q(nlocal) = atof(values[3]); + h_q(nlocal) = force->numeric(FLERR,values[3]); h_x(nlocal,0) = coord[0]; h_x(nlocal,1) = coord[1]; @@ -1520,8 +1520,8 @@ void AtomVecFullKokkos::data_atom(double *coord, imageint imagetmp, int AtomVecFullKokkos::data_atom_hybrid(int nlocal, char **values) { - h_molecule(nlocal) = atoi(values[0]); - h_q(nlocal) = atof(values[1]); + h_molecule(nlocal) = force->inumeric(FLERR,values[0]); + h_q(nlocal) = force->numeric(FLERR,values[1]); h_num_bond(nlocal) = 0; h_num_angle(nlocal) = 0; h_num_dihedral(nlocal) = 0; diff --git a/src/KOKKOS/atom_vec_hybrid_kokkos.cpp b/src/KOKKOS/atom_vec_hybrid_kokkos.cpp index 03cbe1ee5e..88dbdd068a 100644 --- a/src/KOKKOS/atom_vec_hybrid_kokkos.cpp +++ b/src/KOKKOS/atom_vec_hybrid_kokkos.cpp @@ -975,7 +975,7 @@ void AtomVecHybridKokkos::data_atom(double *coord, imageint imagetmp, char **val if (nlocal == nmax) grow(0); h_tag[nlocal] = ATOTAGINT(values[0]); - h_type[nlocal] = atoi(values[1]); + h_type[nlocal] = force->inumeric(FLERR,values[1]); if (h_type[nlocal] <= 0 || h_type[nlocal] > atom->ntypes) error->one(FLERR,"Invalid atom h_type in Atoms section of data file"); @@ -1019,9 +1019,9 @@ void AtomVecHybridKokkos::data_vel(int m, char **values) { atomKK->sync(Host,V_MASK); - h_v(m,0) = atof(values[0]); - h_v(m,1) = atof(values[1]); - h_v(m,2) = atof(values[2]); + h_v(m,0) = force->numeric(FLERR,values[0]); + h_v(m,1) = force->numeric(FLERR,values[1]); + h_v(m,2) = force->numeric(FLERR,values[2]); atomKK->modified(Host,V_MASK); diff --git a/src/KOKKOS/atom_vec_molecular_kokkos.cpp b/src/KOKKOS/atom_vec_molecular_kokkos.cpp index 9ac8ecd264..060228f37e 100644 --- a/src/KOKKOS/atom_vec_molecular_kokkos.cpp +++ b/src/KOKKOS/atom_vec_molecular_kokkos.cpp @@ -1891,9 +1891,9 @@ void AtomVecMolecularKokkos::data_atom(double *coord, imageint imagetmp, if (nlocal == nmax) grow(0); atomKK->modified(Host,ALL_MASK); - h_tag(nlocal) = atoi(values[0]); - h_molecule(nlocal) = atoi(values[1]); - h_type(nlocal) = atoi(values[2]); + h_tag(nlocal) = force->inumeric(FLERR,values[0]); + h_molecule(nlocal) = force->inumeric(FLERR,values[1]); + h_type(nlocal) = force->inumeric(FLERR,values[2]); if (h_type(nlocal) <= 0 || h_type(nlocal) > atom->ntypes) error->one(FLERR,"Invalid atom type in Atoms section of data file"); @@ -1922,7 +1922,7 @@ void AtomVecMolecularKokkos::data_atom(double *coord, imageint imagetmp, int AtomVecMolecularKokkos::data_atom_hybrid(int nlocal, char **values) { - h_molecule(nlocal) = atoi(values[0]); + h_molecule(nlocal) = force->inumeric(FLERR,values[0]); h_num_bond(nlocal) = 0; h_num_angle(nlocal) = 0; h_num_dihedral(nlocal) = 0; diff --git a/src/KOKKOS/atom_vec_sphere_kokkos.cpp b/src/KOKKOS/atom_vec_sphere_kokkos.cpp index 9e8388488f..57dc7ef43d 100644 --- a/src/KOKKOS/atom_vec_sphere_kokkos.cpp +++ b/src/KOKKOS/atom_vec_sphere_kokkos.cpp @@ -2549,15 +2549,15 @@ void AtomVecSphereKokkos::data_atom(double *coord, imageint imagetmp, char **val if (nlocal == nmax) grow(0); tag[nlocal] = ATOTAGINT(values[0]); - type[nlocal] = atoi(values[1]); + type[nlocal] = force->inumeric(FLERR,values[1]); if (type[nlocal] <= 0 || type[nlocal] > atom->ntypes) error->one(FLERR,"Invalid atom type in Atoms section of data file"); - radius[nlocal] = 0.5 * atof(values[2]); + radius[nlocal] = 0.5 * force->numeric(FLERR,values[2]); if (radius[nlocal] < 0.0) error->one(FLERR,"Invalid radius in Atoms section of data file"); - double density = atof(values[3]); + double density = force->numeric(FLERR,values[3]); if (density <= 0.0) error->one(FLERR,"Invalid density in Atoms section of data file"); @@ -2592,11 +2592,11 @@ void AtomVecSphereKokkos::data_atom(double *coord, imageint imagetmp, char **val int AtomVecSphereKokkos::data_atom_hybrid(int nlocal, char **values) { - radius[nlocal] = 0.5 * atof(values[0]); + radius[nlocal] = 0.5 * force->numeric(FLERR,values[0]); if (radius[nlocal] < 0.0) error->one(FLERR,"Invalid radius in Atoms section of data file"); - double density = atof(values[1]); + double density = force->numeric(FLERR,values[1]); if (density <= 0.0) error->one(FLERR,"Invalid density in Atoms section of data file"); @@ -2618,12 +2618,12 @@ int AtomVecSphereKokkos::data_atom_hybrid(int nlocal, char **values) void AtomVecSphereKokkos::data_vel(int m, char **values) { atomKK->sync(Host,V_MASK|OMEGA_MASK); - h_v(m,0) = atof(values[0]); - h_v(m,1) = atof(values[1]); - h_v(m,2) = atof(values[2]); - h_omega(m,0) = atof(values[3]); - h_omega(m,1) = atof(values[4]); - h_omega(m,2) = atof(values[5]); + h_v(m,0) = force->numeric(FLERR,values[0]); + h_v(m,1) = force->numeric(FLERR,values[1]); + h_v(m,2) = force->numeric(FLERR,values[2]); + h_omega(m,0) = force->numeric(FLERR,values[3]); + h_omega(m,1) = force->numeric(FLERR,values[4]); + h_omega(m,2) = force->numeric(FLERR,values[5]); atomKK->modified(Host,V_MASK|OMEGA_MASK); } @@ -2634,9 +2634,9 @@ void AtomVecSphereKokkos::data_vel(int m, char **values) int AtomVecSphereKokkos::data_vel_hybrid(int m, char **values) { atomKK->sync(Host,OMEGA_MASK); - omega[m][0] = atof(values[0]); - omega[m][1] = atof(values[1]); - omega[m][2] = atof(values[2]); + omega[m][0] = force->numeric(FLERR,values[0]); + omega[m][1] = force->numeric(FLERR,values[1]); + omega[m][2] = force->numeric(FLERR,values[2]); atomKK->modified(Host,OMEGA_MASK); return 3; } diff --git a/src/MOLECULE/atom_vec_angle.cpp b/src/MOLECULE/atom_vec_angle.cpp index 6eb5b50fd2..338ac2879e 100644 --- a/src/MOLECULE/atom_vec_angle.cpp +++ b/src/MOLECULE/atom_vec_angle.cpp @@ -793,7 +793,7 @@ void AtomVecAngle::data_atom(double *coord, imageint imagetmp, char **values) tag[nlocal] = ATOTAGINT(values[0]); molecule[nlocal] = ATOTAGINT(values[1]); - type[nlocal] = atoi(values[2]); + type[nlocal] = force->inumeric(FLERR,values[2]); if (type[nlocal] <= 0 || type[nlocal] > atom->ntypes) error->one(FLERR,"Invalid atom type in Atoms section of data file"); diff --git a/src/MOLECULE/atom_vec_bond.cpp b/src/MOLECULE/atom_vec_bond.cpp index 6a7b3585b4..96797bcd55 100644 --- a/src/MOLECULE/atom_vec_bond.cpp +++ b/src/MOLECULE/atom_vec_bond.cpp @@ -739,7 +739,7 @@ void AtomVecBond::data_atom(double *coord, imageint imagetmp, char **values) tag[nlocal] = ATOTAGINT(values[0]); molecule[nlocal] = ATOTAGINT(values[1]); - type[nlocal] = atoi(values[2]); + type[nlocal] = force->inumeric(FLERR,values[2]); if (type[nlocal] <= 0 || type[nlocal] > atom->ntypes) error->one(FLERR,"Invalid atom type in Atoms section of data file"); diff --git a/src/MOLECULE/atom_vec_full.cpp b/src/MOLECULE/atom_vec_full.cpp index d682abf799..bfd1864d6e 100644 --- a/src/MOLECULE/atom_vec_full.cpp +++ b/src/MOLECULE/atom_vec_full.cpp @@ -942,11 +942,11 @@ void AtomVecFull::data_atom(double *coord, imageint imagetmp, char **values) tag[nlocal] = ATOTAGINT(values[0]); molecule[nlocal] = ATOTAGINT(values[1]); - type[nlocal] = atoi(values[2]); + type[nlocal] = force->inumeric(FLERR,values[2]); if (type[nlocal] <= 0 || type[nlocal] > atom->ntypes) error->one(FLERR,"Invalid atom type in Atoms section of data file"); - q[nlocal] = atof(values[3]); + q[nlocal] = force->numeric(FLERR,values[3]); x[nlocal][0] = coord[0]; x[nlocal][1] = coord[1]; @@ -974,7 +974,7 @@ void AtomVecFull::data_atom(double *coord, imageint imagetmp, char **values) int AtomVecFull::data_atom_hybrid(int nlocal, char **values) { molecule[nlocal] = ATOTAGINT(values[0]); - q[nlocal] = atof(values[1]); + q[nlocal] = force->numeric(FLERR,values[1]); num_bond[nlocal] = 0; num_angle[nlocal] = 0; diff --git a/src/MOLECULE/atom_vec_molecular.cpp b/src/MOLECULE/atom_vec_molecular.cpp index cdd3f02505..7e4d4fadad 100644 --- a/src/MOLECULE/atom_vec_molecular.cpp +++ b/src/MOLECULE/atom_vec_molecular.cpp @@ -926,7 +926,7 @@ void AtomVecMolecular::data_atom(double *coord, imageint imagetmp, tag[nlocal] = ATOTAGINT(values[0]); molecule[nlocal] = ATOTAGINT(values[1]); - type[nlocal] = atoi(values[2]); + type[nlocal] = force->inumeric(FLERR,values[2]); if (type[nlocal] <= 0 || type[nlocal] > atom->ntypes) error->one(FLERR,"Invalid atom type in Atoms section of data file"); diff --git a/src/MOLECULE/atom_vec_template.cpp b/src/MOLECULE/atom_vec_template.cpp index 3172804b95..c856684330 100644 --- a/src/MOLECULE/atom_vec_template.cpp +++ b/src/MOLECULE/atom_vec_template.cpp @@ -745,8 +745,8 @@ void AtomVecTemplate::data_atom(double *coord, imageint imagetmp, char **values) error->one(FLERR,"Invalid atom ID in Atoms section of data file"); molecule[nlocal] = ATOTAGINT(values[1]); - molindex[nlocal] = atoi(values[2]) - 1; - molatom[nlocal] = atoi(values[3]) - 1; + molindex[nlocal] = force->inumeric(FLERR,values[2]) - 1; + molatom[nlocal] = force->inumeric(FLERR,values[3]) - 1; if (molindex[nlocal] < 0 || molindex[nlocal] >= nset) error->one(FLERR,"Invalid template index in Atoms section of data file"); @@ -754,7 +754,7 @@ void AtomVecTemplate::data_atom(double *coord, imageint imagetmp, char **values) molatom[nlocal] >= onemols[molindex[nlocal]]->natoms) error->one(FLERR,"Invalid template atom in Atoms section of data file"); - type[nlocal] = atoi(values[4]); + type[nlocal] = force->inumeric(FLERR,values[4]); if (type[nlocal] <= 0 || type[nlocal] > atom->ntypes) error->one(FLERR,"Invalid atom type in Atoms section of data file"); @@ -780,8 +780,8 @@ void AtomVecTemplate::data_atom(double *coord, imageint imagetmp, char **values) int AtomVecTemplate::data_atom_hybrid(int nlocal, char **values) { molecule[nlocal] = ATOTAGINT(values[0]); - molindex[nlocal] = atoi(values[1]) - 1; - molatom[nlocal] = atoi(values[2]) - 1; + molindex[nlocal] = force->inumeric(FLERR,values[1]) - 1; + molatom[nlocal] = force->inumeric(FLERR,values[2]) - 1; return 3; } diff --git a/src/PERI/atom_vec_peri.cpp b/src/PERI/atom_vec_peri.cpp index d78fe27c94..a8a94b86c9 100644 --- a/src/PERI/atom_vec_peri.cpp +++ b/src/PERI/atom_vec_peri.cpp @@ -792,12 +792,12 @@ void AtomVecPeri::data_atom(double *coord, imageint imagetmp, char **values) if (nlocal == nmax) grow(0); tag[nlocal] = ATOTAGINT(values[0]); - type[nlocal] = atoi(values[1]); + type[nlocal] = force->inumeric(FLERR,values[1]); if (type[nlocal] <= 0 || type[nlocal] > atom->ntypes) error->one(FLERR,"Invalid atom type in Atoms section of data file"); - vfrac[nlocal] = atof(values[2]); - rmass[nlocal] = atof(values[3]); + vfrac[nlocal] = force->numeric(FLERR,values[2]); + rmass[nlocal] = force->numeric(FLERR,values[3]); if (rmass[nlocal] <= 0.0) error->one(FLERR,"Invalid mass value"); x[nlocal][0] = coord[0]; @@ -826,8 +826,8 @@ void AtomVecPeri::data_atom(double *coord, imageint imagetmp, char **values) int AtomVecPeri::data_atom_hybrid(int nlocal, char **values) { - vfrac[nlocal] = atof(values[0]); - rmass[nlocal] = atof(values[1]); + vfrac[nlocal] = force->numeric(FLERR,values[0]); + rmass[nlocal] = force->numeric(FLERR,values[1]); if (rmass[nlocal] <= 0.0) error->one(FLERR,"Invalid mass value"); s0[nlocal] = DBL_MAX; diff --git a/src/SPIN/atom_vec_spin.cpp b/src/SPIN/atom_vec_spin.cpp index 37d6fb1e59..1d82114fe8 100644 --- a/src/SPIN/atom_vec_spin.cpp +++ b/src/SPIN/atom_vec_spin.cpp @@ -812,7 +812,7 @@ void AtomVecSpin::data_atom(double *coord, imageint imagetmp, char **values) if (nlocal == nmax) grow(0); tag[nlocal] = ATOTAGINT(values[0]); - type[nlocal] = atoi(values[1]); + type[nlocal] = force->inumeric(FLERR,values[1]); if (type[nlocal] <= 0 || type[nlocal] > atom->ntypes) error->one(FLERR,"Invalid atom type in Atoms section of data file"); @@ -820,10 +820,10 @@ void AtomVecSpin::data_atom(double *coord, imageint imagetmp, char **values) x[nlocal][1] = coord[1]; x[nlocal][2] = coord[2]; - sp[nlocal][3] = atof(values[2]); - sp[nlocal][0] = atof(values[6]); - sp[nlocal][1] = atof(values[7]); - sp[nlocal][2] = atof(values[8]); + sp[nlocal][3] = force->numeric(FLERR,values[2]); + sp[nlocal][0] = force->numeric(FLERR,values[6]); + sp[nlocal][1] = force->numeric(FLERR,values[7]); + sp[nlocal][2] = force->numeric(FLERR,values[8]); double inorm = 1.0/sqrt(sp[nlocal][0]*sp[nlocal][0] + sp[nlocal][1]*sp[nlocal][1] + sp[nlocal][2]*sp[nlocal][2]); @@ -849,16 +849,16 @@ void AtomVecSpin::data_atom(double *coord, imageint imagetmp, char **values) int AtomVecSpin::data_atom_hybrid(int nlocal, char **values) { - sp[nlocal][0] = atof(values[0]); - sp[nlocal][1] = atof(values[1]); - sp[nlocal][2] = atof(values[2]); + sp[nlocal][0] = force->numeric(FLERR,values[0]); + sp[nlocal][1] = force->numeric(FLERR,values[1]); + sp[nlocal][2] = force->numeric(FLERR,values[2]); double inorm = 1.0/sqrt(sp[nlocal][0]*sp[nlocal][0] + sp[nlocal][1]*sp[nlocal][1] + sp[nlocal][2]*sp[nlocal][2]); sp[nlocal][0] *= inorm; sp[nlocal][1] *= inorm; sp[nlocal][2] *= inorm; - sp[nlocal][3] = atof(values[3]); + sp[nlocal][3] = force->numeric(FLERR,values[3]); return 4; } diff --git a/src/USER-AWPMD/atom_vec_wavepacket.cpp b/src/USER-AWPMD/atom_vec_wavepacket.cpp index 7556dd2c8e..912544c860 100644 --- a/src/USER-AWPMD/atom_vec_wavepacket.cpp +++ b/src/USER-AWPMD/atom_vec_wavepacket.cpp @@ -916,19 +916,19 @@ void AtomVecWavepacket::data_atom(double *coord, imageint imagetmp, if (nlocal == nmax) grow(0); tag[nlocal] = ATOTAGINT(values[0]); - type[nlocal] = atoi(values[1]); + type[nlocal] = force->inumeric(FLERR,values[1]); if (type[nlocal] <= 0 || type[nlocal] > atom->ntypes) error->one(FLERR,"Invalid atom type in Atoms section of data file"); - q[nlocal] = atof(values[2]); - spin[nlocal] = atoi(values[3]); - eradius[nlocal] = atof(values[4]); + q[nlocal] = force->numeric(FLERR,values[2]); + spin[nlocal] = force->inumeric(FLERR,values[3]); + eradius[nlocal] = force->numeric(FLERR,values[4]); if (eradius[nlocal] < 0.0) error->one(FLERR,"Invalid eradius in Atoms section of data file"); - etag[nlocal] = atoi(values[5]); - cs[2*nlocal] = atoi(values[6]); - cs[2*nlocal+1] = atof(values[7]); + etag[nlocal] = force->inumeric(FLERR,values[5]); + cs[2*nlocal] = force->inumeric(FLERR,values[6]); + cs[2*nlocal+1] = force->numeric(FLERR,values[7]); x[nlocal][0] = coord[0]; x[nlocal][1] = coord[1]; @@ -952,15 +952,15 @@ void AtomVecWavepacket::data_atom(double *coord, imageint imagetmp, int AtomVecWavepacket::data_atom_hybrid(int nlocal, char **values) { - q[nlocal] = atof(values[0]); - spin[nlocal] = atoi(values[1]); - eradius[nlocal] = atof(values[2]); + q[nlocal] = force->numeric(FLERR,values[0]); + spin[nlocal] = force->inumeric(FLERR,values[1]); + eradius[nlocal] = force->numeric(FLERR,values[2]); if (eradius[nlocal] < 0.0) error->one(FLERR,"Invalid eradius in Atoms section of data file"); - etag[nlocal] = atoi(values[3]); - cs[2*nlocal] = atoi(values[4]); - cs[2*nlocal+1] = atof(values[5]); + etag[nlocal] = force->inumeric(FLERR,values[3]); + cs[2*nlocal] = force->inumeric(FLERR,values[4]); + cs[2*nlocal+1] = force->numeric(FLERR,values[5]); v[nlocal][0] = 0.0; v[nlocal][1] = 0.0; @@ -976,10 +976,10 @@ int AtomVecWavepacket::data_atom_hybrid(int nlocal, char **values) void AtomVecWavepacket::data_vel(int m, char **values) { - v[m][0] = atof(values[0]); - v[m][1] = atof(values[1]); - v[m][2] = atof(values[2]); - ervel[m] = atof(values[3]); + v[m][0] = force->numeric(FLERR,values[0]); + v[m][1] = force->numeric(FLERR,values[1]); + v[m][2] = force->numeric(FLERR,values[2]); + ervel[m] = force->numeric(FLERR,values[3]); } /* ---------------------------------------------------------------------- @@ -988,7 +988,7 @@ void AtomVecWavepacket::data_vel(int m, char **values) int AtomVecWavepacket::data_vel_hybrid(int m, char **values) { - ervel[m] = atof(values[0]); + ervel[m] = force->numeric(FLERR,values[0]); return 1; } diff --git a/src/USER-DPD/atom_vec_dpd.cpp b/src/USER-DPD/atom_vec_dpd.cpp index 4cf6356100..c67034baf2 100644 --- a/src/USER-DPD/atom_vec_dpd.cpp +++ b/src/USER-DPD/atom_vec_dpd.cpp @@ -814,11 +814,11 @@ void AtomVecDPD::data_atom(double *coord, tagint imagetmp, char **values) if (nlocal == nmax) grow(0); tag[nlocal] = ATOTAGINT(values[0]); - type[nlocal] = atoi(values[1]); + type[nlocal] = force->inumeric(FLERR,values[1]); if (type[nlocal] <= 0 || type[nlocal] > atom->ntypes) error->one(FLERR,"Invalid atom type in Atoms section of data file"); - dpdTheta[nlocal] = atof(values[2]); + dpdTheta[nlocal] = force->numeric(FLERR,values[2]); if (dpdTheta[nlocal] <= 0) error->one(FLERR,"Internal temperature in Atoms section of date file must be > zero"); @@ -850,7 +850,7 @@ void AtomVecDPD::data_atom(double *coord, tagint imagetmp, char **values) int AtomVecDPD::data_atom_hybrid(int nlocal, char **values) { - dpdTheta[nlocal] = atof(values[0]); + dpdTheta[nlocal] = force->numeric(FLERR,values[0]); return 1; } diff --git a/src/USER-EFF/atom_vec_electron.cpp b/src/USER-EFF/atom_vec_electron.cpp index 1bc5387c9e..2cf04e189a 100644 --- a/src/USER-EFF/atom_vec_electron.cpp +++ b/src/USER-EFF/atom_vec_electron.cpp @@ -799,15 +799,15 @@ void AtomVecElectron::data_atom(double *coord, imageint imagetmp, char **values) if (nlocal == nmax) grow(0); tag[nlocal] = ATOTAGINT(values[0]); - type[nlocal] = atoi(values[1]); + type[nlocal] = force->inumeric(FLERR,values[1]); if (type[nlocal] <= 0 || type[nlocal] > atom->ntypes) error->one(FLERR,"Invalid atom type in Atoms section of data file"); - q[nlocal] = atof(values[2]); - spin[nlocal] = atoi(values[3]); + q[nlocal] = force->numeric(FLERR,values[2]); + spin[nlocal] = force->inumeric(FLERR,values[3]); if (spin[nlocal] == 3) atom->ecp_flag = 1; - eradius[nlocal] = atof(values[4]); + eradius[nlocal] = force->numeric(FLERR,values[4]); x[nlocal][0] = coord[0]; x[nlocal][1] = coord[1]; @@ -831,9 +831,9 @@ void AtomVecElectron::data_atom(double *coord, imageint imagetmp, char **values) int AtomVecElectron::data_atom_hybrid(int nlocal, char **values) { - q[nlocal] = atof(values[0]); - spin[nlocal] = atoi(values[1]); - eradius[nlocal] = atof(values[2]); + q[nlocal] = force->numeric(FLERR,values[0]); + spin[nlocal] = force->inumeric(FLERR,values[1]); + eradius[nlocal] = force->numeric(FLERR,values[2]); if (eradius[nlocal] < 0.0) error->one(FLERR,"Invalid eradius in Atoms section of data file"); @@ -851,10 +851,10 @@ int AtomVecElectron::data_atom_hybrid(int nlocal, char **values) void AtomVecElectron::data_vel(int m, char **values) { - v[m][0] = atof(values[0]); - v[m][1] = atof(values[1]); - v[m][2] = atof(values[2]); - ervel[m] = atof(values[3]); + v[m][0] = force->numeric(FLERR,values[0]); + v[m][1] = force->numeric(FLERR,values[1]); + v[m][2] = force->numeric(FLERR,values[2]); + ervel[m] = force->numeric(FLERR,values[3]); } /* ---------------------------------------------------------------------- @@ -863,7 +863,7 @@ void AtomVecElectron::data_vel(int m, char **values) int AtomVecElectron::data_vel_hybrid(int m, char **values) { - ervel[m] = atof(values[0]); + ervel[m] = force->numeric(FLERR,values[0]); return 1; } diff --git a/src/USER-MESO/atom_vec_edpd.cpp b/src/USER-MESO/atom_vec_edpd.cpp index d956e914b5..b55573e409 100644 --- a/src/USER-MESO/atom_vec_edpd.cpp +++ b/src/USER-MESO/atom_vec_edpd.cpp @@ -759,12 +759,12 @@ void AtomVecEDPD::data_atom(double *coord, imageint imagetmp, char **values) if (nlocal == nmax) grow(0); tag[nlocal] = ATOTAGINT(values[0]); - type[nlocal] = atoi(values[1]); + type[nlocal] = force->inumeric(FLERR,values[1]); if (type[nlocal] <= 0 || type[nlocal] > atom->ntypes) error->one(FLERR,"Invalid atom type in Atoms section of data file"); - edpd_temp[nlocal] = atof(values[2]); - edpd_cv[nlocal] = atof(values[3]); + edpd_temp[nlocal] = force->numeric(FLERR,values[2]); + edpd_cv[nlocal] = force->numeric(FLERR,values[3]); x[nlocal][0] = coord[0]; x[nlocal][1] = coord[1]; diff --git a/src/USER-MESO/atom_vec_mdpd.cpp b/src/USER-MESO/atom_vec_mdpd.cpp index 5bc5e212ff..47082a3b82 100644 --- a/src/USER-MESO/atom_vec_mdpd.cpp +++ b/src/USER-MESO/atom_vec_mdpd.cpp @@ -798,7 +798,7 @@ void AtomVecMDPD::data_atom(double *coord, imageint imagetmp, char **values) { if (nlocal == nmax) grow(0); tag[nlocal] = ATOTAGINT(values[0]); - type[nlocal] = atoi(values[1]); + type[nlocal] = force->inumeric(FLERR,values[1]); if (type[nlocal] <= 0 || type[nlocal] > atom->ntypes) error->one(FLERR,"Invalid atom type in Atoms section of data file"); @@ -817,7 +817,7 @@ void AtomVecMDPD::data_atom(double *coord, imageint imagetmp, char **values) { vest[nlocal][1] = 0.0; vest[nlocal][2] = 0.0; - rho[nlocal] = atof(values[2]); + rho[nlocal] = force->numeric(FLERR,values[2]); drho[nlocal] = 0.0; atom->nlocal++; @@ -830,7 +830,7 @@ void AtomVecMDPD::data_atom(double *coord, imageint imagetmp, char **values) { int AtomVecMDPD::data_atom_hybrid(int nlocal, char **values) { - rho[nlocal] = atof(values[0]); + rho[nlocal] = force->numeric(FLERR,values[0]); return 3; } diff --git a/src/USER-MESO/atom_vec_tdpd.cpp b/src/USER-MESO/atom_vec_tdpd.cpp index aa0dc93809..261bef1795 100644 --- a/src/USER-MESO/atom_vec_tdpd.cpp +++ b/src/USER-MESO/atom_vec_tdpd.cpp @@ -792,7 +792,7 @@ void AtomVecTDPD::data_atom(double *coord, imageint imagetmp, char **values) if (nlocal == nmax) grow(0); tag[nlocal] = ATOTAGINT(values[0]); - type[nlocal] = atoi(values[1]); + type[nlocal] = force->inumeric(FLERR,values[1]); if (type[nlocal] <= 0 || type[nlocal] > atom->ntypes) error->one(FLERR,"Invalid atom type in Atoms section of data file"); diff --git a/src/USER-SMD/atom_vec_smd.cpp b/src/USER-SMD/atom_vec_smd.cpp index 020284312b..fb2b1ccc69 100644 --- a/src/USER-SMD/atom_vec_smd.cpp +++ b/src/USER-SMD/atom_vec_smd.cpp @@ -1029,7 +1029,7 @@ void AtomVecSMD::data_atom(double *coord, imageint imagetmp, char **values) { tag[nlocal] = ATOTAGINT(values[0]); - type[nlocal] = atoi(values[1]); + type[nlocal] = force->inumeric(FLERR,values[1]); if (type[nlocal] <= 0 || type[nlocal] > atom->ntypes) error->one(FLERR, "Invalid atom type in Atoms section of data file"); @@ -1037,27 +1037,27 @@ void AtomVecSMD::data_atom(double *coord, imageint imagetmp, char **values) { if (molecule[nlocal] <= 0) error->one(FLERR, "Invalid molecule in Atoms section of data file"); - vfrac[nlocal] = atof(values[3]); + vfrac[nlocal] = force->numeric(FLERR,values[3]); if (vfrac[nlocal] < 0.0) error->one(FLERR, "Invalid volume in Atoms section of data file"); - rmass[nlocal] = atof(values[4]); + rmass[nlocal] = force->numeric(FLERR,values[4]); if (rmass[nlocal] == 0.0) error->one(FLERR, "Invalid mass in Atoms section of data file"); - radius[nlocal] = atof(values[5]); + radius[nlocal] = force->numeric(FLERR,values[5]); if (radius[nlocal] < 0.0) error->one(FLERR, "Invalid radius in Atoms section of data file"); - contact_radius[nlocal] = atof(values[6]); + contact_radius[nlocal] = force->numeric(FLERR,values[6]); if (contact_radius[nlocal] < 0.0) error->one(FLERR, "Invalid contact radius in Atoms section of data file"); e[nlocal] = 0.0; - x0[nlocal][0] = atof(values[7]); - x0[nlocal][1] = atof(values[8]); - x0[nlocal][2] = atof(values[9]); + x0[nlocal][0] = force->numeric(FLERR,values[7]); + x0[nlocal][1] = force->numeric(FLERR,values[8]); + x0[nlocal][2] = force->numeric(FLERR,values[9]); x[nlocal][0] = coord[0]; x[nlocal][1] = coord[1]; @@ -1108,12 +1108,12 @@ int AtomVecSMD::data_atom_hybrid(int /*nlocal*/, char **/*values*/) { ------------------------------------------------------------------------- */ void AtomVecSMD::data_vel(int m, char **values) { - v[m][0] = atof(values[0]); - v[m][1] = atof(values[1]); - v[m][2] = atof(values[2]); - vest[m][0] = atof(values[0]); - vest[m][1] = atof(values[1]); - vest[m][2] = atof(values[2]); + v[m][0] = force->numeric(FLERR,values[0]); + v[m][1] = force->numeric(FLERR,values[1]); + v[m][2] = force->numeric(FLERR,values[2]); + vest[m][0] = force->numeric(FLERR,values[0]); + vest[m][1] = force->numeric(FLERR,values[1]); + vest[m][2] = force->numeric(FLERR,values[2]); } /* ---------------------------------------------------------------------- diff --git a/src/USER-SPH/atom_vec_meso.cpp b/src/USER-SPH/atom_vec_meso.cpp index 7dc6c6f7bd..144eaa2433 100644 --- a/src/USER-SPH/atom_vec_meso.cpp +++ b/src/USER-SPH/atom_vec_meso.cpp @@ -843,13 +843,13 @@ void AtomVecMeso::data_atom(double *coord, imageint imagetmp, char **values) { if (nlocal == nmax) grow(0); tag[nlocal] = ATOTAGINT(values[0]); - type[nlocal] = atoi(values[1]); + type[nlocal] = force->inumeric(FLERR,values[1]); if (type[nlocal] <= 0 || type[nlocal] > atom->ntypes) error->one(FLERR,"Invalid atom type in Atoms section of data file"); - rho[nlocal] = atof(values[2]); - e[nlocal] = atof(values[3]); - cv[nlocal] = atof(values[4]); + rho[nlocal] = force->numeric(FLERR,values[2]); + e[nlocal] = force->numeric(FLERR,values[3]); + cv[nlocal] = force->numeric(FLERR,values[4]); x[nlocal][0] = coord[0]; x[nlocal][1] = coord[1]; @@ -881,9 +881,9 @@ void AtomVecMeso::data_atom(double *coord, imageint imagetmp, char **values) { int AtomVecMeso::data_atom_hybrid(int nlocal, char **values) { - rho[nlocal] = atof(values[0]); - e[nlocal] = atof(values[1]); - cv[nlocal] = atof(values[2]); + rho[nlocal] = force->numeric(FLERR,values[0]); + e[nlocal] = force->numeric(FLERR,values[1]); + cv[nlocal] = force->numeric(FLERR,values[2]); return 3; } diff --git a/src/atom_vec.cpp b/src/atom_vec.cpp index a7ca6fcb19..33caea05a2 100644 --- a/src/atom_vec.cpp +++ b/src/atom_vec.cpp @@ -113,9 +113,9 @@ int AtomVec::grow_nmax_bonus(int nmax_bonus) void AtomVec::data_vel(int m, char **values) { double **v = atom->v; - v[m][0] = atof(values[0]); - v[m][1] = atof(values[1]); - v[m][2] = atof(values[2]); + v[m][0] = force->numeric(FLERR,values[0]); + v[m][1] = force->numeric(FLERR,values[1]); + v[m][2] = force->numeric(FLERR,values[2]); } /* ---------------------------------------------------------------------- diff --git a/src/atom_vec_atomic.cpp b/src/atom_vec_atomic.cpp index e1c9a1e524..0f391baae9 100644 --- a/src/atom_vec_atomic.cpp +++ b/src/atom_vec_atomic.cpp @@ -612,7 +612,7 @@ void AtomVecAtomic::data_atom(double *coord, imageint imagetmp, char **values) if (nlocal == nmax) grow(0); tag[nlocal] = ATOTAGINT(values[0]); - type[nlocal] = atoi(values[1]); + type[nlocal] = force->inumeric(FLERR,values[1]); if (type[nlocal] <= 0 || type[nlocal] > atom->ntypes) error->one(FLERR,"Invalid atom type in Atoms section of data file"); diff --git a/src/atom_vec_body.cpp b/src/atom_vec_body.cpp index d5f286c077..f54605fbb0 100644 --- a/src/atom_vec_body.cpp +++ b/src/atom_vec_body.cpp @@ -1280,16 +1280,16 @@ void AtomVecBody::data_atom(double *coord, imageint imagetmp, char **values) if (nlocal == nmax) grow(0); tag[nlocal] = ATOTAGINT(values[0]); - type[nlocal] = atoi(values[1]); + type[nlocal] = force->inumeric(FLERR,values[1]); if (type[nlocal] <= 0 || type[nlocal] > atom->ntypes) error->one(FLERR,"Invalid atom type in Atoms section of data file"); - body[nlocal] = atoi(values[2]); + body[nlocal] = force->inumeric(FLERR,values[2]); if (body[nlocal] == 0) body[nlocal] = -1; else if (body[nlocal] == 1) body[nlocal] = 0; else error->one(FLERR,"Invalid bodyflag in Atoms section of data file"); - rmass[nlocal] = atof(values[3]); + rmass[nlocal] = force->numeric(FLERR,values[3]); if (rmass[nlocal] <= 0.0) error->one(FLERR,"Invalid density in Atoms section of data file"); @@ -1318,12 +1318,12 @@ void AtomVecBody::data_atom(double *coord, imageint imagetmp, char **values) int AtomVecBody::data_atom_hybrid(int nlocal, char **values) { - body[nlocal] = atoi(values[0]); + body[nlocal] = force->inumeric(FLERR,values[0]); if (body[nlocal] == 0) body[nlocal] = -1; else if (body[nlocal] == 1) body[nlocal] = 0; else error->one(FLERR,"Invalid atom type in Atoms section of data file"); - rmass[nlocal] = atof(values[1]); + rmass[nlocal] = force->numeric(FLERR,values[1]); if (rmass[nlocal] <= 0.0) error->one(FLERR,"Invalid density in Atoms section of data file"); @@ -1350,12 +1350,12 @@ void AtomVecBody::data_body(int m, int ninteger, int ndouble, void AtomVecBody::data_vel(int m, char **values) { - v[m][0] = atof(values[0]); - v[m][1] = atof(values[1]); - v[m][2] = atof(values[2]); - angmom[m][0] = atof(values[3]); - angmom[m][1] = atof(values[4]); - angmom[m][2] = atof(values[5]); + v[m][0] = force->numeric(FLERR,values[0]); + v[m][1] = force->numeric(FLERR,values[1]); + v[m][2] = force->numeric(FLERR,values[2]); + angmom[m][0] = force->numeric(FLERR,values[3]); + angmom[m][1] = force->numeric(FLERR,values[4]); + angmom[m][2] = force->numeric(FLERR,values[5]); } /* ---------------------------------------------------------------------- @@ -1364,9 +1364,9 @@ void AtomVecBody::data_vel(int m, char **values) int AtomVecBody::data_vel_hybrid(int m, char **values) { - angmom[m][0] = atof(values[0]); - angmom[m][1] = atof(values[1]); - angmom[m][2] = atof(values[2]); + angmom[m][0] = force->numeric(FLERR,values[0]); + angmom[m][1] = force->numeric(FLERR,values[1]); + angmom[m][2] = force->numeric(FLERR,values[2]); return 3; } diff --git a/src/atom_vec_charge.cpp b/src/atom_vec_charge.cpp index 440393385d..a6fd5962ca 100644 --- a/src/atom_vec_charge.cpp +++ b/src/atom_vec_charge.cpp @@ -663,11 +663,11 @@ void AtomVecCharge::data_atom(double *coord, imageint imagetmp, char **values) if (nlocal == nmax) grow(0); tag[nlocal] = ATOTAGINT(values[0]); - type[nlocal] = atoi(values[1]); + type[nlocal] = force->inumeric(FLERR,values[1]); if (type[nlocal] <= 0 || type[nlocal] > atom->ntypes) error->one(FLERR,"Invalid atom type in Atoms section of data file"); - q[nlocal] = atof(values[2]); + q[nlocal] = force->numeric(FLERR,values[2]); x[nlocal][0] = coord[0]; x[nlocal][1] = coord[1]; @@ -690,7 +690,7 @@ void AtomVecCharge::data_atom(double *coord, imageint imagetmp, char **values) int AtomVecCharge::data_atom_hybrid(int nlocal, char **values) { - q[nlocal] = atof(values[0]); + q[nlocal] = force->numeric(FLERR,values[0]); return 1; } diff --git a/src/atom_vec_ellipsoid.cpp b/src/atom_vec_ellipsoid.cpp index 2bf3f683d0..1fc713e583 100644 --- a/src/atom_vec_ellipsoid.cpp +++ b/src/atom_vec_ellipsoid.cpp @@ -1141,16 +1141,16 @@ void AtomVecEllipsoid::data_atom(double *coord, imageint imagetmp, if (nlocal == nmax) grow(0); tag[nlocal] = ATOTAGINT(values[0]); - type[nlocal] = atoi(values[1]); + type[nlocal] = force->inumeric(FLERR,values[1]); if (type[nlocal] <= 0 || type[nlocal] > atom->ntypes) error->one(FLERR,"Invalid atom type in Atoms section of data file"); - ellipsoid[nlocal] = atoi(values[2]); + ellipsoid[nlocal] = force->inumeric(FLERR,values[2]); if (ellipsoid[nlocal] == 0) ellipsoid[nlocal] = -1; else if (ellipsoid[nlocal] == 1) ellipsoid[nlocal] = 0; else error->one(FLERR,"Invalid ellipsoidflag in Atoms section of data file"); - rmass[nlocal] = atof(values[3]); + rmass[nlocal] = force->numeric(FLERR,values[3]); if (rmass[nlocal] <= 0.0) error->one(FLERR,"Invalid density in Atoms section of data file"); @@ -1178,12 +1178,12 @@ void AtomVecEllipsoid::data_atom(double *coord, imageint imagetmp, int AtomVecEllipsoid::data_atom_hybrid(int nlocal, char **values) { - ellipsoid[nlocal] = atoi(values[0]); + ellipsoid[nlocal] = force->inumeric(FLERR,values[0]); if (ellipsoid[nlocal] == 0) ellipsoid[nlocal] = -1; else if (ellipsoid[nlocal] == 1) ellipsoid[nlocal] = 0; else error->one(FLERR,"Invalid atom type in Atoms section of data file"); - rmass[nlocal] = atof(values[1]); + rmass[nlocal] = force->numeric(FLERR,values[1]); if (rmass[nlocal] <= 0.0) error->one(FLERR,"Invalid density in Atoms section of data file"); @@ -1202,17 +1202,17 @@ void AtomVecEllipsoid::data_atom_bonus(int m, char **values) if (nlocal_bonus == nmax_bonus) grow_bonus(); double *shape = bonus[nlocal_bonus].shape; - shape[0] = 0.5 * atof(values[0]); - shape[1] = 0.5 * atof(values[1]); - shape[2] = 0.5 * atof(values[2]); + shape[0] = 0.5 * force->numeric(FLERR,values[0]); + shape[1] = 0.5 * force->numeric(FLERR,values[1]); + shape[2] = 0.5 * force->numeric(FLERR,values[2]); if (shape[0] <= 0.0 || shape[1] <= 0.0 || shape[2] <= 0.0) error->one(FLERR,"Invalid shape in Ellipsoids section of data file"); double *quat = bonus[nlocal_bonus].quat; - quat[0] = atof(values[3]); - quat[1] = atof(values[4]); - quat[2] = atof(values[5]); - quat[3] = atof(values[6]); + quat[0] = force->numeric(FLERR,values[3]); + quat[1] = force->numeric(FLERR,values[4]); + quat[2] = force->numeric(FLERR,values[5]); + quat[3] = force->numeric(FLERR,values[6]); MathExtra::qnormalize(quat); // reset ellipsoid mass @@ -1230,12 +1230,12 @@ void AtomVecEllipsoid::data_atom_bonus(int m, char **values) void AtomVecEllipsoid::data_vel(int m, char **values) { - v[m][0] = atof(values[0]); - v[m][1] = atof(values[1]); - v[m][2] = atof(values[2]); - angmom[m][0] = atof(values[3]); - angmom[m][1] = atof(values[4]); - angmom[m][2] = atof(values[5]); + v[m][0] = force->numeric(FLERR,values[0]); + v[m][1] = force->numeric(FLERR,values[1]); + v[m][2] = force->numeric(FLERR,values[2]); + angmom[m][0] = force->numeric(FLERR,values[3]); + angmom[m][1] = force->numeric(FLERR,values[4]); + angmom[m][2] = force->numeric(FLERR,values[5]); } /* ---------------------------------------------------------------------- @@ -1244,9 +1244,9 @@ void AtomVecEllipsoid::data_vel(int m, char **values) int AtomVecEllipsoid::data_vel_hybrid(int m, char **values) { - angmom[m][0] = atof(values[0]); - angmom[m][1] = atof(values[1]); - angmom[m][2] = atof(values[2]); + angmom[m][0] = force->numeric(FLERR,values[0]); + angmom[m][1] = force->numeric(FLERR,values[1]); + angmom[m][2] = force->numeric(FLERR,values[2]); return 3; } diff --git a/src/atom_vec_hybrid.cpp b/src/atom_vec_hybrid.cpp index 7e1fb01e5d..cf99a90632 100644 --- a/src/atom_vec_hybrid.cpp +++ b/src/atom_vec_hybrid.cpp @@ -863,7 +863,7 @@ void AtomVecHybrid::data_atom(double *coord, imageint imagetmp, char **values) if (nlocal == nmax) grow(0); tag[nlocal] = ATOTAGINT(values[0]); - type[nlocal] = atoi(values[1]); + type[nlocal] = force->inumeric(FLERR,values[1]); if (type[nlocal] <= 0 || type[nlocal] > atom->ntypes) error->one(FLERR,"Invalid atom type in Atoms section of data file"); @@ -903,9 +903,9 @@ void AtomVecHybrid::data_atom(double *coord, imageint imagetmp, char **values) void AtomVecHybrid::data_vel(int m, char **values) { - v[m][0] = atof(values[0]); - v[m][1] = atof(values[1]); - v[m][2] = atof(values[2]); + v[m][0] = force->numeric(FLERR,values[0]); + v[m][1] = force->numeric(FLERR,values[1]); + v[m][2] = force->numeric(FLERR,values[2]); // each sub-style parses sub-style specific values diff --git a/src/atom_vec_line.cpp b/src/atom_vec_line.cpp index 020b622c93..f229297798 100644 --- a/src/atom_vec_line.cpp +++ b/src/atom_vec_line.cpp @@ -1037,16 +1037,16 @@ void AtomVecLine::data_atom(double *coord, imageint imagetmp, char **values) tag[nlocal] = ATOTAGINT(values[0]); molecule[nlocal] = ATOTAGINT(values[1]); - type[nlocal] = atoi(values[2]); + type[nlocal] = force->inumeric(FLERR,values[2]); if (type[nlocal] <= 0 || type[nlocal] > atom->ntypes) error->one(FLERR,"Invalid atom type in Atoms section of data file"); - line[nlocal] = atoi(values[3]); + line[nlocal] = force->inumeric(FLERR,values[3]); if (line[nlocal] == 0) line[nlocal] = -1; else if (line[nlocal] == 1) line[nlocal] = 0; else error->one(FLERR,"Invalid lineflag in Atoms section of data file"); - rmass[nlocal] = atof(values[4]); + rmass[nlocal] = force->numeric(FLERR,values[4]); if (rmass[nlocal] <= 0.0) error->one(FLERR,"Invalid density in Atoms section of data file"); @@ -1082,12 +1082,12 @@ int AtomVecLine::data_atom_hybrid(int nlocal, char **values) { molecule[nlocal] = ATOTAGINT(values[0]); - line[nlocal] = atoi(values[1]); + line[nlocal] = force->inumeric(FLERR,values[1]); if (line[nlocal] == 0) line[nlocal] = -1; else if (line[nlocal] == 1) line[nlocal] = 0; else error->one(FLERR,"Invalid atom type in Atoms section of data file"); - rmass[nlocal] = atof(values[2]); + rmass[nlocal] = force->numeric(FLERR,values[2]); if (rmass[nlocal] <= 0.0) error->one(FLERR,"Invalid density in Atoms section of data file"); @@ -1110,10 +1110,10 @@ void AtomVecLine::data_atom_bonus(int m, char **values) if (nlocal_bonus == nmax_bonus) grow_bonus(); - double x1 = atof(values[0]); - double y1 = atof(values[1]); - double x2 = atof(values[2]); - double y2 = atof(values[3]); + double x1 = force->numeric(FLERR,values[0]); + double y1 = force->numeric(FLERR,values[1]); + double x2 = force->numeric(FLERR,values[2]); + double y2 = force->numeric(FLERR,values[3]); double dx = x2 - x1; double dy = y2 - y1; double length = sqrt(dx*dx + dy*dy); @@ -1150,12 +1150,12 @@ void AtomVecLine::data_atom_bonus(int m, char **values) void AtomVecLine::data_vel(int m, char **values) { - v[m][0] = atof(values[0]); - v[m][1] = atof(values[1]); - v[m][2] = atof(values[2]); - omega[m][0] = atof(values[3]); - omega[m][1] = atof(values[4]); - omega[m][2] = atof(values[5]); + v[m][0] = force->numeric(FLERR,values[0]); + v[m][1] = force->numeric(FLERR,values[1]); + v[m][2] = force->numeric(FLERR,values[2]); + omega[m][0] = force->numeric(FLERR,values[3]); + omega[m][1] = force->numeric(FLERR,values[4]); + omega[m][2] = force->numeric(FLERR,values[5]); } /* ---------------------------------------------------------------------- @@ -1164,9 +1164,9 @@ void AtomVecLine::data_vel(int m, char **values) int AtomVecLine::data_vel_hybrid(int m, char **values) { - omega[m][0] = atof(values[0]); - omega[m][1] = atof(values[1]); - omega[m][2] = atof(values[2]); + omega[m][0] = force->numeric(FLERR,values[0]); + omega[m][1] = force->numeric(FLERR,values[1]); + omega[m][2] = force->numeric(FLERR,values[2]); return 3; } diff --git a/src/atom_vec_sphere.cpp b/src/atom_vec_sphere.cpp index dec98e5200..705b7411e7 100644 --- a/src/atom_vec_sphere.cpp +++ b/src/atom_vec_sphere.cpp @@ -965,15 +965,15 @@ void AtomVecSphere::data_atom(double *coord, imageint imagetmp, char **values) if (nlocal == nmax) grow(0); tag[nlocal] = ATOTAGINT(values[0]); - type[nlocal] = atoi(values[1]); + type[nlocal] = force->inumeric(FLERR,values[1]); if (type[nlocal] <= 0 || type[nlocal] > atom->ntypes) error->one(FLERR,"Invalid atom type in Atoms section of data file"); - radius[nlocal] = 0.5 * atof(values[2]); + radius[nlocal] = 0.5 * force->numeric(FLERR,values[2]); if (radius[nlocal] < 0.0) error->one(FLERR,"Invalid radius in Atoms section of data file"); - double density = atof(values[3]); + double density = force->numeric(FLERR,values[3]); if (density <= 0.0) error->one(FLERR,"Invalid density in Atoms section of data file"); @@ -1006,11 +1006,11 @@ void AtomVecSphere::data_atom(double *coord, imageint imagetmp, char **values) int AtomVecSphere::data_atom_hybrid(int nlocal, char **values) { - radius[nlocal] = 0.5 * atof(values[0]); + radius[nlocal] = 0.5 * force->numeric(FLERR,values[0]); if (radius[nlocal] < 0.0) error->one(FLERR,"Invalid radius in Atoms section of data file"); - double density = atof(values[1]); + double density = force->numeric(FLERR,values[1]); if (density <= 0.0) error->one(FLERR,"Invalid density in Atoms section of data file"); @@ -1028,12 +1028,12 @@ int AtomVecSphere::data_atom_hybrid(int nlocal, char **values) void AtomVecSphere::data_vel(int m, char **values) { - v[m][0] = atof(values[0]); - v[m][1] = atof(values[1]); - v[m][2] = atof(values[2]); - omega[m][0] = atof(values[3]); - omega[m][1] = atof(values[4]); - omega[m][2] = atof(values[5]); + v[m][0] = force->numeric(FLERR,values[0]); + v[m][1] = force->numeric(FLERR,values[1]); + v[m][2] = force->numeric(FLERR,values[2]); + omega[m][0] = force->numeric(FLERR,values[3]); + omega[m][1] = force->numeric(FLERR,values[4]); + omega[m][2] = force->numeric(FLERR,values[5]); } /* ---------------------------------------------------------------------- @@ -1042,9 +1042,9 @@ void AtomVecSphere::data_vel(int m, char **values) int AtomVecSphere::data_vel_hybrid(int m, char **values) { - omega[m][0] = atof(values[0]); - omega[m][1] = atof(values[1]); - omega[m][2] = atof(values[2]); + omega[m][0] = force->numeric(FLERR,values[0]); + omega[m][1] = force->numeric(FLERR,values[1]); + omega[m][2] = force->numeric(FLERR,values[2]); return 3; } diff --git a/src/atom_vec_tri.cpp b/src/atom_vec_tri.cpp index 8fbe0a92dc..9f4557b63d 100644 --- a/src/atom_vec_tri.cpp +++ b/src/atom_vec_tri.cpp @@ -1436,16 +1436,16 @@ void AtomVecTri::data_atom(double *coord, imageint imagetmp, char **values) tag[nlocal] = ATOTAGINT(values[0]); molecule[nlocal] = ATOTAGINT(values[1]); - type[nlocal] = atoi(values[2]); + type[nlocal] = force->inumeric(FLERR,values[2]); if (type[nlocal] <= 0 || type[nlocal] > atom->ntypes) error->one(FLERR,"Invalid atom type in Atoms section of data file"); - tri[nlocal] = atoi(values[3]); + tri[nlocal] = force->inumeric(FLERR,values[3]); if (tri[nlocal] == 0) tri[nlocal] = -1; else if (tri[nlocal] == 1) tri[nlocal] = 0; else error->one(FLERR,"Invalid triflag in Atoms section of data file"); - rmass[nlocal] = atof(values[4]); + rmass[nlocal] = force->numeric(FLERR,values[4]); if (rmass[nlocal] <= 0.0) error->one(FLERR,"Invalid density in Atoms section of data file"); @@ -1484,12 +1484,12 @@ int AtomVecTri::data_atom_hybrid(int nlocal, char **values) { molecule[nlocal] = ATOTAGINT(values[0]); - tri[nlocal] = atoi(values[1]); + tri[nlocal] = force->inumeric(FLERR,values[1]); if (tri[nlocal] == 0) tri[nlocal] = -1; else if (tri[nlocal] == 1) tri[nlocal] = 0; else error->one(FLERR,"Invalid atom type in Atoms section of data file"); - rmass[nlocal] = atof(values[2]); + rmass[nlocal] = force->numeric(FLERR,values[2]); if (rmass[nlocal] <= 0.0) error->one(FLERR,"Invalid density in Atoms section of data file"); @@ -1513,15 +1513,15 @@ void AtomVecTri::data_atom_bonus(int m, char **values) if (nlocal_bonus == nmax_bonus) grow_bonus(); double c1[3],c2[3],c3[3]; - c1[0] = atof(values[0]); - c1[1] = atof(values[1]); - c1[2] = atof(values[2]); - c2[0] = atof(values[3]); - c2[1] = atof(values[4]); - c2[2] = atof(values[5]); - c3[0] = atof(values[6]); - c3[1] = atof(values[7]); - c3[2] = atof(values[8]); + c1[0] = force->numeric(FLERR,values[0]); + c1[1] = force->numeric(FLERR,values[1]); + c1[2] = force->numeric(FLERR,values[2]); + c2[0] = force->numeric(FLERR,values[3]); + c2[1] = force->numeric(FLERR,values[4]); + c2[2] = force->numeric(FLERR,values[5]); + c3[0] = force->numeric(FLERR,values[6]); + c3[1] = force->numeric(FLERR,values[7]); + c3[2] = force->numeric(FLERR,values[8]); // check for duplicate points @@ -1641,15 +1641,15 @@ void AtomVecTri::data_atom_bonus(int m, char **values) void AtomVecTri::data_vel(int m, char **values) { - v[m][0] = atof(values[0]); - v[m][1] = atof(values[1]); - v[m][2] = atof(values[2]); - omega[m][0] = atof(values[3]); - omega[m][1] = atof(values[4]); - omega[m][2] = atof(values[5]); - angmom[m][0] = atof(values[6]); - angmom[m][1] = atof(values[7]); - angmom[m][2] = atof(values[8]); + v[m][0] = force->numeric(FLERR,values[0]); + v[m][1] = force->numeric(FLERR,values[1]); + v[m][2] = force->numeric(FLERR,values[2]); + omega[m][0] = force->numeric(FLERR,values[3]); + omega[m][1] = force->numeric(FLERR,values[4]); + omega[m][2] = force->numeric(FLERR,values[5]); + angmom[m][0] = force->numeric(FLERR,values[6]); + angmom[m][1] = force->numeric(FLERR,values[7]); + angmom[m][2] = force->numeric(FLERR,values[8]); } /* ---------------------------------------------------------------------- @@ -1658,12 +1658,12 @@ void AtomVecTri::data_vel(int m, char **values) int AtomVecTri::data_vel_hybrid(int m, char **values) { - omega[m][0] = atof(values[0]); - omega[m][1] = atof(values[1]); - omega[m][2] = atof(values[2]); - angmom[m][0] = atof(values[3]); - angmom[m][1] = atof(values[4]); - angmom[m][2] = atof(values[5]); + omega[m][0] = force->numeric(FLERR,values[0]); + omega[m][1] = force->numeric(FLERR,values[1]); + omega[m][2] = force->numeric(FLERR,values[2]); + angmom[m][0] = force->numeric(FLERR,values[3]); + angmom[m][1] = force->numeric(FLERR,values[4]); + angmom[m][2] = force->numeric(FLERR,values[5]); return 6; } -- GitLab From b469ff6791c2d35a417696f6a0cc4df4bac8a082 Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Sun, 7 Jul 2019 16:06:30 -0400 Subject: [PATCH 199/469] need to include 'force.h' header for conversion functions --- src/DIPOLE/atom_vec_dipole.cpp | 1 + src/KOKKOS/atom_vec_angle_kokkos.cpp | 1 + src/KOKKOS/atom_vec_atomic_kokkos.cpp | 1 + src/KOKKOS/atom_vec_bond_kokkos.cpp | 1 + src/KOKKOS/atom_vec_charge_kokkos.cpp | 1 + src/KOKKOS/atom_vec_dpd_kokkos.cpp | 1 + src/KOKKOS/atom_vec_full_kokkos.cpp | 1 + src/KOKKOS/atom_vec_hybrid_kokkos.cpp | 1 + src/KOKKOS/atom_vec_molecular_kokkos.cpp | 1 + src/MOLECULE/atom_vec_angle.cpp | 1 + src/MOLECULE/atom_vec_bond.cpp | 1 + src/MOLECULE/atom_vec_full.cpp | 1 + src/MOLECULE/atom_vec_molecular.cpp | 1 + src/MOLECULE/atom_vec_template.cpp | 1 + src/PERI/atom_vec_peri.cpp | 1 + src/SPIN/atom_vec_spin.cpp | 1 + src/USER-DPD/atom_vec_dpd.cpp | 1 + src/USER-MESO/atom_vec_edpd.cpp | 1 + src/USER-MESO/atom_vec_mdpd.cpp | 1 + src/USER-SPH/atom_vec_meso.cpp | 1 + src/atom_vec_atomic.cpp | 1 + src/atom_vec_charge.cpp | 1 + src/atom_vec_hybrid.cpp | 1 + 23 files changed, 23 insertions(+) diff --git a/src/DIPOLE/atom_vec_dipole.cpp b/src/DIPOLE/atom_vec_dipole.cpp index c6f8fbb432..b469327c80 100644 --- a/src/DIPOLE/atom_vec_dipole.cpp +++ b/src/DIPOLE/atom_vec_dipole.cpp @@ -17,6 +17,7 @@ #include "atom.h" #include "comm.h" #include "domain.h" +#include "force.h" #include "modify.h" #include "fix.h" #include "memory.h" diff --git a/src/KOKKOS/atom_vec_angle_kokkos.cpp b/src/KOKKOS/atom_vec_angle_kokkos.cpp index 36fa47c712..b6cf8ba2b2 100644 --- a/src/KOKKOS/atom_vec_angle_kokkos.cpp +++ b/src/KOKKOS/atom_vec_angle_kokkos.cpp @@ -16,6 +16,7 @@ #include "atom_kokkos.h" #include "comm_kokkos.h" #include "domain.h" +#include "force.h" #include "modify.h" #include "fix.h" #include "atom_masks.h" diff --git a/src/KOKKOS/atom_vec_atomic_kokkos.cpp b/src/KOKKOS/atom_vec_atomic_kokkos.cpp index 61703d1cc8..b0cf4e483a 100644 --- a/src/KOKKOS/atom_vec_atomic_kokkos.cpp +++ b/src/KOKKOS/atom_vec_atomic_kokkos.cpp @@ -16,6 +16,7 @@ #include "atom_kokkos.h" #include "comm_kokkos.h" #include "domain.h" +#include "force.h" #include "modify.h" #include "fix.h" #include "atom_masks.h" diff --git a/src/KOKKOS/atom_vec_bond_kokkos.cpp b/src/KOKKOS/atom_vec_bond_kokkos.cpp index bbf9f58b58..bac06e7845 100644 --- a/src/KOKKOS/atom_vec_bond_kokkos.cpp +++ b/src/KOKKOS/atom_vec_bond_kokkos.cpp @@ -16,6 +16,7 @@ #include "atom_kokkos.h" #include "comm_kokkos.h" #include "domain.h" +#include "force.h" #include "modify.h" #include "fix.h" #include "atom_masks.h" diff --git a/src/KOKKOS/atom_vec_charge_kokkos.cpp b/src/KOKKOS/atom_vec_charge_kokkos.cpp index be267d8b16..44f9a44052 100644 --- a/src/KOKKOS/atom_vec_charge_kokkos.cpp +++ b/src/KOKKOS/atom_vec_charge_kokkos.cpp @@ -16,6 +16,7 @@ #include "atom_kokkos.h" #include "comm_kokkos.h" #include "domain.h" +#include "force.h" #include "modify.h" #include "fix.h" #include "atom_masks.h" diff --git a/src/KOKKOS/atom_vec_dpd_kokkos.cpp b/src/KOKKOS/atom_vec_dpd_kokkos.cpp index ffbfc75a93..d3c3e71331 100644 --- a/src/KOKKOS/atom_vec_dpd_kokkos.cpp +++ b/src/KOKKOS/atom_vec_dpd_kokkos.cpp @@ -16,6 +16,7 @@ #include "atom_kokkos.h" #include "comm_kokkos.h" #include "domain.h" +#include "force.h" #include "modify.h" #include "fix.h" #include "atom_masks.h" diff --git a/src/KOKKOS/atom_vec_full_kokkos.cpp b/src/KOKKOS/atom_vec_full_kokkos.cpp index 1974c12ebb..c10402de8c 100644 --- a/src/KOKKOS/atom_vec_full_kokkos.cpp +++ b/src/KOKKOS/atom_vec_full_kokkos.cpp @@ -16,6 +16,7 @@ #include "atom_kokkos.h" #include "comm_kokkos.h" #include "domain.h" +#include "force.h" #include "modify.h" #include "fix.h" #include "atom_masks.h" diff --git a/src/KOKKOS/atom_vec_hybrid_kokkos.cpp b/src/KOKKOS/atom_vec_hybrid_kokkos.cpp index 88dbdd068a..4c3de20a49 100644 --- a/src/KOKKOS/atom_vec_hybrid_kokkos.cpp +++ b/src/KOKKOS/atom_vec_hybrid_kokkos.cpp @@ -16,6 +16,7 @@ #include "atom_vec_hybrid_kokkos.h" #include "atom_kokkos.h" #include "domain.h" +#include "force.h" #include "modify.h" #include "fix.h" #include "memory_kokkos.h" diff --git a/src/KOKKOS/atom_vec_molecular_kokkos.cpp b/src/KOKKOS/atom_vec_molecular_kokkos.cpp index 060228f37e..0616b3dfe0 100644 --- a/src/KOKKOS/atom_vec_molecular_kokkos.cpp +++ b/src/KOKKOS/atom_vec_molecular_kokkos.cpp @@ -18,6 +18,7 @@ #include "domain.h" #include "modify.h" #include "fix.h" +#include "force.h" #include "atom_masks.h" #include "memory_kokkos.h" #include "error.h" diff --git a/src/MOLECULE/atom_vec_angle.cpp b/src/MOLECULE/atom_vec_angle.cpp index 338ac2879e..594a039463 100644 --- a/src/MOLECULE/atom_vec_angle.cpp +++ b/src/MOLECULE/atom_vec_angle.cpp @@ -16,6 +16,7 @@ #include "atom.h" #include "comm.h" #include "domain.h" +#include "force.h" #include "modify.h" #include "fix.h" #include "memory.h" diff --git a/src/MOLECULE/atom_vec_bond.cpp b/src/MOLECULE/atom_vec_bond.cpp index 96797bcd55..12eafbc6ce 100644 --- a/src/MOLECULE/atom_vec_bond.cpp +++ b/src/MOLECULE/atom_vec_bond.cpp @@ -16,6 +16,7 @@ #include "atom.h" #include "comm.h" #include "domain.h" +#include "force.h" #include "modify.h" #include "fix.h" #include "memory.h" diff --git a/src/MOLECULE/atom_vec_full.cpp b/src/MOLECULE/atom_vec_full.cpp index bfd1864d6e..4cad70f782 100644 --- a/src/MOLECULE/atom_vec_full.cpp +++ b/src/MOLECULE/atom_vec_full.cpp @@ -16,6 +16,7 @@ #include "atom.h" #include "comm.h" #include "domain.h" +#include "force.h" #include "modify.h" #include "fix.h" #include "memory.h" diff --git a/src/MOLECULE/atom_vec_molecular.cpp b/src/MOLECULE/atom_vec_molecular.cpp index 7e4d4fadad..dfd833d1c8 100644 --- a/src/MOLECULE/atom_vec_molecular.cpp +++ b/src/MOLECULE/atom_vec_molecular.cpp @@ -16,6 +16,7 @@ #include "atom.h" #include "comm.h" #include "domain.h" +#include "force.h" #include "modify.h" #include "fix.h" #include "memory.h" diff --git a/src/MOLECULE/atom_vec_template.cpp b/src/MOLECULE/atom_vec_template.cpp index c856684330..2498010888 100644 --- a/src/MOLECULE/atom_vec_template.cpp +++ b/src/MOLECULE/atom_vec_template.cpp @@ -16,6 +16,7 @@ #include "atom_vec_template.h" #include "atom.h" #include "molecule.h" +#include "force.h" #include "comm.h" #include "domain.h" #include "modify.h" diff --git a/src/PERI/atom_vec_peri.cpp b/src/PERI/atom_vec_peri.cpp index a8a94b86c9..9b262477a6 100644 --- a/src/PERI/atom_vec_peri.cpp +++ b/src/PERI/atom_vec_peri.cpp @@ -22,6 +22,7 @@ #include "atom.h" #include "comm.h" #include "domain.h" +#include "force.h" #include "modify.h" #include "fix.h" #include "citeme.h" diff --git a/src/SPIN/atom_vec_spin.cpp b/src/SPIN/atom_vec_spin.cpp index 1d82114fe8..ba33372542 100644 --- a/src/SPIN/atom_vec_spin.cpp +++ b/src/SPIN/atom_vec_spin.cpp @@ -32,6 +32,7 @@ #include "domain.h" #include "error.h" #include "fix.h" +#include "force.h" #include "memory.h" #include "modify.h" diff --git a/src/USER-DPD/atom_vec_dpd.cpp b/src/USER-DPD/atom_vec_dpd.cpp index c67034baf2..776de845ab 100644 --- a/src/USER-DPD/atom_vec_dpd.cpp +++ b/src/USER-DPD/atom_vec_dpd.cpp @@ -20,6 +20,7 @@ #include "atom.h" #include "comm.h" #include "domain.h" +#include "force.h" #include "modify.h" #include "fix.h" #include "memory.h" diff --git a/src/USER-MESO/atom_vec_edpd.cpp b/src/USER-MESO/atom_vec_edpd.cpp index b55573e409..25049ce003 100644 --- a/src/USER-MESO/atom_vec_edpd.cpp +++ b/src/USER-MESO/atom_vec_edpd.cpp @@ -16,6 +16,7 @@ #include "atom.h" #include "comm.h" #include "domain.h" +#include "force.h" #include "modify.h" #include "fix.h" #include "update.h" diff --git a/src/USER-MESO/atom_vec_mdpd.cpp b/src/USER-MESO/atom_vec_mdpd.cpp index 47082a3b82..9952182851 100644 --- a/src/USER-MESO/atom_vec_mdpd.cpp +++ b/src/USER-MESO/atom_vec_mdpd.cpp @@ -17,6 +17,7 @@ #include "atom.h" #include "comm.h" #include "domain.h" +#include "force.h" #include "modify.h" #include "fix.h" #include "update.h" diff --git a/src/USER-SPH/atom_vec_meso.cpp b/src/USER-SPH/atom_vec_meso.cpp index 144eaa2433..763ce5af5a 100644 --- a/src/USER-SPH/atom_vec_meso.cpp +++ b/src/USER-SPH/atom_vec_meso.cpp @@ -17,6 +17,7 @@ #include "atom.h" #include "comm.h" #include "domain.h" +#include "force.h" #include "modify.h" #include "fix.h" #include "memory.h" diff --git a/src/atom_vec_atomic.cpp b/src/atom_vec_atomic.cpp index 0f391baae9..2f01424d9d 100644 --- a/src/atom_vec_atomic.cpp +++ b/src/atom_vec_atomic.cpp @@ -16,6 +16,7 @@ #include "atom.h" #include "comm.h" #include "domain.h" +#include "force.h" #include "modify.h" #include "fix.h" #include "memory.h" diff --git a/src/atom_vec_charge.cpp b/src/atom_vec_charge.cpp index a6fd5962ca..03ef95a2e4 100644 --- a/src/atom_vec_charge.cpp +++ b/src/atom_vec_charge.cpp @@ -16,6 +16,7 @@ #include "atom.h" #include "comm.h" #include "domain.h" +#include "force.h" #include "modify.h" #include "fix.h" #include "memory.h" diff --git a/src/atom_vec_hybrid.cpp b/src/atom_vec_hybrid.cpp index cf99a90632..94391ec9f3 100644 --- a/src/atom_vec_hybrid.cpp +++ b/src/atom_vec_hybrid.cpp @@ -16,6 +16,7 @@ #include "atom_vec_hybrid.h" #include "atom.h" #include "domain.h" +#include "force.h" #include "modify.h" #include "fix.h" #include "memory.h" -- GitLab From 13d4fbdcfbad171fd83ac74d7dcc66170979cd05 Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Sun, 7 Jul 2019 16:23:36 -0400 Subject: [PATCH 200/469] clean up includes in QEQ, REPLICA, and RIGID packages --- src/PERI/pair_peri_ves.cpp | 1 - src/QEQ/fix_qeq.cpp | 12 +----------- src/QEQ/fix_qeq_dynamic.cpp | 5 +---- src/QEQ/fix_qeq_fire.cpp | 5 +---- src/QEQ/fix_qeq_point.cpp | 3 --- src/QEQ/fix_qeq_shielded.cpp | 3 --- src/QEQ/fix_qeq_slater.cpp | 3 --- src/REPLICA/compute_event_displace.cpp | 3 --- src/REPLICA/fix_event.cpp | 8 +------- src/REPLICA/fix_event_hyper.cpp | 9 +-------- src/REPLICA/fix_event_prd.cpp | 9 +-------- src/REPLICA/fix_event_tad.cpp | 9 +-------- src/REPLICA/fix_hyper_global.cpp | 2 -- src/REPLICA/fix_hyper_local.cpp | 3 +-- src/REPLICA/fix_hyper_local.h | 1 - src/REPLICA/fix_neb.cpp | 1 - src/REPLICA/hyper.cpp | 4 +--- src/REPLICA/neb.cpp | 5 ----- src/REPLICA/prd.cpp | 9 --------- src/REPLICA/tad.cpp | 12 ------------ src/REPLICA/temper.cpp | 4 ---- src/REPLICA/verlet_split.cpp | 1 - src/RIGID/compute_erotate_rigid.cpp | 1 - src/RIGID/compute_ke_rigid.cpp | 1 - src/RIGID/compute_rigid_local.cpp | 1 - 25 files changed, 9 insertions(+), 106 deletions(-) diff --git a/src/PERI/pair_peri_ves.cpp b/src/PERI/pair_peri_ves.cpp index 930ecc6812..bd1eaa5fd2 100644 --- a/src/PERI/pair_peri_ves.cpp +++ b/src/PERI/pair_peri_ves.cpp @@ -18,7 +18,6 @@ #include "pair_peri_ves.h" #include #include -#include #include #include "atom.h" #include "domain.h" diff --git a/src/QEQ/fix_qeq.cpp b/src/QEQ/fix_qeq.cpp index 2e0b7edbe5..7768c01a41 100644 --- a/src/QEQ/fix_qeq.cpp +++ b/src/QEQ/fix_qeq.cpp @@ -17,28 +17,18 @@ ------------------------------------------------------------------------- */ #include "fix_qeq.h" +#include #include -#include -#include #include #include "atom.h" #include "comm.h" -#include "domain.h" -#include "neighbor.h" #include "neigh_list.h" -#include "neigh_request.h" #include "update.h" #include "force.h" -#include "kspace.h" -#include "group.h" -#include "pair.h" -#include "respa.h" -#include "math_const.h" #include "memory.h" #include "error.h" using namespace LAMMPS_NS; -using namespace MathConst; using namespace FixConst; #define MAXLINE 1024 diff --git a/src/QEQ/fix_qeq_dynamic.cpp b/src/QEQ/fix_qeq_dynamic.cpp index fb5fd2ddac..a2cc683b56 100644 --- a/src/QEQ/fix_qeq_dynamic.cpp +++ b/src/QEQ/fix_qeq_dynamic.cpp @@ -16,23 +16,20 @@ ------------------------------------------------------------------------- */ #include "fix_qeq_dynamic.h" +#include #include -#include #include #include #include "atom.h" #include "comm.h" -#include "domain.h" #include "neighbor.h" #include "neigh_list.h" #include "neigh_request.h" #include "update.h" #include "force.h" #include "group.h" -#include "pair.h" #include "kspace.h" #include "respa.h" -#include "memory.h" #include "error.h" using namespace LAMMPS_NS; diff --git a/src/QEQ/fix_qeq_fire.cpp b/src/QEQ/fix_qeq_fire.cpp index 561a82b714..265528a089 100644 --- a/src/QEQ/fix_qeq_fire.cpp +++ b/src/QEQ/fix_qeq_fire.cpp @@ -16,25 +16,22 @@ ------------------------------------------------------------------------- */ #include "fix_qeq_fire.h" +#include #include -#include #include #include #include "atom.h" #include "comm.h" -#include "domain.h" #include "neighbor.h" #include "neigh_list.h" #include "neigh_request.h" #include "update.h" #include "force.h" #include "group.h" -#include "pair.h" #include "pair_comb.h" #include "pair_comb3.h" #include "kspace.h" #include "respa.h" -#include "memory.h" #include "error.h" using namespace LAMMPS_NS; diff --git a/src/QEQ/fix_qeq_point.cpp b/src/QEQ/fix_qeq_point.cpp index bb3ce835fc..8fb9fd3273 100644 --- a/src/QEQ/fix_qeq_point.cpp +++ b/src/QEQ/fix_qeq_point.cpp @@ -17,12 +17,9 @@ #include "fix_qeq_point.h" #include -#include -#include #include #include "atom.h" #include "comm.h" -#include "domain.h" #include "neighbor.h" #include "neigh_list.h" #include "neigh_request.h" diff --git a/src/QEQ/fix_qeq_shielded.cpp b/src/QEQ/fix_qeq_shielded.cpp index 60ff62ca07..13e25475ae 100644 --- a/src/QEQ/fix_qeq_shielded.cpp +++ b/src/QEQ/fix_qeq_shielded.cpp @@ -17,12 +17,9 @@ #include "fix_qeq_shielded.h" #include -#include -#include #include #include "atom.h" #include "comm.h" -#include "domain.h" #include "neighbor.h" #include "neigh_list.h" #include "neigh_request.h" diff --git a/src/QEQ/fix_qeq_slater.cpp b/src/QEQ/fix_qeq_slater.cpp index 95105b5ef2..4f5369eb87 100644 --- a/src/QEQ/fix_qeq_slater.cpp +++ b/src/QEQ/fix_qeq_slater.cpp @@ -17,12 +17,10 @@ #include "fix_qeq_slater.h" #include -#include #include #include #include "atom.h" #include "comm.h" -#include "domain.h" #include "neighbor.h" #include "neigh_list.h" #include "neigh_request.h" @@ -33,7 +31,6 @@ #include "kspace.h" #include "respa.h" #include "math_const.h" -#include "memory.h" #include "error.h" using namespace LAMMPS_NS; diff --git a/src/REPLICA/compute_event_displace.cpp b/src/REPLICA/compute_event_displace.cpp index 4c8d022d70..a6abcce85d 100644 --- a/src/REPLICA/compute_event_displace.cpp +++ b/src/REPLICA/compute_event_displace.cpp @@ -17,14 +17,11 @@ #include "compute_event_displace.h" #include -#include -#include #include #include "atom.h" #include "domain.h" #include "modify.h" #include "fix_event.h" -#include "memory.h" #include "error.h" #include "force.h" #include "update.h" diff --git a/src/REPLICA/fix_event.cpp b/src/REPLICA/fix_event.cpp index 8cf1acba94..41f91332cb 100644 --- a/src/REPLICA/fix_event.cpp +++ b/src/REPLICA/fix_event.cpp @@ -16,16 +16,10 @@ ------------------------------------------------------------------------- */ #include "fix_event.h" -#include -#include #include "atom.h" -#include "update.h" #include "domain.h" -#include "neighbor.h" -#include "comm.h" -#include "universe.h" -#include "memory.h" #include "error.h" +#include "memory.h" using namespace LAMMPS_NS; using namespace FixConst; diff --git a/src/REPLICA/fix_event_hyper.cpp b/src/REPLICA/fix_event_hyper.cpp index 3dd1a03eb9..0d32516dee 100644 --- a/src/REPLICA/fix_event_hyper.cpp +++ b/src/REPLICA/fix_event_hyper.cpp @@ -12,16 +12,9 @@ ------------------------------------------------------------------------- */ #include "fix_event_hyper.h" -#include -#include -#include "atom.h" -#include "update.h" -#include "domain.h" -#include "neighbor.h" #include "comm.h" -#include "universe.h" -#include "memory.h" #include "error.h" +#include "update.h" using namespace LAMMPS_NS; using namespace FixConst; diff --git a/src/REPLICA/fix_event_prd.cpp b/src/REPLICA/fix_event_prd.cpp index 63c9c2718b..19a89e988c 100644 --- a/src/REPLICA/fix_event_prd.cpp +++ b/src/REPLICA/fix_event_prd.cpp @@ -16,16 +16,9 @@ ------------------------------------------------------------------------- */ #include "fix_event_prd.h" -#include -#include -#include "atom.h" -#include "update.h" -#include "domain.h" -#include "neighbor.h" #include "comm.h" -#include "universe.h" -#include "memory.h" #include "error.h" +#include "update.h" using namespace LAMMPS_NS; using namespace FixConst; diff --git a/src/REPLICA/fix_event_tad.cpp b/src/REPLICA/fix_event_tad.cpp index b92bc1fd73..d0b94a216b 100644 --- a/src/REPLICA/fix_event_tad.cpp +++ b/src/REPLICA/fix_event_tad.cpp @@ -16,16 +16,9 @@ ------------------------------------------------------------------------- */ #include "fix_event_tad.h" -#include -#include -#include "atom.h" -#include "update.h" -#include "domain.h" -#include "neighbor.h" #include "comm.h" -#include "universe.h" -#include "memory.h" #include "error.h" +#include "update.h" using namespace LAMMPS_NS; using namespace FixConst; diff --git a/src/REPLICA/fix_hyper_global.cpp b/src/REPLICA/fix_hyper_global.cpp index a58798a63e..5e9da02768 100644 --- a/src/REPLICA/fix_hyper_global.cpp +++ b/src/REPLICA/fix_hyper_global.cpp @@ -14,7 +14,6 @@ #include "fix_hyper_global.h" #include #include -#include #include #include "atom.h" #include "update.h" @@ -24,7 +23,6 @@ #include "neighbor.h" #include "neigh_request.h" #include "neigh_list.h" -#include "modify.h" #include "math_extra.h" #include "memory.h" #include "error.h" diff --git a/src/REPLICA/fix_hyper_local.cpp b/src/REPLICA/fix_hyper_local.cpp index 555c5234f6..e8773095d1 100644 --- a/src/REPLICA/fix_hyper_local.cpp +++ b/src/REPLICA/fix_hyper_local.cpp @@ -14,7 +14,6 @@ #include "fix_hyper_local.h" #include #include -#include #include #include "atom.h" #include "update.h" @@ -22,10 +21,10 @@ #include "pair.h" #include "domain.h" #include "comm.h" +#include "my_page.h" #include "neighbor.h" #include "neigh_request.h" #include "neigh_list.h" -#include "modify.h" #include "math_extra.h" #include "memory.h" #include "error.h" diff --git a/src/REPLICA/fix_hyper_local.h b/src/REPLICA/fix_hyper_local.h index 6f13acb606..8fb3a445c2 100644 --- a/src/REPLICA/fix_hyper_local.h +++ b/src/REPLICA/fix_hyper_local.h @@ -21,7 +21,6 @@ FixStyle(hyper/local,FixHyperLocal) #define LMP_FIX_HYPER_LOCAL_H #include "fix_hyper.h" -#include "my_page.h" namespace LAMMPS_NS { diff --git a/src/REPLICA/fix_neb.cpp b/src/REPLICA/fix_neb.cpp index 2803c37b23..7b377ae9ec 100644 --- a/src/REPLICA/fix_neb.cpp +++ b/src/REPLICA/fix_neb.cpp @@ -19,7 +19,6 @@ #include "fix_neb.h" #include #include -#include #include #include "universe.h" #include "update.h" diff --git a/src/REPLICA/hyper.cpp b/src/REPLICA/hyper.cpp index c400ae097d..af2a963616 100644 --- a/src/REPLICA/hyper.cpp +++ b/src/REPLICA/hyper.cpp @@ -12,11 +12,9 @@ ------------------------------------------------------------------------- */ #include "hyper.h" -#include -#include +#include #include #include "update.h" -#include "atom.h" #include "domain.h" #include "region.h" #include "integrate.h" diff --git a/src/REPLICA/neb.cpp b/src/REPLICA/neb.cpp index b670f3d8f1..84337ce8ae 100644 --- a/src/REPLICA/neb.cpp +++ b/src/REPLICA/neb.cpp @@ -11,12 +11,7 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -// lmptype.h must be first b/c this file uses MAXBIGINT and includes mpi.h -// due to OpenMPI bug which sets INT64_MAX via its mpi.h -// before lmptype.h can set flags to insure it is done correctly - #include "neb.h" -#include "lmptype.h" #include #include #include diff --git a/src/REPLICA/prd.cpp b/src/REPLICA/prd.cpp index 19a12ddbbb..f631cc6a0a 100644 --- a/src/REPLICA/prd.cpp +++ b/src/REPLICA/prd.cpp @@ -15,15 +15,8 @@ Contributing author: Mike Brown (SNL) ------------------------------------------------------------------------- */ -// lmptype.h must be first b/c this file uses MAXBIGINT and includes mpi.h -// due to OpenMPI bug which sets INT64_MAX via its mpi.h -// before lmptype.h can set flags to insure it is done correctly - #include "prd.h" -#include "lmptype.h" #include -#include -#include #include #include "universe.h" #include "update.h" @@ -40,11 +33,9 @@ #include "fix.h" #include "fix_event_prd.h" #include "force.h" -#include "pair.h" #include "random_park.h" #include "random_mars.h" #include "output.h" -#include "dump.h" #include "finish.h" #include "timer.h" #include "memory.h" diff --git a/src/REPLICA/tad.cpp b/src/REPLICA/tad.cpp index 90667b8865..8a51f6d00e 100644 --- a/src/REPLICA/tad.cpp +++ b/src/REPLICA/tad.cpp @@ -15,36 +15,24 @@ Contributing author: Aidan Thompson (SNL) ------------------------------------------------------------------------- */ -// lmptype.h must be first b/c this file uses MAXBIGINT and includes mpi.h -// due to OpenMPI bug which sets INT64_MAX via its mpi.h -// before lmptype.h can set flags to insure it is done correctly - #include "tad.h" -#include "lmptype.h" #include #include -#include #include #include "universe.h" #include "update.h" #include "atom.h" #include "domain.h" -#include "region.h" -#include "comm.h" -#include "velocity.h" #include "integrate.h" #include "min.h" #include "neighbor.h" #include "modify.h" #include "neb.h" #include "compute.h" -#include "fix.h" #include "fix_event_tad.h" #include "fix_store.h" #include "force.h" -#include "pair.h" #include "output.h" -#include "dump.h" #include "finish.h" #include "timer.h" #include "memory.h" diff --git a/src/REPLICA/temper.cpp b/src/REPLICA/temper.cpp index 6eb50c8d9f..46fc3af649 100644 --- a/src/REPLICA/temper.cpp +++ b/src/REPLICA/temper.cpp @@ -17,7 +17,6 @@ #include "temper.h" #include -#include #include #include "universe.h" #include "domain.h" @@ -27,13 +26,10 @@ #include "modify.h" #include "compute.h" #include "force.h" -#include "output.h" -#include "thermo.h" #include "fix.h" #include "random_park.h" #include "finish.h" #include "timer.h" -#include "memory.h" #include "error.h" using namespace LAMMPS_NS; diff --git a/src/REPLICA/verlet_split.cpp b/src/REPLICA/verlet_split.cpp index f268afe7f8..a5ed1a671d 100644 --- a/src/REPLICA/verlet_split.cpp +++ b/src/REPLICA/verlet_split.cpp @@ -16,7 +16,6 @@ ------------------------------------------------------------------------- */ #include "verlet_split.h" -#include #include "universe.h" #include "neighbor.h" #include "domain.h" diff --git a/src/RIGID/compute_erotate_rigid.cpp b/src/RIGID/compute_erotate_rigid.cpp index 1a7236e263..e15c0deb82 100644 --- a/src/RIGID/compute_erotate_rigid.cpp +++ b/src/RIGID/compute_erotate_rigid.cpp @@ -12,7 +12,6 @@ ------------------------------------------------------------------------- */ #include "compute_erotate_rigid.h" -#include #include #include "update.h" #include "force.h" diff --git a/src/RIGID/compute_ke_rigid.cpp b/src/RIGID/compute_ke_rigid.cpp index 66b7a92566..031919b7a9 100644 --- a/src/RIGID/compute_ke_rigid.cpp +++ b/src/RIGID/compute_ke_rigid.cpp @@ -12,7 +12,6 @@ ------------------------------------------------------------------------- */ #include "compute_ke_rigid.h" -#include #include #include "update.h" #include "force.h" diff --git a/src/RIGID/compute_rigid_local.cpp b/src/RIGID/compute_rigid_local.cpp index 75334bb759..57f69a64e2 100644 --- a/src/RIGID/compute_rigid_local.cpp +++ b/src/RIGID/compute_rigid_local.cpp @@ -12,7 +12,6 @@ ------------------------------------------------------------------------- */ #include "compute_rigid_local.h" -#include #include #include "atom.h" #include "update.h" -- GitLab From 65e281d661190ed8e1255fd31cff4a1d45d7a63d Mon Sep 17 00:00:00 2001 From: Aidan Thompson Date: Sun, 7 Jul 2019 18:00:07 -0600 Subject: [PATCH 201/469] Fixed a few problems with read_dump xyz --- src/read_dump.cpp | 7 +++++-- src/reader.cpp | 10 ++++++++++ src/reader.h | 2 +- 3 files changed, 16 insertions(+), 3 deletions(-) diff --git a/src/read_dump.cpp b/src/read_dump.cpp index 395f4c8edd..1a0a746c07 100644 --- a/src/read_dump.cpp +++ b/src/read_dump.cpp @@ -507,7 +507,10 @@ void ReadDump::header(int fieldinfo) yhi = box[1][1]; zlo = box[2][0]; zhi = box[2][1]; - if (triclinic_snap) { + + // value of 1 indicates possible change in tilt factors + + if (triclinic_snap == 1) { xy = box[0][2]; xz = box[1][2]; yz = box[2][2]; @@ -546,7 +549,7 @@ void ReadDump::header(int fieldinfo) error->one(FLERR,"Read_dump triclinic status does not match simulation"); } - // error check on requested fields exisiting in dump file + // error check on requested fields existing in dump file if (fieldflag < 0) error->one(FLERR,"Read_dump field not found in dump file"); diff --git a/src/reader.cpp b/src/reader.cpp index cf344b37b3..5292c9c992 100644 --- a/src/reader.cpp +++ b/src/reader.cpp @@ -75,3 +75,13 @@ void Reader::close_file() else fclose(fp); fp = NULL; } + +/* ---------------------------------------------------------------------- + detect unused arguments +------------------------------------------------------------------------- */ + +void Reader::settings(int narg, char** /*args*/) +{ + if (narg > 0) + error->all(FLERR,"Illegal read_dump command"); +} diff --git a/src/reader.h b/src/reader.h index 8f36bf622a..08b0010b81 100644 --- a/src/reader.h +++ b/src/reader.h @@ -25,7 +25,7 @@ class Reader : protected Pointers { Reader(class LAMMPS *); virtual ~Reader() {} - virtual void settings(int, char**) {}; + virtual void settings(int, char**); virtual int read_time(bigint &) = 0; virtual void skip() = 0; -- GitLab From 5b7ae3713b5722fc87871b716f6107885fd6cbe5 Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Sun, 7 Jul 2019 21:02:51 -0400 Subject: [PATCH 202/469] clean up include handling for VORONOI package --- src/VORONOI/compute_voronoi_atom.cpp | 4 +--- 1 file changed, 1 insertion(+), 3 deletions(-) diff --git a/src/VORONOI/compute_voronoi_atom.cpp b/src/VORONOI/compute_voronoi_atom.cpp index 860126fa77..27252fae89 100644 --- a/src/VORONOI/compute_voronoi_atom.cpp +++ b/src/VORONOI/compute_voronoi_atom.cpp @@ -15,16 +15,14 @@ Contributing author: Daniel Schwen ------------------------------------------------------------------------- */ +#include "compute_voronoi_atom.h" #include #include #include -#include #include "voro++.hh" -#include "compute_voronoi_atom.h" #include "atom.h" #include "group.h" #include "update.h" -#include "modify.h" #include "domain.h" #include "memory.h" #include "error.h" -- GitLab From 60a808d25b61d57d68513d05cc5b99491610e53d Mon Sep 17 00:00:00 2001 From: jrgissing Date: Sun, 7 Jul 2019 21:17:23 -0600 Subject: [PATCH 203/469] bond/react: error->all vs. error->one also, correct several incorrect instances of error printing, which could cause code to hang without explanation --- src/USER-MISC/fix_bond_react.cpp | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/src/USER-MISC/fix_bond_react.cpp b/src/USER-MISC/fix_bond_react.cpp index c641912db6..7be8ec9f4f 100644 --- a/src/USER-MISC/fix_bond_react.cpp +++ b/src/USER-MISC/fix_bond_react.cpp @@ -1286,7 +1286,7 @@ void FixBondReact::make_a_guess() for (int i = 0; i < nxspecial[atom->map(glove[pion][1])][0]; i++) { if (atom->map(xspecial[atom->map(glove[pion][1])][i]) < 0) { - error->all(FLERR,"Bond/react: Fix bond/react needs ghost atoms from further away1"); // parallel issues. + error->one(FLERR,"Bond/react: Fix bond/react needs ghost atoms from further away"); // parallel issues. } if (i_limit_tags[(int)atom->map(xspecial[atom->map(glove[pion][1])][i])] != 0) { status = GUESSFAIL; @@ -1397,7 +1397,7 @@ void FixBondReact::check_a_neighbor() //another check for ghost atoms. perhaps remove the one in make_a_guess if (atom->map(glove[(int)onemol_xspecial[pion][neigh]-1][1]) < 0) { - error->all(FLERR,"Bond/react: Fix bond/react needs ghost atoms from further away2"); + error->one(FLERR,"Bond/react: Fix bond/react needs ghost atoms from further away"); } for (int j = 0; j < onemol_nxspecial[onemol_xspecial[pion][neigh]-1][0]; j++) { @@ -1449,7 +1449,7 @@ void FixBondReact::check_a_neighbor() //another check for ghost atoms. perhaps remove the one in make_a_guess if (atom->map(glove[(int)onemol_xspecial[pion][neigh]-1][1]) < 0) { - error->all(FLERR,"Bond/react: Fix bond/react needs ghost atoms from further away3"); + error->one(FLERR,"Bond/react: Fix bond/react needs ghost atoms from further away"); } for (int ii = 0; ii < onemol_nxspecial[onemol_xspecial[pion][neigh]-1][0]; ii++) { @@ -1560,7 +1560,7 @@ void FixBondReact::inner_crosscheck_loop() //another check for ghost atoms. perhaps remove the one in make_a_guess if (atom->map(glove[(int)onemol_xspecial[pion][neigh]-1][1]) < 0) { - error->all(FLERR,"Bond/react: Fix bond/react needs ghost atoms from further away4"); + error->one(FLERR,"Bond/react: Fix bond/react needs ghost atoms from further away"); } if (guess_branch[avail_guesses-1] == 0) avail_guesses--; -- GitLab From 03418be6452b62299638122a183f016751c19cf3 Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Mon, 8 Jul 2019 15:43:57 -0400 Subject: [PATCH 204/469] minor tweaks to already processed files --- src/ASPHERE/pair_line_lj.cpp | 3 --- src/ASPHERE/pair_resquared.cpp | 5 +---- src/ASPHERE/pair_tri_lj.cpp | 3 --- src/CORESHELL/pair_born_coul_long_cs.cpp | 1 - src/GRANULAR/fix_wall_gran_region.cpp | 1 - src/KSPACE/msm.h | 3 --- src/KSPACE/pair_coul_msm.cpp | 1 - src/angle.h | 2 +- src/dump.h | 1 - src/kspace.h | 3 +-- src/mpiio.h | 2 +- src/region.h | 2 +- src/timer.cpp | 1 - src/write_restart.cpp | 1 - 14 files changed, 5 insertions(+), 24 deletions(-) diff --git a/src/ASPHERE/pair_line_lj.cpp b/src/ASPHERE/pair_line_lj.cpp index 0cb603c4fa..fdeb09aac4 100644 --- a/src/ASPHERE/pair_line_lj.cpp +++ b/src/ASPHERE/pair_line_lj.cpp @@ -13,9 +13,6 @@ #include "pair_line_lj.h" #include -#include -#include -#include #include "atom.h" #include "atom_vec_line.h" #include "force.h" diff --git a/src/ASPHERE/pair_resquared.cpp b/src/ASPHERE/pair_resquared.cpp index ba73c5ba0c..f139564320 100644 --- a/src/ASPHERE/pair_resquared.cpp +++ b/src/ASPHERE/pair_resquared.cpp @@ -16,10 +16,8 @@ ------------------------------------------------------------------------- */ #include "pair_resquared.h" +#include #include -#include -#include -#include #include "math_extra.h" #include "atom.h" #include "atom_vec_ellipsoid.h" @@ -27,7 +25,6 @@ #include "force.h" #include "neighbor.h" #include "neigh_list.h" -#include "integrate.h" #include "memory.h" #include "error.h" diff --git a/src/ASPHERE/pair_tri_lj.cpp b/src/ASPHERE/pair_tri_lj.cpp index 3dde2a4f44..0984b0a30c 100644 --- a/src/ASPHERE/pair_tri_lj.cpp +++ b/src/ASPHERE/pair_tri_lj.cpp @@ -13,9 +13,6 @@ #include "pair_tri_lj.h" #include -#include -#include -#include #include "math_extra.h" #include "atom.h" #include "atom_vec_tri.h" diff --git a/src/CORESHELL/pair_born_coul_long_cs.cpp b/src/CORESHELL/pair_born_coul_long_cs.cpp index f6262fa9e7..b56389e180 100644 --- a/src/CORESHELL/pair_born_coul_long_cs.cpp +++ b/src/CORESHELL/pair_born_coul_long_cs.cpp @@ -17,7 +17,6 @@ #include "pair_born_coul_long_cs.h" #include -#include #include "atom.h" #include "force.h" #include "neigh_list.h" diff --git a/src/GRANULAR/fix_wall_gran_region.cpp b/src/GRANULAR/fix_wall_gran_region.cpp index a4b798d6aa..95553b83b7 100644 --- a/src/GRANULAR/fix_wall_gran_region.cpp +++ b/src/GRANULAR/fix_wall_gran_region.cpp @@ -21,7 +21,6 @@ #include "atom.h" #include "domain.h" #include "update.h" -#include "pair.h" #include "memory.h" #include "error.h" #include "comm.h" diff --git a/src/KSPACE/msm.h b/src/KSPACE/msm.h index 0f81eb9c3f..bf393473e7 100644 --- a/src/KSPACE/msm.h +++ b/src/KSPACE/msm.h @@ -20,9 +20,6 @@ KSpaceStyle(msm,MSM) #ifndef LMP_MSM_H #define LMP_MSM_H -#include "lmptype.h" -#include - #include "kspace.h" namespace LAMMPS_NS { diff --git a/src/KSPACE/pair_coul_msm.cpp b/src/KSPACE/pair_coul_msm.cpp index 0917bb9275..5d42e1f046 100644 --- a/src/KSPACE/pair_coul_msm.cpp +++ b/src/KSPACE/pair_coul_msm.cpp @@ -22,7 +22,6 @@ #include "force.h" #include "kspace.h" #include "neigh_list.h" -#include "memory.h" #include "error.h" using namespace LAMMPS_NS; diff --git a/src/angle.h b/src/angle.h index 3e6812c4fd..7a008f7ca7 100644 --- a/src/angle.h +++ b/src/angle.h @@ -14,7 +14,7 @@ #ifndef LMP_ANGLE_H #define LMP_ANGLE_H -#include "pointers.h" +#include "pointers.h" // IWYU pragma: export namespace LAMMPS_NS { diff --git a/src/dump.h b/src/dump.h index 0173aa3112..bc7fd2d5a5 100644 --- a/src/dump.h +++ b/src/dump.h @@ -14,7 +14,6 @@ #ifndef LMP_DUMP_H #define LMP_DUMP_H -#include #include "pointers.h" // IWYU pragma: export namespace LAMMPS_NS { diff --git a/src/kspace.h b/src/kspace.h index 83ce19cd87..c04a0db989 100644 --- a/src/kspace.h +++ b/src/kspace.h @@ -14,8 +14,7 @@ #ifndef LMP_KSPACE_H #define LMP_KSPACE_H -#include -#include "pointers.h" +#include "pointers.h" // IWYU pragma: export #ifdef FFT_SINGLE typedef float FFT_SCALAR; diff --git a/src/mpiio.h b/src/mpiio.h index 4953ade185..0098fca0e1 100644 --- a/src/mpiio.h +++ b/src/mpiio.h @@ -23,7 +23,7 @@ #error "The MPIIO package cannot be compiled in serial with MPI STUBS" #endif -#include "restart_mpiio.h" +#include "restart_mpiio.h" // IWYU pragma: export #else diff --git a/src/region.h b/src/region.h index 6a3806fed7..0dce004a5b 100644 --- a/src/region.h +++ b/src/region.h @@ -14,7 +14,7 @@ #ifndef LMP_REGION_H #define LMP_REGION_H -#include "pointers.h" +#include "pointers.h" // IWYU pragma: export namespace LAMMPS_NS { diff --git a/src/timer.cpp b/src/timer.cpp index 0dad8fb756..0a5e56ab35 100644 --- a/src/timer.cpp +++ b/src/timer.cpp @@ -18,7 +18,6 @@ #include "comm.h" #include "error.h" #include "force.h" -#include "memory.h" #ifdef _WIN32 #include diff --git a/src/write_restart.cpp b/src/write_restart.cpp index 5adb39067c..4b84e790b8 100644 --- a/src/write_restart.cpp +++ b/src/write_restart.cpp @@ -16,7 +16,6 @@ #include #include "atom.h" #include "atom_vec.h" -#include "atom_vec_hybrid.h" #include "group.h" #include "force.h" #include "pair.h" -- GitLab From 31e19e0824893165038f096313c5fe069c53c94a Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Mon, 8 Jul 2019 16:23:49 -0400 Subject: [PATCH 205/469] complete cleaning includes in some more packages --- src/KSPACE/pair_buck_coul_msm.cpp | 6 ------ src/KSPACE/pair_lj_charmm_coul_msm.cpp | 1 - src/KSPACE/pair_lj_cut_coul_long.cpp | 1 + src/KSPACE/pair_lj_cut_coul_msm.cpp | 1 - src/MPIIO/dump_atom_mpiio.cpp | 4 ++-- src/MPIIO/dump_atom_mpiio.h | 1 - src/MPIIO/dump_cfg_mpiio.cpp | 6 ------ src/MPIIO/dump_custom_mpiio.cpp | 5 ----- src/MPIIO/dump_xyz_mpiio.cpp | 7 ------- src/USER-BOCS/fix_bocs.cpp | 1 - src/USER-CGDNA/bond_oxdna2_fene.cpp | 2 -- src/USER-CGDNA/bond_oxdna_fene.cpp | 2 -- src/USER-CGDNA/fix_nve_dot.cpp | 5 ----- src/USER-CGDNA/fix_nve_dotc_langevin.cpp | 2 -- src/USER-CGDNA/pair_oxdna2_coaxstk.cpp | 6 +----- src/USER-CGDNA/pair_oxdna2_dh.cpp | 10 +--------- src/USER-CGDNA/pair_oxdna2_excv.cpp | 4 ---- src/USER-CGDNA/pair_oxdna2_stk.cpp | 4 ---- src/USER-CGDNA/pair_oxdna_coaxstk.cpp | 6 +----- src/USER-CGDNA/pair_oxdna_excv.cpp | 8 +------- src/USER-CGDNA/pair_oxdna_hbond.cpp | 8 +------- src/USER-CGDNA/pair_oxdna_stk.cpp | 10 ++-------- src/USER-CGDNA/pair_oxdna_xstk.cpp | 6 +----- src/USER-DPD/pair_dpd_fdt_energy.cpp | 7 ++----- src/USER-DPD/pair_exp6_rx.cpp | 6 ++---- src/USER-MESO/atom_vec_tdpd.cpp | 1 - src/USER-MESO/compute_edpd_temp_atom.cpp | 3 +-- src/USER-MESO/fix_edpd_source.cpp | 11 ++--------- src/USER-MESO/fix_mvv_edpd.cpp | 4 +--- src/USER-MESO/fix_mvv_tdpd.cpp | 4 +--- src/VORONOI/compute_voronoi_atom.cpp | 2 +- 31 files changed, 21 insertions(+), 123 deletions(-) diff --git a/src/KSPACE/pair_buck_coul_msm.cpp b/src/KSPACE/pair_buck_coul_msm.cpp index 3d7687df90..1355a2f13a 100644 --- a/src/KSPACE/pair_buck_coul_msm.cpp +++ b/src/KSPACE/pair_buck_coul_msm.cpp @@ -13,21 +13,15 @@ #include "pair_buck_coul_msm.h" #include -#include -#include #include #include "atom.h" -#include "comm.h" #include "force.h" #include "kspace.h" -#include "neighbor.h" #include "neigh_list.h" -#include "math_const.h" #include "memory.h" #include "error.h" using namespace LAMMPS_NS; -using namespace MathConst; /* ---------------------------------------------------------------------- */ diff --git a/src/KSPACE/pair_lj_charmm_coul_msm.cpp b/src/KSPACE/pair_lj_charmm_coul_msm.cpp index 804ae5919d..a93a1275f4 100644 --- a/src/KSPACE/pair_lj_charmm_coul_msm.cpp +++ b/src/KSPACE/pair_lj_charmm_coul_msm.cpp @@ -21,7 +21,6 @@ #include "atom.h" #include "force.h" #include "kspace.h" -#include "neighbor.h" #include "neigh_list.h" #include "memory.h" #include "error.h" diff --git a/src/KSPACE/pair_lj_cut_coul_long.cpp b/src/KSPACE/pair_lj_cut_coul_long.cpp index 7921c814c3..fb79451b37 100644 --- a/src/KSPACE/pair_lj_cut_coul_long.cpp +++ b/src/KSPACE/pair_lj_cut_coul_long.cpp @@ -16,6 +16,7 @@ ------------------------------------------------------------------------- */ #include "pair_lj_cut_coul_long.h" +#include #include #include #include "atom.h" diff --git a/src/KSPACE/pair_lj_cut_coul_msm.cpp b/src/KSPACE/pair_lj_cut_coul_msm.cpp index f8021cc180..4ebbcb9a3f 100644 --- a/src/KSPACE/pair_lj_cut_coul_msm.cpp +++ b/src/KSPACE/pair_lj_cut_coul_msm.cpp @@ -21,7 +21,6 @@ #include "atom.h" #include "force.h" #include "kspace.h" -#include "update.h" #include "neigh_list.h" #include "memory.h" #include "error.h" diff --git a/src/MPIIO/dump_atom_mpiio.cpp b/src/MPIIO/dump_atom_mpiio.cpp index cde5b6258b..2b663554cc 100644 --- a/src/MPIIO/dump_atom_mpiio.cpp +++ b/src/MPIIO/dump_atom_mpiio.cpp @@ -16,11 +16,11 @@ ------------------------------------------------------------------------- */ #include "dump_atom_mpiio.h" +#include +#include #include #include "domain.h" -#include "atom.h" #include "update.h" -#include "group.h" #include "memory.h" #include "error.h" diff --git a/src/MPIIO/dump_atom_mpiio.h b/src/MPIIO/dump_atom_mpiio.h index ad49fa1182..36b43e3f08 100644 --- a/src/MPIIO/dump_atom_mpiio.h +++ b/src/MPIIO/dump_atom_mpiio.h @@ -21,7 +21,6 @@ DumpStyle(atom/mpiio,DumpAtomMPIIO) #define LMP_DUMP_ATOM_MPIIO_H #include "dump_atom.h" -#include namespace LAMMPS_NS { diff --git a/src/MPIIO/dump_cfg_mpiio.cpp b/src/MPIIO/dump_cfg_mpiio.cpp index 90f92d094d..31848b550c 100644 --- a/src/MPIIO/dump_cfg_mpiio.cpp +++ b/src/MPIIO/dump_cfg_mpiio.cpp @@ -21,12 +21,6 @@ #include #include "atom.h" #include "domain.h" -#include "comm.h" -#include "modify.h" -#include "compute.h" -#include "input.h" -#include "fix.h" -#include "variable.h" #include "update.h" #include "memory.h" #include "error.h" diff --git a/src/MPIIO/dump_custom_mpiio.cpp b/src/MPIIO/dump_custom_mpiio.cpp index 5838c61124..dca5833c5b 100644 --- a/src/MPIIO/dump_custom_mpiio.cpp +++ b/src/MPIIO/dump_custom_mpiio.cpp @@ -19,16 +19,11 @@ #include #include #include -#include "atom.h" -#include "force.h" #include "domain.h" -#include "region.h" -#include "group.h" #include "input.h" #include "variable.h" #include "update.h" #include "modify.h" -#include "compute.h" #include "fix.h" #include "memory.h" #include "error.h" diff --git a/src/MPIIO/dump_xyz_mpiio.cpp b/src/MPIIO/dump_xyz_mpiio.cpp index 7b647561bf..ee0532399a 100644 --- a/src/MPIIO/dump_xyz_mpiio.cpp +++ b/src/MPIIO/dump_xyz_mpiio.cpp @@ -19,17 +19,10 @@ #include #include #include -#include "atom.h" -#include "force.h" #include "domain.h" -#include "region.h" -#include "group.h" -#include "input.h" -#include "variable.h" #include "update.h" #include "modify.h" #include "compute.h" -#include "fix.h" #include "memory.h" #include "error.h" diff --git a/src/USER-BOCS/fix_bocs.cpp b/src/USER-BOCS/fix_bocs.cpp index e0952086dd..936e5ff58e 100644 --- a/src/USER-BOCS/fix_bocs.cpp +++ b/src/USER-BOCS/fix_bocs.cpp @@ -18,7 +18,6 @@ #include #include #include -#include "math_extra.h" #include "atom.h" #include "force.h" #include "group.h" diff --git a/src/USER-CGDNA/bond_oxdna2_fene.cpp b/src/USER-CGDNA/bond_oxdna2_fene.cpp index 2cd7883600..97005ef5f9 100644 --- a/src/USER-CGDNA/bond_oxdna2_fene.cpp +++ b/src/USER-CGDNA/bond_oxdna2_fene.cpp @@ -15,8 +15,6 @@ ------------------------------------------------------------------------- */ #include "bond_oxdna2_fene.h" -#include -#include using namespace LAMMPS_NS; diff --git a/src/USER-CGDNA/bond_oxdna_fene.cpp b/src/USER-CGDNA/bond_oxdna_fene.cpp index 8b94fd6a5a..8314576d63 100644 --- a/src/USER-CGDNA/bond_oxdna_fene.cpp +++ b/src/USER-CGDNA/bond_oxdna_fene.cpp @@ -16,10 +16,8 @@ #include "bond_oxdna_fene.h" #include -#include #include "atom.h" #include "neighbor.h" -#include "domain.h" #include "comm.h" #include "update.h" #include "force.h" diff --git a/src/USER-CGDNA/fix_nve_dot.cpp b/src/USER-CGDNA/fix_nve_dot.cpp index 3bf6757df7..ff8e1c0ee2 100644 --- a/src/USER-CGDNA/fix_nve_dot.cpp +++ b/src/USER-CGDNA/fix_nve_dot.cpp @@ -15,15 +15,10 @@ ------------------------------------------------------------------------- */ #include "fix_nve_dot.h" -#include -#include -#include #include "math_extra.h" #include "atom.h" #include "atom_vec_ellipsoid.h" -#include "force.h" #include "update.h" -#include "memory.h" #include "error.h" using namespace LAMMPS_NS; diff --git a/src/USER-CGDNA/fix_nve_dotc_langevin.cpp b/src/USER-CGDNA/fix_nve_dotc_langevin.cpp index 61e3552f11..59def4c812 100644 --- a/src/USER-CGDNA/fix_nve_dotc_langevin.cpp +++ b/src/USER-CGDNA/fix_nve_dotc_langevin.cpp @@ -17,7 +17,6 @@ #include "fix_nve_dotc_langevin.h" #include -#include #include #include "math_extra.h" #include "atom.h" @@ -26,7 +25,6 @@ #include "update.h" #include "comm.h" #include "random_mars.h" -#include "memory.h" #include "error.h" using namespace LAMMPS_NS; diff --git a/src/USER-CGDNA/pair_oxdna2_coaxstk.cpp b/src/USER-CGDNA/pair_oxdna2_coaxstk.cpp index 1d0a2eb494..b96da3fa4a 100644 --- a/src/USER-CGDNA/pair_oxdna2_coaxstk.cpp +++ b/src/USER-CGDNA/pair_oxdna2_coaxstk.cpp @@ -15,9 +15,8 @@ ------------------------------------------------------------------------- */ #include "pair_oxdna2_coaxstk.h" +#include #include -#include -#include #include #include "mf_oxdna.h" #include "atom.h" @@ -25,9 +24,6 @@ #include "force.h" #include "neighbor.h" #include "neigh_list.h" -#include "neigh_request.h" -#include "update.h" -#include "integrate.h" #include "math_const.h" #include "memory.h" #include "error.h" diff --git a/src/USER-CGDNA/pair_oxdna2_dh.cpp b/src/USER-CGDNA/pair_oxdna2_dh.cpp index 22fc79dae4..ea1f4f84f4 100644 --- a/src/USER-CGDNA/pair_oxdna2_dh.cpp +++ b/src/USER-CGDNA/pair_oxdna2_dh.cpp @@ -15,28 +15,20 @@ ------------------------------------------------------------------------- */ #include "pair_oxdna2_dh.h" +#include #include -#include -#include #include -#include "mf_oxdna.h" #include "atom.h" #include "comm.h" #include "force.h" #include "neighbor.h" #include "neigh_list.h" -#include "neigh_request.h" -#include "update.h" -#include "integrate.h" -#include "math_const.h" #include "memory.h" #include "error.h" #include "atom_vec_ellipsoid.h" #include "math_extra.h" using namespace LAMMPS_NS; -using namespace MathConst; -using namespace MFOxdna; /* ---------------------------------------------------------------------- */ diff --git a/src/USER-CGDNA/pair_oxdna2_excv.cpp b/src/USER-CGDNA/pair_oxdna2_excv.cpp index de4f8319b9..0a7da8e81a 100644 --- a/src/USER-CGDNA/pair_oxdna2_excv.cpp +++ b/src/USER-CGDNA/pair_oxdna2_excv.cpp @@ -15,10 +15,6 @@ ------------------------------------------------------------------------- */ #include "pair_oxdna2_excv.h" -#include -#include -#include -#include using namespace LAMMPS_NS; diff --git a/src/USER-CGDNA/pair_oxdna2_stk.cpp b/src/USER-CGDNA/pair_oxdna2_stk.cpp index 3b9480bff6..26bae766e1 100644 --- a/src/USER-CGDNA/pair_oxdna2_stk.cpp +++ b/src/USER-CGDNA/pair_oxdna2_stk.cpp @@ -15,10 +15,6 @@ ------------------------------------------------------------------------- */ #include "pair_oxdna2_stk.h" -#include -#include -#include -#include using namespace LAMMPS_NS; diff --git a/src/USER-CGDNA/pair_oxdna_coaxstk.cpp b/src/USER-CGDNA/pair_oxdna_coaxstk.cpp index 7310f60ec3..6e37352ef0 100644 --- a/src/USER-CGDNA/pair_oxdna_coaxstk.cpp +++ b/src/USER-CGDNA/pair_oxdna_coaxstk.cpp @@ -15,9 +15,8 @@ ------------------------------------------------------------------------- */ #include "pair_oxdna_coaxstk.h" +#include #include -#include -#include #include #include "mf_oxdna.h" #include "atom.h" @@ -25,9 +24,6 @@ #include "force.h" #include "neighbor.h" #include "neigh_list.h" -#include "neigh_request.h" -#include "update.h" -#include "integrate.h" #include "math_const.h" #include "memory.h" #include "error.h" diff --git a/src/USER-CGDNA/pair_oxdna_excv.cpp b/src/USER-CGDNA/pair_oxdna_excv.cpp index 68091f4190..9fb3dd041a 100644 --- a/src/USER-CGDNA/pair_oxdna_excv.cpp +++ b/src/USER-CGDNA/pair_oxdna_excv.cpp @@ -15,9 +15,8 @@ ------------------------------------------------------------------------- */ #include "pair_oxdna_excv.h" +#include #include -#include -#include #include #include "mf_oxdna.h" #include "atom.h" @@ -25,17 +24,12 @@ #include "force.h" #include "neighbor.h" #include "neigh_list.h" -#include "neigh_request.h" -#include "update.h" -#include "integrate.h" -#include "math_const.h" #include "memory.h" #include "error.h" #include "atom_vec_ellipsoid.h" #include "math_extra.h" using namespace LAMMPS_NS; -using namespace MathConst; using namespace MFOxdna; /* ---------------------------------------------------------------------- */ diff --git a/src/USER-CGDNA/pair_oxdna_hbond.cpp b/src/USER-CGDNA/pair_oxdna_hbond.cpp index 2de05e66ae..12e4b08c46 100644 --- a/src/USER-CGDNA/pair_oxdna_hbond.cpp +++ b/src/USER-CGDNA/pair_oxdna_hbond.cpp @@ -15,9 +15,8 @@ ------------------------------------------------------------------------- */ #include "pair_oxdna_hbond.h" +#include #include -#include -#include #include #include "mf_oxdna.h" #include "atom.h" @@ -25,17 +24,12 @@ #include "force.h" #include "neighbor.h" #include "neigh_list.h" -#include "neigh_request.h" -#include "update.h" -#include "integrate.h" -#include "math_const.h" #include "memory.h" #include "error.h" #include "atom_vec_ellipsoid.h" #include "math_extra.h" using namespace LAMMPS_NS; -using namespace MathConst; using namespace MFOxdna; // sequence-specific base-pairing strength diff --git a/src/USER-CGDNA/pair_oxdna_stk.cpp b/src/USER-CGDNA/pair_oxdna_stk.cpp index aaa25039ef..022d94f935 100644 --- a/src/USER-CGDNA/pair_oxdna_stk.cpp +++ b/src/USER-CGDNA/pair_oxdna_stk.cpp @@ -15,27 +15,21 @@ ------------------------------------------------------------------------- */ #include "pair_oxdna_stk.h" +#include #include -#include -#include #include +#include #include "mf_oxdna.h" #include "atom.h" #include "comm.h" #include "force.h" #include "neighbor.h" -#include "neigh_list.h" -#include "neigh_request.h" -#include "update.h" -#include "integrate.h" -#include "math_const.h" #include "memory.h" #include "error.h" #include "atom_vec_ellipsoid.h" #include "math_extra.h" using namespace LAMMPS_NS; -using namespace MathConst; using namespace MFOxdna; // sequence-specific stacking strength diff --git a/src/USER-CGDNA/pair_oxdna_xstk.cpp b/src/USER-CGDNA/pair_oxdna_xstk.cpp index 806f8a42c6..384a7768bd 100644 --- a/src/USER-CGDNA/pair_oxdna_xstk.cpp +++ b/src/USER-CGDNA/pair_oxdna_xstk.cpp @@ -15,9 +15,8 @@ ------------------------------------------------------------------------- */ #include "pair_oxdna_xstk.h" +#include #include -#include -#include #include #include "mf_oxdna.h" #include "atom.h" @@ -25,9 +24,6 @@ #include "force.h" #include "neighbor.h" #include "neigh_list.h" -#include "neigh_request.h" -#include "update.h" -#include "integrate.h" #include "math_const.h" #include "memory.h" #include "error.h" diff --git a/src/USER-DPD/pair_dpd_fdt_energy.cpp b/src/USER-DPD/pair_dpd_fdt_energy.cpp index 12e6989c00..22741a055d 100644 --- a/src/USER-DPD/pair_dpd_fdt_energy.cpp +++ b/src/USER-DPD/pair_dpd_fdt_energy.cpp @@ -15,23 +15,20 @@ Contributing author: James Larentzos (U.S. Army Research Laboratory) ------------------------------------------------------------------------- */ +#include "pair_dpd_fdt_energy.h" +#include #include -#include -#include #include #include "atom.h" -#include "atom_vec.h" #include "comm.h" #include "update.h" #include "fix.h" #include "force.h" #include "neighbor.h" #include "neigh_list.h" -#include "neigh_request.h" #include "random_mars.h" #include "memory.h" #include "modify.h" -#include "pair_dpd_fdt_energy.h" #include "error.h" using namespace LAMMPS_NS; diff --git a/src/USER-DPD/pair_exp6_rx.cpp b/src/USER-DPD/pair_exp6_rx.cpp index 13521b52b1..5cf2859ae3 100644 --- a/src/USER-DPD/pair_exp6_rx.cpp +++ b/src/USER-DPD/pair_exp6_rx.cpp @@ -11,17 +11,16 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ +#include "pair_exp6_rx.h" +#include #include -#include #include #include #include -#include "pair_exp6_rx.h" #include "atom.h" #include "comm.h" #include "force.h" #include "neigh_list.h" -#include "math_const.h" #include "math_special.h" #include "memory.h" #include "error.h" @@ -29,7 +28,6 @@ #include "fix.h" using namespace LAMMPS_NS; -using namespace MathConst; using namespace MathSpecial; #define MAXLINE 1024 diff --git a/src/USER-MESO/atom_vec_tdpd.cpp b/src/USER-MESO/atom_vec_tdpd.cpp index aa0dc93809..0db5437c4a 100644 --- a/src/USER-MESO/atom_vec_tdpd.cpp +++ b/src/USER-MESO/atom_vec_tdpd.cpp @@ -23,7 +23,6 @@ #include "update.h" #include "memory.h" #include "error.h" -#include "input.h" using namespace LAMMPS_NS; diff --git a/src/USER-MESO/compute_edpd_temp_atom.cpp b/src/USER-MESO/compute_edpd_temp_atom.cpp index 119e0079d1..9eb6e9752b 100644 --- a/src/USER-MESO/compute_edpd_temp_atom.cpp +++ b/src/USER-MESO/compute_edpd_temp_atom.cpp @@ -11,13 +11,12 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include #include "compute_edpd_temp_atom.h" +#include #include "atom.h" #include "update.h" #include "modify.h" #include "comm.h" -#include "force.h" #include "memory.h" #include "error.h" diff --git a/src/USER-MESO/fix_edpd_source.cpp b/src/USER-MESO/fix_edpd_source.cpp index 24bef2b1f7..e62d9a8a79 100644 --- a/src/USER-MESO/fix_edpd_source.cpp +++ b/src/USER-MESO/fix_edpd_source.cpp @@ -11,17 +11,10 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include -#include #include "fix_edpd_source.h" +#include +#include #include "atom.h" -#include "comm.h" -#include "update.h" -#include "modify.h" -#include "domain.h" -#include "lattice.h" -#include "input.h" -#include "variable.h" #include "error.h" #include "force.h" diff --git a/src/USER-MESO/fix_mvv_edpd.cpp b/src/USER-MESO/fix_mvv_edpd.cpp index 8719d0d262..bd9cd9cc2a 100644 --- a/src/USER-MESO/fix_mvv_edpd.cpp +++ b/src/USER-MESO/fix_mvv_edpd.cpp @@ -29,13 +29,11 @@ Communications, 2015, 51: 11038-11040. ------------------------------------------------------------------------- */ -#include -#include #include "fix_mvv_edpd.h" +#include #include "atom.h" #include "force.h" #include "update.h" -#include "respa.h" #include "error.h" using namespace LAMMPS_NS; diff --git a/src/USER-MESO/fix_mvv_tdpd.cpp b/src/USER-MESO/fix_mvv_tdpd.cpp index 24b1bbcf48..b7fe37d7ee 100644 --- a/src/USER-MESO/fix_mvv_tdpd.cpp +++ b/src/USER-MESO/fix_mvv_tdpd.cpp @@ -25,13 +25,11 @@ -reaction problems". The Journal of Chemical Physics, 2015, 143: 014101. ------------------------------------------------------------------------- */ -#include -#include #include "fix_mvv_tdpd.h" +#include #include "atom.h" #include "force.h" #include "update.h" -#include "respa.h" #include "error.h" using namespace LAMMPS_NS; diff --git a/src/VORONOI/compute_voronoi_atom.cpp b/src/VORONOI/compute_voronoi_atom.cpp index 27252fae89..d5976f85d3 100644 --- a/src/VORONOI/compute_voronoi_atom.cpp +++ b/src/VORONOI/compute_voronoi_atom.cpp @@ -19,7 +19,7 @@ #include #include #include -#include "voro++.hh" +#include #include "atom.h" #include "group.h" #include "update.h" -- GitLab From cfaa53729697d88ecf1c5bb7453306b887823f5a Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Mon, 8 Jul 2019 17:40:30 -0400 Subject: [PATCH 206/469] use alternate implementation of numeric conversion functions these new functions allow to choose between aborting with Error::one() and exiting with Error::all(). in the long run those should replace all of the functions in Force. --- src/DIPOLE/atom_vec_dipole.cpp | 19 +-- src/KOKKOS/atom_vec_angle_kokkos.cpp | 9 +- src/KOKKOS/atom_vec_atomic_kokkos.cpp | 5 +- src/KOKKOS/atom_vec_bond_kokkos.cpp | 9 +- src/KOKKOS/atom_vec_charge_kokkos.cpp | 9 +- src/KOKKOS/atom_vec_dpd_kokkos.cpp | 7 +- src/KOKKOS/atom_vec_full_kokkos.cpp | 13 +- src/KOKKOS/atom_vec_hybrid_kokkos.cpp | 9 +- src/KOKKOS/atom_vec_molecular_kokkos.cpp | 9 +- src/KOKKOS/atom_vec_sphere_kokkos.cpp | 29 ++--- src/MOLECULE/atom_vec_angle.cpp | 3 +- src/MOLECULE/atom_vec_bond.cpp | 3 +- src/MOLECULE/atom_vec_full.cpp | 7 +- src/MOLECULE/atom_vec_molecular.cpp | 3 +- src/MOLECULE/atom_vec_template.cpp | 11 +- src/PERI/atom_vec_peri.cpp | 11 +- src/SPIN/atom_vec_spin.cpp | 19 +-- src/USER-AWPMD/atom_vec_wavepacket.cpp | 37 +++--- src/USER-DPD/atom_vec_dpd.cpp | 7 +- src/USER-EFF/atom_vec_electron.cpp | 25 ++-- src/USER-MESO/atom_vec_edpd.cpp | 7 +- src/USER-MESO/atom_vec_mdpd.cpp | 7 +- src/USER-MESO/atom_vec_tdpd.cpp | 3 +- src/USER-SMD/atom_vec_smd.cpp | 29 ++--- src/USER-SPH/atom_vec_meso.cpp | 15 +-- src/atom_vec.cpp | 7 +- src/atom_vec_atomic.cpp | 3 +- src/atom_vec_body.cpp | 28 ++--- src/atom_vec_charge.cpp | 7 +- src/atom_vec_ellipsoid.cpp | 43 +++---- src/atom_vec_hybrid.cpp | 9 +- src/atom_vec_line.cpp | 37 +++--- src/atom_vec_sphere.cpp | 29 ++--- src/atom_vec_tri.cpp | 59 +++++----- src/utils.cpp | 144 +++++++++++++++++++++++ src/utils.h | 56 ++++++++- 36 files changed, 479 insertions(+), 248 deletions(-) diff --git a/src/DIPOLE/atom_vec_dipole.cpp b/src/DIPOLE/atom_vec_dipole.cpp index b469327c80..47fff1d4c5 100644 --- a/src/DIPOLE/atom_vec_dipole.cpp +++ b/src/DIPOLE/atom_vec_dipole.cpp @@ -22,6 +22,7 @@ #include "fix.h" #include "memory.h" #include "error.h" +#include "utils.h" using namespace LAMMPS_NS; @@ -781,19 +782,19 @@ void AtomVecDipole::data_atom(double *coord, imageint imagetmp, char **values) if (nlocal == nmax) grow(0); tag[nlocal] = ATOTAGINT(values[0]); - type[nlocal] = force->inumeric(FLERR,values[1]); + type[nlocal] = utils::inumeric(FLERR,values[1],true,lmp); if (type[nlocal] <= 0 || type[nlocal] > atom->ntypes) error->one(FLERR,"Invalid atom type in Atoms section of data file"); - q[nlocal] = force->numeric(FLERR,values[2]); + q[nlocal] = utils::numeric(FLERR,values[2],true,lmp); x[nlocal][0] = coord[0]; x[nlocal][1] = coord[1]; x[nlocal][2] = coord[2]; - mu[nlocal][0] = force->numeric(FLERR,values[6]); - mu[nlocal][1] = force->numeric(FLERR,values[7]); - mu[nlocal][2] = force->numeric(FLERR,values[8]); + mu[nlocal][0] = utils::numeric(FLERR,values[6],true,lmp); + mu[nlocal][1] = utils::numeric(FLERR,values[7],true,lmp); + mu[nlocal][2] = utils::numeric(FLERR,values[8],true,lmp); mu[nlocal][3] = sqrt(mu[nlocal][0]*mu[nlocal][0] + mu[nlocal][1]*mu[nlocal][1] + mu[nlocal][2]*mu[nlocal][2]); @@ -815,10 +816,10 @@ void AtomVecDipole::data_atom(double *coord, imageint imagetmp, char **values) int AtomVecDipole::data_atom_hybrid(int nlocal, char **values) { - q[nlocal] = force->numeric(FLERR,values[0]); - mu[nlocal][0] = force->numeric(FLERR,values[1]); - mu[nlocal][1] = force->numeric(FLERR,values[2]); - mu[nlocal][2] = force->numeric(FLERR,values[3]); + q[nlocal] = utils::numeric(FLERR,values[0],true,lmp); + mu[nlocal][0] = utils::numeric(FLERR,values[1],true,lmp); + mu[nlocal][1] = utils::numeric(FLERR,values[2],true,lmp); + mu[nlocal][2] = utils::numeric(FLERR,values[3],true,lmp); mu[nlocal][3] = sqrt(mu[nlocal][0]*mu[nlocal][0] + mu[nlocal][1]*mu[nlocal][1] + mu[nlocal][2]*mu[nlocal][2]); diff --git a/src/KOKKOS/atom_vec_angle_kokkos.cpp b/src/KOKKOS/atom_vec_angle_kokkos.cpp index b6cf8ba2b2..06358289b6 100644 --- a/src/KOKKOS/atom_vec_angle_kokkos.cpp +++ b/src/KOKKOS/atom_vec_angle_kokkos.cpp @@ -22,6 +22,7 @@ #include "atom_masks.h" #include "memory_kokkos.h" #include "error.h" +#include "utils.h" using namespace LAMMPS_NS; @@ -1633,9 +1634,9 @@ void AtomVecAngleKokkos::data_atom(double *coord, imageint imagetmp, if (nlocal == nmax) grow(0); atomKK->modified(Host,ALL_MASK); - h_tag(nlocal) = force->inumeric(FLERR,values[0]); - h_molecule(nlocal) = force->inumeric(FLERR,values[1]); - h_type(nlocal) = force->inumeric(FLERR,values[2]); + h_tag(nlocal) = utils::inumeric(FLERR,values[0],true,lmp); + h_molecule(nlocal) = utils::inumeric(FLERR,values[1],true,lmp); + h_type(nlocal) = utils::inumeric(FLERR,values[2],true,lmp); if (h_type(nlocal) <= 0 || h_type(nlocal) > atom->ntypes) error->one(FLERR,"Invalid atom type in Atoms section of data file"); @@ -1662,7 +1663,7 @@ void AtomVecAngleKokkos::data_atom(double *coord, imageint imagetmp, int AtomVecAngleKokkos::data_atom_hybrid(int nlocal, char **values) { - h_molecule(nlocal) = force->inumeric(FLERR,values[0]); + h_molecule(nlocal) = utils::inumeric(FLERR,values[0],true,lmp); h_num_bond(nlocal) = 0; h_num_angle(nlocal) = 0; return 1; diff --git a/src/KOKKOS/atom_vec_atomic_kokkos.cpp b/src/KOKKOS/atom_vec_atomic_kokkos.cpp index b0cf4e483a..6e530bdbe9 100644 --- a/src/KOKKOS/atom_vec_atomic_kokkos.cpp +++ b/src/KOKKOS/atom_vec_atomic_kokkos.cpp @@ -22,6 +22,7 @@ #include "atom_masks.h" #include "memory_kokkos.h" #include "error.h" +#include "utils.h" using namespace LAMMPS_NS; @@ -824,8 +825,8 @@ void AtomVecAtomicKokkos::data_atom(double *coord, tagint imagetmp, int nlocal = atom->nlocal; if (nlocal == nmax) grow(0); - h_tag[nlocal] = force->inumeric(FLERR,values[0]); - h_type[nlocal] = force->inumeric(FLERR,values[1]); + h_tag[nlocal] = utils::inumeric(FLERR,values[0],true,lmp); + h_type[nlocal] = utils::inumeric(FLERR,values[1],true,lmp); if (type[nlocal] <= 0 || type[nlocal] > atom->ntypes) error->one(FLERR,"Invalid atom type in Atoms section of data file"); diff --git a/src/KOKKOS/atom_vec_bond_kokkos.cpp b/src/KOKKOS/atom_vec_bond_kokkos.cpp index bac06e7845..3195ea0876 100644 --- a/src/KOKKOS/atom_vec_bond_kokkos.cpp +++ b/src/KOKKOS/atom_vec_bond_kokkos.cpp @@ -22,6 +22,7 @@ #include "atom_masks.h" #include "memory_kokkos.h" #include "error.h" +#include "utils.h" using namespace LAMMPS_NS; @@ -1059,9 +1060,9 @@ void AtomVecBondKokkos::data_atom(double *coord, imageint imagetmp, if (nlocal == nmax) grow(0); atomKK->modified(Host,ALL_MASK); - h_tag(nlocal) = force->inumeric(FLERR,values[0]); - h_molecule(nlocal) = force->inumeric(FLERR,values[1]); - h_type(nlocal) = force->inumeric(FLERR,values[2]); + h_tag(nlocal) = utils::inumeric(FLERR,values[0],true,lmp); + h_molecule(nlocal) = utils::inumeric(FLERR,values[1],true,lmp); + h_type(nlocal) = utils::inumeric(FLERR,values[2],true,lmp); if (h_type(nlocal) <= 0 || h_type(nlocal) > atom->ntypes) error->one(FLERR,"Invalid atom type in Atoms section of data file"); @@ -1087,7 +1088,7 @@ void AtomVecBondKokkos::data_atom(double *coord, imageint imagetmp, int AtomVecBondKokkos::data_atom_hybrid(int nlocal, char **values) { - h_molecule(nlocal) = force->inumeric(FLERR,values[0]); + h_molecule(nlocal) = utils::inumeric(FLERR,values[0],true,lmp); h_num_bond(nlocal) = 0; return 1; } diff --git a/src/KOKKOS/atom_vec_charge_kokkos.cpp b/src/KOKKOS/atom_vec_charge_kokkos.cpp index 44f9a44052..77d0c1dae3 100644 --- a/src/KOKKOS/atom_vec_charge_kokkos.cpp +++ b/src/KOKKOS/atom_vec_charge_kokkos.cpp @@ -22,6 +22,7 @@ #include "atom_masks.h" #include "memory_kokkos.h" #include "error.h" +#include "utils.h" using namespace LAMMPS_NS; @@ -960,12 +961,12 @@ void AtomVecChargeKokkos::data_atom(double *coord, imageint imagetmp, int nlocal = atom->nlocal; if (nlocal == nmax) grow(0); - h_tag[nlocal] = force->inumeric(FLERR,values[0]); - h_type[nlocal] = force->inumeric(FLERR,values[1]); + h_tag[nlocal] = utils::inumeric(FLERR,values[0],true,lmp); + h_type[nlocal] = utils::inumeric(FLERR,values[1],true,lmp); if (type[nlocal] <= 0 || type[nlocal] > atom->ntypes) error->one(FLERR,"Invalid atom type in Atoms section of data file"); - h_q[nlocal] = force->numeric(FLERR,values[2]); + h_q[nlocal] = utils::numeric(FLERR,values[2],true,lmp); h_x(nlocal,0) = coord[0]; h_x(nlocal,1) = coord[1]; @@ -989,7 +990,7 @@ void AtomVecChargeKokkos::data_atom(double *coord, imageint imagetmp, int AtomVecChargeKokkos::data_atom_hybrid(int nlocal, char **values) { - h_q[nlocal] = force->numeric(FLERR,values[0]); + h_q[nlocal] = utils::numeric(FLERR,values[0],true,lmp); return 1; } diff --git a/src/KOKKOS/atom_vec_dpd_kokkos.cpp b/src/KOKKOS/atom_vec_dpd_kokkos.cpp index d3c3e71331..93ca976892 100644 --- a/src/KOKKOS/atom_vec_dpd_kokkos.cpp +++ b/src/KOKKOS/atom_vec_dpd_kokkos.cpp @@ -22,6 +22,7 @@ #include "atom_masks.h" #include "memory_kokkos.h" #include "error.h" +#include "utils.h" using namespace LAMMPS_NS; @@ -1724,11 +1725,11 @@ void AtomVecDPDKokkos::data_atom(double *coord, tagint imagetmp, if (nlocal == nmax) grow(0); h_tag[nlocal] = ATOTAGINT(values[0]); - h_type[nlocal] = force->inumeric(FLERR,values[1]); + h_type[nlocal] = utils::inumeric(FLERR,values[1],true,lmp); if (type[nlocal] <= 0 || type[nlocal] > atom->ntypes) error->one(FLERR,"Invalid atom type in Atoms section of data file"); - h_dpdTheta[nlocal] = force->numeric(FLERR,values[2]); + h_dpdTheta[nlocal] = utils::numeric(FLERR,values[2],true,lmp); if (h_dpdTheta[nlocal] <= 0) error->one(FLERR,"Internal temperature in Atoms section of date file must be > zero"); @@ -1762,7 +1763,7 @@ void AtomVecDPDKokkos::data_atom(double *coord, tagint imagetmp, int AtomVecDPDKokkos::data_atom_hybrid(int nlocal, char **values) { - h_dpdTheta(nlocal) = force->numeric(FLERR,values[0]); + h_dpdTheta(nlocal) = utils::numeric(FLERR,values[0],true,lmp); atomKK->modified(Host,DPDTHETA_MASK); diff --git a/src/KOKKOS/atom_vec_full_kokkos.cpp b/src/KOKKOS/atom_vec_full_kokkos.cpp index c10402de8c..19443b231f 100644 --- a/src/KOKKOS/atom_vec_full_kokkos.cpp +++ b/src/KOKKOS/atom_vec_full_kokkos.cpp @@ -22,6 +22,7 @@ #include "atom_masks.h" #include "memory_kokkos.h" #include "error.h" +#include "utils.h" using namespace LAMMPS_NS; @@ -1488,13 +1489,13 @@ void AtomVecFullKokkos::data_atom(double *coord, imageint imagetmp, if (nlocal == nmax) grow(0); atomKK->modified(Host,ALL_MASK); - h_tag(nlocal) = force->inumeric(FLERR,values[0]); - h_molecule(nlocal) = force->inumeric(FLERR,values[1]); - h_type(nlocal) = force->inumeric(FLERR,values[2]); + h_tag(nlocal) = utils::inumeric(FLERR,values[0],true,lmp); + h_molecule(nlocal) = utils::inumeric(FLERR,values[1],true,lmp); + h_type(nlocal) = utils::inumeric(FLERR,values[2],true,lmp); if (h_type(nlocal) <= 0 || h_type(nlocal) > atom->ntypes) error->one(FLERR,"Invalid atom type in Atoms section of data file"); - h_q(nlocal) = force->numeric(FLERR,values[3]); + h_q(nlocal) = utils::numeric(FLERR,values[3],true,lmp); h_x(nlocal,0) = coord[0]; h_x(nlocal,1) = coord[1]; @@ -1521,8 +1522,8 @@ void AtomVecFullKokkos::data_atom(double *coord, imageint imagetmp, int AtomVecFullKokkos::data_atom_hybrid(int nlocal, char **values) { - h_molecule(nlocal) = force->inumeric(FLERR,values[0]); - h_q(nlocal) = force->numeric(FLERR,values[1]); + h_molecule(nlocal) = utils::inumeric(FLERR,values[0],true,lmp); + h_q(nlocal) = utils::numeric(FLERR,values[1],true,lmp); h_num_bond(nlocal) = 0; h_num_angle(nlocal) = 0; h_num_dihedral(nlocal) = 0; diff --git a/src/KOKKOS/atom_vec_hybrid_kokkos.cpp b/src/KOKKOS/atom_vec_hybrid_kokkos.cpp index 4c3de20a49..54dd89bfb3 100644 --- a/src/KOKKOS/atom_vec_hybrid_kokkos.cpp +++ b/src/KOKKOS/atom_vec_hybrid_kokkos.cpp @@ -22,6 +22,7 @@ #include "memory_kokkos.h" #include "error.h" #include "atom_masks.h" +#include "utils.h" using namespace LAMMPS_NS; @@ -976,7 +977,7 @@ void AtomVecHybridKokkos::data_atom(double *coord, imageint imagetmp, char **val if (nlocal == nmax) grow(0); h_tag[nlocal] = ATOTAGINT(values[0]); - h_type[nlocal] = force->inumeric(FLERR,values[1]); + h_type[nlocal] = utils::inumeric(FLERR,values[1],true,lmp); if (h_type[nlocal] <= 0 || h_type[nlocal] > atom->ntypes) error->one(FLERR,"Invalid atom h_type in Atoms section of data file"); @@ -1020,9 +1021,9 @@ void AtomVecHybridKokkos::data_vel(int m, char **values) { atomKK->sync(Host,V_MASK); - h_v(m,0) = force->numeric(FLERR,values[0]); - h_v(m,1) = force->numeric(FLERR,values[1]); - h_v(m,2) = force->numeric(FLERR,values[2]); + h_v(m,0) = utils::numeric(FLERR,values[0],true,lmp); + h_v(m,1) = utils::numeric(FLERR,values[1],true,lmp); + h_v(m,2) = utils::numeric(FLERR,values[2],true,lmp); atomKK->modified(Host,V_MASK); diff --git a/src/KOKKOS/atom_vec_molecular_kokkos.cpp b/src/KOKKOS/atom_vec_molecular_kokkos.cpp index 0616b3dfe0..9871b1247a 100644 --- a/src/KOKKOS/atom_vec_molecular_kokkos.cpp +++ b/src/KOKKOS/atom_vec_molecular_kokkos.cpp @@ -22,6 +22,7 @@ #include "atom_masks.h" #include "memory_kokkos.h" #include "error.h" +#include "utils.h" using namespace LAMMPS_NS; @@ -1892,9 +1893,9 @@ void AtomVecMolecularKokkos::data_atom(double *coord, imageint imagetmp, if (nlocal == nmax) grow(0); atomKK->modified(Host,ALL_MASK); - h_tag(nlocal) = force->inumeric(FLERR,values[0]); - h_molecule(nlocal) = force->inumeric(FLERR,values[1]); - h_type(nlocal) = force->inumeric(FLERR,values[2]); + h_tag(nlocal) = utils::inumeric(FLERR,values[0],true,lmp); + h_molecule(nlocal) = utils::inumeric(FLERR,values[1],true,lmp); + h_type(nlocal) = utils::inumeric(FLERR,values[2],true,lmp); if (h_type(nlocal) <= 0 || h_type(nlocal) > atom->ntypes) error->one(FLERR,"Invalid atom type in Atoms section of data file"); @@ -1923,7 +1924,7 @@ void AtomVecMolecularKokkos::data_atom(double *coord, imageint imagetmp, int AtomVecMolecularKokkos::data_atom_hybrid(int nlocal, char **values) { - h_molecule(nlocal) = force->inumeric(FLERR,values[0]); + h_molecule(nlocal) = utils::inumeric(FLERR,values[0],true,lmp); h_num_bond(nlocal) = 0; h_num_angle(nlocal) = 0; h_num_dihedral(nlocal) = 0; diff --git a/src/KOKKOS/atom_vec_sphere_kokkos.cpp b/src/KOKKOS/atom_vec_sphere_kokkos.cpp index 57dc7ef43d..bc72bcbf5e 100644 --- a/src/KOKKOS/atom_vec_sphere_kokkos.cpp +++ b/src/KOKKOS/atom_vec_sphere_kokkos.cpp @@ -27,6 +27,7 @@ #include "memory.h" #include "error.h" #include "memory_kokkos.h" +#include "utils.h" using namespace LAMMPS_NS; @@ -2549,15 +2550,15 @@ void AtomVecSphereKokkos::data_atom(double *coord, imageint imagetmp, char **val if (nlocal == nmax) grow(0); tag[nlocal] = ATOTAGINT(values[0]); - type[nlocal] = force->inumeric(FLERR,values[1]); + type[nlocal] = utils::inumeric(FLERR,values[1],true,lmp); if (type[nlocal] <= 0 || type[nlocal] > atom->ntypes) error->one(FLERR,"Invalid atom type in Atoms section of data file"); - radius[nlocal] = 0.5 * force->numeric(FLERR,values[2]); + radius[nlocal] = 0.5 * utils::numeric(FLERR,values[2],true,lmp); if (radius[nlocal] < 0.0) error->one(FLERR,"Invalid radius in Atoms section of data file"); - double density = force->numeric(FLERR,values[3]); + double density = utils::numeric(FLERR,values[3],true,lmp); if (density <= 0.0) error->one(FLERR,"Invalid density in Atoms section of data file"); @@ -2592,11 +2593,11 @@ void AtomVecSphereKokkos::data_atom(double *coord, imageint imagetmp, char **val int AtomVecSphereKokkos::data_atom_hybrid(int nlocal, char **values) { - radius[nlocal] = 0.5 * force->numeric(FLERR,values[0]); + radius[nlocal] = 0.5 * utils::numeric(FLERR,values[0],true,lmp); if (radius[nlocal] < 0.0) error->one(FLERR,"Invalid radius in Atoms section of data file"); - double density = force->numeric(FLERR,values[1]); + double density = utils::numeric(FLERR,values[1],true,lmp); if (density <= 0.0) error->one(FLERR,"Invalid density in Atoms section of data file"); @@ -2618,12 +2619,12 @@ int AtomVecSphereKokkos::data_atom_hybrid(int nlocal, char **values) void AtomVecSphereKokkos::data_vel(int m, char **values) { atomKK->sync(Host,V_MASK|OMEGA_MASK); - h_v(m,0) = force->numeric(FLERR,values[0]); - h_v(m,1) = force->numeric(FLERR,values[1]); - h_v(m,2) = force->numeric(FLERR,values[2]); - h_omega(m,0) = force->numeric(FLERR,values[3]); - h_omega(m,1) = force->numeric(FLERR,values[4]); - h_omega(m,2) = force->numeric(FLERR,values[5]); + h_v(m,0) = utils::numeric(FLERR,values[0],true,lmp); + h_v(m,1) = utils::numeric(FLERR,values[1],true,lmp); + h_v(m,2) = utils::numeric(FLERR,values[2],true,lmp); + h_omega(m,0) = utils::numeric(FLERR,values[3],true,lmp); + h_omega(m,1) = utils::numeric(FLERR,values[4],true,lmp); + h_omega(m,2) = utils::numeric(FLERR,values[5],true,lmp); atomKK->modified(Host,V_MASK|OMEGA_MASK); } @@ -2634,9 +2635,9 @@ void AtomVecSphereKokkos::data_vel(int m, char **values) int AtomVecSphereKokkos::data_vel_hybrid(int m, char **values) { atomKK->sync(Host,OMEGA_MASK); - omega[m][0] = force->numeric(FLERR,values[0]); - omega[m][1] = force->numeric(FLERR,values[1]); - omega[m][2] = force->numeric(FLERR,values[2]); + omega[m][0] = utils::numeric(FLERR,values[0],true,lmp); + omega[m][1] = utils::numeric(FLERR,values[1],true,lmp); + omega[m][2] = utils::numeric(FLERR,values[2],true,lmp); atomKK->modified(Host,OMEGA_MASK); return 3; } diff --git a/src/MOLECULE/atom_vec_angle.cpp b/src/MOLECULE/atom_vec_angle.cpp index 594a039463..87220bfad6 100644 --- a/src/MOLECULE/atom_vec_angle.cpp +++ b/src/MOLECULE/atom_vec_angle.cpp @@ -21,6 +21,7 @@ #include "fix.h" #include "memory.h" #include "error.h" +#include "utils.h" using namespace LAMMPS_NS; @@ -794,7 +795,7 @@ void AtomVecAngle::data_atom(double *coord, imageint imagetmp, char **values) tag[nlocal] = ATOTAGINT(values[0]); molecule[nlocal] = ATOTAGINT(values[1]); - type[nlocal] = force->inumeric(FLERR,values[2]); + type[nlocal] = utils::inumeric(FLERR,values[2],true,lmp); if (type[nlocal] <= 0 || type[nlocal] > atom->ntypes) error->one(FLERR,"Invalid atom type in Atoms section of data file"); diff --git a/src/MOLECULE/atom_vec_bond.cpp b/src/MOLECULE/atom_vec_bond.cpp index 12eafbc6ce..6f0c63529b 100644 --- a/src/MOLECULE/atom_vec_bond.cpp +++ b/src/MOLECULE/atom_vec_bond.cpp @@ -21,6 +21,7 @@ #include "fix.h" #include "memory.h" #include "error.h" +#include "utils.h" using namespace LAMMPS_NS; @@ -740,7 +741,7 @@ void AtomVecBond::data_atom(double *coord, imageint imagetmp, char **values) tag[nlocal] = ATOTAGINT(values[0]); molecule[nlocal] = ATOTAGINT(values[1]); - type[nlocal] = force->inumeric(FLERR,values[2]); + type[nlocal] = utils::inumeric(FLERR,values[2],true,lmp); if (type[nlocal] <= 0 || type[nlocal] > atom->ntypes) error->one(FLERR,"Invalid atom type in Atoms section of data file"); diff --git a/src/MOLECULE/atom_vec_full.cpp b/src/MOLECULE/atom_vec_full.cpp index 4cad70f782..0cb95254e3 100644 --- a/src/MOLECULE/atom_vec_full.cpp +++ b/src/MOLECULE/atom_vec_full.cpp @@ -21,6 +21,7 @@ #include "fix.h" #include "memory.h" #include "error.h" +#include "utils.h" using namespace LAMMPS_NS; @@ -943,11 +944,11 @@ void AtomVecFull::data_atom(double *coord, imageint imagetmp, char **values) tag[nlocal] = ATOTAGINT(values[0]); molecule[nlocal] = ATOTAGINT(values[1]); - type[nlocal] = force->inumeric(FLERR,values[2]); + type[nlocal] = utils::inumeric(FLERR,values[2],true,lmp); if (type[nlocal] <= 0 || type[nlocal] > atom->ntypes) error->one(FLERR,"Invalid atom type in Atoms section of data file"); - q[nlocal] = force->numeric(FLERR,values[3]); + q[nlocal] = utils::numeric(FLERR,values[3],true,lmp); x[nlocal][0] = coord[0]; x[nlocal][1] = coord[1]; @@ -975,7 +976,7 @@ void AtomVecFull::data_atom(double *coord, imageint imagetmp, char **values) int AtomVecFull::data_atom_hybrid(int nlocal, char **values) { molecule[nlocal] = ATOTAGINT(values[0]); - q[nlocal] = force->numeric(FLERR,values[1]); + q[nlocal] = utils::numeric(FLERR,values[1],true,lmp); num_bond[nlocal] = 0; num_angle[nlocal] = 0; diff --git a/src/MOLECULE/atom_vec_molecular.cpp b/src/MOLECULE/atom_vec_molecular.cpp index dfd833d1c8..28766fa67d 100644 --- a/src/MOLECULE/atom_vec_molecular.cpp +++ b/src/MOLECULE/atom_vec_molecular.cpp @@ -21,6 +21,7 @@ #include "fix.h" #include "memory.h" #include "error.h" +#include "utils.h" using namespace LAMMPS_NS; @@ -927,7 +928,7 @@ void AtomVecMolecular::data_atom(double *coord, imageint imagetmp, tag[nlocal] = ATOTAGINT(values[0]); molecule[nlocal] = ATOTAGINT(values[1]); - type[nlocal] = force->inumeric(FLERR,values[2]); + type[nlocal] = utils::inumeric(FLERR,values[2],true,lmp); if (type[nlocal] <= 0 || type[nlocal] > atom->ntypes) error->one(FLERR,"Invalid atom type in Atoms section of data file"); diff --git a/src/MOLECULE/atom_vec_template.cpp b/src/MOLECULE/atom_vec_template.cpp index 2498010888..f7cf5f96db 100644 --- a/src/MOLECULE/atom_vec_template.cpp +++ b/src/MOLECULE/atom_vec_template.cpp @@ -23,6 +23,7 @@ #include "fix.h" #include "memory.h" #include "error.h" +#include "utils.h" using namespace LAMMPS_NS; @@ -746,8 +747,8 @@ void AtomVecTemplate::data_atom(double *coord, imageint imagetmp, char **values) error->one(FLERR,"Invalid atom ID in Atoms section of data file"); molecule[nlocal] = ATOTAGINT(values[1]); - molindex[nlocal] = force->inumeric(FLERR,values[2]) - 1; - molatom[nlocal] = force->inumeric(FLERR,values[3]) - 1; + molindex[nlocal] = utils::inumeric(FLERR,values[2],true,lmp) - 1; + molatom[nlocal] = utils::inumeric(FLERR,values[3],true,lmp) - 1; if (molindex[nlocal] < 0 || molindex[nlocal] >= nset) error->one(FLERR,"Invalid template index in Atoms section of data file"); @@ -755,7 +756,7 @@ void AtomVecTemplate::data_atom(double *coord, imageint imagetmp, char **values) molatom[nlocal] >= onemols[molindex[nlocal]]->natoms) error->one(FLERR,"Invalid template atom in Atoms section of data file"); - type[nlocal] = force->inumeric(FLERR,values[4]); + type[nlocal] = utils::inumeric(FLERR,values[4],true,lmp); if (type[nlocal] <= 0 || type[nlocal] > atom->ntypes) error->one(FLERR,"Invalid atom type in Atoms section of data file"); @@ -781,8 +782,8 @@ void AtomVecTemplate::data_atom(double *coord, imageint imagetmp, char **values) int AtomVecTemplate::data_atom_hybrid(int nlocal, char **values) { molecule[nlocal] = ATOTAGINT(values[0]); - molindex[nlocal] = force->inumeric(FLERR,values[1]) - 1; - molatom[nlocal] = force->inumeric(FLERR,values[2]) - 1; + molindex[nlocal] = utils::inumeric(FLERR,values[1],true,lmp) - 1; + molatom[nlocal] = utils::inumeric(FLERR,values[2],true,lmp) - 1; return 3; } diff --git a/src/PERI/atom_vec_peri.cpp b/src/PERI/atom_vec_peri.cpp index 9b262477a6..25a0b8a933 100644 --- a/src/PERI/atom_vec_peri.cpp +++ b/src/PERI/atom_vec_peri.cpp @@ -28,6 +28,7 @@ #include "citeme.h" #include "memory.h" #include "error.h" +#include "utils.h" using namespace LAMMPS_NS; @@ -793,12 +794,12 @@ void AtomVecPeri::data_atom(double *coord, imageint imagetmp, char **values) if (nlocal == nmax) grow(0); tag[nlocal] = ATOTAGINT(values[0]); - type[nlocal] = force->inumeric(FLERR,values[1]); + type[nlocal] = utils::inumeric(FLERR,values[1],true,lmp); if (type[nlocal] <= 0 || type[nlocal] > atom->ntypes) error->one(FLERR,"Invalid atom type in Atoms section of data file"); - vfrac[nlocal] = force->numeric(FLERR,values[2]); - rmass[nlocal] = force->numeric(FLERR,values[3]); + vfrac[nlocal] = utils::numeric(FLERR,values[2],true,lmp); + rmass[nlocal] = utils::numeric(FLERR,values[3],true,lmp); if (rmass[nlocal] <= 0.0) error->one(FLERR,"Invalid mass value"); x[nlocal][0] = coord[0]; @@ -827,8 +828,8 @@ void AtomVecPeri::data_atom(double *coord, imageint imagetmp, char **values) int AtomVecPeri::data_atom_hybrid(int nlocal, char **values) { - vfrac[nlocal] = force->numeric(FLERR,values[0]); - rmass[nlocal] = force->numeric(FLERR,values[1]); + vfrac[nlocal] = utils::numeric(FLERR,values[0],true,lmp); + rmass[nlocal] = utils::numeric(FLERR,values[1],true,lmp); if (rmass[nlocal] <= 0.0) error->one(FLERR,"Invalid mass value"); s0[nlocal] = DBL_MAX; diff --git a/src/SPIN/atom_vec_spin.cpp b/src/SPIN/atom_vec_spin.cpp index ba33372542..63c55759be 100644 --- a/src/SPIN/atom_vec_spin.cpp +++ b/src/SPIN/atom_vec_spin.cpp @@ -35,6 +35,7 @@ #include "force.h" #include "memory.h" #include "modify.h" +#include "utils.h" using namespace LAMMPS_NS; @@ -813,7 +814,7 @@ void AtomVecSpin::data_atom(double *coord, imageint imagetmp, char **values) if (nlocal == nmax) grow(0); tag[nlocal] = ATOTAGINT(values[0]); - type[nlocal] = force->inumeric(FLERR,values[1]); + type[nlocal] = utils::inumeric(FLERR,values[1],true,lmp); if (type[nlocal] <= 0 || type[nlocal] > atom->ntypes) error->one(FLERR,"Invalid atom type in Atoms section of data file"); @@ -821,10 +822,10 @@ void AtomVecSpin::data_atom(double *coord, imageint imagetmp, char **values) x[nlocal][1] = coord[1]; x[nlocal][2] = coord[2]; - sp[nlocal][3] = force->numeric(FLERR,values[2]); - sp[nlocal][0] = force->numeric(FLERR,values[6]); - sp[nlocal][1] = force->numeric(FLERR,values[7]); - sp[nlocal][2] = force->numeric(FLERR,values[8]); + sp[nlocal][3] = utils::numeric(FLERR,values[2],true,lmp); + sp[nlocal][0] = utils::numeric(FLERR,values[6],true,lmp); + sp[nlocal][1] = utils::numeric(FLERR,values[7],true,lmp); + sp[nlocal][2] = utils::numeric(FLERR,values[8],true,lmp); double inorm = 1.0/sqrt(sp[nlocal][0]*sp[nlocal][0] + sp[nlocal][1]*sp[nlocal][1] + sp[nlocal][2]*sp[nlocal][2]); @@ -850,16 +851,16 @@ void AtomVecSpin::data_atom(double *coord, imageint imagetmp, char **values) int AtomVecSpin::data_atom_hybrid(int nlocal, char **values) { - sp[nlocal][0] = force->numeric(FLERR,values[0]); - sp[nlocal][1] = force->numeric(FLERR,values[1]); - sp[nlocal][2] = force->numeric(FLERR,values[2]); + sp[nlocal][0] = utils::numeric(FLERR,values[0],true,lmp); + sp[nlocal][1] = utils::numeric(FLERR,values[1],true,lmp); + sp[nlocal][2] = utils::numeric(FLERR,values[2],true,lmp); double inorm = 1.0/sqrt(sp[nlocal][0]*sp[nlocal][0] + sp[nlocal][1]*sp[nlocal][1] + sp[nlocal][2]*sp[nlocal][2]); sp[nlocal][0] *= inorm; sp[nlocal][1] *= inorm; sp[nlocal][2] *= inorm; - sp[nlocal][3] = force->numeric(FLERR,values[3]); + sp[nlocal][3] = utils::numeric(FLERR,values[3],true,lmp); return 4; } diff --git a/src/USER-AWPMD/atom_vec_wavepacket.cpp b/src/USER-AWPMD/atom_vec_wavepacket.cpp index 912544c860..67eaf94551 100644 --- a/src/USER-AWPMD/atom_vec_wavepacket.cpp +++ b/src/USER-AWPMD/atom_vec_wavepacket.cpp @@ -27,6 +27,7 @@ #include "fix.h" #include "memory.h" #include "error.h" +#include "utils.h" using namespace LAMMPS_NS; @@ -916,19 +917,19 @@ void AtomVecWavepacket::data_atom(double *coord, imageint imagetmp, if (nlocal == nmax) grow(0); tag[nlocal] = ATOTAGINT(values[0]); - type[nlocal] = force->inumeric(FLERR,values[1]); + type[nlocal] = utils::inumeric(FLERR,values[1],true,lmp); if (type[nlocal] <= 0 || type[nlocal] > atom->ntypes) error->one(FLERR,"Invalid atom type in Atoms section of data file"); - q[nlocal] = force->numeric(FLERR,values[2]); - spin[nlocal] = force->inumeric(FLERR,values[3]); - eradius[nlocal] = force->numeric(FLERR,values[4]); + q[nlocal] = utils::numeric(FLERR,values[2],true,lmp); + spin[nlocal] = utils::inumeric(FLERR,values[3],true,lmp); + eradius[nlocal] = utils::numeric(FLERR,values[4],true,lmp); if (eradius[nlocal] < 0.0) error->one(FLERR,"Invalid eradius in Atoms section of data file"); - etag[nlocal] = force->inumeric(FLERR,values[5]); - cs[2*nlocal] = force->inumeric(FLERR,values[6]); - cs[2*nlocal+1] = force->numeric(FLERR,values[7]); + etag[nlocal] = utils::inumeric(FLERR,values[5],true,lmp); + cs[2*nlocal] = utils::inumeric(FLERR,values[6],true,lmp); + cs[2*nlocal+1] = utils::numeric(FLERR,values[7],true,lmp); x[nlocal][0] = coord[0]; x[nlocal][1] = coord[1]; @@ -952,15 +953,15 @@ void AtomVecWavepacket::data_atom(double *coord, imageint imagetmp, int AtomVecWavepacket::data_atom_hybrid(int nlocal, char **values) { - q[nlocal] = force->numeric(FLERR,values[0]); - spin[nlocal] = force->inumeric(FLERR,values[1]); - eradius[nlocal] = force->numeric(FLERR,values[2]); + q[nlocal] = utils::numeric(FLERR,values[0],true,lmp); + spin[nlocal] = utils::inumeric(FLERR,values[1],true,lmp); + eradius[nlocal] = utils::numeric(FLERR,values[2],true,lmp); if (eradius[nlocal] < 0.0) error->one(FLERR,"Invalid eradius in Atoms section of data file"); - etag[nlocal] = force->inumeric(FLERR,values[3]); - cs[2*nlocal] = force->inumeric(FLERR,values[4]); - cs[2*nlocal+1] = force->numeric(FLERR,values[5]); + etag[nlocal] = utils::inumeric(FLERR,values[3],true,lmp); + cs[2*nlocal] = utils::inumeric(FLERR,values[4],true,lmp); + cs[2*nlocal+1] = utils::numeric(FLERR,values[5],true,lmp); v[nlocal][0] = 0.0; v[nlocal][1] = 0.0; @@ -976,10 +977,10 @@ int AtomVecWavepacket::data_atom_hybrid(int nlocal, char **values) void AtomVecWavepacket::data_vel(int m, char **values) { - v[m][0] = force->numeric(FLERR,values[0]); - v[m][1] = force->numeric(FLERR,values[1]); - v[m][2] = force->numeric(FLERR,values[2]); - ervel[m] = force->numeric(FLERR,values[3]); + v[m][0] = utils::numeric(FLERR,values[0],true,lmp); + v[m][1] = utils::numeric(FLERR,values[1],true,lmp); + v[m][2] = utils::numeric(FLERR,values[2],true,lmp); + ervel[m] = utils::numeric(FLERR,values[3],true,lmp); } /* ---------------------------------------------------------------------- @@ -988,7 +989,7 @@ void AtomVecWavepacket::data_vel(int m, char **values) int AtomVecWavepacket::data_vel_hybrid(int m, char **values) { - ervel[m] = force->numeric(FLERR,values[0]); + ervel[m] = utils::numeric(FLERR,values[0],true,lmp); return 1; } diff --git a/src/USER-DPD/atom_vec_dpd.cpp b/src/USER-DPD/atom_vec_dpd.cpp index 776de845ab..2aef55ff9f 100644 --- a/src/USER-DPD/atom_vec_dpd.cpp +++ b/src/USER-DPD/atom_vec_dpd.cpp @@ -25,6 +25,7 @@ #include "fix.h" #include "memory.h" #include "error.h" +#include "utils.h" using namespace LAMMPS_NS; @@ -815,11 +816,11 @@ void AtomVecDPD::data_atom(double *coord, tagint imagetmp, char **values) if (nlocal == nmax) grow(0); tag[nlocal] = ATOTAGINT(values[0]); - type[nlocal] = force->inumeric(FLERR,values[1]); + type[nlocal] = utils::inumeric(FLERR,values[1],true,lmp); if (type[nlocal] <= 0 || type[nlocal] > atom->ntypes) error->one(FLERR,"Invalid atom type in Atoms section of data file"); - dpdTheta[nlocal] = force->numeric(FLERR,values[2]); + dpdTheta[nlocal] = utils::numeric(FLERR,values[2],true,lmp); if (dpdTheta[nlocal] <= 0) error->one(FLERR,"Internal temperature in Atoms section of date file must be > zero"); @@ -851,7 +852,7 @@ void AtomVecDPD::data_atom(double *coord, tagint imagetmp, char **values) int AtomVecDPD::data_atom_hybrid(int nlocal, char **values) { - dpdTheta[nlocal] = force->numeric(FLERR,values[0]); + dpdTheta[nlocal] = utils::numeric(FLERR,values[0],true,lmp); return 1; } diff --git a/src/USER-EFF/atom_vec_electron.cpp b/src/USER-EFF/atom_vec_electron.cpp index 2cf04e189a..e62519d223 100644 --- a/src/USER-EFF/atom_vec_electron.cpp +++ b/src/USER-EFF/atom_vec_electron.cpp @@ -28,6 +28,7 @@ #include "citeme.h" #include "memory.h" #include "error.h" +#include "utils.h" using namespace LAMMPS_NS; @@ -799,15 +800,15 @@ void AtomVecElectron::data_atom(double *coord, imageint imagetmp, char **values) if (nlocal == nmax) grow(0); tag[nlocal] = ATOTAGINT(values[0]); - type[nlocal] = force->inumeric(FLERR,values[1]); + type[nlocal] = utils::inumeric(FLERR,values[1],true,lmp); if (type[nlocal] <= 0 || type[nlocal] > atom->ntypes) error->one(FLERR,"Invalid atom type in Atoms section of data file"); - q[nlocal] = force->numeric(FLERR,values[2]); - spin[nlocal] = force->inumeric(FLERR,values[3]); + q[nlocal] = utils::numeric(FLERR,values[2],true,lmp); + spin[nlocal] = utils::inumeric(FLERR,values[3],true,lmp); if (spin[nlocal] == 3) atom->ecp_flag = 1; - eradius[nlocal] = force->numeric(FLERR,values[4]); + eradius[nlocal] = utils::numeric(FLERR,values[4],true,lmp); x[nlocal][0] = coord[0]; x[nlocal][1] = coord[1]; @@ -831,9 +832,9 @@ void AtomVecElectron::data_atom(double *coord, imageint imagetmp, char **values) int AtomVecElectron::data_atom_hybrid(int nlocal, char **values) { - q[nlocal] = force->numeric(FLERR,values[0]); - spin[nlocal] = force->inumeric(FLERR,values[1]); - eradius[nlocal] = force->numeric(FLERR,values[2]); + q[nlocal] = utils::numeric(FLERR,values[0],true,lmp); + spin[nlocal] = utils::inumeric(FLERR,values[1],true,lmp); + eradius[nlocal] = utils::numeric(FLERR,values[2],true,lmp); if (eradius[nlocal] < 0.0) error->one(FLERR,"Invalid eradius in Atoms section of data file"); @@ -851,10 +852,10 @@ int AtomVecElectron::data_atom_hybrid(int nlocal, char **values) void AtomVecElectron::data_vel(int m, char **values) { - v[m][0] = force->numeric(FLERR,values[0]); - v[m][1] = force->numeric(FLERR,values[1]); - v[m][2] = force->numeric(FLERR,values[2]); - ervel[m] = force->numeric(FLERR,values[3]); + v[m][0] = utils::numeric(FLERR,values[0],true,lmp); + v[m][1] = utils::numeric(FLERR,values[1],true,lmp); + v[m][2] = utils::numeric(FLERR,values[2],true,lmp); + ervel[m] = utils::numeric(FLERR,values[3],true,lmp); } /* ---------------------------------------------------------------------- @@ -863,7 +864,7 @@ void AtomVecElectron::data_vel(int m, char **values) int AtomVecElectron::data_vel_hybrid(int m, char **values) { - ervel[m] = force->numeric(FLERR,values[0]); + ervel[m] = utils::numeric(FLERR,values[0],true,lmp); return 1; } diff --git a/src/USER-MESO/atom_vec_edpd.cpp b/src/USER-MESO/atom_vec_edpd.cpp index 25049ce003..ff8515abc6 100644 --- a/src/USER-MESO/atom_vec_edpd.cpp +++ b/src/USER-MESO/atom_vec_edpd.cpp @@ -22,6 +22,7 @@ #include "update.h" #include "memory.h" #include "error.h" +#include "utils.h" using namespace LAMMPS_NS; @@ -760,12 +761,12 @@ void AtomVecEDPD::data_atom(double *coord, imageint imagetmp, char **values) if (nlocal == nmax) grow(0); tag[nlocal] = ATOTAGINT(values[0]); - type[nlocal] = force->inumeric(FLERR,values[1]); + type[nlocal] = utils::inumeric(FLERR,values[1],true,lmp); if (type[nlocal] <= 0 || type[nlocal] > atom->ntypes) error->one(FLERR,"Invalid atom type in Atoms section of data file"); - edpd_temp[nlocal] = force->numeric(FLERR,values[2]); - edpd_cv[nlocal] = force->numeric(FLERR,values[3]); + edpd_temp[nlocal] = utils::numeric(FLERR,values[2],true,lmp); + edpd_cv[nlocal] = utils::numeric(FLERR,values[3],true,lmp); x[nlocal][0] = coord[0]; x[nlocal][1] = coord[1]; diff --git a/src/USER-MESO/atom_vec_mdpd.cpp b/src/USER-MESO/atom_vec_mdpd.cpp index 9952182851..965891a283 100644 --- a/src/USER-MESO/atom_vec_mdpd.cpp +++ b/src/USER-MESO/atom_vec_mdpd.cpp @@ -23,6 +23,7 @@ #include "update.h" #include "memory.h" #include "error.h" +#include "utils.h" using namespace LAMMPS_NS; @@ -799,7 +800,7 @@ void AtomVecMDPD::data_atom(double *coord, imageint imagetmp, char **values) { if (nlocal == nmax) grow(0); tag[nlocal] = ATOTAGINT(values[0]); - type[nlocal] = force->inumeric(FLERR,values[1]); + type[nlocal] = utils::inumeric(FLERR,values[1],true,lmp); if (type[nlocal] <= 0 || type[nlocal] > atom->ntypes) error->one(FLERR,"Invalid atom type in Atoms section of data file"); @@ -818,7 +819,7 @@ void AtomVecMDPD::data_atom(double *coord, imageint imagetmp, char **values) { vest[nlocal][1] = 0.0; vest[nlocal][2] = 0.0; - rho[nlocal] = force->numeric(FLERR,values[2]); + rho[nlocal] = utils::numeric(FLERR,values[2],true,lmp); drho[nlocal] = 0.0; atom->nlocal++; @@ -831,7 +832,7 @@ void AtomVecMDPD::data_atom(double *coord, imageint imagetmp, char **values) { int AtomVecMDPD::data_atom_hybrid(int nlocal, char **values) { - rho[nlocal] = force->numeric(FLERR,values[0]); + rho[nlocal] = utils::numeric(FLERR,values[0],true,lmp); return 3; } diff --git a/src/USER-MESO/atom_vec_tdpd.cpp b/src/USER-MESO/atom_vec_tdpd.cpp index 261bef1795..def0a8ad7b 100644 --- a/src/USER-MESO/atom_vec_tdpd.cpp +++ b/src/USER-MESO/atom_vec_tdpd.cpp @@ -24,6 +24,7 @@ #include "memory.h" #include "error.h" #include "input.h" +#include "utils.h" using namespace LAMMPS_NS; @@ -792,7 +793,7 @@ void AtomVecTDPD::data_atom(double *coord, imageint imagetmp, char **values) if (nlocal == nmax) grow(0); tag[nlocal] = ATOTAGINT(values[0]); - type[nlocal] = force->inumeric(FLERR,values[1]); + type[nlocal] = utils::inumeric(FLERR,values[1],true,lmp); if (type[nlocal] <= 0 || type[nlocal] > atom->ntypes) error->one(FLERR,"Invalid atom type in Atoms section of data file"); diff --git a/src/USER-SMD/atom_vec_smd.cpp b/src/USER-SMD/atom_vec_smd.cpp index fb2b1ccc69..278652bf43 100644 --- a/src/USER-SMD/atom_vec_smd.cpp +++ b/src/USER-SMD/atom_vec_smd.cpp @@ -36,6 +36,7 @@ #include "math_const.h" #include "memory.h" #include "error.h" +#include "utils.h" using namespace LAMMPS_NS; using namespace MathConst; @@ -1029,7 +1030,7 @@ void AtomVecSMD::data_atom(double *coord, imageint imagetmp, char **values) { tag[nlocal] = ATOTAGINT(values[0]); - type[nlocal] = force->inumeric(FLERR,values[1]); + type[nlocal] = utils::inumeric(FLERR,values[1],true,lmp); if (type[nlocal] <= 0 || type[nlocal] > atom->ntypes) error->one(FLERR, "Invalid atom type in Atoms section of data file"); @@ -1037,27 +1038,27 @@ void AtomVecSMD::data_atom(double *coord, imageint imagetmp, char **values) { if (molecule[nlocal] <= 0) error->one(FLERR, "Invalid molecule in Atoms section of data file"); - vfrac[nlocal] = force->numeric(FLERR,values[3]); + vfrac[nlocal] = utils::numeric(FLERR,values[3],true,lmp); if (vfrac[nlocal] < 0.0) error->one(FLERR, "Invalid volume in Atoms section of data file"); - rmass[nlocal] = force->numeric(FLERR,values[4]); + rmass[nlocal] = utils::numeric(FLERR,values[4],true,lmp); if (rmass[nlocal] == 0.0) error->one(FLERR, "Invalid mass in Atoms section of data file"); - radius[nlocal] = force->numeric(FLERR,values[5]); + radius[nlocal] = utils::numeric(FLERR,values[5],true,lmp); if (radius[nlocal] < 0.0) error->one(FLERR, "Invalid radius in Atoms section of data file"); - contact_radius[nlocal] = force->numeric(FLERR,values[6]); + contact_radius[nlocal] = utils::numeric(FLERR,values[6],true,lmp); if (contact_radius[nlocal] < 0.0) error->one(FLERR, "Invalid contact radius in Atoms section of data file"); e[nlocal] = 0.0; - x0[nlocal][0] = force->numeric(FLERR,values[7]); - x0[nlocal][1] = force->numeric(FLERR,values[8]); - x0[nlocal][2] = force->numeric(FLERR,values[9]); + x0[nlocal][0] = utils::numeric(FLERR,values[7],true,lmp); + x0[nlocal][1] = utils::numeric(FLERR,values[8],true,lmp); + x0[nlocal][2] = utils::numeric(FLERR,values[9],true,lmp); x[nlocal][0] = coord[0]; x[nlocal][1] = coord[1]; @@ -1108,12 +1109,12 @@ int AtomVecSMD::data_atom_hybrid(int /*nlocal*/, char **/*values*/) { ------------------------------------------------------------------------- */ void AtomVecSMD::data_vel(int m, char **values) { - v[m][0] = force->numeric(FLERR,values[0]); - v[m][1] = force->numeric(FLERR,values[1]); - v[m][2] = force->numeric(FLERR,values[2]); - vest[m][0] = force->numeric(FLERR,values[0]); - vest[m][1] = force->numeric(FLERR,values[1]); - vest[m][2] = force->numeric(FLERR,values[2]); + v[m][0] = utils::numeric(FLERR,values[0],true,lmp); + v[m][1] = utils::numeric(FLERR,values[1],true,lmp); + v[m][2] = utils::numeric(FLERR,values[2],true,lmp); + vest[m][0] = utils::numeric(FLERR,values[0],true,lmp); + vest[m][1] = utils::numeric(FLERR,values[1],true,lmp); + vest[m][2] = utils::numeric(FLERR,values[2],true,lmp); } /* ---------------------------------------------------------------------- diff --git a/src/USER-SPH/atom_vec_meso.cpp b/src/USER-SPH/atom_vec_meso.cpp index 763ce5af5a..0960141ae2 100644 --- a/src/USER-SPH/atom_vec_meso.cpp +++ b/src/USER-SPH/atom_vec_meso.cpp @@ -22,6 +22,7 @@ #include "fix.h" #include "memory.h" #include "error.h" +#include "utils.h" using namespace LAMMPS_NS; @@ -844,13 +845,13 @@ void AtomVecMeso::data_atom(double *coord, imageint imagetmp, char **values) { if (nlocal == nmax) grow(0); tag[nlocal] = ATOTAGINT(values[0]); - type[nlocal] = force->inumeric(FLERR,values[1]); + type[nlocal] = utils::inumeric(FLERR,values[1],true,lmp); if (type[nlocal] <= 0 || type[nlocal] > atom->ntypes) error->one(FLERR,"Invalid atom type in Atoms section of data file"); - rho[nlocal] = force->numeric(FLERR,values[2]); - e[nlocal] = force->numeric(FLERR,values[3]); - cv[nlocal] = force->numeric(FLERR,values[4]); + rho[nlocal] = utils::numeric(FLERR,values[2],true,lmp); + e[nlocal] = utils::numeric(FLERR,values[3],true,lmp); + cv[nlocal] = utils::numeric(FLERR,values[4],true,lmp); x[nlocal][0] = coord[0]; x[nlocal][1] = coord[1]; @@ -882,9 +883,9 @@ void AtomVecMeso::data_atom(double *coord, imageint imagetmp, char **values) { int AtomVecMeso::data_atom_hybrid(int nlocal, char **values) { - rho[nlocal] = force->numeric(FLERR,values[0]); - e[nlocal] = force->numeric(FLERR,values[1]); - cv[nlocal] = force->numeric(FLERR,values[2]); + rho[nlocal] = utils::numeric(FLERR,values[0],true,lmp); + e[nlocal] = utils::numeric(FLERR,values[1],true,lmp); + cv[nlocal] = utils::numeric(FLERR,values[2],true,lmp); return 3; } diff --git a/src/atom_vec.cpp b/src/atom_vec.cpp index 33caea05a2..d4bea15d0b 100644 --- a/src/atom_vec.cpp +++ b/src/atom_vec.cpp @@ -18,6 +18,7 @@ #include "force.h" #include "domain.h" #include "error.h" +#include "utils.h" using namespace LAMMPS_NS; @@ -113,9 +114,9 @@ int AtomVec::grow_nmax_bonus(int nmax_bonus) void AtomVec::data_vel(int m, char **values) { double **v = atom->v; - v[m][0] = force->numeric(FLERR,values[0]); - v[m][1] = force->numeric(FLERR,values[1]); - v[m][2] = force->numeric(FLERR,values[2]); + v[m][0] = utils::numeric(FLERR,values[0],true,lmp); + v[m][1] = utils::numeric(FLERR,values[1],true,lmp); + v[m][2] = utils::numeric(FLERR,values[2],true,lmp); } /* ---------------------------------------------------------------------- diff --git a/src/atom_vec_atomic.cpp b/src/atom_vec_atomic.cpp index 2f01424d9d..0574db1d8e 100644 --- a/src/atom_vec_atomic.cpp +++ b/src/atom_vec_atomic.cpp @@ -21,6 +21,7 @@ #include "fix.h" #include "memory.h" #include "error.h" +#include "utils.h" using namespace LAMMPS_NS; @@ -613,7 +614,7 @@ void AtomVecAtomic::data_atom(double *coord, imageint imagetmp, char **values) if (nlocal == nmax) grow(0); tag[nlocal] = ATOTAGINT(values[0]); - type[nlocal] = force->inumeric(FLERR,values[1]); + type[nlocal] = utils::inumeric(FLERR,values[1],true,lmp); if (type[nlocal] <= 0 || type[nlocal] > atom->ntypes) error->one(FLERR,"Invalid atom type in Atoms section of data file"); diff --git a/src/atom_vec_body.cpp b/src/atom_vec_body.cpp index f54605fbb0..4b22933881 100644 --- a/src/atom_vec_body.cpp +++ b/src/atom_vec_body.cpp @@ -1280,16 +1280,16 @@ void AtomVecBody::data_atom(double *coord, imageint imagetmp, char **values) if (nlocal == nmax) grow(0); tag[nlocal] = ATOTAGINT(values[0]); - type[nlocal] = force->inumeric(FLERR,values[1]); + type[nlocal] = utils::inumeric(FLERR,values[1],true,lmp); if (type[nlocal] <= 0 || type[nlocal] > atom->ntypes) error->one(FLERR,"Invalid atom type in Atoms section of data file"); - body[nlocal] = force->inumeric(FLERR,values[2]); + body[nlocal] = utils::inumeric(FLERR,values[2],true,lmp); if (body[nlocal] == 0) body[nlocal] = -1; else if (body[nlocal] == 1) body[nlocal] = 0; else error->one(FLERR,"Invalid bodyflag in Atoms section of data file"); - rmass[nlocal] = force->numeric(FLERR,values[3]); + rmass[nlocal] = utils::numeric(FLERR,values[3],true,lmp); if (rmass[nlocal] <= 0.0) error->one(FLERR,"Invalid density in Atoms section of data file"); @@ -1318,12 +1318,12 @@ void AtomVecBody::data_atom(double *coord, imageint imagetmp, char **values) int AtomVecBody::data_atom_hybrid(int nlocal, char **values) { - body[nlocal] = force->inumeric(FLERR,values[0]); + body[nlocal] = utils::inumeric(FLERR,values[0],true,lmp); if (body[nlocal] == 0) body[nlocal] = -1; else if (body[nlocal] == 1) body[nlocal] = 0; else error->one(FLERR,"Invalid atom type in Atoms section of data file"); - rmass[nlocal] = force->numeric(FLERR,values[1]); + rmass[nlocal] = utils::numeric(FLERR,values[1],true,lmp); if (rmass[nlocal] <= 0.0) error->one(FLERR,"Invalid density in Atoms section of data file"); @@ -1350,12 +1350,12 @@ void AtomVecBody::data_body(int m, int ninteger, int ndouble, void AtomVecBody::data_vel(int m, char **values) { - v[m][0] = force->numeric(FLERR,values[0]); - v[m][1] = force->numeric(FLERR,values[1]); - v[m][2] = force->numeric(FLERR,values[2]); - angmom[m][0] = force->numeric(FLERR,values[3]); - angmom[m][1] = force->numeric(FLERR,values[4]); - angmom[m][2] = force->numeric(FLERR,values[5]); + v[m][0] = utils::numeric(FLERR,values[0],true,lmp); + v[m][1] = utils::numeric(FLERR,values[1],true,lmp); + v[m][2] = utils::numeric(FLERR,values[2],true,lmp); + angmom[m][0] = utils::numeric(FLERR,values[3],true,lmp); + angmom[m][1] = utils::numeric(FLERR,values[4],true,lmp); + angmom[m][2] = utils::numeric(FLERR,values[5],true,lmp); } /* ---------------------------------------------------------------------- @@ -1364,9 +1364,9 @@ void AtomVecBody::data_vel(int m, char **values) int AtomVecBody::data_vel_hybrid(int m, char **values) { - angmom[m][0] = force->numeric(FLERR,values[0]); - angmom[m][1] = force->numeric(FLERR,values[1]); - angmom[m][2] = force->numeric(FLERR,values[2]); + angmom[m][0] = utils::numeric(FLERR,values[0],true,lmp); + angmom[m][1] = utils::numeric(FLERR,values[1],true,lmp); + angmom[m][2] = utils::numeric(FLERR,values[2],true,lmp); return 3; } diff --git a/src/atom_vec_charge.cpp b/src/atom_vec_charge.cpp index 03ef95a2e4..1a78ba0e2d 100644 --- a/src/atom_vec_charge.cpp +++ b/src/atom_vec_charge.cpp @@ -21,6 +21,7 @@ #include "fix.h" #include "memory.h" #include "error.h" +#include "utils.h" using namespace LAMMPS_NS; @@ -664,11 +665,11 @@ void AtomVecCharge::data_atom(double *coord, imageint imagetmp, char **values) if (nlocal == nmax) grow(0); tag[nlocal] = ATOTAGINT(values[0]); - type[nlocal] = force->inumeric(FLERR,values[1]); + type[nlocal] = utils::inumeric(FLERR,values[1],true,lmp); if (type[nlocal] <= 0 || type[nlocal] > atom->ntypes) error->one(FLERR,"Invalid atom type in Atoms section of data file"); - q[nlocal] = force->numeric(FLERR,values[2]); + q[nlocal] = utils::numeric(FLERR,values[2],true,lmp); x[nlocal][0] = coord[0]; x[nlocal][1] = coord[1]; @@ -691,7 +692,7 @@ void AtomVecCharge::data_atom(double *coord, imageint imagetmp, char **values) int AtomVecCharge::data_atom_hybrid(int nlocal, char **values) { - q[nlocal] = force->numeric(FLERR,values[0]); + q[nlocal] = utils::numeric(FLERR,values[0],true,lmp); return 1; } diff --git a/src/atom_vec_ellipsoid.cpp b/src/atom_vec_ellipsoid.cpp index 1fc713e583..0b94359c55 100644 --- a/src/atom_vec_ellipsoid.cpp +++ b/src/atom_vec_ellipsoid.cpp @@ -27,6 +27,7 @@ #include "math_const.h" #include "memory.h" #include "error.h" +#include "utils.h" using namespace LAMMPS_NS; using namespace MathConst; @@ -1141,16 +1142,16 @@ void AtomVecEllipsoid::data_atom(double *coord, imageint imagetmp, if (nlocal == nmax) grow(0); tag[nlocal] = ATOTAGINT(values[0]); - type[nlocal] = force->inumeric(FLERR,values[1]); + type[nlocal] = utils::inumeric(FLERR,values[1],true,lmp); if (type[nlocal] <= 0 || type[nlocal] > atom->ntypes) error->one(FLERR,"Invalid atom type in Atoms section of data file"); - ellipsoid[nlocal] = force->inumeric(FLERR,values[2]); + ellipsoid[nlocal] = utils::inumeric(FLERR,values[2],true,lmp); if (ellipsoid[nlocal] == 0) ellipsoid[nlocal] = -1; else if (ellipsoid[nlocal] == 1) ellipsoid[nlocal] = 0; else error->one(FLERR,"Invalid ellipsoidflag in Atoms section of data file"); - rmass[nlocal] = force->numeric(FLERR,values[3]); + rmass[nlocal] = utils::numeric(FLERR,values[3],true,lmp); if (rmass[nlocal] <= 0.0) error->one(FLERR,"Invalid density in Atoms section of data file"); @@ -1178,12 +1179,12 @@ void AtomVecEllipsoid::data_atom(double *coord, imageint imagetmp, int AtomVecEllipsoid::data_atom_hybrid(int nlocal, char **values) { - ellipsoid[nlocal] = force->inumeric(FLERR,values[0]); + ellipsoid[nlocal] = utils::inumeric(FLERR,values[0],true,lmp); if (ellipsoid[nlocal] == 0) ellipsoid[nlocal] = -1; else if (ellipsoid[nlocal] == 1) ellipsoid[nlocal] = 0; else error->one(FLERR,"Invalid atom type in Atoms section of data file"); - rmass[nlocal] = force->numeric(FLERR,values[1]); + rmass[nlocal] = utils::numeric(FLERR,values[1],true,lmp); if (rmass[nlocal] <= 0.0) error->one(FLERR,"Invalid density in Atoms section of data file"); @@ -1202,17 +1203,17 @@ void AtomVecEllipsoid::data_atom_bonus(int m, char **values) if (nlocal_bonus == nmax_bonus) grow_bonus(); double *shape = bonus[nlocal_bonus].shape; - shape[0] = 0.5 * force->numeric(FLERR,values[0]); - shape[1] = 0.5 * force->numeric(FLERR,values[1]); - shape[2] = 0.5 * force->numeric(FLERR,values[2]); + shape[0] = 0.5 * utils::numeric(FLERR,values[0],true,lmp); + shape[1] = 0.5 * utils::numeric(FLERR,values[1],true,lmp); + shape[2] = 0.5 * utils::numeric(FLERR,values[2],true,lmp); if (shape[0] <= 0.0 || shape[1] <= 0.0 || shape[2] <= 0.0) error->one(FLERR,"Invalid shape in Ellipsoids section of data file"); double *quat = bonus[nlocal_bonus].quat; - quat[0] = force->numeric(FLERR,values[3]); - quat[1] = force->numeric(FLERR,values[4]); - quat[2] = force->numeric(FLERR,values[5]); - quat[3] = force->numeric(FLERR,values[6]); + quat[0] = utils::numeric(FLERR,values[3],true,lmp); + quat[1] = utils::numeric(FLERR,values[4],true,lmp); + quat[2] = utils::numeric(FLERR,values[5],true,lmp); + quat[3] = utils::numeric(FLERR,values[6],true,lmp); MathExtra::qnormalize(quat); // reset ellipsoid mass @@ -1230,12 +1231,12 @@ void AtomVecEllipsoid::data_atom_bonus(int m, char **values) void AtomVecEllipsoid::data_vel(int m, char **values) { - v[m][0] = force->numeric(FLERR,values[0]); - v[m][1] = force->numeric(FLERR,values[1]); - v[m][2] = force->numeric(FLERR,values[2]); - angmom[m][0] = force->numeric(FLERR,values[3]); - angmom[m][1] = force->numeric(FLERR,values[4]); - angmom[m][2] = force->numeric(FLERR,values[5]); + v[m][0] = utils::numeric(FLERR,values[0],true,lmp); + v[m][1] = utils::numeric(FLERR,values[1],true,lmp); + v[m][2] = utils::numeric(FLERR,values[2],true,lmp); + angmom[m][0] = utils::numeric(FLERR,values[3],true,lmp); + angmom[m][1] = utils::numeric(FLERR,values[4],true,lmp); + angmom[m][2] = utils::numeric(FLERR,values[5],true,lmp); } /* ---------------------------------------------------------------------- @@ -1244,9 +1245,9 @@ void AtomVecEllipsoid::data_vel(int m, char **values) int AtomVecEllipsoid::data_vel_hybrid(int m, char **values) { - angmom[m][0] = force->numeric(FLERR,values[0]); - angmom[m][1] = force->numeric(FLERR,values[1]); - angmom[m][2] = force->numeric(FLERR,values[2]); + angmom[m][0] = utils::numeric(FLERR,values[0],true,lmp); + angmom[m][1] = utils::numeric(FLERR,values[1],true,lmp); + angmom[m][2] = utils::numeric(FLERR,values[2],true,lmp); return 3; } diff --git a/src/atom_vec_hybrid.cpp b/src/atom_vec_hybrid.cpp index 94391ec9f3..a7816efbed 100644 --- a/src/atom_vec_hybrid.cpp +++ b/src/atom_vec_hybrid.cpp @@ -21,6 +21,7 @@ #include "fix.h" #include "memory.h" #include "error.h" +#include "utils.h" using namespace LAMMPS_NS; @@ -864,7 +865,7 @@ void AtomVecHybrid::data_atom(double *coord, imageint imagetmp, char **values) if (nlocal == nmax) grow(0); tag[nlocal] = ATOTAGINT(values[0]); - type[nlocal] = force->inumeric(FLERR,values[1]); + type[nlocal] = utils::inumeric(FLERR,values[1],true,lmp); if (type[nlocal] <= 0 || type[nlocal] > atom->ntypes) error->one(FLERR,"Invalid atom type in Atoms section of data file"); @@ -904,9 +905,9 @@ void AtomVecHybrid::data_atom(double *coord, imageint imagetmp, char **values) void AtomVecHybrid::data_vel(int m, char **values) { - v[m][0] = force->numeric(FLERR,values[0]); - v[m][1] = force->numeric(FLERR,values[1]); - v[m][2] = force->numeric(FLERR,values[2]); + v[m][0] = utils::numeric(FLERR,values[0],true,lmp); + v[m][1] = utils::numeric(FLERR,values[1],true,lmp); + v[m][2] = utils::numeric(FLERR,values[2],true,lmp); // each sub-style parses sub-style specific values diff --git a/src/atom_vec_line.cpp b/src/atom_vec_line.cpp index f229297798..6bffc1b0de 100644 --- a/src/atom_vec_line.cpp +++ b/src/atom_vec_line.cpp @@ -24,6 +24,7 @@ #include "math_const.h" #include "memory.h" #include "error.h" +#include "utils.h" using namespace LAMMPS_NS; using namespace MathConst; @@ -1037,16 +1038,16 @@ void AtomVecLine::data_atom(double *coord, imageint imagetmp, char **values) tag[nlocal] = ATOTAGINT(values[0]); molecule[nlocal] = ATOTAGINT(values[1]); - type[nlocal] = force->inumeric(FLERR,values[2]); + type[nlocal] = utils::inumeric(FLERR,values[2],true,lmp); if (type[nlocal] <= 0 || type[nlocal] > atom->ntypes) error->one(FLERR,"Invalid atom type in Atoms section of data file"); - line[nlocal] = force->inumeric(FLERR,values[3]); + line[nlocal] = utils::inumeric(FLERR,values[3],true,lmp); if (line[nlocal] == 0) line[nlocal] = -1; else if (line[nlocal] == 1) line[nlocal] = 0; else error->one(FLERR,"Invalid lineflag in Atoms section of data file"); - rmass[nlocal] = force->numeric(FLERR,values[4]); + rmass[nlocal] = utils::numeric(FLERR,values[4],true,lmp); if (rmass[nlocal] <= 0.0) error->one(FLERR,"Invalid density in Atoms section of data file"); @@ -1082,12 +1083,12 @@ int AtomVecLine::data_atom_hybrid(int nlocal, char **values) { molecule[nlocal] = ATOTAGINT(values[0]); - line[nlocal] = force->inumeric(FLERR,values[1]); + line[nlocal] = utils::inumeric(FLERR,values[1],true,lmp); if (line[nlocal] == 0) line[nlocal] = -1; else if (line[nlocal] == 1) line[nlocal] = 0; else error->one(FLERR,"Invalid atom type in Atoms section of data file"); - rmass[nlocal] = force->numeric(FLERR,values[2]); + rmass[nlocal] = utils::numeric(FLERR,values[2],true,lmp); if (rmass[nlocal] <= 0.0) error->one(FLERR,"Invalid density in Atoms section of data file"); @@ -1110,10 +1111,10 @@ void AtomVecLine::data_atom_bonus(int m, char **values) if (nlocal_bonus == nmax_bonus) grow_bonus(); - double x1 = force->numeric(FLERR,values[0]); - double y1 = force->numeric(FLERR,values[1]); - double x2 = force->numeric(FLERR,values[2]); - double y2 = force->numeric(FLERR,values[3]); + double x1 = utils::numeric(FLERR,values[0],true,lmp); + double y1 = utils::numeric(FLERR,values[1],true,lmp); + double x2 = utils::numeric(FLERR,values[2],true,lmp); + double y2 = utils::numeric(FLERR,values[3],true,lmp); double dx = x2 - x1; double dy = y2 - y1; double length = sqrt(dx*dx + dy*dy); @@ -1150,12 +1151,12 @@ void AtomVecLine::data_atom_bonus(int m, char **values) void AtomVecLine::data_vel(int m, char **values) { - v[m][0] = force->numeric(FLERR,values[0]); - v[m][1] = force->numeric(FLERR,values[1]); - v[m][2] = force->numeric(FLERR,values[2]); - omega[m][0] = force->numeric(FLERR,values[3]); - omega[m][1] = force->numeric(FLERR,values[4]); - omega[m][2] = force->numeric(FLERR,values[5]); + v[m][0] = utils::numeric(FLERR,values[0],true,lmp); + v[m][1] = utils::numeric(FLERR,values[1],true,lmp); + v[m][2] = utils::numeric(FLERR,values[2],true,lmp); + omega[m][0] = utils::numeric(FLERR,values[3],true,lmp); + omega[m][1] = utils::numeric(FLERR,values[4],true,lmp); + omega[m][2] = utils::numeric(FLERR,values[5],true,lmp); } /* ---------------------------------------------------------------------- @@ -1164,9 +1165,9 @@ void AtomVecLine::data_vel(int m, char **values) int AtomVecLine::data_vel_hybrid(int m, char **values) { - omega[m][0] = force->numeric(FLERR,values[0]); - omega[m][1] = force->numeric(FLERR,values[1]); - omega[m][2] = force->numeric(FLERR,values[2]); + omega[m][0] = utils::numeric(FLERR,values[0],true,lmp); + omega[m][1] = utils::numeric(FLERR,values[1],true,lmp); + omega[m][2] = utils::numeric(FLERR,values[2],true,lmp); return 3; } diff --git a/src/atom_vec_sphere.cpp b/src/atom_vec_sphere.cpp index 705b7411e7..b37b853c86 100644 --- a/src/atom_vec_sphere.cpp +++ b/src/atom_vec_sphere.cpp @@ -25,6 +25,7 @@ #include "math_const.h" #include "memory.h" #include "error.h" +#include "utils.h" using namespace LAMMPS_NS; using namespace MathConst; @@ -965,15 +966,15 @@ void AtomVecSphere::data_atom(double *coord, imageint imagetmp, char **values) if (nlocal == nmax) grow(0); tag[nlocal] = ATOTAGINT(values[0]); - type[nlocal] = force->inumeric(FLERR,values[1]); + type[nlocal] = utils::inumeric(FLERR,values[1],true,lmp); if (type[nlocal] <= 0 || type[nlocal] > atom->ntypes) error->one(FLERR,"Invalid atom type in Atoms section of data file"); - radius[nlocal] = 0.5 * force->numeric(FLERR,values[2]); + radius[nlocal] = 0.5 * utils::numeric(FLERR,values[2],true,lmp); if (radius[nlocal] < 0.0) error->one(FLERR,"Invalid radius in Atoms section of data file"); - double density = force->numeric(FLERR,values[3]); + double density = utils::numeric(FLERR,values[3],true,lmp); if (density <= 0.0) error->one(FLERR,"Invalid density in Atoms section of data file"); @@ -1006,11 +1007,11 @@ void AtomVecSphere::data_atom(double *coord, imageint imagetmp, char **values) int AtomVecSphere::data_atom_hybrid(int nlocal, char **values) { - radius[nlocal] = 0.5 * force->numeric(FLERR,values[0]); + radius[nlocal] = 0.5 * utils::numeric(FLERR,values[0],true,lmp); if (radius[nlocal] < 0.0) error->one(FLERR,"Invalid radius in Atoms section of data file"); - double density = force->numeric(FLERR,values[1]); + double density = utils::numeric(FLERR,values[1],true,lmp); if (density <= 0.0) error->one(FLERR,"Invalid density in Atoms section of data file"); @@ -1028,12 +1029,12 @@ int AtomVecSphere::data_atom_hybrid(int nlocal, char **values) void AtomVecSphere::data_vel(int m, char **values) { - v[m][0] = force->numeric(FLERR,values[0]); - v[m][1] = force->numeric(FLERR,values[1]); - v[m][2] = force->numeric(FLERR,values[2]); - omega[m][0] = force->numeric(FLERR,values[3]); - omega[m][1] = force->numeric(FLERR,values[4]); - omega[m][2] = force->numeric(FLERR,values[5]); + v[m][0] = utils::numeric(FLERR,values[0],true,lmp); + v[m][1] = utils::numeric(FLERR,values[1],true,lmp); + v[m][2] = utils::numeric(FLERR,values[2],true,lmp); + omega[m][0] = utils::numeric(FLERR,values[3],true,lmp); + omega[m][1] = utils::numeric(FLERR,values[4],true,lmp); + omega[m][2] = utils::numeric(FLERR,values[5],true,lmp); } /* ---------------------------------------------------------------------- @@ -1042,9 +1043,9 @@ void AtomVecSphere::data_vel(int m, char **values) int AtomVecSphere::data_vel_hybrid(int m, char **values) { - omega[m][0] = force->numeric(FLERR,values[0]); - omega[m][1] = force->numeric(FLERR,values[1]); - omega[m][2] = force->numeric(FLERR,values[2]); + omega[m][0] = utils::numeric(FLERR,values[0],true,lmp); + omega[m][1] = utils::numeric(FLERR,values[1],true,lmp); + omega[m][2] = utils::numeric(FLERR,values[2],true,lmp); return 3; } diff --git a/src/atom_vec_tri.cpp b/src/atom_vec_tri.cpp index 9f4557b63d..4070c6795e 100644 --- a/src/atom_vec_tri.cpp +++ b/src/atom_vec_tri.cpp @@ -25,6 +25,7 @@ #include "math_const.h" #include "memory.h" #include "error.h" +#include "utils.h" using namespace LAMMPS_NS; using namespace MathConst; @@ -1436,16 +1437,16 @@ void AtomVecTri::data_atom(double *coord, imageint imagetmp, char **values) tag[nlocal] = ATOTAGINT(values[0]); molecule[nlocal] = ATOTAGINT(values[1]); - type[nlocal] = force->inumeric(FLERR,values[2]); + type[nlocal] = utils::inumeric(FLERR,values[2],true,lmp); if (type[nlocal] <= 0 || type[nlocal] > atom->ntypes) error->one(FLERR,"Invalid atom type in Atoms section of data file"); - tri[nlocal] = force->inumeric(FLERR,values[3]); + tri[nlocal] = utils::inumeric(FLERR,values[3],true,lmp); if (tri[nlocal] == 0) tri[nlocal] = -1; else if (tri[nlocal] == 1) tri[nlocal] = 0; else error->one(FLERR,"Invalid triflag in Atoms section of data file"); - rmass[nlocal] = force->numeric(FLERR,values[4]); + rmass[nlocal] = utils::numeric(FLERR,values[4],true,lmp); if (rmass[nlocal] <= 0.0) error->one(FLERR,"Invalid density in Atoms section of data file"); @@ -1484,12 +1485,12 @@ int AtomVecTri::data_atom_hybrid(int nlocal, char **values) { molecule[nlocal] = ATOTAGINT(values[0]); - tri[nlocal] = force->inumeric(FLERR,values[1]); + tri[nlocal] = utils::inumeric(FLERR,values[1],true,lmp); if (tri[nlocal] == 0) tri[nlocal] = -1; else if (tri[nlocal] == 1) tri[nlocal] = 0; else error->one(FLERR,"Invalid atom type in Atoms section of data file"); - rmass[nlocal] = force->numeric(FLERR,values[2]); + rmass[nlocal] = utils::numeric(FLERR,values[2],true,lmp); if (rmass[nlocal] <= 0.0) error->one(FLERR,"Invalid density in Atoms section of data file"); @@ -1513,15 +1514,15 @@ void AtomVecTri::data_atom_bonus(int m, char **values) if (nlocal_bonus == nmax_bonus) grow_bonus(); double c1[3],c2[3],c3[3]; - c1[0] = force->numeric(FLERR,values[0]); - c1[1] = force->numeric(FLERR,values[1]); - c1[2] = force->numeric(FLERR,values[2]); - c2[0] = force->numeric(FLERR,values[3]); - c2[1] = force->numeric(FLERR,values[4]); - c2[2] = force->numeric(FLERR,values[5]); - c3[0] = force->numeric(FLERR,values[6]); - c3[1] = force->numeric(FLERR,values[7]); - c3[2] = force->numeric(FLERR,values[8]); + c1[0] = utils::numeric(FLERR,values[0],true,lmp); + c1[1] = utils::numeric(FLERR,values[1],true,lmp); + c1[2] = utils::numeric(FLERR,values[2],true,lmp); + c2[0] = utils::numeric(FLERR,values[3],true,lmp); + c2[1] = utils::numeric(FLERR,values[4],true,lmp); + c2[2] = utils::numeric(FLERR,values[5],true,lmp); + c3[0] = utils::numeric(FLERR,values[6],true,lmp); + c3[1] = utils::numeric(FLERR,values[7],true,lmp); + c3[2] = utils::numeric(FLERR,values[8],true,lmp); // check for duplicate points @@ -1641,15 +1642,15 @@ void AtomVecTri::data_atom_bonus(int m, char **values) void AtomVecTri::data_vel(int m, char **values) { - v[m][0] = force->numeric(FLERR,values[0]); - v[m][1] = force->numeric(FLERR,values[1]); - v[m][2] = force->numeric(FLERR,values[2]); - omega[m][0] = force->numeric(FLERR,values[3]); - omega[m][1] = force->numeric(FLERR,values[4]); - omega[m][2] = force->numeric(FLERR,values[5]); - angmom[m][0] = force->numeric(FLERR,values[6]); - angmom[m][1] = force->numeric(FLERR,values[7]); - angmom[m][2] = force->numeric(FLERR,values[8]); + v[m][0] = utils::numeric(FLERR,values[0],true,lmp); + v[m][1] = utils::numeric(FLERR,values[1],true,lmp); + v[m][2] = utils::numeric(FLERR,values[2],true,lmp); + omega[m][0] = utils::numeric(FLERR,values[3],true,lmp); + omega[m][1] = utils::numeric(FLERR,values[4],true,lmp); + omega[m][2] = utils::numeric(FLERR,values[5],true,lmp); + angmom[m][0] = utils::numeric(FLERR,values[6],true,lmp); + angmom[m][1] = utils::numeric(FLERR,values[7],true,lmp); + angmom[m][2] = utils::numeric(FLERR,values[8],true,lmp); } /* ---------------------------------------------------------------------- @@ -1658,12 +1659,12 @@ void AtomVecTri::data_vel(int m, char **values) int AtomVecTri::data_vel_hybrid(int m, char **values) { - omega[m][0] = force->numeric(FLERR,values[0]); - omega[m][1] = force->numeric(FLERR,values[1]); - omega[m][2] = force->numeric(FLERR,values[2]); - angmom[m][0] = force->numeric(FLERR,values[3]); - angmom[m][1] = force->numeric(FLERR,values[4]); - angmom[m][2] = force->numeric(FLERR,values[5]); + omega[m][0] = utils::numeric(FLERR,values[0],true,lmp); + omega[m][1] = utils::numeric(FLERR,values[1],true,lmp); + omega[m][2] = utils::numeric(FLERR,values[2],true,lmp); + angmom[m][0] = utils::numeric(FLERR,values[3],true,lmp); + angmom[m][1] = utils::numeric(FLERR,values[4],true,lmp); + angmom[m][2] = utils::numeric(FLERR,values[5],true,lmp); return 6; } diff --git a/src/utils.cpp b/src/utils.cpp index 8468b22d8c..bbda22f24c 100644 --- a/src/utils.cpp +++ b/src/utils.cpp @@ -141,6 +141,150 @@ std::string utils::check_packages_for_style(std::string style, return errmsg; } + +/* ---------------------------------------------------------------------- + read a floating point value from a string + generate an error if not a legitimate floating point value + called by various commands to check validity of their arguments +------------------------------------------------------------------------- */ + +double utils::numeric(const char *file, int line, const char *str, + bool do_abort, LAMMPS *lmp) +{ + int n = 0; + + if (str) n = strlen(str); + if (n == 0) { + if (do_abort) + lmp->error->one(file,line,"Expected floating point parameter instead of" + " NULL or empty string in input script or data file"); + else + lmp->error->all(file,line,"Expected floating point parameter instead of" + " NULL or empty string in input script or data file"); + } + + for (int i = 0; i < n; i++) { + if (isdigit(str[i])) continue; + if (str[i] == '-' || str[i] == '+' || str[i] == '.') continue; + if (str[i] == 'e' || str[i] == 'E') continue; + std::string msg("Expected floating point parameter instead of '"); + msg += str; + msg += "' in input script or data file"; + if (do_abort) + lmp->error->one(file,line,msg.c_str()); + else + lmp->error->all(file,line,msg.c_str()); + } + + return atof(str); +} + +/* ---------------------------------------------------------------------- + read an integer value from a string + generate an error if not a legitimate integer value + called by various commands to check validity of their arguments +------------------------------------------------------------------------- */ + +int utils::inumeric(const char *file, int line, const char *str, + bool do_abort, LAMMPS *lmp) +{ + int n = 0; + + if (str) n = strlen(str); + if (n == 0) { + if (do_abort) + lmp->error->one(file,line,"Expected integer parameter instead of " + "NULL or empty string in input script or data file"); + else + lmp->error->all(file,line,"Expected integer parameter instead of " + "NULL or empty string in input script or data file"); + } + + for (int i = 0; i < n; i++) { + if (isdigit(str[i]) || str[i] == '-' || str[i] == '+') continue; + std::string msg("Expected integer parameter instead of '"); + msg += str; + msg += "' in input script or data file"; + if (do_abort) + lmp->error->one(file,line,msg.c_str()); + else + lmp->error->all(file,line,msg.c_str()); + } + + return atoi(str); +} + +/* ---------------------------------------------------------------------- + read a big integer value from a string + generate an error if not a legitimate integer value + called by various commands to check validity of their arguments +------------------------------------------------------------------------- */ + +bigint utils::bnumeric(const char *file, int line, const char *str, + bool do_abort, LAMMPS *lmp) +{ + int n = 0; + + if (str) n = strlen(str); + if (n == 0) { + if (do_abort) + lmp->error->one(file,line,"Expected integer parameter instead of " + "NULL or empty string in input script or data file"); + else + lmp->error->all(file,line,"Expected integer parameter instead of " + "NULL or empty string in input script or data file"); + } + + for (int i = 0; i < n; i++) { + if (isdigit(str[i]) || str[i] == '-' || str[i] == '+') continue; + std::string msg("Expected integer parameter instead of '"); + msg += str; + msg += "' in input script or data file"; + if (do_abort) + lmp->error->one(file,line,msg.c_str()); + else + lmp->error->all(file,line,msg.c_str()); + } + + return ATOBIGINT(str); +} + +/* ---------------------------------------------------------------------- + read a tag integer value from a string + generate an error if not a legitimate integer value + called by various commands to check validity of their arguments +------------------------------------------------------------------------- */ + +tagint utils::tnumeric(const char *file, int line, const char *str, + bool do_abort, LAMMPS *lmp) +{ + int n = 0; + + if (str) n = strlen(str); + if (n == 0) { + if (do_abort) + lmp->error->one(file,line,"Expected integer parameter instead of " + "NULL or empty string in input script or data file"); + else + lmp->error->all(file,line,"Expected integer parameter instead of " + "NULL or empty string in input script or data file"); + } + + for (int i = 0; i < n; i++) { + if (isdigit(str[i]) || str[i] == '-' || str[i] == '+') continue; + std::string msg("Expected integer parameter instead of '"); + msg += str; + msg += "' in input script or data file"; + if (do_abort) + lmp->error->one(file,line,msg.c_str()); + else + lmp->error->all(file,line,msg.c_str()); + } + + return ATOTAGINT(str); +} + + /* ------------------------------------------------------------------ */ extern "C" { diff --git a/src/utils.h b/src/utils.h index 7dfba8ead0..5f71bfae76 100644 --- a/src/utils.h +++ b/src/utils.h @@ -16,6 +16,7 @@ /*! \file utils.h */ +#include "lmptype.h" #include #include @@ -75,7 +76,60 @@ namespace LAMMPS_NS { * \param lmp pointer to top-level LAMMPS class instance * \return string usable for error messages */ - std::string check_packages_for_style(std::string style, std::string name, LAMMPS *lmp); + std::string check_packages_for_style(std::string style, + std::string name, LAMMPS *lmp); + + /** \brief Convert a string to a floating point number while checking + if it is a valid floating point or integer number + * + * \param file name of source file for error message + * \param line in source file for error message + * \param str string to be converted to number + * \param do_abort determines whether to call Error::one() or Error::all() + * \param lmp pointer to top-level LAMMPS class instance + * \return double precision floating point number + */ + double numeric(const char *file, int line, const char *str, + bool do_abort, LAMMPS *lmp); + + /** \brief Convert a string to an integer number while checking + if it is a valid integer number (regular int) + * + * \param file name of source file for error message + * \param line in source file for error message + * \param str string to be converted to number + * \param do_abort determines whether to call Error::one() or Error::all() + * \param lmp pointer to top-level LAMMPS class instance + * \return integer number (regular int) + */ + int inumeric(const char *file, int line, const char *str, + bool do_abort, LAMMPS *lmp); + + /** \brief Convert a string to an integer number while checking + if it is a valid integer number (bigint) + * + * \param file name of source file for error message + * \param line in source file for error message + * \param str string to be converted to number + * \param do_abort determines whether to call Error::one() or Error::all() + * \param lmp pointer to top-level LAMMPS class instance + * \return integer number (bigint) + */ + bigint bnumeric(const char *file, int line, const char *str, + bool do_abort, LAMMPS *lmp); + + /** \brief Convert a string to an integer number while checking + if it is a valid integer number (tagint) + * + * \param file name of source file for error message + * \param line in source file for error message + * \param str string to be converted to number + * \param do_abort determines whether to call Error::one() or Error::all() + * \param lmp pointer to top-level LAMMPS class instance + * \return integer number (tagint) + */ + tagint tnumeric(const char *file, int line, const char *str, + bool do_abort, LAMMPS *lmp); } } -- GitLab From cbdc5dba13399718e0f2f48f545b438e774e49a6 Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Mon, 8 Jul 2019 18:09:41 -0400 Subject: [PATCH 207/469] fix bug in atom style wavepacket --- src/USER-AWPMD/atom_vec_wavepacket.cpp | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/USER-AWPMD/atom_vec_wavepacket.cpp b/src/USER-AWPMD/atom_vec_wavepacket.cpp index 67eaf94551..0edaf7ac02 100644 --- a/src/USER-AWPMD/atom_vec_wavepacket.cpp +++ b/src/USER-AWPMD/atom_vec_wavepacket.cpp @@ -928,7 +928,7 @@ void AtomVecWavepacket::data_atom(double *coord, imageint imagetmp, error->one(FLERR,"Invalid eradius in Atoms section of data file"); etag[nlocal] = utils::inumeric(FLERR,values[5],true,lmp); - cs[2*nlocal] = utils::inumeric(FLERR,values[6],true,lmp); + cs[2*nlocal] = utils::numeric(FLERR,values[6],true,lmp); cs[2*nlocal+1] = utils::numeric(FLERR,values[7],true,lmp); x[nlocal][0] = coord[0]; -- GitLab From 1f47da6c51deaac5f29f56bc532a683965d85a82 Mon Sep 17 00:00:00 2001 From: "Ryan S. Elliott" Date: Mon, 8 Jul 2019 17:46:47 -0500 Subject: [PATCH 208/469] Add fixed_types to kim_init & split to kim_query --- examples/kim/in.query | 7 ++- src/KIM/kim_interactions.cpp | 106 ++++++++++++++++++++--------------- src/KIM/kim_query.cpp | 32 +++++++++-- 3 files changed, 94 insertions(+), 51 deletions(-) diff --git a/examples/kim/in.query b/examples/kim/in.query index 33272dc298..72e739fb52 100644 --- a/examples/kim/in.query +++ b/examples/kim/in.query @@ -4,8 +4,9 @@ # lattice constant for a specific test used for a specific model and then # assigns it to the variable 'latconst' -units metal +kim_init EAM_CubicNaturalSpline_ErcolessiAdams_1994_Al__MO_800509458712_002 metal info variables out log -kim_query latconst get_test_result test=TE_156715955670 species=["Al"] model=MO_800509458712 prop=structure-cubic-crystal-npt keys=["a"] units=["angstrom"] +kim_query latconst split get_test_result test=TE_156715955670 species=["Al"] prop=structure-cubic-crystal-npt keys=["a","a"] units=["angstrom","angstrom"] info variables out log -lattice fcc ${latconst} +lattice fcc ${latconst_1} +lattice fcc ${latconst_2} diff --git a/src/KIM/kim_interactions.cpp b/src/KIM/kim_interactions.cpp index 355df9c3be..d0fbb809d2 100644 --- a/src/KIM/kim_interactions.cpp +++ b/src/KIM/kim_interactions.cpp @@ -115,8 +115,16 @@ void KimInteractions::kim_interactions_log_delimiter( void KimInteractions::do_setup(int narg, char **arg) { - if (narg != atom->ntypes) + bool fixed_types; + if ((narg == 1) && (0 == strcmp("fixed_types",arg[0]))) { + fixed_types = true; + } + else if (narg != atom->ntypes) { error->all(FLERR,"Illegal kim_interactions command"); + } + else { + fixed_types = false; + } char *model_name = NULL; KIM_SimulatorModel *simulatorModel(NULL); @@ -137,53 +145,59 @@ void KimInteractions::do_setup(int narg, char **arg) if (simulatorModel) { - std::string delimiter(""); - std::string atom_type_sym_list; - std::string atom_type_num_list; + if (!fixed_types) { + std::string delimiter(""); + std::string atom_type_sym_list; + std::string atom_type_num_list; - for (int i = 0; i < narg; i++) - { - atom_type_sym_list += delimiter + arg[i]; - atom_type_num_list += delimiter + SNUM(species_to_atomic_no(arg[i])); - delimiter = " "; - } - - KIM_SimulatorModel_AddTemplateMap( - simulatorModel,"atom-type-sym-list",atom_type_sym_list.c_str()); - KIM_SimulatorModel_AddTemplateMap( - simulatorModel,"atom-type-num-list",atom_type_num_list.c_str()); - KIM_SimulatorModel_CloseTemplateMap(simulatorModel); - - int len = strlen(atom_type_sym_list.c_str())+1; - char *strbuf = new char[len]; - char *strword; - - // validate species selection - - int sim_num_species; - bool species_is_supported; - char const *sim_species; - KIM_SimulatorModel_GetNumberOfSupportedSpecies( - simulatorModel,&sim_num_species); - strcpy(strbuf,atom_type_sym_list.c_str()); - strword = strtok(strbuf," \t"); - while (strword) { - species_is_supported = false; - if (strcmp(strword,"NULL") == 0) continue; - for (int i=0; i < sim_num_species; ++i) { - KIM_SimulatorModel_GetSupportedSpecies(simulatorModel,i,&sim_species); - if (strcmp(sim_species,strword) == 0) - species_is_supported = true; + for (int i = 0; i < narg; i++) + { + atom_type_sym_list += delimiter + arg[i]; + atom_type_num_list += delimiter + SNUM(species_to_atomic_no(arg[i])); + delimiter = " "; } - if (!species_is_supported) { - std::string msg("Species '"); - msg += strword; - msg += "' is not supported by this KIM Simulator Model"; - error->all(FLERR,msg.c_str()); + + KIM_SimulatorModel_AddTemplateMap( + simulatorModel,"atom-type-sym-list",atom_type_sym_list.c_str()); + KIM_SimulatorModel_AddTemplateMap( + simulatorModel,"atom-type-num-list",atom_type_num_list.c_str()); + KIM_SimulatorModel_CloseTemplateMap(simulatorModel); + + int len = strlen(atom_type_sym_list.c_str())+1; + char *strbuf = new char[len]; + char *strword; + + // validate species selection + + int sim_num_species; + bool species_is_supported; + char const *sim_species; + KIM_SimulatorModel_GetNumberOfSupportedSpecies( + simulatorModel,&sim_num_species); + strcpy(strbuf,atom_type_sym_list.c_str()); + strword = strtok(strbuf," \t"); + while (strword) { + species_is_supported = false; + if (strcmp(strword,"NULL") == 0) continue; + for (int i=0; i < sim_num_species; ++i) { + KIM_SimulatorModel_GetSupportedSpecies(simulatorModel,i,&sim_species); + if (strcmp(sim_species,strword) == 0) + species_is_supported = true; + } + if (!species_is_supported) { + std::string msg("Species '"); + msg += strword; + msg += "' is not supported by this KIM Simulator Model"; + error->all(FLERR,msg.c_str()); + } + strword = strtok(NULL," \t"); } - strword = strtok(NULL," \t"); + delete[] strbuf; + } + else + { + KIM_SimulatorModel_CloseTemplateMap(simulatorModel); } - delete[] strbuf; // check if units are unchanged @@ -223,6 +237,10 @@ void KimInteractions::do_setup(int narg, char **arg) } else { // not a simulator model. issue pair_style and pair_coeff commands. + + if (fixed_types) + error->all(FLERR,"fixed_types cannot be used with a KIM Portable Model"); + // NOTE: all references to arg must appear before calls to input->one() // as that will reset the argument vector. diff --git a/src/KIM/kim_query.cpp b/src/KIM/kim_query.cpp index 2bb404ec26..cf4efc2b12 100644 --- a/src/KIM/kim_query.cpp +++ b/src/KIM/kim_query.cpp @@ -57,6 +57,7 @@ #include #include #include +#include #include "kim_query.h" #include "comm.h" #include "error.h" @@ -104,6 +105,13 @@ void KimQuery::command(int narg, char **arg) varname = arg[0]; + bool split = false; + if (0 == strcmp("split",arg[1])) { + if (narg == 2) error->all(FLERR,"Illegal kim_query command"); + split = true; + arg++; + narg--; + } function = arg[1]; #if defined(LMP_KIM_CURL) @@ -123,11 +131,27 @@ void KimQuery::command(int narg, char **arg) } char **varcmd = new char*[3]; - varcmd[0] = varname; - varcmd[1] = (char *) "string"; - varcmd[2] = value; + if (split) { + int counter = 1; + std::stringstream ss(value); + std::string token; + varcmd[1] = (char *) "string"; + + while(std::getline(ss, token, ',')) { + std::stringstream splitname; + splitname << varname << "_" << counter++; + varcmd[0] = const_cast(splitname.str().c_str()); + varcmd[2] = const_cast(token.c_str()); + input->variable->set(3,varcmd); + } + } + else { + varcmd[0] = varname; + varcmd[1] = (char *) "string"; + varcmd[2] = value; - input->variable->set(3,varcmd); + input->variable->set(3,varcmd); + } delete[] varcmd; delete[] value; -- GitLab From 74414afdea0563131122228d4318cbcf950c7dfc Mon Sep 17 00:00:00 2001 From: Aidan Thompson Date: Mon, 8 Jul 2019 17:25:23 -0600 Subject: [PATCH 209/469] Added the boxinfo argument --- src/read_dump.cpp | 69 ++++++++++++++++++++++--------------------- src/reader.h | 2 +- src/reader_native.cpp | 3 +- src/reader_native.h | 2 +- src/reader_xyz.cpp | 4 +-- src/reader_xyz.h | 2 +- 6 files changed, 42 insertions(+), 40 deletions(-) diff --git a/src/read_dump.cpp b/src/read_dump.cpp index 1a0a746c07..85e2312a42 100644 --- a/src/read_dump.cpp +++ b/src/read_dump.cpp @@ -483,51 +483,52 @@ bigint ReadDump::next(bigint ncurrent, bigint nlast, int nevery, int nskip) void ReadDump::header(int fieldinfo) { - int triclinic_snap; + int boxinfo, triclinic_snap; int fieldflag,xflag,yflag,zflag; if (filereader) { for (int i = 0; i < nreader; i++) - nsnapatoms[i] = readers[i]->read_header(box,triclinic_snap,fieldinfo, + nsnapatoms[i] = readers[i]->read_header(box,boxinfo,triclinic_snap,fieldinfo, nfield,fieldtype,fieldlabel, scaleflag,wrapflag,fieldflag, xflag,yflag,zflag); } MPI_Bcast(nsnapatoms,nreader,MPI_LMP_BIGINT,0,clustercomm); + MPI_Bcast(&boxinfo,1,MPI_INT,0,clustercomm); MPI_Bcast(&triclinic_snap,1,MPI_INT,0,clustercomm); MPI_Bcast(&box[0][0],9,MPI_DOUBLE,0,clustercomm); // local copy of snapshot box parameters // used in xfield,yfield,zfield when converting dump atom to absolute coords - xlo = box[0][0]; - xhi = box[0][1]; - ylo = box[1][0]; - yhi = box[1][1]; - zlo = box[2][0]; - zhi = box[2][1]; - - // value of 1 indicates possible change in tilt factors - - if (triclinic_snap == 1) { - xy = box[0][2]; - xz = box[1][2]; - yz = box[2][2]; - double xdelta = MIN(0.0,xy); - xdelta = MIN(xdelta,xz); - xdelta = MIN(xdelta,xy+xz); - xlo = xlo - xdelta; - xdelta = MAX(0.0,xy); - xdelta = MAX(xdelta,xz); - xdelta = MAX(xdelta,xy+xz); - xhi = xhi - xdelta; - ylo = ylo - MIN(0.0,yz); - yhi = yhi - MAX(0.0,yz); + if (boxinfo) { + xlo = box[0][0]; + xhi = box[0][1]; + ylo = box[1][0]; + yhi = box[1][1]; + zlo = box[2][0]; + zhi = box[2][1]; + + if (triclinic_snap) { + xy = box[0][2]; + xz = box[1][2]; + yz = box[2][2]; + double xdelta = MIN(0.0,xy); + xdelta = MIN(xdelta,xz); + xdelta = MIN(xdelta,xy+xz); + xlo = xlo - xdelta; + xdelta = MAX(0.0,xy); + xdelta = MAX(xdelta,xz); + xdelta = MAX(xdelta,xy+xz); + xhi = xhi - xdelta; + ylo = ylo - MIN(0.0,yz); + yhi = yhi - MAX(0.0,yz); + } + xprd = xhi - xlo; + yprd = yhi - ylo; + zprd = zhi - zlo; } - xprd = xhi - xlo; - yprd = yhi - ylo; - zprd = zhi - zlo; // done if not checking fields @@ -539,13 +540,13 @@ void ReadDump::header(int fieldinfo) MPI_Bcast(&zflag,1,MPI_INT,0,clustercomm); // error check on current vs new box and fields - // triclinic_snap < 0 means no box info in file + // boxinfo == 0 means no box info in file - if (triclinic_snap < 0 && boxflag > 0) - error->all(FLERR,"No box information in dump, must use 'box no'"); - if (triclinic_snap >= 0) { - if ((triclinic_snap && !triclinic) || - (!triclinic_snap && triclinic)) + if (boxflag) { + if (!boxinfo) + error->all(FLERR,"No box information in dump, must use 'box no'"); + else if ((triclinic_snap && !triclinic) || + (!triclinic_snap && triclinic)) error->one(FLERR,"Read_dump triclinic status does not match simulation"); } diff --git a/src/reader.h b/src/reader.h index 08b0010b81..7b31b666ba 100644 --- a/src/reader.h +++ b/src/reader.h @@ -29,7 +29,7 @@ class Reader : protected Pointers { virtual int read_time(bigint &) = 0; virtual void skip() = 0; - virtual bigint read_header(double [3][3], int &, int, int, int *, char **, + virtual bigint read_header(double [3][3], int &, int &, int, int, int *, char **, int, int, int &, int &, int &, int &) = 0; virtual void read_atoms(int, int, double **) = 0; diff --git a/src/reader_native.cpp b/src/reader_native.cpp index 2c60ffdfd4..7c772ab6b8 100644 --- a/src/reader_native.cpp +++ b/src/reader_native.cpp @@ -103,7 +103,7 @@ void ReaderNative::skip() only called by proc 0 ------------------------------------------------------------------------- */ -bigint ReaderNative::read_header(double box[3][3], int &triclinic, +bigint ReaderNative::read_header(double box[3][3], int &boxinfo, int &triclinic, int fieldinfo, int nfield, int *fieldtype, char **fieldlabel, int scaleflag, int wrapflag, int &fieldflag, @@ -113,6 +113,7 @@ bigint ReaderNative::read_header(double box[3][3], int &triclinic, read_lines(2); sscanf(line,BIGINT_FORMAT,&natoms); + boxinfo = 1; triclinic = 0; box[0][2] = box[1][2] = box[2][2] = 0.0; read_lines(1); diff --git a/src/reader_native.h b/src/reader_native.h index ab99469aa8..de43e43003 100644 --- a/src/reader_native.h +++ b/src/reader_native.h @@ -33,7 +33,7 @@ class ReaderNative : public Reader { int read_time(bigint &); void skip(); - bigint read_header(double [3][3], int &, int, int, int *, char **, + bigint read_header(double [3][3], int &, int &, int, int, int *, char **, int, int, int &, int &, int &, int &); void read_atoms(int, int, double **); diff --git a/src/reader_xyz.cpp b/src/reader_xyz.cpp index 37d30bd740..303c25cd7a 100644 --- a/src/reader_xyz.cpp +++ b/src/reader_xyz.cpp @@ -117,7 +117,7 @@ void ReaderXYZ::skip() only called by proc 0 ------------------------------------------------------------------------- */ -bigint ReaderXYZ::read_header(double /*box*/[3][3], int &triclinic, +bigint ReaderXYZ::read_header(double /*box*/[3][3], int &boxinfo, int &/*triclinic*/, int fieldinfo, int nfield, int *fieldtype, char **/*fieldlabel*/, int scaleflag, int wrapflag, int &fieldflag, @@ -128,7 +128,7 @@ bigint ReaderXYZ::read_header(double /*box*/[3][3], int &triclinic, // signal that we have no box info at all - triclinic = -1; + boxinfo = 0; // if no field info requested, just return diff --git a/src/reader_xyz.h b/src/reader_xyz.h index 698c6ef240..f8b0ebcea1 100644 --- a/src/reader_xyz.h +++ b/src/reader_xyz.h @@ -33,7 +33,7 @@ class ReaderXYZ : public Reader { int read_time(bigint &); void skip(); - bigint read_header(double [3][3], int &, int, int, int *, char **, + bigint read_header(double [3][3], int &, int &, int, int, int *, char **, int, int, int &, int &, int &, int &); void read_atoms(int, int, double **); -- GitLab From 7a62717051277ef0e3ff1d04b676444c18e5f1bd Mon Sep 17 00:00:00 2001 From: Aidan Thompson Date: Mon, 8 Jul 2019 19:40:31 -0600 Subject: [PATCH 210/469] Updated USER-MOLFILE --- src/USER-MOLFILE/reader_molfile.cpp | 18 ++++++++++++++---- src/USER-MOLFILE/reader_molfile.h | 2 +- 2 files changed, 15 insertions(+), 5 deletions(-) diff --git a/src/USER-MOLFILE/reader_molfile.cpp b/src/USER-MOLFILE/reader_molfile.cpp index bbbe65959e..ca1a61850c 100644 --- a/src/USER-MOLFILE/reader_molfile.cpp +++ b/src/USER-MOLFILE/reader_molfile.cpp @@ -195,7 +195,7 @@ void ReaderMolfile::skip() only called by proc 0 ------------------------------------------------------------------------- */ -bigint ReaderMolfile::read_header(double box[3][3], int &triclinic, +bigint ReaderMolfile::read_header(double box[3][3], int &boxinfo, int &triclinic, int fieldinfo, int nfield, int *fieldtype, char ** /* fieldlabel */, int scaleflag, int wrapflag, int &fieldflag, @@ -204,17 +204,24 @@ bigint ReaderMolfile::read_header(double box[3][3], int &triclinic, nid = 0; // signal that we have no box info at all so far. - triclinic = -1; + + boxinfo = 0; + triclinic = 0; // heuristics to determine if we have boxinfo (first if) // and whether we have an orthogonal box (second if) + if (!is_smalldiff(cell[0]*cell[1]*cell[2], 0.0f)) { + boxinfo = 1; if (is_smalldiff(cell[3],90.0f) && is_smalldiff(cell[4],90.0f) && is_smalldiff(cell[5],90.0f)) { + triclinic = 0; + // we have no information about the absolute location // of the box, so we assume that the origin is in the middle. // also we cannot tell periodicity. we assume, yes. + box[0][0] = -0.5*static_cast(cell[0]); box[0][1] = 0.5*static_cast(cell[0]); box[0][2] = 0.0; @@ -224,6 +231,7 @@ bigint ReaderMolfile::read_header(double box[3][3], int &triclinic, box[2][0] = -0.5*static_cast(cell[2]); box[2][1] = 0.5*static_cast(cell[2]); box[2][2] = 0.0; + } else { triclinic = 1; @@ -243,7 +251,8 @@ bigint ReaderMolfile::read_header(double box[3][3], int &triclinic, (lb*lc*cos(alpha/90.0*MY_PI2) - xy*xz) / ly : 0.0; const double lz = sqrt(lc*lc - xz*xz - yz*yz); - /* go from box length to boundary */ + // go from box length to boundary + double xbnd; xbnd = 0.0; @@ -275,7 +284,8 @@ bigint ReaderMolfile::read_header(double box[3][3], int &triclinic, } // if no field info requested, just return - if (!fieldinfo) return natoms; + + if (!fieldinfo) return natoms; memory->create(fieldindex,nfield,"read_dump:fieldindex"); diff --git a/src/USER-MOLFILE/reader_molfile.h b/src/USER-MOLFILE/reader_molfile.h index 5450843d6d..a56a4e0b96 100644 --- a/src/USER-MOLFILE/reader_molfile.h +++ b/src/USER-MOLFILE/reader_molfile.h @@ -35,7 +35,7 @@ class ReaderMolfile : public Reader { virtual int read_time(bigint &); virtual void skip(); - virtual bigint read_header(double [3][3], int &, int, int, int *, char **, + virtual bigint read_header(double [3][3], int &, int &, int, int, int *, char **, int, int, int &, int &, int &, int &); virtual void read_atoms(int, int, double **); -- GitLab From 39c8a7de6e8f4e36f5dc87b775445e7c1c93fd0d Mon Sep 17 00:00:00 2001 From: Ellad Tadmor Date: Tue, 9 Jul 2019 07:35:50 -0400 Subject: [PATCH 211/469] Updated kim_commands doc to descript kim_query split mode --- doc/src/kim_commands.txt | 12 ++++++++++-- 1 file changed, 10 insertions(+), 2 deletions(-) diff --git a/doc/src/kim_commands.txt b/doc/src/kim_commands.txt index 66319d7a08..16d8ea785d 100644 --- a/doc/src/kim_commands.txt +++ b/doc/src/kim_commands.txt @@ -14,13 +14,14 @@ kim_query command :h3 kim_init model user_units unitarg kim_interactions typeargs -kim_query variable query_function queryargs :pre +kim_query variable formatarg query_function queryargs :pre model = name of the KIM interatomic model (the KIM ID for models archived in OpenKIM) user_units = the LAMMPS "units"_units.html style assumed in the LAMMPS input script unitarg = {unit_conversion_mode} (optional) typeargs = atom type to species mapping (one entry per atom type) variable = name of a (string style) variable where the result of the query is stored +formatarg = {split} (optional) query_function = name of the OpenKIM web API query function to be used queryargs = a series of {keyword=value} pairs that represent the web query; supported keywords depend on the query function :ul @@ -377,7 +378,7 @@ changed to: "lattice fcc $\{a0\}*$\{_u_distance\}". kim_init EAM_Dynamo_Mendelev_2007_Zr__MO_848899341753_000 metal boundary p p p -kim_query latconst get_lattice_constant_hcp species=\["Zr"\] units=\["angstrom"\] +kim_query latconst split get_lattice_constant_hcp species=\["Zr"\] units=\["angstrom"\] variable a0 equal latconst_1 variable c0 equal latconst_2 variable c_to_a equal $\{c0\}/$\{a0\} @@ -387,6 +388,13 @@ lattice custom $\{a0\} a1 0.5 -0.866025 0 a2 0.5 0.866025 0 a3 0 0 $\{c In this case the {kim_query} returns two arguments (since the hexagonal close packed (hcp) structure has two independent lattice constants). +The default behavior of {kim_query} returns the result as a string +with the values separated by commas. The optional keyword {split} +separates the result values into individual variables of the form +{prefix_I}, where {prefix} is set to the the {kim_query} {variable} argument +and {I} ranges from 1 to the number of returned values. The number and order of +the returned values is determined by the type of query performed. + In the case where a query returns multiple results, the default behavior for {kim_query} is to split these into individual variables of the form {prefix_I}, where {prefix} is set to the the {kim_query} {variable} argument -- GitLab From 30086950b87ccb019b2a723b6c684fce7fd6fe7f Mon Sep 17 00:00:00 2001 From: Ellad Tadmor Date: Tue, 9 Jul 2019 09:43:34 -0400 Subject: [PATCH 212/469] Added preliminary doc for kim_interactions fixed_types --- doc/src/kim_commands.txt | 18 +++++++++++++++--- 1 file changed, 15 insertions(+), 3 deletions(-) diff --git a/doc/src/kim_commands.txt b/doc/src/kim_commands.txt index 16d8ea785d..437b768df6 100644 --- a/doc/src/kim_commands.txt +++ b/doc/src/kim_commands.txt @@ -19,7 +19,7 @@ kim_query variable formatarg query_function queryargs :pre model = name of the KIM interatomic model (the KIM ID for models archived in OpenKIM) user_units = the LAMMPS "units"_units.html style assumed in the LAMMPS input script unitarg = {unit_conversion_mode} (optional) -typeargs = atom type to species mapping (one entry per atom type) +typeargs = atom type to species mapping (one entry per atom type) or {fixed_types} for models with a preset fixed mapping variable = name of a (string style) variable where the result of the query is stored formatarg = {split} (optional) query_function = name of the OpenKIM web API query function to be used @@ -33,6 +33,8 @@ kim_interactions Si kim_init Sim_LAMMPS_ReaxFF_StrachanVanDuinChakraborty_2003_CHNO__SM_107643900657_000 real kim_init Sim_LAMMPS_ReaxFF_StrachanVanDuinChakraborty_2003_CHNO__SM_107643900657_000 metal unit_conversion_mode kim_interactions C H O +kim_init Sim_LAMMPS_IFF_OtherInfo_AuthorList_Year_Species__SM_064312669787_000 real +kim_interactions fixed_types kim_query a0 get_lattice_constant_fcc species=\["Al"] units=\["angstrom"\] :pre @@ -272,8 +274,13 @@ The second and final step in using an OpenKIM IM is to execute the command and a "create_box"_create_box.html command, which defines the number of atom types {N}. The {kim_interactions} command has one argument {typeargs}. This argument -contains a list of {N} chemical species, which defines a mapping between -atom types in LAMMPS to the available species in the OpenKIM IM. +contains either a list of {N} chemical species, which defines a mapping between +atom types in LAMMPS to the available species in the OpenKIM IM, or the +keyword {fixed_types} for models that have a preset fixed mapping (i.e. +the mapping between LAMMPS atom types and chemical species is defined by +the model and cannot be changed). In the latter case, the user must consult +the model documentation to see how many atom types there are and how they +map to the chemcial species. For example, consider an OpenKIM IM that supports Si and C species. If the LAMMPS simulation has four atom types, where the first three are Si, @@ -282,6 +289,11 @@ and the fourth is C, the following {kim_interactions} command would be used: kim_interactions Si Si Si C :pre +Alternatively, for a model with a fixed mapping the command would be: + +kim_interactions fixed_types +:pre + The {kim_interactions} command performs all the necessary steps to set up the OpenKIM IM selected in the {kim_init} command. The specific actions depend on whether the IM is a KIM PM or a KIM SM. For a KIM PM, -- GitLab From 5013fd699ffcf5c844b2f34cca10c964bbaf967a Mon Sep 17 00:00:00 2001 From: Stan Moore Date: Tue, 9 Jul 2019 09:43:50 -0600 Subject: [PATCH 213/469] Fix issue in Kokkos neighor binning when using non-Kokkos lists on GPUs --- src/KOKKOS/nbin_kokkos.cpp | 1 + src/KOKKOS/neighbor_kokkos.cpp | 1 + src/nbin.cpp | 2 ++ src/nbin.h | 4 ++++ 4 files changed, 8 insertions(+) diff --git a/src/KOKKOS/nbin_kokkos.cpp b/src/KOKKOS/nbin_kokkos.cpp index 090519a5a8..5fc3a89732 100644 --- a/src/KOKKOS/nbin_kokkos.cpp +++ b/src/KOKKOS/nbin_kokkos.cpp @@ -40,6 +40,7 @@ NBinKokkos::NBinKokkos(LAMMPS *lmp) : NBinStandard(lmp) { #endif h_resize() = 1; + kokkos = 1; } /* ---------------------------------------------------------------------- diff --git a/src/KOKKOS/neighbor_kokkos.cpp b/src/KOKKOS/neighbor_kokkos.cpp index e912956a3f..a594c8f7a0 100644 --- a/src/KOKKOS/neighbor_kokkos.cpp +++ b/src/KOKKOS/neighbor_kokkos.cpp @@ -301,6 +301,7 @@ void NeighborKokkos::build_kokkos(int topoflag) if (style != Neighbor::NSQ) { for (int i = 0; i < nbin; i++) { + if (!neigh_bin[i]->kokkos) atomKK->sync(Host,ALL_MASK); neigh_bin[i]->bin_atoms_setup(nall); neigh_bin[i]->bin_atoms(); } diff --git a/src/nbin.cpp b/src/nbin.cpp index a30b76cca0..3e50148a04 100644 --- a/src/nbin.cpp +++ b/src/nbin.cpp @@ -35,6 +35,8 @@ NBin::NBin(LAMMPS *lmp) : Pointers(lmp) dimension = domain->dimension; triclinic = domain->triclinic; + + kokkos = 0; } /* ---------------------------------------------------------------------- */ diff --git a/src/nbin.h b/src/nbin.h index d6022a6a35..54b8da171d 100644 --- a/src/nbin.h +++ b/src/nbin.h @@ -47,6 +47,10 @@ class NBin : protected Pointers { virtual void setup_bins(int) = 0; virtual void bin_atoms() = 0; + // Kokkos package + + int kokkos; // 1 if class stores Kokkos data + protected: // data from Neighbor class -- GitLab From c2dc624ec90575027328f0b3b9ab52fff2b00631 Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Tue, 9 Jul 2019 15:04:41 -0400 Subject: [PATCH 214/469] update packages USER-SPH, USER-SMTBQ, USER-SDPD, USER-TALLY, USER-UEF, USER-YAFF --- src/USER-SDPD/pair_sdpd_taitwater_isothermal.cpp | 3 +-- src/USER-SMTBQ/pair_smtbq.cpp | 7 +++---- src/USER-SPH/compute_meso_e_atom.cpp | 3 +-- src/USER-SPH/compute_meso_rho_atom.cpp | 3 +-- src/USER-SPH/compute_meso_t_atom.cpp | 3 +-- src/USER-SPH/fix_meso.cpp | 12 ------------ src/USER-SPH/fix_meso_stationary.cpp | 12 ------------ src/USER-SPH/pair_sph_heatconduction.cpp | 4 +--- src/USER-SPH/pair_sph_idealgas.cpp | 4 +--- src/USER-SPH/pair_sph_lj.cpp | 4 +--- src/USER-SPH/pair_sph_rhosum.cpp | 2 -- src/USER-SPH/pair_sph_taitwater.cpp | 3 +-- src/USER-SPH/pair_sph_taitwater_morris.cpp | 3 +-- src/USER-TALLY/compute_force_tally.cpp | 4 ++-- src/USER-TALLY/compute_heat_flux_tally.cpp | 2 +- src/USER-TALLY/compute_pe_mol_tally.cpp | 3 +-- src/USER-TALLY/compute_pe_tally.cpp | 2 +- src/USER-TALLY/compute_stress_tally.cpp | 2 +- src/USER-UEF/compute_pressure_uef.cpp | 9 +-------- src/USER-UEF/compute_temp_uef.cpp | 4 +--- src/USER-UEF/dump_cfg_uef.cpp | 6 +----- src/USER-UEF/fix_nh_uef.cpp | 5 +---- src/USER-YAFF/angle_cross.cpp | 4 +--- src/USER-YAFF/angle_cross.h | 1 - src/USER-YAFF/angle_mm3.cpp | 5 ++--- src/USER-YAFF/angle_mm3.h | 1 - src/USER-YAFF/bond_mm3.cpp | 5 ++--- src/USER-YAFF/bond_mm3.h | 1 - src/USER-YAFF/improper_distharm.cpp | 6 ++---- src/USER-YAFF/improper_distharm.h | 1 - src/USER-YAFF/improper_sqdistharm.cpp | 6 ++---- src/USER-YAFF/improper_sqdistharm.h | 1 - src/USER-YAFF/pair_lj_switch3_coulgauss_long.cpp | 8 +++----- src/USER-YAFF/pair_mm3_switch3_coulgauss_long.cpp | 8 +++----- 34 files changed, 37 insertions(+), 110 deletions(-) diff --git a/src/USER-SDPD/pair_sdpd_taitwater_isothermal.cpp b/src/USER-SDPD/pair_sdpd_taitwater_isothermal.cpp index db80debe51..d799869db3 100644 --- a/src/USER-SDPD/pair_sdpd_taitwater_isothermal.cpp +++ b/src/USER-SDPD/pair_sdpd_taitwater_isothermal.cpp @@ -18,9 +18,8 @@ references: Espanol and Revenga, Phys Rev E 67, 026705 (2003) ------------------------------------------------------------------------- */ -#include -#include #include "pair_sdpd_taitwater_isothermal.h" +#include #include "atom.h" #include "force.h" #include "comm.h" diff --git a/src/USER-SMTBQ/pair_smtbq.cpp b/src/USER-SMTBQ/pair_smtbq.cpp index ba7f8eb88c..f61fc1a72e 100644 --- a/src/USER-SMTBQ/pair_smtbq.cpp +++ b/src/USER-SMTBQ/pair_smtbq.cpp @@ -38,25 +38,24 @@ . ------------------------------------------------------------------------- */ +#include "pair_smtbq.h" +#include #include -#include #include #include +#include #include -#include "pair_smtbq.h" #include "atom.h" #include "comm.h" #include "force.h" #include "neighbor.h" #include "neigh_list.h" #include "neigh_request.h" -#include "group.h" #include "update.h" #include "math_const.h" #include "math_special.h" #include "memory.h" #include "error.h" -#include "domain.h" #include #include diff --git a/src/USER-SPH/compute_meso_e_atom.cpp b/src/USER-SPH/compute_meso_e_atom.cpp index e39dee2b5f..c56243e5ed 100644 --- a/src/USER-SPH/compute_meso_e_atom.cpp +++ b/src/USER-SPH/compute_meso_e_atom.cpp @@ -11,13 +11,12 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include #include "compute_meso_e_atom.h" +#include #include "atom.h" #include "update.h" #include "modify.h" #include "comm.h" -#include "force.h" #include "memory.h" #include "error.h" diff --git a/src/USER-SPH/compute_meso_rho_atom.cpp b/src/USER-SPH/compute_meso_rho_atom.cpp index eeb3f987bc..b2fbd2d70a 100644 --- a/src/USER-SPH/compute_meso_rho_atom.cpp +++ b/src/USER-SPH/compute_meso_rho_atom.cpp @@ -11,13 +11,12 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include #include "compute_meso_rho_atom.h" +#include #include "atom.h" #include "update.h" #include "modify.h" #include "comm.h" -#include "force.h" #include "memory.h" #include "error.h" diff --git a/src/USER-SPH/compute_meso_t_atom.cpp b/src/USER-SPH/compute_meso_t_atom.cpp index dc4f3407f1..bab96468dd 100644 --- a/src/USER-SPH/compute_meso_t_atom.cpp +++ b/src/USER-SPH/compute_meso_t_atom.cpp @@ -11,13 +11,12 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include #include "compute_meso_t_atom.h" +#include #include "atom.h" #include "update.h" #include "modify.h" #include "comm.h" -#include "force.h" #include "memory.h" #include "error.h" diff --git a/src/USER-SPH/fix_meso.cpp b/src/USER-SPH/fix_meso.cpp index b688eccfea..4f4e532291 100644 --- a/src/USER-SPH/fix_meso.cpp +++ b/src/USER-SPH/fix_meso.cpp @@ -11,23 +11,11 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include -#include -#include -#include #include "fix_meso.h" #include "atom.h" -#include "comm.h" #include "force.h" -#include "neighbor.h" -#include "neigh_list.h" -#include "neigh_request.h" #include "update.h" -#include "integrate.h" -#include "respa.h" -#include "memory.h" #include "error.h" -#include "pair.h" using namespace LAMMPS_NS; using namespace FixConst; diff --git a/src/USER-SPH/fix_meso_stationary.cpp b/src/USER-SPH/fix_meso_stationary.cpp index 29e8a1554c..b7f0675ef8 100644 --- a/src/USER-SPH/fix_meso_stationary.cpp +++ b/src/USER-SPH/fix_meso_stationary.cpp @@ -11,23 +11,11 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include -#include -#include -#include #include "fix_meso_stationary.h" #include "atom.h" -#include "comm.h" #include "force.h" -#include "neighbor.h" -#include "neigh_list.h" -#include "neigh_request.h" #include "update.h" -#include "integrate.h" -#include "respa.h" -#include "memory.h" #include "error.h" -#include "pair.h" using namespace LAMMPS_NS; using namespace FixConst; diff --git a/src/USER-SPH/pair_sph_heatconduction.cpp b/src/USER-SPH/pair_sph_heatconduction.cpp index bafa26be89..cff9009015 100644 --- a/src/USER-SPH/pair_sph_heatconduction.cpp +++ b/src/USER-SPH/pair_sph_heatconduction.cpp @@ -11,12 +11,10 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include -#include #include "pair_sph_heatconduction.h" +#include #include "atom.h" #include "force.h" -#include "comm.h" #include "memory.h" #include "error.h" #include "neigh_list.h" diff --git a/src/USER-SPH/pair_sph_idealgas.cpp b/src/USER-SPH/pair_sph_idealgas.cpp index db5ec964bc..f206bf68f5 100644 --- a/src/USER-SPH/pair_sph_idealgas.cpp +++ b/src/USER-SPH/pair_sph_idealgas.cpp @@ -11,12 +11,10 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include -#include #include "pair_sph_idealgas.h" +#include #include "atom.h" #include "force.h" -#include "comm.h" #include "neigh_list.h" #include "memory.h" #include "error.h" diff --git a/src/USER-SPH/pair_sph_lj.cpp b/src/USER-SPH/pair_sph_lj.cpp index 7d315c975c..3173e2a47d 100644 --- a/src/USER-SPH/pair_sph_lj.cpp +++ b/src/USER-SPH/pair_sph_lj.cpp @@ -11,12 +11,10 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include -#include #include "pair_sph_lj.h" +#include #include "atom.h" #include "force.h" -#include "comm.h" #include "neigh_list.h" #include "memory.h" #include "error.h" diff --git a/src/USER-SPH/pair_sph_rhosum.cpp b/src/USER-SPH/pair_sph_rhosum.cpp index 842dddc744..fa51dc3781 100644 --- a/src/USER-SPH/pair_sph_rhosum.cpp +++ b/src/USER-SPH/pair_sph_rhosum.cpp @@ -11,8 +11,6 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include -#include #include "pair_sph_rhosum.h" #include "atom.h" #include "force.h" diff --git a/src/USER-SPH/pair_sph_taitwater.cpp b/src/USER-SPH/pair_sph_taitwater.cpp index cf3c0e914b..f2a34d4edd 100644 --- a/src/USER-SPH/pair_sph_taitwater.cpp +++ b/src/USER-SPH/pair_sph_taitwater.cpp @@ -11,9 +11,8 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include -#include #include "pair_sph_taitwater.h" +#include #include "atom.h" #include "force.h" #include "comm.h" diff --git a/src/USER-SPH/pair_sph_taitwater_morris.cpp b/src/USER-SPH/pair_sph_taitwater_morris.cpp index 5cbaa5959f..9ca03e3476 100644 --- a/src/USER-SPH/pair_sph_taitwater_morris.cpp +++ b/src/USER-SPH/pair_sph_taitwater_morris.cpp @@ -11,9 +11,8 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include -#include #include "pair_sph_taitwater_morris.h" +#include #include "atom.h" #include "force.h" #include "comm.h" diff --git a/src/USER-TALLY/compute_force_tally.cpp b/src/USER-TALLY/compute_force_tally.cpp index 3339e0555b..9d15fbc441 100644 --- a/src/USER-TALLY/compute_force_tally.cpp +++ b/src/USER-TALLY/compute_force_tally.cpp @@ -11,9 +11,9 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include -#include #include "compute_force_tally.h" +#include +#include #include "atom.h" #include "group.h" #include "pair.h" diff --git a/src/USER-TALLY/compute_heat_flux_tally.cpp b/src/USER-TALLY/compute_heat_flux_tally.cpp index 2a5f724953..350bc4b4b6 100644 --- a/src/USER-TALLY/compute_heat_flux_tally.cpp +++ b/src/USER-TALLY/compute_heat_flux_tally.cpp @@ -11,8 +11,8 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include #include "compute_heat_flux_tally.h" +#include #include "atom.h" #include "group.h" #include "pair.h" diff --git a/src/USER-TALLY/compute_pe_mol_tally.cpp b/src/USER-TALLY/compute_pe_mol_tally.cpp index 5fabd4a77b..ce647a04c3 100644 --- a/src/USER-TALLY/compute_pe_mol_tally.cpp +++ b/src/USER-TALLY/compute_pe_mol_tally.cpp @@ -11,13 +11,12 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include #include "compute_pe_mol_tally.h" +#include #include "atom.h" #include "group.h" #include "pair.h" #include "update.h" -#include "memory.h" #include "error.h" #include "force.h" #include "comm.h" diff --git a/src/USER-TALLY/compute_pe_tally.cpp b/src/USER-TALLY/compute_pe_tally.cpp index 8e6703bde1..edfa49b1b1 100644 --- a/src/USER-TALLY/compute_pe_tally.cpp +++ b/src/USER-TALLY/compute_pe_tally.cpp @@ -11,8 +11,8 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include #include "compute_pe_tally.h" +#include #include "atom.h" #include "group.h" #include "pair.h" diff --git a/src/USER-TALLY/compute_stress_tally.cpp b/src/USER-TALLY/compute_stress_tally.cpp index 07d685a9c2..1ea096e286 100644 --- a/src/USER-TALLY/compute_stress_tally.cpp +++ b/src/USER-TALLY/compute_stress_tally.cpp @@ -11,8 +11,8 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include #include "compute_stress_tally.h" +#include #include "atom.h" #include "group.h" #include "pair.h" diff --git a/src/USER-UEF/compute_pressure_uef.cpp b/src/USER-UEF/compute_pressure_uef.cpp index 8b62853042..adb9970c12 100644 --- a/src/USER-UEF/compute_pressure_uef.cpp +++ b/src/USER-UEF/compute_pressure_uef.cpp @@ -13,21 +13,14 @@ Contributing author: David Nicholson (MIT) ------------------------------------------------------------------------- */ -#include -#include -#include #include "compute_pressure_uef.h" +#include #include "fix_nh_uef.h" #include "update.h" #include "domain.h" #include "modify.h" #include "fix.h" #include "force.h" -#include "pair.h" -#include "bond.h" -#include "angle.h" -#include "dihedral.h" -#include "improper.h" #include "kspace.h" #include "error.h" diff --git a/src/USER-UEF/compute_temp_uef.cpp b/src/USER-UEF/compute_temp_uef.cpp index 999296ec7e..698c4452c2 100644 --- a/src/USER-UEF/compute_temp_uef.cpp +++ b/src/USER-UEF/compute_temp_uef.cpp @@ -13,11 +13,9 @@ Contributing author: David Nicholson (MIT) ------------------------------------------------------------------------- */ -#include -#include #include "compute_temp_uef.h" +#include #include "fix_nh_uef.h" -#include "update.h" #include "modify.h" #include "fix.h" #include "error.h" diff --git a/src/USER-UEF/dump_cfg_uef.cpp b/src/USER-UEF/dump_cfg_uef.cpp index 58b3ec5a1f..5e3733f422 100644 --- a/src/USER-UEF/dump_cfg_uef.cpp +++ b/src/USER-UEF/dump_cfg_uef.cpp @@ -13,15 +13,11 @@ Contributing Author: David Nicholson (MIT) ------------------------------------------------------------------------- */ - +#include "dump_cfg.h" #include -#include #include -#include "dump_cfg.h" #include "atom.h" -#include "domain.h" #include "modify.h" -#include "compute.h" #include "fix.h" #include "error.h" #include "uef_utils.h" diff --git a/src/USER-UEF/fix_nh_uef.cpp b/src/USER-UEF/fix_nh_uef.cpp index bffcd7849f..8873688eb7 100644 --- a/src/USER-UEF/fix_nh_uef.cpp +++ b/src/USER-UEF/fix_nh_uef.cpp @@ -13,19 +13,16 @@ Contributing author: David Nicholson (MIT) ------------------------------------------------------------------------- */ +#include "fix_nh_uef.h" #include -#include #include -#include "fix_nh_uef.h" #include "atom.h" #include "force.h" -#include "group.h" #include "comm.h" #include "citeme.h" #include "irregular.h" #include "modify.h" #include "compute.h" -#include "kspace.h" #include "update.h" #include "domain.h" #include "error.h" diff --git a/src/USER-YAFF/angle_cross.cpp b/src/USER-YAFF/angle_cross.cpp index 2e6731f494..2ebb08f56b 100644 --- a/src/USER-YAFF/angle_cross.cpp +++ b/src/USER-YAFF/angle_cross.cpp @@ -15,10 +15,8 @@ Contributing author: Steven Vandenbrande ------------------------------------------------------------------------- */ -#include -#include -#include #include "angle_cross.h" +#include #include "atom.h" #include "neighbor.h" #include "domain.h" diff --git a/src/USER-YAFF/angle_cross.h b/src/USER-YAFF/angle_cross.h index 7709c10414..ba958f98ec 100644 --- a/src/USER-YAFF/angle_cross.h +++ b/src/USER-YAFF/angle_cross.h @@ -20,7 +20,6 @@ AngleStyle(cross,AngleCross) #ifndef LMP_ANGLE_CROSS_H #define LMP_ANGLE_CROSS_H -#include #include "angle.h" namespace LAMMPS_NS { diff --git a/src/USER-YAFF/angle_mm3.cpp b/src/USER-YAFF/angle_mm3.cpp index 53cb11b5df..24ce8229ba 100644 --- a/src/USER-YAFF/angle_mm3.cpp +++ b/src/USER-YAFF/angle_mm3.cpp @@ -15,10 +15,9 @@ Contributing author: Steven Vandenbrande ------------------------------------------------------------------------- */ -#include -#include -#include #include "angle_mm3.h" +#include +#include #include "atom.h" #include "neighbor.h" #include "domain.h" diff --git a/src/USER-YAFF/angle_mm3.h b/src/USER-YAFF/angle_mm3.h index 2d19b4d1b4..985c4bb9b4 100644 --- a/src/USER-YAFF/angle_mm3.h +++ b/src/USER-YAFF/angle_mm3.h @@ -20,7 +20,6 @@ AngleStyle(mm3,AngleMM3) #ifndef LMP_ANGLE_MM3_H #define LMP_ANGLE_MM3_H -#include #include "angle.h" namespace LAMMPS_NS { diff --git a/src/USER-YAFF/bond_mm3.cpp b/src/USER-YAFF/bond_mm3.cpp index ee1ebcdd61..2a7d5d1843 100644 --- a/src/USER-YAFF/bond_mm3.cpp +++ b/src/USER-YAFF/bond_mm3.cpp @@ -15,12 +15,11 @@ Contributing author: Steven Vandenbrande ------------------------------------------------------------------------- */ -#include -#include #include "bond_mm3.h" +#include +#include #include "atom.h" #include "neighbor.h" -#include "domain.h" #include "comm.h" #include "force.h" #include "memory.h" diff --git a/src/USER-YAFF/bond_mm3.h b/src/USER-YAFF/bond_mm3.h index 9711d89529..56f3136ea8 100644 --- a/src/USER-YAFF/bond_mm3.h +++ b/src/USER-YAFF/bond_mm3.h @@ -20,7 +20,6 @@ BondStyle(mm3,BondMM3) #ifndef LMP_BOND_MM3_H #define LMP_BOND_MM3_H -#include #include "bond.h" namespace LAMMPS_NS { diff --git a/src/USER-YAFF/improper_distharm.cpp b/src/USER-YAFF/improper_distharm.cpp index b45087a9ab..2b62f827e7 100644 --- a/src/USER-YAFF/improper_distharm.cpp +++ b/src/USER-YAFF/improper_distharm.cpp @@ -16,16 +16,14 @@ improper_distance code by Paolo Raiteri (Curtin University) ------------------------------------------------------------------------- */ -#include -#include -#include #include "improper_distharm.h" +#include +#include #include "atom.h" #include "comm.h" #include "neighbor.h" #include "domain.h" #include "force.h" -#include "update.h" #include "memory.h" #include "error.h" diff --git a/src/USER-YAFF/improper_distharm.h b/src/USER-YAFF/improper_distharm.h index b8b9ae780e..0a8d34ac44 100644 --- a/src/USER-YAFF/improper_distharm.h +++ b/src/USER-YAFF/improper_distharm.h @@ -20,7 +20,6 @@ ImproperStyle(distharm,ImproperDistHarm) #ifndef LMP_IMPROPER_DISTHARM_H #define LMP_IMPROPER_DISTHARM_H -#include #include "improper.h" namespace LAMMPS_NS { diff --git a/src/USER-YAFF/improper_sqdistharm.cpp b/src/USER-YAFF/improper_sqdistharm.cpp index ae702820cb..bcc0549f7e 100644 --- a/src/USER-YAFF/improper_sqdistharm.cpp +++ b/src/USER-YAFF/improper_sqdistharm.cpp @@ -16,16 +16,14 @@ improper_distance code by Paolo Raiteri (Curtin University) ------------------------------------------------------------------------- */ -#include -#include -#include #include "improper_sqdistharm.h" +#include +#include #include "atom.h" #include "comm.h" #include "neighbor.h" #include "domain.h" #include "force.h" -#include "update.h" #include "memory.h" #include "error.h" diff --git a/src/USER-YAFF/improper_sqdistharm.h b/src/USER-YAFF/improper_sqdistharm.h index 301b5066cb..3aceb01a03 100644 --- a/src/USER-YAFF/improper_sqdistharm.h +++ b/src/USER-YAFF/improper_sqdistharm.h @@ -20,7 +20,6 @@ ImproperStyle(sqdistharm,ImproperSQDistHarm) #ifndef LMP_IMPROPER_SQDISTHARM_H #define LMP_IMPROPER_SQDISTHARM_H -#include #include "improper.h" namespace LAMMPS_NS { diff --git a/src/USER-YAFF/pair_lj_switch3_coulgauss_long.cpp b/src/USER-YAFF/pair_lj_switch3_coulgauss_long.cpp index f37dcc3ed1..ab983a78bc 100644 --- a/src/USER-YAFF/pair_lj_switch3_coulgauss_long.cpp +++ b/src/USER-YAFF/pair_lj_switch3_coulgauss_long.cpp @@ -15,17 +15,15 @@ Contributing author: Steven Vandenbrande ------------------------------------------------------------------------- */ -#include -#include -#include -#include #include "pair_lj_switch3_coulgauss_long.h" +#include +#include +#include #include "atom.h" #include "comm.h" #include "force.h" #include "kspace.h" #include "update.h" -#include "integrate.h" #include "respa.h" #include "neighbor.h" #include "neigh_list.h" diff --git a/src/USER-YAFF/pair_mm3_switch3_coulgauss_long.cpp b/src/USER-YAFF/pair_mm3_switch3_coulgauss_long.cpp index 931ed1d116..4175ef915d 100644 --- a/src/USER-YAFF/pair_mm3_switch3_coulgauss_long.cpp +++ b/src/USER-YAFF/pair_mm3_switch3_coulgauss_long.cpp @@ -15,17 +15,15 @@ Contributing author: Steven Vandenbrande ------------------------------------------------------------------------- */ -#include -#include -#include -#include #include "pair_mm3_switch3_coulgauss_long.h" +#include +#include +#include #include "atom.h" #include "comm.h" #include "force.h" #include "kspace.h" #include "update.h" -#include "integrate.h" #include "respa.h" #include "neighbor.h" #include "neigh_list.h" -- GitLab From 2fd327d05738ce6a87521f658256a81851947e88 Mon Sep 17 00:00:00 2001 From: Steve Plimpton Date: Tue, 9 Jul 2019 16:17:54 -0600 Subject: [PATCH 215/469] more robust version of atom exchange size --- src/BODY/body_nparticle.cpp | 1 + src/BODY/body_rounded_polygon.cpp | 1 + src/BODY/body_rounded_polyhedron.cpp | 1 + src/atom_vec.cpp | 2 ++ src/atom_vec.h | 2 ++ src/body.h | 2 ++ src/comm.cpp | 40 ++++++++++++++++++++++++++-- src/comm.h | 15 +++++++---- src/comm_brick.cpp | 30 +++++++++------------ src/comm_brick.h | 1 - src/comm_tiled.cpp | 30 +++++++++------------ src/comm_tiled.h | 1 - src/fix.cpp | 2 ++ src/fix.h | 2 ++ src/fix_neigh_history.cpp | 16 +++++------ src/fix_store.cpp | 1 + 16 files changed, 93 insertions(+), 54 deletions(-) diff --git a/src/BODY/body_nparticle.cpp b/src/BODY/body_nparticle.cpp index 10529ad3af..1a85531a31 100644 --- a/src/BODY/body_nparticle.cpp +++ b/src/BODY/body_nparticle.cpp @@ -44,6 +44,7 @@ BodyNparticle::BodyNparticle(LAMMPS *lmp, int narg, char **arg) : icp = new MyPoolChunk(1,1); dcp = new MyPoolChunk(3*nmin,3*nmax); + maxexchange = 1 + 3*nmax; // icp max + dcp max memory->create(imflag,nmax,"body/nparticle:imflag"); memory->create(imdata,nmax,4,"body/nparticle:imdata"); diff --git a/src/BODY/body_rounded_polygon.cpp b/src/BODY/body_rounded_polygon.cpp index d352c789d7..f4d9cede18 100644 --- a/src/BODY/body_rounded_polygon.cpp +++ b/src/BODY/body_rounded_polygon.cpp @@ -61,6 +61,7 @@ BodyRoundedPolygon::BodyRoundedPolygon(LAMMPS *lmp, int narg, char **arg) : icp = new MyPoolChunk(1,1); dcp = new MyPoolChunk(3*nmin+2*nmin+1+1,3*nmax+2*nmax+1+1); + maxexchange = 1 + 3*nmax+2*nmax+1+1; // icp max + dcp max memory->create(imflag,nmax,"body/rounded/polygon:imflag"); memory->create(imdata,nmax,7,"body/nparticle:imdata"); diff --git a/src/BODY/body_rounded_polyhedron.cpp b/src/BODY/body_rounded_polyhedron.cpp index 99a380a932..6d5824ecc5 100644 --- a/src/BODY/body_rounded_polyhedron.cpp +++ b/src/BODY/body_rounded_polyhedron.cpp @@ -61,6 +61,7 @@ BodyRoundedPolyhedron::BodyRoundedPolyhedron(LAMMPS *lmp, int narg, char **arg) icp = new MyPoolChunk(1,3); dcp = new MyPoolChunk(3*nmin+2+1+1, 3*nmax+2*nmax+MAX_FACE_SIZE*nmax+1+1); + maxexchange = 3 + 3*nmax+2*nmax+MAX_FACE_SIZE*nmax+1+1; // icp max + dcp max memory->create(imflag,2*nmax,"body/rounded/polyhedron:imflag"); memory->create(imdata,2*nmax,7,"body/polyhedron:imdata"); diff --git a/src/atom_vec.cpp b/src/atom_vec.cpp index d4bea15d0b..93433c6bea 100644 --- a/src/atom_vec.cpp +++ b/src/atom_vec.cpp @@ -34,6 +34,8 @@ AtomVec::AtomVec(LAMMPS *lmp) : Pointers(lmp) mass_type = dipole_type = 0; forceclearflag = 0; size_data_bonus = 0; + maxexchange = 0; + kokkosable = 0; nargcopy = 0; diff --git a/src/atom_vec.h b/src/atom_vec.h index 87fb35d9c7..e4e8014cd5 100644 --- a/src/atom_vec.h +++ b/src/atom_vec.h @@ -39,6 +39,8 @@ class AtomVec : protected Pointers { int size_data_vel; // number of values in Velocity line int size_data_bonus; // number of values in Bonus line int xcol_data; // column (1-N) where x is in Atom line + int maxexchange; // max size of exchanged atom + // only needs to be set if size > BUFEXTRA class Molecule **onemols; // list of molecules for style template int nset; // # of molecules in list diff --git a/src/body.h b/src/body.h index 59001620f8..7da08733c5 100644 --- a/src/body.h +++ b/src/body.h @@ -28,6 +28,8 @@ class Body : protected Pointers { char *style; int size_forward; // max extra values packed for comm int size_border; // max extra values packed for border comm + int maxexchange; // max size of exchanged atom + AtomVecBody *avec; // ptr to class that stores body bonus info Body(class LAMMPS *, int, char **); diff --git a/src/comm.cpp b/src/comm.cpp index 052de93793..0356f88be7 100644 --- a/src/comm.cpp +++ b/src/comm.cpp @@ -39,7 +39,7 @@ using namespace LAMMPS_NS; -#define BUFMIN 1000 // also in comm styles +#define BUFEXTRA 1024 enum{ONELEVEL,TWOLEVEL,NUMA,CUSTOM}; enum{CART,CARTREORDER,XYZ}; @@ -65,7 +65,10 @@ Comm::Comm(LAMMPS *lmp) : Pointers(lmp) outfile = NULL; recv_from_partition = send_to_partition = -1; otherflag = 0; - maxexchange_atom = maxexchange_fix = 0; + + maxexchange = maxexchange_atom = maxexchange_fix = 0; + maxexchange_fix_dynamic = 0; + bufextra = BUFEXTRA; grid2proc = NULL; xsplit = ysplit = zsplit = NULL; @@ -225,6 +228,39 @@ void Comm::init() if (force->newton == 0) maxreverse = 0; if (force->pair) maxreverse = MAX(maxreverse,force->pair->comm_reverse_off); + + // maxexchange_atom = size of an exchanged atom, set by AtomVec + // only needs to be set if size > BUFEXTRA + // maxexchange_fix_dynamic = 1 if any fix sets its maxexchange dynamically + + maxexchange_atom = atom->avec->maxexchange; + + int nfix = modify->nfix; + Fix **fix = modify->fix; + + maxexchange_fix_dynamic = 0; + for (int i = 0; i < nfix; i++) + if (fix[i]->maxexchange_dynamic) maxexchange_fix_dynamic = 1; +} + +/* ---------------------------------------------------------------------- + set maxexchange based on AtomVec and fixes +------------------------------------------------------------------------- */ + +void Comm::init_exchange() +{ + int nfix = modify->nfix; + Fix **fix = modify->fix; + + int onefix; + maxexchange_fix = 0; + for (int i = 0; i < nfix; i++) { + onefix = fix[i]->maxexchange; + maxexchange_fix = MAX(maxexchange_fix,onefix); + } + + maxexchange = maxexchange_atom + maxexchange_fix; + bufextra = maxexchange + BUFEXTRA; } /* ---------------------------------------------------------------------- diff --git a/src/comm.h b/src/comm.h index 30360b1059..3367051e3c 100644 --- a/src/comm.h +++ b/src/comm.h @@ -38,9 +38,8 @@ class Comm : protected Pointers { // -1 if no recv or send int other_partition_style; // 0 = recv layout dims must be multiple of // my layout dims - int maxexchange_atom; // max contribution to exchange from AtomVec - int maxexchange_fix; // max contribution to exchange from Fixes - int nthreads; // OpenMP threads per MPI process + + int nthreads; // OpenMP threads per MPI process // public settings specific to layout = UNIFORM, NONUNIFORM @@ -130,8 +129,13 @@ class Comm : protected Pointers { int size_reverse; // # of datums in reverse comm int size_border; // # of datums in forward border comm - int maxforward,maxreverse; // max # of datums in forward/reverse comm - int maxexchange; // max # of datums/atom in exchange comm + int maxforward,maxreverse; // max # of datums in forward/reverse comm + int maxexchange; // max size of one exchanged atom + int maxexchange_atom; // contribution to maxexchange from AtomVec + int maxexchange_fix; // static contribution to maxexchange from Fixes + int maxexchange_fix_dynamic; // 1 if a fix has a dynamic contribution + int bufextra; // augment size of send buf for an exchange atom + int gridflag; // option for creating 3d grid int mapflag; // option for mapping procs to 3d grid @@ -147,6 +151,7 @@ class Comm : protected Pointers { int coregrid[3]; // 3d grid of cores within a node int user_coregrid[3]; // user request for cores in each dim + void init_exchange(); int rendezvous_irregular(int, char *, int, int, int *, int (*)(int, char *, int &, int *&, char *&, void *), int, char *&, int, void *, int); diff --git a/src/comm_brick.cpp b/src/comm_brick.cpp index 330551aaed..97114e5734 100644 --- a/src/comm_brick.cpp +++ b/src/comm_brick.cpp @@ -42,8 +42,7 @@ using namespace LAMMPS_NS; #define BUFFACTOR 1.5 -#define BUFMIN 1000 -#define BUFEXTRA 1000 +#define BUFMIN 1024 #define BIG 1.0e20 /* ---------------------------------------------------------------------- */ @@ -110,14 +109,6 @@ void CommBrick::init_buffers() multilo = multihi = NULL; cutghostmulti = NULL; - // bufextra = max size of one exchanged atom - // = allowed overflow of sendbuf in exchange() - // atomvec, fix reset these 2 maxexchange values if needed - // only necessary if their size > BUFEXTRA - - maxexchange = maxexchange_atom + maxexchange_fix; - bufextra = maxexchange + BUFEXTRA; - maxsend = BUFMIN; memory->create(buf_send,maxsend+bufextra,"comm:buf_send"); maxrecv = BUFMIN; @@ -141,6 +132,10 @@ void CommBrick::init() { Comm::init(); + int bufextra_old = bufextra; + init_exchange(); + if (bufextra > bufextra_old) grow_send(maxsend+bufextra,0); + // memory for multi-style communication if (mode == Comm::MULTI && multilo == NULL) { @@ -603,15 +598,14 @@ void CommBrick::exchange() atom->nghost = 0; atom->avec->clear_bonus(); - // insure send buf is large enough for single atom - // bufextra = max size of one atom = allowed overflow of sendbuf - // fixes can change per-atom size requirement on-the-fly + // insure send buf has extra space for a single atom + // only need to reset if a fix can dynamically add to size of single atom - int bufextra_old = bufextra; - maxexchange = maxexchange_atom + maxexchange_fix; - bufextra = maxexchange + BUFEXTRA; - if (bufextra > bufextra_old) - grow_send(maxsend+bufextra,1); + if (maxexchange_fix_dynamic) { + int bufextra_old = bufextra; + init_exchange(); + if (bufextra > bufextra_old) grow_send(maxsend+bufextra,0); + } // subbox bounds for orthogonal or triclinic diff --git a/src/comm_brick.h b/src/comm_brick.h index b3a3a7e094..05268da63e 100644 --- a/src/comm_brick.h +++ b/src/comm_brick.h @@ -74,7 +74,6 @@ class CommBrick : public Comm { double *buf_send; // send buffer for all comm double *buf_recv; // recv buffer for all comm int maxsend,maxrecv; // current size of send/recv buffer - int bufextra; // extra space beyond maxsend in send buffer int smax,rmax; // max size in atoms of single borders send/recv // NOTE: init_buffers is called from a constructor and must not be made virtual diff --git a/src/comm_tiled.cpp b/src/comm_tiled.cpp index d1d625445a..c9f1a63fbc 100644 --- a/src/comm_tiled.cpp +++ b/src/comm_tiled.cpp @@ -32,8 +32,7 @@ using namespace LAMMPS_NS; #define BUFFACTOR 1.5 #define BUFFACTOR 1.5 -#define BUFMIN 1000 -#define BUFEXTRA 1000 +#define BUFMIN 1024 #define EPSILON 1.0e-6 #define DELTA_PROCS 16 @@ -80,14 +79,6 @@ CommTiled::~CommTiled() void CommTiled::init_buffers() { - // bufextra = max size of one exchanged atom - // = allowed overflow of sendbuf in exchange() - // atomvec, fix reset these 2 maxexchange values if needed - // only necessary if their size > BUFEXTRA - - maxexchange = maxexchange_atom + maxexchange_fix; - bufextra = maxexchange + BUFEXTRA; - maxsend = BUFMIN; memory->create(buf_send,maxsend+bufextra,"comm:buf_send"); maxrecv = BUFMIN; @@ -108,6 +99,10 @@ void CommTiled::init() { Comm::init(); + int bufextra_old = bufextra; + init_exchange(); + if (bufextra > bufextra_old) grow_send(maxsend+bufextra,0); + // temporary restrictions if (triclinic) @@ -644,15 +639,14 @@ void CommTiled::exchange() atom->nghost = 0; atom->avec->clear_bonus(); - // insure send buf is large enough for single atom - // bufextra = max size of one atom = allowed overflow of sendbuf - // fixes can change per-atom size requirement on-the-fly + // insure send buf has extra space for a single atom + // only need to reset if a fix can dynamically add to size of single atom - int bufextra_old = bufextra; - maxexchange = maxexchange_atom + maxexchange_fix; - bufextra = maxexchange + BUFEXTRA; - if (bufextra > bufextra_old) - memory->grow(buf_send,maxsend+bufextra,"comm:buf_send"); + if (maxexchange_fix_dynamic) { + int bufextra_old = bufextra; + init_exchange(); + if (bufextra > bufextra_old) grow_send(maxsend+bufextra,1); + } // domain properties used in exchange method and methods it calls // subbox bounds for orthogonal or triclinic diff --git a/src/comm_tiled.h b/src/comm_tiled.h index 13ecbc4b01..679be195aa 100644 --- a/src/comm_tiled.h +++ b/src/comm_tiled.h @@ -87,7 +87,6 @@ class CommTiled : public Comm { double *buf_send; // send buffer for all comm double *buf_recv; // recv buffer for all comm int maxsend,maxrecv; // current size of send/recv buffer - int bufextra; // extra space beyond maxsend in send buffer int smaxone,rmaxone; // max size in atoms of single borders send/recv int smaxall,rmaxall; // max size in atoms of any borders send/recv // for comm to all procs in one swap diff --git a/src/fix.cpp b/src/fix.cpp index 634bc2393d..2a94340842 100644 --- a/src/fix.cpp +++ b/src/fix.cpp @@ -78,6 +78,8 @@ Fix::Fix(LAMMPS *lmp, int /*narg*/, char **arg) : enforce2d_flag = 0; respa_level_support = 0; respa_level = -1; + maxexchange = 0; + maxexchange_dynamic = 0; scalar_flag = vector_flag = array_flag = 0; peratom_flag = local_flag = 0; diff --git a/src/fix.h b/src/fix.h index 7eaff38bd3..f4bf7f9c01 100644 --- a/src/fix.h +++ b/src/fix.h @@ -56,6 +56,8 @@ class Fix : protected Pointers { int enforce2d_flag; // 1 if has enforce2d method int respa_level_support; // 1 if fix supports fix_modify respa int respa_level; // which respa level to apply fix (1-Nrespa) + int maxexchange; // max # of per-atom values for Comm::exchange() + int maxexchange_dynamic; // 1 if fix sets maxexchange dynamically int scalar_flag; // 0/1 if compute_scalar() function exists int vector_flag; // 0/1 if compute_vector() function exists diff --git a/src/fix_neigh_history.cpp b/src/fix_neigh_history.cpp index 207c409596..7405b6d81f 100644 --- a/src/fix_neigh_history.cpp +++ b/src/fix_neigh_history.cpp @@ -42,6 +42,7 @@ FixNeighHistory::FixNeighHistory(LAMMPS *lmp, int narg, char **arg) : restart_peratom = 1; create_attribute = 1; + maxexchange_dynamic = 1; newton_pair = force->newton_pair; @@ -296,11 +297,11 @@ void FixNeighHistory::pre_exchange_onesided() } // set maxpartner = max # of partners of any owned atom - // bump up comm->maxexchange_fix if necessary + // maxexchange = max # of values for any Comm::exchange() atom maxpartner = 0; for (i = 0; i < nlocal_neigh; i++) maxpartner = MAX(maxpartner,npartner[i]); - comm->maxexchange_fix = MAX(comm->maxexchange_fix,(dnum+1)*maxpartner+1); + maxexchange = (dnum+1)*maxpartner + 1; // zero npartner values from previous nlocal_neigh to current nlocal @@ -424,11 +425,11 @@ void FixNeighHistory::pre_exchange_newton() comm->reverse_comm_fix_variable(this); // set maxpartner = max # of partners of any owned atom - // bump up comm->maxexchange_fix if necessary + // maxexchange = max # of values for any Comm::exchange() atom maxpartner = 0; for (i = 0; i < nlocal_neigh; i++) maxpartner = MAX(maxpartner,npartner[i]); - comm->maxexchange_fix = MAX(comm->maxexchange_fix,(dnum+1)*maxpartner+1); + maxexchange = (dnum+1)*maxpartner + 1; // zero npartner values from previous nlocal_neigh to current nlocal @@ -531,11 +532,11 @@ void FixNeighHistory::pre_exchange_no_newton() } // set maxpartner = max # of partners of any owned atom - // bump up comm->maxexchange_fix if necessary + // maxexchange = max # of values for any Comm::exchange() atom maxpartner = 0; for (i = 0; i < nlocal_neigh; i++) maxpartner = MAX(maxpartner,npartner[i]); - comm->maxexchange_fix = MAX(comm->maxexchange_fix,(dnum+1)*maxpartner+1); + maxexchange = (dnum+1)*maxpartner + 1; // zero npartner values from previous nlocal_neigh to current nlocal @@ -796,9 +797,6 @@ void FixNeighHistory::unpack_reverse_comm(int n, int *list, double *buf) int FixNeighHistory::pack_exchange(int i, double *buf) { - // NOTE: how do I know comm buf is big enough if extreme # of touching neighs - // Comm::BUFEXTRA may need to be increased - int m = 0; buf[m++] = npartner[i]; for (int n = 0; n < npartner[i]; n++) { diff --git a/src/fix_store.cpp b/src/fix_store.cpp index 9db65d0987..941132a837 100644 --- a/src/fix_store.cpp +++ b/src/fix_store.cpp @@ -106,6 +106,7 @@ vstore(NULL), astore(NULL), rbuf(NULL) for (int i = 0; i < nlocal; i++) for (int j = 0; j < nvalues; j++) astore[i][j] = 0.0; + maxexchange = nvalues; } } -- GitLab From 5236497932c7b775480123d6e11516158796f035 Mon Sep 17 00:00:00 2001 From: Ellad Tadmor Date: Tue, 9 Jul 2019 18:36:51 -0400 Subject: [PATCH 216/469] Changed 'bohr_per_atu_si' to 'bohr_per_atu_electron_si' --- src/KIM/kim_units.cpp | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/src/KIM/kim_units.cpp b/src/KIM/kim_units.cpp index 40f4917601..45f9b81a35 100644 --- a/src/KIM/kim_units.cpp +++ b/src/KIM/kim_units.cpp @@ -175,7 +175,7 @@ double const nanometer_per_nanosecond_si = nanometer_si/nanosecond_si; // [m/s] nanometer/nanosecond double const centimeter_per_second_si = centimeter_si; // [m/s] centimeter/second -double const bohr_per_atu_si = +double const bohr_per_atu_electron_si = bohr_si/atu_electron_si; // [m/s] bohr/atu /*---------------------- @@ -803,7 +803,7 @@ double get_velocity_conversion_factor(units from_unit_enum, units to_unit_enum) conv[meter_per_second][angstrom_per_femtosecond] = 1.0/angstrom_per_femtosecond_si; conv[meter_per_second][angstrom_per_picosecond] = 1.0/angstrom_per_picosecond_si; conv[meter_per_second][centimeter_per_second] = 1.0/centimeter_per_second_si; - conv[meter_per_second][bohr_per_atu] = 1.0/bohr_per_atu_si; + conv[meter_per_second][bohr_per_atu] = 1.0/bohr_per_atu_electron_si; conv[meter_per_second][micrometer_per_microsecond] = 1.0/micrometer_per_microsecond_si; conv[meter_per_second][nanometer_per_nanosecond] = 1.0/nanometer_per_nanosecond_si; -- GitLab From 39315268e885fba886a0ff30eccc619ffaa64c5f Mon Sep 17 00:00:00 2001 From: Steve Plimpton Date: Tue, 9 Jul 2019 16:53:19 -0600 Subject: [PATCH 217/469] new versions of jacobi() method --- src/math_extra.cpp | 229 +++++++++++++++++++++++++++++++++------------ src/math_extra.h | 9 +- 2 files changed, 175 insertions(+), 63 deletions(-) diff --git a/src/math_extra.cpp b/src/math_extra.cpp index f7e5bb646b..e72b3d3997 100644 --- a/src/math_extra.cpp +++ b/src/math_extra.cpp @@ -13,6 +13,7 @@ /* ---------------------------------------------------------------------- Contributing author: Mike Brown (SNL) + Arno Mayrhofer (DCS Computing), jacobi() functions ------------------------------------------------------------------------- */ #include @@ -95,83 +96,189 @@ int mldivide3(const double m[3][3], const double *v, double *ans) /* ---------------------------------------------------------------------- compute evalues and evectors of 3x3 real symmetric matrix based on Jacobi rotations - adapted from Numerical Recipes jacobi() function + two variants for passing in matrix + + procedure jacobi(S ∈ Rn×n; out e ∈ Rn; out E ∈ Rn×n) + var + i, k, l, m, state ∈ N + s, c, t, p, y, d, r ∈ R + ind ∈ Nn + changed ∈ Ln + ! init e, E, and arrays ind, changed + E := I; state := n + for k := 1 to n do indk := maxind(k); ek := Skk; changedk := true endfor + while state≠0 do ! next rotation + m := 1 ! find index (k,l) of pivot p + for k := 2 to n−1 do + if │Sk indk│ > │Sm indm│ then m := k endif + endfor + k := m; l := indm; p := Skl + ! calculate c = cos φ, s = sin φ + y := (el−ek)/2; d := │y│+√(p2+y2) + r := √(p2+d2); c := d/r; s := p/r; t := p2/d + if y<0 then s := −s; t := −t endif + Skl := 0.0; update(k,−t); update(l,t) + ! rotate rows and columns k and l + for i := 1 to k−1 do rotate(i,k,i,l) endfor + for i := k+1 to l−1 do rotate(k,i,i,l) endfor + for i := l+1 to n do rotate(k,i,l,i) endfor + ! rotate eigenvectors + for i := 1 to n do + ┌ ┐ ┌ ┐┌ ┐ + │Eik│ │c −s││Eik│ + │ │ := │ ││ │ + │Eil│ │s c││Eil│ + └ ┘ └ ┘└ ┘ + endfor + ! rows k, l have changed, update rows indk, indl + indk := maxind(k); indl := maxind(l) + loop + endproc ------------------------------------------------------------------------- */ int jacobi(double matrix[3][3], double *evalues, double evectors[3][3]) { - int i,j,k; - double tresh,theta,tau,t,sm,s,h,g,c,b[3],z[3]; - - for (i = 0; i < 3; i++) { - for (j = 0; j < 3; j++) evectors[i][j] = 0.0; - evectors[i][i] = 1.0; - } - for (i = 0; i < 3; i++) { - b[i] = evalues[i] = matrix[i][i]; - z[i] = 0.0; - } - - for (int iter = 1; iter <= MAXJACOBI; iter++) { - sm = 0.0; - for (i = 0; i < 2; i++) - for (j = i+1; j < 3; j++) - sm += fabs(matrix[i][j]); - if (sm == 0.0) return 0; - - if (iter < 4) tresh = 0.2*sm/(3*3); - else tresh = 0.0; - - for (i = 0; i < 2; i++) { - for (j = i+1; j < 3; j++) { - g = 100.0*fabs(matrix[i][j]); - if (iter > 4 && fabs(evalues[i])+g == fabs(evalues[i]) - && fabs(evalues[j])+g == fabs(evalues[j])) - matrix[i][j] = 0.0; - else if (fabs(matrix[i][j]) > tresh) { - h = evalues[j]-evalues[i]; - if (fabs(h)+g == fabs(h)) t = (matrix[i][j])/h; - else { - theta = 0.5*h/(matrix[i][j]); - t = 1.0/(fabs(theta)+sqrt(1.0+theta*theta)); - if (theta < 0.0) t = -t; - } - c = 1.0/sqrt(1.0+t*t); - s = t*c; - tau = s/(1.0+c); - h = t*matrix[i][j]; - z[i] -= h; - z[j] += h; - evalues[i] -= h; - evalues[j] += h; - matrix[i][j] = 0.0; - for (k = 0; k < i; k++) rotate(matrix,k,i,k,j,s,tau); - for (k = i+1; k < j; k++) rotate(matrix,i,k,k,j,s,tau); - for (k = j+1; k < 3; k++) rotate(matrix,i,k,j,k,s,tau); - for (k = 0; k < 3; k++) rotate(evectors,k,i,k,j,s,tau); + evectors[0][0] = 1.0; evectors[0][1] = 0.0; evectors[0][2] = 0.0; + evectors[1][0] = 0.0; evectors[1][1] = 1.0; evectors[1][2] = 0.0; + evectors[2][0] = 0.0; evectors[2][1] = 0.0; evectors[2][2] = 1.0; + evalues[0] = 0.0; evalues[1] = 0.0; evalues[2] = 0.0; + double threshold = 0.0; + + for (int i = 0; i < 3; i++) + for (int j = i; j < 3; j++) + threshold += fabs(matrix[i][j]); + + if (threshold < 1.0e-200) return 0; + threshold *= 1.0e-12; + int state = 2; + bool changed[3] = {true, true, true}; + + int iteration = 0; + while (state > 0 && iteration < MAXJACOBI) { + for (int k = 0; k < 2; k++) { + for (int l = k+1; l < 3; l++) { + const double p = matrix[k][l]; + const double y = (matrix[l][l]-matrix[k][k])*0.5; + const double d = fabs(y)+sqrt(p*p + y*y); + const double r = sqrt(p*p + d*d); + const double c = r > threshold ? d/r : 1.0; + double s = r > threshold ? p/r : 0.0; + double t = d > threshold ? p*p/d : 0.0; + if (y < 0.0) { + s *= -1.0; + t *= -1.0; } + matrix[k][l] = 0.0; + update_eigenvalue(matrix[k][k], changed[k], state, -t, threshold); + update_eigenvalue(matrix[l][l], changed[l], state, t, threshold); + for (int i = 0; i < k; i++) + rotate(matrix[i][k], matrix[i][l],c,s); + for (int i = k+1; i < l; i++) + rotate(matrix[k][i], matrix[i][l],c,s); + for (int i = l+1; i < 3; i++) + rotate(matrix[k][i], matrix[l][i],c,s); + for (int i = 0; i < 3; i++) + rotate(evectors[i][k], evectors[i][l],c,s); } } + iteration++; + } + + for (int i = 0; i < 3; i++) + evalues[i] = matrix[i][i]; - for (i = 0; i < 3; i++) { - evalues[i] = b[i] += z[i]; - z[i] = 0.0; + if (iteration == MAXJACOBI) return 1; + return 0; +} + +int jacobi(double **matrix, double *evalues, double **evectors) +{ + evectors[0][0] = 1.0; evectors[0][1] = 0.0; evectors[0][2] = 0.0; + evectors[1][0] = 0.0; evectors[1][1] = 1.0; evectors[1][2] = 0.0; + evectors[2][0] = 0.0; evectors[2][1] = 0.0; evectors[2][2] = 1.0; + evalues[0] = 0.0; evalues[1] = 0.0; evalues[2] = 0.0; + double threshold = 0.0; + + for (int i = 0; i < 3; i++) + for (int j = i; j < 3; j++) + threshold += fabs(matrix[i][j]); + + if (threshold < 1.0e-200) return 0; + threshold *= 1.0e-12; + int state = 2; + bool changed[3] = {true, true, true}; + + int iteration = 0; + while (state > 0 && iteration < MAXJACOBI) { + for (int k = 0; k < 2; k++) { + for (int l = k+1; l < 3; l++) { + const double p = matrix[k][l]; + const double y = (matrix[l][l]-matrix[k][k])*0.5; + const double d = fabs(y)+sqrt(p*p + y*y); + const double r = sqrt(p*p + d*d); + const double c = r > threshold ? d/r : 1.0; + double s = r > threshold ? p/r : 0.0; + double t = d > threshold ? p*p/d : 0.0; + if (y < 0.0) { + s *= -1.0; + t *= -1.0; + } + matrix[k][l] = 0.0; + update_eigenvalue(matrix[k][k], changed[k], state, -t, threshold); + update_eigenvalue(matrix[l][l], changed[l], state, t, threshold); + for (int i = 0; i < k; i++) + rotate(matrix[i][k], matrix[i][l],c,s); + for (int i = k+1; i < l; i++) + rotate(matrix[k][i], matrix[i][l],c,s); + for (int i = l+1; i < 3; i++) + rotate(matrix[k][i], matrix[l][i],c,s); + for (int i = 0; i < 3; i++) + rotate(evectors[i][k], evectors[i][l],c,s); + } } + iteration++; } - return 1; + + for (int i = 0; i < 3; i++) + evalues[i] = matrix[i][i]; + + if (iteration == MAXJACOBI) return 1; + return 0; } /* ---------------------------------------------------------------------- - perform a single Jacobi rotation + perform a single Jacobi rotation of Sij, Skl + ┌ ┐ ┌ ┐┌ ┐ + │Skl│ │c −s││Skl│ + │ │ := │ ││ │ + │Sij│ │s c││Sij│ + └ ┘ └ ┘└ ┘ ------------------------------------------------------------------------- */ -void rotate(double matrix[3][3], int i, int j, int k, int l, - double s, double tau) +void rotate(double &matrix_kl, double &matrix_ij, + const double c, const double s) { - double g = matrix[i][j]; - double h = matrix[k][l]; - matrix[i][j] = g-s*(h+g*tau); - matrix[k][l] = h+s*(g-h*tau); + const double tmp_kl = matrix_kl; + matrix_kl = c*matrix_kl - s*matrix_ij; + matrix_ij = s*tmp_kl + c*matrix_ij; +} + +/* ---------------------------------------------------------------------- + update eigenvalue and its status +------------------------------------------------------------------------- */ + +void update_eigenvalue(double &eigenvalue, bool &changed, int &state, + const double t, const double threshold) +{ + eigenvalue += t; + + if (changed && fabs(t) < threshold) { + changed = false; + state--; + } else if (!changed && fabs(t) > threshold) { + changed = true; + state++; + } } /* ---------------------------------------------------------------------- diff --git a/src/math_extra.h b/src/math_extra.h index 85f57224cf..2befc7ee97 100644 --- a/src/math_extra.h +++ b/src/math_extra.h @@ -77,9 +77,14 @@ namespace MathExtra { void write3(const double mat[3][3]); int mldivide3(const double mat[3][3], const double *vec, double *ans); + int jacobi(double matrix[3][3], double *evalues, double evectors[3][3]); - void rotate(double matrix[3][3], int i, int j, int k, int l, - double s, double tau); + int jacobi(double **matrix, double *evalues, double **evectors); + void rotate(double &matrix_kl, double &matrix_ij, + const double c, const double s); + void update_eigenvalue(double &eigenvalue, bool &changed, int &state, + const double t, const double threshold); + void richardson(double *q, double *m, double *w, double *moments, double dtq); void no_squish_rotate(int k, double *p, double *q, double *inertia, double dt); -- GitLab From d6ed4ee1b12489d126ca35d0005c59c1baf9a93c Mon Sep 17 00:00:00 2001 From: Steve Plimpton Date: Tue, 9 Jul 2019 17:34:54 -0600 Subject: [PATCH 218/469] add missing term to per-atom stress --- src/MANYBODY/pair_bop.cpp | 3 +++ 1 file changed, 3 insertions(+) diff --git a/src/MANYBODY/pair_bop.cpp b/src/MANYBODY/pair_bop.cpp index ac157e071c..39f48cd05e 100644 --- a/src/MANYBODY/pair_bop.cpp +++ b/src/MANYBODY/pair_bop.cpp @@ -3740,6 +3740,9 @@ double PairBOP::sigmaBo(int itmp, int jtmp) if(sigma_f[iij]==0.5&&sigma_k[iij]==0.0) { sigB=dsigB1; pp1=2.0*betaS_ij; + xtmp[0]=x[bt_j][0]-x[bt_i][0]; + xtmp[1]=x[bt_j][1]-x[bt_i][1]; + xtmp[2]=x[bt_j][2]-x[bt_i][2]; for(pp=0;pp<3;pp++) { bt_sg[m].dSigB[pp]=dsigB2*bt_sg[m].dSigB1[pp]; } -- GitLab From 93748a18ae4fd370e43244fed4c5e3b07eae4e4f Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Wed, 10 Jul 2019 00:22:03 -0400 Subject: [PATCH 219/469] further clean up of AtomVec classes after merging PR #1552 to master --- src/DIPOLE/atom_vec_dipole.cpp | 2 -- src/KOKKOS/atom_vec_angle_kokkos.cpp | 2 -- src/KOKKOS/atom_vec_atomic_kokkos.cpp | 2 -- src/KOKKOS/atom_vec_bond_kokkos.cpp | 2 -- src/KOKKOS/atom_vec_charge_kokkos.cpp | 2 -- src/KOKKOS/atom_vec_dpd_kokkos.cpp | 2 -- src/KOKKOS/atom_vec_full_kokkos.cpp | 2 -- src/KOKKOS/atom_vec_hybrid_kokkos.cpp | 2 -- src/KOKKOS/atom_vec_molecular_kokkos.cpp | 2 -- src/KOKKOS/atom_vec_sphere_kokkos.cpp | 2 -- src/MOLECULE/atom_vec_angle.cpp | 2 -- src/MOLECULE/atom_vec_bond.cpp | 2 -- src/MOLECULE/atom_vec_full.cpp | 2 -- src/MOLECULE/atom_vec_molecular.cpp | 2 -- src/MOLECULE/atom_vec_template.cpp | 2 -- src/PERI/atom_vec_peri.cpp | 2 -- src/SPIN/atom_vec_spin.cpp | 2 -- src/USER-AWPMD/atom_vec_wavepacket.cpp | 2 -- src/USER-DPD/atom_vec_dpd.cpp | 2 -- src/USER-EFF/atom_vec_electron.cpp | 3 +-- src/USER-MESO/atom_vec_edpd.cpp | 4 +--- src/USER-MESO/atom_vec_mdpd.cpp | 4 +--- src/USER-MESO/atom_vec_tdpd.cpp | 8 +++----- src/USER-SMD/atom_vec_smd.cpp | 4 +--- src/USER-SPH/atom_vec_meso.cpp | 4 +--- src/atom_vec.cpp | 1 - src/atom_vec_atomic.cpp | 2 -- src/atom_vec_body.cpp | 1 - src/atom_vec_charge.cpp | 2 -- src/atom_vec_ellipsoid.cpp | 1 - src/atom_vec_hybrid.cpp | 2 -- src/atom_vec_line.cpp | 1 - src/atom_vec_sphere.cpp | 1 - src/atom_vec_tri.cpp | 1 - 34 files changed, 8 insertions(+), 69 deletions(-) diff --git a/src/DIPOLE/atom_vec_dipole.cpp b/src/DIPOLE/atom_vec_dipole.cpp index 945732f74b..a3ff3fd0f5 100644 --- a/src/DIPOLE/atom_vec_dipole.cpp +++ b/src/DIPOLE/atom_vec_dipole.cpp @@ -13,11 +13,9 @@ #include "atom_vec_dipole.h" #include -#include #include "atom.h" #include "comm.h" #include "domain.h" -#include "force.h" #include "modify.h" #include "fix.h" #include "memory.h" diff --git a/src/KOKKOS/atom_vec_angle_kokkos.cpp b/src/KOKKOS/atom_vec_angle_kokkos.cpp index b8f5634fa0..736e1c1fca 100644 --- a/src/KOKKOS/atom_vec_angle_kokkos.cpp +++ b/src/KOKKOS/atom_vec_angle_kokkos.cpp @@ -12,11 +12,9 @@ ------------------------------------------------------------------------- */ #include "atom_vec_angle_kokkos.h" -#include #include "atom_kokkos.h" #include "comm_kokkos.h" #include "domain.h" -#include "force.h" #include "modify.h" #include "fix.h" #include "atom_masks.h" diff --git a/src/KOKKOS/atom_vec_atomic_kokkos.cpp b/src/KOKKOS/atom_vec_atomic_kokkos.cpp index f65f34419a..4fec5740d6 100644 --- a/src/KOKKOS/atom_vec_atomic_kokkos.cpp +++ b/src/KOKKOS/atom_vec_atomic_kokkos.cpp @@ -12,11 +12,9 @@ ------------------------------------------------------------------------- */ #include "atom_vec_atomic_kokkos.h" -#include #include "atom_kokkos.h" #include "comm_kokkos.h" #include "domain.h" -#include "force.h" #include "modify.h" #include "fix.h" #include "atom_masks.h" diff --git a/src/KOKKOS/atom_vec_bond_kokkos.cpp b/src/KOKKOS/atom_vec_bond_kokkos.cpp index c36b084637..74c05a506c 100644 --- a/src/KOKKOS/atom_vec_bond_kokkos.cpp +++ b/src/KOKKOS/atom_vec_bond_kokkos.cpp @@ -12,11 +12,9 @@ ------------------------------------------------------------------------- */ #include "atom_vec_bond_kokkos.h" -#include #include "atom_kokkos.h" #include "comm_kokkos.h" #include "domain.h" -#include "force.h" #include "modify.h" #include "fix.h" #include "atom_masks.h" diff --git a/src/KOKKOS/atom_vec_charge_kokkos.cpp b/src/KOKKOS/atom_vec_charge_kokkos.cpp index 631c4b237c..3f26b1e9ea 100644 --- a/src/KOKKOS/atom_vec_charge_kokkos.cpp +++ b/src/KOKKOS/atom_vec_charge_kokkos.cpp @@ -12,11 +12,9 @@ ------------------------------------------------------------------------- */ #include "atom_vec_charge_kokkos.h" -#include #include "atom_kokkos.h" #include "comm_kokkos.h" #include "domain.h" -#include "force.h" #include "modify.h" #include "fix.h" #include "atom_masks.h" diff --git a/src/KOKKOS/atom_vec_dpd_kokkos.cpp b/src/KOKKOS/atom_vec_dpd_kokkos.cpp index e7123037ca..4162b71374 100644 --- a/src/KOKKOS/atom_vec_dpd_kokkos.cpp +++ b/src/KOKKOS/atom_vec_dpd_kokkos.cpp @@ -12,11 +12,9 @@ ------------------------------------------------------------------------- */ #include "atom_vec_dpd_kokkos.h" -#include #include "atom_kokkos.h" #include "comm_kokkos.h" #include "domain.h" -#include "force.h" #include "modify.h" #include "fix.h" #include "atom_masks.h" diff --git a/src/KOKKOS/atom_vec_full_kokkos.cpp b/src/KOKKOS/atom_vec_full_kokkos.cpp index 4b6e413b64..1fdbcbec8c 100644 --- a/src/KOKKOS/atom_vec_full_kokkos.cpp +++ b/src/KOKKOS/atom_vec_full_kokkos.cpp @@ -12,11 +12,9 @@ ------------------------------------------------------------------------- */ #include "atom_vec_full_kokkos.h" -#include #include "atom_kokkos.h" #include "comm_kokkos.h" #include "domain.h" -#include "force.h" #include "modify.h" #include "fix.h" #include "atom_masks.h" diff --git a/src/KOKKOS/atom_vec_hybrid_kokkos.cpp b/src/KOKKOS/atom_vec_hybrid_kokkos.cpp index 630648b3a6..318e79d955 100644 --- a/src/KOKKOS/atom_vec_hybrid_kokkos.cpp +++ b/src/KOKKOS/atom_vec_hybrid_kokkos.cpp @@ -12,11 +12,9 @@ ------------------------------------------------------------------------- */ #include "atom_vec_hybrid_kokkos.h" -#include #include #include "atom_kokkos.h" #include "domain.h" -#include "force.h" #include "modify.h" #include "fix.h" #include "memory_kokkos.h" diff --git a/src/KOKKOS/atom_vec_molecular_kokkos.cpp b/src/KOKKOS/atom_vec_molecular_kokkos.cpp index 8790f0bdbc..f3b4ae98ca 100644 --- a/src/KOKKOS/atom_vec_molecular_kokkos.cpp +++ b/src/KOKKOS/atom_vec_molecular_kokkos.cpp @@ -12,13 +12,11 @@ ------------------------------------------------------------------------- */ #include "atom_vec_molecular_kokkos.h" -#include #include "atom_kokkos.h" #include "comm_kokkos.h" #include "domain.h" #include "modify.h" #include "fix.h" -#include "force.h" #include "atom_masks.h" #include "memory_kokkos.h" #include "error.h" diff --git a/src/KOKKOS/atom_vec_sphere_kokkos.cpp b/src/KOKKOS/atom_vec_sphere_kokkos.cpp index 0f69cc9c5a..d93b98a4b0 100644 --- a/src/KOKKOS/atom_vec_sphere_kokkos.cpp +++ b/src/KOKKOS/atom_vec_sphere_kokkos.cpp @@ -13,14 +13,12 @@ #include "atom_vec_sphere_kokkos.h" #include -#include #include #include "atom_kokkos.h" #include "atom_masks.h" #include "comm_kokkos.h" #include "domain.h" #include "modify.h" -#include "force.h" #include "fix.h" #include "fix_adapt.h" #include "math_const.h" diff --git a/src/MOLECULE/atom_vec_angle.cpp b/src/MOLECULE/atom_vec_angle.cpp index c8053266ca..b6f5a013cb 100644 --- a/src/MOLECULE/atom_vec_angle.cpp +++ b/src/MOLECULE/atom_vec_angle.cpp @@ -12,11 +12,9 @@ ------------------------------------------------------------------------- */ #include "atom_vec_angle.h" -#include #include "atom.h" #include "comm.h" #include "domain.h" -#include "force.h" #include "modify.h" #include "fix.h" #include "memory.h" diff --git a/src/MOLECULE/atom_vec_bond.cpp b/src/MOLECULE/atom_vec_bond.cpp index 0d267d10cc..b9d4177b4f 100644 --- a/src/MOLECULE/atom_vec_bond.cpp +++ b/src/MOLECULE/atom_vec_bond.cpp @@ -12,11 +12,9 @@ ------------------------------------------------------------------------- */ #include "atom_vec_bond.h" -#include #include "atom.h" #include "comm.h" #include "domain.h" -#include "force.h" #include "modify.h" #include "fix.h" #include "memory.h" diff --git a/src/MOLECULE/atom_vec_full.cpp b/src/MOLECULE/atom_vec_full.cpp index 167edde18f..e71e23a661 100644 --- a/src/MOLECULE/atom_vec_full.cpp +++ b/src/MOLECULE/atom_vec_full.cpp @@ -12,11 +12,9 @@ ------------------------------------------------------------------------- */ #include "atom_vec_full.h" -#include #include "atom.h" #include "comm.h" #include "domain.h" -#include "force.h" #include "modify.h" #include "fix.h" #include "memory.h" diff --git a/src/MOLECULE/atom_vec_molecular.cpp b/src/MOLECULE/atom_vec_molecular.cpp index 5ccf5529b4..1bafb6dc43 100644 --- a/src/MOLECULE/atom_vec_molecular.cpp +++ b/src/MOLECULE/atom_vec_molecular.cpp @@ -12,11 +12,9 @@ ------------------------------------------------------------------------- */ #include "atom_vec_molecular.h" -#include #include "atom.h" #include "comm.h" #include "domain.h" -#include "force.h" #include "modify.h" #include "fix.h" #include "memory.h" diff --git a/src/MOLECULE/atom_vec_template.cpp b/src/MOLECULE/atom_vec_template.cpp index ae31870fd0..27c6ab4183 100644 --- a/src/MOLECULE/atom_vec_template.cpp +++ b/src/MOLECULE/atom_vec_template.cpp @@ -12,10 +12,8 @@ ------------------------------------------------------------------------- */ #include "atom_vec_template.h" -#include #include "atom.h" #include "molecule.h" -#include "force.h" #include "comm.h" #include "domain.h" #include "modify.h" diff --git a/src/PERI/atom_vec_peri.cpp b/src/PERI/atom_vec_peri.cpp index 0829dfb1c0..47b88995b8 100644 --- a/src/PERI/atom_vec_peri.cpp +++ b/src/PERI/atom_vec_peri.cpp @@ -17,12 +17,10 @@ #include "atom_vec_peri.h" #include -#include #include #include "atom.h" #include "comm.h" #include "domain.h" -#include "force.h" #include "modify.h" #include "fix.h" #include "citeme.h" diff --git a/src/SPIN/atom_vec_spin.cpp b/src/SPIN/atom_vec_spin.cpp index 345a2d6c04..f5560b6ee9 100644 --- a/src/SPIN/atom_vec_spin.cpp +++ b/src/SPIN/atom_vec_spin.cpp @@ -25,14 +25,12 @@ #include "atom_vec_spin.h" #include -#include #include #include "atom.h" #include "comm.h" #include "domain.h" #include "error.h" #include "fix.h" -#include "force.h" #include "memory.h" #include "modify.h" #include "utils.h" diff --git a/src/USER-AWPMD/atom_vec_wavepacket.cpp b/src/USER-AWPMD/atom_vec_wavepacket.cpp index bafd172254..c12798688e 100644 --- a/src/USER-AWPMD/atom_vec_wavepacket.cpp +++ b/src/USER-AWPMD/atom_vec_wavepacket.cpp @@ -17,13 +17,11 @@ #include "atom_vec_wavepacket.h" #include -#include #include #include "atom.h" #include "comm.h" #include "domain.h" #include "modify.h" -#include "force.h" #include "fix.h" #include "memory.h" #include "error.h" diff --git a/src/USER-DPD/atom_vec_dpd.cpp b/src/USER-DPD/atom_vec_dpd.cpp index 2aef55ff9f..bf11840d1e 100644 --- a/src/USER-DPD/atom_vec_dpd.cpp +++ b/src/USER-DPD/atom_vec_dpd.cpp @@ -15,12 +15,10 @@ Contributing author: James Larentzos (U.S. Army Research Laboratory) ------------------------------------------------------------------------- */ -#include #include "atom_vec_dpd.h" #include "atom.h" #include "comm.h" #include "domain.h" -#include "force.h" #include "modify.h" #include "fix.h" #include "memory.h" diff --git a/src/USER-EFF/atom_vec_electron.cpp b/src/USER-EFF/atom_vec_electron.cpp index cca71545f4..707a75c7c1 100644 --- a/src/USER-EFF/atom_vec_electron.cpp +++ b/src/USER-EFF/atom_vec_electron.cpp @@ -15,9 +15,8 @@ Contributing author: Andres Jaramillo-Botero (Caltech) ------------------------------------------------------------------------- */ -#include -#include #include "atom_vec_electron.h" +#include #include "atom.h" #include "comm.h" #include "domain.h" diff --git a/src/USER-MESO/atom_vec_edpd.cpp b/src/USER-MESO/atom_vec_edpd.cpp index ff8515abc6..dccc8b9efa 100644 --- a/src/USER-MESO/atom_vec_edpd.cpp +++ b/src/USER-MESO/atom_vec_edpd.cpp @@ -10,13 +10,11 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include -#include #include "atom_vec_edpd.h" +#include #include "atom.h" #include "comm.h" #include "domain.h" -#include "force.h" #include "modify.h" #include "fix.h" #include "update.h" diff --git a/src/USER-MESO/atom_vec_mdpd.cpp b/src/USER-MESO/atom_vec_mdpd.cpp index 965891a283..0aa6aedcee 100644 --- a/src/USER-MESO/atom_vec_mdpd.cpp +++ b/src/USER-MESO/atom_vec_mdpd.cpp @@ -11,13 +11,11 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include -#include #include "atom_vec_mdpd.h" +#include #include "atom.h" #include "comm.h" #include "domain.h" -#include "force.h" #include "modify.h" #include "fix.h" #include "update.h" diff --git a/src/USER-MESO/atom_vec_tdpd.cpp b/src/USER-MESO/atom_vec_tdpd.cpp index f19758f884..278baa2024 100644 --- a/src/USER-MESO/atom_vec_tdpd.cpp +++ b/src/USER-MESO/atom_vec_tdpd.cpp @@ -11,12 +11,10 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include -#include #include "atom_vec_tdpd.h" +#include #include "atom.h" #include "comm.h" -#include "force.h" #include "domain.h" #include "modify.h" #include "fix.h" @@ -65,7 +63,7 @@ void AtomVecTDPD::process_args(int narg, char **arg) { if (narg < 1) error->all(FLERR,"Invalid atom_style tdpd command"); - atom->cc_species = force->inumeric(FLERR,arg[0]); + atom->cc_species = utils::inumeric(FLERR,arg[0],false,lmp); cc_species = atom->cc_species; // reset sizes that depend on cc_species @@ -801,7 +799,7 @@ void AtomVecTDPD::data_atom(double *coord, imageint imagetmp, char **values) x[nlocal][2] = coord[2]; for(int k = 0; k < cc_species; k++) - cc[nlocal][k] = atof( values[5+k] ); + cc[nlocal][k] = utils::numeric(FLERR,values[5+k],true,lmp); image[nlocal] = imagetmp; diff --git a/src/USER-SMD/atom_vec_smd.cpp b/src/USER-SMD/atom_vec_smd.cpp index 278652bf43..5cc411a832 100644 --- a/src/USER-SMD/atom_vec_smd.cpp +++ b/src/USER-SMD/atom_vec_smd.cpp @@ -22,15 +22,13 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ +#include "atom_vec_smd.h" #include -#include #include -#include "atom_vec_smd.h" #include "atom.h" #include "comm.h" #include "domain.h" #include "modify.h" -#include "force.h" #include "fix.h" #include "fix_adapt.h" #include "math_const.h" diff --git a/src/USER-SPH/atom_vec_meso.cpp b/src/USER-SPH/atom_vec_meso.cpp index 0960141ae2..59e6638f16 100644 --- a/src/USER-SPH/atom_vec_meso.cpp +++ b/src/USER-SPH/atom_vec_meso.cpp @@ -11,13 +11,11 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include -#include #include "atom_vec_meso.h" +#include #include "atom.h" #include "comm.h" #include "domain.h" -#include "force.h" #include "modify.h" #include "fix.h" #include "memory.h" diff --git a/src/atom_vec.cpp b/src/atom_vec.cpp index 146a503221..1ea085b869 100644 --- a/src/atom_vec.cpp +++ b/src/atom_vec.cpp @@ -13,7 +13,6 @@ #include "atom_vec.h" #include -#include #include "atom.h" #include "force.h" #include "domain.h" diff --git a/src/atom_vec_atomic.cpp b/src/atom_vec_atomic.cpp index f1583ab8cc..3cf037f182 100644 --- a/src/atom_vec_atomic.cpp +++ b/src/atom_vec_atomic.cpp @@ -12,11 +12,9 @@ ------------------------------------------------------------------------- */ #include "atom_vec_atomic.h" -#include #include "atom.h" #include "comm.h" #include "domain.h" -#include "force.h" #include "modify.h" #include "fix.h" #include "memory.h" diff --git a/src/atom_vec_body.cpp b/src/atom_vec_body.cpp index 622b698bd9..53ed708c4e 100644 --- a/src/atom_vec_body.cpp +++ b/src/atom_vec_body.cpp @@ -12,7 +12,6 @@ ------------------------------------------------------------------------- */ #include "atom_vec_body.h" -#include #include #include #include "my_pool_chunk.h" diff --git a/src/atom_vec_charge.cpp b/src/atom_vec_charge.cpp index da863f0949..923d892acd 100644 --- a/src/atom_vec_charge.cpp +++ b/src/atom_vec_charge.cpp @@ -12,11 +12,9 @@ ------------------------------------------------------------------------- */ #include "atom_vec_charge.h" -#include #include "atom.h" #include "comm.h" #include "domain.h" -#include "force.h" #include "modify.h" #include "fix.h" #include "memory.h" diff --git a/src/atom_vec_ellipsoid.cpp b/src/atom_vec_ellipsoid.cpp index 44cd818c9d..586e6a80ff 100644 --- a/src/atom_vec_ellipsoid.cpp +++ b/src/atom_vec_ellipsoid.cpp @@ -16,7 +16,6 @@ ------------------------------------------------------------------------- */ #include "atom_vec_ellipsoid.h" -#include #include #include "math_extra.h" #include "atom.h" diff --git a/src/atom_vec_hybrid.cpp b/src/atom_vec_hybrid.cpp index 25c85b2e3d..9ad07b9032 100644 --- a/src/atom_vec_hybrid.cpp +++ b/src/atom_vec_hybrid.cpp @@ -12,11 +12,9 @@ ------------------------------------------------------------------------- */ #include "atom_vec_hybrid.h" -#include #include #include "atom.h" #include "domain.h" -#include "force.h" #include "modify.h" #include "fix.h" #include "memory.h" diff --git a/src/atom_vec_line.cpp b/src/atom_vec_line.cpp index f9feb9b046..30736c02c9 100644 --- a/src/atom_vec_line.cpp +++ b/src/atom_vec_line.cpp @@ -13,7 +13,6 @@ #include "atom_vec_line.h" #include -#include #include #include "atom.h" #include "comm.h" diff --git a/src/atom_vec_sphere.cpp b/src/atom_vec_sphere.cpp index 1defcf8d01..9d52d005ba 100644 --- a/src/atom_vec_sphere.cpp +++ b/src/atom_vec_sphere.cpp @@ -12,7 +12,6 @@ ------------------------------------------------------------------------- */ #include "atom_vec_sphere.h" -#include #include #include "atom.h" #include "comm.h" diff --git a/src/atom_vec_tri.cpp b/src/atom_vec_tri.cpp index 8835255591..640e0fcb34 100644 --- a/src/atom_vec_tri.cpp +++ b/src/atom_vec_tri.cpp @@ -13,7 +13,6 @@ #include "atom_vec_tri.h" #include -#include #include #include "math_extra.h" #include "atom.h" -- GitLab From 054ff97a5168830fbc6cda3fedcb1ad1f4bdf0aa Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Wed, 10 Jul 2019 00:27:31 -0400 Subject: [PATCH 220/469] replace ATOTAGINT() calls with utils::tnumeric() in AtomVec classes --- src/DIPOLE/atom_vec_dipole.cpp | 2 +- src/KOKKOS/atom_vec_dpd_kokkos.cpp | 2 +- src/KOKKOS/atom_vec_hybrid_kokkos.cpp | 2 +- src/KOKKOS/atom_vec_sphere_kokkos.cpp | 2 +- src/MOLECULE/atom_vec_angle.cpp | 6 +++--- src/MOLECULE/atom_vec_bond.cpp | 6 +++--- src/MOLECULE/atom_vec_full.cpp | 6 +++--- src/MOLECULE/atom_vec_molecular.cpp | 6 +++--- src/MOLECULE/atom_vec_template.cpp | 6 +++--- src/PERI/atom_vec_peri.cpp | 2 +- src/SPIN/atom_vec_spin.cpp | 2 +- src/USER-AWPMD/atom_vec_wavepacket.cpp | 2 +- src/USER-DPD/atom_vec_dpd.cpp | 2 +- src/USER-EFF/atom_vec_electron.cpp | 2 +- src/USER-MESO/atom_vec_edpd.cpp | 2 +- src/USER-MESO/atom_vec_mdpd.cpp | 2 +- src/USER-MESO/atom_vec_tdpd.cpp | 2 +- src/USER-SMD/atom_vec_smd.cpp | 4 ++-- src/USER-SPH/atom_vec_meso.cpp | 2 +- src/atom_vec_atomic.cpp | 2 +- src/atom_vec_body.cpp | 2 +- src/atom_vec_charge.cpp | 2 +- src/atom_vec_ellipsoid.cpp | 2 +- src/atom_vec_hybrid.cpp | 2 +- src/atom_vec_line.cpp | 6 +++--- src/atom_vec_sphere.cpp | 2 +- src/atom_vec_tri.cpp | 6 +++--- 27 files changed, 42 insertions(+), 42 deletions(-) diff --git a/src/DIPOLE/atom_vec_dipole.cpp b/src/DIPOLE/atom_vec_dipole.cpp index 47fff1d4c5..a6f454dc98 100644 --- a/src/DIPOLE/atom_vec_dipole.cpp +++ b/src/DIPOLE/atom_vec_dipole.cpp @@ -781,7 +781,7 @@ void AtomVecDipole::data_atom(double *coord, imageint imagetmp, char **values) int nlocal = atom->nlocal; if (nlocal == nmax) grow(0); - tag[nlocal] = ATOTAGINT(values[0]); + tag[nlocal] = utils::tnumeric(FLERR,values[0],true,lmp); type[nlocal] = utils::inumeric(FLERR,values[1],true,lmp); if (type[nlocal] <= 0 || type[nlocal] > atom->ntypes) error->one(FLERR,"Invalid atom type in Atoms section of data file"); diff --git a/src/KOKKOS/atom_vec_dpd_kokkos.cpp b/src/KOKKOS/atom_vec_dpd_kokkos.cpp index 93ca976892..317914e4f8 100644 --- a/src/KOKKOS/atom_vec_dpd_kokkos.cpp +++ b/src/KOKKOS/atom_vec_dpd_kokkos.cpp @@ -1724,7 +1724,7 @@ void AtomVecDPDKokkos::data_atom(double *coord, tagint imagetmp, int nlocal = atom->nlocal; if (nlocal == nmax) grow(0); - h_tag[nlocal] = ATOTAGINT(values[0]); + h_tag[nlocal] = utils::tnumeric(FLERR,values[0],true,lmp); h_type[nlocal] = utils::inumeric(FLERR,values[1],true,lmp); if (type[nlocal] <= 0 || type[nlocal] > atom->ntypes) error->one(FLERR,"Invalid atom type in Atoms section of data file"); diff --git a/src/KOKKOS/atom_vec_hybrid_kokkos.cpp b/src/KOKKOS/atom_vec_hybrid_kokkos.cpp index 54dd89bfb3..c4dd90ce05 100644 --- a/src/KOKKOS/atom_vec_hybrid_kokkos.cpp +++ b/src/KOKKOS/atom_vec_hybrid_kokkos.cpp @@ -976,7 +976,7 @@ void AtomVecHybridKokkos::data_atom(double *coord, imageint imagetmp, char **val int nlocal = atom->nlocal; if (nlocal == nmax) grow(0); - h_tag[nlocal] = ATOTAGINT(values[0]); + h_tag[nlocal] = utils::tnumeric(FLERR,values[0],true,lmp); h_type[nlocal] = utils::inumeric(FLERR,values[1],true,lmp); if (h_type[nlocal] <= 0 || h_type[nlocal] > atom->ntypes) error->one(FLERR,"Invalid atom h_type in Atoms section of data file"); diff --git a/src/KOKKOS/atom_vec_sphere_kokkos.cpp b/src/KOKKOS/atom_vec_sphere_kokkos.cpp index bc72bcbf5e..3b64ceeb42 100644 --- a/src/KOKKOS/atom_vec_sphere_kokkos.cpp +++ b/src/KOKKOS/atom_vec_sphere_kokkos.cpp @@ -2549,7 +2549,7 @@ void AtomVecSphereKokkos::data_atom(double *coord, imageint imagetmp, char **val int nlocal = atom->nlocal; if (nlocal == nmax) grow(0); - tag[nlocal] = ATOTAGINT(values[0]); + tag[nlocal] = utils::tnumeric(FLERR,values[0],true,lmp); type[nlocal] = utils::inumeric(FLERR,values[1],true,lmp); if (type[nlocal] <= 0 || type[nlocal] > atom->ntypes) error->one(FLERR,"Invalid atom type in Atoms section of data file"); diff --git a/src/MOLECULE/atom_vec_angle.cpp b/src/MOLECULE/atom_vec_angle.cpp index 87220bfad6..bdafdae148 100644 --- a/src/MOLECULE/atom_vec_angle.cpp +++ b/src/MOLECULE/atom_vec_angle.cpp @@ -793,8 +793,8 @@ void AtomVecAngle::data_atom(double *coord, imageint imagetmp, char **values) int nlocal = atom->nlocal; if (nlocal == nmax) grow(0); - tag[nlocal] = ATOTAGINT(values[0]); - molecule[nlocal] = ATOTAGINT(values[1]); + tag[nlocal] = utils::tnumeric(FLERR,values[0],true,lmp); + molecule[nlocal] = utils::tnumeric(FLERR,values[1],true,lmp); type[nlocal] = utils::inumeric(FLERR,values[2],true,lmp); if (type[nlocal] <= 0 || type[nlocal] > atom->ntypes) error->one(FLERR,"Invalid atom type in Atoms section of data file"); @@ -822,7 +822,7 @@ void AtomVecAngle::data_atom(double *coord, imageint imagetmp, char **values) int AtomVecAngle::data_atom_hybrid(int nlocal, char **values) { - molecule[nlocal] = ATOTAGINT(values[0]); + molecule[nlocal] = utils::tnumeric(FLERR,values[0],true,lmp); num_bond[nlocal] = 0; num_angle[nlocal] = 0; diff --git a/src/MOLECULE/atom_vec_bond.cpp b/src/MOLECULE/atom_vec_bond.cpp index 6f0c63529b..275c424941 100644 --- a/src/MOLECULE/atom_vec_bond.cpp +++ b/src/MOLECULE/atom_vec_bond.cpp @@ -739,8 +739,8 @@ void AtomVecBond::data_atom(double *coord, imageint imagetmp, char **values) int nlocal = atom->nlocal; if (nlocal == nmax) grow(0); - tag[nlocal] = ATOTAGINT(values[0]); - molecule[nlocal] = ATOTAGINT(values[1]); + tag[nlocal] = utils::tnumeric(FLERR,values[0],true,lmp); + molecule[nlocal] = utils::tnumeric(FLERR,values[1],true,lmp); type[nlocal] = utils::inumeric(FLERR,values[2],true,lmp); if (type[nlocal] <= 0 || type[nlocal] > atom->ntypes) error->one(FLERR,"Invalid atom type in Atoms section of data file"); @@ -767,7 +767,7 @@ void AtomVecBond::data_atom(double *coord, imageint imagetmp, char **values) int AtomVecBond::data_atom_hybrid(int nlocal, char **values) { - molecule[nlocal] = ATOTAGINT(values[0]); + molecule[nlocal] = utils::tnumeric(FLERR,values[0],true,lmp); num_bond[nlocal] = 0; diff --git a/src/MOLECULE/atom_vec_full.cpp b/src/MOLECULE/atom_vec_full.cpp index 0cb95254e3..036324cb2c 100644 --- a/src/MOLECULE/atom_vec_full.cpp +++ b/src/MOLECULE/atom_vec_full.cpp @@ -942,8 +942,8 @@ void AtomVecFull::data_atom(double *coord, imageint imagetmp, char **values) int nlocal = atom->nlocal; if (nlocal == nmax) grow(0); - tag[nlocal] = ATOTAGINT(values[0]); - molecule[nlocal] = ATOTAGINT(values[1]); + tag[nlocal] = utils::tnumeric(FLERR,values[0],true,lmp); + molecule[nlocal] = utils::tnumeric(FLERR,values[1],true,lmp); type[nlocal] = utils::inumeric(FLERR,values[2],true,lmp); if (type[nlocal] <= 0 || type[nlocal] > atom->ntypes) error->one(FLERR,"Invalid atom type in Atoms section of data file"); @@ -975,7 +975,7 @@ void AtomVecFull::data_atom(double *coord, imageint imagetmp, char **values) int AtomVecFull::data_atom_hybrid(int nlocal, char **values) { - molecule[nlocal] = ATOTAGINT(values[0]); + molecule[nlocal] = utils::tnumeric(FLERR,values[0],true,lmp); q[nlocal] = utils::numeric(FLERR,values[1],true,lmp); num_bond[nlocal] = 0; diff --git a/src/MOLECULE/atom_vec_molecular.cpp b/src/MOLECULE/atom_vec_molecular.cpp index 28766fa67d..49606f0a69 100644 --- a/src/MOLECULE/atom_vec_molecular.cpp +++ b/src/MOLECULE/atom_vec_molecular.cpp @@ -926,8 +926,8 @@ void AtomVecMolecular::data_atom(double *coord, imageint imagetmp, int nlocal = atom->nlocal; if (nlocal == nmax) grow(0); - tag[nlocal] = ATOTAGINT(values[0]); - molecule[nlocal] = ATOTAGINT(values[1]); + tag[nlocal] = utils::tnumeric(FLERR,values[0],true,lmp); + molecule[nlocal] = utils::tnumeric(FLERR,values[1],true,lmp); type[nlocal] = utils::inumeric(FLERR,values[2],true,lmp); if (type[nlocal] <= 0 || type[nlocal] > atom->ntypes) error->one(FLERR,"Invalid atom type in Atoms section of data file"); @@ -957,7 +957,7 @@ void AtomVecMolecular::data_atom(double *coord, imageint imagetmp, int AtomVecMolecular::data_atom_hybrid(int nlocal, char **values) { - molecule[nlocal] = ATOTAGINT(values[0]); + molecule[nlocal] = utils::tnumeric(FLERR,values[0],true,lmp); num_bond[nlocal] = 0; num_angle[nlocal] = 0; diff --git a/src/MOLECULE/atom_vec_template.cpp b/src/MOLECULE/atom_vec_template.cpp index f7cf5f96db..14e7736b50 100644 --- a/src/MOLECULE/atom_vec_template.cpp +++ b/src/MOLECULE/atom_vec_template.cpp @@ -742,11 +742,11 @@ void AtomVecTemplate::data_atom(double *coord, imageint imagetmp, char **values) int nlocal = atom->nlocal; if (nlocal == nmax) grow(0); - tag[nlocal] = ATOTAGINT(values[0]); + tag[nlocal] = utils::tnumeric(FLERR,values[0],true,lmp); if (tag[nlocal] <= 0) error->one(FLERR,"Invalid atom ID in Atoms section of data file"); - molecule[nlocal] = ATOTAGINT(values[1]); + molecule[nlocal] = utils::tnumeric(FLERR,values[1],true,lmp); molindex[nlocal] = utils::inumeric(FLERR,values[2],true,lmp) - 1; molatom[nlocal] = utils::inumeric(FLERR,values[3],true,lmp) - 1; @@ -781,7 +781,7 @@ void AtomVecTemplate::data_atom(double *coord, imageint imagetmp, char **values) int AtomVecTemplate::data_atom_hybrid(int nlocal, char **values) { - molecule[nlocal] = ATOTAGINT(values[0]); + molecule[nlocal] = utils::tnumeric(FLERR,values[0],true,lmp); molindex[nlocal] = utils::inumeric(FLERR,values[1],true,lmp) - 1; molatom[nlocal] = utils::inumeric(FLERR,values[2],true,lmp) - 1; return 3; diff --git a/src/PERI/atom_vec_peri.cpp b/src/PERI/atom_vec_peri.cpp index 25a0b8a933..64ce323a3f 100644 --- a/src/PERI/atom_vec_peri.cpp +++ b/src/PERI/atom_vec_peri.cpp @@ -793,7 +793,7 @@ void AtomVecPeri::data_atom(double *coord, imageint imagetmp, char **values) int nlocal = atom->nlocal; if (nlocal == nmax) grow(0); - tag[nlocal] = ATOTAGINT(values[0]); + tag[nlocal] = utils::tnumeric(FLERR,values[0],true,lmp); type[nlocal] = utils::inumeric(FLERR,values[1],true,lmp); if (type[nlocal] <= 0 || type[nlocal] > atom->ntypes) error->one(FLERR,"Invalid atom type in Atoms section of data file"); diff --git a/src/SPIN/atom_vec_spin.cpp b/src/SPIN/atom_vec_spin.cpp index 63c55759be..5b4173509f 100644 --- a/src/SPIN/atom_vec_spin.cpp +++ b/src/SPIN/atom_vec_spin.cpp @@ -813,7 +813,7 @@ void AtomVecSpin::data_atom(double *coord, imageint imagetmp, char **values) int nlocal = atom->nlocal; if (nlocal == nmax) grow(0); - tag[nlocal] = ATOTAGINT(values[0]); + tag[nlocal] = utils::tnumeric(FLERR,values[0],true,lmp); type[nlocal] = utils::inumeric(FLERR,values[1],true,lmp); if (type[nlocal] <= 0 || type[nlocal] > atom->ntypes) error->one(FLERR,"Invalid atom type in Atoms section of data file"); diff --git a/src/USER-AWPMD/atom_vec_wavepacket.cpp b/src/USER-AWPMD/atom_vec_wavepacket.cpp index 0edaf7ac02..bffe49e6c5 100644 --- a/src/USER-AWPMD/atom_vec_wavepacket.cpp +++ b/src/USER-AWPMD/atom_vec_wavepacket.cpp @@ -916,7 +916,7 @@ void AtomVecWavepacket::data_atom(double *coord, imageint imagetmp, if (nlocal == nmax) grow(0); - tag[nlocal] = ATOTAGINT(values[0]); + tag[nlocal] = utils::tnumeric(FLERR,values[0],true,lmp); type[nlocal] = utils::inumeric(FLERR,values[1],true,lmp); if (type[nlocal] <= 0 || type[nlocal] > atom->ntypes) error->one(FLERR,"Invalid atom type in Atoms section of data file"); diff --git a/src/USER-DPD/atom_vec_dpd.cpp b/src/USER-DPD/atom_vec_dpd.cpp index 2aef55ff9f..de673caec0 100644 --- a/src/USER-DPD/atom_vec_dpd.cpp +++ b/src/USER-DPD/atom_vec_dpd.cpp @@ -815,7 +815,7 @@ void AtomVecDPD::data_atom(double *coord, tagint imagetmp, char **values) int nlocal = atom->nlocal; if (nlocal == nmax) grow(0); - tag[nlocal] = ATOTAGINT(values[0]); + tag[nlocal] = utils::tnumeric(FLERR,values[0],true,lmp); type[nlocal] = utils::inumeric(FLERR,values[1],true,lmp); if (type[nlocal] <= 0 || type[nlocal] > atom->ntypes) error->one(FLERR,"Invalid atom type in Atoms section of data file"); diff --git a/src/USER-EFF/atom_vec_electron.cpp b/src/USER-EFF/atom_vec_electron.cpp index e62519d223..cf4555f02e 100644 --- a/src/USER-EFF/atom_vec_electron.cpp +++ b/src/USER-EFF/atom_vec_electron.cpp @@ -799,7 +799,7 @@ void AtomVecElectron::data_atom(double *coord, imageint imagetmp, char **values) if (nlocal == nmax) grow(0); - tag[nlocal] = ATOTAGINT(values[0]); + tag[nlocal] = utils::tnumeric(FLERR,values[0],true,lmp); type[nlocal] = utils::inumeric(FLERR,values[1],true,lmp); if (type[nlocal] <= 0 || type[nlocal] > atom->ntypes) error->one(FLERR,"Invalid atom type in Atoms section of data file"); diff --git a/src/USER-MESO/atom_vec_edpd.cpp b/src/USER-MESO/atom_vec_edpd.cpp index ff8515abc6..eee8ae25b0 100644 --- a/src/USER-MESO/atom_vec_edpd.cpp +++ b/src/USER-MESO/atom_vec_edpd.cpp @@ -760,7 +760,7 @@ void AtomVecEDPD::data_atom(double *coord, imageint imagetmp, char **values) int nlocal = atom->nlocal; if (nlocal == nmax) grow(0); - tag[nlocal] = ATOTAGINT(values[0]); + tag[nlocal] = utils::tnumeric(FLERR,values[0],true,lmp); type[nlocal] = utils::inumeric(FLERR,values[1],true,lmp); if (type[nlocal] <= 0 || type[nlocal] > atom->ntypes) error->one(FLERR,"Invalid atom type in Atoms section of data file"); diff --git a/src/USER-MESO/atom_vec_mdpd.cpp b/src/USER-MESO/atom_vec_mdpd.cpp index 965891a283..fd3c01f0c6 100644 --- a/src/USER-MESO/atom_vec_mdpd.cpp +++ b/src/USER-MESO/atom_vec_mdpd.cpp @@ -799,7 +799,7 @@ void AtomVecMDPD::data_atom(double *coord, imageint imagetmp, char **values) { int nlocal = atom->nlocal; if (nlocal == nmax) grow(0); - tag[nlocal] = ATOTAGINT(values[0]); + tag[nlocal] = utils::tnumeric(FLERR,values[0],true,lmp); type[nlocal] = utils::inumeric(FLERR,values[1],true,lmp); if (type[nlocal] <= 0 || type[nlocal] > atom->ntypes) error->one(FLERR,"Invalid atom type in Atoms section of data file"); diff --git a/src/USER-MESO/atom_vec_tdpd.cpp b/src/USER-MESO/atom_vec_tdpd.cpp index def0a8ad7b..f91731f8ac 100644 --- a/src/USER-MESO/atom_vec_tdpd.cpp +++ b/src/USER-MESO/atom_vec_tdpd.cpp @@ -792,7 +792,7 @@ void AtomVecTDPD::data_atom(double *coord, imageint imagetmp, char **values) int nlocal = atom->nlocal; if (nlocal == nmax) grow(0); - tag[nlocal] = ATOTAGINT(values[0]); + tag[nlocal] = utils::tnumeric(FLERR,values[0],true,lmp); type[nlocal] = utils::inumeric(FLERR,values[1],true,lmp); if (type[nlocal] <= 0 || type[nlocal] > atom->ntypes) error->one(FLERR,"Invalid atom type in Atoms section of data file"); diff --git a/src/USER-SMD/atom_vec_smd.cpp b/src/USER-SMD/atom_vec_smd.cpp index 278652bf43..9c634be091 100644 --- a/src/USER-SMD/atom_vec_smd.cpp +++ b/src/USER-SMD/atom_vec_smd.cpp @@ -1028,13 +1028,13 @@ void AtomVecSMD::data_atom(double *coord, imageint imagetmp, char **values) { if (nlocal == nmax) grow(0); - tag[nlocal] = ATOTAGINT(values[0]); + tag[nlocal] = utils::tnumeric(FLERR,values[0],true,lmp); type[nlocal] = utils::inumeric(FLERR,values[1],true,lmp); if (type[nlocal] <= 0 || type[nlocal] > atom->ntypes) error->one(FLERR, "Invalid atom type in Atoms section of data file"); - molecule[nlocal] = ATOTAGINT(values[2]); + molecule[nlocal] = utils::tnumeric(FLERR,values[2],true,lmp); if (molecule[nlocal] <= 0) error->one(FLERR, "Invalid molecule in Atoms section of data file"); diff --git a/src/USER-SPH/atom_vec_meso.cpp b/src/USER-SPH/atom_vec_meso.cpp index 0960141ae2..aa3e680c61 100644 --- a/src/USER-SPH/atom_vec_meso.cpp +++ b/src/USER-SPH/atom_vec_meso.cpp @@ -844,7 +844,7 @@ void AtomVecMeso::data_atom(double *coord, imageint imagetmp, char **values) { int nlocal = atom->nlocal; if (nlocal == nmax) grow(0); - tag[nlocal] = ATOTAGINT(values[0]); + tag[nlocal] = utils::tnumeric(FLERR,values[0],true,lmp); type[nlocal] = utils::inumeric(FLERR,values[1],true,lmp); if (type[nlocal] <= 0 || type[nlocal] > atom->ntypes) error->one(FLERR,"Invalid atom type in Atoms section of data file"); diff --git a/src/atom_vec_atomic.cpp b/src/atom_vec_atomic.cpp index 0574db1d8e..af4b4e617d 100644 --- a/src/atom_vec_atomic.cpp +++ b/src/atom_vec_atomic.cpp @@ -613,7 +613,7 @@ void AtomVecAtomic::data_atom(double *coord, imageint imagetmp, char **values) int nlocal = atom->nlocal; if (nlocal == nmax) grow(0); - tag[nlocal] = ATOTAGINT(values[0]); + tag[nlocal] = utils::tnumeric(FLERR,values[0],true,lmp); type[nlocal] = utils::inumeric(FLERR,values[1],true,lmp); if (type[nlocal] <= 0 || type[nlocal] > atom->ntypes) error->one(FLERR,"Invalid atom type in Atoms section of data file"); diff --git a/src/atom_vec_body.cpp b/src/atom_vec_body.cpp index 4b22933881..96cf0ec909 100644 --- a/src/atom_vec_body.cpp +++ b/src/atom_vec_body.cpp @@ -1279,7 +1279,7 @@ void AtomVecBody::data_atom(double *coord, imageint imagetmp, char **values) int nlocal = atom->nlocal; if (nlocal == nmax) grow(0); - tag[nlocal] = ATOTAGINT(values[0]); + tag[nlocal] = utils::tnumeric(FLERR,values[0],true,lmp); type[nlocal] = utils::inumeric(FLERR,values[1],true,lmp); if (type[nlocal] <= 0 || type[nlocal] > atom->ntypes) error->one(FLERR,"Invalid atom type in Atoms section of data file"); diff --git a/src/atom_vec_charge.cpp b/src/atom_vec_charge.cpp index 1a78ba0e2d..fa3c99ca34 100644 --- a/src/atom_vec_charge.cpp +++ b/src/atom_vec_charge.cpp @@ -664,7 +664,7 @@ void AtomVecCharge::data_atom(double *coord, imageint imagetmp, char **values) int nlocal = atom->nlocal; if (nlocal == nmax) grow(0); - tag[nlocal] = ATOTAGINT(values[0]); + tag[nlocal] = utils::tnumeric(FLERR,values[0],true,lmp); type[nlocal] = utils::inumeric(FLERR,values[1],true,lmp); if (type[nlocal] <= 0 || type[nlocal] > atom->ntypes) error->one(FLERR,"Invalid atom type in Atoms section of data file"); diff --git a/src/atom_vec_ellipsoid.cpp b/src/atom_vec_ellipsoid.cpp index 0b94359c55..455e4f192f 100644 --- a/src/atom_vec_ellipsoid.cpp +++ b/src/atom_vec_ellipsoid.cpp @@ -1141,7 +1141,7 @@ void AtomVecEllipsoid::data_atom(double *coord, imageint imagetmp, int nlocal = atom->nlocal; if (nlocal == nmax) grow(0); - tag[nlocal] = ATOTAGINT(values[0]); + tag[nlocal] = utils::tnumeric(FLERR,values[0],true,lmp); type[nlocal] = utils::inumeric(FLERR,values[1],true,lmp); if (type[nlocal] <= 0 || type[nlocal] > atom->ntypes) error->one(FLERR,"Invalid atom type in Atoms section of data file"); diff --git a/src/atom_vec_hybrid.cpp b/src/atom_vec_hybrid.cpp index a7816efbed..18f6fb567d 100644 --- a/src/atom_vec_hybrid.cpp +++ b/src/atom_vec_hybrid.cpp @@ -864,7 +864,7 @@ void AtomVecHybrid::data_atom(double *coord, imageint imagetmp, char **values) int nlocal = atom->nlocal; if (nlocal == nmax) grow(0); - tag[nlocal] = ATOTAGINT(values[0]); + tag[nlocal] = utils::tnumeric(FLERR,values[0],true,lmp); type[nlocal] = utils::inumeric(FLERR,values[1],true,lmp); if (type[nlocal] <= 0 || type[nlocal] > atom->ntypes) error->one(FLERR,"Invalid atom type in Atoms section of data file"); diff --git a/src/atom_vec_line.cpp b/src/atom_vec_line.cpp index 6bffc1b0de..ba59b3d17a 100644 --- a/src/atom_vec_line.cpp +++ b/src/atom_vec_line.cpp @@ -1036,8 +1036,8 @@ void AtomVecLine::data_atom(double *coord, imageint imagetmp, char **values) int nlocal = atom->nlocal; if (nlocal == nmax) grow(0); - tag[nlocal] = ATOTAGINT(values[0]); - molecule[nlocal] = ATOTAGINT(values[1]); + tag[nlocal] = utils::tnumeric(FLERR,values[0],true,lmp); + molecule[nlocal] = utils::tnumeric(FLERR,values[1],true,lmp); type[nlocal] = utils::inumeric(FLERR,values[2],true,lmp); if (type[nlocal] <= 0 || type[nlocal] > atom->ntypes) error->one(FLERR,"Invalid atom type in Atoms section of data file"); @@ -1081,7 +1081,7 @@ void AtomVecLine::data_atom(double *coord, imageint imagetmp, char **values) int AtomVecLine::data_atom_hybrid(int nlocal, char **values) { - molecule[nlocal] = ATOTAGINT(values[0]); + molecule[nlocal] = utils::tnumeric(FLERR,values[0],true,lmp); line[nlocal] = utils::inumeric(FLERR,values[1],true,lmp); if (line[nlocal] == 0) line[nlocal] = -1; diff --git a/src/atom_vec_sphere.cpp b/src/atom_vec_sphere.cpp index b37b853c86..2a77ec418b 100644 --- a/src/atom_vec_sphere.cpp +++ b/src/atom_vec_sphere.cpp @@ -965,7 +965,7 @@ void AtomVecSphere::data_atom(double *coord, imageint imagetmp, char **values) int nlocal = atom->nlocal; if (nlocal == nmax) grow(0); - tag[nlocal] = ATOTAGINT(values[0]); + tag[nlocal] = utils::tnumeric(FLERR,values[0],true,lmp); type[nlocal] = utils::inumeric(FLERR,values[1],true,lmp); if (type[nlocal] <= 0 || type[nlocal] > atom->ntypes) error->one(FLERR,"Invalid atom type in Atoms section of data file"); diff --git a/src/atom_vec_tri.cpp b/src/atom_vec_tri.cpp index 4070c6795e..45418b35fd 100644 --- a/src/atom_vec_tri.cpp +++ b/src/atom_vec_tri.cpp @@ -1435,8 +1435,8 @@ void AtomVecTri::data_atom(double *coord, imageint imagetmp, char **values) int nlocal = atom->nlocal; if (nlocal == nmax) grow(0); - tag[nlocal] = ATOTAGINT(values[0]); - molecule[nlocal] = ATOTAGINT(values[1]); + tag[nlocal] = utils::tnumeric(FLERR,values[0],true,lmp); + molecule[nlocal] = utils::tnumeric(FLERR,values[1],true,lmp); type[nlocal] = utils::inumeric(FLERR,values[2],true,lmp); if (type[nlocal] <= 0 || type[nlocal] > atom->ntypes) error->one(FLERR,"Invalid atom type in Atoms section of data file"); @@ -1483,7 +1483,7 @@ void AtomVecTri::data_atom(double *coord, imageint imagetmp, char **values) int AtomVecTri::data_atom_hybrid(int nlocal, char **values) { - molecule[nlocal] = ATOTAGINT(values[0]); + molecule[nlocal] = utils::tnumeric(FLERR,values[0],true,lmp); tri[nlocal] = utils::inumeric(FLERR,values[1],true,lmp); if (tri[nlocal] == 0) tri[nlocal] = -1; -- GitLab From 0f691de031b8000f91e451172d72f329c937c428 Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Wed, 10 Jul 2019 00:50:34 -0400 Subject: [PATCH 221/469] include file cleanup in some more packages --- src/SPIN/fix_setforce_spin.cpp | 1 - src/USER-CGDNA/bond_oxdna_fene.cpp | 1 + src/USER-CGSDK/angle_sdk.cpp | 2 +- src/USER-CGSDK/pair_lj_sdk.cpp | 7 +------ src/USER-CGSDK/pair_lj_sdk_coul_long.cpp | 8 +------- src/USER-CGSDK/pair_lj_sdk_coul_msm.cpp | 9 --------- src/USER-DIFFRACTION/compute_saed.cpp | 3 +-- src/USER-DIFFRACTION/compute_xrd.cpp | 3 +-- src/USER-DIFFRACTION/fix_saed_vtk.cpp | 5 +---- src/USER-DPD/compute_dpd.cpp | 5 +---- src/USER-DPD/compute_dpd_atom.cpp | 8 +------- src/USER-DPD/fix_dpd_energy.cpp | 4 ---- src/USER-DPD/fix_eos_cv.cpp | 2 -- src/USER-DPD/fix_eos_table.cpp | 3 ++- src/USER-DPD/fix_eos_table_rx.cpp | 3 ++- src/USER-DPD/fix_rx.cpp | 4 ++-- src/USER-DPD/fix_shardlow.cpp | 5 +---- src/USER-DPD/nbin_ssa.cpp | 2 -- src/USER-DPD/npair_half_bin_newton_ssa.cpp | 2 -- src/USER-DPD/nstencil_half_bin_2d_newton_ssa.cpp | 2 -- src/USER-DPD/nstencil_half_bin_3d_newton_ssa.cpp | 2 -- src/USER-DPD/pair_dpd_fdt.cpp | 7 ++----- src/USER-DPD/pair_table_rx.cpp | 4 +--- src/USER-DRUDE/compute_temp_drude.cpp | 8 ++------ src/USER-DRUDE/compute_temp_drude.h | 3 +-- src/USER-DRUDE/fix_drude.cpp | 5 +++-- src/USER-DRUDE/fix_drude_transform.cpp | 4 ++-- src/USER-DRUDE/fix_drude_transform.h | 3 +-- src/USER-DRUDE/fix_langevin_drude.cpp | 5 ++--- src/USER-DRUDE/fix_langevin_drude.h | 3 +-- src/USER-DRUDE/pair_lj_cut_thole_long.cpp | 9 +++------ src/USER-DRUDE/pair_lj_cut_thole_long.h | 3 +-- src/USER-DRUDE/pair_thole.cpp | 7 +++---- src/USER-DRUDE/pair_thole.h | 3 +-- src/USER-EFF/compute_temp_eff.cpp | 3 +-- src/USER-FEP/compute_fep.cpp | 3 +-- src/USER-FEP/fix_adapt_fep.cpp | 4 +--- src/USER-FEP/pair_coul_cut_soft.cpp | 5 ++--- src/USER-FEP/pair_coul_long_soft.cpp | 7 ++----- src/USER-FEP/pair_lj_charmm_coul_long_soft.cpp | 6 ++---- src/USER-FEP/pair_lj_class2_coul_cut_soft.cpp | 5 ++--- src/USER-FEP/pair_lj_class2_coul_long_soft.cpp | 5 ++--- src/USER-FEP/pair_lj_class2_soft.cpp | 5 ++--- src/USER-FEP/pair_lj_cut_coul_cut_soft.cpp | 5 ++--- src/USER-FEP/pair_lj_cut_coul_long_soft.cpp | 6 ++---- src/USER-FEP/pair_lj_cut_soft.cpp | 6 ++---- src/USER-FEP/pair_lj_cut_tip4p_long_soft.cpp | 9 ++------- src/USER-FEP/pair_morse_soft.cpp | 5 ++--- src/USER-FEP/pair_tip4p_long_soft.cpp | 9 ++------- src/USER-MESO/fix_mvv_dpd.cpp | 4 +--- src/USER-MESO/fix_tdpd_source.cpp | 11 ++--------- src/USER-MESO/pair_edpd.cpp | 6 ++---- src/USER-MESO/pair_mdpd.cpp | 6 ++---- src/USER-MESO/pair_mdpd_rhosum.cpp | 5 +---- src/USER-MESO/pair_tdpd.cpp | 5 +---- 55 files changed, 75 insertions(+), 190 deletions(-) diff --git a/src/SPIN/fix_setforce_spin.cpp b/src/SPIN/fix_setforce_spin.cpp index 15e5aacfb6..e36a9d260d 100644 --- a/src/SPIN/fix_setforce_spin.cpp +++ b/src/SPIN/fix_setforce_spin.cpp @@ -22,7 +22,6 @@ ------------------------------------------------------------------------- */ #include "fix_setforce_spin.h" -#include #include "atom.h" #include "update.h" #include "modify.h" diff --git a/src/USER-CGDNA/bond_oxdna_fene.cpp b/src/USER-CGDNA/bond_oxdna_fene.cpp index 8314576d63..2f76e67ef4 100644 --- a/src/USER-CGDNA/bond_oxdna_fene.cpp +++ b/src/USER-CGDNA/bond_oxdna_fene.cpp @@ -15,6 +15,7 @@ ------------------------------------------------------------------------- */ #include "bond_oxdna_fene.h" +#include #include #include "atom.h" #include "neighbor.h" diff --git a/src/USER-CGSDK/angle_sdk.cpp b/src/USER-CGSDK/angle_sdk.cpp index 575b0fae69..862c165bbd 100644 --- a/src/USER-CGSDK/angle_sdk.cpp +++ b/src/USER-CGSDK/angle_sdk.cpp @@ -19,8 +19,8 @@ ------------------------------------------------------------------------- */ #include "angle_sdk.h" +#include #include -#include #include "atom.h" #include "neighbor.h" #include "pair.h" diff --git a/src/USER-CGSDK/pair_lj_sdk.cpp b/src/USER-CGSDK/pair_lj_sdk.cpp index b22469566e..6ad77a6183 100644 --- a/src/USER-CGSDK/pair_lj_sdk.cpp +++ b/src/USER-CGSDK/pair_lj_sdk.cpp @@ -17,18 +17,13 @@ ------------------------------------------------------------------------- */ #include "pair_lj_sdk.h" +#include #include -#include -#include #include #include "atom.h" #include "comm.h" #include "force.h" -#include "neighbor.h" #include "neigh_list.h" -#include "neigh_request.h" -#include "update.h" -#include "integrate.h" #include "math_const.h" #include "memory.h" #include "error.h" diff --git a/src/USER-CGSDK/pair_lj_sdk_coul_long.cpp b/src/USER-CGSDK/pair_lj_sdk_coul_long.cpp index 5fba8cde66..62acf00d27 100644 --- a/src/USER-CGSDK/pair_lj_sdk_coul_long.cpp +++ b/src/USER-CGSDK/pair_lj_sdk_coul_long.cpp @@ -17,9 +17,8 @@ ------------------------------------------------------------------------- */ #include "pair_lj_sdk_coul_long.h" +#include #include -#include -#include #include #include "atom.h" #include "comm.h" @@ -27,10 +26,6 @@ #include "kspace.h" #include "neighbor.h" #include "neigh_list.h" -#include "neigh_request.h" -#include "update.h" -#include "integrate.h" -#include "math_const.h" #include "memory.h" #include "error.h" @@ -38,7 +33,6 @@ #include "lj_sdk_common.h" using namespace LAMMPS_NS; -using namespace MathConst; using namespace LJSDKParms; #define EWALD_F 1.12837917 diff --git a/src/USER-CGSDK/pair_lj_sdk_coul_msm.cpp b/src/USER-CGSDK/pair_lj_sdk_coul_msm.cpp index b61ed5528f..1095521de3 100644 --- a/src/USER-CGSDK/pair_lj_sdk_coul_msm.cpp +++ b/src/USER-CGSDK/pair_lj_sdk_coul_msm.cpp @@ -18,26 +18,17 @@ #include "pair_lj_sdk_coul_msm.h" #include -#include -#include #include #include "atom.h" -#include "comm.h" #include "force.h" #include "kspace.h" -#include "neighbor.h" #include "neigh_list.h" -#include "neigh_request.h" -#include "update.h" -#include "integrate.h" -#include "math_const.h" #include "memory.h" #include "error.h" #include "lj_sdk_common.h" using namespace LAMMPS_NS; -using namespace MathConst; using namespace LJSDKParms; /* ---------------------------------------------------------------------- */ diff --git a/src/USER-DIFFRACTION/compute_saed.cpp b/src/USER-DIFFRACTION/compute_saed.cpp index dcafe57ba8..971d9bd380 100644 --- a/src/USER-DIFFRACTION/compute_saed.cpp +++ b/src/USER-DIFFRACTION/compute_saed.cpp @@ -15,13 +15,12 @@ Contributing authors: Shawn Coleman & Douglas Spearot (Arkansas) ------------------------------------------------------------------------- */ +#include "compute_saed.h" #include #include #include -#include #include #include "math_const.h" -#include "compute_saed.h" #include "compute_saed_consts.h" #include "atom.h" #include "comm.h" diff --git a/src/USER-DIFFRACTION/compute_xrd.cpp b/src/USER-DIFFRACTION/compute_xrd.cpp index d6b7549272..f48951f1ff 100644 --- a/src/USER-DIFFRACTION/compute_xrd.cpp +++ b/src/USER-DIFFRACTION/compute_xrd.cpp @@ -16,13 +16,12 @@ Updated: 06/17/2015-2 ------------------------------------------------------------------------- */ +#include "compute_xrd.h" #include #include #include -#include #include #include "math_const.h" -#include "compute_xrd.h" #include "compute_xrd_consts.h" #include "atom.h" #include "comm.h" diff --git a/src/USER-DIFFRACTION/fix_saed_vtk.cpp b/src/USER-DIFFRACTION/fix_saed_vtk.cpp index 4d9af66818..c3a72e494b 100644 --- a/src/USER-DIFFRACTION/fix_saed_vtk.cpp +++ b/src/USER-DIFFRACTION/fix_saed_vtk.cpp @@ -16,17 +16,14 @@ Incorporating SAED: Shawn Coleman (Arkansas) ------------------------------------------------------------------------- */ +#include "fix_saed_vtk.h" #include #include #include -#include "fix_saed_vtk.h" #include "update.h" #include "modify.h" #include "compute.h" #include "compute_saed.h" -#include "group.h" -#include "input.h" -#include "variable.h" #include "memory.h" #include "error.h" #include "force.h" diff --git a/src/USER-DPD/compute_dpd.cpp b/src/USER-DPD/compute_dpd.cpp index 08aa19bcdf..0ef7868164 100644 --- a/src/USER-DPD/compute_dpd.cpp +++ b/src/USER-DPD/compute_dpd.cpp @@ -15,13 +15,10 @@ Contributing author: James Larentzos (U.S. Army Research Laboratory) ------------------------------------------------------------------------- */ -#include #include "compute_dpd.h" +#include #include "atom.h" #include "update.h" -#include "force.h" -#include "domain.h" -#include "group.h" #include "error.h" using namespace LAMMPS_NS; diff --git a/src/USER-DPD/compute_dpd_atom.cpp b/src/USER-DPD/compute_dpd_atom.cpp index 78f842a68f..0fd732f669 100644 --- a/src/USER-DPD/compute_dpd_atom.cpp +++ b/src/USER-DPD/compute_dpd_atom.cpp @@ -15,21 +15,15 @@ Contributing author: James Larentzos (U.S. Army Research Laboratory) ------------------------------------------------------------------------- */ -#include -#include -#include #include "compute_dpd_atom.h" +#include #include "atom.h" #include "update.h" #include "modify.h" -#include "domain.h" -#include "group.h" #include "memory.h" #include "error.h" #include "comm.h" -#include - using namespace LAMMPS_NS; /* ---------------------------------------------------------------------- */ diff --git a/src/USER-DPD/fix_dpd_energy.cpp b/src/USER-DPD/fix_dpd_energy.cpp index 5759a164f5..6ee88ea88a 100644 --- a/src/USER-DPD/fix_dpd_energy.cpp +++ b/src/USER-DPD/fix_dpd_energy.cpp @@ -11,14 +11,10 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include -#include #include "fix_dpd_energy.h" #include "atom.h" #include "force.h" #include "update.h" -#include "respa.h" -#include "modify.h" #include "error.h" #include "pair_dpd_fdt_energy.h" diff --git a/src/USER-DPD/fix_eos_cv.cpp b/src/USER-DPD/fix_eos_cv.cpp index 919e6829f3..5b25519a40 100644 --- a/src/USER-DPD/fix_eos_cv.cpp +++ b/src/USER-DPD/fix_eos_cv.cpp @@ -15,8 +15,6 @@ Contributing author: James Larentzos (U.S. Army Research Laboratory) ------------------------------------------------------------------------- */ -#include -#include #include "fix_eos_cv.h" #include "atom.h" #include "error.h" diff --git a/src/USER-DPD/fix_eos_table.cpp b/src/USER-DPD/fix_eos_table.cpp index 7d701f5fb8..ff9a186c47 100644 --- a/src/USER-DPD/fix_eos_table.cpp +++ b/src/USER-DPD/fix_eos_table.cpp @@ -15,9 +15,10 @@ Contributing author: James Larentzos (U.S. Army Research Laboratory) ------------------------------------------------------------------------- */ +#include "fix_eos_table.h" +#include #include #include -#include "fix_eos_table.h" #include "atom.h" #include "error.h" #include "force.h" diff --git a/src/USER-DPD/fix_eos_table_rx.cpp b/src/USER-DPD/fix_eos_table_rx.cpp index 779cee0e8b..9f1bd6a3bb 100644 --- a/src/USER-DPD/fix_eos_table_rx.cpp +++ b/src/USER-DPD/fix_eos_table_rx.cpp @@ -15,10 +15,11 @@ Contributing author: James Larentzos (U.S. Army Research Laboratory) ------------------------------------------------------------------------- */ +#include "fix_eos_table_rx.h" +#include #include #include #include -#include "fix_eos_table_rx.h" #include "atom.h" #include "error.h" #include "force.h" diff --git a/src/USER-DPD/fix_rx.cpp b/src/USER-DPD/fix_rx.cpp index cb8349786f..03e8ae49a4 100644 --- a/src/USER-DPD/fix_rx.cpp +++ b/src/USER-DPD/fix_rx.cpp @@ -11,12 +11,12 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include +#include "fix_rx.h" +#include #include #include #include #include // DBL_EPSILON -#include "fix_rx.h" #include "atom.h" #include "error.h" #include "group.h" diff --git a/src/USER-DPD/fix_shardlow.cpp b/src/USER-DPD/fix_shardlow.cpp index 4e133480ad..f181436f91 100644 --- a/src/USER-DPD/fix_shardlow.cpp +++ b/src/USER-DPD/fix_shardlow.cpp @@ -33,15 +33,13 @@ 135, 204105. ------------------------------------------------------------------------- */ -#include +#include "fix_shardlow.h" #include #include #include -#include "fix_shardlow.h" #include "atom.h" #include "force.h" #include "update.h" -#include "respa.h" #include "error.h" #include "atom_vec.h" #include "comm.h" @@ -53,7 +51,6 @@ #include "modify.h" #include "pair_dpd_fdt.h" #include "pair_dpd_fdt_energy.h" -#include "pair.h" #include "npair_half_bin_newton_ssa.h" #include "citeme.h" diff --git a/src/USER-DPD/nbin_ssa.cpp b/src/USER-DPD/nbin_ssa.cpp index dcd434cb4a..e3fa71aedf 100644 --- a/src/USER-DPD/nbin_ssa.cpp +++ b/src/USER-DPD/nbin_ssa.cpp @@ -21,8 +21,6 @@ #include "update.h" #include "group.h" #include "domain.h" -#include "memory.h" -#include "error.h" using namespace LAMMPS_NS; diff --git a/src/USER-DPD/npair_half_bin_newton_ssa.cpp b/src/USER-DPD/npair_half_bin_newton_ssa.cpp index ba90ebc465..2139173d47 100644 --- a/src/USER-DPD/npair_half_bin_newton_ssa.cpp +++ b/src/USER-DPD/npair_half_bin_newton_ssa.cpp @@ -17,7 +17,6 @@ ------------------------------------------------------------------------- */ #include "npair_half_bin_newton_ssa.h" -#include "neighbor.h" #include "nstencil_ssa.h" #include "nbin_ssa.h" #include "neigh_list.h" @@ -25,7 +24,6 @@ #include "atom_vec.h" #include "molecule.h" #include "domain.h" -#include "group.h" #include "memory.h" #include "my_page.h" #include "error.h" diff --git a/src/USER-DPD/nstencil_half_bin_2d_newton_ssa.cpp b/src/USER-DPD/nstencil_half_bin_2d_newton_ssa.cpp index 451381c104..9953fca62c 100644 --- a/src/USER-DPD/nstencil_half_bin_2d_newton_ssa.cpp +++ b/src/USER-DPD/nstencil_half_bin_2d_newton_ssa.cpp @@ -17,8 +17,6 @@ ------------------------------------------------------------------------- */ #include "nstencil_half_bin_2d_newton_ssa.h" -#include "neighbor.h" -#include "neigh_list.h" using namespace LAMMPS_NS; diff --git a/src/USER-DPD/nstencil_half_bin_3d_newton_ssa.cpp b/src/USER-DPD/nstencil_half_bin_3d_newton_ssa.cpp index cdd3b8856f..4dd3c4a5fe 100644 --- a/src/USER-DPD/nstencil_half_bin_3d_newton_ssa.cpp +++ b/src/USER-DPD/nstencil_half_bin_3d_newton_ssa.cpp @@ -17,8 +17,6 @@ ------------------------------------------------------------------------- */ #include "nstencil_half_bin_3d_newton_ssa.h" -#include "neighbor.h" -#include "neigh_list.h" using namespace LAMMPS_NS; diff --git a/src/USER-DPD/pair_dpd_fdt.cpp b/src/USER-DPD/pair_dpd_fdt.cpp index 07ef8190f0..1cb9d68d06 100644 --- a/src/USER-DPD/pair_dpd_fdt.cpp +++ b/src/USER-DPD/pair_dpd_fdt.cpp @@ -15,23 +15,20 @@ Contributing author: James Larentzos (U.S. Army Research Laboratory) ------------------------------------------------------------------------- */ +#include "pair_dpd_fdt.h" +#include #include -#include -#include #include #include "atom.h" -#include "atom_vec.h" #include "comm.h" #include "update.h" #include "fix.h" #include "force.h" #include "neighbor.h" #include "neigh_list.h" -#include "neigh_request.h" #include "random_mars.h" #include "memory.h" #include "modify.h" -#include "pair_dpd_fdt.h" #include "error.h" using namespace LAMMPS_NS; diff --git a/src/USER-DPD/pair_table_rx.cpp b/src/USER-DPD/pair_table_rx.cpp index f2d0d7b1fb..e767f93367 100644 --- a/src/USER-DPD/pair_table_rx.cpp +++ b/src/USER-DPD/pair_table_rx.cpp @@ -15,14 +15,12 @@ Contributing author: Paul Crozier (SNL) ------------------------------------------------------------------------- */ +#include "pair_table_rx.h" #include #include -#include #include -#include "pair_table_rx.h" #include "atom.h" #include "force.h" -#include "comm.h" #include "neigh_list.h" #include "memory.h" #include "error.h" diff --git a/src/USER-DRUDE/compute_temp_drude.cpp b/src/USER-DRUDE/compute_temp_drude.cpp index 4830e950d0..a12c248680 100644 --- a/src/USER-DRUDE/compute_temp_drude.cpp +++ b/src/USER-DRUDE/compute_temp_drude.cpp @@ -11,19 +11,15 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ +#include "compute_temp_drude.h" #include -#include #include -#include "compute_temp_drude.h" #include "atom.h" #include "update.h" #include "force.h" -#include "group.h" #include "modify.h" -#include "fix.h" +#include "fix_drude.h" #include "domain.h" -#include "lattice.h" -#include "memory.h" #include "error.h" #include "comm.h" diff --git a/src/USER-DRUDE/compute_temp_drude.h b/src/USER-DRUDE/compute_temp_drude.h index 88d767f8b7..530c84ce3d 100644 --- a/src/USER-DRUDE/compute_temp_drude.h +++ b/src/USER-DRUDE/compute_temp_drude.h @@ -21,7 +21,6 @@ ComputeStyle(temp/drude,ComputeTempDrude) #define LMP_COMPUTE_TEMP_DRUDE_H #include "compute.h" -#include "fix_drude.h" namespace LAMMPS_NS { @@ -37,7 +36,7 @@ class ComputeTempDrude : public Compute { private: int fix_dof; - FixDrude * fix_drude; + class FixDrude * fix_drude; char *id_temp; class Compute *temperature; bigint dof_core, dof_drude; diff --git a/src/USER-DRUDE/fix_drude.cpp b/src/USER-DRUDE/fix_drude.cpp index 7800efe7ff..080408459c 100644 --- a/src/USER-DRUDE/fix_drude.cpp +++ b/src/USER-DRUDE/fix_drude.cpp @@ -11,9 +11,10 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include -#include #include "fix_drude.h" +#include +#include +#include #include "atom.h" #include "comm.h" #include "modify.h" diff --git a/src/USER-DRUDE/fix_drude_transform.cpp b/src/USER-DRUDE/fix_drude_transform.cpp index 34742a0683..8e85f1dffd 100644 --- a/src/USER-DRUDE/fix_drude_transform.cpp +++ b/src/USER-DRUDE/fix_drude_transform.cpp @@ -12,15 +12,15 @@ ------------------------------------------------------------------------- */ /** Fix Drude Transform ******************************************************/ +#include "fix_drude_transform.h" #include #include -#include "fix_drude_transform.h" +#include "fix_drude.h" #include "atom.h" #include "domain.h" #include "comm.h" #include "error.h" #include "modify.h" -#include "force.h" using namespace LAMMPS_NS; using namespace FixConst; diff --git a/src/USER-DRUDE/fix_drude_transform.h b/src/USER-DRUDE/fix_drude_transform.h index 41f4e147ed..b74a500c95 100644 --- a/src/USER-DRUDE/fix_drude_transform.h +++ b/src/USER-DRUDE/fix_drude_transform.h @@ -22,7 +22,6 @@ FixStyle(drude/transform/inverse,FixDrudeTransform) #define LMP_FIX_DRUDE_TRANSFORM_H #include "fix.h" -#include "fix_drude.h" namespace LAMMPS_NS { @@ -42,7 +41,7 @@ class FixDrudeTransform : public Fix { void unpack_forward_comm(int n, int first, double *buf); protected: double * mcoeff; - FixDrude * fix_drude; + class FixDrude * fix_drude; }; } diff --git a/src/USER-DRUDE/fix_langevin_drude.cpp b/src/USER-DRUDE/fix_langevin_drude.cpp index b9d1139f83..1a16c3df96 100644 --- a/src/USER-DRUDE/fix_langevin_drude.cpp +++ b/src/USER-DRUDE/fix_langevin_drude.cpp @@ -11,17 +11,16 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ +#include "fix_langevin_drude.h" #include -#include #include -#include "fix_langevin_drude.h" +#include "fix_drude.h" #include "atom.h" #include "force.h" #include "comm.h" #include "input.h" #include "variable.h" #include "random_mars.h" -#include "group.h" #include "update.h" #include "modify.h" #include "compute.h" diff --git a/src/USER-DRUDE/fix_langevin_drude.h b/src/USER-DRUDE/fix_langevin_drude.h index d65440582c..9437883ba3 100644 --- a/src/USER-DRUDE/fix_langevin_drude.h +++ b/src/USER-DRUDE/fix_langevin_drude.h @@ -21,7 +21,6 @@ FixStyle(langevin/drude,FixLangevinDrude) #define LMP_FIX_LANGEVIN_DRUDE_H #include "fix.h" -#include "fix_drude.h" namespace LAMMPS_NS { @@ -51,7 +50,7 @@ class FixLangevinDrude : public Fix { class RanMars *random_core, *random_drude; int zero; bigint ncore; - FixDrude * fix_drude; + class FixDrude * fix_drude; class Compute *temperature; char *id_temp; }; diff --git a/src/USER-DRUDE/pair_lj_cut_thole_long.cpp b/src/USER-DRUDE/pair_lj_cut_thole_long.cpp index 1ebe4a4c2d..851effd89c 100644 --- a/src/USER-DRUDE/pair_lj_cut_thole_long.cpp +++ b/src/USER-DRUDE/pair_lj_cut_thole_long.cpp @@ -15,20 +15,17 @@ Contributing author: Paul Crozier (SNL) ------------------------------------------------------------------------- */ +#include "pair_lj_cut_thole_long.h" +#include #include -#include -#include #include -#include "pair_lj_cut_thole_long.h" +#include "fix_drude.h" #include "atom.h" #include "comm.h" #include "force.h" #include "kspace.h" -#include "update.h" -#include "integrate.h" #include "neighbor.h" #include "neigh_list.h" -#include "neigh_request.h" #include "math_const.h" #include "memory.h" #include "error.h" diff --git a/src/USER-DRUDE/pair_lj_cut_thole_long.h b/src/USER-DRUDE/pair_lj_cut_thole_long.h index 27a917c737..4c3a883064 100644 --- a/src/USER-DRUDE/pair_lj_cut_thole_long.h +++ b/src/USER-DRUDE/pair_lj_cut_thole_long.h @@ -21,7 +21,6 @@ PairStyle(lj/cut/thole/long,PairLJCutTholeLong) #define LMP_PAIR_LJ_CUT_THOLE_LONG_H #include "pair.h" -#include "fix_drude.h" namespace LAMMPS_NS { @@ -58,7 +57,7 @@ class PairLJCutTholeLong : public Pair { double cut_global; double **cut,**scale; double **polar,**thole,**ascreen; - FixDrude *fix_drude; + class FixDrude *fix_drude; virtual void allocate(); }; diff --git a/src/USER-DRUDE/pair_thole.cpp b/src/USER-DRUDE/pair_thole.cpp index 1bb75af825..1f81263e95 100644 --- a/src/USER-DRUDE/pair_thole.cpp +++ b/src/USER-DRUDE/pair_thole.cpp @@ -11,11 +11,10 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ +#include "pair_thole.h" +#include #include -#include -#include #include -#include "pair_thole.h" #include "atom.h" #include "comm.h" #include "force.h" @@ -24,7 +23,7 @@ #include "memory.h" #include "error.h" #include "fix.h" -#include "fix_store.h" +#include "fix_drude.h" #include "domain.h" #include "modify.h" diff --git a/src/USER-DRUDE/pair_thole.h b/src/USER-DRUDE/pair_thole.h index 2c462b431a..88c00b6d20 100644 --- a/src/USER-DRUDE/pair_thole.h +++ b/src/USER-DRUDE/pair_thole.h @@ -21,7 +21,6 @@ PairStyle(thole,PairThole) #define LMP_PAIR_THOLE_H #include "pair.h" -#include "fix_drude.h" namespace LAMMPS_NS { @@ -46,7 +45,7 @@ class PairThole : public Pair { double cut_global; double **cut,**scale; double **polar,**thole,**ascreen; - FixDrude * fix_drude; + class FixDrude * fix_drude; virtual void allocate(); }; diff --git a/src/USER-EFF/compute_temp_eff.cpp b/src/USER-EFF/compute_temp_eff.cpp index d745269ff5..8e07e390fa 100644 --- a/src/USER-EFF/compute_temp_eff.cpp +++ b/src/USER-EFF/compute_temp_eff.cpp @@ -15,9 +15,8 @@ Contributing author: Andres Jaramillo-Botero (Caltech) ------------------------------------------------------------------------- */ -#include -#include #include "compute_temp_eff.h" +#include #include "atom.h" #include "update.h" #include "force.h" diff --git a/src/USER-FEP/compute_fep.cpp b/src/USER-FEP/compute_fep.cpp index dc0b71e71b..1853828db3 100644 --- a/src/USER-FEP/compute_fep.cpp +++ b/src/USER-FEP/compute_fep.cpp @@ -15,7 +15,7 @@ Contributing author: Agilio Padua (Univ Blaise Pascal & CNRS) ------------------------------------------------------------------------- */ -#include +#include "compute_fep.h" #include #include #include @@ -34,7 +34,6 @@ #include "timer.h" #include "memory.h" #include "error.h" -#include "compute_fep.h" using namespace LAMMPS_NS; diff --git a/src/USER-FEP/fix_adapt_fep.cpp b/src/USER-FEP/fix_adapt_fep.cpp index 7304bc4ef6..46cf32cf0b 100644 --- a/src/USER-FEP/fix_adapt_fep.cpp +++ b/src/USER-FEP/fix_adapt_fep.cpp @@ -15,10 +15,8 @@ Charges by type and after option: Agilio Padua (Univ Blaise Pascal & CNRS) ------------------------------------------------------------------------- */ -#include -#include -#include #include "fix_adapt_fep.h" +#include #include "atom.h" #include "update.h" #include "group.h" diff --git a/src/USER-FEP/pair_coul_cut_soft.cpp b/src/USER-FEP/pair_coul_cut_soft.cpp index 86a6d02819..a4ff3ca846 100644 --- a/src/USER-FEP/pair_coul_cut_soft.cpp +++ b/src/USER-FEP/pair_coul_cut_soft.cpp @@ -15,11 +15,10 @@ Soft-core version: Agilio Padua (Univ Blaise Pascal & CNRS) ------------------------------------------------------------------------- */ +#include "pair_coul_cut_soft.h" +#include #include -#include -#include #include -#include "pair_coul_cut_soft.h" #include "atom.h" #include "comm.h" #include "force.h" diff --git a/src/USER-FEP/pair_coul_long_soft.cpp b/src/USER-FEP/pair_coul_long_soft.cpp index 9d3ffc0da1..c0030f8935 100644 --- a/src/USER-FEP/pair_coul_long_soft.cpp +++ b/src/USER-FEP/pair_coul_long_soft.cpp @@ -16,19 +16,16 @@ Soft-core version: Agilio Padua (Univ Blaise Pascal & CNRS) ------------------------------------------------------------------------- */ +#include "pair_coul_long_soft.h" +#include #include -#include -#include #include -#include "pair_coul_long_soft.h" #include "atom.h" #include "comm.h" #include "force.h" #include "kspace.h" #include "neighbor.h" #include "neigh_list.h" -#include "update.h" -#include "integrate.h" #include "memory.h" #include "error.h" diff --git a/src/USER-FEP/pair_lj_charmm_coul_long_soft.cpp b/src/USER-FEP/pair_lj_charmm_coul_long_soft.cpp index ac6f1e6384..4c3be6addb 100644 --- a/src/USER-FEP/pair_lj_charmm_coul_long_soft.cpp +++ b/src/USER-FEP/pair_lj_charmm_coul_long_soft.cpp @@ -16,17 +16,15 @@ Soft-core version: Agilio Padua (Univ Blaise Pascal & CNRS) ------------------------------------------------------------------------- */ +#include "pair_lj_charmm_coul_long_soft.h" +#include #include -#include -#include #include -#include "pair_lj_charmm_coul_long_soft.h" #include "atom.h" #include "comm.h" #include "force.h" #include "kspace.h" #include "update.h" -#include "integrate.h" #include "respa.h" #include "neighbor.h" #include "neigh_list.h" diff --git a/src/USER-FEP/pair_lj_class2_coul_cut_soft.cpp b/src/USER-FEP/pair_lj_class2_coul_cut_soft.cpp index ae79515488..bbe67e4ff3 100644 --- a/src/USER-FEP/pair_lj_class2_coul_cut_soft.cpp +++ b/src/USER-FEP/pair_lj_class2_coul_cut_soft.cpp @@ -11,11 +11,10 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ +#include "pair_lj_class2_coul_cut_soft.h" +#include #include -#include -#include #include -#include "pair_lj_class2_coul_cut_soft.h" #include "atom.h" #include "comm.h" #include "force.h" diff --git a/src/USER-FEP/pair_lj_class2_coul_long_soft.cpp b/src/USER-FEP/pair_lj_class2_coul_long_soft.cpp index 275486d1e2..a3e0f732a2 100644 --- a/src/USER-FEP/pair_lj_class2_coul_long_soft.cpp +++ b/src/USER-FEP/pair_lj_class2_coul_long_soft.cpp @@ -11,11 +11,10 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ +#include "pair_lj_class2_coul_long_soft.h" +#include #include -#include -#include #include -#include "pair_lj_class2_coul_long_soft.h" #include "atom.h" #include "comm.h" #include "force.h" diff --git a/src/USER-FEP/pair_lj_class2_soft.cpp b/src/USER-FEP/pair_lj_class2_soft.cpp index d22cd53883..d98a5db5f3 100644 --- a/src/USER-FEP/pair_lj_class2_soft.cpp +++ b/src/USER-FEP/pair_lj_class2_soft.cpp @@ -11,11 +11,10 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ +#include "pair_lj_class2_soft.h" +#include #include -#include -#include #include -#include "pair_lj_class2_soft.h" #include "atom.h" #include "comm.h" #include "force.h" diff --git a/src/USER-FEP/pair_lj_cut_coul_cut_soft.cpp b/src/USER-FEP/pair_lj_cut_coul_cut_soft.cpp index 35c9162dbc..38fcb6fc07 100644 --- a/src/USER-FEP/pair_lj_cut_coul_cut_soft.cpp +++ b/src/USER-FEP/pair_lj_cut_coul_cut_soft.cpp @@ -15,11 +15,10 @@ Soft-core version: Agilio Padua (Univ Blaise Pascal & CNRS) ------------------------------------------------------------------------- */ +#include "pair_lj_cut_coul_cut_soft.h" +#include #include -#include -#include #include -#include "pair_lj_cut_coul_cut_soft.h" #include "atom.h" #include "comm.h" #include "force.h" diff --git a/src/USER-FEP/pair_lj_cut_coul_long_soft.cpp b/src/USER-FEP/pair_lj_cut_coul_long_soft.cpp index 79253d2b9c..740daabf62 100644 --- a/src/USER-FEP/pair_lj_cut_coul_long_soft.cpp +++ b/src/USER-FEP/pair_lj_cut_coul_long_soft.cpp @@ -16,17 +16,15 @@ Soft-core version: Agilio Padua (Univ Blaise Pascal & CNRS) ------------------------------------------------------------------------- */ +#include "pair_lj_cut_coul_long_soft.h" +#include #include -#include -#include #include -#include "pair_lj_cut_coul_long_soft.h" #include "atom.h" #include "comm.h" #include "force.h" #include "kspace.h" #include "update.h" -#include "integrate.h" #include "respa.h" #include "neighbor.h" #include "neigh_list.h" diff --git a/src/USER-FEP/pair_lj_cut_soft.cpp b/src/USER-FEP/pair_lj_cut_soft.cpp index 4192d6546b..5e9a77877e 100644 --- a/src/USER-FEP/pair_lj_cut_soft.cpp +++ b/src/USER-FEP/pair_lj_cut_soft.cpp @@ -16,11 +16,10 @@ Soft-core version: Agilio Padua (Univ Blaise Pascal & CNRS) ------------------------------------------------------------------------- */ +#include "pair_lj_cut_soft.h" +#include #include -#include -#include #include -#include "pair_lj_cut_soft.h" #include "atom.h" #include "comm.h" #include "force.h" @@ -28,7 +27,6 @@ #include "neigh_list.h" #include "neigh_request.h" #include "update.h" -#include "integrate.h" #include "respa.h" #include "math_const.h" #include "memory.h" diff --git a/src/USER-FEP/pair_lj_cut_tip4p_long_soft.cpp b/src/USER-FEP/pair_lj_cut_tip4p_long_soft.cpp index 8ac28f9fa9..d4f6dcb910 100644 --- a/src/USER-FEP/pair_lj_cut_tip4p_long_soft.cpp +++ b/src/USER-FEP/pair_lj_cut_tip4p_long_soft.cpp @@ -17,23 +17,18 @@ Soft-core version: Agilio Padua (Univ Blaise Pascal & CNRS) ------------------------------------------------------------------------- */ +#include "pair_lj_cut_tip4p_long_soft.h" +#include #include -#include -#include #include -#include "pair_lj_cut_tip4p_long_soft.h" #include "angle.h" #include "atom.h" #include "bond.h" #include "comm.h" #include "domain.h" #include "force.h" -#include "kspace.h" -#include "update.h" -#include "respa.h" #include "neighbor.h" #include "neigh_list.h" -#include "neigh_request.h" #include "memory.h" #include "error.h" diff --git a/src/USER-FEP/pair_morse_soft.cpp b/src/USER-FEP/pair_morse_soft.cpp index 21f616a082..2803e7df49 100644 --- a/src/USER-FEP/pair_morse_soft.cpp +++ b/src/USER-FEP/pair_morse_soft.cpp @@ -11,11 +11,10 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ +#include "pair_morse_soft.h" +#include #include -#include -#include #include -#include "pair_morse_soft.h" #include "atom.h" #include "comm.h" #include "force.h" diff --git a/src/USER-FEP/pair_tip4p_long_soft.cpp b/src/USER-FEP/pair_tip4p_long_soft.cpp index 9b6a6841fe..9cea5b54c5 100644 --- a/src/USER-FEP/pair_tip4p_long_soft.cpp +++ b/src/USER-FEP/pair_tip4p_long_soft.cpp @@ -17,23 +17,18 @@ Soft-core version: Agilio Padua (Univ Blaise Pascal & CNRS) ------------------------------------------------------------------------- */ +#include "pair_tip4p_long_soft.h" +#include #include -#include -#include #include -#include "pair_tip4p_long_soft.h" #include "angle.h" #include "atom.h" #include "bond.h" #include "comm.h" #include "domain.h" #include "force.h" -#include "kspace.h" -#include "update.h" -#include "respa.h" #include "neighbor.h" #include "neigh_list.h" -#include "neigh_request.h" #include "memory.h" #include "error.h" diff --git a/src/USER-MESO/fix_mvv_dpd.cpp b/src/USER-MESO/fix_mvv_dpd.cpp index f663165f78..116bbf506a 100644 --- a/src/USER-MESO/fix_mvv_dpd.cpp +++ b/src/USER-MESO/fix_mvv_dpd.cpp @@ -20,13 +20,11 @@ Email: zhen_li@brown.edu ------------------------------------------------------------------------- */ -#include -#include #include "fix_mvv_dpd.h" +#include #include "atom.h" #include "force.h" #include "update.h" -#include "respa.h" #include "error.h" using namespace LAMMPS_NS; diff --git a/src/USER-MESO/fix_tdpd_source.cpp b/src/USER-MESO/fix_tdpd_source.cpp index 89e8005b43..990f6a5b78 100644 --- a/src/USER-MESO/fix_tdpd_source.cpp +++ b/src/USER-MESO/fix_tdpd_source.cpp @@ -11,17 +11,10 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include -#include #include "fix_tdpd_source.h" +#include +#include #include "atom.h" -#include "comm.h" -#include "update.h" -#include "modify.h" -#include "domain.h" -#include "lattice.h" -#include "input.h" -#include "variable.h" #include "error.h" #include "force.h" diff --git a/src/USER-MESO/pair_edpd.cpp b/src/USER-MESO/pair_edpd.cpp index e428b02822..f72b6d6b93 100644 --- a/src/USER-MESO/pair_edpd.cpp +++ b/src/USER-MESO/pair_edpd.cpp @@ -16,14 +16,12 @@ Email: zhen_li@brown.edu ------------------------------------------------------------------------- */ +#include "pair_edpd.h" +#include #include -#include -#include #include #include -#include "pair_edpd.h" #include "atom.h" -#include "atom_vec.h" #include "comm.h" #include "update.h" #include "force.h" diff --git a/src/USER-MESO/pair_mdpd.cpp b/src/USER-MESO/pair_mdpd.cpp index 4102499d46..56adad26ce 100644 --- a/src/USER-MESO/pair_mdpd.cpp +++ b/src/USER-MESO/pair_mdpd.cpp @@ -16,13 +16,11 @@ Email: zhen_li@brown.edu ------------------------------------------------------------------------- */ +#include "pair_mdpd.h" +#include #include -#include -#include #include -#include "pair_mdpd.h" #include "atom.h" -#include "atom_vec.h" #include "comm.h" #include "update.h" #include "force.h" diff --git a/src/USER-MESO/pair_mdpd_rhosum.cpp b/src/USER-MESO/pair_mdpd_rhosum.cpp index 2fd238088c..05cb123f61 100644 --- a/src/USER-MESO/pair_mdpd_rhosum.cpp +++ b/src/USER-MESO/pair_mdpd_rhosum.cpp @@ -19,9 +19,8 @@ Contributing author: Zhen Li (Brown University) ------------------------------------------------------------------------- */ -#include -#include #include "pair_mdpd_rhosum.h" +#include #include "atom.h" #include "force.h" #include "comm.h" @@ -30,8 +29,6 @@ #include "memory.h" #include "error.h" #include "neighbor.h" -#include "update.h" -#include "domain.h" using namespace LAMMPS_NS; diff --git a/src/USER-MESO/pair_tdpd.cpp b/src/USER-MESO/pair_tdpd.cpp index 7df9d6d163..346401b1ba 100644 --- a/src/USER-MESO/pair_tdpd.cpp +++ b/src/USER-MESO/pair_tdpd.cpp @@ -16,13 +16,10 @@ Email: zhen_li@brown.edu ------------------------------------------------------------------------- */ +#include "pair_tdpd.h" #include -#include -#include #include -#include "pair_tdpd.h" #include "atom.h" -#include "atom_vec.h" #include "comm.h" #include "update.h" #include "force.h" -- GitLab From 872d43f02f8e9cc274344baba158366106c338c0 Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Wed, 10 Jul 2019 07:29:29 -0400 Subject: [PATCH 222/469] recover compilation of USER-OMP package --- src/USER-OMP/pair_lj_cut_thole_long_omp.cpp | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/src/USER-OMP/pair_lj_cut_thole_long_omp.cpp b/src/USER-OMP/pair_lj_cut_thole_long_omp.cpp index 85cab4fe7b..d0db6262b1 100644 --- a/src/USER-OMP/pair_lj_cut_thole_long_omp.cpp +++ b/src/USER-OMP/pair_lj_cut_thole_long_omp.cpp @@ -15,13 +15,14 @@ Contributing author: Paul Crozier (SNL) ------------------------------------------------------------------------- */ +#include "pair_lj_cut_thole_long_omp.h" #include #include #include #include -#include "pair_lj_cut_thole_long_omp.h" #include "atom.h" #include "comm.h" +#include "fix_drude.h" #include "force.h" #include "neighbor.h" #include "neigh_list.h" -- GitLab From c5044d648463ae307bcbd1aa90565077489442df Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Wed, 10 Jul 2019 08:49:16 -0400 Subject: [PATCH 223/469] continuing include file handling cleanup --- src/USER-MANIFOLD/fix_manifoldforce.cpp | 5 +- src/USER-MANIFOLD/fix_manifoldforce.h | 2 +- src/USER-MANIFOLD/fix_nve_manifold_rattle.cpp | 10 +- src/USER-MANIFOLD/fix_nve_manifold_rattle.h | 6 +- src/USER-MANIFOLD/fix_nvt_manifold_rattle.cpp | 9 +- src/USER-MANIFOLD/manifold_factory.h | 11 +- src/USER-MANIFOLD/manifold_thylakoid.cpp | 2 +- src/USER-MANIFOLD/manifold_thylakoid.h | 4 +- src/USER-MEAMC/meam.h | 2 +- src/USER-MEAMC/meam_dens_final.cpp | 1 - src/USER-MEAMC/meam_dens_init.cpp | 2 + src/USER-MEAMC/meam_force.cpp | 3 +- src/USER-MEAMC/meam_impl.cpp | 1 + src/USER-MEAMC/meam_setup_done.cpp | 6 +- src/USER-MEAMC/pair_meamc.cpp | 6 +- src/USER-MEAMC/pair_meamc.h | 1 - src/USER-MGPT/mgpt_linalg.cpp | 2 - src/USER-MGPT/mgpt_readpot.h | 4 +- src/USER-MGPT/pair_mgpt.cpp | 5 +- src/USER-MGPT/pair_mgpt.h | 381 +++++++++--------- src/USER-MISC/angle_cosine_shift.cpp | 4 +- src/USER-MISC/angle_cosine_shift_exp.cpp | 4 +- src/USER-MISC/angle_dipole.cpp | 4 +- src/USER-MISC/angle_fourier.cpp | 4 +- src/USER-MISC/angle_fourier_simple.cpp | 4 +- src/USER-MISC/angle_quartic.cpp | 4 +- src/USER-MISC/bond_harmonic_shift.cpp | 5 +- src/USER-MISC/bond_harmonic_shift_cut.cpp | 5 +- src/USER-MISC/compute_cnp_atom.cpp | 5 +- src/USER-MISC/compute_entropy_atom.cpp | 5 +- src/USER-MISC/compute_pressure_cylinder.cpp | 6 +- src/USER-MISC/compute_pressure_grem.cpp | 6 +- src/USER-MISC/compute_stress_mop.cpp | 6 +- src/USER-MISC/compute_stress_mop_profile.cpp | 6 +- src/USER-MISC/compute_temp_rotate.cpp | 5 +- src/USER-MISC/dihedral_cosine_shift_exp.cpp | 4 +- src/USER-MISC/dihedral_fourier.cpp | 5 +- src/USER-MISC/dihedral_nharmonic.cpp | 5 +- src/USER-MISC/dihedral_quadratic.cpp | 5 +- src/USER-MISC/dihedral_spherical.cpp | 5 +- src/USER-MISC/dihedral_table.cpp | 9 +- src/USER-MISC/dihedral_table_cut.cpp | 14 +- src/USER-MISC/fix_addtorque.cpp | 5 +- src/USER-MISC/fix_ave_correlate_long.cpp | 3 +- src/USER-MISC/fix_bond_react.cpp | 3 +- src/USER-MISC/fix_electron_stopping.cpp | 4 +- src/USER-MISC/fix_ffl.cpp | 14 +- src/USER-MISC/fix_filter_corotate.cpp | 17 +- src/USER-MISC/fix_flow_gauss.cpp | 5 +- src/USER-MISC/fix_gle.cpp | 11 +- src/USER-MISC/fix_grem.cpp | 7 +- src/USER-MISC/fix_ipi.cpp | 7 +- src/USER-MISC/fix_nvk.cpp | 6 +- src/USER-MISC/fix_pimd.cpp | 3 +- src/USER-MISC/fix_rhok.cpp | 5 +- src/USER-MISC/fix_smd.cpp | 4 +- src/USER-MISC/fix_srp.cpp | 9 +- src/USER-MISC/fix_ti_spring.cpp | 4 +- src/USER-MISC/fix_ttm_mod.cpp | 5 +- src/USER-MISC/fix_wall_ees.cpp | 10 +- src/USER-MISC/fix_wall_region_ees.cpp | 7 +- 61 files changed, 302 insertions(+), 410 deletions(-) diff --git a/src/USER-MANIFOLD/fix_manifoldforce.cpp b/src/USER-MANIFOLD/fix_manifoldforce.cpp index 00293bfec7..74a9a1833f 100644 --- a/src/USER-MANIFOLD/fix_manifoldforce.cpp +++ b/src/USER-MANIFOLD/fix_manifoldforce.cpp @@ -11,9 +11,9 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include +#include "fix_manifoldforce.h" // For stuff +#include #include -#include #include "atom.h" #include "update.h" #include "respa.h" @@ -21,7 +21,6 @@ #include "force.h" #include "manifold.h" -#include "fix_manifoldforce.h" // For stuff #include "manifold_factory.h" // For constructing manifold diff --git a/src/USER-MANIFOLD/fix_manifoldforce.h b/src/USER-MANIFOLD/fix_manifoldforce.h index 527bee3f86..1d5afc7afc 100644 --- a/src/USER-MANIFOLD/fix_manifoldforce.h +++ b/src/USER-MANIFOLD/fix_manifoldforce.h @@ -43,9 +43,9 @@ FixStyle(manifoldforce,FixManifoldForce) #define LMP_FIX_MANIFOLDFORCE_H #include "fix.h" -#include "manifold.h" namespace LAMMPS_NS { +namespace user_manifold { class manifold; } class FixManifoldForce : public Fix { public: diff --git a/src/USER-MANIFOLD/fix_nve_manifold_rattle.cpp b/src/USER-MANIFOLD/fix_nve_manifold_rattle.cpp index de134e32ed..7f8d9d5675 100644 --- a/src/USER-MANIFOLD/fix_nve_manifold_rattle.cpp +++ b/src/USER-MANIFOLD/fix_nve_manifold_rattle.cpp @@ -32,24 +32,18 @@ ------------------------------------------------------------------------- */ -#include -#include +#include "fix_nve_manifold_rattle.h" +#include #include #include "atom.h" #include "force.h" #include "update.h" -#include "respa.h" #include "error.h" -#include "group.h" -#include #include "input.h" #include "variable.h" #include "citeme.h" -#include "memory.h" #include "comm.h" - -#include "fix_nve_manifold_rattle.h" #include "manifold_factory.h" #include "manifold.h" diff --git a/src/USER-MANIFOLD/fix_nve_manifold_rattle.h b/src/USER-MANIFOLD/fix_nve_manifold_rattle.h index 2bc821ab04..581ecf36d3 100644 --- a/src/USER-MANIFOLD/fix_nve_manifold_rattle.h +++ b/src/USER-MANIFOLD/fix_nve_manifold_rattle.h @@ -42,12 +42,10 @@ FixStyle(nve/manifold/rattle,FixNVEManifoldRattle) #define LMP_FIX_NVE_MANIFOLD_RATTLE_H #include "fix.h" -#include "manifold.h" - namespace LAMMPS_NS { -// namespace user_manifold { +namespace user_manifold { class manifold; } class FixNVEManifoldRattle : public Fix { public: @@ -98,9 +96,7 @@ namespace LAMMPS_NS { user_manifold::manifold *ptr_m; - void print_stats( const char * ); - int was_var( const char * ); virtual void update_var_params(); diff --git a/src/USER-MANIFOLD/fix_nvt_manifold_rattle.cpp b/src/USER-MANIFOLD/fix_nvt_manifold_rattle.cpp index a4eed66336..2789f8738a 100644 --- a/src/USER-MANIFOLD/fix_nvt_manifold_rattle.cpp +++ b/src/USER-MANIFOLD/fix_nvt_manifold_rattle.cpp @@ -32,25 +32,18 @@ ------------------------------------------------------------------------- */ -#include -#include +#include "fix_nvt_manifold_rattle.h" #include #include #include "atom.h" #include "force.h" #include "update.h" -#include "respa.h" #include "error.h" #include "group.h" -#include "input.h" -#include "variable.h" #include "citeme.h" -#include "memory.h" -#include "comm.h" #include "modify.h" #include "compute.h" -#include "fix_nvt_manifold_rattle.h" #include "manifold.h" diff --git a/src/USER-MANIFOLD/manifold_factory.h b/src/USER-MANIFOLD/manifold_factory.h index cc3e1245bf..ac2aee8a26 100644 --- a/src/USER-MANIFOLD/manifold_factory.h +++ b/src/USER-MANIFOLD/manifold_factory.h @@ -35,8 +35,7 @@ #ifndef LMP_MANIFOLD_FACTORY_H #define LMP_MANIFOLD_FACTORY_H - -#include "manifold.h" +#include #include /* @@ -79,14 +78,16 @@ static FILE *screen = fopen("/dev/stdout","w"); #define FLERR __FILE__,__LINE__ // Equivalent to definition in pointers.h #endif // USE_PHONY_LAMMPS - - /* Here the actual implementation of LAMMPS-related functions begins. */ namespace LAMMPS_NS { +class LAMMPS; namespace user_manifold { +// forward declaration +class manifold; + // Templated, so needs to be in header. template void make_manifold_if( manifold **man_ptr, const char *name, @@ -103,8 +104,6 @@ namespace user_manifold { int , char ** ); } // namespace user_manifold - } // namespace LAMMPS_NS - #endif // LMP_MANIFOLD_FACTORY_H diff --git a/src/USER-MANIFOLD/manifold_thylakoid.cpp b/src/USER-MANIFOLD/manifold_thylakoid.cpp index 530e0a876d..e4ef039832 100644 --- a/src/USER-MANIFOLD/manifold_thylakoid.cpp +++ b/src/USER-MANIFOLD/manifold_thylakoid.cpp @@ -1,6 +1,6 @@ #include "manifold_thylakoid.h" #include - +#include "manifold_thylakoid_shared.h" #include "comm.h" #include "domain.h" // For some checks regarding the simulation box. #include "error.h" diff --git a/src/USER-MANIFOLD/manifold_thylakoid.h b/src/USER-MANIFOLD/manifold_thylakoid.h index d8ebe2e94f..35ad4dfd9c 100644 --- a/src/USER-MANIFOLD/manifold_thylakoid.h +++ b/src/USER-MANIFOLD/manifold_thylakoid.h @@ -4,12 +4,10 @@ #include "manifold.h" #include -#include "manifold_thylakoid_shared.h" - namespace LAMMPS_NS { namespace user_manifold { - + struct thyla_part; class manifold_thylakoid : public manifold { public: diff --git a/src/USER-MEAMC/meam.h b/src/USER-MEAMC/meam.h index 74b1eb0e54..da55805790 100644 --- a/src/USER-MEAMC/meam.h +++ b/src/USER-MEAMC/meam.h @@ -1,12 +1,12 @@ #ifndef LMP_MEAM_H #define LMP_MEAM_H -#include "memory.h" #include #define maxelt 5 namespace LAMMPS_NS { +class Memory; typedef enum { FCC, BCC, HCP, DIM, DIA, B1, C11, L12, B2 } lattice_t; diff --git a/src/USER-MEAMC/meam_dens_final.cpp b/src/USER-MEAMC/meam_dens_final.cpp index c55b1b45c4..867106df88 100644 --- a/src/USER-MEAMC/meam_dens_final.cpp +++ b/src/USER-MEAMC/meam_dens_final.cpp @@ -1,5 +1,4 @@ #include "meam.h" -#include "math_special.h" using namespace LAMMPS_NS; diff --git a/src/USER-MEAMC/meam_dens_init.cpp b/src/USER-MEAMC/meam_dens_init.cpp index 3bb9328142..155941422c 100644 --- a/src/USER-MEAMC/meam_dens_init.cpp +++ b/src/USER-MEAMC/meam_dens_init.cpp @@ -1,4 +1,6 @@ #include "meam.h" +#include +#include "memory.h" #include "math_special.h" using namespace LAMMPS_NS; diff --git a/src/USER-MEAMC/meam_force.cpp b/src/USER-MEAMC/meam_force.cpp index 06fbb57adb..09aad90111 100644 --- a/src/USER-MEAMC/meam_force.cpp +++ b/src/USER-MEAMC/meam_force.cpp @@ -1,6 +1,7 @@ #include "meam.h" -#include "math_special.h" +#include #include +#include "math_special.h" using namespace LAMMPS_NS; diff --git a/src/USER-MEAMC/meam_impl.cpp b/src/USER-MEAMC/meam_impl.cpp index b099ead8d5..3b40a2b612 100644 --- a/src/USER-MEAMC/meam_impl.cpp +++ b/src/USER-MEAMC/meam_impl.cpp @@ -16,6 +16,7 @@ ------------------------------------------------------------------------- */ #include "meam.h" +#include #include "memory.h" using namespace LAMMPS_NS; diff --git a/src/USER-MEAMC/meam_setup_done.cpp b/src/USER-MEAMC/meam_setup_done.cpp index 2a762d1204..7000eac6ae 100644 --- a/src/USER-MEAMC/meam_setup_done.cpp +++ b/src/USER-MEAMC/meam_setup_done.cpp @@ -1,6 +1,10 @@ #include "meam.h" -#include "math_special.h" +#include +#include #include +#include "math_special.h" +#include "memory.h" + using namespace LAMMPS_NS; void diff --git a/src/USER-MEAMC/pair_meamc.cpp b/src/USER-MEAMC/pair_meamc.cpp index 7c96fadb44..a9034a1af3 100644 --- a/src/USER-MEAMC/pair_meamc.cpp +++ b/src/USER-MEAMC/pair_meamc.cpp @@ -15,16 +15,14 @@ Contributing author: Greg Wagner (SNL) ------------------------------------------------------------------------- */ -#include -#include +#include "pair_meamc.h" +#include #include #include #include "meam.h" -#include "pair_meamc.h" #include "atom.h" #include "force.h" #include "comm.h" -#include "memory.h" #include "neighbor.h" #include "neigh_list.h" #include "neigh_request.h" diff --git a/src/USER-MEAMC/pair_meamc.h b/src/USER-MEAMC/pair_meamc.h index a006e70bdb..31dd8ba022 100644 --- a/src/USER-MEAMC/pair_meamc.h +++ b/src/USER-MEAMC/pair_meamc.h @@ -24,7 +24,6 @@ PairStyle(meam,PairMEAMC) #include "pair.h" namespace LAMMPS_NS { -class MEAM; class PairMEAMC : public Pair { public: diff --git a/src/USER-MGPT/mgpt_linalg.cpp b/src/USER-MGPT/mgpt_linalg.cpp index 68701037f4..bc15873739 100644 --- a/src/USER-MGPT/mgpt_linalg.cpp +++ b/src/USER-MGPT/mgpt_linalg.cpp @@ -20,8 +20,6 @@ #include #include -#include -#include #define restrict __restrict__ diff --git a/src/USER-MGPT/mgpt_readpot.h b/src/USER-MGPT/mgpt_readpot.h index 62f66883b6..8f46592e8a 100644 --- a/src/USER-MGPT/mgpt_readpot.h +++ b/src/USER-MGPT/mgpt_readpot.h @@ -19,7 +19,9 @@ #ifndef READPOT__ #define READPOT__ - +#include +#include +#include #include "mgpt_splinetab.h" struct potdata { diff --git a/src/USER-MGPT/pair_mgpt.cpp b/src/USER-MGPT/pair_mgpt.cpp index 91c624eec5..0634872c70 100644 --- a/src/USER-MGPT/pair_mgpt.cpp +++ b/src/USER-MGPT/pair_mgpt.cpp @@ -21,17 +21,16 @@ (2011). See LLNL copyright notice at bottom of this file. ------------------------------------------------------------------------- */ +#include "pair_mgpt.h" +#include #include -#include #include #include #include -#include "pair_mgpt.h" #include "atom.h" #include "force.h" #include "comm.h" -#include "memory.h" #include "neighbor.h" #include "neigh_list.h" #include "neigh_request.h" diff --git a/src/USER-MGPT/pair_mgpt.h b/src/USER-MGPT/pair_mgpt.h index 70b36364b1..3e861a0198 100644 --- a/src/USER-MGPT/pair_mgpt.h +++ b/src/USER-MGPT/pair_mgpt.h @@ -32,6 +32,7 @@ PairStyle(mgpt,PairMGPT) #include #include +#include #include #include "pair.h" @@ -77,29 +78,29 @@ public: Link(const K &k,Link *n) : next(n),key(k),hits(1) {} static void *operator new(std::size_t sz) { - const size_t align = 32; - size_t x = (size_t) (void *) ::operator new(sz+align); - size_t y = (x + align) - ((x+align)&(align-1)); - assert(sizeof(void *) <= align); - assert((x & (sizeof(void *)-1)) == 0); - ((void **) y)[-1] = (void *) x; - return (void *) y; + const size_t align = 32; + size_t x = (size_t) (void *) ::operator new(sz+align); + size_t y = (x + align) - ((x+align)&(align-1)); + assert(sizeof(void *) <= align); + assert((x & (sizeof(void *)-1)) == 0); + ((void **) y)[-1] = (void *) x; + return (void *) y; } static void operator delete(void *ptr) { - ::operator delete(((void **) ptr)[-1]); + ::operator delete(((void **) ptr)[-1]); } }; int isprime(int x) { if(x%2 == 0) - return 0; + return 0; else { - int k = 3; - while(k*k <= x) { - if(x%k == 0) return 0; - k = k+2; - } - return 1; + int k = 3; + while(k*k <= x) { + if(x%k == 0) return 0; + k = k+2; + } + return 1; } } @@ -117,25 +118,25 @@ public: Iterator(Hash &HH) : H(HH),idx(-1),p(0) { next(); } Iterator(Hash &HH,int iidx,Link *pp) : H(HH),idx(iidx),p(pp) {} void next() { - if(idx >= H.Size()) return; - if(p != 0) p = p->next; - if(p == 0) { - do { - idx = idx+1; - if(idx >= H.Size()) return; - p = H.table[idx]; - } while(p == 0); - } + if(idx >= H.Size()) return; + if(p != 0) p = p->next; + if(p == 0) { + do { + idx = idx+1; + if(idx >= H.Size()) return; + p = H.table[idx]; + } while(p == 0); + } } K *key() { return &p->key; } T *data() { return &p->data; } Link *link() { return p; } int operator==(const Iterator &a) { - return idx==a.idx && p==a.p; + return idx==a.idx && p==a.p; } int operator!=(const Iterator &a) { - return !(*this == a); + return !(*this == a); } }; @@ -147,7 +148,7 @@ public: table = new Link *[size]; for(int i = 0; inext; - delete p; - p = q; - } + Link *p = table[i]; + while(p != 0) { + Link *q = p->next; + delete p; + p = q; + } } delete[] table; } @@ -179,24 +180,24 @@ public: int idx = key.hash() % size; if(idx < 0) idx = idx + size; if(idx >= size || idx < 0) { - printf("(1) Damn... key = %d, idx = %d, size = %d\n",key.hash(),idx,size); - exit(1); + printf("(1) Damn... key = %d, idx = %d, size = %d\n",key.hash(),idx,size); + exit(1); } used = used + 1; if(1) { - table[idx] = new Link(key,table[idx]); - return &table[idx]->data; + table[idx] = new Link(key,table[idx]); + return &table[idx]->data; } else { /* This is for threading... and incomplete */ - typedef Link *LinkPtr; - LinkPtr ptr = table[idx],last = 0,dataptr = new Link(key,0); - - while(ptr != 0) { - last = ptr; - ptr = ptr->next; - } - *((volatile LinkPtr *) &(last->next)) = dataptr; - return &(dataptr->data); + typedef Link *LinkPtr; + LinkPtr ptr = table[idx],last = 0,dataptr = new Link(key,0); + + while(ptr != 0) { + last = ptr; + ptr = ptr->next; + } + *((volatile LinkPtr *) &(last->next)) = dataptr; + return &(dataptr->data); } } void Remove(const K &key) { @@ -205,28 +206,28 @@ public: int count = 1; if(idx < 0) idx = idx + size; if(idx >= size || idx < 0) { - printf("(2) Damn... key = %d, idx = %d, size = %d\n",key.hash(),idx,size); - exit(1); + printf("(2) Damn... key = %d, idx = %d, size = %d\n",key.hash(),idx,size); + exit(1); } p = table[idx]; while(p != 0 && !(p->key == key)) { - last = p; - p = p->next; - count = count + 1; + last = p; + p = p->next; + count = count + 1; } if(p != 0) { - used = used - 1; - if(last == 0) - table[idx] = p->next; - else - last->next = p->next; - delete p; + used = used - 1; + if(last == 0) + table[idx] = p->next; + else + last->next = p->next; + delete p; } if(count > maxlength) - maxlength = count; + maxlength = count; nsearch = nsearch + 1; nstep = nstep + count; } @@ -236,19 +237,19 @@ public: int count = 1; if(idx < 0) idx = idx + size; if(idx >= size || idx < 0) { - printf("(3) Damn... key = %d, idx = %d, size = %d\n",key.hash(),idx,size); - exit(1); + printf("(3) Damn... key = %d, idx = %d, size = %d\n",key.hash(),idx,size); + exit(1); } p = table[idx]; while(p != 0 && !(p->key == key)) { - p = p->next; - count = count + 1; + p = p->next; + count = count + 1; } if(count > maxlength) - maxlength = count; + maxlength = count; nsearch = nsearch + 1; nstep = nstep + count; @@ -283,46 +284,46 @@ public: } void zero() { for(int i = 0; i<8; i++) - for(int j = 0; j<8; j++) - m[i][j] = 0.0; + for(int j = 0; j<8; j++) + m[i][j] = 0.0; } void operator=(const Matrix &A) { for(int i = 1; i<=sz; i++) - for(int j = 1; j<=sz; j++) - m[i][j] = A.m[i][j]; + for(int j = 1; j<=sz; j++) + m[i][j] = A.m[i][j]; } void operator=(double x) { for(int i = 1; i<=sz; i++) - for(int j = 1; j<=sz; j++) - m[i][j] = x; + for(int j = 1; j<=sz; j++) + m[i][j] = x; } Matrix operator+(const Matrix &B) const { Matrix s; for(int i = 1; i<=sz; i++) - for(int j = 1; j<=sz; j++) - s.m[i][j] = m[i][j] + B.m[i][j]; + for(int j = 1; j<=sz; j++) + s.m[i][j] = m[i][j] + B.m[i][j]; return s; } Matrix operator-(const Matrix &B) const { Matrix s; for(int i = 1; i<=sz; i++) - for(int j = 1; j<=sz; j++) - s.m[i][j] = m[i][j] - B.m[i][j]; + for(int j = 1; j<=sz; j++) + s.m[i][j] = m[i][j] - B.m[i][j]; return s; } Matrix operator-() const { Matrix s; for(int i = 1; i<=sz; i++) - for(int j = 1; j<=sz; j++) - s.m[i][j] = -m[i][j]; + for(int j = 1; j<=sz; j++) + s.m[i][j] = -m[i][j]; return s; } Matrix operator*(double x) const { Matrix P; for(int i = 1; i<=sz; i++) - for(int j = 0; j<=sz; j++) - P.m[i][j] = m[i][j] * x; + for(int j = 0; j<=sz; j++) + P.m[i][j] = m[i][j] * x; return P; } Matrix operator/(double x) const { @@ -331,8 +332,8 @@ public: Matrix transpose() const { Matrix T; for(int i = 1; i<=sz; i++) - for(int j = 1; j<=sz; j++) - T.m[j][i] = m[i][j]; + for(int j = 1; j<=sz; j++) + T.m[j][i] = m[i][j]; return T; } }; @@ -374,13 +375,13 @@ public: int align_check() { return - (H1H2.align_check() << 0) | - (H1xH2.align_check() << 1) | - (H1yH2.align_check() << 2) | - (H1zH2.align_check() << 3) | - (H1H2x.align_check() << 4) | - (H1H2y.align_check() << 5) | - (H1H2z.align_check() << 6) ; + (H1H2.align_check() << 0) | + (H1xH2.align_check() << 1) | + (H1yH2.align_check() << 2) | + (H1zH2.align_check() << 3) | + (H1H2x.align_check() << 4) | + (H1H2y.align_check() << 5) | + (H1H2z.align_check() << 6) ; } void zero() { @@ -396,18 +397,18 @@ public: void make_bond(const double xx[][3],int i,int j,bond_data *bptr); void make_triplet(bond_data *ij_bond,bond_data *ik_bond,triplet_data *triptr); triplet_data *get_triplet(const double xx[][3],int i,int j,int k, - Hash *bhash,triplet_data *twork, - double *dvir_ij_p,double *dvir_ik_p); + Hash *bhash,triplet_data *twork, + double *dvir_ij_p,double *dvir_ik_p); int c1_outside(const double a[3], - int triclinic,const double alpha[3]) { + int triclinic,const double alpha[3]) { const double stol = 1e-5; if(triclinic) { for(int p = 0; p<3; p++) { - double cog = a[p]; - if(cog < domain->sublo_lamda[p]-0.5*rmax*alpha[p]-stol) return 1; - if(cog > domain->subhi_lamda[p]+0.5*rmax*alpha[p]+stol) return 1; + double cog = a[p]; + if(cog < domain->sublo_lamda[p]-0.5*rmax*alpha[p]-stol) return 1; + if(cog > domain->subhi_lamda[p]+0.5*rmax*alpha[p]+stol) return 1; } } else { @@ -415,63 +416,63 @@ public: for(int p = 0; p<3; p++) { - double cog = a[p]; - if(cog < domain->sublo[p]-0.5*rmax-stol) return 1; - if(cog > domain->subhi[p]+0.5*rmax+stol) return 1; - - if(cog < domain->sublo[p]-stol) { - double t = cog - (domain->sublo[p]-stol); - rout = rout + t*t; - } else if(cog > domain->subhi[p]+stol) { - double t = cog - (domain->subhi[p]+stol); - rout = rout + t*t; - } + double cog = a[p]; + if(cog < domain->sublo[p]-0.5*rmax-stol) return 1; + if(cog > domain->subhi[p]+0.5*rmax+stol) return 1; + + if(cog < domain->sublo[p]-stol) { + double t = cog - (domain->sublo[p]-stol); + rout = rout + t*t; + } else if(cog > domain->subhi[p]+stol) { + double t = cog - (domain->subhi[p]+stol); + rout = rout + t*t; + } } if(rout > 0.25*rmax*rmax) - return 1; + return 1; } return 0; } int c2_outside(const double a[3],const double b[3], - int triclinic,const double alpha[3]) { + int triclinic,const double alpha[3]) { const double stol = 1e-5; if(triclinic) { for(int p = 0; p<3; p++) { - double cog = 0.5*(a[p] + b[p]); - if(cog < domain->sublo_lamda[p]-0.5*rcrit*alpha[p]-stol) return 1; - if(cog > domain->subhi_lamda[p]+0.5*rcrit*alpha[p]+stol) return 1; + double cog = 0.5*(a[p] + b[p]); + if(cog < domain->sublo_lamda[p]-0.5*rcrit*alpha[p]-stol) return 1; + if(cog > domain->subhi_lamda[p]+0.5*rcrit*alpha[p]+stol) return 1; } } else { double rout = 0.0; for(int p = 0; p<3; p++) { - double cog = 0.5*(a[p] + b[p]); - if(cog < domain->sublo[p]-0.5*rcrit-stol) return 1; - if(cog > domain->subhi[p]+0.5*rcrit+stol) return 1; - - if(cog < domain->sublo[p]-stol) { - double t = cog - (domain->sublo[p]-stol); - rout = rout + t*t; - } else if(cog > domain->subhi[p]+stol) { - double t = cog - (domain->subhi[p]+stol); - rout = rout + t*t; - } + double cog = 0.5*(a[p] + b[p]); + if(cog < domain->sublo[p]-0.5*rcrit-stol) return 1; + if(cog > domain->subhi[p]+0.5*rcrit+stol) return 1; + + if(cog < domain->sublo[p]-stol) { + double t = cog - (domain->sublo[p]-stol); + rout = rout + t*t; + } else if(cog > domain->subhi[p]+stol) { + double t = cog - (domain->subhi[p]+stol); + rout = rout + t*t; + } } if(rout > 0.25*rcrit*rcrit) - return 1; + return 1; } return 0; } double get_weight(const int triclinic, - const double a[3] = 0,const double b[3] = 0, - const double c[3] = 0,const double d[3] = 0) { + const double a[3] = 0,const double b[3] = 0, + const double c[3] = 0,const double d[3] = 0) { const double *s0 = triclinic ? domain->sublo_lamda : domain->sublo, *s1 = triclinic ? domain->subhi_lamda : domain->subhi; @@ -498,46 +499,46 @@ public: } void force_debug_3t(double xx[][3], - int i0,int j0,int k0, - int i ,int j ,int k , - double dfix,double dfiy,double dfiz, - double dfjx,double dfjy,double dfjz, - double dfkx,double dfky,double dfkz); + int i0,int j0,int k0, + int i ,int j ,int k , + double dfix,double dfiy,double dfiz, + double dfjx,double dfjy,double dfjz, + double dfkx,double dfky,double dfkz); void force_debug_3v(double xx[][3], - int i0,int j0,int k0, - int i ,int j ,int k , - double dfix,double dfiy,double dfiz, - double dfjx,double dfjy,double dfjz, - double dfkx,double dfky,double dfkz); + int i0,int j0,int k0, + int i ,int j ,int k , + double dfix,double dfiy,double dfiz, + double dfjx,double dfjy,double dfjz, + double dfkx,double dfky,double dfkz); void force_debug_4(double xx[][3], - int i0,int j0,int k0,int m0, - int i ,int j ,int k ,int m , - double dfix,double dfiy,double dfiz, - double dfjx,double dfjy,double dfjz, - double dfkx,double dfky,double dfkz, - double dfmx,double dfmy,double dfmz); + int i0,int j0,int k0,int m0, + int i ,int j ,int k ,int m , + double dfix,double dfiy,double dfiz, + double dfjx,double dfjy,double dfjz, + double dfkx,double dfky,double dfkz, + double dfmx,double dfmy,double dfmz); double numderiv3t(double xx[][3],int i,int j,int k,int p); double numderiv3v(double xx[][3],int i,int j,int k,int p,int ipert); double numderiv4(double xx[][3],int i,int j,int k,int m,int p); void compute_x(const int *nnei,const int * const *nlist, - double *e_s,double *e_p,double *e_t,double *e_q, - int evflag,int newton_pair); + double *e_s,double *e_p,double *e_t,double *e_q, + int evflag,int newton_pair); /* Reimplementation of bond matrix computation */ void fl_deriv_new(double r,double ri,double xhat,double yhat,double zhat, - double &fl_0,double &fl_x,double &fl_y,double &fl_z, - double &fl_rp,double &fl_p1,double &fl_r0,double &fl_al); + double &fl_0,double &fl_x,double &fl_y,double &fl_z, + double &fl_rp,double &fl_p1,double &fl_r0,double &fl_al); void hamltn_5_raw(const double xin,const double yin,const double zin, - double M [8][8],double Mx[8][8], - double My[8][8],double Mz[8][8], - double *fl_deriv_sum_p); + double M [8][8],double Mx[8][8], + double My[8][8],double Mz[8][8], + double *fl_deriv_sum_p); void hamltn_7_raw(const double xin,const double yin,const double zin, - double M [8][8],double Mx[8][8], - double My[8][8],double Mz[8][8], - double *fl_deriv_sum_p); + double M [8][8],double Mx[8][8], + double My[8][8],double Mz[8][8], + double *fl_deriv_sum_p); /* * */ // Old matrix routines, only used in force debug routines. @@ -546,9 +547,9 @@ public: Matrix h; for(int l = 1; l <= lmax; l++) { for(int n = 1; n <= lmax; n++) { - h.m[l][n] = 0.0; - for(int m = 1; m <= lmax; m++) - h.m[l][n] += ha.m[l][m] * hb.m[m][n]; + h.m[l][n] = 0.0; + for(int m = 1; m <= lmax; m++) + h.m[l][n] += ha.m[l][m] * hb.m[m][n]; } } return h; @@ -560,7 +561,7 @@ public: for(int n = 1; n <= lmax; n++) { double cquan = 0.0; for(int m = 1; m <= lmax; m++) - cquan += ha.m[n][m] * hb.m[m][n]; + cquan += ha.m[n][m] * hb.m[m][n]; zquan += cquan; } return zquan; @@ -572,32 +573,32 @@ public: int i,j,k; if(lmax == 5) { - const int n = 5; - for(i = 1; i<=n; i++) - for(j = 1; j<=n; j++) { - double s = 0.0; - for(k = 1; k<=n; k++) - s = s + a.m[i][k]*b.m[j][k]; - c.m[i][j] = s; - } + const int n = 5; + for(i = 1; i<=n; i++) + for(j = 1; j<=n; j++) { + double s = 0.0; + for(k = 1; k<=n; k++) + s = s + a.m[i][k]*b.m[j][k]; + c.m[i][j] = s; + } } else if(lmax == 7) { - const int n = 7; - for(i = 1; i<=n; i++) - for(j = 1; j<=n; j++) { - double s = 0.0; - for(k = 1; k<=n; k++) - s = s + a.m[i][k]*b.m[j][k]; - c.m[i][j] = s; - } + const int n = 7; + for(i = 1; i<=n; i++) + for(j = 1; j<=n; j++) { + double s = 0.0; + for(k = 1; k<=n; k++) + s = s + a.m[i][k]*b.m[j][k]; + c.m[i][j] = s; + } } else { - const int n = lmax; - for(i = 1; i<=n; i++) - for(j = 1; j<=n; j++) { - double s = 0.0; - for(k = 1; k<=n; k++) - s = s + a.m[i][k]*b.m[j][k]; - c.m[i][j] = s; - } + const int n = lmax; + for(i = 1; i<=n; i++) + for(j = 1; j<=n; j++) { + double s = 0.0; + for(k = 1; k<=n; k++) + s = s + a.m[i][k]*b.m[j][k]; + c.m[i][j] = s; + } } } @@ -608,7 +609,7 @@ public: for(i = 0; i -#include #include "angle_cosine_shift.h" +#include +#include #include "atom.h" #include "neighbor.h" #include "domain.h" diff --git a/src/USER-MISC/angle_cosine_shift_exp.cpp b/src/USER-MISC/angle_cosine_shift_exp.cpp index 8c6282de20..79cb0fea7c 100644 --- a/src/USER-MISC/angle_cosine_shift_exp.cpp +++ b/src/USER-MISC/angle_cosine_shift_exp.cpp @@ -15,9 +15,9 @@ Contributing author: Carsten Svaneborg, science@zqex.dk ------------------------------------------------------------------------- */ -#include -#include #include "angle_cosine_shift_exp.h" +#include +#include #include "atom.h" #include "neighbor.h" #include "domain.h" diff --git a/src/USER-MISC/angle_dipole.cpp b/src/USER-MISC/angle_dipole.cpp index 781da46869..0956ba3b8f 100644 --- a/src/USER-MISC/angle_dipole.cpp +++ b/src/USER-MISC/angle_dipole.cpp @@ -15,9 +15,9 @@ Contributing authors: Mario Orsi & Wei Ding (QMUL), m.orsi@qmul.ac.uk ------------------------------------------------------------------------- */ -#include -#include #include "angle_dipole.h" +#include +#include #include "atom.h" #include "neighbor.h" #include "domain.h" diff --git a/src/USER-MISC/angle_fourier.cpp b/src/USER-MISC/angle_fourier.cpp index 8f5074ff5d..dcf5080431 100644 --- a/src/USER-MISC/angle_fourier.cpp +++ b/src/USER-MISC/angle_fourier.cpp @@ -16,9 +16,9 @@ [ based on angle_cosine_squared.cpp Naveen Michaud-Agrawal (Johns Hopkins U)] ------------------------------------------------------------------------- */ -#include -#include #include "angle_fourier.h" +#include +#include #include "atom.h" #include "neighbor.h" #include "domain.h" diff --git a/src/USER-MISC/angle_fourier_simple.cpp b/src/USER-MISC/angle_fourier_simple.cpp index 615556bbe7..bbe3f8520b 100644 --- a/src/USER-MISC/angle_fourier_simple.cpp +++ b/src/USER-MISC/angle_fourier_simple.cpp @@ -16,9 +16,9 @@ [ based on angle_cosine_squared.cpp Naveen Michaud-Agrawal (Johns Hopkins U)] ------------------------------------------------------------------------- */ -#include -#include #include "angle_fourier_simple.h" +#include +#include #include "atom.h" #include "neighbor.h" #include "domain.h" diff --git a/src/USER-MISC/angle_quartic.cpp b/src/USER-MISC/angle_quartic.cpp index 21a96100aa..5c5f3411e4 100644 --- a/src/USER-MISC/angle_quartic.cpp +++ b/src/USER-MISC/angle_quartic.cpp @@ -16,9 +16,9 @@ [ based on angle_harmonic.cpp] ------------------------------------------------------------------------- */ -#include -#include #include "angle_quartic.h" +#include +#include #include "atom.h" #include "neighbor.h" #include "domain.h" diff --git a/src/USER-MISC/bond_harmonic_shift.cpp b/src/USER-MISC/bond_harmonic_shift.cpp index c7e4444cce..fdd3111783 100644 --- a/src/USER-MISC/bond_harmonic_shift.cpp +++ b/src/USER-MISC/bond_harmonic_shift.cpp @@ -15,12 +15,11 @@ Contributing author: Carsten Svaneborg, science@zqex.dk ------------------------------------------------------------------------- */ -#include -#include #include "bond_harmonic_shift.h" +#include +#include #include "atom.h" #include "neighbor.h" -#include "domain.h" #include "comm.h" #include "force.h" #include "memory.h" diff --git a/src/USER-MISC/bond_harmonic_shift_cut.cpp b/src/USER-MISC/bond_harmonic_shift_cut.cpp index 5b396f5d72..0688cb428a 100644 --- a/src/USER-MISC/bond_harmonic_shift_cut.cpp +++ b/src/USER-MISC/bond_harmonic_shift_cut.cpp @@ -15,12 +15,11 @@ Contributing author: Carsten Svaneborg, science@zqex.dk ------------------------------------------------------------------------- */ -#include -#include #include "bond_harmonic_shift_cut.h" +#include +#include #include "atom.h" #include "neighbor.h" -#include "domain.h" #include "comm.h" #include "force.h" #include "memory.h" diff --git a/src/USER-MISC/compute_cnp_atom.cpp b/src/USER-MISC/compute_cnp_atom.cpp index 6fa16f1a9a..ba97be25d4 100644 --- a/src/USER-MISC/compute_cnp_atom.cpp +++ b/src/USER-MISC/compute_cnp_atom.cpp @@ -21,11 +21,10 @@ branicio@usc.edu ------------------------------------------------------------------------- */ +#include "compute_cnp_atom.h" +#include #include -#include #include - -#include "compute_cnp_atom.h" #include "atom.h" #include "update.h" #include "modify.h" diff --git a/src/USER-MISC/compute_entropy_atom.cpp b/src/USER-MISC/compute_entropy_atom.cpp index 0367d7fe6d..00f7e6dc8b 100644 --- a/src/USER-MISC/compute_entropy_atom.cpp +++ b/src/USER-MISC/compute_entropy_atom.cpp @@ -15,10 +15,9 @@ Contributing author: Pablo Piaggi (EPFL Lausanne) ------------------------------------------------------------------------- */ +#include "compute_entropy_atom.h" #include #include -#include -#include "compute_entropy_atom.h" #include "atom.h" #include "update.h" #include "modify.h" @@ -28,13 +27,11 @@ #include "force.h" #include "pair.h" #include "comm.h" -#include "math_extra.h" #include "math_const.h" #include "memory.h" #include "error.h" #include "domain.h" - using namespace LAMMPS_NS; using namespace MathConst; diff --git a/src/USER-MISC/compute_pressure_cylinder.cpp b/src/USER-MISC/compute_pressure_cylinder.cpp index c250eaf677..6d2509d685 100644 --- a/src/USER-MISC/compute_pressure_cylinder.cpp +++ b/src/USER-MISC/compute_pressure_cylinder.cpp @@ -11,10 +11,9 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include -#include -#include #include "compute_pressure_cylinder.h" +#include +#include #include "atom.h" #include "update.h" #include "force.h" @@ -22,7 +21,6 @@ #include "neighbor.h" #include "neigh_request.h" #include "neigh_list.h" -#include "group.h" #include "memory.h" #include "error.h" #include "citeme.h" diff --git a/src/USER-MISC/compute_pressure_grem.cpp b/src/USER-MISC/compute_pressure_grem.cpp index 087c01bd8e..ba949727b0 100644 --- a/src/USER-MISC/compute_pressure_grem.cpp +++ b/src/USER-MISC/compute_pressure_grem.cpp @@ -11,17 +11,13 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include -#include -#include #include "compute_pressure_grem.h" -#include "atom.h" +#include #include "update.h" #include "domain.h" #include "modify.h" #include "fix.h" #include "force.h" -#include "pair.h" #include "kspace.h" #include "error.h" diff --git a/src/USER-MISC/compute_stress_mop.cpp b/src/USER-MISC/compute_stress_mop.cpp index cb2a0b9713..2f932321e1 100644 --- a/src/USER-MISC/compute_stress_mop.cpp +++ b/src/USER-MISC/compute_stress_mop.cpp @@ -15,18 +15,14 @@ Contributing Authors : Romain Vermorel (LFCR), Laurent Joly (ULyon) --------------------------------------------------------------------------*/ +#include "compute_stress_mop.h" #include #include #include -#include -#include "compute_stress_mop.h" #include "atom.h" #include "update.h" #include "domain.h" -#include "group.h" -#include "modify.h" -#include "fix.h" #include "neighbor.h" #include "force.h" #include "pair.h" diff --git a/src/USER-MISC/compute_stress_mop_profile.cpp b/src/USER-MISC/compute_stress_mop_profile.cpp index 5499a37a46..5f6d0a36b2 100644 --- a/src/USER-MISC/compute_stress_mop_profile.cpp +++ b/src/USER-MISC/compute_stress_mop_profile.cpp @@ -15,18 +15,14 @@ Contributing Authors : Romain Vermorel (LFCR), Laurent Joly (ULyon) --------------------------------------------------------------------------*/ +#include "compute_stress_mop_profile.h" #include #include #include -#include -#include "compute_stress_mop_profile.h" #include "atom.h" #include "update.h" #include "domain.h" -#include "group.h" -#include "modify.h" -#include "fix.h" #include "neighbor.h" #include "force.h" #include "pair.h" diff --git a/src/USER-MISC/compute_temp_rotate.cpp b/src/USER-MISC/compute_temp_rotate.cpp index 36093bd1e1..94c6115186 100644 --- a/src/USER-MISC/compute_temp_rotate.cpp +++ b/src/USER-MISC/compute_temp_rotate.cpp @@ -15,16 +15,13 @@ Contributing author: Laurent Joly (U Lyon, France), ljoly.ulyon@gmail.com ------------------------------------------------------------------------- */ -#include -#include -#include #include "compute_temp_rotate.h" +#include #include "atom.h" #include "update.h" #include "force.h" #include "group.h" #include "domain.h" -#include "lattice.h" #include "error.h" #include "memory.h" diff --git a/src/USER-MISC/dihedral_cosine_shift_exp.cpp b/src/USER-MISC/dihedral_cosine_shift_exp.cpp index c411ea8150..820dfabdeb 100644 --- a/src/USER-MISC/dihedral_cosine_shift_exp.cpp +++ b/src/USER-MISC/dihedral_cosine_shift_exp.cpp @@ -15,14 +15,12 @@ Contributing author: Carsten Svaneborg, science@zqex.dk ------------------------------------------------------------------------- */ +#include "dihedral_cosine_shift_exp.h" #include #include -#include -#include "dihedral_cosine_shift_exp.h" #include "atom.h" #include "comm.h" #include "neighbor.h" -#include "domain.h" #include "force.h" #include "update.h" #include "memory.h" diff --git a/src/USER-MISC/dihedral_fourier.cpp b/src/USER-MISC/dihedral_fourier.cpp index af86259c01..7cc250b1a8 100644 --- a/src/USER-MISC/dihedral_fourier.cpp +++ b/src/USER-MISC/dihedral_fourier.cpp @@ -16,16 +16,13 @@ [ based on dihedral_charmm.cpp Paul Crozier (SNL) ] ------------------------------------------------------------------------- */ +#include "dihedral_fourier.h" #include #include -#include -#include "dihedral_fourier.h" #include "atom.h" #include "comm.h" #include "neighbor.h" -#include "domain.h" #include "force.h" -#include "pair.h" #include "update.h" #include "math_const.h" #include "memory.h" diff --git a/src/USER-MISC/dihedral_nharmonic.cpp b/src/USER-MISC/dihedral_nharmonic.cpp index ea2b76f415..f1e0018689 100644 --- a/src/USER-MISC/dihedral_nharmonic.cpp +++ b/src/USER-MISC/dihedral_nharmonic.cpp @@ -16,12 +16,11 @@ [ based on dihedral_multi_harmonic.cpp Mathias Puetz (SNL) and friends ] ------------------------------------------------------------------------- */ -#include -#include #include "dihedral_nharmonic.h" +#include +#include #include "atom.h" #include "neighbor.h" -#include "domain.h" #include "comm.h" #include "force.h" #include "update.h" diff --git a/src/USER-MISC/dihedral_quadratic.cpp b/src/USER-MISC/dihedral_quadratic.cpp index 8436e73c5c..02effc2f4f 100644 --- a/src/USER-MISC/dihedral_quadratic.cpp +++ b/src/USER-MISC/dihedral_quadratic.cpp @@ -16,12 +16,11 @@ [ based on dihedral_helix.cpp Paul Crozier (SNL) ] ------------------------------------------------------------------------- */ -#include -#include #include "dihedral_quadratic.h" +#include +#include #include "atom.h" #include "neighbor.h" -#include "domain.h" #include "comm.h" #include "force.h" #include "update.h" diff --git a/src/USER-MISC/dihedral_spherical.cpp b/src/USER-MISC/dihedral_spherical.cpp index 3b30121551..78d45f923d 100644 --- a/src/USER-MISC/dihedral_spherical.cpp +++ b/src/USER-MISC/dihedral_spherical.cpp @@ -17,22 +17,19 @@ and Paul Crozier (SNL) ] ------------------------------------------------------------------------- */ +#include "dihedral_spherical.h" #include #include -#include #include #include "atom.h" #include "comm.h" #include "neighbor.h" #include "domain.h" #include "force.h" -#include "pair.h" -#include "update.h" #include "math_const.h" #include "math_extra.h" #include "memory.h" #include "error.h" -#include "dihedral_spherical.h" using namespace std; using namespace LAMMPS_NS; diff --git a/src/USER-MISC/dihedral_table.cpp b/src/USER-MISC/dihedral_table.cpp index a97ae3649f..7fa871d3be 100644 --- a/src/USER-MISC/dihedral_table.cpp +++ b/src/USER-MISC/dihedral_table.cpp @@ -17,21 +17,20 @@ the "tridiag.c" written by Gerard Jungman for GSL ------------------------------------------------------------------------- */ +#include +#include #include #include #include -#include #include -#include -#include -#include +#include // IWYU pragma: keep +#include // IWYU pragma: keep #include "atom.h" #include "comm.h" #include "neighbor.h" #include "domain.h" #include "force.h" -#include "update.h" #include "memory.h" #include "error.h" #include "dihedral_table.h" diff --git a/src/USER-MISC/dihedral_table_cut.cpp b/src/USER-MISC/dihedral_table_cut.cpp index 18a645cd75..71f9ea0df1 100644 --- a/src/USER-MISC/dihedral_table_cut.cpp +++ b/src/USER-MISC/dihedral_table_cut.cpp @@ -16,25 +16,23 @@ Based on tabulated dihedral (dihedral_table.cpp) by Andrew Jewett ------------------------------------------------------------------------- */ +#include "dihedral_table_cut.h" +#include +#include #include #include #include -#include #include -#include -#include -#include +#include // IWYU pragma: keep +#include // IWYU pragma: keep -#include "dihedral_table_cut.h" #include "atom.h" #include "neighbor.h" #include "update.h" -#include "domain.h" #include "comm.h" #include "force.h" #include "citeme.h" #include "math_const.h" -#include "math_extra.h" #include "memory.h" #include "error.h" #include "utils.h" @@ -42,8 +40,6 @@ using namespace LAMMPS_NS; using namespace MathConst; using namespace std; -using namespace MathExtra; - static const char cite_dihedral_tablecut[] = "dihedral_style table/cut command:\n\n" diff --git a/src/USER-MISC/fix_addtorque.cpp b/src/USER-MISC/fix_addtorque.cpp index 2cd1ac7527..665f1d4a60 100644 --- a/src/USER-MISC/fix_addtorque.cpp +++ b/src/USER-MISC/fix_addtorque.cpp @@ -15,9 +15,9 @@ Contributing author: Laurent Joly (U Lyon, France), ljoly.ulyon@gmail.com ------------------------------------------------------------------------- */ -#include -#include #include "fix_addtorque.h" +#include +#include #include "atom.h" #include "update.h" #include "modify.h" @@ -25,7 +25,6 @@ #include "respa.h" #include "input.h" #include "variable.h" -#include "memory.h" #include "error.h" #include "group.h" #include "force.h" diff --git a/src/USER-MISC/fix_ave_correlate_long.cpp b/src/USER-MISC/fix_ave_correlate_long.cpp index dc52d94b14..b1bcc07fa7 100644 --- a/src/USER-MISC/fix_ave_correlate_long.cpp +++ b/src/USER-MISC/fix_ave_correlate_long.cpp @@ -21,11 +21,12 @@ see J. Chem. Phys. 133, 154103 (2010) ------------------------------------------------------------------------- */ +#include "fix_ave_correlate_long.h" +#include #include #include #include #include -#include "fix_ave_correlate_long.h" #include "update.h" #include "modify.h" #include "compute.h" diff --git a/src/USER-MISC/fix_bond_react.cpp b/src/USER-MISC/fix_bond_react.cpp index c641912db6..ef23f98d64 100644 --- a/src/USER-MISC/fix_bond_react.cpp +++ b/src/USER-MISC/fix_bond_react.cpp @@ -15,11 +15,10 @@ See the README file in the top-level LAMMPS directory. Contributing Author: Jacob Gissinger (jacob.gissinger@colorado.edu) ------------------------------------------------------------------------- */ +#include "fix_bond_react.h" #include #include #include -#include -#include "fix_bond_react.h" #include "update.h" #include "modify.h" #include "respa.h" diff --git a/src/USER-MISC/fix_electron_stopping.cpp b/src/USER-MISC/fix_electron_stopping.cpp index 0831ebcf89..2130f07420 100644 --- a/src/USER-MISC/fix_electron_stopping.cpp +++ b/src/USER-MISC/fix_electron_stopping.cpp @@ -16,16 +16,14 @@ Information: k.avchachov@gmail.com ------------------------------------------------------------------------- */ +#include "fix_electron_stopping.h" #include -#include #include -#include "fix_electron_stopping.h" #include "mpi.h" #include "atom.h" #include "update.h" #include "domain.h" #include "region.h" -#include "group.h" #include "force.h" #include "fix.h" #include "memory.h" diff --git a/src/USER-MISC/fix_ffl.cpp b/src/USER-MISC/fix_ffl.cpp index 9ab113aeaa..a245b6b4e5 100644 --- a/src/USER-MISC/fix_ffl.cpp +++ b/src/USER-MISC/fix_ffl.cpp @@ -18,31 +18,21 @@ /* ---------------------------------------------------------------------- Contributing authors: Lionel Constantin (EPFL), David M. Wilkins (EPFL), - Michele Ceriotti (EPFL) + Michele Ceriotti (EPFL) ------------------------------------------------------------------------- */ +#include "fix_ffl.h" #include #include #include -#include -#include "fix_ffl.h" -#include "math_extra.h" #include "atom.h" -#include "atom_vec_ellipsoid.h" #include "force.h" #include "update.h" -#include "modify.h" -#include "compute.h" -#include "domain.h" -#include "region.h" #include "respa.h" #include "comm.h" -#include "input.h" -#include "variable.h" #include "random_mars.h" #include "memory.h" #include "error.h" -#include "group.h" using namespace LAMMPS_NS; using namespace FixConst; diff --git a/src/USER-MISC/fix_filter_corotate.cpp b/src/USER-MISC/fix_filter_corotate.cpp index f6cc1c435f..bfc5f58f93 100644 --- a/src/USER-MISC/fix_filter_corotate.cpp +++ b/src/USER-MISC/fix_filter_corotate.cpp @@ -16,30 +16,25 @@ some subroutines are from fix_shake.cpp ------------------------------------------------------------------------- */ +#include "fix_filter_corotate.h" #include +#include +#include #include #include -#include "fix_filter_corotate.h" #include "atom.h" #include "atom_vec.h" -#include "molecule.h" -#include "bond.h" +#include "comm.h" +#include "domain.h" #include "angle.h" +#include "bond.h" #include "math_const.h" #include "update.h" #include "modify.h" -#include "domain.h" -#include "region.h" #include "memory.h" #include "error.h" #include "force.h" -#include "comm.h" -#include "error.h" -#include "memory.h" -#include "domain.h" -#include "integrate.h" #include "respa.h" -#include "neighbor.h" #include "citeme.h" using namespace LAMMPS_NS; diff --git a/src/USER-MISC/fix_flow_gauss.cpp b/src/USER-MISC/fix_flow_gauss.cpp index b6366ec509..70be1f1e45 100644 --- a/src/USER-MISC/fix_flow_gauss.cpp +++ b/src/USER-MISC/fix_flow_gauss.cpp @@ -16,13 +16,12 @@ Joel.Eaves@Colorado.edu ------------------------------------------------------------------------- */ -#include -#include #include "fix_flow_gauss.h" +#include +#include #include "atom.h" #include "force.h" #include "group.h" -#include "comm.h" #include "update.h" #include "domain.h" #include "error.h" diff --git a/src/USER-MISC/fix_gle.cpp b/src/USER-MISC/fix_gle.cpp index 01da7f87cf..b8bdc66d08 100644 --- a/src/USER-MISC/fix_gle.cpp +++ b/src/USER-MISC/fix_gle.cpp @@ -16,28 +16,19 @@ Axel Kohylmeyer (Temple U) ------------------------------------------------------------------------- */ +#include "fix_gle.h" #include #include #include #include -#include "fix_gle.h" -#include "math_extra.h" #include "atom.h" -#include "atom_vec_ellipsoid.h" #include "force.h" #include "update.h" -#include "modify.h" -#include "compute.h" -#include "domain.h" -#include "region.h" #include "respa.h" #include "comm.h" -#include "input.h" -#include "variable.h" #include "random_mars.h" #include "memory.h" #include "error.h" -#include "group.h" using namespace LAMMPS_NS; using namespace FixConst; diff --git a/src/USER-MISC/fix_grem.cpp b/src/USER-MISC/fix_grem.cpp index 635acf705c..4272740068 100644 --- a/src/USER-MISC/fix_grem.cpp +++ b/src/USER-MISC/fix_grem.cpp @@ -22,19 +22,14 @@ Tom Keyes (Boston University) ------------------------------------------------------------------------- */ -#include -#include -#include -#include "comm.h" #include "fix_grem.h" +#include #include "atom.h" #include "force.h" #include "update.h" #include "modify.h" #include "domain.h" -#include "input.h" #include "compute.h" -#include "memory.h" #include "error.h" using namespace LAMMPS_NS; diff --git a/src/USER-MISC/fix_ipi.cpp b/src/USER-MISC/fix_ipi.cpp index 32892d87a8..08b39ee89b 100644 --- a/src/USER-MISC/fix_ipi.cpp +++ b/src/USER-MISC/fix_ipi.cpp @@ -15,15 +15,12 @@ Contributing author: Michele Ceriotti (EPFL), Axel Kohlmeyer (Temple U) ------------------------------------------------------------------------- */ +#include "fix_ipi.h" #include -#include #include -#include -#include "fix_ipi.h" #include "atom.h" #include "force.h" #include "update.h" -#include "respa.h" #include "error.h" #include "kspace.h" #include "modify.h" @@ -32,8 +29,6 @@ #include "neighbor.h" #include "irregular.h" #include "domain.h" -#include "compute_pressure.h" -#include using namespace LAMMPS_NS; using namespace FixConst; diff --git a/src/USER-MISC/fix_nvk.cpp b/src/USER-MISC/fix_nvk.cpp index 2ac2a7c9fc..410a269f8c 100644 --- a/src/USER-MISC/fix_nvk.cpp +++ b/src/USER-MISC/fix_nvk.cpp @@ -15,18 +15,16 @@ Contributing author: Efrem Braun (UC Berkeley) ------------------------------------------------------------------------- */ +#include "fix_nvk.h" +#include #include -#include #include -#include "fix_nvk.h" #include "atom.h" #include "force.h" #include "update.h" #include "respa.h" #include "error.h" -#include "compute.h" #include "math_extra.h" -#include "domain.h" using namespace LAMMPS_NS; using namespace FixConst; diff --git a/src/USER-MISC/fix_pimd.cpp b/src/USER-MISC/fix_pimd.cpp index 3929d47d6b..8f790f0a59 100644 --- a/src/USER-MISC/fix_pimd.cpp +++ b/src/USER-MISC/fix_pimd.cpp @@ -21,10 +21,11 @@ Version 1.0 ------------------------------------------------------------------------- */ +#include "fix_pimd.h" +#include #include #include #include -#include "fix_pimd.h" #include "universe.h" #include "comm.h" #include "force.h" diff --git a/src/USER-MISC/fix_rhok.cpp b/src/USER-MISC/fix_rhok.cpp index 6a6e71ebaa..c638adf6a4 100644 --- a/src/USER-MISC/fix_rhok.cpp +++ b/src/USER-MISC/fix_rhok.cpp @@ -13,12 +13,11 @@ Contributing author: Ulf R. Pedersen, ulf@urp.dk ------------------------------------------------------------------------- */ -#include -#include +#include "fix_rhok.h" +#include #include #include -#include "fix_rhok.h" #include "atom.h" #include "domain.h" #include "error.h" diff --git a/src/USER-MISC/fix_smd.cpp b/src/USER-MISC/fix_smd.cpp index cbebdebdbf..32c040c2b4 100644 --- a/src/USER-MISC/fix_smd.cpp +++ b/src/USER-MISC/fix_smd.cpp @@ -16,10 +16,10 @@ based on fix spring by: Paul Crozier (SNL) ------------------------------------------------------------------------- */ +#include "fix_smd.h" +#include #include -#include #include -#include "fix_smd.h" #include "atom.h" #include "comm.h" #include "update.h" diff --git a/src/USER-MISC/fix_srp.cpp b/src/USER-MISC/fix_srp.cpp index ebc161ff99..c0db252db4 100644 --- a/src/USER-MISC/fix_srp.cpp +++ b/src/USER-MISC/fix_srp.cpp @@ -15,9 +15,10 @@ Contributing authors: Timothy Sirk (ARL), Pieter in't Veld (BASF) ------------------------------------------------------------------------- */ -#include -#include #include "fix_srp.h" +#include +#include +#include #include "atom.h" #include "force.h" #include "domain.h" @@ -635,11 +636,11 @@ void FixSRP::restart(char *buf) int FixSRP::modify_param(int /*narg*/, char **arg) { if (strcmp(arg[0],"btype") == 0) { - btype = atoi(arg[1]); + btype = force->inumeric(FLERR,arg[1]); return 2; } if (strcmp(arg[0],"bptype") == 0) { - bptype = atoi(arg[1]); + bptype = force->inumeric(FLERR,arg[1]); return 2; } return 0; diff --git a/src/USER-MISC/fix_ti_spring.cpp b/src/USER-MISC/fix_ti_spring.cpp index 305e29e033..8481b34a6b 100644 --- a/src/USER-MISC/fix_ti_spring.cpp +++ b/src/USER-MISC/fix_ti_spring.cpp @@ -18,9 +18,9 @@ Maurice de Koning (Unicamp/Brazil) - dekoning@ifi.unicamp.br ------------------------------------------------------------------------- */ -#include -#include #include "fix_ti_spring.h" +#include +#include #include "atom.h" #include "update.h" #include "domain.h" diff --git a/src/USER-MISC/fix_ttm_mod.cpp b/src/USER-MISC/fix_ttm_mod.cpp index a34c2eb42f..55526a9149 100644 --- a/src/USER-MISC/fix_ttm_mod.cpp +++ b/src/USER-MISC/fix_ttm_mod.cpp @@ -17,17 +17,14 @@ Vasily Pisarev (Joint Institute for High Temperatures of RAS) ------------------------------------------------------------------------- */ -#include "lmptype.h" +#include "fix_ttm_mod.h" #include #include #include -#include -#include "fix_ttm_mod.h" #include "atom.h" #include "force.h" #include "update.h" #include "domain.h" -#include "region.h" #include "respa.h" #include "comm.h" #include "random_mars.h" diff --git a/src/USER-MISC/fix_wall_ees.cpp b/src/USER-MISC/fix_wall_ees.cpp index 5ca16ebdad..bd7e230472 100644 --- a/src/USER-MISC/fix_wall_ees.cpp +++ b/src/USER-MISC/fix_wall_ees.cpp @@ -15,21 +15,13 @@ Contributing author: Abdoreza Ershadinia, a.ershadinia at gmail.com ------------------------------------------------------------------------- */ +#include "fix_wall_ees.h" #include #include "math_extra.h" -#include "fix_wall_ees.h" #include "atom.h" #include "atom_vec.h" #include "atom_vec_ellipsoid.h" -#include "domain.h" -#include "region.h" -#include "force.h" -#include "lattice.h" -#include "update.h" -#include "output.h" -#include "respa.h" #include "error.h" -#include "math_extra.h" using namespace LAMMPS_NS; using namespace FixConst; diff --git a/src/USER-MISC/fix_wall_region_ees.cpp b/src/USER-MISC/fix_wall_region_ees.cpp index 33bf636e64..5c6bb1874b 100644 --- a/src/USER-MISC/fix_wall_region_ees.cpp +++ b/src/USER-MISC/fix_wall_region_ees.cpp @@ -15,19 +15,16 @@ Contributing author: Abdoreza Ershadinia, a.ershadinia at gmail.com ------------------------------------------------------------------------- */ +#include "fix_wall_region_ees.h" +#include #include -#include #include -#include "fix_wall_region_ees.h" #include "atom.h" -#include "atom_vec.h" #include "atom_vec_ellipsoid.h" #include "domain.h" #include "region.h" #include "force.h" -#include "lattice.h" #include "update.h" -#include "output.h" #include "respa.h" #include "error.h" #include "math_extra.h" -- GitLab From 89af88bd10343585de91b695c0348252f109f04e Mon Sep 17 00:00:00 2001 From: Steve Plimpton Date: Wed, 10 Jul 2019 08:41:27 -0600 Subject: [PATCH 224/469] more changes to robustify comm buf_send length --- src/atom_vec_hybrid.cpp | 3 ++ src/comm.h | 2 +- src/comm_brick.cpp | 27 ++++++++++------- src/comm_tiled.cpp | 23 +++++++++------ src/irregular.cpp | 64 ++++++++++++++++++++++++++++++++--------- src/irregular.h | 2 ++ 6 files changed, 87 insertions(+), 34 deletions(-) diff --git a/src/atom_vec_hybrid.cpp b/src/atom_vec_hybrid.cpp index a7816efbed..d0e8ed62ed 100644 --- a/src/atom_vec_hybrid.cpp +++ b/src/atom_vec_hybrid.cpp @@ -95,6 +95,7 @@ void AtomVecHybrid::process_args(int narg, char **arg) size_data_atom = 5; size_data_vel = 4; xcol_data = 3; + maxexchange = 0; for (int k = 0; k < nstyles; k++) { if ((styles[k]->molecular == 1 && molecular == 2) || @@ -120,6 +121,8 @@ void AtomVecHybrid::process_args(int narg, char **arg) size_border += styles[k]->size_border - 6; size_data_atom += styles[k]->size_data_atom - 5; size_data_vel += styles[k]->size_data_vel - 4; + + maxexchange += styles[k]->maxexchange; } size_velocity = 3; diff --git a/src/comm.h b/src/comm.h index 3367051e3c..967af0a014 100644 --- a/src/comm.h +++ b/src/comm.h @@ -134,7 +134,7 @@ class Comm : protected Pointers { int maxexchange_atom; // contribution to maxexchange from AtomVec int maxexchange_fix; // static contribution to maxexchange from Fixes int maxexchange_fix_dynamic; // 1 if a fix has a dynamic contribution - int bufextra; // augment size of send buf for an exchange atom + int bufextra; // augment send buf size for an exchange atom int gridflag; // option for creating 3d grid diff --git a/src/comm_brick.cpp b/src/comm_brick.cpp index 97114e5734..5c5fec47c0 100644 --- a/src/comm_brick.cpp +++ b/src/comm_brick.cpp @@ -109,9 +109,9 @@ void CommBrick::init_buffers() multilo = multihi = NULL; cutghostmulti = NULL; - maxsend = BUFMIN; - memory->create(buf_send,maxsend+bufextra,"comm:buf_send"); - maxrecv = BUFMIN; + buf_send = buf_recv = NULL; + maxsend = maxrecv = BUFMIN; + grow_send(maxsend,2); memory->create(buf_recv,maxrecv,"comm:buf_recv"); nswap = 0; @@ -134,7 +134,7 @@ void CommBrick::init() int bufextra_old = bufextra; init_exchange(); - if (bufextra > bufextra_old) grow_send(maxsend+bufextra,0); + if (bufextra > bufextra_old) grow_send(maxsend+bufextra,2); // memory for multi-style communication @@ -604,7 +604,7 @@ void CommBrick::exchange() if (maxexchange_fix_dynamic) { int bufextra_old = bufextra; init_exchange(); - if (bufextra > bufextra_old) grow_send(maxsend+bufextra,0); + if (bufextra > bufextra_old) grow_send(maxsend+bufextra,2); } // subbox bounds for orthogonal or triclinic @@ -1346,18 +1346,23 @@ int CommBrick::exchange_variable(int n, double *inbuf, double *&outbuf) /* ---------------------------------------------------------------------- realloc the size of the send buffer as needed with BUFFACTOR and bufextra - if flag = 1, realloc - if flag = 0, don't need to realloc with copy, just free/malloc + flag = 0, don't need to realloc with copy, just free/malloc w/ BUFFACTOR + flag = 1, realloc with BUFFACTOR + flag = 2, free/malloc w/out BUFFACTOR ------------------------------------------------------------------------- */ void CommBrick::grow_send(int n, int flag) { - maxsend = static_cast (BUFFACTOR * n); - if (flag) - memory->grow(buf_send,maxsend+bufextra,"comm:buf_send"); - else { + if (flag == 0) { + maxsend = static_cast (BUFFACTOR * n); memory->destroy(buf_send); memory->create(buf_send,maxsend+bufextra,"comm:buf_send"); + } else if (flag == 1) { + maxsend = static_cast (BUFFACTOR * n); + memory->grow(buf_send,maxsend+bufextra,"comm:buf_send"); + } else { + memory->destroy(buf_send); + memory->grow(buf_send,maxsend+bufextra,"comm:buf_send"); } } diff --git a/src/comm_tiled.cpp b/src/comm_tiled.cpp index c9f1a63fbc..2e04aa2978 100644 --- a/src/comm_tiled.cpp +++ b/src/comm_tiled.cpp @@ -79,9 +79,9 @@ CommTiled::~CommTiled() void CommTiled::init_buffers() { - maxsend = BUFMIN; - memory->create(buf_send,maxsend+bufextra,"comm:buf_send"); - maxrecv = BUFMIN; + buf_send = buf_recv = NULL; + maxsend = maxrecv = BUFMIN; + grow_send(maxsend,2); memory->create(buf_recv,maxrecv,"comm:buf_recv"); maxoverlap = 0; @@ -1804,18 +1804,23 @@ int CommTiled::coord2proc(double *x, int &igx, int &igy, int &igz) /* ---------------------------------------------------------------------- realloc the size of the send buffer as needed with BUFFACTOR and bufextra - if flag = 1, realloc - if flag = 0, don't need to realloc with copy, just free/malloc + flag = 0, don't need to realloc with copy, just free/malloc w/ BUFFACTOR + flag = 1, realloc with BUFFACTOR + flag = 2, free/malloc w/out BUFFACTOR ------------------------------------------------------------------------- */ void CommTiled::grow_send(int n, int flag) { - maxsend = static_cast (BUFFACTOR * n); - if (flag) - memory->grow(buf_send,maxsend+bufextra,"comm:buf_send"); - else { + if (flag == 0) { + maxsend = static_cast (BUFFACTOR * n); memory->destroy(buf_send); memory->create(buf_send,maxsend+bufextra,"comm:buf_send"); + } else if (flag == 1) { + maxsend = static_cast (BUFFACTOR * n); + memory->grow(buf_send,maxsend+bufextra,"comm:buf_send"); + } else { + memory->destroy(buf_send); + memory->grow(buf_send,maxsend+bufextra,"comm:buf_send"); } } diff --git a/src/irregular.cpp b/src/irregular.cpp index 1865f9cbf6..9851770612 100644 --- a/src/irregular.cpp +++ b/src/irregular.cpp @@ -19,6 +19,8 @@ #include "atom_vec.h" #include "domain.h" #include "comm.h" +#include "modify.h" +#include "fix.h" #include "memory.h" using namespace LAMMPS_NS; @@ -35,8 +37,8 @@ static int compare_standalone(const int, const int, void *); #endif #define BUFFACTOR 1.5 -#define BUFMIN 1000 -#define BUFEXTRA 1000 +#define BUFMIN 1024 +#define BUFEXTRA 1024 /* ---------------------------------------------------------------------- */ @@ -69,9 +71,10 @@ Irregular::Irregular(LAMMPS *lmp) : Pointers(lmp) // initialize buffers for migrate atoms, not used for datum comm // these can persist for multiple irregular operations - maxsend = BUFMIN; - memory->create(buf_send,maxsend+BUFEXTRA,"comm:buf_send"); - maxrecv = BUFMIN; + buf_send = buf_recv = NULL; + maxsend = maxrecv = BUFMIN; + bufextra = BUFEXTRA; + grow_send(maxsend,2); memory->create(buf_recv,maxrecv,"comm:buf_recv"); } @@ -103,6 +106,13 @@ Irregular::~Irregular() void Irregular::migrate_atoms(int sortflag, int preassign, int *procassign) { + // check if buf_send needs to be extended due to atom style or per-atom fixes + // same as in Comm::exchange() + + int bufextra_old = bufextra; + init_exchange(); + if (bufextra > bufextra_old) grow_send(maxsend+bufextra,2); + // clear global->local map since atoms move to new procs // clear old ghosts so map_set() at end will operate only on local atoms // exchange() doesn't need to clear ghosts b/c borders() @@ -983,24 +993,52 @@ void Irregular::destroy_data() } /* ---------------------------------------------------------------------- - realloc the size of the send buffer as needed with BUFFACTOR & BUFEXTRA - if flag = 1, realloc - if flag = 0, don't need to realloc with copy, just free/malloc + set bufextra based on AtomVec and fixes + similar to Comm::init_exchange() +------------------------------------------------------------------------- */ + +void Irregular::init_exchange() +{ + int nfix = modify->nfix; + Fix **fix = modify->fix; + + int onefix; + int maxexchange_fix = 0; + for (int i = 0; i < nfix; i++) { + onefix = fix[i]->maxexchange; + maxexchange_fix = MAX(maxexchange_fix,onefix); + } + + int maxexchange = atom->avec->maxexchange + maxexchange_fix; + bufextra = maxexchange + BUFEXTRA; +} + +/* ---------------------------------------------------------------------- + realloc the size of the send buffer as needed with BUFFACTOR and bufextra + flag = 0, don't need to realloc with copy, just free/malloc w/ BUFFACTOR + flag = 1, realloc with BUFFACTOR + flag = 2, free/malloc w/out BUFFACTOR + same as Comm::grow_send() ------------------------------------------------------------------------- */ void Irregular::grow_send(int n, int flag) { - maxsend = static_cast (BUFFACTOR * n); - if (flag) - memory->grow(buf_send,maxsend+BUFEXTRA,"comm:buf_send"); - else { + if (flag == 0) { + maxsend = static_cast (BUFFACTOR * n); + memory->destroy(buf_send); + memory->create(buf_send,maxsend+bufextra,"comm:buf_send"); + } else if (flag == 1) { + maxsend = static_cast (BUFFACTOR * n); + memory->grow(buf_send,maxsend+bufextra,"comm:buf_send"); + } else { memory->destroy(buf_send); - memory->create(buf_send,maxsend+BUFEXTRA,"comm:buf_send"); + memory->grow(buf_send,maxsend+bufextra,"comm:buf_send"); } } /* ---------------------------------------------------------------------- free/malloc the size of the recv buffer as needed with BUFFACTOR + same as Comm::grow_recv() ------------------------------------------------------------------------- */ void Irregular::grow_recv(int n) diff --git a/src/irregular.h b/src/irregular.h index d56bcb253d..01fe40c46b 100644 --- a/src/irregular.h +++ b/src/irregular.h @@ -43,6 +43,7 @@ class Irregular : protected Pointers { int triclinic; int map_style; + int bufextra; // augment send buf size for a migrating atom int maxsend,maxrecv; // size of buf send/recv in # of doubles double *buf_send,*buf_recv; // bufs used in migrate_atoms int maxdbuf; // size of double buf in bytes @@ -91,6 +92,7 @@ class Irregular : protected Pointers { int binary(double, int, double *); + void init_exchange(); // reset bufxtra void grow_send(int,int); // reallocate send buffer void grow_recv(int); // free/allocate recv buffer }; -- GitLab From 941607595aff199660cc3e5a1fc682e29a213a5c Mon Sep 17 00:00:00 2001 From: Steve Plimpton Date: Wed, 10 Jul 2019 08:48:33 -0600 Subject: [PATCH 225/469] one more change --- src/comm_tiled.cpp | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/src/comm_tiled.cpp b/src/comm_tiled.cpp index 2e04aa2978..652bb7add9 100644 --- a/src/comm_tiled.cpp +++ b/src/comm_tiled.cpp @@ -101,7 +101,7 @@ void CommTiled::init() int bufextra_old = bufextra; init_exchange(); - if (bufextra > bufextra_old) grow_send(maxsend+bufextra,0); + if (bufextra > bufextra_old) grow_send(maxsend+bufextra,2); // temporary restrictions @@ -645,7 +645,7 @@ void CommTiled::exchange() if (maxexchange_fix_dynamic) { int bufextra_old = bufextra; init_exchange(); - if (bufextra > bufextra_old) grow_send(maxsend+bufextra,1); + if (bufextra > bufextra_old) grow_send(maxsend+bufextra,2); } // domain properties used in exchange method and methods it calls -- GitLab From ea68db964a3dcbdab7aec33f9e4edee404469d53 Mon Sep 17 00:00:00 2001 From: "Ryan S. Elliott" Date: Wed, 10 Jul 2019 14:21:07 -0500 Subject: [PATCH 226/469] trim (left and right) strings from kim_query xxxx split --- src/KIM/kim_query.cpp | 2 ++ 1 file changed, 2 insertions(+) diff --git a/src/KIM/kim_query.cpp b/src/KIM/kim_query.cpp index cf4efc2b12..221dc9e804 100644 --- a/src/KIM/kim_query.cpp +++ b/src/KIM/kim_query.cpp @@ -138,6 +138,8 @@ void KimQuery::command(int narg, char **arg) varcmd[1] = (char *) "string"; while(std::getline(ss, token, ',')) { + token.erase(0,token.find_first_not_of(" \n\r\t")); // ltrim + token.erase(token.find_last_not_of(" \n\r\t") + 1); // rtrim std::stringstream splitname; splitname << varname << "_" << counter++; varcmd[0] = const_cast(splitname.str().c_str()); -- GitLab From 956d21ec0ead2d94220c22dd5ba97c0bbe45189f Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Wed, 10 Jul 2019 15:38:41 -0400 Subject: [PATCH 227/469] update include lists in packages USER-MISC, USER-MOFF, USER-PTM, and USER-SMD --- src/USER-MISC/fix_imd.cpp | 2 -- src/USER-MISC/improper_cossq.cpp | 4 +--- src/USER-MISC/improper_distance.cpp | 4 +--- src/USER-MISC/improper_fourier.cpp | 5 +---- src/USER-MISC/improper_ring.cpp | 5 +---- src/USER-MISC/pair_agni.cpp | 6 ++---- src/USER-MISC/pair_buck_mdf.cpp | 7 ++----- src/USER-MISC/pair_coul_diel.cpp | 6 ++---- src/USER-MISC/pair_coul_shield.cpp | 5 +---- src/USER-MISC/pair_drip.cpp | 6 ++---- src/USER-MISC/pair_drip.h | 2 -- src/USER-MISC/pair_e3b.cpp | 8 +++----- src/USER-MISC/pair_edip.cpp | 4 ++-- src/USER-MISC/pair_edip_multi.cpp | 5 ++--- src/USER-MISC/pair_extep.cpp | 4 ++-- src/USER-MISC/pair_extep.h | 1 - src/USER-MISC/pair_gauss_cut.cpp | 9 ++------- src/USER-MISC/pair_ilp_graphene_hbn.cpp | 3 +-- src/USER-MISC/pair_ilp_graphene_hbn.h | 2 -- src/USER-MISC/pair_kolmogorov_crespi_full.cpp | 3 +-- src/USER-MISC/pair_kolmogorov_crespi_full.h | 2 -- src/USER-MISC/pair_kolmogorov_crespi_z.cpp | 4 ++-- src/USER-MISC/pair_lebedeva_z.cpp | 4 ++-- src/USER-MISC/pair_lennard_mdf.cpp | 6 ++---- src/USER-MISC/pair_list.cpp | 10 +++------- src/USER-MISC/pair_lj_expand_coul_long.cpp | 6 ++---- src/USER-MISC/pair_lj_mdf.cpp | 6 ++---- src/USER-MISC/pair_lj_sf_dipole_sf.cpp | 4 ++-- src/USER-MISC/pair_meam_spline.cpp | 4 +--- src/USER-MISC/pair_meam_sw_spline.cpp | 4 +--- src/USER-MISC/pair_momb.cpp | 5 ++--- src/USER-MISC/pair_morse_smooth_linear.cpp | 5 ++--- src/USER-MISC/pair_srp.cpp | 4 +++- src/USER-MISC/pair_tersoff_table.cpp | 4 ++-- src/USER-MISC/temper_grem.cpp | 7 +------ src/USER-MISC/temper_npt.cpp | 6 +----- src/USER-MOFFF/angle_class2_p6.cpp | 4 ++-- src/USER-MOFFF/angle_cosine_buck6d.cpp | 6 ++---- src/USER-MOFFF/improper_inversion_harmonic.cpp | 6 +----- src/USER-MOFFF/pair_buck6d_coul_gauss_dsf.cpp | 4 +--- src/USER-MOFFF/pair_buck6d_coul_gauss_long.cpp | 7 ++----- src/USER-PTM/compute_ptm_atom.cpp | 4 +--- src/USER-PTM/ptm_convex_hull_incremental.cpp | 1 - src/USER-PTM/ptm_index.cpp | 4 ---- src/USER-PTM/ptm_initialize_data.cpp | 8 +------- src/USER-PTM/ptm_neighbour_ordering.cpp | 5 ++--- src/USER-PTM/ptm_polar.h | 1 - src/USER-PTM/ptm_quat.cpp | 2 +- src/USER-PTM/ptm_voronoi_cell.cpp | 2 +- src/USER-PTM/ptm_voronoi_cell.h | 3 --- src/USER-SMD/atom_vec_smd.cpp | 5 +---- src/USER-SMD/compute_smd_contact_radius.cpp | 3 +-- src/USER-SMD/compute_smd_damage.cpp | 3 +-- src/USER-SMD/compute_smd_internal_energy.cpp | 1 - src/USER-SMD/compute_smd_plastic_strain.cpp | 3 +-- src/USER-SMD/compute_smd_plastic_strain_rate.cpp | 3 +-- src/USER-SMD/compute_smd_rho.cpp | 3 +-- src/USER-SMD/compute_smd_tlsph_defgrad.cpp | 8 ++------ src/USER-SMD/compute_smd_tlsph_shape.cpp | 6 +----- src/USER-SMD/compute_smd_tlsph_strain.cpp | 5 +---- src/USER-SMD/compute_smd_tlsph_stress.cpp | 3 ++- src/USER-SMD/compute_smd_triangle_vertices.cpp | 9 +-------- src/USER-SMD/compute_smd_ulsph_strain.cpp | 9 +-------- src/USER-SMD/compute_smd_ulsph_stress.cpp | 3 ++- src/USER-SMD/compute_smd_vol.cpp | 4 ++-- src/USER-SMD/fix_smd_adjust_dt.cpp | 11 ++--------- src/USER-SMD/fix_smd_integrate_tlsph.cpp | 10 ++-------- src/USER-SMD/fix_smd_integrate_ulsph.cpp | 11 +---------- src/USER-SMD/fix_smd_move_triangulated_surface.cpp | 14 ++------------ src/USER-SMD/fix_smd_setvel.cpp | 4 ++-- .../fix_smd_tlsph_reference_configuration.cpp | 6 +----- .../fix_smd_tlsph_reference_configuration.h | 1 - src/USER-SMD/fix_smd_wall_surface.cpp | 12 +++--------- src/USER-SMD/pair_smd_hertz.cpp | 7 ++----- src/USER-SMD/pair_smd_tlsph.cpp | 11 +++-------- src/USER-SMD/pair_smd_triangulated_surface.cpp | 9 ++------- src/USER-SMD/pair_smd_ulsph.cpp | 8 +------- src/USER-SMD/smd_material_models.cpp | 4 ++++ 78 files changed, 111 insertions(+), 294 deletions(-) diff --git a/src/USER-MISC/fix_imd.cpp b/src/USER-MISC/fix_imd.cpp index 1c3eafdc46..10aaa285a5 100644 --- a/src/USER-MISC/fix_imd.cpp +++ b/src/USER-MISC/fix_imd.cpp @@ -58,8 +58,6 @@ negotiate an appropriate license for such distribution." #include "group.h" #include "memory.h" -#include -#include #include #include diff --git a/src/USER-MISC/improper_cossq.cpp b/src/USER-MISC/improper_cossq.cpp index c8eb0808fb..2ea804b95d 100644 --- a/src/USER-MISC/improper_cossq.cpp +++ b/src/USER-MISC/improper_cossq.cpp @@ -16,14 +16,12 @@ gvog@chemeng.ntua.gr ------------------------------------------------------------------------- */ +#include "improper_cossq.h" #include #include -#include -#include "improper_cossq.h" #include "atom.h" #include "comm.h" #include "neighbor.h" -#include "domain.h" #include "force.h" #include "update.h" #include "memory.h" diff --git a/src/USER-MISC/improper_distance.cpp b/src/USER-MISC/improper_distance.cpp index 50babcc84e..2efab8b5f8 100644 --- a/src/USER-MISC/improper_distance.cpp +++ b/src/USER-MISC/improper_distance.cpp @@ -15,16 +15,14 @@ Contributing author: Paolo Raiteri (Curtin University) ------------------------------------------------------------------------- */ +#include "improper_distance.h" #include #include -#include -#include "improper_distance.h" #include "atom.h" #include "comm.h" #include "neighbor.h" #include "domain.h" #include "force.h" -#include "update.h" #include "memory.h" #include "error.h" diff --git a/src/USER-MISC/improper_fourier.cpp b/src/USER-MISC/improper_fourier.cpp index 288d888d12..a0ef3a2058 100644 --- a/src/USER-MISC/improper_fourier.cpp +++ b/src/USER-MISC/improper_fourier.cpp @@ -16,15 +16,12 @@ [ based on improper_umbrella.cpp Tod A Pascal (Caltech) ] ------------------------------------------------------------------------- */ +#include "improper_fourier.h" #include #include -#include -#include -#include "improper_fourier.h" #include "atom.h" #include "comm.h" #include "neighbor.h" -#include "domain.h" #include "force.h" #include "update.h" #include "memory.h" diff --git a/src/USER-MISC/improper_ring.cpp b/src/USER-MISC/improper_ring.cpp index 36ba73af0f..48db5a41e9 100644 --- a/src/USER-MISC/improper_ring.cpp +++ b/src/USER-MISC/improper_ring.cpp @@ -36,16 +36,13 @@ of j. ------------------------------------------------------------------------- */ +#include "improper_ring.h" #include #include -#include -#include "improper_ring.h" #include "atom.h" #include "comm.h" #include "neighbor.h" -#include "domain.h" #include "force.h" -#include "update.h" #include "math_const.h" #include "math_special.h" #include "memory.h" diff --git a/src/USER-MISC/pair_agni.cpp b/src/USER-MISC/pair_agni.cpp index 21a6f1deee..b3abc647ef 100644 --- a/src/USER-MISC/pair_agni.cpp +++ b/src/USER-MISC/pair_agni.cpp @@ -15,18 +15,16 @@ Contributing authors: Axel Kohlmeyer (Temple U), Venkatesh Botu ------------------------------------------------------------------------- */ +#include "pair_agni.h" +#include #include -#include #include #include -#include "pair_agni.h" #include "atom.h" #include "neighbor.h" #include "neigh_request.h" #include "force.h" #include "comm.h" -#include "memory.h" -#include "neighbor.h" #include "neigh_list.h" #include "memory.h" #include "error.h" diff --git a/src/USER-MISC/pair_buck_mdf.cpp b/src/USER-MISC/pair_buck_mdf.cpp index afd15d7fdb..e977197522 100644 --- a/src/USER-MISC/pair_buck_mdf.cpp +++ b/src/USER-MISC/pair_buck_mdf.cpp @@ -15,21 +15,18 @@ Contributing author: Paolo Raiteri (Curtin University) ------------------------------------------------------------------------- */ +#include "pair_buck_mdf.h" +#include #include -#include -#include #include -#include "pair_buck_mdf.h" #include "atom.h" #include "comm.h" #include "force.h" #include "neigh_list.h" -#include "math_const.h" #include "memory.h" #include "error.h" using namespace LAMMPS_NS; -using namespace MathConst; /* ---------------------------------------------------------------------- */ diff --git a/src/USER-MISC/pair_coul_diel.cpp b/src/USER-MISC/pair_coul_diel.cpp index a86921d296..a375901ecd 100644 --- a/src/USER-MISC/pair_coul_diel.cpp +++ b/src/USER-MISC/pair_coul_diel.cpp @@ -14,11 +14,9 @@ Contributiong authors: Arben Jusufi, Axel Kohlmeyer (Temple U.) ------------------------------------------------------------------------- */ -#include -#include -#include -#include #include "pair_coul_diel.h" +#include +#include #include "atom.h" #include "comm.h" #include "force.h" diff --git a/src/USER-MISC/pair_coul_shield.cpp b/src/USER-MISC/pair_coul_shield.cpp index f74dcfe7d8..9264e51287 100644 --- a/src/USER-MISC/pair_coul_shield.cpp +++ b/src/USER-MISC/pair_coul_shield.cpp @@ -18,11 +18,8 @@ [Maaravi et al, J. Phys. Chem. C 121, 22826-22835 (2017)] ------------------------------------------------------------------------- */ -#include -#include -#include -#include #include "pair_coul_shield.h" +#include #include "atom.h" #include "comm.h" #include "force.h" diff --git a/src/USER-MISC/pair_drip.cpp b/src/USER-MISC/pair_drip.cpp index 118c033b5c..20ec3abcf9 100644 --- a/src/USER-MISC/pair_drip.cpp +++ b/src/USER-MISC/pair_drip.cpp @@ -20,19 +20,17 @@ Phys. Rev. B, 98, 235404 (2018). ------------------------------------------------------------------------- */ +#include "pair_drip.h" +#include #include -#include #include #include -#include -#include "pair_drip.h" #include "atom.h" #include "comm.h" #include "force.h" #include "neighbor.h" #include "neigh_list.h" #include "neigh_request.h" -#include "my_page.h" #include "memory.h" #include "error.h" diff --git a/src/USER-MISC/pair_drip.h b/src/USER-MISC/pair_drip.h index 0a8f90dfc2..3ea6c735a6 100644 --- a/src/USER-MISC/pair_drip.h +++ b/src/USER-MISC/pair_drip.h @@ -31,8 +31,6 @@ PairStyle(drip, PairDRIP) #define LMP_PAIR_DRIP_H #include "pair.h" -#include "my_page.h" -#include namespace LAMMPS_NS { diff --git a/src/USER-MISC/pair_e3b.cpp b/src/USER-MISC/pair_e3b.cpp index 43b472594a..aa19849baa 100644 --- a/src/USER-MISC/pair_e3b.cpp +++ b/src/USER-MISC/pair_e3b.cpp @@ -14,16 +14,14 @@ contact: stevene.strong at gmail dot com ------------------------------------------------------------------------- */ +#include "pair_e3b.h" +#include #include -#include -#include #include - -#include "pair_e3b.h" +#include #include "atom.h" #include "neighbor.h" -#include "neigh_request.h" #include "neigh_list.h" #include "force.h" #include "comm.h" diff --git a/src/USER-MISC/pair_edip.cpp b/src/USER-MISC/pair_edip.cpp index 0b5220fdfd..8dee4a606b 100644 --- a/src/USER-MISC/pair_edip.cpp +++ b/src/USER-MISC/pair_edip.cpp @@ -21,12 +21,12 @@ Phys. Rev. B 58, 2539 (1998) ------------------------------------------------------------------------- */ +#include "pair_edip.h" +#include #include #include -#include #include #include -#include "pair_edip.h" #include "atom.h" #include "neighbor.h" #include "neigh_list.h" diff --git a/src/USER-MISC/pair_edip_multi.cpp b/src/USER-MISC/pair_edip_multi.cpp index ab48fbaa73..9f953610de 100644 --- a/src/USER-MISC/pair_edip_multi.cpp +++ b/src/USER-MISC/pair_edip_multi.cpp @@ -17,12 +17,11 @@ Contributing author: Chao Jiang ------------------------------------------------------------------------- */ +#include "pair_edip_multi.h" +#include #include -#include -#include #include #include -#include "pair_edip_multi.h" #include "atom.h" #include "neighbor.h" #include "neigh_list.h" diff --git a/src/USER-MISC/pair_extep.cpp b/src/USER-MISC/pair_extep.cpp index bd5da71f4a..8507fd49f6 100644 --- a/src/USER-MISC/pair_extep.cpp +++ b/src/USER-MISC/pair_extep.cpp @@ -15,12 +15,12 @@ Contributing author: Jan Los ------------------------------------------------------------------------- */ +#include "pair_extep.h" +#include #include -#include #include #include #include -#include "pair_extep.h" #include "atom.h" #include "neighbor.h" #include "neigh_list.h" diff --git a/src/USER-MISC/pair_extep.h b/src/USER-MISC/pair_extep.h index 535e7261e3..1f127b71e0 100644 --- a/src/USER-MISC/pair_extep.h +++ b/src/USER-MISC/pair_extep.h @@ -21,7 +21,6 @@ PairStyle(extep,PairExTeP) #define LMP_PAIR_EXTEP_H #include "pair.h" -#include "my_page.h" #define MAXTYPES 8 #define NSPLINE 5 diff --git a/src/USER-MISC/pair_gauss_cut.cpp b/src/USER-MISC/pair_gauss_cut.cpp index 24d0b191d8..e6cfc02f63 100644 --- a/src/USER-MISC/pair_gauss_cut.cpp +++ b/src/USER-MISC/pair_gauss_cut.cpp @@ -15,18 +15,13 @@ Contributing authors: Arben Jusufi, Axel Kohlmeyer (Temple U.) ------------------------------------------------------------------------- */ -#include -#include -#include -#include #include "pair_gauss_cut.h" +#include +#include #include "atom.h" #include "comm.h" #include "force.h" -#include "neighbor.h" #include "neigh_list.h" -#include "update.h" -#include "integrate.h" #include "memory.h" #include "error.h" #include "math_const.h" diff --git a/src/USER-MISC/pair_ilp_graphene_hbn.cpp b/src/USER-MISC/pair_ilp_graphene_hbn.cpp index a41c660b7b..b94db6a871 100644 --- a/src/USER-MISC/pair_ilp_graphene_hbn.cpp +++ b/src/USER-MISC/pair_ilp_graphene_hbn.cpp @@ -20,12 +20,11 @@ [Kolmogorov & Crespi, Phys. Rev. B 71, 235415 (2005)] ------------------------------------------------------------------------- */ +#include "pair_ilp_graphene_hbn.h" #include #include -#include #include #include -#include "pair_ilp_graphene_hbn.h" #include "atom.h" #include "comm.h" #include "force.h" diff --git a/src/USER-MISC/pair_ilp_graphene_hbn.h b/src/USER-MISC/pair_ilp_graphene_hbn.h index 07c3b2e97b..ae4662cdc5 100644 --- a/src/USER-MISC/pair_ilp_graphene_hbn.h +++ b/src/USER-MISC/pair_ilp_graphene_hbn.h @@ -21,8 +21,6 @@ PairStyle(ilp/graphene/hbn,PairILPGrapheneHBN) #define LMP_PAIR_ILP_GRAPHENE_HBN_H #include "pair.h" -#include "my_page.h" -#include namespace LAMMPS_NS { diff --git a/src/USER-MISC/pair_kolmogorov_crespi_full.cpp b/src/USER-MISC/pair_kolmogorov_crespi_full.cpp index e73278968d..0009531ca8 100644 --- a/src/USER-MISC/pair_kolmogorov_crespi_full.cpp +++ b/src/USER-MISC/pair_kolmogorov_crespi_full.cpp @@ -20,12 +20,11 @@ [Kolmogorov & Crespi, Phys. Rev. B 71, 235415 (2005)] ------------------------------------------------------------------------- */ +#include "pair_kolmogorov_crespi_full.h" #include -#include #include #include #include -#include "pair_kolmogorov_crespi_full.h" #include "atom.h" #include "comm.h" #include "force.h" diff --git a/src/USER-MISC/pair_kolmogorov_crespi_full.h b/src/USER-MISC/pair_kolmogorov_crespi_full.h index 9923b409a7..68dede0dd5 100644 --- a/src/USER-MISC/pair_kolmogorov_crespi_full.h +++ b/src/USER-MISC/pair_kolmogorov_crespi_full.h @@ -21,8 +21,6 @@ PairStyle(kolmogorov/crespi/full,PairKolmogorovCrespiFull) #define LMP_PAIR_KolmogorovCrespi_FULL_H #include "pair.h" -#include "my_page.h" -#include namespace LAMMPS_NS { diff --git a/src/USER-MISC/pair_kolmogorov_crespi_z.cpp b/src/USER-MISC/pair_kolmogorov_crespi_z.cpp index 79d6aa3daf..61c326ac87 100644 --- a/src/USER-MISC/pair_kolmogorov_crespi_z.cpp +++ b/src/USER-MISC/pair_kolmogorov_crespi_z.cpp @@ -21,11 +21,11 @@ The simplification is that all normals are taken along the z-direction ------------------------------------------------------------------------- */ +#include "pair_kolmogorov_crespi_z.h" +#include #include -#include #include #include -#include "pair_kolmogorov_crespi_z.h" #include "atom.h" #include "comm.h" #include "force.h" diff --git a/src/USER-MISC/pair_lebedeva_z.cpp b/src/USER-MISC/pair_lebedeva_z.cpp index c9d90e2850..8930042cef 100644 --- a/src/USER-MISC/pair_lebedeva_z.cpp +++ b/src/USER-MISC/pair_lebedeva_z.cpp @@ -22,11 +22,11 @@ [Lebedeva et al., Physica E, 44(6), 949-954, 2012.] ------------------------------------------------------------------------- */ +#include "pair_lebedeva_z.h" +#include #include -#include #include #include -#include "pair_lebedeva_z.h" #include "atom.h" #include "comm.h" #include "force.h" diff --git a/src/USER-MISC/pair_lennard_mdf.cpp b/src/USER-MISC/pair_lennard_mdf.cpp index e2e81e4943..50f59107a0 100644 --- a/src/USER-MISC/pair_lennard_mdf.cpp +++ b/src/USER-MISC/pair_lennard_mdf.cpp @@ -16,15 +16,13 @@ Contributing author: Paolo Raiteri (Curtin University) ------------------------------------------------------------------------- */ +#include "pair_lennard_mdf.h" +#include #include -#include -#include #include -#include "pair_lennard_mdf.h" #include "atom.h" #include "comm.h" #include "force.h" -#include "neighbor.h" #include "neigh_list.h" #include "memory.h" #include "error.h" diff --git a/src/USER-MISC/pair_list.cpp b/src/USER-MISC/pair_list.cpp index 562a60aa99..2f4e886a61 100644 --- a/src/USER-MISC/pair_list.cpp +++ b/src/USER-MISC/pair_list.cpp @@ -16,19 +16,15 @@ ------------------------------------------------------------------------- */ #include "pair_list.h" +#include +#include +#include #include "atom.h" #include "comm.h" -#include "domain.h" #include "force.h" #include "memory.h" - #include "error.h" -#include -#include -#include -#include - using namespace LAMMPS_NS; static const char * const stylename[] = { diff --git a/src/USER-MISC/pair_lj_expand_coul_long.cpp b/src/USER-MISC/pair_lj_expand_coul_long.cpp index fe21538f2d..ffa828826f 100644 --- a/src/USER-MISC/pair_lj_expand_coul_long.cpp +++ b/src/USER-MISC/pair_lj_expand_coul_long.cpp @@ -15,17 +15,15 @@ Contributing author: Trung Nguyen (Northwestern) ------------------------------------------------------------------------- */ +#include "pair_lj_expand_coul_long.h" +#include #include -#include -#include #include -#include "pair_lj_expand_coul_long.h" #include "atom.h" #include "comm.h" #include "force.h" #include "kspace.h" #include "update.h" -#include "integrate.h" #include "respa.h" #include "neighbor.h" #include "neigh_list.h" diff --git a/src/USER-MISC/pair_lj_mdf.cpp b/src/USER-MISC/pair_lj_mdf.cpp index cfe125f21f..3fe0fa6bf9 100644 --- a/src/USER-MISC/pair_lj_mdf.cpp +++ b/src/USER-MISC/pair_lj_mdf.cpp @@ -16,15 +16,13 @@ Contributing author: Paolo Raiteri (Curtin University) ------------------------------------------------------------------------- */ +#include "pair_lj_mdf.h" +#include #include -#include -#include #include -#include "pair_lj_mdf.h" #include "atom.h" #include "comm.h" #include "force.h" -#include "neighbor.h" #include "neigh_list.h" #include "memory.h" #include "error.h" diff --git a/src/USER-MISC/pair_lj_sf_dipole_sf.cpp b/src/USER-MISC/pair_lj_sf_dipole_sf.cpp index af7d23370d..758962ce29 100644 --- a/src/USER-MISC/pair_lj_sf_dipole_sf.cpp +++ b/src/USER-MISC/pair_lj_sf_dipole_sf.cpp @@ -16,10 +16,10 @@ Samuel Genheden (University of Southampton) ------------------------------------------------------------------------- */ +#include "pair_lj_sf_dipole_sf.h" +#include #include -#include #include -#include "pair_lj_sf_dipole_sf.h" #include "atom.h" #include "neighbor.h" #include "neigh_list.h" diff --git a/src/USER-MISC/pair_meam_spline.cpp b/src/USER-MISC/pair_meam_spline.cpp index f09919ce0f..79e7ac7e09 100644 --- a/src/USER-MISC/pair_meam_spline.cpp +++ b/src/USER-MISC/pair_meam_spline.cpp @@ -31,15 +31,13 @@ conform with pairing, updated to LAMMPS style ------------------------------------------------------------------------- */ +#include "pair_meam_spline.h" #include -#include #include #include -#include "pair_meam_spline.h" #include "atom.h" #include "force.h" #include "comm.h" -#include "memory.h" #include "neighbor.h" #include "neigh_list.h" #include "neigh_request.h" diff --git a/src/USER-MISC/pair_meam_sw_spline.cpp b/src/USER-MISC/pair_meam_sw_spline.cpp index af1e8788bd..eeadacf33a 100644 --- a/src/USER-MISC/pair_meam_sw_spline.cpp +++ b/src/USER-MISC/pair_meam_sw_spline.cpp @@ -23,15 +23,13 @@ * 01-Aug-12 - RER: First code version. ------------------------------------------------------------------------- */ +#include "pair_meam_sw_spline.h" #include -#include #include #include -#include "pair_meam_sw_spline.h" #include "atom.h" #include "force.h" #include "comm.h" -#include "memory.h" #include "neighbor.h" #include "neigh_list.h" #include "neigh_request.h" diff --git a/src/USER-MISC/pair_momb.cpp b/src/USER-MISC/pair_momb.cpp index 1716149a98..29d5715302 100644 --- a/src/USER-MISC/pair_momb.cpp +++ b/src/USER-MISC/pair_momb.cpp @@ -16,10 +16,9 @@ Ya Zhou (Penn State University) ------------------------------------------------------------------------- */ -#include -#include -#include #include "pair_momb.h" +#include +#include #include "atom.h" #include "comm.h" #include "force.h" diff --git a/src/USER-MISC/pair_morse_smooth_linear.cpp b/src/USER-MISC/pair_morse_smooth_linear.cpp index 7c7973f830..c3cbe39db7 100644 --- a/src/USER-MISC/pair_morse_smooth_linear.cpp +++ b/src/USER-MISC/pair_morse_smooth_linear.cpp @@ -11,11 +11,10 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ +#include "pair_morse_smooth_linear.h" +#include #include -#include -#include #include -#include "pair_morse_smooth_linear.h" #include "atom.h" #include "comm.h" #include "force.h" diff --git a/src/USER-MISC/pair_srp.cpp b/src/USER-MISC/pair_srp.cpp index 01deaf0fbe..416ace8132 100644 --- a/src/USER-MISC/pair_srp.cpp +++ b/src/USER-MISC/pair_srp.cpp @@ -25,9 +25,11 @@ There is an example script for this package in examples/USER/srp. Please contact Timothy Sirk for questions (tim.sirk@us.army.mil). ------------------------------------------------------------------------- */ +#include "pair_srp.h" +#include +#include #include #include -#include "pair_srp.h" #include "atom.h" #include "comm.h" #include "force.h" diff --git a/src/USER-MISC/pair_tersoff_table.cpp b/src/USER-MISC/pair_tersoff_table.cpp index e0985d1dce..5c4f60f354 100644 --- a/src/USER-MISC/pair_tersoff_table.cpp +++ b/src/USER-MISC/pair_tersoff_table.cpp @@ -20,11 +20,11 @@ 1) Tersoff, Phys. Rev. B 39, 5566 (1988) ------------------------------------------------------------------------- */ +#include "pair_tersoff_table.h" +#include #include -#include #include #include -#include "pair_tersoff_table.h" #include "atom.h" #include "neighbor.h" #include "neigh_list.h" diff --git a/src/USER-MISC/temper_grem.cpp b/src/USER-MISC/temper_grem.cpp index 031a449689..d0e2fa5606 100644 --- a/src/USER-MISC/temper_grem.cpp +++ b/src/USER-MISC/temper_grem.cpp @@ -15,26 +15,21 @@ Contributing author: David Stelter (BU) ------------------------------------------------------------------------- */ +#include "temper_grem.h" #include -#include #include -#include "temper_grem.h" #include "fix_grem.h" #include "universe.h" #include "domain.h" -#include "atom.h" #include "update.h" #include "integrate.h" #include "modify.h" #include "compute.h" #include "force.h" -#include "output.h" -#include "thermo.h" #include "fix.h" #include "random_park.h" #include "finish.h" #include "timer.h" -#include "memory.h" #include "error.h" using namespace LAMMPS_NS; diff --git a/src/USER-MISC/temper_npt.cpp b/src/USER-MISC/temper_npt.cpp index 7cf8fbab9b..9fd4bd6d06 100644 --- a/src/USER-MISC/temper_npt.cpp +++ b/src/USER-MISC/temper_npt.cpp @@ -17,10 +17,9 @@ Contact Email: amulyapervaje@gmail.com ------------------------------------------------------------------------- */ +#include "temper_npt.h" #include -#include #include -#include "temper_npt.h" #include "universe.h" #include "domain.h" #include "atom.h" @@ -29,13 +28,10 @@ #include "modify.h" #include "compute.h" #include "force.h" -#include "output.h" -#include "thermo.h" #include "fix.h" #include "random_park.h" #include "finish.h" #include "timer.h" -#include "memory.h" #include "error.h" using namespace LAMMPS_NS; diff --git a/src/USER-MOFFF/angle_class2_p6.cpp b/src/USER-MOFFF/angle_class2_p6.cpp index e8e6f279de..bb0a01d546 100644 --- a/src/USER-MOFFF/angle_class2_p6.cpp +++ b/src/USER-MOFFF/angle_class2_p6.cpp @@ -16,10 +16,10 @@ and Rochus Schmid (Ruhr-Universitaet Bochum) ------------------------------------------------------------------------- */ +#include "angle_class2_p6.h" +#include #include #include -#include -#include "angle_class2_p6.h" #include "atom.h" #include "neighbor.h" #include "domain.h" diff --git a/src/USER-MOFFF/angle_cosine_buck6d.cpp b/src/USER-MOFFF/angle_cosine_buck6d.cpp index 3829d2b8dc..c17b2a1dba 100644 --- a/src/USER-MOFFF/angle_cosine_buck6d.cpp +++ b/src/USER-MOFFF/angle_cosine_buck6d.cpp @@ -16,9 +16,9 @@ and Rochus Schmid (Ruhr-Universitaet Bochum) ------------------------------------------------------------------------- */ -#include -#include #include "angle_cosine_buck6d.h" +#include +#include #include "atom.h" #include "neighbor.h" #include "domain.h" @@ -26,13 +26,11 @@ #include "force.h" #include "pair.h" #include "math_const.h" -#include "math_special.h" #include "memory.h" #include "error.h" using namespace LAMMPS_NS; using namespace MathConst; -using namespace MathSpecial; #define SMALL 0.001 diff --git a/src/USER-MOFFF/improper_inversion_harmonic.cpp b/src/USER-MOFFF/improper_inversion_harmonic.cpp index 3f1e61e54a..12f7062ccc 100644 --- a/src/USER-MOFFF/improper_inversion_harmonic.cpp +++ b/src/USER-MOFFF/improper_inversion_harmonic.cpp @@ -19,17 +19,13 @@ [ abbreviated from and verified via DLPOLY2.0 ] ------------------------------------------------------------------------- */ +#include "improper_inversion_harmonic.h" #include #include -#include -#include -#include "improper_inversion_harmonic.h" #include "atom.h" #include "comm.h" #include "neighbor.h" -#include "domain.h" #include "force.h" -#include "update.h" #include "math_const.h" #include "memory.h" #include "error.h" diff --git a/src/USER-MOFFF/pair_buck6d_coul_gauss_dsf.cpp b/src/USER-MOFFF/pair_buck6d_coul_gauss_dsf.cpp index 282bb0c58f..9c917d1c19 100644 --- a/src/USER-MOFFF/pair_buck6d_coul_gauss_dsf.cpp +++ b/src/USER-MOFFF/pair_buck6d_coul_gauss_dsf.cpp @@ -18,11 +18,9 @@ Fennell and Gezelter, JCP 124, 234104 (2006) ------------------------------------------------------------------------- */ +#include "pair_buck6d_coul_gauss_dsf.h" #include -#include -#include #include -#include "pair_buck6d_coul_gauss_dsf.h" #include "atom.h" #include "comm.h" #include "force.h" diff --git a/src/USER-MOFFF/pair_buck6d_coul_gauss_long.cpp b/src/USER-MOFFF/pair_buck6d_coul_gauss_long.cpp index d6a4121d21..953507ce21 100644 --- a/src/USER-MOFFF/pair_buck6d_coul_gauss_long.cpp +++ b/src/USER-MOFFF/pair_buck6d_coul_gauss_long.cpp @@ -17,11 +17,10 @@ References: Bureekaew and Schmid, Phys. Status Solidi B 250, 1128 (2013) ------------------------------------------------------------------------- */ +#include "pair_buck6d_coul_gauss_long.h" +#include #include -#include -#include #include -#include "pair_buck6d_coul_gauss_long.h" #include "atom.h" #include "comm.h" #include "force.h" @@ -29,12 +28,10 @@ #include "neighbor.h" #include "neigh_list.h" #include "memory.h" -#include "math_const.h" #include "error.h" #include "math_special.h" using namespace LAMMPS_NS; -using namespace MathConst; #define EWALD_F 1.12837917 diff --git a/src/USER-PTM/compute_ptm_atom.cpp b/src/USER-PTM/compute_ptm_atom.cpp index 41e6540b97..ad3d3facdb 100644 --- a/src/USER-PTM/compute_ptm_atom.cpp +++ b/src/USER-PTM/compute_ptm_atom.cpp @@ -16,15 +16,14 @@ under Contributing author: PM Larsen (MIT) ------------------------------------------------------------------------- */ +#include "compute_ptm_atom.h" #include #include -#include #include #include #include "atom.h" #include "comm.h" -#include "compute_ptm_atom.h" #include "error.h" #include "force.h" #include "memory.h" @@ -32,7 +31,6 @@ under #include "neigh_list.h" #include "neigh_request.h" #include "neighbor.h" -#include "pair.h" #include "update.h" #include "ptm_functions.h" diff --git a/src/USER-PTM/ptm_convex_hull_incremental.cpp b/src/USER-PTM/ptm_convex_hull_incremental.cpp index 45643ec515..8dd06e8168 100644 --- a/src/USER-PTM/ptm_convex_hull_incremental.cpp +++ b/src/USER-PTM/ptm_convex_hull_incremental.cpp @@ -11,7 +11,6 @@ THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLI #include #include #include -#include #include "ptm_convex_hull_incremental.h" #include "ptm_constants.h" diff --git a/src/USER-PTM/ptm_index.cpp b/src/USER-PTM/ptm_index.cpp index 3068e7a7f6..b50e5c4333 100644 --- a/src/USER-PTM/ptm_index.cpp +++ b/src/USER-PTM/ptm_index.cpp @@ -12,19 +12,15 @@ THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLI #include "ptm_convex_hull_incremental.h" #include "ptm_deformation_gradient.h" #include "ptm_functions.h" -#include "ptm_graph_data.h" #include "ptm_initialize_data.h" #include "ptm_neighbour_ordering.h" #include "ptm_normalize_vertices.h" #include "ptm_polar.h" #include "ptm_quat.h" #include "ptm_structure_matcher.h" -#include #include -#include #include #include -#include #include static double calculate_interatomic_distance(int type, double scale) { diff --git a/src/USER-PTM/ptm_initialize_data.cpp b/src/USER-PTM/ptm_initialize_data.cpp index 49dc6f2323..1f0a5c94af 100644 --- a/src/USER-PTM/ptm_initialize_data.cpp +++ b/src/USER-PTM/ptm_initialize_data.cpp @@ -7,14 +7,8 @@ The above copyright notice and this permission notice shall be included in all c THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ -#include -#include -#include -#include -#include -#include -#include #include "ptm_initialize_data.h" +#include static void make_facets_clockwise(int num_facets, int8_t (*facets)[3], const double (*points)[3]) diff --git a/src/USER-PTM/ptm_neighbour_ordering.cpp b/src/USER-PTM/ptm_neighbour_ordering.cpp index cb72a43711..1332b8819b 100644 --- a/src/USER-PTM/ptm_neighbour_ordering.cpp +++ b/src/USER-PTM/ptm_neighbour_ordering.cpp @@ -9,16 +9,15 @@ THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLI //todo: normalize vertices -#include +#include "ptm_neighbour_ordering.h" #include #include #include #include #include +#include #include "ptm_constants.h" #include "ptm_voronoi_cell.h" -#include "ptm_neighbour_ordering.h" -#include "ptm_normalize_vertices.h" namespace ptm { diff --git a/src/USER-PTM/ptm_polar.h b/src/USER-PTM/ptm_polar.h index e03963048b..f11dd98ee9 100644 --- a/src/USER-PTM/ptm_polar.h +++ b/src/USER-PTM/ptm_polar.h @@ -11,7 +11,6 @@ THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLI #define PTM_POLAR_H #include -#include namespace ptm { diff --git a/src/USER-PTM/ptm_quat.cpp b/src/USER-PTM/ptm_quat.cpp index 4a93499b3a..527f4d1116 100644 --- a/src/USER-PTM/ptm_quat.cpp +++ b/src/USER-PTM/ptm_quat.cpp @@ -7,9 +7,9 @@ The above copyright notice and this permission notice shall be included in all c THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ +#include "ptm_quat.h" #include #include -#include #include diff --git a/src/USER-PTM/ptm_voronoi_cell.cpp b/src/USER-PTM/ptm_voronoi_cell.cpp index dfe61eb24f..dc4ce4e747 100644 --- a/src/USER-PTM/ptm_voronoi_cell.cpp +++ b/src/USER-PTM/ptm_voronoi_cell.cpp @@ -52,7 +52,7 @@ such enhancements or derivative works thereof, in binary and source code form. * \brief Function implementations for the voronoicell and related classes. */ #include -#include +#include #include #include "ptm_voronoi_config.h" #include "ptm_voronoi_cell.h" diff --git a/src/USER-PTM/ptm_voronoi_cell.h b/src/USER-PTM/ptm_voronoi_cell.h index eb091dd36b..69e3b5bdc4 100644 --- a/src/USER-PTM/ptm_voronoi_cell.h +++ b/src/USER-PTM/ptm_voronoi_cell.h @@ -56,9 +56,6 @@ such enhancements or derivative works thereof, in binary and source code form. #define PTM_VOROPP_CELL_HH #include -#include - -#include "ptm_voronoi_config.h" namespace ptm_voro { diff --git a/src/USER-SMD/atom_vec_smd.cpp b/src/USER-SMD/atom_vec_smd.cpp index 93a6f1308f..604504c5a7 100644 --- a/src/USER-SMD/atom_vec_smd.cpp +++ b/src/USER-SMD/atom_vec_smd.cpp @@ -23,21 +23,18 @@ ------------------------------------------------------------------------- */ #include "atom_vec_smd.h" -#include #include #include "atom.h" #include "comm.h" #include "domain.h" #include "modify.h" #include "fix.h" -#include "fix_adapt.h" -#include "math_const.h" #include "memory.h" #include "error.h" #include "utils.h" using namespace LAMMPS_NS; -using namespace MathConst; + #define NMAT_FULL 9 #define NMAT_SYMM 6 diff --git a/src/USER-SMD/compute_smd_contact_radius.cpp b/src/USER-SMD/compute_smd_contact_radius.cpp index 8193ad6ccf..46cbc602f2 100644 --- a/src/USER-SMD/compute_smd_contact_radius.cpp +++ b/src/USER-SMD/compute_smd_contact_radius.cpp @@ -23,13 +23,12 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include #include "compute_smd_contact_radius.h" +#include #include "atom.h" #include "update.h" #include "modify.h" #include "comm.h" -#include "force.h" #include "memory.h" #include "error.h" diff --git a/src/USER-SMD/compute_smd_damage.cpp b/src/USER-SMD/compute_smd_damage.cpp index 9603fd5c64..96a936cd82 100644 --- a/src/USER-SMD/compute_smd_damage.cpp +++ b/src/USER-SMD/compute_smd_damage.cpp @@ -23,13 +23,12 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include #include "compute_smd_damage.h" +#include #include "atom.h" #include "update.h" #include "modify.h" #include "comm.h" -#include "force.h" #include "memory.h" #include "error.h" diff --git a/src/USER-SMD/compute_smd_internal_energy.cpp b/src/USER-SMD/compute_smd_internal_energy.cpp index d937aa98a4..f88da8bc33 100644 --- a/src/USER-SMD/compute_smd_internal_energy.cpp +++ b/src/USER-SMD/compute_smd_internal_energy.cpp @@ -29,7 +29,6 @@ #include "update.h" #include "modify.h" #include "comm.h" -#include "force.h" #include "memory.h" #include "error.h" diff --git a/src/USER-SMD/compute_smd_plastic_strain.cpp b/src/USER-SMD/compute_smd_plastic_strain.cpp index 67466ebb72..c1c001a5dd 100644 --- a/src/USER-SMD/compute_smd_plastic_strain.cpp +++ b/src/USER-SMD/compute_smd_plastic_strain.cpp @@ -23,13 +23,12 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include #include "compute_smd_plastic_strain.h" +#include #include "atom.h" #include "update.h" #include "modify.h" #include "comm.h" -#include "force.h" #include "memory.h" #include "error.h" diff --git a/src/USER-SMD/compute_smd_plastic_strain_rate.cpp b/src/USER-SMD/compute_smd_plastic_strain_rate.cpp index 20dfa64edd..272a2c59e5 100644 --- a/src/USER-SMD/compute_smd_plastic_strain_rate.cpp +++ b/src/USER-SMD/compute_smd_plastic_strain_rate.cpp @@ -23,13 +23,12 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include #include "compute_smd_plastic_strain_rate.h" +#include #include "atom.h" #include "update.h" #include "modify.h" #include "comm.h" -#include "force.h" #include "memory.h" #include "error.h" diff --git a/src/USER-SMD/compute_smd_rho.cpp b/src/USER-SMD/compute_smd_rho.cpp index 5c78e604b6..d9c0a99b07 100644 --- a/src/USER-SMD/compute_smd_rho.cpp +++ b/src/USER-SMD/compute_smd_rho.cpp @@ -22,13 +22,12 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include #include "compute_smd_rho.h" +#include #include "atom.h" #include "update.h" #include "modify.h" #include "comm.h" -#include "force.h" #include "memory.h" #include "error.h" diff --git a/src/USER-SMD/compute_smd_tlsph_defgrad.cpp b/src/USER-SMD/compute_smd_tlsph_defgrad.cpp index 37ad78dcea..09aeeea74a 100644 --- a/src/USER-SMD/compute_smd_tlsph_defgrad.cpp +++ b/src/USER-SMD/compute_smd_tlsph_defgrad.cpp @@ -22,20 +22,16 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include -#include +#include "compute_smd_tlsph_defgrad.h" #include -#include #include -#include "compute_smd_tlsph_defgrad.h" #include "atom.h" #include "update.h" #include "modify.h" #include "comm.h" -#include "force.h" #include "memory.h" #include "error.h" -#include "pair.h" + using namespace Eigen; using namespace std; using namespace LAMMPS_NS; diff --git a/src/USER-SMD/compute_smd_tlsph_shape.cpp b/src/USER-SMD/compute_smd_tlsph_shape.cpp index bbab274b5c..ba1a9306ef 100644 --- a/src/USER-SMD/compute_smd_tlsph_shape.cpp +++ b/src/USER-SMD/compute_smd_tlsph_shape.cpp @@ -22,13 +22,9 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include -#include +#include "compute_smd_tlsph_shape.h" #include -#include #include -#include -#include "compute_smd_tlsph_shape.h" #include "atom.h" #include "update.h" #include "modify.h" diff --git a/src/USER-SMD/compute_smd_tlsph_strain.cpp b/src/USER-SMD/compute_smd_tlsph_strain.cpp index a94a3cd511..f0061bf7a1 100644 --- a/src/USER-SMD/compute_smd_tlsph_strain.cpp +++ b/src/USER-SMD/compute_smd_tlsph_strain.cpp @@ -23,12 +23,9 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include -#include +#include "compute_smd_tlsph_strain.h" #include -#include #include -#include "compute_smd_tlsph_strain.h" #include "atom.h" #include "update.h" #include "modify.h" diff --git a/src/USER-SMD/compute_smd_tlsph_stress.cpp b/src/USER-SMD/compute_smd_tlsph_stress.cpp index a54b07dd1e..9c78b192ce 100644 --- a/src/USER-SMD/compute_smd_tlsph_stress.cpp +++ b/src/USER-SMD/compute_smd_tlsph_stress.cpp @@ -22,9 +22,10 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ +#include "compute_smd_tlsph_stress.h" +#include #include #include -#include "compute_smd_tlsph_stress.h" #include "atom.h" #include "update.h" #include "modify.h" diff --git a/src/USER-SMD/compute_smd_triangle_vertices.cpp b/src/USER-SMD/compute_smd_triangle_vertices.cpp index b24223b8b5..06706a85ad 100644 --- a/src/USER-SMD/compute_smd_triangle_vertices.cpp +++ b/src/USER-SMD/compute_smd_triangle_vertices.cpp @@ -23,22 +23,15 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include -#include -#include -#include -#include #include "compute_smd_triangle_vertices.h" +#include #include "atom.h" #include "update.h" #include "modify.h" #include "comm.h" -#include "force.h" #include "memory.h" #include "error.h" -#include "pair.h" -using namespace Eigen; using namespace std; using namespace LAMMPS_NS; diff --git a/src/USER-SMD/compute_smd_ulsph_strain.cpp b/src/USER-SMD/compute_smd_ulsph_strain.cpp index 89b85f7bc1..cf1535759c 100644 --- a/src/USER-SMD/compute_smd_ulsph_strain.cpp +++ b/src/USER-SMD/compute_smd_ulsph_strain.cpp @@ -23,22 +23,15 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include -#include -#include -#include -#include #include "compute_smd_ulsph_strain.h" +#include #include "atom.h" #include "update.h" #include "modify.h" #include "comm.h" -#include "force.h" #include "memory.h" #include "error.h" -#include "pair.h" -using namespace Eigen; using namespace std; using namespace LAMMPS_NS; diff --git a/src/USER-SMD/compute_smd_ulsph_stress.cpp b/src/USER-SMD/compute_smd_ulsph_stress.cpp index 7f1bbc4c29..ea477375ce 100644 --- a/src/USER-SMD/compute_smd_ulsph_stress.cpp +++ b/src/USER-SMD/compute_smd_ulsph_stress.cpp @@ -22,9 +22,10 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ +#include "compute_smd_ulsph_stress.h" +#include #include #include -#include "compute_smd_ulsph_stress.h" #include "atom.h" #include "update.h" #include "modify.h" diff --git a/src/USER-SMD/compute_smd_vol.cpp b/src/USER-SMD/compute_smd_vol.cpp index 17a6b556e8..eb1f144275 100644 --- a/src/USER-SMD/compute_smd_vol.cpp +++ b/src/USER-SMD/compute_smd_vol.cpp @@ -22,13 +22,13 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include #include "compute_smd_vol.h" +#include +#include #include "atom.h" #include "update.h" #include "modify.h" #include "comm.h" -#include "force.h" #include "memory.h" #include "error.h" diff --git a/src/USER-SMD/fix_smd_adjust_dt.cpp b/src/USER-SMD/fix_smd_adjust_dt.cpp index f015c6c4df..ab6dd5ef5c 100644 --- a/src/USER-SMD/fix_smd_adjust_dt.cpp +++ b/src/USER-SMD/fix_smd_adjust_dt.cpp @@ -22,21 +22,14 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include -#include -#include #include "fix_smd_adjust_dt.h" -#include "atom.h" +#include +#include #include "update.h" -#include "integrate.h" -#include "domain.h" -#include "lattice.h" #include "force.h" #include "pair.h" #include "modify.h" #include "fix.h" -#include "output.h" -#include "dump.h" #include "comm.h" #include "error.h" diff --git a/src/USER-SMD/fix_smd_integrate_tlsph.cpp b/src/USER-SMD/fix_smd_integrate_tlsph.cpp index f931ae94ff..8464bed609 100644 --- a/src/USER-SMD/fix_smd_integrate_tlsph.cpp +++ b/src/USER-SMD/fix_smd_integrate_tlsph.cpp @@ -22,22 +22,16 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include -#include +#include "fix_smd_integrate_tlsph.h" +#include #include -#include #include -#include "fix_smd_integrate_tlsph.h" #include "atom.h" #include "force.h" #include "update.h" #include "error.h" #include "pair.h" -#include "neigh_list.h" -#include "domain.h" -#include "neighbor.h" #include "comm.h" -#include "modify.h" using namespace Eigen; using namespace LAMMPS_NS; diff --git a/src/USER-SMD/fix_smd_integrate_ulsph.cpp b/src/USER-SMD/fix_smd_integrate_ulsph.cpp index 6c4705eb96..0f0d224f95 100644 --- a/src/USER-SMD/fix_smd_integrate_ulsph.cpp +++ b/src/USER-SMD/fix_smd_integrate_ulsph.cpp @@ -22,25 +22,16 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include +#include "fix_smd_integrate_ulsph.h" #include -#include #include #include -#include "fix_smd_integrate_ulsph.h" #include "atom.h" #include "comm.h" #include "force.h" -#include "neighbor.h" -#include "neigh_list.h" -#include "neigh_request.h" #include "update.h" -#include "integrate.h" -#include "respa.h" -#include "memory.h" #include "error.h" #include "pair.h" -#include "domain.h" using namespace Eigen; using namespace LAMMPS_NS; diff --git a/src/USER-SMD/fix_smd_move_triangulated_surface.cpp b/src/USER-SMD/fix_smd_move_triangulated_surface.cpp index fe8695b23e..cbaad9ac4c 100644 --- a/src/USER-SMD/fix_smd_move_triangulated_surface.cpp +++ b/src/USER-SMD/fix_smd_move_triangulated_surface.cpp @@ -22,25 +22,15 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include -#include +#include "fix_smd_move_triangulated_surface.h" #include -#include +#include #include -#include "fix_smd_move_triangulated_surface.h" #include "atom.h" #include "comm.h" #include "force.h" -#include "neighbor.h" -#include "neigh_list.h" -#include "neigh_request.h" #include "update.h" -#include "integrate.h" -#include "respa.h" -#include "memory.h" #include "error.h" -#include "pair.h" -#include "domain.h" #include "math_const.h" using namespace Eigen; diff --git a/src/USER-SMD/fix_smd_setvel.cpp b/src/USER-SMD/fix_smd_setvel.cpp index 4bc8b5127b..2964ded544 100644 --- a/src/USER-SMD/fix_smd_setvel.cpp +++ b/src/USER-SMD/fix_smd_setvel.cpp @@ -23,9 +23,9 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include -#include #include "fix_smd_setvel.h" +#include +#include #include "atom.h" #include "update.h" #include "modify.h" diff --git a/src/USER-SMD/fix_smd_tlsph_reference_configuration.cpp b/src/USER-SMD/fix_smd_tlsph_reference_configuration.cpp index a2813cc3ca..6aa23fe3b2 100644 --- a/src/USER-SMD/fix_smd_tlsph_reference_configuration.cpp +++ b/src/USER-SMD/fix_smd_tlsph_reference_configuration.cpp @@ -24,20 +24,16 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ +#include "fix_smd_tlsph_reference_configuration.h" #include -#include -#include #include -#include "fix_smd_tlsph_reference_configuration.h" #include "atom.h" #include "comm.h" -#include "neighbor.h" #include "neigh_list.h" #include "lattice.h" #include "force.h" #include "pair.h" #include "update.h" -#include "modify.h" #include "memory.h" #include "error.h" #include "domain.h" diff --git a/src/USER-SMD/fix_smd_tlsph_reference_configuration.h b/src/USER-SMD/fix_smd_tlsph_reference_configuration.h index 8549621c2f..5f952bde93 100644 --- a/src/USER-SMD/fix_smd_tlsph_reference_configuration.h +++ b/src/USER-SMD/fix_smd_tlsph_reference_configuration.h @@ -35,7 +35,6 @@ FixStyle(SMD_TLSPH_NEIGHBORS,FixSMD_TLSPH_ReferenceConfiguration) #define LMP_FIX_SMD_TLSPH_REFERENCE_H #include "fix.h" -#include "my_page.h" namespace LAMMPS_NS { diff --git a/src/USER-SMD/fix_smd_wall_surface.cpp b/src/USER-SMD/fix_smd_wall_surface.cpp index a37ba67a80..9183bcd9ea 100644 --- a/src/USER-SMD/fix_smd_wall_surface.cpp +++ b/src/USER-SMD/fix_smd_wall_surface.cpp @@ -15,21 +15,15 @@ Contributing authors: Mike Parks (SNL), Ezwanur Rahman, J.T. Foster (UTSA) ------------------------------------------------------------------------- */ -#include +#include "fix_smd_wall_surface.h" +#include #include -#include +#include #include -#include "fix_smd_wall_surface.h" #include "atom.h" #include "domain.h" #include "force.h" #include "comm.h" -#include "update.h" -#include "neighbor.h" -#include "neigh_list.h" -#include "neigh_request.h" -#include "pair.h" -#include "lattice.h" #include "memory.h" #include "error.h" #include "atom_vec.h" diff --git a/src/USER-SMD/pair_smd_hertz.cpp b/src/USER-SMD/pair_smd_hertz.cpp index 541be9f05c..97be94d833 100644 --- a/src/USER-SMD/pair_smd_hertz.cpp +++ b/src/USER-SMD/pair_smd_hertz.cpp @@ -26,17 +26,14 @@ Contributing author: Mike Parks (SNL) ------------------------------------------------------------------------- */ +#include "pair_smd_hertz.h" +#include #include -#include #include #include -#include "pair_smd_hertz.h" #include "atom.h" #include "domain.h" #include "force.h" -#include "update.h" -#include "modify.h" -#include "fix.h" #include "comm.h" #include "neighbor.h" #include "neigh_list.h" diff --git a/src/USER-SMD/pair_smd_tlsph.cpp b/src/USER-SMD/pair_smd_tlsph.cpp index 1d7bbca780..0dff905962 100644 --- a/src/USER-SMD/pair_smd_tlsph.cpp +++ b/src/USER-SMD/pair_smd_tlsph.cpp @@ -22,15 +22,13 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ +#include "pair_smd_tlsph.h" +#include #include -#include -#include #include -#include +#include #include -#include #include -#include "pair_smd_tlsph.h" #include "fix_smd_tlsph_reference_configuration.h" #include "atom.h" #include "domain.h" @@ -41,12 +39,9 @@ #include "fix.h" #include "comm.h" #include "neighbor.h" -#include "neigh_list.h" #include "neigh_request.h" #include "memory.h" #include "error.h" -#include "math_special.h" -#include "update.h" #include "smd_material_models.h" #include "smd_kernels.h" #include "smd_math.h" diff --git a/src/USER-SMD/pair_smd_triangulated_surface.cpp b/src/USER-SMD/pair_smd_triangulated_surface.cpp index d3a4983379..f9052be087 100644 --- a/src/USER-SMD/pair_smd_triangulated_surface.cpp +++ b/src/USER-SMD/pair_smd_triangulated_surface.cpp @@ -26,20 +26,15 @@ Contributing author: Mike Parks (SNL) ------------------------------------------------------------------------- */ +#include "pair_smd_triangulated_surface.h" +#include #include -#include #include #include -#include -#include #include -#include "pair_smd_triangulated_surface.h" #include "atom.h" #include "domain.h" #include "force.h" -#include "update.h" -#include "modify.h" -#include "fix.h" #include "comm.h" #include "neighbor.h" #include "neigh_list.h" diff --git a/src/USER-SMD/pair_smd_ulsph.cpp b/src/USER-SMD/pair_smd_ulsph.cpp index 2c4a2de989..9e824ded3c 100644 --- a/src/USER-SMD/pair_smd_ulsph.cpp +++ b/src/USER-SMD/pair_smd_ulsph.cpp @@ -22,19 +22,13 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ +#include "pair_smd_ulsph.h" #include -#include -#include #include -#include -#include -#include "pair_smd_ulsph.h" #include "atom.h" #include "domain.h" #include "force.h" #include "update.h" -#include "modify.h" -#include "fix.h" #include "comm.h" #include "neighbor.h" #include "neigh_list.h" diff --git a/src/USER-SMD/smd_material_models.cpp b/src/USER-SMD/smd_material_models.cpp index 4213428872..5ee67fbb4e 100644 --- a/src/USER-SMD/smd_material_models.cpp +++ b/src/USER-SMD/smd_material_models.cpp @@ -21,6 +21,10 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ +#include "smd_material_models.h" +#include +#include +#include #include #include #include "math_special.h" -- GitLab From 39873fb7a3367367a6bba05fe4dffdf2dbd11cd8 Mon Sep 17 00:00:00 2001 From: Stan Moore Date: Wed, 10 Jul 2019 16:53:26 -0600 Subject: [PATCH 228/469] Fix issue in Kokkos neigh list when using half-from-full --- src/KOKKOS/neigh_list_kokkos.cpp | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/KOKKOS/neigh_list_kokkos.cpp b/src/KOKKOS/neigh_list_kokkos.cpp index 1c78fe3a68..a5d832cab6 100644 --- a/src/KOKKOS/neigh_list_kokkos.cpp +++ b/src/KOKKOS/neigh_list_kokkos.cpp @@ -36,7 +36,7 @@ void NeighListKokkos::grow(int nmax) { // skip if this list is already long enough to store nmax atoms - if (nmax <= maxatoms) return; + if (nmax <= maxatoms && d_neighbors.extent(1) >= maxneighs) return; maxatoms = nmax; k_ilist = -- GitLab From 789d6a991eba4840315c239f69e51d96aa5bf49f Mon Sep 17 00:00:00 2001 From: Stan Moore Date: Wed, 10 Jul 2019 17:01:46 -0600 Subject: [PATCH 229/469] Update comment --- src/KOKKOS/neigh_list_kokkos.cpp | 1 + 1 file changed, 1 insertion(+) diff --git a/src/KOKKOS/neigh_list_kokkos.cpp b/src/KOKKOS/neigh_list_kokkos.cpp index a5d832cab6..2b9c5ef645 100644 --- a/src/KOKKOS/neigh_list_kokkos.cpp +++ b/src/KOKKOS/neigh_list_kokkos.cpp @@ -35,6 +35,7 @@ template void NeighListKokkos::grow(int nmax) { // skip if this list is already long enough to store nmax atoms + // and maxneighs neighbors if (nmax <= maxatoms && d_neighbors.extent(1) >= maxneighs) return; maxatoms = nmax; -- GitLab From 1a0662c3860a68a38ee370812b069b58f8f7821d Mon Sep 17 00:00:00 2001 From: "Ryan S. Elliott" Date: Wed, 10 Jul 2019 22:11:47 -0500 Subject: [PATCH 230/469] Some corrections and additions to kim_commands docs --- doc/src/kim_commands.txt | 14 +++++++++----- 1 file changed, 9 insertions(+), 5 deletions(-) diff --git a/doc/src/kim_commands.txt b/doc/src/kim_commands.txt index 437b768df6..1356ade9e2 100644 --- a/doc/src/kim_commands.txt +++ b/doc/src/kim_commands.txt @@ -35,7 +35,7 @@ kim_init Sim_LAMMPS_ReaxFF_StrachanVanDuinChakraborty_2003_CHNO__SM_107643900657 kim_interactions C H O kim_init Sim_LAMMPS_IFF_OtherInfo_AuthorList_Year_Species__SM_064312669787_000 real kim_interactions fixed_types -kim_query a0 get_lattice_constant_fcc species=\["Al"] units=\["angstrom"\] :pre +kim_query a0 get_lattice_constant_fcc species=\["Al"\] units=\["angstrom"\] :pre [Description:] @@ -105,12 +105,16 @@ The URL for such a page is constructed from the "extended KIM ID"_https://openkim.org/about-kim-ids/ of the IM: https://openkim.org/id/extended_KIM_ID +or +https://openkim.org/id/short_KIM_ID :pre For example for the Stillinger-Weber potential listed above the Model Page is located at: "https://openkim.org/id/SW_StillingerWeber_1985_Si__MO_405512056662_005"_https://openkim.org/id/SW_StillingerWeber_1985_Si__MO_405512056662_005 +or +"https://openkim.org/id/MO_405512056662_005"_https://openkim.org/id/MO_405512056662_005 :pre See the "current list of KIM PMs and SMs archived in OpenKIM"_https://openkim.org/browse/models/by-species. @@ -271,8 +275,8 @@ OpenKIM IM Execution ({kim_interactions}) :h5 The second and final step in using an OpenKIM IM is to execute the {kim_interactions} command. This command must be preceded by a {kim_init} -command and a "create_box"_create_box.html command, -which defines the number of atom types {N}. +command and a command that creates the simulation box (such as +"create_box"_create_box.html), which defines the number of atom types {N}. The {kim_interactions} command has one argument {typeargs}. This argument contains either a list of {N} chemical species, which defines a mapping between atom types in LAMMPS to the available species in the OpenKIM IM, or the @@ -338,7 +342,7 @@ Note also that parameters like cutoff radii and charge tolerances, which have an effect on IM predictions, are also included in the SM definition ensuring reproducibility. -NOTE: When using using {kim_init} and {kim_interactions} to select +NOTE: When using {kim_init} and {kim_interactions} to select and set up an OpenKIM IM, other LAMMPS commands for the same functions (such as pair_style, pair_coeff, bond_style, bond_coeff, fixes related to charge equilibration, etc.) should normally @@ -356,7 +360,7 @@ argument of the {kim_query command}. The second required argument (e.g. {get_lattice_constant_fcc}). All following arguments are parameters handed over to the web query in the format {keyword=value}. The list of supported keywords and -and the type and format of their values depend on the query function +the type and format of their values depend on the query function used. NOTE: The current list of supported query functions is available on the OpenKIM -- GitLab From d05787ab99994e3cb6533280265026e55679e8aa Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Thu, 11 Jul 2019 07:16:53 -0400 Subject: [PATCH 231/469] clean up include in USER-REAXC --- src/USER-REAXC/compute_spec_atom.cpp | 8 +------- src/USER-REAXC/compute_spec_atom.h | 1 - src/USER-REAXC/fix_qeq_reax.cpp | 7 +++---- src/USER-REAXC/fix_reaxc.cpp | 2 -- src/USER-REAXC/fix_reaxc_bonds.cpp | 12 ++---------- src/USER-REAXC/fix_reaxc_bonds.h | 1 - src/USER-REAXC/fix_reaxc_species.cpp | 12 ++++-------- src/USER-REAXC/fix_reaxc_species.h | 5 ----- src/USER-REAXC/pair_reaxc.cpp | 9 ++++++--- src/USER-REAXC/reaxc_allocate.cpp | 7 +++---- src/USER-REAXC/reaxc_bond_orders.cpp | 6 ++++-- src/USER-REAXC/reaxc_bonds.cpp | 7 +++---- src/USER-REAXC/reaxc_control.cpp | 4 ++-- src/USER-REAXC/reaxc_ffield.cpp | 8 +++++--- src/USER-REAXC/reaxc_ffield.h | 1 + src/USER-REAXC/reaxc_forces.cpp | 9 +++------ src/USER-REAXC/reaxc_hydrogen_bonds.cpp | 5 +++-- src/USER-REAXC/reaxc_init_md.cpp | 9 +++++---- src/USER-REAXC/reaxc_init_md.h | 2 +- src/USER-REAXC/reaxc_io_tools.cpp | 10 +++------- src/USER-REAXC/reaxc_list.cpp | 2 +- src/USER-REAXC/reaxc_lookup.cpp | 5 +++-- src/USER-REAXC/reaxc_lookup.h | 6 ++++-- src/USER-REAXC/reaxc_multi_body.cpp | 8 ++++---- src/USER-REAXC/reaxc_nonbonded.cpp | 7 ++++--- src/USER-REAXC/reaxc_reset_tools.cpp | 4 ++-- src/USER-REAXC/reaxc_system_props.cpp | 6 ++---- src/USER-REAXC/reaxc_system_props.h | 1 + src/USER-REAXC/reaxc_tool_box.cpp | 6 ++++-- src/USER-REAXC/reaxc_tool_box.h | 2 +- src/USER-REAXC/reaxc_torsion_angles.cpp | 6 +++--- src/USER-REAXC/reaxc_traj.cpp | 8 +++++--- src/USER-REAXC/reaxc_valence_angles.cpp | 5 +++-- src/USER-REAXC/reaxc_vector.cpp | 4 ++-- src/USER-REAXC/reaxc_vector.h | 2 -- 35 files changed, 88 insertions(+), 109 deletions(-) diff --git a/src/USER-REAXC/compute_spec_atom.cpp b/src/USER-REAXC/compute_spec_atom.cpp index 77b82b3e55..bc5b26b699 100644 --- a/src/USER-REAXC/compute_spec_atom.cpp +++ b/src/USER-REAXC/compute_spec_atom.cpp @@ -11,19 +11,13 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include -#include #include "compute_spec_atom.h" -#include "math_extra.h" +#include #include "atom.h" #include "update.h" #include "force.h" -#include "domain.h" #include "memory.h" #include "error.h" - -#include "reaxc_defs.h" -#include "reaxc_types.h" #include "pair_reaxc.h" using namespace LAMMPS_NS; diff --git a/src/USER-REAXC/compute_spec_atom.h b/src/USER-REAXC/compute_spec_atom.h index 4d5cb86d71..cf0aa0215d 100644 --- a/src/USER-REAXC/compute_spec_atom.h +++ b/src/USER-REAXC/compute_spec_atom.h @@ -21,7 +21,6 @@ ComputeStyle(SPEC/ATOM,ComputeSpecAtom) #define LMP_COMPUTE_SPEC_ATOM_H #include "compute.h" -#include "pointers.h" namespace LAMMPS_NS { diff --git a/src/USER-REAXC/fix_qeq_reax.cpp b/src/USER-REAXC/fix_qeq_reax.cpp index faa0632608..be6eccf764 100644 --- a/src/USER-REAXC/fix_qeq_reax.cpp +++ b/src/USER-REAXC/fix_qeq_reax.cpp @@ -18,15 +18,13 @@ Hybrid and sub-group capabilities: Ray Shan (Sandia) ------------------------------------------------------------------------- */ +#include "fix_qeq_reax.h" +#include #include -#include -#include #include -#include "fix_qeq_reax.h" #include "pair_reaxc.h" #include "atom.h" #include "comm.h" -#include "domain.h" #include "neighbor.h" #include "neigh_list.h" #include "neigh_request.h" @@ -39,6 +37,7 @@ #include "citeme.h" #include "error.h" #include "reaxc_defs.h" +#include "reaxc_types.h" using namespace LAMMPS_NS; using namespace FixConst; diff --git a/src/USER-REAXC/fix_reaxc.cpp b/src/USER-REAXC/fix_reaxc.cpp index dc67ad6ffb..c98adf5b45 100644 --- a/src/USER-REAXC/fix_reaxc.cpp +++ b/src/USER-REAXC/fix_reaxc.cpp @@ -23,8 +23,6 @@ #include "fix_reaxc.h" #include "atom.h" -#include "pair.h" -#include "comm.h" #include "memory.h" using namespace LAMMPS_NS; diff --git a/src/USER-REAXC/fix_reaxc_bonds.cpp b/src/USER-REAXC/fix_reaxc_bonds.cpp index 9dc347826f..f7ad7ed6d4 100644 --- a/src/USER-REAXC/fix_reaxc_bonds.cpp +++ b/src/USER-REAXC/fix_reaxc_bonds.cpp @@ -15,22 +15,14 @@ Contributing author: Ray Shan (Sandia, tnshan@sandia.gov) ------------------------------------------------------------------------- */ -#include -#include -#include "fix_ave_atom.h" #include "fix_reaxc_bonds.h" +#include +#include #include "atom.h" #include "update.h" #include "pair_reaxc.h" -#include "modify.h" -#include "neighbor.h" #include "neigh_list.h" -#include "neigh_request.h" -#include "comm.h" #include "force.h" -#include "compute.h" -#include "input.h" -#include "variable.h" #include "memory.h" #include "error.h" #include "reaxc_list.h" diff --git a/src/USER-REAXC/fix_reaxc_bonds.h b/src/USER-REAXC/fix_reaxc_bonds.h index 60f41beb02..e83e01f1d5 100644 --- a/src/USER-REAXC/fix_reaxc_bonds.h +++ b/src/USER-REAXC/fix_reaxc_bonds.h @@ -21,7 +21,6 @@ FixStyle(reax/c/bonds,FixReaxCBonds) #define LMP_FIX_REAXC_BONDS_H #include "fix.h" -#include "pointers.h" namespace LAMMPS_NS { diff --git a/src/USER-REAXC/fix_reaxc_species.cpp b/src/USER-REAXC/fix_reaxc_species.cpp index 46426d484a..74692f1c9b 100644 --- a/src/USER-REAXC/fix_reaxc_species.cpp +++ b/src/USER-REAXC/fix_reaxc_species.cpp @@ -16,27 +16,23 @@ Oleg Sergeev (VNIIA, sergeev@vniia.ru) ------------------------------------------------------------------------- */ +#include "fix_reaxc_species.h" +#include #include -#include #include #include "fix_ave_atom.h" -#include "fix_reaxc_species.h" #include "atom.h" #include "domain.h" #include "update.h" -#include "pair_reaxc.h" #include "modify.h" #include "neighbor.h" #include "neigh_list.h" -#include "neigh_request.h" #include "comm.h" #include "force.h" -#include "compute.h" -#include "input.h" -#include "variable.h" #include "memory.h" #include "error.h" -#include "reaxc_list.h" +#include "pair_reaxc.h" +#include "reaxc_defs.h" using namespace LAMMPS_NS; using namespace FixConst; diff --git a/src/USER-REAXC/fix_reaxc_species.h b/src/USER-REAXC/fix_reaxc_species.h index 23a470fd0a..937af98527 100644 --- a/src/USER-REAXC/fix_reaxc_species.h +++ b/src/USER-REAXC/fix_reaxc_species.h @@ -21,11 +21,6 @@ FixStyle(reax/c/species,FixReaxCSpecies) #define LMP_FIX_REAXC_SPECIES_H #include "fix.h" -#include "pointers.h" - -#include "pair_reaxc.h" -#include "reaxc_types.h" -#include "reaxc_defs.h" #define BUFLEN 1000 diff --git a/src/USER-REAXC/pair_reaxc.cpp b/src/USER-REAXC/pair_reaxc.cpp index 224f3e2568..959405576e 100644 --- a/src/USER-REAXC/pair_reaxc.cpp +++ b/src/USER-REAXC/pair_reaxc.cpp @@ -20,8 +20,12 @@ Hybrid and hybrid/overlay compatibility added by Ray Shan (Sandia) ------------------------------------------------------------------------- */ -#include #include "pair_reaxc.h" +#include +#include +#include +#include +#include #include "atom.h" #include "update.h" #include "force.h" @@ -36,6 +40,7 @@ #include "memory.h" #include "error.h" +#include "reaxc_defs.h" #include "reaxc_types.h" #include "reaxc_allocate.h" #include "reaxc_control.h" @@ -46,9 +51,7 @@ #include "reaxc_list.h" #include "reaxc_lookup.h" #include "reaxc_reset_tools.h" -#include "reaxc_traj.h" #include "reaxc_vector.h" -#include "fix_reaxc_bonds.h" using namespace LAMMPS_NS; diff --git a/src/USER-REAXC/reaxc_allocate.cpp b/src/USER-REAXC/reaxc_allocate.cpp index 460f8aeb6a..6303db5619 100644 --- a/src/USER-REAXC/reaxc_allocate.cpp +++ b/src/USER-REAXC/reaxc_allocate.cpp @@ -24,14 +24,13 @@ . ----------------------------------------------------------------------*/ -#include "pair_reaxc.h" #include "reaxc_allocate.h" +#include +#include "reaxc_defs.h" #include "reaxc_list.h" -#include "reaxc_reset_tools.h" #include "reaxc_tool_box.h" -#include "reaxc_vector.h" -#if defined(_OPENMP) +#if defined(LMP_USER_OMP) && defined(_OPENMP) #include #endif diff --git a/src/USER-REAXC/reaxc_bond_orders.cpp b/src/USER-REAXC/reaxc_bond_orders.cpp index 1ed58a0bfd..869e796661 100644 --- a/src/USER-REAXC/reaxc_bond_orders.cpp +++ b/src/USER-REAXC/reaxc_bond_orders.cpp @@ -24,9 +24,11 @@ . ----------------------------------------------------------------------*/ -#include "pair_reaxc.h" -#include "reaxc_types.h" #include "reaxc_bond_orders.h" +#include +#include "pair.h" +#include "reaxc_defs.h" +#include "reaxc_types.h" #include "reaxc_list.h" #include "reaxc_vector.h" diff --git a/src/USER-REAXC/reaxc_bonds.cpp b/src/USER-REAXC/reaxc_bonds.cpp index 48fb872324..4cfd2a3c3a 100644 --- a/src/USER-REAXC/reaxc_bonds.cpp +++ b/src/USER-REAXC/reaxc_bonds.cpp @@ -24,12 +24,11 @@ . ----------------------------------------------------------------------*/ -#include "pair_reaxc.h" #include "reaxc_bonds.h" -#include "reaxc_bond_orders.h" +#include +#include "pair.h" +#include "reaxc_defs.h" #include "reaxc_list.h" -#include "reaxc_tool_box.h" -#include "reaxc_vector.h" void Bonds( reax_system *system, control_params * /*control*/, simulation_data *data, storage *workspace, reax_list **lists, diff --git a/src/USER-REAXC/reaxc_control.cpp b/src/USER-REAXC/reaxc_control.cpp index 060c1a0342..12aa989fa2 100644 --- a/src/USER-REAXC/reaxc_control.cpp +++ b/src/USER-REAXC/reaxc_control.cpp @@ -24,10 +24,10 @@ . ----------------------------------------------------------------------*/ +#include "reaxc_control.h" #include #include -#include "pair_reaxc.h" -#include "reaxc_control.h" +#include "reaxc_defs.h" #include "reaxc_tool_box.h" #include "error.h" diff --git a/src/USER-REAXC/reaxc_ffield.cpp b/src/USER-REAXC/reaxc_ffield.cpp index 2160d180cf..e3a6645fc2 100644 --- a/src/USER-REAXC/reaxc_ffield.cpp +++ b/src/USER-REAXC/reaxc_ffield.cpp @@ -24,14 +24,16 @@ . ----------------------------------------------------------------------*/ +#include "reaxc_ffield.h" +#include +#include +#include #include #include -#include "pair_reaxc.h" +#include "reaxc_defs.h" #include "error.h" -#include "reaxc_ffield.h" #include "reaxc_tool_box.h" - char Read_Force_Field( FILE *fp, reax_interaction *reax, control_params *control ) { diff --git a/src/USER-REAXC/reaxc_ffield.h b/src/USER-REAXC/reaxc_ffield.h index 7cef730f91..b6fe1c9ea9 100644 --- a/src/USER-REAXC/reaxc_ffield.h +++ b/src/USER-REAXC/reaxc_ffield.h @@ -28,6 +28,7 @@ #define __FFIELD_H_ #include "reaxc_types.h" +#include char Read_Force_Field( FILE*, reax_interaction*, control_params* ); diff --git a/src/USER-REAXC/reaxc_forces.cpp b/src/USER-REAXC/reaxc_forces.cpp index 79094ece43..6cd627f05d 100644 --- a/src/USER-REAXC/reaxc_forces.cpp +++ b/src/USER-REAXC/reaxc_forces.cpp @@ -24,25 +24,22 @@ . ----------------------------------------------------------------------*/ -#include -#include "pair_reaxc.h" #include "reaxc_forces.h" +#include +#include +#include #include "reaxc_bond_orders.h" #include "reaxc_bonds.h" #include "reaxc_hydrogen_bonds.h" -#include "reaxc_io_tools.h" #include "reaxc_list.h" -#include "reaxc_lookup.h" #include "reaxc_multi_body.h" #include "reaxc_nonbonded.h" -#include "reaxc_tool_box.h" #include "reaxc_torsion_angles.h" #include "reaxc_valence_angles.h" #include "reaxc_vector.h" #include "error.h" - interaction_function Interaction_Functions[NUM_INTRS]; void Dummy_Interaction( reax_system * /*system*/, control_params * /*control*/, diff --git a/src/USER-REAXC/reaxc_hydrogen_bonds.cpp b/src/USER-REAXC/reaxc_hydrogen_bonds.cpp index be34df7571..5929703bad 100644 --- a/src/USER-REAXC/reaxc_hydrogen_bonds.cpp +++ b/src/USER-REAXC/reaxc_hydrogen_bonds.cpp @@ -24,9 +24,10 @@ . ----------------------------------------------------------------------*/ -#include "pair_reaxc.h" #include "reaxc_hydrogen_bonds.h" -#include "reaxc_bond_orders.h" +#include +#include "pair.h" +#include "reaxc_defs.h" #include "reaxc_list.h" #include "reaxc_valence_angles.h" #include "reaxc_vector.h" diff --git a/src/USER-REAXC/reaxc_init_md.cpp b/src/USER-REAXC/reaxc_init_md.cpp index a0e15e98f5..966ad78c34 100644 --- a/src/USER-REAXC/reaxc_init_md.cpp +++ b/src/USER-REAXC/reaxc_init_md.cpp @@ -24,18 +24,19 @@ . ----------------------------------------------------------------------*/ -#include -#include "pair_reaxc.h" #include "reaxc_init_md.h" +#include +#include +#include +#include +#include "reaxc_defs.h" #include "reaxc_allocate.h" #include "reaxc_forces.h" #include "reaxc_io_tools.h" #include "reaxc_list.h" #include "reaxc_lookup.h" #include "reaxc_reset_tools.h" -#include "reaxc_system_props.h" #include "reaxc_tool_box.h" -#include "reaxc_vector.h" #include "error.h" diff --git a/src/USER-REAXC/reaxc_init_md.h b/src/USER-REAXC/reaxc_init_md.h index ab519a4c72..5d593f50ea 100644 --- a/src/USER-REAXC/reaxc_init_md.h +++ b/src/USER-REAXC/reaxc_init_md.h @@ -28,7 +28,7 @@ #define __INIT_MD_H_ #include "reaxc_types.h" - +#include void Initialize( reax_system*, control_params*, simulation_data*, storage*, reax_list**, output_controls*, mpi_datatypes*, MPI_Comm ); diff --git a/src/USER-REAXC/reaxc_io_tools.cpp b/src/USER-REAXC/reaxc_io_tools.cpp index f4a1486c48..f68a2a2abb 100644 --- a/src/USER-REAXC/reaxc_io_tools.cpp +++ b/src/USER-REAXC/reaxc_io_tools.cpp @@ -24,16 +24,12 @@ . ----------------------------------------------------------------------*/ -#include -#include "pair_reaxc.h" -#include "update.h" #include "reaxc_io_tools.h" -#include "reaxc_list.h" -#include "reaxc_reset_tools.h" +#include +#include +#include "reaxc_defs.h" #include "reaxc_system_props.h" -#include "reaxc_tool_box.h" #include "reaxc_traj.h" -#include "reaxc_vector.h" int Init_Output_Files( reax_system *system, control_params *control, output_controls *out_control, mpi_datatypes *mpi_data, diff --git a/src/USER-REAXC/reaxc_list.cpp b/src/USER-REAXC/reaxc_list.cpp index cd4f815286..53bd05bc8d 100644 --- a/src/USER-REAXC/reaxc_list.cpp +++ b/src/USER-REAXC/reaxc_list.cpp @@ -24,8 +24,8 @@ . ----------------------------------------------------------------------*/ -#include "pair_reaxc.h" #include "reaxc_list.h" +#include "reaxc_defs.h" #include "reaxc_tool_box.h" #include "error.h" diff --git a/src/USER-REAXC/reaxc_lookup.cpp b/src/USER-REAXC/reaxc_lookup.cpp index 8d33a33fba..622483fdc9 100644 --- a/src/USER-REAXC/reaxc_lookup.cpp +++ b/src/USER-REAXC/reaxc_lookup.cpp @@ -24,12 +24,13 @@ . ----------------------------------------------------------------------*/ -#include "pair_reaxc.h" #include "reaxc_lookup.h" +#include +#include +#include "reaxc_defs.h" #include "reaxc_nonbonded.h" #include "reaxc_tool_box.h" - void Tridiagonal_Solve( const double *a, const double *b, double *c, double *d, double *x, unsigned int n){ int i; diff --git a/src/USER-REAXC/reaxc_lookup.h b/src/USER-REAXC/reaxc_lookup.h index 3fd0c2581a..3aae7e0b63 100644 --- a/src/USER-REAXC/reaxc_lookup.h +++ b/src/USER-REAXC/reaxc_lookup.h @@ -28,6 +28,7 @@ #define __LOOKUP_H_ #include "reaxc_types.h" +namespace LAMMPS_NS { class Error; } void Tridiagonal_Solve( const double *a, const double *b, double *c, double *d, double *x, unsigned int n); @@ -35,8 +36,9 @@ void Tridiagonal_Solve( const double *a, const double *b, void Natural_Cubic_Spline( LAMMPS_NS::Error*, const double *h, const double *f, cubic_spline_coef *coef, unsigned int n ); -void Complete_Cubic_Spline( LAMMPS_NS::Error*, const double *h, const double *f, double v0, double vlast, - cubic_spline_coef *coef, unsigned int n ); +void Complete_Cubic_Spline( LAMMPS_NS::Error*, const double *h, const double *f, + double v0, double vlast, cubic_spline_coef *coef, + unsigned int n ); int Init_Lookup_Tables( reax_system*, control_params*, storage*, mpi_datatypes*, char* ); diff --git a/src/USER-REAXC/reaxc_multi_body.cpp b/src/USER-REAXC/reaxc_multi_body.cpp index 371b8ed65e..ed1a3d5ac1 100644 --- a/src/USER-REAXC/reaxc_multi_body.cpp +++ b/src/USER-REAXC/reaxc_multi_body.cpp @@ -24,12 +24,12 @@ . ----------------------------------------------------------------------*/ -#include -#include "pair_reaxc.h" #include "reaxc_multi_body.h" -#include "reaxc_bond_orders.h" +#include +#include +#include "pair.h" +#include "reaxc_defs.h" #include "reaxc_list.h" -#include "reaxc_vector.h" void Atom_Energy( reax_system *system, control_params *control, simulation_data *data, storage *workspace, reax_list **lists, diff --git a/src/USER-REAXC/reaxc_nonbonded.cpp b/src/USER-REAXC/reaxc_nonbonded.cpp index b0fea8c1b9..497a1a0ebe 100644 --- a/src/USER-REAXC/reaxc_nonbonded.cpp +++ b/src/USER-REAXC/reaxc_nonbonded.cpp @@ -24,10 +24,11 @@ . ----------------------------------------------------------------------*/ -#include "pair_reaxc.h" -#include "reaxc_types.h" #include "reaxc_nonbonded.h" -#include "reaxc_bond_orders.h" +#include +#include "pair.h" +#include "reaxc_defs.h" +#include "reaxc_types.h" #include "reaxc_list.h" #include "reaxc_vector.h" diff --git a/src/USER-REAXC/reaxc_reset_tools.cpp b/src/USER-REAXC/reaxc_reset_tools.cpp index c72ccbadcd..91b1a9e14f 100644 --- a/src/USER-REAXC/reaxc_reset_tools.cpp +++ b/src/USER-REAXC/reaxc_reset_tools.cpp @@ -24,9 +24,9 @@ . ----------------------------------------------------------------------*/ -#include -#include "pair_reaxc.h" #include "reaxc_reset_tools.h" +#include +#include "reaxc_defs.h" #include "reaxc_list.h" #include "reaxc_tool_box.h" #include "reaxc_vector.h" diff --git a/src/USER-REAXC/reaxc_system_props.cpp b/src/USER-REAXC/reaxc_system_props.cpp index 5024feffcf..166f070be6 100644 --- a/src/USER-REAXC/reaxc_system_props.cpp +++ b/src/USER-REAXC/reaxc_system_props.cpp @@ -24,11 +24,9 @@ . ----------------------------------------------------------------------*/ -#include "pair_reaxc.h" #include "reaxc_system_props.h" -#include "reaxc_tool_box.h" -#include "reaxc_vector.h" - +#include +#include "reaxc_defs.h" void Compute_System_Energy( reax_system *system, simulation_data *data, MPI_Comm comm ) diff --git a/src/USER-REAXC/reaxc_system_props.h b/src/USER-REAXC/reaxc_system_props.h index 161060e184..4d80e22966 100644 --- a/src/USER-REAXC/reaxc_system_props.h +++ b/src/USER-REAXC/reaxc_system_props.h @@ -28,6 +28,7 @@ #define __SYSTEM_PROP_H_ #include "reaxc_types.h" +#include void Compute_System_Energy( reax_system*, simulation_data*, MPI_Comm ); diff --git a/src/USER-REAXC/reaxc_tool_box.cpp b/src/USER-REAXC/reaxc_tool_box.cpp index 2cf66d8655..811c2ed0ee 100644 --- a/src/USER-REAXC/reaxc_tool_box.cpp +++ b/src/USER-REAXC/reaxc_tool_box.cpp @@ -24,9 +24,11 @@ . ----------------------------------------------------------------------*/ -#include -#include "pair_reaxc.h" #include "reaxc_tool_box.h" +#include +#include +#include +#include "reaxc_defs.h" #if !defined(_MSC_VER) #include diff --git a/src/USER-REAXC/reaxc_tool_box.h b/src/USER-REAXC/reaxc_tool_box.h index 0465376dba..b325819265 100644 --- a/src/USER-REAXC/reaxc_tool_box.h +++ b/src/USER-REAXC/reaxc_tool_box.h @@ -28,7 +28,7 @@ #define __TOOL_BOX_H_ #include "reaxc_types.h" -#include "reaxc_defs.h" +namespace LAMMPS_NS { class Error; } /* from system_props.h */ double Get_Time( ); diff --git a/src/USER-REAXC/reaxc_torsion_angles.cpp b/src/USER-REAXC/reaxc_torsion_angles.cpp index ed76368d68..ce944b217f 100644 --- a/src/USER-REAXC/reaxc_torsion_angles.cpp +++ b/src/USER-REAXC/reaxc_torsion_angles.cpp @@ -24,11 +24,11 @@ . ----------------------------------------------------------------------*/ -#include "pair_reaxc.h" #include "reaxc_torsion_angles.h" -#include "reaxc_bond_orders.h" +#include +#include "pair.h" +#include "reaxc_defs.h" #include "reaxc_list.h" -#include "reaxc_tool_box.h" #include "reaxc_vector.h" #define MIN_SINE 1e-10 diff --git a/src/USER-REAXC/reaxc_traj.cpp b/src/USER-REAXC/reaxc_traj.cpp index a536445113..fb493feae5 100644 --- a/src/USER-REAXC/reaxc_traj.cpp +++ b/src/USER-REAXC/reaxc_traj.cpp @@ -24,11 +24,13 @@ . ----------------------------------------------------------------------*/ -#include -#include "pair_reaxc.h" #include "reaxc_traj.h" +#include +#include +#include +#include +#include "reaxc_defs.h" #include "reaxc_list.h" -#include "reaxc_tool_box.h" #include "error.h" diff --git a/src/USER-REAXC/reaxc_valence_angles.cpp b/src/USER-REAXC/reaxc_valence_angles.cpp index 4ba870b6d9..560955fa9d 100644 --- a/src/USER-REAXC/reaxc_valence_angles.cpp +++ b/src/USER-REAXC/reaxc_valence_angles.cpp @@ -24,9 +24,10 @@ . ----------------------------------------------------------------------*/ -#include "pair_reaxc.h" #include "reaxc_valence_angles.h" -#include "reaxc_bond_orders.h" +#include +#include "pair.h" +#include "reaxc_defs.h" #include "reaxc_list.h" #include "reaxc_vector.h" diff --git a/src/USER-REAXC/reaxc_vector.cpp b/src/USER-REAXC/reaxc_vector.cpp index b54d329ce9..207d745df3 100644 --- a/src/USER-REAXC/reaxc_vector.cpp +++ b/src/USER-REAXC/reaxc_vector.cpp @@ -24,9 +24,9 @@ . ----------------------------------------------------------------------*/ -#include "pair_reaxc.h" #include "reaxc_vector.h" - +#include +#include "reaxc_defs.h" void rvec_Copy( rvec dest, rvec src ) { diff --git a/src/USER-REAXC/reaxc_vector.h b/src/USER-REAXC/reaxc_vector.h index 906b200dc9..549c1f927c 100644 --- a/src/USER-REAXC/reaxc_vector.h +++ b/src/USER-REAXC/reaxc_vector.h @@ -27,9 +27,7 @@ #ifndef __VECTOR_H_ #define __VECTOR_H_ -#include "pair.h" #include "reaxc_types.h" -#include "reaxc_defs.h" void rvec_Copy( rvec, rvec ); void rvec_Scale( rvec, double, rvec ); -- GitLab From ca4b26ddf8e0c0a6f7060387c999b21c3f13c9db Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Thu, 11 Jul 2019 07:22:41 -0400 Subject: [PATCH 232/469] fix up some leftover include issues that got overlooked in previous changes --- src/USER-PTM/ptm_structure_matcher.cpp | 8 ++------ src/USER-PTM/ptm_structure_matcher.h | 2 +- src/USER-QTB/fix_qbmsst.cpp | 11 +---------- src/USER-QTB/fix_qtb.cpp | 9 +-------- src/USER-SDPD/fix_meso_move.cpp | 3 +-- src/USER-SDPD/fix_rigid_meso.cpp | 7 ------- src/USER-SMD/pair_smd_ulsph.cpp | 3 +++ src/USER-UEF/dump_cfg_uef.cpp | 1 - src/USER-YAFF/angle_cross.cpp | 1 + src/USER-YAFF/angle_mm3.cpp | 2 +- 10 files changed, 11 insertions(+), 36 deletions(-) diff --git a/src/USER-PTM/ptm_structure_matcher.cpp b/src/USER-PTM/ptm_structure_matcher.cpp index d50676a3c1..b587ad225f 100644 --- a/src/USER-PTM/ptm_structure_matcher.cpp +++ b/src/USER-PTM/ptm_structure_matcher.cpp @@ -7,20 +7,16 @@ The above copyright notice and this permission notice shall be included in all c THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ -#include -#include +#include "ptm_structure_matcher.h" #include #include -#include -#include -#include +#include #include "ptm_convex_hull_incremental.h" #include "ptm_canonical_coloured.h" #include "ptm_graph_data.h" #include "ptm_graph_tools.h" #include "ptm_normalize_vertices.h" #include "ptm_polar.h" -#include "ptm_structure_matcher.h" #include "ptm_constants.h" diff --git a/src/USER-PTM/ptm_structure_matcher.h b/src/USER-PTM/ptm_structure_matcher.h index e75892f8cb..63bc5ed1fe 100644 --- a/src/USER-PTM/ptm_structure_matcher.h +++ b/src/USER-PTM/ptm_structure_matcher.h @@ -12,7 +12,7 @@ THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLI #include "ptm_initialize_data.h" #include "ptm_constants.h" - +#include "ptm_convex_hull_incremental.h" namespace ptm { diff --git a/src/USER-QTB/fix_qbmsst.cpp b/src/USER-QTB/fix_qbmsst.cpp index b9b07664d2..abbf1701b8 100644 --- a/src/USER-QTB/fix_qbmsst.cpp +++ b/src/USER-QTB/fix_qbmsst.cpp @@ -16,31 +16,22 @@ Implementation of the Multi-Scale Shock Method with quantum nuclear effects ------------------------------------------------------------------------- */ +#include "fix_qbmsst.h" #include #include #include #include -#include "fix_qbmsst.h" -#include "math_extra.h" #include "atom.h" -#include "atom_vec_ellipsoid.h" #include "force.h" #include "update.h" #include "modify.h" #include "compute.h" #include "domain.h" -#include "region.h" -#include "respa.h" #include "comm.h" -#include "input.h" -#include "output.h" -#include "variable.h" #include "random_mars.h" #include "memory.h" #include "error.h" -#include "group.h" #include "kspace.h" -#include "thermo.h" #include "utils.h" using namespace LAMMPS_NS; diff --git a/src/USER-QTB/fix_qtb.cpp b/src/USER-QTB/fix_qtb.cpp index 015f953b8e..593ca31006 100644 --- a/src/USER-QTB/fix_qtb.cpp +++ b/src/USER-QTB/fix_qtb.cpp @@ -16,28 +16,21 @@ Implementation of the colored thermostat for quantum nuclear effects ------------------------------------------------------------------------- */ +#include "fix_qtb.h" #include #include #include #include -#include "fix_qtb.h" -#include "math_extra.h" #include "atom.h" -#include "atom_vec_ellipsoid.h" #include "force.h" #include "update.h" #include "modify.h" #include "compute.h" -#include "domain.h" -#include "region.h" #include "respa.h" #include "comm.h" -#include "input.h" -#include "variable.h" #include "random_mars.h" #include "memory.h" #include "error.h" -#include "group.h" using namespace LAMMPS_NS; using namespace FixConst; diff --git a/src/USER-SDPD/fix_meso_move.cpp b/src/USER-SDPD/fix_meso_move.cpp index 85b08a2af7..176cd8b895 100644 --- a/src/USER-SDPD/fix_meso_move.cpp +++ b/src/USER-SDPD/fix_meso_move.cpp @@ -16,11 +16,10 @@ Morteza Jalalvand (IASBS) jalalvand.m AT gmail.com ------------------------------------------------------------------------- */ +#include "fix_meso_move.h" #include #include -#include "fix_meso_move.h" #include "atom.h" -#include "group.h" #include "update.h" #include "modify.h" #include "force.h" diff --git a/src/USER-SDPD/fix_rigid_meso.cpp b/src/USER-SDPD/fix_rigid_meso.cpp index 49c9ca8614..e93c543e72 100644 --- a/src/USER-SDPD/fix_rigid_meso.cpp +++ b/src/USER-SDPD/fix_rigid_meso.cpp @@ -27,17 +27,10 @@ and all codes relevant to that has been removed ------------------------------------------------------------------------- */ -#include #include "fix_rigid_meso.h" #include "math_extra.h" #include "atom.h" -#include "compute.h" #include "domain.h" -#include "update.h" -#include "modify.h" -#include "group.h" -#include "force.h" -#include "output.h" #include "memory.h" #include "error.h" diff --git a/src/USER-SMD/pair_smd_ulsph.cpp b/src/USER-SMD/pair_smd_ulsph.cpp index 9e824ded3c..b53eb779de 100644 --- a/src/USER-SMD/pair_smd_ulsph.cpp +++ b/src/USER-SMD/pair_smd_ulsph.cpp @@ -23,8 +23,11 @@ ------------------------------------------------------------------------- */ #include "pair_smd_ulsph.h" +#include #include #include +#include +#include #include "atom.h" #include "domain.h" #include "force.h" diff --git a/src/USER-UEF/dump_cfg_uef.cpp b/src/USER-UEF/dump_cfg_uef.cpp index 5e3733f422..8e6268eee6 100644 --- a/src/USER-UEF/dump_cfg_uef.cpp +++ b/src/USER-UEF/dump_cfg_uef.cpp @@ -14,7 +14,6 @@ ------------------------------------------------------------------------- */ #include "dump_cfg.h" -#include #include #include "atom.h" #include "modify.h" diff --git a/src/USER-YAFF/angle_cross.cpp b/src/USER-YAFF/angle_cross.cpp index 2ebb08f56b..0f8861cdf5 100644 --- a/src/USER-YAFF/angle_cross.cpp +++ b/src/USER-YAFF/angle_cross.cpp @@ -16,6 +16,7 @@ ------------------------------------------------------------------------- */ #include "angle_cross.h" +#include #include #include "atom.h" #include "neighbor.h" diff --git a/src/USER-YAFF/angle_mm3.cpp b/src/USER-YAFF/angle_mm3.cpp index 24ce8229ba..b90db37afa 100644 --- a/src/USER-YAFF/angle_mm3.cpp +++ b/src/USER-YAFF/angle_mm3.cpp @@ -16,8 +16,8 @@ ------------------------------------------------------------------------- */ #include "angle_mm3.h" +#include #include -#include #include "atom.h" #include "neighbor.h" #include "domain.h" -- GitLab From 01524d9850ab0896adb905d8c64d6b72a99cf1de Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Thu, 11 Jul 2019 08:13:03 -0400 Subject: [PATCH 233/469] recover compilation of USER-OMP --- src/USER-OMP/reaxc_bond_orders_omp.cpp | 3 ++- src/USER-OMP/reaxc_bonds_omp.cpp | 5 +++-- src/USER-OMP/reaxc_forces_omp.cpp | 3 ++- src/USER-OMP/reaxc_hydrogen_bonds_omp.cpp | 4 ++-- src/USER-OMP/reaxc_init_md_omp.cpp | 3 ++- src/USER-OMP/reaxc_multi_body_omp.cpp | 3 ++- src/USER-OMP/reaxc_nonbonded_omp.cpp | 1 + src/USER-OMP/reaxc_torsion_angles_omp.cpp | 3 ++- src/USER-OMP/reaxc_valence_angles_omp.cpp | 3 ++- 9 files changed, 18 insertions(+), 10 deletions(-) diff --git a/src/USER-OMP/reaxc_bond_orders_omp.cpp b/src/USER-OMP/reaxc_bond_orders_omp.cpp index 33780f5e3f..17715c6e26 100644 --- a/src/USER-OMP/reaxc_bond_orders_omp.cpp +++ b/src/USER-OMP/reaxc_bond_orders_omp.cpp @@ -26,9 +26,10 @@ . ----------------------------------------------------------------------*/ +#include "reaxc_bond_orders_omp.h" +#include "reaxc_defs.h" #include "pair_reaxc_omp.h" #include "reaxc_types.h" -#include "reaxc_bond_orders_omp.h" #include "reaxc_list.h" #include "reaxc_vector.h" diff --git a/src/USER-OMP/reaxc_bonds_omp.cpp b/src/USER-OMP/reaxc_bonds_omp.cpp index 5160c6f55d..12ba1dcbfe 100644 --- a/src/USER-OMP/reaxc_bonds_omp.cpp +++ b/src/USER-OMP/reaxc_bonds_omp.cpp @@ -26,10 +26,11 @@ . ----------------------------------------------------------------------*/ -#include "pair_reaxc_omp.h" - #include "reaxc_bonds_omp.h" +#include "reaxc_defs.h" #include "reaxc_bond_orders_omp.h" +#include "pair_reaxc_omp.h" + #include "reaxc_list.h" #include "reaxc_tool_box.h" #include "reaxc_vector.h" diff --git a/src/USER-OMP/reaxc_forces_omp.cpp b/src/USER-OMP/reaxc_forces_omp.cpp index 0a08bd6a46..1ada5e7e71 100644 --- a/src/USER-OMP/reaxc_forces_omp.cpp +++ b/src/USER-OMP/reaxc_forces_omp.cpp @@ -26,10 +26,11 @@ . ----------------------------------------------------------------------*/ +#include "reaxc_forces_omp.h" +#include "reaxc_defs.h" #include "pair_reaxc_omp.h" #include "thr_data.h" -#include "reaxc_forces_omp.h" #include "reaxc_bond_orders_omp.h" #include "reaxc_bonds_omp.h" #include "reaxc_hydrogen_bonds_omp.h" diff --git a/src/USER-OMP/reaxc_hydrogen_bonds_omp.cpp b/src/USER-OMP/reaxc_hydrogen_bonds_omp.cpp index 7acf26262e..e3c034a12e 100644 --- a/src/USER-OMP/reaxc_hydrogen_bonds_omp.cpp +++ b/src/USER-OMP/reaxc_hydrogen_bonds_omp.cpp @@ -26,9 +26,9 @@ . ----------------------------------------------------------------------*/ -#include "pair_reaxc_omp.h" - #include "reaxc_hydrogen_bonds_omp.h" +#include "pair_reaxc_omp.h" +#include "reaxc_defs.h" #include "reaxc_bond_orders_omp.h" #include "reaxc_list.h" #include "reaxc_valence_angles.h" // To access Calculate_Theta() diff --git a/src/USER-OMP/reaxc_init_md_omp.cpp b/src/USER-OMP/reaxc_init_md_omp.cpp index fe7682d035..847e916666 100644 --- a/src/USER-OMP/reaxc_init_md_omp.cpp +++ b/src/USER-OMP/reaxc_init_md_omp.cpp @@ -26,8 +26,9 @@ . ----------------------------------------------------------------------*/ -#include "pair_reaxc_omp.h" #include "reaxc_init_md_omp.h" +#include "pair_reaxc_omp.h" +#include "reaxc_defs.h" #include "reaxc_allocate.h" #include "reaxc_forces.h" #include "reaxc_forces_omp.h" diff --git a/src/USER-OMP/reaxc_multi_body_omp.cpp b/src/USER-OMP/reaxc_multi_body_omp.cpp index d791f945a8..164999b986 100644 --- a/src/USER-OMP/reaxc_multi_body_omp.cpp +++ b/src/USER-OMP/reaxc_multi_body_omp.cpp @@ -26,11 +26,12 @@ . ----------------------------------------------------------------------*/ +#include "reaxc_multi_body_omp.h" #include #include "pair_reaxc_omp.h" #include "thr_data.h" +#include "reaxc_defs.h" -#include "reaxc_multi_body_omp.h" #include "reaxc_bond_orders_omp.h" #include "reaxc_list.h" #include "reaxc_vector.h" diff --git a/src/USER-OMP/reaxc_nonbonded_omp.cpp b/src/USER-OMP/reaxc_nonbonded_omp.cpp index ea92e0c210..564088880a 100644 --- a/src/USER-OMP/reaxc_nonbonded_omp.cpp +++ b/src/USER-OMP/reaxc_nonbonded_omp.cpp @@ -29,6 +29,7 @@ #include "pair_reaxc_omp.h" #include "thr_data.h" +#include "reaxc_defs.h" #include "reaxc_types.h" #include "reaxc_nonbonded.h" diff --git a/src/USER-OMP/reaxc_torsion_angles_omp.cpp b/src/USER-OMP/reaxc_torsion_angles_omp.cpp index d290dc264f..9cd716b594 100644 --- a/src/USER-OMP/reaxc_torsion_angles_omp.cpp +++ b/src/USER-OMP/reaxc_torsion_angles_omp.cpp @@ -26,11 +26,12 @@ . ----------------------------------------------------------------------*/ +#include "reaxc_torsion_angles_omp.h" #include "pair_reaxc_omp.h" #include "thr_data.h" +#include "reaxc_defs.h" #include "reaxc_types.h" -#include "reaxc_torsion_angles_omp.h" #include "reaxc_bond_orders_omp.h" #include "reaxc_list.h" #include "reaxc_tool_box.h" diff --git a/src/USER-OMP/reaxc_valence_angles_omp.cpp b/src/USER-OMP/reaxc_valence_angles_omp.cpp index 195f16a75d..7fbe87d6e5 100644 --- a/src/USER-OMP/reaxc_valence_angles_omp.cpp +++ b/src/USER-OMP/reaxc_valence_angles_omp.cpp @@ -26,12 +26,13 @@ . ----------------------------------------------------------------------*/ +#include "reaxc_valence_angles_omp.h" #include "pair_reaxc_omp.h" #include "thr_data.h" +#include "reaxc_defs.h" #include "reaxc_types.h" #include "reaxc_valence_angles.h" -#include "reaxc_valence_angles_omp.h" #include "reaxc_bond_orders_omp.h" #include "reaxc_list.h" #include "reaxc_vector.h" -- GitLab From b5fea1f4a7528776cf1944508b7ce445c97e0217 Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Thu, 11 Jul 2019 09:19:26 -0400 Subject: [PATCH 234/469] no need to zero out Ec_meam twice --- src/USER-MEAMC/meam_impl.cpp | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/USER-MEAMC/meam_impl.cpp b/src/USER-MEAMC/meam_impl.cpp index 3b40a2b612..74e8af1cde 100644 --- a/src/USER-MEAMC/meam_impl.cpp +++ b/src/USER-MEAMC/meam_impl.cpp @@ -44,7 +44,7 @@ MEAM::MEAM(Memory* mem) rho_ref_meam[i] = ibar_meam[i] = ielt_meam[i] = 0.0; for (int j = 0; j < maxelt; j++) { lattce_meam[i][j] = FCC; - Ec_meam[i][j] = re_meam[i][j] = alpha_meam[i][j] = delta_meam[i][j] = Ec_meam[i][j] = ebound_meam[i][j] = attrac_meam[i][j] = repuls_meam[i][j] = 0.0; + Ec_meam[i][j] = re_meam[i][j] = alpha_meam[i][j] = delta_meam[i][j] = ebound_meam[i][j] = attrac_meam[i][j] = repuls_meam[i][j] = 0.0; nn2_meam[i][j] = zbl_meam[i][j] = eltind[i][j] = 0; } } -- GitLab From b1f8c3f38acd9490fe4a17977428c31d20558e00 Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Thu, 11 Jul 2019 11:25:44 -0400 Subject: [PATCH 235/469] silence some compiler warnings --- src/MANYBODY/pair_airebo.cpp | 161 ++++++++++++++++++----------------- 1 file changed, 81 insertions(+), 80 deletions(-) diff --git a/src/MANYBODY/pair_airebo.cpp b/src/MANYBODY/pair_airebo.cpp index 818663222f..fcc3a3efd2 100644 --- a/src/MANYBODY/pair_airebo.cpp +++ b/src/MANYBODY/pair_airebo.cpp @@ -3193,6 +3193,7 @@ double PairAIREBO::piRCSpline(double Nij, double Nji, double Nijconj, dN3[0]=0.0; dN3[1]=0.0; dN3[2]=0.0; + piRC=0.0; if (typei==0 && typej==0) { @@ -4343,70 +4344,70 @@ void PairAIREBO::Sptricubic_patch_coeffs( ) { const double C_inv[64][32] = { // output_matrix(2, 8*4, get_matrix(3)) - 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, - 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 0, 0, 0, 0, 0, 0, - -3, 3, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, -2, -1, 0, 0, 0, 0, 0, 0, - 2, -2, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 1, 0, 0, 0, 0, 0, 0, - 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, - 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, - 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, -3, 3, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, - 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 2, -2, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, - -3, 0, 3, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, -2, 0, -1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, - 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, -3, 0, 3, 0, 0, 0, 0, 0, - 9, -9, -9, 9, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 6, -6, 3, -3, 0, 0, 0, 0, 6, 3, -6, -3, 0, 0, 0, 0, - -6, 6, 6, -6, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, -4, 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0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0}, + { 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, -6, 6, 0, 0, 6, -6, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0}, + { 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 4, -4, 0, 0, -4, 4, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0}, + {-6, 0, 6, 0, 6, 0, -6, 0, -3, 0, 3, 0, -3, 0, 3, 0, -4, 0, -2, 0, 4, 0, 2, 0, 0, 0, 0, 0, 0, 0, 0, 0}, + { 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, -6, 0, 6, 0, 6, 0, -6, 0}, + {18,-18,-18, 18,-18, 18, 18,-18, 9, -9, -9, 9, 9, -9, -9, 9, 12,-12, 6, -6,-12, 12, -6, 6, 12, 6,-12, -6,-12, -6, 12, 6}, + {-12,12, 12,-12, 12,-12,-12, 12, -6, 6, 6, -6, -6, 6, 6, -6, -8, 8, -4, 4, 8, -8, 4, -4, -6, -6, 6, 6, 6, 6, -6, -6}, + { 4, 0, -4, 0, -4, 0, 4, 0, 2, 0, -2, 0, 2, 0, -2, 0, 2, 0, 2, 0, -2, 0, -2, 0, 0, 0, 0, 0, 0, 0, 0, 0}, + { 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 4, 0, -4, 0, -4, 0, 4, 0}, + {-12,12, 12,-12, 12,-12,-12, 12, -6, 6, 6, -6, -6, 6, 6, -6, -6, 6, -6, 6, 6, -6, 6, -6, -8, -4, 8, 4, 8, 4, -8, -4}, + { 8, -8, -8, 8, -8, 8, 8, -8, 4, -4, -4, 4, 4, -4, -4, 4, 4, -4, 4, -4, -4, 4, -4, 4, 4, 4, -4, -4, -4, -4, 4, 4} }; double dx = xmax - xmin; double dy = ymax - ymin; @@ -4456,22 +4457,22 @@ void PairAIREBO::Spbicubic_patch_coeffs( ) { const double C_inv[16][12] = { // output_matrix(1, 4*3, get_matrix(2)) - 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, - 0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 0, 0, - -3, 3, 0, 0, 0, 0, 0, 0,-2,-1, 0, 0, - 2,-2, 0, 0, 0, 0, 0, 0, 1, 1, 0, 0, - 0, 0, 0, 0, 1, 0, 0, 0, 0, 0, 0, 0, - 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, - 0, 0, 0, 0,-3, 3, 0, 0, 0, 0, 0, 0, - 0, 0, 0, 0, 2,-2, 0, 0, 0, 0, 0, 0, - -3, 0, 3, 0,-2, 0,-1, 0, 0, 0, 0, 0, - 0, 0, 0, 0, 0, 0, 0, 0,-3, 0, 3, 0, - 9,-9,-9, 9, 6,-6, 3,-3, 6, 3,-6,-3, - -6, 6, 6,-6,-4, 4,-2, 2,-3,-3, 3, 3, - 2, 0,-2, 0, 1, 0, 1, 0, 0, 0, 0, 0, - 0, 0, 0, 0, 0, 0, 0, 0, 2, 0,-2, 0, - -6, 6, 6,-6,-3, 3,-3, 3,-4,-2, 4, 2, - 4,-4,-4, 4, 2,-2, 2,-2, 2, 2,-2,-2, + { 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0}, + { 0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 0, 0}, + {-3, 3, 0, 0, 0, 0, 0, 0,-2,-1, 0, 0}, + { 2,-2, 0, 0, 0, 0, 0, 0, 1, 1, 0, 0}, + { 0, 0, 0, 0, 1, 0, 0, 0, 0, 0, 0, 0}, + { 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0}, + { 0, 0, 0, 0,-3, 3, 0, 0, 0, 0, 0, 0}, + { 0, 0, 0, 0, 2,-2, 0, 0, 0, 0, 0, 0}, + {-3, 0, 3, 0,-2, 0,-1, 0, 0, 0, 0, 0}, + { 0, 0, 0, 0, 0, 0, 0, 0,-3, 0, 3, 0}, + { 9,-9,-9, 9, 6,-6, 3,-3, 6, 3,-6,-3}, + {-6, 6, 6,-6,-4, 4,-2, 2,-3,-3, 3, 3}, + { 2, 0,-2, 0, 1, 0, 1, 0, 0, 0, 0, 0}, + { 0, 0, 0, 0, 0, 0, 0, 0, 2, 0,-2, 0}, + {-6, 6, 6,-6,-3, 3,-3, 3,-4,-2, 4, 2}, + { 4,-4,-4, 4, 2,-2, 2,-2, 2, 2,-2,-2} }; double dx = xmax - xmin; double dy = ymax - ymin; -- GitLab From dbd0158d3f03abba93a219f8e7c40f097998d72e Mon Sep 17 00:00:00 2001 From: "Ryan S. Elliott" Date: Thu, 11 Jul 2019 12:01:35 -0500 Subject: [PATCH 236/469] Adjust/update kim_query do_query() routine --- src/KIM/kim_query.cpp | 21 ++++++++++++++------- 1 file changed, 14 insertions(+), 7 deletions(-) diff --git a/src/KIM/kim_query.cpp b/src/KIM/kim_query.cpp index 221dc9e804..6e77b8f859 100644 --- a/src/KIM/kim_query.cpp +++ b/src/KIM/kim_query.cpp @@ -124,7 +124,7 @@ void KimQuery::command(int narg, char **arg) // that was returned by the web server if (0 == strlen(value)) { - char errmsg[512]; + char errmsg[1024]; sprintf(errmsg,"OpenKIM query failed: %s",value+1); error->all(FLERR,errmsg); @@ -258,9 +258,15 @@ char *do_query(char *qfunction, char * model_name, int narg, char **arg, if (value[0] == '[') { int len = strlen(value)-1; - retval = new char[len]; - value[len] = '\0'; - strcpy(retval,value+1); + if (value[len-1] == ']') { + retval = new char[len]; + value[len-1] = '\0'; + strcpy(retval,value+1); + } else { + retval = new char[len+2]; + retval[0] = '\0'; + strcpy(retval+1,value); + } } else if (value[0] == '\0') { int len = strlen(value+1)+2; retval = new char[len]; @@ -268,10 +274,11 @@ char *do_query(char *qfunction, char * model_name, int narg, char **arg, strcpy(retval+1,value+1); } else { // unknown response type. we should not get here. - // copy response without modifications. - int len = strlen(value)+1; + // we return an "empty" string but add error message after it + int len = strlen(value)+2; retval = new char[len]; - strcpy(retval,value); + retval[0] = '\0'; + strcpy(retval+1,value); } return retval; } -- GitLab From 8e2f3e48832115af044efe39861b9a35480327fd Mon Sep 17 00:00:00 2001 From: Ellad Tadmor Date: Thu, 11 Jul 2019 12:04:54 -0500 Subject: [PATCH 237/469] Wording changes and removed duplicate text --- doc/src/kim_commands.txt | 8 +------- 1 file changed, 1 insertion(+), 7 deletions(-) diff --git a/doc/src/kim_commands.txt b/doc/src/kim_commands.txt index 437b768df6..f9615b8d5f 100644 --- a/doc/src/kim_commands.txt +++ b/doc/src/kim_commands.txt @@ -58,7 +58,7 @@ Reliability :h5 All content archived in OpenKIM is reviewed by the "KIM Editor"_https://openkim.org/governance/ for quality. IMs in OpenKIM are archived with full provenance control. Each is associated with a maintainer responsible for the integrity of the content. All changes are tracked and recorded. -IMs in OpenKIM are exhaustively tested using "KIM Tests"_https://openkim.org/getting-started/kim-tests/ that compute a host of material properties, and "KIM Verification Checks"_https://openkim.org/about-verification-checks/ that provide the user with information on various aspects of the IM behavior and coding correctness. This information is displayed on the IM's page on "OpenKIM"_https://openkim.org. :ul +IMs in OpenKIM are exhaustively tested using "KIM Tests"_https://openkim.org/getting-started/kim-tests/ that compute a host of material properties, and "KIM Verification Checks"_https://openkim.org/about-verification-checks/ that provide the user with information on various aspects of the IM behavior and coding correctness. This information is displayed on the IM's page accessible through the "OpenKIM browse interface"_https://openkim.org/browse. :ul Reproducibility :h5 @@ -407,12 +407,6 @@ separates the result values into individual variables of the form and {I} ranges from 1 to the number of returned values. The number and order of the returned values is determined by the type of query performed. -In the case where a query returns multiple results, the default behavior -for {kim_query} is to split these into individual variables of the form -{prefix_I}, where {prefix} is set to the the {kim_query} {variable} argument -and {I} ranges from 1 to the number of returned values. The number and order of -the returned values is determined by the type of query performed. - [Define a crystal at finite temperature accounting for thermal expansion] kim_init EAM_Dynamo_ErcolessiAdams_1994_Al__MO_123629422045_005 metal -- GitLab From 3349ed00133553e8f2feac931b18b4cf4903cbdc Mon Sep 17 00:00:00 2001 From: Ellad Tadmor Date: Thu, 11 Jul 2019 12:22:36 -0500 Subject: [PATCH 238/469] Changed PM Page and SM Page to "Model Page" --- doc/src/kim_commands.txt | 5 ++--- 1 file changed, 2 insertions(+), 3 deletions(-) diff --git a/doc/src/kim_commands.txt b/doc/src/kim_commands.txt index 2a8f83e7a8..604aba4449 100644 --- a/doc/src/kim_commands.txt +++ b/doc/src/kim_commands.txt @@ -95,13 +95,12 @@ By convention SM prefixes begin with {Sim_} to readily identify them. SW_StillingerWeber_1985_Si__MO_405512056662_005 Sim_LAMMPS_ReaxFF_StrachanVanDuinChakraborty_2003_CHNO__SM_107643900657_000 :pre -Each OpenKIM IM has a dedicated page on "OpenKIM"_https://openkim.org +Each OpenKIM IM has a dedicated "Model Page" on "OpenKIM"_https://openkim.org providing all the information on the IM including a title, description, authorship and citation information, test and verification check results, visualizations of results, a wiki with documentation and user comments, and access to raw files, and other information. -This is referred to as the "PM Page" or "SM Page". -The URL for such a page is constructed from the +The URL for the Model Page is constructed from the "extended KIM ID"_https://openkim.org/about-kim-ids/ of the IM: https://openkim.org/id/extended_KIM_ID -- GitLab From 9f6bbe1d8e390a3614a10413dee95deb4d3c55cd Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Thu, 11 Jul 2019 14:21:55 -0400 Subject: [PATCH 239/469] recover compilation of KOKKOS package --- src/KOKKOS/fix_reaxc_species_kokkos.cpp | 1 + 1 file changed, 1 insertion(+) diff --git a/src/KOKKOS/fix_reaxc_species_kokkos.cpp b/src/KOKKOS/fix_reaxc_species_kokkos.cpp index 71aacba68d..f32bea2c67 100644 --- a/src/KOKKOS/fix_reaxc_species_kokkos.cpp +++ b/src/KOKKOS/fix_reaxc_species_kokkos.cpp @@ -23,6 +23,7 @@ #include "fix_ave_atom.h" #include "domain.h" #include "update.h" +#include "reaxc_defs.h" #include "pair_reaxc_kokkos.h" #include "modify.h" #include "neighbor.h" -- GitLab From 9718b99af969900fdd62614e9c0ccda418408eb6 Mon Sep 17 00:00:00 2001 From: Ellad Tadmor Date: Thu, 11 Jul 2019 13:23:46 -0500 Subject: [PATCH 240/469] Clarification on what preceeds in kim_interactions --- doc/src/kim_commands.txt | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/doc/src/kim_commands.txt b/doc/src/kim_commands.txt index 604aba4449..a6551734f1 100644 --- a/doc/src/kim_commands.txt +++ b/doc/src/kim_commands.txt @@ -274,8 +274,8 @@ OpenKIM IM Execution ({kim_interactions}) :h5 The second and final step in using an OpenKIM IM is to execute the {kim_interactions} command. This command must be preceded by a {kim_init} -command and a command that creates the simulation box (such as -"create_box"_create_box.html), which defines the number of atom types {N}. +command and a command that defines the number of atom types {N} (such as +"create_box"_create_box.html). The {kim_interactions} command has one argument {typeargs}. This argument contains either a list of {N} chemical species, which defines a mapping between atom types in LAMMPS to the available species in the OpenKIM IM, or the -- GitLab From 48c73567436964589dd0a99d741be7e49530e53d Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Thu, 11 Jul 2019 16:51:48 -0400 Subject: [PATCH 241/469] starting to work on includes in USER-OMP --- src/USER-OMP/angle_charmm_omp.cpp | 8 ++------ src/USER-OMP/angle_class2_omp.cpp | 8 ++------ src/USER-OMP/angle_cosine_delta_omp.cpp | 8 ++------ src/USER-OMP/angle_cosine_omp.cpp | 8 ++------ src/USER-OMP/angle_cosine_periodic_omp.cpp | 8 ++------ src/USER-OMP/angle_cosine_shift_exp_omp.cpp | 8 ++------ src/USER-OMP/angle_cosine_shift_omp.cpp | 2 +- src/USER-OMP/angle_cosine_squared_omp.cpp | 8 ++------ src/USER-OMP/angle_dipole_omp.cpp | 8 ++------ src/USER-OMP/angle_fourier_omp.cpp | 2 +- src/USER-OMP/angle_fourier_simple_omp.cpp | 8 ++------ src/USER-OMP/angle_harmonic_omp.cpp | 8 ++------ src/USER-OMP/angle_quartic_omp.cpp | 2 +- src/USER-OMP/angle_sdk_omp.cpp | 8 ++------ src/USER-OMP/angle_table_omp.cpp | 8 ++------ src/USER-OMP/bond_class2_omp.cpp | 2 +- src/USER-OMP/bond_fene_expand_omp.cpp | 2 +- src/USER-OMP/bond_fene_omp.cpp | 2 +- src/USER-OMP/bond_gromos_omp.cpp | 2 +- src/USER-OMP/bond_harmonic_omp.cpp | 2 +- src/USER-OMP/bond_harmonic_shift_cut_omp.cpp | 2 +- src/USER-OMP/bond_harmonic_shift_omp.cpp | 2 +- src/USER-OMP/bond_morse_omp.cpp | 2 +- src/USER-OMP/bond_nonlinear_omp.cpp | 2 +- src/USER-OMP/bond_quartic_omp.cpp | 2 +- src/USER-OMP/bond_table_omp.cpp | 2 +- src/USER-OMP/dihedral_charmm_omp.cpp | 2 +- src/USER-OMP/dihedral_class2_omp.cpp | 2 +- src/USER-OMP/dihedral_cosine_shift_exp_omp.cpp | 2 +- src/USER-OMP/dihedral_fourier_omp.cpp | 2 +- src/USER-OMP/dihedral_harmonic_omp.cpp | 2 +- src/USER-OMP/dihedral_helix_omp.cpp | 2 +- src/USER-OMP/dihedral_multi_harmonic_omp.cpp | 2 +- src/USER-OMP/dihedral_nharmonic_omp.cpp | 2 +- src/USER-OMP/dihedral_opls_omp.cpp | 2 +- src/USER-OMP/dihedral_quadratic_omp.cpp | 2 +- src/USER-OMP/dihedral_table_omp.cpp | 3 ++- src/USER-OMP/domain_omp.cpp | 1 - src/USER-OMP/fix_gravity_omp.cpp | 2 +- src/USER-OMP/fix_nh_omp.cpp | 4 +--- src/USER-OMP/fix_nh_sphere_omp.cpp | 3 --- src/USER-OMP/fix_nvt_sllod_omp.cpp | 5 +++-- src/USER-OMP/fix_omp.cpp | 10 +++++----- src/USER-OMP/fix_qeq_reax_omp.cpp | 2 +- src/USER-OMP/fix_rigid_nh_omp.cpp | 5 ++--- src/USER-OMP/fix_rigid_nph_omp.cpp | 2 +- src/USER-OMP/fix_rigid_npt_omp.cpp | 2 +- src/USER-OMP/fix_rigid_omp.cpp | 7 +++---- src/USER-OMP/fix_rigid_small_omp.cpp | 1 + src/USER-OMP/improper_class2_omp.cpp | 2 +- src/USER-OMP/improper_cossq_omp.cpp | 2 +- src/USER-OMP/improper_cvff_omp.cpp | 2 +- src/USER-OMP/improper_fourier_omp.cpp | 2 +- src/USER-OMP/improper_harmonic_omp.cpp | 2 +- src/USER-OMP/improper_ring_omp.cpp | 2 +- src/USER-OMP/improper_umbrella_omp.cpp | 2 +- src/USER-OMP/msm_cg_omp.cpp | 4 ++-- src/USER-OMP/msm_omp.cpp | 3 ++- src/USER-OMP/npair_full_bin_atomonly_omp.cpp | 1 + src/USER-OMP/npair_half_bin_atomonly_newton_omp.cpp | 2 +- src/USER-OMP/npair_halffull_newtoff_omp.cpp | 2 +- src/USER-OMP/npair_halffull_newton_omp.cpp | 2 +- src/USER-OMP/pair_brownian_omp.cpp | 3 ++- src/USER-OMP/pair_brownian_poly_omp.cpp | 2 +- src/USER-OMP/pair_lj_cut_thole_long_omp.cpp | 3 ++- src/USER-OMP/pair_lj_cut_tip4p_long_omp.cpp | 2 +- src/USER-OMP/pair_lubricate_poly_omp.cpp | 2 +- src/USER-OMP/pppm_cg_omp.cpp | 3 ++- src/USER-OMP/pppm_disp_omp.cpp | 3 ++- src/USER-OMP/pppm_disp_tip4p_omp.cpp | 3 ++- src/USER-OMP/pppm_omp.cpp | 3 ++- src/USER-OMP/respa_omp.cpp | 3 ++- src/USER-OMP/thr_data.h | 8 ++------ src/USER-OMP/thr_omp.cpp | 2 -- src/USER-OMP/thr_omp.h | 9 +++++---- src/special.cpp | 2 +- 76 files changed, 109 insertions(+), 158 deletions(-) diff --git a/src/USER-OMP/angle_charmm_omp.cpp b/src/USER-OMP/angle_charmm_omp.cpp index 118ba00226..f135446915 100644 --- a/src/USER-OMP/angle_charmm_omp.cpp +++ b/src/USER-OMP/angle_charmm_omp.cpp @@ -16,19 +16,15 @@ ------------------------------------------------------------------------- */ #include "angle_charmm_omp.h" +#include #include "atom.h" #include "comm.h" #include "force.h" #include "neighbor.h" -#include "domain.h" - -#include "math_const.h" - -#include +#include "timer.h" #include "suffix.h" using namespace LAMMPS_NS; -using namespace MathConst; #define SMALL 0.001 diff --git a/src/USER-OMP/angle_class2_omp.cpp b/src/USER-OMP/angle_class2_omp.cpp index e072d136e1..0cf5489663 100644 --- a/src/USER-OMP/angle_class2_omp.cpp +++ b/src/USER-OMP/angle_class2_omp.cpp @@ -16,19 +16,15 @@ ------------------------------------------------------------------------- */ #include "angle_class2_omp.h" +#include #include "atom.h" #include "comm.h" #include "force.h" #include "neighbor.h" -#include "domain.h" - -#include "math_const.h" - -#include +#include "timer.h" #include "suffix.h" using namespace LAMMPS_NS; -using namespace MathConst; #define SMALL 0.001 diff --git a/src/USER-OMP/angle_cosine_delta_omp.cpp b/src/USER-OMP/angle_cosine_delta_omp.cpp index a6dfb20433..7f4d994c4f 100644 --- a/src/USER-OMP/angle_cosine_delta_omp.cpp +++ b/src/USER-OMP/angle_cosine_delta_omp.cpp @@ -16,19 +16,15 @@ ------------------------------------------------------------------------- */ #include "angle_cosine_delta_omp.h" +#include #include "atom.h" #include "comm.h" #include "force.h" #include "neighbor.h" -#include "domain.h" - -#include "math_const.h" - -#include +#include "timer.h" #include "suffix.h" using namespace LAMMPS_NS; -using namespace MathConst; #define SMALL 0.001 diff --git a/src/USER-OMP/angle_cosine_omp.cpp b/src/USER-OMP/angle_cosine_omp.cpp index 9097c8569c..0543c94799 100644 --- a/src/USER-OMP/angle_cosine_omp.cpp +++ b/src/USER-OMP/angle_cosine_omp.cpp @@ -16,19 +16,15 @@ ------------------------------------------------------------------------- */ #include "angle_cosine_omp.h" +#include #include "atom.h" #include "comm.h" #include "force.h" #include "neighbor.h" -#include "domain.h" - -#include "math_const.h" - -#include +#include "timer.h" #include "suffix.h" using namespace LAMMPS_NS; -using namespace MathConst; #define SMALL 0.001 diff --git a/src/USER-OMP/angle_cosine_periodic_omp.cpp b/src/USER-OMP/angle_cosine_periodic_omp.cpp index 3fcea7ad1d..907315f83b 100644 --- a/src/USER-OMP/angle_cosine_periodic_omp.cpp +++ b/src/USER-OMP/angle_cosine_periodic_omp.cpp @@ -16,20 +16,16 @@ ------------------------------------------------------------------------- */ #include "angle_cosine_periodic_omp.h" +#include #include "atom.h" #include "comm.h" #include "force.h" #include "neighbor.h" -#include "domain.h" - -#include "math_const.h" +#include "timer.h" #include "math_special.h" -#include - #include "suffix.h" using namespace LAMMPS_NS; -using namespace MathConst; using namespace MathSpecial; #define SMALL 0.001 diff --git a/src/USER-OMP/angle_cosine_shift_exp_omp.cpp b/src/USER-OMP/angle_cosine_shift_exp_omp.cpp index 6bd2feb023..6c42319905 100644 --- a/src/USER-OMP/angle_cosine_shift_exp_omp.cpp +++ b/src/USER-OMP/angle_cosine_shift_exp_omp.cpp @@ -16,19 +16,15 @@ ------------------------------------------------------------------------- */ #include "angle_cosine_shift_exp_omp.h" +#include #include "atom.h" #include "comm.h" #include "force.h" #include "neighbor.h" -#include "domain.h" - -#include "math_const.h" - -#include +#include "timer.h" #include "suffix.h" using namespace LAMMPS_NS; -using namespace MathConst; #define SMALL 0.001 diff --git a/src/USER-OMP/angle_cosine_shift_omp.cpp b/src/USER-OMP/angle_cosine_shift_omp.cpp index 56486faac1..2eea790595 100644 --- a/src/USER-OMP/angle_cosine_shift_omp.cpp +++ b/src/USER-OMP/angle_cosine_shift_omp.cpp @@ -20,7 +20,7 @@ #include "comm.h" #include "force.h" #include "neighbor.h" -#include "domain.h" +#include "timer.h" #include "math_const.h" diff --git a/src/USER-OMP/angle_cosine_squared_omp.cpp b/src/USER-OMP/angle_cosine_squared_omp.cpp index 6dd2a3bb3b..27c47b90d8 100644 --- a/src/USER-OMP/angle_cosine_squared_omp.cpp +++ b/src/USER-OMP/angle_cosine_squared_omp.cpp @@ -16,19 +16,15 @@ ------------------------------------------------------------------------- */ #include "angle_cosine_squared_omp.h" +#include #include "atom.h" #include "comm.h" #include "force.h" #include "neighbor.h" -#include "domain.h" - -#include "math_const.h" - -#include +#include "timer.h" #include "suffix.h" using namespace LAMMPS_NS; -using namespace MathConst; #define SMALL 0.001 diff --git a/src/USER-OMP/angle_dipole_omp.cpp b/src/USER-OMP/angle_dipole_omp.cpp index da2e819ee2..6af5b44a03 100644 --- a/src/USER-OMP/angle_dipole_omp.cpp +++ b/src/USER-OMP/angle_dipole_omp.cpp @@ -16,20 +16,16 @@ ------------------------------------------------------------------------- */ #include "angle_dipole_omp.h" +#include #include "atom.h" #include "comm.h" #include "error.h" #include "force.h" #include "neighbor.h" -#include "domain.h" - -#include "math_const.h" - -#include +#include "timer.h" #include "suffix.h" using namespace LAMMPS_NS; -using namespace MathConst; #define SMALL 0.001 diff --git a/src/USER-OMP/angle_fourier_omp.cpp b/src/USER-OMP/angle_fourier_omp.cpp index b2f9b47e05..52736ca60f 100644 --- a/src/USER-OMP/angle_fourier_omp.cpp +++ b/src/USER-OMP/angle_fourier_omp.cpp @@ -20,7 +20,7 @@ #include "comm.h" #include "force.h" #include "neighbor.h" -#include "domain.h" +#include "timer.h" #include "math_const.h" diff --git a/src/USER-OMP/angle_fourier_simple_omp.cpp b/src/USER-OMP/angle_fourier_simple_omp.cpp index 93532a30e5..71d0197b72 100644 --- a/src/USER-OMP/angle_fourier_simple_omp.cpp +++ b/src/USER-OMP/angle_fourier_simple_omp.cpp @@ -16,19 +16,15 @@ ------------------------------------------------------------------------- */ #include "angle_fourier_simple_omp.h" +#include #include "atom.h" #include "comm.h" #include "force.h" #include "neighbor.h" -#include "domain.h" - -#include "math_const.h" - -#include +#include "timer.h" #include "suffix.h" using namespace LAMMPS_NS; -using namespace MathConst; #define SMALL 0.001 diff --git a/src/USER-OMP/angle_harmonic_omp.cpp b/src/USER-OMP/angle_harmonic_omp.cpp index 824b254287..ee08bbd8ad 100644 --- a/src/USER-OMP/angle_harmonic_omp.cpp +++ b/src/USER-OMP/angle_harmonic_omp.cpp @@ -16,19 +16,15 @@ ------------------------------------------------------------------------- */ #include "angle_harmonic_omp.h" +#include #include "atom.h" #include "comm.h" #include "force.h" #include "neighbor.h" -#include "domain.h" - -#include "math_const.h" - -#include +#include "timer.h" #include "suffix.h" using namespace LAMMPS_NS; -using namespace MathConst; #define SMALL 0.001 diff --git a/src/USER-OMP/angle_quartic_omp.cpp b/src/USER-OMP/angle_quartic_omp.cpp index fff08ddb39..f97f39b16a 100644 --- a/src/USER-OMP/angle_quartic_omp.cpp +++ b/src/USER-OMP/angle_quartic_omp.cpp @@ -20,7 +20,7 @@ #include "comm.h" #include "force.h" #include "neighbor.h" -#include "domain.h" +#include "timer.h" #include "math_const.h" diff --git a/src/USER-OMP/angle_sdk_omp.cpp b/src/USER-OMP/angle_sdk_omp.cpp index e8c762092c..e0b1da0baf 100644 --- a/src/USER-OMP/angle_sdk_omp.cpp +++ b/src/USER-OMP/angle_sdk_omp.cpp @@ -16,20 +16,16 @@ ------------------------------------------------------------------------- */ #include "angle_sdk_omp.h" +#include #include "atom.h" #include "neighbor.h" -#include "domain.h" +#include "timer.h" #include "comm.h" #include "force.h" -#include "math_const.h" - -#include - #include "lj_sdk_common.h" #include "suffix.h" using namespace LAMMPS_NS; -using namespace MathConst; using namespace LJSDKParms; #define SMALL 0.001 diff --git a/src/USER-OMP/angle_table_omp.cpp b/src/USER-OMP/angle_table_omp.cpp index d9d80b744d..4f6edf2073 100644 --- a/src/USER-OMP/angle_table_omp.cpp +++ b/src/USER-OMP/angle_table_omp.cpp @@ -16,19 +16,15 @@ ------------------------------------------------------------------------- */ #include "angle_table_omp.h" +#include #include "atom.h" #include "comm.h" #include "force.h" #include "neighbor.h" -#include "domain.h" - -#include "math_const.h" - -#include +#include "timer.h" #include "suffix.h" using namespace LAMMPS_NS; -using namespace MathConst; #define SMALL 0.001 diff --git a/src/USER-OMP/bond_class2_omp.cpp b/src/USER-OMP/bond_class2_omp.cpp index fdd73c20b0..7d1b693faf 100644 --- a/src/USER-OMP/bond_class2_omp.cpp +++ b/src/USER-OMP/bond_class2_omp.cpp @@ -20,7 +20,7 @@ #include "comm.h" #include "force.h" #include "neighbor.h" -#include "domain.h" +#include "timer.h" #include diff --git a/src/USER-OMP/bond_fene_expand_omp.cpp b/src/USER-OMP/bond_fene_expand_omp.cpp index a8eec11760..aefae6dcf7 100644 --- a/src/USER-OMP/bond_fene_expand_omp.cpp +++ b/src/USER-OMP/bond_fene_expand_omp.cpp @@ -20,7 +20,7 @@ #include "comm.h" #include "force.h" #include "neighbor.h" -#include "domain.h" +#include "timer.h" #include "error.h" #include "update.h" diff --git a/src/USER-OMP/bond_fene_omp.cpp b/src/USER-OMP/bond_fene_omp.cpp index be7dcd4b49..2b579114ba 100644 --- a/src/USER-OMP/bond_fene_omp.cpp +++ b/src/USER-OMP/bond_fene_omp.cpp @@ -20,7 +20,7 @@ #include "comm.h" #include "force.h" #include "neighbor.h" -#include "domain.h" +#include "timer.h" #include "error.h" #include "update.h" diff --git a/src/USER-OMP/bond_gromos_omp.cpp b/src/USER-OMP/bond_gromos_omp.cpp index 8f0926c0e9..88ef1dc23e 100644 --- a/src/USER-OMP/bond_gromos_omp.cpp +++ b/src/USER-OMP/bond_gromos_omp.cpp @@ -20,7 +20,7 @@ #include "comm.h" #include "force.h" #include "neighbor.h" -#include "domain.h" +#include "timer.h" #include diff --git a/src/USER-OMP/bond_harmonic_omp.cpp b/src/USER-OMP/bond_harmonic_omp.cpp index a3bb69c53c..5515284f9a 100644 --- a/src/USER-OMP/bond_harmonic_omp.cpp +++ b/src/USER-OMP/bond_harmonic_omp.cpp @@ -20,7 +20,7 @@ #include "comm.h" #include "force.h" #include "neighbor.h" -#include "domain.h" +#include "timer.h" #include diff --git a/src/USER-OMP/bond_harmonic_shift_cut_omp.cpp b/src/USER-OMP/bond_harmonic_shift_cut_omp.cpp index 5c16e27a32..a871fa8c04 100644 --- a/src/USER-OMP/bond_harmonic_shift_cut_omp.cpp +++ b/src/USER-OMP/bond_harmonic_shift_cut_omp.cpp @@ -20,7 +20,7 @@ #include "comm.h" #include "force.h" #include "neighbor.h" -#include "domain.h" +#include "timer.h" #include diff --git a/src/USER-OMP/bond_harmonic_shift_omp.cpp b/src/USER-OMP/bond_harmonic_shift_omp.cpp index 39e957c137..4117da9159 100644 --- a/src/USER-OMP/bond_harmonic_shift_omp.cpp +++ b/src/USER-OMP/bond_harmonic_shift_omp.cpp @@ -20,7 +20,7 @@ #include "comm.h" #include "force.h" #include "neighbor.h" -#include "domain.h" +#include "timer.h" #include diff --git a/src/USER-OMP/bond_morse_omp.cpp b/src/USER-OMP/bond_morse_omp.cpp index c0203de0d6..e6526dc8dc 100644 --- a/src/USER-OMP/bond_morse_omp.cpp +++ b/src/USER-OMP/bond_morse_omp.cpp @@ -20,7 +20,7 @@ #include "comm.h" #include "force.h" #include "neighbor.h" -#include "domain.h" +#include "timer.h" #include diff --git a/src/USER-OMP/bond_nonlinear_omp.cpp b/src/USER-OMP/bond_nonlinear_omp.cpp index 8fa3daf8ab..0d1a648415 100644 --- a/src/USER-OMP/bond_nonlinear_omp.cpp +++ b/src/USER-OMP/bond_nonlinear_omp.cpp @@ -20,7 +20,7 @@ #include "comm.h" #include "force.h" #include "neighbor.h" -#include "domain.h" +#include "timer.h" #include diff --git a/src/USER-OMP/bond_quartic_omp.cpp b/src/USER-OMP/bond_quartic_omp.cpp index fd0ccaf79d..60d3a5601c 100644 --- a/src/USER-OMP/bond_quartic_omp.cpp +++ b/src/USER-OMP/bond_quartic_omp.cpp @@ -20,7 +20,7 @@ #include "comm.h" #include "force.h" #include "neighbor.h" -#include "domain.h" +#include "timer.h" #include "pair.h" #include diff --git a/src/USER-OMP/bond_table_omp.cpp b/src/USER-OMP/bond_table_omp.cpp index 1616988385..8e1e792c73 100644 --- a/src/USER-OMP/bond_table_omp.cpp +++ b/src/USER-OMP/bond_table_omp.cpp @@ -20,7 +20,7 @@ #include "comm.h" #include "force.h" #include "neighbor.h" -#include "domain.h" +#include "timer.h" #include diff --git a/src/USER-OMP/dihedral_charmm_omp.cpp b/src/USER-OMP/dihedral_charmm_omp.cpp index b09863613e..49dbd54035 100644 --- a/src/USER-OMP/dihedral_charmm_omp.cpp +++ b/src/USER-OMP/dihedral_charmm_omp.cpp @@ -21,7 +21,7 @@ #include "atom.h" #include "comm.h" #include "neighbor.h" -#include "domain.h" +#include "timer.h" #include "force.h" #include "pair.h" #include "update.h" diff --git a/src/USER-OMP/dihedral_class2_omp.cpp b/src/USER-OMP/dihedral_class2_omp.cpp index 03ac9d9bab..6c2bc02ff4 100644 --- a/src/USER-OMP/dihedral_class2_omp.cpp +++ b/src/USER-OMP/dihedral_class2_omp.cpp @@ -20,7 +20,7 @@ #include "atom.h" #include "comm.h" #include "neighbor.h" -#include "domain.h" +#include "timer.h" #include "force.h" #include "update.h" #include "error.h" diff --git a/src/USER-OMP/dihedral_cosine_shift_exp_omp.cpp b/src/USER-OMP/dihedral_cosine_shift_exp_omp.cpp index c64cad9fc3..d77e9d6b3e 100644 --- a/src/USER-OMP/dihedral_cosine_shift_exp_omp.cpp +++ b/src/USER-OMP/dihedral_cosine_shift_exp_omp.cpp @@ -20,7 +20,7 @@ #include "atom.h" #include "comm.h" #include "neighbor.h" -#include "domain.h" +#include "timer.h" #include "force.h" #include "update.h" #include "error.h" diff --git a/src/USER-OMP/dihedral_fourier_omp.cpp b/src/USER-OMP/dihedral_fourier_omp.cpp index 94bdae3795..e853f56051 100644 --- a/src/USER-OMP/dihedral_fourier_omp.cpp +++ b/src/USER-OMP/dihedral_fourier_omp.cpp @@ -20,7 +20,7 @@ #include "atom.h" #include "comm.h" #include "neighbor.h" -#include "domain.h" +#include "timer.h" #include "force.h" #include "update.h" #include "error.h" diff --git a/src/USER-OMP/dihedral_harmonic_omp.cpp b/src/USER-OMP/dihedral_harmonic_omp.cpp index 10ccbd3d9f..84aa584d9e 100644 --- a/src/USER-OMP/dihedral_harmonic_omp.cpp +++ b/src/USER-OMP/dihedral_harmonic_omp.cpp @@ -20,7 +20,7 @@ #include "atom.h" #include "comm.h" #include "neighbor.h" -#include "domain.h" +#include "timer.h" #include "force.h" #include "update.h" #include "error.h" diff --git a/src/USER-OMP/dihedral_helix_omp.cpp b/src/USER-OMP/dihedral_helix_omp.cpp index 8c8e29cac0..51b07754e2 100644 --- a/src/USER-OMP/dihedral_helix_omp.cpp +++ b/src/USER-OMP/dihedral_helix_omp.cpp @@ -20,7 +20,7 @@ #include "atom.h" #include "comm.h" #include "neighbor.h" -#include "domain.h" +#include "timer.h" #include "force.h" #include "update.h" #include "math_const.h" diff --git a/src/USER-OMP/dihedral_multi_harmonic_omp.cpp b/src/USER-OMP/dihedral_multi_harmonic_omp.cpp index 38961e1746..4cb6919a96 100644 --- a/src/USER-OMP/dihedral_multi_harmonic_omp.cpp +++ b/src/USER-OMP/dihedral_multi_harmonic_omp.cpp @@ -20,7 +20,7 @@ #include "atom.h" #include "comm.h" #include "neighbor.h" -#include "domain.h" +#include "timer.h" #include "force.h" #include "update.h" #include "error.h" diff --git a/src/USER-OMP/dihedral_nharmonic_omp.cpp b/src/USER-OMP/dihedral_nharmonic_omp.cpp index e74238265d..203884531b 100644 --- a/src/USER-OMP/dihedral_nharmonic_omp.cpp +++ b/src/USER-OMP/dihedral_nharmonic_omp.cpp @@ -20,10 +20,10 @@ #include "atom.h" #include "comm.h" #include "neighbor.h" -#include "domain.h" #include "force.h" #include "update.h" #include "error.h" +#include "timer.h" #include "suffix.h" using namespace LAMMPS_NS; diff --git a/src/USER-OMP/dihedral_opls_omp.cpp b/src/USER-OMP/dihedral_opls_omp.cpp index 64eaffe6fe..af12bb866e 100644 --- a/src/USER-OMP/dihedral_opls_omp.cpp +++ b/src/USER-OMP/dihedral_opls_omp.cpp @@ -20,7 +20,7 @@ #include "atom.h" #include "comm.h" #include "neighbor.h" -#include "domain.h" +#include "timer.h" #include "force.h" #include "update.h" #include "error.h" diff --git a/src/USER-OMP/dihedral_quadratic_omp.cpp b/src/USER-OMP/dihedral_quadratic_omp.cpp index 8df622b847..8cea62aaea 100644 --- a/src/USER-OMP/dihedral_quadratic_omp.cpp +++ b/src/USER-OMP/dihedral_quadratic_omp.cpp @@ -20,10 +20,10 @@ #include "atom.h" #include "comm.h" #include "neighbor.h" -#include "domain.h" #include "force.h" #include "update.h" #include "error.h" +#include "timer.h" #include "suffix.h" using namespace LAMMPS_NS; diff --git a/src/USER-OMP/dihedral_table_omp.cpp b/src/USER-OMP/dihedral_table_omp.cpp index 792ee90c26..928af079e8 100644 --- a/src/USER-OMP/dihedral_table_omp.cpp +++ b/src/USER-OMP/dihedral_table_omp.cpp @@ -22,11 +22,12 @@ #include "dihedral_table_omp.h" #include "atom.h" #include "comm.h" -#include "neighbor.h" #include "domain.h" +#include "neighbor.h" #include "force.h" #include "update.h" #include "error.h" +#include "timer.h" #include "math_const.h" #include "math_extra.h" diff --git a/src/USER-OMP/domain_omp.cpp b/src/USER-OMP/domain_omp.cpp index 584e56b1f0..a18931c551 100644 --- a/src/USER-OMP/domain_omp.cpp +++ b/src/USER-OMP/domain_omp.cpp @@ -15,7 +15,6 @@ Contributing author : Axel Kohlmeyer (Temple U) ------------------------------------------------------------------------- */ -#include "domain.h" #include "accelerator_omp.h" #include "atom.h" diff --git a/src/USER-OMP/fix_gravity_omp.cpp b/src/USER-OMP/fix_gravity_omp.cpp index eae918ec52..ae00c44ffb 100644 --- a/src/USER-OMP/fix_gravity_omp.cpp +++ b/src/USER-OMP/fix_gravity_omp.cpp @@ -22,7 +22,7 @@ #include "fix_gravity_omp.h" #include "atom.h" #include "update.h" -#include "domain.h" +#include "timer.h" #include "input.h" #include "modify.h" #include "respa.h" diff --git a/src/USER-OMP/fix_nh_omp.cpp b/src/USER-OMP/fix_nh_omp.cpp index 76a47b71fd..2abd739f71 100644 --- a/src/USER-OMP/fix_nh_omp.cpp +++ b/src/USER-OMP/fix_nh_omp.cpp @@ -16,15 +16,13 @@ ------------------------------------------------------------------------- */ #include "fix_nh_omp.h" +#include #include "atom.h" #include "compute.h" #include "domain.h" #include "error.h" #include "modify.h" -#include -#include - using namespace LAMMPS_NS; using namespace FixConst; diff --git a/src/USER-OMP/fix_nh_sphere_omp.cpp b/src/USER-OMP/fix_nh_sphere_omp.cpp index a32f0f8b51..64bc536bb0 100644 --- a/src/USER-OMP/fix_nh_sphere_omp.cpp +++ b/src/USER-OMP/fix_nh_sphere_omp.cpp @@ -15,12 +15,9 @@ Contributing author: Axel Kohlmeyer (Temple U) ------------------------------------------------------------------------- */ -#include #include "fix_nh_sphere_omp.h" #include "atom.h" -#include "atom_vec.h" #include "compute.h" -#include "group.h" #include "error.h" using namespace LAMMPS_NS; diff --git a/src/USER-OMP/fix_nvt_sllod_omp.cpp b/src/USER-OMP/fix_nvt_sllod_omp.cpp index e439647c12..6944cf15af 100644 --- a/src/USER-OMP/fix_nvt_sllod_omp.cpp +++ b/src/USER-OMP/fix_nvt_sllod_omp.cpp @@ -15,18 +15,19 @@ Contributing author: Axel Kohlmeyer (Temple U) ------------------------------------------------------------------------- */ +#include "fix_nvt_sllod_omp.h" #include #include -#include "fix_nvt_sllod_omp.h" #include "math_extra.h" #include "atom.h" -#include "domain.h" #include "group.h" #include "modify.h" #include "fix.h" #include "fix_deform.h" #include "compute.h" #include "error.h" +#include "domain.h" +#include "timer.h" using namespace LAMMPS_NS; using namespace FixConst; diff --git a/src/USER-OMP/fix_omp.cpp b/src/USER-OMP/fix_omp.cpp index a4587b1c14..1fca1e739b 100644 --- a/src/USER-OMP/fix_omp.cpp +++ b/src/USER-OMP/fix_omp.cpp @@ -24,13 +24,10 @@ #include "neigh_request.h" #include "universe.h" #include "update.h" -#include "integrate.h" -#include "min.h" #include "timer.h" #include "fix_omp.h" #include "thr_data.h" -#include "thr_omp.h" #include "pair_hybrid.h" #include "bond_hybrid.h" @@ -40,8 +37,11 @@ #include "kspace.h" #include -#include -#include + +#if defined(_OPENMP) +#include +#endif + #include "suffix.h" diff --git a/src/USER-OMP/fix_qeq_reax_omp.cpp b/src/USER-OMP/fix_qeq_reax_omp.cpp index 45da91305d..5c50c54bff 100644 --- a/src/USER-OMP/fix_qeq_reax_omp.cpp +++ b/src/USER-OMP/fix_qeq_reax_omp.cpp @@ -39,7 +39,7 @@ #include "pair_reaxc_omp.h" #include "atom.h" #include "comm.h" -#include "domain.h" +#include "timer.h" #include "neighbor.h" #include "neigh_list.h" #include "neigh_request.h" diff --git a/src/USER-OMP/fix_rigid_nh_omp.cpp b/src/USER-OMP/fix_rigid_nh_omp.cpp index e6a6e065bf..74b2a92775 100644 --- a/src/USER-OMP/fix_rigid_nh_omp.cpp +++ b/src/USER-OMP/fix_rigid_nh_omp.cpp @@ -15,11 +15,9 @@ Contributing author: Axel Kohlmeyer (Temple U) ------------------------------------------------------------------------- */ +#include "fix_rigid_nh_omp.h" #include #include - -#include "fix_rigid_nh_omp.h" - #include "atom.h" #include "atom_vec_ellipsoid.h" #include "atom_vec_line.h" @@ -32,6 +30,7 @@ #include "kspace.h" #include "modify.h" #include "update.h" +#include "timer.h" #if defined(_OPENMP) #include diff --git a/src/USER-OMP/fix_rigid_nph_omp.cpp b/src/USER-OMP/fix_rigid_nph_omp.cpp index 7db45ed9bf..af59b65996 100644 --- a/src/USER-OMP/fix_rigid_nph_omp.cpp +++ b/src/USER-OMP/fix_rigid_nph_omp.cpp @@ -19,7 +19,7 @@ #include #include "fix_rigid_nph_omp.h" -#include "domain.h" +#include "timer.h" #include "modify.h" #include "error.h" diff --git a/src/USER-OMP/fix_rigid_npt_omp.cpp b/src/USER-OMP/fix_rigid_npt_omp.cpp index a041706f38..744b27ce01 100644 --- a/src/USER-OMP/fix_rigid_npt_omp.cpp +++ b/src/USER-OMP/fix_rigid_npt_omp.cpp @@ -19,7 +19,7 @@ #include #include "fix_rigid_npt_omp.h" -#include "domain.h" +#include "timer.h" #include "modify.h" #include "error.h" diff --git a/src/USER-OMP/fix_rigid_omp.cpp b/src/USER-OMP/fix_rigid_omp.cpp index 20478b3ca1..2e97adab35 100644 --- a/src/USER-OMP/fix_rigid_omp.cpp +++ b/src/USER-OMP/fix_rigid_omp.cpp @@ -15,18 +15,17 @@ Contributing author: Axel Kohlmeyer (Temple U) ------------------------------------------------------------------------- */ +#include "fix_rigid_omp.h" #include #include - -#include "fix_rigid_omp.h" - #include "atom.h" #include "atom_vec_ellipsoid.h" #include "atom_vec_line.h" #include "atom_vec_tri.h" #include "comm.h" -#include "domain.h" #include "error.h" +#include "domain.h" +#include "timer.h" #if defined(_OPENMP) #include diff --git a/src/USER-OMP/fix_rigid_small_omp.cpp b/src/USER-OMP/fix_rigid_small_omp.cpp index 1f6173497d..f8fea815c8 100644 --- a/src/USER-OMP/fix_rigid_small_omp.cpp +++ b/src/USER-OMP/fix_rigid_small_omp.cpp @@ -25,6 +25,7 @@ #include "atom_vec_tri.h" #include "comm.h" #include "domain.h" +#include "timer.h" #if defined(_OPENMP) #include diff --git a/src/USER-OMP/improper_class2_omp.cpp b/src/USER-OMP/improper_class2_omp.cpp index c2b493f425..3bff179b44 100644 --- a/src/USER-OMP/improper_class2_omp.cpp +++ b/src/USER-OMP/improper_class2_omp.cpp @@ -20,7 +20,7 @@ #include "atom.h" #include "comm.h" #include "neighbor.h" -#include "domain.h" +#include "timer.h" #include "force.h" #include "update.h" #include "error.h" diff --git a/src/USER-OMP/improper_cossq_omp.cpp b/src/USER-OMP/improper_cossq_omp.cpp index 3b328e5b78..0f99f2732f 100644 --- a/src/USER-OMP/improper_cossq_omp.cpp +++ b/src/USER-OMP/improper_cossq_omp.cpp @@ -20,7 +20,7 @@ #include "atom.h" #include "comm.h" #include "neighbor.h" -#include "domain.h" +#include "timer.h" #include "force.h" #include "update.h" #include "error.h" diff --git a/src/USER-OMP/improper_cvff_omp.cpp b/src/USER-OMP/improper_cvff_omp.cpp index fe1fc45bec..fdc29c74b1 100644 --- a/src/USER-OMP/improper_cvff_omp.cpp +++ b/src/USER-OMP/improper_cvff_omp.cpp @@ -20,7 +20,7 @@ #include "atom.h" #include "comm.h" #include "neighbor.h" -#include "domain.h" +#include "timer.h" #include "force.h" #include "update.h" #include "error.h" diff --git a/src/USER-OMP/improper_fourier_omp.cpp b/src/USER-OMP/improper_fourier_omp.cpp index b5af428cb9..b49b895c78 100644 --- a/src/USER-OMP/improper_fourier_omp.cpp +++ b/src/USER-OMP/improper_fourier_omp.cpp @@ -20,7 +20,7 @@ #include "atom.h" #include "comm.h" #include "neighbor.h" -#include "domain.h" +#include "timer.h" #include "force.h" #include "update.h" #include "error.h" diff --git a/src/USER-OMP/improper_harmonic_omp.cpp b/src/USER-OMP/improper_harmonic_omp.cpp index 6e02d0968e..32e837fdfe 100644 --- a/src/USER-OMP/improper_harmonic_omp.cpp +++ b/src/USER-OMP/improper_harmonic_omp.cpp @@ -20,7 +20,7 @@ #include "atom.h" #include "comm.h" #include "neighbor.h" -#include "domain.h" +#include "timer.h" #include "force.h" #include "update.h" #include "error.h" diff --git a/src/USER-OMP/improper_ring_omp.cpp b/src/USER-OMP/improper_ring_omp.cpp index e198b99337..6d6c1094ec 100644 --- a/src/USER-OMP/improper_ring_omp.cpp +++ b/src/USER-OMP/improper_ring_omp.cpp @@ -20,7 +20,7 @@ #include "atom.h" #include "comm.h" #include "neighbor.h" -#include "domain.h" +#include "timer.h" #include "force.h" #include "update.h" #include "error.h" diff --git a/src/USER-OMP/improper_umbrella_omp.cpp b/src/USER-OMP/improper_umbrella_omp.cpp index ceaca35074..f3fdf4570f 100644 --- a/src/USER-OMP/improper_umbrella_omp.cpp +++ b/src/USER-OMP/improper_umbrella_omp.cpp @@ -20,7 +20,7 @@ #include "atom.h" #include "comm.h" #include "neighbor.h" -#include "domain.h" +#include "timer.h" #include "force.h" #include "update.h" #include "error.h" diff --git a/src/USER-OMP/msm_cg_omp.cpp b/src/USER-OMP/msm_cg_omp.cpp index 8a920e05d5..94c64cd0cf 100644 --- a/src/USER-OMP/msm_cg_omp.cpp +++ b/src/USER-OMP/msm_cg_omp.cpp @@ -16,6 +16,7 @@ Original MSM class by: Paul Crozier, Stan Moore, Stephen Bond, (all SNL) ------------------------------------------------------------------------- */ +#include "msm_cg_omp.h" #include #include #include @@ -29,9 +30,8 @@ #include "force.h" #include "neighbor.h" #include "memory.h" -#include "msm_cg_omp.h" - #include "math_const.h" +#include "timer.h" using namespace LAMMPS_NS; using namespace MathConst; diff --git a/src/USER-OMP/msm_omp.cpp b/src/USER-OMP/msm_omp.cpp index 74cbb56be7..51aaa35d63 100644 --- a/src/USER-OMP/msm_omp.cpp +++ b/src/USER-OMP/msm_omp.cpp @@ -16,6 +16,7 @@ ------------------------------------------------------------------------- */ #include "msm_omp.h" +#include #include "atom.h" #include "comm.h" #include "domain.h" @@ -23,8 +24,8 @@ #include "force.h" #include "memory.h" #include "math_const.h" +#include "timer.h" -#include #if defined(_OPENMP) #include diff --git a/src/USER-OMP/npair_full_bin_atomonly_omp.cpp b/src/USER-OMP/npair_full_bin_atomonly_omp.cpp index d9e0fb9297..a6a3f3e748 100644 --- a/src/USER-OMP/npair_full_bin_atomonly_omp.cpp +++ b/src/USER-OMP/npair_full_bin_atomonly_omp.cpp @@ -20,6 +20,7 @@ #include "domain.h" #include "my_page.h" #include "error.h" +#include "timer.h" using namespace LAMMPS_NS; using namespace NeighConst; diff --git a/src/USER-OMP/npair_half_bin_atomonly_newton_omp.cpp b/src/USER-OMP/npair_half_bin_atomonly_newton_omp.cpp index 02d98ff6ab..5a87ad1ea6 100644 --- a/src/USER-OMP/npair_half_bin_atomonly_newton_omp.cpp +++ b/src/USER-OMP/npair_half_bin_atomonly_newton_omp.cpp @@ -18,7 +18,7 @@ #include "atom.h" #include "atom_vec.h" #include "molecule.h" -#include "domain.h" +#include "timer.h" #include "my_page.h" #include "error.h" diff --git a/src/USER-OMP/npair_halffull_newtoff_omp.cpp b/src/USER-OMP/npair_halffull_newtoff_omp.cpp index 947e4e1ad2..6f90f82752 100644 --- a/src/USER-OMP/npair_halffull_newtoff_omp.cpp +++ b/src/USER-OMP/npair_halffull_newtoff_omp.cpp @@ -18,7 +18,7 @@ #include "atom.h" #include "atom_vec.h" #include "molecule.h" -#include "domain.h" +#include "timer.h" #include "my_page.h" #include "error.h" diff --git a/src/USER-OMP/npair_halffull_newton_omp.cpp b/src/USER-OMP/npair_halffull_newton_omp.cpp index 6e158d372d..6cf8ab8ac2 100644 --- a/src/USER-OMP/npair_halffull_newton_omp.cpp +++ b/src/USER-OMP/npair_halffull_newton_omp.cpp @@ -18,7 +18,7 @@ #include "atom.h" #include "atom_vec.h" #include "molecule.h" -#include "domain.h" +#include "timer.h" #include "my_page.h" #include "error.h" diff --git a/src/USER-OMP/pair_brownian_omp.cpp b/src/USER-OMP/pair_brownian_omp.cpp index cef9fb0955..6367976c7d 100644 --- a/src/USER-OMP/pair_brownian_omp.cpp +++ b/src/USER-OMP/pair_brownian_omp.cpp @@ -12,8 +12,8 @@ Contributing author: Axel Kohlmeyer (Temple U) ------------------------------------------------------------------------- */ -#include #include "pair_brownian_omp.h" +#include #include "atom.h" #include "comm.h" #include "domain.h" @@ -26,6 +26,7 @@ #include "random_mars.h" #include "math_const.h" #include "math_special.h" +#include "timer.h" #include "fix_wall.h" diff --git a/src/USER-OMP/pair_brownian_poly_omp.cpp b/src/USER-OMP/pair_brownian_poly_omp.cpp index 239a820242..dcb4124634 100644 --- a/src/USER-OMP/pair_brownian_poly_omp.cpp +++ b/src/USER-OMP/pair_brownian_poly_omp.cpp @@ -12,8 +12,8 @@ Contributing author: Axel Kohlmeyer (Temple U) ------------------------------------------------------------------------- */ -#include #include "pair_brownian_poly_omp.h" +#include #include "atom.h" #include "comm.h" #include "domain.h" diff --git a/src/USER-OMP/pair_lj_cut_thole_long_omp.cpp b/src/USER-OMP/pair_lj_cut_thole_long_omp.cpp index d0db6262b1..87d637e80d 100644 --- a/src/USER-OMP/pair_lj_cut_thole_long_omp.cpp +++ b/src/USER-OMP/pair_lj_cut_thole_long_omp.cpp @@ -22,6 +22,7 @@ #include #include "atom.h" #include "comm.h" +#include "domain.h" #include "fix_drude.h" #include "force.h" #include "neighbor.h" @@ -30,7 +31,7 @@ #include "math_const.h" #include "error.h" #include "suffix.h" -#include "domain.h" +#include "timer.h" using namespace LAMMPS_NS; using namespace MathConst; diff --git a/src/USER-OMP/pair_lj_cut_tip4p_long_omp.cpp b/src/USER-OMP/pair_lj_cut_tip4p_long_omp.cpp index e2c1da1a89..18fc207015 100644 --- a/src/USER-OMP/pair_lj_cut_tip4p_long_omp.cpp +++ b/src/USER-OMP/pair_lj_cut_tip4p_long_omp.cpp @@ -12,8 +12,8 @@ Contributing author: Axel Kohlmeyer (Temple U) ------------------------------------------------------------------------- */ -#include #include "pair_lj_cut_tip4p_long_omp.h" +#include #include "atom.h" #include "domain.h" #include "comm.h" diff --git a/src/USER-OMP/pair_lubricate_poly_omp.cpp b/src/USER-OMP/pair_lubricate_poly_omp.cpp index 3a5f03364d..04ac59b121 100644 --- a/src/USER-OMP/pair_lubricate_poly_omp.cpp +++ b/src/USER-OMP/pair_lubricate_poly_omp.cpp @@ -12,8 +12,8 @@ Contributing author: Axel Kohlmeyer (Temple U) ------------------------------------------------------------------------- */ -#include #include "pair_lubricate_poly_omp.h" +#include #include "atom.h" #include "comm.h" #include "domain.h" diff --git a/src/USER-OMP/pppm_cg_omp.cpp b/src/USER-OMP/pppm_cg_omp.cpp index 2b4619f685..f20fa37683 100644 --- a/src/USER-OMP/pppm_cg_omp.cpp +++ b/src/USER-OMP/pppm_cg_omp.cpp @@ -15,9 +15,9 @@ Contributing author: Axel Kohlmeyer (Temple U) ------------------------------------------------------------------------- */ +#include "pppm_cg_omp.h" #include #include -#include "pppm_cg_omp.h" #include "atom.h" #include "comm.h" #include "domain.h" @@ -28,6 +28,7 @@ #include "memory.h" #include "math_const.h" #include "math_special.h" +#include "timer.h" #include "suffix.h" using namespace LAMMPS_NS; diff --git a/src/USER-OMP/pppm_disp_omp.cpp b/src/USER-OMP/pppm_disp_omp.cpp index 435341a31c..295bd66266 100644 --- a/src/USER-OMP/pppm_disp_omp.cpp +++ b/src/USER-OMP/pppm_disp_omp.cpp @@ -16,15 +16,16 @@ Rolf Isele-Holder (RWTH Aachen University) ------------------------------------------------------------------------- */ +#include "pppm_disp_omp.h" #include #include -#include "pppm_disp_omp.h" #include "atom.h" #include "comm.h" #include "domain.h" #include "force.h" #include "memory.h" #include "math_const.h" +#include "timer.h" #include "suffix.h" using namespace LAMMPS_NS; diff --git a/src/USER-OMP/pppm_disp_tip4p_omp.cpp b/src/USER-OMP/pppm_disp_tip4p_omp.cpp index a53c5b2ac5..04dec7365e 100644 --- a/src/USER-OMP/pppm_disp_tip4p_omp.cpp +++ b/src/USER-OMP/pppm_disp_tip4p_omp.cpp @@ -15,9 +15,9 @@ Contributing author: Axel Kohlmeyer (Temple U) ------------------------------------------------------------------------- */ +#include "pppm_disp_tip4p_omp.h" #include #include -#include "pppm_disp_tip4p_omp.h" #include "atom.h" #include "comm.h" #include "domain.h" @@ -27,6 +27,7 @@ #include "memory.h" #include "math_const.h" #include "math_special.h" +#include "timer.h" #include "suffix.h" using namespace LAMMPS_NS; diff --git a/src/USER-OMP/pppm_omp.cpp b/src/USER-OMP/pppm_omp.cpp index 66190b3f51..73b257efa9 100644 --- a/src/USER-OMP/pppm_omp.cpp +++ b/src/USER-OMP/pppm_omp.cpp @@ -15,9 +15,9 @@ Contributing author: Axel Kohlmeyer (Temple U) ------------------------------------------------------------------------- */ +#include "pppm_omp.h" #include #include -#include "pppm_omp.h" #include "atom.h" #include "comm.h" #include "domain.h" @@ -27,6 +27,7 @@ #include "memory.h" #include "math_const.h" #include "math_special.h" +#include "timer.h" #include "suffix.h" using namespace LAMMPS_NS; diff --git a/src/USER-OMP/respa_omp.cpp b/src/USER-OMP/respa_omp.cpp index 9c8555c66d..4a7757723f 100644 --- a/src/USER-OMP/respa_omp.cpp +++ b/src/USER-OMP/respa_omp.cpp @@ -19,9 +19,9 @@ #include #include "respa_omp.h" #include "neighbor.h" -#include "domain.h" #include "comm.h" #include "atom.h" +#include "domain.h" #include "force.h" #include "pair.h" #include "bond.h" @@ -37,6 +37,7 @@ #include "timer.h" #include "memory.h" #include "error.h" +#include "timer.h" #if defined(_OPENMP) #include diff --git a/src/USER-OMP/thr_data.h b/src/USER-OMP/thr_data.h index 3cea1b0018..edff17cad3 100644 --- a/src/USER-OMP/thr_data.h +++ b/src/USER-OMP/thr_data.h @@ -18,10 +18,6 @@ #ifndef LMP_THR_DATA_H #define LMP_THR_DATA_H -#if defined(_OPENMP) -#include -#endif - #include "timer.h" namespace LAMMPS_NS { @@ -35,7 +31,7 @@ class ThrData { public: ThrData(int tid, class Timer *t); - ~ThrData() { delete _timer; _timer = NULL; }; + ~ThrData() { delete _timer; _timer = nullptr; }; void check_tid(int); // thread id consistency check int get_tid() const { return _tid; }; // our thread id. @@ -140,7 +136,7 @@ class ThrData { // disabled default methods private: - ThrData() : _tid(-1), _timer(NULL) {}; + ThrData() : _tid(-1), _timer(nullptr) {}; }; //////////////////////////////////////////////////////////////////////// diff --git a/src/USER-OMP/thr_omp.cpp b/src/USER-OMP/thr_omp.cpp index 22f751e6c0..51030358d3 100644 --- a/src/USER-OMP/thr_omp.cpp +++ b/src/USER-OMP/thr_omp.cpp @@ -22,7 +22,6 @@ #include "comm.h" #include "error.h" #include "force.h" -#include "memory.h" #include "modify.h" #include "neighbor.h" #include "timer.h" @@ -34,7 +33,6 @@ #include "angle.h" #include "dihedral.h" #include "improper.h" -#include "kspace.h" #include "compute.h" #include "math_const.h" diff --git a/src/USER-OMP/thr_omp.h b/src/USER-OMP/thr_omp.h index 87d921290e..062d77bc0e 100644 --- a/src/USER-OMP/thr_omp.h +++ b/src/USER-OMP/thr_omp.h @@ -18,10 +18,13 @@ #ifndef LMP_THR_OMP_H #define LMP_THR_OMP_H +#if defined(_OPENMP) +#include +#endif #include "pointers.h" #include "error.h" -#include "fix_omp.h" -#include "thr_data.h" +#include "fix_omp.h" // IWYU pragma: export +#include "thr_data.h" // IWYU pragma: export namespace LAMMPS_NS { @@ -31,8 +34,6 @@ class Bond; class Angle; class Dihedral; class Improper; -class KSpace; -class Fix; class ThrOMP { diff --git a/src/special.cpp b/src/special.cpp index b64aa96e2b..3dd817bc7f 100644 --- a/src/special.cpp +++ b/src/special.cpp @@ -19,7 +19,7 @@ #include "comm.h" #include "modify.h" #include "fix.h" -#include "accelerator_kokkos.h" +#include "accelerator_kokkos.h" // IWYU pragma: export #include "atom_masks.h" #include "memory.h" -- GitLab From 944c3bc91d3b372397f5dc30f843cca787110cb0 Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Thu, 11 Jul 2019 17:42:58 -0400 Subject: [PATCH 242/469] fix bug reported by jesse carter on lammps-users --- src/USER-INTEL/fix_nh_intel.cpp | 2 +- src/USER-INTEL/fix_nve_intel.cpp | 11 +++++++++++ 2 files changed, 12 insertions(+), 1 deletion(-) diff --git a/src/USER-INTEL/fix_nh_intel.cpp b/src/USER-INTEL/fix_nh_intel.cpp index bf4764f104..a072e823a4 100644 --- a/src/USER-INTEL/fix_nh_intel.cpp +++ b/src/USER-INTEL/fix_nh_intel.cpp @@ -335,7 +335,7 @@ void FixNHIntel::reset_dt() if (nlocal > _nlocal_max) { if (_nlocal_max) memory->destroy(_dtfm); _nlocal_max = static_cast(1.20 * nlocal); - memory->create(_dtfm, _nlocal_max * 3, "fix_nve_intel:dtfm"); + memory->create(_dtfm, _nlocal_max * 3, "fix_nh_intel:dtfm"); } _nlocal3 = nlocal * 3; diff --git a/src/USER-INTEL/fix_nve_intel.cpp b/src/USER-INTEL/fix_nve_intel.cpp index 7dee31d2f4..f5d0513b65 100644 --- a/src/USER-INTEL/fix_nve_intel.cpp +++ b/src/USER-INTEL/fix_nve_intel.cpp @@ -75,6 +75,7 @@ void FixNVEIntel::initial_integrate(int /*vflag*/) x[i] += dtv * v[i]; } } else if (igroup == 0) { + if (neighbor->ago == 0) reset_dt(); #if defined(LMP_SIMD_COMPILER) #pragma vector aligned #pragma simd @@ -84,6 +85,7 @@ void FixNVEIntel::initial_integrate(int /*vflag*/) x[i] += dtv * v[i]; } } else { + if (neighbor->ago == 0) reset_dt(); #if defined(LMP_SIMD_COMPILER) #pragma vector aligned #pragma simd @@ -114,6 +116,15 @@ void FixNVEIntel::final_integrate() #endif for (int i = 0; i < _nlocal3; i++) v[i] += dtfm * f[i]; + } else if (igroup == 0) { + if (neighbor->ago == 0) reset_dt(); + #if defined(LMP_SIMD_COMPILER) + #pragma vector aligned + #pragma simd + #endif + for (int i = 0; i < _nlocal3; i++) { + v[i] += _dtfm[i] * f[i]; + } } else { if (neighbor->ago == 0) reset_dt(); #if defined(LMP_SIMD_COMPILER) -- GitLab From b4f60ef477d86cf541bb10d7e3262e03c3fed036 Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Thu, 11 Jul 2019 16:51:48 -0400 Subject: [PATCH 243/469] starting to work on includes in USER-OMP --- src/USER-OMP/angle_charmm_omp.cpp | 8 ++------ src/USER-OMP/angle_class2_omp.cpp | 8 ++------ src/USER-OMP/angle_cosine_delta_omp.cpp | 8 ++------ src/USER-OMP/angle_cosine_omp.cpp | 8 ++------ src/USER-OMP/angle_cosine_periodic_omp.cpp | 8 ++------ src/USER-OMP/angle_cosine_shift_exp_omp.cpp | 8 ++------ src/USER-OMP/angle_cosine_shift_omp.cpp | 8 ++------ src/USER-OMP/angle_cosine_squared_omp.cpp | 8 ++------ src/USER-OMP/angle_dipole_omp.cpp | 8 ++------ src/USER-OMP/angle_fourier_omp.cpp | 8 ++------ src/USER-OMP/angle_fourier_simple_omp.cpp | 8 ++------ src/USER-OMP/angle_harmonic_omp.cpp | 8 ++------ src/USER-OMP/angle_quartic_omp.cpp | 8 ++------ src/USER-OMP/angle_sdk_omp.cpp | 8 ++------ src/USER-OMP/angle_table_omp.cpp | 8 ++------ src/USER-OMP/bond_class2_omp.cpp | 2 +- src/USER-OMP/bond_fene_expand_omp.cpp | 2 +- src/USER-OMP/bond_fene_omp.cpp | 2 +- src/USER-OMP/bond_gromos_omp.cpp | 4 +--- src/USER-OMP/bond_harmonic_omp.cpp | 2 +- src/USER-OMP/bond_harmonic_shift_cut_omp.cpp | 2 +- src/USER-OMP/bond_harmonic_shift_omp.cpp | 2 +- src/USER-OMP/bond_morse_omp.cpp | 2 +- src/USER-OMP/bond_nonlinear_omp.cpp | 2 +- src/USER-OMP/bond_quartic_omp.cpp | 2 +- src/USER-OMP/bond_table_omp.cpp | 2 +- src/USER-OMP/dihedral_charmm_omp.cpp | 5 ++--- src/USER-OMP/dihedral_class2_omp.cpp | 2 +- .../dihedral_cosine_shift_exp_omp.cpp | 2 +- src/USER-OMP/dihedral_fourier_omp.cpp | 6 ++---- src/USER-OMP/dihedral_harmonic_omp.cpp | 2 +- src/USER-OMP/dihedral_helix_omp.cpp | 2 +- src/USER-OMP/dihedral_multi_harmonic_omp.cpp | 2 +- src/USER-OMP/dihedral_nharmonic_omp.cpp | 2 +- src/USER-OMP/dihedral_opls_omp.cpp | 2 +- src/USER-OMP/dihedral_quadratic_omp.cpp | 2 +- src/USER-OMP/dihedral_table_omp.cpp | 11 +++-------- src/USER-OMP/domain_omp.cpp | 1 - src/USER-OMP/ewald_omp.cpp | 7 +++---- src/USER-OMP/fix_gravity_omp.cpp | 7 ------- src/USER-OMP/fix_neigh_history_omp.cpp | 7 +------ src/USER-OMP/fix_nh_omp.cpp | 4 +--- src/USER-OMP/fix_nh_sphere_omp.cpp | 3 --- src/USER-OMP/fix_nve_omp.cpp | 1 - src/USER-OMP/fix_nve_sphere_omp.cpp | 8 +------- src/USER-OMP/fix_nvt_sllod_omp.cpp | 5 ++--- src/USER-OMP/fix_omp.cpp | 10 +++++----- src/USER-OMP/fix_qeq_comb_omp.cpp | 8 ++------ src/USER-OMP/fix_qeq_reax_omp.cpp | 19 +++++++------------ src/USER-OMP/fix_rigid_nh_omp.cpp | 5 ++--- src/USER-OMP/fix_rigid_nph_omp.cpp | 3 +-- src/USER-OMP/fix_rigid_npt_omp.cpp | 3 +-- src/USER-OMP/fix_rigid_omp.cpp | 7 +++---- src/USER-OMP/fix_rigid_small_omp.cpp | 4 +--- src/USER-OMP/improper_class2_omp.cpp | 2 +- src/USER-OMP/improper_cossq_omp.cpp | 2 +- src/USER-OMP/improper_cvff_omp.cpp | 2 +- src/USER-OMP/improper_fourier_omp.cpp | 2 +- src/USER-OMP/improper_harmonic_omp.cpp | 2 +- src/USER-OMP/improper_ring_omp.cpp | 6 ++---- src/USER-OMP/improper_umbrella_omp.cpp | 2 +- src/USER-OMP/msm_cg_omp.cpp | 10 ++++++---- src/USER-OMP/msm_omp.cpp | 8 ++------ src/USER-OMP/npair_full_bin_atomonly_omp.cpp | 2 -- src/USER-OMP/npair_full_bin_ghost_omp.cpp | 1 - src/USER-OMP/npair_full_multi_omp.cpp | 1 - src/USER-OMP/npair_full_nsq_ghost_omp.cpp | 1 - src/USER-OMP/npair_full_nsq_omp.cpp | 1 - .../npair_half_bin_atomonly_newton_omp.cpp | 3 --- .../npair_half_bin_newtoff_ghost_omp.cpp | 1 - src/USER-OMP/npair_half_bin_newtoff_omp.cpp | 1 - src/USER-OMP/npair_half_bin_newton_omp.cpp | 2 -- .../npair_half_bin_newton_tri_omp.cpp | 1 - src/USER-OMP/npair_half_multi_newtoff_omp.cpp | 1 - src/USER-OMP/npair_half_multi_newton_omp.cpp | 1 - src/USER-OMP/npair_halffull_newtoff_omp.cpp | 2 +- src/USER-OMP/npair_halffull_newton_omp.cpp | 2 +- src/USER-OMP/pair_brownian_omp.cpp | 3 ++- src/USER-OMP/pair_brownian_poly_omp.cpp | 2 +- src/USER-OMP/pair_lj_cut_thole_long_omp.cpp | 3 ++- src/USER-OMP/pair_lj_cut_tip4p_long_omp.cpp | 2 +- src/USER-OMP/pair_lubricate_poly_omp.cpp | 2 +- src/USER-OMP/pppm_cg_omp.cpp | 12 ++++++------ src/USER-OMP/pppm_disp_omp.cpp | 9 +++++++-- src/USER-OMP/pppm_disp_tip4p_omp.cpp | 11 +++++------ src/USER-OMP/pppm_omp.cpp | 11 +++++++---- src/USER-OMP/pppm_tip4p_omp.cpp | 9 ++++++--- src/USER-OMP/reaxc_multi_body_omp.cpp | 7 +++---- src/USER-OMP/reaxc_valence_angles_omp.cpp | 6 ++++-- src/USER-OMP/respa_omp.cpp | 9 ++------- src/USER-OMP/thr_data.h | 8 ++------ src/USER-OMP/thr_omp.cpp | 2 -- src/USER-OMP/thr_omp.h | 9 +++++---- src/USER-SMD/pair_smd_tlsph.cpp | 8 +++----- src/special.cpp | 2 +- 95 files changed, 162 insertions(+), 293 deletions(-) diff --git a/src/USER-OMP/angle_charmm_omp.cpp b/src/USER-OMP/angle_charmm_omp.cpp index 118ba00226..f135446915 100644 --- a/src/USER-OMP/angle_charmm_omp.cpp +++ b/src/USER-OMP/angle_charmm_omp.cpp @@ -16,19 +16,15 @@ ------------------------------------------------------------------------- */ #include "angle_charmm_omp.h" +#include #include "atom.h" #include "comm.h" #include "force.h" #include "neighbor.h" -#include "domain.h" - -#include "math_const.h" - -#include +#include "timer.h" #include "suffix.h" using namespace LAMMPS_NS; -using namespace MathConst; #define SMALL 0.001 diff --git a/src/USER-OMP/angle_class2_omp.cpp b/src/USER-OMP/angle_class2_omp.cpp index e072d136e1..0cf5489663 100644 --- a/src/USER-OMP/angle_class2_omp.cpp +++ b/src/USER-OMP/angle_class2_omp.cpp @@ -16,19 +16,15 @@ ------------------------------------------------------------------------- */ #include "angle_class2_omp.h" +#include #include "atom.h" #include "comm.h" #include "force.h" #include "neighbor.h" -#include "domain.h" - -#include "math_const.h" - -#include +#include "timer.h" #include "suffix.h" using namespace LAMMPS_NS; -using namespace MathConst; #define SMALL 0.001 diff --git a/src/USER-OMP/angle_cosine_delta_omp.cpp b/src/USER-OMP/angle_cosine_delta_omp.cpp index a6dfb20433..7f4d994c4f 100644 --- a/src/USER-OMP/angle_cosine_delta_omp.cpp +++ b/src/USER-OMP/angle_cosine_delta_omp.cpp @@ -16,19 +16,15 @@ ------------------------------------------------------------------------- */ #include "angle_cosine_delta_omp.h" +#include #include "atom.h" #include "comm.h" #include "force.h" #include "neighbor.h" -#include "domain.h" - -#include "math_const.h" - -#include +#include "timer.h" #include "suffix.h" using namespace LAMMPS_NS; -using namespace MathConst; #define SMALL 0.001 diff --git a/src/USER-OMP/angle_cosine_omp.cpp b/src/USER-OMP/angle_cosine_omp.cpp index 9097c8569c..0543c94799 100644 --- a/src/USER-OMP/angle_cosine_omp.cpp +++ b/src/USER-OMP/angle_cosine_omp.cpp @@ -16,19 +16,15 @@ ------------------------------------------------------------------------- */ #include "angle_cosine_omp.h" +#include #include "atom.h" #include "comm.h" #include "force.h" #include "neighbor.h" -#include "domain.h" - -#include "math_const.h" - -#include +#include "timer.h" #include "suffix.h" using namespace LAMMPS_NS; -using namespace MathConst; #define SMALL 0.001 diff --git a/src/USER-OMP/angle_cosine_periodic_omp.cpp b/src/USER-OMP/angle_cosine_periodic_omp.cpp index 3fcea7ad1d..907315f83b 100644 --- a/src/USER-OMP/angle_cosine_periodic_omp.cpp +++ b/src/USER-OMP/angle_cosine_periodic_omp.cpp @@ -16,20 +16,16 @@ ------------------------------------------------------------------------- */ #include "angle_cosine_periodic_omp.h" +#include #include "atom.h" #include "comm.h" #include "force.h" #include "neighbor.h" -#include "domain.h" - -#include "math_const.h" +#include "timer.h" #include "math_special.h" -#include - #include "suffix.h" using namespace LAMMPS_NS; -using namespace MathConst; using namespace MathSpecial; #define SMALL 0.001 diff --git a/src/USER-OMP/angle_cosine_shift_exp_omp.cpp b/src/USER-OMP/angle_cosine_shift_exp_omp.cpp index 6bd2feb023..6c42319905 100644 --- a/src/USER-OMP/angle_cosine_shift_exp_omp.cpp +++ b/src/USER-OMP/angle_cosine_shift_exp_omp.cpp @@ -16,19 +16,15 @@ ------------------------------------------------------------------------- */ #include "angle_cosine_shift_exp_omp.h" +#include #include "atom.h" #include "comm.h" #include "force.h" #include "neighbor.h" -#include "domain.h" - -#include "math_const.h" - -#include +#include "timer.h" #include "suffix.h" using namespace LAMMPS_NS; -using namespace MathConst; #define SMALL 0.001 diff --git a/src/USER-OMP/angle_cosine_shift_omp.cpp b/src/USER-OMP/angle_cosine_shift_omp.cpp index 56486faac1..5c0afcf316 100644 --- a/src/USER-OMP/angle_cosine_shift_omp.cpp +++ b/src/USER-OMP/angle_cosine_shift_omp.cpp @@ -16,19 +16,15 @@ ------------------------------------------------------------------------- */ #include "angle_cosine_shift_omp.h" +#include #include "atom.h" #include "comm.h" #include "force.h" #include "neighbor.h" -#include "domain.h" - -#include "math_const.h" - -#include +#include "timer.h" #include "suffix.h" using namespace LAMMPS_NS; -using namespace MathConst; #define SMALL 0.001 diff --git a/src/USER-OMP/angle_cosine_squared_omp.cpp b/src/USER-OMP/angle_cosine_squared_omp.cpp index 6dd2a3bb3b..27c47b90d8 100644 --- a/src/USER-OMP/angle_cosine_squared_omp.cpp +++ b/src/USER-OMP/angle_cosine_squared_omp.cpp @@ -16,19 +16,15 @@ ------------------------------------------------------------------------- */ #include "angle_cosine_squared_omp.h" +#include #include "atom.h" #include "comm.h" #include "force.h" #include "neighbor.h" -#include "domain.h" - -#include "math_const.h" - -#include +#include "timer.h" #include "suffix.h" using namespace LAMMPS_NS; -using namespace MathConst; #define SMALL 0.001 diff --git a/src/USER-OMP/angle_dipole_omp.cpp b/src/USER-OMP/angle_dipole_omp.cpp index da2e819ee2..6af5b44a03 100644 --- a/src/USER-OMP/angle_dipole_omp.cpp +++ b/src/USER-OMP/angle_dipole_omp.cpp @@ -16,20 +16,16 @@ ------------------------------------------------------------------------- */ #include "angle_dipole_omp.h" +#include #include "atom.h" #include "comm.h" #include "error.h" #include "force.h" #include "neighbor.h" -#include "domain.h" - -#include "math_const.h" - -#include +#include "timer.h" #include "suffix.h" using namespace LAMMPS_NS; -using namespace MathConst; #define SMALL 0.001 diff --git a/src/USER-OMP/angle_fourier_omp.cpp b/src/USER-OMP/angle_fourier_omp.cpp index b2f9b47e05..98527c2028 100644 --- a/src/USER-OMP/angle_fourier_omp.cpp +++ b/src/USER-OMP/angle_fourier_omp.cpp @@ -16,19 +16,15 @@ ------------------------------------------------------------------------- */ #include "angle_fourier_omp.h" +#include #include "atom.h" #include "comm.h" #include "force.h" #include "neighbor.h" -#include "domain.h" - -#include "math_const.h" - -#include +#include "timer.h" #include "suffix.h" using namespace LAMMPS_NS; -using namespace MathConst; #define SMALL 0.001 diff --git a/src/USER-OMP/angle_fourier_simple_omp.cpp b/src/USER-OMP/angle_fourier_simple_omp.cpp index 93532a30e5..71d0197b72 100644 --- a/src/USER-OMP/angle_fourier_simple_omp.cpp +++ b/src/USER-OMP/angle_fourier_simple_omp.cpp @@ -16,19 +16,15 @@ ------------------------------------------------------------------------- */ #include "angle_fourier_simple_omp.h" +#include #include "atom.h" #include "comm.h" #include "force.h" #include "neighbor.h" -#include "domain.h" - -#include "math_const.h" - -#include +#include "timer.h" #include "suffix.h" using namespace LAMMPS_NS; -using namespace MathConst; #define SMALL 0.001 diff --git a/src/USER-OMP/angle_harmonic_omp.cpp b/src/USER-OMP/angle_harmonic_omp.cpp index 824b254287..ee08bbd8ad 100644 --- a/src/USER-OMP/angle_harmonic_omp.cpp +++ b/src/USER-OMP/angle_harmonic_omp.cpp @@ -16,19 +16,15 @@ ------------------------------------------------------------------------- */ #include "angle_harmonic_omp.h" +#include #include "atom.h" #include "comm.h" #include "force.h" #include "neighbor.h" -#include "domain.h" - -#include "math_const.h" - -#include +#include "timer.h" #include "suffix.h" using namespace LAMMPS_NS; -using namespace MathConst; #define SMALL 0.001 diff --git a/src/USER-OMP/angle_quartic_omp.cpp b/src/USER-OMP/angle_quartic_omp.cpp index fff08ddb39..5745948222 100644 --- a/src/USER-OMP/angle_quartic_omp.cpp +++ b/src/USER-OMP/angle_quartic_omp.cpp @@ -16,19 +16,15 @@ ------------------------------------------------------------------------- */ #include "angle_quartic_omp.h" +#include #include "atom.h" #include "comm.h" #include "force.h" #include "neighbor.h" -#include "domain.h" - -#include "math_const.h" - -#include +#include "timer.h" #include "suffix.h" using namespace LAMMPS_NS; -using namespace MathConst; #define SMALL 0.001 diff --git a/src/USER-OMP/angle_sdk_omp.cpp b/src/USER-OMP/angle_sdk_omp.cpp index e8c762092c..e0b1da0baf 100644 --- a/src/USER-OMP/angle_sdk_omp.cpp +++ b/src/USER-OMP/angle_sdk_omp.cpp @@ -16,20 +16,16 @@ ------------------------------------------------------------------------- */ #include "angle_sdk_omp.h" +#include #include "atom.h" #include "neighbor.h" -#include "domain.h" +#include "timer.h" #include "comm.h" #include "force.h" -#include "math_const.h" - -#include - #include "lj_sdk_common.h" #include "suffix.h" using namespace LAMMPS_NS; -using namespace MathConst; using namespace LJSDKParms; #define SMALL 0.001 diff --git a/src/USER-OMP/angle_table_omp.cpp b/src/USER-OMP/angle_table_omp.cpp index d9d80b744d..4f6edf2073 100644 --- a/src/USER-OMP/angle_table_omp.cpp +++ b/src/USER-OMP/angle_table_omp.cpp @@ -16,19 +16,15 @@ ------------------------------------------------------------------------- */ #include "angle_table_omp.h" +#include #include "atom.h" #include "comm.h" #include "force.h" #include "neighbor.h" -#include "domain.h" - -#include "math_const.h" - -#include +#include "timer.h" #include "suffix.h" using namespace LAMMPS_NS; -using namespace MathConst; #define SMALL 0.001 diff --git a/src/USER-OMP/bond_class2_omp.cpp b/src/USER-OMP/bond_class2_omp.cpp index fdd73c20b0..7d1b693faf 100644 --- a/src/USER-OMP/bond_class2_omp.cpp +++ b/src/USER-OMP/bond_class2_omp.cpp @@ -20,7 +20,7 @@ #include "comm.h" #include "force.h" #include "neighbor.h" -#include "domain.h" +#include "timer.h" #include diff --git a/src/USER-OMP/bond_fene_expand_omp.cpp b/src/USER-OMP/bond_fene_expand_omp.cpp index a8eec11760..aefae6dcf7 100644 --- a/src/USER-OMP/bond_fene_expand_omp.cpp +++ b/src/USER-OMP/bond_fene_expand_omp.cpp @@ -20,7 +20,7 @@ #include "comm.h" #include "force.h" #include "neighbor.h" -#include "domain.h" +#include "timer.h" #include "error.h" #include "update.h" diff --git a/src/USER-OMP/bond_fene_omp.cpp b/src/USER-OMP/bond_fene_omp.cpp index be7dcd4b49..2b579114ba 100644 --- a/src/USER-OMP/bond_fene_omp.cpp +++ b/src/USER-OMP/bond_fene_omp.cpp @@ -20,7 +20,7 @@ #include "comm.h" #include "force.h" #include "neighbor.h" -#include "domain.h" +#include "timer.h" #include "error.h" #include "update.h" diff --git a/src/USER-OMP/bond_gromos_omp.cpp b/src/USER-OMP/bond_gromos_omp.cpp index 8f0926c0e9..ba23217a1f 100644 --- a/src/USER-OMP/bond_gromos_omp.cpp +++ b/src/USER-OMP/bond_gromos_omp.cpp @@ -20,9 +20,7 @@ #include "comm.h" #include "force.h" #include "neighbor.h" -#include "domain.h" - -#include +#include "timer.h" #include "suffix.h" using namespace LAMMPS_NS; diff --git a/src/USER-OMP/bond_harmonic_omp.cpp b/src/USER-OMP/bond_harmonic_omp.cpp index a3bb69c53c..5515284f9a 100644 --- a/src/USER-OMP/bond_harmonic_omp.cpp +++ b/src/USER-OMP/bond_harmonic_omp.cpp @@ -20,7 +20,7 @@ #include "comm.h" #include "force.h" #include "neighbor.h" -#include "domain.h" +#include "timer.h" #include diff --git a/src/USER-OMP/bond_harmonic_shift_cut_omp.cpp b/src/USER-OMP/bond_harmonic_shift_cut_omp.cpp index 5c16e27a32..a871fa8c04 100644 --- a/src/USER-OMP/bond_harmonic_shift_cut_omp.cpp +++ b/src/USER-OMP/bond_harmonic_shift_cut_omp.cpp @@ -20,7 +20,7 @@ #include "comm.h" #include "force.h" #include "neighbor.h" -#include "domain.h" +#include "timer.h" #include diff --git a/src/USER-OMP/bond_harmonic_shift_omp.cpp b/src/USER-OMP/bond_harmonic_shift_omp.cpp index 39e957c137..4117da9159 100644 --- a/src/USER-OMP/bond_harmonic_shift_omp.cpp +++ b/src/USER-OMP/bond_harmonic_shift_omp.cpp @@ -20,7 +20,7 @@ #include "comm.h" #include "force.h" #include "neighbor.h" -#include "domain.h" +#include "timer.h" #include diff --git a/src/USER-OMP/bond_morse_omp.cpp b/src/USER-OMP/bond_morse_omp.cpp index c0203de0d6..e6526dc8dc 100644 --- a/src/USER-OMP/bond_morse_omp.cpp +++ b/src/USER-OMP/bond_morse_omp.cpp @@ -20,7 +20,7 @@ #include "comm.h" #include "force.h" #include "neighbor.h" -#include "domain.h" +#include "timer.h" #include diff --git a/src/USER-OMP/bond_nonlinear_omp.cpp b/src/USER-OMP/bond_nonlinear_omp.cpp index 8fa3daf8ab..0d1a648415 100644 --- a/src/USER-OMP/bond_nonlinear_omp.cpp +++ b/src/USER-OMP/bond_nonlinear_omp.cpp @@ -20,7 +20,7 @@ #include "comm.h" #include "force.h" #include "neighbor.h" -#include "domain.h" +#include "timer.h" #include diff --git a/src/USER-OMP/bond_quartic_omp.cpp b/src/USER-OMP/bond_quartic_omp.cpp index fd0ccaf79d..60d3a5601c 100644 --- a/src/USER-OMP/bond_quartic_omp.cpp +++ b/src/USER-OMP/bond_quartic_omp.cpp @@ -20,7 +20,7 @@ #include "comm.h" #include "force.h" #include "neighbor.h" -#include "domain.h" +#include "timer.h" #include "pair.h" #include diff --git a/src/USER-OMP/bond_table_omp.cpp b/src/USER-OMP/bond_table_omp.cpp index 1616988385..8e1e792c73 100644 --- a/src/USER-OMP/bond_table_omp.cpp +++ b/src/USER-OMP/bond_table_omp.cpp @@ -20,7 +20,7 @@ #include "comm.h" #include "force.h" #include "neighbor.h" -#include "domain.h" +#include "timer.h" #include diff --git a/src/USER-OMP/dihedral_charmm_omp.cpp b/src/USER-OMP/dihedral_charmm_omp.cpp index b09863613e..95ad9af6a6 100644 --- a/src/USER-OMP/dihedral_charmm_omp.cpp +++ b/src/USER-OMP/dihedral_charmm_omp.cpp @@ -15,13 +15,12 @@ Contributing author: Axel Kohlmeyer (Temple U) ------------------------------------------------------------------------- */ -#include -#include #include "dihedral_charmm_omp.h" +#include #include "atom.h" #include "comm.h" #include "neighbor.h" -#include "domain.h" +#include "timer.h" #include "force.h" #include "pair.h" #include "update.h" diff --git a/src/USER-OMP/dihedral_class2_omp.cpp b/src/USER-OMP/dihedral_class2_omp.cpp index 03ac9d9bab..6c2bc02ff4 100644 --- a/src/USER-OMP/dihedral_class2_omp.cpp +++ b/src/USER-OMP/dihedral_class2_omp.cpp @@ -20,7 +20,7 @@ #include "atom.h" #include "comm.h" #include "neighbor.h" -#include "domain.h" +#include "timer.h" #include "force.h" #include "update.h" #include "error.h" diff --git a/src/USER-OMP/dihedral_cosine_shift_exp_omp.cpp b/src/USER-OMP/dihedral_cosine_shift_exp_omp.cpp index c64cad9fc3..d77e9d6b3e 100644 --- a/src/USER-OMP/dihedral_cosine_shift_exp_omp.cpp +++ b/src/USER-OMP/dihedral_cosine_shift_exp_omp.cpp @@ -20,7 +20,7 @@ #include "atom.h" #include "comm.h" #include "neighbor.h" -#include "domain.h" +#include "timer.h" #include "force.h" #include "update.h" #include "error.h" diff --git a/src/USER-OMP/dihedral_fourier_omp.cpp b/src/USER-OMP/dihedral_fourier_omp.cpp index 94bdae3795..93dbd773ca 100644 --- a/src/USER-OMP/dihedral_fourier_omp.cpp +++ b/src/USER-OMP/dihedral_fourier_omp.cpp @@ -15,20 +15,18 @@ Contributing author: Axel Kohlmeyer (Temple U) ------------------------------------------------------------------------- */ -#include #include "dihedral_fourier_omp.h" +#include #include "atom.h" #include "comm.h" #include "neighbor.h" -#include "domain.h" +#include "timer.h" #include "force.h" #include "update.h" #include "error.h" -#include "math_const.h" #include "suffix.h" using namespace LAMMPS_NS; -using namespace MathConst; #define TOLERANCE 0.05 diff --git a/src/USER-OMP/dihedral_harmonic_omp.cpp b/src/USER-OMP/dihedral_harmonic_omp.cpp index 10ccbd3d9f..84aa584d9e 100644 --- a/src/USER-OMP/dihedral_harmonic_omp.cpp +++ b/src/USER-OMP/dihedral_harmonic_omp.cpp @@ -20,7 +20,7 @@ #include "atom.h" #include "comm.h" #include "neighbor.h" -#include "domain.h" +#include "timer.h" #include "force.h" #include "update.h" #include "error.h" diff --git a/src/USER-OMP/dihedral_helix_omp.cpp b/src/USER-OMP/dihedral_helix_omp.cpp index 8c8e29cac0..51b07754e2 100644 --- a/src/USER-OMP/dihedral_helix_omp.cpp +++ b/src/USER-OMP/dihedral_helix_omp.cpp @@ -20,7 +20,7 @@ #include "atom.h" #include "comm.h" #include "neighbor.h" -#include "domain.h" +#include "timer.h" #include "force.h" #include "update.h" #include "math_const.h" diff --git a/src/USER-OMP/dihedral_multi_harmonic_omp.cpp b/src/USER-OMP/dihedral_multi_harmonic_omp.cpp index 38961e1746..4cb6919a96 100644 --- a/src/USER-OMP/dihedral_multi_harmonic_omp.cpp +++ b/src/USER-OMP/dihedral_multi_harmonic_omp.cpp @@ -20,7 +20,7 @@ #include "atom.h" #include "comm.h" #include "neighbor.h" -#include "domain.h" +#include "timer.h" #include "force.h" #include "update.h" #include "error.h" diff --git a/src/USER-OMP/dihedral_nharmonic_omp.cpp b/src/USER-OMP/dihedral_nharmonic_omp.cpp index e74238265d..203884531b 100644 --- a/src/USER-OMP/dihedral_nharmonic_omp.cpp +++ b/src/USER-OMP/dihedral_nharmonic_omp.cpp @@ -20,10 +20,10 @@ #include "atom.h" #include "comm.h" #include "neighbor.h" -#include "domain.h" #include "force.h" #include "update.h" #include "error.h" +#include "timer.h" #include "suffix.h" using namespace LAMMPS_NS; diff --git a/src/USER-OMP/dihedral_opls_omp.cpp b/src/USER-OMP/dihedral_opls_omp.cpp index 64eaffe6fe..af12bb866e 100644 --- a/src/USER-OMP/dihedral_opls_omp.cpp +++ b/src/USER-OMP/dihedral_opls_omp.cpp @@ -20,7 +20,7 @@ #include "atom.h" #include "comm.h" #include "neighbor.h" -#include "domain.h" +#include "timer.h" #include "force.h" #include "update.h" #include "error.h" diff --git a/src/USER-OMP/dihedral_quadratic_omp.cpp b/src/USER-OMP/dihedral_quadratic_omp.cpp index 8df622b847..8cea62aaea 100644 --- a/src/USER-OMP/dihedral_quadratic_omp.cpp +++ b/src/USER-OMP/dihedral_quadratic_omp.cpp @@ -20,10 +20,10 @@ #include "atom.h" #include "comm.h" #include "neighbor.h" -#include "domain.h" #include "force.h" #include "update.h" #include "error.h" +#include "timer.h" #include "suffix.h" using namespace LAMMPS_NS; diff --git a/src/USER-OMP/dihedral_table_omp.cpp b/src/USER-OMP/dihedral_table_omp.cpp index 792ee90c26..6b10027b9d 100644 --- a/src/USER-OMP/dihedral_table_omp.cpp +++ b/src/USER-OMP/dihedral_table_omp.cpp @@ -15,19 +15,14 @@ Contributing author: Axel Kohlmeyer (Temple U) ------------------------------------------------------------------------- */ -#include -#include -#include - #include "dihedral_table_omp.h" +#include #include "atom.h" #include "comm.h" -#include "neighbor.h" #include "domain.h" +#include "neighbor.h" #include "force.h" -#include "update.h" -#include "error.h" - +#include "timer.h" #include "math_const.h" #include "math_extra.h" diff --git a/src/USER-OMP/domain_omp.cpp b/src/USER-OMP/domain_omp.cpp index 584e56b1f0..a18931c551 100644 --- a/src/USER-OMP/domain_omp.cpp +++ b/src/USER-OMP/domain_omp.cpp @@ -15,7 +15,6 @@ Contributing author : Axel Kohlmeyer (Temple U) ------------------------------------------------------------------------- */ -#include "domain.h" #include "accelerator_omp.h" #include "atom.h" diff --git a/src/USER-OMP/ewald_omp.cpp b/src/USER-OMP/ewald_omp.cpp index b56fc25142..aadf63741d 100644 --- a/src/USER-OMP/ewald_omp.cpp +++ b/src/USER-OMP/ewald_omp.cpp @@ -15,15 +15,14 @@ Contributing authors: Roy Pollock (LLNL), Paul Crozier (SNL) ------------------------------------------------------------------------- */ -#include #include "ewald_omp.h" +#include +#include #include "atom.h" #include "comm.h" #include "force.h" #include "memory.h" - -#include - +#include "timer.h" #include "math_const.h" #include "suffix.h" diff --git a/src/USER-OMP/fix_gravity_omp.cpp b/src/USER-OMP/fix_gravity_omp.cpp index eae918ec52..fa6b698821 100644 --- a/src/USER-OMP/fix_gravity_omp.cpp +++ b/src/USER-OMP/fix_gravity_omp.cpp @@ -15,19 +15,12 @@ Contributing author: Axel Kohlmeyer (Temple U) ------------------------------------------------------------------------- */ -#include -#include -#include -#include #include "fix_gravity_omp.h" #include "atom.h" #include "update.h" -#include "domain.h" #include "input.h" #include "modify.h" -#include "respa.h" #include "variable.h" -#include "error.h" using namespace LAMMPS_NS; using namespace FixConst; diff --git a/src/USER-OMP/fix_neigh_history_omp.cpp b/src/USER-OMP/fix_neigh_history_omp.cpp index be03e1d8f2..c2bc8af5e0 100644 --- a/src/USER-OMP/fix_neigh_history_omp.cpp +++ b/src/USER-OMP/fix_neigh_history_omp.cpp @@ -11,19 +11,14 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include -#include #include "fix_neigh_history_omp.h" +#include #include "my_page.h" #include "atom.h" #include "comm.h" -#include "neighbor.h" #include "neigh_list.h" -#include "force.h" #include "pair.h" -#include "update.h" #include "memory.h" -#include "modify.h" #include "error.h" #if defined(_OPENMP) diff --git a/src/USER-OMP/fix_nh_omp.cpp b/src/USER-OMP/fix_nh_omp.cpp index 76a47b71fd..2abd739f71 100644 --- a/src/USER-OMP/fix_nh_omp.cpp +++ b/src/USER-OMP/fix_nh_omp.cpp @@ -16,15 +16,13 @@ ------------------------------------------------------------------------- */ #include "fix_nh_omp.h" +#include #include "atom.h" #include "compute.h" #include "domain.h" #include "error.h" #include "modify.h" -#include -#include - using namespace LAMMPS_NS; using namespace FixConst; diff --git a/src/USER-OMP/fix_nh_sphere_omp.cpp b/src/USER-OMP/fix_nh_sphere_omp.cpp index a32f0f8b51..64bc536bb0 100644 --- a/src/USER-OMP/fix_nh_sphere_omp.cpp +++ b/src/USER-OMP/fix_nh_sphere_omp.cpp @@ -15,12 +15,9 @@ Contributing author: Axel Kohlmeyer (Temple U) ------------------------------------------------------------------------- */ -#include #include "fix_nh_sphere_omp.h" #include "atom.h" -#include "atom_vec.h" #include "compute.h" -#include "group.h" #include "error.h" using namespace LAMMPS_NS; diff --git a/src/USER-OMP/fix_nve_omp.cpp b/src/USER-OMP/fix_nve_omp.cpp index c61ad7155c..61ed82b16f 100644 --- a/src/USER-OMP/fix_nve_omp.cpp +++ b/src/USER-OMP/fix_nve_omp.cpp @@ -13,7 +13,6 @@ #include "fix_nve_omp.h" #include "atom.h" -#include "force.h" using namespace LAMMPS_NS; using namespace FixConst; diff --git a/src/USER-OMP/fix_nve_sphere_omp.cpp b/src/USER-OMP/fix_nve_sphere_omp.cpp index 2286120bee..ccdd654874 100644 --- a/src/USER-OMP/fix_nve_sphere_omp.cpp +++ b/src/USER-OMP/fix_nve_sphere_omp.cpp @@ -11,16 +11,10 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include -#include -#include #include "fix_nve_sphere_omp.h" +#include #include "atom.h" -#include "atom_vec.h" -#include "update.h" -#include "respa.h" #include "force.h" -#include "error.h" #include "math_vector.h" #include "math_extra.h" diff --git a/src/USER-OMP/fix_nvt_sllod_omp.cpp b/src/USER-OMP/fix_nvt_sllod_omp.cpp index e439647c12..208dfb9432 100644 --- a/src/USER-OMP/fix_nvt_sllod_omp.cpp +++ b/src/USER-OMP/fix_nvt_sllod_omp.cpp @@ -15,18 +15,17 @@ Contributing author: Axel Kohlmeyer (Temple U) ------------------------------------------------------------------------- */ -#include -#include #include "fix_nvt_sllod_omp.h" +#include #include "math_extra.h" #include "atom.h" -#include "domain.h" #include "group.h" #include "modify.h" #include "fix.h" #include "fix_deform.h" #include "compute.h" #include "error.h" +#include "domain.h" using namespace LAMMPS_NS; using namespace FixConst; diff --git a/src/USER-OMP/fix_omp.cpp b/src/USER-OMP/fix_omp.cpp index a4587b1c14..1fca1e739b 100644 --- a/src/USER-OMP/fix_omp.cpp +++ b/src/USER-OMP/fix_omp.cpp @@ -24,13 +24,10 @@ #include "neigh_request.h" #include "universe.h" #include "update.h" -#include "integrate.h" -#include "min.h" #include "timer.h" #include "fix_omp.h" #include "thr_data.h" -#include "thr_omp.h" #include "pair_hybrid.h" #include "bond_hybrid.h" @@ -40,8 +37,11 @@ #include "kspace.h" #include -#include -#include + +#if defined(_OPENMP) +#include +#endif + #include "suffix.h" diff --git a/src/USER-OMP/fix_qeq_comb_omp.cpp b/src/USER-OMP/fix_qeq_comb_omp.cpp index 2f0a90a790..b0573dfa97 100644 --- a/src/USER-OMP/fix_qeq_comb_omp.cpp +++ b/src/USER-OMP/fix_qeq_comb_omp.cpp @@ -15,24 +15,20 @@ Contributing author: Axel Kohlmeyer (Temple U) ------------------------------------------------------------------------- */ +#include "fix_qeq_comb_omp.h" #include #include #include -#include "fix_qeq_comb_omp.h" -#include "fix_omp.h" +#include "pair_comb.h" #include "atom.h" #include "comm.h" #include "force.h" #include "group.h" #include "memory.h" -#include "modify.h" #include "error.h" -#include "neighbor.h" #include "neigh_list.h" -#include "neigh_request.h" #include "respa.h" #include "update.h" -#include "pair_comb_omp.h" using namespace LAMMPS_NS; using namespace FixConst; diff --git a/src/USER-OMP/fix_qeq_reax_omp.cpp b/src/USER-OMP/fix_qeq_reax_omp.cpp index 45da91305d..55e2b73812 100644 --- a/src/USER-OMP/fix_qeq_reax_omp.cpp +++ b/src/USER-OMP/fix_qeq_reax_omp.cpp @@ -31,27 +31,22 @@ High Performance Computing Applications, to appear. ------------------------------------------------------------------------- */ -#include -#include -#include -#include #include "fix_qeq_reax_omp.h" -#include "pair_reaxc_omp.h" +#include +#include +#include "pair_reaxc.h" #include "atom.h" #include "comm.h" -#include "domain.h" -#include "neighbor.h" #include "neigh_list.h" -#include "neigh_request.h" #include "update.h" -#include "force.h" -#include "group.h" -#include "pair.h" -#include "respa.h" #include "memory.h" #include "error.h" #include "reaxc_defs.h" +#if defined(_OPENMP) +#include +#endif + using namespace LAMMPS_NS; using namespace FixConst; diff --git a/src/USER-OMP/fix_rigid_nh_omp.cpp b/src/USER-OMP/fix_rigid_nh_omp.cpp index e6a6e065bf..74b2a92775 100644 --- a/src/USER-OMP/fix_rigid_nh_omp.cpp +++ b/src/USER-OMP/fix_rigid_nh_omp.cpp @@ -15,11 +15,9 @@ Contributing author: Axel Kohlmeyer (Temple U) ------------------------------------------------------------------------- */ +#include "fix_rigid_nh_omp.h" #include #include - -#include "fix_rigid_nh_omp.h" - #include "atom.h" #include "atom_vec_ellipsoid.h" #include "atom_vec_line.h" @@ -32,6 +30,7 @@ #include "kspace.h" #include "modify.h" #include "update.h" +#include "timer.h" #if defined(_OPENMP) #include diff --git a/src/USER-OMP/fix_rigid_nph_omp.cpp b/src/USER-OMP/fix_rigid_nph_omp.cpp index 7db45ed9bf..31d53868c8 100644 --- a/src/USER-OMP/fix_rigid_nph_omp.cpp +++ b/src/USER-OMP/fix_rigid_nph_omp.cpp @@ -17,9 +17,8 @@ Miller et al., J Chem Phys. 116, 8649-8659 (2002) ------------------------------------------------------------------------- */ -#include #include "fix_rigid_nph_omp.h" -#include "domain.h" +#include #include "modify.h" #include "error.h" diff --git a/src/USER-OMP/fix_rigid_npt_omp.cpp b/src/USER-OMP/fix_rigid_npt_omp.cpp index a041706f38..1e7c139d52 100644 --- a/src/USER-OMP/fix_rigid_npt_omp.cpp +++ b/src/USER-OMP/fix_rigid_npt_omp.cpp @@ -17,9 +17,8 @@ Miller et al., J Chem Phys. 116, 8649-8659 (2002) ------------------------------------------------------------------------- */ -#include #include "fix_rigid_npt_omp.h" -#include "domain.h" +#include #include "modify.h" #include "error.h" diff --git a/src/USER-OMP/fix_rigid_omp.cpp b/src/USER-OMP/fix_rigid_omp.cpp index 20478b3ca1..b807ddba7c 100644 --- a/src/USER-OMP/fix_rigid_omp.cpp +++ b/src/USER-OMP/fix_rigid_omp.cpp @@ -15,18 +15,17 @@ Contributing author: Axel Kohlmeyer (Temple U) ------------------------------------------------------------------------- */ +#include "fix_rigid_omp.h" #include +#include #include - -#include "fix_rigid_omp.h" - #include "atom.h" #include "atom_vec_ellipsoid.h" #include "atom_vec_line.h" #include "atom_vec_tri.h" #include "comm.h" -#include "domain.h" #include "error.h" +#include "domain.h" #if defined(_OPENMP) #include diff --git a/src/USER-OMP/fix_rigid_small_omp.cpp b/src/USER-OMP/fix_rigid_small_omp.cpp index 1f6173497d..0aa15ee408 100644 --- a/src/USER-OMP/fix_rigid_small_omp.cpp +++ b/src/USER-OMP/fix_rigid_small_omp.cpp @@ -15,10 +15,8 @@ Contributing author: Axel Kohlmeyer (Temple U) ------------------------------------------------------------------------- */ -#include - #include "fix_rigid_small_omp.h" - +#include #include "atom.h" #include "atom_vec_ellipsoid.h" #include "atom_vec_line.h" diff --git a/src/USER-OMP/improper_class2_omp.cpp b/src/USER-OMP/improper_class2_omp.cpp index c2b493f425..3bff179b44 100644 --- a/src/USER-OMP/improper_class2_omp.cpp +++ b/src/USER-OMP/improper_class2_omp.cpp @@ -20,7 +20,7 @@ #include "atom.h" #include "comm.h" #include "neighbor.h" -#include "domain.h" +#include "timer.h" #include "force.h" #include "update.h" #include "error.h" diff --git a/src/USER-OMP/improper_cossq_omp.cpp b/src/USER-OMP/improper_cossq_omp.cpp index 3b328e5b78..0f99f2732f 100644 --- a/src/USER-OMP/improper_cossq_omp.cpp +++ b/src/USER-OMP/improper_cossq_omp.cpp @@ -20,7 +20,7 @@ #include "atom.h" #include "comm.h" #include "neighbor.h" -#include "domain.h" +#include "timer.h" #include "force.h" #include "update.h" #include "error.h" diff --git a/src/USER-OMP/improper_cvff_omp.cpp b/src/USER-OMP/improper_cvff_omp.cpp index fe1fc45bec..fdc29c74b1 100644 --- a/src/USER-OMP/improper_cvff_omp.cpp +++ b/src/USER-OMP/improper_cvff_omp.cpp @@ -20,7 +20,7 @@ #include "atom.h" #include "comm.h" #include "neighbor.h" -#include "domain.h" +#include "timer.h" #include "force.h" #include "update.h" #include "error.h" diff --git a/src/USER-OMP/improper_fourier_omp.cpp b/src/USER-OMP/improper_fourier_omp.cpp index b5af428cb9..b49b895c78 100644 --- a/src/USER-OMP/improper_fourier_omp.cpp +++ b/src/USER-OMP/improper_fourier_omp.cpp @@ -20,7 +20,7 @@ #include "atom.h" #include "comm.h" #include "neighbor.h" -#include "domain.h" +#include "timer.h" #include "force.h" #include "update.h" #include "error.h" diff --git a/src/USER-OMP/improper_harmonic_omp.cpp b/src/USER-OMP/improper_harmonic_omp.cpp index 6e02d0968e..32e837fdfe 100644 --- a/src/USER-OMP/improper_harmonic_omp.cpp +++ b/src/USER-OMP/improper_harmonic_omp.cpp @@ -20,7 +20,7 @@ #include "atom.h" #include "comm.h" #include "neighbor.h" -#include "domain.h" +#include "timer.h" #include "force.h" #include "update.h" #include "error.h" diff --git a/src/USER-OMP/improper_ring_omp.cpp b/src/USER-OMP/improper_ring_omp.cpp index e198b99337..c8fe685faa 100644 --- a/src/USER-OMP/improper_ring_omp.cpp +++ b/src/USER-OMP/improper_ring_omp.cpp @@ -15,15 +15,13 @@ Contributing author: Axel Kohlmeyer (Temple U) ------------------------------------------------------------------------- */ -#include #include "improper_ring_omp.h" +#include #include "atom.h" #include "comm.h" #include "neighbor.h" -#include "domain.h" +#include "timer.h" #include "force.h" -#include "update.h" -#include "error.h" #include "math_special.h" #include "suffix.h" diff --git a/src/USER-OMP/improper_umbrella_omp.cpp b/src/USER-OMP/improper_umbrella_omp.cpp index ceaca35074..f3fdf4570f 100644 --- a/src/USER-OMP/improper_umbrella_omp.cpp +++ b/src/USER-OMP/improper_umbrella_omp.cpp @@ -20,7 +20,7 @@ #include "atom.h" #include "comm.h" #include "neighbor.h" -#include "domain.h" +#include "timer.h" #include "force.h" #include "update.h" #include "error.h" diff --git a/src/USER-OMP/msm_cg_omp.cpp b/src/USER-OMP/msm_cg_omp.cpp index 8a920e05d5..3c5439db5d 100644 --- a/src/USER-OMP/msm_cg_omp.cpp +++ b/src/USER-OMP/msm_cg_omp.cpp @@ -16,10 +16,10 @@ Original MSM class by: Paul Crozier, Stan Moore, Stephen Bond, (all SNL) ------------------------------------------------------------------------- */ +#include "msm_cg_omp.h" #include #include #include -#include #include #include "atom.h" @@ -29,12 +29,14 @@ #include "force.h" #include "neighbor.h" #include "memory.h" -#include "msm_cg_omp.h" +#include "thr_omp.h" +#include "timer.h" -#include "math_const.h" +#if defined(_OPENMP) +#include +#endif using namespace LAMMPS_NS; -using namespace MathConst; #define OFFSET 16384 #define SMALLQ 0.00001 diff --git a/src/USER-OMP/msm_omp.cpp b/src/USER-OMP/msm_omp.cpp index 74cbb56be7..81f84e8f6f 100644 --- a/src/USER-OMP/msm_omp.cpp +++ b/src/USER-OMP/msm_omp.cpp @@ -16,15 +16,11 @@ ------------------------------------------------------------------------- */ #include "msm_omp.h" -#include "atom.h" +#include #include "comm.h" #include "domain.h" #include "error.h" -#include "force.h" -#include "memory.h" -#include "math_const.h" - -#include +#include "timer.h" #if defined(_OPENMP) #include diff --git a/src/USER-OMP/npair_full_bin_atomonly_omp.cpp b/src/USER-OMP/npair_full_bin_atomonly_omp.cpp index d9e0fb9297..0f791e204d 100644 --- a/src/USER-OMP/npair_full_bin_atomonly_omp.cpp +++ b/src/USER-OMP/npair_full_bin_atomonly_omp.cpp @@ -13,11 +13,9 @@ #include "npair_full_bin_atomonly_omp.h" #include "npair_omp.h" -#include "neighbor.h" #include "neigh_list.h" #include "atom.h" #include "atom_vec.h" -#include "domain.h" #include "my_page.h" #include "error.h" diff --git a/src/USER-OMP/npair_full_bin_ghost_omp.cpp b/src/USER-OMP/npair_full_bin_ghost_omp.cpp index b915aca002..d541381143 100644 --- a/src/USER-OMP/npair_full_bin_ghost_omp.cpp +++ b/src/USER-OMP/npair_full_bin_ghost_omp.cpp @@ -13,7 +13,6 @@ #include "npair_full_bin_ghost_omp.h" #include "npair_omp.h" -#include "neighbor.h" #include "neigh_list.h" #include "atom.h" #include "atom_vec.h" diff --git a/src/USER-OMP/npair_full_multi_omp.cpp b/src/USER-OMP/npair_full_multi_omp.cpp index 9bc196e17a..57b60f665b 100644 --- a/src/USER-OMP/npair_full_multi_omp.cpp +++ b/src/USER-OMP/npair_full_multi_omp.cpp @@ -13,7 +13,6 @@ #include "npair_full_multi_omp.h" #include "npair_omp.h" -#include "neighbor.h" #include "neigh_list.h" #include "atom.h" #include "atom_vec.h" diff --git a/src/USER-OMP/npair_full_nsq_ghost_omp.cpp b/src/USER-OMP/npair_full_nsq_ghost_omp.cpp index b33f76bb22..242c4e300c 100644 --- a/src/USER-OMP/npair_full_nsq_ghost_omp.cpp +++ b/src/USER-OMP/npair_full_nsq_ghost_omp.cpp @@ -13,7 +13,6 @@ #include "npair_full_nsq_ghost_omp.h" #include "npair_omp.h" -#include "neighbor.h" #include "neigh_list.h" #include "atom.h" #include "atom_vec.h" diff --git a/src/USER-OMP/npair_full_nsq_omp.cpp b/src/USER-OMP/npair_full_nsq_omp.cpp index 1d0f26d638..08a034d5ab 100644 --- a/src/USER-OMP/npair_full_nsq_omp.cpp +++ b/src/USER-OMP/npair_full_nsq_omp.cpp @@ -13,7 +13,6 @@ #include "npair_full_nsq_omp.h" #include "npair_omp.h" -#include "neighbor.h" #include "neigh_list.h" #include "atom.h" #include "atom_vec.h" diff --git a/src/USER-OMP/npair_half_bin_atomonly_newton_omp.cpp b/src/USER-OMP/npair_half_bin_atomonly_newton_omp.cpp index 02d98ff6ab..a69779d96d 100644 --- a/src/USER-OMP/npair_half_bin_atomonly_newton_omp.cpp +++ b/src/USER-OMP/npair_half_bin_atomonly_newton_omp.cpp @@ -13,12 +13,9 @@ #include "npair_half_bin_atomonly_newton_omp.h" #include "npair_omp.h" -#include "neighbor.h" #include "neigh_list.h" #include "atom.h" #include "atom_vec.h" -#include "molecule.h" -#include "domain.h" #include "my_page.h" #include "error.h" diff --git a/src/USER-OMP/npair_half_bin_newtoff_ghost_omp.cpp b/src/USER-OMP/npair_half_bin_newtoff_ghost_omp.cpp index 24fe75ec55..5f8ffdab29 100644 --- a/src/USER-OMP/npair_half_bin_newtoff_ghost_omp.cpp +++ b/src/USER-OMP/npair_half_bin_newtoff_ghost_omp.cpp @@ -13,7 +13,6 @@ #include "npair_half_bin_newtoff_ghost_omp.h" #include "npair_omp.h" -#include "neighbor.h" #include "neigh_list.h" #include "atom.h" #include "atom_vec.h" diff --git a/src/USER-OMP/npair_half_bin_newtoff_omp.cpp b/src/USER-OMP/npair_half_bin_newtoff_omp.cpp index ff74b54d7d..35807645cf 100644 --- a/src/USER-OMP/npair_half_bin_newtoff_omp.cpp +++ b/src/USER-OMP/npair_half_bin_newtoff_omp.cpp @@ -13,7 +13,6 @@ #include "npair_half_bin_newtoff_omp.h" #include "npair_omp.h" -#include "neighbor.h" #include "neigh_list.h" #include "atom.h" #include "atom_vec.h" diff --git a/src/USER-OMP/npair_half_bin_newton_omp.cpp b/src/USER-OMP/npair_half_bin_newton_omp.cpp index f7d969ba27..2700d6863b 100644 --- a/src/USER-OMP/npair_half_bin_newton_omp.cpp +++ b/src/USER-OMP/npair_half_bin_newton_omp.cpp @@ -13,11 +13,9 @@ #include "npair_half_bin_newton_omp.h" #include "npair_omp.h" -#include "neighbor.h" #include "neigh_list.h" #include "atom.h" #include "atom_vec.h" -#include "group.h" #include "molecule.h" #include "domain.h" #include "my_page.h" diff --git a/src/USER-OMP/npair_half_bin_newton_tri_omp.cpp b/src/USER-OMP/npair_half_bin_newton_tri_omp.cpp index c843d623cd..d94845898c 100644 --- a/src/USER-OMP/npair_half_bin_newton_tri_omp.cpp +++ b/src/USER-OMP/npair_half_bin_newton_tri_omp.cpp @@ -13,7 +13,6 @@ #include "npair_half_bin_newton_tri_omp.h" #include "npair_omp.h" -#include "neighbor.h" #include "neigh_list.h" #include "atom.h" #include "atom_vec.h" diff --git a/src/USER-OMP/npair_half_multi_newtoff_omp.cpp b/src/USER-OMP/npair_half_multi_newtoff_omp.cpp index 705d1b8d9f..c06737dc1c 100644 --- a/src/USER-OMP/npair_half_multi_newtoff_omp.cpp +++ b/src/USER-OMP/npair_half_multi_newtoff_omp.cpp @@ -13,7 +13,6 @@ #include "npair_half_multi_newtoff_omp.h" #include "npair_omp.h" -#include "neighbor.h" #include "neigh_list.h" #include "atom.h" #include "atom_vec.h" diff --git a/src/USER-OMP/npair_half_multi_newton_omp.cpp b/src/USER-OMP/npair_half_multi_newton_omp.cpp index f16dd027a0..50df756be4 100644 --- a/src/USER-OMP/npair_half_multi_newton_omp.cpp +++ b/src/USER-OMP/npair_half_multi_newton_omp.cpp @@ -13,7 +13,6 @@ #include "npair_half_multi_newton_omp.h" #include "npair_omp.h" -#include "neighbor.h" #include "neigh_list.h" #include "atom.h" #include "atom_vec.h" diff --git a/src/USER-OMP/npair_halffull_newtoff_omp.cpp b/src/USER-OMP/npair_halffull_newtoff_omp.cpp index 947e4e1ad2..6f90f82752 100644 --- a/src/USER-OMP/npair_halffull_newtoff_omp.cpp +++ b/src/USER-OMP/npair_halffull_newtoff_omp.cpp @@ -18,7 +18,7 @@ #include "atom.h" #include "atom_vec.h" #include "molecule.h" -#include "domain.h" +#include "timer.h" #include "my_page.h" #include "error.h" diff --git a/src/USER-OMP/npair_halffull_newton_omp.cpp b/src/USER-OMP/npair_halffull_newton_omp.cpp index 6e158d372d..6cf8ab8ac2 100644 --- a/src/USER-OMP/npair_halffull_newton_omp.cpp +++ b/src/USER-OMP/npair_halffull_newton_omp.cpp @@ -18,7 +18,7 @@ #include "atom.h" #include "atom_vec.h" #include "molecule.h" -#include "domain.h" +#include "timer.h" #include "my_page.h" #include "error.h" diff --git a/src/USER-OMP/pair_brownian_omp.cpp b/src/USER-OMP/pair_brownian_omp.cpp index cef9fb0955..6367976c7d 100644 --- a/src/USER-OMP/pair_brownian_omp.cpp +++ b/src/USER-OMP/pair_brownian_omp.cpp @@ -12,8 +12,8 @@ Contributing author: Axel Kohlmeyer (Temple U) ------------------------------------------------------------------------- */ -#include #include "pair_brownian_omp.h" +#include #include "atom.h" #include "comm.h" #include "domain.h" @@ -26,6 +26,7 @@ #include "random_mars.h" #include "math_const.h" #include "math_special.h" +#include "timer.h" #include "fix_wall.h" diff --git a/src/USER-OMP/pair_brownian_poly_omp.cpp b/src/USER-OMP/pair_brownian_poly_omp.cpp index 239a820242..dcb4124634 100644 --- a/src/USER-OMP/pair_brownian_poly_omp.cpp +++ b/src/USER-OMP/pair_brownian_poly_omp.cpp @@ -12,8 +12,8 @@ Contributing author: Axel Kohlmeyer (Temple U) ------------------------------------------------------------------------- */ -#include #include "pair_brownian_poly_omp.h" +#include #include "atom.h" #include "comm.h" #include "domain.h" diff --git a/src/USER-OMP/pair_lj_cut_thole_long_omp.cpp b/src/USER-OMP/pair_lj_cut_thole_long_omp.cpp index d0db6262b1..87d637e80d 100644 --- a/src/USER-OMP/pair_lj_cut_thole_long_omp.cpp +++ b/src/USER-OMP/pair_lj_cut_thole_long_omp.cpp @@ -22,6 +22,7 @@ #include #include "atom.h" #include "comm.h" +#include "domain.h" #include "fix_drude.h" #include "force.h" #include "neighbor.h" @@ -30,7 +31,7 @@ #include "math_const.h" #include "error.h" #include "suffix.h" -#include "domain.h" +#include "timer.h" using namespace LAMMPS_NS; using namespace MathConst; diff --git a/src/USER-OMP/pair_lj_cut_tip4p_long_omp.cpp b/src/USER-OMP/pair_lj_cut_tip4p_long_omp.cpp index e2c1da1a89..18fc207015 100644 --- a/src/USER-OMP/pair_lj_cut_tip4p_long_omp.cpp +++ b/src/USER-OMP/pair_lj_cut_tip4p_long_omp.cpp @@ -12,8 +12,8 @@ Contributing author: Axel Kohlmeyer (Temple U) ------------------------------------------------------------------------- */ -#include #include "pair_lj_cut_tip4p_long_omp.h" +#include #include "atom.h" #include "domain.h" #include "comm.h" diff --git a/src/USER-OMP/pair_lubricate_poly_omp.cpp b/src/USER-OMP/pair_lubricate_poly_omp.cpp index 3a5f03364d..04ac59b121 100644 --- a/src/USER-OMP/pair_lubricate_poly_omp.cpp +++ b/src/USER-OMP/pair_lubricate_poly_omp.cpp @@ -12,8 +12,8 @@ Contributing author: Axel Kohlmeyer (Temple U) ------------------------------------------------------------------------- */ -#include #include "pair_lubricate_poly_omp.h" +#include #include "atom.h" #include "comm.h" #include "domain.h" diff --git a/src/USER-OMP/pppm_cg_omp.cpp b/src/USER-OMP/pppm_cg_omp.cpp index 2b4619f685..1117979f1f 100644 --- a/src/USER-OMP/pppm_cg_omp.cpp +++ b/src/USER-OMP/pppm_cg_omp.cpp @@ -15,20 +15,20 @@ Contributing author: Axel Kohlmeyer (Temple U) ------------------------------------------------------------------------- */ +#include "pppm_cg_omp.h" +#include #include #include -#include "pppm_cg_omp.h" #include "atom.h" #include "comm.h" #include "domain.h" -#include "error.h" -#include "fix_omp.h" #include "force.h" -#include "neighbor.h" -#include "memory.h" #include "math_const.h" #include "math_special.h" - +#include "timer.h" +#if defined(_OPENMP) +#include +#endif #include "suffix.h" using namespace LAMMPS_NS; using namespace MathConst; diff --git a/src/USER-OMP/pppm_disp_omp.cpp b/src/USER-OMP/pppm_disp_omp.cpp index 435341a31c..de902b1a57 100644 --- a/src/USER-OMP/pppm_disp_omp.cpp +++ b/src/USER-OMP/pppm_disp_omp.cpp @@ -16,15 +16,20 @@ Rolf Isele-Holder (RWTH Aachen University) ------------------------------------------------------------------------- */ +#include "pppm_disp_omp.h" +#include #include #include -#include "pppm_disp_omp.h" #include "atom.h" #include "comm.h" #include "domain.h" +#include "error.h" #include "force.h" -#include "memory.h" #include "math_const.h" +#include "timer.h" +#if defined(_OPENMP) +#include +#endif #include "suffix.h" using namespace LAMMPS_NS; diff --git a/src/USER-OMP/pppm_disp_tip4p_omp.cpp b/src/USER-OMP/pppm_disp_tip4p_omp.cpp index a53c5b2ac5..fc9466e395 100644 --- a/src/USER-OMP/pppm_disp_tip4p_omp.cpp +++ b/src/USER-OMP/pppm_disp_tip4p_omp.cpp @@ -15,23 +15,22 @@ Contributing author: Axel Kohlmeyer (Temple U) ------------------------------------------------------------------------- */ +#include "pppm_disp_tip4p_omp.h" +#include #include #include -#include "pppm_disp_tip4p_omp.h" #include "atom.h" #include "comm.h" #include "domain.h" #include "error.h" -#include "fix_omp.h" #include "force.h" -#include "memory.h" #include "math_const.h" -#include "math_special.h" - +#if defined(_OPENMP) +#include +#endif #include "suffix.h" using namespace LAMMPS_NS; using namespace MathConst; -using namespace MathSpecial; #ifdef FFT_SINGLE #define ZEROF 0.0f diff --git a/src/USER-OMP/pppm_omp.cpp b/src/USER-OMP/pppm_omp.cpp index 66190b3f51..3ef3de1ab7 100644 --- a/src/USER-OMP/pppm_omp.cpp +++ b/src/USER-OMP/pppm_omp.cpp @@ -15,18 +15,21 @@ Contributing author: Axel Kohlmeyer (Temple U) ------------------------------------------------------------------------- */ +#include "pppm_omp.h" +#include #include #include -#include "pppm_omp.h" #include "atom.h" #include "comm.h" #include "domain.h" -#include "error.h" -#include "fix_omp.h" #include "force.h" -#include "memory.h" #include "math_const.h" #include "math_special.h" +#include "timer.h" + +#if defined(_OPENMP) +#include +#endif #include "suffix.h" using namespace LAMMPS_NS; diff --git a/src/USER-OMP/pppm_tip4p_omp.cpp b/src/USER-OMP/pppm_tip4p_omp.cpp index 5fe44d2b71..d7c12613d9 100644 --- a/src/USER-OMP/pppm_tip4p_omp.cpp +++ b/src/USER-OMP/pppm_tip4p_omp.cpp @@ -15,18 +15,21 @@ Contributing author: Axel Kohlmeyer (Temple U) ------------------------------------------------------------------------- */ +#include "pppm_tip4p_omp.h" +#include #include #include -#include "pppm_tip4p_omp.h" #include "atom.h" #include "comm.h" #include "domain.h" #include "error.h" -#include "fix_omp.h" #include "force.h" -#include "memory.h" #include "math_const.h" #include "math_special.h" +#include "timer.h" +#if defined(_OPENMP) +#include +#endif #include "suffix.h" using namespace LAMMPS_NS; diff --git a/src/USER-OMP/reaxc_multi_body_omp.cpp b/src/USER-OMP/reaxc_multi_body_omp.cpp index 164999b986..5f4b6d4eb0 100644 --- a/src/USER-OMP/reaxc_multi_body_omp.cpp +++ b/src/USER-OMP/reaxc_multi_body_omp.cpp @@ -27,14 +27,13 @@ ----------------------------------------------------------------------*/ #include "reaxc_multi_body_omp.h" +#include +#include +#include "fix_omp.h" #include #include "pair_reaxc_omp.h" -#include "thr_data.h" #include "reaxc_defs.h" - -#include "reaxc_bond_orders_omp.h" #include "reaxc_list.h" -#include "reaxc_vector.h" #if defined(_OPENMP) #include diff --git a/src/USER-OMP/reaxc_valence_angles_omp.cpp b/src/USER-OMP/reaxc_valence_angles_omp.cpp index 7fbe87d6e5..104fadbbae 100644 --- a/src/USER-OMP/reaxc_valence_angles_omp.cpp +++ b/src/USER-OMP/reaxc_valence_angles_omp.cpp @@ -27,13 +27,15 @@ ----------------------------------------------------------------------*/ #include "reaxc_valence_angles_omp.h" +#include +#include #include "pair_reaxc_omp.h" -#include "thr_data.h" +#include "fix_omp.h" +#include "error.h" #include "reaxc_defs.h" #include "reaxc_types.h" #include "reaxc_valence_angles.h" -#include "reaxc_bond_orders_omp.h" #include "reaxc_list.h" #include "reaxc_vector.h" diff --git a/src/USER-OMP/respa_omp.cpp b/src/USER-OMP/respa_omp.cpp index 9c8555c66d..5add419253 100644 --- a/src/USER-OMP/respa_omp.cpp +++ b/src/USER-OMP/respa_omp.cpp @@ -15,13 +15,11 @@ Contributing authors: Mark Stevens (SNL), Paul Crozier (SNL) ------------------------------------------------------------------------- */ -#include -#include #include "respa_omp.h" #include "neighbor.h" -#include "domain.h" #include "comm.h" #include "atom.h" +#include "domain.h" #include "force.h" #include "pair.h" #include "bond.h" @@ -32,11 +30,8 @@ #include "output.h" #include "update.h" #include "modify.h" -#include "compute.h" -#include "fix_respa.h" -#include "timer.h" -#include "memory.h" #include "error.h" +#include "timer.h" #if defined(_OPENMP) #include diff --git a/src/USER-OMP/thr_data.h b/src/USER-OMP/thr_data.h index 3cea1b0018..edff17cad3 100644 --- a/src/USER-OMP/thr_data.h +++ b/src/USER-OMP/thr_data.h @@ -18,10 +18,6 @@ #ifndef LMP_THR_DATA_H #define LMP_THR_DATA_H -#if defined(_OPENMP) -#include -#endif - #include "timer.h" namespace LAMMPS_NS { @@ -35,7 +31,7 @@ class ThrData { public: ThrData(int tid, class Timer *t); - ~ThrData() { delete _timer; _timer = NULL; }; + ~ThrData() { delete _timer; _timer = nullptr; }; void check_tid(int); // thread id consistency check int get_tid() const { return _tid; }; // our thread id. @@ -140,7 +136,7 @@ class ThrData { // disabled default methods private: - ThrData() : _tid(-1), _timer(NULL) {}; + ThrData() : _tid(-1), _timer(nullptr) {}; }; //////////////////////////////////////////////////////////////////////// diff --git a/src/USER-OMP/thr_omp.cpp b/src/USER-OMP/thr_omp.cpp index 22f751e6c0..51030358d3 100644 --- a/src/USER-OMP/thr_omp.cpp +++ b/src/USER-OMP/thr_omp.cpp @@ -22,7 +22,6 @@ #include "comm.h" #include "error.h" #include "force.h" -#include "memory.h" #include "modify.h" #include "neighbor.h" #include "timer.h" @@ -34,7 +33,6 @@ #include "angle.h" #include "dihedral.h" #include "improper.h" -#include "kspace.h" #include "compute.h" #include "math_const.h" diff --git a/src/USER-OMP/thr_omp.h b/src/USER-OMP/thr_omp.h index 87d921290e..062d77bc0e 100644 --- a/src/USER-OMP/thr_omp.h +++ b/src/USER-OMP/thr_omp.h @@ -18,10 +18,13 @@ #ifndef LMP_THR_OMP_H #define LMP_THR_OMP_H +#if defined(_OPENMP) +#include +#endif #include "pointers.h" #include "error.h" -#include "fix_omp.h" -#include "thr_data.h" +#include "fix_omp.h" // IWYU pragma: export +#include "thr_data.h" // IWYU pragma: export namespace LAMMPS_NS { @@ -31,8 +34,6 @@ class Bond; class Angle; class Dihedral; class Improper; -class KSpace; -class Fix; class ThrOMP { diff --git a/src/USER-SMD/pair_smd_tlsph.cpp b/src/USER-SMD/pair_smd_tlsph.cpp index 0dff905962..82b7c8ff9d 100644 --- a/src/USER-SMD/pair_smd_tlsph.cpp +++ b/src/USER-SMD/pair_smd_tlsph.cpp @@ -1776,9 +1776,8 @@ void PairTlsph::init_style() { optional granular history list ------------------------------------------------------------------------- */ -void PairTlsph::init_list(int id, NeighList *ptr) { - if (id == 0) - list = ptr; +void PairTlsph::init_list(int id, class NeighList *ptr) { + if (id == 0) list = ptr; } /* ---------------------------------------------------------------------- @@ -1786,8 +1785,7 @@ void PairTlsph::init_list(int id, NeighList *ptr) { ------------------------------------------------------------------------- */ double PairTlsph::memory_usage() { - - return 118 * nmax * sizeof(double); + return 118.0 * nmax * sizeof(double); } /* ---------------------------------------------------------------------- diff --git a/src/special.cpp b/src/special.cpp index b64aa96e2b..3dd817bc7f 100644 --- a/src/special.cpp +++ b/src/special.cpp @@ -19,7 +19,7 @@ #include "comm.h" #include "modify.h" #include "fix.h" -#include "accelerator_kokkos.h" +#include "accelerator_kokkos.h" // IWYU pragma: export #include "atom_masks.h" #include "memory.h" -- GitLab From 2f646150873b170cbbd4318bc937967effc0d195 Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Thu, 11 Jul 2019 22:31:16 -0400 Subject: [PATCH 244/469] more work on includes in USER-OMP --- src/USER-OMP/npair_full_bin_atomonly_omp.cpp | 2 -- src/USER-OMP/npair_full_bin_ghost_omp.cpp | 1 - src/USER-OMP/npair_full_bin_omp.cpp | 2 -- src/USER-OMP/npair_full_multi_omp.cpp | 1 - src/USER-OMP/npair_full_nsq_ghost_omp.cpp | 1 - src/USER-OMP/npair_full_nsq_omp.cpp | 1 - src/USER-OMP/npair_half_multi_newton_tri_omp.cpp | 1 - src/USER-OMP/npair_half_nsq_newtoff_ghost_omp.cpp | 1 - src/USER-OMP/npair_half_nsq_newtoff_omp.cpp | 1 - src/USER-OMP/npair_half_nsq_newton_omp.cpp | 1 - src/USER-OMP/npair_half_respa_bin_newtoff_omp.cpp | 1 - src/USER-OMP/npair_half_respa_bin_newton_omp.cpp | 1 - src/USER-OMP/npair_half_respa_bin_newton_tri_omp.cpp | 1 - src/USER-OMP/npair_half_respa_nsq_newtoff_omp.cpp | 1 - src/USER-OMP/npair_half_respa_nsq_newton_omp.cpp | 1 - src/USER-OMP/npair_half_size_bin_newtoff_omp.cpp | 2 -- src/USER-OMP/npair_half_size_bin_newton_omp.cpp | 2 -- src/USER-OMP/npair_half_size_bin_newton_tri_omp.cpp | 1 - src/USER-OMP/npair_half_size_nsq_newtoff_omp.cpp | 2 -- src/USER-OMP/npair_half_size_nsq_newton_omp.cpp | 2 -- src/USER-OMP/npair_halffull_newtoff_omp.cpp | 4 ---- src/USER-OMP/npair_halffull_newton_omp.cpp | 3 --- src/USER-OMP/pair_beck_omp.cpp | 4 ++-- src/USER-OMP/pair_born_coul_wolf_omp.cpp | 4 ++-- src/USER-OMP/pair_born_omp.cpp | 4 ++-- src/USER-OMP/pair_buck_omp.cpp | 4 ++-- src/USER-OMP/pair_coul_cut_omp.cpp | 4 ++-- src/USER-OMP/pair_coul_debye_omp.cpp | 4 ++-- src/USER-OMP/pair_coul_dsf_omp.cpp | 5 ++--- src/USER-OMP/pair_coul_wolf_omp.cpp | 4 ++-- src/USER-OMP/pair_dpd_omp.cpp | 4 ++-- 31 files changed, 18 insertions(+), 52 deletions(-) diff --git a/src/USER-OMP/npair_full_bin_atomonly_omp.cpp b/src/USER-OMP/npair_full_bin_atomonly_omp.cpp index 09c4f2d78d..3bda2e4c5a 100644 --- a/src/USER-OMP/npair_full_bin_atomonly_omp.cpp +++ b/src/USER-OMP/npair_full_bin_atomonly_omp.cpp @@ -18,10 +18,8 @@ #include "atom_vec.h" #include "my_page.h" #include "error.h" -#include "timer.h" using namespace LAMMPS_NS; -using namespace NeighConst; /* ---------------------------------------------------------------------- */ diff --git a/src/USER-OMP/npair_full_bin_ghost_omp.cpp b/src/USER-OMP/npair_full_bin_ghost_omp.cpp index d541381143..b0b0070df5 100644 --- a/src/USER-OMP/npair_full_bin_ghost_omp.cpp +++ b/src/USER-OMP/npair_full_bin_ghost_omp.cpp @@ -22,7 +22,6 @@ #include "error.h" using namespace LAMMPS_NS; -using namespace NeighConst; /* ---------------------------------------------------------------------- */ diff --git a/src/USER-OMP/npair_full_bin_omp.cpp b/src/USER-OMP/npair_full_bin_omp.cpp index e1f75c06e2..d3e30b4932 100644 --- a/src/USER-OMP/npair_full_bin_omp.cpp +++ b/src/USER-OMP/npair_full_bin_omp.cpp @@ -13,7 +13,6 @@ #include "npair_full_bin_omp.h" #include "npair_omp.h" -#include "neighbor.h" #include "neigh_list.h" #include "atom.h" #include "atom_vec.h" @@ -23,7 +22,6 @@ #include "error.h" using namespace LAMMPS_NS; -using namespace NeighConst; /* ---------------------------------------------------------------------- */ diff --git a/src/USER-OMP/npair_full_multi_omp.cpp b/src/USER-OMP/npair_full_multi_omp.cpp index 57b60f665b..707db2edcf 100644 --- a/src/USER-OMP/npair_full_multi_omp.cpp +++ b/src/USER-OMP/npair_full_multi_omp.cpp @@ -22,7 +22,6 @@ #include "error.h" using namespace LAMMPS_NS; -using namespace NeighConst; /* ---------------------------------------------------------------------- */ diff --git a/src/USER-OMP/npair_full_nsq_ghost_omp.cpp b/src/USER-OMP/npair_full_nsq_ghost_omp.cpp index 242c4e300c..527df58fd6 100644 --- a/src/USER-OMP/npair_full_nsq_ghost_omp.cpp +++ b/src/USER-OMP/npair_full_nsq_ghost_omp.cpp @@ -22,7 +22,6 @@ #include "error.h" using namespace LAMMPS_NS; -using namespace NeighConst; /* ---------------------------------------------------------------------- */ diff --git a/src/USER-OMP/npair_full_nsq_omp.cpp b/src/USER-OMP/npair_full_nsq_omp.cpp index 08a034d5ab..2719f5dc2c 100644 --- a/src/USER-OMP/npair_full_nsq_omp.cpp +++ b/src/USER-OMP/npair_full_nsq_omp.cpp @@ -23,7 +23,6 @@ #include "error.h" using namespace LAMMPS_NS; -using namespace NeighConst; /* ---------------------------------------------------------------------- */ diff --git a/src/USER-OMP/npair_half_multi_newton_tri_omp.cpp b/src/USER-OMP/npair_half_multi_newton_tri_omp.cpp index ce93e85485..8b78b311dd 100644 --- a/src/USER-OMP/npair_half_multi_newton_tri_omp.cpp +++ b/src/USER-OMP/npair_half_multi_newton_tri_omp.cpp @@ -13,7 +13,6 @@ #include "npair_half_multi_newton_tri_omp.h" #include "npair_omp.h" -#include "neighbor.h" #include "neigh_list.h" #include "atom.h" #include "atom_vec.h" diff --git a/src/USER-OMP/npair_half_nsq_newtoff_ghost_omp.cpp b/src/USER-OMP/npair_half_nsq_newtoff_ghost_omp.cpp index add4c44d9e..f0eb211425 100644 --- a/src/USER-OMP/npair_half_nsq_newtoff_ghost_omp.cpp +++ b/src/USER-OMP/npair_half_nsq_newtoff_ghost_omp.cpp @@ -13,7 +13,6 @@ #include "npair_half_nsq_newtoff_ghost_omp.h" #include "npair_omp.h" -#include "neighbor.h" #include "neigh_list.h" #include "atom.h" #include "atom_vec.h" diff --git a/src/USER-OMP/npair_half_nsq_newtoff_omp.cpp b/src/USER-OMP/npair_half_nsq_newtoff_omp.cpp index 01da73cf1e..55b9f9e512 100644 --- a/src/USER-OMP/npair_half_nsq_newtoff_omp.cpp +++ b/src/USER-OMP/npair_half_nsq_newtoff_omp.cpp @@ -13,7 +13,6 @@ #include "npair_half_nsq_newtoff_omp.h" #include "npair_omp.h" -#include "neighbor.h" #include "neigh_list.h" #include "atom.h" #include "atom_vec.h" diff --git a/src/USER-OMP/npair_half_nsq_newton_omp.cpp b/src/USER-OMP/npair_half_nsq_newton_omp.cpp index 3815b1b85b..223da622e8 100644 --- a/src/USER-OMP/npair_half_nsq_newton_omp.cpp +++ b/src/USER-OMP/npair_half_nsq_newton_omp.cpp @@ -13,7 +13,6 @@ #include "npair_half_nsq_newton_omp.h" #include "npair_omp.h" -#include "neighbor.h" #include "neigh_list.h" #include "atom.h" #include "atom_vec.h" diff --git a/src/USER-OMP/npair_half_respa_bin_newtoff_omp.cpp b/src/USER-OMP/npair_half_respa_bin_newtoff_omp.cpp index f094691b71..9bb4d277fe 100644 --- a/src/USER-OMP/npair_half_respa_bin_newtoff_omp.cpp +++ b/src/USER-OMP/npair_half_respa_bin_newtoff_omp.cpp @@ -13,7 +13,6 @@ #include "npair_half_respa_bin_newtoff_omp.h" #include "npair_omp.h" -#include "neighbor.h" #include "neigh_list.h" #include "atom.h" #include "atom_vec.h" diff --git a/src/USER-OMP/npair_half_respa_bin_newton_omp.cpp b/src/USER-OMP/npair_half_respa_bin_newton_omp.cpp index de7ef5f7d5..9ed0ae482d 100644 --- a/src/USER-OMP/npair_half_respa_bin_newton_omp.cpp +++ b/src/USER-OMP/npair_half_respa_bin_newton_omp.cpp @@ -12,7 +12,6 @@ ------------------------------------------------------------------------- */ #include "npair_half_respa_bin_newton_omp.h" -#include "neighbor.h" #include "npair_omp.h" #include "neigh_list.h" #include "atom.h" diff --git a/src/USER-OMP/npair_half_respa_bin_newton_tri_omp.cpp b/src/USER-OMP/npair_half_respa_bin_newton_tri_omp.cpp index f20d101bc9..cd03684940 100644 --- a/src/USER-OMP/npair_half_respa_bin_newton_tri_omp.cpp +++ b/src/USER-OMP/npair_half_respa_bin_newton_tri_omp.cpp @@ -13,7 +13,6 @@ #include "npair_half_respa_bin_newton_tri_omp.h" #include "npair_omp.h" -#include "neighbor.h" #include "neigh_list.h" #include "atom.h" #include "atom_vec.h" diff --git a/src/USER-OMP/npair_half_respa_nsq_newtoff_omp.cpp b/src/USER-OMP/npair_half_respa_nsq_newtoff_omp.cpp index 0f726cdd7f..b1e7467ec7 100644 --- a/src/USER-OMP/npair_half_respa_nsq_newtoff_omp.cpp +++ b/src/USER-OMP/npair_half_respa_nsq_newtoff_omp.cpp @@ -13,7 +13,6 @@ #include "npair_half_respa_nsq_newtoff_omp.h" #include "npair_omp.h" -#include "neighbor.h" #include "neigh_list.h" #include "atom.h" #include "atom_vec.h" diff --git a/src/USER-OMP/npair_half_respa_nsq_newton_omp.cpp b/src/USER-OMP/npair_half_respa_nsq_newton_omp.cpp index 2783e1255e..c22965895d 100644 --- a/src/USER-OMP/npair_half_respa_nsq_newton_omp.cpp +++ b/src/USER-OMP/npair_half_respa_nsq_newton_omp.cpp @@ -13,7 +13,6 @@ #include "npair_half_respa_nsq_newton_omp.h" #include "npair_omp.h" -#include "neighbor.h" #include "neigh_list.h" #include "atom.h" #include "atom_vec.h" diff --git a/src/USER-OMP/npair_half_size_bin_newtoff_omp.cpp b/src/USER-OMP/npair_half_size_bin_newtoff_omp.cpp index dff2a762d5..1b437482c4 100644 --- a/src/USER-OMP/npair_half_size_bin_newtoff_omp.cpp +++ b/src/USER-OMP/npair_half_size_bin_newtoff_omp.cpp @@ -11,10 +11,8 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include #include "npair_half_size_bin_newtoff_omp.h" #include "npair_omp.h" -#include "neighbor.h" #include "neigh_list.h" #include "atom.h" #include "atom_vec.h" diff --git a/src/USER-OMP/npair_half_size_bin_newton_omp.cpp b/src/USER-OMP/npair_half_size_bin_newton_omp.cpp index 3053b81594..8e0581d4ce 100644 --- a/src/USER-OMP/npair_half_size_bin_newton_omp.cpp +++ b/src/USER-OMP/npair_half_size_bin_newton_omp.cpp @@ -11,10 +11,8 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include #include "npair_half_size_bin_newton_omp.h" #include "npair_omp.h" -#include "neighbor.h" #include "neigh_list.h" #include "atom.h" #include "atom_vec.h" diff --git a/src/USER-OMP/npair_half_size_bin_newton_tri_omp.cpp b/src/USER-OMP/npair_half_size_bin_newton_tri_omp.cpp index b02bfa345e..38a2c0d61f 100644 --- a/src/USER-OMP/npair_half_size_bin_newton_tri_omp.cpp +++ b/src/USER-OMP/npair_half_size_bin_newton_tri_omp.cpp @@ -13,7 +13,6 @@ #include "npair_half_size_bin_newton_tri_omp.h" #include "npair_omp.h" -#include "neighbor.h" #include "neigh_list.h" #include "atom.h" #include "atom_vec.h" diff --git a/src/USER-OMP/npair_half_size_nsq_newtoff_omp.cpp b/src/USER-OMP/npair_half_size_nsq_newtoff_omp.cpp index 717012b226..d1505e1b2e 100644 --- a/src/USER-OMP/npair_half_size_nsq_newtoff_omp.cpp +++ b/src/USER-OMP/npair_half_size_nsq_newtoff_omp.cpp @@ -11,10 +11,8 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include #include "npair_half_size_nsq_newtoff_omp.h" #include "npair_omp.h" -#include "neighbor.h" #include "neigh_list.h" #include "atom.h" #include "atom_vec.h" diff --git a/src/USER-OMP/npair_half_size_nsq_newton_omp.cpp b/src/USER-OMP/npair_half_size_nsq_newton_omp.cpp index 5a55029d30..9027b0728d 100644 --- a/src/USER-OMP/npair_half_size_nsq_newton_omp.cpp +++ b/src/USER-OMP/npair_half_size_nsq_newton_omp.cpp @@ -11,10 +11,8 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include #include "npair_half_size_nsq_newton_omp.h" #include "npair_omp.h" -#include "neighbor.h" #include "neigh_list.h" #include "atom.h" #include "atom_vec.h" diff --git a/src/USER-OMP/npair_halffull_newtoff_omp.cpp b/src/USER-OMP/npair_halffull_newtoff_omp.cpp index 6f90f82752..7d2fe4f109 100644 --- a/src/USER-OMP/npair_halffull_newtoff_omp.cpp +++ b/src/USER-OMP/npair_halffull_newtoff_omp.cpp @@ -13,12 +13,8 @@ #include "npair_halffull_newtoff_omp.h" #include "npair_omp.h" -#include "neighbor.h" #include "neigh_list.h" -#include "atom.h" #include "atom_vec.h" -#include "molecule.h" -#include "timer.h" #include "my_page.h" #include "error.h" diff --git a/src/USER-OMP/npair_halffull_newton_omp.cpp b/src/USER-OMP/npair_halffull_newton_omp.cpp index 6cf8ab8ac2..3fcc8c2e98 100644 --- a/src/USER-OMP/npair_halffull_newton_omp.cpp +++ b/src/USER-OMP/npair_halffull_newton_omp.cpp @@ -13,12 +13,9 @@ #include "npair_halffull_newton_omp.h" #include "npair_omp.h" -#include "neighbor.h" #include "neigh_list.h" #include "atom.h" #include "atom_vec.h" -#include "molecule.h" -#include "timer.h" #include "my_page.h" #include "error.h" diff --git a/src/USER-OMP/pair_beck_omp.cpp b/src/USER-OMP/pair_beck_omp.cpp index 90c3777932..8d0605fae9 100644 --- a/src/USER-OMP/pair_beck_omp.cpp +++ b/src/USER-OMP/pair_beck_omp.cpp @@ -12,14 +12,14 @@ Contributing author: Axel Kohlmeyer (Temple U) ------------------------------------------------------------------------- */ -#include #include "pair_beck_omp.h" +#include #include "atom.h" #include "comm.h" #include "force.h" -#include "neighbor.h" #include "neigh_list.h" #include "math_special.h" +#include "timer.h" #include "suffix.h" using namespace LAMMPS_NS; diff --git a/src/USER-OMP/pair_born_coul_wolf_omp.cpp b/src/USER-OMP/pair_born_coul_wolf_omp.cpp index 567eddc9cb..55da972c4e 100644 --- a/src/USER-OMP/pair_born_coul_wolf_omp.cpp +++ b/src/USER-OMP/pair_born_coul_wolf_omp.cpp @@ -12,14 +12,14 @@ Contributing author: Axel Kohlmeyer (Temple U) ------------------------------------------------------------------------- */ -#include #include "pair_born_coul_wolf_omp.h" +#include #include "atom.h" #include "comm.h" #include "force.h" -#include "neighbor.h" #include "neigh_list.h" #include "math_const.h" +#include "timer.h" #include "suffix.h" using namespace LAMMPS_NS; diff --git a/src/USER-OMP/pair_born_omp.cpp b/src/USER-OMP/pair_born_omp.cpp index fce2013745..35ad4fcb48 100644 --- a/src/USER-OMP/pair_born_omp.cpp +++ b/src/USER-OMP/pair_born_omp.cpp @@ -12,13 +12,13 @@ Contributing author: Axel Kohlmeyer (Temple U) ------------------------------------------------------------------------- */ -#include #include "pair_born_omp.h" +#include #include "atom.h" #include "comm.h" #include "force.h" -#include "neighbor.h" #include "neigh_list.h" +#include "timer.h" #include "suffix.h" using namespace LAMMPS_NS; diff --git a/src/USER-OMP/pair_buck_omp.cpp b/src/USER-OMP/pair_buck_omp.cpp index cc7e81b9c5..8d5c80513a 100644 --- a/src/USER-OMP/pair_buck_omp.cpp +++ b/src/USER-OMP/pair_buck_omp.cpp @@ -12,13 +12,13 @@ Contributing author: Axel Kohlmeyer (Temple U) ------------------------------------------------------------------------- */ -#include #include "pair_buck_omp.h" +#include #include "atom.h" #include "comm.h" #include "force.h" -#include "neighbor.h" #include "neigh_list.h" +#include "timer.h" #include "suffix.h" using namespace LAMMPS_NS; diff --git a/src/USER-OMP/pair_coul_cut_omp.cpp b/src/USER-OMP/pair_coul_cut_omp.cpp index 056daf210a..267beeecbd 100644 --- a/src/USER-OMP/pair_coul_cut_omp.cpp +++ b/src/USER-OMP/pair_coul_cut_omp.cpp @@ -12,13 +12,13 @@ Contributing author: Axel Kohlmeyer (Temple U) ------------------------------------------------------------------------- */ -#include #include "pair_coul_cut_omp.h" +#include #include "atom.h" #include "comm.h" #include "force.h" -#include "neighbor.h" #include "neigh_list.h" +#include "timer.h" #include "suffix.h" using namespace LAMMPS_NS; diff --git a/src/USER-OMP/pair_coul_debye_omp.cpp b/src/USER-OMP/pair_coul_debye_omp.cpp index d202e314bf..4d3f92c495 100644 --- a/src/USER-OMP/pair_coul_debye_omp.cpp +++ b/src/USER-OMP/pair_coul_debye_omp.cpp @@ -12,13 +12,13 @@ Contributing author: Axel Kohlmeyer (Temple U) ------------------------------------------------------------------------- */ -#include #include "pair_coul_debye_omp.h" +#include #include "atom.h" #include "comm.h" #include "force.h" -#include "neighbor.h" #include "neigh_list.h" +#include "timer.h" #include "suffix.h" using namespace LAMMPS_NS; diff --git a/src/USER-OMP/pair_coul_dsf_omp.cpp b/src/USER-OMP/pair_coul_dsf_omp.cpp index 217fb844c3..bd7f5cfed2 100644 --- a/src/USER-OMP/pair_coul_dsf_omp.cpp +++ b/src/USER-OMP/pair_coul_dsf_omp.cpp @@ -12,14 +12,13 @@ Contributing author: Axel Kohlmeyer (Temple U) ------------------------------------------------------------------------- */ -#include #include "pair_coul_dsf_omp.h" +#include #include "atom.h" #include "comm.h" #include "force.h" -#include "neighbor.h" #include "neigh_list.h" - +#include "timer.h" #include "suffix.h" #include "math_const.h" using namespace LAMMPS_NS; diff --git a/src/USER-OMP/pair_coul_wolf_omp.cpp b/src/USER-OMP/pair_coul_wolf_omp.cpp index 0913a2b188..92d5bd7b15 100644 --- a/src/USER-OMP/pair_coul_wolf_omp.cpp +++ b/src/USER-OMP/pair_coul_wolf_omp.cpp @@ -12,14 +12,14 @@ Contributing author: Axel Kohlmeyer (Temple U) ------------------------------------------------------------------------- */ -#include #include "pair_coul_wolf_omp.h" +#include #include "atom.h" #include "comm.h" #include "force.h" -#include "neighbor.h" #include "neigh_list.h" #include "math_const.h" +#include "timer.h" #include "suffix.h" using namespace LAMMPS_NS; diff --git a/src/USER-OMP/pair_dpd_omp.cpp b/src/USER-OMP/pair_dpd_omp.cpp index 77db3d9183..b7f3a7f4d4 100644 --- a/src/USER-OMP/pair_dpd_omp.cpp +++ b/src/USER-OMP/pair_dpd_omp.cpp @@ -12,15 +12,15 @@ Contributing author: Axel Kohlmeyer (Temple U) ------------------------------------------------------------------------- */ -#include #include "pair_dpd_omp.h" +#include #include "atom.h" #include "comm.h" #include "force.h" -#include "neighbor.h" #include "neigh_list.h" #include "update.h" #include "random_mars.h" +#include "timer.h" #include "suffix.h" using namespace LAMMPS_NS; -- GitLab From 08ed046a690ec57e1a045e95584a2dcac5f025a8 Mon Sep 17 00:00:00 2001 From: Aidan Thompson Date: Fri, 12 Jul 2019 11:29:14 -0600 Subject: [PATCH 245/469] Removed TEMPLATED_FIX_LANGEVIN ifdef --- src/fix_langevin.cpp | 11 ----------- src/fix_langevin.h | 8 +------- 2 files changed, 1 insertion(+), 18 deletions(-) diff --git a/src/fix_langevin.cpp b/src/fix_langevin.cpp index 36ea47daf6..3f2ec20db0 100644 --- a/src/fix_langevin.cpp +++ b/src/fix_langevin.cpp @@ -304,7 +304,6 @@ void FixLangevin::post_force(int /*vflag*/) // this avoids testing them inside inner loop: // TSTYLEATOM, GJF, TALLY, BIAS, RMASS, ZERO -#ifdef TEMPLATED_FIX_LANGEVIN if (tstyle == ATOM) if (gjfflag) if (tallyflag) @@ -431,10 +430,6 @@ void FixLangevin::post_force(int /*vflag*/) else if (zeroflag) post_force_templated<0,0,0,0,0,1>(); else post_force_templated<0,0,0,0,0,0>(); -#else - post_force_untemplated(int(tstyle==ATOM), gjfflag, tallyflag, - int(tbiasflag==BIAS), int(rmass!=NULL), zeroflag); -#endif } /* ---------------------------------------------------------------------- */ @@ -448,15 +443,9 @@ void FixLangevin::post_force_respa(int vflag, int ilevel, int /*iloop*/) modify forces using one of the many Langevin styles ------------------------------------------------------------------------- */ -#ifdef TEMPLATED_FIX_LANGEVIN template < int Tp_TSTYLEATOM, int Tp_GJF, int Tp_TALLY, int Tp_BIAS, int Tp_RMASS, int Tp_ZERO > void FixLangevin::post_force_templated() -#else -void FixLangevin::post_force_untemplated - (int Tp_TSTYLEATOM, int Tp_GJF, int Tp_TALLY, - int Tp_BIAS, int Tp_RMASS, int Tp_ZERO) -#endif { double gamma1,gamma2; diff --git a/src/fix_langevin.h b/src/fix_langevin.h index 024e7a9539..4b5570ac2e 100644 --- a/src/fix_langevin.h +++ b/src/fix_langevin.h @@ -72,16 +72,10 @@ class FixLangevin : public Fix { class RanMars *random; int seed; - // comment next line to turn off templating -#define TEMPLATED_FIX_LANGEVIN -#ifdef TEMPLATED_FIX_LANGEVIN template < int Tp_TSTYLEATOM, int Tp_GJF, int Tp_TALLY, int Tp_BIAS, int Tp_RMASS, int Tp_ZERO > void post_force_templated(); -#else - void post_force_untemplated(int, int, int, - int, int, int); -#endif + void omega_thermostat(); void angmom_thermostat(); void compute_target(); -- GitLab From a51479a62b7b3f827e0e537a40c6e6d7245237d3 Mon Sep 17 00:00:00 2001 From: Stan Moore Date: Fri, 12 Jul 2019 11:53:32 -0600 Subject: [PATCH 246/469] Fix bug in fix_setforce_kokkos --- src/KOKKOS/fix_setforce_kokkos.cpp | 2 ++ 1 file changed, 2 insertions(+) diff --git a/src/KOKKOS/fix_setforce_kokkos.cpp b/src/KOKKOS/fix_setforce_kokkos.cpp index 5d15b88d76..634bc05ac3 100644 --- a/src/KOKKOS/fix_setforce_kokkos.cpp +++ b/src/KOKKOS/fix_setforce_kokkos.cpp @@ -47,6 +47,7 @@ FixSetForceKokkos::FixSetForceKokkos(LAMMPS *lmp, int narg, char **a memory->destroy(sforce); memoryKK->create_kokkos(k_sforce,sforce,maxatom,3,"setforce:sforce"); + d_sforce = k_sforce.view(); } /* ---------------------------------------------------------------------- */ @@ -103,6 +104,7 @@ void FixSetForceKokkos::post_force(int vflag) maxatom = atom->nmax; memoryKK->destroy_kokkos(k_sforce,sforce); memoryKK->create_kokkos(k_sforce,sforce,maxatom,3,"setforce:sforce"); + d_sforce = k_sforce.view(); } foriginal[0] = foriginal[1] = foriginal[2] = 0.0; -- GitLab From e832b5d50bae37c49f12f652cffb8b421e9dd372 Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Fri, 12 Jul 2019 15:42:16 -0400 Subject: [PATCH 247/469] make clang++ happy when trying to compile the GPU library --- lib/gpu/lal_answer.cpp | 4 ++-- lib/gpu/lal_atom.cpp | 4 ++-- lib/gpu/lal_base_atomic.cpp | 5 +++-- lib/gpu/lal_base_charge.cpp | 4 ++-- lib/gpu/lal_base_dipole.cpp | 4 ++-- lib/gpu/lal_base_dpd.cpp | 4 ++-- lib/gpu/lal_base_ellipsoid.cpp | 4 ++-- lib/gpu/lal_base_three.cpp | 4 ++-- lib/gpu/lal_beck.cpp | 3 ++- lib/gpu/lal_born.cpp | 3 ++- lib/gpu/lal_born_coul_long.cpp | 3 ++- lib/gpu/lal_born_coul_long_cs.cpp | 3 ++- lib/gpu/lal_born_coul_wolf.cpp | 3 ++- lib/gpu/lal_born_coul_wolf_cs.cpp | 3 ++- lib/gpu/lal_buck.cpp | 3 ++- lib/gpu/lal_buck_coul.cpp | 3 ++- lib/gpu/lal_buck_coul_long.cpp | 3 ++- lib/gpu/lal_charmm_long.cpp | 3 ++- lib/gpu/lal_colloid.cpp | 3 ++- lib/gpu/lal_coul.cpp | 3 ++- lib/gpu/lal_coul_debye.cpp | 3 ++- lib/gpu/lal_coul_dsf.cpp | 3 ++- lib/gpu/lal_coul_long.cpp | 3 ++- lib/gpu/lal_coul_long_cs.cpp | 3 ++- lib/gpu/lal_device.cpp | 5 +++-- lib/gpu/lal_dipole_lj.cpp | 3 ++- lib/gpu/lal_dipole_lj_sf.cpp | 3 ++- lib/gpu/lal_dipole_long_lj.cpp | 3 ++- lib/gpu/lal_dpd.cpp | 3 ++- lib/gpu/lal_eam.cpp | 3 ++- lib/gpu/lal_gauss.cpp | 3 ++- lib/gpu/lal_gayberne.cpp | 4 ++-- lib/gpu/lal_lj.cpp | 3 ++- lib/gpu/lal_lj96.cpp | 3 ++- lib/gpu/lal_lj_class2_long.cpp | 4 ++-- lib/gpu/lal_lj_coul.cpp | 3 ++- lib/gpu/lal_lj_coul_debye.cpp | 3 ++- lib/gpu/lal_lj_coul_long.cpp | 3 ++- lib/gpu/lal_lj_coul_msm.cpp | 3 ++- lib/gpu/lal_lj_cubic.cpp | 3 ++- lib/gpu/lal_lj_dsf.cpp | 3 ++- lib/gpu/lal_lj_expand.cpp | 3 ++- lib/gpu/lal_lj_expand_coul_long.cpp | 3 ++- lib/gpu/lal_lj_gromacs.cpp | 3 ++- lib/gpu/lal_lj_sdk.cpp | 3 ++- lib/gpu/lal_lj_sdk_long.cpp | 3 ++- lib/gpu/lal_mie.cpp | 3 ++- lib/gpu/lal_morse.cpp | 4 ++-- lib/gpu/lal_pppm.cpp | 3 ++- lib/gpu/lal_re_squared.cpp | 4 ++-- lib/gpu/lal_soft.cpp | 3 ++- lib/gpu/lal_sw.cpp | 4 ++-- lib/gpu/lal_table.cpp | 3 ++- lib/gpu/lal_tersoff.cpp | 4 ++-- lib/gpu/lal_tersoff_mod.cpp | 4 ++-- lib/gpu/lal_tersoff_zbl.cpp | 4 ++-- lib/gpu/lal_ufm.cpp | 3 ++- lib/gpu/lal_vashishta.cpp | 4 ++-- lib/gpu/lal_yukawa.cpp | 3 ++- lib/gpu/lal_yukawa_colloid.cpp | 3 ++- lib/gpu/lal_zbl.cpp | 3 ++- 61 files changed, 124 insertions(+), 79 deletions(-) diff --git a/lib/gpu/lal_answer.cpp b/lib/gpu/lal_answer.cpp index bd8c7ef843..aa6d33d334 100644 --- a/lib/gpu/lal_answer.cpp +++ b/lib/gpu/lal_answer.cpp @@ -15,7 +15,7 @@ #include "lal_answer.h" -using namespace LAMMPS_AL; +namespace LAMMPS_AL { #define AnswerT Answer template @@ -311,4 +311,4 @@ void AnswerT::cq(const int cq_index) { } template class Answer; - +} diff --git a/lib/gpu/lal_atom.cpp b/lib/gpu/lal_atom.cpp index 222ba0525e..bc25c00d93 100644 --- a/lib/gpu/lal_atom.cpp +++ b/lib/gpu/lal_atom.cpp @@ -15,7 +15,7 @@ #include "lal_atom.h" -using namespace LAMMPS_AL; +namespace LAMMPS_AL { #define AtomT Atom template @@ -349,4 +349,4 @@ void AtomT::compile_kernels(UCL_Device &dev) { #endif template class Atom; - +} diff --git a/lib/gpu/lal_base_atomic.cpp b/lib/gpu/lal_base_atomic.cpp index da54f1dca3..4aadd3754c 100644 --- a/lib/gpu/lal_base_atomic.cpp +++ b/lib/gpu/lal_base_atomic.cpp @@ -14,7 +14,8 @@ ***************************************************************************/ #include "lal_base_atomic.h" -using namespace LAMMPS_AL; + +namespace LAMMPS_AL { #define BaseAtomicT BaseAtomic extern Device global_device; @@ -285,4 +286,4 @@ void BaseAtomicT::compile_kernels(UCL_Device &dev, const void *pair_str, } template class BaseAtomic; - +} diff --git a/lib/gpu/lal_base_charge.cpp b/lib/gpu/lal_base_charge.cpp index a3ec710baa..760e759201 100644 --- a/lib/gpu/lal_base_charge.cpp +++ b/lib/gpu/lal_base_charge.cpp @@ -15,7 +15,7 @@ ***************************************************************************/ #include "lal_base_charge.h" -using namespace LAMMPS_AL; +namespace LAMMPS_AL { #define BaseChargeT BaseCharge extern Device global_device; @@ -302,4 +302,4 @@ void BaseChargeT::compile_kernels(UCL_Device &dev, const void *pair_str, } template class BaseCharge; - +} diff --git a/lib/gpu/lal_base_dipole.cpp b/lib/gpu/lal_base_dipole.cpp index 9fc7e1b235..56dcaf8e12 100644 --- a/lib/gpu/lal_base_dipole.cpp +++ b/lib/gpu/lal_base_dipole.cpp @@ -15,7 +15,7 @@ ***************************************************************************/ #include "lal_base_dipole.h" -using namespace LAMMPS_AL; +namespace LAMMPS_AL { #define BaseDipoleT BaseDipole extern Device global_device; @@ -311,4 +311,4 @@ void BaseDipoleT::compile_kernels(UCL_Device &dev, const void *pair_str, } template class BaseDipole; - +} diff --git a/lib/gpu/lal_base_dpd.cpp b/lib/gpu/lal_base_dpd.cpp index eb5c2088a6..66c8cf09e9 100644 --- a/lib/gpu/lal_base_dpd.cpp +++ b/lib/gpu/lal_base_dpd.cpp @@ -15,7 +15,7 @@ ***************************************************************************/ #include "lal_base_dpd.h" -using namespace LAMMPS_AL; +namespace LAMMPS_AL { #define BaseDPDT BaseDPD extern Device global_device; @@ -308,4 +308,4 @@ void BaseDPDT::compile_kernels(UCL_Device &dev, const void *pair_str, } template class BaseDPD; - +} diff --git a/lib/gpu/lal_base_ellipsoid.cpp b/lib/gpu/lal_base_ellipsoid.cpp index eea5344e33..b8d0b7a666 100644 --- a/lib/gpu/lal_base_ellipsoid.cpp +++ b/lib/gpu/lal_base_ellipsoid.cpp @@ -15,7 +15,7 @@ #include "lal_base_ellipsoid.h" #include -using namespace LAMMPS_AL; +namespace LAMMPS_AL { #if defined(USE_OPENCL) #include "ellipsoid_nbor_cl.h" @@ -488,4 +488,4 @@ void BaseEllipsoidT::compile_kernels(UCL_Device &dev, } template class BaseEllipsoid; - +} diff --git a/lib/gpu/lal_base_three.cpp b/lib/gpu/lal_base_three.cpp index 0510b84d92..dc5678dd24 100644 --- a/lib/gpu/lal_base_three.cpp +++ b/lib/gpu/lal_base_three.cpp @@ -14,7 +14,7 @@ ***************************************************************************/ #include "lal_base_three.h" -using namespace LAMMPS_AL; +namespace LAMMPS_AL { #define BaseThreeT BaseThree extern Device global_device; @@ -397,4 +397,4 @@ void BaseThreeT::compile_kernels(UCL_Device &dev, const void *pair_str, } template class BaseThree; - +} diff --git a/lib/gpu/lal_beck.cpp b/lib/gpu/lal_beck.cpp index 165a02b71a..be1722c32c 100644 --- a/lib/gpu/lal_beck.cpp +++ b/lib/gpu/lal_beck.cpp @@ -23,7 +23,7 @@ const char *beck=0; #include "lal_beck.h" #include -using namespace LAMMPS_AL; +namespace LAMMPS_AL { #define BeckT Beck extern Device device; @@ -150,3 +150,4 @@ void BeckT::loop(const bool _eflag, const bool _vflag) { } template class Beck; +} diff --git a/lib/gpu/lal_born.cpp b/lib/gpu/lal_born.cpp index 7c1ed944d3..4a6b789687 100644 --- a/lib/gpu/lal_born.cpp +++ b/lib/gpu/lal_born.cpp @@ -23,7 +23,7 @@ const char *born=0; #include "lal_born.h" #include -using namespace LAMMPS_AL; +namespace LAMMPS_AL { #define BornT Born extern Device device; @@ -179,3 +179,4 @@ void BornT::loop(const bool _eflag, const bool _vflag) { } template class Born; +} diff --git a/lib/gpu/lal_born_coul_long.cpp b/lib/gpu/lal_born_coul_long.cpp index 116d44d58f..1b147395f6 100644 --- a/lib/gpu/lal_born_coul_long.cpp +++ b/lib/gpu/lal_born_coul_long.cpp @@ -23,7 +23,7 @@ const char *born_coul_long=0; #include "lal_born_coul_long.h" #include -using namespace LAMMPS_AL; +namespace LAMMPS_AL { #define BornCoulLongT BornCoulLong extern Device device; @@ -173,3 +173,4 @@ void BornCoulLongT::loop(const bool _eflag, const bool _vflag) { } template class BornCoulLong; +} diff --git a/lib/gpu/lal_born_coul_long_cs.cpp b/lib/gpu/lal_born_coul_long_cs.cpp index e7fb946f14..24de1e3a06 100644 --- a/lib/gpu/lal_born_coul_long_cs.cpp +++ b/lib/gpu/lal_born_coul_long_cs.cpp @@ -23,7 +23,7 @@ const char *born_coul_long_cs=0; #include "lal_born_coul_long_cs.h" #include -using namespace LAMMPS_AL; +namespace LAMMPS_AL { #define BornCoulLongCST BornCoulLongCS extern Device device; @@ -93,3 +93,4 @@ int BornCoulLongCST::init(const int ntypes, double **host_cutsq, double **host_r } template class BornCoulLongCS; +} diff --git a/lib/gpu/lal_born_coul_wolf.cpp b/lib/gpu/lal_born_coul_wolf.cpp index c44b841463..1624dd9d50 100644 --- a/lib/gpu/lal_born_coul_wolf.cpp +++ b/lib/gpu/lal_born_coul_wolf.cpp @@ -23,7 +23,7 @@ const char *born_coul_wolf=0; #include "lal_born_coul_wolf.h" #include -using namespace LAMMPS_AL; +namespace LAMMPS_AL { #define BornCoulWolfT BornCoulWolf extern Device device; @@ -174,3 +174,4 @@ void BornCoulWolfT::loop(const bool _eflag, const bool _vflag) { } template class BornCoulWolf; +} diff --git a/lib/gpu/lal_born_coul_wolf_cs.cpp b/lib/gpu/lal_born_coul_wolf_cs.cpp index bdb1c31e55..8deceeb1f4 100644 --- a/lib/gpu/lal_born_coul_wolf_cs.cpp +++ b/lib/gpu/lal_born_coul_wolf_cs.cpp @@ -23,7 +23,7 @@ const char *born_coul_wolf_cs=0; #include "lal_born_coul_wolf_cs.h" #include -using namespace LAMMPS_AL; +namespace LAMMPS_AL { #define BornCoulWolfCST BornCoulWolfCS extern Device device; @@ -95,3 +95,4 @@ int BornCoulWolfCST::init(const int ntypes, double **host_cutsq, double **host_r } template class BornCoulWolfCS; +} diff --git a/lib/gpu/lal_buck.cpp b/lib/gpu/lal_buck.cpp index 0da4068d51..5a335a1e51 100644 --- a/lib/gpu/lal_buck.cpp +++ b/lib/gpu/lal_buck.cpp @@ -23,7 +23,7 @@ const char *buck=0; #include "lal_buck.h" #include -using namespace LAMMPS_AL; +namespace LAMMPS_AL { #define BuckT Buck extern Device device; @@ -168,3 +168,4 @@ void BuckT::loop(const bool _eflag, const bool _vflag) { } template class Buck; +} diff --git a/lib/gpu/lal_buck_coul.cpp b/lib/gpu/lal_buck_coul.cpp index e4f829fc5c..25607eae17 100644 --- a/lib/gpu/lal_buck_coul.cpp +++ b/lib/gpu/lal_buck_coul.cpp @@ -23,7 +23,7 @@ const char *buck_coul=0; #include "lal_buck_coul.h" #include -using namespace LAMMPS_AL; +namespace LAMMPS_AL { #define BuckCoulT BuckCoul extern Device device; @@ -161,3 +161,4 @@ void BuckCoulT::loop(const bool _eflag, const bool _vflag) { } template class BuckCoul; +} diff --git a/lib/gpu/lal_buck_coul_long.cpp b/lib/gpu/lal_buck_coul_long.cpp index 81faada116..1c0288c2d8 100644 --- a/lib/gpu/lal_buck_coul_long.cpp +++ b/lib/gpu/lal_buck_coul_long.cpp @@ -23,7 +23,7 @@ const char *buck_coul_long=0; #include "lal_buck_coul_long.h" #include -using namespace LAMMPS_AL; +namespace LAMMPS_AL { #define BuckCoulLongT BuckCoulLong extern Device device; @@ -166,3 +166,4 @@ void BuckCoulLongT::loop(const bool _eflag, const bool _vflag) { } template class BuckCoulLong; +} diff --git a/lib/gpu/lal_charmm_long.cpp b/lib/gpu/lal_charmm_long.cpp index 9cd032b3c6..a78996a7d5 100644 --- a/lib/gpu/lal_charmm_long.cpp +++ b/lib/gpu/lal_charmm_long.cpp @@ -23,7 +23,7 @@ const char *charmm_long=0; #include "lal_charmm_long.h" #include -using namespace LAMMPS_AL; +namespace LAMMPS_AL { #define CHARMMLongT CHARMMLong extern Device device; @@ -174,3 +174,4 @@ void CHARMMLongT::loop(const bool _eflag, const bool _vflag) { } template class CHARMMLong; +} diff --git a/lib/gpu/lal_colloid.cpp b/lib/gpu/lal_colloid.cpp index fb2b643e5e..c441d50968 100644 --- a/lib/gpu/lal_colloid.cpp +++ b/lib/gpu/lal_colloid.cpp @@ -23,7 +23,7 @@ const char *colloid=0; #include "lal_colloid.h" #include -using namespace LAMMPS_AL; +namespace LAMMPS_AL { #define ColloidT Colloid extern Device device; @@ -179,3 +179,4 @@ void ColloidT::loop(const bool _eflag, const bool _vflag) { } template class Colloid; +} diff --git a/lib/gpu/lal_coul.cpp b/lib/gpu/lal_coul.cpp index a06a29e610..3e29215c91 100644 --- a/lib/gpu/lal_coul.cpp +++ b/lib/gpu/lal_coul.cpp @@ -23,7 +23,7 @@ const char *coul=0; #include "lal_coul.h" #include -using namespace LAMMPS_AL; +namespace LAMMPS_AL { #define CoulT Coul extern Device device; @@ -164,3 +164,4 @@ void CoulT::loop(const bool _eflag, const bool _vflag) { } template class Coul; +} diff --git a/lib/gpu/lal_coul_debye.cpp b/lib/gpu/lal_coul_debye.cpp index 9098aeacb1..08ceb99300 100644 --- a/lib/gpu/lal_coul_debye.cpp +++ b/lib/gpu/lal_coul_debye.cpp @@ -23,7 +23,7 @@ const char *coul_debye=0; #include "lal_coul_debye.h" #include -using namespace LAMMPS_AL; +namespace LAMMPS_AL { #define CoulDebyeT CoulDebye extern Device device; @@ -165,3 +165,4 @@ void CoulDebyeT::loop(const bool _eflag, const bool _vflag) { } template class CoulDebye; +} diff --git a/lib/gpu/lal_coul_dsf.cpp b/lib/gpu/lal_coul_dsf.cpp index 32c4342fbe..fe1fbfede7 100644 --- a/lib/gpu/lal_coul_dsf.cpp +++ b/lib/gpu/lal_coul_dsf.cpp @@ -23,7 +23,7 @@ const char *coul_dsf=0; #include "lal_coul_dsf.h" #include -using namespace LAMMPS_AL; +namespace LAMMPS_AL { #define CoulDSFT CoulDSF extern Device device; @@ -151,3 +151,4 @@ void CoulDSFT::loop(const bool _eflag, const bool _vflag) { } template class CoulDSF; +} diff --git a/lib/gpu/lal_coul_long.cpp b/lib/gpu/lal_coul_long.cpp index b4c6a44d2f..02097a2c61 100644 --- a/lib/gpu/lal_coul_long.cpp +++ b/lib/gpu/lal_coul_long.cpp @@ -23,7 +23,7 @@ const char *coul_long=0; #include "lal_coul_long.h" #include -using namespace LAMMPS_AL; +namespace LAMMPS_AL { #define CoulLongT CoulLong extern Device pair_gpu_device; @@ -156,3 +156,4 @@ void CoulLongT::loop(const bool _eflag, const bool _vflag) { } template class CoulLong; +} diff --git a/lib/gpu/lal_coul_long_cs.cpp b/lib/gpu/lal_coul_long_cs.cpp index 7afa0ae5d2..32b5691610 100644 --- a/lib/gpu/lal_coul_long_cs.cpp +++ b/lib/gpu/lal_coul_long_cs.cpp @@ -23,7 +23,7 @@ const char *coul_long_cs=0; #include "lal_coul_long_cs.h" #include -using namespace LAMMPS_AL; +namespace LAMMPS_AL { #define CoulLongCST CoulLongCS extern Device pair_gpu_device; @@ -76,3 +76,4 @@ int CoulLongCST::init(const int ntypes, double **host_scale, } template class CoulLongCS; +} diff --git a/lib/gpu/lal_device.cpp b/lib/gpu/lal_device.cpp index 9410cc5250..5bd306ea5b 100644 --- a/lib/gpu/lal_device.cpp +++ b/lib/gpu/lal_device.cpp @@ -30,7 +30,7 @@ const char *device=0; #include "device_cubin.h" #endif -using namespace LAMMPS_AL; +namespace LAMMPS_AL { #define DeviceT Device template @@ -762,7 +762,9 @@ double DeviceT::host_memory_usage() const { template class Device; Device global_device; +} +using namespace LAMMPS_AL; int lmp_init_device(MPI_Comm world, MPI_Comm replica, const int first_gpu, const int last_gpu, const int gpu_mode, const double particle_split, const int nthreads, @@ -781,4 +783,3 @@ double lmp_gpu_forces(double **f, double **tor, double *eatom, double **vatom, double *virial, double &ecoul) { return global_device.fix_gpu(f,tor,eatom,vatom,virial,ecoul); } - diff --git a/lib/gpu/lal_dipole_lj.cpp b/lib/gpu/lal_dipole_lj.cpp index c97b76c820..b0929e2ffb 100644 --- a/lib/gpu/lal_dipole_lj.cpp +++ b/lib/gpu/lal_dipole_lj.cpp @@ -23,7 +23,7 @@ const char *dipole_lj=0; #include "lal_dipole_lj.h" #include -using namespace LAMMPS_AL; +namespace LAMMPS_AL { #define DipoleLJT DipoleLJ extern Device device; @@ -168,3 +168,4 @@ void DipoleLJT::loop(const bool _eflag, const bool _vflag) { } template class DipoleLJ; +} diff --git a/lib/gpu/lal_dipole_lj_sf.cpp b/lib/gpu/lal_dipole_lj_sf.cpp index a33f38084f..dcf95bb126 100644 --- a/lib/gpu/lal_dipole_lj_sf.cpp +++ b/lib/gpu/lal_dipole_lj_sf.cpp @@ -23,7 +23,7 @@ const char *dipole_lj_sf=0; #include "lal_dipole_lj_sf.h" #include -using namespace LAMMPS_AL; +namespace LAMMPS_AL { #define DipoleLJSFT DipoleLJSF extern Device device; @@ -168,3 +168,4 @@ void DipoleLJSFT::loop(const bool _eflag, const bool _vflag) { } template class DipoleLJSF; +} diff --git a/lib/gpu/lal_dipole_long_lj.cpp b/lib/gpu/lal_dipole_long_lj.cpp index 251e1def92..9648e9b15e 100644 --- a/lib/gpu/lal_dipole_long_lj.cpp +++ b/lib/gpu/lal_dipole_long_lj.cpp @@ -23,7 +23,7 @@ const char *dipole_long_lj=0; #include "lal_dipole_long_lj.h" #include -using namespace LAMMPS_AL; +namespace LAMMPS_AL { #define DipoleLongLJT DipoleLongLJ extern Device device; @@ -171,3 +171,4 @@ void DipoleLongLJT::loop(const bool _eflag, const bool _vflag) { } template class DipoleLongLJ; +} diff --git a/lib/gpu/lal_dpd.cpp b/lib/gpu/lal_dpd.cpp index 4f6f2d641f..c5cbc7eb53 100644 --- a/lib/gpu/lal_dpd.cpp +++ b/lib/gpu/lal_dpd.cpp @@ -23,7 +23,7 @@ const char *dpd=0; #include "lal_dpd.h" #include -using namespace LAMMPS_AL; +namespace LAMMPS_AL { #define DPDT DPD extern Device device; @@ -168,3 +168,4 @@ void DPDT::update_coeff(int ntypes, double **host_a0, double **host_gamma, } template class DPD; +} diff --git a/lib/gpu/lal_eam.cpp b/lib/gpu/lal_eam.cpp index b83972f4db..8c81353f36 100644 --- a/lib/gpu/lal_eam.cpp +++ b/lib/gpu/lal_eam.cpp @@ -23,7 +23,7 @@ const char *eam=0; #include "lal_eam.h" #include -using namespace LAMMPS_AL; +namespace LAMMPS_AL { #define EAMT EAM @@ -531,3 +531,4 @@ void EAMT::loop2(const bool _eflag, const bool _vflag) { } template class EAM; +} diff --git a/lib/gpu/lal_gauss.cpp b/lib/gpu/lal_gauss.cpp index 1ef215d7ff..2f965758eb 100644 --- a/lib/gpu/lal_gauss.cpp +++ b/lib/gpu/lal_gauss.cpp @@ -23,7 +23,7 @@ const char *gauss=0; #include "lal_gauss.h" #include -using namespace LAMMPS_AL; +namespace LAMMPS_AL { #define GaussT Gauss extern Device device; @@ -159,3 +159,4 @@ void GaussT::loop(const bool _eflag, const bool _vflag) { } template class Gauss; +} diff --git a/lib/gpu/lal_gayberne.cpp b/lib/gpu/lal_gayberne.cpp index ba15af672e..f17fc50f5f 100644 --- a/lib/gpu/lal_gayberne.cpp +++ b/lib/gpu/lal_gayberne.cpp @@ -26,7 +26,7 @@ const char *gayberne_lj=0; #include "lal_gayberne.h" #include -using namespace LAMMPS_AL; +namespace LAMMPS_AL { #define GayBerneT GayBerne extern Device device; @@ -315,4 +315,4 @@ void GayBerneT::loop(const bool _eflag, const bool _vflag) { } template class GayBerne; - +} diff --git a/lib/gpu/lal_lj.cpp b/lib/gpu/lal_lj.cpp index 978b33e5d7..5bd015e364 100644 --- a/lib/gpu/lal_lj.cpp +++ b/lib/gpu/lal_lj.cpp @@ -23,7 +23,7 @@ const char *lj=0; #include "lal_lj.h" #include -using namespace LAMMPS_AL; +namespace LAMMPS_AL { #define LJT LJ extern Device device; @@ -168,3 +168,4 @@ void LJT::loop(const bool _eflag, const bool _vflag) { } template class LJ; +} diff --git a/lib/gpu/lal_lj96.cpp b/lib/gpu/lal_lj96.cpp index 191f211ae4..6f74cd0f19 100644 --- a/lib/gpu/lal_lj96.cpp +++ b/lib/gpu/lal_lj96.cpp @@ -23,7 +23,7 @@ const char *lj96=0; #include "lal_lj96.h" #include -using namespace LAMMPS_AL; +namespace LAMMPS_AL { #define LJ96T LJ96 extern Device device; @@ -152,3 +152,4 @@ void LJ96T::loop(const bool _eflag, const bool _vflag) { } template class LJ96; +} diff --git a/lib/gpu/lal_lj_class2_long.cpp b/lib/gpu/lal_lj_class2_long.cpp index 497e5989ad..24b07212ed 100644 --- a/lib/gpu/lal_lj_class2_long.cpp +++ b/lib/gpu/lal_lj_class2_long.cpp @@ -23,7 +23,7 @@ const char *lj_class2_long=0; #include "lal_lj_class2_long.h" #include -using namespace LAMMPS_AL; +namespace LAMMPS_AL { #define LJClass2LongT LJClass2Long @@ -164,4 +164,4 @@ void LJClass2LongT::loop(const bool _eflag, const bool _vflag) { } template class LJClass2Long; - +} diff --git a/lib/gpu/lal_lj_coul.cpp b/lib/gpu/lal_lj_coul.cpp index a8255318bd..59ce9c5e61 100644 --- a/lib/gpu/lal_lj_coul.cpp +++ b/lib/gpu/lal_lj_coul.cpp @@ -23,7 +23,7 @@ const char *lj_coul=0; #include "lal_lj_coul.h" #include -using namespace LAMMPS_AL; +namespace LAMMPS_AL { #define LJCoulT LJCoul extern Device device; @@ -164,3 +164,4 @@ void LJCoulT::loop(const bool _eflag, const bool _vflag) { } template class LJCoul; +} diff --git a/lib/gpu/lal_lj_coul_debye.cpp b/lib/gpu/lal_lj_coul_debye.cpp index 92167f314f..556a0a5cd3 100644 --- a/lib/gpu/lal_lj_coul_debye.cpp +++ b/lib/gpu/lal_lj_coul_debye.cpp @@ -23,7 +23,7 @@ const char *lj_coul_debye=0; #include "lal_lj_coul_debye.h" #include -using namespace LAMMPS_AL; +namespace LAMMPS_AL { #define LJCoulDebyeT LJCoulDebye extern Device device; @@ -166,3 +166,4 @@ void LJCoulDebyeT::loop(const bool _eflag, const bool _vflag) { } template class LJCoulDebye; +} diff --git a/lib/gpu/lal_lj_coul_long.cpp b/lib/gpu/lal_lj_coul_long.cpp index 29d648bed2..66897a4aa7 100644 --- a/lib/gpu/lal_lj_coul_long.cpp +++ b/lib/gpu/lal_lj_coul_long.cpp @@ -23,7 +23,7 @@ const char *lj_coul_long=0; #include "lal_lj_coul_long.h" #include -using namespace LAMMPS_AL; +namespace LAMMPS_AL { #define LJCoulLongT LJCoulLong extern Device device; @@ -181,3 +181,4 @@ void LJCoulLongT::loop(const bool _eflag, const bool _vflag) { } template class LJCoulLong; +} diff --git a/lib/gpu/lal_lj_coul_msm.cpp b/lib/gpu/lal_lj_coul_msm.cpp index 1358de9ee1..9a17d068ec 100644 --- a/lib/gpu/lal_lj_coul_msm.cpp +++ b/lib/gpu/lal_lj_coul_msm.cpp @@ -23,7 +23,7 @@ const char *lj_coul_msm=0; #include "lal_lj_coul_msm.h" #include -using namespace LAMMPS_AL; +namespace LAMMPS_AL { #define LJCoulMSMT LJCoulMSM extern Device device; @@ -198,3 +198,4 @@ void LJCoulMSMT::loop(const bool _eflag, const bool _vflag) { } template class LJCoulMSM; +} diff --git a/lib/gpu/lal_lj_cubic.cpp b/lib/gpu/lal_lj_cubic.cpp index 21ea22845c..f8200ec037 100644 --- a/lib/gpu/lal_lj_cubic.cpp +++ b/lib/gpu/lal_lj_cubic.cpp @@ -23,7 +23,7 @@ const char *lj_cubic=0; #include "lal_lj_cubic.h" #include -using namespace LAMMPS_AL; +namespace LAMMPS_AL { #define LJCubicT LJCubic extern Device device; @@ -157,3 +157,4 @@ void LJCubicT::loop(const bool _eflag, const bool _vflag) { } template class LJCubic; +} diff --git a/lib/gpu/lal_lj_dsf.cpp b/lib/gpu/lal_lj_dsf.cpp index 1efac3e821..b888f33f00 100644 --- a/lib/gpu/lal_lj_dsf.cpp +++ b/lib/gpu/lal_lj_dsf.cpp @@ -23,7 +23,7 @@ const char *lj_dsf=0; #include "lal_lj_dsf.h" #include -using namespace LAMMPS_AL; +namespace LAMMPS_AL { #define LJDSFT LJDSF extern Device device; @@ -166,3 +166,4 @@ void LJDSFT::loop(const bool _eflag, const bool _vflag) { } template class LJDSF; +} diff --git a/lib/gpu/lal_lj_expand.cpp b/lib/gpu/lal_lj_expand.cpp index 34a4d71c0b..1c58cecfae 100644 --- a/lib/gpu/lal_lj_expand.cpp +++ b/lib/gpu/lal_lj_expand.cpp @@ -23,7 +23,7 @@ const char *lj_expand=0; #include "lal_lj_expand.h" #include -using namespace LAMMPS_AL; +namespace LAMMPS_AL { #define LJExpandT LJExpand extern Device device; @@ -171,3 +171,4 @@ void LJExpandT::loop(const bool _eflag, const bool _vflag) { } template class LJExpand; +} diff --git a/lib/gpu/lal_lj_expand_coul_long.cpp b/lib/gpu/lal_lj_expand_coul_long.cpp index 32a4f8120e..3e5e00ef6a 100644 --- a/lib/gpu/lal_lj_expand_coul_long.cpp +++ b/lib/gpu/lal_lj_expand_coul_long.cpp @@ -23,7 +23,7 @@ const char *lj_expand_coul_long=0; #include "lal_lj_expand_coul_long.h" #include -using namespace LAMMPS_AL; +namespace LAMMPS_AL { #define LJExpandCoulLongT LJExpandCoulLong extern Device device; @@ -181,3 +181,4 @@ void LJExpandCoulLongT::loop(const bool _eflag, const bool _vflag) { } template class LJExpandCoulLong; +} diff --git a/lib/gpu/lal_lj_gromacs.cpp b/lib/gpu/lal_lj_gromacs.cpp index 75f5a41917..0563151ddd 100644 --- a/lib/gpu/lal_lj_gromacs.cpp +++ b/lib/gpu/lal_lj_gromacs.cpp @@ -23,7 +23,7 @@ const char *lj_gromacs=0; #include "lal_lj_gromacs.h" #include -using namespace LAMMPS_AL; +namespace LAMMPS_AL { #define LJGROMACST LJGROMACS extern Device device; @@ -162,3 +162,4 @@ void LJGROMACST::loop(const bool _eflag, const bool _vflag) { } template class LJGROMACS; +} diff --git a/lib/gpu/lal_lj_sdk.cpp b/lib/gpu/lal_lj_sdk.cpp index 618555e38a..c6a282576c 100644 --- a/lib/gpu/lal_lj_sdk.cpp +++ b/lib/gpu/lal_lj_sdk.cpp @@ -23,7 +23,7 @@ const char *lj_sdk=0; #include "lal_lj_sdk.h" #include -using namespace LAMMPS_AL; +namespace LAMMPS_AL { #define CGCMMT CGCMM extern Device device; @@ -152,3 +152,4 @@ void CGCMMT::loop(const bool _eflag, const bool _vflag) { } template class CGCMM; +} diff --git a/lib/gpu/lal_lj_sdk_long.cpp b/lib/gpu/lal_lj_sdk_long.cpp index 46caf6bd36..74dbfc40e3 100644 --- a/lib/gpu/lal_lj_sdk_long.cpp +++ b/lib/gpu/lal_lj_sdk_long.cpp @@ -23,7 +23,7 @@ const char *lj_sdk_long=0; #include "lal_lj_sdk_long.h" #include -using namespace LAMMPS_AL; +namespace LAMMPS_AL { #define CGCMMLongT CGCMMLong extern Device device; @@ -164,3 +164,4 @@ void CGCMMLongT::loop(const bool _eflag, const bool _vflag) { } template class CGCMMLong; +} diff --git a/lib/gpu/lal_mie.cpp b/lib/gpu/lal_mie.cpp index 1510275047..394d1f8a2f 100644 --- a/lib/gpu/lal_mie.cpp +++ b/lib/gpu/lal_mie.cpp @@ -23,7 +23,7 @@ const char *mie=0; #include "lal_mie.h" #include -using namespace LAMMPS_AL; +namespace LAMMPS_AL { #define MieT Mie extern Device device; @@ -150,3 +150,4 @@ void MieT::loop(const bool _eflag, const bool _vflag) { } template class Mie; +} diff --git a/lib/gpu/lal_morse.cpp b/lib/gpu/lal_morse.cpp index cbdf928863..09da65d252 100644 --- a/lib/gpu/lal_morse.cpp +++ b/lib/gpu/lal_morse.cpp @@ -23,7 +23,7 @@ const char *morse=0; #include "lal_morse.h" #include -using namespace LAMMPS_AL; +namespace LAMMPS_AL { #define MorseT Morse extern Device device; @@ -150,4 +150,4 @@ void MorseT::loop(const bool _eflag, const bool _vflag) { } template class Morse; - +} diff --git a/lib/gpu/lal_pppm.cpp b/lib/gpu/lal_pppm.cpp index fefa1172ab..8b5012f312 100644 --- a/lib/gpu/lal_pppm.cpp +++ b/lib/gpu/lal_pppm.cpp @@ -25,7 +25,7 @@ const char *pppm_d=0; #include "lal_pppm.h" #include -using namespace LAMMPS_AL; +namespace LAMMPS_AL { #define PPPMT PPPM extern Device global_device; @@ -402,3 +402,4 @@ void PPPMT::compile_kernels(UCL_Device &dev) { template class PPPM; template class PPPM; +} diff --git a/lib/gpu/lal_re_squared.cpp b/lib/gpu/lal_re_squared.cpp index 9513f5a633..81dc3b13a4 100644 --- a/lib/gpu/lal_re_squared.cpp +++ b/lib/gpu/lal_re_squared.cpp @@ -26,7 +26,7 @@ const char *re_squared_lj=0; #include "lal_re_squared.h" #include -using namespace LAMMPS_AL; +namespace LAMMPS_AL { #define RESquaredT RESquared extern Device device; @@ -315,4 +315,4 @@ void RESquaredT::loop(const bool _eflag, const bool _vflag) { } template class RESquared; - +} diff --git a/lib/gpu/lal_soft.cpp b/lib/gpu/lal_soft.cpp index 727b112ea5..8e944fa0a5 100644 --- a/lib/gpu/lal_soft.cpp +++ b/lib/gpu/lal_soft.cpp @@ -23,7 +23,7 @@ const char *soft=0; #include "lal_soft.h" #include -using namespace LAMMPS_AL; +namespace LAMMPS_AL { #define SoftT Soft extern Device device; @@ -158,3 +158,4 @@ void SoftT::loop(const bool _eflag, const bool _vflag) { } template class Soft; +} diff --git a/lib/gpu/lal_sw.cpp b/lib/gpu/lal_sw.cpp index 46b6382a60..5c7bd45c76 100644 --- a/lib/gpu/lal_sw.cpp +++ b/lib/gpu/lal_sw.cpp @@ -23,7 +23,7 @@ const char *sw=0; #include "lal_sw.h" #include -using namespace LAMMPS_AL; +namespace LAMMPS_AL { #define SWT SW extern Device device; @@ -262,4 +262,4 @@ void SWT::loop(const bool _eflag, const bool _vflag, const int evatom) { } template class SW; - +} diff --git a/lib/gpu/lal_table.cpp b/lib/gpu/lal_table.cpp index 0de59c84b2..d07b2716e4 100644 --- a/lib/gpu/lal_table.cpp +++ b/lib/gpu/lal_table.cpp @@ -23,7 +23,7 @@ const char *table=0; #include "lal_table.h" #include -using namespace LAMMPS_AL; +namespace LAMMPS_AL { #define TableT Table #define LOOKUP 0 @@ -337,3 +337,4 @@ void TableT::loop(const bool _eflag, const bool _vflag) { } template class Table; +} diff --git a/lib/gpu/lal_tersoff.cpp b/lib/gpu/lal_tersoff.cpp index ef55b98a2d..27143acb0c 100644 --- a/lib/gpu/lal_tersoff.cpp +++ b/lib/gpu/lal_tersoff.cpp @@ -23,7 +23,7 @@ const char *tersoff=0; #include "lal_tersoff.h" #include -using namespace LAMMPS_AL; +namespace LAMMPS_AL { #define TersoffT Tersoff extern Device device; @@ -329,4 +329,4 @@ void TersoffT::loop(const bool _eflag, const bool _vflag, const int evatom) { } template class Tersoff; - +} diff --git a/lib/gpu/lal_tersoff_mod.cpp b/lib/gpu/lal_tersoff_mod.cpp index 3cbb488cab..182859bdd4 100644 --- a/lib/gpu/lal_tersoff_mod.cpp +++ b/lib/gpu/lal_tersoff_mod.cpp @@ -23,7 +23,7 @@ const char *tersoff_mod=0; #include "lal_tersoff_mod.h" #include -using namespace LAMMPS_AL; +namespace LAMMPS_AL { #define TersoffMT TersoffMod extern Device device; @@ -329,4 +329,4 @@ void TersoffMT::loop(const bool _eflag, const bool _vflag, const int evatom) { } template class TersoffMod; - +} diff --git a/lib/gpu/lal_tersoff_zbl.cpp b/lib/gpu/lal_tersoff_zbl.cpp index ebf67285ed..92db59679e 100644 --- a/lib/gpu/lal_tersoff_zbl.cpp +++ b/lib/gpu/lal_tersoff_zbl.cpp @@ -23,7 +23,7 @@ const char *tersoff_zbl=0; #include "lal_tersoff_zbl.h" #include -using namespace LAMMPS_AL; +namespace LAMMPS_AL { #define TersoffZT TersoffZBL extern Device device; @@ -355,4 +355,4 @@ void TersoffZT::loop(const bool _eflag, const bool _vflag, const int evatom) { } template class TersoffZBL; - +} diff --git a/lib/gpu/lal_ufm.cpp b/lib/gpu/lal_ufm.cpp index c7aa2cca39..9b7d42dec9 100644 --- a/lib/gpu/lal_ufm.cpp +++ b/lib/gpu/lal_ufm.cpp @@ -25,7 +25,7 @@ const char *ufm=0; #include "lal_ufm.h" #include -using namespace LAMMPS_AL; +namespace LAMMPS_AL { #define UFMT UFM extern Device device; @@ -170,3 +170,4 @@ void UFMT::loop(const bool _eflag, const bool _vflag) { } template class UFM; +} diff --git a/lib/gpu/lal_vashishta.cpp b/lib/gpu/lal_vashishta.cpp index 5a01a9bd46..350ae8e8fd 100644 --- a/lib/gpu/lal_vashishta.cpp +++ b/lib/gpu/lal_vashishta.cpp @@ -23,7 +23,7 @@ const char *vashishta=0; #include "lal_vashishta.h" #include -using namespace LAMMPS_AL; +namespace LAMMPS_AL { #define VashishtaT Vashishta extern Device device; @@ -295,4 +295,4 @@ void VashishtaT::loop(const bool _eflag, const bool _vflag, const int evatom) { } template class Vashishta; - +} diff --git a/lib/gpu/lal_yukawa.cpp b/lib/gpu/lal_yukawa.cpp index a316d195ac..453139e537 100644 --- a/lib/gpu/lal_yukawa.cpp +++ b/lib/gpu/lal_yukawa.cpp @@ -23,7 +23,7 @@ const char *yukawa=0; #include "lal_yukawa.h" #include -using namespace LAMMPS_AL; +namespace LAMMPS_AL { #define YukawaT Yukawa extern Device device; @@ -147,3 +147,4 @@ void YukawaT::loop(const bool _eflag, const bool _vflag) { } template class Yukawa; +} diff --git a/lib/gpu/lal_yukawa_colloid.cpp b/lib/gpu/lal_yukawa_colloid.cpp index af29938a68..e71e962ffd 100644 --- a/lib/gpu/lal_yukawa_colloid.cpp +++ b/lib/gpu/lal_yukawa_colloid.cpp @@ -23,7 +23,7 @@ const char *yukawa_colloid=0; #include "lal_yukawa_colloid.h" #include -using namespace LAMMPS_AL; +namespace LAMMPS_AL { #define YukawaColloidT YukawaColloid extern Device device; @@ -289,3 +289,4 @@ void YukawaColloidT::loop(const bool _eflag, const bool _vflag) { } template class YukawaColloid; +} diff --git a/lib/gpu/lal_zbl.cpp b/lib/gpu/lal_zbl.cpp index 77e55a62f9..2bf3369174 100644 --- a/lib/gpu/lal_zbl.cpp +++ b/lib/gpu/lal_zbl.cpp @@ -23,7 +23,7 @@ const char *zbl=0; #include "lal_zbl.h" #include -using namespace LAMMPS_AL; +namespace LAMMPS_AL { #define ZBLT ZBL extern Device device; @@ -157,3 +157,4 @@ void ZBLT::loop(const bool _eflag, const bool _vflag) { } template class ZBL; +} -- GitLab From a1f0c0079de6d0c7d94fc63f6d9cd76e70b5ce2b Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Fri, 12 Jul 2019 15:40:24 -0400 Subject: [PATCH 248/469] some cleanup for missed steps in previous change sets --- src/KSPACE/pppm.h | 5 +---- src/KSPACE/pppm_disp.h | 5 +---- src/MPIIO/dump_xyz_mpiio.cpp | 1 - src/USER-AWPMD/atom_vec_wavepacket.cpp | 1 - src/USER-AWPMD/fix_nve_awpmd.cpp | 7 +++---- src/USER-AWPMD/fix_nve_awpmd.h | 3 +-- src/USER-AWPMD/pair_awpmd_cut.cpp | 8 ++++++-- src/USER-BOCS/compute_pressure_bocs.cpp | 1 + src/USER-CGSDK/pair_lj_sdk.cpp | 2 -- src/USER-CGSDK/pair_lj_sdk_coul_msm.cpp | 1 - src/USER-DPD/fix_shardlow.cpp | 3 ++- src/USER-OMP/pair_reaxc_omp.cpp | 11 ++++------- src/accelerator_kokkos.h | 16 ++++++++-------- src/finish.cpp | 4 ++-- 14 files changed, 29 insertions(+), 39 deletions(-) diff --git a/src/KSPACE/pppm.h b/src/KSPACE/pppm.h index 1ce1a0d666..b84dfe26c4 100644 --- a/src/KSPACE/pppm.h +++ b/src/KSPACE/pppm.h @@ -20,8 +20,7 @@ KSpaceStyle(pppm,PPPM) #ifndef LMP_PPPM_H #define LMP_PPPM_H -#include "lmptype.h" -#include +#include "kspace.h" #ifdef FFT_SINGLE typedef float FFT_SCALAR; @@ -31,8 +30,6 @@ typedef double FFT_SCALAR; #define MPI_FFT_SCALAR MPI_DOUBLE #endif -#include "kspace.h" - namespace LAMMPS_NS { class PPPM : public KSpace { diff --git a/src/KSPACE/pppm_disp.h b/src/KSPACE/pppm_disp.h index ccbeb60f3c..8582e98acd 100644 --- a/src/KSPACE/pppm_disp.h +++ b/src/KSPACE/pppm_disp.h @@ -20,8 +20,7 @@ KSpaceStyle(pppm/disp,PPPMDisp) #ifndef LMP_PPPM_DISP_H #define LMP_PPPM_DISP_H -#include "lmptype.h" -#include +#include "kspace.h" #ifdef FFT_SINGLE typedef float FFT_SCALAR; @@ -31,8 +30,6 @@ typedef double FFT_SCALAR; #define MPI_FFT_SCALAR MPI_DOUBLE #endif -#include "kspace.h" - namespace LAMMPS_NS { diff --git a/src/MPIIO/dump_xyz_mpiio.cpp b/src/MPIIO/dump_xyz_mpiio.cpp index ee0532399a..f5caab3a9c 100644 --- a/src/MPIIO/dump_xyz_mpiio.cpp +++ b/src/MPIIO/dump_xyz_mpiio.cpp @@ -21,7 +21,6 @@ #include #include "domain.h" #include "update.h" -#include "modify.h" #include "compute.h" #include "memory.h" #include "error.h" diff --git a/src/USER-AWPMD/atom_vec_wavepacket.cpp b/src/USER-AWPMD/atom_vec_wavepacket.cpp index 3dc624e4b8..bce334a7b3 100644 --- a/src/USER-AWPMD/atom_vec_wavepacket.cpp +++ b/src/USER-AWPMD/atom_vec_wavepacket.cpp @@ -16,7 +16,6 @@ ------------------------------------------------------------------------- */ #include "atom_vec_wavepacket.h" -#include #include #include "atom.h" #include "comm.h" diff --git a/src/USER-AWPMD/fix_nve_awpmd.cpp b/src/USER-AWPMD/fix_nve_awpmd.cpp index 57ad17f3e6..a147a11081 100644 --- a/src/USER-AWPMD/fix_nve_awpmd.cpp +++ b/src/USER-AWPMD/fix_nve_awpmd.cpp @@ -16,14 +16,13 @@ ------------------------------------------------------------------------- */ #include "fix_nve_awpmd.h" -#include -#include -#include +#include "pair_awpmd_cut.h" #include "atom.h" #include "force.h" #include "update.h" #include "respa.h" #include "error.h" +#include "utils.h" #include "TCP/wpmd_split.h" @@ -62,7 +61,7 @@ void FixNVEAwpmd::init() dtv = update->dt; dtf = 0.5 * update->dt * force->ftm2v; - if (strstr(update->integrate_style,"respa")) + if (utils::strmatch(update->integrate_style,"^respa")) step_respa = ((Respa *) update->integrate)->step; awpmd_pair=(PairAWPMDCut *)force->pair; diff --git a/src/USER-AWPMD/fix_nve_awpmd.h b/src/USER-AWPMD/fix_nve_awpmd.h index 140d234308..832f5821a3 100644 --- a/src/USER-AWPMD/fix_nve_awpmd.h +++ b/src/USER-AWPMD/fix_nve_awpmd.h @@ -25,7 +25,6 @@ FixStyle(nve/awpmd,FixNVEAwpmd) #define LMP_FIX_NVE_awpmd_H #include "fix.h" -#include "pair_awpmd_cut.h" namespace LAMMPS_NS { @@ -45,7 +44,7 @@ class FixNVEAwpmd : public Fix { double *step_respa; int mass_require; - PairAWPMDCut *awpmd_pair; + class PairAWPMDCut *awpmd_pair; }; } diff --git a/src/USER-AWPMD/pair_awpmd_cut.cpp b/src/USER-AWPMD/pair_awpmd_cut.cpp index ae2fbc59fa..75ebb0e251 100644 --- a/src/USER-AWPMD/pair_awpmd_cut.cpp +++ b/src/USER-AWPMD/pair_awpmd_cut.cpp @@ -16,10 +16,11 @@ ------------------------------------------------------------------------- */ #include "pair_awpmd_cut.h" +#include #include -#include -#include #include +#include +#include #include "atom.h" #include "update.h" #include "min.h" @@ -32,6 +33,9 @@ #include "memory.h" #include "error.h" +#include "logexc.h" +#include "vector_3.h" +#include "TCP/wpmd.h" #include "TCP/wpmd_split.h" using namespace LAMMPS_NS; diff --git a/src/USER-BOCS/compute_pressure_bocs.cpp b/src/USER-BOCS/compute_pressure_bocs.cpp index ee1ad33f88..d0a24b99a3 100644 --- a/src/USER-BOCS/compute_pressure_bocs.cpp +++ b/src/USER-BOCS/compute_pressure_bocs.cpp @@ -16,6 +16,7 @@ #include "compute_pressure_bocs.h" #include +#include #include #include #include "atom.h" diff --git a/src/USER-CGSDK/pair_lj_sdk.cpp b/src/USER-CGSDK/pair_lj_sdk.cpp index 6ad77a6183..1301dc4155 100644 --- a/src/USER-CGSDK/pair_lj_sdk.cpp +++ b/src/USER-CGSDK/pair_lj_sdk.cpp @@ -24,7 +24,6 @@ #include "comm.h" #include "force.h" #include "neigh_list.h" -#include "math_const.h" #include "memory.h" #include "error.h" @@ -32,7 +31,6 @@ #include "lj_sdk_common.h" using namespace LAMMPS_NS; -using namespace MathConst; using namespace LJSDKParms; /* ---------------------------------------------------------------------- */ diff --git a/src/USER-CGSDK/pair_lj_sdk_coul_msm.cpp b/src/USER-CGSDK/pair_lj_sdk_coul_msm.cpp index 1095521de3..f168089fae 100644 --- a/src/USER-CGSDK/pair_lj_sdk_coul_msm.cpp +++ b/src/USER-CGSDK/pair_lj_sdk_coul_msm.cpp @@ -23,7 +23,6 @@ #include "force.h" #include "kspace.h" #include "neigh_list.h" -#include "memory.h" #include "error.h" #include "lj_sdk_common.h" diff --git a/src/USER-DPD/fix_shardlow.cpp b/src/USER-DPD/fix_shardlow.cpp index f181436f91..b0efeb634d 100644 --- a/src/USER-DPD/fix_shardlow.cpp +++ b/src/USER-DPD/fix_shardlow.cpp @@ -37,15 +37,16 @@ #include #include #include +#include #include "atom.h" #include "force.h" #include "update.h" #include "error.h" -#include "atom_vec.h" #include "comm.h" #include "neighbor.h" #include "neigh_list.h" #include "neigh_request.h" +#include "npair.h" #include "memory.h" #include "domain.h" #include "modify.h" diff --git a/src/USER-OMP/pair_reaxc_omp.cpp b/src/USER-OMP/pair_reaxc_omp.cpp index 2f17515130..aedd438066 100644 --- a/src/USER-OMP/pair_reaxc_omp.cpp +++ b/src/USER-OMP/pair_reaxc_omp.cpp @@ -34,6 +34,8 @@ ------------------------------------------------------------------------- */ #include "pair_reaxc_omp.h" +#include +#include #include "atom.h" #include "update.h" #include "force.h" @@ -42,32 +44,27 @@ #include "neigh_list.h" #include "neigh_request.h" #include "modify.h" -#include "fix.h" #include "fix_reaxc.h" #include "citeme.h" #include "memory.h" #include "error.h" #include "timer.h" +#include "reaxc_defs.h" #include "reaxc_types.h" #include "reaxc_allocate.h" -#include "reaxc_control.h" -#include "reaxc_ffield.h" #include "reaxc_forces_omp.h" #include "reaxc_init_md_omp.h" #include "reaxc_io_tools.h" #include "reaxc_list.h" -#include "reaxc_lookup.h" #include "reaxc_reset_tools.h" #include "reaxc_tool_box.h" -#include "reaxc_traj.h" -#include "reaxc_vector.h" -#include "fix_reaxc_bonds.h" #if defined(_OPENMP) #include #endif +#include "suffix.h" using namespace LAMMPS_NS; #ifdef OMP_TIMING diff --git a/src/accelerator_kokkos.h b/src/accelerator_kokkos.h index 74bd470572..a3fff2fe16 100644 --- a/src/accelerator_kokkos.h +++ b/src/accelerator_kokkos.h @@ -19,14 +19,14 @@ #ifdef LMP_KOKKOS -#include "kokkos.h" -#include "atom_kokkos.h" -#include "comm_kokkos.h" -#include "comm_tiled_kokkos.h" -#include "domain_kokkos.h" -#include "neighbor_kokkos.h" -#include "memory_kokkos.h" -#include "modify_kokkos.h" +#include "kokkos.h" // IWYU pragma: export +#include "atom_kokkos.h" // IWYU pragma: export +#include "comm_kokkos.h" // IWYU pragma: export +#include "comm_tiled_kokkos.h" // IWYU pragma: export +#include "domain_kokkos.h" // IWYU pragma: export +#include "neighbor_kokkos.h" // IWYU pragma: export +#include "memory_kokkos.h" // IWYU pragma: export +#include "modify_kokkos.h" // IWYU pragma: export #define LAMMPS_INLINE KOKKOS_INLINE_FUNCTION diff --git a/src/finish.cpp b/src/finish.cpp index bef3ae89eb..9ab97ae410 100644 --- a/src/finish.cpp +++ b/src/finish.cpp @@ -16,8 +16,6 @@ #include #include #include -#include "timer.h" -#include "universe.h" #include "accelerator_kokkos.h" #include "atom.h" #include "atom_vec.h" @@ -32,6 +30,8 @@ #include "neigh_request.h" #include "memory.h" #include "error.h" +#include "timer.h" +#include "universe.h" #ifdef LMP_USER_OMP #include "modify.h" -- GitLab From 3d157e5ab4c7f8481ec2170ff3d557f0bd1b37cc Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Fri, 12 Jul 2019 18:00:59 -0400 Subject: [PATCH 249/469] more include handling cleanup in USER packages --- src/USER-DRUDE/fix_drude_transform.cpp | 1 + src/USER-DRUDE/fix_langevin_drude.cpp | 1 + src/USER-EFF/compute_temp_eff.cpp | 1 + src/USER-LB/fix_lb_fluid.cpp | 5 ++--- src/USER-LB/fix_lb_momentum.cpp | 5 ++--- src/USER-LB/fix_lb_pc.cpp | 5 +---- src/USER-LB/fix_lb_rigid_pc_sphere.cpp | 7 ++----- src/USER-LB/fix_lb_viscous.cpp | 4 +--- src/USER-MGPT/pair_mgpt.h | 2 -- src/USER-MOLFILE/dump_molfile.cpp | 5 ++--- src/USER-MOLFILE/reader_molfile.cpp | 4 +--- src/USER-OMP/fix_qeq_reax_omp.cpp | 1 + src/USER-OMP/pair_reaxc_omp.h | 1 - src/USER-OMP/reaxc_bond_orders_omp.cpp | 3 +++ src/USER-OMP/reaxc_bonds_omp.cpp | 7 +++---- src/USER-OMP/reaxc_forces_omp.cpp | 7 +++---- src/USER-OMP/reaxc_forces_omp.h | 1 - src/USER-OMP/reaxc_hydrogen_bonds_omp.cpp | 4 +++- src/USER-OMP/reaxc_init_md_omp.cpp | 7 ++----- src/USER-OMP/reaxc_torsion_angles_omp.cpp | 5 ++--- src/USER-PTM/ptm_index.cpp | 1 + src/USER-PTM/ptm_initialize_data.cpp | 4 ++++ src/USER-PTM/ptm_initialize_data.h | 4 ---- 23 files changed, 36 insertions(+), 49 deletions(-) diff --git a/src/USER-DRUDE/fix_drude_transform.cpp b/src/USER-DRUDE/fix_drude_transform.cpp index 8e85f1dffd..4128c508d6 100644 --- a/src/USER-DRUDE/fix_drude_transform.cpp +++ b/src/USER-DRUDE/fix_drude_transform.cpp @@ -13,6 +13,7 @@ /** Fix Drude Transform ******************************************************/ #include "fix_drude_transform.h" +#include #include #include #include "fix_drude.h" diff --git a/src/USER-DRUDE/fix_langevin_drude.cpp b/src/USER-DRUDE/fix_langevin_drude.cpp index 1a16c3df96..d413c31bd7 100644 --- a/src/USER-DRUDE/fix_langevin_drude.cpp +++ b/src/USER-DRUDE/fix_langevin_drude.cpp @@ -12,6 +12,7 @@ ------------------------------------------------------------------------- */ #include "fix_langevin_drude.h" +#include #include #include #include "fix_drude.h" diff --git a/src/USER-EFF/compute_temp_eff.cpp b/src/USER-EFF/compute_temp_eff.cpp index 8e07e390fa..e9295ea680 100644 --- a/src/USER-EFF/compute_temp_eff.cpp +++ b/src/USER-EFF/compute_temp_eff.cpp @@ -17,6 +17,7 @@ #include "compute_temp_eff.h" #include +#include #include "atom.h" #include "update.h" #include "force.h" diff --git a/src/USER-LB/fix_lb_fluid.cpp b/src/USER-LB/fix_lb_fluid.cpp index 31c54aee76..8ad3dbe33e 100644 --- a/src/USER-LB/fix_lb_fluid.cpp +++ b/src/USER-LB/fix_lb_fluid.cpp @@ -20,15 +20,14 @@ #include #include #include -#include #include +#include +#include #include "comm.h" #include "memory.h" #include "error.h" #include "domain.h" #include "atom.h" -#include -#include #include "group.h" #include "random_mars.h" #include "update.h" diff --git a/src/USER-LB/fix_lb_momentum.cpp b/src/USER-LB/fix_lb_momentum.cpp index df17561380..10fffed018 100644 --- a/src/USER-LB/fix_lb_momentum.cpp +++ b/src/USER-LB/fix_lb_momentum.cpp @@ -18,16 +18,15 @@ Contributing author: Naveen Michaud-Agrawal (Johns Hopkins U) ------------------------------------------------------------------------- */ +#include "fix_lb_momentum.h" +#include #include #include -#include "fix_lb_momentum.h" #include "atom.h" -#include "domain.h" #include "group.h" #include "error.h" #include "fix_lb_fluid.h" #include "modify.h" -#include "comm.h" using namespace LAMMPS_NS; using namespace FixConst; diff --git a/src/USER-LB/fix_lb_pc.cpp b/src/USER-LB/fix_lb_pc.cpp index ce6ca0c9a1..d61692419a 100644 --- a/src/USER-LB/fix_lb_pc.cpp +++ b/src/USER-LB/fix_lb_pc.cpp @@ -15,17 +15,14 @@ Contributing authors: Frances Mackay, Santtu Ollila, Colin Denniston (UWO) ------------------------------------------------------------------------- */ +#include "fix_lb_pc.h" #include -#include #include -#include "fix_lb_pc.h" #include "atom.h" #include "force.h" #include "update.h" -#include "respa.h" #include "error.h" #include "memory.h" -#include "comm.h" #include "domain.h" #include "fix_lb_fluid.h" #include "modify.h" diff --git a/src/USER-LB/fix_lb_rigid_pc_sphere.cpp b/src/USER-LB/fix_lb_rigid_pc_sphere.cpp index 83dc751631..af1b01043d 100644 --- a/src/USER-LB/fix_lb_rigid_pc_sphere.cpp +++ b/src/USER-LB/fix_lb_rigid_pc_sphere.cpp @@ -16,21 +16,18 @@ Based on fix_rigid (version from 2008). ------------------------------------------------------------------------- */ +#include "fix_lb_rigid_pc_sphere.h" +#include #include -#include #include #include -#include "fix_lb_rigid_pc_sphere.h" #include "atom.h" -#include "atom_vec.h" #include "domain.h" #include "update.h" -#include "respa.h" #include "modify.h" #include "group.h" #include "comm.h" #include "force.h" -#include "output.h" #include "memory.h" #include "error.h" #include "fix_lb_fluid.h" diff --git a/src/USER-LB/fix_lb_viscous.cpp b/src/USER-LB/fix_lb_viscous.cpp index afe23477be..59fddebd67 100644 --- a/src/USER-LB/fix_lb_viscous.cpp +++ b/src/USER-LB/fix_lb_viscous.cpp @@ -15,10 +15,8 @@ Contributing authors: Frances Mackay, Santtu Ollila, Colin Denniston (UWO) ------------------------------------------------------------------------- */ -#include -#include -#include #include "fix_lb_viscous.h" +#include #include "atom.h" #include "update.h" #include "respa.h" diff --git a/src/USER-MGPT/pair_mgpt.h b/src/USER-MGPT/pair_mgpt.h index 3e861a0198..ff71edc9f3 100644 --- a/src/USER-MGPT/pair_mgpt.h +++ b/src/USER-MGPT/pair_mgpt.h @@ -30,8 +30,6 @@ PairStyle(mgpt,PairMGPT) #ifndef LMP_PAIR_MGPT_H #define LMP_PAIR_MGPT_H -#include -#include #include #include diff --git a/src/USER-MOLFILE/dump_molfile.cpp b/src/USER-MOLFILE/dump_molfile.cpp index 732fea74bd..d9d8ec3c97 100644 --- a/src/USER-MOLFILE/dump_molfile.cpp +++ b/src/USER-MOLFILE/dump_molfile.cpp @@ -15,15 +15,14 @@ Contributing author: Axel Kohlmeyer (Temple U) ------------------------------------------------------------------------- */ -#include +#include "dump_molfile.h" +#include #include #include -#include "dump_molfile.h" #include "domain.h" #include "atom.h" #include "comm.h" #include "update.h" -#include "output.h" #include "group.h" #include "memory.h" #include "error.h" diff --git a/src/USER-MOLFILE/reader_molfile.cpp b/src/USER-MOLFILE/reader_molfile.cpp index ca1a61850c..5cff56753b 100644 --- a/src/USER-MOLFILE/reader_molfile.cpp +++ b/src/USER-MOLFILE/reader_molfile.cpp @@ -15,11 +15,9 @@ Contributing author: Axel Kohlmeyer (Temple U) ------------------------------------------------------------------------- */ -#include +#include "reader_molfile.h" #include #include -#include "reader_molfile.h" -#include "atom.h" #include "comm.h" #include "memory.h" #include "error.h" diff --git a/src/USER-OMP/fix_qeq_reax_omp.cpp b/src/USER-OMP/fix_qeq_reax_omp.cpp index 55e2b73812..f7945b5579 100644 --- a/src/USER-OMP/fix_qeq_reax_omp.cpp +++ b/src/USER-OMP/fix_qeq_reax_omp.cpp @@ -42,6 +42,7 @@ #include "memory.h" #include "error.h" #include "reaxc_defs.h" +#include "reaxc_types.h" #if defined(_OPENMP) #include diff --git a/src/USER-OMP/pair_reaxc_omp.h b/src/USER-OMP/pair_reaxc_omp.h index ad8c368aaf..0cae28f56b 100644 --- a/src/USER-OMP/pair_reaxc_omp.h +++ b/src/USER-OMP/pair_reaxc_omp.h @@ -22,7 +22,6 @@ PairStyle(reax/c/omp,PairReaxCOMP) #include "pair_reaxc.h" #include "thr_omp.h" -#include "suffix.h" namespace LAMMPS_NS { diff --git a/src/USER-OMP/reaxc_bond_orders_omp.cpp b/src/USER-OMP/reaxc_bond_orders_omp.cpp index 17715c6e26..d581819e00 100644 --- a/src/USER-OMP/reaxc_bond_orders_omp.cpp +++ b/src/USER-OMP/reaxc_bond_orders_omp.cpp @@ -27,6 +27,9 @@ ----------------------------------------------------------------------*/ #include "reaxc_bond_orders_omp.h" +#include +#include +#include "fix_omp.h" #include "reaxc_defs.h" #include "pair_reaxc_omp.h" #include "reaxc_types.h" diff --git a/src/USER-OMP/reaxc_bonds_omp.cpp b/src/USER-OMP/reaxc_bonds_omp.cpp index 12ba1dcbfe..b6a76b3f3a 100644 --- a/src/USER-OMP/reaxc_bonds_omp.cpp +++ b/src/USER-OMP/reaxc_bonds_omp.cpp @@ -27,13 +27,12 @@ ----------------------------------------------------------------------*/ #include "reaxc_bonds_omp.h" +#include +#include +#include "fix_omp.h" #include "reaxc_defs.h" -#include "reaxc_bond_orders_omp.h" #include "pair_reaxc_omp.h" - #include "reaxc_list.h" -#include "reaxc_tool_box.h" -#include "reaxc_vector.h" #if defined(_OPENMP) #include diff --git a/src/USER-OMP/reaxc_forces_omp.cpp b/src/USER-OMP/reaxc_forces_omp.cpp index 1ada5e7e71..971667cc2d 100644 --- a/src/USER-OMP/reaxc_forces_omp.cpp +++ b/src/USER-OMP/reaxc_forces_omp.cpp @@ -27,19 +27,18 @@ ----------------------------------------------------------------------*/ #include "reaxc_forces_omp.h" +#include +#include +#include "fix_omp.h" #include "reaxc_defs.h" #include "pair_reaxc_omp.h" -#include "thr_data.h" #include "reaxc_bond_orders_omp.h" #include "reaxc_bonds_omp.h" #include "reaxc_hydrogen_bonds_omp.h" -#include "reaxc_io_tools.h" #include "reaxc_list.h" -#include "reaxc_lookup.h" #include "reaxc_multi_body_omp.h" #include "reaxc_nonbonded_omp.h" -#include "reaxc_tool_box.h" #include "reaxc_torsion_angles_omp.h" #include "reaxc_valence_angles_omp.h" #include "reaxc_vector.h" diff --git a/src/USER-OMP/reaxc_forces_omp.h b/src/USER-OMP/reaxc_forces_omp.h index d1e2a5c65a..6df0288656 100644 --- a/src/USER-OMP/reaxc_forces_omp.h +++ b/src/USER-OMP/reaxc_forces_omp.h @@ -30,7 +30,6 @@ #define __FORCES_OMP_H_ #include "reaxc_types.h" -#include "reaxc_defs.h" void Init_Force_FunctionsOMP( control_params* ); void Compute_ForcesOMP( reax_system*, control_params*, simulation_data*, diff --git a/src/USER-OMP/reaxc_hydrogen_bonds_omp.cpp b/src/USER-OMP/reaxc_hydrogen_bonds_omp.cpp index e3c034a12e..d06966a92d 100644 --- a/src/USER-OMP/reaxc_hydrogen_bonds_omp.cpp +++ b/src/USER-OMP/reaxc_hydrogen_bonds_omp.cpp @@ -27,9 +27,11 @@ ----------------------------------------------------------------------*/ #include "reaxc_hydrogen_bonds_omp.h" +#include +#include +#include "fix_omp.h" #include "pair_reaxc_omp.h" #include "reaxc_defs.h" -#include "reaxc_bond_orders_omp.h" #include "reaxc_list.h" #include "reaxc_valence_angles.h" // To access Calculate_Theta() #include "reaxc_valence_angles_omp.h" // To access Calculate_dCos_ThetaOMP() diff --git a/src/USER-OMP/reaxc_init_md_omp.cpp b/src/USER-OMP/reaxc_init_md_omp.cpp index 847e916666..9d40479ddf 100644 --- a/src/USER-OMP/reaxc_init_md_omp.cpp +++ b/src/USER-OMP/reaxc_init_md_omp.cpp @@ -27,18 +27,15 @@ ----------------------------------------------------------------------*/ #include "reaxc_init_md_omp.h" -#include "pair_reaxc_omp.h" +#include #include "reaxc_defs.h" -#include "reaxc_allocate.h" #include "reaxc_forces.h" #include "reaxc_forces_omp.h" #include "reaxc_io_tools.h" #include "reaxc_list.h" #include "reaxc_lookup.h" -#include "reaxc_reset_tools.h" -#include "reaxc_system_props.h" #include "reaxc_tool_box.h" -#include "reaxc_vector.h" +#include "error.h" // Functions defined in reaxc_init_md.cpp extern int Init_MPI_Datatypes(reax_system*, storage*, mpi_datatypes*, MPI_Comm, char*); diff --git a/src/USER-OMP/reaxc_torsion_angles_omp.cpp b/src/USER-OMP/reaxc_torsion_angles_omp.cpp index 9cd716b594..68bacb7202 100644 --- a/src/USER-OMP/reaxc_torsion_angles_omp.cpp +++ b/src/USER-OMP/reaxc_torsion_angles_omp.cpp @@ -27,14 +27,13 @@ ----------------------------------------------------------------------*/ #include "reaxc_torsion_angles_omp.h" +#include +#include "fix_omp.h" #include "pair_reaxc_omp.h" -#include "thr_data.h" #include "reaxc_defs.h" #include "reaxc_types.h" -#include "reaxc_bond_orders_omp.h" #include "reaxc_list.h" -#include "reaxc_tool_box.h" #include "reaxc_vector.h" #if defined(_OPENMP) diff --git a/src/USER-PTM/ptm_index.cpp b/src/USER-PTM/ptm_index.cpp index b50e5c4333..cedd35126d 100644 --- a/src/USER-PTM/ptm_index.cpp +++ b/src/USER-PTM/ptm_index.cpp @@ -22,6 +22,7 @@ THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLI #include #include #include +#include static double calculate_interatomic_distance(int type, double scale) { assert(type >= 1 && type <= 8); diff --git a/src/USER-PTM/ptm_initialize_data.cpp b/src/USER-PTM/ptm_initialize_data.cpp index 1f0a5c94af..ff8245fe44 100644 --- a/src/USER-PTM/ptm_initialize_data.cpp +++ b/src/USER-PTM/ptm_initialize_data.cpp @@ -8,6 +8,10 @@ THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLI */ #include "ptm_initialize_data.h" +#include "ptm_canonical_coloured.h" +#include "ptm_convex_hull_incremental.h" +#include "ptm_graph_tools.h" +#include "ptm_neighbour_ordering.h" #include diff --git a/src/USER-PTM/ptm_initialize_data.h b/src/USER-PTM/ptm_initialize_data.h index 20c9921962..4e7f3e8f0a 100644 --- a/src/USER-PTM/ptm_initialize_data.h +++ b/src/USER-PTM/ptm_initialize_data.h @@ -12,12 +12,8 @@ THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLI #include "ptm_graph_data.h" -#include "ptm_graph_tools.h" #include "ptm_deformation_gradient.h" #include "ptm_fundamental_mappings.h" -#include "ptm_neighbour_ordering.h" -#include "ptm_canonical_coloured.h" -#include "ptm_convex_hull_incremental.h" #include "ptm_alt_templates.h" -- GitLab From 226e68a784ca00aaa69db53ef91a4a847a877216 Mon Sep 17 00:00:00 2001 From: Andrew Schultz Date: Fri, 12 Jul 2019 22:42:23 -0400 Subject: [PATCH 250/469] Rename Pair::pairTensor() => Pair::hessian_twobody() --- src/pair.cpp | 2 +- src/pair.h | 2 +- src/pair_lj_smooth_linear.cpp | 2 +- 3 files changed, 3 insertions(+), 3 deletions(-) diff --git a/src/pair.cpp b/src/pair.cpp index 43fc9bc907..ea2ad9509e 100644 --- a/src/pair.cpp +++ b/src/pair.cpp @@ -1746,7 +1746,7 @@ void Pair::init_bitmap(double inner, double outer, int ntablebits, /* ---------------------------------------------------------------------- */ -void Pair::pairTensor(double fforce, double dfac, double delr[3], double phiTensor[6]) { +void Pair::hessian_twobody(double fforce, double dfac, double delr[3], double phiTensor[6]) { int m = 0; for (int k=0; k<3; k++) { phiTensor[m] = fforce; diff --git a/src/pair.h b/src/pair.h index d85b9af0c3..38772d2f5d 100644 --- a/src/pair.h +++ b/src/pair.h @@ -149,7 +149,7 @@ class Pair : protected Pointers { return 0.0; } - void pairTensor(double fforce, double dfac, double delr[3], double phiTensor[6]); + void hessian_twobody(double fforce, double dfac, double delr[3], double phiTensor[6]); virtual double single_hessian(int, int, int, int, double, double[3], double, double, diff --git a/src/pair_lj_smooth_linear.cpp b/src/pair_lj_smooth_linear.cpp index 3ebdda4143..8d77436780 100644 --- a/src/pair_lj_smooth_linear.cpp +++ b/src/pair_lj_smooth_linear.cpp @@ -368,6 +368,6 @@ double PairLJSmoothLinear::single_hessian(int /*i*/, int /*j*/, int itype, int j + (r-cut[itype][jtype])*dljcut[itype][jtype]; double d2r = factor_lj * r6inv * (13.0*lj1[itype][jtype]*r6inv - 7.0*lj2[itype][jtype])/rsq; - pairTensor(fforce, -(fforce + d2r) / rsq, delr, d2u); + hessian_twobody(fforce, -(fforce + d2r) / rsq, delr, d2u); return factor_lj*philj; } -- GitLab From 2a04e41287dd9b86e5fcce026da8bef296933481 Mon Sep 17 00:00:00 2001 From: Andrew Schultz Date: Fri, 12 Jul 2019 22:43:05 -0400 Subject: [PATCH 251/469] Add pointers between doc pages for compute hma and dynamical matrix --- doc/src/compute_hma.txt | 6 +++++- doc/src/dynamical_matrix.txt | 3 +++ 2 files changed, 8 insertions(+), 1 deletion(-) diff --git a/doc/src/compute_hma.txt b/doc/src/compute_hma.txt index 35a92664df..863ee86159 100644 --- a/doc/src/compute_hma.txt +++ b/doc/src/compute_hma.txt @@ -159,7 +159,7 @@ scalar value will be in energy "units"_units.html. [Restrictions:] -This compute is distributed as the USER-HMA package. It is only +This compute is part of the USER-MISC package. It is only enabled if LAMMPS was built with that package. See the "Build package"_Build_package.html doc page for more info. @@ -169,6 +169,10 @@ Usage restricted to canonical (NVT) ensemble simulation only. "compute pe"_compute_pe.html, "compute pressure"_compute_pressure.html +"dynamical matrix"_dynamical_matrix.html provides a finite difference +formulation of the hessian provided by Pair's single_hessian, which is used by +this compute. + [Default:] none :line diff --git a/doc/src/dynamical_matrix.txt b/doc/src/dynamical_matrix.txt index a7dc4e442e..6291bdec52 100644 --- a/doc/src/dynamical_matrix.txt +++ b/doc/src/dynamical_matrix.txt @@ -47,6 +47,9 @@ package"_Build_package.html doc page for more info. "fix phonon"_fix_phonon.html +"compute hma"_compute_hma.html uses an analytic formulation of the hessian +provided by Pair's single_hessian. + [Default:] The default settings are file = "dynmat.dyn", binary = no -- GitLab From 2b5a6d3b7fe4cd96240c9970aa0ce089c318f8f5 Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Mon, 15 Jul 2019 18:05:20 -0400 Subject: [PATCH 252/469] clean up (some) includes in KOKKOS package --- src/KOKKOS/fix_dpd_energy_kokkos.cpp | 5 ----- src/KOKKOS/fix_eos_table_rx_kokkos.cpp | 3 --- src/KOKKOS/fix_langevin_kokkos.cpp | 7 ++----- src/KOKKOS/fix_qeq_reax_kokkos.cpp | 7 ------- src/KOKKOS/fix_reaxc_bonds_kokkos.cpp | 13 ------------- src/KOKKOS/fix_reaxc_species_kokkos.cpp | 10 ---------- src/KOKKOS/fix_rx_kokkos.cpp | 2 -- src/KOKKOS/fix_setforce_kokkos.cpp | 4 +--- src/KOKKOS/fix_setforce_kokkos.h | 3 +-- src/KOKKOS/fix_shardlow_kokkos.cpp | 10 +--------- src/KOKKOS/improper_class2_kokkos.cpp | 7 ------- src/KOKKOS/improper_harmonic_kokkos.cpp | 6 ------ src/KOKKOS/nbin_ssa_kokkos.cpp | 3 --- src/KOKKOS/npair_copy_kokkos.cpp | 7 ------- src/KOKKOS/npair_skip_kokkos.cpp | 4 ---- src/KOKKOS/pair_buck_coul_cut_kokkos.cpp | 4 ---- src/KOKKOS/pair_buck_coul_long_kokkos.cpp | 6 ------ src/KOKKOS/pair_buck_kokkos.cpp | 6 ------ src/KOKKOS/pair_coul_cut_kokkos.cpp | 9 --------- src/KOKKOS/pair_coul_debye_kokkos.cpp | 6 ------ src/KOKKOS/pair_coul_dsf_kokkos.cpp | 7 ------- src/KOKKOS/pair_coul_long_kokkos.cpp | 6 ------ src/KOKKOS/pair_coul_wolf_kokkos.cpp | 7 ------- src/KOKKOS/pair_dpd_fdt_energy_kokkos.cpp | 6 ------ src/KOKKOS/pair_eam_alloy_kokkos.cpp | 2 -- src/KOKKOS/pair_eam_fs_kokkos.cpp | 2 -- src/KOKKOS/pair_eam_kokkos.cpp | 3 --- src/KOKKOS/pair_exp6_rx_kokkos.cpp | 4 ---- src/KOKKOS/pair_hybrid_kokkos.cpp | 5 ----- src/KOKKOS/pair_hybrid_overlay_kokkos.cpp | 3 --- .../pair_lj_charmm_coul_charmm_implicit_kokkos.cpp | 7 ------- src/KOKKOS/pair_lj_charmm_coul_charmm_kokkos.cpp | 6 ------ src/KOKKOS/pair_lj_charmm_coul_long_kokkos.cpp | 6 ------ src/KOKKOS/pair_lj_class2_coul_cut_kokkos.cpp | 5 ----- src/KOKKOS/pair_lj_class2_coul_long_kokkos.cpp | 6 ------ src/KOKKOS/pair_lj_class2_kokkos.cpp | 6 ------ src/KOKKOS/pair_lj_cut_coul_cut_kokkos.cpp | 6 ------ src/KOKKOS/pair_lj_cut_coul_debye_kokkos.cpp | 6 ------ src/KOKKOS/pair_lj_cut_coul_dsf_kokkos.cpp | 4 ---- src/KOKKOS/pair_lj_cut_coul_long_kokkos.cpp | 4 ---- src/KOKKOS/pair_lj_cut_kokkos.cpp | 7 ------- src/KOKKOS/pair_lj_expand_kokkos.cpp | 6 ------ src/KOKKOS/pair_lj_gromacs_coul_gromacs_kokkos.cpp | 6 ------ src/KOKKOS/pair_lj_gromacs_kokkos.cpp | 6 ------ src/KOKKOS/pair_lj_sdk_kokkos.cpp | 5 ----- src/KOKKOS/pair_morse_kokkos.cpp | 4 ---- src/KOKKOS/pair_multi_lucy_rx_kokkos.cpp | 5 ----- src/KOKKOS/pair_reaxc_kokkos.cpp | 5 ----- src/KOKKOS/pair_sw_kokkos.cpp | 4 ---- src/KOKKOS/pair_table_kokkos.cpp | 4 ---- src/KOKKOS/pair_table_rx_kokkos.cpp | 1 - src/KOKKOS/pair_tersoff_kokkos.cpp | 6 ------ src/KOKKOS/pair_tersoff_mod_kokkos.cpp | 6 ------ src/KOKKOS/pair_tersoff_zbl_kokkos.cpp | 4 ---- src/KOKKOS/pair_vashishta_kokkos.cpp | 4 ---- src/KOKKOS/pair_yukawa_kokkos.cpp | 5 ----- src/KOKKOS/pair_zbl_kokkos.cpp | 6 ------ src/KOKKOS/pppm_kokkos.cpp | 5 ----- src/KOKKOS/region_block_kokkos.cpp | 4 ---- src/KOKKOS/verlet_kokkos.cpp | 7 ------- 60 files changed, 5 insertions(+), 318 deletions(-) diff --git a/src/KOKKOS/fix_dpd_energy_kokkos.cpp b/src/KOKKOS/fix_dpd_energy_kokkos.cpp index debad0407a..20579a6dc5 100644 --- a/src/KOKKOS/fix_dpd_energy_kokkos.cpp +++ b/src/KOKKOS/fix_dpd_energy_kokkos.cpp @@ -12,14 +12,9 @@ ------------------------------------------------------------------------- */ #include "fix_dpd_energy_kokkos.h" -#include -#include #include "atom_masks.h" #include "atom_kokkos.h" -#include "force.h" #include "update.h" -#include "respa.h" -#include "modify.h" #include "error.h" using namespace LAMMPS_NS; diff --git a/src/KOKKOS/fix_eos_table_rx_kokkos.cpp b/src/KOKKOS/fix_eos_table_rx_kokkos.cpp index d0280eeef0..89561c9a92 100644 --- a/src/KOKKOS/fix_eos_table_rx_kokkos.cpp +++ b/src/KOKKOS/fix_eos_table_rx_kokkos.cpp @@ -16,15 +16,12 @@ ------------------------------------------------------------------------- */ #include "fix_eos_table_rx_kokkos.h" -#include -#include #include "atom_kokkos.h" #include "error.h" #include "force.h" #include "memory_kokkos.h" #include "comm.h" #include -#include "modify.h" #include "atom_masks.h" #define MAXLINE 1024 diff --git a/src/KOKKOS/fix_langevin_kokkos.cpp b/src/KOKKOS/fix_langevin_kokkos.cpp index 23a43b38ef..651f790a25 100644 --- a/src/KOKKOS/fix_langevin_kokkos.cpp +++ b/src/KOKKOS/fix_langevin_kokkos.cpp @@ -13,21 +13,18 @@ #include "fix_langevin_kokkos.h" #include -#include -#include #include "atom_masks.h" #include "atom_kokkos.h" #include "force.h" +#include "group.h" #include "update.h" -#include "respa.h" #include "error.h" #include "memory_kokkos.h" -#include "group.h" -#include "random_mars.h" #include "compute.h" #include "comm.h" #include "modify.h" #include "input.h" +#include "region.h" #include "variable.h" using namespace LAMMPS_NS; diff --git a/src/KOKKOS/fix_qeq_reax_kokkos.cpp b/src/KOKKOS/fix_qeq_reax_kokkos.cpp index 6f8392ab16..e51fbacaaf 100644 --- a/src/KOKKOS/fix_qeq_reax_kokkos.cpp +++ b/src/KOKKOS/fix_qeq_reax_kokkos.cpp @@ -18,24 +18,17 @@ #include "fix_qeq_reax_kokkos.h" #include -#include -#include -#include #include "kokkos.h" #include "atom.h" #include "atom_masks.h" #include "atom_kokkos.h" #include "comm.h" #include "force.h" -#include "group.h" -#include "modify.h" #include "neighbor.h" #include "neigh_list_kokkos.h" #include "neigh_request.h" #include "update.h" #include "integrate.h" -#include "respa.h" -#include "math_const.h" #include "memory_kokkos.h" #include "error.h" #include "pair_reaxc_kokkos.h" diff --git a/src/KOKKOS/fix_reaxc_bonds_kokkos.cpp b/src/KOKKOS/fix_reaxc_bonds_kokkos.cpp index 347c477476..51702bc603 100644 --- a/src/KOKKOS/fix_reaxc_bonds_kokkos.cpp +++ b/src/KOKKOS/fix_reaxc_bonds_kokkos.cpp @@ -15,26 +15,13 @@ Contributing author: Stan Moore (Sandia) ------------------------------------------------------------------------- */ -#include "fix_ave_atom.h" -#include -#include #include "fix_reaxc_bonds_kokkos.h" #include "atom.h" -#include "update.h" #include "pair_reaxc_kokkos.h" -#include "modify.h" -#include "neighbor.h" -#include "neigh_list.h" -#include "neigh_request.h" -#include "comm.h" #include "force.h" #include "compute.h" -#include "input.h" -#include "variable.h" #include "memory_kokkos.h" #include "error.h" -#include "reaxc_list.h" -#include "reaxc_types.h" #include "reaxc_defs.h" #include "atom_masks.h" diff --git a/src/KOKKOS/fix_reaxc_species_kokkos.cpp b/src/KOKKOS/fix_reaxc_species_kokkos.cpp index f32bea2c67..f3bce2f9c0 100644 --- a/src/KOKKOS/fix_reaxc_species_kokkos.cpp +++ b/src/KOKKOS/fix_reaxc_species_kokkos.cpp @@ -16,27 +16,17 @@ ------------------------------------------------------------------------- */ #include "fix_reaxc_species_kokkos.h" -#include -#include #include "atom.h" -#include #include "fix_ave_atom.h" -#include "domain.h" -#include "update.h" #include "reaxc_defs.h" #include "pair_reaxc_kokkos.h" -#include "modify.h" -#include "neighbor.h" #include "neigh_list.h" #include "neigh_request.h" #include "comm.h" #include "force.h" -#include "compute.h" #include "input.h" -#include "variable.h" #include "memory_kokkos.h" #include "error.h" -#include "reaxc_list.h" #include "atom_masks.h" using namespace LAMMPS_NS; diff --git a/src/KOKKOS/fix_rx_kokkos.cpp b/src/KOKKOS/fix_rx_kokkos.cpp index 050dda2400..e06fc14585 100644 --- a/src/KOKKOS/fix_rx_kokkos.cpp +++ b/src/KOKKOS/fix_rx_kokkos.cpp @@ -12,14 +12,12 @@ ------------------------------------------------------------------------- */ #include "fix_rx_kokkos.h" -#include #include #include "atom_masks.h" #include "atom_kokkos.h" #include "force.h" #include "memory_kokkos.h" #include "update.h" -#include "respa.h" #include "modify.h" #include "neighbor.h" #include "neigh_list_kokkos.h" diff --git a/src/KOKKOS/fix_setforce_kokkos.cpp b/src/KOKKOS/fix_setforce_kokkos.cpp index 03cfd3afb2..4165b100f5 100644 --- a/src/KOKKOS/fix_setforce_kokkos.cpp +++ b/src/KOKKOS/fix_setforce_kokkos.cpp @@ -13,20 +13,18 @@ #include "fix_setforce_kokkos.h" #include -#include #include "atom_kokkos.h" #include "update.h" #include "modify.h" #include "domain.h" #include "region.h" -#include "respa.h" #include "input.h" #include "variable.h" #include "memory_kokkos.h" #include "error.h" -#include "force.h" #include "atom_masks.h" #include "kokkos_base.h" +#include "region.h" using namespace LAMMPS_NS; using namespace FixConst; diff --git a/src/KOKKOS/fix_setforce_kokkos.h b/src/KOKKOS/fix_setforce_kokkos.h index 3cbf3d3720..ecbfd71e36 100644 --- a/src/KOKKOS/fix_setforce_kokkos.h +++ b/src/KOKKOS/fix_setforce_kokkos.h @@ -23,7 +23,6 @@ FixStyle(setforce/kk/host,FixSetForceKokkos) #define LMP_FIX_SET_FORCE_KOKKOS_H #include "fix_setforce.h" -#include "region.h" #include "kokkos_type.h" namespace LAMMPS_NS { @@ -82,7 +81,7 @@ class FixSetForceKokkos : public FixSetForce { typename AT::t_f_array f; typename AT::t_int_1d_randomread mask; - Region* region; + class Region* region; }; } diff --git a/src/KOKKOS/fix_shardlow_kokkos.cpp b/src/KOKKOS/fix_shardlow_kokkos.cpp index 96f67ccb5e..9bd8594341 100644 --- a/src/KOKKOS/fix_shardlow_kokkos.cpp +++ b/src/KOKKOS/fix_shardlow_kokkos.cpp @@ -34,30 +34,22 @@ ------------------------------------------------------------------------- */ #include "fix_shardlow_kokkos.h" -#include +#include #include -#include #include "atom.h" #include "atom_masks.h" #include "atom_kokkos.h" #include "force.h" #include "update.h" -#include "respa.h" #include "error.h" -#include -#include "atom_vec.h" #include "comm.h" #include "neighbor.h" #include "neigh_list_kokkos.h" #include "neigh_request.h" #include "memory_kokkos.h" #include "domain.h" -#include "modify.h" -// #include "pair_dpd_fdt.h" #include "pair_dpd_fdt_energy_kokkos.h" -#include "pair.h" #include "npair_ssa_kokkos.h" -#include "citeme.h" using namespace LAMMPS_NS; using namespace FixConst; diff --git a/src/KOKKOS/improper_class2_kokkos.cpp b/src/KOKKOS/improper_class2_kokkos.cpp index 84b721bd2a..defd5e16f5 100644 --- a/src/KOKKOS/improper_class2_kokkos.cpp +++ b/src/KOKKOS/improper_class2_kokkos.cpp @@ -16,22 +16,15 @@ ------------------------------------------------------------------------- */ #include "improper_class2_kokkos.h" -#include #include -#include #include "atom_kokkos.h" -#include "comm.h" #include "neighbor_kokkos.h" -#include "domain.h" #include "force.h" -#include "update.h" -#include "math_const.h" #include "memory_kokkos.h" #include "error.h" #include "atom_masks.h" using namespace LAMMPS_NS; -using namespace MathConst; #define TOLERANCE 0.05 #define SMALL 0.001 diff --git a/src/KOKKOS/improper_harmonic_kokkos.cpp b/src/KOKKOS/improper_harmonic_kokkos.cpp index 262ffe7700..7d6437dbf5 100644 --- a/src/KOKKOS/improper_harmonic_kokkos.cpp +++ b/src/KOKKOS/improper_harmonic_kokkos.cpp @@ -16,22 +16,16 @@ ------------------------------------------------------------------------- */ #include "improper_harmonic_kokkos.h" -#include #include -#include #include "atom_kokkos.h" #include "comm.h" #include "neighbor_kokkos.h" -#include "domain.h" #include "force.h" -#include "update.h" -#include "math_const.h" #include "memory_kokkos.h" #include "error.h" #include "atom_masks.h" using namespace LAMMPS_NS; -using namespace MathConst; #define TOLERANCE 0.05 #define SMALL 0.001 diff --git a/src/KOKKOS/nbin_ssa_kokkos.cpp b/src/KOKKOS/nbin_ssa_kokkos.cpp index ecf0e08535..0e46f7fc61 100644 --- a/src/KOKKOS/nbin_ssa_kokkos.cpp +++ b/src/KOKKOS/nbin_ssa_kokkos.cpp @@ -19,11 +19,8 @@ #include "nbin_ssa_kokkos.h" #include "neighbor.h" #include "atom_kokkos.h" -#include "group.h" #include "domain.h" -#include "comm.h" #include "update.h" -#include "error.h" #include "atom_masks.h" // #include "memory_kokkos.h" diff --git a/src/KOKKOS/npair_copy_kokkos.cpp b/src/KOKKOS/npair_copy_kokkos.cpp index 7dde05745c..0ce0f4d3ff 100644 --- a/src/KOKKOS/npair_copy_kokkos.cpp +++ b/src/KOKKOS/npair_copy_kokkos.cpp @@ -12,14 +12,7 @@ ------------------------------------------------------------------------- */ #include "npair_copy_kokkos.h" -#include "neighbor.h" #include "neigh_list_kokkos.h" -#include "atom.h" -#include "atom_vec.h" -#include "molecule.h" -#include "domain.h" -#include "my_page.h" -#include "error.h" using namespace LAMMPS_NS; diff --git a/src/KOKKOS/npair_skip_kokkos.cpp b/src/KOKKOS/npair_skip_kokkos.cpp index e614e624c9..bb393c9b95 100644 --- a/src/KOKKOS/npair_skip_kokkos.cpp +++ b/src/KOKKOS/npair_skip_kokkos.cpp @@ -12,13 +12,9 @@ ------------------------------------------------------------------------- */ #include "npair_skip_kokkos.h" -#include "neighbor.h" #include "neigh_list_kokkos.h" #include "atom_kokkos.h" #include "atom_vec.h" -#include "molecule.h" -#include "domain.h" -#include "my_page.h" #include "error.h" #include "atom_masks.h" diff --git a/src/KOKKOS/pair_buck_coul_cut_kokkos.cpp b/src/KOKKOS/pair_buck_coul_cut_kokkos.cpp index e3843262a5..2a72617525 100644 --- a/src/KOKKOS/pair_buck_coul_cut_kokkos.cpp +++ b/src/KOKKOS/pair_buck_coul_cut_kokkos.cpp @@ -17,18 +17,14 @@ #include "pair_buck_coul_cut_kokkos.h" #include -#include -#include #include #include "kokkos.h" #include "atom_kokkos.h" -#include "comm.h" #include "force.h" #include "neighbor.h" #include "neigh_list.h" #include "neigh_request.h" #include "update.h" -#include "integrate.h" #include "respa.h" #include "math_const.h" #include "memory_kokkos.h" diff --git a/src/KOKKOS/pair_buck_coul_long_kokkos.cpp b/src/KOKKOS/pair_buck_coul_long_kokkos.cpp index 7457a0988f..fdf395684a 100644 --- a/src/KOKKOS/pair_buck_coul_long_kokkos.cpp +++ b/src/KOKKOS/pair_buck_coul_long_kokkos.cpp @@ -17,26 +17,20 @@ #include "pair_buck_coul_long_kokkos.h" #include -#include -#include #include #include "kokkos.h" #include "atom_kokkos.h" -#include "comm.h" #include "force.h" #include "neighbor.h" #include "neigh_list.h" #include "neigh_request.h" #include "update.h" -#include "integrate.h" #include "respa.h" -#include "math_const.h" #include "memory_kokkos.h" #include "error.h" #include "atom_masks.h" using namespace LAMMPS_NS; -using namespace MathConst; #define KOKKOS_CUDA_MAX_THREADS 256 #define KOKKOS_CUDA_MIN_BLOCKS 8 diff --git a/src/KOKKOS/pair_buck_kokkos.cpp b/src/KOKKOS/pair_buck_kokkos.cpp index 131622cac5..375d0dc1ea 100644 --- a/src/KOKKOS/pair_buck_kokkos.cpp +++ b/src/KOKKOS/pair_buck_kokkos.cpp @@ -17,26 +17,20 @@ #include "pair_buck_kokkos.h" #include -#include -#include #include #include "kokkos.h" #include "atom_kokkos.h" -#include "comm.h" #include "force.h" #include "neighbor.h" #include "neigh_list.h" #include "neigh_request.h" #include "update.h" -#include "integrate.h" #include "respa.h" -#include "math_const.h" #include "memory_kokkos.h" #include "error.h" #include "atom_masks.h" using namespace LAMMPS_NS; -using namespace MathConst; #define KOKKOS_CUDA_MAX_THREADS 256 #define KOKKOS_CUDA_MIN_BLOCKS 8 diff --git a/src/KOKKOS/pair_coul_cut_kokkos.cpp b/src/KOKKOS/pair_coul_cut_kokkos.cpp index e79f103363..5a1a6eefac 100644 --- a/src/KOKKOS/pair_coul_cut_kokkos.cpp +++ b/src/KOKKOS/pair_coul_cut_kokkos.cpp @@ -13,26 +13,17 @@ #include "pair_coul_cut_kokkos.h" #include -#include -#include -#include #include "kokkos.h" #include "atom_kokkos.h" -#include "comm.h" #include "force.h" #include "neighbor.h" #include "neigh_list.h" #include "neigh_request.h" -#include "update.h" -#include "integrate.h" -#include "respa.h" -#include "math_const.h" #include "memory_kokkos.h" #include "error.h" #include "atom_masks.h" using namespace LAMMPS_NS; -using namespace MathConst; #define KOKKOS_CUDA_MAX_THREADS 256 #define KOKKOS_CUDA_MIN_BLOCKS 8 diff --git a/src/KOKKOS/pair_coul_debye_kokkos.cpp b/src/KOKKOS/pair_coul_debye_kokkos.cpp index 0fe03af043..8dd7e4f3d2 100644 --- a/src/KOKKOS/pair_coul_debye_kokkos.cpp +++ b/src/KOKKOS/pair_coul_debye_kokkos.cpp @@ -17,26 +17,20 @@ #include "pair_coul_debye_kokkos.h" #include -#include -#include #include #include "kokkos.h" #include "atom_kokkos.h" -#include "comm.h" #include "force.h" #include "neighbor.h" #include "neigh_list.h" #include "neigh_request.h" #include "update.h" -#include "integrate.h" #include "respa.h" -#include "math_const.h" #include "memory_kokkos.h" #include "error.h" #include "atom_masks.h" using namespace LAMMPS_NS; -using namespace MathConst; #define KOKKOS_CUDA_MAX_THREADS 256 #define KOKKOS_CUDA_MIN_BLOCKS 8 diff --git a/src/KOKKOS/pair_coul_dsf_kokkos.cpp b/src/KOKKOS/pair_coul_dsf_kokkos.cpp index e94aae4754..836b12ba39 100644 --- a/src/KOKKOS/pair_coul_dsf_kokkos.cpp +++ b/src/KOKKOS/pair_coul_dsf_kokkos.cpp @@ -17,20 +17,13 @@ #include "pair_coul_dsf_kokkos.h" #include -#include -#include -#include #include "kokkos.h" #include "atom_kokkos.h" -#include "comm.h" #include "force.h" #include "neighbor.h" #include "neigh_list_kokkos.h" #include "neigh_request.h" #include "memory_kokkos.h" -#include "update.h" -#include "integrate.h" -#include "respa.h" #include "math_const.h" #include "error.h" #include "atom_masks.h" diff --git a/src/KOKKOS/pair_coul_long_kokkos.cpp b/src/KOKKOS/pair_coul_long_kokkos.cpp index 67132e11f6..84b89c6373 100644 --- a/src/KOKKOS/pair_coul_long_kokkos.cpp +++ b/src/KOKKOS/pair_coul_long_kokkos.cpp @@ -17,26 +17,20 @@ #include "pair_coul_long_kokkos.h" #include -#include -#include #include #include "kokkos.h" #include "atom_kokkos.h" -#include "comm.h" #include "force.h" #include "neighbor.h" #include "neigh_list.h" #include "neigh_request.h" #include "update.h" -#include "integrate.h" #include "respa.h" -#include "math_const.h" #include "memory_kokkos.h" #include "error.h" #include "atom_masks.h" using namespace LAMMPS_NS; -using namespace MathConst; #define KOKKOS_CUDA_MAX_THREADS 256 #define KOKKOS_CUDA_MIN_BLOCKS 8 diff --git a/src/KOKKOS/pair_coul_wolf_kokkos.cpp b/src/KOKKOS/pair_coul_wolf_kokkos.cpp index dbbb865961..3ca8f16a79 100644 --- a/src/KOKKOS/pair_coul_wolf_kokkos.cpp +++ b/src/KOKKOS/pair_coul_wolf_kokkos.cpp @@ -17,19 +17,12 @@ #include "pair_coul_wolf_kokkos.h" #include -#include -#include -#include #include "kokkos.h" #include "atom_kokkos.h" -#include "comm.h" #include "force.h" #include "neighbor.h" #include "neigh_list_kokkos.h" #include "neigh_request.h" -#include "update.h" -#include "integrate.h" -#include "respa.h" #include "math_const.h" #include "memory_kokkos.h" #include "error.h" diff --git a/src/KOKKOS/pair_dpd_fdt_energy_kokkos.cpp b/src/KOKKOS/pair_dpd_fdt_energy_kokkos.cpp index 27a7a59c2a..21fd32a2c8 100644 --- a/src/KOKKOS/pair_dpd_fdt_energy_kokkos.cpp +++ b/src/KOKKOS/pair_dpd_fdt_energy_kokkos.cpp @@ -17,20 +17,14 @@ #include "pair_dpd_fdt_energy_kokkos.h" #include -#include -#include -#include #include "atom_kokkos.h" -#include "atom_vec.h" #include "comm.h" #include "update.h" -#include "fix.h" #include "force.h" #include "neighbor.h" #include "neigh_list.h" #include "neigh_request.h" #include "memory_kokkos.h" -#include "modify.h" #include "error.h" #include "atom_masks.h" #include "kokkos.h" diff --git a/src/KOKKOS/pair_eam_alloy_kokkos.cpp b/src/KOKKOS/pair_eam_alloy_kokkos.cpp index aa33d44eee..48bf63386a 100644 --- a/src/KOKKOS/pair_eam_alloy_kokkos.cpp +++ b/src/KOKKOS/pair_eam_alloy_kokkos.cpp @@ -17,8 +17,6 @@ #include "pair_eam_alloy_kokkos.h" #include -#include -#include #include #include "kokkos.h" #include "pair_kokkos.h" diff --git a/src/KOKKOS/pair_eam_fs_kokkos.cpp b/src/KOKKOS/pair_eam_fs_kokkos.cpp index 9832a16a73..6536dd745a 100644 --- a/src/KOKKOS/pair_eam_fs_kokkos.cpp +++ b/src/KOKKOS/pair_eam_fs_kokkos.cpp @@ -17,8 +17,6 @@ #include "pair_eam_fs_kokkos.h" #include -#include -#include #include #include "kokkos.h" #include "pair_kokkos.h" diff --git a/src/KOKKOS/pair_eam_kokkos.cpp b/src/KOKKOS/pair_eam_kokkos.cpp index 4c6fadfe92..f6eef5b53c 100644 --- a/src/KOKKOS/pair_eam_kokkos.cpp +++ b/src/KOKKOS/pair_eam_kokkos.cpp @@ -17,9 +17,6 @@ #include "pair_eam_kokkos.h" #include -#include -#include -#include #include "kokkos.h" #include "pair_kokkos.h" #include "atom_kokkos.h" diff --git a/src/KOKKOS/pair_exp6_rx_kokkos.cpp b/src/KOKKOS/pair_exp6_rx_kokkos.cpp index 31a48fe154..8698687377 100644 --- a/src/KOKKOS/pair_exp6_rx_kokkos.cpp +++ b/src/KOKKOS/pair_exp6_rx_kokkos.cpp @@ -17,18 +17,15 @@ #include "pair_exp6_rx_kokkos.h" #include -#include #include #include #include "atom.h" #include "comm.h" #include "force.h" #include "neigh_list.h" -#include "math_const.h" #include "math_special_kokkos.h" #include "memory_kokkos.h" #include "error.h" -#include "modify.h" #include "fix.h" #include #include "atom_masks.h" @@ -41,7 +38,6 @@ #endif using namespace LAMMPS_NS; -using namespace MathConst; using namespace MathSpecialKokkos; #define MAXLINE 1024 diff --git a/src/KOKKOS/pair_hybrid_kokkos.cpp b/src/KOKKOS/pair_hybrid_kokkos.cpp index c767d9f470..b5b0a9d02b 100644 --- a/src/KOKKOS/pair_hybrid_kokkos.cpp +++ b/src/KOKKOS/pair_hybrid_kokkos.cpp @@ -12,19 +12,14 @@ ------------------------------------------------------------------------- */ #include "pair_hybrid_kokkos.h" -#include -#include #include -#include #include "atom_kokkos.h" #include "force.h" #include "pair.h" #include "neighbor.h" #include "neigh_request.h" #include "update.h" -#include "comm.h" #include "memory_kokkos.h" -#include "error.h" #include "respa.h" #include "atom_masks.h" #include "kokkos.h" diff --git a/src/KOKKOS/pair_hybrid_overlay_kokkos.cpp b/src/KOKKOS/pair_hybrid_overlay_kokkos.cpp index cb1389d38e..0cebd79c88 100644 --- a/src/KOKKOS/pair_hybrid_overlay_kokkos.cpp +++ b/src/KOKKOS/pair_hybrid_overlay_kokkos.cpp @@ -12,13 +12,10 @@ ------------------------------------------------------------------------- */ #include "pair_hybrid_overlay_kokkos.h" -#include #include #include #include "atom.h" #include "force.h" -#include "neighbor.h" -#include "neigh_request.h" #include "error.h" using namespace LAMMPS_NS; diff --git a/src/KOKKOS/pair_lj_charmm_coul_charmm_implicit_kokkos.cpp b/src/KOKKOS/pair_lj_charmm_coul_charmm_implicit_kokkos.cpp index b7c3766d5f..ae6cb61b60 100644 --- a/src/KOKKOS/pair_lj_charmm_coul_charmm_implicit_kokkos.cpp +++ b/src/KOKKOS/pair_lj_charmm_coul_charmm_implicit_kokkos.cpp @@ -16,27 +16,20 @@ ------------------------------------------------------------------------- */ #include "pair_lj_charmm_coul_charmm_implicit_kokkos.h" -#include -#include -#include #include #include "kokkos.h" #include "atom_kokkos.h" -#include "comm.h" #include "force.h" #include "neighbor.h" #include "neigh_list.h" #include "neigh_request.h" #include "update.h" -#include "integrate.h" #include "respa.h" -#include "math_const.h" #include "memory_kokkos.h" #include "error.h" #include "atom_masks.h" using namespace LAMMPS_NS; -using namespace MathConst; #define KOKKOS_CUDA_MAX_THREADS 256 #define KOKKOS_CUDA_MIN_BLOCKS 8 diff --git a/src/KOKKOS/pair_lj_charmm_coul_charmm_kokkos.cpp b/src/KOKKOS/pair_lj_charmm_coul_charmm_kokkos.cpp index c6a1e3211d..9cdef267e2 100644 --- a/src/KOKKOS/pair_lj_charmm_coul_charmm_kokkos.cpp +++ b/src/KOKKOS/pair_lj_charmm_coul_charmm_kokkos.cpp @@ -17,26 +17,20 @@ #include "pair_lj_charmm_coul_charmm_kokkos.h" #include -#include -#include #include #include "kokkos.h" #include "atom_kokkos.h" -#include "comm.h" #include "force.h" #include "neighbor.h" #include "neigh_list.h" #include "neigh_request.h" #include "update.h" -#include "integrate.h" #include "respa.h" -#include "math_const.h" #include "memory_kokkos.h" #include "error.h" #include "atom_masks.h" using namespace LAMMPS_NS; -using namespace MathConst; #define KOKKOS_CUDA_MAX_THREADS 256 #define KOKKOS_CUDA_MIN_BLOCKS 8 diff --git a/src/KOKKOS/pair_lj_charmm_coul_long_kokkos.cpp b/src/KOKKOS/pair_lj_charmm_coul_long_kokkos.cpp index 4ba0651601..441070248d 100644 --- a/src/KOKKOS/pair_lj_charmm_coul_long_kokkos.cpp +++ b/src/KOKKOS/pair_lj_charmm_coul_long_kokkos.cpp @@ -17,26 +17,20 @@ #include "pair_lj_charmm_coul_long_kokkos.h" #include -#include -#include #include #include "kokkos.h" #include "atom_kokkos.h" -#include "comm.h" #include "force.h" #include "neighbor.h" #include "neigh_list.h" #include "neigh_request.h" #include "update.h" -#include "integrate.h" #include "respa.h" -#include "math_const.h" #include "memory_kokkos.h" #include "error.h" #include "atom_masks.h" using namespace LAMMPS_NS; -using namespace MathConst; #define KOKKOS_CUDA_MAX_THREADS 256 #define KOKKOS_CUDA_MIN_BLOCKS 8 diff --git a/src/KOKKOS/pair_lj_class2_coul_cut_kokkos.cpp b/src/KOKKOS/pair_lj_class2_coul_cut_kokkos.cpp index ef8fe7a128..1f7642e965 100644 --- a/src/KOKKOS/pair_lj_class2_coul_cut_kokkos.cpp +++ b/src/KOKKOS/pair_lj_class2_coul_cut_kokkos.cpp @@ -13,8 +13,6 @@ #include "pair_lj_class2_coul_cut_kokkos.h" #include -#include -#include #include #include "kokkos.h" #include "atom_kokkos.h" @@ -24,15 +22,12 @@ #include "neigh_list.h" #include "neigh_request.h" #include "update.h" -#include "integrate.h" #include "respa.h" -#include "math_const.h" #include "memory_kokkos.h" #include "error.h" #include "atom_masks.h" using namespace LAMMPS_NS; -using namespace MathConst; #define KOKKOS_CUDA_MAX_THREADS 256 #define KOKKOS_CUDA_MIN_BLOCKS 8 diff --git a/src/KOKKOS/pair_lj_class2_coul_long_kokkos.cpp b/src/KOKKOS/pair_lj_class2_coul_long_kokkos.cpp index 5a25d0250b..c88ff9378e 100644 --- a/src/KOKKOS/pair_lj_class2_coul_long_kokkos.cpp +++ b/src/KOKKOS/pair_lj_class2_coul_long_kokkos.cpp @@ -13,26 +13,20 @@ #include "pair_lj_class2_coul_long_kokkos.h" #include -#include -#include #include #include "kokkos.h" #include "atom_kokkos.h" -#include "comm.h" #include "force.h" #include "neighbor.h" #include "neigh_list.h" #include "neigh_request.h" #include "update.h" -#include "integrate.h" #include "respa.h" -#include "math_const.h" #include "memory_kokkos.h" #include "error.h" #include "atom_masks.h" using namespace LAMMPS_NS; -using namespace MathConst; #define KOKKOS_CUDA_MAX_THREADS 256 #define KOKKOS_CUDA_MIN_BLOCKS 8 diff --git a/src/KOKKOS/pair_lj_class2_kokkos.cpp b/src/KOKKOS/pair_lj_class2_kokkos.cpp index 6d673b2d01..9900e7361f 100644 --- a/src/KOKKOS/pair_lj_class2_kokkos.cpp +++ b/src/KOKKOS/pair_lj_class2_kokkos.cpp @@ -17,26 +17,20 @@ #include "pair_lj_class2_kokkos.h" #include -#include -#include #include #include "kokkos.h" #include "atom_kokkos.h" -#include "comm.h" #include "force.h" #include "neighbor.h" #include "neigh_list.h" #include "neigh_request.h" #include "update.h" -#include "integrate.h" #include "respa.h" -#include "math_const.h" #include "memory_kokkos.h" #include "error.h" #include "atom_masks.h" using namespace LAMMPS_NS; -using namespace MathConst; #define KOKKOS_CUDA_MAX_THREADS 256 #define KOKKOS_CUDA_MIN_BLOCKS 8 diff --git a/src/KOKKOS/pair_lj_cut_coul_cut_kokkos.cpp b/src/KOKKOS/pair_lj_cut_coul_cut_kokkos.cpp index 9201a116b5..1601e4a4b2 100644 --- a/src/KOKKOS/pair_lj_cut_coul_cut_kokkos.cpp +++ b/src/KOKKOS/pair_lj_cut_coul_cut_kokkos.cpp @@ -13,26 +13,20 @@ #include "pair_lj_cut_coul_cut_kokkos.h" #include -#include -#include #include #include "kokkos.h" #include "atom_kokkos.h" -#include "comm.h" #include "force.h" #include "neighbor.h" #include "neigh_list.h" #include "neigh_request.h" #include "update.h" -#include "integrate.h" #include "respa.h" -#include "math_const.h" #include "memory_kokkos.h" #include "error.h" #include "atom_masks.h" using namespace LAMMPS_NS; -using namespace MathConst; #define KOKKOS_CUDA_MAX_THREADS 256 #define KOKKOS_CUDA_MIN_BLOCKS 8 diff --git a/src/KOKKOS/pair_lj_cut_coul_debye_kokkos.cpp b/src/KOKKOS/pair_lj_cut_coul_debye_kokkos.cpp index 8935333c74..6e7d1eeb8b 100644 --- a/src/KOKKOS/pair_lj_cut_coul_debye_kokkos.cpp +++ b/src/KOKKOS/pair_lj_cut_coul_debye_kokkos.cpp @@ -17,26 +17,20 @@ #include "pair_lj_cut_coul_debye_kokkos.h" #include -#include -#include #include #include "kokkos.h" #include "atom_kokkos.h" -#include "comm.h" #include "force.h" #include "neighbor.h" #include "neigh_list.h" #include "neigh_request.h" #include "update.h" -#include "integrate.h" #include "respa.h" -#include "math_const.h" #include "memory_kokkos.h" #include "error.h" #include "atom_masks.h" using namespace LAMMPS_NS; -using namespace MathConst; #define KOKKOS_CUDA_MAX_THREADS 256 #define KOKKOS_CUDA_MIN_BLOCKS 8 diff --git a/src/KOKKOS/pair_lj_cut_coul_dsf_kokkos.cpp b/src/KOKKOS/pair_lj_cut_coul_dsf_kokkos.cpp index aea70faec4..b7dc7cc26d 100644 --- a/src/KOKKOS/pair_lj_cut_coul_dsf_kokkos.cpp +++ b/src/KOKKOS/pair_lj_cut_coul_dsf_kokkos.cpp @@ -17,18 +17,14 @@ #include "pair_lj_cut_coul_dsf_kokkos.h" #include -#include -#include #include #include "kokkos.h" #include "atom_kokkos.h" -#include "comm.h" #include "force.h" #include "neighbor.h" #include "neigh_list.h" #include "neigh_request.h" #include "update.h" -#include "integrate.h" #include "respa.h" #include "math_const.h" #include "memory_kokkos.h" diff --git a/src/KOKKOS/pair_lj_cut_coul_long_kokkos.cpp b/src/KOKKOS/pair_lj_cut_coul_long_kokkos.cpp index 53d27f2447..122d59af82 100644 --- a/src/KOKKOS/pair_lj_cut_coul_long_kokkos.cpp +++ b/src/KOKKOS/pair_lj_cut_coul_long_kokkos.cpp @@ -13,18 +13,14 @@ #include "pair_lj_cut_coul_long_kokkos.h" #include -#include -#include #include #include "kokkos.h" #include "atom_kokkos.h" -#include "comm.h" #include "force.h" #include "neighbor.h" #include "neigh_list.h" #include "neigh_request.h" #include "update.h" -#include "integrate.h" #include "respa.h" #include "math_const.h" #include "memory_kokkos.h" diff --git a/src/KOKKOS/pair_lj_cut_kokkos.cpp b/src/KOKKOS/pair_lj_cut_kokkos.cpp index ee29e12322..df750b7524 100644 --- a/src/KOKKOS/pair_lj_cut_kokkos.cpp +++ b/src/KOKKOS/pair_lj_cut_kokkos.cpp @@ -12,27 +12,20 @@ ------------------------------------------------------------------------- */ #include "pair_lj_cut_kokkos.h" -#include -#include -#include #include #include "kokkos.h" #include "atom_kokkos.h" -#include "comm.h" #include "force.h" #include "neighbor.h" #include "neigh_list.h" #include "neigh_request.h" #include "update.h" -#include "integrate.h" #include "respa.h" -#include "math_const.h" #include "memory_kokkos.h" #include "error.h" #include "atom_masks.h" using namespace LAMMPS_NS; -using namespace MathConst; #define KOKKOS_CUDA_MAX_THREADS 256 #define KOKKOS_CUDA_MIN_BLOCKS 8 diff --git a/src/KOKKOS/pair_lj_expand_kokkos.cpp b/src/KOKKOS/pair_lj_expand_kokkos.cpp index 061fc205fb..38bebc364f 100644 --- a/src/KOKKOS/pair_lj_expand_kokkos.cpp +++ b/src/KOKKOS/pair_lj_expand_kokkos.cpp @@ -17,26 +17,20 @@ #include "pair_lj_expand_kokkos.h" #include -#include -#include #include #include "kokkos.h" #include "atom_kokkos.h" -#include "comm.h" #include "force.h" #include "neighbor.h" #include "neigh_list.h" #include "neigh_request.h" #include "update.h" -#include "integrate.h" #include "respa.h" -#include "math_const.h" #include "memory_kokkos.h" #include "error.h" #include "atom_masks.h" using namespace LAMMPS_NS; -using namespace MathConst; #define KOKKOS_CUDA_MAX_THREADS 256 #define KOKKOS_CUDA_MIN_BLOCKS 8 diff --git a/src/KOKKOS/pair_lj_gromacs_coul_gromacs_kokkos.cpp b/src/KOKKOS/pair_lj_gromacs_coul_gromacs_kokkos.cpp index 4df9fdea9e..a46a5c0441 100644 --- a/src/KOKKOS/pair_lj_gromacs_coul_gromacs_kokkos.cpp +++ b/src/KOKKOS/pair_lj_gromacs_coul_gromacs_kokkos.cpp @@ -17,26 +17,20 @@ #include "pair_lj_gromacs_coul_gromacs_kokkos.h" #include -#include -#include #include #include "kokkos.h" #include "atom_kokkos.h" -#include "comm.h" #include "force.h" #include "neighbor.h" #include "neigh_list.h" #include "neigh_request.h" #include "update.h" -#include "integrate.h" #include "respa.h" -#include "math_const.h" #include "memory_kokkos.h" #include "error.h" #include "atom_masks.h" using namespace LAMMPS_NS; -using namespace MathConst; #define KOKKOS_CUDA_MAX_THREADS 256 #define KOKKOS_CUDA_MIN_BLOCKS 8 diff --git a/src/KOKKOS/pair_lj_gromacs_kokkos.cpp b/src/KOKKOS/pair_lj_gromacs_kokkos.cpp index 2d395c39d5..23ed5e5595 100644 --- a/src/KOKKOS/pair_lj_gromacs_kokkos.cpp +++ b/src/KOKKOS/pair_lj_gromacs_kokkos.cpp @@ -17,26 +17,20 @@ #include "pair_lj_gromacs_kokkos.h" #include -#include -#include #include #include "kokkos.h" #include "atom_kokkos.h" -#include "comm.h" #include "force.h" #include "neighbor.h" #include "neigh_list.h" #include "neigh_request.h" #include "update.h" -#include "integrate.h" #include "respa.h" -#include "math_const.h" #include "memory_kokkos.h" #include "error.h" #include "atom_masks.h" using namespace LAMMPS_NS; -using namespace MathConst; #define KOKKOS_CUDA_MAX_THREADS 256 #define KOKKOS_CUDA_MIN_BLOCKS 8 diff --git a/src/KOKKOS/pair_lj_sdk_kokkos.cpp b/src/KOKKOS/pair_lj_sdk_kokkos.cpp index 14c53c38bf..25f081d255 100644 --- a/src/KOKKOS/pair_lj_sdk_kokkos.cpp +++ b/src/KOKKOS/pair_lj_sdk_kokkos.cpp @@ -14,19 +14,15 @@ #include "pair_lj_sdk_kokkos.h" #include #include -#include #include #include "kokkos.h" #include "atom_kokkos.h" #include "comm.h" #include "force.h" #include "neighbor.h" -#include "neigh_list.h" #include "neigh_request.h" #include "update.h" -#include "integrate.h" #include "respa.h" -#include "math_const.h" #include "memory_kokkos.h" #include "error.h" #include "atom_masks.h" @@ -34,7 +30,6 @@ #include "lj_sdk_common.h" using namespace LAMMPS_NS; -using namespace MathConst; using namespace LJSDKParms; #define KOKKOS_CUDA_MAX_THREADS 256 diff --git a/src/KOKKOS/pair_morse_kokkos.cpp b/src/KOKKOS/pair_morse_kokkos.cpp index d679477321..d3e3042a34 100644 --- a/src/KOKKOS/pair_morse_kokkos.cpp +++ b/src/KOKKOS/pair_morse_kokkos.cpp @@ -17,18 +17,14 @@ #include "pair_morse_kokkos.h" #include -#include -#include #include #include "kokkos.h" #include "atom_kokkos.h" -#include "comm.h" #include "force.h" #include "neighbor.h" #include "neigh_list.h" #include "neigh_request.h" #include "update.h" -#include "integrate.h" #include "respa.h" #include "math_const.h" #include "memory_kokkos.h" diff --git a/src/KOKKOS/pair_multi_lucy_rx_kokkos.cpp b/src/KOKKOS/pair_multi_lucy_rx_kokkos.cpp index 81a4aa7a82..75247859ed 100644 --- a/src/KOKKOS/pair_multi_lucy_rx_kokkos.cpp +++ b/src/KOKKOS/pair_multi_lucy_rx_kokkos.cpp @@ -22,9 +22,7 @@ ------------------------------------------------------------------------------------------- */ #include "pair_multi_lucy_rx_kokkos.h" -#include #include -#include #include #include "math_const.h" #include "atom_kokkos.h" @@ -33,9 +31,6 @@ #include "neigh_list.h" #include "memory_kokkos.h" #include "error.h" -#include "citeme.h" -#include "modify.h" -#include "fix.h" #include "atom_masks.h" #include "neigh_request.h" #include "kokkos.h" diff --git a/src/KOKKOS/pair_reaxc_kokkos.cpp b/src/KOKKOS/pair_reaxc_kokkos.cpp index ca897a377c..d0ad1f1b09 100644 --- a/src/KOKKOS/pair_reaxc_kokkos.cpp +++ b/src/KOKKOS/pair_reaxc_kokkos.cpp @@ -17,7 +17,6 @@ #include "pair_reaxc_kokkos.h" #include -#include #include #include #include "kokkos.h" @@ -27,9 +26,6 @@ #include "neighbor.h" #include "neigh_request.h" #include "neigh_list_kokkos.h" -#include "update.h" -#include "integrate.h" -#include "respa.h" #include "math_const.h" #include "math_special.h" #include "memory_kokkos.h" @@ -38,7 +34,6 @@ #include "reaxc_defs.h" #include "reaxc_lookup.h" #include "reaxc_tool_box.h" -#include "modify.h" #define TEAMSIZE 128 diff --git a/src/KOKKOS/pair_sw_kokkos.cpp b/src/KOKKOS/pair_sw_kokkos.cpp index dbd45747f0..e85afa362f 100644 --- a/src/KOKKOS/pair_sw_kokkos.cpp +++ b/src/KOKKOS/pair_sw_kokkos.cpp @@ -17,9 +17,6 @@ #include "pair_sw_kokkos.h" #include -#include -#include -#include #include "kokkos.h" #include "pair_kokkos.h" #include "atom_kokkos.h" @@ -30,7 +27,6 @@ #include "memory_kokkos.h" #include "neighbor.h" #include "neigh_list_kokkos.h" -#include "memory_kokkos.h" #include "error.h" #include "atom_masks.h" #include "math_const.h" diff --git a/src/KOKKOS/pair_table_kokkos.cpp b/src/KOKKOS/pair_table_kokkos.cpp index 01966d708a..5ee24ad479 100644 --- a/src/KOKKOS/pair_table_kokkos.cpp +++ b/src/KOKKOS/pair_table_kokkos.cpp @@ -16,14 +16,10 @@ ------------------------------------------------------------------------- */ #include "pair_table_kokkos.h" -#include -#include -#include #include #include "kokkos.h" #include "atom.h" #include "force.h" -#include "comm.h" #include "neighbor.h" #include "neigh_list.h" #include "neigh_request.h" diff --git a/src/KOKKOS/pair_table_rx_kokkos.cpp b/src/KOKKOS/pair_table_rx_kokkos.cpp index 7c2d20c68d..daebeda8db 100644 --- a/src/KOKKOS/pair_table_rx_kokkos.cpp +++ b/src/KOKKOS/pair_table_rx_kokkos.cpp @@ -18,7 +18,6 @@ #include "pair_table_rx_kokkos.h" #include #include -#include #include #include "kokkos.h" #include "atom.h" diff --git a/src/KOKKOS/pair_tersoff_kokkos.cpp b/src/KOKKOS/pair_tersoff_kokkos.cpp index b68af84425..b360b20ef3 100644 --- a/src/KOKKOS/pair_tersoff_kokkos.cpp +++ b/src/KOKKOS/pair_tersoff_kokkos.cpp @@ -17,9 +17,6 @@ #include "pair_tersoff_kokkos.h" #include -#include -#include -#include #include "kokkos.h" #include "atom_kokkos.h" #include "comm.h" @@ -27,9 +24,6 @@ #include "neighbor.h" #include "neigh_request.h" #include "neigh_list_kokkos.h" -#include "update.h" -#include "integrate.h" -#include "respa.h" #include "math_const.h" #include "memory_kokkos.h" #include "error.h" diff --git a/src/KOKKOS/pair_tersoff_mod_kokkos.cpp b/src/KOKKOS/pair_tersoff_mod_kokkos.cpp index b6921179c0..81ef486999 100644 --- a/src/KOKKOS/pair_tersoff_mod_kokkos.cpp +++ b/src/KOKKOS/pair_tersoff_mod_kokkos.cpp @@ -17,9 +17,6 @@ #include "pair_tersoff_mod_kokkos.h" #include -#include -#include -#include #include "kokkos.h" #include "atom_kokkos.h" #include "comm.h" @@ -27,9 +24,6 @@ #include "neighbor.h" #include "neigh_request.h" #include "neigh_list_kokkos.h" -#include "update.h" -#include "integrate.h" -#include "respa.h" #include "math_const.h" #include "memory_kokkos.h" #include "error.h" diff --git a/src/KOKKOS/pair_tersoff_zbl_kokkos.cpp b/src/KOKKOS/pair_tersoff_zbl_kokkos.cpp index 60ff0a7269..4593f32e36 100644 --- a/src/KOKKOS/pair_tersoff_zbl_kokkos.cpp +++ b/src/KOKKOS/pair_tersoff_zbl_kokkos.cpp @@ -17,8 +17,6 @@ #include "pair_tersoff_zbl_kokkos.h" #include -#include -#include #include #include "kokkos.h" #include "atom_kokkos.h" @@ -28,8 +26,6 @@ #include "neigh_request.h" #include "neigh_list_kokkos.h" #include "update.h" -#include "integrate.h" -#include "respa.h" #include "math_const.h" #include "memory_kokkos.h" #include "error.h" diff --git a/src/KOKKOS/pair_vashishta_kokkos.cpp b/src/KOKKOS/pair_vashishta_kokkos.cpp index febb171c83..614d3334d5 100644 --- a/src/KOKKOS/pair_vashishta_kokkos.cpp +++ b/src/KOKKOS/pair_vashishta_kokkos.cpp @@ -17,8 +17,6 @@ #include "pair_vashishta_kokkos.h" #include -#include -#include #include #include "kokkos.h" #include "pair_kokkos.h" @@ -28,9 +26,7 @@ #include "force.h" #include "comm.h" #include "memory_kokkos.h" -#include "neighbor.h" #include "neigh_list_kokkos.h" -#include "memory_kokkos.h" #include "error.h" #include "atom_masks.h" #include "math_const.h" diff --git a/src/KOKKOS/pair_yukawa_kokkos.cpp b/src/KOKKOS/pair_yukawa_kokkos.cpp index acfeb2fbdc..6dfffd4a54 100644 --- a/src/KOKKOS/pair_yukawa_kokkos.cpp +++ b/src/KOKKOS/pair_yukawa_kokkos.cpp @@ -17,24 +17,19 @@ #include "pair_yukawa_kokkos.h" #include -#include #include "kokkos.h" #include "atom_kokkos.h" -#include "comm.h" #include "force.h" #include "neighbor.h" #include "neigh_list.h" #include "neigh_request.h" #include "update.h" -#include "integrate.h" #include "respa.h" -#include "math_const.h" #include "memory_kokkos.h" #include "error.h" #include "atom_masks.h" using namespace LAMMPS_NS; -using namespace MathConst; #define KOKKOS_CUDA_MAX_THREADS 256 #define KOKKOS_CUDA_MIN_BLOCKS 8 diff --git a/src/KOKKOS/pair_zbl_kokkos.cpp b/src/KOKKOS/pair_zbl_kokkos.cpp index 0f21331266..5697dd5b00 100644 --- a/src/KOKKOS/pair_zbl_kokkos.cpp +++ b/src/KOKKOS/pair_zbl_kokkos.cpp @@ -17,19 +17,14 @@ #include "pair_zbl_kokkos.h" #include -#include -#include #include #include "atom_kokkos.h" -#include "comm.h" #include "force.h" #include "neighbor.h" #include "neigh_list.h" #include "neigh_request.h" #include "update.h" -#include "integrate.h" #include "respa.h" -#include "math_const.h" #include "memory_kokkos.h" #include "error.h" #include "atom_masks.h" @@ -39,7 +34,6 @@ // "The Stopping and Range of Ions in Matter" volume 1, Pergamon, 1985. using namespace LAMMPS_NS; -using namespace MathConst; using namespace PairZBLConstants; /* ---------------------------------------------------------------------- */ diff --git a/src/KOKKOS/pppm_kokkos.cpp b/src/KOKKOS/pppm_kokkos.cpp index 1842524e23..3e70602f67 100644 --- a/src/KOKKOS/pppm_kokkos.cpp +++ b/src/KOKKOS/pppm_kokkos.cpp @@ -17,9 +17,6 @@ #include "pppm_kokkos.h" #include -#include -#include -#include #include #include "atom_kokkos.h" #include "comm.h" @@ -27,8 +24,6 @@ #include "neighbor.h" #include "force.h" #include "pair.h" -#include "bond.h" -#include "angle.h" #include "domain.h" #include "fft3d_wrap.h" #include "remap_wrap.h" diff --git a/src/KOKKOS/region_block_kokkos.cpp b/src/KOKKOS/region_block_kokkos.cpp index a5734f6ba7..b28230290e 100644 --- a/src/KOKKOS/region_block_kokkos.cpp +++ b/src/KOKKOS/region_block_kokkos.cpp @@ -12,10 +12,6 @@ ------------------------------------------------------------------------- */ #include "region_block_kokkos.h" -#include -#include -#include "domain.h" -#include "force.h" #include "atom_kokkos.h" #include "atom_masks.h" diff --git a/src/KOKKOS/verlet_kokkos.cpp b/src/KOKKOS/verlet_kokkos.cpp index d555b74d23..2d2f0a9815 100644 --- a/src/KOKKOS/verlet_kokkos.cpp +++ b/src/KOKKOS/verlet_kokkos.cpp @@ -12,11 +12,9 @@ ------------------------------------------------------------------------- */ #include "verlet_kokkos.h" -#include #include "neighbor.h" #include "domain.h" #include "comm.h" -#include "atom.h" #include "atom_kokkos.h" #include "atom_masks.h" #include "force.h" @@ -29,15 +27,10 @@ #include "output.h" #include "update.h" #include "modify.h" -#include "compute.h" -#include "fix.h" #include "timer.h" #include "memory_kokkos.h" -#include "error.h" #include "kokkos.h" -#include - using namespace LAMMPS_NS; template -- GitLab From 658cda9b670da84e66a695d4f98364ac5202c4f4 Mon Sep 17 00:00:00 2001 From: Ellad Tadmor Date: Tue, 16 Jul 2019 15:02:24 -0500 Subject: [PATCH 253/469] Updated kim_query documentation to new format --- doc/src/kim_commands.txt | 71 +++++++++++++++++++++++++++------------- 1 file changed, 48 insertions(+), 23 deletions(-) diff --git a/doc/src/kim_commands.txt b/doc/src/kim_commands.txt index a6551734f1..46e437a871 100644 --- a/doc/src/kim_commands.txt +++ b/doc/src/kim_commands.txt @@ -35,8 +35,7 @@ kim_init Sim_LAMMPS_ReaxFF_StrachanVanDuinChakraborty_2003_CHNO__SM_107643900657 kim_interactions C H O kim_init Sim_LAMMPS_IFF_OtherInfo_AuthorList_Year_Species__SM_064312669787_000 real kim_interactions fixed_types -kim_query a0 get_lattice_constant_fcc species=\["Al"\] units=\["angstrom"\] :pre - +kim_query a0 get_lattice_constant_cubic crystal=\["fcc"\] species=\["Al"\] units=\["angstrom"\] :pre [Description:] @@ -104,16 +103,12 @@ The URL for the Model Page is constructed from the "extended KIM ID"_https://openkim.org/about-kim-ids/ of the IM: https://openkim.org/id/extended_KIM_ID -or -https://openkim.org/id/short_KIM_ID :pre For example for the Stillinger-Weber potential listed above the Model Page is located at: "https://openkim.org/id/SW_StillingerWeber_1985_Si__MO_405512056662_005"_https://openkim.org/id/SW_StillingerWeber_1985_Si__MO_405512056662_005 -or -"https://openkim.org/id/MO_405512056662_005"_https://openkim.org/id/MO_405512056662_005 :pre See the "current list of KIM PMs and SMs archived in OpenKIM"_https://openkim.org/browse/models/by-species. @@ -354,16 +349,34 @@ of the IM set by {kim_init} for material properties archived in "OpenKIM"_https://openkim.org. The {kim_query} command must be preceded by a {kim_init} command. The result of the query is stored in a "string style variable"_variable.html, the name of which is given as the first -argument of the {kim_query command}. The second required argument -{query_function} is the name of the query function to be called -(e.g. {get_lattice_constant_fcc}). -All following arguments are parameters handed over to the web query -in the format {keyword=value}. The list of supported keywords and -the type and format of their values depend on the query function -used. - -NOTE: The current list of supported query functions is available on the OpenKIM -webpage at "https://query.openkim.org"_https://query.openkim.org/ +argument of the {kim_query command}. (For the case of multiple +return values, the optional {split} keyword can be used after the +variable name to separate the results into multiple variables; see +the "example"_#split_example below.) +The second required argument {query_function} is the name of the +query function to be called (e.g. {get_lattice_constant_cubic}). +All following "arguments"_Commands_parse.html are parameters handed over to +the web query in the format {keyword=value}, where {value} is always +an array of one or more comma-separated items in brackets. +The list of supported keywords and the type and format of their values +depend on the query function used. The current list of query functions +is available on the OpenKIM webpage at +"https://openkim.org/doc/repository/kim-query"_https://openkim.org/doc/repository/kim-query. + +NOTE: All query functions require the {model} keyword, which identifies +the IM whose predictions are being queried. This keyword is automatically +generated by {kim_query} based on the IM set in {kim_init} and must not +be specified as an argument to {kim_query}. + +NOTE: Each {query_function} is associated with a default method (implemented +as a "KIM Test"_https://openkim.org/getting-started/kim-tests/) +used to compute this property. In cases where there are multiple +methods in OpenKIM for computing a property, a {method} keyword can +be provided to select the method of choice. See the +"query documentation"_https://openkim.org/doc/repository/kim-query +to see which methods are available for a given {query function}. + +{kim_query} Usage Examples and Further Clarifications: :h6 The data obtained by {kim_query} commands can be used as part of the setup or analysis phases of LAMMPS simulations. Some examples are given below. @@ -372,7 +385,7 @@ or analysis phases of LAMMPS simulations. Some examples are given below. kim_init EAM_Dynamo_ErcolessiAdams_1994_Al__MO_123629422045_005 metal boundary p p p -kim_query a0 get_lattice_constant_fcc species=\["Al"\] units=\["angstrom"\] +kim_query a0 get_lattice_constant_cubic crystal=\["fcc"\] species=\["Al"\] units=\["angstrom"\] lattice fcc $\{a0\} ... :pre @@ -389,11 +402,12 @@ Note that in {unit_conversion_mode} the results obtained from a For example, in the above script, the lattice command would need to be changed to: "lattice fcc $\{a0\}*$\{_u_distance\}". +:link(split_example) [Define an equilibrium hcp crystal] kim_init EAM_Dynamo_Mendelev_2007_Zr__MO_848899341753_000 metal boundary p p p -kim_query latconst split get_lattice_constant_hcp species=\["Zr"\] units=\["angstrom"\] +kim_query latconst split get_lattice_constant_hexagonal crystal=\["hcp"\] species=\["Zr"\] units=\["angstrom"\] variable a0 equal latconst_1 variable c0 equal latconst_2 variable c_to_a equal $\{c0\}/$\{a0\} @@ -414,16 +428,27 @@ the returned values is determined by the type of query performed. kim_init EAM_Dynamo_ErcolessiAdams_1994_Al__MO_123629422045_005 metal boundary p p p -kim_query a0 get_lattice_constant_fcc species=\["Al"\] units=\["angstrom"\] -kim_query alpha get_linear_thermal_expansion_fcc species=\["Al"\] units=\{"1/K"\} +kim_query a0 get_lattice_constant_cubic crystal=\["fcc"\] species=\["Al"\] units=\["angstrom"\] +kim_query alpha get_linear_thermal_expansion_constant_cubic crystal=\["fcc"\] species=\["Al"\] units=\{"1/K"\} temperature=[293.15] temperature_units=["K"] variable DeltaT equal 300 lattice fcc $\{a0\}*$\{alpha\}*$\{DeltaT\} ... :pre As in the previous example, the equilibrium lattice constant is obtained for the Ercolessi and Adams (1994) potential. However, in this case the -crystal is scaled to the appropriate lattice constant at 300 K by using -the linear thermal expansion coefficient predicted by the potential. +crystal is scaled to the appropriate lattice constant at room temperature +(293.15 K) by using the linear thermal expansion constant predicted by the +potential. + +NOTE: When passing numerical values as arguments (as in the case +of the temperature in the above example) it is also possible to pass a +tolerance indicating how close to the value is considered a match. +If no tolerance is passed a default value is used. If multiple results +are returned (indicating that the tolerance is too large), {kim_query} +will return an error. See the +"query documentation"_https://openkim.org/doc/repository/kim-query +to see which numerical arguments and tolerances are available for a +given {query function}. [Compute defect formation energy] @@ -432,7 +457,7 @@ kim_init EAM_Dynamo_ErcolessiAdams_1994_Al__MO_123629422045_005 metal ... Build fcc crystal containing some defect and compute the total energy ... which is stored in the variable {Etot} ... -kim_query Ec get_cohesive_energy_fcc species=\["Al"\] units=\["eV"\] +kim_query Ec get_cohesive_energy_cubic crystal=\["fcc"\] species=\["Al"\] units=\["eV"\] variable Eform equal $\{Etot\} - count(all)*$\{Ec\} ... :pre -- GitLab From b61b48235b3e3551a6ad71e188995d6532a5a622 Mon Sep 17 00:00:00 2001 From: Ellad Tadmor Date: Tue, 16 Jul 2019 15:19:28 -0500 Subject: [PATCH 254/469] Updated openkim.org documentation URLs to new /doc/* locations --- doc/src/kim_commands.txt | 19 ++++++++++--------- 1 file changed, 10 insertions(+), 9 deletions(-) diff --git a/doc/src/kim_commands.txt b/doc/src/kim_commands.txt index 46e437a871..7c88fd084a 100644 --- a/doc/src/kim_commands.txt +++ b/doc/src/kim_commands.txt @@ -57,17 +57,17 @@ Reliability :h5 All content archived in OpenKIM is reviewed by the "KIM Editor"_https://openkim.org/governance/ for quality. IMs in OpenKIM are archived with full provenance control. Each is associated with a maintainer responsible for the integrity of the content. All changes are tracked and recorded. -IMs in OpenKIM are exhaustively tested using "KIM Tests"_https://openkim.org/getting-started/kim-tests/ that compute a host of material properties, and "KIM Verification Checks"_https://openkim.org/about-verification-checks/ that provide the user with information on various aspects of the IM behavior and coding correctness. This information is displayed on the IM's page accessible through the "OpenKIM browse interface"_https://openkim.org/browse. :ul +IMs in OpenKIM are exhaustively tested using "KIM Tests"_https://openkim.org/doc/evaluation/kim-tests/ that compute a host of material properties, and "KIM Verification Checks"_https://openkim.org/doc/evaluation/kim-verification-checks/ that provide the user with information on various aspects of the IM behavior and coding correctness. This information is displayed on the IM's page accessible through the "OpenKIM browse interface"_https://openkim.org/browse. :ul Reproducibility :h5 -Each IM in OpenKIM is issued a unique identifier ("KIM ID"_https://openkim.org/about-kim-ids/), which includes a version number (last three digits). Any changes that can result in different numerical values lead to a version increment in the KIM ID. This makes it possible to reproduce simulations since the specific version of a specific IM used can be retrieved using its KIM ID. +Each IM in OpenKIM is issued a unique identifier ("KIM ID"_https://openkim.org/doc/schema/kim-ids/), which includes a version number (last three digits). Any changes that can result in different numerical values lead to a version increment in the KIM ID. This makes it possible to reproduce simulations since the specific version of a specific IM used can be retrieved using its KIM ID. OpenKIM is a member organization of "DataCite"_https://datacite.org/ and issues digital object identifiers (DOIs) to all IMs archived in OpenKIM. This makes it possible to cite the IM code used in a simulation in a publications to give credit to the developers and further facilitate reproducibility. :ul Convenience :h5 IMs in OpenKIM are distributed in binary form along with LAMMPS and can be used in a LAMMPS input script simply by providing their KIM ID in the {kim_init} command documented on this page. -The {kim_query} web query tool provides the ability to use the predictions of IMs for supported material properties (computed via "KIM Tests"_https://openkim.org/getting-started/kim-tests/) as part of a LAMMPS input script setup and analysis. +The {kim_query} web query tool provides the ability to use the predictions of IMs for supported material properties (computed via "KIM Tests"_https://openkim.org/doc/evaluation/kim-tests/) as part of a LAMMPS input script setup and analysis. Support is provided for unit conversion between the "unit style"_units.html used in the LAMMPS input script and the units required by the OpenKIM IM. This makes it possible to use a single input script with IMs using different units without change and minimizes the likelihood of errors due to incompatible units. :ul :link(IM_types) @@ -80,10 +80,11 @@ The second type is called a {KIM Simulator Model} (SM). A KIM SM is an IM that i With these two IM types, OpenKIM can archive and test almost all IMs that can be used by LAMMPS. (It is easy to contribute new IMs to OpenKIM, see -the "upload instructions"_https://openkim.org/getting-started/adding-content/.) +the "upload instructions"_https://openkim.org/doc/repository/adding-content/.) OpenKIM IMs are uniquely identified by a -"KIM ID"_https://openkim.org/about-kim-ids/. The extended KIM ID consists of +"KIM ID"_https://openkim.org/doc/schema/kim-ids/. +The extended KIM ID consists of a human-readable prefix identifying the type of IM, authors, publication year, and supported species, separated by two underscores from the KIM ID itself, which begins with an IM code @@ -100,7 +101,7 @@ authorship and citation information, test and verification check results, visualizations of results, a wiki with documentation and user comments, and access to raw files, and other information. The URL for the Model Page is constructed from the -"extended KIM ID"_https://openkim.org/about-kim-ids/ of the IM: +"extended KIM ID"_https://openkim.org/doc/schema/kim-ids/ of the IM: https://openkim.org/id/extended_KIM_ID :pre @@ -141,7 +142,7 @@ would not include {units} and {atom_style} commands. The required arguments of {kim_init} are the {model} name of the IM to be used in the simulation (for an IM archived in OpenKIM this is -its "extended KIM ID"_https://openkim.org/about-kim-ids/), and +its "extended KIM ID"_https://openkim.org/doc/schema/kim-ids/, and the {user_units}, which are the LAMMPS "units style"_units.html used in the input script. (Any dimensioned numerical values in the input script and values read in from files are expected to be in the @@ -219,7 +220,7 @@ _u_density :pre If desired, the input script can be designed to work with these conversion factors so that the script will work without change with any OpenKIM IM. (This approach is used in the -"OpenKIM Testing Framework"_https://openkim.org/getting-started/kim-tests/.) +"OpenKIM Testing Framework"_https://openkim.org/doc/evaluation/kim-tests/.) For example, the script given above for the cohesive energy of fcc Al can be rewritten to work with any IM regardless of units. The following script constructs an fcc lattice with a lattice parameter defined in @@ -369,7 +370,7 @@ generated by {kim_query} based on the IM set in {kim_init} and must not be specified as an argument to {kim_query}. NOTE: Each {query_function} is associated with a default method (implemented -as a "KIM Test"_https://openkim.org/getting-started/kim-tests/) +as a "KIM Test"_https://openkim.org/doc/evaluation/kim-tests/) used to compute this property. In cases where there are multiple methods in OpenKIM for computing a property, a {method} keyword can be provided to select the method of choice. See the -- GitLab From 5b4f77b919b251ba8130abb9b15946999f738faa Mon Sep 17 00:00:00 2001 From: "Ryan S. Elliott" Date: Tue, 16 Jul 2019 16:20:48 -0500 Subject: [PATCH 255/469] kim_query check for explicit 'model=' key in arguments (give error if present). --- src/KIM/kim_query.cpp | 11 +++++++++-- 1 file changed, 9 insertions(+), 2 deletions(-) diff --git a/src/KIM/kim_query.cpp b/src/KIM/kim_query.cpp index 6e77b8f859..dc8d0544f6 100644 --- a/src/KIM/kim_query.cpp +++ b/src/KIM/kim_query.cpp @@ -113,6 +113,13 @@ void KimQuery::command(int narg, char **arg) narg--; } function = arg[1]; + for (int i = 2; i < narg; ++i) + { + if (0 == strncmp("model=",arg[i], 6)) { + error->all(FLERR,"Illegal 'model' key in kim_query command"); + } + } + #if defined(LMP_KIM_CURL) @@ -258,9 +265,9 @@ char *do_query(char *qfunction, char * model_name, int narg, char **arg, if (value[0] == '[') { int len = strlen(value)-1; - if (value[len-1] == ']') { + if (value[len] == ']') { retval = new char[len]; - value[len-1] = '\0'; + value[len] = '\0'; strcpy(retval,value+1); } else { retval = new char[len+2]; -- GitLab From 354f4d19fd67094ca50ef83cb627abdf85f9a087 Mon Sep 17 00:00:00 2001 From: "Ryan S. Elliott" Date: Tue, 16 Jul 2019 22:11:23 -0500 Subject: [PATCH 256/469] Update to kim-api-2.1.0 release --- cmake/Modules/Packages/KIM.cmake | 6 ++---- 1 file changed, 2 insertions(+), 4 deletions(-) diff --git a/cmake/Modules/Packages/KIM.cmake b/cmake/Modules/Packages/KIM.cmake index 5803ea23c4..5c0b8e2ee8 100644 --- a/cmake/Modules/Packages/KIM.cmake +++ b/cmake/Modules/Packages/KIM.cmake @@ -21,10 +21,8 @@ if(PKG_KIM) enable_language(Fortran) include(ExternalProject) ExternalProject_Add(kim_build - GIT_REPOSITORY https://github.com/openkim/kim-api.git - GIT_TAG SimulatorModels - #URL https://s3.openkim.org/kim-api/kim-api-2.0.2.txz - #URL_MD5 537d9c0abd30f85b875ebb584f9143fa + URL https://s3.openkim.org/kim-api/kim-api-2.1.0.txz + URL_MD5 9ada58e677a545a1987b1ecb98e39d7e BINARY_DIR build CMAKE_ARGS -DCMAKE_C_COMPILER=${CMAKE_C_COMPILER} -DCMAKE_CXX_COMPILER=${CMAKE_CXX_COMPILER} -- GitLab From 06275b03c06f3615d6442ef9243a41ffecbcae19 Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Wed, 17 Jul 2019 15:46:39 -0400 Subject: [PATCH 257/469] refactor FFT handling in CMake module for KSPACE. This also improves the FFT info output in the PPPM styles --- cmake/CMakeLists.txt | 7 ++++++- cmake/Modules/Packages/KSPACE.cmake | 28 ++++++++++++++++------------ src/KOKKOS/pppm_kokkos.cpp | 10 ++-------- src/KSPACE/pppm.cpp | 10 ++-------- src/KSPACE/pppm.h | 11 +++++++++++ src/KSPACE/pppm_disp.cpp | 10 ++-------- src/KSPACE/pppm_disp.h | 10 ++++++++++ 7 files changed, 49 insertions(+), 37 deletions(-) diff --git a/cmake/CMakeLists.txt b/cmake/CMakeLists.txt index bde36aa896..4b528f280e 100644 --- a/cmake/CMakeLists.txt +++ b/cmake/CMakeLists.txt @@ -673,5 +673,10 @@ if(PKG_KOKKOS) message(STATUS "Kokkos Arch: ${KOKKOS_ARCH}") endif() if(PKG_KSPACE) - message(STATUS "Using ${FFT} as FFT") + message(STATUS "Using ${FFT} as primary FFT library") + if(FFT_SINGLE) + message(STATUS "Using single precision FFTs") + else() + message(STATUS "Using double precision FFTs") + endif() endif() diff --git a/cmake/Modules/Packages/KSPACE.cmake b/cmake/Modules/Packages/KSPACE.cmake index 6938a93a36..63c42baf2d 100644 --- a/cmake/Modules/Packages/KSPACE.cmake +++ b/cmake/Modules/Packages/KSPACE.cmake @@ -1,5 +1,5 @@ if(PKG_KSPACE) - option(FFT_SINGLE "Use single precision FFT instead of double" OFF) + option(FFT_SINGLE "Use single precision FFTs instead of double precision FFTs" OFF) set(FFTW "FFTW3") if(FFT_SINGLE) set(FFTW "FFTW3F") @@ -7,26 +7,30 @@ if(PKG_KSPACE) endif() find_package(${FFTW} QUIET) if(${FFTW}_FOUND) - set(FFT "${FFTW}" CACHE STRING "FFT library for KSPACE package") + set(FFT "FFTW3" CACHE STRING "FFT library for KSPACE package") else() set(FFT "KISS" CACHE STRING "FFT library for KSPACE package") endif() - set(FFT_VALUES KISS ${FFTW} MKL) + set(FFT_VALUES KISS FFTW3 MKL) set_property(CACHE FFT PROPERTY STRINGS ${FFT_VALUES}) validate_option(FFT FFT_VALUES) string(TOUPPER ${FFT} FFT) - if(NOT FFT STREQUAL "KISS") - find_package(${FFT} REQUIRED) - if(NOT FFT STREQUAL "FFTW3F") - add_definitions(-DFFT_FFTW) - else() - add_definitions(-DFFT_${FFT}) - endif() - include_directories(${${FFT}_INCLUDE_DIRS}) - list(APPEND LAMMPS_LINK_LIBS ${${FFT}_LIBRARIES}) + + if(FFT STREQUAL "FFTW3") + find_package(${FFTW} REQUIRED) + add_definitions(-DFFT_FFTW3) + include_directories(${${FFTW}_INCLUDE_DIRS}) + list(APPEND LAMMPS_LINK_LIBS ${${FFTW}_LIBRARIES}) + elseif(FFT STREQUAL "MKL") + find_package(MKL REQUIRED) + add_definitions(-DFFT_MKL) + include_directories(${MKL_INCLUDE_DIRS}) + list(APPEND LAMMPS_LINK_LIBS ${MKL_LIBRARIES}) else() + # last option is KISSFFT add_definitions(-DFFT_KISS) endif() + set(FFT_PACK "array" CACHE STRING "Optimization for FFT") set(FFT_PACK_VALUES array pointer memcpy) set_property(CACHE FFT_PACK PROPERTY STRINGS ${FFT_PACK_VALUES}) diff --git a/src/KOKKOS/pppm_kokkos.cpp b/src/KOKKOS/pppm_kokkos.cpp index 7c01adc510..c9c0d6d1d4 100644 --- a/src/KOKKOS/pppm_kokkos.cpp +++ b/src/KOKKOS/pppm_kokkos.cpp @@ -306,12 +306,6 @@ void PPPMKokkos::init() if (me == 0) { -#ifdef FFT_SINGLE - const char fft_prec[] = "single"; -#else - const char fft_prec[] = "double"; -#endif - if (screen) { fprintf(screen," G vector (1/distance) = %g\n",g_ewald); fprintf(screen," grid = %d %d %d\n",nx_pppm,ny_pppm,nz_pppm); @@ -320,7 +314,7 @@ void PPPMKokkos::init() estimated_accuracy); fprintf(screen," estimated relative force accuracy = %g\n", estimated_accuracy/two_charge_force); - fprintf(screen," using %s precision FFTs\n",fft_prec); + fprintf(screen," using " LMP_FFT_PREC " precision " LMP_FFT_LIB "\n"); fprintf(screen," 3d grid and FFT values/proc = %d %d\n", ngrid_max,nfft_both_max); } @@ -332,7 +326,7 @@ void PPPMKokkos::init() estimated_accuracy); fprintf(logfile," estimated relative force accuracy = %g\n", estimated_accuracy/two_charge_force); - fprintf(logfile," using %s precision FFTs\n",fft_prec); + fprintf(logfile," using " LMP_FFT_PREC " precision " LMP_FFT_LIB "\n"); fprintf(logfile," 3d grid and FFT values/proc = %d %d\n", ngrid_max,nfft_both_max); } diff --git a/src/KSPACE/pppm.cpp b/src/KSPACE/pppm.cpp index 53c18804a5..1abb19e947 100644 --- a/src/KSPACE/pppm.cpp +++ b/src/KSPACE/pppm.cpp @@ -350,12 +350,6 @@ void PPPM::init() if (me == 0) { -#ifdef FFT_SINGLE - const char fft_prec[] = "single"; -#else - const char fft_prec[] = "double"; -#endif - if (screen) { fprintf(screen," G vector (1/distance) = %g\n",g_ewald); fprintf(screen," grid = %d %d %d\n",nx_pppm,ny_pppm,nz_pppm); @@ -364,7 +358,7 @@ void PPPM::init() estimated_accuracy); fprintf(screen," estimated relative force accuracy = %g\n", estimated_accuracy/two_charge_force); - fprintf(screen," using %s precision FFTs\n",fft_prec); + fprintf(screen," using " LMP_FFT_PREC " precision " LMP_FFT_LIB "\n"); fprintf(screen," 3d grid and FFT values/proc = %d %d\n", ngrid_max,nfft_both_max); } @@ -376,7 +370,7 @@ void PPPM::init() estimated_accuracy); fprintf(logfile," estimated relative force accuracy = %g\n", estimated_accuracy/two_charge_force); - fprintf(logfile," using %s precision FFTs\n",fft_prec); + fprintf(logfile," using " LMP_FFT_PREC " precision " LMP_FFT_LIB "\n"); fprintf(logfile," 3d grid and FFT values/proc = %d %d\n", ngrid_max,nfft_both_max); } diff --git a/src/KSPACE/pppm.h b/src/KSPACE/pppm.h index 1ce1a0d666..6426b9c22d 100644 --- a/src/KSPACE/pppm.h +++ b/src/KSPACE/pppm.h @@ -23,11 +23,22 @@ KSpaceStyle(pppm,PPPM) #include "lmptype.h" #include +#if defined(FFT_FFTW3) +#define LMP_FFT_LIB "FFTW3" +#elif defined(FFT_MKL) +#define LMP_FFT_LIB "MKL FFT" +#else +#define LMP_FFT_LIB "KISS FFT" +#endif + #ifdef FFT_SINGLE typedef float FFT_SCALAR; +#define LMP_FFT_PREC "single" #define MPI_FFT_SCALAR MPI_FLOAT #else + typedef double FFT_SCALAR; +#define LMP_FFT_PREC "double" #define MPI_FFT_SCALAR MPI_DOUBLE #endif diff --git a/src/KSPACE/pppm_disp.cpp b/src/KSPACE/pppm_disp.cpp index 45dce0895b..ba0e85bbba 100644 --- a/src/KSPACE/pppm_disp.cpp +++ b/src/KSPACE/pppm_disp.cpp @@ -474,12 +474,6 @@ void PPPMDisp::init() MPI_Allreduce(&nfft_both,&nfft_both_max,1,MPI_INT,MPI_MAX,world); if (me == 0) { - #ifdef FFT_SINGLE - const char fft_prec[] = "single"; - #else - const char fft_prec[] = "double"; - #endif - if (screen) { fprintf(screen," Coulomb G vector (1/distance)= %g\n",g_ewald); fprintf(screen," Coulomb grid = %d %d %d\n",nx_pppm,ny_pppm,nz_pppm); @@ -488,7 +482,7 @@ void PPPMDisp::init() acc); fprintf(screen," Coulomb estimated relative force accuracy = %g\n", acc/two_charge_force); - fprintf(screen," using %s precision FFTs\n",fft_prec); + fprintf(screen," using " LMP_FFT_PREC " precision " LMP_FFT_LIB "\n"); fprintf(screen," 3d grid and FFT values/proc = %d %d\n", ngrid_max, nfft_both_max); } @@ -501,7 +495,7 @@ void PPPMDisp::init() acc); fprintf(logfile," Coulomb estimated relative force accuracy = %g\n", acc/two_charge_force); - fprintf(logfile," using %s precision FFTs\n",fft_prec); + fprintf(logfile," using " LMP_FFT_PREC " precision " LMP_FFT_LIB "\n"); fprintf(logfile," 3d grid and FFT values/proc = %d %d\n", ngrid_max, nfft_both_max); } diff --git a/src/KSPACE/pppm_disp.h b/src/KSPACE/pppm_disp.h index ccbeb60f3c..8674669274 100644 --- a/src/KSPACE/pppm_disp.h +++ b/src/KSPACE/pppm_disp.h @@ -23,11 +23,21 @@ KSpaceStyle(pppm/disp,PPPMDisp) #include "lmptype.h" #include +#if defined(FFT_FFTW3) +#define LMP_FFT_LIB "FFTW3" +#elif defined(FFT_MKL) +#define LMP_FFT_LIB "MKL FFT" +#else +#define LMP_FFT_LIB "KISS FFT" +#endif + #ifdef FFT_SINGLE typedef float FFT_SCALAR; +#define LMP_FFT_PREC "single" #define MPI_FFT_SCALAR MPI_FLOAT #else typedef double FFT_SCALAR; +#define LMP_FFT_PREC "double" #define MPI_FFT_SCALAR MPI_DOUBLE #endif -- GitLab From bcf600d7814df4eefe4b73d3de7ac344a8decc16 Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Wed, 17 Jul 2019 15:47:28 -0400 Subject: [PATCH 258/469] let CMake configuration default to Release with debug settings this way we can more easily get detailed stack traces from people compiling with CMake --- cmake/CMakeLists.txt | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/cmake/CMakeLists.txt b/cmake/CMakeLists.txt index 4b528f280e..0f99cc6274 100644 --- a/cmake/CMakeLists.txt +++ b/cmake/CMakeLists.txt @@ -37,7 +37,7 @@ include(PreventInSourceBuilds) if(NOT CMAKE_BUILD_TYPE AND NOT CMAKE_CXX_FLAGS) #release comes with -O3 by default - set(CMAKE_BUILD_TYPE Release CACHE STRING "Choose the type of build, options are: None Debug Release RelWithDebInfo MinSizeRel." FORCE) + set(CMAKE_BUILD_TYPE RelWithDebInfo CACHE STRING "Choose the type of build, options are: None Debug Release RelWithDebInfo MinSizeRel." FORCE) endif(NOT CMAKE_BUILD_TYPE AND NOT CMAKE_CXX_FLAGS) string(TOUPPER "${CMAKE_BUILD_TYPE}" BTYPE) -- GitLab From 02b0fb454f7adbb412ea3d2fd7d324ff5004446b Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Wed, 17 Jul 2019 16:34:43 -0400 Subject: [PATCH 259/469] include rmass[] in border communication. will otherwise trigger issues with fix shake. --- src/PERI/atom_vec_peri.cpp | 11 ++++++++++- src/atom_vec_ellipsoid.cpp | 11 ++++++++++- 2 files changed, 20 insertions(+), 2 deletions(-) diff --git a/src/PERI/atom_vec_peri.cpp b/src/PERI/atom_vec_peri.cpp index 64ce323a3f..c4fa0bd43b 100644 --- a/src/PERI/atom_vec_peri.cpp +++ b/src/PERI/atom_vec_peri.cpp @@ -55,7 +55,7 @@ AtomVecPeri::AtomVecPeri(LAMMPS *lmp) : AtomVec(lmp) comm_f_only = 1; size_forward = 4; size_reverse = 3; - size_border = 11; + size_border = 12; size_velocity = 3; size_data_atom = 7; size_data_vel = 4; @@ -357,6 +357,7 @@ int AtomVecPeri::pack_border(int n, int *list, double *buf, buf[m++] = ubuf(type[j]).d; buf[m++] = ubuf(mask[j]).d; buf[m++] = vfrac[j]; + buf[m++] = rmass[j]; buf[m++] = s0[j]; buf[m++] = x0[j][0]; buf[m++] = x0[j][1]; @@ -381,6 +382,7 @@ int AtomVecPeri::pack_border(int n, int *list, double *buf, buf[m++] = ubuf(type[j]).d; buf[m++] = ubuf(mask[j]).d; buf[m++] = vfrac[j]; + buf[m++] = rmass[j]; buf[m++] = s0[j]; buf[m++] = x0[j][0]; buf[m++] = x0[j][1]; @@ -414,6 +416,7 @@ int AtomVecPeri::pack_border_vel(int n, int *list, double *buf, buf[m++] = ubuf(type[j]).d; buf[m++] = ubuf(mask[j]).d; buf[m++] = vfrac[j]; + buf[m++] = rmass[j]; buf[m++] = s0[j]; buf[m++] = x0[j][0]; buf[m++] = x0[j][1]; @@ -442,6 +445,7 @@ int AtomVecPeri::pack_border_vel(int n, int *list, double *buf, buf[m++] = ubuf(type[j]).d; buf[m++] = ubuf(mask[j]).d; buf[m++] = vfrac[j]; + buf[m++] = rmass[j]; buf[m++] = s0[j]; buf[m++] = x0[j][0]; buf[m++] = x0[j][1]; @@ -463,6 +467,7 @@ int AtomVecPeri::pack_border_vel(int n, int *list, double *buf, buf[m++] = ubuf(type[j]).d; buf[m++] = ubuf(mask[j]).d; buf[m++] = vfrac[j]; + buf[m++] = rmass[j]; buf[m++] = s0[j]; buf[m++] = x0[j][0]; buf[m++] = x0[j][1]; @@ -497,6 +502,7 @@ int AtomVecPeri::pack_border_hybrid(int n, int *list, double *buf) for (i = 0; i < n; i++) { j = list[i]; buf[m++] = vfrac[j]; + buf[m++] = rmass[j]; buf[m++] = s0[j]; buf[m++] = x0[j][0]; buf[m++] = x0[j][1]; @@ -522,6 +528,7 @@ void AtomVecPeri::unpack_border(int n, int first, double *buf) type[i] = (int) ubuf(buf[m++]).i; mask[i] = (int) ubuf(buf[m++]).i; vfrac[i] = buf[m++]; + rmass[i] = buf[m++]; s0[i] = buf[m++]; x0[i][0] = buf[m++]; x0[i][1] = buf[m++]; @@ -551,6 +558,7 @@ void AtomVecPeri::unpack_border_vel(int n, int first, double *buf) type[i] = (int) ubuf(buf[m++]).i; mask[i] = (int) ubuf(buf[m++]).i; vfrac[i] = buf[m++]; + rmass[i] = buf[m++]; s0[i] = buf[m++]; x0[i][0] = buf[m++]; x0[i][1] = buf[m++]; @@ -576,6 +584,7 @@ int AtomVecPeri::unpack_border_hybrid(int n, int first, double *buf) last = first + n; for (i = first; i < last; i++) { vfrac[i] = buf[m++]; + rmass[i] = buf[m++]; s0[i] = buf[m++]; x0[i][0] = buf[m++]; x0[i][1] = buf[m++]; diff --git a/src/atom_vec_ellipsoid.cpp b/src/atom_vec_ellipsoid.cpp index 455e4f192f..7bb29bd6bc 100644 --- a/src/atom_vec_ellipsoid.cpp +++ b/src/atom_vec_ellipsoid.cpp @@ -41,7 +41,7 @@ AtomVecEllipsoid::AtomVecEllipsoid(LAMMPS *lmp) : AtomVec(lmp) comm_x_only = comm_f_only = 0; size_forward = 7; size_reverse = 6; - size_border = 14; + size_border = 15; size_velocity = 6; size_data_atom = 7; size_data_vel = 7; @@ -544,6 +544,7 @@ int AtomVecEllipsoid::pack_border(int n, int *list, double *buf, buf[m++] = ubuf(tag[j]).d; buf[m++] = ubuf(type[j]).d; buf[m++] = ubuf(mask[j]).d; + buf[m++] = rmass[j]; if (ellipsoid[j] < 0) buf[m++] = ubuf(0).d; else { buf[m++] = ubuf(1).d; @@ -576,6 +577,7 @@ int AtomVecEllipsoid::pack_border(int n, int *list, double *buf, buf[m++] = ubuf(tag[j]).d; buf[m++] = ubuf(type[j]).d; buf[m++] = ubuf(mask[j]).d; + buf[m++] = rmass[j]; if (ellipsoid[j] < 0) buf[m++] = ubuf(0).d; else { buf[m++] = ubuf(1).d; @@ -618,6 +620,7 @@ int AtomVecEllipsoid::pack_border_vel(int n, int *list, double *buf, buf[m++] = ubuf(tag[j]).d; buf[m++] = ubuf(type[j]).d; buf[m++] = ubuf(mask[j]).d; + buf[m++] = rmass[j]; if (ellipsoid[j] < 0) buf[m++] = ubuf(0).d; else { buf[m++] = ubuf(1).d; @@ -657,6 +660,7 @@ int AtomVecEllipsoid::pack_border_vel(int n, int *list, double *buf, buf[m++] = ubuf(tag[j]).d; buf[m++] = ubuf(type[j]).d; buf[m++] = ubuf(mask[j]).d; + buf[m++] = rmass[j]; if (ellipsoid[j] < 0) buf[m++] = ubuf(0).d; else { buf[m++] = ubuf(1).d; @@ -689,6 +693,7 @@ int AtomVecEllipsoid::pack_border_vel(int n, int *list, double *buf, buf[m++] = ubuf(tag[j]).d; buf[m++] = ubuf(type[j]).d; buf[m++] = ubuf(mask[j]).d; + buf[m++] = rmass[j]; if (ellipsoid[j] < 0) buf[m++] = ubuf(0).d; else { buf[m++] = ubuf(1).d; @@ -735,6 +740,7 @@ int AtomVecEllipsoid::pack_border_hybrid(int n, int *list, double *buf) m = 0; for (i = 0; i < n; i++) { j = list[i]; + buf[m++] = rmass[j]; if (ellipsoid[j] < 0) buf[m++] = ubuf(0).d; else { buf[m++] = ubuf(1).d; @@ -769,6 +775,7 @@ void AtomVecEllipsoid::unpack_border(int n, int first, double *buf) tag[i] = (tagint) ubuf(buf[m++]).i; type[i] = (int) ubuf(buf[m++]).i; mask[i] = (int) ubuf(buf[m++]).i; + rmass[i] = buf[m++]; ellipsoid[i] = (int) ubuf(buf[m++]).i; if (ellipsoid[i] == 0) ellipsoid[i] = -1; else { @@ -812,6 +819,7 @@ void AtomVecEllipsoid::unpack_border_vel(int n, int first, double *buf) tag[i] = (tagint) ubuf(buf[m++]).i; type[i] = (int) ubuf(buf[m++]).i; mask[i] = (int) ubuf(buf[m++]).i; + rmass[i] = buf[m++]; ellipsoid[i] = (int) ubuf(buf[m++]).i; if (ellipsoid[i] == 0) ellipsoid[i] = -1; else { @@ -854,6 +862,7 @@ int AtomVecEllipsoid::unpack_border_hybrid(int n, int first, double *buf) m = 0; last = first + n; for (i = first; i < last; i++) { + rmass[i] = buf[m++]; ellipsoid[i] = (int) ubuf(buf[m++]).i; if (ellipsoid[i] == 0) ellipsoid[i] = -1; else { -- GitLab From 856efa28aab9a140f37875a7ed5df96419280ad0 Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Wed, 17 Jul 2019 19:37:08 -0400 Subject: [PATCH 260/469] fix issue #1568 --- src/utils.cpp | 1 + 1 file changed, 1 insertion(+) diff --git a/src/utils.cpp b/src/utils.cpp index bbda22f24c..34e6e6fae6 100644 --- a/src/utils.cpp +++ b/src/utils.cpp @@ -13,6 +13,7 @@ #include #include +#include #include "utils.h" #include "lammps.h" #include "error.h" -- GitLab From 60ebc08d0f6da5b9b74011b9728c069cb6973cee Mon Sep 17 00:00:00 2001 From: julient31 Date: Wed, 17 Jul 2019 21:49:26 -0600 Subject: [PATCH 261/469] Commit JT 071719 - added doc for read_data spin - corrected an error in pack/unpack data hybrid - added mask flags in fix_nve_spin::initial_integrate - removed spin renormalization in min_spin (was causing a bug) --- doc/src/read_data.txt | 3 ++ src/SPIN/atom_vec_spin.cpp | 18 +++++------ src/SPIN/fix_nve_spin.cpp | 66 +++++++++++++++++++++++--------------- src/SPIN/min_spin.cpp | 6 ---- 4 files changed, 53 insertions(+), 40 deletions(-) diff --git a/doc/src/read_data.txt b/doc/src/read_data.txt index 62112ea886..5fb91ba797 100644 --- a/doc/src/read_data.txt +++ b/doc/src/read_data.txt @@ -565,6 +565,7 @@ molecular: atom-ID molecule-ID atom-type x y z peri: atom-ID atom-type volume density x y z smd: atom-ID atom-type molecule volume mass kernel-radius contact-radius x y z sphere: atom-ID atom-type diameter density x y z +spin: atom-ID atom-type sp x y z spx spy spz template: atom-ID molecule-ID template-index template-atom atom-type x y z tri: atom-ID molecule-ID atom-type triangleflag density x y z wavepacket: atom-ID atom-type charge spin eradius etag cs_re cs_im x y z @@ -595,6 +596,8 @@ mux,muy,muz = components of dipole moment of atom (dipole units) q = charge on atom (charge units) rho = density (need units) for SPH particles spin = electron spin (+1/-1), 0 = nuclei, 2 = fixed-core, 3 = pseudo-cores (i.e. ECP) +sp = norm of magnetic spin of atom (in number of Bohr magnetons) +spx,spy,spz = components of magnetic spin of atom (adim normalized vector) template-atom = which atom within a template molecule the atom is template-index = which molecule within the molecule template the atom is part of theta = internal temperature of a DPD particle diff --git a/src/SPIN/atom_vec_spin.cpp b/src/SPIN/atom_vec_spin.cpp index 5b4173509f..8cc38dbc15 100644 --- a/src/SPIN/atom_vec_spin.cpp +++ b/src/SPIN/atom_vec_spin.cpp @@ -263,10 +263,10 @@ int AtomVecSpin::pack_comm_hybrid(int n, int *list, double *buf) m = 0; for (i = 0; i < n; i++) { j = list[i]; + buf[m++] = sp[j][3]; buf[m++] = sp[j][0]; buf[m++] = sp[j][1]; buf[m++] = sp[j][2]; - buf[m++] = sp[j][3]; } return m; } @@ -321,10 +321,10 @@ int AtomVecSpin::unpack_comm_hybrid(int n, int first, double *buf) m = 0; last = first + n; for (i = first; i < last; i++) { + sp[i][3] = buf[m++]; sp[i][0] = buf[m++]; sp[i][1] = buf[m++]; sp[i][2] = buf[m++]; - sp[i][3] = buf[m++]; } return m; } @@ -524,10 +524,10 @@ int AtomVecSpin::pack_border_hybrid(int n, int *list, double *buf) m = 0; for (i = 0; i < n; i++) { j = list[i]; + buf[m++] = sp[j][3]; buf[m++] = sp[j][0]; buf[m++] = sp[j][1]; buf[m++] = sp[j][2]; - buf[m++] = sp[j][3]; } return m; @@ -603,10 +603,10 @@ int AtomVecSpin::unpack_border_hybrid(int n, int first, double *buf) m = 0; last = first + n; for (i = first; i < last; i++) { + sp[i][3] = buf[m++]; sp[i][0] = buf[m++]; sp[i][1] = buf[m++]; sp[i][2] = buf[m++]; - sp[i][3] = buf[m++]; } return m; @@ -894,10 +894,10 @@ void AtomVecSpin::pack_data(double **buf) int AtomVecSpin::pack_data_hybrid(int i, double *buf) { - buf[0] = sp[i][0]; - buf[1] = sp[i][1]; - buf[2] = sp[i][2]; - buf[3] = sp[i][3]; + buf[0] = sp[i][3]; + buf[1] = sp[i][0]; + buf[2] = sp[i][1]; + buf[3] = sp[i][2]; return 4; } @@ -924,7 +924,7 @@ void AtomVecSpin::write_data(FILE *fp, int n, double **buf) int AtomVecSpin::write_data_hybrid(FILE *fp, double *buf) { - fprintf(fp," %-1.16e %-1.16e %-1.16e %-1.16e %-1.16e",buf[0],buf[1],buf[2],buf[3],buf[4]); + fprintf(fp," %-1.16e %-1.16e %-1.16e %-1.16e",buf[0],buf[1],buf[2],buf[3]); return 4; } diff --git a/src/SPIN/fix_nve_spin.cpp b/src/SPIN/fix_nve_spin.cpp index 595ddb0cc2..b992f17cc3 100644 --- a/src/SPIN/fix_nve_spin.cpp +++ b/src/SPIN/fix_nve_spin.cpp @@ -312,29 +312,37 @@ void FixNVESpin::initial_integrate(int /*vflag*/) comm->forward_comm(); int i = stack_foot[j]; while (i >= 0) { - ComputeInteractionsSpin(i); - AdvanceSingleSpin(i); - i = forward_stacks[i]; + if (mask[i] & groupbit) { + ComputeInteractionsSpin(i); + AdvanceSingleSpin(i); + i = forward_stacks[i]; + } } } for (int j = nsectors-1; j >= 0; j--) { // advance quarter s for nlocal comm->forward_comm(); int i = stack_head[j]; while (i >= 0) { - ComputeInteractionsSpin(i); - AdvanceSingleSpin(i); - i = backward_stacks[i]; + if (mask[i] & groupbit) { + ComputeInteractionsSpin(i); + AdvanceSingleSpin(i); + i = backward_stacks[i]; + } } } } else if (sector_flag == 0) { // serial seq. update comm->forward_comm(); // comm. positions of ghost atoms for (int i = 0; i < nlocal; i++){ // advance quarter s for nlocal - ComputeInteractionsSpin(i); - AdvanceSingleSpin(i); + if (mask[i] & groupbit) { + ComputeInteractionsSpin(i); + AdvanceSingleSpin(i); + } } for (int i = nlocal-1; i >= 0; i--){ // advance quarter s for nlocal - ComputeInteractionsSpin(i); - AdvanceSingleSpin(i); + if (mask[i] & groupbit) { + ComputeInteractionsSpin(i); + AdvanceSingleSpin(i); + } } } else error->all(FLERR,"Illegal fix NVE/spin command"); @@ -357,29 +365,37 @@ void FixNVESpin::initial_integrate(int /*vflag*/) comm->forward_comm(); int i = stack_foot[j]; while (i >= 0) { - ComputeInteractionsSpin(i); - AdvanceSingleSpin(i); - i = forward_stacks[i]; + if (mask[i] & groupbit) { + ComputeInteractionsSpin(i); + AdvanceSingleSpin(i); + i = forward_stacks[i]; + } } } for (int j = nsectors-1; j >= 0; j--) { // advance quarter s for nlocal comm->forward_comm(); int i = stack_head[j]; while (i >= 0) { - ComputeInteractionsSpin(i); - AdvanceSingleSpin(i); - i = backward_stacks[i]; + if (mask[i] & groupbit) { + ComputeInteractionsSpin(i); + AdvanceSingleSpin(i); + i = backward_stacks[i]; + } } } } else if (sector_flag == 0) { // serial seq. update comm->forward_comm(); // comm. positions of ghost atoms for (int i = 0; i < nlocal; i++){ // advance quarter s for nlocal-1 - ComputeInteractionsSpin(i); - AdvanceSingleSpin(i); + if (mask[i] & groupbit) { + ComputeInteractionsSpin(i); + AdvanceSingleSpin(i); + } } for (int i = nlocal-1; i >= 0; i--){ // advance quarter s for nlocal-1 - ComputeInteractionsSpin(i); - AdvanceSingleSpin(i); + if (mask[i] & groupbit) { + ComputeInteractionsSpin(i); + AdvanceSingleSpin(i); + } } } else error->all(FLERR,"Illegal fix NVE/spin command"); @@ -613,11 +629,11 @@ void FixNVESpin::AdvanceSingleSpin(int i) // renormalization (check if necessary) - //msq = g[0]*g[0] + g[1]*g[1] + g[2]*g[2]; - //scale = 1.0/sqrt(msq); - //sp[i][0] *= scale; - //sp[i][1] *= scale; - //sp[i][2] *= scale; + // msq = g[0]*g[0] + g[1]*g[1] + g[2]*g[2]; + // scale = 1.0/sqrt(msq); + // sp[i][0] *= scale; + // sp[i][1] *= scale; + // sp[i][2] *= scale; // comm. sp[i] to atoms with same tag (for serial algo) diff --git a/src/SPIN/min_spin.cpp b/src/SPIN/min_spin.cpp index 2bddc110e7..dda414ff97 100644 --- a/src/SPIN/min_spin.cpp +++ b/src/SPIN/min_spin.cpp @@ -287,12 +287,6 @@ void MinSpin::advance_spins(double dts) // renormalization (check if necessary) - msq = g[0]*g[0] + g[1]*g[1] + g[2]*g[2]; - scale = 1.0/sqrt(msq); - sp[i][0] *= scale; - sp[i][1] *= scale; - sp[i][2] *= scale; - // no comm. to atoms with same tag // because no need for simplecticity } -- GitLab From 22b73a316fb59f691660ba2c404b1c36a3ce49bc Mon Sep 17 00:00:00 2001 From: julient31 Date: Wed, 17 Jul 2019 22:15:23 -0600 Subject: [PATCH 262/469] Commit2 JT 071719 - added 'magnetons' to false-positive for doc --- doc/utils/sphinx-config/false_positives.txt | 1 + 1 file changed, 1 insertion(+) diff --git a/doc/utils/sphinx-config/false_positives.txt b/doc/utils/sphinx-config/false_positives.txt index 9a46983539..da5c869075 100644 --- a/doc/utils/sphinx-config/false_positives.txt +++ b/doc/utils/sphinx-config/false_positives.txt @@ -1521,6 +1521,7 @@ Magdeburg magelec Maginn magneton +magnetons mainboard mainboards makefile -- GitLab From 92518e53f4146abf236a73e5ffed4b5db0b0e37d Mon Sep 17 00:00:00 2001 From: jrgissing Date: Wed, 17 Jul 2019 22:58:40 -0600 Subject: [PATCH 263/469] Revert "spelling: attempt add file paths to false positives" This reverts commit 0c4af8b820f4d6f559d07086db91a2c1dee67a47. --- doc/utils/sphinx-config/conf.py | 3 --- doc/utils/sphinx-config/custom_filters.py | 9 --------- 2 files changed, 12 deletions(-) delete mode 100644 doc/utils/sphinx-config/custom_filters.py diff --git a/doc/utils/sphinx-config/conf.py b/doc/utils/sphinx-config/conf.py index 646fbd2e94..29de3af156 100644 --- a/doc/utils/sphinx-config/conf.py +++ b/doc/utils/sphinx-config/conf.py @@ -312,6 +312,3 @@ if spelling_spec: spelling_lang='en_US' spelling_word_list_filename='false_positives.txt' - - from custom_filters import PathFilter - spelling_filters = [PathFilter] diff --git a/doc/utils/sphinx-config/custom_filters.py b/doc/utils/sphinx-config/custom_filters.py deleted file mode 100644 index 3df26854e4..0000000000 --- a/doc/utils/sphinx-config/custom_filters.py +++ /dev/null @@ -1,9 +0,0 @@ -class PathFilter(Filter): - r"""Filter skipping over simple file paths - """ - _DOC_ERRORS = ["zA"] - _pattern = re.compile(r"\/[^\s].*") - def _skip(self,word): - if self._pattern.match(word): - return True - return False -- GitLab From 8cf1084decf4a5c765ab67b6d94c73aadac6e9e3 Mon Sep 17 00:00:00 2001 From: jrgissing Date: Wed, 17 Jul 2019 23:05:28 -0600 Subject: [PATCH 264/469] bond/react: use Unix path in docs --- doc/src/fix_bond_react.txt | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/doc/src/fix_bond_react.txt b/doc/src/fix_bond_react.txt index 7310545e1c..37b916cbea 100644 --- a/doc/src/fix_bond_react.txt +++ b/doc/src/fix_bond_react.txt @@ -52,7 +52,7 @@ react = mandatory argument indicating new reaction specification :l [Examples:] -For unabridged example scripts and files, see \examples\USER\misc\bond_react. +For unabridged example scripts and files, see examples/USER/misc/bond_react. molecule mol1 pre_reacted_topology.txt molecule mol2 post_reacted_topology.txt -- GitLab From 87154da7f5c95ed22d3f7085e0d5a40733788dca Mon Sep 17 00:00:00 2001 From: jrgissing Date: Wed, 17 Jul 2019 23:24:12 -0600 Subject: [PATCH 265/469] another Unix path correction --- doc/src/fix_bond_react.txt | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/doc/src/fix_bond_react.txt b/doc/src/fix_bond_react.txt index 37b916cbea..3f428e2103 100644 --- a/doc/src/fix_bond_react.txt +++ b/doc/src/fix_bond_react.txt @@ -135,7 +135,7 @@ constant-topology parts of your system separately. The dynamic group contains only atoms not involved in a reaction at a given timestep, and therefore should be used by a subsequent system-wide time integrator such as nvt, npt, or nve, as shown in the second example -above (full examples can be found at \examples\USER\misc\bond_react). +above (full examples can be found at examples/USER/misc/bond_react). The time integration command should be placed after the fix bond/react command due to the internal dynamic grouping performed by fix bond/react. -- GitLab From e5fffa59ef5e244f5516415ef5822ce8d645cde6 Mon Sep 17 00:00:00 2001 From: Stan Moore Date: Thu, 18 Jul 2019 15:29:45 -0600 Subject: [PATCH 266/469] Add optimized version of Kokkos SNAP --- src/KOKKOS/pair_snap_kokkos.h | 48 +- src/KOKKOS/pair_snap_kokkos_impl.h | 431 +++++++++--------- src/KOKKOS/sna_kokkos.h | 97 ++-- src/KOKKOS/sna_kokkos_impl.h | 681 ++++++++++------------------- 4 files changed, 526 insertions(+), 731 deletions(-) diff --git a/src/KOKKOS/pair_snap_kokkos.h b/src/KOKKOS/pair_snap_kokkos.h index 8be0bf9afb..2193e9ff24 100644 --- a/src/KOKKOS/pair_snap_kokkos.h +++ b/src/KOKKOS/pair_snap_kokkos.h @@ -31,10 +31,17 @@ PairStyle(snap/kk/host,PairSNAPKokkos) namespace LAMMPS_NS { template -struct TagPairSNAPCompute{}; +struct TagPairSNAPComputeForce{}; struct TagPairSNAPBeta{}; -struct TagPairSNAPBispectrum{}; +struct TagPairSNAPComputeNeigh{}; +struct TagPairSNAPPreUi{}; +struct TagPairSNAPComputeUi{}; +struct TagPairSNAPComputeZi{}; +struct TagPairSNAPComputeBi{}; +struct TagPairSNAPComputeYi{}; +struct TagPairSNAPComputeDuidrj{}; +struct TagPairSNAPComputeDeidrj{}; template class PairSNAPKokkos : public PairSNAP { @@ -56,17 +63,38 @@ public: template KOKKOS_INLINE_FUNCTION - void operator() (TagPairSNAPCompute,const typename Kokkos::TeamPolicy >::member_type& team) const; + void operator() (TagPairSNAPComputeForce,const typename Kokkos::TeamPolicy >::member_type& team) const; template KOKKOS_INLINE_FUNCTION - void operator() (TagPairSNAPCompute,const typename Kokkos::TeamPolicy >::member_type& team, EV_FLOAT&) const; + void operator() (TagPairSNAPComputeForce,const typename Kokkos::TeamPolicy >::member_type& team, EV_FLOAT&) const; KOKKOS_INLINE_FUNCTION - void operator() (TagPairSNAPBeta,const typename Kokkos::TeamPolicy::member_type& team) const; + void operator() (TagPairSNAPComputeNeigh,const typename Kokkos::TeamPolicy::member_type& team) const; + + KOKKOS_INLINE_FUNCTION + void operator() (TagPairSNAPPreUi,const typename Kokkos::TeamPolicy::member_type& team) const; + + KOKKOS_INLINE_FUNCTION + void operator() (TagPairSNAPComputeUi,const typename Kokkos::TeamPolicy::member_type& team) const; + + KOKKOS_INLINE_FUNCTION + void operator() (TagPairSNAPComputeZi,const typename Kokkos::TeamPolicy::member_type& team) const; + + KOKKOS_INLINE_FUNCTION + void operator() (TagPairSNAPComputeBi,const typename Kokkos::TeamPolicy::member_type& team) const; + + KOKKOS_INLINE_FUNCTION + void operator() (TagPairSNAPComputeYi,const typename Kokkos::TeamPolicy::member_type& team) const; + + KOKKOS_INLINE_FUNCTION + void operator() (TagPairSNAPComputeDuidrj,const typename Kokkos::TeamPolicy::member_type& team) const; + + KOKKOS_INLINE_FUNCTION + void operator() (TagPairSNAPComputeDeidrj,const typename Kokkos::TeamPolicy::member_type& team) const; KOKKOS_INLINE_FUNCTION - void operator() (TagPairSNAPBispectrum,const typename Kokkos::TeamPolicy::member_type& team) const; + void operator() (TagPairSNAPBeta,const typename Kokkos::TeamPolicy::member_type& team) const; template KOKKOS_INLINE_FUNCTION @@ -90,15 +118,10 @@ protected: t_dbvec dbvec; SNAKokkos snaKK; - // How much parallelism to use within an interaction - int vector_length,team_size; - int team_scratch_size; - int thread_scratch_size; + int inum,max_neighs,chunk_offset; int eflag,vflag; - void compute_beta(); - void compute_bispectrum(); void allocate(); //void read_files(char *, char *); /*template @@ -131,6 +154,7 @@ inline double dist2(double* x,double* y); Kokkos::View d_wjelem; // elements weights Kokkos::View d_coeffelem; // element bispectrum coefficients Kokkos::View d_map; // mapping from atom types to elements + Kokkos::View d_ninside; // ninside for all atoms in list Kokkos::View d_beta; // betas for all atoms in list Kokkos::View d_bispectrum; // bispectrum components for all atoms in list diff --git a/src/KOKKOS/pair_snap_kokkos_impl.h b/src/KOKKOS/pair_snap_kokkos_impl.h index 8d72d1fac4..645521a17b 100644 --- a/src/KOKKOS/pair_snap_kokkos_impl.h +++ b/src/KOKKOS/pair_snap_kokkos_impl.h @@ -57,7 +57,6 @@ PairSNAPKokkos::PairSNAPKokkos(LAMMPS *lmp) : PairSNAP(lmp) datamask_read = EMPTY_MASK; datamask_modify = EMPTY_MASK; - vector_length = 8; k_cutsq = tdual_fparams("PairSNAPKokkos::cutsq",atom->ntypes+1,atom->ntypes+1); auto d_cutsq = k_cutsq.template view(); rnd_cutsq = d_cutsq; @@ -164,7 +163,7 @@ void PairSNAPKokkos::compute(int eflag_in, int vflag_in) d_numneigh = k_list->d_numneigh; d_neighbors = k_list->d_neighbors; d_ilist = k_list->d_ilist; - int inum = list->inum; + inum = list->inum; need_dup = lmp->kokkos->need_dup(); if (need_dup) { @@ -181,70 +180,112 @@ void PairSNAPKokkos::compute(int eflag_in, int vflag_in) const int num_neighs = neighs_i.get_num_neighs(); if (max_neighs(k_list), Kokkos::Experimental::Max(max_neighs)); - snaKK.nmax = max_neighs; - - team_scratch_size = snaKK.size_team_scratch_arrays(); - thread_scratch_size = snaKK.size_thread_scratch_arrays(); - - //printf("Sizes: %i %i\n",team_scratch_size/1024,thread_scratch_size/1024); + int vector_length = 1; + int ui_vector_length = 1; + int team_size = 1; + int yi_team_size = 1; int team_size_max = Kokkos::TeamPolicy::team_size_max(*this); - vector_length = 8; #ifdef KOKKOS_ENABLE_CUDA team_size = 32;//max_neighs; if (team_size*vector_length > team_size_max) team_size = team_size_max/vector_length; -#else - team_size = 1; + + yi_team_size = 256; + if (yi_team_size*vector_length > team_size_max) + yi_team_size = team_size_max/vector_length; + + ui_vector_length = 8; + if (team_size*ui_vector_length > team_size_max) + team_size = team_size_max/ui_vector_length; #endif - if (beta_max < list->inum) { - d_beta = Kokkos::View("PairSNAPKokkos:beta", - list->inum,ncoeff); - d_bispectrum = Kokkos::View("PairSNAPKokkos:bispectrum", - list->inum,ncoeff); - beta_max = list->inum; + if (beta_max < inum) { + beta_max = inum; + d_beta = Kokkos::View("PairSNAPKokkos:beta",inum,ncoeff); + d_ninside = Kokkos::View("PairSNAPKokkos:ninside",inum); } - // compute dE_i/dB_i = beta_i for all i in list + int chunk_size = 2000; + chunk_offset = 0; - if (quadraticflag || eflag) - compute_bispectrum(); - compute_beta(); + snaKK.grow_rij(chunk_size,max_neighs); EV_FLOAT ev; - if (eflag) { - if (neighflag == HALF) { - typename Kokkos::TeamPolicy > policy(inum,team_size,vector_length); - Kokkos::parallel_reduce(policy - .set_scratch_size(1,Kokkos::PerThread(thread_scratch_size)) - .set_scratch_size(1,Kokkos::PerTeam(team_scratch_size)) - ,*this,ev); - } else if (neighflag == HALFTHREAD) { - typename Kokkos::TeamPolicy > policy(inum,team_size,vector_length); - Kokkos::parallel_reduce(policy - .set_scratch_size(1,Kokkos::PerThread(thread_scratch_size)) - .set_scratch_size(1,Kokkos::PerTeam(team_scratch_size)) - ,*this,ev); + while (chunk_offset < inum) { // chunk up loop to prevent running out of memory + + EV_FLOAT ev_tmp; + + if (chunk_size > inum - chunk_offset) + chunk_size = inum - chunk_offset; + + //ComputeNeigh + typename Kokkos::TeamPolicy policy_neigh(chunk_size,team_size,vector_length); + Kokkos::parallel_for("ComputeNeigh",policy_neigh,*this); + + //PreUi + typename Kokkos::TeamPolicy policy_preui(chunk_size,team_size,vector_length); + Kokkos::parallel_for("PreUi",policy_preui,*this); + + //ComputeUi + typename Kokkos::TeamPolicy policy_ui(((inum+team_size-1)/team_size)*max_neighs,team_size,ui_vector_length); + Kokkos::parallel_for("ComputeUi",policy_ui,*this); + + //Compute bispectrum + if (quadraticflag || eflag) { + //ComputeZi + typename Kokkos::TeamPolicy policy_zi(chunk_size,team_size,vector_length); + Kokkos::parallel_for("ComputeZi",policy_zi,*this); + + //ComputeBi + typename Kokkos::TeamPolicy policy_bi(chunk_size,team_size,vector_length); + Kokkos::parallel_for("ComputeBi",policy_bi,*this); } - } else { - if (neighflag == HALF) { - typename Kokkos::TeamPolicy > policy(inum,team_size,vector_length); - Kokkos::parallel_for(policy - .set_scratch_size(1,Kokkos::PerThread(thread_scratch_size)) - .set_scratch_size(1,Kokkos::PerTeam(team_scratch_size)) - ,*this); - } else if (neighflag == HALFTHREAD) { - typename Kokkos::TeamPolicy > policy(inum,team_size,vector_length); - Kokkos::parallel_for(policy - .set_scratch_size(1,Kokkos::PerThread(thread_scratch_size)) - .set_scratch_size(1,Kokkos::PerTeam(team_scratch_size)) - ,*this); + + //Compute beta = dE_i/dB_i for all i in list + typename Kokkos::TeamPolicy policy_beta(chunk_size,team_size,vector_length); + Kokkos::parallel_for("ComputeBeta",policy_beta,*this); + + //ComputeYi + typename Kokkos::TeamPolicy policy_yi(chunk_size,yi_team_size,vector_length); + Kokkos::parallel_for("ComputeYi",policy_yi,*this); + + //ComputeDuidrj + typename Kokkos::TeamPolicy policy_duidrj(((inum+team_size-1)/team_size)*max_neighs,team_size,vector_length); + Kokkos::parallel_for("ComputeDuidrj",policy_duidrj,*this); + + //ComputeDeidrj + typename Kokkos::TeamPolicy policy_deidrj(((inum+team_size-1)/team_size)*max_neighs,team_size,vector_length); + Kokkos::parallel_for("ComputeDeidrj",policy_deidrj,*this); + + //ComputeForce + if (eflag) { + if (neighflag == HALF) { + typename Kokkos::TeamPolicy > policy_force(chunk_size,team_size,vector_length); + Kokkos::parallel_reduce(policy_force + ,*this,ev_tmp); + } else if (neighflag == HALFTHREAD) { + typename Kokkos::TeamPolicy > policy_force(chunk_size,team_size,vector_length); + Kokkos::parallel_reduce(policy_force + ,*this,ev_tmp); + } + } else { + if (neighflag == HALF) { + typename Kokkos::TeamPolicy > policy_force(chunk_size,team_size,vector_length); + Kokkos::parallel_for(policy_force + ,*this); + } else if (neighflag == HALFTHREAD) { + typename Kokkos::TeamPolicy > policy_force(chunk_size,team_size,vector_length); + Kokkos::parallel_for(policy_force + ,*this); + } } - } + ev += ev_tmp; + chunk_offset += chunk_size; + } // end while if (need_dup) Kokkos::Experimental::contribute(f, dup_f); @@ -284,32 +325,19 @@ void PairSNAPKokkos::compute(int eflag_in, int vflag_in) } } -/* ---------------------------------------------------------------------- - compute beta -------------------------------------------------------------------------- */ - -template -void PairSNAPKokkos::compute_beta() -{ - // TODO: use RangePolicy instead, or thread over ncoeff? - int inum = list->inum; - typename Kokkos::TeamPolicy policy(inum,team_size,vector_length); - Kokkos::parallel_for(policy - .set_scratch_size(1,Kokkos::PerThread(thread_scratch_size)) - .set_scratch_size(1,Kokkos::PerTeam(team_scratch_size)) - ,*this); -} - /* ---------------------------------------------------------------------- */ template KOKKOS_INLINE_FUNCTION void PairSNAPKokkos::operator() (TagPairSNAPBeta,const typename Kokkos::TeamPolicy::member_type& team) const { + // TODO: use RangePolicy instead, or thread over ncoeff? const int ii = team.league_rank(); - const int i = d_ilist[ii]; + const int i = d_ilist[ii + chunk_offset]; const int itype = type[i]; const int ielem = d_map[itype]; + SNAKokkos my_sna = snaKK; + Kokkos::View> d_coeffi(d_coeffelem,ielem,Kokkos::ALL); @@ -319,11 +347,11 @@ void PairSNAPKokkos::operator() (TagPairSNAPBeta,const typename Kokk if (quadraticflag) { int k = ncoeff+1; for (int icoeff = 0; icoeff < ncoeff; icoeff++) { - double bveci = d_bispectrum(ii,icoeff); + double bveci = my_sna.blist(ii,icoeff); d_beta(ii,icoeff) += d_coeffi[k]*bveci; k++; for (int jcoeff = icoeff+1; jcoeff < ncoeff; jcoeff++) { - double bvecj = d_bispectrum(ii,jcoeff); + double bvecj = my_sna.blist(ii,jcoeff); d_beta(ii,icoeff) += d_coeffi[k]*bvecj; d_beta(ii,jcoeff) += d_coeffi[k]*bveci; k++; @@ -332,105 +360,6 @@ void PairSNAPKokkos::operator() (TagPairSNAPBeta,const typename Kokk } } -/* ---------------------------------------------------------------------- - compute bispectrum -------------------------------------------------------------------------- */ - -template -void PairSNAPKokkos::compute_bispectrum() -{ - int inum = list->inum; - typename Kokkos::TeamPolicy policy(inum,team_size,vector_length); - Kokkos::parallel_for(policy - .set_scratch_size(1,Kokkos::PerThread(thread_scratch_size)) - .set_scratch_size(1,Kokkos::PerTeam(team_scratch_size)) - ,*this); -} - -/* ---------------------------------------------------------------------- */ - -template -KOKKOS_INLINE_FUNCTION -void PairSNAPKokkos::operator() (TagPairSNAPBispectrum,const typename Kokkos::TeamPolicy::member_type& team) const { - - const int ii = team.league_rank(); - const int i = d_ilist[ii]; - SNAKokkos my_sna(snaKK,team); - const double xtmp = x(i,0); - const double ytmp = x(i,1); - const double ztmp = x(i,2); - const int itype = type[i]; - const int ielem = d_map[itype]; - const double radi = d_radelem[ielem]; - - const int num_neighs = d_numneigh[i]; - - // rij[][3] = displacements between atom I and those neighbors - // inside = indices of neighbors of I within cutoff - // wj = weights for neighbors of I within cutoff - // rcutij = cutoffs for neighbors of I within cutoff - // note Rij sign convention => dU/dRij = dU/dRj = -dU/dRi - - int ninside = 0; - Kokkos::parallel_reduce(Kokkos::TeamThreadRange(team,num_neighs), - [&] (const int jj, int& count) { - Kokkos::single(Kokkos::PerThread(team), [&] (){ - T_INT j = d_neighbors(i,jj); - const F_FLOAT dx = x(j,0) - xtmp; - const F_FLOAT dy = x(j,1) - ytmp; - const F_FLOAT dz = x(j,2) - ztmp; - - const int jtype = type(j); - const F_FLOAT rsq = dx*dx + dy*dy + dz*dz; - const int elem_j = d_map[jtype]; - - if ( rsq < rnd_cutsq(itype,jtype) ) - count++; - }); - },ninside); - - if (team.team_rank() == 0) - Kokkos::parallel_scan(Kokkos::ThreadVectorRange(team,num_neighs), - [&] (const int jj, int& offset, bool final) { - //for (int jj = 0; jj < num_neighs; jj++) { - T_INT j = d_neighbors(i,jj); - const F_FLOAT dx = x(j,0) - xtmp; - const F_FLOAT dy = x(j,1) - ytmp; - const F_FLOAT dz = x(j,2) - ztmp; - - const int jtype = type(j); - const F_FLOAT rsq = dx*dx + dy*dy + dz*dz; - const int elem_j = d_map[jtype]; - - if ( rsq < rnd_cutsq(itype,jtype) ) { - if (final) { - my_sna.rij(offset,0) = dx; - my_sna.rij(offset,1) = dy; - my_sna.rij(offset,2) = dz; - my_sna.inside[offset] = j; - my_sna.wj[offset] = d_wjelem[elem_j]; - my_sna.rcutij[offset] = (radi + d_radelem[elem_j])*rcutfac; - } - offset++; - } - }); - team.team_barrier(); - - // compute Ui, Zi, and Bi for atom I - - my_sna.compute_ui(team,ninside); - team.team_barrier(); - - my_sna.compute_zi(team); - team.team_barrier(); - - my_sna.compute_bi(team); - team.team_barrier(); - - for (int icoeff = 0; icoeff < ncoeff; icoeff++) - d_bispectrum(ii,icoeff) = my_sna.blist[icoeff]; -} - /* ---------------------------------------------------------------------- allocate all arrays ------------------------------------------------------------------------- */ @@ -496,30 +425,21 @@ void PairSNAPKokkos::coeff(int narg, char **arg) Kokkos::deep_copy(d_coeffelem,h_coeffelem); Kokkos::deep_copy(d_map,h_map); - // allocate memory for per OpenMP thread data which - // is wrapped into the sna class - snaKK = SNAKokkos(rfac0,twojmax, rmin0,switchflag,bzeroflag); - snaKK.grow_rij(0); + snaKK.grow_rij(0,0); snaKK.init(); } /* ---------------------------------------------------------------------- */ template -template KOKKOS_INLINE_FUNCTION -void PairSNAPKokkos::operator() (TagPairSNAPCompute,const typename Kokkos::TeamPolicy >::member_type& team, EV_FLOAT& ev) const { - - // The f array is duplicated for OpenMP, atomic for CUDA, and neither for Serial - - auto v_f = ScatterViewHelper::value,decltype(dup_f),decltype(ndup_f)>::get(dup_f,ndup_f); - auto a_f = v_f.template access::value>(); +void PairSNAPKokkos::operator() (TagPairSNAPComputeNeigh,const typename Kokkos::TeamPolicy::member_type& team) const { const int ii = team.league_rank(); - const int i = d_ilist[ii]; - SNAKokkos my_sna(snaKK,team); + const int i = d_ilist[ii + chunk_offset]; + SNAKokkos my_sna = snaKK; const double xtmp = x(i,0); const double ytmp = x(i,1); const double ztmp = x(i,2); @@ -553,6 +473,8 @@ void PairSNAPKokkos::operator() (TagPairSNAPCompute::operator() (TagPairSNAPCompute +KOKKOS_INLINE_FUNCTION +void PairSNAPKokkos::operator() (TagPairSNAPPreUi,const typename Kokkos::TeamPolicy::member_type& team) const { + const int ii = team.league_rank(); + SNAKokkos my_sna = snaKK; + my_sna.pre_ui(team,ii); +} - my_sna.compute_ui(team,ninside); - team.team_barrier(); +template +KOKKOS_INLINE_FUNCTION +void PairSNAPKokkos::operator() (TagPairSNAPComputeUi,const typename Kokkos::TeamPolicy::member_type& team) const { + SNAKokkos my_sna = snaKK; - // for neighbors of I within cutoff: - // compute Fij = dEi/dRj = -dEi/dRi - // add to Fi, subtract from Fj + // Extract the atom number + const int ii = team.team_rank() + team.team_size() * (team.league_rank() % ((inum+team.team_size()-1)/team.team_size())); + if (ii >= inum) return; - my_sna.compute_yi(team,d_beta,ii); - team.team_barrier(); + // Extract the neighbor number + const int jj = team.league_rank() / ((inum+team.team_size()-1)/team.team_size()); + const int ninside = d_ninside(ii); + if (jj >= ninside) return; - Kokkos::View> - d_coeffi(d_coeffelem,ielem,Kokkos::ALL); + my_sna.compute_ui(team,ii,jj); +} + +template +KOKKOS_INLINE_FUNCTION +void PairSNAPKokkos::operator() (TagPairSNAPComputeYi,const typename Kokkos::TeamPolicy::member_type& team) const { + const int ii = team.league_rank(); + SNAKokkos my_sna = snaKK; + my_sna.compute_yi(team,ii,d_beta); +} + +template +KOKKOS_INLINE_FUNCTION +void PairSNAPKokkos::operator() (TagPairSNAPComputeZi,const typename Kokkos::TeamPolicy::member_type& team) const { + const int ii = team.league_rank(); + SNAKokkos my_sna = snaKK; + my_sna.compute_zi(team,ii); +} + +template +KOKKOS_INLINE_FUNCTION +void PairSNAPKokkos::operator() (TagPairSNAPComputeBi,const typename Kokkos::TeamPolicy::member_type& team) const { + const int ii = team.league_rank(); + SNAKokkos my_sna = snaKK; + my_sna.compute_bi(team,ii); +} + +template +KOKKOS_INLINE_FUNCTION +void PairSNAPKokkos::operator() (TagPairSNAPComputeDuidrj,const typename Kokkos::TeamPolicy::member_type& team) const { + SNAKokkos my_sna = snaKK; + + // Extract the atom number + const int ii = team.team_rank() + team.team_size() * (team.league_rank() % ((inum+team.team_size()-1)/team.team_size())); + if (ii >= inum) return; + + // Extract the neighbor number + const int jj = team.league_rank() / ((inum+team.team_size()-1)/team.team_size()); + const int ninside = d_ninside(ii); + if (jj >= ninside) return; + + my_sna.compute_duidrj(team,ii,jj); +} + +template +KOKKOS_INLINE_FUNCTION +void PairSNAPKokkos::operator() (TagPairSNAPComputeDeidrj,const typename Kokkos::TeamPolicy::member_type& team) const { + SNAKokkos my_sna = snaKK; + + // Extract the atom number + const int ii = team.team_rank() + team.team_size() * (team.league_rank() % ((inum+team.team_size()-1)/team.team_size())); + if (ii >= inum) return; + + // Extract the neighbor number + const int jj = team.league_rank() / ((inum+team.team_size()-1)/team.team_size()); + const int ninside = d_ninside(ii); + if (jj >= ninside) return; + + my_sna.compute_deidrj(team,ii,jj); +} + +template +template +KOKKOS_INLINE_FUNCTION +void PairSNAPKokkos::operator() (TagPairSNAPComputeForce,const typename Kokkos::TeamPolicy >::member_type& team, EV_FLOAT& ev) const { + + // The f array is duplicated for OpenMP, atomic for CUDA, and neither for Serial + + auto v_f = ScatterViewHelper::value,decltype(dup_f),decltype(ndup_f)>::get(dup_f,ndup_f); + auto a_f = v_f.template access::value>(); + + const int ii = team.league_rank(); + const int i = d_ilist[ii + chunk_offset]; + SNAKokkos my_sna = snaKK; + const int ninside = d_ninside(ii); Kokkos::parallel_for (Kokkos::TeamThreadRange(team,ninside), [&] (const int jj) { - //for (int jj = 0; jj < ninside; jj++) { - int j = my_sna.inside[jj]; - - my_sna.compute_duidrj(team,&my_sna.rij(jj,0), - my_sna.wj[jj],my_sna.rcutij[jj],jj); + int j = my_sna.inside(ii,jj); F_FLOAT fij[3]; - my_sna.compute_deidrj(team,fij); + fij[0] = my_sna.dedr(ii,jj,0); + fij[1] = my_sna.dedr(ii,jj,1); + fij[2] = my_sna.dedr(ii,jj,2); Kokkos::single(Kokkos::PerThread(team), [&] (){ a_f(i,0) += fij[0]; @@ -620,8 +623,8 @@ void PairSNAPKokkos::operator() (TagPairSNAPCompute(ev,i,j, fij[0],fij[1],fij[2], - -my_sna.rij(jj,0),-my_sna.rij(jj,1), - -my_sna.rij(jj,2)); + -my_sna.rij(ii,jj,0),-my_sna.rij(ii,jj,1), + -my_sna.rij(ii,jj,2)); } } @@ -633,6 +636,11 @@ void PairSNAPKokkos::operator() (TagPairSNAPCompute> + d_coeffi(d_coeffelem,ielem,Kokkos::ALL); + Kokkos::single(Kokkos::PerTeam(team), [&] () { // evdwl = energy of atom I, sum over coeffs_k * Bi_k @@ -640,21 +648,21 @@ void PairSNAPKokkos::operator() (TagPairSNAPCompute::operator() (TagPairSNAPCompute template KOKKOS_INLINE_FUNCTION -void PairSNAPKokkos::operator() (TagPairSNAPCompute,const typename Kokkos::TeamPolicy >::member_type& team) const { +void PairSNAPKokkos::operator() (TagPairSNAPComputeForce,const typename Kokkos::TeamPolicy >::member_type& team) const { EV_FLOAT ev; - this->template operator()(TagPairSNAPCompute(), team, ev); + this->template operator()(TagPairSNAPComputeForce(), team, ev); } /* ---------------------------------------------------------------------- */ @@ -738,4 +746,5 @@ double PairSNAPKokkos::memory_usage() bytes += snaKK.memory_usage(); return bytes; } + } diff --git a/src/KOKKOS/sna_kokkos.h b/src/KOKKOS/sna_kokkos.h index a53a614229..2dbfdcb47c 100644 --- a/src/KOKKOS/sna_kokkos.h +++ b/src/KOKKOS/sna_kokkos.h @@ -25,6 +25,9 @@ namespace LAMMPS_NS { +typedef double SNAreal; +typedef struct { SNAreal re, im; } SNAcomplex; + struct SNAKK_ZINDICES { int j1, j2, j, ma1min, ma2max, mb1min, mb2max, na, nb, jju; }; @@ -39,12 +42,22 @@ class SNAKokkos { public: typedef Kokkos::View t_sna_1i; typedef Kokkos::View t_sna_1d; - typedef Kokkos::View > t_sna_1d_atomic; - typedef Kokkos::View t_sna_2d; - typedef Kokkos::View t_sna_3d; - typedef Kokkos::View t_sna_4d; - typedef Kokkos::View t_sna_3d3; - typedef Kokkos::View t_sna_5d; + typedef Kokkos::View > t_sna_1d_atomic; + typedef Kokkos::View t_sna_2i; + typedef Kokkos::View t_sna_2d; + typedef Kokkos::View t_sna_3d; + typedef Kokkos::View t_sna_4d; + typedef Kokkos::View t_sna_3d3; + typedef Kokkos::View t_sna_5d; + + typedef Kokkos::View t_sna_1c; + typedef Kokkos::View > t_sna_1c_atomic; + typedef Kokkos::View t_sna_2c; + typedef Kokkos::View t_sna_2c_cpu; + typedef Kokkos::View t_sna_3c; + typedef Kokkos::View t_sna_4c; + typedef Kokkos::View t_sna_3c3; + typedef Kokkos::View t_sna_5c; inline SNAKokkos() {}; @@ -63,36 +76,31 @@ inline inline void init(); // -inline - T_INT size_team_scratch_arrays(); - -inline - T_INT size_thread_scratch_arrays(); - double memory_usage(); int ncoeff; // functions for bispectrum coefficients - KOKKOS_INLINE_FUNCTION - void compute_ui(const typename Kokkos::TeamPolicy::member_type& team, int); // ForceSNAP + void pre_ui(const typename Kokkos::TeamPolicy::member_type& team, int); // ForceSNAP + KOKKOS_INLINE_FUNCTION + void compute_ui(const typename Kokkos::TeamPolicy::member_type& team, int, int); // ForceSNAP + KOKKOS_INLINE_FUNCTION + void compute_ui_orig(const typename Kokkos::TeamPolicy::member_type& team, int, int); // ForceSNAP KOKKOS_INLINE_FUNCTION - void compute_zi(const typename Kokkos::TeamPolicy::member_type& team); // ForceSNAP + void compute_zi(const typename Kokkos::TeamPolicy::member_type& team, int); // ForceSNAP KOKKOS_INLINE_FUNCTION - void compute_yi(const typename Kokkos::TeamPolicy::member_type& team, - const Kokkos::View &beta, const int ii); // ForceSNAP + void compute_yi(const typename Kokkos::TeamPolicy::member_type& team, int, + const Kokkos::View &beta); // ForceSNAP KOKKOS_INLINE_FUNCTION - void compute_bi(const typename Kokkos::TeamPolicy::member_type& team); // ForceSNAP + void compute_bi(const typename Kokkos::TeamPolicy::member_type& team, int); // ForceSNAP // functions for derivatives KOKKOS_INLINE_FUNCTION - void compute_duidrj(const typename Kokkos::TeamPolicy::member_type& team, double*, double, double, int); //ForceSNAP + void compute_duidrj(const typename Kokkos::TeamPolicy::member_type& team, int, int); //ForceSNAP KOKKOS_INLINE_FUNCTION - void compute_dbidrj(const typename Kokkos::TeamPolicy::member_type& team); //ForceSNAP - KOKKOS_INLINE_FUNCTION - void compute_deidrj(const typename Kokkos::TeamPolicy::member_type& team, double *); // ForceSNAP + void compute_deidrj(const typename Kokkos::TeamPolicy::member_type& team, int, int); // ForceSNAP KOKKOS_INLINE_FUNCTION double compute_sfac(double, double); // add_uarraytot, compute_duarray KOKKOS_INLINE_FUNCTION @@ -109,29 +117,26 @@ inline // Per InFlight Particle - t_sna_2d rij; - t_sna_1i inside; - t_sna_1d wj; - t_sna_1d rcutij; - int nmax; + t_sna_3d rij; + t_sna_2i inside; + t_sna_2d wj; + t_sna_2d rcutij; + t_sna_3d dedr; + int natom, nmax; - void grow_rij(int); + void grow_rij(int, int); int twojmax, diagonalstyle; - // Per InFlight Particle - t_sna_1d blist; - t_sna_1d ulisttot_r, ulisttot_i; - t_sna_1d_atomic ulisttot_r_a, ulisttot_i_a; - t_sna_1d zlist_r, zlist_i; - t_sna_2d ulist_r_ij, ulist_i_ij; + + t_sna_2d blist; + t_sna_2c_cpu ulisttot; + t_sna_2c zlist; - // Per InFlight Interaction - t_sna_1d ulist_r, ulist_i; - t_sna_1d_atomic ylist_r, ylist_i; + t_sna_3c ulist; + t_sna_2c ylist; // derivatives of data - t_sna_2d dulist_r, dulist_i; - t_sna_2d dblist; + t_sna_4c dulist; private: double rmin0, rfac0; @@ -168,14 +173,14 @@ inline inline void init_rootpqarray(); // init() KOKKOS_INLINE_FUNCTION - void zero_uarraytot(const typename Kokkos::TeamPolicy::member_type& team); // compute_ui + void zero_uarraytot(const typename Kokkos::TeamPolicy::member_type& team, int); // compute_ui KOKKOS_INLINE_FUNCTION - void addself_uarraytot(const typename Kokkos::TeamPolicy::member_type& team, double); // compute_ui + void addself_uarraytot(const typename Kokkos::TeamPolicy::member_type& team, int, double); // compute_ui KOKKOS_INLINE_FUNCTION - void add_uarraytot(const typename Kokkos::TeamPolicy::member_type& team, double, double, double, int); // compute_ui + void add_uarraytot(const typename Kokkos::TeamPolicy::member_type& team, int, int, double, double, double); // compute_ui KOKKOS_INLINE_FUNCTION - void compute_uarray(const typename Kokkos::TeamPolicy::member_type& team, + void compute_uarray(const typename Kokkos::TeamPolicy::member_type& team, int, int, double, double, double, double, double); // compute_ui inline @@ -184,9 +189,9 @@ inline inline int compute_ncoeff(); // SNAKokkos() KOKKOS_INLINE_FUNCTION - void compute_duarray(const typename Kokkos::TeamPolicy::member_type& team, + void compute_duarray(const typename Kokkos::TeamPolicy::member_type& team, int, int, double, double, double, // compute_duidrj - double, double, double, double, double, int); + double, double, double, double, double); // Sets the style for the switching function // 0 = none @@ -197,7 +202,7 @@ inline double wself; int bzero_flag; // 1 if bzero subtracted from barray - Kokkos::View bzero; // array of B values for isolated atoms + Kokkos::View bzero; // array of B values for isolated atoms }; } diff --git a/src/KOKKOS/sna_kokkos_impl.h b/src/KOKKOS/sna_kokkos_impl.h index f0d45cb5c2..36765e9cd6 100644 --- a/src/KOKKOS/sna_kokkos_impl.h +++ b/src/KOKKOS/sna_kokkos_impl.h @@ -41,8 +41,6 @@ SNAKokkos::SNAKokkos(double rfac0_in, ncoeff = compute_ncoeff(); - //create_twojmax_arrays(); - nmax = 0; build_indexlist(); @@ -63,37 +61,6 @@ SNAKokkos::SNAKokkos(double rfac0_in, } } -template -KOKKOS_INLINE_FUNCTION -SNAKokkos::SNAKokkos(const SNAKokkos& sna, const typename Kokkos::TeamPolicy::member_type& team) { - wself = sna.wself; - - rfac0 = sna.rfac0; - rmin0 = sna.rmin0; - switch_flag = sna.switch_flag; - bzero_flag = sna.bzero_flag; - - twojmax = sna.twojmax; - - ncoeff = sna.ncoeff; - nmax = sna.nmax; - idxz = sna.idxz; - idxb = sna.idxb; - idxcg_max = sna.idxcg_max; - idxu_max = sna.idxu_max; - idxz_max = sna.idxz_max; - idxb_max = sna.idxb_max; - idxcg_block = sna.idxcg_block; - idxu_block = sna.idxu_block; - idxz_block = sna.idxz_block; - idxb_block = sna.idxb_block; - cglist = sna.cglist; - rootpqarray = sna.rootpqarray; - bzero = sna.bzero; - create_team_scratch_arrays(team); - create_thread_scratch_arrays(team); -} - /* ---------------------------------------------------------------------- */ template @@ -245,18 +212,80 @@ void SNAKokkos::init() template inline -void SNAKokkos::grow_rij(int newnmax) +void SNAKokkos::grow_rij(int newnatom, int newnmax) { - if(newnmax <= nmax) return; + if(newnatom <= natom && newnmax <= nmax) return; + natom = newnatom; nmax = newnmax; + + rij = t_sna_3d("sna:rij",natom,nmax,3); + inside = t_sna_2i("sna:inside",natom,nmax); + wj = t_sna_2d("sna:wj",natom,nmax); + rcutij = t_sna_2d("sna:rcutij",natom,nmax); + dedr = t_sna_3d("sna:dedr",natom,nmax,3); + + blist = t_sna_2d("sna:blist",natom,idxb_max); + ulisttot = t_sna_2c_cpu("sna:ulisttot",natom,idxu_max); + zlist = t_sna_2c("sna:zlist",natom,idxz_max); + + ulist = t_sna_3c("sna:ulist",natom,nmax,idxu_max); + ylist = t_sna_2c("sna:ylist",natom,idxu_max); + + dulist = t_sna_4c("sna:dulist",natom,nmax,idxu_max); } + +/* ---------------------------------------------------------------------- + * compute Ui by summing over neighbors j + * ------------------------------------------------------------------------- */ + +template +KOKKOS_INLINE_FUNCTION +void SNAKokkos::pre_ui(const typename Kokkos::TeamPolicy::member_type& team, int iatom) +{ + if(team.team_rank() == 0) { + zero_uarraytot(team,iatom); + //Kokkos::single(Kokkos::PerThread(team), [&] (){ + addself_uarraytot(team,iatom,wself); + //}); + } + team.team_barrier(); +} + /* ---------------------------------------------------------------------- compute Ui by summing over neighbors j ------------------------------------------------------------------------- */ template KOKKOS_INLINE_FUNCTION -void SNAKokkos::compute_ui(const typename Kokkos::TeamPolicy::member_type& team, int jnum) +void SNAKokkos::compute_ui(const typename Kokkos::TeamPolicy::member_type& team, int iatom, int jnbor) +{ + double rsq, r, x, y, z, z0, theta0; + + // utot(j,ma,mb) = 0 for all j,ma,ma + // utot(j,ma,ma) = 1 for all j,ma + // for j in neighbors of i: + // compute r0 = (x,y,z,z0) + // utot(j,ma,mb) += u(r0;j,ma,mb) for all j,ma,mb + + x = rij(iatom,jnbor,0); + y = rij(iatom,jnbor,1); + z = rij(iatom,jnbor,2); + rsq = x * x + y * y + z * z; + r = sqrt(rsq); + + theta0 = (r - rmin0) * rfac0 * MY_PI / (rcutij(iatom,jnbor) - rmin0); + // theta0 = (r - rmin0) * rscale0; + z0 = r / tan(theta0); + + compute_uarray(team, iatom, jnbor, x, y, z, z0, r); + //Kokkos::single(Kokkos::PerThread(team), [&] (){ + add_uarraytot(team, iatom, jnbor, r, wj(iatom,jnbor), rcutij(iatom,jnbor)); + //}); +} + +template +KOKKOS_INLINE_FUNCTION +void SNAKokkos::compute_ui_orig(const typename Kokkos::TeamPolicy::member_type& team, int iatom, int jnum) { double rsq, r, x, y, z, z0, theta0; @@ -267,9 +296,9 @@ void SNAKokkos::compute_ui(const typename Kokkos::TeamPolicy::compute_ui(const typename Kokkos::TeamPolicy::compute_ui(const typename Kokkos::TeamPolicy KOKKOS_INLINE_FUNCTION -void SNAKokkos::compute_zi(const typename Kokkos::TeamPolicy::member_type& team) +void SNAKokkos::compute_zi(const typename Kokkos::TeamPolicy::member_type& team, int iatom) { Kokkos::parallel_for(Kokkos::TeamThreadRange(team,idxz_max), [&] (const int& jjz) { @@ -318,8 +347,8 @@ void SNAKokkos::compute_zi(const typename Kokkos::TeamPolicy::compute_zi(const typename Kokkos::TeamPolicy::compute_zi(const typename Kokkos::TeamPolicy KOKKOS_INLINE_FUNCTION -void SNAKokkos::compute_yi(const typename Kokkos::TeamPolicy::member_type& team, - const Kokkos::View &beta, const int ii) +void SNAKokkos::compute_yi(const typename Kokkos::TeamPolicy::member_type& team, int iatom, + const Kokkos::View &beta) { double betaj; + const int ii = iatom; { - double* const ptr = ylist_r.data(); - Kokkos::parallel_for(Kokkos::TeamThreadRange(team,ylist_r.span()), + Kokkos::parallel_for(Kokkos::TeamThreadRange(team,ylist.extent(1)), [&] (const int& i) { - ptr[i] = 0.0; - }); - } - { - double* const ptr = ylist_i.data(); - Kokkos::parallel_for(Kokkos::TeamThreadRange(team,ylist_i.span()), - [&] (const int& i) { - ptr[i] = 0.0; + ylist(iatom,i).re = 0.0; + ylist(iatom,i).im = 0.0; }); } + //int flopsum = 0; + Kokkos::parallel_for(Kokkos::TeamThreadRange(team,idxz_max), [&] (const int& jjz) { //for(int jjz = 0; jjz < idxz_max; jjz++) { @@ -410,18 +430,15 @@ void SNAKokkos::compute_yi(const typename Kokkos::TeamPolicy::compute_yi(const typename Kokkos::TeamPolicy::compute_yi(const typename Kokkos::TeamPolicy KOKKOS_INLINE_FUNCTION -void SNAKokkos::compute_deidrj(const typename Kokkos::TeamPolicy::member_type& team, double* dedr) +void SNAKokkos::compute_deidrj(const typename Kokkos::TeamPolicy::member_type& team, int iatom, int jnbor) { t_scalar3 sum; @@ -482,9 +501,9 @@ void SNAKokkos::compute_deidrj(const typename Kokkos::TeamPolicy::compute_deidrj(const typename Kokkos::TeamPolicy::compute_deidrj(const typename Kokkos::TeamPolicy KOKKOS_INLINE_FUNCTION -void SNAKokkos::compute_bi(const typename Kokkos::TeamPolicy::member_type& team) +void SNAKokkos::compute_bi(const typename Kokkos::TeamPolicy::member_type& team, int iatom) { // for j1 = 0,...,twojmax // for j2 = 0,twojmax @@ -555,8 +575,8 @@ void SNAKokkos::compute_bi(const typename Kokkos::TeamPolicy::compute_bi(const typename Kokkos::TeamPolicy::compute_bi(const typename Kokkos::TeamPolicy::compute_bi(const typename Kokkos::TeamPolicy -KOKKOS_INLINE_FUNCTION -void SNAKokkos::compute_dbidrj(const typename Kokkos::TeamPolicy::member_type& team) -{ - // for j1 = 0,...,twojmax - // for j2 = 0,twojmax - // for j = |j1-j2|,Min(twojmax,j1+j2),2 - // zdb = 0 - // for mb = 0,...,jmid - // for ma = 0,...,j - // zdb += - // Conj(dudr(j,ma,mb))*z(j1,j2,j,ma,mb) - // dbdr(j1,j2,j) += 2*zdb - // zdb = 0 - // for mb1 = 0,...,j1mid - // for ma1 = 0,...,j1 - // zdb += - // Conj(dudr(j1,ma1,mb1))*z(j,j2,j1,ma1,mb1) - // dbdr(j1,j2,j) += 2*zdb*(j+1)/(j1+1) - // zdb = 0 - // for mb2 = 0,...,j2mid - // for ma2 = 0,...,j2 - // zdb += - // Conj(dudr(j2,ma2,mb2))*z(j1,j,j2,ma2,mb2) - // dbdr(j1,j2,j) += 2*zdb*(j+1)/(j2+1) - - - Kokkos::parallel_for(Kokkos::ThreadVectorRange(team,idxb_max), - [&] (const int& jjb) { - //for(int jjb = 0; jjb < idxb_max; jjb++) { - const int j1 = idxb[jjb].j1; - const int j2 = idxb[jjb].j2; - const int j = idxb[jjb].j; - -// dbdr = dblist(jjb); -// dbdr[0] = 0.0; -// dbdr[1] = 0.0; -// dbdr[2] = 0.0; - - t_scalar3 dbdr,sumzdu_r; - // Sum terms Conj(dudr(j,ma,mb))*z(j1,j2,j,ma,mb) - - int jjz = idxz_block(j1,j2,j); - int jju = idxu_block[j]; - - for(int mb = 0; 2*mb < j; mb++) - for(int ma = 0; ma <= j; ma++) { - const int jju_index = jju+mb*(j+1)+ma; - const int jjz_index = jjz+mb*(j+1)+ma; - sumzdu_r.x += (dulist_r(jju_index,0) * zlist_r[jjz_index] + dulist_i(jju_index,0) * zlist_i[jjz_index]); - sumzdu_r.y += (dulist_r(jju_index,1) * zlist_r[jjz_index] + dulist_i(jju_index,1) * zlist_i[jjz_index]); - sumzdu_r.z += (dulist_r(jju_index,2) * zlist_r[jjz_index] + dulist_i(jju_index,2) * zlist_i[jjz_index]); - } //end loop over ma mb - - // For j even, handle middle column - - if (j%2 == 0) { - int mb = j/2; - for(int ma = 0; ma <= mb; ma++) { - const int jju_index = jju+(mb-1)*(j+1)+(j+1)+ma; - const int jjz_index = jjz+(mb-1)*(j+1)+(j+1)+ma; - sumzdu_r.x += (dulist_r(jju_index,0) * zlist_r[jjz_index] + dulist_i(jju_index,0) * zlist_i[jjz_index]); - sumzdu_r.y += (dulist_r(jju_index,1) * zlist_r[jjz_index] + dulist_i(jju_index,1) * zlist_i[jjz_index]); - sumzdu_r.z += (dulist_r(jju_index,2) * zlist_r[jjz_index] + dulist_i(jju_index,2) * zlist_i[jjz_index]); - } - int ma = mb; - const int jju_index = jju+(mb-1)*(j+1)+(j+1)+ma; - const int jjz_index = jjz+(mb-1)*(j+1)+(j+1)+ma; - for(int k = 0; k < 3; k++) { - sumzdu_r.x += (dulist_r(jju_index,0) * zlist_r[jjz] + dulist_i(jju_index,0) * zlist_i[jjz_index])*0.5; - sumzdu_r.y += (dulist_r(jju_index,1) * zlist_r[jjz] + dulist_i(jju_index,1) * zlist_i[jjz_index])*0.5; - sumzdu_r.z += (dulist_r(jju_index,2) * zlist_r[jjz] + dulist_i(jju_index,2) * zlist_i[jjz_index])*0.5; - } - } // end if jeven - - dbdr += 2.0*sumzdu_r; - - // Sum over Conj(dudr(j1,ma1,mb1))*z(j,j2,j1,ma1,mb1) - - double j1fac = (j+1)/(j1+1.0); - - jjz = idxz_block(j,j2,j1); - jju = idxu_block[j1]; - - sumzdu_r.x = 0.0; sumzdu_r.y = 0.0; sumzdu_r.z = 0.0; - - for(int mb = 0; 2*mb < j1; mb++) - for(int ma = 0; ma <= j1; ma++) { - const int jju_index = jju+mb*(j1+1)+ma; - const int jjz_index = jjz+mb*(j1+1)+ma; - sumzdu_r.x += (dulist_r(jju_index,0) * zlist_r[jjz_index] + dulist_i(jju_index,0) * zlist_i[jjz_index]); - sumzdu_r.y += (dulist_r(jju_index,1) * zlist_r[jjz_index] + dulist_i(jju_index,1) * zlist_i[jjz_index]); - sumzdu_r.z += (dulist_r(jju_index,2) * zlist_r[jjz_index] + dulist_i(jju_index,2) * zlist_i[jjz_index]); - } //end loop over ma1 mb1 - - // For j1 even, handle middle column - - if (j1%2 == 0) { - const int mb = j1/2; - for(int ma = 0; ma <= mb; ma++) { - const int jju_index = jju+(mb-1)*(j1+1)+(j1+1)+ma; - const int jjz_index = jjz+(mb-1)*(j1+1)+(j1+1)+ma; - sumzdu_r.x += (dulist_r(jju_index,0) * zlist_r[jjz_index] + dulist_i(jju_index,0) * zlist_i[jjz_index]); - sumzdu_r.y += (dulist_r(jju_index,1) * zlist_r[jjz_index] + dulist_i(jju_index,1) * zlist_i[jjz_index]); - sumzdu_r.z += (dulist_r(jju_index,2) * zlist_r[jjz_index] + dulist_i(jju_index,2) * zlist_i[jjz_index]); - } - int ma = mb; - const int jju_index = jju+(mb-1)*(j1+1)+(j1+1)+ma; - const int jjz_index = jjz+(mb-1)*(j1+1)+(j1+1)+ma; - for(int k = 0; k < 3; k++) { - sumzdu_r.x += (dulist_r(jju_index,0) * zlist_r[jjz] + dulist_i(jju_index,0) * zlist_i[jjz_index])*0.5; - sumzdu_r.y += (dulist_r(jju_index,1) * zlist_r[jjz] + dulist_i(jju_index,1) * zlist_i[jjz_index])*0.5; - sumzdu_r.z += (dulist_r(jju_index,2) * zlist_r[jjz] + dulist_i(jju_index,2) * zlist_i[jjz_index])*0.5; - } - } // end if j1even - - dbdr += 2.0*sumzdu_r*j1fac; - - // Sum over Conj(dudr(j2,ma2,mb2))*z(j1,j,j2,ma2,mb2) - - double j2fac = (j+1)/(j2+1.0); - - jjz = idxz_block(j,j1,j2); - jju = idxu_block[j2]; - - sumzdu_r.x = 0.0; sumzdu_r.y = 0.0; sumzdu_r.z = 0.0; - - for(int mb = 0; 2*mb < j2; mb++) - for(int ma = 0; ma <= j2; ma++) { - const int jju_index = jju+mb*(j2+1)+ma; - const int jjz_index = jjz+mb*(j2+1)+ma; - sumzdu_r.x += (dulist_r(jju_index,0) * zlist_r[jjz_index] + dulist_i(jju_index,0) * zlist_i[jjz_index]); - sumzdu_r.y += (dulist_r(jju_index,1) * zlist_r[jjz_index] + dulist_i(jju_index,1) * zlist_i[jjz_index]); - sumzdu_r.z += (dulist_r(jju_index,2) * zlist_r[jjz_index] + dulist_i(jju_index,2) * zlist_i[jjz_index]); - } //end loop over ma2 mb2 - - // For j2 even, handle middle column - - if (j2%2 == 0) { - const int mb = j2/2; - for(int ma = 0; ma <= mb; ma++) { - const int jju_index = jju+(mb-1)*(j2+1)+(j2+1)+ma; - const int jjz_index = jjz+(mb-1)*(j2+1)+(j2+1)+ma; - sumzdu_r.x += (dulist_r(jju_index,0) * zlist_r[jjz_index] + dulist_i(jju_index,0) * zlist_i[jjz_index]); - sumzdu_r.y += (dulist_r(jju_index,1) * zlist_r[jjz_index] + dulist_i(jju_index,1) * zlist_i[jjz_index]); - sumzdu_r.z += (dulist_r(jju_index,2) * zlist_r[jjz_index] + dulist_i(jju_index,2) * zlist_i[jjz_index]); - } - int ma = mb; - const int jju_index = jju+(mb-1)*(j2+1)+(j2+1)+ma; - const int jjz_index = jjz+(mb-1)*(j2+1)+(j2+1)+ma; - for(int k = 0; k < 3; k++) { - sumzdu_r.x += (dulist_r(jju_index,0) * zlist_r[jjz] + dulist_i(jju_index,0) * zlist_i[jjz_index])*0.5; - sumzdu_r.y += (dulist_r(jju_index,1) * zlist_r[jjz] + dulist_i(jju_index,1) * zlist_i[jjz_index])*0.5; - sumzdu_r.z += (dulist_r(jju_index,2) * zlist_r[jjz] + dulist_i(jju_index,2) * zlist_i[jjz_index])*0.5; - } - } // end if j2even - - dbdr += 2.0*sumzdu_r*j2fac; - dblist(jjb,0) = dbdr.x; - dblist(jjb,1) = dbdr.y; - dblist(jjb,2) = dbdr.z; - - }); //end loop over j1 j2 j -} - /* ---------------------------------------------------------------------- calculate derivative of Ui w.r.t. atom j ------------------------------------------------------------------------- */ template KOKKOS_INLINE_FUNCTION -void SNAKokkos::compute_duidrj(const typename Kokkos::TeamPolicy::member_type& team, - double* rij, double wj, double rcut, int jj) +void SNAKokkos::compute_duidrj(const typename Kokkos::TeamPolicy::member_type& team, int iatom, int jnbor) { double rsq, r, x, y, z, z0, theta0, cs, sn; double dz0dr; - x = rij[0]; - y = rij[1]; - z = rij[2]; + x = rij(iatom,jnbor,0); + y = rij(iatom,jnbor,1); + z = rij(iatom,jnbor,2); rsq = x * x + y * y + z * z; r = sqrt(rsq); - double rscale0 = rfac0 * MY_PI / (rcut - rmin0); + double rscale0 = rfac0 * MY_PI / (rcutij(iatom,jnbor) - rmin0); theta0 = (r - rmin0) * rscale0; cs = cos(theta0); sn = sin(theta0); z0 = r * cs / sn; dz0dr = z0 / r - (r*rscale0) * (rsq + z0 * z0) / rsq; - compute_duarray(team, x, y, z, z0, r, dz0dr, wj, rcut, jj); + compute_duarray(team, iatom, jnbor, x, y, z, z0, r, dz0dr, wj(iatom,jnbor), rcutij(iatom,jnbor)); } /* ---------------------------------------------------------------------- */ template KOKKOS_INLINE_FUNCTION -void SNAKokkos::zero_uarraytot(const typename Kokkos::TeamPolicy::member_type& team) +void SNAKokkos::zero_uarraytot(const typename Kokkos::TeamPolicy::member_type& team, int iatom) { { - double* const ptr = ulisttot_r.data(); - Kokkos::parallel_for(Kokkos::ThreadVectorRange(team,ulisttot_r.span()), - [&] (const int& i) { - ptr[i] = 0.0; - }); - } - { - double* const ptr = ulisttot_i.data(); - Kokkos::parallel_for(Kokkos::ThreadVectorRange(team,ulisttot_i.span()), + Kokkos::parallel_for(Kokkos::ThreadVectorRange(team,ulisttot.extent(1)), [&] (const int& i) { - ptr[i] = 0.0; + ulisttot(iatom,i).re = 0.0; + ulisttot(iatom,i).im = 0.0; }); } } @@ -822,15 +663,15 @@ void SNAKokkos::zero_uarraytot(const typename Kokkos::TeamPolicy KOKKOS_INLINE_FUNCTION -void SNAKokkos::addself_uarraytot(const typename Kokkos::TeamPolicy::member_type& team, double wself_in) +void SNAKokkos::addself_uarraytot(const typename Kokkos::TeamPolicy::member_type& team, int iatom, double wself_in) { Kokkos::parallel_for(Kokkos::ThreadVectorRange(team,twojmax+1), [&] (const int& j) { //for (int j = 0; j <= twojmax; j++) int jju = idxu_block[j]; for (int ma = 0; ma <= j; ma++) { - ulisttot_r[jju] = wself_in; - ulisttot_i[jju] = 0.0; + ulisttot(iatom,jju).re = wself_in; + ulisttot(iatom,jju).im = 0.0; jju += j+2; } }); @@ -842,28 +683,15 @@ void SNAKokkos::addself_uarraytot(const typename Kokkos::TeamPolicy< template KOKKOS_INLINE_FUNCTION -void SNAKokkos::add_uarraytot(const typename Kokkos::TeamPolicy::member_type& team, - double r, double wj, double rcut, int j) +void SNAKokkos::add_uarraytot(const typename Kokkos::TeamPolicy::member_type& team, int iatom, int jnbor, + double r, double wj, double rcut) { const double sfac = compute_sfac(r, rcut) * wj; - const double* const ptr_r = ulist_r.data(); - const double* const ptr_i = ulist_i.data(); - double* const ptrtot_r = ulisttot_r.data(); - double* const ptrtot_i = ulisttot_i.data(); - - Kokkos::View> - ulist_r_j(ulist_r_ij,j,Kokkos::ALL); - Kokkos::View> - ulist_i_j(ulist_i_ij,j,Kokkos::ALL); - - Kokkos::parallel_for(Kokkos::ThreadVectorRange(team,ulisttot_r.span()), + Kokkos::parallel_for(Kokkos::ThreadVectorRange(team,ulisttot.extent(1)), [&] (const int& i) { - Kokkos::atomic_add(ptrtot_r+i, sfac * ptr_r[i]); - Kokkos::atomic_add(ptrtot_i+i, sfac * ptr_i[i]); - - ulist_r_j(i) = ulist_r(i); - ulist_i_j(i) = ulist_i(i); + Kokkos::atomic_add(&(ulisttot(iatom,i).re), sfac * ulist(iatom,jnbor,i).re); + Kokkos::atomic_add(&(ulisttot(iatom,i).im), sfac * ulist(iatom,jnbor,i).im); }); } @@ -873,7 +701,7 @@ void SNAKokkos::add_uarraytot(const typename Kokkos::TeamPolicy KOKKOS_INLINE_FUNCTION -void SNAKokkos::compute_uarray(const typename Kokkos::TeamPolicy::member_type& team, +void SNAKokkos::compute_uarray(const typename Kokkos::TeamPolicy::member_type& team, int iatom, int jnbor, double x, double y, double z, double z0, double r) { @@ -891,8 +719,8 @@ void SNAKokkos::compute_uarray(const typename Kokkos::TeamPolicy::compute_uarray(const typename Kokkos::TeamPolicy::compute_uarray(const typename Kokkos::TeamPolicy::compute_uarray(const typename Kokkos::TeamPolicy KOKKOS_INLINE_FUNCTION -void SNAKokkos::compute_duarray(const typename Kokkos::TeamPolicy::member_type& team, +void SNAKokkos::compute_duarray(const typename Kokkos::TeamPolicy::member_type& team, int iatom, int jnbor, double x, double y, double z, double z0, double r, double dz0dr, - double wj, double rcut, int jj) + double wj, double rcut) { double r0inv; double a_r, a_i, b_r, b_i; @@ -1012,17 +840,12 @@ void SNAKokkos::compute_duarray(const typename Kokkos::TeamPolicy> - ulist_r(ulist_r_ij,jj,Kokkos::ALL); - Kokkos::View> - ulist_i(ulist_i_ij,jj,Kokkos::ALL); - - dulist_r(0,0) = 0.0; - dulist_r(0,1) = 0.0; - dulist_r(0,2) = 0.0; - dulist_i(0,0) = 0.0; - dulist_i(0,1) = 0.0; - dulist_i(0,2) = 0.0; + dulist(iatom,jnbor,0,0).re = 0.0; + dulist(iatom,jnbor,0,1).re = 0.0; + dulist(iatom,jnbor,0,2).re = 0.0; + dulist(iatom,jnbor,0,0).im = 0.0; + dulist(iatom,jnbor,0,1).im = 0.0; + dulist(iatom,jnbor,0,2).im = 0.0; for (int j = 1; j <= twojmax; j++) { int jju = idxu_block[j]; @@ -1031,42 +854,42 @@ void SNAKokkos::compute_duarray(const typename Kokkos::TeamPolicy::compute_duarray(const typename Kokkos::TeamPolicy::compute_duarray(const typename Kokkos::TeamPolicy -KOKKOS_INLINE_FUNCTION -void SNAKokkos::create_team_scratch_arrays(const typename Kokkos::TeamPolicy::member_type& team) -{ - ulisttot_r_a = ulisttot_r = t_sna_1d(team.team_scratch(1),idxu_max); - ulisttot_i_a = ulisttot_i = t_sna_1d(team.team_scratch(1),idxu_max); - ylist_r = t_sna_1d(team.team_scratch(1),idxu_max); - ylist_i = t_sna_1d(team.team_scratch(1),idxu_max); - zlist_r = t_sna_1d(team.team_scratch(1),idxz_max); - zlist_i = t_sna_1d(team.team_scratch(1),idxz_max); - blist = t_sna_1d(team.team_scratch(1),idxb_max); - - rij = t_sna_2d(team.team_scratch(1),nmax,3); - rcutij = t_sna_1d(team.team_scratch(1),nmax); - wj = t_sna_1d(team.team_scratch(1),nmax); - inside = t_sna_1i(team.team_scratch(1),nmax); - ulist_r_ij = t_sna_2d(team.team_scratch(1),nmax,idxu_max); - ulist_i_ij = t_sna_2d(team.team_scratch(1),nmax,idxu_max); -} - -template -inline -T_INT SNAKokkos::size_team_scratch_arrays() { - T_INT size = 0; - - size += t_sna_1d::shmem_size(idxu_max)*2; // ulisttot - size += t_sna_1d::shmem_size(idxu_max)*2; // ylist - size += t_sna_1d::shmem_size(idxz_max)*2; // zlist - size += t_sna_1d::shmem_size(idxb_max); // blist - - size += t_sna_2d::shmem_size(nmax,3); // rij - size += t_sna_1d::shmem_size(nmax); // rcutij - size += t_sna_1d::shmem_size(nmax); // wj - size += t_sna_1i::shmem_size(nmax); // inside - size += t_sna_2d::shmem_size(nmax,idxu_max)*2; // ulist_ij - - return size; -} - -/* ---------------------------------------------------------------------- */ - -template -KOKKOS_INLINE_FUNCTION -void SNAKokkos::create_thread_scratch_arrays(const typename Kokkos::TeamPolicy::member_type& team) -{ - dblist = t_sna_2d(team.thread_scratch(1),idxb_max,3); - ulist_r = t_sna_1d(team.thread_scratch(1),idxu_max); - ulist_i = t_sna_1d(team.thread_scratch(1),idxu_max); - dulist_r = t_sna_2d(team.thread_scratch(1),idxu_max,3); - dulist_i = t_sna_2d(team.thread_scratch(1),idxu_max,3); -} - -template -inline -T_INT SNAKokkos::size_thread_scratch_arrays() { - T_INT size = 0; - - size += t_sna_2d::shmem_size(idxb_max,3); // dblist - size += t_sna_1d::shmem_size(idxu_max)*2; // ulist - size += t_sna_2d::shmem_size(idxu_max,3)*2; // dulist - return size; -} - /* ---------------------------------------------------------------------- factorial n, wrapper for precomputed table ------------------------------------------------------------------------- */ @@ -1558,14 +1316,13 @@ double SNAKokkos::memory_usage() bytes += jdimpq*jdimpq * sizeof(double); // pqarray bytes += idxcg_max * sizeof(double); // cglist - bytes += idxu_max * sizeof(double) * 2; // ulist - bytes += idxu_max * sizeof(double) * 2; // ulisttot - bytes += idxu_max * 3 * sizeof(double) * 2; // dulist - - bytes += idxz_max * sizeof(double) * 2; // zlist - bytes += idxb_max * sizeof(double); // blist - bytes += idxb_max * 3 * sizeof(double); // dblist - bytes += idxu_max * sizeof(double) * 2; // ylist + bytes += natom * idxu_max * sizeof(double) * 2; // ulist + bytes += natom * idxu_max * sizeof(double) * 2; // ulisttot + bytes += natom * idxu_max * 3 * sizeof(double) * 2; // dulist + + bytes += natom * idxz_max * sizeof(double) * 2; // zlist + bytes += natom * idxb_max * sizeof(double); // blist + bytes += natom * idxu_max * sizeof(double) * 2; // ylist bytes += jdim * jdim * jdim * sizeof(int); // idxcg_block bytes += jdim * sizeof(int); // idxu_block @@ -1577,11 +1334,11 @@ double SNAKokkos::memory_usage() bytes += jdim * sizeof(double); // bzero - bytes += nmax * 3 * sizeof(double); // rij - bytes += nmax * sizeof(int); // inside - bytes += nmax * sizeof(double); // wj - bytes += nmax * sizeof(double); // rcutij - bytes += nmax * idxu_max * sizeof(double) * 2; // ulist_ij + bytes += natom * nmax * 3 * sizeof(double); // rij + bytes += natom * nmax * sizeof(int); // inside + bytes += natom * nmax * sizeof(double); // wj + bytes += natom * nmax * sizeof(double); // rcutij + bytes += natom * nmax * idxu_max * sizeof(double) * 2; // ulist_ij return bytes; } -- GitLab From 3acb09e3b10d81ff26d1cf58996271a6dcaf6991 Mon Sep 17 00:00:00 2001 From: Oliver Henrich Date: Fri, 19 Jul 2019 11:09:47 +0100 Subject: [PATCH 267/469] Corrected virial, altered calculation of stacking strength --- doc/src/pair_oxdna.txt | 8 +- doc/src/pair_oxdna2.txt | 12 +- src/USER-CGDNA/bond_oxdna2_fene.cpp | 4 +- src/USER-CGDNA/bond_oxdna2_fene.h | 3 +- src/USER-CGDNA/bond_oxdna_fene.cpp | 98 ++++++++++++++- src/USER-CGDNA/bond_oxdna_fene.h | 4 +- src/USER-CGDNA/pair_oxdna2_coaxstk.cpp | 6 +- src/USER-CGDNA/pair_oxdna2_dh.cpp | 8 +- src/USER-CGDNA/pair_oxdna2_excv.cpp | 4 +- src/USER-CGDNA/pair_oxdna2_excv.h | 2 +- src/USER-CGDNA/pair_oxdna2_stk.cpp | 50 -------- src/USER-CGDNA/pair_oxdna2_stk.h | 53 --------- src/USER-CGDNA/pair_oxdna_coaxstk.cpp | 6 +- src/USER-CGDNA/pair_oxdna_excv.cpp | 44 +++---- src/USER-CGDNA/pair_oxdna_excv.h | 2 +- src/USER-CGDNA/pair_oxdna_hbond.cpp | 6 +- src/USER-CGDNA/pair_oxdna_stk.cpp | 159 ++++++++++++++++++++----- src/USER-CGDNA/pair_oxdna_stk.h | 4 +- src/USER-CGDNA/pair_oxdna_xstk.cpp | 6 +- 19 files changed, 294 insertions(+), 185 deletions(-) delete mode 100644 src/USER-CGDNA/pair_oxdna2_stk.cpp delete mode 100644 src/USER-CGDNA/pair_oxdna2_stk.h diff --git a/doc/src/pair_oxdna.txt b/doc/src/pair_oxdna.txt index b63b5371cf..dfcd93c9a8 100644 --- a/doc/src/pair_oxdna.txt +++ b/doc/src/pair_oxdna.txt @@ -23,9 +23,11 @@ style1 = {hybrid/overlay oxdna/excv oxdna/stk oxdna/hbond oxdna/xstk oxdna/coaxs style2 = {oxdna/excv} or {oxdna/stk} or {oxdna/hbond} or {oxdna/xstk} or {oxdna/coaxstk} args = list of arguments for these particular styles :ul - {oxdna/stk} args = seq T 6.0 0.4 0.9 0.32 0.6 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2.0 0.65 2.0 0.65 + {oxdna/stk} args = seq T xi kappa 6.0 0.4 0.9 0.32 0.6 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2.0 0.65 2.0 0.65 seq = seqav (for average sequence stacking strength) or seqdep (for sequence-dependent stacking strength) T = temperature (oxDNA units, 0.1 = 300 K) + xi = temperature-independent coefficient in stacking strength + kappa = coefficient of linear temperature dependence in stacking strength {oxdna/hbond} args = seq eps 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45 seq = seqav (for average sequence base-pairing strength) or seqdep (for sequence-dependent base-pairing strength) eps = 1.077 (between base pairs A-T and C-G) or 0 (all other pairs) :pre @@ -34,7 +36,7 @@ args = list of arguments for these particular styles :ul pair_style hybrid/overlay oxdna/excv oxdna/stk oxdna/hbond oxdna/xstk oxdna/coaxstk pair_coeff * * oxdna/excv 2.0 0.7 0.675 2.0 0.515 0.5 2.0 0.33 0.32 -pair_coeff * * oxdna/stk seqdep 0.1 6.0 0.4 0.9 0.32 0.6 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2.0 0.65 2.0 0.65 +pair_coeff * * oxdna/stk seqdep 0.1 1.3448 2.6568 6.0 0.4 0.9 0.32 0.6 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2.0 0.65 2.0 0.65 pair_coeff * * oxdna/hbond seqdep 0.0 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45 pair_coeff 1 4 oxdna/hbond seqdep 1.077 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45 pair_coeff 2 3 oxdna/hbond seqdep 1.077 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45 @@ -62,7 +64,7 @@ NOTE: These pair styles have to be used together with the related oxDNA bond sty {oxdna/fene} for the connectivity of the phosphate backbone (see also documentation of "bond_style oxdna/fene"_bond_oxdna.html). Most of the coefficients in the above example have to be kept fixed and cannot be changed without reparameterizing the entire model. -Exceptions are the first and second coefficient after {oxdna/stk} (seq=seqdep and T=0.1 in the above example) +Exceptions are the first four coefficients after {oxdna/stk} (seq=seqdep, T=0.1, xi=1.3448 and kappa=2.6568 in the above example) and the first coefficient after {oxdna/hbond} (seq=seqdep in the above example). When using a Langevin thermostat, e.g. through "fix langevin"_fix_langevin.html or "fix nve/dotc/langevin"_fix_nve_dotc_langevin.html diff --git a/doc/src/pair_oxdna2.txt b/doc/src/pair_oxdna2.txt index f2963f7b17..3e462f384d 100644 --- a/doc/src/pair_oxdna2.txt +++ b/doc/src/pair_oxdna2.txt @@ -24,10 +24,12 @@ style1 = {hybrid/overlay oxdna2/excv oxdna2/stk oxdna2/hbond oxdna2/xstk oxdna2/ style2 = {oxdna2/excv} or {oxdna2/stk} or {oxdna2/hbond} or {oxdna2/xstk} or {oxdna2/coaxstk} or {oxdna2/dh} args = list of arguments for these particular styles :ul - {oxdna2/stk} args = seq T 6.0 0.4 0.9 0.32 0.6 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2.0 0.65 2.0 0.65 + {oxdna2/stk} args = seq T xi kappa 6.0 0.4 0.9 0.32 0.6 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2.0 0.65 2.0 0.65 seq = seqav (for average sequence stacking strength) or seqdep (for sequence-dependent stacking strength) T = temperature (oxDNA units, 0.1 = 300 K) - {oxdna/hbond} args = seq eps 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45 + xi = temperature-independent coefficient in stacking strength + kappa = coefficient of linear temperature dependence in stacking strength + {oxdna2/hbond} args = seq eps 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45 seq = seqav (for average sequence base-pairing strength) or seqdep (for sequence-dependent base-pairing strength) eps = 1.0678 (between base pairs A-T and C-G) or 0 (all other pairs) {oxdna2/dh} args = T rhos qeff @@ -39,7 +41,7 @@ args = list of arguments for these particular styles :ul pair_style hybrid/overlay oxdna2/excv oxdna2/stk oxdna2/hbond oxdna2/xstk oxdna2/coaxstk oxdna2/dh pair_coeff * * oxdna2/excv 2.0 0.7 0.675 2.0 0.515 0.5 2.0 0.33 0.32 -pair_coeff * * oxdna2/stk seqdep 0.1 6.0 0.4 0.9 0.32 0.6 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2.0 0.65 2.0 0.65 +pair_coeff * * oxdna2/stk seqdep 0.1 1.3523 2.6717 6.0 0.4 0.9 0.32 0.6 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2.0 0.65 2.0 0.65 pair_coeff * * oxdna2/hbond seqdep 0.0 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45 pair_coeff 1 4 oxdna2/hbond seqdep 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45 pair_coeff 2 3 oxdna2/hbond seqdep 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45 @@ -68,8 +70,8 @@ NOTE: These pair styles have to be used together with the related oxDNA2 bond st {oxdna2/fene} for the connectivity of the phosphate backbone (see also documentation of "bond_style oxdna2/fene"_bond_oxdna.html). Most of the coefficients in the above example have to be kept fixed and cannot be changed without reparameterizing the entire model. -Exceptions are the first and the second coefficient after {oxdna2/stk} (seq=seqdep and T=0.1 in the above example), -the first coefficient after {oxdna/hbond} (seq=seqdep in the above example) and the three coefficients +Exceptions are the first four coefficients after {oxdna2/stk} (seq=seqdep, T=0.1, xi=1.3523 and kappa=2.6717 in the above example), +the first coefficient after {oxdna2/hbond} (seq=seqdep in the above example) and the three coefficients after {oxdna2/dh} (T=0.1, rhos=1.0, qeff=0.815 in the above example). When using a Langevin thermostat e.g. through "fix langevin"_fix_langevin.html or "fix nve/dotc/langevin"_fix_nve_dotc_langevin.html the temperature coefficients have to be matched to the one used in the fix. diff --git a/src/USER-CGDNA/bond_oxdna2_fene.cpp b/src/USER-CGDNA/bond_oxdna2_fene.cpp index 39cbb04f88..557d62aac6 100644 --- a/src/USER-CGDNA/bond_oxdna2_fene.cpp +++ b/src/USER-CGDNA/bond_oxdna2_fene.cpp @@ -37,8 +37,8 @@ BondOxdna2Fene::~BondOxdna2Fene() /* ---------------------------------------------------------------------- compute vector COM-sugar-phosphate backbone interaction site in oxDNA2 ------------------------------------------------------------------------- */ -void BondOxdna2Fene::compute_interaction_sites(double e1[3], - double e2[3], double r[3]) +void BondOxdna2Fene::compute_interaction_sites(double e1[3], double e2[3], + double /*e3*/[3], double r[3]) { double d_cs_x=-0.34, d_cs_y=+0.3408; diff --git a/src/USER-CGDNA/bond_oxdna2_fene.h b/src/USER-CGDNA/bond_oxdna2_fene.h index 0654c37a9c..4bcce337ed 100644 --- a/src/USER-CGDNA/bond_oxdna2_fene.h +++ b/src/USER-CGDNA/bond_oxdna2_fene.h @@ -28,7 +28,8 @@ class BondOxdna2Fene : public BondOxdnaFene { public: BondOxdna2Fene(class LAMMPS *); virtual ~BondOxdna2Fene(); - virtual void compute_interaction_sites(double *, double *, double *); + virtual void compute_interaction_sites(double *, double *, double *, + double *); }; } diff --git a/src/USER-CGDNA/bond_oxdna_fene.cpp b/src/USER-CGDNA/bond_oxdna_fene.cpp index 8271668e3f..9d6453f5a8 100644 --- a/src/USER-CGDNA/bond_oxdna_fene.cpp +++ b/src/USER-CGDNA/bond_oxdna_fene.cpp @@ -55,8 +55,8 @@ BondOxdnaFene::~BondOxdnaFene() /* ---------------------------------------------------------------------- compute vector COM-sugar-phosphate backbone interaction site in oxDNA ------------------------------------------------------------------------- */ -void BondOxdnaFene::compute_interaction_sites(double e1[3], - double /*e2*/[3], double r[3]) +void BondOxdnaFene::compute_interaction_sites(double e1[3], double /*e2*/[3], + double /*e3*/[3], double r[3]) { double d_cs=-0.4; @@ -66,6 +66,90 @@ void BondOxdnaFene::compute_interaction_sites(double e1[3], } +/* ---------------------------------------------------------------------- + tally energy and virial into global and per-atom accumulators +------------------------------------------------------------------------- */ + +void BondOxdnaFene::ev_tally_xyz(int i, int j, int nlocal, int newton_bond, + double ebond, + double fx, double fy, double fz, + double delx, double dely, double delz) +{ + double ebondhalf,v[6]; + + if (eflag_either) { + if (eflag_global) { + if (newton_bond) energy += ebond; + else { + ebondhalf = 0.5*ebond; + if (i < nlocal) energy += ebondhalf; + if (j < nlocal) energy += ebondhalf; + } + } + if (eflag_atom) { + ebondhalf = 0.5*ebond; + if (newton_bond || i < nlocal) eatom[i] += ebondhalf; + if (newton_bond || j < nlocal) eatom[j] += ebondhalf; + } + } + + if (vflag_either) { + v[0] = delx*fx; + v[1] = dely*fy; + v[2] = delz*fz; + v[3] = delx*fy; + v[4] = delx*fz; + v[5] = dely*fz; + + if (vflag_global) { + if (newton_bond) { + virial[0] += v[0]; + virial[1] += v[1]; + virial[2] += v[2]; + virial[3] += v[3]; + virial[4] += v[4]; + virial[5] += v[5]; + } else { + if (i < nlocal) { + virial[0] += 0.5*v[0]; + virial[1] += 0.5*v[1]; + virial[2] += 0.5*v[2]; + virial[3] += 0.5*v[3]; + virial[4] += 0.5*v[4]; + virial[5] += 0.5*v[5]; + } + if (j < nlocal) { + virial[0] += 0.5*v[0]; + virial[1] += 0.5*v[1]; + virial[2] += 0.5*v[2]; + virial[3] += 0.5*v[3]; + virial[4] += 0.5*v[4]; + virial[5] += 0.5*v[5]; + } + } + } + + if (vflag_atom) { + if (newton_bond || i < nlocal) { + vatom[i][0] += 0.5*v[0]; + vatom[i][1] += 0.5*v[1]; + vatom[i][2] += 0.5*v[2]; + vatom[i][3] += 0.5*v[3]; + vatom[i][4] += 0.5*v[4]; + vatom[i][5] += 0.5*v[5]; + } + if (newton_bond || j < nlocal) { + vatom[j][0] += 0.5*v[0]; + vatom[j][1] += 0.5*v[1]; + vatom[j][2] += 0.5*v[2]; + vatom[j][3] += 0.5*v[3]; + vatom[j][4] += 0.5*v[4]; + vatom[j][5] += 0.5*v[5]; + } + } + } +} + /* ---------------------------------------------------------------------- compute function for oxDNA FENE-bond interaction s=sugar-phosphate backbone site, b=base site, st=stacking site @@ -112,8 +196,8 @@ void BondOxdnaFene::compute(int eflag, int vflag) MathExtra::q_to_exyz(qb,bx,by,bz); // vector COM-backbone site a and b - compute_interaction_sites(ax,ay,ra_cs); - compute_interaction_sites(bx,by,rb_cs); + compute_interaction_sites(ax,ay,az,ra_cs); + compute_interaction_sites(bx,by,bz,rb_cs); // vector backbone site b to a delr[0] = x[a][0] + ra_cs[0] - x[b][0] - rb_cs[0]; @@ -182,7 +266,11 @@ void BondOxdnaFene::compute(int eflag, int vflag) } // increment energy and virial - if (evflag) ev_tally(a,b,nlocal,newton_bond,ebond,fbond,delr[0],delr[1],delr[2]); + // NOTE: The virial is calculated on the 'molecular' basis. + // (see G. Ciccotti and J.P. Ryckaert, Comp. Phys. Rep. 4, 345-392 (1986)) + + if (evflag) ev_tally_xyz(a,b,nlocal,newton_bond,ebond, + delf[0],delf[1],delf[2],x[a][0]-x[b][0],x[a][1]-x[b][1],x[a][2]-x[b][2]); } diff --git a/src/USER-CGDNA/bond_oxdna_fene.h b/src/USER-CGDNA/bond_oxdna_fene.h index 318ac31fc6..0c702d719a 100644 --- a/src/USER-CGDNA/bond_oxdna_fene.h +++ b/src/USER-CGDNA/bond_oxdna_fene.h @@ -28,7 +28,8 @@ class BondOxdnaFene : public Bond { public: BondOxdnaFene(class LAMMPS *); virtual ~BondOxdnaFene(); - virtual void compute_interaction_sites(double *, double *, double *); + virtual void compute_interaction_sites(double *, double *, double *, + double *); virtual void compute(int, int); void coeff(int, char **); void init_style(); @@ -42,6 +43,7 @@ class BondOxdnaFene : public Bond { double *k,*Delta,*r0; // FENE void allocate(); + void ev_tally_xyz(int, int, int, int, double, double, double, double, double, double, double); }; } diff --git a/src/USER-CGDNA/pair_oxdna2_coaxstk.cpp b/src/USER-CGDNA/pair_oxdna2_coaxstk.cpp index dfea97f0bf..4fde5e37b4 100644 --- a/src/USER-CGDNA/pair_oxdna2_coaxstk.cpp +++ b/src/USER-CGDNA/pair_oxdna2_coaxstk.cpp @@ -383,7 +383,11 @@ void PairOxdna2Coaxstk::compute(int eflag, int vflag) } // increment energy and virial - if (evflag) ev_tally(a,b,nlocal,newton_pair,evdwl,0.0,fpair,delr_st[0],delr_st[1],delr_st[2]); + // NOTE: The virial is calculated on the 'molecular' basis. + // (see G. Ciccotti and J.P. Ryckaert, Comp. Phys. Rep. 4, 345-392 (1986)) + + if (evflag) ev_tally_xyz(a,b,nlocal,newton_pair,evdwl,0.0, + delf[0],delf[1],delf[2],x[a][0]-x[b][0],x[a][1]-x[b][1],x[a][2]-x[b][2]); // pure torques not expressible as r x f diff --git a/src/USER-CGDNA/pair_oxdna2_dh.cpp b/src/USER-CGDNA/pair_oxdna2_dh.cpp index b4afad12db..ca5f44b815 100644 --- a/src/USER-CGDNA/pair_oxdna2_dh.cpp +++ b/src/USER-CGDNA/pair_oxdna2_dh.cpp @@ -223,10 +223,14 @@ void PairOxdna2Dh::compute(int eflag, int vflag) } + // increment energy and virial + // NOTE: The virial is calculated on the 'molecular' basis. + // (see G. Ciccotti and J.P. Ryckaert, Comp. Phys. Rep. 4, 345-392 (1986)) + + if (evflag) ev_tally_xyz(a,b,nlocal,newton_pair,evdwl,0.0, + delf[0],delf[1],delf[2],x[a][0]-x[b][0],x[a][1]-x[b][1],x[a][2]-x[b][2]); - if (evflag) ev_tally(a,b,nlocal,newton_pair, - evdwl,0.0,fpair,delr[0],delr[1],delr[2]); } } diff --git a/src/USER-CGDNA/pair_oxdna2_excv.cpp b/src/USER-CGDNA/pair_oxdna2_excv.cpp index 4329fbe071..f2fb77b3b2 100644 --- a/src/USER-CGDNA/pair_oxdna2_excv.cpp +++ b/src/USER-CGDNA/pair_oxdna2_excv.cpp @@ -39,8 +39,8 @@ PairOxdna2Excv::~PairOxdna2Excv() /* ---------------------------------------------------------------------- compute vector COM-excluded volume interaction sites in oxDNA2 ------------------------------------------------------------------------- */ -void PairOxdna2Excv::compute_interaction_sites(double e1[3], - double e2[3], double rs[3], double rb[3]) +void PairOxdna2Excv::compute_interaction_sites(double e1[3], double e2[3], + double /*e3*/[3], double rs[3], double rb[3]) { double d_cs_x=-0.34, d_cs_y=+0.3408, d_cb=+0.4; diff --git a/src/USER-CGDNA/pair_oxdna2_excv.h b/src/USER-CGDNA/pair_oxdna2_excv.h index 33eacbed9c..d61317009b 100644 --- a/src/USER-CGDNA/pair_oxdna2_excv.h +++ b/src/USER-CGDNA/pair_oxdna2_excv.h @@ -28,7 +28,7 @@ class PairOxdna2Excv : public PairOxdnaExcv { public: PairOxdna2Excv(class LAMMPS *); virtual ~PairOxdna2Excv(); - virtual void compute_interaction_sites(double *, + virtual void compute_interaction_sites(double *, double *, double *, double *, double *); }; diff --git a/src/USER-CGDNA/pair_oxdna2_stk.cpp b/src/USER-CGDNA/pair_oxdna2_stk.cpp deleted file mode 100644 index f479572aa6..0000000000 --- a/src/USER-CGDNA/pair_oxdna2_stk.cpp +++ /dev/null @@ -1,50 +0,0 @@ -/* ---------------------------------------------------------------------- - LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov - - Copyright (2003) Sandia Corporation. Under the terms of Contract - DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains - certain rights in this software. This software is distributed under - the GNU General Public License. - - See the README file in the top-level LAMMPS directory. -------------------------------------------------------------------------- */ -/* ---------------------------------------------------------------------- - Contributing author: Oliver Henrich (University of Strathclyde, Glasgow) -------------------------------------------------------------------------- */ - -#include -#include -#include -#include -#include "pair_oxdna2_stk.h" - -using namespace LAMMPS_NS; - -/* ---------------------------------------------------------------------- */ - -PairOxdna2Stk::PairOxdna2Stk(LAMMPS *lmp) : PairOxdnaStk(lmp) -{ - -} - -/* ---------------------------------------------------------------------- */ - -PairOxdna2Stk::~PairOxdna2Stk() -{ - -} - -/* ---------------------------------------------------------------------- - return temperature dependent oxDNA2 stacking strength -------------------------------------------------------------------------- */ - -double PairOxdna2Stk::stacking_strength(double T) -{ - double eps; - - eps = 1.3523 + 2.6717 * T; - - return eps; -} diff --git a/src/USER-CGDNA/pair_oxdna2_stk.h b/src/USER-CGDNA/pair_oxdna2_stk.h deleted file mode 100644 index 7654e5db2f..0000000000 --- a/src/USER-CGDNA/pair_oxdna2_stk.h +++ /dev/null @@ -1,53 +0,0 @@ -/* -*- c++ -*- ---------------------------------------------------------- - LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov - - Copyright (2003) Sandia Corporation. Under the terms of Contract - DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains - certain rights in this software. This software is distributed under - the GNU General Public License. - - See the README file in the top-level LAMMPS directory. -------------------------------------------------------------------------- */ - -#ifdef PAIR_CLASS - -PairStyle(oxdna2/stk,PairOxdna2Stk) - -#else - -#ifndef LMP_PAIR_OXDNA2_STK_H -#define LMP_PAIR_OXDNA2_STK_H - -#include "pair_oxdna_stk.h" - -namespace LAMMPS_NS { - -class PairOxdna2Stk : public PairOxdnaStk { - public: - PairOxdna2Stk(class LAMMPS *); - virtual ~PairOxdna2Stk(); - - protected: - virtual double stacking_strength(double); -}; - -} - -#endif -#endif - -/* ERROR/WARNING messages: - -E: Illegal ... command - -Self-explanatory. Check the input script syntax and compare to the -documentation for the command. You can use -echo screen as a -command-line option when running LAMMPS to see the offending line. - -E: Incorrect args for pair coefficients - -Self-explanatory. Check the input script or data file. - -*/ diff --git a/src/USER-CGDNA/pair_oxdna_coaxstk.cpp b/src/USER-CGDNA/pair_oxdna_coaxstk.cpp index 6f3fa4fa4e..6b10117f91 100644 --- a/src/USER-CGDNA/pair_oxdna_coaxstk.cpp +++ b/src/USER-CGDNA/pair_oxdna_coaxstk.cpp @@ -450,7 +450,11 @@ void PairOxdnaCoaxstk::compute(int eflag, int vflag) } // increment energy and virial - if (evflag) ev_tally(a,b,nlocal,newton_pair,evdwl,0.0,fpair,delr_st[0],delr_st[1],delr_st[2]); + // NOTE: The virial is calculated on the 'molecular' basis. + // (see G. Ciccotti and J.P. Ryckaert, Comp. Phys. Rep. 4, 345-392 (1986)) + + if (evflag) ev_tally_xyz(a,b,nlocal,newton_pair,evdwl,0.0, + delf[0],delf[1],delf[2],x[a][0]-x[b][0],x[a][1]-x[b][1],x[a][2]-x[b][2]); // pure torques not expressible as r x f diff --git a/src/USER-CGDNA/pair_oxdna_excv.cpp b/src/USER-CGDNA/pair_oxdna_excv.cpp index 82af5ed1c7..ddfe32946c 100644 --- a/src/USER-CGDNA/pair_oxdna_excv.cpp +++ b/src/USER-CGDNA/pair_oxdna_excv.cpp @@ -91,8 +91,8 @@ PairOxdnaExcv::~PairOxdnaExcv() /* ---------------------------------------------------------------------- compute vector COM-excluded volume interaction sites in oxDNA ------------------------------------------------------------------------- */ -void PairOxdnaExcv::compute_interaction_sites(double e1[3], - double /*e2*/[3], double rs[3], double rb[3]) +void PairOxdnaExcv::compute_interaction_sites(double e1[3], double /*e2*/[3], + double /*e3*/[3], double rs[3], double rb[3]) { double d_cs=-0.4, d_cb=+0.4; @@ -162,7 +162,7 @@ void PairOxdnaExcv::compute(int eflag, int vflag) MathExtra::q_to_exyz(qa,ax,ay,az); // vector COM - backbone and base site a - compute_interaction_sites(ax,ay,ra_cs,ra_cb); + compute_interaction_sites(ax,ay,az,ra_cs,ra_cb); rtmp_s[0] = x[a][0] + ra_cs[0]; rtmp_s[1] = x[a][1] + ra_cs[1]; @@ -187,7 +187,7 @@ void PairOxdnaExcv::compute(int eflag, int vflag) MathExtra::q_to_exyz(qb,bx,by,bz); // vector COM - backbone and base site b - compute_interaction_sites(bx,by,rb_cs,rb_cb); + compute_interaction_sites(bx,by,bz,rb_cs,rb_cb); // vector backbone site b to a delr_ss[0] = rtmp_s[0] - (x[b][0] + rb_cs[0]); @@ -225,14 +225,17 @@ void PairOxdnaExcv::compute(int eflag, int vflag) fpair *= factor_lj; evdwl *= factor_lj; - // increment energy and virial - if (evflag) ev_tally(a,b,nlocal,newton_pair, - evdwl,0.0,fpair,delr_ss[0],delr_ss[1],delr_ss[2]); - delf[0] = delr_ss[0]*fpair; delf[1] = delr_ss[1]*fpair; delf[2] = delr_ss[2]*fpair; + // increment energy and virial + // NOTE: The virial is calculated on the 'molecular' basis. + // (see G. Ciccotti and J.P. Ryckaert, Comp. Phys. Rep. 4, 345-392 (1986)) + + if (evflag) ev_tally_xyz(a,b,nlocal,newton_pair,evdwl,0.0, + delf[0],delf[1],delf[2],x[a][0]-x[b][0],x[a][1]-x[b][1],x[a][2]-x[b][2]); + f[a][0] += delf[0]; f[a][1] += delf[1]; f[a][2] += delf[2]; @@ -259,21 +262,20 @@ void PairOxdnaExcv::compute(int eflag, int vflag) } - // backbone-base if (rsq_sb < cutsq_sb_c[atype][btype]) { evdwl = F3(rsq_sb,cutsq_sb_ast[atype][btype],cut_sb_c[atype][btype],lj1_sb[atype][btype], lj2_sb[atype][btype],epsilon_sb[atype][btype],b_sb[atype][btype],fpair); - // increment energy and virial - if (evflag) ev_tally(a,b,nlocal,newton_pair, - evdwl,0.0,fpair,delr_sb[0],delr_sb[1],delr_sb[2]); - delf[0] = delr_sb[0]*fpair; delf[1] = delr_sb[1]*fpair; delf[2] = delr_sb[2]*fpair; + // increment energy and virial + if (evflag) ev_tally_xyz(a,b,nlocal,newton_pair,evdwl,0.0, + delf[0],delf[1],delf[2],x[a][0]-x[b][0],x[a][1]-x[b][1],x[a][2]-x[b][2]); + f[a][0] += delf[0]; f[a][1] += delf[1]; f[a][2] += delf[2]; @@ -306,14 +308,14 @@ void PairOxdnaExcv::compute(int eflag, int vflag) evdwl = F3(rsq_bs,cutsq_sb_ast[atype][btype],cut_sb_c[atype][btype],lj1_sb[atype][btype], lj2_sb[atype][btype],epsilon_sb[atype][btype],b_sb[atype][btype],fpair); - // increment energy and virial - if (evflag) ev_tally(a,b,nlocal,newton_pair, - evdwl,0.0,fpair,delr_bs[0],delr_bs[1],delr_bs[2]); - delf[0] = delr_bs[0]*fpair; delf[1] = delr_bs[1]*fpair; delf[2] = delr_bs[2]*fpair; + // increment energy and virial + if (evflag) ev_tally_xyz(a,b,nlocal,newton_pair,evdwl,0.0, + delf[0],delf[1],delf[2],x[a][0]-x[b][0],x[a][1]-x[b][1],x[a][2]-x[b][2]); + f[a][0] += delf[0]; f[a][1] += delf[1]; f[a][2] += delf[2]; @@ -346,14 +348,14 @@ void PairOxdnaExcv::compute(int eflag, int vflag) evdwl = F3(rsq_bb,cutsq_bb_ast[atype][btype],cut_bb_c[atype][btype],lj1_bb[atype][btype], lj2_bb[atype][btype],epsilon_bb[atype][btype],b_bb[atype][btype],fpair); - // increment energy and virial - if (evflag) ev_tally(a,b,nlocal,newton_pair, - evdwl,0.0,fpair,delr_bb[0],delr_bb[1],delr_bb[2]); - delf[0] = delr_bb[0]*fpair; delf[1] = delr_bb[1]*fpair; delf[2] = delr_bb[2]*fpair; + // increment energy and virial + if (evflag) ev_tally_xyz(a,b,nlocal,newton_pair,evdwl,0.0, + delf[0],delf[1],delf[2],x[a][0]-x[b][0],x[a][1]-x[b][1],x[a][2]-x[b][2]); + f[a][0] += delf[0]; f[a][1] += delf[1]; f[a][2] += delf[2]; diff --git a/src/USER-CGDNA/pair_oxdna_excv.h b/src/USER-CGDNA/pair_oxdna_excv.h index 9cae6ac528..c80a112fec 100644 --- a/src/USER-CGDNA/pair_oxdna_excv.h +++ b/src/USER-CGDNA/pair_oxdna_excv.h @@ -28,7 +28,7 @@ class PairOxdnaExcv : public Pair { public: PairOxdnaExcv(class LAMMPS *); virtual ~PairOxdnaExcv(); - virtual void compute_interaction_sites(double *, double *, + virtual void compute_interaction_sites(double *, double *, double *, double *, double *); virtual void compute(int, int); void settings(int, char **); diff --git a/src/USER-CGDNA/pair_oxdna_hbond.cpp b/src/USER-CGDNA/pair_oxdna_hbond.cpp index 8cd28f10c8..03e83e1324 100644 --- a/src/USER-CGDNA/pair_oxdna_hbond.cpp +++ b/src/USER-CGDNA/pair_oxdna_hbond.cpp @@ -410,7 +410,11 @@ void PairOxdnaHbond::compute(int eflag, int vflag) } // increment energy and virial - if (evflag) ev_tally(a,b,nlocal,newton_pair,evdwl,0.0,fpair,delr_hb[0],delr_hb[1],delr_hb[2]); + // NOTE: The virial is calculated on the 'molecular' basis. + // (see G. Ciccotti and J.P. Ryckaert, Comp. Phys. Rep. 4, 345-392 (1986)) + + if (evflag) ev_tally_xyz(a,b,nlocal,newton_pair,evdwl,0.0, + delf[0],delf[1],delf[2],x[a][0]-x[b][0],x[a][1]-x[b][1],x[a][2]-x[b][2]); // pure torques not expressible as r x f diff --git a/src/USER-CGDNA/pair_oxdna_stk.cpp b/src/USER-CGDNA/pair_oxdna_stk.cpp index 93c65979ac..3c7a3f05bc 100644 --- a/src/USER-CGDNA/pair_oxdna_stk.cpp +++ b/src/USER-CGDNA/pair_oxdna_stk.cpp @@ -106,6 +106,94 @@ PairOxdnaStk::~PairOxdnaStk() } } +/* ---------------------------------------------------------------------- + tally energy and virial into global and per-atom accumulators + + NOTE: Although this is a pair style interaction, the algorithm below + follows the virial incrementation of the bond style. This is because + the bond topology is used in the main compute loop. +------------------------------------------------------------------------- */ + +void PairOxdnaStk::ev_tally_xyz(int i, int j, int nlocal, int newton_bond, + double evdwl, + double fx, double fy, double fz, + double delx, double dely, double delz) +{ + double evdwlhalf,v[6]; + + if (eflag_either) { + if (eflag_global) { + if (newton_bond) eng_vdwl += evdwl; + else { + evdwlhalf = 0.5*evdwl; + if (i < nlocal) eng_vdwl += evdwlhalf; + if (j < nlocal) eng_vdwl += evdwlhalf; + } + } + if (eflag_atom) { + evdwlhalf = 0.5*evdwl; + if (newton_bond || i < nlocal) eatom[i] += evdwlhalf; + if (newton_bond || j < nlocal) eatom[j] += evdwlhalf; + } + } + + if (vflag_either) { + v[0] = delx*fx; + v[1] = dely*fy; + v[2] = delz*fz; + v[3] = delx*fy; + v[4] = delx*fz; + v[5] = dely*fz; + + if (vflag_global) { + if (newton_bond) { + virial[0] += v[0]; + virial[1] += v[1]; + virial[2] += v[2]; + virial[3] += v[3]; + virial[4] += v[4]; + virial[5] += v[5]; + } else { + if (i < nlocal) { + virial[0] += 0.5*v[0]; + virial[1] += 0.5*v[1]; + virial[2] += 0.5*v[2]; + virial[3] += 0.5*v[3]; + virial[4] += 0.5*v[4]; + virial[5] += 0.5*v[5]; + } + if (j < nlocal) { + virial[0] += 0.5*v[0]; + virial[1] += 0.5*v[1]; + virial[2] += 0.5*v[2]; + virial[3] += 0.5*v[3]; + virial[4] += 0.5*v[4]; + virial[5] += 0.5*v[5]; + } + } + } + + if (vflag_atom) { + if (newton_bond || i < nlocal) { + vatom[i][0] += 0.5*v[0]; + vatom[i][1] += 0.5*v[1]; + vatom[i][2] += 0.5*v[2]; + vatom[i][3] += 0.5*v[3]; + vatom[i][4] += 0.5*v[4]; + vatom[i][5] += 0.5*v[5]; + } + if (newton_bond || j < nlocal) { + vatom[j][0] += 0.5*v[0]; + vatom[j][1] += 0.5*v[1]; + vatom[j][2] += 0.5*v[2]; + vatom[j][3] += 0.5*v[3]; + vatom[j][4] += 0.5*v[4]; + vatom[j][5] += 0.5*v[5]; + } + } + } +} + /* ---------------------------------------------------------------------- compute function for oxDNA pair interactions s=sugar-phosphate backbone site, b=base site, st=stacking site @@ -295,9 +383,6 @@ void PairOxdnaStk::compute(int eflag, int vflag) // early rejection criterium if (evdwl) { - // increment energy - if (evflag) ev_tally(a,b,nlocal,newton_bond,evdwl,0.0,0.0,0.0,0.0,0.0); - df1 = DF1(r_st, epsilon_st[atype][btype], a_st[atype][btype], cut_st_0[atype][btype], cut_st_lc[atype][btype], cut_st_hc[atype][btype], cut_st_lo[atype][btype], cut_st_hi[atype][btype], b_st_lo[atype][btype], b_st_hi[atype][btype]); @@ -366,7 +451,7 @@ void PairOxdnaStk::compute(int eflag, int vflag) } - // increment forces, torques and virial + // increment forces and torques if (newton_bond || a < nlocal) { @@ -402,7 +487,12 @@ void PairOxdnaStk::compute(int eflag, int vflag) } - if (evflag) ev_tally(a,b,nlocal,newton_bond,0.0,0.0,fpair,delr_st[0],delr_st[1],delr_st[2]); + // increment energy and virial + // NOTE: The virial is calculated on the 'molecular' basis. + // (see G. Ciccotti and J.P. Ryckaert, Comp. Phys. Rep. 4, 345-392 (1986)) + + if (evflag) ev_tally_xyz(a,b,nlocal,newton_bond,evdwl, + delf[0],delf[1],delf[2],x[a][0]-x[b][0],x[a][1]-x[b][1],x[a][2]-x[b][2]); // force, torque and virial contribution for forces between backbone sites @@ -444,7 +534,7 @@ void PairOxdnaStk::compute(int eflag, int vflag) } - // increment forces, torques and virial + // increment forces and torques if (newton_bond || a < nlocal) { @@ -480,8 +570,9 @@ void PairOxdnaStk::compute(int eflag, int vflag) } - if (evflag) ev_tally(a,b,nlocal,newton_bond,0.0,0.0,fpair,delr_ss[0],delr_ss[1],delr_ss[2]); - + // increment virial only + if (evflag) ev_tally_xyz(a,b,nlocal,newton_bond,0.0, + delf[0],delf[1],delf[2],x[a][0]-x[b][0],x[a][1]-x[b][1],x[a][2]-x[b][2]); // pure torques not expressible as r x f @@ -656,11 +747,11 @@ void PairOxdnaStk::settings(int narg, char **/*arg*/) return temperature dependent oxDNA stacking strength ------------------------------------------------------------------------- */ -double PairOxdnaStk::stacking_strength(double T) +double PairOxdnaStk::stacking_strength(double xi_st, double kappa_st, double T) { double eps; - eps = 1.3448 + 2.6568 * T; + eps = xi_st + kappa_st * T; return eps; } @@ -673,7 +764,7 @@ void PairOxdnaStk::coeff(int narg, char **arg) { int count; - if (narg != 22) error->all(FLERR,"Incorrect args for pair coefficients in oxdna/stk"); + if (narg != 24) error->all(FLERR,"Incorrect args for pair coefficients in oxdna/stk"); if (!allocated) allocate(); int ilo,ihi,jlo,jhi; @@ -683,7 +774,7 @@ void PairOxdnaStk::coeff(int narg, char **arg) // stacking interaction count = 0; - double T, epsilon_st_one, a_st_one, b_st_lo_one, b_st_hi_one; + double T, epsilon_st_one, xi_st_one, kappa_st_one, a_st_one, b_st_lo_one, b_st_hi_one; double cut_st_0_one, cut_st_c_one, cut_st_lo_one, cut_st_hi_one; double cut_st_lc_one, cut_st_hc_one, tmp, shift_st_one; @@ -706,27 +797,29 @@ void PairOxdnaStk::coeff(int narg, char **arg) if (strcmp(arg[2],"seqdep") == 0) seqdepflag = 1; T = force->numeric(FLERR,arg[3]); - epsilon_st_one = stacking_strength(T); - - a_st_one = force->numeric(FLERR,arg[4]); - cut_st_0_one = force->numeric(FLERR,arg[5]); - cut_st_c_one = force->numeric(FLERR,arg[6]); - cut_st_lo_one = force->numeric(FLERR,arg[7]); - cut_st_hi_one = force->numeric(FLERR,arg[8]); - - a_st4_one = force->numeric(FLERR,arg[9]); - theta_st4_0_one = force->numeric(FLERR,arg[10]); - dtheta_st4_ast_one = force->numeric(FLERR,arg[11]); - a_st5_one = force->numeric(FLERR,arg[12]); - theta_st5_0_one = force->numeric(FLERR,arg[13]); - dtheta_st5_ast_one = force->numeric(FLERR,arg[14]); - a_st6_one = force->numeric(FLERR,arg[15]); - theta_st6_0_one = force->numeric(FLERR,arg[16]); - dtheta_st6_ast_one = force->numeric(FLERR,arg[17]); - a_st1_one = force->numeric(FLERR,arg[18]); - cosphi_st1_ast_one = force->numeric(FLERR,arg[19]); - a_st2_one = force->numeric(FLERR,arg[20]); - cosphi_st2_ast_one = force->numeric(FLERR,arg[21]); + xi_st_one = force->numeric(FLERR,arg[4]); + kappa_st_one = force->numeric(FLERR,arg[5]); + epsilon_st_one = stacking_strength(xi_st_one, kappa_st_one, T); + + a_st_one = force->numeric(FLERR,arg[6]); + cut_st_0_one = force->numeric(FLERR,arg[7]); + cut_st_c_one = force->numeric(FLERR,arg[8]); + cut_st_lo_one = force->numeric(FLERR,arg[9]); + cut_st_hi_one = force->numeric(FLERR,arg[10]); + + a_st4_one = force->numeric(FLERR,arg[11]); + theta_st4_0_one = force->numeric(FLERR,arg[12]); + dtheta_st4_ast_one = force->numeric(FLERR,arg[13]); + a_st5_one = force->numeric(FLERR,arg[14]); + theta_st5_0_one = force->numeric(FLERR,arg[15]); + dtheta_st5_ast_one = force->numeric(FLERR,arg[16]); + a_st6_one = force->numeric(FLERR,arg[17]); + theta_st6_0_one = force->numeric(FLERR,arg[18]); + dtheta_st6_ast_one = force->numeric(FLERR,arg[19]); + a_st1_one = force->numeric(FLERR,arg[20]); + cosphi_st1_ast_one = force->numeric(FLERR,arg[21]); + a_st2_one = force->numeric(FLERR,arg[22]); + cosphi_st2_ast_one = force->numeric(FLERR,arg[23]); b_st_lo_one = 2*a_st_one*exp(-a_st_one*(cut_st_lo_one-cut_st_0_one))* 2*a_st_one*exp(-a_st_one*(cut_st_lo_one-cut_st_0_one))* diff --git a/src/USER-CGDNA/pair_oxdna_stk.h b/src/USER-CGDNA/pair_oxdna_stk.h index 74a9a6bf68..581e87f4b2 100644 --- a/src/USER-CGDNA/pair_oxdna_stk.h +++ b/src/USER-CGDNA/pair_oxdna_stk.h @@ -14,6 +14,7 @@ #ifdef PAIR_CLASS PairStyle(oxdna/stk,PairOxdnaStk) +PairStyle(oxdna2/stk,PairOxdnaStk) #else @@ -44,7 +45,7 @@ class PairOxdnaStk : public Pair { protected: // stacking interaction - virtual double stacking_strength(double); + double stacking_strength(double, double, double); double **epsilon_st, **a_st, **cut_st_0, **cut_st_c; double **cut_st_lo, **cut_st_hi; double **cut_st_lc, **cut_st_hc, **b_st_lo, **b_st_hi, **shift_st; @@ -61,6 +62,7 @@ class PairOxdnaStk : public Pair { int seqdepflag; virtual void allocate(); + void ev_tally_xyz(int, int, int, int, double, double, double, double, double, double, double); }; } diff --git a/src/USER-CGDNA/pair_oxdna_xstk.cpp b/src/USER-CGDNA/pair_oxdna_xstk.cpp index 1365d0d2b2..d5248937ca 100644 --- a/src/USER-CGDNA/pair_oxdna_xstk.cpp +++ b/src/USER-CGDNA/pair_oxdna_xstk.cpp @@ -422,7 +422,11 @@ void PairOxdnaXstk::compute(int eflag, int vflag) } // increment energy and virial - if (evflag) ev_tally(a,b,nlocal,newton_pair,evdwl,0.0,fpair,delr_hb[0],delr_hb[1],delr_hb[2]); + // NOTE: The virial is calculated on the 'molecular' basis. + // (see G. Ciccotti and J.P. Ryckaert, Comp. Phys. Rep. 4, 345-392 (1986)) + + if (evflag) ev_tally_xyz(a,b,nlocal,newton_pair,evdwl,0.0, + delf[0],delf[1],delf[2],x[a][0]-x[b][0],x[a][1]-x[b][1],x[a][2]-x[b][2]); // pure torques not expressible as r x f -- GitLab From 7bf97577551dd496f8dca8aa7b9cdb00d1bd6c91 Mon Sep 17 00:00:00 2001 From: Oliver Henrich Date: Fri, 19 Jul 2019 11:57:58 +0100 Subject: [PATCH 268/469] Updated input and log files, amended comment in data files --- .../cgdna/examples/oxDNA/duplex1/data.duplex1 | 2 +- .../cgdna/examples/oxDNA/duplex1/in.duplex1 | 9 +- .../oxDNA/duplex1/log.18Jun19.duplex1.g++.1 | 1165 ++++++++++++++++ .../oxDNA/duplex1/log.18Jun19.duplex1.g++.4 | 1165 ++++++++++++++++ .../oxDNA/duplex1/log.27Nov18.duplex1.g++.1 | 172 --- .../oxDNA/duplex1/log.27Nov18.duplex1.g++.4 | 172 --- .../cgdna/examples/oxDNA/duplex2/data.duplex2 | 2 +- .../cgdna/examples/oxDNA/duplex2/in.duplex2 | 9 +- .../oxDNA/duplex2/log.18Jun19.duplex2.g++.1 | 1167 ++++++++++++++++ .../oxDNA/duplex2/log.18Jun19.duplex2.g++.4 | 1167 ++++++++++++++++ .../oxDNA/duplex2/log.27Nov18.duplex2.g++.1 | 172 --- .../oxDNA/duplex2/log.27Nov18.duplex2.g++.4 | 172 --- .../examples/oxDNA2/duplex1/data.duplex1 | 2 +- .../cgdna/examples/oxDNA2/duplex1/in.duplex1 | 11 +- .../oxDNA2/duplex1/log.18Jun19.duplex1.g++.1 | 1172 ++++++++++++++++ .../oxDNA2/duplex1/log.18Jun19.duplex1.g++.4 | 1172 ++++++++++++++++ .../oxDNA2/duplex1/log.27Nov18.duplex1.g++.1 | 178 --- .../oxDNA2/duplex1/log.27Nov18.duplex1.g++.4 | 178 --- .../examples/oxDNA2/duplex2/data.duplex2 | 2 +- .../cgdna/examples/oxDNA2/duplex2/in.duplex2 | 12 +- .../oxDNA2/duplex2/log.18Jun19.duplex2.g++.1 | 1173 +++++++++++++++++ .../oxDNA2/duplex2/log.18Jun19.duplex2.g++.4 | 1173 +++++++++++++++++ .../oxDNA2/duplex2/log.27Nov18.duplex2.g++.1 | 178 --- .../oxDNA2/duplex2/log.27Nov18.duplex2.g++.4 | 178 --- .../examples/oxDNA2/duplex3/data.duplex3 | 73 + .../cgdna/examples/oxDNA2/duplex3/in.duplex3 | 79 ++ .../oxDNA2/duplex3/log.18Jun19.duplex3.g++.1 | 1172 ++++++++++++++++ .../oxDNA2/duplex3/log.18Jun19.duplex3.g++.4 | 1172 ++++++++++++++++ 28 files changed, 11876 insertions(+), 1423 deletions(-) create mode 100644 examples/USER/cgdna/examples/oxDNA/duplex1/log.18Jun19.duplex1.g++.1 create mode 100644 examples/USER/cgdna/examples/oxDNA/duplex1/log.18Jun19.duplex1.g++.4 delete mode 100644 examples/USER/cgdna/examples/oxDNA/duplex1/log.27Nov18.duplex1.g++.1 delete mode 100644 examples/USER/cgdna/examples/oxDNA/duplex1/log.27Nov18.duplex1.g++.4 create mode 100644 examples/USER/cgdna/examples/oxDNA/duplex2/log.18Jun19.duplex2.g++.1 create mode 100644 examples/USER/cgdna/examples/oxDNA/duplex2/log.18Jun19.duplex2.g++.4 delete mode 100644 examples/USER/cgdna/examples/oxDNA/duplex2/log.27Nov18.duplex2.g++.1 delete mode 100644 examples/USER/cgdna/examples/oxDNA/duplex2/log.27Nov18.duplex2.g++.4 create mode 100644 examples/USER/cgdna/examples/oxDNA2/duplex1/log.18Jun19.duplex1.g++.1 create mode 100644 examples/USER/cgdna/examples/oxDNA2/duplex1/log.18Jun19.duplex1.g++.4 delete mode 100644 examples/USER/cgdna/examples/oxDNA2/duplex1/log.27Nov18.duplex1.g++.1 delete mode 100644 examples/USER/cgdna/examples/oxDNA2/duplex1/log.27Nov18.duplex1.g++.4 create mode 100644 examples/USER/cgdna/examples/oxDNA2/duplex2/log.18Jun19.duplex2.g++.1 create mode 100644 examples/USER/cgdna/examples/oxDNA2/duplex2/log.18Jun19.duplex2.g++.4 delete mode 100644 examples/USER/cgdna/examples/oxDNA2/duplex2/log.27Nov18.duplex2.g++.1 delete mode 100644 examples/USER/cgdna/examples/oxDNA2/duplex2/log.27Nov18.duplex2.g++.4 create mode 100644 examples/USER/cgdna/examples/oxDNA2/duplex3/data.duplex3 create mode 100644 examples/USER/cgdna/examples/oxDNA2/duplex3/in.duplex3 create mode 100644 examples/USER/cgdna/examples/oxDNA2/duplex3/log.18Jun19.duplex3.g++.1 create mode 100644 examples/USER/cgdna/examples/oxDNA2/duplex3/log.18Jun19.duplex3.g++.4 diff --git a/examples/USER/cgdna/examples/oxDNA/duplex1/data.duplex1 b/examples/USER/cgdna/examples/oxDNA/duplex1/data.duplex1 index 6aee3233dd..0ef671c603 100644 --- a/examples/USER/cgdna/examples/oxDNA/duplex1/data.duplex1 +++ b/examples/USER/cgdna/examples/oxDNA/duplex1/data.duplex1 @@ -32,7 +32,7 @@ Atoms 9 3 4.860249842674775e-01 3.518234140414733e-01 3.897628551303121e-01 2 1 1 10 4 5.999999999999996e-01 -1.332267629550188e-16 -1.110223024625157e-16 2 1 1 -# Atom-ID, translational, rotational velocity +# Atom-ID, translational velocity, angular momentum Velocities 1 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 diff --git a/examples/USER/cgdna/examples/oxDNA/duplex1/in.duplex1 b/examples/USER/cgdna/examples/oxDNA/duplex1/in.duplex1 index 6485312731..34e17380af 100644 --- a/examples/USER/cgdna/examples/oxDNA/duplex1/in.duplex1 +++ b/examples/USER/cgdna/examples/oxDNA/duplex1/in.duplex1 @@ -1,6 +1,7 @@ variable number equal 1 variable ofreq equal 1000 variable efreq equal 1000 +variable T equal 0.1 units lj @@ -30,7 +31,7 @@ bond_coeff * 2.0 0.25 0.7525 # oxDNA pair interactions pair_style hybrid/overlay oxdna/excv oxdna/stk oxdna/hbond oxdna/xstk oxdna/coaxstk pair_coeff * * oxdna/excv 2.0 0.7 0.675 2.0 0.515 0.5 2.0 0.33 0.32 -pair_coeff * * oxdna/stk seqav 0.1 6.0 0.4 0.9 0.32 0.6 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2.0 0.65 2.0 0.65 +pair_coeff * * oxdna/stk seqav ${T} 1.3448 2.6568 6.0 0.4 0.9 0.32 0.6 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2.0 0.65 2.0 0.65 pair_coeff * * oxdna/hbond seqav 0.0 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45 pair_coeff 1 4 oxdna/hbond seqav 1.077 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45 pair_coeff 2 3 oxdna/hbond seqav 1.077 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45 @@ -39,9 +40,9 @@ pair_coeff * * oxdna/coaxstk 46.0 0.4 0.6 0.22 0.58 2.0 2.541592653589793 0.65 1 # NVE ensemble fix 1 all nve/dot -#fix 1 all nve/dotc/langevin 0.1 0.1 0.03 457145 angmom 10 +#fix 1 all nve/dotc/langevin ${T} ${T} 0.03 457145 angmom 10 #fix 1 all nve/asphere -#fix 2 all langevin 0.1 0.1 0.03 457145 angmom 10 +#fix 2 all langevin ${T} ${T} 0.03 457145 angmom 10 timestep 1e-5 @@ -72,6 +73,6 @@ fix 5 all print ${efreq} "$(step) ekin = ${ekin} | erot = ${erot} | epot = ${e #dump_modify out sort id #dump_modify out format line "%d %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le" -run 10000 +run 1000000 #write_restart config.${number}.* diff --git a/examples/USER/cgdna/examples/oxDNA/duplex1/log.18Jun19.duplex1.g++.1 b/examples/USER/cgdna/examples/oxDNA/duplex1/log.18Jun19.duplex1.g++.1 new file mode 100644 index 0000000000..8b1c5c3807 --- /dev/null +++ b/examples/USER/cgdna/examples/oxDNA/duplex1/log.18Jun19.duplex1.g++.1 @@ -0,0 +1,1165 @@ +LAMMPS (18 Jun 2019) +variable number equal 1 +variable ofreq equal 1000 +variable efreq equal 1000 +variable T equal 0.1 + +units lj + +dimension 3 + +newton off + +boundary p p p + +atom_style hybrid bond ellipsoid +atom_modify sort 0 1.0 + +# Pair interactions require lists of neighbours to be calculated +neighbor 1.0 bin +neigh_modify every 1 delay 0 check yes + +read_data data.duplex1 + orthogonal box = (-20 -20 -20) to (20 20 20) + 1 by 1 by 1 MPI processor grid + reading atoms ... + 10 atoms + reading velocities ... + 10 velocities + 10 ellipsoids + scanning bonds ... + 2 = max bonds/atom + reading bonds ... + 8 bonds + 2 = max # of 1-2 neighbors + 2 = max # of 1-3 neighbors + 2 = max # of 1-4 neighbors + 4 = max # of special neighbors + special bonds CPU = 5e-05 secs + read_data CPU = 0.001522 secs + +set atom * mass 3.1575 + 10 settings made for mass + +group all type 1 4 +10 atoms in group all + +# oxDNA bond interactions - FENE backbone +bond_style oxdna/fene +bond_coeff * 2.0 0.25 0.7525 + +# oxDNA pair interactions +pair_style hybrid/overlay oxdna/excv oxdna/stk oxdna/hbond oxdna/xstk oxdna/coaxstk +pair_coeff * * oxdna/excv 2.0 0.7 0.675 2.0 0.515 0.5 2.0 0.33 0.32 +pair_coeff * * oxdna/stk seqav ${T} 1.3448 2.6568 6.0 0.4 0.9 0.32 0.6 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2.0 0.65 2.0 0.65 +pair_coeff * * oxdna/stk seqav 0.1 1.3448 2.6568 6.0 0.4 0.9 0.32 0.6 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2.0 0.65 2.0 0.65 +pair_coeff * * oxdna/hbond seqav 0.0 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45 +pair_coeff 1 4 oxdna/hbond seqav 1.077 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45 +pair_coeff 2 3 oxdna/hbond seqav 1.077 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45 +pair_coeff * * oxdna/xstk 47.5 0.575 0.675 0.495 0.655 2.25 0.791592653589793 0.58 1.7 1.0 0.68 1.7 1.0 0.68 1.5 0 0.65 1.7 0.875 0.68 1.7 0.875 0.68 +pair_coeff * * oxdna/coaxstk 46.0 0.4 0.6 0.22 0.58 2.0 2.541592653589793 0.65 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2.0 -0.65 2.0 -0.65 + +# NVE ensemble +fix 1 all nve/dot +#fix 1 all nve/dotc/langevin ${T} ${T} 0.03 457145 angmom 10 +#fix 1 all nve/asphere +#fix 2 all langevin ${T} ${T} 0.03 457145 angmom 10 + +timestep 1e-5 + +#comm_style tiled +#fix 3 all balance 10000 1.1 rcb + +#compute mol all chunk/atom molecule +#compute mychunk all vcm/chunk mol +#fix 4 all ave/time 10000 1 10000 c_mychunk[1] c_mychunk[2] c_mychunk[3] file vcm.txt mode vector + +#dump pos all xyz ${ofreq} traj.${number}.xyz + +#compute quat all property/atom quatw quati quatj quatk +#dump quat all custom ${ofreq} quat.${number}.txt id c_quat[1] c_quat[2] c_quat[3] c_quat[4] +#dump_modify quat sort id +#dump_modify quat format line "%d %13.6le %13.6le %13.6le %13.6le" + +compute erot all erotate/asphere +compute ekin all ke +compute epot all pe +variable erot equal c_erot +variable ekin equal c_ekin +variable epot equal c_epot +variable etot equal c_erot+c_ekin+c_epot +fix 5 all print ${efreq} "$(step) ekin = ${ekin} | erot = ${erot} | epot = ${epot} | etot = ${etot}" screen yes +fix 5 all print 1000 "$(step) ekin = ${ekin} | erot = ${erot} | epot = ${epot} | etot = ${etot}" screen yes + +#dump out all custom ${ofreq} out.${number}.txt id x y z vx vy vz fx fy fz tqx tqy tqz +#dump_modify out sort id +#dump_modify out format line "%d %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le" + +run 1000000 +Neighbor list info ... + update every 1 steps, delay 0 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 1.92828 + ghost atom cutoff = 1.92828 + binsize = 0.964142, bins = 42 42 42 + 5 neighbor lists, perpetual/occasional/extra = 5 0 0 + (1) pair oxdna/excv, perpetual + attributes: half, newton off + pair build: half/bin/newtoff + stencil: half/bin/3d/newtoff + bin: standard + (2) pair oxdna/stk, perpetual, copy from (1) + attributes: half, newton off + pair build: copy + stencil: none + bin: none + (3) pair oxdna/hbond, perpetual, copy from (1) + attributes: half, newton off + pair build: copy + stencil: none + bin: none + (4) pair oxdna/xstk, perpetual, copy from (1) + attributes: half, newton off + pair build: copy + stencil: none + bin: none + (5) pair oxdna/coaxstk, perpetual, copy from (1) + attributes: half, newton off + pair build: copy + stencil: none + bin: none +Per MPI rank memory allocation (min/avg/max) = 2.859 | 2.859 | 2.859 Mbytes +Step Temp E_pair E_mol TotEng Press + 0 0 -1.4711818 0.0069384985 -1.4642433 2.5836586e-06 +1000 ekin = 0.00113448721737003 | erot = 0.00413455947734281 | epot = -14.6477022915193 | etot = -14.6424332448246 +2000 ekin = 0.00449927223902336 | erot = 0.0164446434455805 | epot = -14.6633771605337 | etot = -14.6424332448491 +3000 ekin = 0.00997964450841065 | erot = 0.0366523356056461 | epot = -14.6890652250033 | etot = -14.6424332448892 +4000 ekin = 0.0173888111295073 | erot = 0.0643039804300224 | epot = -14.7241260365031 | etot = -14.6424332449436 +5000 ekin = 0.0264744514136619 | erot = 0.0987844033142069 | epot = -14.7676920997383 | etot = -14.6424332450104 +6000 ekin = 0.0369277948556079 | erot = 0.139336571052566 | epot = -14.8186976109956 | etot = -14.6424332450875 +7000 ekin = 0.04839505571915 | erot = 0.185086295692081 | epot = -14.8759145965832 | etot = -14.642433245172 +8000 ekin = 0.0604909336920643 | erot = 0.235071307523532 | epot = -14.9379954864767 | etot = -14.6424332452611 +9000 ekin = 0.0728137406440561 | erot = 0.288273694501538 | epot = -15.003520680497 | etot = -14.6424332453514 +10000 ekin = 0.0849615563085878 | erot = 0.343654369293473 | epot = -15.0710491710418 | etot = -14.6424332454398 +11000 ekin = 0.0965486715045649 | erot = 0.400187932108223 | epot = -15.1391698491357 | etot = -14.6424332455229 +12000 ekin = 0.10722146628289 | erot = 0.456896095459165 | epot = -15.20655080734 | etot = -14.642433245598 +13000 ekin = 0.116672809719548 | erot = 0.512877765427643 | epot = -15.2719838208099 | etot = -14.6424332456627 +14000 ekin = 0.12465407373104 | erot = 0.567333962045116 | epot = -15.3344212814913 | etot = -14.6424332457151 +15000 ekin = 0.13098393968427 | erot = 0.619586028256667 | epot = -15.3930032136954 | etot = -14.6424332457544 +16000 ekin = 0.135553354544872 | erot = 0.669086028489761 | epot = -15.447072628815 | etot = -14.6424332457804 +17000 ekin = 0.138326263958247 | erot = 0.715418858085449 | epot = -15.4961783678372 | etot = -14.6424332457935 +18000 ekin = 0.139336096664052 | erot = 0.758296324627745 | epot = -15.5400656670872 | etot = -14.6424332457954 +19000 ekin = 0.138678360045177 | erot = 0.797544234275864 | epot = -15.5786558401088 | etot = -14.6424332457878 +20000 ekin = 0.136500074655373 | erot = 0.83308420441103 | epot = -15.6120175248394 | etot = -14.642433245773 +21000 ekin = 0.132987065285671 | erot = 0.864912408452581 | epot = -15.6403327194916 | etot = -14.6424332457533 +22000 ekin = 0.128350288213556 | erot = 0.893077649557994 | epot = -15.6638611835027 | etot = -14.6424332457311 +23000 ekin = 0.122812385135508 | erot = 0.917661024683964 | epot = -15.6829066555277 | etot = -14.6424332457083 +24000 ekin = 0.116595521408284 | erot = 0.938759014332096 | epot = -15.6977877814267 | etot = -14.6424332456863 +25000 ekin = 0.109911323474816 | erot = 0.956471207347236 | epot = -15.7088157764882 | etot = -14.6424332456662 +26000 ekin = 0.102953426207644 | erot = 0.970893163953198 | epot = -15.7162798358091 | etot = -14.6424332456483 +27000 ekin = 0.0958928250746637 | erot = 0.982114250194049 | epot = -15.7204403209013 | etot = -14.6424332456326 +28000 ekin = 0.0888759410950343 | erot = 0.990219731539835 | epot = -15.7215289182535 | etot = -14.6424332456186 +29000 ekin = 0.0820250748773376 | erot = 0.995296041202909 | epot = -15.719754361686 | etot = -14.6424332456058 +30000 ekin = 0.0754407616839748 | erot = 0.997437949320991 | epot = -15.7153119565981 | etot = -14.6424332455932 +31000 ekin = 0.0692054432610605 | erot = 0.996756332762285 | epot = -15.7083950216035 | etot = -14.6424332455802 +32000 ekin = 0.0633878377978472 | erot = 0.993385345349211 | epot = -15.699206428713 | etot = -14.6424332455659 +33000 ekin = 0.0580474070871663 | erot = 0.987487973309961 | epot = -15.6879686259471 | etot = -14.64243324555 +34000 ekin = 0.0532383791888181 | erot = 0.979259192921736 | epot = -15.6749308176426 | etot = -14.642433245532 +35000 ekin = 0.0490128758307997 | erot = 0.968926197407215 | epot = -15.66037231875 | etot = -14.642433245512 +36000 ekin = 0.0454228081410747 | erot = 0.95674540962595 | epot = -15.6446014632576 | etot = -14.6424332454906 +37000 ekin = 0.0425203357176436 | erot = 0.942996238000708 | epot = -15.6279498191869 | etot = -14.6424332454685 +38000 ekin = 0.0403568280949567 | erot = 0.92797176661665 | epot = -15.6107618401582 | etot = -14.6424332454466 +39000 ekin = 0.0389804214212708 | erot = 0.911966804110001 | epot = -15.5933804709572 | etot = -14.642433245426 +40000 ekin = 0.0384324238856422 | erot = 0.8952639595629 | epot = -15.5761296288567 | etot = -14.6424332454081 +41000 ekin = 0.0387429860408521 | erot = 0.878118672838247 | epot = -15.5592949042733 | etot = -14.6424332453942 +42000 ekin = 0.0399266053637504 | erot = 0.860744395135471 | epot = -15.5431042458848 | etot = -14.6424332453856 +43000 ekin = 0.0419781561011205 | erot = 0.843299365355946 | epot = -15.52771076684 | etot = -14.6424332453829 +44000 ekin = 0.0448701894086706 | erot = 0.825876603312506 | epot = -15.5131800381079 | etot = -14.6424332453867 +45000 ekin = 0.0485521857411509 | erot = 0.808498758184836 | epot = -15.4994841893228 | etot = -14.6424332453969 +46000 ekin = 0.0529522094031963 | erot = 0.791119212186772 | epot = -15.4865046670025 | etot = -14.6424332454125 +47000 ekin = 0.0579809824236739 | erot = 0.773630265882115 | epot = -15.4740444937379 | etot = -14.6424332454321 +48000 ekin = 0.063537784649307 | erot = 0.755878310836066 | epot = -15.4618493409392 | etot = -14.6424332454538 +49000 ekin = 0.0695169124457283 | erot = 0.737684732482629 | epot = -15.4496348904038 | etot = -14.6424332454754 +50000 ekin = 0.0758129058454745 | erot = 0.718870126218063 | epot = -15.4371162775588 | etot = -14.6424332454952 +51000 ekin = 0.082322663864191 | erot = 0.69927859951883 | epot = -15.4240345088949 | etot = -14.6424332455119 +52000 ekin = 0.0889431481334984 | erot = 0.67879880709845 | epot = -15.4101752007568 | etot = -14.6424332455248 +53000 ekin = 0.0955646689255781 | erot = 0.657379086769954 | epot = -15.3953770012299 | etot = -14.6424332455344 +54000 ekin = 0.102061477509349 | erot = 0.635035489168609 | epot = -15.3795302122192 | etot = -14.6424332455412 +55000 ekin = 0.108282960174 | erot = 0.611853171347129 | epot = -15.3625693770671 | etot = -14.6424332455459 +56000 ekin = 0.114049426281782 | erot = 0.58798294592476 | epot = -15.3444656177551 | etot = -14.6424332455485 +57000 ekin = 0.119155806186856 | erot = 0.563635255923989 | epot = -15.3252243076595 | etot = -14.6424332455486 +58000 ekin = 0.123384552305436 | erot = 0.539073355224011 | epot = -15.3048911530747 | etot = -14.6424332455453 +59000 ekin = 0.126526300954942 | erot = 0.514606324860975 | epot = -15.2835658713528 | etot = -14.6424332455369 +60000 ekin = 0.128404399836505 | erot = 0.490581338842491 | epot = -15.2614189842015 | etot = -14.6424332455225 +61000 ekin = 0.128898142362338 | erot = 0.46737389240369 | epot = -15.2387052802676 | etot = -14.6424332455016 +62000 ekin = 0.127959880290304 | erot = 0.445374820089083 | epot = -15.2157679458544 | etot = -14.642433245475 +63000 ekin = 0.125622870624957 | erot = 0.424973765390021 | epot = -15.1930298814589 | etot = -14.6424332454439 +64000 ekin = 0.121999044843205 | erot = 0.406539918574829 | epot = -15.1709722088285 | etot = -14.6424332454105 +65000 ekin = 0.117268056619305 | erot = 0.390401831022814 | epot = -15.1501031330194 | etot = -14.6424332453773 +66000 ekin = 0.111660385257246 | erot = 0.376828594080988 | epot = -15.1309222246848 | etot = -14.6424332453465 +67000 ekin = 0.105437746905138 | erot = 0.366014539812675 | epot = -15.1138855320384 | etot = -14.6424332453205 +68000 ekin = 0.0988737375607886 | erot = 0.3580690141562 | epot = -15.0993759970177 | etot = -14.6424332453007 +69000 ekin = 0.0922368286502271 | erot = 0.353011948772473 | epot = -15.0876820227105 | etot = -14.6424332452878 +70000 ekin = 0.085776901527448 | erot = 0.350775174164851 | epot = -15.0789853209745 | etot = -14.6424332452822 +71000 ekin = 0.0797156921642142 | erot = 0.351208844244805 | epot = -15.0733577816926 | etot = -14.6424332452835 +72000 ekin = 0.0742409440406418 | erot = 0.354092037745935 | epot = -15.0707662270776 | etot = -14.6424332452911 +73000 ekin = 0.0695037498701448 | erot = 0.359146526959505 | epot = -15.0710835221334 | etot = -14.6424332453038 +74000 ekin = 0.0656184497423043 | erot = 0.366052769876549 | epot = -15.0741044649392 | etot = -14.6424332453204 +75000 ekin = 0.0626644690389266 | erot = 0.374467290031506 | epot = -15.07956500441 | etot = -14.6424332453396 +76000 ekin = 0.0606895535086054 | erot = 0.384040683400738 | epot = -15.0871634822693 | etot = -14.64243324536 +77000 ekin = 0.0597139401235012 | erot = 0.394435495890075 | epot = -15.0965826813934 | etot = -14.6424332453798 +78000 ekin = 0.059735062986913 | erot = 0.405343151479082 | epot = -15.1075114598642 | etot = -14.6424332453982 +79000 ekin = 0.0607324264355555 | erot = 0.416499017639937 | epot = -15.1196646894892 | etot = -14.6424332454137 +80000 ekin = 0.06267229049498 | erot = 0.427694630236126 | epot = -15.1328001661568 | etot = -14.6424332454257 +81000 ekin = 0.0655118235328765 | erot = 0.438786127846728 | epot = -15.1467311968131 | etot = -14.6424332454335 +82000 ekin = 0.0692024020835893 | erot = 0.449698113828473 | epot = -15.1613337613493 | etot = -14.6424332454372 +83000 ekin = 0.0736917936906618 | erot = 0.460422490738957 | epot = -15.1765475298665 | etot = -14.6424332454369 +84000 ekin = 0.0789250526546722 | erot = 0.471012272293582 | epot = -15.1923705703818 | etot = -14.6424332454336 +85000 ekin = 0.0848440878750035 | erot = 0.481570908649162 | epot = -15.2088482419522 | etot = -14.642433245428 +86000 ekin = 0.0913860133254624 | erot = 0.492238169205216 | epot = -15.2260574279521 | etot = -14.6424332454214 +87000 ekin = 0.0984805441200046 | erot = 0.503174014616525 | epot = -15.2440878041518 | etot = -14.6424332454153 +88000 ekin = 0.106046830304297 | erot = 0.514542076496056 | epot = -15.263022152211 | etot = -14.6424332454106 +89000 ekin = 0.113990204127984 | erot = 0.526494309539207 | epot = -15.2829177590758 | etot = -14.6424332454087 +90000 ekin = 0.122199339151894 | erot = 0.539158097285698 | epot = -15.3037906818477 | etot = -14.6424332454101 +91000 ekin = 0.130544275971403 | erot = 0.552626637865723 | epot = -15.3256041592524 | etot = -14.6424332454152 +92000 ekin = 0.138875666148815 | erot = 0.566952900962156 | epot = -15.3482618125355 | etot = -14.6424332454245 +93000 ekin = 0.147025440614642 | erot = 0.582146933737432 | epot = -15.3716056197897 | etot = -14.6424332454376 +94000 ekin = 0.154808946847822 | erot = 0.598175891801207 | epot = -15.3954180841032 | etot = -14.6424332454542 +95000 ekin = 0.162028449602152 | erot = 0.614965942453837 | epot = -15.4194276375299 | etot = -14.6424332454739 +96000 ekin = 0.168477779667818 | erot = 0.632405154082029 | epot = -15.4433161792459 | etot = -14.642433245496 +97000 ekin = 0.17394786302672 | erot = 0.650346631628325 | epot = -15.4667277401752 | etot = -14.6424332455201 +98000 ekin = 0.178232875004242 | erot = 0.668611435745948 | epot = -15.4892775562957 | etot = -14.6424332455455 +99000 ekin = 0.181136831926353 | erot = 0.686991165056211 | epot = -15.5105612425543 | etot = -14.6424332455718 +100000 ekin = 0.182480533643598 | erot = 0.705250413407778 | epot = -15.5301641926495 | etot = -14.6424332455981 +101000 ekin = 0.182108871451935 | erot = 0.723129571003179 | epot = -15.547671688079 | etot = -14.6424332456239 +102000 ekin = 0.179898581170268 | erot = 0.740348571090314 | epot = -15.5626803979088 | etot = -14.6424332456482 +103000 ekin = 0.175766517608084 | erot = 0.756612167825837 | epot = -15.5748119311039 | etot = -14.64243324567 +104000 ekin = 0.169678431535445 | erot = 0.771617166851602 | epot = -15.5837288440751 | etot = -14.6424332456881 +105000 ekin = 0.161658036036865 | erot = 0.785061742962005 | epot = -15.5891530247 | etot = -14.6424332457012 +106000 ekin = 0.151795867650478 | erot = 0.796656613424597 | epot = -15.5908857267829 | etot = -14.6424332457078 +107000 ekin = 0.140257112952727 | erot = 0.806137449197231 | epot = -15.5888278078568 | etot = -14.6424332457068 +108000 ekin = 0.127287240201241 | erot = 0.813277564481104 | epot = -15.5829980503796 | etot = -14.6424332456973 +109000 ekin = 0.113214025490917 | erot = 0.817899691734432 | epot = -15.573546962904 | etot = -14.6424332456787 +110000 ekin = 0.0984444823805213 | erot = 0.819885578053921 | epot = -15.5607633060856 | etot = -14.6424332456512 +111000 ekin = 0.0834553769364569 | erot = 0.819182262545785 | epot = -15.545070885098 | etot = -14.6424332456157 +112000 ekin = 0.0687764915871027 | erot = 0.815804215094415 | epot = -15.5270139522555 | etot = -14.642433245574 +113000 ekin = 0.0549665904028903 | erot = 0.809830999844441 | epot = -15.5072308357759 | etot = -14.6424332455285 +114000 ekin = 0.0425830583120619 | erot = 0.801400700350953 | epot = -15.4864170041452 | etot = -14.6424332454821 +115000 ekin = 0.032147280213263 | erot = 0.790699910049051 | epot = -15.4652804357003 | etot = -14.642433245438 +116000 ekin = 0.024108778034577 | erot = 0.777951546674724 | epot = -15.4444935701085 | etot = -14.6424332453992 +117000 ekin = 0.0188117102728931 | erot = 0.763402004774069 | epot = -15.4246469604154 | etot = -14.6424332453684 +118000 ekin = 0.0164673894159043 | erot = 0.747309167856945 | epot = -15.4062098026203 | etot = -14.6424332453474 +119000 ekin = 0.0171359296532898 | erot = 0.729932564575393 | epot = -15.3895017395657 | etot = -14.642433245337 +120000 ekin = 0.0207190822430497 | erot = 0.711526526250247 | epot = -15.3746788538305 | etot = -14.6424332453372 +121000 ekin = 0.0269649552319816 | erot = 0.692336677373422 | epot = -15.3617348779522 | etot = -14.6424332453468 +122000 ekin = 0.0354839220297736 | erot = 0.672599570214091 | epot = -15.3505167376079 | etot = -14.642433245364 +123000 ekin = 0.0457738626451366 | erot = 0.652544850165416 | epot = -15.3407519581971 | etot = -14.6424332453865 +124000 ekin = 0.0572521324296466 | erot = 0.632399068066114 | epot = -15.3320844459074 | etot = -14.6424332454117 +125000 ekin = 0.0692913736002564 | erot = 0.612390156186006 | epot = -15.324114775223 | etot = -14.6424332454368 +126000 ekin = 0.0812564128172846 | erot = 0.592751635109578 | epot = -15.3164412933862 | etot = -14.6424332454593 +127000 ekin = 0.0925398817823717 | erot = 0.573725774407888 | epot = -15.3086989016675 | etot = -14.6424332454772 +128000 ekin = 0.102594692018529 | erot = 0.55556513894369 | epot = -15.3005930764509 | etot = -14.6424332454887 +129000 ekin = 0.110961953873462 | erot = 0.538532171478003 | epot = -15.291927370844 | etot = -14.6424332454925 +130000 ekin = 0.117293279472125 | erot = 0.52289666445339 | epot = -15.2826231894136 | etot = -14.642433245488 +131000 ekin = 0.121366644774014 | erot = 0.508931150171021 | epot = -15.2727310404203 | etot = -14.6424332454752 +132000 ekin = 0.123095155538848 | erot = 0.49690439090507 | epot = -15.2624327918984 | etot = -14.6424332454545 +133000 ekin = 0.122528239670491 | erot = 0.487073282996463 | epot = -15.2520347680938 | etot = -14.6424332454268 +134000 ekin = 0.119845042600695 | erot = 0.47967360116923 | epot = -15.2419518891638 | etot = -14.6424332453939 +135000 ekin = 0.115340171966309 | erot = 0.474910093714588 | epot = -15.2326835110385 | etot = -14.6424332453576 +136000 ekin = 0.10940241928465 | erot = 0.472946484072521 | epot = -15.2247821486777 | etot = -14.6424332453205 +137000 ekin = 0.102487634021818 | erot = 0.473895929917005 | epot = -15.2188168092237 | etot = -14.6424332452849 +138000 ekin = 0.0950874634047233 | erot = 0.477812435582745 | epot = -15.2153331442409 | etot = -14.6424332452534 +139000 ekin = 0.0876961121512815 | erot = 0.484683617748011 | epot = -15.2148129751279 | etot = -14.6424332452286 +140000 ekin = 0.0807775418431626 | erot = 0.494425108537478 | epot = -15.2176358955931 | etot = -14.6424332452125 +141000 ekin = 0.0747355681577817 | erot = 0.50687677080795 | epot = -15.2240455841725 | etot = -14.6424332452068 +142000 ekin = 0.0698891098450116 | erot = 0.521800821238808 | epot = -15.2341231762965 | etot = -14.6424332452127 +143000 ekin = 0.0664544171866063 | erot = 0.538881922424094 | epot = -15.2477695848413 | etot = -14.6424332452306 +144000 ekin = 0.0645355104692083 | erot = 0.557729316020225 | epot = -15.2646980717496 | etot = -14.6424332452602 +145000 ekin = 0.0641233595162911 | erot = 0.577881111412627 | epot = -15.2844377162297 | etot = -14.6424332453008 +146000 ekin = 0.0651036077515188 | erot = 0.598810893851628 | epot = -15.3063477469538 | etot = -14.6424332453507 +147000 ekin = 0.0672719578973601 | erot = 0.619936843681753 | epot = -15.3296420469868 | etot = -14.6424332454077 +148000 ekin = 0.0703557492692045 | erot = 0.640633538190902 | epot = -15.3534225329294 | etot = -14.6424332454693 +149000 ekin = 0.0740398128642427 | erot = 0.660246523237691 | epot = -15.3767195816347 | etot = -14.6424332455328 +150000 ekin = 0.0779944201058678 | erot = 0.678109590376156 | epot = -15.398537256077 | etot = -14.642433245595 +151000 ekin = 0.0819030604172323 | erot = 0.693564488648094 | epot = -15.4179007947185 | etot = -14.6424332456531 +152000 ekin = 0.0854878938552624 | erot = 0.705982563003889 | epot = -15.4339037025634 | etot = -14.6424332457043 +153000 ekin = 0.0885310147328532 | erot = 0.714787575382088 | epot = -15.4457518358609 | etot = -14.6424332457459 +154000 ekin = 0.0908901012887555 | erot = 0.719478762727528 | epot = -15.4528021097924 | etot = -14.6424332457761 +155000 ekin = 0.092507570371455 | erot = 0.719653046097721 | epot = -15.4545938622626 | etot = -14.6424332457934 +156000 ekin = 0.0934129479728847 | erot = 0.715025243753982 | epot = -15.4508714375239 | etot = -14.642433245797 +157000 ekin = 0.0937187435779626 | erot = 0.705445163946324 | epot = -15.4415971533109 | etot = -14.6424332457866 +158000 ekin = 0.0936106185393401 | erot = 0.690910554325706 | epot = -15.4269544186278 | etot = -14.6424332457627 +159000 ekin = 0.0933330174010987 | erot = 0.671575051659785 | epot = -15.4073413147871 | etot = -14.6424332457262 +160000 ekin = 0.0931716565242322 | erot = 0.647750492120645 | epot = -15.3833553943234 | etot = -14.6424332456785 +161000 ekin = 0.0934343296231438 | erot = 0.619903194016586 | epot = -15.3557707692612 | etot = -14.6424332456215 +162000 ekin = 0.0944314104804186 | erot = 0.588644098979611 | epot = -15.3255087550173 | etot = -14.6424332455572 +163000 ekin = 0.0964572425739502 | erot = 0.55471294345392 | epot = -15.2936034315161 | etot = -14.6424332454882 +164000 ekin = 0.0997733472806136 | erot = 0.518956918561936 | epot = -15.2611635112594 | etot = -14.6424332454169 +165000 ekin = 0.104594102019911 | erot = 0.482304549422426 | epot = -15.2293318967882 | etot = -14.6424332453459 +166000 ekin = 0.11107527651625 | erot = 0.445735768512381 | epot = -15.1992442903065 | etot = -14.6424332452778 +167000 ekin = 0.11930559751358 | erot = 0.410249354728318 | epot = -15.1719881974571 | etot = -14.6424332452152 +168000 ekin = 0.129301354725086 | erot = 0.37682904617874 | epot = -15.1485636460642 | etot = -14.6424332451604 +169000 ekin = 0.14100396578975 | erot = 0.346409702527097 | epot = -15.1298469134321 | etot = -14.6424332451152 +170000 ekin = 0.154280377439942 | erot = 0.319844892417961 | epot = -15.1165585149394 | etot = -14.6424332450815 +171000 ekin = 0.168926178621544 | erot = 0.297877221606916 | epot = -15.109236645289 | etot = -14.6424332450606 +172000 ekin = 0.184671319364511 | erot = 0.281112611137243 | epot = -15.108217175555 | etot = -14.6424332450532 +173000 ekin = 0.201188345437118 | erot = 0.269999595570268 | epot = -15.1136211860672 | etot = -14.6424332450598 +174000 ekin = 0.218103052207035 | erot = 0.264814547402982 | epot = -15.12535084469 | etot = -14.6424332450799 +175000 ekin = 0.235007413035623 | erot = 0.265653545950115 | epot = -15.1430942040986 | etot = -14.6424332451129 +176000 ekin = 0.251474534267915 | erot = 0.272431389432266 | epot = -15.1663391688573 | etot = -14.6424332451571 +177000 ekin = 0.267075225143436 | erot = 0.284887984978803 | epot = -15.1943964553329 | etot = -14.6424332452107 +178000 ekin = 0.281395553895287 | erot = 0.302602030915412 | epot = -15.2264308300819 | etot = -14.6424332452712 +179000 ekin = 0.294054514411866 | erot = 0.325011526057904 | epot = -15.2614992858055 | etot = -14.6424332453358 +180000 ekin = 0.304720692896942 | erot = 0.351440214935852 | epot = -15.2985941532343 | etot = -14.6424332454015 +181000 ekin = 0.313126658918426 | erot = 0.381128639602688 | epot = -15.3366885439866 | etot = -14.6424332454655 +182000 ekin = 0.319079775823621 | erot = 0.413268071114152 | epot = -15.374781092463 | etot = -14.6424332455252 +183000 ekin = 0.322468290005762 | erot = 0.447035301736728 | epot = -15.4119368373208 | etot = -14.6424332455783 +184000 ekin = 0.323261947554671 | erot = 0.48162615508044 | epot = -15.4473213482583 | etot = -14.6424332456231 +185000 ekin = 0.321506983530827 | erot = 0.516285658867815 | epot = -15.4802258880574 | etot = -14.6424332456588 +186000 ekin = 0.317316057633682 | erot = 0.550333132629112 | epot = -15.5100824359478 | etot = -14.642433245685 +187000 ekin = 0.310854440590084 | erot = 0.583180936761968 | epot = -15.5364686230541 | etot = -14.642433245702 +188000 ekin = 0.302324329763947 | erot = 0.614346238385429 | epot = -15.55910381386 | etot = -14.6424332457106 +189000 ekin = 0.291949445197116 | erot = 0.64345577901281 | epot = -15.5778384699217 | etot = -14.6424332457118 +190000 ekin = 0.279961942768254 | erot = 0.67024418570442 | epot = -15.5926393741794 | etot = -14.6424332457067 +191000 ekin = 0.266593185653664 | erot = 0.694546781233348 | epot = -15.6035732125832 | etot = -14.6424332456962 +192000 ekin = 0.252069141623363 | erot = 0.716288088786984 | epot = -15.6107904760917 | etot = -14.6424332456814 +193000 ekin = 0.236610293254145 | erot = 0.735467302242536 | epot = -15.6145108411597 | etot = -14.642433245663 +194000 ekin = 0.22043514940511 | erot = 0.75214194302714 | epot = -15.615010338074 | etot = -14.6424332456418 +195000 ekin = 0.20376588009334 | erot = 0.76641079902996 | epot = -15.6126099247417 | etot = -14.6424332456184 +196000 ekin = 0.186834339037366 | erot = 0.778397083250806 | epot = -15.6076646678817 | etot = -14.6424332455935 +197000 ekin = 0.169886782294183 | erot = 0.788232586070618 | epot = -15.6005526139326 | etot = -14.6424332455678 +198000 ekin = 0.153185871077985 | erot = 0.796043434538987 | epot = -15.5916625511591 | etot = -14.6424332455421 +199000 ekin = 0.137008972987403 | erot = 0.801937915798979 | epot = -15.581380134304 | etot = -14.6424332455176 +200000 ekin = 0.121642272364804 | erot = 0.805996673261661 | epot = -15.5700721911217 | etot = -14.6424332454953 +201000 ekin = 0.107370722656483 | erot = 0.808265456806726 | epot = -15.5580694249396 | etot = -14.6424332454764 +202000 ekin = 0.0944644042392164 | erot = 0.808750524310001 | epot = -15.5456481740113 | etot = -14.6424332454621 +203000 ekin = 0.0831623790893979 | erot = 0.807416772443554 | epot = -15.5330123969865 | etot = -14.6424332454535 +204000 ekin = 0.0736556272335549 | erot = 0.80418872541979 | epot = -15.5202775981049 | etot = -14.6424332454516 +205000 ekin = 0.0660710401675949 | erot = 0.79895460735586 | epot = -15.50745889298 | etot = -14.6424332454565 +206000 ekin = 0.0604586317681684 | erot = 0.791573809424189 | epot = -15.4944656866607 | etot = -14.6424332454683 +207000 ekin = 0.0567840026883034 | erot = 0.781888054798422 | epot = -15.4811053029728 | etot = -14.642433245486 +208000 ekin = 0.0549275971601569 | erot = 0.769736381379661 | epot = -15.4670972240478 | etot = -14.642433245508 +209000 ekin = 0.054691444753805 | erot = 0.754973659533912 | epot = -15.4520983498196 | etot = -14.6424332455319 +210000 ekin = 0.055813012677523 | erot = 0.737491764374765 | epot = -15.4357380226072 | etot = -14.6424332455549 +211000 ekin = 0.0579847210238433 | erot = 0.717241838880031 | epot = -15.417659805478 | etot = -14.6424332455742 +212000 ekin = 0.0608768356205362 | erot = 0.694255492639193 | epot = -15.3975655738466 | etot = -14.6424332455869 +213000 ekin = 0.06416104270831 | erot = 0.668662476163316 | epot = -15.3752567644624 | etot = -14.6424332455907 +214000 ekin = 0.0675321043587428 | erot = 0.64070249551798 | epot = -15.3506678454611 | etot = -14.6424332455844 +215000 ekin = 0.070725533636788 | erot = 0.610729417267909 | epot = -15.3238881964721 | etot = -14.6424332455674 +216000 ekin = 0.0735300437834057 | erot = 0.579207054837054 | epot = -15.2951703441606 | etot = -14.6424332455401 +217000 ekin = 0.0757943994895767 | erot = 0.546696813208958 | epot = -15.2649244582023 | etot = -14.6424332455037 +218000 ekin = 0.0774290394184473 | erot = 0.513838451215592 | epot = -15.2337007360942 | etot = -14.6424332454601 +219000 ekin = 0.0784033323161932 | erot = 0.481325894960063 | epot = -15.2021624726878 | etot = -14.6424332454116 +220000 ekin = 0.0787395495628362 | erot = 0.449880299616975 | epot = -15.1710530945401 | etot = -14.6424332453603 +221000 ekin = 0.0785046319692606 | erot = 0.420222425154575 | epot = -15.1411603024325 | etot = -14.6424332453087 +222000 ekin = 0.0778006814288784 | erot = 0.393045972165179 | epot = -15.1132798988531 | etot = -14.642433245259 +223000 ekin = 0.0767549035403029 | erot = 0.368992968905302 | epot = -15.0881811176588 | etot = -14.6424332452132 +224000 ekin = 0.0755095293719489 | erot = 0.348631757026569 | epot = -15.0665745315716 | etot = -14.6424332451731 +225000 ekin = 0.0742120885680923 | erot = 0.332437700423116 | epot = -15.0490830341315 | etot = -14.6424332451403 +226000 ekin = 0.0730063028703669 | erot = 0.320776497496383 | epot = -15.0362160454828 | etot = -14.6424332451161 +227000 ekin = 0.072023814088989 | erot = 0.313889923623787 | epot = -15.0283469828147 | etot = -14.642433245102 +228000 ekin = 0.0713769419944175 | erot = 0.31188394524302 | epot = -15.025694132336 | etot = -14.6424332450985 +229000 ekin = 0.0711526728859894 | erot = 0.314719386436074 | epot = -15.0283053044287 | etot = -14.6424332451066 +230000 ekin = 0.0714080974064438 | erot = 0.322205638587393 | epot = -15.0360469811206 | etot = -14.6424332451268 +231000 ekin = 0.0721675361185073 | erot = 0.333998222200335 | epot = -15.0485990034776 | etot = -14.6424332451588 +232000 ekin = 0.073421602289788 | erot = 0.349601270465542 | epot = -15.0654561179573 | etot = -14.6424332452019 +233000 ekin = 0.0751284397495051 | erot = 0.368376135876568 | epot = -15.0859378208814 | etot = -14.6424332452553 +234000 ekin = 0.0772173235430231 | erot = 0.389557254435346 | epot = -15.1092078232955 | etot = -14.6424332453172 +235000 ekin = 0.0795947059788063 | erot = 0.412276079792834 | epot = -15.1343040311561 | etot = -14.6424332453845 +236000 ekin = 0.0821526186131156 | erot = 0.435593295650787 | epot = -15.1601791597182 | etot = -14.6424332454543 +237000 ekin = 0.084779101422344 | erot = 0.458538653868273 | epot = -15.1857510008135 | etot = -14.6424332455229 +238000 ekin = 0.0873700423841441 | erot = 0.480156759890549 | epot = -15.2099600478608 | etot = -14.6424332455861 +239000 ekin = 0.0898415153120331 | erot = 0.499556095556538 | epot = -15.2318308565087 | etot = -14.6424332456401 +240000 ekin = 0.0921414623518645 | erot = 0.515957735404849 | epot = -15.2505324434381 | etot = -14.6424332456814 +241000 ekin = 0.0942594490127862 | erot = 0.528739776890127 | epot = -15.2654324716098 | etot = -14.6424332457069 +242000 ekin = 0.0962332805866192 | erot = 0.537473606139427 | epot = -15.276140132441 | etot = -14.6424332457149 +243000 ekin = 0.0981515319325858 | erot = 0.541948785982857 | epot = -15.2825335636204 | etot = -14.642433245705 +244000 ekin = 0.100151482350114 | erot = 0.542184479376275 | epot = -15.2847692074041 | etot = -14.6424332456777 +245000 ekin = 0.102412491094951 | erot = 0.538426702319034 | epot = -15.2832724390489 | etot = -14.642433245635 +246000 ekin = 0.105145395544293 | erot = 0.531132085866979 | epot = -15.2787107269906 | etot = -14.6424332455793 +247000 ekin = 0.108578961411821 | erot = 0.52093999420686 | epot = -15.271952201133 | etot = -14.6424332455143 +248000 ekin = 0.112944688754725 | erot = 0.50863565229471 | epot = -15.2640135864931 | etot = -14.6424332454436 +249000 ekin = 0.118461348905719 | erot = 0.495107336752391 | epot = -15.2560019310293 | etot = -14.6424332453712 +250000 ekin = 0.125320510714173 | erot = 0.481300713195434 | epot = -15.2490544692103 | etot = -14.6424332453007 +251000 ekin = 0.133674056956427 | erot = 0.468173145421896 | epot = -15.2442804476139 | etot = -14.6424332452356 +252000 ekin = 0.143624355874461 | erot = 0.456650355971834 | epot = -15.2427079570251 | etot = -14.6424332451788 +253000 ekin = 0.155217400156353 | erot = 0.447587277163379 | epot = -15.2452379224523 | etot = -14.6424332451326 +254000 ekin = 0.168438906846637 | erot = 0.441734376015244 | epot = -15.2526065279605 | etot = -14.6424332450987 +255000 ekin = 0.183213121646734 | erot = 0.439710227351439 | epot = -15.2653565940763 | etot = -14.6424332450781 +256000 ekin = 0.199403908834921 | erot = 0.441980689731424 | epot = -15.283817843638 | etot = -14.6424332450717 +257000 ekin = 0.216817638464824 | erot = 0.448844730303074 | epot = -15.3080956138475 | etot = -14.6424332450796 +258000 ekin = 0.235207399038843 | erot = 0.460426746273175 | epot = -15.3380673904137 | etot = -14.6424332451017 +259000 ekin = 0.254278151369354 | erot = 0.476675120646266 | epot = -15.3733865171527 | etot = -14.6424332451371 +260000 ekin = 0.273692576680278 | erot = 0.497366691704049 | epot = -15.4134925135692 | etot = -14.6424332451849 +261000 ekin = 0.293077534076593 | erot = 0.522116767902341 | epot = -15.4576275472227 | etot = -14.6424332452438 +262000 ekin = 0.312031202024041 | erot = 0.550394247117889 | epot = -15.5048586944538 | etot = -14.6424332453119 +263000 ekin = 0.330131107619666 | erot = 0.58154128199589 | epot = -15.5541056350029 | etot = -14.6424332453873 +264000 ekin = 0.346943319973835 | erot = 0.614796773442864 | epot = -15.6041733388843 | etot = -14.6424332454676 +265000 ekin = 0.36203307825833 | erot = 0.649322794992431 | epot = -15.6537891188012 | etot = -14.6424332455505 +266000 ekin = 0.374977027500473 | erot = 0.684232889055386 | epot = -15.7016431621889 | etot = -14.6424332456331 +267000 ekin = 0.385377045185273 | erot = 0.718621072058621 | epot = -15.7464313629566 | etot = -14.6424332457127 +268000 ekin = 0.392875374680177 | erot = 0.751590369461549 | epot = -15.7868989899282 | etot = -14.6424332457865 +269000 ekin = 0.397170471139152 | erot = 0.782279784272065 | epot = -15.8218835012632 | etot = -14.6424332458519 +270000 ekin = 0.398032662028036 | erot = 0.809888771673587 | epot = -15.8503546796086 | etot = -14.642433245907 +271000 ekin = 0.395318487598681 | erot = 0.833698516709737 | epot = -15.8714502502579 | etot = -14.6424332459495 +272000 ekin = 0.388982474352113 | erot = 0.853089551908481 | epot = -15.8845052722386 | etot = -14.642433245978 +273000 ekin = 0.379085147931406 | erot = 0.867555470405084 | epot = -15.8890738643282 | etot = -14.6424332459917 +274000 ekin = 0.36579632219322 | erot = 0.876712662629334 | epot = -15.8849422308128 | etot = -14.6424332459903 +275000 ekin = 0.349393082921511 | erot = 0.880306121913819 | epot = -15.8721324508092 | etot = -14.6424332459739 +276000 ekin = 0.330252358905648 | erot = 0.878211432148985 | epot = -15.8508970369982 | etot = -14.6424332459435 +277000 ekin = 0.308838461220188 | erot = 0.870433084876957 | epot = -15.8217047919976 | etot = -14.6424332459005 +278000 ekin = 0.285686394604086 | erot = 0.857099294885159 | epot = -15.7852189353358 | etot = -14.6424332458466 +279000 ekin = 0.261382042766412 | erot = 0.838453513181032 | epot = -15.7422688017312 | etot = -14.6424332457837 +280000 ekin = 0.23654047332595 | erot = 0.814842890587961 | epot = -15.6938166096284 | etot = -14.6424332457145 +281000 ekin = 0.211783602608016 | erot = 0.78670403285839 | epot = -15.6409208811076 | etot = -14.6424332456411 +282000 ekin = 0.187718337271894 | erot = 0.754546508157669 | epot = -15.5846980909958 | etot = -14.6424332455662 +283000 ekin = 0.164916115090795 | erot = 0.718934708845181 | epot = -15.5262840694281 | etot = -14.6424332454921 +284000 ekin = 0.143894549221715 | erot = 0.680468811939352 | epot = -15.4667966065823 | etot = -14.6424332454213 +285000 ekin = 0.125101678372295 | erot = 0.639765701847641 | epot = -15.4073006255757 | etot = -14.6424332453557 +286000 ekin = 0.108903164107394 | erot = 0.597440790010453 | epot = -15.3487771994148 | etot = -14.6424332452969 +287000 ekin = 0.0955726645551815 | erot = 0.554091668604978 | epot = -15.2920975784066 | etot = -14.6424332452464 +288000 ekin = 0.0852855448006968 | erot = 0.510284456822097 | epot = -15.2380032468277 | etot = -14.6424332452049 +289000 ekin = 0.07811604131029 | erot = 0.466543535623142 | epot = -15.1870928221065 | etot = -14.6424332451731 +290000 ekin = 0.0740379578618433 | erot = 0.423345127589082 | epot = -15.1398163306018 | etot = -14.6424332451509 +291000 ekin = 0.072928910063375 | erot = 0.381114879437431 | epot = -15.0964770346385 | etot = -14.6424332451377 +292000 ekin = 0.0745780357927571 | erot = 0.340229271737873 | epot = -15.0572405526631 | etot = -14.6424332451325 +293000 ekin = 0.0786969407539254 | erot = 0.301020346548472 | epot = -15.0221505324365 | etot = -14.6424332451341 +294000 ekin = 0.0849334564702411 | erot = 0.263782947588667 | epot = -14.9911496491996 | etot = -14.6424332451407 +295000 ekin = 0.0928875723607584 | erot = 0.228783448806939 | epot = -14.9641042663184 | etot = -14.6424332451507 +296000 ekin = 0.102128697507195 | erot = 0.19626884038738 | epot = -14.9408307830571 | etot = -14.6424332451625 +297000 ekin = 0.112213252496717 | erot = 0.166475068218863 | epot = -14.9211215658901 | etot = -14.6424332451745 +298000 ekin = 0.122701527066801 | erot = 0.139633685446912 | epot = -14.9047684576991 | etot = -14.6424332451854 +299000 ekin = 0.13317279291057 | erot = 0.115976150690173 | epot = -14.8915821887951 | etot = -14.6424332451943 +300000 ekin = 0.143237839707087 | erot = 0.0957354521215326 | epot = -14.8814065370293 | etot = -14.6424332452007 +301000 ekin = 0.152548387988438 | erot = 0.0791450908732747 | epot = -14.8741267240661 | etot = -14.6424332452044 +302000 ekin = 0.160803184299453 | erot = 0.0664357608561943 | epot = -14.8696721903613 | etot = -14.6424332452057 +303000 ekin = 0.167750948486611 | erot = 0.0578302677257495 | epot = -14.868014461417 | etot = -14.6424332452046 +304000 ekin = 0.173190665587053 | erot = 0.0535373136372916 | epot = -14.8691612244265 | etot = -14.6424332452022 +305000 ekin = 0.176969952948865 | erot = 0.0537447402909072 | epot = -14.8731479384385 | etot = -14.6424332451988 +306000 ekin = 0.178982363290529 | erot = 0.0586126977876584 | epot = -14.8800283062732 | etot = -14.642433245195 +307000 ekin = 0.179164502944002 | erot = 0.0682670321056827 | epot = -14.8898647802413 | etot = -14.6424332451916 +308000 ekin = 0.177493763288021 | erot = 0.0827930029186529 | epot = -14.9027200113955 | etot = -14.6424332451889 +309000 ekin = 0.173987301150961 | erot = 0.102229291870645 | epot = -14.9186498382089 | etot = -14.6424332451873 +310000 ekin = 0.168702678647172 | erot = 0.126562162216051 | epot = -14.9376980860502 | etot = -14.642433245187 +311000 ekin = 0.16174029700891 | erot = 0.155719593406526 | epot = -14.9598931356034 | etot = -14.642433245188 +312000 ekin = 0.15324744012492 | erot = 0.189565237977728 | epot = -14.985245923293 | etot = -14.6424332451904 +313000 ekin = 0.14342338999696 | erot = 0.227892126760383 | epot = -15.0137487619518 | etot = -14.6424332451944 +314000 ekin = 0.132524706018464 | erot = 0.270416174780403 | epot = -15.0453741259986 | etot = -14.6424332451998 +315000 ekin = 0.120869409552541 | erot = 0.31676970828902 | epot = -15.0800723630488 | etot = -14.6424332452072 +316000 ekin = 0.108838546104728 | erot = 0.366495437994318 | epot = -15.1177672293161 | etot = -14.642433245217 +317000 ekin = 0.0968734934277246 | erot = 0.419041536809129 | epot = -15.1583482754668 | etot = -14.6424332452299 +318000 ekin = 0.0854675378549793 | erot = 0.47375872576408 | epot = -15.2016595088657 | etot = -14.6424332452467 +319000 ekin = 0.0751507271451901 | erot = 0.529900497448216 | epot = -15.247484469862 | etot = -14.6424332452686 +320000 ekin = 0.0664678443364345 | erot = 0.586627760739854 | epot = -15.2955288503729 | etot = -14.6424332452966 +321000 ekin = 0.0599504590563252 | erot = 0.643019202691537 | epot = -15.3454029070798 | etot = -14.6424332453319 +322000 ekin = 0.0560852142800011 | erot = 0.698088453267024 | epot = -15.3966069129217 | etot = -14.6424332453747 +323000 ekin = 0.0552815181248971 | erot = 0.750808639916102 | epot = -15.4485234034659 | etot = -14.6424332454249 +324000 ekin = 0.057842325520568 | erot = 0.800144112657426 | epot = -15.5004196836595 | etot = -14.6424332454815 +325000 ekin = 0.0639414864634492 | erot = 0.845088070114938 | epot = -15.5514628021208 | etot = -14.6424332455424 +326000 ekin = 0.0736101694210054 | erot = 0.884703689967212 | epot = -15.6007471049934 | etot = -14.6424332456052 +327000 ekin = 0.0867333560896964 | erot = 0.91816541981297 | epot = -15.6473320215697 | etot = -14.642433245667 +328000 ekin = 0.103055779603987 | erot = 0.944796600223873 | epot = -15.6902856255527 | etot = -14.6424332457249 +329000 ekin = 0.12219544617078 | erot = 0.964099781594463 | epot = -15.7287284735416 | etot = -14.6424332457764 +330000 ekin = 0.143662406710238 | erot = 0.975776996237359 | epot = -15.7618726487672 | etot = -14.6424332458196 +331000 ekin = 0.166880785133575 | erot = 0.979738667517989 | epot = -15.7890526985047 | etot = -14.6424332458532 +332000 ekin = 0.191212923969923 | erot = 0.976101405902871 | epot = -15.8097475757491 | etot = -14.6424332458763 +333000 ekin = 0.215985355319577 | erot = 0.965176233539036 | epot = -15.8235948347474 | etot = -14.6424332458887 +334000 ekin = 0.240516656831147 | erot = 0.947449485112495 | epot = -15.8303993878336 | etot = -14.64243324589 +335000 ekin = 0.264146896086235 | erot = 0.923558676868035 | epot = -15.8301388188342 | etot = -14.6424332458799 +336000 ekin = 0.286267467754231 | erot = 0.894265184760612 | epot = -15.8229658983734 | etot = -14.6424332458586 +337000 ekin = 0.306349134750088 | erot = 0.860424939336672 | epot = -15.809207319913 | etot = -14.6424332458262 +338000 ekin = 0.323965497674696 | erot = 0.822957838322753 | epot = -15.7893565817813 | etot = -14.6424332457838 +339000 ekin = 0.338809250788985 | erot = 0.782816380150479 | epot = -15.7640588766724 | etot = -14.6424332457329 +340000 ekin = 0.35069944423374 | erot = 0.740954141303117 | epot = -15.7340868312125 | etot = -14.6424332456757 +341000 ekin = 0.359579293536495 | erot = 0.698295027831847 | epot = -15.700307566983 | etot = -14.6424332456147 +342000 ekin = 0.365505462154926 | erot = 0.655704542034982 | epot = -15.6636432497426 | etot = -14.6424332455527 +343000 ekin = 0.368630832661383 | erot = 0.613964463465552 | epot = -15.6250285416195 | etot = -14.6424332454926 +344000 ekin = 0.369183369589215 | erot = 0.573752273080787 | epot = -15.5853688881069 | etot = -14.6424332454369 +345000 ekin = 0.367443732824289 | erot = 0.535626361233146 | epot = -15.5455033394448 | etot = -14.6424332453874 +346000 ekin = 0.36372393313177 | erot = 0.500017626276193 | epot = -15.5061748047535 | etot = -14.6424332453455 +347000 ekin = 0.358348705277679 | erot = 0.467227585427262 | epot = -15.4680095360169 | etot = -14.642433245312 +348000 ekin = 0.351640582954838 | erot = 0.437432666908102 | epot = -15.4315064951499 | etot = -14.642433245287 +349000 ekin = 0.343909024694815 | erot = 0.410693986169929 | epot = -15.3970362561344 | etot = -14.6424332452696 +350000 ekin = 0.335443435968793 | erot = 0.386971649880727 | epot = -15.3648483311092 | etot = -14.6424332452597 +351000 ekin = 0.326509584093778 | erot = 0.366142474251511 | epot = -15.3350853036005 | etot = -14.6424332452552 +352000 ekin = 0.317348699022207 | erot = 0.34801993040111 | epot = -15.3078018746784 | etot = -14.6424332452551 +353000 ekin = 0.30817846664876 | erot = 0.332375117501944 | epot = -15.2829868294085 | etot = -14.6424332452578 +354000 ekin = 0.299195119854399 | erot = 0.318957598139001 | epot = -15.2605859632553 | etot = -14.6424332452619 +355000 ekin = 0.290575888248862 | erot = 0.307515001370356 | epot = -15.2405241348854 | etot = -14.6424332452662 +356000 ekin = 0.282481160312497 | erot = 0.29781040621721 | epot = -15.2227248117992 | etot = -14.6424332452695 +357000 ekin = 0.275055828993789 | erot = 0.289636664277857 | epot = -15.2071257385429 | etot = -14.6424332452713 +358000 ekin = 0.26842942725494 | erot = 0.282827006912222 | epot = -15.1936896794383 | etot = -14.6424332452711 +359000 ekin = 0.262714810201762 | erot = 0.277261507858003 | epot = -15.1824095633288 | etot = -14.642433245269 +360000 ekin = 0.258005302569436 | erot = 0.272869227748658 | epot = -15.1733077755836 | etot = -14.6424332452655 +361000 ekin = 0.254370400621781 | erot = 0.269626137802017 | epot = -15.1664297836851 | etot = -14.6424332452613 +362000 ekin = 0.251850290178651 | erot = 0.267549186087959 | epot = -15.1618327215239 | etot = -14.6424332452573 +363000 ekin = 0.250449609862751 | erot = 0.266687109597485 | epot = -15.159569964715 | etot = -14.6424332452548 +364000 ekin = 0.250131041863336 | erot = 0.267108788857729 | epot = -15.1596730759762 | etot = -14.6424332452551 +365000 ekin = 0.250809442162066 | erot = 0.268890073928026 | epot = -15.1621327613494 | etot = -14.6424332452593 +366000 ekin = 0.25234731876335 | erot = 0.272100073006091 | epot = -15.1668806370379 | etot = -14.6424332452684 +367000 ekin = 0.254552520178511 | erot = 0.276787886819413 | epot = -15.1737736522811 | etot = -14.6424332452832 +368000 ekin = 0.257178996153298 | erot = 0.282970699523766 | epot = -15.1825829409812 | etot = -14.6424332453042 +369000 ekin = 0.259931424908708 | erot = 0.29062401114344 | epot = -15.1929886813832 | etot = -14.642433245331 +370000 ekin = 0.262474349326632 | erot = 0.299674631814998 | epot = -15.2045822265049 | etot = -14.6424332453633 +371000 ekin = 0.264446209428301 | erot = 0.309996869297344 | epot = -15.2168763241253 | etot = -14.6424332453996 +372000 ekin = 0.265478281861433 | erot = 0.321412142686654 | epot = -15.2293236699864 | etot = -14.6424332454383 +373000 ekin = 0.265218028290041 | erot = 0.333692059448718 | epot = -15.2413433332161 | etot = -14.6424332454774 +374000 ekin = 0.26335572124772 | erot = 0.346564809671271 | epot = -15.2523537764331 | etot = -14.6424332455141 +375000 ekin = 0.259652497500777 | erot = 0.359724567998165 | epot = -15.2618103110451 | etot = -14.6424332455462 +376000 ekin = 0.253967268934319 | erot = 0.372843454384699 | epot = -15.2692439688902 | etot = -14.6424332455711 +377000 ekin = 0.246279333497663 | erot = 0.385585491299193 | epot = -15.2742980703837 | etot = -14.6424332455868 +378000 ekin = 0.236703249874173 | erot = 0.397621906702965 | epot = -15.2767584021691 | etot = -14.642433245592 +379000 ekin = 0.22549275694072 | erot = 0.408647066936832 | epot = -15.2765730694637 | etot = -14.6424332455862 +380000 ekin = 0.213031377534934 | erot = 0.418394279001949 | epot = -15.2738589021069 | etot = -14.64243324557 +381000 ekin = 0.19980887731166 | erot = 0.426650676217107 | epot = -15.2688927990735 | etot = -14.6424332455448 +382000 ekin = 0.186384809014969 | erot = 0.433270396060972 | epot = -15.2620884505889 | etot = -14.642433245513 +383000 ekin = 0.173342616140343 | erot = 0.4381852790555 | epot = -15.2539611406731 | etot = -14.6424332454773 +384000 ekin = 0.161239700828087 | erot = 0.441412371407271 | epot = -15.2450853176757 | etot = -14.6424332454403 +385000 ekin = 0.15055995464474 | erot = 0.443057612556821 | epot = -15.2360508126064 | etot = -14.6424332454049 +386000 ekin = 0.141675129696877 | erot = 0.443315241526503 | epot = -15.2274236165962 | etot = -14.6424332453728 +387000 ekin = 0.134820015696259 | erot = 0.442462667351556 | epot = -15.2197159283931 | etot = -14.6424332453452 +388000 ekin = 0.130083976412379 | erot = 0.44085081351593 | epot = -15.2133680352507 | etot = -14.6424332453224 +389000 ekin = 0.12741857023722 | erot = 0.43889024628032 | epot = -15.2087420618216 | etot = -14.6424332453041 +390000 ekin = 0.126658423092956 | erot = 0.43703370208669 | epot = -15.2061253704692 | etot = -14.6424332452895 +391000 ekin = 0.127550804261056 | erot = 0.435755902066133 | epot = -15.2057399516053 | etot = -14.6424332452781 +392000 ekin = 0.129788752936039 | erot = 0.435531744058152 | epot = -15.2077537422634 | etot = -14.6424332452692 +393000 ekin = 0.133043055316541 | erot = 0.43681406507717 | epot = -15.2122903656559 | etot = -14.6424332452622 +394000 ekin = 0.136989561466299 | erot = 0.440012156509965 | epot = -15.2194349632336 | etot = -14.6424332452574 +395000 ekin = 0.141329833042564 | erot = 0.445472096884898 | epot = -15.2292351751821 | etot = -14.6424332452547 +396000 ekin = 0.145804542777373 | erot = 0.45345976764831 | epot = -15.2416975556805 | etot = -14.6424332452548 +397000 ekin = 0.150200153188676 | erot = 0.464147173461378 | epot = -15.2567805719085 | etot = -14.6424332452585 +398000 ekin = 0.154350089766152 | erot = 0.477602441558481 | epot = -15.2743857765906 | etot = -14.642433245266 +399000 ekin = 0.158131920622366 | erot = 0.493783661155649 | epot = -15.2943488270562 | etot = -14.6424332452782 +400000 ekin = 0.161462056173796 | erot = 0.512536568006325 | epot = -15.3164318694755 | etot = -14.6424332452953 +401000 ekin = 0.164289301181072 | erot = 0.533595989002473 | epot = -15.3403185355012 | etot = -14.6424332453177 +402000 ekin = 0.166588323050693 | erot = 0.556590928839834 | epot = -15.3656124972355 | etot = -14.642433245345 +403000 ekin = 0.168353810379696 | erot = 0.581053183644485 | epot = -15.3918402394011 | etot = -14.6424332453769 +404000 ekin = 0.169595821301193 | erot = 0.606429376023291 | epot = -15.4184584427372 | etot = -14.6424332454127 +405000 ekin = 0.170336578562018 | erot = 0.63209629254071 | epot = -15.444866116554 | etot = -14.6424332454513 +406000 ekin = 0.170608761978812 | erot = 0.65737934451496 | epot = -15.4704213519851 | etot = -14.6424332454913 +407000 ekin = 0.170455178567329 | erot = 0.681573854094723 | epot = -15.4944622781935 | etot = -14.6424332455315 +408000 ekin = 0.169929554809759 | erot = 0.703968692151394 | epot = -15.5163314925311 | etot = -14.64243324557 +409000 ekin = 0.169098093451394 | erot = 0.723871579521683 | epot = -15.5354029185781 | etot = -14.6424332456051 +410000 ekin = 0.168041369040759 | erot = 0.740635137248624 | epot = -15.5511097519242 | etot = -14.6424332456348 +411000 ekin = 0.166856102809036 | erot = 0.753682569971393 | epot = -15.5629719184382 | etot = -14.6424332456577 +412000 ekin = 0.165656359033239 | erot = 0.762531725093238 | epot = -15.5706213297988 | etot = -14.6424332456724 +413000 ekin = 0.164573741711749 | erot = 0.766816218739624 | epot = -15.5738232061291 | etot = -14.6424332456777 +414000 ekin = 0.163756240957875 | erot = 0.766302377571564 | epot = -15.5724918642026 | etot = -14.6424332456732 +415000 ekin = 0.163365479945837 | erot = 0.76090092022446 | epot = -15.5666996458289 | etot = -14.6424332456586 +416000 ekin = 0.16357224009456 | erot = 0.750672586698944 | epot = -15.556678072428 | etot = -14.6424332456345 +417000 ekin = 0.164550286199954 | erot = 0.7358272978906 | epot = -15.5428108296923 | etot = -14.6424332456018 +418000 ekin = 0.166468663393413 | erot = 0.716716857299939 | epot = -15.5256187662552 | etot = -14.6424332455618 +419000 ekin = 0.169482781127082 | erot = 0.693821649098591 | epot = -15.5057376757421 | etot = -14.6424332455164 +420000 ekin = 0.173724722667737 | erot = 0.66773219168281 | epot = -15.4838901598182 | etot = -14.6424332454677 +421000 ekin = 0.179293310761201 | erot = 0.639126725581016 | epot = -15.4608532817598 | etot = -14.6424332454176 +422000 ekin = 0.18624451452154 | erot = 0.608746211198834 | epot = -15.437423971089 | etot = -14.6424332453687 +423000 ekin = 0.194582798147166 | erot = 0.577368165576623 | epot = -15.4143842090466 | etot = -14.6424332453228 +424000 ekin = 0.204253993032127 | erot = 0.545780680985215 | epot = -15.3924679192995 | etot = -14.6424332452822 +425000 ekin = 0.215140228919709 | erot = 0.514757766830984 | epot = -15.3723312409989 | etot = -14.6424332452482 +426000 ekin = 0.227057395200028 | erot = 0.485036881514174 | epot = -15.354527521936 | etot = -14.6424332452218 +427000 ekin = 0.239755526228602 | erot = 0.457299221560653 | epot = -15.3394879929934 | etot = -14.6424332452042 +428000 ekin = 0.252922416271923 | erot = 0.432153058134052 | epot = -15.3275087196016 | etot = -14.6424332451956 +429000 ekin = 0.266190667181531 | erot = 0.410120192007372 | epot = -15.3187441043849 | etot = -14.642433245196 +430000 ekin = 0.279148248287616 | erot = 0.391625457761957 | epot = -15.3132069512549 | etot = -14.6424332452053 +431000 ekin = 0.291352495295092 | erot = 0.376989149810484 | epot = -15.3107748903279 | etot = -14.6424332452223 +432000 ekin = 0.302347287571197 | erot = 0.366422254466197 | epot = -15.311202787284 | etot = -14.6424332452466 +433000 ekin = 0.311682921771834 | erot = 0.360024429012416 | epot = -15.3141405960599 | etot = -14.6424332452756 +434000 ekin = 0.318937954387398 | erot = 0.357784738270779 | epot = -15.3191559379664 | etot = -14.6424332453082 +435000 ekin = 0.323742037714837 | erot = 0.359585207272863 | epot = -15.3257604903308 | etot = -14.6424332453431 +436000 ekin = 0.325798554031316 | erot = 0.365207245305789 | epot = -15.3334390447156 | etot = -14.6424332453785 +437000 ekin = 0.324905697097303 | erot = 0.374340922349983 | epot = -15.3416798648586 | etot = -14.6424332454113 +438000 ekin = 0.320974589858357 | erot = 0.386596930160468 | epot = -15.3500047654588 | etot = -14.64243324544 +439000 ekin = 0.314043077746361 | erot = 0.401520852185505 | epot = -15.3579971753956 | etot = -14.6424332454637 +440000 ekin = 0.304283988020539 | erot = 0.41860913221399 | epot = -15.3653263657148 | etot = -14.6424332454802 +441000 ekin = 0.292006859111611 | erot = 0.437325916193047 | epot = -15.3717660207934 | etot = -14.6424332454888 +442000 ekin = 0.277652365815072 | erot = 0.457119792518877 | epot = -15.3772054038232 | etot = -14.6424332454893 +443000 ekin = 0.261778853590747 | erot = 0.477439412175799 | epot = -15.3816515112488 | etot = -14.6424332454822 +444000 ekin = 0.245040553434245 | erot = 0.497747053376455 | epot = -15.3852208522799 | etot = -14.6424332454692 +445000 ekin = 0.22815726042029 | erot = 0.517529408202492 | epot = -15.3881199140742 | etot = -14.6424332454515 +446000 ekin = 0.211875681729375 | erot = 0.536305196856599 | epot = -15.3906141240179 | etot = -14.6424332454319 +447000 ekin = 0.196923472681452 | erot = 0.553629632753464 | epot = -15.3929863508487 | etot = -14.6424332454138 +448000 ekin = 0.183958277880794 | erot = 0.569096233371 | epot = -15.3954877566523 | etot = -14.6424332454005 +449000 ekin = 0.173515771313211 | erot = 0.582336947151656 | epot = -15.3982859638601 | etot = -14.6424332453953 +450000 ekin = 0.16596236119942 | erot = 0.593021970145928 | epot = -15.4014175767459 | etot = -14.6424332454006 +451000 ekin = 0.161459280835239 | erot = 0.600860851249481 | epot = -15.4047533775022 | etot = -14.6424332454175 +452000 ekin = 0.159944578253891 | erot = 0.605606408076383 | epot = -15.4079842317757 | etot = -14.6424332454454 +453000 ekin = 0.161137653115343 | erot = 0.607062496368097 | epot = -15.410633394965 | etot = -14.6424332454815 +454000 ekin = 0.164567591513362 | erot = 0.605095779306141 | epot = -15.4120966163413 | etot = -14.6424332455218 +455000 ekin = 0.169622334209561 | erot = 0.599650455421321 | epot = -15.4117060351916 | etot = -14.6424332455607 +456000 ekin = 0.175611802350685 | erot = 0.590763702894581 | epot = -15.4088087508385 | etot = -14.6424332455932 +457000 ekin = 0.181835621982265 | erot = 0.578578749363229 | epot = -15.40284761696 | etot = -14.6424332456146 +458000 ekin = 0.187645727030889 | erot = 0.563352302649372 | epot = -15.3934312753016 | etot = -14.6424332456214 +459000 ekin = 0.192495880384907 | erot = 0.54545371714964 | epot = -15.380382843147 | etot = -14.6424332456124 +460000 ekin = 0.195973381637234 | erot = 0.525354597712022 | epot = -15.3637612249374 | etot = -14.6424332455881 +461000 ekin = 0.197811920991222 | erot = 0.503609203464283 | epot = -15.3438543700064 | etot = -14.6424332455509 +462000 ekin = 0.197887724919133 | erot = 0.480827560284776 | epot = -15.3211485307076 | etot = -14.6424332455037 +463000 ekin = 0.196203198485172 | erot = 0.457644248439133 | epot = -15.2962806923751 | etot = -14.6424332454508 +464000 ekin = 0.192863034125905 | erot = 0.434686220431894 | epot = -15.2699824999537 | etot = -14.6424332453959 +465000 ekin = 0.188047435822221 | erot = 0.412542760094015 | epot = -15.2430234412586 | etot = -14.6424332453423 +466000 ekin = 0.181986107552773 | erot = 0.39174001067487 | epot = -15.2161593635207 | etot = -14.642433245293 +467000 ekin = 0.174935400197984 | erot = 0.372721626737719 | epot = -15.1900902721857 | etot = -14.64243324525 +468000 ekin = 0.167159826102143 | erot = 0.355836258353913 | epot = -15.1654293296704 | etot = -14.6424332452144 +469000 ekin = 0.158918218022589 | erot = 0.34133189076746 | epot = -15.1426833539768 | etot = -14.6424332451868 +470000 ekin = 0.150454185653206 | erot = 0.329356584635659 | epot = -15.1222440154559 | etot = -14.642433245167 +471000 ekin = 0.141990180749416 | erot = 0.319964871778407 | epot = -15.1043882976824 | etot = -14.6424332451545 +472000 ekin = 0.13372435386821 | erot = 0.313128906246327 | epot = -15.089286505263 | etot = -14.6424332451484 +473000 ekin = 0.12582939810187 | erot = 0.308753392325055 | epot = -15.0770160355743 | etot = -14.6424332451474 +474000 ekin = 0.118452666363187 | erot = 0.306693264414364 | epot = -15.0675791759277 | etot = -14.6424332451502 +475000 ekin = 0.111716976218892 | erot = 0.306773053291038 | epot = -15.0609232746652 | etot = -14.6424332451553 +476000 ekin = 0.105721655633223 | erot = 0.308806833537935 | epot = -15.0569617343327 | etot = -14.6424332451616 +477000 ekin = 0.100543523675713 | erot = 0.312617617130682 | epot = -15.055594385974 | etot = -14.6424332451676 +478000 ekin = 0.0962376398644524 | erot = 0.31805505563592 | epot = -15.0567259406729 | etot = -14.6424332451726 +479000 ekin = 0.0928377950023796 | erot = 0.325010357031072 | epot = -15.0602813972091 | etot = -14.6424332451757 +480000 ekin = 0.0903568546344123 | erot = 0.333427427764652 | epot = -15.0662175275756 | etot = -14.6424332451766 +481000 ekin = 0.0887871989354825 | erot = 0.343309423711621 | epot = -15.074529867822 | etot = -14.6424332451749 +482000 ekin = 0.0881016191313879 | erot = 0.354720133059457 | epot = -15.085254997362 | etot = -14.6424332451711 +483000 ekin = 0.0882551127429667 | erot = 0.367779908275293 | epot = -15.0984682661837 | etot = -14.6424332451655 +484000 ekin = 0.0891880440123837 | erot = 0.382656193510863 | epot = -15.1142774826819 | etot = -14.6424332451586 +485000 ekin = 0.0908310739090695 | erot = 0.399549033149904 | epot = -15.1328133522102 | etot = -14.6424332451512 +486000 ekin = 0.0931120890965809 | erot = 0.418672269926982 | epot = -15.1542176041678 | etot = -14.6424332451442 +487000 ekin = 0.0959650526362282 | erot = 0.440231422324969 | epot = -15.1786297200997 | etot = -14.6424332451385 +488000 ekin = 0.09934026138313 | erot = 0.464399451388414 | epot = -15.2061729579063 | etot = -14.6424332451348 +489000 ekin = 0.103214957393528 | erot = 0.491291775407016 | epot = -15.2369399779348 | etot = -14.6424332451343 +490000 ekin = 0.107602676592561 | erot = 0.520941965501655 | epot = -15.2709778872321 | etot = -14.6424332451379 +491000 ekin = 0.112559247659633 | erot = 0.553279563919971 | epot = -15.3082720567263 | etot = -14.6424332451467 +492000 ekin = 0.118183136718381 | erot = 0.588111425310919 | epot = -15.3487278071915 | etot = -14.6424332451622 +493000 ekin = 0.124608040121107 | erot = 0.625107908280808 | epot = -15.3921491935878 | etot = -14.6424332451858 +494000 ekin = 0.131986393307421 | erot = 0.663795156036237 | epot = -15.4382147945631 | etot = -14.6424332452194 +495000 ekin = 0.140463823895351 | erot = 0.703554605722113 | epot = -15.4864516748821 | etot = -14.6424332452647 +496000 ekin = 0.150146408031555 | erot = 0.743630741562816 | epot = -15.5362103949171 | etot = -14.6424332453228 +497000 ekin = 0.161064579067727 | erot = 0.783147917316502 | epot = -15.5866457417786 | etot = -14.6424332453944 +498000 ekin = 0.173139219154636 | erot = 0.821136754971001 | epot = -15.6367092196045 | etot = -14.6424332454789 +499000 ekin = 0.186156317831577 | erot = 0.856570103854305 | epot = -15.6851596672597 | etot = -14.6424332455738 +500000 ekin = 0.199756195068125 | erot = 0.888407758271075 | epot = -15.7305971990145 | etot = -14.6424332456753 +501000 ekin = 0.213441517837528 | erot = 0.915648078729389 | epot = -15.7715228423447 | etot = -14.6424332457778 +502000 ekin = 0.226605416599141 | erot = 0.93738343364528 | epot = -15.8064220961188 | etot = -14.6424332458744 +503000 ekin = 0.238577508979596 | erot = 0.952855183120654 | epot = -15.833865938058 | etot = -14.6424332459578 +504000 ekin = 0.24868234701908 | erot = 0.961503066783773 | epot = -15.852618659824 | etot = -14.6424332460212 +505000 ekin = 0.256302488972939 | erot = 0.96300365636181 | epot = -15.8617393913938 | etot = -14.6424332460591 +506000 ekin = 0.26093758314799 | erot = 0.957293217915516 | epot = -15.8606640471316 | etot = -14.6424332460681 +507000 ekin = 0.262251679303339 | erot = 0.944571918253385 | epot = -15.8492568436041 | etot = -14.6424332460474 +508000 ekin = 0.260103184115661 | erot = 0.92528856492912 | epot = -15.8278249950432 | etot = -14.6424332459984 +509000 ekin = 0.254554875284732 | erot = 0.900107536932478 | epot = -15.7970956581425 | etot = -14.6424332459253 +510000 ekin = 0.245864483352381 | erot = 0.86986171798002 | epot = -15.7581594471659 | etot = -14.6424332458335 +511000 ekin = 0.234458914530907 | erot = 0.835496660121178 | epot = -15.7123888203816 | etot = -14.6424332457296 +512000 ekin = 0.220896820243755 | erot = 0.798011684060757 | epot = -15.6613417499247 | etot = -14.6424332456202 +513000 ekin = 0.205824805091356 | erot = 0.758403224573394 | epot = -15.6066612751765 | etot = -14.6424332455118 +514000 ekin = 0.189932244119312 | erot = 0.717614706855625 | epot = -15.5499801963846 | etot = -14.6424332454096 +515000 ekin = 0.173908748202557 | erot = 0.676495918868222 | epot = -15.4928379123889 | etot = -14.6424332453181 +516000 ekin = 0.158407108511411 | erot = 0.63577351602134 | epot = -15.4366138697731 | etot = -14.6424332452404 +517000 ekin = 0.144013350185933 | erot = 0.596033149114553 | epot = -15.3824797444789 | etot = -14.6424332451784 +518000 ekin = 0.131224514119668 | erot = 0.55771282568585 | epot = -15.3313705849382 | etot = -14.6424332451327 +519000 ekin = 0.120434042407116 | erot = 0.521106495595107 | epot = -15.2839737831051 | etot = -14.6424332451028 +520000 ekin = 0.111924165177635 | erot = 0.486376443197646 | epot = -15.240733853463 | etot = -14.6424332450877 +521000 ekin = 0.105864424816456 | erot = 0.453572806058813 | epot = -15.2018704759605 | etot = -14.6424332450853 +522000 ekin = 0.102315362067633 | erot = 0.422658367130362 | epot = -15.1674069742913 | etot = -14.6424332450933 +523000 ekin = 0.101236366465094 | erot = 0.393536647096269 | epot = -15.1372062586706 | etot = -14.6424332451092 +524000 ekin = 0.102496717236358 | erot = 0.366081244307823 | epot = -15.1110112066744 | etot = -14.6424332451302 +525000 ekin = 0.105888887335355 | erot = 0.340164343214516 | epot = -15.0884864757035 | etot = -14.6424332451536 +526000 ekin = 0.111143247849968 | erot = 0.315682368378613 | epot = -15.0692588614059 | etot = -14.6424332451774 +527000 ekin = 0.117943398961207 | erot = 0.292576937806905 | epot = -15.0529535819675 | etot = -14.6424332451994 +528000 ekin = 0.125941474254371 | erot = 0.270849598243589 | epot = -15.0392243177162 | etot = -14.6424332452183 +529000 ekin = 0.134772916008756 | erot = 0.250569317238961 | epot = -15.0277754784808 | etot = -14.642433245233 +530000 ekin = 0.144070383401965 | erot = 0.231872340651302 | epot = -15.0183759692967 | etot = -14.6424332452434 +531000 ekin = 0.153476601968781 | erot = 0.214954741433939 | epot = -15.0108645886523 | etot = -14.6424332452495 +532000 ekin = 0.162656054076991 | erot = 0.200058697647332 | epot = -15.0051479969763 | etot = -14.642433245252 +533000 ekin = 0.171305419079578 | erot = 0.18745414318241 | epot = -15.0011928075133 | etot = -14.6424332452513 +534000 ekin = 0.179162595538559 | erot = 0.177417842692309 | epot = -14.9990136834797 | etot = -14.6424332452488 +535000 ekin = 0.186014006484955 | erot = 0.17021209444076 | epot = -14.9986593461708 | etot = -14.6424332452451 +536000 ekin = 0.191699759238898 | erot = 0.166065149224471 | epot = -15.0001981537044 | etot = -14.642433245241 +537000 ekin = 0.196116169930243 | erot = 0.165155084977473 | epot = -15.003704500145 | etot = -14.6424332452373 +538000 ekin = 0.199215220532696 | erot = 0.167598364569312 | epot = -15.0092468303365 | etot = -14.6424332452345 +539000 ekin = 0.20100070966893 | erot = 0.173443713615195 | epot = -15.0168776685174 | etot = -14.6424332452333 +540000 ekin = 0.201521164037735 | erot = 0.182671367030132 | epot = -15.0266257763018 | etot = -14.6424332452339 +541000 ekin = 0.200859940141596 | erot = 0.195197211440065 | epot = -15.0384903968184 | etot = -14.6424332452368 +542000 ekin = 0.199123298889485 | erot = 0.210880936221535 | epot = -15.0524374803529 | etot = -14.6424332452419 +543000 ekin = 0.196427519384798 | erot = 0.229537017788165 | epot = -15.0683977824221 | etot = -14.6424332452492 +544000 ekin = 0.192886294946265 | erot = 0.25094720200201 | epot = -15.0862667422075 | etot = -14.6424332452593 +545000 ekin = 0.188599710888656 | erot = 0.274873110236005 | epot = -15.1059060663961 | etot = -14.6424332452715 +546000 ekin = 0.18364604524401 | erot = 0.301067663120887 | epot = -15.1271469536507 | etot = -14.6424332452858 +547000 ekin = 0.178077473819964 | erot = 0.329284179376543 | epot = -15.1497948984983 | etot = -14.6424332453018 +548000 ekin = 0.171920510268456 | erot = 0.359282253787671 | epot = -15.1736360093753 | etot = -14.6424332453191 +549000 ekin = 0.165181670578856 | erot = 0.390829837836003 | epot = -15.1984447537518 | etot = -14.6424332453369 +550000 ekin = 0.15785840865594 | erot = 0.423701326923092 | epot = -15.2239929809337 | etot = -14.6424332453547 +551000 ekin = 0.149954809005835 | erot = 0.457671882722257 | epot = -15.2500599370996 | etot = -14.6424332453715 +552000 ekin = 0.141500835822419 | erot = 0.492508662666464 | epot = -15.2764427438757 | etot = -14.6424332453869 +553000 ekin = 0.132573145480449 | erot = 0.527960055130273 | epot = -15.3029664460107 | etot = -14.6424332453999 +554000 ekin = 0.123314645146749 | erot = 0.563744383275372 | epot = -15.3294922738325 | etot = -14.6424332454104 +555000 ekin = 0.113949270900195 | erot = 0.599539792628959 | epot = -15.3559223089471 | etot = -14.642433245418 +556000 ekin = 0.104788088804118 | erot = 0.634977129568407 | epot = -15.3821984637958 | etot = -14.6424332454232 +557000 ekin = 0.0962230654738397 | erot = 0.669637513728588 | epot = -15.4082938246296 | etot = -14.6424332454272 +558000 ekin = 0.0887059614381524 | erot = 0.703055990484034 | epot = -15.4341951973535 | etot = -14.6424332454313 +559000 ekin = 0.0827118847692362 | erot = 0.734732129426798 | epot = -15.4598772596337 | etot = -14.6424332454377 +560000 ekin = 0.0786899547209647 | erot = 0.764147748400966 | epot = -15.4852709485704 | etot = -14.6424332454485 +561000 ekin = 0.0770067720584792 | erot = 0.790791153077553 | epot = -15.5102311706015 | etot = -14.6424332454654 +562000 ekin = 0.0778911706718854 | erot = 0.814186471630276 | epot = -15.5345108877916 | etot = -14.6424332454895 +563000 ekin = 0.0813901113631692 | erot = 0.833925925483943 | epot = -15.5577492823672 | etot = -14.6424332455201 +564000 ekin = 0.0873448530183735 | erot = 0.849702302566485 | epot = -15.5794804011401 | etot = -14.6424332455553 +565000 ekin = 0.0953935152513606 | erot = 0.861338569497979 | epot = -15.5991653303409 | etot = -14.6424332455915 +566000 ekin = 0.105001366117363 | erot = 0.868811531658242 | epot = -15.6162461434002 | etot = -14.6424332456246 +567000 ekin = 0.11551478920907 | erot = 0.872266750929345 | epot = -15.6302147857879 | etot = -14.6424332456494 +568000 ekin = 0.126230320989268 | erot = 0.872022546762513 | epot = -15.6406861134138 | etot = -14.642433245662 +569000 ekin = 0.13646757520452 | erot = 0.868561781939776 | epot = -15.6474626028035 | etot = -14.6424332456592 +570000 ekin = 0.145634823228517 | erot = 0.862511177264942 | epot = -15.6505792461335 | etot = -14.6424332456401 +571000 ekin = 0.153278250259444 | erot = 0.85460899135856 | epot = -15.6503204872235 | etot = -14.6424332456055 +572000 ekin = 0.159109636953228 | erot = 0.845662918619192 | epot = -15.6472058011307 | etot = -14.6424332455583 +573000 ekin = 0.163011362016512 | erot = 0.836500892322368 | epot = -15.6419454998419 | etot = -14.642433245503 +574000 ekin = 0.165021239079037 | erot = 0.827918058207513 | epot = -15.6353725427317 | etot = -14.6424332454451 +575000 ekin = 0.165302195907189 | erot = 0.820623479706097 | epot = -15.6283589210035 | etot = -14.6424332453902 +576000 ekin = 0.164102988099436 | erot = 0.815190165400348 | epot = -15.6217263988437 | etot = -14.642433245344 +577000 ekin = 0.161716152385033 | erot = 0.812011817945282 | epot = -15.6161612156414 | etot = -14.6424332453111 +578000 ekin = 0.158438569369342 | erot = 0.811269345694562 | epot = -15.6121411603589 | etot = -14.642433245295 +579000 ekin = 0.154538688866582 | erot = 0.812909695779756 | epot = -15.609881629944 | etot = -14.6424332452977 +580000 ekin = 0.150232988451456 | erot = 0.816638977239882 | epot = -15.6093052110108 | etot = -14.6424332453195 +581000 ekin = 0.145672809811769 | erot = 0.821931135408107 | epot = -15.610037190579 | etot = -14.6424332453591 +582000 ekin = 0.140941476788221 | erot = 0.828052590347089 | epot = -15.6114273125489 | etot = -14.6424332454136 +583000 ekin = 0.136060602595884 | erot = 0.834102246891801 | epot = -15.6125960949663 | etot = -14.6424332454786 +584000 ekin = 0.131003759893416 | erot = 0.839065139153076 | epot = -15.6125021445954 | etot = -14.6424332455489 +585000 ekin = 0.125715216480047 | erot = 0.841876757443314 | epot = -15.610025219542 | etot = -14.6424332456187 +586000 ekin = 0.120131224766283 | erot = 0.841493945660697 | epot = -15.6040584161089 | etot = -14.6424332456819 +587000 ekin = 0.114201380569862 | erot = 0.836967317747552 | epot = -15.5936019440503 | etot = -14.6424332457329 +588000 ekin = 0.107907808224941 | erot = 0.82750959597709 | epot = -15.577850649969 | etot = -14.642433245767 +589000 ekin = 0.101280337908465 | erot = 0.812554260667714 | epot = -15.5562678443569 | etot = -14.6424332457808 +590000 ekin = 0.0944063548781498 | erot = 0.791799488415112 | epot = -15.5286390890655 | etot = -14.6424332457722 +591000 ekin = 0.0874345511051164 | erot = 0.765233519218438 | epot = -15.4951013160648 | etot = -14.6424332457413 +592000 ekin = 0.0805723392090151 | erot = 0.733139214281057 | epot = -15.4561447991796 | etot = -14.6424332456895 +593000 ekin = 0.0740771594091624 | erot = 0.696077455345293 | epot = -15.4125878603745 | etot = -14.6424332456201 +594000 ekin = 0.0682423089615835 | erot = 0.654850963355498 | epot = -15.3655265178546 | etot = -14.6424332455375 +595000 ekin = 0.0633782539035135 | erot = 0.610451848321739 | epot = -15.3162633476725 | etot = -14.6424332454472 +596000 ekin = 0.0597906540673872 | erot = 0.563997548399991 | epot = -15.2662214478226 | etot = -14.6424332453552 +597000 ekin = 0.0577565493651072 | erot = 0.516660644083797 | epot = -15.2168504387165 | etot = -14.6424332452676 +598000 ekin = 0.0575003158564822 | erot = 0.469598294353737 | epot = -15.1695318554 | etot = -14.6424332451897 +599000 ekin = 0.0591710965315271 | erot = 0.423886769451641 | epot = -15.1254911111098 | etot = -14.6424332451266 +600000 ekin = 0.0628234356919084 | erot = 0.380465849282374 | epot = -15.085722530056 | etot = -14.6424332450817 +601000 ekin = 0.0684027903404234 | erot = 0.340096852290236 | epot = -15.0509328876879 | etot = -14.6424332450572 +602000 ekin = 0.0757374499151454 | erot = 0.303336891510158 | epot = -15.0215075864789 | etot = -14.6424332450536 +603000 ekin = 0.0845381560125067 | erot = 0.270530726253859 | epot = -14.9975021273365 | etot = -14.6424332450701 +604000 ekin = 0.0944063594091286 | erot = 0.241820347964902 | epot = -14.9786599524778 | etot = -14.6424332451038 +605000 ekin = 0.10485156246129 | erot = 0.217171224792453 | epot = -14.9644560324042 | etot = -14.6424332451505 +606000 ekin = 0.115317556389963 | erot = 0.19641293035746 | epot = -14.9541637319522 | etot = -14.6424332452047 +607000 ekin = 0.125216580352814 | erot = 0.179290709848685 | epot = -14.9469405354619 | etot = -14.6424332452604 +608000 ekin = 0.133969542489555 | erot = 0.165523445158836 | epot = -14.9419262329593 | etot = -14.6424332453109 +609000 ekin = 0.141049537027034 | erot = 0.154862582266178 | epot = -14.9383453646431 | etot = -14.6424332453499 +610000 ekin = 0.146025095174092 | erot = 0.1471460408894 | epot = -14.9356043814358 | etot = -14.6424332453723 +611000 ekin = 0.148599079333654 | erot = 0.142341118194537 | epot = -14.9333734429025 | etot = -14.6424332453743 +612000 ekin = 0.148639027540038 | erot = 0.140571068728109 | epot = -14.9316433416225 | etot = -14.6424332453543 +613000 ekin = 0.146195193891189 | erot = 0.14212144139606 | epot = -14.9307498806004 | etot = -14.6424332453132 +614000 ekin = 0.141503544703117 | erot = 0.147424293659367 | epot = -14.9313610836164 | etot = -14.6424332452539 +615000 ekin = 0.134972482667994 | erot = 0.157020849768205 | epot = -14.9344265776182 | etot = -14.642433245182 +616000 ekin = 0.127153892886345 | erot = 0.171505679771382 | epot = -14.9410928177621 | etot = -14.6424332451044 +617000 ekin = 0.118700960496639 | erot = 0.191457667913243 | epot = -14.9525918734392 | etot = -14.6424332450293 +618000 ekin = 0.110316794781978 | erot = 0.217364584488656 | epot = -14.9701146242355 | etot = -14.6424332449648 +619000 ekin = 0.102698942666746 | erot = 0.249548776229802 | epot = -14.9946809638153 | etot = -14.6424332449188 +620000 ekin = 0.0964852203328029 | erot = 0.28810131748882 | epot = -15.0270197827189 | etot = -14.6424332448972 +621000 ekin = 0.0922059091543824 | erot = 0.332831044361685 | epot = -15.0674701984207 | etot = -14.6424332449047 +622000 ekin = 0.0902463647122828 | erot = 0.383233451857076 | epot = -15.1159130615124 | etot = -14.6424332449431 +623000 ekin = 0.0908226920728038 | erot = 0.438482716259981 | epot = -15.1717386533448 | etot = -14.642433245012 +624000 ekin = 0.0939716062548715 | erot = 0.497448307331879 | epot = -15.2338531586956 | etot = -14.6424332451088 +625000 ekin = 0.0995541611252495 | erot = 0.55873588677621 | epot = -15.3007232931297 | etot = -14.6424332452283 +626000 ekin = 0.107271859328467 | erot = 0.620750477447864 | epot = -15.37045558214 | etot = -14.6424332453637 +627000 ekin = 0.116692826740179 | erot = 0.681778220892588 | epot = -15.4409042931397 | etot = -14.642433245507 +628000 ekin = 0.127285245275851 | erot = 0.740081431761277 | epot = -15.5097999226863 | etot = -14.6424332456492 +629000 ekin = 0.138455039155779 | erot = 0.794000196762996 | epot = -15.5748884817003 | etot = -14.6424332457815 +630000 ekin = 0.14958484293864 | erot = 0.842052640233787 | epot = -15.6340707290682 | etot = -14.6424332458958 +631000 ekin = 0.160071499854153 | erot = 0.883025442872994 | epot = -15.6855301887124 | etot = -14.6424332459852 +632000 ekin = 0.169359720293479 | erot = 0.916046503422886 | epot = -15.7278394697615 | etot = -14.6424332460451 +633000 ekin = 0.176970053692838 | erot = 0.940632922938759 | epot = -15.7600362227044 | etot = -14.6424332460728 +634000 ekin = 0.18251996128985 | erot = 0.956709735133355 | epot = -15.7816629424915 | etot = -14.6424332460683 +635000 ekin = 0.185737466035171 | erot = 0.964597760207225 | epot = -15.7927684722762 | etot = -14.6424332460338 +636000 ekin = 0.186467519302491 | erot = 0.964972204258569 | epot = -15.7938729695347 | etot = -14.6424332459737 +637000 ekin = 0.184671774603369 | erot = 0.958796660379843 | epot = -15.7859016808768 | etot = -14.6424332458936 +638000 ekin = 0.18042282577668 | erot = 0.947239527077098 | epot = -15.770095598654 | etot = -14.6424332458002 +639000 ekin = 0.173894119063272 | erot = 0.931581224200833 | epot = -15.7479085889646 | etot = -14.6424332457005 +640000 ekin = 0.165346701826059 | erot = 0.913120838758217 | epot = -15.720900786185 | etot = -14.6424332456007 +641000 ekin = 0.155113786101867 | erot = 0.893090060094414 | epot = -15.6906370917029 | etot = -14.6424332455066 +642000 ekin = 0.143583869242346 | erot = 0.872580710310524 | epot = -15.6585978249756 | etot = -14.6424332454227 +643000 ekin = 0.131182953687712 | erot = 0.85249016805802 | epot = -15.626106367098 | etot = -14.6424332453522 +644000 ekin = 0.118356305759397 | erot = 0.833486853993089 | epot = -15.5942764050497 | etot = -14.6424332452972 +645000 ekin = 0.105550209083444 | erot = 0.815995971214604 | epot = -15.5639794255564 | etot = -14.6424332452583 +646000 ekin = 0.0931942744180207 | erot = 0.800204061931992 | epot = -15.5358315815853 | etot = -14.6424332452353 +647000 ekin = 0.0816850001788838 | erot = 0.786079744440617 | epot = -15.5101979898464 | etot = -14.6424332452269 +648000 ekin = 0.0713713598428998 | erot = 0.773407243191854 | epot = -15.4872118482658 | etot = -14.6424332452311 +649000 ekin = 0.0625431628711437 | erot = 0.761828976528577 | epot = -15.466805384645 | etot = -14.6424332452453 +650000 ekin = 0.0554227735501042 | erot = 0.750893453411344 | epot = -15.4487494722283 | etot = -14.6424332452669 +651000 ekin = 0.0501605027659902 | erot = 0.740104978445366 | epot = -15.4326987265041 | etot = -14.6424332452927 +652000 ekin = 0.0468336713668948 | erot = 0.728972100417369 | epot = -15.4182390171042 | etot = -14.64243324532 +653000 ekin = 0.0454490492583012 | erot = 0.71705228594169 | epot = -15.4049345805459 | etot = -14.6424332453459 +654000 ekin = 0.0459481524956013 | erot = 0.703990869780751 | epot = -15.3923722676445 | etot = -14.6424332453682 +655000 ekin = 0.0482147495301563 | erot = 0.689552835103781 | epot = -15.3802008300186 | etot = -14.6424332453846 +656000 ekin = 0.052083876127999 | erot = 0.6736463327468 | epot = -15.3681634542687 | etot = -14.6424332453939 +657000 ekin = 0.0573516620867098 | erot = 0.656337023113139 | epot = -15.3561219305948 | etot = -14.6424332453949 +658000 ekin = 0.0637853134946659 | erot = 0.637852348218005 | epot = -15.3440709071003 | etot = -14.6424332453876 +659000 ekin = 0.0711326702887129 | erot = 0.618574815847064 | epot = -15.3321407315083 | etot = -14.6424332453725 +660000 ekin = 0.0791308828116024 | erot = 0.599023454708815 | epot = -15.3205875828713 | etot = -14.6424332453509 +661000 ekin = 0.0875139366244679 | erot = 0.579822939748233 | epot = -15.3097701216978 | etot = -14.6424332453251 +662000 ekin = 0.0960190004205311 | erot = 0.561660610348993 | epot = -15.3001128560677 | etot = -14.6424332452982 +663000 ekin = 0.104391848885269 | erot = 0.54523274605647 | epot = -15.2920578402154 | etot = -14.6424332452737 +664000 ekin = 0.112391863389534 | erot = 0.531182949320087 | epot = -15.286008057965 | etot = -14.6424332452554 +665000 ekin = 0.119797262719802 | erot = 0.520037124798746 | epot = -15.2822676327654 | etot = -14.6424332452468 +666000 ekin = 0.126411190061237 | erot = 0.512141060962394 | epot = -15.2809854962748 | etot = -14.6424332452511 +667000 ekin = 0.132069035722096 | erot = 0.507607681730268 | epot = -15.2821099627224 | etot = -14.64243324527 +668000 ekin = 0.13664691453854 | erot = 0.506281315754884 | epot = -15.2853614755972 | etot = -14.6424332453038 +669000 ekin = 0.140070616008884 | erot = 0.507725566171511 | epot = -15.2902294275315 | etot = -14.6424332453511 +670000 ekin = 0.142323740902266 | erot = 0.511239425097731 | epot = -15.2959964114084 | etot = -14.6424332454084 +671000 ekin = 0.143453306298606 | erot = 0.515903234043229 | epot = -15.3017897858128 | etot = -14.642433245471 +672000 ekin = 0.143571012728166 | erot = 0.520652256715664 | epot = -15.3066565149767 | etot = -14.6424332455328 +673000 ekin = 0.142848733833156 | erot = 0.52437156335394 | epot = -15.3096535427749 | etot = -14.6424332455878 +674000 ekin = 0.1415076132746 | erot = 0.526002362927187 | epot = -15.3099432218319 | etot = -14.6424332456301 +675000 ekin = 0.13980130282334 | erot = 0.524647629020819 | epot = -15.3068821774991 | etot = -14.6424332456549 +676000 ekin = 0.137995095209388 | erot = 0.519664439037725 | epot = -15.3000927799067 | etot = -14.6424332456596 +677000 ekin = 0.136343677284998 | erot = 0.510732098514415 | epot = -15.2895090214424 | etot = -14.642433245643 +678000 ekin = 0.135070664123473 | erot = 0.497888575253319 | epot = -15.2753924849829 | etot = -14.6424332456061 +679000 ekin = 0.134352810446714 | erot = 0.481532294129922 | epot = -15.2583183501282 | etot = -14.6424332455516 +680000 ekin = 0.134310862658442 | erot = 0.462390968603332 | epot = -15.2391350767452 | etot = -14.6424332454834 +681000 ekin = 0.135007638926465 | erot = 0.441462941783532 | epot = -15.2189038261164 | etot = -14.6424332454064 +682000 ekin = 0.136452461528359 | erot = 0.419938865037162 | epot = -15.1988245718911 | etot = -14.6424332453256 +683000 ekin = 0.138609887401901 | erot = 0.399112293315355 | epot = -15.1801554259633 | etot = -14.642433245246 +684000 ekin = 0.141410065652158 | erot = 0.380287181762659 | epot = -15.1641304925878 | etot = -14.642433245173 +685000 ekin = 0.144758102725849 | erot = 0.364688846299896 | epot = -15.1518801941367 | etot = -14.6424332451109 +686000 ekin = 0.148540467122542 | erot = 0.353383275614958 | epot = -15.1443569878014 | etot = -14.6424332450639 +687000 ekin = 0.152627512101174 | erot = 0.347208212231079 | epot = -15.1422689693677 | etot = -14.6424332450355 +688000 ekin = 0.156872371009907 | erot = 0.346718408270883 | epot = -15.1460240243093 | etot = -14.6424332450285 +689000 ekin = 0.161107527975576 | erot = 0.352146941114484 | epot = -15.1556877141346 | etot = -14.6424332450445 +690000 ekin = 0.165141087380535 | erot = 0.363384304940302 | epot = -15.1709586374048 | etot = -14.642433245084 +691000 ekin = 0.16875504264806 | erot = 0.379976931153832 | epot = -15.1911652189475 | etot = -14.6424332451456 +692000 ekin = 0.171707649701815 | erot = 0.401146558394006 | epot = -15.2152874533222 | etot = -14.6424332452264 +693000 ekin = 0.173741393440444 | erot = 0.425831232783773 | epot = -15.2420058715459 | etot = -14.6424332453217 +694000 ekin = 0.174597110621473 | erot = 0.452747528134232 | epot = -15.2697778841809 | etot = -14.6424332454252 +695000 ekin = 0.174033757468432 | erot = 0.480471830915669 | epot = -15.2969388339132 | etot = -14.6424332455291 +696000 ekin = 0.171852263360605 | erot = 0.507536398150921 | epot = -15.3218219071368 | etot = -14.6424332456253 +697000 ekin = 0.167921065286616 | erot = 0.532533688685243 | epot = -15.3428879996772 | etot = -14.6424332457054 +698000 ekin = 0.162200409472727 | erot = 0.55422061991701 | epot = -15.3588542751519 | etot = -14.6424332457621 +699000 ekin = 0.15476241571153 | erot = 0.5716133610199 | epot = -15.3688090225212 | etot = -14.6424332457897 +700000 ekin = 0.14580423000504 | erot = 0.584063387080082 | epot = -15.3723008628698 | etot = -14.6424332457847 +701000 ekin = 0.135652269555348 | erot = 0.591306922713837 | epot = -15.3693924380155 | etot = -14.6424332457463 +702000 ekin = 0.124756460204831 | erot = 0.59348246434204 | epot = -15.3606721702235 | etot = -14.6424332456766 +703000 ekin = 0.113674325949313 | erot = 0.591114401850656 | epot = -15.3472219733804 | etot = -14.6424332455805 +704000 ekin = 0.10304567594439 | erot = 0.585064323190966 | epot = -15.3305432446002 | etot = -14.6424332454648 +705000 ekin = 0.0935593581958762 | erot = 0.576454826529771 | epot = -15.3124474300639 | etot = -14.6424332453383 +706000 ekin = 0.0859140824287833 | erot = 0.566573150252444 | epot = -15.2949204778916 | etot = -14.6424332452103 +707000 ekin = 0.0807756759567746 | erot = 0.556763427605772 | epot = -15.2799723486536 | etot = -14.642433245091 +708000 ekin = 0.0787333622616091 | erot = 0.548316855287971 | epot = -15.2694834625388 | etot = -14.6424332449892 +709000 ekin = 0.0802577669172368 | erot = 0.542368667950884 | epot = -15.2650596797811 | etot = -14.642433244913 +710000 ekin = 0.0856633545554253 | erot = 0.539809747046289 | epot = -15.2679063464703 | etot = -14.6424332448686 +711000 ekin = 0.0950778519056264 | erot = 0.541219180888341 | epot = -15.2787302776541 | etot = -14.6424332448601 +712000 ekin = 0.108420876625267 | erot = 0.546822307908336 | epot = -15.2976764294225 | etot = -14.6424332448889 +713000 ekin = 0.125393451698069 | erot = 0.556476834654442 | epot = -15.3243035313066 | etot = -14.642433244954 +714000 ekin = 0.145479367624701 | erot = 0.569687600115953 | epot = -15.3576002127927 | etot = -14.642433245052 +715000 ekin = 0.167958541120038 | erot = 0.585648522299648 | epot = -15.3960403085969 | etot = -14.6424332451773 +716000 ekin = 0.191931735854292 | erot = 0.603308292527993 | epot = -15.4376732737045 | etot = -14.6424332453222 +717000 ekin = 0.216355400179768 | erot = 0.621454592033853 | epot = -15.4802432376918 | etot = -14.6424332454782 +718000 ekin = 0.240085056513064 | erot = 0.638810139728766 | epot = -15.5213284418775 | etot = -14.6424332456357 +719000 ekin = 0.261925698577658 | erot = 0.654132895983949 | epot = -15.5584918403468 | etot = -14.6424332457852 +720000 ekin = 0.280687969313511 | erot = 0.666312379865697 | epot = -15.5894335950967 | etot = -14.6424332459175 +721000 ekin = 0.295249345590605 | erot = 0.674454385927248 | epot = -15.6121369775423 | etot = -14.6424332460244 +722000 ekin = 0.304619886334631 | erot = 0.677947410255691 | epot = -15.625000542689 | etot = -14.6424332460987 +723000 ekin = 0.308011983728238 | erot = 0.676505724572098 | epot = -15.626950954435 | etot = -14.6424332461346 +724000 ekin = 0.304912667283913 | erot = 0.670186105902335 | epot = -15.6175320193145 | etot = -14.6424332461282 +725000 ekin = 0.295155116710332 | erot = 0.659377522493187 | epot = -15.5969658852808 | etot = -14.6424332460772 +726000 ekin = 0.278983134898071 | erot = 0.644765363163033 | epot = -15.5661817440431 | etot = -14.642433245982 +727000 ekin = 0.257098790791563 | erot = 0.627273860368268 | epot = -15.5268058970054 | etot = -14.6424332458455 +728000 ekin = 0.230680158271426 | erot = 0.607992016186298 | epot = -15.4811054201321 | etot = -14.6424332456743 +729000 ekin = 0.201354496272596 | erot = 0.588089464040467 | epot = -15.431877205792 | etot = -14.6424332454789 +730000 ekin = 0.171114103974836 | erot = 0.568729214721698 | epot = -15.3822765639703 | etot = -14.6424332452738 +731000 ekin = 0.142168923907651 | erot = 0.550984135076315 | epot = -15.3355863040605 | etot = -14.6424332450765 +732000 ekin = 0.116742007096091 | erot = 0.535763349049021 | epot = -15.2949386010514 | etot = -14.6424332449063 +733000 ekin = 0.0968293027534119 | erot = 0.523753647326195 | epot = -15.2630161948611 | etot = -14.6424332447815 +734000 ekin = 0.0839596135584089 | erot = 0.515379592342255 | epot = -15.2417724506168 | etot = -14.6424332447161 +735000 ekin = 0.0789983701762997 | erot = 0.510784464198618 | epot = -15.2322160790924 | etot = -14.6424332447175 +736000 ekin = 0.0820355551921124 | erot = 0.509832642267912 | epot = -15.2343014422445 | etot = -14.6424332447845 +737000 ekin = 0.092382712385484 | erot = 0.512132550856022 | epot = -15.246948508149 | etot = -14.6424332449075 +738000 ekin = 0.108680448513128 | erot = 0.517077971027173 | epot = -15.2681916646103 | etot = -14.64243324507 +739000 ekin = 0.129093715682691 | erot = 0.523904364925655 | epot = -15.2954313258603 | etot = -14.642433245252 +740000 ekin = 0.151555277793326 | erot = 0.531755895778055 | epot = -15.3257444190045 | etot = -14.6424332454331 +741000 ekin = 0.174012721806035 | erot = 0.539758083451399 | epot = -15.3562040508525 | etot = -14.6424332455951 +742000 ekin = 0.194640916830793 | erot = 0.547090549697037 | epot = -15.384164712252 | etot = -14.6424332457242 +743000 ekin = 0.211995737397977 | erot = 0.553054125335024 | epot = -15.4074831085446 | etot = -14.6424332458116 +744000 ekin = 0.225100508722008 | erot = 0.557126762307225 | epot = -15.4246605168831 | etot = -14.6424332458539 +745000 ekin = 0.233469424485825 | erot = 0.559003260236789 | epot = -15.4349059305745 | etot = -14.6424332458519 +746000 ekin = 0.23707991346408 | erot = 0.558614810498058 | epot = -15.4381279697723 | etot = -14.6424332458102 +747000 ekin = 0.236308652983949 | erot = 0.556125790081372 | epot = -15.4348676888016 | etot = -14.6424332457363 +748000 ekin = 0.231845097886983 | erot = 0.551907079329025 | epot = -15.4261854228555 | etot = -14.6424332456395 +749000 ekin = 0.224593843483339 | erot = 0.546487360028757 | epot = -15.4135144490424 | etot = -14.6424332455303 +750000 ekin = 0.215574369391403 | erot = 0.540486233484167 | epot = -15.3984938482956 | etot = -14.64243324542 +751000 ekin = 0.205824583426058 | erot = 0.534535356763698 | epot = -15.382793185509 | etot = -14.6424332453192 +752000 ekin = 0.196313335741561 | erot = 0.52919581521731 | epot = -15.3679423961964 | etot = -14.6424332452375 +753000 ekin = 0.187866475787076 | erot = 0.524881252730185 | epot = -15.3551809736995 | etot = -14.6424332451822 +754000 ekin = 0.181110613625657 | erot = 0.521796491095279 | epot = -15.345340349879 | etot = -14.6424332451581 +755000 ekin = 0.176438042203778 | erot = 0.519900210803623 | epot = -15.3387714981735 | etot = -14.6424332451661 +756000 ekin = 0.173994962646486 | erot = 0.518897676280608 | epot = -15.3353258841311 | etot = -14.642433245204 +757000 ekin = 0.173693190270073 | erot = 0.518265706177119 | epot = -15.3343921417132 | etot = -14.642433245266 +758000 ekin = 0.175243155014324 | erot = 0.517307659815294 | epot = -15.3349840601735 | etot = -14.6424332453439 +759000 ekin = 0.178203703092602 | erot = 0.515231902157482 | epot = -15.3358688506779 | etot = -14.6424332454278 +760000 ekin = 0.182042463548487 | erot = 0.51124383794149 | epot = -15.3357195469977 | etot = -14.6424332455077 +761000 ekin = 0.186199747761053 | erot = 0.50463982554006 | epot = -15.3332728188755 | etot = -14.6424332455744 +762000 ekin = 0.190149235945104 | erot = 0.494891409026585 | epot = -15.3274738905921 | etot = -14.6424332456204 +763000 ekin = 0.193449921094625 | erot = 0.481710238280476 | epot = -15.3175934050158 | etot = -14.6424332456407 +764000 ekin = 0.195785552426496 | erot = 0.465087294345703 | epot = -15.3033060924053 | etot = -14.6424332456331 +765000 ekin = 0.196989678184872 | erot = 0.445303873487263 | epot = -15.2847267972702 | etot = -14.6424332455981 +766000 ekin = 0.197055919182987 | erot = 0.422915440288454 | epot = -15.2624046050099 | etot = -14.6424332455385 +767000 ekin = 0.19613407649406 | erot = 0.398712320920584 | epot = -15.2372796428736 | etot = -14.6424332454589 +768000 ekin = 0.194513096652813 | erot = 0.37366293895697 | epot = -15.2106092809754 | etot = -14.6424332453656 +769000 ekin = 0.192592017627635 | erot = 0.348845887484862 | epot = -15.183871150378 | etot = -14.6424332452655 +770000 ekin = 0.190840163686923 | erot = 0.325376840212478 | epot = -15.1586502490658 | etot = -14.6424332451664 +771000 ekin = 0.189748397228249 | erot = 0.304335529900872 | epot = -15.1365171722054 | etot = -14.6424332450763 +772000 ekin = 0.18977434185156 | erot = 0.286697153922422 | epot = -15.1189047407765 | etot = -14.6424332450026 +773000 ekin = 0.191286034501482 | erot = 0.273271857838015 | epot = -15.1069911372911 | etot = -14.6424332449516 +774000 ekin = 0.194510000609465 | erot = 0.264655458971731 | epot = -15.1015987045099 | etot = -14.6424332449287 +775000 ekin = 0.199490639679827 | erot = 0.261194193157327 | epot = -15.1031180777734 | etot = -14.6424332449363 +776000 ekin = 0.206067477065984 | erot = 0.26296580393673 | epot = -15.1114665259772 | etot = -14.6424332449745 +777000 ekin = 0.213875019086146 | erot = 0.269778568413633 | epot = -15.1260868325404 | etot = -14.6424332450407 +778000 ekin = 0.222366868965164 | erot = 0.281188790676632 | epot = -15.1459889047712 | etot = -14.6424332451294 +779000 ekin = 0.230862102268941 | erot = 0.2965359441758 | epot = -15.1698312916782 | etot = -14.6424332452334 +780000 ekin = 0.238608567019415 | erot = 0.314993169090579 | epot = -15.1960349814538 | etot = -14.6424332453438 +781000 ekin = 0.244855557741695 | erot = 0.335629445234049 | epot = -15.222918248427 | etot = -14.6424332454513 +782000 ekin = 0.248927612478521 | erot = 0.357478674283205 | epot = -15.2488395323088 | etot = -14.642433245547 +783000 ekin = 0.250291897529516 | erot = 0.379610269023755 | epot = -15.2723354121766 | etot = -14.6424332456234 +784000 ekin = 0.248613283253053 | erot = 0.401195731117637 | epot = -15.2922422600447 | etot = -14.642433245674 +785000 ekin = 0.243793133450592 | erot = 0.421566090460737 | epot = -15.3077924696064 | etot = -14.6424332456951 +786000 ekin = 0.23598950185229 | erot = 0.440255905200772 | epot = -15.3186786527377 | etot = -14.6424332456846 +787000 ekin = 0.225617610784087 | erot = 0.457030673426299 | epot = -15.3250815298539 | etot = -14.6424332456436 +788000 ekin = 0.213330260901152 | erot = 0.471895861690097 | epot = -15.3276593681662 | etot = -14.642433245575 +789000 ekin = 0.19997849967651 | erot = 0.485087183877581 | epot = -15.3274989290384 | etot = -14.6424332454844 +790000 ekin = 0.186553834702627 | erot = 0.497043141237974 | epot = -15.3260302213197 | etot = -14.6424332453791 +791000 ekin = 0.174114766792028 | erot = 0.508362048565589 | epot = -15.3249100606257 | etot = -14.6424332452681 +792000 ekin = 0.163702420431615 | erot = 0.519746739177318 | epot = -15.3258824047698 | etot = -14.6424332451609 +793000 ekin = 0.156252224966357 | erot = 0.531940822986537 | epot = -15.3306262930203 | etot = -14.6424332450674 +794000 ekin = 0.152510350035351 | erot = 0.545660777312736 | epot = -15.3406043723442 | etot = -14.6424332449961 +795000 ekin = 0.152964251158983 | erot = 0.561528326979184 | epot = -15.3569258230923 | etot = -14.6424332449541 +796000 ekin = 0.157795747358379 | erot = 0.58000757877651 | epot = -15.3802365710807 | etot = -14.6424332449459 +797000 ekin = 0.166862457859208 | erot = 0.601351255568297 | epot = -15.4106469584007 | etot = -14.6424332449732 +798000 ekin = 0.179709603433377 | erot = 0.625560121844245 | epot = -15.4477029703127 | etot = -14.642433245035 +799000 ekin = 0.195609966062416 | erot = 0.65235924717518 | epot = -15.4904024583651 | etot = -14.6424332451275 +800000 ekin = 0.213626158791744 | erot = 0.681194021872009 | epot = -15.5372534259083 | etot = -14.6424332452445 +801000 ekin = 0.232687040193829 | erot = 0.711247726384584 | epot = -15.5863680119569 | etot = -14.6424332453785 +802000 ekin = 0.251669429106226 | erot = 0.741480919833726 | epot = -15.6355835944605 | etot = -14.6424332455205 +803000 ekin = 0.269477067858271 | erot = 0.77069100841835 | epot = -15.6826013219381 | etot = -14.6424332456615 +804000 ekin = 0.2851105414574 | erot = 0.797588259155217 | epot = -15.7251320464048 | etot = -14.6424332457922 +805000 ekin = 0.297723982505655 | erot = 0.82088252879607 | epot = -15.7610397572062 | etot = -14.6424332459044 +806000 ekin = 0.306666387686443 | erot = 0.839373432909784 | epot = -15.7884730665875 | etot = -14.6424332459913 +807000 ekin = 0.311506975554881 | erot = 0.852035914442116 | epot = -15.8059761360445 | etot = -14.6424332460475 +808000 ekin = 0.31204517625202 | erot = 0.858093398524567 | epot = -15.8125718208467 | etot = -14.6424332460701 +809000 ekin = 0.308306642386009 | erot = 0.857071970755237 | epot = -15.8078118591995 | etot = -14.6424332460582 +810000 ekin = 0.3005272205585 | erot = 0.848831113925777 | epot = -15.7917915804977 | etot = -14.6424332460134 +811000 ekin = 0.289127204417746 | erot = 0.83356913861968 | epot = -15.7651295889766 | etot = -14.6424332459392 +812000 ekin = 0.274678427598231 | erot = 0.811804116491095 | epot = -15.7289157899298 | etot = -14.6424332458404 +813000 ekin = 0.257866835579171 | erot = 0.784333459541309 | epot = -15.684633540844 | etot = -14.6424332457235 +814000 ekin = 0.23945308058907 | erot = 0.752176980195558 | epot = -15.63406330638 | etot = -14.6424332455953 +815000 ekin = 0.220233415146299 | erot = 0.716509170266206 | epot = -15.5791758308753 | etot = -14.6424332454628 +816000 ekin = 0.201002751041202 | erot = 0.678586569747871 | epot = -15.5220225661217 | etot = -14.6424332453326 +817000 ekin = 0.18252126107488 | erot = 0.639675603864852 | epot = -15.4646301101504 | etot = -14.6424332452107 +818000 ekin = 0.165485401522705 | erot = 0.600985363831257 | epot = -15.4089040104563 | etot = -14.6424332451023 +819000 ekin = 0.150503789775637 | erot = 0.563608719248849 | epot = -15.356545754036 | etot = -14.6424332450115 +820000 ekin = 0.138078032174191 | erot = 0.528474068971486 | epot = -15.3089853460871 | etot = -14.6424332449414 +821000 ekin = 0.128588386726458 | erot = 0.496309093116269 | epot = -15.2673307247368 | etot = -14.6424332448941 +822000 ekin = 0.122284066133841 | erot = 0.467617125513468 | epot = -15.2323344365177 | etot = -14.6424332448704 +823000 ekin = 0.119278020922153 | erot = 0.442666228475553 | epot = -15.2043774942682 | etot = -14.6424332448705 +824000 ekin = 0.119546158602336 | erot = 0.421490682734476 | epot = -15.1834700862298 | etot = -14.642433244893 +825000 ekin = 0.122931110514093 | erot = 0.403904342218594 | epot = -15.1692686976687 | etot = -14.6424332449361 +826000 ekin = 0.129150803764777 | erot = 0.389525074993895 | epot = -15.1611091237552 | etot = -14.6424332449966 +827000 ekin = 0.137812176400527 | erot = 0.377809252263535 | epot = -15.1580546737348 | etot = -14.6424332450707 +828000 ekin = 0.148430331610601 | erot = 0.368094906955077 | epot = -15.1589584837195 | etot = -14.6424332451538 +829000 ekin = 0.160453205764727 | erot = 0.359651737503703 | epot = -15.1625381885089 | etot = -14.6424332452404 +830000 ekin = 0.173291382900529 | erot = 0.351735589536635 | epot = -15.1674602177621 | etot = -14.642433245325 +831000 ekin = 0.186352012967339 | erot = 0.343644456321088 | epot = -15.17242971469 | etot = -14.6424332454015 +832000 ekin = 0.199074924610278 | erot = 0.334772487912379 | epot = -15.1762806579876 | etot = -14.6424332454649 +833000 ekin = 0.210968084885577 | erot = 0.324658115180513 | epot = -15.1780594455764 | etot = -14.6424332455103 +834000 ekin = 0.22163875726204 | erot = 0.313022323434694 | epot = -15.1770943262316 | etot = -14.6424332455348 +835000 ekin = 0.230816330006794 | erot = 0.299793483319765 | epot = -15.1730430588635 | etot = -14.6424332455369 +836000 ekin = 0.238363132178559 | erot = 0.285116039954826 | epot = -15.1659124176508 | etot = -14.6424332455174 +837000 ekin = 0.244270841534548 | erot = 0.269341751254572 | epot = -15.1560458382684 | etot = -14.6424332454793 +838000 ekin = 0.248642320238245 | erot = 0.253003904099761 | epot = -15.144079469765 | etot = -14.642433245427 +839000 ekin = 0.251661569328948 | erot = 0.236776758984022 | epot = -15.1308715736795 | etot = -14.6424332453665 +840000 ekin = 0.253557306828097 | erot = 0.221424057159249 | epot = -15.1174146092912 | etot = -14.6424332453038 +841000 ekin = 0.254567562695129 | erot = 0.20774147574213 | epot = -15.1047422836817 | etot = -14.6424332452444 +842000 ekin = 0.254912814680555 | erot = 0.196498262353486 | epot = -15.0938443222266 | etot = -14.6424332451926 +843000 ekin = 0.25478313076125 | erot = 0.188382921786766 | epot = -15.0855992976989 | etot = -14.6424332451509 +844000 ekin = 0.254340789692162 | erot = 0.183956927272162 | epot = -15.0807309620847 | etot = -14.6424332451204 +845000 ekin = 0.253734932885183 | erot = 0.183619247980868 | epot = -15.0797874259671 | etot = -14.6424332451011 +846000 ekin = 0.253120504189248 | erot = 0.187583282240197 | epot = -15.0831370315218 | etot = -14.6424332450923 +847000 ekin = 0.252671650081459 | erot = 0.195866742639432 | epot = -15.0909716378146 | etot = -14.6424332450937 +848000 ekin = 0.252580915304066 | erot = 0.208294222463377 | epot = -15.103308382873 | etot = -14.6424332451056 +849000 ekin = 0.253039966843089 | erot = 0.224511555531961 | epot = -15.1199847675035 | etot = -14.6424332451285 +850000 ekin = 0.254204001794782 | erot = 0.244010590097847 | epot = -15.1406478370558 | etot = -14.6424332451632 +851000 ekin = 0.256148339024743 | erot = 0.266162563602639 | epot = -15.1647441478372 | etot = -14.6424332452098 +852000 ekin = 0.258829686440357 | erot = 0.290257858698255 | epot = -15.1915207904057 | etot = -14.6424332452671 +853000 ekin = 0.262064657830147 | erot = 0.315549558167899 | epot = -15.2200474613301 | etot = -14.642433245332 +854000 ekin = 0.265534116125842 | erot = 0.341297947736774 | epot = -15.2492653092626 | etot = -14.6424332454 +855000 ekin = 0.268815174658127 | erot = 0.36681300443161 | epot = -15.2780614245547 | etot = -14.642433245465 +856000 ekin = 0.271435486960143 | erot = 0.391492007902569 | epot = -15.3053607403836 | etot = -14.6424332455209 +857000 ekin = 0.272939108069131 | erot = 0.414849750475003 | epot = -15.3302221041064 | etot = -14.6424332455623 +858000 ekin = 0.272951155046072 | erot = 0.436539390690098 | epot = -15.3519237913214 | etot = -14.6424332455852 +859000 ekin = 0.271229880682515 | erot = 0.456362750061876 | epot = -15.3700258763321 | etot = -14.6424332455877 +860000 ekin = 0.267698633839345 | erot = 0.474269718463609 | epot = -15.3844015978732 | etot = -14.6424332455702 +861000 ekin = 0.262455001757423 | erot = 0.490347316011031 | epot = -15.3952355633033 | etot = -14.6424332455349 +862000 ekin = 0.255758797180063 | erot = 0.504799761302306 | epot = -15.4029918039677 | etot = -14.6424332454854 +863000 ekin = 0.248003564343451 | erot = 0.517921532815844 | epot = -15.4083583425857 | etot = -14.6424332454264 +864000 ekin = 0.239677655585439 | erot = 0.530065823506495 | epot = -15.412176724455 | etot = -14.642433245363 +865000 ekin = 0.23132088944446 | erot = 0.541610953536998 | epot = -15.4153650882816 | etot = -14.6424332453002 +866000 ekin = 0.223481813673878 | erot = 0.552927233334005 | epot = -15.41884229225 | etot = -14.6424332452421 +867000 ekin = 0.216679174488124 | erot = 0.564346499433549 | epot = -15.4234589191144 | etot = -14.6424332451927 +868000 ekin = 0.211369750013082 | erot = 0.576136138939065 | epot = -15.4299391341069 | etot = -14.6424332451547 +869000 ekin = 0.207923502302006 | erot = 0.588478941150607 | epot = -15.4388356885827 | etot = -14.64243324513 +870000 ekin = 0.206606152993159 | erot = 0.601459626888393 | epot = -15.4504990250012 | etot = -14.6424332451197 +871000 ekin = 0.207568796750574 | erot = 0.615058451102447 | epot = -15.4650604929769 | etot = -14.6424332451239 +872000 ekin = 0.210843969893514 | erot = 0.629151875755212 | epot = -15.4824290907906 | etot = -14.6424332451419 +873000 ekin = 0.216347593110671 | erot = 0.643519970828197 | epot = -15.5023008091114 | etot = -14.6424332451726 +874000 ekin = 0.223886305134761 | erot = 0.65785990972427 | epot = -15.5241794600729 | etot = -14.6424332452139 +875000 ekin = 0.233169807544781 | erot = 0.671804662203727 | epot = -15.5474077150118 | etot = -14.6424332452633 +876000 ekin = 0.243827877955837 | erot = 0.684945735792129 | epot = -15.5712068590658 | etot = -14.6424332453179 +877000 ekin = 0.255431632539029 | erot = 0.69685856734628 | epot = -15.5947234452596 | etot = -14.6424332453743 +878000 ekin = 0.267518408507424 | erot = 0.707128927380235 | epot = -15.6170805813169 | etot = -14.6424332454292 +879000 ekin = 0.279619300254511 | erot = 0.715378495712557 | epot = -15.6374310414462 | etot = -14.6424332454792 +880000 ekin = 0.291287955017456 | erot = 0.721287639190631 | epot = -15.6550088397293 | etot = -14.6424332455213 +881000 ekin = 0.302128778463176 | erot = 0.724613422802369 | epot = -15.6691754468184 | etot = -14.6424332455529 +882000 ekin = 0.311822304069024 | erot = 0.725201068168812 | epot = -15.6794566178103 | etot = -14.6424332455725 +883000 ekin = 0.320145243789556 | erot = 0.722987481096488 | epot = -15.6855659704653 | etot = -14.6424332455793 +884000 ekin = 0.326982762202337 | erot = 0.717996120151906 | epot = -15.6874121279283 | etot = -14.642433245574 +885000 ekin = 0.332330882217347 | erot = 0.710323349665211 | epot = -15.6850874774409 | etot = -14.6424332455584 +886000 ekin = 0.336287673337102 | erot = 0.700117442969765 | epot = -15.6788383618422 | etot = -14.6424332455353 +887000 ekin = 0.33903296415872 | erot = 0.687552454430858 | epot = -15.6690186640981 | etot = -14.6424332455086 +888000 ekin = 0.340797654552155 | erot = 0.67280010093964 | epot = -15.6560310009741 | etot = -14.6424332454823 +889000 ekin = 0.341825106167166 | erot = 0.656003407096678 | epot = -15.6402617587246 | etot = -14.6424332454608 +890000 ekin = 0.342328347583419 | erot = 0.637256013160556 | epot = -15.6220176061914 | etot = -14.6424332454474 +891000 ekin = 0.342447730500021 | erot = 0.616590618565289 | epot = -15.6014715945102 | etot = -14.6424332454449 +892000 ekin = 0.342214057419104 | erot = 0.593979026501831 | epot = -15.5786263293753 | etot = -14.6424332454543 +893000 ekin = 0.34152200491664 | erot = 0.569344767729407 | epot = -15.5533000181212 | etot = -14.6424332454752 +894000 ekin = 0.340117934122997 | erot = 0.542587519912816 | epot = -15.525138699541 | etot = -14.6424332455052 +895000 ekin = 0.337605044786637 | erot = 0.513616778977938 | epot = -15.4936550693051 | etot = -14.6424332455405 +896000 ekin = 0.333467462875054 | erot = 0.48239077517223 | epot = -15.4582914836235 | etot = -14.6424332455762 +897000 ekin = 0.327113397523327 | erot = 0.448955709001807 | epot = -15.4185023521314 | etot = -14.6424332456062 +898000 ekin = 0.317936017621265 | erot = 0.413480165458539 | epot = -15.3738494287041 | etot = -14.6424332456243 +899000 ekin = 0.305389123795979 | erot = 0.376280077469313 | epot = -15.3241024468894 | etot = -14.6424332456241 +900000 ekin = 0.289072881395148 | erot = 0.337830752319287 | epot = -15.2693368793143 | etot = -14.6424332455999 +901000 ekin = 0.268822686259622 | erot = 0.298764046957452 | epot = -15.2100199787646 | etot = -14.6424332455475 +902000 ekin = 0.244791653968919 | erot = 0.259850521118035 | epot = -15.1470754205513 | etot = -14.6424332454644 +903000 ekin = 0.217514571462472 | erot = 0.221968047210473 | epot = -15.0819158640236 | etot = -14.6424332453507 +904000 ekin = 0.187939204411346 | erot = 0.186059692012592 | epot = -15.0164321416341 | etot = -14.6424332452102 +905000 ekin = 0.157410847731204 | erot = 0.153084564883822 | epot = -14.9529286576653 | etot = -14.6424332450503 +906000 ekin = 0.127599356271268 | erot = 0.123965703545286 | epot = -14.8939983046991 | etot = -14.6424332448825 +907000 ekin = 0.100365589130667 | erot = 0.0995389863896931 | epot = -14.8423378202422 | etot = -14.6424332447218 +908000 ekin = 0.0775759855945855 | erot = 0.0805066337401435 | epot = -14.800515863919 | etot = -14.6424332445842 +909000 ekin = 0.0608876950034 | erot = 0.0673982354567511 | epot = -14.7707191749454 | etot = -14.6424332444853 +910000 ekin = 0.0515382922989042 | erot = 0.0605415547706379 | epot = -14.7545130915067 | etot = -14.6424332444371 +911000 ekin = 0.0501789452911252 | erot = 0.0600446989620123 | epot = -14.7526568886991 | etot = -14.642433244446 +912000 ekin = 0.0567846925755769 | erot = 0.0657906450221707 | epot = -14.7650085821085 | etot = -14.6424332445108 +913000 ekin = 0.0706603747975489 | erot = 0.0774445361855688 | epot = -14.790538155607 | etot = -14.6424332446239 +914000 ekin = 0.0905398584143666 | erot = 0.0944735694282315 | epot = -14.8274466726145 | etot = -14.6424332447719 +915000 ekin = 0.114756144633904 | erot = 0.116178630204502 | epot = -14.8733680197774 | etot = -14.642433244939 +916000 ekin = 0.141447043407684 | erot = 0.141736093135102 | epot = -14.9256163816514 | etot = -14.6424332451087 +917000 ekin = 0.168758535424836 | erot = 0.170247440483737 | epot = -14.9814392211754 | etot = -14.6424332452668 +918000 ekin = 0.195014913443954 | erot = 0.200793639362701 | epot = -15.0382417982093 | etot = -14.6424332454026 +919000 ekin = 0.218837422087121 | erot = 0.232490666329554 | epot = -15.0937613339258 | etot = -14.6424332455091 +920000 ekin = 0.239206641026195 | erot = 0.264542267085039 | epot = -15.1461821536945 | etot = -14.6424332455832 +921000 ekin = 0.25547457715008 | erot = 0.296286050795184 | epot = -15.1941938735701 | etot = -14.6424332456248 +922000 ekin = 0.267338631216139 | erot = 0.327229363198297 | epot = -15.2370012400506 | etot = -14.6424332456361 +923000 ekin = 0.274791412213564 | erot = 0.357072039930916 | epot = -15.2742966977653 | etot = -14.6424332456208 +924000 ekin = 0.278059017514789 | erot = 0.385714059426418 | epot = -15.306206322525 | etot = -14.6424332455838 +925000 ekin = 0.277537405165931 | erot = 0.413247220089643 | epot = -15.333217870786 | etot = -14.6424332455304 +926000 ekin = 0.273733135235124 | erot = 0.439931173656047 | epot = -15.3560975543575 | etot = -14.6424332454664 +927000 ekin = 0.267211859637652 | erot = 0.466155363877246 | epot = -15.3758004689123 | etot = -14.6424332453974 +928000 ekin = 0.258555847531632 | erot = 0.492389553497958 | epot = -15.3933786463587 | etot = -14.6424332453291 +929000 ekin = 0.248330567886967 | erot = 0.519126582977394 | epot = -15.4098903961312 | etot = -14.6424332452668 +930000 ekin = 0.23705974716086 | erot = 0.546821711627624 | epot = -15.4263147040038 | etot = -14.6424332452153 +931000 ekin = 0.225208144800234 | erot = 0.575833282919438 | epot = -15.4434746728981 | etot = -14.6424332451784 +932000 ekin = 0.213171319360063 | erot = 0.606369490847652 | epot = -15.4619740553666 | etot = -14.6424332451589 +933000 ekin = 0.201271722990057 | erot = 0.638445690374705 | epot = -15.4821506585231 | etot = -14.6424332451583 +934000 ekin = 0.189760460104366 | erot = 0.67185600669489 | epot = -15.5040497119762 | etot = -14.6424332451769 +935000 ekin = 0.178823941832753 | erot = 0.706161996583042 | epot = -15.5274191836291 | etot = -14.6424332452133 +936000 ekin = 0.168594479109611 | erot = 0.74069986583281 | epot = -15.5517275902074 | etot = -14.642433245265 +937000 ekin = 0.159163635629916 | erot = 0.774606336201627 | epot = -15.5762032171597 | etot = -14.6424332453281 +938000 ekin = 0.150596971910416 | erot = 0.806861786791798 | epot = -15.5998920041003 | etot = -14.6424332453981 +939000 ekin = 0.142948711628538 | erot = 0.83634788352242 | epot = -15.6217298406206 | etot = -14.6424332454696 +940000 ekin = 0.136274889167971 | erot = 0.861915676024924 | epot = -15.6406238107303 | etot = -14.6424332455374 +941000 ekin = 0.130643703196498 | erot = 0.882459199117052 | epot = -15.6555361479098 | etot = -14.6424332455962 +942000 ekin = 0.126142088159105 | erot = 0.896989065169274 | epot = -15.66556439897 | etot = -14.6424332456417 +943000 ekin = 0.122877886109369 | erot = 0.904700444356692 | epot = -15.6700115761362 | etot = -14.6424332456702 +944000 ekin = 0.120977407412015 | erot = 0.905030230235472 | epot = -15.6684408833271 | etot = -14.6424332456797 +945000 ekin = 0.120578563691314 | erot = 0.897699054744981 | epot = -15.6607108641056 | etot = -14.6424332456693 +946000 ekin = 0.121820103594724 | erot = 0.882735070928503 | epot = -15.646988420163 | etot = -14.6424332456398 +947000 ekin = 0.124827761130805 | erot = 0.860477935596992 | epot = -15.6277389423211 | etot = -14.6424332455933 +948000 ekin = 0.129698334170726 | erot = 0.831563037038998 | epot = -15.6036946167428 | etot = -14.642433245533 +949000 ekin = 0.136482857560392 | erot = 0.796887554723542 | epot = -15.5758036577472 | etot = -14.6424332454633 +950000 ekin = 0.145170138933426 | erot = 0.757561255989732 | epot = -15.5451646403121 | etot = -14.642433245389 +951000 ekin = 0.155672002997215 | erot = 0.714845916095059 | epot = -15.5129511644075 | etot = -14.6424332453152 +952000 ekin = 0.167811650837965 | erot = 0.67008783325118 | epot = -15.480332729336 | etot = -14.6424332452469 +953000 ekin = 0.181316579472455 | erot = 0.624648095212333 | epot = -15.4483979198734 | etot = -14.6424332451886 +954000 ekin = 0.195817500701693 | erot = 0.579835080695355 | epot = -15.4180858265408 | etot = -14.6424332451437 +955000 ekin = 0.210854606876419 | erot = 0.536843219767442 | epot = -15.3901310717585 | etot = -14.6424332451147 +956000 ekin = 0.22589229983617 | erot = 0.496701376789191 | epot = -15.3650269217278 | etot = -14.6424332451025 +957000 ekin = 0.240343066496498 | erot = 0.460233438090612 | epot = -15.3430097496938 | etot = -14.6424332451067 +958000 ekin = 0.253600493836355 | erot = 0.428032849889929 | epot = -15.3240665888515 | etot = -14.6424332451252 +959000 ekin = 0.265080433744447 | erot = 0.400452005453988 | epot = -15.3079656843532 | etot = -14.6424332451548 +960000 ekin = 0.274268068126047 | erot = 0.37760654944402 | epot = -15.294307862761 | etot = -14.6424332451909 +961000 ekin = 0.280767177998564 | erot = 0.359393861243516 | epot = -15.2825942844706 | etot = -14.6424332452285 +962000 ekin = 0.284346484058158 | erot = 0.34552419881024 | epot = -15.2723039281308 | etot = -14.6424332452624 +963000 ekin = 0.284976816084592 | erot = 0.335562232322765 | epot = -15.2629722936953 | etot = -14.6424332452879 +964000 ekin = 0.282852494243092 | erot = 0.328975986490651 | epot = -15.2542617260353 | etot = -14.6424332453015 +965000 ekin = 0.278391086611333 | erot = 0.325189577593016 | epot = -15.2460139095058 | etot = -14.6424332453015 +966000 ekin = 0.272207924676324 | erot = 0.323635640145639 | epot = -15.2382768101098 | etot = -14.6424332452879 +967000 ekin = 0.265065367868708 | erot = 0.323803079983033 | epot = -15.2313016931144 | etot = -14.6424332452627 +968000 ekin = 0.257801293713459 | erot = 0.325275872287221 | epot = -15.2255104112304 | etot = -14.6424332452297 +969000 ekin = 0.251245661475255 | erot = 0.327759142573571 | epot = -15.2214380492424 | etot = -14.6424332451936 +970000 ekin = 0.246137008995617 | erot = 0.331089781179348 | epot = -15.2196600353345 | etot = -14.6424332451595 +971000 ekin = 0.243051319619918 | erot = 0.335230325664218 | epot = -15.220714890416 | etot = -14.6424332451318 +972000 ekin = 0.242353409643632 | erot = 0.340246678804405 | epot = -15.2250333335622 | etot = -14.6424332451142 +973000 ekin = 0.2441763381681 | erot = 0.346272190710886 | epot = -15.2328817739879 | etot = -14.642433245109 +974000 ekin = 0.248428661663904 | erot = 0.353462430362299 | epot = -15.2443243371435 | etot = -14.6424332451173 +975000 ekin = 0.254824314808745 | erot = 0.361946299431111 | epot = -15.2592038593792 | etot = -14.6424332451394 +976000 ekin = 0.26292684882563 | erot = 0.371779749930331 | epot = -15.2771398439303 | etot = -14.6424332451743 +977000 ekin = 0.27219923533505 | erot = 0.382908123264369 | epot = -15.29754060382 | etot = -14.6424332452206 +978000 ekin = 0.282052066854694 | erot = 0.395142048097406 | epot = -15.3196273602282 | etot = -14.6424332452761 +979000 ekin = 0.291885751915604 | erot = 0.408150081470976 | epot = -15.3424690787245 | etot = -14.6424332453379 +980000 ekin = 0.301125083790157 | erot = 0.421469125221772 | epot = -15.3650274544147 | etot = -14.6424332454028 +981000 ekin = 0.309246535916217 | erot = 0.434531423655031 | epot = -15.3862112050381 | etot = -14.6424332454669 +982000 ekin = 0.315799497488439 | erot = 0.446704965614828 | epot = -15.4049377086292 | etot = -14.642433245526 +983000 ekin = 0.320422573217629 | erot = 0.457342632741568 | epot = -15.4201984515353 | etot = -14.6424332455761 +984000 ekin = 0.322855465254252 | erot = 0.465834622596749 | epot = -15.4311233334646 | etot = -14.6424332456136 +985000 ekin = 0.322946302470394 | erot = 0.47165859097122 | epot = -15.4370381390773 | etot = -14.6424332456357 +986000 ekin = 0.320653917800696 | erot = 0.474422556587648 | epot = -15.437509720029 | etot = -14.6424332456406 +987000 ekin = 0.31604462735714 | erot = 0.473896755512796 | epot = -15.4323746284979 | etot = -14.642433245628 +988000 ekin = 0.309283477263999 | erot = 0.470032116942454 | epot = -15.4217488398048 | etot = -14.6424332455984 +989000 ekin = 0.300620522164939 | erot = 0.462964620619315 | epot = -15.406018388338 | etot = -14.6424332455537 +990000 ekin = 0.290373280687637 | erot = 0.453006262992374 | epot = -15.3858127891766 | etot = -14.6424332454965 +991000 ekin = 0.278906915702925 | erot = 0.440624526216757 | epot = -15.3619646873499 | etot = -14.6424332454302 +992000 ekin = 0.266613826413316 | erot = 0.42641300688875 | epot = -15.3354600786602 | etot = -14.6424332453582 +993000 ekin = 0.253894212445666 | erot = 0.411056197521998 | epot = -15.3073836552517 | etot = -14.6424332452841 +994000 ekin = 0.241138837000196 | erot = 0.395291372385701 | epot = -15.2788634545969 | etot = -14.642433245211 +995000 ekin = 0.228714768908018 | erot = 0.379870207852185 | epot = -15.2510182219023 | etot = -14.6424332451421 +996000 ekin = 0.216954417472331 | erot = 0.365522282703969 | epot = -15.2249099452561 | etot = -14.6424332450798 +997000 ekin = 0.206147766458768 | erot = 0.352922066134627 | epot = -15.2015030776195 | etot = -14.6424332450261 +998000 ekin = 0.196537413161314 | erot = 0.34266049598664 | epot = -15.1816311541306 | etot = -14.6424332449827 +999000 ekin = 0.188315843917132 | erot = 0.335221830000276 | epot = -15.1659709188677 | etot = -14.6424332449503 +1000000 ekin = 0.181624323072266 | erot = 0.330966139643081 | epot = -15.1550237076453 | etot = -14.6424332449299 + 1000000 0.013453654 -1.5270261 0.011523695 -1.4973399 -8.4815516e-05 +Loop time of 18.9591 on 1 procs for 1000000 steps with 10 atoms + +Performance: 45571.887 tau/day, 52745.239 timesteps/s +98.5% CPU use with 1 MPI tasks x no OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 15.272 | 15.272 | 15.272 | 0.0 | 80.55 +Bond | 0.58511 | 0.58511 | 0.58511 | 0.0 | 3.09 +Neigh | 0 | 0 | 0 | 0.0 | 0.00 +Comm | 0.19027 | 0.19027 | 0.19027 | 0.0 | 1.00 +Output | 8e-06 | 8e-06 | 8e-06 | 0.0 | 0.00 +Modify | 2.6225 | 2.6225 | 2.6225 | 0.0 | 13.83 +Other | | 0.2893 | | | 1.53 + +Nlocal: 10 ave 10 max 10 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 0 ave 0 max 0 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 43 ave 43 max 43 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 43 +Ave neighs/atom = 4.3 +Ave special neighs/atom = 3.6 +Neighbor list builds = 0 +Dangerous builds = 0 + +#write_restart config.${number}.* +Total wall time: 0:00:18 diff --git a/examples/USER/cgdna/examples/oxDNA/duplex1/log.18Jun19.duplex1.g++.4 b/examples/USER/cgdna/examples/oxDNA/duplex1/log.18Jun19.duplex1.g++.4 new file mode 100644 index 0000000000..59800043d3 --- /dev/null +++ b/examples/USER/cgdna/examples/oxDNA/duplex1/log.18Jun19.duplex1.g++.4 @@ -0,0 +1,1165 @@ +LAMMPS (18 Jun 2019) +variable number equal 1 +variable ofreq equal 1000 +variable efreq equal 1000 +variable T equal 0.1 + +units lj + +dimension 3 + +newton off + +boundary p p p + +atom_style hybrid bond ellipsoid +atom_modify sort 0 1.0 + +# Pair interactions require lists of neighbours to be calculated +neighbor 1.0 bin +neigh_modify every 1 delay 0 check yes + +read_data data.duplex1 + orthogonal box = (-20 -20 -20) to (20 20 20) + 1 by 2 by 2 MPI processor grid + reading atoms ... + 10 atoms + reading velocities ... + 10 velocities + 10 ellipsoids + scanning bonds ... + 2 = max bonds/atom + reading bonds ... + 8 bonds + 2 = max # of 1-2 neighbors + 2 = max # of 1-3 neighbors + 2 = max # of 1-4 neighbors + 4 = max # of special neighbors + special bonds CPU = 0.000462 secs + read_data CPU = 0.004857 secs + +set atom * mass 3.1575 + 10 settings made for mass + +group all type 1 4 +10 atoms in group all + +# oxDNA bond interactions - FENE backbone +bond_style oxdna/fene +bond_coeff * 2.0 0.25 0.7525 + +# oxDNA pair interactions +pair_style hybrid/overlay oxdna/excv oxdna/stk oxdna/hbond oxdna/xstk oxdna/coaxstk +pair_coeff * * oxdna/excv 2.0 0.7 0.675 2.0 0.515 0.5 2.0 0.33 0.32 +pair_coeff * * oxdna/stk seqav ${T} 1.3448 2.6568 6.0 0.4 0.9 0.32 0.6 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2.0 0.65 2.0 0.65 +pair_coeff * * oxdna/stk seqav 0.1 1.3448 2.6568 6.0 0.4 0.9 0.32 0.6 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2.0 0.65 2.0 0.65 +pair_coeff * * oxdna/hbond seqav 0.0 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45 +pair_coeff 1 4 oxdna/hbond seqav 1.077 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45 +pair_coeff 2 3 oxdna/hbond seqav 1.077 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45 +pair_coeff * * oxdna/xstk 47.5 0.575 0.675 0.495 0.655 2.25 0.791592653589793 0.58 1.7 1.0 0.68 1.7 1.0 0.68 1.5 0 0.65 1.7 0.875 0.68 1.7 0.875 0.68 +pair_coeff * * oxdna/coaxstk 46.0 0.4 0.6 0.22 0.58 2.0 2.541592653589793 0.65 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2.0 -0.65 2.0 -0.65 + +# NVE ensemble +fix 1 all nve/dot +#fix 1 all nve/dotc/langevin ${T} ${T} 0.03 457145 angmom 10 +#fix 1 all nve/asphere +#fix 2 all langevin ${T} ${T} 0.03 457145 angmom 10 + +timestep 1e-5 + +#comm_style tiled +#fix 3 all balance 10000 1.1 rcb + +#compute mol all chunk/atom molecule +#compute mychunk all vcm/chunk mol +#fix 4 all ave/time 10000 1 10000 c_mychunk[1] c_mychunk[2] c_mychunk[3] file vcm.txt mode vector + +#dump pos all xyz ${ofreq} traj.${number}.xyz + +#compute quat all property/atom quatw quati quatj quatk +#dump quat all custom ${ofreq} quat.${number}.txt id c_quat[1] c_quat[2] c_quat[3] c_quat[4] +#dump_modify quat sort id +#dump_modify quat format line "%d %13.6le %13.6le %13.6le %13.6le" + +compute erot all erotate/asphere +compute ekin all ke +compute epot all pe +variable erot equal c_erot +variable ekin equal c_ekin +variable epot equal c_epot +variable etot equal c_erot+c_ekin+c_epot +fix 5 all print ${efreq} "$(step) ekin = ${ekin} | erot = ${erot} | epot = ${epot} | etot = ${etot}" screen yes +fix 5 all print 1000 "$(step) ekin = ${ekin} | erot = ${erot} | epot = ${epot} | etot = ${etot}" screen yes + +#dump out all custom ${ofreq} out.${number}.txt id x y z vx vy vz fx fy fz tqx tqy tqz +#dump_modify out sort id +#dump_modify out format line "%d %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le" + +run 1000000 +Neighbor list info ... + update every 1 steps, delay 0 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 1.92828 + ghost atom cutoff = 1.92828 + binsize = 0.964142, bins = 42 42 42 + 5 neighbor lists, perpetual/occasional/extra = 5 0 0 + (1) pair oxdna/excv, perpetual + attributes: half, newton off + pair build: half/bin/newtoff + stencil: half/bin/3d/newtoff + bin: standard + (2) pair oxdna/stk, perpetual, copy from (1) + attributes: half, newton off + pair build: copy + stencil: none + bin: none + (3) pair oxdna/hbond, perpetual, copy from (1) + attributes: half, newton off + pair build: copy + stencil: none + bin: none + (4) pair oxdna/xstk, perpetual, copy from (1) + attributes: half, newton off + pair build: copy + stencil: none + bin: none + (5) pair oxdna/coaxstk, perpetual, copy from (1) + attributes: half, newton off + pair build: copy + stencil: none + bin: none +Per MPI rank memory allocation (min/avg/max) = 7.341 | 7.523 | 7.705 Mbytes +Step Temp E_pair E_mol TotEng Press + 0 0 -1.4711818 0.0069384985 -1.4642433 2.5836586e-06 +1000 ekin = 0.00113448721737009 | erot = 0.0041345594773427 | epot = -14.6477022915193 | etot = -14.6424332448246 +2000 ekin = 0.00449927223902292 | erot = 0.0164446434455803 | epot = -14.6633771605337 | etot = -14.6424332448491 +3000 ekin = 0.00997964450840756 | erot = 0.0366523356056466 | epot = -14.6890652250033 | etot = -14.6424332448892 +4000 ekin = 0.017388811129498 | erot = 0.0643039804300251 | epot = -14.7241260365031 | etot = -14.6424332449436 +5000 ekin = 0.0264744514136422 | erot = 0.0987844033142134 | epot = -14.7676920997383 | etot = -14.6424332450104 +6000 ekin = 0.0369277948555727 | erot = 0.13933657105258 | epot = -14.8186976109956 | etot = -14.6424332450875 +7000 ekin = 0.0483950557190949 | erot = 0.18508629569211 | epot = -14.8759145965832 | etot = -14.642433245172 +8000 ekin = 0.0604909336919856 | erot = 0.235071307523581 | epot = -14.9379954864767 | etot = -14.6424332452611 +9000 ekin = 0.0728137406439518 | erot = 0.288273694501614 | epot = -15.003520680497 | etot = -14.6424332453514 +10000 ekin = 0.0849615563084574 | erot = 0.343654369293588 | epot = -15.0710491710418 | etot = -14.6424332454398 +11000 ekin = 0.0965486715044103 | erot = 0.400187932108392 | epot = -15.1391698491357 | etot = -14.6424332455229 +12000 ekin = 0.107221466282716 | erot = 0.456896095459393 | epot = -15.2065508073401 | etot = -14.642433245598 +13000 ekin = 0.116672809719361 | erot = 0.512877765427946 | epot = -15.27198382081 | etot = -14.6424332456627 +14000 ekin = 0.124654073730849 | erot = 0.567333962045503 | epot = -15.3344212814915 | etot = -14.6424332457151 +15000 ekin = 0.130983939684084 | erot = 0.619586028257146 | epot = -15.3930032136957 | etot = -14.6424332457544 +16000 ekin = 0.135553354544703 | erot = 0.66908602849033 | epot = -15.4470726288154 | etot = -14.6424332457804 +17000 ekin = 0.138326263958104 | erot = 0.715418858086103 | epot = -15.4961783678378 | etot = -14.6424332457936 +18000 ekin = 0.139336096663942 | erot = 0.758296324628468 | epot = -15.5400656670878 | etot = -14.6424332457954 +19000 ekin = 0.138678360045107 | erot = 0.797544234276629 | epot = -15.5786558401095 | etot = -14.6424332457878 +20000 ekin = 0.136500074655344 | erot = 0.83308420441182 | epot = -15.6120175248401 | etot = -14.642433245773 +21000 ekin = 0.13298706528568 | erot = 0.864912408453368 | epot = -15.6403327194924 | etot = -14.6424332457533 +22000 ekin = 0.128350288213599 | erot = 0.893077649558725 | epot = -15.6638611835035 | etot = -14.6424332457311 +23000 ekin = 0.122812385135574 | erot = 0.917661024684598 | epot = -15.6829066555285 | etot = -14.6424332457083 +24000 ekin = 0.116595521408358 | erot = 0.938759014332585 | epot = -15.6977877814273 | etot = -14.6424332456863 +25000 ekin = 0.109911323474882 | erot = 0.95647120734756 | epot = -15.7088157764886 | etot = -14.6424332456662 +26000 ekin = 0.102953426207684 | erot = 0.970893163953299 | epot = -15.7162798358093 | etot = -14.6424332456483 +27000 ekin = 0.0958928250746602 | erot = 0.982114250193902 | epot = -15.7204403209011 | etot = -14.6424332456326 +28000 ekin = 0.08887594109497 | erot = 0.990219731539409 | epot = -15.721528918253 | etot = -14.6424332456186 +29000 ekin = 0.0820250748771992 | erot = 0.995296041202176 | epot = -15.7197543616852 | etot = -14.6424332456058 +30000 ekin = 0.0754407616837525 | erot = 0.997437949319921 | epot = -15.7153119565969 | etot = -14.6424332455933 +31000 ekin = 0.0692054432607511 | erot = 0.996756332760935 | epot = -15.708395021602 | etot = -14.6424332455803 +32000 ekin = 0.0633878377974532 | erot = 0.993385345347625 | epot = -15.6992064287111 | etot = -14.6424332455661 +33000 ekin = 0.0580474070866977 | erot = 0.987487973308193 | epot = -15.6879686259451 | etot = -14.6424332455502 +34000 ekin = 0.0532383791882916 | erot = 0.979259192919847 | epot = -15.6749308176403 | etot = -14.6424332455322 +35000 ekin = 0.0490128758302373 | erot = 0.96892619740531 | epot = -15.6603723187477 | etot = -14.6424332455122 +36000 ekin = 0.0454228081405034 | erot = 0.956745409624112 | epot = -15.6446014632554 | etot = -14.6424332454908 +37000 ekin = 0.0425203357170931 | erot = 0.942996237999014 | epot = -15.6279498191848 | etot = -14.6424332454687 +38000 ekin = 0.0403568280944582 | erot = 0.927971766615185 | epot = -15.6107618401563 | etot = -14.6424332454467 +39000 ekin = 0.0389804214208553 | erot = 0.911966804108842 | epot = -15.5933804709559 | etot = -14.6424332454262 +40000 ekin = 0.0384324238853386 | erot = 0.89526395956212 | epot = -15.5761296288558 | etot = -14.6424332454083 +41000 ekin = 0.0387429860406854 | erot = 0.878118672837898 | epot = -15.559294904273 | etot = -14.6424332453944 +42000 ekin = 0.0399266053637397 | erot = 0.860744395135588 | epot = -15.543104245885 | etot = -14.6424332453857 +43000 ekin = 0.041978156101278 | erot = 0.84329936535652 | epot = -15.5277107668409 | etot = -14.6424332453831 +44000 ekin = 0.044870189409001 | erot = 0.825876603313516 | epot = -15.5131800381094 | etot = -14.6424332453868 +45000 ekin = 0.0485521857416513 | erot = 0.808498758186241 | epot = -15.4994841893249 | etot = -14.642433245397 +46000 ekin = 0.0529522094038552 | erot = 0.791119212188506 | epot = -15.486504667005 | etot = -14.6424332454127 +47000 ekin = 0.0579809824244721 | erot = 0.773630265884098 | epot = -15.4740444937409 | etot = -14.6424332454323 +48000 ekin = 0.0635377846502182 | erot = 0.755878310838203 | epot = -15.4618493409424 | etot = -14.6424332454539 +49000 ekin = 0.0695169124467202 | erot = 0.737684732484798 | epot = -15.4496348904071 | etot = -14.6424332454756 +50000 ekin = 0.0758129058465097 | erot = 0.718870126220151 | epot = -15.437116277562 | etot = -14.6424332454953 +51000 ekin = 0.0823226638652294 | erot = 0.699278599520714 | epot = -15.424034508898 | etot = -14.642433245512 +52000 ekin = 0.0889431481344998 | erot = 0.67879880710002 | epot = -15.4101752007595 | etot = -14.642433245525 +53000 ekin = 0.0955646689265025 | erot = 0.657379086771117 | epot = -15.3953770012321 | etot = -14.6424332455345 +54000 ekin = 0.10206147751016 | erot = 0.635035489169276 | epot = -15.3795302122208 | etot = -14.6424332455414 +55000 ekin = 0.108282960174665 | erot = 0.611853171347244 | epot = -15.362569377068 | etot = -14.6424332455461 +56000 ekin = 0.114049426282277 | erot = 0.587982945924297 | epot = -15.3444656177552 | etot = -14.6424332455486 +57000 ekin = 0.119155806187163 | erot = 0.563635255922951 | epot = -15.3252243076589 | etot = -14.6424332455488 +58000 ekin = 0.123384552305545 | erot = 0.539073355222428 | epot = -15.3048911530734 | etot = -14.6424332455454 +59000 ekin = 0.126526300954853 | erot = 0.514606324858911 | epot = -15.2835658713509 | etot = -14.6424332455371 +60000 ekin = 0.128404399836229 | erot = 0.490581338840044 | epot = -15.261418984199 | etot = -14.6424332455227 +61000 ekin = 0.128898142361897 | erot = 0.467373892400972 | epot = -15.2387052802646 | etot = -14.6424332455018 +62000 ekin = 0.127959880289726 | erot = 0.445374820086222 | epot = -15.2157679458511 | etot = -14.6424332454752 +63000 ekin = 0.125622870624277 | erot = 0.424973765387148 | epot = -15.1930298814554 | etot = -14.642433245444 +64000 ekin = 0.121999044842466 | erot = 0.406539918572074 | epot = -15.1709722088251 | etot = -14.6424332454105 +65000 ekin = 0.117268056618551 | erot = 0.390401831020312 | epot = -15.1501031330161 | etot = -14.6424332453772 +66000 ekin = 0.11166038525652 | erot = 0.376828594078856 | epot = -15.1309222246818 | etot = -14.6424332453464 +67000 ekin = 0.105437746904482 | erot = 0.366014539811009 | epot = -15.1138855320359 | etot = -14.6424332453204 +68000 ekin = 0.0988737375602389 | erot = 0.358069014155077 | epot = -15.0993759970158 | etot = -14.6424332453005 +69000 ekin = 0.0922368286498126 | erot = 0.353011948771943 | epot = -15.0876820227093 | etot = -14.6424332452876 +70000 ekin = 0.0857769015271899 | erot = 0.350775174164931 | epot = -15.078985320974 | etot = -14.6424332452819 +71000 ekin = 0.0797156921641249 | erot = 0.351208844245481 | epot = -15.0733577816927 | etot = -14.6424332452831 +72000 ekin = 0.0742409440407228 | erot = 0.354092037747166 | epot = -15.0707662270784 | etot = -14.6424332452906 +73000 ekin = 0.069503749870388 | erot = 0.359146526961232 | epot = -15.0710835221349 | etot = -14.6424332453033 +74000 ekin = 0.065618449742691 | erot = 0.366052769878692 | epot = -15.0741044649412 | etot = -14.6424332453199 +75000 ekin = 0.0626644690394284 | erot = 0.374467290033975 | epot = -15.0795650044124 | etot = -14.642433245339 +76000 ekin = 0.0606895535091863 | erot = 0.384040683403432 | epot = -15.087163482272 | etot = -14.6424332453594 +77000 ekin = 0.0597139401241188 | erot = 0.394435495892894 | epot = -15.0965826813962 | etot = -14.6424332453792 +78000 ekin = 0.0597350629875199 | erot = 0.405343151481916 | epot = -15.107511459867 | etot = -14.6424332453975 +79000 ekin = 0.0607324264361021 | erot = 0.4164990176427 | epot = -15.1196646894919 | etot = -14.6424332454131 +80000 ekin = 0.0626722904954161 | erot = 0.427694630238743 | epot = -15.1328001661592 | etot = -14.6424332454251 +81000 ekin = 0.0655118235331528 | erot = 0.438786127849131 | epot = -15.1467311968152 | etot = -14.6424332454329 +82000 ekin = 0.0692024020836604 | erot = 0.449698113830624 | epot = -15.1613337613509 | etot = -14.6424332454366 +83000 ekin = 0.0736917936904884 | erot = 0.460422490740831 | epot = -15.1765475298676 | etot = -14.6424332454363 +84000 ekin = 0.0789250526542207 | erot = 0.471012272295187 | epot = -15.1923705703823 | etot = -14.6424332454329 +85000 ekin = 0.0848440878742484 | erot = 0.481570908650517 | epot = -15.2088482419521 | etot = -14.6424332454273 +86000 ekin = 0.0913860133243867 | erot = 0.492238169206351 | epot = -15.2260574279515 | etot = -14.6424332454207 +87000 ekin = 0.0984805441186007 | erot = 0.503174014617495 | epot = -15.2440878041506 | etot = -14.6424332454146 +88000 ekin = 0.106046830302566 | erot = 0.514542076496893 | epot = -15.2630221522094 | etot = -14.6424332454099 +89000 ekin = 0.113990204125935 | erot = 0.526494309539958 | epot = -15.2829177590739 | etot = -14.642433245408 +90000 ekin = 0.122199339149549 | erot = 0.539158097286396 | epot = -15.3037906818453 | etot = -14.6424332454094 +91000 ekin = 0.130544275968789 | erot = 0.552626637866402 | epot = -15.3256041592497 | etot = -14.6424332454146 +92000 ekin = 0.138875666145969 | erot = 0.566952900962838 | epot = -15.3482618125326 | etot = -14.6424332454238 +93000 ekin = 0.14702544061161 | erot = 0.582146933738122 | epot = -15.3716056197866 | etot = -14.6424332454369 +94000 ekin = 0.154808946844654 | erot = 0.598175891801918 | epot = -15.3954180841001 | etot = -14.6424332454535 +95000 ekin = 0.162028449598908 | erot = 0.614965942454569 | epot = -15.4194276375267 | etot = -14.6424332454732 +96000 ekin = 0.168477779664562 | erot = 0.632405154082769 | epot = -15.4433161792427 | etot = -14.6424332454953 +97000 ekin = 0.173947863023519 | erot = 0.650346631629065 | epot = -15.466727740172 | etot = -14.6424332455194 +98000 ekin = 0.178232875001165 | erot = 0.668611435746703 | epot = -15.4892775562927 | etot = -14.6424332455449 +99000 ekin = 0.181136831923469 | erot = 0.686991165056991 | epot = -15.5105612425515 | etot = -14.6424332455711 +100000 ekin = 0.182480533640974 | erot = 0.705250413408614 | epot = -15.530164192647 | etot = -14.6424332455974 +101000 ekin = 0.182108871449632 | erot = 0.723129571004103 | epot = -15.5476716880769 | etot = -14.6424332456232 +102000 ekin = 0.179898581168339 | erot = 0.740348571091352 | epot = -15.5626803979071 | etot = -14.6424332456474 +103000 ekin = 0.17576651760657 | erot = 0.756612167827034 | epot = -15.5748119311029 | etot = -14.6424332456693 +104000 ekin = 0.169678431534372 | erot = 0.771617166852996 | epot = -15.5837288440748 | etot = -14.6424332456874 +105000 ekin = 0.161658036036246 | erot = 0.785061742963598 | epot = -15.5891530247003 | etot = -14.6424332457005 +106000 ekin = 0.151795867650305 | erot = 0.796656613426427 | epot = -15.5908857267839 | etot = -14.6424332457071 +107000 ekin = 0.140257112952978 | erot = 0.806137449199291 | epot = -15.5888278078584 | etot = -14.6424332457061 +108000 ekin = 0.127287240201874 | erot = 0.813277564483374 | epot = -15.5829980503819 | etot = -14.6424332456966 +109000 ekin = 0.113214025491877 | erot = 0.817899691736857 | epot = -15.5735469629067 | etot = -14.642433245678 +110000 ekin = 0.0984444823817425 | erot = 0.819885578056442 | epot = -15.5607633060887 | etot = -14.6424332456505 +111000 ekin = 0.0834553769378644 | erot = 0.819182262548316 | epot = -15.5450708851012 | etot = -14.6424332456151 +112000 ekin = 0.0687764915886182 | erot = 0.815804215096852 | epot = -15.5270139522588 | etot = -14.6424332455734 +113000 ekin = 0.0549665904044371 | erot = 0.809830999846678 | epot = -15.507230835779 | etot = -14.6424332455279 +114000 ekin = 0.04258305831357 | erot = 0.801400700352889 | epot = -15.486417004148 | etot = -14.6424332454815 +115000 ekin = 0.0321472802146729 | erot = 0.790699910050576 | epot = -15.4652804357026 | etot = -14.6424332454374 +116000 ekin = 0.0241087780358441 | erot = 0.77795154667576 | epot = -15.4444935701102 | etot = -14.6424332453986 +117000 ekin = 0.0188117102739907 | erot = 0.763402004774545 | epot = -15.4246469604164 | etot = -14.6424332453678 +118000 ekin = 0.0164673894168237 | erot = 0.747309167856841 | epot = -15.4062098026205 | etot = -14.6424332453468 +119000 ekin = 0.0171359296540399 | erot = 0.72993256457469 | epot = -15.3895017395652 | etot = -14.6424332453364 +120000 ekin = 0.0207190822436548 | erot = 0.711526526248979 | epot = -15.3746788538292 | etot = -14.6424332453366 +121000 ekin = 0.0269649552324778 | erot = 0.692336677371657 | epot = -15.3617348779503 | etot = -14.6424332453462 +122000 ekin = 0.0354839220302051 | erot = 0.672599570211917 | epot = -15.3505167376055 | etot = -14.6424332453634 +123000 ekin = 0.0457738626455503 | erot = 0.652544850162978 | epot = -15.3407519581944 | etot = -14.6424332453859 +124000 ekin = 0.0572521324300892 | erot = 0.632399068063538 | epot = -15.3320844459047 | etot = -14.6424332454111 +125000 ekin = 0.0692913736007693 | erot = 0.612390156183436 | epot = -15.3241147752204 | etot = -14.6424332454362 +126000 ekin = 0.0812564128179015 | erot = 0.592751635107163 | epot = -15.3164412933838 | etot = -14.6424332454587 +127000 ekin = 0.0925398817831139 | erot = 0.573725774405781 | epot = -15.3086989016655 | etot = -14.6424332454766 +128000 ekin = 0.102594692019405 | erot = 0.555565138942023 | epot = -15.3005930764495 | etot = -14.6424332454881 +129000 ekin = 0.110961953874467 | erot = 0.538532171476875 | epot = -15.2919273708433 | etot = -14.6424332454919 +130000 ekin = 0.117293279473242 | erot = 0.52289666445288 | epot = -15.2826231894136 | etot = -14.6424332454874 +131000 ekin = 0.121366644775211 | erot = 0.508931150171171 | epot = -15.272731040421 | etot = -14.6424332454746 +132000 ekin = 0.123095155540088 | erot = 0.496904390905875 | epot = -15.2624327918998 | etot = -14.6424332454539 +133000 ekin = 0.122528239671731 | erot = 0.487073282997897 | epot = -15.2520347680959 | etot = -14.6424332454262 +134000 ekin = 0.119845042601891 | erot = 0.47967360117123 | epot = -15.2419518891664 | etot = -14.6424332453933 +135000 ekin = 0.115340171967418 | erot = 0.474910093717058 | epot = -15.2326835110415 | etot = -14.642433245357 +136000 ekin = 0.109402419285639 | erot = 0.472946484075354 | epot = -15.2247821486809 | etot = -14.6424332453199 +137000 ekin = 0.102487634022662 | erot = 0.473895929920083 | epot = -15.218816809227 | etot = -14.6424332452843 +138000 ekin = 0.0950874634054098 | erot = 0.477812435585943 | epot = -15.2153331442442 | etot = -14.6424332452528 +139000 ekin = 0.0876961121518108 | erot = 0.484683617751208 | epot = -15.2148129751311 | etot = -14.6424332452281 +140000 ekin = 0.0807775418435451 | erot = 0.494425108540545 | epot = -15.217635895596 | etot = -14.6424332452119 +141000 ekin = 0.0747355681580393 | erot = 0.506876770810791 | epot = -15.2240455841751 | etot = -14.6424332452063 +142000 ekin = 0.0698891098451726 | erot = 0.521800821241339 | epot = -15.2341231762987 | etot = -14.6424332452121 +143000 ekin = 0.0664544171867034 | erot = 0.538881922426252 | epot = -15.247769584843 | etot = -14.64243324523 +144000 ekin = 0.064535510469277 | erot = 0.557729316021967 | epot = -15.2646980717509 | etot = -14.6424332452596 +145000 ekin = 0.0641233595163659 | erot = 0.577881111413926 | epot = -15.2844377162305 | etot = -14.6424332453002 +146000 ekin = 0.065103607751629 | erot = 0.598810893852487 | epot = -15.3063477469542 | etot = -14.6424332453501 +147000 ekin = 0.0672719578975296 | erot = 0.619936843682188 | epot = -15.3296420469869 | etot = -14.6424332454072 +148000 ekin = 0.0703557492694474 | erot = 0.64063353819095 | epot = -15.3534225329292 | etot = -14.6424332454688 +149000 ekin = 0.0740398128645644 | erot = 0.660246523237392 | epot = -15.3767195816342 | etot = -14.6424332455323 +150000 ekin = 0.0779944201062649 | erot = 0.67810959037558 | epot = -15.3985372560763 | etot = -14.6424332455945 +151000 ekin = 0.0819030604176924 | erot = 0.693564488647308 | epot = -15.4179007947176 | etot = -14.6424332456526 +152000 ekin = 0.0854878938557652 | erot = 0.705982563002958 | epot = -15.4339037025624 | etot = -14.6424332457037 +153000 ekin = 0.0885310147333713 | erot = 0.714787575381071 | epot = -15.4457518358598 | etot = -14.6424332457454 +154000 ekin = 0.0908901012892559 | erot = 0.719478762726488 | epot = -15.4528021097913 | etot = -14.6424332457756 +155000 ekin = 0.0925075703719017 | erot = 0.719653046096719 | epot = -15.4545938622615 | etot = -14.6424332457929 +156000 ekin = 0.0934129479732407 | erot = 0.715025243753081 | epot = -15.4508714375228 | etot = -14.6424332457965 +157000 ekin = 0.0937187435781918 | erot = 0.70544516394557 | epot = -15.4415971533099 | etot = -14.6424332457861 +158000 ekin = 0.093610618539412 | erot = 0.690910554325135 | epot = -15.4269544186267 | etot = -14.6424332457622 +159000 ekin = 0.093333017400989 | erot = 0.671575051659432 | epot = -15.4073413147861 | etot = -14.6424332457257 +160000 ekin = 0.0931716565239226 | erot = 0.647750492120542 | epot = -15.3833553943224 | etot = -14.642433245678 +161000 ekin = 0.0934343296226242 | erot = 0.619903194016743 | epot = -15.3557707692603 | etot = -14.6424332456209 +162000 ekin = 0.0944314104796886 | erot = 0.588644098980031 | epot = -15.3255087550164 | etot = -14.6424332455567 +163000 ekin = 0.0964572425730171 | erot = 0.554712943454593 | epot = -15.2936034315153 | etot = -14.6424332454877 +164000 ekin = 0.0997733472794941 | erot = 0.518956918562839 | epot = -15.2611635112587 | etot = -14.6424332454164 +165000 ekin = 0.10459410201863 | erot = 0.482304549423526 | epot = -15.2293318967876 | etot = -14.6424332453454 +166000 ekin = 0.111075276514836 | erot = 0.445735768513645 | epot = -15.1992442903058 | etot = -14.6424332452774 +167000 ekin = 0.119305597512064 | erot = 0.410249354729672 | epot = -15.1719881974565 | etot = -14.6424332452148 +168000 ekin = 0.129301354723501 | erot = 0.376829046180125 | epot = -15.1485636460635 | etot = -14.6424332451599 +169000 ekin = 0.141003965788129 | erot = 0.346409702528434 | epot = -15.1298469134313 | etot = -14.6424332451147 +170000 ekin = 0.154280377438315 | erot = 0.319844892419163 | epot = -15.1165585149384 | etot = -14.642433245081 +171000 ekin = 0.168926178619937 | erot = 0.297877221607912 | epot = -15.1092366452878 | etot = -14.64243324506 +172000 ekin = 0.184671319362945 | erot = 0.281112611137957 | epot = -15.1082171755535 | etot = -14.6424332450526 +173000 ekin = 0.201188345435608 | erot = 0.269999595570643 | epot = -15.1136211860654 | etot = -14.6424332450591 +174000 ekin = 0.218103052205593 | erot = 0.264814547402958 | epot = -15.1253508446879 | etot = -14.6424332450793 +175000 ekin = 0.235007413034248 | erot = 0.26565354594967 | epot = -15.1430942040961 | etot = -14.6424332451122 +176000 ekin = 0.251474534266605 | erot = 0.272431389431399 | epot = -15.1663391688545 | etot = -14.6424332451565 +177000 ekin = 0.267075225142185 | erot = 0.284887984977542 | epot = -15.1943964553297 | etot = -14.64243324521 +178000 ekin = 0.281395553894086 | erot = 0.302602030913814 | epot = -15.2264308300784 | etot = -14.6424332452705 +179000 ekin = 0.294054514410706 | erot = 0.325011526056047 | epot = -15.2614992858018 | etot = -14.642433245335 +180000 ekin = 0.304720692895809 | erot = 0.351440214933843 | epot = -15.2985941532305 | etot = -14.6424332454008 +181000 ekin = 0.31312665891731 | erot = 0.381128639600658 | epot = -15.3366885439828 | etot = -14.6424332454648 +182000 ekin = 0.319079775822511 | erot = 0.413268071112237 | epot = -15.3747810924591 | etot = -14.6424332455244 +183000 ekin = 0.322468290004652 | erot = 0.447035301735071 | epot = -15.4119368373172 | etot = -14.6424332455774 +184000 ekin = 0.323261947553553 | erot = 0.481626155079182 | epot = -15.447321348255 | etot = -14.6424332456223 +185000 ekin = 0.321506983529694 | erot = 0.516285658867092 | epot = -15.4802258880547 | etot = -14.6424332456579 +186000 ekin = 0.317316057632528 | erot = 0.55033313262905 | epot = -15.5100824359457 | etot = -14.6424332456841 +187000 ekin = 0.310854440588901 | erot = 0.583180936762646 | epot = -15.5364686230527 | etot = -14.6424332457011 +188000 ekin = 0.302324329762727 | erot = 0.614346238386904 | epot = -15.5591038138593 | etot = -14.6424332457097 +189000 ekin = 0.291949445195851 | erot = 0.643455779015123 | epot = -15.5778384699218 | etot = -14.6424332457108 +190000 ekin = 0.279961942766932 | erot = 0.670244185707557 | epot = -15.5926393741802 | etot = -14.6424332457057 +191000 ekin = 0.266593185652274 | erot = 0.694546781237238 | epot = -15.6035732125847 | etot = -14.6424332456952 +192000 ekin = 0.252069141621898 | erot = 0.716288088791539 | epot = -15.6107904760939 | etot = -14.6424332456804 +193000 ekin = 0.236610293252604 | erot = 0.735467302247627 | epot = -15.6145108411624 | etot = -14.6424332456621 +194000 ekin = 0.220435149403497 | erot = 0.752141943032621 | epot = -15.615010338077 | etot = -14.6424332456409 +195000 ekin = 0.203765880091669 | erot = 0.766410799035668 | epot = -15.6126099247448 | etot = -14.6424332456175 +196000 ekin = 0.18683433903566 | erot = 0.778397083256566 | epot = -15.6076646678848 | etot = -14.6424332455926 +197000 ekin = 0.169886782292475 | erot = 0.788232586076231 | epot = -15.6005526139356 | etot = -14.6424332455669 +198000 ekin = 0.153185871076313 | erot = 0.796043434544288 | epot = -15.5916625511618 | etot = -14.6424332455412 +199000 ekin = 0.137008972985806 | erot = 0.801937915803797 | epot = -15.5813801343063 | etot = -14.6424332455167 +200000 ekin = 0.121642272363325 | erot = 0.805996673265862 | epot = -15.5700721911235 | etot = -14.6424332454943 +201000 ekin = 0.107370722655158 | erot = 0.80826545681021 | epot = -15.5580694249408 | etot = -14.6424332454755 +202000 ekin = 0.0944644042380686 | erot = 0.808750524312687 | epot = -15.5456481740119 | etot = -14.6424332454612 +203000 ekin = 0.0831623790884404 | erot = 0.807416772445398 | epot = -15.5330123969864 | etot = -14.6424332454526 +204000 ekin = 0.0736556272327849 | erot = 0.80418872542083 | epot = -15.5202775981042 | etot = -14.6424332454506 +205000 ekin = 0.066071040166992 | erot = 0.798954607356127 | epot = -15.5074588929787 | etot = -14.6424332454556 +206000 ekin = 0.0604586317676969 | erot = 0.791573809423779 | epot = -15.4944656866589 | etot = -14.6424332454674 +207000 ekin = 0.0567840026879154 | erot = 0.781888054797448 | epot = -15.4811053029705 | etot = -14.6424332454851 +208000 ekin = 0.0549275971597956 | erot = 0.769736381378278 | epot = -15.4670972240452 | etot = -14.6424332455071 +209000 ekin = 0.0546914447534107 | erot = 0.754973659532307 | epot = -15.4520983498168 | etot = -14.642433245531 +210000 ekin = 0.0558130126770382 | erot = 0.737491764373139 | epot = -15.4357380226042 | etot = -14.642433245554 +211000 ekin = 0.0579847210232175 | erot = 0.717241838878594 | epot = -15.4176598054751 | etot = -14.6424332455733 +212000 ekin = 0.0608768356197291 | erot = 0.694255492638144 | epot = -15.3975655738438 | etot = -14.642433245586 +213000 ekin = 0.0641610427072956 | erot = 0.668662476162839 | epot = -15.37525676446 | etot = -14.6424332455898 +214000 ekin = 0.06753210435751 | erot = 0.640702495518234 | epot = -15.3506678454592 | etot = -14.6424332455835 +215000 ekin = 0.0707255336353407 | erot = 0.610729417269012 | epot = -15.3238881964708 | etot = -14.6424332455665 +216000 ekin = 0.0735300437817614 | erot = 0.579207054839078 | epot = -15.2951703441601 | etot = -14.6424332455392 +217000 ekin = 0.0757943994877656 | erot = 0.546696813211925 | epot = -15.2649244582025 | etot = -14.6424332455028 +218000 ekin = 0.0774290394165114 | erot = 0.51383845121948 | epot = -15.2337007360952 | etot = -14.6424332454592 +219000 ekin = 0.0784033323141814 | erot = 0.481325894964792 | epot = -15.2021624726897 | etot = -14.6424332454107 +220000 ekin = 0.0787395495608023 | erot = 0.449880299622429 | epot = -15.1710530945426 | etot = -14.6424332453594 +221000 ekin = 0.0785046319672615 | erot = 0.420222425160601 | epot = -15.1411603024356 | etot = -14.6424332453078 +222000 ekin = 0.0778006814269721 | erot = 0.39304597217159 | epot = -15.1132798988567 | etot = -14.6424332452581 +223000 ekin = 0.0767549035385447 | erot = 0.368992968911897 | epot = -15.0881811176628 | etot = -14.6424332452123 +224000 ekin = 0.0755095293703893 | erot = 0.348631757033145 | epot = -15.0665745315757 | etot = -14.6424332451722 +225000 ekin = 0.0742120885667742 | erot = 0.332437700429458 | epot = -15.0490830341357 | etot = -14.6424332451395 +226000 ekin = 0.073006302869323 | erot = 0.320776497502283 | epot = -15.0362160454868 | etot = -14.6424332451152 +227000 ekin = 0.0720238140882433 | erot = 0.313889923629061 | epot = -15.0283469828184 | etot = -14.6424332451011 +228000 ekin = 0.0713769419939847 | erot = 0.311883945247506 | epot = -15.0256941323392 | etot = -14.6424332450977 +229000 ekin = 0.0711526728858743 | erot = 0.314719386439641 | epot = -15.0283053044313 | etot = -14.6424332451058 +230000 ekin = 0.0714080974066408 | erot = 0.322205638589943 | epot = -15.0360469811226 | etot = -14.642433245126 +231000 ekin = 0.0721675361190023 | erot = 0.333998222201819 | epot = -15.0485990034788 | etot = -14.642433245158 +232000 ekin = 0.0734216022905603 | erot = 0.349601270465958 | epot = -15.0654561179576 | etot = -14.6424332452011 +233000 ekin = 0.0751284397505271 | erot = 0.368376135875951 | epot = -15.085937820881 | etot = -14.6424332452545 +234000 ekin = 0.0772173235442621 | erot = 0.389557254433776 | epot = -15.1092078232944 | etot = -14.6424332453164 +235000 ekin = 0.0795947059802265 | erot = 0.412276079790441 | epot = -15.1343040311543 | etot = -14.6424332453836 +236000 ekin = 0.0821526186146775 | erot = 0.43559329564772 | epot = -15.160179159716 | etot = -14.6424332454536 +237000 ekin = 0.0847791014240061 | erot = 0.458538653864716 | epot = -15.1857510008108 | etot = -14.6424332455221 +238000 ekin = 0.0873700423858637 | erot = 0.480156759886701 | epot = -15.2099600478579 | etot = -14.6424332455853 +239000 ekin = 0.0898415153137649 | erot = 0.499556095552604 | epot = -15.2318308565057 | etot = -14.6424332456393 +240000 ekin = 0.0921414623535621 | erot = 0.515957735401017 | epot = -15.2505324434351 | etot = -14.6424332456806 +241000 ekin = 0.0942594490144011 | erot = 0.528739776886579 | epot = -15.2654324716071 | etot = -14.6424332457061 +242000 ekin = 0.0962332805881029 | erot = 0.537473606136305 | epot = -15.2761401324386 | etot = -14.6424332457142 +243000 ekin = 0.0981515319338902 | erot = 0.541948785980292 | epot = -15.2825335636184 | etot = -14.6424332457042 +244000 ekin = 0.100151482351193 | erot = 0.542184479374338 | epot = -15.2847692074024 | etot = -14.6424332456769 +245000 ekin = 0.102412491095761 | erot = 0.538426702317763 | epot = -15.2832724390477 | etot = -14.6424332456342 +246000 ekin = 0.105145395544795 | erot = 0.531132085866374 | epot = -15.2787107269897 | etot = -14.6424332455785 +247000 ekin = 0.108578961411983 | erot = 0.520939994206881 | epot = -15.2719522011324 | etot = -14.6424332455135 +248000 ekin = 0.112944688754523 | erot = 0.508635652295277 | epot = -15.2640135864926 | etot = -14.6424332454428 +249000 ekin = 0.11846134890514 | erot = 0.495107336753422 | epot = -15.2560019310289 | etot = -14.6424332453704 +250000 ekin = 0.125320510713214 | erot = 0.48130071319683 | epot = -15.2490544692099 | etot = -14.6424332452999 +251000 ekin = 0.133674056955099 | erot = 0.468173145423569 | epot = -15.2442804476134 | etot = -14.6424332452347 +252000 ekin = 0.143624355872782 | erot = 0.456650355973676 | epot = -15.2427079570244 | etot = -14.6424332451779 +253000 ekin = 0.155217400154351 | erot = 0.447587277165331 | epot = -15.2452379224514 | etot = -14.6424332451318 +254000 ekin = 0.168438906844348 | erot = 0.441734376017242 | epot = -15.2526065279594 | etot = -14.6424332450978 +255000 ekin = 0.183213121644194 | erot = 0.43971022735347 | epot = -15.2653565940749 | etot = -14.6424332450772 +256000 ekin = 0.199403908832166 | erot = 0.441980689733479 | epot = -15.2838178436365 | etot = -14.6424332450708 +257000 ekin = 0.216817638461889 | erot = 0.448844730305189 | epot = -15.3080956138459 | etot = -14.6424332450788 +258000 ekin = 0.235207399035754 | erot = 0.460426746275392 | epot = -15.338067390412 | etot = -14.6424332451008 +259000 ekin = 0.254278151366129 | erot = 0.476675120648644 | epot = -15.373386517151 | etot = -14.6424332451362 +260000 ekin = 0.273692576676924 | erot = 0.49736669170667 | epot = -15.4134925135676 | etot = -14.642433245184 +261000 ekin = 0.293077534073102 | erot = 0.522116767905281 | epot = -15.4576275472213 | etot = -14.6424332452429 +262000 ekin = 0.312031202020399 | erot = 0.550394247121215 | epot = -15.5048586944527 | etot = -14.642433245311 +263000 ekin = 0.330131107615849 | erot = 0.581541281999657 | epot = -15.554105635002 | etot = -14.6424332453865 +264000 ekin = 0.346943319969814 | erot = 0.614796773447099 | epot = -15.6041733388837 | etot = -14.6424332454667 +265000 ekin = 0.362033078254078 | erot = 0.64932279499714 | epot = -15.6537891188008 | etot = -14.6424332455496 +266000 ekin = 0.374977027495969 | erot = 0.684232889060528 | epot = -15.7016431621888 | etot = -14.6424332456323 +267000 ekin = 0.385377045180505 | erot = 0.718621072064159 | epot = -15.7464313629565 | etot = -14.6424332457118 +268000 ekin = 0.392875374675151 | erot = 0.75159036946739 | epot = -15.7868989899282 | etot = -14.6424332457857 +269000 ekin = 0.397170471133891 | erot = 0.782279784278107 | epot = -15.8218835012631 | etot = -14.6424332458511 +270000 ekin = 0.398032662022584 | erot = 0.809888771679725 | epot = -15.8503546796085 | etot = -14.6424332459062 +271000 ekin = 0.395318487593106 | erot = 0.833698516715849 | epot = -15.8714502502576 | etot = -14.6424332459487 +272000 ekin = 0.3889824743465 | erot = 0.853089551914417 | epot = -15.8845052722381 | etot = -14.6424332459772 +273000 ekin = 0.379085147925856 | erot = 0.867555470410714 | epot = -15.8890738643275 | etot = -14.6424332459909 +274000 ekin = 0.365796322187845 | erot = 0.876712662634537 | epot = -15.8849422308118 | etot = -14.6424332459894 +275000 ekin = 0.349393082916426 | erot = 0.880306121918472 | epot = -15.872132450808 | etot = -14.6424332459731 +276000 ekin = 0.330252358900968 | erot = 0.878211432153003 | epot = -15.8508970369967 | etot = -14.6424332459427 +277000 ekin = 0.308838461216024 | erot = 0.870433084880285 | epot = -15.821704791996 | etot = -14.6424332458996 +278000 ekin = 0.285686394600537 | erot = 0.857099294887754 | epot = -15.785218935334 | etot = -14.6424332458457 +279000 ekin = 0.261382042763559 | erot = 0.838453513182875 | epot = -15.7422688017293 | etot = -14.6424332457829 +280000 ekin = 0.236540473323853 | erot = 0.814842890589049 | epot = -15.6938166096265 | etot = -14.6424332457136 +281000 ekin = 0.211783602606715 | erot = 0.786704032858738 | epot = -15.6409208811057 | etot = -14.6424332456403 +282000 ekin = 0.187718337271409 | erot = 0.754546508157302 | epot = -15.5846980909941 | etot = -14.6424332455654 +283000 ekin = 0.16491611509112 | erot = 0.718934708844168 | epot = -15.5262840694266 | etot = -14.6424332454913 +284000 ekin = 0.143894549222822 | erot = 0.680468811937736 | epot = -15.466796606581 | etot = -14.6424332454204 +285000 ekin = 0.125101678374138 | erot = 0.639765701845489 | epot = -15.4073006255745 | etot = -14.6424332453549 +286000 ekin = 0.108903164109909 | erot = 0.597440790007828 | epot = -15.3487771994138 | etot = -14.6424332452961 +287000 ekin = 0.0955726645582895 | erot = 0.554091668601936 | epot = -15.2920975784057 | etot = -14.6424332452455 +288000 ekin = 0.0852855448043095 | erot = 0.510284456818714 | epot = -15.2380032468271 | etot = -14.6424332452041 +289000 ekin = 0.0781160413143099 | erot = 0.466543535619487 | epot = -15.187092822106 | etot = -14.6424332451722 +290000 ekin = 0.0740379578661698 | erot = 0.423345127585219 | epot = -15.1398163306013 | etot = -14.6424332451499 +291000 ekin = 0.0729289100679055 | erot = 0.38111487943343 | epot = -15.0964770346381 | etot = -14.6424332451368 +292000 ekin = 0.07457803579739 | erot = 0.340229271733799 | epot = -15.0572405526628 | etot = -14.6424332451316 +293000 ekin = 0.0786969407585632 | erot = 0.301020346544403 | epot = -15.0221505324361 | etot = -14.6424332451332 +294000 ekin = 0.0849334564747931 | erot = 0.263782947584683 | epot = -14.9911496491992 | etot = -14.6424332451397 +295000 ekin = 0.0928875723651433 | erot = 0.228783448803118 | epot = -14.964104266318 | etot = -14.6424332451498 +296000 ekin = 0.102128697511344 | erot = 0.196268840383812 | epot = -14.9408307830567 | etot = -14.6424332451616 +297000 ekin = 0.112213252500573 | erot = 0.166475068215632 | epot = -14.9211215658898 | etot = -14.6424332451736 +298000 ekin = 0.122701527070322 | erot = 0.139633685444096 | epot = -14.9047684576989 | etot = -14.6424332451845 +299000 ekin = 0.133172792913731 | erot = 0.115976150687847 | epot = -14.891582188795 | etot = -14.6424332451934 +300000 ekin = 0.143237839709879 | erot = 0.0957354521197614 | epot = -14.8814065370294 | etot = -14.6424332451998 +301000 ekin = 0.152548387990868 | erot = 0.079145090872109 | epot = -14.8741267240665 | etot = -14.6424332452036 +302000 ekin = 0.160803184301541 | erot = 0.0664357608556664 | epot = -14.869672190362 | etot = -14.6424332452048 +303000 ekin = 0.167750948488392 | erot = 0.0578302677258683 | epot = -14.8680144614181 | etot = -14.6424332452038 +304000 ekin = 0.173190665588574 | erot = 0.053537313638039 | epot = -14.869161224428 | etot = -14.6424332452014 +305000 ekin = 0.17696995295018 | erot = 0.0537447402922378 | epot = -14.8731479384404 | etot = -14.642433245198 +306000 ekin = 0.178982363291699 | erot = 0.0586126977894969 | epot = -14.8800283062755 | etot = -14.6424332451943 +307000 ekin = 0.179164502945091 | erot = 0.0682670321079287 | epot = -14.8898647802439 | etot = -14.6424332451908 +308000 ekin = 0.177493763289092 | erot = 0.0827930029211812 | epot = -14.9027200113984 | etot = -14.6424332451881 +309000 ekin = 0.173987301152073 | erot = 0.102229291873313 | epot = -14.9186498382119 | etot = -14.6424332451865 +310000 ekin = 0.168702678648375 | erot = 0.126562162218708 | epot = -14.9376980860533 | etot = -14.6424332451862 +311000 ekin = 0.161740297010248 | erot = 0.155719593409014 | epot = -14.9598931356065 | etot = -14.6424332451872 +312000 ekin = 0.153247440126422 | erot = 0.189565237979898 | epot = -14.985245923296 | etot = -14.6424332451897 +313000 ekin = 0.143423389998644 | erot = 0.227892126762103 | epot = -15.0137487619544 | etot = -14.6424332451937 +314000 ekin = 0.132524706020331 | erot = 0.270416174781571 | epot = -15.0453741260009 | etot = -14.642433245199 +315000 ekin = 0.120869409554577 | erot = 0.316769708289568 | epot = -15.0800723630506 | etot = -14.6424332452064 +316000 ekin = 0.1088385461069 | erot = 0.366495437994219 | epot = -15.1177672293174 | etot = -14.6424332452162 +317000 ekin = 0.0968734934299854 | erot = 0.419041536808397 | epot = -15.1583482754675 | etot = -14.6424332452291 +318000 ekin = 0.0854675378572642 | erot = 0.473758725762781 | epot = -15.2016595088659 | etot = -14.6424332452459 +319000 ekin = 0.0751507271474209 | erot = 0.529900497446471 | epot = -15.2474844698617 | etot = -14.6424332452678 +320000 ekin = 0.0664678443385232 | erot = 0.586627760737817 | epot = -15.2955288503722 | etot = -14.6424332452959 +321000 ekin = 0.0599504590581789 | erot = 0.643019202689382 | epot = -15.3454029070786 | etot = -14.6424332453311 +322000 ekin = 0.0560852142815269 | erot = 0.698088453264983 | epot = -15.3966069129204 | etot = -14.6424332453739 +323000 ekin = 0.0552815181260071 | erot = 0.750808639914411 | epot = -15.4485234034645 | etot = -14.6424332454241 +324000 ekin = 0.057842325521187 | erot = 0.800144112656294 | epot = -15.5004196836582 | etot = -14.6424332454807 +325000 ekin = 0.063941486463515 | erot = 0.845088070114582 | epot = -15.5514628021197 | etot = -14.6424332455416 +326000 ekin = 0.0736101694204757 | erot = 0.8847036899678 | epot = -15.6007471049927 | etot = -14.6424332456044 +327000 ekin = 0.0867333560885493 | erot = 0.918165419814647 | epot = -15.6473320215694 | etot = -14.6424332456662 +328000 ekin = 0.103055779602218 | erot = 0.944796600226722 | epot = -15.690285625553 | etot = -14.642433245724 +329000 ekin = 0.122195446168401 | erot = 0.964099781598492 | epot = -15.7287284735425 | etot = -14.6424332457756 +330000 ekin = 0.143662406707274 | erot = 0.97577699624252 | epot = -15.7618726487685 | etot = -14.6424332458188 +331000 ekin = 0.166880785130066 | erot = 0.979738667524184 | epot = -15.7890526985066 | etot = -14.6424332458523 +332000 ekin = 0.191212923965916 | erot = 0.976101405909932 | epot = -15.8097475757513 | etot = -14.6424332458755 +333000 ekin = 0.215985355315126 | erot = 0.96517623354676 | epot = -15.8235948347498 | etot = -14.6424332458879 +334000 ekin = 0.240516656826312 | erot = 0.947449485120633 | epot = -15.8303993878361 | etot = -14.6424332458891 +335000 ekin = 0.264146896081082 | erot = 0.923558676876312 | epot = -15.8301388188364 | etot = -14.642433245879 +336000 ekin = 0.286267467748831 | erot = 0.894265184768772 | epot = -15.8229658983753 | etot = -14.6424332458577 +337000 ekin = 0.306349134744516 | erot = 0.86042493934443 | epot = -15.8092073199143 | etot = -14.6424332458253 +338000 ekin = 0.323965497669028 | erot = 0.822957838329898 | epot = -15.7893565817819 | etot = -14.642433245783 +339000 ekin = 0.338809250783309 | erot = 0.782816380156821 | epot = -15.7640588766722 | etot = -14.6424332457321 +340000 ekin = 0.350699444228147 | erot = 0.740954141308479 | epot = -15.7340868312114 | etot = -14.6424332456748 +341000 ekin = 0.359579293531077 | erot = 0.698295027836124 | epot = -15.700307566981 | etot = -14.6424332456138 +342000 ekin = 0.365505462149771 | erot = 0.65570454203815 | epot = -15.6636432497397 | etot = -14.6424332455518 +343000 ekin = 0.368630832656574 | erot = 0.613964463467596 | epot = -15.6250285416159 | etot = -14.6424332454917 +344000 ekin = 0.369183369584824 | erot = 0.573752273081762 | epot = -15.5853688881025 | etot = -14.6424332454359 +345000 ekin = 0.367443732820381 | erot = 0.535626361233121 | epot = -15.5455033394399 | etot = -14.6424332453864 +346000 ekin = 0.363723933128391 | erot = 0.500017626275295 | epot = -15.5061748047483 | etot = -14.6424332453446 +347000 ekin = 0.358348705274855 | erot = 0.467227585425635 | epot = -15.4680095360116 | etot = -14.6424332453111 +348000 ekin = 0.351640582952574 | erot = 0.437432666905905 | epot = -15.4315064951445 | etot = -14.642433245286 +349000 ekin = 0.343909024693095 | erot = 0.41069398616735 | epot = -15.3970362561291 | etot = -14.6424332452687 +350000 ekin = 0.335443435967589 | erot = 0.386971649877954 | epot = -15.3648483311043 | etot = -14.6424332452587 +351000 ekin = 0.326509584093047 | erot = 0.366142474248719 | epot = -15.335085303596 | etot = -14.6424332452542 +352000 ekin = 0.31734869902189 | erot = 0.348019930398469 | epot = -15.3078018746744 | etot = -14.642433245254 +353000 ekin = 0.308178466648795 | erot = 0.332375117499601 | epot = -15.2829868294052 | etot = -14.6424332452568 +354000 ekin = 0.299195119854714 | erot = 0.318957598137068 | epot = -15.2605859632527 | etot = -14.6424332452609 +355000 ekin = 0.290575888249386 | erot = 0.307515001368932 | epot = -15.2405241348834 | etot = -14.6424332452651 +356000 ekin = 0.282481160313163 | erot = 0.297810406216367 | epot = -15.222724811798 | etot = -14.6424332452684 +357000 ekin = 0.275055828994536 | erot = 0.289636664277623 | epot = -15.2071257385424 | etot = -14.6424332452702 +358000 ekin = 0.268429427255716 | erot = 0.2828270069126 | epot = -15.1936896794383 | etot = -14.64243324527 +359000 ekin = 0.262714810202527 | erot = 0.277261507858961 | epot = -15.1824095633294 | etot = -14.6424332452679 +360000 ekin = 0.258005302570158 | erot = 0.272869227750137 | epot = -15.1733077755847 | etot = -14.6424332452644 +361000 ekin = 0.254370400622446 | erot = 0.269626137803926 | epot = -15.1664297836866 | etot = -14.6424332452602 +362000 ekin = 0.251850290179257 | erot = 0.267549186090192 | epot = -15.1618327215256 | etot = -14.6424332452562 +363000 ekin = 0.250449609863309 | erot = 0.266687109599918 | epot = -15.1595699647169 | etot = -14.6424332452537 +364000 ekin = 0.250131041863869 | erot = 0.267108788860229 | epot = -15.1596730759781 | etot = -14.642433245254 +365000 ekin = 0.250809442162608 | erot = 0.268890073930453 | epot = -15.1621327613513 | etot = -14.6424332452583 +366000 ekin = 0.252347318763942 | erot = 0.272100073008303 | epot = -15.1668806370396 | etot = -14.6424332452674 +367000 ekin = 0.254552520179202 | erot = 0.276787886821285 | epot = -15.1737736522826 | etot = -14.6424332452822 +368000 ekin = 0.257178996154138 | erot = 0.282970699525187 | epot = -15.1825829409824 | etot = -14.6424332453031 +369000 ekin = 0.259931424909754 | erot = 0.290624011144305 | epot = -15.192988681384 | etot = -14.64243324533 +370000 ekin = 0.262474349327938 | erot = 0.299674631815232 | epot = -15.2045822265054 | etot = -14.6424332453622 +371000 ekin = 0.264446209429919 | erot = 0.30999686929688 | epot = -15.2168763241253 | etot = -14.6424332453985 +372000 ekin = 0.265478281863403 | erot = 0.321412142685467 | epot = -15.2293236699861 | etot = -14.6424332454372 +373000 ekin = 0.265218028292392 | erot = 0.333692059446794 | epot = -15.2413433332155 | etot = -14.6424332454763 +374000 ekin = 0.263355721250465 | erot = 0.346564809668633 | epot = -15.2523537764321 | etot = -14.642433245513 +375000 ekin = 0.259652497503914 | erot = 0.35972456799486 | epot = -15.2618103110439 | etot = -14.6424332455451 +376000 ekin = 0.253967268937827 | erot = 0.372843454380799 | epot = -15.2692439688887 | etot = -14.6424332455701 +377000 ekin = 0.246279333501497 | erot = 0.385585491294786 | epot = -15.274298070382 | etot = -14.6424332455857 +378000 ekin = 0.236703249878266 | erot = 0.397621906698155 | epot = -15.2767584021673 | etot = -14.6424332455909 +379000 ekin = 0.225492756944983 | erot = 0.408647066931749 | epot = -15.2765730694618 | etot = -14.6424332455851 +380000 ekin = 0.213031377539262 | erot = 0.418394278996725 | epot = -15.2738589021049 | etot = -14.6424332455689 +381000 ekin = 0.199808877315933 | erot = 0.42665067621188 | epot = -15.2688927990715 | etot = -14.6424332455437 +382000 ekin = 0.186384809019062 | erot = 0.433270396055884 | epot = -15.2620884505868 | etot = -14.6424332455119 +383000 ekin = 0.173342616144133 | erot = 0.438185279050674 | epot = -15.2539611406711 | etot = -14.6424332454762 +384000 ekin = 0.161239700831467 | erot = 0.441412371402834 | epot = -15.2450853176736 | etot = -14.6424332454393 +385000 ekin = 0.15055995464762 | erot = 0.44305761255288 | epot = -15.2360508126044 | etot = -14.6424332454039 +386000 ekin = 0.1416751296992 | erot = 0.443315241523152 | epot = -15.2274236165942 | etot = -14.6424332453718 +387000 ekin = 0.134820015698004 | erot = 0.442462667348858 | epot = -15.2197159283911 | etot = -14.6424332453442 +388000 ekin = 0.130083976413563 | erot = 0.440850813513923 | epot = -15.2133680352489 | etot = -14.6424332453214 +389000 ekin = 0.127418570237896 | erot = 0.438890246279034 | epot = -15.20874206182 | etot = -14.6424332453031 +390000 ekin = 0.126658423093211 | erot = 0.437033702086108 | epot = -15.2061253704679 | etot = -14.6424332452886 +391000 ekin = 0.127550804261002 | erot = 0.435755902066214 | epot = -15.2057399516043 | etot = -14.6424332452771 +392000 ekin = 0.129788752935804 | erot = 0.435531744058807 | epot = -15.2077537422628 | etot = -14.6424332452682 +393000 ekin = 0.13304305531626 | erot = 0.436814065078312 | epot = -15.2122903656558 | etot = -14.6424332452612 +394000 ekin = 0.136989561466103 | erot = 0.440012156511487 | epot = -15.2194349632339 | etot = -14.6424332452563 +395000 ekin = 0.14132983304257 | erot = 0.44547209688668 | epot = -15.2292351751828 | etot = -14.6424332452536 +396000 ekin = 0.145804542777681 | erot = 0.453459767650225 | epot = -15.2416975556816 | etot = -14.6424332452537 +397000 ekin = 0.150200153189366 | erot = 0.464147173463303 | epot = -15.25678057191 | etot = -14.6424332452573 +398000 ekin = 0.154350089767278 | erot = 0.477602441560288 | epot = -15.2743857765924 | etot = -14.6424332452648 +399000 ekin = 0.158131920623957 | erot = 0.49378366115725 | epot = -15.2943488270583 | etot = -14.6424332452771 +400000 ekin = 0.161462056175852 | erot = 0.512536568007638 | epot = -15.3164318694777 | etot = -14.6424332452942 +401000 ekin = 0.164289301183564 | erot = 0.533595989003432 | epot = -15.3403185355036 | etot = -14.6424332453166 +402000 ekin = 0.16658832305357 | erot = 0.556590928840415 | epot = -15.3656124972378 | etot = -14.6424332453438 +403000 ekin = 0.168353810382888 | erot = 0.581053183644666 | epot = -15.3918402394033 | etot = -14.6424332453758 +404000 ekin = 0.169595821304612 | erot = 0.606429376023098 | epot = -15.4184584427392 | etot = -14.6424332454115 +405000 ekin = 0.170336578565562 | erot = 0.63209629254019 | epot = -15.4448661165559 | etot = -14.6424332454501 +406000 ekin = 0.170608761982373 | erot = 0.657379344514174 | epot = -15.4704213519868 | etot = -14.6424332454903 +407000 ekin = 0.170455178570794 | erot = 0.681573854093766 | epot = -15.494462278195 | etot = -14.6424332455304 +408000 ekin = 0.169929554813017 | erot = 0.703968692150334 | epot = -15.5163314925322 | etot = -14.6424332455689 +409000 ekin = 0.169098093454334 | erot = 0.723871579520639 | epot = -15.5354029185788 | etot = -14.6424332456039 +410000 ekin = 0.168041369043284 | erot = 0.740635137247676 | epot = -15.5511097519246 | etot = -14.6424332456336 +411000 ekin = 0.16685610281106 | erot = 0.753682569970645 | epot = -15.5629719184382 | etot = -14.6424332456565 +412000 ekin = 0.165656359034691 | erot = 0.762531725092763 | epot = -15.5706213297985 | etot = -14.6424332456711 +413000 ekin = 0.16457374171258 | erot = 0.766816218739503 | epot = -15.5738232061285 | etot = -14.6424332456764 +414000 ekin = 0.163756240958051 | erot = 0.766302377571847 | epot = -15.5724918642017 | etot = -14.6424332456718 +415000 ekin = 0.163365479945346 | erot = 0.760900920225164 | epot = -15.5666996458277 | etot = -14.6424332456572 +416000 ekin = 0.16357224009341 | erot = 0.75067258670007 | epot = -15.5566780724265 | etot = -14.642433245633 +417000 ekin = 0.164550286198177 | erot = 0.735827297892157 | epot = -15.5428108296905 | etot = -14.6424332456002 +418000 ekin = 0.166468663391054 | erot = 0.71671685730188 | epot = -15.5256187662531 | etot = -14.6424332455602 +419000 ekin = 0.169482781124205 | erot = 0.69382164910088 | epot = -15.5057376757398 | etot = -14.6424332455147 +420000 ekin = 0.17372472266442 | erot = 0.667732191685371 | epot = -15.4838901598156 | etot = -14.6424332454658 +421000 ekin = 0.179293310757533 | erot = 0.639126725583772 | epot = -15.460853281757 | etot = -14.6424332454157 +422000 ekin = 0.18624451451762 | erot = 0.608746211201687 | epot = -15.437423971086 | etot = -14.6424332453667 +423000 ekin = 0.194582798143094 | erot = 0.577368165579487 | epot = -15.4143842090434 | etot = -14.6424332453208 +424000 ekin = 0.204253993028008 | erot = 0.545780680988006 | epot = -15.392467919296 | etot = -14.64243324528 +425000 ekin = 0.215140228915644 | erot = 0.514757766833632 | epot = -15.3723312409951 | etot = -14.6424332452459 +426000 ekin = 0.22705739519611 | erot = 0.485036881516617 | epot = -15.3545275219322 | etot = -14.6424332452194 +427000 ekin = 0.239755526224917 | erot = 0.457299221562847 | epot = -15.3394879929896 | etot = -14.6424332452018 +428000 ekin = 0.252922416268543 | erot = 0.432153058135964 | epot = -15.3275087195978 | etot = -14.6424332451933 +429000 ekin = 0.266190667178511 | erot = 0.410120192008996 | epot = -15.3187441043811 | etot = -14.6424332451936 +430000 ekin = 0.279148248284993 | erot = 0.391625457763317 | epot = -15.3132069512512 | etot = -14.6424332452029 +431000 ekin = 0.291352495292879 | erot = 0.376989149811629 | epot = -15.3107748903245 | etot = -14.64243324522 +432000 ekin = 0.302347287569384 | erot = 0.366422254467196 | epot = -15.3112027872808 | etot = -14.6424332452442 +433000 ekin = 0.311682921770386 | erot = 0.360024429013363 | epot = -15.314140596057 | etot = -14.6424332452733 +434000 ekin = 0.318937954386255 | erot = 0.357784738271778 | epot = -15.3191559379639 | etot = -14.6424332453059 +435000 ekin = 0.323742037713914 | erot = 0.359585207274041 | epot = -15.3257604903287 | etot = -14.6424332453407 +436000 ekin = 0.325798554030506 | erot = 0.365207245307274 | epot = -15.3334390447139 | etot = -14.6424332453761 +437000 ekin = 0.324905697096481 | erot = 0.374340922351912 | epot = -15.3416798648573 | etot = -14.642433245409 +438000 ekin = 0.320974589857387 | erot = 0.38659693016297 | epot = -15.350004765458 | etot = -14.6424332454377 +439000 ekin = 0.314043077745106 | erot = 0.401520852188694 | epot = -15.3579971753951 | etot = -14.6424332454613 +440000 ekin = 0.304283988018871 | erot = 0.418609132217954 | epot = -15.3653263657147 | etot = -14.6424332454779 +441000 ekin = 0.292006859109421 | erot = 0.437325916197858 | epot = -15.3717660207937 | etot = -14.6424332454864 +442000 ekin = 0.277652365812285 | erot = 0.457119792524558 | epot = -15.3772054038237 | etot = -14.6424332454869 +443000 ekin = 0.261778853587334 | erot = 0.477439412182338 | epot = -15.3816515112496 | etot = -14.6424332454799 +444000 ekin = 0.245040553430229 | erot = 0.497747053383812 | epot = -15.3852208522809 | etot = -14.6424332454669 +445000 ekin = 0.228157260415745 | erot = 0.517529408210577 | epot = -15.3881199140755 | etot = -14.6424332454491 +446000 ekin = 0.211875681724426 | erot = 0.536305196865301 | epot = -15.3906141240194 | etot = -14.6424332454296 +447000 ekin = 0.196923472676264 | erot = 0.553629632762624 | epot = -15.3929863508503 | etot = -14.6424332454114 +448000 ekin = 0.183958277875564 | erot = 0.569096233380439 | epot = -15.3954877566541 | etot = -14.6424332453981 +449000 ekin = 0.173515771308145 | erot = 0.582336947161166 | epot = -15.3982859638623 | etot = -14.6424332453929 +450000 ekin = 0.165962361194716 | erot = 0.593021970155278 | epot = -15.4014175767483 | etot = -14.6424332453983 +451000 ekin = 0.161459280831071 | erot = 0.600860851258448 | epot = -15.4047533775048 | etot = -14.6424332454152 +452000 ekin = 0.159944578250394 | erot = 0.605606408084745 | epot = -15.4079842317782 | etot = -14.6424332454431 +453000 ekin = 0.161137653112604 | erot = 0.607062496375647 | epot = -15.4106333949675 | etot = -14.6424332454792 +454000 ekin = 0.164567591511419 | erot = 0.605095779312697 | epot = -15.4120966163436 | etot = -14.6424332455194 +455000 ekin = 0.169622334208404 | erot = 0.599650455426745 | epot = -15.4117060351936 | etot = -14.6424332455584 +456000 ekin = 0.175611802350263 | erot = 0.590763702898767 | epot = -15.4088087508399 | etot = -14.6424332455909 +457000 ekin = 0.181835621982496 | erot = 0.578578749366124 | epot = -15.4028476169608 | etot = -14.6424332456122 +458000 ekin = 0.18764572703167 | erot = 0.563352302650977 | epot = -15.3934312753017 | etot = -14.6424332456191 +459000 ekin = 0.192495880386128 | erot = 0.545453717150014 | epot = -15.3803828431463 | etot = -14.6424332456101 +460000 ekin = 0.19597338163879 | erot = 0.525354597711273 | epot = -15.3637612249358 | etot = -14.6424332455858 +461000 ekin = 0.197811920993009 | erot = 0.503609203462558 | epot = -15.3438543700042 | etot = -14.6424332455486 +462000 ekin = 0.19788772492106 | erot = 0.480827560282267 | epot = -15.3211485307047 | etot = -14.6424332455014 +463000 ekin = 0.196203198487162 | erot = 0.457644248436047 | epot = -15.2962806923717 | etot = -14.6424332454485 +464000 ekin = 0.192863034127886 | erot = 0.434686220428428 | epot = -15.2699824999498 | etot = -14.6424332453935 +465000 ekin = 0.188047435824139 | erot = 0.412542760090385 | epot = -15.2430234412545 | etot = -14.64243324534 +466000 ekin = 0.181986107554585 | erot = 0.391740010671268 | epot = -15.2161593635165 | etot = -14.6424332452907 +467000 ekin = 0.174935400199653 | erot = 0.372721626734306 | epot = -15.1900902721816 | etot = -14.6424332452476 +468000 ekin = 0.167159826103645 | erot = 0.355836258350829 | epot = -15.1654293296665 | etot = -14.642433245212 +469000 ekin = 0.158918218023908 | erot = 0.341331890764793 | epot = -15.1426833539731 | etot = -14.6424332451844 +470000 ekin = 0.15045418565433 | erot = 0.32935658463347 | epot = -15.1222440154524 | etot = -14.6424332451646 +471000 ekin = 0.141990180750341 | erot = 0.319964871776709 | epot = -15.1043882976792 | etot = -14.6424332451522 +472000 ekin = 0.133724353868939 | erot = 0.313128906245089 | epot = -15.08928650526 | etot = -14.642433245146 +473000 ekin = 0.125829398102414 | erot = 0.308753392324214 | epot = -15.0770160355716 | etot = -14.642433245145 +474000 ekin = 0.118452666363562 | erot = 0.306693264413826 | epot = -15.0675791759251 | etot = -14.6424332451477 +475000 ekin = 0.111716976219122 | erot = 0.306773053290683 | epot = -15.0609232746627 | etot = -14.6424332451529 +476000 ekin = 0.10572165563334 | erot = 0.308806833537627 | epot = -15.0569617343301 | etot = -14.6424332451591 +477000 ekin = 0.100543523675759 | erot = 0.312617617130285 | epot = -15.0555943859712 | etot = -14.6424332451652 +478000 ekin = 0.0962376398644792 | erot = 0.31805505563531 | epot = -15.0567259406699 | etot = -14.6424332451701 +479000 ekin = 0.0928377950024481 | erot = 0.325010357030128 | epot = -15.0602813972058 | etot = -14.6424332451732 +480000 ekin = 0.0903568546345918 | erot = 0.33342742776329 | epot = -15.066217527572 | etot = -14.6424332451741 +481000 ekin = 0.0887871989358495 | erot = 0.343309423709778 | epot = -15.0745298678181 | etot = -14.6424332451725 +482000 ekin = 0.0881016191320247 | erot = 0.354720133057113 | epot = -15.0852549973578 | etot = -14.6424332451687 +483000 ekin = 0.0882551127439553 | erot = 0.367779908272464 | epot = -15.0984682661794 | etot = -14.642433245163 +484000 ekin = 0.0891880440138003 | erot = 0.382656193507601 | epot = -15.1142774826776 | etot = -14.6424332451562 +485000 ekin = 0.0908310739109808 | erot = 0.399549033146284 | epot = -15.1328133522061 | etot = -14.6424332451488 +486000 ekin = 0.0931120890990374 | erot = 0.418672269923129 | epot = -15.1542176041639 | etot = -14.6424332451417 +487000 ekin = 0.0959650526392593 | erot = 0.440231422321011 | epot = -15.1786297200963 | etot = -14.642433245136 +488000 ekin = 0.0993402613867364 | erot = 0.464399451384487 | epot = -15.2061729579036 | etot = -14.6424332451324 +489000 ekin = 0.103214957397678 | erot = 0.491291775403258 | epot = -15.2369399779328 | etot = -14.6424332451318 +490000 ekin = 0.107602676597184 | erot = 0.520941965498208 | epot = -15.2709778872308 | etot = -14.6424332451354 +491000 ekin = 0.112559247664622 | erot = 0.553279563916956 | epot = -15.3082720567259 | etot = -14.6424332451443 +492000 ekin = 0.118183136723597 | erot = 0.588111425308452 | epot = -15.3487278071918 | etot = -14.6424332451598 +493000 ekin = 0.12460804012638 | erot = 0.62510790827898 | epot = -15.3921491935888 | etot = -14.6424332451834 +494000 ekin = 0.131986393312561 | erot = 0.663795156035111 | epot = -15.4382147945646 | etot = -14.6424332452169 +495000 ekin = 0.140463823900159 | erot = 0.703554605721736 | epot = -15.4864516748841 | etot = -14.6424332452622 +496000 ekin = 0.15014640803584 | erot = 0.743630741563187 | epot = -15.5362103949193 | etot = -14.6424332453203 +497000 ekin = 0.161064579071316 | erot = 0.783147917317585 | epot = -15.5866457417809 | etot = -14.642433245392 +498000 ekin = 0.173139219157384 | erot = 0.821136754972775 | epot = -15.6367092196065 | etot = -14.6424332454764 +499000 ekin = 0.186156317833383 | erot = 0.856570103856722 | epot = -15.6851596672614 | etot = -14.6424332455713 +500000 ekin = 0.199756195068936 | erot = 0.888407758274067 | epot = -15.7305971990159 | etot = -14.6424332456729 +501000 ekin = 0.21344151783734 | erot = 0.915648078732879 | epot = -15.7715228423456 | etot = -14.6424332457754 +502000 ekin = 0.226605416598004 | erot = 0.937383433649205 | epot = -15.8064220961192 | etot = -14.642433245872 +503000 ekin = 0.238577508977599 | erot = 0.952855183124955 | epot = -15.833865938058 | etot = -14.6424332459554 +504000 ekin = 0.248682347016341 | erot = 0.961503066788411 | epot = -15.8526186598236 | etot = -14.6424332460188 +505000 ekin = 0.256302488969601 | erot = 0.963003656366721 | epot = -15.8617393913931 | etot = -14.6424332460567 +506000 ekin = 0.260937583144201 | erot = 0.957293217920631 | epot = -15.8606640471306 | etot = -14.6424332460658 +507000 ekin = 0.262251679299254 | erot = 0.944571918258648 | epot = -15.8492568436029 | etot = -14.642433246045 +508000 ekin = 0.260103184111419 | erot = 0.925288564934488 | epot = -15.827824995042 | etot = -14.6424332459961 +509000 ekin = 0.254554875280464 | erot = 0.90010753693787 | epot = -15.7970956581413 | etot = -14.642433245923 +510000 ekin = 0.245864483348196 | erot = 0.869861717985383 | epot = -15.7581594471648 | etot = -14.6424332458312 +511000 ekin = 0.234458914526896 | erot = 0.835496660126456 | epot = -15.7123888203806 | etot = -14.6424332457273 +512000 ekin = 0.22089682023999 | erot = 0.798011684065881 | epot = -15.6613417499238 | etot = -14.642433245618 +513000 ekin = 0.205824805087888 | erot = 0.758403224578321 | epot = -15.6066612751757 | etot = -14.6424332455095 +514000 ekin = 0.189932244116178 | erot = 0.717614706860286 | epot = -15.5499801963839 | etot = -14.6424332454074 +515000 ekin = 0.17390874819978 | erot = 0.676495918872563 | epot = -15.4928379123882 | etot = -14.6424332453159 +516000 ekin = 0.158407108509004 | erot = 0.635773516025323 | epot = -15.4366138697724 | etot = -14.6424332452381 +517000 ekin = 0.1440133501839 | erot = 0.596033149118113 | epot = -15.3824797444781 | etot = -14.6424332451761 +518000 ekin = 0.131224514118008 | erot = 0.557712825688944 | epot = -15.3313705849373 | etot = -14.6424332451304 +519000 ekin = 0.120434042405821 | erot = 0.521106495597703 | epot = -15.283973783104 | etot = -14.6424332451005 +520000 ekin = 0.111924165176696 | erot = 0.48637644319974 | epot = -15.2407338534618 | etot = -14.6424332450854 +521000 ekin = 0.105864424815862 | erot = 0.453572806060421 | epot = -15.2018704759592 | etot = -14.6424332450829 +522000 ekin = 0.102315362067372 | erot = 0.422658367131508 | epot = -15.1674069742899 | etot = -14.642433245091 +523000 ekin = 0.101236366465152 | erot = 0.393536647097 | epot = -15.137206258669 | etot = -14.6424332451069 +524000 ekin = 0.102496717236721 | erot = 0.366081244308229 | epot = -15.1110112066728 | etot = -14.6424332451279 +525000 ekin = 0.105888887336008 | erot = 0.340164343214705 | epot = -15.088486475702 | etot = -14.6424332451513 +526000 ekin = 0.111143247850893 | erot = 0.315682368378702 | epot = -15.0692588614046 | etot = -14.642433245175 +527000 ekin = 0.117943398962381 | erot = 0.292576937807028 | epot = -15.0529535819665 | etot = -14.6424332451971 +528000 ekin = 0.125941474255768 | erot = 0.270849598243881 | epot = -15.0392243177156 | etot = -14.6424332452159 +529000 ekin = 0.134772916010344 | erot = 0.250569317239541 | epot = -15.0277754784805 | etot = -14.6424332452306 +530000 ekin = 0.144070383403707 | erot = 0.231872340652279 | epot = -15.0183759692969 | etot = -14.6424332452409 +531000 ekin = 0.153476601970632 | erot = 0.214954741435395 | epot = -15.010864588653 | etot = -14.642433245247 +532000 ekin = 0.1626560540789 | erot = 0.200058697649321 | epot = -15.0051479969777 | etot = -14.6424332452495 +533000 ekin = 0.171305419081489 | erot = 0.187454143184939 | epot = -15.0011928075153 | etot = -14.6424332452489 +534000 ekin = 0.179162595540411 | erot = 0.177417842695355 | epot = -14.9990136834822 | etot = -14.6424332452464 +535000 ekin = 0.186014006486684 | erot = 0.170212094444257 | epot = -14.9986593461736 | etot = -14.6424332452427 +536000 ekin = 0.191699759240443 | erot = 0.166065149228308 | epot = -15.0001981537074 | etot = -14.6424332452386 +537000 ekin = 0.196116169931545 | erot = 0.165155084981508 | epot = -15.0037045001479 | etot = -14.6424332452349 +538000 ekin = 0.199215220533704 | erot = 0.167598364573368 | epot = -15.0092468303392 | etot = -14.6424332452321 +539000 ekin = 0.201000709669604 | erot = 0.173443713619075 | epot = -15.0168776685195 | etot = -14.6424332452308 +540000 ekin = 0.201521164038046 | erot = 0.182671367033628 | epot = -15.026625776303 | etot = -14.6424332452313 +541000 ekin = 0.200859940141535 | erot = 0.195197211442984 | epot = -15.0384903968185 | etot = -14.642433245234 +542000 ekin = 0.199123298889063 | erot = 0.210880936223687 | epot = -15.0524374803519 | etot = -14.6424332452391 +543000 ekin = 0.196427519384046 | erot = 0.2295370177894 | epot = -15.0683977824198 | etot = -14.6424332452464 +544000 ekin = 0.192886294945241 | erot = 0.25094720200222 | epot = -15.0862667422039 | etot = -14.6424332452565 +545000 ekin = 0.188599710887441 | erot = 0.274873110235132 | epot = -15.1059060663912 | etot = -14.6424332452687 +546000 ekin = 0.183646045242704 | erot = 0.301067663118917 | epot = -15.1271469536446 | etot = -14.642433245283 +547000 ekin = 0.178077473818685 | erot = 0.329284179373518 | epot = -15.1497948984912 | etot = -14.642433245299 +548000 ekin = 0.171920510267331 | erot = 0.359282253783689 | epot = -15.1736360093672 | etot = -14.6424332453162 +549000 ekin = 0.165181670578021 | erot = 0.390829837831202 | epot = -15.1984447537431 | etot = -14.6424332453339 +550000 ekin = 0.157858408655527 | erot = 0.423701326917663 | epot = -15.2239929809248 | etot = -14.6424332453516 +551000 ekin = 0.149954809005965 | erot = 0.457671882716405 | epot = -15.2500599370908 | etot = -14.6424332453685 +552000 ekin = 0.141500835823196 | erot = 0.492508662660419 | epot = -15.2764427438674 | etot = -14.6424332453838 +553000 ekin = 0.132573145481942 | erot = 0.527960055124252 | epot = -15.3029664460031 | etot = -14.6424332453969 +554000 ekin = 0.123314645148993 | erot = 0.563744383269579 | epot = -15.329492273826 | etot = -14.6424332454074 +555000 ekin = 0.11394927090318 | erot = 0.599539792623581 | epot = -15.3559223089418 | etot = -14.642433245415 +556000 ekin = 0.104788088807789 | erot = 0.634977129563578 | epot = -15.3821984637916 | etot = -14.6424332454203 +557000 ekin = 0.0962230654780937 | erot = 0.669637513724418 | epot = -15.4082938246266 | etot = -14.6424332454241 +558000 ekin = 0.0887059614428439 | erot = 0.703055990480566 | epot = -15.4341951973516 | etot = -14.6424332454282 +559000 ekin = 0.0827118847741871 | erot = 0.734732129424035 | epot = -15.4598772596329 | etot = -14.6424332454346 +560000 ekin = 0.0786899547259807 | erot = 0.764147748398847 | epot = -15.4852709485702 | etot = -14.6424332454454 +561000 ekin = 0.0770067720633659 | erot = 0.790791153075989 | epot = -15.5102311706017 | etot = -14.6424332454624 +562000 ekin = 0.0778911706764631 | erot = 0.814186471629129 | epot = -15.534510887792 | etot = -14.6424332454864 +563000 ekin = 0.0813901113672907 | erot = 0.833925925483065 | epot = -15.5577492823675 | etot = -14.6424332455171 +564000 ekin = 0.0873448530219359 | erot = 0.849702302565726 | epot = -15.57948040114 | etot = -14.6424332455523 +565000 ekin = 0.0953935152543113 | erot = 0.861338569497175 | epot = -15.5991653303401 | etot = -14.6424332455886 +566000 ekin = 0.105001366119702 | erot = 0.868811531657282 | epot = -15.6162461433985 | etot = -14.6424332456215 +567000 ekin = 0.115514789210848 | erot = 0.872266750928135 | epot = -15.6302147857853 | etot = -14.6424332456464 +568000 ekin = 0.126230320990576 | erot = 0.872022546760986 | epot = -15.6406861134105 | etot = -14.6424332456589 +569000 ekin = 0.136467575205475 | erot = 0.868561781937934 | epot = -15.6474626027995 | etot = -14.6424332456561 +570000 ekin = 0.145634823229257 | erot = 0.862511177262809 | epot = -15.650579246129 | etot = -14.642433245637 +571000 ekin = 0.153278250260102 | erot = 0.854608991356203 | epot = -15.6503204872187 | etot = -14.6424332456024 +572000 ekin = 0.159109636953932 | erot = 0.845662918616737 | epot = -15.6472058011258 | etot = -14.6424332455552 +573000 ekin = 0.163011362017374 | erot = 0.836500892319944 | epot = -15.6419454998372 | etot = -14.6424332454999 +574000 ekin = 0.165021239080146 | erot = 0.82791805820528 | epot = -15.6353725427274 | etot = -14.642433245442 +575000 ekin = 0.165302195908609 | erot = 0.820623479704234 | epot = -15.628358921 | etot = -14.6424332453872 +576000 ekin = 0.164102988101204 | erot = 0.815190165399022 | epot = -15.6217263988411 | etot = -14.6424332453409 +577000 ekin = 0.16171615238716 | erot = 0.812011817944629 | epot = -15.6161612156398 | etot = -14.642433245308 +578000 ekin = 0.158438569371814 | erot = 0.811269345694708 | epot = -15.6121411603584 | etot = -14.6424332452919 +579000 ekin = 0.154538688869361 | erot = 0.812909695780807 | epot = -15.6098816299448 | etot = -14.6424332452946 +580000 ekin = 0.150232988454484 | erot = 0.816638977241892 | epot = -15.6093052110128 | etot = -14.6424332453164 +581000 ekin = 0.145672809814972 | erot = 0.821931135411058 | epot = -15.610037190582 | etot = -14.642433245356 +582000 ekin = 0.140941476791515 | erot = 0.828052590350937 | epot = -15.6114273125529 | etot = -14.6424332454104 +583000 ekin = 0.136060602599172 | erot = 0.834102246896438 | epot = -15.6125960949711 | etot = -14.6424332454755 +584000 ekin = 0.131003759896596 | erot = 0.839065139158377 | epot = -15.6125021446008 | etot = -14.6424332455458 +585000 ekin = 0.125715216483019 | erot = 0.841876757449112 | epot = -15.6100252195477 | etot = -14.6424332456156 +586000 ekin = 0.120131224768949 | erot = 0.841493945666844 | epot = -15.6040584161145 | etot = -14.6424332456787 +587000 ekin = 0.114201380572134 | erot = 0.836967317753832 | epot = -15.5936019440557 | etot = -14.6424332457297 +588000 ekin = 0.107907808226742 | erot = 0.827509595983301 | epot = -15.5778506499739 | etot = -14.6424332457638 +589000 ekin = 0.101280337909734 | erot = 0.81255426067366 | epot = -15.5562678443609 | etot = -14.6424332457776 +590000 ekin = 0.0944063548788447 | erot = 0.791799488420614 | epot = -15.5286390890685 | etot = -14.642433245769 +591000 ekin = 0.0874345511052151 | erot = 0.76523351922336 | epot = -15.4951013160666 | etot = -14.642433245738 +592000 ekin = 0.0805723392085189 | erot = 0.733139214285282 | epot = -15.45614479918 | etot = -14.6424332456862 +593000 ekin = 0.0740771594080953 | erot = 0.696077455348749 | epot = -15.4125878603736 | etot = -14.6424332456168 +594000 ekin = 0.0682423089599914 | erot = 0.654850963358167 | epot = -15.3655265178524 | etot = -14.6424332455342 +595000 ekin = 0.0633782539014622 | erot = 0.610451848323624 | epot = -15.316263347669 | etot = -14.6424332454439 +596000 ekin = 0.0597906540649622 | erot = 0.563997548401124 | epot = -15.266221447818 | etot = -14.6424332453519 +597000 ekin = 0.0577565493624107 | erot = 0.516660644084268 | epot = -15.2168504387109 | etot = -14.6424332452643 +598000 ekin = 0.0575003158536292 | erot = 0.46959829435364 | epot = -15.1695318553937 | etot = -14.6424332451864 +599000 ekin = 0.0591710965286411 | erot = 0.423886769451092 | epot = -15.125491111103 | etot = -14.6424332451233 +600000 ekin = 0.0628234356891151 | erot = 0.380465849281473 | epot = -15.085722530049 | etot = -14.6424332450784 +601000 ekin = 0.0684027903378462 | erot = 0.340096852289088 | epot = -15.0509328876808 | etot = -14.6424332450539 +602000 ekin = 0.0757374499128992 | erot = 0.303336891508859 | epot = -15.0215075864721 | etot = -14.6424332450503 +603000 ekin = 0.0845381560106908 | erot = 0.270530726252483 | epot = -14.9975021273299 | etot = -14.6424332450667 +604000 ekin = 0.0944063594078219 | erot = 0.241820347963514 | epot = -14.9786599524718 | etot = -14.6424332451004 +605000 ekin = 0.104851562460546 | erot = 0.217171224791095 | epot = -14.9644560323987 | etot = -14.6424332451471 +606000 ekin = 0.115317556389809 | erot = 0.196412930356164 | epot = -14.9541637319473 | etot = -14.6424332452013 +607000 ekin = 0.125216580353243 | erot = 0.179290709847465 | epot = -14.9469405354577 | etot = -14.6424332452569 +608000 ekin = 0.133969542490526 | erot = 0.165523445157702 | epot = -14.9419262329557 | etot = -14.6424332453075 +609000 ekin = 0.141049537028475 | erot = 0.154862582265136 | epot = -14.9383453646401 | etot = -14.6424332453465 +610000 ekin = 0.146025095175903 | erot = 0.147146040888474 | epot = -14.9356043814332 | etot = -14.6424332453689 +611000 ekin = 0.148599079335708 | erot = 0.142341118193759 | epot = -14.9333734429004 | etot = -14.6424332453709 +612000 ekin = 0.148639027542189 | erot = 0.140571068727531 | epot = -14.9316433416207 | etot = -14.6424332453509 +613000 ekin = 0.146195193893286 | erot = 0.142121441395761 | epot = -14.9307498805988 | etot = -14.6424332453097 +614000 ekin = 0.141503544705005 | erot = 0.147424293659447 | epot = -14.931361083615 | etot = -14.6424332452505 +615000 ekin = 0.134972482669537 | erot = 0.157020849768784 | epot = -14.9344265776169 | etot = -14.6424332451786 +616000 ekin = 0.127153892887427 | erot = 0.171505679772597 | epot = -14.941092817761 | etot = -14.642433245101 +617000 ekin = 0.11870096049717 | erot = 0.191457667915229 | epot = -14.9525918734383 | etot = -14.6424332450259 +618000 ekin = 0.110316794781908 | erot = 0.217364584491545 | epot = -14.9701146242349 | etot = -14.6424332449614 +619000 ekin = 0.102698942666063 | erot = 0.24954877623369 | epot = -14.9946809638151 | etot = -14.6424332449153 +620000 ekin = 0.0964852203315362 | erot = 0.288101317493775 | epot = -15.0270197827191 | etot = -14.6424332448938 +621000 ekin = 0.0922059091525968 | erot = 0.332831044367712 | epot = -15.0674701984216 | etot = -14.6424332449013 +622000 ekin = 0.0902463647100715 | erot = 0.38323345186412 | epot = -15.1159130615138 | etot = -14.6424332449397 +623000 ekin = 0.0908226920702821 | erot = 0.438482716267927 | epot = -15.1717386533468 | etot = -14.6424332450086 +624000 ekin = 0.0939716062521676 | erot = 0.497448307340542 | epot = -15.2338531586981 | etot = -14.6424332451054 +625000 ekin = 0.0995541611224928 | erot = 0.558735886785353 | epot = -15.3007232931327 | etot = -14.6424332452249 +626000 ekin = 0.10727185932578 | erot = 0.620750477457182 | epot = -15.3704555821433 | etot = -14.6424332453603 +627000 ekin = 0.11669282673767 | erot = 0.681778220901769 | epot = -15.440904293143 | etot = -14.6424332455036 +628000 ekin = 0.127285245273611 | erot = 0.740081431769978 | epot = -15.5097999226894 | etot = -14.6424332456458 +629000 ekin = 0.138455039153878 | erot = 0.794000196770909 | epot = -15.574888481703 | etot = -14.6424332457782 +630000 ekin = 0.149584842937125 | erot = 0.842052640240603 | epot = -15.6340707290701 | etot = -14.6424332458924 +631000 ekin = 0.16007149985305 | erot = 0.883025442878479 | epot = -15.6855301887134 | etot = -14.6424332459819 +632000 ekin = 0.169359720292797 | erot = 0.916046503426873 | epot = -15.7278394697614 | etot = -14.6424332460418 +633000 ekin = 0.17697005369257 | erot = 0.940632922941154 | epot = -15.7600362227032 | etot = -14.6424332460695 +634000 ekin = 0.182519961289978 | erot = 0.956709735134137 | epot = -15.781662942489 | etot = -14.6424332460649 +635000 ekin = 0.185737466035669 | erot = 0.964597760206484 | epot = -15.7927684722726 | etot = -14.6424332460304 +636000 ekin = 0.186467519303327 | erot = 0.964972204256472 | epot = -15.7938729695301 | etot = -14.6424332459703 +637000 ekin = 0.184671774604503 | erot = 0.958796660376594 | epot = -15.7859016808714 | etot = -14.6424332458903 +638000 ekin = 0.180422825778069 | erot = 0.947239527072976 | epot = -15.770095598648 | etot = -14.6424332457969 +639000 ekin = 0.173894119064868 | erot = 0.931581224196161 | epot = -15.7479085889582 | etot = -14.6424332456971 +640000 ekin = 0.165346701827808 | erot = 0.913120838753317 | epot = -15.7209007861785 | etot = -14.6424332455974 +641000 ekin = 0.155113786103713 | erot = 0.893090060089577 | epot = -15.6906370916966 | etot = -14.6424332455033 +642000 ekin = 0.143583869244232 | erot = 0.872580710306069 | epot = -15.6585978249697 | etot = -14.6424332454194 +643000 ekin = 0.131182953689577 | erot = 0.852490168054228 | epot = -15.6261063670927 | etot = -14.6424332453489 +644000 ekin = 0.11835630576118 | erot = 0.833486853990155 | epot = -15.5942764050452 | etot = -14.6424332452939 +645000 ekin = 0.105550209085084 | erot = 0.815995971212681 | epot = -15.5639794255528 | etot = -14.642433245255 +646000 ekin = 0.093194274419463 | erot = 0.800204061931152 | epot = -15.5358315815826 | etot = -14.642433245232 +647000 ekin = 0.0816850001800759 | erot = 0.786079744440879 | epot = -15.5101979898445 | etot = -14.6424332452235 +648000 ekin = 0.0713713598437969 | erot = 0.773407243193161 | epot = -15.4872118482646 | etot = -14.6424332452277 +649000 ekin = 0.0625431628717073 | erot = 0.761828976530834 | epot = -15.4668053846445 | etot = -14.642433245242 +650000 ekin = 0.0554227735503065 | erot = 0.750893453414394 | epot = -15.4487494722282 | etot = -14.6424332452635 +651000 ekin = 0.0501605027658154 | erot = 0.740104978449003 | epot = -15.4326987265042 | etot = -14.6424332452894 +652000 ekin = 0.0468336713663407 | erot = 0.728972100421355 | epot = -15.4182390171044 | etot = -14.6424332453167 +653000 ekin = 0.0454490492573823 | erot = 0.717052285945779 | epot = -15.4049345805458 | etot = -14.6424332453426 +654000 ekin = 0.0459481524943509 | erot = 0.70399086978471 | epot = -15.392372267644 | etot = -14.6424332453649 +655000 ekin = 0.0482147495286276 | erot = 0.689552835107397 | epot = -15.3802008300174 | etot = -14.6424332453814 +656000 ekin = 0.0520838761262644 | erot = 0.673646332749874 | epot = -15.3681634542669 | etot = -14.6424332453908 +657000 ekin = 0.0573516620848622 | erot = 0.656337023115527 | epot = -15.3561219305923 | etot = -14.6424332453919 +658000 ekin = 0.0637853134928166 | erot = 0.637852348219607 | epot = -15.344070907097 | etot = -14.6424332453846 +659000 ekin = 0.0711326702869886 | erot = 0.618574815847844 | epot = -15.3321407315043 | etot = -14.6424332453694 +660000 ekin = 0.0791308828101371 | erot = 0.599023454708784 | epot = -15.3205875828668 | etot = -14.6424332453479 +661000 ekin = 0.0875139366233974 | erot = 0.57982293974748 | epot = -15.309770121693 | etot = -14.6424332453222 +662000 ekin = 0.0960190004199823 | erot = 0.561660610347651 | epot = -15.3001128560629 | etot = -14.6424332452952 +663000 ekin = 0.104391848885353 | erot = 0.545232746054702 | epot = -15.2920578402108 | etot = -14.6424332452707 +664000 ekin = 0.112391863390337 | erot = 0.531182949318112 | epot = -15.2860080579609 | etot = -14.6424332452524 +665000 ekin = 0.119797262721372 | erot = 0.520037124796779 | epot = -15.2822676327621 | etot = -14.6424332452439 +666000 ekin = 0.126411190063575 | erot = 0.512141060960667 | epot = -15.2809854962725 | etot = -14.6424332452483 +667000 ekin = 0.132069035725156 | erot = 0.50760768172899 | epot = -15.2821099627212 | etot = -14.6424332452671 +668000 ekin = 0.136646914542223 | erot = 0.506281315754211 | epot = -15.2853614755972 | etot = -14.6424332453008 +669000 ekin = 0.140070616013037 | erot = 0.507725566171581 | epot = -15.2902294275325 | etot = -14.6424332453479 +670000 ekin = 0.142323740906691 | erot = 0.511239425098608 | epot = -15.2959964114102 | etot = -14.6424332454049 +671000 ekin = 0.143453306303075 | erot = 0.515903234044913 | epot = -15.3017897858151 | etot = -14.6424332454671 +672000 ekin = 0.143571012732429 | erot = 0.520652256718095 | epot = -15.3066565149792 | etot = -14.6424332455287 +673000 ekin = 0.142848733836965 | erot = 0.524371563356991 | epot = -15.3096535427773 | etot = -14.6424332455833 +674000 ekin = 0.141507613277731 | erot = 0.526002362930676 | epot = -15.3099432218337 | etot = -14.6424332456253 +675000 ekin = 0.139801302825604 | erot = 0.524647629024546 | epot = -15.3068821775003 | etot = -14.6424332456501 +676000 ekin = 0.137995095210655 | erot = 0.519664439041476 | epot = -15.3000927799068 | etot = -14.6424332456546 +677000 ekin = 0.136343677285201 | erot = 0.510732098517963 | epot = -15.2895090214411 | etot = -14.6424332456379 +678000 ekin = 0.135070664122621 | erot = 0.497888575256477 | epot = -15.2753924849801 | etot = -14.642433245601 +679000 ekin = 0.134352810444884 | erot = 0.481532294132544 | epot = -15.2583183501238 | etot = -14.6424332455464 +680000 ekin = 0.134310862655773 | erot = 0.462390968605323 | epot = -15.2391350767392 | etot = -14.6424332454781 +681000 ekin = 0.135007638923145 | erot = 0.441462941784857 | epot = -15.218903826109 | etot = -14.642433245401 +682000 ekin = 0.13645246152461 | erot = 0.419938865037855 | epot = -15.1988245718826 | etot = -14.6424332453201 +683000 ekin = 0.138609887397967 | erot = 0.399112293315506 | epot = -15.180155425954 | etot = -14.6424332452405 +684000 ekin = 0.141410065648281 | erot = 0.38028718176242 | epot = -15.164130492578 | etot = -14.6424332451673 +685000 ekin = 0.144758102722259 | erot = 0.364688846299456 | epot = -15.1518801941268 | etot = -14.6424332451051 +686000 ekin = 0.148540467119441 | erot = 0.353383275614529 | epot = -15.1443569877921 | etot = -14.6424332450581 +687000 ekin = 0.152627512098729 | erot = 0.347208212230897 | epot = -15.1422689693592 | etot = -14.6424332450296 +688000 ekin = 0.156872371008247 | erot = 0.346718408271177 | epot = -15.1460240243021 | etot = -14.6424332450226 +689000 ekin = 0.161107527974783 | erot = 0.35214694111545 | epot = -15.1556877141289 | etot = -14.6424332450387 +690000 ekin = 0.165141087380649 | erot = 0.36338430494212 | epot = -15.1709586374008 | etot = -14.6424332450781 +691000 ekin = 0.168755042649078 | erot = 0.379976931156632 | epot = -15.1911652189454 | etot = -14.6424332451396 +692000 ekin = 0.171707649703689 | erot = 0.401146558397852 | epot = -15.215287453322 | etot = -14.6424332452204 +693000 ekin = 0.173741393443089 | erot = 0.42583123278867 | epot = -15.2420058715475 | etot = -14.6424332453157 +694000 ekin = 0.174597110624771 | erot = 0.452747528140126 | epot = -15.2697778841841 | etot = -14.6424332454192 +695000 ekin = 0.174033757472238 | erot = 0.480471830922422 | epot = -15.2969388339178 | etot = -14.6424332455232 +696000 ekin = 0.171852263364757 | erot = 0.507536398158356 | epot = -15.3218219071425 | etot = -14.6424332456194 +697000 ekin = 0.167921065290933 | erot = 0.532533688693164 | epot = -15.3428879996837 | etot = -14.6424332456996 +698000 ekin = 0.162200409477029 | erot = 0.554220619925199 | epot = -15.3588542751586 | etot = -14.6424332457564 +699000 ekin = 0.154762415715643 | erot = 0.571613361028106 | epot = -15.3688090225278 | etot = -14.642433245784 +700000 ekin = 0.145804230008803 | erot = 0.584063387088072 | epot = -15.3723008628759 | etot = -14.6424332457791 +701000 ekin = 0.135652269558616 | erot = 0.591306922721422 | epot = -15.3693924380207 | etot = -14.6424332457407 +702000 ekin = 0.124756460207487 | erot = 0.593482464349051 | epot = -15.3606721702277 | etot = -14.6424332456711 +703000 ekin = 0.113674325951271 | erot = 0.591114401856995 | epot = -15.3472219733833 | etot = -14.642433245575 +704000 ekin = 0.1030456759456 | erot = 0.585064323196589 | epot = -15.3305432446015 | etot = -14.6424332454593 +705000 ekin = 0.0935593581963262 | erot = 0.576454826534689 | epot = -15.3124474300639 | etot = -14.6424332453329 +706000 ekin = 0.0859140824284925 | erot = 0.566573150256724 | epot = -15.2949204778902 | etot = -14.642433245205 +707000 ekin = 0.0807756759557919 | erot = 0.556763427609511 | epot = -15.279972348651 | etot = -14.6424332450857 +708000 ekin = 0.0787333622600079 | erot = 0.548316855291324 | epot = -15.2694834625352 | etot = -14.6424332449839 +709000 ekin = 0.0802577669151073 | erot = 0.542368667954005 | epot = -15.2650596797768 | etot = -14.6424332449077 +710000 ekin = 0.0856633545528672 | erot = 0.539809747049325 | epot = -15.2679063464655 | etot = -14.6424332448633 +711000 ekin = 0.095077851902745 | erot = 0.541219180891425 | epot = -15.278730277649 | etot = -14.6424332448548 +712000 ekin = 0.108420876622167 | erot = 0.546822307911541 | epot = -15.2976764294173 | etot = -14.6424332448836 +713000 ekin = 0.125393451694849 | erot = 0.556476834657793 | epot = -15.3243035313014 | etot = -14.6424332449487 +714000 ekin = 0.145479367621451 | erot = 0.56968760011942 | epot = -15.3576002127876 | etot = -14.6424332450467 +715000 ekin = 0.167958541116837 | erot = 0.585648522303156 | epot = -15.396040308592 | etot = -14.642433245172 +716000 ekin = 0.191931735851211 | erot = 0.603308292531433 | epot = -15.4376732736996 | etot = -14.6424332453169 +717000 ekin = 0.216355400176877 | erot = 0.621454592037058 | epot = -15.4802432376869 | etot = -14.6424332454729 +718000 ekin = 0.24008505651043 | erot = 0.638810139731555 | epot = -15.5213284418724 | etot = -14.6424332456304 +719000 ekin = 0.261925698575348 | erot = 0.654132895986132 | epot = -15.5584918403414 | etot = -14.6424332457799 +720000 ekin = 0.280687969311602 | erot = 0.6663123798671 | epot = -15.5894335950909 | etot = -14.6424332459122 +721000 ekin = 0.295249345589177 | erot = 0.674454385927726 | epot = -15.612136977536 | etot = -14.6424332460191 +722000 ekin = 0.304619886333769 | erot = 0.677947410255128 | epot = -15.6250005426823 | etot = -14.6424332460934 +723000 ekin = 0.308011983728025 | erot = 0.676505724570436 | epot = -15.6269509544278 | etot = -14.6424332461294 +724000 ekin = 0.304912667284422 | erot = 0.670186105899586 | epot = -15.617532019307 | etot = -14.642433246123 +725000 ekin = 0.295155116711621 | erot = 0.659377522489412 | epot = -15.596965885273 | etot = -14.642433246072 +726000 ekin = 0.278983134900163 | erot = 0.644765363158375 | epot = -15.5661817440352 | etot = -14.6424332459767 +727000 ekin = 0.257098790794435 | erot = 0.627273860362892 | epot = -15.5268058969976 | etot = -14.6424332458402 +728000 ekin = 0.230680158274999 | erot = 0.607992016180427 | epot = -15.4811054201245 | etot = -14.6424332456691 +729000 ekin = 0.201354496276734 | erot = 0.588089464034349 | epot = -15.4318772057847 | etot = -14.6424332454737 +730000 ekin = 0.171114103979347 | erot = 0.56872921471559 | epot = -15.3822765639634 | etot = -14.6424332452685 +731000 ekin = 0.142168923912302 | erot = 0.55098413507048 | epot = -15.335586304054 | etot = -14.6424332450712 +732000 ekin = 0.116742007100633 | erot = 0.535763349043665 | epot = -15.2949386010453 | etot = -14.642433244901 +733000 ekin = 0.09682930275761 | erot = 0.523753647321524 | epot = -15.2630161948552 | etot = -14.6424332447761 +734000 ekin = 0.0839596135620733 | erot = 0.515379592338451 | epot = -15.2417724506113 | etot = -14.6424332447107 +735000 ekin = 0.0789983701793142 | erot = 0.510784464195818 | epot = -15.2322160790872 | etot = -14.6424332447121 +736000 ekin = 0.0820355551944443 | erot = 0.509832642266179 | epot = -15.2343014422398 | etot = -14.6424332447791 +737000 ekin = 0.0923827123871823 | erot = 0.512132550855379 | epot = -15.2469485081446 | etot = -14.642433244902 +738000 ekin = 0.10868044851431 | erot = 0.517077971027559 | epot = -15.2681916646065 | etot = -14.6424332450646 +739000 ekin = 0.129093715683514 | erot = 0.523904364926965 | epot = -15.2954313258571 | etot = -14.6424332452466 +740000 ekin = 0.151555277793959 | erot = 0.531755895780137 | epot = -15.3257444190018 | etot = -14.6424332454277 +741000 ekin = 0.174012721806636 | erot = 0.539758083454087 | epot = -15.3562040508504 | etot = -14.6424332455896 +742000 ekin = 0.194640916831482 | erot = 0.54709054970013 | epot = -15.3841647122503 | etot = -14.6424332457187 +743000 ekin = 0.211995737398838 | erot = 0.553054125338314 | epot = -15.4074831085433 | etot = -14.6424332458062 +744000 ekin = 0.225100508723079 | erot = 0.557126762310524 | epot = -15.424660516882 | etot = -14.6424332458484 +745000 ekin = 0.233469424487108 | erot = 0.559003260239957 | epot = -15.4349059305735 | etot = -14.6424332458464 +746000 ekin = 0.237079913465558 | erot = 0.558614810500983 | epot = -15.4381279697713 | etot = -14.6424332458048 +747000 ekin = 0.236308652985589 | erot = 0.556125790084016 | epot = -15.4348676888005 | etot = -14.6424332457309 +748000 ekin = 0.231845097888752 | erot = 0.55190707933143 | epot = -15.4261854228542 | etot = -14.642433245634 +749000 ekin = 0.224593843485221 | erot = 0.546487360031015 | epot = -15.4135144490412 | etot = -14.6424332455249 +750000 ekin = 0.215574369393402 | erot = 0.540486233486425 | epot = -15.3984938482944 | etot = -14.6424332454146 +751000 ekin = 0.205824583428198 | erot = 0.534535356766148 | epot = -15.3827931855081 | etot = -14.6424332453138 +752000 ekin = 0.196313335743884 | erot = 0.52919581522017 | epot = -15.3679423961961 | etot = -14.642433245232 +753000 ekin = 0.187866475789629 | erot = 0.524881252733656 | epot = -15.3551809737001 | etot = -14.6424332451768 +754000 ekin = 0.181110613628486 | erot = 0.521796491099562 | epot = -15.3453403498807 | etot = -14.6424332451526 +755000 ekin = 0.176438042206913 | erot = 0.519900210808863 | epot = -15.3387714981765 | etot = -14.6424332451607 +756000 ekin = 0.173994962649932 | erot = 0.518897676286876 | epot = -15.3353258841353 | etot = -14.6424332451985 +757000 ekin = 0.173693190273803 | erot = 0.518265706184404 | epot = -15.3343921417187 | etot = -14.6424332452605 +758000 ekin = 0.175243155018275 | erot = 0.517307659823502 | epot = -15.3349840601801 | etot = -14.6424332453383 +759000 ekin = 0.178203703096672 | erot = 0.515231902166426 | epot = -15.3358688506853 | etot = -14.6424332454222 +760000 ekin = 0.182042463552542 | erot = 0.511243837950911 | epot = -15.3357195470056 | etot = -14.6424332455021 +761000 ekin = 0.186199747764937 | erot = 0.504639825549636 | epot = -15.3332728188833 | etot = -14.6424332455687 +762000 ekin = 0.190149235948647 | erot = 0.494891409035961 | epot = -15.3274738905993 | etot = -14.6424332456147 +763000 ekin = 0.193449921097656 | erot = 0.48171023828929 | epot = -15.3175934050219 | etot = -14.642433245635 +764000 ekin = 0.195785552428858 | erot = 0.465087294353624 | epot = -15.3033060924099 | etot = -14.6424332456274 +765000 ekin = 0.196989678186435 | erot = 0.445303873494018 | epot = -15.2847267972728 | etot = -14.6424332455924 +766000 ekin = 0.197055919183657 | erot = 0.422915440293833 | epot = -15.2624046050103 | etot = -14.6424332455328 +767000 ekin = 0.196134076493791 | erot = 0.398712320924463 | epot = -15.2372796428714 | etot = -14.6424332454532 +768000 ekin = 0.19451309665161 | erot = 0.373662938959324 | epot = -15.2106092809708 | etot = -14.6424332453598 +769000 ekin = 0.192592017625545 | erot = 0.348845887485747 | epot = -15.183871150371 | etot = -14.6424332452597 +770000 ekin = 0.190840163684042 | erot = 0.325376840212043 | epot = -15.1586502490567 | etot = -14.6424332451606 +771000 ekin = 0.189748397224706 | erot = 0.304335529899335 | epot = -15.1365171721945 | etot = -14.6424332450705 +772000 ekin = 0.189774341847512 | erot = 0.286697153920059 | epot = -15.1189047407643 | etot = -14.6424332449968 +773000 ekin = 0.191286034497103 | erot = 0.273271857835136 | epot = -15.1069911372781 | etot = -14.6424332449458 +774000 ekin = 0.194510000604928 | erot = 0.264655458968671 | epot = -15.1015987044965 | etot = -14.6424332449229 +775000 ekin = 0.1994906396753 | erot = 0.261194193154413 | epot = -15.1031180777602 | etot = -14.6424332449305 +776000 ekin = 0.20606747706162 | erot = 0.262965803934266 | epot = -15.1114665259645 | etot = -14.6424332449687 +777000 ekin = 0.213875019082075 | erot = 0.269778568411878 | epot = -15.1260868325288 | etot = -14.6424332450348 +778000 ekin = 0.222366868961501 | erot = 0.281188790675803 | epot = -15.1459889047609 | etot = -14.6424332451236 +779000 ekin = 0.23086210226578 | erot = 0.296535944176041 | epot = -15.1698312916694 | etot = -14.6424332452276 +780000 ekin = 0.238608567016832 | erot = 0.314993169091967 | epot = -15.1960349814467 | etot = -14.6424332453379 +781000 ekin = 0.244855557739749 | erot = 0.335629445236581 | epot = -15.2229182484218 | etot = -14.6424332454454 +782000 ekin = 0.24892761247725 | erot = 0.357478674286814 | epot = -15.2488395323052 | etot = -14.6424332455412 +783000 ekin = 0.250291897528933 | erot = 0.379610269028307 | epot = -15.2723354121746 | etot = -14.6424332456174 +784000 ekin = 0.248613283253142 | erot = 0.401195731122951 | epot = -15.2922422600441 | etot = -14.642433245668 +785000 ekin = 0.243793133451306 | erot = 0.421566090466591 | epot = -15.307792469607 | etot = -14.6424332456891 +786000 ekin = 0.235989501853544 | erot = 0.440255905206922 | epot = -15.3186786527391 | etot = -14.6424332456787 +787000 ekin = 0.225617610785755 | erot = 0.457030673432498 | epot = -15.3250815298558 | etot = -14.6424332456375 +788000 ekin = 0.213330260903068 | erot = 0.471895861696116 | epot = -15.3276593681681 | etot = -14.6424332455689 +789000 ekin = 0.199978499678474 | erot = 0.485087183883212 | epot = -15.3274989290401 | etot = -14.6424332454784 +790000 ekin = 0.186553834704413 | erot = 0.497043141243068 | epot = -15.3260302213206 | etot = -14.6424332453731 +791000 ekin = 0.174114766793401 | erot = 0.508362048570016 | epot = -15.3249100606255 | etot = -14.6424332452621 +792000 ekin = 0.163702420432354 | erot = 0.519746739181041 | epot = -15.3258824047684 | etot = -14.642433245155 +793000 ekin = 0.156252224966272 | erot = 0.531940822989567 | epot = -15.3306262930174 | etot = -14.6424332450615 +794000 ekin = 0.152510350034305 | erot = 0.545660777315136 | epot = -15.3406043723396 | etot = -14.6424332449902 +795000 ekin = 0.15296425115691 | erot = 0.561528326981077 | epot = -15.3569258230862 | etot = -14.6424332449482 +796000 ekin = 0.157795747355293 | erot = 0.58000757877803 | epot = -15.3802365710733 | etot = -14.64243324494 +797000 ekin = 0.166862457855209 | erot = 0.601351255569628 | epot = -15.4106469583921 | etot = -14.6424332449673 +798000 ekin = 0.179709603428639 | erot = 0.625560121845548 | epot = -15.4477029703033 | etot = -14.6424332450291 +799000 ekin = 0.195609966057174 | erot = 0.652359247176621 | epot = -15.4904024583554 | etot = -14.6424332451216 +800000 ekin = 0.213626158786275 | erot = 0.681194021873727 | epot = -15.5372534258987 | etot = -14.6424332452387 +801000 ekin = 0.23268704018842 | erot = 0.711247726386662 | epot = -15.5863680119477 | etot = -14.6424332453727 +802000 ekin = 0.251669429101161 | erot = 0.74148091983623 | epot = -15.6355835944521 | etot = -14.6424332455147 +803000 ekin = 0.269477067853805 | erot = 0.77069100842129 | epot = -15.6826013219308 | etot = -14.6424332456557 +804000 ekin = 0.285110541453744 | erot = 0.797588259158567 | epot = -15.7251320463987 | etot = -14.6424332457864 +805000 ekin = 0.297723982502972 | erot = 0.820882528799733 | epot = -15.7610397572013 | etot = -14.6424332458986 +806000 ekin = 0.306666387684833 | erot = 0.839373432913609 | epot = -15.7884730665839 | etot = -14.6424332459854 +807000 ekin = 0.31150697555439 | erot = 0.852035914445983 | epot = -15.805976136042 | etot = -14.6424332460416 +808000 ekin = 0.312045176252642 | erot = 0.858093398528306 | epot = -15.8125718208452 | etot = -14.6424332460642 +809000 ekin = 0.308306642387692 | erot = 0.857071970758726 | epot = -15.8078118591988 | etot = -14.6424332460524 +810000 ekin = 0.300527220561155 | erot = 0.848831113928873 | epot = -15.7917915804976 | etot = -14.6424332460076 +811000 ekin = 0.289127204421254 | erot = 0.833569138622274 | epot = -15.7651295889768 | etot = -14.6424332459333 +812000 ekin = 0.274678427602453 | erot = 0.81180411649313 | epot = -15.7289157899302 | etot = -14.6424332458346 +813000 ekin = 0.25786683558395 | erot = 0.784333459542784 | epot = -15.6846335408444 | etot = -14.6424332457177 +814000 ekin = 0.239453080594243 | erot = 0.752176980196514 | epot = -15.6340633063802 | etot = -14.6424332455895 +815000 ekin = 0.220233415151703 | erot = 0.716509170266734 | epot = -15.5791758308754 | etot = -14.642433245457 +816000 ekin = 0.201002751046678 | erot = 0.678586569748113 | epot = -15.5220225661216 | etot = -14.6424332453268 +817000 ekin = 0.182521261080269 | erot = 0.639675603864976 | epot = -15.4646301101501 | etot = -14.6424332452049 +818000 ekin = 0.16548540152786 | erot = 0.600985363831456 | epot = -15.4089040104558 | etot = -14.6424332450964 +819000 ekin = 0.15050378978042 | erot = 0.563608719249299 | epot = -15.3565457540354 | etot = -14.6424332450057 +820000 ekin = 0.138078032178478 | erot = 0.528474068972393 | epot = -15.3089853460865 | etot = -14.6424332449356 +821000 ekin = 0.128588386730135 | erot = 0.496309093117806 | epot = -15.2673307247362 | etot = -14.6424332448883 +822000 ekin = 0.122284066136812 | erot = 0.467617125515789 | epot = -15.2323344365172 | etot = -14.6424332448646 +823000 ekin = 0.119278020924339 | erot = 0.44266622847877 | epot = -15.2043774942677 | etot = -14.6424332448646 +824000 ekin = 0.119546158603677 | erot = 0.421490682738665 | epot = -15.1834700862295 | etot = -14.6424332448872 +825000 ekin = 0.122931110514549 | erot = 0.403904342223771 | epot = -15.1692686976685 | etot = -14.6424332449302 +826000 ekin = 0.129150803764327 | erot = 0.389525075000029 | epot = -15.161109123755 | etot = -14.6424332449907 +827000 ekin = 0.137812176399179 | erot = 0.377809252270532 | epot = -15.1580546737345 | etot = -14.6424332450648 +828000 ekin = 0.148430331608382 | erot = 0.368094906962796 | epot = -15.1589584837191 | etot = -14.6424332451479 +829000 ekin = 0.160453205761696 | erot = 0.359651737511967 | epot = -15.1625381885082 | etot = -14.6424332452346 +830000 ekin = 0.17329138289678 | erot = 0.351735589545236 | epot = -15.1674602177611 | etot = -14.6424332453191 +831000 ekin = 0.186352012962992 | erot = 0.343644456329796 | epot = -15.1724297146884 | etot = -14.6424332453957 +832000 ekin = 0.19907492460549 | erot = 0.334772487920949 | epot = -15.1762806579855 | etot = -14.642433245459 +833000 ekin = 0.21096808488054 | erot = 0.324658115188717 | epot = -15.1780594455737 | etot = -14.6424332455044 +834000 ekin = 0.22163875725698 | erot = 0.313022323442326 | epot = -15.1770943262282 | etot = -14.6424332455289 +835000 ekin = 0.230816330001966 | erot = 0.299793483326653 | epot = -15.1730430588596 | etot = -14.642433245531 +836000 ekin = 0.238363132174234 | erot = 0.28511603996084 | epot = -15.1659124176466 | etot = -14.6424332455115 +837000 ekin = 0.244270841530998 | erot = 0.269341751259632 | epot = -15.1560458382641 | etot = -14.6424332454734 +838000 ekin = 0.248642320235733 | erot = 0.25300390410384 | epot = -15.1440794697607 | etot = -14.6424332454212 +839000 ekin = 0.251661569327697 | erot = 0.23677675898714 | epot = -15.1308715736755 | etot = -14.6424332453607 +840000 ekin = 0.253557306828274 | erot = 0.221424057161473 | epot = -15.1174146092878 | etot = -14.642433245298 +841000 ekin = 0.254567562696821 | erot = 0.207741475743574 | epot = -15.104742283679 | etot = -14.6424332452386 +842000 ekin = 0.254912814683751 | erot = 0.196498262354278 | epot = -15.0938443222248 | etot = -14.6424332451868 +843000 ekin = 0.254783130765828 | erot = 0.188382921787058 | epot = -15.085599297698 | etot = -14.6424332451451 +844000 ekin = 0.254340789697888 | erot = 0.183956927272106 | epot = -15.0807309620847 | etot = -14.6424332451147 +845000 ekin = 0.253734932891713 | erot = 0.183619247980611 | epot = -15.0797874259676 | etot = -14.6424332450953 +846000 ekin = 0.253120504196155 | erot = 0.187583282239862 | epot = -15.0831370315226 | etot = -14.6424332450866 +847000 ekin = 0.252671650088266 | erot = 0.195866742639111 | epot = -15.0909716378154 | etot = -14.642433245088 +848000 ekin = 0.25258091531028 | erot = 0.20829422246314 | epot = -15.1033083828732 | etot = -14.6424332450998 +849000 ekin = 0.253039966848252 | erot = 0.224511555531826 | epot = -15.1199847675027 | etot = -14.6424332451227 +850000 ekin = 0.254204001798515 | erot = 0.244010590097797 | epot = -15.1406478370536 | etot = -14.6424332451573 +851000 ekin = 0.256148339026787 | erot = 0.26616256360263 | epot = -15.1647441478333 | etot = -14.6424332452039 +852000 ekin = 0.258829686440588 | erot = 0.290257858698213 | epot = -15.1915207904 | etot = -14.6424332452612 +853000 ekin = 0.262064657828587 | erot = 0.315549558167727 | epot = -15.2200474613225 | etot = -14.6424332453262 +854000 ekin = 0.265534116122648 | erot = 0.341297947736379 | epot = -15.2492653092531 | etot = -14.6424332453941 +855000 ekin = 0.26881517465358 | erot = 0.366813004430893 | epot = -15.2780614245436 | etot = -14.6424332454591 +856000 ekin = 0.271435486954603 | erot = 0.391492007901445 | epot = -15.305360740371 | etot = -14.642433245515 +857000 ekin = 0.272939108063008 | erot = 0.414849750473414 | epot = -15.3302221040928 | etot = -14.6424332455564 +858000 ekin = 0.272951155039785 | erot = 0.436539390688027 | epot = -15.3519237913071 | etot = -14.6424332455793 +859000 ekin = 0.271229880676472 | erot = 0.456362750059341 | epot = -15.3700258763176 | etot = -14.6424332455817 +860000 ekin = 0.267698633833911 | erot = 0.474269718460682 | epot = -15.3844015978589 | etot = -14.6424332455643 +861000 ekin = 0.262455001752904 | erot = 0.490347316007815 | epot = -15.3952355632896 | etot = -14.6424332455289 +862000 ekin = 0.255758797176706 | erot = 0.504799761298941 | epot = -15.402991803955 | etot = -14.6424332454794 +863000 ekin = 0.248003564341433 | erot = 0.517921532812514 | epot = -15.4083583425743 | etot = -14.6424332454204 +864000 ekin = 0.23967765558487 | erot = 0.5300658235034 | epot = -15.4121767244453 | etot = -14.642433245357 +865000 ekin = 0.23132088944539 | erot = 0.541610953534341 | epot = -15.4153650882739 | etot = -14.6424332452941 +866000 ekin = 0.223481813676297 | erot = 0.552927233331988 | epot = -15.4188422922445 | etot = -14.6424332452362 +867000 ekin = 0.216679174491969 | erot = 0.564346499432351 | epot = -15.4234589191111 | etot = -14.6424332451867 +868000 ekin = 0.211369750018244 | erot = 0.57613613893885 | epot = -15.4299391341058 | etot = -14.6424332451487 +869000 ekin = 0.207923502308331 | erot = 0.588478941151472 | epot = -15.4388356885839 | etot = -14.6424332451241 +870000 ekin = 0.206606153000455 | erot = 0.601459626890416 | epot = -15.4504990250046 | etot = -14.6424332451137 +871000 ekin = 0.207568796758621 | erot = 0.615058451105655 | epot = -15.4650604929822 | etot = -14.6424332451179 +872000 ekin = 0.210843969902065 | erot = 0.62915187575959 | epot = -15.4824290907976 | etot = -14.642433245136 +873000 ekin = 0.216347593119461 | erot = 0.643519970833663 | epot = -15.5023008091198 | etot = -14.6424332451666 +874000 ekin = 0.223886305143511 | erot = 0.65785990973072 | epot = -15.5241794600822 | etot = -14.6424332452079 +875000 ekin = 0.233169807553207 | erot = 0.67180466221101 | epot = -15.5474077150216 | etot = -14.6424332452574 +876000 ekin = 0.243827877963662 | erot = 0.684945735800061 | epot = -15.5712068590757 | etot = -14.642433245312 +877000 ekin = 0.255431632545988 | erot = 0.696858567354671 | epot = -15.5947234452691 | etot = -14.6424332453684 +878000 ekin = 0.267518408513276 | erot = 0.707128927388885 | epot = -15.6170805813255 | etot = -14.6424332454234 +879000 ekin = 0.279619300259048 | erot = 0.71537849572129 | epot = -15.6374310414537 | etot = -14.6424332454734 +880000 ekin = 0.291287955020511 | erot = 0.721287639199272 | epot = -15.6550088397353 | etot = -14.6424332455155 +881000 ekin = 0.30212877846463 | erot = 0.724613422810775 | epot = -15.6691754468226 | etot = -14.6424332455472 +882000 ekin = 0.311822304068824 | erot = 0.725201068176889 | epot = -15.6794566178125 | etot = -14.6424332455668 +883000 ekin = 0.320145243787706 | erot = 0.722987481104172 | epot = -15.6855659704655 | etot = -14.6424332455736 +884000 ekin = 0.326982762198909 | erot = 0.717996120159159 | epot = -15.6874121279265 | etot = -14.6424332455684 +885000 ekin = 0.332330882212481 | erot = 0.710323349672059 | epot = -15.6850874774374 | etot = -14.6424332455528 +886000 ekin = 0.33628767333099 | erot = 0.700117442976239 | epot = -15.678838361837 | etot = -14.6424332455298 +887000 ekin = 0.339032964151614 | erot = 0.687552454437006 | epot = -15.6690186640916 | etot = -14.642433245503 +888000 ekin = 0.340797654544347 | erot = 0.67280010094551 | epot = -15.6560310009666 | etot = -14.6424332454768 +889000 ekin = 0.341825106158976 | erot = 0.656003407102339 | epot = -15.6402617587166 | etot = -14.6424332454552 +890000 ekin = 0.342328347575176 | erot = 0.63725601316603 | epot = -15.6220176061831 | etot = -14.6424332454419 +891000 ekin = 0.342447730492056 | erot = 0.616590618570594 | epot = -15.601471594502 | etot = -14.6424332454393 +892000 ekin = 0.342214057411724 | erot = 0.593979026506924 | epot = -15.5786263293674 | etot = -14.6424332454488 +893000 ekin = 0.341522004910123 | erot = 0.569344767734232 | epot = -15.5533000181139 | etot = -14.6424332454695 +894000 ekin = 0.340117934117577 | erot = 0.542587519917294 | epot = -15.5251386995343 | etot = -14.6424332454994 +895000 ekin = 0.337605044782497 | erot = 0.51361677898196 | epot = -15.4936550692992 | etot = -14.6424332455348 +896000 ekin = 0.333467462872322 | erot = 0.482390775175684 | epot = -15.4582914836184 | etot = -14.6424332455704 +897000 ekin = 0.327113397522066 | erot = 0.448955709004578 | epot = -15.418502352127 | etot = -14.6424332456003 +898000 ekin = 0.317936017621476 | erot = 0.413480165460528 | epot = -15.3738494287003 | etot = -14.6424332456182 +899000 ekin = 0.305389123797598 | erot = 0.376280077470489 | epot = -15.3241024468861 | etot = -14.642433245618 +900000 ekin = 0.289072881398049 | erot = 0.337830752319602 | epot = -15.2693368793114 | etot = -14.6424332455938 +901000 ekin = 0.268822686263612 | erot = 0.298764046956934 | epot = -15.2100199787618 | etot = -14.6424332455413 +902000 ekin = 0.244791653973738 | erot = 0.259850521116738 | epot = -15.1470754205486 | etot = -14.6424332454581 +903000 ekin = 0.217514571467803 | erot = 0.221968047208507 | epot = -15.0819158640206 | etot = -14.6424332453443 +904000 ekin = 0.187939204416829 | erot = 0.186059692010109 | epot = -15.0164321416307 | etot = -14.6424332452037 +905000 ekin = 0.157410847736455 | erot = 0.153084564881008 | epot = -14.9529286576612 | etot = -14.6424332450437 +906000 ekin = 0.127599356275899 | erot = 0.123965703542346 | epot = -14.8939983046941 | etot = -14.6424332448759 +907000 ekin = 0.100365589134322 | erot = 0.0995389863868474 | epot = -14.8423378202363 | etot = -14.6424332447151 +908000 ekin = 0.077575985596966 | erot = 0.0805066337376087 | epot = -14.800515863912 | etot = -14.6424332445775 +909000 ekin = 0.0608876950043041 | erot = 0.0673982354547353 | epot = -14.7707191749375 | etot = -14.6424332444784 +910000 ekin = 0.0515382922982525 | erot = 0.0605415547693243 | epot = -14.7545130914978 | etot = -14.6424332444302 +911000 ekin = 0.0501789452889699 | erot = 0.0600446989615507 | epot = -14.7526568886895 | etot = -14.642433244439 +912000 ekin = 0.0567846925720978 | erot = 0.065790645022677 | epot = -14.7650085820984 | etot = -14.6424332445036 +913000 ekin = 0.0706603747930292 | erot = 0.0774445361871137 | epot = -14.7905381555968 | etot = -14.6424332446166 +914000 ekin = 0.0905398584091615 | erot = 0.0944735694308371 | epot = -14.8274466726047 | etot = -14.6424332447647 +915000 ekin = 0.114756144628398 | erot = 0.116178630208142 | epot = -14.8733680197681 | etot = -14.6424332449316 +916000 ekin = 0.141447043402251 | erot = 0.141736093139704 | epot = -14.9256163816432 | etot = -14.6424332451012 +917000 ekin = 0.168758535419812 | erot = 0.170247440489189 | epot = -14.9814392211683 | etot = -14.6424332452593 +918000 ekin = 0.195014913439607 | erot = 0.200793639368855 | epot = -15.0382417982036 | etot = -14.6424332453951 +919000 ekin = 0.218837422083647 | erot = 0.232490666336242 | epot = -15.0937613339215 | etot = -14.6424332455016 +920000 ekin = 0.239206641023718 | erot = 0.264542267092076 | epot = -15.1461821536915 | etot = -14.6424332455757 +921000 ekin = 0.255474577148654 | erot = 0.296286050802385 | epot = -15.1941938735684 | etot = -14.6424332456174 +922000 ekin = 0.267338631215765 | erot = 0.327229363205489 | epot = -15.2370012400499 | etot = -14.6424332456286 +923000 ekin = 0.274791412214202 | erot = 0.357072039937939 | epot = -15.2742966977655 | etot = -14.6424332456134 +924000 ekin = 0.278059017516371 | erot = 0.385714059433155 | epot = -15.3062063225259 | etot = -14.6424332455763 +925000 ekin = 0.277537405168372 | erot = 0.41324722009601 | epot = -15.3332178707874 | etot = -14.642433245523 +926000 ekin = 0.273733135238329 | erot = 0.439931173662005 | epot = -15.3560975543592 | etot = -14.6424332454589 +927000 ekin = 0.267211859641524 | erot = 0.466155363882809 | epot = -15.3758004689143 | etot = -14.6424332453899 +928000 ekin = 0.258555847536078 | erot = 0.492389553503158 | epot = -15.3933786463609 | etot = -14.6424332453217 +929000 ekin = 0.248330567891891 | erot = 0.519126582982283 | epot = -15.4098903961336 | etot = -14.6424332452594 +930000 ekin = 0.237059747166165 | erot = 0.546821711632301 | epot = -15.4263147040064 | etot = -14.6424332452079 +931000 ekin = 0.22520814480582 | erot = 0.575833282923993 | epot = -15.4434746729008 | etot = -14.6424332451709 +932000 ekin = 0.213171319365827 | erot = 0.606369490852174 | epot = -15.4619740553694 | etot = -14.6424332451514 +933000 ekin = 0.201271722995889 | erot = 0.63844569037927 | epot = -15.482150658526 | etot = -14.6424332451508 +934000 ekin = 0.189760460110152 | erot = 0.671856006699522 | epot = -15.5040497119791 | etot = -14.6424332451694 +935000 ekin = 0.178823941838377 | erot = 0.706161996587761 | epot = -15.527419183632 | etot = -14.6424332452058 +936000 ekin = 0.168594479114955 | erot = 0.740699865837585 | epot = -15.55172759021 | etot = -14.6424332452575 +937000 ekin = 0.159163635634861 | erot = 0.774606336206385 | epot = -15.5762032171619 | etot = -14.6424332453207 +938000 ekin = 0.150596971914849 | erot = 0.806861786796458 | epot = -15.5998920041019 | etot = -14.6424332453906 +939000 ekin = 0.142948711632359 | erot = 0.836347883526831 | epot = -15.6217298406214 | etot = -14.6424332454622 +940000 ekin = 0.136274889171099 | erot = 0.861915676028948 | epot = -15.64062381073 | etot = -14.6424332455299 +941000 ekin = 0.130643703198872 | erot = 0.882459199120565 | epot = -15.6555361479082 | etot = -14.6424332455888 +942000 ekin = 0.126142088160694 | erot = 0.896989065172162 | epot = -15.6655643989671 | etot = -14.6424332456342 +943000 ekin = 0.122877886110172 | erot = 0.904700444358873 | epot = -15.6700115761318 | etot = -14.6424332456628 +944000 ekin = 0.120977407412063 | erot = 0.905030230236876 | epot = -15.6684408833212 | etot = -14.6424332456723 +945000 ekin = 0.120578563690669 | erot = 0.897699054745604 | epot = -15.6607108640983 | etot = -14.642433245662 +946000 ekin = 0.12182010359348 | erot = 0.882735070928404 | epot = -15.6469884201544 | etot = -14.6424332456325 +947000 ekin = 0.124827761129084 | erot = 0.86047793559626 | epot = -15.6277389423113 | etot = -14.642433245586 +948000 ekin = 0.129698334168674 | erot = 0.831563037037796 | epot = -15.6036946167321 | etot = -14.6424332455257 +949000 ekin = 0.13648285755817 | erot = 0.796887554722047 | epot = -15.5758036577362 | etot = -14.6424332454559 +950000 ekin = 0.14517013893121 | erot = 0.757561255988166 | epot = -15.545164640301 | etot = -14.6424332453816 +951000 ekin = 0.155672002995183 | erot = 0.71484591609363 | epot = -15.5129511643966 | etot = -14.6424332453078 +952000 ekin = 0.167811650836291 | erot = 0.670087833250127 | epot = -15.480332729326 | etot = -14.6424332452396 +953000 ekin = 0.181316579471303 | erot = 0.624648095211848 | epot = -15.4483979198644 | etot = -14.6424332451812 +954000 ekin = 0.195817500701208 | erot = 0.579835080695611 | epot = -15.4180858265331 | etot = -14.6424332451363 +955000 ekin = 0.21085460687672 | erot = 0.536843219768569 | epot = -15.3901310717525 | etot = -14.6424332451072 +956000 ekin = 0.225892299837344 | erot = 0.496701376791255 | epot = -15.3650269217236 | etot = -14.642433245095 +957000 ekin = 0.240343066498587 | erot = 0.460233438093626 | epot = -15.3430097496914 | etot = -14.6424332450992 +958000 ekin = 0.253600493839353 | erot = 0.428032849893872 | epot = -15.324066588851 | etot = -14.6424332451178 +959000 ekin = 0.265080433748287 | erot = 0.400452005458765 | epot = -15.3079656843544 | etot = -14.6424332451473 +960000 ekin = 0.274268068130606 | erot = 0.377606549449485 | epot = -15.2943078627635 | etot = -14.6424332451834 +961000 ekin = 0.280767178003658 | erot = 0.359393861249483 | epot = -15.2825942844742 | etot = -14.642433245221 +962000 ekin = 0.284346484063545 | erot = 0.345524198816493 | epot = -15.2723039281349 | etot = -14.6424332452549 +963000 ekin = 0.28497681608998 | erot = 0.33556223232907 | epot = -15.2629722936994 | etot = -14.6424332452804 +964000 ekin = 0.282852494248157 | erot = 0.328975986496775 | epot = -15.2542617260389 | etot = -14.642433245294 +965000 ekin = 0.278391086615737 | erot = 0.325189577598745 | epot = -15.2460139095084 | etot = -14.6424332452939 +966000 ekin = 0.272207924679743 | erot = 0.323635640150781 | epot = -15.2382768101107 | etot = -14.6424332452802 +967000 ekin = 0.265065367870864 | erot = 0.323803079987444 | epot = -15.2313016931133 | etot = -14.642433245255 +968000 ekin = 0.25780129371415 | erot = 0.325275872290811 | epot = -15.2255104112269 | etot = -14.6424332452219 +969000 ekin = 0.251245661474385 | erot = 0.327759142576306 | epot = -15.2214380492365 | etot = -14.6424332451859 +970000 ekin = 0.246137008993216 | erot = 0.331089781181249 | epot = -15.2196600353262 | etot = -14.6424332451517 +971000 ekin = 0.243051319616145 | erot = 0.33523032566537 | epot = -15.2207148904055 | etot = -14.642433245124 +972000 ekin = 0.242353409638764 | erot = 0.340246678804933 | epot = -15.2250333335501 | etot = -14.6424332451064 +973000 ekin = 0.244176338162503 | erot = 0.346272190710957 | epot = -15.2328817739746 | etot = -14.6424332451011 +974000 ekin = 0.248428661658007 | erot = 0.353462430362089 | epot = -15.2443243371296 | etot = -14.6424332451095 +975000 ekin = 0.254824314802991 | erot = 0.361946299430811 | epot = -15.2592038593653 | etot = -14.6424332451315 +976000 ekin = 0.262926848820441 | erot = 0.371779749930123 | epot = -15.277139843917 | etot = -14.6424332451665 +977000 ekin = 0.272199235330791 | erot = 0.382908123264411 | epot = -15.2975406038079 | etot = -14.6424332452127 +978000 ekin = 0.282052066851645 | erot = 0.395142048097818 | epot = -15.3196273602177 | etot = -14.6424332452682 +979000 ekin = 0.291885751913936 | erot = 0.408150081471835 | epot = -15.3424690787158 | etot = -14.6424332453301 +980000 ekin = 0.301125083789936 | erot = 0.421469125223117 | epot = -15.365027454408 | etot = -14.642433245395 +981000 ekin = 0.309246535917406 | erot = 0.434531423656849 | epot = -15.3862112050333 | etot = -14.642433245459 +982000 ekin = 0.315799497490907 | erot = 0.446704965617073 | epot = -15.4049377086261 | etot = -14.6424332455181 +983000 ekin = 0.320422573221183 | erot = 0.457342632744156 | epot = -15.4201984515336 | etot = -14.6424332455683 +984000 ekin = 0.322855465258642 | erot = 0.465834622599602 | epot = -15.431123333464 | etot = -14.6424332456058 +985000 ekin = 0.322946302475343 | erot = 0.471658590974231 | epot = -15.4370381390774 | etot = -14.6424332456279 +986000 ekin = 0.320653917805922 | erot = 0.474422556590712 | epot = -15.4375097200295 | etot = -14.6424332456328 +987000 ekin = 0.316044627362369 | erot = 0.473896755515841 | epot = -15.4323746284984 | etot = -14.6424332456202 +988000 ekin = 0.309283477268975 | erot = 0.470032116945433 | epot = -15.421748839805 | etot = -14.6424332455906 +989000 ekin = 0.300620522169441 | erot = 0.462964620622199 | epot = -15.4060183883375 | etot = -14.6424332455459 +990000 ekin = 0.290373280691476 | erot = 0.45300626299518 | epot = -15.3858127891754 | etot = -14.6424332454887 +991000 ekin = 0.278906915705959 | erot = 0.440624526219509 | epot = -15.3619646873478 | etot = -14.6424332454224 +992000 ekin = 0.266613826415441 | erot = 0.426413006891514 | epot = -15.3354600786573 | etot = -14.6424332453503 +993000 ekin = 0.253894212446822 | erot = 0.411056197524864 | epot = -15.3073836552479 | etot = -14.6424332452762 +994000 ekin = 0.241138837000364 | erot = 0.395291372388786 | epot = -15.2788634545923 | etot = -14.6424332452032 +995000 ekin = 0.228714768907212 | erot = 0.379870207855612 | epot = -15.2510182218971 | etot = -14.6424332451343 +996000 ekin = 0.2169544174706 | erot = 0.365522282707863 | epot = -15.2249099452504 | etot = -14.642433245072 +997000 ekin = 0.206147766456188 | erot = 0.352922066139109 | epot = -15.2015030776136 | etot = -14.6424332450183 +998000 ekin = 0.196537413157987 | erot = 0.342660495991805 | epot = -15.1816311541246 | etot = -14.6424332449748 +999000 ekin = 0.188315843913178 | erot = 0.335221830006205 | epot = -15.1659709188618 | etot = -14.6424332449424 +1000000 ekin = 0.181624323067817 | erot = 0.330966139649826 | epot = -15.1550237076397 | etot = -14.642433244922 + 1000000 0.013453654 -1.5270261 0.011523695 -1.4973399 -8.4815516e-05 +Loop time of 29.1595 on 4 procs for 1000000 steps with 10 atoms + +Performance: 29630.171 tau/day, 34294.179 timesteps/s +96.5% CPU use with 4 MPI tasks x no OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0.8549 | 9.7585 | 17.369 | 226.0 | 33.47 +Bond | 0.12382 | 0.38401 | 0.60938 | 32.9 | 1.32 +Neigh | 0 | 0 | 0 | 0.0 | 0.00 +Comm | 2.9104 | 3.7862 | 4.6404 | 31.7 | 12.98 +Output | 2e-05 | 2.775e-05 | 3.1e-05 | 0.0 | 0.00 +Modify | 0.27411 | 1.1629 | 1.994 | 64.7 | 3.99 +Other | | 14.07 | | | 48.24 + +Nlocal: 2.5 ave 5 max 0 min +Histogram: 1 0 1 0 0 0 0 0 1 1 +Nghost: 7.5 ave 10 max 5 min +Histogram: 1 0 1 0 0 0 0 0 1 1 +Neighs: 17.5 ave 33 max 0 min +Histogram: 1 0 1 0 0 0 0 0 1 1 + +Total # of neighbors = 70 +Ave neighs/atom = 7 +Ave special neighs/atom = 3.6 +Neighbor list builds = 0 +Dangerous builds = 0 + +#write_restart config.${number}.* +Total wall time: 0:00:29 diff --git a/examples/USER/cgdna/examples/oxDNA/duplex1/log.27Nov18.duplex1.g++.1 b/examples/USER/cgdna/examples/oxDNA/duplex1/log.27Nov18.duplex1.g++.1 deleted file mode 100644 index abbd917f05..0000000000 --- a/examples/USER/cgdna/examples/oxDNA/duplex1/log.27Nov18.duplex1.g++.1 +++ /dev/null @@ -1,172 +0,0 @@ -LAMMPS (27 Nov 2018) - using 1 OpenMP thread(s) per MPI task -variable number equal 1 -variable ofreq equal 1000 -variable efreq equal 1000 - -units lj - -dimension 3 - -newton off - -boundary p p p - -atom_style hybrid bond ellipsoid -atom_modify sort 0 1.0 - -# Pair interactions require lists of neighbours to be calculated -neighbor 1.0 bin -neigh_modify every 1 delay 0 check yes - -read_data data.duplex1 - orthogonal box = (-20 -20 -20) to (20 20 20) - 1 by 1 by 1 MPI processor grid - reading atoms ... - 10 atoms - reading velocities ... - 10 velocities - 10 ellipsoids - scanning bonds ... - 2 = max bonds/atom - reading bonds ... - 8 bonds - 2 = max # of 1-2 neighbors - 2 = max # of 1-3 neighbors - 2 = max # of 1-4 neighbors - 4 = max # of special neighbors - -set atom * mass 3.1575 - 10 settings made for mass - -group all type 1 4 -10 atoms in group all - -# oxDNA bond interactions - FENE backbone -bond_style oxdna/fene -bond_coeff * 2.0 0.25 0.7525 - -# oxDNA pair interactions -pair_style hybrid/overlay oxdna/excv oxdna/stk oxdna/hbond oxdna/xstk oxdna/coaxstk -pair_coeff * * oxdna/excv 2.0 0.7 0.675 2.0 0.515 0.5 2.0 0.33 0.32 -pair_coeff * * oxdna/stk seqav 0.1 6.0 0.4 0.9 0.32 0.6 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2.0 0.65 2.0 0.65 -pair_coeff * * oxdna/hbond seqav 0.0 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45 -pair_coeff 1 4 oxdna/hbond seqav 1.077 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45 -pair_coeff 2 3 oxdna/hbond seqav 1.077 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45 -pair_coeff * * oxdna/xstk 47.5 0.575 0.675 0.495 0.655 2.25 0.791592653589793 0.58 1.7 1.0 0.68 1.7 1.0 0.68 1.5 0 0.65 1.7 0.875 0.68 1.7 0.875 0.68 -pair_coeff * * oxdna/coaxstk 46.0 0.4 0.6 0.22 0.58 2.0 2.541592653589793 0.65 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2.0 -0.65 2.0 -0.65 - -# NVE ensemble -fix 1 all nve/dot -#fix 1 all nve/dotc/langevin 0.1 0.1 0.03 457145 angmom 10 -#fix 1 all nve/asphere -#fix 2 all langevin 0.1 0.1 0.03 457145 angmom 10 - -timestep 1e-5 - -#comm_style tiled -#fix 3 all balance 10000 1.1 rcb - -#compute mol all chunk/atom molecule -#compute mychunk all vcm/chunk mol -#fix 4 all ave/time 10000 1 10000 c_mychunk[1] c_mychunk[2] c_mychunk[3] file vcm.txt mode vector - -#dump pos all xyz ${ofreq} traj.${number}.xyz - -#compute quat all property/atom quatw quati quatj quatk -#dump quat all custom ${ofreq} quat.${number}.txt id c_quat[1] c_quat[2] c_quat[3] c_quat[4] -#dump_modify quat sort id -#dump_modify quat format line "%d %13.6le %13.6le %13.6le %13.6le" - -compute erot all erotate/asphere -compute ekin all ke -compute epot all pe -variable erot equal c_erot -variable ekin equal c_ekin -variable epot equal c_epot -variable etot equal c_erot+c_ekin+c_epot -fix 5 all print ${efreq} "$(step) ekin = ${ekin} | erot = ${erot} | epot = ${epot} | etot = ${etot}" screen yes -fix 5 all print 1000 "$(step) ekin = ${ekin} | erot = ${erot} | epot = ${epot} | etot = ${etot}" screen yes - -#dump out all custom ${ofreq} out.${number}.txt id x y z vx vy vz fx fy fz tqx tqy tqz -#dump_modify out sort id -#dump_modify out format line "%d %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le" - -run 10000 -Neighbor list info ... - update every 1 steps, delay 0 steps, check yes - max neighbors/atom: 2000, page size: 100000 - master list distance cutoff = 1.92828 - ghost atom cutoff = 1.92828 - binsize = 0.964142, bins = 42 42 42 - 5 neighbor lists, perpetual/occasional/extra = 5 0 0 - (1) pair oxdna/excv, perpetual - attributes: half, newton off - pair build: half/bin/newtoff - stencil: half/bin/3d/newtoff - bin: standard - (2) pair oxdna/stk, perpetual, copy from (1) - attributes: half, newton off - pair build: copy - stencil: none - bin: none - (3) pair oxdna/hbond, perpetual, copy from (1) - attributes: half, newton off - pair build: copy - stencil: none - bin: none - (4) pair oxdna/xstk, perpetual, copy from (1) - attributes: half, newton off - pair build: copy - stencil: none - bin: none - (5) pair oxdna/coaxstk, perpetual, copy from (1) - attributes: half, newton off - pair build: copy - stencil: none - bin: none -Per MPI rank memory allocation (min/avg/max) = 2.859 | 2.859 | 2.859 Mbytes -Step Temp E_pair E_mol TotEng Press - 0 0 -1.4711818 0.0069384985 -1.4642433 -6.2745089e-05 -1000 ekin = 0.00113448721737003 | erot = 0.00413455947734281 | epot = -14.6477022915193 | etot = -14.6424332448246 -2000 ekin = 0.00449927223902336 | erot = 0.0164446434455805 | epot = -14.6633771605337 | etot = -14.6424332448491 -3000 ekin = 0.00997964450841065 | erot = 0.0366523356056461 | epot = -14.6890652250033 | etot = -14.6424332448892 -4000 ekin = 0.0173888111295073 | erot = 0.0643039804300221 | epot = -14.7241260365031 | etot = -14.6424332449436 -5000 ekin = 0.0264744514136619 | erot = 0.0987844033142066 | epot = -14.7676920997383 | etot = -14.6424332450104 -6000 ekin = 0.0369277948556079 | erot = 0.139336571052565 | epot = -14.8186976109956 | etot = -14.6424332450875 -7000 ekin = 0.04839505571915 | erot = 0.18508629569208 | epot = -14.8759145965832 | etot = -14.642433245172 -8000 ekin = 0.0604909336920643 | erot = 0.23507130752353 | epot = -14.9379954864767 | etot = -14.6424332452611 -9000 ekin = 0.0728137406440561 | erot = 0.288273694501537 | epot = -15.003520680497 | etot = -14.6424332453514 -10000 ekin = 0.0849615563085879 | erot = 0.343654369293472 | epot = -15.0710491710418 | etot = -14.6424332454398 - 10000 0.0062934486 -1.5138305 0.0067255788 -1.4986088 -9.9021593e-05 -Loop time of 0.141929 on 1 procs for 10000 steps with 10 atoms - -Performance: 60875.649 tau/day, 70457.927 timesteps/s -99.9% CPU use with 1 MPI tasks x 1 OpenMP threads - -MPI task timing breakdown: -Section | min time | avg time | max time |%varavg| %total ---------------------------------------------------------------- -Pair | 0.11467 | 0.11467 | 0.11467 | 0.0 | 80.79 -Bond | 0.0050094 | 0.0050094 | 0.0050094 | 0.0 | 3.53 -Neigh | 0 | 0 | 0 | 0.0 | 0.00 -Comm | 0.0013616 | 0.0013616 | 0.0013616 | 0.0 | 0.96 -Output | 4.0531e-06 | 4.0531e-06 | 4.0531e-06 | 0.0 | 0.00 -Modify | 0.017901 | 0.017901 | 0.017901 | 0.0 | 12.61 -Other | | 0.002982 | | | 2.10 - -Nlocal: 10 ave 10 max 10 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Nghost: 0 ave 0 max 0 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Neighs: 43 ave 43 max 43 min -Histogram: 1 0 0 0 0 0 0 0 0 0 - -Total # of neighbors = 43 -Ave neighs/atom = 4.3 -Ave special neighs/atom = 3.6 -Neighbor list builds = 0 -Dangerous builds = 0 - -#write_restart config.${number}.* -Total wall time: 0:00:00 diff --git a/examples/USER/cgdna/examples/oxDNA/duplex1/log.27Nov18.duplex1.g++.4 b/examples/USER/cgdna/examples/oxDNA/duplex1/log.27Nov18.duplex1.g++.4 deleted file mode 100644 index 78712bf913..0000000000 --- a/examples/USER/cgdna/examples/oxDNA/duplex1/log.27Nov18.duplex1.g++.4 +++ /dev/null @@ -1,172 +0,0 @@ -LAMMPS (27 Nov 2018) - using 1 OpenMP thread(s) per MPI task -variable number equal 1 -variable ofreq equal 1000 -variable efreq equal 1000 - -units lj - -dimension 3 - -newton off - -boundary p p p - -atom_style hybrid bond ellipsoid -atom_modify sort 0 1.0 - -# Pair interactions require lists of neighbours to be calculated -neighbor 1.0 bin -neigh_modify every 1 delay 0 check yes - -read_data data.duplex1 - orthogonal box = (-20 -20 -20) to (20 20 20) - 1 by 2 by 2 MPI processor grid - reading atoms ... - 10 atoms - reading velocities ... - 10 velocities - 10 ellipsoids - scanning bonds ... - 2 = max bonds/atom - reading bonds ... - 8 bonds - 2 = max # of 1-2 neighbors - 2 = max # of 1-3 neighbors - 2 = max # of 1-4 neighbors - 4 = max # of special neighbors - -set atom * mass 3.1575 - 10 settings made for mass - -group all type 1 4 -10 atoms in group all - -# oxDNA bond interactions - FENE backbone -bond_style oxdna/fene -bond_coeff * 2.0 0.25 0.7525 - -# oxDNA pair interactions -pair_style hybrid/overlay oxdna/excv oxdna/stk oxdna/hbond oxdna/xstk oxdna/coaxstk -pair_coeff * * oxdna/excv 2.0 0.7 0.675 2.0 0.515 0.5 2.0 0.33 0.32 -pair_coeff * * oxdna/stk seqav 0.1 6.0 0.4 0.9 0.32 0.6 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2.0 0.65 2.0 0.65 -pair_coeff * * oxdna/hbond seqav 0.0 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45 -pair_coeff 1 4 oxdna/hbond seqav 1.077 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45 -pair_coeff 2 3 oxdna/hbond seqav 1.077 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45 -pair_coeff * * oxdna/xstk 47.5 0.575 0.675 0.495 0.655 2.25 0.791592653589793 0.58 1.7 1.0 0.68 1.7 1.0 0.68 1.5 0 0.65 1.7 0.875 0.68 1.7 0.875 0.68 -pair_coeff * * oxdna/coaxstk 46.0 0.4 0.6 0.22 0.58 2.0 2.541592653589793 0.65 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2.0 -0.65 2.0 -0.65 - -# NVE ensemble -fix 1 all nve/dot -#fix 1 all nve/dotc/langevin 0.1 0.1 0.03 457145 angmom 10 -#fix 1 all nve/asphere -#fix 2 all langevin 0.1 0.1 0.03 457145 angmom 10 - -timestep 1e-5 - -#comm_style tiled -#fix 3 all balance 10000 1.1 rcb - -#compute mol all chunk/atom molecule -#compute mychunk all vcm/chunk mol -#fix 4 all ave/time 10000 1 10000 c_mychunk[1] c_mychunk[2] c_mychunk[3] file vcm.txt mode vector - -#dump pos all xyz ${ofreq} traj.${number}.xyz - -#compute quat all property/atom quatw quati quatj quatk -#dump quat all custom ${ofreq} quat.${number}.txt id c_quat[1] c_quat[2] c_quat[3] c_quat[4] -#dump_modify quat sort id -#dump_modify quat format line "%d %13.6le %13.6le %13.6le %13.6le" - -compute erot all erotate/asphere -compute ekin all ke -compute epot all pe -variable erot equal c_erot -variable ekin equal c_ekin -variable epot equal c_epot -variable etot equal c_erot+c_ekin+c_epot -fix 5 all print ${efreq} "$(step) ekin = ${ekin} | erot = ${erot} | epot = ${epot} | etot = ${etot}" screen yes -fix 5 all print 1000 "$(step) ekin = ${ekin} | erot = ${erot} | epot = ${epot} | etot = ${etot}" screen yes - -#dump out all custom ${ofreq} out.${number}.txt id x y z vx vy vz fx fy fz tqx tqy tqz -#dump_modify out sort id -#dump_modify out format line "%d %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le" - -run 10000 -Neighbor list info ... - update every 1 steps, delay 0 steps, check yes - max neighbors/atom: 2000, page size: 100000 - master list distance cutoff = 1.92828 - ghost atom cutoff = 1.92828 - binsize = 0.964142, bins = 42 42 42 - 5 neighbor lists, perpetual/occasional/extra = 5 0 0 - (1) pair oxdna/excv, perpetual - attributes: half, newton off - pair build: half/bin/newtoff - stencil: half/bin/3d/newtoff - bin: standard - (2) pair oxdna/stk, perpetual, copy from (1) - attributes: half, newton off - pair build: copy - stencil: none - bin: none - (3) pair oxdna/hbond, perpetual, copy from (1) - attributes: half, newton off - pair build: copy - stencil: none - bin: none - (4) pair oxdna/xstk, perpetual, copy from (1) - attributes: half, newton off - pair build: copy - stencil: none - bin: none - (5) pair oxdna/coaxstk, perpetual, copy from (1) - attributes: half, newton off - pair build: copy - stencil: none - bin: none -Per MPI rank memory allocation (min/avg/max) = 7.341 | 7.523 | 7.705 Mbytes -Step Temp E_pair E_mol TotEng Press - 0 0 -1.4711818 0.0069384985 -1.4642433 -6.2745089e-05 -1000 ekin = 0.00113448721737009 | erot = 0.0041345594773427 | epot = -14.6477022915193 | etot = -14.6424332448246 -2000 ekin = 0.00449927223902292 | erot = 0.0164446434455803 | epot = -14.6633771605337 | etot = -14.6424332448491 -3000 ekin = 0.00997964450840756 | erot = 0.0366523356056465 | epot = -14.6890652250033 | etot = -14.6424332448892 -4000 ekin = 0.017388811129498 | erot = 0.0643039804300254 | epot = -14.7241260365031 | etot = -14.6424332449436 -5000 ekin = 0.0264744514136422 | erot = 0.098784403314214 | epot = -14.7676920997383 | etot = -14.6424332450104 -6000 ekin = 0.0369277948555727 | erot = 0.139336571052581 | epot = -14.8186976109956 | etot = -14.6424332450875 -7000 ekin = 0.0483950557190949 | erot = 0.185086295692111 | epot = -14.8759145965832 | etot = -14.642433245172 -8000 ekin = 0.0604909336919856 | erot = 0.235071307523583 | epot = -14.9379954864767 | etot = -14.6424332452611 -9000 ekin = 0.0728137406439517 | erot = 0.288273694501617 | epot = -15.003520680497 | etot = -14.6424332453514 -10000 ekin = 0.0849615563084573 | erot = 0.34365436929359 | epot = -15.0710491710418 | etot = -14.6424332454398 - 10000 0.0062934486 -1.5138305 0.0067255788 -1.4986088 -0.00010196899 -Loop time of 0.134536 on 4 procs for 10000 steps with 10 atoms - -Performance: 64220.659 tau/day, 74329.466 timesteps/s -97.3% CPU use with 4 MPI tasks x 1 OpenMP threads - -MPI task timing breakdown: -Section | min time | avg time | max time |%varavg| %total ---------------------------------------------------------------- -Pair | 0.0030077 | 0.052212 | 0.093066 | 17.4 | 38.81 -Bond | 0.00061846 | 0.00234 | 0.0039451 | 2.8 | 1.74 -Neigh | 0 | 0 | 0 | 0.0 | 0.00 -Comm | 0.013431 | 0.014091 | 0.014596 | 0.4 | 10.47 -Output | 5.0783e-05 | 5.1141e-05 | 5.1498e-05 | 0.0 | 0.04 -Modify | 0.0011578 | 0.0059478 | 0.010331 | 4.8 | 4.42 -Other | | 0.05989 | | | 44.52 - -Nlocal: 2.5 ave 5 max 0 min -Histogram: 1 0 1 0 0 0 0 0 1 1 -Nghost: 7.5 ave 10 max 5 min -Histogram: 1 0 1 0 0 0 0 0 1 1 -Neighs: 17.5 ave 33 max 0 min -Histogram: 1 0 1 0 0 0 0 0 1 1 - -Total # of neighbors = 70 -Ave neighs/atom = 7 -Ave special neighs/atom = 3.6 -Neighbor list builds = 0 -Dangerous builds = 0 - -#write_restart config.${number}.* -Total wall time: 0:00:00 diff --git a/examples/USER/cgdna/examples/oxDNA/duplex2/data.duplex2 b/examples/USER/cgdna/examples/oxDNA/duplex2/data.duplex2 index 6547def910..72872d431a 100644 --- a/examples/USER/cgdna/examples/oxDNA/duplex2/data.duplex2 +++ b/examples/USER/cgdna/examples/oxDNA/duplex2/data.duplex2 @@ -38,7 +38,7 @@ Atoms 15 3 4.860249842674773e-01 3.518234140414733e-01 3.897628551303119e-01 2 1 1 16 4 5.999999999999995e-01 -3.330669073875470e-17 -3.330669073875470e-16 2 1 1 -# Atom-ID, translational, rotational velocity +# Atom-ID, translational velocity, angular momentum Velocities 1 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 diff --git a/examples/USER/cgdna/examples/oxDNA/duplex2/in.duplex2 b/examples/USER/cgdna/examples/oxDNA/duplex2/in.duplex2 index a5a09af9f4..d80e7bbc0e 100644 --- a/examples/USER/cgdna/examples/oxDNA/duplex2/in.duplex2 +++ b/examples/USER/cgdna/examples/oxDNA/duplex2/in.duplex2 @@ -1,6 +1,7 @@ variable number equal 2 variable ofreq equal 1000 variable efreq equal 1000 +variable T equal 0.1 units lj @@ -30,7 +31,7 @@ bond_coeff * 2.0 0.25 0.7525 # oxDNA pair interactions pair_style hybrid/overlay oxdna/excv oxdna/stk oxdna/hbond oxdna/xstk oxdna/coaxstk pair_coeff * * oxdna/excv 2.0 0.7 0.675 2.0 0.515 0.5 2.0 0.33 0.32 -pair_coeff * * oxdna/stk seqav 0.1 6.0 0.4 0.9 0.32 0.6 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2.0 0.65 2.0 0.65 +pair_coeff * * oxdna/stk seqav ${T} 1.3448 2.6568 6.0 0.4 0.9 0.32 0.6 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2.0 0.65 2.0 0.65 pair_coeff * * oxdna/hbond seqav 0.0 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45 pair_coeff 1 4 oxdna/hbond seqav 1.077 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45 pair_coeff 2 3 oxdna/hbond seqav 1.077 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45 @@ -39,9 +40,9 @@ pair_coeff * * oxdna/coaxstk 46.0 0.4 0.6 0.22 0.58 2.0 2.541592653589793 0.65 1 # NVE ensemble #fix 1 all nve/dot -fix 1 all nve/dotc/langevin 0.1 0.1 0.03 457145 angmom 10 +fix 1 all nve/dotc/langevin ${T} ${T} 0.03 457145 angmom 10 #fix 1 all nve/asphere -#fix 2 all langevin 0.1 0.1 0.03 457145 angmom 10 +#fix 2 all langevin ${T} ${T} 0.03 457145 angmom 10 timestep 1e-5 @@ -72,6 +73,6 @@ fix 5 all print ${efreq} "$(step) ekin = ${ekin} | erot = ${erot} | epot = ${e #dump_modify out sort id #dump_modify out format line "%d %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le" -run 10000 +run 1000000 #write_restart config.${number}.* diff --git a/examples/USER/cgdna/examples/oxDNA/duplex2/log.18Jun19.duplex2.g++.1 b/examples/USER/cgdna/examples/oxDNA/duplex2/log.18Jun19.duplex2.g++.1 new file mode 100644 index 0000000000..29eaec2dab --- /dev/null +++ b/examples/USER/cgdna/examples/oxDNA/duplex2/log.18Jun19.duplex2.g++.1 @@ -0,0 +1,1167 @@ +LAMMPS (18 Jun 2019) +variable number equal 2 +variable ofreq equal 1000 +variable efreq equal 1000 +variable T equal 0.1 + +units lj + +dimension 3 + +newton off + +boundary p p p + +atom_style hybrid bond ellipsoid +atom_modify sort 0 1.0 + +# Pair interactions require lists of neighbours to be calculated +neighbor 1.0 bin +neigh_modify every 1 delay 0 check yes + +read_data data.duplex2 + orthogonal box = (-20 -20 -20) to (20 20 20) + 1 by 1 by 1 MPI processor grid + reading atoms ... + 16 atoms + reading velocities ... + 16 velocities + 16 ellipsoids + scanning bonds ... + 2 = max bonds/atom + reading bonds ... + 13 bonds + 2 = max # of 1-2 neighbors + 2 = max # of 1-3 neighbors + 4 = max # of 1-4 neighbors + 6 = max # of special neighbors + special bonds CPU = 0.000135 secs + read_data CPU = 0.002118 secs + +set atom * mass 3.1575 + 16 settings made for mass + +group all type 1 4 +16 atoms in group all + +# oxDNA bond interactions - FENE backbone +bond_style oxdna/fene +bond_coeff * 2.0 0.25 0.7525 + +# oxDNA pair interactions +pair_style hybrid/overlay oxdna/excv oxdna/stk oxdna/hbond oxdna/xstk oxdna/coaxstk +pair_coeff * * oxdna/excv 2.0 0.7 0.675 2.0 0.515 0.5 2.0 0.33 0.32 +pair_coeff * * oxdna/stk seqav ${T} 1.3448 2.6568 6.0 0.4 0.9 0.32 0.6 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2.0 0.65 2.0 0.65 +pair_coeff * * oxdna/stk seqav 0.1 1.3448 2.6568 6.0 0.4 0.9 0.32 0.6 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2.0 0.65 2.0 0.65 +pair_coeff * * oxdna/hbond seqav 0.0 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45 +pair_coeff 1 4 oxdna/hbond seqav 1.077 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45 +pair_coeff 2 3 oxdna/hbond seqav 1.077 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45 +pair_coeff * * oxdna/xstk 47.5 0.575 0.675 0.495 0.655 2.25 0.791592653589793 0.58 1.7 1.0 0.68 1.7 1.0 0.68 1.5 0 0.65 1.7 0.875 0.68 1.7 0.875 0.68 +pair_coeff * * oxdna/coaxstk 46.0 0.4 0.6 0.22 0.58 2.0 2.541592653589793 0.65 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2.0 -0.65 2.0 -0.65 + +# NVE ensemble +#fix 1 all nve/dot +fix 1 all nve/dotc/langevin ${T} ${T} 0.03 457145 angmom 10 +fix 1 all nve/dotc/langevin 0.1 ${T} 0.03 457145 angmom 10 +fix 1 all nve/dotc/langevin 0.1 0.1 0.03 457145 angmom 10 +#fix 1 all nve/asphere +#fix 2 all langevin ${T} ${T} 0.03 457145 angmom 10 + +timestep 1e-5 + +#comm_style tiled +#fix 3 all balance 10000 1.1 rcb + +#compute mol all chunk/atom molecule +#compute mychunk all vcm/chunk mol +#fix 4 all ave/time 10000 1 10000 c_mychunk[1] c_mychunk[2] c_mychunk[3] file vcm.txt mode vector + +#dump pos all xyz ${ofreq} traj.${number}.xyz + +#compute quat all property/atom quatw quati quatj quatk +#dump quat all custom ${ofreq} quat.${number}.txt id c_quat[1] c_quat[2] c_quat[3] c_quat[4] +#dump_modify quat sort id +#dump_modify quat format line "%d %13.6le %13.6le %13.6le %13.6le" + +compute erot all erotate/asphere +compute ekin all ke +compute epot all pe +variable erot equal c_erot +variable ekin equal c_ekin +variable epot equal c_epot +variable etot equal c_erot+c_ekin+c_epot +fix 5 all print ${efreq} "$(step) ekin = ${ekin} | erot = ${erot} | epot = ${epot} | etot = ${etot}" screen yes +fix 5 all print 1000 "$(step) ekin = ${ekin} | erot = ${erot} | epot = ${epot} | etot = ${etot}" screen yes + +#dump out all custom ${ofreq} out.${number}.txt id x y z vx vy vz fx fy fz tqx tqy tqz +#dump_modify out sort id +#dump_modify out format line "%d %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le" + +run 1000000 +Neighbor list info ... + update every 1 steps, delay 0 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 1.92828 + ghost atom cutoff = 1.92828 + binsize = 0.964142, bins = 42 42 42 + 5 neighbor lists, perpetual/occasional/extra = 5 0 0 + (1) pair oxdna/excv, perpetual + attributes: half, newton off + pair build: half/bin/newtoff + stencil: half/bin/3d/newtoff + bin: standard + (2) pair oxdna/stk, perpetual, copy from (1) + attributes: half, newton off + pair build: copy + stencil: none + bin: none + (3) pair oxdna/hbond, perpetual, copy from (1) + attributes: half, newton off + pair build: copy + stencil: none + bin: none + (4) pair oxdna/xstk, perpetual, copy from (1) + attributes: half, newton off + pair build: copy + stencil: none + bin: none + (5) pair oxdna/coaxstk, perpetual, copy from (1) + attributes: half, newton off + pair build: copy + stencil: none + bin: none +Per MPI rank memory allocation (min/avg/max) = 2.861 | 2.861 | 2.861 Mbytes +Step Temp E_pair E_mol TotEng Press + 0 0 -1.5402493 0.0070469125 -1.5332024 6.0760034e-06 +1000 ekin = 1.54234964773389 | erot = 1.71563526070267 | epot = -24.5477045187653 | etot = -21.2897196103287 +2000 ekin = 1.85988866919215 | erot = 1.9424302796508 | epot = -24.4843044999595 | etot = -20.6819855511165 +3000 ekin = 2.68354339452998 | erot = 2.14216528317607 | epot = -24.4019350693561 | etot = -19.57622639165 +4000 ekin = 2.04461800191989 | erot = 1.49015219763161 | epot = -24.2959428773347 | etot = -20.7611726777832 +5000 ekin = 1.76794859210155 | erot = 2.54289684465819 | epot = -24.2337587736863 | etot = -19.9229133369266 +6000 ekin = 3.1106424806079 | erot = 2.04409805200893 | epot = -24.1585729744133 | etot = -19.0038324417964 +7000 ekin = 3.21360097519306 | erot = 2.71941303605722 | epot = -24.0566262531609 | etot = -18.1236122419107 +8000 ekin = 2.82489935901743 | erot = 2.66790555575695 | epot = -24.0194805097633 | etot = -18.526675594989 +9000 ekin = 2.69381302856378 | erot = 2.59107820129446 | epot = -23.9216126050554 | etot = -18.6367213751972 +10000 ekin = 2.65765007662471 | erot = 1.95562671446597 | epot = -23.7978334881241 | etot = -19.1845566970334 +11000 ekin = 2.33860420545645 | erot = 2.067780391377 | epot = -23.6589739475584 | etot = -19.2525893507249 +12000 ekin = 2.71377849618258 | erot = 2.08757199120023 | epot = -23.5483571834756 | etot = -18.7470066960928 +13000 ekin = 2.62930153930326 | erot = 2.36926332727578 | epot = -23.4509629615768 | etot = -18.4523980949977 +14000 ekin = 3.08200416316113 | erot = 2.52340746291244 | epot = -23.3378147651053 | etot = -17.7324031390317 +15000 ekin = 2.98008664779269 | erot = 1.871644860882 | epot = -23.1940665570191 | etot = -18.3423350483444 +16000 ekin = 2.18422481774796 | erot = 2.13029325858584 | epot = -23.0709946755646 | etot = -18.7564765992308 +17000 ekin = 1.86029951221073 | erot = 2.30856215831156 | epot = -22.9148241979648 | etot = -18.7459625274425 +18000 ekin = 2.26757205264074 | erot = 1.23282183419698 | epot = -22.7667657090377 | etot = -19.2663718222 +19000 ekin = 2.39717301992408 | erot = 2.43814713185077 | epot = -22.6249045514987 | etot = -17.7895843997239 +20000 ekin = 2.4972090427325 | erot = 2.14695469209109 | epot = -22.4687873897505 | etot = -17.824623654927 +21000 ekin = 2.97591775854817 | erot = 2.40996811711195 | epot = -22.580475447988 | etot = -17.1945895723278 +22000 ekin = 3.04727168578733 | erot = 1.83825256427932 | epot = -22.6695853833015 | etot = -17.7840611332348 +23000 ekin = 2.64835731773193 | erot = 2.22162785501705 | epot = -22.6565689169972 | etot = -17.7865837442483 +24000 ekin = 2.64866576787001 | erot = 2.80157082833922 | epot = -22.6222797420052 | etot = -17.172043145796 +25000 ekin = 2.29527970143855 | erot = 2.22049811939069 | epot = -22.6228421013006 | etot = -18.1070642804714 +26000 ekin = 1.6242512251805 | erot = 2.52390475262917 | epot = -22.6746055892862 | etot = -18.5264496114765 +27000 ekin = 1.74746467550781 | erot = 3.7138606202505 | epot = -22.7150312690973 | etot = -17.253705973339 +28000 ekin = 2.26500128280479 | erot = 2.34791343563183 | epot = -22.7926648585827 | etot = -18.179750140146 +29000 ekin = 2.04774074424512 | erot = 1.86347261547111 | epot = -22.8081204933408 | etot = -18.8969071336246 +30000 ekin = 2.41140146125466 | erot = 1.86296915421469 | epot = -22.7764612164305 | etot = -18.5020906009612 +31000 ekin = 2.76447800297261 | erot = 2.7393253404681 | epot = -22.7808698156252 | etot = -17.2770664721845 +32000 ekin = 2.08103539953574 | erot = 2.81216171106146 | epot = -22.8081908465747 | etot = -17.9149937359775 +33000 ekin = 2.08672340074227 | erot = 3.65510023442519 | epot = -22.7575363468642 | etot = -17.0157127116967 +34000 ekin = 2.34180742039869 | erot = 3.10027175201874 | epot = -22.6657421559553 | etot = -17.2236629835378 +35000 ekin = 2.32430602395272 | erot = 2.01607522370048 | epot = -22.5813705492547 | etot = -18.2409893016015 +36000 ekin = 1.91917507775106 | erot = 1.97289747304336 | epot = -22.481118994336 | etot = -18.5890464435416 +37000 ekin = 1.57560528527468 | erot = 2.63029511887642 | epot = -22.4456699464305 | etot = -18.2397695422794 +38000 ekin = 2.20652731867584 | erot = 2.89671984141264 | epot = -22.3965902387972 | etot = -17.2933430787087 +39000 ekin = 2.54765822667968 | erot = 2.47352619735437 | epot = -22.3525131983352 | etot = -17.3313287743012 +40000 ekin = 2.24172560748699 | erot = 1.87314319107769 | epot = -22.3791956830638 | etot = -18.2643268844991 +41000 ekin = 2.45176361826215 | erot = 2.49992612251747 | epot = -22.4441192111887 | etot = -17.492429470409 +42000 ekin = 2.68254780786499 | erot = 2.04382131696989 | epot = -22.4352265851614 | etot = -17.7088574603266 +43000 ekin = 2.39383336858508 | erot = 1.66587291396325 | epot = -22.4337243898148 | etot = -18.3740181072664 +44000 ekin = 2.30758870966958 | erot = 2.39381816537748 | epot = -22.4636201484766 | etot = -17.7622132734295 +45000 ekin = 1.84308929771583 | erot = 2.25880380151546 | epot = -22.5697712917435 | etot = -18.4678781925122 +46000 ekin = 1.98608215049724 | erot = 3.02136983211363 | epot = -22.5606085774834 | etot = -17.5531565948725 +47000 ekin = 1.31457586857024 | erot = 1.99780932836913 | epot = -22.5522289127255 | etot = -19.2398437157862 +48000 ekin = 2.59855199680394 | erot = 1.90772345027383 | epot = -22.5972680906756 | etot = -18.0909926435978 +49000 ekin = 2.32140483916261 | erot = 2.72932938830521 | epot = -22.6070371995253 | etot = -17.5563029720575 +50000 ekin = 2.48248035385828 | erot = 3.42713570109107 | epot = -22.5294064222472 | etot = -16.6197903672979 +51000 ekin = 2.73677705777971 | erot = 1.43285265191038 | epot = -22.4272695862992 | etot = -18.2576398766091 +52000 ekin = 3.03746109762767 | erot = 1.97878223690383 | epot = -22.4105817052324 | etot = -17.3943383707009 +53000 ekin = 2.4689045601064 | erot = 4.26434186327668 | epot = -22.4059567857723 | etot = -15.6727103623892 +54000 ekin = 2.48025904071626 | erot = 2.36957879662632 | epot = -22.4049729842648 | etot = -17.5551351469222 +55000 ekin = 2.28269445417385 | erot = 1.92149293107792 | epot = -22.4643082993723 | etot = -18.2601209141205 +56000 ekin = 2.36225428889468 | erot = 2.21818002425493 | epot = -22.5516502452859 | etot = -17.9712159321363 +57000 ekin = 2.5222034650231 | erot = 2.87044520913643 | epot = -22.6517599833465 | etot = -17.259111309187 +58000 ekin = 2.50677816066749 | erot = 2.80087142998998 | epot = -22.7046490897181 | etot = -17.3969994990606 +59000 ekin = 2.7442153349817 | erot = 2.17375311266844 | epot = -22.7630968852437 | etot = -17.8451284375935 +60000 ekin = 3.28881699963202 | erot = 1.98491245229834 | epot = -22.7493813857704 | etot = -17.47565193384 +61000 ekin = 2.42749732003947 | erot = 1.80500042748845 | epot = -22.6954080097403 | etot = -18.4629102622124 +62000 ekin = 2.82051548232979 | erot = 1.69220614985812 | epot = -22.5840860651657 | etot = -18.0713644329778 +63000 ekin = 3.66818847100113 | erot = 1.91510536540651 | epot = -22.4235299160084 | etot = -16.8402360796008 +64000 ekin = 3.60192162647095 | erot = 3.02302140162941 | epot = -22.4028966408394 | etot = -15.777953612739 +65000 ekin = 3.37797300912952 | erot = 3.90646944425564 | epot = -22.3508227873685 | etot = -15.0663803339833 +66000 ekin = 2.90796062513305 | erot = 2.46538835419998 | epot = -22.2656130116827 | etot = -16.8922640323497 +67000 ekin = 2.57641483706472 | erot = 2.1063925708314 | epot = -22.1586423836372 | etot = -17.4758349757411 +68000 ekin = 2.5516902727465 | erot = 2.46870040285813 | epot = -22.1454741588102 | etot = -17.1250834832056 +69000 ekin = 2.42897294997603 | erot = 2.86774435615082 | epot = -22.1788582092806 | etot = -16.8821409031537 +70000 ekin = 3.08406596014674 | erot = 2.51171720098584 | epot = -22.2680651617951 | etot = -16.6722820006626 +71000 ekin = 2.55052721315253 | erot = 2.49486492124423 | epot = -22.3940848075589 | etot = -17.3486926731621 +72000 ekin = 1.77666138705941 | erot = 2.52301579845699 | epot = -22.4956655989824 | etot = -18.195988413466 +73000 ekin = 1.86857924146303 | erot = 2.33110810852355 | epot = -22.5401005215029 | etot = -18.3404131715163 +74000 ekin = 3.14875320805144 | erot = 2.12002807961601 | epot = -22.5354282257998 | etot = -17.2666469381323 +75000 ekin = 2.60566180511119 | erot = 2.16421143606062 | epot = -22.5109742574449 | etot = -17.7411010162731 +76000 ekin = 1.94500512300058 | erot = 1.94681992806367 | epot = -22.5134561384461 | etot = -18.6216310873819 +77000 ekin = 2.09005510206219 | erot = 2.13354294429721 | epot = -22.5157248384152 | etot = -18.2921267920558 +78000 ekin = 2.48381695181472 | erot = 2.49598603867482 | epot = -22.449809286019 | etot = -17.4700062955295 +79000 ekin = 3.09582217320064 | erot = 2.46630074007712 | epot = -22.3464652405845 | etot = -16.7843423273068 +80000 ekin = 2.51380629427529 | erot = 1.89207626467031 | epot = -22.2775752521275 | etot = -17.8716926931819 +81000 ekin = 2.32322780911516 | erot = 2.24954513249787 | epot = -22.2655235360186 | etot = -17.6927505944055 +82000 ekin = 1.54779729878415 | erot = 2.01487148845307 | epot = -22.2126473128098 | etot = -18.6499785255726 +83000 ekin = 2.24267653112482 | erot = 3.34721522119025 | epot = -22.2063282117648 | etot = -16.6164364594498 +84000 ekin = 2.86948852339533 | erot = 2.11915315181827 | epot = -22.2055386975617 | etot = -17.2168970223481 +85000 ekin = 3.13802387827786 | erot = 2.93900498543376 | epot = -22.2240733080824 | etot = -16.1470444443708 +86000 ekin = 3.46160079449538 | erot = 2.80798287444336 | epot = -22.2732645073155 | etot = -16.0036808383767 +87000 ekin = 3.63139446909085 | erot = 2.3166794204513 | epot = -22.2567856660101 | etot = -16.308711776468 +88000 ekin = 3.15348314879937 | erot = 2.2785763709033 | epot = -22.2154422326699 | etot = -16.7833827129672 +89000 ekin = 3.30271147105659 | erot = 1.80791256125564 | epot = -22.1564153597823 | etot = -17.04579132747 +90000 ekin = 2.42655906518194 | erot = 2.24507038389518 | epot = -21.9481188512569 | etot = -17.2764894021798 +91000 ekin = 1.89051217909395 | erot = 2.51049066719493 | epot = -21.7877769537306 | etot = -17.3867741074417 +92000 ekin = 2.07833668466679 | erot = 2.218324246302 | epot = -21.6997103074282 | etot = -17.4030493764594 +93000 ekin = 1.94321435585196 | erot = 2.99473985773914 | epot = -21.6748650469777 | etot = -16.7369108333866 +94000 ekin = 2.07878576812463 | erot = 3.37631892101902 | epot = -21.7659932416399 | etot = -16.3108885524963 +95000 ekin = 2.10517721407769 | erot = 2.08345895044788 | epot = -21.8951718799354 | etot = -17.7065357154098 +96000 ekin = 2.68821593238919 | erot = 1.86988637992409 | epot = -21.9622848400866 | etot = -17.4041825277733 +97000 ekin = 1.95061152706206 | erot = 2.81054215683073 | epot = -22.0229813258884 | etot = -17.2618276419957 +98000 ekin = 1.98463063611221 | erot = 2.05732763357977 | epot = -22.0930102039112 | etot = -18.0510519342192 +99000 ekin = 2.51292852217217 | erot = 3.54194472638845 | epot = -22.199088757298 | etot = -16.1442155087374 +100000 ekin = 1.8757570387949 | erot = 2.3690785580876 | epot = -22.348409587438 | etot = -18.1035739905555 +101000 ekin = 1.66160772204006 | erot = 3.59766032223856 | epot = -22.3604908173889 | etot = -17.1012227731103 +102000 ekin = 1.62075182718474 | erot = 3.3442006848817 | epot = -22.3063629504087 | etot = -17.3414104383422 +103000 ekin = 2.00871148652538 | erot = 2.33677124900284 | epot = -22.275557852692 | etot = -17.9300751171637 +104000 ekin = 2.04513709976292 | erot = 2.74664593650967 | epot = -22.2818713634637 | etot = -17.4900883271911 +105000 ekin = 1.87027868596139 | erot = 1.98922389218239 | epot = -22.223503909299 | etot = -18.3640013311552 +106000 ekin = 1.71540784443942 | erot = 1.9177953110688 | epot = -22.2562839843324 | etot = -18.6230808288242 +107000 ekin = 2.61024905591622 | erot = 1.57446439985464 | epot = -22.3171357124015 | etot = -18.1324222566306 +108000 ekin = 2.13751756724178 | erot = 2.18822458113098 | epot = -22.2268794585969 | etot = -17.9011373102241 +109000 ekin = 2.24408198608307 | erot = 2.11438299352724 | epot = -22.076564108576 | etot = -17.7180991289657 +110000 ekin = 1.66706562020821 | erot = 2.50986066169373 | epot = -22.0833343008135 | etot = -17.9064080189116 +111000 ekin = 2.30463895640872 | erot = 2.24982560856989 | epot = -22.0940837732696 | etot = -17.539619208291 +112000 ekin = 2.63019524472749 | erot = 2.43696110420532 | epot = -22.0953344558745 | etot = -17.0281781069417 +113000 ekin = 2.42282638113981 | erot = 3.06190927482913 | epot = -22.1061661458173 | etot = -16.6214304898484 +114000 ekin = 2.34214572325658 | erot = 2.31899235523686 | epot = -22.0941430549288 | etot = -17.4330049764353 +115000 ekin = 1.70336449422736 | erot = 3.10166879044198 | epot = -22.1252095896431 | etot = -17.3201763049738 +116000 ekin = 1.51705870113214 | erot = 2.21425252709695 | epot = -22.1823772627204 | etot = -18.4510660344913 +117000 ekin = 1.70129809180508 | erot = 2.34142425076372 | epot = -22.2067668262467 | etot = -18.1640444836779 +118000 ekin = 2.20482827236051 | erot = 2.3179714809504 | epot = -22.1855414590757 | etot = -17.6627417057647 +119000 ekin = 2.54272629601484 | erot = 2.46528921750297 | epot = -22.2113175246519 | etot = -17.2033020111341 +120000 ekin = 1.76640390552554 | erot = 2.16116304616032 | epot = -22.1536331723646 | etot = -18.2260662206787 +121000 ekin = 2.81281157959688 | erot = 2.31761005518346 | epot = -22.1492969323239 | etot = -17.0188752975435 +122000 ekin = 3.25156823587966 | erot = 3.31679050874322 | epot = -22.2050361016166 | etot = -15.6366773569938 +123000 ekin = 2.87462309654081 | erot = 3.25604816714397 | epot = -22.1785374359393 | etot = -16.0478661722546 +124000 ekin = 2.18213410260632 | erot = 2.77182209342785 | epot = -22.0161464482698 | etot = -17.0621902522356 +125000 ekin = 1.85317252616068 | erot = 1.36623599567638 | epot = -21.8721650279344 | etot = -18.6527565060973 +126000 ekin = 2.47747071965844 | erot = 3.09909384826334 | epot = -21.8840309142636 | etot = -16.3074663463419 +127000 ekin = 2.42177426273027 | erot = 2.35209644429656 | epot = -21.8861939604609 | etot = -17.1123232534341 +128000 ekin = 2.76000040231245 | erot = 1.8231678837239 | epot = -21.8538456680958 | etot = -17.2706773820595 +129000 ekin = 2.78355536315491 | erot = 2.88851981621501 | epot = -21.9251039267855 | etot = -16.2530287474156 +130000 ekin = 3.26834278926799 | erot = 2.56228354573336 | epot = -22.0546105678549 | etot = -16.2239842328536 +131000 ekin = 2.64714688907849 | erot = 2.51107513446137 | epot = -22.0961160192681 | etot = -16.9378939957282 +132000 ekin = 2.61847248883524 | erot = 3.38899164334156 | epot = -22.1218916777659 | etot = -16.1144275455891 +133000 ekin = 2.03408861514006 | erot = 2.87401070790187 | epot = -22.0785989417621 | etot = -17.1704996187202 +134000 ekin = 1.64140897264888 | erot = 1.66986416585675 | epot = -22.0323643102285 | etot = -18.7210911717228 +135000 ekin = 2.46650096367446 | erot = 2.111120611107 | epot = -21.9976572593399 | etot = -17.4200356845585 +136000 ekin = 2.32880805911731 | erot = 3.05940125193231 | epot = -21.8983392007847 | etot = -16.5101298897351 +137000 ekin = 2.7601019905106 | erot = 2.47443779429795 | epot = -21.752125264204 | etot = -16.5175854793954 +138000 ekin = 3.30162084678948 | erot = 1.73084735415554 | epot = -21.7423849642075 | etot = -16.7099167632625 +139000 ekin = 2.76669064053124 | erot = 1.72642745910431 | epot = -21.8898577306654 | etot = -17.3967396310298 +140000 ekin = 2.73595287215366 | erot = 2.46891829250481 | epot = -21.9884857831833 | etot = -16.7836146185249 +141000 ekin = 2.79316289615844 | erot = 2.46753088695597 | epot = -22.0064855648443 | etot = -16.7457917817299 +142000 ekin = 3.51694745558129 | erot = 3.49862438784827 | epot = -21.9623193335451 | etot = -14.9467474901156 +143000 ekin = 2.58689934548697 | erot = 2.04008576044027 | epot = -21.9563338194557 | etot = -17.3293487135285 +144000 ekin = 3.72611917000993 | erot = 3.04855733322793 | epot = -21.9536376487796 | etot = -15.1789611455417 +145000 ekin = 3.61191106831147 | erot = 2.71915407989904 | epot = -21.870542665333 | etot = -15.5394775171225 +146000 ekin = 3.85060594912677 | erot = 2.47210219931339 | epot = -21.8285858153921 | etot = -15.505877666952 +147000 ekin = 3.26481933196161 | erot = 2.06864347299802 | epot = -21.6752809049183 | etot = -16.3418180999587 +148000 ekin = 2.47977997895053 | erot = 1.65169267241014 | epot = -21.4172781734276 | etot = -17.2858055220669 +149000 ekin = 2.70771685463074 | erot = 2.28028425953227 | epot = -21.2324293178539 | etot = -16.2444282036909 +150000 ekin = 2.60726181496431 | erot = 2.88955230103659 | epot = -21.126549406853 | etot = -15.6297352908521 +151000 ekin = 2.06865005733849 | erot = 2.13537039813292 | epot = -21.0304193709383 | etot = -16.8263989154669 +152000 ekin = 2.41210154812787 | erot = 2.60104053370075 | epot = -20.8967777045302 | etot = -15.8836356227016 +153000 ekin = 2.12406231442824 | erot = 2.25444655142795 | epot = -20.9199278716094 | etot = -16.5414190057532 +154000 ekin = 2.34622678455546 | erot = 2.58439374093403 | epot = -21.0040588663533 | etot = -16.0734383408638 +155000 ekin = 2.08240965570452 | erot = 3.02621505767145 | epot = -21.0204738431416 | etot = -15.9118491297656 +156000 ekin = 2.04576145796301 | erot = 3.17151405834467 | epot = -20.8558463949479 | etot = -15.6385708786402 +157000 ekin = 2.36459548410747 | erot = 1.89207417055424 | epot = -20.8025485082277 | etot = -16.545878853566 +158000 ekin = 2.16996178916575 | erot = 2.46547727482113 | epot = -20.8673070433024 | etot = -16.2318679793155 +159000 ekin = 2.86272730849306 | erot = 2.27590841865057 | epot = -20.9710387207245 | etot = -15.8324029935809 +160000 ekin = 2.19288173853782 | erot = 2.36312829884111 | epot = -21.0403123366075 | etot = -16.4843022992286 +161000 ekin = 2.14059248149909 | erot = 2.4287283799048 | epot = -21.1333683100403 | etot = -16.5640474486365 +162000 ekin = 1.76077466564934 | erot = 2.66561836368342 | epot = -21.1782130850259 | etot = -16.7518200556931 +163000 ekin = 2.23068698955417 | erot = 2.02664945757243 | epot = -21.3281780197228 | etot = -17.0708415725963 +164000 ekin = 2.75358320318999 | erot = 1.43717365990088 | epot = -21.4675480212853 | etot = -17.2767911581945 +165000 ekin = 2.65171600986478 | erot = 2.29632253260765 | epot = -21.493178025826 | etot = -16.5451394833536 +166000 ekin = 3.27298673277591 | erot = 2.41252396730596 | epot = -21.4477711984927 | etot = -15.7622604984108 +167000 ekin = 3.02574105268454 | erot = 2.02770436019795 | epot = -21.5236773217566 | etot = -16.4702319088741 +168000 ekin = 3.14659813654158 | erot = 1.8374607941321 | epot = -21.5547269116736 | etot = -16.5706679809999 +169000 ekin = 2.22493755697302 | erot = 2.67175500860652 | epot = -21.4662206077311 | etot = -16.5695280421515 +170000 ekin = 2.41921977325643 | erot = 2.49142716001801 | epot = -21.3123035293873 | etot = -16.4016565961128 +171000 ekin = 1.89798915040775 | erot = 2.39492100285877 | epot = -21.2153991969519 | etot = -16.9224890436853 +172000 ekin = 2.86894215563086 | erot = 3.22914449693158 | epot = -21.1827352206441 | etot = -15.0846485680816 +173000 ekin = 2.74888252418688 | erot = 2.13556434483052 | epot = -21.2166792789418 | etot = -16.3322324099244 +174000 ekin = 2.45887587066864 | erot = 2.23682521338056 | epot = -21.2633056658561 | etot = -16.5676045818069 +175000 ekin = 2.84703517745999 | erot = 2.39381254916381 | epot = -21.2430876358358 | etot = -16.002239909212 +176000 ekin = 2.14025231000119 | erot = 1.89894722702466 | epot = -21.3238321496633 | etot = -17.2846326126375 +177000 ekin = 2.5795061901144 | erot = 2.75365074391219 | epot = -21.3022195274207 | etot = -15.9690625933941 +178000 ekin = 1.83122028490793 | erot = 2.59468068841507 | epot = -21.2483113201278 | etot = -16.8224103468048 +179000 ekin = 2.50706581632049 | erot = 2.3918046623687 | epot = -21.3152464598324 | etot = -16.4163759811432 +180000 ekin = 1.88211034410738 | erot = 2.47063835849692 | epot = -21.4741119346399 | etot = -17.1213632320356 +181000 ekin = 1.74209654097779 | erot = 3.05723824722444 | epot = -21.4808621715442 | etot = -16.681527383342 +182000 ekin = 1.55789914013104 | erot = 2.05767448814763 | epot = -21.423526482018 | etot = -17.8079528537394 +183000 ekin = 2.00937540548925 | erot = 2.80898978674436 | epot = -21.491360735728 | etot = -16.6729955434944 +184000 ekin = 2.69285960778353 | erot = 2.42969439668747 | epot = -21.6024209898208 | etot = -16.4798669853498 +185000 ekin = 3.01326925127938 | erot = 3.19083239326424 | epot = -21.6730258967931 | etot = -15.4689242522495 +186000 ekin = 3.2083067153638 | erot = 2.42899016869201 | epot = -21.7143665695974 | etot = -16.0770696855416 +187000 ekin = 2.672906100919 | erot = 3.41560404715603 | epot = -21.6726605039613 | etot = -15.5841503558862 +188000 ekin = 2.89349337388582 | erot = 3.06258669113775 | epot = -21.6216664732832 | etot = -15.6655864082597 +189000 ekin = 2.65435973176118 | erot = 1.82043381700644 | epot = -21.5604872976485 | etot = -17.0856937488809 +190000 ekin = 2.21855159698309 | erot = 1.84826944038784 | epot = -21.5263477340278 | etot = -17.4595266966569 +191000 ekin = 2.26980616064111 | erot = 2.05944589507645 | epot = -21.4543005141097 | etot = -17.1250484583921 +192000 ekin = 2.27219103053707 | erot = 3.11210788791052 | epot = -21.4899273087562 | etot = -16.1056283903086 +193000 ekin = 1.95008147026928 | erot = 1.89648921534019 | epot = -21.4843079374128 | etot = -17.6377372518033 +194000 ekin = 2.45477671526091 | erot = 2.0272304242676 | epot = -21.3709228769337 | etot = -16.8889157374052 +195000 ekin = 3.09567411006595 | erot = 2.10081767143638 | epot = -21.3012041149762 | etot = -16.1047123334739 +196000 ekin = 2.67423122149492 | erot = 2.50738189755519 | epot = -21.2164124023053 | etot = -16.0347992832552 +197000 ekin = 2.50338730962556 | erot = 2.07349764616723 | epot = -21.041867486922 | etot = -16.4649825311292 +198000 ekin = 2.66945928982616 | erot = 1.79012921820209 | epot = -21.0169215356766 | etot = -16.5573330276483 +199000 ekin = 2.53947964790256 | erot = 2.33176467953655 | epot = -21.0171165577067 | etot = -16.1458722302676 +200000 ekin = 2.90451062704866 | erot = 1.42170066957004 | epot = -21.0113804229743 | etot = -16.6851691263556 +201000 ekin = 2.68927776239674 | erot = 1.56650335894554 | epot = -21.0245916399581 | etot = -16.7688105186158 +202000 ekin = 2.2601329351618 | erot = 2.25401443373177 | epot = -20.9769308007641 | etot = -16.4627834318706 +203000 ekin = 2.12073487355488 | erot = 2.03553028991747 | epot = -20.919035946492 | etot = -16.7627707830197 +204000 ekin = 2.11829086582788 | erot = 1.89731962488617 | epot = -20.9376264283538 | etot = -16.9220159376397 +205000 ekin = 1.30964171332167 | erot = 2.12770406224885 | epot = -20.9991335630718 | etot = -17.5617877875013 +206000 ekin = 1.39940057572522 | erot = 2.24496791209126 | epot = -20.963919219062 | etot = -17.3195507312455 +207000 ekin = 1.8871608804017 | erot = 1.79849326266382 | epot = -21.0552898160204 | etot = -17.3696356729549 +208000 ekin = 1.81558541079753 | erot = 3.24210836817276 | epot = -21.3060144768834 | etot = -16.2483206979131 +209000 ekin = 2.79588064252181 | erot = 2.3467149173832 | epot = -21.4301997554495 | etot = -16.2876041955445 +210000 ekin = 3.17544887511567 | erot = 3.12704516116654 | epot = -21.5100449360932 | etot = -15.2075508998109 +211000 ekin = 2.47442327377226 | erot = 2.0990867711376 | epot = -21.6455723047062 | etot = -17.0720622597963 +212000 ekin = 2.36672302145397 | erot = 1.93445871446419 | epot = -21.7283038297487 | etot = -17.4271220938306 +213000 ekin = 1.91045426241161 | erot = 2.52535628540462 | epot = -21.8158508544504 | etot = -17.3800403066341 +214000 ekin = 1.99794025866061 | erot = 2.49896939492127 | epot = -21.8606548137084 | etot = -17.3637451601266 +215000 ekin = 1.97741561009525 | erot = 3.17667494473254 | epot = -21.8701701582032 | etot = -16.7160796033754 +216000 ekin = 1.88829990821377 | erot = 1.87402623825167 | epot = -21.8343889393413 | etot = -18.0720627928759 +217000 ekin = 2.10000293878932 | erot = 1.95052404495887 | epot = -21.8965404786646 | etot = -17.8460134949164 +218000 ekin = 2.34753598782339 | erot = 1.69695019504401 | epot = -21.8560027679962 | etot = -17.8115165851288 +219000 ekin = 2.497223564463 | erot = 2.20999914485705 | epot = -21.8797649478059 | etot = -17.1725422384859 +220000 ekin = 1.75274593087921 | erot = 3.03992746556406 | epot = -21.8491595252171 | etot = -17.0564861287739 +221000 ekin = 1.78874686645809 | erot = 2.79359542964647 | epot = -21.869798634642 | etot = -17.2874563385375 +222000 ekin = 2.63608430516661 | erot = 2.86817933637385 | epot = -21.8351218383832 | etot = -16.3308581968427 +223000 ekin = 3.02706758581511 | erot = 1.93888641555348 | epot = -21.8582453001765 | etot = -16.8922912988079 +224000 ekin = 2.71704451339112 | erot = 2.42079327531441 | epot = -21.8188420875657 | etot = -16.6810042988601 +225000 ekin = 2.04245190508395 | erot = 3.38216222891907 | epot = -21.8232190868647 | etot = -16.3986049528616 +226000 ekin = 2.37968015829255 | erot = 2.38384696857065 | epot = -21.8913549487127 | etot = -17.1278278218495 +227000 ekin = 2.73883397024414 | erot = 2.62491632372019 | epot = -21.9496900700867 | etot = -16.5859397761223 +228000 ekin = 2.06833362780412 | erot = 2.25049628751225 | epot = -21.9946760345141 | etot = -17.6758461191977 +229000 ekin = 1.78618617304217 | erot = 1.80509591500329 | epot = -22.0671964085329 | etot = -18.4759143204874 +230000 ekin = 2.76967283780387 | erot = 2.22492545317995 | epot = -22.0913590121729 | etot = -17.0967607211891 +231000 ekin = 3.15653922952316 | erot = 2.77099247609325 | epot = -22.0635255129442 | etot = -16.1359938073278 +232000 ekin = 1.86633326635991 | erot = 1.70672288688982 | epot = -22.0959715052869 | etot = -18.5229153520371 +233000 ekin = 1.75856846080021 | erot = 1.55694263125625 | epot = -22.0729289884755 | etot = -18.7574178964191 +234000 ekin = 2.32322575892498 | erot = 2.05793864740336 | epot = -21.9849429433607 | etot = -17.6037785370324 +235000 ekin = 1.95327191686568 | erot = 2.52519338885861 | epot = -21.9357201856672 | etot = -17.4572548799429 +236000 ekin = 2.25952484966859 | erot = 1.90005304846995 | epot = -21.9422471368741 | etot = -17.7826692387355 +237000 ekin = 2.49082301609303 | erot = 2.65327564887437 | epot = -22.0049130762794 | etot = -16.860814411312 +238000 ekin = 2.21076048871751 | erot = 2.74154862479023 | epot = -22.0553236426831 | etot = -17.1030145291754 +239000 ekin = 2.71464884454142 | erot = 2.48739530580561 | epot = -22.0661894571024 | etot = -16.8641453067554 +240000 ekin = 3.08961933821573 | erot = 2.17857064931927 | epot = -21.9596599475175 | etot = -16.6914699599825 +241000 ekin = 3.04172562407922 | erot = 2.64442433974962 | epot = -21.872950064824 | etot = -16.1868001009951 +242000 ekin = 2.21355627539455 | erot = 2.33429157450905 | epot = -21.7850463200938 | etot = -17.2371984701902 +243000 ekin = 1.52065138183895 | erot = 2.81375224845254 | epot = -21.724672004357 | etot = -17.3902683740655 +244000 ekin = 1.90352576583831 | erot = 2.43821138840079 | epot = -21.6320468184555 | etot = -17.2903096642164 +245000 ekin = 1.96342069667742 | erot = 2.61760141174562 | epot = -21.509789944958 | etot = -16.928767836535 +246000 ekin = 2.05478829283868 | erot = 2.42643933263093 | epot = -21.4781109635143 | etot = -16.9968833380447 +247000 ekin = 1.54618395739204 | erot = 2.28537401295509 | epot = -21.4411828355572 | etot = -17.6096248652101 +248000 ekin = 1.83924983769609 | erot = 2.55904554412921 | epot = -21.4587985205918 | etot = -17.0605031387665 +249000 ekin = 1.78703007063825 | erot = 2.03411349475431 | epot = -21.516607560139 | etot = -17.6954639947464 +250000 ekin = 1.69317901626952 | erot = 3.382620023581 | epot = -21.5380480709889 | etot = -16.4622490311384 +251000 ekin = 2.13799462687096 | erot = 3.25868442484789 | epot = -21.5254595658408 | etot = -16.1287805141219 +252000 ekin = 2.04357045453396 | erot = 2.53079336098227 | epot = -21.5456931883614 | etot = -16.9713293728452 +253000 ekin = 1.63287738205387 | erot = 3.20992823373492 | epot = -21.5622010587548 | etot = -16.719395442966 +254000 ekin = 2.31269246359595 | erot = 3.10766702207071 | epot = -21.5505863172024 | etot = -16.1302268315358 +255000 ekin = 2.50767926641465 | erot = 2.76631276495167 | epot = -21.5288449153183 | etot = -16.254852883952 +256000 ekin = 1.97163698305487 | erot = 2.61682132599931 | epot = -21.5273539828767 | etot = -16.9388956738225 +257000 ekin = 2.21091422886157 | erot = 3.2624387389365 | epot = -21.5385504601779 | etot = -16.0651974923798 +258000 ekin = 2.0351730783025 | erot = 1.84693461512361 | epot = -21.6544556001779 | etot = -17.7723479067518 +259000 ekin = 2.85718947138204 | erot = 2.78701165242275 | epot = -21.7587237542941 | etot = -16.1145226304893 +260000 ekin = 2.90387286634678 | erot = 2.18817434737477 | epot = -21.8080383126913 | etot = -16.7159910989698 +261000 ekin = 2.76190440948559 | erot = 2.33968169215532 | epot = -21.8592909726424 | etot = -16.7577048710015 +262000 ekin = 3.50919242681178 | erot = 1.76925994550144 | epot = -21.8779228441577 | etot = -16.5994704718445 +263000 ekin = 3.07696270254058 | erot = 2.41477320555763 | epot = -21.8078566004281 | etot = -16.3161206923299 +264000 ekin = 2.26633389925754 | erot = 2.04161743361595 | epot = -21.8372928128571 | etot = -17.5293414799836 +265000 ekin = 1.95747124461577 | erot = 2.5081300879884 | epot = -21.8490876266416 | etot = -17.3834862940375 +266000 ekin = 2.34517905801099 | erot = 3.31486209922478 | epot = -21.8287737874741 | etot = -16.1687326302383 +267000 ekin = 1.74030193361906 | erot = 2.23366459528059 | epot = -21.699850097441 | etot = -17.7258835685413 +268000 ekin = 2.04858677018814 | erot = 3.28744422098426 | epot = -21.6459408923623 | etot = -16.3099099011899 +269000 ekin = 1.93146929709294 | erot = 2.79280735598121 | epot = -21.549773802712 | etot = -16.8254971496378 +270000 ekin = 2.19788894271016 | erot = 2.64563279687103 | epot = -21.4165389672397 | etot = -16.5730172276585 +271000 ekin = 2.21923220579694 | erot = 3.10768708967444 | epot = -21.2197121954353 | etot = -15.8927928999639 +272000 ekin = 2.54992061853163 | erot = 2.29721880581853 | epot = -21.0816515756819 | etot = -16.2345121513317 +273000 ekin = 1.914618407838 | erot = 2.01420401968473 | epot = -21.0503637141725 | etot = -17.1215412866498 +274000 ekin = 1.89671513770876 | erot = 2.24334386161735 | epot = -21.0967103438301 | etot = -16.9566513445039 +275000 ekin = 1.78930707116537 | erot = 3.09754687865994 | epot = -21.1385700371941 | etot = -16.2517160873688 +276000 ekin = 3.37110328153971 | erot = 2.41957324257529 | epot = -21.0908388312033 | etot = -15.3001623070883 +277000 ekin = 2.38921825148496 | erot = 1.50604988822737 | epot = -21.034620883997 | etot = -17.1393527442847 +278000 ekin = 2.51997301930638 | erot = 2.14026171776896 | epot = -21.0117379332914 | etot = -16.351503196216 +279000 ekin = 1.88315206280857 | erot = 2.37342905263994 | epot = -20.9993757709145 | etot = -16.742794655466 +280000 ekin = 2.33534713190787 | erot = 3.58626468287222 | epot = -20.8573252930133 | etot = -14.9357134782332 +281000 ekin = 1.75252641954511 | erot = 1.7907930540809 | epot = -20.9036528826792 | etot = -17.3603334090531 +282000 ekin = 2.26373977259215 | erot = 3.04032073608633 | epot = -20.8497513702237 | etot = -15.5456908615452 +283000 ekin = 2.1783387139443 | erot = 2.20833158301333 | epot = -20.8002776734785 | etot = -16.4136073765209 +284000 ekin = 1.9148667268656 | erot = 2.21521993135969 | epot = -20.8277491648056 | etot = -16.6976625065804 +285000 ekin = 3.15634443167765 | erot = 1.80033231604849 | epot = -21.0046435881196 | etot = -16.0479668403934 +286000 ekin = 3.84877574957331 | erot = 1.82969969667577 | epot = -21.1628555811447 | etot = -15.4843801348956 +287000 ekin = 3.60615742824732 | erot = 2.91608688151215 | epot = -21.2126952882302 | etot = -14.6904509784708 +288000 ekin = 3.19613259393802 | erot = 1.67736393077137 | epot = -21.1713552834963 | etot = -16.297858758787 +289000 ekin = 2.45584885114799 | erot = 2.77781979747336 | epot = -21.1669115721543 | etot = -15.9332429235329 +290000 ekin = 2.74570408981357 | erot = 2.40443247852242 | epot = -21.1874427766533 | etot = -16.0373062083173 +291000 ekin = 2.10295274468233 | erot = 2.37092484671539 | epot = -21.2419107014544 | etot = -16.7680331100567 +292000 ekin = 2.36118713930732 | erot = 2.05558127949017 | epot = -21.3137361602548 | etot = -16.8969677414573 +293000 ekin = 2.2786196308825 | erot = 2.35874555054765 | epot = -21.4302415460533 | etot = -16.7928763646231 +294000 ekin = 2.93315982813019 | erot = 2.90313008187785 | epot = -21.5210917917479 | etot = -15.6848018817399 +295000 ekin = 2.66360761710434 | erot = 2.28100565751945 | epot = -21.6885021477336 | etot = -16.7438888731098 +296000 ekin = 2.18767827164471 | erot = 2.90589885547353 | epot = -21.7355037190159 | etot = -16.6419265918977 +297000 ekin = 2.15987738107365 | erot = 3.29819575592636 | epot = -21.7177655658756 | etot = -16.2596924288756 +298000 ekin = 2.92956976611296 | erot = 2.36377210613469 | epot = -21.6748271071566 | etot = -16.3814852349089 +299000 ekin = 3.19167138064488 | erot = 2.23480811780853 | epot = -21.8042612344918 | etot = -16.3777817360384 +300000 ekin = 3.3133572846982 | erot = 1.38932157247169 | epot = -21.8799906137235 | etot = -17.1773117565536 +301000 ekin = 2.39061971962408 | erot = 3.30110260608963 | epot = -21.8919200817915 | etot = -16.2001977560778 +302000 ekin = 2.954460706029 | erot = 3.2304815881765 | epot = -21.8557645140423 | etot = -15.6708222198368 +303000 ekin = 2.44700205353933 | erot = 2.60676303242282 | epot = -21.8414046718167 | etot = -16.7876395858546 +304000 ekin = 2.23578509140697 | erot = 2.68770420047938 | epot = -21.7680601199659 | etot = -16.8445708280796 +305000 ekin = 2.35505207220215 | erot = 2.3823003115585 | epot = -21.7344089784493 | etot = -16.9970565946887 +306000 ekin = 1.91790567526689 | erot = 2.90107494003232 | epot = -21.7170004822351 | etot = -16.8980198669359 +307000 ekin = 2.48241777758708 | erot = 2.0836708009946 | epot = -21.6510481218459 | etot = -17.0849595432642 +308000 ekin = 2.77531620706104 | erot = 2.63103510715158 | epot = -21.6349123878086 | etot = -16.2285610735959 +309000 ekin = 2.30440955942791 | erot = 2.1249829765834 | epot = -21.5927938975113 | etot = -17.1634013615 +310000 ekin = 2.50879527040005 | erot = 3.21338829421535 | epot = -21.6043932917725 | etot = -15.8822097271571 +311000 ekin = 2.31939145866558 | erot = 3.03649241514151 | epot = -21.6247503351754 | etot = -16.2688664613683 +312000 ekin = 1.78383134659847 | erot = 3.26262247889992 | epot = -21.4948144284683 | etot = -16.4483606029699 +313000 ekin = 1.6465994694839 | erot = 2.08133087588833 | epot = -21.4920309735611 | etot = -17.7641006281889 +314000 ekin = 2.2552391830868 | erot = 2.55077633299239 | epot = -21.5103692936944 | etot = -16.7043537776152 +315000 ekin = 2.5352734391515 | erot = 2.13089997124613 | epot = -21.5923709217299 | etot = -16.9261975113323 +316000 ekin = 1.99944427781285 | erot = 1.80072924409704 | epot = -21.6039893771529 | etot = -17.803815855243 +317000 ekin = 2.11848744585804 | erot = 2.01459693810075 | epot = -21.5948976630665 | etot = -17.4618132791077 +318000 ekin = 2.29013024301854 | erot = 1.92405818620914 | epot = -21.5643695946921 | etot = -17.3501811654644 +319000 ekin = 1.97314693278018 | erot = 1.67996578959134 | epot = -21.4554808400841 | etot = -17.8023681177126 +320000 ekin = 2.45681719546631 | erot = 3.07835144499744 | epot = -21.3924125538101 | etot = -15.8572439133463 +321000 ekin = 1.85729238455498 | erot = 2.67083565671245 | epot = -21.433818829251 | etot = -16.9056907879836 +322000 ekin = 1.96132292396412 | erot = 3.36792274118279 | epot = -21.3663490830085 | etot = -16.0371034178616 +323000 ekin = 1.94437285233567 | erot = 2.09558156605687 | epot = -21.4151250968679 | etot = -17.3751706784754 +324000 ekin = 2.229181524904 | erot = 2.4674418745061 | epot = -21.532385908563 | etot = -16.8357625091529 +325000 ekin = 2.74582842770392 | erot = 2.36717454305098 | epot = -21.6443544237971 | etot = -16.5313514530422 +326000 ekin = 1.91124551133375 | erot = 1.93084217743114 | epot = -21.7077957426602 | etot = -17.8657080538953 +327000 ekin = 3.05627483509655 | erot = 1.67325209460963 | epot = -21.7948818019128 | etot = -17.0653548722066 +328000 ekin = 2.73933273476856 | erot = 1.92380912803777 | epot = -21.8364014823586 | etot = -17.1732596195523 +329000 ekin = 2.95907896099514 | erot = 3.15654168356681 | epot = -21.898199971646 | etot = -15.7825793270841 +330000 ekin = 2.90795110595274 | erot = 2.01765890034968 | epot = -21.9037795505258 | etot = -16.9781695442234 +331000 ekin = 2.27446048340228 | erot = 2.03754878634056 | epot = -21.8760842049291 | etot = -17.5640749351863 +332000 ekin = 2.43262938612094 | erot = 3.19219171897213 | epot = -21.9305186945662 | etot = -16.3056975894732 +333000 ekin = 2.47357651298171 | erot = 2.70061045814697 | epot = -22.0416691323271 | etot = -16.8674821611985 +334000 ekin = 2.38171387374892 | erot = 3.00424927873366 | epot = -22.0746318522988 | etot = -16.6886686998162 +335000 ekin = 2.10465470910016 | erot = 3.57382014016833 | epot = -22.1175420615632 | etot = -16.4390672122947 +336000 ekin = 2.61374577374183 | erot = 2.13386927281299 | epot = -22.08988251196 | etot = -17.3422674654052 +337000 ekin = 2.72124526751511 | erot = 2.74800480481403 | epot = -22.0768537131621 | etot = -16.607603640833 +338000 ekin = 1.83524121485421 | erot = 2.24338894827196 | epot = -22.1591955034455 | etot = -18.0805653403194 +339000 ekin = 1.54928432997334 | erot = 2.49812246084905 | epot = -22.202239883467 | etot = -18.1548330926446 +340000 ekin = 1.44405714940632 | erot = 4.0451327092417 | epot = -22.1149458734013 | etot = -16.6257560147533 +341000 ekin = 1.67447392575555 | erot = 2.77749751745982 | epot = -22.0760831546714 | etot = -17.624111711456 +342000 ekin = 1.9825676117275 | erot = 2.71655566521084 | epot = -22.1563522566984 | etot = -17.45722897976 +343000 ekin = 2.68213676683887 | erot = 3.16686462846914 | epot = -22.2498477633288 | etot = -16.4008463680208 +344000 ekin = 1.77905771753907 | erot = 2.19153667254074 | epot = -22.2907212723871 | etot = -18.3201268823073 +345000 ekin = 1.5460499615042 | erot = 1.85960255696712 | epot = -22.3447003428977 | etot = -18.9390478244264 +346000 ekin = 1.71554664484034 | erot = 1.79880968736714 | epot = -22.3117022609055 | etot = -18.797345928698 +347000 ekin = 1.38672912049481 | erot = 2.61484473767931 | epot = -22.332503239512 | etot = -18.3309293813379 +348000 ekin = 2.15015924850684 | erot = 2.86300326453563 | epot = -22.3337312775957 | etot = -17.3205687645532 +349000 ekin = 1.83066085453602 | erot = 1.9844132649487 | epot = -22.3967822584585 | etot = -18.5817081389738 +350000 ekin = 1.83318738252649 | erot = 2.56907029661254 | epot = -22.4577827539416 | etot = -18.0555250748026 +351000 ekin = 1.72790505260219 | erot = 2.87456274671834 | epot = -22.5159555107051 | etot = -17.9134877113846 +352000 ekin = 2.80786740016944 | erot = 2.08750448125769 | epot = -22.6549834386892 | etot = -17.7596115572621 +353000 ekin = 3.5492801472091 | erot = 1.42584537334883 | epot = -22.6849212734238 | etot = -17.7097957528659 +354000 ekin = 3.49129244374804 | erot = 2.25156548638802 | epot = -22.604182620693 | etot = -16.861324690557 +355000 ekin = 2.06248783371663 | erot = 2.92733565233054 | epot = -22.5494488364627 | etot = -17.5596253504155 +356000 ekin = 2.13415426306312 | erot = 3.32668319049641 | epot = -22.6122425286523 | etot = -17.1514050750927 +357000 ekin = 2.75897049849731 | erot = 2.51843165594436 | epot = -22.6042888591885 | etot = -17.3268867047468 +358000 ekin = 2.51778220496547 | erot = 2.28374144764325 | epot = -22.5654155469984 | etot = -17.7638918943897 +359000 ekin = 3.2037278512604 | erot = 2.5552016027623 | epot = -22.6749569097326 | etot = -16.91602745571 +360000 ekin = 2.52669169359923 | erot = 1.97563796824025 | epot = -22.7314557612254 | etot = -18.229126099386 +361000 ekin = 2.60424632123629 | erot = 2.51068088850826 | epot = -22.7715023743751 | etot = -17.6565751646306 +362000 ekin = 2.43350156723209 | erot = 3.84566788758402 | epot = -22.7352151098034 | etot = -16.4560456549873 +363000 ekin = 2.91069717970492 | erot = 1.99710098714122 | epot = -22.6302259934474 | etot = -17.7224278266013 +364000 ekin = 2.2553832868325 | erot = 1.87832387363455 | epot = -22.5083625296191 | etot = -18.374655369152 +365000 ekin = 2.04575884197224 | erot = 2.797742068412 | epot = -22.332262738426 | etot = -17.4887618280417 +366000 ekin = 2.26894187965217 | erot = 1.94379382552235 | epot = -22.2788727984906 | etot = -18.0661370933161 +367000 ekin = 2.82509630766737 | erot = 2.50361468767084 | epot = -22.3209381619452 | etot = -16.992227166607 +368000 ekin = 2.81542036602322 | erot = 2.18733627644489 | epot = -22.4297259451244 | etot = -17.4269693026563 +369000 ekin = 2.30426035796382 | erot = 2.85653411706989 | epot = -22.4923286665588 | etot = -17.3315341915251 +370000 ekin = 2.67871033327547 | erot = 2.11464921695177 | epot = -22.578069860797 | etot = -17.7847103105697 +371000 ekin = 2.19281044135007 | erot = 3.60165960664287 | epot = -22.6424730832337 | etot = -16.8480030352407 +372000 ekin = 1.77481259468411 | erot = 3.406547444381 | epot = -22.7147683829008 | etot = -17.5334083438357 +373000 ekin = 2.15551547517191 | erot = 2.7877825236183 | epot = -22.7559497214321 | etot = -17.8126517226419 +374000 ekin = 2.71938368055486 | erot = 3.58127823243842 | epot = -22.9084433694729 | etot = -16.6077814564796 +375000 ekin = 2.42759321485976 | erot = 2.9742127178716 | epot = -22.9740378563778 | etot = -17.5722319236464 +376000 ekin = 3.39126830110572 | erot = 3.24733797625004 | epot = -22.9874015798135 | etot = -16.3487953024578 +377000 ekin = 3.20966733323472 | erot = 2.65934060364476 | epot = -22.9452111216365 | etot = -17.076203184757 +378000 ekin = 1.56095946168131 | erot = 2.66159033944991 | epot = -22.9575870308253 | etot = -18.7350372296941 +379000 ekin = 1.9498568748538 | erot = 2.54085216255828 | epot = -22.9834751642939 | etot = -18.4927661268818 +380000 ekin = 2.65820438237073 | erot = 2.88045867212573 | epot = -22.9984703542083 | etot = -17.4598072997118 +381000 ekin = 2.97084599252829 | erot = 2.18892549461574 | epot = -23.0341895570111 | etot = -17.8744180698671 +382000 ekin = 2.61355176942653 | erot = 2.02938704043227 | epot = -23.00841197151 | etot = -18.3654731616512 +383000 ekin = 2.03830671072154 | erot = 2.50516194855525 | epot = -23.0393965606452 | etot = -18.4959279013684 +384000 ekin = 2.1060608733416 | erot = 2.2184025045895 | epot = -23.0602182522593 | etot = -18.7357548743282 +385000 ekin = 1.89114918519107 | erot = 1.63701051320103 | epot = -23.0834434146806 | etot = -19.5552837162885 +386000 ekin = 1.55124380123707 | erot = 1.36147797265396 | epot = -23.1300518396949 | etot = -20.2173300658039 +387000 ekin = 2.19627825752355 | erot = 1.75751396098972 | epot = -23.1280875332419 | etot = -19.1742953147287 +388000 ekin = 1.96387084539616 | erot = 1.95852585326804 | epot = -23.0327752892415 | etot = -19.1103785905773 +389000 ekin = 2.50801560941705 | erot = 2.32519825784836 | epot = -23.0011464671235 | etot = -18.1679325998581 +390000 ekin = 2.03596866068489 | erot = 1.88295618907177 | epot = -22.8810338311575 | etot = -18.9621089814009 +391000 ekin = 1.8098591016452 | erot = 2.39622167162874 | epot = -22.81955664632 | etot = -18.613475873046 +392000 ekin = 2.17725370142733 | erot = 2.87094426544089 | epot = -22.7839731045438 | etot = -17.7357751376756 +393000 ekin = 2.14224634181997 | erot = 3.17242974303658 | epot = -22.8435025538357 | etot = -17.5288264689792 +394000 ekin = 1.97769550804367 | erot = 2.16375300420729 | epot = -22.8342667825711 | etot = -18.6928182703201 +395000 ekin = 2.03687268736298 | erot = 2.49567469731651 | epot = -22.8892034986303 | etot = -18.3566561139508 +396000 ekin = 2.16189109047463 | erot = 1.95308746486161 | epot = -22.9781386034885 | etot = -18.8631600481523 +397000 ekin = 2.41744222422408 | erot = 1.65310699287476 | epot = -23.0900453292844 | etot = -19.0194961121856 +398000 ekin = 3.58905654436294 | erot = 2.51930256503331 | epot = -23.2070733343384 | etot = -17.0987142249422 +399000 ekin = 2.65051654249497 | erot = 1.78138450529865 | epot = -23.3040478764215 | etot = -18.8721468286279 +400000 ekin = 2.49402752614129 | erot = 2.10290777432183 | epot = -23.3608759462318 | etot = -18.7639406457687 +401000 ekin = 2.04176177605462 | erot = 2.154995213856 | epot = -23.4039603394011 | etot = -19.2072033494905 +402000 ekin = 2.44505875861459 | erot = 2.11318097973378 | epot = -23.3975262709888 | etot = -18.8392865326404 +403000 ekin = 2.54858079745147 | erot = 2.81138206601919 | epot = -23.476064698677 | etot = -18.1161018352063 +404000 ekin = 2.21063952462117 | erot = 2.64710865829565 | epot = -23.574696037266 | etot = -18.7169478543492 +405000 ekin = 2.47328118101332 | erot = 2.40933750599425 | epot = -23.5927917139469 | etot = -18.7101730269393 +406000 ekin = 2.24891173527799 | erot = 2.23777884116047 | epot = -23.6086191890417 | etot = -19.1219286126032 +407000 ekin = 2.0107940045037 | erot = 2.78642832526904 | epot = -23.5246032469978 | etot = -18.727380917225 +408000 ekin = 2.59464051790823 | erot = 2.59123578102097 | epot = -23.4198302602656 | etot = -18.2339539613364 +409000 ekin = 2.37170880608734 | erot = 2.26136902851213 | epot = -23.317258193724 | etot = -18.6841803591245 +410000 ekin = 1.99754661347185 | erot = 1.95523998485755 | epot = -23.2950402043273 | etot = -19.3422536059979 +411000 ekin = 1.8693657058423 | erot = 2.63899492681176 | epot = -23.2490367633041 | etot = -18.74067613065 +412000 ekin = 1.98214047746227 | erot = 2.68315820775202 | epot = -23.1987357483281 | etot = -18.5334370631139 +413000 ekin = 2.39078873487373 | erot = 2.65589562872907 | epot = -23.1435198518627 | etot = -18.0968354882599 +414000 ekin = 2.40821090859775 | erot = 1.75574324408225 | epot = -23.0725048141377 | etot = -18.9085506614577 +415000 ekin = 2.74601981183015 | erot = 2.43675176686816 | epot = -23.1211711904486 | etot = -17.9383996117503 +416000 ekin = 2.08828454200993 | erot = 2.76783506526218 | epot = -23.1383119239965 | etot = -18.2821923167244 +417000 ekin = 2.01455344430628 | erot = 1.95306265456051 | epot = -23.1433633505287 | etot = -19.1757472516619 +418000 ekin = 2.42716528853985 | erot = 2.57642821145486 | epot = -23.127531797131 | etot = -18.1239382971363 +419000 ekin = 3.04095103685797 | erot = 2.58427576972734 | epot = -23.0602279332617 | etot = -17.4350011266764 +420000 ekin = 2.6360746280152 | erot = 2.44478111019393 | epot = -22.982092315172 | etot = -17.9012365769629 +421000 ekin = 2.53019765722915 | erot = 1.78389585255477 | epot = -22.9707435541329 | etot = -18.6566500443489 +422000 ekin = 2.72457425772367 | erot = 1.67768634886349 | epot = -22.9542997027495 | etot = -18.5520390961623 +423000 ekin = 2.11402997037893 | erot = 2.55034580375608 | epot = -22.8263851956497 | etot = -18.1620094215147 +424000 ekin = 1.8895880210325 | erot = 2.31332431343561 | epot = -22.772666888172 | etot = -18.5697545537039 +425000 ekin = 2.3595116370971 | erot = 1.95762380637298 | epot = -22.7752082759346 | etot = -18.4580728324645 +426000 ekin = 2.23706657164627 | erot = 2.60016134755148 | epot = -22.7844114251539 | etot = -17.9471835059562 +427000 ekin = 1.88801598248841 | erot = 2.12415782350886 | epot = -22.9416586386639 | etot = -18.9294848326666 +428000 ekin = 1.92849031333042 | erot = 2.44097902588716 | epot = -23.0611368174399 | etot = -18.6916674782223 +429000 ekin = 1.70536802258415 | erot = 2.14916257389792 | epot = -23.0556586745393 | etot = -19.2011280780572 +430000 ekin = 2.30226095973205 | erot = 2.14689932813604 | epot = -23.0606502516208 | etot = -18.6114899637527 +431000 ekin = 2.45988288454318 | erot = 2.42278380298657 | epot = -23.0729777223881 | etot = -18.1903110348583 +432000 ekin = 2.80869332724974 | erot = 2.19954129490925 | epot = -23.0939746542044 | etot = -18.0857400320454 +433000 ekin = 2.21130556188282 | erot = 1.62882156110628 | epot = -23.1534080352157 | etot = -19.3132809122266 +434000 ekin = 2.60574953870752 | erot = 2.36088790768803 | epot = -23.1901717047879 | etot = -18.2235342583923 +435000 ekin = 2.30377529593091 | erot = 2.53917715731259 | epot = -23.1716983948432 | etot = -18.3287459415997 +436000 ekin = 2.42707603554825 | erot = 2.75234181061924 | epot = -23.2197996577197 | etot = -18.0403818115522 +437000 ekin = 1.65090540276074 | erot = 3.25345231298367 | epot = -23.2216366145388 | etot = -18.3172788987944 +438000 ekin = 1.56145302974407 | erot = 2.60950810563796 | epot = -23.1303770792278 | etot = -18.9594159438458 +439000 ekin = 2.30955439722234 | erot = 1.94011743371103 | epot = -23.1353170794497 | etot = -18.8856452485163 +440000 ekin = 2.53037674867674 | erot = 3.0652704286103 | epot = -23.196858945292 | etot = -17.601211768005 +441000 ekin = 2.80107707952534 | erot = 2.53664155736544 | epot = -23.1712373428919 | etot = -17.8335187060011 +442000 ekin = 2.92536323090713 | erot = 2.88384500930017 | epot = -23.1123001627208 | etot = -17.3030919225135 +443000 ekin = 1.96543935969482 | erot = 1.753449631552 | epot = -23.0380529084377 | etot = -19.3191639171909 +444000 ekin = 2.00309477401363 | erot = 2.23897509587739 | epot = -22.9472103119533 | etot = -18.7051404420623 +445000 ekin = 2.20302071819722 | erot = 2.06928381371828 | epot = -22.7775434364172 | etot = -18.5052389045017 +446000 ekin = 2.43487889302299 | erot = 2.37751556007798 | epot = -22.6838190597697 | etot = -17.8714246066687 +447000 ekin = 2.2620819636031 | erot = 2.41400188145197 | epot = -22.7082516636546 | etot = -18.0321678185995 +448000 ekin = 2.16184472791984 | erot = 1.93539407204278 | epot = -22.8144859493263 | etot = -18.7172471493637 +449000 ekin = 2.21107967973114 | erot = 2.34659682978741 | epot = -22.9059503054159 | etot = -18.3482737958974 +450000 ekin = 2.74677740004439 | erot = 1.97222921372039 | epot = -22.860755926716 | etot = -18.1417493129513 +451000 ekin = 2.2050889378155 | erot = 2.13042736119389 | epot = -22.8862608894796 | etot = -18.5507445904702 +452000 ekin = 2.52760608607095 | erot = 2.34006815636601 | epot = -22.9138111972133 | etot = -18.0461369547763 +453000 ekin = 2.23448825172916 | erot = 1.77834418215733 | epot = -22.8879238301791 | etot = -18.8750913962926 +454000 ekin = 2.4343851915949 | erot = 2.59700848533281 | epot = -22.8184361849036 | etot = -17.7870425079759 +455000 ekin = 2.04195793930991 | erot = 2.79639043747681 | epot = -22.6032980500354 | etot = -17.7649496732487 +456000 ekin = 2.00799933710202 | erot = 2.53653815407518 | epot = -22.4355596266522 | etot = -17.891022135475 +457000 ekin = 2.60426208759883 | erot = 2.46609612876191 | epot = -22.3409120082078 | etot = -17.270553791847 +458000 ekin = 2.01368468059037 | erot = 1.9961381624531 | epot = -22.2549400327205 | etot = -18.2451171896771 +459000 ekin = 1.73688781588865 | erot = 2.48572034306896 | epot = -22.2282088298767 | etot = -18.0056006709191 +460000 ekin = 1.91682575775988 | erot = 2.08308677023944 | epot = -22.2211874714416 | etot = -18.2212749434423 +461000 ekin = 1.54933673126938 | erot = 1.29454502815255 | epot = -22.1945151049368 | etot = -19.3506333455148 +462000 ekin = 2.44160489340629 | erot = 1.34721473707676 | epot = -22.284671307697 | etot = -18.495851677214 +463000 ekin = 2.63165365707667 | erot = 2.08143760128039 | epot = -22.4004513395625 | etot = -17.6873600812055 +464000 ekin = 2.67929276186416 | erot = 3.72563793061087 | epot = -22.5200042545289 | etot = -16.1150735620538 +465000 ekin = 1.94880111369479 | erot = 2.23148844819348 | epot = -22.685554296329 | etot = -18.5052647344407 +466000 ekin = 2.13853049638891 | erot = 2.95056624305957 | epot = -22.7822881705531 | etot = -17.6931914311046 +467000 ekin = 2.46452767169615 | erot = 2.1077848077008 | epot = -22.9485753844866 | etot = -18.3762629050896 +468000 ekin = 1.98589158006998 | erot = 1.62816092182055 | epot = -23.0180008829524 | etot = -19.4039483810618 +469000 ekin = 2.498810820967 | erot = 2.6361546272592 | epot = -23.0547833968841 | etot = -17.9198179486579 +470000 ekin = 2.91491361681313 | erot = 3.19115611298998 | epot = -23.0448741101699 | etot = -16.9388043803668 +471000 ekin = 2.37554627514204 | erot = 1.71739792236247 | epot = -22.9932329645513 | etot = -18.9002887670468 +472000 ekin = 2.18486807923518 | erot = 2.00687069908099 | epot = -22.9563182572702 | etot = -18.764579478954 +473000 ekin = 2.36185345820899 | erot = 2.86259041401023 | epot = -22.9161024426125 | etot = -17.6916585703933 +474000 ekin = 2.17077693495272 | erot = 2.59376596740919 | epot = -22.7894018760352 | etot = -18.0248589736733 +475000 ekin = 2.37844153079293 | erot = 2.01112751381907 | epot = -22.6793191497969 | etot = -18.2897501051849 +476000 ekin = 2.0876367643964 | erot = 2.59647624455221 | epot = -22.6700039875052 | etot = -17.9858909785566 +477000 ekin = 2.52249432714936 | erot = 3.55251934739867 | epot = -22.6424099194916 | etot = -16.5673962449436 +478000 ekin = 2.40424947791157 | erot = 2.7323911725861 | epot = -22.544776325228 | etot = -17.4081356747303 +479000 ekin = 1.27637524434413 | erot = 2.99749792697945 | epot = -22.4994949498981 | etot = -18.2256217785745 +480000 ekin = 1.81374950293817 | erot = 2.14389317135939 | epot = -22.4678405170784 | etot = -18.5101978427809 +481000 ekin = 2.39496774186199 | erot = 3.18299441824521 | epot = -22.4930736763177 | etot = -16.9151115162105 +482000 ekin = 3.21051763720184 | erot = 2.40962326270833 | epot = -22.4479376181304 | etot = -16.8277967182202 +483000 ekin = 3.06081116762377 | erot = 2.49856996934407 | epot = -22.4288948733283 | etot = -16.8695137363604 +484000 ekin = 2.7452293328759 | erot = 2.53012629993099 | epot = -22.483756332919 | etot = -17.2084007001121 +485000 ekin = 3.33103095180521 | erot = 2.42091818181918 | epot = -22.4922555047182 | etot = -16.7403063710938 +486000 ekin = 1.99323479363108 | erot = 1.76127718142275 | epot = -22.5432098594131 | etot = -18.7886978843593 +487000 ekin = 2.64825718911654 | erot = 2.50204426232017 | epot = -22.6407366935241 | etot = -17.4904352420874 +488000 ekin = 1.76385891719471 | erot = 2.64266555173498 | epot = -22.6990728058786 | etot = -18.2925483369489 +489000 ekin = 2.10357630534276 | erot = 2.95613916443127 | epot = -22.7877124402073 | etot = -17.7279969704332 +490000 ekin = 2.33515649128314 | erot = 2.32995416999058 | epot = -22.7920703811403 | etot = -18.1269597198666 +491000 ekin = 2.48752587426647 | erot = 2.58310949760555 | epot = -22.7834811495388 | etot = -17.7128457776668 +492000 ekin = 3.29820665204489 | erot = 2.18682924183924 | epot = -22.7674519489923 | etot = -17.2824160551082 +493000 ekin = 3.40238156707506 | erot = 2.35717041222451 | epot = -22.7149408840448 | etot = -16.9553889047452 +494000 ekin = 3.59348050162499 | erot = 2.23182460532058 | epot = -22.7081682295491 | etot = -16.8828631226035 +495000 ekin = 2.52030309238562 | erot = 2.16229430067423 | epot = -22.6973031832711 | etot = -18.0147057902113 +496000 ekin = 1.96100991422337 | erot = 3.58581695215166 | epot = -22.7342002900882 | etot = -17.1873734237132 +497000 ekin = 2.2228647925968 | erot = 2.49495319949133 | epot = -22.752706201593 | etot = -18.0348882095048 +498000 ekin = 1.71033952564695 | erot = 2.41331591511584 | epot = -22.7131621100867 | etot = -18.589506669324 +499000 ekin = 2.41919864300729 | erot = 2.82349519531821 | epot = -22.7304918052927 | etot = -17.4877979669672 +500000 ekin = 2.76271068346558 | erot = 2.22796445937143 | epot = -22.810945568044 | etot = -17.820270425207 +501000 ekin = 2.97642553987186 | erot = 1.97769778889399 | epot = -22.8306304048616 | etot = -17.8765070760957 +502000 ekin = 2.96175345860856 | erot = 1.80859086419487 | epot = -22.8525538190094 | etot = -18.082209496206 +503000 ekin = 2.51126831088417 | erot = 2.88572311841927 | epot = -22.8673362278446 | etot = -17.4703447985412 +504000 ekin = 2.84611165351303 | erot = 2.67626783872459 | epot = -22.784891957601 | etot = -17.2625124653634 +505000 ekin = 2.96124584448914 | erot = 2.59100575301934 | epot = -22.8251284225258 | etot = -17.2728768250174 +506000 ekin = 2.19858217910528 | erot = 1.97142936872076 | epot = -22.8530995461462 | etot = -18.6830879983201 +507000 ekin = 2.27398115142402 | erot = 2.68837996151517 | epot = -22.8141163798141 | etot = -17.8517552668749 +508000 ekin = 2.64439339973837 | erot = 2.04756467869449 | epot = -22.8146247157345 | etot = -18.1226666373017 +509000 ekin = 2.96023637315629 | erot = 2.90549934754532 | epot = -22.8719625385967 | etot = -17.0062268178951 +510000 ekin = 2.26067558634546 | erot = 2.80864918519521 | epot = -22.9774448292236 | etot = -17.9081200576829 +511000 ekin = 2.88512738978599 | erot = 2.15263877534437 | epot = -23.086672848248 | etot = -18.0489066831176 +512000 ekin = 2.17783748155516 | erot = 2.31389139764186 | epot = -23.1520181882638 | etot = -18.6602893090668 +513000 ekin = 1.69717952556151 | erot = 2.88265468656805 | epot = -23.1640284548407 | etot = -18.5841942427111 +514000 ekin = 1.72432024724117 | erot = 2.32742209152174 | epot = -23.1602225830814 | etot = -19.1084802443185 +515000 ekin = 2.00525337522086 | erot = 1.80102864435032 | epot = -23.1548763180746 | etot = -19.3485942985034 +516000 ekin = 3.04706172157038 | erot = 1.54171785431326 | epot = -23.1202751246552 | etot = -18.5314955487716 +517000 ekin = 2.47323892251936 | erot = 2.10799615007355 | epot = -23.0942246440307 | etot = -18.5129895714378 +518000 ekin = 2.03556879740597 | erot = 2.51531294708502 | epot = -23.01998934344 | etot = -18.4691075989491 +519000 ekin = 1.59255614728459 | erot = 1.63520468579907 | epot = -22.9787913166931 | etot = -19.7510304836094 +520000 ekin = 2.17210761761845 | erot = 1.8975366735392 | epot = -22.9877149955356 | etot = -18.918070704378 +521000 ekin = 1.98466680078867 | erot = 2.09219045542651 | epot = -23.0348541858322 | etot = -18.9579969296171 +522000 ekin = 2.72098469914434 | erot = 2.19565658619456 | epot = -23.1001210576502 | etot = -18.1834797723113 +523000 ekin = 2.26033454380754 | erot = 1.67112114369622 | epot = -23.1475509854345 | etot = -19.2160952979307 +524000 ekin = 2.34603831546138 | erot = 2.1054661011949 | epot = -23.1746761633773 | etot = -18.723171746721 +525000 ekin = 2.13671314300235 | erot = 2.07172081705863 | epot = -23.241177743004 | etot = -19.032743782943 +526000 ekin = 2.50849953901566 | erot = 2.27662230434506 | epot = -23.3179050583979 | etot = -18.5327832150372 +527000 ekin = 3.04322527932213 | erot = 1.8128057083239 | epot = -23.3977373118239 | etot = -18.5417063241779 +528000 ekin = 2.572303182379 | erot = 2.54386055260816 | epot = -23.4208428708383 | etot = -18.3046791358511 +529000 ekin = 2.39361269633634 | erot = 1.91637577362227 | epot = -23.3966015599491 | etot = -19.0866130899905 +530000 ekin = 3.3562937907424 | erot = 3.41683815876463 | epot = -23.2977853851852 | etot = -16.5246534356781 +531000 ekin = 2.52741741752381 | erot = 2.34075342407645 | epot = -23.1721175623278 | etot = -18.3039467207275 +532000 ekin = 2.78397051305127 | erot = 1.78575123294094 | epot = -23.2171711834401 | etot = -18.6474494374479 +533000 ekin = 2.27408274334042 | erot = 2.01427501035043 | epot = -23.2885684059727 | etot = -19.0002106522818 +534000 ekin = 2.54998010491125 | erot = 2.0164545364507 | epot = -23.340767920006 | etot = -18.7743332786441 +535000 ekin = 2.49595662250557 | erot = 2.09586427439366 | epot = -23.3878755759449 | etot = -18.7960546790457 +536000 ekin = 2.47717157546008 | erot = 1.92116873587364 | epot = -23.3847675210095 | etot = -18.9864272096758 +537000 ekin = 1.75235621440219 | erot = 2.11852052216092 | epot = -23.4590860280326 | etot = -19.5882092914695 +538000 ekin = 2.19317209186629 | erot = 2.75191518419657 | epot = -23.5517834707225 | etot = -18.6066961946597 +539000 ekin = 2.16135327665114 | erot = 2.25935011393788 | epot = -23.5718250119029 | etot = -19.1511216213139 +540000 ekin = 2.35701554620647 | erot = 1.6449529057333 | epot = -23.5490867129451 | etot = -19.5471182610054 +541000 ekin = 2.61451212811978 | erot = 2.52550284426682 | epot = -23.5334576350385 | etot = -18.3934426626519 +542000 ekin = 2.78909215024063 | erot = 2.09346850400965 | epot = -23.5754619290989 | etot = -18.6929012748486 +543000 ekin = 2.77024528778678 | erot = 1.84116991183092 | epot = -23.4849560716084 | etot = -18.8735408719907 +544000 ekin = 2.15807529188369 | erot = 1.50139575300257 | epot = -23.4530822422947 | etot = -19.7936111974084 +545000 ekin = 1.72860204886329 | erot = 2.56468335549414 | epot = -23.4524953434144 | etot = -19.159209939057 +546000 ekin = 2.38494138419348 | erot = 1.87772638427254 | epot = -23.4950389557033 | etot = -19.2323711872372 +547000 ekin = 2.44871634556835 | erot = 2.44464466893214 | epot = -23.544915775382 | etot = -18.6515547608815 +548000 ekin = 2.36962922994878 | erot = 2.40235228488721 | epot = -23.5548428056052 | etot = -18.7828612907692 +549000 ekin = 2.57958168249614 | erot = 2.04930779813674 | epot = -23.5565149978683 | etot = -18.9276255172355 +550000 ekin = 1.9793136647427 | erot = 1.85207468704394 | epot = -23.5614067919063 | etot = -19.7300184401196 +551000 ekin = 2.4121774327081 | erot = 2.0348936886299 | epot = -23.5115216908382 | etot = -19.0644505695002 +552000 ekin = 2.6621149390197 | erot = 1.41279265378133 | epot = -23.3450678435402 | etot = -19.2701602507391 +553000 ekin = 1.76359346131444 | erot = 2.63019210822711 | epot = -23.1435570943958 | etot = -18.7497715248542 +554000 ekin = 2.29840754300073 | erot = 2.34424452982823 | epot = -23.1114395278817 | etot = -18.4687874550527 +555000 ekin = 3.29672420152566 | erot = 1.64146930698359 | epot = -23.0891292168918 | etot = -18.1509357083825 +556000 ekin = 2.92076699655596 | erot = 2.59602967895818 | epot = -23.0268314200472 | etot = -17.5100347445331 +557000 ekin = 2.90322014804994 | erot = 3.16052668894921 | epot = -23.0146480567181 | etot = -16.950901219719 +558000 ekin = 2.78018761002222 | erot = 2.59826947006759 | epot = -22.7877399275349 | etot = -17.4092828474451 +559000 ekin = 2.48661596771862 | erot = 3.22596665511856 | epot = -22.8226574327834 | etot = -17.1100748099462 +560000 ekin = 2.34942852601698 | erot = 2.32773162877396 | epot = -22.8255608134696 | etot = -18.1484006586786 +561000 ekin = 2.0520192544917 | erot = 2.90306975046936 | epot = -22.8488516051139 | etot = -17.8937626001529 +562000 ekin = 2.18821919117372 | erot = 3.66499439159819 | epot = -22.7618817506902 | etot = -16.9086681679183 +563000 ekin = 3.11505518852414 | erot = 2.28057725990564 | epot = -22.791430640287 | etot = -17.3957981918572 +564000 ekin = 2.45343120006931 | erot = 2.36321638506708 | epot = -22.75807077839 | etot = -17.9414231932536 +565000 ekin = 2.77835835502221 | erot = 2.07073547186409 | epot = -22.7486053888412 | etot = -17.8995115619549 +566000 ekin = 2.43655641927934 | erot = 2.19832280178868 | epot = -22.7227654505166 | etot = -18.0878862294486 +567000 ekin = 2.71233133108494 | erot = 2.01281091173405 | epot = -22.8839744455115 | etot = -18.1588322026925 +568000 ekin = 3.12450796157708 | erot = 1.93520150351061 | epot = -22.9625972279254 | etot = -17.9028877628377 +569000 ekin = 3.72714267701977 | erot = 2.06562452789051 | epot = -22.9814174117752 | etot = -17.1886502068649 +570000 ekin = 2.68808623045676 | erot = 2.36042122391805 | epot = -22.998959026692 | etot = -17.9504515723172 +571000 ekin = 1.97223467321356 | erot = 2.85558181274648 | epot = -22.9369001315648 | etot = -18.1090836456047 +572000 ekin = 2.4182049732123 | erot = 2.40910077907643 | epot = -22.934930836907 | etot = -18.1076250846182 +573000 ekin = 1.76702714285012 | erot = 2.31739567602694 | epot = -22.9768902017483 | etot = -18.8924673828712 +574000 ekin = 2.08740259214111 | erot = 2.59288012722136 | epot = -23.0518321557917 | etot = -18.3715494364293 +575000 ekin = 2.34020490338786 | erot = 2.78500973557001 | epot = -23.106579446946 | etot = -17.9813648079881 +576000 ekin = 2.15506609467459 | erot = 3.3045287538029 | epot = -23.1521162771299 | etot = -17.6925214286524 +577000 ekin = 2.45698150895878 | erot = 2.31876672704204 | epot = -23.1781917242715 | etot = -18.4024434882707 +578000 ekin = 2.59353106592521 | erot = 2.33790294336519 | epot = -23.2101395643707 | etot = -18.2787055550803 +579000 ekin = 2.58102015460712 | erot = 1.71748063175117 | epot = -23.1865014452815 | etot = -18.8880006589232 +580000 ekin = 2.30361750578347 | erot = 2.87410564379621 | epot = -23.2045008793077 | etot = -18.026777729728 +581000 ekin = 2.45915247103344 | erot = 2.59640238490727 | epot = -23.1882783600354 | etot = -18.1327235040947 +582000 ekin = 2.33801590725494 | erot = 3.19256035650617 | epot = -23.2501410058056 | etot = -17.7195647420445 +583000 ekin = 1.95982078382855 | erot = 2.81944051586213 | epot = -23.4085593869414 | etot = -18.6292980872508 +584000 ekin = 2.00358327245437 | erot = 1.7126727026301 | epot = -23.4960310960901 | etot = -19.7797751210056 +585000 ekin = 2.28859150562676 | erot = 2.06309046911262 | epot = -23.5306230166998 | etot = -19.1789410419604 +586000 ekin = 2.21858454582016 | erot = 1.97776854350186 | epot = -23.4873397268816 | etot = -19.2909866375596 +587000 ekin = 3.70065233550663 | erot = 1.82187748311298 | epot = -23.4652388428899 | etot = -17.9427090242702 +588000 ekin = 3.49447328534893 | erot = 2.31981981591506 | epot = -23.3985567739262 | etot = -17.5842636726622 +589000 ekin = 2.66144502802388 | erot = 3.02756546370717 | epot = -23.2783756079917 | etot = -17.5893651162607 +590000 ekin = 1.52141257336428 | erot = 2.09874614600563 | epot = -23.1290158071881 | etot = -19.5088570878182 +591000 ekin = 1.82897193042274 | erot = 1.75592223095374 | epot = -23.0622736076073 | etot = -19.4773794462309 +592000 ekin = 2.49491276892191 | erot = 2.5482988197852 | epot = -23.054885494985 | etot = -18.0116739062779 +593000 ekin = 2.36845716276159 | erot = 1.78503341410575 | epot = -23.005264310194 | etot = -18.8517737333267 +594000 ekin = 2.07907010887474 | erot = 2.14563658430187 | epot = -22.9611396232755 | etot = -18.7364329300989 +595000 ekin = 2.62736231723874 | erot = 2.0397582574453 | epot = -22.9495489717352 | etot = -18.2824283970512 +596000 ekin = 2.58985967531625 | erot = 2.12449830164849 | epot = -22.9908505579803 | etot = -18.2764925810155 +597000 ekin = 3.02540042664856 | erot = 3.14256707367048 | epot = -22.9740991012936 | etot = -16.8061316009746 +598000 ekin = 3.44397104083287 | erot = 2.8605790839857 | epot = -23.0035411551228 | etot = -16.6989910303042 +599000 ekin = 2.13932500926498 | erot = 3.49187029024979 | epot = -22.9657391359988 | etot = -17.334543836484 +600000 ekin = 2.19758597945326 | erot = 2.49610822362376 | epot = -22.9452235009931 | etot = -18.2515292979161 +601000 ekin = 2.80918982916752 | erot = 2.81768433603376 | epot = -22.8970508934525 | etot = -17.2701767282513 +602000 ekin = 2.30031523379463 | erot = 2.40907304500534 | epot = -22.8523950981499 | etot = -18.1430068193499 +603000 ekin = 1.91335501396421 | erot = 1.99518053980753 | epot = -22.7884152302358 | etot = -18.879879676464 +604000 ekin = 2.5976715095492 | erot = 3.14351403383687 | epot = -22.7430641975849 | etot = -17.0018786541988 +605000 ekin = 2.63203298717972 | erot = 2.07906613894389 | epot = -22.7307949909783 | etot = -18.0196958648547 +606000 ekin = 2.94678399289781 | erot = 2.03982213630799 | epot = -22.6555302524726 | etot = -17.6689241232668 +607000 ekin = 2.85272606479019 | erot = 2.36693467257681 | epot = -22.6318548820144 | etot = -17.4121941446474 +608000 ekin = 3.6642968125636 | erot = 2.46706737589234 | epot = -22.5724662590778 | etot = -16.4411020706219 +609000 ekin = 2.69343886620625 | erot = 2.25873504143679 | epot = -22.6007364465805 | etot = -17.6485625389374 +610000 ekin = 2.99904616523658 | erot = 2.13621966615343 | epot = -22.5973658485054 | etot = -17.4621000171154 +611000 ekin = 3.86832985948944 | erot = 2.12096644577641 | epot = -22.5702925425382 | etot = -16.5809962372724 +612000 ekin = 2.88515301824618 | erot = 2.45910554524357 | epot = -22.4848584522585 | etot = -17.1405998887688 +613000 ekin = 2.9367425327116 | erot = 2.14436169371533 | epot = -22.465526703267 | etot = -17.3844224768401 +614000 ekin = 2.79116462876301 | erot = 2.024409539648 | epot = -22.5207406301148 | etot = -17.7051664617038 +615000 ekin = 2.29338048298908 | erot = 2.38828872470982 | epot = -22.6082782403584 | etot = -17.9266090326595 +616000 ekin = 1.78195169789474 | erot = 2.45334803626968 | epot = -22.6887534547644 | etot = -18.4534537206 +617000 ekin = 2.57505808534158 | erot = 2.55345758187858 | epot = -22.701463839496 | etot = -17.5729481722758 +618000 ekin = 2.29561379442387 | erot = 2.68043259355499 | epot = -22.629958627306 | etot = -17.6539122393272 +619000 ekin = 1.94323313590202 | erot = 2.00964911157699 | epot = -22.56819110474 | etot = -18.6153088572609 +620000 ekin = 2.92263589097657 | erot = 2.15657756066215 | epot = -22.6264664894927 | etot = -17.547253037854 +621000 ekin = 2.90437881656455 | erot = 1.70649555848315 | epot = -22.665419447573 | etot = -18.0545450725253 +622000 ekin = 2.03426149564846 | erot = 2.51826459248401 | epot = -22.6086250578043 | etot = -18.0560989696718 +623000 ekin = 1.98348786592096 | erot = 3.08484972830227 | epot = -22.6234743341759 | etot = -17.5551367399527 +624000 ekin = 2.08463083558977 | erot = 2.64004606903047 | epot = -22.6266529328942 | etot = -17.901976028274 +625000 ekin = 2.52963490334089 | erot = 2.37033264022622 | epot = -22.6750436783156 | etot = -17.7750761347485 +626000 ekin = 2.73147680333726 | erot = 2.07051651598004 | epot = -22.7272383647964 | etot = -17.9252450454791 +627000 ekin = 2.23447399123207 | erot = 2.35288557052269 | epot = -22.7136740507756 | etot = -18.1263144890208 +628000 ekin = 2.28933754695897 | erot = 2.29676268895054 | epot = -22.6176528573237 | etot = -18.0315526214142 +629000 ekin = 2.5355466362136 | erot = 1.92082543033528 | epot = -22.5693331526924 | etot = -18.1129610861435 +630000 ekin = 3.11700824717166 | erot = 2.51611049765935 | epot = -22.5144695759915 | etot = -16.8813508311605 +631000 ekin = 2.38844807455604 | erot = 3.31601650504458 | epot = -22.5190998334878 | etot = -16.8146352538871 +632000 ekin = 2.59939587493746 | erot = 2.51496212358955 | epot = -22.4711049664696 | etot = -17.3567469679426 +633000 ekin = 2.45338619933597 | erot = 1.89874016257143 | epot = -22.4394257686937 | etot = -18.0872994067863 +634000 ekin = 2.23819111967047 | erot = 1.98305652730466 | epot = -22.3433365860708 | etot = -18.1220889390957 +635000 ekin = 2.22438000857702 | erot = 1.95893208021227 | epot = -22.2877959440852 | etot = -18.1044838552959 +636000 ekin = 2.26938644192167 | erot = 2.77816773779856 | epot = -22.304696935737 | etot = -17.2571427560168 +637000 ekin = 1.97799147515645 | erot = 2.59610837639352 | epot = -22.3353238115758 | etot = -17.7612239600258 +638000 ekin = 2.54901279963355 | erot = 3.14232301833368 | epot = -22.3113570318407 | etot = -16.6200212138734 +639000 ekin = 2.38194254982011 | erot = 2.49468098011844 | epot = -22.2696251856514 | etot = -17.3930016557128 +640000 ekin = 2.07438054408915 | erot = 2.20336226777045 | epot = -22.1673693230788 | etot = -17.8896265112192 +641000 ekin = 2.49150296422893 | erot = 3.53882164550033 | epot = -22.047323387435 | etot = -16.0169987777057 +642000 ekin = 3.37964058409635 | erot = 2.18458831029801 | epot = -21.9324522713976 | etot = -16.3682233770032 +643000 ekin = 2.80862431007863 | erot = 2.40815089193716 | epot = -21.8726014240441 | etot = -16.6558262220283 +644000 ekin = 2.952235016065 | erot = 1.92776262379328 | epot = -21.826057423183 | etot = -16.9460597833247 +645000 ekin = 4.10488984334312 | erot = 1.89062109330214 | epot = -21.7981661301139 | etot = -15.8026551934687 +646000 ekin = 2.50234872105284 | erot = 2.00205075040523 | epot = -21.7221642434957 | etot = -17.2177647720377 +647000 ekin = 2.52267281239589 | erot = 2.19481558810105 | epot = -21.7438885460027 | etot = -17.0264001455058 +648000 ekin = 2.99344241657584 | erot = 2.11139263207284 | epot = -21.7373240000025 | etot = -16.6324889513538 +649000 ekin = 2.55027365085816 | erot = 3.20350991793738 | epot = -21.7192481424448 | etot = -15.9654645736493 +650000 ekin = 3.75163896052813 | erot = 2.44189212282279 | epot = -21.6756681314987 | etot = -15.4821370481478 +651000 ekin = 3.29740056237165 | erot = 2.36780448747275 | epot = -21.5372361691658 | etot = -15.8720311193214 +652000 ekin = 2.54645886055823 | erot = 2.99097829596978 | epot = -21.4549655298412 | etot = -15.9175283733132 +653000 ekin = 2.88682688109756 | erot = 2.53633970608342 | epot = -21.4696471597398 | etot = -16.0464805725588 +654000 ekin = 2.28614085804932 | erot = 2.12026601708473 | epot = -21.5642684321318 | etot = -17.1578615569978 +655000 ekin = 2.20709609517087 | erot = 2.10729950549551 | epot = -21.5349466292622 | etot = -17.2205510285959 +656000 ekin = 2.40310876229413 | erot = 2.09663823500903 | epot = -21.5631924595209 | etot = -17.0634454622178 +657000 ekin = 2.7886551346751 | erot = 2.19608839827219 | epot = -21.794507747247 | etot = -16.8097642142998 +658000 ekin = 3.1025713807162 | erot = 2.59154293692773 | epot = -21.96675599421 | etot = -16.2726416765661 +659000 ekin = 2.88891106020275 | erot = 3.47010878893494 | epot = -22.0542552611187 | etot = -15.695235411981 +660000 ekin = 2.90074521854052 | erot = 1.62850743298554 | epot = -22.1003034196589 | etot = -17.5710507681328 +661000 ekin = 3.26666543815737 | erot = 1.86223225384175 | epot = -22.202664217118 | etot = -17.0737665251189 +662000 ekin = 3.1558491019044 | erot = 2.16868634291728 | epot = -22.3049478747805 | etot = -16.9804124299588 +663000 ekin = 1.94349853674083 | erot = 2.45687952722591 | epot = -22.3908978754178 | etot = -17.990519811451 +664000 ekin = 1.45445820960401 | erot = 1.37641815749115 | epot = -22.5088813854798 | etot = -19.6780050183846 +665000 ekin = 1.57568561901953 | erot = 2.30379312359823 | epot = -22.5957949572927 | etot = -18.7163162146749 +666000 ekin = 2.46162449261636 | erot = 1.76978614573263 | epot = -22.7431602236664 | etot = -18.5117495853174 +667000 ekin = 2.82410423268351 | erot = 2.3383666365949 | epot = -22.9350563238978 | etot = -17.7725854546194 +668000 ekin = 2.73717686116191 | erot = 3.18779777915035 | epot = -23.0188768131827 | etot = -17.0939021728704 +669000 ekin = 3.41035672635339 | erot = 2.45479601777612 | epot = -23.0718232403886 | etot = -17.2066704962591 +670000 ekin = 2.54649164859505 | erot = 1.99520979169172 | epot = -23.0246775830826 | etot = -18.4829761427959 +671000 ekin = 2.3802025684166 | erot = 3.00742736998541 | epot = -23.0023479116088 | etot = -17.6147179732068 +672000 ekin = 3.0126952152146 | erot = 2.55297219144565 | epot = -22.9947723733502 | etot = -17.4291049666899 +673000 ekin = 3.39486270740071 | erot = 2.3808700262033 | epot = -22.9033457919095 | etot = -17.1276130583054 +674000 ekin = 3.13698489626099 | erot = 2.10609113054063 | epot = -22.8089270617647 | etot = -17.5658510349631 +675000 ekin = 2.32294130821675 | erot = 1.5285851482073 | epot = -22.6840603385672 | etot = -18.8325338821432 +676000 ekin = 2.43564726401376 | erot = 2.26860623636408 | epot = -22.6133446272028 | etot = -17.909091126825 +677000 ekin = 2.75162757613842 | erot = 1.94219014743457 | epot = -22.7039380847023 | etot = -18.0101203611293 +678000 ekin = 2.86321973687601 | erot = 1.66387788364136 | epot = -22.7223510604726 | etot = -18.1952534399553 +679000 ekin = 2.35079208772869 | erot = 2.70386328048641 | epot = -22.7977445343495 | etot = -17.7430891661344 +680000 ekin = 2.48449675729004 | erot = 2.90645575582477 | epot = -22.8559375688936 | etot = -17.4649850557788 +681000 ekin = 1.91581136662333 | erot = 2.58179603882022 | epot = -22.7891325966099 | etot = -18.2915251911664 +682000 ekin = 2.10466427353705 | erot = 2.69470735868807 | epot = -22.6959043279182 | etot = -17.896532695693 +683000 ekin = 2.34504535409021 | erot = 2.11592035700791 | epot = -22.5718670441909 | etot = -18.1109013330928 +684000 ekin = 2.87198876498958 | erot = 2.65732173958706 | epot = -22.4986977268025 | etot = -16.9693872222258 +685000 ekin = 3.03375238110975 | erot = 2.18190577381518 | epot = -22.4634189289575 | etot = -17.2477607740326 +686000 ekin = 2.46248931777656 | erot = 2.43025710170918 | epot = -22.4079029677658 | etot = -17.5151565482801 +687000 ekin = 2.74662486817896 | erot = 1.79609152562411 | epot = -22.3360381567114 | etot = -17.7933217629083 +688000 ekin = 1.81703718003042 | erot = 2.06511603415635 | epot = -22.3083758541198 | etot = -18.426222639933 +689000 ekin = 2.84202633430564 | erot = 1.92033962884777 | epot = -22.3752571185822 | etot = -17.6128911554288 +690000 ekin = 2.07525448405017 | erot = 2.46342632176817 | epot = -22.4633535431152 | etot = -17.9246727372969 +691000 ekin = 2.12558517800138 | erot = 2.52961097164 | epot = -22.483426266766 | etot = -17.8282301171246 +692000 ekin = 2.86720433292881 | erot = 2.65102150657025 | epot = -22.4003374064863 | etot = -16.8821115669873 +693000 ekin = 2.30143055084864 | erot = 2.52290946383361 | epot = -22.2859681228792 | etot = -17.4616281081969 +694000 ekin = 2.88400701080875 | erot = 2.34320802755437 | epot = -22.206318584282 | etot = -16.9791035459189 +695000 ekin = 2.93184722112895 | erot = 2.22933507376834 | epot = -22.2348177906806 | etot = -17.0736354957833 +696000 ekin = 2.63173546326796 | erot = 2.34275369570833 | epot = -22.274597219839 | etot = -17.3001080608627 +697000 ekin = 1.87084079501972 | erot = 1.78050094908734 | epot = -22.2730387150935 | etot = -18.6216969709865 +698000 ekin = 2.19791428580687 | erot = 2.82883581756349 | epot = -22.2819378523405 | etot = -17.2551877489701 +699000 ekin = 2.34279295545267 | erot = 2.07514436344563 | epot = -22.2061425261575 | etot = -17.7882052072592 +700000 ekin = 2.576803119019 | erot = 2.32167543064962 | epot = -22.1658685747825 | etot = -17.2673900251139 +701000 ekin = 2.9943865807539 | erot = 1.89982533986206 | epot = -22.2191193266439 | etot = -17.324907406028 +702000 ekin = 2.68548464757459 | erot = 2.65050744453208 | epot = -22.2547415922757 | etot = -16.918749500169 +703000 ekin = 2.01996957402024 | erot = 2.04032822241737 | epot = -22.3253693056515 | etot = -18.2650715092139 +704000 ekin = 1.58871069317829 | erot = 1.64014270467762 | epot = -22.3617232281452 | etot = -19.1328698302893 +705000 ekin = 2.3089415754982 | erot = 1.90252913035993 | epot = -22.4307958564623 | etot = -18.2193251506042 +706000 ekin = 2.61729186445574 | erot = 3.21879868039103 | epot = -22.5603358780911 | etot = -16.7242453332443 +707000 ekin = 2.60797107906866 | erot = 2.31455039977396 | epot = -22.7102471053997 | etot = -17.7877256265571 +708000 ekin = 1.81633850341999 | erot = 2.3482257566942 | epot = -22.841408787855 | etot = -18.6768445277408 +709000 ekin = 1.83541322105378 | erot = 2.51792380003796 | epot = -23.0137235815795 | etot = -18.6603865604878 +710000 ekin = 2.2142058326246 | erot = 1.92378721690473 | epot = -23.1433453130909 | etot = -19.0053522635615 +711000 ekin = 2.06744054454467 | erot = 2.3981170935319 | epot = -23.1532717948855 | etot = -18.687714156809 +712000 ekin = 2.1727947270635 | erot = 1.75362175342097 | epot = -23.0479262273955 | etot = -19.121509746911 +713000 ekin = 2.87118830138474 | erot = 1.54943993787555 | epot = -22.8430575230906 | etot = -18.4224292838303 +714000 ekin = 2.0107946674397 | erot = 1.87510988392751 | epot = -22.9212969433221 | etot = -19.0353923919549 +715000 ekin = 2.4992182958927 | erot = 1.91934008289236 | epot = -22.9679126658062 | etot = -18.5493542870211 +716000 ekin = 2.94666510633353 | erot = 2.18714442405523 | epot = -23.033997097429 | etot = -17.9001875670402 +717000 ekin = 3.07404079722085 | erot = 2.46628262765133 | epot = -23.1869721551174 | etot = -17.6466487302452 +718000 ekin = 3.47060078371109 | erot = 2.28206620506093 | epot = -23.2524492340768 | etot = -17.4997822453048 +719000 ekin = 4.08343792096552 | erot = 3.10429377075217 | epot = -23.2448292181926 | etot = -16.0570975264749 +720000 ekin = 2.52774819763971 | erot = 1.92867508904585 | epot = -23.1435084559682 | etot = -18.6870851692826 +721000 ekin = 2.58294244811584 | erot = 2.0383053178033 | epot = -23.0601633758883 | etot = -18.4389156099691 +722000 ekin = 1.9445888545086 | erot = 2.32008660802523 | epot = -22.9811929404572 | etot = -18.7165174779234 +723000 ekin = 2.41998340576259 | erot = 2.12369728979369 | epot = -23.0570939793876 | etot = -18.5134132838314 +724000 ekin = 1.90406371300861 | erot = 1.97533505769876 | epot = -23.1267629042383 | etot = -19.247364133531 +725000 ekin = 2.14287056473422 | erot = 2.79289687450022 | epot = -23.1695632046138 | etot = -18.2337957653794 +726000 ekin = 2.26423317099721 | erot = 2.55343019202652 | epot = -23.2432909083709 | etot = -18.4256275453472 +727000 ekin = 1.69816397656716 | erot = 2.64011919415556 | epot = -23.298837689321 | etot = -18.9605545185982 +728000 ekin = 2.23000862561934 | erot = 3.58521470578671 | epot = -23.3528245832467 | etot = -17.5376012518407 +729000 ekin = 2.70076566380343 | erot = 1.73367306410751 | epot = -23.3971276122796 | etot = -18.9626888843686 +730000 ekin = 2.54818673802759 | erot = 2.77394958410256 | epot = -23.3988686964744 | etot = -18.0767323743443 +731000 ekin = 2.69782550956093 | erot = 2.04855826523075 | epot = -23.4310969813891 | etot = -18.6847132065974 +732000 ekin = 2.79613002753752 | erot = 1.87867430486715 | epot = -23.4885161441653 | etot = -18.8137118117607 +733000 ekin = 2.20346728125046 | erot = 2.64365594749975 | epot = -23.5261309431819 | etot = -18.6790077144317 +734000 ekin = 1.69780111261443 | erot = 2.30917909560787 | epot = -23.5188046470475 | etot = -19.5118244388252 +735000 ekin = 2.18402736165936 | erot = 2.72051620230871 | epot = -23.4712689506938 | etot = -18.5667253867257 +736000 ekin = 2.26138696009404 | erot = 1.17083930058803 | epot = -23.4348107178754 | etot = -20.0025844571934 +737000 ekin = 2.22219419044796 | erot = 3.14114682990362 | epot = -23.3869288757725 | etot = -18.0235878554209 +738000 ekin = 1.75464981631084 | erot = 2.28485941478058 | epot = -23.2709893028052 | etot = -19.2314800717138 +739000 ekin = 1.41806378584362 | erot = 2.16714034112821 | epot = -23.2213775300889 | etot = -19.636173403117 +740000 ekin = 1.90901017596351 | erot = 2.27102763422491 | epot = -23.1829198366046 | etot = -19.0028820264162 +741000 ekin = 1.9930994487751 | erot = 2.73523269523399 | epot = -23.1169670577824 | etot = -18.3886349137733 +742000 ekin = 1.99876411117685 | erot = 1.89882876917754 | epot = -23.0300825800851 | etot = -19.1324896997307 +743000 ekin = 1.96472814667687 | erot = 2.79504722629174 | epot = -22.8990488521609 | etot = -18.1392734791923 +744000 ekin = 2.02442646092311 | erot = 2.35044838626024 | epot = -22.8186526150799 | etot = -18.4437777678966 +745000 ekin = 1.65344231988822 | erot = 1.87919095141018 | epot = -22.7624827109091 | etot = -19.2298494396107 +746000 ekin = 2.1034668185472 | erot = 2.03078530569663 | epot = -22.743454277698 | etot = -18.6092021534542 +747000 ekin = 3.06690414848489 | erot = 1.6754029786949 | epot = -22.7625979159322 | etot = -18.0202907887524 +748000 ekin = 3.06965414483401 | erot = 1.86014593098643 | epot = -22.8118567150739 | etot = -17.8820566392535 +749000 ekin = 2.53718696167217 | erot = 2.02710579059033 | epot = -22.8431046011969 | etot = -18.2788118489344 +750000 ekin = 2.75657354808099 | erot = 2.34953156046291 | epot = -22.9548205390759 | etot = -17.848715430532 +751000 ekin = 2.52290020835147 | erot = 2.34873763599977 | epot = -23.0238691402084 | etot = -18.1522312958572 +752000 ekin = 2.47222247869325 | erot = 1.68679846444683 | epot = -22.9958559112491 | etot = -18.8368349681091 +753000 ekin = 2.48263277172423 | erot = 1.54669382815742 | epot = -23.0858212396418 | etot = -19.0564946397602 +754000 ekin = 2.54806257410878 | erot = 2.26636466676163 | epot = -23.1896472696842 | etot = -18.3752200288138 +755000 ekin = 1.53168409517921 | erot = 2.22665478278013 | epot = -23.2059118234918 | etot = -19.4475729455324 +756000 ekin = 2.10751715527953 | erot = 2.40525774326678 | epot = -23.114150245375 | etot = -18.6013753468287 +757000 ekin = 2.93395895491028 | erot = 2.05821177584909 | epot = -23.0783355599275 | etot = -18.0861648291682 +758000 ekin = 2.38307945406232 | erot = 2.50598165375058 | epot = -22.9691152621287 | etot = -18.0800541543158 +759000 ekin = 2.60292884338835 | erot = 2.36916677072548 | epot = -22.7987274767845 | etot = -17.8266318626707 +760000 ekin = 3.2284318196987 | erot = 2.73822716520638 | epot = -22.6756147646272 | etot = -16.7089557797221 +761000 ekin = 3.41868727786494 | erot = 1.68975765213408 | epot = -22.5638952547581 | etot = -17.4554503247591 +762000 ekin = 3.43033946346107 | erot = 2.5283975140253 | epot = -22.3549032489322 | etot = -16.3961662714458 +763000 ekin = 2.65773094814485 | erot = 1.83975133975562 | epot = -22.234833339183 | etot = -17.7373510512825 +764000 ekin = 2.3815484472129 | erot = 2.70684992442147 | epot = -22.0890752688231 | etot = -17.0006768971887 +765000 ekin = 2.23212803588897 | erot = 1.94868597739427 | epot = -21.9918715237933 | etot = -17.81105751051 +766000 ekin = 2.49097891886066 | erot = 1.96764603993156 | epot = -21.8443436680801 | etot = -17.3857187092879 +767000 ekin = 2.3457921497675 | erot = 2.64636009163513 | epot = -21.7634962034012 | etot = -16.7713439619986 +768000 ekin = 1.87671147825106 | erot = 2.05549869178485 | epot = -21.7324638416528 | etot = -17.8002536716169 +769000 ekin = 3.05058687860239 | erot = 2.66104171022372 | epot = -21.66792195987 | etot = -15.9562933710439 +770000 ekin = 2.44115683640633 | erot = 1.97554932479751 | epot = -21.6448820664751 | etot = -17.2281759052712 +771000 ekin = 2.23687464004429 | erot = 2.55040970708789 | epot = -21.5811924169692 | etot = -16.793908069837 +772000 ekin = 2.76529680592008 | erot = 1.97873499811185 | epot = -21.6543448952384 | etot = -16.9103130912064 +773000 ekin = 2.14632888240094 | erot = 2.41330587525514 | epot = -21.7728828090228 | etot = -17.2132480513667 +774000 ekin = 2.19848545803079 | erot = 1.9765131024719 | epot = -21.8398858604883 | etot = -17.6648872999856 +775000 ekin = 2.52300137989083 | erot = 2.80935365273515 | epot = -22.0219985274259 | etot = -16.6896434947999 +776000 ekin = 3.15842485269274 | erot = 2.47066157093645 | epot = -22.183029096161 | etot = -16.5539426725319 +777000 ekin = 1.91784338934576 | erot = 1.76045300517081 | epot = -22.2259652888115 | etot = -18.547668894295 +778000 ekin = 2.93738066043324 | erot = 2.29457842490289 | epot = -22.2339481852394 | etot = -17.0019890999032 +779000 ekin = 3.09847206114319 | erot = 2.0455771700605 | epot = -22.240438366259 | etot = -17.0963891350553 +780000 ekin = 2.86127568397807 | erot = 3.12055135138658 | epot = -22.1865692766137 | etot = -16.204742241249 +781000 ekin = 2.36069914420785 | erot = 3.53186431088487 | epot = -22.1210563364352 | etot = -16.2284928813425 +782000 ekin = 2.31592690319261 | erot = 2.85730598644035 | epot = -22.0302855151548 | etot = -16.8570526255218 +783000 ekin = 1.86647729944746 | erot = 3.03450246093099 | epot = -21.886014367949 | etot = -16.9850346075705 +784000 ekin = 2.04055627573201 | erot = 2.26047908607293 | epot = -21.7534271639393 | etot = -17.4523918021343 +785000 ekin = 2.02248469828703 | erot = 2.13950421850547 | epot = -21.6318967501918 | etot = -17.4699078333993 +786000 ekin = 2.34211746551602 | erot = 2.34838133643265 | epot = -21.5890308210084 | etot = -16.8985320190598 +787000 ekin = 2.74971447554938 | erot = 2.24123553296042 | epot = -21.5192132515563 | etot = -16.5282632430465 +788000 ekin = 2.14142056672039 | erot = 2.27008574684965 | epot = -21.4982362621714 | etot = -17.0867299486013 +789000 ekin = 1.98580913341303 | erot = 2.00702444041791 | epot = -21.5235331659838 | etot = -17.5306995921529 +790000 ekin = 1.68578263083924 | erot = 1.43485602862151 | epot = -21.6440081593601 | etot = -18.5233694998993 +791000 ekin = 2.13583938840528 | erot = 2.5373009545894 | epot = -21.7916440698418 | etot = -17.1185037268471 +792000 ekin = 1.71937483898028 | erot = 2.19563804216011 | epot = -21.8794946709408 | etot = -17.9644817898004 +793000 ekin = 3.15868943755338 | erot = 1.94575875708421 | epot = -22.0398145404617 | etot = -16.9353663458242 +794000 ekin = 2.45478602538954 | erot = 3.00825554959563 | epot = -22.0843165283013 | etot = -16.6212749533161 +795000 ekin = 2.87760320917193 | erot = 3.06920266633565 | epot = -22.1595628991904 | etot = -16.2127570236829 +796000 ekin = 2.29816690595058 | erot = 1.61510864654315 | epot = -22.1869705548184 | etot = -18.2736950023247 +797000 ekin = 2.1901525606721 | erot = 3.65734446008353 | epot = -22.1432608090644 | etot = -16.2957637883088 +798000 ekin = 2.12018787925578 | erot = 2.92822258455555 | epot = -22.1311312789224 | etot = -17.0827208151111 +799000 ekin = 2.49416140154829 | erot = 2.73328283280216 | epot = -22.0825726051882 | etot = -16.8551283708378 +800000 ekin = 2.18932007838552 | erot = 2.97640731559393 | epot = -21.979362152191 | etot = -16.8136347582115 +801000 ekin = 2.58827112124838 | erot = 2.7440442483726 | epot = -21.9108490336924 | etot = -16.5785336640714 +802000 ekin = 3.07870342348167 | erot = 2.87961505564287 | epot = -21.822560433681 | etot = -15.8642419545565 +803000 ekin = 2.2398624368064 | erot = 2.50525058807596 | epot = -21.72759408181 | etot = -16.9824810569277 +804000 ekin = 2.91885860068426 | erot = 1.57889040451428 | epot = -21.6896376725624 | etot = -17.1918886673638 +805000 ekin = 2.68277363980193 | erot = 3.05527868915738 | epot = -21.6710764398127 | etot = -15.9330241108534 +806000 ekin = 2.77769607049014 | erot = 2.1888727690908 | epot = -21.6314833902337 | etot = -16.6649145506527 +807000 ekin = 2.12673239079668 | erot = 2.86003407600806 | epot = -21.7295924017744 | etot = -16.7428259349697 +808000 ekin = 1.89599614774678 | erot = 2.29237053227662 | epot = -21.7511361510417 | etot = -17.5627694710183 +809000 ekin = 1.96405066221971 | erot = 1.92110393348368 | epot = -21.7075506883706 | etot = -17.8223960926672 +810000 ekin = 2.01518137594275 | erot = 2.60119247286596 | epot = -21.6788385874729 | etot = -17.0624647386642 +811000 ekin = 2.31084800889289 | erot = 1.75270367309064 | epot = -21.6837819033719 | etot = -17.6202302213883 +812000 ekin = 2.5770103100209 | erot = 2.34932304073588 | epot = -21.7246716033188 | etot = -16.798338252562 +813000 ekin = 2.87706904926076 | erot = 2.35686610624154 | epot = -21.8375922236049 | etot = -16.6036570681026 +814000 ekin = 2.89908405023866 | erot = 2.31423299883226 | epot = -21.8379261473901 | etot = -16.6246090983192 +815000 ekin = 2.54050064212256 | erot = 2.82732568868829 | epot = -21.6068952707049 | etot = -16.2390689398941 +816000 ekin = 2.17040404256387 | erot = 2.53711088209172 | epot = -21.5560322071983 | etot = -16.8485172825427 +817000 ekin = 1.7842696071831 | erot = 2.67810959410576 | epot = -21.8738878035325 | etot = -17.4115086022437 +818000 ekin = 2.29659398017838 | erot = 2.63718862373664 | epot = -22.164277271391 | etot = -17.230494667476 +819000 ekin = 2.15801167884062 | erot = 2.62095572928877 | epot = -22.1816109590116 | etot = -17.4026435508822 +820000 ekin = 1.94384548213955 | erot = 2.28597987799275 | epot = -22.0986187375022 | etot = -17.8687933773699 +821000 ekin = 2.10513194007576 | erot = 2.38698175569219 | epot = -22.1146754444785 | etot = -17.6225617487105 +822000 ekin = 2.24819716786441 | erot = 2.15258805680875 | epot = -22.0539472940486 | etot = -17.6531620693754 +823000 ekin = 2.26584952085583 | erot = 2.60619852526611 | epot = -22.0924201800579 | etot = -17.220372133936 +824000 ekin = 1.65187935478514 | erot = 1.48703119037228 | epot = -22.1682955997986 | etot = -19.0293850546412 +825000 ekin = 1.60213094818648 | erot = 1.98592524368393 | epot = -22.1687104063708 | etot = -18.5806542145004 +826000 ekin = 1.97430720107255 | erot = 2.19175014677159 | epot = -22.1061881978655 | etot = -17.9401308500213 +827000 ekin = 2.1793755983405 | erot = 2.44975419075935 | epot = -21.9704586607304 | etot = -17.3413288716305 +828000 ekin = 1.90399088418588 | erot = 2.72532994798816 | epot = -21.9585923270583 | etot = -17.3292714948842 +829000 ekin = 2.06478103068884 | erot = 2.9658303540259 | epot = -21.9849402038682 | etot = -16.9543288191534 +830000 ekin = 1.98920675238979 | erot = 2.15331250444996 | epot = -22.0339146439702 | etot = -17.8913953871305 +831000 ekin = 2.33567462674689 | erot = 2.36888807413497 | epot = -22.1271573756461 | etot = -17.4225946747643 +832000 ekin = 2.0119470999192 | erot = 1.94769143293625 | epot = -22.2038482709588 | etot = -18.2442097381034 +833000 ekin = 2.26025933495881 | erot = 2.16012558191462 | epot = -22.2882501045414 | etot = -17.867865187668 +834000 ekin = 2.11529426445865 | erot = 1.52405523315358 | epot = -22.3075608649826 | etot = -18.6682113673703 +835000 ekin = 2.8992075090551 | erot = 2.73801081751029 | epot = -22.3942491248321 | etot = -16.7570307982667 +836000 ekin = 3.33069528982658 | erot = 2.4277126780786 | epot = -22.4321737300744 | etot = -16.6737657621692 +837000 ekin = 2.74831774333782 | erot = 2.31991750378628 | epot = -22.4290234552872 | etot = -17.3607882081631 +838000 ekin = 3.13714871682188 | erot = 3.21601751721777 | epot = -22.4642383906451 | etot = -16.1110721566054 +839000 ekin = 2.73358272751807 | erot = 2.60144488190506 | epot = -22.4062682687368 | etot = -17.0712406593137 +840000 ekin = 2.96121930874637 | erot = 1.42725942278118 | epot = -22.3293755621294 | etot = -17.9408968306018 +841000 ekin = 2.95134811170866 | erot = 2.67666861874608 | epot = -22.2936348151224 | etot = -16.6656180846677 +842000 ekin = 2.15783928636401 | erot = 2.30287195796693 | epot = -22.2978011147172 | etot = -17.8370898703863 +843000 ekin = 2.84565152669617 | erot = 2.0510801477514 | epot = -22.3162908719779 | etot = -17.4195591975303 +844000 ekin = 2.99645803669157 | erot = 1.50433298006521 | epot = -22.3768320579304 | etot = -17.8760410411736 +845000 ekin = 3.20248025697125 | erot = 2.27246140825564 | epot = -22.3985708422076 | etot = -16.9236291769807 +846000 ekin = 3.35773945734322 | erot = 2.54074745551552 | epot = -22.4144833015876 | etot = -16.5159963887289 +847000 ekin = 2.17779203733109 | erot = 2.73817581188461 | epot = -22.3524825149514 | etot = -17.4365146657357 +848000 ekin = 2.51627348417144 | erot = 2.81170686694717 | epot = -22.2066307862469 | etot = -16.8786504351283 +849000 ekin = 1.99679455190557 | erot = 2.56855846773092 | epot = -22.0763062134929 | etot = -17.5109531938564 +850000 ekin = 2.05799123916876 | erot = 1.80888056240785 | epot = -22.0665032506706 | etot = -18.1996314490939 +851000 ekin = 2.0888979376792 | erot = 1.86172181790289 | epot = -22.0629711763889 | etot = -18.1123514208068 +852000 ekin = 1.68990805178902 | erot = 1.42763535981882 | epot = -22.002100112701 | etot = -18.8845567010931 +853000 ekin = 1.99310886654811 | erot = 3.05226969048292 | epot = -22.0306903552278 | etot = -16.9853117981968 +854000 ekin = 2.98378700534986 | erot = 2.2310274524054 | epot = -22.1115820238811 | etot = -16.8967675661258 +855000 ekin = 2.17087415585277 | erot = 2.8378147226879 | epot = -22.1115106395971 | etot = -17.1028217610564 +856000 ekin = 2.42228475387308 | erot = 1.53328604594478 | epot = -22.0841888628209 | etot = -18.128618063003 +857000 ekin = 2.50431566526894 | erot = 2.80498769176516 | epot = -21.9881235267534 | etot = -16.6788201697193 +858000 ekin = 2.17333686672378 | erot = 2.8259111550717 | epot = -21.9093201368614 | etot = -16.9100721150659 +859000 ekin = 2.29930070497243 | erot = 2.32417368939061 | epot = -21.8849849636104 | etot = -17.2615105692473 +860000 ekin = 1.99153024057672 | erot = 1.94674638600151 | epot = -21.8998709373217 | etot = -17.9615943107434 +861000 ekin = 2.69177523559624 | erot = 2.23997750036373 | epot = -21.8915522194994 | etot = -16.9597994835394 +862000 ekin = 2.86117050047984 | erot = 2.41530060322761 | epot = -21.876687883023 | etot = -16.6002167793156 +863000 ekin = 2.59841547044276 | erot = 3.3501705008543 | epot = -21.8162649771437 | etot = -15.8676790058467 +864000 ekin = 2.92496272611018 | erot = 2.30350236144453 | epot = -21.7820358973268 | etot = -16.5535708097721 +865000 ekin = 1.94718216128952 | erot = 2.16572180916633 | epot = -21.7000823492195 | etot = -17.5871783787636 +866000 ekin = 1.99006127871689 | erot = 1.65011901234952 | epot = -21.6190182409268 | etot = -17.9788379498604 +867000 ekin = 1.76250718110787 | erot = 3.37958608370307 | epot = -21.5401486584561 | etot = -16.3980553936452 +868000 ekin = 1.845623450314 | erot = 2.78812196028616 | epot = -21.5771917352235 | etot = -16.9434463246234 +869000 ekin = 2.39300849969205 | erot = 2.38301618173176 | epot = -21.6710790825578 | etot = -16.895054401134 +870000 ekin = 1.91899243212541 | erot = 3.22222440717393 | epot = -21.6734733803871 | etot = -16.5322565410878 +871000 ekin = 3.10255827845531 | erot = 2.95454268850896 | epot = -21.5913249106744 | etot = -15.5342239437101 +872000 ekin = 2.94582883077842 | erot = 1.38261935263093 | epot = -21.4597055547833 | etot = -17.1312573713739 +873000 ekin = 2.72830997927423 | erot = 2.23223699637274 | epot = -21.3657566950046 | etot = -16.4052097193577 +874000 ekin = 2.41464704842015 | erot = 2.10351476791496 | epot = -21.2635161734954 | etot = -16.7453543571603 +875000 ekin = 2.99468455803482 | erot = 2.72761242382524 | epot = -21.2488881289381 | etot = -15.526591147078 +876000 ekin = 2.13382009818493 | erot = 2.23152059294678 | epot = -21.2388603913311 | etot = -16.8735197001994 +877000 ekin = 1.839391763993 | erot = 1.607279977226 | epot = -21.2015948102408 | etot = -17.7549230690218 +878000 ekin = 2.01267175782178 | erot = 2.73109796378376 | epot = -21.2125253160263 | etot = -16.4687555944208 +879000 ekin = 1.42911941081343 | erot = 2.17371661448622 | epot = -21.1345316334464 | etot = -17.5316956081468 +880000 ekin = 2.10605339224633 | erot = 2.5884751778913 | epot = -21.0787246891645 | etot = -16.3841961190269 +881000 ekin = 1.54924791070118 | erot = 2.0068513915418 | epot = -21.1356465207066 | etot = -17.5795472184637 +882000 ekin = 2.199643157135 | erot = 2.65509097106007 | epot = -21.2389026935677 | etot = -16.3841685653726 +883000 ekin = 2.20850404171077 | erot = 2.22833605977577 | epot = -21.3067394383395 | etot = -16.869899336853 +884000 ekin = 2.76978562647275 | erot = 2.10395845939756 | epot = -21.3429618615585 | etot = -16.4692177756882 +885000 ekin = 1.93339807672781 | erot = 1.77156241344967 | epot = -21.3858074096933 | etot = -17.6808469195158 +886000 ekin = 2.00408769971894 | erot = 3.10736267931439 | epot = -21.3935346347812 | etot = -16.2820842557479 +887000 ekin = 1.96987943750801 | erot = 2.82035886899744 | epot = -21.3967073105593 | etot = -16.6064690040538 +888000 ekin = 1.91464371566411 | erot = 2.33371232948867 | epot = -21.4767119016419 | etot = -17.2283558564891 +889000 ekin = 1.88227414130201 | erot = 2.45915914930408 | epot = -21.5790392436829 | etot = -17.2376059530768 +890000 ekin = 1.84515176532447 | erot = 2.24992378831499 | epot = -21.6747594004542 | etot = -17.5796838468148 +891000 ekin = 2.6016566869706 | erot = 2.34500453305753 | epot = -21.8016735536793 | etot = -16.8550123336512 +892000 ekin = 2.71287751886859 | erot = 2.69544224573131 | epot = -21.9063749565585 | etot = -16.4980551919586 +893000 ekin = 2.17862714611329 | erot = 2.98452123742221 | epot = -21.9155556335137 | etot = -16.7524072499782 +894000 ekin = 2.52079948361477 | erot = 2.46355933674925 | epot = -21.915110079455 | etot = -16.930751259091 +895000 ekin = 2.53566097944338 | erot = 2.4513045444294 | epot = -21.947786087834 | etot = -16.9608205639612 +896000 ekin = 1.84455393639213 | erot = 2.77499090684945 | epot = -21.9167554809878 | etot = -17.2972106377463 +897000 ekin = 2.38519326880694 | erot = 2.019802873173 | epot = -21.8644918203993 | etot = -17.4594956784193 +898000 ekin = 2.14354914407572 | erot = 1.89196669459414 | epot = -21.7953104274974 | etot = -17.7597945888276 +899000 ekin = 2.65485657727374 | erot = 2.3237456003819 | epot = -21.6964754705568 | etot = -16.7178732929012 +900000 ekin = 2.1437154528087 | erot = 2.28119066740275 | epot = -21.6934954112434 | etot = -17.2685892910319 +901000 ekin = 1.93965814946881 | erot = 1.81495571440908 | epot = -21.7369092433376 | etot = -17.9822953794597 +902000 ekin = 2.60993957981555 | erot = 2.50321386623391 | epot = -21.6842517568354 | etot = -16.571098310786 +903000 ekin = 1.87484955546757 | erot = 2.17008893987962 | epot = -21.6383913984978 | etot = -17.5934529031506 +904000 ekin = 1.87454064845764 | erot = 2.32484081519398 | epot = -21.5866637125315 | etot = -17.3872822488799 +905000 ekin = 2.31407473814844 | erot = 2.15094868542391 | epot = -21.5154415841816 | etot = -17.0504181606093 +906000 ekin = 2.49583383758853 | erot = 2.25091096848461 | epot = -21.5170853902294 | etot = -16.7703405841563 +907000 ekin = 4.19798796104344 | erot = 2.5030532322807 | epot = -21.5976736513859 | etot = -14.8966324580618 +908000 ekin = 3.26730891548756 | erot = 2.11222217905481 | epot = -21.7526644402476 | etot = -16.3731333457052 +909000 ekin = 2.64106561110374 | erot = 1.92197432194202 | epot = -21.8748043207924 | etot = -17.3117643877467 +910000 ekin = 2.61805562731904 | erot = 2.90737422678703 | epot = -21.9709470207745 | etot = -16.4455171666685 +911000 ekin = 2.62012718860141 | erot = 4.35318528241844 | epot = -22.0282478750366 | etot = -15.0549354040167 +912000 ekin = 3.07628909273118 | erot = 3.69371809788395 | epot = -22.0511180009901 | etot = -15.281110810375 +913000 ekin = 2.82956898268831 | erot = 2.17078429141201 | epot = -22.0149543706266 | etot = -17.0146010965263 +914000 ekin = 2.16386655780066 | erot = 1.22303673036133 | epot = -21.9243495493208 | etot = -18.5374462611589 +915000 ekin = 1.59447095066509 | erot = 2.95966391292002 | epot = -21.8264580452026 | etot = -17.2723231816175 +916000 ekin = 2.58365539107523 | erot = 3.75147270955029 | epot = -21.8922962938608 | etot = -15.5571681932352 +917000 ekin = 3.01643029206973 | erot = 2.88035639021004 | epot = -21.9150526568514 | etot = -16.0182659745717 +918000 ekin = 2.89929776900147 | erot = 2.64137394041291 | epot = -21.9078998623094 | etot = -16.367228152895 +919000 ekin = 3.20476671865012 | erot = 2.76036957969153 | epot = -21.8878055443404 | etot = -15.9226692459988 +920000 ekin = 2.28949350558683 | erot = 2.38558870046816 | epot = -21.8659406759967 | etot = -17.1908584699418 +921000 ekin = 2.39158312157105 | erot = 2.44959700788167 | epot = -21.8638974869225 | etot = -17.0227173574697 +922000 ekin = 2.30678787768012 | erot = 2.42145678067298 | epot = -21.8218369909645 | etot = -17.0935923326114 +923000 ekin = 2.49697778842282 | erot = 2.66565493744118 | epot = -21.8078634464733 | etot = -16.6452307206093 +924000 ekin = 1.55676047489501 | erot = 2.97115254541007 | epot = -21.7829722234117 | etot = -17.2550592031067 +925000 ekin = 1.86603413909288 | erot = 1.96274861601779 | epot = -21.7288604040749 | etot = -17.9000776489642 +926000 ekin = 1.36993364395821 | erot = 2.11749584641399 | epot = -21.7083442855147 | etot = -18.2209147951426 +927000 ekin = 2.55718977538496 | erot = 2.08109095048881 | epot = -21.7242353526192 | etot = -17.0859546267455 +928000 ekin = 2.0974272910786 | erot = 2.73922911267236 | epot = -21.7673808868819 | etot = -16.9307244831309 +929000 ekin = 1.85550591174834 | erot = 1.84990976935039 | epot = -21.8639426090857 | etot = -18.158526927987 +930000 ekin = 1.99594723517184 | erot = 2.09151231016387 | epot = -21.8461015073053 | etot = -17.7586419619696 +931000 ekin = 2.45331651079283 | erot = 1.86703658018613 | epot = -21.7382799817762 | etot = -17.4179268907972 +932000 ekin = 2.76909250526759 | erot = 2.34990175754269 | epot = -21.7639792890094 | etot = -16.6449850261991 +933000 ekin = 3.04747366335481 | erot = 2.52740756503515 | epot = -21.6783727845496 | etot = -16.1034915561597 +934000 ekin = 2.93463275640818 | erot = 2.48893095891026 | epot = -21.5784996926914 | etot = -16.1549359773729 +935000 ekin = 2.77799347567549 | erot = 2.1392935841225 | epot = -21.5334239467005 | etot = -16.6161368869025 +936000 ekin = 2.96529953690398 | erot = 2.07095365726714 | epot = -21.5249249864244 | etot = -16.4886717922533 +937000 ekin = 3.0485053770175 | erot = 2.32432162998051 | epot = -21.4386642161072 | etot = -16.0658372091092 +938000 ekin = 2.9926262850536 | erot = 2.35224559307843 | epot = -21.3457080466208 | etot = -16.0008361684887 +939000 ekin = 2.61238181353703 | erot = 2.26780356837292 | epot = -21.3079422537804 | etot = -16.4277568718705 +940000 ekin = 2.65930112044942 | erot = 2.75497479722395 | epot = -21.2170493356504 | etot = -15.802773417977 +941000 ekin = 2.27574261339217 | erot = 2.61419196501686 | epot = -21.1297657597673 | etot = -16.2398311813583 +942000 ekin = 1.89172011891055 | erot = 2.82029488513784 | epot = -21.0410099256114 | etot = -16.328994921563 +943000 ekin = 2.47643464476757 | erot = 2.34737109151876 | epot = -21.046668772798 | etot = -16.2228630365117 +944000 ekin = 2.13883995897326 | erot = 1.92577316206138 | epot = -21.0114219746514 | etot = -16.9468088536167 +945000 ekin = 2.57768697869113 | erot = 2.21470136124069 | epot = -21.0634624131725 | etot = -16.2710740732407 +946000 ekin = 2.36420709243625 | erot = 2.89647330776424 | epot = -21.088814693033 | etot = -15.8281342928325 +947000 ekin = 2.07104171538467 | erot = 1.86575631327232 | epot = -21.1004860950452 | etot = -17.1636880663882 +948000 ekin = 1.85532958802997 | erot = 1.36952834086551 | epot = -21.1364231315616 | etot = -17.9115652026661 +949000 ekin = 1.76206591178366 | erot = 2.31737328558629 | epot = -21.1463744779337 | etot = -17.0669352805638 +950000 ekin = 1.72021033353108 | erot = 2.24191394295309 | epot = -21.1376324866856 | etot = -17.1755082102014 +951000 ekin = 1.96140007830504 | erot = 2.32248863487758 | epot = -21.1955927656813 | etot = -16.9117040524987 +952000 ekin = 2.93256201500608 | erot = 2.74550490827503 | epot = -21.234781024541 | etot = -15.5567141012599 +953000 ekin = 2.95031285986317 | erot = 2.39822873263993 | epot = -21.252609183133 | etot = -15.9040675906299 +954000 ekin = 3.09579074538114 | erot = 1.98159252445734 | epot = -21.1641538136742 | etot = -16.0867705438357 +955000 ekin = 3.59360323486038 | erot = 2.06789679071821 | epot = -21.0522880782498 | etot = -15.3907880526712 +956000 ekin = 2.97416074498497 | erot = 3.66953591785751 | epot = -20.9097603766373 | etot = -14.2660637137948 +957000 ekin = 3.03140562067951 | erot = 2.66078083760708 | epot = -20.741905867784 | etot = -15.0497194094974 +958000 ekin = 2.68913434704072 | erot = 2.94057112873834 | epot = -20.5488384129041 | etot = -14.9191329371251 +959000 ekin = 1.93264217407773 | erot = 2.45198406257092 | epot = -20.468781161493 | etot = -16.0841549248444 +960000 ekin = 1.49632279167952 | erot = 3.13346348599987 | epot = -20.4844974178568 | etot = -15.8547111401774 +961000 ekin = 1.96353429663481 | erot = 2.07553358516994 | epot = -20.4805590123497 | etot = -16.441491130545 +962000 ekin = 2.02830196392007 | erot = 1.88908496389356 | epot = -20.5374211599971 | etot = -16.6200342321835 +963000 ekin = 1.80829526034561 | erot = 2.46258345726267 | epot = -20.5841835730967 | etot = -16.3133048554884 +964000 ekin = 2.79449124937198 | erot = 2.42527551362846 | epot = -20.623880544448 | etot = -15.4041137814476 +965000 ekin = 2.53493670506137 | erot = 2.27804362684503 | epot = -20.6549300812151 | etot = -15.8419497493087 +966000 ekin = 2.0920817650402 | erot = 2.27478990703181 | epot = -20.704473904241 | etot = -16.337602232169 +967000 ekin = 1.55562260797661 | erot = 3.55543363172458 | epot = -20.739375276301 | etot = -15.6283190365998 +968000 ekin = 1.93439891222236 | erot = 2.37295903815892 | epot = -20.7189229543385 | etot = -16.4115650039572 +969000 ekin = 2.16199728898303 | erot = 2.4601205252494 | epot = -20.6747113173023 | etot = -16.0525935030699 +970000 ekin = 1.84926216722517 | erot = 2.96951777569267 | epot = -20.6011599981509 | etot = -15.7823800552331 +971000 ekin = 1.93656411083027 | erot = 3.08724923997924 | epot = -20.5835250734812 | etot = -15.5597117226717 +972000 ekin = 1.90452783927713 | erot = 2.5823076678316 | epot = -20.5782905980209 | etot = -16.0914550909122 +973000 ekin = 2.1922712122506 | erot = 2.92686386394502 | epot = -20.5868173702649 | etot = -15.4676822940693 +974000 ekin = 2.53094641465528 | erot = 2.69271305556795 | epot = -20.5382547781502 | etot = -15.314595307927 +975000 ekin = 3.41187201669925 | erot = 2.32917219553093 | epot = -20.5109803919917 | etot = -14.7699361797616 +976000 ekin = 2.88156114272554 | erot = 3.10474521611246 | epot = -20.5158119249461 | etot = -14.5295055661081 +977000 ekin = 2.73962881168093 | erot = 2.50884169958543 | epot = -20.4964590297999 | etot = -15.2479885185336 +978000 ekin = 1.79682802545478 | erot = 2.06924041504343 | epot = -20.4730821934977 | etot = -16.6070137529995 +979000 ekin = 1.86521389998383 | erot = 2.22151626929011 | epot = -20.4069392895634 | etot = -16.3202091202894 +980000 ekin = 1.92383169177414 | erot = 1.56425965548877 | epot = -20.3533353734708 | etot = -16.8652440262079 +981000 ekin = 1.55110199282939 | erot = 2.05381225133935 | epot = -20.3970890782076 | etot = -16.7921748340389 +982000 ekin = 1.85559395816058 | erot = 1.96991369841493 | epot = -20.499354149896 | etot = -16.6738464933205 +983000 ekin = 2.75061857015333 | erot = 1.7944840218308 | epot = -20.5241519929378 | etot = -15.9790494009537 +984000 ekin = 3.65069712553537 | erot = 2.64237329124733 | epot = -20.6374699142712 | etot = -14.3443994974885 +985000 ekin = 2.9563732193106 | erot = 2.18846412126773 | epot = -20.8122975273334 | etot = -15.6674601867551 +986000 ekin = 2.87072902054599 | erot = 2.18810434250119 | epot = -20.9390290724605 | etot = -15.8801957094134 +987000 ekin = 3.37463328642758 | erot = 2.5371366667467 | epot = -21.0098323012658 | etot = -15.0980623480916 +988000 ekin = 3.45107854450338 | erot = 3.23625536313169 | epot = -21.0554260480417 | etot = -14.3680921404067 +989000 ekin = 2.83591404363756 | erot = 2.20564156324817 | epot = -21.19499265416 | etot = -16.1534370472743 +990000 ekin = 2.79864389348437 | erot = 1.83178426663539 | epot = -21.1880268304373 | etot = -16.5575986703175 +991000 ekin = 3.14781925181036 | erot = 3.2078247180891 | epot = -21.1115234865128 | etot = -14.7558795166133 +992000 ekin = 3.30033725309946 | erot = 2.62749912694387 | epot = -21.0030296251662 | etot = -15.0751932451229 +993000 ekin = 3.07374297249949 | erot = 2.22697230616356 | epot = -20.9385586572609 | etot = -15.6378433785979 +994000 ekin = 3.21461776403449 | erot = 2.80599707993708 | epot = -20.8790524582442 | etot = -14.8584376142727 +995000 ekin = 3.25071478747345 | erot = 1.73415439498321 | epot = -20.8037804714002 | etot = -15.8189112889436 +996000 ekin = 3.07999632962569 | erot = 3.18107550500824 | epot = -20.7805295335828 | etot = -14.5194576989488 +997000 ekin = 2.97118118001025 | erot = 3.14046656474894 | epot = -20.7334885248756 | etot = -14.6218407801164 +998000 ekin = 3.09169861594907 | erot = 1.99060706981745 | epot = -20.6553134096535 | etot = -15.573007723887 +999000 ekin = 2.07498130576584 | erot = 2.75045972766921 | epot = -20.616091526295 | etot = -15.79065049286 +1000000 ekin = 2.07851119592057 | erot = 2.11869313853035 | epot = -20.4539417072875 | etot = -16.2567373728366 + 1000000 0.092378275 -1.3359709 0.057599499 -1.1484644 2.8477973e-05 +Loop time of 38.201 on 1 procs for 1000000 steps with 16 atoms + +Performance: 22617.237 tau/day, 26177.358 timesteps/s +98.6% CPU use with 1 MPI tasks x no OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 27.344 | 27.344 | 27.344 | 0.0 | 71.58 +Bond | 0.88043 | 0.88043 | 0.88043 | 0.0 | 2.30 +Neigh | 0 | 0 | 0 | 0.0 | 0.00 +Comm | 0.2073 | 0.2073 | 0.2073 | 0.0 | 0.54 +Output | 7e-06 | 7e-06 | 7e-06 | 0.0 | 0.00 +Modify | 9.4379 | 9.4379 | 9.4379 | 0.0 | 24.71 +Other | | 0.331 | | | 0.87 + +Nlocal: 16 ave 16 max 16 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 0 ave 0 max 0 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 88 ave 88 max 88 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 88 +Ave neighs/atom = 5.5 +Ave special neighs/atom = 3.75 +Neighbor list builds = 0 +Dangerous builds = 0 + +#write_restart config.${number}.* +Total wall time: 0:00:38 diff --git a/examples/USER/cgdna/examples/oxDNA/duplex2/log.18Jun19.duplex2.g++.4 b/examples/USER/cgdna/examples/oxDNA/duplex2/log.18Jun19.duplex2.g++.4 new file mode 100644 index 0000000000..3010570379 --- /dev/null +++ b/examples/USER/cgdna/examples/oxDNA/duplex2/log.18Jun19.duplex2.g++.4 @@ -0,0 +1,1167 @@ +LAMMPS (18 Jun 2019) +variable number equal 2 +variable ofreq equal 1000 +variable efreq equal 1000 +variable T equal 0.1 + +units lj + +dimension 3 + +newton off + +boundary p p p + +atom_style hybrid bond ellipsoid +atom_modify sort 0 1.0 + +# Pair interactions require lists of neighbours to be calculated +neighbor 1.0 bin +neigh_modify every 1 delay 0 check yes + +read_data data.duplex2 + orthogonal box = (-20 -20 -20) to (20 20 20) + 1 by 2 by 2 MPI processor grid + reading atoms ... + 16 atoms + reading velocities ... + 16 velocities + 16 ellipsoids + scanning bonds ... + 2 = max bonds/atom + reading bonds ... + 13 bonds + 2 = max # of 1-2 neighbors + 2 = max # of 1-3 neighbors + 4 = max # of 1-4 neighbors + 6 = max # of special neighbors + special bonds CPU = 0.000189 secs + read_data CPU = 0.003505 secs + +set atom * mass 3.1575 + 16 settings made for mass + +group all type 1 4 +16 atoms in group all + +# oxDNA bond interactions - FENE backbone +bond_style oxdna/fene +bond_coeff * 2.0 0.25 0.7525 + +# oxDNA pair interactions +pair_style hybrid/overlay oxdna/excv oxdna/stk oxdna/hbond oxdna/xstk oxdna/coaxstk +pair_coeff * * oxdna/excv 2.0 0.7 0.675 2.0 0.515 0.5 2.0 0.33 0.32 +pair_coeff * * oxdna/stk seqav ${T} 1.3448 2.6568 6.0 0.4 0.9 0.32 0.6 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2.0 0.65 2.0 0.65 +pair_coeff * * oxdna/stk seqav 0.1 1.3448 2.6568 6.0 0.4 0.9 0.32 0.6 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2.0 0.65 2.0 0.65 +pair_coeff * * oxdna/hbond seqav 0.0 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45 +pair_coeff 1 4 oxdna/hbond seqav 1.077 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45 +pair_coeff 2 3 oxdna/hbond seqav 1.077 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45 +pair_coeff * * oxdna/xstk 47.5 0.575 0.675 0.495 0.655 2.25 0.791592653589793 0.58 1.7 1.0 0.68 1.7 1.0 0.68 1.5 0 0.65 1.7 0.875 0.68 1.7 0.875 0.68 +pair_coeff * * oxdna/coaxstk 46.0 0.4 0.6 0.22 0.58 2.0 2.541592653589793 0.65 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2.0 -0.65 2.0 -0.65 + +# NVE ensemble +#fix 1 all nve/dot +fix 1 all nve/dotc/langevin ${T} ${T} 0.03 457145 angmom 10 +fix 1 all nve/dotc/langevin 0.1 ${T} 0.03 457145 angmom 10 +fix 1 all nve/dotc/langevin 0.1 0.1 0.03 457145 angmom 10 +#fix 1 all nve/asphere +#fix 2 all langevin ${T} ${T} 0.03 457145 angmom 10 + +timestep 1e-5 + +#comm_style tiled +#fix 3 all balance 10000 1.1 rcb + +#compute mol all chunk/atom molecule +#compute mychunk all vcm/chunk mol +#fix 4 all ave/time 10000 1 10000 c_mychunk[1] c_mychunk[2] c_mychunk[3] file vcm.txt mode vector + +#dump pos all xyz ${ofreq} traj.${number}.xyz + +#compute quat all property/atom quatw quati quatj quatk +#dump quat all custom ${ofreq} quat.${number}.txt id c_quat[1] c_quat[2] c_quat[3] c_quat[4] +#dump_modify quat sort id +#dump_modify quat format line "%d %13.6le %13.6le %13.6le %13.6le" + +compute erot all erotate/asphere +compute ekin all ke +compute epot all pe +variable erot equal c_erot +variable ekin equal c_ekin +variable epot equal c_epot +variable etot equal c_erot+c_ekin+c_epot +fix 5 all print ${efreq} "$(step) ekin = ${ekin} | erot = ${erot} | epot = ${epot} | etot = ${etot}" screen yes +fix 5 all print 1000 "$(step) ekin = ${ekin} | erot = ${erot} | epot = ${epot} | etot = ${etot}" screen yes + +#dump out all custom ${ofreq} out.${number}.txt id x y z vx vy vz fx fy fz tqx tqy tqz +#dump_modify out sort id +#dump_modify out format line "%d %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le" + +run 1000000 +Neighbor list info ... + update every 1 steps, delay 0 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 1.92828 + ghost atom cutoff = 1.92828 + binsize = 0.964142, bins = 42 42 42 + 5 neighbor lists, perpetual/occasional/extra = 5 0 0 + (1) pair oxdna/excv, perpetual + attributes: half, newton off + pair build: half/bin/newtoff + stencil: half/bin/3d/newtoff + bin: standard + (2) pair oxdna/stk, perpetual, copy from (1) + attributes: half, newton off + pair build: copy + stencil: none + bin: none + (3) pair oxdna/hbond, perpetual, copy from (1) + attributes: half, newton off + pair build: copy + stencil: none + bin: none + (4) pair oxdna/xstk, perpetual, copy from (1) + attributes: half, newton off + pair build: copy + stencil: none + bin: none + (5) pair oxdna/coaxstk, perpetual, copy from (1) + attributes: half, newton off + pair build: copy + stencil: none + bin: none +Per MPI rank memory allocation (min/avg/max) = 7.466 | 7.648 | 7.83 Mbytes +Step Temp E_pair E_mol TotEng Press + 0 0 -1.5402493 0.0070469125 -1.5332024 6.0760034e-06 +1000 ekin = 1.34565986428024 | erot = 2.31051421234078 | epot = -24.5061991591502 | etot = -20.8500250825292 +2000 ekin = 2.15911766687235 | erot = 2.16031365874706 | epot = -24.4723177103698 | etot = -20.1528863847504 +3000 ekin = 3.26561948796015 | erot = 2.75651822936605 | epot = -24.412573068346 | etot = -18.3904353510198 +4000 ekin = 1.92438809241066 | erot = 2.12016940074985 | epot = -24.3496233970111 | etot = -20.3050659038505 +5000 ekin = 1.35986357015476 | erot = 1.99413493074226 | epot = -24.2789445616949 | etot = -20.9249460607979 +6000 ekin = 2.19432475124593 | erot = 1.74281260409078 | epot = -24.2128064295788 | etot = -20.2756690742421 +7000 ekin = 2.65619274477635 | erot = 1.74094257048458 | epot = -24.1673462333493 | etot = -19.7702109180883 +8000 ekin = 2.51333548501169 | erot = 2.34649854571052 | epot = -24.0812769481836 | etot = -19.2214429174614 +9000 ekin = 2.24506493169711 | erot = 2.0652555461504 | epot = -23.9906736063989 | etot = -19.6803531285514 +10000 ekin = 2.36632635249862 | erot = 1.79592471761529 | epot = -23.9002627850602 | etot = -19.7380117149463 +11000 ekin = 2.03296432220126 | erot = 1.687070009478 | epot = -23.8527188138995 | etot = -20.1326844822202 +12000 ekin = 2.65352743446956 | erot = 2.50226345616878 | epot = -23.8480805937578 | etot = -18.6922897031194 +13000 ekin = 1.89067421214403 | erot = 2.35043092595414 | epot = -23.7714712440931 | etot = -19.5303661059949 +14000 ekin = 1.90680463918722 | erot = 2.127459870274 | epot = -23.7545354032947 | etot = -19.7202708938335 +15000 ekin = 2.40428667481004 | erot = 2.06172433796653 | epot = -23.6726347642127 | etot = -19.2066237514361 +16000 ekin = 2.7510166356243 | erot = 1.18896277635345 | epot = -23.5745121257654 | etot = -19.6345327137876 +17000 ekin = 2.44090826892662 | erot = 2.38166706806442 | epot = -23.5888433865641 | etot = -18.766268049573 +18000 ekin = 2.16977970545217 | erot = 2.46915729098831 | epot = -23.6023194416344 | etot = -18.9633824451939 +19000 ekin = 2.19378610033861 | erot = 2.45183819484608 | epot = -23.5449084745393 | etot = -18.8992841793546 +20000 ekin = 2.07734013817241 | erot = 1.81448496219961 | epot = -23.5782673056894 | etot = -19.6864422053173 +21000 ekin = 2.27781532351243 | erot = 2.76369118136087 | epot = -23.5986545956161 | etot = -18.5571480907428 +22000 ekin = 2.69375785791379 | erot = 1.86436952967315 | epot = -23.5521083325077 | etot = -18.9939809449208 +23000 ekin = 1.99952884103097 | erot = 2.28032953163858 | epot = -23.4448504933921 | etot = -19.1649921207226 +24000 ekin = 2.19993258930349 | erot = 2.97916455146846 | epot = -23.365299008021 | etot = -18.1862018672491 +25000 ekin = 2.28089469652686 | erot = 2.97627567077201 | epot = -23.2873526827526 | etot = -18.0301823154537 +26000 ekin = 1.99390998801618 | erot = 2.79250495479073 | epot = -23.1859723519608 | etot = -18.3995574091539 +27000 ekin = 2.00992865272585 | erot = 2.66533768693446 | epot = -23.0781687640813 | etot = -18.402902424421 +28000 ekin = 2.00322172723407 | erot = 2.36418499091004 | epot = -23.0032647032354 | etot = -18.6358579850913 +29000 ekin = 2.52361436071784 | erot = 2.06140753694879 | epot = -22.9685706338047 | etot = -18.383548736138 +30000 ekin = 1.94969919616482 | erot = 2.13601590002587 | epot = -22.8657664932105 | etot = -18.7800513970198 +31000 ekin = 1.81286761012387 | erot = 2.31717861791922 | epot = -22.8372197907213 | etot = -18.7071735626782 +32000 ekin = 1.88389491638451 | erot = 2.00512246825909 | epot = -22.9321024454487 | etot = -19.0430850608051 +33000 ekin = 1.78524470387102 | erot = 1.83154598239148 | epot = -22.9538943248059 | etot = -19.3371036385434 +34000 ekin = 2.28023843988047 | erot = 3.11357086039976 | epot = -23.0617618407572 | etot = -17.6679525404769 +35000 ekin = 2.88795920533174 | erot = 1.81662227096288 | epot = -23.1342233361349 | etot = -18.4296418598403 +36000 ekin = 2.40018487148211 | erot = 2.59182059399979 | epot = -23.2153198761915 | etot = -18.2233144107096 +37000 ekin = 2.22699211630433 | erot = 1.73889017332476 | epot = -23.2291614908027 | etot = -19.2632792011736 +38000 ekin = 2.13593461964592 | erot = 3.07590136326317 | epot = -23.1607724763685 | etot = -17.9489364934594 +39000 ekin = 2.08839393640823 | erot = 2.80471150509565 | epot = -23.1352878747759 | etot = -18.242182433272 +40000 ekin = 2.94982054413846 | erot = 2.19484102372242 | epot = -23.1842229043853 | etot = -18.0395613365244 +41000 ekin = 2.47855373480178 | erot = 3.46795094832273 | epot = -23.1698888629099 | etot = -17.2233841797854 +42000 ekin = 2.57225931171306 | erot = 3.11160980977123 | epot = -23.0914425999525 | etot = -17.4075734784682 +43000 ekin = 2.16695829201326 | erot = 2.67063324875933 | epot = -22.9841690345739 | etot = -18.1465774938013 +44000 ekin = 2.3251045436594 | erot = 3.31069456451417 | epot = -22.9099977707014 | etot = -17.2741986625278 +45000 ekin = 1.8593572517472 | erot = 3.48256913429863 | epot = -22.7853293556222 | etot = -17.4434029695763 +46000 ekin = 2.59906260222482 | erot = 2.2320785378511 | epot = -22.67184319375 | etot = -17.8407020536741 +47000 ekin = 1.9041935097682 | erot = 3.39352467596442 | epot = -22.5624536061979 | etot = -17.2647354204653 +48000 ekin = 2.46191536162938 | erot = 2.50024189038396 | epot = -22.5888330081063 | etot = -17.626675756093 +49000 ekin = 3.18008619674965 | erot = 2.18329398142911 | epot = -22.6110647388653 | etot = -17.2476845606865 +50000 ekin = 2.92380640638808 | erot = 1.5483538313346 | epot = -22.6682279672282 | etot = -18.1960677295055 +51000 ekin = 2.86729503225236 | erot = 2.67529217516738 | epot = -22.6748886664557 | etot = -17.132301459036 +52000 ekin = 2.30283827457731 | erot = 1.82645474029553 | epot = -22.6607030819086 | etot = -18.5314100670358 +53000 ekin = 3.18697616339313 | erot = 1.67211265049679 | epot = -22.7158951183044 | etot = -17.8568063044145 +54000 ekin = 2.63274995193146 | erot = 1.96664130685844 | epot = -22.7877787224364 | etot = -18.1883874636465 +55000 ekin = 3.18311630681888 | erot = 2.85127254864952 | epot = -22.8390589862477 | etot = -16.8046701307793 +56000 ekin = 2.55275960671527 | erot = 3.05720384772627 | epot = -22.8187750450683 | etot = -17.2088115906267 +57000 ekin = 2.43682051944963 | erot = 3.45782031837861 | epot = -22.7770565571277 | etot = -16.8824157192995 +58000 ekin = 1.93888380963701 | erot = 2.51321017005842 | epot = -22.7135987564736 | etot = -18.2615047767781 +59000 ekin = 2.5584899615086 | erot = 3.52166542523796 | epot = -22.6623202639297 | etot = -16.5821648771831 +60000 ekin = 2.80661395039301 | erot = 2.89055248290059 | epot = -22.5801959967487 | etot = -16.8830295634551 +61000 ekin = 2.68598657973729 | erot = 2.54741083070049 | epot = -22.4806361765055 | etot = -17.2472387660677 +62000 ekin = 2.74493324548126 | erot = 2.23648307303268 | epot = -22.4129547813458 | etot = -17.4315384628319 +63000 ekin = 2.65627195091608 | erot = 2.46107949280746 | epot = -22.3986334001314 | etot = -17.2812819564079 +64000 ekin = 2.12379240032878 | erot = 2.79203441675508 | epot = -22.3495990435982 | etot = -17.4337722265143 +65000 ekin = 1.86782238979936 | erot = 2.70277079938775 | epot = -22.3710220966341 | etot = -17.800428907447 +66000 ekin = 2.74983103317414 | erot = 1.93532287297328 | epot = -22.3642892005435 | etot = -17.6791352943961 +67000 ekin = 2.51092055125345 | erot = 2.46618624666164 | epot = -22.3997780561407 | etot = -17.4226712582257 +68000 ekin = 2.95469759114172 | erot = 1.97026833535316 | epot = -22.465077041847 | etot = -17.5401111153521 +69000 ekin = 2.60179538487173 | erot = 2.27022574694886 | epot = -22.4013876082186 | etot = -17.529366476398 +70000 ekin = 2.38624525335423 | erot = 2.82124637267728 | epot = -22.3329612644329 | etot = -17.1254696384013 +71000 ekin = 2.62641919853461 | erot = 2.89332429923839 | epot = -22.3324946257813 | etot = -16.8127511280083 +72000 ekin = 2.93199679301318 | erot = 2.83600213853038 | epot = -22.4418753486332 | etot = -16.6738764170897 +73000 ekin = 2.20521324648382 | erot = 3.0506384171445 | epot = -22.5078076718832 | etot = -17.2519560082549 +74000 ekin = 2.16594519672766 | erot = 2.82993872672918 | epot = -22.5187768617569 | etot = -17.5228929383001 +75000 ekin = 1.52753824412461 | erot = 1.91758574309003 | epot = -22.6434864113427 | etot = -19.198362424128 +76000 ekin = 1.89477517532868 | erot = 2.83145375092217 | epot = -22.7507099037207 | etot = -18.0244809774699 +77000 ekin = 2.84722966394523 | erot = 3.20523918524771 | epot = -22.8263123696514 | etot = -16.7738435204585 +78000 ekin = 2.44900478430451 | erot = 2.80964787966682 | epot = -22.8119237303111 | etot = -17.5532710663397 +79000 ekin = 2.16549328835506 | erot = 1.67531288307153 | epot = -22.8278994273521 | etot = -18.9870932559255 +80000 ekin = 2.38929173610466 | erot = 2.58355997375491 | epot = -22.7453472674483 | etot = -17.7724955575887 +81000 ekin = 2.74182188148999 | erot = 1.92580771183151 | epot = -22.6872721828913 | etot = -18.0196425895698 +82000 ekin = 1.90254633515813 | erot = 1.70958501101745 | epot = -22.5904815431895 | etot = -18.9783501970139 +83000 ekin = 1.63862423461032 | erot = 1.87668722448406 | epot = -22.5030898166236 | etot = -18.9877783575292 +84000 ekin = 1.65768128899531 | erot = 2.10186039233844 | epot = -22.4199436013011 | etot = -18.6604019199674 +85000 ekin = 2.40787065796921 | erot = 2.04965431830703 | epot = -22.3401854879212 | etot = -17.882660511645 +86000 ekin = 2.51073542405177 | erot = 1.79768841940749 | epot = -22.3948638623201 | etot = -18.0864400188608 +87000 ekin = 2.13729284484532 | erot = 1.97886338867606 | epot = -22.4457225556767 | etot = -18.3295663221553 +88000 ekin = 1.7511616822056 | erot = 2.36434608342924 | epot = -22.4232555875236 | etot = -18.3077478218887 +89000 ekin = 1.85498863251071 | erot = 3.29466014836527 | epot = -22.4615925106509 | etot = -17.3119437297749 +90000 ekin = 2.22730928223451 | erot = 2.36761183779185 | epot = -22.5498488806969 | etot = -17.9549277606706 +91000 ekin = 2.40026068010467 | erot = 3.1312454261103 | epot = -22.5445138059197 | etot = -17.0130076997047 +92000 ekin = 2.69184894487886 | erot = 3.01111638487596 | epot = -22.5488335054242 | etot = -16.8458681756693 +93000 ekin = 3.04452081584098 | erot = 3.0289315825034 | epot = -22.4857514998612 | etot = -16.4122991015169 +94000 ekin = 3.21054020599498 | erot = 1.87554208928457 | epot = -22.58235617796 | etot = -17.4962738826805 +95000 ekin = 3.49164555041805 | erot = 2.89107259754101 | epot = -22.651746211573 | etot = -16.2690280636139 +96000 ekin = 2.8961145983777 | erot = 2.38403691628048 | epot = -22.6376886129393 | etot = -17.3575370982811 +97000 ekin = 1.94001816357315 | erot = 2.09603205774619 | epot = -22.6212143095229 | etot = -18.5851640882036 +98000 ekin = 2.21812472183551 | erot = 3.66512951907029 | epot = -22.5400207863669 | etot = -16.6567665454611 +99000 ekin = 1.96304801418099 | erot = 2.78092002528644 | epot = -22.4500077741119 | etot = -17.7060397346444 +100000 ekin = 1.78146596589238 | erot = 2.66087063973067 | epot = -22.3806285021859 | etot = -17.9382918965629 +101000 ekin = 2.13576431486591 | erot = 2.39189697670582 | epot = -22.3671198416411 | etot = -17.8394585500694 +102000 ekin = 1.54265458925823 | erot = 2.31301627489861 | epot = -22.3596033820568 | etot = -18.5039325179 +103000 ekin = 1.6493299781162 | erot = 2.82700146777614 | epot = -22.4044472055819 | etot = -17.9281157596895 +104000 ekin = 1.88425130865015 | erot = 3.36695629589132 | epot = -22.4614117565727 | etot = -17.2102041520312 +105000 ekin = 2.0873628063424 | erot = 1.99902589912497 | epot = -22.4857870795246 | etot = -18.3993983740572 +106000 ekin = 2.85192200005481 | erot = 1.96124421177818 | epot = -22.4885148263279 | etot = -17.6753486144949 +107000 ekin = 2.27699301124082 | erot = 1.54572940373457 | epot = -22.4328687856414 | etot = -18.610146370666 +108000 ekin = 2.43341212242248 | erot = 1.7101452395327 | epot = -22.4750159709763 | etot = -18.3314586090212 +109000 ekin = 2.3240302459673 | erot = 2.92730273400661 | epot = -22.4544447404649 | etot = -17.203111760491 +110000 ekin = 2.75939007795593 | erot = 2.3726124845783 | epot = -22.4066316113363 | etot = -17.2746290488021 +111000 ekin = 2.30202775259985 | erot = 2.09098171366697 | epot = -22.340628179725 | etot = -17.9476187134581 +112000 ekin = 2.89672803093986 | erot = 1.84536318388285 | epot = -22.189229344937 | etot = -17.4471381301143 +113000 ekin = 2.802868120203 | erot = 1.68317583122193 | epot = -22.1739192926257 | etot = -17.6878753412008 +114000 ekin = 3.41134331362353 | erot = 2.66279011393036 | epot = -22.2993892060878 | etot = -16.2252557785339 +115000 ekin = 3.04096848543598 | erot = 1.72164164793761 | epot = -22.3101669297006 | etot = -17.547556796327 +116000 ekin = 3.18249263106367 | erot = 3.21872780579631 | epot = -22.3766120310369 | etot = -15.975391594177 +117000 ekin = 3.04033644338918 | erot = 2.4163277414929 | epot = -22.3406101341932 | etot = -16.8839459493111 +118000 ekin = 3.2297663279461 | erot = 1.46870208555873 | epot = -22.262910646297 | etot = -17.5644422327922 +119000 ekin = 2.35815331598994 | erot = 3.07464675916892 | epot = -22.21629705762 | etot = -16.7834969824611 +120000 ekin = 1.93901604028919 | erot = 2.21087803685818 | epot = -22.1596747789505 | etot = -18.0097807018031 +121000 ekin = 1.94791988346889 | erot = 3.06697908719322 | epot = -22.1473490758084 | etot = -17.1324501051462 +122000 ekin = 1.69642311218451 | erot = 1.71065948591522 | epot = -22.235021693017 | etot = -18.8279390949172 +123000 ekin = 1.74537927001903 | erot = 2.31042772730644 | epot = -22.3250546948603 | etot = -18.2692476975348 +124000 ekin = 2.74229806685692 | erot = 1.94346011848795 | epot = -22.3376426377462 | etot = -17.6518844524013 +125000 ekin = 2.77628031613761 | erot = 1.95737420539167 | epot = -22.3561899601979 | etot = -17.6225354386686 +126000 ekin = 2.05898577806786 | erot = 1.47493157618749 | epot = -22.3918669376121 | etot = -18.8579495833568 +127000 ekin = 1.88620727578863 | erot = 1.58698481884328 | epot = -22.3753405588623 | etot = -18.9021484642304 +128000 ekin = 1.65027256647601 | erot = 1.87589048163674 | epot = -22.3576574967822 | etot = -18.8314944486694 +129000 ekin = 2.51771860981078 | erot = 2.38745668871875 | epot = -22.3622404512641 | etot = -17.4570651527346 +130000 ekin = 1.60778116741171 | erot = 2.81983062254802 | epot = -22.3043401463426 | etot = -17.8767283563829 +131000 ekin = 2.27966529707091 | erot = 2.29465997580789 | epot = -22.1860056729234 | etot = -17.6116804000446 +132000 ekin = 2.94605151024306 | erot = 2.34727265039698 | epot = -22.1004107829512 | etot = -16.8070866223112 +133000 ekin = 2.00184520718143 | erot = 2.13597622566089 | epot = -22.0860804435183 | etot = -17.948259010676 +134000 ekin = 1.54536260297594 | erot = 2.86019181856985 | epot = -22.0324797134652 | etot = -17.6269252919194 +135000 ekin = 1.7899169229158 | erot = 2.40585579784188 | epot = -22.0564792277569 | etot = -17.8607065069992 +136000 ekin = 1.63315069688348 | erot = 2.13968964990471 | epot = -22.0645410751455 | etot = -18.2917007283573 +137000 ekin = 2.36475220491125 | erot = 1.93075105476848 | epot = -22.101884847306 | etot = -17.8063815876262 +138000 ekin = 2.9554682114977 | erot = 1.58329215843879 | epot = -22.158920719349 | etot = -17.6201603494125 +139000 ekin = 3.18559985564368 | erot = 2.24978247982886 | epot = -22.2766713145625 | etot = -16.84128897909 +140000 ekin = 2.25331500051846 | erot = 3.04264261269698 | epot = -22.4413209794807 | etot = -17.1453633662653 +141000 ekin = 1.8939664036255 | erot = 3.12730191483887 | epot = -22.6943708703895 | etot = -17.6731025519251 +142000 ekin = 2.48698722341786 | erot = 2.50204475841097 | epot = -22.8022645411412 | etot = -17.8132325593124 +143000 ekin = 2.39031114354901 | erot = 2.72027514737474 | epot = -22.7789363640121 | etot = -17.6683500730884 +144000 ekin = 1.93009742932803 | erot = 2.68112648713777 | epot = -22.6600942975092 | etot = -18.0488703810434 +145000 ekin = 1.81543048110687 | erot = 1.73927524532866 | epot = -22.6290694904769 | etot = -19.0743637640413 +146000 ekin = 2.4125202126428 | erot = 2.0856902293417 | epot = -22.560764077018 | etot = -18.0625536350335 +147000 ekin = 1.44642974398304 | erot = 1.86921415702345 | epot = -22.4437745695725 | etot = -19.128130668566 +148000 ekin = 1.94224767107089 | erot = 2.57935525538892 | epot = -22.4110987100046 | etot = -17.8894957835448 +149000 ekin = 2.03195649040454 | erot = 3.31786202502786 | epot = -22.312227106758 | etot = -16.9624085913256 +150000 ekin = 2.47792894576431 | erot = 2.68612874200302 | epot = -22.1392843642772 | etot = -16.9752266765099 +151000 ekin = 2.75692645092955 | erot = 1.88122565848133 | epot = -21.9329416416722 | etot = -17.2947895322613 +152000 ekin = 2.7753834344323 | erot = 1.78115734250796 | epot = -21.745072490984 | etot = -17.1885317140438 +153000 ekin = 3.09316888168833 | erot = 1.80744228044955 | epot = -21.6451473427313 | etot = -16.7445361805934 +154000 ekin = 2.31433640945477 | erot = 2.19304386678896 | epot = -21.5946356595636 | etot = -17.0872553833199 +155000 ekin = 1.94169881401553 | erot = 2.67959698479411 | epot = -21.6941053409436 | etot = -17.0728095421339 +156000 ekin = 2.69151609119638 | erot = 2.25048211983205 | epot = -21.7610571974251 | etot = -16.8190589863966 +157000 ekin = 3.89507004263776 | erot = 2.74501587672577 | epot = -21.8157728797742 | etot = -15.1756869604107 +158000 ekin = 2.88173407476086 | erot = 2.69702262693026 | epot = -21.8854957137509 | etot = -16.3067390120597 +159000 ekin = 3.15173323195919 | erot = 2.61743473710129 | epot = -21.8245251626835 | etot = -16.055357193623 +160000 ekin = 2.54983562435716 | erot = 3.26037467643908 | epot = -21.8527884226329 | etot = -16.0425781218366 +161000 ekin = 2.47569624391789 | erot = 2.44418416527208 | epot = -21.7973550812186 | etot = -16.8774746720287 +162000 ekin = 2.9422872213738 | erot = 2.59784970938383 | epot = -21.7813251561028 | etot = -16.2411882253452 +163000 ekin = 3.25812805712343 | erot = 2.2523933100784 | epot = -21.820089307521 | etot = -16.3095679403192 +164000 ekin = 3.52786799143084 | erot = 2.22392713421413 | epot = -21.7646946348872 | etot = -16.0128995092422 +165000 ekin = 2.47839548873417 | erot = 2.58744140761171 | epot = -21.679095294504 | etot = -16.6132583981582 +166000 ekin = 2.14435847552791 | erot = 3.04732688845808 | epot = -21.6219995979976 | etot = -16.4303142340116 +167000 ekin = 2.77664659649902 | erot = 2.89037999868329 | epot = -21.5339928834654 | etot = -15.8669662882831 +168000 ekin = 1.74464407802389 | erot = 2.78052653338967 | epot = -21.4288999288374 | etot = -16.9037293174239 +169000 ekin = 1.80689129093329 | erot = 2.46391033708927 | epot = -21.4128285618694 | etot = -17.1420269338468 +170000 ekin = 1.6949814594151 | erot = 2.88911238881154 | epot = -21.4319269866203 | etot = -16.8478331383937 +171000 ekin = 2.15326316196645 | erot = 1.61346547801869 | epot = -21.2861470779283 | etot = -17.5194184379432 +172000 ekin = 1.67904916339532 | erot = 2.36509147316375 | epot = -21.1250864759441 | etot = -17.080945839385 +173000 ekin = 2.05349972960735 | erot = 2.1886466510775 | epot = -21.0744450592631 | etot = -16.8322986785782 +174000 ekin = 2.49402795941962 | erot = 3.10392317000879 | epot = -20.9332609664624 | etot = -15.335309837034 +175000 ekin = 2.60611029063986 | erot = 2.90993176119182 | epot = -20.8533230180668 | etot = -15.3372809662352 +176000 ekin = 2.14535974511637 | erot = 2.67710511021539 | epot = -20.8508037764829 | etot = -16.0283389211511 +177000 ekin = 2.82654664242577 | erot = 2.80647819657321 | epot = -20.9303681620826 | etot = -15.2973433230836 +178000 ekin = 3.17006270723388 | erot = 1.88204403688962 | epot = -21.0665744865168 | etot = -16.0144677423933 +179000 ekin = 2.33834827123178 | erot = 2.84870047825869 | epot = -21.1082901606943 | etot = -15.9212414112039 +180000 ekin = 2.39362550925045 | erot = 2.94575326168227 | epot = -21.1089731290028 | etot = -15.7695943580701 +181000 ekin = 2.78703231260152 | erot = 3.29998898392537 | epot = -21.0761138110654 | etot = -14.9890925145385 +182000 ekin = 3.02338391239199 | erot = 2.32533107462881 | epot = -21.0444377426861 | etot = -15.6957227556653 +183000 ekin = 2.44126401356994 | erot = 2.19853056632819 | epot = -20.8846280234405 | etot = -16.2448334435424 +184000 ekin = 2.56448211253962 | erot = 2.77267067014066 | epot = -20.6657911214549 | etot = -15.3286383387746 +185000 ekin = 2.16427057092672 | erot = 1.95880146934286 | epot = -20.5647658775173 | etot = -16.4416938372477 +186000 ekin = 2.06536030915311 | erot = 3.14593463137772 | epot = -20.4537584304771 | etot = -15.2424634899463 +187000 ekin = 2.43846121057803 | erot = 1.93593042270703 | epot = -20.4775765627296 | etot = -16.1031849294445 +188000 ekin = 2.28827356508696 | erot = 2.89699235589217 | epot = -20.6028880527163 | etot = -15.4176221317372 +189000 ekin = 1.67206333515898 | erot = 3.05807378739729 | epot = -20.6184572736204 | etot = -15.8883201510642 +190000 ekin = 1.96995062226968 | erot = 2.94301967439401 | epot = -20.6150380630742 | etot = -15.7020677664105 +191000 ekin = 2.31558303301195 | erot = 2.65062200614568 | epot = -20.5845049099943 | etot = -15.6182998708367 +192000 ekin = 3.58105122568799 | erot = 2.89866835149675 | epot = -20.555036456006 | etot = -14.0753168788213 +193000 ekin = 2.69738971383614 | erot = 3.08390984677749 | epot = -20.5718609412494 | etot = -14.7905613806358 +194000 ekin = 2.65963556416735 | erot = 2.28486501061268 | epot = -20.4488832942326 | etot = -15.5043827194526 +195000 ekin = 1.85289053427901 | erot = 2.65318671222087 | epot = -20.3816844231208 | etot = -15.8756071766209 +196000 ekin = 2.28257181147918 | erot = 2.31175601065462 | epot = -20.4051132325268 | etot = -15.810785410393 +197000 ekin = 2.49770460330585 | erot = 2.55587879440511 | epot = -20.4716020539923 | etot = -15.4180186562814 +198000 ekin = 2.01700960777427 | erot = 1.51922008609382 | epot = -20.4907970823156 | etot = -16.9545673884475 +199000 ekin = 1.50027537520987 | erot = 2.19604462463446 | epot = -20.5138434458212 | etot = -16.8175234459769 +200000 ekin = 1.64850512926723 | erot = 2.4596633548257 | epot = -20.4934420686449 | etot = -16.385273584552 +201000 ekin = 2.62997533994907 | erot = 2.61637339049483 | epot = -20.5569645618355 | etot = -15.3106158313916 +202000 ekin = 2.3089517547524 | erot = 2.5565329388766 | epot = -20.6262537118088 | etot = -15.7607690181798 +203000 ekin = 1.64768887888551 | erot = 2.11556417528285 | epot = -20.6617888215465 | etot = -16.8985357673782 +204000 ekin = 2.01924097320136 | erot = 1.97748949636931 | epot = -20.7002685556682 | etot = -16.7035380860975 +205000 ekin = 2.97656554045711 | erot = 3.25408007971553 | epot = -20.9425038008424 | etot = -14.7118581806698 +206000 ekin = 2.56613069661945 | erot = 2.21624244224461 | epot = -21.0621833598182 | etot = -16.2798102209542 +207000 ekin = 3.44850636848559 | erot = 2.48816050856267 | epot = -21.2038849430867 | etot = -15.2672180660384 +208000 ekin = 2.54208934028226 | erot = 2.22605232144502 | epot = -21.3476404533667 | etot = -16.5794987916394 +209000 ekin = 3.84151461096732 | erot = 2.16534559513903 | epot = -21.4932373455843 | etot = -15.486377139478 +210000 ekin = 3.06873591712904 | erot = 2.24760815652574 | epot = -21.6427793540355 | etot = -16.3264352803807 +211000 ekin = 1.64176280869923 | erot = 2.17721976802011 | epot = -21.8130439048272 | etot = -17.9940613281078 +212000 ekin = 2.5985934050661 | erot = 2.41520703335869 | epot = -21.9964648294563 | etot = -16.9826643910315 +213000 ekin = 2.51136104390039 | erot = 1.99503544560738 | epot = -22.161492842604 | etot = -17.6550963530962 +214000 ekin = 2.77089845962619 | erot = 3.17247228684199 | epot = -22.208715104286 | etot = -16.2653443578179 +215000 ekin = 2.53408528186206 | erot = 1.84963848601798 | epot = -22.1148567901871 | etot = -17.7311330223071 +216000 ekin = 2.52671619876928 | erot = 2.77873014449688 | epot = -22.1370884570131 | etot = -16.8316421137469 +217000 ekin = 2.50171921508545 | erot = 1.89238935467003 | epot = -22.226079201001 | etot = -17.8319706312455 +218000 ekin = 2.43936294263937 | erot = 2.41974828067303 | epot = -22.2447049583244 | etot = -17.385593735012 +219000 ekin = 2.30221269367205 | erot = 2.65120674162376 | epot = -22.2807164841742 | etot = -17.3272970488784 +220000 ekin = 1.70065256620687 | erot = 2.34758543213915 | epot = -22.2809933538228 | etot = -18.2327553554768 +221000 ekin = 2.09298237125575 | erot = 2.47886481595909 | epot = -22.267957001012 | etot = -17.6961098137972 +222000 ekin = 1.58469709510937 | erot = 2.14490786301286 | epot = -22.1867412404881 | etot = -18.4571362823659 +223000 ekin = 1.83926923346352 | erot = 1.89456034969536 | epot = -22.131893392038 | etot = -18.3980638088791 +224000 ekin = 2.59583657132575 | erot = 2.93869915115497 | epot = -22.1425986650605 | etot = -16.6080629425798 +225000 ekin = 3.29351563254165 | erot = 2.8433953581414 | epot = -22.12757310355 | etot = -15.9906621128669 +226000 ekin = 3.03135339447922 | erot = 2.08293143143602 | epot = -22.15283624886 | etot = -17.0385514229448 +227000 ekin = 2.50176282992082 | erot = 3.15084128846394 | epot = -22.2250438959744 | etot = -16.5724397775897 +228000 ekin = 2.32013498351673 | erot = 2.67554406359439 | epot = -22.3177515383563 | etot = -17.3220724912452 +229000 ekin = 2.89545450975319 | erot = 2.90735055857068 | epot = -22.4361496683348 | etot = -16.6333446000109 +230000 ekin = 2.28321229485933 | erot = 3.48420465632866 | epot = -22.548785995051 | etot = -16.781369043863 +231000 ekin = 2.0778632375453 | erot = 3.10673973696436 | epot = -22.5896609633152 | etot = -17.4050579888055 +232000 ekin = 2.1202374109541 | erot = 1.98747810033065 | epot = -22.5738924334392 | etot = -18.4661769221544 +233000 ekin = 2.33571877855589 | erot = 2.83585090202738 | epot = -22.5402065195541 | etot = -17.3686368389708 +234000 ekin = 2.10578223747154 | erot = 2.07381218733635 | epot = -22.5507693150833 | etot = -18.3711748902754 +235000 ekin = 2.44321041214394 | erot = 2.80846352304318 | epot = -22.5606929563186 | etot = -17.3090190211315 +236000 ekin = 2.93630791731799 | erot = 3.0631591853173 | epot = -22.4860653874722 | etot = -16.4865982848369 +237000 ekin = 3.21264879506079 | erot = 3.26866508478298 | epot = -22.3683553437862 | etot = -15.8870414639424 +238000 ekin = 2.46595539123277 | erot = 2.32502019506664 | epot = -22.3144456769666 | etot = -17.5234700906672 +239000 ekin = 2.10325864915823 | erot = 2.47631139904042 | epot = -22.3011392921811 | etot = -17.7215692439825 +240000 ekin = 1.77270999777839 | erot = 2.60141429112664 | epot = -22.2344206081543 | etot = -17.8602963192493 +241000 ekin = 1.94952922244078 | erot = 1.39715216866764 | epot = -22.2207225048761 | etot = -18.8740411137677 +242000 ekin = 3.05687991591411 | erot = 2.00862394928705 | epot = -22.2213200390944 | etot = -17.1558161738932 +243000 ekin = 2.86735711945299 | erot = 1.79948118674678 | epot = -22.2697610280427 | etot = -17.6029227218429 +244000 ekin = 2.00525854269389 | erot = 2.36445341214555 | epot = -22.2726788994494 | etot = -17.90296694461 +245000 ekin = 2.28011102404838 | erot = 2.787005205328 | epot = -22.2995433574618 | etot = -17.2324271280854 +246000 ekin = 2.06819738789813 | erot = 2.24624952782285 | epot = -22.2551680110138 | etot = -17.9407210952928 +247000 ekin = 1.69964711256213 | erot = 3.22260619239827 | epot = -22.1916408256116 | etot = -17.2693875206512 +248000 ekin = 1.92997585194759 | erot = 3.61155944514373 | epot = -22.0096484177853 | etot = -16.4681131206939 +249000 ekin = 2.16278530892653 | erot = 3.27771891456709 | epot = -21.8856058980727 | etot = -16.4451016745791 +250000 ekin = 2.32204054211024 | erot = 2.46317574116847 | epot = -21.8028762710592 | etot = -17.0176599877804 +251000 ekin = 1.23768964067254 | erot = 2.24150533762101 | epot = -21.763065707404 | etot = -18.2838707291104 +252000 ekin = 1.79818833522214 | erot = 2.12556386664128 | epot = -21.7586349357285 | etot = -17.8348827338651 +253000 ekin = 2.12809689846393 | erot = 2.59685639208402 | epot = -21.7226495687758 | etot = -16.9976962782278 +254000 ekin = 2.46813261968532 | erot = 2.00391812662869 | epot = -21.7113918037362 | etot = -17.2393410574222 +255000 ekin = 2.3156672908729 | erot = 2.03619058028117 | epot = -21.7265453183257 | etot = -17.3746874471716 +256000 ekin = 2.87223929491326 | erot = 2.61790933826624 | epot = -21.659332511914 | etot = -16.1691838787345 +257000 ekin = 2.85756762932927 | erot = 2.081746739162 | epot = -21.6161821054731 | etot = -16.6768677369819 +258000 ekin = 2.06111021157734 | erot = 2.32748664972428 | epot = -21.5132485706727 | etot = -17.124651709371 +259000 ekin = 2.23305784057759 | erot = 2.88843859953735 | epot = -21.5040039667855 | etot = -16.3825075266705 +260000 ekin = 2.49862397932476 | erot = 2.38336885848389 | epot = -21.488210637319 | etot = -16.6062177995103 +261000 ekin = 2.09280296934734 | erot = 2.39632540029205 | epot = -21.4325331777953 | etot = -16.9434048081559 +262000 ekin = 2.33576913564289 | erot = 2.67273419354397 | epot = -21.3832241450035 | etot = -16.3747208158166 +263000 ekin = 2.20536189489354 | erot = 2.71530627040565 | epot = -21.4329409070981 | etot = -16.5122727417989 +264000 ekin = 2.2858247573423 | erot = 2.76839346219664 | epot = -21.39310844316 | etot = -16.338890223621 +265000 ekin = 1.70928536820409 | erot = 1.79395423442894 | epot = -21.2682341921474 | etot = -17.7649945895144 +266000 ekin = 2.48721735474525 | erot = 2.08745460533224 | epot = -21.1746995817337 | etot = -16.6000276216562 +267000 ekin = 2.69283567987773 | erot = 2.10301910407211 | epot = -21.1705161290062 | etot = -16.3746613450564 +268000 ekin = 3.00000233743719 | erot = 2.80954585635721 | epot = -21.164752112651 | etot = -15.3552039188566 +269000 ekin = 3.50713810468527 | erot = 2.35763817348003 | epot = -21.1537110688984 | etot = -15.2889347907331 +270000 ekin = 3.50686942248863 | erot = 1.86462765875888 | epot = -21.1925508822801 | etot = -15.8210538010326 +271000 ekin = 3.57026082273992 | erot = 2.08172467795384 | epot = -21.2775817182941 | etot = -15.6255962176003 +272000 ekin = 2.4484752533773 | erot = 3.08466485039761 | epot = -21.3619851902072 | etot = -15.8288450864322 +273000 ekin = 2.39748176307241 | erot = 3.13355050446718 | epot = -21.4386234252579 | etot = -15.9075911577183 +274000 ekin = 2.48208144431863 | erot = 2.00552494041967 | epot = -21.4476232953882 | etot = -16.9600169106499 +275000 ekin = 2.48721081149369 | erot = 3.05413598233603 | epot = -21.4713984309062 | etot = -15.9300516370765 +276000 ekin = 2.82709589676966 | erot = 2.88384306577856 | epot = -21.4434590118161 | etot = -15.7325200492679 +277000 ekin = 2.23479555963313 | erot = 2.20310851955638 | epot = -21.3883073251199 | etot = -16.9504032459304 +278000 ekin = 2.81418916407429 | erot = 3.24537052192613 | epot = -21.3155364074003 | etot = -15.2559767213999 +279000 ekin = 2.57366525203699 | erot = 1.81705578305929 | epot = -21.2862101233851 | etot = -16.8954890882888 +280000 ekin = 2.41063464320149 | erot = 1.76282693004731 | epot = -21.2549625280961 | etot = -17.0815009548473 +281000 ekin = 2.58126226070487 | erot = 2.29258221702166 | epot = -21.306394928225 | etot = -16.4325504504985 +282000 ekin = 3.02016903398222 | erot = 2.43094523890341 | epot = -21.4340900724633 | etot = -15.9829757995777 +283000 ekin = 2.59269149790331 | erot = 2.11330689541033 | epot = -21.6296517079942 | etot = -16.9236533146806 +284000 ekin = 2.51704243107537 | erot = 3.13156683036761 | epot = -21.7452694753527 | etot = -16.0966602139097 +285000 ekin = 2.4236537221525 | erot = 1.77228258125507 | epot = -21.8557019037769 | etot = -17.6597656003693 +286000 ekin = 1.9446719552166 | erot = 2.0366097411672 | epot = -21.901435736722 | etot = -17.9201540403382 +287000 ekin = 2.56319670376172 | erot = 2.60867050510166 | epot = -21.90675099349 | etot = -16.7348837846266 +288000 ekin = 2.19574207425738 | erot = 1.69805542160023 | epot = -21.8143855675961 | etot = -17.9205880717385 +289000 ekin = 2.35326278833027 | erot = 1.65840109676146 | epot = -21.6976038565284 | etot = -17.6859399714367 +290000 ekin = 2.3519456177505 | erot = 1.99444238353744 | epot = -21.6551012116075 | etot = -17.3087132103195 +291000 ekin = 1.48585281531715 | erot = 2.66475825861554 | epot = -21.56036793472 | etot = -17.4097568607873 +292000 ekin = 2.10739944756451 | erot = 2.42809824662638 | epot = -21.4451596117638 | etot = -16.9096619175729 +293000 ekin = 2.11618090223716 | erot = 1.86694554151198 | epot = -21.3593625692767 | etot = -17.3762361255276 +294000 ekin = 2.06078090566332 | erot = 2.13941873359476 | epot = -21.2326233100941 | etot = -17.032423670836 +295000 ekin = 2.11467178034793 | erot = 2.3267343667518 | epot = -21.1123588667461 | etot = -16.6709527196464 +296000 ekin = 1.53087058859331 | erot = 2.94008409149153 | epot = -21.2112197533848 | etot = -16.7402650732999 +297000 ekin = 2.52732986791196 | erot = 2.18380855337858 | epot = -21.1955190508786 | etot = -16.4843806295881 +298000 ekin = 1.89033945823196 | erot = 2.02521913176001 | epot = -21.2593750718296 | etot = -17.3438164818376 +299000 ekin = 1.87142873048436 | erot = 1.66404563221549 | epot = -21.2919162310488 | etot = -17.7564418683489 +300000 ekin = 2.23872615546788 | erot = 1.50807257618897 | epot = -21.3339204593826 | etot = -17.5871217277258 +301000 ekin = 1.99965506724558 | erot = 2.00145094516844 | epot = -21.4707589194325 | etot = -17.4696529070184 +302000 ekin = 1.76370349732521 | erot = 2.23787708901487 | epot = -21.5675275978257 | etot = -17.5659470114856 +303000 ekin = 2.69610887251788 | erot = 1.6995722142974 | epot = -21.5563765448092 | etot = -17.1606954579939 +304000 ekin = 2.55447143501921 | erot = 2.02060813090349 | epot = -21.5692327321341 | etot = -16.9941531662114 +305000 ekin = 2.38230604232717 | erot = 2.31489374428114 | epot = -21.5335950166329 | etot = -16.8363952300246 +306000 ekin = 2.07785475765118 | erot = 2.4523066068597 | epot = -21.4550895345847 | etot = -16.9249281700738 +307000 ekin = 3.17130424567278 | erot = 3.29574614566806 | epot = -21.4151535289883 | etot = -14.9481031376474 +308000 ekin = 3.40959217051674 | erot = 2.68389483402973 | epot = -21.4778643688409 | etot = -15.3843773642944 +309000 ekin = 2.36068264180093 | erot = 2.91715332823342 | epot = -21.5794336507741 | etot = -16.3015976807398 +310000 ekin = 2.4995235722922 | erot = 2.36028950896138 | epot = -21.5982142524176 | etot = -16.738401171164 +311000 ekin = 2.53288726180906 | erot = 2.29596940545851 | epot = -21.6418553661547 | etot = -16.8129986988871 +312000 ekin = 2.05123272208704 | erot = 2.92023923411834 | epot = -21.7377547517075 | etot = -16.7662827955022 +313000 ekin = 1.80834719374888 | erot = 2.29357283142125 | epot = -21.7993116362532 | etot = -17.6973916110831 +314000 ekin = 2.30684015099018 | erot = 2.20859462712272 | epot = -21.8029398081388 | etot = -17.2875050300259 +315000 ekin = 1.86413924486173 | erot = 2.14748794238475 | epot = -21.8550418960799 | etot = -17.8434147088335 +316000 ekin = 2.20558056533516 | erot = 3.03447287931582 | epot = -21.8868412075709 | etot = -16.6467877629199 +317000 ekin = 2.47820931125479 | erot = 3.56870099099487 | epot = -21.9902146748519 | etot = -15.9433043726022 +318000 ekin = 2.36582343801679 | erot = 3.01887804681552 | epot = -22.1178732891163 | etot = -16.733171804284 +319000 ekin = 2.40464629760758 | erot = 3.15910789488741 | epot = -22.2289401281565 | etot = -16.6651859356615 +320000 ekin = 1.80206494109346 | erot = 2.83527990295434 | epot = -22.3120263401861 | etot = -17.6746814961383 +321000 ekin = 2.91146951948762 | erot = 2.25772268449837 | epot = -22.3029455835947 | etot = -17.1337533796087 +322000 ekin = 2.8226351296685 | erot = 2.67950826833977 | epot = -22.3041650189947 | etot = -16.8020216209865 +323000 ekin = 2.067323568424 | erot = 2.319752847753 | epot = -22.3338840353559 | etot = -17.9468076191789 +324000 ekin = 2.6012747278288 | erot = 2.58351861537749 | epot = -22.3215168526944 | etot = -17.1367235094881 +325000 ekin = 3.45560055552843 | erot = 2.50162515355505 | epot = -22.1825527777624 | etot = -16.2253270686789 +326000 ekin = 3.51422890604519 | erot = 2.84426061018012 | epot = -22.0201095272525 | etot = -15.6616200110272 +327000 ekin = 2.63551490316295 | erot = 2.20570805472231 | epot = -21.9384479867007 | etot = -17.0972250288154 +328000 ekin = 1.8043914440792 | erot = 2.37599512200968 | epot = -21.861980397642 | etot = -17.6815938315531 +329000 ekin = 2.15766181563134 | erot = 2.45286496267961 | epot = -21.8518523862112 | etot = -17.2413256079002 +330000 ekin = 1.8483425992464 | erot = 2.03367429366601 | epot = -21.768409525242 | etot = -17.8863926323296 +331000 ekin = 2.3531484336258 | erot = 1.80165819621476 | epot = -21.7197009414848 | etot = -17.5648943116443 +332000 ekin = 1.67855936307207 | erot = 2.5334121965131 | epot = -21.7336434355881 | etot = -17.5216718760029 +333000 ekin = 1.60376334688456 | erot = 2.14058675025446 | epot = -21.835637958395 | etot = -18.091287861256 +334000 ekin = 2.26551990081779 | erot = 2.62486254825415 | epot = -21.8794971078471 | etot = -16.9891146587751 +335000 ekin = 2.91208137486081 | erot = 3.11052870452009 | epot = -21.9161692767172 | etot = -15.8935591973363 +336000 ekin = 2.73132973682385 | erot = 2.56213100489412 | epot = -21.8312488568505 | etot = -16.5377881151325 +337000 ekin = 3.15411918141902 | erot = 3.87512819831194 | epot = -21.9061152574783 | etot = -14.8768678777473 +338000 ekin = 2.33141760424507 | erot = 2.13211945089677 | epot = -21.913746111238 | etot = -17.4502090560962 +339000 ekin = 1.71915361945719 | erot = 2.31270220754042 | epot = -21.904207477372 | etot = -17.8723516503744 +340000 ekin = 1.62199393011804 | erot = 3.16990972384471 | epot = -21.8898233676232 | etot = -17.0979197136604 +341000 ekin = 1.71588704296646 | erot = 3.17642860992459 | epot = -21.8345558128149 | etot = -16.9422401599239 +342000 ekin = 1.82178091247658 | erot = 2.58875985611024 | epot = -21.7161502950573 | etot = -17.3056095264705 +343000 ekin = 3.08559255942693 | erot = 2.94813449265471 | epot = -21.7030445300997 | etot = -15.669317478018 +344000 ekin = 2.95985387154984 | erot = 3.1154751585035 | epot = -21.6815483295521 | etot = -15.6062192994987 +345000 ekin = 2.33428072266864 | erot = 2.88044431283017 | epot = -21.6567075042343 | etot = -16.4419824687355 +346000 ekin = 2.02077664062698 | erot = 3.45936833964707 | epot = -21.5877268821218 | etot = -16.1075819018478 +347000 ekin = 2.34924784800441 | erot = 1.93056350805623 | epot = -21.4896151766055 | etot = -17.2098038205448 +348000 ekin = 2.79839267202794 | erot = 2.79408776517963 | epot = -21.4682057474678 | etot = -15.8757253102602 +349000 ekin = 2.33820470114614 | erot = 3.12966318670513 | epot = -21.5603039389198 | etot = -16.0924360510685 +350000 ekin = 2.22383234890832 | erot = 2.38886870388011 | epot = -21.5375784703117 | etot = -16.9248774175233 +351000 ekin = 2.33329735253339 | erot = 2.84447430695179 | epot = -21.5078106306152 | etot = -16.33003897113 +352000 ekin = 2.74923373919408 | erot = 2.76796181793625 | epot = -21.5537134920816 | etot = -16.0365179349512 +353000 ekin = 1.76111836153717 | erot = 2.12255592617518 | epot = -21.5037017999955 | etot = -17.6200275122832 +354000 ekin = 2.29967358188085 | erot = 2.37615363620183 | epot = -21.559257977819 | etot = -16.8834307597364 +355000 ekin = 2.32956787601564 | erot = 2.41406261152025 | epot = -21.5311925684016 | etot = -16.7875620808657 +356000 ekin = 2.99536507165417 | erot = 3.0133786789017 | epot = -21.461213826164 | etot = -15.4524700756081 +357000 ekin = 1.79487551861702 | erot = 2.14781775756832 | epot = -21.4425100027869 | etot = -17.4998167266016 +358000 ekin = 2.06856992699964 | erot = 1.9158505155371 | epot = -21.4597512525557 | etot = -17.475330810019 +359000 ekin = 2.03457633089973 | erot = 2.13725650388114 | epot = -21.434584367242 | etot = -17.2627515324611 +360000 ekin = 2.64289898809605 | erot = 2.45722294398598 | epot = -21.3798303659973 | etot = -16.2797084339152 +361000 ekin = 2.44681633772951 | erot = 2.40323525392197 | epot = -21.4535746870958 | etot = -16.6035230954443 +362000 ekin = 2.27284400709389 | erot = 2.04866562998477 | epot = -21.4444048899961 | etot = -17.1228952529175 +363000 ekin = 3.23945885057604 | erot = 1.79247859381387 | epot = -21.4992698914106 | etot = -16.4673324470207 +364000 ekin = 3.01124200487831 | erot = 2.16495867321708 | epot = -21.5330648567406 | etot = -16.3568641786452 +365000 ekin = 2.51472285580867 | erot = 2.29864111879035 | epot = -21.6252096459669 | etot = -16.8118456713679 +366000 ekin = 2.59356655410022 | erot = 2.21031948632573 | epot = -21.6397726115723 | etot = -16.8358865711464 +367000 ekin = 2.23422490605626 | erot = 1.85375489374336 | epot = -21.7036464131406 | etot = -17.615666613341 +368000 ekin = 2.47747707853682 | erot = 2.36511710555106 | epot = -21.7442459693683 | etot = -16.9016517852804 +369000 ekin = 2.03854183495619 | erot = 2.80790943599038 | epot = -21.829546112742 | etot = -16.9830948417954 +370000 ekin = 2.08495509326204 | erot = 2.15717784784087 | epot = -21.8579547558588 | etot = -17.6158218147559 +371000 ekin = 2.1649158804987 | erot = 2.10731342711637 | epot = -21.750730287247 | etot = -17.4785009796319 +372000 ekin = 1.83416420958724 | erot = 1.90082367490453 | epot = -21.6784224725519 | etot = -17.9434345880602 +373000 ekin = 1.97176482573297 | erot = 1.77796007890949 | epot = -21.6393712386778 | etot = -17.8896463340354 +374000 ekin = 2.89940710658305 | erot = 1.91194262525378 | epot = -21.5337545453636 | etot = -16.7224048135267 +375000 ekin = 2.32339676163341 | erot = 1.92362318361284 | epot = -21.4217091025191 | etot = -17.1746891572728 +376000 ekin = 2.59047552311153 | erot = 2.32394149083979 | epot = -21.4139727856534 | etot = -16.4995557717021 +377000 ekin = 2.24598863840517 | erot = 1.65770205797294 | epot = -21.3405339068232 | etot = -17.4368432104451 +378000 ekin = 2.38351514056703 | erot = 2.54156262207207 | epot = -21.3122380587448 | etot = -16.3871602961057 +379000 ekin = 2.08457212928958 | erot = 2.11819645676889 | epot = -21.2663127721437 | etot = -17.0635441860853 +380000 ekin = 2.62168026009058 | erot = 2.36576073073357 | epot = -21.2469701231192 | etot = -16.259529132295 +381000 ekin = 2.42554871977308 | erot = 2.21588725182519 | epot = -21.2594018196931 | etot = -16.6179658480948 +382000 ekin = 2.04454090532126 | erot = 3.35199327879852 | epot = -21.3507561156204 | etot = -15.9542219315006 +383000 ekin = 2.57756769789846 | erot = 1.58356833947095 | epot = -21.4206473136967 | etot = -17.2595112763272 +384000 ekin = 2.32411392435712 | erot = 2.07034159075996 | epot = -21.425401700327 | etot = -17.03094618521 +385000 ekin = 1.93815279071873 | erot = 3.29970374476252 | epot = -21.4993838182002 | etot = -16.2615272827189 +386000 ekin = 2.10645704249442 | erot = 2.94380940917572 | epot = -21.5050572923383 | etot = -16.4547908406681 +387000 ekin = 2.28625118399721 | erot = 2.404880226949 | epot = -21.4350466670762 | etot = -16.74391525613 +388000 ekin = 2.84183807689895 | erot = 2.72440789072405 | epot = -21.448767296848 | etot = -15.882521329225 +389000 ekin = 3.39750799106372 | erot = 3.08194517695386 | epot = -21.6559630447603 | etot = -15.1765098767427 +390000 ekin = 2.82211920760115 | erot = 2.04880343622589 | epot = -21.7229608878358 | etot = -16.8520382440088 +391000 ekin = 2.25113345866117 | erot = 2.45876014532077 | epot = -21.7793475672488 | etot = -17.0694539632668 +392000 ekin = 2.6777973992177 | erot = 2.75278604715789 | epot = -21.9200377033298 | etot = -16.4894542569542 +393000 ekin = 2.07336639249413 | erot = 1.66102921524042 | epot = -22.0500496423094 | etot = -18.3156540345748 +394000 ekin = 2.1138614951422 | erot = 2.4065490584156 | epot = -22.0647062581752 | etot = -17.5442957046174 +395000 ekin = 2.46967791557607 | erot = 2.46187607744978 | epot = -22.0113006362931 | etot = -17.0797466432672 +396000 ekin = 3.17858061422168 | erot = 1.60030928107608 | epot = -21.9570022338792 | etot = -17.1781123385814 +397000 ekin = 2.37483507726776 | erot = 2.17387816921976 | epot = -21.8769234701935 | etot = -17.3282102237059 +398000 ekin = 2.29815779154461 | erot = 2.2014862703049 | epot = -21.8293641014529 | etot = -17.3297200396034 +399000 ekin = 2.66620669497936 | erot = 2.78316441348845 | epot = -21.7420307764657 | etot = -16.2926596679979 +400000 ekin = 1.8196142363994 | erot = 2.77573291920477 | epot = -21.7225828560707 | etot = -17.1272357004666 +401000 ekin = 2.39347596566753 | erot = 3.11237720134102 | epot = -21.7632198127751 | etot = -16.2573666457665 +402000 ekin = 4.01379092525261 | erot = 3.58756310879361 | epot = -21.6952307126456 | etot = -14.0938766785994 +403000 ekin = 3.64238723358271 | erot = 3.44210139074533 | epot = -21.6932224157202 | etot = -14.6087337913922 +404000 ekin = 2.52116102522202 | erot = 2.99286839639893 | epot = -21.7395466120138 | etot = -16.2255171903929 +405000 ekin = 2.80514548558626 | erot = 3.09807228440149 | epot = -21.809681120553 | etot = -15.9064633505653 +406000 ekin = 2.32696376764902 | erot = 2.03572639782902 | epot = -21.9111381639248 | etot = -17.5484479984468 +407000 ekin = 2.33504128016395 | erot = 1.91320949168965 | epot = -21.9359478399848 | etot = -17.6876970681312 +408000 ekin = 1.90942025822265 | erot = 2.20375631379574 | epot = -21.9849314014528 | etot = -17.8717548294344 +409000 ekin = 1.98818542800297 | erot = 1.95540808206523 | epot = -22.0378349759701 | etot = -18.0942414659019 +410000 ekin = 1.59823476401333 | erot = 1.91272967852491 | epot = -22.0830507565096 | etot = -18.5720863139714 +411000 ekin = 1.87320182179615 | erot = 2.46575148951076 | epot = -22.1911106440468 | etot = -17.8521573327399 +412000 ekin = 2.51909186028136 | erot = 2.65534868642724 | epot = -22.281680067606 | etot = -17.1072395208974 +413000 ekin = 2.80929435327118 | erot = 3.19888285052217 | epot = -22.1907679968741 | etot = -16.1825907930808 +414000 ekin = 2.79014519733558 | erot = 2.7251519541093 | epot = -22.144863024243 | etot = -16.6295658727981 +415000 ekin = 2.46789019087319 | erot = 2.24891720770208 | epot = -22.1977268949425 | etot = -17.4809194963672 +416000 ekin = 3.30766536008866 | erot = 1.55878918639505 | epot = -22.1694878213559 | etot = -17.3030332748722 +417000 ekin = 3.95074944679108 | erot = 2.44780201516577 | epot = -22.1018895242095 | etot = -15.7033380622526 +418000 ekin = 2.77340936693415 | erot = 2.68993840817536 | epot = -21.977327562767 | etot = -16.5139797876575 +419000 ekin = 2.38275203991917 | erot = 2.97769109273478 | epot = -21.9010102007429 | etot = -16.5405670680889 +420000 ekin = 1.80397709765343 | erot = 1.82715488758969 | epot = -21.8849019003165 | etot = -18.2537699150734 +421000 ekin = 1.35294173647286 | erot = 1.7746327595132 | epot = -21.8324727162455 | etot = -18.7048982202595 +422000 ekin = 1.39101035408781 | erot = 2.74626781088313 | epot = -21.8922044238521 | etot = -17.7549262588811 +423000 ekin = 1.58313118355036 | erot = 3.0798858727609 | epot = -21.9303489156376 | etot = -17.2673318593263 +424000 ekin = 2.38308976422853 | erot = 2.0290563283423 | epot = -22.0003513420112 | etot = -17.5882052494403 +425000 ekin = 2.32292982636642 | erot = 2.54472792699355 | epot = -22.0461884305753 | etot = -17.1785306772154 +426000 ekin = 2.07274921207622 | erot = 3.12068562025985 | epot = -21.9899604929779 | etot = -16.7965256606419 +427000 ekin = 2.16499158921497 | erot = 2.43609860560844 | epot = -21.883756502818 | etot = -17.2826663079946 +428000 ekin = 1.81001230881454 | erot = 1.6518491031194 | epot = -21.8651168729134 | etot = -18.4032554609795 +429000 ekin = 1.67080799563552 | erot = 2.55829004033943 | epot = -21.823203822061 | etot = -17.5941057860861 +430000 ekin = 2.68658781224627 | erot = 2.8591925337156 | epot = -21.8545360487503 | etot = -16.3087557027885 +431000 ekin = 2.77334901985549 | erot = 1.57746917070686 | epot = -21.8360353910944 | etot = -17.485217200532 +432000 ekin = 2.50244674166436 | erot = 1.60779258881598 | epot = -21.7381087453319 | etot = -17.6278694148516 +433000 ekin = 1.85649371322473 | erot = 2.4917335891794 | epot = -21.7919912827364 | etot = -17.4437639803323 +434000 ekin = 2.89302367450635 | erot = 2.7989004560269 | epot = -21.923157505168 | etot = -16.2312333746348 +435000 ekin = 3.67647442700572 | erot = 1.38588132381276 | epot = -22.1019777057281 | etot = -17.0396219549097 +436000 ekin = 3.05510329104703 | erot = 2.00142902882896 | epot = -22.1034257027066 | etot = -17.0468933828306 +437000 ekin = 3.2334117289381 | erot = 1.78346855436481 | epot = -22.1137020887251 | etot = -17.0968218054222 +438000 ekin = 2.86378458795303 | erot = 1.84588842157479 | epot = -22.072414124752 | etot = -17.3627411152242 +439000 ekin = 2.41407153953135 | erot = 2.70066632790346 | epot = -22.0535011599236 | etot = -16.9387632924888 +440000 ekin = 2.22110309163132 | erot = 3.0167468581899 | epot = -22.0773629228072 | etot = -16.839512972986 +441000 ekin = 2.8952003347941 | erot = 2.87911130379518 | epot = -22.2098492363511 | etot = -16.4355375977618 +442000 ekin = 2.05598301233622 | erot = 1.73562369066667 | epot = -22.2689079268812 | etot = -18.4773012238783 +443000 ekin = 1.86650631344267 | erot = 2.00816178040311 | epot = -22.3072964279925 | etot = -18.4326283341467 +444000 ekin = 2.06088560705618 | erot = 2.15265011198712 | epot = -22.3186686701219 | etot = -18.1051329510786 +445000 ekin = 2.10029110633057 | erot = 2.2800331405132 | epot = -22.3739249314238 | etot = -17.9936006845801 +446000 ekin = 2.42121462246176 | erot = 2.85365097104764 | epot = -22.4030820729314 | etot = -17.128216479422 +447000 ekin = 2.19905370994782 | erot = 2.98216231903379 | epot = -22.4760062523442 | etot = -17.2947902233625 +448000 ekin = 2.35344530580996 | erot = 2.94496431571713 | epot = -22.4927466941727 | etot = -17.1943370726456 +449000 ekin = 2.39032460069844 | erot = 2.92889137252356 | epot = -22.5027878081879 | etot = -17.1835718349659 +450000 ekin = 1.87543018481826 | erot = 1.69603328668916 | epot = -22.4562462785528 | etot = -18.8847828070454 +451000 ekin = 2.01850498861611 | erot = 1.92812989993404 | epot = -22.4817672986218 | etot = -18.5351324100716 +452000 ekin = 1.36652609658347 | erot = 1.87105620810406 | epot = -22.4501755877893 | etot = -19.2125932831018 +453000 ekin = 2.0599225820261 | erot = 2.56027964608567 | epot = -22.2765869721545 | etot = -17.6563847440428 +454000 ekin = 1.47421749728914 | erot = 2.19120144206327 | epot = -22.1381671023588 | etot = -18.4727481630064 +455000 ekin = 1.65550022307771 | erot = 2.72165814308168 | epot = -21.9904394751434 | etot = -17.613281108984 +456000 ekin = 2.34827062603187 | erot = 2.00722438151074 | epot = -21.9105114729144 | etot = -17.5550164653718 +457000 ekin = 2.01338249991754 | erot = 2.37170378033695 | epot = -21.8819790372449 | etot = -17.4968927569904 +458000 ekin = 1.72815421955305 | erot = 2.26329746701056 | epot = -21.9116044050661 | etot = -17.9201527185024 +459000 ekin = 2.48347398227002 | erot = 2.32376196929941 | epot = -21.9949404038568 | etot = -17.1877044522874 +460000 ekin = 2.18770854699575 | erot = 2.00081662918322 | epot = -21.9585322440375 | etot = -17.7700070678586 +461000 ekin = 2.27716435663744 | erot = 2.9019565626907 | epot = -21.8877682177659 | etot = -16.7086472984378 +462000 ekin = 2.61244889701715 | erot = 1.79757533309513 | epot = -21.9143949779912 | etot = -17.5043707478789 +463000 ekin = 2.55684814656524 | erot = 3.31200610027657 | epot = -21.8497749242034 | etot = -15.9809206773616 +464000 ekin = 2.15312235839157 | erot = 2.38947690136822 | epot = -21.7825241097983 | etot = -17.2399248500385 +465000 ekin = 2.5257577253008 | erot = 3.61331808321477 | epot = -21.70727052519 | etot = -15.5681947166744 +466000 ekin = 1.97943618964772 | erot = 2.88688528337621 | epot = -21.7222514097774 | etot = -16.8559299367535 +467000 ekin = 1.62882257493983 | erot = 2.60892282315519 | epot = -21.8080861041928 | etot = -17.5703407060978 +468000 ekin = 1.09823854644375 | erot = 3.35073251937299 | epot = -21.8523811012329 | etot = -17.4034100354162 +469000 ekin = 1.70229597385131 | erot = 2.7588984072639 | epot = -21.8665756757502 | etot = -17.405381294635 +470000 ekin = 1.85844768422772 | erot = 2.8706546217625 | epot = -21.9036130079376 | etot = -17.1745107019474 +471000 ekin = 2.74399539924327 | erot = 2.34943354955083 | epot = -21.9543989717239 | etot = -16.8609700229298 +472000 ekin = 2.7182617922689 | erot = 2.13581917182001 | epot = -22.0449294707038 | etot = -17.1908485066149 +473000 ekin = 2.29380642077304 | erot = 2.07595163501546 | epot = -22.0706135180041 | etot = -17.7008554622156 +474000 ekin = 2.22690782122656 | erot = 2.1647059901395 | epot = -22.0704871162386 | etot = -17.6788733048726 +475000 ekin = 2.4978679533329 | erot = 2.09510196885223 | epot = -22.0509742163569 | etot = -17.4580042941718 +476000 ekin = 2.20264299239668 | erot = 1.76757923556403 | epot = -21.9427521555982 | etot = -17.9725299276375 +477000 ekin = 2.45872237399503 | erot = 2.38426997478539 | epot = -21.9051474088983 | etot = -17.0621550601178 +478000 ekin = 1.89905964030889 | erot = 2.04864356713722 | epot = -21.9114508304737 | etot = -17.9637476230276 +479000 ekin = 2.27133902137491 | erot = 3.08755197682257 | epot = -21.8872829373266 | etot = -16.5283919391291 +480000 ekin = 1.67015605151468 | erot = 2.76560365045837 | epot = -21.8968158425889 | etot = -17.4610561406158 +481000 ekin = 1.81882995680354 | erot = 2.94136105971067 | epot = -21.8571304925407 | etot = -17.0969394760265 +482000 ekin = 2.15305069632653 | erot = 2.07327897823918 | epot = -21.8152992914385 | etot = -17.5889696168728 +483000 ekin = 1.50004535981758 | erot = 1.99364343935404 | epot = -21.7843644990947 | etot = -18.2906756999231 +484000 ekin = 1.85234844255529 | erot = 2.34000231202781 | epot = -21.8614293841666 | etot = -17.6690786295835 +485000 ekin = 1.64682178328831 | erot = 2.50437862576679 | epot = -21.8969405008956 | etot = -17.7457400918405 +486000 ekin = 1.86104257115938 | erot = 2.15995925522771 | epot = -21.8879397421696 | etot = -17.8669379157825 +487000 ekin = 2.34639026339217 | erot = 3.11622773972825 | epot = -21.9707194220382 | etot = -16.5081014189178 +488000 ekin = 2.27484994031488 | erot = 3.28147617368226 | epot = -21.9426475486812 | etot = -16.3863214346841 +489000 ekin = 2.38811933287365 | erot = 2.56070014238266 | epot = -21.8600861168089 | etot = -16.9112666415526 +490000 ekin = 2.12976254880773 | erot = 3.54525746010289 | epot = -21.7617637919249 | etot = -16.0867437830143 +491000 ekin = 2.20850764560417 | erot = 2.48919239454317 | epot = -21.6468680069132 | etot = -16.9491679667658 +492000 ekin = 2.43957739853024 | erot = 2.76323186690378 | epot = -21.6230951653168 | etot = -16.4202858998828 +493000 ekin = 1.79391622496105 | erot = 2.29052518470042 | epot = -21.6945975278841 | etot = -17.6101561182226 +494000 ekin = 2.11542949642227 | erot = 3.01313865872481 | epot = -21.7637004472039 | etot = -16.6351322920568 +495000 ekin = 2.1568591957283 | erot = 2.49005677705245 | epot = -21.8783556810053 | etot = -17.2314397082246 +496000 ekin = 2.06037552826019 | erot = 2.60698629104699 | epot = -21.9276220332962 | etot = -17.260260213989 +497000 ekin = 2.52228141248763 | erot = 1.710130192768 | epot = -21.8769629373864 | etot = -17.6445513321307 +498000 ekin = 2.15394500805411 | erot = 1.78777085700022 | epot = -21.8243748366056 | etot = -17.8826589715513 +499000 ekin = 3.01296343053108 | erot = 1.73934813146708 | epot = -21.8392632680439 | etot = -17.0869517060458 +500000 ekin = 2.76642119718551 | erot = 2.50182215373002 | epot = -21.830671988603 | etot = -16.5624286376875 +501000 ekin = 2.69367571720338 | erot = 2.99042817784739 | epot = -21.7039103667138 | etot = -16.0198064716631 +502000 ekin = 1.91666556639459 | erot = 3.89815239299714 | epot = -21.5845300715443 | etot = -15.7697121121525 +503000 ekin = 1.80513448090424 | erot = 2.94463129244922 | epot = -21.408846856306 | etot = -16.6590810829525 +504000 ekin = 1.70082883689617 | erot = 3.04312463877848 | epot = -21.3315058298563 | etot = -16.5875523541817 +505000 ekin = 2.75953000022913 | erot = 2.14635942194519 | epot = -21.3525103549444 | etot = -16.4466209327701 +506000 ekin = 2.29728093923375 | erot = 2.04403144683579 | epot = -21.3794572010067 | etot = -17.0381448149372 +507000 ekin = 3.17636857959624 | erot = 2.42164349794529 | epot = -21.4731108320934 | etot = -15.8750987545519 +508000 ekin = 2.53590109429522 | erot = 2.52790695399208 | epot = -21.6300410847596 | etot = -16.5662330364723 +509000 ekin = 2.12748393236722 | erot = 2.83071060777933 | epot = -21.7781347526393 | etot = -16.8199402124927 +510000 ekin = 2.16138023827908 | erot = 1.44739524871434 | epot = -21.8661383228762 | etot = -18.2573628358828 +511000 ekin = 2.5432337386743 | erot = 2.77108674378182 | epot = -21.9670096484361 | etot = -16.65268916598 +512000 ekin = 2.32820226144235 | erot = 2.8042493163404 | epot = -22.0177071813425 | etot = -16.8852556035598 +513000 ekin = 2.47700215188743 | erot = 2.17127792631492 | epot = -22.0110285387343 | etot = -17.3627484605319 +514000 ekin = 2.76651136580707 | erot = 2.55680467976047 | epot = -22.0909970005814 | etot = -16.7676809550138 +515000 ekin = 2.5202331965388 | erot = 1.82499891391154 | epot = -22.1712715169565 | etot = -17.8260394065062 +516000 ekin = 2.81741012640848 | erot = 2.22255273815334 | epot = -22.2621950124766 | etot = -17.2222321479148 +517000 ekin = 2.03287831599844 | erot = 2.04932227860395 | epot = -22.2794486174447 | etot = -18.1972480228423 +518000 ekin = 2.18753527424292 | erot = 2.76011341951323 | epot = -22.2667176836093 | etot = -17.3190689898532 +519000 ekin = 2.23127004412533 | erot = 2.23036422155453 | epot = -22.3641437250361 | etot = -17.9025094593562 +520000 ekin = 1.88835704965194 | erot = 2.20137678015021 | epot = -22.4547788180201 | etot = -18.365044988218 +521000 ekin = 2.57911594310157 | erot = 1.87216207270883 | epot = -22.6071563154982 | etot = -18.1558782996878 +522000 ekin = 3.47551915105823 | erot = 1.7762374523623 | epot = -22.6852629490162 | etot = -17.4335063455956 +523000 ekin = 2.84545293485784 | erot = 2.47507537559667 | epot = -22.727728352182 | etot = -17.4072000417275 +524000 ekin = 2.40278895519472 | erot = 2.37529684497552 | epot = -22.6643160930411 | etot = -17.8862302928709 +525000 ekin = 1.59507033575009 | erot = 2.61508341973268 | epot = -22.5633164974795 | etot = -18.3531627419968 +526000 ekin = 1.67007684014044 | erot = 1.59545284095808 | epot = -22.511319978416 | etot = -19.2457902973175 +527000 ekin = 2.19667533945247 | erot = 1.93330231246752 | epot = -22.4181345854017 | etot = -18.2881569334817 +528000 ekin = 2.6386695788743 | erot = 2.84200507572115 | epot = -22.4271496272375 | etot = -16.946474972642 +529000 ekin = 2.71685924097597 | erot = 3.01195511036354 | epot = -22.4607209136928 | etot = -16.7319065623533 +530000 ekin = 2.59646038482582 | erot = 2.1317692819235 | epot = -22.3209630404852 | etot = -17.5927333737358 +531000 ekin = 2.96818211550215 | erot = 2.35836906019033 | epot = -22.2240561584028 | etot = -16.8975049827103 +532000 ekin = 2.54400448114086 | erot = 2.32266423688292 | epot = -22.2383323718678 | etot = -17.3716636538441 +533000 ekin = 2.47235456553948 | erot = 2.96337386592411 | epot = -22.2434312615742 | etot = -16.8077028301106 +534000 ekin = 2.104894788263 | erot = 2.03894640697441 | epot = -22.2624131617689 | etot = -18.1185719665315 +535000 ekin = 3.76811893478762 | erot = 2.64694643296526 | epot = -22.2342741399369 | etot = -15.819208772184 +536000 ekin = 2.78932048770646 | erot = 1.95046774407585 | epot = -22.1710588414062 | etot = -17.4312706096239 +537000 ekin = 2.84547413963846 | erot = 2.6235440651257 | epot = -22.0792539675812 | etot = -16.610235762817 +538000 ekin = 2.67615418297317 | erot = 2.08962546790895 | epot = -21.9560559397441 | etot = -17.190276288862 +539000 ekin = 2.73041224389434 | erot = 2.35761678189143 | epot = -22.0360310245606 | etot = -16.9480019987748 +540000 ekin = 2.45513520817505 | erot = 2.4980712479617 | epot = -22.1997448500024 | etot = -17.2465383938656 +541000 ekin = 3.48268229748523 | erot = 2.77797330372245 | epot = -22.2939060084685 | etot = -16.0332504072608 +542000 ekin = 2.48960436886327 | erot = 2.87332479229809 | epot = -22.3004887690915 | etot = -16.9375596079301 +543000 ekin = 2.34699181381528 | erot = 2.86167842257193 | epot = -22.3027783678197 | etot = -17.0941081314325 +544000 ekin = 2.22918134297116 | erot = 1.4682792461716 | epot = -22.2757921511235 | etot = -18.5783315619807 +545000 ekin = 2.45393652663684 | erot = 2.14178562937392 | epot = -22.2696521197313 | etot = -17.6739299637206 +546000 ekin = 1.98434977645849 | erot = 2.24144093113159 | epot = -22.232171992891 | etot = -18.0063812853009 +547000 ekin = 2.56230350196472 | erot = 1.8957462591202 | epot = -22.2013923967025 | etot = -17.7433426356176 +548000 ekin = 1.72907614338158 | erot = 1.64127030305735 | epot = -22.1897325934373 | etot = -18.8193861469984 +549000 ekin = 1.95696682165776 | erot = 2.64539988943055 | epot = -22.3281210018679 | etot = -17.7257542907796 +550000 ekin = 1.80672944936439 | erot = 1.58554489058937 | epot = -22.4379557312283 | etot = -19.0456813912745 +551000 ekin = 2.19785864069661 | erot = 2.26344341600386 | epot = -22.4944444264338 | etot = -18.0331423697333 +552000 ekin = 2.074442528674 | erot = 2.49246441473273 | epot = -22.5313734934249 | etot = -17.9644665500182 +553000 ekin = 2.94841939583913 | erot = 2.1230978630074 | epot = -22.5870982488507 | etot = -17.5155809900042 +554000 ekin = 2.86687820100223 | erot = 1.9428729838172 | epot = -22.755332978123 | etot = -17.9455817933036 +555000 ekin = 2.43102414091851 | erot = 2.28708167460996 | epot = -22.8409516497233 | etot = -18.1228458341949 +556000 ekin = 2.31020008885682 | erot = 2.55815314755913 | epot = -22.8777743355338 | etot = -18.0094210991179 +557000 ekin = 2.81359485404958 | erot = 1.42586137655665 | epot = -22.93912738 | etot = -18.6996711493938 +558000 ekin = 2.7970970853355 | erot = 1.99545051650404 | epot = -22.9823826800611 | etot = -18.1898350782216 +559000 ekin = 3.34842854089643 | erot = 2.30939572175805 | epot = -23.0558646505447 | etot = -17.3980403878902 +560000 ekin = 3.12583165184862 | erot = 2.33613566970363 | epot = -23.0537007225862 | etot = -17.591733401034 +561000 ekin = 2.9127609673679 | erot = 2.07459481236913 | epot = -22.982260765434 | etot = -17.994904985697 +562000 ekin = 3.33017095598494 | erot = 2.52215992853225 | epot = -22.8889363116257 | etot = -17.0366054271086 +563000 ekin = 2.70200701416854 | erot = 1.64770113379199 | epot = -22.8712722594835 | etot = -18.521564111523 +564000 ekin = 2.82953631474813 | erot = 2.52900560163798 | epot = -22.8387855460795 | etot = -17.4802436296934 +565000 ekin = 2.67999888917708 | erot = 2.05091800967453 | epot = -22.7937507048715 | etot = -18.0628338060199 +566000 ekin = 2.32986557500305 | erot = 2.16379904557213 | epot = -22.8028233873669 | etot = -18.3091587667917 +567000 ekin = 1.92319601586312 | erot = 2.83258522428556 | epot = -22.7588270107033 | etot = -18.0030457705546 +568000 ekin = 2.1767237164987 | erot = 2.23391201707386 | epot = -22.7857243432792 | etot = -18.3750886097066 +569000 ekin = 2.44197408396629 | erot = 2.6515953630557 | epot = -22.7197314796374 | etot = -17.6261620326154 +570000 ekin = 2.43177406209051 | erot = 1.89764945519458 | epot = -22.6963472615904 | etot = -18.3669237443054 +571000 ekin = 2.86160521289847 | erot = 2.96804382024775 | epot = -22.6961835038031 | etot = -16.8665344706569 +572000 ekin = 1.92662919536387 | erot = 3.79135909534691 | epot = -22.6587081618987 | etot = -16.940719871188 +573000 ekin = 2.40137439242946 | erot = 2.29982613356341 | epot = -22.6365074046858 | etot = -17.935306878693 +574000 ekin = 1.68882589350908 | erot = 2.3209740449249 | epot = -22.6783832960445 | etot = -18.6685833576105 +575000 ekin = 1.85490665091732 | erot = 1.8564080891142 | epot = -22.7444448136904 | etot = -19.0331300736588 +576000 ekin = 3.24775679594035 | erot = 2.9556926821431 | epot = -22.6991990620437 | etot = -16.4957495839603 +577000 ekin = 2.89423151645282 | erot = 2.87486712706735 | epot = -22.628436560802 | etot = -16.8593379172818 +578000 ekin = 2.4046091667757 | erot = 2.78216711024699 | epot = -22.4348874817265 | etot = -17.2481112047039 +579000 ekin = 2.40580528046576 | erot = 1.9955781448253 | epot = -22.288913673667 | etot = -17.887530248376 +580000 ekin = 2.69817090358906 | erot = 1.94741864170502 | epot = -22.1754486864787 | etot = -17.5298591411846 +581000 ekin = 2.06309668646281 | erot = 2.97621367011722 | epot = -22.0670098600828 | etot = -17.0276995035027 +582000 ekin = 2.33869527454826 | erot = 3.07898324506955 | epot = -21.9478320300713 | etot = -16.5301535104535 +583000 ekin = 2.23428959741495 | erot = 2.68476693088864 | epot = -21.837983720672 | etot = -16.9189271923684 +584000 ekin = 2.94321016295282 | erot = 2.59995039730549 | epot = -21.7517635625832 | etot = -16.2086030023248 +585000 ekin = 2.36063475490835 | erot = 2.49112677628938 | epot = -21.7173359488816 | etot = -16.8655744176839 +586000 ekin = 3.56583702163525 | erot = 2.02487858259688 | epot = -21.7707868137138 | etot = -16.1800712094817 +587000 ekin = 3.53727585853243 | erot = 1.9725893265202 | epot = -21.7665121756112 | etot = -16.2566469905585 +588000 ekin = 2.82339556293757 | erot = 1.59340504807046 | epot = -21.7545319340972 | etot = -17.3377313230892 +589000 ekin = 2.31627310139818 | erot = 2.20582604523299 | epot = -21.8199173705563 | etot = -17.2978182239252 +590000 ekin = 2.57616671531331 | erot = 1.72768273328208 | epot = -21.8427138199642 | etot = -17.5388643713688 +591000 ekin = 1.91473306171853 | erot = 3.80604384238379 | epot = -21.9351393124187 | etot = -16.2143624083164 +592000 ekin = 2.11222958764659 | erot = 2.84208333850205 | epot = -21.9639458839076 | etot = -17.0096329577589 +593000 ekin = 1.66462149590471 | erot = 2.46217253451014 | epot = -21.9921445323971 | etot = -17.8653505019822 +594000 ekin = 1.86314045588476 | erot = 2.37275936142268 | epot = -22.1149191228505 | etot = -17.879019305543 +595000 ekin = 1.6397125755004 | erot = 2.1497024679856 | epot = -22.2960530768755 | etot = -18.5066380333895 +596000 ekin = 1.86247376576131 | erot = 1.5693809542787 | epot = -22.4014957466218 | etot = -18.9696410265818 +597000 ekin = 2.210739014067 | erot = 2.3087175693751 | epot = -22.4599242604733 | etot = -17.9404676770312 +598000 ekin = 1.8660134932493 | erot = 3.02311727399809 | epot = -22.5165298316334 | etot = -17.627399064386 +599000 ekin = 2.86271635930755 | erot = 2.19928854437227 | epot = -22.536599708025 | etot = -17.4745948043452 +600000 ekin = 2.65062163067179 | erot = 2.14533898812782 | epot = -22.4620537969303 | etot = -17.6660931781307 +601000 ekin = 2.97018864875202 | erot = 3.19824090103877 | epot = -22.3271949752462 | etot = -16.1587654254554 +602000 ekin = 2.93416893709001 | erot = 2.68627449040958 | epot = -22.2245183728173 | etot = -16.6040749453177 +603000 ekin = 2.5987545006459 | erot = 2.71301833029982 | epot = -22.1705323477201 | etot = -16.8587595167744 +604000 ekin = 1.79059859762797 | erot = 2.11515305424796 | epot = -22.1931056020217 | etot = -18.2873539501458 +605000 ekin = 1.82914051863723 | erot = 2.27656979248766 | epot = -22.2183915784731 | etot = -18.1126812673482 +606000 ekin = 2.33864125390345 | erot = 2.204164937778 | epot = -22.1617656383863 | etot = -17.6189594467048 +607000 ekin = 2.72666217259876 | erot = 2.97710334336218 | epot = -22.1572786906588 | etot = -16.4535131746978 +608000 ekin = 2.45226937954678 | erot = 2.41232790919959 | epot = -22.1263051367364 | etot = -17.2617078479901 +609000 ekin = 1.91032127854288 | erot = 2.62712516529567 | epot = -22.0127581830193 | etot = -17.4753117391807 +610000 ekin = 3.01319055031108 | erot = 2.17098104720965 | epot = -21.930499629869 | etot = -16.7463280323483 +611000 ekin = 2.44410994437293 | erot = 2.75159061185424 | epot = -21.9258193850468 | etot = -16.7301188288197 +612000 ekin = 2.50271115837174 | erot = 2.16817640692169 | epot = -21.9676183236645 | etot = -17.2967307583711 +613000 ekin = 3.01842230632868 | erot = 2.12784419676567 | epot = -22.0277467117807 | etot = -16.8814802086864 +614000 ekin = 2.25331711369829 | erot = 2.99334048390158 | epot = -22.0701464667307 | etot = -16.8234888691309 +615000 ekin = 1.66376443031995 | erot = 2.63613776051569 | epot = -21.9985978951916 | etot = -17.698695704356 +616000 ekin = 1.89454248699046 | erot = 2.87318355169532 | epot = -22.0041678369046 | etot = -17.2364417982189 +617000 ekin = 2.14789714287838 | erot = 2.51249074123957 | epot = -22.0251474680604 | etot = -17.3647595839425 +618000 ekin = 3.11174934178844 | erot = 2.74374306269141 | epot = -21.980284295602 | etot = -16.1247918911221 +619000 ekin = 3.41036213968179 | erot = 2.10616794159728 | epot = -21.9557959924962 | etot = -16.4392659112171 +620000 ekin = 4.28430989238205 | erot = 2.19572475327593 | epot = -21.9033881020935 | etot = -15.4233534564355 +621000 ekin = 3.095687767491 | erot = 2.55794040804605 | epot = -21.8286763731363 | etot = -16.1750481975993 +622000 ekin = 2.76030419206697 | erot = 2.60754397958254 | epot = -21.7459002641757 | etot = -16.3780520925262 +623000 ekin = 2.87269212022169 | erot = 2.90401311950186 | epot = -21.5853226709315 | etot = -15.8086174312079 +624000 ekin = 2.01889500087932 | erot = 3.41825755609791 | epot = -21.4095311686242 | etot = -15.972378611647 +625000 ekin = 2.87966631754697 | erot = 2.69115421564283 | epot = -21.2859406043045 | etot = -15.7151200711147 +626000 ekin = 2.56087279949319 | erot = 2.15801254335177 | epot = -21.2329175358055 | etot = -16.5140321929606 +627000 ekin = 2.30197939613517 | erot = 2.40176668957967 | epot = -21.2932794652839 | etot = -16.589533379569 +628000 ekin = 2.23988628353727 | erot = 2.75332535542195 | epot = -21.4558642198861 | etot = -16.4626525809268 +629000 ekin = 2.20891060851904 | erot = 1.97036896055006 | epot = -21.6109313731644 | etot = -17.4316518040953 +630000 ekin = 2.48711004105954 | erot = 2.14055508379566 | epot = -21.6286281269545 | etot = -17.0009630020993 +631000 ekin = 2.05035510102044 | erot = 1.78519131042561 | epot = -21.633635046353 | etot = -17.798088634907 +632000 ekin = 1.65439924450982 | erot = 3.28310987077496 | epot = -21.6999899301469 | etot = -16.7624808148621 +633000 ekin = 2.34657988531209 | erot = 2.34109631044869 | epot = -21.8317647703271 | etot = -17.1440885745664 +634000 ekin = 2.31570267703931 | erot = 2.471293173825 | epot = -21.8814211467029 | etot = -17.0944252958386 +635000 ekin = 1.99068848818427 | erot = 3.35493927676214 | epot = -21.9111632351734 | etot = -16.565535470227 +636000 ekin = 2.5015676385862 | erot = 2.48847742334419 | epot = -21.8752689055209 | etot = -16.8852238435905 +637000 ekin = 2.76558055064046 | erot = 2.80410341825293 | epot = -21.7874464522772 | etot = -16.2177624833838 +638000 ekin = 2.45488734924466 | erot = 2.81516363335622 | epot = -21.897362338598 | etot = -16.6273113559971 +639000 ekin = 1.89221088715375 | erot = 2.13319565970052 | epot = -21.932098303477 | etot = -17.9066917566227 +640000 ekin = 2.12173400886946 | erot = 3.32302167857403 | epot = -21.8808288554836 | etot = -16.4360731680401 +641000 ekin = 2.09554541112562 | erot = 2.23098450754968 | epot = -21.9203390995502 | etot = -17.5938091808749 +642000 ekin = 2.28696138506763 | erot = 2.67378976619349 | epot = -21.9723604262128 | etot = -17.0116092749517 +643000 ekin = 2.74450005384908 | erot = 2.20403941809548 | epot = -21.9235240791533 | etot = -16.9749846072088 +644000 ekin = 2.87909523138453 | erot = 3.40688779630214 | epot = -21.9417833997402 | etot = -15.6558003720535 +645000 ekin = 2.38284095628021 | erot = 2.10846397463902 | epot = -21.8306349073152 | etot = -17.339329976396 +646000 ekin = 2.68568471833193 | erot = 1.8085210536706 | epot = -21.6853054888873 | etot = -17.1910997168848 +647000 ekin = 2.44462012552757 | erot = 2.00446720103467 | epot = -21.4974635292911 | etot = -17.0483762027288 +648000 ekin = 2.22150753159449 | erot = 1.69679185313772 | epot = -21.5947311257684 | etot = -17.6764317410362 +649000 ekin = 2.55943952639507 | erot = 1.77203724563615 | epot = -22.016770390185 | etot = -17.6852936181538 +650000 ekin = 2.7234725572106 | erot = 2.20418229003755 | epot = -22.1594214535889 | etot = -17.2317666063407 +651000 ekin = 2.25383373914402 | erot = 3.26326768595798 | epot = -22.2274805933885 | etot = -16.7103791682865 +652000 ekin = 2.35810253390822 | erot = 2.29591208392313 | epot = -22.2332195197311 | etot = -17.5792049018997 +653000 ekin = 2.06421004499471 | erot = 2.1417184547457 | epot = -22.2265612208312 | etot = -18.0206327210908 +654000 ekin = 2.30460304373657 | erot = 1.85567946278894 | epot = -22.2521914868228 | etot = -18.0919089802973 +655000 ekin = 2.11188824015111 | erot = 1.79072614414006 | epot = -22.2262193909715 | etot = -18.3236050066803 +656000 ekin = 2.44561836830367 | erot = 2.32567811025775 | epot = -22.1872376286341 | etot = -17.4159411500727 +657000 ekin = 2.45751083141108 | erot = 2.86439216413734 | epot = -22.1805503246548 | etot = -16.8586473291064 +658000 ekin = 2.49955432693124 | erot = 2.85472680235227 | epot = -22.1390040132353 | etot = -16.7847228839518 +659000 ekin = 3.37980090980363 | erot = 2.77552992994233 | epot = -21.9898923341708 | etot = -15.8345614944249 +660000 ekin = 2.6941462621918 | erot = 1.99094454704574 | epot = -21.839770569098 | etot = -17.1546797598605 +661000 ekin = 2.21049176877594 | erot = 2.52393650500608 | epot = -21.6857326790217 | etot = -16.9513044052397 +662000 ekin = 2.06962867519899 | erot = 2.53976085175021 | epot = -21.6239147287108 | etot = -17.0145252017616 +663000 ekin = 2.27770295544224 | erot = 2.30124717941155 | epot = -21.5870186127932 | etot = -17.0080684779394 +664000 ekin = 2.39061717453214 | erot = 1.87616423363735 | epot = -21.4930500427881 | etot = -17.2262686346187 +665000 ekin = 2.66924405123179 | erot = 2.29240983153227 | epot = -21.4402310096658 | etot = -16.4785771269017 +666000 ekin = 1.66318176263893 | erot = 2.30827907651666 | epot = -21.3477804932103 | etot = -17.3763196540548 +667000 ekin = 1.65573830146343 | erot = 2.8261361193353 | epot = -21.2651811028886 | etot = -16.7833066820899 +668000 ekin = 2.50126196238916 | erot = 3.29062396521939 | epot = -21.1310768281354 | etot = -15.3391909005269 +669000 ekin = 1.61008562219097 | erot = 2.65727107854378 | epot = -21.0513800034042 | etot = -16.7840233026694 +670000 ekin = 2.21851826153844 | erot = 2.60770568109394 | epot = -20.9727942140714 | etot = -16.146570271439 +671000 ekin = 2.25905318343359 | erot = 2.15965495575029 | epot = -20.920836534986 | etot = -16.5021283958021 +672000 ekin = 1.93426342346647 | erot = 1.65365047668441 | epot = -20.8333028169839 | etot = -17.245388916833 +673000 ekin = 1.880896686753 | erot = 2.07483128120029 | epot = -20.79952620348 | etot = -16.8437982355267 +674000 ekin = 2.06783468057301 | erot = 2.16234064938726 | epot = -20.8176950919606 | etot = -16.5875197620003 +675000 ekin = 2.03952283590142 | erot = 2.48129689359269 | epot = -20.8297865902612 | etot = -16.3089668607671 +676000 ekin = 2.44687523374789 | erot = 2.77932995735251 | epot = -20.8513819036485 | etot = -15.6251767125481 +677000 ekin = 2.18851088067448 | erot = 2.6192892566419 | epot = -20.8589021998565 | etot = -16.0511020625401 +678000 ekin = 2.13451298865477 | erot = 2.78742961560772 | epot = -20.7380850837789 | etot = -15.8161424795164 +679000 ekin = 2.15556981522704 | erot = 2.17593910434841 | epot = -20.629255081746 | etot = -16.2977461621706 +680000 ekin = 2.0771745141444 | erot = 2.68436897198806 | epot = -20.6512705044545 | etot = -15.889727018322 +681000 ekin = 2.16836766753576 | erot = 1.82666294843077 | epot = -20.7392652191906 | etot = -16.744234603224 +682000 ekin = 3.01810965188601 | erot = 2.39774897550361 | epot = -20.7185667085479 | etot = -15.3027080811583 +683000 ekin = 2.84169666492797 | erot = 2.09885122074905 | epot = -20.7261705834808 | etot = -15.7856226978037 +684000 ekin = 1.9625035286937 | erot = 2.99543980855394 | epot = -20.7697045673731 | etot = -15.8117612301254 +685000 ekin = 1.50086016290167 | erot = 2.04478648729578 | epot = -20.7788952528481 | etot = -17.2332486026506 +686000 ekin = 2.3009298353038 | erot = 2.55442118756325 | epot = -20.7673358731011 | etot = -15.9119848502341 +687000 ekin = 1.86053862979306 | erot = 2.84846934037481 | epot = -20.7009117540898 | etot = -15.9919037839219 +688000 ekin = 2.56859020075852 | erot = 2.23263295871676 | epot = -20.6563366249257 | etot = -15.8551134654504 +689000 ekin = 2.7493014170063 | erot = 2.68327386026116 | epot = -20.8092642099637 | etot = -15.3766889326963 +690000 ekin = 2.67477310841297 | erot = 2.52397256899153 | epot = -21.0730303416649 | etot = -15.8742846642604 +691000 ekin = 2.28465281003006 | erot = 2.52273866559282 | epot = -21.2401157605126 | etot = -16.4327242848897 +692000 ekin = 2.42087744380444 | erot = 3.24812320332686 | epot = -21.2665776826931 | etot = -15.5975770355618 +693000 ekin = 2.37642605279041 | erot = 2.99546830568891 | epot = -21.3330277418611 | etot = -15.9611333833818 +694000 ekin = 2.69750178365984 | erot = 2.53085866970816 | epot = -21.521485598392 | etot = -16.293125145024 +695000 ekin = 2.49230316198816 | erot = 1.18105864485318 | epot = -21.6959912399269 | etot = -18.0226294330856 +696000 ekin = 1.86075498586631 | erot = 1.46501529683133 | epot = -21.6808441671222 | etot = -18.3550738844245 +697000 ekin = 2.40460770445908 | erot = 2.10461647488794 | epot = -21.7143559347048 | etot = -17.2051317553578 +698000 ekin = 2.32098148261586 | erot = 1.91506962097515 | epot = -21.7787361369849 | etot = -17.5426850333939 +699000 ekin = 2.44943497732062 | erot = 2.56143482106644 | epot = -21.7638026578475 | etot = -16.7529328594605 +700000 ekin = 2.13119890669415 | erot = 2.28802336161954 | epot = -21.6714710604343 | etot = -17.2522487921206 +701000 ekin = 2.15013169314239 | erot = 2.18565847708907 | epot = -21.5488216255628 | etot = -17.2130314553313 +702000 ekin = 1.57482438035702 | erot = 1.99931097090508 | epot = -21.5047640382371 | etot = -17.930628686975 +703000 ekin = 2.08829522236785 | erot = 2.17557396869524 | epot = -21.5242713758434 | etot = -17.2604021847803 +704000 ekin = 2.82144699483839 | erot = 1.94479401958833 | epot = -21.5462466947694 | etot = -16.7800056803427 +705000 ekin = 2.81019786745821 | erot = 2.16662483548889 | epot = -21.497690476826 | etot = -16.5208677738789 +706000 ekin = 1.97639068263159 | erot = 2.31468002405233 | epot = -21.494117475981 | etot = -17.2030467692971 +707000 ekin = 1.90740387464487 | erot = 2.04436544372037 | epot = -21.5505486138142 | etot = -17.5987792954489 +708000 ekin = 2.4927128838246 | erot = 2.15829540621563 | epot = -21.5728746117359 | etot = -16.9218663216957 +709000 ekin = 2.89296518644075 | erot = 2.58120965850485 | epot = -21.6152997801578 | etot = -16.1411249352122 +710000 ekin = 2.18515172086139 | erot = 2.27924743097097 | epot = -21.5865916502444 | etot = -17.122192498412 +711000 ekin = 2.31589231212299 | erot = 1.40143925977899 | epot = -21.6089597508522 | etot = -17.8916281789502 +712000 ekin = 2.55835611026778 | erot = 2.27281573655802 | epot = -21.7227687229586 | etot = -16.8915968761328 +713000 ekin = 1.95615391137192 | erot = 2.3180685223896 | epot = -21.8059432402922 | etot = -17.5317208065307 +714000 ekin = 2.56238583099812 | erot = 2.10850361056242 | epot = -21.8681675013087 | etot = -17.1972780597481 +715000 ekin = 2.42321114653449 | erot = 3.74023135295615 | epot = -21.8498336266088 | etot = -15.6863911271181 +716000 ekin = 2.83316600532177 | erot = 2.84850242081136 | epot = -21.7640231598546 | etot = -16.0823547337214 +717000 ekin = 3.45113934412558 | erot = 3.20598462177201 | epot = -21.667790662391 | etot = -15.0106666964934 +718000 ekin = 3.10736232683018 | erot = 3.94031338601797 | epot = -21.5629179727886 | etot = -14.5152422599405 +719000 ekin = 2.38564322644681 | erot = 2.95089811755838 | epot = -21.5481188237003 | etot = -16.2115774796951 +720000 ekin = 2.22543420991222 | erot = 3.14305432696276 | epot = -21.5381615962024 | etot = -16.1696730593274 +721000 ekin = 1.71709109813907 | erot = 2.23939430363989 | epot = -21.4645851946691 | etot = -17.5080997928902 +722000 ekin = 1.93213958129581 | erot = 2.81573218276728 | epot = -21.4896847080113 | etot = -16.7418129439482 +723000 ekin = 2.3814534534689 | erot = 2.55666957995948 | epot = -21.4374887927968 | etot = -16.4993657593684 +724000 ekin = 1.74740284448188 | erot = 2.4555617568904 | epot = -21.4125175551609 | etot = -17.2095529537886 +725000 ekin = 2.29233638352032 | erot = 2.9526701477774 | epot = -21.4751392844086 | etot = -16.2301327531109 +726000 ekin = 1.63503646092182 | erot = 2.30649262262117 | epot = -21.5156851039584 | etot = -17.5741560204154 +727000 ekin = 2.46705454176008 | erot = 3.19802987014479 | epot = -21.5382715508196 | etot = -15.8731871389148 +728000 ekin = 2.21709576272191 | erot = 2.16616227421244 | epot = -21.5244744557248 | etot = -17.1412164187904 +729000 ekin = 1.89396537247993 | erot = 1.66596987620967 | epot = -21.5644109232526 | etot = -18.004475674563 +730000 ekin = 1.78155182892059 | erot = 2.15399661961713 | epot = -21.5594738957829 | etot = -17.6239254472452 +731000 ekin = 2.16713092512296 | erot = 2.96875570154118 | epot = -21.4952326145865 | etot = -16.3593459879223 +732000 ekin = 2.40927355189018 | erot = 2.27189990077002 | epot = -21.3831563581627 | etot = -16.7019829055024 +733000 ekin = 3.04824198143784 | erot = 2.57289903054807 | epot = -21.429005165309 | etot = -15.8078641533231 +734000 ekin = 2.36703883022855 | erot = 2.04468815017469 | epot = -21.4926214065432 | etot = -17.0808944261399 +735000 ekin = 2.13292788677937 | erot = 1.55097035487251 | epot = -21.5455592190822 | etot = -17.8616609774303 +736000 ekin = 2.13562110082196 | erot = 3.45795834862287 | epot = -21.6515763333194 | etot = -16.0579968838746 +737000 ekin = 1.73550703692746 | erot = 3.58781244645382 | epot = -21.6785680654269 | etot = -16.3552485820456 +738000 ekin = 2.01136680767019 | erot = 2.50533140705366 | epot = -21.7068415263434 | etot = -17.1901433116196 +739000 ekin = 1.85122466968333 | erot = 2.19323904324285 | epot = -21.7211705032462 | etot = -17.6767067903201 +740000 ekin = 2.84677298867337 | erot = 2.79086338446698 | epot = -21.7460997683893 | etot = -16.108463395249 +741000 ekin = 2.47281769013274 | erot = 2.90867674862121 | epot = -21.8038806031312 | etot = -16.4223861643772 +742000 ekin = 2.74212748781964 | erot = 3.26601844940295 | epot = -21.9417105639309 | etot = -15.9335646267083 +743000 ekin = 2.23337436613032 | erot = 3.20752099935254 | epot = -22.0769938861091 | etot = -16.6360985206262 +744000 ekin = 2.01007582963959 | erot = 3.79208398827071 | epot = -22.1581491314472 | etot = -16.3559893135369 +745000 ekin = 3.14168435406402 | erot = 2.32756039064277 | epot = -22.1552791709709 | etot = -16.6860344262642 +746000 ekin = 2.96147960587595 | erot = 2.64919778641529 | epot = -22.131657657659 | etot = -16.5209802653678 +747000 ekin = 2.31713973406909 | erot = 2.0538838502724 | epot = -22.1362115743712 | etot = -17.7651879900297 +748000 ekin = 2.36228107661837 | erot = 2.41530550223615 | epot = -22.1703943251347 | etot = -17.3928077462802 +749000 ekin = 2.07006713072585 | erot = 2.7743291960411 | epot = -22.1708421357978 | etot = -17.3264458090308 +750000 ekin = 1.65834656870048 | erot = 2.38415657369843 | epot = -22.2465520170919 | etot = -18.204048874693 +751000 ekin = 1.79302728344389 | erot = 2.827102160061 | epot = -22.3488339479635 | etot = -17.7287045044586 +752000 ekin = 1.35555517803007 | erot = 1.46019783589209 | epot = -22.4342877547318 | etot = -19.6185347408096 +753000 ekin = 1.88586262445723 | erot = 2.44014879801272 | epot = -22.3837690917336 | etot = -18.0577576692636 +754000 ekin = 1.74745498380874 | erot = 2.73612011854199 | epot = -22.2852965474798 | etot = -17.8017214451291 +755000 ekin = 2.39590781949902 | erot = 2.41019902787154 | epot = -22.2066358684386 | etot = -17.400529021068 +756000 ekin = 1.83745653598818 | erot = 2.79024351605605 | epot = -22.133592240187 | etot = -17.5058921881428 +757000 ekin = 1.97281200687049 | erot = 2.57792722235948 | epot = -22.0604464398181 | etot = -17.5097072105881 +758000 ekin = 1.18945619136922 | erot = 2.72372183682492 | epot = -21.9899494795137 | etot = -18.0767714513196 +759000 ekin = 2.16230453116658 | erot = 1.39722896511084 | epot = -22.0003304659983 | etot = -18.4407969697208 +760000 ekin = 2.57253050230035 | erot = 2.33269711137819 | epot = -22.0357457302398 | etot = -17.1305181165612 +761000 ekin = 2.08545216810511 | erot = 2.24940559703297 | epot = -22.1132097744113 | etot = -17.7783520092733 +762000 ekin = 2.13509249172209 | erot = 1.66078369856518 | epot = -22.1380840935026 | etot = -18.3422079032154 +763000 ekin = 2.42851727622128 | erot = 3.36016749294484 | epot = -22.2079173436287 | etot = -16.4192325744626 +764000 ekin = 2.84703530894743 | erot = 2.79172375883345 | epot = -22.2143624032421 | etot = -16.5756033354612 +765000 ekin = 1.81325658345262 | erot = 2.77448180912351 | epot = -22.1194010453623 | etot = -17.5316626527862 +766000 ekin = 2.64831101430988 | erot = 2.3138164970859 | epot = -21.9919179324216 | etot = -17.0297904210258 +767000 ekin = 2.58949745571041 | erot = 2.86718473216884 | epot = -21.9087370669524 | etot = -16.4520548790732 +768000 ekin = 1.86313167956692 | erot = 2.78552244417217 | epot = -21.9381577980074 | etot = -17.2895036742683 +769000 ekin = 2.40162376419982 | erot = 2.31402374045875 | epot = -22.0373843590672 | etot = -17.3217368544087 +770000 ekin = 2.49146487205159 | erot = 3.23101926076328 | epot = -22.1439576198693 | etot = -16.4214734870544 +771000 ekin = 2.33226337742861 | erot = 2.27787220200643 | epot = -22.1812213688414 | etot = -17.5710857894063 +772000 ekin = 2.28990016215835 | erot = 2.99389364569332 | epot = -22.2765115340955 | etot = -16.9927177262439 +773000 ekin = 2.23002457595115 | erot = 1.82240115552767 | epot = -22.3379686916384 | etot = -18.2855429601596 +774000 ekin = 2.82350297312971 | erot = 2.21054815770298 | epot = -22.331524297742 | etot = -17.2974731669093 +775000 ekin = 1.82305982105504 | erot = 1.87100336542221 | epot = -22.2729891281483 | etot = -18.578925941671 +776000 ekin = 1.39169167990077 | erot = 3.16027505319296 | epot = -22.2459295451276 | etot = -17.6939628120339 +777000 ekin = 1.6265637770548 | erot = 2.80881827044756 | epot = -22.1611617112313 | etot = -17.7257796637289 +778000 ekin = 1.49436478903862 | erot = 2.24161236856226 | epot = -22.1732646444852 | etot = -18.4372874868843 +779000 ekin = 1.88107404119766 | erot = 1.90732846459751 | epot = -22.2125828989308 | etot = -18.4241803931357 +780000 ekin = 1.70209634464211 | erot = 2.30515299210351 | epot = -22.2800747799124 | etot = -18.2728254431668 +781000 ekin = 2.12615575710868 | erot = 2.5606535839807 | epot = -22.3657963731658 | etot = -17.6789870320765 +782000 ekin = 2.60319344794517 | erot = 1.9571688066736 | epot = -22.278889588664 | etot = -17.7185273340452 +783000 ekin = 2.19489638548848 | erot = 2.9003350616753 | epot = -22.2004563501245 | etot = -17.1052249029607 +784000 ekin = 2.84914111009349 | erot = 2.24051018422878 | epot = -22.2093010900996 | etot = -17.1196497957773 +785000 ekin = 3.14240765153577 | erot = 2.92860772919915 | epot = -22.2500274240077 | etot = -16.1790120432728 +786000 ekin = 2.83372300736036 | erot = 3.44593690351849 | epot = -22.2923595270367 | etot = -16.0126996161579 +787000 ekin = 2.41074903520556 | erot = 3.01381650302092 | epot = -22.2329745868673 | etot = -16.8084090486408 +788000 ekin = 1.99557665602945 | erot = 2.01600225895996 | epot = -22.1996915458458 | etot = -18.1881126308564 +789000 ekin = 2.46258971641133 | erot = 2.27406771625316 | epot = -22.1314921413931 | etot = -17.3948347087286 +790000 ekin = 3.5794195002921 | erot = 2.82440864812442 | epot = -22.0691321886934 | etot = -15.6653040402769 +791000 ekin = 3.1240271028451 | erot = 2.42401718962737 | epot = -22.0808685046086 | etot = -16.5328242121361 +792000 ekin = 3.95429056548242 | erot = 1.97241939137157 | epot = -22.0156932891881 | etot = -16.0889833323341 +793000 ekin = 2.26828416500901 | erot = 2.58677202552917 | epot = -21.9219598803777 | etot = -17.0669036898395 +794000 ekin = 2.16106559150924 | erot = 2.44310931274122 | epot = -21.7619518452423 | etot = -17.1577769409919 +795000 ekin = 1.62519700428841 | erot = 2.41826691867446 | epot = -21.6012749849542 | etot = -17.5578110619913 +796000 ekin = 2.18377144801669 | erot = 2.13093440679001 | epot = -21.4820337714693 | etot = -17.1673279166626 +797000 ekin = 1.81427862345353 | erot = 1.99534051513419 | epot = -21.4739195915569 | etot = -17.6643004529692 +798000 ekin = 2.2201219513299 | erot = 2.51363796316553 | epot = -21.5008270155092 | etot = -16.7670671010138 +799000 ekin = 1.88984581553595 | erot = 2.87047971528298 | epot = -21.4708608053325 | etot = -16.7105352745136 +800000 ekin = 2.14235800297794 | erot = 2.35196377273805 | epot = -21.3792596865246 | etot = -16.8849379108086 +801000 ekin = 1.84302686949433 | erot = 1.65480855802629 | epot = -21.2211741734437 | etot = -17.7233387459231 +802000 ekin = 2.20305615004888 | erot = 2.22355768328245 | epot = -21.1073599995259 | etot = -16.6807461661946 +803000 ekin = 2.64836814873033 | erot = 1.90761871804858 | epot = -21.0752041885471 | etot = -16.5192173217682 +804000 ekin = 2.34495845479317 | erot = 2.89112045330492 | epot = -21.0176734836814 | etot = -15.7815945755833 +805000 ekin = 1.79915640284781 | erot = 2.71685844764875 | epot = -20.8858433761952 | etot = -16.3698285256987 +806000 ekin = 1.74992507845556 | erot = 2.08517047523252 | epot = -20.8503301901419 | etot = -17.0152346364538 +807000 ekin = 1.57172452594494 | erot = 1.70422569898767 | epot = -20.9092333967053 | etot = -17.6332831717727 +808000 ekin = 2.08106901002531 | erot = 2.4036706521883 | epot = -20.9858691795981 | etot = -16.5011295173845 +809000 ekin = 2.61736488835992 | erot = 1.51251405170843 | epot = -20.9790910298502 | etot = -16.8492120897819 +810000 ekin = 3.07344763503492 | erot = 2.65428122600395 | epot = -20.896297890317 | etot = -15.1685690292781 +811000 ekin = 3.028899831017 | erot = 3.61686315729187 | epot = -20.939661602879 | etot = -14.2938986145701 +812000 ekin = 2.13832655324419 | erot = 2.7919099294265 | epot = -21.0260005012597 | etot = -16.095764018589 +813000 ekin = 2.19077235410927 | erot = 3.16158040032406 | epot = -21.2169108164964 | etot = -15.8645580620631 +814000 ekin = 1.70775111413747 | erot = 2.98436840501864 | epot = -21.3089511890131 | etot = -16.6168316698569 +815000 ekin = 2.14630779714624 | erot = 2.27335416843263 | epot = -21.3099230783927 | etot = -16.8902611128138 +816000 ekin = 2.70331501775258 | erot = 1.53093796189124 | epot = -21.3384418834226 | etot = -17.1041889037788 +817000 ekin = 2.55738086811903 | erot = 2.58558173150041 | epot = -21.4691891608916 | etot = -16.3262265612722 +818000 ekin = 2.27829786328906 | erot = 2.26089725682103 | epot = -21.5162183667694 | etot = -16.9770232466593 +819000 ekin = 2.10478260130361 | erot = 3.02380855832961 | epot = -21.5292309310153 | etot = -16.4006397713821 +820000 ekin = 2.50608188233135 | erot = 2.71783485224719 | epot = -21.5036816055507 | etot = -16.2797648709722 +821000 ekin = 2.62609848062629 | erot = 2.55164634943844 | epot = -21.478766185164 | etot = -16.3010213550993 +822000 ekin = 3.63941681915299 | erot = 2.20246894917129 | epot = -21.4688230156577 | etot = -15.6269372473334 +823000 ekin = 3.58953515450024 | erot = 2.73556206545619 | epot = -21.4650227341943 | etot = -15.1399255142378 +824000 ekin = 4.11304720722591 | erot = 3.2917459513548 | epot = -21.4062011377905 | etot = -14.0014079792098 +825000 ekin = 2.90620097853796 | erot = 3.46409084826251 | epot = -21.2436944546109 | etot = -14.8734026278105 +826000 ekin = 1.72188438195169 | erot = 1.97028277378148 | epot = -21.0473904580338 | etot = -17.3552233023007 +827000 ekin = 1.9124069409458 | erot = 2.55760488338657 | epot = -20.9206700763425 | etot = -16.4506582520101 +828000 ekin = 2.38145056979363 | erot = 2.55544957149182 | epot = -20.8204865756543 | etot = -15.8835864343689 +829000 ekin = 2.24733826946605 | erot = 1.78474837345228 | epot = -20.7084449579388 | etot = -16.6763583150204 +830000 ekin = 2.52795893691035 | erot = 2.34146724282711 | epot = -20.5883731027638 | etot = -15.7189469230264 +831000 ekin = 2.68310001004752 | erot = 2.07407005901145 | epot = -20.4364451382899 | etot = -15.679275069231 +832000 ekin = 2.6732342426401 | erot = 2.02167788192499 | epot = -20.3691783993746 | etot = -15.6742662748095 +833000 ekin = 2.55071664949192 | erot = 2.59972899624767 | epot = -20.3036213925319 | etot = -15.1531757467923 +834000 ekin = 2.87089088359563 | erot = 2.32463192225235 | epot = -20.2984653371648 | etot = -15.1029425313168 +835000 ekin = 2.77558903596269 | erot = 2.73757154391999 | epot = -20.4022293845421 | etot = -14.8890688046595 +836000 ekin = 2.57713146919653 | erot = 2.85322310545496 | epot = -20.5403137141641 | etot = -15.1099591395126 +837000 ekin = 1.78075406754283 | erot = 1.97503243561096 | epot = -20.5889142070484 | etot = -16.8331277038946 +838000 ekin = 1.98032617531701 | erot = 2.7982946707394 | epot = -20.6049667376349 | etot = -15.8263458915785 +839000 ekin = 2.0003179521848 | erot = 2.70198331564815 | epot = -20.5921495833285 | etot = -15.8898483154955 +840000 ekin = 1.70031236242703 | erot = 2.95685689490568 | epot = -20.6678372916037 | etot = -16.010668034271 +841000 ekin = 2.77705100359315 | erot = 2.84742847205069 | epot = -20.7929304121763 | etot = -15.1684509365325 +842000 ekin = 2.54393458307436 | erot = 2.87172695192627 | epot = -20.8173418291016 | etot = -15.401680294101 +843000 ekin = 2.00273625390939 | erot = 2.63437491598434 | epot = -20.8053999188197 | etot = -16.1682887489259 +844000 ekin = 1.52900749569349 | erot = 1.92882434140971 | epot = -20.8427655387949 | etot = -17.3849337016917 +845000 ekin = 2.27176799938834 | erot = 2.308436365406 | epot = -20.9384881501645 | etot = -16.3582837853702 +846000 ekin = 2.06718804989496 | erot = 2.33108662324981 | epot = -21.008503215967 | etot = -16.6102285428222 +847000 ekin = 2.457310325364 | erot = 2.64112097293887 | epot = -20.9624761048838 | etot = -15.8640448065809 +848000 ekin = 2.13894899278459 | erot = 1.46487099434192 | epot = -20.9909626022984 | etot = -17.3871426151719 +849000 ekin = 2.0007946308419 | erot = 2.48568109050424 | epot = -20.9995492646628 | etot = -16.5130735433167 +850000 ekin = 2.54186297995285 | erot = 2.66929613872204 | epot = -20.9906717645298 | etot = -15.7795126458549 +851000 ekin = 2.16443404123472 | erot = 2.92830981454153 | epot = -20.9932718794597 | etot = -15.9005280236835 +852000 ekin = 2.48255398040851 | erot = 2.46238001266592 | epot = -21.018749118108 | etot = -16.0738151250336 +853000 ekin = 2.41541467016921 | erot = 2.97520224443385 | epot = -20.9598722543997 | etot = -15.5692553397966 +854000 ekin = 2.35150751079563 | erot = 2.85453387569363 | epot = -20.8693696367608 | etot = -15.6633282502715 +855000 ekin = 2.36749640703667 | erot = 2.0675340835823 | epot = -20.8980197782034 | etot = -16.4629892875844 +856000 ekin = 2.52164598863741 | erot = 2.75265020302047 | epot = -20.800830948998 | etot = -15.5265347573401 +857000 ekin = 2.55862872070476 | erot = 3.03030828592914 | epot = -20.6910887919773 | etot = -15.1021517853434 +858000 ekin = 3.12628251408762 | erot = 2.1455460426107 | epot = -20.6394579492303 | etot = -15.367629392532 +859000 ekin = 2.91259413572113 | erot = 2.23773675238284 | epot = -20.6611486479508 | etot = -15.5108177598468 +860000 ekin = 2.88318377110752 | erot = 1.51972062646443 | epot = -20.6828066069552 | etot = -16.2799022093833 +861000 ekin = 2.33529167415754 | erot = 2.85116617791259 | epot = -20.6796212139896 | etot = -15.4931633619195 +862000 ekin = 3.06091745354043 | erot = 1.86960550588563 | epot = -20.7257485328209 | etot = -15.7952255733949 +863000 ekin = 2.88295223464283 | erot = 1.77743902656171 | epot = -20.8340328987095 | etot = -16.173641637505 +864000 ekin = 2.95602292127633 | erot = 2.6505641071531 | epot = -21.016295456145 | etot = -15.4097084277156 +865000 ekin = 3.3172549369506 | erot = 2.24347319046513 | epot = -21.1441095096619 | etot = -15.5833813822461 +866000 ekin = 2.8446879555804 | erot = 3.16802464112883 | epot = -21.2275167371632 | etot = -15.214804140454 +867000 ekin = 2.74149808612435 | erot = 3.09628634794253 | epot = -21.2140642048229 | etot = -15.376279770756 +868000 ekin = 2.19141484864809 | erot = 2.23765996064101 | epot = -21.1661691183494 | etot = -16.7370943090603 +869000 ekin = 2.92726848075923 | erot = 2.49663936074752 | epot = -21.1109612585256 | etot = -15.6870534170189 +870000 ekin = 2.47986538741064 | erot = 2.11907230969515 | epot = -21.0900293946685 | etot = -16.4910916975627 +871000 ekin = 2.18342640526418 | erot = 2.37474045896628 | epot = -20.9804914418025 | etot = -16.422324577572 +872000 ekin = 1.52873571215978 | erot = 2.08908078804674 | epot = -20.9343176993392 | etot = -17.3165011991327 +873000 ekin = 1.39281578471524 | erot = 2.29034780878957 | epot = -21.0007866828842 | etot = -17.3176230893794 +874000 ekin = 1.40786554880768 | erot = 2.77007970032348 | epot = -21.160084274243 | etot = -16.9821390251118 +875000 ekin = 1.18320018517441 | erot = 2.7305884288351 | epot = -21.2959059488291 | etot = -17.3821173348196 +876000 ekin = 1.8300189393038 | erot = 2.99586941144887 | epot = -21.3298635968753 | etot = -16.5039752461226 +877000 ekin = 2.38032906471076 | erot = 2.03722695211227 | epot = -21.4152790752831 | etot = -16.99772305846 +878000 ekin = 2.1293851684127 | erot = 1.75666654131943 | epot = -21.412657760354 | etot = -17.5266060506219 +879000 ekin = 2.23837299177368 | erot = 2.71307243504657 | epot = -21.4006541150457 | etot = -16.4492086882254 +880000 ekin = 2.68032631557358 | erot = 2.78439945590096 | epot = -21.4462782448912 | etot = -15.9815524734167 +881000 ekin = 2.86810525851389 | erot = 2.35959915589952 | epot = -21.4314549447334 | etot = -16.20375053032 +882000 ekin = 2.33172283615115 | erot = 2.17176020371467 | epot = -21.369535469283 | etot = -16.8660524294172 +883000 ekin = 2.36331150998289 | erot = 1.97634374053966 | epot = -21.1748990104138 | etot = -16.8352437598913 +884000 ekin = 2.53782271833829 | erot = 2.25243670168427 | epot = -21.0795767771653 | etot = -16.2893173571427 +885000 ekin = 2.86057103069745 | erot = 2.27462544190307 | epot = -21.0782171958267 | etot = -15.9430207232262 +886000 ekin = 3.17034195996096 | erot = 1.74832646729409 | epot = -21.1280719510453 | etot = -16.2094035237903 +887000 ekin = 2.66023408534638 | erot = 2.49426802108016 | epot = -21.1909579488462 | etot = -16.0364558424197 +888000 ekin = 2.14156056158802 | erot = 2.83065920295552 | epot = -21.2749898508176 | etot = -16.302770086274 +889000 ekin = 2.13776380125426 | erot = 2.19994227158624 | epot = -21.1902576201104 | etot = -16.8525515472699 +890000 ekin = 1.76446650263826 | erot = 2.97354753014624 | epot = -21.2518724314555 | etot = -16.513858398671 +891000 ekin = 1.64433607192947 | erot = 2.28044235221045 | epot = -21.3759471910581 | etot = -17.4511687669181 +892000 ekin = 1.97381907006142 | erot = 2.35969977765342 | epot = -21.5200869372681 | etot = -17.1865680895533 +893000 ekin = 1.77998159671209 | erot = 1.83959134574388 | epot = -21.5960425863495 | etot = -17.9764696438935 +894000 ekin = 2.8098996128374 | erot = 2.80337844303785 | epot = -21.6896955865519 | etot = -16.0764175306767 +895000 ekin = 2.03570642281182 | erot = 2.73641442629084 | epot = -21.77632807541 | etot = -17.0042072263074 +896000 ekin = 1.6670401968188 | erot = 2.55842313387756 | epot = -21.9079691828366 | etot = -17.6825058521403 +897000 ekin = 1.79364820755772 | erot = 2.35937074837063 | epot = -22.0466195733302 | etot = -17.8936006174018 +898000 ekin = 1.84103348909591 | erot = 2.4159698011209 | epot = -22.0792153246985 | etot = -17.8222120344817 +899000 ekin = 1.6644807831865 | erot = 3.06295573986192 | epot = -22.0050930291629 | etot = -17.2776565061145 +900000 ekin = 2.15301263014261 | erot = 2.62503812958044 | epot = -21.9769631774149 | etot = -17.1989124176918 +901000 ekin = 2.43323525076021 | erot = 2.69661561775585 | epot = -22.0455467285607 | etot = -16.9156958600446 +902000 ekin = 2.57983518470479 | erot = 2.40634661051271 | epot = -22.0504126836938 | etot = -17.0642308884763 +903000 ekin = 2.38804084084236 | erot = 2.40369143268286 | epot = -22.0548572254258 | etot = -17.2631249519006 +904000 ekin = 1.9975679938241 | erot = 3.15736733739655 | epot = -22.0783783499621 | etot = -16.9234430187414 +905000 ekin = 2.28042135995781 | erot = 2.20746001153526 | epot = -22.092475444409 | etot = -17.604594072916 +906000 ekin = 2.49914497220395 | erot = 1.67106173041057 | epot = -22.0649292741971 | etot = -17.8947225715826 +907000 ekin = 2.34170753461351 | erot = 2.16830189815579 | epot = -21.9182395193391 | etot = -17.4082300865698 +908000 ekin = 2.83101675354561 | erot = 2.39226452568031 | epot = -21.9393923471479 | etot = -16.7161110679219 +909000 ekin = 3.13519044247878 | erot = 2.07053636961478 | epot = -22.044039894957 | etot = -16.8383130828634 +910000 ekin = 2.91492350277448 | erot = 3.54269221448408 | epot = -22.1774209001616 | etot = -15.719805182903 +911000 ekin = 1.86299522014884 | erot = 2.75425299355676 | epot = -22.2318842654016 | etot = -17.614636051696 +912000 ekin = 2.64270620869814 | erot = 1.86916034984858 | epot = -22.2816929482531 | etot = -17.7698263897064 +913000 ekin = 2.45835259040075 | erot = 2.03343540339216 | epot = -22.4051980318983 | etot = -17.9134100381054 +914000 ekin = 2.01630257583653 | erot = 3.01931541129968 | epot = -22.505580829989 | etot = -17.4699628428528 +915000 ekin = 2.73550820750709 | erot = 2.14051989379169 | epot = -22.5067223019054 | etot = -17.6306942006067 +916000 ekin = 2.38833694849903 | erot = 3.26236542376325 | epot = -22.5299732656691 | etot = -16.8792708934068 +917000 ekin = 2.21211072529667 | erot = 2.24425221182159 | epot = -22.5175498112378 | etot = -18.0611868741195 +918000 ekin = 2.11721632678553 | erot = 2.05681940825278 | epot = -22.4485798442659 | etot = -18.2745441092275 +919000 ekin = 2.6606540164524 | erot = 2.41853759346262 | epot = -22.4819256778217 | etot = -17.4027340679066 +920000 ekin = 3.26471044916532 | erot = 2.75531911342505 | epot = -22.5858600689149 | etot = -16.5658305063245 +921000 ekin = 2.72028388628927 | erot = 1.9696059637128 | epot = -22.639440275186 | etot = -17.949550425184 +922000 ekin = 1.43428549123066 | erot = 1.52428475569853 | epot = -22.6914991306332 | etot = -19.732928883704 +923000 ekin = 1.67603986848274 | erot = 1.86522020655464 | epot = -22.7510571233686 | etot = -19.2097970483313 +924000 ekin = 2.15000311118185 | erot = 1.53327070095755 | epot = -22.722341324193 | etot = -19.0390675120536 +925000 ekin = 2.27769316315993 | erot = 1.3558291477729 | epot = -22.6317669747038 | etot = -18.9982446637709 +926000 ekin = 2.0037075380337 | erot = 2.07123237010034 | epot = -22.5811533157097 | etot = -18.5062134075756 +927000 ekin = 2.5163142824884 | erot = 1.98711239136866 | epot = -22.6957752134474 | etot = -18.1923485395904 +928000 ekin = 2.57502157703452 | erot = 2.51449316644151 | epot = -22.8486668477058 | etot = -17.7591521042298 +929000 ekin = 2.66015175923782 | erot = 1.82991995656989 | epot = -22.8894816710891 | etot = -18.3994099552814 +930000 ekin = 2.41758548277495 | erot = 2.00977019739402 | epot = -22.9023129289068 | etot = -18.4749572487378 +931000 ekin = 3.01936517399357 | erot = 2.11115283295647 | epot = -22.8598478032752 | etot = -17.7293297963252 +932000 ekin = 2.34904883629147 | erot = 1.87134929534042 | epot = -22.900230384769 | etot = -18.6798322531371 +933000 ekin = 2.16775611540091 | erot = 2.83796264813669 | epot = -22.9075292968864 | etot = -17.9018105333488 +934000 ekin = 2.17428610858913 | erot = 2.11891276299501 | epot = -22.9275911153101 | etot = -18.634392243726 +935000 ekin = 2.35380058127247 | erot = 2.22719757040085 | epot = -22.9178791070039 | etot = -18.3368809553306 +936000 ekin = 2.29398857252167 | erot = 2.52122883801967 | epot = -23.0254587453496 | etot = -18.2102413348082 +937000 ekin = 2.32405492839276 | erot = 2.82571975062453 | epot = -23.1134869099967 | etot = -17.9637122309794 +938000 ekin = 2.46190818228192 | erot = 1.99586541720566 | epot = -23.1690855883853 | etot = -18.7113119888978 +939000 ekin = 2.99494633358444 | erot = 2.1120057997909 | epot = -23.1621265982256 | etot = -18.0551744648503 +940000 ekin = 3.76773061527755 | erot = 2.67954167018356 | epot = -23.1020260319689 | etot = -16.6547537465078 +941000 ekin = 3.15108874053801 | erot = 2.26610050109568 | epot = -23.0042404655517 | etot = -17.587051223918 +942000 ekin = 3.50311245643907 | erot = 1.88373602143018 | epot = -22.9671180112669 | etot = -17.5802695333976 +943000 ekin = 3.82043792465856 | erot = 2.71285823250348 | epot = -22.9404059827705 | etot = -16.4071098256085 +944000 ekin = 2.68278476017665 | erot = 2.75585489458161 | epot = -22.919058077481 | etot = -17.4804184227228 +945000 ekin = 2.55880828345198 | erot = 2.02741981318914 | epot = -22.8232630911495 | etot = -18.2370349945083 +946000 ekin = 2.47548691870273 | erot = 1.66864059361738 | epot = -22.6586979544826 | etot = -18.5145704421625 +947000 ekin = 2.41867478100658 | erot = 1.99274780926995 | epot = -22.5542133657 | etot = -18.1427907754235 +948000 ekin = 3.54970439277899 | erot = 2.57756240201333 | epot = -22.4104376157296 | etot = -16.2831708209373 +949000 ekin = 2.98589976166071 | erot = 2.44208964275302 | epot = -22.1971411230011 | etot = -16.7691517185873 +950000 ekin = 1.82147308870195 | erot = 3.05083899379338 | epot = -22.0435130221227 | etot = -17.1712009396274 +951000 ekin = 2.20031505253436 | erot = 2.38004890424644 | epot = -22.0174402075992 | etot = -17.4370762508184 +952000 ekin = 2.14165422682636 | erot = 1.67045420750585 | epot = -21.9875031647927 | etot = -18.1753947304605 +953000 ekin = 2.2983346942831 | erot = 1.97349532600851 | epot = -21.9532851584681 | etot = -17.6814551381765 +954000 ekin = 1.48835290094507 | erot = 3.35692451991831 | epot = -21.8812774176255 | etot = -17.0359999967621 +955000 ekin = 1.87513794155827 | erot = 2.65898918540887 | epot = -21.7919528937348 | etot = -17.2578257667677 +956000 ekin = 1.6947359470094 | erot = 2.15427252360414 | epot = -21.7268035908356 | etot = -17.877795120222 +957000 ekin = 1.75579814865835 | erot = 1.63901039608816 | epot = -21.700727032202 | etot = -18.3059184874555 +958000 ekin = 1.59869777656518 | erot = 2.20104985114387 | epot = -21.7023937250484 | etot = -17.9026460973393 +959000 ekin = 2.58438881562724 | erot = 2.4897790743314 | epot = -21.7153511733982 | etot = -16.6411832834396 +960000 ekin = 2.53916903929276 | erot = 2.05995138561213 | epot = -21.7134163297425 | etot = -17.1142959048376 +961000 ekin = 2.28282707786747 | erot = 2.18347157951504 | epot = -21.7152390799838 | etot = -17.2489404226013 +962000 ekin = 1.65520100959905 | erot = 3.51416445242775 | epot = -21.7329558565076 | etot = -16.5635903944808 +963000 ekin = 1.99568689924178 | erot = 1.50126173817713 | epot = -21.6847527677603 | etot = -18.1878041303413 +964000 ekin = 2.18616111169191 | erot = 2.27601428306196 | epot = -21.621271673579 | etot = -17.1590962788252 +965000 ekin = 2.12688674785305 | erot = 2.31141713690626 | epot = -21.6018715374842 | etot = -17.1635676527249 +966000 ekin = 3.18043989665769 | erot = 3.42455452205085 | epot = -21.638305203769 | etot = -15.0333107850605 +967000 ekin = 3.07300409154252 | erot = 2.17511749698304 | epot = -21.5951488445701 | etot = -16.3470272560445 +968000 ekin = 2.08663150655529 | erot = 2.13997027735021 | epot = -21.5232721871232 | etot = -17.2966704032177 +969000 ekin = 2.26951411936363 | erot = 2.21822796004341 | epot = -21.4611553284775 | etot = -16.9734132490705 +970000 ekin = 2.49167396599781 | erot = 2.62083774678039 | epot = -21.4077353682587 | etot = -16.2952236554805 +971000 ekin = 2.497450596106 | erot = 2.64553775005007 | epot = -21.3712924820092 | etot = -16.2283041358532 +972000 ekin = 3.2069302084461 | erot = 2.4701129448845 | epot = -21.3144344371103 | etot = -15.6373912837797 +973000 ekin = 3.35935448087941 | erot = 2.62917582888825 | epot = -21.2433830591837 | etot = -15.254852749416 +974000 ekin = 2.71069552226069 | erot = 2.13944446989067 | epot = -21.1404268855179 | etot = -16.2902868933666 +975000 ekin = 1.81165819781674 | erot = 2.10218924092727 | epot = -21.0499905566304 | etot = -17.1361431178864 +976000 ekin = 2.36984742020937 | erot = 1.38488988265325 | epot = -20.9803229653515 | etot = -17.2255856624889 +977000 ekin = 2.83728662155799 | erot = 3.02976542728586 | epot = -21.086860961914 | etot = -15.2198089130701 +978000 ekin = 3.14169266917128 | erot = 3.0279981203262 | epot = -21.1408187166748 | etot = -14.9711279271773 +979000 ekin = 3.63725915757345 | erot = 2.47075910077982 | epot = -21.0348329782418 | etot = -14.9268147198885 +980000 ekin = 3.42622785415583 | erot = 3.24164435781272 | epot = -20.9604411583362 | etot = -14.2925689463677 +981000 ekin = 2.9282364939793 | erot = 2.44516658563954 | epot = -20.999389015838 | etot = -15.6259859362192 +982000 ekin = 2.0455891107008 | erot = 2.21302288881361 | epot = -21.0172581853275 | etot = -16.7586461858131 +983000 ekin = 2.56053983213181 | erot = 1.98406283304104 | epot = -21.0054554868711 | etot = -16.4608528216982 +984000 ekin = 2.31455025377678 | erot = 2.58584391470351 | epot = -21.0528748947299 | etot = -16.1524807262496 +985000 ekin = 2.31703817263368 | erot = 2.99965025262552 | epot = -21.1270579315131 | etot = -15.8103695062539 +986000 ekin = 2.05103854432386 | erot = 2.1535155091137 | epot = -21.2182405597612 | etot = -17.0136865063236 +987000 ekin = 2.41899263793244 | erot = 1.58416150281503 | epot = -21.1906087726859 | etot = -17.1874546319384 +988000 ekin = 2.75135283132848 | erot = 2.70498731016258 | epot = -21.09026978368 | etot = -15.633929642189 +989000 ekin = 2.29408577956131 | erot = 2.85656205344493 | epot = -21.0178170251465 | etot = -15.8671691921403 +990000 ekin = 2.23414139649767 | erot = 2.58987928207187 | epot = -20.9412338597721 | etot = -16.1172131812026 +991000 ekin = 2.20140095465642 | erot = 2.53421928109187 | epot = -20.8284298905317 | etot = -16.0928096547834 +992000 ekin = 1.73516341340694 | erot = 2.49726908126814 | epot = -20.8981414535471 | etot = -16.665708958872 +993000 ekin = 1.38883779880922 | erot = 1.96818984395137 | epot = -20.9939445972527 | etot = -17.6369169544921 +994000 ekin = 1.48978908674571 | erot = 2.95636513336706 | epot = -21.0608370227912 | etot = -16.6146828026784 +995000 ekin = 2.31404204513712 | erot = 1.67482961392509 | epot = -21.1264761824825 | etot = -17.1376045234203 +996000 ekin = 2.89776504847011 | erot = 2.85063328331353 | epot = -21.0879631716189 | etot = -15.3395648398353 +997000 ekin = 3.12980664910277 | erot = 2.14994147346883 | epot = -21.0789162715404 | etot = -15.7991681489688 +998000 ekin = 2.21592279552962 | erot = 3.03017611615784 | epot = -20.9989402817529 | etot = -15.7528413700654 +999000 ekin = 2.60947995309596 | erot = 1.73829419308785 | epot = -20.9136108602423 | etot = -16.5658367140585 +1000000 ekin = 2.32269547490306 | erot = 2.87794942105203 | epot = -20.9071852604882 | etot = -15.7065403645331 + 1000000 0.10323091 -1.356822 0.050122912 -1.1615306 0.00013791576 +Loop time of 52.0267 on 4 procs for 1000000 steps with 16 atoms + +Performance: 16606.850 tau/day, 19220.892 timesteps/s +96.4% CPU use with 4 MPI tasks x no OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0.92946 | 16.932 | 31.787 | 338.2 | 32.55 +Bond | 0.12904 | 0.54878 | 0.89134 | 46.8 | 1.05 +Neigh | 0 | 0 | 0 | 0.0 | 0.00 +Comm | 4.2008 | 5.1678 | 6.1197 | 36.6 | 9.93 +Output | 2.1e-05 | 3.15e-05 | 3.6e-05 | 0.0 | 0.00 +Modify | 0.32128 | 3.4221 | 6.4024 | 143.6 | 6.58 +Other | | 25.96 | | | 49.89 + +Nlocal: 4 ave 8 max 0 min +Histogram: 1 1 0 0 0 0 0 0 1 1 +Nghost: 9 ave 10 max 8 min +Histogram: 1 0 0 0 0 2 0 0 0 1 +Neighs: 34.5 ave 67 max 0 min +Histogram: 1 1 0 0 0 0 0 0 0 2 + +Total # of neighbors = 138 +Ave neighs/atom = 8.625 +Ave special neighs/atom = 3.75 +Neighbor list builds = 0 +Dangerous builds = 0 + +#write_restart config.${number}.* +Total wall time: 0:00:52 diff --git a/examples/USER/cgdna/examples/oxDNA/duplex2/log.27Nov18.duplex2.g++.1 b/examples/USER/cgdna/examples/oxDNA/duplex2/log.27Nov18.duplex2.g++.1 deleted file mode 100644 index 56f1b72277..0000000000 --- a/examples/USER/cgdna/examples/oxDNA/duplex2/log.27Nov18.duplex2.g++.1 +++ /dev/null @@ -1,172 +0,0 @@ -LAMMPS (27 Nov 2018) - using 1 OpenMP thread(s) per MPI task -variable number equal 2 -variable ofreq equal 1000 -variable efreq equal 1000 - -units lj - -dimension 3 - -newton off - -boundary p p p - -atom_style hybrid bond ellipsoid -atom_modify sort 0 1.0 - -# Pair interactions require lists of neighbours to be calculated -neighbor 1.0 bin -neigh_modify every 1 delay 0 check yes - -read_data data.duplex2 - orthogonal box = (-20 -20 -20) to (20 20 20) - 1 by 1 by 1 MPI processor grid - reading atoms ... - 16 atoms - reading velocities ... - 16 velocities - 16 ellipsoids - scanning bonds ... - 2 = max bonds/atom - reading bonds ... - 13 bonds - 2 = max # of 1-2 neighbors - 2 = max # of 1-3 neighbors - 4 = max # of 1-4 neighbors - 6 = max # of special neighbors - -set atom * mass 3.1575 - 16 settings made for mass - -group all type 1 4 -16 atoms in group all - -# oxDNA bond interactions - FENE backbone -bond_style oxdna/fene -bond_coeff * 2.0 0.25 0.7525 - -# oxDNA pair interactions -pair_style hybrid/overlay oxdna/excv oxdna/stk oxdna/hbond oxdna/xstk oxdna/coaxstk -pair_coeff * * oxdna/excv 2.0 0.7 0.675 2.0 0.515 0.5 2.0 0.33 0.32 -pair_coeff * * oxdna/stk seqav 0.1 6.0 0.4 0.9 0.32 0.6 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2.0 0.65 2.0 0.65 -pair_coeff * * oxdna/hbond seqav 0.0 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45 -pair_coeff 1 4 oxdna/hbond seqav 1.077 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45 -pair_coeff 2 3 oxdna/hbond seqav 1.077 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45 -pair_coeff * * oxdna/xstk 47.5 0.575 0.675 0.495 0.655 2.25 0.791592653589793 0.58 1.7 1.0 0.68 1.7 1.0 0.68 1.5 0 0.65 1.7 0.875 0.68 1.7 0.875 0.68 -pair_coeff * * oxdna/coaxstk 46.0 0.4 0.6 0.22 0.58 2.0 2.541592653589793 0.65 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2.0 -0.65 2.0 -0.65 - -# NVE ensemble -#fix 1 all nve/dot -fix 1 all nve/dotc/langevin 0.1 0.1 0.03 457145 angmom 10 -#fix 1 all nve/asphere -#fix 2 all langevin 0.1 0.1 0.03 457145 angmom 10 - -timestep 1e-5 - -#comm_style tiled -#fix 3 all balance 10000 1.1 rcb - -#compute mol all chunk/atom molecule -#compute mychunk all vcm/chunk mol -#fix 4 all ave/time 10000 1 10000 c_mychunk[1] c_mychunk[2] c_mychunk[3] file vcm.txt mode vector - -#dump pos all xyz ${ofreq} traj.${number}.xyz - -#compute quat all property/atom quatw quati quatj quatk -#dump quat all custom ${ofreq} quat.${number}.txt id c_quat[1] c_quat[2] c_quat[3] c_quat[4] -#dump_modify quat sort id -#dump_modify quat format line "%d %13.6le %13.6le %13.6le %13.6le" - -compute erot all erotate/asphere -compute ekin all ke -compute epot all pe -variable erot equal c_erot -variable ekin equal c_ekin -variable epot equal c_epot -variable etot equal c_erot+c_ekin+c_epot -fix 5 all print ${efreq} "$(step) ekin = ${ekin} | erot = ${erot} | epot = ${epot} | etot = ${etot}" screen yes -fix 5 all print 1000 "$(step) ekin = ${ekin} | erot = ${erot} | epot = ${epot} | etot = ${etot}" screen yes - -#dump out all custom ${ofreq} out.${number}.txt id x y z vx vy vz fx fy fz tqx tqy tqz -#dump_modify out sort id -#dump_modify out format line "%d %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le" - -run 10000 -Neighbor list info ... - update every 1 steps, delay 0 steps, check yes - max neighbors/atom: 2000, page size: 100000 - master list distance cutoff = 1.92828 - ghost atom cutoff = 1.92828 - binsize = 0.964142, bins = 42 42 42 - 5 neighbor lists, perpetual/occasional/extra = 5 0 0 - (1) pair oxdna/excv, perpetual - attributes: half, newton off - pair build: half/bin/newtoff - stencil: half/bin/3d/newtoff - bin: standard - (2) pair oxdna/stk, perpetual, copy from (1) - attributes: half, newton off - pair build: copy - stencil: none - bin: none - (3) pair oxdna/hbond, perpetual, copy from (1) - attributes: half, newton off - pair build: copy - stencil: none - bin: none - (4) pair oxdna/xstk, perpetual, copy from (1) - attributes: half, newton off - pair build: copy - stencil: none - bin: none - (5) pair oxdna/coaxstk, perpetual, copy from (1) - attributes: half, newton off - pair build: copy - stencil: none - bin: none -Per MPI rank memory allocation (min/avg/max) = 2.861 | 2.861 | 2.861 Mbytes -Step Temp E_pair E_mol TotEng Press - 0 0 -1.5402493 0.0070469125 -1.5332024 -8.5641987e-05 -1000 ekin = 1.54234964773389 | erot = 1.71563526070267 | epot = -24.5477045187653 | etot = -21.2897196103287 -2000 ekin = 1.85988866919215 | erot = 1.9424302796508 | epot = -24.4843044999595 | etot = -20.6819855511165 -3000 ekin = 2.68354339452998 | erot = 2.14216528317607 | epot = -24.4019350693561 | etot = -19.57622639165 -4000 ekin = 2.04461800191989 | erot = 1.49015219763162 | epot = -24.2959428773347 | etot = -20.7611726777832 -5000 ekin = 1.76794859210155 | erot = 2.54289684465818 | epot = -24.2337587736863 | etot = -19.9229133369266 -6000 ekin = 3.1106424806079 | erot = 2.04409805200892 | epot = -24.1585729744133 | etot = -19.0038324417964 -7000 ekin = 3.21360097519306 | erot = 2.71941303605722 | epot = -24.0566262531609 | etot = -18.1236122419107 -8000 ekin = 2.82489935901743 | erot = 2.66790555575696 | epot = -24.0194805097633 | etot = -18.526675594989 -9000 ekin = 2.69381302856378 | erot = 2.59107820129446 | epot = -23.9216126050554 | etot = -18.6367213751972 -10000 ekin = 2.65765007662471 | erot = 1.95562671446597 | epot = -23.7978334881241 | etot = -19.1845566970334 - 10000 0.11811778 -1.4992295 0.011864944 -1.3212615 -0.00013416809 -Loop time of 0.295538 on 1 procs for 10000 steps with 16 atoms - -Performance: 29234.801 tau/day, 33836.575 timesteps/s -99.7% CPU use with 1 MPI tasks x 1 OpenMP threads - -MPI task timing breakdown: -Section | min time | avg time | max time |%varavg| %total ---------------------------------------------------------------- -Pair | 0.20959 | 0.20959 | 0.20959 | 0.0 | 70.92 -Bond | 0.0073669 | 0.0073669 | 0.0073669 | 0.0 | 2.49 -Neigh | 0 | 0 | 0 | 0.0 | 0.00 -Comm | 0.0016472 | 0.0016472 | 0.0016472 | 0.0 | 0.56 -Output | 5.0068e-06 | 5.0068e-06 | 5.0068e-06 | 0.0 | 0.00 -Modify | 0.073117 | 0.073117 | 0.073117 | 0.0 | 24.74 -Other | | 0.003813 | | | 1.29 - -Nlocal: 16 ave 16 max 16 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Nghost: 0 ave 0 max 0 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Neighs: 88 ave 88 max 88 min -Histogram: 1 0 0 0 0 0 0 0 0 0 - -Total # of neighbors = 88 -Ave neighs/atom = 5.5 -Ave special neighs/atom = 3.75 -Neighbor list builds = 0 -Dangerous builds = 0 - -#write_restart config.${number}.* -Total wall time: 0:00:00 diff --git a/examples/USER/cgdna/examples/oxDNA/duplex2/log.27Nov18.duplex2.g++.4 b/examples/USER/cgdna/examples/oxDNA/duplex2/log.27Nov18.duplex2.g++.4 deleted file mode 100644 index 5cb953cd8c..0000000000 --- a/examples/USER/cgdna/examples/oxDNA/duplex2/log.27Nov18.duplex2.g++.4 +++ /dev/null @@ -1,172 +0,0 @@ -LAMMPS (27 Nov 2018) - using 1 OpenMP thread(s) per MPI task -variable number equal 2 -variable ofreq equal 1000 -variable efreq equal 1000 - -units lj - -dimension 3 - -newton off - -boundary p p p - -atom_style hybrid bond ellipsoid -atom_modify sort 0 1.0 - -# Pair interactions require lists of neighbours to be calculated -neighbor 1.0 bin -neigh_modify every 1 delay 0 check yes - -read_data data.duplex2 - orthogonal box = (-20 -20 -20) to (20 20 20) - 1 by 2 by 2 MPI processor grid - reading atoms ... - 16 atoms - reading velocities ... - 16 velocities - 16 ellipsoids - scanning bonds ... - 2 = max bonds/atom - reading bonds ... - 13 bonds - 2 = max # of 1-2 neighbors - 2 = max # of 1-3 neighbors - 4 = max # of 1-4 neighbors - 6 = max # of special neighbors - -set atom * mass 3.1575 - 16 settings made for mass - -group all type 1 4 -16 atoms in group all - -# oxDNA bond interactions - FENE backbone -bond_style oxdna/fene -bond_coeff * 2.0 0.25 0.7525 - -# oxDNA pair interactions -pair_style hybrid/overlay oxdna/excv oxdna/stk oxdna/hbond oxdna/xstk oxdna/coaxstk -pair_coeff * * oxdna/excv 2.0 0.7 0.675 2.0 0.515 0.5 2.0 0.33 0.32 -pair_coeff * * oxdna/stk seqav 0.1 6.0 0.4 0.9 0.32 0.6 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2.0 0.65 2.0 0.65 -pair_coeff * * oxdna/hbond seqav 0.0 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45 -pair_coeff 1 4 oxdna/hbond seqav 1.077 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45 -pair_coeff 2 3 oxdna/hbond seqav 1.077 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45 -pair_coeff * * oxdna/xstk 47.5 0.575 0.675 0.495 0.655 2.25 0.791592653589793 0.58 1.7 1.0 0.68 1.7 1.0 0.68 1.5 0 0.65 1.7 0.875 0.68 1.7 0.875 0.68 -pair_coeff * * oxdna/coaxstk 46.0 0.4 0.6 0.22 0.58 2.0 2.541592653589793 0.65 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2.0 -0.65 2.0 -0.65 - -# NVE ensemble -#fix 1 all nve/dot -fix 1 all nve/dotc/langevin 0.1 0.1 0.03 457145 angmom 10 -#fix 1 all nve/asphere -#fix 2 all langevin 0.1 0.1 0.03 457145 angmom 10 - -timestep 1e-5 - -#comm_style tiled -#fix 3 all balance 10000 1.1 rcb - -#compute mol all chunk/atom molecule -#compute mychunk all vcm/chunk mol -#fix 4 all ave/time 10000 1 10000 c_mychunk[1] c_mychunk[2] c_mychunk[3] file vcm.txt mode vector - -#dump pos all xyz ${ofreq} traj.${number}.xyz - -#compute quat all property/atom quatw quati quatj quatk -#dump quat all custom ${ofreq} quat.${number}.txt id c_quat[1] c_quat[2] c_quat[3] c_quat[4] -#dump_modify quat sort id -#dump_modify quat format line "%d %13.6le %13.6le %13.6le %13.6le" - -compute erot all erotate/asphere -compute ekin all ke -compute epot all pe -variable erot equal c_erot -variable ekin equal c_ekin -variable epot equal c_epot -variable etot equal c_erot+c_ekin+c_epot -fix 5 all print ${efreq} "$(step) ekin = ${ekin} | erot = ${erot} | epot = ${epot} | etot = ${etot}" screen yes -fix 5 all print 1000 "$(step) ekin = ${ekin} | erot = ${erot} | epot = ${epot} | etot = ${etot}" screen yes - -#dump out all custom ${ofreq} out.${number}.txt id x y z vx vy vz fx fy fz tqx tqy tqz -#dump_modify out sort id -#dump_modify out format line "%d %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le" - -run 10000 -Neighbor list info ... - update every 1 steps, delay 0 steps, check yes - max neighbors/atom: 2000, page size: 100000 - master list distance cutoff = 1.92828 - ghost atom cutoff = 1.92828 - binsize = 0.964142, bins = 42 42 42 - 5 neighbor lists, perpetual/occasional/extra = 5 0 0 - (1) pair oxdna/excv, perpetual - attributes: half, newton off - pair build: half/bin/newtoff - stencil: half/bin/3d/newtoff - bin: standard - (2) pair oxdna/stk, perpetual, copy from (1) - attributes: half, newton off - pair build: copy - stencil: none - bin: none - (3) pair oxdna/hbond, perpetual, copy from (1) - attributes: half, newton off - pair build: copy - stencil: none - bin: none - (4) pair oxdna/xstk, perpetual, copy from (1) - attributes: half, newton off - pair build: copy - stencil: none - bin: none - (5) pair oxdna/coaxstk, perpetual, copy from (1) - attributes: half, newton off - pair build: copy - stencil: none - bin: none -Per MPI rank memory allocation (min/avg/max) = 7.466 | 7.648 | 7.83 Mbytes -Step Temp E_pair E_mol TotEng Press - 0 0 -1.5402493 0.0070469125 -1.5332024 -8.5641987e-05 -1000 ekin = 1.34565986428024 | erot = 2.31051421234078 | epot = -24.5061991591502 | etot = -20.8500250825292 -2000 ekin = 2.15911766687235 | erot = 2.16031365874707 | epot = -24.4723177103698 | etot = -20.1528863847504 -3000 ekin = 3.26561948796015 | erot = 2.75651822936604 | epot = -24.412573068346 | etot = -18.3904353510198 -4000 ekin = 1.92438809241066 | erot = 2.12016940074985 | epot = -24.3496233970111 | etot = -20.3050659038506 -5000 ekin = 1.35986357015476 | erot = 1.99413493074226 | epot = -24.2789445616949 | etot = -20.9249460607979 -6000 ekin = 2.19432475124593 | erot = 1.74281260409078 | epot = -24.2128064295788 | etot = -20.2756690742421 -7000 ekin = 2.65619274477635 | erot = 1.74094257048458 | epot = -24.1673462333493 | etot = -19.7702109180883 -8000 ekin = 2.51333548501168 | erot = 2.34649854571051 | epot = -24.0812769481836 | etot = -19.2214429174614 -9000 ekin = 2.24506493169711 | erot = 2.0652555461504 | epot = -23.9906736063989 | etot = -19.6803531285514 -10000 ekin = 2.36632635249862 | erot = 1.7959247176153 | epot = -23.9002627850602 | etot = -19.7380117149463 - 10000 0.10517006 -1.5057137 0.011947302 -1.345871 -9.5924016e-05 -Loop time of 0.251867 on 4 procs for 10000 steps with 16 atoms - -Performance: 34303.820 tau/day, 39703.495 timesteps/s -97.8% CPU use with 4 MPI tasks x 1 OpenMP threads - -MPI task timing breakdown: -Section | min time | avg time | max time |%varavg| %total ---------------------------------------------------------------- -Pair | 0.0035377 | 0.092047 | 0.17435 | 26.0 | 36.55 -Bond | 0.00065637 | 0.0031857 | 0.0053554 | 3.8 | 1.26 -Neigh | 0 | 0 | 0 | 0.0 | 0.00 -Comm | 0.013929 | 0.01497 | 0.015733 | 0.6 | 5.94 -Output | 5.0783e-05 | 5.2691e-05 | 5.3883e-05 | 0.0 | 0.02 -Modify | 0.0013576 | 0.020825 | 0.040231 | 11.8 | 8.27 -Other | | 0.1208 | | | 47.96 - -Nlocal: 4 ave 8 max 0 min -Histogram: 1 1 0 0 0 0 0 0 1 1 -Nghost: 9 ave 10 max 8 min -Histogram: 1 0 0 0 0 2 0 0 0 1 -Neighs: 34.5 ave 67 max 0 min -Histogram: 1 1 0 0 0 0 0 0 0 2 - -Total # of neighbors = 138 -Ave neighs/atom = 8.625 -Ave special neighs/atom = 3.75 -Neighbor list builds = 0 -Dangerous builds = 0 - -#write_restart config.${number}.* -Total wall time: 0:00:00 diff --git a/examples/USER/cgdna/examples/oxDNA2/duplex1/data.duplex1 b/examples/USER/cgdna/examples/oxDNA2/duplex1/data.duplex1 index 6aee3233dd..0ef671c603 100644 --- a/examples/USER/cgdna/examples/oxDNA2/duplex1/data.duplex1 +++ b/examples/USER/cgdna/examples/oxDNA2/duplex1/data.duplex1 @@ -32,7 +32,7 @@ Atoms 9 3 4.860249842674775e-01 3.518234140414733e-01 3.897628551303121e-01 2 1 1 10 4 5.999999999999996e-01 -1.332267629550188e-16 -1.110223024625157e-16 2 1 1 -# Atom-ID, translational, rotational velocity +# Atom-ID, translational velocity, angular momentum Velocities 1 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 diff --git a/examples/USER/cgdna/examples/oxDNA2/duplex1/in.duplex1 b/examples/USER/cgdna/examples/oxDNA2/duplex1/in.duplex1 index 5260e51330..9ff9d3c4db 100644 --- a/examples/USER/cgdna/examples/oxDNA2/duplex1/in.duplex1 +++ b/examples/USER/cgdna/examples/oxDNA2/duplex1/in.duplex1 @@ -1,6 +1,7 @@ variable number equal 1 variable ofreq equal 1000 variable efreq equal 1000 +variable T equal 0.1 units lj @@ -30,19 +31,19 @@ bond_coeff * 2.0 0.25 0.7564 # oxDNA pair interactions pair_style hybrid/overlay oxdna2/excv oxdna2/stk oxdna2/hbond oxdna2/xstk oxdna2/coaxstk oxdna2/dh pair_coeff * * oxdna2/excv 2.0 0.7 0.675 2.0 0.515 0.5 2.0 0.33 0.32 -pair_coeff * * oxdna2/stk seqav 0.1 6.0 0.4 0.9 0.32 0.6 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2.0 0.65 2.0 0.65 +pair_coeff * * oxdna2/stk seqav ${T} 1.3523 2.6717 6.0 0.4 0.9 0.32 0.6 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2.0 0.65 2.0 0.65 pair_coeff * * oxdna2/hbond seqav 0.0 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45 pair_coeff 1 4 oxdna2/hbond seqav 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45 pair_coeff 2 3 oxdna2/hbond seqav 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45 pair_coeff * * oxdna2/xstk 47.5 0.575 0.675 0.495 0.655 2.25 0.791592653589793 0.58 1.7 1.0 0.68 1.7 1.0 0.68 1.5 0 0.65 1.7 0.875 0.68 1.7 0.875 0.68 pair_coeff * * oxdna2/coaxstk 58.5 0.4 0.6 0.22 0.58 2.0 2.891592653589793 0.65 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 40.0 3.116592653589793 -pair_coeff * * oxdna2/dh 0.1 1.0 0.815 +pair_coeff * * oxdna2/dh ${T} 1.0 0.815 # NVE ensemble fix 1 all nve/dot -#fix 1 all nve/dotc/langevin 0.1 0.1 0.03 457145 angmom 10 +#fix 1 all nve/dotc/langevin ${T} ${T} 0.03 457145 angmom 10 #fix 1 all nve/asphere -#fix 2 all langevin 0.1 0.1 0.03 457145 angmom 10 +#fix 2 all langevin ${T} ${T} 0.03 457145 angmom 10 timestep 1e-5 @@ -73,6 +74,6 @@ fix 5 all print ${efreq} "$(step) ekin = ${ekin} | erot = ${erot} | epot = ${e #dump_modify out sort id #dump_modify out format line "%d %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le" -run 10000 +run 1000000 #write_restart config.${number}.* diff --git a/examples/USER/cgdna/examples/oxDNA2/duplex1/log.18Jun19.duplex1.g++.1 b/examples/USER/cgdna/examples/oxDNA2/duplex1/log.18Jun19.duplex1.g++.1 new file mode 100644 index 0000000000..a699d8726d --- /dev/null +++ b/examples/USER/cgdna/examples/oxDNA2/duplex1/log.18Jun19.duplex1.g++.1 @@ -0,0 +1,1172 @@ +LAMMPS (18 Jun 2019) +variable number equal 1 +variable ofreq equal 1000 +variable efreq equal 1000 +variable T equal 0.1 + +units lj + +dimension 3 + +newton off + +boundary p p p + +atom_style hybrid bond ellipsoid +atom_modify sort 0 1.0 + +# Pair interactions require lists of neighbours to be calculated +neighbor 1.0 bin +neigh_modify every 1 delay 0 check yes + +read_data data.duplex1 + orthogonal box = (-20 -20 -20) to (20 20 20) + 1 by 1 by 1 MPI processor grid + reading atoms ... + 10 atoms + reading velocities ... + 10 velocities + 10 ellipsoids + scanning bonds ... + 2 = max bonds/atom + reading bonds ... + 8 bonds + 2 = max # of 1-2 neighbors + 2 = max # of 1-3 neighbors + 2 = max # of 1-4 neighbors + 4 = max # of special neighbors + special bonds CPU = 0.000102 secs + read_data CPU = 0.002436 secs + +set atom * mass 3.1575 + 10 settings made for mass + +group all type 1 4 +10 atoms in group all + +# oxDNA bond interactions - FENE backbone +bond_style oxdna2/fene +bond_coeff * 2.0 0.25 0.7564 + +# oxDNA pair interactions +pair_style hybrid/overlay oxdna2/excv oxdna2/stk oxdna2/hbond oxdna2/xstk oxdna2/coaxstk oxdna2/dh +pair_coeff * * oxdna2/excv 2.0 0.7 0.675 2.0 0.515 0.5 2.0 0.33 0.32 +pair_coeff * * oxdna2/stk seqav ${T} 1.3523 2.6717 6.0 0.4 0.9 0.32 0.6 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2.0 0.65 2.0 0.65 +pair_coeff * * oxdna2/stk seqav 0.1 1.3523 2.6717 6.0 0.4 0.9 0.32 0.6 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2.0 0.65 2.0 0.65 +pair_coeff * * oxdna2/hbond seqav 0.0 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45 +pair_coeff 1 4 oxdna2/hbond seqav 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45 +pair_coeff 2 3 oxdna2/hbond seqav 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45 +pair_coeff * * oxdna2/xstk 47.5 0.575 0.675 0.495 0.655 2.25 0.791592653589793 0.58 1.7 1.0 0.68 1.7 1.0 0.68 1.5 0 0.65 1.7 0.875 0.68 1.7 0.875 0.68 +pair_coeff * * oxdna2/coaxstk 58.5 0.4 0.6 0.22 0.58 2.0 2.891592653589793 0.65 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 40.0 3.116592653589793 +pair_coeff * * oxdna2/dh ${T} 1.0 0.815 +pair_coeff * * oxdna2/dh 0.1 1.0 0.815 + +# NVE ensemble +fix 1 all nve/dot +#fix 1 all nve/dotc/langevin ${T} ${T} 0.03 457145 angmom 10 +#fix 1 all nve/asphere +#fix 2 all langevin ${T} ${T} 0.03 457145 angmom 10 + +timestep 1e-5 + +#comm_style tiled +#fix 3 all balance 10000 1.1 rcb + +#compute mol all chunk/atom molecule +#compute mychunk all vcm/chunk mol +#fix 4 all ave/time 10000 1 10000 c_mychunk[1] c_mychunk[2] c_mychunk[3] file vcm.txt mode vector + +#dump pos all xyz ${ofreq} traj.${number}.xyz + +#compute quat all property/atom quatw quati quatj quatk +#dump quat all custom ${ofreq} quat.${number}.txt id c_quat[1] c_quat[2] c_quat[3] c_quat[4] +#dump_modify quat sort id +#dump_modify quat format line "%d %13.6le %13.6le %13.6le %13.6le" + +compute erot all erotate/asphere +compute ekin all ke +compute epot all pe +variable erot equal c_erot +variable ekin equal c_ekin +variable epot equal c_epot +variable etot equal c_erot+c_ekin+c_epot +fix 5 all print ${efreq} "$(step) ekin = ${ekin} | erot = ${erot} | epot = ${epot} | etot = ${etot}" screen yes +fix 5 all print 1000 "$(step) ekin = ${ekin} | erot = ${erot} | epot = ${epot} | etot = ${etot}" screen yes + +#dump out all custom ${ofreq} out.${number}.txt id x y z vx vy vz fx fy fz tqx tqy tqz +#dump_modify out sort id +#dump_modify out format line "%d %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le" + +run 1000000 +Neighbor list info ... + update every 1 steps, delay 0 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 2.6274 + ghost atom cutoff = 2.6274 + binsize = 1.3137, bins = 31 31 31 + 6 neighbor lists, perpetual/occasional/extra = 6 0 0 + (1) pair oxdna2/excv, perpetual + attributes: half, newton off + pair build: half/bin/newtoff + stencil: half/bin/3d/newtoff + bin: standard + (2) pair oxdna2/stk, perpetual, copy from (1) + attributes: half, newton off + pair build: copy + stencil: none + bin: none + (3) pair oxdna2/hbond, perpetual, copy from (1) + attributes: half, newton off + pair build: copy + stencil: none + bin: none + (4) pair oxdna2/xstk, perpetual, copy from (1) + attributes: half, newton off + pair build: copy + stencil: none + bin: none + (5) pair oxdna2/coaxstk, perpetual, copy from (1) + attributes: half, newton off + pair build: copy + stencil: none + bin: none + (6) pair oxdna2/dh, perpetual, copy from (1) + attributes: half, newton off + pair build: copy + stencil: none + bin: none +Per MPI rank memory allocation (min/avg/max) = 3.023 | 3.023 | 3.023 Mbytes +Step Temp E_pair E_mol TotEng Press + 0 0 -1.4712768 0.009525411 -1.4617514 4.663076e-06 +1000 ekin = 0.00113086229080528 | erot = 0.0043101016040658 | epot = -14.6229549982368 | etot = -14.617514034342 +2000 ekin = 0.0044853322434243 | erot = 0.0171407706505008 | epot = -14.6391401372615 | etot = -14.6175140343675 +3000 ekin = 0.00995035259649285 | erot = 0.0381961780846484 | epot = -14.6656605650904 | etot = -14.6175140344093 +4000 ekin = 0.0173418024862054 | erot = 0.0669935184860634 | epot = -14.7018493554381 | etot = -14.6175140344659 +5000 ekin = 0.0264109356286075 | erot = 0.102878288094517 | epot = -14.7468032582586 | etot = -14.6175140345355 +6000 ekin = 0.0368533113591442 | erot = 0.14504542056987 | epot = -14.7994127665447 | etot = -14.6175140346157 +7000 ekin = 0.0483200640564843 | erot = 0.192565862515508 | epot = -14.8583999612756 | etot = -14.6175140347036 +8000 ekin = 0.0604312317605998 | erot = 0.244417870131508 | epot = -14.9223631366883 | etot = -14.6175140347962 +9000 ekin = 0.0727907119671751 | erot = 0.299521949931839 | epot = -14.989826696789 | etot = -14.6175140348899 +10000 ekin = 0.0850022498875221 | erot = 0.356777997217902 | epot = -15.0592942820869 | etot = -14.6175140349815 +11000 ekin = 0.0966857134041704 | erot = 0.415102860829614 | epot = -15.1293026093013 | etot = -14.6175140350675 +12000 ekin = 0.107492790688446 | erot = 0.473466334178045 | epot = -15.1984731600115 | etot = -14.617514035145 +13000 ekin = 0.117121180381715 | erot = 0.530923485009724 | epot = -15.2655587006029 | etot = -14.6175140352115 +14000 ekin = 0.125326348459166 | erot = 0.586641324447693 | epot = -15.329481708172 | etot = -14.6175140352651 +15000 ekin = 0.131930017119452 | erot = 0.639918104234695 | epot = -15.389362156659 | etot = -14.6175140353048 +16000 ekin = 0.136824741331535 | erot = 0.690194029501056 | epot = -15.4445328061632 | etot = -14.6175140353306 +17000 ekin = 0.139974218116303 | erot = 0.73705286614779 | epot = -15.4945411196072 | etot = -14.6175140353432 +18000 ekin = 0.141409342139924 | erot = 0.780214750583505 | epot = -15.5391381280674 | etot = -14.617514035344 +19000 ekin = 0.14122042490348 | erot = 0.819521373491594 | epot = -15.5782558337303 | etot = -14.6175140353352 +20000 ekin = 0.139546371890615 | erot = 0.854915474127934 | epot = -15.6119758813378 | etot = -14.6175140353193 +21000 ekin = 0.136561897558623 | erot = 0.886417110947779 | epot = -15.6404930438051 | etot = -14.6175140352987 +22000 ekin = 0.132464002543739 | erot = 0.914099368829953 | epot = -15.6640774066495 | etot = -14.6175140352758 +23000 ekin = 0.127458921012922 | erot = 0.938065991541773 | epot = -15.6830389478072 | etot = -14.6175140352525 +24000 ekin = 0.121750582423385 | erot = 0.958432936326242 | epot = -15.6976975539802 | etot = -14.6175140352305 +25000 ekin = 0.115531361418989 | erot = 0.97531514293118 | epot = -15.7083605395609 | etot = -14.6175140352107 +26000 ekin = 0.108975565586104 | erot = 0.988819027952036 | epot = -15.7153086287315 | etot = -14.6175140351934 +27000 ekin = 0.102235785319049 | erot = 0.999040485514132 | epot = -15.7187903060115 | etot = -14.6175140351783 +28000 ekin = 0.095441943431881 | erot = 1.00606759140964 | epot = -15.7190235700066 | etot = -14.6175140351651 +29000 ekin = 0.0887026587343887 | erot = 1.00998681843601 | epot = -15.7162035123233 | etot = -14.6175140351529 +30000 ekin = 0.0821083868014372 | erot = 1.01089138149893 | epot = -15.7105138034411 | etot = -14.6175140351407 +31000 ekin = 0.0757357206087773 | erot = 1.00889031641317 | epot = -15.7021400721498 | etot = -14.6175140351278 +32000 ekin = 0.0696522149388972 | erot = 1.00411701389994 | epot = -15.691283263952 | etot = -14.6175140351132 +33000 ekin = 0.0639211300028632 | erot = 0.996736133735177 | epot = -15.6781712988344 | etot = -14.6175140350964 +34000 ekin = 0.0586055597939536 | erot = 0.986948071943124 | epot = -15.6630676668141 | etot = -14.617514035077 +35000 ekin = 0.0537715085519321 | erot = 0.97499041461744 | epot = -15.6462759582244 | etot = -14.617514035055 +36000 ekin = 0.0494895953264297 | erot = 0.961136064967259 | epot = -15.6281396953245 | etot = -14.6175140350308 +37000 ekin = 0.0458351949405726 | erot = 0.945687966086967 | epot = -15.6090371960325 | etot = -14.617514035005 +38000 ekin = 0.0428869588016531 | erot = 0.928970560852795 | epot = -15.5893715546332 | etot = -14.6175140349787 +39000 ekin = 0.0407237982122988 | erot = 0.9113183396798 | epot = -15.5695561728451 | etot = -14.617514034953 +40000 ekin = 0.0394205547754457 | erot = 0.893062038097747 | epot = -15.5499966278026 | etot = -14.6175140349294 +41000 ekin = 0.0390427256107104 | erot = 0.874513269990878 | epot = -15.5310700305109 | etot = -14.6175140349093 +42000 ekin = 0.0396407506458402 | erot = 0.855948622306271 | epot = -15.5131034078461 | etot = -14.617514034894 +43000 ekin = 0.0412444930542154 | erot = 0.837594480923697 | epot = -15.4963530088628 | etot = -14.6175140348849 +44000 ekin = 0.0438586280730372 | erot = 0.819614069272971 | epot = -15.4809867322287 | etot = -14.6175140348826 +45000 ekin = 0.0474596621516281 | erot = 0.802098297010783 | epot = -15.4670719940501 | etot = -14.6175140348877 +46000 ekin = 0.0519951857192148 | erot = 0.785061947877571 | epot = -15.4545711684965 | etot = -14.6175140348997 +47000 ekin = 0.0573856747191636 | erot = 0.76844639238657 | epot = -15.4433461020232 | etot = -14.6175140349174 +48000 ekin = 0.0635286843632004 | erot = 0.75212933501618 | epot = -15.433172054319 | etot = -14.6175140349396 +49000 ekin = 0.070304673538874 | erot = 0.735941123250837 | epot = -15.4237598317539 | etot = -14.6175140349642 +50000 ekin = 0.0775831019857076 | erot = 0.719686007781425 | epot = -15.4147831447563 | etot = -14.6175140349892 +51000 ekin = 0.0852270843845694 | erot = 0.703165726695028 | epot = -15.4059068460928 | etot = -14.6175140350132 +52000 ekin = 0.0930950223451647 | erot = 0.686202231166125 | epot = -15.396811288546 | etot = -14.6175140350347 +53000 ekin = 0.101038429252995 | erot = 0.668656546988927 | epot = -15.3872090112954 | etot = -14.6175140350535 +54000 ekin = 0.10889654098061 | erot = 0.650441726174306 | epot = -15.3768523022246 | etot = -14.6175140350697 +55000 ekin = 0.116489881626234 | erot = 0.631529329348001 | epot = -15.3655332460579 | etot = -14.6175140350836 +56000 ekin = 0.12361610349192 | erot = 0.611950383382611 | epot = -15.35308052197 | etot = -14.6175140350954 +57000 ekin = 0.130051530401153 | erot = 0.591792721317295 | epot = -15.3393582868232 | etot = -14.6175140351048 +58000 ekin = 0.135560625193501 | erot = 0.571196690673292 | epot = -15.3242713509773 | etot = -14.6175140351105 +59000 ekin = 0.139913350827135 | erot = 0.550350463180279 | epot = -15.307777849119 | etot = -14.6175140351115 +60000 ekin = 0.142907875045794 | erot = 0.529485019662529 | epot = -15.2899069298147 | etot = -14.6175140351063 +61000 ekin = 0.144394224777542 | erot = 0.508867904998907 | epot = -15.2707761648706 | etot = -14.6175140350941 +62000 ekin = 0.144294003785763 | erot = 0.488794507592477 | epot = -15.2506025464531 | etot = -14.6175140350748 +63000 ekin = 0.142612256998146 | erot = 0.469576039421557 | epot = -15.2297023314688 | etot = -14.6175140350491 +64000 ekin = 0.139439544726902 | erot = 0.45152434495459 | epot = -15.2084779247003 | etot = -14.6175140350188 +65000 ekin = 0.134944526553566 | erot = 0.434934714913839 | epot = -15.1873932764535 | etot = -14.6175140349861 +66000 ekin = 0.129359146358223 | erot = 0.420068607767106 | epot = -15.1669417890788 | etot = -14.6175140349535 +67000 ekin = 0.122959458764236 | erot = 0.407138362059705 | epot = -15.1476118557469 | etot = -14.617514034923 +68000 ekin = 0.116045210525559 | erot = 0.396295631876262 | epot = -15.1298548772986 | etot = -14.6175140348968 +69000 ekin = 0.108920722072365 | erot = 0.38762458997195 | epot = -15.1140593469202 | etot = -14.6175140348758 +70000 ekin = 0.101878740729572 | erot = 0.381140173640836 | epot = -15.1005329492313 | etot = -14.6175140348609 +71000 ekin = 0.0951880561484016 | erot = 0.376791007701538 | epot = -15.0894930987019 | etot = -14.617514034852 +72000 ekin = 0.0890849677261927 | erot = 0.374466237250371 | epot = -15.0810652398255 | etot = -14.6175140348489 +73000 ekin = 0.0837682427021612 | erot = 0.374005347599889 | epot = -15.0752876251531 | etot = -14.617514034851 +74000 ekin = 0.0793969849744096 | erot = 0.375210076750601 | epot = -15.0721210965825 | etot = -14.6175140348575 +75000 ekin = 0.0760907865069267 | erot = 0.377857644572265 | epot = -15.0714624659463 | etot = -14.6175140348671 +76000 ekin = 0.0739315834908328 | erot = 0.381714646755152 | epot = -15.0731602651247 | etot = -14.6175140348788 +77000 ekin = 0.0729667273608161 | erot = 0.386551032956121 | epot = -15.0770317952083 | etot = -14.6175140348914 +78000 ekin = 0.073212865507933 | erot = 0.392153586683229 | epot = -15.0828804870951 | etot = -14.617514034904 +79000 ekin = 0.074660287835072 | erot = 0.398338263929461 | epot = -15.09051258668 | etot = -14.6175140349155 +80000 ekin = 0.0772774298944847 | erot = 0.404960669863083 | epot = -15.0997521346826 | etot = -14.6175140349251 +81000 ekin = 0.0810152396746107 | erot = 0.411923913359048 | epot = -15.1104531879657 | etot = -14.617514034932 +82000 ekin = 0.0858111278279411 | erot = 0.419183131304986 | epot = -15.1225082940691 | etot = -14.6175140349362 +83000 ekin = 0.0915922459205373 | erot = 0.426746154030553 | epot = -15.1358524348887 | etot = -14.6175140349376 +84000 ekin = 0.0982778862653023 | erot = 0.434670094582779 | epot = -15.1504620157846 | etot = -14.6175140349365 +85000 ekin = 0.105780875252123 | erot = 0.443054055542032 | epot = -15.1663489657278 | etot = -14.6175140349337 +86000 ekin = 0.114007936320491 | erot = 0.452028591870552 | epot = -15.183550563121 | etot = -14.6175140349299 +87000 ekin = 0.122859117093021 | erot = 0.461742961599068 | epot = -15.2021161136185 | etot = -14.6175140349264 +88000 ekin = 0.132226490250365 | erot = 0.472351454260961 | epot = -15.2220919794351 | etot = -14.6175140349238 +89000 ekin = 0.14199243043518 | erot = 0.484000150228927 | epot = -15.2435066155872 | etot = -14.6175140349231 +90000 ekin = 0.152027823848745 | erot = 0.49681531383988 | epot = -15.2663571726137 | etot = -14.6175140349251 +91000 ekin = 0.162190574344125 | erot = 0.510894287760631 | epot = -15.2905988970349 | etot = -14.6175140349302 +92000 ekin = 0.172324730223241 | erot = 0.526299304076712 | epot = -15.3161380692387 | etot = -14.6175140349387 +93000 ekin = 0.182260479602514 | erot = 0.543054150883983 | epot = -15.342828665437 | etot = -14.6175140349505 +94000 ekin = 0.191815166424497 | erot = 0.561143224560487 | epot = -15.3704724259505 | etot = -14.6175140349655 +95000 ekin = 0.200795384589871 | erot = 0.580512230413669 | epot = -15.398821649987 | etot = -14.6175140349834 +96000 ekin = 0.209000133284301 | erot = 0.601069706845445 | epot = -15.4275838751336 | etot = -14.6175140350039 +97000 ekin = 0.216224974983076 | erot = 0.622688639933065 | epot = -15.4564276499427 | etot = -14.6175140350266 +98000 ekin = 0.222267131485452 | erot = 0.645207670246426 | epot = -15.4849888367829 | etot = -14.617514035051 +99000 ekin = 0.226931474008822 | erot = 0.668431711040234 | epot = -15.5128772201258 | etot = -14.6175140350768 +100000 ekin = 0.230037392185194 | erot = 0.692132125756912 | epot = -15.5396835530455 | etot = -14.6175140351034 +101000 ekin = 0.231426538774339 | erot = 0.716046886549487 | epot = -15.5649874604541 | etot = -14.6175140351302 +102000 ekin = 0.230971416186116 | erot = 0.739881303910906 | epot = -15.5883667552535 | etot = -14.6175140351565 +103000 ekin = 0.228584676860968 | erot = 0.763309953365433 | epot = -15.6094086654079 | etot = -14.6175140351815 +104000 ekin = 0.224228843046698 | erot = 0.785980326921886 | epot = -15.6277232051725 | etot = -14.6175140352039 +105000 ekin = 0.217925953180593 | erot = 0.807518535460022 | epot = -15.6429585238635 | etot = -14.6175140352229 +106000 ekin = 0.209766205881976 | erot = 0.827537066837565 | epot = -15.6548173079567 | etot = -14.6175140352372 +107000 ekin = 0.19991466311948 | erot = 0.845644346598459 | epot = -15.6630730449638 | etot = -14.6175140352459 +108000 ekin = 0.188614735691129 | erot = 0.861455562303715 | epot = -15.6675843332431 | etot = -14.6175140352483 +109000 ekin = 0.176187061061687 | erot = 0.874603999194433 | epot = -15.6683050955002 | etot = -14.6175140352441 +110000 ekin = 0.163022626611995 | erot = 0.88475208463374 | epot = -15.6652887464792 | etot = -14.6175140352335 +111000 ekin = 0.14956938211077 | erot = 0.89160140093568 | epot = -15.6586848182637 | etot = -14.6175140352173 +112000 ekin = 0.136312261124986 | erot = 0.8949011206007 | epot = -15.6487274169225 | etot = -14.6175140351968 +113000 ekin = 0.123747404857758 | erot = 0.894454602033368 | epot = -15.6357160420648 | etot = -14.6175140351736 +114000 ekin = 0.112352324429831 | erot = 0.890124196452667 | epot = -15.6199905560322 | etot = -14.6175140351497 +115000 ekin = 0.102554569787556 | erot = 0.881834585426713 | epot = -15.6019031903412 | etot = -14.6175140351269 +116000 ekin = 0.0947020047096738 | erot = 0.869575126614186 | epot = -15.5817911664307 | etot = -14.6175140351068 +117000 ekin = 0.0890378681937318 | erot = 0.853401690493949 | epot = -15.559953593778 | etot = -14.6175140350903 +118000 ekin = 0.0856833736308548 | erot = 0.833438318818926 | epot = -15.5366357275277 | etot = -14.6175140350779 +119000 ekin = 0.0846297171118248 | erot = 0.809878764032089 | epot = -15.5120225162133 | etot = -14.6175140350694 +120000 ekin = 0.0857402026936468 | erot = 0.782987649501416 | epot = -15.4862418872589 | etot = -14.6175140350638 +121000 ekin = 0.088761978164944 | erot = 0.753100709615785 | epot = -15.4593767228408 | etot = -14.61751403506 +122000 ekin = 0.0933458418336512 | erot = 0.720623403982127 | epot = -15.4314832808722 | etot = -14.6175140350564 +123000 ekin = 0.0990718975139699 | erot = 0.68602719834959 | epot = -15.4026131309152 | etot = -14.6175140350516 +124000 ekin = 0.105478567535099 | erot = 0.649842971567299 | epot = -15.3728355741467 | etot = -14.6175140350443 +125000 ekin = 0.112092583657528 | erot = 0.61265130691034 | epot = -15.3422579256011 | etot = -14.6175140350332 +126000 ekin = 0.118457948670349 | erot = 0.575069793125981 | epot = -15.3110417768144 | etot = -14.617514035018 +127000 ekin = 0.124162352097832 | erot = 0.537737821903371 | epot = -15.2794142089993 | etot = -14.6175140349981 +128000 ekin = 0.128860000475183 | erot = 0.501299660072983 | epot = -15.2476736955218 | etot = -14.6175140349736 +129000 ekin = 0.132290197681538 | erot = 0.466386755141783 | epot = -15.2161909877681 | etot = -14.6175140349448 +130000 ekin = 0.134291248323408 | erot = 0.433600287194685 | epot = -15.1854055704302 | etot = -14.6175140349121 +131000 ekin = 0.134809368079367 | erot = 0.403494917851113 | epot = -15.1558183208069 | etot = -14.6175140348764 +132000 ekin = 0.133902311413259 | erot = 0.376564532721602 | epot = -15.1279808789733 | etot = -14.6175140348385 +133000 ekin = 0.131737425950174 | erot = 0.353230559449875 | epot = -15.1024820201993 | etot = -14.6175140347993 +134000 ekin = 0.128583872250139 | erot = 0.333833200745338 | epot = -15.0799311077557 | etot = -14.6175140347602 +135000 ekin = 0.124798858319487 | erot = 0.31862567876175 | epot = -15.0609385718037 | etot = -14.6175140347224 +136000 ekin = 0.12080796695122 | erot = 0.307771366705934 | epot = -15.0460933683448 | etot = -14.6175140346877 +137000 ekin = 0.117080018573556 | erot = 0.301343503849859 | epot = -15.0359375570811 | etot = -14.6175140346577 +138000 ekin = 0.114097404451637 | erot = 0.299327064918768 | epot = -15.0309385040046 | etot = -14.6175140346342 +139000 ekin = 0.112323403877397 | erot = 0.301622293047273 | epot = -15.0314597315437 | etot = -14.6175140346191 +140000 ekin = 0.112168587317134 | erot = 0.308049410073558 | epot = -15.0377320320047 | etot = -14.617514034614 +141000 ekin = 0.113958896787483 | erot = 0.318354084563277 | epot = -15.0498270159712 | etot = -14.6175140346204 +142000 ekin = 0.117908250110044 | erot = 0.332213334114174 | epot = -15.0676356188633 | etot = -14.6175140346391 +143000 ekin = 0.124098500240116 | erot = 0.349241744868859 | epot = -15.0908542797794 | etot = -14.6175140346704 +144000 ekin = 0.132469049162244 | erot = 0.36899804234383 | epot = -15.1189811262199 | etot = -14.6175140347138 +145000 ekin = 0.142817534773294 | erot = 0.390992018433025 | epot = -15.1513235879745 | etot = -14.6175140347682 +146000 ekin = 0.154812002594044 | erot = 0.414692148538822 | epot = -15.1870181859643 | etot = -14.6175140348315 +147000 ekin = 0.168013608208165 | erot = 0.43953414756317 | epot = -15.2250617906724 | etot = -14.6175140349011 +148000 ekin = 0.181907755044192 | erot = 0.46493071599216 | epot = -15.2643525060103 | etot = -14.617514034974 +149000 ekin = 0.195940689918404 | erot = 0.490282644230507 | epot = -15.3037373691959 | etot = -14.6175140350469 +150000 ekin = 0.209558115498161 | erot = 0.514991307802203 | epot = -15.3420634584171 | etot = -14.6175140351168 +151000 ekin = 0.222242375358722 | erot = 0.538472447669863 | epot = -15.3782288582089 | etot = -14.6175140351803 +152000 ekin = 0.233545181100895 | erot = 0.560170967504241 | epot = -15.4112301838403 | etot = -14.6175140352351 +153000 ekin = 0.243113638171897 | erot = 0.579575715963473 | epot = -15.4402033894145 | etot = -14.6175140352791 +154000 ekin = 0.250708030719563 | erot = 0.596234520730074 | epot = -15.4644565867606 | etot = -14.617514035311 +155000 ekin = 0.256210874594961 | erot = 0.609768185048496 | epot = -15.4834930949732 | etot = -14.6175140353298 +156000 ekin = 0.259627463842806 | erot = 0.619882772314079 | epot = -15.4970242714923 | etot = -14.6175140353354 +157000 ekin = 0.26107875673392 | erot = 0.626379517381585 | epot = -15.5049723094438 | etot = -14.6175140353283 +158000 ekin = 0.260787877594978 | erot = 0.629161788909624 | epot = -15.5074637018139 | etot = -14.6175140353093 +159000 ekin = 0.259061752299553 | erot = 0.628238692725195 | epot = -15.5048144803046 | etot = -14.6175140352799 +160000 ekin = 0.256269476948141 | erot = 0.623725097357881 | epot = -15.4975086095477 | etot = -14.6175140352417 +161000 ekin = 0.252818974262866 | erot = 0.615838055765116 | epot = -15.4861710652245 | etot = -14.6175140351965 +162000 ekin = 0.249133354781009 | erot = 0.604889772114047 | epot = -15.4715371620415 | etot = -14.6175140351465 +163000 ekin = 0.245628201594233 | erot = 0.591277407066157 | epot = -15.4544196437542 | etot = -14.6175140350938 +164000 ekin = 0.242690765770646 | erot = 0.5754701254003 | epot = -15.4356749262112 | etot = -14.6175140350402 +165000 ekin = 0.240661818237773 | erot = 0.557993868664013 | epot = -15.4161697218898 | etot = -14.617514034988 +166000 ekin = 0.239820672159938 | erot = 0.539414388849556 | epot = -15.3967490959484 | etot = -14.6175140349389 +167000 ekin = 0.24037368261711 | erot = 0.520319112884873 | epot = -15.3782068303964 | etot = -14.6175140348944 +168000 ekin = 0.24244635767351 | erot = 0.501298426047331 | epot = -15.3612588185771 | etot = -14.6175140348562 +169000 ekin = 0.246079081489649 | erot = 0.482926967022199 | epot = -15.3465200833372 | etot = -14.6175140348253 +170000 ekin = 0.2512263556708 | erot = 0.465745518941327 | epot = -15.334485909415 | etot = -14.6175140348028 +171000 ekin = 0.257759407502687 | erot = 0.450244072412507 | epot = -15.3255175147045 | etot = -14.6175140347893 +172000 ekin = 0.265471962315305 | erot = 0.436846557572436 | epot = -15.3198325546728 | etot = -14.617514034785 +173000 ekin = 0.274088992052948 | erot = 0.425897760801831 | epot = -15.3175007876449 | etot = -14.6175140347901 +174000 ekin = 0.283278228108448 | erot = 0.417652965987037 | epot = -15.3184452288997 | etot = -14.6175140348042 +175000 ekin = 0.292664164217591 | erot = 0.412270652066437 | epot = -15.3224488511105 | etot = -14.6175140348264 +176000 ekin = 0.301844276744599 | erot = 0.409808663992694 | epot = -15.3291669755931 | etot = -14.6175140348558 +177000 ekin = 0.310407103278429 | erot = 0.410224178772685 | epot = -15.3381453169418 | etot = -14.6175140348907 +178000 ekin = 0.317951707449239 | erot = 0.413377690532346 | epot = -15.3488434329111 | etot = -14.6175140349295 +179000 ekin = 0.324107901132174 | erot = 0.419041092198358 | epot = -15.3606630283006 | etot = -14.6175140349701 +180000 ekin = 0.328556397749118 | erot = 0.426909726006353 | epot = -15.3729801587658 | etot = -14.6175140350103 +181000 ekin = 0.331047834154798 | erot = 0.436618006901549 | epot = -15.3851798761042 | etot = -14.6175140350478 +182000 ekin = 0.331419420115411 | erot = 0.447757936313848 | epot = -15.3966913915096 | etot = -14.6175140350804 +183000 ekin = 0.329607792338432 | erot = 0.459899520064776 | epot = -15.4070213475094 | etot = -14.6175140351062 +184000 ekin = 0.325656516855951 | erot = 0.472611792132538 | epot = -15.4157823441122 | etot = -14.6175140351237 +185000 ekin = 0.319716934488103 | erot = 0.485483030926984 | epot = -15.4227140005474 | etot = -14.6175140351323 +186000 ekin = 0.312041347783061 | erot = 0.498138700397667 | epot = -15.4276940833127 | etot = -14.6175140351319 +187000 ekin = 0.302968200961952 | erot = 0.510255791848641 | epot = -15.4307380279341 | etot = -14.6175140351235 +188000 ekin = 0.292899787357099 | erot = 0.521572552051206 | epot = -15.4319863745165 | etot = -14.6175140351082 +189000 ekin = 0.282274048056294 | erot = 0.531893031493142 | epot = -15.4316811146379 | etot = -14.6175140350885 +190000 ekin = 0.271533034589587 | erot = 0.541086413296707 | epot = -15.4301334829529 | etot = -14.6175140350666 +191000 ekin = 0.261091384545769 | erot = 0.54908161018572 | epot = -15.4276870297764 | etot = -14.6175140350449 +192000 ekin = 0.251308489708551 | erot = 0.555858063434352 | epot = -15.4246805881686 | etot = -14.6175140350257 +193000 ekin = 0.242467771120031 | erot = 0.561433978654736 | epot = -15.4214157847852 | etot = -14.6175140350104 +194000 ekin = 0.2347655816246 | erot = 0.565853352187793 | epot = -15.4181329688123 | etot = -14.6175140349999 +195000 ekin = 0.228310848061445 | erot = 0.569173077812631 | epot = -15.4149979608682 | etot = -14.6175140349941 +196000 ekin = 0.223134890550306 | erot = 0.57145120860725 | epot = -15.4121001341502 | etot = -14.6175140349926 +197000 ekin = 0.219209242156003 | erot = 0.572737138233763 | epot = -15.409460415384 | etot = -14.6175140349943 +198000 ekin = 0.216468062809104 | erot = 0.573064123808166 | epot = -15.4070462216152 | etot = -14.6175140349979 +199000 ekin = 0.214831137522652 | erot = 0.572444258403913 | epot = -15.4047894309289 | etot = -14.6175140350023 +200000 ekin = 0.214223573902254 | erot = 0.57086576066316 | epot = -15.4026033695722 | etot = -14.6175140350067 +201000 ekin = 0.214589119166907 | erot = 0.568292309386801 | epot = -15.4003954635645 | etot = -14.6175140350107 +202000 ekin = 0.215895325602457 | erot = 0.564664121433424 | epot = -15.3980734820503 | etot = -14.6175140350145 +203000 ekin = 0.218130347570136 | erot = 0.559900543318492 | epot = -15.395544925907 | etot = -14.6175140350184 +204000 ekin = 0.221292667473869 | erot = 0.553904074217835 | epot = -15.3927107767149 | etot = -14.6175140350232 +205000 ekin = 0.225376258610798 | erot = 0.546565915588112 | epot = -15.3894562092286 | etot = -14.6175140350297 +206000 ekin = 0.230354397529151 | erot = 0.537773288683187 | epot = -15.3856417212507 | etot = -14.6175140350384 +207000 ekin = 0.236165428414771 | erot = 0.527418806929786 | epot = -15.3810982703936 | etot = -14.617514035049 +208000 ekin = 0.242703261860427 | erot = 0.515412077175151 | epot = -15.3756293740966 | etot = -14.617514035061 +209000 ekin = 0.249814382550021 | erot = 0.501693407691568 | epot = -15.3690218253148 | etot = -14.6175140350732 +210000 ekin = 0.257301864855649 | erot = 0.486249049965564 | epot = -15.361064949905 | etot = -14.6175140350838 +211000 ekin = 0.264935635394273 | erot = 0.469126912720557 | epot = -15.3515765832057 | etot = -14.6175140350909 +212000 ekin = 0.272467183646406 | erot = 0.450451153648061 | epot = -15.3404323723872 | etot = -14.6175140350927 +213000 ekin = 0.279646306736793 | erot = 0.430433702677846 | epot = -15.3275940445023 | etot = -14.6175140350876 +214000 ekin = 0.286237611276688 | erot = 0.409381288017783 | epot = -15.3131329343691 | etot = -14.6175140350746 +215000 ekin = 0.292034643872632 | erot = 0.387696263734527 | epot = -15.2972449426606 | etot = -14.6175140350534 +216000 ekin = 0.296870258152624 | erot = 0.365870567411729 | epot = -15.2802548605889 | etot = -14.6175140350245 +217000 ekin = 0.300622666324868 | erot = 0.344472695102956 | epot = -15.2626093964168 | etot = -14.617514034989 +218000 ekin = 0.303217269541043 | erot = 0.324128407398458 | epot = -15.2448597118882 | etot = -14.6175140349487 +219000 ekin = 0.304624843911682 | erot = 0.305496496152239 | epot = -15.2276353749694 | etot = -14.6175140349055 +220000 ekin = 0.304856982073792 | erot = 0.289241221676068 | epot = -15.2116122386118 | etot = -14.6175140348619 +221000 ekin = 0.303959749544065 | erot = 0.276003133762455 | epot = -15.1974769181266 | etot = -14.61751403482 +222000 ekin = 0.302006434070655 | erot = 0.266369862265548 | epot = -15.1858903311184 | etot = -14.6175140347822 +223000 ekin = 0.299090105490396 | erot = 0.260848208954625 | epot = -15.1774523491954 | etot = -14.6175140347503 +224000 ekin = 0.29531650374511 | erot = 0.259838588557332 | epot = -15.1726691270288 | etot = -14.6175140347264 +225000 ekin = 0.290797600317434 | erot = 0.263612591735795 | epot = -15.1719242267649 | etot = -14.6175140347117 +226000 ekin = 0.285646103232653 | erot = 0.272294318080247 | epot = -15.1754544560203 | etot = -14.6175140347074 +227000 ekin = 0.279971018689074 | erot = 0.285846075011501 | epot = -15.1833311284151 | etot = -14.6175140347145 +228000 ekin = 0.273874374727583 | erot = 0.304059069119542 | epot = -15.1954474785804 | etot = -14.6175140347333 +229000 ekin = 0.267449174159942 | erot = 0.326549807965912 | epot = -15.2115130168895 | etot = -14.6175140347636 +230000 ekin = 0.260778614118952 | erot = 0.352763004039877 | epot = -15.2310556529637 | etot = -14.6175140348048 +231000 ekin = 0.253936564976955 | erot = 0.381981763344646 | epot = -15.2534323631772 | etot = -14.6175140348556 +232000 ekin = 0.24698923084228 | erot = 0.413345683736504 | epot = -15.2778489494931 | etot = -14.6175140349143 +233000 ekin = 0.239997814735683 | erot = 0.445877135783545 | epot = -15.3033889854978 | etot = -14.6175140349785 +234000 ekin = 0.233021891669698 | erot = 0.478515439398703 | epot = -15.3290513661138 | etot = -14.6175140350454 +235000 ekin = 0.226123071286244 | erot = 0.510157919201248 | epot = -15.3537950255994 | etot = -14.6175140351119 +236000 ekin = 0.219368436952614 | erot = 0.539706010633753 | epot = -15.3765884827609 | etot = -14.6175140351745 +237000 ekin = 0.212833212708479 | erot = 0.566113832023268 | epot = -15.3964610799618 | etot = -14.6175140352301 +238000 ekin = 0.206602165162757 | erot = 0.588436180449468 | epot = -15.412552380888 | etot = -14.6175140352757 +239000 ekin = 0.200769360307635 | erot = 0.605872583258753 | epot = -15.4241559788757 | etot = -14.6175140353093 +240000 ekin = 0.195436190928488 | erot = 0.617803458378408 | epot = -15.4307536846362 | etot = -14.6175140353293 +241000 ekin = 0.190707920284559 | erot = 0.623817360381655 | epot = -15.4320393160013 | etot = -14.6175140353351 +242000 ekin = 0.186689132523883 | erot = 0.623726737660644 | epot = -15.4279299055112 | etot = -14.6175140353267 +243000 ekin = 0.18347888087463 | erot = 0.61757185737741 | epot = -15.418564773557 | etot = -14.617514035305 +244000 ekin = 0.181166166759762 | erot = 0.60561292371356 | epot = -15.4042931257446 | etot = -14.6175140352713 +245000 ekin = 0.179826690515581 | erot = 0.588311983398978 | epot = -15.3856527091421 | etot = -14.6175140352276 +246000 ekin = 0.179521473344392 | erot = 0.566306329740652 | epot = -15.3633418382609 | etot = -14.6175140351758 +247000 ekin = 0.180297726608685 | erot = 0.54037552872489 | epot = -15.3381872904519 | etot = -14.6175140351184 +248000 ekin = 0.182192022180427 | erot = 0.511404282992934 | epot = -15.3111103402306 | etot = -14.6175140350572 +249000 ekin = 0.185235475058219 | erot = 0.480343275338998 | epot = -15.2830927853917 | etot = -14.6175140349945 +250000 ekin = 0.18946032457762 | erot = 0.448169956263045 | epot = -15.2551443157728 | etot = -14.6175140349321 +251000 ekin = 0.194907020011059 | erot = 0.415851007133659 | epot = -15.2282720620165 | etot = -14.6175140348718 +252000 ekin = 0.201630699422451 | erot = 0.384307951122869 | epot = -15.2034526853603 | etot = -14.617514034815 +253000 ekin = 0.209705815254746 | erot = 0.354387113740477 | epot = -15.1816069637584 | etot = -14.6175140347632 +254000 ekin = 0.219227629545986 | erot = 0.326834860919931 | epot = -15.1635765251836 | etot = -14.6175140347177 +255000 ekin = 0.230309407956005 | erot = 0.302278768995696 | epot = -15.1501022116313 | etot = -14.6175140346796 +256000 ekin = 0.243074422920893 | erot = 0.281215109558497 | epot = -15.1418035671295 | etot = -14.6175140346501 +257000 ekin = 0.257642364628865 | erot = 0.264002762945737 | epot = -15.139159162205 | etot = -14.6175140346304 +258000 ekin = 0.274110461102935 | erot = 0.250863404057276 | epot = -15.1424878997817 | etot = -14.6175140346215 +259000 ekin = 0.292530483428745 | erot = 0.241887528332562 | epot = -15.1519320463858 | etot = -14.6175140346245 +260000 ekin = 0.312883750214262 | erot = 0.237045600990929 | epot = -15.167443385845 | etot = -14.6175140346398 +261000 ekin = 0.335057071665646 | erot = 0.23620332462488 | epot = -15.1887744309582 | etot = -14.6175140346677 +262000 ekin = 0.358823075932977 | erot = 0.239139750883904 | epot = -15.2154768615246 | etot = -14.6175140347077 +263000 ekin = 0.383828346058697 | erot = 0.24556675356939 | epot = -15.2469091343868 | etot = -14.6175140347588 +264000 ekin = 0.409592161639846 | erot = 0.25514829095879 | epot = -15.2822544874178 | etot = -14.6175140348192 +265000 ekin = 0.435517425641053 | erot = 0.267517972446926 | epot = -15.3205494329745 | etot = -14.6175140348865 +266000 ekin = 0.460913759434934 | erot = 0.28229374222826 | epot = -15.3607215366211 | etot = -14.6175140349579 +267000 ekin = 0.485031075314244 | erot = 0.299088986461549 | epot = -15.4016340968062 | etot = -14.6175140350304 +268000 ekin = 0.507100517474285 | erot = 0.317519986657596 | epot = -15.4421345392328 | etot = -14.6175140351009 +269000 ekin = 0.526378761164296 | erot = 0.337210258004039 | epot = -15.4811030543346 | etot = -14.6175140351662 +270000 ekin = 0.542191399558024 | erot = 0.357792786171182 | epot = -15.5174982209533 | etot = -14.6175140352241 +271000 ekin = 0.55397150127625 | erot = 0.378911394713957 | epot = -15.5503969312626 | etot = -14.6175140352724 +272000 ekin = 0.561290243477908 | erot = 0.400222387434508 | epot = -15.579026666222 | etot = -14.6175140353095 +273000 ekin = 0.563877614618956 | erot = 0.421397250044594 | epot = -15.6027888999983 | etot = -14.6175140353347 +274000 ekin = 0.561632338448697 | erot = 0.442126671656052 | epot = -15.6212730454525 | etot = -14.6175140353478 +275000 ekin = 0.554621238225524 | erot = 0.462125606775959 | epot = -15.6342608803503 | etot = -14.6175140353488 +276000 ekin = 0.543069132888247 | erot = 0.481138682332307 | epot = -15.6417218505594 | etot = -14.6175140353389 +277000 ekin = 0.527340979966703 | erot = 0.498945052082944 | epot = -15.6438000673687 | etot = -14.617514035319 +278000 ekin = 0.507918337218215 | erot = 0.515361832412993 | epot = -15.6407942049222 | etot = -14.617514035291 +279000 ekin = 0.485372319602766 | erot = 0.53024547360125 | epot = -15.6331318284605 | etot = -14.6175140352565 +280000 ekin = 0.460335116507262 | erot = 0.543490744710295 | epot = -15.6213398964351 | etot = -14.6175140352175 +281000 ekin = 0.433471859961099 | erot = 0.555027349455695 | epot = -15.606013244593 | etot = -14.6175140351762 +282000 ekin = 0.405454262481042 | erot = 0.564814480005611 | epot = -15.5877827776215 | etot = -14.6175140351348 +283000 ekin = 0.376937038993841 | erot = 0.572833827991569 | epot = -15.56728490208 | etot = -14.6175140350946 +284000 ekin = 0.348537747962758 | erot = 0.579081711929156 | epot = -15.5451334949486 | etot = -14.6175140350567 +285000 ekin = 0.320820372083395 | erot = 0.583561068644996 | epot = -15.5218954757513 | etot = -14.6175140350229 +286000 ekin = 0.294282726921591 | erot = 0.586274110944376 | epot = -15.49807087286 | etot = -14.617514034994 +287000 ekin = 0.269347634013421 | erot = 0.58721647590847 | epot = -15.4740781448926 | etot = -14.6175140349707 +288000 ekin = 0.246357704467551 | erot = 0.586373659771232 | epot = -15.450245399192 | etot = -14.6175140349532 +289000 ekin = 0.22557352214567 | erot = 0.583720426230562 | epot = -15.4268079833179 | etot = -14.6175140349417 +290000 ekin = 0.207174962818393 | erot = 0.57922365744791 | epot = -15.4039126552014 | etot = -14.6175140349351 +291000 ekin = 0.191265313940187 | erot = 0.572848780862473 | epot = -15.3816281297352 | etot = -14.6175140349326 +292000 ekin = 0.177877757396419 | erot = 0.564569470031942 | epot = -15.3599612623613 | etot = -14.617514034933 +293000 ekin = 0.166983649288418 | erot = 0.554379837681261 | epot = -15.3388775219044 | etot = -14.6175140349348 +294000 ekin = 0.158501898150678 | erot = 0.542307895558042 | epot = -15.3183238286452 | etot = -14.6175140349364 +295000 ekin = 0.152308641379645 | erot = 0.528428741575596 | epot = -15.298251417892 | etot = -14.6175140349367 +296000 ekin = 0.148246390134139 | erot = 0.512875830575803 | epot = -15.2786362556445 | etot = -14.6175140349346 +297000 ekin = 0.146131889948737 | erot = 0.495848833634457 | epot = -15.2594947585125 | etot = -14.6175140349293 +298000 ekin = 0.145762142540829 | erot = 0.477616979344766 | epot = -15.2408931568064 | etot = -14.6175140349208 +299000 ekin = 0.146918339842591 | erot = 0.458517327975552 | epot = -15.2229497027275 | etot = -14.6175140349094 +300000 ekin = 0.149367830717969 | erot = 0.438948042713275 | epot = -15.205829908327 | etot = -14.6175140348958 +301000 ekin = 0.152864610233931 | erot = 0.419357266834875 | epot = -15.1897359119496 | etot = -14.6175140348808 +302000 ekin = 0.157149122640062 | erot = 0.400228590599294 | epot = -15.1748917481051 | etot = -14.6175140348658 +303000 ekin = 0.16194834771892 | erot = 0.382064246008704 | epot = -15.1615266285792 | etot = -14.6175140348516 +304000 ekin = 0.166977167327322 | erot = 0.365367110080369 | epot = -15.1498583122469 | etot = -14.6175140348392 +305000 ekin = 0.171941885875759 | erot = 0.350622387002877 | epot = -15.1400783077083 | etot = -14.6175140348297 +306000 ekin = 0.176546522696758 | erot = 0.338279561365245 | epot = -15.1323401188853 | etot = -14.6175140348233 +307000 ekin = 0.180502080572099 | erot = 0.328734935092634 | epot = -15.1267510504853 | etot = -14.6175140348206 +308000 ekin = 0.183539117579173 | erot = 0.32231506851894 | epot = -15.1233682209196 | etot = -14.6175140348214 +309000 ekin = 0.185422589168761 | erot = 0.31926113518105 | epot = -15.1221977591756 | etot = -14.6175140348258 +310000 ekin = 0.18596838252546 | erot = 0.319714556778101 | epot = -15.1231969741369 | etot = -14.6175140348333 +311000 ekin = 0.185060444471766 | erot = 0.323704474533048 | epot = -15.1262789538485 | etot = -14.6175140348436 +312000 ekin = 0.18266705569995 | erot = 0.331137883754578 | epot = -15.1313189743107 | etot = -14.6175140348562 +313000 ekin = 0.178854671448202 | erot = 0.341793554574001 | epot = -15.1381622608926 | etot = -14.6175140348704 +314000 ekin = 0.173797674113419 | erot = 0.355321045101389 | epot = -15.1466327541005 | etot = -14.6175140348857 +315000 ekin = 0.167782440686126 | erot = 0.371246117949507 | epot = -15.1565425935371 | etot = -14.6175140349014 +316000 ekin = 0.161204347699483 | erot = 0.388983636697569 | epot = -15.1677020193138 | etot = -14.6175140349167 +317000 ekin = 0.154556738723145 | erot = 0.407858516720337 | epot = -15.1799292903744 | etot = -14.6175140349309 +318000 ekin = 0.148411457828143 | erot = 0.427134549770667 | epot = -15.1930600425422 | etot = -14.6175140349434 +319000 ekin = 0.143391260343367 | erot = 0.446049980955804 | epot = -15.2069552762529 | etot = -14.6175140349537 +320000 ekin = 0.140135163879429 | erot = 0.463857713006082 | epot = -15.2215069118471 | etot = -14.6175140349616 +321000 ekin = 0.139258496830789 | erot = 0.479867117343116 | epot = -15.2366396491412 | etot = -14.6175140349673 +322000 ekin = 0.141309963686665 | erot = 0.493483840953484 | epot = -15.2523078396112 | etot = -14.6175140349711 +323000 ekin = 0.146728465401823 | erot = 0.504243890594755 | epot = -15.2684863909706 | etot = -14.6175140349741 +324000 ekin = 0.155802740978128 | erot = 0.511838753068286 | epot = -15.285155529024 | etot = -14.6175140349776 +325000 ekin = 0.168637192339279 | erot = 0.516129344219886 | epot = -15.3022805715426 | etot = -14.6175140349834 +326000 ekin = 0.185127492740314 | erot = 0.517147991937071 | epot = -15.31978951967 | etot = -14.6175140349926 +327000 ekin = 0.204949583924698 | erot = 0.515089155112464 | epot = -15.3375527740434 | etot = -14.6175140350062 +328000 ekin = 0.227565145375698 | erot = 0.510290835145397 | epot = -15.3553700155455 | etot = -14.6175140350244 +329000 ekin = 0.252245305620947 | erot = 0.503209396461946 | epot = -15.3729687371292 | etot = -14.6175140350463 +330000 ekin = 0.278112223737838 | erot = 0.494390678508285 | epot = -15.3900169373164 | etot = -14.6175140350703 +331000 ekin = 0.304195517643728 | erot = 0.484439927615862 | epot = -15.4061494803532 | etot = -14.6175140350936 +332000 ekin = 0.329497983391289 | erot = 0.473992405220338 | epot = -15.4210044237253 | etot = -14.6175140351137 +333000 ekin = 0.353063353197021 | erot = 0.463685785197061 | epot = -15.4342631735221 | etot = -14.617514035128 +334000 ekin = 0.374038491014966 | erot = 0.454134842084351 | epot = -15.4456873682339 | etot = -14.6175140351346 +335000 ekin = 0.391723520498624 | erot = 0.44590856262641 | epot = -15.4551461182577 | etot = -14.6175140351327 +336000 ekin = 0.405605581596876 | erot = 0.439509690041266 | epot = -15.4626293067607 | etot = -14.6175140351225 +337000 ekin = 0.415374601836511 | erot = 0.435356764652945 | epot = -15.4682454015947 | etot = -14.6175140351053 +338000 ekin = 0.420921997008494 | erot = 0.4337688621957 | epot = -15.4722048942871 | etot = -14.6175140350829 +339000 ekin = 0.422325110445994 | erot = 0.434953376212245 | epot = -15.4747925217162 | etot = -14.6175140350579 +340000 ekin = 0.419821259879065 | erot = 0.438997304560045 | epot = -15.4763325994719 | etot = -14.6175140350328 +341000 ekin = 0.413775534579932 | erot = 0.445862573585468 | epot = -15.4771521431752 | etot = -14.6175140350098 +342000 ekin = 0.404646174019828 | erot = 0.455385967573506 | epot = -15.4775461765844 | etot = -14.617514034991 +343000 ekin = 0.392950705832007 | erot = 0.467284215126369 | epot = -15.4777489559361 | etot = -14.6175140349777 +344000 ekin = 0.379235231728315 | erot = 0.481164689425287 | epot = -15.4779139561242 | etot = -14.6175140349706 +345000 ekin = 0.364048459932831 | erot = 0.49654196729344 | epot = -15.4781044621959 | etot = -14.6175140349696 +346000 ekin = 0.347921358320248 | erot = 0.512860132814242 | epot = -15.4782955261082 | etot = -14.6175140349738 +347000 ekin = 0.331352665808313 | erot = 0.529520204052381 | epot = -15.4783869048424 | etot = -14.6175140349817 +348000 ekin = 0.314799955037007 | erot = 0.545911447468509 | epot = -15.478225437497 | etot = -14.6175140349915 +349000 ekin = 0.298675493175969 | erot = 0.561444708833552 | epot = -15.4776342370106 | etot = -14.6175140350011 +350000 ekin = 0.28334581552179 | erot = 0.575585348315622 | epot = -15.4764451988457 | etot = -14.6175140350083 +351000 ekin = 0.269133730328657 | erot = 0.587883045338955 | epot = -15.474530810679 | etot = -14.6175140350114 +352000 ekin = 0.256321431306528 | erot = 0.597995738138102 | epot = -15.4718312044538 | etot = -14.6175140350092 +353000 ekin = 0.245153509655857 | erot = 0.605705335206491 | epot = -15.4683728798634 | etot = -14.617514035001 +354000 ekin = 0.235838910987786 | erot = 0.610923562934953 | epot = -15.4642765089099 | etot = -14.6175140349872 +355000 ekin = 0.228551231301984 | erot = 0.613687305426088 | epot = -15.4597525716969 | etot = -14.6175140349688 +356000 ekin = 0.223427131308619 | erot = 0.61414390282533 | epot = -15.4550850690815 | etot = -14.6175140349475 +357000 ekin = 0.220563006919496 | erot = 0.612527933402533 | epot = -15.4506049752473 | etot = -14.6175140349253 +358000 ekin = 0.220010333199303 | erot = 0.609131855544879 | epot = -15.4466562236489 | etot = -14.6175140349047 +359000 ekin = 0.221770268741646 | erot = 0.604273418958276 | epot = -15.443557722588 | etot = -14.6175140348881 +360000 ekin = 0.225788163654918 | erot = 0.598262925571842 | epot = -15.4415651241044 | etot = -14.6175140348777 +361000 ekin = 0.231948578438913 | erot = 0.59137325198523 | epot = -15.4408358652996 | etot = -14.6175140348754 +362000 ekin = 0.240071331019464 | erot = 0.583815109039738 | epot = -15.4414004749418 | etot = -14.6175140348826 +363000 ekin = 0.249908988059078 | erot = 0.575719406612622 | epot = -15.4431424295716 | etot = -14.6175140348999 +364000 ekin = 0.261146140583132 | erot = 0.56712790648618 | epot = -15.4457880819966 | etot = -14.6175140349273 +365000 ekin = 0.273400773646818 | erot = 0.557992653604894 | epot = -15.4489074622159 | etot = -14.6175140349642 +366000 ekin = 0.286228056504663 | erot = 0.548184015757871 | epot = -15.4519261072718 | etot = -14.6175140350093 +367000 ekin = 0.299126926926786 | erot = 0.537506547610907 | epot = -15.4541475095983 | etot = -14.6175140350606 +368000 ekin = 0.311549892639084 | erot = 0.525721330951755 | epot = -15.4547852587065 | etot = -14.6175140351156 +369000 ekin = 0.322916493342769 | erot = 0.512572942753926 | epot = -15.4530034712682 | etot = -14.6175140351715 +370000 ekin = 0.332630833324557 | erot = 0.497818805481132 | epot = -15.4479636740308 | etot = -14.6175140352251 +371000 ekin = 0.340103492446634 | erot = 0.481258447415918 | epot = -15.4388759751356 | etot = -14.6175140352731 +372000 ekin = 0.344777943664193 | erot = 0.462760223983496 | epot = -15.4250522029596 | etot = -14.6175140353119 +373000 ekin = 0.346161332162081 | erot = 0.442283380417406 | epot = -15.405958747918 | etot = -14.6175140353385 +374000 ekin = 0.343859062980667 | erot = 0.419893962766177 | epot = -15.3812670610967 | etot = -14.6175140353498 +375000 ekin = 0.337612023151491 | erot = 0.395773904235502 | epot = -15.35089996273 | etot = -14.617514035343 +376000 ekin = 0.327334336193659 | erot = 0.370223433835828 | epot = -15.3150718053453 | etot = -14.6175140353159 +377000 ekin = 0.313148263712968 | erot = 0.3436575453366 | epot = -15.2743198443167 | etot = -14.6175140352671 +378000 ekin = 0.295411338277735 | erot = 0.316597454537734 | epot = -15.2295228280119 | etot = -14.6175140351964 +379000 ekin = 0.274729408510529 | erot = 0.289657740939432 | epot = -15.1819011845551 | etot = -14.6175140351051 +380000 ekin = 0.251948675267414 | erot = 0.263529414055011 | epot = -15.1329921243187 | etot = -14.6175140349963 +381000 ekin = 0.228120837035203 | erot = 0.238958749468097 | epot = -15.0845936213794 | etot = -14.6175140348761 +382000 ekin = 0.204438854506746 | erot = 0.216721270519329 | epot = -15.0386741597779 | etot = -14.6175140347518 +383000 ekin = 0.182146263755385 | erot = 0.19759188098445 | epot = -14.9972521793722 | etot = -14.6175140346323 +384000 ekin = 0.162429780679522 | erot = 0.182311896924387 | epot = -14.9622557121308 | etot = -14.6175140345269 +385000 ekin = 0.146310622123822 | erot = 0.171555128911536 | epot = -14.9353797854792 | etot = -14.6175140344439 +386000 ekin = 0.134552389652403 | erot = 0.165895597224741 | epot = -14.9179620212657 | etot = -14.6175140343886 +387000 ekin = 0.127600986328395 | erot = 0.165779213534325 | epot = -14.9108942342266 | etot = -14.6175140343639 +388000 ekin = 0.125565151523028 | erot = 0.171500950984996 | epot = -14.9145801368772 | etot = -14.6175140343691 +389000 ekin = 0.128237001096973 | erot = 0.183188026636525 | epot = -14.9289390621349 | etot = -14.6175140344014 +390000 ekin = 0.135143637923168 | erot = 0.200788930663413 | epot = -14.9534466030433 | etot = -14.6175140344567 +391000 ekin = 0.145616156499953 | erot = 0.224068074688611 | epot = -14.9871982657191 | etot = -14.6175140345306 +392000 ekin = 0.158862235246809 | erot = 0.252606362171908 | epot = -15.0289826320371 | etot = -14.6175140346184 +393000 ekin = 0.174032087603698 | erot = 0.285808726839658 | epot = -15.0773548491589 | etot = -14.6175140347155 +394000 ekin = 0.190272707003915 | erot = 0.322920107512839 | epot = -15.1307068493349 | etot = -14.6175140348181 +395000 ekin = 0.206769905102427 | erot = 0.363051013228117 | epot = -15.1873349532527 | etot = -14.6175140349221 +396000 ekin = 0.222780272470673 | erot = 0.405212687947373 | epot = -15.2455069954414 | etot = -14.6175140350234 +397000 ekin = 0.23765569871957 | erot = 0.448360183482314 | epot = -15.3035299173199 | etot = -14.6175140351181 +398000 ekin = 0.250862154070766 | erot = 0.491439914329229 | epot = -15.3598161036022 | etot = -14.6175140352022 +399000 ekin = 0.261993055954332 | erot = 0.533437059170124 | epot = -15.4129441503972 | etot = -14.6175140352727 +400000 ekin = 0.270776550507805 | erot = 0.573417887949055 | epot = -15.4617084737844 | etot = -14.6175140353276 +401000 ekin = 0.277075831016468 | erot = 0.610562842823512 | epot = -15.505152709206 | etot = -14.617514035366 +402000 ekin = 0.280882158892238 | erot = 0.644187798759056 | epot = -15.5425839930397 | etot = -14.6175140353884 +403000 ekin = 0.282301228579434 | erot = 0.673752968641712 | epot = -15.5735682326173 | etot = -14.6175140353962 +404000 ekin = 0.281534519812515 | erot = 0.698860907481931 | epot = -15.5979094626858 | etot = -14.6175140353913 +405000 ekin = 0.278857975737129 | erot = 0.719246574878154 | epot = -15.6156185859915 | etot = -14.6175140353763 +406000 ekin = 0.274600555759475 | erot = 0.73476315739679 | epot = -15.6268777485094 | etot = -14.6175140353531 +407000 ekin = 0.269124923358509 | erot = 0.745367259285065 | epot = -15.6320062179673 | etot = -14.6175140353237 +408000 ekin = 0.262811853165719 | erot = 0.751106276665231 | epot = -15.63143216512 | etot = -14.6175140352891 +409000 ekin = 0.256049112192117 | erot = 0.752109968276187 | epot = -15.6256731157185 | etot = -14.6175140352502 +410000 ekin = 0.249224269809732 | erot = 0.74858433225965 | epot = -15.6153226372768 | etot = -14.6175140352074 +411000 ekin = 0.242720888553437 | erot = 0.740809103918433 | epot = -15.6010440276326 | etot = -14.6175140351607 +412000 ekin = 0.236916379506095 | erot = 0.729136085380854 | epot = -15.5835664999974 | etot = -14.6175140351104 +413000 ekin = 0.232179735243653 | erot = 0.713985498456999 | epot = -15.5636792687578 | etot = -14.6175140350572 +414000 ekin = 0.228867632642243 | erot = 0.695838652585891 | epot = -15.5422203202302 | etot = -14.6175140350021 +415000 ekin = 0.227317772307856 | erot = 0.675225695396218 | epot = -15.5200575026509 | etot = -14.6175140349469 +416000 ekin = 0.227838940777607 | erot = 0.652708261105161 | epot = -15.4980612367764 | etot = -14.6175140348937 +417000 ekin = 0.230697970866891 | erot = 0.628857925336047 | epot = -15.4770699310479 | etot = -14.617514034845 +418000 ekin = 0.236104416120681 | erot = 0.604232291329749 | epot = -15.4578507422538 | etot = -14.6175140348034 +419000 ekin = 0.244194252200401 | erot = 0.579351108945114 | epot = -15.4410593959166 | etot = -14.6175140347711 +420000 ekin = 0.255014214168464 | erot = 0.554674986841152 | epot = -15.4272032357598 | etot = -14.6175140347502 +421000 ekin = 0.268508458340295 | erot = 0.530589008736334 | epot = -15.4166115018185 | etot = -14.6175140347418 +422000 ekin = 0.284509119560496 | erot = 0.507392982380571 | epot = -15.4094161366875 | etot = -14.6175140347464 +423000 ekin = 0.302732060426934 | erot = 0.485299248118979 | epot = -15.4055453433093 | etot = -14.6175140347634 +424000 ekin = 0.322778728051398 | erot = 0.464438075670481 | epot = -15.4047308385137 | etot = -14.6175140347918 +425000 ekin = 0.344144594922637 | erot = 0.444869796712131 | epot = -15.4065284264641 | etot = -14.6175140348293 +426000 ekin = 0.366234204300038 | erot = 0.426602052983704 | epot = -15.4103502921573 | etot = -14.6175140348735 +427000 ekin = 0.388382398339816 | erot = 0.409609962240036 | epot = -15.4155063955013 | etot = -14.6175140349214 +428000 ekin = 0.409880900047524 | erot = 0.393856678091899 | epot = -15.4212516131094 | etot = -14.6175140349699 +429000 ekin = 0.430009061106479 | erot = 0.379311788381591 | epot = -15.4268348845041 | etot = -14.617514035016 +430000 ekin = 0.448067283636575 | erot = 0.3659652824005 | epot = -15.4315466010941 | etot = -14.617514035057 +431000 ekin = 0.463411378723588 | erot = 0.353835411175161 | epot = -15.4347608249895 | etot = -14.6175140350907 +432000 ekin = 0.475485941535269 | erot = 0.342969616703674 | epot = -15.4359695933546 | etot = -14.6175140351156 +433000 ekin = 0.483854704021334 | erot = 0.333438714396283 | epot = -15.4348074535483 | etot = -14.6175140351307 +434000 ekin = 0.488225698519521 | erot = 0.325325491782385 | epot = -15.4310652254377 | etot = -14.6175140351358 +435000 ekin = 0.48846961521868 | erot = 0.318709988965965 | epot = -15.4246936393157 | etot = -14.6175140351311 +436000 ekin = 0.484629100798397 | erot = 0.313653867974891 | epot = -15.4157970038909 | etot = -14.6175140351176 +437000 ekin = 0.476917712285193 | erot = 0.310186654191006 | epot = -15.4046184015729 | etot = -14.6175140350967 +438000 ekin = 0.465707830236428 | erot = 0.308296241623089 | epot = -15.3915181069294 | etot = -14.6175140350699 +439000 ekin = 0.45150753680146 | erot = 0.30792515377069 | epot = -15.3769467256113 | etot = -14.6175140350391 +440000 ekin = 0.434927659014138 | erot = 0.308973010492868 | epot = -15.3614147045135 | etot = -14.6175140350065 +441000 ekin = 0.416641657349937 | erot = 0.311304747383582 | epot = -15.3454604397074 | etot = -14.6175140349739 +442000 ekin = 0.397341542601571 | erot = 0.314762618736297 | epot = -15.3296181962812 | etot = -14.6175140349433 +443000 ekin = 0.377694362715545 | erot = 0.319179725729324 | epot = -15.314388123361 | etot = -14.6175140349161 +444000 ekin = 0.358304425136817 | erot = 0.32439329819003 | epot = -15.3002117582203 | etot = -14.6175140348934 +445000 ekin = 0.339684383335156 | erot = 0.330254911559461 | epot = -15.2874533297707 | etot = -14.6175140348761 +446000 ekin = 0.322237701351822 | erot = 0.336636009508 | epot = -15.2763877457241 | etot = -14.6175140348643 +447000 ekin = 0.30625308658371 | erot = 0.34342824275766 | epot = -15.2671953641993 | etot = -14.6175140348579 +448000 ekin = 0.291909091343975 | erot = 0.350538602019967 | epot = -15.2599617282208 | etot = -14.6175140348568 +449000 ekin = 0.279285717664377 | erot = 0.357880263087886 | epot = -15.254680015613 | etot = -14.6175140348608 +450000 ekin = 0.268379332693754 | erot = 0.365360767815974 | epot = -15.2512541353793 | etot = -14.6175140348696 +451000 ekin = 0.259117719163031 | erot = 0.372869677558793 | epot = -15.2495014316051 | etot = -14.6175140348833 +452000 ekin = 0.251373384973835 | erot = 0.380268095669032 | epot = -15.2491555155445 | etot = -14.6175140349017 +453000 ekin = 0.24497482412797 | erot = 0.387382402362676 | epot = -15.2498712614149 | etot = -14.6175140349243 +454000 ekin = 0.239716691076598 | erot = 0.394004131859313 | epot = -15.251234857886 | etot = -14.6175140349501 +455000 ekin = 0.235370413814522 | erot = 0.399897145639913 | epot = -15.252781594432 | etot = -14.6175140349776 +456000 ekin = 0.231696513790871 | erot = 0.404812188422525 | epot = -15.254022737218 | etot = -14.6175140350046 +457000 ekin = 0.22845901443235 | erot = 0.408507709512969 | epot = -15.2544807589739 | etot = -14.6175140350285 +458000 ekin = 0.225441196082656 | erot = 0.41077470562198 | epot = -15.2537299367515 | etot = -14.6175140350469 +459000 ekin = 0.22246101894078 | erot = 0.411462514810095 | epot = -15.251437568808 | etot = -14.6175140350572 +460000 ekin = 0.219384094438714 | erot = 0.410502136527495 | epot = -15.2474002660241 | etot = -14.6175140350579 +461000 ekin = 0.21613224524022 | erot = 0.40792384413126 | epot = -15.2415701244196 | etot = -14.6175140350481 +462000 ekin = 0.212686361973382 | erot = 0.403866554422734 | epot = -15.2340669514243 | etot = -14.6175140350282 +463000 ekin = 0.209083218482854 | erot = 0.398577486489151 | epot = -15.2251747399712 | etot = -14.6175140349992 +464000 ekin = 0.20540688826373 | erot = 0.392401883856613 | epot = -15.2153228070836 | etot = -14.6175140349633 +465000 ekin = 0.201776197881068 | erot = 0.385763783461919 | epot = -15.2050540162659 | etot = -14.6175140349229 +466000 ekin = 0.198330130961181 | erot = 0.379139817336986 | epot = -15.1949839831793 | etot = -14.6175140348811 +467000 ekin = 0.195213224017124 | erot = 0.373028711257475 | epot = -15.1857559701151 | etot = -14.6175140348405 +468000 ekin = 0.192562810062158 | erot = 0.367919448414916 | epot = -15.1779962932808 | etot = -14.6175140348037 +469000 ekin = 0.190499545154769 | erot = 0.364261004085612 | epot = -15.1722745840131 | etot = -14.6175140347727 +470000 ekin = 0.18912208603274 | erot = 0.362436180586983 | epot = -15.1690723013684 | etot = -14.6175140347487 +471000 ekin = 0.188506156938867 | erot = 0.362741456207278 | epot = -15.1687616478786 | etot = -14.6175140347325 +472000 ekin = 0.188707621222394 | erot = 0.365373993438347 | epot = -15.1715956493845 | etot = -14.6175140347238 +473000 ekin = 0.189768618622282 | erot = 0.370426120543888 | epot = -15.1777087738883 | etot = -14.6175140347222 +474000 ekin = 0.191725397341772 | erot = 0.377886798112635 | epot = -15.1871262301808 | etot = -14.6175140347264 +475000 ekin = 0.194616213071371 | erot = 0.387648901412467 | epot = -15.1997791492193 | etot = -14.6175140347354 +476000 ekin = 0.19848763616133 | erot = 0.399520678155556 | epot = -15.2155223490651 | etot = -14.6175140347483 +477000 ekin = 0.203397790430575 | erot = 0.413239540254448 | epot = -15.234151365449 | etot = -14.617514034764 +478000 ekin = 0.209415519783994 | erot = 0.428486466926518 | epot = -15.2554160214928 | etot = -14.6175140347823 +479000 ekin = 0.216615156595488 | erot = 0.444899686771521 | epot = -15.2790288781697 | etot = -14.6175140348027 +480000 ekin = 0.225067223158495 | erot = 0.462086880017487 | epot = -15.3046681380014 | etot = -14.6175140348255 +481000 ekin = 0.234826185148526 | erot = 0.479635803738694 | epot = -15.3319760237382 | etot = -14.6175140348509 +482000 ekin = 0.24591693935593 | erot = 0.497123799837189 | epot = -15.3605547740723 | etot = -14.6175140348792 +483000 ekin = 0.258322039581471 | erot = 0.514126984880484 | epot = -15.3899630593723 | etot = -14.6175140349103 +484000 ekin = 0.271971667055458 | erot = 0.530229960568097 | epot = -15.4197156625675 | etot = -14.617514034944 +485000 ekin = 0.286738030810237 | erot = 0.545036619609161 | epot = -15.4492886853988 | etot = -14.6175140349794 +486000 ekin = 0.302435294442602 | erot = 0.558182125190157 | epot = -15.4781314546481 | etot = -14.6175140350154 +487000 ekin = 0.318825369858635 | erot = 0.569345540302413 | epot = -15.5056849452114 | etot = -14.6175140350504 +488000 ekin = 0.335629120856599 | erot = 0.578262027782435 | epot = -15.5314051837218 | etot = -14.6175140350827 +489000 ekin = 0.352541803825719 | erot = 0.584733173542254 | epot = -15.5547890124787 | etot = -14.6175140351108 +490000 ekin = 0.369251041133798 | erot = 0.58863390237619 | epot = -15.5753989786432 | etot = -14.6175140351332 +491000 ekin = 0.385455339944008 | erot = 0.589914693970058 | epot = -15.5928840690631 | etot = -14.6175140351491 +492000 ekin = 0.40088115647899 | erot = 0.588598334680754 | epot = -15.6069935263179 | etot = -14.6175140351581 +493000 ekin = 0.415296746377553 | erot = 0.584771169137649 | epot = -15.6175819506758 | etot = -14.6175140351606 +494000 ekin = 0.428521503102931 | erot = 0.578569614095801 | epot = -15.6246051523561 | etot = -14.6175140351573 +495000 ekin = 0.440430011858771 | erot = 0.570163426568569 | epot = -15.6281074735768 | etot = -14.6175140351495 +496000 ekin = 0.450950706316734 | erot = 0.559737766477586 | epot = -15.628202507933 | etot = -14.6175140351387 +497000 ekin = 0.460059581798191 | erot = 0.547476355485745 | epot = -15.6250499724103 | etot = -14.6175140351264 +498000 ekin = 0.467769906492318 | erot = 0.533547985555278 | epot = -15.6188319271617 | etot = -14.6175140351141 +499000 ekin = 0.474119221073082 | erot = 0.518098277332704 | epot = -15.6097315335085 | etot = -14.6175140351027 +500000 ekin = 0.47915510663518 | erot = 0.501247978937513 | epot = -15.5979171206656 | etot = -14.6175140350929 +501000 ekin = 0.482921233338969 | erot = 0.483098304082662 | epot = -15.5835335725064 | etot = -14.6175140350848 +502000 ekin = 0.485445093649088 | erot = 0.463742920559554 | epot = -15.5667020492864 | etot = -14.6175140350777 +503000 ekin = 0.486728599209648 | erot = 0.443285305605623 | epot = -15.5475279398862 | etot = -14.6175140350709 +504000 ekin = 0.486742408087926 | erot = 0.421859374631785 | epot = -15.5261158177828 | etot = -14.6175140350631 +505000 ekin = 0.485424480827694 | erot = 0.399650657768087 | epot = -15.5025891736488 | etot = -14.617514035053 +506000 ekin = 0.48268297341187 | erot = 0.376914939267219 | epot = -15.4771119477182 | etot = -14.6175140350392 +507000 ekin = 0.478403198154612 | erot = 0.353991273961029 | epot = -15.4499085071364 | etot = -14.6175140350208 +508000 ekin = 0.472458052935441 | erot = 0.331306710133916 | epot = -15.4212787980666 | etot = -14.6175140349972 +509000 ekin = 0.46472106285539 | erot = 0.309370883447747 | epot = -15.3916059812718 | etot = -14.6175140349687 +510000 ekin = 0.455081004104095 | erot = 0.288759823578743 | epot = -15.3613548626186 | etot = -14.6175140349358 +511000 ekin = 0.443456979180403 | erot = 0.270089690707411 | epot = -15.3310607047875 | etot = -14.6175140348996 +512000 ekin = 0.429812848219575 | erot = 0.25398253489869 | epot = -15.3013094179802 | etot = -14.6175140348619 +513000 ekin = 0.414169942618988 | erot = 0.241027258547328 | epot = -15.2727112359908 | etot = -14.6175140348245 +514000 ekin = 0.396617122319459 | erot = 0.231739657368316 | epot = -15.245870814477 | etot = -14.6175140347893 +515000 ekin = 0.377317407138787 | erot = 0.226525548757195 | epot = -15.2213569906539 | etot = -14.6175140347579 +516000 ekin = 0.356510629533613 | erot = 0.225650587239684 | epot = -15.1996752515051 | etot = -14.6175140347318 +517000 ekin = 0.334511811731556 | erot = 0.229219509886492 | epot = -15.1812453563299 | etot = -14.6175140347118 +518000 ekin = 0.311705249160021 | erot = 0.23716641592675 | epot = -15.1663856997854 | etot = -14.6175140346987 +519000 ekin = 0.288534562405509 | erot = 0.249256456193826 | epot = -15.1553050532917 | etot = -14.6175140346923 +520000 ekin = 0.265489234982404 | erot = 0.265098165451267 | epot = -15.1481014351262 | etot = -14.6175140346925 +521000 ekin = 0.243088358087729 | erot = 0.284164745160129 | epot = -15.1447671379464 | etot = -14.6175140346986 +522000 ekin = 0.221862437060792 | erot = 0.305821970140486 | epot = -15.1451984419111 | etot = -14.6175140347098 +523000 ekin = 0.202334169776215 | erot = 0.329360070797338 | epot = -15.149208275299 | etot = -14.6175140347255 +524000 ekin = 0.184999091076189 | erot = 0.354026911471086 | epot = -15.1565400372918 | etot = -14.6175140347445 +525000 ekin = 0.170306912739355 | erot = 0.379059948771691 | epot = -15.1668808962774 | etot = -14.6175140347664 +526000 ekin = 0.158644243148445 | erot = 0.403715126925631 | epot = -15.1798734048646 | etot = -14.6175140347905 +527000 ekin = 0.150319367666608 | erot = 0.427291025812717 | epot = -15.1951244282958 | etot = -14.6175140348165 +528000 ekin = 0.145549592055318 | erot = 0.449147424933815 | epot = -15.2122110518333 | etot = -14.6175140348441 +529000 ekin = 0.144451603984815 | erot = 0.46871812185095 | epot = -15.2306837607091 | etot = -14.6175140348734 +530000 ekin = 0.147035267138349 | erot = 0.485518371011605 | epot = -15.2500676730542 | etot = -14.6175140349042 +531000 ekin = 0.153201203684292 | erot = 0.499147835497304 | epot = -15.2698630741182 | etot = -14.6175140349366 +532000 ekin = 0.162742448479717 | erot = 0.509290301682708 | epot = -15.2895467851327 | etot = -14.6175140349702 +533000 ekin = 0.175350354881916 | erot = 0.515711587206721 | epot = -15.3085759770934 | etot = -14.6175140350047 +534000 ekin = 0.190624856013519 | erot = 0.518257146630614 | epot = -15.3263960376834 | etot = -14.6175140350393 +535000 ekin = 0.208088493536824 | erot = 0.516850140104756 | epot = -15.3424526687142 | etot = -14.6175140350726 +536000 ekin = 0.227204325842689 | erot = 0.511491240065728 | epot = -15.3562096010119 | etot = -14.6175140351035 +537000 ekin = 0.247396768812984 | erot = 0.502260311074185 | epot = -15.3671711150173 | etot = -14.6175140351302 +538000 ekin = 0.268074342413392 | erot = 0.489319600961478 | epot = -15.3749079785256 | etot = -14.6175140351508 +539000 ekin = 0.288653182933449 | erot = 0.4729176796722 | epot = -15.3790848977693 | etot = -14.6175140351637 +540000 ekin = 0.308579985825782 | erot = 0.453392904739592 | epot = -15.3794869257329 | etot = -14.6175140351675 +541000 ekin = 0.327353008191246 | erot = 0.431174973010967 | epot = -15.3760420163633 | etot = -14.6175140351611 +542000 ekin = 0.344539853506965 | erot = 0.406783142889028 | epot = -15.3688370315399 | etot = -14.6175140351439 +543000 ekin = 0.359790986513993 | erot = 0.380819988063805 | epot = -15.3581250096939 | etot = -14.6175140351161 +544000 ekin = 0.37284826309085 | erot = 0.353960030672464 | epot = -15.344322328842 | etot = -14.6175140350787 +545000 ekin = 0.383548167009815 | erot = 0.326933212481791 | epot = -15.3279954145248 | etot = -14.6175140350332 +546000 ekin = 0.391819867385749 | erot = 0.300503784237994 | epot = -15.3098376866053 | etot = -14.6175140349815 +547000 ekin = 0.397678590182396 | erot = 0.275445713887096 | epot = -15.2906383389958 | etot = -14.6175140349263 +548000 ekin = 0.401215088504832 | erot = 0.252516050366015 | epot = -15.2712451737408 | etot = -14.6175140348699 +549000 ekin = 0.402582175512791 | erot = 0.232427794767637 | epot = -15.2525240050959 | etot = -14.6175140348155 +550000 ekin = 0.401979352687969 | erot = 0.215823740833009 | epot = -15.2353171282862 | etot = -14.6175140347652 +551000 ekin = 0.399636550193996 | erot = 0.203252510909739 | epot = -15.220403095825 | etot = -14.6175140347213 +552000 ekin = 0.395797934840894 | erot = 0.195147714573778 | epot = -15.2084596841007 | etot = -14.617514034686 +553000 ekin = 0.390706676476196 | erot = 0.191810879117336 | epot = -15.2000315902546 | etot = -14.6175140346611 +554000 ekin = 0.384591526958096 | erot = 0.19339860945437 | epot = -15.1955041710601 | etot = -14.6175140346476 +555000 ekin = 0.377656068332676 | erot = 0.199914362894006 | epot = -15.1950844658734 | etot = -14.6175140346467 +556000 ekin = 0.370071512615683 | erot = 0.211205266307111 | epot = -15.1987908135806 | etot = -14.6175140346578 +557000 ekin = 0.361973939272813 | erot = 0.226964515102972 | epot = -15.2064524890562 | etot = -14.6175140346805 +558000 ekin = 0.353466765020817 | erot = 0.246739996102199 | epot = -15.2177207958362 | etot = -14.6175140347132 +559000 ekin = 0.344628961765223 | erot = 0.269949765670651 | epot = -15.2320927621895 | etot = -14.6175140347536 +560000 ekin = 0.335528980568065 | erot = 0.295904778796298 | epot = -15.248947794163 | etot = -14.6175140347986 +561000 ekin = 0.326243446081694 | erot = 0.32383871490908 | epot = -15.2675961958353 | etot = -14.6175140348445 +562000 ekin = 0.316878486813705 | erot = 0.352943857553535 | epot = -15.2873363792542 | etot = -14.617514034887 +563000 ekin = 0.307590234581993 | erot = 0.382410843957943 | epot = -15.3075151134627 | etot = -14.6175140349227 +564000 ekin = 0.298599911427723 | erot = 0.411468934029848 | epot = -15.3275828804063 | etot = -14.6175140349488 +565000 ekin = 0.290198521501613 | erot = 0.439422606477982 | epot = -15.3471351629436 | etot = -14.617514034964 +566000 ekin = 0.282736992095915 | erot = 0.465680158920146 | epot = -15.3659311859852 | etot = -14.6175140349691 +567000 ekin = 0.276599956454237 | erot = 0.489770841523137 | epot = -15.3838848329439 | etot = -14.6175140349665 +568000 ekin = 0.272165052790849 | erot = 0.51134888782089 | epot = -15.4010279755719 | etot = -14.6175140349602 +569000 ekin = 0.269753809413351 | erot = 0.530185258477429 | epot = -15.4174531028455 | etot = -14.6175140349547 +570000 ekin = 0.269583567607364 | erot = 0.546150320474836 | epot = -15.4332479230362 | etot = -14.617514034954 +571000 ekin = 0.271731068577875 | erot = 0.559192265325752 | epot = -15.4484373688642 | etot = -14.6175140349606 +572000 ekin = 0.276116495687091 | erot = 0.569316321634121 | epot = -15.4629468522959 | etot = -14.6175140349747 +573000 ekin = 0.282512256444534 | erot = 0.576569321998237 | epot = -15.4765956134374 | etot = -14.6175140349946 +574000 ekin = 0.290574483947443 | erot = 0.58103049076154 | epot = -15.4891190097262 | etot = -14.6175140350172 +575000 ekin = 0.299890113326593 | erot = 0.582808418137594 | epot = -15.5002125665028 | etot = -14.6175140350386 +576000 ekin = 0.310029076130859 | erot = 0.582041678954832 | epot = -15.5095847901412 | etot = -14.6175140350555 +577000 ekin = 0.320591144135675 | erot = 0.578899817193377 | epot = -15.5170049963946 | etot = -14.6175140350655 +578000 ekin = 0.331239680817734 | erot = 0.573581904321388 | epot = -15.5223356202072 | etot = -14.6175140350681 +579000 ekin = 0.341718767395713 | erot = 0.566311213814816 | epot = -15.5255440162742 | etot = -14.6175140350637 +580000 ekin = 0.351854361646192 | erot = 0.557326170820746 | epot = -15.5266945675209 | etot = -14.617514035054 +581000 ekin = 0.361543170719959 | erot = 0.546869043111512 | epot = -15.5259262488727 | etot = -14.6175140350412 +582000 ekin = 0.370734291431731 | erot = 0.535174473618127 | epot = -15.5234228000774 | etot = -14.6175140350275 +583000 ekin = 0.37940854514636 | erot = 0.522459863754317 | epot = -15.5193824439152 | etot = -14.6175140350145 +584000 ekin = 0.387559338332064 | erot = 0.50891899993969 | epot = -15.5139923732753 | etot = -14.6175140350036 +585000 ekin = 0.395177418309436 | erot = 0.494719483694829 | epot = -15.5074109369994 | etot = -14.6175140349952 +586000 ekin = 0.402240533516594 | erot = 0.480003760424791 | epot = -15.4997583289309 | etot = -14.6175140349895 +587000 ekin = 0.408707997145263 | erot = 0.464893014294175 | epot = -15.4911150464257 | etot = -14.6175140349862 +588000 ekin = 0.41451954577295 | erot = 0.449492951760516 | epot = -15.4815265325182 | etot = -14.6175140349847 +589000 ekin = 0.419597612555334 | erot = 0.43390048790532 | epot = -15.4710121354448 | etot = -14.6175140349841 +590000 ekin = 0.423852083806567 | erot = 0.418210489542958 | epot = -15.4595766083332 | etot = -14.6175140349837 +591000 ekin = 0.427186671517479 | erot = 0.402521929657892 | epot = -15.447222636158 | etot = -14.6175140349826 +592000 ekin = 0.429506137373686 | erot = 0.386943005728737 | epot = -15.4339631780827 | etot = -14.6175140349802 +593000 ekin = 0.430723706116615 | erot = 0.371594936609099 | epot = -15.4198326777017 | etot = -14.617514034976 +594000 ekin = 0.430768094953839 | erot = 0.356614269836478 | epot = -15.4048963997596 | etot = -14.6175140349693 +595000 ekin = 0.42958966483036 | erot = 0.34215360916983 | epot = -15.3892573089602 | etot = -14.61751403496 +596000 ekin = 0.427165296133674 | erot = 0.328380718540701 | epot = -15.3730600496226 | etot = -14.6175140349482 +597000 ekin = 0.423501658500188 | erot = 0.315475989401846 | epot = -15.3564916828361 | etot = -14.617514034934 +598000 ekin = 0.418636501255824 | erot = 0.30362835958022 | epot = -15.3397788957539 | etot = -14.6175140349178 +599000 ekin = 0.412638207582771 | erot = 0.293029673722298 | epot = -15.3231819162053 | etot = -14.6175140349002 +600000 ekin = 0.405603414753992 | erot = 0.283867637225037 | epot = -15.306985086861 | etot = -14.6175140348819 +601000 ekin = 0.397652939448924 | erot = 0.27631757335997 | epot = -15.2914845476729 | etot = -14.617514034864 +602000 ekin = 0.388926339151977 | erot = 0.270533300127966 | epot = -15.2769736741272 | etot = -14.6175140348472 +603000 ekin = 0.379575547711323 | erot = 0.266637582798157 | epot = -15.2637271653422 | etot = -14.6175140348327 +604000 ekin = 0.369758112224678 | erot = 0.264712769809213 | epot = -15.2519849168553 | etot = -14.6175140348214 +605000 ekin = 0.359630614964776 | erot = 0.264792359550131 | epot = -15.241937009329 | etot = -14.617514034814 +606000 ekin = 0.349342882571482 | erot = 0.266854337886994 | epot = -15.2337112552696 | etot = -14.6175140348111 +607000 ekin = 0.339033558751721 | erot = 0.270817131627805 | epot = -15.2273647251923 | etot = -14.6175140348128 +608000 ekin = 0.328827538259558 | erot = 0.276538908097645 | epot = -15.2228804811762 | etot = -14.617514034819 +609000 ekin = 0.318835621087791 | erot = 0.283820700144912 | epot = -15.2201703560617 | etot = -14.617514034829 +610000 ekin = 0.309156542568471 | erot = 0.292413461056483 | epot = -15.2190840384669 | etot = -14.617514034842 +611000 ekin = 0.29988127210835 | erot = 0.302028697870677 | epot = -15.2194240048356 | etot = -14.6175140348566 +612000 ekin = 0.291099167856382 | erot = 0.312351863790435 | epot = -15.2209650665183 | etot = -14.6175140348715 +613000 ekin = 0.282905257831731 | erot = 0.323057294042835 | epot = -15.2234765867597 | etot = -14.6175140348851 +614000 ekin = 0.275407632339994 | erot = 0.333823223653581 | epot = -15.2267448908899 | etot = -14.6175140348963 +615000 ekin = 0.268733725567278 | erot = 0.344345386321387 | epot = -15.2305931467927 | etot = -14.617514034904 +616000 ekin = 0.263034181136557 | erot = 0.35434787992739 | epot = -15.2348960959719 | etot = -14.6175140349079 +617000 ekin = 0.258483071857821 | erot = 0.363590372787447 | epot = -15.2395874795532 | etot = -14.6175140349079 +618000 ekin = 0.255273496413574 | erot = 0.371871254538827 | epot = -15.2446587858571 | etot = -14.6175140349047 +619000 ekin = 0.253608004174632 | erot = 0.37902692128715 | epot = -15.2501489603613 | etot = -14.6175140348995 +620000 ekin = 0.253683881421992 | erot = 0.384927934513618 | epot = -15.2561258508295 | etot = -14.6175140348939 +621000 ekin = 0.255674023709804 | erot = 0.389473226071993 | epot = -15.2626612846714 | etot = -14.6175140348896 +622000 ekin = 0.25970485336757 | erot = 0.392583779639758 | epot = -15.2698026678959 | etot = -14.6175140348885 +623000 ekin = 0.265833429999403 | erot = 0.394197274405735 | epot = -15.2775447392974 | etot = -14.6175140348923 +624000 ekin = 0.274026439188228 | erot = 0.394265031624551 | epot = -15.2858055057147 | etot = -14.6175140349019 +625000 ekin = 0.284144015738384 | erot = 0.392752285176118 | epot = -15.2944103358322 | etot = -14.6175140349177 +626000 ekin = 0.295931256226139 | erot = 0.389642344380343 | epot = -15.3030876355457 | etot = -14.6175140349392 +627000 ekin = 0.309019727829663 | erot = 0.38494467650416 | epot = -15.3114784392987 | etot = -14.6175140349649 +628000 ekin = 0.322940275279064 | erot = 0.378706350959343 | epot = -15.3191606612307 | etot = -14.6175140349923 +629000 ekin = 0.337147043698277 | erot = 0.37102569897414 | epot = -15.3256867776908 | etot = -14.6175140350184 +630000 ekin = 0.351051052994981 | erot = 0.362066500826367 | epot = -15.3306315888613 | etot = -14.6175140350399 +631000 ekin = 0.364060148819096 | erot = 0.352070586245494 | epot = -15.333644770118 | etot = -14.6175140350534 +632000 ekin = 0.375621025661737 | erot = 0.341366514680777 | epot = -15.3345015753988 | etot = -14.6175140350563 +633000 ekin = 0.385258541224816 | erot = 0.33037209230534 | epot = -15.3331446685769 | etot = -14.6175140350467 +634000 ekin = 0.392607865616762 | erot = 0.31958895649352 | epot = -15.3297108571345 | etot = -14.6175140350242 +635000 ekin = 0.39743609727868 | erot = 0.309588318033271 | epot = -15.3245384503017 | etot = -14.6175140349897 +636000 ekin = 0.399651602685353 | erot = 0.30098809437835 | epot = -15.318153732009 | etot = -14.6175140349453 +637000 ekin = 0.399301141333129 | erot = 0.294422893568983 | epot = -15.3112380697961 | etot = -14.617514034894 +638000 ekin = 0.396556439147407 | erot = 0.290509369489655 | epot = -15.3045798434767 | etot = -14.6175140348397 +639000 ekin = 0.391692975513997 | erot = 0.289810143797434 | epot = -15.2990171540975 | etot = -14.617514034786 +640000 ekin = 0.385064212934161 | erot = 0.292799653113688 | epot = -15.2953779007847 | etot = -14.6175140347369 +641000 ekin = 0.377074355551302 | erot = 0.299834934663062 | epot = -15.2944233249094 | etot = -14.6175140346951 +642000 ekin = 0.368152133961515 | erot = 0.311133625026309 | epot = -15.2967997936509 | etot = -14.6175140346631 +643000 ekin = 0.358727298275111 | erot = 0.326760494743868 | epot = -15.3030018276614 | etot = -14.6175140346424 +644000 ekin = 0.349210670243499 | erot = 0.346622862554325 | epot = -15.3133475674317 | etot = -14.6175140346339 +645000 ekin = 0.339977915474886 | erot = 0.370474376280189 | epot = -15.3279663263927 | etot = -14.6175140346376 +646000 ekin = 0.331356734049287 | erot = 0.397926004729598 | epot = -15.3467967734319 | etot = -14.617514034653 +647000 ekin = 0.323616951062021 | erot = 0.428462692622343 | epot = -15.3695936783637 | etot = -14.6175140346794 +648000 ekin = 0.316962984679749 | erot = 0.461463981264525 | epot = -15.3959410006599 | etot = -14.6175140347156 +649000 ekin = 0.311528303721769 | erot = 0.496226945506609 | epot = -15.4252692839889 | etot = -14.6175140347605 +650000 ekin = 0.307371814502051 | erot = 0.53199011331203 | epot = -15.4568759626267 | etot = -14.6175140348127 +651000 ekin = 0.304476169211528 | erot = 0.567957247023637 | epot = -15.4899474511057 | etot = -14.6175140348705 +652000 ekin = 0.302748327843063 | erot = 0.603320352539344 | epot = -15.523582715315 | etot = -14.6175140349325 +653000 ekin = 0.302022769689561 | erot = 0.637281675063983 | epot = -15.5568184797505 | etot = -14.617514034997 +654000 ekin = 0.302067723594154 | erot = 0.669074745116258 | epot = -15.5886565037723 | etot = -14.6175140350619 +655000 ekin = 0.302594671774775 | erot = 0.697984728110365 | epot = -15.6180934350103 | etot = -14.6175140351252 +656000 ekin = 0.303271161273661 | erot = 0.723368330432067 | epot = -15.6441535268902 | etot = -14.6175140351845 +657000 ekin = 0.303736663270792 | erot = 0.744673311812443 | epot = -15.6659240103206 | etot = -14.6175140352373 +658000 ekin = 0.303620889262384 | erot = 0.761457272710392 | epot = -15.6825921972542 | etot = -14.6175140352814 +659000 ekin = 0.302563666907984 | erot = 0.773404945481054 | epot = -15.6934826477032 | etot = -14.6175140353142 +660000 ekin = 0.300235395695091 | erot = 0.780343280385843 | epot = -15.698092711415 | etot = -14.6175140353341 +661000 ekin = 0.296355710531902 | erot = 0.782250083093143 | epot = -15.6961198289647 | etot = -14.6175140353397 +662000 ekin = 0.290710478297184 | erot = 0.779257959177687 | epot = -15.6874824728051 | etot = -14.6175140353302 +663000 ekin = 0.283165147463639 | erot = 0.77165065199169 | epot = -15.6723298347614 | etot = -14.6175140353061 +664000 ekin = 0.273673427176448 | erot = 0.759850562455872 | epot = -15.6510380249006 | etot = -14.6175140352683 +665000 ekin = 0.262280913452385 | erot = 0.744397727319057 | epot = -15.6241926759903 | etot = -14.6175140352189 +666000 ekin = 0.249123647022483 | erot = 0.7259212317447 | epot = -15.5925589139278 | etot = -14.6175140351606 +667000 ekin = 0.234422061210147 | erot = 0.705104954965032 | epot = -15.5570410512716 | etot = -14.6175140350964 +668000 ekin = 0.218471158369324 | erot = 0.682650243124776 | epot = -15.5186354365237 | etot = -14.6175140350296 +669000 ekin = 0.201627981911843 | erot = 0.659238455806553 | epot = -15.4783804726815 | etot = -14.6175140349632 +670000 ekin = 0.184297501939065 | erot = 0.635496303880898 | epot = -15.43730784072 | etot = -14.6175140349001 +671000 ekin = 0.166917915805004 | erot = 0.611966525748027 | epot = -15.3963984763956 | etot = -14.6175140348426 +672000 ekin = 0.149946120674196 | erot = 0.589085832361493 | epot = -15.3565459878282 | etot = -14.6175140347926 +673000 ekin = 0.133843801904582 | erot = 0.567171306812613 | epot = -15.318529143468 | etot = -14.6175140347508 +674000 ekin = 0.119064262674576 | erot = 0.546415679820867 | epot = -15.2829939772136 | etot = -14.6175140347181 +675000 ekin = 0.106039855017085 | erot = 0.526891195482506 | epot = -15.250445085194 | etot = -14.6175140346944 +676000 ekin = 0.0951697078773878 | erot = 0.508561175678473 | epot = -15.2212449182352 | etot = -14.6175140346793 +677000 ekin = 0.086807451986192 | erot = 0.491297978909966 | epot = -15.1956194655683 | etot = -14.6175140346722 +678000 ekin = 0.0812485969712828 | erot = 0.474905301099178 | epot = -15.1736679327427 | etot = -14.6175140346722 +679000 ekin = 0.0787177619800211 | erot = 0.459143233464763 | epot = -15.1553750301234 | etot = -14.6175140346787 +680000 ekin = 0.0793562024648552 | erot = 0.443753980649329 | epot = -15.140624217805 | etot = -14.6175140346908 +681000 ekin = 0.0832104900789999 | erot = 0.428486254341784 | epot = -15.1292107791285 | etot = -14.6175140347077 +682000 ekin = 0.0902236865225188 | erot = 0.413116880933304 | epot = -15.1208546021847 | etot = -14.6175140347289 +683000 ekin = 0.100230543462408 | erot = 0.397468585264377 | epot = -15.11521316348 | etot = -14.6175140347533 +684000 ekin = 0.112958164258869 | erot = 0.381423459018597 | epot = -15.1118956580574 | etot = -14.6175140347799 +685000 ekin = 0.128033094046148 | erot = 0.364932120277307 | epot = -15.1104792491311 | etot = -14.6175140348076 +686000 ekin = 0.144995008361601 | erot = 0.348018922992647 | epot = -15.1105279661894 | etot = -14.6175140348351 +687000 ekin = 0.163316207854767 | erot = 0.330783730221022 | epot = -15.1116139729365 | etot = -14.6175140348607 +688000 ekin = 0.182425234215551 | erot = 0.313400732953855 | epot = -15.1133400020525 | etot = -14.6175140348831 +689000 ekin = 0.201732335852577 | erot = 0.296114640201443 | epot = -15.1153610109551 | etot = -14.6175140349011 +690000 ekin = 0.220654383891154 | erot = 0.279234374240434 | epot = -15.1174027930453 | etot = -14.6175140349137 +691000 ekin = 0.23863718992453 | erot = 0.263124260136862 | epot = -15.1192754849819 | etot = -14.6175140349205 +692000 ekin = 0.255173895596428 | erot = 0.248192653897472 | epot = -15.1208805844156 | etot = -14.6175140349217 +693000 ekin = 0.269818995118043 | erot = 0.234878024009109 | epot = -15.1222110540446 | etot = -14.6175140349175 +694000 ekin = 0.282198402189113 | erot = 0.223632668706427 | epot = -15.1233451058044 | etot = -14.6175140349089 +695000 ekin = 0.292016609393231 | erot = 0.214904477348993 | epot = -15.124435121639 | etot = -14.6175140348968 +696000 ekin = 0.299062308191112 | erot = 0.209117382947945 | epot = -15.1256937260212 | etot = -14.6175140348821 +697000 ekin = 0.30321380997214 | erot = 0.206651361568493 | epot = -15.1273792064064 | etot = -14.6175140348658 +698000 ekin = 0.30444525619219 | erot = 0.207822979229873 | epot = -15.1297822702705 | etot = -14.6175140348484 +699000 ekin = 0.302833983904948 | erot = 0.212867544425277 | epot = -15.1332155631607 | etot = -14.6175140348305 +700000 ekin = 0.29856859634332 | erot = 0.221923881123336 | epot = -15.1380065122785 | etot = -14.6175140348118 +701000 ekin = 0.291956369738242 | erot = 0.235022588976831 | epot = -15.1444929935074 | etot = -14.6175140347924 +702000 ekin = 0.283427734153835 | erot = 0.252078414121472 | epot = -15.153020183048 | etot = -14.6175140347727 +703000 ekin = 0.273534855576746 | erot = 0.272887068861365 | epot = -15.1639359591909 | etot = -14.6175140347528 +704000 ekin = 0.262941046164233 | erot = 0.297126498876432 | epot = -15.1775815797744 | etot = -14.6175140347337 +705000 ekin = 0.252398060444365 | erot = 0.324362359960393 | epot = -15.194274455122 | etot = -14.6175140347173 +706000 ekin = 0.242709489752073 | erot = 0.354057349893491 | epot = -15.2142808743513 | etot = -14.6175140347058 +707000 ekin = 0.234680465258637 | erot = 0.385584073394242 | epot = -15.2377785733552 | etot = -14.6175140347023 +708000 ekin = 0.229056562326157 | erot = 0.418241319394871 | epot = -15.264811916431 | etot = -14.61751403471 +709000 ekin = 0.226457657533258 | erot = 0.451273895783649 | epot = -15.2952455880485 | etot = -14.6175140347316 +710000 ekin = 0.227314828595311 | erot = 0.483896330830945 | epot = -15.3287251941949 | etot = -14.6175140347687 +711000 ekin = 0.231819479497128 | erot = 0.515320742171203 | epot = -15.3646542564898 | etot = -14.6175140348215 +712000 ekin = 0.239893150548963 | erot = 0.544788749312711 | epot = -15.4021959347498 | etot = -14.6175140348881 +713000 ekin = 0.251183758823288 | erot = 0.571606341188824 | epot = -15.4403041349766 | etot = -14.6175140349645 +714000 ekin = 0.265090036185525 | erot = 0.595179886372787 | epot = -15.4777839576035 | etot = -14.6175140350452 +715000 ekin = 0.280811306968559 | erot = 0.615050345044272 | epot = -15.5133756871366 | etot = -14.6175140351238 +716000 ekin = 0.297415784950407 | erot = 0.630922165703626 | epot = -15.5458519858478 | etot = -14.6175140351937 +717000 ekin = 0.313918116237917 | erot = 0.642683345316706 | epot = -15.5741154968041 | etot = -14.6175140352494 +718000 ekin = 0.329356373327112 | erot = 0.650413757300199 | epot = -15.597284165914 | etot = -14.6175140352867 +719000 ekin = 0.342860093484457 | erot = 0.654380316354483 | epot = -15.6147544451421 | etot = -14.6175140353032 +720000 ekin = 0.353703497403049 | erot = 0.655019233384572 | epot = -15.6262367660863 | etot = -14.6175140352987 +721000 ekin = 0.361340844905849 | erot = 0.652906431496321 | epot = -15.6317613116767 | etot = -14.6175140352745 +722000 ekin = 0.365423978941575 | erot = 0.648719378780931 | epot = -15.6316573929561 | etot = -14.6175140352336 +723000 ekin = 0.365803989072306 | erot = 0.643193727890481 | epot = -15.6265117521426 | etot = -14.6175140351798 +724000 ekin = 0.362520178745313 | erot = 0.637078359573022 | epot = -15.6171125734355 | etot = -14.6175140351172 +725000 ekin = 0.355779938480366 | erot = 0.631092082280502 | epot = -15.604386055811 | etot = -14.6175140350501 +726000 ekin = 0.345932952941823 | erot = 0.625884613514235 | epot = -15.5893316014386 | etot = -14.6175140349825 +727000 ekin = 0.333442641405672 | erot = 0.622003743386422 | epot = -15.5729604197101 | etot = -14.617514034918 +728000 ekin = 0.318857050497248 | erot = 0.619869891937897 | epot = -15.5562409772948 | etot = -14.6175140348596 +729000 ekin = 0.302780724957378 | erot = 0.619758691690217 | epot = -15.5400534514572 | etot = -14.6175140348096 +730000 ekin = 0.285848455041315 | erot = 0.621791770570811 | epot = -15.5251542603814 | etot = -14.6175140347693 +731000 ekin = 0.268701272205162 | erot = 0.625935552811657 | epot = -15.5121508597566 | etot = -14.6175140347398 +732000 ekin = 0.251964649664151 | erot = 0.632007594592174 | epot = -15.5014862789777 | etot = -14.6175140347214 +733000 ekin = 0.236228569496788 | erot = 0.639689689353094 | epot = -15.4934322935639 | etot = -14.617514034714 +734000 ekin = 0.222028960746823 | erot = 0.648546698715163 | epot = -15.4880896941794 | etot = -14.6175140347174 +735000 ekin = 0.209830023527925 | erot = 0.658049804517654 | epot = -15.4853938627761 | etot = -14.6175140347305 +736000 ekin = 0.200007166761159 | erot = 0.667602683399479 | epot = -15.4851238849135 | etot = -14.6175140347528 +737000 ekin = 0.192830719625055 | erot = 0.676569044421098 | epot = -15.4869137988298 | etot = -14.6175140347837 +738000 ekin = 0.188451200585547 | erot = 0.684300102137718 | epot = -15.4902653375453 | etot = -14.6175140348221 +739000 ekin = 0.186887639936592 | erot = 0.690160900651566 | epot = -15.4945625754552 | etot = -14.617514034867 +740000 ekin = 0.188021068410451 | erot = 0.693554915034906 | epot = -15.4990900183625 | etot = -14.6175140349172 +741000 ekin = 0.191595568995028 | erot = 0.693946922730537 | epot = -15.5030565266959 | etot = -14.6175140349703 +742000 ekin = 0.197228843628196 | erot = 0.690884208638673 | epot = -15.5056270872912 | etot = -14.6175140350243 +743000 ekin = 0.20443350363757 | erot = 0.684016821527744 | epot = -15.5059643602408 | etot = -14.6175140350755 +744000 ekin = 0.212648433381533 | erot = 0.673116668202852 | epot = -15.5032791367049 | etot = -14.6175140351205 +745000 ekin = 0.221277722248148 | erot = 0.658094727365387 | epot = -15.496886484769 | etot = -14.6175140351555 +746000 ekin = 0.229733012317517 | erot = 0.639014583781424 | epot = -15.4862616312763 | etot = -14.6175140351774 +747000 ekin = 0.2374740441444 | erot = 0.61610009667291 | epot = -15.4710881760011 | etot = -14.6175140351838 +748000 ekin = 0.244042266762953 | erot = 0.5897348727874 | epot = -15.4512911747243 | etot = -14.617514035174 +749000 ekin = 0.249083597953252 | erot = 0.56045151840338 | epot = -15.4270491515053 | etot = -14.6175140351487 +750000 ekin = 0.252358330147216 | erot = 0.528910066811307 | epot = -15.3987824320685 | etot = -14.61751403511 +751000 ekin = 0.253738423481735 | erot = 0.495866496254582 | epot = -15.3671189547979 | etot = -14.6175140350616 +752000 ekin = 0.253194394015788 | erot = 0.462133785333153 | epot = -15.3328422143563 | etot = -14.6175140350074 +753000 ekin = 0.250775308155868 | erot = 0.428539072350445 | epot = -15.2968284154581 | etot = -14.6175140349518 +754000 ekin = 0.246585878547032 | erot = 0.395880964578706 | epot = -15.2599808780244 | etot = -14.6175140348987 +755000 ekin = 0.240764398113293 | erot = 0.364890850085532 | epot = -15.2231692830501 | etot = -14.6175140348513 +756000 ekin = 0.23346447104344 | erot = 0.33620133003045 | epot = -15.1871798358857 | etot = -14.6175140348118 +757000 ekin = 0.224842467158388 | erot = 0.310323830730243 | epot = -15.1526803326699 | etot = -14.6175140347812 +758000 ekin = 0.215051562421428 | erot = 0.287636293952697 | epot = -15.120201891134 | etot = -14.6175140347599 +759000 ekin = 0.204242275876271 | erot = 0.268380753509857 | epot = -15.0901370641325 | etot = -14.6175140347464 +760000 ekin = 0.192568636065474 | erot = 0.252669695562842 | epot = -15.0627523663679 | etot = -14.6175140347396 +761000 ekin = 0.180198520175885 | erot = 0.240499428911651 | epot = -15.0382119838247 | etot = -14.6175140347371 +762000 ekin = 0.167326299029189 | erot = 0.231768292967787 | epot = -15.0166086267339 | etot = -14.6175140347369 +763000 ekin = 0.154185685901956 | erot = 0.226297425416186 | epot = -14.9979971460548 | etot = -14.6175140347367 +764000 ekin = 0.141060632748886 | erot = 0.22385200334864 | epot = -14.9824266708322 | etot = -14.6175140347347 +765000 ekin = 0.128292252296688 | erot = 0.224161332818126 | epot = -14.9699676198447 | etot = -14.6175140347299 +766000 ekin = 0.116280064488099 | erot = 0.226936813023238 | epot = -14.9607309122326 | etot = -14.6175140347212 +767000 ekin = 0.105476340626969 | erot = 0.23188750727037 | epot = -14.9548778826066 | etot = -14.6175140347093 +768000 ekin = 0.096372890945937 | erot = 0.238733641345087 | epot = -14.9526205669852 | etot = -14.6175140346942 +769000 ekin = 0.0894802427431669 | erot = 0.247218655409017 | epot = -14.9542129328294 | etot = -14.6175140346772 +770000 ekin = 0.0852997361093092 | erot = 0.257120353608164 | epot = -14.9599341243773 | etot = -14.6175140346598 +771000 ekin = 0.0842896183570599 | erot = 0.268261228608835 | epot = -14.9700648816096 | etot = -14.6175140346437 +772000 ekin = 0.0868267987477346 | erot = 0.280517313419992 | epot = -14.9848581467989 | etot = -14.6175140346312 +773000 ekin = 0.0931666172480206 | erot = 0.293824162660099 | epot = -15.0045048145328 | etot = -14.6175140346247 +774000 ekin = 0.103403843826671 | erot = 0.308178073397117 | epot = -15.0290959518505 | etot = -14.6175140346267 +775000 ekin = 0.117439110045757 | erot = 0.323630675217794 | epot = -15.0585838199034 | etot = -14.6175140346399 +776000 ekin = 0.134955835365974 | erot = 0.340275613675452 | epot = -15.0927454837074 | etot = -14.617514034666 +777000 ekin = 0.155413263635979 | erot = 0.358227842745911 | epot = -15.131155141088 | etot = -14.6175140347061 +778000 ekin = 0.178060391221893 | erot = 0.377596905889502 | epot = -15.1731713318714 | etot = -14.61751403476 +779000 ekin = 0.201973803865647 | erot = 0.398457850158065 | epot = -15.2179456888489 | etot = -14.6175140348252 +780000 ekin = 0.226119091214274 | erot = 0.420824480238275 | epot = -15.2644576063504 | etot = -14.6175140348978 +781000 ekin = 0.249431156626622 | erot = 0.444629585314847 | epot = -15.3115747769139 | etot = -14.6175140349725 +782000 ekin = 0.270904470269639 | erot = 0.469715692367583 | epot = -15.3581341976801 | etot = -14.6175140350429 +783000 ekin = 0.289681273783551 | erot = 0.495837747641305 | epot = -15.4030330565279 | etot = -14.617514035103 +784000 ekin = 0.305125009986927 | erot = 0.522676532161923 | epot = -15.445315577297 | etot = -14.6175140351482 +785000 ekin = 0.316868262923434 | erot = 0.549859353707342 | epot = -15.4842416518064 | etot = -14.6175140351756 +786000 ekin = 0.324828845889255 | erot = 0.576983310023016 | epot = -15.5193261910972 | etot = -14.6175140351849 +787000 ekin = 0.32919323387939 | erot = 0.603636505801527 | epot = -15.550343774859 | etot = -14.617514035178 +788000 ekin = 0.330371864852151 | erot = 0.629413875563716 | epot = -15.5772997755747 | etot = -14.6175140351588 +789000 ekin = 0.328934711355495 | erot = 0.653926193132344 | epot = -15.6003749396201 | etot = -14.6175140351322 +790000 ekin = 0.32553731947378 | erot = 0.676802790006292 | epot = -15.6198541445837 | etot = -14.6175140351036 +791000 ekin = 0.320847267933459 | erot = 0.697689943211487 | epot = -15.6360512462227 | etot = -14.6175140350777 +792000 ekin = 0.315479253539392 | erot = 0.716247584423973 | epot = -15.6492408730215 | etot = -14.6175140350582 +793000 ekin = 0.309944490982107 | erot = 0.732146955922051 | epot = -15.6596054819516 | etot = -14.6175140350474 +794000 ekin = 0.304617480925239 | erot = 0.745071299199412 | epot = -15.6672028151708 | etot = -14.6175140350461 +795000 ekin = 0.299720880976423 | erot = 0.754720862084592 | epot = -15.6719557781148 | etot = -14.6175140350538 +796000 ekin = 0.295327396180162 | erot = 0.760822658787278 | epot = -15.6736640900359 | etot = -14.6175140350685 +797000 ekin = 0.291376296851675 | erot = 0.763144639344914 | epot = -15.6720349712838 | etot = -14.6175140350872 +798000 ekin = 0.287701294703707 | erot = 0.761513269131401 | epot = -15.6667285989415 | etot = -14.6175140351064 +799000 ekin = 0.284065979572222 | erot = 0.755832991336602 | epot = -15.6574130060307 | etot = -14.6175140351219 +800000 ekin = 0.280202790631652 | erot = 0.746105645863969 | epot = -15.643822471626 | etot = -14.6175140351304 +801000 ekin = 0.275851560112653 | erot = 0.732447665813264 | epot = -15.6258132610543 | etot = -14.6175140351284 +802000 ekin = 0.270794034433592 | erot = 0.715102809072576 | epot = -15.6034108786199 | etot = -14.6175140351138 +803000 ekin = 0.264881442636465 | erot = 0.694448356025832 | epot = -15.5768438337476 | etot = -14.6175140350853 +804000 ekin = 0.258053167891105 | erot = 0.670993199746629 | epot = -15.5465604026808 | etot = -14.6175140350431 +805000 ekin = 0.250345604728483 | erot = 0.645366941436678 | epot = -15.5132265811537 | etot = -14.6175140349885 +806000 ekin = 0.241890533712104 | erot = 0.618299214644422 | epot = -15.4777037832803 | etot = -14.6175140349238 +807000 ekin = 0.232905655207387 | erot = 0.590591287736433 | epot = -15.4410109777962 | etot = -14.6175140348524 +808000 ekin = 0.223678061733381 | erot = 0.563080896688429 | epot = -15.4042729931999 | etot = -14.6175140347781 +809000 ekin = 0.21454303523099 | erot = 0.536602758842029 | epot = -15.3686598287782 | etot = -14.6175140347052 +810000 ekin = 0.205860488313568 | erot = 0.511947500023896 | epot = -15.3353220229752 | etot = -14.6175140346377 +811000 ekin = 0.197991117806005 | erot = 0.489821758278081 | epot = -15.3053269106636 | etot = -14.6175140345795 +812000 ekin = 0.191273941671524 | erot = 0.470812030934271 | epot = -15.2796000071394 | etot = -14.6175140345336 +813000 ekin = 0.186006404369985 | erot = 0.455354451062655 | epot = -15.2588748899354 | etot = -14.6175140345028 +814000 ekin = 0.18242775371236 | erot = 0.443712201374096 | epot = -15.243653989575 | etot = -14.6175140344885 +815000 ekin = 0.18070598633541 | erot = 0.435961774091635 | epot = -15.234181794919 | etot = -14.617514034492 +816000 ekin = 0.180928373605491 | erot = 0.431988814113314 | epot = -15.2304312222317 | etot = -14.6175140345129 +817000 ekin = 0.183095431234183 | erot = 0.431493858263631 | epot = -15.2321033240486 | etot = -14.6175140345508 +818000 ekin = 0.187118173911464 | erot = 0.434007895069526 | epot = -15.2386401035849 | etot = -14.6175140346039 +819000 ekin = 0.192818568053382 | erot = 0.43891728680681 | epot = -15.2492498895299 | etot = -14.6175140346697 +820000 ekin = 0.199933211814771 | erot = 0.445497181488374 | epot = -15.2629444280486 | etot = -14.6175140347454 +821000 ekin = 0.208120374081953 | erot = 0.452952069483821 | epot = -15.2785864783931 | etot = -14.6175140348273 +822000 ekin = 0.216970558498266 | erot = 0.460461605795678 | epot = -15.2949461992054 | etot = -14.6175140349114 +823000 ekin = 0.226020685629111 | erot = 0.467229260922827 | epot = -15.3107639815452 | etot = -14.6175140349933 +824000 ekin = 0.234771793851546 | erot = 0.47253085821668 | epot = -15.3248166871369 | etot = -14.6175140350687 +825000 ekin = 0.242709867661982 | erot = 0.475759712130438 | epot = -15.3359836149259 | etot = -14.6175140351335 +826000 ekin = 0.249329060857897 | erot = 0.476465014357233 | epot = -15.3433081103994 | etot = -14.6175140351843 +827000 ekin = 0.254156259485738 | erot = 0.474380409602743 | epot = -15.3460507043067 | etot = -14.6175140352182 +828000 ekin = 0.256775693170762 | erot = 0.46944038334452 | epot = -15.3437301117489 | etot = -14.6175140352336 +829000 ekin = 0.256852201216661 | erot = 0.461783092102077 | epot = -15.3361493285486 | etot = -14.6175140352298 +830000 ekin = 0.254151805816721 | erot = 0.451739467041208 | epot = -15.3234053080651 | etot = -14.6175140352072 +831000 ekin = 0.248558416433736 | erot = 0.439809632306583 | epot = -15.3058820839077 | etot = -14.6175140351674 +832000 ekin = 0.240085737091052 | erot = 0.426628719076076 | epot = -15.2842284912797 | etot = -14.6175140351126 +833000 ekin = 0.228883712687689 | erot = 0.412924890624274 | epot = -15.2593226383577 | etot = -14.6175140350458 +834000 ekin = 0.215239082681844 | erot = 0.399472764056086 | epot = -15.2322258817084 | etot = -14.6175140349705 +835000 ekin = 0.199569787294665 | erot = 0.387045440519586 | epot = -15.2041292627046 | etot = -14.6175140348904 +836000 ekin = 0.182413100763772 | erot = 0.376368114580803 | epot = -15.1762952501539 | etot = -14.6175140348093 +837000 ekin = 0.164407483062706 | erot = 0.36807582593139 | epot = -15.1499973437255 | etot = -14.6175140347314 +838000 ekin = 0.146268295773454 | erot = 0.362677435797712 | epot = -15.1264597662312 | etot = -14.61751403466 +839000 ekin = 0.128757768426402 | erot = 0.360527421580405 | epot = -15.1067992246056 | etot = -14.6175140345988 +840000 ekin = 0.112649960717984 | erot = 0.361806618656283 | epot = -15.091970613925 | etot = -14.6175140345507 +841000 ekin = 0.0986919456677054 | erot = 0.366512603929069 | epot = -15.0827185841153 | etot = -14.6175140345185 +842000 ekin = 0.0875630029234395 | erot = 0.374460003555771 | epot = -15.0795370409833 | etot = -14.6175140345041 +843000 ekin = 0.0798341847686366 | erot = 0.385290606532762 | epot = -15.08263882581 | etot = -14.6175140345086 +844000 ekin = 0.0759310929907395 | erot = 0.3984927697296 | epot = -15.0919378972525 | etot = -14.6175140345322 +845000 ekin = 0.076102961020352 | erot = 0.413429207168617 | epot = -15.107046202763 | etot = -14.617514034574 +846000 ekin = 0.0804010613290235 | erot = 0.429371869322532 | epot = -15.1272869652841 | etot = -14.6175140346325 +847000 ekin = 0.0886689809240873 | erot = 0.445542241998021 | epot = -15.1517252576265 | etot = -14.6175140347044 +848000 ekin = 0.100546421459775 | erot = 0.461155038711605 | epot = -15.179215494957 | etot = -14.6175140347856 +849000 ekin = 0.115486960010826 | erot = 0.475462945351677 | epot = -15.208463940234 | etot = -14.6175140348715 +850000 ekin = 0.132788806695669 | erot = 0.487799837752774 | epot = -15.2381026794056 | etot = -14.6175140349571 +851000 ekin = 0.15163622778631 | erot = 0.49761978557658 | epot = -15.2667700483999 | etot = -14.617514035037 +852000 ekin = 0.171148194576093 | erot = 0.5045292426275 | epot = -15.2931914723102 | etot = -14.6175140351066 +853000 ekin = 0.19043015939564 | erot = 0.508310157461229 | epot = -15.3162543520185 | etot = -14.6175140351617 +854000 ekin = 0.208624756899512 | erot = 0.508932337650922 | epot = -15.3350711297497 | etot = -14.6175140351993 +855000 ekin = 0.224957674812131 | erot = 0.506554231539335 | epot = -15.3490259415692 | etot = -14.6175140352178 +856000 ekin = 0.238775816538934 | erot = 0.501512259960027 | epot = -15.3578021117156 | etot = -14.6175140352166 +857000 ekin = 0.249575992233887 | erot = 0.494299801981668 | epot = -15.3613898294122 | etot = -14.6175140351967 +858000 ekin = 0.257023502073677 | erot = 0.485537766821904 | epot = -15.3600753040553 | etot = -14.6175140351598 +859000 ekin = 0.260960921285557 | erot = 0.47593924761589 | epot = -15.3544142040099 | etot = -14.6175140351084 +860000 ekin = 0.261408037072254 | erot = 0.466270984604724 | epot = -15.3451930567227 | etot = -14.6175140350457 +861000 ekin = 0.258554187538227 | erot = 0.457314264403266 | epot = -15.3333824869164 | etot = -14.6175140349749 +862000 ekin = 0.252744258033032 | erot = 0.449827506886351 | epot = -15.3200857998187 | etot = -14.6175140348993 +863000 ekin = 0.24445941779656 | erot = 0.444512141834286 | epot = -15.3064855944532 | etot = -14.6175140348224 +864000 ekin = 0.234293368840191 | erot = 0.441983030939893 | epot = -15.2937904345275 | etot = -14.6175140347474 +865000 ekin = 0.222924696624028 | erot = 0.442744308395087 | epot = -15.2831830396966 | etot = -14.6175140346775 +866000 ekin = 0.211086026109153 | erot = 0.447169652381141 | epot = -15.275769713106 | etot = -14.6175140346157 +867000 ekin = 0.199530465892741 | erot = 0.455487658924214 | epot = -15.2725321593816 | etot = -14.6175140345647 +868000 ekin = 0.188996288427104 | erot = 0.467771811643747 | epot = -15.2742821345979 | etot = -14.6175140345271 +869000 ekin = 0.180171161859106 | erot = 0.483934855626885 | epot = -15.2816200519912 | etot = -14.6175140345052 +870000 ekin = 0.17365741386822 | erot = 0.503727420429673 | epot = -15.2948988687985 | etot = -14.6175140345006 +871000 ekin = 0.169940429081846 | erot = 0.52674119313203 | epot = -15.3141956567285 | etot = -14.6175140345146 +872000 ekin = 0.169362274178155 | erot = 0.552417088945952 | epot = -15.3392933976716 | etot = -14.6175140345475 +873000 ekin = 0.172102391201285 | erot = 0.580058846014358 | epot = -15.3696752718142 | etot = -14.6175140345986 +874000 ekin = 0.17816700290151 | erot = 0.608852557307893 | epot = -15.4045335948759 | etot = -14.6175140346665 +875000 ekin = 0.187388233890407 | erot = 0.637892396630087 | epot = -15.4427946652692 | etot = -14.6175140347487 +876000 ekin = 0.19943318136702 | erot = 0.666212376945529 | epot = -15.4831595931541 | etot = -14.6175140348415 +877000 ekin = 0.213822249050307 | erot = 0.692823325238237 | epot = -15.5241596092293 | etot = -14.6175140349407 +878000 ekin = 0.229955728385699 | erot = 0.71675421264508 | epot = -15.5642239760723 | etot = -14.6175140350415 +879000 ekin = 0.24714610464469 | erot = 0.737095186135096 | epot = -15.6017553259188 | etot = -14.617514035139 +880000 ekin = 0.264653797001986 | erot = 0.753040153406107 | epot = -15.6352079856364 | etot = -14.6175140352283 +881000 ekin = 0.281723784261025 | erot = 0.763926241591362 | epot = -15.6631640611574 | etot = -14.617514035305 +882000 ekin = 0.297620641606497 | erot = 0.769267373447878 | epot = -15.6844020504201 | etot = -14.6175140353657 +883000 ekin = 0.31165996716591 | erot = 0.768779581882635 | epot = -15.6979535844562 | etot = -14.6175140354077 +884000 ekin = 0.32323477376766 | erot = 0.762396270684418 | epot = -15.7031450798815 | etot = -14.6175140354294 +885000 ekin = 0.331836099624976 | erot = 0.750272396067649 | epot = -15.6996225311232 | etot = -14.6175140354305 +886000 ekin = 0.33706775156376 | erot = 0.73277738526586 | epot = -15.6873591722413 | etot = -14.6175140354116 +887000 ekin = 0.33865564976609 | erot = 0.710477420750346 | epot = -15.6666471058906 | etot = -14.6175140353742 +888000 ekin = 0.336452632420724 | erot = 0.684108417156207 | epot = -15.6380750848973 | etot = -14.6175140353203 +889000 ekin = 0.330439768515565 | erot = 0.654541548240145 | epot = -15.6024953520085 | etot = -14.6175140352528 +890000 ekin = 0.320725208484774 | erot = 0.622743520027188 | epot = -15.5609827636863 | etot = -14.6175140351743 +891000 ekin = 0.30754138620901 | erot = 0.589733936087593 | epot = -15.5147893573847 | etot = -14.6175140350881 +892000 ekin = 0.291240998129824 | erot = 0.55654208039805 | epot = -15.4652971135248 | etot = -14.6175140349969 +893000 ekin = 0.272291667891339 | erot = 0.524165278720875 | epot = -15.413970981516 | etot = -14.6175140349038 +894000 ekin = 0.251268620703469 | erot = 0.493530718297772 | epot = -15.3623133738123 | etot = -14.617514034811 +895000 ekin = 0.228844131843647 | erot = 0.465462234286628 | epot = -15.3118204008517 | etot = -14.6175140347214 +896000 ekin = 0.205772103521931 | erot = 0.44065313730724 | epot = -15.2639392754666 | etot = -14.6175140346374 +897000 ekin = 0.182866017803037 | erot = 0.419645693758354 | epot = -15.2200257461231 | etot = -14.6175140345617 +898000 ekin = 0.160968870008541 | erot = 0.402817425242934 | epot = -15.1813003297485 | etot = -14.617514034497 +899000 ekin = 0.140914625128407 | erot = 0.390374024162942 | epot = -15.1488026837377 | etot = -14.6175140344464 +900000 ekin = 0.123482269337592 | erot = 0.382348451689143 | epot = -15.1233447554393 | etot = -14.6175140344126 +901000 ekin = 0.109345484385137 | erot = 0.3786057375543 | epot = -15.1054652563377 | etot = -14.6175140343982 +902000 ekin = 0.0990229789068443 | erot = 0.378853140166087 | epot = -15.0953901534781 | etot = -14.6175140344052 +903000 ekin = 0.0928360184564003 | erot = 0.382655585825594 | epot = -15.0930056387161 | etot = -14.6175140344341 +904000 ekin = 0.0908801123879861 | erot = 0.389456554773426 | epot = -15.0978507016452 | etot = -14.6175140344838 +905000 ekin = 0.0930167096525759 | erot = 0.398604648849945 | epot = -15.109135393054 | etot = -14.6175140345515 +906000 ekin = 0.0988880708462299 | erot = 0.409385812369135 | epot = -15.1257879178477 | etot = -14.6175140346323 +907000 ekin = 0.107954659147321 | erot = 0.421060528764021 | epot = -15.1465292226317 | etot = -14.6175140347203 +908000 ekin = 0.119550305154264 | erot = 0.432904367174404 | epot = -15.1699687071371 | etot = -14.6175140348085 +909000 ekin = 0.132947118364171 | erot = 0.44424923215812 | epot = -15.1947103854124 | etot = -14.6175140348901 +910000 ekin = 0.147420543333256 | erot = 0.454521879656354 | epot = -15.2194564579492 | etot = -14.6175140349595 +911000 ekin = 0.162305506309105 | erot = 0.463275978359162 | epot = -15.243095519681 | etot = -14.6175140350127 +912000 ekin = 0.177037050912775 | erot = 0.470214361754759 | epot = -15.264765447715 | etot = -14.6175140350475 +913000 ekin = 0.191172462463145 | erot = 0.47519909256641 | epot = -15.2838855900937 | etot = -14.6175140350641 +914000 ekin = 0.204395616840717 | erot = 0.478248345048037 | epot = -15.3001579969529 | etot = -14.6175140350642 +915000 ekin = 0.216507238695372 | erot = 0.479520616572283 | epot = -15.3135418903184 | etot = -14.6175140350507 +916000 ekin = 0.227406352399354 | erot = 0.479288139236181 | epot = -15.324208526663 | etot = -14.6175140350275 +917000 ekin = 0.237068358848421 | erot = 0.47790239272317 | epot = -15.3324847865699 | etot = -14.6175140349983 +918000 ekin = 0.245524170399261 | erot = 0.475755244752224 | epot = -15.3387934501184 | etot = -14.6175140349669 +919000 ekin = 0.252843202023974 | erot = 0.473239468155706 | epot = -15.343596705116 | etot = -14.6175140349363 +920000 ekin = 0.259121284815254 | erot = 0.470712244290015 | epot = -15.3473475640143 | etot = -14.617514034909 +921000 ekin = 0.264473144076574 | erot = 0.468464808092157 | epot = -15.3504519870554 | etot = -14.6175140348867 +922000 ekin = 0.269028180853983 | erot = 0.466700668341734 | epot = -15.3532428840659 | etot = -14.6175140348701 +923000 ekin = 0.272927944745736 | erot = 0.465523908452108 | epot = -15.3559658880573 | etot = -14.6175140348595 +924000 ekin = 0.276323793829006 | erot = 0.464938026324777 | epot = -15.3587758550082 | etot = -14.6175140348544 +925000 ekin = 0.279373649323259 | erot = 0.46485472138072 | epot = -15.361742405558 | etot = -14.617514034854 +926000 ekin = 0.282237300897742 | erot = 0.465111106681027 | epot = -15.3648624424358 | etot = -14.617514034857 +927000 ekin = 0.285070250341507 | erot = 0.465493135293317 | epot = -15.368077420497 | etot = -14.6175140348622 +928000 ekin = 0.288016501944515 | erot = 0.465762600718122 | epot = -15.3712931375312 | etot = -14.6175140348685 +929000 ekin = 0.291201026098165 | erot = 0.465684740678949 | epot = -15.3743998016517 | etot = -14.6175140348746 +930000 ekin = 0.294722459178849 | erot = 0.465054261989122 | epot = -15.3772907560474 | etot = -14.6175140348794 +931000 ekin = 0.298646764015069 | erot = 0.463717248452617 | epot = -15.37987804735 | etot = -14.6175140348823 +932000 ekin = 0.303002304639518 | erot = 0.461587311532337 | epot = -15.3821036510548 | etot = -14.6175140348829 +933000 ekin = 0.307776651094703 | erot = 0.458654945590446 | epot = -15.3839456315665 | etot = -14.6175140348813 +934000 ekin = 0.312915338271949 | erot = 0.454989722654232 | epot = -15.3854190958038 | etot = -14.6175140348776 +935000 ekin = 0.318322768321298 | erot = 0.450735625549576 | epot = -15.3865724287433 | etot = -14.6175140348724 +936000 ekin = 0.323865441581078 | erot = 0.4461003856938 | epot = -15.3874798621412 | etot = -14.6175140348663 +937000 ekin = 0.329377658420705 | erot = 0.441340069469478 | epot = -15.3882317627502 | etot = -14.61751403486 +938000 ekin = 0.334669609401419 | erot = 0.43674015463711 | epot = -15.3889237988925 | etot = -14.617514034854 +939000 ekin = 0.339538182698638 | erot = 0.43259572362611 | epot = -15.3896479411737 | etot = -14.6175140348489 +940000 ekin = 0.343779460435286 | erot = 0.429190561371808 | epot = -15.3904840566521 | etot = -14.617514034845 +941000 ekin = 0.347202304174038 | erot = 0.426777065358206 | epot = -15.3914934043749 | etot = -14.6175140348427 +942000 ekin = 0.349642062607923 | erot = 0.425558062624919 | epot = -15.3927141600748 | etot = -14.617514034842 +943000 ekin = 0.350973206935894 | erot = 0.425671371650785 | epot = -15.3941586134297 | etot = -14.617514034843 +944000 ekin = 0.351119786154916 | erot = 0.427178062459289 | epot = -15.3958118834598 | etot = -14.6175140348456 +945000 ekin = 0.350062816508881 | erot = 0.430055404933721 | epot = -15.3976322562924 | etot = -14.6175140348498 +946000 ekin = 0.347844068536826 | erot = 0.43419544779 | epot = -15.399553551182 | etot = -14.6175140348552 +947000 ekin = 0.344566017441624 | erot = 0.439410327984555 | epot = -15.4014903802875 | etot = -14.6175140348614 +948000 ekin = 0.340388212507466 | erot = 0.445444378277408 | epot = -15.4033466256523 | etot = -14.6175140348674 +949000 ekin = 0.335520427168573 | erot = 0.451992965714934 | epot = -15.405027427756 | etot = -14.6175140348725 +950000 ekin = 0.330213181196302 | erot = 0.458727107975965 | epot = -15.4064543240477 | etot = -14.6175140348755 +951000 ekin = 0.32474581655651 | erot = 0.465321341197607 | epot = -15.4075811926297 | etot = -14.6175140348755 +952000 ekin = 0.319412679962215 | erot = 0.471482169177628 | epot = -15.4084088840117 | etot = -14.6175140348718 +953000 ekin = 0.314508037100187 | erot = 0.476974139327395 | epot = -15.4089962112918 | etot = -14.6175140348642 +954000 ekin = 0.310309685024338 | erot = 0.48163943141798 | epot = -15.4094631512954 | etot = -14.6175140348531 +955000 ekin = 0.307061947765172 | erot = 0.485408201613879 | epot = -15.4099841842186 | etot = -14.6175140348396 +956000 ekin = 0.304958921288845 | erot = 0.488297803841432 | epot = -15.4107707599557 | etot = -14.6175140348254 +957000 ekin = 0.304129209168544 | erot = 0.490400499132465 | epot = -15.412043743114 | etot = -14.617514034813 +958000 ekin = 0.30462371461979 | erot = 0.491860923621405 | epot = -15.4139986730458 | etot = -14.6175140348046 +959000 ekin = 0.306408207891338 | erot = 0.492846142548894 | epot = -15.4167683852429 | etot = -14.6175140348027 +960000 ekin = 0.309362278812989 | erot = 0.493512316198202 | epot = -15.4203886298201 | etot = -14.6175140348089 +961000 ekin = 0.313285873784586 | erot = 0.493972653387296 | epot = -15.4247725619958 | etot = -14.6175140348239 +962000 ekin = 0.31791392478401 | erot = 0.494271324762717 | epot = -15.429699284394 | etot = -14.6175140348473 +963000 ekin = 0.322938673952677 | erot = 0.49436733773729 | epot = -15.4348200465674 | etot = -14.6175140348775 +964000 ekin = 0.328038281530642 | erot = 0.494131108238433 | epot = -15.4396834246807 | etot = -14.6175140349116 +965000 ekin = 0.332909295682699 | erot = 0.493354750676295 | epot = -15.4437780813051 | etot = -14.6175140349461 +966000 ekin = 0.33729968976251 | erot = 0.491775167781853 | epot = -15.4465888925212 | etot = -14.6175140349768 +967000 ekin = 0.341038574326505 | erot = 0.489107134739274 | epot = -15.4476597440655 | etot = -14.6175140349998 +968000 ekin = 0.344058508086205 | erot = 0.485082040988283 | epot = -15.446654584086 | etot = -14.6175140350116 +969000 ekin = 0.346406687226292 | erot = 0.479487053292162 | epot = -15.4434077755287 | etot = -14.6175140350102 +970000 ekin = 0.348242259950603 | erot = 0.472199376075359 | epot = -15.4379556710211 | etot = -14.6175140349951 +971000 ekin = 0.34981857790832 | erot = 0.46321104020783 | epot = -15.4305436530838 | etot = -14.6175140349677 +972000 ekin = 0.351451221504254 | erot = 0.452641107454446 | epot = -15.4216063638894 | etot = -14.6175140349307 +973000 ekin = 0.353474851841754 | erot = 0.440734047140903 | epot = -15.4117229338711 | etot = -14.6175140348884 +974000 ekin = 0.356193968986792 | erot = 0.42784496232361 | epot = -15.4015529661561 | etot = -14.6175140348457 +975000 ekin = 0.359834072253393 | erot = 0.414413971021987 | epot = -15.3917620780828 | etot = -14.6175140348074 +976000 ekin = 0.364500158165202 | erot = 0.400933139115816 | epot = -15.3829473320587 | etot = -14.6175140347777 +977000 ekin = 0.370148756532482 | erot = 0.387909813697021 | epot = -15.3755726049891 | etot = -14.6175140347596 +978000 ekin = 0.376577842833215 | erot = 0.375830059083025 | epot = -15.3699219366707 | etot = -14.6175140347545 +979000 ekin = 0.38343628910019 | erot = 0.365125297246779 | epot = -15.3660756211092 | etot = -14.6175140347622 +980000 ekin = 0.390251542223294 | erot = 0.35614439745949 | epot = -15.3639099744643 | etot = -14.6175140347816 +981000 ekin = 0.396471539317082 | erot = 0.349132547197932 | epot = -15.3631181213249 | etot = -14.6175140348099 +982000 ekin = 0.401514997593021 | erot = 0.344217435799683 | epot = -15.3632464682369 | etot = -14.6175140348442 +983000 ekin = 0.40482345877132 | erot = 0.341402706416172 | epot = -15.3637402000689 | etot = -14.6175140348814 +984000 ekin = 0.40590886668651 | erot = 0.340568324597744 | epot = -15.3639912262029 | etot = -14.6175140349187 +985000 ekin = 0.40439180306127 | erot = 0.341477444720355 | epot = -15.3633832827352 | etot = -14.6175140349536 +986000 ekin = 0.400027422801574 | erot = 0.34378943446128 | epot = -15.361330892247 | etot = -14.6175140349842 +987000 ekin = 0.392718180745197 | erot = 0.347078806738211 | epot = -15.3573110224925 | etot = -14.617514035009 +988000 ekin = 0.38251423921461 | erot = 0.35085976914659 | epot = -15.3508880433883 | etot = -14.6175140350271 +989000 ekin = 0.369603726654237 | erot = 0.354615837188711 | epot = -15.3417335988804 | etot = -14.6175140350375 +990000 ekin = 0.354295674461643 | erot = 0.357833454087933 | epot = -15.3296431635888 | etot = -14.6175140350392 +991000 ekin = 0.336998529351755 | erot = 0.360037895318059 | epot = -15.3145504597015 | etot = -14.6175140350317 +992000 ekin = 0.318196763890793 | erot = 0.360829065190808 | epot = -15.2965398640958 | etot = -14.6175140350142 +993000 ekin = 0.298427479538949 | erot = 0.359914303089432 | epot = -15.275855817615 | etot = -14.6175140349866 +994000 ekin = 0.278258203580391 | erot = 0.357135170965373 | epot = -15.2529074094948 | etot = -14.617514034949 +995000 ekin = 0.258266471895345 | erot = 0.352485480212691 | epot = -15.2282659870101 | etot = -14.617514034902 +996000 ekin = 0.239021351636229 | erot = 0.346118523027927 | epot = -15.2026539095112 | etot = -14.617514034847 +997000 ekin = 0.221066818081289 | erot = 0.338342492442898 | epot = -15.1769233453102 | etot = -14.617514034786 +998000 ekin = 0.204906835818331 | erot = 0.329604233509071 | epot = -15.1520251040488 | etot = -14.6175140347214 +999000 ekin = 0.190992053959174 | erot = 0.320462575795008 | epot = -15.1289686644104 | etot = -14.6175140346562 +1000000 ekin = 0.179708146665509 | erot = 0.311553394429298 | epot = -15.1087755756885 | etot = -14.6175140345937 + 1000000 0.013311715 -1.5443684 0.033490821 -1.4929067 -3.7544839e-05 +Loop time of 20.4903 on 1 procs for 1000000 steps with 10 atoms + +Performance: 42166.322 tau/day, 48803.614 timesteps/s +98.3% CPU use with 1 MPI tasks x no OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 16.542 | 16.542 | 16.542 | 0.0 | 80.73 +Bond | 0.62224 | 0.62224 | 0.62224 | 0.0 | 3.04 +Neigh | 0 | 0 | 0 | 0.0 | 0.00 +Comm | 0.21974 | 0.21974 | 0.21974 | 0.0 | 1.07 +Output | 7e-06 | 7e-06 | 7e-06 | 0.0 | 0.00 +Modify | 2.7798 | 2.7798 | 2.7798 | 0.0 | 13.57 +Other | | 0.3269 | | | 1.60 + +Nlocal: 10 ave 10 max 10 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 0 ave 0 max 0 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 45 ave 45 max 45 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 45 +Ave neighs/atom = 4.5 +Ave special neighs/atom = 3.6 +Neighbor list builds = 0 +Dangerous builds = 0 + +#write_restart config.${number}.* +Total wall time: 0:00:20 diff --git a/examples/USER/cgdna/examples/oxDNA2/duplex1/log.18Jun19.duplex1.g++.4 b/examples/USER/cgdna/examples/oxDNA2/duplex1/log.18Jun19.duplex1.g++.4 new file mode 100644 index 0000000000..9856a9c95b --- /dev/null +++ b/examples/USER/cgdna/examples/oxDNA2/duplex1/log.18Jun19.duplex1.g++.4 @@ -0,0 +1,1172 @@ +LAMMPS (18 Jun 2019) +variable number equal 1 +variable ofreq equal 1000 +variable efreq equal 1000 +variable T equal 0.1 + +units lj + +dimension 3 + +newton off + +boundary p p p + +atom_style hybrid bond ellipsoid +atom_modify sort 0 1.0 + +# Pair interactions require lists of neighbours to be calculated +neighbor 1.0 bin +neigh_modify every 1 delay 0 check yes + +read_data data.duplex1 + orthogonal box = (-20 -20 -20) to (20 20 20) + 1 by 2 by 2 MPI processor grid + reading atoms ... + 10 atoms + reading velocities ... + 10 velocities + 10 ellipsoids + scanning bonds ... + 2 = max bonds/atom + reading bonds ... + 8 bonds + 2 = max # of 1-2 neighbors + 2 = max # of 1-3 neighbors + 2 = max # of 1-4 neighbors + 4 = max # of special neighbors + special bonds CPU = 0.000196 secs + read_data CPU = 0.003266 secs + +set atom * mass 3.1575 + 10 settings made for mass + +group all type 1 4 +10 atoms in group all + +# oxDNA bond interactions - FENE backbone +bond_style oxdna2/fene +bond_coeff * 2.0 0.25 0.7564 + +# oxDNA pair interactions +pair_style hybrid/overlay oxdna2/excv oxdna2/stk oxdna2/hbond oxdna2/xstk oxdna2/coaxstk oxdna2/dh +pair_coeff * * oxdna2/excv 2.0 0.7 0.675 2.0 0.515 0.5 2.0 0.33 0.32 +pair_coeff * * oxdna2/stk seqav ${T} 1.3523 2.6717 6.0 0.4 0.9 0.32 0.6 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2.0 0.65 2.0 0.65 +pair_coeff * * oxdna2/stk seqav 0.1 1.3523 2.6717 6.0 0.4 0.9 0.32 0.6 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2.0 0.65 2.0 0.65 +pair_coeff * * oxdna2/hbond seqav 0.0 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45 +pair_coeff 1 4 oxdna2/hbond seqav 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45 +pair_coeff 2 3 oxdna2/hbond seqav 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45 +pair_coeff * * oxdna2/xstk 47.5 0.575 0.675 0.495 0.655 2.25 0.791592653589793 0.58 1.7 1.0 0.68 1.7 1.0 0.68 1.5 0 0.65 1.7 0.875 0.68 1.7 0.875 0.68 +pair_coeff * * oxdna2/coaxstk 58.5 0.4 0.6 0.22 0.58 2.0 2.891592653589793 0.65 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 40.0 3.116592653589793 +pair_coeff * * oxdna2/dh ${T} 1.0 0.815 +pair_coeff * * oxdna2/dh 0.1 1.0 0.815 + +# NVE ensemble +fix 1 all nve/dot +#fix 1 all nve/dotc/langevin ${T} ${T} 0.03 457145 angmom 10 +#fix 1 all nve/asphere +#fix 2 all langevin ${T} ${T} 0.03 457145 angmom 10 + +timestep 1e-5 + +#comm_style tiled +#fix 3 all balance 10000 1.1 rcb + +#compute mol all chunk/atom molecule +#compute mychunk all vcm/chunk mol +#fix 4 all ave/time 10000 1 10000 c_mychunk[1] c_mychunk[2] c_mychunk[3] file vcm.txt mode vector + +#dump pos all xyz ${ofreq} traj.${number}.xyz + +#compute quat all property/atom quatw quati quatj quatk +#dump quat all custom ${ofreq} quat.${number}.txt id c_quat[1] c_quat[2] c_quat[3] c_quat[4] +#dump_modify quat sort id +#dump_modify quat format line "%d %13.6le %13.6le %13.6le %13.6le" + +compute erot all erotate/asphere +compute ekin all ke +compute epot all pe +variable erot equal c_erot +variable ekin equal c_ekin +variable epot equal c_epot +variable etot equal c_erot+c_ekin+c_epot +fix 5 all print ${efreq} "$(step) ekin = ${ekin} | erot = ${erot} | epot = ${epot} | etot = ${etot}" screen yes +fix 5 all print 1000 "$(step) ekin = ${ekin} | erot = ${erot} | epot = ${epot} | etot = ${etot}" screen yes + +#dump out all custom ${ofreq} out.${number}.txt id x y z vx vy vz fx fy fz tqx tqy tqz +#dump_modify out sort id +#dump_modify out format line "%d %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le" + +run 1000000 +Neighbor list info ... + update every 1 steps, delay 0 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 2.6274 + ghost atom cutoff = 2.6274 + binsize = 1.3137, bins = 31 31 31 + 6 neighbor lists, perpetual/occasional/extra = 6 0 0 + (1) pair oxdna2/excv, perpetual + attributes: half, newton off + pair build: half/bin/newtoff + stencil: half/bin/3d/newtoff + bin: standard + (2) pair oxdna2/stk, perpetual, copy from (1) + attributes: half, newton off + pair build: copy + stencil: none + bin: none + (3) pair oxdna2/hbond, perpetual, copy from (1) + attributes: half, newton off + pair build: copy + stencil: none + bin: none + (4) pair oxdna2/xstk, perpetual, copy from (1) + attributes: half, newton off + pair build: copy + stencil: none + bin: none + (5) pair oxdna2/coaxstk, perpetual, copy from (1) + attributes: half, newton off + pair build: copy + stencil: none + bin: none + (6) pair oxdna2/dh, perpetual, copy from (1) + attributes: half, newton off + pair build: copy + stencil: none + bin: none +Per MPI rank memory allocation (min/avg/max) = 7.652 | 7.834 | 8.016 Mbytes +Step Temp E_pair E_mol TotEng Press + 0 0 -1.4712768 0.009525411 -1.4617514 4.663076e-06 +1000 ekin = 0.00113086229080478 | erot = 0.00431010160406708 | epot = -14.6229549982368 | etot = -14.617514034342 +2000 ekin = 0.00448533224342286 | erot = 0.0171407706505013 | epot = -14.6391401372615 | etot = -14.6175140343675 +3000 ekin = 0.0099503525964896 | erot = 0.0381961780846439 | epot = -14.6656605650904 | etot = -14.6175140344093 +4000 ekin = 0.0173418024861991 | erot = 0.0669935184860482 | epot = -14.7018493554381 | etot = -14.6175140344659 +5000 ekin = 0.0264109356285965 | erot = 0.102878288094483 | epot = -14.7468032582586 | etot = -14.6175140345355 +6000 ekin = 0.0368533113591267 | erot = 0.14504542056981 | epot = -14.7994127665446 | etot = -14.6175140346157 +7000 ekin = 0.0483200640564583 | erot = 0.192565862515414 | epot = -14.8583999612755 | etot = -14.6175140347036 +8000 ekin = 0.0604312317605635 | erot = 0.244417870131371 | epot = -14.9223631366881 | etot = -14.6175140347962 +9000 ekin = 0.072790711967127 | erot = 0.299521949931656 | epot = -14.9898266967887 | etot = -14.6175140348899 +10000 ekin = 0.0850022498874609 | erot = 0.356777997217668 | epot = -15.0592942820866 | etot = -14.6175140349815 +11000 ekin = 0.0966857134040954 | erot = 0.415102860829322 | epot = -15.1293026093009 | etot = -14.6175140350675 +12000 ekin = 0.107492790688356 | erot = 0.473466334177699 | epot = -15.1984731600111 | etot = -14.617514035145 +13000 ekin = 0.117121180381612 | erot = 0.530923485009329 | epot = -15.2655587006024 | etot = -14.6175140352115 +14000 ekin = 0.125326348459051 | erot = 0.586641324447251 | epot = -15.3294817081714 | etot = -14.6175140352651 +15000 ekin = 0.131930017119328 | erot = 0.63991810423422 | epot = -15.3893621566583 | etot = -14.6175140353048 +16000 ekin = 0.136824741331405 | erot = 0.690194029500566 | epot = -15.4445328061626 | etot = -14.6175140353306 +17000 ekin = 0.139974218116171 | erot = 0.737052866147306 | epot = -15.4945411196066 | etot = -14.6175140353432 +18000 ekin = 0.141409342139797 | erot = 0.780214750583043 | epot = -15.5391381280668 | etot = -14.617514035344 +19000 ekin = 0.141220424903361 | erot = 0.819521373491177 | epot = -15.5782558337298 | etot = -14.6175140353352 +20000 ekin = 0.139546371890511 | erot = 0.854915474127585 | epot = -15.6119758813374 | etot = -14.6175140353193 +21000 ekin = 0.136561897558541 | erot = 0.886417110947522 | epot = -15.6404930438047 | etot = -14.6175140352986 +22000 ekin = 0.132464002543684 | erot = 0.914099368829796 | epot = -15.6640774066492 | etot = -14.6175140352758 +23000 ekin = 0.127458921012898 | erot = 0.938065991541741 | epot = -15.6830389478072 | etot = -14.6175140352525 +24000 ekin = 0.121750582423396 | erot = 0.958432936326346 | epot = -15.6976975539803 | etot = -14.6175140352306 +25000 ekin = 0.115531361419039 | erot = 0.975315142931434 | epot = -15.7083605395612 | etot = -14.6175140352107 +26000 ekin = 0.108975565586195 | erot = 0.988819027952452 | epot = -15.715308628732 | etot = -14.6175140351934 +27000 ekin = 0.102235785319183 | erot = 0.999040485514706 | epot = -15.7187903060122 | etot = -14.6175140351783 +28000 ekin = 0.0954419434320554 | erot = 1.00606759141037 | epot = -15.7190235700075 | etot = -14.6175140351651 +29000 ekin = 0.0887026587346012 | erot = 1.00998681843686 | epot = -15.7162035123244 | etot = -14.6175140351529 +30000 ekin = 0.0821083868016836 | erot = 1.01089138149989 | epot = -15.7105138034423 | etot = -14.6175140351407 +31000 ekin = 0.0757357206090521 | erot = 1.00889031641421 | epot = -15.702140072151 | etot = -14.6175140351278 +32000 ekin = 0.0696522149391935 | erot = 1.00411701390103 | epot = -15.6912832639534 | etot = -14.6175140351132 +33000 ekin = 0.0639211300031737 | erot = 0.996736133736263 | epot = -15.6781712988358 | etot = -14.6175140350964 +34000 ekin = 0.0586055597942697 | erot = 0.986948071944207 | epot = -15.6630676668155 | etot = -14.617514035077 +35000 ekin = 0.0537715085522448 | erot = 0.974990414618501 | epot = -15.6462759582258 | etot = -14.617514035055 +36000 ekin = 0.0494895953267295 | erot = 0.961136064968264 | epot = -15.6281396953257 | etot = -14.6175140350307 +37000 ekin = 0.0458351949408502 | erot = 0.945687966087874 | epot = -15.6090371960337 | etot = -14.617514035005 +38000 ekin = 0.0428869588018996 | erot = 0.928970560853581 | epot = -15.5893715546342 | etot = -14.6175140349787 +39000 ekin = 0.0407237982125063 | erot = 0.911318339680438 | epot = -15.5695561728459 | etot = -14.617514034953 +40000 ekin = 0.0394205547756063 | erot = 0.893062038098217 | epot = -15.5499966278032 | etot = -14.6175140349294 +41000 ekin = 0.0390427256108178 | erot = 0.874513269991183 | epot = -15.5310700305113 | etot = -14.6175140349092 +42000 ekin = 0.0396407506458889 | erot = 0.855948622306388 | epot = -15.5131034078463 | etot = -14.617514034894 +43000 ekin = 0.0412444930542012 | erot = 0.837594480923648 | epot = -15.4963530088627 | etot = -14.6175140348848 +44000 ekin = 0.0438586280729573 | erot = 0.819614069272763 | epot = -15.4809867322283 | etot = -14.6175140348826 +45000 ekin = 0.0474596621514809 | erot = 0.802098297010425 | epot = -15.4670719940496 | etot = -14.6175140348876 +46000 ekin = 0.0519951857190001 | erot = 0.785061947877089 | epot = -15.4545711684958 | etot = -14.6175140348997 +47000 ekin = 0.0573856747188828 | erot = 0.768446392385995 | epot = -15.4433461020223 | etot = -14.6175140349174 +48000 ekin = 0.0635286843628562 | erot = 0.752129335015535 | epot = -15.433172054318 | etot = -14.6175140349396 +49000 ekin = 0.0703046735384702 | erot = 0.735941123250163 | epot = -15.4237598317528 | etot = -14.6175140349642 +50000 ekin = 0.0775831019852491 | erot = 0.719686007780774 | epot = -15.4147831447551 | etot = -14.6175140349891 +51000 ekin = 0.0852270843840623 | erot = 0.703165726694424 | epot = -15.4059068460916 | etot = -14.6175140350132 +52000 ekin = 0.0930950223446157 | erot = 0.686202231165621 | epot = -15.3968112885448 | etot = -14.6175140350346 +53000 ekin = 0.101038429252411 | erot = 0.668656546988554 | epot = -15.3872090112944 | etot = -14.6175140350534 +54000 ekin = 0.108896540979999 | erot = 0.65044172617409 | epot = -15.3768523022237 | etot = -14.6175140350696 +55000 ekin = 0.116489881625605 | erot = 0.631529329347953 | epot = -15.3655332460571 | etot = -14.6175140350836 +56000 ekin = 0.12361610349128 | erot = 0.611950383382754 | epot = -15.3530805219694 | etot = -14.6175140350954 +57000 ekin = 0.130051530400511 | erot = 0.591792721317636 | epot = -15.3393582868229 | etot = -14.6175140351047 +58000 ekin = 0.135560625192868 | erot = 0.571196690673809 | epot = -15.3242713509772 | etot = -14.6175140351105 +59000 ekin = 0.13991335082652 | erot = 0.550350463180971 | epot = -15.307777849119 | etot = -14.6175140351115 +60000 ekin = 0.142907875045205 | erot = 0.529485019663366 | epot = -15.2899069298149 | etot = -14.6175140351063 +61000 ekin = 0.144394224776987 | erot = 0.508867904999859 | epot = -15.2707761648709 | etot = -14.6175140350941 +62000 ekin = 0.14429400378525 | erot = 0.488794507593493 | epot = -15.2506025464535 | etot = -14.6175140350748 +63000 ekin = 0.142612256997681 | erot = 0.469576039422599 | epot = -15.2297023314693 | etot = -14.617514035049 +64000 ekin = 0.139439544726489 | erot = 0.451524344955609 | epot = -15.2084779247008 | etot = -14.6175140350187 +65000 ekin = 0.134944526553205 | erot = 0.434934714914789 | epot = -15.1873932764541 | etot = -14.6175140349861 +66000 ekin = 0.129359146357915 | erot = 0.42006860776795 | epot = -15.1669417890793 | etot = -14.6175140349534 +67000 ekin = 0.122959458763979 | erot = 0.407138362060406 | epot = -15.1476118557473 | etot = -14.6175140349229 +68000 ekin = 0.116045210525348 | erot = 0.396295631876791 | epot = -15.1298548772989 | etot = -14.6175140348967 +69000 ekin = 0.108920722072196 | erot = 0.387624589972286 | epot = -15.1140593469203 | etot = -14.6175140348758 +70000 ekin = 0.10187874072944 | erot = 0.381140173640969 | epot = -15.1005329492312 | etot = -14.6175140348608 +71000 ekin = 0.0951880561483024 | erot = 0.376791007701474 | epot = -15.0894930987017 | etot = -14.6175140348519 +72000 ekin = 0.0890849677261225 | erot = 0.374466237250124 | epot = -15.0810652398251 | etot = -14.6175140348489 +73000 ekin = 0.0837682427021172 | erot = 0.37400534759948 | epot = -15.0752876251526 | etot = -14.617514034851 +74000 ekin = 0.0793969849743902 | erot = 0.375210076750066 | epot = -15.0721210965819 | etot = -14.6175140348574 +75000 ekin = 0.0760907865069309 | erot = 0.377857644571635 | epot = -15.0714624659456 | etot = -14.617514034867 +76000 ekin = 0.073931583490861 | erot = 0.381714646754472 | epot = -15.073160265124 | etot = -14.6175140348787 +77000 ekin = 0.0729667273608691 | erot = 0.386551032955436 | epot = -15.0770317952076 | etot = -14.6175140348913 +78000 ekin = 0.0732128655080132 | erot = 0.392153586682573 | epot = -15.0828804870945 | etot = -14.6175140349039 +79000 ekin = 0.0746602878351816 | erot = 0.398338263928879 | epot = -15.0905125866795 | etot = -14.6175140349154 +80000 ekin = 0.0772774298946258 | erot = 0.404960669862598 | epot = -15.0997521346822 | etot = -14.617514034925 +81000 ekin = 0.0810152396747851 | erot = 0.411923913358685 | epot = -15.1104531879654 | etot = -14.617514034932 +82000 ekin = 0.0858111278281503 | erot = 0.419183131304765 | epot = -15.122508294069 | etot = -14.6175140349361 +83000 ekin = 0.0915922459207823 | erot = 0.426746154030485 | epot = -15.1358524348888 | etot = -14.6175140349375 +84000 ekin = 0.0982778862655832 | erot = 0.434670094582864 | epot = -15.1504620157849 | etot = -14.6175140349364 +85000 ekin = 0.105780875252437 | erot = 0.443054055542249 | epot = -15.1663489657283 | etot = -14.6175140349336 +86000 ekin = 0.114007936320836 | erot = 0.452028591870875 | epot = -15.1835505631216 | etot = -14.6175140349299 +87000 ekin = 0.122859117093393 | erot = 0.461742961599463 | epot = -15.2021161136192 | etot = -14.6175140349264 +88000 ekin = 0.132226490250757 | erot = 0.472351454261397 | epot = -15.2220919794359 | etot = -14.6175140349237 +89000 ekin = 0.141992430435586 | erot = 0.48400015022936 | epot = -15.243506615588 | etot = -14.6175140349231 +90000 ekin = 0.152027823849156 | erot = 0.496815313840275 | epot = -15.2663571726144 | etot = -14.617514034925 +91000 ekin = 0.162190574344531 | erot = 0.510894287760946 | epot = -15.2905988970356 | etot = -14.6175140349301 +92000 ekin = 0.172324730223634 | erot = 0.526299304076921 | epot = -15.3161380692392 | etot = -14.6175140349387 +93000 ekin = 0.182260479602882 | erot = 0.543054150884053 | epot = -15.3428286654374 | etot = -14.6175140349505 +94000 ekin = 0.19181516642483 | erot = 0.561143224560411 | epot = -15.3704724259507 | etot = -14.6175140349654 +95000 ekin = 0.200795384590157 | erot = 0.580512230413436 | epot = -15.398821649987 | etot = -14.6175140349834 +96000 ekin = 0.209000133284529 | erot = 0.601069706845066 | epot = -15.4275838751334 | etot = -14.6175140350038 +97000 ekin = 0.216224974983237 | erot = 0.62268863993255 | epot = -15.4564276499423 | etot = -14.6175140350265 +98000 ekin = 0.222267131485539 | erot = 0.6452076702458 | epot = -15.4849888367823 | etot = -14.617514035051 +99000 ekin = 0.226931474008825 | erot = 0.668431711039527 | epot = -15.5128772201251 | etot = -14.6175140350767 +100000 ekin = 0.230037392185109 | erot = 0.692132125756159 | epot = -15.5396835530446 | etot = -14.6175140351033 +101000 ekin = 0.231426538774162 | erot = 0.716046886548711 | epot = -15.5649874604531 | etot = -14.6175140351302 +102000 ekin = 0.230971416185847 | erot = 0.739881303910146 | epot = -15.5883667552525 | etot = -14.6175140351565 +103000 ekin = 0.228584676860608 | erot = 0.763309953364731 | epot = -15.6094086654068 | etot = -14.6175140351814 +104000 ekin = 0.224228843046253 | erot = 0.78598032692129 | epot = -15.6277232051714 | etot = -14.6175140352039 +105000 ekin = 0.217925953180068 | erot = 0.807518535459536 | epot = -15.6429585238624 | etot = -14.6175140352228 +106000 ekin = 0.209766205881383 | erot = 0.827537066837229 | epot = -15.6548173079557 | etot = -14.6175140352371 +107000 ekin = 0.199914663118832 | erot = 0.845644346598305 | epot = -15.6630730449629 | etot = -14.6175140352458 +108000 ekin = 0.188614735690438 | erot = 0.86145556230374 | epot = -15.6675843332424 | etot = -14.6175140352482 +109000 ekin = 0.176187061060969 | erot = 0.874603999194657 | epot = -15.6683050954996 | etot = -14.617514035244 +110000 ekin = 0.163022626611269 | erot = 0.884752084634178 | epot = -15.6652887464788 | etot = -14.6175140352334 +111000 ekin = 0.149569382110055 | erot = 0.891601400936344 | epot = -15.6586848182636 | etot = -14.6175140352172 +112000 ekin = 0.136312261124298 | erot = 0.894901120601569 | epot = -15.6487274169225 | etot = -14.6175140351967 +113000 ekin = 0.123747404857111 | erot = 0.894454602034433 | epot = -15.635716042065 | etot = -14.6175140351735 +114000 ekin = 0.112352324429236 | erot = 0.89012419645392 | epot = -15.6199905560327 | etot = -14.6175140351496 +115000 ekin = 0.102554569787019 | erot = 0.881834585428133 | epot = -15.601903190342 | etot = -14.6175140351268 +116000 ekin = 0.094702004709198 | erot = 0.869575126615747 | epot = -15.5817911664316 | etot = -14.6175140351067 +117000 ekin = 0.0890378681933156 | erot = 0.853401690495617 | epot = -15.5599535937792 | etot = -14.6175140350902 +118000 ekin = 0.0856833736304911 | erot = 0.833438318820653 | epot = -15.536635727529 | etot = -14.6175140350778 +119000 ekin = 0.0846297171115028 | erot = 0.809878764033866 | epot = -15.5120225162146 | etot = -14.6175140350693 +120000 ekin = 0.0857402026933537 | erot = 0.782987649503194 | epot = -15.4862418872603 | etot = -14.6175140350638 +121000 ekin = 0.0887619781646647 | erot = 0.753100709617513 | epot = -15.4593767228421 | etot = -14.61751403506 +122000 ekin = 0.0933458418333701 | erot = 0.720623403983765 | epot = -15.4314832808735 | etot = -14.6175140350564 +123000 ekin = 0.0990718975136712 | erot = 0.686027198351099 | epot = -15.4026131309163 | etot = -14.6175140350515 +124000 ekin = 0.10547856753477 | erot = 0.649842971568616 | epot = -15.3728355741476 | etot = -14.6175140350442 +125000 ekin = 0.112092583657157 | erot = 0.612651306911466 | epot = -15.3422579256018 | etot = -14.6175140350331 +126000 ekin = 0.118457948669929 | erot = 0.575069793126885 | epot = -15.3110417768148 | etot = -14.6175140350179 +127000 ekin = 0.12416235209736 | erot = 0.537737821904032 | epot = -15.2794142089994 | etot = -14.617514034998 +128000 ekin = 0.12886000047466 | erot = 0.50129966007338 | epot = -15.2476736955216 | etot = -14.6175140349735 +129000 ekin = 0.132290197680968 | erot = 0.466386755141928 | epot = -15.2161909877676 | etot = -14.6175140349447 +130000 ekin = 0.134291248322799 | erot = 0.433600287194598 | epot = -15.1854055704295 | etot = -14.6175140349121 +131000 ekin = 0.134809368078731 | erot = 0.403494917850824 | epot = -15.1558183208059 | etot = -14.6175140348763 +132000 ekin = 0.133902311412609 | erot = 0.376564532721137 | epot = -15.1279808789722 | etot = -14.6175140348384 +133000 ekin = 0.131737425949523 | erot = 0.35323055944927 | epot = -15.102482020198 | etot = -14.6175140347992 +134000 ekin = 0.128583872249503 | erot = 0.333833200744645 | epot = -15.0799311077543 | etot = -14.6175140347601 +135000 ekin = 0.124798858318881 | erot = 0.318625678761018 | epot = -15.0609385718023 | etot = -14.6175140347224 +136000 ekin = 0.120807966950657 | erot = 0.307771366705204 | epot = -15.0460933683435 | etot = -14.6175140346876 +137000 ekin = 0.117080018573046 | erot = 0.301343503849178 | epot = -15.0359375570798 | etot = -14.6175140346576 +138000 ekin = 0.11409740445119 | erot = 0.299327064918184 | epot = -15.0309385040035 | etot = -14.6175140346342 +139000 ekin = 0.112323403877017 | erot = 0.30162229304682 | epot = -15.0314597315429 | etot = -14.6175140346191 +140000 ekin = 0.112168587316825 | erot = 0.308049410073269 | epot = -15.0377320320041 | etot = -14.617514034614 +141000 ekin = 0.113958896787242 | erot = 0.318354084563179 | epot = -15.0498270159708 | etot = -14.6175140346204 +142000 ekin = 0.117908250109871 | erot = 0.332213334114279 | epot = -15.0676356188632 | etot = -14.6175140346391 +143000 ekin = 0.124098500240005 | erot = 0.349241744869171 | epot = -15.0908542797795 | etot = -14.6175140346704 +144000 ekin = 0.132469049162189 | erot = 0.368998042344344 | epot = -15.1189811262203 | etot = -14.6175140347138 +145000 ekin = 0.142817534773286 | erot = 0.390992018433719 | epot = -15.1513235879751 | etot = -14.6175140347681 +146000 ekin = 0.154812002594074 | erot = 0.414692148539669 | epot = -15.1870181859652 | etot = -14.6175140348314 +147000 ekin = 0.168013608208222 | erot = 0.439534147564146 | epot = -15.2250617906734 | etot = -14.617514034901 +148000 ekin = 0.181907755044263 | erot = 0.464930715993231 | epot = -15.2643525060114 | etot = -14.617514034974 +149000 ekin = 0.195940689918476 | erot = 0.490282644231627 | epot = -15.303737369197 | etot = -14.6175140350469 +150000 ekin = 0.209558115498224 | erot = 0.514991307803342 | epot = -15.3420634584183 | etot = -14.6175140351167 +151000 ekin = 0.222242375358764 | erot = 0.538472447670959 | epot = -15.37822885821 | etot = -14.6175140351803 +152000 ekin = 0.233545181100908 | erot = 0.560170967505261 | epot = -15.4112301838413 | etot = -14.6175140352351 +153000 ekin = 0.243113638171877 | erot = 0.579575715964384 | epot = -15.4402033894153 | etot = -14.6175140352791 +154000 ekin = 0.250708030719506 | erot = 0.596234520730852 | epot = -15.4644565867613 | etot = -14.617514035311 +155000 ekin = 0.256210874594867 | erot = 0.60976818504912 | epot = -15.4834930949737 | etot = -14.6175140353297 +156000 ekin = 0.259627463842678 | erot = 0.619882772314523 | epot = -15.4970242714926 | etot = -14.6175140353354 +157000 ekin = 0.261078756733762 | erot = 0.626379517381851 | epot = -15.5049723094439 | etot = -14.6175140353283 +158000 ekin = 0.260787877594799 | erot = 0.629161788909728 | epot = -15.5074637018138 | etot = -14.6175140353093 +159000 ekin = 0.259061752299363 | erot = 0.628238692725143 | epot = -15.5048144803044 | etot = -14.6175140352799 +160000 ekin = 0.256269476947947 | erot = 0.623725097357694 | epot = -15.4975086095473 | etot = -14.6175140352416 +161000 ekin = 0.252818974262676 | erot = 0.615838055764808 | epot = -15.486171065224 | etot = -14.6175140351965 +162000 ekin = 0.249133354780831 | erot = 0.604889772113657 | epot = -15.471537162041 | etot = -14.6175140351465 +163000 ekin = 0.245628201594069 | erot = 0.591277407065719 | epot = -15.4544196437535 | etot = -14.6175140350937 +164000 ekin = 0.242690765770497 | erot = 0.575470125399849 | epot = -15.4356749262106 | etot = -14.6175140350402 +165000 ekin = 0.240661818237638 | erot = 0.557993868663582 | epot = -15.4161697218892 | etot = -14.617514034988 +166000 ekin = 0.239820672159809 | erot = 0.53941438884916 | epot = -15.3967490959478 | etot = -14.6175140349388 +167000 ekin = 0.240373682616981 | erot = 0.520319112884548 | epot = -15.3782068303959 | etot = -14.6175140348944 +168000 ekin = 0.24244635767337 | erot = 0.501298426047094 | epot = -15.3612588185766 | etot = -14.6175140348562 +169000 ekin = 0.246079081489486 | erot = 0.482926967022081 | epot = -15.3465200833369 | etot = -14.6175140348253 +170000 ekin = 0.251226355670601 | erot = 0.465745518941346 | epot = -15.3344859094148 | etot = -14.6175140348028 +171000 ekin = 0.257759407502439 | erot = 0.450244072412675 | epot = -15.3255175147044 | etot = -14.6175140347893 +172000 ekin = 0.265471962314995 | erot = 0.43684655757276 | epot = -15.3198325546728 | etot = -14.617514034785 +173000 ekin = 0.274088992052566 | erot = 0.425897760802307 | epot = -15.317500787645 | etot = -14.6175140347901 +174000 ekin = 0.283278228107989 | erot = 0.417652965987653 | epot = -15.3184452288998 | etot = -14.6175140348041 +175000 ekin = 0.292664164217049 | erot = 0.41227065206718 | epot = -15.3224488511106 | etot = -14.6175140348264 +176000 ekin = 0.301844276743974 | erot = 0.409808663993543 | epot = -15.3291669755933 | etot = -14.6175140348558 +177000 ekin = 0.310407103277722 | erot = 0.410224178773613 | epot = -15.338145316942 | etot = -14.6175140348907 +178000 ekin = 0.317951707448459 | erot = 0.413377690533319 | epot = -15.3488434329112 | etot = -14.6175140349295 +179000 ekin = 0.324107901131331 | erot = 0.419041092199345 | epot = -15.3606630283007 | etot = -14.61751403497 +180000 ekin = 0.328556397748226 | erot = 0.426909726007329 | epot = -15.3729801587658 | etot = -14.6175140350103 +181000 ekin = 0.331047834153872 | erot = 0.436618006902467 | epot = -15.3851798761041 | etot = -14.6175140350478 +182000 ekin = 0.331419420114469 | erot = 0.447757936314679 | epot = -15.3966913915095 | etot = -14.6175140350803 +183000 ekin = 0.32960779233749 | erot = 0.459899520065503 | epot = -15.4070213475091 | etot = -14.6175140351061 +184000 ekin = 0.325656516855028 | erot = 0.472611792133139 | epot = -15.4157823441118 | etot = -14.6175140351236 +185000 ekin = 0.319716934487211 | erot = 0.485483030927449 | epot = -15.4227140005469 | etot = -14.6175140351322 +186000 ekin = 0.312041347782212 | erot = 0.498138700398001 | epot = -15.4276940833121 | etot = -14.6175140351319 +187000 ekin = 0.302968200961153 | erot = 0.510255791848845 | epot = -15.4307380279334 | etot = -14.6175140351234 +188000 ekin = 0.292899787356355 | erot = 0.5215725520513 | epot = -15.4319863745157 | etot = -14.6175140351081 +189000 ekin = 0.282274048055605 | erot = 0.531893031493143 | epot = -15.4316811146372 | etot = -14.6175140350884 +190000 ekin = 0.271533034588949 | erot = 0.541086413296656 | epot = -15.4301334829521 | etot = -14.6175140350665 +191000 ekin = 0.261091384545176 | erot = 0.549081610185661 | epot = -15.4276870297757 | etot = -14.6175140350448 +192000 ekin = 0.251308489707993 | erot = 0.555858063434326 | epot = -15.4246805881679 | etot = -14.6175140350256 +193000 ekin = 0.242467771119499 | erot = 0.561433978654792 | epot = -15.4214157847846 | etot = -14.6175140350103 +194000 ekin = 0.234765581624083 | erot = 0.565853352187983 | epot = -15.4181329688119 | etot = -14.6175140349998 +195000 ekin = 0.228310848060933 | erot = 0.569173077812972 | epot = -15.414997960868 | etot = -14.6175140349941 +196000 ekin = 0.223134890549791 | erot = 0.571451208607789 | epot = -15.4121001341501 | etot = -14.6175140349925 +197000 ekin = 0.219209242155479 | erot = 0.572737138234515 | epot = -15.4094604153842 | etot = -14.6175140349942 +198000 ekin = 0.216468062808567 | erot = 0.573064123809139 | epot = -15.4070462216157 | etot = -14.6175140349979 +199000 ekin = 0.214831137522102 | erot = 0.572444258405115 | epot = -15.4047894309295 | etot = -14.6175140350023 +200000 ekin = 0.214223573901692 | erot = 0.570865760664587 | epot = -15.402603369573 | etot = -14.6175140350067 +201000 ekin = 0.214589119166338 | erot = 0.568292309388425 | epot = -15.4003954635655 | etot = -14.6175140350107 +202000 ekin = 0.215895325601886 | erot = 0.564664121435212 | epot = -15.3980734820515 | etot = -14.6175140350144 +203000 ekin = 0.218130347569574 | erot = 0.559900543320399 | epot = -15.3955449259083 | etot = -14.6175140350184 +204000 ekin = 0.221292667473328 | erot = 0.553904074219812 | epot = -15.3927107767163 | etot = -14.6175140350232 +205000 ekin = 0.225376258610291 | erot = 0.546565915590092 | epot = -15.3894562092301 | etot = -14.6175140350297 +206000 ekin = 0.230354397528691 | erot = 0.537773288685112 | epot = -15.3856417212522 | etot = -14.6175140350384 +207000 ekin = 0.236165428414371 | erot = 0.527418806931585 | epot = -15.3810982703949 | etot = -14.617514035049 +208000 ekin = 0.242703261860097 | erot = 0.515412077176746 | epot = -15.3756293740978 | etot = -14.617514035061 +209000 ekin = 0.249814382549771 | erot = 0.501693407692903 | epot = -15.3690218253159 | etot = -14.6175140350732 +210000 ekin = 0.257301864855487 | erot = 0.486249049966596 | epot = -15.3610649499059 | etot = -14.6175140350838 +211000 ekin = 0.264935635394204 | erot = 0.469126912721243 | epot = -15.3515765832063 | etot = -14.6175140350909 +212000 ekin = 0.272467183646431 | erot = 0.450451153648371 | epot = -15.3404323723875 | etot = -14.6175140350927 +213000 ekin = 0.279646306736912 | erot = 0.430433702677772 | epot = -15.3275940445023 | etot = -14.6175140350876 +214000 ekin = 0.286237611276899 | erot = 0.409381288017331 | epot = -15.3131329343688 | etot = -14.6175140350746 +215000 ekin = 0.29203464387293 | erot = 0.387696263733711 | epot = -15.29724494266 | etot = -14.6175140350534 +216000 ekin = 0.296870258153004 | erot = 0.365870567410591 | epot = -15.2802548605881 | etot = -14.6175140350245 +217000 ekin = 0.300622666325324 | erot = 0.344472695101547 | epot = -15.2626093964159 | etot = -14.617514034989 +218000 ekin = 0.303217269541564 | erot = 0.324128407396835 | epot = -15.244859711887 | etot = -14.6175140349486 +219000 ekin = 0.30462484391226 | erot = 0.305496496150474 | epot = -15.2276353749682 | etot = -14.6175140349055 +220000 ekin = 0.304856982074418 | erot = 0.289241221674229 | epot = -15.2116122386105 | etot = -14.6175140348619 +221000 ekin = 0.303959749544728 | erot = 0.276003133760616 | epot = -15.1974769181253 | etot = -14.61751403482 +222000 ekin = 0.302006434071345 | erot = 0.266369862263779 | epot = -15.1858903311172 | etot = -14.6175140347821 +223000 ekin = 0.299090105491099 | erot = 0.260848208952979 | epot = -15.1774523491944 | etot = -14.6175140347503 +224000 ekin = 0.295316503745815 | erot = 0.259838588555865 | epot = -15.172669127028 | etot = -14.6175140347263 +225000 ekin = 0.29079760031813 | erot = 0.263612591734547 | epot = -15.1719242267643 | etot = -14.6175140347116 +226000 ekin = 0.28564610323333 | erot = 0.272294318079248 | epot = -15.1754544560199 | etot = -14.6175140347074 +227000 ekin = 0.279971018689722 | erot = 0.285846075010758 | epot = -15.1833311284149 | etot = -14.6175140347144 +228000 ekin = 0.27387437472819 | erot = 0.304059069119049 | epot = -15.1954474785804 | etot = -14.6175140347332 +229000 ekin = 0.2674491741605 | erot = 0.326549807965654 | epot = -15.2115130168897 | etot = -14.6175140347636 +230000 ekin = 0.260778614119455 | erot = 0.352763004039831 | epot = -15.2310556529641 | etot = -14.6175140348048 +231000 ekin = 0.253936564977397 | erot = 0.381981763344761 | epot = -15.2534323631777 | etot = -14.6175140348555 +232000 ekin = 0.246989230842658 | erot = 0.413345683736738 | epot = -15.2778489494936 | etot = -14.6175140349142 +233000 ekin = 0.239997814735998 | erot = 0.445877135783837 | epot = -15.3033889854983 | etot = -14.6175140349784 +234000 ekin = 0.233021891669953 | erot = 0.478515439398998 | epot = -15.3290513661143 | etot = -14.6175140350454 +235000 ekin = 0.226123071286445 | erot = 0.510157919201484 | epot = -15.3537950255997 | etot = -14.6175140351118 +236000 ekin = 0.21936843695277 | erot = 0.539706010633891 | epot = -15.3765884827611 | etot = -14.6175140351745 +237000 ekin = 0.212833212708602 | erot = 0.566113832023262 | epot = -15.3964610799619 | etot = -14.61751403523 +238000 ekin = 0.206602165162865 | erot = 0.588436180449287 | epot = -15.4125523808878 | etot = -14.6175140352757 +239000 ekin = 0.200769360307748 | erot = 0.605872583258365 | epot = -15.4241559788754 | etot = -14.6175140353093 +240000 ekin = 0.195436190928625 | erot = 0.61780345837781 | epot = -15.4307536846357 | etot = -14.6175140353293 +241000 ekin = 0.190707920284743 | erot = 0.623817360380854 | epot = -15.4320393160006 | etot = -14.617514035335 +242000 ekin = 0.186689132524135 | erot = 0.623726737659666 | epot = -15.4279299055104 | etot = -14.6175140353266 +243000 ekin = 0.183478880874969 | erot = 0.617571857376273 | epot = -15.4185647735561 | etot = -14.6175140353049 +244000 ekin = 0.181166166760206 | erot = 0.605612923712308 | epot = -15.4042931257437 | etot = -14.6175140352712 +245000 ekin = 0.179826690516145 | erot = 0.588311983397642 | epot = -15.3856527091413 | etot = -14.6175140352275 +246000 ekin = 0.179521473345086 | erot = 0.566306329739288 | epot = -15.3633418382601 | etot = -14.6175140351758 +247000 ekin = 0.180297726609514 | erot = 0.540375528723551 | epot = -15.3381872904514 | etot = -14.6175140351183 +248000 ekin = 0.182192022181392 | erot = 0.511404282991666 | epot = -15.3111103402302 | etot = -14.6175140350572 +249000 ekin = 0.185235475059313 | erot = 0.480343275337858 | epot = -15.2830927853916 | etot = -14.6175140349945 +250000 ekin = 0.189460324578832 | erot = 0.448169956262064 | epot = -15.255144315773 | etot = -14.6175140349321 +251000 ekin = 0.19490702001237 | erot = 0.415851007132868 | epot = -15.228272062017 | etot = -14.6175140348717 +252000 ekin = 0.201630699423836 | erot = 0.384307951122289 | epot = -15.2034526853611 | etot = -14.617514034815 +253000 ekin = 0.209705815256177 | erot = 0.354387113740113 | epot = -15.1816069637594 | etot = -14.6175140347631 +254000 ekin = 0.219227629547432 | erot = 0.326834860919775 | epot = -15.1635765251848 | etot = -14.6175140347176 +255000 ekin = 0.230309407957432 | erot = 0.302278768995733 | epot = -15.1501022116327 | etot = -14.6175140346795 +256000 ekin = 0.243074422922267 | erot = 0.281215109558701 | epot = -15.141803567131 | etot = -14.61751403465 +257000 ekin = 0.257642364630153 | erot = 0.264002762946067 | epot = -15.1391591622066 | etot = -14.6175140346304 +258000 ekin = 0.274110461104108 | erot = 0.250863404057697 | epot = -15.1424878997833 | etot = -14.6175140346215 +259000 ekin = 0.292530483429775 | erot = 0.241887528333024 | epot = -15.1519320463872 | etot = -14.6175140346244 +260000 ekin = 0.312883750215128 | erot = 0.237045600991386 | epot = -15.1674433858462 | etot = -14.6175140346397 +261000 ekin = 0.335057071666333 | erot = 0.236203324625284 | epot = -15.1887744309592 | etot = -14.6175140346676 +262000 ekin = 0.358823075933473 | erot = 0.239139750884213 | epot = -15.2154768615253 | etot = -14.6175140347076 +263000 ekin = 0.383828346058996 | erot = 0.245566753569572 | epot = -15.2469091343872 | etot = -14.6175140347587 +264000 ekin = 0.409592161639947 | erot = 0.255148290958814 | epot = -15.2822544874178 | etot = -14.6175140348191 +265000 ekin = 0.435517425640964 | erot = 0.267517972446782 | epot = -15.3205494329741 | etot = -14.6175140348864 +266000 ekin = 0.460913759434661 | erot = 0.282293742227942 | epot = -15.3607215366204 | etot = -14.6175140349578 +267000 ekin = 0.485031075313793 | erot = 0.299088986461059 | epot = -15.4016340968052 | etot = -14.6175140350303 +268000 ekin = 0.50710051747368 | erot = 0.317519986656956 | epot = -15.4421345392314 | etot = -14.6175140351007 +269000 ekin = 0.526378761163555 | erot = 0.33721025800327 | epot = -15.4811030543329 | etot = -14.6175140351661 +270000 ekin = 0.542191399557166 | erot = 0.357792786170323 | epot = -15.5174982209515 | etot = -14.617514035224 +271000 ekin = 0.553971501275297 | erot = 0.378911394713051 | epot = -15.5503969312606 | etot = -14.6175140352722 +272000 ekin = 0.561290243476884 | erot = 0.400222387433604 | epot = -15.5790266662199 | etot = -14.6175140353094 +273000 ekin = 0.563877614617889 | erot = 0.421397250043755 | epot = -15.6027888999963 | etot = -14.6175140353346 +274000 ekin = 0.561632338447609 | erot = 0.442126671655328 | epot = -15.6212730454506 | etot = -14.6175140353477 +275000 ekin = 0.554621238224436 | erot = 0.462125606775396 | epot = -15.6342608803486 | etot = -14.6175140353487 +276000 ekin = 0.543069132887187 | erot = 0.481138682331962 | epot = -15.6417218505579 | etot = -14.6175140353387 +277000 ekin = 0.527340979965694 | erot = 0.498945052082853 | epot = -15.6438000673675 | etot = -14.6175140353189 +278000 ekin = 0.507918337217276 | erot = 0.515361832413196 | epot = -15.6407942049214 | etot = -14.617514035291 +279000 ekin = 0.485372319601914 | erot = 0.530245473601771 | epot = -15.6331318284601 | etot = -14.6175140352564 +280000 ekin = 0.46033511650651 | erot = 0.543490744711146 | epot = -15.6213398964351 | etot = -14.6175140352175 +281000 ekin = 0.433471859960453 | erot = 0.555027349456868 | epot = -15.6060132445935 | etot = -14.6175140351761 +282000 ekin = 0.405454262480505 | erot = 0.564814480007104 | epot = -15.5877827776223 | etot = -14.6175140351347 +283000 ekin = 0.376937038993415 | erot = 0.572833827993335 | epot = -15.5672849020813 | etot = -14.6175140350945 +284000 ekin = 0.348537747962441 | erot = 0.579081711931139 | epot = -15.5451334949501 | etot = -14.6175140350565 +285000 ekin = 0.320820372083179 | erot = 0.583561068647143 | epot = -15.5218954757531 | etot = -14.6175140350227 +286000 ekin = 0.294282726921465 | erot = 0.586274110946605 | epot = -15.4980708728619 | etot = -14.6175140349939 +287000 ekin = 0.269347634013372 | erot = 0.587216475910704 | epot = -15.4740781448946 | etot = -14.6175140349706 +288000 ekin = 0.246357704467567 | erot = 0.586373659773396 | epot = -15.4502453991941 | etot = -14.6175140349531 +289000 ekin = 0.225573522145737 | erot = 0.583720426232575 | epot = -15.4268079833199 | etot = -14.6175140349416 +290000 ekin = 0.207174962818498 | erot = 0.579223657449698 | epot = -15.4039126552032 | etot = -14.617514034935 +291000 ekin = 0.191265313940317 | erot = 0.57284878086397 | epot = -15.3816281297368 | etot = -14.6175140349325 +292000 ekin = 0.177877757396561 | erot = 0.564569470033103 | epot = -15.3599612623625 | etot = -14.6175140349328 +293000 ekin = 0.166983649288562 | erot = 0.55437983768204 | epot = -15.3388775219052 | etot = -14.6175140349346 +294000 ekin = 0.158501898150816 | erot = 0.542307895558416 | epot = -15.3183238286456 | etot = -14.6175140349363 +295000 ekin = 0.152308641379775 | erot = 0.528428741575564 | epot = -15.2982514178919 | etot = -14.6175140349366 +296000 ekin = 0.14824639013426 | erot = 0.512875830575376 | epot = -15.2786362556441 | etot = -14.6175140349344 +297000 ekin = 0.146131889948848 | erot = 0.49584883363365 | epot = -15.2594947585117 | etot = -14.6175140349292 +298000 ekin = 0.145762142540934 | erot = 0.47761697934363 | epot = -15.2408931568053 | etot = -14.6175140349207 +299000 ekin = 0.146918339842692 | erot = 0.458517327974144 | epot = -15.2229497027261 | etot = -14.6175140349093 +300000 ekin = 0.149367830718069 | erot = 0.438948042711649 | epot = -15.2058299083254 | etot = -14.6175140348957 +301000 ekin = 0.152864610234033 | erot = 0.419357266833102 | epot = -15.1897359119478 | etot = -14.6175140348807 +302000 ekin = 0.157149122640169 | erot = 0.400228590597444 | epot = -15.1748917481033 | etot = -14.6175140348656 +303000 ekin = 0.161948347719032 | erot = 0.382064246006851 | epot = -15.1615266285773 | etot = -14.6175140348514 +304000 ekin = 0.166977167327436 | erot = 0.365367110078575 | epot = -15.1498583122451 | etot = -14.6175140348391 +305000 ekin = 0.171941885875871 | erot = 0.350622387001196 | epot = -15.1400783077067 | etot = -14.6175140348296 +306000 ekin = 0.176546522696863 | erot = 0.338279561363742 | epot = -15.1323401188838 | etot = -14.6175140348232 +307000 ekin = 0.180502080572192 | erot = 0.32873493509135 | epot = -15.126751050484 | etot = -14.6175140348205 +308000 ekin = 0.183539117579248 | erot = 0.322315068517915 | epot = -15.1233682209185 | etot = -14.6175140348213 +309000 ekin = 0.18542258916881 | erot = 0.31926113518031 | epot = -15.1221977591748 | etot = -14.6175140348257 +310000 ekin = 0.185968382525478 | erot = 0.319714556777655 | epot = -15.1231969741364 | etot = -14.6175140348332 +311000 ekin = 0.185060444471749 | erot = 0.323704474532897 | epot = -15.1262789538482 | etot = -14.6175140348435 +312000 ekin = 0.182667055699898 | erot = 0.331137883754702 | epot = -15.1313189743107 | etot = -14.6175140348561 +313000 ekin = 0.178854671448117 | erot = 0.341793554574368 | epot = -15.1381622608928 | etot = -14.6175140348703 +314000 ekin = 0.173797674113305 | erot = 0.355321045101964 | epot = -15.1466327541009 | etot = -14.6175140348857 +315000 ekin = 0.167782440685989 | erot = 0.371246117950244 | epot = -15.1565425935376 | etot = -14.6175140349013 +316000 ekin = 0.161204347699333 | erot = 0.388983636698412 | epot = -15.1677020193144 | etot = -14.6175140349166 +317000 ekin = 0.154556738722997 | erot = 0.407858516721222 | epot = -15.179929290375 | etot = -14.6175140349308 +318000 ekin = 0.148411457828014 | erot = 0.427134549771526 | epot = -15.1930600425429 | etot = -14.6175140349434 +319000 ekin = 0.143391260343274 | erot = 0.446049980956587 | epot = -15.2069552762535 | etot = -14.6175140349536 +320000 ekin = 0.140135163879389 | erot = 0.463857713006731 | epot = -15.2215069118477 | etot = -14.6175140349616 +321000 ekin = 0.13925849683082 | erot = 0.47986711734359 | epot = -15.2366396491416 | etot = -14.6175140349672 +322000 ekin = 0.141309963686786 | erot = 0.493483840953745 | epot = -15.2523078396115 | etot = -14.617514034971 +323000 ekin = 0.146728465402049 | erot = 0.504243890594766 | epot = -15.2684863909708 | etot = -14.617514034974 +324000 ekin = 0.155802740978474 | erot = 0.511838753068047 | epot = -15.2851555290241 | etot = -14.6175140349776 +325000 ekin = 0.168637192339758 | erot = 0.516129344219392 | epot = -15.3022805715425 | etot = -14.6175140349833 +326000 ekin = 0.185127492740937 | erot = 0.517147991936341 | epot = -15.3197895196698 | etot = -14.6175140349925 +327000 ekin = 0.204949583925474 | erot = 0.515089155111526 | epot = -15.3375527740431 | etot = -14.6175140350061 +328000 ekin = 0.227565145376632 | erot = 0.510290835144293 | epot = -15.3553700155453 | etot = -14.6175140350243 +329000 ekin = 0.252245305622037 | erot = 0.503209396460715 | epot = -15.372968737129 | etot = -14.6175140350463 +330000 ekin = 0.278112223739082 | erot = 0.494390678506977 | epot = -15.3900169373163 | etot = -14.6175140350702 +331000 ekin = 0.304195517645115 | erot = 0.484439927614521 | epot = -15.4061494803532 | etot = -14.6175140350935 +332000 ekin = 0.329497983392802 | erot = 0.473992405219011 | epot = -15.4210044237255 | etot = -14.6175140351136 +333000 ekin = 0.353063353198636 | erot = 0.463685785195801 | epot = -15.4342631735224 | etot = -14.617514035128 +334000 ekin = 0.374038491016654 | erot = 0.454134842083192 | epot = -15.4456873682344 | etot = -14.6175140351345 +335000 ekin = 0.391723520500355 | erot = 0.445908562625392 | epot = -15.4551461182584 | etot = -14.6175140351326 +336000 ekin = 0.405605581598612 | erot = 0.439509690040415 | epot = -15.4626293067615 | etot = -14.6175140351225 +337000 ekin = 0.415374601838216 | erot = 0.435356764652285 | epot = -15.4682454015957 | etot = -14.6175140351052 +338000 ekin = 0.42092199701013 | erot = 0.433768862195237 | epot = -15.4722048942883 | etot = -14.6175140350829 +339000 ekin = 0.422325110447523 | erot = 0.434953376211998 | epot = -15.4747925217174 | etot = -14.6175140350579 +340000 ekin = 0.419821259880453 | erot = 0.438997304560007 | epot = -15.4763325994732 | etot = -14.6175140350327 +341000 ekin = 0.413775534581149 | erot = 0.445862573585633 | epot = -15.4771521431765 | etot = -14.6175140350097 +342000 ekin = 0.404646174020848 | erot = 0.455385967573857 | epot = -15.4775461765857 | etot = -14.617514034991 +343000 ekin = 0.39295070583281 | erot = 0.467284215126884 | epot = -15.4777489559374 | etot = -14.6175140349777 +344000 ekin = 0.379235231728883 | erot = 0.481164689425934 | epot = -15.4779139561254 | etot = -14.6175140349706 +345000 ekin = 0.364048459933153 | erot = 0.496541967294177 | epot = -15.4781044621969 | etot = -14.6175140349695 +346000 ekin = 0.347921358320316 | erot = 0.512860132815006 | epot = -15.478295526109 | etot = -14.6175140349737 +347000 ekin = 0.331352665808126 | erot = 0.529520204053122 | epot = -15.4783869048429 | etot = -14.6175140349817 +348000 ekin = 0.314799955036566 | erot = 0.545911447469168 | epot = -15.4782254374972 | etot = -14.6175140349915 +349000 ekin = 0.298675493175281 | erot = 0.561444708834092 | epot = -15.4776342370104 | etot = -14.6175140350011 +350000 ekin = 0.283345815520869 | erot = 0.575585348315993 | epot = -15.4764451988451 | etot = -14.6175140350083 +351000 ekin = 0.269133730327523 | erot = 0.587883045339117 | epot = -15.474530810678 | etot = -14.6175140350114 +352000 ekin = 0.256321431305203 | erot = 0.597995738138039 | epot = -15.4718312044524 | etot = -14.6175140350092 +353000 ekin = 0.24515350965437 | erot = 0.605705335206206 | epot = -15.4683728798616 | etot = -14.617514035001 +354000 ekin = 0.235838910986168 | erot = 0.610923562934476 | epot = -15.4642765089078 | etot = -14.6175140349872 +355000 ekin = 0.228551231300269 | erot = 0.613687305425456 | epot = -15.4597525716945 | etot = -14.6175140349688 +356000 ekin = 0.223427131306842 | erot = 0.61414390282459 | epot = -15.4550850690789 | etot = -14.6175140349475 +357000 ekin = 0.220563006917694 | erot = 0.612527933401747 | epot = -15.4506049752447 | etot = -14.6175140349253 +358000 ekin = 0.22001033319751 | erot = 0.60913185554411 | epot = -15.4466562236463 | etot = -14.6175140349046 +359000 ekin = 0.221770268739896 | erot = 0.604273418957587 | epot = -15.4435577225855 | etot = -14.617514034888 +360000 ekin = 0.225788163653238 | erot = 0.598262925571301 | epot = -15.4415651241022 | etot = -14.6175140348777 +361000 ekin = 0.231948578437327 | erot = 0.591373251984918 | epot = -15.4408358652977 | etot = -14.6175140348754 +362000 ekin = 0.240071331017989 | erot = 0.583815109039703 | epot = -15.4414004749403 | etot = -14.6175140348826 +363000 ekin = 0.249908988057725 | erot = 0.5757194066129 | epot = -15.4431424295705 | etot = -14.6175140348999 +364000 ekin = 0.261146140581906 | erot = 0.567127906486804 | epot = -15.445788081996 | etot = -14.6175140349273 +365000 ekin = 0.273400773645715 | erot = 0.55799265360587 | epot = -15.4489074622158 | etot = -14.6175140349642 +366000 ekin = 0.286228056503678 | erot = 0.548184015759183 | epot = -15.4519261072721 | etot = -14.6175140350092 +367000 ekin = 0.299126926925909 | erot = 0.537506547612528 | epot = -15.454147509599 | etot = -14.6175140350606 +368000 ekin = 0.311549892638302 | erot = 0.525721330953642 | epot = -15.4547852587076 | etot = -14.6175140351156 +369000 ekin = 0.32291649334207 | erot = 0.512572942756027 | epot = -15.4530034712696 | etot = -14.6175140351715 +370000 ekin = 0.332630833323927 | erot = 0.497818805483382 | epot = -15.4479636740324 | etot = -14.6175140352251 +371000 ekin = 0.340103492446064 | erot = 0.481258447418256 | epot = -15.4388759751374 | etot = -14.617514035273 +372000 ekin = 0.344777943663672 | erot = 0.462760223985855 | epot = -15.4250522029614 | etot = -14.6175140353119 +373000 ekin = 0.346161332161602 | erot = 0.442283380419715 | epot = -15.4059587479198 | etot = -14.6175140353385 +374000 ekin = 0.343859062980226 | erot = 0.419893962768359 | epot = -15.3812670610984 | etot = -14.6175140353498 +375000 ekin = 0.337612023151089 | erot = 0.395773904237503 | epot = -15.3508999627316 | etot = -14.617514035343 +376000 ekin = 0.327334336193297 | erot = 0.370223433837585 | epot = -15.3150718053467 | etot = -14.6175140353159 +377000 ekin = 0.31314826371265 | erot = 0.343657545338067 | epot = -15.2743198443178 | etot = -14.6175140352671 +378000 ekin = 0.295411338277465 | erot = 0.316597454538877 | epot = -15.2295228280127 | etot = -14.6175140351964 +379000 ekin = 0.274729408510311 | erot = 0.289657740940239 | epot = -15.1819011845556 | etot = -14.6175140351051 +380000 ekin = 0.251948675267255 | erot = 0.263529414055484 | epot = -15.1329921243191 | etot = -14.6175140349963 +381000 ekin = 0.228120837035106 | erot = 0.238958749468258 | epot = -15.0845936213795 | etot = -14.6175140348762 +382000 ekin = 0.204438854506711 | erot = 0.21672127051921 | epot = -15.0386741597778 | etot = -14.6175140347519 +383000 ekin = 0.182146263755408 | erot = 0.197591880984099 | epot = -14.9972521793719 | etot = -14.6175140346324 +384000 ekin = 0.162429780679591 | erot = 0.182311896923862 | epot = -14.9622557121303 | etot = -14.6175140345269 +385000 ekin = 0.14631062212392 | erot = 0.171555128910903 | epot = -14.9353797854787 | etot = -14.6175140344438 +386000 ekin = 0.134552389652504 | erot = 0.165895597224072 | epot = -14.9179620212652 | etot = -14.6175140343886 +387000 ekin = 0.127600986328474 | erot = 0.165779213533691 | epot = -14.9108942342261 | etot = -14.6175140343639 +388000 ekin = 0.125565151523057 | erot = 0.171500950984465 | epot = -14.9145801368767 | etot = -14.6175140343691 +389000 ekin = 0.128237001096924 | erot = 0.183188026636153 | epot = -14.9289390621345 | etot = -14.6175140344014 +390000 ekin = 0.135143637923019 | erot = 0.200788930663243 | epot = -14.953446603043 | etot = -14.6175140344567 +391000 ekin = 0.145616156499687 | erot = 0.224068074688667 | epot = -14.9871982657189 | etot = -14.6175140345306 +392000 ekin = 0.158862235246419 | erot = 0.252606362172197 | epot = -15.028982632037 | etot = -14.6175140346184 +393000 ekin = 0.174032087603182 | erot = 0.285808726840173 | epot = -15.0773548491589 | etot = -14.6175140347155 +394000 ekin = 0.190272707003279 | erot = 0.32292010751355 | epot = -15.130706849335 | etot = -14.6175140348181 +395000 ekin = 0.206769905101682 | erot = 0.363051013228993 | epot = -15.1873349532528 | etot = -14.6175140349222 +396000 ekin = 0.222780272469837 | erot = 0.405212687948367 | epot = -15.2455069954416 | etot = -14.6175140350234 +397000 ekin = 0.237655698718666 | erot = 0.448360183483368 | epot = -15.3035299173201 | etot = -14.6175140351181 +398000 ekin = 0.250862154069819 | erot = 0.491439914330298 | epot = -15.3598161036023 | etot = -14.6175140352022 +399000 ekin = 0.261993055953367 | erot = 0.533437059171161 | epot = -15.4129441503973 | etot = -14.6175140352727 +400000 ekin = 0.27077655050685 | erot = 0.573417887950022 | epot = -15.4617084737844 | etot = -14.6175140353276 +401000 ekin = 0.277075831015552 | erot = 0.610562842824378 | epot = -15.505152709206 | etot = -14.6175140353661 +402000 ekin = 0.280882158891387 | erot = 0.644187798759806 | epot = -15.5425839930396 | etot = -14.6175140353885 +403000 ekin = 0.282301228578668 | erot = 0.673752968642337 | epot = -15.5735682326172 | etot = -14.6175140353962 +404000 ekin = 0.281534519811851 | erot = 0.698860907482421 | epot = -15.5979094626856 | etot = -14.6175140353913 +405000 ekin = 0.278857975736577 | erot = 0.719246574878491 | epot = -15.6156185859914 | etot = -14.6175140353763 +406000 ekin = 0.27460055575904 | erot = 0.734763157396981 | epot = -15.6268777485092 | etot = -14.6175140353531 +407000 ekin = 0.269124923358191 | erot = 0.745367259285135 | epot = -15.632006217967 | etot = -14.6175140353237 +408000 ekin = 0.262811853165513 | erot = 0.75110627666519 | epot = -15.6314321651198 | etot = -14.6175140352891 +409000 ekin = 0.256049112192014 | erot = 0.752109968276038 | epot = -15.6256731157183 | etot = -14.6175140352503 +410000 ekin = 0.249224269809724 | erot = 0.748584332259421 | epot = -15.6153226372766 | etot = -14.6175140352074 +411000 ekin = 0.242720888553515 | erot = 0.74080910391814 | epot = -15.6010440276324 | etot = -14.6175140351607 +412000 ekin = 0.236916379506249 | erot = 0.729136085380527 | epot = -15.5835664999973 | etot = -14.6175140351105 +413000 ekin = 0.232179735243875 | erot = 0.713985498456682 | epot = -15.5636792687578 | etot = -14.6175140350572 +414000 ekin = 0.228867632642529 | erot = 0.695838652585608 | epot = -15.5422203202303 | etot = -14.6175140350022 +415000 ekin = 0.227317772308198 | erot = 0.675225695396014 | epot = -15.5200575026511 | etot = -14.6175140349469 +416000 ekin = 0.227838940778005 | erot = 0.65270826110506 | epot = -15.4980612367768 | etot = -14.6175140348937 +417000 ekin = 0.23069797086734 | erot = 0.628857925336074 | epot = -15.4770699310485 | etot = -14.6175140348451 +418000 ekin = 0.236104416121177 | erot = 0.604232291329939 | epot = -15.4578507422545 | etot = -14.6175140348034 +419000 ekin = 0.244194252200936 | erot = 0.579351108945467 | epot = -15.4410593959176 | etot = -14.6175140347712 +420000 ekin = 0.255014214169025 | erot = 0.554674986841681 | epot = -15.427203235761 | etot = -14.6175140347503 +421000 ekin = 0.268508458340867 | erot = 0.530589008737006 | epot = -15.4166115018197 | etot = -14.6175140347419 +422000 ekin = 0.284509119561056 | erot = 0.507392982381358 | epot = -15.4094161366888 | etot = -14.6175140347464 +423000 ekin = 0.302732060427453 | erot = 0.485299248119848 | epot = -15.4055453433108 | etot = -14.6175140347635 +424000 ekin = 0.322778728051846 | erot = 0.464438075671392 | epot = -15.4047308385151 | etot = -14.6175140347918 +425000 ekin = 0.344144594922978 | erot = 0.444869796713037 | epot = -15.4065284264654 | etot = -14.6175140348294 +426000 ekin = 0.366234204300236 | erot = 0.426602052984558 | epot = -15.4103502921584 | etot = -14.6175140348736 +427000 ekin = 0.388382398339839 | erot = 0.409609962240785 | epot = -15.4155063955021 | etot = -14.6175140349215 +428000 ekin = 0.409880900047347 | erot = 0.393856678092514 | epot = -15.4212516131098 | etot = -14.61751403497 +429000 ekin = 0.430009061106081 | erot = 0.379311788382045 | epot = -15.4268348845042 | etot = -14.617514035016 +430000 ekin = 0.448067283635938 | erot = 0.365965282400769 | epot = -15.4315466010937 | etot = -14.617514035057 +431000 ekin = 0.463411378722709 | erot = 0.353835411175237 | epot = -15.4347608249887 | etot = -14.6175140350907 +432000 ekin = 0.47548594153415 | erot = 0.342969616703567 | epot = -15.4359695933534 | etot = -14.6175140351157 +433000 ekin = 0.483854704019995 | erot = 0.333438714396017 | epot = -15.4348074535468 | etot = -14.6175140351308 +434000 ekin = 0.488225698517989 | erot = 0.325325491781988 | epot = -15.4310652254358 | etot = -14.6175140351358 +435000 ekin = 0.488469615216989 | erot = 0.318709988965469 | epot = -15.4246936393136 | etot = -14.6175140351312 +436000 ekin = 0.48462910079659 | erot = 0.313653867974335 | epot = -15.4157970038886 | etot = -14.6175140351176 +437000 ekin = 0.476917712283315 | erot = 0.310186654190433 | epot = -15.4046184015705 | etot = -14.6175140350967 +438000 ekin = 0.465707830234525 | erot = 0.308296241622533 | epot = -15.3915181069269 | etot = -14.6175140350699 +439000 ekin = 0.451507536799582 | erot = 0.307925153770196 | epot = -15.376946725609 | etot = -14.6175140350392 +440000 ekin = 0.434927659012326 | erot = 0.308973010492473 | epot = -15.3614147045113 | etot = -14.6175140350065 +441000 ekin = 0.416641657348227 | erot = 0.311304747383323 | epot = -15.3454604397054 | etot = -14.6175140349739 +442000 ekin = 0.397341542599983 | erot = 0.3147626187362 | epot = -15.3296181962795 | etot = -14.6175140349433 +443000 ekin = 0.377694362714098 | erot = 0.319179725729427 | epot = -15.3143881233596 | etot = -14.6175140349161 +444000 ekin = 0.358304425135514 | erot = 0.324393298190365 | epot = -15.3002117582193 | etot = -14.6175140348935 +445000 ekin = 0.339684383333994 | erot = 0.330254911560057 | epot = -15.2874533297702 | etot = -14.6175140348761 +446000 ekin = 0.322237701350787 | erot = 0.336636009508874 | epot = -15.276387745724 | etot = -14.6175140348643 +447000 ekin = 0.306253086582787 | erot = 0.343428242758822 | epot = -15.2671953641996 | etot = -14.617514034858 +448000 ekin = 0.291909091343146 | erot = 0.350538602021414 | epot = -15.2599617282214 | etot = -14.6175140348569 +449000 ekin = 0.279285717663623 | erot = 0.35788026308961 | epot = -15.2546800156141 | etot = -14.6175140348608 +450000 ekin = 0.268379332693062 | erot = 0.365360767817965 | epot = -15.2512541353807 | etot = -14.6175140348697 +451000 ekin = 0.259117719162389 | erot = 0.372869677561009 | epot = -15.2495014316067 | etot = -14.6175140348833 +452000 ekin = 0.251373384973236 | erot = 0.380268095671436 | epot = -15.2491555155464 | etot = -14.6175140349017 +453000 ekin = 0.244974824127414 | erot = 0.387382402365197 | epot = -15.249871261417 | etot = -14.6175140349243 +454000 ekin = 0.239716691076083 | erot = 0.39400413186188 | epot = -15.2512348578882 | etot = -14.6175140349502 +455000 ekin = 0.235370413814051 | erot = 0.399897145642462 | epot = -15.2527815944342 | etot = -14.6175140349777 +456000 ekin = 0.231696513790449 | erot = 0.40481218842498 | epot = -15.2540227372201 | etot = -14.6175140350047 +457000 ekin = 0.228459014431981 | erot = 0.40850770951526 | epot = -15.2544807589758 | etot = -14.6175140350286 +458000 ekin = 0.225441196082345 | erot = 0.410774705624049 | epot = -15.2537299367533 | etot = -14.6175140350469 +459000 ekin = 0.222461018940529 | erot = 0.411462514811891 | epot = -15.2514375688097 | etot = -14.6175140350572 +460000 ekin = 0.219384094438522 | erot = 0.410502136529 | epot = -15.2474002660254 | etot = -14.6175140350579 +461000 ekin = 0.216132245240083 | erot = 0.40792384413244 | epot = -15.2415701244207 | etot = -14.6175140350482 +462000 ekin = 0.212686361973293 | erot = 0.403866554423589 | epot = -15.2340669514251 | etot = -14.6175140350283 +463000 ekin = 0.209083218482802 | erot = 0.398577486489706 | epot = -15.2251747399718 | etot = -14.6175140349993 +464000 ekin = 0.205406888263705 | erot = 0.392401883856904 | epot = -15.2153228070839 | etot = -14.6175140349633 +465000 ekin = 0.201776197881055 | erot = 0.385763783461981 | epot = -15.205054016266 | etot = -14.617514034923 +466000 ekin = 0.198330130961163 | erot = 0.379139817336875 | epot = -15.1949839831792 | etot = -14.6175140348812 +467000 ekin = 0.195213224017084 | erot = 0.373028711257248 | epot = -15.1857559701149 | etot = -14.6175140348406 +468000 ekin = 0.192562810062079 | erot = 0.367919448414624 | epot = -15.1779962932805 | etot = -14.6175140348038 +469000 ekin = 0.190499545154634 | erot = 0.364261004085315 | epot = -15.1722745840127 | etot = -14.6175140347728 +470000 ekin = 0.189122086032537 | erot = 0.362436180586744 | epot = -15.1690723013681 | etot = -14.6175140347488 +471000 ekin = 0.188506156938585 | erot = 0.362741456207124 | epot = -15.1687616478783 | etot = -14.6175140347325 +472000 ekin = 0.188707621222025 | erot = 0.365373993438314 | epot = -15.1715956493842 | etot = -14.6175140347239 +473000 ekin = 0.189768618621823 | erot = 0.370426120543997 | epot = -15.1777087738881 | etot = -14.6175140347222 +474000 ekin = 0.191725397341228 | erot = 0.377886798112909 | epot = -15.1871262301805 | etot = -14.6175140347264 +475000 ekin = 0.194616213070748 | erot = 0.387648901412907 | epot = -15.1997791492191 | etot = -14.6175140347355 +476000 ekin = 0.19848763616064 | erot = 0.39952067815615 | epot = -15.2155223490651 | etot = -14.6175140347483 +477000 ekin = 0.203397790429832 | erot = 0.413239540255182 | epot = -15.2341513654491 | etot = -14.6175140347641 +478000 ekin = 0.209415519783212 | erot = 0.428486466927375 | epot = -15.2554160214929 | etot = -14.6175140347823 +479000 ekin = 0.216615156594683 | erot = 0.444899686772466 | epot = -15.2790288781699 | etot = -14.6175140348028 +480000 ekin = 0.225067223157677 | erot = 0.462086880018489 | epot = -15.3046681380017 | etot = -14.6175140348255 +481000 ekin = 0.234826185147703 | erot = 0.479635803739713 | epot = -15.3319760237384 | etot = -14.617514034851 +482000 ekin = 0.245916939355107 | erot = 0.497123799838186 | epot = -15.3605547740726 | etot = -14.6175140348793 +483000 ekin = 0.258322039580648 | erot = 0.514126984881418 | epot = -15.3899630593725 | etot = -14.6175140349104 +484000 ekin = 0.27197166705463 | erot = 0.530229960568927 | epot = -15.4197156625676 | etot = -14.6175140349441 +485000 ekin = 0.286738030809397 | erot = 0.545036619609846 | epot = -15.4492886853987 | etot = -14.6175140349795 +486000 ekin = 0.302435294441744 | erot = 0.55818212519067 | epot = -15.4781314546478 | etot = -14.6175140350154 +487000 ekin = 0.31882536985775 | erot = 0.569345540302742 | epot = -15.5056849452109 | etot = -14.6175140350504 +488000 ekin = 0.33562912085568 | erot = 0.578262027782569 | epot = -15.531405183721 | etot = -14.6175140350828 +489000 ekin = 0.352541803824768 | erot = 0.584733173542191 | epot = -15.5547890124778 | etot = -14.6175140351108 +490000 ekin = 0.369251041132819 | erot = 0.588633902375943 | epot = -15.575398978642 | etot = -14.6175140351332 +491000 ekin = 0.38545533994301 | erot = 0.589914693969638 | epot = -15.5928840690618 | etot = -14.6175140351491 +492000 ekin = 0.400881156477994 | erot = 0.588598334680196 | epot = -15.6069935263164 | etot = -14.6175140351582 +493000 ekin = 0.41529674637658 | erot = 0.584771169136983 | epot = -15.6175819506742 | etot = -14.6175140351607 +494000 ekin = 0.42852150310201 | erot = 0.578569614095072 | epot = -15.6246051523544 | etot = -14.6175140351573 +495000 ekin = 0.440430011857935 | erot = 0.570163426567811 | epot = -15.6281074735753 | etot = -14.6175140351496 +496000 ekin = 0.45095070631601 | erot = 0.559737766476832 | epot = -15.6282025079316 | etot = -14.6175140351387 +497000 ekin = 0.460059581797609 | erot = 0.547476355485017 | epot = -15.6250499724091 | etot = -14.6175140351264 +498000 ekin = 0.467769906491902 | erot = 0.533547985554597 | epot = -15.6188319271606 | etot = -14.6175140351141 +499000 ekin = 0.474119221072851 | erot = 0.51809827733209 | epot = -15.6097315335077 | etot = -14.6175140351027 +500000 ekin = 0.47915510663515 | erot = 0.501247978936972 | epot = -15.5979171206651 | etot = -14.617514035093 +501000 ekin = 0.482921233339145 | erot = 0.48309830408219 | epot = -15.5835335725062 | etot = -14.6175140350848 +502000 ekin = 0.485445093649468 | erot = 0.463742920559152 | epot = -15.5667020492864 | etot = -14.6175140350778 +503000 ekin = 0.486728599210218 | erot = 0.443285305605287 | epot = -15.5475279398865 | etot = -14.617514035071 +504000 ekin = 0.486742408088666 | erot = 0.421859374631512 | epot = -15.5261158177833 | etot = -14.6175140350632 +505000 ekin = 0.485424480828576 | erot = 0.399650657767878 | epot = -15.5025891736495 | etot = -14.617514035053 +506000 ekin = 0.482682973412862 | erot = 0.376914939267073 | epot = -15.4771119477192 | etot = -14.6175140350392 +507000 ekin = 0.478403198155678 | erot = 0.353991273960951 | epot = -15.4499085071374 | etot = -14.6175140350208 +508000 ekin = 0.472458052936543 | erot = 0.331306710133899 | epot = -15.4212787980677 | etot = -14.6175140349973 +509000 ekin = 0.464721062856492 | erot = 0.309370883447797 | epot = -15.3916059812731 | etot = -14.6175140349688 +510000 ekin = 0.455081004105159 | erot = 0.288759823578861 | epot = -15.3613548626198 | etot = -14.6175140349358 +511000 ekin = 0.443456979181393 | erot = 0.270089690707588 | epot = -15.3310607047887 | etot = -14.6175140348997 +512000 ekin = 0.42981284822046 | erot = 0.253982534898902 | epot = -15.3013094179813 | etot = -14.6175140348619 +513000 ekin = 0.414169942619743 | erot = 0.241027258547542 | epot = -15.2727112359918 | etot = -14.6175140348246 +514000 ekin = 0.396617122320061 | erot = 0.231739657368506 | epot = -15.2458708144779 | etot = -14.6175140347893 +515000 ekin = 0.377317407139222 | erot = 0.226525548757325 | epot = -15.2213569906545 | etot = -14.6175140347579 +516000 ekin = 0.356510629533878 | erot = 0.225650587239722 | epot = -15.1996752515054 | etot = -14.6175140347318 +517000 ekin = 0.334511811731657 | erot = 0.2292195098864 | epot = -15.1812453563299 | etot = -14.6175140347119 +518000 ekin = 0.311705249159968 | erot = 0.237166415926506 | epot = -15.1663856997852 | etot = -14.6175140346987 +519000 ekin = 0.288534562405324 | erot = 0.249256456193412 | epot = -15.1553050532911 | etot = -14.6175140346924 +520000 ekin = 0.265489234982117 | erot = 0.265098165450665 | epot = -15.1481014351253 | etot = -14.6175140346926 +521000 ekin = 0.243088358087376 | erot = 0.28416474515935 | epot = -15.1447671379453 | etot = -14.6175140346986 +522000 ekin = 0.221862437060409 | erot = 0.305821970139557 | epot = -15.1451984419098 | etot = -14.6175140347099 +523000 ekin = 0.202334169775844 | erot = 0.329360070796281 | epot = -15.1492082752976 | etot = -14.6175140347255 +524000 ekin = 0.18499909107587 | erot = 0.354026911469942 | epot = -15.1565400372904 | etot = -14.6175140347446 +525000 ekin = 0.170306912739125 | erot = 0.379059948770509 | epot = -15.1668808962761 | etot = -14.6175140347665 +526000 ekin = 0.158644243148338 | erot = 0.403715126924459 | epot = -15.1798734048633 | etot = -14.6175140347905 +527000 ekin = 0.150319367666652 | erot = 0.427291025811595 | epot = -15.1951244282948 | etot = -14.6175140348166 +528000 ekin = 0.145549592055536 | erot = 0.449147424932796 | epot = -15.2122110518326 | etot = -14.6175140348442 +529000 ekin = 0.144451603985221 | erot = 0.468718121850073 | epot = -15.2306837607087 | etot = -14.6175140348734 +530000 ekin = 0.14703526713895 | erot = 0.485518371010905 | epot = -15.2500676730542 | etot = -14.6175140349043 +531000 ekin = 0.153201203685084 | erot = 0.499147835496798 | epot = -15.2698630741185 | etot = -14.6175140349366 +532000 ekin = 0.162742448480689 | erot = 0.509290301682419 | epot = -15.2895467851334 | etot = -14.6175140349703 +533000 ekin = 0.175350354883052 | erot = 0.515711587206659 | epot = -15.3085759770945 | etot = -14.6175140350048 +534000 ekin = 0.190624856014791 | erot = 0.518257146630773 | epot = -15.3263960376849 | etot = -14.6175140350393 +535000 ekin = 0.2080884935382 | erot = 0.516850140105121 | epot = -15.342452668716 | etot = -14.6175140350727 +536000 ekin = 0.227204325844129 | erot = 0.511491240066285 | epot = -15.356209601014 | etot = -14.6175140351035 +537000 ekin = 0.247396768814447 | erot = 0.502260311074919 | epot = -15.3671711150196 | etot = -14.6175140351302 +538000 ekin = 0.268074342414832 | erot = 0.489319600962367 | epot = -15.374907978528 | etot = -14.6175140351508 +539000 ekin = 0.288653182934819 | erot = 0.472917679673217 | epot = -15.3790848977717 | etot = -14.6175140351637 +540000 ekin = 0.308579985827036 | erot = 0.453392904740712 | epot = -15.3794869257353 | etot = -14.6175140351676 +541000 ekin = 0.32735300819234 | erot = 0.431174973012169 | epot = -15.3760420163656 | etot = -14.6175140351611 +542000 ekin = 0.344539853507862 | erot = 0.406783142890278 | epot = -15.368837031542 | etot = -14.6175140351439 +543000 ekin = 0.359790986514659 | erot = 0.380819988065077 | epot = -15.3581250096959 | etot = -14.6175140351161 +544000 ekin = 0.372848263091261 | erot = 0.353960030673725 | epot = -15.3443223288437 | etot = -14.6175140350787 +545000 ekin = 0.383548167009949 | erot = 0.326933212483018 | epot = -15.3279954145262 | etot = -14.6175140350332 +546000 ekin = 0.391819867385597 | erot = 0.30050378423916 | epot = -15.3098376866063 | etot = -14.6175140349815 +547000 ekin = 0.397678590181961 | erot = 0.275445713888184 | epot = -15.2906383389964 | etot = -14.6175140349263 +548000 ekin = 0.401215088504123 | erot = 0.252516050367 | epot = -15.2712451737411 | etot = -14.6175140348699 +549000 ekin = 0.402582175511822 | erot = 0.232427794768509 | epot = -15.2525240050958 | etot = -14.6175140348155 +550000 ekin = 0.401979352686767 | erot = 0.215823740833757 | epot = -15.2353171282858 | etot = -14.6175140347652 +551000 ekin = 0.399636550192594 | erot = 0.203252510910356 | epot = -15.2204030958242 | etot = -14.6175140347213 +552000 ekin = 0.39579793483933 | erot = 0.19514771457426 | epot = -15.2084596840996 | etot = -14.617514034686 +553000 ekin = 0.390706676474511 | erot = 0.191810879117678 | epot = -15.2000315902533 | etot = -14.6175140346611 +554000 ekin = 0.384591526956334 | erot = 0.193398609454572 | epot = -15.1955041710586 | etot = -14.6175140346477 +555000 ekin = 0.37765606833088 | erot = 0.19991436289407 | epot = -15.1950844658717 | etot = -14.6175140346467 +556000 ekin = 0.370071512613894 | erot = 0.211205266307038 | epot = -15.1987908135787 | etot = -14.6175140346578 +557000 ekin = 0.361973939271072 | erot = 0.22696451510277 | epot = -15.2064524890543 | etot = -14.6175140346805 +558000 ekin = 0.353466765019157 | erot = 0.246739996101886 | epot = -15.2177207958342 | etot = -14.6175140347132 +559000 ekin = 0.344628961763677 | erot = 0.269949765670226 | epot = -15.2320927621875 | etot = -14.6175140347536 +560000 ekin = 0.335528980566657 | erot = 0.295904778795777 | epot = -15.2489477941611 | etot = -14.6175140347987 +561000 ekin = 0.326243446080443 | erot = 0.323838714908469 | epot = -15.2675961958334 | etot = -14.6175140348445 +562000 ekin = 0.31687848681263 | erot = 0.35294385755285 | epot = -15.2873363792525 | etot = -14.617514034887 +563000 ekin = 0.307590234581101 | erot = 0.382410843957197 | epot = -15.3075151134611 | etot = -14.6175140349228 +564000 ekin = 0.298599911427017 | erot = 0.411468934029061 | epot = -15.3275828804049 | etot = -14.6175140349488 +565000 ekin = 0.290198521501092 | erot = 0.439422606477171 | epot = -15.3471351629423 | etot = -14.617514034964 +566000 ekin = 0.282736992095573 | erot = 0.46568015891933 | epot = -15.365931185984 | etot = -14.6175140349691 +567000 ekin = 0.276599956454062 | erot = 0.489770841522339 | epot = -15.3838848329429 | etot = -14.6175140349665 +568000 ekin = 0.272165052790826 | erot = 0.511348887820125 | epot = -15.4010279755712 | etot = -14.6175140349602 +569000 ekin = 0.269753809413461 | erot = 0.530185258476706 | epot = -15.4174531028449 | etot = -14.6175140349547 +570000 ekin = 0.269583567607582 | erot = 0.546150320474166 | epot = -15.4332479230358 | etot = -14.617514034954 +571000 ekin = 0.271731068578169 | erot = 0.559192265325146 | epot = -15.4484373688639 | etot = -14.6175140349606 +572000 ekin = 0.27611649568743 | erot = 0.569316321633573 | epot = -15.4629468522957 | etot = -14.6175140349747 +573000 ekin = 0.282512256444883 | erot = 0.576569321997748 | epot = -15.4765956134373 | etot = -14.6175140349947 +574000 ekin = 0.290574483947772 | erot = 0.581030490761115 | epot = -15.4891190097262 | etot = -14.6175140350173 +575000 ekin = 0.299890113326873 | erot = 0.582808418137228 | epot = -15.5002125665028 | etot = -14.6175140350387 +576000 ekin = 0.310029076131071 | erot = 0.582041678954515 | epot = -15.5095847901411 | etot = -14.6175140350555 +577000 ekin = 0.320591144135804 | erot = 0.578899817193121 | epot = -15.5170049963945 | etot = -14.6175140350656 +578000 ekin = 0.331239680817777 | erot = 0.573581904321184 | epot = -15.5223356202071 | etot = -14.6175140350681 +579000 ekin = 0.341718767395671 | erot = 0.566311213814667 | epot = -15.5255440162741 | etot = -14.6175140350637 +580000 ekin = 0.351854361646072 | erot = 0.557326170820678 | epot = -15.5266945675208 | etot = -14.6175140350541 +581000 ekin = 0.361543170719775 | erot = 0.54686904311153 | epot = -15.5259262488726 | etot = -14.6175140350413 +582000 ekin = 0.370734291431498 | erot = 0.535174473618245 | epot = -15.5234228000773 | etot = -14.6175140350275 +583000 ekin = 0.37940854514609 | erot = 0.522459863754552 | epot = -15.5193824439152 | etot = -14.6175140350145 +584000 ekin = 0.38755933833177 | erot = 0.50891899994006 | epot = -15.5139923732754 | etot = -14.6175140350036 +585000 ekin = 0.395177418309126 | erot = 0.494719483695348 | epot = -15.5074109369997 | etot = -14.6175140349952 +586000 ekin = 0.402240533516271 | erot = 0.480003760425467 | epot = -15.4997583289313 | etot = -14.6175140349896 +587000 ekin = 0.408707997144929 | erot = 0.464893014295021 | epot = -15.4911150464262 | etot = -14.6175140349863 +588000 ekin = 0.414519545772604 | erot = 0.449492951761529 | epot = -15.4815265325189 | etot = -14.6175140349848 +589000 ekin = 0.419597612554971 | erot = 0.433900487906506 | epot = -15.4710121354457 | etot = -14.6175140349842 +590000 ekin = 0.423852083806182 | erot = 0.418210489544302 | epot = -15.4595766083342 | etot = -14.6175140349837 +591000 ekin = 0.42718667151707 | erot = 0.402521929659384 | epot = -15.4472226361591 | etot = -14.6175140349827 +592000 ekin = 0.429506137373247 | erot = 0.386943005730352 | epot = -15.4339631780839 | etot = -14.6175140349803 +593000 ekin = 0.430723706116147 | erot = 0.371594936610811 | epot = -15.4198326777029 | etot = -14.617514034976 +594000 ekin = 0.430768094953345 | erot = 0.356614269838259 | epot = -15.4048963997609 | etot = -14.6175140349693 +595000 ekin = 0.429589664829847 | erot = 0.342153609171636 | epot = -15.3892573089616 | etot = -14.6175140349601 +596000 ekin = 0.427165296133148 | erot = 0.328380718542492 | epot = -15.3730600496239 | etot = -14.6175140349483 +597000 ekin = 0.42350165849966 | erot = 0.315475989403582 | epot = -15.3564916828373 | etot = -14.6175140349341 +598000 ekin = 0.418636501255305 | erot = 0.303628359581859 | epot = -15.339778895755 | etot = -14.6175140349179 +599000 ekin = 0.412638207582272 | erot = 0.293029673723798 | epot = -15.3231819162063 | etot = -14.6175140349002 +600000 ekin = 0.405603414753522 | erot = 0.28386763722636 | epot = -15.3069850868619 | etot = -14.617514034882 +601000 ekin = 0.397652939448492 | erot = 0.276317573361084 | epot = -15.2914845476736 | etot = -14.617514034864 +602000 ekin = 0.388926339151588 | erot = 0.270533300128844 | epot = -15.2769736741277 | etot = -14.6175140348473 +603000 ekin = 0.379575547710976 | erot = 0.266637582798786 | epot = -15.2637271653425 | etot = -14.6175140348328 +604000 ekin = 0.369758112224373 | erot = 0.264712769809576 | epot = -15.2519849168554 | etot = -14.6175140348215 +605000 ekin = 0.35963061496451 | erot = 0.264792359550224 | epot = -15.2419370093288 | etot = -14.6175140348141 +606000 ekin = 0.349342882571248 | erot = 0.266854337886836 | epot = -15.2337112552692 | etot = -14.6175140348112 +607000 ekin = 0.339033558751512 | erot = 0.270817131627415 | epot = -15.2273647251918 | etot = -14.6175140348128 +608000 ekin = 0.32882753825937 | erot = 0.276538908097057 | epot = -15.2228804811754 | etot = -14.617514034819 +609000 ekin = 0.318835621087622 | erot = 0.283820700144174 | epot = -15.2201703560608 | etot = -14.617514034829 +610000 ekin = 0.309156542568317 | erot = 0.292413461055651 | epot = -15.219084038466 | etot = -14.617514034842 +611000 ekin = 0.299881272108214 | erot = 0.302028697869802 | epot = -15.2194240048347 | etot = -14.6175140348566 +612000 ekin = 0.291099167856268 | erot = 0.312351863789569 | epot = -15.2209650665173 | etot = -14.6175140348715 +613000 ekin = 0.282905257831642 | erot = 0.323057294042038 | epot = -15.2234765867589 | etot = -14.6175140348852 +614000 ekin = 0.275407632339941 | erot = 0.333823223652897 | epot = -15.2267448908892 | etot = -14.6175140348963 +615000 ekin = 0.26873372556727 | erot = 0.344345386320857 | epot = -15.2305931467922 | etot = -14.6175140349041 +616000 ekin = 0.263034181136603 | erot = 0.354347879927045 | epot = -15.2348960959716 | etot = -14.617514034908 +617000 ekin = 0.258483071857928 | erot = 0.363590372787296 | epot = -15.2395874795532 | etot = -14.617514034908 +618000 ekin = 0.255273496413749 | erot = 0.371871254538884 | epot = -15.2446587858574 | etot = -14.6175140349047 +619000 ekin = 0.253608004174875 | erot = 0.379026921287401 | epot = -15.2501489603618 | etot = -14.6175140348996 +620000 ekin = 0.253683881422301 | erot = 0.384927934514049 | epot = -15.2561258508302 | etot = -14.6175140348939 +621000 ekin = 0.255674023710173 | erot = 0.389473226072584 | epot = -15.2626612846724 | etot = -14.6175140348896 +622000 ekin = 0.25970485336799 | erot = 0.392583779640473 | epot = -15.269802667897 | etot = -14.6175140348886 +623000 ekin = 0.265833429999859 | erot = 0.394197274406549 | epot = -15.2775447392987 | etot = -14.6175140348923 +624000 ekin = 0.274026439188702 | erot = 0.394265031625425 | epot = -15.2858055057161 | etot = -14.6175140349019 +625000 ekin = 0.28414401573885 | erot = 0.392752285177019 | epot = -15.2944103358336 | etot = -14.6175140349177 +626000 ekin = 0.295931256226573 | erot = 0.389642344381245 | epot = -15.303087635547 | etot = -14.6175140349392 +627000 ekin = 0.309019727830035 | erot = 0.384944676505037 | epot = -15.3114784393 | etot = -14.6175140349649 +628000 ekin = 0.322940275279346 | erot = 0.378706350960174 | epot = -15.3191606612318 | etot = -14.6175140349923 +629000 ekin = 0.337147043698441 | erot = 0.371025698974895 | epot = -15.3256867776918 | etot = -14.6175140350184 +630000 ekin = 0.351051052995002 | erot = 0.362066500827022 | epot = -15.330631588862 | etot = -14.61751403504 +631000 ekin = 0.364060148818953 | erot = 0.352070586246035 | epot = -15.3336447701185 | etot = -14.6175140350535 +632000 ekin = 0.375621025661416 | erot = 0.341366514681189 | epot = -15.334501575399 | etot = -14.6175140350563 +633000 ekin = 0.385258541224309 | erot = 0.330372092305621 | epot = -15.3331446685767 | etot = -14.6175140350468 +634000 ekin = 0.392607865616072 | erot = 0.319588956493667 | epot = -15.329710857134 | etot = -14.6175140350243 +635000 ekin = 0.397436097277817 | erot = 0.309588318033289 | epot = -15.3245384503008 | etot = -14.6175140349897 +636000 ekin = 0.399651602684335 | erot = 0.300988094378234 | epot = -15.3181537320079 | etot = -14.6175140349453 +637000 ekin = 0.399301141331978 | erot = 0.294422893568735 | epot = -15.3112380697947 | etot = -14.617514034894 +638000 ekin = 0.396556439146157 | erot = 0.290509369489293 | epot = -15.3045798434752 | etot = -14.6175140348397 +639000 ekin = 0.391692975512685 | erot = 0.289810143796979 | epot = -15.2990171540957 | etot = -14.6175140347861 +640000 ekin = 0.385064212932825 | erot = 0.29279965311316 | epot = -15.2953779007829 | etot = -14.6175140347369 +641000 ekin = 0.377074355549984 | erot = 0.299834934662478 | epot = -15.2944233249076 | etot = -14.6175140346951 +642000 ekin = 0.368152133960252 | erot = 0.311133625025682 | epot = -15.2967997936491 | etot = -14.6175140346632 +643000 ekin = 0.35872729827394 | erot = 0.326760494743215 | epot = -15.3030018276596 | etot = -14.6175140346425 +644000 ekin = 0.349210670242454 | erot = 0.346622862553666 | epot = -15.3133475674301 | etot = -14.6175140346339 +645000 ekin = 0.339977915473995 | erot = 0.370474376279531 | epot = -15.3279663263912 | etot = -14.6175140346376 +646000 ekin = 0.331356734048571 | erot = 0.397926004728945 | epot = -15.3467967734306 | etot = -14.6175140346531 +647000 ekin = 0.323616951061498 | erot = 0.428462692621698 | epot = -15.3695936783626 | etot = -14.6175140346794 +648000 ekin = 0.316962984679426 | erot = 0.461463981263885 | epot = -15.395941000659 | etot = -14.6175140347157 +649000 ekin = 0.311528303721651 | erot = 0.496226945505972 | epot = -15.4252692839882 | etot = -14.6175140347606 +650000 ekin = 0.307371814502134 | erot = 0.531990113311391 | epot = -15.4568759626263 | etot = -14.6175140348127 +651000 ekin = 0.304476169211803 | erot = 0.567957247022998 | epot = -15.4899474511054 | etot = -14.6175140348706 +652000 ekin = 0.302748327843514 | erot = 0.603320352538697 | epot = -15.5235827153148 | etot = -14.6175140349326 +653000 ekin = 0.302022769690169 | erot = 0.637281675063339 | epot = -15.5568184797505 | etot = -14.617514034997 +654000 ekin = 0.302067723594894 | erot = 0.669074745115614 | epot = -15.5886565037725 | etot = -14.617514035062 +655000 ekin = 0.30259467177562 | erot = 0.697984728109731 | epot = -15.6180934350106 | etot = -14.6175140351253 +656000 ekin = 0.30327116127458 | erot = 0.723368330431443 | epot = -15.6441535268905 | etot = -14.6175140351845 +657000 ekin = 0.303736663271753 | erot = 0.744673311811842 | epot = -15.665924010321 | etot = -14.6175140352374 +658000 ekin = 0.303620889263354 | erot = 0.761457272709825 | epot = -15.6825921972547 | etot = -14.6175140352815 +659000 ekin = 0.302563666908929 | erot = 0.773404945480537 | epot = -15.6934826477038 | etot = -14.6175140353143 +660000 ekin = 0.300235395695977 | erot = 0.780343280385416 | epot = -15.6980927114156 | etot = -14.6175140353342 +661000 ekin = 0.2963557105327 | erot = 0.782250083092817 | epot = -15.6961198289653 | etot = -14.6175140353398 +662000 ekin = 0.290710478297869 | erot = 0.779257959177475 | epot = -15.6874824728057 | etot = -14.6175140353303 +663000 ekin = 0.283165147464189 | erot = 0.771650651991606 | epot = -15.672329834762 | etot = -14.6175140353062 +664000 ekin = 0.27367342717685 | erot = 0.75985056245593 | epot = -15.6510380249012 | etot = -14.6175140352684 +665000 ekin = 0.262280913452633 | erot = 0.744397727319261 | epot = -15.6241926759909 | etot = -14.617514035219 +666000 ekin = 0.249123647022576 | erot = 0.725921231745041 | epot = -15.5925589139283 | etot = -14.6175140351607 +667000 ekin = 0.234422061210095 | erot = 0.705104954965518 | epot = -15.5570410512721 | etot = -14.6175140350965 +668000 ekin = 0.218471158369142 | erot = 0.682650243125394 | epot = -15.5186354365242 | etot = -14.6175140350297 +669000 ekin = 0.201627981911554 | erot = 0.659238455807285 | epot = -15.4783804726821 | etot = -14.6175140349633 +670000 ekin = 0.184297501938695 | erot = 0.635496303881749 | epot = -15.4373078407206 | etot = -14.6175140349002 +671000 ekin = 0.166917915804586 | erot = 0.611966525748987 | epot = -15.3963984763963 | etot = -14.6175140348427 +672000 ekin = 0.149946120673763 | erot = 0.589085832362546 | epot = -15.3565459878289 | etot = -14.6175140347926 +673000 ekin = 0.133843801904168 | erot = 0.567171306813735 | epot = -15.3185291434688 | etot = -14.6175140347509 +674000 ekin = 0.119064262674211 | erot = 0.546415679822031 | epot = -15.2829939772145 | etot = -14.6175140347182 +675000 ekin = 0.106039855016797 | erot = 0.526891195483695 | epot = -15.250445085195 | etot = -14.6175140346945 +676000 ekin = 0.0951697078771964 | erot = 0.508561175679673 | epot = -15.2212449182363 | etot = -14.6175140346794 +677000 ekin = 0.0868074519861108 | erot = 0.491297978911151 | epot = -15.1956194655695 | etot = -14.6175140346723 +678000 ekin = 0.0812485969713162 | erot = 0.47490530110032 | epot = -15.173667932744 | etot = -14.6175140346723 +679000 ekin = 0.0787177619801643 | erot = 0.459143233465844 | epot = -15.1553750301248 | etot = -14.6175140346788 +680000 ekin = 0.079356202465094 | erot = 0.443753980650321 | epot = -15.1406242178063 | etot = -14.6175140346909 +681000 ekin = 0.0832104900793129 | erot = 0.428486254342671 | epot = -15.1292107791298 | etot = -14.6175140347078 +682000 ekin = 0.0902236865228784 | erot = 0.41311688093406 | epot = -15.1208546021859 | etot = -14.617514034729 +683000 ekin = 0.100230543462783 | erot = 0.397468585264983 | epot = -15.1152131634811 | etot = -14.6175140347533 +684000 ekin = 0.112958164259223 | erot = 0.38142345901904 | epot = -15.1118956580582 | etot = -14.61751403478 +685000 ekin = 0.128033094046448 | erot = 0.364932120277571 | epot = -15.1104792491317 | etot = -14.6175140348077 +686000 ekin = 0.144995008361815 | erot = 0.348018922992721 | epot = -15.1105279661897 | etot = -14.6175140348351 +687000 ekin = 0.163316207854869 | erot = 0.330783730220898 | epot = -15.1116139729366 | etot = -14.6175140348608 +688000 ekin = 0.18242523421552 | erot = 0.313400732953528 | epot = -15.1133400020522 | etot = -14.6175140348832 +689000 ekin = 0.201732335852404 | erot = 0.296114640200911 | epot = -15.1153610109544 | etot = -14.6175140349011 +690000 ekin = 0.220654383890837 | erot = 0.2792343742397 | epot = -15.1174027930443 | etot = -14.6175140349138 +691000 ekin = 0.238637189924079 | erot = 0.263124260135935 | epot = -15.1192754849806 | etot = -14.6175140349206 +692000 ekin = 0.255173895595862 | erot = 0.248192653896372 | epot = -15.120880584414 | etot = -14.6175140349217 +693000 ekin = 0.269818995117389 | erot = 0.23487802400786 | epot = -15.1222110540428 | etot = -14.6175140349175 +694000 ekin = 0.282198402188406 | erot = 0.223632668705058 | epot = -15.1233451058024 | etot = -14.6175140349089 +695000 ekin = 0.292016609392508 | erot = 0.214904477347547 | epot = -15.1244351216369 | etot = -14.6175140348968 +696000 ekin = 0.299062308190414 | erot = 0.209117382946464 | epot = -15.125693726019 | etot = -14.6175140348821 +697000 ekin = 0.303213809971508 | erot = 0.20665136156702 | epot = -15.1273792064044 | etot = -14.6175140348658 +698000 ekin = 0.304445256191661 | erot = 0.207822979228463 | epot = -15.1297822702686 | etot = -14.6175140348484 +699000 ekin = 0.302833983904557 | erot = 0.212867544423975 | epot = -15.133215563159 | etot = -14.6175140348305 +700000 ekin = 0.298568596343091 | erot = 0.221923881122192 | epot = -15.1380065122771 | etot = -14.6175140348118 +701000 ekin = 0.291956369738192 | erot = 0.235022588975887 | epot = -15.1444929935065 | etot = -14.6175140347924 +702000 ekin = 0.283427734153971 | erot = 0.252078414120766 | epot = -15.1530201830474 | etot = -14.6175140347727 +703000 ekin = 0.273534855577063 | erot = 0.272887068860917 | epot = -15.1639359591908 | etot = -14.6175140347528 +704000 ekin = 0.262941046164718 | erot = 0.297126498876258 | epot = -15.1775815797747 | etot = -14.6175140347337 +705000 ekin = 0.252398060444993 | erot = 0.324362359960494 | epot = -15.1942744551228 | etot = -14.6175140347173 +706000 ekin = 0.242709489752809 | erot = 0.35405734989386 | epot = -15.2142808743525 | etot = -14.6175140347058 +707000 ekin = 0.23468046525944 | erot = 0.385584073394854 | epot = -15.2377785733566 | etot = -14.6175140347023 +708000 ekin = 0.229056562326985 | erot = 0.418241319395694 | epot = -15.2648119164327 | etot = -14.61751403471 +709000 ekin = 0.226457657534062 | erot = 0.451273895784643 | epot = -15.2952455880503 | etot = -14.6175140347316 +710000 ekin = 0.227314828596047 | erot = 0.483896330832059 | epot = -15.3287251941968 | etot = -14.6175140347687 +711000 ekin = 0.231819479497758 | erot = 0.51532074217238 | epot = -15.3646542564917 | etot = -14.6175140348216 +712000 ekin = 0.239893150549453 | erot = 0.544788749313893 | epot = -15.4021959347515 | etot = -14.6175140348881 +713000 ekin = 0.251183758823612 | erot = 0.571606341189966 | epot = -15.4403041349782 | etot = -14.6175140349646 +714000 ekin = 0.265090036185669 | erot = 0.595179886373849 | epot = -15.4777839576048 | etot = -14.6175140350453 +715000 ekin = 0.280811306968513 | erot = 0.615050345045216 | epot = -15.5133756871376 | etot = -14.6175140351238 +716000 ekin = 0.297415784950172 | erot = 0.63092216570443 | epot = -15.5458519858484 | etot = -14.6175140351938 +717000 ekin = 0.313918116237496 | erot = 0.642683345317361 | epot = -15.5741154968044 | etot = -14.6175140352495 +718000 ekin = 0.329356373326515 | erot = 0.650413757300699 | epot = -15.597284165914 | etot = -14.6175140352868 +719000 ekin = 0.342860093483698 | erot = 0.654380316354833 | epot = -15.6147544451418 | etot = -14.6175140353033 +720000 ekin = 0.353703497402146 | erot = 0.655019233384794 | epot = -15.6262367660857 | etot = -14.6175140352987 +721000 ekin = 0.361340844904821 | erot = 0.652906431496425 | epot = -15.6317613116759 | etot = -14.6175140352746 +722000 ekin = 0.365423978940444 | erot = 0.648719378780955 | epot = -15.6316573929551 | etot = -14.6175140352337 +723000 ekin = 0.365803989071099 | erot = 0.643193727890457 | epot = -15.6265117521414 | etot = -14.6175140351799 +724000 ekin = 0.362520178744054 | erot = 0.637078359572984 | epot = -15.6171125734343 | etot = -14.6175140351172 +725000 ekin = 0.355779938479084 | erot = 0.631092082280464 | epot = -15.6043860558097 | etot = -14.6175140350502 +726000 ekin = 0.345932952940548 | erot = 0.625884613514222 | epot = -15.5893316014373 | etot = -14.6175140349826 +727000 ekin = 0.333442641404433 | erot = 0.622003743386452 | epot = -15.572960419709 | etot = -14.6175140349181 +728000 ekin = 0.31885705049608 | erot = 0.619869891937983 | epot = -15.5562409772938 | etot = -14.6175140348597 +729000 ekin = 0.30278072495631 | erot = 0.61975869169039 | epot = -15.5400534514564 | etot = -14.6175140348097 +730000 ekin = 0.285848455040377 | erot = 0.621791770571061 | epot = -15.5251542603808 | etot = -14.6175140347694 +731000 ekin = 0.26870127220438 | erot = 0.625935552811994 | epot = -15.5121508597562 | etot = -14.6175140347399 +732000 ekin = 0.251964649663544 | erot = 0.632007594592584 | epot = -15.5014862789777 | etot = -14.6175140347215 +733000 ekin = 0.236228569496369 | erot = 0.639689689353592 | epot = -15.4934322935641 | etot = -14.6175140347141 +734000 ekin = 0.2220289607466 | erot = 0.64854669871573 | epot = -15.4880896941798 | etot = -14.6175140347175 +735000 ekin = 0.209830023527896 | erot = 0.658049804518268 | epot = -15.4853938627768 | etot = -14.6175140347306 +736000 ekin = 0.20000716676131 | erot = 0.667602683400117 | epot = -15.4851238849144 | etot = -14.6175140347529 +737000 ekin = 0.192830719625365 | erot = 0.676569044421737 | epot = -15.4869137988309 | etot = -14.6175140347838 +738000 ekin = 0.188451200585985 | erot = 0.684300102138329 | epot = -15.4902653375465 | etot = -14.6175140348222 +739000 ekin = 0.186887639937117 | erot = 0.6901609006521 | epot = -15.4945625754563 | etot = -14.6175140348671 +740000 ekin = 0.18802106841102 | erot = 0.693554915035337 | epot = -15.4990900183636 | etot = -14.6175140349173 +741000 ekin = 0.191595568995591 | erot = 0.693946922730827 | epot = -15.5030565266968 | etot = -14.6175140349704 +742000 ekin = 0.197228843628703 | erot = 0.690884208638806 | epot = -15.5056270872919 | etot = -14.6175140350244 +743000 ekin = 0.204433503637974 | erot = 0.684016821527692 | epot = -15.5059643602413 | etot = -14.6175140350756 +744000 ekin = 0.212648433381792 | erot = 0.673116668202608 | epot = -15.503279136705 | etot = -14.6175140351206 +745000 ekin = 0.221277722248228 | erot = 0.658094727364962 | epot = -15.4968864847688 | etot = -14.6175140351556 +746000 ekin = 0.229733012317398 | erot = 0.639014583780834 | epot = -15.4862616312757 | etot = -14.6175140351775 +747000 ekin = 0.23747404414407 | erot = 0.616100096672176 | epot = -15.4710881760002 | etot = -14.6175140351839 +748000 ekin = 0.244042266762415 | erot = 0.589734872786552 | epot = -15.4512911747231 | etot = -14.6175140351741 +749000 ekin = 0.249083597952522 | erot = 0.560451518402465 | epot = -15.4270491515038 | etot = -14.6175140351488 +750000 ekin = 0.25235833014632 | erot = 0.528910066810374 | epot = -15.3987824320668 | etot = -14.6175140351102 +751000 ekin = 0.253738423480709 | erot = 0.495866496253692 | epot = -15.3671189547962 | etot = -14.6175140350618 +752000 ekin = 0.253194394014668 | erot = 0.462133785332355 | epot = -15.3328422143545 | etot = -14.6175140350075 +753000 ekin = 0.250775308154698 | erot = 0.428539072349797 | epot = -15.2968284154564 | etot = -14.6175140349519 +754000 ekin = 0.246585878545855 | erot = 0.395880964578259 | epot = -15.2599808780229 | etot = -14.6175140348988 +755000 ekin = 0.240764398112151 | erot = 0.364890850085332 | epot = -15.2231692830489 | etot = -14.6175140348514 +756000 ekin = 0.233464471042371 | erot = 0.33620133003052 | epot = -15.1871798358848 | etot = -14.6175140348119 +757000 ekin = 0.224842467157428 | erot = 0.310323830730607 | epot = -15.1526803326694 | etot = -14.6175140347814 +758000 ekin = 0.215051562420606 | erot = 0.287636293953365 | epot = -15.1202018911339 | etot = -14.61751403476 +759000 ekin = 0.204242275875609 | erot = 0.268380753510832 | epot = -15.090137064133 | etot = -14.6175140347465 +760000 ekin = 0.192568636064991 | erot = 0.252669695564108 | epot = -15.0627523663688 | etot = -14.6175140347397 +761000 ekin = 0.180198520175589 | erot = 0.240499428913179 | epot = -15.038211983826 | etot = -14.6175140347373 +762000 ekin = 0.167326299029085 | erot = 0.231768292969539 | epot = -15.0166086267357 | etot = -14.617514034737 +763000 ekin = 0.15418568590204 | erot = 0.226297425418118 | epot = -14.997997146057 | etot = -14.6175140347368 +764000 ekin = 0.141060632749147 | erot = 0.223852003350697 | epot = -14.9824266708347 | etot = -14.6175140347349 +765000 ekin = 0.128292252297103 | erot = 0.224161332820243 | epot = -14.9699676198474 | etot = -14.61751403473 +766000 ekin = 0.116280064488639 | erot = 0.226936813025351 | epot = -14.9607309122354 | etot = -14.6175140347214 +767000 ekin = 0.105476340627594 | erot = 0.231887507272404 | epot = -14.9548778826094 | etot = -14.6175140347094 +768000 ekin = 0.0963728909465988 | erot = 0.23873364134698 | epot = -14.952620566988 | etot = -14.6175140346944 +769000 ekin = 0.0894802427438104 | erot = 0.247218655410706 | epot = -14.9542129328319 | etot = -14.6175140346774 +770000 ekin = 0.0852997361098734 | erot = 0.257120353609604 | epot = -14.9599341243794 | etot = -14.6175140346599 +771000 ekin = 0.0842896183574806 | erot = 0.268261228609983 | epot = -14.9700648816113 | etot = -14.6175140346438 +772000 ekin = 0.0868267987479503 | erot = 0.280517313420827 | epot = -14.9848581468001 | etot = -14.6175140346313 +773000 ekin = 0.0931666172479738 | erot = 0.29382416266062 | epot = -15.0045048145334 | etot = -14.6175140346248 +774000 ekin = 0.103403843826315 | erot = 0.308178073397328 | epot = -15.0290959518505 | etot = -14.6175140346269 +775000 ekin = 0.117439110045059 | erot = 0.323630675217718 | epot = -15.0585838199028 | etot = -14.61751403464 +776000 ekin = 0.134955835364923 | erot = 0.340275613675133 | epot = -15.0927454837062 | etot = -14.6175140346661 +777000 ekin = 0.155413263634583 | erot = 0.3582278427454 | epot = -15.1311551410863 | etot = -14.6175140347063 +778000 ekin = 0.178060391220183 | erot = 0.377596905888865 | epot = -15.1731713318691 | etot = -14.6175140347601 +779000 ekin = 0.201973803863677 | erot = 0.398457850157374 | epot = -15.2179456888463 | etot = -14.6175140348253 +780000 ekin = 0.226119091212116 | erot = 0.420824480237598 | epot = -15.2644576063476 | etot = -14.6175140348979 +781000 ekin = 0.249431156624362 | erot = 0.444629585314245 | epot = -15.3115747769111 | etot = -14.6175140349725 +782000 ekin = 0.27090447026737 | erot = 0.469715692367108 | epot = -15.3581341976774 | etot = -14.617514035043 +783000 ekin = 0.289681273781371 | erot = 0.495837747641005 | epot = -15.4030330565255 | etot = -14.6175140351031 +784000 ekin = 0.305125009984925 | erot = 0.522676532161846 | epot = -15.4453155772951 | etot = -14.6175140351483 +785000 ekin = 0.316868262921689 | erot = 0.549859353707494 | epot = -15.4842416518049 | etot = -14.6175140351757 +786000 ekin = 0.324828845887827 | erot = 0.57698331002341 | epot = -15.5193261910962 | etot = -14.617514035185 +787000 ekin = 0.32919323387832 | erot = 0.60363650580216 | epot = -15.5503437748586 | etot = -14.6175140351781 +788000 ekin = 0.33037186485146 | erot = 0.629413875564563 | epot = -15.5772997755749 | etot = -14.6175140351589 +789000 ekin = 0.328934711355184 | erot = 0.653926193133396 | epot = -15.6003749396209 | etot = -14.6175140351323 +790000 ekin = 0.325537319473833 | erot = 0.676802790007515 | epot = -15.619854144585 | etot = -14.6175140351037 +791000 ekin = 0.320847267933844 | erot = 0.697689943212853 | epot = -15.6360512462245 | etot = -14.6175140350778 +792000 ekin = 0.315479253540059 | erot = 0.716247584425432 | epot = -15.6492408730237 | etot = -14.6175140350582 +793000 ekin = 0.309944490982995 | erot = 0.732146955923568 | epot = -15.659605481954 | etot = -14.6175140350475 +794000 ekin = 0.304617480926279 | erot = 0.745071299200936 | epot = -15.6672028151733 | etot = -14.6175140350461 +795000 ekin = 0.299720880977542 | erot = 0.754720862086076 | epot = -15.6719557781174 | etot = -14.6175140350538 +796000 ekin = 0.295327396181288 | erot = 0.760822658788699 | epot = -15.6736640900385 | etot = -14.6175140350685 +797000 ekin = 0.291376296852734 | erot = 0.763144639346229 | epot = -15.6720349712862 | etot = -14.6175140350872 +798000 ekin = 0.287701294704638 | erot = 0.761513269132583 | epot = -15.6667285989436 | etot = -14.6175140351064 +799000 ekin = 0.284065979572969 | erot = 0.755832991337638 | epot = -15.6574130060325 | etot = -14.6175140351219 +800000 ekin = 0.280202790632173 | erot = 0.746105645864818 | epot = -15.6438224716274 | etot = -14.6175140351304 +801000 ekin = 0.275851560112921 | erot = 0.732447665813908 | epot = -15.6258132610552 | etot = -14.6175140351284 +802000 ekin = 0.270794034433598 | erot = 0.715102809072986 | epot = -15.6034108786203 | etot = -14.6175140351137 +803000 ekin = 0.264881442636211 | erot = 0.694448356025999 | epot = -15.5768438337475 | etot = -14.6175140350853 +804000 ekin = 0.258053167890611 | erot = 0.670993199746564 | epot = -15.5465604026803 | etot = -14.6175140350431 +805000 ekin = 0.250345604727777 | erot = 0.645366941436383 | epot = -15.5132265811527 | etot = -14.6175140349885 +806000 ekin = 0.241890533711227 | erot = 0.618299214643911 | epot = -15.4777037832789 | etot = -14.6175140349238 +807000 ekin = 0.232905655206386 | erot = 0.59059128773573 | epot = -15.4410109777945 | etot = -14.6175140348524 +808000 ekin = 0.223678061732307 | erot = 0.563080896687569 | epot = -15.404272993198 | etot = -14.6175140347781 +809000 ekin = 0.21454303522989 | erot = 0.536602758841035 | epot = -15.3686598287761 | etot = -14.6175140347052 +810000 ekin = 0.205860488312487 | erot = 0.511947500022813 | epot = -15.335322022973 | etot = -14.6175140346377 +811000 ekin = 0.197991117804985 | erot = 0.489821758276953 | epot = -15.3053269106614 | etot = -14.6175140345795 +812000 ekin = 0.191273941670598 | erot = 0.470812030933133 | epot = -15.2796000071373 | etot = -14.6175140345336 +813000 ekin = 0.18600640436918 | erot = 0.455354451061547 | epot = -15.2588748899335 | etot = -14.6175140345028 +814000 ekin = 0.182427753711695 | erot = 0.443712201373049 | epot = -15.2436539895733 | etot = -14.6175140344886 +815000 ekin = 0.180705986334899 | erot = 0.435961774090678 | epot = -15.2341817949176 | etot = -14.617514034492 +816000 ekin = 0.180928373605138 | erot = 0.431988814112469 | epot = -15.2304312222306 | etot = -14.617514034513 +817000 ekin = 0.183095431233989 | erot = 0.431493858262917 | epot = -15.2321033240477 | etot = -14.6175140345508 +818000 ekin = 0.187118173911423 | erot = 0.43400789506895 | epot = -15.2386401035843 | etot = -14.6175140346039 +819000 ekin = 0.192818568053485 | erot = 0.438917286806367 | epot = -15.2492498895297 | etot = -14.6175140346698 +820000 ekin = 0.199933211815007 | erot = 0.445497181488063 | epot = -15.2629444280486 | etot = -14.6175140347455 +821000 ekin = 0.208120374082307 | erot = 0.452952069483619 | epot = -15.2785864783934 | etot = -14.6175140348274 +822000 ekin = 0.216970558498724 | erot = 0.460461605795572 | epot = -15.2949461992058 | etot = -14.6175140349115 +823000 ekin = 0.226020685629653 | erot = 0.467229260922794 | epot = -15.3107639815457 | etot = -14.6175140349933 +824000 ekin = 0.234771793852154 | erot = 0.472530858216694 | epot = -15.3248166871376 | etot = -14.6175140350687 +825000 ekin = 0.242709867662635 | erot = 0.475759712130466 | epot = -15.3359836149267 | etot = -14.6175140351336 +826000 ekin = 0.249329060858575 | erot = 0.476465014357238 | epot = -15.3433081104001 | etot = -14.6175140351843 +827000 ekin = 0.25415625948642 | erot = 0.474380409602698 | epot = -15.3460507043074 | etot = -14.6175140352183 +828000 ekin = 0.256775693171424 | erot = 0.469440383344404 | epot = -15.3437301117495 | etot = -14.6175140352337 +829000 ekin = 0.256852201217284 | erot = 0.46178309210187 | epot = -15.336149328549 | etot = -14.6175140352299 +830000 ekin = 0.254151805817283 | erot = 0.451739467040903 | epot = -15.3234053080654 | etot = -14.6175140352073 +831000 ekin = 0.248558416434218 | erot = 0.439809632306185 | epot = -15.3058820839079 | etot = -14.6175140351675 +832000 ekin = 0.240085737091441 | erot = 0.426628719075599 | epot = -15.2842284912797 | etot = -14.6175140351126 +833000 ekin = 0.228883712687973 | erot = 0.412924890623741 | epot = -15.2593226383575 | etot = -14.6175140350458 +834000 ekin = 0.215239082682017 | erot = 0.399472764055522 | epot = -15.2322258817081 | etot = -14.6175140349705 +835000 ekin = 0.199569787294727 | erot = 0.387045440519038 | epot = -15.2041292627042 | etot = -14.6175140348904 +836000 ekin = 0.182413100763729 | erot = 0.376368114580306 | epot = -15.1762952501535 | etot = -14.6175140348094 +837000 ekin = 0.164407483062571 | erot = 0.368075825930997 | epot = -15.149997343725 | etot = -14.6175140347315 +838000 ekin = 0.146268295773245 | erot = 0.362677435797452 | epot = -15.1264597662308 | etot = -14.6175140346601 +839000 ekin = 0.128757768426142 | erot = 0.360527421580312 | epot = -15.1067992246053 | etot = -14.6175140345989 +840000 ekin = 0.112649960717701 | erot = 0.36180661865639 | epot = -15.0919706139249 | etot = -14.6175140345508 +841000 ekin = 0.0986919456674289 | erot = 0.36651260392939 | epot = -15.0827185841154 | etot = -14.6175140345186 +842000 ekin = 0.0875630029231973 | erot = 0.374460003556307 | epot = -15.0795370409836 | etot = -14.6175140345041 +843000 ekin = 0.0798341847684568 | erot = 0.385290606533499 | epot = -15.0826388258105 | etot = -14.6175140345086 +844000 ekin = 0.0759310929906455 | erot = 0.398492769730518 | epot = -15.0919378972534 | etot = -14.6175140345322 +845000 ekin = 0.0761029610203614 | erot = 0.413429207169692 | epot = -15.1070462027642 | etot = -14.6175140345741 +846000 ekin = 0.0804010613291467 | erot = 0.429371869323724 | epot = -15.1272869652855 | etot = -14.6175140346326 +847000 ekin = 0.0886689809243283 | erot = 0.445542241999283 | epot = -15.151725257628 | etot = -14.6175140347044 +848000 ekin = 0.100546421460129 | erot = 0.46115503871289 | epot = -15.1792154949586 | etot = -14.6175140347856 +849000 ekin = 0.115486960011282 | erot = 0.475462945352927 | epot = -15.2084639402358 | etot = -14.6175140348716 +850000 ekin = 0.132788806696208 | erot = 0.487799837753942 | epot = -15.2381026794073 | etot = -14.6175140349572 +851000 ekin = 0.151636227786906 | erot = 0.497619785577632 | epot = -15.2667700484016 | etot = -14.6175140350371 +852000 ekin = 0.171148194576718 | erot = 0.504529242628412 | epot = -15.2931914723118 | etot = -14.6175140351066 +853000 ekin = 0.190430159396265 | erot = 0.50831015746196 | epot = -15.31625435202 | etot = -14.6175140351617 +854000 ekin = 0.208624756900111 | erot = 0.508932337651449 | epot = -15.3350711297509 | etot = -14.6175140351993 +855000 ekin = 0.224957674812678 | erot = 0.506554231539646 | epot = -15.3490259415702 | etot = -14.6175140352179 +856000 ekin = 0.238775816539412 | erot = 0.501512259960127 | epot = -15.3578021117162 | etot = -14.6175140352167 +857000 ekin = 0.249575992234284 | erot = 0.494299801981541 | epot = -15.3613898294126 | etot = -14.6175140351967 +858000 ekin = 0.257023502073991 | erot = 0.485537766821542 | epot = -15.3600753040553 | etot = -14.6175140351598 +859000 ekin = 0.260960921285794 | erot = 0.475939247615297 | epot = -15.3544142040096 | etot = -14.6175140351085 +860000 ekin = 0.261408037072425 | erot = 0.466270984603931 | epot = -15.3451930567221 | etot = -14.6175140350458 +861000 ekin = 0.258554187538353 | erot = 0.457314264402295 | epot = -15.3333824869156 | etot = -14.6175140349749 +862000 ekin = 0.252744258033141 | erot = 0.449827506885222 | epot = -15.3200857998177 | etot = -14.6175140348993 +863000 ekin = 0.244459417796683 | erot = 0.444512141833012 | epot = -15.3064855944521 | etot = -14.6175140348224 +864000 ekin = 0.23429336884036 | erot = 0.441983030938511 | epot = -15.2937904345263 | etot = -14.6175140347475 +865000 ekin = 0.222924696624272 | erot = 0.442744308393629 | epot = -15.2831830396954 | etot = -14.6175140346775 +866000 ekin = 0.211086026109497 | erot = 0.447169652379628 | epot = -15.2757697131049 | etot = -14.6175140346158 +867000 ekin = 0.199530465893205 | erot = 0.455487658922675 | epot = -15.2725321593806 | etot = -14.6175140345647 +868000 ekin = 0.188996288427701 | erot = 0.467771811642206 | epot = -15.274282134597 | etot = -14.6175140345271 +869000 ekin = 0.180171161859839 | erot = 0.483934855625384 | epot = -15.2816200519904 | etot = -14.6175140345052 +870000 ekin = 0.173657413869083 | erot = 0.503727420428225 | epot = -15.2948988687979 | etot = -14.6175140345006 +871000 ekin = 0.169940429082826 | erot = 0.526741193130643 | epot = -15.3141956567281 | etot = -14.6175140345146 +872000 ekin = 0.169362274179231 | erot = 0.55241708894464 | epot = -15.3392933976713 | etot = -14.6175140345475 +873000 ekin = 0.172102391202432 | erot = 0.580058846013128 | epot = -15.3696752718142 | etot = -14.6175140345986 +874000 ekin = 0.178167002902699 | erot = 0.608852557306752 | epot = -15.404533594876 | etot = -14.6175140346666 +875000 ekin = 0.187388233891608 | erot = 0.637892396629037 | epot = -15.4427946652693 | etot = -14.6175140347487 +876000 ekin = 0.199433181368205 | erot = 0.666212376944565 | epot = -15.4831595931543 | etot = -14.6175140348416 +877000 ekin = 0.213822249051452 | erot = 0.69282332523737 | epot = -15.5241596092296 | etot = -14.6175140349407 +878000 ekin = 0.229955728386783 | erot = 0.716754212644293 | epot = -15.5642239760726 | etot = -14.6175140350415 +879000 ekin = 0.247146104645698 | erot = 0.737095186134375 | epot = -15.6017553259191 | etot = -14.617514035139 +880000 ekin = 0.264653797002906 | erot = 0.753040153405454 | epot = -15.6352079856366 | etot = -14.6175140352283 +881000 ekin = 0.28172378426185 | erot = 0.763926241590771 | epot = -15.6631640611577 | etot = -14.617514035305 +882000 ekin = 0.297620641607227 | erot = 0.769267373447333 | epot = -15.6844020504203 | etot = -14.6175140353657 +883000 ekin = 0.311659967166543 | erot = 0.768779581882131 | epot = -15.6979535844564 | etot = -14.6175140354077 +884000 ekin = 0.323234773768197 | erot = 0.762396270683944 | epot = -15.7031450798816 | etot = -14.6175140354294 +885000 ekin = 0.331836099625417 | erot = 0.750272396067174 | epot = -15.6996225311231 | etot = -14.6175140354305 +886000 ekin = 0.337067751564103 | erot = 0.732777385265373 | epot = -15.6873591722411 | etot = -14.6175140354117 +887000 ekin = 0.338655649766336 | erot = 0.710477420749848 | epot = -15.6666471058904 | etot = -14.6175140353742 +888000 ekin = 0.336452632420875 | erot = 0.684108417155686 | epot = -15.6380750848969 | etot = -14.6175140353203 +889000 ekin = 0.330439768515621 | erot = 0.654541548239603 | epot = -15.602495352008 | etot = -14.6175140352528 +890000 ekin = 0.320725208484741 | erot = 0.62274352002662 | epot = -15.5609827636857 | etot = -14.6175140351743 +891000 ekin = 0.307541386208895 | erot = 0.589733936087021 | epot = -15.514789357384 | etot = -14.6175140350881 +892000 ekin = 0.291240998129636 | erot = 0.556542080397485 | epot = -15.465297113524 | etot = -14.6175140349969 +893000 ekin = 0.272291667891092 | erot = 0.524165278720341 | epot = -15.4139709815152 | etot = -14.6175140349038 +894000 ekin = 0.251268620703177 | erot = 0.493530718297282 | epot = -15.3623133738115 | etot = -14.6175140348111 +895000 ekin = 0.228844131843334 | erot = 0.465462234286213 | epot = -15.311820400851 | etot = -14.6175140347214 +896000 ekin = 0.205772103521623 | erot = 0.440653137306931 | epot = -15.263939275466 | etot = -14.6175140346374 +897000 ekin = 0.18286601780276 | erot = 0.419645693758162 | epot = -15.2200257461227 | etot = -14.6175140345617 +898000 ekin = 0.160968870008327 | erot = 0.40281742524286 | epot = -15.1813003297482 | etot = -14.617514034497 +899000 ekin = 0.140914625128286 | erot = 0.390374024162985 | epot = -15.1488026837377 | etot = -14.6175140344464 +900000 ekin = 0.123482269337591 | erot = 0.382348451689304 | epot = -15.1233447554395 | etot = -14.6175140344126 +901000 ekin = 0.109345484385278 | erot = 0.378605737554559 | epot = -15.1054652563381 | etot = -14.6175140343982 +902000 ekin = 0.0990229789071406 | erot = 0.37885314016642 | epot = -15.0953901534788 | etot = -14.6175140344052 +903000 ekin = 0.0928360184568559 | erot = 0.382655585825979 | epot = -15.093005638717 | etot = -14.6175140344341 +904000 ekin = 0.0908801123885926 | erot = 0.389456554773827 | epot = -15.0978507016463 | etot = -14.6175140344838 +905000 ekin = 0.0930167096533132 | erot = 0.398604648850322 | epot = -15.1091353930552 | etot = -14.6175140345515 +906000 ekin = 0.0988880708470662 | erot = 0.409385812369458 | epot = -15.1257879178489 | etot = -14.6175140346324 +907000 ekin = 0.107954659148216 | erot = 0.421060528764254 | epot = -15.1465292226329 | etot = -14.6175140347204 +908000 ekin = 0.119550305155171 | erot = 0.432904367174519 | epot = -15.1699687071382 | etot = -14.6175140348085 +909000 ekin = 0.132947118365042 | erot = 0.444249232158093 | epot = -15.1947103854133 | etot = -14.6175140348902 +910000 ekin = 0.14742054333404 | erot = 0.45452187965619 | epot = -15.2194564579498 | etot = -14.6175140349596 +911000 ekin = 0.162305506309761 | erot = 0.463275978358842 | epot = -15.2430955196813 | etot = -14.6175140350127 +912000 ekin = 0.177037050913266 | erot = 0.470214361754283 | epot = -15.2647654477151 | etot = -14.6175140350476 +913000 ekin = 0.191172462463443 | erot = 0.475199092565798 | epot = -15.2838855900934 | etot = -14.6175140350642 +914000 ekin = 0.204395616840806 | erot = 0.478248345047313 | epot = -15.3001579969523 | etot = -14.6175140350642 +915000 ekin = 0.21650723869525 | erot = 0.479520616571472 | epot = -15.3135418903175 | etot = -14.6175140350508 +916000 ekin = 0.22740635239903 | erot = 0.479288139235308 | epot = -15.3242085266619 | etot = -14.6175140350276 +917000 ekin = 0.237068358847916 | erot = 0.477902392722287 | epot = -15.3324847865686 | etot = -14.6175140349984 +918000 ekin = 0.245524170398606 | erot = 0.475755244751368 | epot = -15.338793450117 | etot = -14.617514034967 +919000 ekin = 0.252843202023207 | erot = 0.473239468154926 | epot = -15.3435967051145 | etot = -14.6175140349364 +920000 ekin = 0.259121284814418 | erot = 0.470712244289352 | epot = -15.3473475640129 | etot = -14.6175140349091 +921000 ekin = 0.264473144075716 | erot = 0.468464808091652 | epot = -15.3504519870541 | etot = -14.6175140348868 +922000 ekin = 0.269028180853147 | erot = 0.466700668341421 | epot = -15.3532428840648 | etot = -14.6175140348703 +923000 ekin = 0.272927944744965 | erot = 0.465523908452019 | epot = -15.3559658880565 | etot = -14.6175140348596 +924000 ekin = 0.276323793828338 | erot = 0.464938026324942 | epot = -15.3587758550077 | etot = -14.6175140348544 +925000 ekin = 0.279373649322719 | erot = 0.464854721381143 | epot = -15.3617424055579 | etot = -14.6175140348541 +926000 ekin = 0.282237300897349 | erot = 0.465111106681717 | epot = -15.3648624424361 | etot = -14.6175140348571 +927000 ekin = 0.285070250341268 | erot = 0.465493135294266 | epot = -15.3680774204978 | etot = -14.6175140348623 +928000 ekin = 0.288016501944426 | erot = 0.465762600719312 | epot = -15.3712931375323 | etot = -14.6175140348686 +929000 ekin = 0.291201026098215 | erot = 0.465684740680354 | epot = -15.3743998016532 | etot = -14.6175140348747 +930000 ekin = 0.294722459179014 | erot = 0.465054261990702 | epot = -15.3772907560492 | etot = -14.6175140348795 +931000 ekin = 0.29864676401532 | erot = 0.463717248454336 | epot = -15.3798780473521 | etot = -14.6175140348824 +932000 ekin = 0.30300230463982 | erot = 0.461587311534142 | epot = -15.382103651057 | etot = -14.617514034883 +933000 ekin = 0.307776651095021 | erot = 0.458654945592281 | epot = -15.3839456315687 | etot = -14.6175140348814 +934000 ekin = 0.312915338272243 | erot = 0.454989722656041 | epot = -15.385419095806 | etot = -14.6175140348777 +935000 ekin = 0.318322768321537 | erot = 0.4507356255513 | epot = -15.3865724287453 | etot = -14.6175140348725 +936000 ekin = 0.323865441581232 | erot = 0.446100385695392 | epot = -15.3874798621431 | etot = -14.6175140348664 +937000 ekin = 0.329377658420751 | erot = 0.441340069470884 | epot = -15.3882317627517 | etot = -14.6175140348601 +938000 ekin = 0.334669609401342 | erot = 0.436740154638299 | epot = -15.3889237988938 | etot = -14.6175140348541 +939000 ekin = 0.339538182698431 | erot = 0.432595723627041 | epot = -15.3896479411745 | etot = -14.617514034849 +940000 ekin = 0.343779460434951 | erot = 0.429190561372456 | epot = -15.3904840566526 | etot = -14.6175140348452 +941000 ekin = 0.347202304173587 | erot = 0.426777065358565 | epot = -15.391493404375 | etot = -14.6175140348428 +942000 ekin = 0.349642062607373 | erot = 0.425558062624985 | epot = -15.3927141600744 | etot = -14.6175140348421 +943000 ekin = 0.350973206935267 | erot = 0.425671371650545 | epot = -15.3941586134289 | etot = -14.6175140348431 +944000 ekin = 0.351119786154239 | erot = 0.427178062458757 | epot = -15.3958118834587 | etot = -14.6175140348457 +945000 ekin = 0.350062816508182 | erot = 0.430055404932911 | epot = -15.397632256291 | etot = -14.6175140348499 +946000 ekin = 0.347844068536133 | erot = 0.434195447788936 | epot = -15.3995535511804 | etot = -14.6175140348553 +947000 ekin = 0.344566017440968 | erot = 0.439410327983271 | epot = -15.4014903802857 | etot = -14.6175140348614 +948000 ekin = 0.340388212506876 | erot = 0.445444378275944 | epot = -15.4033466256503 | etot = -14.6175140348675 +949000 ekin = 0.335520427168076 | erot = 0.451992965713332 | epot = -15.405027427754 | etot = -14.6175140348726 +950000 ekin = 0.330213181195925 | erot = 0.458727107974287 | epot = -15.4064543240458 | etot = -14.6175140348756 +951000 ekin = 0.324745816556271 | erot = 0.465321341195901 | epot = -15.4075811926278 | etot = -14.6175140348756 +952000 ekin = 0.319412679962131 | erot = 0.471482169175953 | epot = -15.4084088840101 | etot = -14.617514034872 +953000 ekin = 0.314508037100271 | erot = 0.476974139325801 | epot = -15.4089962112904 | etot = -14.6175140348643 +954000 ekin = 0.310309685024597 | erot = 0.481639431416524 | epot = -15.4094631512943 | etot = -14.6175140348532 +955000 ekin = 0.30706194776561 | erot = 0.485408201612597 | epot = -15.4099841842179 | etot = -14.6175140348397 +956000 ekin = 0.304958921289462 | erot = 0.488297803840355 | epot = -15.4107707599554 | etot = -14.6175140348255 +957000 ekin = 0.304129209169334 | erot = 0.490400499131601 | epot = -15.4120437431141 | etot = -14.6175140348131 +958000 ekin = 0.304623714620741 | erot = 0.491860923620763 | epot = -15.4139986730463 | etot = -14.6175140348048 +959000 ekin = 0.306408207892433 | erot = 0.492846142548468 | epot = -15.4167683852438 | etot = -14.6175140348029 +960000 ekin = 0.309362278814204 | erot = 0.493512316197963 | epot = -15.4203886298212 | etot = -14.617514034809 +961000 ekin = 0.313285873785893 | erot = 0.493972653387203 | epot = -15.4247725619971 | etot = -14.617514034824 +962000 ekin = 0.317913924785377 | erot = 0.494271324762721 | epot = -15.4296992843955 | etot = -14.6175140348474 +963000 ekin = 0.322938673954067 | erot = 0.494367337737335 | epot = -15.434820046569 | etot = -14.6175140348776 +964000 ekin = 0.32803828153202 | erot = 0.494131108238476 | epot = -15.4396834246822 | etot = -14.6175140349118 +965000 ekin = 0.332909295684033 | erot = 0.493354750676285 | epot = -15.4437780813066 | etot = -14.6175140349462 +966000 ekin = 0.337299689763766 | erot = 0.491775167781745 | epot = -15.4465888925225 | etot = -14.617514034977 +967000 ekin = 0.341038574327655 | erot = 0.489107134739062 | epot = -15.4476597440666 | etot = -14.6175140349999 +968000 ekin = 0.344058508087222 | erot = 0.485082040987952 | epot = -15.4466545840868 | etot = -14.6175140350117 +969000 ekin = 0.346406687227151 | erot = 0.479487053291702 | epot = -15.4434077755292 | etot = -14.6175140350103 +970000 ekin = 0.348242259951282 | erot = 0.472199376074787 | epot = -15.4379556710213 | etot = -14.6175140349953 +971000 ekin = 0.349818577908804 | erot = 0.463211040207177 | epot = -15.4305436530837 | etot = -14.6175140349678 +972000 ekin = 0.351451221504524 | erot = 0.452641107453752 | epot = -15.4216063638891 | etot = -14.6175140349308 +973000 ekin = 0.3534748518418 | erot = 0.440734047140215 | epot = -15.4117229338706 | etot = -14.6175140348885 +974000 ekin = 0.356193968986606 | erot = 0.427844962322964 | epot = -15.4015529661554 | etot = -14.6175140348458 +975000 ekin = 0.359834072252968 | erot = 0.414413971021433 | epot = -15.3917620780819 | etot = -14.6175140348075 +976000 ekin = 0.364500158164541 | erot = 0.400933139115399 | epot = -15.3829473320578 | etot = -14.6175140347778 +977000 ekin = 0.370148756531594 | erot = 0.387909813696784 | epot = -15.3755726049881 | etot = -14.6175140347597 +978000 ekin = 0.376577842832112 | erot = 0.37583005908299 | epot = -15.3699219366697 | etot = -14.6175140347546 +979000 ekin = 0.383436289098897 | erot = 0.365125297246974 | epot = -15.3660756211082 | etot = -14.6175140347623 +980000 ekin = 0.390251542221838 | erot = 0.356144397459927 | epot = -15.3639099744635 | etot = -14.6175140347817 +981000 ekin = 0.396471539315499 | erot = 0.349132547198626 | epot = -15.3631181213241 | etot = -14.61751403481 +982000 ekin = 0.401514997591354 | erot = 0.344217435800631 | epot = -15.3632464682362 | etot = -14.6175140348443 +983000 ekin = 0.404823458769612 | erot = 0.341402706417366 | epot = -15.3637402000685 | etot = -14.6175140348815 +984000 ekin = 0.405908866684804 | erot = 0.34056832459917 | epot = -15.3639912262027 | etot = -14.6175140349188 +985000 ekin = 0.404391803059605 | erot = 0.341477444721989 | epot = -15.3633832827353 | etot = -14.6175140349537 +986000 ekin = 0.400027422799988 | erot = 0.343789434463081 | epot = -15.3613308922474 | etot = -14.6175140349843 +987000 ekin = 0.392718180743718 | erot = 0.347078806740141 | epot = -15.357311022493 | etot = -14.6175140350092 +988000 ekin = 0.382514239213264 | erot = 0.350859769148604 | epot = -15.3508880433891 | etot = -14.6175140350273 +989000 ekin = 0.36960372665304 | erot = 0.354615837190747 | epot = -15.3417335988814 | etot = -14.6175140350376 +990000 ekin = 0.354295674460603 | erot = 0.357833454089941 | epot = -15.3296431635899 | etot = -14.6175140350393 +991000 ekin = 0.336998529350877 | erot = 0.360037895319979 | epot = -15.3145504597026 | etot = -14.6175140350318 +992000 ekin = 0.318196763890073 | erot = 0.360829065192576 | epot = -15.296539864097 | etot = -14.6175140350143 +993000 ekin = 0.298427479538382 | erot = 0.359914303090994 | epot = -15.2758558176161 | etot = -14.6175140349867 +994000 ekin = 0.278258203579966 | erot = 0.357135170966681 | epot = -15.2529074094957 | etot = -14.6175140349491 +995000 ekin = 0.258266471895044 | erot = 0.352485480213702 | epot = -15.2282659870109 | etot = -14.6175140349022 +996000 ekin = 0.239021351636038 | erot = 0.346118523028621 | epot = -15.2026539095118 | etot = -14.6175140348471 +997000 ekin = 0.221066818081191 | erot = 0.338342492443265 | epot = -15.1769233453106 | etot = -14.6175140347861 +998000 ekin = 0.204906835818307 | erot = 0.329604233509113 | epot = -15.152025104049 | etot = -14.6175140347215 +999000 ekin = 0.190992053959209 | erot = 0.320462575794744 | epot = -15.1289686644103 | etot = -14.6175140346563 +1000000 ekin = 0.179708146665587 | erot = 0.311553394428757 | epot = -15.1087755756882 | etot = -14.6175140345938 + 1000000 0.013311715 -1.5443684 0.033490821 -1.4929067 -3.7544839e-05 +Loop time of 28.9854 on 4 procs for 1000000 steps with 10 atoms + +Performance: 29808.075 tau/day, 34500.086 timesteps/s +96.6% CPU use with 4 MPI tasks x no OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0.85571 | 9.8341 | 18.111 | 228.8 | 33.93 +Bond | 0.12393 | 0.38078 | 0.62324 | 32.7 | 1.31 +Neigh | 0 | 0 | 0 | 0.0 | 0.00 +Comm | 2.795 | 3.6269 | 4.4228 | 30.4 | 12.51 +Output | 1.8e-05 | 2.575e-05 | 2.9e-05 | 0.0 | 0.00 +Modify | 0.24721 | 1.1083 | 1.9206 | 64.1 | 3.82 +Other | | 14.04 | | | 48.42 + +Nlocal: 2.5 ave 5 max 0 min +Histogram: 1 0 1 0 0 0 0 0 1 1 +Nghost: 7.5 ave 10 max 5 min +Histogram: 1 0 1 0 0 0 0 0 1 1 +Neighs: 18.5 ave 35 max 0 min +Histogram: 1 0 1 0 0 0 0 0 1 1 + +Total # of neighbors = 74 +Ave neighs/atom = 7.4 +Ave special neighs/atom = 3.6 +Neighbor list builds = 0 +Dangerous builds = 0 + +#write_restart config.${number}.* +Total wall time: 0:00:28 diff --git a/examples/USER/cgdna/examples/oxDNA2/duplex1/log.27Nov18.duplex1.g++.1 b/examples/USER/cgdna/examples/oxDNA2/duplex1/log.27Nov18.duplex1.g++.1 deleted file mode 100644 index 2c09a4f99d..0000000000 --- a/examples/USER/cgdna/examples/oxDNA2/duplex1/log.27Nov18.duplex1.g++.1 +++ /dev/null @@ -1,178 +0,0 @@ -LAMMPS (27 Nov 2018) - using 1 OpenMP thread(s) per MPI task -variable number equal 1 -variable ofreq equal 1000 -variable efreq equal 1000 - -units lj - -dimension 3 - -newton off - -boundary p p p - -atom_style hybrid bond ellipsoid -atom_modify sort 0 1.0 - -# Pair interactions require lists of neighbours to be calculated -neighbor 1.0 bin -neigh_modify every 1 delay 0 check yes - -read_data data.duplex1 - orthogonal box = (-20 -20 -20) to (20 20 20) - 1 by 1 by 1 MPI processor grid - reading atoms ... - 10 atoms - reading velocities ... - 10 velocities - 10 ellipsoids - scanning bonds ... - 2 = max bonds/atom - reading bonds ... - 8 bonds - 2 = max # of 1-2 neighbors - 2 = max # of 1-3 neighbors - 2 = max # of 1-4 neighbors - 4 = max # of special neighbors - -set atom * mass 3.1575 - 10 settings made for mass - -group all type 1 4 -10 atoms in group all - -# oxDNA bond interactions - FENE backbone -bond_style oxdna2/fene -bond_coeff * 2.0 0.25 0.7564 - -# oxDNA pair interactions -pair_style hybrid/overlay oxdna2/excv oxdna2/stk oxdna2/hbond oxdna2/xstk oxdna2/coaxstk oxdna2/dh -pair_coeff * * oxdna2/excv 2.0 0.7 0.675 2.0 0.515 0.5 2.0 0.33 0.32 -pair_coeff * * oxdna2/stk seqav 0.1 6.0 0.4 0.9 0.32 0.6 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2.0 0.65 2.0 0.65 -pair_coeff * * oxdna2/hbond seqav 0.0 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45 -pair_coeff 1 4 oxdna2/hbond seqav 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45 -pair_coeff 2 3 oxdna2/hbond seqav 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45 -pair_coeff * * oxdna2/xstk 47.5 0.575 0.675 0.495 0.655 2.25 0.791592653589793 0.58 1.7 1.0 0.68 1.7 1.0 0.68 1.5 0 0.65 1.7 0.875 0.68 1.7 0.875 0.68 -pair_coeff * * oxdna2/coaxstk 58.5 0.4 0.6 0.22 0.58 2.0 2.891592653589793 0.65 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 40.0 3.116592653589793 -pair_coeff * * oxdna2/dh 0.1 1.0 0.815 - -# NVE ensemble -fix 1 all nve/dot -#fix 1 all nve/dotc/langevin 0.1 0.1 0.03 457145 angmom 10 -#fix 1 all nve/asphere -#fix 2 all langevin 0.1 0.1 0.03 457145 angmom 10 - -timestep 1e-5 - -#comm_style tiled -#fix 3 all balance 10000 1.1 rcb - -#compute mol all chunk/atom molecule -#compute mychunk all vcm/chunk mol -#fix 4 all ave/time 10000 1 10000 c_mychunk[1] c_mychunk[2] c_mychunk[3] file vcm.txt mode vector - -#dump pos all xyz ${ofreq} traj.${number}.xyz - -#compute quat all property/atom quatw quati quatj quatk -#dump quat all custom ${ofreq} quat.${number}.txt id c_quat[1] c_quat[2] c_quat[3] c_quat[4] -#dump_modify quat sort id -#dump_modify quat format line "%d %13.6le %13.6le %13.6le %13.6le" - -compute erot all erotate/asphere -compute ekin all ke -compute epot all pe -variable erot equal c_erot -variable ekin equal c_ekin -variable epot equal c_epot -variable etot equal c_erot+c_ekin+c_epot -fix 5 all print ${efreq} "$(step) ekin = ${ekin} | erot = ${erot} | epot = ${epot} | etot = ${etot}" screen yes -fix 5 all print 1000 "$(step) ekin = ${ekin} | erot = ${erot} | epot = ${epot} | etot = ${etot}" screen yes - -#dump out all custom ${ofreq} out.${number}.txt id x y z vx vy vz fx fy fz tqx tqy tqz -#dump_modify out sort id -#dump_modify out format line "%d %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le" - -run 10000 -Neighbor list info ... - update every 1 steps, delay 0 steps, check yes - max neighbors/atom: 2000, page size: 100000 - master list distance cutoff = 2.6274 - ghost atom cutoff = 2.6274 - binsize = 1.3137, bins = 31 31 31 - 6 neighbor lists, perpetual/occasional/extra = 6 0 0 - (1) pair oxdna2/excv, perpetual - attributes: half, newton off - pair build: half/bin/newtoff - stencil: half/bin/3d/newtoff - bin: standard - (2) pair oxdna2/stk, perpetual, copy from (1) - attributes: half, newton off - pair build: copy - stencil: none - bin: none - (3) pair oxdna2/hbond, perpetual, copy from (1) - attributes: half, newton off - pair build: copy - stencil: none - bin: none - (4) pair oxdna2/xstk, perpetual, copy from (1) - attributes: half, newton off - pair build: copy - stencil: none - bin: none - (5) pair oxdna2/coaxstk, perpetual, copy from (1) - attributes: half, newton off - pair build: copy - stencil: none - bin: none - (6) pair oxdna2/dh, perpetual, copy from (1) - attributes: half, newton off - pair build: copy - stencil: none - bin: none -Per MPI rank memory allocation (min/avg/max) = 3.023 | 3.023 | 3.023 Mbytes -Step Temp E_pair E_mol TotEng Press - 0 0 -1.4712768 0.009525411 -1.4617514 -5.8922361e-05 -1000 ekin = 0.00113086229080528 | erot = 0.0043101016040658 | epot = -14.6229549982368 | etot = -14.617514034342 -2000 ekin = 0.0044853322434243 | erot = 0.0171407706505008 | epot = -14.6391401372615 | etot = -14.6175140343675 -3000 ekin = 0.00995035259649284 | erot = 0.0381961780846485 | epot = -14.6656605650904 | etot = -14.6175140344093 -4000 ekin = 0.0173418024862054 | erot = 0.0669935184860634 | epot = -14.7018493554381 | etot = -14.6175140344659 -5000 ekin = 0.0264109356286075 | erot = 0.102878288094517 | epot = -14.7468032582586 | etot = -14.6175140345355 -6000 ekin = 0.0368533113591442 | erot = 0.14504542056987 | epot = -14.7994127665447 | etot = -14.6175140346157 -7000 ekin = 0.0483200640564843 | erot = 0.19256586251551 | epot = -14.8583999612756 | etot = -14.6175140347036 -8000 ekin = 0.0604312317605998 | erot = 0.24441787013151 | epot = -14.9223631366883 | etot = -14.6175140347962 -9000 ekin = 0.0727907119671751 | erot = 0.299521949931843 | epot = -14.989826696789 | etot = -14.6175140348899 -10000 ekin = 0.0850022498875221 | erot = 0.356777997217908 | epot = -15.0592942820869 | etot = -14.6175140349815 - 10000 0.006296463 -1.5144685 0.0085391004 -1.4974292 -0.00010794792 -Loop time of 0.149406 on 1 procs for 10000 steps with 10 atoms - -Performance: 57828.835 tau/day, 66931.522 timesteps/s -99.9% CPU use with 1 MPI tasks x 1 OpenMP threads - -MPI task timing breakdown: -Section | min time | avg time | max time |%varavg| %total ---------------------------------------------------------------- -Pair | 0.11971 | 0.11971 | 0.11971 | 0.0 | 80.12 -Bond | 0.0051196 | 0.0051196 | 0.0051196 | 0.0 | 3.43 -Neigh | 0 | 0 | 0 | 0.0 | 0.00 -Comm | 0.0013614 | 0.0013614 | 0.0013614 | 0.0 | 0.91 -Output | 5.0068e-06 | 5.0068e-06 | 5.0068e-06 | 0.0 | 0.00 -Modify | 0.018941 | 0.018941 | 0.018941 | 0.0 | 12.68 -Other | | 0.004268 | | | 2.86 - -Nlocal: 10 ave 10 max 10 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Nghost: 0 ave 0 max 0 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Neighs: 45 ave 45 max 45 min -Histogram: 1 0 0 0 0 0 0 0 0 0 - -Total # of neighbors = 45 -Ave neighs/atom = 4.5 -Ave special neighs/atom = 3.6 -Neighbor list builds = 0 -Dangerous builds = 0 - -#write_restart config.${number}.* -Total wall time: 0:00:00 diff --git a/examples/USER/cgdna/examples/oxDNA2/duplex1/log.27Nov18.duplex1.g++.4 b/examples/USER/cgdna/examples/oxDNA2/duplex1/log.27Nov18.duplex1.g++.4 deleted file mode 100644 index a326248cdb..0000000000 --- a/examples/USER/cgdna/examples/oxDNA2/duplex1/log.27Nov18.duplex1.g++.4 +++ /dev/null @@ -1,178 +0,0 @@ -LAMMPS (27 Nov 2018) - using 1 OpenMP thread(s) per MPI task -variable number equal 1 -variable ofreq equal 1000 -variable efreq equal 1000 - -units lj - -dimension 3 - -newton off - -boundary p p p - -atom_style hybrid bond ellipsoid -atom_modify sort 0 1.0 - -# Pair interactions require lists of neighbours to be calculated -neighbor 1.0 bin -neigh_modify every 1 delay 0 check yes - -read_data data.duplex1 - orthogonal box = (-20 -20 -20) to (20 20 20) - 1 by 2 by 2 MPI processor grid - reading atoms ... - 10 atoms - reading velocities ... - 10 velocities - 10 ellipsoids - scanning bonds ... - 2 = max bonds/atom - reading bonds ... - 8 bonds - 2 = max # of 1-2 neighbors - 2 = max # of 1-3 neighbors - 2 = max # of 1-4 neighbors - 4 = max # of special neighbors - -set atom * mass 3.1575 - 10 settings made for mass - -group all type 1 4 -10 atoms in group all - -# oxDNA bond interactions - FENE backbone -bond_style oxdna2/fene -bond_coeff * 2.0 0.25 0.7564 - -# oxDNA pair interactions -pair_style hybrid/overlay oxdna2/excv oxdna2/stk oxdna2/hbond oxdna2/xstk oxdna2/coaxstk oxdna2/dh -pair_coeff * * oxdna2/excv 2.0 0.7 0.675 2.0 0.515 0.5 2.0 0.33 0.32 -pair_coeff * * oxdna2/stk seqav 0.1 6.0 0.4 0.9 0.32 0.6 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2.0 0.65 2.0 0.65 -pair_coeff * * oxdna2/hbond seqav 0.0 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45 -pair_coeff 1 4 oxdna2/hbond seqav 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45 -pair_coeff 2 3 oxdna2/hbond seqav 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45 -pair_coeff * * oxdna2/xstk 47.5 0.575 0.675 0.495 0.655 2.25 0.791592653589793 0.58 1.7 1.0 0.68 1.7 1.0 0.68 1.5 0 0.65 1.7 0.875 0.68 1.7 0.875 0.68 -pair_coeff * * oxdna2/coaxstk 58.5 0.4 0.6 0.22 0.58 2.0 2.891592653589793 0.65 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 40.0 3.116592653589793 -pair_coeff * * oxdna2/dh 0.1 1.0 0.815 - -# NVE ensemble -fix 1 all nve/dot -#fix 1 all nve/dotc/langevin 0.1 0.1 0.03 457145 angmom 10 -#fix 1 all nve/asphere -#fix 2 all langevin 0.1 0.1 0.03 457145 angmom 10 - -timestep 1e-5 - -#comm_style tiled -#fix 3 all balance 10000 1.1 rcb - -#compute mol all chunk/atom molecule -#compute mychunk all vcm/chunk mol -#fix 4 all ave/time 10000 1 10000 c_mychunk[1] c_mychunk[2] c_mychunk[3] file vcm.txt mode vector - -#dump pos all xyz ${ofreq} traj.${number}.xyz - -#compute quat all property/atom quatw quati quatj quatk -#dump quat all custom ${ofreq} quat.${number}.txt id c_quat[1] c_quat[2] c_quat[3] c_quat[4] -#dump_modify quat sort id -#dump_modify quat format line "%d %13.6le %13.6le %13.6le %13.6le" - -compute erot all erotate/asphere -compute ekin all ke -compute epot all pe -variable erot equal c_erot -variable ekin equal c_ekin -variable epot equal c_epot -variable etot equal c_erot+c_ekin+c_epot -fix 5 all print ${efreq} "$(step) ekin = ${ekin} | erot = ${erot} | epot = ${epot} | etot = ${etot}" screen yes -fix 5 all print 1000 "$(step) ekin = ${ekin} | erot = ${erot} | epot = ${epot} | etot = ${etot}" screen yes - -#dump out all custom ${ofreq} out.${number}.txt id x y z vx vy vz fx fy fz tqx tqy tqz -#dump_modify out sort id -#dump_modify out format line "%d %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le" - -run 10000 -Neighbor list info ... - update every 1 steps, delay 0 steps, check yes - max neighbors/atom: 2000, page size: 100000 - master list distance cutoff = 2.6274 - ghost atom cutoff = 2.6274 - binsize = 1.3137, bins = 31 31 31 - 6 neighbor lists, perpetual/occasional/extra = 6 0 0 - (1) pair oxdna2/excv, perpetual - attributes: half, newton off - pair build: half/bin/newtoff - stencil: half/bin/3d/newtoff - bin: standard - (2) pair oxdna2/stk, perpetual, copy from (1) - attributes: half, newton off - pair build: copy - stencil: none - bin: none - (3) pair oxdna2/hbond, perpetual, copy from (1) - attributes: half, newton off - pair build: copy - stencil: none - bin: none - (4) pair oxdna2/xstk, perpetual, copy from (1) - attributes: half, newton off - pair build: copy - stencil: none - bin: none - (5) pair oxdna2/coaxstk, perpetual, copy from (1) - attributes: half, newton off - pair build: copy - stencil: none - bin: none - (6) pair oxdna2/dh, perpetual, copy from (1) - attributes: half, newton off - pair build: copy - stencil: none - bin: none -Per MPI rank memory allocation (min/avg/max) = 7.652 | 7.834 | 8.016 Mbytes -Step Temp E_pair E_mol TotEng Press - 0 0 -1.4712768 0.009525411 -1.4617514 -5.8922361e-05 -1000 ekin = 0.00113086229080478 | erot = 0.00431010160406708 | epot = -14.6229549982368 | etot = -14.617514034342 -2000 ekin = 0.00448533224342286 | erot = 0.0171407706505013 | epot = -14.6391401372615 | etot = -14.6175140343675 -3000 ekin = 0.0099503525964896 | erot = 0.0381961780846438 | epot = -14.6656605650904 | etot = -14.6175140344093 -4000 ekin = 0.0173418024861991 | erot = 0.0669935184860479 | epot = -14.7018493554381 | etot = -14.6175140344659 -5000 ekin = 0.0264109356285965 | erot = 0.102878288094482 | epot = -14.7468032582586 | etot = -14.6175140345355 -6000 ekin = 0.0368533113591268 | erot = 0.145045420569809 | epot = -14.7994127665446 | etot = -14.6175140346156 -7000 ekin = 0.0483200640564584 | erot = 0.192565862515413 | epot = -14.8583999612755 | etot = -14.6175140347036 -8000 ekin = 0.0604312317605635 | erot = 0.24441787013137 | epot = -14.9223631366881 | etot = -14.6175140347962 -9000 ekin = 0.072790711967127 | erot = 0.299521949931654 | epot = -14.9898266967887 | etot = -14.6175140348899 -10000 ekin = 0.0850022498874609 | erot = 0.356777997217666 | epot = -15.0592942820866 | etot = -14.6175140349815 - 10000 0.006296463 -1.5144685 0.0085391004 -1.4974292 -0.00010794792 -Loop time of 0.14583 on 4 procs for 10000 steps with 10 atoms - -Performance: 59247.054 tau/day, 68572.979 timesteps/s -97.5% CPU use with 4 MPI tasks x 1 OpenMP threads - -MPI task timing breakdown: -Section | min time | avg time | max time |%varavg| %total ---------------------------------------------------------------- -Pair | 0.0034175 | 0.055587 | 0.10059 | 17.9 | 38.12 -Bond | 0.00064635 | 0.002131 | 0.0035357 | 2.5 | 1.46 -Neigh | 0 | 0 | 0 | 0.0 | 0.00 -Comm | 0.014538 | 0.014932 | 0.015271 | 0.2 | 10.24 -Output | 5.7459e-05 | 5.7697e-05 | 5.7936e-05 | 0.0 | 0.04 -Modify | 0.0012829 | 0.0063873 | 0.011321 | 5.2 | 4.38 -Other | | 0.06674 | | | 45.76 - -Nlocal: 2.5 ave 5 max 0 min -Histogram: 1 0 1 0 0 0 0 0 1 1 -Nghost: 7.5 ave 10 max 5 min -Histogram: 1 0 1 0 0 0 0 0 1 1 -Neighs: 18.5 ave 35 max 0 min -Histogram: 1 0 1 0 0 0 0 0 1 1 - -Total # of neighbors = 74 -Ave neighs/atom = 7.4 -Ave special neighs/atom = 3.6 -Neighbor list builds = 0 -Dangerous builds = 0 - -#write_restart config.${number}.* -Total wall time: 0:00:00 diff --git a/examples/USER/cgdna/examples/oxDNA2/duplex2/data.duplex2 b/examples/USER/cgdna/examples/oxDNA2/duplex2/data.duplex2 index 6547def910..72872d431a 100644 --- a/examples/USER/cgdna/examples/oxDNA2/duplex2/data.duplex2 +++ b/examples/USER/cgdna/examples/oxDNA2/duplex2/data.duplex2 @@ -38,7 +38,7 @@ Atoms 15 3 4.860249842674773e-01 3.518234140414733e-01 3.897628551303119e-01 2 1 1 16 4 5.999999999999995e-01 -3.330669073875470e-17 -3.330669073875470e-16 2 1 1 -# Atom-ID, translational, rotational velocity +# Atom-ID, translational velocity, angular momentum Velocities 1 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 diff --git a/examples/USER/cgdna/examples/oxDNA2/duplex2/in.duplex2 b/examples/USER/cgdna/examples/oxDNA2/duplex2/in.duplex2 index 3d4393e09b..3850dfcedf 100644 --- a/examples/USER/cgdna/examples/oxDNA2/duplex2/in.duplex2 +++ b/examples/USER/cgdna/examples/oxDNA2/duplex2/in.duplex2 @@ -1,7 +1,7 @@ variable number equal 2 variable ofreq equal 1000 variable efreq equal 1000 - +variable T equal 0.1 units lj dimension 3 @@ -30,19 +30,19 @@ bond_coeff * 2.0 0.25 0.7564 # oxDNA pair interactions pair_style hybrid/overlay oxdna2/excv oxdna2/stk oxdna2/hbond oxdna2/xstk oxdna2/coaxstk oxdna2/dh pair_coeff * * oxdna2/excv 2.0 0.7 0.675 2.0 0.515 0.5 2.0 0.33 0.32 -pair_coeff * * oxdna2/stk seqav 0.1 6.0 0.4 0.9 0.32 0.6 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2.0 0.65 2.0 0.65 +pair_coeff * * oxdna2/stk seqav ${T} 1.3523 2.6717 6.0 0.4 0.9 0.32 0.6 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2.0 0.65 2.0 0.65 pair_coeff * * oxdna2/hbond seqav 0.0 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45 pair_coeff 1 4 oxdna2/hbond seqav 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45 pair_coeff 2 3 oxdna2/hbond seqav 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45 pair_coeff * * oxdna2/xstk 47.5 0.575 0.675 0.495 0.655 2.25 0.791592653589793 0.58 1.7 1.0 0.68 1.7 1.0 0.68 1.5 0 0.65 1.7 0.875 0.68 1.7 0.875 0.68 pair_coeff * * oxdna2/coaxstk 58.5 0.4 0.6 0.22 0.58 2.0 2.891592653589793 0.65 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 40.0 3.116592653589793 -pair_coeff * * oxdna2/dh 0.1 1.0 0.815 +pair_coeff * * oxdna2/dh ${T} 1.0 0.815 # NVE ensemble #fix 1 all nve/dot -fix 1 all nve/dotc/langevin 0.1 0.1 0.03 457145 angmom 10 +fix 1 all nve/dotc/langevin ${T} ${T} 0.03 457145 angmom 10 #fix 1 all nve/asphere -#fix 2 all langevin 0.1 0.1 0.03 457145 angmom 10 +#fix 2 all langevin ${T} ${T} 0.03 457145 angmom 10 timestep 1e-5 @@ -73,6 +73,6 @@ fix 5 all print ${efreq} "$(step) ekin = ${ekin} | erot = ${erot} | epot = ${e #dump_modify out sort id #dump_modify out format line "%d %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le" -run 10000 +run 1000000 #write_restart config.${number}.* diff --git a/examples/USER/cgdna/examples/oxDNA2/duplex2/log.18Jun19.duplex2.g++.1 b/examples/USER/cgdna/examples/oxDNA2/duplex2/log.18Jun19.duplex2.g++.1 new file mode 100644 index 0000000000..e4478a8942 --- /dev/null +++ b/examples/USER/cgdna/examples/oxDNA2/duplex2/log.18Jun19.duplex2.g++.1 @@ -0,0 +1,1173 @@ +LAMMPS (18 Jun 2019) +variable number equal 2 +variable ofreq equal 1000 +variable efreq equal 1000 +variable T equal 0.1 +units lj + +dimension 3 + +newton off + +boundary p p p + +atom_style hybrid bond ellipsoid +atom_modify sort 0 1.0 + +# Pair interactions require lists of neighbours to be calculated +neighbor 1.0 bin +neigh_modify every 1 delay 0 check yes + +read_data data.duplex2 + orthogonal box = (-20 -20 -20) to (20 20 20) + 1 by 1 by 1 MPI processor grid + reading atoms ... + 16 atoms + reading velocities ... + 16 velocities + 16 ellipsoids + scanning bonds ... + 2 = max bonds/atom + reading bonds ... + 13 bonds + 2 = max # of 1-2 neighbors + 2 = max # of 1-3 neighbors + 4 = max # of 1-4 neighbors + 6 = max # of special neighbors + special bonds CPU = 0.000103 secs + read_data CPU = 0.00215 secs + +set atom * mass 3.1575 + 16 settings made for mass + +group all type 1 4 +16 atoms in group all + +# oxDNA bond interactions - FENE backbone +bond_style oxdna2/fene +bond_coeff * 2.0 0.25 0.7564 + +# oxDNA pair interactions +pair_style hybrid/overlay oxdna2/excv oxdna2/stk oxdna2/hbond oxdna2/xstk oxdna2/coaxstk oxdna2/dh +pair_coeff * * oxdna2/excv 2.0 0.7 0.675 2.0 0.515 0.5 2.0 0.33 0.32 +pair_coeff * * oxdna2/stk seqav ${T} 1.3523 2.6717 6.0 0.4 0.9 0.32 0.6 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2.0 0.65 2.0 0.65 +pair_coeff * * oxdna2/stk seqav 0.1 1.3523 2.6717 6.0 0.4 0.9 0.32 0.6 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2.0 0.65 2.0 0.65 +pair_coeff * * oxdna2/hbond seqav 0.0 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45 +pair_coeff 1 4 oxdna2/hbond seqav 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45 +pair_coeff 2 3 oxdna2/hbond seqav 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45 +pair_coeff * * oxdna2/xstk 47.5 0.575 0.675 0.495 0.655 2.25 0.791592653589793 0.58 1.7 1.0 0.68 1.7 1.0 0.68 1.5 0 0.65 1.7 0.875 0.68 1.7 0.875 0.68 +pair_coeff * * oxdna2/coaxstk 58.5 0.4 0.6 0.22 0.58 2.0 2.891592653589793 0.65 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 40.0 3.116592653589793 +pair_coeff * * oxdna2/dh ${T} 1.0 0.815 +pair_coeff * * oxdna2/dh 0.1 1.0 0.815 + +# NVE ensemble +#fix 1 all nve/dot +fix 1 all nve/dotc/langevin ${T} ${T} 0.03 457145 angmom 10 +fix 1 all nve/dotc/langevin 0.1 ${T} 0.03 457145 angmom 10 +fix 1 all nve/dotc/langevin 0.1 0.1 0.03 457145 angmom 10 +#fix 1 all nve/asphere +#fix 2 all langevin ${T} ${T} 0.03 457145 angmom 10 + +timestep 1e-5 + +#comm_style tiled +#fix 3 all balance 10000 1.1 rcb + +#compute mol all chunk/atom molecule +#compute mychunk all vcm/chunk mol +#fix 4 all ave/time 10000 1 10000 c_mychunk[1] c_mychunk[2] c_mychunk[3] file vcm.txt mode vector + +#dump pos all xyz ${ofreq} traj.${number}.xyz + +#compute quat all property/atom quatw quati quatj quatk +#dump quat all custom ${ofreq} quat.${number}.txt id c_quat[1] c_quat[2] c_quat[3] c_quat[4] +#dump_modify quat sort id +#dump_modify quat format line "%d %13.6le %13.6le %13.6le %13.6le" + +compute erot all erotate/asphere +compute ekin all ke +compute epot all pe +variable erot equal c_erot +variable ekin equal c_ekin +variable epot equal c_epot +variable etot equal c_erot+c_ekin+c_epot +fix 5 all print ${efreq} "$(step) ekin = ${ekin} | erot = ${erot} | epot = ${epot} | etot = ${etot}" screen yes +fix 5 all print 1000 "$(step) ekin = ${ekin} | erot = ${erot} | epot = ${epot} | etot = ${etot}" screen yes + +#dump out all custom ${ofreq} out.${number}.txt id x y z vx vy vz fx fy fz tqx tqy tqz +#dump_modify out sort id +#dump_modify out format line "%d %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le" + +run 1000000 +Neighbor list info ... + update every 1 steps, delay 0 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 2.6274 + ghost atom cutoff = 2.6274 + binsize = 1.3137, bins = 31 31 31 + 6 neighbor lists, perpetual/occasional/extra = 6 0 0 + (1) pair oxdna2/excv, perpetual + attributes: half, newton off + pair build: half/bin/newtoff + stencil: half/bin/3d/newtoff + bin: standard + (2) pair oxdna2/stk, perpetual, copy from (1) + attributes: half, newton off + pair build: copy + stencil: none + bin: none + (3) pair oxdna2/hbond, perpetual, copy from (1) + attributes: half, newton off + pair build: copy + stencil: none + bin: none + (4) pair oxdna2/xstk, perpetual, copy from (1) + attributes: half, newton off + pair build: copy + stencil: none + bin: none + (5) pair oxdna2/coaxstk, perpetual, copy from (1) + attributes: half, newton off + pair build: copy + stencil: none + bin: none + (6) pair oxdna2/dh, perpetual, copy from (1) + attributes: half, newton off + pair build: copy + stencil: none + bin: none +Per MPI rank memory allocation (min/avg/max) = 3.025 | 3.025 | 3.025 Mbytes +Step Temp E_pair E_mol TotEng Press + 0 0 -1.5358787 0.0096742456 -1.5262045 1.0127369e-05 +1000 ekin = 1.54282272464468 | erot = 1.71757897250772 | epot = -24.4403527731341 | etot = -21.1799510759817 +2000 ekin = 1.86109566690716 | erot = 1.93804145796026 | epot = -24.3759816748265 | etot = -20.5768445499591 +3000 ekin = 2.68769182431188 | erot = 2.14559269500086 | epot = -24.2916556822451 | etot = -19.4583711629324 +4000 ekin = 2.04710303757243 | erot = 1.48774072590987 | epot = -24.190371461807 | etot = -20.6555276983247 +5000 ekin = 1.77654023802719 | erot = 2.53418650522101 | epot = -24.1246365663843 | etot = -19.8139098231361 +6000 ekin = 3.12253137872527 | erot = 2.04028266818831 | epot = -24.0491248750916 | etot = -18.8863108281781 +7000 ekin = 3.22418765752177 | erot = 2.72037570174022 | epot = -23.9458569915548 | etot = -18.0012936322928 +8000 ekin = 2.83204202112963 | erot = 2.67060276413776 | epot = -23.9211291529766 | etot = -18.4184843677092 +9000 ekin = 2.69585642754481 | erot = 2.59559820250212 | epot = -23.8340823338302 | etot = -18.5426277037833 +10000 ekin = 2.66058119525512 | erot = 1.95965933336077 | epot = -23.7132443170725 | etot = -19.0930037884567 +11000 ekin = 2.34346978235591 | erot = 2.0608750207871 | epot = -23.5779637301072 | etot = -19.1736189269642 +12000 ekin = 2.71430148816282 | erot = 2.08352509995717 | epot = -23.4639027443831 | etot = -18.6660761562631 +13000 ekin = 2.61978682102879 | erot = 2.37135270083347 | epot = -23.3602247027812 | etot = -18.3690851809189 +14000 ekin = 3.07648218347461 | erot = 2.513719767243 | epot = -23.2345584968309 | etot = -17.6443565461133 +15000 ekin = 2.98155804409324 | erot = 1.87766202539412 | epot = -23.0833749664029 | etot = -18.2241548969156 +16000 ekin = 2.18215330648447 | erot = 2.12621179836828 | epot = -22.9601160092383 | etot = -18.6517509043856 +17000 ekin = 1.85636180329758 | erot = 2.31208745603367 | epot = -22.8022922969143 | etot = -18.633843037583 +18000 ekin = 2.26768559168017 | erot = 1.2389450409061 | epot = -22.668242963885 | etot = -19.1616123312987 +19000 ekin = 2.41605854545852 | erot = 2.44791952321404 | epot = -22.5387095337131 | etot = -17.6747314650405 +20000 ekin = 2.51175765558337 | erot = 2.15047735899709 | epot = -22.3909493829452 | etot = -17.7287143683647 +21000 ekin = 2.9915110961596 | erot = 2.41132105778464 | epot = -22.5047205397251 | etot = -17.1018883857809 +22000 ekin = 3.06067007914886 | erot = 1.83986675392832 | epot = -22.6049739626141 | etot = -17.7044371295369 +23000 ekin = 2.66061083480474 | erot = 2.22251362834379 | epot = -22.5979829967718 | etot = -17.7148585336233 +24000 ekin = 2.65745533322327 | erot = 2.79344397300952 | epot = -22.5688422615674 | etot = -17.1179429553346 +25000 ekin = 2.30064465907917 | erot = 2.20975367009042 | epot = -22.5633453862602 | etot = -18.0529470570906 +26000 ekin = 1.6282588103248 | erot = 2.51914272742421 | epot = -22.6015006270016 | etot = -18.4540990892526 +27000 ekin = 1.76021840072103 | erot = 3.70719293889859 | epot = -22.6409357152274 | etot = -17.1735243756077 +28000 ekin = 2.28064774169505 | erot = 2.34192414128161 | epot = -22.7124772012735 | etot = -18.0899053182968 +29000 ekin = 2.05883865245349 | erot = 1.85387249117169 | epot = -22.7242388348361 | etot = -18.811527691211 +30000 ekin = 2.41090888362676 | erot = 1.86304539977924 | epot = -22.6876650006964 | etot = -18.4137107172904 +31000 ekin = 2.76955959719985 | erot = 2.74117025737249 | epot = -22.6962463526981 | etot = -17.1855164981257 +32000 ekin = 2.08562644954365 | erot = 2.81609166367558 | epot = -22.7309387973059 | etot = -17.8292206840867 +33000 ekin = 2.08306771838837 | erot = 3.6412168312574 | epot = -22.671701882331 | etot = -16.9474173326852 +34000 ekin = 2.32648544880974 | erot = 3.09480128654123 | epot = -22.5637155764017 | etot = -17.1424288410507 +35000 ekin = 2.32492461599899 | erot = 2.02549181832456 | epot = -22.4811871522455 | etot = -18.1307707179219 +36000 ekin = 1.9160219633488 | erot = 1.97655634076097 | epot = -22.3849871062612 | etot = -18.4924088021514 +37000 ekin = 1.57338784336504 | erot = 2.62872199467344 | epot = -22.3528406869297 | etot = -18.1507308488912 +38000 ekin = 2.21547906806797 | erot = 2.89630123965964 | epot = -22.3056616105138 | etot = -17.1938813027862 +39000 ekin = 2.55049061085212 | erot = 2.46486573403212 | epot = -22.2602280028032 | etot = -17.244871657919 +40000 ekin = 2.25628181110086 | erot = 1.87515483835113 | epot = -22.2878959489406 | etot = -18.1564592994886 +41000 ekin = 2.46478791133629 | erot = 2.50742704532316 | epot = -22.3614598606398 | etot = -17.3892449039804 +42000 ekin = 2.69217693496336 | erot = 2.04021031621289 | epot = -22.3505245167544 | etot = -17.6181372655782 +43000 ekin = 2.40211339309477 | erot = 1.6668978842528 | epot = -22.353509525279 | etot = -18.2844982479314 +44000 ekin = 2.30891568897327 | erot = 2.40213237626172 | epot = -22.3871831090405 | etot = -17.6761350438055 +45000 ekin = 1.83275065976638 | erot = 2.26068140262528 | epot = -22.4994702091406 | etot = -18.406038146749 +46000 ekin = 1.97585087518641 | erot = 3.0186371421683 | epot = -22.4902643909032 | etot = -17.4957763735485 +47000 ekin = 1.30702141485601 | erot = 1.99592830992523 | epot = -22.4679405795691 | etot = -19.1649908547879 +48000 ekin = 2.58893650014613 | erot = 1.90050780837457 | epot = -22.5072015009757 | etot = -18.017757192455 +49000 ekin = 2.30293607053961 | erot = 2.71885537559561 | epot = -22.5026363414396 | etot = -17.4808448953044 +50000 ekin = 2.47053682632632 | erot = 3.4216531112208 | epot = -22.415032340787 | etot = -16.5228424032399 +51000 ekin = 2.70972992123879 | erot = 1.4301791663753 | epot = -22.3056750708571 | etot = -18.165765983243 +52000 ekin = 3.01390456844682 | erot = 1.97787470370191 | epot = -22.2827481318966 | etot = -17.2909688597479 +53000 ekin = 2.43796472406694 | erot = 4.25598325759163 | epot = -22.2611961774508 | etot = -15.5672481957922 +54000 ekin = 2.47286167616923 | erot = 2.3677730007818 | epot = -22.243519577301 | etot = -17.40288490035 +55000 ekin = 2.25994505035907 | erot = 1.91872181759988 | epot = -22.2996523252175 | etot = -18.1209854572585 +56000 ekin = 2.3461223108806 | erot = 2.20461695689782 | epot = -22.370356062429 | etot = -17.8196167946505 +57000 ekin = 2.51587877543148 | erot = 2.87451767129977 | epot = -22.4723343857415 | etot = -17.0819379390103 +58000 ekin = 2.49925674722554 | erot = 2.80569508565646 | epot = -22.5303780310556 | etot = -17.2254261981736 +59000 ekin = 2.75080755995156 | erot = 2.17181245800364 | epot = -22.5861118023788 | etot = -17.6634917844236 +60000 ekin = 3.2849676836621 | erot = 1.98487748777051 | epot = -22.5789662701264 | etot = -17.3091210986938 +61000 ekin = 2.4147550327795 | erot = 1.80972454908232 | epot = -22.5207352876114 | etot = -18.2962557057495 +62000 ekin = 2.82665653061546 | erot = 1.68517769072779 | epot = -22.4078181490349 | etot = -17.8959839276917 +63000 ekin = 3.70002607874218 | erot = 1.92704686824234 | epot = -22.2626867402007 | etot = -16.6356137932161 +64000 ekin = 3.61736288982706 | erot = 3.03600982585025 | epot = -22.2659045523542 | etot = -15.6125318366769 +65000 ekin = 3.40363639902008 | erot = 3.89044870099903 | epot = -22.2274777177663 | etot = -14.9333926177472 +66000 ekin = 2.94418257190202 | erot = 2.45963190668857 | epot = -22.1363667635561 | etot = -16.7325522849655 +67000 ekin = 2.60477940218663 | erot = 2.10479080523513 | epot = -22.038362895265 | etot = -17.3287926878432 +68000 ekin = 2.57158327795866 | erot = 2.46431755410219 | epot = -22.0244560205645 | etot = -16.9885551885036 +69000 ekin = 2.43845102321476 | erot = 2.85996177461682 | epot = -22.0620804569545 | etot = -16.7636676591229 +70000 ekin = 3.08348233524936 | erot = 2.49640850205841 | epot = -22.1433186271748 | etot = -16.563427789867 +71000 ekin = 2.5576093427884 | erot = 2.50957641127969 | epot = -22.2697187660694 | etot = -17.2025330120013 +72000 ekin = 1.7831483145096 | erot = 2.52806261120156 | epot = -22.3815818044114 | etot = -18.0703708787002 +73000 ekin = 1.86053585113659 | erot = 2.3350857968737 | epot = -22.4387359493251 | etot = -18.2431143013148 +74000 ekin = 3.14016175467449 | erot = 2.13186507521504 | epot = -22.447062887188 | etot = -17.1750360572984 +75000 ekin = 2.60368665360454 | erot = 2.18680067560206 | epot = -22.4438479629936 | etot = -17.653360633787 +76000 ekin = 1.9633244939079 | erot = 1.96057322365503 | epot = -22.4704022140376 | etot = -18.5465044964747 +77000 ekin = 2.09841107775422 | erot = 2.1471460143176 | epot = -22.4970899098551 | etot = -18.2515328177832 +78000 ekin = 2.49484391610508 | erot = 2.50538853212234 | epot = -22.4472882748805 | etot = -17.4470558266531 +79000 ekin = 3.10058476014063 | erot = 2.47637061915656 | epot = -22.3558276087081 | etot = -16.7788722294109 +80000 ekin = 2.52610159631253 | erot = 1.89085194000216 | epot = -22.2951000287249 | etot = -17.8781464924102 +81000 ekin = 2.34286765202483 | erot = 2.2376810918426 | epot = -22.2933034850974 | etot = -17.71275474123 +82000 ekin = 1.55517061572748 | erot = 2.02195112736337 | epot = -22.2470532436032 | etot = -18.6699315005123 +83000 ekin = 2.27421747802727 | erot = 3.34135950792192 | epot = -22.2406089881454 | etot = -16.6250320021963 +84000 ekin = 2.91603956429582 | erot = 2.09861057599124 | epot = -22.2305865946953 | etot = -17.2159364544083 +85000 ekin = 3.17172070756641 | erot = 2.91883241347319 | epot = -22.2381339647476 | etot = -16.147580843708 +86000 ekin = 3.48918734688943 | erot = 2.79711547316344 | epot = -22.2890012778608 | etot = -16.0026984578079 +87000 ekin = 3.648834525211 | erot = 2.30637362835037 | epot = -22.2817018896603 | etot = -16.3264937360989 +88000 ekin = 3.16156585935194 | erot = 2.24503314085539 | epot = -22.2225172277202 | etot = -16.8159182275129 +89000 ekin = 3.32092350591891 | erot = 1.79966969251215 | epot = -22.1549711261911 | etot = -17.03437792776 +90000 ekin = 2.41383485147934 | erot = 2.22694238351369 | epot = -21.9352492588881 | etot = -17.294472023895 +91000 ekin = 1.87769980964557 | erot = 2.50898156232204 | epot = -21.766796868726 | etot = -17.3801154967584 +92000 ekin = 2.06420930396832 | erot = 2.23853979300919 | epot = -21.6902828653619 | etot = -17.3875337683844 +93000 ekin = 1.94960374605101 | erot = 3.00245663654886 | epot = -21.6771969695753 | etot = -16.7251365869754 +94000 ekin = 2.07633340602167 | erot = 3.38669471112637 | epot = -21.7794316475531 | etot = -16.3164035304051 +95000 ekin = 2.09307446139111 | erot = 2.0811295310408 | epot = -21.9165143849258 | etot = -17.7423103924939 +96000 ekin = 2.66782345206074 | erot = 1.87453507536254 | epot = -21.9748225431664 | etot = -17.4324640157432 +97000 ekin = 1.93962158410337 | erot = 2.81228342262069 | epot = -22.0301811391172 | etot = -17.2782761323932 +98000 ekin = 1.98651083318125 | erot = 2.05358325550364 | epot = -22.1050988415859 | etot = -18.065004752901 +99000 ekin = 2.50729461715162 | erot = 3.55227490812968 | epot = -22.2148658268239 | etot = -16.1552963015426 +100000 ekin = 1.87954195221303 | erot = 2.38994009743578 | epot = -22.3826768493088 | etot = -18.11319479966 +101000 ekin = 1.66917867676911 | erot = 3.61296864361924 | epot = -22.4122779848186 | etot = -17.1301306644303 +102000 ekin = 1.63707836649616 | erot = 3.33958463197985 | epot = -22.3664797586262 | etot = -17.3898167601502 +103000 ekin = 2.00216132457488 | erot = 2.34409134088738 | epot = -22.338100531932 | etot = -17.9918478664698 +104000 ekin = 2.03704734920245 | erot = 2.74903331701925 | epot = -22.3478074938274 | etot = -17.5617268276057 +105000 ekin = 1.85601249652044 | erot = 2.00020228548217 | epot = -22.2937670136133 | etot = -18.4375522316107 +106000 ekin = 1.70582694215149 | erot = 1.90992656339968 | epot = -22.3252996603125 | etot = -18.7095461547614 +107000 ekin = 2.61183521416777 | erot = 1.56756438600251 | epot = -22.3815585845482 | etot = -18.2021589843779 +108000 ekin = 2.13345133147477 | erot = 2.1967764492834 | epot = -22.2873637709221 | etot = -17.9571359901639 +109000 ekin = 2.23517703897427 | erot = 2.12289589403282 | epot = -22.1519605830327 | etot = -17.7938876500256 +110000 ekin = 1.66340581480182 | erot = 2.52573727214601 | epot = -22.1681066766204 | etot = -17.9789635896725 +111000 ekin = 2.28529122032929 | erot = 2.24044883756493 | epot = -22.1711980210611 | etot = -17.6454579631669 +112000 ekin = 2.60405127944181 | erot = 2.43646974545776 | epot = -22.1582164438795 | etot = -17.11769541898 +113000 ekin = 2.40208651796091 | erot = 3.06270264515793 | epot = -22.1587051510952 | etot = -16.6939159879764 +114000 ekin = 2.34302229470158 | erot = 2.30426477746864 | epot = -22.1439772736805 | etot = -17.4966902015103 +115000 ekin = 1.69616053999229 | erot = 3.11049212247371 | epot = -22.1736739038021 | etot = -17.3670212413361 +116000 ekin = 1.51961045217859 | erot = 2.22203808801726 | epot = -22.2355447345615 | etot = -18.4938961943657 +117000 ekin = 1.69355164638512 | erot = 2.33913072714747 | epot = -22.2671845473364 | etot = -18.2345021738038 +118000 ekin = 2.1960991163694 | erot = 2.33815079858085 | epot = -22.2453229868293 | etot = -17.7110730718791 +119000 ekin = 2.55982892523823 | erot = 2.47378749563683 | epot = -22.2824155531543 | etot = -17.2487991322793 +120000 ekin = 1.76091001620491 | erot = 2.1741296357231 | epot = -22.2369948282136 | etot = -18.3019551762855 +121000 ekin = 2.80671234452976 | erot = 2.30128219469303 | epot = -22.2260257995407 | etot = -17.1180312603179 +122000 ekin = 3.23136903340218 | erot = 3.30036165167127 | epot = -22.2515019863338 | etot = -15.7197713012603 +123000 ekin = 2.8561114897291 | erot = 3.24294818442618 | epot = -22.2018342366988 | etot = -16.1027745625435 +124000 ekin = 2.14842162472016 | erot = 2.7693802805091 | epot = -22.0303368839078 | etot = -17.1125349786785 +125000 ekin = 1.83317468651689 | erot = 1.37271219749613 | epot = -21.8885764971633 | etot = -18.6826896131502 +126000 ekin = 2.45181092117661 | erot = 3.08753876167365 | epot = -21.8912653158441 | etot = -16.3519156329938 +127000 ekin = 2.39800706812202 | erot = 2.35255982488708 | epot = -21.8786845575463 | etot = -17.1281176645372 +128000 ekin = 2.72073389273301 | erot = 1.81206134758344 | epot = -21.8246886433981 | etot = -17.2918934030816 +129000 ekin = 2.76648233159587 | erot = 2.90133130407443 | epot = -21.9103698595755 | etot = -16.2425562239052 +130000 ekin = 3.26919771496399 | erot = 2.56804213542044 | epot = -22.0468205769693 | etot = -16.2095807265849 +131000 ekin = 2.65797021501453 | erot = 2.51912811588696 | epot = -22.1046945041584 | etot = -16.9275961732569 +132000 ekin = 2.60615175826329 | erot = 3.39821871959342 | epot = -22.1393658191679 | etot = -16.1349953413112 +133000 ekin = 2.01702653257964 | erot = 2.88164356754679 | epot = -22.1083395633022 | etot = -17.2096694631758 +134000 ekin = 1.62732528940444 | erot = 1.66916296573806 | epot = -22.0617984863721 | etot = -18.7653102312296 +135000 ekin = 2.44472224525446 | erot = 2.12100291286044 | epot = -22.0290071826116 | etot = -17.4632820244967 +136000 ekin = 2.29361895961086 | erot = 3.04813516280966 | epot = -21.9240579822781 | etot = -16.5823038598575 +137000 ekin = 2.71943103843212 | erot = 2.46250134466529 | epot = -21.759346222065 | etot = -16.5774138389676 +138000 ekin = 3.29026615453928 | erot = 1.74005246857097 | epot = -21.7424803627639 | etot = -16.7121617396537 +139000 ekin = 2.76078280183931 | erot = 1.72093988964439 | epot = -21.8915740702781 | etot = -17.4098513787944 +140000 ekin = 2.72717929836212 | erot = 2.46093572161851 | epot = -21.9730696792527 | etot = -16.784954659272 +141000 ekin = 2.79178566984556 | erot = 2.45152416051809 | epot = -21.9760531770405 | etot = -16.7327433466769 +142000 ekin = 3.51808959230238 | erot = 3.47662361887462 | epot = -21.9144706671159 | etot = -14.9197574559389 +143000 ekin = 2.56674276565954 | erot = 2.02320192154355 | epot = -21.887847774869 | etot = -17.2979030876659 +144000 ekin = 3.71876753045239 | erot = 3.03518010984555 | epot = -21.8693810552709 | etot = -15.115433414973 +145000 ekin = 3.61067898932004 | erot = 2.70461629179152 | epot = -21.7768865247848 | etot = -15.4615912436733 +146000 ekin = 3.85672431702576 | erot = 2.48360222237068 | epot = -21.7383083831155 | etot = -15.3979818437191 +147000 ekin = 3.26264642879795 | erot = 2.07790943830875 | epot = -21.612808589745 | etot = -16.2722527226383 +148000 ekin = 2.49411629896921 | erot = 1.64570933977901 | epot = -21.3601881264357 | etot = -17.2203624876875 +149000 ekin = 2.73353556199719 | erot = 2.27529903215971 | epot = -21.180923940444 | etot = -16.1720893462871 +150000 ekin = 2.6282457385967 | erot = 2.90058901460194 | epot = -21.0864924194498 | etot = -15.5576576662512 +151000 ekin = 2.07954165316093 | erot = 2.1164125590575 | epot = -20.9951076802445 | etot = -16.7991534680261 +152000 ekin = 2.41868973763601 | erot = 2.60413735099777 | epot = -20.8520585412647 | etot = -15.8292314526309 +153000 ekin = 2.12569822788918 | erot = 2.25674944787518 | epot = -20.8874716791535 | etot = -16.5050240033891 +154000 ekin = 2.34486280100484 | erot = 2.61050919353092 | epot = -20.9924730886396 | etot = -16.0371010941038 +155000 ekin = 2.06912274657395 | erot = 3.0299583491991 | epot = -21.0207700832301 | etot = -15.921688987457 +156000 ekin = 2.03235057930374 | erot = 3.18386486882217 | epot = -20.8574059636368 | etot = -15.6411905155109 +157000 ekin = 2.3579061324469 | erot = 1.91132393217369 | epot = -20.8256173876826 | etot = -16.556387323062 +158000 ekin = 2.17332819176356 | erot = 2.47832446500284 | epot = -20.9206749462161 | etot = -16.2690222894497 +159000 ekin = 2.87139796431922 | erot = 2.29125458595932 | epot = -21.0425793637301 | etot = -15.8799268134516 +160000 ekin = 2.19495281512895 | erot = 2.37206762182712 | epot = -21.12868212155 | etot = -16.5616616845939 +161000 ekin = 2.13209841436583 | erot = 2.44149028746738 | epot = -21.2267263358883 | etot = -16.6531376340551 +162000 ekin = 1.75046056470489 | erot = 2.66847316377717 | epot = -21.2792984888785 | etot = -16.8603647603965 +163000 ekin = 2.22203312194875 | erot = 2.03600602857084 | epot = -21.4244626156303 | etot = -17.1664234651107 +164000 ekin = 2.74926161019501 | erot = 1.42936965542836 | epot = -21.5631783920293 | etot = -17.384547126406 +165000 ekin = 2.66465183950737 | erot = 2.28908630196103 | epot = -21.572272285795 | etot = -16.6185341443266 +166000 ekin = 3.29267065001881 | erot = 2.38564084157004 | epot = -21.5039232020267 | etot = -15.8256117104378 +167000 ekin = 3.03664818915841 | erot = 2.03669674074452 | epot = -21.5747204885882 | etot = -16.5013755586853 +168000 ekin = 3.16556842965113 | erot = 1.85206282714724 | epot = -21.6223493129218 | etot = -16.6047180561234 +169000 ekin = 2.24511985727904 | erot = 2.66889068764969 | epot = -21.5368970033532 | etot = -16.6228864584245 +170000 ekin = 2.43734116474603 | erot = 2.49716986363814 | epot = -21.3912465276853 | etot = -16.4567354993011 +171000 ekin = 1.90620260936893 | erot = 2.39687883544744 | epot = -21.3008997539566 | etot = -16.9978183091402 +172000 ekin = 2.87444998880216 | erot = 3.21713663160875 | epot = -21.2616188758685 | etot = -15.1700322554576 +173000 ekin = 2.74942738368889 | erot = 2.14120450530294 | epot = -21.2850360200821 | etot = -16.3944041310903 +174000 ekin = 2.4529377396394 | erot = 2.23261644076142 | epot = -21.3299047479428 | etot = -16.644350567542 +175000 ekin = 2.84864650053625 | erot = 2.37733794803682 | epot = -21.2943230039461 | etot = -16.068338555373 +176000 ekin = 2.13647755199109 | erot = 1.89602819204849 | epot = -21.3605335602015 | etot = -17.3280278161619 +177000 ekin = 2.57740970525463 | erot = 2.74252419383388 | epot = -21.3306809364134 | etot = -16.0107470373249 +178000 ekin = 1.83680522170069 | erot = 2.5856914127028 | epot = -21.2632846497336 | etot = -16.8407880153301 +179000 ekin = 2.51484018139121 | erot = 2.38459479892641 | epot = -21.325303559771 | etot = -16.4258685794534 +180000 ekin = 1.88523508330591 | erot = 2.46381998482447 | epot = -21.4811020579528 | etot = -17.1320469898224 +181000 ekin = 1.75689043588625 | erot = 3.04324017089631 | epot = -21.474228259015 | etot = -16.6740976522324 +182000 ekin = 1.56534231241504 | erot = 2.04864866727399 | epot = -21.4129540971941 | etot = -17.798963117505 +183000 ekin = 2.00287899563344 | erot = 2.82515065812734 | epot = -21.49258719815 | etot = -16.6645575443892 +184000 ekin = 2.68544625765532 | erot = 2.43626281495748 | epot = -21.6103862218356 | etot = -16.4886771492228 +185000 ekin = 2.99891111533195 | erot = 3.19602779235331 | epot = -21.6822175762628 | etot = -15.4872786685775 +186000 ekin = 3.18195376963592 | erot = 2.43765957688182 | epot = -21.7117512273523 | etot = -16.0921378808346 +187000 ekin = 2.64722090162018 | erot = 3.43145857630564 | epot = -21.6694156065006 | etot = -15.5907361285748 +188000 ekin = 2.8593721905413 | erot = 3.05764002667605 | epot = -21.6129263142805 | etot = -15.6959140970631 +189000 ekin = 2.64258352431382 | erot = 1.81957536948003 | epot = -21.5503774009301 | etot = -17.0882185071363 +190000 ekin = 2.2190608435254 | erot = 1.84740673329965 | epot = -21.5105703637082 | etot = -17.4441027868831 +191000 ekin = 2.27442549063464 | erot = 2.06581774328105 | epot = -21.4485511972947 | etot = -17.108307963379 +192000 ekin = 2.27419285809427 | erot = 3.10822480468651 | epot = -21.4844439428341 | etot = -16.1020262800533 +193000 ekin = 1.95256612457884 | erot = 1.88944690058107 | epot = -21.4719648319093 | etot = -17.6299518067494 +194000 ekin = 2.46290863552507 | erot = 2.02714246570739 | epot = -21.3483686370757 | etot = -16.8583175358433 +195000 ekin = 3.12615833704228 | erot = 2.09882827884293 | epot = -21.2854694780647 | etot = -16.0604828621794 +196000 ekin = 2.70126861243405 | erot = 2.51307250710585 | epot = -21.2052184052664 | etot = -15.9908772857265 +197000 ekin = 2.55113347479427 | erot = 2.07490331769114 | epot = -21.0379488001649 | etot = -16.4119120076795 +198000 ekin = 2.7091171175815 | erot = 1.79542986755821 | epot = -21.0311079948236 | etot = -16.5265610096839 +199000 ekin = 2.57086088527333 | erot = 2.33194065149168 | epot = -21.0448935828999 | etot = -16.1420920461349 +200000 ekin = 2.89149033048946 | erot = 1.42165157230865 | epot = -21.03770919399 | etot = -16.7245672911919 +201000 ekin = 2.68304721320748 | erot = 1.55647352804279 | epot = -21.0368254418007 | etot = -16.7973047005504 +202000 ekin = 2.2656487707054 | erot = 2.24246330836477 | epot = -20.9783437689148 | etot = -16.4702316898446 +203000 ekin = 2.11263799464235 | erot = 2.0311722239375 | epot = -20.9045528293636 | etot = -16.7607426107837 +204000 ekin = 2.10289033168206 | erot = 1.89431766090034 | epot = -20.917707897003 | etot = -16.9204999044206 +205000 ekin = 1.32594040742044 | erot = 2.12787440210413 | epot = -20.9650467335179 | etot = -17.5112319239933 +206000 ekin = 1.37942510627947 | erot = 2.255876437166 | epot = -20.9344799697865 | etot = -17.299178426341 +207000 ekin = 1.89707208497052 | erot = 1.80792832329628 | epot = -21.0372131039119 | etot = -17.3322126956451 +208000 ekin = 1.82394216235567 | erot = 3.24636401083921 | epot = -21.2905133091558 | etot = -16.2202071359609 +209000 ekin = 2.80235035495642 | erot = 2.34817422826193 | epot = -21.4119988544966 | etot = -16.2614742712782 +210000 ekin = 3.17268831077415 | erot = 3.11920168004874 | epot = -21.4880486169942 | etot = -15.1961586261713 +211000 ekin = 2.46911290485391 | erot = 2.09583435351186 | epot = -21.6131156278285 | etot = -17.0481683694628 +212000 ekin = 2.36983963899524 | erot = 1.93490727968814 | epot = -21.6916906588951 | etot = -17.3869437402117 +213000 ekin = 1.90089387455099 | erot = 2.5187405361218 | epot = -21.7688631446424 | etot = -17.3492287339696 +214000 ekin = 1.97453946438608 | erot = 2.49804990679736 | epot = -21.7968032544022 | etot = -17.3242138832188 +215000 ekin = 1.97170537707849 | erot = 3.1720109210939 | epot = -21.7980499435109 | etot = -16.6543336453385 +216000 ekin = 1.89064429395263 | erot = 1.88113651267029 | epot = -21.7625464985643 | etot = -17.9907656919414 +217000 ekin = 2.0626433286583 | erot = 1.95286476791462 | epot = -21.8181895344454 | etot = -17.8026814378725 +218000 ekin = 2.31967181974704 | erot = 1.6896622434335 | epot = -21.7699992955268 | etot = -17.7606652323462 +219000 ekin = 2.46739391618502 | erot = 2.20775453602831 | epot = -21.776978875084 | etot = -17.1018304228706 +220000 ekin = 1.73785505731585 | erot = 3.0372433480804 | epot = -21.7321393101048 | etot = -16.9570409047086 +221000 ekin = 1.778697043089 | erot = 2.7846909329313 | epot = -21.7425830987872 | etot = -17.1791951227669 +222000 ekin = 2.62634865011186 | erot = 2.86077326472522 | epot = -21.7007933593054 | etot = -16.2136714444683 +223000 ekin = 3.04431297723215 | erot = 1.94008328047868 | epot = -21.7188465939138 | etot = -16.734450336203 +224000 ekin = 2.71939424183677 | erot = 2.42480251627533 | epot = -21.6866518782312 | etot = -16.5424551201191 +225000 ekin = 2.02593449761365 | erot = 3.37613250979673 | epot = -21.6919775986917 | etot = -16.2899105912813 +226000 ekin = 2.36496088602628 | erot = 2.39060577783945 | epot = -21.7612411053054 | etot = -17.0056744414397 +227000 ekin = 2.73527371921374 | erot = 2.63040468048003 | epot = -21.8235720454426 | etot = -16.4578936457488 +228000 ekin = 2.09009153610323 | erot = 2.26861924367323 | epot = -21.8859446312141 | etot = -17.5272338514377 +229000 ekin = 1.80131280326501 | erot = 1.7963110804324 | epot = -21.9677974652423 | etot = -18.3701735815449 +230000 ekin = 2.77436270232913 | erot = 2.22792046726092 | epot = -21.9902739646399 | etot = -16.9879907950498 +231000 ekin = 3.15789416871844 | erot = 2.77494856675301 | epot = -21.9771750398138 | etot = -16.0443323043424 +232000 ekin = 1.86920525086143 | erot = 1.70617009970185 | epot = -22.0127465263534 | etot = -18.4373711757901 +233000 ekin = 1.75915660001321 | erot = 1.56505378532405 | epot = -21.9936912811375 | etot = -18.6694808958002 +234000 ekin = 2.33631680564953 | erot = 2.05523369254154 | epot = -21.9151391633044 | etot = -17.5235886651133 +235000 ekin = 1.95729755108493 | erot = 2.52297007842176 | epot = -21.8622583087295 | etot = -17.3819906792228 +236000 ekin = 2.26174488772854 | erot = 1.90926942275389 | epot = -21.8776848863915 | etot = -17.7066705759091 +237000 ekin = 2.48859859508474 | erot = 2.6489237604941 | epot = -21.9479801146397 | etot = -16.8104577590608 +238000 ekin = 2.21074117955686 | erot = 2.74245988956904 | epot = -22.0027094279364 | etot = -17.0495083588105 +239000 ekin = 2.72897236706913 | erot = 2.49153579775713 | epot = -22.0211522435864 | etot = -16.8006440787602 +240000 ekin = 3.10410575629688 | erot = 2.19185039149975 | epot = -21.9285399490843 | etot = -16.6325838012877 +241000 ekin = 3.04659381738443 | erot = 2.65407823399251 | epot = -21.8553999209703 | etot = -16.1547278695933 +242000 ekin = 2.22634814860329 | erot = 2.33710119371497 | epot = -21.778295180705 | etot = -17.2148458383868 +243000 ekin = 1.53739989500925 | erot = 2.804422651144 | epot = -21.7210994015014 | etot = -17.3792768553481 +244000 ekin = 1.91594160283678 | erot = 2.43897673315061 | epot = -21.6239948430905 | etot = -17.2690765071031 +245000 ekin = 1.9573212108497 | erot = 2.60792757585164 | epot = -21.4969890421964 | etot = -16.931740255495 +246000 ekin = 2.07155268659352 | erot = 2.40712847472271 | epot = -21.4555802858827 | etot = -16.9768991245664 +247000 ekin = 1.55687592357629 | erot = 2.27937051296287 | epot = -21.415801560854 | etot = -17.5795551243148 +248000 ekin = 1.83815644169539 | erot = 2.56757546633135 | epot = -21.4396063392852 | etot = -17.0338744312585 +249000 ekin = 1.79880701831597 | erot = 2.0439839568354 | epot = -21.5116552123395 | etot = -17.6688642371882 +250000 ekin = 1.6819474109243 | erot = 3.39458382990459 | epot = -21.5432862054069 | etot = -16.466754964578 +251000 ekin = 2.13148829031636 | erot = 3.25959517865089 | epot = -21.5335137503413 | etot = -16.142430281374 +252000 ekin = 2.05395839402013 | erot = 2.53819950912971 | epot = -21.5603119938518 | etot = -16.9681540907019 +253000 ekin = 1.65837982841157 | erot = 3.21084156386521 | epot = -21.5856483774528 | etot = -16.716426985176 +254000 ekin = 2.32607189562296 | erot = 3.10904441141191 | epot = -21.5835562113995 | etot = -16.1484399043647 +255000 ekin = 2.50516183463011 | erot = 2.76806754476897 | epot = -21.5622650070292 | etot = -16.2890356276301 +256000 ekin = 1.97348594928106 | erot = 2.62554900973971 | epot = -21.5549569513865 | etot = -16.9559219923657 +257000 ekin = 2.23010268129159 | erot = 3.26394503338319 | epot = -21.5756937773404 | etot = -16.0816460626656 +258000 ekin = 2.0447966409083 | erot = 1.84671550533958 | epot = -21.6926265414806 | etot = -17.8011143952327 +259000 ekin = 2.87403716266236 | erot = 2.7890686554313 | epot = -21.799948240906 | etot = -16.1368424228124 +260000 ekin = 2.90780294403218 | erot = 2.19263097772001 | epot = -21.8560884935551 | etot = -16.7556545718029 +261000 ekin = 2.76828016335186 | erot = 2.34066383431491 | epot = -21.904753347489 | etot = -16.7958093498223 +262000 ekin = 3.52268021990509 | erot = 1.77075610541266 | epot = -21.923252751046 | etot = -16.6298164257282 +263000 ekin = 3.08420493567484 | erot = 2.42539400967894 | epot = -21.8573813915989 | etot = -16.3477824462451 +264000 ekin = 2.24745015945595 | erot = 2.03541588430139 | epot = -21.8692313889178 | etot = -17.5863653451605 +265000 ekin = 1.92522220276231 | erot = 2.5003676829468 | epot = -21.7418152763709 | etot = -17.3162253906618 +266000 ekin = 2.39641107663208 | erot = 3.25288398956727 | epot = -21.6961161037834 | etot = -16.046821037584 +267000 ekin = 1.71111784450077 | erot = 2.23671058890166 | epot = -21.6618183077995 | etot = -17.7139898743971 +268000 ekin = 2.10089423119538 | erot = 3.22434301936133 | epot = -21.6199098144813 | etot = -16.2946725639246 +269000 ekin = 1.9625053447265 | erot = 2.78709438989466 | epot = -21.512378343547 | etot = -16.7627786089258 +270000 ekin = 2.11347862898579 | erot = 2.66955708081142 | epot = -21.4131997021519 | etot = -16.6301639923547 +271000 ekin = 2.18755627878071 | erot = 3.10635949745237 | epot = -21.231195119641 | etot = -15.9372793434079 +272000 ekin = 2.53142755489725 | erot = 2.28018838604503 | epot = -21.0716416692008 | etot = -16.2600257282585 +273000 ekin = 1.9364743445402 | erot = 1.99261296885892 | epot = -21.007557675667 | etot = -17.0784703622679 +274000 ekin = 1.91013630831847 | erot = 2.2120127665723 | epot = -21.0477834541013 | etot = -16.9256343792105 +275000 ekin = 1.79273258693701 | erot = 3.10050032804429 | epot = -21.0858519409205 | etot = -16.1926190259392 +276000 ekin = 3.35719138398128 | erot = 2.41111345420191 | epot = -21.0304226706007 | etot = -15.2621178324176 +277000 ekin = 2.41774397151369 | erot = 1.50719443697989 | epot = -20.9759671563228 | etot = -17.0510287478292 +278000 ekin = 2.53951758510302 | erot = 2.14756601555722 | epot = -20.9653070148297 | etot = -16.2782234141694 +279000 ekin = 1.90856122527452 | erot = 2.38982437581387 | epot = -20.9745429336076 | etot = -16.6761573325192 +280000 ekin = 2.37131544290542 | erot = 3.59489996493466 | epot = -20.85613421052 | etot = -14.8899188026799 +281000 ekin = 1.76889591811704 | erot = 1.7951894912658 | epot = -20.9289254822807 | etot = -17.3648400728979 +282000 ekin = 2.27070827347114 | erot = 3.05009551199377 | epot = -20.8916515658568 | etot = -15.5708477803919 +283000 ekin = 2.18685960365006 | erot = 2.20812220616949 | epot = -20.8474969045899 | etot = -16.4525150947704 +284000 ekin = 1.91940159973892 | erot = 2.20890146173499 | epot = -20.8751887573221 | etot = -16.7468856958482 +285000 ekin = 3.15509933694634 | erot = 1.80738796351619 | epot = -21.0554892608396 | etot = -16.0930019603771 +286000 ekin = 3.87415003559708 | erot = 1.83530883692693 | epot = -21.2366462656484 | etot = -15.5271873931244 +287000 ekin = 3.65191681280166 | erot = 2.913547855761 | epot = -21.3085830740657 | etot = -14.7431184055031 +288000 ekin = 3.25566521528532 | erot = 1.61409275051713 | epot = -21.3016538192157 | etot = -16.4318958534132 +289000 ekin = 2.57277357969492 | erot = 2.7865509468974 | epot = -21.2753452951968 | etot = -15.9160207686044 +290000 ekin = 2.70842209282674 | erot = 2.41918512811132 | epot = -21.2877903800065 | etot = -16.1601831590685 +291000 ekin = 2.06014704473036 | erot = 2.36104758138505 | epot = -21.2845199368975 | etot = -16.8633253107821 +292000 ekin = 2.28556270655109 | erot = 2.04929815389926 | epot = -21.3435089189608 | etot = -17.0086480585104 +293000 ekin = 2.24999256733429 | erot = 2.35234276421049 | epot = -21.4532864362272 | etot = -16.8509511046824 +294000 ekin = 2.93128079968628 | erot = 2.88901294012339 | epot = -21.5344832077337 | etot = -15.7141894679241 +295000 ekin = 2.66786158124138 | erot = 2.29144551421467 | epot = -21.6972562684637 | etot = -16.7379491730076 +296000 ekin = 2.20703931624838 | erot = 2.91798090137806 | epot = -21.7499994740518 | etot = -16.6249792564254 +297000 ekin = 2.17711857895463 | erot = 3.3139407196584 | epot = -21.7438418246471 | etot = -16.2527825260341 +298000 ekin = 2.91263821701566 | erot = 2.35687557807243 | epot = -21.7003108484957 | etot = -16.4307970534076 +299000 ekin = 3.16765240032233 | erot = 2.23927360570976 | epot = -21.8111744518828 | etot = -16.4042484458507 +300000 ekin = 3.29571242152463 | erot = 1.38932168050636 | epot = -21.8854995787115 | etot = -17.2004654766805 +301000 ekin = 2.38336849338668 | erot = 3.30873138065989 | epot = -21.9040100279112 | etot = -16.2119101538647 +302000 ekin = 2.92546415072637 | erot = 3.247691767578 | epot = -21.8700812142841 | etot = -15.6969252959798 +303000 ekin = 2.4103373416559 | erot = 2.62018947425678 | epot = -21.8591741279587 | etot = -16.828647312046 +304000 ekin = 2.22974120288231 | erot = 2.69525972032883 | epot = -21.7977946057185 | etot = -16.8727936825074 +305000 ekin = 2.37900884029014 | erot = 2.39016080950149 | epot = -21.7722637572341 | etot = -17.0030941074424 +306000 ekin = 1.9446171443063 | erot = 2.89927908625624 | epot = -21.772518921465 | etot = -16.9286226909024 +307000 ekin = 2.51296678773709 | erot = 2.07871985749639 | epot = -21.7145354205816 | etot = -17.1228487753482 +308000 ekin = 2.81300442192371 | erot = 2.63068774502107 | epot = -21.7059595575782 | etot = -16.2622673906334 +309000 ekin = 2.33295752921531 | erot = 2.12114847477695 | epot = -21.6789859227475 | etot = -17.2248799187552 +310000 ekin = 2.52283407385729 | erot = 3.21577684610766 | epot = -21.6977338722704 | etot = -15.9591229523054 +311000 ekin = 2.34905401714491 | erot = 3.03961744974846 | epot = -21.7112095513776 | etot = -16.3225380844842 +312000 ekin = 1.82668239636477 | erot = 3.25882975871633 | epot = -21.5839087054203 | etot = -16.4983965503392 +313000 ekin = 1.63596397844578 | erot = 2.08106491982899 | epot = -21.6088054377576 | etot = -17.8917765394829 +314000 ekin = 2.27268061655198 | erot = 2.56861774872119 | epot = -21.622333325343 | etot = -16.7810349600698 +315000 ekin = 2.53123691731374 | erot = 2.1324731770604 | epot = -21.7018350864597 | etot = -17.0381249920856 +316000 ekin = 1.99511026234591 | erot = 1.80085053236165 | epot = -21.7165753862862 | etot = -17.9206145915787 +317000 ekin = 2.11342130166581 | erot = 2.00931752224566 | epot = -21.7049091699378 | etot = -17.5821703460263 +318000 ekin = 2.29657040201996 | erot = 1.9218952520588 | epot = -21.6732020643863 | etot = -17.4547364103076 +319000 ekin = 1.98100978177984 | erot = 1.68241530251755 | epot = -21.5700337503682 | etot = -17.9066086660708 +320000 ekin = 2.46277902525288 | erot = 3.0707129249839 | epot = -21.5118277867106 | etot = -15.9783358364738 +321000 ekin = 1.8533722862421 | erot = 2.67441728470359 | epot = -21.5413634192757 | etot = -17.01357384833 +322000 ekin = 1.94543884879318 | erot = 3.3613066315754 | epot = -21.4649757180038 | etot = -16.1582302376352 +323000 ekin = 1.92582236335168 | erot = 2.08582462630249 | epot = -21.5020070864549 | etot = -17.4903600968007 +324000 ekin = 2.21385975174577 | erot = 2.45972054558752 | epot = -21.6040339423077 | etot = -16.9304536449744 +325000 ekin = 2.71973574551436 | erot = 2.37172075216282 | epot = -21.7154750081878 | etot = -16.6240185105106 +326000 ekin = 1.88834012476607 | erot = 1.92160793718507 | epot = -21.7697066104337 | etot = -17.9597585484825 +327000 ekin = 3.03100650626309 | erot = 1.66914039489952 | epot = -21.8474776692767 | etot = -17.1473307681141 +328000 ekin = 2.74123304387623 | erot = 1.9170666048058 | epot = -21.8856206551572 | etot = -17.2273210064752 +329000 ekin = 2.94158338898171 | erot = 3.13997083102765 | epot = -21.9406516192959 | etot = -15.8590973992865 +330000 ekin = 2.91669398329971 | erot = 2.01301123001111 | epot = -21.9369752911326 | etot = -17.0072700778218 +331000 ekin = 2.28417665381006 | erot = 2.04960167200569 | epot = -21.927160006304 | etot = -17.5933816804883 +332000 ekin = 2.4148148688836 | erot = 3.18178691603942 | epot = -21.9797962539673 | etot = -16.3831944690443 +333000 ekin = 2.45630818257634 | erot = 2.70954264697347 | epot = -22.0834375892948 | etot = -16.917586759745 +334000 ekin = 2.37347521855933 | erot = 2.99534828037212 | epot = -22.119902754337 | etot = -16.7510792554055 +335000 ekin = 2.11274250313861 | erot = 3.56585847378427 | epot = -22.1620352555629 | etot = -16.48343427864 +336000 ekin = 2.63429420241716 | erot = 2.12841745309053 | epot = -22.1384285356293 | etot = -17.3757168801216 +337000 ekin = 2.74014146566976 | erot = 2.73588205536329 | epot = -22.1194416289215 | etot = -16.6434181078884 +338000 ekin = 1.84480508690214 | erot = 2.23455733552335 | epot = -22.1965093971539 | etot = -18.1171469747284 +339000 ekin = 1.56183988387053 | erot = 2.489100411134 | epot = -22.2396203002948 | etot = -18.1886800052903 +340000 ekin = 1.46409027371678 | erot = 4.0512372950447 | epot = -22.1584645354502 | etot = -16.6431369666887 +341000 ekin = 1.68589245970878 | erot = 2.79353148184118 | epot = -22.1393063295445 | etot = -17.6598823879945 +342000 ekin = 1.9632055547669 | erot = 2.74455536956775 | epot = -22.2008946996018 | etot = -17.4931337752671 +343000 ekin = 2.66782090058793 | erot = 3.18156117072004 | epot = -22.2922370675599 | etot = -16.4428549962519 +344000 ekin = 1.78878469299216 | erot = 2.18063379585249 | epot = -22.3229742728833 | etot = -18.3535557840387 +345000 ekin = 1.540972096623 | erot = 1.85836807653953 | epot = -22.3669594635967 | etot = -18.9676192904341 +346000 ekin = 1.69306131915114 | erot = 1.80797582028411 | epot = -22.3312791976866 | etot = -18.8302420582514 +347000 ekin = 1.37617258934979 | erot = 2.61616357123582 | epot = -22.3534264320593 | etot = -18.3610902714737 +348000 ekin = 2.13829045790164 | erot = 2.85908731375532 | epot = -22.3464198630052 | etot = -17.3490420913483 +349000 ekin = 1.82945196641201 | erot = 1.97678849263654 | epot = -22.3619223728943 | etot = -18.5556819138458 +350000 ekin = 1.78944470920989 | erot = 2.50950790539659 | epot = -22.3467767277336 | etot = -18.0478241131271 +351000 ekin = 1.68749587286921 | erot = 2.81742906170281 | epot = -22.4171372510498 | etot = -17.9122123164778 +352000 ekin = 2.77021178817643 | erot = 2.15256178979697 | epot = -22.5877268787862 | etot = -17.6649533008128 +353000 ekin = 3.5651579503159 | erot = 1.46627940614144 | epot = -22.6396840781933 | etot = -17.608246721736 +354000 ekin = 3.44763260550689 | erot = 2.25092776011915 | epot = -22.5553143373262 | etot = -16.8567539717001 +355000 ekin = 2.03402845200418 | erot = 2.90906782343746 | epot = -22.5137132330461 | etot = -17.5706169576044 +356000 ekin = 2.10644486273696 | erot = 3.31938387624324 | epot = -22.5442634045104 | etot = -17.1184346655302 +357000 ekin = 2.76535001946383 | erot = 2.50873330135166 | epot = -22.52215971412 | etot = -17.2480763933045 +358000 ekin = 2.53751054023787 | erot = 2.26477084741189 | epot = -22.5103746530379 | etot = -17.7080932653881 +359000 ekin = 3.23570364771486 | erot = 2.52813698122051 | epot = -22.6019986378314 | etot = -16.838158008896 +360000 ekin = 2.59175576606819 | erot = 1.97223576668381 | epot = -22.6470028729806 | etot = -18.0830113402286 +361000 ekin = 2.61182361704566 | erot = 2.50385714239847 | epot = -22.6927829246934 | etot = -17.5771021652493 +362000 ekin = 2.38475515872101 | erot = 3.84233912950958 | epot = -22.6454854809905 | etot = -16.4183911927599 +363000 ekin = 2.88487115582968 | erot = 1.98709532428838 | epot = -22.5316518293815 | etot = -17.6596853492635 +364000 ekin = 2.24456282663807 | erot = 1.87857741688963 | epot = -22.4065988337859 | etot = -18.2834585902582 +365000 ekin = 2.04295690198209 | erot = 2.81008642631349 | epot = -22.2314366274422 | etot = -17.3783932991466 +366000 ekin = 2.266544192376 | erot = 1.95642386899595 | epot = -22.1933765521819 | etot = -17.97040849081 +367000 ekin = 2.81580114465084 | erot = 2.51878026336671 | epot = -22.2503978612043 | etot = -16.9158164531867 +368000 ekin = 2.81616947616975 | erot = 2.18673959088794 | epot = -22.3700662776457 | etot = -17.367157210588 +369000 ekin = 2.31685128708704 | erot = 2.8485166214536 | epot = -22.4347113127671 | etot = -17.2693434042264 +370000 ekin = 2.66633369096824 | erot = 2.10373843245294 | epot = -22.5097473869516 | etot = -17.7396752635304 +371000 ekin = 2.19554700980946 | erot = 3.61136788339347 | epot = -22.5751109079912 | etot = -16.7681960147883 +372000 ekin = 1.77355024694411 | erot = 3.42422008956619 | epot = -22.6682235461143 | etot = -17.470453209604 +373000 ekin = 2.14882393689494 | erot = 2.79102164241389 | epot = -22.7183823639386 | etot = -17.7785367846297 +374000 ekin = 2.69471790401649 | erot = 3.57888941010137 | epot = -22.8644350080836 | etot = -16.5908276939657 +375000 ekin = 2.40588229328688 | erot = 2.98559431132055 | epot = -22.9231560989464 | etot = -17.5316794943389 +376000 ekin = 3.36525975858234 | erot = 3.24749522030667 | epot = -22.9448546765658 | etot = -16.3320996976767 +377000 ekin = 3.1898535090454 | erot = 2.65440981370779 | epot = -22.8890189773608 | etot = -17.0447556546076 +378000 ekin = 1.54661929765086 | erot = 2.66304115784623 | epot = -22.8894135140088 | etot = -18.6797530585117 +379000 ekin = 1.93848939303329 | erot = 2.54534330055222 | epot = -22.9081180555037 | etot = -18.4242853619182 +380000 ekin = 2.66258042260528 | erot = 2.88895789126712 | epot = -22.9376621442708 | etot = -17.3861238303984 +381000 ekin = 2.95374671041029 | erot = 2.1769850563328 | epot = -22.9816080577256 | etot = -17.8508762909825 +382000 ekin = 2.58850292280408 | erot = 2.01885613358327 | epot = -22.9279053853416 | etot = -18.3205463289542 +383000 ekin = 2.01542491830335 | erot = 2.50444856286716 | epot = -22.9509700194999 | etot = -18.4310965383294 +384000 ekin = 2.10088918623931 | erot = 2.19861971638621 | epot = -22.9637245689725 | etot = -18.664215666347 +385000 ekin = 1.91381637067085 | erot = 1.63023926713733 | epot = -22.9798616984434 | etot = -19.4358060606352 +386000 ekin = 1.55997375471681 | erot = 1.35864886272388 | epot = -23.026401230456 | etot = -20.1077786130153 +387000 ekin = 2.21265030198491 | erot = 1.7501227932087 | epot = -23.0266356759123 | etot = -19.0638625807187 +388000 ekin = 1.98732621523102 | erot = 1.96003045102707 | epot = -22.9343684877508 | etot = -18.9870118214927 +389000 ekin = 2.5418388293764 | erot = 2.33933777400626 | epot = -22.9288764120935 | etot = -18.0476998087109 +390000 ekin = 2.07840415144685 | erot = 1.88714080084969 | epot = -22.8368099519711 | etot = -18.8712649996745 +391000 ekin = 1.85201287716429 | erot = 2.41309749069991 | epot = -22.8035614550317 | etot = -18.5384510871675 +392000 ekin = 2.19897450334475 | erot = 2.90002030847564 | epot = -22.8026053664846 | etot = -17.7036105546642 +393000 ekin = 2.15250422129825 | erot = 3.1954140871906 | epot = -22.8935871868038 | etot = -17.5456688783149 +394000 ekin = 1.99220043003136 | erot = 2.14720550675182 | epot = -22.8839525821639 | etot = -18.7445466453807 +395000 ekin = 2.03384825587122 | erot = 2.5026704188622 | epot = -22.9355340107645 | etot = -18.3990153360311 +396000 ekin = 2.14388612805494 | erot = 1.95887569078926 | epot = -23.0314147787906 | etot = -18.9286529599464 +397000 ekin = 2.39817268086959 | erot = 1.65198489715495 | epot = -23.1381610188687 | etot = -19.0880034408442 +398000 ekin = 3.5848529329223 | erot = 2.5137795193631 | epot = -23.2493671328086 | etot = -17.1507346805232 +399000 ekin = 2.65690410152896 | erot = 1.78815540583896 | epot = -23.3551071826471 | etot = -18.9100476752792 +400000 ekin = 2.5116972230557 | erot = 2.10904464709597 | epot = -23.4242760069967 | etot = -18.803534136845 +401000 ekin = 2.05111703519218 | erot = 2.15375363886755 | epot = -23.4796569613041 | etot = -19.2747862872443 +402000 ekin = 2.43372934314587 | erot = 2.11260100954187 | epot = -23.4682554876931 | etot = -18.9219251350053 +403000 ekin = 2.53598880596584 | erot = 2.81278076880176 | epot = -23.5378775828587 | etot = -18.1891080080911 +404000 ekin = 2.18194702425602 | erot = 2.63711249102604 | epot = -23.6244518702206 | etot = -18.8053923549385 +405000 ekin = 2.45121967393562 | erot = 2.40500763090291 | epot = -23.6357713162683 | etot = -18.7795440114298 +406000 ekin = 2.21958671378093 | erot = 2.24922226746756 | epot = -23.6553601287 | etot = -19.1865511474515 +407000 ekin = 1.98564574231222 | erot = 2.77863717556005 | epot = -23.5607032705187 | etot = -18.7964203526464 +408000 ekin = 2.57646591315375 | erot = 2.58095218000659 | epot = -23.4398366413677 | etot = -18.2824185482073 +409000 ekin = 2.36945583486912 | erot = 2.25935935813466 | epot = -23.3294611001761 | etot = -18.7006459071724 +410000 ekin = 2.02254604345491 | erot = 1.96483214055515 | epot = -23.3122760741247 | etot = -19.3248978901146 +411000 ekin = 1.87895167522371 | erot = 2.65152784802951 | epot = -23.2919254735047 | etot = -18.7614459502515 +412000 ekin = 1.99369299492691 | erot = 2.68971636909523 | epot = -23.2559513781021 | etot = -18.57254201408 +413000 ekin = 2.38900558877156 | erot = 2.64564764432049 | epot = -23.2013938450539 | etot = -18.1667406119618 +414000 ekin = 2.42764300748033 | erot = 1.75174590229272 | epot = -23.1266922276306 | etot = -18.9473033178576 +415000 ekin = 2.76414124953308 | erot = 2.44215852210494 | epot = -23.1817305186064 | etot = -17.9754307469683 +416000 ekin = 2.08280868301927 | erot = 2.76578542751831 | epot = -23.1905832299196 | etot = -18.341989119382 +417000 ekin = 1.99968890800012 | erot = 1.95787693284286 | epot = -23.194417716001 | etot = -19.236851875158 +418000 ekin = 2.38298881868294 | erot = 2.55898711987873 | epot = -23.1586352965619 | etot = -18.2166593580002 +419000 ekin = 2.9839633883085 | erot = 2.57065203496089 | epot = -23.0544780894577 | etot = -17.4998626661883 +420000 ekin = 2.60178854557762 | erot = 2.46052060802045 | epot = -22.9622762729971 | etot = -17.899967119399 +421000 ekin = 2.51720276737396 | erot = 1.77804167911051 | epot = -22.9515897224038 | etot = -18.6563452759193 +422000 ekin = 2.7320348139792 | erot = 1.67298118116889 | epot = -22.9404137463627 | etot = -18.5353977512146 +423000 ekin = 2.13282380031375 | erot = 2.54987675813572 | epot = -22.8157706530705 | etot = -18.133070094621 +424000 ekin = 1.90610672595356 | erot = 2.31894231724673 | epot = -22.7787002443962 | etot = -18.553651201196 +425000 ekin = 2.37366400687573 | erot = 1.95578603620107 | epot = -22.7873996262579 | etot = -18.4579495831811 +426000 ekin = 2.23502410344739 | erot = 2.60951465135819 | epot = -22.8069525247999 | etot = -17.9624137699943 +427000 ekin = 1.88572309905852 | erot = 2.12675775194484 | epot = -22.973782602072 | etot = -18.9613017510686 +428000 ekin = 1.93180562731872 | erot = 2.45432362930894 | epot = -23.1062681387344 | etot = -18.7201388821067 +429000 ekin = 1.72618205037519 | erot = 2.1638575670951 | epot = -23.1203764425356 | etot = -19.2303368250654 +430000 ekin = 2.31236502680075 | erot = 2.14057167953237 | epot = -23.127316365141 | etot = -18.6743796588079 +431000 ekin = 2.45859340033276 | erot = 2.41557475448707 | epot = -23.137683007962 | etot = -18.2635148531422 +432000 ekin = 2.80043339920945 | erot = 2.19140888866301 | epot = -23.1459051340744 | etot = -18.1540628462019 +433000 ekin = 2.2038223816989 | erot = 1.62239062651454 | epot = -23.1902054552061 | etot = -19.3639924469927 +434000 ekin = 2.59117398719482 | erot = 2.35262979682601 | epot = -23.2174180769097 | etot = -18.2736142928889 +435000 ekin = 2.29283868462832 | erot = 2.54026007379789 | epot = -23.1968654207439 | etot = -18.3637666623176 +436000 ekin = 2.43256920688117 | erot = 2.74968424233253 | epot = -23.2466230085986 | etot = -18.0643695593849 +437000 ekin = 1.64425125112848 | erot = 3.23329270267647 | epot = -23.2380191669749 | etot = -18.3604752131699 +438000 ekin = 1.56124620606823 | erot = 2.60252333491232 | epot = -23.1341667906033 | etot = -18.9703972496228 +439000 ekin = 2.30501653948793 | erot = 1.93890022921162 | epot = -23.14170715719 | etot = -18.8977903884904 +440000 ekin = 2.52023257151789 | erot = 3.04669715760005 | epot = -23.2021590525686 | etot = -17.6352293234507 +441000 ekin = 2.79903748157629 | erot = 2.54578114158762 | epot = -23.1760357267403 | etot = -17.8312171035764 +442000 ekin = 2.93503932875119 | erot = 2.87674150367343 | epot = -23.1192988997858 | etot = -17.3075180673612 +443000 ekin = 1.96853850230447 | erot = 1.76444304280728 | epot = -23.0474504745021 | etot = -19.3144689293904 +444000 ekin = 2.00740903163919 | erot = 2.25338146232896 | epot = -22.9768126386128 | etot = -18.7160221446446 +445000 ekin = 2.22543241532629 | erot = 2.06325853122729 | epot = -22.8128736901554 | etot = -18.5241827436018 +446000 ekin = 2.44497213168066 | erot = 2.37296472072563 | epot = -22.7182187420116 | etot = -17.9002818896053 +447000 ekin = 2.27682912672612 | erot = 2.40590062157627 | epot = -22.73821768508 | etot = -18.0554879367776 +448000 ekin = 2.17717815648414 | erot = 1.94002353369628 | epot = -22.8515885285926 | etot = -18.7343868384122 +449000 ekin = 2.21957974285234 | erot = 2.34288028472299 | epot = -22.9413256171992 | etot = -18.3788655896239 +450000 ekin = 2.75054329798646 | erot = 1.97942707751151 | epot = -22.8960066852305 | etot = -18.1660363097325 +451000 ekin = 2.21127283509867 | erot = 2.13383865709095 | epot = -22.93012845553 | etot = -18.5850169633403 +452000 ekin = 2.54342208027875 | erot = 2.35725031977164 | epot = -22.9678192920236 | etot = -18.0671468919732 +453000 ekin = 2.22826691368246 | erot = 1.78505555998555 | epot = -22.9525856519538 | etot = -18.9392631782858 +454000 ekin = 2.43963081757063 | erot = 2.59545869820689 | epot = -22.8816014548474 | etot = -17.8465119390699 +455000 ekin = 2.04579285921012 | erot = 2.79600798010941 | epot = -22.6671256943706 | etot = -17.8253248550511 +456000 ekin = 2.02054568037702 | erot = 2.5142933737518 | epot = -22.4807651427491 | etot = -17.9459260886202 +457000 ekin = 2.62427297855768 | erot = 2.43881475758852 | epot = -22.3628471473124 | etot = -17.2997594111662 +458000 ekin = 2.00982157063058 | erot = 1.99237218757745 | epot = -22.2563036448067 | etot = -18.2541098865987 +459000 ekin = 1.75248702434071 | erot = 2.49686008961238 | epot = -22.2467888503062 | etot = -17.9974417363531 +460000 ekin = 1.91910131837566 | erot = 2.07619395094217 | epot = -22.2400567481829 | etot = -18.2447614788651 +461000 ekin = 1.56844353839394 | erot = 1.28973659789019 | epot = -22.2093526564538 | etot = -19.3511725201697 +462000 ekin = 2.45174884293064 | erot = 1.36031689293857 | epot = -22.3089787954009 | etot = -18.4969130595317 +463000 ekin = 2.64349839520108 | erot = 2.07831354185085 | epot = -22.4300376076151 | etot = -17.7082256705631 +464000 ekin = 2.67299819724031 | erot = 3.73615881795558 | epot = -22.554470130186 | etot = -16.1453131149901 +465000 ekin = 1.95390361110071 | erot = 2.23920710641231 | epot = -22.7384686297881 | etot = -18.545357912275 +466000 ekin = 2.13348556167989 | erot = 2.96280610170109 | epot = -22.8443072066537 | etot = -17.7480155432727 +467000 ekin = 2.46613760277875 | erot = 2.11616591175904 | epot = -23.0265043956358 | etot = -18.444200881098 +468000 ekin = 1.99036864211387 | erot = 1.62858187482038 | epot = -23.0961237334908 | etot = -19.4771732165565 +469000 ekin = 2.49659836745282 | erot = 2.63661728128629 | epot = -23.1411267023576 | etot = -18.0079110536185 +470000 ekin = 2.92199371715687 | erot = 3.21712399422296 | epot = -23.1457817109815 | etot = -17.0066639996017 +471000 ekin = 2.36477645073574 | erot = 1.72314859686431 | epot = -23.1045733261495 | etot = -19.0166482785494 +472000 ekin = 2.18519498855062 | erot = 2.00240720258206 | epot = -23.072627104452 | etot = -18.8850249133193 +473000 ekin = 2.3714321613692 | erot = 2.86124663404655 | epot = -23.0328429128019 | etot = -17.8001641173862 +474000 ekin = 2.1857949588469 | erot = 2.60051446256873 | epot = -22.9136735669303 | etot = -18.1273641455147 +475000 ekin = 2.39661135768768 | erot = 2.01358694537797 | epot = -22.813046501162 | etot = -18.4028481980963 +476000 ekin = 2.10676579065005 | erot = 2.60327856915634 | epot = -22.8119267991277 | etot = -18.1018824393213 +477000 ekin = 2.53295314095718 | erot = 3.55510942450984 | epot = -22.7955031957515 | etot = -16.7074406302845 +478000 ekin = 2.40630114318287 | erot = 2.73236241457618 | epot = -22.7034337758127 | etot = -17.5647702180536 +479000 ekin = 1.27745698905519 | erot = 2.99245403250463 | epot = -22.6605920931777 | etot = -18.3906810716179 +480000 ekin = 1.82390564518045 | erot = 2.13920354248295 | epot = -22.6299626931083 | etot = -18.6668535054449 +481000 ekin = 2.3880478628611 | erot = 3.18399864702822 | epot = -22.6553769169915 | etot = -17.0833304071022 +482000 ekin = 3.20116727691415 | erot = 2.41976760575225 | epot = -22.6125762236254 | etot = -16.991641340959 +483000 ekin = 3.03846588981692 | erot = 2.48627946336888 | epot = -22.5774232520165 | etot = -17.0526778988307 +484000 ekin = 2.70181776439228 | erot = 2.52677846233176 | epot = -22.6070502809988 | etot = -17.3784540542748 +485000 ekin = 3.27224317472663 | erot = 2.42431335826243 | epot = -22.5997277235211 | etot = -16.9031711905321 +486000 ekin = 1.96596043103987 | erot = 1.75891125021975 | epot = -22.642547970919 | etot = -18.9176762896594 +487000 ekin = 2.6234378417876 | erot = 2.50755895035553 | epot = -22.7339556642929 | etot = -17.6029588721497 +488000 ekin = 1.75208074499658 | erot = 2.6448687233026 | epot = -22.7917400975639 | etot = -18.3947906292648 +489000 ekin = 2.08733298303259 | erot = 2.9523180967106 | epot = -22.881879447047 | etot = -17.8422283673038 +490000 ekin = 2.30760030156363 | erot = 2.33161319100248 | epot = -22.8847649865187 | etot = -18.2455514939526 +491000 ekin = 2.48196214295004 | erot = 2.59523958504393 | epot = -22.8776771178079 | etot = -17.800475389814 +492000 ekin = 3.28209206383218 | erot = 2.1852502939697 | epot = -22.8577625078557 | etot = -17.3904201500538 +493000 ekin = 3.37967323337949 | erot = 2.35355143859173 | epot = -22.8047552632571 | etot = -17.0715305912858 +494000 ekin = 3.57464120696614 | erot = 2.24853455202993 | epot = -22.8042956353342 | etot = -16.9811198763381 +495000 ekin = 2.5052992174061 | erot = 2.15850924694968 | epot = -22.7996067752132 | etot = -18.1357983108574 +496000 ekin = 1.95429188426678 | erot = 3.5825937389492 | epot = -22.837298805698 | etot = -17.3004131824821 +497000 ekin = 2.22186292996358 | erot = 2.46502235984734 | epot = -22.8432554612651 | etot = -18.1563701714542 +498000 ekin = 1.72648192614392 | erot = 2.39641281876546 | epot = -22.7792810810776 | etot = -18.6563863361682 +499000 ekin = 2.44591165293457 | erot = 2.82720242160824 | epot = -22.7953427712295 | etot = -17.5222286966867 +500000 ekin = 2.7851302139546 | erot = 2.23270136622152 | epot = -22.8991185931508 | etot = -17.8812870129746 +501000 ekin = 2.99439211318652 | erot = 1.97783069072832 | epot = -22.9279475016441 | etot = -17.9557246977292 +502000 ekin = 2.9862206030979 | erot = 1.79973926744011 | epot = -22.956155459855 | etot = -18.170195589317 +503000 ekin = 2.51500932637374 | erot = 2.88863666961797 | epot = -22.9858023469845 | etot = -17.5821563509928 +504000 ekin = 2.84387999289216 | erot = 2.69340549636984 | epot = -22.9170131486245 | etot = -17.3797276593625 +505000 ekin = 2.95569075243612 | erot = 2.602585876956 | epot = -22.9907249028698 | etot = -17.4324482734777 +506000 ekin = 2.19812159740513 | erot = 1.96718410179931 | epot = -23.0318373952185 | etot = -18.8665316960141 +507000 ekin = 2.26250501037088 | erot = 2.70461320689487 | epot = -22.9974394720575 | etot = -18.0303212547917 +508000 ekin = 2.63634784309456 | erot = 2.05036585895923 | epot = -23.0090804345496 | etot = -18.3223667324958 +509000 ekin = 2.94151668821484 | erot = 2.91160221114196 | epot = -23.0621014211554 | etot = -17.2089825217986 +510000 ekin = 2.26258273420884 | erot = 2.8155823326395 | epot = -23.1767418648115 | etot = -18.0985767979631 +511000 ekin = 2.89871784417207 | erot = 2.15651428734314 | epot = -23.2992796007865 | etot = -18.2440474692713 +512000 ekin = 2.18241701331153 | erot = 2.32471024525139 | epot = -23.3744961479659 | etot = -18.867368889403 +513000 ekin = 1.69086971293502 | erot = 2.8783745660792 | epot = -23.3843289700052 | etot = -18.8150846909909 +514000 ekin = 1.72546832120935 | erot = 2.33325616873572 | epot = -23.3798363194193 | etot = -19.3211118294743 +515000 ekin = 1.99840202228396 | erot = 1.80255577214453 | epot = -23.3747953532199 | etot = -19.5738375587914 +516000 ekin = 3.02853898966319 | erot = 1.54004582498168 | epot = -23.3386782444955 | etot = -18.7700934298506 +517000 ekin = 2.46344499126943 | erot = 2.11388687673044 | epot = -23.3135548350045 | etot = -18.7362229670046 +518000 ekin = 2.0362169291028 | erot = 2.51796163147274 | epot = -23.2504637438686 | etot = -18.6962851832931 +519000 ekin = 1.58660977959654 | erot = 1.63211831489779 | epot = -23.2081782818072 | etot = -19.9894501873129 +520000 ekin = 2.16318611090781 | erot = 1.89658879288914 | epot = -23.2096974204855 | etot = -19.1499225166885 +521000 ekin = 1.97684804456375 | erot = 2.08731550434085 | epot = -23.2527315496486 | etot = -19.188568000744 +522000 ekin = 2.69827007409924 | erot = 2.19560826391663 | epot = -23.3133573112007 | etot = -18.4194789731848 +523000 ekin = 2.2478363305578 | erot = 1.67442261891177 | epot = -23.3604551637841 | etot = -19.4381962143146 +524000 ekin = 2.34895041229461 | erot = 2.10078601700867 | epot = -23.381233923661 | etot = -18.9314974943577 +525000 ekin = 2.13155817393156 | erot = 2.07239357304026 | epot = -23.4395046885398 | etot = -19.235552941568 +526000 ekin = 2.50234900291801 | erot = 2.25431525777582 | epot = -23.4988198653879 | etot = -18.7421556046941 +527000 ekin = 3.03511403104629 | erot = 1.80504692374136 | epot = -23.5562539149297 | etot = -18.7160929601421 +528000 ekin = 2.56074044727573 | erot = 2.54331285469023 | epot = -23.5735936308822 | etot = -18.4695403289162 +529000 ekin = 2.37500349152887 | erot = 1.93006279746846 | epot = -23.5580125050353 | etot = -19.252946216038 +530000 ekin = 3.34194424343389 | erot = 3.41373524710891 | epot = -23.4507267657596 | etot = -16.6950472752168 +531000 ekin = 2.42341072166937 | erot = 2.35978455298084 | epot = -23.1501712562452 | etot = -18.366975981595 +532000 ekin = 2.58886764526949 | erot = 1.86996947608086 | epot = -23.1663546344342 | etot = -18.7075175130839 +533000 ekin = 2.18022742299593 | erot = 2.16045486833456 | epot = -23.380637574335 | etot = -19.0399552830045 +534000 ekin = 2.34791679374047 | erot = 2.03855517230123 | epot = -23.463831563993 | etot = -19.0773595979513 +535000 ekin = 2.37817813408508 | erot = 2.07397219148902 | epot = -23.4832900392636 | etot = -19.0311397136895 +536000 ekin = 2.46210672665338 | erot = 1.8947790016655 | epot = -23.4672059982835 | etot = -19.1103202699646 +537000 ekin = 1.71186030024847 | erot = 2.1344462698512 | epot = -23.5555571897054 | etot = -19.7092506196057 +538000 ekin = 2.16671541009104 | erot = 2.76559932728314 | epot = -23.6609154290595 | etot = -18.7286006916853 +539000 ekin = 2.16621132370208 | erot = 2.29104148484627 | epot = -23.7377569804062 | etot = -19.2805041718579 +540000 ekin = 2.37610335621453 | erot = 1.63780764528448 | epot = -23.7325177726622 | etot = -19.7186067711632 +541000 ekin = 2.61201541528826 | erot = 2.52498155703037 | epot = -23.6623419839272 | etot = -18.5253450116085 +542000 ekin = 2.72898292667725 | erot = 2.10989431729706 | epot = -23.7000798212983 | etot = -18.861202577324 +543000 ekin = 2.72070152721044 | erot = 1.85641764017256 | epot = -23.6069628280622 | etot = -19.0298436606792 +544000 ekin = 2.11779438939827 | erot = 1.50576740930398 | epot = -23.5826778503359 | etot = -19.9591160516337 +545000 ekin = 1.70778076743634 | erot = 2.56995673058895 | epot = -23.583343914622 | etot = -19.3056064165967 +546000 ekin = 2.3805758278215 | erot = 1.86648142267507 | epot = -23.6114100683877 | etot = -19.3643528178911 +547000 ekin = 2.45245186799104 | erot = 2.45758854207408 | epot = -23.6611856045782 | etot = -18.7511451945131 +548000 ekin = 2.39042546399151 | erot = 2.39603897463391 | epot = -23.6735607421256 | etot = -18.8870963035002 +549000 ekin = 2.59234094316699 | erot = 2.03286284306236 | epot = -23.6646331709071 | etot = -19.0394293846778 +550000 ekin = 1.99320521419403 | erot = 1.84894458030441 | epot = -23.6669378249973 | etot = -19.8247880304988 +551000 ekin = 2.44898809443739 | erot = 2.0219242208942 | epot = -23.6235443659669 | etot = -19.1526320506353 +552000 ekin = 2.69502802037877 | erot = 1.40870700355959 | epot = -23.4610294466586 | etot = -19.3572944227202 +553000 ekin = 1.76133393557171 | erot = 2.61023484195893 | epot = -23.254624102607 | etot = -18.8830553250764 +554000 ekin = 2.30411800065654 | erot = 2.33064249173903 | epot = -23.2181242479504 | etot = -18.5833637555548 +555000 ekin = 3.27047384641377 | erot = 1.6422371773255 | epot = -23.1973795659522 | etot = -18.2846685422129 +556000 ekin = 2.90314776795354 | erot = 2.59897046564306 | epot = -23.1460736374982 | etot = -17.6439554039016 +557000 ekin = 2.91673821282758 | erot = 3.16411852075219 | epot = -23.1459806883625 | etot = -17.0651239547827 +558000 ekin = 2.82902946234823 | erot = 2.71147602500681 | epot = -23.1195640745749 | etot = -17.5790585872199 +559000 ekin = 2.44501247164481 | erot = 3.2946921444891 | epot = -23.1638653139107 | etot = -17.4241606977768 +560000 ekin = 2.31903153876872 | erot = 2.34794389762528 | epot = -23.1221343768987 | etot = -18.4551589405047 +561000 ekin = 2.04778211145284 | erot = 2.88230317636058 | epot = -23.0254469759625 | etot = -18.0953616881491 +562000 ekin = 2.23097749779459 | erot = 3.71637560430596 | epot = -22.8954878936692 | etot = -16.9481347915687 +563000 ekin = 3.13589796296721 | erot = 2.30360204009239 | epot = -22.9672461823823 | etot = -17.5277461793227 +564000 ekin = 2.43468506100309 | erot = 2.37780089042927 | epot = -22.9400399192094 | etot = -18.127553967777 +565000 ekin = 2.74707381978168 | erot = 2.07635638038451 | epot = -22.9404100305402 | etot = -18.116979830374 +566000 ekin = 2.4222424655432 | erot = 2.23675573588529 | epot = -22.964317030412 | etot = -18.3053188289835 +567000 ekin = 2.66075150820169 | erot = 2.00813116398473 | epot = -23.0598382212572 | etot = -18.3909555490708 +568000 ekin = 3.04180913535304 | erot = 1.98452490185762 | epot = -23.1129541055894 | etot = -18.0866200683787 +569000 ekin = 3.57499094364799 | erot = 2.06992850387417 | epot = -23.117960007112 | etot = -17.4730405595898 +570000 ekin = 2.66020768003306 | erot = 2.34012507933247 | epot = -23.1339632056245 | etot = -18.133630446259 +571000 ekin = 1.94924082891001 | erot = 2.84220462440654 | epot = -23.0609933320748 | etot = -18.2695478787583 +572000 ekin = 2.41536650984725 | erot = 2.40871845587551 | epot = -23.0560879925718 | etot = -18.232003026849 +573000 ekin = 1.75696177901838 | erot = 2.31680084915611 | epot = -23.107424588529 | etot = -19.0336619603545 +574000 ekin = 2.1071071848933 | erot = 2.59270710144433 | epot = -23.1966129698341 | etot = -18.4967986834965 +575000 ekin = 2.37668274547159 | erot = 2.79832262601946 | epot = -23.2697902014998 | etot = -18.0947848300088 +576000 ekin = 2.17648663043414 | erot = 3.28534323951364 | epot = -23.3035961850707 | etot = -17.8417663151229 +577000 ekin = 2.48653402473871 | erot = 2.29382004189646 | epot = -23.3348256872303 | etot = -18.5544716205951 +578000 ekin = 2.63497646120015 | erot = 2.38541222697017 | epot = -23.3938829535157 | etot = -18.3734942653454 +579000 ekin = 2.68807604490538 | erot = 1.70832449354964 | epot = -23.3711370904455 | etot = -18.9747365519905 +580000 ekin = 2.35405412912148 | erot = 2.8553242408976 | epot = -23.3804498064804 | etot = -18.1710714364613 +581000 ekin = 2.45622900796811 | erot = 2.60461398742566 | epot = -23.3507481421638 | etot = -18.28990514677 +582000 ekin = 2.33821855888559 | erot = 3.20610340688907 | epot = -23.4193095100182 | etot = -17.8749875442436 +583000 ekin = 1.96183085357235 | erot = 2.81826367270291 | epot = -23.5872275727996 | etot = -18.8071330465243 +584000 ekin = 2.00096559581716 | erot = 1.71662185522173 | epot = -23.6766993596687 | etot = -19.9591119086298 +585000 ekin = 2.2650842350347 | erot = 2.08204874292297 | epot = -23.7234738719865 | etot = -19.3763408940288 +586000 ekin = 2.20207640113325 | erot = 1.96861811478536 | epot = -23.6859240119471 | etot = -19.5152294960285 +587000 ekin = 3.67938790357027 | erot = 1.82484412869377 | epot = -23.6634672548209 | etot = -18.1592352225569 +588000 ekin = 3.48089636122829 | erot = 2.30691916064612 | epot = -23.5643712718911 | etot = -17.7765557500167 +589000 ekin = 2.63030533099327 | erot = 2.9702466869305 | epot = -23.3767694123201 | etot = -17.7762173943963 +590000 ekin = 1.60813837628253 | erot = 2.03263132264272 | epot = -23.1946522249358 | etot = -19.5538825260106 +591000 ekin = 1.81653381805571 | erot = 1.75591263591366 | epot = -23.1302877005862 | etot = -19.5578412466168 +592000 ekin = 2.57247249135485 | erot = 2.59257155085885 | epot = -23.1533569826366 | etot = -17.9883129404229 +593000 ekin = 2.43678836763256 | erot = 1.78797409267748 | epot = -23.1035527853187 | etot = -18.8787903250087 +594000 ekin = 2.12126425466624 | erot = 2.16319102375819 | epot = -23.0537965790237 | etot = -18.7693413005993 +595000 ekin = 2.61494655403376 | erot = 2.04015446622256 | epot = -23.041588630948 | etot = -18.3864876106917 +596000 ekin = 2.58385979830463 | erot = 2.125984026295 | epot = -23.0987578414776 | etot = -18.388914016878 +597000 ekin = 3.0356528884646 | erot = 3.13920569000609 | epot = -23.0959220060406 | etot = -16.92106342757 +598000 ekin = 3.448018111133 | erot = 2.86438132305443 | epot = -23.1524961324829 | etot = -16.8400966982954 +599000 ekin = 2.14568317629689 | erot = 3.49762367929462 | epot = -23.1236320419091 | etot = -17.4803251863176 +600000 ekin = 2.20856388598401 | erot = 2.50873295237986 | epot = -23.1229244675557 | etot = -18.4056276291918 +601000 ekin = 2.82305805419651 | erot = 2.82785171484619 | epot = -23.093817009667 | etot = -17.4429072406243 +602000 ekin = 2.33756515640057 | erot = 2.3814563165261 | epot = -23.0592036595801 | etot = -18.3401821866535 +603000 ekin = 1.93163217766375 | erot = 1.95544716703194 | epot = -22.941151667404 | etot = -19.0540723227083 +604000 ekin = 2.67918576808855 | erot = 3.14415640026539 | epot = -22.9119901406973 | etot = -17.0886479723434 +605000 ekin = 2.72017891571417 | erot = 2.06410352610178 | epot = -22.9250944568005 | etot = -18.1408120149845 +606000 ekin = 2.99653903957879 | erot = 2.03201724640129 | epot = -22.8426486789921 | etot = -17.814092393012 +607000 ekin = 2.88290327274547 | erot = 2.37629823895312 | epot = -22.8265624505584 | etot = -17.5673609388598 +608000 ekin = 3.6564890765792 | erot = 2.46096427245297 | epot = -22.7637531347954 | etot = -16.6462997857633 +609000 ekin = 2.67772613172483 | erot = 2.28052588350936 | epot = -22.784032519386 | etot = -17.8257805041518 +610000 ekin = 2.96660977711584 | erot = 2.13935236193287 | epot = -22.7753012812081 | etot = -17.6693391421594 +611000 ekin = 3.84936812341098 | erot = 2.13515328821562 | epot = -22.7555358965927 | etot = -16.7710144849661 +612000 ekin = 2.85991416578252 | erot = 2.46799936153364 | epot = -22.6670923038619 | etot = -17.3391787765458 +613000 ekin = 2.93458428860956 | erot = 2.15612272200133 | epot = -22.6620509726505 | etot = -17.5713439620396 +614000 ekin = 2.80109550846435 | erot = 2.03413630963325 | epot = -22.735929073337 | etot = -17.9006972552394 +615000 ekin = 2.29275572188425 | erot = 2.37295436060996 | epot = -22.8265717932651 | etot = -18.1608617107709 +616000 ekin = 1.78880182339297 | erot = 2.46512387757483 | epot = -22.9181914142038 | etot = -18.664265713236 +617000 ekin = 2.58548247747108 | erot = 2.53734413400793 | epot = -22.9371325341202 | etot = -17.8143059226412 +618000 ekin = 2.31891017470357 | erot = 2.68587322473765 | epot = -22.8737927646705 | etot = -17.8690093652293 +619000 ekin = 1.95260275466613 | erot = 2.00546202293513 | epot = -22.8346556656307 | etot = -18.8765908880295 +620000 ekin = 2.9312355259843 | erot = 2.17154966265513 | epot = -22.9093263040915 | etot = -17.806541115452 +621000 ekin = 2.92251791603671 | erot = 1.69365790820559 | epot = -22.9491849521548 | etot = -18.3330091279125 +622000 ekin = 2.04583493083921 | erot = 2.52347309118728 | epot = -22.8885087146283 | etot = -18.3192006926018 +623000 ekin = 1.97949309574552 | erot = 3.07796024634624 | epot = -22.899088756596 | etot = -17.8416354145043 +624000 ekin = 2.09648243468335 | erot = 2.65430331108241 | epot = -22.914733999871 | etot = -18.1639482541052 +625000 ekin = 2.53179488470072 | erot = 2.36095144458489 | epot = -22.9722766139489 | etot = -18.0795302846633 +626000 ekin = 2.71471201325311 | erot = 2.038002303651 | epot = -23.0006194176227 | etot = -18.2479051007186 +627000 ekin = 2.22374294193216 | erot = 2.35282114621755 | epot = -22.9588355159151 | etot = -18.3822714277654 +628000 ekin = 2.28003968408293 | erot = 2.28859673286464 | epot = -22.8537881524811 | etot = -18.2851517355335 +629000 ekin = 2.52123014813329 | erot = 1.89624895610832 | epot = -22.7908976494591 | etot = -18.3734185452175 +630000 ekin = 3.09551469183927 | erot = 2.51634259883875 | epot = -22.7156574639271 | etot = -17.1038001732491 +631000 ekin = 2.38491234780997 | erot = 3.31746706623938 | epot = -22.7274824388449 | etot = -17.0251030247955 +632000 ekin = 2.58509546960735 | erot = 2.52764681234154 | epot = -22.6801845001954 | etot = -17.5674422182465 +633000 ekin = 2.43450196234921 | erot = 1.9074646477535 | epot = -22.6545806388637 | etot = -18.312614028761 +634000 ekin = 2.22577935817066 | erot = 2.00781737526926 | epot = -22.5723806994747 | etot = -18.3387839660348 +635000 ekin = 2.21833116743445 | erot = 1.98256884900851 | epot = -22.5422908112103 | etot = -18.3413907947673 +636000 ekin = 2.25207449335774 | erot = 2.77890466668274 | epot = -22.5736742647701 | etot = -17.5426951047296 +637000 ekin = 1.94359576469155 | erot = 2.6121109986752 | epot = -22.6035657643129 | etot = -18.0478590009461 +638000 ekin = 2.53947002676468 | erot = 3.14006412371943 | epot = -22.5826147275244 | etot = -16.9030805770402 +639000 ekin = 2.37745481188141 | erot = 2.49540365345358 | epot = -22.5449630195302 | etot = -17.6721045541952 +640000 ekin = 2.08212454926531 | erot = 2.21940536991445 | epot = -22.453303862966 | etot = -18.1517739437862 +641000 ekin = 2.47971433110368 | erot = 3.55852071727848 | epot = -22.3500233136602 | etot = -16.3117882652781 +642000 ekin = 3.38958957156561 | erot = 2.18184701440171 | epot = -22.2389727056174 | etot = -16.6675361196501 +643000 ekin = 2.84881174665207 | erot = 2.413254877821 | epot = -22.1927147648616 | etot = -16.9306481403886 +644000 ekin = 2.9788163296922 | erot = 1.93799042516405 | epot = -22.1764728944767 | etot = -17.2596661396204 +645000 ekin = 4.12550859701587 | erot = 1.89960014649319 | epot = -22.1706973334318 | etot = -16.1455885899228 +646000 ekin = 2.52696357860359 | erot = 2.00637360005821 | epot = -22.1102258356952 | etot = -17.5768886570333 +647000 ekin = 2.55512268942677 | erot = 2.20922204555245 | epot = -22.1538572894812 | etot = -17.389512554502 +648000 ekin = 3.02957533574521 | erot = 2.11325139659861 | epot = -22.1575349215939 | etot = -17.0147081892501 +649000 ekin = 2.58453912449214 | erot = 3.20631221677863 | epot = -22.1339073532352 | etot = -16.3430560119644 +650000 ekin = 3.77204744414227 | erot = 2.43066777037188 | epot = -22.0837500061792 | etot = -15.8810347916651 +651000 ekin = 3.31369677202991 | erot = 2.36221103045568 | epot = -21.9243902112032 | etot = -16.2484824087176 +652000 ekin = 2.49262898649827 | erot = 3.02155153905954 | epot = -21.7253342697997 | etot = -16.2111537442419 +653000 ekin = 2.82559687485827 | erot = 2.53899564631137 | epot = -21.7211782659414 | etot = -16.3565857447718 +654000 ekin = 2.35170683287638 | erot = 2.15925543988734 | epot = -21.9219546077978 | etot = -17.4109923350341 +655000 ekin = 2.2746913368331 | erot = 2.12498780379593 | epot = -21.9020101665877 | etot = -17.5023310259586 +656000 ekin = 2.33856358324454 | erot = 2.10525554685067 | epot = -21.9227166217961 | etot = -17.4788974917008 +657000 ekin = 2.74434355807405 | erot = 2.19006149870653 | epot = -22.1368388094875 | etot = -17.2024337527069 +658000 ekin = 3.04721032533817 | erot = 2.59752520159664 | epot = -22.2936626687419 | etot = -16.6489271418071 +659000 ekin = 2.86427564828999 | erot = 3.42151988715138 | epot = -22.2986314842237 | etot = -16.0128359487823 +660000 ekin = 2.92506899234012 | erot = 1.63381738879488 | epot = -22.3375917964994 | etot = -17.7787054153644 +661000 ekin = 3.22051797741487 | erot = 1.86658559874782 | epot = -22.4692759662967 | etot = -17.382172390134 +662000 ekin = 3.06008561550976 | erot = 2.20194497946945 | epot = -22.5616874184536 | etot = -17.2996568234744 +663000 ekin = 1.91383924631387 | erot = 2.47155788641765 | epot = -22.6270449564058 | etot = -18.2416478236743 +664000 ekin = 1.43175220258741 | erot = 1.36481827202384 | epot = -22.714938601816 | etot = -19.9183681272047 +665000 ekin = 1.55751729325324 | erot = 2.30904543593978 | epot = -22.7903483651339 | etot = -18.9237856359409 +666000 ekin = 2.44554812999981 | erot = 1.7728381640758 | epot = -22.9292683336281 | etot = -18.7108820395525 +667000 ekin = 2.81292959120154 | erot = 2.33182461186713 | epot = -23.1152300896738 | etot = -17.9704758866051 +668000 ekin = 2.71701517852366 | erot = 3.1927510370022 | epot = -23.1898047541379 | etot = -17.2800385386121 +669000 ekin = 3.4211844979108 | erot = 2.4483988547294 | epot = -23.2367567149657 | etot = -17.3671733623255 +670000 ekin = 2.540272537006 | erot = 1.98108817711494 | epot = -23.1773017073799 | etot = -18.655940993259 +671000 ekin = 2.38054183576284 | erot = 2.98341127846263 | epot = -23.1403357669317 | etot = -17.7763826527062 +672000 ekin = 3.02714775234025 | erot = 2.54429912094893 | epot = -23.1240813931427 | etot = -17.5526345198536 +673000 ekin = 3.42342714962536 | erot = 2.36764796314287 | epot = -23.0365834633316 | etot = -17.2455083505634 +674000 ekin = 3.1787369792725 | erot = 2.10003598211897 | epot = -22.9565366380298 | etot = -17.6777636766383 +675000 ekin = 2.35379506516488 | erot = 1.53509045481238 | epot = -22.8504434741329 | etot = -18.9615579541557 +676000 ekin = 2.44888744246419 | erot = 2.24653163842729 | epot = -22.7725645250621 | etot = -18.0771454441706 +677000 ekin = 2.75831894151647 | erot = 1.93124166774781 | epot = -22.8527844251281 | etot = -18.1632238158638 +678000 ekin = 2.86751481243524 | erot = 1.65310315497864 | epot = -22.8648869805436 | etot = -18.3442690131297 +679000 ekin = 2.34238342331609 | erot = 2.69036620616395 | epot = -22.9330609670147 | etot = -17.9003113375347 +680000 ekin = 2.47092831167294 | erot = 2.90821987338148 | epot = -22.9893989293305 | etot = -17.610250744276 +681000 ekin = 1.90592213851373 | erot = 2.57738203916981 | epot = -22.9226803153478 | etot = -18.4393761376642 +682000 ekin = 2.11776015116235 | erot = 2.69956516894844 | epot = -22.8385618600593 | etot = -18.0212365399485 +683000 ekin = 2.36569744411279 | erot = 2.12377742206911 | epot = -22.7248964050232 | etot = -18.2354215388413 +684000 ekin = 2.87481829504096 | erot = 2.65568540935019 | epot = -22.6557781340276 | etot = -17.1252744296364 +685000 ekin = 3.04590812681261 | erot = 2.17384411148381 | epot = -22.6239841629455 | etot = -17.4042319246491 +686000 ekin = 2.45732454887051 | erot = 2.42727693460545 | epot = -22.5554269158738 | etot = -17.6708254323979 +687000 ekin = 2.74615797772517 | erot = 1.80419114366277 | epot = -22.4906419692597 | etot = -17.9402928478718 +688000 ekin = 1.7920739822545 | erot = 2.04572898801195 | epot = -22.4080555397627 | etot = -18.5702525694962 +689000 ekin = 2.87658871003945 | erot = 1.89509928788519 | epot = -22.4597913998897 | etot = -17.6881034019651 +690000 ekin = 2.12362847773645 | erot = 2.42433705189552 | epot = -22.5737079170673 | etot = -18.0257423874353 +691000 ekin = 2.15963929746743 | erot = 2.52975117929537 | epot = -22.5896382204305 | etot = -17.9002477436677 +692000 ekin = 2.88714768351631 | erot = 2.65189982514091 | epot = -22.4796475018852 | etot = -16.9405999932279 +693000 ekin = 2.30934205113368 | erot = 2.51896960835911 | epot = -22.3454093965687 | etot = -17.5170977370759 +694000 ekin = 2.90083400146798 | erot = 2.34214046553658 | epot = -22.2620689836397 | etot = -17.0190945166351 +695000 ekin = 2.9577943585455 | erot = 2.23887088042094 | epot = -22.303054593607 | etot = -17.1063893546405 +696000 ekin = 2.65803880066321 | erot = 2.33953886943022 | epot = -22.3444459486844 | etot = -17.3468682785909 +697000 ekin = 1.89104688866877 | erot = 1.78290264315477 | epot = -22.3519476787994 | etot = -18.6779981469758 +698000 ekin = 2.22763370474282 | erot = 2.82521193129044 | epot = -22.374966668557 | etot = -17.3221210325237 +699000 ekin = 2.35357258316915 | erot = 2.06864522211151 | epot = -22.302995332199 | etot = -17.8807775269184 +700000 ekin = 2.58206368687336 | erot = 2.33093601350411 | epot = -22.2613878464485 | etot = -17.3483881460711 +701000 ekin = 2.99704307093403 | erot = 1.89954183386767 | epot = -22.3232249760621 | etot = -17.4266400712604 +702000 ekin = 2.67512006336489 | erot = 2.64729282748452 | epot = -22.3604874692709 | etot = -17.0380745784215 +703000 ekin = 2.02348242287829 | erot = 2.03755058248806 | epot = -22.4348344343157 | etot = -18.3738014289493 +704000 ekin = 1.59657624705204 | erot = 1.63613322855987 | epot = -22.4674717825454 | etot = -19.2347623069335 +705000 ekin = 2.34019771505867 | erot = 1.91006554831154 | epot = -22.5441024225864 | etot = -18.2938391592161 +706000 ekin = 2.47926998793354 | erot = 3.26999075651193 | epot = -22.5117539612542 | etot = -16.7624932168087 +707000 ekin = 2.38604341038216 | erot = 2.41699636933021 | epot = -22.604009927914 | etot = -17.8009701482016 +708000 ekin = 1.68115636633466 | erot = 2.34002138995268 | epot = -22.7466665621618 | etot = -18.7254888058744 +709000 ekin = 1.80992626994918 | erot = 2.57911114058356 | epot = -23.0637398035031 | etot = -18.6747023929704 +710000 ekin = 2.07665974484992 | erot = 1.83617776589231 | epot = -23.1977961917903 | etot = -19.2849586810481 +711000 ekin = 1.95352231029107 | erot = 2.41454578486037 | epot = -23.2358193849337 | etot = -18.8677512897822 +712000 ekin = 2.13370686414587 | erot = 1.78661700982467 | epot = -23.2645434465923 | etot = -19.3442195726217 +713000 ekin = 2.90695161716251 | erot = 1.55091931636559 | epot = -23.1835772351912 | etot = -18.7257063016631 +714000 ekin = 2.06629801094757 | erot = 1.86611085535956 | epot = -23.2239032864041 | etot = -19.2914944200969 +715000 ekin = 2.52903922778277 | erot = 1.94261958015835 | epot = -23.1658397986034 | etot = -18.6941809906622 +716000 ekin = 3.03498992772823 | erot = 2.21064066235538 | epot = -23.2216970852983 | etot = -17.9760664952147 +717000 ekin = 3.07971375394894 | erot = 2.47094593918087 | epot = -23.3639588975855 | etot = -17.8132992044557 +718000 ekin = 3.49703192209654 | erot = 2.27170758510088 | epot = -23.4199184473786 | etot = -17.6511789401811 +719000 ekin = 4.06139770605771 | erot = 3.10418818480813 | epot = -23.4072026156126 | etot = -16.2416167247468 +720000 ekin = 2.49828440590245 | erot = 1.90909738802778 | epot = -23.262316602338 | etot = -18.8549348084078 +721000 ekin = 2.57931762358207 | erot = 1.98570897250437 | epot = -23.1440560046385 | etot = -18.579029408552 +722000 ekin = 2.01081836336836 | erot = 2.2747167647488 | epot = -23.1040519922181 | etot = -18.8185168641009 +723000 ekin = 2.44097316114449 | erot = 2.07630856281912 | epot = -23.1828606158314 | etot = -18.6655788918678 +724000 ekin = 1.90797367222605 | erot = 1.93592443836535 | epot = -23.2376437089983 | etot = -19.3937455984069 +725000 ekin = 2.19373210936071 | erot = 2.80513028222362 | epot = -23.2888134461385 | etot = -18.2899510545542 +726000 ekin = 2.2764864004673 | erot = 2.54378150467671 | epot = -23.3354979947709 | etot = -18.5152300896268 +727000 ekin = 1.72219216954142 | erot = 2.62563304726333 | epot = -23.3703740298761 | etot = -19.0225488130713 +728000 ekin = 2.25087046178847 | erot = 3.59486012962608 | epot = -23.435416924773 | etot = -17.5896863333584 +729000 ekin = 2.68839033328484 | erot = 1.72111131116557 | epot = -23.4784810452544 | etot = -19.0689794008039 +730000 ekin = 2.5329756962683 | erot = 2.7666773813211 | epot = -23.4899025882625 | etot = -18.1902495106731 +731000 ekin = 2.6760609901083 | erot = 2.04579712240261 | epot = -23.5241973416199 | etot = -18.802339229109 +732000 ekin = 2.77848516459028 | erot = 1.88432734797838 | epot = -23.5774208145874 | etot = -18.9146083020187 +733000 ekin = 2.18895381088671 | erot = 2.63471719118119 | epot = -23.6107634586383 | etot = -18.7870924565704 +734000 ekin = 1.69467760927658 | erot = 2.30338410687055 | epot = -23.5936446347431 | etot = -19.595582918596 +735000 ekin = 2.17749689272956 | erot = 2.71618098412724 | epot = -23.5330417303215 | etot = -18.6393638534647 +736000 ekin = 2.29375858428166 | erot = 1.1740900723812 | epot = -23.503450790287 | etot = -20.0356021336242 +737000 ekin = 2.20827752624533 | erot = 3.11531250945766 | epot = -23.4552023795231 | etot = -18.1316123438201 +738000 ekin = 1.72303720787712 | erot = 2.28747842674015 | epot = -23.3309270174989 | etot = -19.3204113828816 +739000 ekin = 1.39492824364512 | erot = 2.17488386602882 | epot = -23.28548996576 | etot = -19.7156778560861 +740000 ekin = 1.90426261774289 | erot = 2.27825159935278 | epot = -23.2514184467463 | etot = -19.0689042296506 +741000 ekin = 2.02024508457136 | erot = 2.72073546284876 | epot = -23.1876217096301 | etot = -18.4466411622099 +742000 ekin = 1.97487019042321 | erot = 1.87541960482772 | epot = -23.0929182320365 | etot = -19.2426284367856 +743000 ekin = 1.96486238454688 | erot = 2.76982785281128 | epot = -22.9318899502109 | etot = -18.1971997128528 +744000 ekin = 2.04909521933131 | erot = 2.34373814592941 | epot = -22.8510525613065 | etot = -18.4582191960458 +745000 ekin = 1.66771130319646 | erot = 1.87270341329448 | epot = -22.7977076876185 | etot = -19.2572929711276 +746000 ekin = 2.11650515037838 | erot = 2.03542197982564 | epot = -22.7785820280378 | etot = -18.6266548978338 +747000 ekin = 3.07964448387158 | erot = 1.66910106460583 | epot = -22.8037757029139 | etot = -18.0550301544365 +748000 ekin = 3.03811477337698 | erot = 1.85631102018694 | epot = -22.8436239146773 | etot = -17.9491981211133 +749000 ekin = 2.53753852426481 | erot = 2.01199117356573 | epot = -22.860297041716 | etot = -18.3107673438855 +750000 ekin = 2.77210902960465 | erot = 2.32628560304478 | epot = -22.9528220918576 | etot = -17.8544274592082 +751000 ekin = 2.52040431872467 | erot = 2.34903725042469 | epot = -23.0127359055533 | etot = -18.1432943364039 +752000 ekin = 2.46408285580806 | erot = 1.68868786663082 | epot = -22.9901282704654 | etot = -18.8373575480265 +753000 ekin = 2.47364326188914 | erot = 1.55776271670366 | epot = -23.1135680684223 | etot = -19.0821620898295 +754000 ekin = 2.5278916038673 | erot = 2.29496804643662 | epot = -23.2403939606523 | etot = -18.4175343103483 +755000 ekin = 1.52934303772527 | erot = 2.21322404979637 | epot = -23.262110017443 | etot = -19.5195429299214 +756000 ekin = 2.10423967353423 | erot = 2.40303050505255 | epot = -23.1685739957517 | etot = -18.6613038171649 +757000 ekin = 2.92559629660516 | erot = 2.0691293568206 | epot = -23.1502917576405 | etot = -18.1555661042147 +758000 ekin = 2.37300490719645 | erot = 2.51363215153151 | epot = -23.0495756460038 | etot = -18.1629385872758 +759000 ekin = 2.6014595730178 | erot = 2.39657042348208 | epot = -22.9025259489071 | etot = -17.9044959524072 +760000 ekin = 3.23086874355225 | erot = 2.77072134903012 | epot = -22.8089299952235 | etot = -16.8073399026412 +761000 ekin = 3.41475369307092 | erot = 1.70180532416599 | epot = -22.7404708369396 | etot = -17.6239118197027 +762000 ekin = 3.40874473404401 | erot = 2.52147443954634 | epot = -22.5276669204419 | etot = -16.5974477468515 +763000 ekin = 2.64281892112082 | erot = 1.82464895439093 | epot = -22.3890167593186 | etot = -17.9215488838069 +764000 ekin = 2.38098664175603 | erot = 2.71455563654527 | epot = -22.2309521785191 | etot = -17.1354099002178 +765000 ekin = 2.24221473762586 | erot = 1.94826539133556 | epot = -22.122583392123 | etot = -17.9321032631616 +766000 ekin = 2.50645584526003 | erot = 1.96129579948818 | epot = -21.9857907119498 | etot = -17.5180390672015 +767000 ekin = 2.34028568638226 | erot = 2.64592471376141 | epot = -21.9051815399867 | etot = -16.918971139843 +768000 ekin = 1.86752761821211 | erot = 2.06138447840236 | epot = -21.8874171216963 | etot = -17.9585050250818 +769000 ekin = 3.03590459157853 | erot = 2.66440802561784 | epot = -21.8247140853503 | etot = -16.124401468154 +770000 ekin = 2.42567220683552 | erot = 1.97830158892933 | epot = -21.8110526122117 | etot = -17.4070788164468 +771000 ekin = 2.20056711884501 | erot = 2.53255190976195 | epot = -21.7341162461991 | etot = -17.0009972175921 +772000 ekin = 2.75016173617492 | erot = 1.98403019503999 | epot = -21.8164316952287 | etot = -17.0822397640138 +773000 ekin = 2.14723076845117 | erot = 2.41512334908793 | epot = -21.9576017041203 | etot = -17.3952475865812 +774000 ekin = 2.20536023895281 | erot = 1.98379412617599 | epot = -22.043759647449 | etot = -17.8546052823202 +775000 ekin = 2.53158393271132 | erot = 2.8225938280108 | epot = -22.2469056379858 | etot = -16.8927278772637 +776000 ekin = 3.15988726149912 | erot = 2.46223044860468 | epot = -22.4204382258798 | etot = -16.798320515776 +777000 ekin = 1.91542872566335 | erot = 1.75408058586262 | epot = -22.4517075164596 | etot = -18.7821982049336 +778000 ekin = 2.94665474162607 | erot = 2.31805831302194 | epot = -22.4632153304498 | etot = -17.1985022758018 +779000 ekin = 3.10970934270731 | erot = 2.04446179405629 | epot = -22.4851490287702 | etot = -17.3309778920066 +780000 ekin = 2.85215832341045 | erot = 3.13312086675091 | epot = -22.4501531708741 | etot = -16.4648739807127 +781000 ekin = 2.36733074493229 | erot = 3.56399648845806 | epot = -22.4171363625471 | etot = -16.4858091291567 +782000 ekin = 2.32796510372074 | erot = 2.86343667143255 | epot = -22.3438054250098 | etot = -17.1524036498565 +783000 ekin = 1.86439500745061 | erot = 3.05233385447291 | epot = -22.2079509833896 | etot = -17.2912221214661 +784000 ekin = 2.05476588420882 | erot = 2.29789997988689 | epot = -22.1006364427793 | etot = -17.7479705786836 +785000 ekin = 2.03879516593738 | erot = 2.15052527915338 | epot = -22.0056061371158 | etot = -17.816285692025 +786000 ekin = 2.3752160296601 | erot = 2.32156698168742 | epot = -21.9727988200248 | etot = -17.2760158086773 +787000 ekin = 2.76686314352376 | erot = 2.23625261993099 | epot = -21.8969600931556 | etot = -16.8938443297008 +788000 ekin = 2.13318993659091 | erot = 2.25162748275281 | epot = -21.8604178455632 | etot = -17.4756004262194 +789000 ekin = 1.98216852118508 | erot = 1.98058785261598 | epot = -21.844134033761 | etot = -17.8813776599599 +790000 ekin = 1.67847851427146 | erot = 1.42560334440858 | epot = -21.941301490604 | etot = -18.837219631924 +791000 ekin = 2.12689982203095 | erot = 2.53200907087448 | epot = -22.0864434478656 | etot = -17.4275345549602 +792000 ekin = 1.72797703494859 | erot = 2.22448376175168 | epot = -22.1854190028922 | etot = -18.2329582061919 +793000 ekin = 3.18409314211953 | erot = 1.94056710411296 | epot = -22.3760603901177 | etot = -17.2514001438852 +794000 ekin = 2.49071782059139 | erot = 3.01186430180266 | epot = -22.4315505782774 | etot = -16.9289684558833 +795000 ekin = 2.89844296027926 | erot = 3.07659510288655 | epot = -22.5164404652995 | etot = -16.5414024021337 +796000 ekin = 2.32845268798927 | erot = 1.62708270564126 | epot = -22.5660647482766 | etot = -18.6105293546461 +797000 ekin = 2.20766900620157 | erot = 3.6597733457204 | epot = -22.5351911425215 | etot = -16.6677487905995 +798000 ekin = 2.12139450500735 | erot = 2.94419809776829 | epot = -22.53586560158 | etot = -17.4702729988044 +799000 ekin = 2.48452434226029 | erot = 2.7415786036137 | epot = -22.4941328101442 | etot = -17.2680298642702 +800000 ekin = 2.17521613585505 | erot = 2.96480330538541 | epot = -22.3818079549674 | etot = -17.2417885137269 +801000 ekin = 2.54690065539559 | erot = 2.74966931670846 | epot = -22.3008594124712 | etot = -17.0042894403671 +802000 ekin = 3.02823775407486 | erot = 2.8915936784506 | epot = -22.2024149184001 | etot = -16.2825834858746 +803000 ekin = 2.21042161290743 | erot = 2.51594019231142 | epot = -22.1069208353333 | etot = -17.3805590301145 +804000 ekin = 2.91061289296152 | erot = 1.5830418961718 | epot = -22.0839512655924 | etot = -17.5902964764591 +805000 ekin = 2.67762522194669 | erot = 3.06970455948968 | epot = -22.0793101970619 | etot = -16.3319804156255 +806000 ekin = 2.75979804034939 | erot = 2.2176860954027 | epot = -22.0549669082474 | etot = -17.0774827724953 +807000 ekin = 2.11041519443391 | erot = 2.83915265443807 | epot = -22.1073292774231 | etot = -17.1577614285511 +808000 ekin = 1.84392510139081 | erot = 2.29797054411878 | epot = -22.0753255923415 | etot = -17.9334299468319 +809000 ekin = 1.93171652686567 | erot = 1.94021167949754 | epot = -22.0668297694372 | etot = -18.194901563074 +810000 ekin = 1.97774334424761 | erot = 2.6472977913531 | epot = -22.1020544833021 | etot = -17.4770133477014 +811000 ekin = 2.2417092413671 | erot = 1.75505259459069 | epot = -22.1062654329495 | etot = -18.1095035969917 +812000 ekin = 2.49053159164605 | erot = 2.33986799245713 | epot = -22.124141511127 | etot = -17.2937419270238 +813000 ekin = 3.01755249739549 | erot = 2.24004680047387 | epot = -22.1167722656682 | etot = -16.8591729677989 +814000 ekin = 2.86045886242639 | erot = 2.24119269343823 | epot = -22.1084535534804 | etot = -17.0068019976158 +815000 ekin = 2.57503557502156 | erot = 2.76212054641368 | epot = -21.9950519676046 | etot = -16.6578958461694 +816000 ekin = 2.19961906931023 | erot = 2.59194277056134 | epot = -22.0843443380244 | etot = -17.2927824981528 +817000 ekin = 1.75062364873707 | erot = 2.66165019507354 | epot = -22.3739862599355 | etot = -17.9617124161249 +818000 ekin = 2.24809257416679 | erot = 2.59026399650675 | epot = -22.5610524731389 | etot = -17.7226959024654 +819000 ekin = 2.12537334404071 | erot = 2.59618311382673 | epot = -22.5606510650104 | etot = -17.839094607143 +820000 ekin = 1.93414650390356 | erot = 2.29085663493509 | epot = -22.4839314706954 | etot = -18.2589283318568 +821000 ekin = 2.11382182469737 | erot = 2.38685226676536 | epot = -22.47627897247 | etot = -17.9756048810073 +822000 ekin = 2.2613431095799 | erot = 2.12056938305333 | epot = -22.370909843474 | etot = -17.9889973508408 +823000 ekin = 2.31560863750917 | erot = 2.60350436456086 | epot = -22.4988996092736 | etot = -17.5797866072036 +824000 ekin = 1.73697879038959 | erot = 1.5185057021212 | epot = -22.6200401147494 | etot = -19.3645556222386 +825000 ekin = 1.63614248894086 | erot = 1.97731468932685 | epot = -22.6198150724223 | etot = -19.0063578941546 +826000 ekin = 2.00841233147246 | erot = 2.17850248200248 | epot = -22.5466518143203 | etot = -18.3597370008454 +827000 ekin = 2.18457105279113 | erot = 2.44711764942285 | epot = -22.4005870169979 | etot = -17.7688983147839 +828000 ekin = 1.91039404464085 | erot = 2.73449242191012 | epot = -22.3948651441296 | etot = -17.7499786775786 +829000 ekin = 2.07228257188588 | erot = 2.97134747466499 | epot = -22.4347910090961 | etot = -17.3911609625452 +830000 ekin = 1.99293621346915 | erot = 2.15765133255911 | epot = -22.4843800017124 | etot = -18.3337924556842 +831000 ekin = 2.33241187954984 | erot = 2.37634533076884 | epot = -22.5757045912718 | etot = -17.8669473809531 +832000 ekin = 2.02856108052035 | erot = 1.94729581180225 | epot = -22.6670251626246 | etot = -18.691168270302 +833000 ekin = 2.28623411522758 | erot = 2.15108044390973 | epot = -22.7566850878713 | etot = -18.319370528734 +834000 ekin = 2.12105013529711 | erot = 1.5116778668129 | epot = -22.7735851481702 | etot = -19.1408571460602 +835000 ekin = 2.88531776933573 | erot = 2.74027641398136 | epot = -22.8585330533172 | etot = -17.2329388700001 +836000 ekin = 3.32070208623905 | erot = 2.42231134749978 | epot = -22.8959107751695 | etot = -17.1528973414306 +837000 ekin = 2.74149226799164 | erot = 2.32127198719276 | epot = -22.8906677110002 | etot = -17.8279034558158 +838000 ekin = 3.13302338440878 | erot = 3.19829232559053 | epot = -22.9166668544453 | etot = -16.585351144446 +839000 ekin = 2.73522885875602 | erot = 2.61100294075548 | epot = -22.8499426413711 | etot = -17.5037108418596 +840000 ekin = 2.97139629828009 | erot = 1.43157972743722 | epot = -22.7763904271576 | etot = -18.3734144014403 +841000 ekin = 2.9571795545775 | erot = 2.67280681737836 | epot = -22.7408850128302 | etot = -17.1108986408743 +842000 ekin = 2.17222575948606 | erot = 2.30478646820068 | epot = -22.7382440804492 | etot = -18.2612318527624 +843000 ekin = 2.83292824269634 | erot = 2.04165126380544 | epot = -22.7426687858571 | etot = -17.8680892793554 +844000 ekin = 2.95938970875204 | erot = 1.50198210425589 | epot = -22.783719790782 | etot = -18.3223479777741 +845000 ekin = 3.16076837184522 | erot = 2.28216144351779 | epot = -22.7913524647186 | etot = -17.3484226493555 +846000 ekin = 3.3398977708405 | erot = 2.53602189023877 | epot = -22.7943227793905 | etot = -16.9184031183113 +847000 ekin = 2.14145435242079 | erot = 2.75036267291773 | epot = -22.7255800042885 | etot = -17.83376297895 +848000 ekin = 2.48912550447967 | erot = 2.81875176956459 | epot = -22.5834297802211 | etot = -17.2755525061768 +849000 ekin = 1.98023552181666 | erot = 2.5692134285068 | epot = -22.4587431120173 | etot = -17.9092941616939 +850000 ekin = 2.0475383789703 | erot = 1.80627608629883 | epot = -22.442868440532 | etot = -18.5890539752628 +851000 ekin = 2.09704360250612 | erot = 1.85768640504848 | epot = -22.4344168330881 | etot = -18.4796868255335 +852000 ekin = 1.70813487206096 | erot = 1.42387059402563 | epot = -22.3764553852037 | etot = -19.2444499191171 +853000 ekin = 2.00140314580349 | erot = 3.04689599134399 | epot = -22.4103147041128 | etot = -17.3620155669653 +854000 ekin = 3.02149896921022 | erot = 2.22990677084323 | epot = -22.4965128093929 | etot = -17.2451070693394 +855000 ekin = 2.19607047478225 | erot = 2.83672007906388 | epot = -22.5083573431917 | etot = -17.4755667893456 +856000 ekin = 2.44947669543341 | erot = 1.52884872890501 | epot = -22.4898047833717 | etot = -18.5114793590332 +857000 ekin = 2.53345481305323 | erot = 2.80399799726174 | epot = -22.39864736443 | etot = -17.061194554115 +858000 ekin = 2.20266598505728 | erot = 2.82477658278041 | epot = -22.322749893257 | etot = -17.2953073254193 +859000 ekin = 2.30655855498922 | erot = 2.31428920065484 | epot = -22.299458676259 | etot = -17.6786109206149 +860000 ekin = 1.99697183524065 | erot = 1.95028062775308 | epot = -22.3156691349687 | etot = -18.3684166719749 +861000 ekin = 2.69687116915107 | erot = 2.24433771449493 | epot = -22.3086232893581 | etot = -17.3674144057121 +862000 ekin = 2.86022987586877 | erot = 2.41684736135787 | epot = -22.2874375572893 | etot = -17.0103603200626 +863000 ekin = 2.60871204568914 | erot = 3.3557366458487 | epot = -22.2313024399491 | etot = -16.2668537484113 +864000 ekin = 2.90978326967391 | erot = 2.29745178043259 | epot = -22.1985713670251 | etot = -16.9913363169186 +865000 ekin = 1.92892881804686 | erot = 2.15731715168145 | epot = -22.0984656787339 | etot = -18.0122197090056 +866000 ekin = 1.96990768776308 | erot = 1.64764578107637 | epot = -21.9980087709689 | etot = -18.3804553021294 +867000 ekin = 1.75218832670564 | erot = 3.37220276943672 | epot = -21.9060579112704 | etot = -16.781666815128 +868000 ekin = 1.82818126605702 | erot = 2.79449094294287 | epot = -21.9401796601767 | etot = -17.3175074511768 +869000 ekin = 2.38095838431442 | erot = 2.38587739965205 | epot = -22.0329803939138 | etot = -17.2661446099473 +870000 ekin = 1.91334960398162 | erot = 3.22058637313173 | epot = -22.0372634175766 | etot = -16.9033274404632 +871000 ekin = 3.11762256076551 | erot = 2.95337521110721 | epot = -21.9585521021423 | etot = -15.8875543302696 +872000 ekin = 2.97995457097216 | erot = 1.38589789821627 | epot = -21.8388140547637 | etot = -17.4729615855753 +873000 ekin = 2.75063242740213 | erot = 2.24384409185972 | epot = -21.7621446383558 | etot = -16.767668119094 +874000 ekin = 2.42548187796032 | erot = 2.11160399589529 | epot = -21.6726796153781 | etot = -17.1355937415225 +875000 ekin = 2.99029080863986 | erot = 2.74119845235593 | epot = -21.6681717382462 | etot = -15.9366824772504 +876000 ekin = 2.13275197859305 | erot = 2.233203194222 | epot = -21.6687594523732 | etot = -17.3028042795581 +877000 ekin = 1.83070162423874 | erot = 1.6010526911626 | epot = -21.6263742280813 | etot = -18.19461991268 +878000 ekin = 2.01997494895548 | erot = 2.72070409004295 | epot = -21.632105565574 | etot = -16.8914265265756 +879000 ekin = 1.43444833027133 | erot = 2.17422677437648 | epot = -21.5501867528963 | etot = -17.9415116482485 +880000 ekin = 2.09181862571921 | erot = 2.57771231025419 | epot = -21.4847603093162 | etot = -16.8152293733428 +881000 ekin = 1.54081572899847 | erot = 1.98591498012594 | epot = -21.5197472943257 | etot = -17.9930165852013 +882000 ekin = 2.2061903789583 | erot = 2.64808794630213 | epot = -21.6149395754995 | etot = -16.760661250239 +883000 ekin = 2.22398786469444 | erot = 2.23146516226547 | epot = -21.6814015671086 | etot = -17.2259485401487 +884000 ekin = 2.78668802039765 | erot = 2.10130089852047 | epot = -21.7272273228039 | etot = -16.8392384038858 +885000 ekin = 1.92361997638943 | erot = 1.77572378933155 | epot = -21.7696517903878 | etot = -18.0703080246668 +886000 ekin = 1.99836032534883 | erot = 3.11596676947403 | epot = -21.7879382713548 | etot = -16.673611176532 +887000 ekin = 1.98879909318866 | erot = 2.81589132946027 | epot = -21.7923091863043 | etot = -16.9876187636554 +888000 ekin = 1.92041141945741 | erot = 2.3252911526479 | epot = -21.8607011941373 | etot = -17.614998622032 +889000 ekin = 1.8806357075667 | erot = 2.46119753007268 | epot = -21.9506056361693 | etot = -17.6087723985299 +890000 ekin = 1.86005551534237 | erot = 2.25705356539098 | epot = -22.0523870894554 | etot = -17.9352780087221 +891000 ekin = 2.60384568426052 | erot = 2.35330960558484 | epot = -22.1900620535717 | etot = -17.2329067637263 +892000 ekin = 2.68682478776143 | erot = 2.69192226449536 | epot = -22.2913421142228 | etot = -16.9125950619661 +893000 ekin = 2.17360632388892 | erot = 2.98553431183659 | epot = -22.2913111245685 | etot = -17.132170488843 +894000 ekin = 2.52600330506545 | erot = 2.45861329518365 | epot = -22.2813523194117 | etot = -17.2967357191626 +895000 ekin = 2.51964265942842 | erot = 2.458508768977 | epot = -22.3090530666537 | etot = -17.3309016382482 +896000 ekin = 1.83970949418621 | erot = 2.7876698428861 | epot = -22.2816769795447 | etot = -17.6542976424724 +897000 ekin = 2.36177466310812 | erot = 2.0208895092276 | epot = -22.2244555724411 | etot = -17.8417914001054 +898000 ekin = 2.11475930620727 | erot = 1.90142689771282 | epot = -22.1399515435435 | etot = -18.1237653396234 +899000 ekin = 2.62628238826603 | erot = 2.33607509693707 | epot = -22.040854543184 | etot = -17.0784970579809 +900000 ekin = 2.1134311489616 | erot = 2.28923041198217 | epot = -22.042922147544 | etot = -17.6402605866003 +901000 ekin = 1.9156742929676 | erot = 1.81441237665855 | epot = -22.0776682049659 | etot = -18.3475815353397 +902000 ekin = 2.56902181313363 | erot = 2.49856756454338 | epot = -22.0065137105888 | etot = -16.9389243329118 +903000 ekin = 1.85774740371253 | erot = 2.17490444163848 | epot = -21.9440961512363 | etot = -17.9114443058853 +904000 ekin = 1.86493397406833 | erot = 2.32873873815716 | epot = -21.8931358584844 | etot = -17.6994631462589 +905000 ekin = 2.31979070947169 | erot = 2.14360558294755 | epot = -21.824385320242 | etot = -17.3609890278228 +906000 ekin = 2.49844805906095 | erot = 2.24842339845928 | epot = -21.8343155675942 | etot = -17.087444110074 +907000 ekin = 4.2050069684007 | erot = 2.50213003512293 | epot = -21.926981437738 | etot = -15.2198444342144 +908000 ekin = 3.27384188266606 | erot = 2.113986364986 | epot = -22.0851390841283 | etot = -16.6973108364762 +909000 ekin = 2.63126156907554 | erot = 1.92589592890071 | epot = -22.2067426627273 | etot = -17.649585164751 +910000 ekin = 2.59247391196527 | erot = 2.91530974700789 | epot = -22.3083595488238 | etot = -16.8005758898507 +911000 ekin = 2.58542931349158 | erot = 4.35273181589072 | epot = -22.3703725466068 | etot = -15.4322114172245 +912000 ekin = 3.05788115941417 | erot = 3.70629270837706 | epot = -22.3924331468687 | etot = -15.6282592790774 +913000 ekin = 2.82179099955174 | erot = 2.17271040546975 | epot = -22.3592523787226 | etot = -17.3647509737011 +914000 ekin = 2.15502438011904 | erot = 1.21668409626845 | epot = -22.2678100512732 | etot = -18.8961015748857 +915000 ekin = 1.59606663662058 | erot = 2.96270026674799 | epot = -22.1740650061606 | etot = -17.615298102792 +916000 ekin = 2.59113116114426 | erot = 3.74925276784446 | epot = -22.2376802645764 | etot = -15.8972963355877 +917000 ekin = 3.04931771481537 | erot = 2.87183708314021 | epot = -22.2631766381559 | etot = -16.3420218402004 +918000 ekin = 2.92188996322642 | erot = 2.63336986904281 | epot = -22.2586011448583 | etot = -16.7033413125891 +919000 ekin = 3.21078589975638 | erot = 2.75946192406924 | epot = -22.2354679015341 | etot = -16.2652200777085 +920000 ekin = 2.28588196467068 | erot = 2.37332214874002 | epot = -22.2033589800159 | etot = -17.5441548666052 +921000 ekin = 2.38962275209347 | erot = 2.43661594631483 | epot = -22.1850468087942 | etot = -17.3588081103859 +922000 ekin = 2.30444121290069 | erot = 2.41446680487179 | epot = -22.1364838134968 | etot = -17.4175757957243 +923000 ekin = 2.49328668364371 | erot = 2.66692739305866 | epot = -22.1214525565084 | etot = -16.961238479806 +924000 ekin = 1.53749552443357 | erot = 2.96826070169594 | epot = -22.0894201538095 | etot = -17.58366392768 +925000 ekin = 1.85840160112661 | erot = 1.96300614534087 | epot = -22.0261080308484 | etot = -18.2047002843809 +926000 ekin = 1.36444139420093 | erot = 2.1171911056521 | epot = -22.0105169062661 | etot = -18.5288844064131 +927000 ekin = 2.55080456695379 | erot = 2.08771192494034 | epot = -22.0296775970306 | etot = -17.3911611051365 +928000 ekin = 2.08687563155734 | erot = 2.73937352627042 | epot = -22.0655254209395 | etot = -17.2392762631117 +929000 ekin = 1.85842465674464 | erot = 1.85229951899858 | epot = -22.161879510768 | etot = -18.4511553350248 +930000 ekin = 1.98312460976539 | erot = 2.1107410982594 | epot = -22.14836282055 | etot = -18.0544971125252 +931000 ekin = 2.44403538776918 | erot = 1.87099700190232 | epot = -22.0455015122594 | etot = -17.7304691225879 +932000 ekin = 2.7450847259232 | erot = 2.34428750425033 | epot = -22.0610452671158 | etot = -16.9716730369423 +933000 ekin = 3.03611053551161 | erot = 2.51768120120295 | epot = -21.9625013660046 | etot = -16.4087096292901 +934000 ekin = 2.94656859108538 | erot = 2.48807299457996 | epot = -21.861427363924 | etot = -16.4267857782587 +935000 ekin = 2.79276097099932 | erot = 2.14683659927043 | epot = -21.8273092000012 | etot = -16.8877116297315 +936000 ekin = 2.97178317336133 | erot = 2.07585468409967 | epot = -21.8285263420326 | etot = -16.7808884845716 +937000 ekin = 3.04678623330025 | erot = 2.3469475727902 | epot = -21.7540111620946 | etot = -16.3602773560041 +938000 ekin = 2.98751343731959 | erot = 2.36094469095133 | epot = -21.6698990656412 | etot = -16.3214409373703 +939000 ekin = 2.58148991378899 | erot = 2.28540307033942 | epot = -21.641624391377 | etot = -16.7747314072486 +940000 ekin = 2.64449140269543 | erot = 2.76444805229845 | epot = -21.5519193090555 | etot = -16.1429798540616 +941000 ekin = 2.27119597888968 | erot = 2.6047011226429 | epot = -21.4613787017959 | etot = -16.5854816002633 +942000 ekin = 1.87372343217533 | erot = 2.80846718394805 | epot = -21.3627475231486 | etot = -16.6805569070252 +943000 ekin = 2.47144243861285 | erot = 2.33780411758964 | epot = -21.3635196463293 | etot = -16.5542730901269 +944000 ekin = 2.13395812695593 | erot = 1.92152946754219 | epot = -21.3250397924826 | etot = -17.2695521979844 +945000 ekin = 2.55906013749132 | erot = 2.2064112111687 | epot = -21.3688330068161 | etot = -16.6033616581561 +946000 ekin = 2.36057360323902 | erot = 2.87561909021941 | epot = -21.3642087487724 | etot = -16.128016055314 +947000 ekin = 2.0664007802554 | erot = 1.8712733843037 | epot = -21.3615863875836 | etot = -17.4239122230245 +948000 ekin = 1.84827298766581 | erot = 1.37746869479931 | epot = -21.4042186851624 | etot = -18.1784770026972 +949000 ekin = 1.76268582715986 | erot = 2.31704980534492 | epot = -21.4240851264671 | etot = -17.3443494939624 +950000 ekin = 1.71596526195605 | erot = 2.24238613701562 | epot = -21.4136184248624 | etot = -17.4552670258908 +951000 ekin = 1.97739431794919 | erot = 2.32356723589743 | epot = -21.4746626443703 | etot = -17.1737010905236 +952000 ekin = 2.93969915889367 | erot = 2.72641565709973 | epot = -21.5183559681327 | etot = -15.8522411521393 +953000 ekin = 2.94576770934606 | erot = 2.38856498634115 | epot = -21.5141407104899 | etot = -16.1798080148027 +954000 ekin = 3.09120782928501 | erot = 1.98547863545544 | epot = -21.4220978424351 | etot = -16.3454113776947 +955000 ekin = 3.57635302907509 | erot = 2.07344226252239 | epot = -21.3055276294275 | etot = -15.65573233783 +956000 ekin = 2.96199697760255 | erot = 3.68176573533001 | epot = -21.1569123839441 | etot = -14.5131496710115 +957000 ekin = 2.99343140156395 | erot = 2.6641673976979 | epot = -20.9767503534011 | etot = -15.3191515541393 +958000 ekin = 2.66519710291016 | erot = 2.94296730915348 | epot = -20.778322783175 | etot = -15.1701583711114 +959000 ekin = 1.92859078964251 | erot = 2.44737003089627 | epot = -20.7022563699757 | etot = -16.3262955494369 +960000 ekin = 1.49451727360012 | erot = 3.13583888779427 | epot = -20.7118848436939 | etot = -16.0815286822995 +961000 ekin = 1.95030797402212 | erot = 2.08601754519332 | epot = -20.7116280307748 | etot = -16.6753025115593 +962000 ekin = 2.02519672504697 | erot = 1.8993614904036 | epot = -20.7772856698007 | etot = -16.8527274543501 +963000 ekin = 1.81866098250674 | erot = 2.47413067985077 | epot = -20.8446590259958 | etot = -16.5518673636383 +964000 ekin = 2.82274927013719 | erot = 2.43518028535965 | epot = -20.9038261011269 | etot = -15.64589654563 +965000 ekin = 2.55107687208175 | erot = 2.29878175210651 | epot = -20.9717669792334 | etot = -16.1219083550452 +966000 ekin = 2.1200913755337 | erot = 2.2846988725502 | epot = -21.0606259488472 | etot = -16.6558357007633 +967000 ekin = 1.58229605946639 | erot = 3.55757301639252 | epot = -21.1224849810159 | etot = -15.982615905157 +968000 ekin = 1.95011274740584 | erot = 2.3752003899703 | epot = -21.1147445818894 | etot = -16.7894314445132 +969000 ekin = 2.19259033480515 | erot = 2.45911844664679 | epot = -21.0841141670188 | etot = -16.4324053855669 +970000 ekin = 1.87048608890169 | erot = 2.95646346755995 | epot = -21.0142741201673 | etot = -16.1873245637056 +971000 ekin = 1.950153162929 | erot = 3.0717285905854 | epot = -20.9854323440231 | etot = -15.9635505905087 +972000 ekin = 1.93197938125398 | erot = 2.56232300543577 | epot = -20.9700672251306 | etot = -16.4757648384409 +973000 ekin = 2.21536036218028 | erot = 2.92680374210101 | epot = -20.9735070987956 | etot = -15.8313429945143 +974000 ekin = 2.53787477442507 | erot = 2.68950390909793 | epot = -20.9249780227203 | etot = -15.6975993391973 +975000 ekin = 3.3832404833891 | erot = 2.33888514036507 | epot = -20.8975294326534 | etot = -15.1754038088992 +976000 ekin = 2.84644457799265 | erot = 3.11578234174529 | epot = -20.8919958508098 | etot = -14.9297689310719 +977000 ekin = 2.71728271399263 | erot = 2.50842582300821 | epot = -20.8689034899506 | etot = -15.6431949529497 +978000 ekin = 1.79447160570111 | erot = 2.0736426807417 | epot = -20.8420102217514 | etot = -16.9738959353086 +979000 ekin = 1.87121723303036 | erot = 2.21930404593537 | epot = -20.7748213462523 | etot = -16.6843000672865 +980000 ekin = 1.92329753072694 | erot = 1.58075512357095 | epot = -20.7449893755876 | etot = -17.2409367212897 +981000 ekin = 1.54378956643562 | erot = 2.05667260838343 | epot = -20.8055475552994 | etot = -17.2050853804803 +982000 ekin = 1.84106018589786 | erot = 1.96434982363189 | epot = -20.9115392638984 | etot = -17.1061292543687 +983000 ekin = 2.72419781781661 | erot = 1.79041192395563 | epot = -20.935370561762 | etot = -16.4207608199898 +984000 ekin = 3.62592878226169 | erot = 2.63360520982709 | epot = -21.0391300854773 | etot = -14.7795960933885 +985000 ekin = 2.94852029277516 | erot = 2.17123324675229 | epot = -21.210668025134 | etot = -16.0909144856065 +986000 ekin = 2.87308205004233 | erot = 2.17802315487852 | epot = -21.3375937115616 | etot = -16.2864885066408 +987000 ekin = 3.37012638403781 | erot = 2.51985184465596 | epot = -21.4043627880157 | etot = -15.514384559322 +988000 ekin = 3.46870329025365 | erot = 3.24288958557111 | epot = -21.4574256625201 | etot = -14.7458327866953 +989000 ekin = 2.84167714920458 | erot = 2.20794124486355 | epot = -21.6063889534189 | etot = -16.5567705593508 +990000 ekin = 2.79616762915596 | erot = 1.83962543905575 | epot = -21.6049428673847 | etot = -16.969149799173 +991000 ekin = 3.12376374867622 | erot = 3.19217780569165 | epot = -21.5124272449002 | etot = -15.1964856905324 +992000 ekin = 3.28266282243327 | erot = 2.63435990952508 | epot = -21.3973672594977 | etot = -15.4803445275393 +993000 ekin = 3.03845590773447 | erot = 2.22451011589011 | epot = -21.3214832241627 | etot = -16.0585172005382 +994000 ekin = 3.17417330085466 | erot = 2.79358287085479 | epot = -21.2400043434466 | etot = -15.2722481717371 +995000 ekin = 3.20646780888655 | erot = 1.72565517852613 | epot = -21.1372155372729 | etot = -16.2050925498602 +996000 ekin = 3.05109485375234 | erot = 3.18000631651671 | epot = -21.0952864235923 | etot = -14.8641852533233 +997000 ekin = 2.95625677593347 | erot = 3.15916554858247 | epot = -21.058148007987 | etot = -14.942725683471 +998000 ekin = 3.06605914614908 | erot = 1.97682176881012 | epot = -20.9834240684974 | etot = -15.9405431535382 +999000 ekin = 2.08919327368179 | erot = 2.76364485800616 | epot = -20.9705413117635 | etot = -16.1177031800756 +1000000 ekin = 2.11761701334905 | erot = 2.1409630347026 | epot = -20.9096627221725 | etot = -16.6510826741208 + 1000000 0.094116312 -1.3659956 0.059141691 -1.1745029 -3.0654283e-05 +Loop time of 43.6978 on 1 procs for 1000000 steps with 16 atoms + +Performance: 19772.150 tau/day, 22884.433 timesteps/s +98.6% CPU use with 1 MPI tasks x no OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 32.769 | 32.769 | 32.769 | 0.0 | 74.99 +Bond | 0.93071 | 0.93071 | 0.93071 | 0.0 | 2.13 +Neigh | 0 | 0 | 0 | 0.0 | 0.00 +Comm | 0.19584 | 0.19584 | 0.19584 | 0.0 | 0.45 +Output | 1e-05 | 1e-05 | 1e-05 | 0.0 | 0.00 +Modify | 9.4507 | 9.4507 | 9.4507 | 0.0 | 21.63 +Other | | 0.3515 | | | 0.80 + +Nlocal: 16 ave 16 max 16 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 0 ave 0 max 0 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 116 ave 116 max 116 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 116 +Ave neighs/atom = 7.25 +Ave special neighs/atom = 3.75 +Neighbor list builds = 0 +Dangerous builds = 0 + +#write_restart config.${number}.* +Total wall time: 0:00:43 diff --git a/examples/USER/cgdna/examples/oxDNA2/duplex2/log.18Jun19.duplex2.g++.4 b/examples/USER/cgdna/examples/oxDNA2/duplex2/log.18Jun19.duplex2.g++.4 new file mode 100644 index 0000000000..8989bce5ef --- /dev/null +++ b/examples/USER/cgdna/examples/oxDNA2/duplex2/log.18Jun19.duplex2.g++.4 @@ -0,0 +1,1173 @@ +LAMMPS (18 Jun 2019) +variable number equal 2 +variable ofreq equal 1000 +variable efreq equal 1000 +variable T equal 0.1 +units lj + +dimension 3 + +newton off + +boundary p p p + +atom_style hybrid bond ellipsoid +atom_modify sort 0 1.0 + +# Pair interactions require lists of neighbours to be calculated +neighbor 1.0 bin +neigh_modify every 1 delay 0 check yes + +read_data data.duplex2 + orthogonal box = (-20 -20 -20) to (20 20 20) + 1 by 2 by 2 MPI processor grid + reading atoms ... + 16 atoms + reading velocities ... + 16 velocities + 16 ellipsoids + scanning bonds ... + 2 = max bonds/atom + reading bonds ... + 13 bonds + 2 = max # of 1-2 neighbors + 2 = max # of 1-3 neighbors + 4 = max # of 1-4 neighbors + 6 = max # of special neighbors + special bonds CPU = 0.000162 secs + read_data CPU = 0.002971 secs + +set atom * mass 3.1575 + 16 settings made for mass + +group all type 1 4 +16 atoms in group all + +# oxDNA bond interactions - FENE backbone +bond_style oxdna2/fene +bond_coeff * 2.0 0.25 0.7564 + +# oxDNA pair interactions +pair_style hybrid/overlay oxdna2/excv oxdna2/stk oxdna2/hbond oxdna2/xstk oxdna2/coaxstk oxdna2/dh +pair_coeff * * oxdna2/excv 2.0 0.7 0.675 2.0 0.515 0.5 2.0 0.33 0.32 +pair_coeff * * oxdna2/stk seqav ${T} 1.3523 2.6717 6.0 0.4 0.9 0.32 0.6 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2.0 0.65 2.0 0.65 +pair_coeff * * oxdna2/stk seqav 0.1 1.3523 2.6717 6.0 0.4 0.9 0.32 0.6 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2.0 0.65 2.0 0.65 +pair_coeff * * oxdna2/hbond seqav 0.0 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45 +pair_coeff 1 4 oxdna2/hbond seqav 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45 +pair_coeff 2 3 oxdna2/hbond seqav 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45 +pair_coeff * * oxdna2/xstk 47.5 0.575 0.675 0.495 0.655 2.25 0.791592653589793 0.58 1.7 1.0 0.68 1.7 1.0 0.68 1.5 0 0.65 1.7 0.875 0.68 1.7 0.875 0.68 +pair_coeff * * oxdna2/coaxstk 58.5 0.4 0.6 0.22 0.58 2.0 2.891592653589793 0.65 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 40.0 3.116592653589793 +pair_coeff * * oxdna2/dh ${T} 1.0 0.815 +pair_coeff * * oxdna2/dh 0.1 1.0 0.815 + +# NVE ensemble +#fix 1 all nve/dot +fix 1 all nve/dotc/langevin ${T} ${T} 0.03 457145 angmom 10 +fix 1 all nve/dotc/langevin 0.1 ${T} 0.03 457145 angmom 10 +fix 1 all nve/dotc/langevin 0.1 0.1 0.03 457145 angmom 10 +#fix 1 all nve/asphere +#fix 2 all langevin ${T} ${T} 0.03 457145 angmom 10 + +timestep 1e-5 + +#comm_style tiled +#fix 3 all balance 10000 1.1 rcb + +#compute mol all chunk/atom molecule +#compute mychunk all vcm/chunk mol +#fix 4 all ave/time 10000 1 10000 c_mychunk[1] c_mychunk[2] c_mychunk[3] file vcm.txt mode vector + +#dump pos all xyz ${ofreq} traj.${number}.xyz + +#compute quat all property/atom quatw quati quatj quatk +#dump quat all custom ${ofreq} quat.${number}.txt id c_quat[1] c_quat[2] c_quat[3] c_quat[4] +#dump_modify quat sort id +#dump_modify quat format line "%d %13.6le %13.6le %13.6le %13.6le" + +compute erot all erotate/asphere +compute ekin all ke +compute epot all pe +variable erot equal c_erot +variable ekin equal c_ekin +variable epot equal c_epot +variable etot equal c_erot+c_ekin+c_epot +fix 5 all print ${efreq} "$(step) ekin = ${ekin} | erot = ${erot} | epot = ${epot} | etot = ${etot}" screen yes +fix 5 all print 1000 "$(step) ekin = ${ekin} | erot = ${erot} | epot = ${epot} | etot = ${etot}" screen yes + +#dump out all custom ${ofreq} out.${number}.txt id x y z vx vy vz fx fy fz tqx tqy tqz +#dump_modify out sort id +#dump_modify out format line "%d %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le" + +run 1000000 +Neighbor list info ... + update every 1 steps, delay 0 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 2.6274 + ghost atom cutoff = 2.6274 + binsize = 1.3137, bins = 31 31 31 + 6 neighbor lists, perpetual/occasional/extra = 6 0 0 + (1) pair oxdna2/excv, perpetual + attributes: half, newton off + pair build: half/bin/newtoff + stencil: half/bin/3d/newtoff + bin: standard + (2) pair oxdna2/stk, perpetual, copy from (1) + attributes: half, newton off + pair build: copy + stencil: none + bin: none + (3) pair oxdna2/hbond, perpetual, copy from (1) + attributes: half, newton off + pair build: copy + stencil: none + bin: none + (4) pair oxdna2/xstk, perpetual, copy from (1) + attributes: half, newton off + pair build: copy + stencil: none + bin: none + (5) pair oxdna2/coaxstk, perpetual, copy from (1) + attributes: half, newton off + pair build: copy + stencil: none + bin: none + (6) pair oxdna2/dh, perpetual, copy from (1) + attributes: half, newton off + pair build: copy + stencil: none + bin: none +Per MPI rank memory allocation (min/avg/max) = 7.777 | 7.959 | 8.142 Mbytes +Step Temp E_pair E_mol TotEng Press + 0 0 -1.5358787 0.0096742456 -1.5262045 1.0127369e-05 +1000 ekin = 1.34554291364716 | erot = 2.30525041754444 | epot = -24.3924150888896 | etot = -20.741621757698 +2000 ekin = 2.15972469811184 | erot = 2.1628675965276 | epot = -24.3548203354875 | etot = -20.0322280408481 +3000 ekin = 3.26433550542939 | erot = 2.76107866472087 | epot = -24.2947953202752 | etot = -18.269381150125 +4000 ekin = 1.9203212531997 | erot = 2.133394384253 | epot = -24.234098584123 | etot = -20.1803829466703 +5000 ekin = 1.35481075814721 | erot = 2.00854026688447 | epot = -24.1768963201279 | etot = -20.8135452950963 +6000 ekin = 2.18974627635306 | erot = 1.73271671162436 | epot = -24.1096616118305 | etot = -20.1871986238531 +7000 ekin = 2.65472853187395 | erot = 1.73258720631297 | epot = -24.0561118130561 | etot = -19.6687960748691 +8000 ekin = 2.51192327964357 | erot = 2.34132844779952 | epot = -23.9708695663488 | etot = -19.1176178389058 +9000 ekin = 2.24554900802464 | erot = 2.0522939078286 | epot = -23.874757758319 | etot = -19.5769148424658 +10000 ekin = 2.36227360512089 | erot = 1.80185994066737 | epot = -23.7793375260418 | etot = -19.6152039802535 +11000 ekin = 2.03264234985168 | erot = 1.68707706801736 | epot = -23.7396221351636 | etot = -20.0199027172945 +12000 ekin = 2.66329111303325 | erot = 2.49804687909781 | epot = -23.7366995564469 | etot = -18.5753615643158 +13000 ekin = 1.89677055811531 | erot = 2.34624821263612 | epot = -23.6591067615901 | etot = -19.4160879908387 +14000 ekin = 1.91279445145792 | erot = 2.13129118502405 | epot = -23.6468743458148 | etot = -19.6027887093328 +15000 ekin = 2.41876331112169 | erot = 2.07362128417238 | epot = -23.5767792498568 | etot = -19.0843946545628 +16000 ekin = 2.76615310647131 | erot = 1.19495009524763 | epot = -23.4862363509196 | etot = -19.5251331492006 +17000 ekin = 2.45632569069911 | erot = 2.37627186077148 | epot = -23.500787861849 | etot = -18.6681903103784 +18000 ekin = 2.18348858414473 | erot = 2.46933014500077 | epot = -23.5223047738331 | etot = -18.8694860446876 +19000 ekin = 2.2074746303434 | erot = 2.45349372324724 | epot = -23.4618353655003 | etot = -18.8008670119096 +20000 ekin = 2.06964129991908 | erot = 1.80832666230414 | epot = -23.4930879797962 | etot = -19.615120017573 +21000 ekin = 2.26572194434983 | erot = 2.76680470094409 | epot = -23.5023070260553 | etot = -18.4697803807614 +22000 ekin = 2.69295306575102 | erot = 1.86984875574017 | epot = -23.4463493063166 | etot = -18.8835474848254 +23000 ekin = 1.99930153068661 | erot = 2.27735339437466 | epot = -23.3493214662276 | etot = -19.0726665411663 +24000 ekin = 2.20679650752062 | erot = 2.98147599881873 | epot = -23.273517698415 | etot = -18.0852451920757 +25000 ekin = 2.28085541692287 | erot = 2.99165466281124 | epot = -23.2072100929465 | etot = -17.9347000132124 +26000 ekin = 1.9530124305314 | erot = 2.81680126246586 | epot = -23.0636678500934 | etot = -18.2938541570962 +27000 ekin = 1.96948983508855 | erot = 2.69266617300682 | epot = -22.9870601707012 | etot = -18.3249041626058 +28000 ekin = 2.02061868464074 | erot = 2.37038530969117 | epot = -22.9383598315964 | etot = -18.5473558372645 +29000 ekin = 2.51387846128098 | erot = 2.0265039132053 | epot = -22.888959880923 | etot = -18.3485775064367 +30000 ekin = 1.95889729807242 | erot = 2.1170713545074 | epot = -22.7896312662562 | etot = -18.7136626136764 +31000 ekin = 1.81775203419098 | erot = 2.326796842935 | epot = -22.7561124537192 | etot = -18.6115635765932 +32000 ekin = 1.87947265787065 | erot = 2.0009346769358 | epot = -22.8533570528062 | etot = -18.9729497179997 +33000 ekin = 1.77435214491107 | erot = 1.82826131933673 | epot = -22.8632647352802 | etot = -19.2606512710324 +34000 ekin = 2.27098719472917 | erot = 3.11275511420439 | epot = -22.9527052663856 | etot = -17.5689629574521 +35000 ekin = 2.88921171289845 | erot = 1.82538384737236 | epot = -23.0316569923336 | etot = -18.3170614320628 +36000 ekin = 2.40471013682393 | erot = 2.59817148723643 | epot = -23.1277697887139 | etot = -18.1248881646536 +37000 ekin = 2.23499312928139 | erot = 1.74662115184433 | epot = -23.1542126827759 | etot = -19.1725984016501 +38000 ekin = 2.13875747252781 | erot = 3.07733571118648 | epot = -23.0916051545794 | etot = -17.8755119708651 +39000 ekin = 2.08901196654187 | erot = 2.81975762995374 | epot = -23.0796147800379 | etot = -18.1708451835423 +40000 ekin = 2.95155149177527 | erot = 2.19459039829335 | epot = -23.141500571363 | etot = -17.9953586812944 +41000 ekin = 2.49235596566196 | erot = 3.45295839915509 | epot = -23.115526015811 | etot = -17.1702116509939 +42000 ekin = 2.58401591894786 | erot = 3.0976076851145 | epot = -23.0181097727229 | etot = -17.3364861686605 +43000 ekin = 2.17593293893362 | erot = 2.65403748718844 | epot = -22.8962504257564 | etot = -18.0662799996343 +44000 ekin = 2.34068034665607 | erot = 3.294882771572 | epot = -22.8143844644656 | etot = -17.1788213462375 +45000 ekin = 1.87200112415306 | erot = 3.49863859200052 | epot = -22.6989374637074 | etot = -17.3282977475538 +46000 ekin = 2.60943921333194 | erot = 2.23170007842725 | epot = -22.5884035122493 | etot = -17.7472642204901 +47000 ekin = 1.89594756436345 | erot = 3.4002587629387 | epot = -22.4938472923117 | etot = -17.1976409650096 +48000 ekin = 2.49339593279701 | erot = 2.5104785556399 | epot = -22.5372062210456 | etot = -17.5333317326087 +49000 ekin = 3.2041407554348 | erot = 2.17669016194865 | epot = -22.5688036423094 | etot = -17.1879727249259 +50000 ekin = 2.93024070185999 | erot = 1.55416219951966 | epot = -22.6087903765995 | etot = -18.1243874752199 +51000 ekin = 2.8585759501124 | erot = 2.69193261792584 | epot = -22.6228353253324 | etot = -17.0723267572942 +52000 ekin = 2.3079418078843 | erot = 1.84260643306147 | epot = -22.6230480697441 | etot = -18.4724998287983 +53000 ekin = 3.1803685919024 | erot = 1.67451273370508 | epot = -22.6834814309773 | etot = -17.8286001053698 +54000 ekin = 2.6151376953128 | erot = 1.96091197875017 | epot = -22.7484551927013 | etot = -18.1724055186384 +55000 ekin = 3.1639577845443 | erot = 2.86286196426802 | epot = -22.7917236196438 | etot = -16.7649038708315 +56000 ekin = 2.52994034294643 | erot = 3.05544364249365 | epot = -22.7651844773103 | etot = -17.1798004918702 +57000 ekin = 2.40889871674401 | erot = 3.4525690879514 | epot = -22.7113139496974 | etot = -16.849846145002 +58000 ekin = 1.9363727739706 | erot = 2.52762778976703 | epot = -22.6468058892224 | etot = -18.1828053254848 +59000 ekin = 2.55505415922972 | erot = 3.52385701835933 | epot = -22.6037443858311 | etot = -16.5248332082421 +60000 ekin = 2.80945252332612 | erot = 2.88606183204889 | epot = -22.5227874119079 | etot = -16.8272730565329 +61000 ekin = 2.69750183117722 | erot = 2.55373633146433 | epot = -22.4306469225965 | etot = -17.1794087599549 +62000 ekin = 2.74494354639602 | erot = 2.23074517653766 | epot = -22.3675792436719 | etot = -17.3918905207383 +63000 ekin = 2.66335513293138 | erot = 2.46159865380861 | epot = -22.3527707145482 | etot = -17.2278169278082 +64000 ekin = 2.12832019835147 | erot = 2.78772793164811 | epot = -22.3048690294469 | etot = -17.3888208994473 +65000 ekin = 1.88429801911228 | erot = 2.70719871478483 | epot = -22.3342736701749 | etot = -17.7427769362778 +66000 ekin = 2.77106091929282 | erot = 1.94126620531915 | epot = -22.338257942783 | etot = -17.625930818171 +67000 ekin = 2.53561386235746 | erot = 2.45901054739082 | epot = -22.3780784743028 | etot = -17.3834540645545 +68000 ekin = 2.9678648663671 | erot = 1.95502711706149 | epot = -22.4420512915713 | etot = -17.5191593081427 +69000 ekin = 2.61501630036274 | erot = 2.2429513448561 | epot = -22.3607835407198 | etot = -17.502815895501 +70000 ekin = 2.41492598760663 | erot = 2.80885610657203 | epot = -22.2905725083407 | etot = -17.066790414162 +71000 ekin = 2.65062529541957 | erot = 2.88868401392431 | epot = -22.2951070257787 | etot = -16.7557977164349 +72000 ekin = 2.93273744051009 | erot = 2.82552508252073 | epot = -22.4016757930526 | etot = -16.6434132700218 +73000 ekin = 2.18922665452238 | erot = 3.03559183860538 | epot = -22.4509770394845 | etot = -17.2261585463568 +74000 ekin = 2.16074843540078 | erot = 2.83668185121384 | epot = -22.4374624006144 | etot = -17.4400321139998 +75000 ekin = 1.52329638473031 | erot = 1.91520672578907 | epot = -22.5623153080324 | etot = -19.123812197513 +76000 ekin = 1.89250964827726 | erot = 2.83358650938892 | epot = -22.6698326202442 | etot = -17.943736462578 +77000 ekin = 2.82066630152179 | erot = 3.19779433197964 | epot = -22.7402096770599 | etot = -16.7217490435584 +78000 ekin = 2.42603824235662 | erot = 2.82319136688957 | epot = -22.7334053911689 | etot = -17.4841757819227 +79000 ekin = 2.1571494738421 | erot = 1.67722302323495 | epot = -22.7616861631187 | etot = -18.9273136660417 +80000 ekin = 2.3760789053548 | erot = 2.58372913427157 | epot = -22.6889139769023 | etot = -17.729105937276 +81000 ekin = 2.73468961033338 | erot = 1.92748741387075 | epot = -22.6388260929897 | etot = -17.9766490687856 +82000 ekin = 1.90565370838817 | erot = 1.71715050303634 | epot = -22.5547415381056 | etot = -18.9319373266811 +83000 ekin = 1.63698443616271 | erot = 1.88092293220519 | epot = -22.4792739412377 | etot = -18.9613665728698 +84000 ekin = 1.65571812906993 | erot = 2.10290321918187 | epot = -22.4031972735297 | etot = -18.6445759252779 +85000 ekin = 2.40863681830855 | erot = 2.04741059095057 | epot = -22.321221903585 | etot = -17.8651744943259 +86000 ekin = 2.50560893716733 | erot = 1.80624308622105 | epot = -22.3789065133115 | etot = -18.0670544899231 +87000 ekin = 2.13576456371582 | erot = 1.97115993651017 | epot = -22.4335511413526 | etot = -18.3266266411266 +88000 ekin = 1.74897318407528 | erot = 2.37233945814529 | epot = -22.4142028246849 | etot = -18.2928901824643 +89000 ekin = 1.85559683216276 | erot = 3.29559734355419 | epot = -22.4519626048678 | etot = -17.3007684291509 +90000 ekin = 2.22181579992018 | erot = 2.33948779846394 | epot = -22.5289826258985 | etot = -17.9676790275144 +91000 ekin = 2.40596540834273 | erot = 3.11545124680293 | epot = -22.4975752624166 | etot = -16.9761586072709 +92000 ekin = 2.6773157744569 | erot = 3.00279439655287 | epot = -22.4834827179575 | etot = -16.8033725469477 +93000 ekin = 3.0427813598525 | erot = 3.03722776158512 | epot = -22.4121259471479 | etot = -16.3321168257103 +94000 ekin = 3.20507830840023 | erot = 1.86440047317737 | epot = -22.5079833350679 | etot = -17.4385045534903 +95000 ekin = 3.4839955648833 | erot = 2.87934575393031 | epot = -22.5675869456428 | etot = -16.2042456268292 +96000 ekin = 2.8873631080951 | erot = 2.38554372248299 | epot = -22.5453635283434 | etot = -17.2724566977653 +97000 ekin = 1.92899149350272 | erot = 2.09886479790579 | epot = -22.5208382020819 | etot = -18.4929819106733 +98000 ekin = 2.21420868967462 | erot = 3.66528252896999 | epot = -22.4426781355708 | etot = -16.5631869169262 +99000 ekin = 1.98238051924192 | erot = 2.77358159119584 | epot = -22.3579409961467 | etot = -17.6019788857089 +100000 ekin = 1.80278462349605 | erot = 2.65457154995031 | epot = -22.2926900475079 | etot = -17.8353338740616 +101000 ekin = 2.14042196591663 | erot = 2.38610603254675 | epot = -22.2789462117326 | etot = -17.7524182132692 +102000 ekin = 1.54923043145398 | erot = 2.30485616158943 | epot = -22.27519637673 | etot = -18.4211097836866 +103000 ekin = 1.66618004359352 | erot = 2.82192794888076 | epot = -22.3284746660305 | etot = -17.8403666735562 +104000 ekin = 1.8840390723585 | erot = 3.37607054348826 | epot = -22.4068162519772 | etot = -17.1467066361304 +105000 ekin = 2.08970806137592 | erot = 2.01278733908098 | epot = -22.450865561264 | etot = -18.3483701608071 +106000 ekin = 2.87186619049714 | erot = 1.95029477179727 | epot = -22.46479383237 | etot = -17.6426328700756 +107000 ekin = 2.28516102595382 | erot = 1.55115426482475 | epot = -22.420448971169 | etot = -18.5841336803904 +108000 ekin = 2.4440862469061 | erot = 1.71323205815914 | epot = -22.4934628688132 | etot = -18.336144563748 +109000 ekin = 2.33376449416318 | erot = 2.92962175925398 | epot = -22.4792154966925 | etot = -17.2158292432753 +110000 ekin = 2.7815613020599 | erot = 2.36483486971455 | epot = -22.4384263756784 | etot = -17.2920302039039 +111000 ekin = 2.32472851347632 | erot = 2.09554567134105 | epot = -22.3756448055424 | etot = -17.955370620725 +112000 ekin = 2.91126509700492 | erot = 1.8278781240038 | epot = -22.2278235937356 | etot = -17.4886803727269 +113000 ekin = 2.82522334536064 | erot = 1.67936756938672 | epot = -22.2030639545535 | etot = -17.6984730398062 +114000 ekin = 3.42964629994365 | erot = 2.67287683722422 | epot = -22.3274259722919 | etot = -16.224902835124 +115000 ekin = 3.0542495603856 | erot = 1.72370226125566 | epot = -22.3530732875163 | etot = -17.575121465875 +116000 ekin = 3.19934505541307 | erot = 3.20304074939432 | epot = -22.4112422200445 | etot = -16.0088564152371 +117000 ekin = 3.03942349360439 | erot = 2.40720645224432 | epot = -22.3646852618703 | etot = -16.9180553160216 +118000 ekin = 3.21704225120818 | erot = 1.46425401673931 | epot = -22.2864155249032 | etot = -17.6051192569557 +119000 ekin = 2.33989996826882 | erot = 3.07668030790319 | epot = -22.2283862990246 | etot = -16.8118060228526 +120000 ekin = 1.93772242476321 | erot = 2.20130457047854 | epot = -22.1620199969907 | etot = -18.022993001749 +121000 ekin = 1.94013950333198 | erot = 3.08987281123525 | epot = -22.1565667857742 | etot = -17.126554471207 +122000 ekin = 1.68663003450368 | erot = 1.73461876453175 | epot = -22.2565715090021 | etot = -18.8353227099667 +123000 ekin = 1.72841976989173 | erot = 2.32750063038672 | epot = -22.3665160016578 | etot = -18.3105956013793 +124000 ekin = 2.73468934475335 | erot = 1.93313584543739 | epot = -22.378088078826 | etot = -17.7102628886353 +125000 ekin = 2.77507735763211 | erot = 1.95244582221334 | epot = -22.3863676939847 | etot = -17.6588445141392 +126000 ekin = 2.04549959008918 | erot = 1.485897173428 | epot = -22.4226219879524 | etot = -18.8912252244352 +127000 ekin = 1.86410777734907 | erot = 1.58829497411524 | epot = -22.4027380289015 | etot = -18.9503352774372 +128000 ekin = 1.63329448006254 | erot = 1.88032753965974 | epot = -22.3918784566533 | etot = -18.8782564369311 +129000 ekin = 2.51522192674941 | erot = 2.38822614049102 | epot = -22.396225517968 | etot = -17.4927774507275 +130000 ekin = 1.61191166117177 | erot = 2.81688343133435 | epot = -22.341565060394 | etot = -17.9127699678878 +131000 ekin = 2.29569747740708 | erot = 2.2886876976091 | epot = -22.2184139794107 | etot = -17.6340288043945 +132000 ekin = 2.97393694467802 | erot = 2.3613525440602 | epot = -22.1410658382525 | etot = -16.8057763495143 +133000 ekin = 2.01357676743257 | erot = 2.125828419273 | epot = -22.1312019600638 | etot = -17.9917967733582 +134000 ekin = 1.56048037412857 | erot = 2.84208065022547 | epot = -22.0682869067536 | etot = -17.6657258823995 +135000 ekin = 1.79811942319758 | erot = 2.40075843487508 | epot = -22.0853555614258 | etot = -17.8864777033532 +136000 ekin = 1.63631696233012 | erot = 2.13166656554854 | epot = -22.0879615470249 | etot = -18.3199780191463 +137000 ekin = 2.36040439516093 | erot = 1.93785486632901 | epot = -22.1234845924018 | etot = -17.8252253309118 +138000 ekin = 2.94591421775872 | erot = 1.58866111192914 | epot = -22.1783168558241 | etot = -17.6437415261363 +139000 ekin = 3.17560544591524 | erot = 2.24933296614107 | epot = -22.2966418842012 | etot = -16.8717034721449 +140000 ekin = 2.24781162873235 | erot = 3.05934139328612 | epot = -22.4681108223249 | etot = -17.1609578003064 +141000 ekin = 1.89078628042285 | erot = 3.13246933186326 | epot = -22.730922227649 | etot = -17.7076666153629 +142000 ekin = 2.51033894675651 | erot = 2.4942894309123 | epot = -22.8404165502847 | etot = -17.8357881726159 +143000 ekin = 2.40438807844298 | erot = 2.71461817456284 | epot = -22.8207220890738 | etot = -17.7017158360679 +144000 ekin = 1.9307425487964 | erot = 2.67760329085926 | epot = -22.6973757396236 | etot = -18.0890298999679 +145000 ekin = 1.82681171280412 | erot = 1.73674169257736 | epot = -22.6628534675149 | etot = -19.0993000621335 +146000 ekin = 2.42423538163981 | erot = 2.0908776294658 | epot = -22.6072904345337 | etot = -18.0921774234281 +147000 ekin = 1.44607209743073 | erot = 1.8801263906251 | epot = -22.5001275476876 | etot = -19.1739290596318 +148000 ekin = 1.9349809420382 | erot = 2.57774390934154 | epot = -22.4721664357448 | etot = -17.9594415843651 +149000 ekin = 2.02370265642699 | erot = 3.3179576458013 | epot = -22.3745153112138 | etot = -17.0328550089855 +150000 ekin = 2.48124469844233 | erot = 2.68185291250579 | epot = -22.1950329772129 | etot = -17.0319353662648 +151000 ekin = 2.76319440452884 | erot = 1.87355938382631 | epot = -21.986630645846 | etot = -17.3498768574909 +152000 ekin = 2.77453107952051 | erot = 1.77016628972892 | epot = -21.7977108098427 | etot = -17.2530134405933 +153000 ekin = 3.08827014622555 | erot = 1.80976617511255 | epot = -21.6910123469878 | etot = -16.7929760256497 +154000 ekin = 2.32051051770812 | erot = 2.18004857730092 | epot = -21.6406733490634 | etot = -17.1401142540543 +155000 ekin = 1.95766873014157 | erot = 2.67064554154836 | epot = -21.7315745360126 | etot = -17.1032602643227 +156000 ekin = 2.69830438989808 | erot = 2.24987636164771 | epot = -21.7962907570244 | etot = -16.8481100054786 +157000 ekin = 3.89340900899948 | erot = 2.73733315325155 | epot = -21.8437967078712 | etot = -15.2130545456202 +158000 ekin = 2.84737207100033 | erot = 2.70157958556583 | epot = -21.878244439129 | etot = -16.3292927825628 +159000 ekin = 3.1312088996125 | erot = 2.65375527842548 | epot = -21.8350703791794 | etot = -16.0501062011414 +160000 ekin = 2.54316260055464 | erot = 3.27950281054041 | epot = -21.8888467298127 | etot = -16.0661813187176 +161000 ekin = 2.49549109190181 | erot = 2.45028506429479 | epot = -21.8585593359585 | etot = -16.9127831797619 +162000 ekin = 3.05200272259994 | erot = 2.59164651185653 | epot = -21.8439750046483 | etot = -16.2003257701918 +163000 ekin = 3.30374280597553 | erot = 2.24193960212662 | epot = -21.8717863279577 | etot = -16.3261039198555 +164000 ekin = 3.53081155329031 | erot = 2.22419322011391 | epot = -21.8162094860939 | etot = -16.0612047126897 +165000 ekin = 2.48919804649027 | erot = 2.59105984700639 | epot = -21.7395563276218 | etot = -16.6592984341251 +166000 ekin = 2.14880495285182 | erot = 3.05770380831398 | epot = -21.6850566092694 | etot = -16.4785478481036 +167000 ekin = 2.78181890034675 | erot = 2.90402826001928 | epot = -21.5971987360122 | etot = -15.9113515756462 +168000 ekin = 1.74726050172142 | erot = 2.76898886506121 | epot = -21.490566893224 | etot = -16.9743175264414 +169000 ekin = 1.8134289785439 | erot = 2.45780601602371 | epot = -21.4680710936728 | etot = -17.1968360991052 +170000 ekin = 1.69364478039988 | erot = 2.87928997590297 | epot = -21.4668806356843 | etot = -16.8939458793814 +171000 ekin = 2.14879448642638 | erot = 1.61442218455815 | epot = -21.3172106430715 | etot = -17.553993972087 +172000 ekin = 1.68431962963431 | erot = 2.36087816720612 | epot = -21.1539793618528 | etot = -17.1087815650124 +173000 ekin = 2.05784071815669 | erot = 2.17142592689102 | epot = -21.0926393885011 | etot = -16.8633727434534 +174000 ekin = 2.49611606122761 | erot = 3.09665692560806 | epot = -20.9460348670979 | etot = -15.3532618802622 +175000 ekin = 2.61673440848865 | erot = 2.88720331620426 | epot = -20.8525764091519 | etot = -15.348638684459 +176000 ekin = 2.16190213742438 | erot = 2.672518464664 | epot = -20.8442274508468 | etot = -16.0098068487584 +177000 ekin = 2.83236394902013 | erot = 2.81489135382763 | epot = -20.925759607446 | etot = -15.2785043045983 +178000 ekin = 3.17804494293424 | erot = 1.88346790512585 | epot = -21.0677853312893 | etot = -16.0062724832292 +179000 ekin = 2.33267448424065 | erot = 2.85731052069525 | epot = -21.1181390109479 | etot = -15.928154006012 +180000 ekin = 2.39061531304011 | erot = 2.93791308776 | epot = -21.1146449531392 | etot = -15.786116552339 +181000 ekin = 2.79990361156737 | erot = 3.28891520287386 | epot = -21.0834365456108 | etot = -14.9946177311695 +182000 ekin = 3.02616507870526 | erot = 2.3341432703009 | epot = -21.0600545808659 | etot = -15.6997462318597 +183000 ekin = 2.45290144562467 | erot = 2.21141617846262 | epot = -20.911866387917 | etot = -16.2475487638297 +184000 ekin = 2.56560515060991 | erot = 2.7739810551646 | epot = -20.6989716212004 | etot = -15.3593854154259 +185000 ekin = 2.17586139274635 | erot = 1.95913868179524 | epot = -20.5985322435751 | etot = -16.4635321690335 +186000 ekin = 2.07303044902321 | erot = 3.15122816264525 | epot = -20.4965070011281 | etot = -15.2722483894597 +187000 ekin = 2.44319481307615 | erot = 1.92784212082443 | epot = -20.5124982035642 | etot = -16.1414612696636 +188000 ekin = 2.28870879542405 | erot = 2.8871121346017 | epot = -20.6323506293031 | etot = -15.4565296992773 +189000 ekin = 1.68047280237829 | erot = 3.05535775765803 | epot = -20.6378101864803 | etot = -15.901979626444 +190000 ekin = 1.97184665786397 | erot = 2.95271452778009 | epot = -20.6376534135265 | etot = -15.7130922278825 +191000 ekin = 2.30626539196432 | erot = 2.64854814117512 | epot = -20.6037323569656 | etot = -15.6489188238262 +192000 ekin = 3.54976671698926 | erot = 2.91090725702116 | epot = -20.5525508832509 | etot = -14.0918769092405 +193000 ekin = 2.63938438600422 | erot = 3.14409581682352 | epot = -20.5892132844066 | etot = -14.8057330815789 +194000 ekin = 2.67903757365037 | erot = 2.30768318132376 | epot = -20.4753987179501 | etot = -15.488677962976 +195000 ekin = 1.89257615363314 | erot = 2.64508051866103 | epot = -20.4197880125065 | etot = -15.8821313402123 +196000 ekin = 2.29151017050607 | erot = 2.32636787964875 | epot = -20.4440761857987 | etot = -15.8261981356438 +197000 ekin = 2.48344018982905 | erot = 2.5654400941963 | epot = -20.516126938087 | etot = -15.4672466540616 +198000 ekin = 2.01386156849612 | erot = 1.52779840514975 | epot = -20.537160292649 | etot = -16.9955003190031 +199000 ekin = 1.50729232131931 | erot = 2.19878124720506 | epot = -20.5584754599868 | etot = -16.8524018914625 +200000 ekin = 1.64236235330806 | erot = 2.46736341802316 | epot = -20.5387924113648 | etot = -16.4290666400336 +201000 ekin = 2.627066472214 | erot = 2.61321940355396 | epot = -20.6089911163939 | etot = -15.3687052406259 +202000 ekin = 2.3129503751722 | erot = 2.54874856259559 | epot = -20.6732219111123 | etot = -15.8115229733445 +203000 ekin = 1.63961009223968 | erot = 2.10835750593015 | epot = -20.7002051999767 | etot = -16.9522376018069 +204000 ekin = 2.0558049009161 | erot = 1.9161072834091 | epot = -20.8154459612946 | etot = -16.8435337769694 +205000 ekin = 3.04603860094189 | erot = 3.24233043438682 | epot = -20.9297600758299 | etot = -14.6413910405012 +206000 ekin = 2.56775422508359 | erot = 2.20992928465512 | epot = -21.0192669133083 | etot = -16.2415834035696 +207000 ekin = 3.46597997409567 | erot = 2.48427015330086 | epot = -21.151399026488 | etot = -15.2011488990915 +208000 ekin = 2.51159742060494 | erot = 2.22948191756652 | epot = -21.2942477400986 | etot = -16.5531684019271 +209000 ekin = 3.78908644724162 | erot = 2.17660742759513 | epot = -21.4499700336111 | etot = -15.4842761587743 +210000 ekin = 3.03133642129733 | erot = 2.21595982730352 | epot = -21.5648709610245 | etot = -16.3175747124237 +211000 ekin = 1.63075564056512 | erot = 2.12650387194819 | epot = -21.6099552204253 | etot = -17.852695707912 +212000 ekin = 2.67694215598975 | erot = 2.47186432110288 | epot = -21.8481434074352 | etot = -16.6993369303425 +213000 ekin = 2.70688282449408 | erot = 1.96666534072978 | epot = -22.1170796448084 | etot = -17.4435314795845 +214000 ekin = 2.88993887341392 | erot = 3.16392577542175 | epot = -22.1689844550676 | etot = -16.1151198062319 +215000 ekin = 2.59587305508913 | erot = 1.84775314628517 | epot = -22.0799472955547 | etot = -17.6363210941804 +216000 ekin = 2.59710486720184 | erot = 2.79170232594871 | epot = -22.123050002636 | etot = -16.7342428094855 +217000 ekin = 2.50043297628753 | erot = 1.89569946865143 | epot = -22.2232445790842 | etot = -17.8271121341452 +218000 ekin = 2.42608117861514 | erot = 2.42380011003409 | epot = -22.2442965405807 | etot = -17.3944152519314 +219000 ekin = 2.31038806457503 | erot = 2.64910389607574 | epot = -22.2862511100887 | etot = -17.3267591494379 +220000 ekin = 1.69989575631519 | erot = 2.34717348369245 | epot = -22.2936253261379 | etot = -18.2465560861303 +221000 ekin = 2.0597604328414 | erot = 2.4617257870959 | epot = -22.2693428350923 | etot = -17.747856615155 +222000 ekin = 1.56778478035701 | erot = 2.12765432596982 | epot = -22.1639011265163 | etot = -18.4684620201895 +223000 ekin = 1.84761048251748 | erot = 1.88006246465219 | epot = -22.0932628941083 | etot = -18.3655899469387 +224000 ekin = 2.59436846043989 | erot = 2.94714248251079 | epot = -22.1101977210218 | etot = -16.5686867780711 +225000 ekin = 3.30446830369106 | erot = 2.86069163428051 | epot = -22.1130335717329 | etot = -15.9478736337614 +226000 ekin = 3.03148439961004 | erot = 2.0857715841185 | epot = -22.1515480756285 | etot = -17.0342920918999 +227000 ekin = 2.52473737037052 | erot = 3.1515233037479 | epot = -22.2272979755786 | etot = -16.5510373014602 +228000 ekin = 2.32773029487822 | erot = 2.67887550863523 | epot = -22.3289846157579 | etot = -17.3223788122445 +229000 ekin = 2.908632187774 | erot = 2.89972099244786 | epot = -22.4590990625921 | etot = -16.6507458823703 +230000 ekin = 2.30901008738396 | erot = 3.48892218468534 | epot = -22.5811133380347 | etot = -16.7831810659654 +231000 ekin = 2.09445974553368 | erot = 3.10137653837903 | epot = -22.6273628788262 | etot = -17.4315265949135 +232000 ekin = 2.11347252785341 | erot = 1.99214840222577 | epot = -22.6148559367411 | etot = -18.5092350066619 +233000 ekin = 2.31469131808302 | erot = 2.82702779723524 | epot = -22.573468078272 | etot = -17.4317489629538 +234000 ekin = 2.08691986790862 | erot = 2.09006771152617 | epot = -22.5768924885421 | etot = -18.3999049091073 +235000 ekin = 2.43602788311011 | erot = 2.79756094595935 | epot = -22.5841308018507 | etot = -17.3505419727812 +236000 ekin = 2.93232983655883 | erot = 3.05945149934941 | epot = -22.5011281720659 | etot = -16.5093468361576 +237000 ekin = 3.2236915032749 | erot = 3.26810349425041 | epot = -22.3869936414794 | etot = -15.8951986439541 +238000 ekin = 2.4674995923353 | erot = 2.31630563795609 | epot = -22.3210409459325 | etot = -17.5372357156411 +239000 ekin = 2.10887317283391 | erot = 2.47562990634415 | epot = -22.3008221039947 | etot = -17.7163190248166 +240000 ekin = 1.76092230208337 | erot = 2.62077674301801 | epot = -22.2503883436816 | etot = -17.8686892985802 +241000 ekin = 1.93966929781469 | erot = 1.41063904300121 | epot = -22.2367099354244 | etot = -18.8864015946085 +242000 ekin = 3.03220831764684 | erot = 2.02809667614523 | epot = -22.2529237351145 | etot = -17.1926187413224 +243000 ekin = 2.84396619393303 | erot = 1.7910064306681 | epot = -22.2768680265869 | etot = -17.6418954019858 +244000 ekin = 1.94630661585721 | erot = 2.3722540427007 | epot = -22.2272698315535 | etot = -17.9087091729956 +245000 ekin = 2.21268964174709 | erot = 2.75899365563147 | epot = -22.1926413343766 | etot = -17.2209580369981 +246000 ekin = 2.07547606015104 | erot = 2.22089229769683 | epot = -22.119471822751 | etot = -17.8231034649032 +247000 ekin = 1.58341517009487 | erot = 3.06778333448391 | epot = -22.0033087190277 | etot = -17.3521102144489 +248000 ekin = 2.1365138975527 | erot = 3.53502738921423 | epot = -21.8495423719646 | etot = -16.1780010851977 +249000 ekin = 2.17149547481658 | erot = 3.29316066315612 | epot = -21.813933670884 | etot = -16.3492775329113 +250000 ekin = 2.39365756609179 | erot = 2.39580124119371 | epot = -21.767733544404 | etot = -16.9782747371185 +251000 ekin = 1.2828204065042 | erot = 2.24293125468609 | epot = -21.7209613352709 | etot = -18.1952096740806 +252000 ekin = 1.76792385357404 | erot = 2.13774913157991 | epot = -21.715743646839 | etot = -17.8100706616851 +253000 ekin = 2.15844787240193 | erot = 2.59910839140098 | epot = -21.6939194867273 | etot = -16.9363632229244 +254000 ekin = 2.46988601582316 | erot = 1.99393049965303 | epot = -21.6738244724958 | etot = -17.2100079570196 +255000 ekin = 2.31014544453096 | erot = 2.03140480982291 | epot = -21.6888108217887 | etot = -17.3472605674348 +256000 ekin = 2.90570988017011 | erot = 2.61779108741197 | epot = -21.6304219101588 | etot = -16.1069209425767 +257000 ekin = 2.87227426842454 | erot = 2.08598550349753 | epot = -21.5998306482426 | etot = -16.6415708763206 +258000 ekin = 2.06365418401471 | erot = 2.33103720962373 | epot = -21.5019981919811 | etot = -17.1073067983427 +259000 ekin = 2.23106413601668 | erot = 2.88992031738565 | epot = -21.4929751490585 | etot = -16.3719906956562 +260000 ekin = 2.49064109684832 | erot = 2.38083177290805 | epot = -21.4659963710747 | etot = -16.5945235013183 +261000 ekin = 2.09140199827797 | erot = 2.40209752473156 | epot = -21.4076397934529 | etot = -16.9141402704433 +262000 ekin = 2.36091906713393 | erot = 2.66652490187927 | epot = -21.359937125592 | etot = -16.3324931565788 +263000 ekin = 2.2112169796158 | erot = 2.73059503173094 | epot = -21.4187723839513 | etot = -16.4769603726046 +264000 ekin = 2.28961718487933 | erot = 2.75455515229635 | epot = -21.370776058554 | etot = -16.3266037213783 +265000 ekin = 1.71596203334806 | erot = 1.76104932073225 | epot = -21.2034176623527 | etot = -17.7264063082724 +266000 ekin = 2.51424635704546 | erot = 2.09488481391075 | epot = -21.0818656942669 | etot = -16.4727345233107 +267000 ekin = 2.81393895925601 | erot = 2.14232705328249 | epot = -21.1259701200622 | etot = -16.1697041075237 +268000 ekin = 3.10191854871686 | erot = 2.80451383793942 | epot = -21.0933882633302 | etot = -15.1869558766739 +269000 ekin = 3.52550118014125 | erot = 2.35973600910593 | epot = -21.0585255577117 | etot = -15.1732883684645 +270000 ekin = 3.50731584216641 | erot = 1.86855463358785 | epot = -21.093710946541 | etot = -15.7178404707867 +271000 ekin = 3.5675331453682 | erot = 2.0823459971557 | epot = -21.1717850302959 | etot = -15.521905887772 +272000 ekin = 2.43382567191708 | erot = 3.09591378837425 | epot = -21.2584464912718 | etot = -15.7287070309805 +273000 ekin = 2.38177594135517 | erot = 3.14028416008422 | epot = -21.3418702267283 | etot = -15.8198101252889 +274000 ekin = 2.46408091312732 | erot = 2.01407385193325 | epot = -21.3513679347441 | etot = -16.8732131696836 +275000 ekin = 2.45653813926169 | erot = 3.06780010281641 | epot = -21.3769507768006 | etot = -15.8526125347225 +276000 ekin = 2.79508720985829 | erot = 2.87011619931109 | epot = -21.3368600634473 | etot = -15.671656654278 +277000 ekin = 2.21394865880382 | erot = 2.19504097967885 | epot = -21.2606836087454 | etot = -16.8516939702627 +278000 ekin = 2.75723780567064 | erot = 3.25107227641375 | epot = -21.1755556732391 | etot = -15.1672455911547 +279000 ekin = 2.50738352588257 | erot = 1.80312795092014 | epot = -21.119949297869 | etot = -16.8094378210662 +280000 ekin = 2.35419479075042 | erot = 1.7566104351529 | epot = -21.0612865360217 | etot = -16.9504813101184 +281000 ekin = 2.54091624756361 | erot = 2.29354970120309 | epot = -21.0950091005497 | etot = -16.260543151783 +282000 ekin = 2.99712896075656 | erot = 2.42094408338315 | epot = -21.2220089565004 | etot = -15.8039359123607 +283000 ekin = 2.56696810638689 | erot = 2.10068113035835 | epot = -21.403161576838 | etot = -16.7355123400928 +284000 ekin = 2.50149529685552 | erot = 3.12894850572552 | epot = -21.5256946024495 | etot = -15.8952507998684 +285000 ekin = 2.42104861452631 | erot = 1.7773884250687 | epot = -21.6343236201921 | etot = -17.4358865805971 +286000 ekin = 1.95703367775988 | erot = 2.02947038358402 | epot = -21.6777606373854 | etot = -17.6912565760415 +287000 ekin = 2.563069553437 | erot = 2.57822888294094 | epot = -21.7096788412169 | etot = -16.568380404839 +288000 ekin = 2.18408141161779 | erot = 1.69724000161796 | epot = -21.6059228036045 | etot = -17.7246013903687 +289000 ekin = 2.32975723406079 | erot = 1.67288237726622 | epot = -21.4690249265465 | etot = -17.4663853152195 +290000 ekin = 2.22773933829104 | erot = 2.00568808096403 | epot = -21.3936416309443 | etot = -17.1602142116892 +291000 ekin = 1.46140048209222 | erot = 2.68187349132486 | epot = -21.320309661152 | etot = -17.177035687735 +292000 ekin = 2.07752653885401 | erot = 2.42042811850752 | epot = -21.2225710152689 | etot = -16.7246163579074 +293000 ekin = 2.14598735312316 | erot = 1.87232699516306 | epot = -21.1503112105659 | etot = -17.1319968622797 +294000 ekin = 2.15249843510191 | erot = 2.17548638187737 | epot = -21.1209057143321 | etot = -16.7929208973528 +295000 ekin = 2.13417246804068 | erot = 2.31578295657371 | epot = -21.023273761855 | etot = -16.5733183372406 +296000 ekin = 1.52381700282724 | erot = 2.92433462308731 | epot = -21.0839283123442 | etot = -16.6357766864297 +297000 ekin = 2.45165869902145 | erot = 2.17953392904489 | epot = -21.0491333291916 | etot = -16.4179407011252 +298000 ekin = 1.77920935759369 | erot = 2.01251348063453 | epot = -21.0971977522748 | etot = -17.3054749140465 +299000 ekin = 1.87538650376616 | erot = 1.65135039658661 | epot = -21.119277949862 | etot = -17.5925410495092 +300000 ekin = 2.3167056751994 | erot = 1.510902648654 | epot = -21.178913099451 | etot = -17.3513047755976 +301000 ekin = 2.00567209290794 | erot = 2.01270349508404 | epot = -21.2857234594098 | etot = -17.2673478714178 +302000 ekin = 1.78598592595272 | erot = 2.2354055492879 | epot = -21.3905601140029 | etot = -17.3691686387622 +303000 ekin = 2.73278841880507 | erot = 1.64856089415774 | epot = -21.3608973804115 | etot = -16.9795480674487 +304000 ekin = 2.5809493598196 | erot = 2.00558555026353 | epot = -21.400198286629 | etot = -16.8136633765459 +305000 ekin = 2.43647384348742 | erot = 2.28275438290435 | epot = -21.3863075230184 | etot = -16.6670792966266 +306000 ekin = 2.14332823539982 | erot = 2.4338461634411 | epot = -21.3233075109442 | etot = -16.7461331121032 +307000 ekin = 3.21424191196812 | erot = 3.27591538479569 | epot = -21.289790084126 | etot = -14.7996327873622 +308000 ekin = 3.45838026839176 | erot = 2.68116130354006 | epot = -21.3419403426811 | etot = -15.2023987707493 +309000 ekin = 2.38041738433959 | erot = 2.92081370932153 | epot = -21.4463399141034 | etot = -16.1451088204423 +310000 ekin = 2.50977269558789 | erot = 2.34824464102402 | epot = -21.4648074532888 | etot = -16.6067901166769 +311000 ekin = 2.57488628819259 | erot = 2.293754673538 | epot = -21.5151382155269 | etot = -16.6464972537963 +312000 ekin = 2.09623150906876 | erot = 2.93795890592974 | epot = -21.6260240426366 | etot = -16.5918336276381 +313000 ekin = 1.8184499729194 | erot = 2.28463898505893 | epot = -21.6999003790643 | etot = -17.5968114210859 +314000 ekin = 2.3228324174232 | erot = 2.19580475273396 | epot = -21.6870491287185 | etot = -17.1684119585613 +315000 ekin = 1.84546653836013 | erot = 2.13886071139629 | epot = -21.7312132691438 | etot = -17.7468860193873 +316000 ekin = 2.1657114199577 | erot = 3.03124199276298 | epot = -21.7430929234306 | etot = -16.5461395107099 +317000 ekin = 2.42793755919909 | erot = 3.57187833839244 | epot = -21.8303487369249 | etot = -15.8305328393334 +318000 ekin = 2.31418145055206 | erot = 3.02858542885927 | epot = -21.9347898317926 | etot = -16.5920229523813 +319000 ekin = 2.35032973997068 | erot = 3.16078759112674 | epot = -22.0387665246751 | etot = -16.5276491935776 +320000 ekin = 1.78202525445684 | erot = 2.83297321443624 | epot = -22.1187616541783 | etot = -17.5037631852852 +321000 ekin = 2.87441941784728 | erot = 2.26223197636944 | epot = -22.1065455913123 | etot = -16.9698941970956 +322000 ekin = 2.79013397204362 | erot = 2.68769432639935 | epot = -22.1121405540937 | etot = -16.6343122556507 +323000 ekin = 2.070121980457 | erot = 2.31830584817612 | epot = -22.1539458855415 | etot = -17.7655180569083 +324000 ekin = 2.58383941134683 | erot = 2.58296807603305 | epot = -22.1539753505051 | etot = -16.9871678631253 +325000 ekin = 3.43451304817783 | erot = 2.45405386180802 | epot = -21.938960387404 | etot = -16.0503934774181 +326000 ekin = 3.49680929786584 | erot = 2.85196633398113 | epot = -21.8204400999953 | etot = -15.4716644681484 +327000 ekin = 2.68799300805475 | erot = 2.21805195956654 | epot = -21.7892073548558 | etot = -16.8831623872345 +328000 ekin = 1.81477491971657 | erot = 2.35891534842888 | epot = -21.7275637950057 | etot = -17.5538735268602 +329000 ekin = 2.19319322627006 | erot = 2.40717958919081 | epot = -21.6826095784948 | etot = -17.0822367630339 +330000 ekin = 1.87131927244382 | erot = 2.03694340108429 | epot = -21.5934239674847 | etot = -17.6851612939566 +331000 ekin = 2.37197683084608 | erot = 1.80087022346348 | epot = -21.5641185835514 | etot = -17.3912715292419 +332000 ekin = 1.69601394569048 | erot = 2.54947032294377 | epot = -21.5986464339748 | etot = -17.3531621653406 +333000 ekin = 1.59867443991714 | erot = 2.14911483871162 | epot = -21.7162173059518 | etot = -17.9684280273231 +334000 ekin = 2.25811733625553 | erot = 2.62323988136568 | epot = -21.7749416190679 | etot = -16.8935844014467 +335000 ekin = 2.93433632601273 | erot = 3.10350297573268 | epot = -21.7966831809595 | etot = -15.7588438792141 +336000 ekin = 2.76337640462581 | erot = 2.54930710489019 | epot = -21.7180312833467 | etot = -16.4053477738307 +337000 ekin = 3.19235531401951 | erot = 3.87146146874103 | epot = -21.8022396262892 | etot = -14.7384228435286 +338000 ekin = 2.33305125173566 | erot = 2.13094194678887 | epot = -21.8068682042896 | etot = -17.3428750057651 +339000 ekin = 1.71673308889604 | erot = 2.30964121170968 | epot = -21.7941224580796 | etot = -17.7677481574739 +340000 ekin = 1.59424151294027 | erot = 3.16324993863714 | epot = -21.7679173396748 | etot = -17.0104258880973 +341000 ekin = 1.69465464335694 | erot = 3.18694861883744 | epot = -21.7067352043109 | etot = -16.8251319421165 +342000 ekin = 1.81243763026219 | erot = 2.60448215582795 | epot = -21.5993126794634 | etot = -17.1823928933732 +343000 ekin = 3.08243814047349 | erot = 2.9217466333323 | epot = -21.5855979229594 | etot = -15.5814131491536 +344000 ekin = 2.94964594107348 | erot = 3.10231272046816 | epot = -21.5506154266351 | etot = -15.4986567650935 +345000 ekin = 2.34525111670595 | erot = 2.88045261854212 | epot = -21.530734043011 | etot = -16.3050303077629 +346000 ekin = 2.03136740406842 | erot = 3.44352096435563 | epot = -21.4703041890966 | etot = -15.9954158206726 +347000 ekin = 2.34515762081498 | erot = 1.91414074840886 | epot = -21.3488386855954 | etot = -17.0895403163716 +348000 ekin = 2.76763212340836 | erot = 2.78035348102326 | epot = -21.3102796687364 | etot = -15.7622940643048 +349000 ekin = 2.29342234253801 | erot = 3.14526664575919 | epot = -21.3922932631024 | etot = -15.9536042748052 +350000 ekin = 2.17828641691343 | erot = 2.38211689163937 | epot = -21.3570978647003 | etot = -16.7966945561475 +351000 ekin = 2.2787342054874 | erot = 2.85568682453813 | epot = -21.3165609660186 | etot = -16.182139935993 +352000 ekin = 2.70894563927919 | erot = 2.77656375044279 | epot = -21.3565059314145 | etot = -15.8709965416925 +353000 ekin = 1.74748047732915 | erot = 2.14191122851256 | epot = -21.3195625770357 | etot = -17.430170871194 +354000 ekin = 2.30492780756568 | erot = 2.37159952583724 | epot = -21.3742968901642 | etot = -16.6977695567612 +355000 ekin = 2.32493886573112 | erot = 2.38411746089983 | epot = -21.339340741587 | etot = -16.6302844149561 +356000 ekin = 2.9749649543268 | erot = 2.9916655517553 | epot = -21.2468948072712 | etot = -15.2802643011891 +357000 ekin = 1.79541671946026 | erot = 2.13971792108731 | epot = -21.2216819829681 | etot = -17.2865473424205 +358000 ekin = 2.06637919290965 | erot = 1.9076530715578 | epot = -21.2447441674953 | etot = -17.2707119030278 +359000 ekin = 2.02344077580052 | erot = 2.11726163321539 | epot = -21.2183688961264 | etot = -17.0776664871105 +360000 ekin = 2.64012587839158 | erot = 2.43776362828977 | epot = -21.1472477161847 | etot = -16.0693582095033 +361000 ekin = 2.41850555983882 | erot = 2.39054736245265 | epot = -21.2133787743639 | etot = -16.4043258520724 +362000 ekin = 2.2486199222758 | erot = 2.04489136793498 | epot = -21.2088914287919 | etot = -16.9153801385811 +363000 ekin = 3.21904252076974 | erot = 1.79717950163013 | epot = -21.2620537293498 | etot = -16.24583170695 +364000 ekin = 2.9845697448498 | erot = 2.18316673460243 | epot = -21.2883338312843 | etot = -16.120597351832 +365000 ekin = 2.49427392981412 | erot = 2.31205455481896 | epot = -21.4001153296815 | etot = -16.5937868450484 +366000 ekin = 2.61706523565788 | erot = 2.20229130507574 | epot = -21.4506718008962 | etot = -16.6313152601626 +367000 ekin = 2.24650816549397 | erot = 1.87906237362998 | epot = -21.5207044850599 | etot = -17.3951339459359 +368000 ekin = 2.46672276241562 | erot = 2.37638546053105 | epot = -21.5628581383216 | etot = -16.7197499153749 +369000 ekin = 2.03614635149851 | erot = 2.85426887707092 | epot = -21.6803034764487 | etot = -16.7898882478793 +370000 ekin = 2.13410724028005 | erot = 2.17304603842012 | epot = -21.7343761700058 | etot = -17.4272228913057 +371000 ekin = 2.21722409826115 | erot = 2.11058746733929 | epot = -21.6422617131998 | etot = -17.3144501475994 +372000 ekin = 1.88083333566673 | erot = 1.90617172826127 | epot = -21.6005499693118 | etot = -17.8135449053838 +373000 ekin = 1.98298204516521 | erot = 1.78267682128409 | epot = -21.5708808628646 | etot = -17.8052219964153 +374000 ekin = 2.88981201933268 | erot = 1.90326894499807 | epot = -21.4624711307906 | etot = -16.6693901664599 +375000 ekin = 2.31951869092549 | erot = 1.92779670517485 | epot = -21.3521768069862 | etot = -17.1048614108859 +376000 ekin = 2.60113015271722 | erot = 2.31181306588444 | epot = -21.34681055463 | etot = -16.4338673360283 +377000 ekin = 2.23867315344604 | erot = 1.65923992926403 | epot = -21.2611852709131 | etot = -17.363272188203 +378000 ekin = 2.38125181613766 | erot = 2.54002618279121 | epot = -21.2390275318703 | etot = -16.3177495329414 +379000 ekin = 2.06952281308678 | erot = 2.11888196225292 | epot = -21.194025606577 | etot = -17.0056208312373 +380000 ekin = 2.59961269461524 | erot = 2.3751200788503 | epot = -21.1885781090515 | etot = -16.2138453355859 +381000 ekin = 2.42019573552876 | erot = 2.20667402504614 | epot = -21.1989968748535 | etot = -16.5721271142786 +382000 ekin = 2.04746564398744 | erot = 3.34439482672214 | epot = -21.2903574441545 | etot = -15.8984969734449 +383000 ekin = 2.65699216362738 | erot = 1.56546061375907 | epot = -21.3572338418187 | etot = -17.1347810644322 +384000 ekin = 2.43156675693926 | erot = 2.00097327452753 | epot = -21.3434156392382 | etot = -16.9108756077714 +385000 ekin = 1.95152101616516 | erot = 3.28345377140313 | epot = -21.4173973675698 | etot = -16.1824225800015 +386000 ekin = 2.10919215730741 | erot = 2.90700736383436 | epot = -21.3963452767614 | etot = -16.3801457556197 +387000 ekin = 2.34448447096483 | erot = 2.50155013212484 | epot = -21.3487258248084 | etot = -16.5026912217187 +388000 ekin = 2.71771591111729 | erot = 2.76803950274557 | epot = -21.3515918112166 | etot = -15.8658363973537 +389000 ekin = 3.06825183100775 | erot = 3.06148533146046 | epot = -21.4826430036711 | etot = -15.3529058412029 +390000 ekin = 2.56997560639923 | erot = 2.05646161654304 | epot = -21.5623801506968 | etot = -16.9359429277546 +391000 ekin = 2.1110114400687 | erot = 2.44612603817531 | epot = -21.6052888202632 | etot = -17.0481513420191 +392000 ekin = 2.58328475785099 | erot = 2.75249392862464 | epot = -21.7336094646938 | etot = -16.3978307782182 +393000 ekin = 2.03977041996533 | erot = 1.67448219405536 | epot = -21.8740604202474 | etot = -18.1598078062267 +394000 ekin = 2.1229408356241 | erot = 2.43410977254954 | epot = -21.9094739378951 | etot = -17.3524233297214 +395000 ekin = 2.48696003315341 | erot = 2.48225062557349 | epot = -21.8799685903484 | etot = -16.9107579316215 +396000 ekin = 3.18909661029635 | erot = 1.62675064803775 | epot = -21.8520000277039 | etot = -17.0361527693698 +397000 ekin = 2.39161566907255 | erot = 2.17052346752458 | epot = -21.7939512244376 | etot = -17.2318120878404 +398000 ekin = 2.29946433742664 | erot = 2.18115834594542 | epot = -21.7285069861955 | etot = -17.2478843028235 +399000 ekin = 2.65449075133045 | erot = 2.80318185995816 | epot = -21.6503181327212 | etot = -16.1926455214325 +400000 ekin = 1.800915604111 | erot = 2.76596769548035 | epot = -21.6418619272709 | etot = -17.0749786276795 +401000 ekin = 2.35073130822393 | erot = 3.1229922205774 | epot = -21.6675586342212 | etot = -16.1938351054199 +402000 ekin = 3.95550191914708 | erot = 3.58855023837881 | epot = -21.5840051268208 | etot = -14.0399529692949 +403000 ekin = 3.59615502379622 | erot = 3.44558176696768 | epot = -21.5781150073617 | etot = -14.5363782165978 +404000 ekin = 2.50360365952137 | erot = 3.01285184176069 | epot = -21.6258060641303 | etot = -16.1093505628483 +405000 ekin = 2.77241560720113 | erot = 3.10596549510783 | epot = -21.704678917892 | etot = -15.826297815583 +406000 ekin = 2.33934923007339 | erot = 2.04671975867729 | epot = -21.819104286388 | etot = -17.4330352976373 +407000 ekin = 2.34277955096234 | erot = 1.89301717692526 | epot = -21.8450916691373 | etot = -17.6092949412497 +408000 ekin = 1.91561948833426 | erot = 2.19551604353608 | epot = -21.8744041835349 | etot = -17.7632686516646 +409000 ekin = 1.98819074442449 | erot = 1.93870533007334 | epot = -21.921903026697 | etot = -17.9950069521992 +410000 ekin = 1.59047218684375 | erot = 1.93259851333214 | epot = -21.969890787558 | etot = -18.4468200873821 +411000 ekin = 1.88305362601542 | erot = 2.47249081001963 | epot = -22.0985208042931 | etot = -17.742976368258 +412000 ekin = 2.51301623282815 | erot = 2.67550740966365 | epot = -22.2078537029906 | etot = -17.0193300604988 +413000 ekin = 2.81407439938451 | erot = 3.21402559358062 | epot = -22.1310120840187 | etot = -16.1029120910536 +414000 ekin = 2.79247479268938 | erot = 2.73425265524033 | epot = -22.0977113063587 | etot = -16.570983858429 +415000 ekin = 2.47916660937974 | erot = 2.2538291443672 | epot = -22.1646477745644 | etot = -17.4316520208175 +416000 ekin = 3.33232223339091 | erot = 1.56386062957 | epot = -22.1461937000839 | etot = -17.250010837123 +417000 ekin = 3.95877285814837 | erot = 2.43917045295873 | epot = -22.0789469190762 | etot = -15.6810036079691 +418000 ekin = 2.77978041892218 | erot = 2.67961998913593 | epot = -21.9429456651673 | etot = -16.4835452571092 +419000 ekin = 2.38024484823696 | erot = 2.99229133054455 | epot = -21.8677152868896 | etot = -16.4951791081081 +420000 ekin = 1.80871194953159 | erot = 1.84151089264678 | epot = -21.8596865313185 | etot = -18.2094636891401 +421000 ekin = 1.25971024821532 | erot = 1.84154088985399 | epot = -21.8144945739243 | etot = -18.713243435855 +422000 ekin = 1.38801644153196 | erot = 2.76287955544763 | epot = -21.9448046693442 | etot = -17.7939086723646 +423000 ekin = 1.61378102360038 | erot = 3.08643589903684 | epot = -21.9876910184367 | etot = -17.2874740957995 +424000 ekin = 2.38187559636676 | erot = 2.03497345340564 | epot = -22.0529622043822 | etot = -17.6361131546098 +425000 ekin = 2.30172600419957 | erot = 2.56124787306544 | epot = -22.0909144547264 | etot = -17.2279405774613 +426000 ekin = 2.08135734353848 | erot = 3.11029155110106 | epot = -22.0318884881515 | etot = -16.8402395935119 +427000 ekin = 2.14905284759742 | erot = 2.44063059706749 | epot = -21.9221859408584 | etot = -17.3325024961935 +428000 ekin = 1.77884336055357 | erot = 1.65616500997461 | epot = -21.9003025672496 | etot = -18.4652941967214 +429000 ekin = 1.64634843235491 | erot = 2.54977814749917 | epot = -21.8505053104909 | etot = -17.6543787306368 +430000 ekin = 2.66566369380165 | erot = 2.85826638798746 | epot = -21.8749831872768 | etot = -16.3510531054877 +431000 ekin = 2.77262842672213 | erot = 1.57008239418362 | epot = -21.8682859290024 | etot = -17.5255751080967 +432000 ekin = 2.55459213758159 | erot = 1.62943387255927 | epot = -21.8357562133881 | etot = -17.6517302032472 +433000 ekin = 1.99645419170627 | erot = 2.46386731011038 | epot = -21.9426115259012 | etot = -17.4822900240846 +434000 ekin = 3.03855037499723 | erot = 2.70114732868002 | epot = -22.0521183162706 | etot = -16.3124206125934 +435000 ekin = 3.56249359412514 | erot = 1.3916907800745 | epot = -22.1907087359577 | etot = -17.236524361758 +436000 ekin = 2.9919519436941 | erot = 2.00780906096746 | epot = -22.1944569501235 | etot = -17.194695945462 +437000 ekin = 3.22983002449305 | erot = 1.78457838368284 | epot = -22.2079862630257 | etot = -17.1935778548498 +438000 ekin = 2.89357954274282 | erot = 1.84712438388029 | epot = -22.1640149633625 | etot = -17.4233110367394 +439000 ekin = 2.43548109922482 | erot = 2.69725667220989 | epot = -22.15552566419 | etot = -17.0227878927552 +440000 ekin = 2.2623759777343 | erot = 3.0053291392984 | epot = -22.1911581748161 | etot = -16.9234530577834 +441000 ekin = 2.91169601545459 | erot = 2.87109172357543 | epot = -22.3349024428918 | etot = -16.5521147038618 +442000 ekin = 2.09099397022228 | erot = 1.73520313922453 | epot = -22.4051258365299 | etot = -18.5789287270831 +443000 ekin = 1.89190436364779 | erot = 2.00338805773041 | epot = -22.4571595679749 | etot = -18.5618671465967 +444000 ekin = 2.07260612589383 | erot = 2.15261859961606 | epot = -22.4762155543905 | etot = -18.2509908288806 +445000 ekin = 2.10794043544074 | erot = 2.27849500108989 | epot = -22.5289113655649 | etot = -18.1424759290343 +446000 ekin = 2.43249129570082 | erot = 2.85798785841701 | epot = -22.5578450371516 | etot = -17.2673658830337 +447000 ekin = 2.18427449291498 | erot = 2.99487058702881 | epot = -22.633209665243 | etot = -17.4540645852992 +448000 ekin = 2.33125251154888 | erot = 2.9537271150568 | epot = -22.6544934614541 | etot = -17.3695138348484 +449000 ekin = 2.34830834177129 | erot = 2.93433423081578 | epot = -22.6524261630772 | etot = -17.3697835904901 +450000 ekin = 1.83059864091627 | erot = 1.69583085832556 | epot = -22.5959718193007 | etot = -19.0695423200588 +451000 ekin = 1.97008420530444 | erot = 1.93005789483906 | epot = -22.6042016377466 | etot = -18.7040595376031 +452000 ekin = 1.36031716300771 | erot = 1.88416646481667 | epot = -22.5654500281941 | etot = -19.3209664003698 +453000 ekin = 2.08394677326601 | erot = 2.55637003071468 | epot = -22.3996731437447 | etot = -17.759356339764 +454000 ekin = 1.46122132979162 | erot = 2.1932504558799 | epot = -22.2559783518549 | etot = -18.6015065661834 +455000 ekin = 1.66159562683808 | erot = 2.72214658377912 | epot = -22.1100881227337 | etot = -17.7263459121165 +456000 ekin = 2.35139002285135 | erot = 1.99736695780608 | epot = -22.0265180206658 | etot = -17.6777610400084 +457000 ekin = 2.02337666353787 | erot = 2.36288174917835 | epot = -21.9870419865869 | etot = -17.6007835738707 +458000 ekin = 1.74388716034853 | erot = 2.25704341258625 | epot = -22.0124765184275 | etot = -18.0115459454927 +459000 ekin = 2.51302694941202 | erot = 2.31610812350976 | epot = -22.0905335599533 | etot = -17.2613984870315 +460000 ekin = 2.20235980851235 | erot = 2.00073208070752 | epot = -22.0624281815267 | etot = -17.8593362923069 +461000 ekin = 2.27697813860512 | erot = 2.92153186175593 | epot = -22.0043780203814 | etot = -16.8058680200203 +462000 ekin = 2.61751250591993 | erot = 1.79446367088042 | epot = -22.034566251344 | etot = -17.6225900745436 +463000 ekin = 2.59076396942114 | erot = 3.29959067151568 | epot = -21.9680597931617 | etot = -16.0777051522249 +464000 ekin = 2.18897688760924 | erot = 2.37342380725927 | epot = -21.9014176363544 | etot = -17.3390169414859 +465000 ekin = 2.55336811292171 | erot = 3.60208553232432 | epot = -21.8218243406516 | etot = -15.6663706954055 +466000 ekin = 1.98087073364117 | erot = 2.88377492118972 | epot = -21.8240279062597 | etot = -16.9593822514288 +467000 ekin = 1.63963444033068 | erot = 2.61720118783829 | epot = -21.9072568806945 | etot = -17.6504212525255 +468000 ekin = 1.11353612829142 | erot = 3.36362638075105 | epot = -21.9675488944805 | etot = -17.490386385438 +469000 ekin = 1.72228182007047 | erot = 2.77659856111655 | epot = -21.9967286251288 | etot = -17.4978482439417 +470000 ekin = 1.86957223270987 | erot = 2.88200736733016 | epot = -22.0532435258199 | etot = -17.3016639257798 +471000 ekin = 2.73889257490363 | erot = 2.33805868565127 | epot = -22.1018048913227 | etot = -17.0248536307678 +472000 ekin = 2.69336835751318 | erot = 2.14497398823592 | epot = -22.1783319655624 | etot = -17.3399896198133 +473000 ekin = 2.2834012228809 | erot = 2.08779065134065 | epot = -22.2062566289287 | etot = -17.8350647547071 +474000 ekin = 2.23753393343421 | erot = 2.18021358366907 | epot = -22.2186470965394 | etot = -17.8008995794361 +475000 ekin = 2.52144972759887 | erot = 2.10742888877791 | epot = -22.2200376200674 | etot = -17.5911590036907 +476000 ekin = 2.21750839437398 | erot = 1.76993465858266 | epot = -22.1228407781581 | etot = -18.1353977252014 +477000 ekin = 2.49639604606981 | erot = 2.38997154938614 | epot = -22.0914213950017 | etot = -17.2050537995458 +478000 ekin = 1.92476411077776 | erot = 2.05068061613981 | epot = -22.1165013146126 | etot = -18.141056587695 +479000 ekin = 2.27814065534966 | erot = 3.09902158675158 | epot = -22.1039609371193 | etot = -16.726798695018 +480000 ekin = 1.67684718675217 | erot = 2.75298455656157 | epot = -22.107572084908 | etot = -17.6777403415942 +481000 ekin = 1.82004035403442 | erot = 2.94243611851488 | epot = -22.0570042571709 | etot = -17.2945277846216 +482000 ekin = 2.15620792762657 | erot = 2.07225318674483 | epot = -22.0195504604851 | etot = -17.7910893461137 +483000 ekin = 1.49597937205778 | erot = 1.99748154603235 | epot = -21.9846691787552 | etot = -18.4912082606651 +484000 ekin = 1.84801031899852 | erot = 2.3383930614213 | epot = -22.057622803598 | etot = -17.8712194231781 +485000 ekin = 1.63994449952444 | erot = 2.49474020960602 | epot = -22.0873319631203 | etot = -17.9526472539898 +486000 ekin = 1.86878710017944 | erot = 2.15121977781065 | epot = -22.0738722433192 | etot = -18.0538653653291 +487000 ekin = 2.36575535267025 | erot = 3.10125401276719 | epot = -22.1449283981519 | etot = -16.6779190327145 +488000 ekin = 2.28442246943194 | erot = 3.25683393002513 | epot = -22.0988506325681 | etot = -16.557594233111 +489000 ekin = 2.42271484675 | erot = 2.54542145912102 | epot = -22.0089541135478 | etot = -17.0408178076768 +490000 ekin = 2.15700463004959 | erot = 3.54046810332719 | epot = -21.9046622319151 | etot = -16.2071894985383 +491000 ekin = 2.21877065503535 | erot = 2.48745097433189 | epot = -21.7908019627883 | etot = -17.084580333421 +492000 ekin = 2.42517437413502 | erot = 2.76311171529555 | epot = -21.7601749752715 | etot = -16.5718888858409 +493000 ekin = 1.78704503482097 | erot = 2.27560531894265 | epot = -21.8193757259442 | etot = -17.7567253721806 +494000 ekin = 2.08676036701357 | erot = 2.99995787427429 | epot = -21.8611051542237 | etot = -16.7743869129358 +495000 ekin = 2.13526814465422 | erot = 2.49327519100043 | epot = -21.9512664264056 | etot = -17.322723090751 +496000 ekin = 2.04396376951351 | erot = 2.616205394925 | epot = -21.9926597066748 | etot = -17.3324905422363 +497000 ekin = 2.5138400992253 | erot = 1.7082513952147 | epot = -21.9316573881385 | etot = -17.7095658936985 +498000 ekin = 2.15599563393455 | erot = 1.7954584756616 | epot = -21.8684844569259 | etot = -17.9170303473298 +499000 ekin = 3.01748439271979 | erot = 1.75754764004202 | epot = -21.8933218662966 | etot = -17.1182898335348 +500000 ekin = 2.75260982901106 | erot = 2.51842805388796 | epot = -21.8943946135574 | etot = -16.6233567306584 +501000 ekin = 2.67931288903133 | erot = 3.01160406637169 | epot = -21.7750232065095 | etot = -16.0841062511065 +502000 ekin = 1.89360306182664 | erot = 3.89791941021244 | epot = -21.6573468922303 | etot = -15.8658244201912 +503000 ekin = 1.79321931974651 | erot = 2.94204976962205 | epot = -21.4684952360274 | etot = -16.7332261466588 +504000 ekin = 1.67757593959819 | erot = 3.03667519772553 | epot = -21.3740498051044 | etot = -16.6597986677806 +505000 ekin = 2.71879314198246 | erot = 2.13553052885653 | epot = -21.3748517524097 | etot = -16.5205280815707 +506000 ekin = 2.26416011641767 | erot = 2.0398390357387 | epot = -21.3744734731022 | etot = -17.0704743209458 +507000 ekin = 3.1361217829786 | erot = 2.43598082432092 | epot = -21.4637546760327 | etot = -15.8916520687332 +508000 ekin = 2.50986106907072 | erot = 2.54739392181407 | epot = -21.6231060681634 | etot = -16.5658510772786 +509000 ekin = 2.11468804004737 | erot = 2.82565642150503 | epot = -21.7737120459513 | etot = -16.8333675843989 +510000 ekin = 2.15001055304937 | erot = 1.42727017491937 | epot = -21.8417870574445 | etot = -18.2645063294758 +511000 ekin = 2.52545394756595 | erot = 2.75161712587392 | epot = -21.9086876613652 | etot = -16.6316165879253 +512000 ekin = 2.30866784309731 | erot = 2.74554976662385 | epot = -21.9096028664776 | etot = -16.8553852567564 +513000 ekin = 2.48902345599678 | erot = 2.14823762928075 | epot = -21.8729373600799 | etot = -17.2356762748023 +514000 ekin = 2.80071109914887 | erot = 2.54489890263222 | epot = -22.0260959105663 | etot = -16.6804859087852 +515000 ekin = 2.54951114466539 | erot = 1.81830545608794 | epot = -22.1182236024141 | etot = -17.7504070016608 +516000 ekin = 2.82429114749713 | erot = 2.22223190254033 | epot = -22.2027443448738 | etot = -17.1562212948364 +517000 ekin = 2.0440652856654 | erot = 2.05268379810237 | epot = -22.2270328001489 | etot = -18.1302837163811 +518000 ekin = 2.19098614618396 | erot = 2.7523349010516 | epot = -22.2209877154936 | etot = -17.2776666682581 +519000 ekin = 2.24036502705842 | erot = 2.22532553600967 | epot = -22.3180679614818 | etot = -17.8523773984137 +520000 ekin = 1.89058003919379 | erot = 2.20041260684313 | epot = -22.4024099853452 | etot = -18.3114173393082 +521000 ekin = 2.59235690452872 | erot = 1.87867658572832 | epot = -22.562076955749 | etot = -18.0910434654919 +522000 ekin = 3.47612340255834 | erot = 1.7709131526267 | epot = -22.6560013672146 | etot = -17.4089648120295 +523000 ekin = 2.8697331156896 | erot = 2.45931135481363 | epot = -22.7015468187877 | etot = -17.3725023482845 +524000 ekin = 2.43256318748704 | erot = 2.35726786724124 | epot = -22.6382055947878 | etot = -17.8483745400596 +525000 ekin = 1.5862220801759 | erot = 2.67712917770356 | epot = -22.6016118927226 | etot = -18.3382606348432 +526000 ekin = 1.68941966580457 | erot = 1.5638733848976 | epot = -22.5489288531345 | etot = -19.2956358024323 +527000 ekin = 2.25322718958956 | erot = 1.91908592764601 | epot = -22.4417549635527 | etot = -18.2694418463171 +528000 ekin = 2.66412422381676 | erot = 2.81704928468163 | epot = -22.4249217233809 | etot = -16.9437482148825 +529000 ekin = 2.68379060052796 | erot = 3.01205280488721 | epot = -22.4295574265689 | etot = -16.7337140211537 +530000 ekin = 2.58073227215729 | erot = 2.12870295195894 | epot = -22.2883086480464 | etot = -17.5788734239302 +531000 ekin = 2.96770457160389 | erot = 2.35391742452841 | epot = -22.1856711738739 | etot = -16.8640491777416 +532000 ekin = 2.56038964370913 | erot = 2.30878740571672 | epot = -22.1997799918585 | etot = -17.3306029424327 +533000 ekin = 2.47143825522096 | erot = 2.96338918263318 | epot = -22.2065233272061 | etot = -16.7716958893519 +534000 ekin = 2.10112886915673 | erot = 2.06170735341251 | epot = -22.2366529232829 | etot = -18.0738167007137 +535000 ekin = 3.76894732289841 | erot = 2.64646203076619 | epot = -22.2276744548843 | etot = -15.8122651012197 +536000 ekin = 2.7696162230836 | erot = 1.95805234771211 | epot = -22.1654529173378 | etot = -17.4377843465421 +537000 ekin = 2.84154244437419 | erot = 2.62704512023094 | epot = -22.0849688339382 | etot = -16.6163812693331 +538000 ekin = 2.68442563578381 | erot = 2.11441739965432 | epot = -22.0125688846837 | etot = -17.2137258492456 +539000 ekin = 2.71421145807769 | erot = 2.40915133591281 | epot = -22.1313332530722 | etot = -17.0079704590817 +540000 ekin = 2.43518407250594 | erot = 2.49363815768251 | epot = -22.2749632551308 | etot = -17.3461410249423 +541000 ekin = 3.40444579850308 | erot = 2.79359613706622 | epot = -22.3466180642397 | etot = -16.1485761286704 +542000 ekin = 2.43275262454037 | erot = 2.8926712949891 | epot = -22.3556133688796 | etot = -17.0301894493501 +543000 ekin = 2.33375802900842 | erot = 2.87822266703542 | epot = -22.354503031092 | etot = -17.1425223350481 +544000 ekin = 2.20372430185484 | erot = 1.45976141003991 | epot = -22.3227611685585 | etot = -18.6592754566638 +545000 ekin = 2.44172510086271 | erot = 2.14426798374485 | epot = -22.3064237448696 | etot = -17.720430660262 +546000 ekin = 1.97339115566054 | erot = 2.22847557914697 | epot = -22.2636677476263 | etot = -18.0618010128188 +547000 ekin = 2.54002001617723 | erot = 1.88945501268906 | epot = -22.2158143598027 | etot = -17.7863393309365 +548000 ekin = 1.68526456618955 | erot = 1.65049155866197 | epot = -22.1214578510425 | etot = -18.785701726191 +549000 ekin = 1.87014690614356 | erot = 2.68376307045224 | epot = -22.3040985050477 | etot = -17.7501885284519 +550000 ekin = 1.81229877740871 | erot = 1.59166644509217 | epot = -22.4560870327802 | etot = -19.0521218102793 +551000 ekin = 2.18773128797504 | erot = 2.27087388044657 | epot = -22.5158361799812 | etot = -18.0572310115596 +552000 ekin = 2.05249497087455 | erot = 2.50761265901319 | epot = -22.5719393540102 | etot = -18.0118317241225 +553000 ekin = 2.95454924363313 | erot = 2.14558063826841 | epot = -22.6616695566088 | etot = -17.5615396747072 +554000 ekin = 2.82907288726943 | erot = 1.93583607418193 | epot = -22.8114472173086 | etot = -18.0465382558572 +555000 ekin = 2.39144194814065 | erot = 2.2690346714923 | epot = -22.8607776699892 | etot = -18.2003010503562 +556000 ekin = 2.29377130416531 | erot = 2.58082229477443 | epot = -22.9123559572369 | etot = -18.0377623582971 +557000 ekin = 2.83942594504113 | erot = 1.46630323732685 | epot = -22.9955247836668 | etot = -18.6897956012988 +558000 ekin = 2.74466783679159 | erot = 2.01704787654692 | epot = -23.0269943374553 | etot = -18.2652786241168 +559000 ekin = 3.32013685758138 | erot = 2.33070588278053 | epot = -23.0724440783111 | etot = -17.4216013379492 +560000 ekin = 3.06575014862304 | erot = 2.3240772361437 | epot = -23.058452120381 | etot = -17.6686247356143 +561000 ekin = 2.86678914129224 | erot = 2.08494050984238 | epot = -22.9757329649367 | etot = -18.0240033138021 +562000 ekin = 3.27279507804287 | erot = 2.51484206553918 | epot = -22.8763400547029 | etot = -17.0887029111208 +563000 ekin = 2.66038070150058 | erot = 1.64116530766161 | epot = -22.8496252506975 | etot = -18.5480792415353 +564000 ekin = 2.80463843262516 | erot = 2.5266606313835 | epot = -22.8040898690867 | etot = -17.4727908050781 +565000 ekin = 2.64623234011006 | erot = 2.04560086917498 | epot = -22.7528472206811 | etot = -18.061014011396 +566000 ekin = 2.31861442156789 | erot = 2.17941765713979 | epot = -22.7559143900141 | etot = -18.2578823113064 +567000 ekin = 1.93226018038665 | erot = 2.82020539323088 | epot = -22.7113049006743 | etot = -17.9588393270567 +568000 ekin = 2.20139908423163 | erot = 2.2173471641442 | epot = -22.7309883250972 | etot = -18.3122420767214 +569000 ekin = 2.47190977966691 | erot = 2.65968832242268 | epot = -22.6724326928842 | etot = -17.5408345907946 +570000 ekin = 2.43697670060318 | erot = 1.88669477532771 | epot = -22.6652860601546 | etot = -18.3416145842237 +571000 ekin = 2.89014026085716 | erot = 2.95617526869999 | epot = -22.6585089246084 | etot = -16.8121933950513 +572000 ekin = 1.93596118948626 | erot = 3.77290573984751 | epot = -22.617986049283 | etot = -16.9091191199493 +573000 ekin = 2.4045463471171 | erot = 2.31316721466246 | epot = -22.5941857447927 | etot = -17.8764721830131 +574000 ekin = 1.69171540489496 | erot = 2.32939319863948 | epot = -22.6485181547002 | etot = -18.6274095511658 +575000 ekin = 1.84147438222145 | erot = 1.86451086977537 | epot = -22.7257563443532 | etot = -19.0197710923563 +576000 ekin = 3.22125710715105 | erot = 2.95826776175095 | epot = -22.6735851458116 | etot = -16.4940602769096 +577000 ekin = 2.86653117003728 | erot = 2.88010628292138 | epot = -22.6061554079341 | etot = -16.8595179549754 +578000 ekin = 2.38032268318987 | erot = 2.76710196021751 | epot = -22.4015577816723 | etot = -17.2541331382649 +579000 ekin = 2.40088404436444 | erot = 1.99411758494037 | epot = -22.2441807849414 | etot = -17.8491791556366 +580000 ekin = 2.62022193893445 | erot = 1.97772953708398 | epot = -22.0981459564787 | etot = -17.5001944804602 +581000 ekin = 2.04609920382364 | erot = 3.0202197191752 | epot = -21.9713515823037 | etot = -16.9050326593048 +582000 ekin = 2.17556767215606 | erot = 3.10885810822424 | epot = -21.8451828402321 | etot = -16.5607570598518 +583000 ekin = 2.12792577884129 | erot = 2.7142175246668 | epot = -21.8090540347999 | etot = -16.9669107312918 +584000 ekin = 2.99197492146328 | erot = 2.6185428756741 | epot = -21.8014711662179 | etot = -16.1909533690805 +585000 ekin = 2.41600413666429 | erot = 2.49968403996098 | epot = -21.7582079751419 | etot = -16.8425197985166 +586000 ekin = 3.57880609498067 | erot = 1.99026777936244 | epot = -21.7793800190221 | etot = -16.210306144679 +587000 ekin = 3.53569318795882 | erot = 1.96660845702856 | epot = -21.7574182658133 | etot = -16.255116620826 +588000 ekin = 2.80385841316338 | erot = 1.58927534150911 | epot = -21.7290695763864 | etot = -17.3359358217139 +589000 ekin = 2.31178332958482 | erot = 2.19605556561577 | epot = -21.7771889269559 | etot = -17.2693500317553 +590000 ekin = 2.57159955455667 | erot = 1.71441305781987 | epot = -21.7801644206484 | etot = -17.4941518082718 +591000 ekin = 1.90027597697965 | erot = 3.80794292513097 | epot = -21.8693595444135 | etot = -16.1611406423028 +592000 ekin = 2.10287592275467 | erot = 2.85572724854609 | epot = -21.913245820329 | etot = -16.9546426490283 +593000 ekin = 1.6630679389305 | erot = 2.45937970675131 | epot = -21.9499391362603 | etot = -17.8274914905785 +594000 ekin = 1.85147249869391 | erot = 2.37596539021724 | epot = -22.0748010854883 | etot = -17.8473631965771 +595000 ekin = 1.62801913987931 | erot = 2.13760745860405 | epot = -22.2650343535207 | etot = -18.4994077550374 +596000 ekin = 1.8507787756783 | erot = 1.55277904845736 | epot = -22.3618759263936 | etot = -18.9583181022579 +597000 ekin = 2.21873580046471 | erot = 2.31247364510899 | epot = -22.4218283315557 | etot = -17.890618885982 +598000 ekin = 1.87152940931079 | erot = 3.02770945247868 | epot = -22.4928956008977 | etot = -17.5936567391082 +599000 ekin = 2.84160333456022 | erot = 2.19202304201413 | epot = -22.5210806388342 | etot = -17.4874542622599 +600000 ekin = 2.63824255094171 | erot = 2.13280883838531 | epot = -22.4361553764614 | etot = -17.6651039871344 +601000 ekin = 2.95991744971104 | erot = 3.20891387142304 | epot = -22.3089419175364 | etot = -16.1401105964023 +602000 ekin = 2.94287171911394 | erot = 2.6801544694314 | epot = -22.2205146380182 | etot = -16.5974884494729 +603000 ekin = 2.59651768027528 | erot = 2.70994674634417 | epot = -22.1626040385702 | etot = -16.8561396119508 +604000 ekin = 1.79237423166219 | erot = 2.11638057359598 | epot = -22.1934477586593 | etot = -18.2846929534011 +605000 ekin = 1.83068473031177 | erot = 2.2795743818689 | epot = -22.2254684973409 | etot = -18.1152093851602 +606000 ekin = 2.3318585405123 | erot = 2.19626289047853 | epot = -22.1692552740621 | etot = -17.6411338430713 +607000 ekin = 2.71184010988538 | erot = 2.97108975720824 | epot = -22.1536579122904 | etot = -16.4707280451968 +608000 ekin = 2.42009843612052 | erot = 2.41609650030392 | epot = -22.110570505977 | etot = -17.2743755695526 +609000 ekin = 1.88829617874732 | erot = 2.63290748875975 | epot = -21.9999822454274 | etot = -17.4787785779203 +610000 ekin = 3.00361337450473 | erot = 2.17709909276457 | epot = -21.9226199750059 | etot = -16.7419075077366 +611000 ekin = 2.45804405292799 | erot = 2.74756316868512 | epot = -21.9190479764513 | etot = -16.7134407548382 +612000 ekin = 2.52217588638913 | erot = 2.13391253924555 | epot = -21.9544188877756 | etot = -17.2983304621409 +613000 ekin = 3.03676008822021 | erot = 2.11841016157454 | epot = -22.0017416346015 | etot = -16.8465713848068 +614000 ekin = 2.28555718180926 | erot = 3.0054092802111 | epot = -22.0761965028491 | etot = -16.7852300408287 +615000 ekin = 1.68510287809685 | erot = 2.62386193001633 | epot = -22.0327006368424 | etot = -17.7237358287293 +616000 ekin = 1.93880828018173 | erot = 2.84237691352502 | epot = -22.0612297066235 | etot = -17.2800445129167 +617000 ekin = 2.16704933019324 | erot = 2.51662857724103 | epot = -22.0595683849495 | etot = -17.3758904775152 +618000 ekin = 3.09933970351517 | erot = 2.74545743402536 | epot = -22.0170483082271 | etot = -16.1722511706866 +619000 ekin = 3.43176670397203 | erot = 2.12195823326365 | epot = -21.9875785418916 | etot = -16.4338536046559 +620000 ekin = 4.28780554984769 | erot = 2.22709196760532 | epot = -21.9605251543896 | etot = -15.4456276369365 +621000 ekin = 3.08171244822519 | erot = 2.57159564010567 | epot = -21.9025163812385 | etot = -16.2492082929076 +622000 ekin = 2.7316886075754 | erot = 2.62820058118157 | epot = -21.8412338594045 | etot = -16.4813446706475 +623000 ekin = 2.85452079274903 | erot = 2.89943500147414 | epot = -21.6852443941174 | etot = -15.9312885998942 +624000 ekin = 2.03273271064347 | erot = 3.41737453659275 | epot = -21.5180611078538 | etot = -16.0679538606176 +625000 ekin = 2.93860287466086 | erot = 2.6777302302364 | epot = -21.3855450802948 | etot = -15.7692119753975 +626000 ekin = 2.62772208534213 | erot = 2.18165419852424 | epot = -21.3747765229082 | etot = -16.5654002390418 +627000 ekin = 2.31977818310487 | erot = 2.39484209061113 | epot = -21.4372090577008 | etot = -16.7225887839848 +628000 ekin = 2.22183190227213 | erot = 2.76412054255638 | epot = -21.5969078027883 | etot = -16.6109553579598 +629000 ekin = 2.21761787409423 | erot = 1.98066149405245 | epot = -21.7578561859453 | etot = -17.5595768177986 +630000 ekin = 2.47350494176362 | erot = 2.13931642231374 | epot = -21.7773766650218 | etot = -17.1645553009445 +631000 ekin = 2.05047278007876 | erot = 1.79296462014617 | epot = -21.7869475538217 | etot = -17.9435101535968 +632000 ekin = 1.64845667747476 | erot = 3.28396465847893 | epot = -21.8333012025329 | etot = -16.9008798665792 +633000 ekin = 2.3500132343185 | erot = 2.3390975332878 | epot = -21.9539301797825 | etot = -17.2648194121762 +634000 ekin = 2.35704893279043 | erot = 2.46483254513169 | epot = -22.0204072629832 | etot = -17.1985257850611 +635000 ekin = 1.98907577162676 | erot = 3.37071781675284 | epot = -22.0690924871448 | etot = -16.7092988987652 +636000 ekin = 2.50984196335062 | erot = 2.48688994533939 | epot = -22.0714906026256 | etot = -17.0747586939356 +637000 ekin = 2.77501317112847 | erot = 2.80709332215511 | epot = -21.9923972278242 | etot = -16.4102907345407 +638000 ekin = 2.43799129572064 | erot = 2.7900719850463 | epot = -22.0591413868446 | etot = -16.8310781060777 +639000 ekin = 1.88073995546173 | erot = 2.09679843998312 | epot = -22.0499554202513 | etot = -18.0724170248065 +640000 ekin = 2.08188045172846 | erot = 3.35894090591918 | epot = -21.9976614802368 | etot = -16.5568401225891 +641000 ekin = 2.09182367506332 | erot = 2.24091541077085 | epot = -22.0969663672431 | etot = -17.7642272814089 +642000 ekin = 2.29630816296813 | erot = 2.69496533496291 | epot = -22.1529742829376 | etot = -17.1617007850065 +643000 ekin = 2.73580847855276 | erot = 2.20074971448877 | epot = -22.0965451673466 | etot = -17.1599869743051 +644000 ekin = 2.877547382531 | erot = 3.41752705378106 | epot = -22.1314614085221 | etot = -15.8363869722101 +645000 ekin = 2.42917363330758 | erot = 2.10617126422418 | epot = -22.0684179655268 | etot = -17.533073067995 +646000 ekin = 2.69471397724187 | erot = 1.80009045225372 | epot = -21.8990804127739 | etot = -17.4042759832783 +647000 ekin = 2.47700110999565 | erot = 1.99221351689819 | epot = -21.6986646197608 | etot = -17.229449992867 +648000 ekin = 2.27330015032657 | erot = 1.67398094476719 | epot = -21.7984825454864 | etot = -17.8512014503927 +649000 ekin = 2.5628574039565 | erot = 1.74923984575743 | epot = -22.1937498986979 | etot = -17.881652648984 +650000 ekin = 2.76035969172866 | erot = 2.20984080080438 | epot = -22.3536470081185 | etot = -17.3834465155854 +651000 ekin = 2.262551545237 | erot = 3.27496991661067 | epot = -22.4274148303114 | etot = -16.8898933684638 +652000 ekin = 2.3727982819665 | erot = 2.29630046443082 | epot = -22.4456643066011 | etot = -17.7765655602038 +653000 ekin = 2.07651844100825 | erot = 2.14699861111497 | epot = -22.4487464586908 | etot = -18.2252294065676 +654000 ekin = 2.31499263290336 | erot = 1.84798657187726 | epot = -22.471548114837 | etot = -18.3085689100564 +655000 ekin = 2.12344600536595 | erot = 1.79742316518918 | epot = -22.4407504825061 | etot = -18.519881311951 +656000 ekin = 2.44238672537433 | erot = 2.33314467296101 | epot = -22.4050518721077 | etot = -17.6295204737724 +657000 ekin = 2.44684720738067 | erot = 2.87010904355218 | epot = -22.3954429054341 | etot = -17.0784866545012 +658000 ekin = 2.49369435044193 | erot = 2.86933833355583 | epot = -22.3577847118898 | etot = -16.9947520278921 +659000 ekin = 3.38707666874149 | erot = 2.79117377884123 | epot = -22.2233688708269 | etot = -16.0451184232442 +660000 ekin = 2.69464750718905 | erot = 1.98877163007961 | epot = -22.0868371976707 | etot = -17.403418060402 +661000 ekin = 2.2148438610813 | erot = 2.52686187560576 | epot = -21.9324475602905 | etot = -17.1907418236035 +662000 ekin = 2.04483468145689 | erot = 2.52786214958084 | epot = -21.8656118118386 | etot = -17.2929149808009 +663000 ekin = 2.25554994547888 | erot = 2.29981193022507 | epot = -21.812115133329 | etot = -17.256753257625 +664000 ekin = 2.38378154392877 | erot = 1.87242521142835 | epot = -21.7163692740767 | etot = -17.4601625187195 +665000 ekin = 2.64936843119576 | erot = 2.2989986114753 | epot = -21.6597356727187 | etot = -16.7113686300476 +666000 ekin = 1.64494457505824 | erot = 2.30638161556456 | epot = -21.5641898301393 | etot = -17.6128636395165 +667000 ekin = 1.65735220589392 | erot = 2.82614341732318 | epot = -21.4751653585362 | etot = -16.9916697353191 +668000 ekin = 2.49844825113869 | erot = 3.27950898400314 | epot = -21.3387145475146 | etot = -15.5607573123727 +669000 ekin = 1.61611201967415 | erot = 2.67203522811057 | epot = -21.2655442255718 | etot = -16.9773969777871 +670000 ekin = 2.23077474650818 | erot = 2.61363425835144 | epot = -21.2008892493679 | etot = -16.3564802445083 +671000 ekin = 2.26765830930916 | erot = 2.16388121545907 | epot = -21.1515274648835 | etot = -16.7199879401153 +672000 ekin = 1.94916146819698 | erot = 1.65479713709716 | epot = -21.0650678898704 | etot = -17.4611092845762 +673000 ekin = 1.92556066199439 | erot = 2.07900172108796 | epot = -21.0394363569888 | etot = -17.0348739739065 +674000 ekin = 2.12432357869025 | erot = 2.16781085660272 | epot = -21.0725830613714 | etot = -16.7804486260784 +675000 ekin = 2.06851819258986 | erot = 2.48317287761026 | epot = -21.1036073609477 | etot = -16.5519162907476 +676000 ekin = 2.45484997181755 | erot = 2.79183078710855 | epot = -21.1301283632782 | etot = -15.8834476043521 +677000 ekin = 2.20334154136532 | erot = 2.62444584525113 | epot = -21.1495626618894 | etot = -16.321775275273 +678000 ekin = 2.1472401432145 | erot = 2.79545747432262 | epot = -21.0405241444794 | etot = -16.0978265269423 +679000 ekin = 2.17033413623502 | erot = 2.18513653140294 | epot = -20.9421185444833 | etot = -16.5866478768454 +680000 ekin = 2.0995303513191 | erot = 2.68744418062154 | epot = -20.96987060062 | etot = -16.1828960686793 +681000 ekin = 2.18304447310098 | erot = 1.84812119436561 | epot = -21.0743862151371 | etot = -17.0432205476705 +682000 ekin = 3.04278123794939 | erot = 2.40409586716963 | epot = -21.0797568548333 | etot = -15.6328797497143 +683000 ekin = 2.86269023881706 | erot = 2.09728443896194 | epot = -21.0991655055583 | etot = -16.1391908277793 +684000 ekin = 1.98767037715953 | erot = 2.99591968828981 | epot = -21.1362036730577 | etot = -16.1526136076083 +685000 ekin = 1.57295457528713 | erot = 2.03034771002018 | epot = -21.146987158564 | etot = -17.5436848732567 +686000 ekin = 2.37743960028747 | erot = 2.54064910359146 | epot = -21.1479154694211 | etot = -16.2298267655421 +687000 ekin = 1.90905424981708 | erot = 2.87649471802563 | epot = -21.1390488337729 | etot = -16.3534998659302 +688000 ekin = 2.6274055742777 | erot = 2.25087525520177 | epot = -21.1259808926564 | etot = -16.2477000631769 +689000 ekin = 2.6802663035185 | erot = 2.65264291183039 | epot = -21.2405393346747 | etot = -15.9076301193258 +690000 ekin = 2.56393304559926 | erot = 2.48495065222978 | epot = -21.4016015121778 | etot = -16.3527178143488 +691000 ekin = 2.1927043501829 | erot = 2.52704457861404 | epot = -21.506826556612 | etot = -16.787077627815 +692000 ekin = 2.34077396593209 | erot = 3.24867065054243 | epot = -21.5176021816804 | etot = -15.9281575652059 +693000 ekin = 2.29029075483228 | erot = 3.0057489559252 | epot = -21.5358866889499 | etot = -16.2398469781924 +694000 ekin = 2.65674046511192 | erot = 2.58629868712489 | epot = -21.7490636357026 | etot = -16.5060244834658 +695000 ekin = 2.43126197328691 | erot = 1.19706323700546 | epot = -21.9401398969726 | etot = -18.3118146866802 +696000 ekin = 1.81474808623754 | erot = 1.46920096781106 | epot = -21.9089223337524 | etot = -18.6249732797038 +697000 ekin = 2.39476771383886 | erot = 2.11183502257124 | epot = -21.9420332766104 | etot = -17.4354305402003 +698000 ekin = 2.35926337724266 | erot = 1.92783320549514 | epot = -22.0277191263435 | etot = -17.7406225436058 +699000 ekin = 2.48176872675362 | erot = 2.56000644090342 | epot = -22.0212596021869 | etot = -16.9794844345298 +700000 ekin = 2.14129959772679 | erot = 2.29861037684922 | epot = -21.9318234409146 | etot = -17.4919134663386 +701000 ekin = 2.17049668499625 | erot = 2.20225192400486 | epot = -21.8245513288874 | etot = -17.4518027198863 +702000 ekin = 1.5627527155292 | erot = 2.01171151000641 | epot = -21.7865003044461 | etot = -18.2120360789105 +703000 ekin = 2.06065227779357 | erot = 2.17329473717683 | epot = -21.8026608939335 | etot = -17.5687138789631 +704000 ekin = 2.81952809577903 | erot = 1.94266087393333 | epot = -21.8212186788769 | etot = -17.0590297091645 +705000 ekin = 2.82050127519937 | erot = 2.18154028834385 | epot = -21.7752102636878 | etot = -16.7731687001446 +706000 ekin = 1.98267828238497 | erot = 2.32706466032389 | epot = -21.7893242385512 | etot = -17.4795812958423 +707000 ekin = 1.9119199256382 | erot = 2.05897787647106 | epot = -21.8430722730707 | etot = -17.8721744709615 +708000 ekin = 2.5016490217549 | erot = 2.18383615173375 | epot = -21.8544847432183 | etot = -17.1689995697297 +709000 ekin = 2.87304116461984 | erot = 2.56843564623617 | epot = -21.904442472254 | etot = -16.462965661398 +710000 ekin = 2.19867234802447 | erot = 2.26714812026436 | epot = -21.8819798989583 | etot = -17.4161594306695 +711000 ekin = 2.3389229861775 | erot = 1.44633862250317 | epot = -21.9197827259336 | etot = -18.1345211172529 +712000 ekin = 2.57005480809076 | erot = 2.28706559960511 | epot = -22.0346026838636 | etot = -17.1774822761678 +713000 ekin = 1.98393390580317 | erot = 2.33525788511068 | epot = -22.1280127822608 | etot = -17.8088209913469 +714000 ekin = 2.59844561627729 | erot = 2.10769412707773 | epot = -22.1916311346269 | etot = -17.4854913912719 +715000 ekin = 2.41851974197058 | erot = 3.7488852557719 | epot = -22.1607861798611 | etot = -15.9933811821187 +716000 ekin = 2.8418023132582 | erot = 2.85971600497616 | epot = -22.0686589684412 | etot = -16.3671406502068 +717000 ekin = 3.4484144493586 | erot = 3.22605040091157 | epot = -21.9727882885698 | etot = -15.2983234382996 +718000 ekin = 3.10436184228427 | erot = 3.94950630255782 | epot = -21.8709253031511 | etot = -14.817057158309 +719000 ekin = 2.37806574336789 | erot = 2.95502686702168 | epot = -21.8563367317646 | etot = -16.523244121375 +720000 ekin = 2.2124258408194 | erot = 3.13473166149202 | epot = -21.832964450767 | etot = -16.4858069484555 +721000 ekin = 1.6946894391771 | erot = 2.23193742756367 | epot = -21.7424084526643 | etot = -17.8157815859235 +722000 ekin = 1.90287140868432 | erot = 2.80483524098531 | epot = -21.7497487144859 | etot = -17.0420420648163 +723000 ekin = 2.36731223380046 | erot = 2.56327951769445 | epot = -21.6831418267135 | etot = -16.7525500752186 +724000 ekin = 1.73555921199202 | erot = 2.45238016332295 | epot = -21.6581802464112 | etot = -17.4702408710962 +725000 ekin = 2.29059437023039 | erot = 2.94575894857246 | epot = -21.7174261464808 | etot = -16.481072827678 +726000 ekin = 1.63483147798521 | erot = 2.30383185500799 | epot = -21.7564933587679 | etot = -17.8178300257747 +727000 ekin = 2.48240653489464 | erot = 3.20354227059193 | epot = -21.7912108634863 | etot = -16.1052620579997 +728000 ekin = 2.22769215153326 | erot = 2.1648907299462 | epot = -21.7890771091799 | etot = -17.3964942277004 +729000 ekin = 1.89768095869013 | erot = 1.65721672588089 | epot = -21.828690265207 | etot = -18.273792580636 +730000 ekin = 1.81050835100381 | erot = 2.15777747975243 | epot = -21.8264469741817 | etot = -17.8581611434255 +731000 ekin = 2.19898236908282 | erot = 2.98408098832205 | epot = -21.78613179764 | etot = -16.6030684402352 +732000 ekin = 2.43355047343304 | erot = 2.27170844305628 | epot = -21.6883863408736 | etot = -16.9831274243842 +733000 ekin = 3.07212273972684 | erot = 2.56783751855608 | epot = -21.7364921079322 | etot = -16.0965318496493 +734000 ekin = 2.38307322516835 | erot = 2.02726646964742 | epot = -21.7939757502944 | etot = -17.3836360554786 +735000 ekin = 2.14195880954704 | erot = 1.55624807241878 | epot = -21.8426856981853 | etot = -18.1444788162195 +736000 ekin = 2.14667447582536 | erot = 3.43698049451811 | epot = -21.9502105525335 | etot = -16.36655558219 +737000 ekin = 1.74866123585724 | erot = 3.5826697540454 | epot = -21.968815658378 | etot = -16.6374846684753 +738000 ekin = 2.03996249374858 | erot = 2.50844136963082 | epot = -22.0013918784186 | etot = -17.4529880150392 +739000 ekin = 1.85238190118677 | erot = 2.20010970404146 | epot = -22.0186271684577 | etot = -17.9661355632295 +740000 ekin = 2.8386294530065 | erot = 2.79090377324796 | epot = -22.0338814904879 | etot = -16.4043482642334 +741000 ekin = 2.46678702773208 | erot = 2.91050038280044 | epot = -22.0853235069127 | etot = -16.7080360963801 +742000 ekin = 2.7152902937519 | erot = 3.273956530725 | epot = -22.2140748190892 | etot = -16.2248279946123 +743000 ekin = 2.22536600879677 | erot = 3.2117924712642 | epot = -22.3431375024118 | etot = -16.9059790223509 +744000 ekin = 2.01371736615449 | erot = 3.7760139384218 | epot = -22.4261509869247 | etot = -16.6364196823485 +745000 ekin = 3.15730296333415 | erot = 2.31558796250712 | epot = -22.4108926873302 | etot = -16.9380017614889 +746000 ekin = 2.9774013013854 | erot = 2.63107362961469 | epot = -22.3694265664286 | etot = -16.7609516354285 +747000 ekin = 2.34209064832563 | erot = 2.04683419375202 | epot = -22.3628627944521 | etot = -17.9739379523744 +748000 ekin = 2.37156256463875 | erot = 2.40538773919509 | epot = -22.3979208424336 | etot = -17.6209705385998 +749000 ekin = 2.06136855553991 | erot = 2.76585915349199 | epot = -22.3831536512816 | etot = -17.5559259422497 +750000 ekin = 1.64656775002689 | erot = 2.38368935068671 | epot = -22.444703911786 | etot = -18.4144468110724 +751000 ekin = 1.78122844885826 | erot = 2.81833836133587 | epot = -22.533438976529 | etot = -17.9338721663349 +752000 ekin = 1.34730592473948 | erot = 1.45838401317446 | epot = -22.6090848823224 | etot = -19.8033949444084 +753000 ekin = 1.87571626319838 | erot = 2.4535466519722 | epot = -22.5588053116254 | etot = -18.2295423964548 +754000 ekin = 1.7497031355263 | erot = 2.74314075044427 | epot = -22.4698920344377 | etot = -17.9770481484671 +755000 ekin = 2.42081076696332 | erot = 2.41217357398055 | epot = -22.3964223120253 | etot = -17.5634379710815 +756000 ekin = 1.85475003398 | erot = 2.78259891044772 | epot = -22.3205962727121 | etot = -17.6832473282843 +757000 ekin = 1.97578050121357 | erot = 2.51781218539581 | epot = -22.1263927786386 | etot = -17.6328000920292 +758000 ekin = 1.22826853890876 | erot = 2.60763168332874 | epot = -21.9863700054334 | etot = -18.1504697831958 +759000 ekin = 2.21637457917735 | erot = 1.43949125248239 | epot = -22.1514665432947 | etot = -18.495600711635 +760000 ekin = 2.68033406797323 | erot = 2.41719679588396 | epot = -22.2590376675296 | etot = -17.1615068036724 +761000 ekin = 2.1753744063555 | erot = 2.27171718649737 | epot = -22.3344047362676 | etot = -17.8873131434147 +762000 ekin = 2.18577068124737 | erot = 1.66829735822053 | epot = -22.3621686129861 | etot = -18.5081005735182 +763000 ekin = 2.45478818575913 | erot = 3.35299551820638 | epot = -22.4281249366375 | etot = -16.620341232672 +764000 ekin = 2.82872579097199 | erot = 2.78775814269904 | epot = -22.4216595904294 | etot = -16.8051756567583 +765000 ekin = 1.82575545759014 | erot = 2.7623896973924 | epot = -22.3222506299713 | etot = -17.7341054749887 +766000 ekin = 2.64667028577447 | erot = 2.30816231818549 | epot = -22.1784504992491 | etot = -17.2236178952891 +767000 ekin = 2.5751886312018 | erot = 2.85636091304187 | epot = -22.0829371218307 | etot = -16.651387577587 +768000 ekin = 1.86419535586237 | erot = 2.77038508826208 | epot = -22.1032134089885 | etot = -17.4686329648641 +769000 ekin = 2.39682103653439 | erot = 2.30725355924694 | epot = -22.1808553751715 | etot = -17.4767807793902 +770000 ekin = 2.47007838986712 | erot = 3.23244425991329 | epot = -22.2845706013469 | etot = -16.5820479515665 +771000 ekin = 2.32978280625416 | erot = 2.29082247939232 | epot = -22.3223780040389 | etot = -17.7017727183924 +772000 ekin = 2.26109456847871 | erot = 3.00930315380545 | epot = -22.420252339108 | etot = -17.1498546168239 +773000 ekin = 2.23291379974972 | erot = 1.81993150945886 | epot = -22.4876821856977 | etot = -18.4348368764892 +774000 ekin = 2.82112723374611 | erot = 2.20399964233337 | epot = -22.478004597296 | etot = -17.4528777212165 +775000 ekin = 1.80765894464447 | erot = 1.85918506821001 | epot = -22.4072882679054 | etot = -18.7404442550509 +776000 ekin = 1.40021367363829 | erot = 3.15411215412014 | epot = -22.3650958887673 | etot = -17.8107700610088 +777000 ekin = 1.64184304615234 | erot = 2.80565056199556 | epot = -22.2758630382018 | etot = -17.8283694300539 +778000 ekin = 1.48552010960747 | erot = 2.23385655322065 | epot = -22.280627961357 | etot = -18.5612512985288 +779000 ekin = 1.8612416844269 | erot = 1.89467011122749 | epot = -22.3098169150752 | etot = -18.5539051194208 +780000 ekin = 1.69992943470698 | erot = 2.31253245347 | epot = -22.3678364729486 | etot = -18.3553745847716 +781000 ekin = 2.09952906112345 | erot = 2.56012058482576 | epot = -22.4462778123775 | etot = -17.7866281664283 +782000 ekin = 2.5656681981454 | erot = 1.9584872929859 | epot = -22.3478635193415 | etot = -17.8237080282102 +783000 ekin = 2.16529384416182 | erot = 2.88344914114146 | epot = -22.2446053910143 | etot = -17.1958624057111 +784000 ekin = 2.82003342353258 | erot = 2.22795791523759 | epot = -22.2211041777196 | etot = -17.1731128389495 +785000 ekin = 3.1175846654813 | erot = 2.90935771938994 | epot = -22.2344563156641 | etot = -16.2075139307928 +786000 ekin = 2.80016717549673 | erot = 3.42867564957491 | epot = -22.2496451559719 | etot = -16.0208023309003 +787000 ekin = 2.38498105317564 | erot = 3.01080705704523 | epot = -22.1644901078413 | etot = -16.7687019976204 +788000 ekin = 1.98689482841944 | erot = 2.00265266168408 | epot = -22.1102205855985 | etot = -18.120673095495 +789000 ekin = 2.4429381578802 | erot = 2.28303571912852 | epot = -22.0438356575627 | etot = -17.317861780554 +790000 ekin = 3.54942607073523 | erot = 2.80791853998027 | epot = -21.9672470303852 | etot = -15.6099024196697 +791000 ekin = 3.07978044254695 | erot = 2.4184479370232 | epot = -21.9558944305006 | etot = -16.4576660509305 +792000 ekin = 3.91878473045569 | erot = 1.9731825502165 | epot = -21.8851857762129 | etot = -15.9932184955407 +793000 ekin = 2.24379464034279 | erot = 2.58359475602037 | epot = -21.774610681239 | etot = -16.9472212848759 +794000 ekin = 2.14799943871595 | erot = 2.45378042225321 | epot = -21.6055963838422 | etot = -17.0038165228731 +795000 ekin = 1.62858645550717 | erot = 2.41208539626204 | epot = -21.4428264365968 | etot = -17.4021545848276 +796000 ekin = 2.20626767900772 | erot = 2.13905661758329 | epot = -21.3317362060421 | etot = -16.9864119094511 +797000 ekin = 1.82996184067328 | erot = 1.99906119944911 | epot = -21.3393574083459 | etot = -17.5103343682236 +798000 ekin = 2.25667499558209 | erot = 2.51245793531 | epot = -21.3768565865699 | etot = -16.6077236556778 +799000 ekin = 1.90911035219009 | erot = 2.87369878279891 | epot = -21.3617435253194 | etot = -16.5789343903304 +800000 ekin = 2.1677625897713 | erot = 2.34740172956008 | epot = -21.2761013083254 | etot = -16.7609369889941 +801000 ekin = 1.87638787205728 | erot = 1.64434088909028 | epot = -21.119685062831 | etot = -17.5989563016834 +802000 ekin = 2.22686790237101 | erot = 2.21112245128271 | epot = -21.0065136937552 | etot = -16.5685233401014 +803000 ekin = 2.68797844582697 | erot = 1.9055042783616 | epot = -20.977533512373 | etot = -16.3840507881845 +804000 ekin = 2.34860603481643 | erot = 2.89571698053518 | epot = -20.9203141084123 | etot = -15.6759910930607 +805000 ekin = 1.76197291834029 | erot = 2.71253740465393 | epot = -20.7889998983483 | etot = -16.3144895753541 +806000 ekin = 1.7473508020381 | erot = 2.06758975379032 | epot = -20.7361939926422 | etot = -16.9212534368137 +807000 ekin = 1.56935370454674 | erot = 1.70438269927346 | epot = -20.7922156879383 | etot = -17.5184792841181 +808000 ekin = 2.10918656723178 | erot = 2.39856508826456 | epot = -20.8730295437323 | etot = -16.3652778882359 +809000 ekin = 2.64218178293791 | erot = 1.51718119689586 | epot = -20.8620425969582 | etot = -16.7026796171244 +810000 ekin = 3.0961523233869 | erot = 2.66382304688042 | epot = -20.7945446198551 | etot = -15.0345692495878 +811000 ekin = 3.04477285154901 | erot = 3.63336291459452 | epot = -20.8540215443024 | etot = -14.1758857781589 +812000 ekin = 2.15160716251188 | erot = 2.79673763715996 | epot = -20.9409883926875 | etot = -15.9926435930157 +813000 ekin = 2.1868093512261 | erot = 3.1736283575579 | epot = -21.1408022790474 | etot = -15.7803645702634 +814000 ekin = 1.7209257269681 | erot = 2.995751260245 | epot = -21.2437075371712 | etot = -16.5270305499581 +815000 ekin = 2.15299829462668 | erot = 2.27035656487164 | epot = -21.2458654890398 | etot = -16.8225106295415 +816000 ekin = 2.708122450654 | erot = 1.52125307187336 | epot = -21.2616781989935 | etot = -17.0323026764662 +817000 ekin = 2.58901717437677 | erot = 2.58536627670115 | epot = -21.3956545078514 | etot = -16.2212710567734 +818000 ekin = 2.27875756856437 | erot = 2.24624264725757 | epot = -21.4318935062254 | etot = -16.9068932904035 +819000 ekin = 2.10656184615865 | erot = 3.01130039050673 | epot = -21.4327594058408 | etot = -16.3148971691754 +820000 ekin = 2.45661353119087 | erot = 2.7077529494413 | epot = -21.3798106611917 | etot = -16.2154441805595 +821000 ekin = 2.56789243532195 | erot = 2.54922758508947 | epot = -21.3170915318809 | etot = -16.1999715114695 +822000 ekin = 3.57333066089329 | erot = 2.21054956102185 | epot = -21.2861057645663 | etot = -15.5022255426512 +823000 ekin = 3.55383413213106 | erot = 2.72435850620162 | epot = -21.2727846567927 | etot = -14.99459201846 +824000 ekin = 4.1160622349429 | erot = 3.29139599112171 | epot = -21.2039659493683 | etot = -13.7965077233036 +825000 ekin = 2.91568774544338 | erot = 3.47057612959321 | epot = -21.0618933558847 | etot = -14.6756294808481 +826000 ekin = 1.71667097443836 | erot = 1.97830555981831 | epot = -20.8776766681461 | etot = -17.1827001338894 +827000 ekin = 1.87676981471836 | erot = 2.56467088925009 | epot = -20.7862250182709 | etot = -16.3447843143025 +828000 ekin = 2.38071607948713 | erot = 2.54624446499464 | epot = -20.7057379171108 | etot = -15.778777372629 +829000 ekin = 2.23087866970087 | erot = 1.78456567522682 | epot = -20.6078136299299 | etot = -16.5923692850022 +830000 ekin = 2.54758016482261 | erot = 2.32440405635605 | epot = -20.4881081818274 | etot = -15.6161239606488 +831000 ekin = 2.68445862644274 | erot = 2.08263260479755 | epot = -20.3542193485845 | etot = -15.5871281173442 +832000 ekin = 2.63412360308726 | erot = 2.01244922883234 | epot = -20.215817212176 | etot = -15.5692443802564 +833000 ekin = 2.52816532834198 | erot = 2.59604450500368 | epot = -20.1546011863619 | etot = -15.0303913530162 +834000 ekin = 2.89178882882708 | erot = 2.32656568068785 | epot = -20.154457994043 | etot = -14.9361034845281 +835000 ekin = 2.77377023733645 | erot = 2.76167763911259 | epot = -20.2925945781538 | etot = -14.7571467017048 +836000 ekin = 2.5461758373878 | erot = 2.86272526489883 | epot = -20.4572179712235 | etot = -15.0483168689368 +837000 ekin = 1.73852270651188 | erot = 1.97943492340463 | epot = -20.5100877279363 | etot = -16.7921300980198 +838000 ekin = 1.97190789156808 | erot = 2.79058337256635 | epot = -20.5305299708184 | etot = -15.7680387066839 +839000 ekin = 1.97773711155226 | erot = 2.72413991034567 | epot = -20.5265807034224 | etot = -15.8247036815245 +840000 ekin = 1.7232963874871 | erot = 2.96738113282628 | epot = -20.6321231069653 | etot = -15.9414455866519 +841000 ekin = 2.83071457484449 | erot = 2.84941397463216 | epot = -20.7926258530586 | etot = -15.112497303582 +842000 ekin = 2.59731855411368 | erot = 2.84178819703383 | epot = -20.8313063579289 | etot = -15.3921996067814 +843000 ekin = 2.04928376150596 | erot = 2.6128843549826 | epot = -20.8099267672999 | etot = -16.1477586508114 +844000 ekin = 1.54583411960153 | erot = 1.93893729147582 | epot = -20.8613105352918 | etot = -17.3765391242145 +845000 ekin = 2.313825406008 | erot = 2.32466241883302 | epot = -20.9823282893206 | etot = -16.3438404644796 +846000 ekin = 2.08903634512998 | erot = 2.31578856009952 | epot = -21.0646153757685 | etot = -16.659790470539 +847000 ekin = 2.4800137362118 | erot = 2.63006614696695 | epot = -21.0262265568772 | etot = -15.9161466736984 +848000 ekin = 2.15184282735255 | erot = 1.47311006297176 | epot = -21.0583979355086 | etot = -17.4334450451843 +849000 ekin = 2.01842760273387 | erot = 2.48110730715332 | epot = -21.0805165806607 | etot = -16.5809816707735 +850000 ekin = 2.55741512224125 | erot = 2.68263416508461 | epot = -21.0773082596903 | etot = -15.8372589723645 +851000 ekin = 2.18005669935449 | erot = 2.93569398882535 | epot = -21.0924777064982 | etot = -15.9767270183184 +852000 ekin = 2.4696261459638 | erot = 2.4702657660563 | epot = -21.121182921383 | etot = -16.1812910093629 +853000 ekin = 2.39950550338299 | erot = 2.98750142132015 | epot = -21.0612995182632 | etot = -15.67429259356 +854000 ekin = 2.33465924490093 | erot = 2.85274307519464 | epot = -20.968723969517 | etot = -15.7813216494214 +855000 ekin = 2.34227388182979 | erot = 2.06894784165371 | epot = -20.9841257021182 | etot = -16.5729039786347 +856000 ekin = 2.50117711580693 | erot = 2.74791206324422 | epot = -20.8738269143244 | etot = -15.6247377352733 +857000 ekin = 2.54090672086302 | erot = 3.01990349760065 | epot = -20.7453092144205 | etot = -15.1844989959569 +858000 ekin = 3.06946696795817 | erot = 2.15496603972173 | epot = -20.6851307548641 | etot = -15.4606977471842 +859000 ekin = 2.8502330341827 | erot = 2.24419946408453 | epot = -20.6787263175177 | etot = -15.5842938192505 +860000 ekin = 2.81341243833324 | erot = 1.5197461937082 | epot = -20.6783502445099 | etot = -16.3451916124685 +861000 ekin = 2.27419936469317 | erot = 2.84736568193217 | epot = -20.6476685348769 | etot = -15.5261034882516 +862000 ekin = 2.99814535919906 | erot = 1.87200304458178 | epot = -20.6714218686896 | etot = -15.8012734649088 +863000 ekin = 2.82320132781549 | erot = 1.77959785908837 | epot = -20.7642045825074 | etot = -16.1614053956036 +864000 ekin = 2.91892607599648 | erot = 2.64325528924267 | epot = -20.9317153856013 | etot = -15.3695340203621 +865000 ekin = 3.32989545880503 | erot = 2.25510784979563 | epot = -21.0557741374338 | etot = -15.4707708288331 +866000 ekin = 2.85710406140164 | erot = 3.16185395635697 | epot = -21.1425088224093 | etot = -15.1235508046507 +867000 ekin = 2.74742982523498 | erot = 3.06773761977147 | epot = -21.134531707449 | etot = -15.3193642624426 +868000 ekin = 2.1948650568198 | erot = 2.22458860510737 | epot = -21.0697126630058 | etot = -16.6502590010787 +869000 ekin = 2.92239964068215 | erot = 2.50065925324415 | epot = -21.0149378764857 | etot = -15.5918789825594 +870000 ekin = 2.48931117933877 | erot = 2.13038554226924 | epot = -20.9976655364141 | etot = -16.3779688148061 +871000 ekin = 2.19107246828585 | erot = 2.37839051284131 | epot = -20.8765191273408 | etot = -16.3070561462136 +872000 ekin = 1.55081886521514 | erot = 2.09762459684259 | epot = -20.8521940121747 | etot = -17.2037505501169 +873000 ekin = 1.3896067615701 | erot = 2.27757856660909 | epot = -20.9255865429236 | etot = -17.2584012147444 +874000 ekin = 1.41282979514325 | erot = 2.76881886831623 | epot = -21.0901483490343 | etot = -16.9084996855748 +875000 ekin = 1.18979270807644 | erot = 2.71872907877545 | epot = -21.2270266717576 | etot = -17.3185048849058 +876000 ekin = 1.81100671707876 | erot = 2.98963277694409 | epot = -21.2472610575188 | etot = -16.4466215634959 +877000 ekin = 2.36243541111364 | erot = 2.03609143795483 | epot = -21.3277863705839 | etot = -16.9292595215154 +878000 ekin = 2.1245196182468 | erot = 1.75451707226955 | epot = -21.3222506595257 | etot = -17.4432139690093 +879000 ekin = 2.2716997631568 | erot = 2.70191568133046 | epot = -21.3119311913778 | etot = -16.3383157468906 +880000 ekin = 2.68326313012635 | erot = 2.77340532358103 | epot = -21.3535728447366 | etot = -15.8969043910292 +881000 ekin = 2.87483307600208 | erot = 2.33652901733377 | epot = -21.3292700652532 | etot = -16.1179079719173 +882000 ekin = 2.32758906799515 | erot = 2.16795489269516 | epot = -21.2584233833351 | etot = -16.7628794226448 +883000 ekin = 2.35908631800798 | erot = 1.97904048991531 | epot = -21.0655746410777 | etot = -16.7274478331544 +884000 ekin = 2.52269362644082 | erot = 2.25025361307445 | epot = -20.9641879640375 | etot = -16.1912407245222 +885000 ekin = 2.8471189843883 | erot = 2.26506458535077 | epot = -20.9641383727441 | etot = -15.8519548030051 +886000 ekin = 3.18322288605135 | erot = 1.73470875511279 | epot = -21.0012427194847 | etot = -16.0833110783206 +887000 ekin = 2.68813414464725 | erot = 2.50204216522368 | epot = -21.067976555709 | etot = -15.8778002458381 +888000 ekin = 2.15187544250473 | erot = 2.83221089603913 | epot = -21.17639007923 | etot = -16.1923037406862 +889000 ekin = 2.16956995574787 | erot = 2.20198656261183 | epot = -21.1017572530618 | etot = -16.7302007347021 +890000 ekin = 1.78556825977743 | erot = 2.98410700070926 | epot = -21.186208638226 | etot = -16.4165333777393 +891000 ekin = 1.64917016933854 | erot = 2.27750403923458 | epot = -21.3189640243096 | etot = -17.3922898157365 +892000 ekin = 1.96583947510742 | erot = 2.36271973263346 | epot = -21.4596361006042 | etot = -17.1310768928633 +893000 ekin = 1.79314340564254 | erot = 1.8411107489992 | epot = -21.5470179462123 | etot = -17.9127637915705 +894000 ekin = 2.81442382935654 | erot = 2.80759818283316 | epot = -21.6538835081476 | etot = -16.0318614959579 +895000 ekin = 2.0070369904664 | erot = 2.75374249882318 | epot = -21.7499760057857 | etot = -16.9891965164961 +896000 ekin = 1.6507008342202 | erot = 2.56296228195539 | epot = -21.8927812332095 | etot = -17.6791181170339 +897000 ekin = 1.78139405234358 | erot = 2.35356223356246 | epot = -22.0286409132692 | etot = -17.8936846273632 +898000 ekin = 1.85207490030026 | erot = 2.3928555728648 | epot = -22.0495390022753 | etot = -17.8046085291102 +899000 ekin = 1.66216066819287 | erot = 3.04222938639382 | epot = -21.9579747350567 | etot = -17.25358468047 +900000 ekin = 2.15165827067079 | erot = 2.62356927804175 | epot = -21.9156104880732 | etot = -17.1403829393607 +901000 ekin = 2.41248642142908 | erot = 2.69714418093217 | epot = -21.9837417963999 | etot = -16.8741111940386 +902000 ekin = 2.57545214239909 | erot = 2.40635843208183 | epot = -21.996436412966 | etot = -17.0146258384851 +903000 ekin = 2.40335601179059 | erot = 2.4057541752901 | epot = -22.0230111828253 | etot = -17.2139009957446 +904000 ekin = 1.99365997109403 | erot = 3.12264199705152 | epot = -22.0954468558152 | etot = -16.9791448876697 +905000 ekin = 2.45160047861299 | erot = 2.11889478277434 | epot = -22.0620083174753 | etot = -17.4915130560879 +906000 ekin = 2.69446662881178 | erot = 1.66991631401456 | epot = -22.0555442490735 | etot = -17.6911613062471 +907000 ekin = 2.5734498863711 | erot = 2.16877319112329 | epot = -22.0376984236082 | etot = -17.2954753461138 +908000 ekin = 2.9646776076989 | erot = 2.40252252045294 | epot = -22.0191047803794 | etot = -16.6519046522276 +909000 ekin = 3.12793409264582 | erot = 2.12009742665766 | epot = -22.0610667288554 | etot = -16.8130352095519 +910000 ekin = 2.92206025021313 | erot = 3.50302372345592 | epot = -22.1277774480557 | etot = -15.7026934743867 +911000 ekin = 1.85381948048669 | erot = 2.73401011795404 | epot = -22.1683975531304 | etot = -17.5805679546896 +912000 ekin = 2.64405242900445 | erot = 1.86324838607163 | epot = -22.2002570143971 | etot = -17.692956199321 +913000 ekin = 2.46824283660223 | erot = 2.0308633546605 | epot = -22.3203806242275 | etot = -17.8212744329647 +914000 ekin = 2.01871966356282 | erot = 2.94283156821207 | epot = -22.3513452914152 | etot = -17.3897940596404 +915000 ekin = 2.82676643872102 | erot = 2.11643553756712 | epot = -22.3640471312087 | etot = -17.4208451549205 +916000 ekin = 2.54227707175729 | erot = 3.23335822897873 | epot = -22.4652663102875 | etot = -16.6896310095515 +917000 ekin = 2.31676859881433 | erot = 2.2427200582576 | epot = -22.463585281336 | etot = -17.9040966242641 +918000 ekin = 2.08681780124233 | erot = 2.05685815910104 | epot = -22.3748058531193 | etot = -18.231129892776 +919000 ekin = 2.60282015977208 | erot = 2.38968293687319 | epot = -22.3822670579485 | etot = -17.3897639613032 +920000 ekin = 3.21847224306531 | erot = 2.75010700480466 | epot = -22.4646189595793 | etot = -16.4960397117093 +921000 ekin = 2.67829101318104 | erot = 1.98386933580364 | epot = -22.5250186592845 | etot = -17.8628583102998 +922000 ekin = 1.43283799739773 | erot = 1.5210967069851 | epot = -22.5925015236451 | etot = -19.6385668192623 +923000 ekin = 1.69052063428542 | erot = 1.88300391650268 | epot = -22.66377714455 | etot = -19.0902525937619 +924000 ekin = 2.14340021014736 | erot = 1.52248843908134 | epot = -22.6402388027506 | etot = -18.9743501535219 +925000 ekin = 2.26091939109784 | erot = 1.33050454776921 | epot = -22.5227280014394 | etot = -18.9313040625724 +926000 ekin = 2.00930540350536 | erot = 2.07372939007629 | epot = -22.4428200376094 | etot = -18.3597852440277 +927000 ekin = 2.53289082621251 | erot = 1.99783542507574 | epot = -22.5727269691716 | etot = -18.0420007178833 +928000 ekin = 2.57275295957812 | erot = 2.50503787417693 | epot = -22.7397714760282 | etot = -17.6619806422732 +929000 ekin = 2.66131598383108 | erot = 1.82871097568713 | epot = -22.7889092091996 | etot = -18.2988822496814 +930000 ekin = 2.41369096322635 | erot = 2.00598415451171 | epot = -22.802343205586 | etot = -18.3826680878479 +931000 ekin = 3.02636364754007 | erot = 2.115962250161 | epot = -22.7562575819635 | etot = -17.6139316842625 +932000 ekin = 2.34573343934799 | erot = 1.88269819474441 | epot = -22.8028018252265 | etot = -18.5743701911341 +933000 ekin = 2.16951834533283 | erot = 2.85677231086964 | epot = -22.8240172791919 | etot = -17.7977266229894 +934000 ekin = 2.17177152489559 | erot = 2.1194660688678 | epot = -22.8652321779361 | etot = -18.5739945841727 +935000 ekin = 2.34485090948927 | erot = 2.23417606918545 | epot = -22.85888707632 | etot = -18.2798600976452 +936000 ekin = 2.28188124919415 | erot = 2.53015822921572 | epot = -22.9782518612072 | etot = -18.1662123827973 +937000 ekin = 2.3061925494295 | erot = 2.82857457174385 | epot = -23.071665648819 | etot = -17.9368985276457 +938000 ekin = 2.44229226509271 | erot = 2.00737414808353 | epot = -23.1363676072136 | etot = -18.6867011940373 +939000 ekin = 2.97744015155649 | erot = 2.1021287084213 | epot = -23.1206613400026 | etot = -18.0410924800248 +940000 ekin = 3.74219661265262 | erot = 2.68184060115531 | epot = -23.0494489680042 | etot = -16.6254117541962 +941000 ekin = 3.1130700754106 | erot = 2.2870034463699 | epot = -22.9451834918749 | etot = -17.5451099700944 +942000 ekin = 3.46654816859628 | erot = 1.87509182259239 | epot = -22.9048558084884 | etot = -17.5632158172997 +943000 ekin = 3.79224818385641 | erot = 2.70927084823339 | epot = -22.8698482349086 | etot = -16.3683292028188 +944000 ekin = 2.65995525590795 | erot = 2.74912726816423 | epot = -22.8317889960132 | etot = -17.422706471941 +945000 ekin = 2.54659137616624 | erot = 2.02239421261018 | epot = -22.725938832337 | etot = -18.1569532435606 +946000 ekin = 2.46388617435412 | erot = 1.67037983156324 | epot = -22.5545307163887 | etot = -18.4202647104713 +947000 ekin = 2.40803821488282 | erot = 1.99424876436282 | epot = -22.4581247656853 | etot = -18.0558377864397 +948000 ekin = 3.53604042034895 | erot = 2.57997877434838 | epot = -22.3226574127033 | etot = -16.206638218006 +949000 ekin = 2.98854271807069 | erot = 2.434764866082 | epot = -22.1081978358246 | etot = -16.6848902516719 +950000 ekin = 1.85098760333696 | erot = 3.0113849918017 | epot = -21.9481390655564 | etot = -17.0857664704178 +951000 ekin = 2.24140231384639 | erot = 2.36101456496684 | epot = -21.9054305662226 | etot = -17.3030136874094 +952000 ekin = 2.1767459614223 | erot = 1.66164476273624 | epot = -21.8857446244283 | etot = -18.0473539002697 +953000 ekin = 2.32434436644844 | erot = 1.96780923551529 | epot = -21.864089307184 | etot = -17.5719357052203 +954000 ekin = 1.49071594272054 | erot = 3.34931219540537 | epot = -21.7966718941878 | etot = -16.9566437560618 +955000 ekin = 1.88457697665867 | erot = 2.69006961792184 | epot = -21.7221575712775 | etot = -17.147510976697 +956000 ekin = 1.69307087749046 | erot = 2.16469646035311 | epot = -21.6721199805376 | etot = -17.814352642694 +957000 ekin = 1.73487330688787 | erot = 1.64307450157792 | epot = -21.6559256952543 | etot = -18.2779778867885 +958000 ekin = 1.60385894866933 | erot = 2.19168737006627 | epot = -21.6476897105175 | etot = -17.8521433917819 +959000 ekin = 2.59262245343361 | erot = 2.48219361032086 | epot = -21.6596277279706 | etot = -16.5848116642161 +960000 ekin = 2.55386671368679 | erot = 2.05771846301768 | epot = -21.6626200672138 | etot = -17.0510348905093 +961000 ekin = 2.27765806186204 | erot = 2.17958354193562 | epot = -21.6544957188758 | etot = -17.1972541150782 +962000 ekin = 1.66004639932187 | erot = 3.51004740828816 | epot = -21.6650529510449 | etot = -16.4949591434349 +963000 ekin = 1.98935936955203 | erot = 1.50490949194663 | epot = -21.6088711497269 | etot = -18.1146022882282 +964000 ekin = 2.17983717879189 | erot = 2.29031074234418 | epot = -21.5586262428098 | etot = -17.0884783216737 +965000 ekin = 2.10787439045543 | erot = 2.3221077885109 | epot = -21.5497920382512 | etot = -17.1198098592849 +966000 ekin = 3.1408040905672 | erot = 3.41823133718854 | epot = -21.5836404263088 | etot = -15.024604998553 +967000 ekin = 3.0568623124503 | erot = 2.1733206632131 | epot = -21.5260931467358 | etot = -16.2959101710724 +968000 ekin = 2.05064192877792 | erot = 2.14124924922397 | epot = -21.4479972163209 | etot = -17.256106038319 +969000 ekin = 2.21517858837652 | erot = 2.21735686304378 | epot = -21.3822587820383 | etot = -16.949723330618 +970000 ekin = 2.44665062708039 | erot = 2.63919176763313 | epot = -21.3192840477868 | etot = -16.2334416530733 +971000 ekin = 2.47241679333997 | erot = 2.68621090896417 | epot = -21.3036698600044 | etot = -16.1450421577003 +972000 ekin = 3.18976408247808 | erot = 2.45901954667695 | epot = -21.2523934460448 | etot = -15.6036098168898 +973000 ekin = 3.35475115149161 | erot = 2.61012752320778 | epot = -21.183068859057 | etot = -15.2181901843576 +974000 ekin = 2.71127807449815 | erot = 2.12974355852032 | epot = -21.0816906098712 | etot = -16.2406689768528 +975000 ekin = 1.81295894463494 | erot = 2.0759564976921 | epot = -20.9964165264669 | etot = -17.1075010841398 +976000 ekin = 2.37619926790761 | erot = 1.37981441384236 | epot = -20.8930101654836 | etot = -17.1369964837336 +977000 ekin = 2.85555210767404 | erot = 3.03619369635208 | epot = -21.0095574945917 | etot = -15.1178116905656 +978000 ekin = 3.13849116757388 | erot = 3.01118356119965 | epot = -21.0732326779663 | etot = -14.9235579491928 +979000 ekin = 3.64170438280054 | erot = 2.4612126795782 | epot = -20.9593695826044 | etot = -14.8564525202257 +980000 ekin = 3.43680535726821 | erot = 3.27333588575053 | epot = -20.9004670674903 | etot = -14.1903258244715 +981000 ekin = 2.95806185202903 | erot = 2.46811293942083 | epot = -20.9868038459701 | etot = -15.5606290545202 +982000 ekin = 2.05823037945997 | erot = 2.23573651589999 | epot = -21.0420814071854 | etot = -16.7481145118254 +983000 ekin = 2.5553610304344 | erot = 1.97272050888114 | epot = -21.0434200461188 | etot = -16.5153385068032 +984000 ekin = 2.32140326985734 | erot = 2.58284655378618 | epot = -21.0826601835729 | etot = -16.1784103599294 +985000 ekin = 2.30327577152247 | erot = 3.01569210622987 | epot = -21.1731422974947 | etot = -15.8541744197424 +986000 ekin = 2.0247579133688 | erot = 2.17885674714069 | epot = -21.2745593334952 | etot = -17.0709446729857 +987000 ekin = 2.38610984160001 | erot = 1.60437579739602 | epot = -21.2569575649582 | etot = -17.2664719259622 +988000 ekin = 2.73926231299059 | erot = 2.71146350841208 | epot = -21.1552791211025 | etot = -15.7045532996999 +989000 ekin = 2.26697151561908 | erot = 2.87750604798637 | epot = -21.0937789068058 | etot = -15.9493013432004 +990000 ekin = 2.20943106152859 | erot = 2.59684886899357 | epot = -21.0203331776818 | etot = -16.2140532471596 +991000 ekin = 2.18249266283082 | erot = 2.54649657411172 | epot = -20.9130337682104 | etot = -16.1840445312679 +992000 ekin = 1.6979885228163 | erot = 2.49592807829765 | epot = -20.97584958751 | etot = -16.781932986396 +993000 ekin = 1.37413745875443 | erot = 1.97736806672932 | epot = -21.0653195519547 | etot = -17.713814026471 +994000 ekin = 1.46489942286098 | erot = 2.9578292103502 | epot = -21.126186746174 | etot = -16.7034581129629 +995000 ekin = 2.313206084368 | erot = 1.68064795849453 | epot = -21.1907262676309 | etot = -17.1968722247684 +996000 ekin = 2.91635623044139 | erot = 2.86817278212845 | epot = -21.1749728841882 | etot = -15.3904438716184 +997000 ekin = 3.14117227050211 | erot = 2.13892951607983 | epot = -21.1714996184258 | etot = -15.8913978318439 +998000 ekin = 2.24297046385175 | erot = 3.02327291553881 | epot = -21.1032039558864 | etot = -15.8369605764958 +999000 ekin = 2.61553981530106 | erot = 1.7387289184571 | epot = -21.0217257279766 | etot = -16.6674569942185 +1000000 ekin = 2.34012577497833 | erot = 2.86436388995813 | epot = -21.0201566044041 | etot = -15.8156669394676 + 1000000 0.10400559 -1.3746133 0.060853481 -1.1675019 0.00013752759 +Loop time of 59.4195 on 4 procs for 1000000 steps with 16 atoms + +Performance: 14540.686 tau/day, 16829.497 timesteps/s +96.3% CPU use with 4 MPI tasks x no OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 1.0304 | 20.212 | 37.839 | 369.5 | 34.02 +Bond | 0.12844 | 0.57006 | 0.95643 | 49.6 | 0.96 +Neigh | 0 | 0 | 0 | 0.0 | 0.00 +Comm | 4.3935 | 5.5635 | 6.7052 | 44.2 | 9.36 +Output | 2.3e-05 | 3.575e-05 | 4.1e-05 | 0.0 | 0.00 +Modify | 0.3513 | 3.4695 | 6.4366 | 144.3 | 5.84 +Other | | 29.6 | | | 49.82 + +Nlocal: 4 ave 8 max 0 min +Histogram: 1 1 0 0 0 0 0 0 1 1 +Nghost: 11 ave 14 max 8 min +Histogram: 1 1 0 0 0 0 0 0 1 1 +Neighs: 46 ave 89 max 0 min +Histogram: 1 1 0 0 0 0 0 0 0 2 + +Total # of neighbors = 184 +Ave neighs/atom = 11.5 +Ave special neighs/atom = 3.75 +Neighbor list builds = 0 +Dangerous builds = 0 + +#write_restart config.${number}.* +Total wall time: 0:00:59 diff --git a/examples/USER/cgdna/examples/oxDNA2/duplex2/log.27Nov18.duplex2.g++.1 b/examples/USER/cgdna/examples/oxDNA2/duplex2/log.27Nov18.duplex2.g++.1 deleted file mode 100644 index ba36d696fb..0000000000 --- a/examples/USER/cgdna/examples/oxDNA2/duplex2/log.27Nov18.duplex2.g++.1 +++ /dev/null @@ -1,178 +0,0 @@ -LAMMPS (27 Nov 2018) - using 1 OpenMP thread(s) per MPI task -variable number equal 2 -variable ofreq equal 1000 -variable efreq equal 1000 - -units lj - -dimension 3 - -newton off - -boundary p p p - -atom_style hybrid bond ellipsoid -atom_modify sort 0 1.0 - -# Pair interactions require lists of neighbours to be calculated -neighbor 1.0 bin -neigh_modify every 1 delay 0 check yes - -read_data data.duplex2 - orthogonal box = (-20 -20 -20) to (20 20 20) - 1 by 1 by 1 MPI processor grid - reading atoms ... - 16 atoms - reading velocities ... - 16 velocities - 16 ellipsoids - scanning bonds ... - 2 = max bonds/atom - reading bonds ... - 13 bonds - 2 = max # of 1-2 neighbors - 2 = max # of 1-3 neighbors - 4 = max # of 1-4 neighbors - 6 = max # of special neighbors - -set atom * mass 3.1575 - 16 settings made for mass - -group all type 1 4 -16 atoms in group all - -# oxDNA bond interactions - FENE backbone -bond_style oxdna2/fene -bond_coeff * 2.0 0.25 0.7564 - -# oxDNA pair interactions -pair_style hybrid/overlay oxdna2/excv oxdna2/stk oxdna2/hbond oxdna2/xstk oxdna2/coaxstk oxdna2/dh -pair_coeff * * oxdna2/excv 2.0 0.7 0.675 2.0 0.515 0.5 2.0 0.33 0.32 -pair_coeff * * oxdna2/stk seqav 0.1 6.0 0.4 0.9 0.32 0.6 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2.0 0.65 2.0 0.65 -pair_coeff * * oxdna2/hbond seqav 0.0 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45 -pair_coeff 1 4 oxdna2/hbond seqav 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45 -pair_coeff 2 3 oxdna2/hbond seqav 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45 -pair_coeff * * oxdna2/xstk 47.5 0.575 0.675 0.495 0.655 2.25 0.791592653589793 0.58 1.7 1.0 0.68 1.7 1.0 0.68 1.5 0 0.65 1.7 0.875 0.68 1.7 0.875 0.68 -pair_coeff * * oxdna2/coaxstk 58.5 0.4 0.6 0.22 0.58 2.0 2.891592653589793 0.65 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 40.0 3.116592653589793 -pair_coeff * * oxdna2/dh 0.1 1.0 0.815 - -# NVE ensemble -#fix 1 all nve/dot -fix 1 all nve/dotc/langevin 0.1 0.1 0.03 457145 angmom 10 -#fix 1 all nve/asphere -#fix 2 all langevin 0.1 0.1 0.03 457145 angmom 10 - -timestep 1e-5 - -#comm_style tiled -#fix 3 all balance 10000 1.1 rcb - -#compute mol all chunk/atom molecule -#compute mychunk all vcm/chunk mol -#fix 4 all ave/time 10000 1 10000 c_mychunk[1] c_mychunk[2] c_mychunk[3] file vcm.txt mode vector - -#dump pos all xyz ${ofreq} traj.${number}.xyz - -#compute quat all property/atom quatw quati quatj quatk -#dump quat all custom ${ofreq} quat.${number}.txt id c_quat[1] c_quat[2] c_quat[3] c_quat[4] -#dump_modify quat sort id -#dump_modify quat format line "%d %13.6le %13.6le %13.6le %13.6le" - -compute erot all erotate/asphere -compute ekin all ke -compute epot all pe -variable erot equal c_erot -variable ekin equal c_ekin -variable epot equal c_epot -variable etot equal c_erot+c_ekin+c_epot -fix 5 all print ${efreq} "$(step) ekin = ${ekin} | erot = ${erot} | epot = ${epot} | etot = ${etot}" screen yes -fix 5 all print 1000 "$(step) ekin = ${ekin} | erot = ${erot} | epot = ${epot} | etot = ${etot}" screen yes - -#dump out all custom ${ofreq} out.${number}.txt id x y z vx vy vz fx fy fz tqx tqy tqz -#dump_modify out sort id -#dump_modify out format line "%d %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le" - -run 10000 -Neighbor list info ... - update every 1 steps, delay 0 steps, check yes - max neighbors/atom: 2000, page size: 100000 - master list distance cutoff = 2.6274 - ghost atom cutoff = 2.6274 - binsize = 1.3137, bins = 31 31 31 - 6 neighbor lists, perpetual/occasional/extra = 6 0 0 - (1) pair oxdna2/excv, perpetual - attributes: half, newton off - pair build: half/bin/newtoff - stencil: half/bin/3d/newtoff - bin: standard - (2) pair oxdna2/stk, perpetual, copy from (1) - attributes: half, newton off - pair build: copy - stencil: none - bin: none - (3) pair oxdna2/hbond, perpetual, copy from (1) - attributes: half, newton off - pair build: copy - stencil: none - bin: none - (4) pair oxdna2/xstk, perpetual, copy from (1) - attributes: half, newton off - pair build: copy - stencil: none - bin: none - (5) pair oxdna2/coaxstk, perpetual, copy from (1) - attributes: half, newton off - pair build: copy - stencil: none - bin: none - (6) pair oxdna2/dh, perpetual, copy from (1) - attributes: half, newton off - pair build: copy - stencil: none - bin: none -Per MPI rank memory allocation (min/avg/max) = 3.025 | 3.025 | 3.025 Mbytes -Step Temp E_pair E_mol TotEng Press - 0 0 -1.5358787 0.0096742456 -1.5262045 -7.9568629e-05 -1000 ekin = 1.54282272464468 | erot = 1.71757897250772 | epot = -24.4403527731341 | etot = -21.1799510759817 -2000 ekin = 1.86109566690716 | erot = 1.93804145796026 | epot = -24.3759816748265 | etot = -20.5768445499591 -3000 ekin = 2.68769182431188 | erot = 2.14559269500086 | epot = -24.2916556822451 | etot = -19.4583711629324 -4000 ekin = 2.04710303757243 | erot = 1.48774072590987 | epot = -24.190371461807 | etot = -20.6555276983247 -5000 ekin = 1.77654023802719 | erot = 2.534186505221 | epot = -24.1246365663843 | etot = -19.8139098231361 -6000 ekin = 3.12253137872527 | erot = 2.04028266818831 | epot = -24.0491248750916 | etot = -18.886310828178 -7000 ekin = 3.22418765752177 | erot = 2.72037570174023 | epot = -23.9458569915548 | etot = -18.0012936322928 -8000 ekin = 2.83204202112963 | erot = 2.67060276413777 | epot = -23.9211291529766 | etot = -18.4184843677092 -9000 ekin = 2.69585642754481 | erot = 2.59559820250212 | epot = -23.8340823338302 | etot = -18.5426277037833 -10000 ekin = 2.66058119525512 | erot = 1.95965933336077 | epot = -23.7132443170725 | etot = -19.0930037884566 - 10000 0.11824805 -1.4953627 0.013284973 -1.3157914 -0.00012999454 -Loop time of 0.32781 on 1 procs for 10000 steps with 16 atoms - -Performance: 26356.746 tau/day, 30505.493 timesteps/s -99.9% CPU use with 1 MPI tasks x 1 OpenMP threads - -MPI task timing breakdown: -Section | min time | avg time | max time |%varavg| %total ---------------------------------------------------------------- -Pair | 0.24211 | 0.24211 | 0.24211 | 0.0 | 73.86 -Bond | 0.0075173 | 0.0075173 | 0.0075173 | 0.0 | 2.29 -Neigh | 0 | 0 | 0 | 0.0 | 0.00 -Comm | 0.0014515 | 0.0014515 | 0.0014515 | 0.0 | 0.44 -Output | 5.4836e-06 | 5.4836e-06 | 5.4836e-06 | 0.0 | 0.00 -Modify | 0.073331 | 0.073331 | 0.073331 | 0.0 | 22.37 -Other | | 0.003398 | | | 1.04 - -Nlocal: 16 ave 16 max 16 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Nghost: 0 ave 0 max 0 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Neighs: 116 ave 116 max 116 min -Histogram: 1 0 0 0 0 0 0 0 0 0 - -Total # of neighbors = 116 -Ave neighs/atom = 7.25 -Ave special neighs/atom = 3.75 -Neighbor list builds = 0 -Dangerous builds = 0 - -#write_restart config.${number}.* -Total wall time: 0:00:00 diff --git a/examples/USER/cgdna/examples/oxDNA2/duplex2/log.27Nov18.duplex2.g++.4 b/examples/USER/cgdna/examples/oxDNA2/duplex2/log.27Nov18.duplex2.g++.4 deleted file mode 100644 index 3237d4849e..0000000000 --- a/examples/USER/cgdna/examples/oxDNA2/duplex2/log.27Nov18.duplex2.g++.4 +++ /dev/null @@ -1,178 +0,0 @@ -LAMMPS (27 Nov 2018) - using 1 OpenMP thread(s) per MPI task -variable number equal 2 -variable ofreq equal 1000 -variable efreq equal 1000 - -units lj - -dimension 3 - -newton off - -boundary p p p - -atom_style hybrid bond ellipsoid -atom_modify sort 0 1.0 - -# Pair interactions require lists of neighbours to be calculated -neighbor 1.0 bin -neigh_modify every 1 delay 0 check yes - -read_data data.duplex2 - orthogonal box = (-20 -20 -20) to (20 20 20) - 1 by 2 by 2 MPI processor grid - reading atoms ... - 16 atoms - reading velocities ... - 16 velocities - 16 ellipsoids - scanning bonds ... - 2 = max bonds/atom - reading bonds ... - 13 bonds - 2 = max # of 1-2 neighbors - 2 = max # of 1-3 neighbors - 4 = max # of 1-4 neighbors - 6 = max # of special neighbors - -set atom * mass 3.1575 - 16 settings made for mass - -group all type 1 4 -16 atoms in group all - -# oxDNA bond interactions - FENE backbone -bond_style oxdna2/fene -bond_coeff * 2.0 0.25 0.7564 - -# oxDNA pair interactions -pair_style hybrid/overlay oxdna2/excv oxdna2/stk oxdna2/hbond oxdna2/xstk oxdna2/coaxstk oxdna2/dh -pair_coeff * * oxdna2/excv 2.0 0.7 0.675 2.0 0.515 0.5 2.0 0.33 0.32 -pair_coeff * * oxdna2/stk seqav 0.1 6.0 0.4 0.9 0.32 0.6 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2.0 0.65 2.0 0.65 -pair_coeff * * oxdna2/hbond seqav 0.0 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45 -pair_coeff 1 4 oxdna2/hbond seqav 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45 -pair_coeff 2 3 oxdna2/hbond seqav 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45 -pair_coeff * * oxdna2/xstk 47.5 0.575 0.675 0.495 0.655 2.25 0.791592653589793 0.58 1.7 1.0 0.68 1.7 1.0 0.68 1.5 0 0.65 1.7 0.875 0.68 1.7 0.875 0.68 -pair_coeff * * oxdna2/coaxstk 58.5 0.4 0.6 0.22 0.58 2.0 2.891592653589793 0.65 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 40.0 3.116592653589793 -pair_coeff * * oxdna2/dh 0.1 1.0 0.815 - -# NVE ensemble -#fix 1 all nve/dot -fix 1 all nve/dotc/langevin 0.1 0.1 0.03 457145 angmom 10 -#fix 1 all nve/asphere -#fix 2 all langevin 0.1 0.1 0.03 457145 angmom 10 - -timestep 1e-5 - -#comm_style tiled -#fix 3 all balance 10000 1.1 rcb - -#compute mol all chunk/atom molecule -#compute mychunk all vcm/chunk mol -#fix 4 all ave/time 10000 1 10000 c_mychunk[1] c_mychunk[2] c_mychunk[3] file vcm.txt mode vector - -#dump pos all xyz ${ofreq} traj.${number}.xyz - -#compute quat all property/atom quatw quati quatj quatk -#dump quat all custom ${ofreq} quat.${number}.txt id c_quat[1] c_quat[2] c_quat[3] c_quat[4] -#dump_modify quat sort id -#dump_modify quat format line "%d %13.6le %13.6le %13.6le %13.6le" - -compute erot all erotate/asphere -compute ekin all ke -compute epot all pe -variable erot equal c_erot -variable ekin equal c_ekin -variable epot equal c_epot -variable etot equal c_erot+c_ekin+c_epot -fix 5 all print ${efreq} "$(step) ekin = ${ekin} | erot = ${erot} | epot = ${epot} | etot = ${etot}" screen yes -fix 5 all print 1000 "$(step) ekin = ${ekin} | erot = ${erot} | epot = ${epot} | etot = ${etot}" screen yes - -#dump out all custom ${ofreq} out.${number}.txt id x y z vx vy vz fx fy fz tqx tqy tqz -#dump_modify out sort id -#dump_modify out format line "%d %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le" - -run 10000 -Neighbor list info ... - update every 1 steps, delay 0 steps, check yes - max neighbors/atom: 2000, page size: 100000 - master list distance cutoff = 2.6274 - ghost atom cutoff = 2.6274 - binsize = 1.3137, bins = 31 31 31 - 6 neighbor lists, perpetual/occasional/extra = 6 0 0 - (1) pair oxdna2/excv, perpetual - attributes: half, newton off - pair build: half/bin/newtoff - stencil: half/bin/3d/newtoff - bin: standard - (2) pair oxdna2/stk, perpetual, copy from (1) - attributes: half, newton off - pair build: copy - stencil: none - bin: none - (3) pair oxdna2/hbond, perpetual, copy from (1) - attributes: half, newton off - pair build: copy - stencil: none - bin: none - (4) pair oxdna2/xstk, perpetual, copy from (1) - attributes: half, newton off - pair build: copy - stencil: none - bin: none - (5) pair oxdna2/coaxstk, perpetual, copy from (1) - attributes: half, newton off - pair build: copy - stencil: none - bin: none - (6) pair oxdna2/dh, perpetual, copy from (1) - attributes: half, newton off - pair build: copy - stencil: none - bin: none -Per MPI rank memory allocation (min/avg/max) = 7.777 | 7.959 | 8.142 Mbytes -Step Temp E_pair E_mol TotEng Press - 0 0 -1.5358787 0.0096742456 -1.5262045 -7.9568629e-05 -1000 ekin = 1.34554291364716 | erot = 2.30525041754444 | epot = -24.3924150888896 | etot = -20.741621757698 -2000 ekin = 2.15972469811184 | erot = 2.1628675965276 | epot = -24.3548203354875 | etot = -20.0322280408481 -3000 ekin = 3.26433550542939 | erot = 2.76107866472085 | epot = -24.2947953202752 | etot = -18.269381150125 -4000 ekin = 1.9203212531997 | erot = 2.13339438425299 | epot = -24.234098584123 | etot = -20.1803829466703 -5000 ekin = 1.35481075814721 | erot = 2.00854026688447 | epot = -24.1768963201279 | etot = -20.8135452950963 -6000 ekin = 2.18974627635306 | erot = 1.73271671162435 | epot = -24.1096616118305 | etot = -20.1871986238531 -7000 ekin = 2.65472853187395 | erot = 1.73258720631296 | epot = -24.0561118130561 | etot = -19.6687960748691 -8000 ekin = 2.51192327964357 | erot = 2.34132844779952 | epot = -23.9708695663488 | etot = -19.1176178389058 -9000 ekin = 2.24554900802464 | erot = 2.0522939078286 | epot = -23.874757758319 | etot = -19.5769148424658 -10000 ekin = 2.36227360512089 | erot = 1.80185994066737 | epot = -23.7793375260418 | etot = -19.6152039802535 - 10000 0.10498994 -1.5020657 0.015857071 -1.3385665 -8.8930899e-05 -Loop time of 0.291642 on 4 procs for 10000 steps with 16 atoms - -Performance: 29625.313 tau/day, 34288.557 timesteps/s -96.6% CPU use with 4 MPI tasks x 1 OpenMP threads - -MPI task timing breakdown: -Section | min time | avg time | max time |%varavg| %total ---------------------------------------------------------------- -Pair | 0.0035026 | 0.1107 | 0.20674 | 28.3 | 37.96 -Bond | 0.00062203 | 0.0029532 | 0.0049176 | 3.6 | 1.01 -Neigh | 0 | 0 | 0 | 0.0 | 0.00 -Comm | 0.016712 | 0.018041 | 0.01914 | 0.7 | 6.19 -Output | 5.0306e-05 | 5.424e-05 | 5.579e-05 | 0.0 | 0.02 -Modify | 0.0013862 | 0.020914 | 0.039594 | 11.7 | 7.17 -Other | | 0.139 | | | 47.65 - -Nlocal: 4 ave 8 max 0 min -Histogram: 1 1 0 0 0 0 0 0 1 1 -Nghost: 11 ave 14 max 8 min -Histogram: 1 1 0 0 0 0 0 0 1 1 -Neighs: 46 ave 89 max 0 min -Histogram: 1 1 0 0 0 0 0 0 0 2 - -Total # of neighbors = 184 -Ave neighs/atom = 11.5 -Ave special neighs/atom = 3.75 -Neighbor list builds = 0 -Dangerous builds = 0 - -#write_restart config.${number}.* -Total wall time: 0:00:00 diff --git a/examples/USER/cgdna/examples/oxDNA2/duplex3/data.duplex3 b/examples/USER/cgdna/examples/oxDNA2/duplex3/data.duplex3 new file mode 100644 index 0000000000..bbd584163b --- /dev/null +++ b/examples/USER/cgdna/examples/oxDNA2/duplex3/data.duplex3 @@ -0,0 +1,73 @@ +# LAMMPS data file +10 atoms +10 ellipsoids +8 bonds + +4 atom types +1 bond types + +# System size +-20.000000 20.000000 xlo xhi +-20.000000 20.000000 ylo yhi +-20.000000 20.000000 zlo zhi + +Masses + +1 1.0 +2 1.0 +3 1.0 +4 1.0 + +# Atom-ID, type, position, molecule-ID, ellipsoid flag, density +Atoms + +1 1 -6.000000000000001e-01 0.000000000000000e+00 0.000000000000000e+00 1 1 1 +2 2 -4.860249842674776e-01 -3.518234140414736e-01 3.897628551303122e-01 1 1 1 +3 3 -1.874009511073395e-01 -5.699832309147915e-01 7.795257102606244e-01 1 1 1 +4 4 1.824198365552941e-01 -5.715968887521518e-01 1.169288565390937e+00 1 1 1 +5 1 4.829362784135484e-01 -3.560513319622209e-01 1.559051420521249e+00 1 1 1 +6 4 -4.829362784135484e-01 3.560513319622209e-01 1.559051420521249e+00 2 1 1 +7 1 -1.824198365552941e-01 5.715968887521516e-01 1.169288565390937e+00 2 1 1 +8 2 1.874009511073395e-01 5.699832309147913e-01 7.795257102606243e-01 2 1 1 +9 3 4.860249842674775e-01 3.518234140414733e-01 3.897628551303121e-01 2 1 1 +10 4 5.999999999999996e-01 -1.332267629550188e-16 -1.110223024625157e-16 2 1 1 + +# Atom-ID, translational velocity, angular momentum +Velocities + +1 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 +2 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 +3 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 +4 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 +5 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 +6 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 +7 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 +8 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 +9 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 +10 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 + +# Atom-ID, shape, quaternion +Ellipsoids + +1 3.1622776601683795+00 3.1622776601683795+00 3.1622776601683795+00 1.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 +2 3.1622776601683795+00 3.1622776601683795+00 3.1622776601683795+00 9.513258223252946e-01 0.000000000000000e+00 0.000000000000000e+00 3.081869234362515e-01 +3 3.1622776601683795+00 3.1622776601683795+00 3.1622776601683795+00 8.100416404457962e-01 0.000000000000000e+00 0.000000000000000e+00 5.863723567357894e-01 +4 3.1622776601683795+00 3.1622776601683795+00 3.1622776601683795+00 5.899012371043606e-01 0.000000000000000e+00 0.000000000000000e+00 8.074754054847398e-01 +5 3.1622776601683795+00 3.1622776601683795+00 3.1622776601683795+00 3.123349185122326e-01 0.000000000000000e+00 0.000000000000000e+00 9.499720515246527e-01 +6 3.1622776601683795+00 3.1622776601683795+00 3.1622776601683795+00 0.000000000000000e+00 9.499720515246527e-01 -3.123349185122326e-01 -0.000000000000000e+00 +7 3.1622776601683795+00 3.1622776601683795+00 3.1622776601683795+00 0.000000000000000e+00 8.074754054847401e-01 -5.899012371043604e-01 0.000000000000000e+00 +8 3.1622776601683795+00 3.1622776601683795+00 3.1622776601683795+00 0.000000000000000e+00 5.863723567357896e-01 -8.100416404457959e-01 0.000000000000000e+00 +9 3.1622776601683795+00 3.1622776601683795+00 3.1622776601683795+00 -0.000000000000000e+00 -3.081869234362514e-01 9.513258223252947e-01 0.000000000000000e+00 +10 3.1622776601683795+00 3.1622776601683795+00 3.1622776601683795+00 -0.000000000000000e+00 1.110223024625157e-16 1.000000000000000e+00 -0.000000000000000e+00 + +# Bond topology +Bonds + +1 1 1 2 +2 1 2 3 +3 1 3 4 +4 1 4 5 +5 1 6 7 +6 1 7 8 +7 1 8 9 +8 1 9 10 diff --git a/examples/USER/cgdna/examples/oxDNA2/duplex3/in.duplex3 b/examples/USER/cgdna/examples/oxDNA2/duplex3/in.duplex3 new file mode 100644 index 0000000000..51d6334f55 --- /dev/null +++ b/examples/USER/cgdna/examples/oxDNA2/duplex3/in.duplex3 @@ -0,0 +1,79 @@ +variable number equal 1 +variable ofreq equal 1000 +variable efreq equal 1000 +variable T equal 0.1 + +units lj + +dimension 3 + +newton off + +boundary p p p + +atom_style hybrid bond ellipsoid +atom_modify sort 0 1.0 + +# Pair interactions require lists of neighbours to be calculated +neighbor 1.0 bin +neigh_modify every 1 delay 0 check yes + +read_data data.duplex3 + +set atom * mass 1.0 + +group all type 1 4 + +# oxDNA bond interactions - FENE backbone +bond_style oxdna2/fene +bond_coeff * 2.0 0.25 0.7564 + +# oxDNA pair interactions +pair_style hybrid/overlay oxdna2/excv oxdna2/stk oxdna2/hbond oxdna2/xstk oxdna2/coaxstk oxdna2/dh +pair_coeff * * oxdna2/excv 2.0 0.7 0.675 2.0 0.515 0.5 2.0 0.33 0.32 +pair_coeff * * oxdna2/stk seqdep ${T} 1.3523 2.6717 6.0 0.4 0.9 0.32 0.6 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2.0 0.65 2.0 0.65 +pair_coeff * * oxdna2/hbond seqdep 0.0 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45 +pair_coeff 1 4 oxdna2/hbond seqdep 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45 +pair_coeff 2 3 oxdna2/hbond seqdep 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45 +pair_coeff * * oxdna2/xstk 47.5 0.575 0.675 0.495 0.655 2.25 0.791592653589793 0.58 1.7 1.0 0.68 1.7 1.0 0.68 1.5 0 0.65 1.7 0.875 0.68 1.7 0.875 0.68 +pair_coeff * * oxdna2/coaxstk 58.5 0.4 0.6 0.22 0.58 2.0 2.891592653589793 0.65 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 40.0 3.116592653589793 +pair_coeff * * oxdna2/dh ${T} 1.0 0.815 + +# NVE ensemble +fix 1 all nve/dot +#fix 1 all nve/dotc/langevin ${T} ${T} 0.03 457145 angmom 10 +#fix 1 all nve/asphere +#fix 2 all langevin ${T} ${T} 0.03 457145 angmom 10 + +timestep 1e-5 + +#comm_style tiled +#fix 3 all balance 10000 1.1 rcb + +#compute mol all chunk/atom molecule +#compute mychunk all vcm/chunk mol +#fix 4 all ave/time 10000 1 10000 c_mychunk[1] c_mychunk[2] c_mychunk[3] file vcm.txt mode vector + +#dump pos all xyz ${ofreq} traj.${number}.xyz + +#compute quat all property/atom quatw quati quatj quatk +#dump quat all custom ${ofreq} quat.${number}.txt id c_quat[1] c_quat[2] c_quat[3] c_quat[4] +#dump_modify quat sort id +#dump_modify quat format line "%d %13.6le %13.6le %13.6le %13.6le" + +compute erot all erotate/asphere +compute ekin all ke +compute epot all pe +variable erot equal c_erot +variable ekin equal c_ekin +variable epot equal c_epot +variable etot equal c_erot+c_ekin+c_epot +fix 5 all print ${efreq} "$(step) ekin = ${ekin} | erot = ${erot} | epot = ${epot} | etot = ${etot}" screen yes + +#dump out all custom ${ofreq} out.${number}.txt id x y z vx vy vz fx fy fz tqx tqy tqz +#dump_modify out sort id +#dump_modify out format line "%d %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le" + +run 1000000 + +#write_restart config.${number}.* diff --git a/examples/USER/cgdna/examples/oxDNA2/duplex3/log.18Jun19.duplex3.g++.1 b/examples/USER/cgdna/examples/oxDNA2/duplex3/log.18Jun19.duplex3.g++.1 new file mode 100644 index 0000000000..6b8b7161d5 --- /dev/null +++ b/examples/USER/cgdna/examples/oxDNA2/duplex3/log.18Jun19.duplex3.g++.1 @@ -0,0 +1,1172 @@ +LAMMPS (18 Jun 2019) +variable number equal 1 +variable ofreq equal 1000 +variable efreq equal 1000 +variable T equal 0.1 + +units lj + +dimension 3 + +newton off + +boundary p p p + +atom_style hybrid bond ellipsoid +atom_modify sort 0 1.0 + +# Pair interactions require lists of neighbours to be calculated +neighbor 1.0 bin +neigh_modify every 1 delay 0 check yes + +read_data data.duplex3 + orthogonal box = (-20 -20 -20) to (20 20 20) + 1 by 1 by 1 MPI processor grid + reading atoms ... + 10 atoms + reading velocities ... + 10 velocities + 10 ellipsoids + scanning bonds ... + 2 = max bonds/atom + reading bonds ... + 8 bonds + 2 = max # of 1-2 neighbors + 2 = max # of 1-3 neighbors + 2 = max # of 1-4 neighbors + 4 = max # of special neighbors + special bonds CPU = 0.000113 secs + read_data CPU = 0.00275 secs + +set atom * mass 1.0 + 10 settings made for mass + +group all type 1 4 +10 atoms in group all + +# oxDNA bond interactions - FENE backbone +bond_style oxdna2/fene +bond_coeff * 2.0 0.25 0.7564 + +# oxDNA pair interactions +pair_style hybrid/overlay oxdna2/excv oxdna2/stk oxdna2/hbond oxdna2/xstk oxdna2/coaxstk oxdna2/dh +pair_coeff * * oxdna2/excv 2.0 0.7 0.675 2.0 0.515 0.5 2.0 0.33 0.32 +pair_coeff * * oxdna2/stk seqdep ${T} 1.3523 2.6717 6.0 0.4 0.9 0.32 0.6 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2.0 0.65 2.0 0.65 +pair_coeff * * oxdna2/stk seqdep 0.1 1.3523 2.6717 6.0 0.4 0.9 0.32 0.6 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2.0 0.65 2.0 0.65 +pair_coeff * * oxdna2/hbond seqdep 0.0 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45 +pair_coeff 1 4 oxdna2/hbond seqdep 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45 +pair_coeff 2 3 oxdna2/hbond seqdep 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45 +pair_coeff * * oxdna2/xstk 47.5 0.575 0.675 0.495 0.655 2.25 0.791592653589793 0.58 1.7 1.0 0.68 1.7 1.0 0.68 1.5 0 0.65 1.7 0.875 0.68 1.7 0.875 0.68 +pair_coeff * * oxdna2/coaxstk 58.5 0.4 0.6 0.22 0.58 2.0 2.891592653589793 0.65 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 40.0 3.116592653589793 +pair_coeff * * oxdna2/dh ${T} 1.0 0.815 +pair_coeff * * oxdna2/dh 0.1 1.0 0.815 + +# NVE ensemble +fix 1 all nve/dot +#fix 1 all nve/dotc/langevin ${T} ${T} 0.03 457145 angmom 10 +#fix 1 all nve/asphere +#fix 2 all langevin ${T} ${T} 0.03 457145 angmom 10 + +timestep 1e-5 + +#comm_style tiled +#fix 3 all balance 10000 1.1 rcb + +#compute mol all chunk/atom molecule +#compute mychunk all vcm/chunk mol +#fix 4 all ave/time 10000 1 10000 c_mychunk[1] c_mychunk[2] c_mychunk[3] file vcm.txt mode vector + +#dump pos all xyz ${ofreq} traj.${number}.xyz + +#compute quat all property/atom quatw quati quatj quatk +#dump quat all custom ${ofreq} quat.${number}.txt id c_quat[1] c_quat[2] c_quat[3] c_quat[4] +#dump_modify quat sort id +#dump_modify quat format line "%d %13.6le %13.6le %13.6le %13.6le" + +compute erot all erotate/asphere +compute ekin all ke +compute epot all pe +variable erot equal c_erot +variable ekin equal c_ekin +variable epot equal c_epot +variable etot equal c_erot+c_ekin+c_epot +fix 5 all print ${efreq} "$(step) ekin = ${ekin} | erot = ${erot} | epot = ${epot} | etot = ${etot}" screen yes +fix 5 all print 1000 "$(step) ekin = ${ekin} | erot = ${erot} | epot = ${epot} | etot = ${etot}" screen yes + +#dump out all custom ${ofreq} out.${number}.txt id x y z vx vy vz fx fy fz tqx tqy tqz +#dump_modify out sort id +#dump_modify out format line "%d %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le" + +run 1000000 +Neighbor list info ... + update every 1 steps, delay 0 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 2.6274 + ghost atom cutoff = 2.6274 + binsize = 1.3137, bins = 31 31 31 + 6 neighbor lists, perpetual/occasional/extra = 6 0 0 + (1) pair oxdna2/excv, perpetual + attributes: half, newton off + pair build: half/bin/newtoff + stencil: half/bin/3d/newtoff + bin: standard + (2) pair oxdna2/stk, perpetual, copy from (1) + attributes: half, newton off + pair build: copy + stencil: none + bin: none + (3) pair oxdna2/hbond, perpetual, copy from (1) + attributes: half, newton off + pair build: copy + stencil: none + bin: none + (4) pair oxdna2/xstk, perpetual, copy from (1) + attributes: half, newton off + pair build: copy + stencil: none + bin: none + (5) pair oxdna2/coaxstk, perpetual, copy from (1) + attributes: half, newton off + pair build: copy + stencil: none + bin: none + (6) pair oxdna2/dh, perpetual, copy from (1) + attributes: half, newton off + pair build: copy + stencil: none + bin: none +Per MPI rank memory allocation (min/avg/max) = 3.023 | 3.023 | 3.023 Mbytes +Step Temp E_pair E_mol TotEng Press + 0 0 -1.4720158 0.009525411 -1.4624904 3.1370518e-06 +1000 ekin = 0.00366431201929618 | erot = 0.00193726360267488 | epot = -14.630505317301 | etot = -14.624903741679 +2000 ekin = 0.0144775076075466 | erot = 0.00770914672938582 | epot = -14.6470903960565 | etot = -14.6249037417196 +3000 ekin = 0.0319122186081549 | erot = 0.0171972328649101 | epot = -14.6740131932573 | etot = -14.6249037417842 +4000 ekin = 0.0551283043509704 | erot = 0.0302085305548002 | epot = -14.7102405767754 | etot = -14.6249037418696 +5000 ekin = 0.0830285165715823 | erot = 0.0464820547541705 | epot = -14.7544143132963 | etot = -14.6249037419705 +6000 ekin = 0.114331121546757 | erot = 0.0656980211282096 | epot = -14.8049328847556 | etot = -14.6249037420806 +7000 ekin = 0.147653866561892 | erot = 0.0874894888755386 | epot = -14.860047097631 | etot = -14.6249037421936 +8000 ekin = 0.181602099560207 | erot = 0.111456095727703 | epot = -14.9179619375911 | etot = -14.6249037423032 +9000 ekin = 0.214852894725919 | erot = 0.137179311245174 | epot = -14.9769359483746 | etot = -14.6249037424035 +10000 ekin = 0.246227151956033 | erot = 0.164238435218395 | epot = -15.0353693296648 | etot = -14.6249037424904 +11000 ekin = 0.274743080419051 | erot = 0.192226420003239 | epot = -15.0918732429829 | etot = -14.6249037425607 +12000 ekin = 0.2996471417657 | erot = 0.220764512146651 | epot = -15.1453153965252 | etot = -14.6249037426128 +13000 ekin = 0.320421918860966 | erot = 0.249514690530541 | epot = -15.1948403520385 | etot = -14.624903742647 +14000 ekin = 0.33677373488436 | erot = 0.27818893373049 | epot = -15.2398664112793 | etot = -14.6249037426645 +15000 ekin = 0.348605413762901 | erot = 0.306554508009418 | epot = -15.2800636644399 | etot = -14.6249037426675 +16000 ekin = 0.355980829097854 | erot = 0.334434770083744 | epot = -15.3153193418402 | etot = -14.6249037426586 +17000 ekin = 0.35908770105941 | erot = 0.361705441666512 | epot = -15.3456968853664 | etot = -14.6249037426405 +18000 ekin = 0.358203710992239 | erot = 0.388286889516313 | epot = -15.3713943431242 | etot = -14.6249037426156 +19000 ekin = 0.353668912555234 | erot = 0.414133518537107 | epot = -15.3927061736788 | etot = -14.6249037425864 +20000 ekin = 0.345865220775291 | erot = 0.439221805285432 | epot = -15.4099907686153 | etot = -14.6249037425546 +21000 ekin = 0.335201981146472 | erot = 0.463538642606515 | epot = -15.4236443662748 | etot = -14.6249037425218 +22000 ekin = 0.322105588834903 | erot = 0.487071492273063 | epot = -15.4340808235971 | etot = -14.6249037424892 +23000 ekin = 0.307010918596165 | erot = 0.509801406229371 | epot = -15.4417160672832 | etot = -14.6249037424577 +24000 ekin = 0.290352786033169 | erot = 0.531699400501692 | epot = -15.446955928963 | etot = -14.6249037424281 +25000 ekin = 0.272556500902037 | erot = 0.552726088759198 | epot = -15.4501863320622 | etot = -14.624903742401 +26000 ekin = 0.254027484079049 | erot = 0.572834017299018 | epot = -15.4517652437547 | etot = -14.6249037423766 +27000 ekin = 0.23514066521633 | erot = 0.591971851501221 | epot = -15.4520162590729 | etot = -14.6249037423553 +28000 ekin = 0.216230835846198 | erot = 0.610089455964333 | epot = -15.4512240341478 | etot = -14.6249037423373 +29000 ekin = 0.197585285158555 | erot = 0.627142960082633 | epot = -15.4496319875635 | etot = -14.6249037423223 +30000 ekin = 0.179439940173318 | erot = 0.643099062793407 | epot = -15.4474427452769 | etot = -14.6249037423102 +31000 ekin = 0.161979935826124 | erot = 0.657938056392308 | epot = -15.4448217345186 | etot = -14.6249037423001 +32000 ekin = 0.145345108983022 | erot = 0.671655297433962 | epot = -15.4419041487086 | etot = -14.6249037422916 +33000 ekin = 0.12964040034519 | erot = 0.684261083518556 | epot = -15.4388052261475 | etot = -14.6249037422838 +34000 ekin = 0.114950474500008 | erot = 0.695779112936504 | epot = -15.4356333297121 | etot = -14.6249037422756 +35000 ekin = 0.10135710346033 | erot = 0.706243888527894 | epot = -15.4325047342544 | etot = -14.6249037422662 +36000 ekin = 0.088957633457107 | erot = 0.715697403164625 | epot = -15.4295587788764 | etot = -14.6249037422546 +37000 ekin = 0.0778817390290652 | erot = 0.72418563863568 | epot = -15.4269711199052 | etot = -14.6249037422404 +38000 ekin = 0.068303709154812 | erot = 0.731755309647473 | epot = -15.4249627610255 | etot = -14.6249037422232 +39000 ekin = 0.0604476327394706 | erot = 0.738451228922909 | epot = -15.4238026038659 | etot = -14.6249037422035 +40000 ekin = 0.0545835914676979 | erot = 0.7443145576821 | epot = -15.4238018913318 | etot = -14.624903742182 +41000 ekin = 0.0510142787133839 | erot = 0.749382063190735 | epot = -15.4253000840641 | etot = -14.6249037421599 +42000 ekin = 0.0500531571157636 | erot = 0.753686350478931 | epot = -15.428643249734 | etot = -14.6249037421393 +43000 ekin = 0.0519969858278391 | erot = 0.757256889238991 | epot = -15.4341576171885 | etot = -14.6249037421217 +44000 ekin = 0.0570968352184469 | erot = 0.760121540481399 | epot = -15.4421221178085 | etot = -14.6249037421087 +45000 ekin = 0.065532155346979 | erot = 0.762308219230476 | epot = -15.4527441166789 | etot = -14.6249037421014 +46000 ekin = 0.077391880036746 | erot = 0.763846321567568 | epot = -15.4661419437049 | etot = -14.6249037421006 +47000 ekin = 0.0926650518887463 | erot = 0.764767599959976 | epot = -15.4823363939546 | etot = -14.6249037421059 +48000 ekin = 0.111241466891021 | erot = 0.76510628368957 | epot = -15.5012514926977 | etot = -14.6249037421171 +49000 ekin = 0.132920935183101 | erot = 0.764898395951945 | epot = -15.5227230732685 | etot = -14.6249037421334 +50000 ekin = 0.157428432862297 | erot = 0.764180392178817 | epot = -15.5465125671951 | etot = -14.624903742154 +51000 ekin = 0.184431879186394 | erot = 0.762987403181186 | epot = -15.5723230245453 | etot = -14.6249037421777 +52000 ekin = 0.213559336999611 | erot = 0.761351471408957 | epot = -15.5998145506125 | etot = -14.6249037422039 +53000 ekin = 0.244412677541745 | erot = 0.759300175100897 | epot = -15.6286165948748 | etot = -14.6249037422322 +54000 ekin = 0.276574826726797 | erot = 0.756855909736049 | epot = -15.6583344787255 | etot = -14.6249037422626 +55000 ekin = 0.30960770869724 | erot = 0.754035838659133 | epot = -15.6885472896526 | etot = -14.6249037422962 +56000 ekin = 0.343038597242155 | erot = 0.750852192167397 | epot = -15.7187945317444 | etot = -14.6249037423348 +57000 ekin = 0.376334705011604 | erot = 0.747312289063754 | epot = -15.7485507364561 | etot = -14.6249037423808 +58000 ekin = 0.408870193943412 | erot = 0.743417624903535 | epot = -15.7771915612832 | etot = -14.6249037424363 +59000 ekin = 0.439895666476021 | erot = 0.739161690570186 | epot = -15.803961099549 | etot = -14.6249037425028 +60000 ekin = 0.468524372325726 | erot = 0.734526514748657 | epot = -15.8279546296536 | etot = -14.6249037425792 +61000 ekin = 0.493750804630799 | erot = 0.729479048550173 | epot = -15.8481335958428 | etot = -14.6249037426618 +62000 ekin = 0.514511417905549 | erot = 0.723968952963015 | epot = -15.8633841136119 | etot = -14.6249037427433 +63000 ekin = 0.529785687820656 | erot = 0.717929490923262 | epot = -15.8726189215586 | etot = -14.6249037428146 +64000 ekin = 0.538722043349821 | erot = 0.711282639870032 | epot = -15.874908426086 | etot = -14.6249037428661 +65000 ekin = 0.540763046401741 | erot = 0.703948378732647 | epot = -15.8696151680245 | etot = -14.6249037428901 +66000 ekin = 0.535742115226795 | erot = 0.69585678068686 | epot = -15.856502638796 | etot = -14.6249037428824 +67000 ekin = 0.523930969354056 | erot = 0.686960578434575 | epot = -15.8357952906315 | etot = -14.6249037428429 +68000 ekin = 0.506029704478054 | erot = 0.677245632040232 | epot = -15.8081790792936 | etot = -14.6249037427753 +69000 ekin = 0.483104826199992 | erot = 0.666737270644537 | epot = -15.774745839531 | etot = -14.6249037426865 +70000 ekin = 0.456490218293252 | erot = 0.655501536743317 | epot = -15.7368954976212 | etot = -14.6249037425847 +71000 ekin = 0.427669918862549 | erot = 0.643641521526345 | epot = -15.6962151828672 | etot = -14.6249037424783 +72000 ekin = 0.398160338931557 | erot = 0.631289876691081 | epot = -15.654353957998 | etot = -14.6249037423754 +73000 ekin = 0.369405258276815 | erot = 0.618599034382849 | epot = -15.6129080349415 | etot = -14.6249037422819 +74000 ekin = 0.342691749042209 | erot = 0.605730669564501 | epot = -15.5733261608092 | etot = -14.6249037422025 +75000 ekin = 0.31909052680686 | erot = 0.59284563490598 | epot = -15.5368399038529 | etot = -14.62490374214 +76000 ekin = 0.299420611427412 | erot = 0.580095163563671 | epot = -15.5044195170868 | etot = -14.6249037420957 +77000 ekin = 0.284235504574989 | erot = 0.567613716752661 | epot = -15.4767529633973 | etot = -14.6249037420697 +78000 ekin = 0.273826140866561 | erot = 0.555513536864305 | epot = -15.454243419792 | etot = -14.6249037420611 +79000 ekin = 0.268234635497613 | erot = 0.54388078034572 | epot = -15.4370191579124 | etot = -14.624903742069 +80000 ekin = 0.267272602906451 | erot = 0.532773036269929 | epot = -15.4249493812687 | etot = -14.6249037420923 +81000 ekin = 0.270538934182559 | erot = 0.522218059775773 | epot = -15.4176607360884 | etot = -14.6249037421301 +82000 ekin = 0.277434574359295 | erot = 0.512213638248342 | epot = -15.4145519547894 | etot = -14.6249037421818 +83000 ekin = 0.287175732620333 | erot = 0.50272864056942 | epot = -15.414808115436 | etot = -14.6249037422462 +84000 ekin = 0.298811175848678 | erot = 0.493705451301681 | epot = -15.4174203694717 | etot = -14.6249037423214 +85000 ekin = 0.311252369949697 | erot = 0.485064122067565 | epot = -15.4212202344211 | etot = -14.6249037424038 +86000 ekin = 0.323325626375984 | erot = 0.476708618161036 | epot = -15.424937987025 | etot = -14.624903742488 +87000 ekin = 0.333851795518747 | erot = 0.468535420697862 | epot = -15.4272909587828 | etot = -14.6249037425662 +88000 ekin = 0.341751109758396 | erot = 0.460444399763919 | epot = -15.427099252152 | etot = -14.6249037426296 +89000 ekin = 0.346159825920001 | erot = 0.452351304178873 | epot = -15.4234148727693 | etot = -14.6249037426704 +90000 ekin = 0.346534667470265 | erot = 0.444200535918399 | epot = -15.4156389460718 | etot = -14.6249037426831 +91000 ekin = 0.342715665475867 | erot = 0.435976333753397 | epot = -15.4035957418967 | etot = -14.6249037426674 +92000 ekin = 0.3349227158513 | erot = 0.427710377227648 | epot = -15.3875368357071 | etot = -14.6249037426282 +93000 ekin = 0.323677844433752 | erot = 0.419484336039963 | epot = -15.3680659230484 | etot = -14.6249037425747 +94000 ekin = 0.30966978292125 | erot = 0.411426964072553 | epot = -15.3460004895119 | etot = -14.6249037425181 +95000 ekin = 0.293600014861622 | erot = 0.403706586473099 | epot = -15.3222103438021 | etot = -14.6249037424674 +96000 ekin = 0.276058284884091 | erot = 0.396520701306161 | epot = -15.2974827286175 | etot = -14.6249037424272 +97000 ekin = 0.25746445629565 | erot = 0.390084510982946 | epot = -15.2724527096753 | etot = -14.6249037423967 +98000 ekin = 0.238086767082953 | erot = 0.384619533405539 | epot = -15.2476100428595 | etot = -14.624903742371 +99000 ekin = 0.218116994125883 | erot = 0.380342481668092 | epot = -15.2233632181382 | etot = -14.6249037423442 +100000 ekin = 0.197764845956536 | erot = 0.377453964065333 | epot = -15.2001225523339 | etot = -14.624903742312 +101000 ekin = 0.177333852671335 | erot = 0.376126621697227 | epot = -15.1783642166414 | etot = -14.6249037422728 +102000 ekin = 0.157255732179445 | erot = 0.376493003927733 | epot = -15.1586524783356 | etot = -14.6249037422284 +103000 ekin = 0.138079925448889 | erot = 0.378634329970018 | epot = -15.1416179976015 | etot = -14.6249037421826 +104000 ekin = 0.120430234291316 | erot = 0.382571791335251 | epot = -15.1279057677665 | etot = -14.6249037421399 +105000 ekin = 0.10494672239352 | erot = 0.388261944551333 | epot = -15.118112409049 | etot = -14.6249037421041 +106000 ekin = 0.0922291289493497 | erot = 0.395597086392468 | epot = -15.11272995742 | etot = -14.6249037420782 +107000 ekin = 0.0827918191991084 | erot = 0.404410579138465 | epot = -15.112106140401 | etot = -14.6249037420634 +108000 ekin = 0.0770336430609741 | erot = 0.414486225075992 | epot = -15.116423610197 | etot = -14.62490374206 +109000 ekin = 0.075221312117861 | erot = 0.425570202879186 | epot = -15.1256952570646 | etot = -14.6249037420675 +110000 ekin = 0.0774826364247882 | erot = 0.437383858086522 | epot = -15.1397702365965 | etot = -14.6249037420852 +111000 ekin = 0.0838057148048547 | erot = 0.449635759436015 | epot = -15.1583452163526 | etot = -14.6249037421117 +112000 ekin = 0.0940411317710077 | erot = 0.462031808376879 | epot = -15.1809766822946 | etot = -14.6249037421467 +113000 ekin = 0.107905661684195 | erot = 0.474282718869093 | epot = -15.2070921227426 | etot = -14.6249037421893 +114000 ekin = 0.124987416380568 | erot = 0.486108767327343 | epot = -15.2359999259468 | etot = -14.6249037422389 +115000 ekin = 0.14475347442169 | erot = 0.497242253023055 | epot = -15.2668994697394 | etot = -14.6249037422947 +116000 ekin = 0.166561593123301 | erot = 0.507428522971045 | epot = -15.2988938584499 | etot = -14.6249037423555 +117000 ekin = 0.189677527330859 | erot = 0.516426638198687 | epot = -15.3310079079495 | etot = -14.6249037424199 +118000 ekin = 0.213298790897302 | erot = 0.524010758771369 | epot = -15.3622132921543 | etot = -14.6249037424857 +119000 ekin = 0.23658457696156 | erot = 0.529973112381439 | epot = -15.3914614318934 | etot = -14.6249037425504 +120000 ekin = 0.25869030185824 | erot = 0.534129034925715 | epot = -15.4177230793952 | etot = -14.6249037426113 +121000 ekin = 0.278804196532859 | erot = 0.536324108799716 | epot = -15.4400320479982 | etot = -14.6249037426656 +122000 ekin = 0.296182819519396 | erot = 0.536442962870823 | epot = -15.4575295251008 | etot = -14.6249037427106 +123000 ekin = 0.310182446405815 | erot = 0.534418915104236 | epot = -15.4695051042542 | etot = -14.6249037427442 +124000 ekin = 0.320283972930007 | erot = 0.530243389137678 | epot = -15.4754311048322 | etot = -14.6249037427645 +125000 ekin = 0.326110081462184 | erot = 0.523973945236141 | epot = -15.474987769469 | etot = -14.6249037427707 +126000 ekin = 0.327434709614433 | erot = 0.515739832556637 | epot = -15.4680782849335 | etot = -14.6249037427625 +127000 ekin = 0.324186046690112 | erot = 0.505744172152634 | epot = -15.4548339615826 | etot = -14.6249037427399 +128000 ekin = 0.316445106703942 | erot = 0.49426218578474 | epot = -15.4356110351922 | etot = -14.6249037427035 +129000 ekin = 0.304442167762443 | erot = 0.481635256753056 | epot = -15.4109811671698 | etot = -14.6249037426543 +130000 ekin = 0.288552887156219 | erot = 0.468261006625427 | epot = -15.381717636375 | etot = -14.6249037425933 +131000 ekin = 0.269294696165104 | erot = 0.454579955598623 | epot = -15.3487783942857 | etot = -14.624903742522 +132000 ekin = 0.247322351785515 | erot = 0.44105966132284 | epot = -15.3132857555502 | etot = -14.6249037424419 +133000 ekin = 0.223419723871429 | erot = 0.428177456066543 | epot = -15.276500922293 | etot = -14.6249037423551 +134000 ekin = 0.198483666316777 | erot = 0.416402982921072 | epot = -15.2397903915022 | etot = -14.6249037422644 +135000 ekin = 0.173495806295108 | erot = 0.40618164100245 | epot = -15.2045811894712 | etot = -14.6249037421736 +136000 ekin = 0.149479658252647 | erot = 0.397919790440824 | epot = -15.1723031907806 | etot = -14.6249037420871 +137000 ekin = 0.127443476996608 | erot = 0.391972186713592 | epot = -15.1443194057199 | etot = -14.6249037420097 +138000 ekin = 0.10831297052536 | erot = 0.388631700836367 | epot = -15.1218484133082 | etot = -14.6249037419464 +139000 ekin = 0.0928612988418002 | erot = 0.388121053034821 | epot = -15.1058860937783 | etot = -14.6249037419017 +140000 ekin = 0.0816456573910084 | erot = 0.390586148388801 | epot = -15.0971355476587 | etot = -14.6249037418789 +141000 ekin = 0.0749596349872437 | erot = 0.396090706683564 | epot = -15.0959540835505 | etot = -14.6249037418797 +142000 ekin = 0.0728085537690405 | erot = 0.404612196534891 | epot = -15.1023244922084 | etot = -14.6249037419044 +143000 ekin = 0.0749117535383842 | erot = 0.416039504837645 | epot = -15.1158550003269 | etot = -14.6249037419509 +144000 ekin = 0.0807320498020964 | erot = 0.43017313668478 | epot = -15.1358089285024 | etot = -14.6249037420156 +145000 ekin = 0.08952902558338 | erot = 0.446728893938156 | epot = -15.1611616616151 | etot = -14.6249037420935 +146000 ekin = 0.100429851263191 | erot = 0.465345829669622 | epot = -15.1906794231115 | etot = -14.6249037421787 +147000 ekin = 0.112509264558581 | erot = 0.485598823528122 | epot = -15.2230118303515 | etot = -14.6249037422648 +148000 ekin = 0.124869425792591 | erot = 0.507015469189552 | epot = -15.2567886373282 | etot = -14.6249037423461 +149000 ekin = 0.136710750658436 | erot = 0.529096273051187 | epot = -15.290710766127 | etot = -14.6249037424174 +150000 ekin = 0.147386480806171 | erot = 0.551336607352345 | epot = -15.323626830634 | etot = -14.6249037424755 +151000 ekin = 0.156436378416032 | erot = 0.573248570645276 | epot = -15.3545886915794 | etot = -14.6249037425181 +152000 ekin = 0.163597998371653 | erot = 0.594380933602923 | epot = -15.3828826745196 | etot = -14.624903742545 +153000 ekin = 0.168796920199611 | erot = 0.614335653334474 | epot = -15.4080363160912 | etot = -14.6249037425571 +154000 ekin = 0.172119667637745 | erot = 0.63277992909172 | epot = -15.4298033392862 | etot = -14.6249037425567 +155000 ekin = 0.173774602206285 | erot = 0.649453329865168 | epot = -15.448131674618 | etot = -14.6249037425466 +156000 ekin = 0.174046854480021 | erot = 0.664170048550552 | epot = -15.4631206455605 | etot = -14.62490374253 +157000 ekin = 0.173253451016122 | erot = 0.676816762702534 | epot = -15.4749739562284 | etot = -14.6249037425097 +158000 ekin = 0.171704281293749 | erot = 0.687346881268012 | epot = -15.48395490505 | etot = -14.6249037424883 +159000 ekin = 0.169673443699862 | erot = 0.695772131173121 | epot = -15.4903493173403 | etot = -14.6249037424673 +160000 ekin = 0.167383826014546 | erot = 0.702152502586509 | epot = -15.4944400710487 | etot = -14.6249037424476 +161000 ekin = 0.165005624031702 | erot = 0.706585545944493 | epot = -15.4964949124054 | etot = -14.6249037424292 +162000 ekin = 0.162667154471752 | erot = 0.709195914790859 | epot = -15.4967668116741 | etot = -14.6249037424115 +163000 ekin = 0.160474189581485 | erot = 0.710125892129829 | epot = -15.4955038241048 | etot = -14.6249037423935 +164000 ekin = 0.158532578972596 | erot = 0.709527441008927 | epot = -15.4929637623557 | etot = -14.6249037423742 +165000 ekin = 0.156968465370669 | erot = 0.707556101121189 | epot = -15.4894283088449 | etot = -14.624903742353 +166000 ekin = 0.155941053191124 | erot = 0.704366832058078 | epot = -15.4852116275794 | etot = -14.6249037423302 +167000 ekin = 0.155644496809548 | erot = 0.700111698658369 | epot = -15.4806599377741 | etot = -14.6249037423062 +168000 ekin = 0.156297672988182 | erot = 0.694939119112873 | epot = -15.4761405343834 | etot = -14.6249037422823 +169000 ekin = 0.158122923325456 | erot = 0.688994262094025 | epot = -15.4720209276801 | etot = -14.6249037422606 +170000 ekin = 0.161316852937676 | erot = 0.682420091513849 | epot = -15.4686406866943 | etot = -14.6249037422428 +171000 ekin = 0.166017619146822 | erot = 0.675358520304806 | epot = -15.4662798816825 | etot = -14.6249037422309 +172000 ekin = 0.172273671159511 | erot = 0.667951149520835 | epot = -15.4651285629069 | etot = -14.6249037422266 +173000 ekin = 0.180018623556049 | erot = 0.660339136127854 | epot = -15.4652615019149 | etot = -14.624903742231 +174000 ekin = 0.189056055744924 | erot = 0.65266185183192 | epot = -15.4666216498214 | etot = -14.6249037422445 +175000 ekin = 0.199056860650113 | erot = 0.645054167286172 | epot = -15.4690147702031 | etot = -14.6249037422668 +176000 ekin = 0.209570701317552 | erot = 0.637642422787005 | epot = -15.4721168664013 | etot = -14.6249037422967 +177000 ekin = 0.220052442974625 | erot = 0.630539423737628 | epot = -15.4754956090443 | etot = -14.6249037423321 +178000 ekin = 0.229904071991194 | erot = 0.623839102439311 | epot = -15.4786469168001 | etot = -14.6249037423696 +179000 ekin = 0.238532114427982 | erot = 0.617611757777875 | epot = -15.4810476146108 | etot = -14.624903742405 +180000 ekin = 0.245419064060292 | erot = 0.611900922402653 | epot = -15.4822237288957 | etot = -14.6249037424328 +181000 ekin = 0.250203926055771 | erot = 0.606722796615248 | epot = -15.4818304651186 | etot = -14.6249037424476 +182000 ekin = 0.252761402919565 | erot = 0.602068750131856 | epot = -15.4797338954959 | etot = -14.6249037424445 +183000 ekin = 0.253262634974054 | erot = 0.597910660168588 | epot = -15.4760770375641 | etot = -14.6249037424214 +184000 ekin = 0.252195762131878 | erot = 0.594208023726969 | epot = -15.4713075282387 | etot = -14.6249037423799 +185000 ekin = 0.250326113306321 | erot = 0.59091517967259 | epot = -15.4661450353052 | etot = -14.6249037423263 +186000 ekin = 0.248586758541649 | erot = 0.587986907734566 | epot = -15.4614774085478 | etot = -14.6249037422716 +187000 ekin = 0.247909630265846 | erot = 0.585381224303701 | epot = -15.4581945967982 | etot = -14.6249037422286 +188000 ekin = 0.2490290523945 | erot = 0.583059148733781 | epot = -15.4569919433378 | etot = -14.6249037422095 +189000 ekin = 0.252303803181127 | erot = 0.580982165409763 | epot = -15.4581897108128 | etot = -14.6249037422219 +190000 ekin = 0.25760376351551 | erot = 0.579108718145144 | epot = -15.4616162239281 | etot = -14.6249037422675 +191000 ekin = 0.264292655598098 | erot = 0.577391223758838 | epot = -15.4665876216975 | etot = -14.6249037423406 +192000 ekin = 0.271315385056409 | erot = 0.575774831089113 | epot = -15.4719939585751 | etot = -14.6249037424296 +193000 ekin = 0.277374539132748 | erot = 0.574198584868256 | epot = -15.4764768665202 | etot = -14.6249037425192 +194000 ekin = 0.281161076019677 | erot = 0.572598913484698 | epot = -15.478663732098 | etot = -14.6249037425936 +195000 ekin = 0.281592637347121 | erot = 0.570914645865623 | epot = -15.4774110258523 | etot = -14.6249037426396 +196000 ekin = 0.278011867235596 | erot = 0.569092314484759 | epot = -15.4720079243693 | etot = -14.624903742649 +197000 ekin = 0.270307527592762 | erot = 0.567090473639989 | epot = -15.4623017438531 | etot = -14.6249037426204 +198000 ekin = 0.258940359975855 | erot = 0.564882125458807 | epot = -15.4487262279927 | etot = -14.6249037425581 +199000 ekin = 0.244877476699234 | erot = 0.562454912721902 | epot = -15.4322361318925 | etot = -14.6249037424713 +200000 ekin = 0.229456931018641 | erot = 0.559809284042077 | epot = -15.4141699574324 | etot = -14.6249037423716 +201000 ekin = 0.214214012278847 | erot = 0.556955381706859 | epot = -15.3960731362566 | etot = -14.6249037422709 +202000 ekin = 0.200701376135036 | erot = 0.553909032488863 | epot = -15.3795141508034 | etot = -14.6249037421795 +203000 ekin = 0.190329688710817 | erot = 0.550687503827512 | epot = -15.3659209346435 | etot = -14.6249037421052 +204000 ekin = 0.184246973275337 | erot = 0.547306655840007 | epot = -15.356457371168 | etot = -14.6249037420527 +205000 ekin = 0.183262973705813 | erot = 0.543779043729278 | epot = -15.3519457594592 | etot = -14.6249037420241 +206000 ekin = 0.187816949073515 | erot = 0.540113432736619 | epot = -15.3528341238291 | etot = -14.624903742019 +207000 ekin = 0.197980929490512 | erot = 0.536315658388676 | epot = -15.3592003299145 | etot = -14.6249037420353 +208000 ekin = 0.213487612677366 | erot = 0.53239049820727 | epot = -15.3707818529549 | etot = -14.6249037420703 +209000 ekin = 0.233772362712521 | erot = 0.528344018725095 | epot = -15.3870201235584 | etot = -14.6249037421208 +210000 ekin = 0.258021408692355 | erot = 0.524185756556833 | epot = -15.4071109074329 | etot = -14.6249037421837 +211000 ekin = 0.285222208429996 | erot = 0.519930104708342 | epot = -15.4300560553942 | etot = -14.6249037422558 +212000 ekin = 0.314215813604987 | erot = 0.515596398128489 | epot = -15.454715954067 | etot = -14.6249037423335 +213000 ekin = 0.343753634043937 | erot = 0.511207450608882 | epot = -15.4798648270658 | etot = -14.624903742413 +214000 ekin = 0.372561594270316 | erot = 0.506786560075337 | epot = -15.5042518968352 | etot = -14.6249037424895 +215000 ekin = 0.399412456462858 | erot = 0.502353347158712 | epot = -15.5266695461799 | etot = -14.6249037425583 +216000 ekin = 0.423202666203616 | erot = 0.497919155944113 | epot = -15.5460255647623 | etot = -14.6249037426146 +217000 ekin = 0.443025226540025 | erot = 0.493483013679004 | epot = -15.5614119828738 | etot = -14.6249037426548 +218000 ekin = 0.458227302378849 | erot = 0.489029294856436 | epot = -15.5721603399122 | etot = -14.6249037426769 +219000 ekin = 0.46844301918404 | erot = 0.484528125251435 | epot = -15.5778748871159 | etot = -14.6249037426804 +220000 ekin = 0.473598483116685 | erot = 0.479939108990801 | epot = -15.5784413347739 | etot = -14.6249037426664 +221000 ekin = 0.473894168318713 | erot = 0.475218183432529 | epot = -15.5740160943878 | etot = -14.6249037426366 +222000 ekin = 0.46977401404952 | erot = 0.470326483973494 | epot = -15.565004240616 | etot = -14.624903742593 +223000 ekin = 0.461887320397438 | erot = 0.465239349169368 | epot = -15.552030412105 | etot = -14.6249037425382 +224000 ekin = 0.45104133642262 | erot = 0.459953336121611 | epot = -15.5358984150202 | etot = -14.624903742476 +225000 ekin = 0.438137198422833 | erot = 0.454489515561399 | epot = -15.5175304563959 | etot = -14.6249037424116 +226000 ekin = 0.424086332826247 | erot = 0.448892294163513 | epot = -15.4978823693413 | etot = -14.6249037423516 +227000 ekin = 0.409717105195145 | erot = 0.443224250669953 | epot = -15.4778450981665 | etot = -14.6249037423014 +228000 ekin = 0.395692916861505 | erot = 0.437558473222737 | epot = -15.4581551323492 | etot = -14.6249037422649 +229000 ekin = 0.382463318564619 | erot = 0.431970318931211 | epot = -15.4393373797385 | etot = -14.6249037422426 +230000 ekin = 0.370258116730603 | erot = 0.426530223272752 | epot = -15.421692082236 | etot = -14.6249037422326 +231000 ekin = 0.359118625017489 | erot = 0.421298440292615 | epot = -15.4053208075415 | etot = -14.6249037422314 +232000 ekin = 0.348949729121418 | erot = 0.416321816462733 | epot = -15.3901752878198 | etot = -14.6249037422357 +233000 ekin = 0.339575284188205 | erot = 0.411632247273789 | epot = -15.3761112737045 | etot = -14.6249037422425 +234000 ekin = 0.330784909163314 | erot = 0.407246384303571 | epot = -15.362935035717 | etot = -14.6249037422501 +235000 ekin = 0.322367248495157 | erot = 0.403166248673602 | epot = -15.350437239426 | etot = -14.6249037422572 +236000 ekin = 0.314129851889501 | erot = 0.399380677843556 | epot = -15.3384142719966 | etot = -14.6249037422635 +237000 ekin = 0.305908300164827 | erot = 0.395867600047935 | epot = -15.3266796424818 | etot = -14.624903742269 +238000 ekin = 0.297568064657773 | erot = 0.39259715720464 | epot = -15.3150689641361 | etot = -14.6249037422737 +239000 ekin = 0.289002756414808 | erot = 0.389535643317172 | epot = -15.3034421420093 | etot = -14.6249037422773 +240000 ekin = 0.280132201614557 | erot = 0.386650129641611 | epot = -15.291686073536 | etot = -14.6249037422798 +241000 ekin = 0.270903172980175 | erot = 0.383913574227223 | epot = -15.2797204894877 | etot = -14.6249037422803 +242000 ekin = 0.261294311101929 | erot = 0.381310019034114 | epot = -15.2675080724141 | etot = -14.624903742278 +243000 ekin = 0.251325265433967 | erot = 0.378839435319614 | epot = -15.255068443025 | etot = -14.6249037422714 +244000 ekin = 0.241068460184099 | erot = 0.376521662813181 | epot = -15.2424938652571 | etot = -14.6249037422598 +245000 ekin = 0.230660579660543 | erot = 0.374398842117411 | epot = -15.2299631640205 | etot = -14.6249037422425 +246000 ekin = 0.220310176855077 | erot = 0.372535772164605 | epot = -15.2177496912391 | etot = -14.6249037422194 +247000 ekin = 0.21029792040831 | erot = 0.371017759432739 | epot = -15.2062194220324 | etot = -14.6249037421913 +248000 ekin = 0.200966973970282 | erot = 0.369945779906298 | epot = -15.1958164960366 | etot = -14.62490374216 +249000 ekin = 0.19270275205643 | erot = 0.369429135338942 | epot = -15.1870356295232 | etot = -14.6249037421279 +250000 ekin = 0.18590352409262 | erot = 0.369576201101644 | epot = -15.1803834672921 | etot = -14.6249037420978 +251000 ekin = 0.180945546219597 | erot = 0.370484246994953 | epot = -15.1763335352872 | etot = -14.6249037420727 +252000 ekin = 0.178147956309677 | erot = 0.372229589272508 | epot = -15.1752812876371 | etot = -14.624903742055 +253000 ekin = 0.177743031465493 | erot = 0.374859230993345 | epot = -15.1775060045052 | etot = -14.6249037420463 +254000 ekin = 0.179856300055144 | erot = 0.378385037101541 | epot = -15.1831450792041 | etot = -14.6249037420475 +255000 ekin = 0.184498455786623 | erot = 0.382781080046676 | epot = -15.1921832778916 | etot = -14.6249037420583 +256000 ekin = 0.191568141873245 | erot = 0.387983970946509 | epot = -15.2044558548979 | etot = -14.6249037420781 +257000 ekin = 0.200862084874684 | erot = 0.39389562099413 | epot = -15.2196614479746 | etot = -14.6249037421058 +258000 ekin = 0.212087875567067 | erot = 0.400387498987617 | epot = -15.2373791166953 | etot = -14.6249037421406 +259000 ekin = 0.22487530619229 | erot = 0.407305396776974 | epot = -15.2570844451511 | etot = -14.6249037421818 +260000 ekin = 0.238784314763371 | erot = 0.414473950040919 | epot = -15.2781620070334 | etot = -14.6249037422291 +261000 ekin = 0.253310397642053 | erot = 0.42170059668304 | epot = -15.2999147366073 | etot = -14.6249037422822 +262000 ekin = 0.267890750412286 | erot = 0.428779149459046 | epot = -15.3215736422117 | etot = -14.6249037423403 +263000 ekin = 0.281915541777785 | erot = 0.435493571930371 | epot = -15.3423128561102 | etot = -14.6249037424021 +264000 ekin = 0.294748319449044 | erot = 0.441622773940652 | epot = -15.3612748358547 | etot = -14.624903742465 +265000 ekin = 0.305757851305137 | erot = 0.446947232466447 | epot = -15.3776088262971 | etot = -14.6249037425255 +266000 ekin = 0.314361275702132 | erot = 0.451257984268096 | epot = -15.3905230025497 | etot = -14.6249037425794 +267000 ekin = 0.320075758813841 | erot = 0.454368036195507 | epot = -15.3993475376314 | etot = -14.624903742622 +268000 ekin = 0.322573111285627 | erot = 0.456125517716869 | epot = -15.403602371651 | etot = -14.6249037426485 +269000 ekin = 0.321728949456794 | erot = 0.456427019949868 | epot = -15.403059712062 | etot = -14.6249037426553 +270000 ekin = 0.31765519820333 | erot = 0.45522869606994 | epot = -15.3977876369143 | etot = -14.624903742641 +271000 ekin = 0.310703151367432 | erot = 0.452552178355822 | epot = -15.3881590723309 | etot = -14.6249037426077 +272000 ekin = 0.301426233536413 | erot = 0.448482664562071 | epot = -15.3748126406594 | etot = -14.6249037425609 +273000 ekin = 0.290499502093209 | erot = 0.443158007811074 | epot = -15.3585612524138 | etot = -14.6249037425095 +274000 ekin = 0.278606962226069 | erot = 0.436750209657617 | epot = -15.3402609143468 | etot = -14.6249037424631 +275000 ekin = 0.26632348034077 | erot = 0.429443553158618 | epot = -15.3206707759287 | etot = -14.6249037424293 +276000 ekin = 0.254026977158081 | erot = 0.421415402004818 | epot = -15.3003461215739 | etot = -14.624903742411 +277000 ekin = 0.241871064453538 | erot = 0.412825312322111 | epot = -15.2796001191811 | etot = -14.6249037424054 +278000 ekin = 0.229828041579721 | erot = 0.403815416629946 | epot = -15.2585472006151 | etot = -14.6249037424054 +279000 ekin = 0.217786141146189 | erot = 0.394521119096963 | epot = -15.2372110026452 | etot = -14.624903742402 +280000 ekin = 0.205666064593732 | erot = 0.38508770303191 | epot = -15.2156575100133 | etot = -14.6249037423876 +281000 ekin = 0.19351860427424 | erot = 0.375686870762611 | epot = -15.194109217395 | etot = -14.6249037423581 +282000 ekin = 0.181576720747694 | erot = 0.366527860021383 | epot = -15.1730083230829 | etot = -14.6249037423139 +283000 ekin = 0.170254050626048 | erot = 0.357859944223912 | epot = -15.1530177371086 | etot = -14.6249037422586 +284000 ekin = 0.16009863107041 | erot = 0.349965713705531 | epot = -15.1349680869742 | etot = -14.6249037421982 +285000 ekin = 0.151720356670754 | erot = 0.343146625519695 | epot = -15.1197707243297 | etot = -14.6249037421393 +286000 ekin = 0.145712559183906 | erot = 0.337703485420487 | epot = -15.1083197866921 | etot = -14.6249037420877 +287000 ekin = 0.142584250545045 | erot = 0.33391483609244 | epot = -15.1014028286853 | etot = -14.6249037420479 +288000 ekin = 0.14271294134083 | erot = 0.33201595204223 | epot = -15.0996326354053 | etot = -14.6249037420222 +289000 ekin = 0.146320998448773 | erot = 0.332180585089635 | epot = -15.1034053255502 | etot = -14.6249037420118 +290000 ekin = 0.153472816921521 | erot = 0.334506983378674 | epot = -15.1128835423164 | etot = -14.6249037420162 +291000 ekin = 0.16408646566307 | erot = 0.339009144348004 | epot = -15.1279993520452 | etot = -14.6249037420341 +292000 ekin = 0.177952173600894 | erot = 0.345613807734655 | epot = -15.1484697233998 | etot = -14.6249037420642 +293000 ekin = 0.194750859969321 | erot = 0.354163344443058 | epot = -15.1738179465174 | etot = -14.624903742105 +294000 ekin = 0.214068309159694 | erot = 0.364424408222029 | epot = -15.2033964595369 | etot = -14.6249037421551 +295000 ekin = 0.23540371040359 | erot = 0.376101928511103 | epot = -15.2364093811279 | etot = -14.6249037422133 +296000 ekin = 0.258174229753498 | erot = 0.388857685536646 | epot = -15.2719356575678 | etot = -14.6249037422776 +297000 ekin = 0.281719360135706 | erot = 0.402332315571764 | epot = -15.3089554180538 | etot = -14.6249037423463 +298000 ekin = 0.305309684523697 | erot = 0.416169191335652 | epot = -15.3463826182759 | etot = -14.6249037424165 +299000 ekin = 0.328164426016654 | erot = 0.430038291827268 | epot = -15.3831064603292 | etot = -14.6249037424853 +300000 ekin = 0.349480947255048 | erot = 0.443657997414315 | epot = -15.4180426872181 | etot = -14.6249037425488 +301000 ekin = 0.368477349759193 | erot = 0.456812763608568 | epot = -15.4501938559701 | etot = -14.6249037426023 +302000 ekin = 0.384446573101124 | erot = 0.469364841860938 | epot = -15.4787151576043 | etot = -14.6249037426422 +303000 ekin = 0.396817065634558 | erot = 0.481258609604811 | epot = -15.5029794179039 | etot = -14.6249037426646 +304000 ekin = 0.405211709647007 | erot = 0.492516637287636 | epot = -15.5226320896017 | etot = -14.624903742667 +305000 ekin = 0.409494186865868 | erot = 0.503227368870062 | epot = -15.5376252983853 | etot = -14.6249037426493 +306000 ekin = 0.409791521882642 | erot = 0.513525227982917 | epot = -15.5482204924792 | etot = -14.6249037426137 +307000 ekin = 0.406484029567507 | erot = 0.523565033268454 | epot = -15.5549528054007 | etot = -14.6249037425647 +308000 ekin = 0.400159443093576 | erot = 0.533493670193517 | epot = -15.5585568557963 | etot = -14.6249037425092 +309000 ekin = 0.391535685673409 | erot = 0.543422788904487 | epot = -15.5598622170328 | etot = -14.6249037424549 +310000 ekin = 0.381364662749467 | erot = 0.553406603763533 | epot = -15.559675008922 | etot = -14.624903742409 +311000 ekin = 0.370335174700701 | erot = 0.563428434509133 | epot = -15.5586673515868 | etot = -14.624903742377 +312000 ekin = 0.358994462073939 | erot = 0.573398378860855 | epot = -15.5572965832959 | etot = -14.6249037423611 +313000 ekin = 0.347704062021925 | erot = 0.583162598674903 | epot = -15.5557704030573 | etot = -14.6249037423605 +314000 ekin = 0.33663740290675 | erot = 0.592522528333923 | epot = -15.5540636736116 | etot = -14.6249037423709 +315000 ekin = 0.325816357219143 | erot = 0.601260411441213 | epot = -15.5519805110473 | etot = -14.6249037423869 +316000 ekin = 0.31517501281672 | erot = 0.60916645196768 | epot = -15.5492452071863 | etot = -14.6249037424019 +317000 ekin = 0.304633856553889 | erot = 0.616062831072119 | epot = -15.5456004300365 | etot = -14.6249037424105 +318000 ekin = 0.294167456686821 | erot = 0.621820866636781 | epot = -15.5408920657325 | etot = -14.6249037424089 +319000 ekin = 0.283852816310689 | erot = 0.626369338624031 | epot = -15.5351258973307 | etot = -14.6249037423959 +320000 ekin = 0.273891844373646 | erot = 0.62969394858388 | epot = -15.5284895353295 | etot = -14.624903742372 +321000 ekin = 0.264607615830763 | erot = 0.631829520445007 | epot = -15.5213408786157 | etot = -14.6249037423399 +322000 ekin = 0.256418665980724 | erot = 0.632847556381818 | epot = -15.5141699646656 | etot = -14.6249037423031 +323000 ekin = 0.249797892887888 | erot = 0.632842055921319 | epot = -15.5075436910747 | etot = -14.6249037422655 +324000 ekin = 0.245223011939643 | erot = 0.631916211662829 | epot = -15.5020429658332 | etot = -14.6249037422308 +325000 ekin = 0.243124676660885 | erot = 0.630171930979599 | epot = -15.4982003498433 | etot = -14.6249037422029 +326000 ekin = 0.243837159968202 | erot = 0.62770331019607 | epot = -15.4964442123487 | etot = -14.6249037421844 +327000 ekin = 0.247555458534598 | erot = 0.624594349329564 | epot = -15.4970535500418 | etot = -14.6249037421777 +328000 ekin = 0.254302069317208 | erot = 0.620920422826662 | epot = -15.5001262343276 | etot = -14.6249037421837 +329000 ekin = 0.263906382978448 | erot = 0.616752378549749 | epot = -15.5055625037309 | etot = -14.6249037422027 +330000 ekin = 0.275999298196581 | erot = 0.612161709808553 | epot = -15.513064750239 | etot = -14.6249037422339 +331000 ekin = 0.290024872454518 | erot = 0.6072251384784 | epot = -15.5221537532081 | etot = -14.6249037422752 +332000 ekin = 0.305269328205317 | erot = 0.602027230533175 | epot = -15.5322003010622 | etot = -14.6249037423237 +333000 ekin = 0.32090561137506 | erot = 0.59666030333851 | epot = -15.5424696570894 | etot = -14.6249037423759 +334000 ekin = 0.336049438962957 | erot = 0.59122171045733 | epot = -15.5521748918481 | etot = -14.6249037424278 +335000 ekin = 0.349821102707528 | erot = 0.585809355783074 | epot = -15.5605342009664 | etot = -14.6249037424758 +336000 ekin = 0.361406827299004 | erot = 0.580516763971273 | epot = -15.5668273337865 | etot = -14.6249037425162 +337000 ekin = 0.370114335989199 | erot = 0.575429096256477 | epot = -15.570447174792 | etot = -14.6249037425463 +338000 ekin = 0.375418963131835 | erot = 0.570621177508979 | epot = -15.5709438832047 | etot = -14.6249037425639 +339000 ekin = 0.376998306684161 | erot = 0.566157982091391 | epot = -15.5680600313428 | etot = -14.6249037425673 +340000 ekin = 0.374754278532076 | erot = 0.562097189039027 | epot = -15.561755210127 | etot = -14.6249037425559 +341000 ekin = 0.368821588409674 | erot = 0.558493134368603 | epot = -15.5522184653082 | etot = -14.6249037425299 +342000 ekin = 0.359561251230654 | erot = 0.555400700218385 | epot = -15.5398656939398 | etot = -14.6249037424907 +343000 ekin = 0.347537853254552 | erot = 0.552877785918206 | epot = -15.5253193816135 | etot = -14.6249037424408 +344000 ekin = 0.333480374963866 | erot = 0.5509852684009 | epot = -15.5093693857484 | etot = -14.6249037423837 +345000 ekin = 0.318228359784356 | erot = 0.549783918348281 | epot = -15.4929160204566 | etot = -14.6249037423239 +346000 ekin = 0.302667555547469 | erot = 0.549328430110417 | epot = -15.4768997279243 | etot = -14.6249037422664 +347000 ekin = 0.28766105744341 | erot = 0.549659363310447 | epot = -15.4622241629696 | etot = -14.6249037422157 +348000 ekin = 0.273982878354205 | erot = 0.550794243902763 | epot = -15.4496808644331 | etot = -14.6249037421761 +349000 ekin = 0.262260631617843 | erot = 0.552719272009514 | epot = -15.439883645778 | etot = -14.6249037421507 +350000 ekin = 0.252932884528192 | erot = 0.555383042233133 | epot = -15.4332196689026 | etot = -14.6249037421413 +351000 ekin = 0.246225113234617 | erot = 0.55869341876511 | epot = -15.4298222741477 | etot = -14.624903742148 +352000 ekin = 0.242146418558379 | erot = 0.562518344425243 | epot = -15.4295685051533 | etot = -14.6249037421697 +353000 ekin = 0.240507191582831 | erot = 0.566690733134613 | epot = -15.4321016669209 | etot = -14.6249037422035 +354000 ekin = 0.240955911174275 | erot = 0.571016874087082 | epot = -15.4368765275071 | etot = -14.6249037422458 +355000 ekin = 0.243030568944454 | erot = 0.575286990707861 | epot = -15.4432213019444 | etot = -14.624903742292 +356000 ekin = 0.246218336341954 | erot = 0.579286102670435 | epot = -15.4504081813504 | etot = -14.6249037423381 +357000 ekin = 0.250015504867581 | erot = 0.58280308408374 | epot = -15.4577223313315 | etot = -14.6249037423802 +358000 ekin = 0.253980003728839 | erot = 0.585636256510467 | epot = -15.4645200026551 | etot = -14.6249037424158 +359000 ekin = 0.257771924238821 | erot = 0.587595069854197 | epot = -15.4702707365363 | etot = -14.6249037424433 +360000 ekin = 0.261178006692924 | erot = 0.588498175296143 | epot = -15.4745799244512 | etot = -14.6249037424621 +361000 ekin = 0.264121303804436 | erot = 0.588169931158563 | epot = -15.4771949774355 | etot = -14.6249037424725 +362000 ekin = 0.26665626894814 | erot = 0.586437607933123 | epot = -15.4779976193568 | etot = -14.6249037424755 +363000 ekin = 0.268947338174106 | erot = 0.583131261384995 | epot = -15.4769823420322 | etot = -14.6249037424731 +364000 ekin = 0.271226723299596 | erot = 0.578087502910441 | epot = -15.4742179686788 | etot = -14.6249037424688 +365000 ekin = 0.273728224388818 | erot = 0.571157191000725 | epot = -15.469789157857 | etot = -14.6249037424674 +366000 ekin = 0.27660157052003 | erot = 0.562216266683608 | epot = -15.4637215796777 | etot = -14.624903742474 +367000 ekin = 0.279824898676208 | erot = 0.551178529879214 | epot = -15.4559071710475 | etot = -14.6249037424921 +368000 ekin = 0.283144751011421 | erot = 0.538009090150606 | epot = -15.446057583683 | etot = -14.624903742521 +369000 ekin = 0.286073979195429 | erot = 0.522737270878628 | epot = -15.43371499263 | etot = -14.6249037425559 +370000 ekin = 0.287962637923178 | erot = 0.50546765170011 | epot = -15.4183340322108 | etot = -14.6249037425875 +371000 ekin = 0.288129562576893 | erot = 0.486387667907303 | epot = -15.3994209730894 | etot = -14.6249037426052 +372000 ekin = 0.286016270828215 | erot = 0.465769998081936 | epot = -15.3766900115109 | etot = -14.6249037426008 +373000 ekin = 0.281314492917267 | erot = 0.443968246943336 | epot = -15.3501864824312 | etot = -14.6249037425706 +374000 ekin = 0.274029637541304 | erot = 0.421405384813941 | epot = -15.3203387648723 | etot = -14.6249037425171 +375000 ekin = 0.264468317323927 | erot = 0.398555847613352 | epot = -15.2879279073837 | etot = -14.6249037424464 +376000 ekin = 0.253165169267974 | erot = 0.375923572596667 | epot = -15.2539924842319 | etot = -14.6249037423673 +377000 ekin = 0.240780733674519 | erot = 0.354018931407049 | epot = -15.2197034073693 | etot = -14.6249037422878 +378000 ekin = 0.228003530692849 | erot = 0.333337224177657 | epot = -15.1862444970844 | etot = -14.6249037422138 +379000 ekin = 0.215478669427367 | erot = 0.314340303318035 | epot = -15.1547227148943 | etot = -14.6249037421489 +380000 ekin = 0.203769466320298 | erot = 0.297441561967809 | epot = -15.1261147703827 | etot = -14.6249037420946 +381000 ekin = 0.193344913038602 | erot = 0.282993579610754 | epot = -15.1012422347007 | etot = -14.6249037420513 +382000 ekin = 0.1845790971167 | erot = 0.271277560103436 | epot = -15.0807603992401 | etot = -14.62490374202 +383000 ekin = 0.177749902922622 | erot = 0.26249431847454 | epot = -15.0651479633984 | etot = -14.6249037420012 +384000 ekin = 0.173031383434508 | erot = 0.256757595375745 | epot = -15.0546927208059 | etot = -14.6249037419956 +385000 ekin = 0.170483112154869 | erot = 0.254091341095724 | epot = -15.049478195254 | etot = -14.6249037420034 +386000 ekin = 0.170046361592442 | erot = 0.254432809989109 | epot = -15.0493829136049 | etot = -14.6249037420233 +387000 ekin = 0.171558026227206 | erot = 0.257642587604648 | epot = -15.0541043558835 | etot = -14.6249037420517 +388000 ekin = 0.174787865439128 | erot = 0.263521131370077 | epot = -15.0632127388927 | etot = -14.6249037420835 +389000 ekin = 0.179494526901848 | erot = 0.271829477565643 | epot = -15.0762277465811 | etot = -14.6249037421136 +390000 ekin = 0.185484901052496 | erot = 0.282310127810724 | epot = -15.0926987710012 | etot = -14.624903742138 +391000 ekin = 0.192654775276086 | erot = 0.294703495236184 | epot = -15.1122620126683 | etot = -14.624903742156 +392000 ekin = 0.200990711955861 | erot = 0.308756153372879 | epot = -15.1346506074993 | etot = -14.6249037421705 +393000 ekin = 0.210524629688573 | erot = 0.324219483681282 | epot = -15.1596478555577 | etot = -14.6249037421878 +394000 ekin = 0.22125039811835 | erot = 0.340840530849664 | epot = -15.1869946711827 | etot = -14.6249037422146 +395000 ekin = 0.233028912153826 | erot = 0.358349828151301 | epot = -15.2162824825616 | etot = -14.6249037422565 +396000 ekin = 0.2455168348482 | erot = 0.376452447324096 | epot = -15.2468730244869 | etot = -14.6249037423146 +397000 ekin = 0.25814964628924 | erot = 0.394827815017667 | epot = -15.2778812036919 | etot = -14.624903742385 +398000 ekin = 0.270192540270399 | erot = 0.4131410333725 | epot = -15.3082373161018 | etot = -14.6249037424589 +399000 ekin = 0.280849396853854 | erot = 0.431064534842813 | epot = -15.3368176742223 | etot = -14.6249037425256 +400000 ekin = 0.289399657315509 | erot = 0.448305349545533 | epot = -15.3626087494363 | etot = -14.6249037425752 +401000 ekin = 0.295323233787914 | erot = 0.464631356382232 | epot = -15.3848583327717 | etot = -14.6249037426015 +402000 ekin = 0.298377750401429 | erot = 0.479890206670972 | epot = -15.4031716996757 | etot = -14.6249037426033 +403000 ekin = 0.298608046776847 | erot = 0.494016844836358 | epot = -15.4175286341982 | etot = -14.624903742585 +404000 ekin = 0.296288720276099 | erot = 0.507028747324982 | epot = -15.4282212101551 | etot = -14.624903742554 +405000 ekin = 0.29181945089068 | erot = 0.519011022290344 | epot = -15.4357342157007 | etot = -14.6249037425197 +406000 ekin = 0.285604695316787 | erot = 0.530095491696252 | epot = -15.440603929503 | etot = -14.62490374249 +407000 ekin = 0.27795179501284 | erot = 0.540438449781457 | epot = -15.4432939872644 | etot = -14.6249037424701 +408000 ekin = 0.269015012492725 | erot = 0.550201084797105 | epot = -15.4441198397503 | etot = -14.6249037424605 +409000 ekin = 0.258799683406998 | erot = 0.559535019811799 | epot = -15.4432384456764 | etot = -14.6249037424576 +410000 ekin = 0.247223943172304 | erot = 0.568573648692186 | epot = -15.4407013343195 | etot = -14.624903742455 +411000 ekin = 0.234219542826644 | erot = 0.577428429926533 | epot = -15.4365517151989 | etot = -14.6249037424457 +412000 ekin = 0.219842320368382 | erot = 0.5861883861288 | epot = -15.4309344489209 | etot = -14.6249037424237 +413000 ekin = 0.204359948374925 | erot = 0.594920843620856 | epot = -15.4241845343826 | etot = -14.6249037423868 +414000 ekin = 0.188290368309528 | erot = 0.603671832826723 | epot = -15.4168659434726 | etot = -14.6249037423363 +415000 ekin = 0.17237708181679 | erot = 0.612465324291743 | epot = -15.4097461483867 | etot = -14.6249037422781 +416000 ekin = 0.157503657630917 | erot = 0.621301324615619 | epot = -15.4037087244673 | etot = -14.6249037422208 +417000 ekin = 0.144565276806003 | erot = 0.630153567596961 | epot = -15.3996225865765 | etot = -14.6249037421735 +418000 ekin = 0.134326161306162 | erot = 0.638967960411851 | epot = -15.3981978638625 | etot = -14.6249037421445 +419000 ekin = 0.127295713866961 | erot = 0.647663024756136 | epot = -15.3998624807615 | etot = -14.6249037421384 +420000 ekin = 0.123652074078926 | erot = 0.656133267678405 | epot = -15.404689083913 | etot = -14.6249037421557 +421000 ekin = 0.123230332545423 | erot = 0.664256043547052 | epot = -15.4123901182846 | etot = -14.6249037421921 +422000 ekin = 0.125576493084645 | erot = 0.671901405101299 | epot = -15.4223816404261 | etot = -14.6249037422401 +423000 ekin = 0.130051930466291 | erot = 0.678943694027994 | epot = -15.4338993667851 | etot = -14.6249037422908 +424000 ekin = 0.135961143238941 | erot = 0.68527308622734 | epot = -15.4461379718019 | etot = -14.6249037423356 +425000 ekin = 0.142671659965653 | erot = 0.690804983811737 | epot = -15.4583803861463 | etot = -14.6249037423689 +426000 ekin = 0.149699767318955 | erot = 0.69548556134855 | epot = -15.4700890710557 | etot = -14.6249037423882 +427000 ekin = 0.156747049208564 | erot = 0.699292628464386 | epot = -15.4809434200676 | etot = -14.6249037423947 +428000 ekin = 0.163686553654653 | erot = 0.702231990285693 | epot = -15.4908222863327 | etot = -14.6249037423924 +429000 ekin = 0.170509683514881 | erot = 0.704330315301697 | epot = -15.4997437412031 | etot = -14.6249037423865 +430000 ekin = 0.177252892951705 | erot = 0.705626025883602 | epot = -15.5077826612176 | etot = -14.6249037423823 +431000 ekin = 0.183925691222895 | erot = 0.706159951516283 | epot = -15.5149893851227 | etot = -14.6249037423835 +432000 ekin = 0.19045785108011 | erot = 0.705966883793978 | epot = -15.5213284772661 | etot = -14.624903742392 +433000 ekin = 0.196676887389506 | erot = 0.705069371776843 | epot = -15.5266500015735 | etot = -14.6249037424072 +434000 ekin = 0.202317433899842 | erot = 0.703474477741428 | epot = -15.5306956540681 | etot = -14.6249037424269 +435000 ekin = 0.207056046506956 | erot = 0.701173837003811 | epot = -15.5331336259585 | etot = -14.6249037424477 +436000 ekin = 0.210560164857125 | erot = 0.698146912242933 | epot = -15.5336108195661 | etot = -14.6249037424661 +437000 ekin = 0.212539330538931 | erot = 0.694366864819831 | epot = -15.5318099378377 | etot = -14.624903742479 +438000 ekin = 0.212789433625871 | erot = 0.689808070113593 | epot = -15.5275012462235 | etot = -14.624903742484 +439000 ekin = 0.211224885327214 | erot = 0.684454087056214 | epot = -15.5205827148631 | etot = -14.6249037424797 +440000 ekin = 0.207897417438809 | erot = 0.678304934040255 | epot = -15.5111060939441 | etot = -14.624903742465 +441000 ekin = 0.203002684917561 | erot = 0.671382822496918 | epot = -15.4992892498548 | etot = -14.6249037424403 +442000 ekin = 0.196876783893415 | erot = 0.66373594678721 | epot = -15.4855164730867 | etot = -14.6249037424061 +443000 ekin = 0.189984458135294 | erot = 0.655440346227568 | epot = -15.4703285467262 | etot = -14.6249037423634 +444000 ekin = 0.182899715135625 | erot = 0.646600090308741 | epot = -15.4544035477581 | etot = -14.6249037423138 +445000 ekin = 0.176278659807151 | erot = 0.637346059016373 | epot = -15.4385284610832 | etot = -14.6249037422597 +446000 ekin = 0.170824489262207 | erot = 0.627833490901199 | epot = -15.4235617223673 | etot = -14.6249037422039 +447000 ekin = 0.16724611578148 | erot = 0.618238375507256 | epot = -15.4103882334382 | etot = -14.6249037421495 +448000 ekin = 0.166214016011086 | erot = 0.608752709243579 | epot = -15.3998704673542 | etot = -14.6249037420995 +449000 ekin = 0.1683180025474 | erot = 0.599578546514547 | epot = -15.3928002911186 | etot = -14.6249037420567 +450000 ekin = 0.174030350885976 | erot = 0.590920601688637 | epot = -15.3898546945984 | etot = -14.6249037420238 +451000 ekin = 0.183674309612486 | erot = 0.582976972209394 | epot = -15.3915550238252 | etot = -14.6249037420033 +452000 ekin = 0.197394458885248 | erot = 0.575927582956616 | epot = -15.39822578384 | etot = -14.6249037419981 +453000 ekin = 0.215124290963754 | erot = 0.569920414705972 | epot = -15.4099484476811 | etot = -14.6249037420114 +454000 ekin = 0.236549344238332 | erot = 0.565056494271021 | epot = -15.4265095805559 | etot = -14.6249037420465 +455000 ekin = 0.261070666492934 | erot = 0.561375729612865 | epot = -15.4473501382115 | etot = -14.6249037421057 +456000 ekin = 0.287780783019101 | erot = 0.558846520705115 | epot = -15.4715310459133 | etot = -14.6249037421891 +457000 ekin = 0.315469350479039 | erot = 0.557362227354604 | epot = -15.4977353201268 | etot = -14.6249037422931 +458000 ekin = 0.342675461161211 | erot = 0.556746783054113 | epot = -15.5243259866255 | etot = -14.6249037424101 +459000 ekin = 0.367796771324328 | erot = 0.556770049266128 | epot = -15.5494705631189 | etot = -14.6249037425284 +460000 ekin = 0.3892528364295 | erot = 0.557171234683844 | epot = -15.5713278137471 | etot = -14.6249037426338 +461000 ekin = 0.405683830372718 | erot = 0.557686417732241 | epot = -15.5882739908163 | etot = -14.6249037427113 +462000 ekin = 0.416150509763905 | erot = 0.558074591842708 | epot = -15.5991288443566 | etot = -14.6249037427499 +463000 ekin = 0.420292029665246 | erot = 0.558136338549459 | epot = -15.6033321109587 | etot = -14.624903742744 +464000 ekin = 0.418399545178514 | erot = 0.557720582601952 | epot = -15.6010238704768 | etot = -14.6249037426963 +465000 ekin = 0.411377435968826 | erot = 0.55671776612672 | epot = -15.5929989447132 | etot = -14.6249037426177 +466000 ekin = 0.400588481170777 | erot = 0.555041504869193 | epot = -15.5805337285653 | etot = -14.6249037425253 +467000 ekin = 0.387608315925912 | erot = 0.552604267015981 | epot = -15.5651163253807 | etot = -14.6249037424389 +468000 ekin = 0.373939506071419 | erot = 0.549294716065778 | epot = -15.5481379645134 | etot = -14.6249037423762 +469000 ekin = 0.360748545285941 | erot = 0.544964338611031 | epot = -15.5306166262458 | etot = -14.6249037423488 +470000 ekin = 0.348685397522481 | erot = 0.539428754142283 | epot = -15.5130178940239 | etot = -14.6249037423591 +471000 ekin = 0.33782542530965 | erot = 0.53248528288589 | epot = -15.495214450596 | etot = -14.6249037424005 +472000 ekin = 0.327743216876187 | erot = 0.523944004295118 | epot = -15.4765909636299 | etot = -14.6249037424586 +473000 ekin = 0.317695625905249 | erot = 0.513665869846711 | epot = -15.4562652382675 | etot = -14.6249037425155 +474000 ekin = 0.306866206292903 | erot = 0.501599410558902 | epot = -15.4333693594053 | etot = -14.6249037425535 +475000 ekin = 0.294611572516014 | erot = 0.487807694339925 | epot = -15.4073230094157 | etot = -14.6249037425598 +476000 ekin = 0.280654133645735 | erot = 0.472479343853221 | epot = -15.3780372200274 | etot = -14.6249037425284 +477000 ekin = 0.265182667318346 | erot = 0.455920989277164 | epot = -15.3460073990571 | etot = -14.6249037424615 +478000 ekin = 0.248846579355896 | erot = 0.438532535944716 | epot = -15.3122828576688 | etot = -14.6249037423682 +479000 ekin = 0.232654569020801 | erot = 0.420770062233786 | epot = -15.2783283735167 | etot = -14.6249037422621 +480000 ekin = 0.217807844646274 | erot = 0.403103245642895 | epot = -15.2458148324472 | etot = -14.624903742158 +481000 ekin = 0.205508255202274 | erot = 0.385974572360121 | epot = -15.2163865696318 | etot = -14.6249037420694 +482000 ekin = 0.196781566941766 | erot = 0.36976631024765 | epot = -15.1914516191951 | etot = -14.6249037420057 +483000 ekin = 0.19234694356787 | erot = 0.354778814406374 | epot = -15.1720294999463 | etot = -14.6249037419721 +484000 ekin = 0.192548846646396 | erot = 0.341220938396507 | epot = -15.1586735270111 | etot = -14.6249037419682 +485000 ekin = 0.197351634264796 | erot = 0.329210924265182 | epot = -15.1514663005207 | etot = -14.6249037419907 +486000 ekin = 0.206384571112674 | erot = 0.318784712513058 | epot = -15.1500730256597 | etot = -14.624903742034 +487000 ekin = 0.219018661981128 | erot = 0.309908337315953 | epot = -15.1538307413883 | etot = -14.6249037420912 +488000 ekin = 0.234457053485615 | erot = 0.302491737711597 | epot = -15.1618525333532 | etot = -14.6249037421559 +489000 ekin = 0.251825722282228 | erot = 0.296402451840807 | epot = -15.1731319163449 | etot = -14.6249037422219 +490000 ekin = 0.270257579252373 | erot = 0.291478772534408 | epot = -15.1866400940707 | etot = -14.6249037422839 +491000 ekin = 0.288968023940477 | erot = 0.287542686829702 | epot = -15.2014144531066 | etot = -14.6249037423364 +492000 ekin = 0.307321746939982 | erot = 0.28441316533236 | epot = -15.2166386546473 | etot = -14.624903742375 +493000 ekin = 0.32488919226749 | erot = 0.281920128741024 | epot = -15.2317130634052 | etot = -14.6249037423967 +494000 ekin = 0.341487883386483 | erot = 0.279918789013753 | epot = -15.2463104147992 | etot = -14.624903742399 +495000 ekin = 0.35720080106069 | erot = 0.278303167954071 | epot = -15.2604077113969 | etot = -14.6249037423821 +496000 ekin = 0.372363075866133 | erot = 0.277016625443694 | epot = -15.274283443659 | etot = -14.6249037423491 +497000 ekin = 0.387510424729673 | erot = 0.276056483801325 | epot = -15.288470650837 | etot = -14.624903742306 +498000 ekin = 0.403287744735438 | erot = 0.275469725413168 | epot = -15.3036612124104 | etot = -14.6249037422618 +499000 ekin = 0.42032292393259 | erot = 0.275337682298044 | epot = -15.320564348458 | etot = -14.6249037422274 +500000 ekin = 0.43907820686993 | erot = 0.275749832423184 | epot = -15.3397317815074 | etot = -14.6249037422143 +501000 ekin = 0.459699055393576 | erot = 0.27677002458897 | epot = -15.3613728222153 | etot = -14.6249037422327 +502000 ekin = 0.481887975238202 | erot = 0.278401857022776 | epot = -15.3851935745495 | etot = -14.6249037422885 +503000 ekin = 0.504836001700849 | erot = 0.28056227342693 | epot = -15.410302017509 | etot = -14.6249037423813 +504000 ekin = 0.527242963721984 | erot = 0.283072520273731 | epot = -15.4352192264977 | etot = -14.624903742502 +505000 ekin = 0.547444055756082 | erot = 0.285672032586838 | epot = -15.458019830977 | etot = -14.6249037426341 +506000 ekin = 0.563636138784674 | erot = 0.288055811209927 | epot = -15.47659569275 | etot = -14.6249037427554 +507000 ekin = 0.574166796919909 | erot = 0.289928574131153 | epot = -15.4889991138946 | etot = -14.6249037428436 +508000 ekin = 0.577825151301095 | erot = 0.29106332686132 | epot = -15.4937922210437 | etot = -14.6249037428812 +509000 ekin = 0.574066827021787 | erot = 0.291350176078735 | epot = -15.4903207459605 | etot = -14.6249037428599 +510000 ekin = 0.563118031118052 | erot = 0.290823209378379 | epot = -15.478844983279 | etot = -14.6249037427826 +511000 ekin = 0.545937816053849 | erot = 0.289659846600108 | epot = -15.4605014053159 | etot = -14.624903742662 +512000 ekin = 0.524051924661522 | erot = 0.288153919329358 | epot = -15.4371095865082 | etot = -14.6249037425174 +513000 ekin = 0.49930007419802 | erot = 0.286670443869403 | epot = -15.4108742604374 | etot = -14.6249037423699 +514000 ekin = 0.473556830410389 | erot = 0.285593013544029 | epot = -15.3840535861934 | etot = -14.624903742239 +515000 ekin = 0.448481344234872 | erot = 0.285274677057468 | epot = -15.3586597634305 | etot = -14.6249037421382 +516000 ekin = 0.425336124988155 | erot = 0.286000471485139 | epot = -15.3362403385481 | etot = -14.6249037420748 +517000 ekin = 0.404895133580943 | erot = 0.2879658116616 | epot = -15.3177646872915 | etot = -14.6249037420489 +518000 ekin = 0.38744137195972 | erot = 0.291271247088022 | epot = -15.303616361103 | etot = -14.6249037420552 +519000 ekin = 0.372839035852851 | erot = 0.295931281214127 | epot = -15.2936740591517 | etot = -14.6249037420847 +520000 ekin = 0.360656186943069 | erot = 0.301893194868317 | epot = -15.2874531239377 | etot = -14.6249037421263 +521000 ekin = 0.350310207443456 | erot = 0.30906098360489 | epot = -15.284274933218 | etot = -14.6249037421697 +522000 ekin = 0.341208800539667 | erot = 0.3173194084493 | epot = -15.2834319511953 | etot = -14.6249037422063 +523000 ekin = 0.332862997936835 | erot = 0.326553653087588 | epot = -15.284320393256 | etot = -14.6249037422315 +524000 ekin = 0.324955020060083 | erot = 0.336661144000867 | epot = -15.2865199063051 | etot = -14.6249037422441 +525000 ekin = 0.317352570821523 | erot = 0.347553686772997 | epot = -15.2898099998415 | etot = -14.624903742247 +526000 ekin = 0.310071537936527 | erot = 0.359150063852877 | epot = -15.2941253440357 | etot = -14.6249037422463 +527000 ekin = 0.30319969763022 | erot = 0.371361343285068 | epot = -15.2994647831647 | etot = -14.6249037422494 +528000 ekin = 0.296802852838113 | erot = 0.38407297047912 | epot = -15.3057795655799 | etot = -14.6249037422627 +529000 ekin = 0.290839689447243 | erot = 0.397128838352394 | epot = -15.31287227009 | etot = -14.6249037422904 +530000 ekin = 0.285110822260533 | erot = 0.410322608856898 | epot = -15.3203371734496 | etot = -14.6249037423322 +531000 ekin = 0.279260366287321 | erot = 0.423400398731777 | epot = -15.3275645074024 | etot = -14.6249037423833 +532000 ekin = 0.2728357059054 | erot = 0.436076588369062 | epot = -15.3338160367096 | etot = -14.6249037424351 +533000 ekin = 0.265395406955423 | erot = 0.448061330488706 | epot = -15.3383604799205 | etot = -14.6249037424763 +534000 ekin = 0.25664035180014 | erot = 0.45909504502717 | epot = -15.3406391393241 | etot = -14.6249037424968 +535000 ekin = 0.24653363369425 | erot = 0.468982742180589 | epot = -15.3404201183648 | etot = -14.62490374249 +536000 ekin = 0.235373881374767 | erot = 0.477620282696299 | epot = -15.3378979065254 | etot = -14.6249037424543 +537000 ekin = 0.223795203401825 | erot = 0.485006039595742 | epot = -15.3337049853926 | etot = -14.624903742395 +538000 ekin = 0.212682661997717 | erot = 0.491234540507922 | epot = -15.32882094483 | etot = -14.6249037423243 +539000 ekin = 0.203011536568094 | erot = 0.496472671628212 | epot = -15.324387950454 | etot = -14.6249037422577 +540000 ekin = 0.195638496925756 | erot = 0.500922912276288 | epot = -15.3214651514142 | etot = -14.6249037422122 +541000 ekin = 0.191090437373868 | erot = 0.504781043299473 | epot = -15.3207752228743 | etot = -14.624903742201 +542000 ekin = 0.189407567632351 | erot = 0.508197267609666 | epot = -15.3225085774711 | etot = -14.6249037422291 +543000 ekin = 0.190094034780963 | erot = 0.511249275631094 | epot = -15.3262470527038 | etot = -14.6249037422917 +544000 ekin = 0.192205662500001 | erot = 0.513933300996131 | epot = -15.3310427058706 | etot = -14.6249037423745 +545000 ekin = 0.194562943958398 | erot = 0.516174993404786 | epot = -15.3356416798198 | etot = -14.6249037424566 +546000 ekin = 0.196033343259865 | erot = 0.517857026727595 | epot = -15.3387941125054 | etot = -14.624903742518 +547000 ekin = 0.195801439086576 | erot = 0.518856237019659 | epot = -15.3395614186507 | etot = -14.6249037425445 +548000 ekin = 0.193552178457624 | erot = 0.519081068513043 | epot = -15.3375369895016 | etot = -14.6249037425309 +549000 ekin = 0.189527872077782 | erot = 0.518500763845595 | epot = -15.3329323784042 | etot = -14.6249037424808 +550000 ekin = 0.18446469719282 | erot = 0.517160608016848 | epot = -15.326529047614 | etot = -14.6249037424043 +551000 ekin = 0.17944751961377 | erot = 0.515181377053922 | epot = -15.3195326389815 | etot = -14.6249037423138 +552000 ekin = 0.175731062295071 | erot = 0.512744588095586 | epot = -15.3133793926126 | etot = -14.6249037422219 +553000 ekin = 0.174564310046339 | erot = 0.510067400325356 | epot = -15.3095354525118 | etot = -14.6249037421401 +554000 ekin = 0.177036897101121 | erot = 0.507372062614127 | epot = -15.309312701793 | etot = -14.6249037420777 +555000 ekin = 0.183953653121541 | erot = 0.50485506124058 | epot = -15.3137124564044 | etot = -14.6249037420423 +556000 ekin = 0.195740677804154 | erot = 0.502660902828886 | epot = -15.3233053226714 | etot = -14.6249037420384 +557000 ekin = 0.212389174813395 | erot = 0.500864749566249 | epot = -15.3381576664467 | etot = -14.6249037420671 +558000 ekin = 0.233445020972978 | erot = 0.499466731744177 | epot = -15.3578154948427 | etot = -14.6249037421256 +559000 ekin = 0.258048678278145 | erot = 0.498398734229532 | epot = -15.381351154715 | etot = -14.6249037422073 +560000 ekin = 0.285022157939727 | erot = 0.497541950864641 | epot = -15.4074678511075 | etot = -14.6249037423031 +561000 ekin = 0.312990622171893 | erot = 0.496751658908829 | epot = -15.4346460234834 | etot = -14.6249037424027 +562000 ekin = 0.340519848730057 | erot = 0.495884310852853 | epot = -15.461307902079 | etot = -14.6249037424961 +563000 ekin = 0.366249237356341 | erot = 0.494821962715706 | epot = -15.4859749426471 | etot = -14.6249037425751 +564000 ekin = 0.389003340228864 | erot = 0.493490109026347 | epot = -15.5073971918896 | etot = -14.6249037426344 +565000 ekin = 0.407871381975787 | erot = 0.491866632343088 | epot = -15.5246417569901 | etot = -14.6249037426712 +566000 ekin = 0.422251605413063 | erot = 0.489981232303539 | epot = -15.537136580402 | etot = -14.6249037426854 +567000 ekin = 0.431863045464991 | erot = 0.487906470955931 | epot = -15.5446732590994 | etot = -14.6249037426785 +568000 ekin = 0.436733840918529 | erot = 0.485743252286281 | epot = -15.5473808358582 | etot = -14.6249037426534 +569000 ekin = 0.437172173179269 | erot = 0.483603786385196 | epot = -15.5456797021777 | etot = -14.6249037426133 +570000 ekin = 0.43372713864672 | erot = 0.48159597879343 | epot = -15.5402268600018 | etot = -14.6249037425617 +571000 ekin = 0.42714180814445 | erot = 0.479812578148079 | epot = -15.5318581287948 | etot = -14.6249037425023 +572000 ekin = 0.418294466662065 | erot = 0.478326721683348 | epot = -15.5215249307851 | etot = -14.6249037424397 +573000 ekin = 0.408121101336508 | erot = 0.477193277919927 | epot = -15.5102181216365 | etot = -14.6249037423801 +574000 ekin = 0.397514818218918 | erot = 0.476453234966625 | epot = -15.4988717955165 | etot = -14.624903742331 +575000 ekin = 0.387207144490505 | erot = 0.476137354469736 | epot = -15.4882482412605 | etot = -14.6249037423002 +576000 ekin = 0.377649119218454 | erot = 0.476266044932873 | epot = -15.4788189064457 | etot = -14.6249037422944 +577000 ekin = 0.368920817133122 | erot = 0.476844730976094 | epot = -15.4706692904255 | etot = -14.6249037423163 +578000 ekin = 0.360700785231361 | erot = 0.47785688313413 | epot = -15.4634614107286 | etot = -14.6249037423631 +579000 ekin = 0.352319179858645 | erot = 0.479258927576455 | epot = -15.4564818498607 | etot = -14.6249037424256 +580000 ekin = 0.342901425190256 | erot = 0.480981430412058 | epot = -15.4487865980916 | etot = -14.6249037424893 +581000 ekin = 0.331586894252413 | erot = 0.482939076923234 | epot = -15.4394297137118 | etot = -14.6249037425361 +582000 ekin = 0.317784488003658 | erot = 0.485048781538909 | epot = -15.427737012092 | etot = -14.6249037425495 +583000 ekin = 0.301409490235786 | erot = 0.487252029394123 | epot = -15.4135652621474 | etot = -14.6249037425175 +584000 ekin = 0.283039202393456 | erot = 0.489535511255409 | epot = -15.3974784560865 | etot = -14.6249037424376 +585000 ekin = 0.263933313486932 | erot = 0.491944128119358 | epot = -15.3807811839248 | etot = -14.6249037423185 +586000 ekin = 0.245890887800014 | erot = 0.494582820570716 | epot = -15.36537745055 | etot = -14.6249037421793 +587000 ekin = 0.230956405619767 | erot = 0.497607010278002 | epot = -15.3534671579441 | etot = -14.6249037420464 +588000 ekin = 0.221033841917334 | erot = 0.501205839010304 | epot = -15.3471434228726 | etot = -14.6249037419449 +589000 ekin = 0.217504428503198 | erot = 0.505584588307916 | epot = -15.3479927587054 | etot = -14.6249037418943 +590000 ekin = 0.220953423088802 | erot = 0.510952138425678 | epot = -15.3568093034149 | etot = -14.6249037419004 +591000 ekin = 0.231083134064877 | erot = 0.517515644130037 | epot = -15.3735025201503 | etot = -14.6249037419554 +592000 ekin = 0.246829245753809 | erot = 0.525479282586983 | epot = -15.3972122703829 | etot = -14.6249037420421 +593000 ekin = 0.266628949730648 | erot = 0.535039778666154 | epot = -15.4265724705373 | etot = -14.6249037421405 +594000 ekin = 0.288743434935948 | erot = 0.546371032865159 | epot = -15.4600182100359 | etot = -14.6249037422348 +595000 ekin = 0.311533695301854 | erot = 0.559594229359111 | epot = -15.4960316669784 | etot = -14.6249037423174 +596000 ekin = 0.333624348261494 | erot = 0.574736425374244 | epot = -15.5332645160249 | etot = -14.6249037423892 +597000 ekin = 0.353943370598259 | erot = 0.591686591895167 | epot = -15.5705337049495 | etot = -14.6249037424561 +598000 ekin = 0.371670846224399 | erot = 0.610160828223706 | epot = -15.6067354169733 | etot = -14.6249037425252 +599000 ekin = 0.386151688530232 | erot = 0.629687420924543 | epot = -15.6407428520551 | etot = -14.6249037426004 +600000 ekin = 0.396824670884392 | erot = 0.649618644309618 | epot = -15.6713470578743 | etot = -14.6249037426803 +601000 ekin = 0.403202067553724 | erot = 0.669171693344937 | epot = -15.6972775036568 | etot = -14.6249037427581 +602000 ekin = 0.404908528299605 | erot = 0.687495721385225 | epot = -15.7173079925077 | etot = -14.6249037428229 +603000 ekin = 0.401765041348441 | erot = 0.703757265562351 | epot = -15.7304260497729 | etot = -14.6249037428621 +604000 ekin = 0.393886240081566 | erot = 0.717231476889447 | epot = -15.7360214598369 | etot = -14.6249037428659 +605000 ekin = 0.381750384954784 | erot = 0.727382711583162 | epot = -15.7340368393681 | etot = -14.6249037428302 +606000 ekin = 0.366205114567235 | erot = 0.733917584159895 | epot = -15.725026441486 | etot = -14.6249037427589 +607000 ekin = 0.348389460815329 | erot = 0.736798185090343 | epot = -15.7100913885696 | etot = -14.624903742664 +608000 ekin = 0.329579787369629 | erot = 0.73621262347853 | epot = -15.6906961534103 | etot = -14.6249037425622 +609000 ekin = 0.310994196072014 | erot = 0.732511274794253 | epot = -15.6684092133371 | etot = -14.6249037424709 +610000 ekin = 0.29360483588481 | erot = 0.726125549058504 | epot = -15.644634127347 | etot = -14.6249037424037 +611000 ekin = 0.278004208602607 | erot = 0.717488389874772 | epot = -15.6203963408453 | etot = -14.624903742368 +612000 ekin = 0.264353214553523 | erot = 0.706972008379557 | epot = -15.5962289652967 | etot = -14.6249037423637 +613000 ekin = 0.252415280668682 | erot = 0.694851301360247 | epot = -15.5721703244136 | etot = -14.6249037423847 +614000 ekin = 0.241662201717183 | erot = 0.681294462599197 | epot = -15.5478604067366 | etot = -14.6249037424202 +615000 ekin = 0.231427318529533 | erot = 0.666377599991891 | epot = -15.5227086609789 | etot = -14.6249037424574 +616000 ekin = 0.221078258759054 | erot = 0.650117838828839 | epot = -15.496099840071 | etot = -14.6249037424831 +617000 ekin = 0.21018039046722 | erot = 0.632518274251072 | epot = -15.4676024072045 | etot = -14.6249037424862 +618000 ekin = 0.198621509656023 | erot = 0.613617132100535 | epot = -15.4371423842165 | etot = -14.6249037424599 +619000 ekin = 0.18667044221321 | erot = 0.593532504056809 | epot = -15.405106688674 | etot = -14.624903742404 +620000 ekin = 0.174951539061334 | erot = 0.572493952083576 | epot = -15.3723492334691 | etot = -14.6249037423242 +621000 ekin = 0.164335257151748 | erot = 0.550854196820334 | epot = -15.3400931962044 | etot = -14.6249037422324 +622000 ekin = 0.155768039681223 | erot = 0.529078173717901 | epot = -15.3097499555421 | etot = -14.6249037421429 +623000 ekin = 0.150083571178067 | erot = 0.507711807337581 | epot = -15.2826991205843 | etot = -14.6249037420687 +624000 ekin = 0.147843467415026 | erot = 0.487337070698877 | epot = -15.2600842801327 | etot = -14.6249037420188 +625000 ekin = 0.149245521580685 | erot = 0.468521842126521 | epot = -15.2426711057039 | etot = -14.6249037419967 +626000 ekin = 0.154116108891011 | erot = 0.451772481731706 | epot = -15.230792332623 | etot = -14.6249037420003 +627000 ekin = 0.161979086426243 | erot = 0.437494698740521 | epot = -15.2243775271906 | etot = -14.6249037420239 +628000 ekin = 0.172174902879429 | erot = 0.425965324893993 | epot = -15.2230439698331 | etot = -14.6249037420597 +629000 ekin = 0.183995029152745 | erot = 0.417314987668754 | epot = -15.2262137589225 | etot = -14.624903742101 +630000 ekin = 0.196798066695247 | erot = 0.411519917957055 | epot = -15.2332217267955 | etot = -14.6249037421432 +631000 ekin = 0.210082131922237 | erot = 0.408400457424511 | epot = -15.2433863315318 | etot = -14.6249037421851 +632000 ekin = 0.223500184826661 | erot = 0.407624312389748 | epot = -15.2560282394451 | etot = -14.6249037422287 +633000 ekin = 0.236818662197368 | erot = 0.40871410814115 | epot = -15.2704365126172 | etot = -14.6249037422787 +634000 ekin = 0.249833574953511 | erot = 0.411060882467202 | epot = -15.2857981997609 | etot = -14.6249037423402 +635000 ekin = 0.262270239999869 | erot = 0.413946987960319 | epot = -15.3011209703766 | etot = -14.6249037424164 +636000 ekin = 0.273700147362094 | erot = 0.41658241201687 | epot = -15.3151863018853 | etot = -14.6249037425063 +637000 ekin = 0.283507856899951 | erot = 0.418156955202178 | epot = -15.3265685547055 | etot = -14.6249037426034 +638000 ekin = 0.290930324554581 | erot = 0.417906927432974 | epot = -15.3337409946828 | etot = -14.6249037426952 +639000 ekin = 0.295171730169445 | erot = 0.415189912095163 | epot = -15.3352653850311 | etot = -14.6249037427665 +640000 ekin = 0.295573453214757 | erot = 0.409556450349425 | epot = -15.330033646366 | etot = -14.6249037428018 +641000 ekin = 0.291798784614159 | erot = 0.400805216305592 | epot = -15.3175077437094 | etot = -14.6249037427896 +642000 ekin = 0.283982821763191 | erot = 0.389009767281871 | epot = -15.2978963317709 | etot = -14.6249037427259 +643000 ekin = 0.272803834295014 | erot = 0.374510198235057 | epot = -15.2722177751454 | etot = -14.6249037426153 +644000 ekin = 0.259451287281783 | erot = 0.357870303235152 | epot = -15.242225332988 | etot = -14.6249037424711 +645000 ekin = 0.245490538509252 | erot = 0.339807577758131 | epot = -15.2102018585797 | etot = -14.6249037423123 +646000 ekin = 0.232646751226996 | erot = 0.321107525182603 | epot = -15.1786580185706 | etot = -14.624903742161 +647000 ekin = 0.22254581022401 | erot = 0.302534738054871 | epot = -15.1499842903174 | etot = -14.6249037420385 +648000 ekin = 0.216457466201459 | erot = 0.284752019408104 | epot = -15.1261132275716 | etot = -14.624903741962 +649000 ekin = 0.215087078764693 | erot = 0.268256849270417 | epot = -15.1082476699768 | etot = -14.6249037419417 +650000 ekin = 0.218457489209268 | erot = 0.253342374384922 | epot = -15.0967036055725 | etot = -14.6249037419783 +651000 ekin = 0.225910420497663 | erot = 0.240087663214968 | epot = -15.090901825775 | etot = -14.6249037420623 +652000 ekin = 0.236236377394858 | erot = 0.228379019530766 | epot = -15.0895191391013 | etot = -14.6249037421757 +653000 ekin = 0.247915496412395 | erot = 0.217959688822015 | epot = -15.0907789275287 | etot = -14.6249037422943 +654000 ekin = 0.259425494352476 | erot = 0.208500305716241 | epot = -15.0928295424619 | etot = -14.6249037423932 +655000 ekin = 0.26955455820855 | erot = 0.199677958220202 | epot = -15.0941362588805 | etot = -14.6249037424517 +656000 ekin = 0.277652649609351 | erot = 0.191249336850371 | epot = -15.0938057289177 | etot = -14.624903742458 +657000 ekin = 0.283765747905513 | erot = 0.183104207684416 | epot = -15.0917736980008 | etot = -14.6249037424109 +658000 ekin = 0.288620908153495 | erot = 0.175289536735997 | epot = -15.0888141872111 | etot = -14.6249037423216 +659000 ekin = 0.293459924910638 | erot = 0.168001027405567 | epot = -15.0863646945267 | etot = -14.6249037422105 +660000 ekin = 0.299750121924058 | erot = 0.16154591329551 | epot = -15.0861997773236 | etot = -14.624903742104 +661000 ekin = 0.30882794580118 | erot = 0.15628680849445 | epot = -15.0900184963236 | etot = -14.624903742028 +662000 ekin = 0.321550844182007 | erot = 0.152579955314563 | epot = -15.0990345414996 | etot = -14.624903742003 +663000 ekin = 0.338040404322879 | erot = 0.150721656676574 | epot = -15.1136658030369 | etot = -14.6249037420375 +664000 ekin = 0.357588696379433 | erot = 0.150913925254324 | epot = -15.1334063637592 | etot = -14.6249037421255 +665000 ekin = 0.378766116435926 | erot = 0.153254852725576 | epot = -15.1569247114086 | etot = -14.6249037422471 +666000 ekin = 0.399716130930416 | erot = 0.157752003176736 | epot = -15.1823718764813 | etot = -14.6249037423741 +667000 ekin = 0.418564373573455 | erot = 0.164350192887448 | epot = -15.2078183089391 | etot = -14.6249037424782 +668000 ekin = 0.433827740573898 | erot = 0.172960630436554 | epot = -15.2316921135493 | etot = -14.6249037425388 +669000 ekin = 0.444701001629873 | erot = 0.183478145302767 | epot = -15.2530828894839 | etot = -14.6249037425513 +670000 ekin = 0.451136418416049 | erot = 0.195778468141822 | epot = -15.2718186290842 | etot = -14.6249037425263 +671000 ekin = 0.453701004148981 | erot = 0.209695862328768 | epot = -15.2883006089635 | etot = -14.6249037424857 +672000 ekin = 0.453273827001077 | erot = 0.224990306458558 | epot = -15.3031678759134 | etot = -14.6249037424538 +673000 ekin = 0.450699702661522 | erot = 0.241319095058617 | epot = -15.3169225401686 | etot = -14.6249037424485 +674000 ekin = 0.446523488450417 | erot = 0.258227823778676 | epot = -15.3296550547043 | etot = -14.6249037424752 +675000 ekin = 0.44088962459253 | erot = 0.275170305159689 | epot = -15.3409636722772 | etot = -14.624903742525 +676000 ekin = 0.433624481153454 | erot = 0.291558306506453 | epot = -15.350086530239 | etot = -14.6249037425791 +677000 ekin = 0.424453634856828 | erot = 0.306833290383679 | epot = -15.3561906678562 | etot = -14.6249037426157 +678000 ekin = 0.41326517646593 | erot = 0.320546114279227 | epot = -15.3587150333616 | etot = -14.6249037426165 +679000 ekin = 0.400321537247193 | erot = 0.332428088763687 | epot = -15.3576533685842 | etot = -14.6249037425733 +680000 ekin = 0.386341988793522 | erot = 0.342437977068841 | epot = -15.3536837083529 | etot = -14.6249037424906 +681000 ekin = 0.372417408219175 | erot = 0.350774050474234 | epot = -15.3480952010788 | etot = -14.6249037423854 +682000 ekin = 0.35976964508921 | erot = 0.357847594354926 | epot = -15.342520981727 | etot = -14.6249037422829 +683000 ekin = 0.349419724484302 | erot = 0.364223142873746 | epot = -15.3385466095668 | etot = -14.6249037422088 +684000 ekin = 0.341867426589136 | erot = 0.370539083005818 | epot = -15.3373102517758 | etot = -14.6249037421809 +685000 ekin = 0.336892967752833 | erot = 0.37742728588017 | epot = -15.3392239958362 | etot = -14.6249037422032 +686000 ekin = 0.333560575456658 | erot = 0.385449795148896 | epot = -15.343914112869 | etot = -14.6249037422634 +687000 ekin = 0.330440845244727 | erot = 0.395064019974615 | epot = -15.3504086075565 | etot = -14.6249037423372 +688000 ekin = 0.325996654362847 | erot = 0.406617593545496 | epot = -15.3575179903034 | etot = -14.624903742395 +689000 ekin = 0.319023752377333 | erot = 0.420363991129467 | epot = -15.3642914859188 | etot = -14.624903742412 +690000 ekin = 0.309020969988424 | erot = 0.436483939357874 | epot = -15.3704086517213 | etot = -14.624903742375 +691000 ekin = 0.296388973948975 | erot = 0.455097572739774 | epot = -15.3763902889748 | etot = -14.6249037422861 +692000 ekin = 0.282408410636019 | erot = 0.476257707732204 | epot = -15.3835698605304 | etot = -14.6249037421622 +693000 ekin = 0.269008530851688 | erot = 0.499923033173812 | epot = -15.393835306056 | etot = -14.6249037420305 +694000 ekin = 0.258387685788622 | erot = 0.525918285140571 | epot = -15.4092097128506 | etot = -14.6249037419214 +695000 ekin = 0.25257627520821 | erot = 0.553894058809888 | epot = -15.43137407588 | etot = -14.6249037418619 +696000 ekin = 0.253038186235009 | erot = 0.583300660396584 | epot = -15.4612425885012 | etot = -14.6249037418696 +697000 ekin = 0.260392018277579 | erot = 0.613388418368988 | epot = -15.4986841785954 | etot = -14.6249037419489 +698000 ekin = 0.274304391463509 | erot = 0.64324187918294 | epot = -15.5424500127365 | etot = -14.6249037420901 +699000 ekin = 0.293570250406769 | erot = 0.671848180609457 | epot = -15.5903221732877 | etot = -14.6249037422715 +700000 ekin = 0.316355070233514 | erot = 0.698191700483047 | epot = -15.639450513181 | etot = -14.6249037424644 +701000 ekin = 0.340538337282332 | erot = 0.721359481466447 | epot = -15.6868015613885 | etot = -14.6249037426397 +702000 ekin = 0.364075443764615 | erot = 0.740637254695032 | epot = -15.7296164412337 | etot = -14.6249037427741 +703000 ekin = 0.385294321874606 | erot = 0.75557636945477 | epot = -15.7657744341848 | etot = -14.6249037428555 +704000 ekin = 0.40306671671928 | erot = 0.766018576887906 | epot = -15.7939890364911 | etot = -14.6249037428839 +705000 ekin = 0.416833588997184 | erot = 0.772075474100319 | epot = -15.8138128059668 | etot = -14.6249037428693 +706000 ekin = 0.426510451501955 | erot = 0.774072055032491 | epot = -15.8254862493611 | etot = -14.6249037428266 +707000 ekin = 0.432328070473605 | erot = 0.772470813770598 | epot = -15.8297026270152 | etot = -14.624903742771 +708000 ekin = 0.434671210546145 | erot = 0.767794279505844 | epot = -15.8273692327653 | etot = -14.6249037427133 +709000 ekin = 0.433963855683832 | erot = 0.760560754832635 | epot = -15.8194283531753 | etot = -14.6249037426588 +710000 ekin = 0.430621214402396 | erot = 0.751241421805773 | epot = -15.8067663788157 | etot = -14.6249037426076 +711000 ekin = 0.42506102881634 | erot = 0.740240555545717 | epot = -15.7902053269187 | etot = -14.6249037425567 +712000 ekin = 0.417748693286703 | erot = 0.727895913280697 | epot = -15.7705483490698 | etot = -14.6249037425024 +713000 ekin = 0.409245407745788 | erot = 0.714493617369859 | epot = -15.7486427675576 | etot = -14.624903742442 +714000 ekin = 0.400233112897398 | erot = 0.700290376394005 | epot = -15.7254272316667 | etot = -14.6249037423753 +715000 ekin = 0.391499218630518 | erot = 0.685535269234734 | epot = -15.7019382301705 | etot = -14.6249037423053 +716000 ekin = 0.383874653287396 | erot = 0.67048382480872 | epot = -15.6792622203348 | etot = -14.6249037422387 +717000 ekin = 0.378129665172728 | erot = 0.655399296057203 | epot = -15.6584327034143 | etot = -14.6249037421843 +718000 ekin = 0.374843116814185 | erot = 0.640539821856989 | epot = -15.640286680823 | etot = -14.6249037421519 +719000 ekin = 0.374271424141624 | erot = 0.626134666228549 | epot = -15.6253098325193 | etot = -14.6249037421492 +720000 ekin = 0.376249546442097 | erot = 0.612356169201246 | epot = -15.6135094578233 | etot = -14.62490374218 +721000 ekin = 0.380155783156075 | erot = 0.599295758360148 | epot = -15.6043552837583 | etot = -14.6249037422421 +722000 ekin = 0.38496276143876 | erot = 0.586951574249477 | epot = -15.5968180780148 | etot = -14.6249037423265 +723000 ekin = 0.389379823381561 | erot = 0.57523200329734 | epot = -15.5895155690971 | etot = -14.6249037424182 +724000 ekin = 0.392071125783968 | erot = 0.563975606696704 | epot = -15.5809504749797 | etot = -14.624903742499 +725000 ekin = 0.391913283458913 | erot = 0.552983740178136 | epot = -15.5698007661881 | etot = -14.624903742551 +726000 ekin = 0.388241956532947 | erot = 0.542058916015296 | epot = -15.5552046151089 | etot = -14.6249037425607 +727000 ekin = 0.381032991792247 | erot = 0.531040454531364 | epot = -15.5369771888453 | etot = -14.6249037425217 +728000 ekin = 0.370971903191936 | erot = 0.51982908237483 | epot = -15.5157047280045 | etot = -14.6249037424377 +729000 ekin = 0.359388263612697 | erot = 0.508395729808055 | epot = -15.4926877357429 | etot = -14.6249037423222 +730000 ekin = 0.348057580439693 | erot = 0.496773021024349 | epot = -15.4697343436589 | etot = -14.6249037421949 +731000 ekin = 0.338902689199426 | erot = 0.48503267140759 | epot = -15.4488391026866 | etot = -14.6249037420796 +732000 ekin = 0.333649662945475 | erot = 0.473255762296962 | epot = -15.4318091672413 | etot = -14.6249037419988 +733000 ekin = 0.333505576676606 | erot = 0.461504910073432 | epot = -15.4199142287184 | etot = -14.6249037419684 +734000 ekin = 0.338924758984327 | erot = 0.449807254483215 | epot = -15.4136357554618 | etot = -14.6249037419943 +735000 ekin = 0.349515468577354 | erot = 0.438154711902627 | epot = -15.412573922551 | etot = -14.624903742071 +736000 ekin = 0.364111355274983 | erot = 0.426523255164317 | epot = -15.4155383526214 | etot = -14.6249037421821 +737000 ekin = 0.380995719774913 | erot = 0.414906900972836 | epot = -15.4208063630518 | etot = -14.6249037423041 +738000 ekin = 0.398229414671756 | erot = 0.403356227833025 | epot = -15.4264893849167 | etot = -14.6249037424119 +739000 ekin = 0.41400586007365 | erot = 0.392007798568608 | epot = -15.4309174011284 | etot = -14.6249037424862 +740000 ekin = 0.426948743963044 | erot = 0.381091720704502 | epot = -15.4329442071847 | etot = -14.6249037425172 +741000 ekin = 0.436283647683231 | erot = 0.370910229391922 | epot = -15.4320976195822 | etot = -14.6249037425071 +742000 ekin = 0.441850001827036 | erot = 0.361789064611271 | epot = -15.4285428089074 | etot = -14.6249037424691 +743000 ekin = 0.443963491147379 | erot = 0.354012421291793 | epot = -15.4228796548618 | etot = -14.6249037424227 +744000 ekin = 0.443178108515845 | erot = 0.347758127978261 | epot = -15.4158399788819 | etot = -14.6249037423878 +745000 ekin = 0.440021184885117 | erot = 0.343050543545259 | epot = -15.4079754708099 | etot = -14.6249037423795 +746000 ekin = 0.434779146250806 | erot = 0.339744491074207 | epot = -15.3994273797282 | etot = -14.6249037424032 +747000 ekin = 0.427396883605164 | erot = 0.337545938413876 | epot = -15.3898465644715 | etot = -14.6249037424524 +748000 ekin = 0.417523045840964 | erot = 0.336066252171354 | epot = -15.378493040523 | etot = -14.6249037425106 +749000 ekin = 0.404692764111769 | erot = 0.334898725161342 | epot = -15.3644952318284 | etot = -14.6249037425553 +750000 ekin = 0.38859628761696 | erot = 0.333700338300268 | epot = -15.3472003684814 | etot = -14.6249037425641 +751000 ekin = 0.369348367994352 | erot = 0.332259621152217 | epot = -15.3265117316697 | etot = -14.6249037425232 +752000 ekin = 0.347662572337044 | erot = 0.330533807749388 | epot = -15.3031001225185 | etot = -14.6249037424321 +753000 ekin = 0.32485637347094 | erot = 0.328645172901279 | epot = -15.2784052886778 | etot = -14.6249037423055 +754000 ekin = 0.302664104351826 | erot = 0.326836116135493 | epot = -15.2544039626575 | etot = -14.6249037421702 +755000 ekin = 0.282898405306331 | erot = 0.32539267738901 | epot = -15.2331948247533 | etot = -14.6249037420579 +756000 ekin = 0.267052130149665 | erot = 0.324553861438981 | epot = -15.216509733585 | etot = -14.6249037419963 +757000 ekin = 0.255952872034765 | erot = 0.32442748097694 | epot = -15.2052840950137 | etot = -14.624903742002 +758000 ekin = 0.24956686325818 | erot = 0.324931841855881 | epot = -15.1994024471896 | etot = -14.6249037420755 +759000 ekin = 0.247007285742243 | erot = 0.325777353497121 | epot = -15.1976883814409 | etot = -14.6249037422016 +760000 ekin = 0.246749335490674 | erot = 0.326494279608963 | epot = -15.1981473574513 | etot = -14.6249037423517 +761000 ekin = 0.247004464362755 | erot = 0.32650345690093 | epot = -15.1984116637543 | etot = -14.6249037424906 +762000 ekin = 0.246168267682973 | erot = 0.325217160867496 | epot = -15.196289171135 | etot = -14.6249037425846 +763000 ekin = 0.243236270174414 | erot = 0.32214932288445 | epot = -15.1902893356681 | etot = -14.6249037426092 +764000 ekin = 0.238083572627797 | erot = 0.31701054114624 | epot = -15.1799978563308 | etot = -14.6249037425568 +765000 ekin = 0.231530329805837 | erot = 0.309765883620828 | epot = -15.1661999558649 | etot = -14.6249037424383 +766000 ekin = 0.225163449189513 | erot = 0.300642577937803 | epot = -15.1507097694085 | etot = -14.6249037422812 +767000 ekin = 0.22094703764136 | erot = 0.290087936283322 | epot = -15.1359387160482 | etot = -14.6249037421235 +768000 ekin = 0.220714417705591 | erot = 0.278690999515505 | epot = -15.1243091592243 | etot = -14.6249037420032 +769000 ekin = 0.225674230585282 | erot = 0.267090069999639 | epot = -15.1176680425329 | etot = -14.6249037419479 +770000 ekin = 0.236066860406118 | erot = 0.255889903618327 | epot = -15.1168605059916 | etot = -14.6249037419672 +771000 ekin = 0.251070223471381 | erot = 0.245606888556436 | epot = -15.1215808540782 | etot = -14.6249037420503 +772000 ekin = 0.268985032795184 | erot = 0.236650197272858 | epot = -15.130538972238 | etot = -14.6249037421699 +773000 ekin = 0.287649902236207 | erot = 0.229335047808925 | epot = -15.1418886923348 | etot = -14.6249037422896 +774000 ekin = 0.304971347443521 | erot = 0.223914516380439 | epot = -15.1537896061995 | etot = -14.6249037423755 +775000 ekin = 0.319422560281353 | erot = 0.220611402282044 | epot = -15.1649377049685 | etot = -14.6249037424051 +776000 ekin = 0.330375903029014 | erot = 0.219632840721417 | epot = -15.1749124861243 | etot = -14.6249037423739 +777000 ekin = 0.338182326481318 | erot = 0.221157252264488 | epot = -15.1842433210425 | etot = -14.6249037422967 +778000 ekin = 0.34398099350531 | erot = 0.22529363977163 | epot = -15.1941783754801 | etot = -14.6249037422031 +779000 ekin = 0.349294202147492 | erot = 0.232023926337254 | epot = -15.2062218706139 | etot = -14.6249037421291 +780000 ekin = 0.355517983707864 | erot = 0.241146781675322 | epot = -15.2215685074905 | etot = -14.6249037421074 +781000 ekin = 0.36344584750217 | erot = 0.25224414994015 | epot = -15.2405937395998 | etot = -14.6249037421575 +782000 ekin = 0.372957766808887 | erot = 0.264688770758124 | epot = -15.2625502798461 | etot = -14.6249037422791 +783000 ekin = 0.38296926774882 | erot = 0.277702579812121 | epot = -15.2855755900113 | etot = -14.6249037424504 +784000 ekin = 0.391670514066059 | erot = 0.290462881206425 | epot = -15.3070371379046 | etot = -14.6249037426321 +785000 ekin = 0.397003136152363 | erot = 0.302237882822127 | epot = -15.3241447617524 | etot = -14.6249037427779 +786000 ekin = 0.397244540913185 | erot = 0.312520082335045 | epot = -15.3346683660963 | etot = -14.6249037428481 +787000 ekin = 0.391525061079143 | erot = 0.321121025638669 | epot = -15.33754982954 | etot = -14.6249037428222 +788000 ekin = 0.380116514494114 | erot = 0.328198366844194 | epot = -15.3332186240437 | etot = -14.6249037427054 +789000 ekin = 0.364402868102804 | erot = 0.334204933643257 | epot = -15.323511544273 | etot = -14.6249037425269 +790000 ekin = 0.346547882835914 | erot = 0.339772664564402 | epot = -15.3112242897307 | etot = -14.6249037423304 +791000 ekin = 0.328969533926533 | erot = 0.345562661329726 | epot = -15.2994359374168 | etot = -14.6249037421606 +792000 ekin = 0.313783234687151 | erot = 0.352120250332853 | epot = -15.290807227072 | etot = -14.624903742052 +793000 ekin = 0.302371973145348 | erot = 0.359769001653092 | epot = -15.2870447168183 | etot = -14.6249037420198 +794000 ekin = 0.295192752069156 | erot = 0.368565036951925 | epot = -15.2886615310787 | etot = -14.6249037420576 +795000 ekin = 0.291854072001083 | erot = 0.378316728407065 | epot = -15.2950745425492 | etot = -14.624903742141 +796000 ekin = 0.291420477240231 | erot = 0.388659220599418 | epot = -15.3049834400759 | etot = -14.6249037422363 +797000 ekin = 0.292835767594049 | erot = 0.399160677915359 | epot = -15.3169001878201 | etot = -14.6249037423107 +798000 ekin = 0.295321690655136 | erot = 0.40942991973209 | epot = -15.3296553527312 | etot = -14.624903742344 +799000 ekin = 0.298615606685619 | erot = 0.419195269464138 | epot = -15.3427146184843 | etot = -14.6249037423346 +800000 ekin = 0.302963113079283 | erot = 0.428333265393292 | epot = -15.3562001207729 | etot = -14.6249037423003 +801000 ekin = 0.308869807419017 | erot = 0.436842111958073 | epot = -15.3706156616482 | etot = -14.6249037422711 +802000 ekin = 0.316711643346418 | erot = 0.444773620895252 | epot = -15.3863890065178 | etot = -14.6249037422762 +803000 ekin = 0.326365730602249 | erot = 0.452151664704984 | epot = -15.403421137639 | etot = -14.6249037423317 +804000 ekin = 0.337019280358016 | erot = 0.458909057451227 | epot = -15.4208320802433 | etot = -14.6249037424341 +805000 ekin = 0.347244531512768 | erot = 0.464865921886024 | epot = -15.4370141959588 | etot = -14.62490374256 +806000 ekin = 0.355321558015419 | erot = 0.469755825324061 | epot = -15.449981126015 | etot = -14.6249037426755 +807000 ekin = 0.359699244804511 | erot = 0.473288399899576 | epot = -15.457891387451 | etot = -14.6249037427469 +808000 ekin = 0.35944291943687 | erot = 0.475225772200724 | epot = -15.4595724343888 | etot = -14.6249037427512 +809000 ekin = 0.354532149711152 | erot = 0.475448148012716 | epot = -15.4548840404063 | etot = -14.6249037426824 +810000 ekin = 0.34592712151575 | erot = 0.473990365430488 | epot = -15.4448212294989 | etot = -14.6249037425527 +811000 ekin = 0.335391497319932 | erot = 0.47104235524006 | epot = -15.4313375949483 | etot = -14.6249037423883 +812000 ekin = 0.325122479809716 | erot = 0.466917662640269 | epot = -15.4169438846729 | etot = -14.624903742223 +813000 ekin = 0.317281832618796 | erot = 0.462001954841414 | epot = -15.4041875295496 | etot = -14.6249037420894 +814000 ekin = 0.313538689251802 | erot = 0.456696276151744 | epot = -15.3951387074161 | etot = -14.6249037420126 +815000 ekin = 0.314725301427551 | erot = 0.451368238943745 | epot = -15.3909972823755 | etot = -14.6249037420042 +816000 ekin = 0.320674745952841 | erot = 0.446320054204994 | epot = -15.3918985422197 | etot = -14.6249037420619 +817000 ekin = 0.330264402530169 | erot = 0.441777145070237 | epot = -15.3969452897705 | etot = -14.6249037421701 +818000 ekin = 0.341643112116294 | erot = 0.437896324121931 | epot = -15.4044431785426 | etot = -14.6249037423044 +819000 ekin = 0.352584467965985 | erot = 0.434788688971306 | epot = -15.4122768993744 | etot = -14.6249037424371 +820000 ekin = 0.360890006680584 | erot = 0.432549774287109 | epot = -15.4183435235104 | etot = -14.6249037425427 +821000 ekin = 0.364764924967109 | erot = 0.43128829359489 | epot = -15.420956961164 | etot = -14.624903742602 +822000 ekin = 0.363101323048021 | erot = 0.431144612410221 | epot = -15.419149678064 | etot = -14.6249037426058 +823000 ekin = 0.355627506071419 | erot = 0.43229307921143 | epot = -15.4128243278382 | etot = -14.6249037425554 +824000 ekin = 0.342909507999076 | erot = 0.434926118199362 | epot = -15.4027393686599 | etot = -14.6249037424615 +825000 ekin = 0.326218347990279 | erot = 0.439222871854997 | epot = -15.390344962187 | etot = -14.6249037423417 +826000 ekin = 0.307298067026364 | erot = 0.445309293137064 | epot = -15.3775111023799 | etot = -14.6249037422164 +827000 ekin = 0.288081469809457 | erot = 0.453218819733404 | epot = -15.3662040316486 | etot = -14.6249037421057 +828000 ekin = 0.270403517643933 | erot = 0.462862712071296 | epot = -15.358169971741 | etot = -14.6249037420258 +829000 ekin = 0.255756724313351 | erot = 0.474017347276038 | epot = -15.3546778135762 | etot = -14.6249037419868 +830000 ekin = 0.245120383539822 | erot = 0.48633201659407 | epot = -15.3563561421258 | etot = -14.624903741992 +831000 ekin = 0.238883956789673 | erot = 0.499357971990034 | epot = -15.3631456708166 | etot = -14.6249037420369 +832000 ekin = 0.236868645663221 | erot = 0.512595315427615 | epot = -15.3743677032019 | etot = -14.6249037421111 +833000 ekin = 0.238435989569064 | erot = 0.525550909042522 | epot = -15.3888906408114 | etot = -14.6249037421998 +834000 ekin = 0.242658569128244 | erot = 0.537797737790336 | epot = -15.405360049206 | etot = -14.6249037422874 +835000 ekin = 0.248518315376458 | erot = 0.549024910269567 | epot = -15.4224469680061 | etot = -14.62490374236 +836000 ekin = 0.255095050223297 | erot = 0.559068449138061 | epot = -15.4390672417691 | etot = -14.6249037424078 +837000 ekin = 0.261712817640754 | erot = 0.567916383627862 | epot = -15.4545329436951 | etot = -14.6249037424265 +838000 ekin = 0.268023056778799 | erot = 0.575686784519135 | epot = -15.468613583716 | etot = -14.6249037424181 +839000 ekin = 0.274018270323247 | erot = 0.582582979366575 | epot = -15.481504992079 | etot = -14.6249037423892 +840000 ekin = 0.279983100774044 | erot = 0.588834754839254 | epot = -15.493721597963 | etot = -14.6249037423497 +841000 ekin = 0.286398274628748 | erot = 0.594637024330571 | epot = -15.5059390412695 | etot = -14.6249037423102 +842000 ekin = 0.293816650983671 | erot = 0.600098453280244 | epot = -15.5188188465455 | etot = -14.6249037422816 +843000 ekin = 0.302726774569864 | erot = 0.605208920748267 | epot = -15.5328394375906 | etot = -14.6249037422725 +844000 ekin = 0.313421069061913 | erot = 0.609833296484503 | epot = -15.5481581078352 | etot = -14.6249037422888 +845000 ekin = 0.325887895395929 | erot = 0.613733577818103 | epot = -15.5645252155455 | etot = -14.6249037423314 +846000 ekin = 0.33975240096389 | erot = 0.616615984720062 | epot = -15.5812721280797 | etot = -14.6249037423957 +847000 ekin = 0.354292335350613 | erot = 0.618194079532099 | epot = -15.5973901573538 | etot = -14.624903742471 +848000 ekin = 0.368542667425734 | erot = 0.618254639141467 | epot = -15.6117010491094 | etot = -14.6249037425422 +849000 ekin = 0.381474241846711 | erot = 0.616711095272622 | epot = -15.6230890797133 | etot = -14.624903742594 +850000 ekin = 0.392198266664605 | erot = 0.613631554978577 | epot = -15.6307335642585 | etot = -14.6249037426153 +851000 ekin = 0.400129367739792 | erot = 0.609234588534973 | epot = -15.6342676988789 | etot = -14.6249037426041 +852000 ekin = 0.405049998800082 | erot = 0.603854451145949 | epot = -15.6338081925133 | etot = -14.6249037425673 +853000 ekin = 0.407056563943438 | erot = 0.597885334647268 | epot = -15.6298456411094 | etot = -14.6249037425187 +854000 ekin = 0.406415158940066 | erot = 0.591718979209663 | epot = -15.623037880623 | etot = -14.6249037424732 +855000 ekin = 0.403390043513582 | erot = 0.585690332508252 | epot = -15.6139841184641 | etot = -14.6249037424422 +856000 ekin = 0.398116166002876 | erot = 0.580042463524147 | epot = -15.6030623719562 | etot = -14.6249037424292 +857000 ekin = 0.39056801615961 | erot = 0.574915889724005 | epot = -15.5903876483121 | etot = -14.6249037424285 +858000 ekin = 0.380638245095305 | erot = 0.570361176879803 | epot = -15.5759031644036 | etot = -14.6249037424285 +859000 ekin = 0.368297168913566 | erot = 0.566367903414504 | epot = -15.5595688147431 | etot = -14.624903742415 +860000 ekin = 0.353771484485059 | erot = 0.56289933566622 | epot = -15.5415745625294 | etot = -14.6249037423781 +861000 ekin = 0.33766818907467 | erot = 0.559921190515333 | epot = -15.5224931219057 | etot = -14.6249037423157 +862000 ekin = 0.320982687533336 | erot = 0.557415114411014 | epot = -15.5033015441806 | etot = -14.6249037422363 +863000 ekin = 0.304965814690107 | erot = 0.555372641471618 | epot = -15.485242198319 | etot = -14.6249037421573 +864000 ekin = 0.290872653002407 | erot = 0.5537720825734 | epot = -15.4695484776756 | etot = -14.6249037420998 +865000 ekin = 0.27966077424891 | erot = 0.552546988654679 | epot = -15.4571115049861 | etot = -14.6249037420825 +866000 ekin = 0.271730646598884 | erot = 0.551558423385933 | epot = -15.4481928120997 | etot = -14.6249037421148 +867000 ekin = 0.266795961580335 | erot = 0.550582916185739 | epot = -15.442282619959 | etot = -14.6249037421929 +868000 ekin = 0.263936467175558 | erot = 0.549323573879739 | epot = -15.4381637833552 | etot = -14.6249037422999 +869000 ekin = 0.261831470221842 | erot = 0.547444696243082 | epot = -15.4341799088743 | etot = -14.6249037424094 +870000 ekin = 0.259116433169414 | erot = 0.544622620095275 | epot = -15.4286427957584 | etot = -14.6249037424937 +871000 ekin = 0.254766113418661 | erot = 0.540599894777671 | epot = -15.4202697507265 | etot = -14.6249037425302 +872000 ekin = 0.248397230691804 | erot = 0.535228153627548 | epot = -15.4085291268285 | etot = -14.6249037425092 +873000 ekin = 0.240403953826285 | erot = 0.528487826572583 | epot = -15.3937955228344 | etot = -14.6249037424355 +874000 ekin = 0.231884125783745 | erot = 0.520479317821078 | epot = -15.3772671859334 | etot = -14.6249037423285 +875000 ekin = 0.224371090313998 | erot = 0.511388489700788 | epot = -15.3606633222313 | etot = -14.6249037422165 +876000 ekin = 0.219440883380304 | erot = 0.501436812694108 | epot = -15.3457814382033 | etot = -14.6249037421289 +877000 ekin = 0.218302972736541 | erot = 0.490831150818269 | epot = -15.3340378656425 | etot = -14.6249037420877 +878000 ekin = 0.221492456263516 | erot = 0.479728387736696 | epot = -15.3261245861012 | etot = -14.624903742101 +879000 ekin = 0.228756262275047 | erot = 0.468225594693746 | epot = -15.3218855991288 | etot = -14.62490374216 +880000 ekin = 0.23916916008879 | erot = 0.456378166082174 | epot = -15.3204510684128 | etot = -14.6249037422418 +881000 ekin = 0.251443176614632 | erot = 0.444238659513065 | epot = -15.3205855784454 | etot = -14.6249037423177 +882000 ekin = 0.264330844663881 | erot = 0.43190128969608 | epot = -15.3211358767216 | etot = -14.6249037423616 +883000 ekin = 0.276992343361879 | erot = 0.419534292632584 | epot = -15.3214303783539 | etot = -14.6249037423594 +884000 ekin = 0.289210952362963 | erot = 0.407386172192775 | epot = -15.3215008668683 | etot = -14.6249037423126 +885000 ekin = 0.301394205511005 | erot = 0.395760928443894 | epot = -15.3220588761927 | etot = -14.6249037422378 +886000 ekin = 0.31436859920589 | erot = 0.384968165379889 | epot = -15.3242405067469 | etot = -14.6249037421611 +887000 ekin = 0.329038341775477 | erot = 0.375262338090619 | epot = -15.3292044219764 | etot = -14.6249037421103 +888000 ekin = 0.346015111155314 | erot = 0.366788650328168 | epot = -15.3377075035892 | etot = -14.6249037421057 +889000 ekin = 0.365329693883282 | erot = 0.35955094737734 | epot = -15.3497843834164 | etot = -14.6249037421558 +890000 ekin = 0.386310696216818 | erot = 0.353410826838142 | epot = -15.3646252653079 | etot = -14.6249037422529 +891000 ekin = 0.407668087054666 | erot = 0.348119126036796 | epot = -15.3806909554674 | etot = -14.6249037423759 +892000 ekin = 0.427761236102702 | erot = 0.343372786942168 | epot = -15.396037765541 | etot = -14.6249037424962 +893000 ekin = 0.444977236018704 | erot = 0.338883525692821 | epot = -15.4087645042964 | etot = -14.6249037425849 +894000 ekin = 0.458112158679596 | erot = 0.334441343917346 | epot = -15.4174572452184 | etot = -14.6249037426214 +895000 ekin = 0.466648008330968 | erot = 0.329956933565266 | epot = -15.4215086844955 | etot = -14.6249037425992 +896000 ekin = 0.470850232518833 | erot = 0.325472374552695 | epot = -15.421226349598 | etot = -14.6249037425264 +897000 ekin = 0.471664510487189 | erot = 0.321137893833246 | epot = -15.4177061467443 | etot = -14.6249037424239 +898000 ekin = 0.470447771985121 | erot = 0.31716128210791 | epot = -15.4125127964118 | etot = -14.6249037423187 +899000 ekin = 0.468609320535131 | erot = 0.31374324783162 | epot = -15.4072563106044 | etot = -14.6249037422377 +900000 ekin = 0.467255363896452 | erot = 0.311015004595572 | epot = -15.4031741106926 | etot = -14.6249037422006 +901000 ekin = 0.466923299456765 | erot = 0.308993431077939 | epot = -15.4008204727507 | etot = -14.624903742216 +902000 ekin = 0.467466399705909 | erot = 0.307564919774022 | epot = -15.3999350617589 | etot = -14.624903742279 +903000 ekin = 0.468112799245423 | erot = 0.30650258938551 | epot = -15.3995191310034 | etot = -14.6249037423724 +904000 ekin = 0.467682260081114 | erot = 0.305513914729626 | epot = -15.3980999172821 | etot = -14.6249037424714 +905000 ekin = 0.464906903208319 | erot = 0.304308207539406 | epot = -15.3941188532968 | etot = -14.6249037425491 +906000 ekin = 0.458775313350499 | erot = 0.302667437698498 | epot = -15.3863464936332 | etot = -14.6249037425842 +907000 ekin = 0.448811106797387 | erot = 0.300501710925559 | epot = -15.3742165602889 | etot = -14.624903742566 +908000 ekin = 0.435212888278633 | erot = 0.297873922704189 | epot = -15.3579905534804 | etot = -14.6249037424975 +909000 ekin = 0.418821166579361 | erot = 0.294986492955396 | epot = -15.3387114019291 | etot = -14.6249037423944 +910000 ekin = 0.400928155652502 | erot = 0.292134043124591 | epot = -15.3179659410567 | etot = -14.6249037422796 +911000 ekin = 0.38299073131904 | erot = 0.289635345607532 | epot = -15.2975298191036 | etot = -14.624903742177 +912000 ekin = 0.366329155570265 | erot = 0.287762457046 | epot = -15.2789953547218 | etot = -14.6249037421055 +913000 ekin = 0.351888443631644 | erot = 0.286683662572436 | epot = -15.263475848279 | etot = -14.6249037420749 +914000 ekin = 0.340111462795988 | erot = 0.286431278414276 | epot = -15.2514464832956 | etot = -14.6249037420854 +915000 ekin = 0.330936398540546 | erot = 0.286898247266849 | epot = -15.2427383879358 | etot = -14.6249037421284 +916000 ekin = 0.32389927160205 | erot = 0.287861143478129 | epot = -15.2366641572708 | etot = -14.6249037421907 +917000 ekin = 0.318302399047882 | erot = 0.289022784864801 | epot = -15.2322289261694 | etot = -14.6249037422567 +918000 ekin = 0.313403328232211 | erot = 0.290065205370544 | epot = -15.2283722759156 | etot = -14.6249037423128 +919000 ekin = 0.308582994047746 | erot = 0.290702987753655 | epot = -15.2241897241503 | etot = -14.6249037423489 +920000 ekin = 0.303462620955297 | erot = 0.290727692024701 | epot = -15.2190940553404 | etot = -14.6249037423604 +921000 ekin = 0.297952758523176 | erot = 0.290036267627134 | epot = -15.2128927684984 | etot = -14.624903742348 +922000 ekin = 0.292232329167479 | erot = 0.288639696922892 | epot = -15.2057757684081 | etot = -14.6249037423177 +923000 ekin = 0.286668877938219 | erot = 0.286652137103033 | epot = -15.1982247573198 | etot = -14.6249037422785 +924000 ekin = 0.281701868658443 | erot = 0.284264668755385 | epot = -15.1908702796542 | etot = -14.6249037422404 +925000 ekin = 0.277717553237889 | erot = 0.281710557644916 | epot = -15.1843318530949 | etot = -14.6249037422121 +926000 ekin = 0.274945509179126 | erot = 0.279230091666523 | epot = -15.1790793430443 | etot = -14.6249037421987 +927000 ekin = 0.273402631519641 | erot = 0.277042382113033 | epot = -15.1753487558335 | etot = -14.6249037422009 +928000 ekin = 0.272900230271313 | erot = 0.27532923254522 | epot = -15.1731332050308 | etot = -14.6249037422143 +929000 ekin = 0.273115271900815 | erot = 0.274232799537056 | epot = -15.1722518136686 | etot = -14.6249037422307 +930000 ekin = 0.273710515355576 | erot = 0.273865029643896 | epot = -15.1724792872395 | etot = -14.6249037422401 +931000 ekin = 0.274474107139751 | erot = 0.274323617228769 | epot = -15.1737014666023 | etot = -14.6249037422338 +932000 ekin = 0.275440857683152 | erot = 0.275707340216854 | epot = -15.176051940107 | etot = -14.624903742207 +933000 ekin = 0.276957575781874 | erot = 0.278123705988361 | epot = -15.1799850239313 | etot = -14.6249037421611 +934000 ekin = 0.279664435383878 | erot = 0.281683992543418 | epot = -15.1862521700318 | etot = -14.6249037421045 +935000 ekin = 0.284382433296915 | erot = 0.286484503522641 | epot = -15.1957706788708 | etot = -14.6249037420512 +936000 ekin = 0.291920557579979 | erot = 0.292577187598074 | epot = -15.2094014871964 | etot = -14.6249037420184 +937000 ekin = 0.302840159169775 | erot = 0.299936553990588 | epot = -15.2276804551825 | etot = -14.6249037420221 +938000 ekin = 0.317231541763407 | erot = 0.308432066638773 | epot = -15.2505673504752 | etot = -14.6249037420731 +939000 ekin = 0.334562734704664 | erot = 0.317815317270636 | epot = -15.2772817941479 | etot = -14.6249037421726 +940000 ekin = 0.353649521805238 | erot = 0.327729086105133 | epot = -15.3062823502217 | etot = -14.6249037423114 +941000 ekin = 0.372770367646981 | erot = 0.337741122003566 | epot = -15.3354152321204 | etot = -14.6249037424699 +942000 ekin = 0.389915662531947 | erot = 0.347399749799135 | epot = -15.3622191549531 | etot = -14.6249037426221 +943000 ekin = 0.403126345739486 | erot = 0.356302369934052 | epot = -15.3843324584141 | etot = -14.6249037427406 +944000 ekin = 0.410851754406517 | erot = 0.364163156178947 | epot = -15.3999186533885 | etot = -14.624903742803 +945000 ekin = 0.412247920960694 | erot = 0.370864511414574 | epot = -15.4080161751724 | etot = -14.6249037427972 +946000 ekin = 0.407348747780355 | erot = 0.376479254457633 | epot = -15.4087317449614 | etot = -14.6249037427235 +947000 ekin = 0.397071124217177 | erot = 0.381256899558804 | epot = -15.4032317663713 | etot = -14.6249037425953 +948000 ekin = 0.383053455726579 | erot = 0.385576026491136 | epot = -15.3935332246539 | etot = -14.6249037424362 +949000 ekin = 0.367364810070546 | erot = 0.389872987609663 | epot = -15.382141539954 | etot = -14.6249037422738 +950000 ekin = 0.352149150211141 | erot = 0.394562514443112 | epot = -15.371615406789 | etot = -14.6249037421348 +951000 ekin = 0.339280178143099 | erot = 0.399966938641359 | epot = -15.3641508588234 | etot = -14.6249037420389 +952000 ekin = 0.330096120379237 | erot = 0.406268489131811 | epot = -15.3612683515071 | etot = -14.6249037419961 +953000 ekin = 0.325261831669684 | erot = 0.413492937870729 | epot = -15.3636585115451 | etot = -14.6249037420047 +954000 ekin = 0.324774911929383 | erot = 0.421526046053159 | epot = -15.3712047000361 | etot = -14.6249037420535 +955000 ekin = 0.328098170459405 | erot = 0.43015685816017 | epot = -15.3831587707447 | etot = -14.6249037421252 +956000 ekin = 0.334370903123805 | erot = 0.439135698166764 | epot = -15.3984103434923 | etot = -14.6249037422018 +957000 ekin = 0.342633913360331 | erot = 0.448231239799098 | epot = -15.415768895429 | etot = -14.6249037422696 +958000 ekin = 0.352004139469646 | erot = 0.457271615167415 | epot = -15.4341794969597 | etot = -14.6249037423226 +959000 ekin = 0.361755395785228 | erot = 0.466159587643494 | epot = -15.4528187257923 | etot = -14.6249037423635 +960000 ekin = 0.371296348402955 | erot = 0.474860087932416 | epot = -15.4710601787363 | etot = -14.6249037424009 +961000 ekin = 0.380073790912418 | erot = 0.483367158174937 | epot = -15.4883446915324 | etot = -14.624903742445 +962000 ekin = 0.387455548950117 | erot = 0.491663490520803 | epot = -15.5040227819739 | etot = -14.624903742503 +963000 ekin = 0.392654097311874 | erot = 0.49968729563245 | epot = -15.5172451355191 | etot = -14.6249037425748 +964000 ekin = 0.394737939559185 | erot = 0.507318071995981 | epot = -15.5269597542072 | etot = -14.624903742652 +965000 ekin = 0.392748486467115 | erot = 0.514386334667554 | epot = -15.5320385638537 | etot = -14.6249037427191 +966000 ekin = 0.38590547325284 | erot = 0.520705106527849 | epot = -15.5315143225377 | etot = -14.624903742757 +967000 ekin = 0.373852021645421 | erot = 0.526114369234909 | epot = -15.5248701336288 | etot = -14.6249037427485 +968000 ekin = 0.356869417135994 | erot = 0.530525868585158 | epot = -15.5122990284054 | etot = -14.6249037426842 +969000 ekin = 0.335986889834556 | erot = 0.533955228284217 | epot = -15.4948458606857 | etot = -14.624903742567 +970000 ekin = 0.312927788672648 | erot = 0.536531428461786 | epot = -15.4743629595477 | etot = -14.6249037424133 +971000 ekin = 0.289872105907182 | erot = 0.538479668129509 | epot = -15.4532555162878 | etot = -14.6249037422511 +972000 ekin = 0.269070232407033 | erot = 0.540080898361602 | epot = -15.4340548728818 | etot = -14.6249037421131 +973000 ekin = 0.252397022945933 | erot = 0.54161782723094 | epot = -15.4189185922051 | etot = -14.6249037420282 +974000 ekin = 0.240964852823081 | erot = 0.543321042152107 | epot = -15.4091896369882 | etot = -14.624903742013 +975000 ekin = 0.23490216482483 | erot = 0.545328986458791 | epot = -15.4051348933517 | etot = -14.6249037420681 +976000 ekin = 0.233353466622718 | erot = 0.547671994180028 | epot = -15.4059292029808 | etot = -14.624903742178 +977000 ekin = 0.23469220109011 | erot = 0.550284513867316 | epot = -15.4098804572738 | etot = -14.6249037423163 +978000 ekin = 0.236887903181319 | erot = 0.553043053342949 | epot = -15.4148346989756 | etot = -14.6249037424513 +979000 ekin = 0.237945797132614 | erot = 0.555821040963938 | epot = -15.4186705806485 | etot = -14.624903742552 +980000 ekin = 0.236334546964098 | erot = 0.558547250125554 | epot = -15.4197855396836 | etot = -14.624903742594 +981000 ekin = 0.231322843924842 | erot = 0.561252158433111 | epot = -15.4174787449233 | etot = -14.6249037425653 +982000 ekin = 0.223154169545187 | erot = 0.564087592075058 | epot = -15.4121455040898 | etot = -14.6249037424696 +983000 ekin = 0.213008719539848 | erot = 0.567310103887051 | epot = -15.405222565754 | etot = -14.6249037423271 +984000 ekin = 0.202740628548823 | erot = 0.571227590062905 | epot = -15.3988719607832 | etot = -14.6249037421715 +985000 ekin = 0.19443566515497 | erot = 0.576119771488149 | epot = -15.395459178685 | etot = -14.6249037420419 +986000 ekin = 0.189894304519326 | erot = 0.582152858152867 | epot = -15.3969509046438 | etot = -14.6249037419716 +987000 ekin = 0.190182835425093 | erot = 0.589313613953994 | epot = -15.4044001913574 | etot = -14.6249037419783 +988000 ekin = 0.195390213187501 | erot = 0.597385005524193 | epot = -15.4176789607687 | etot = -14.624903742057 +989000 ekin = 0.204671362362471 | erot = 0.605974905403898 | epot = -15.4355500099488 | etot = -14.6249037421824 +990000 ekin = 0.216563394578787 | erot = 0.614593273597699 | epot = -15.4560604104926 | etot = -14.6249037423161 +991000 ekin = 0.229465191862139 | erot = 0.622757127490779 | epot = -15.4771260617733 | etot = -14.6249037424204 +992000 ekin = 0.242114271128949 | erot = 0.630092599917091 | epot = -15.4971106135164 | etot = -14.6249037424704 +993000 ekin = 0.253902581480084 | erot = 0.636403793831659 | epot = -15.5152101177729 | etot = -14.6249037424612 +994000 ekin = 0.264939510335902 | erot = 0.641689105048086 | epot = -15.5315323577919 | etot = -14.6249037424079 +995000 ekin = 0.275864888579236 | erot = 0.646102898208602 | epot = -15.5468715291263 | etot = -14.6249037423384 +996000 ekin = 0.287497820770256 | erot = 0.649877086441226 | epot = -15.5622786494954 | etot = -14.6249037422839 +997000 ekin = 0.300450307467438 | erot = 0.65322742357329 | epot = -15.5785814733092 | etot = -14.6249037422685 +998000 ekin = 0.314829914377602 | erot = 0.656270894957618 | epot = -15.5960045516385 | etot = -14.6249037423033 +999000 ekin = 0.330110494517114 | erot = 0.658973630822449 | epot = -15.6139878677246 | etot = -14.624903742385 +1000000 ekin = 0.345190458650495 | erot = 0.661138339466907 | epot = -15.6312325406154 | etot = -14.624903742498 + 1000000 0.025569664 -1.5839232 0.020799898 -1.5286042 -3.5789082e-06 +Loop time of 20.5464 on 1 procs for 1000000 steps with 10 atoms + +Performance: 42051.215 tau/day, 48670.388 timesteps/s +98.3% CPU use with 1 MPI tasks x no OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 16.716 | 16.716 | 16.716 | 0.0 | 81.36 +Bond | 0.6285 | 0.6285 | 0.6285 | 0.0 | 3.06 +Neigh | 0 | 0 | 0 | 0.0 | 0.00 +Comm | 0.187 | 0.187 | 0.187 | 0.0 | 0.91 +Output | 6e-06 | 6e-06 | 6e-06 | 0.0 | 0.00 +Modify | 2.7186 | 2.7186 | 2.7186 | 0.0 | 13.23 +Other | | 0.2965 | | | 1.44 + +Nlocal: 10 ave 10 max 10 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 0 ave 0 max 0 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 45 ave 45 max 45 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 45 +Ave neighs/atom = 4.5 +Ave special neighs/atom = 3.6 +Neighbor list builds = 0 +Dangerous builds = 0 + +#write_restart config.${number}.* +Total wall time: 0:00:20 diff --git a/examples/USER/cgdna/examples/oxDNA2/duplex3/log.18Jun19.duplex3.g++.4 b/examples/USER/cgdna/examples/oxDNA2/duplex3/log.18Jun19.duplex3.g++.4 new file mode 100644 index 0000000000..60722d1063 --- /dev/null +++ b/examples/USER/cgdna/examples/oxDNA2/duplex3/log.18Jun19.duplex3.g++.4 @@ -0,0 +1,1172 @@ +LAMMPS (18 Jun 2019) +variable number equal 1 +variable ofreq equal 1000 +variable efreq equal 1000 +variable T equal 0.1 + +units lj + +dimension 3 + +newton off + +boundary p p p + +atom_style hybrid bond ellipsoid +atom_modify sort 0 1.0 + +# Pair interactions require lists of neighbours to be calculated +neighbor 1.0 bin +neigh_modify every 1 delay 0 check yes + +read_data data.duplex3 + orthogonal box = (-20 -20 -20) to (20 20 20) + 1 by 2 by 2 MPI processor grid + reading atoms ... + 10 atoms + reading velocities ... + 10 velocities + 10 ellipsoids + scanning bonds ... + 2 = max bonds/atom + reading bonds ... + 8 bonds + 2 = max # of 1-2 neighbors + 2 = max # of 1-3 neighbors + 2 = max # of 1-4 neighbors + 4 = max # of special neighbors + special bonds CPU = 0.000189 secs + read_data CPU = 0.003302 secs + +set atom * mass 1.0 + 10 settings made for mass + +group all type 1 4 +10 atoms in group all + +# oxDNA bond interactions - FENE backbone +bond_style oxdna2/fene +bond_coeff * 2.0 0.25 0.7564 + +# oxDNA pair interactions +pair_style hybrid/overlay oxdna2/excv oxdna2/stk oxdna2/hbond oxdna2/xstk oxdna2/coaxstk oxdna2/dh +pair_coeff * * oxdna2/excv 2.0 0.7 0.675 2.0 0.515 0.5 2.0 0.33 0.32 +pair_coeff * * oxdna2/stk seqdep ${T} 1.3523 2.6717 6.0 0.4 0.9 0.32 0.6 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2.0 0.65 2.0 0.65 +pair_coeff * * oxdna2/stk seqdep 0.1 1.3523 2.6717 6.0 0.4 0.9 0.32 0.6 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2.0 0.65 2.0 0.65 +pair_coeff * * oxdna2/hbond seqdep 0.0 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45 +pair_coeff 1 4 oxdna2/hbond seqdep 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45 +pair_coeff 2 3 oxdna2/hbond seqdep 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45 +pair_coeff * * oxdna2/xstk 47.5 0.575 0.675 0.495 0.655 2.25 0.791592653589793 0.58 1.7 1.0 0.68 1.7 1.0 0.68 1.5 0 0.65 1.7 0.875 0.68 1.7 0.875 0.68 +pair_coeff * * oxdna2/coaxstk 58.5 0.4 0.6 0.22 0.58 2.0 2.891592653589793 0.65 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 40.0 3.116592653589793 +pair_coeff * * oxdna2/dh ${T} 1.0 0.815 +pair_coeff * * oxdna2/dh 0.1 1.0 0.815 + +# NVE ensemble +fix 1 all nve/dot +#fix 1 all nve/dotc/langevin ${T} ${T} 0.03 457145 angmom 10 +#fix 1 all nve/asphere +#fix 2 all langevin ${T} ${T} 0.03 457145 angmom 10 + +timestep 1e-5 + +#comm_style tiled +#fix 3 all balance 10000 1.1 rcb + +#compute mol all chunk/atom molecule +#compute mychunk all vcm/chunk mol +#fix 4 all ave/time 10000 1 10000 c_mychunk[1] c_mychunk[2] c_mychunk[3] file vcm.txt mode vector + +#dump pos all xyz ${ofreq} traj.${number}.xyz + +#compute quat all property/atom quatw quati quatj quatk +#dump quat all custom ${ofreq} quat.${number}.txt id c_quat[1] c_quat[2] c_quat[3] c_quat[4] +#dump_modify quat sort id +#dump_modify quat format line "%d %13.6le %13.6le %13.6le %13.6le" + +compute erot all erotate/asphere +compute ekin all ke +compute epot all pe +variable erot equal c_erot +variable ekin equal c_ekin +variable epot equal c_epot +variable etot equal c_erot+c_ekin+c_epot +fix 5 all print ${efreq} "$(step) ekin = ${ekin} | erot = ${erot} | epot = ${epot} | etot = ${etot}" screen yes +fix 5 all print 1000 "$(step) ekin = ${ekin} | erot = ${erot} | epot = ${epot} | etot = ${etot}" screen yes + +#dump out all custom ${ofreq} out.${number}.txt id x y z vx vy vz fx fy fz tqx tqy tqz +#dump_modify out sort id +#dump_modify out format line "%d %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le" + +run 1000000 +Neighbor list info ... + update every 1 steps, delay 0 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 2.6274 + ghost atom cutoff = 2.6274 + binsize = 1.3137, bins = 31 31 31 + 6 neighbor lists, perpetual/occasional/extra = 6 0 0 + (1) pair oxdna2/excv, perpetual + attributes: half, newton off + pair build: half/bin/newtoff + stencil: half/bin/3d/newtoff + bin: standard + (2) pair oxdna2/stk, perpetual, copy from (1) + attributes: half, newton off + pair build: copy + stencil: none + bin: none + (3) pair oxdna2/hbond, perpetual, copy from (1) + attributes: half, newton off + pair build: copy + stencil: none + bin: none + (4) pair oxdna2/xstk, perpetual, copy from (1) + attributes: half, newton off + pair build: copy + stencil: none + bin: none + (5) pair oxdna2/coaxstk, perpetual, copy from (1) + attributes: half, newton off + pair build: copy + stencil: none + bin: none + (6) pair oxdna2/dh, perpetual, copy from (1) + attributes: half, newton off + pair build: copy + stencil: none + bin: none +Per MPI rank memory allocation (min/avg/max) = 7.652 | 7.834 | 8.016 Mbytes +Step Temp E_pair E_mol TotEng Press + 0 0 -1.4720158 0.009525411 -1.4624904 3.1370518e-06 +1000 ekin = 0.00366431201929595 | erot = 0.00193726360268106 | epot = -14.630505317301 | etot = -14.624903741679 +2000 ekin = 0.0144775076075461 | erot = 0.00770914672939826 | epot = -14.6470903960565 | etot = -14.6249037417196 +3000 ekin = 0.0319122186081537 | erot = 0.017197232864929 | epot = -14.6740131932573 | etot = -14.6249037417842 +4000 ekin = 0.055128304350968 | erot = 0.0302085305548261 | epot = -14.7102405767754 | etot = -14.6249037418696 +5000 ekin = 0.0830285165715777 | erot = 0.0464820547542036 | epot = -14.7544143132963 | etot = -14.6249037419705 +6000 ekin = 0.11433112154675 | erot = 0.0656980211282502 | epot = -14.8049328847556 | etot = -14.6249037420806 +7000 ekin = 0.14765386656188 | erot = 0.0874894888755877 | epot = -14.8600470976311 | etot = -14.6249037421936 +8000 ekin = 0.18160209956019 | erot = 0.111456095727761 | epot = -14.9179619375912 | etot = -14.6249037423032 +9000 ekin = 0.214852894725897 | erot = 0.137179311245239 | epot = -14.9769359483746 | etot = -14.6249037424035 +10000 ekin = 0.246227151956005 | erot = 0.164238435218469 | epot = -15.0353693296649 | etot = -14.6249037424904 +11000 ekin = 0.274743080419017 | erot = 0.192226420003323 | epot = -15.091873242983 | etot = -14.6249037425607 +12000 ekin = 0.299647141765663 | erot = 0.220764512146746 | epot = -15.1453153965252 | etot = -14.6249037426128 +13000 ekin = 0.320421918860927 | erot = 0.249514690530647 | epot = -15.1948403520386 | etot = -14.624903742647 +14000 ekin = 0.336773734884323 | erot = 0.278188933730603 | epot = -15.2398664112794 | etot = -14.6249037426645 +15000 ekin = 0.34860541376287 | erot = 0.306554508009539 | epot = -15.2800636644399 | etot = -14.6249037426675 +16000 ekin = 0.355980829097832 | erot = 0.334434770083873 | epot = -15.3153193418403 | etot = -14.6249037426586 +17000 ekin = 0.359087701059401 | erot = 0.361705441666651 | epot = -15.3456968853665 | etot = -14.6249037426405 +18000 ekin = 0.358203710992248 | erot = 0.388286889516457 | epot = -15.3713943431244 | etot = -14.6249037426157 +19000 ekin = 0.353668912555266 | erot = 0.414133518537258 | epot = -15.3927061736789 | etot = -14.6249037425864 +20000 ekin = 0.345865220775347 | erot = 0.439221805285588 | epot = -15.4099907686155 | etot = -14.6249037425546 +21000 ekin = 0.335201981146553 | erot = 0.463538642606666 | epot = -15.423644366275 | etot = -14.6249037425218 +22000 ekin = 0.322105588835009 | erot = 0.487071492273222 | epot = -15.4340808235974 | etot = -14.6249037424892 +23000 ekin = 0.307010918596293 | erot = 0.509801406229522 | epot = -15.4417160672835 | etot = -14.6249037424577 +24000 ekin = 0.290352786033317 | erot = 0.53169940050183 | epot = -15.4469559289633 | etot = -14.6249037424281 +25000 ekin = 0.272556500902201 | erot = 0.552726088759337 | epot = -15.4501863320625 | etot = -14.624903742401 +26000 ekin = 0.254027484079225 | erot = 0.572834017299149 | epot = -15.451765243755 | etot = -14.6249037423766 +27000 ekin = 0.235140665216512 | erot = 0.591971851501351 | epot = -15.4520162590732 | etot = -14.6249037423553 +28000 ekin = 0.216230835846381 | erot = 0.610089455964456 | epot = -15.4512240341482 | etot = -14.6249037423373 +29000 ekin = 0.197585285158732 | erot = 0.627142960082751 | epot = -15.4496319875638 | etot = -14.6249037423223 +30000 ekin = 0.179439940173485 | erot = 0.643099062793524 | epot = -15.4474427452772 | etot = -14.6249037423102 +31000 ekin = 0.161979935826275 | erot = 0.657938056392414 | epot = -15.4448217345188 | etot = -14.6249037423001 +32000 ekin = 0.145345108983154 | erot = 0.671655297434073 | epot = -15.4419041487088 | etot = -14.6249037422916 +33000 ekin = 0.129640400345301 | erot = 0.684261083518649 | epot = -15.4388052261477 | etot = -14.6249037422838 +34000 ekin = 0.114950474500096 | erot = 0.695779112936577 | epot = -15.4356333297123 | etot = -14.6249037422756 +35000 ekin = 0.101357103460395 | erot = 0.706243888527945 | epot = -15.4325047342545 | etot = -14.6249037422661 +36000 ekin = 0.0889576334571495 | erot = 0.715697403164658 | epot = -15.4295587788764 | etot = -14.6249037422546 +37000 ekin = 0.0778817390290869 | erot = 0.724185638635694 | epot = -15.4269711199052 | etot = -14.6249037422404 +38000 ekin = 0.0683037091548152 | erot = 0.731755309647459 | epot = -15.4249627610255 | etot = -14.6249037422232 +39000 ekin = 0.0604476327394574 | erot = 0.738451228922887 | epot = -15.4238026038658 | etot = -14.6249037422035 +40000 ekin = 0.0545835914676698 | erot = 0.744314557682062 | epot = -15.4238018913317 | etot = -14.624903742182 +41000 ekin = 0.0510142787133431 | erot = 0.749382063190686 | epot = -15.425300084064 | etot = -14.6249037421599 +42000 ekin = 0.0500531571157122 | erot = 0.753686350478873 | epot = -15.4286432497339 | etot = -14.6249037421393 +43000 ekin = 0.0519969858277791 | erot = 0.757256889238925 | epot = -15.4341576171884 | etot = -14.6249037421217 +44000 ekin = 0.0570968352183795 | erot = 0.760121540481331 | epot = -15.4421221178083 | etot = -14.6249037421086 +45000 ekin = 0.0655321553469052 | erot = 0.762308219230389 | epot = -15.4527441166787 | etot = -14.6249037421014 +46000 ekin = 0.077391880036667 | erot = 0.763846321567477 | epot = -15.4661419437046 | etot = -14.6249037421005 +47000 ekin = 0.0926650518886644 | erot = 0.764767599959881 | epot = -15.4823363939543 | etot = -14.6249037421058 +48000 ekin = 0.111241466890937 | erot = 0.765106283689481 | epot = -15.5012514926974 | etot = -14.624903742117 +49000 ekin = 0.132920935183018 | erot = 0.764898395951864 | epot = -15.5227230732682 | etot = -14.6249037421333 +50000 ekin = 0.157428432862217 | erot = 0.764180392178735 | epot = -15.5465125671948 | etot = -14.6249037421538 +51000 ekin = 0.184431879186323 | erot = 0.762987403181098 | epot = -15.572323024545 | etot = -14.6249037421776 +52000 ekin = 0.213559336999553 | erot = 0.761351471408863 | epot = -15.5998145506122 | etot = -14.6249037422038 +53000 ekin = 0.244412677541706 | erot = 0.759300175100794 | epot = -15.6286165948746 | etot = -14.6249037422321 +54000 ekin = 0.276574826726782 | erot = 0.756855909735936 | epot = -15.6583344787253 | etot = -14.6249037422625 +55000 ekin = 0.309607708697251 | erot = 0.754035838659022 | epot = -15.6885472896524 | etot = -14.6249037422961 +56000 ekin = 0.343038597242195 | erot = 0.750852192167276 | epot = -15.7187945317442 | etot = -14.6249037423347 +57000 ekin = 0.376334705011675 | erot = 0.747312289063632 | epot = -15.748550736456 | etot = -14.6249037423806 +58000 ekin = 0.408870193943514 | erot = 0.743417624903406 | epot = -15.7771915612831 | etot = -14.6249037424361 +59000 ekin = 0.439895666476151 | erot = 0.739161690570044 | epot = -15.8039610995489 | etot = -14.6249037425027 +60000 ekin = 0.468524372325882 | erot = 0.734526514748492 | epot = -15.8279546296535 | etot = -14.6249037425791 +61000 ekin = 0.493750804630977 | erot = 0.729479048549992 | epot = -15.8481335958426 | etot = -14.6249037426617 +62000 ekin = 0.514511417905742 | erot = 0.723968952962828 | epot = -15.8633841136118 | etot = -14.6249037427432 +63000 ekin = 0.529785687820863 | erot = 0.717929490923054 | epot = -15.8726189215585 | etot = -14.6249037428146 +64000 ekin = 0.538722043350041 | erot = 0.711282639869802 | epot = -15.8749084260858 | etot = -14.624903742866 +65000 ekin = 0.540763046401972 | erot = 0.703948378732391 | epot = -15.8696151680244 | etot = -14.62490374289 +66000 ekin = 0.535742115227036 | erot = 0.695856780686584 | epot = -15.8565026387959 | etot = -14.6249037428823 +67000 ekin = 0.523930969354304 | erot = 0.68696057843429 | epot = -15.8357952906313 | etot = -14.6249037428428 +68000 ekin = 0.506029704478312 | erot = 0.677245632039928 | epot = -15.8081790792934 | etot = -14.6249037427752 +69000 ekin = 0.483104826200259 | erot = 0.666737270644213 | epot = -15.7747458395309 | etot = -14.6249037426864 +70000 ekin = 0.456490218293525 | erot = 0.655501536742973 | epot = -15.7368954976211 | etot = -14.6249037425846 +71000 ekin = 0.427669918862827 | erot = 0.643641521525979 | epot = -15.696215182867 | etot = -14.6249037424782 +72000 ekin = 0.398160338931837 | erot = 0.631289876690699 | epot = -15.6543539579978 | etot = -14.6249037423753 +73000 ekin = 0.369405258277091 | erot = 0.618599034382457 | epot = -15.6129080349413 | etot = -14.6249037422818 +74000 ekin = 0.342691749042478 | erot = 0.605730669564096 | epot = -15.573326160809 | etot = -14.6249037422024 +75000 ekin = 0.319090526807116 | erot = 0.592845634905565 | epot = -15.5368399038526 | etot = -14.6249037421399 +76000 ekin = 0.299420611427649 | erot = 0.580095163563256 | epot = -15.5044195170865 | etot = -14.6249037420956 +77000 ekin = 0.284235504575202 | erot = 0.567613716752232 | epot = -15.476752963397 | etot = -14.6249037420696 +78000 ekin = 0.273826140866745 | erot = 0.555513536863883 | epot = -15.4542434197916 | etot = -14.624903742061 +79000 ekin = 0.268234635497765 | erot = 0.54388078034531 | epot = -15.437019157912 | etot = -14.6249037420689 +80000 ekin = 0.267272602906572 | erot = 0.532773036269537 | epot = -15.4249493812683 | etot = -14.6249037420922 +81000 ekin = 0.270538934182649 | erot = 0.522218059775401 | epot = -15.417660736088 | etot = -14.62490374213 +82000 ekin = 0.27743457435936 | erot = 0.512213638247992 | epot = -15.414551954789 | etot = -14.6249037421817 +83000 ekin = 0.287175732620383 | erot = 0.502728640569106 | epot = -15.4148081154356 | etot = -14.6249037422461 +84000 ekin = 0.298811175848726 | erot = 0.493705451301405 | epot = -15.4174203694714 | etot = -14.6249037423213 +85000 ekin = 0.311252369949757 | erot = 0.485064122067327 | epot = -15.4212202344208 | etot = -14.6249037424038 +86000 ekin = 0.323325626376074 | erot = 0.476708618160845 | epot = -15.4249379870248 | etot = -14.6249037424879 +87000 ekin = 0.33385179551888 | erot = 0.468535420697723 | epot = -15.4272909587828 | etot = -14.6249037425662 +88000 ekin = 0.341751109758587 | erot = 0.460444399763838 | epot = -15.427099252152 | etot = -14.6249037426296 +89000 ekin = 0.346159825920252 | erot = 0.452351304178841 | epot = -15.4234148727694 | etot = -14.6249037426704 +90000 ekin = 0.346534667470577 | erot = 0.444200535918418 | epot = -15.4156389460721 | etot = -14.6249037426831 +91000 ekin = 0.342715665476236 | erot = 0.435976333753466 | epot = -15.4035957418971 | etot = -14.6249037426674 +92000 ekin = 0.334922715851711 | erot = 0.427710377227768 | epot = -15.3875368357076 | etot = -14.6249037426281 +93000 ekin = 0.323677844434189 | erot = 0.419484336040122 | epot = -15.368065923049 | etot = -14.6249037425747 +94000 ekin = 0.309669782921695 | erot = 0.411426964072737 | epot = -15.3460004895125 | etot = -14.624903742518 +95000 ekin = 0.293600014862055 | erot = 0.403706586473305 | epot = -15.3222103438027 | etot = -14.6249037424673 +96000 ekin = 0.2760582848845 | erot = 0.396520701306389 | epot = -15.297482728618 | etot = -14.6249037424272 +97000 ekin = 0.257464456296026 | erot = 0.390084510983188 | epot = -15.2724527096758 | etot = -14.6249037423966 +98000 ekin = 0.238086767083294 | erot = 0.384619533405776 | epot = -15.24761004286 | etot = -14.6249037423709 +99000 ekin = 0.218116994126189 | erot = 0.380342481668315 | epot = -15.2233632181387 | etot = -14.6249037423442 +100000 ekin = 0.197764845956813 | erot = 0.377453964065525 | epot = -15.2001225523343 | etot = -14.6249037423119 +101000 ekin = 0.177333852671588 | erot = 0.37612662169739 | epot = -15.1783642166417 | etot = -14.6249037422727 +102000 ekin = 0.157255732179676 | erot = 0.376493003927858 | epot = -15.1586524783359 | etot = -14.6249037422283 +103000 ekin = 0.138079925449103 | erot = 0.378634329970109 | epot = -15.1416179976017 | etot = -14.6249037421825 +104000 ekin = 0.120430234291513 | erot = 0.38257179133531 | epot = -15.1279057677667 | etot = -14.6249037421398 +105000 ekin = 0.104946722393699 | erot = 0.388261944551355 | epot = -15.1181124090491 | etot = -14.6249037421041 +106000 ekin = 0.0922291289495077 | erot = 0.395597086392455 | epot = -15.1127299574201 | etot = -14.6249037420781 +107000 ekin = 0.0827918191992449 | erot = 0.404410579138415 | epot = -15.112106140401 | etot = -14.6249037420633 +108000 ekin = 0.0770336430610872 | erot = 0.414486225075909 | epot = -15.116423610197 | etot = -14.62490374206 +109000 ekin = 0.0752213121179505 | erot = 0.425570202879076 | epot = -15.1256952570645 | etot = -14.6249037420675 +110000 ekin = 0.077482636424855 | erot = 0.437383858086389 | epot = -15.1397702365963 | etot = -14.6249037420851 +111000 ekin = 0.0838057148049012 | erot = 0.449635759435866 | epot = -15.1583452163524 | etot = -14.6249037421117 +112000 ekin = 0.094041131771038 | erot = 0.462031808376727 | epot = -15.1809766822944 | etot = -14.6249037421466 +113000 ekin = 0.107905661684216 | erot = 0.47428271886895 | epot = -15.2070921227424 | etot = -14.6249037421893 +114000 ekin = 0.124987416380585 | erot = 0.486108767327206 | epot = -15.2359999259466 | etot = -14.6249037422388 +115000 ekin = 0.144753474421712 | erot = 0.497242253022929 | epot = -15.2668994697393 | etot = -14.6249037422947 +116000 ekin = 0.166561593123338 | erot = 0.507428522970937 | epot = -15.2988938584497 | etot = -14.6249037423555 +117000 ekin = 0.189677527330919 | erot = 0.516426638198595 | epot = -15.3310079079494 | etot = -14.6249037424199 +118000 ekin = 0.213298790897393 | erot = 0.524010758771299 | epot = -15.3622132921543 | etot = -14.6249037424856 +119000 ekin = 0.236584576961686 | erot = 0.529973112381402 | epot = -15.3914614318934 | etot = -14.6249037425503 +120000 ekin = 0.258690301858407 | erot = 0.5341290349257 | epot = -15.4177230793954 | etot = -14.6249037426112 +121000 ekin = 0.278804196533067 | erot = 0.536324108799723 | epot = -15.4400320479983 | etot = -14.6249037426655 +122000 ekin = 0.296182819519644 | erot = 0.536442962870851 | epot = -15.4575295251011 | etot = -14.6249037427106 +123000 ekin = 0.310182446406097 | erot = 0.534418915104283 | epot = -15.4695051042545 | etot = -14.6249037427441 +124000 ekin = 0.320283972930319 | erot = 0.530243389137748 | epot = -15.4754311048325 | etot = -14.6249037427644 +125000 ekin = 0.326110081462518 | erot = 0.523973945236228 | epot = -15.4749877694694 | etot = -14.6249037427707 +126000 ekin = 0.32743470961478 | erot = 0.515739832556742 | epot = -15.468078284934 | etot = -14.6249037427624 +127000 ekin = 0.324186046690464 | erot = 0.505744172152755 | epot = -15.4548339615831 | etot = -14.6249037427398 +128000 ekin = 0.316445106704291 | erot = 0.494262185784872 | epot = -15.4356110351926 | etot = -14.6249037427034 +129000 ekin = 0.304442167762781 | erot = 0.481635256753188 | epot = -15.4109811671702 | etot = -14.6249037426542 +130000 ekin = 0.288552887156539 | erot = 0.468261006625544 | epot = -15.3817176363753 | etot = -14.6249037425933 +131000 ekin = 0.269294696165401 | erot = 0.45457995559872 | epot = -15.3487783942861 | etot = -14.6249037425219 +132000 ekin = 0.247322351785784 | erot = 0.441059661322916 | epot = -15.3132857555505 | etot = -14.6249037424418 +133000 ekin = 0.223419723871666 | erot = 0.428177456066593 | epot = -15.2765009222933 | etot = -14.624903742355 +134000 ekin = 0.19848366631698 | erot = 0.416402982921093 | epot = -15.2397903915024 | etot = -14.6249037422643 +135000 ekin = 0.173495806295277 | erot = 0.406181641002432 | epot = -15.2045811894713 | etot = -14.6249037421736 +136000 ekin = 0.149479658252776 | erot = 0.397919790440761 | epot = -15.1723031907806 | etot = -14.6249037420871 +137000 ekin = 0.127443476996694 | erot = 0.391972186713497 | epot = -15.1443194057198 | etot = -14.6249037420096 +138000 ekin = 0.108312970525399 | erot = 0.38863170083623 | epot = -15.121848413308 | etot = -14.6249037419464 +139000 ekin = 0.0928612988417865 | erot = 0.388121053034643 | epot = -15.1058860937781 | etot = -14.6249037419017 +140000 ekin = 0.0816456573909381 | erot = 0.390586148388578 | epot = -15.0971355476584 | etot = -14.6249037418789 +141000 ekin = 0.074959634987115 | erot = 0.396090706683305 | epot = -15.0959540835502 | etot = -14.6249037418797 +142000 ekin = 0.072808553768854 | erot = 0.404612196534598 | epot = -15.1023244922079 | etot = -14.6249037419044 +143000 ekin = 0.0749117535381453 | erot = 0.416039504837322 | epot = -15.1158550003263 | etot = -14.6249037419509 +144000 ekin = 0.0807320498018154 | erot = 0.430173136684429 | epot = -15.1358089285018 | etot = -14.6249037420155 +145000 ekin = 0.0895290255830711 | erot = 0.44672889393778 | epot = -15.1611616616143 | etot = -14.6249037420935 +146000 ekin = 0.100429851262872 | erot = 0.46534582966922 | epot = -15.1906794231108 | etot = -14.6249037421787 +147000 ekin = 0.112509264558272 | erot = 0.485598823527704 | epot = -15.2230118303508 | etot = -14.6249037422648 +148000 ekin = 0.124869425792311 | erot = 0.507015469189125 | epot = -15.2567886373275 | etot = -14.6249037423461 +149000 ekin = 0.136710750658201 | erot = 0.529096273050756 | epot = -15.2907107661264 | etot = -14.6249037424174 +150000 ekin = 0.147386480805994 | erot = 0.551336607351909 | epot = -15.3236268306334 | etot = -14.6249037424755 +151000 ekin = 0.156436378415923 | erot = 0.573248570644847 | epot = -15.3545886915789 | etot = -14.6249037425181 +152000 ekin = 0.163597998371616 | erot = 0.594380933602504 | epot = -15.3828826745191 | etot = -14.624903742545 +153000 ekin = 0.168796920199645 | erot = 0.614335653334077 | epot = -15.4080363160909 | etot = -14.6249037425571 +154000 ekin = 0.172119667637843 | erot = 0.632779929091333 | epot = -15.4298033392859 | etot = -14.6249037425567 +155000 ekin = 0.173774602206439 | erot = 0.649453329864798 | epot = -15.4481316746178 | etot = -14.6249037425466 +156000 ekin = 0.174046854480218 | erot = 0.664170048550206 | epot = -15.4631206455604 | etot = -14.62490374253 +157000 ekin = 0.17325345101635 | erot = 0.67681676270221 | epot = -15.4749739562283 | etot = -14.6249037425097 +158000 ekin = 0.171704281293994 | erot = 0.687346881267705 | epot = -15.48395490505 | etot = -14.6249037424883 +159000 ekin = 0.169673443700116 | erot = 0.695772131172833 | epot = -15.4903493173403 | etot = -14.6249037424673 +160000 ekin = 0.167383826014799 | erot = 0.702152502586226 | epot = -15.4944400710487 | etot = -14.6249037424476 +161000 ekin = 0.165005624031947 | erot = 0.706585545944227 | epot = -15.4964949124054 | etot = -14.6249037424292 +162000 ekin = 0.162667154471987 | erot = 0.7091959147906 | epot = -15.4967668116741 | etot = -14.6249037424115 +163000 ekin = 0.160474189581708 | erot = 0.710125892129571 | epot = -15.4955038241048 | etot = -14.6249037423935 +164000 ekin = 0.158532578972808 | erot = 0.709527441008673 | epot = -15.4929637623557 | etot = -14.6249037423742 +165000 ekin = 0.156968465370873 | erot = 0.707556101120943 | epot = -15.4894283088449 | etot = -14.624903742353 +166000 ekin = 0.155941053191322 | erot = 0.704366832057858 | epot = -15.4852116275794 | etot = -14.6249037423302 +167000 ekin = 0.15564449680974 | erot = 0.700111698658167 | epot = -15.4806599377741 | etot = -14.6249037423062 +168000 ekin = 0.156297672988367 | erot = 0.694939119112688 | epot = -15.4761405343834 | etot = -14.6249037422823 +169000 ekin = 0.158122923325633 | erot = 0.688994262093866 | epot = -15.4720209276801 | etot = -14.6249037422606 +170000 ekin = 0.161316852937839 | erot = 0.682420091513715 | epot = -15.4686406866943 | etot = -14.6249037422428 +171000 ekin = 0.166017619146964 | erot = 0.675358520304694 | epot = -15.4662798816826 | etot = -14.6249037422309 +172000 ekin = 0.172273671159624 | erot = 0.667951149520755 | epot = -15.465128562907 | etot = -14.6249037422266 +173000 ekin = 0.180018623556126 | erot = 0.660339136127817 | epot = -15.465261501915 | etot = -14.624903742231 +174000 ekin = 0.189056055744959 | erot = 0.652661851831919 | epot = -15.4666216498214 | etot = -14.6249037422446 +175000 ekin = 0.199056860650102 | erot = 0.645054167286212 | epot = -15.4690147702031 | etot = -14.6249037422668 +176000 ekin = 0.209570701317496 | erot = 0.637642422787083 | epot = -15.4721168664013 | etot = -14.6249037422968 +177000 ekin = 0.220052442974529 | erot = 0.630539423737744 | epot = -15.4754956090444 | etot = -14.6249037423321 +178000 ekin = 0.229904071991068 | erot = 0.623839102439468 | epot = -15.4786469168001 | etot = -14.6249037423696 +179000 ekin = 0.238532114427838 | erot = 0.617611757778078 | epot = -15.4810476146109 | etot = -14.624903742405 +180000 ekin = 0.245419064060145 | erot = 0.611900922402911 | epot = -15.4822237288958 | etot = -14.6249037424328 +181000 ekin = 0.250203926055637 | erot = 0.606722796615544 | epot = -15.4818304651187 | etot = -14.6249037424476 +182000 ekin = 0.252761402919458 | erot = 0.602068750132192 | epot = -15.4797338954962 | etot = -14.6249037424445 +183000 ekin = 0.253262634973987 | erot = 0.597910660168958 | epot = -15.4760770375644 | etot = -14.6249037424214 +184000 ekin = 0.252195762131854 | erot = 0.594208023727366 | epot = -15.4713075282391 | etot = -14.6249037423799 +185000 ekin = 0.250326113306337 | erot = 0.590915179672999 | epot = -15.4661450353057 | etot = -14.6249037423263 +186000 ekin = 0.248586758541696 | erot = 0.587986907734991 | epot = -15.4614774085483 | etot = -14.6249037422716 +187000 ekin = 0.247909630265907 | erot = 0.585381224304124 | epot = -15.4581945967987 | etot = -14.6249037422287 +188000 ekin = 0.249029052394555 | erot = 0.583059148734203 | epot = -15.4569919433383 | etot = -14.6249037422095 +189000 ekin = 0.25230380318116 | erot = 0.580982165410166 | epot = -15.4581897108133 | etot = -14.624903742222 +190000 ekin = 0.257603763515512 | erot = 0.579108718145525 | epot = -15.4616162239286 | etot = -14.6249037422675 +191000 ekin = 0.264292655598072 | erot = 0.577391223759195 | epot = -15.4665876216979 | etot = -14.6249037423406 +192000 ekin = 0.271315385056371 | erot = 0.575774831089445 | epot = -15.4719939585754 | etot = -14.6249037424296 +193000 ekin = 0.277374539132726 | erot = 0.574198584868558 | epot = -15.4764768665205 | etot = -14.6249037425192 +194000 ekin = 0.281161076019698 | erot = 0.572598913484966 | epot = -15.4786637320983 | etot = -14.6249037425936 +195000 ekin = 0.28159263734721 | erot = 0.570914645865857 | epot = -15.4774110258526 | etot = -14.6249037426396 +196000 ekin = 0.278011867235767 | erot = 0.569092314484949 | epot = -15.4720079243697 | etot = -14.624903742649 +197000 ekin = 0.270307527593016 | erot = 0.567090473640134 | epot = -15.4623017438535 | etot = -14.6249037426204 +198000 ekin = 0.258940359976181 | erot = 0.564882125458909 | epot = -15.4487262279932 | etot = -14.6249037425581 +199000 ekin = 0.244877476699608 | erot = 0.562454912721969 | epot = -15.432236131893 | etot = -14.6249037424714 +200000 ekin = 0.229456931019031 | erot = 0.559809284042109 | epot = -15.4141699574328 | etot = -14.6249037423717 +201000 ekin = 0.214214012279214 | erot = 0.556955381706857 | epot = -15.396073136257 | etot = -14.6249037422709 +202000 ekin = 0.200701376135343 | erot = 0.553909032488835 | epot = -15.3795141508038 | etot = -14.6249037421796 +203000 ekin = 0.190329688711031 | erot = 0.550687503827458 | epot = -15.3659209346438 | etot = -14.6249037421053 +204000 ekin = 0.184246973275431 | erot = 0.547306655839924 | epot = -15.3564573711681 | etot = -14.6249037420528 +205000 ekin = 0.183262973705765 | erot = 0.543779043729182 | epot = -15.3519457594592 | etot = -14.6249037420242 +206000 ekin = 0.187816949073314 | erot = 0.5401134327365 | epot = -15.3528341238289 | etot = -14.6249037420191 +207000 ekin = 0.197980929490155 | erot = 0.536315658388532 | epot = -15.3592003299141 | etot = -14.6249037420354 +208000 ekin = 0.213487612676859 | erot = 0.532390498207104 | epot = -15.3707818529543 | etot = -14.6249037420704 +209000 ekin = 0.23377236271188 | erot = 0.528344018724915 | epot = -15.3870201235577 | etot = -14.6249037421209 +210000 ekin = 0.258021408691598 | erot = 0.524185756556645 | epot = -15.4071109074321 | etot = -14.6249037421838 +211000 ekin = 0.285222208429149 | erot = 0.519930104708152 | epot = -15.4300560553932 | etot = -14.6249037422559 +212000 ekin = 0.314215813604078 | erot = 0.515596398128299 | epot = -15.454715954066 | etot = -14.6249037423336 +213000 ekin = 0.343753634042999 | erot = 0.511207450608694 | epot = -15.4798648270648 | etot = -14.6249037424131 +214000 ekin = 0.372561594269383 | erot = 0.506786560075164 | epot = -15.5042518968341 | etot = -14.6249037424896 +215000 ekin = 0.399412456461965 | erot = 0.502353347158559 | epot = -15.5266695461789 | etot = -14.6249037425584 +216000 ekin = 0.423202666202795 | erot = 0.497919155943979 | epot = -15.5460255647614 | etot = -14.6249037426146 +217000 ekin = 0.443025226539309 | erot = 0.49348301367888 | epot = -15.561411982873 | etot = -14.6249037426548 +218000 ekin = 0.458227302378268 | erot = 0.48902929485633 | epot = -15.5721603399116 | etot = -14.624903742677 +219000 ekin = 0.468443019183614 | erot = 0.484528125251351 | epot = -15.5778748871154 | etot = -14.6249037426804 +220000 ekin = 0.473598483116428 | erot = 0.479939108990727 | epot = -15.5784413347736 | etot = -14.6249037426664 +221000 ekin = 0.473894168318623 | erot = 0.475218183432471 | epot = -15.5740160943877 | etot = -14.6249037426366 +222000 ekin = 0.469774014049581 | erot = 0.470326483973439 | epot = -15.5650042406161 | etot = -14.6249037425931 +223000 ekin = 0.461887320397625 | erot = 0.465239349169327 | epot = -15.5520304121052 | etot = -14.6249037425383 +224000 ekin = 0.451041336422898 | erot = 0.459953336121568 | epot = -15.5358984150205 | etot = -14.6249037424761 +225000 ekin = 0.438137198423164 | erot = 0.454489515561359 | epot = -15.5175304563962 | etot = -14.6249037424117 +226000 ekin = 0.424086332826599 | erot = 0.448892294163476 | epot = -15.4978823693417 | etot = -14.6249037423516 +227000 ekin = 0.409717105195494 | erot = 0.443224250669919 | epot = -15.4778450981669 | etot = -14.6249037423015 +228000 ekin = 0.395692916861841 | erot = 0.437558473222699 | epot = -15.4581551323495 | etot = -14.624903742265 +229000 ekin = 0.382463318564939 | erot = 0.431970318931165 | epot = -15.4393373797388 | etot = -14.6249037422427 +230000 ekin = 0.37025811673091 | erot = 0.426530223272703 | epot = -15.4216920822363 | etot = -14.6249037422326 +231000 ekin = 0.359118625017792 | erot = 0.42129844029256 | epot = -15.4053208075418 | etot = -14.6249037422314 +232000 ekin = 0.348949729121723 | erot = 0.416321816462675 | epot = -15.3901752878201 | etot = -14.6249037422357 +233000 ekin = 0.339575284188518 | erot = 0.411632247273729 | epot = -15.3761112737048 | etot = -14.6249037422426 +234000 ekin = 0.330784909163637 | erot = 0.407246384303507 | epot = -15.3629350357173 | etot = -14.6249037422502 +235000 ekin = 0.322367248495492 | erot = 0.403166248673538 | epot = -15.3504372394263 | etot = -14.6249037422572 +236000 ekin = 0.314129851889848 | erot = 0.399380677843492 | epot = -15.3384142719969 | etot = -14.6249037422636 +237000 ekin = 0.305908300165184 | erot = 0.395867600047875 | epot = -15.3266796424821 | etot = -14.624903742269 +238000 ekin = 0.297568064658136 | erot = 0.392597157204584 | epot = -15.3150689641364 | etot = -14.6249037422737 +239000 ekin = 0.289002756415172 | erot = 0.389535643317114 | epot = -15.3034421420096 | etot = -14.6249037422774 +240000 ekin = 0.280132201614914 | erot = 0.386650129641556 | epot = -15.2916860735363 | etot = -14.6249037422798 +241000 ekin = 0.270903172980511 | erot = 0.383913574227165 | epot = -15.2797204894881 | etot = -14.6249037422804 +242000 ekin = 0.261294311102232 | erot = 0.381310019034049 | epot = -15.2675080724143 | etot = -14.6249037422781 +243000 ekin = 0.251325265434219 | erot = 0.378839435319532 | epot = -15.2550684430252 | etot = -14.6249037422715 +244000 ekin = 0.241068460184283 | erot = 0.376521662813082 | epot = -15.2424938652572 | etot = -14.6249037422598 +245000 ekin = 0.230660579660644 | erot = 0.374398842117291 | epot = -15.2299631640205 | etot = -14.6249037422425 +246000 ekin = 0.220310176855083 | erot = 0.372535772164452 | epot = -15.217749691239 | etot = -14.6249037422195 +247000 ekin = 0.210297920408214 | erot = 0.371017759432552 | epot = -15.2062194220322 | etot = -14.6249037421914 +248000 ekin = 0.200966973970082 | erot = 0.36994577990608 | epot = -15.1958164960362 | etot = -14.6249037421601 +249000 ekin = 0.192702752056133 | erot = 0.369429135338683 | epot = -15.1870356295227 | etot = -14.6249037421279 +250000 ekin = 0.185903524092239 | erot = 0.369576201101353 | epot = -15.1803834672915 | etot = -14.6249037420979 +251000 ekin = 0.180945546219151 | erot = 0.370484246994623 | epot = -15.1763335352865 | etot = -14.6249037420727 +252000 ekin = 0.178147956309189 | erot = 0.372229589272153 | epot = -15.1752812876364 | etot = -14.624903742055 +253000 ekin = 0.177743031464987 | erot = 0.374859230992971 | epot = -15.1775060045044 | etot = -14.6249037420464 +254000 ekin = 0.179856300054645 | erot = 0.378385037101156 | epot = -15.1831450792033 | etot = -14.6249037420475 +255000 ekin = 0.184498455786156 | erot = 0.382781080046288 | epot = -15.1921832778908 | etot = -14.6249037420584 +256000 ekin = 0.191568141872831 | erot = 0.387983970946124 | epot = -15.2044558548971 | etot = -14.6249037420782 +257000 ekin = 0.20086208487434 | erot = 0.39389562099376 | epot = -15.2196614479739 | etot = -14.6249037421058 +258000 ekin = 0.212087875566807 | erot = 0.400387498987271 | epot = -15.2373791166947 | etot = -14.6249037421406 +259000 ekin = 0.224875306192123 | erot = 0.407305396776656 | epot = -15.2570844451507 | etot = -14.6249037421819 +260000 ekin = 0.238784314763303 | erot = 0.414473950040634 | epot = -15.2781620070332 | etot = -14.6249037422292 +261000 ekin = 0.253310397642086 | erot = 0.421700596682803 | epot = -15.2999147366071 | etot = -14.6249037422822 +262000 ekin = 0.26789075041242 | erot = 0.428779149458854 | epot = -15.3215736422117 | etot = -14.6249037423404 +263000 ekin = 0.281915541778016 | erot = 0.435493571930236 | epot = -15.3423128561104 | etot = -14.6249037424021 +264000 ekin = 0.294748319449364 | erot = 0.441622773940569 | epot = -15.3612748358549 | etot = -14.624903742465 +265000 ekin = 0.305757851305535 | erot = 0.446947232466421 | epot = -15.3776088262975 | etot = -14.6249037425255 +266000 ekin = 0.314361275702592 | erot = 0.451257984268131 | epot = -15.3905230025502 | etot = -14.6249037425794 +267000 ekin = 0.320075758814341 | erot = 0.454368036195608 | epot = -15.399347537632 | etot = -14.624903742622 +268000 ekin = 0.322573111286139 | erot = 0.456125517717021 | epot = -15.4036023716517 | etot = -14.6249037426486 +269000 ekin = 0.321728949457285 | erot = 0.456427019950081 | epot = -15.4030597120627 | etot = -14.6249037426554 +270000 ekin = 0.317655198203759 | erot = 0.455228696070215 | epot = -15.397787636915 | etot = -14.624903742641 +271000 ekin = 0.310703151367757 | erot = 0.452552178356157 | epot = -15.3881590723317 | etot = -14.6249037426077 +272000 ekin = 0.3014262335366 | erot = 0.448482664562447 | epot = -15.37481264066 | etot = -14.624903742561 +273000 ekin = 0.290499502093233 | erot = 0.443158007811504 | epot = -15.3585612524143 | etot = -14.6249037425096 +274000 ekin = 0.278606962225926 | erot = 0.436750209658098 | epot = -15.3402609143472 | etot = -14.6249037424632 +275000 ekin = 0.266323480340475 | erot = 0.429443553159133 | epot = -15.320670775929 | etot = -14.6249037424294 +276000 ekin = 0.254026977157675 | erot = 0.421415402005373 | epot = -15.3003461215741 | etot = -14.6249037424111 +277000 ekin = 0.241871064453077 | erot = 0.412825312322701 | epot = -15.2796001191813 | etot = -14.6249037424055 +278000 ekin = 0.229828041579266 | erot = 0.403815416630584 | epot = -15.2585472006154 | etot = -14.6249037424055 +279000 ekin = 0.217786141145793 | erot = 0.394521119097645 | epot = -15.2372110026455 | etot = -14.6249037424021 +280000 ekin = 0.205666064593437 | erot = 0.385087703032635 | epot = -15.2156575100138 | etot = -14.6249037423877 +281000 ekin = 0.193518604274061 | erot = 0.375686870763365 | epot = -15.1941092173957 | etot = -14.6249037423582 +282000 ekin = 0.18157672074763 | erot = 0.366527860022155 | epot = -15.1730083230837 | etot = -14.624903742314 +283000 ekin = 0.170254050626075 | erot = 0.357859944224688 | epot = -15.1530177371095 | etot = -14.6249037422587 +284000 ekin = 0.160098631070491 | erot = 0.349965713706295 | epot = -15.1349680869751 | etot = -14.6249037421983 +285000 ekin = 0.151720356670846 | erot = 0.34314662552044 | epot = -15.1197707243306 | etot = -14.6249037421394 +286000 ekin = 0.145712559183964 | erot = 0.337703485421193 | epot = -15.1083197866929 | etot = -14.6249037420878 +287000 ekin = 0.142584250545026 | erot = 0.333914836093095 | epot = -15.1014028286861 | etot = -14.624903742048 +288000 ekin = 0.1427129413407 | erot = 0.33201595204283 | epot = -15.0996326354059 | etot = -14.6249037420224 +289000 ekin = 0.146320998448507 | erot = 0.332180585090171 | epot = -15.1034053255506 | etot = -14.6249037420119 +290000 ekin = 0.153472816921105 | erot = 0.334506983379138 | epot = -15.1128835423165 | etot = -14.6249037420163 +291000 ekin = 0.164086465662505 | erot = 0.339009144348392 | epot = -15.1279993520451 | etot = -14.6249037420342 +292000 ekin = 0.177952173600193 | erot = 0.345613807734964 | epot = -15.1484697233995 | etot = -14.6249037420643 +293000 ekin = 0.194750859968512 | erot = 0.354163344443286 | epot = -15.1738179465169 | etot = -14.6249037421051 +294000 ekin = 0.214068309158811 | erot = 0.364424408222176 | epot = -15.2033964595362 | etot = -14.6249037421552 +295000 ekin = 0.235403710402673 | erot = 0.376101928511166 | epot = -15.2364093811272 | etot = -14.6249037422133 +296000 ekin = 0.258174229752594 | erot = 0.388857685536638 | epot = -15.2719356575669 | etot = -14.6249037422777 +297000 ekin = 0.28171936013486 | erot = 0.402332315571688 | epot = -15.308955418053 | etot = -14.6249037423465 +298000 ekin = 0.30530968452295 | erot = 0.416169191335505 | epot = -15.3463826182751 | etot = -14.6249037424166 +299000 ekin = 0.328164426016042 | erot = 0.430038291827055 | epot = -15.3831064603285 | etot = -14.6249037424854 +300000 ekin = 0.349480947254597 | erot = 0.443657997414049 | epot = -15.4180426872175 | etot = -14.6249037425489 +301000 ekin = 0.368477349758915 | erot = 0.456812763608253 | epot = -15.4501938559697 | etot = -14.6249037426025 +302000 ekin = 0.384446573101029 | erot = 0.469364841860584 | epot = -15.478715157604 | etot = -14.6249037426423 +303000 ekin = 0.396817065634643 | erot = 0.481258609604428 | epot = -15.5029794179037 | etot = -14.6249037426647 +304000 ekin = 0.405211709647263 | erot = 0.492516637287232 | epot = -15.5226320896016 | etot = -14.6249037426671 +305000 ekin = 0.409494186866275 | erot = 0.503227368869637 | epot = -15.5376252983854 | etot = -14.6249037426495 +306000 ekin = 0.409791521883174 | erot = 0.513525227982492 | epot = -15.5482204924795 | etot = -14.6249037426138 +307000 ekin = 0.406484029568133 | erot = 0.523565033268022 | epot = -15.554952805401 | etot = -14.6249037425649 +308000 ekin = 0.400159443094258 | erot = 0.533493670193094 | epot = -15.5585568557967 | etot = -14.6249037425093 +309000 ekin = 0.391535685674106 | erot = 0.543422788904079 | epot = -15.5598622170332 | etot = -14.624903742455 +310000 ekin = 0.381364662750139 | erot = 0.553406603763137 | epot = -15.5596750089224 | etot = -14.6249037424091 +311000 ekin = 0.370335174701307 | erot = 0.563428434508751 | epot = -15.5586673515872 | etot = -14.6249037423771 +312000 ekin = 0.358994462074446 | erot = 0.573398378860501 | epot = -15.5572965832962 | etot = -14.6249037423613 +313000 ekin = 0.347704062022306 | erot = 0.583162598674582 | epot = -15.5557704030575 | etot = -14.6249037423606 +314000 ekin = 0.336637402906986 | erot = 0.592522528333631 | epot = -15.5540636736117 | etot = -14.624903742371 +315000 ekin = 0.325816357219225 | erot = 0.601260411440956 | epot = -15.5519805110472 | etot = -14.624903742387 +316000 ekin = 0.315175012816655 | erot = 0.609166451967456 | epot = -15.5492452071862 | etot = -14.6249037424021 +317000 ekin = 0.304633856553691 | erot = 0.616062831071924 | epot = -15.5456004300362 | etot = -14.6249037424106 +318000 ekin = 0.294167456686513 | erot = 0.62182086663663 | epot = -15.5408920657322 | etot = -14.624903742409 +319000 ekin = 0.283852816310304 | erot = 0.626369338623922 | epot = -15.5351258973303 | etot = -14.624903742396 +320000 ekin = 0.273891844373217 | erot = 0.629693948583815 | epot = -15.5284895353292 | etot = -14.6249037423721 +321000 ekin = 0.264607615830326 | erot = 0.631829520444979 | epot = -15.5213408786153 | etot = -14.62490374234 +322000 ekin = 0.256418665980307 | erot = 0.632847556381831 | epot = -15.5141699646654 | etot = -14.6249037423032 +323000 ekin = 0.249797892887523 | erot = 0.632842055921361 | epot = -15.5075436910745 | etot = -14.6249037422657 +324000 ekin = 0.245223011939351 | erot = 0.631916211662891 | epot = -15.5020429658331 | etot = -14.6249037422309 +325000 ekin = 0.243124676660684 | erot = 0.630171930979688 | epot = -15.4982003498434 | etot = -14.624903742203 +326000 ekin = 0.243837159968099 | erot = 0.627703310196172 | epot = -15.4964442123488 | etot = -14.6249037421845 +327000 ekin = 0.247555458534595 | erot = 0.624594349329669 | epot = -15.4970535500421 | etot = -14.6249037421778 +328000 ekin = 0.254302069317299 | erot = 0.620920422826771 | epot = -15.5001262343279 | etot = -14.6249037421838 +329000 ekin = 0.263906382978619 | erot = 0.616752378549859 | epot = -15.5055625037313 | etot = -14.6249037422028 +330000 ekin = 0.275999298196813 | erot = 0.612161709808654 | epot = -15.5130647502395 | etot = -14.624903742234 +331000 ekin = 0.290024872454789 | erot = 0.607225138478484 | epot = -15.5221537532086 | etot = -14.6249037422753 +332000 ekin = 0.305269328205604 | erot = 0.602027230533244 | epot = -15.5322003010627 | etot = -14.6249037423238 +333000 ekin = 0.320905611375339 | erot = 0.596660303338559 | epot = -15.5424696570899 | etot = -14.624903742376 +334000 ekin = 0.33604943896321 | erot = 0.591221710457376 | epot = -15.5521748918485 | etot = -14.6249037424279 +335000 ekin = 0.349821102707738 | erot = 0.585809355783106 | epot = -15.5605342009668 | etot = -14.624903742476 +336000 ekin = 0.361406827299164 | erot = 0.580516763971287 | epot = -15.5668273337868 | etot = -14.6249037425163 +337000 ekin = 0.370114335989308 | erot = 0.575429096256479 | epot = -15.5704471747923 | etot = -14.6249037425465 +338000 ekin = 0.375418963131897 | erot = 0.570621177508977 | epot = -15.5709438832049 | etot = -14.624903742564 +339000 ekin = 0.37699830668418 | erot = 0.566157982091382 | epot = -15.568060031343 | etot = -14.6249037425674 +340000 ekin = 0.374754278532065 | erot = 0.562097189039008 | epot = -15.5617552101272 | etot = -14.6249037425561 +341000 ekin = 0.368821588409643 | erot = 0.558493134368575 | epot = -15.5522184653083 | etot = -14.62490374253 +342000 ekin = 0.359561251230613 | erot = 0.555400700218343 | epot = -15.5398656939398 | etot = -14.6249037424909 +343000 ekin = 0.34753785325451 | erot = 0.55287778591816 | epot = -15.5253193816136 | etot = -14.6249037424409 +344000 ekin = 0.33348037496383 | erot = 0.55098526840084 | epot = -15.5093693857485 | etot = -14.6249037423838 +345000 ekin = 0.318228359784329 | erot = 0.549783918348214 | epot = -15.4929160204567 | etot = -14.6249037423241 +346000 ekin = 0.302667555547452 | erot = 0.54932843011035 | epot = -15.4768997279244 | etot = -14.6249037422666 +347000 ekin = 0.287661057443402 | erot = 0.549659363310377 | epot = -15.4622241629697 | etot = -14.6249037422159 +348000 ekin = 0.273982878354199 | erot = 0.550794243902694 | epot = -15.4496808644332 | etot = -14.6249037421763 +349000 ekin = 0.262260631617831 | erot = 0.552719272009444 | epot = -15.4398836457781 | etot = -14.6249037421509 +350000 ekin = 0.252932884528162 | erot = 0.555383042233064 | epot = -15.4332196689026 | etot = -14.6249037421414 +351000 ekin = 0.246225113234554 | erot = 0.558693418765032 | epot = -15.4298222741477 | etot = -14.6249037421482 +352000 ekin = 0.242146418558272 | erot = 0.56251834442516 | epot = -15.4295685051533 | etot = -14.6249037421699 +353000 ekin = 0.240507191582667 | erot = 0.566690733134521 | epot = -15.4321016669209 | etot = -14.6249037422037 +354000 ekin = 0.240955911174045 | erot = 0.571016874086999 | epot = -15.436876527507 | etot = -14.6249037422459 +355000 ekin = 0.243030568944153 | erot = 0.575286990707781 | epot = -15.4432213019441 | etot = -14.6249037422922 +356000 ekin = 0.246218336341581 | erot = 0.579286102670368 | epot = -15.4504081813502 | etot = -14.6249037423382 +357000 ekin = 0.250015504867143 | erot = 0.582803084083675 | epot = -15.4577223313313 | etot = -14.6249037423804 +358000 ekin = 0.253980003728345 | erot = 0.585636256510411 | epot = -15.4645200026548 | etot = -14.6249037424161 +359000 ekin = 0.257771924238285 | erot = 0.587595069854159 | epot = -15.470270736536 | etot = -14.6249037424435 +360000 ekin = 0.261178006692362 | erot = 0.588498175296126 | epot = -15.4745799244509 | etot = -14.6249037424624 +361000 ekin = 0.264121303803865 | erot = 0.588169931158578 | epot = -15.4771949774352 | etot = -14.6249037424728 +362000 ekin = 0.266656268947586 | erot = 0.586437607933159 | epot = -15.4779976193564 | etot = -14.6249037424757 +363000 ekin = 0.268947338173594 | erot = 0.583131261385069 | epot = -15.4769823420319 | etot = -14.6249037424733 +364000 ekin = 0.271226723299151 | erot = 0.578087502910549 | epot = -15.4742179686787 | etot = -14.624903742469 +365000 ekin = 0.273728224388467 | erot = 0.571157191000871 | epot = -15.4697891578569 | etot = -14.6249037424676 +366000 ekin = 0.276601570519792 | erot = 0.562216266683795 | epot = -15.4637215796778 | etot = -14.6249037424742 +367000 ekin = 0.279824898676098 | erot = 0.551178529879434 | epot = -15.4559071710478 | etot = -14.6249037424923 +368000 ekin = 0.283144751011445 | erot = 0.538009090150866 | epot = -15.4460575836835 | etot = -14.6249037425212 +369000 ekin = 0.286073979195581 | erot = 0.522737270878923 | epot = -15.4337149926306 | etot = -14.6249037425561 +370000 ekin = 0.287962637923446 | erot = 0.505467651700438 | epot = -15.4183340322116 | etot = -14.6249037425877 +371000 ekin = 0.288129562577258 | erot = 0.486387667907668 | epot = -15.3994209730903 | etot = -14.6249037426054 +372000 ekin = 0.286016270828658 | erot = 0.46576999808234 | epot = -15.3766900115119 | etot = -14.6249037426009 +373000 ekin = 0.28131449291777 | erot = 0.44396824694377 | epot = -15.3501864824323 | etot = -14.6249037425708 +374000 ekin = 0.274029637541844 | erot = 0.421405384814399 | epot = -15.3203387648735 | etot = -14.6249037425173 +375000 ekin = 0.264468317324484 | erot = 0.398555847613824 | epot = -15.2879279073849 | etot = -14.6249037424466 +376000 ekin = 0.253165169268526 | erot = 0.375923572597148 | epot = -15.2539924842331 | etot = -14.6249037423675 +377000 ekin = 0.240780733675043 | erot = 0.354018931407531 | epot = -15.2197034073705 | etot = -14.6249037422879 +378000 ekin = 0.228003530693319 | erot = 0.333337224178132 | epot = -15.1862444970855 | etot = -14.624903742214 +379000 ekin = 0.215478669427759 | erot = 0.314340303318484 | epot = -15.1547227148953 | etot = -14.624903742149 +380000 ekin = 0.203769466320592 | erot = 0.297441561968215 | epot = -15.1261147703835 | etot = -14.6249037420947 +381000 ekin = 0.193344913038784 | erot = 0.28299357961111 | epot = -15.1012422347014 | etot = -14.6249037420515 +382000 ekin = 0.184579097116762 | erot = 0.271277560103732 | epot = -15.0807603992407 | etot = -14.6249037420202 +383000 ekin = 0.177749902922565 | erot = 0.262494318474771 | epot = -15.0651479633987 | etot = -14.6249037420014 +384000 ekin = 0.173031383434342 | erot = 0.256757595375907 | epot = -15.0546927208061 | etot = -14.6249037419958 +385000 ekin = 0.170483112154611 | erot = 0.254091341095815 | epot = -15.049478195254 | etot = -14.6249037420036 +386000 ekin = 0.170046361592112 | erot = 0.254432809989126 | epot = -15.0493829136047 | etot = -14.6249037420235 +387000 ekin = 0.171558026226825 | erot = 0.257642587604582 | epot = -15.0541043558832 | etot = -14.6249037420518 +388000 ekin = 0.174787865438713 | erot = 0.263521131369935 | epot = -15.0632127388923 | etot = -14.6249037420836 +389000 ekin = 0.179494526901415 | erot = 0.271829477565432 | epot = -15.0762277465806 | etot = -14.6249037421138 +390000 ekin = 0.185484901052056 | erot = 0.282310127810448 | epot = -15.0926987710007 | etot = -14.6249037421382 +391000 ekin = 0.192654775275645 | erot = 0.294703495235847 | epot = -15.1122620126676 | etot = -14.6249037421561 +392000 ekin = 0.200990711955422 | erot = 0.308756153372483 | epot = -15.1346506074986 | etot = -14.6249037421707 +393000 ekin = 0.210524629688135 | erot = 0.324219483680835 | epot = -15.1596478555569 | etot = -14.624903742188 +394000 ekin = 0.221250398117909 | erot = 0.340840530849171 | epot = -15.1869946711819 | etot = -14.6249037422148 +395000 ekin = 0.233028912153377 | erot = 0.358349828150776 | epot = -15.2162824825608 | etot = -14.6249037422566 +396000 ekin = 0.24551683484774 | erot = 0.376452447323546 | epot = -15.246873024486 | etot = -14.6249037423147 +397000 ekin = 0.258149646288765 | erot = 0.394827815017102 | epot = -15.277881203691 | etot = -14.6249037423851 +398000 ekin = 0.270192540269911 | erot = 0.413141033371924 | epot = -15.3082373161009 | etot = -14.624903742459 +399000 ekin = 0.280849396853359 | erot = 0.431064534842246 | epot = -15.3368176742213 | etot = -14.6249037425257 +400000 ekin = 0.289399657315015 | erot = 0.448305349544995 | epot = -15.3626087494354 | etot = -14.6249037425754 +401000 ekin = 0.295323233787434 | erot = 0.464631356381723 | epot = -15.3848583327708 | etot = -14.6249037426017 +402000 ekin = 0.298377750400983 | erot = 0.479890206670516 | epot = -15.403171699675 | etot = -14.6249037426035 +403000 ekin = 0.298608046776455 | erot = 0.49401684483596 | epot = -15.4175286341975 | etot = -14.6249037425851 +404000 ekin = 0.296288720275777 | erot = 0.507028747324647 | epot = -15.4282212101546 | etot = -14.6249037425541 +405000 ekin = 0.291819450890444 | erot = 0.519011022290083 | epot = -15.4357342157004 | etot = -14.6249037425198 +406000 ekin = 0.285604695316647 | erot = 0.530095491696055 | epot = -15.4406039295028 | etot = -14.6249037424901 +407000 ekin = 0.2779517950128 | erot = 0.540438449781317 | epot = -15.4432939872644 | etot = -14.6249037424703 +408000 ekin = 0.269015012492784 | erot = 0.550201084797022 | epot = -15.4441198397505 | etot = -14.6249037424607 +409000 ekin = 0.258799683407146 | erot = 0.559535019811769 | epot = -15.4432384456767 | etot = -14.6249037424578 +410000 ekin = 0.247223943172528 | erot = 0.568573648692213 | epot = -15.4407013343199 | etot = -14.6249037424552 +411000 ekin = 0.234219542826923 | erot = 0.577428429926601 | epot = -15.4365517151993 | etot = -14.6249037424458 +412000 ekin = 0.219842320368698 | erot = 0.586188386128906 | epot = -15.4309344489214 | etot = -14.6249037424238 +413000 ekin = 0.20435994837526 | erot = 0.594920843620994 | epot = -15.4241845343832 | etot = -14.6249037423869 +414000 ekin = 0.188290368309867 | erot = 0.603671832826878 | epot = -15.4168659434732 | etot = -14.6249037423364 +415000 ekin = 0.17237708181712 | erot = 0.6124653242919 | epot = -15.4097461483873 | etot = -14.6249037422783 +416000 ekin = 0.157503657631228 | erot = 0.621301324615769 | epot = -15.4037087244679 | etot = -14.6249037422209 +417000 ekin = 0.144565276806289 | erot = 0.630153567597092 | epot = -15.399622586577 | etot = -14.6249037421736 +418000 ekin = 0.134326161306418 | erot = 0.638967960411968 | epot = -15.398197863863 | etot = -14.6249037421446 +419000 ekin = 0.127295713867183 | erot = 0.647663024756225 | epot = -15.3998624807619 | etot = -14.6249037421385 +420000 ekin = 0.123652074079106 | erot = 0.656133267678458 | epot = -15.4046890839134 | etot = -14.6249037421558 +421000 ekin = 0.123230332545554 | erot = 0.664256043547071 | epot = -15.4123901182848 | etot = -14.6249037421922 +422000 ekin = 0.125576493084721 | erot = 0.671901405101286 | epot = -15.4223816404263 | etot = -14.6249037422402 +423000 ekin = 0.130051930466301 | erot = 0.678943694027942 | epot = -15.4338993667852 | etot = -14.6249037422909 +424000 ekin = 0.135961143238876 | erot = 0.685273086227244 | epot = -15.4461379718019 | etot = -14.6249037423358 +425000 ekin = 0.142671659965505 | erot = 0.69080498381162 | epot = -15.4583803861461 | etot = -14.624903742369 +426000 ekin = 0.149699767318722 | erot = 0.695485561348404 | epot = -15.4700890710554 | etot = -14.6249037423883 +427000 ekin = 0.156747049208244 | erot = 0.699292628464214 | epot = -15.4809434200673 | etot = -14.6249037423948 +428000 ekin = 0.163686553654253 | erot = 0.702231990285515 | epot = -15.4908222863323 | etot = -14.6249037423925 +429000 ekin = 0.170509683514413 | erot = 0.70433031530151 | epot = -15.4997437412025 | etot = -14.6249037423866 +430000 ekin = 0.177252892951188 | erot = 0.705626025883397 | epot = -15.507782661217 | etot = -14.6249037423824 +431000 ekin = 0.183925691222352 | erot = 0.706159951516081 | epot = -15.5149893851221 | etot = -14.6249037423836 +432000 ekin = 0.190457851079565 | erot = 0.70596688379378 | epot = -15.5213284772654 | etot = -14.6249037423921 +433000 ekin = 0.196676887388984 | erot = 0.705069371776661 | epot = -15.5266500015729 | etot = -14.6249037424073 +434000 ekin = 0.202317433899364 | erot = 0.703474477741261 | epot = -15.5306956540676 | etot = -14.624903742427 +435000 ekin = 0.207056046506538 | erot = 0.701173837003675 | epot = -15.533133625958 | etot = -14.6249037424478 +436000 ekin = 0.210560164856777 | erot = 0.698146912242834 | epot = -15.5336108195658 | etot = -14.6249037424662 +437000 ekin = 0.212539330538657 | erot = 0.69436686481977 | epot = -15.5318099378375 | etot = -14.6249037424791 +438000 ekin = 0.212789433625669 | erot = 0.689808070113577 | epot = -15.5275012462234 | etot = -14.6249037424842 +439000 ekin = 0.211224885327081 | erot = 0.684454087056256 | epot = -15.5205827148631 | etot = -14.6249037424798 +440000 ekin = 0.207897417438738 | erot = 0.678304934040362 | epot = -15.5111060939442 | etot = -14.6249037424651 +441000 ekin = 0.203002684917544 | erot = 0.671382822497087 | epot = -15.4992892498551 | etot = -14.6249037424404 +442000 ekin = 0.196876783893444 | erot = 0.663735946787442 | epot = -15.485516473087 | etot = -14.6249037424062 +443000 ekin = 0.189984458135359 | erot = 0.655440346227863 | epot = -15.4703285467267 | etot = -14.6249037423634 +444000 ekin = 0.182899715135716 | erot = 0.646600090309095 | epot = -15.4544035477587 | etot = -14.6249037423138 +445000 ekin = 0.176278659807256 | erot = 0.637346059016788 | epot = -15.4385284610839 | etot = -14.6249037422598 +446000 ekin = 0.170824489262319 | erot = 0.627833490901675 | epot = -15.4235617223679 | etot = -14.6249037422039 +447000 ekin = 0.167246115781588 | erot = 0.618238375507795 | epot = -15.4103882334389 | etot = -14.6249037421495 +448000 ekin = 0.166214016011178 | erot = 0.608752709244163 | epot = -15.3998704673549 | etot = -14.6249037420996 +449000 ekin = 0.168318002547464 | erot = 0.599578546515158 | epot = -15.3928002911194 | etot = -14.6249037420568 +450000 ekin = 0.174030350885997 | erot = 0.590920601689278 | epot = -15.3898546945991 | etot = -14.6249037420239 +451000 ekin = 0.183674309612449 | erot = 0.582976972210044 | epot = -15.3915550238259 | etot = -14.6249037420034 +452000 ekin = 0.197394458885136 | erot = 0.575927582957288 | epot = -15.3982257838406 | etot = -14.6249037419982 +453000 ekin = 0.21512429096355 | erot = 0.569920414706644 | epot = -15.4099484476817 | etot = -14.6249037420115 +454000 ekin = 0.236549344238021 | erot = 0.565056494271684 | epot = -15.4265095805563 | etot = -14.6249037420466 +455000 ekin = 0.26107066649251 | erot = 0.561375729613514 | epot = -15.4473501382118 | etot = -14.6249037421058 +456000 ekin = 0.287780783018564 | erot = 0.558846520705737 | epot = -15.4715310459135 | etot = -14.6249037421892 +457000 ekin = 0.315469350478398 | erot = 0.557362227355198 | epot = -15.4977353201268 | etot = -14.6249037422932 +458000 ekin = 0.342675461160486 | erot = 0.556746783054669 | epot = -15.5243259866254 | etot = -14.6249037424102 +459000 ekin = 0.367796771323547 | erot = 0.556770049266648 | epot = -15.5494705631187 | etot = -14.6249037425286 +460000 ekin = 0.389252836428699 | erot = 0.557171234684316 | epot = -15.5713278137469 | etot = -14.6249037426338 +461000 ekin = 0.405683830371934 | erot = 0.557686417732654 | epot = -15.588273990816 | etot = -14.6249037427114 +462000 ekin = 0.41615050976317 | erot = 0.558074591843087 | epot = -15.5991288443563 | etot = -14.62490374275 +463000 ekin = 0.420292029664587 | erot = 0.558136338549784 | epot = -15.6033321109585 | etot = -14.6249037427441 +464000 ekin = 0.418399545177946 | erot = 0.557720582602229 | epot = -15.6010238704766 | etot = -14.6249037426964 +465000 ekin = 0.411377435968348 | erot = 0.556717766126943 | epot = -15.592998944713 | etot = -14.6249037426177 +466000 ekin = 0.400588481170385 | erot = 0.555041504869352 | epot = -15.5805337285651 | etot = -14.6249037425254 +467000 ekin = 0.387608315925592 | erot = 0.552604267016079 | epot = -15.5651163253806 | etot = -14.6249037424389 +468000 ekin = 0.373939506071155 | erot = 0.549294716065804 | epot = -15.5481379645132 | etot = -14.6249037423763 +469000 ekin = 0.360748545285724 | erot = 0.544964338610985 | epot = -15.5306166262455 | etot = -14.6249037423488 +470000 ekin = 0.348685397522308 | erot = 0.539428754142175 | epot = -15.5130178940236 | etot = -14.6249037423592 +471000 ekin = 0.337825425309533 | erot = 0.532485282885717 | epot = -15.4952144505958 | etot = -14.6249037424005 +472000 ekin = 0.327743216876142 | erot = 0.523944004294882 | epot = -15.4765909636297 | etot = -14.6249037424587 +473000 ekin = 0.317695625905302 | erot = 0.513665869846428 | epot = -15.4562652382673 | etot = -14.6249037425156 +474000 ekin = 0.306866206293077 | erot = 0.501599410558585 | epot = -15.4333693594052 | etot = -14.6249037425536 +475000 ekin = 0.294611572516325 | erot = 0.487807694339578 | epot = -15.4073230094157 | etot = -14.6249037425598 +476000 ekin = 0.280654133646186 | erot = 0.472479343852861 | epot = -15.3780372200275 | etot = -14.6249037425285 +477000 ekin = 0.265182667318923 | erot = 0.45592098927681 | epot = -15.3460073990573 | etot = -14.6249037424616 +478000 ekin = 0.248846579356572 | erot = 0.438532535944384 | epot = -15.3122828576692 | etot = -14.6249037423683 +479000 ekin = 0.232654569021534 | erot = 0.420770062233477 | epot = -15.2783283735172 | etot = -14.6249037422622 +480000 ekin = 0.217807844647013 | erot = 0.403103245642619 | epot = -15.2458148324477 | etot = -14.6249037421581 +481000 ekin = 0.205508255202962 | erot = 0.385974572359883 | epot = -15.2163865696323 | etot = -14.6249037420695 +482000 ekin = 0.19678156694235 | erot = 0.369766310247464 | epot = -15.1914516191956 | etot = -14.6249037420058 +483000 ekin = 0.192346943568308 | erot = 0.354778814406232 | epot = -15.1720294999467 | etot = -14.6249037419722 +484000 ekin = 0.192548846646656 | erot = 0.341220938396417 | epot = -15.1586735270114 | etot = -14.6249037419683 +485000 ekin = 0.197351634264863 | erot = 0.329210924265139 | epot = -15.1514663005208 | etot = -14.6249037419908 +486000 ekin = 0.20638457111255 | erot = 0.318784712513067 | epot = -15.1500730256597 | etot = -14.6249037420341 +487000 ekin = 0.219018661980825 | erot = 0.30990833731601 | epot = -15.1538307413881 | etot = -14.6249037420913 +488000 ekin = 0.234457053485159 | erot = 0.302491737711703 | epot = -15.1618525333529 | etot = -14.624903742156 +489000 ekin = 0.251825722281652 | erot = 0.296402451840958 | epot = -15.1731319163445 | etot = -14.6249037422219 +490000 ekin = 0.270257579251709 | erot = 0.291478772534598 | epot = -15.1866400940702 | etot = -14.6249037422839 +491000 ekin = 0.288968023939754 | erot = 0.287542686829926 | epot = -15.2014144531061 | etot = -14.6249037423365 +492000 ekin = 0.307321746939228 | erot = 0.284413165332613 | epot = -15.2166386546469 | etot = -14.6249037423751 +493000 ekin = 0.324889192266724 | erot = 0.281920128741297 | epot = -15.2317130634048 | etot = -14.6249037423968 +494000 ekin = 0.34148788338571 | erot = 0.279918789014045 | epot = -15.2463104147988 | etot = -14.6249037423991 +495000 ekin = 0.357200801059907 | erot = 0.27830316795437 | epot = -15.2604077113965 | etot = -14.6249037423822 +496000 ekin = 0.372363075865331 | erot = 0.277016625443997 | epot = -15.2742834436586 | etot = -14.6249037423492 +497000 ekin = 0.387510424728836 | erot = 0.276056483801624 | epot = -15.2884706508366 | etot = -14.6249037423061 +498000 ekin = 0.40328774473455 | erot = 0.275469725413449 | epot = -15.3036612124099 | etot = -14.6249037422619 +499000 ekin = 0.420322923931638 | erot = 0.275337682298311 | epot = -15.3205643484574 | etot = -14.6249037422275 +500000 ekin = 0.439078206868906 | erot = 0.275749832423424 | epot = -15.3397317815068 | etot = -14.6249037422144 +501000 ekin = 0.459699055392479 | erot = 0.27677002458918 | epot = -15.3613728222145 | etot = -14.6249037422328 +502000 ekin = 0.481887975237045 | erot = 0.278401857022953 | epot = -15.3851935745487 | etot = -14.6249037422887 +503000 ekin = 0.504836001699661 | erot = 0.280562273427077 | epot = -15.4103020175081 | etot = -14.6249037423814 +504000 ekin = 0.527242963720809 | erot = 0.283072520273854 | epot = -15.4352192264968 | etot = -14.6249037425021 +505000 ekin = 0.547444055754969 | erot = 0.285672032586941 | epot = -15.4580198309761 | etot = -14.6249037426342 +506000 ekin = 0.563636138783675 | erot = 0.288055811210013 | epot = -15.4765956927492 | etot = -14.6249037427555 +507000 ekin = 0.574166796919079 | erot = 0.289928574131231 | epot = -15.488999113894 | etot = -14.6249037428437 +508000 ekin = 0.57782515130048 | erot = 0.291063326861402 | epot = -15.4937922210432 | etot = -14.6249037428813 +509000 ekin = 0.574066827021413 | erot = 0.291350176078827 | epot = -15.4903207459603 | etot = -14.6249037428601 +510000 ekin = 0.563118031117931 | erot = 0.290823209378486 | epot = -15.4788449832791 | etot = -14.6249037427827 +511000 ekin = 0.545937816053972 | erot = 0.289659846600232 | epot = -15.4605014053163 | etot = -14.6249037426621 +512000 ekin = 0.52405192466186 | erot = 0.2881539193295 | epot = -15.4371095865088 | etot = -14.6249037425175 +513000 ekin = 0.499300074198536 | erot = 0.28667044386956 | epot = -15.4108742604381 | etot = -14.62490374237 +514000 ekin = 0.473556830411034 | erot = 0.285593013544196 | epot = -15.3840535861943 | etot = -14.6249037422391 +515000 ekin = 0.448481344235602 | erot = 0.285274677057636 | epot = -15.3586597634315 | etot = -14.6249037421383 +516000 ekin = 0.425336124988924 | erot = 0.286000471485298 | epot = -15.3362403385491 | etot = -14.6249037420749 +517000 ekin = 0.404895133581714 | erot = 0.287965811661741 | epot = -15.3177646872924 | etot = -14.624903742049 +518000 ekin = 0.387441371960463 | erot = 0.29127124708814 | epot = -15.3036163611039 | etot = -14.6249037420553 +519000 ekin = 0.372839035853544 | erot = 0.295931281214217 | epot = -15.2936740591526 | etot = -14.6249037420848 +520000 ekin = 0.360656186943702 | erot = 0.301893194868378 | epot = -15.2874531239385 | etot = -14.6249037421264 +521000 ekin = 0.350310207444023 | erot = 0.30906098360492 | epot = -15.2842749332187 | etot = -14.6249037421697 +522000 ekin = 0.341208800540165 | erot = 0.317319408449295 | epot = -15.2834319511959 | etot = -14.6249037422064 +523000 ekin = 0.332862997937259 | erot = 0.326553653087547 | epot = -15.2843203932564 | etot = -14.6249037422316 +524000 ekin = 0.324955020060425 | erot = 0.336661144000779 | epot = -15.2865199063054 | etot = -14.6249037422442 +525000 ekin = 0.317352570821777 | erot = 0.347553686772866 | epot = -15.2898099998417 | etot = -14.6249037422471 +526000 ekin = 0.310071537936686 | erot = 0.359150063852697 | epot = -15.2941253440357 | etot = -14.6249037422464 +527000 ekin = 0.30319969763028 | erot = 0.371361343284829 | epot = -15.2994647831646 | etot = -14.6249037422495 +528000 ekin = 0.296802852838071 | erot = 0.384072970478812 | epot = -15.3057795655796 | etot = -14.6249037422627 +529000 ekin = 0.290839689447108 | erot = 0.397128838352017 | epot = -15.3128722700896 | etot = -14.6249037422905 +530000 ekin = 0.285110822260319 | erot = 0.410322608856454 | epot = -15.320337173449 | etot = -14.6249037423323 +531000 ekin = 0.279260366287054 | erot = 0.423400398731268 | epot = -15.3275645074017 | etot = -14.6249037423834 +532000 ekin = 0.272835705905111 | erot = 0.4360765883685 | epot = -15.3338160367088 | etot = -14.6249037424352 +533000 ekin = 0.265395406955148 | erot = 0.448061330488109 | epot = -15.3383604799197 | etot = -14.6249037424764 +534000 ekin = 0.256640351799918 | erot = 0.459095045026538 | epot = -15.3406391393234 | etot = -14.6249037424969 +535000 ekin = 0.246533633694114 | erot = 0.46898274217995 | epot = -15.3404201183641 | etot = -14.62490374249 +536000 ekin = 0.235373881374739 | erot = 0.477620282695672 | epot = -15.3378979065248 | etot = -14.6249037424544 +537000 ekin = 0.223795203401919 | erot = 0.485006039595133 | epot = -15.3337049853922 | etot = -14.6249037423951 +538000 ekin = 0.212682661997928 | erot = 0.491234540507361 | epot = -15.3288209448297 | etot = -14.6249037423244 +539000 ekin = 0.203011536568405 | erot = 0.496472671627705 | epot = -15.3243879504539 | etot = -14.6249037422578 +540000 ekin = 0.195638496926135 | erot = 0.50092291227584 | epot = -15.3214651514142 | etot = -14.6249037422123 +541000 ekin = 0.191090437374276 | erot = 0.504781043299091 | epot = -15.3207752228744 | etot = -14.624903742201 +542000 ekin = 0.189407567632742 | erot = 0.508197267609352 | epot = -15.3225085774713 | etot = -14.6249037422292 +543000 ekin = 0.190094034781292 | erot = 0.511249275630852 | epot = -15.326247052704 | etot = -14.6249037422918 +544000 ekin = 0.192205662500225 | erot = 0.513933300995961 | epot = -15.3310427058708 | etot = -14.6249037423746 +545000 ekin = 0.194562943958487 | erot = 0.516174993404676 | epot = -15.3356416798199 | etot = -14.6249037424567 +546000 ekin = 0.196033343259802 | erot = 0.517857026727554 | epot = -15.3387941125054 | etot = -14.624903742518 +547000 ekin = 0.19580143908636 | erot = 0.518856237019682 | epot = -15.3395614186506 | etot = -14.6249037425445 +548000 ekin = 0.193552178457268 | erot = 0.519081068513129 | epot = -15.3375369895014 | etot = -14.624903742531 +549000 ekin = 0.189527872077315 | erot = 0.518500763845738 | epot = -15.332932378404 | etot = -14.6249037424809 +550000 ekin = 0.184464697192282 | erot = 0.517160608017039 | epot = -15.3265290476137 | etot = -14.6249037424044 +551000 ekin = 0.179447519613205 | erot = 0.515181377054168 | epot = -15.3195326389812 | etot = -14.6249037423139 +552000 ekin = 0.175731062294521 | erot = 0.512744588095886 | epot = -15.3133793926124 | etot = -14.624903742222 +553000 ekin = 0.174564310045835 | erot = 0.510067400325703 | epot = -15.3095354525117 | etot = -14.6249037421402 +554000 ekin = 0.177036897100683 | erot = 0.507372062614515 | epot = -15.309312701793 | etot = -14.6249037420778 +555000 ekin = 0.183953653121175 | erot = 0.504855061241007 | epot = -15.3137124564046 | etot = -14.6249037420424 +556000 ekin = 0.195740677803854 | erot = 0.502660902829331 | epot = -15.3233053226717 | etot = -14.6249037420385 +557000 ekin = 0.212389174813147 | erot = 0.500864749566708 | epot = -15.338157666447 | etot = -14.6249037420672 +558000 ekin = 0.23344502097276 | erot = 0.499466731744655 | epot = -15.357815494843 | etot = -14.6249037421256 +559000 ekin = 0.258048678277938 | erot = 0.498398734230019 | epot = -15.3813511547153 | etot = -14.6249037422074 +560000 ekin = 0.285022157939512 | erot = 0.49754195086514 | epot = -15.4074678511078 | etot = -14.6249037423032 +561000 ekin = 0.312990622171654 | erot = 0.496751658909336 | epot = -15.4346460234837 | etot = -14.6249037424027 +562000 ekin = 0.340519848729776 | erot = 0.495884310853372 | epot = -15.4613079020793 | etot = -14.6249037424961 +563000 ekin = 0.366249237356 | erot = 0.494821962716246 | epot = -15.4859749426474 | etot = -14.6249037425751 +564000 ekin = 0.389003340228442 | erot = 0.493490109026911 | epot = -15.5073971918898 | etot = -14.6249037426344 +565000 ekin = 0.407871381975258 | erot = 0.491866632343677 | epot = -15.5246417569902 | etot = -14.6249037426713 +566000 ekin = 0.422251605412405 | erot = 0.489981232304148 | epot = -15.537136580402 | etot = -14.6249037426854 +567000 ekin = 0.431863045464181 | erot = 0.48790647095657 | epot = -15.5446732590993 | etot = -14.6249037426785 +568000 ekin = 0.436733840917554 | erot = 0.485743252286935 | epot = -15.5473808358579 | etot = -14.6249037426534 +569000 ekin = 0.437172173178126 | erot = 0.483603786385869 | epot = -15.5456797021773 | etot = -14.6249037426133 +570000 ekin = 0.433727138645419 | erot = 0.481595978794116 | epot = -15.5402268600013 | etot = -14.6249037425617 +571000 ekin = 0.427141808143026 | erot = 0.479812578148763 | epot = -15.5318581287941 | etot = -14.6249037425023 +572000 ekin = 0.418294466660563 | erot = 0.478326721684033 | epot = -15.5215249307844 | etot = -14.6249037424398 +573000 ekin = 0.408121101334992 | erot = 0.477193277920611 | epot = -15.5102181216358 | etot = -14.6249037423802 +574000 ekin = 0.397514818217457 | erot = 0.476453234967311 | epot = -15.4988717955158 | etot = -14.6249037423311 +575000 ekin = 0.387207144489171 | erot = 0.476137354470425 | epot = -15.4882482412599 | etot = -14.6249037423003 +576000 ekin = 0.377649119217314 | erot = 0.476266044933562 | epot = -15.4788189064453 | etot = -14.6249037422944 +577000 ekin = 0.368920817132226 | erot = 0.476844730976786 | epot = -15.4706692904254 | etot = -14.6249037423164 +578000 ekin = 0.360700785230741 | erot = 0.477856883134822 | epot = -15.4634614107288 | etot = -14.6249037423632 +579000 ekin = 0.352319179858308 | erot = 0.479258927577157 | epot = -15.4564818498611 | etot = -14.6249037424256 +580000 ekin = 0.342901425190187 | erot = 0.480981430412776 | epot = -15.4487865980922 | etot = -14.6249037424893 +581000 ekin = 0.331586894252575 | erot = 0.482939076923953 | epot = -15.4394297137127 | etot = -14.6249037425362 +582000 ekin = 0.317784488003998 | erot = 0.485048781539638 | epot = -15.4277370120932 | etot = -14.6249037425495 +583000 ekin = 0.301409490236239 | erot = 0.487252029394849 | epot = -15.4135652621486 | etot = -14.6249037425175 +584000 ekin = 0.283039202393957 | erot = 0.489535511256142 | epot = -15.3974784560878 | etot = -14.6249037424377 +585000 ekin = 0.263933313487419 | erot = 0.491944128120081 | epot = -15.380781183926 | etot = -14.6249037423185 +586000 ekin = 0.245890887800433 | erot = 0.494582820571413 | epot = -15.3653774505512 | etot = -14.6249037421793 +587000 ekin = 0.230956405620081 | erot = 0.497607010278675 | epot = -15.3534671579451 | etot = -14.6249037420464 +588000 ekin = 0.221033841917523 | erot = 0.501205839010948 | epot = -15.3471434228734 | etot = -14.624903741945 +589000 ekin = 0.21750442850326 | erot = 0.505584588308524 | epot = -15.3479927587061 | etot = -14.6249037418943 +590000 ekin = 0.220953423088753 | erot = 0.510952138426249 | epot = -15.3568093034155 | etot = -14.6249037419005 +591000 ekin = 0.231083134064746 | erot = 0.517515644130575 | epot = -15.3735025201508 | etot = -14.6249037419554 +592000 ekin = 0.246829245753635 | erot = 0.525479282587494 | epot = -15.3972122703833 | etot = -14.6249037420422 +593000 ekin = 0.26662894973047 | erot = 0.535039778666637 | epot = -15.4265724705377 | etot = -14.6249037421406 +594000 ekin = 0.288743434935807 | erot = 0.546371032865614 | epot = -15.4600182100362 | etot = -14.6249037422348 +595000 ekin = 0.311533695301779 | erot = 0.559594229359546 | epot = -15.4960316669788 | etot = -14.6249037423175 +596000 ekin = 0.3336243482615 | erot = 0.574736425374656 | epot = -15.5332645160253 | etot = -14.6249037423892 +597000 ekin = 0.353943370598348 | erot = 0.591686591895555 | epot = -15.57053370495 | etot = -14.6249037424561 +598000 ekin = 0.371670846224556 | erot = 0.610160828224063 | epot = -15.6067354169738 | etot = -14.6249037425252 +599000 ekin = 0.386151688530433 | erot = 0.629687420924883 | epot = -15.6407428520557 | etot = -14.6249037426004 +600000 ekin = 0.396824670884606 | erot = 0.649618644309941 | epot = -15.6713470578748 | etot = -14.6249037426803 +601000 ekin = 0.403202067553919 | erot = 0.669171693345246 | epot = -15.6972775036573 | etot = -14.6249037427582 +602000 ekin = 0.40490852829975 | erot = 0.687495721385519 | epot = -15.7173079925082 | etot = -14.6249037428229 +603000 ekin = 0.401765041348506 | erot = 0.703757265562631 | epot = -15.7304260497733 | etot = -14.6249037428622 +604000 ekin = 0.393886240081525 | erot = 0.717231476889702 | epot = -15.7360214598372 | etot = -14.624903742866 +605000 ekin = 0.38175038495462 | erot = 0.727382711583425 | epot = -15.7340368393683 | etot = -14.6249037428302 +606000 ekin = 0.366205114566941 | erot = 0.733917584160155 | epot = -15.725026441486 | etot = -14.6249037427589 +607000 ekin = 0.348389460814908 | erot = 0.736798185090599 | epot = -15.7100913885695 | etot = -14.624903742664 +608000 ekin = 0.329579787369096 | erot = 0.736212623478789 | epot = -15.6906961534101 | etot = -14.6249037425622 +609000 ekin = 0.310994196071395 | erot = 0.73251127479451 | epot = -15.6684092133368 | etot = -14.6249037424709 +610000 ekin = 0.293604835884145 | erot = 0.726125549058765 | epot = -15.6446341273466 | etot = -14.6249037424037 +611000 ekin = 0.278004208601941 | erot = 0.717488389875027 | epot = -15.620396340845 | etot = -14.624903742368 +612000 ekin = 0.264353214552908 | erot = 0.706972008379807 | epot = -15.5962289652964 | etot = -14.6249037423637 +613000 ekin = 0.252415280668165 | erot = 0.694851301360494 | epot = -15.5721703244133 | etot = -14.6249037423847 +614000 ekin = 0.241662201716805 | erot = 0.681294462599433 | epot = -15.5478604067365 | etot = -14.6249037424203 +615000 ekin = 0.231427318529322 | erot = 0.666377599992121 | epot = -15.5227086609789 | etot = -14.6249037424574 +616000 ekin = 0.221078258759027 | erot = 0.650117838829056 | epot = -15.4960998400712 | etot = -14.6249037424831 +617000 ekin = 0.210180390467373 | erot = 0.632518274251274 | epot = -15.4676024072048 | etot = -14.6249037424862 +618000 ekin = 0.19862150965634 | erot = 0.61361713210071 | epot = -15.437142384217 | etot = -14.6249037424599 +619000 ekin = 0.186670442213662 | erot = 0.593532504056955 | epot = -15.4051066886746 | etot = -14.6249037424039 +620000 ekin = 0.174951539061879 | erot = 0.572493952083693 | epot = -15.3723492334697 | etot = -14.6249037423241 +621000 ekin = 0.164335257152339 | erot = 0.550854196820419 | epot = -15.3400931962051 | etot = -14.6249037422323 +622000 ekin = 0.15576803968181 | erot = 0.529078173717942 | epot = -15.3097499555427 | etot = -14.6249037421429 +623000 ekin = 0.150083571178598 | erot = 0.507711807337566 | epot = -15.2826991205848 | etot = -14.6249037420687 +624000 ekin = 0.147843467415458 | erot = 0.487337070698791 | epot = -15.2600842801331 | etot = -14.6249037420188 +625000 ekin = 0.149245521580975 | erot = 0.468521842126362 | epot = -15.242671105704 | etot = -14.6249037419967 +626000 ekin = 0.154116108891131 | erot = 0.451772481731462 | epot = -15.2307923326229 | etot = -14.6249037420003 +627000 ekin = 0.161979086426179 | erot = 0.437494698740194 | epot = -15.2243775271902 | etot = -14.6249037420239 +628000 ekin = 0.172174902879175 | erot = 0.425965324893585 | epot = -15.2230439698325 | etot = -14.6249037420598 +629000 ekin = 0.183995029152314 | erot = 0.417314987668265 | epot = -15.2262137589216 | etot = -14.624903742101 +630000 ekin = 0.196798066694665 | erot = 0.411519917956496 | epot = -15.2332217267944 | etot = -14.6249037421432 +631000 ekin = 0.210082131921541 | erot = 0.408400457423892 | epot = -15.2433863315305 | etot = -14.6249037421851 +632000 ekin = 0.223500184825895 | erot = 0.407624312389087 | epot = -15.2560282394437 | etot = -14.6249037422287 +633000 ekin = 0.236818662196578 | erot = 0.408714108140466 | epot = -15.2704365126158 | etot = -14.6249037422787 +634000 ekin = 0.249833574952738 | erot = 0.411060882466515 | epot = -15.2857981997594 | etot = -14.6249037423402 +635000 ekin = 0.262270239999152 | erot = 0.413946987959646 | epot = -15.3011209703752 | etot = -14.6249037424164 +636000 ekin = 0.273700147361468 | erot = 0.416582412016232 | epot = -15.315186301884 | etot = -14.6249037425063 +637000 ekin = 0.283507856899438 | erot = 0.418156955201586 | epot = -15.3265685547044 | etot = -14.6249037426034 +638000 ekin = 0.290930324554196 | erot = 0.417906927432445 | epot = -15.3337409946819 | etot = -14.6249037426952 +639000 ekin = 0.295171730169193 | erot = 0.415189912094696 | epot = -15.3352653850304 | etot = -14.6249037427665 +640000 ekin = 0.29557345321463 | erot = 0.409556450349033 | epot = -15.3300336463655 | etot = -14.6249037428018 +641000 ekin = 0.291798784614145 | erot = 0.400805216305268 | epot = -15.3175077437091 | etot = -14.6249037427896 +642000 ekin = 0.283982821763269 | erot = 0.389009767281603 | epot = -15.2978963317707 | etot = -14.6249037427259 +643000 ekin = 0.272803834295158 | erot = 0.374510198234827 | epot = -15.2722177751453 | etot = -14.6249037426153 +644000 ekin = 0.259451287281963 | erot = 0.35787030323495 | epot = -15.242225332988 | etot = -14.6249037424711 +645000 ekin = 0.24549053850944 | erot = 0.339807577757951 | epot = -15.2102018585798 | etot = -14.6249037423124 +646000 ekin = 0.232646751227162 | erot = 0.321107525182429 | epot = -15.1786580185707 | etot = -14.6249037421611 +647000 ekin = 0.222545810224123 | erot = 0.302534738054695 | epot = -15.1499842903174 | etot = -14.6249037420386 +648000 ekin = 0.216457466201495 | erot = 0.28475201940792 | epot = -15.1261132275715 | etot = -14.624903741962 +649000 ekin = 0.215087078764636 | erot = 0.268256849270223 | epot = -15.1082476699766 | etot = -14.6249037419418 +650000 ekin = 0.218457489209105 | erot = 0.253342374384717 | epot = -15.0967036055721 | etot = -14.6249037419783 +651000 ekin = 0.225910420497396 | erot = 0.240087663214758 | epot = -15.0909018257745 | etot = -14.6249037420624 +652000 ekin = 0.236236377394498 | erot = 0.228379019530553 | epot = -15.0895191391008 | etot = -14.6249037421757 +653000 ekin = 0.247915496411967 | erot = 0.217959688821804 | epot = -15.0907789275281 | etot = -14.6249037422943 +654000 ekin = 0.259425494352017 | erot = 0.20850030571605 | epot = -15.0928295424613 | etot = -14.6249037423932 +655000 ekin = 0.269554558208103 | erot = 0.199677958220037 | epot = -15.0941362588799 | etot = -14.6249037424518 +656000 ekin = 0.277652649608963 | erot = 0.191249336850249 | epot = -15.0938057289172 | etot = -14.624903742458 +657000 ekin = 0.283765747905228 | erot = 0.183104207684344 | epot = -15.0917736980005 | etot = -14.6249037424109 +658000 ekin = 0.288620908153343 | erot = 0.175289536735983 | epot = -15.088814187211 | etot = -14.6249037423216 +659000 ekin = 0.293459924910629 | erot = 0.16800102740562 | epot = -15.0863646945268 | etot = -14.6249037422106 +660000 ekin = 0.299750121924184 | erot = 0.161545913295631 | epot = -15.0861997773238 | etot = -14.624903742104 +661000 ekin = 0.30882794580141 | erot = 0.156286808494636 | epot = -15.0900184963241 | etot = -14.624903742028 +662000 ekin = 0.321550844182293 | erot = 0.152579955314811 | epot = -15.0990345415002 | etot = -14.6249037420031 +663000 ekin = 0.338040404323162 | erot = 0.150721656676881 | epot = -15.1136658030376 | etot = -14.6249037420375 +664000 ekin = 0.35758869637966 | erot = 0.150913925254683 | epot = -15.1334063637598 | etot = -14.6249037421255 +665000 ekin = 0.378766116436051 | erot = 0.153254852725981 | epot = -15.1569247114091 | etot = -14.6249037422471 +666000 ekin = 0.399716130930405 | erot = 0.157752003177184 | epot = -15.1823718764818 | etot = -14.6249037423742 +667000 ekin = 0.418564373573293 | erot = 0.16435019288794 | epot = -15.2078183089394 | etot = -14.6249037424782 +668000 ekin = 0.433827740573583 | erot = 0.172960630437096 | epot = -15.2316921135496 | etot = -14.6249037425389 +669000 ekin = 0.444701001629416 | erot = 0.183478145303361 | epot = -15.2530828894841 | etot = -14.6249037425513 +670000 ekin = 0.451136418415458 | erot = 0.195778468142474 | epot = -15.2718186290843 | etot = -14.6249037425264 +671000 ekin = 0.453701004148267 | erot = 0.209695862329476 | epot = -15.2883006089635 | etot = -14.6249037424858 +672000 ekin = 0.453273827000247 | erot = 0.224990306459319 | epot = -15.3031678759134 | etot = -14.6249037424539 +673000 ekin = 0.450699702660583 | erot = 0.241319095059427 | epot = -15.3169225401685 | etot = -14.6249037424485 +674000 ekin = 0.446523488449384 | erot = 0.258227823779524 | epot = -15.3296550547041 | etot = -14.6249037424752 +675000 ekin = 0.440889624591433 | erot = 0.275170305160563 | epot = -15.3409636722771 | etot = -14.6249037425251 +676000 ekin = 0.43362448115233 | erot = 0.29155830650734 | epot = -15.3500865302388 | etot = -14.6249037425792 +677000 ekin = 0.424453634855728 | erot = 0.306833290384575 | epot = -15.356190667856 | etot = -14.6249037426157 +678000 ekin = 0.413265176464919 | erot = 0.320546114280114 | epot = -15.3587150333616 | etot = -14.6249037426165 +679000 ekin = 0.400321537246337 | erot = 0.33242808876456 | epot = -15.3576533685843 | etot = -14.6249037425734 +680000 ekin = 0.386341988792883 | erot = 0.342437977069693 | epot = -15.3536837083532 | etot = -14.6249037424906 +681000 ekin = 0.372417408218802 | erot = 0.350774050475061 | epot = -15.3480952010793 | etot = -14.6249037423855 +682000 ekin = 0.359769645089127 | erot = 0.357847594355724 | epot = -15.3425209817278 | etot = -14.624903742283 +683000 ekin = 0.349419724484513 | erot = 0.364223142874507 | epot = -15.3385466095678 | etot = -14.6249037422088 +684000 ekin = 0.341867426589617 | erot = 0.370539083006542 | epot = -15.3373102517771 | etot = -14.6249037421809 +685000 ekin = 0.336892967753541 | erot = 0.377427285880855 | epot = -15.3392239958376 | etot = -14.6249037422032 +686000 ekin = 0.333560575457532 | erot = 0.385449795149527 | epot = -15.3439141128706 | etot = -14.6249037422635 +687000 ekin = 0.330440845245698 | erot = 0.395064019975185 | epot = -15.3504086075581 | etot = -14.6249037423373 +688000 ekin = 0.325996654363842 | erot = 0.406617593545993 | epot = -15.3575179903049 | etot = -14.6249037423951 +689000 ekin = 0.31902375237829 | erot = 0.420363991129875 | epot = -15.3642914859202 | etot = -14.6249037424121 +690000 ekin = 0.309020969989285 | erot = 0.436483939358184 | epot = -15.3704086517225 | etot = -14.624903742375 +691000 ekin = 0.296388973949697 | erot = 0.455097572739975 | epot = -15.3763902889758 | etot = -14.6249037422861 +692000 ekin = 0.282408410636572 | erot = 0.476257707732277 | epot = -15.383569860531 | etot = -14.6249037421622 +693000 ekin = 0.26900853085206 | erot = 0.499923033173746 | epot = -15.3938353060564 | etot = -14.6249037420305 +694000 ekin = 0.258387685788816 | erot = 0.525918285140374 | epot = -15.4092097128507 | etot = -14.6249037419215 +695000 ekin = 0.252576275208241 | erot = 0.553894058809539 | epot = -15.4313740758797 | etot = -14.624903741862 +696000 ekin = 0.253038186234903 | erot = 0.583300660396082 | epot = -15.4612425885006 | etot = -14.6249037418696 +697000 ekin = 0.260392018277369 | erot = 0.613388418368354 | epot = -15.4986841785946 | etot = -14.6249037419489 +698000 ekin = 0.274304391463235 | erot = 0.643241879182175 | epot = -15.5424500127355 | etot = -14.6249037420901 +699000 ekin = 0.293570250406476 | erot = 0.671848180608583 | epot = -15.5903221732866 | etot = -14.6249037422715 +700000 ekin = 0.316355070233252 | erot = 0.698191700482076 | epot = -15.6394505131798 | etot = -14.6249037424645 +701000 ekin = 0.340538337282147 | erot = 0.721359481465404 | epot = -15.6868015613873 | etot = -14.6249037426397 +702000 ekin = 0.364075443764542 | erot = 0.740637254693957 | epot = -15.7296164412326 | etot = -14.6249037427741 +703000 ekin = 0.385294321874673 | erot = 0.755576369453691 | epot = -15.7657744341838 | etot = -14.6249037428555 +704000 ekin = 0.403066716719495 | erot = 0.766018576886853 | epot = -15.7939890364902 | etot = -14.6249037428839 +705000 ekin = 0.416833588997526 | erot = 0.772075474099313 | epot = -15.8138128059661 | etot = -14.6249037428693 +706000 ekin = 0.426510451502379 | erot = 0.774072055031553 | epot = -15.8254862493606 | etot = -14.6249037428266 +707000 ekin = 0.432328070474044 | erot = 0.772470813769757 | epot = -15.8297026270148 | etot = -14.624903742771 +708000 ekin = 0.434671210546527 | erot = 0.76779427950511 | epot = -15.827369232765 | etot = -14.6249037427133 +709000 ekin = 0.433963855684076 | erot = 0.760560754832016 | epot = -15.8194283531749 | etot = -14.6249037426588 +710000 ekin = 0.430621214402443 | erot = 0.751241421805289 | epot = -15.8067663788153 | etot = -14.6249037426076 +711000 ekin = 0.425061028816158 | erot = 0.740240555545361 | epot = -15.7902053269182 | etot = -14.6249037425567 +712000 ekin = 0.417748693286293 | erot = 0.727895913280463 | epot = -15.7705483490692 | etot = -14.6249037425024 +713000 ekin = 0.409245407745191 | erot = 0.714493617369743 | epot = -15.748642767557 | etot = -14.624903742442 +714000 ekin = 0.400233112896686 | erot = 0.700290376393996 | epot = -15.725427231666 | etot = -14.6249037423753 +715000 ekin = 0.391499218629782 | erot = 0.685535269234813 | epot = -15.7019382301699 | etot = -14.6249037423053 +716000 ekin = 0.38387465328674 | erot = 0.670483824808895 | epot = -15.6792622203343 | etot = -14.6249037422387 +717000 ekin = 0.37812966517224 | erot = 0.655399296057453 | epot = -15.6584327034141 | etot = -14.6249037421844 +718000 ekin = 0.374843116813924 | erot = 0.640539821857324 | epot = -15.6402866808232 | etot = -14.6249037421519 +719000 ekin = 0.374271424141617 | erot = 0.626134666228947 | epot = -15.6253098325198 | etot = -14.6249037421492 +720000 ekin = 0.376249546442333 | erot = 0.612356169201708 | epot = -15.6135094578241 | etot = -14.62490374218 +721000 ekin = 0.38015578315651 | erot = 0.599295758360665 | epot = -15.6043552837594 | etot = -14.6249037422422 +722000 ekin = 0.384962761439327 | erot = 0.586951574250039 | epot = -15.5968180780159 | etot = -14.6249037423266 +723000 ekin = 0.38937982338218 | erot = 0.575232003297926 | epot = -15.5895155690983 | etot = -14.6249037424182 +724000 ekin = 0.392071125784558 | erot = 0.563975606697306 | epot = -15.5809504749809 | etot = -14.6249037424991 +725000 ekin = 0.391913283459399 | erot = 0.552983740178749 | epot = -15.5698007661892 | etot = -14.6249037425511 +726000 ekin = 0.388241956533271 | erot = 0.542058916015903 | epot = -15.5552046151099 | etot = -14.6249037425608 +727000 ekin = 0.381032991792366 | erot = 0.531040454531963 | epot = -15.5369771888461 | etot = -14.6249037425218 +728000 ekin = 0.370971903191828 | erot = 0.519829082375402 | epot = -15.515704728005 | etot = -14.6249037424378 +729000 ekin = 0.359388263612358 | erot = 0.50839572980859 | epot = -15.4926877357432 | etot = -14.6249037423222 +730000 ekin = 0.348057580439132 | erot = 0.496773021024845 | epot = -15.4697343436589 | etot = -14.6249037421949 +731000 ekin = 0.338902689198661 | erot = 0.485032671408036 | epot = -15.4488391026864 | etot = -14.6249037420797 +732000 ekin = 0.333649662944534 | erot = 0.473255762297357 | epot = -15.4318091672407 | etot = -14.6249037419988 +733000 ekin = 0.333505576675517 | erot = 0.461504910073763 | epot = -15.4199142287177 | etot = -14.6249037419685 +734000 ekin = 0.338924758983124 | erot = 0.44980725448349 | epot = -15.4136357554609 | etot = -14.6249037419943 +735000 ekin = 0.34951546857607 | erot = 0.438154711902834 | epot = -15.41257392255 | etot = -14.6249037420711 +736000 ekin = 0.364111355273647 | erot = 0.426523255164468 | epot = -15.4155383526203 | etot = -14.6249037421822 +737000 ekin = 0.38099571977356 | erot = 0.414906900972945 | epot = -15.4208063630506 | etot = -14.6249037423041 +738000 ekin = 0.398229414670415 | erot = 0.403356227833102 | epot = -15.4264893849155 | etot = -14.624903742412 +739000 ekin = 0.414005860072354 | erot = 0.392007798568672 | epot = -15.4309174011272 | etot = -14.6249037424862 +740000 ekin = 0.426948743961824 | erot = 0.381091720704565 | epot = -15.4329442071836 | etot = -14.6249037425172 +741000 ekin = 0.43628364768211 | erot = 0.370910229391996 | epot = -15.4320976195812 | etot = -14.6249037425071 +742000 ekin = 0.44185000182603 | erot = 0.361789064611378 | epot = -15.4285428089066 | etot = -14.6249037424692 +743000 ekin = 0.443963491146499 | erot = 0.354012421291944 | epot = -15.4228796548611 | etot = -14.6249037424227 +744000 ekin = 0.4431781085151 | erot = 0.347758127978473 | epot = -15.4158399788814 | etot = -14.6249037423879 +745000 ekin = 0.440021184884499 | erot = 0.343050543545547 | epot = -15.4079754708096 | etot = -14.6249037423796 +746000 ekin = 0.434779146250304 | erot = 0.339744491074578 | epot = -15.3994273797281 | etot = -14.6249037424032 +747000 ekin = 0.427396883604757 | erot = 0.337545938414333 | epot = -15.3898465644716 | etot = -14.6249037424525 +748000 ekin = 0.417523045840628 | erot = 0.336066252171896 | epot = -15.3784930405232 | etot = -14.6249037425107 +749000 ekin = 0.404692764111473 | erot = 0.334898725161965 | epot = -15.3644952318288 | etot = -14.6249037425554 +750000 ekin = 0.388596287616679 | erot = 0.333700338300972 | epot = -15.3472003684819 | etot = -14.6249037425642 +751000 ekin = 0.369348367994066 | erot = 0.332259621152988 | epot = -15.3265117316703 | etot = -14.6249037425233 +752000 ekin = 0.347662572336739 | erot = 0.330533807750213 | epot = -15.3031001225191 | etot = -14.6249037424322 +753000 ekin = 0.324856373470614 | erot = 0.328645172902147 | epot = -15.2784052886784 | etot = -14.6249037423056 +754000 ekin = 0.302664104351481 | erot = 0.326836116136386 | epot = -15.2544039626582 | etot = -14.6249037421703 +755000 ekin = 0.28289840530598 | erot = 0.325392677389915 | epot = -15.2331948247539 | etot = -14.624903742058 +756000 ekin = 0.267052130149329 | erot = 0.324553861439878 | epot = -15.2165097335856 | etot = -14.6249037419964 +757000 ekin = 0.255952872034472 | erot = 0.324427480977821 | epot = -15.2052840950144 | etot = -14.6249037420021 +758000 ekin = 0.24956686325796 | erot = 0.324931841856735 | epot = -15.1994024471903 | etot = -14.6249037420756 +759000 ekin = 0.247007285742123 | erot = 0.325777353497946 | epot = -15.1976883814417 | etot = -14.6249037422016 +760000 ekin = 0.246749335490671 | erot = 0.326494279609754 | epot = -15.1981473574522 | etot = -14.6249037423518 +761000 ekin = 0.247004464362874 | erot = 0.326503456901681 | epot = -15.1984116637553 | etot = -14.6249037424907 +762000 ekin = 0.246168267683208 | erot = 0.325217160868209 | epot = -15.1962891711361 | etot = -14.6249037425847 +763000 ekin = 0.243236270174742 | erot = 0.322149322885115 | epot = -15.1902893356692 | etot = -14.6249037426093 +764000 ekin = 0.238083572628182 | erot = 0.31701054114686 | epot = -15.1799978563319 | etot = -14.6249037425569 +765000 ekin = 0.231530329806237 | erot = 0.309765883621403 | epot = -15.166199955866 | etot = -14.6249037424384 +766000 ekin = 0.225163449189886 | erot = 0.300642577938324 | epot = -15.1507097694095 | etot = -14.6249037422813 +767000 ekin = 0.220947037641663 | erot = 0.29008793628379 | epot = -15.1359387160491 | etot = -14.6249037421236 +768000 ekin = 0.220714417705789 | erot = 0.278690999515915 | epot = -15.1243091592251 | etot = -14.6249037420034 +769000 ekin = 0.225674230585351 | erot = 0.267090069999984 | epot = -15.1176680425334 | etot = -14.6249037419481 +770000 ekin = 0.23606686040605 | erot = 0.255889903618604 | epot = -15.1168605059919 | etot = -14.6249037419673 +771000 ekin = 0.251070223471186 | erot = 0.245606888556646 | epot = -15.1215808540782 | etot = -14.6249037420504 +772000 ekin = 0.268985032794879 | erot = 0.236650197272996 | epot = -15.1305389722379 | etot = -14.62490374217 +773000 ekin = 0.287649902235825 | erot = 0.229335047808992 | epot = -15.1418886923345 | etot = -14.6249037422897 +774000 ekin = 0.304971347443094 | erot = 0.223914516380436 | epot = -15.1537896061991 | etot = -14.6249037423756 +775000 ekin = 0.319422560280909 | erot = 0.220611402281974 | epot = -15.1649377049681 | etot = -14.6249037424052 +776000 ekin = 0.330375903028573 | erot = 0.21963284072128 | epot = -15.1749124861238 | etot = -14.624903742374 +777000 ekin = 0.338182326480891 | erot = 0.221157252264285 | epot = -15.184243321042 | etot = -14.6249037422968 +778000 ekin = 0.343980993504904 | erot = 0.225293639771365 | epot = -15.1941783754794 | etot = -14.6249037422032 +779000 ekin = 0.349294202147107 | erot = 0.232023926336935 | epot = -15.2062218706133 | etot = -14.6249037421292 +780000 ekin = 0.355517983707508 | erot = 0.241146781674954 | epot = -15.2215685074899 | etot = -14.6249037421074 +781000 ekin = 0.363445847501857 | erot = 0.252244149939742 | epot = -15.2405937395992 | etot = -14.6249037421576 +782000 ekin = 0.372957766808644 | erot = 0.264688770757683 | epot = -15.2625502798455 | etot = -14.6249037422792 +783000 ekin = 0.382969267748679 | erot = 0.277702579811651 | epot = -15.2855755900109 | etot = -14.6249037424505 +784000 ekin = 0.391670514066047 | erot = 0.290462881205936 | epot = -15.3070371379042 | etot = -14.6249037426322 +785000 ekin = 0.397003136152503 | erot = 0.30223788282162 | epot = -15.3241447617521 | etot = -14.624903742778 +786000 ekin = 0.397244540913489 | erot = 0.312520082334536 | epot = -15.3346683660962 | etot = -14.6249037428482 +787000 ekin = 0.391525061079608 | erot = 0.321121025638165 | epot = -15.3375498295401 | etot = -14.6249037428223 +788000 ekin = 0.380116514494719 | erot = 0.328198366843703 | epot = -15.3332186240439 | etot = -14.6249037427055 +789000 ekin = 0.364402868103514 | erot = 0.334204933642789 | epot = -15.3235115442733 | etot = -14.624903742527 +790000 ekin = 0.34654788283668 | erot = 0.339772664563971 | epot = -15.3112242897311 | etot = -14.6249037423304 +791000 ekin = 0.328969533927298 | erot = 0.345562661329334 | epot = -15.2994359374173 | etot = -14.6249037421606 +792000 ekin = 0.313783234687856 | erot = 0.352120250332508 | epot = -15.2908072270725 | etot = -14.6249037420521 +793000 ekin = 0.302371973145943 | erot = 0.359769001652795 | epot = -15.2870447168187 | etot = -14.6249037420199 +794000 ekin = 0.295192752069597 | erot = 0.368565036951676 | epot = -15.288661531079 | etot = -14.6249037420577 +795000 ekin = 0.291854072001344 | erot = 0.378316728406861 | epot = -15.2950745425493 | etot = -14.6249037421411 +796000 ekin = 0.291420477240303 | erot = 0.388659220599258 | epot = -15.3049834400759 | etot = -14.6249037422364 +797000 ekin = 0.292835767593939 | erot = 0.39916067791523 | epot = -15.3169001878199 | etot = -14.6249037423108 +798000 ekin = 0.295321690654866 | erot = 0.409429919731993 | epot = -15.329655352731 | etot = -14.6249037423441 +799000 ekin = 0.298615606685225 | erot = 0.41919526946406 | epot = -15.3427146184839 | etot = -14.6249037423347 +800000 ekin = 0.302963113078809 | erot = 0.428333265393227 | epot = -15.3562001207724 | etot = -14.6249037423004 +801000 ekin = 0.30886980741851 | erot = 0.436842111958024 | epot = -15.3706156616477 | etot = -14.6249037422712 +802000 ekin = 0.316711643345927 | erot = 0.444773620895207 | epot = -15.3863890065174 | etot = -14.6249037422763 +803000 ekin = 0.326365730601817 | erot = 0.452151664704948 | epot = -15.4034211376386 | etot = -14.6249037423318 +804000 ekin = 0.337019280357668 | erot = 0.458909057451191 | epot = -15.4208320802431 | etot = -14.6249037424342 +805000 ekin = 0.347244531512514 | erot = 0.464865921885975 | epot = -15.4370141959586 | etot = -14.6249037425601 +806000 ekin = 0.355321558015248 | erot = 0.469755825323994 | epot = -15.4499811260149 | etot = -14.6249037426756 +807000 ekin = 0.359699244804389 | erot = 0.47328839989947 | epot = -15.4578913874509 | etot = -14.624903742747 +808000 ekin = 0.359442919436746 | erot = 0.475225772200574 | epot = -15.4595724343886 | etot = -14.6249037427513 +809000 ekin = 0.354532149710961 | erot = 0.475448148012512 | epot = -15.454884040406 | etot = -14.6249037426825 +810000 ekin = 0.345927121515436 | erot = 0.473990365430211 | epot = -15.4448212294985 | etot = -14.6249037425528 +811000 ekin = 0.335391497319453 | erot = 0.471042355239708 | epot = -15.4313375949476 | etot = -14.6249037423884 +812000 ekin = 0.325122479809057 | erot = 0.466917662639856 | epot = -15.416943884672 | etot = -14.6249037422231 +813000 ekin = 0.31728183261798 | erot = 0.462001954840949 | epot = -15.4041875295485 | etot = -14.6249037420896 +814000 ekin = 0.313538689250887 | erot = 0.456696276151244 | epot = -15.3951387074148 | etot = -14.6249037420127 +815000 ekin = 0.314725301426621 | erot = 0.451368238943233 | epot = -15.3909972823742 | etot = -14.6249037420043 +816000 ekin = 0.320674745952002 | erot = 0.446320054204494 | epot = -15.3918985422185 | etot = -14.624903742062 +817000 ekin = 0.330264402529528 | erot = 0.441777145069773 | epot = -15.3969452897695 | etot = -14.6249037421702 +818000 ekin = 0.341643112115936 | erot = 0.437896324121525 | epot = -15.404443178542 | etot = -14.6249037423045 +819000 ekin = 0.352584467965967 | erot = 0.43478868897098 | epot = -15.4122768993742 | etot = -14.6249037424372 +820000 ekin = 0.360890006680921 | erot = 0.432549774286878 | epot = -15.4183435235106 | etot = -14.6249037425428 +821000 ekin = 0.364764924967774 | erot = 0.431288293594747 | epot = -15.4209569611646 | etot = -14.624903742602 +822000 ekin = 0.36310132304895 | erot = 0.431144612410167 | epot = -15.419149678065 | etot = -14.6249037426059 +823000 ekin = 0.355627506072524 | erot = 0.432293079211457 | epot = -15.4128243278395 | etot = -14.6249037425555 +824000 ekin = 0.342909508000251 | erot = 0.43492611819946 | epot = -15.4027393686613 | etot = -14.6249037424616 +825000 ekin = 0.326218347991422 | erot = 0.439222871855163 | epot = -15.3903449621884 | etot = -14.6249037423418 +826000 ekin = 0.307298067027383 | erot = 0.445309293137298 | epot = -15.3775111023813 | etot = -14.6249037422166 +827000 ekin = 0.288081469810276 | erot = 0.453218819733682 | epot = -15.3662040316499 | etot = -14.6249037421059 +828000 ekin = 0.270403517644502 | erot = 0.462862712071626 | epot = -15.358169971742 | etot = -14.6249037420259 +829000 ekin = 0.255756724313645 | erot = 0.474017347276416 | epot = -15.354677813577 | etot = -14.624903741987 +830000 ekin = 0.245120383539843 | erot = 0.486332016594477 | epot = -15.3563561421264 | etot = -14.6249037419921 +831000 ekin = 0.238883956789448 | erot = 0.499357971990473 | epot = -15.3631456708169 | etot = -14.624903742037 +832000 ekin = 0.236868645662797 | erot = 0.512595315428093 | epot = -15.3743677032021 | etot = -14.6249037421112 +833000 ekin = 0.238435989568506 | erot = 0.525550909043033 | epot = -15.3888906408115 | etot = -14.6249037421999 +834000 ekin = 0.242658569127625 | erot = 0.537797737790879 | epot = -15.405360049206 | etot = -14.6249037422875 +835000 ekin = 0.248518315375854 | erot = 0.549024910270133 | epot = -15.4224469680061 | etot = -14.6249037423601 +836000 ekin = 0.255095050222772 | erot = 0.559068449138662 | epot = -15.4390672417693 | etot = -14.6249037424078 +837000 ekin = 0.261712817640357 | erot = 0.567916383628495 | epot = -15.4545329436954 | etot = -14.6249037424265 +838000 ekin = 0.268023056778553 | erot = 0.575686784519793 | epot = -15.4686135837165 | etot = -14.6249037424181 +839000 ekin = 0.27401827032314 | erot = 0.582582979367263 | epot = -15.4815049920797 | etot = -14.6249037423893 +840000 ekin = 0.279983100774025 | erot = 0.588834754839967 | epot = -15.4937215979637 | etot = -14.6249037423497 +841000 ekin = 0.286398274628728 | erot = 0.59463702433131 | epot = -15.5059390412703 | etot = -14.6249037423103 +842000 ekin = 0.293816650983536 | erot = 0.600098453281003 | epot = -15.5188188465462 | etot = -14.6249037422817 +843000 ekin = 0.302726774569486 | erot = 0.605208920749049 | epot = -15.5328394375911 | etot = -14.6249037422726 +844000 ekin = 0.313421069061172 | erot = 0.609833296485301 | epot = -15.5481581078353 | etot = -14.6249037422889 +845000 ekin = 0.325887895394733 | erot = 0.613733577818912 | epot = -15.5645252155452 | etot = -14.6249037423315 +846000 ekin = 0.339752400962196 | erot = 0.616615984720894 | epot = -15.5812721280789 | etot = -14.6249037423958 +847000 ekin = 0.354292335348444 | erot = 0.61819407953295 | epot = -15.5973901573525 | etot = -14.6249037424711 +848000 ekin = 0.368542667423182 | erot = 0.618254639142345 | epot = -15.6117010491079 | etot = -14.6249037425423 +849000 ekin = 0.381474241843926 | erot = 0.616711095273524 | epot = -15.6230890797115 | etot = -14.6249037425941 +850000 ekin = 0.392198266661771 | erot = 0.613631554979492 | epot = -15.6307335642567 | etot = -14.6249037426155 +851000 ekin = 0.40012936773711 | erot = 0.609234588535909 | epot = -15.6342676988772 | etot = -14.6249037426042 +852000 ekin = 0.405049998797733 | erot = 0.603854451146916 | epot = -15.633808192512 | etot = -14.6249037425674 +853000 ekin = 0.407056563941561 | erot = 0.597885334648249 | epot = -15.6298456411086 | etot = -14.6249037425187 +854000 ekin = 0.406415158938748 | erot = 0.591718979210661 | epot = -15.6230378806227 | etot = -14.6249037424733 +855000 ekin = 0.403390043512858 | erot = 0.585690332509252 | epot = -15.6139841184645 | etot = -14.6249037424423 +856000 ekin = 0.398116166002726 | erot = 0.580042463525136 | epot = -15.6030623719571 | etot = -14.6249037424293 +857000 ekin = 0.390568016159967 | erot = 0.574915889724967 | epot = -15.5903876483136 | etot = -14.6249037424286 +858000 ekin = 0.380638245096081 | erot = 0.570361176880736 | epot = -15.5759031644054 | etot = -14.6249037424286 +859000 ekin = 0.368297168914653 | erot = 0.566367903415377 | epot = -15.5595688147452 | etot = -14.6249037424151 +860000 ekin = 0.353771484486348 | erot = 0.56289933566704 | epot = -15.5415745625316 | etot = -14.6249037423782 +861000 ekin = 0.337668189076058 | erot = 0.55992119051608 | epot = -15.522493121908 | etot = -14.6249037423159 +862000 ekin = 0.320982687534733 | erot = 0.55741511441171 | epot = -15.5033015441828 | etot = -14.6249037422364 +863000 ekin = 0.304965814691443 | erot = 0.555372641472256 | epot = -15.4852421983211 | etot = -14.6249037421574 +864000 ekin = 0.290872653003623 | erot = 0.553772082573975 | epot = -15.4695484776774 | etot = -14.6249037420998 +865000 ekin = 0.279660774249956 | erot = 0.552546988655193 | epot = -15.4571115049878 | etot = -14.6249037420826 +866000 ekin = 0.271730646599716 | erot = 0.551558423386406 | epot = -15.448192812101 | etot = -14.6249037421149 +867000 ekin = 0.266795961580917 | erot = 0.550582916186157 | epot = -15.44228261996 | etot = -14.624903742193 +868000 ekin = 0.263936467175858 | erot = 0.549323573880104 | epot = -15.4381637833559 | etot = -14.6249037422999 +869000 ekin = 0.261831470221839 | erot = 0.547444696243376 | epot = -15.4341799088748 | etot = -14.6249037424095 +870000 ekin = 0.259116433169107 | erot = 0.544622620095519 | epot = -15.4286427957584 | etot = -14.6249037424938 +871000 ekin = 0.25476611341807 | erot = 0.540599894777859 | epot = -15.4202697507262 | etot = -14.6249037425303 +872000 ekin = 0.248397230690975 | erot = 0.535228153627688 | epot = -15.4085291268279 | etot = -14.6249037425092 +873000 ekin = 0.240403953825284 | erot = 0.528487826572668 | epot = -15.3937955228335 | etot = -14.6249037424356 +874000 ekin = 0.23188412578265 | erot = 0.52047931782111 | epot = -15.3772671859324 | etot = -14.6249037423286 +875000 ekin = 0.224371090312889 | erot = 0.51138848970078 | epot = -15.3606633222303 | etot = -14.6249037422166 +876000 ekin = 0.219440883379249 | erot = 0.501436812694071 | epot = -15.3457814382023 | etot = -14.624903742129 +877000 ekin = 0.218302972735591 | erot = 0.490831150818216 | epot = -15.3340378656416 | etot = -14.6249037420878 +878000 ekin = 0.221492456262699 | erot = 0.479728387736622 | epot = -15.3261245861005 | etot = -14.6249037421012 +879000 ekin = 0.228756262274367 | erot = 0.468225594693664 | epot = -15.3218855991281 | etot = -14.6249037421601 +880000 ekin = 0.239169160088235 | erot = 0.456378166082075 | epot = -15.3204510684122 | etot = -14.6249037422419 +881000 ekin = 0.251443176614178 | erot = 0.444238659512956 | epot = -15.3205855784449 | etot = -14.6249037423178 +882000 ekin = 0.264330844663498 | erot = 0.431901289695958 | epot = -15.3211358767212 | etot = -14.6249037423617 +883000 ekin = 0.276992343361542 | erot = 0.419534292632451 | epot = -15.3214303783535 | etot = -14.6249037423595 +884000 ekin = 0.289210952362652 | erot = 0.407386172192625 | epot = -15.321500866868 | etot = -14.6249037423127 +885000 ekin = 0.301394205510712 | erot = 0.395760928443729 | epot = -15.3220588761924 | etot = -14.6249037422379 +886000 ekin = 0.314368599205627 | erot = 0.384968165379708 | epot = -15.3242405067466 | etot = -14.6249037421612 +887000 ekin = 0.329038341775269 | erot = 0.375262338090432 | epot = -15.3292044219761 | etot = -14.6249037421104 +888000 ekin = 0.3460151111552 | erot = 0.366788650327974 | epot = -15.337707503589 | etot = -14.6249037421058 +889000 ekin = 0.365329693883301 | erot = 0.359550947377142 | epot = -15.3497843834163 | etot = -14.6249037421559 +890000 ekin = 0.386310696217007 | erot = 0.353410826837943 | epot = -15.364625265308 | etot = -14.6249037422531 +891000 ekin = 0.40766808705505 | erot = 0.348119126036606 | epot = -15.3806909554677 | etot = -14.624903742376 +892000 ekin = 0.427761236103282 | erot = 0.343372786941987 | epot = -15.3960377655415 | etot = -14.6249037424963 +893000 ekin = 0.444977236019449 | erot = 0.33888352569265 | epot = -15.4087645042971 | etot = -14.624903742585 +894000 ekin = 0.458112158680458 | erot = 0.334441343917185 | epot = -15.4174572452192 | etot = -14.6249037426215 +895000 ekin = 0.466648008331883 | erot = 0.329956933565113 | epot = -15.4215086844963 | etot = -14.6249037425993 +896000 ekin = 0.470850232519732 | erot = 0.325472374552551 | epot = -15.4212263495988 | etot = -14.6249037425265 +897000 ekin = 0.471664510488006 | erot = 0.321137893833118 | epot = -15.4177061467451 | etot = -14.624903742424 +898000 ekin = 0.470447771985807 | erot = 0.317161282107798 | epot = -15.4125127964124 | etot = -14.6249037423188 +899000 ekin = 0.468609320535655 | erot = 0.313743247831532 | epot = -15.407256310605 | etot = -14.6249037422378 +900000 ekin = 0.467255363896805 | erot = 0.311015004595507 | epot = -15.403174110693 | etot = -14.6249037422007 +901000 ekin = 0.466923299456955 | erot = 0.308993431077898 | epot = -15.4008204727509 | etot = -14.624903742216 +902000 ekin = 0.467466399705958 | erot = 0.307564919774008 | epot = -15.3999350617591 | etot = -14.6249037422791 +903000 ekin = 0.468112799245358 | erot = 0.306502589385531 | epot = -15.3995191310034 | etot = -14.6249037423725 +904000 ekin = 0.467682260080958 | erot = 0.305513914729679 | epot = -15.398099917282 | etot = -14.6249037424714 +905000 ekin = 0.464906903208091 | erot = 0.304308207539486 | epot = -15.3941188532968 | etot = -14.6249037425492 +906000 ekin = 0.458775313350218 | erot = 0.302667437698602 | epot = -15.386346493633 | etot = -14.6249037425842 +907000 ekin = 0.448811106797068 | erot = 0.300501710925682 | epot = -15.3742165602888 | etot = -14.624903742566 +908000 ekin = 0.435212888278286 | erot = 0.297873922704326 | epot = -15.3579905534802 | etot = -14.6249037424976 +909000 ekin = 0.418821166578994 | erot = 0.294986492955548 | epot = -15.338711401929 | etot = -14.6249037423944 +910000 ekin = 0.400928155652122 | erot = 0.292134043124749 | epot = -15.3179659410565 | etot = -14.6249037422796 +911000 ekin = 0.382990731318649 | erot = 0.289635345607696 | epot = -15.2975298191034 | etot = -14.6249037421771 +912000 ekin = 0.366329155569864 | erot = 0.28776245704618 | epot = -15.2789953547216 | etot = -14.6249037421055 +913000 ekin = 0.351888443631227 | erot = 0.286683662572629 | epot = -15.2634758482788 | etot = -14.624903742075 +914000 ekin = 0.340111462795541 | erot = 0.286431278414487 | epot = -15.2514464832954 | etot = -14.6249037420854 +915000 ekin = 0.330936398540049 | erot = 0.286898247267082 | epot = -15.2427383879356 | etot = -14.6249037421284 +916000 ekin = 0.323899271601486 | erot = 0.287861143478391 | epot = -15.2366641572706 | etot = -14.6249037421907 +917000 ekin = 0.318302399047232 | erot = 0.289022784865087 | epot = -15.2322289261691 | etot = -14.6249037422568 +918000 ekin = 0.313403328231463 | erot = 0.290065205370856 | epot = -15.2283722759152 | etot = -14.6249037423129 +919000 ekin = 0.308582994046901 | erot = 0.290702987753991 | epot = -15.2241897241499 | etot = -14.624903742349 +920000 ekin = 0.303462620954368 | erot = 0.290727692025052 | epot = -15.2190940553399 | etot = -14.6249037423605 +921000 ekin = 0.297952758522196 | erot = 0.290036267627498 | epot = -15.2128927684978 | etot = -14.6249037423481 +922000 ekin = 0.29223232916649 | erot = 0.28863969692327 | epot = -15.2057757684075 | etot = -14.6249037423178 +923000 ekin = 0.286668877937277 | erot = 0.286652137103424 | epot = -15.1982247573193 | etot = -14.6249037422786 +924000 ekin = 0.28170186865761 | erot = 0.28426466875578 | epot = -15.1908702796539 | etot = -14.6249037422405 +925000 ekin = 0.277717553237222 | erot = 0.281710557645316 | epot = -15.1843318530947 | etot = -14.6249037422121 +926000 ekin = 0.274945509178671 | erot = 0.279230091666927 | epot = -15.1790793430443 | etot = -14.6249037421988 +927000 ekin = 0.273402631519431 | erot = 0.277042382113437 | epot = -15.1753487558338 | etot = -14.624903742201 +928000 ekin = 0.272900230271358 | erot = 0.275329232545622 | epot = -15.1731332050314 | etot = -14.6249037422144 +929000 ekin = 0.273115271901108 | erot = 0.274232799537457 | epot = -15.1722518136694 | etot = -14.6249037422308 +930000 ekin = 0.273710515356084 | erot = 0.273865029644295 | epot = -15.1724792872405 | etot = -14.6249037422402 +931000 ekin = 0.274474107140427 | erot = 0.274323617229163 | epot = -15.1737014666035 | etot = -14.6249037422339 +932000 ekin = 0.275440857683932 | erot = 0.275707340217243 | epot = -15.1760519401082 | etot = -14.624903742207 +933000 ekin = 0.276957575782685 | erot = 0.278123705988738 | epot = -15.1799850239326 | etot = -14.6249037421612 +934000 ekin = 0.279664435384645 | erot = 0.281683992543778 | epot = -15.186252170033 | etot = -14.6249037421046 +935000 ekin = 0.284382433297568 | erot = 0.286484503522986 | epot = -15.1957706788719 | etot = -14.6249037420513 +936000 ekin = 0.291920557580458 | erot = 0.292577187598382 | epot = -15.2094014871973 | etot = -14.6249037420184 +937000 ekin = 0.302840159170039 | erot = 0.299936553990847 | epot = -15.2276804551831 | etot = -14.6249037420222 +938000 ekin = 0.317231541763436 | erot = 0.308432066638964 | epot = -15.2505673504756 | etot = -14.6249037420732 +939000 ekin = 0.334562734704465 | erot = 0.317815317270747 | epot = -15.277281794148 | etot = -14.6249037421728 +940000 ekin = 0.35364952180483 | erot = 0.327729086105148 | epot = -15.3062823502215 | etot = -14.6249037423115 +941000 ekin = 0.372770367646405 | erot = 0.337741122003473 | epot = -15.3354152321199 | etot = -14.62490374247 +942000 ekin = 0.389915662531244 | erot = 0.34739974979893 | epot = -15.3622191549524 | etot = -14.6249037426222 +943000 ekin = 0.403126345738701 | erot = 0.356302369933728 | epot = -15.3843324584131 | etot = -14.6249037427407 +944000 ekin = 0.410851754405684 | erot = 0.364163156178504 | epot = -15.3999186533874 | etot = -14.6249037428032 +945000 ekin = 0.41224792095984 | erot = 0.370864511414023 | epot = -15.4080161751712 | etot = -14.6249037427973 +946000 ekin = 0.407348747779498 | erot = 0.376479254456982 | epot = -15.4087317449601 | etot = -14.6249037427236 +947000 ekin = 0.397071124216324 | erot = 0.381256899558077 | epot = -15.4032317663699 | etot = -14.6249037425955 +948000 ekin = 0.38305345572573 | erot = 0.385576026490354 | epot = -15.3935332246524 | etot = -14.6249037424363 +949000 ekin = 0.367364810069699 | erot = 0.389872987608877 | epot = -15.3821415399525 | etot = -14.624903742274 +950000 ekin = 0.352149150210297 | erot = 0.394562514442363 | epot = -15.3716154067876 | etot = -14.6249037421349 +951000 ekin = 0.339280178142264 | erot = 0.399966938640697 | epot = -15.364150858822 | etot = -14.6249037420391 +952000 ekin = 0.330096120378427 | erot = 0.406268489131276 | epot = -15.3612683515059 | etot = -14.6249037419962 +953000 ekin = 0.32526183166892 | erot = 0.413492937870355 | epot = -15.3636585115441 | etot = -14.6249037420048 +954000 ekin = 0.324774911928697 | erot = 0.421526046052984 | epot = -15.3712047000353 | etot = -14.6249037420537 +955000 ekin = 0.328098170458837 | erot = 0.430156858160225 | epot = -15.3831587707443 | etot = -14.6249037421253 +956000 ekin = 0.334370903123397 | erot = 0.439135698167057 | epot = -15.3984103434923 | etot = -14.6249037422019 +957000 ekin = 0.342633913360124 | erot = 0.44823123979963 | epot = -15.4157688954295 | etot = -14.6249037422697 +958000 ekin = 0.352004139469675 | erot = 0.457271615168161 | epot = -15.4341794969606 | etot = -14.6249037423228 +959000 ekin = 0.361755395785515 | erot = 0.466159587644429 | epot = -15.4528187257936 | etot = -14.6249037423637 +960000 ekin = 0.37129634840351 | erot = 0.474860087933521 | epot = -15.4710601787381 | etot = -14.624903742401 +961000 ekin = 0.380073790913227 | erot = 0.483367158176183 | epot = -15.4883446915346 | etot = -14.6249037424452 +962000 ekin = 0.387455548951145 | erot = 0.491663490522134 | epot = -15.5040227819764 | etot = -14.6249037425031 +963000 ekin = 0.392654097313064 | erot = 0.499687295633833 | epot = -15.5172451355218 | etot = -14.6249037425749 +964000 ekin = 0.394737939560465 | erot = 0.507318071997362 | epot = -15.52695975421 | etot = -14.6249037426522 +965000 ekin = 0.392748486468401 | erot = 0.514386334668901 | epot = -15.5320385638565 | etot = -14.6249037427192 +966000 ekin = 0.385905473254046 | erot = 0.520705106529118 | epot = -15.5315143225403 | etot = -14.6249037427571 +967000 ekin = 0.373852021646475 | erot = 0.526114369236053 | epot = -15.5248701336312 | etot = -14.6249037427486 +968000 ekin = 0.356869417136842 | erot = 0.530525868586128 | epot = -15.5122990284073 | etot = -14.6249037426844 +969000 ekin = 0.335986889835165 | erot = 0.533955228285004 | epot = -15.4948458606873 | etot = -14.6249037425671 +970000 ekin = 0.312927788673001 | erot = 0.536531428462375 | epot = -15.4743629595488 | etot = -14.6249037424134 +971000 ekin = 0.289872105907279 | erot = 0.538479668129898 | epot = -15.4532555162884 | etot = -14.6249037422512 +972000 ekin = 0.269070232406882 | erot = 0.5400808983618 | epot = -15.4340548728819 | etot = -14.6249037421133 +973000 ekin = 0.252397022945549 | erot = 0.54161782723096 | epot = -15.4189185922049 | etot = -14.6249037420284 +974000 ekin = 0.240964852822479 | erot = 0.543321042151966 | epot = -15.4091896369876 | etot = -14.6249037420132 +975000 ekin = 0.23490216482404 | erot = 0.545328986458525 | epot = -15.4051348933507 | etot = -14.6249037420682 +976000 ekin = 0.233353466621782 | erot = 0.547671994179659 | epot = -15.4059292029795 | etot = -14.6249037421781 +977000 ekin = 0.234692201089083 | erot = 0.550284513866881 | epot = -15.4098804572724 | etot = -14.6249037423164 +978000 ekin = 0.236887903180263 | erot = 0.553043053342472 | epot = -15.4148346989741 | etot = -14.6249037424514 +979000 ekin = 0.237945797131594 | erot = 0.555821040963433 | epot = -15.4186705806471 | etot = -14.6249037425521 +980000 ekin = 0.236334546963168 | erot = 0.558547250125055 | epot = -15.4197855396823 | etot = -14.6249037425941 +981000 ekin = 0.231322843924042 | erot = 0.561252158432646 | epot = -15.4174787449221 | etot = -14.6249037425654 +982000 ekin = 0.223154169544533 | erot = 0.564087592074629 | epot = -15.4121455040889 | etot = -14.6249037424697 +983000 ekin = 0.213008719539339 | erot = 0.567310103886669 | epot = -15.4052225657532 | etot = -14.6249037423272 +984000 ekin = 0.202740628548441 | erot = 0.571227590062575 | epot = -15.3988719607827 | etot = -14.6249037421716 +985000 ekin = 0.194435665154694 | erot = 0.576119771487871 | epot = -15.3954591786846 | etot = -14.624903742042 +986000 ekin = 0.189894304519126 | erot = 0.58215285815263 | epot = -15.3969509046435 | etot = -14.6249037419717 +987000 ekin = 0.190182835424942 | erot = 0.589313613953793 | epot = -15.4044001913571 | etot = -14.6249037419783 +988000 ekin = 0.195390213187374 | erot = 0.597385005524008 | epot = -15.4176789607685 | etot = -14.6249037420571 +989000 ekin = 0.204671362362343 | erot = 0.605974905403727 | epot = -15.4355500099486 | etot = -14.6249037421825 +990000 ekin = 0.216563394578633 | erot = 0.614593273597528 | epot = -15.4560604104923 | etot = -14.6249037423162 +991000 ekin = 0.229465191861939 | erot = 0.622757127490605 | epot = -15.477126061773 | etot = -14.6249037424204 +992000 ekin = 0.24211427112869 | erot = 0.630092599916922 | epot = -15.4971106135161 | etot = -14.6249037424704 +993000 ekin = 0.253902581479766 | erot = 0.636403793831493 | epot = -15.5152101177725 | etot = -14.6249037424612 +994000 ekin = 0.264939510335544 | erot = 0.641689105047928 | epot = -15.5315323577914 | etot = -14.6249037424079 +995000 ekin = 0.275864888578878 | erot = 0.646102898208469 | epot = -15.5468715291258 | etot = -14.6249037423384 +996000 ekin = 0.287497820769962 | erot = 0.649877086441122 | epot = -15.562278649495 | etot = -14.6249037422839 +997000 ekin = 0.300450307467282 | erot = 0.653227423573226 | epot = -15.578581473309 | etot = -14.6249037422685 +998000 ekin = 0.314829914377661 | erot = 0.656270894957595 | epot = -15.5960045516386 | etot = -14.6249037423033 +999000 ekin = 0.330110494517446 | erot = 0.658973630822486 | epot = -15.613987867725 | etot = -14.6249037423851 +1000000 ekin = 0.345190458651126 | erot = 0.66113833946702 | epot = -15.6312325406162 | etot = -14.624903742498 + 1000000 0.025569664 -1.5839232 0.020799898 -1.5286042 -3.5789082e-06 +Loop time of 30.1999 on 4 procs for 1000000 steps with 10 atoms + +Performance: 28609.339 tau/day, 33112.661 timesteps/s +96.4% CPU use with 4 MPI tasks x no OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0.90762 | 10.291 | 18.476 | 234.3 | 34.08 +Bond | 0.11783 | 0.39332 | 0.61914 | 34.0 | 1.30 +Neigh | 0 | 0 | 0 | 0.0 | 0.00 +Comm | 2.8711 | 3.8042 | 4.7159 | 34.0 | 12.60 +Output | 2e-05 | 3.15e-05 | 3.6e-05 | 0.0 | 0.00 +Modify | 0.27052 | 1.1583 | 1.9428 | 63.9 | 3.84 +Other | | 14.55 | | | 48.19 + +Nlocal: 2.5 ave 5 max 0 min +Histogram: 1 0 1 0 0 0 0 0 1 1 +Nghost: 7.5 ave 10 max 5 min +Histogram: 1 0 1 0 0 0 0 0 1 1 +Neighs: 18.5 ave 35 max 0 min +Histogram: 1 0 1 0 0 0 0 0 1 1 + +Total # of neighbors = 74 +Ave neighs/atom = 7.4 +Ave special neighs/atom = 3.6 +Neighbor list builds = 0 +Dangerous builds = 0 + +#write_restart config.${number}.* +Total wall time: 0:00:30 -- GitLab From e2a7cdc4f75ea7f316bf9b555fa5198afd5eab9b Mon Sep 17 00:00:00 2001 From: Oliver Henrich Date: Fri, 19 Jul 2019 12:20:56 +0100 Subject: [PATCH 269/469] Updated extended documentation --- doc/src/PDF/USER-CGDNA.pdf | Bin 4230705 -> 4230823 bytes 1 file changed, 0 insertions(+), 0 deletions(-) diff --git a/doc/src/PDF/USER-CGDNA.pdf b/doc/src/PDF/USER-CGDNA.pdf index 7fcf3660156a903ec1ea7ec984ef4f8b11c73bbe..2577875f687a372fd334748c1eabc0e44fba7f6a 100644 GIT binary patch delta 71735 zcmdlur-^C#+$N?8DvT!6C+0b5*0)A^m)|+I@!sq3Gg|C6?MGNIRNT9|R5LPA=yac_ z{Cw$1Zh?$*3db0dZCrfoYG18hb?i()!ls$;^uBD~B^Mv+zu{(H)7jtVjnnSi?)f?Y z{oxwnWBWQUXMFy!h4b(Q|4TWOmoAiF^6=Thdo`cl{VI}pd-nIj9INQ~yEAk?zMK7b zYCY%Pox01Hy>Gc@@A>oF%7;qmKD@AfS>`jU0qYxkRy>t{{0o)%=x?piLB z8vJwFhi((EncRhM#3T3Z?92#0)gpiU+3C<^~LudRaPmmD!?KsWr`Sx!GQ(fXLeM)}4 ze5KYGWM^_}e%bMjE01Mo9bH&nFIu(#Ps!A$_ug);`M)%K-;KnaWsjfk_?@}Kt0&xV z_bS_KVaNC9pDw&@zqsD}+1~!8*&jac^(%`{^s(Q1#7Xw!>G-D-$1YqIjXWk}ocZv$ 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z*~!Gn!r8^r!qw2+(a7A*&D`15$jQRl(Z$)o$-u(N$xgwBkdo=sx*RO)BXdGRW!OG^ zF5PvmWY@(k?XAYKkxQDc+_TEfQV zX6#UDV^f~>LqTxy5%%kUgoQWi|H?4oWpV8C-h2P}Y5n^WR_ft?l| z&Basoe9E>QNYrpzq~dqVgVWyDt*^c~f@gp7Rm0GOTc64*J_ zTMJ@&ANDfc)4eZlRBia=3%4ToUcM9ec`Uz%pAh=8RVk>aWk z?`LPXy6nzU`94`~l7j9M$hR>(4r~mZcxqoWx+*ZP)jaZE{C?d5#p%?|5)iJ8goHF_03?>V>ct>d$`+FpxK z#CU1Gb$#}#=aOB@=KET`iq@CcPI3Qsv)JqLiGB4^nf6VG(v~uFSlybcCh*1HbfHP- zgClp_d=)F!xx7?p;`i5-b=vT4_oc)qzoMrsn^^r)bnkVu2~khtYD{&mKa%`z|Mn<{ V!Svcb2L&!u10ya~RabvEE&$qqUJ?KR -- GitLab From 57fd9723a5720a62e2a4fcb81413712a8bb693ef Mon Sep 17 00:00:00 2001 From: Oliver Henrich Date: Fri, 19 Jul 2019 12:30:01 +0100 Subject: [PATCH 270/469] Added comment on new duplex3 --- examples/USER/cgdna/README | 8 ++++++++ 1 file changed, 8 insertions(+) diff --git a/examples/USER/cgdna/README b/examples/USER/cgdna/README index 7b05418661..e97910d2e1 100644 --- a/examples/USER/cgdna/README +++ b/examples/USER/cgdna/README @@ -22,6 +22,14 @@ A - C - G - T - A - C - G - T | | | | | | | | T - G - C - A T - G - C - A +/examples/duplex3: +This is basically the duplex1 run with both nucleotide mass and moment +of inertia set to the values of the standalone implementation of oxDNA, +which are M=I=1. To achieve this, the masses were set directly, whereas +the diameter of the ellipsoid in the data file was changed to 3.16227766. +This allows direct comparision of e.g. trajectory data or energies on a +per-timestep basis until numerical noise leads eventually to deviations. + /util: This directory contains a simple python setup tool which creates single straight or helical DNA strands, DNA duplexes or arrays of DNA -- GitLab From 0ee0ea109caae1c8416c579b8db88f80fc4dbd02 Mon Sep 17 00:00:00 2001 From: Oliver Henrich Date: Fri, 19 Jul 2019 12:43:37 +0100 Subject: [PATCH 271/469] Removed references to pair_oxdna2_stk --- src/USER-CGDNA/Install.sh | 2 -- src/USER-CGDNA/README | 2 +- 2 files changed, 1 insertion(+), 3 deletions(-) diff --git a/src/USER-CGDNA/Install.sh b/src/USER-CGDNA/Install.sh index a0721d5bde..fa62b0daf2 100755 --- a/src/USER-CGDNA/Install.sh +++ b/src/USER-CGDNA/Install.sh @@ -48,9 +48,7 @@ action pair_oxdna2_excv.h atom_vec_ellipsoid.h action pair_oxdna_hbond.cpp atom_vec_ellipsoid.h action pair_oxdna_hbond.h atom_vec_ellipsoid.h action pair_oxdna_stk.cpp atom_vec_ellipsoid.h -action pair_oxdna2_stk.cpp atom_vec_ellipsoid.h action pair_oxdna_stk.h atom_vec_ellipsoid.h -action pair_oxdna2_stk.h atom_vec_ellipsoid.h action pair_oxdna_xstk.cpp atom_vec_ellipsoid.h action pair_oxdna_xstk.h atom_vec_ellipsoid.h action pair_oxdna2_dh.cpp atom_vec_ellipsoid.h diff --git a/src/USER-CGDNA/README b/src/USER-CGDNA/README index 8e3f16372c..48d6178d13 100644 --- a/src/USER-CGDNA/README +++ b/src/USER-CGDNA/README @@ -73,7 +73,7 @@ pair_oxdna_xstk.cpp: cross-stacking interaction between nucleotides pair_oxdna_coaxstk.cpp: coaxial stacking interaction between nucleotides -pair_oxdna2_excv.cpp, pair_oxdna2_stk.cpp, pair_oxdna2_coaxstk.cpp: +pair_oxdna2_excv.cpp, pair_oxdna2_coaxstk.cpp: corresponding pair styles in oxDNA2 (see [3]) pair_oxdna2_dh.cpp: Debye-Hueckel electrostatic interaction between backbone -- GitLab From c2643a519e1b81bed24cd862c7589bfe706974c8 Mon Sep 17 00:00:00 2001 From: Oliver Henrich Date: Fri, 19 Jul 2019 13:29:39 +0100 Subject: [PATCH 272/469] Clarified explanation of new example3 --- examples/USER/cgdna/README | 15 +++++++++------ 1 file changed, 9 insertions(+), 6 deletions(-) diff --git a/examples/USER/cgdna/README b/examples/USER/cgdna/README index e97910d2e1..8a9dc44359 100644 --- a/examples/USER/cgdna/README +++ b/examples/USER/cgdna/README @@ -23,12 +23,15 @@ A - C - G - T - A - C - G - T T - G - C - A T - G - C - A /examples/duplex3: -This is basically the duplex1 run with both nucleotide mass and moment -of inertia set to the values of the standalone implementation of oxDNA, -which are M=I=1. To achieve this, the masses were set directly, whereas -the diameter of the ellipsoid in the data file was changed to 3.16227766. -This allows direct comparision of e.g. trajectory data or energies on a -per-timestep basis until numerical noise leads eventually to deviations. +This is basically the duplex1 run with sequence-dependent stacking +and hydrogen-bonding strengths enabled and both nucleotide mass and +moment of inertia set to the value of the standalone implementation +of oxDNA (M = I = 1). To achieve this, the masses can be set directly +in the input and data file, whereas the moment of inertia is set via +the diameter of the ellipsoid in the data file and has a value of 3.16227766. +The change of mass and moment of inertia allows direct comparision of +e.g. trajectory data, energies or time-dependent observables on a per-timestep +basis until numerical noise causes deviations at later simulation times. /util: This directory contains a simple python setup tool which creates -- GitLab From babbdaff2c37c5d6e7fdcaa0b1b05c2cf67c55ac Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Fri, 19 Jul 2019 08:31:04 -0400 Subject: [PATCH 273/469] step version string for next patch release --- doc/lammps.1 | 2 +- doc/src/Manual.txt | 4 ++-- src/version.h | 2 +- 3 files changed, 4 insertions(+), 4 deletions(-) diff --git a/doc/lammps.1 b/doc/lammps.1 index 7ba31bfd06..4685ad22a3 100644 --- a/doc/lammps.1 +++ b/doc/lammps.1 @@ -1,4 +1,4 @@ -.TH LAMMPS "18 June 2019" "2019-06-18" +.TH LAMMPS "19 July 2019" "2019-07-19" .SH NAME .B LAMMPS \- Molecular Dynamics Simulator. diff --git a/doc/src/Manual.txt b/doc/src/Manual.txt index ba6ab8aac7..80d72aac57 100644 --- a/doc/src/Manual.txt +++ b/doc/src/Manual.txt @@ -1,7 +1,7 @@ LAMMPS Users Manual - + @@ -21,7 +21,7 @@ :line LAMMPS Documentation :c,h1 -18 Jun 2019 version :c,h2 +19 Jul 2019 version :c,h2 "What is a LAMMPS version?"_Manual_version.html diff --git a/src/version.h b/src/version.h index c2f6fcaf92..8a8cbec57e 100644 --- a/src/version.h +++ b/src/version.h @@ -1 +1 @@ -#define LAMMPS_VERSION "18 Jun 2019" +#define LAMMPS_VERSION "19 Jul 2019" -- GitLab From 4c328bf846a2f0543f06e2bae0c7ec62411d5b4d Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Fri, 19 Jul 2019 10:39:06 -0400 Subject: [PATCH 274/469] add metachars '\i' and '\f' to regexp for interger and floating point number chars --- src/utils.cpp | 29 +++++++++++++++++++++++++++++ 1 file changed, 29 insertions(+) diff --git a/src/utils.cpp b/src/utils.cpp index bbda22f24c..a27a53e600 100644 --- a/src/utils.cpp +++ b/src/utils.cpp @@ -39,6 +39,10 @@ * '\W' Non-alphanumeric * '\d' Digits, [0-9] * '\D' Non-digits + * '\i' Integer chars, [0-9], '+' and '-' + * '\I' Non-integers + * '\f' Floating point number chars, [0-9], '.', 'e', 'E', '+' and '-' + * '\F' Non-floats * * *NOT* supported: * '[^abc]' Inverted class @@ -307,6 +311,7 @@ extern "C" { enum { UNUSED, DOT, BEGIN, END, QUESTIONMARK, STAR, PLUS, CHAR, CHAR_CLASS, INV_CHAR_CLASS, DIGIT, NOT_DIGIT, + INTEGER, NOT_INTEGER, FLOAT, NOT_FLOAT, ALPHA, NOT_ALPHA, WHITESPACE, NOT_WHITESPACE /*, BRANCH */ }; typedef struct regex_t { @@ -324,6 +329,8 @@ extern "C" { static int matchplus(regex_t p, regex_t *pattern, const char *text); static int matchone(regex_t p, char c); static int matchdigit(char c); + static int matchint(char c); + static int matchfloat(char c); static int matchalpha(char c); static int matchwhitespace(char c); static int matchmetachar(char c, const char *str); @@ -395,6 +402,10 @@ extern "C" { /* Meta-character: */ case 'd': { re_compiled[j].type = DIGIT; } break; case 'D': { re_compiled[j].type = NOT_DIGIT; } break; + case 'i': { re_compiled[j].type = INTEGER; } break; + case 'I': { re_compiled[j].type = NOT_INTEGER; } break; + case 'f': { re_compiled[j].type = FLOAT; } break; + case 'F': { re_compiled[j].type = NOT_FLOAT; } break; case 'w': { re_compiled[j].type = ALPHA; } break; case 'W': { re_compiled[j].type = NOT_ALPHA; } break; case 's': { re_compiled[j].type = WHITESPACE; } break; @@ -467,6 +478,16 @@ extern "C" { return ((c >= '0') && (c <= '9')); } + static int matchint(char c) + { + return (matchdigit(c) || (c == '-') || (c == '+')); + } + + static int matchfloat(char c) + { + return (matchint(c) || (c == '.') || (c == 'e') || (c == 'E')); + } + static int matchalpha(char c) { return ((c >= 'a') && (c <= 'z')) || ((c >= 'A') && (c <= 'Z')); @@ -502,6 +523,10 @@ extern "C" { switch (str[0]) { case 'd': return matchdigit(c); case 'D': return !matchdigit(c); + case 'i': return matchint(c); + case 'I': return !matchint(c); + case 'f': return matchfloat(c); + case 'F': return !matchfloat(c); case 'w': return matchalphanum(c); case 'W': return !matchalphanum(c); case 's': return matchwhitespace(c); @@ -544,6 +569,10 @@ extern "C" { case INV_CHAR_CLASS: return !matchcharclass(c, (const char *)p.ccl); case DIGIT: return matchdigit(c); case NOT_DIGIT: return !matchdigit(c); + case INTEGER: return matchint(c); + case NOT_INTEGER: return !matchint(c); + case FLOAT: return matchfloat(c); + case NOT_FLOAT: return !matchfloat(c); case ALPHA: return matchalphanum(c); case NOT_ALPHA: return !matchalphanum(c); case WHITESPACE: return matchwhitespace(c); -- GitLab From 4f7c95d87e77f880415405910f3e06c4b70b1ca6 Mon Sep 17 00:00:00 2001 From: Evangelos Voyiatzis Date: Fri, 19 Jul 2019 17:13:38 +0200 Subject: [PATCH 275/469] Update compute.txt Addition of a few one-liners --- doc/src/compute.txt | 89 ++++++++++++++++++++++----------------------- 1 file changed, 43 insertions(+), 46 deletions(-) diff --git a/doc/src/compute.txt b/doc/src/compute.txt index 87dbee57d6..53ed373aa5 100644 --- a/doc/src/compute.txt +++ b/doc/src/compute.txt @@ -171,42 +171,40 @@ The individual style names on the "Commands compute"_Commands_compute.html doc page are followed by one or more of (g,i,k,o,t) to indicate which accelerated styles exist. -"ackland/atom"_compute_ackland_atom.html - +"ackland/atom"_compute_ackland_atom.html - determines the local lattice structure based on the Ackland formulation "adf"_compute_adf.html - angular distribution function of triples of atoms "aggregate/atom"_compute_cluster_atom.html - aggregate ID for each atom -"angle"_compute_angle.html - -"angle/local"_compute_angle_local.html - -"angle/local"_compute_bond_local.html - theta and energy of each angle +"angle"_compute_angle.html - energy of each angle sub-style +"angle/local"_compute_angle_local.html - theta and energy of each angle "angmom/chunk"_compute_angmom_chunk.html - angular momentum for each chunk -"basal/atom"_compute_basal_atom.html - +"basal/atom"_compute_basal_atom.html - calculates the hexagonal close-packed “c” lattice vector of each atom "body/local"_compute_body_local.html - attributes of body sub-particles -"bond"_compute_bond.html - values computed by a bond style +"bond"_compute_bond.html - energy of each bond sub-style "bond/local"_compute_bond_local.html - distance and energy of each bond "centro/atom"_compute_centro_atom.html - centro-symmetry parameter for each atom "chunk/atom"_compute_chunk_atom.html - assign chunk IDs to each atom "chunk/spread/atom"_compute_chunk_spread_atom.html - spreads chunk values to each atom in chunk "cluster/atom"_compute_cluster_atom.html - cluster ID for each atom "cna/atom"_compute_cna_atom.html - common neighbor analysis (CNA) for each atom -"cnp/atom"_compute_cnp_atom.html - +"cnp/atom"_compute_cnp_atom.html - common neighborhood parameter (CNP) for each atom "com"_compute_com.html - center-of-mass of group of atoms "com/chunk"_compute_com_chunk.html - center-of-mass for each chunk "contact/atom"_compute_contact_atom.html - contact count for each spherical particle "coord/atom"_compute_coord_atom.html - coordination number for each atom "damage/atom"_compute_damage_atom.html - Peridynamic damage for each atom -"dihedral"_compute_dihedral.html - +"dihedral"_compute_dihedral.html - energy of each dihedral sub-style "dihedral/local"_compute_dihedral_local.html - angle of each dihedral "dilatation/atom"_compute_dilatation_atom.html - Peridynamic dilatation for each atom -"dipole/chunk"_compute_dipole_chunk.html - +"dipole/chunk"_compute_dipole_chunk.html - dipole vector and total dipole for each chunk "displace/atom"_compute_displace_atom.html - displacement of each atom "dpd"_compute_dpd.html - "dpd/atom"_compute_dpd_atom.html - -"edpd/temp/atom"_compute_edpd_temp_atom.html - -"entropy/atom"_compute_entropy_atom.html - +"edpd/temp/atom"_compute_edpd_temp_atom.html - per-atom temperature for each eDPD particle in a group +"entropy/atom"_compute_entropy_atom.html - pair entropy fingerprint of each atom "erotate/asphere"_compute_erotate_asphere.html - rotational energy of aspherical particles "erotate/rigid"_compute_erotate_rigid.html - rotational energy of rigid bodies "erotate/sphere"_compute_erotate_sphere.html - rotational energy of spherical particles -"erotate/sphere/atom"_compute_erotate_sphere.html - rotational energy for each spherical particle -"erotate/sphere/atom"_compute_erotate_sphere_atom.html - +"erotate/sphere/atom"_compute_erotate_sphere_atom.html - rotational energy for each spherical particle "event/displace"_compute_event_displace.html - detect event on atom displacement "fep"_compute_fep.html - "force/tally"_compute_tally.html - @@ -218,17 +216,17 @@ compute"_Commands_compute.html doc page are followed by one or more of "heat/flux"_compute_heat_flux.html - heat flux through a group of atoms "heat/flux/tally"_compute_tally.html - "hexorder/atom"_compute_hexorder_atom.html - bond orientational order parameter q6 -"improper"_compute_improper.html - +"improper"_compute_improper.html - energy of each improper sub-style "improper/local"_compute_improper_local.html - angle of each improper "inertia/chunk"_compute_inertia_chunk.html - inertia tensor for each chunk "ke"_compute_ke.html - translational kinetic energy "ke/atom"_compute_ke_atom.html - kinetic energy for each atom -"ke/atom/eff"_compute_ke_atom_eff.html - -"ke/eff"_compute_ke_eff.html - +"ke/atom/eff"_compute_ke_atom_eff.html - per-atom translational and radial kinetic energy in the electron force field model +"ke/eff"_compute_ke_eff.html - kinetic energy of a group of nuclei and electrons in the electron force field model "ke/rigid"_compute_ke_rigid.html - translational kinetic energy of rigid bodies -"meso/e/atom"_compute_meso_e_atom.html - -"meso/rho/atom"_compute_meso_rho_atom.html - -"meso/t/atom"_compute_meso_t_atom.html - +"meso/e/atom"_compute_meso_e_atom.html - per-atom internal energy of Smooth-Particle Hydrodynamics atoms +"meso/rho/atom"_compute_meso_rho_atom.html - per-atom mesoscopic density of Smooth-Particle Hydrodynamics atoms +"meso/t/atom"_compute_meso_t_atom.html - per-atom internal temperature of Smooth-Particle Hydrodynamics atoms "msd"_compute_msd.html - mean-squared displacement of group of atoms "msd/chunk"_compute_msd_chunk.html - mean-squared displacement for each chunk "msd/nongauss"_compute_msd_nongauss.html - MSD and non-Gaussian parameter of group of atoms @@ -242,73 +240,72 @@ compute"_Commands_compute.html doc page are followed by one or more of "pe/tally"_compute_tally.html - "plasticity/atom"_compute_plasticity_atom.html - Peridynamic plasticity for each atom "pressure"_compute_pressure.html - total pressure and pressure tensor -"pressure/cylinder"_compute_pressure_cylinder.html - -"pressure/uef"_compute_pressure_uef.html - +"pressure/cylinder"_compute_pressure_cylinder.html - pressure tensor in cylindrical coordinates +"pressure/uef"_compute_pressure_uef.html - pressure tensor in the reference frame of an applied flow field "property/atom"_compute_property_atom.html - convert atom attributes to per-atom vectors/arrays "property/chunk"_compute_property_chunk.html - extract various per-chunk attributes "property/local"_compute_property_local.html - convert local attributes to localvectors/arrays -"ptm/atom"_compute_ptm_atom.html - +"ptm/atom"_compute_ptm_atom.html - determines the local lattice structure based on the Polyhedral Template Matching method "rdf"_compute_rdf.html - radial distribution function g(r) histogram of group of atoms "reduce"_compute_reduce.html - combine per-atom quantities into a single global value "reduce/chunk"_compute_reduce_chunk.html - reduce per-atom quantities within each chunk "reduce/region"_compute_reduce.html - same as compute reduce, within a region "rigid/local"_compute_rigid_local.html - extract rigid body attributes -"saed"_compute_saed.html - +"saed"_compute_saed.html - electron diffraction intensity on a mesh of reciprocal lattice nodes "slice"_compute_slice.html - extract values from global vector or array "smd/contact/radius"_compute_smd_contact_radius.html - -"smd/damage"_compute_smd_damage.html - +"smd/damage"_compute_smd_damage.html - damage status of SPH particles in Smooth Mach Dynamics "smd/hourglass/error"_compute_smd_hourglass_error.html - -"smd/internal/energy"_compute_smd_internal_energy.html - -"smd/plastic/strain"_compute_smd_plastic_strain.html - -"smd/plastic/strain/rate"_compute_smd_plastic_strain_rate.html - -"smd/rho"_compute_smd_rho.html - -"smd/tlsph/defgrad"_compute_smd_tlsph_defgrad.html - -"smd/tlsph/dt"_compute_smd_tlsph_dt.html - +"smd/internal/energy"_compute_smd_internal_energy.html - per-particle enthalpy in Smooth Mach Dynamics +"smd/plastic/strain"_compute_smd_plastic_strain.html - equivalent plastic strain per particle in Smooth Mach Dynamics +"smd/plastic/strain/rate"_compute_smd_plastic_strain_rate.html - time rate of the equivalent plastic strain in Smooth Mach Dynamics +"smd/rho"_compute_smd_rho.html - per-particle mass density in Smooth Mach Dynamics +"smd/tlsph/defgrad"_compute_smd_tlsph_defgrad.html - deformation gradient in Smooth Mach Dynamics +"smd/tlsph/dt"_compute_smd_tlsph_dt.html - CFL-stable time increment per particle in Smooth Mach Dynamics "smd/tlsph/num/neighs"_compute_smd_tlsph_num_neighs.html - "smd/tlsph/shape"_compute_smd_tlsph_shape.html - "smd/tlsph/strain"_compute_smd_tlsph_strain.html - "smd/tlsph/strain/rate"_compute_smd_tlsph_strain_rate.html - -"smd/tlsph/stress"_compute_smd_tlsph_stress.html - -"smd/triangle/vertices"_compute_smd_triangle_vertices.html - +"smd/tlsph/stress"_compute_smd_tlsph_stress.html - per-particle Cauchy stress tensor for SPH particles "smd/triangle/vertices"_compute_smd_triangle_vertices.html - "smd/ulsph/num/neighs"_compute_smd_ulsph_num_neighs.html - "smd/ulsph/strain"_compute_smd_ulsph_strain.html - "smd/ulsph/strain/rate"_compute_smd_ulsph_strain_rate.html - -"smd/ulsph/stress"_compute_smd_ulsph_stress.html - -"smd/vol"_compute_smd_vol.html - +"smd/ulsph/stress"_compute_smd_ulsph_stress.html - per-particle Cauchy stress tensor and von Mises equivalent stress in Smooth Mach Dynamics +"smd/vol"_compute_smd_vol.html - per-particle volumes and their sum in Smooth Mach Dynamics "sna/atom"_compute_sna_atom.html - calculate bispectrum coefficients for each atom "snad/atom"_compute_sna_atom.html - derivative of bispectrum coefficients for each atom "snav/atom"_compute_sna_atom.html - virial contribution from bispectrum coefficients for each atom -"spin"_compute_spin.html - +"spin"_compute_spin.html - magnetic quantities for a system of atoms having spins "stress/atom"_compute_stress_atom.html - stress tensor for each atom -"stress/mop"_compute_stress_mop.html - -"stress/mop/profile"_compute_stress_mop.html - +"stress/mop"_compute_stress_mop.html - normal components of the local stress tensor using the method of planes +"stress/mop/profile"_compute_stress_mop.html - profile of the normal components of the local stress tensor using the method of planes "stress/tally"_compute_tally.html - -"tdpd/cc/atom"_compute_tdpd_cc_atom.html - +"tdpd/cc/atom"_compute_tdpd_cc_atom.html - per-atom chemical concentration of a specified species for each tDPD particle "temp"_compute_temp.html - temperature of group of atoms "temp/asphere"_compute_temp_asphere.html - temperature of aspherical particles "temp/body"_compute_temp_body.html - temperature of body particles "temp/chunk"_compute_temp_chunk.html - temperature of each chunk "temp/com"_compute_temp_com.html - temperature after subtracting center-of-mass velocity -"temp/cs"_compute_temp_cs.html - +"temp/cs"_compute_temp_cs.html - temperature based on the center-of-mass velocity of atom pairs that are bonded to each other "temp/deform"_compute_temp_deform.html - temperature excluding box deformation velocity -"temp/deform/eff"_compute_temp_deform_eff.html - -"temp/drude"_compute_temp_drude.html - -"temp/eff"_compute_temp_eff.html - +"temp/deform/eff"_compute_temp_deform_eff.html - temperature excluding box deformation velocity in the electron force field model +"temp/drude"_compute_temp_drude.html - temperature of Core-Drude pairs +"temp/eff"_compute_temp_eff.html - temperature of a group of nuclei and electrons in the electron force field model "temp/partial"_compute_temp_partial.html - temperature excluding one or more dimensions of velocity "temp/profile"_compute_temp_profile.html - temperature excluding a binned velocity profile "temp/ramp"_compute_temp_ramp.html - temperature excluding ramped velocity component "temp/region"_compute_temp_region.html - temperature of a region of atoms -"temp/region/eff"_compute_temp_region_eff.html - -"temp/rotate"_compute_temp_rotate.html - +"temp/region/eff"_compute_temp_region_eff.html - temperature of a region of nuclei and electrons in the electron force field model +"temp/rotate"_compute_temp_rotate.html - temperature of a group of atoms after subtracting out their center-of-mass and angular velocities "temp/sphere"_compute_temp_sphere.html - temperature of spherical particles -"temp/uef"_compute_temp_uef.html - +"temp/uef"_compute_temp_uef.html - kinetic energy tensor in the reference frame of an applied flow field "ti"_compute_ti.html - thermodynamic integration free energy values "torque/chunk"_compute_torque_chunk.html - torque applied on each chunk "vacf"_compute_vacf.html - velocity auto-correlation function of group of atoms "vcm/chunk"_compute_vcm_chunk.html - velocity of center-of-mass for each chunk "voronoi/atom"_compute_voronoi_atom.html - Voronoi volume and neighbors for each atom -"xrd"_compute_xrd.html - :ul +"xrd"_compute_xrd.html - x-ray diffraction intensity on a mesh of reciprocal lattice nodes :ul [Restrictions:] none -- GitLab From 8526e7a4cdb16bb29e00e049e62de472eb9ee6de Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Fri, 19 Jul 2019 11:14:39 -0400 Subject: [PATCH 276/469] checking return value of ?scanf() calls to detect problems parsing files --- doc/src/Errors_messages.txt | 5 +++++ src/REPLICA/neb.cpp | 23 ++++++++++++--------- src/USER-REAXC/fix_qeq_reax.cpp | 8 +++++--- src/atom.cpp | 36 ++++++++++++++++++++------------- src/atom.h | 5 +++++ src/reader_native.cpp | 32 ++++++++++++++++++++--------- src/reader_xyz.cpp | 6 ++++-- 7 files changed, 77 insertions(+), 38 deletions(-) diff --git a/doc/src/Errors_messages.txt b/doc/src/Errors_messages.txt index 1d635ed841..c55d3743ab 100644 --- a/doc/src/Errors_messages.txt +++ b/doc/src/Errors_messages.txt @@ -5890,6 +5890,11 @@ The element names in the ADP file do not match those requested. :dd The element names in the EAM file do not match those requested. :dd +{Incorrect format of ... section in data file} :dt + +Number or type of values per line in the given section of the data file +is not consistent with the requirements for this section. :dd + {Incorrect format in COMB potential file} :dt Incorrect number of words per line in the potential file. :dd diff --git a/src/REPLICA/neb.cpp b/src/REPLICA/neb.cpp index 6b68c52dbb..4061ec6541 100644 --- a/src/REPLICA/neb.cpp +++ b/src/REPLICA/neb.cpp @@ -397,28 +397,33 @@ void NEB::readfile(char *file, int flag) open(file); while (1) { eof = fgets(line,MAXLINE,fp); - if (eof == NULL) error->one(FLERR,"Unexpected end of neb file"); + if (eof == NULL) error->one(FLERR,"Unexpected end of NEB file"); start = &line[strspn(line," \t\n\v\f\r")]; if (*start != '\0' && *start != '#') break; } - sscanf(line,"%d",&nlines); + int rv = sscanf(line,"%d",&nlines); + if (rv != 1) nlines = -1; } MPI_Bcast(&nlines,1,MPI_INT,0,uworld); - + if (nlines < 0) + error->universe_all(FLERR,"Incorrectly formatted NEB file"); } else { if (me == 0) { if (ireplica) { open(file); while (1) { eof = fgets(line,MAXLINE,fp); - if (eof == NULL) error->one(FLERR,"Unexpected end of neb file"); + if (eof == NULL) error->one(FLERR,"Unexpected end of NEB file"); start = &line[strspn(line," \t\n\v\f\r")]; if (*start != '\0' && *start != '#') break; } - sscanf(line,"%d",&nlines); + int rv = sscanf(line,"%d",&nlines); + if (rv != 1) nlines = -1; } else nlines = 0; } MPI_Bcast(&nlines,1,MPI_INT,0,world); + if (nlines < 0) + error->all(FLERR,"Incorrectly formatted NEB file"); } char *buffer = new char[CHUNK*MAXLINE]; @@ -442,7 +447,7 @@ void NEB::readfile(char *file, int flag) eofflag = comm->read_lines_from_file_universe(fp,nchunk,MAXLINE,buffer); else eofflag = comm->read_lines_from_file(fp,nchunk,MAXLINE,buffer); - if (eofflag) error->all(FLERR,"Unexpected end of neb file"); + if (eofflag) error->all(FLERR,"Unexpected end of NEB file"); buf = buffer; next = strchr(buf,'\n'); @@ -451,7 +456,7 @@ void NEB::readfile(char *file, int flag) *next = '\n'; if (nwords != ATTRIBUTE_PERLINE) - error->all(FLERR,"Incorrect atom format in neb file"); + error->all(FLERR,"Incorrect atom format in NEB file"); // loop over lines of atom coords // tokenize the line into values @@ -509,12 +514,12 @@ void NEB::readfile(char *file, int flag) int ntotal; MPI_Allreduce(&ncount,&ntotal,1,MPI_INT,MPI_SUM,uworld); if (ntotal != nreplica*nlines) - error->universe_all(FLERR,"Invalid atom IDs in neb file"); + error->universe_all(FLERR,"Invalid atom IDs in NEB file"); } else { int ntotal; MPI_Allreduce(&ncount,&ntotal,1,MPI_INT,MPI_SUM,world); if (ntotal != nlines) - error->all(FLERR,"Invalid atom IDs in neb file"); + error->all(FLERR,"Invalid atom IDs in NEB file"); } // clean up diff --git a/src/USER-REAXC/fix_qeq_reax.cpp b/src/USER-REAXC/fix_qeq_reax.cpp index faa0632608..6c0da278c2 100644 --- a/src/USER-REAXC/fix_qeq_reax.cpp +++ b/src/USER-REAXC/fix_qeq_reax.cpp @@ -200,7 +200,7 @@ void FixQEqReax::pertype_parameters(char *arg) return; } - int i,itype,ntypes; + int i,itype,ntypes,rv; double v1,v2,v3; FILE *pf; @@ -216,9 +216,11 @@ void FixQEqReax::pertype_parameters(char *arg) error->one(FLERR,"Fix qeq/reax parameter file could not be found"); for (i = 1; i <= ntypes && !feof(pf); i++) { - fscanf(pf,"%d %lg %lg %lg",&itype,&v1,&v2,&v3); + rv = fscanf(pf,"%d %lg %lg %lg",&itype,&v1,&v2,&v3); + if (rv != 4) + error->one(FLERR,"Fix qeq/reax: Incorrect format of param file"); if (itype < 1 || itype > ntypes) - error->one(FLERR,"Fix qeq/reax invalid atom type in param file"); + error->one(FLERR,"Fix qeq/reax: invalid atom type in param file"); chi[itype] = v1; eta[itype] = v2; gamma[itype] = v3; diff --git a/src/atom.cpp b/src/atom.cpp index 1f5d5a80c4..e5a982d620 100644 --- a/src/atom.cpp +++ b/src/atom.cpp @@ -1071,7 +1071,7 @@ void Atom::data_vels(int n, char *buf, tagint id_offset) void Atom::data_bonds(int n, char *buf, int *count, tagint id_offset, int type_offset) { - int m,tmp,itype; + int m,tmp,itype,rv; tagint atom1,atom2; char *next; int newton_bond = force->newton_bond; @@ -1079,8 +1079,10 @@ void Atom::data_bonds(int n, char *buf, int *count, tagint id_offset, for (int i = 0; i < n; i++) { next = strchr(buf,'\n'); *next = '\0'; - sscanf(buf,"%d %d " TAGINT_FORMAT " " TAGINT_FORMAT, - &tmp,&itype,&atom1,&atom2); + rv = sscanf(buf,"%d %d " TAGINT_FORMAT " " TAGINT_FORMAT, + &tmp,&itype,&atom1,&atom2); + if (rv != 4) + error->one(FLERR,"Incorrect format of Bonds section in data file"); if (id_offset) { atom1 += id_offset; atom2 += id_offset; @@ -1124,7 +1126,7 @@ void Atom::data_bonds(int n, char *buf, int *count, tagint id_offset, void Atom::data_angles(int n, char *buf, int *count, tagint id_offset, int type_offset) { - int m,tmp,itype; + int m,tmp,itype,rv; tagint atom1,atom2,atom3; char *next; int newton_bond = force->newton_bond; @@ -1132,8 +1134,10 @@ void Atom::data_angles(int n, char *buf, int *count, tagint id_offset, for (int i = 0; i < n; i++) { next = strchr(buf,'\n'); *next = '\0'; - sscanf(buf,"%d %d " TAGINT_FORMAT " " TAGINT_FORMAT " " TAGINT_FORMAT, - &tmp,&itype,&atom1,&atom2,&atom3); + rv = sscanf(buf,"%d %d " TAGINT_FORMAT " " TAGINT_FORMAT " " TAGINT_FORMAT, + &tmp,&itype,&atom1,&atom2,&atom3); + if (rv != 5) + error->one(FLERR,"Incorrect format of Angles section in data file"); if (id_offset) { atom1 += id_offset; atom2 += id_offset; @@ -1194,7 +1198,7 @@ void Atom::data_angles(int n, char *buf, int *count, tagint id_offset, void Atom::data_dihedrals(int n, char *buf, int *count, tagint id_offset, int type_offset) { - int m,tmp,itype; + int m,tmp,itype,rv; tagint atom1,atom2,atom3,atom4; char *next; int newton_bond = force->newton_bond; @@ -1202,9 +1206,11 @@ void Atom::data_dihedrals(int n, char *buf, int *count, tagint id_offset, for (int i = 0; i < n; i++) { next = strchr(buf,'\n'); *next = '\0'; - sscanf(buf,"%d %d " - TAGINT_FORMAT " " TAGINT_FORMAT " " TAGINT_FORMAT " " TAGINT_FORMAT, - &tmp,&itype,&atom1,&atom2,&atom3,&atom4); + rv = sscanf(buf,"%d %d " TAGINT_FORMAT " " TAGINT_FORMAT + " " TAGINT_FORMAT " " TAGINT_FORMAT, + &tmp,&itype,&atom1,&atom2,&atom3,&atom4); + if (rv != 6) + error->one(FLERR,"Incorrect format of Dihedrals section in data file"); if (id_offset) { atom1 += id_offset; atom2 += id_offset; @@ -1283,7 +1289,7 @@ void Atom::data_dihedrals(int n, char *buf, int *count, tagint id_offset, void Atom::data_impropers(int n, char *buf, int *count, tagint id_offset, int type_offset) { - int m,tmp,itype; + int m,tmp,itype,rv; tagint atom1,atom2,atom3,atom4; char *next; int newton_bond = force->newton_bond; @@ -1291,9 +1297,11 @@ void Atom::data_impropers(int n, char *buf, int *count, tagint id_offset, for (int i = 0; i < n; i++) { next = strchr(buf,'\n'); *next = '\0'; - sscanf(buf,"%d %d " - TAGINT_FORMAT " " TAGINT_FORMAT " " TAGINT_FORMAT " " TAGINT_FORMAT, - &tmp,&itype,&atom1,&atom2,&atom3,&atom4); + rv = sscanf(buf,"%d %d " + TAGINT_FORMAT " " TAGINT_FORMAT " " TAGINT_FORMAT " " TAGINT_FORMAT, + &tmp,&itype,&atom1,&atom2,&atom3,&atom4); + if (rv != 6) + error->one(FLERR,"Incorrect format of Impropers section in data file"); if (id_offset) { atom1 += id_offset; atom2 += id_offset; diff --git a/src/atom.h b/src/atom.h index 5cd9ca819b..81f643c007 100644 --- a/src/atom.h +++ b/src/atom.h @@ -426,6 +426,11 @@ E: Incorrect atom format in data file Number of values per atom line in the data file is not consistent with the atom style. +E: Incorrect format of ... section in data file + +Number or type of values per line in the given section of the data file +is not consistent with the requirements for this section. + E: Invalid atom type in Atoms section of data file Atom types must range from 1 to specified # of types. diff --git a/src/reader_native.cpp b/src/reader_native.cpp index 7c772ab6b8..60b7ecd764 100644 --- a/src/reader_native.cpp +++ b/src/reader_native.cpp @@ -59,8 +59,9 @@ int ReaderNative::read_time(bigint &ntimestep) if (strstr(line,"ITEM: TIMESTEP") != line) error->one(FLERR,"Dump file is incorrectly formatted"); read_lines(1); - sscanf(line,BIGINT_FORMAT,&ntimestep); - + int rv = sscanf(line,BIGINT_FORMAT,&ntimestep); + if (rv != 1) + error->one(FLERR,"Dump file is incorrectly formatted"); return 0; } @@ -73,7 +74,9 @@ void ReaderNative::skip() { read_lines(2); bigint natoms; - sscanf(line,BIGINT_FORMAT,&natoms); + int rv = sscanf(line,BIGINT_FORMAT,&natoms); + if (rv != 1) + error->one(FLERR,"Dump file is incorrectly formatted"); read_lines(5); @@ -110,8 +113,12 @@ bigint ReaderNative::read_header(double box[3][3], int &boxinfo, int &triclinic, int &xflag, int &yflag, int &zflag) { bigint natoms; + int rv; + read_lines(2); - sscanf(line,BIGINT_FORMAT,&natoms); + rv = sscanf(line,BIGINT_FORMAT,&natoms); + if (rv != 1) + error->one(FLERR,"Dump file is incorrectly formatted"); boxinfo = 1; triclinic = 0; @@ -120,14 +127,19 @@ bigint ReaderNative::read_header(double box[3][3], int &boxinfo, int &triclinic, if (line[strlen("ITEM: BOX BOUNDS ")] == 'x') triclinic = 1; read_lines(1); - if (!triclinic) sscanf(line,"%lg %lg",&box[0][0],&box[0][1]); - else sscanf(line,"%lg %lg %lg",&box[0][0],&box[0][1],&box[0][2]); + if (!triclinic) rv = 2 - sscanf(line,"%lg %lg",&box[0][0],&box[0][1]); + else rv = 3 - sscanf(line,"%lg %lg %lg",&box[0][0],&box[0][1],&box[0][2]); + if (rv != 0) error->one(FLERR,"Dump file is incorrectly formatted"); + read_lines(1); - if (!triclinic) sscanf(line,"%lg %lg",&box[1][0],&box[1][1]); - else sscanf(line,"%lg %lg %lg",&box[1][0],&box[1][1],&box[1][2]); + if (!triclinic) rv = 2 - sscanf(line,"%lg %lg",&box[1][0],&box[1][1]); + else rv = 3 - sscanf(line,"%lg %lg %lg",&box[1][0],&box[1][1],&box[1][2]); + if (rv != 0) error->one(FLERR,"Dump file is incorrectly formatted"); + read_lines(1); - if (!triclinic) sscanf(line,"%lg %lg",&box[2][0],&box[2][1]); - else sscanf(line,"%lg %lg %lg",&box[2][0],&box[2][1],&box[2][2]); + if (!triclinic) rv = 2 - sscanf(line,"%lg %lg",&box[2][0],&box[2][1]); + else rv = 3 - sscanf(line,"%lg %lg %lg",&box[2][0],&box[2][1],&box[2][2]); + if (rv != 0) error->one(FLERR,"Dump file is incorrectly formatted"); read_lines(1); diff --git a/src/reader_xyz.cpp b/src/reader_xyz.cpp index 303c25cd7a..040eb9d460 100644 --- a/src/reader_xyz.cpp +++ b/src/reader_xyz.cpp @@ -170,7 +170,7 @@ bigint ReaderXYZ::read_header(double /*box*/[3][3], int &boxinfo, int &/*triclin void ReaderXYZ::read_atoms(int n, int nfield, double **fields) { - int i,m; + int i,m,rv; char *eof; int mytype; double myx, myy, myz; @@ -180,7 +180,9 @@ void ReaderXYZ::read_atoms(int n, int nfield, double **fields) if (eof == NULL) error->one(FLERR,"Unexpected end of dump file"); ++nid; - sscanf(line,"%*s%lg%lg%lg", &myx, &myy, &myz); + rv = sscanf(line,"%*s%lg%lg%lg", &myx, &myy, &myz); + if (rv != 3) + error->one("Dump file is incorrectly formatted"); // XXX: we could insert an element2type translation here // XXX: for now we flag unrecognized types as type 0, -- GitLab From 1de00aaab0baf227c49bb7e7bc33ab5f559416cf Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Fri, 19 Jul 2019 11:16:41 -0400 Subject: [PATCH 277/469] improve parsing of data file header the header lines are now checked using regular expressions instead of strstr() which allows for stricter checking, but also is more forgiving in terms of extra or different whitespace return value of sscanf() calls is checked and on failure LAMMPS errors out --- src/read_data.cpp | 132 +++++++++++++++++++++++++++++++++------------- 1 file changed, 94 insertions(+), 38 deletions(-) diff --git a/src/read_data.cpp b/src/read_data.cpp index e70a526c38..989f989269 100644 --- a/src/read_data.cpp +++ b/src/read_data.cpp @@ -45,6 +45,7 @@ #include "irregular.h" #include "error.h" #include "memory.h" +#include "utils.h" using namespace LAMMPS_NS; @@ -999,74 +1000,115 @@ void ReadData::header(int firstpass) // customize for new header lines // check for triangles before angles so "triangles" not matched as "angles" int extra_flag_value = 0; + int rv; - if (strstr(line,"atoms")) { - sscanf(line,BIGINT_FORMAT,&natoms); + if (utils::strmatch(line,"^\\s*\\d+\\s+atoms\\s")) { + rv = sscanf(line,BIGINT_FORMAT,&natoms); + if (rv != 1) + error->all(FLERR,"Could not parse 'atoms' line in data file header"); if (addflag == NONE) atom->natoms = natoms; else if (firstpass) atom->natoms += natoms; - } else if (strstr(line,"ellipsoids")) { + } else if (utils::strmatch(line,"^\\s*\\d+\\s+ellipsoids\\s")) { if (!avec_ellipsoid) error->all(FLERR,"No ellipsoids allowed with this atom style"); - sscanf(line,BIGINT_FORMAT,&nellipsoids); + rv = sscanf(line,BIGINT_FORMAT,&nellipsoids); + if (rv != 1) + error->all(FLERR,"Could not parse 'ellipsoids' line in data file header"); if (addflag == NONE) atom->nellipsoids = nellipsoids; else if (firstpass) atom->nellipsoids += nellipsoids; - } else if (strstr(line,"lines")) { + } else if (utils::strmatch(line,"^\\s*\\d+\\s+lines\\s")) { if (!avec_line) error->all(FLERR,"No lines allowed with this atom style"); - sscanf(line,BIGINT_FORMAT,&nlines); + rv = sscanf(line,BIGINT_FORMAT,&nlines); + if (rv != 1) + error->all(FLERR,"Could not parse 'lines' line in data file header"); if (addflag == NONE) atom->nlines = nlines; else if (firstpass) atom->nlines += nlines; - } else if (strstr(line,"triangles")) { + } else if (utils::strmatch(line,"^\\s*\\d+\\s+triangles\\s")) { if (!avec_tri) error->all(FLERR,"No triangles allowed with this atom style"); - sscanf(line,BIGINT_FORMAT,&ntris); + rv = sscanf(line,BIGINT_FORMAT,&ntris); + if (rv != 1) + error->all(FLERR,"Could not parse 'triangles' line in data file header"); if (addflag == NONE) atom->ntris = ntris; else if (firstpass) atom->ntris += ntris; - } else if (strstr(line,"bodies")) { + } else if (utils::strmatch(line,"^\\s*\\d+\\s+bodies\\s")) { if (!avec_body) error->all(FLERR,"No bodies allowed with this atom style"); - sscanf(line,BIGINT_FORMAT,&nbodies); + rv = sscanf(line,BIGINT_FORMAT,&nbodies); + if (rv != 1) + error->all(FLERR,"Could not parse 'bodies' line in data file header"); if (addflag == NONE) atom->nbodies = nbodies; else if (firstpass) atom->nbodies += nbodies; - } else if (strstr(line,"bonds")) { - sscanf(line,BIGINT_FORMAT,&nbonds); + } else if (utils::strmatch(line,"^\\s*\\d+\\s+bonds\\s")) { + rv = sscanf(line,BIGINT_FORMAT,&nbonds); + if (rv != 1) + error->all(FLERR,"Could not parse 'bonds' line in data file header"); if (addflag == NONE) atom->nbonds = nbonds; else if (firstpass) atom->nbonds += nbonds; - } else if (strstr(line,"angles")) { - sscanf(line,BIGINT_FORMAT,&nangles); + + } else if (utils::strmatch(line,"^\\s*\\d+\\s+angles\\s")) { + rv = sscanf(line,BIGINT_FORMAT,&nangles); + if (rv != 1) + error->all(FLERR,"Could not parse 'angles' line in data file header"); if (addflag == NONE) atom->nangles = nangles; else if (firstpass) atom->nangles += nangles; - } else if (strstr(line,"dihedrals")) { - sscanf(line,BIGINT_FORMAT,&ndihedrals); + + } else if (utils::strmatch(line,"^\\s*\\d+\\s+dihedrals\\s")) { + rv = sscanf(line,BIGINT_FORMAT,&ndihedrals); + if (rv != 1) + error->all(FLERR,"Could not parse 'dihedrals' line in data file header"); if (addflag == NONE) atom->ndihedrals = ndihedrals; else if (firstpass) atom->ndihedrals += ndihedrals; - } else if (strstr(line,"impropers")) { - sscanf(line,BIGINT_FORMAT,&nimpropers); + + } else if (utils::strmatch(line,"^\\s*\\d+\\s+impropers\\s")) { + rv = sscanf(line,BIGINT_FORMAT,&nimpropers); + if (rv != 1) + error->all(FLERR,"Could not parse 'impropers' line in data file header"); if (addflag == NONE) atom->nimpropers = nimpropers; else if (firstpass) atom->nimpropers += nimpropers; // Atom class type settings are only set by first data file - } else if (strstr(line,"atom types")) { - sscanf(line,"%d",&ntypes); + } else if (utils::strmatch(line,"^\\s*\\d+\\s+atom\\s+types\\s")) { + rv = sscanf(line,"%d",&ntypes); + if (rv != 1) + error->all(FLERR,"Could not parse 'atom types' line " + "in data file header"); if (addflag == NONE) atom->ntypes = ntypes + extra_atom_types; - } else if (strstr(line,"bond types")) { - sscanf(line,"%d",&nbondtypes); + + } else if (utils::strmatch(line,"\\s*\\d+\\s+bond\\s+types\\s")) { + rv = sscanf(line,"%d",&nbondtypes); + if (rv != 1) + error->all(FLERR,"Could not parse 'bond types' line " + "in data file header"); if (addflag == NONE) atom->nbondtypes = nbondtypes + extra_bond_types; - } else if (strstr(line,"angle types")) { - sscanf(line,"%d",&nangletypes); + + } else if (utils::strmatch(line,"^\\s*\\d+\\s+angle\\s+types\\s")) { + rv = sscanf(line,"%d",&nangletypes); + if (rv != 1) + error->all(FLERR,"Could not parse 'angle types' line " + "in data file header"); if (addflag == NONE) atom->nangletypes = nangletypes + extra_angle_types; - } else if (strstr(line,"dihedral types")) { - sscanf(line,"%d",&ndihedraltypes); + + } else if (utils::strmatch(line,"^\\s*\\d+\\s+dihedral\\s+types\\s")) { + rv = sscanf(line,"%d",&ndihedraltypes); + if (rv != 1) + error->all(FLERR,"Could not parse 'dihedral types' line " + "in data file header"); if (addflag == NONE) atom->ndihedraltypes = ndihedraltypes + extra_dihedral_types; - } else if (strstr(line,"improper types")) { - sscanf(line,"%d",&nimpropertypes); + + } else if (utils::strmatch(line,"^\\s*\\d+\\s+improper\\s+types\\s")) { + rv = sscanf(line,"%d",&nimpropertypes); + if (rv != 1) + error->all(FLERR,"Could not parse 'improper types' line " + "in data file header"); if (addflag == NONE) atom->nimpropertypes = nimpropertypes + extra_improper_types; @@ -1095,15 +1137,27 @@ void ReadData::header(int firstpass) // local copy of box info // so can treat differently for first vs subsequent data files - } else if (strstr(line,"xlo xhi")) { - sscanf(line,"%lg %lg",&boxlo[0],&boxhi[0]); - } else if (strstr(line,"ylo yhi")) { - sscanf(line,"%lg %lg",&boxlo[1],&boxhi[1]); - } else if (strstr(line,"zlo zhi")) { - sscanf(line,"%lg %lg",&boxlo[2],&boxhi[2]); - } else if (strstr(line,"xy xz yz")) { + } else if (utils::strmatch(line,"^\\s*\\f+\\s+\\f+\\s+xlo\\s+xhi\\s")) { + rv = sscanf(line,"%lg %lg",&boxlo[0],&boxhi[0]); + if (rv != 2) + error->all(FLERR,"Could not parse 'xlo xhi' line in data file header"); + + } else if (utils::strmatch(line,"^\\s*\\f+\\s+\\f+\\s+ylo\\s+yhi\\s")) { + rv = sscanf(line,"%lg %lg",&boxlo[1],&boxhi[1]); + if (rv != 2) + error->all(FLERR,"Could not parse 'ylo yhi' line in data file header"); + + } else if (utils::strmatch(line,"^\\s*\\f+\\s+\\f+\\s+zlo\\s+zhi\\s")) { + rv = sscanf(line,"%lg %lg",&boxlo[2],&boxhi[2]); + if (rv != 2) + error->all(FLERR,"Could not parse 'zlo zhi' line in data file header"); + + } else if (utils::strmatch(line,"^\\s*\\f+\\s+\\f+\\s+\\f+" + "\\s+xy\\s+xz\\s+yz\\s")) { triclinic = 1; - sscanf(line,"%lg %lg %lg",&xy,&xz,&yz); + rv = sscanf(line,"%lg %lg %lg",&xy,&xz,&yz); + if (rv != 3) + error->all(FLERR,"Could not parse 'xy xz yz' line in data file header"); } else break; } @@ -1638,7 +1692,7 @@ void ReadData::bonus(bigint nbonus, AtomVec *ptr, const char *type) void ReadData::bodies(int firstpass) { - int m,nchunk,nline,nmax,ninteger,ndouble,nword,ncount,onebody,tmp; + int m,nchunk,nline,nmax,ninteger,ndouble,nword,ncount,onebody,tmp,rv; char *eof; int mapflag = 0; @@ -1666,7 +1720,9 @@ void ReadData::bodies(int firstpass) while (nchunk < nmax && nline <= CHUNK-MAXBODY) { eof = fgets(&buffer[m],MAXLINE,fp); if (eof == NULL) error->one(FLERR,"Unexpected end of data file"); - sscanf(&buffer[m],"%d %d %d",&tmp,&ninteger,&ndouble); + rv = sscanf(&buffer[m],"%d %d %d",&tmp,&ninteger,&ndouble); + if (rv != 3) + error->one(FLERR,"Incorrect format in Bodies section of data file"); m += strlen(&buffer[m]); // read lines one at a time into buffer and count words -- GitLab From d730ef5b19dfe7b14327ddb9a0733f49c04baf4b Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Fri, 19 Jul 2019 11:31:45 -0400 Subject: [PATCH 278/469] fix typo --- src/reader_xyz.cpp | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/reader_xyz.cpp b/src/reader_xyz.cpp index 040eb9d460..19f0ff2135 100644 --- a/src/reader_xyz.cpp +++ b/src/reader_xyz.cpp @@ -182,7 +182,7 @@ void ReaderXYZ::read_atoms(int n, int nfield, double **fields) ++nid; rv = sscanf(line,"%*s%lg%lg%lg", &myx, &myy, &myz); if (rv != 3) - error->one("Dump file is incorrectly formatted"); + error->one(FLERR,"Dump file is incorrectly formatted"); // XXX: we could insert an element2type translation here // XXX: for now we flag unrecognized types as type 0, -- GitLab From c7bccc5e7a21a53ffc595d1a30979f78f4a15cc4 Mon Sep 17 00:00:00 2001 From: Stan Moore Date: Fri, 19 Jul 2019 09:40:19 -0600 Subject: [PATCH 279/469] Workaround for GCC internal compiler error --- src/KOKKOS/pair_snap_kokkos_impl.h | 20 ++++++++++---------- 1 file changed, 10 insertions(+), 10 deletions(-) diff --git a/src/KOKKOS/pair_snap_kokkos_impl.h b/src/KOKKOS/pair_snap_kokkos_impl.h index 645521a17b..e53332050a 100644 --- a/src/KOKKOS/pair_snap_kokkos_impl.h +++ b/src/KOKKOS/pair_snap_kokkos_impl.h @@ -332,7 +332,7 @@ KOKKOS_INLINE_FUNCTION void PairSNAPKokkos::operator() (TagPairSNAPBeta,const typename Kokkos::TeamPolicy::member_type& team) const { // TODO: use RangePolicy instead, or thread over ncoeff? - const int ii = team.league_rank(); + int ii = team.league_rank(); const int i = d_ilist[ii + chunk_offset]; const int itype = type[i]; const int ielem = d_map[itype]; @@ -437,7 +437,7 @@ template KOKKOS_INLINE_FUNCTION void PairSNAPKokkos::operator() (TagPairSNAPComputeNeigh,const typename Kokkos::TeamPolicy::member_type& team) const { - const int ii = team.league_rank(); + int ii = team.league_rank(); const int i = d_ilist[ii + chunk_offset]; SNAKokkos my_sna = snaKK; const double xtmp = x(i,0); @@ -505,7 +505,7 @@ void PairSNAPKokkos::operator() (TagPairSNAPComputeNeigh,const typen template KOKKOS_INLINE_FUNCTION void PairSNAPKokkos::operator() (TagPairSNAPPreUi,const typename Kokkos::TeamPolicy::member_type& team) const { - const int ii = team.league_rank(); + int ii = team.league_rank(); SNAKokkos my_sna = snaKK; my_sna.pre_ui(team,ii); } @@ -516,7 +516,7 @@ void PairSNAPKokkos::operator() (TagPairSNAPComputeUi,const typename SNAKokkos my_sna = snaKK; // Extract the atom number - const int ii = team.team_rank() + team.team_size() * (team.league_rank() % ((inum+team.team_size()-1)/team.team_size())); + int ii = team.team_rank() + team.team_size() * (team.league_rank() % ((inum+team.team_size()-1)/team.team_size())); if (ii >= inum) return; // Extract the neighbor number @@ -530,7 +530,7 @@ void PairSNAPKokkos::operator() (TagPairSNAPComputeUi,const typename template KOKKOS_INLINE_FUNCTION void PairSNAPKokkos::operator() (TagPairSNAPComputeYi,const typename Kokkos::TeamPolicy::member_type& team) const { - const int ii = team.league_rank(); + int ii = team.league_rank(); SNAKokkos my_sna = snaKK; my_sna.compute_yi(team,ii,d_beta); } @@ -538,7 +538,7 @@ void PairSNAPKokkos::operator() (TagPairSNAPComputeYi,const typename template KOKKOS_INLINE_FUNCTION void PairSNAPKokkos::operator() (TagPairSNAPComputeZi,const typename Kokkos::TeamPolicy::member_type& team) const { - const int ii = team.league_rank(); + int ii = team.league_rank(); SNAKokkos my_sna = snaKK; my_sna.compute_zi(team,ii); } @@ -546,7 +546,7 @@ void PairSNAPKokkos::operator() (TagPairSNAPComputeZi,const typename template KOKKOS_INLINE_FUNCTION void PairSNAPKokkos::operator() (TagPairSNAPComputeBi,const typename Kokkos::TeamPolicy::member_type& team) const { - const int ii = team.league_rank(); + int ii = team.league_rank(); SNAKokkos my_sna = snaKK; my_sna.compute_bi(team,ii); } @@ -557,7 +557,7 @@ void PairSNAPKokkos::operator() (TagPairSNAPComputeDuidrj,const type SNAKokkos my_sna = snaKK; // Extract the atom number - const int ii = team.team_rank() + team.team_size() * (team.league_rank() % ((inum+team.team_size()-1)/team.team_size())); + int ii = team.team_rank() + team.team_size() * (team.league_rank() % ((inum+team.team_size()-1)/team.team_size())); if (ii >= inum) return; // Extract the neighbor number @@ -574,7 +574,7 @@ void PairSNAPKokkos::operator() (TagPairSNAPComputeDeidrj,const type SNAKokkos my_sna = snaKK; // Extract the atom number - const int ii = team.team_rank() + team.team_size() * (team.league_rank() % ((inum+team.team_size()-1)/team.team_size())); + int ii = team.team_rank() + team.team_size() * (team.league_rank() % ((inum+team.team_size()-1)/team.team_size())); if (ii >= inum) return; // Extract the neighbor number @@ -595,7 +595,7 @@ void PairSNAPKokkos::operator() (TagPairSNAPComputeForce::value,decltype(dup_f),decltype(ndup_f)>::get(dup_f,ndup_f); auto a_f = v_f.template access::value>(); - const int ii = team.league_rank(); + int ii = team.league_rank(); const int i = d_ilist[ii + chunk_offset]; SNAKokkos my_sna = snaKK; const int ninside = d_ninside(ii); -- GitLab From e72aef2a9621118f7662f53be37a226037669d30 Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Fri, 19 Jul 2019 12:01:16 -0400 Subject: [PATCH 280/469] more sscanf() return value checking --- src/procmap.cpp | 9 ++++++--- src/universe.cpp | 10 +++++----- src/variable.cpp | 4 ++-- 3 files changed, 13 insertions(+), 10 deletions(-) diff --git a/src/procmap.cpp b/src/procmap.cpp index 9d1ed83e73..8207b61f4c 100644 --- a/src/procmap.cpp +++ b/src/procmap.cpp @@ -301,7 +301,8 @@ void ProcMap::custom_grid(char *cfile, int nprocs, MPI_Bcast(&n,1,MPI_INT,0,world); MPI_Bcast(line,n,MPI_CHAR,0,world); - sscanf(line,"%d %d %d",&procgrid[0],&procgrid[1],&procgrid[2]); + int rv = sscanf(line,"%d %d %d",&procgrid[0],&procgrid[1],&procgrid[2]); + if (rv != 3) error->all(FLERR,"Processors custom grid file is inconsistent"); int flag = 0; if (procgrid[0]*procgrid[1]*procgrid[2] != nprocs) flag = 1; @@ -320,8 +321,10 @@ void ProcMap::custom_grid(char *cfile, int nprocs, for (int i = 0; i < nprocs; i++) { if (!fgets(line,MAXLINE,fp)) error->one(FLERR,"Unexpected end of custom file"); - sscanf(line,"%d %d %d %d", - &cmap[i][0],&cmap[i][1],&cmap[i][2],&cmap[i][3]); + rv = sscanf(line,"%d %d %d %d", + &cmap[i][0],&cmap[i][1],&cmap[i][2],&cmap[i][3]); + if (rv != 4) + error->one(FLERR,"Processors custom grid file is inconsistent"); } fclose(fp); } diff --git a/src/universe.cpp b/src/universe.cpp index f078590103..dba31f8b76 100644 --- a/src/universe.cpp +++ b/src/universe.cpp @@ -114,19 +114,19 @@ void Universe::reorder(char *style, char *arg) // read nprocs lines // uni2orig = inverse mapping - int me_orig,me_new; - sscanf(line,"%d %d",&me_orig,&me_new); + int me_orig,me_new,rv; + rv = sscanf(line,"%d %d",&me_orig,&me_new); if (me_orig < 0 || me_orig >= nprocs || - me_new < 0 || me_new >= nprocs) + me_new < 0 || me_new >= nprocs || rv != 2) error->one(FLERR,"Invalid entry in -reorder file"); uni2orig[me_new] = me_orig; for (int i = 1; i < nprocs; i++) { if (!fgets(line,MAXLINE,fp)) error->one(FLERR,"Unexpected end of -reorder file"); - sscanf(line,"%d %d",&me_orig,&me_new); + rv = sscanf(line,"%d %d",&me_orig,&me_new); if (me_orig < 0 || me_orig >= nprocs || - me_new < 0 || me_new >= nprocs) + me_new < 0 || me_new >= nprocs || rv != 2) error->one(FLERR,"Invalid entry in -reorder file"); uni2orig[me_new] = me_orig; } diff --git a/src/variable.cpp b/src/variable.cpp index ea7f3044d7..63a425bcf5 100644 --- a/src/variable.cpp +++ b/src/variable.cpp @@ -5162,8 +5162,8 @@ int VarReader::read_peratom() for (i = 0; i < nchunk; i++) { next = strchr(buf,'\n'); *next = '\0'; - sscanf(buf,TAGINT_FORMAT " %lg",&tag,&value); - if (tag <= 0 || tag > map_tag_max) + int rv = sscanf(buf,TAGINT_FORMAT " %lg",&tag,&value); + if (tag <= 0 || tag > map_tag_max || rv != 2) error->one(FLERR,"Invalid atom ID in variable file"); if ((m = atom->map(tag)) >= 0) vstore[m] = value; buf = next + 1; -- GitLab From 276e3b2df10e5f3ea160986f090651182b56aa5d Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Fri, 19 Jul 2019 14:00:24 -0400 Subject: [PATCH 281/469] update fix tmd input similar to read_data --- src/fix_tmd.cpp | 32 +++++++++++++++++++------------- 1 file changed, 19 insertions(+), 13 deletions(-) diff --git a/src/fix_tmd.cpp b/src/fix_tmd.cpp index 4cbb244bc0..10315a750d 100644 --- a/src/fix_tmd.cpp +++ b/src/fix_tmd.cpp @@ -30,6 +30,7 @@ #include "force.h" #include "memory.h" #include "error.h" +#include "utils.h" using namespace LAMMPS_NS; using namespace FixConst; @@ -164,7 +165,7 @@ void FixTMD::init() dtv = update->dt; dtf = update->dt * force->ftm2v; - if (strstr(update->integrate_style,"respa")) + if (utils::strmatch(update->integrate_style,"^respa")) step_respa = ((Respa *) update->integrate)->step; } @@ -423,21 +424,27 @@ void FixTMD::readfile(char *file) *next = '\0'; if (firstline) { - if (strstr(bufptr,"xlo xhi")) { + if (utils::strmatch(bufptr,"^\\s*\\f+\\s+\\f+\\s+xlo\\s+xhi")) { double lo,hi; - sscanf(bufptr,"%lg %lg",&lo,&hi); + n = sscanf(bufptr,"%lg %lg",&lo,&hi); + if (n != 2) + error->all(FLERR,"Incorrect format in TMD target file"); xprd = hi - lo; bufptr = next + 1; continue; - } else if (strstr(bufptr,"ylo yhi")) { + } else if (utils::strmatch(bufptr,"^\\s*\\f+\\s+\\f+\\s+ylo\\s+yhi")) { double lo,hi; - sscanf(bufptr,"%lg %lg",&lo,&hi); + n = sscanf(bufptr,"%lg %lg",&lo,&hi); + if (n != 2) + error->all(FLERR,"Incorrect format in TMD target file"); yprd = hi - lo; bufptr = next + 1; continue; - } else if (strstr(bufptr,"zlo zhi")) { + } else if (utils::strmatch(bufptr,"^\\s*\\f+\\s+\\f+\\s+zlo\\s+zhi")) { double lo,hi; - sscanf(bufptr,"%lg %lg",&lo,&hi); + n = sscanf(bufptr,"%lg %lg",&lo,&hi); + if (n != 2) + error->all(FLERR,"Incorrect format in TMD target file"); zprd = hi - lo; bufptr = next + 1; continue; @@ -455,14 +462,13 @@ void FixTMD::readfile(char *file) } if (imageflag) - n = sscanf(bufptr,TAGINT_FORMAT " %lg %lg %lg %d %d %d", - &itag,&x,&y,&z,&ix,&iy,&iz); + n = 7 - sscanf(bufptr,TAGINT_FORMAT " %lg %lg %lg %d %d %d", + &itag,&x,&y,&z,&ix,&iy,&iz); else - n = sscanf(bufptr,TAGINT_FORMAT " %lg %lg %lg",&itag,&x,&y,&z); + n = 4 - sscanf(bufptr,TAGINT_FORMAT " %lg %lg %lg",&itag,&x,&y,&z); - if (n < 0) { - if (me == 0) error->warning(FLERR,"Ignoring empty or incorrectly" - " formatted line in target file"); + if (n != 0) { + error->all(FLERR,"Incorrectly formatted line in TMD target file"); bufptr = next + 1; continue; } -- GitLab From 502fbfb78a76b2e77b3ff32d7807deb29631ad64 Mon Sep 17 00:00:00 2001 From: Stan Moore Date: Fri, 19 Jul 2019 15:20:22 -0600 Subject: [PATCH 282/469] Fix memory issue --- src/KOKKOS/pair_snap_kokkos_impl.h | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/KOKKOS/pair_snap_kokkos_impl.h b/src/KOKKOS/pair_snap_kokkos_impl.h index e53332050a..95afcc5ec7 100644 --- a/src/KOKKOS/pair_snap_kokkos_impl.h +++ b/src/KOKKOS/pair_snap_kokkos_impl.h @@ -208,7 +208,7 @@ void PairSNAPKokkos::compute(int eflag_in, int vflag_in) d_ninside = Kokkos::View("PairSNAPKokkos:ninside",inum); } - int chunk_size = 2000; + int chunk_size = MIN(2000,inum); chunk_offset = 0; snaKK.grow_rij(chunk_size,max_neighs); -- GitLab From 9239c9dedb0563aa00ffe12d08d54a44c574af47 Mon Sep 17 00:00:00 2001 From: Adrian-Diaz Date: Fri, 19 Jul 2019 17:13:44 -0600 Subject: [PATCH 283/469] patch niche rcb issue --- src/rcb.cpp | 32 ++++++++++++++++++++++++++++++++ 1 file changed, 32 insertions(+) diff --git a/src/rcb.cpp b/src/rcb.cpp index 83cdccdf80..ac7ac60b1f 100644 --- a/src/rcb.cpp +++ b/src/rcb.cpp @@ -467,6 +467,38 @@ void RCB::compute(int dimension, int n, double **x, double *wt, } } + //check if zero box width is the result due to dots being on box vertices + //select half of the box in this case along the best dim + //the best dim is chosen according to the optimum volume (to minimize surface area) + + if(largest==0.0){ + double best_volume=0; + double current_volume; + int dim1o,dim2o; + for (dim = 0; dim < dimension; dim++){ + if(dim==0){ + dim1o=1; + dim2o=2; + } + if(dim==1){ + dim1o=0; + dim2o=2; + } + if(dim==2){ + dim1o=0; + dim2o=1; + } + valuehalf = 0.5*(lo[dim] + hi[dim]); + current_volume = (hi[dim1o]-lo[dim1o]) + *(hi[dim2o]-lo[dim2o])*(valuehalf-lo[dim]); + //chose cut that minimizes surface area by maximizing volume; + if(current_volume>best_volume){ best_volume = current_volume; + valuehalf_select = valuehalf; + dim_select = dim; + } + } + } + // copy results for best dim cut into dim,valuehalf,dotmark dim = dim_select; -- GitLab From f2978475afd78e28232289b19b7bd7b1fbe2d7a2 Mon Sep 17 00:00:00 2001 From: "Ryan S. Elliott" Date: Sun, 21 Jul 2019 15:17:53 -0500 Subject: [PATCH 284/469] Update docs * bring homebrew install notes up-to-date * update openkim docs --- doc/src/Build_extras.txt | 18 ++++++---------- doc/src/Examples.txt | 4 +++- doc/src/Install_mac.txt | 43 +++++++++++++------------------------- doc/src/Intro_features.txt | 4 ++-- doc/src/fix_adapt.txt | 3 +-- doc/src/kim_commands.txt | 3 +++ 6 files changed, 30 insertions(+), 45 deletions(-) diff --git a/doc/src/Build_extras.txt b/doc/src/Build_extras.txt index 1d9a7abfcf..e6791de21b 100644 --- a/doc/src/Build_extras.txt +++ b/doc/src/Build_extras.txt @@ -176,19 +176,13 @@ use with LAMMPS. If you want to use the "kim_query"_kim_commands.html command, you also need to have libcurl installed with the matching development headers and the curl-config tool. -Note that in LAMMPS jargon, a KIM model driver is a pair style -(e.g. EAM or Tersoff). A KIM model is a pair style for a particular -element or alloy and set of parameters, e.g. EAM for Cu with a -specific EAM potential file. Also note that when downloading and -installing from source -the KIM API library with all its models, may take a long time (tens of -minutes to hours) to build. Of course you only need to do that once. - -See the list of KIM model drivers here: -https://openkim.org/browse/model-drivers/alphabetical +See "Obtaining KIM Models"_http://openkim.org/doc/usage/obtaining-models to +learn how to install a pre-build binary of the OpenKIM Repository of Models. +See the list of all KIM models here: https://openkim.org/browse/models -See the list of all KIM models here: -https://openkim.org/browse/models/by-model-drivers +(Also note that when downloading and installing from source +the KIM API library with all its models, may take a long time (tens of +minutes to hours) to build. Of course you only need to do that once.) [CMake build]: diff --git a/doc/src/Examples.txt b/doc/src/Examples.txt index fcf01de383..36d0ac86f9 100644 --- a/doc/src/Examples.txt +++ b/doc/src/Examples.txt @@ -73,7 +73,7 @@ granregion: use of fix wall/region/gran as boundary on granular particles hugoniostat: Hugoniostat shock dynamics hyper: global and local hyperdynamics of diffusion on Pt surface indent: spherical indenter into a 2d solid -kim: use of potentials in Knowledge Base for Interatomic Models (KIM) +kim: use of potentials from the "OpenKIM Repository"_openkim latte: examples for using fix latte for DFTB via the LATTE library meam: MEAM test for SiC and shear (same as shear examples) melt: rapid melt of 3d LJ system @@ -153,3 +153,5 @@ illustrate how to use the command(s) provided in that package. Many of the sub-directories have their own README files which give further instructions. See the "Packages_details"_Packages_details.html doc page for more info on specific USER packages. + +:link(openkim,https://openkim.org) diff --git a/doc/src/Install_mac.txt b/doc/src/Install_mac.txt index 3ab119522c..e277f7e0e4 100644 --- a/doc/src/Install_mac.txt +++ b/doc/src/Install_mac.txt @@ -10,47 +10,34 @@ Documentation"_ld - "LAMMPS Commands"_lc :c Download an executable for Mac :h3 LAMMPS can be downloaded, built, and configured for OS X on a Mac with -"Homebrew"_homebrew. Only four of the LAMMPS packages are unavailable -at this time because of additional needs not yet met: KIM, GPU, -USER-INTEL, USER-ATC. +"Homebrew"_homebrew. The following LAMMPS packages are unavailable at this +time because of additional needs not yet met: GPU, KOKKOS, LATTE, MSCG, +MESSAGE, MPIIO POEMS VORONOI. After installing Homebrew, you can install LAMMPS on your system with the following commands: -% brew tap homebrew/science -% brew install lammps # serial version -% brew install lammps --with-mpi # mpi support :pre +% brew install lammps :pre -This will install the executable "lammps", a python module named -"lammps", and additional resources with all the standard packages. To -get the location of the additional resources type this: - -% brew info lammps :pre - -This command also tells you additional installation options available. -The user-packages are available as options, just install them like -this example for the USER-OMP package: - -% brew install lammps --enable-user-omp :pre - -It is usually best to install LAMMPS with the most up to date source -files, which can be done with the "--HEAD" option: - -% brew install lammps --HEAD :pre - -To re-install the LAMMPS HEAD, run this command occasionally (make sure -to use the desired options). - -% brew install --force lammps --HEAD $\{options\} :pre +This will install the executables "lammps_serial" and "lammps_mpi", as well as +the LAMMPS "doc", "potentials", "tools", "bench", and "examples" directories. Once LAMMPS is installed, you can test the installation with the Lennard-Jones benchmark file: % brew test lammps -v :pre +The LAMMPS binary is built with the "KIM package"_Build_extras#kim which +results in homebrew also installing the `kim-api` binaries when LAMMPS is +installed. In order to use potentials from "openkim.org"_openkim, you can +install the `openkim-models` package + +% brew install openkim-models :pre + If you have problems with the installation you can post issues to "this link"_homebrew. Thanks to Derek Thomas (derekt at cello.t.u-tokyo.ac.jp) for setting up the Homebrew capability. -:link(homebrew,https://github.com/Homebrew/homebrew-science/issues) +:link(homebrew,https://github.com/Homebrew/homebrew-core/issues) +:link(openkim,https://openkim.org) diff --git a/doc/src/Intro_features.txt b/doc/src/Intro_features.txt index 629e8210b7..d133fd8064 100644 --- a/doc/src/Intro_features.txt +++ b/doc/src/Intro_features.txt @@ -92,8 +92,8 @@ commands) implicit solvent potentials: hydrodynamic lubrication, Debye force-field compatibility with common CHARMM, AMBER, DREIDING, \ OPLS, GROMACS, COMPASS options - access to "KIM archive"_http://openkim.org of potentials via \ - "pair kim"_pair_kim.html + access to the "OpenKIM Repository"_http://openkim.org of potentials via \ + "kim_init, kim_interactions, and kim_query"_kim_commands.html commands hybrid potentials: multiple pair, bond, angle, dihedral, improper \ potentials can be used in one simulation overlaid potentials: superposition of multiple pair potentials :ul diff --git a/doc/src/fix_adapt.txt b/doc/src/fix_adapt.txt index 0d862a890d..4f047ec42d 100644 --- a/doc/src/fix_adapt.txt +++ b/doc/src/fix_adapt.txt @@ -149,8 +149,7 @@ meaning of these parameters: "spin/neel"_pair_spin_neel.html: coulombic_cutoff: type global: "table"_pair_table.html: table_cutoff: type pairs: "ufm"_pair_ufm.html: epsilon,sigma: type pairs: -"soft"_pair_soft.html: a: type pairs: -"kim"_pair_kim.html: PARAM_FREE_*:i,j,...: global :tb(c=3,s=:) +"soft"_pair_soft.html: a: type pairs: :tb(c=3,s=:) NOTE: It is easy to add new pairwise potentials and their parameters to this list. All it typically takes is adding an extract() method to diff --git a/doc/src/kim_commands.txt b/doc/src/kim_commands.txt index 7c88fd084a..169f96e6e8 100644 --- a/doc/src/kim_commands.txt +++ b/doc/src/kim_commands.txt @@ -116,6 +116,9 @@ See the "current list of KIM PMs and SMs archived in OpenKIM"_https://openkim.or This list is sorted by species and can be filtered to display only IMs for certain species combinations. +See "Obtaining KIM Models"_http://openkim.org/doc/usage/obtaining-models to +learn how to install a pre-build binary of the OpenKIM Repository of Models. + NOTE: It is also possible to locally install IMs not archived in OpenKIM, in which case their names do not have to conform to the KIM ID format. -- GitLab From c831cee21dad5e5009960498930e0543f692c2a2 Mon Sep 17 00:00:00 2001 From: Rupert Nash Date: Mon, 22 Jul 2019 09:46:01 +0100 Subject: [PATCH 285/469] Fix typos in documentation --- doc/src/compute_momentum.txt | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/doc/src/compute_momentum.txt b/doc/src/compute_momentum.txt index fc5243583e..2c6ec78cf3 100644 --- a/doc/src/compute_momentum.txt +++ b/doc/src/compute_momentum.txt @@ -29,7 +29,7 @@ the mass and velocity of the particle. [Output info:] -This compute calculates a global vector (the summed momentum) on +This compute calculates a global vector (the summed momentum) of length 3. This value can be used by any command that uses a global vector value from a compute as input. See the "Howto output"_Howto_output.html doc page for an overview of LAMMPS output -- GitLab From f5beb418e8e983d6eb32908cb1da18168b0820ca Mon Sep 17 00:00:00 2001 From: Ellad Tadmor Date: Mon, 22 Jul 2019 10:54:53 -0500 Subject: [PATCH 286/469] Put in KIM ID for IFF model in kim_commands usage examples --- doc/src/kim_commands.txt | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/doc/src/kim_commands.txt b/doc/src/kim_commands.txt index 7c88fd084a..dbe0608b5e 100644 --- a/doc/src/kim_commands.txt +++ b/doc/src/kim_commands.txt @@ -33,7 +33,7 @@ kim_interactions Si kim_init Sim_LAMMPS_ReaxFF_StrachanVanDuinChakraborty_2003_CHNO__SM_107643900657_000 real kim_init Sim_LAMMPS_ReaxFF_StrachanVanDuinChakraborty_2003_CHNO__SM_107643900657_000 metal unit_conversion_mode kim_interactions C H O -kim_init Sim_LAMMPS_IFF_OtherInfo_AuthorList_Year_Species__SM_064312669787_000 real +Sim_LAMMPS_IFF_PCFF_HeinzMishraLinEmami_2015Ver1v5_FccmetalsMineralsSolvents Polymers__SM_064312669787_000 real kim_interactions fixed_types kim_query a0 get_lattice_constant_cubic crystal=\["fcc"\] species=\["Al"\] units=\["angstrom"\] :pre -- GitLab From 320be3bcef1b9e08a9a6c4b184fe6b1f687509da Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Mon, 22 Jul 2019 14:22:36 -0400 Subject: [PATCH 287/469] undo changes to poems library and package as they fail regression testing --- lib/poems/POEMSChain.h | 99 +++--- lib/poems/SystemProcessor.h | 439 ++++++++++++----------- lib/poems/body.cpp | 15 +- lib/poems/body.h | 23 +- lib/poems/body23joint.cpp | 17 +- lib/poems/body23joint.h | 9 +- lib/poems/colmatmap.cpp | 2 - lib/poems/colmatmap.h | 6 +- lib/poems/colmatrix.cpp | 5 +- lib/poems/colmatrix.h | 45 ++- lib/poems/defines.h | 7 +- lib/poems/eulerparameters.cpp | 46 ++- lib/poems/eulerparameters.h | 9 +- lib/poems/fastmatrixops.cpp | 143 ++++---- lib/poems/fastmatrixops.h | 17 +- lib/poems/fixedpoint.cpp | 5 - lib/poems/fixedpoint.h | 5 +- lib/poems/freebodyjoint.cpp | 136 ++++--- lib/poems/freebodyjoint.h | 11 +- lib/poems/inertialframe.cpp | 6 +- lib/poems/inertialframe.h | 7 +- lib/poems/joint.cpp | 23 +- lib/poems/joint.h | 12 +- lib/poems/mat3x3.cpp | 5 +- lib/poems/mat3x3.h | 17 +- lib/poems/mat4x4.cpp | 4 - lib/poems/mat4x4.h | 15 +- lib/poems/mat6x6.cpp | 4 - lib/poems/mat6x6.h | 6 +- lib/poems/matrices.h | 13 +- lib/poems/matrix.cpp | 2 - lib/poems/matrix.h | 10 +- lib/poems/matrixfun.cpp | 58 ++- lib/poems/matrixfun.h | 35 +- lib/poems/mixedjoint.cpp | 141 ++++---- lib/poems/mixedjoint.h | 16 +- lib/poems/norm.cpp | 8 - lib/poems/norm.h | 14 +- lib/poems/onbody.cpp | 9 +- lib/poems/onbody.h | 118 +++--- lib/poems/onfunctions.cpp | 49 ++- lib/poems/onfunctions.h | 8 +- lib/poems/onsolver.cpp | 16 +- lib/poems/onsolver.h | 51 ++- lib/poems/particle.cpp | 3 +- lib/poems/particle.h | 12 +- lib/poems/poemslist.h | 74 ++-- lib/poems/poemsnodelib.h | 11 +- lib/poems/poemsobject.cpp | 2 - lib/poems/poemsobject.h | 4 +- lib/poems/poemstree.h | 4 +- lib/poems/poemstreenode.cpp | 2 - lib/poems/poemstreenode.h | 47 +-- lib/poems/point.cpp | 8 +- lib/poems/point.h | 18 +- lib/poems/prismaticjoint.cpp | 6 - lib/poems/prismaticjoint.h | 9 +- lib/poems/revolutejoint.cpp | 6 - lib/poems/revolutejoint.h | 8 +- lib/poems/rigidbody.cpp | 5 +- lib/poems/rigidbody.h | 5 +- lib/poems/rowmatrix.cpp | 4 +- lib/poems/rowmatrix.h | 6 +- lib/poems/solver.cpp | 5 +- lib/poems/solver.h | 23 +- lib/poems/sphericaljoint.cpp | 206 ++++++----- lib/poems/sphericaljoint.h | 9 +- lib/poems/system.cpp | 632 ++++++++++++++++----------------- lib/poems/system.h | 58 ++- lib/poems/vect3.cpp | 11 - lib/poems/vect3.h | 12 +- lib/poems/vect4.cpp | 4 - lib/poems/vect4.h | 13 +- lib/poems/vect6.cpp | 4 - lib/poems/vect6.h | 6 +- lib/poems/virtualcolmatrix.cpp | 2 - lib/poems/virtualcolmatrix.h | 40 +-- lib/poems/virtualmatrix.cpp | 6 +- lib/poems/virtualmatrix.h | 3 +- lib/poems/virtualrowmatrix.cpp | 2 - lib/poems/virtualrowmatrix.h | 11 +- lib/poems/workspace.cpp | 21 +- lib/poems/workspace.h | 78 ++-- src/POEMS/fix_poems.cpp | 2 +- src/POEMS/fix_poems.h | 3 +- 85 files changed, 1407 insertions(+), 1664 deletions(-) diff --git a/lib/poems/POEMSChain.h b/lib/poems/POEMSChain.h index 8baa293dbd..9f0db59333 100644 --- a/lib/poems/POEMSChain.h +++ b/lib/poems/POEMSChain.h @@ -3,7 +3,7 @@ * POEMS: PARALLELIZABLE OPEN SOURCE EFFICIENT MULTIBODY SOFTWARE * * DESCRIPTION: SEE READ-ME * * FILE NAME: PoemsChain.h * - * AUTHORS: See Author List * + * AUTHORS: See Author List * * GRANTS: See Grants List * * COPYRIGHT: (C) 2005 by Authors as listed in Author's List * * LICENSE: Please see License Agreement * @@ -11,7 +11,7 @@ * ADMINISTRATOR: Prof. Kurt Anderson * * Computational Dynamics Lab * * Rensselaer Polytechnic Institute * - * 110 8th St. Troy NY 12180 * + * 110 8th St. Troy NY 12180 * * CONTACT: anderk5@rpi.edu * *_________________________________________________________________________*/ @@ -19,59 +19,56 @@ #define POEMSCHAIN_H_ #include "poemslist.h" -#include -namespace POEMS { struct ChildRingData { - List * childRing; - int entranceNodeId; + List * childRing; + int entranceNodeId; }; struct POEMSChain{ - ~POEMSChain(){ - for(int i = 0; i < childChains.GetNumElements(); i++) - { - delete childChains(i); - } - listOfNodes.DeleteValues(); - } - //void printTreeStructure(int tabs); - //void getTreeAsList(List * temp); - List listOfNodes; - List childChains; - POEMSChain * parentChain; - List childRings; - - - void printTreeStructure(int tabs){ - for(int i = 0; i < tabs; i++) - { - std::cout << "\t"; - } - std::cout << "Chain: "; - for(int i = 0; i < listOfNodes.GetNumElements(); i++) - { - std::cout << *(listOfNodes(i)) << " "; - } - std::cout << std::endl; - for(int i = 0; i < childChains.GetNumElements(); i++) - { - childChains(i)->printTreeStructure(tabs + 1); - } - } - void getTreeAsList(List * temp) - { - for(int i = 0; i < listOfNodes.GetNumElements(); i++) - { - int * integer = new int; - *integer = *(listOfNodes(i)); - temp->Append(integer); - } - for(int i = 0; i < childChains.GetNumElements(); i++) - { - childChains(i)->getTreeAsList(temp); - } - } + ~POEMSChain(){ + for(int i = 0; i < childChains.GetNumElements(); i++) + { + delete childChains(i); + } + listOfNodes.DeleteValues(); + } + //void printTreeStructure(int tabs); + //void getTreeAsList(List * temp); + List listOfNodes; + List childChains; + POEMSChain * parentChain; + List childRings; + + + void printTreeStructure(int tabs){ + for(int i = 0; i < tabs; i++) + { + cout << "\t"; + } + cout << "Chain: "; + for(int i = 0; i < listOfNodes.GetNumElements(); i++) + { + cout << *(listOfNodes(i)) << " "; + } + cout << endl; + for(int i = 0; i < childChains.GetNumElements(); i++) + { + childChains(i)->printTreeStructure(tabs + 1); + } + } + void getTreeAsList(List * temp) + { + for(int i = 0; i < listOfNodes.GetNumElements(); i++) + { + int * integer = new int; + *integer = *(listOfNodes(i)); + temp->Append(integer); + } + for(int i = 0; i < childChains.GetNumElements(); i++) + { + childChains(i)->getTreeAsList(temp); + } + } }; -} #endif diff --git a/lib/poems/SystemProcessor.h b/lib/poems/SystemProcessor.h index a6001d96d0..3be168c34d 100644 --- a/lib/poems/SystemProcessor.h +++ b/lib/poems/SystemProcessor.h @@ -3,7 +3,7 @@ * POEMS: PARALLELIZABLE OPEN SOURCE EFFICIENT MULTIBODY SOFTWARE * * DESCRIPTION: SEE READ-ME * * FILE NAME: SystemProcessor.h * - * AUTHORS: See Author List * + * AUTHORS: See Author List * * GRANTS: See Grants List * * COPYRIGHT: (C) 2005 by Authors as listed in Author's List * * LICENSE: Please see License Agreement * @@ -11,61 +11,59 @@ * ADMINISTRATOR: Prof. Kurt Anderson * * Computational Dynamics Lab * * Rensselaer Polytechnic Institute * - * 110 8th St. Troy NY 12180 * + * 110 8th St. Troy NY 12180 * * CONTACT: anderk5@rpi.edu * *_________________________________________________________________________*/ #ifndef _SYS_PROCESSOR_H_ #define _SYS_PROCESSOR_H_ -#include #include "poemslist.h" #include "poemstree.h" #include "POEMSChain.h" -namespace POEMS { struct POEMSNode { - List links; - List taken; - int idNumber; - bool visited; - - ~POEMSNode(){ - for(int i = 0; i < taken.GetNumElements(); i++) - { - delete taken(i); - } - }; + List links; + List taken; + int idNumber; + bool visited; + + ~POEMSNode(){ + for(int i = 0; i < taken.GetNumElements(); i++) + { + delete taken(i); + } + }; }; class SystemProcessor{ private: - Tree nodes; - static void POEMSNodeDelete_cb(void *node) { - delete (POEMSNode *) node; - } - List headsOfSystems; - List > ringsInSystem; - POEMSNode * findSingleLink(TreeNode * aNode); - POEMSChain * AddNewChain(POEMSNode * currentNode); - bool setLinkVisited(POEMSNode * firstNode, POEMSNode * secondNode); + Tree nodes; + static void POEMSNodeDelete_cb(void *node) { + delete (POEMSNode *) node; + } + List headsOfSystems; + List > ringsInSystem; + POEMSNode * findSingleLink(TreeNode * aNode); + POEMSChain * AddNewChain(POEMSNode * currentNode); + bool setLinkVisited(POEMSNode * firstNode, POEMSNode * secondNode); public: - SystemProcessor(void); - - ~SystemProcessor(void) { - headsOfSystems.DeleteValues(); - for(int i = 0; i < ringsInSystem.GetNumElements(); i++) - { - for(int k = 0; k < ringsInSystem(i)->GetNumElements(); i++) - { - delete (*ringsInSystem(i))(k); - } - } - }; - void processArray(int** links, int numLinks); - List * getSystemData(); - int getNumberOfHeadChains(); + SystemProcessor(void); + + ~SystemProcessor(void) { + headsOfSystems.DeleteValues(); + for(int i = 0; i < ringsInSystem.GetNumElements(); i++) + { + for(int k = 0; k < ringsInSystem(i)->GetNumElements(); i++) + { + delete (*ringsInSystem(i))(k); + } + } + }; + void processArray(int** links, int numLinks); + List * getSystemData(); + int getNumberOfHeadChains(); }; SystemProcessor::SystemProcessor(void){ @@ -75,145 +73,145 @@ SystemProcessor::SystemProcessor(void){ void SystemProcessor::processArray(int** links, int numLinks) { - bool * false_var; //holds the value false; needed because a constant cannot be put into a list; the list requires a - //reference. - for(int i = 0; i < numLinks; i++) //go through all the links in the input array - { - if(!nodes.Find(links[i][0])) //if the first node in the pair is not found in the storage tree - { - POEMSNode * newNode = new POEMSNode; //make a new node -// forDeletion.Append(newNode); - newNode->idNumber = links[i][0]; //set its ID to the value - newNode->visited = false; //set it to be unvisited - nodes.Insert(links[i][0], links[i][0], (void *) newNode); //and add it to the tree storage structure - } - if(!nodes.Find(links[i][1])) //repeat process for the other half of each link - { - POEMSNode * newNode = new POEMSNode; -// forDeletion.Append(newNode); - newNode->idNumber = links[i][1]; - newNode->visited = false; - nodes.Insert(links[i][1], links[i][1], (void *) newNode); - } - POEMSNode * firstNode = (POEMSNode *)nodes.Find(links[i][0]); //now that we are sure both nodes exist, - POEMSNode * secondNode = (POEMSNode *)nodes.Find(links[i][1]); //we can get both of them out of the tree - firstNode->links.Append(secondNode); //and add the link from the first to the second... - false_var = new bool; - *false_var = false; //make a new false boolean to note that the link between these two - firstNode->taken.Append(false_var); //has not already been taken, and append it to the taken list - secondNode->links.Append(firstNode); //repeat process for link from second node to first - false_var = new bool; - *false_var = false; - secondNode->taken.Append(false_var); - } - - TreeNode * temp = nodes.GetRoot(); //get the root node of the node storage tree - POEMSNode * currentNode; - do - { - currentNode = findSingleLink(temp); //find the start of the next available chain - if(currentNode != NULL) - { - headsOfSystems.Append(AddNewChain(currentNode)); //and add it to the headsOfSystems list of chains - } - } - while(currentNode != NULL); //repeat this until all chains have been added + bool * false_var; //holds the value false; needed because a constant cannot be put into a list; the list requires a + //reference. + for(int i = 0; i < numLinks; i++) //go through all the links in the input array + { + if(!nodes.Find(links[i][0])) //if the first node in the pair is not found in the storage tree + { + POEMSNode * newNode = new POEMSNode; //make a new node +// forDeletion.Append(newNode); + newNode->idNumber = links[i][0]; //set its ID to the value + newNode->visited = false; //set it to be unvisited + nodes.Insert(links[i][0], links[i][0], (void *) newNode); //and add it to the tree storage structure + } + if(!nodes.Find(links[i][1])) //repeat process for the other half of each link + { + POEMSNode * newNode = new POEMSNode; +// forDeletion.Append(newNode); + newNode->idNumber = links[i][1]; + newNode->visited = false; + nodes.Insert(links[i][1], links[i][1], (void *) newNode); + } + POEMSNode * firstNode = (POEMSNode *)nodes.Find(links[i][0]); //now that we are sure both nodes exist, + POEMSNode * secondNode = (POEMSNode *)nodes.Find(links[i][1]); //we can get both of them out of the tree + firstNode->links.Append(secondNode); //and add the link from the first to the second... + false_var = new bool; + *false_var = false; //make a new false boolean to note that the link between these two + firstNode->taken.Append(false_var); //has not already been taken, and append it to the taken list + secondNode->links.Append(firstNode); //repeat process for link from second node to first + false_var = new bool; + *false_var = false; + secondNode->taken.Append(false_var); + } + + TreeNode * temp = nodes.GetRoot(); //get the root node of the node storage tree + POEMSNode * currentNode; + do + { + currentNode = findSingleLink(temp); //find the start of the next available chain + if(currentNode != NULL) + { + headsOfSystems.Append(AddNewChain(currentNode)); //and add it to the headsOfSystems list of chains + } + } + while(currentNode != NULL); //repeat this until all chains have been added } POEMSChain * SystemProcessor::AddNewChain(POEMSNode * currentNode){ - if(currentNode == NULL) //Termination condition; if the currentNode is null, then return null - { - return NULL; - } - int * tmp; - POEMSNode * nextNode = NULL; //nextNode stores the proposed next node to add to the chain. this will be checked to make sure no backtracking is occuring before being assigned as the current node. - POEMSChain * newChain = new POEMSChain; //make a new POEMSChain object. This will be the object returned + if(currentNode == NULL) //Termination condition; if the currentNode is null, then return null + { + return NULL; + } + int * tmp; + POEMSNode * nextNode = NULL; //nextNode stores the proposed next node to add to the chain. this will be checked to make sure no backtracking is occuring before being assigned as the current node. + POEMSChain * newChain = new POEMSChain; //make a new POEMSChain object. This will be the object returned - if(currentNode->links.GetNumElements() == 0) //if we have no links from this node, then the whole chain is only one node. Add this node to the chain and return it; mark node as visited for future reference - { - currentNode->visited = true; - tmp = new int; - *tmp = currentNode->idNumber; - newChain->listOfNodes.Append(tmp); - return newChain; - } - while(currentNode->links.GetNumElements() <= 2) //we go until we get to a node that branches, or both branches have already been taken both branches can already be taken if a loop with no spurs is found in the input data - { - currentNode->visited = true; - tmp = new int; - *tmp = currentNode->idNumber; - newChain->listOfNodes.Append(tmp); //append the current node to the chain & mark as visited - //std::cout << "Appending node " << currentNode->idNumber << " to chain" << std::endl; - nextNode = currentNode->links.GetHeadElement()->value; //the next node is the first or second value stored in the links array - //of the current node. We get the first value... - if(!setLinkVisited(currentNode, nextNode)) //...and see if it points back to where we came from. If it does... - { //either way, we set this link as visited - if(currentNode->links.GetNumElements() == 1) //if it does, then if that is the only link to this node, we're done with the chain, so append the chain to the list and return the newly created chain - { -// headsOfSystems.Append(newChain); - return newChain; - } - nextNode = currentNode->links.GetHeadElement()->next->value;//follow the other link if there is one, so we go down the chain - if(!setLinkVisited(currentNode, nextNode)) //mark link as followed, so we know not to backtrack - { - // headsOfSystems.Append(newChain); - return newChain; //This condition, where no branches have occurred but both links have already - //been taken can only occur in a loop with no spurs; add this loop to the - //system (currently added as a chain for consistency), and return. - } - } - currentNode = nextNode; //set the current node to be the next node in the chain - } - currentNode->visited = true; - tmp = new int; - *tmp = currentNode->idNumber; - newChain->listOfNodes.Append(tmp); //append the last node before branch (node shared jointly with branch chains) - //re-mark as visited, just to make sure - ListElement * tempNode = currentNode->links.GetHeadElement(); //go through all of the links, one at a time that branch - POEMSChain * tempChain = NULL; //temporary variable to hold data - while(tempNode != NULL) //when we have followed all links, stop - { - if(setLinkVisited(tempNode->value, currentNode)) //dont backtrack, or create closed loops - { - tempChain = AddNewChain(tempNode->value); //Add a new chain created out of the next node down that link - tempChain->parentChain = newChain; //set the parent to be this chain - newChain->childChains.Append(tempChain); //append the chain to this chain's list of child chains - } - tempNode = tempNode->next; //go to process the next chain - } - //headsOfSystems.Append(newChain); //append this chain to the system list - return newChain; + if(currentNode->links.GetNumElements() == 0) //if we have no links from this node, then the whole chain is only one node. Add this node to the chain and return it; mark node as visited for future reference + { + currentNode->visited = true; + tmp = new int; + *tmp = currentNode->idNumber; + newChain->listOfNodes.Append(tmp); + return newChain; + } + while(currentNode->links.GetNumElements() <= 2) //we go until we get to a node that branches, or both branches have already been taken both branches can already be taken if a loop with no spurs is found in the input data + { + currentNode->visited = true; + tmp = new int; + *tmp = currentNode->idNumber; + newChain->listOfNodes.Append(tmp); //append the current node to the chain & mark as visited + //cout << "Appending node " << currentNode->idNumber << " to chain" << endl; + nextNode = currentNode->links.GetHeadElement()->value; //the next node is the first or second value stored in the links array + //of the current node. We get the first value... + if(!setLinkVisited(currentNode, nextNode)) //...and see if it points back to where we came from. If it does... + { //either way, we set this link as visited + if(currentNode->links.GetNumElements() == 1) //if it does, then if that is the only link to this node, we're done with the chain, so append the chain to the list and return the newly created chain + { +// headsOfSystems.Append(newChain); + return newChain; + } + nextNode = currentNode->links.GetHeadElement()->next->value;//follow the other link if there is one, so we go down the chain + if(!setLinkVisited(currentNode, nextNode)) //mark link as followed, so we know not to backtrack + { + // headsOfSystems.Append(newChain); + return newChain; //This condition, where no branches have occurred but both links have already + //been taken can only occur in a loop with no spurs; add this loop to the + //system (currently added as a chain for consistency), and return. + } + } + currentNode = nextNode; //set the current node to be the next node in the chain + } + currentNode->visited = true; + tmp = new int; + *tmp = currentNode->idNumber; + newChain->listOfNodes.Append(tmp); //append the last node before branch (node shared jointly with branch chains) + //re-mark as visited, just to make sure + ListElement * tempNode = currentNode->links.GetHeadElement(); //go through all of the links, one at a time that branch + POEMSChain * tempChain = NULL; //temporary variable to hold data + while(tempNode != NULL) //when we have followed all links, stop + { + if(setLinkVisited(tempNode->value, currentNode)) //dont backtrack, or create closed loops + { + tempChain = AddNewChain(tempNode->value); //Add a new chain created out of the next node down that link + tempChain->parentChain = newChain; //set the parent to be this chain + newChain->childChains.Append(tempChain); //append the chain to this chain's list of child chains + } + tempNode = tempNode->next; //go to process the next chain + } + //headsOfSystems.Append(newChain); //append this chain to the system list + return newChain; } POEMSNode * SystemProcessor::findSingleLink(TreeNode * aNode) //This function takes the root of a search tree containing POEMSNodes and returns a POEMSNode corresponding to the start of a chain in the //system. It finds a node that has not been visited before, and only has one link; this node will be used as the head of the chain. { - if(aNode == NULL) - { - return NULL; - } - POEMSNode * returnVal = (POEMSNode *)aNode->GetAuxData(); //get the poemsnode data out of the treenode - POEMSNode * detectLoneLoops = NULL; //is used to handle a loop that has no protruding chains - if(returnVal->visited == false) - { - detectLoneLoops = returnVal; //if we find any node that has not been visited yet, save it - } - if(returnVal->links.GetNumElements() == 1 && returnVal->visited == false) //see if it has one element and hasnt been visited already - { - return returnVal; //return the node is it meets this criteria - } - returnVal = findSingleLink(aNode->Left()); //otherwise, check the left subtree - if(returnVal == NULL) //and if we find nothing... - { - returnVal = findSingleLink(aNode->Right()); //check the right subtree - } - if(returnVal == NULL) //if we could not find any chains - { - returnVal = detectLoneLoops; //see if we found any nodes at all that havent been processed - } - return returnVal; //return what we find (will be NULL if no new chains are - //found) + if(aNode == NULL) + { + return NULL; + } + POEMSNode * returnVal = (POEMSNode *)aNode->GetAuxData(); //get the poemsnode data out of the treenode + POEMSNode * detectLoneLoops = NULL; //is used to handle a loop that has no protruding chains + if(returnVal->visited == false) + { + detectLoneLoops = returnVal; //if we find any node that has not been visited yet, save it + } + if(returnVal->links.GetNumElements() == 1 && returnVal->visited == false) //see if it has one element and hasnt been visited already + { + return returnVal; //return the node is it meets this criteria + } + returnVal = findSingleLink(aNode->Left()); //otherwise, check the left subtree + if(returnVal == NULL) //and if we find nothing... + { + returnVal = findSingleLink(aNode->Right()); //check the right subtree + } + if(returnVal == NULL) //if we could not find any chains + { + returnVal = detectLoneLoops; //see if we found any nodes at all that havent been processed + } + return returnVal; //return what we find (will be NULL if no new chains are + //found) } bool SystemProcessor::setLinkVisited(POEMSNode * firstNode, POEMSNode * secondNode) @@ -225,66 +223,65 @@ bool SystemProcessor::setLinkVisited(POEMSNode * firstNode, POEMSNode * secondNo //value for that particular link. Because each link is represented twice, (once at each node in the link), both of the boolean values need //to be set in the event that the link has to be set as visited. { - //std::cout << "Checking link between nodes " << firstNode->idNumber << " and " << secondNode->idNumber << "... "; - ListElement * tmp = firstNode->links.GetHeadElement(); //get the head element of the list of pointers for node 1 - ListElement * tmp2 = firstNode->taken.GetHeadElement(); //get the head element of the list of bool isVisited flags for node 1 - while(tmp->value != NULL || tmp2->value != NULL) //go through untill we reach the end of the lists - { - if(tmp->value == secondNode) //if we find the link to the other node - { - if(*(tmp2->value) == true) //if the link has already been visited - { - //std::cout << "visited already" << std::endl; - return false; //return false to indicate that the link has been visited before this attempt - } - else //otherwise, visit it - { - *tmp2->value = true; - } - break; - } - tmp = tmp->next; //go check next link - tmp2 = tmp2->next; - } + //cout << "Checking link between nodes " << firstNode->idNumber << " and " << secondNode->idNumber << "... "; + ListElement * tmp = firstNode->links.GetHeadElement(); //get the head element of the list of pointers for node 1 + ListElement * tmp2 = firstNode->taken.GetHeadElement(); //get the head element of the list of bool isVisited flags for node 1 + while(tmp->value != NULL || tmp2->value != NULL) //go through untill we reach the end of the lists + { + if(tmp->value == secondNode) //if we find the link to the other node + { + if(*(tmp2->value) == true) //if the link has already been visited + { + //cout << "visited already" << endl; + return false; //return false to indicate that the link has been visited before this attempt + } + else //otherwise, visit it + { + *tmp2->value = true; + } + break; + } + tmp = tmp->next; //go check next link + tmp2 = tmp2->next; + } - tmp = secondNode->links.GetHeadElement(); //now, if the link was unvisited, we need to go set the other node's list such that - //it also knows this link is being visited - tmp2 = secondNode->taken.GetHeadElement(); - while(tmp->value != NULL || tmp2->value != NULL) //go through the list - { - if(tmp->value == firstNode) //if we find the link - { - if(*(tmp2->value) == true) //and it has already been visited, then signal an error; this shouldnt ever happen - { - std::cout << "Error in parsing structure! Should never reach this condition! \n" << - "Record of visited links out of synch between two adjacent nodes.\n"; - return false; - } - else - { - *tmp2->value = true; //set the appropriate value to true to indicate this link has been visited - } - break; - } - tmp = tmp->next; - tmp2 = tmp2->next; - } - //std::cout << "not visited" << std::endl; - return true; //return true to indicate that this is the first time the link has been visited + tmp = secondNode->links.GetHeadElement(); //now, if the link was unvisited, we need to go set the other node's list such that + //it also knows this link is being visited + tmp2 = secondNode->taken.GetHeadElement(); + while(tmp->value != NULL || tmp2->value != NULL) //go through the list + { + if(tmp->value == firstNode) //if we find the link + { + if(*(tmp2->value) == true) //and it has already been visited, then signal an error; this shouldnt ever happen + { + cout << "Error in parsing structure! Should never reach this condition! \n" << + "Record of visited links out of synch between two adjacent nodes.\n"; + return false; + } + else + { + *tmp2->value = true; //set the appropriate value to true to indicate this link has been visited + } + break; + } + tmp = tmp->next; + tmp2 = tmp2->next; + } + //cout << "not visited" << endl; + return true; //return true to indicate that this is the first time the link has been visited } -List * SystemProcessor::getSystemData(void) //Gets the list of POEMSChains that comprise the system. Might eventually only - //return chains linked to the reference plane, but currently returns every chain - //in the system. +List * SystemProcessor::getSystemData(void) //Gets the list of POEMSChains that comprise the system. Might eventually only + //return chains linked to the reference plane, but currently returns every chain + //in the system. { - return &headsOfSystems; + return &headsOfSystems; } int SystemProcessor::getNumberOfHeadChains(void) //This function isnt implemented yet, and might be taken out entirely; this was a holdover - //from when I intended to return an array of chain pointers, rather than a list of chains - //It will probably be deleted once I finish figuring out exactly what needs to be returned + //from when I intended to return an array of chain pointers, rather than a list of chains + //It will probably be deleted once I finish figuring out exactly what needs to be returned { - return 0; -} + return 0; } #endif diff --git a/lib/poems/body.cpp b/lib/poems/body.cpp index 6825941b93..4ef05dd1e6 100644 --- a/lib/poems/body.cpp +++ b/lib/poems/body.cpp @@ -14,20 +14,11 @@ * 110 8th St. Troy NY 12180 * * CONTACT: anderk5@rpi.edu * *_________________________________________________________________________*/ - -#include - -#include "body.h" -#include "inertialframe.h" -#include "mat3x3.h" -#include "particle.h" -#include "poemslist.h" + +#include "bodies.h" #include "point.h" -#include "rigidbody.h" -#include "vect3.h" using namespace std; -using namespace POEMS; Body::Body() { @@ -131,7 +122,7 @@ void Body::AddPoint(Point* point){ // global body functions // -Body* POEMS::NewBody(int type){ +Body* NewBody(int type){ switch( BodyType(type) ) { case INERTIALFRAME : // The inertial reference frame diff --git a/lib/poems/body.h b/lib/poems/body.h index e2394b40aa..f8e0f6a5a3 100644 --- a/lib/poems/body.h +++ b/lib/poems/body.h @@ -19,29 +19,30 @@ #ifndef BODY_H #define BODY_H -#include #include "poemslist.h" +#include #include "poemsobject.h" -#include "mat3x3.h" -#include "vect3.h" -namespace POEMS { +#include "matrices.h" + + + // emumerated type enum BodyType { INERTIALFRAME = 0, PARTICLE = 1, RIGIDBODY = 2 }; - + class Point; class Joint; - +class CompBody; class Body : public POEMSObject { public: double mass; Mat3x3 inertia; - + Vect3 r; Vect3 v; Vect3 v_k; @@ -53,13 +54,13 @@ public: Vect3 alpha; Vect3 alpha_t; double KE; - + List joints; List points; Body(); - + bool ReadIn(std::istream& in); void WriteOut(std::ostream& out); bool ReadInPoints(std::istream& in); @@ -67,7 +68,7 @@ public: Point* GetPoint(int p); void AddJoint(Joint* joint); void AddPoint(Point* point); - + virtual bool ReadInBodyData(std::istream& in) = 0; virtual void WriteOutBodyData(std::ostream& out) = 0; virtual ~Body(); @@ -76,5 +77,5 @@ public: // global body functions Body* NewBody(int type); -} + #endif diff --git a/lib/poems/body23joint.cpp b/lib/poems/body23joint.cpp index e3ef32b2a9..8cd0a95bca 100644 --- a/lib/poems/body23joint.cpp +++ b/lib/poems/body23joint.cpp @@ -14,21 +14,18 @@ * 110 8th St. Troy NY 12180 * * CONTACT: anderk5@rpi.edu * *_________________________________________________________________________*/ + -#include #include "body23joint.h" +#include "point.h" +#include "matrixfun.h" #include "body.h" -#include "colmatrix.h" -#include "eulerparameters.h" #include "fastmatrixops.h" -#include "mat3x3.h" -#include "matrixfun.h" -#include "point.h" -#include "vect3.h" -#include "virtualmatrix.h" +#include "norm.h" +#include "eulerparameters.h" +#include "matrices.h" +#include -using namespace std; -using namespace POEMS; Body23Joint::Body23Joint(){ DimQandU(4,2); diff --git a/lib/poems/body23joint.h b/lib/poems/body23joint.h index 43a727c815..60253ac8a4 100644 --- a/lib/poems/body23joint.h +++ b/lib/poems/body23joint.h @@ -18,11 +18,12 @@ #ifndef BODY23JOINT_H #define BODY23JOINT_H -#include #include "joint.h" -#include "matrix.h" +#include "vect3.h" +#include "mat3x3.h" + + -namespace POEMS { class Body23Joint : public Joint { Matrix const_sP; public: @@ -39,5 +40,5 @@ public: void ForwardKinematics(); void BackwardKinematics(); }; -} + #endif diff --git a/lib/poems/colmatmap.cpp b/lib/poems/colmatmap.cpp index 34a95feb03..1954e7ff15 100644 --- a/lib/poems/colmatmap.cpp +++ b/lib/poems/colmatmap.cpp @@ -21,8 +21,6 @@ #include using namespace std; -using namespace POEMS; - ColMatMap::ColMatMap(){ numrows = 0; diff --git a/lib/poems/colmatmap.h b/lib/poems/colmatmap.h index 5a12cf487f..3a6267a247 100644 --- a/lib/poems/colmatmap.h +++ b/lib/poems/colmatmap.h @@ -19,12 +19,8 @@ #ifndef COLMATMAP_H #define COLMATMAP_H -#include - #include "virtualcolmatrix.h" -#include "virtualmatrix.h" -namespace POEMS { class ColMatrix; class ColMatMap : public VirtualColMatrix { @@ -65,5 +61,5 @@ public: friend void FastCKRK5(ColMatMap& X, ColMatrix& Xi, ColMatrix* f, double* c, double dt); friend void FastFRK5(ColMatMap& X, ColMatrix& Xi, ColMatrix* f, double* c, double dt); }; -} + #endif diff --git a/lib/poems/colmatrix.cpp b/lib/poems/colmatrix.cpp index 0cc666645a..dc6f49be2b 100644 --- a/lib/poems/colmatrix.cpp +++ b/lib/poems/colmatrix.cpp @@ -16,13 +16,12 @@ *_________________________________________________________________________*/ #include "colmatrix.h" - +#include "rowmatrix.h" #include +#include #include using namespace std; -using namespace POEMS; - ColMatrix::ColMatrix(){ numrows = 0; diff --git a/lib/poems/colmatrix.h b/lib/poems/colmatrix.h index bcfa86843a..11fd85a928 100644 --- a/lib/poems/colmatrix.h +++ b/lib/poems/colmatrix.h @@ -19,18 +19,15 @@ #ifndef COLMATRIX_H #define COLMATRIX_H -#include #include "virtualcolmatrix.h" -#include "virtualmatrix.h" +#include "colmatmap.h" -namespace POEMS { class Matrix; class Vect6; class Mat3x3; class Vect3; class ColMatrix : public VirtualColMatrix { -protected: double* elements; public: ColMatrix(); @@ -60,28 +57,28 @@ public: ColMatrix& operator=(const VirtualMatrix& A); // overloaded = ColMatrix& operator*=(double b); - void Abs(); - void BasicMax(double& value, int& index); - void BasicMin(double& value, int& index); + void Abs(); + void BasicMax(double& value, int& index); + void BasicMin(double& value, int& index); // fast matrix operations - friend void FastQuaternions(ColMatrix& q, Mat3x3& C); - friend void FastInvQuaternions(Mat3x3& C, ColMatrix& q); - friend void FastQuaternionDerivatives(ColMatrix& q, ColMatrix& omega, ColMatrix& qdot); - friend void FastTMult(Matrix& A, Vect6& B, ColMatrix& C); - friend void FastMult(Matrix& A, ColMatrix& B, Vect6& C); - friend void FastAssign(ColMatrix& A, ColMatrix& C); + friend void FastQuaternions(ColMatrix& q, Mat3x3& C); + friend void FastInvQuaternions(Mat3x3& C, ColMatrix& q); + friend void FastQuaternionDerivatives(ColMatrix& q, ColMatrix& omega, ColMatrix& qdot); + friend void FastTMult(Matrix& A, Vect6& B, ColMatrix& C); + friend void FastMult(Matrix& A, ColMatrix& B, Vect6& C); + friend void FastAssign(ColMatrix& A, ColMatrix& C); - friend void FastMult(Mat3x3& A, ColMatrix& B, Vect3& C); - friend void FastMult(Mat3x3& A, Vect3& B, ColMatrix& C); - friend void FastAssign(ColMatrix&A, Vect3& C); - - friend void EP_Derivatives(ColMatrix& q, ColMatrix& u, ColMatrix& qdot); - friend void EP_Transformation(ColMatrix& q, Mat3x3& C); - friend void EP_FromTransformation(ColMatrix& q, Mat3x3& C); - friend void EP_Normalize(ColMatrix& q); - friend void EPdotdot_udot(ColMatrix& Audot, ColMatrix& Aqdot, ColMatrix& Aq,ColMatrix& Aqddot); - friend void qdot_to_u(ColMatrix& q, ColMatrix& u, ColMatrix& qdot); + friend void FastMult(Mat3x3& A, ColMatrix& B, Vect3& C); + friend void FastMult(Mat3x3& A, Vect3& B, ColMatrix& C); + friend void FastAssign(ColMatrix&A, Vect3& C); + + friend void EP_Derivatives(ColMatrix& q, ColMatrix& u, ColMatrix& qdot); + friend void EP_Transformation(ColMatrix& q, Mat3x3& C); + friend void EP_FromTransformation(ColMatrix& q, Mat3x3& C); + friend void EP_Normalize(ColMatrix& q); + friend void EPdotdot_udot(ColMatrix& Audot, ColMatrix& Aqdot, ColMatrix& Aq,ColMatrix& Aqddot); + friend void qdot_to_u(ColMatrix& q, ColMatrix& u, ColMatrix& qdot); }; -} + #endif diff --git a/lib/poems/defines.h b/lib/poems/defines.h index 877bc0fa0b..455bc298d5 100644 --- a/lib/poems/defines.h +++ b/lib/poems/defines.h @@ -15,14 +15,13 @@ * CONTACT: anderk5@rpi.edu * *_________________________________________________________________________*/ -#ifndef POEMS_DEFINES_H -#define POEMS_DEFINES_H +#ifndef _DEFINES_H_ +#define _DEFINES_H_ -namespace POEMS { enum SolverType { ONSOLVER = 0, PARTICLESOLVER = 1 }; -} + #endif diff --git a/lib/poems/eulerparameters.cpp b/lib/poems/eulerparameters.cpp index bb8d676796..032bc7da82 100644 --- a/lib/poems/eulerparameters.cpp +++ b/lib/poems/eulerparameters.cpp @@ -3,7 +3,7 @@ * POEMS: PARALLELIZABLE OPEN SOURCE EFFICIENT MULTIBODY SOFTWARE * * DESCRIPTION: SEE READ-ME * * FILE NAME: eulerparameters.cpp * - * AUTHORS: See Author List * + * AUTHORS: See Author List * * GRANTS: See Grants List * * COPYRIGHT: (C) 2005 by Authors as listed in Author's List * * LICENSE: Please see License Agreement * @@ -11,22 +11,16 @@ * ADMINISTRATOR: Prof. Kurt Anderson * * Computational Dynamics Lab * * Rensselaer Polytechnic Institute * - * 110 8th St. Troy NY 12180 * + * 110 8th St. Troy NY 12180 * * CONTACT: anderk5@rpi.edu * *_________________________________________________________________________*/ #include "eulerparameters.h" - #include -#include "colmatrix.h" -#include "mat3x3.h" - using namespace std; -using namespace POEMS; - -void POEMS::EP_Derivatives(ColMatrix& q, ColMatrix& u, ColMatrix& qdot){ +void EP_Derivatives(ColMatrix& q, ColMatrix& u, ColMatrix& qdot){ EP_Normalize(q); int num=u.GetNumRows(); if (3 - +#include #include "fastmatrixops.h" -#include "colmatmap.h" -#include "colmatrix.h" -#include "mat3x3.h" -#include "mat4x4.h" -#include "mat6x6.h" -#include "matrix.h" -#include "vect3.h" -#include "vect4.h" -#include "vect6.h" +#include using namespace std; -using namespace POEMS; - // // Cross Product (friend of Vect3) // -void POEMS::FastCross(Vect3& a, Vect3& b, Vect3& c){ +void FastCross(Vect3& a, Vect3& b, Vect3& c){ c.elements[0] = a.elements[1]*b.elements[2] - a.elements[2]*b.elements[1]; c.elements[1] = a.elements[2]*b.elements[0] - a.elements[0]*b.elements[2]; c.elements[2] = a.elements[0]*b.elements[1] - a.elements[1]*b.elements[0]; @@ -46,7 +35,7 @@ void POEMS::FastCross(Vect3& a, Vect3& b, Vect3& c){ // Simple Rotation (friend of Vect3 and Mat3x3) // -void POEMS::FastSimpleRotation(Vect3& v, double q, Mat3x3& C){ +void FastSimpleRotation(Vect3& v, double q, Mat3x3& C){ // intermediate quantities double cq = cos(q); double sq = sin(q); @@ -71,7 +60,7 @@ void POEMS::FastSimpleRotation(Vect3& v, double q, Mat3x3& C){ // Quaternion Functions // -void POEMS::FastQuaternions(ColMatrix& q, Mat3x3& C){ +void FastQuaternions(ColMatrix& q, Mat3x3& C){ double* e = q.elements; // normalize the quaternions @@ -96,7 +85,7 @@ void POEMS::FastQuaternions(ColMatrix& q, Mat3x3& C){ C.elements[2][1] = 2 * (e[2]*e[3] + e[0]*e[1]); } -void POEMS::FastQuaternionDerivatives(ColMatrix& q, ColMatrix& omega, ColMatrix& qdot){ +void FastQuaternionDerivatives(ColMatrix& q, ColMatrix& omega, ColMatrix& qdot){ double* w = omega.elements; double* e = q.elements; @@ -106,7 +95,7 @@ void POEMS::FastQuaternionDerivatives(ColMatrix& q, ColMatrix& omega, ColMatrix& qdot.elements[3] = 0.5 * ( w[2]*e[0] + w[1]*e[1] - w[0]*e[2]); } -void POEMS::FastInvQuaternions(Mat3x3& C, ColMatrix& q){ +void FastInvQuaternions(Mat3x3& C, ColMatrix& q){ } // @@ -123,7 +112,7 @@ void POEMS::FastInvQuaternions(Mat3x3& C, ColMatrix& q){ // // friend of Matrix -void POEMS::FastLDLT(Matrix& A, Matrix& C){ // C is the LD of the LDL^T decomposition of A (SPD) +void FastLDLT(Matrix& A, Matrix& C){ // C is the LD of the LDL^T decomposition of A (SPD) double Lv; int n = A.numrows; @@ -145,7 +134,7 @@ void POEMS::FastLDLT(Matrix& A, Matrix& C){ // C is the LD of the LDL^T decompos // friend of Mat6x6 -void POEMS::FastLDLT(Mat6x6& A, Mat6x6& C){ // C is the LD of the LDL^T decomposition of A (SPD) +void FastLDLT(Mat6x6& A, Mat6x6& C){ // C is the LD of the LDL^T decomposition of A (SPD) double v[6]; double Lv; @@ -167,7 +156,7 @@ void POEMS::FastLDLT(Mat6x6& A, Mat6x6& C){ // C is the LD of the LDL^T decompos } // friend of Matrix -void POEMS::FastLDLTSubs(Matrix& LD, Matrix& B, Matrix& C){ +void FastLDLTSubs(Matrix& LD, Matrix& B, Matrix& C){ int n = B.numrows; int c = B.numcols; double temp; @@ -192,7 +181,7 @@ void POEMS::FastLDLTSubs(Matrix& LD, Matrix& B, Matrix& C){ } // friend of Matrix -void POEMS::FastLDLTSubsLH(Matrix& B, Matrix& LD, Matrix& C){ +void FastLDLTSubsLH(Matrix& B, Matrix& LD, Matrix& C){ int n = B.numcols; int c = B.numrows; double temp; @@ -217,7 +206,7 @@ void POEMS::FastLDLTSubsLH(Matrix& B, Matrix& LD, Matrix& C){ } // friend of Mat6x6 -void POEMS::FastLDLTSubs(Mat6x6& LD, Mat6x6& B, Mat6x6& C){ +void FastLDLTSubs(Mat6x6& LD, Mat6x6& B, Mat6x6& C){ double temp; for(int k=0;k<6;k++){ @@ -240,7 +229,7 @@ void POEMS::FastLDLTSubs(Mat6x6& LD, Mat6x6& B, Mat6x6& C){ } // friend of Mat6x6 & Vect6 -void POEMS::FastLDLTSubs(Mat6x6& LD, Vect6& B, Vect6& C){ +void FastLDLTSubs(Mat6x6& LD, Vect6& B, Vect6& C){ double temp; for(int i=0;i<6;i++){ @@ -261,7 +250,7 @@ void POEMS::FastLDLTSubs(Mat6x6& LD, Vect6& B, Vect6& C){ } // friend of Matrix -void POEMS::FastLU(Matrix& A, Matrix& LU, int *indx){ // LU is the LU decomposition of A +void FastLU(Matrix& A, Matrix& LU, int *indx){ // LU is the LU decomposition of A int i,imax=0,j,k; int n = A.numrows; double big, dum, sum, temp; @@ -311,7 +300,7 @@ void POEMS::FastLU(Matrix& A, Matrix& LU, int *indx){ // LU is the LU decomposit } // friend of Mat3x3 -void POEMS::FastLU(Mat3x3& A, Mat3x3& LU, int *indx){ // LU is the LU decomposition of A +void FastLU(Mat3x3& A, Mat3x3& LU, int *indx){ // LU is the LU decomposition of A int i,imax=0,j,k; double big, dum, sum, temp; double vv[10000]; @@ -359,7 +348,7 @@ void POEMS::FastLU(Mat3x3& A, Mat3x3& LU, int *indx){ // LU is the LU decomposit } // friend of Mat4x4 -void POEMS::FastLU(Mat4x4& A, Mat4x4& LU, int *indx){ // LU is the LU decomposition of A +void FastLU(Mat4x4& A, Mat4x4& LU, int *indx){ // LU is the LU decomposition of A int i,imax=0,j,k; double big, dum, sum, temp; double vv[10000]; @@ -407,7 +396,7 @@ void POEMS::FastLU(Mat4x4& A, Mat4x4& LU, int *indx){ // LU is the LU decomposit } // friend of Mat6x6 -void POEMS::FastLU(Mat6x6& A, Mat6x6& LU, int *indx){ // LU is the LU decomposition of A +void FastLU(Mat6x6& A, Mat6x6& LU, int *indx){ // LU is the LU decomposition of A int i,imax=0,j,k; double big, dum, sum, temp; double vv[10000]; @@ -455,7 +444,7 @@ void POEMS::FastLU(Mat6x6& A, Mat6x6& LU, int *indx){ // LU is the LU decomposit } // friend of Matrix -void POEMS::FastLUSubs(Matrix& LU, Matrix& B, Matrix& C, int *indx){ // Appropriate Forward and Back Substitution +void FastLUSubs(Matrix& LU, Matrix& B, Matrix& C, int *indx){ // Appropriate Forward and Back Substitution int i,ip,j,k; int n = B.numrows; int c = B.numcols; @@ -479,7 +468,7 @@ void POEMS::FastLUSubs(Matrix& LU, Matrix& B, Matrix& C, int *indx){ // Appropri } // friend of Matrix and Mat3x3 -void POEMS::FastLUSubs(Mat3x3& LU, Matrix& B, Matrix& C, int *indx){ // Appropriate Forward and Back Substitution +void FastLUSubs(Mat3x3& LU, Matrix& B, Matrix& C, int *indx){ // Appropriate Forward and Back Substitution int i,ip,j,k; int n = B.numrows; int c = B.numcols; @@ -503,7 +492,7 @@ void POEMS::FastLUSubs(Mat3x3& LU, Matrix& B, Matrix& C, int *indx){ // Appropri } // friend of Matrix and Mat4x4 -void POEMS::FastLUSubs(Mat4x4& LU, Matrix& B, Matrix& C, int *indx){ // Appropriate Forward and Back Substitution +void FastLUSubs(Mat4x4& LU, Matrix& B, Matrix& C, int *indx){ // Appropriate Forward and Back Substitution int i,ip,j,k; int n = B.numrows; int c = B.numcols; @@ -527,7 +516,7 @@ void POEMS::FastLUSubs(Mat4x4& LU, Matrix& B, Matrix& C, int *indx){ // Appropri } // friend of Matrix and Mat6x6 -void POEMS::FastLUSubs(Mat6x6& LU, Matrix& B, Matrix& C, int *indx){ // Appropriate Forward and Back Substitution +void FastLUSubs(Mat6x6& LU, Matrix& B, Matrix& C, int *indx){ // Appropriate Forward and Back Substitution int i,ip,j,k; int n = B.numrows; int c = B.numcols; @@ -553,7 +542,7 @@ void POEMS::FastLUSubs(Mat6x6& LU, Matrix& B, Matrix& C, int *indx){ // Appropri // The following LUSubsLH routine is incomplete at the moment. // friend of Matrix -void POEMS::FastLUSubsLH(Matrix& LU, Matrix& B, Matrix& C, int *indx){ // Appropriate Forward and Back Substitution +void FastLUSubsLH(Matrix& LU, Matrix& B, Matrix& C, int *indx){ // Appropriate Forward and Back Substitution int i,ip,j,k; int n = B.numcols; int c = B.numrows; @@ -584,13 +573,13 @@ void POEMS::FastLUSubsLH(Matrix& LU, Matrix& B, Matrix& C, int *indx){ // Approp // Triple sum // -void POEMS::FastTripleSum(Vect3& a, Vect3& b, Vect3& c, Vect3& d){ // d = a+b+c +void FastTripleSum(Vect3& a, Vect3& b, Vect3& c, Vect3& d){ // d = a+b+c d.elements[0] = a.elements[0]+b.elements[0]+c.elements[0]; d.elements[1] = a.elements[1]+b.elements[1]+c.elements[1]; d.elements[2] = a.elements[2]+b.elements[2]+c.elements[2]; } -void POEMS::FastTripleSumPPM(Vect3& a, Vect3& b, Vect3& c, Vect3& d){ // d = a+b-c +void FastTripleSumPPM(Vect3& a, Vect3& b, Vect3& c, Vect3& d){ // d = a+b-c d.elements[0] = a.elements[0]+b.elements[0]-c.elements[0]; d.elements[1] = a.elements[1]+b.elements[1]-c.elements[1]; d.elements[2] = a.elements[2]+b.elements[2]-c.elements[2]; @@ -601,7 +590,7 @@ void POEMS::FastTripleSumPPM(Vect3& a, Vect3& b, Vect3& c, Vect3& d){ // d = a+b // // friend of matrix -void POEMS::FastMult(Matrix& A, Matrix& B, Matrix& C){ // C = A*B +void FastMult(Matrix& A, Matrix& B, Matrix& C){ // C = A*B // assumes dimensions are already correct! int r = A.numrows; int ca = A.numcols; @@ -617,7 +606,7 @@ void POEMS::FastMult(Matrix& A, Matrix& B, Matrix& C){ // C = A*B } // friend of matrix -void POEMS::FastTMult(Matrix& A, Matrix& B, Matrix& C){ // C = A*B +void FastTMult(Matrix& A, Matrix& B, Matrix& C){ // C = A*B // assumes dimensions are already correct! int r = A.numcols; int ca = A.numrows; @@ -633,14 +622,14 @@ void POEMS::FastTMult(Matrix& A, Matrix& B, Matrix& C){ // C = A*B } // friend of Mat3x3 & Vect3 -void POEMS::FastMult(Mat3x3& A, Vect3& B, Vect3& C){ // C = A*B +void FastMult(Mat3x3& A, Vect3& B, Vect3& C){ // C = A*B C.elements[0] = A.elements[0][0]*B.elements[0] + A.elements[0][1]*B.elements[1] + A.elements[0][2]*B.elements[2]; C.elements[1] = A.elements[1][0]*B.elements[0] + A.elements[1][1]*B.elements[1] + A.elements[1][2]*B.elements[2]; C.elements[2] = A.elements[2][0]*B.elements[0] + A.elements[2][1]*B.elements[1] + A.elements[2][2]*B.elements[2]; } // friend of Mat3x3, ColMatrix, & Vect3 -void POEMS::FastMult(Mat3x3& A, ColMatrix& B, Vect3& C){ // C = A*B +void FastMult(Mat3x3& A, ColMatrix& B, Vect3& C){ // C = A*B C.elements[0] = A.elements[0][0]*B.elements[0] + A.elements[0][1]*B.elements[1] + A.elements[0][2]*B.elements[2]; C.elements[1] = A.elements[1][0]*B.elements[0] + A.elements[1][1]*B.elements[1] + A.elements[1][2]*B.elements[2]; C.elements[2] = A.elements[2][0]*B.elements[0] + A.elements[2][1]*B.elements[1] + A.elements[2][2]*B.elements[2]; @@ -648,42 +637,42 @@ void POEMS::FastMult(Mat3x3& A, ColMatrix& B, Vect3& C){ // C = A*B // friend of Mat3x3, ColMatrix, & Vect3 -void POEMS::FastMult(Mat3x3& A, Vect3& B, ColMatrix& C){ // C = A*B +void FastMult(Mat3x3& A, Vect3& B, ColMatrix& C){ // C = A*B C.elements[0] = A.elements[0][0]*B.elements[0] + A.elements[0][1]*B.elements[1] + A.elements[0][2]*B.elements[2]; C.elements[1] = A.elements[1][0]*B.elements[0] + A.elements[1][1]*B.elements[1] + A.elements[1][2]*B.elements[2]; C.elements[2] = A.elements[2][0]*B.elements[0] + A.elements[2][1]*B.elements[1] + A.elements[2][2]*B.elements[2]; } // friend of Mat3x3 & Vect3 -void POEMS::FastTMult(Mat3x3& A, Vect3& B, Vect3& C){ // C = A^T*B +void FastTMult(Mat3x3& A, Vect3& B, Vect3& C){ // C = A^T*B C.elements[0] = A.elements[0][0]*B.elements[0] + A.elements[1][0]*B.elements[1] + A.elements[2][0]*B.elements[2]; C.elements[1] = A.elements[0][1]*B.elements[0] + A.elements[1][1]*B.elements[1] + A.elements[2][1]*B.elements[2]; C.elements[2] = A.elements[0][2]*B.elements[0] + A.elements[1][2]*B.elements[1] + A.elements[2][2]*B.elements[2]; } // friend of Mat3x3 & Vect3 -void POEMS::FastNegMult(Mat3x3& A, Vect3& B, Vect3& C){ // C = -A*B +void FastNegMult(Mat3x3& A, Vect3& B, Vect3& C){ // C = -A*B C.elements[0] = -A.elements[0][0]*B.elements[0] - A.elements[0][1]*B.elements[1] - A.elements[0][2]*B.elements[2]; C.elements[1] = -A.elements[1][0]*B.elements[0] - A.elements[1][1]*B.elements[1] - A.elements[1][2]*B.elements[2]; C.elements[2] = -A.elements[2][0]*B.elements[0] - A.elements[2][1]*B.elements[1] - A.elements[2][2]*B.elements[2]; } // friend of Mat3x3 & Vect3 -void POEMS::FastNegTMult(Mat3x3& A, Vect3& B, Vect3& C){ // C = -A^T*B +void FastNegTMult(Mat3x3& A, Vect3& B, Vect3& C){ // C = -A^T*B C.elements[0] = -A.elements[0][0]*B.elements[0] - A.elements[1][0]*B.elements[1] - A.elements[2][0]*B.elements[2]; C.elements[1] = -A.elements[0][1]*B.elements[0] - A.elements[1][1]*B.elements[1] - A.elements[2][1]*B.elements[2]; C.elements[2] = -A.elements[0][2]*B.elements[0] - A.elements[1][2]*B.elements[1] - A.elements[2][2]*B.elements[2]; } // friend of Vect3 -void POEMS::FastMult(double a, Vect3& B, Vect3& C){ // C = a*B +void FastMult(double a, Vect3& B, Vect3& C){ // C = a*B C.elements[0] = a*B.elements[0]; C.elements[1] = a*B.elements[1]; C.elements[2] = a*B.elements[2]; } // friend of Mat4x4 & Vect4 -void POEMS::FastMult(Mat4x4& A, Vect4& B, Vect4& C){ // C = A*B +void FastMult(Mat4x4& A, Vect4& B, Vect4& C){ // C = A*B C.elements[0] = A.elements[0][0]*B.elements[0] + A.elements[0][1]*B.elements[1] + A.elements[0][2]*B.elements[2] + A.elements[0][3]*B.elements[3]; C.elements[1] = A.elements[1][0]*B.elements[0] + A.elements[1][1]*B.elements[1] + A.elements[1][2]*B.elements[2] + A.elements[1][3]*B.elements[3]; C.elements[2] = A.elements[2][0]*B.elements[0] + A.elements[2][1]*B.elements[1] + A.elements[2][2]*B.elements[2] + A.elements[2][3]*B.elements[3]; @@ -691,7 +680,7 @@ void POEMS::FastMult(Mat4x4& A, Vect4& B, Vect4& C){ // C = A*B } // friend of Mat4x4 & Vect4 -void POEMS::FastTMult(Mat4x4& A, Vect4& B, Vect4& C){ // C = A^T*B +void FastTMult(Mat4x4& A, Vect4& B, Vect4& C){ // C = A^T*B C.elements[0] = A.elements[0][0]*B.elements[0] + A.elements[1][0]*B.elements[1] + A.elements[2][0]*B.elements[2] + A.elements[3][0]*B.elements[3]; C.elements[1] = A.elements[0][1]*B.elements[0] + A.elements[1][1]*B.elements[1] + A.elements[2][1]*B.elements[2] + A.elements[3][1]*B.elements[3]; C.elements[2] = A.elements[0][2]*B.elements[0] + A.elements[1][2]*B.elements[1] + A.elements[2][2]*B.elements[2] + A.elements[3][2]*B.elements[3]; @@ -699,7 +688,7 @@ void POEMS::FastTMult(Mat4x4& A, Vect4& B, Vect4& C){ // C = A^T*B } // friend of Mat4x4 & Vect4 -void POEMS::FastNegMult(Mat4x4& A, Vect4& B, Vect4& C){ // C = -A*B +void FastNegMult(Mat4x4& A, Vect4& B, Vect4& C){ // C = -A*B C.elements[0] = -A.elements[0][0]*B.elements[0] - A.elements[0][1]*B.elements[1] - A.elements[0][2]*B.elements[2] - A.elements[0][3]*B.elements[3]; C.elements[1] = -A.elements[1][0]*B.elements[0] - A.elements[1][1]*B.elements[1] - A.elements[1][2]*B.elements[2] - A.elements[1][3]*B.elements[3]; C.elements[2] = -A.elements[2][0]*B.elements[0] - A.elements[2][1]*B.elements[1] - A.elements[2][2]*B.elements[2] - A.elements[2][3]*B.elements[3]; @@ -707,7 +696,7 @@ void POEMS::FastNegMult(Mat4x4& A, Vect4& B, Vect4& C){ // C = -A*B } // friend of Mat4x4 & Vect4 -void POEMS::FastNegTMult(Mat4x4& A, Vect4& B, Vect4& C){ // C = -A^T*B +void FastNegTMult(Mat4x4& A, Vect4& B, Vect4& C){ // C = -A^T*B C.elements[0] = -A.elements[0][0]*B.elements[0] - A.elements[1][0]*B.elements[1] - A.elements[2][0]*B.elements[2] - A.elements[3][0]*B.elements[3]; C.elements[1] = -A.elements[0][1]*B.elements[0] - A.elements[1][1]*B.elements[1] - A.elements[2][1]*B.elements[2] - A.elements[3][1]*B.elements[3]; C.elements[2] = -A.elements[0][2]*B.elements[0] - A.elements[1][2]*B.elements[1] - A.elements[2][2]*B.elements[2] - A.elements[3][2]*B.elements[3]; @@ -715,7 +704,7 @@ void POEMS::FastNegTMult(Mat4x4& A, Vect4& B, Vect4& C){ // C = -A^T*B } // friend of Vect4 -void POEMS::FastMult(double a, Vect4& B, Vect4& C){ // C = a*B +void FastMult(double a, Vect4& B, Vect4& C){ // C = a*B C.elements[0] = a*B.elements[0]; C.elements[1] = a*B.elements[1]; C.elements[2] = a*B.elements[2]; @@ -723,7 +712,7 @@ void POEMS::FastMult(double a, Vect4& B, Vect4& C){ // C = a*B } // friend of Matrix & Mat6x6 -void POEMS::FastMultT(Matrix& A, Matrix& B, Mat6x6& C){ // C = A*B^T +void FastMultT(Matrix& A, Matrix& B, Mat6x6& C){ // C = A*B^T int i,j,k,n; n = A.numcols; @@ -736,7 +725,7 @@ void POEMS::FastMultT(Matrix& A, Matrix& B, Mat6x6& C){ // C = A*B^T } // friend Matrix, Vect6, ColMatrix -void POEMS::FastMult(Matrix& A, ColMatrix& B, Vect6& C){ +void FastMult(Matrix& A, ColMatrix& B, Vect6& C){ int ca = A.numcols; int i,k; @@ -748,7 +737,7 @@ void POEMS::FastMult(Matrix& A, ColMatrix& B, Vect6& C){ } // friend of Matrix & Mat6x6 -void POEMS::FastMult(Mat6x6& A, Matrix& B, Matrix& C){ // C = A*B +void FastMult(Mat6x6& A, Matrix& B, Matrix& C){ // C = A*B // assumes dimensions are already correct! int cb = B.numcols; @@ -762,7 +751,7 @@ void POEMS::FastMult(Mat6x6& A, Matrix& B, Matrix& C){ // C = A*B } // friend Matrix, Vect6, ColMatrix -void POEMS::FastTMult(Matrix& A, Vect6& B, ColMatrix& C){ // C = A^T*B +void FastTMult(Matrix& A, Vect6& B, ColMatrix& C){ // C = A^T*B int n = C.numrows; int i,k; for(i=0;i #include -#include "virtualmatrix.h" - using namespace std; -using namespace POEMS; - FixedPoint::FixedPoint(){ } diff --git a/lib/poems/fixedpoint.h b/lib/poems/fixedpoint.h index 5da1d6d69c..b5ecb23906 100644 --- a/lib/poems/fixedpoint.h +++ b/lib/poems/fixedpoint.h @@ -19,12 +19,9 @@ #ifndef FIXEDPOINT_H #define FIXEDPOINT_H -#include - #include "point.h" #include "vect3.h" -namespace POEMS { class FixedPoint : public Point { public: FixedPoint(); @@ -36,5 +33,5 @@ public: bool ReadInPointData(std::istream& in); void WriteOutPointData(std::ostream& out); }; -} + #endif diff --git a/lib/poems/freebodyjoint.cpp b/lib/poems/freebodyjoint.cpp index 0022ebd9ff..d00f0bdb98 100644 --- a/lib/poems/freebodyjoint.cpp +++ b/lib/poems/freebodyjoint.cpp @@ -3,7 +3,7 @@ * POEMS: PARALLELIZABLE OPEN SOURCE EFFICIENT MULTIBODY SOFTWARE * * DESCRIPTION: SEE READ-ME * * FILE NAME: freebodyjoint.cpp * - * AUTHORS: See Author List * + * AUTHORS: See Author List * * GRANTS: See Grants List * * COPYRIGHT: (C) 2005 by Authors as listed in Author's List * * LICENSE: Please see License Agreement * @@ -11,29 +11,23 @@ * ADMINISTRATOR: Prof. Kurt Anderson * * Computational Dynamics Lab * * Rensselaer Polytechnic Institute * - * 110 8th St. Troy NY 12180 * + * 110 8th St. Troy NY 12180 * * CONTACT: anderk5@rpi.edu * *_________________________________________________________________________*/ - + #include "freebodyjoint.h" - -#include - +#include "point.h" #include "matrixfun.h" #include "body.h" #include "fastmatrixops.h" +#include "norm.h" #include "eulerparameters.h" -#include "colmatrix.h" -#include "mat3x3.h" -#include "mat6x6.h" -#include "vect3.h" -#include "virtualmatrix.h" - -using namespace POEMS; - +#include "matrices.h" +#include + FreeBodyJoint::FreeBodyJoint(){ - DimQandU(7,6); + DimQandU(7,6); } FreeBodyJoint::~FreeBodyJoint(){ @@ -51,112 +45,112 @@ void FreeBodyJoint::WriteOutJointData(std::ostream& out){ } void FreeBodyJoint::ComputeLocalTransform(){ - Mat3x3 ko_C_k; - EP_Transformation(q, ko_C_k); - FastMult(pk_C_ko,ko_C_k,pk_C_k); + Mat3x3 ko_C_k; + EP_Transformation(q, ko_C_k); + FastMult(pk_C_ko,ko_C_k,pk_C_k); } Matrix FreeBodyJoint::GetForward_sP(){ Mat6x6 sP; - //sP.Identity(); - - sP.Zeros(); + //sP.Identity(); + + sP.Zeros(); Mat3x3 temp0=T(pk_C_k); for(int i=1;i<4;i++){ sP(i,i)=1.0; for(int j=1;j<4;j++){ sP(3+i,3+j)=temp0(i,j); } - } - return sP; + } + return sP; } Matrix FreeBodyJoint::GetBackward_sP(){ Mat6x6 sP; - sP.Identity(); + sP.Identity(); sP =-1.0*sP; - std::cout<<"Did I come here in "<r); - - //COMMENT STEP3: CALCULATE QDOT + + FastAssign(r12,body2->r); + + //COMMENT STEP3: CALCULATE QDOT qdot_to_u(q, u, qdot); - - + + Vect3 WN; WN.BasicSet(0,u.BasicGet(0)); WN.BasicSet(1,u.BasicGet(1)); WN.BasicSet(2,u.BasicGet(2)); - - Vect3 VN; + + Vect3 VN; VN.BasicSet(0,u.BasicGet(3)); VN.BasicSet(1,u.BasicGet(4)); - VN.BasicSet(2,u.BasicGet(5)); - - FastAssign(WN,body2->omega_k); - + VN.BasicSet(2,u.BasicGet(5)); + + FastAssign(WN,body2->omega_k); + Vect3 pk_w_k; - FastMult(body2->n_C_k,WN,pk_w_k); + FastMult(body2->n_C_k,WN,pk_w_k); FastAssign(pk_w_k,body2->omega); - - - - //COMMENT STEP5: CALCULATE VELOCITES - FastAssign(VN,body2->v); - FastTMult(body2->n_C_k,body2->v,body2->v_k); - - - //CALCULATE KE - + + + + //COMMENT STEP5: CALCULATE VELOCITES + FastAssign(VN,body2->v); + FastTMult(body2->n_C_k,body2->v,body2->v_k); + + + //CALCULATE KE + Matrix tempke; - tempke = T(body2->v)*(body2->v); + tempke = T(body2->v)*(body2->v); double ke = 0.0; - ke = body2->mass*tempke(1,1); + ke = body2->mass*tempke(1,1); FastMult(body2->inertia,body2->omega_k,result1); - tempke= T(body2->omega_k)*result1; + tempke= T(body2->omega_k)*result1; ke = 0.5*ke + 0.5*tempke(1,1); body2->KE=ke; - - + + //COMMENT STEP6: CALCULATE STATE EXPLICIT ANGULAR ACCELERATIONS body2->alpha_t.Zeros(); - - + + //COMMENT STEP7: CALCULATE STATE EXPLICIT ACCELERATIONS - body2->a_t.Zeros(); - + body2->a_t.Zeros(); + } void FreeBodyJoint::BackwardKinematics(){ -std::cout<<"Did I come here "< - #include "joint.h" -#include "matrix.h" -namespace POEMS { + class FreeBodyJoint : public Joint{ -public: +public: FreeBodyJoint(); ~FreeBodyJoint(); - + JointType GetType(); bool ReadInJointData(std::istream& in); void WriteOutJointData(std::ostream& out); @@ -40,5 +37,5 @@ public: void ForwardKinematics(); void BackwardKinematics(); }; -} + #endif diff --git a/lib/poems/inertialframe.cpp b/lib/poems/inertialframe.cpp index 19ca7cdb0b..6c97b2f584 100644 --- a/lib/poems/inertialframe.cpp +++ b/lib/poems/inertialframe.cpp @@ -16,13 +16,9 @@ *_________________________________________________________________________*/ #include "inertialframe.h" - -#include "mat3x3.h" -#include "virtualmatrix.h" +#include "fixedpoint.h" using namespace std; -using namespace POEMS; - InertialFrame::InertialFrame(){ gravity.Zeros(); diff --git a/lib/poems/inertialframe.h b/lib/poems/inertialframe.h index ae987cdc56..08d0279a1e 100644 --- a/lib/poems/inertialframe.h +++ b/lib/poems/inertialframe.h @@ -19,12 +19,9 @@ #ifndef INERTIALFRAME_H #define INERTIALFRAME_H -#include - #include "body.h" -#include "vect3.h" -namespace POEMS { + class InertialFrame : public Body { Vect3 gravity; public: @@ -36,5 +33,5 @@ public: bool ReadInBodyData(std::istream& in); void WriteOutBodyData(std::ostream& out); }; -} + #endif diff --git a/lib/poems/joint.cpp b/lib/poems/joint.cpp index 3e356337cb..3bdd7b5fcd 100644 --- a/lib/poems/joint.cpp +++ b/lib/poems/joint.cpp @@ -16,28 +16,15 @@ *_________________________________________________________________________*/ -#include -#include -#include - +#include "joints.h" #include "body.h" #include "point.h" +#include +#include "matrixfun.h" #include "fastmatrixops.h" -#include "body23joint.h" -#include "colmatrix.h" -#include "freebodyjoint.h" -#include "joint.h" -#include "mat3x3.h" -#include "matrix.h" -#include "mixedjoint.h" -#include "prismaticjoint.h" -#include "revolutejoint.h" -#include "sphericaljoint.h" -#include "virtualmatrix.h" +#include using namespace std; -using namespace POEMS; - Joint::Joint(){ body1 = body2 = 0; @@ -247,7 +234,7 @@ void Joint::ComputeBackwardGlobalTransform(){ // global joint functions // -Joint* POEMS::NewJoint(int type){ +Joint* NewJoint(int type){ switch( JointType(type) ) { case FREEBODYJOINT : return new FreeBodyJoint; diff --git a/lib/poems/joint.h b/lib/poems/joint.h index fa9b6826a7..17122af775 100644 --- a/lib/poems/joint.h +++ b/lib/poems/joint.h @@ -18,15 +18,9 @@ #ifndef JOINT_H #define JOINT_H -#include #include "poemsobject.h" -#include "colmatrix.h" -#include "mat3x3.h" -#include "matrix.h" -#include "vect3.h" - -namespace POEMS { -class VirtualMatrix; +#include +#include "matrices.h" enum JointType { XYZJOINT = 0, @@ -125,5 +119,5 @@ public: // global joint functions Joint* NewJoint(int type); -} + #endif diff --git a/lib/poems/mat3x3.cpp b/lib/poems/mat3x3.cpp index 8a5098ff59..df24d4b108 100644 --- a/lib/poems/mat3x3.cpp +++ b/lib/poems/mat3x3.cpp @@ -16,13 +16,10 @@ *_________________________________________________________________________*/ -#include -#include #include "mat3x3.h" +#include using namespace std; -using namespace POEMS; - Mat3x3::Mat3x3(){ numrows = numcols = 3; diff --git a/lib/poems/mat3x3.h b/lib/poems/mat3x3.h index bc38e6d393..4362b3ad9c 100644 --- a/lib/poems/mat3x3.h +++ b/lib/poems/mat3x3.h @@ -3,7 +3,7 @@ * POEMS: PARALLELIZABLE OPEN SOURCE EFFICIENT MULTIBODY SOFTWARE * * DESCRIPTION: SEE READ-ME * * FILE NAME: mat3x3.h * - * AUTHORS: See Author List * + * AUTHORS: See Author List * * GRANTS: See Grants List * * COPYRIGHT: (C) 2005 by Authors as listed in Author's List * * LICENSE: Please see License Agreement * @@ -11,19 +11,19 @@ * ADMINISTRATOR: Prof. Kurt Anderson * * Computational Dynamics Lab * * Rensselaer Polytechnic Institute * - * 110 8th St. Troy NY 12180 * + * 110 8th St. Troy NY 12180 * * CONTACT: anderk5@rpi.edu * *_________________________________________________________________________*/ #ifndef MAT3X3_H #define MAT3X3_H -#include #include "virtualmatrix.h" -namespace POEMS { + class Vect3; class Mat6x6; +class Matrix; class ColMatrix; class Mat3x3 : public VirtualMatrix { @@ -68,15 +68,16 @@ public: friend void FastMult(Mat3x3& A, Mat3x3& B, Mat3x3& C); friend void FastMultT(Mat3x3& A, Mat3x3& B, Mat3x3& C); friend void FastAssignT(Mat3x3& A, Mat3x3& C); - friend void FastMult(Mat3x3& A, Vect3& B, ColMatrix& C); - + friend void FastMult(Mat3x3& A, Vect3& B, ColMatrix& C); + friend void OnPopulateSC(Vect3& gamma, Mat3x3& C, Mat6x6& SC); friend void OnPopulateSI(Mat3x3& inertia, double mass, Mat6x6& sI); friend void FastMult(Mat3x3& A, ColMatrix& B, Vect3& C); - + friend void EP_Transformation(ColMatrix& q, Mat3x3& C); friend void EP_FromTransformation(ColMatrix& q, Mat3x3& C); + }; -} + #endif diff --git a/lib/poems/mat4x4.cpp b/lib/poems/mat4x4.cpp index 9a0e7b8d56..4a611a6796 100644 --- a/lib/poems/mat4x4.cpp +++ b/lib/poems/mat4x4.cpp @@ -16,13 +16,9 @@ *_________________________________________________________________________*/ #include "mat4x4.h" - #include -#include using namespace std; -using namespace POEMS; - Mat4x4::Mat4x4(){ numrows = numcols = 4; diff --git a/lib/poems/mat4x4.h b/lib/poems/mat4x4.h index 3f6d97ba15..d7942b248e 100644 --- a/lib/poems/mat4x4.h +++ b/lib/poems/mat4x4.h @@ -3,7 +3,7 @@ * POEMS: PARALLELIZABLE OPEN SOURCE EFFICIENT MULTIBODY SOFTWARE * * DESCRIPTION: SEE READ-ME * * FILE NAME: mat4x4.h * - * AUTHORS: See Author List * + * AUTHORS: See Author List * * GRANTS: See Grants List * * COPYRIGHT: (C) 2005 by Authors as listed in Author's List * * LICENSE: Please see License Agreement * @@ -11,28 +11,27 @@ * ADMINISTRATOR: Prof. Kurt Anderson * * Computational Dynamics Lab * * Rensselaer Polytechnic Institute * - * 110 8th St. Troy NY 12180 * + * 110 8th St. Troy NY 12180 * * CONTACT: anderk5@rpi.edu * *_________________________________________________________________________*/ #ifndef MAT4X4_H #define MAT4X4_H -#include #include "virtualmatrix.h" +#include "matrix.h" + -namespace POEMS { class Vect4; -class Matrix; class Mat4x4 : public VirtualMatrix { double elements[4][4]; -public: +public: Mat4x4(); ~Mat4x4(); Mat4x4(const Mat4x4& A); // copy constructor Mat4x4(const VirtualMatrix& A); // copy constructor - + double& operator_2int (int i, int j); // array access double Get_2int(int i, int j) const; void Set_2int(int i, int j, double value); @@ -65,5 +64,5 @@ public: friend void FastMultT(Mat4x4& A, Mat4x4& B, Mat4x4& C); friend void FastAssignT(Mat4x4& A, Mat4x4& C); }; -} + #endif diff --git a/lib/poems/mat6x6.cpp b/lib/poems/mat6x6.cpp index e9dde2fe87..16bffc5026 100644 --- a/lib/poems/mat6x6.cpp +++ b/lib/poems/mat6x6.cpp @@ -16,13 +16,9 @@ *_________________________________________________________________________*/ #include "mat6x6.h" - #include -#include using namespace std; -using namespace POEMS; - Mat6x6::Mat6x6(){ numrows = numcols = 6; diff --git a/lib/poems/mat6x6.h b/lib/poems/mat6x6.h index a611bc8283..11951b0442 100644 --- a/lib/poems/mat6x6.h +++ b/lib/poems/mat6x6.h @@ -17,11 +17,9 @@ #ifndef MAT6X6_H #define MAT6X6_H -#include - #include "virtualmatrix.h" -namespace POEMS { + class Matrix; class Mat3x3; class Vect6; @@ -74,5 +72,5 @@ public: friend void OnPopulateSC(Vect3& gamma, Mat3x3& C, Mat6x6& SC); friend void OnPopulateSI(Mat3x3& inertia, double mass, Mat6x6& sI); }; -} + #endif diff --git a/lib/poems/matrices.h b/lib/poems/matrices.h index 15f0d3ad23..7a7e2c4b58 100644 --- a/lib/poems/matrices.h +++ b/lib/poems/matrices.h @@ -3,7 +3,7 @@ * POEMS: PARALLELIZABLE OPEN SOURCE EFFICIENT MULTIBODY SOFTWARE * * DESCRIPTION: SEE READ-ME * * FILE NAME: matrices.h * - * AUTHORS: See Author List * + * AUTHORS: See Author List * * GRANTS: See Grants List * * COPYRIGHT: (C) 2005 by Authors as listed in Author's List * * LICENSE: Please see License Agreement * @@ -11,7 +11,7 @@ * ADMINISTRATOR: Prof. Kurt Anderson * * Computational Dynamics Lab * * Rensselaer Polytechnic Institute * - * 110 8th St. Troy NY 12180 * + * 110 8th St. Troy NY 12180 * * CONTACT: anderk5@rpi.edu * *_________________________________________________________________________*/ @@ -20,14 +20,23 @@ #define MATRICES_H #include "matrix.h" + #include "colmatrix.h" + #include "rowmatrix.h" + #include "mat3x3.h" + #include "vect3.h" + #include "mat4x4.h" + #include "vect4.h" + #include "mat6x6.h" + #include "vect6.h" + #include "colmatmap.h" #endif diff --git a/lib/poems/matrix.cpp b/lib/poems/matrix.cpp index f7b0c631f2..f05d6f815c 100644 --- a/lib/poems/matrix.cpp +++ b/lib/poems/matrix.cpp @@ -21,8 +21,6 @@ #include using namespace std; -using namespace POEMS; - Matrix::Matrix(){ numrows = numcols = 0; diff --git a/lib/poems/matrix.h b/lib/poems/matrix.h index c2ed92873c..63699b9835 100644 --- a/lib/poems/matrix.h +++ b/lib/poems/matrix.h @@ -3,7 +3,7 @@ * POEMS: PARALLELIZABLE OPEN SOURCE EFFICIENT MULTIBODY SOFTWARE * * DESCRIPTION: SEE READ-ME * * FILE NAME: matrix.h * - * AUTHORS: See Author List * + * AUTHORS: See Author List * * GRANTS: See Grants List * * COPYRIGHT: (C) 2005 by Authors as listed in Author's List * * LICENSE: Please see License Agreement * @@ -11,18 +11,15 @@ * ADMINISTRATOR: Prof. Kurt Anderson * * Computational Dynamics Lab * * Rensselaer Polytechnic Institute * - * 110 8th St. Troy NY 12180 * + * 110 8th St. Troy NY 12180 * * CONTACT: anderk5@rpi.edu * *_________________________________________________________________________*/ #ifndef MATRIX_H #define MATRIX_H -#include - #include "virtualmatrix.h" -namespace POEMS { class Mat3x3; class Mat4x4; class Mat6x6; @@ -74,6 +71,7 @@ public: friend void FastMult(Mat6x6& A, Matrix& B, Matrix& C); friend void FastMult(Matrix& A, ColMatrix& B, Vect6& C); friend void FastMultT(Matrix& A, Matrix& B, Mat6x6& C); + }; -} + #endif diff --git a/lib/poems/matrixfun.cpp b/lib/poems/matrixfun.cpp index 037e986a99..d193114679 100644 --- a/lib/poems/matrixfun.cpp +++ b/lib/poems/matrixfun.cpp @@ -16,25 +16,17 @@ *_________________________________________________________________________*/ #include "matrixfun.h" - -#include -#include - +#include #include "fastmatrixops.h" -#include "vect4.h" -#include "virtualcolmatrix.h" -#include "virtualmatrix.h" -#include "virtualrowmatrix.h" +#include using namespace std; -using namespace POEMS; - // // Create a new matrix // -VirtualMatrix* POEMS::NewMatrix(int type){ +VirtualMatrix* NewMatrix(int type){ switch( MatrixType(type) ) { case MATRIX : return new Matrix; @@ -52,7 +44,7 @@ VirtualMatrix* POEMS::NewMatrix(int type){ // Transpose // -Matrix POEMS::T(const VirtualMatrix& A){ +Matrix T(const VirtualMatrix& A){ int numrows = A.GetNumRows(); int numcols = A.GetNumCols(); Matrix C(numcols,numrows); @@ -62,8 +54,8 @@ Matrix POEMS::T(const VirtualMatrix& A){ return C; } -Mat3x3 POEMS::T(const Mat3x3& A){ - Mat3x3 C; +Mat3x3 T(const Mat3x3& A){ + Mat3x3 C; C.elements[0][0] = A.elements[0][0]; C.elements[1][1] = A.elements[1][1]; C.elements[2][2] = A.elements[2][2]; @@ -78,7 +70,7 @@ Mat3x3 POEMS::T(const Mat3x3& A){ return C; } -Mat6x6 POEMS::T(const Mat6x6& A){ +Mat6x6 T(const Mat6x6& A){ Mat6x6 C; int i,j; for(i=0;i<6;i++) @@ -88,7 +80,7 @@ Mat6x6 POEMS::T(const Mat6x6& A){ return C; } -Matrix POEMS::T(const Vect3& A){ +Matrix T(const Vect3& A){ Matrix C(1,3); C.BasicSet(0,0,A.elements[0]); C.BasicSet(0,1,A.elements[1]); @@ -97,7 +89,7 @@ Matrix POEMS::T(const Vect3& A){ return C; } -Matrix POEMS::T(const Vect6& A){ +Matrix T(const Vect6& A){ Matrix C(1,6); C.BasicSet(0,0,A.elements[0]); C.BasicSet(0,1,A.elements[1]); @@ -109,7 +101,7 @@ Matrix POEMS::T(const Vect6& A){ return C; } -RowMatrix POEMS::T(const VirtualColMatrix &A){ +RowMatrix T(const VirtualColMatrix &A){ int numele = A.GetNumRows(); RowMatrix C(numele); for(int i=0;i - +#include "point.h" #include "matrixfun.h" #include "body.h" #include "fastmatrixops.h" +#include "norm.h" #include "eulerparameters.h" -#include "colmatrix.h" -#include "mat3x3.h" -#include "mat6x6.h" -#include "vect3.h" -#include "virtualmatrix.h" - -using namespace POEMS; -using namespace std; +#include "matrices.h" + -MixedJoint::MixedJoint(){ +MixedJoint::MixedJoint(){ } MixedJoint::~MixedJoint(){ @@ -56,23 +49,23 @@ void MixedJoint::SetsP(Matrix& sPr, Vect6& temp_dofs, int i, int j){ numrots = i; numtrans = j; if (numrots < 2) - DimQandU(numrots+numtrans,numrots+numtrans); - else - DimQandU((4+numtrans),(numrots+numtrans)); + DimQandU(numrots+numtrans,numrots+numtrans); + else + DimQandU((4+numtrans),(numrots+numtrans)); cout<<"Check "<<4+numtrans<<" "< 1) EP_Normalize(q); // COMMENT STEP1: CALCULATE ORIENTATIONS - ComputeForwardTransforms(); - - + ComputeForwardTransforms(); + + //COMMENT STEP2: CALCULATE POSITION VECTORS - Vect3 result1, result2, result3, result4; + Vect3 result1, result2, result3, result4; result1.Zeros(); for (int k=0; k<3; k++){ if( dofs(3+k) != 0.0 ){ @@ -118,32 +111,32 @@ void MixedJoint::ForwardKinematics(){ result1.BasicSet(k,q.BasicGet(4 + k)); else result1.BasicSet(k,q.BasicGet(numrots + k)); - } + } } - - - - FastAssign(result1,r12); // r12 in parents basis i.e. Newtonian - FastNegMult(k_C_pk,r12,r21); // r21 in body basis - - FastAssign(r12,body2->r); // This is right - - //COMMENT STEP3: CALCULATE QDOT + + + + FastAssign(result1,r12); // r12 in parents basis i.e. Newtonian + FastNegMult(k_C_pk,r12,r21); // r21 in body basis + + FastAssign(r12,body2->r); // This is right + + //COMMENT STEP3: CALCULATE QDOT int pp = 0; if (numrots > 1){ ColMatrix temp_u(3+numtrans); qdot_to_u(q,temp_u,qdot); for (int k=1;k<=6;k++){ if(dofs(k) != 0.0){ - u.BasicSet(pp,temp_u.BasicGet(k-1)); + u.BasicSet(pp,temp_u.BasicGet(k-1)); pp = pp+1; - } + } } } else u = qdot; - - + + Vect3 WN; WN.Zeros(); int p = 0; for (int k=0;k<3;k++){ @@ -153,51 +146,51 @@ void MixedJoint::ForwardKinematics(){ } }// WN is in body basis - - Vect3 VN; VN.Zeros(); + + Vect3 VN; VN.Zeros(); for (int k=0;k<3;k++){ if( dofs(3+k+1) != 0.0 ) { VN.BasicSet(k,u.BasicGet(p)); p=p+1; } }// VN is the vector of translational velocities in Newtonian basis + + FastAssign(WN,body2->omega_k); - FastAssign(WN,body2->omega_k); - - // cout<<"Angular Velocity "<n_C_k,WN,pk_w_k); + FastMult(body2->n_C_k,WN,pk_w_k); FastAssign(pk_w_k,body2->omega); - - - - //COMMENT STEP5: CALCULATE VELOCITES - FastAssign(VN,body2->v); - FastTMult(body2->n_C_k,body2->v,body2->v_k); - - - //CALCULATE KE - + + + + //COMMENT STEP5: CALCULATE VELOCITES + FastAssign(VN,body2->v); + FastTMult(body2->n_C_k,body2->v,body2->v_k); + + + //CALCULATE KE + Matrix tempke; - tempke = T(body2->v)*(body2->v); + tempke = T(body2->v)*(body2->v); double ke = 0.0; - ke = body2->mass*tempke(1,1); + ke = body2->mass*tempke(1,1); FastMult(body2->inertia,body2->omega_k,result1); - tempke= T(body2->omega_k)*result1; + tempke= T(body2->omega_k)*result1; ke = 0.5*ke + 0.5*tempke(1,1); body2->KE=ke; - - + + //COMMENT STEP6: CALCULATE STATE EXPLICIT ANGULAR ACCELERATIONS body2->alpha_t.Zeros(); - - + + //COMMENT STEP7: CALCULATE STATE EXPLICIT ACCELERATIONS - body2->a_t.Zeros(); - + body2->a_t.Zeros(); + } void MixedJoint::BackwardKinematics(){ cout<<"Did I come here "< - #include "joint.h" -#include "matrix.h" -#include "vect6.h" -namespace POEMS { + class MixedJoint : public Joint{ Matrix const_sP; int numrots; int numtrans; Vect6 dofs; -public: +public: MixedJoint(); ~MixedJoint(); - + JointType GetType(); bool ReadInJointData(std::istream& in); void WriteOutJointData(std::ostream& out); @@ -46,5 +42,5 @@ public: void ForwardKinematics(); void BackwardKinematics(); }; -} + #endif diff --git a/lib/poems/norm.cpp b/lib/poems/norm.cpp index 6c983dd06f..0f918cf968 100644 --- a/lib/poems/norm.cpp +++ b/lib/poems/norm.cpp @@ -16,15 +16,7 @@ *_________________________________________________________________________*/ #include - #include "norm.h" -#include "colmatrix.h" -#include "rowmatrix.h" -#include "vect3.h" -#include "vect4.h" -#include "vect6.h" - -using namespace POEMS; double Magnitude(ColMatrix& A){ double G; diff --git a/lib/poems/norm.h b/lib/poems/norm.h index 808be609e8..963a2ec5b2 100644 --- a/lib/poems/norm.h +++ b/lib/poems/norm.h @@ -3,7 +3,7 @@ * POEMS: PARALLELIZABLE OPEN SOURCE EFFICIENT MULTIBODY SOFTWARE * * DESCRIPTION: SEE READ-ME * * FILE NAME: norm.h * - * AUTHORS: See Author List * + * AUTHORS: See Author List * * GRANTS: See Grants List * * COPYRIGHT: (C) 2005 by Authors as listed in Author's List * * LICENSE: Please see License Agreement * @@ -11,24 +11,20 @@ * ADMINISTRATOR: Prof. Kurt Anderson * * Computational Dynamics Lab * * Rensselaer Polytechnic Institute * - * 110 8th St. Troy NY 12180 * + * 110 8th St. Troy NY 12180 * * CONTACT: anderk5@rpi.edu * *_________________________________________________________________________*/ #ifndef NORM_H #define NORM_H -namespace POEMS { -class ColMatrix; -class RowMatrix; -class Vect3; -class Vect4; -class Vect6; +#include "matrices.h" + double Magnitude(ColMatrix& A); double Magnitude(RowMatrix& A); double Magnitude(Vect3& A); double Magnitude(Vect4& A); double Magnitude(Vect6& A); -} + #endif diff --git a/lib/poems/onbody.cpp b/lib/poems/onbody.cpp index 7cea2d2f25..102900df8d 100644 --- a/lib/poems/onbody.cpp +++ b/lib/poems/onbody.cpp @@ -16,22 +16,17 @@ *_________________________________________________________________________*/ #include "onbody.h" - -#include -#include - #include "body.h" #include "inertialframe.h" #include "joint.h" #include "onfunctions.h" #include "virtualmatrix.h" #include "matrixfun.h" +#include +#include "norm.h" #include "eulerparameters.h" -#include "colmatrix.h" using namespace std; -using namespace POEMS; - OnBody::OnBody(){ diff --git a/lib/poems/onbody.h b/lib/poems/onbody.h index df82709ad5..d9923773c7 100644 --- a/lib/poems/onbody.h +++ b/lib/poems/onbody.h @@ -3,7 +3,7 @@ * POEMS: PARALLELIZABLE OPEN SOURCE EFFICIENT MULTIBODY SOFTWARE * * DESCRIPTION: SEE READ-ME * * FILE NAME: onbody.h * - * AUTHORS: See Author List * + * AUTHORS: See Author List * * GRANTS: See Grants List * * COPYRIGHT: (C) 2005 by Authors as listed in Author's List * * LICENSE: Please see License Agreement * @@ -11,7 +11,7 @@ * ADMINISTRATOR: Prof. Kurt Anderson * * Computational Dynamics Lab * * Rensselaer Polytechnic Institute * - * 110 8th St. Troy NY 12180 * + * 110 8th St. Troy NY 12180 * * CONTACT: anderk5@rpi.edu * *_________________________________________________________________________*/ @@ -22,14 +22,6 @@ #include "matrix.h" #include "vect6.h" #include "mat6x6.h" -#include "joint.h" -#include "mat3x3.h" -#include "vect3.h" - -namespace POEMS { -class Body; -class ColMatrix; -class InertialFrame; // emumerated type enum Direction { @@ -37,65 +29,71 @@ enum Direction { FORWARD= 1 }; -class OnBody { - Body* system_body; - Joint* system_joint; - OnBody* parent; - List children; - - Direction joint_dir; - void (Joint::*kinfun)(); // kinematics function - void (Joint::*updatesP)(Matrix&); // sP update function - Vect3* gamma; // pointer to gamma vector - Mat3x3* pk_C_k; // pointer to transformation +class Body; +class InertialFrame; +class Joint; +class OnSolver; +class OnBody { + Body* system_body; + Joint* system_joint; + OnBody* parent; + List children; - Mat6x6 sI; // spatial inertias - Mat6x6 sIhat; // recursive spatial inertias - Mat6x6 sSC; // spatial shift - Mat6x6 sT; // spatial triangularization + Direction joint_dir; + void (Joint::*kinfun)(); // kinematics function + void (Joint::*updatesP)(Matrix&); // sP update function + Vect3* gamma; // pointer to gamma vector + Mat3x3* pk_C_k; // pointer to transformation - Vect6 sF; // spatial forces - Vect6 sFhat; // recursive spatial forces - Vect6 sAhat; // recursive spatial acceleration + + Mat6x6 sI; // spatial inertias + Mat6x6 sIhat; // recursive spatial inertias + Mat6x6 sSC; // spatial shift + Mat6x6 sT; // spatial triangularization - Matrix sP; // spatial partial velocities - Matrix sM; // triangularized mass matrix diagonal elements - Matrix sMinv; // inverse of sM - Matrix sPsMinv; - Matrix sIhatsP; + Vect6 sF; // spatial forces + Vect6 sFhat; // recursive spatial forces + Vect6 sAhat; // recursive spatial acceleration - // states and state derivatives - ColMatrix* q; - ColMatrix* u; - ColMatrix* qdot; - ColMatrix* udot; - ColMatrix* qdotdot; + Matrix sP; // spatial partial velocities + Matrix sM; // triangularized mass matrix diagonal elements + Matrix sMinv; // inverse of sM + Matrix sPsMinv; + Matrix sIhatsP; - ColMatrix* r; - ColMatrix* acc; - ColMatrix* ang; + // states and state derivatives + ColMatrix* q; + ColMatrix* u; + ColMatrix* qdot; + ColMatrix* udot; + ColMatrix* qdotdot; + + ColMatrix* r; + ColMatrix* acc; + ColMatrix* ang; // friend classes friend class OnSolver; + -public: - OnBody(); - ~OnBody(); - int RecursiveSetup(InertialFrame* basebody); - int RecursiveSetup(int ID, OnBody* parentbody, Joint* sys_joint); - void RecursiveKinematics(); - void RecursiveTriangularization(); - void RecursiveForwardSubstitution(); - Mat3x3 GetN_C_K(); - Vect3 LocalCart(); - int GetBodyID(); - void CalculateAcceleration(); - void Setup(); - void SetupInertialFrame(); - void LocalKinematics(); - void LocalTriangularization(Vect3& Torque, Vect3& Force); - void LocalForwardSubstitution(); +public: + OnBody(); + ~OnBody(); + int RecursiveSetup(InertialFrame* basebody); + int RecursiveSetup(int ID, OnBody* parentbody, Joint* sys_joint); + void RecursiveKinematics(); + void RecursiveTriangularization(); + void RecursiveForwardSubstitution(); + Mat3x3 GetN_C_K(); + Vect3 LocalCart(); + int GetBodyID(); + void CalculateAcceleration(); + void Setup(); + void SetupInertialFrame(); + void LocalKinematics(); + void LocalTriangularization(Vect3& Torque, Vect3& Force); + void LocalForwardSubstitution(); }; -} + #endif diff --git a/lib/poems/onfunctions.cpp b/lib/poems/onfunctions.cpp index cfc0c60936..582ab8cf8b 100644 --- a/lib/poems/onfunctions.cpp +++ b/lib/poems/onfunctions.cpp @@ -3,7 +3,7 @@ * POEMS: PARALLELIZABLE OPEN SOURCE EFFICIENT MULTIBODY SOFTWARE * * DESCRIPTION: SEE READ-ME * * FILE NAME: onfunction.cpp * - * AUTHORS: See Author List * + * AUTHORS: See Author List * * GRANTS: See Grants List * * COPYRIGHT: (C) 2005 by Authors as listed in Author's List * * LICENSE: Please see License Agreement * @@ -11,25 +11,18 @@ * ADMINISTRATOR: Prof. Kurt Anderson * * Computational Dynamics Lab * * Rensselaer Polytechnic Institute * - * 110 8th St. Troy NY 12180 * + * 110 8th St. Troy NY 12180 * * CONTACT: anderk5@rpi.edu * *_________________________________________________________________________*/ - + #include "onfunctions.h" - -#include "mat3x3.h" -#include "mat6x6.h" -#include "vect3.h" -#include "vect6.h" -#include "virtualmatrix.h" - +#include "matrixfun.h" +#include using namespace std; -using namespace POEMS; - // friend of Vect3 & Vect6 -void POEMS::OnPopulateSVect(Vect3& angular, Vect3& linear, Vect6& sV){ +void OnPopulateSVect(Vect3& angular, Vect3& linear, Vect6& sV){ sV.elements[0] = angular.elements[0]; sV.elements[1] = angular.elements[1]; sV.elements[2] = angular.elements[2]; @@ -39,38 +32,38 @@ void POEMS::OnPopulateSVect(Vect3& angular, Vect3& linear, Vect6& sV){ } // friend of Vect3, Mat3x3, & Mat6x6 -void POEMS::OnPopulateSC(Vect3& gamma, Mat3x3& C, Mat6x6& SC){ +void OnPopulateSC(Vect3& gamma, Mat3x3& C, Mat6x6& SC){ // the block diagonals - + // the gamma cross with transform Mat3x3 temp; Mat3x3 temp2; SC.Zeros(); - temp.Zeros(); + temp.Zeros(); temp2.Zeros(); - //FastTMult(C,gamma,temp); + //FastTMult(C,gamma,temp); temp(1,2)= -gamma(3); temp(1,3)= gamma(2); temp(2,1)= gamma(3); - temp(2,3)= -gamma(1); temp(3,1)= -gamma(2); temp(3,2)= gamma(1); + temp(2,3)= -gamma(1); temp(3,1)= -gamma(2); temp(3,2)= gamma(1); FastMult(temp,C,temp2); - + SC(1,4)=temp2(1,1); SC(2,4)=temp2(2,1); SC(3,4)=temp2(3,1); SC(1,5)=temp2(1,2); SC(2,5)=temp2(2,2); SC(3,5)=temp2(3,2); SC(1,6)=temp2(1,3); SC(2,6)=temp2(2,3); SC(3,6)=temp2(3,3); - + SC(1,1)=C(1,1); SC(2,1)=C(2,1); SC(3,1)=C(3,1); SC(1,2)=C(1,2); SC(2,2)=C(2,2); SC(3,2)=C(3,2); SC(1,3)=C(1,3); SC(2,3)=C(2,3); SC(3,3)=C(3,3); SC(4,4)=C(1,1); SC(5,4)=C(2,1); SC(6,4)=C(3,1); SC(4,5)=C(1,2); SC(5,5)=C(2,2); SC(6,5)=C(3,2); - SC(4,6)=C(1,3); SC(5,6)=C(2,3); SC(6,6)=C(3,3); - + SC(4,6)=C(1,3); SC(5,6)=C(2,3); SC(6,6)=C(3,3); + } // friend of Mat3x3 & Mat6x6 -void POEMS::OnPopulateSI(Mat3x3& inertia, double mass, Mat6x6& sI){ - - sI(4,4)=mass; sI(5,5)=mass; sI(6,6)=mass; - sI(1,1)=inertia(1,1); sI(1,2)=inertia(1,2); sI(1,3)=inertia(1,3); - sI(2,1)=inertia(2,1); sI(2,2)=inertia(2,2); sI(2,3)=inertia(2,3); - sI(3,1)=inertia(3,1); sI(3,2)=inertia(3,2); sI(3,3)=inertia(3,3); +void OnPopulateSI(Mat3x3& inertia, double mass, Mat6x6& sI){ + + sI(4,4)=mass; sI(5,5)=mass; sI(6,6)=mass; + sI(1,1)=inertia(1,1); sI(1,2)=inertia(1,2); sI(1,3)=inertia(1,3); + sI(2,1)=inertia(2,1); sI(2,2)=inertia(2,2); sI(2,3)=inertia(2,3); + sI(3,1)=inertia(3,1); sI(3,2)=inertia(3,2); sI(3,3)=inertia(3,3); } diff --git a/lib/poems/onfunctions.h b/lib/poems/onfunctions.h index bb07425b85..8a69694095 100644 --- a/lib/poems/onfunctions.h +++ b/lib/poems/onfunctions.h @@ -18,11 +18,7 @@ #ifndef ONFUNCTIONS_H #define ONFUNCTIONS_H -namespace POEMS { -class Mat3x3; -class Mat6x6; -class Vect3; -class Vect6; +#include "matrices.h" void OnPopulateSVect(Vect3& angular, Vect3& linear, Vect6& sV); void OnPopulateSC(Vect3& gamma, Mat3x3& C, Mat6x6& SC); @@ -31,5 +27,5 @@ void OnPopulateSI(Mat3x3& inertia, double mass, Mat6x6& sI); void Create_Map(int MM); int ICELL(int IX,int IY,int IZ, int MM); -} + #endif diff --git a/lib/poems/onsolver.cpp b/lib/poems/onsolver.cpp index 609ef32613..ad04d7e9e3 100644 --- a/lib/poems/onsolver.cpp +++ b/lib/poems/onsolver.cpp @@ -16,25 +16,15 @@ *_________________________________________________________________________*/ -#include -#include - #include "onsolver.h" #include "system.h" #include "onbody.h" #include "body.h" -#include "colmatmap.h" -#include "colmatrix.h" -#include "defines.h" -#include "inertialframe.h" -#include "matrix.h" -#include "poemslist.h" -#include "vect3.h" -#include "virtualmatrix.h" +#include "matrixfun.h" +#include -using namespace std; -using namespace POEMS; +using namespace std; OnSolver::OnSolver(){ numbodies = 0; diff --git a/lib/poems/onsolver.h b/lib/poems/onsolver.h index 1e850b8fc1..f32b5880a9 100644 --- a/lib/poems/onsolver.h +++ b/lib/poems/onsolver.h @@ -3,7 +3,7 @@ * POEMS: PARALLELIZABLE OPEN SOURCE EFFICIENT MULTIBODY SOFTWARE * * DESCRIPTION: SEE READ-ME * * FILE NAME: onsolver.h * - * AUTHORS: See Author List * + * AUTHORS: See Author List * * GRANTS: See Grants List * * COPYRIGHT: (C) 2005 by Authors as listed in Author's List * * LICENSE: Please see License Agreement * @@ -11,7 +11,7 @@ * ADMINISTRATOR: Prof. Kurt Anderson * * Computational Dynamics Lab * * Rensselaer Polytechnic Institute * - * 110 8th St. Troy NY 12180 * + * 110 8th St. Troy NY 12180 * * CONTACT: anderk5@rpi.edu * *_________________________________________________________________________*/ @@ -21,32 +21,31 @@ #include "solver.h" #include "onbody.h" +#include -namespace POEMS { -class ColMatrix; -class Matrix; + class OnSolver : public Solver { - OnBody inertialframe; - int numbodies; - OnBody** bodyarray; - ColMatrix** q; - ColMatrix** qdot; - ColMatrix** qdotdot; - ColMatrix** u; - ColMatrix** udot; - - - - void DeleteModel(); - int CreateTopologyArray(int i, OnBody* body); - void CreateStateMatrixMaps(); - void GetType(); -public: - OnSolver(); - ~OnSolver(); - void CreateModel(); - void Solve(double time, Matrix& FF); + OnBody inertialframe; + int numbodies; + OnBody** bodyarray; + ColMatrix** q; + ColMatrix** qdot; + ColMatrix** qdotdot; + ColMatrix** u; + ColMatrix** udot; + + + + void DeleteModel(); + int CreateTopologyArray(int i, OnBody* body); + void CreateStateMatrixMaps(); + void GetType(); +public: + OnSolver(); + ~OnSolver(); + void CreateModel(); + void Solve(double time, Matrix& FF); }; -} + #endif diff --git a/lib/poems/particle.cpp b/lib/poems/particle.cpp index 37ec790666..3496bc1906 100644 --- a/lib/poems/particle.cpp +++ b/lib/poems/particle.cpp @@ -17,8 +17,7 @@ #include "particle.h" - -using namespace POEMS; +#include "fixedpoint.h" Particle::Particle(){ } diff --git a/lib/poems/particle.h b/lib/poems/particle.h index 8a7a521451..20aa4831ea 100644 --- a/lib/poems/particle.h +++ b/lib/poems/particle.h @@ -3,7 +3,7 @@ * POEMS: PARALLELIZABLE OPEN SOURCE EFFICIENT MULTIBODY SOFTWARE * * DESCRIPTION: SEE READ-ME * * FILE NAME: particle.h * - * AUTHORS: See Author List * + * AUTHORS: See Author List * * GRANTS: See Grants List * * COPYRIGHT: (C) 2005 by Authors as listed in Author's List * * LICENSE: Please see License Agreement * @@ -11,7 +11,7 @@ * ADMINISTRATOR: Prof. Kurt Anderson * * Computational Dynamics Lab * * Rensselaer Polytechnic Institute * - * 110 8th St. Troy NY 12180 * + * 110 8th St. Troy NY 12180 * * CONTACT: anderk5@rpi.edu * *_________________________________________________________________________*/ @@ -19,18 +19,16 @@ #ifndef PARTICLE_H #define PARTICLE_H -#include - #include "body.h" -namespace POEMS { + class Particle : public Body { -public: +public: Particle(); ~Particle(); BodyType GetType(); bool ReadInBodyData(std::istream& in); void WriteOutBodyData(std::ostream& out); }; -} + #endif diff --git a/lib/poems/poemslist.h b/lib/poems/poemslist.h index bd0c1456b4..9882af013a 100644 --- a/lib/poems/poemslist.h +++ b/lib/poems/poemslist.h @@ -3,7 +3,7 @@ * POEMS: PARALLELIZABLE OPEN SOURCE EFFICIENT MULTIBODY SOFTWARE * * DESCRIPTION: SEE READ-ME * * FILE NAME: poemslist.h * - * AUTHORS: See Author List * + * AUTHORS: See Author List * * GRANTS: See Grants List * * COPYRIGHT: (C) 2005 by Authors as listed in Author's List * * LICENSE: Please see License Agreement * @@ -11,7 +11,7 @@ * ADMINISTRATOR: Prof. Kurt Anderson * * Computational Dynamics Lab * * Rensselaer Polytechnic Institute * - * 110 8th St. Troy NY 12180 * + * 110 8th St. Troy NY 12180 * * CONTACT: anderk5@rpi.edu * *_________________________________________________________________________*/ @@ -21,7 +21,8 @@ #include #include -namespace POEMS { +using namespace std; + template class ListElement{ public: ListElement* prev; @@ -50,7 +51,7 @@ public: S* operator()(int id); void Append(List * listToAppend); void DeleteValues(); - void RemoveElementAndDeleteValue(ListElement* ele); + void RemoveElementAndDeleteValue(ListElement* ele); void PrintList(); }; @@ -89,9 +90,9 @@ template List::~List(){ template void List::Append(List * listToAppend) { - tail->next = listToAppend->head; - listToAppend->head->prev = tail; - tail = listToAppend->tail; + tail->next = listToAppend->head; + listToAppend->head->prev = tail; + tail = listToAppend->tail; } template int List::GetNumElements(){ @@ -103,17 +104,17 @@ template ListElement* List::GetHeadElement(){ } template ListElement* List::GetTailElement(){ - return tail; + return tail; } template void List::Remove(ListElement* ele){ if(!ele){ - std::cerr << "ERROR: ListElement to be removed not defined" << std::endl; + cerr << "ERROR: ListElement to be removed not defined" << endl; exit(0); } if(!numelements){ - std::cerr << "ERROR: List is empty" << std::endl; + cerr << "ERROR: List is empty" << endl; exit(0); } @@ -134,7 +135,7 @@ template void List::Remove(ListElement* ele){ template ListElement* List::Append(S* v){ if(!v){ - std::cerr << "ERROR: cannot add null Body to list" << std::endl; + cerr << "ERROR: cannot add null Body to list" << endl; exit(0); } @@ -144,22 +145,22 @@ template ListElement* List::Append(S* v){ if(numelements==1) head = tail = ele; else{ - /* + /* tail->next = ele; ele->prev = tail; - tail = ele;*/ - - ele->prev = tail; - tail = ele; - ele->prev->next = ele; - - } + tail = ele;*/ + + ele->prev = tail; + tail = ele; + ele->prev->next = ele; + + } return ele; } template ListElement* List::Prepend(S* v){ if(!v){ - std::cerr << "ERROR: cannot add null Body to list" << std::endl; + cerr << "ERROR: cannot add null Body to list" << endl; exit(0); } @@ -169,9 +170,9 @@ template ListElement* List::Prepend(S* v){ if(numelements==1) head = tail = ele; else{ - ele->next = head; - head = ele; - ele->next->prev = ele; + ele->next = head; + head = ele; + ele->next->prev = ele; } return ele; } @@ -189,15 +190,15 @@ template S** List::CreateArray(){ template S* List::operator()(int id){ if(id >= numelements){ - std::cerr << "ERROR: subscript out of bounds" << std::endl; + cerr << "ERROR: subscript out of bounds" << endl; exit(0); } - + ListElement* ele = head; for(int i=0;inext; } - + return ele->value; } @@ -213,15 +214,16 @@ template void List::RemoveElementAndDeleteValue(ListElement* ele) } template void List::PrintList(){ - std::cout << "Printing List " << std::endl; - ListElement* ele = head; - std::cout << *(ele->value) << " "; - ele = ele->next; - for(int k =2; kvalue) << " "; - ele = ele->next; - } - std::cout << *(ele->value) << std::endl; -} + cout<<"Printing List "<* ele = head; + cout<<*(ele->value)<<" "; + ele = ele->next; + for(int k =2; kvalue)<<" "; + ele = ele->next; + } + cout<<*(ele->value)< -namespace POEMS { +using namespace std; + + TreeNode *GetTreeNode(int item,TreeNode *lptr = NULL,TreeNode *rptr =NULL); void FreeTreeNode(TreeNode *p); @@ -79,7 +81,7 @@ TreeNode *GetTreeNode(int item,TreeNode *lptr,TreeNode *rptr) // if insufficient memory, terminatewith an error message if (p == NULL) { - std::cerr << "Memory allocation failure!\n"; + cerr << "Memory allocation failure!\n"; exit(1); } @@ -138,7 +140,7 @@ void IndentBlanks(int num) // const int indentblock = 6; for(int i = 0; i < num; i++) - std::cout << " "; + cout << " "; } void PrintTree (TreeNode *t, int level) @@ -151,11 +153,10 @@ void PrintTree (TreeNode *t, int level) PrintTree(t->Right(),level + 1); // indent to current level; output node data IndentBlanks(indentUnit*level); - std::cout << t->GetData() << std::endl; + cout << t->GetData() << endl; // print left branch of tree t PrintTree(t->Left(),level + 1); } } -} #endif diff --git a/lib/poems/poemsobject.cpp b/lib/poems/poemsobject.cpp index dfdd95953e..7c3f1ca872 100644 --- a/lib/poems/poemsobject.cpp +++ b/lib/poems/poemsobject.cpp @@ -19,8 +19,6 @@ #include "poemsobject.h" #include -using namespace POEMS; - POEMSObject::POEMSObject(){ name = 0; ChangeName((const char*)"unnamed"); diff --git a/lib/poems/poemsobject.h b/lib/poems/poemsobject.h index 173d9da7ab..63b2915638 100644 --- a/lib/poems/poemsobject.h +++ b/lib/poems/poemsobject.h @@ -19,7 +19,7 @@ #ifndef POEMSOBJECT_H #define POEMSOBJECT_H -namespace POEMS { + class POEMSObject { char* name; int ID; @@ -31,5 +31,5 @@ public: int GetID(); void SetID(int id); }; -} + #endif diff --git a/lib/poems/poemstree.h b/lib/poems/poemstree.h index d49a0d0a88..8f8e80ab66 100644 --- a/lib/poems/poemstree.h +++ b/lib/poems/poemstree.h @@ -21,7 +21,7 @@ #include "poemstreenode.h" #include "poemsnodelib.h" -namespace POEMS { + // constants to indicate the balance factor of a node const int leftheavy = -1; const int balanced = 0; @@ -609,5 +609,5 @@ void Tree::ClearList(void) delete current; size = 0; } -} + #endif diff --git a/lib/poems/poemstreenode.cpp b/lib/poems/poemstreenode.cpp index ca4307f69f..051e13d6e0 100644 --- a/lib/poems/poemstreenode.cpp +++ b/lib/poems/poemstreenode.cpp @@ -17,8 +17,6 @@ #include "poemstreenode.h" -using namespace POEMS; - // constructor; initialize the data and pointer fields // The pointer value NULL assigns a empty subtree TreeNode::TreeNode (const int & item, TreeNode *lptr,TreeNode *rptr, diff --git a/lib/poems/poemstreenode.h b/lib/poems/poemstreenode.h index 69f3caf958..b8f46031a5 100644 --- a/lib/poems/poemstreenode.h +++ b/lib/poems/poemstreenode.h @@ -3,7 +3,7 @@ * POEMS: PARALLELIZABLE OPEN SOURCE EFFICIENT MULTIBODY SOFTWARE * * DESCRIPTION: SEE READ-ME * * FILE NAME: poemstreenode.h * - * AUTHORS: See Author List * + * AUTHORS: See Author List * * GRANTS: See Grants List * * COPYRIGHT: (C) 2005 by Authors as listed in Author's List * * LICENSE: Please see License Agreement * @@ -11,37 +11,42 @@ * ADMINISTRATOR: Prof. Kurt Anderson * * Computational Dynamics Lab * * Rensselaer Polytechnic Institute * - * 110 8th St. Troy NY 12180 * + * 110 8th St. Troy NY 12180 * * CONTACT: anderk5@rpi.edu * *_________________________________________________________________________*/ #ifndef TREENODE_H #define TREENODE_H -namespace POEMS { +//#define NULL 0 + + +//Tree depends on TreeNode +class Tree; + // declares a tree node object for a binary tree class TreeNode{ private: // points to the left and right children of the node - TreeNode *left; - TreeNode *right; - - int balanceFactor; - int data; - void * aux_data; -public: - // make Tree a friend because it needs access to left and right pointer fields of a node - friend class Tree; - TreeNode * Left(); - TreeNode * Right(); - int GetData(); - void * GetAuxData() {return aux_data;}; - void SetAuxData(void * AuxData) {aux_data = AuxData;}; - int GetBalanceFactor(); - TreeNode(const int &item, TreeNode *lptr, TreeNode *rptr, int balfac = 0); - //friend class DCASolver; + TreeNode *left; + TreeNode *right; + + int balanceFactor; + int data; + void * aux_data; +public: + // make Tree a friend because it needs access to left and right pointer fields of a node + friend class Tree; + TreeNode * Left(); + TreeNode * Right(); + int GetData(); + void * GetAuxData() {return aux_data;}; + void SetAuxData(void * AuxData) {aux_data = AuxData;}; + int GetBalanceFactor(); + TreeNode(const int &item, TreeNode *lptr, TreeNode *rptr, int balfac = 0); + //friend class DCASolver; }; -} + #endif diff --git a/lib/poems/point.cpp b/lib/poems/point.cpp index f648b58d3d..4383844736 100644 --- a/lib/poems/point.cpp +++ b/lib/poems/point.cpp @@ -16,11 +16,7 @@ *_________________________________________________________________________*/ -#include "fixedpoint.h" -#include "point.h" -#include "vect3.h" - -using namespace POEMS; +#include "points.h" Point::Point(){ position.Zeros(); @@ -37,7 +33,7 @@ void Point::WriteOut(std::ostream& out){ WriteOutPointData(out); } -Point* POEMS::NewPoint(int type){ +Point* NewPoint(int type){ switch( PointType(type) ) { case FIXEDPOINT : // A Fixed Point diff --git a/lib/poems/point.h b/lib/poems/point.h index c08e92db0d..746a527cd7 100644 --- a/lib/poems/point.h +++ b/lib/poems/point.h @@ -3,7 +3,7 @@ * POEMS: PARALLELIZABLE OPEN SOURCE EFFICIENT MULTIBODY SOFTWARE * * DESCRIPTION: SEE READ-ME * * FILE NAME: point.h * - * AUTHORS: See Author List * + * AUTHORS: See Author List * * GRANTS: See Grants List * * COPYRIGHT: (C) 2005 by Authors as listed in Author's List * * LICENSE: Please see License Agreement * @@ -11,7 +11,7 @@ * ADMINISTRATOR: Prof. Kurt Anderson * * Computational Dynamics Lab * * Rensselaer Polytechnic Institute * - * 110 8th St. Troy NY 12180 * + * 110 8th St. Troy NY 12180 * * CONTACT: anderk5@rpi.edu * *_________________________________________________________________________*/ @@ -22,21 +22,21 @@ #include "poemsobject.h" #include "vect3.h" -namespace POEMS { + // emumerated type enum PointType { FIXEDPOINT = 0 }; class Point : public POEMSObject { -public: +public: Vect3 position; - Point(); - bool ReadIn(std::istream& in); + Point(); + bool ReadIn(std::istream& in); void WriteOut(std::ostream& out); - - virtual ~Point(); + + virtual ~Point(); virtual PointType GetType() = 0; virtual Vect3 GetPoint() = 0; virtual bool ReadInPointData(std::istream& in) = 0; @@ -45,5 +45,5 @@ public: // global point functions Point* NewPoint(int type); -} + #endif diff --git a/lib/poems/prismaticjoint.cpp b/lib/poems/prismaticjoint.cpp index 3e649f0d22..7c01667a86 100644 --- a/lib/poems/prismaticjoint.cpp +++ b/lib/poems/prismaticjoint.cpp @@ -16,16 +16,10 @@ *_________________________________________________________________________*/ #include "prismaticjoint.h" - #include "point.h" #include "matrixfun.h" #include "body.h" #include "fastmatrixops.h" -#include "colmatrix.h" -#include "mat3x3.h" -#include "virtualmatrix.h" - -using namespace POEMS; PrismaticJoint::PrismaticJoint(){ q.Dim(1); diff --git a/lib/poems/prismaticjoint.h b/lib/poems/prismaticjoint.h index df3ab3195c..17cf050a78 100644 --- a/lib/poems/prismaticjoint.h +++ b/lib/poems/prismaticjoint.h @@ -18,13 +18,12 @@ #ifndef PRISMATICJOINT_H #define PRISMATICJOINT_H -#include - #include "joint.h" #include "vect3.h" -#include "matrix.h" +#include "mat3x3.h" + + -namespace POEMS { class PrismaticJoint : public Joint { Vect3 axis_pk; // unit vector in body1 basis Vect3 axis_k; // unit vector in body2 basis @@ -44,5 +43,5 @@ public: void ForwardKinematics(); void BackwardKinematics(); }; -} + #endif diff --git a/lib/poems/revolutejoint.cpp b/lib/poems/revolutejoint.cpp index 6b11acbf0f..ec5b1bec02 100644 --- a/lib/poems/revolutejoint.cpp +++ b/lib/poems/revolutejoint.cpp @@ -16,16 +16,10 @@ *_________________________________________________________________________*/ #include "revolutejoint.h" - #include "point.h" #include "matrixfun.h" #include "body.h" #include "fastmatrixops.h" -#include "colmatrix.h" -#include "mat3x3.h" -#include "virtualmatrix.h" - -using namespace POEMS; RevoluteJoint::RevoluteJoint(){ DimQandU(1); diff --git a/lib/poems/revolutejoint.h b/lib/poems/revolutejoint.h index 10a38114df..478d48dbb9 100644 --- a/lib/poems/revolutejoint.h +++ b/lib/poems/revolutejoint.h @@ -18,13 +18,11 @@ #ifndef REVOLUTEJOINT_H #define REVOLUTEJOINT_H -#include #include "joint.h" #include "vect3.h" -#include "matrix.h" +#include "mat3x3.h" + -namespace POEMS { -class VirtualMatrix; class RevoluteJoint : public Joint { Vect3 axis_pk; // unit vector in body1 basis @@ -45,5 +43,5 @@ public: void ForwardKinematics(); void BackwardKinematics(); }; -} + #endif diff --git a/lib/poems/rigidbody.cpp b/lib/poems/rigidbody.cpp index a7d4f9f19f..3ac424f9e9 100644 --- a/lib/poems/rigidbody.cpp +++ b/lib/poems/rigidbody.cpp @@ -16,12 +16,9 @@ *_________________________________________________________________________*/ #include "rigidbody.h" -#include "mat3x3.h" -#include "virtualmatrix.h" +#include "fixedpoint.h" using namespace std; -using namespace POEMS; - RigidBody::RigidBody(){ } diff --git a/lib/poems/rigidbody.h b/lib/poems/rigidbody.h index d4be92ebcf..0bb2a3ece2 100644 --- a/lib/poems/rigidbody.h +++ b/lib/poems/rigidbody.h @@ -18,11 +18,8 @@ #ifndef RIGIDBODY_H #define RIGIDBODY_H -#include - #include "body.h" -namespace POEMS { class RigidBody : public Body { public: RigidBody(); @@ -31,5 +28,5 @@ public: bool ReadInBodyData(std::istream& in); void WriteOutBodyData(std::ostream& out); }; -} + #endif diff --git a/lib/poems/rowmatrix.cpp b/lib/poems/rowmatrix.cpp index eac8fbef5d..feb185070e 100644 --- a/lib/poems/rowmatrix.cpp +++ b/lib/poems/rowmatrix.cpp @@ -16,13 +16,11 @@ *_________________________________________________________________________*/ #include "rowmatrix.h" - +#include "colmatrix.h" #include #include using namespace std; -using namespace POEMS; - RowMatrix::RowMatrix(){ numcols = 0; diff --git a/lib/poems/rowmatrix.h b/lib/poems/rowmatrix.h index 8e8d7b5f99..b04113e8ed 100644 --- a/lib/poems/rowmatrix.h +++ b/lib/poems/rowmatrix.h @@ -19,12 +19,8 @@ #ifndef ROWMATRIX_H #define ROWMATRIX_H -#include - #include "virtualrowmatrix.h" -#include "virtualmatrix.h" -namespace POEMS { class RowMatrix : public VirtualRowMatrix { double* elements; public: @@ -53,5 +49,5 @@ public: RowMatrix& operator=(const VirtualMatrix& A); // overloaded = RowMatrix& operator*=(double b); }; -} + #endif diff --git a/lib/poems/solver.cpp b/lib/poems/solver.cpp index 04afb27945..67f5b607e3 100644 --- a/lib/poems/solver.cpp +++ b/lib/poems/solver.cpp @@ -15,12 +15,9 @@ * CONTACT: anderk5@rpi.edu * *_________________________________________________________________________*/ -#include #include "solver.h" #include "system.h" -#include "onsolver.h" - -using namespace POEMS; +#include "matrices.h" Solver::Solver(){ diff --git a/lib/poems/solver.h b/lib/poems/solver.h index 489e6d41f1..45564dd1ef 100644 --- a/lib/poems/solver.h +++ b/lib/poems/solver.h @@ -3,7 +3,7 @@ * POEMS: PARALLELIZABLE OPEN SOURCE EFFICIENT MULTIBODY SOFTWARE * * DESCRIPTION: SEE READ-ME * * FILE NAME: solver.h * - * AUTHORS: See Author List * + * AUTHORS: See Author List * * GRANTS: See Grants List * * COPYRIGHT: (C) 2005 by Authors as listed in Author's List * * LICENSE: Please see License Agreement * @@ -11,29 +11,28 @@ * ADMINISTRATOR: Prof. Kurt Anderson * * Computational Dynamics Lab * * Rensselaer Polytechnic Institute * - * 110 8th St. Troy NY 12180 * + * 110 8th St. Troy NY 12180 * * CONTACT: anderk5@rpi.edu * *_________________________________________________________________________*/ #ifndef SOLVER_H #define SOLVER_H - +#include #include "colmatmap.h" +#include "matrices.h" #include "defines.h" -namespace POEMS { class System; -class Matrix; class Solver{ protected: System* system; - + double time; ColMatMap state; ColMatMap statedot; - ColMatMap statedoubledot; + ColMatMap statedoubledot; SolverType type; @@ -48,13 +47,13 @@ public: virtual void DeleteModel() = 0; virtual void CreateModel() = 0; - virtual void Solve(double time, Matrix& FF) = 0; - - - + virtual void Solve(double time, Matrix& FF) = 0; + + + ColMatMap* GetState(); ColMatMap* GetStateDerivative(); ColMatMap* GetStateDerivativeDerivative(); }; -} + #endif diff --git a/lib/poems/sphericaljoint.cpp b/lib/poems/sphericaljoint.cpp index 996bb5a887..fb5330db17 100644 --- a/lib/poems/sphericaljoint.cpp +++ b/lib/poems/sphericaljoint.cpp @@ -3,7 +3,7 @@ * POEMS: PARALLELIZABLE OPEN SOURCE EFFICIENT MULTIBODY SOFTWARE * * DESCRIPTION: SEE READ-ME * * FILE NAME: sphericaljoint.cpp * - * AUTHORS: See Author List * + * AUTHORS: See Author List * * GRANTS: See Grants List * * COPYRIGHT: (C) 2005 by Authors as listed in Author's List * * LICENSE: Please see License Agreement * @@ -11,27 +11,21 @@ * ADMINISTRATOR: Prof. Kurt Anderson * * Computational Dynamics Lab * * Rensselaer Polytechnic Institute * - * 110 8th St. Troy NY 12180 * + * 110 8th St. Troy NY 12180 * * CONTACT: anderk5@rpi.edu * *_________________________________________________________________________*/ - + #include "sphericaljoint.h" - -#include - #include "point.h" #include "matrixfun.h" #include "body.h" #include "fastmatrixops.h" +#include "norm.h" #include "eulerparameters.h" -#include "colmatrix.h" -#include "mat3x3.h" -#include "vect3.h" -#include "virtualmatrix.h" +#include "matrices.h" +#include -using namespace std; -using namespace POEMS; SphericalJoint::SphericalJoint(){ DimQandU(4,3); @@ -50,24 +44,24 @@ bool SphericalJoint::ReadInJointData(std::istream& in){ void SphericalJoint::WriteOutJointData(std::ostream& out){ } -Matrix SphericalJoint::GetForward_sP(){ +Matrix SphericalJoint::GetForward_sP(){ Mat3x3 sPa,sPl; Matrix sP(6,3); - sPa.Identity(); + sPa.Identity(); sPl.Zeros(); - Vect3 temp = -(point2->position); - + Vect3 temp = -(point2->position); + sPl(1,2) = temp(3); sPl(1,3) = -temp(2); - + sPl(2,1) = -temp(3); sPl(2,3) = temp(1); - - sPl(3,1) = temp(2); + + sPl(3,1) = temp(2); sPl(3,2) = -temp(1); - - sP=Stack(sPa,sPl); - return sP; + + sP=Stack(sPa,sPl); + return sP; } void SphericalJoint::UpdateForward_sP( Matrix& sP){ @@ -81,15 +75,15 @@ Matrix SphericalJoint::GetBackward_sP(){ cout<<" -----------"<position(1)); - sPl(2,3)=-(point2->position(1)); + sPa.Identity(); + sPl.Zeros(); + sPl(3,2)=(point2->position(1)); + sPl(2,3)=-(point2->position(1)); sP=Stack(sPa,sPl); - return sP; + return sP; } -void SphericalJoint::UpdateBackward_sP( Matrix& sP){ +void SphericalJoint::UpdateBackward_sP( Matrix& sP){ // sP is constant, do nothing. } @@ -98,106 +92,106 @@ void SphericalJoint::ComputeLocalTransform(){ // Obtain the transformation matrix from euler parameters EP_Transformation(q, ko_C_k); FastMult(pk_C_ko,ko_C_k,pk_C_k); - } + } void SphericalJoint::ForwardKinematics(){ Vect3 result1,result2,result3,result4,result5; Vect3 pk_w_k; - + //cout<<"Check in spherical "<position,result1); // parents basis - FastAdd(result1,point1->position,r12); - - // compute position vector r21 - FastNegMult(k_C_pk,r12,r21); - - - + // COMPUTE POSITION VECTOR R12 aka GAMMA + + FastNegMult(pk_C_k,point2->position,result1); // parents basis + FastAdd(result1,point1->position,r12); + + // compute position vector r21 + FastNegMult(k_C_pk,r12,r21); + + + //----------------------------------// - // COMPUTE GLOBAL LOCATION - FastMult(body1->n_C_k,(body1->GetPoint(2))->position,result1); - FastAdd(result1,body1->r,result1); - FastNegMult(body2->n_C_k,(body2->GetPoint(1))->position,result2); - FastAdd(result1,result2,body2->r); - - qdot_to_u(q, u, qdot); - - - //----------------------------------- - // angular velocities - + // COMPUTE GLOBAL LOCATION + FastMult(body1->n_C_k,(body1->GetPoint(2))->position,result1); + FastAdd(result1,body1->r,result1); + FastNegMult(body2->n_C_k,(body2->GetPoint(1))->position,result2); + FastAdd(result1,result2,body2->r); + + qdot_to_u(q, u, qdot); + + + //----------------------------------- + // angular velocities + FastAssign(u,pk_w_k); - FastTMult(pk_C_k,body1->omega_k,result1); + FastTMult(pk_C_k,body1->omega_k,result1); FastAdd(result1,pk_w_k,body2->omega_k); - FastMult(body2->n_C_k,body2->omega_k,body2->omega); - - - - //----------------------------------- - - // compute velocities - FastCross(body1->omega_k,(body1->GetPoint(2))->position,result1); + FastMult(body2->n_C_k,body2->omega_k,body2->omega); + + + + //----------------------------------- + + // compute velocities + FastCross(body1->omega_k,(body1->GetPoint(2))->position,result1); FastAdd(body1->v_k,result1,result2); - FastTMult(pk_C_k,result2,result1); // In body basis - - FastCross((body2->GetPoint(1))->position,body2->omega_k,result2); - FastAdd(result1,result2,body2->v_k); // In body basis - FastMult(body2->n_C_k,body2->v_k,body2->v); - - + FastTMult(pk_C_k,result2,result1); // In body basis + + FastCross((body2->GetPoint(1))->position,body2->omega_k,result2); + FastAdd(result1,result2,body2->v_k); // In body basis + FastMult(body2->n_C_k,body2->v_k,body2->v); + + //------------------------------------------ - //Compute the KE + //Compute the KE Matrix tempke; - tempke = T(body2->v)*(body2->v); + tempke = T(body2->v)*(body2->v); double ke = 0.0; - ke = body2->mass*tempke(1,1); + ke = body2->mass*tempke(1,1); FastMult(body2->inertia,body2->omega_k,result1); - tempke= T(body2->omega_k)*result1; + tempke= T(body2->omega_k)*result1; ke = 0.5*ke + 0.5*tempke(1,1); body2->KE=ke; - //----------------------------------- - // compute state explicit angular acceleration // Has to be in body basis - FastTMult(pk_C_k,body1->alpha_t,result2); + //----------------------------------- + // compute state explicit angular acceleration // Has to be in body basis + FastTMult(pk_C_k,body1->alpha_t,result2); FastCross(body2->omega_k,pk_w_k,result1); - FastAdd(result1,result2,body2->alpha_t); - - //----------------------------------- - // compute state explicit acceleration - // NEED TO DO THIS COMPLETELY IN BODY BASIS - + FastAdd(result1,result2,body2->alpha_t); + + //----------------------------------- + // compute state explicit acceleration + // NEED TO DO THIS COMPLETELY IN BODY BASIS + FastCross(body1->omega_k,(body1->GetPoint(2))->position,result1); - FastCross(body1->omega_k,result1,result2); - FastTMult(pk_C_k,result2,result1); - - //FastCross(body2->omega_k,-(body2->GetPoint(1))->position,result3); - FastCross((body2->GetPoint(1))->position,body2->omega_k,result3); - FastCross(body2->omega_k,result3,result2); - FastAdd(result1,result2,result3); //wxwxr in body basis - - FastCross(body1->alpha_t,(body1->GetPoint(2))->position,result4); - FastTMult(pk_C_k,result4,result5); + FastCross(body1->omega_k,result1,result2); + FastTMult(pk_C_k,result2,result1); + + //FastCross(body2->omega_k,-(body2->GetPoint(1))->position,result3); + FastCross((body2->GetPoint(1))->position,body2->omega_k,result3); + FastCross(body2->omega_k,result3,result2); + FastAdd(result1,result2,result3); //wxwxr in body basis + + FastCross(body1->alpha_t,(body1->GetPoint(2))->position,result4); + FastTMult(pk_C_k,result4,result5); FastAssign(result5,result4); - - FastCross((body2->GetPoint(1))->position,body2->alpha_t,result2); - FastAdd(result2,result4,result1); //alphaxr in body basis - + + FastCross((body2->GetPoint(1))->position,body2->alpha_t,result2); + FastAdd(result2,result4,result1); //alphaxr in body basis + FastTMult(pk_C_k,body1->a_t,result2); - FastTripleSum(result3,result1,result2,body2->a_t); // in body basis - - - //----------------------------------- + FastTripleSum(result3,result1,result2,body2->a_t); // in body basis + + + //----------------------------------- } // NOTE: NOT USING BACKWARDKINEMATICS AT PRESENT @@ -208,13 +202,13 @@ void SphericalJoint::BackwardKinematics(){ // orientations ComputeBackwardTransforms(); - + // compute position vector r21 //r21 = point2->position - k_C_pk * point1->position; FastMult(k_C_pk,point1->position,result1); FastSubt(point2->position,result1,r21); - + // compute position vector r21 FastNegMult(pk_C_k,r21,r12); @@ -233,7 +227,7 @@ void SphericalJoint::BackwardKinematics(){ EP_Derivatives(q,u,qdot); // angular velocities - + FastMult(body2->n_C_k,u,result2); FastAdd(body2->omega,result2,body1->omega); FastAssign(u,k_w_pk); @@ -253,7 +247,7 @@ void SphericalJoint::BackwardKinematics(){ FastCross(body1->omega_k,k_w_pk,result1); FastMult(pk_C_k,body2->alpha_t,result2); FastAdd(result1,result2,body1->alpha_t); - + // compute state explicit acceleration FastCross(body2->alpha_t,point2->position,result1); FastCross(body2->omega_k,point2->position,result2); @@ -266,5 +260,5 @@ void SphericalJoint::BackwardKinematics(){ FastCross(body1->omega_k,result2,result3); FastTripleSum(result5,result1,result3,body1->a_t); - + } diff --git a/lib/poems/sphericaljoint.h b/lib/poems/sphericaljoint.h index db048e5544..ef29f8e38e 100644 --- a/lib/poems/sphericaljoint.h +++ b/lib/poems/sphericaljoint.h @@ -18,11 +18,12 @@ #ifndef SPHERICALJOINT_H #define SPHERICALJOINT_H -#include #include "joint.h" -#include "matrix.h" +#include "vect3.h" +#include "mat3x3.h" + + -namespace POEMS { class SphericalJoint : public Joint { Matrix const_sP; public: @@ -39,5 +40,5 @@ public: void ForwardKinematics(); void BackwardKinematics(); }; -} + #endif diff --git a/lib/poems/system.cpp b/lib/poems/system.cpp index 8515588424..369213f7d0 100644 --- a/lib/poems/system.cpp +++ b/lib/poems/system.cpp @@ -3,7 +3,7 @@ * POEMS: PARALLELIZABLE OPEN SOURCE EFFICIENT MULTIBODY SOFTWARE * * DESCRIPTION: SEE READ-ME * * FILE NAME: system.cpp * - * AUTHORS: See Author List * + * AUTHORS: See Author List * * GRANTS: See Grants List * * COPYRIGHT: (C) 2005 by Authors as listed in Author's List * * LICENSE: Please see License Agreement * @@ -11,37 +11,19 @@ * ADMINISTRATOR: Prof. Kurt Anderson * * Computational Dynamics Lab * * Rensselaer Polytechnic Institute * - * 110 8th St. Troy NY 12180 * + * 110 8th St. Troy NY 12180 * * CONTACT: anderk5@rpi.edu * *_________________________________________________________________________*/ #include "system.h" - -#include -#include - #include "body.h" #include "joint.h" -#include "colmatrix.h" -#include "eulerparameters.h" -#include "fixedpoint.h" -#include "freebodyjoint.h" -#include "inertialframe.h" -#include "mat3x3.h" -#include "matrix.h" -#include "matrixfun.h" -#include "rigidbody.h" -#include "sphericaljoint.h" -#include "vect3.h" -#include "virtualmatrix.h" - -namespace POEMS { class Point; } -using namespace std; -using namespace POEMS; +#include + System::System(){ - mappings = NULL; + mappings = NULL; } System::~System(){ @@ -60,7 +42,7 @@ int System::GetNumBodies(){ int * System::GetMappings() { - return mappings; + return mappings; } void System::AddBody(Body* body){ @@ -79,16 +61,16 @@ double System::GetTime(){ return time; } -void System::ComputeForces(){ - // NOT DOING ANYTHING AT THIS TIME - } - +void System::ComputeForces(){ + // NOT DOING ANYTHING AT THIS TIME + } + bool System::ReadIn(istream& in){ int numbodies; Body* body; int bodytype; char bodyname[256]; - int index; + int index; // get number of bodies in >> numbodies; @@ -166,12 +148,12 @@ bool System::ReadIn(istream& in){ delete [] bodyarray; return false; } - + joint->SetBodies(bodyarray[body1], bodyarray[body2]); bodyarray[body1]->AddJoint(joint); bodyarray[body2]->AddJoint(joint); - + in >> point1 >> point2; joint->SetPoints(bodyarray[body1]->GetPoint(point1),bodyarray[body2]->GetPoint(point2)); @@ -204,7 +186,7 @@ void System::WriteOut(ostream& out){ // set the body ID for later identification body->SetID(i); - + // write out the data body->WriteOut(out); @@ -212,7 +194,7 @@ void System::WriteOut(ostream& out){ } // number of joints - out << joints.GetNumElements() << endl; + out << joints.GetNumElements() << endl; // joints loop i = 0; @@ -227,7 +209,7 @@ void System::WriteOut(ostream& out){ // write out the data joint->WriteOut(out); - + i++; j_ele = j_ele->next; } } @@ -253,68 +235,68 @@ void System::ClearJointIDs(){ void System::Create_DegenerateSystem(int& nfree, int*freelist, double *&masstotal, double **&inertia, double **&xcm, double **&vcm, double **&omega, double **&ex_space, double **&ey_space, double **&ez_space){ - //-------------------------------------------------------------------------// - // Declaring Temporary Entities - //-------------------------------------------------------------------------// + //-------------------------------------------------------------------------// + // Declaring Temporary Entities + //-------------------------------------------------------------------------// Body* body = NULL; Body* prev; Body* Inertial; Point* origin; Joint* joint; - Point* point_CM; - Point* point_p; - Point* point_k; + Point* point_CM; + Point* point_p; + Point* point_k; Point* point_ch = NULL; - Vect3 r1,r2,r3,v1,v2,v3; + Vect3 r1,r2,r3,v1,v2,v3; Mat3x3 IM, N, PKCK,PKCN ; ColMatrix qo, uo, q, qdot,w; - - mappings = new int[nfree]; - for(int i = 0; i < nfree; i++) - { - mappings[i] = freelist[i]; - } + + mappings = new int[nfree]; + for(int i = 0; i < nfree; i++) + { + mappings[i] = freelist[i]; + } qo.Dim(4); uo.Dim(3); q.Dim(4); - qdot.Dim(4); + qdot.Dim(4); PKCN.Identity(); PKCK.Identity(); w.Dim(3); - -//-------------------------------------------------------------------------// - // Setting up Inertial Frame, gravity and Origin + +//-------------------------------------------------------------------------// + // Setting up Inertial Frame, gravity and Origin //-------------------------------------------------------------------------// - Inertial= new InertialFrame; + Inertial= new InertialFrame; AddBody(Inertial); - - Vect3 temp1; - temp1.Zeros(); - ((InertialFrame*) Inertial)->SetGravity(temp1); + + Vect3 temp1; + temp1.Zeros(); + ((InertialFrame*) Inertial)->SetGravity(temp1); origin= new FixedPoint(temp1); - Inertial->AddPoint(origin); -//-------------------------------------------------------------------------// - double ** xh1 = new double*[nfree]; - double ** xh2 = new double*[nfree]; - - for (int i=0; iAddPoint(origin); //-------------------------------------------------------------------------// + double ** xh1 = new double*[nfree]; + double ** xh2 = new double*[nfree]; + + for (int i=0; imass=masstotal[mappings[i]-1]; IM(1,1)=inertia[mappings[i]-1][0]; IM(2,2)=inertia[mappings[i]-1][1]; @@ -325,49 +307,49 @@ void System::Create_DegenerateSystem(int& nfree, int*freelist, double *&masstota IM(2,1)=IM(1,2); IM(3,1)=IM(1,3); IM(3,2)=IM(2,3); - body->inertia = IM; - -//-------------------------------------------------------// - - - for (int k=0;k<3;k++){ - r1(k+1)=xh1[i][k]-xcm[mappings[i]-1][k]; - r3(k+1) = xcm[mappings[i]-1][k]; - r3(k+1)=xh2[i][k]-xcm[mappings[i]-1][k]; - } - - r2.Zeros(); - - for (int k=1;k<=3;k++){ - N(k,1)=ex_space[mappings[i]-1][k-1]; - N(k,2)=ey_space[mappings[i]-1][k-1]; - N(k,3)=ez_space[mappings[i]-1][k-1]; - } - + body->inertia = IM; + +//-------------------------------------------------------// + + + for (int k=0;k<3;k++){ + r1(k+1)=xh1[i][k]-xcm[mappings[i]-1][k]; + r3(k+1) = xcm[mappings[i]-1][k]; + r3(k+1)=xh2[i][k]-xcm[mappings[i]-1][k]; + } + + r2.Zeros(); + + for (int k=1;k<=3;k++){ + N(k,1)=ex_space[mappings[i]-1][k-1]; + N(k,2)=ey_space[mappings[i]-1][k-1]; + N(k,3)=ez_space[mappings[i]-1][k-1]; + } + PKCK=T(N); PKCN=T(N); - - q.Zeros(); + + q.Zeros(); EP_FromTransformation(q,N); - + r1=PKCN*r1; r3=PKCN*r3; - + for (int k=1;k<=3;k++){ - w(k)=omega[mappings[i]-1][k-1]; - } - + w(k)=omega[mappings[i]-1][k-1]; + } + Vect3 cart_r, cart_v; for (int k=1;k<=3;k++){ - cart_r(k)=xcm[mappings[i]-1][k-1]; - cart_v(k)=vcm[mappings[i]-1][k-1]; - } - - w=PKCN*w; - EP_Derivatives(q,w,qdot); - - -//-------------------------------------------------------------------------// + cart_r(k)=xcm[mappings[i]-1][k-1]; + cart_v(k)=vcm[mappings[i]-1][k-1]; + } + + w=PKCN*w; + EP_Derivatives(q,w,qdot); + + +//-------------------------------------------------------------------------// // Create bodies and joints with associated properties for POEMS //-------------------------------------------------------------------------// @@ -377,12 +359,12 @@ void System::Create_DegenerateSystem(int& nfree, int*freelist, double *&masstota body->AddPoint(point_CM); body->AddPoint(point_k); body->AddPoint(point_ch); - AddBody(body); - + AddBody(body); + Mat3x3 One; - One.Identity(); - ColMatrix qq=Stack(q,cart_r); - ColMatrix vv=Stack(qdot,cart_v); + One.Identity(); + ColMatrix qq=Stack(q,cart_r); + ColMatrix vv=Stack(qdot,cart_v); joint=new FreeBodyJoint; AddJoint(joint); joint->SetBodies(prev,body); @@ -392,225 +374,225 @@ void System::Create_DegenerateSystem(int& nfree, int*freelist, double *&masstota joint->SetZeroOrientation(One); joint->DimQandU(7,6); joint->SetInitialState(qq,vv); - joint->ForwardKinematics(); + joint->ForwardKinematics(); } for(int i = 0; i < nfree; i++) { - delete [] xh1[i]; - delete [] xh2[i]; + delete [] xh1[i]; + delete [] xh2[i]; } delete [] xh1; - delete [] xh2; + delete [] xh2; } void System::Create_System_LAMMPS(int numbodies, double *mass,double **inertia, double ** xcm, double ** xjoint,double **vcm,double **omega,double **ex_space, double **ey_space, double **ez_space, int b, int * mapping, int count){ - //-------------------------------------------------------------------------// - // Declaring Temporary Entities - //-------------------------------------------------------------------------// - - Body* body = NULL; - Body* prev; - Body* Inertial; - Point* origin; - Joint* joint; - Point* point_CM; - Point* point_p; - Point* point_k; - Point* point_ch = NULL; - Vect3 r1,r2,r3,v1,v2,v3; - Mat3x3 IM, N, PKCK,PKCN ; - ColMatrix qo, uo, q, qdot,w; - Vect3 cart_r, cart_v; - mappings = new int[b]; - for(int i = 0; i < b; i++){ - mappings[i] = mapping[i]; - } - - - qo.Dim(4); - uo.Dim(3); - q.Dim(4); - qdot.Dim(4); - PKCN.Identity(); - PKCK.Identity(); - w.Dim(3); - - //-------------------------------------------------------------------------// - // Setting up Inertial Frame, gravity and Origin - //-------------------------------------------------------------------------// - Inertial= new InertialFrame; - AddBody(Inertial); - - Vect3 temp1; - temp1.Zeros(); - ((InertialFrame*) Inertial)->SetGravity(temp1); - origin= new FixedPoint(temp1); - Inertial->AddPoint(origin); - //-------------------------------------------------------------------------// - - double ** xh1; - double ** xh2; - - xh1 = new double*[b]; - xh2 = new double*[b]; - - - for (int i=0; iSetGravity(temp1); + origin= new FixedPoint(temp1); + Inertial->AddPoint(origin); + //-------------------------------------------------------------------------// + + double ** xh1; + double ** xh2; + + xh1 = new double*[b]; + xh2 = new double*[b]; + + + for (int i=0; imass=mass[mapping[i]-1]; - IM(1,1)=inertia[mapping[i]-1][0]; - IM(2,2)=inertia[mapping[i]-1][1]; - IM(3,3)=inertia[mapping[i]-1][2]; - IM(1,2)=0.0; - IM(1,3)=0.0; - IM(2,3)=0.0; - IM(2,1)=IM(1,2); - IM(3,1)=IM(1,3); - IM(3,2)=IM(2,3); - body->inertia = IM; - - //-------------------------------------------------------// - - for (int k=0;k<3;k++){ - r1(k+1)=xh1[i][k]-xcm[mapping[i]-1][k]; - r3(k+1)=xh2[i][k]-xcm[mapping[i]-1][k]; - } - r2.Zeros(); - - for (int k=1;k<=3;k++){ - N(k,1)=ex_space[mapping[i]-1][k-1]; - N(k,2)=ey_space[mapping[i]-1][k-1]; - N(k,3)=ez_space[mapping[i]-1][k-1]; - } - - - if (i==0){ - PKCK=T(N); - PKCN=T(N); - - q.Zeros(); - EP_FromTransformation(q,N); - - r1=PKCN*r1; - r3=PKCN*r3; - - for (int k=1;k<=3;k++){ - w(k)=omega[mappings[i]-1][k-1]; - } - - for (int k=1;k<=3;k++){ - cart_r(k)=xcm[mappings[i]-1][k-1]; - cart_v(k)=vcm[mappings[i]-1][k-1]; - } - w=PKCN*w; - EP_Derivatives(q,w,qdot); - - } - else{ - PKCK=PKCN*N; - PKCN=T(N); - - q.Zeros(); - EP_FromTransformation(q,PKCK); - - r1=PKCN*r1; - r3=PKCN*r3; - - for (int k=1;k<=3;k++){ - w(k)=omega[mapping[i]-1][k-1]-omega[mapping[i-1]-1][k-1]; - } - - w=PKCN*w; - EP_Derivatives(q, w, qdot); - } - - - //-------------------------------------------------------------------------// + //-------------------------------------------------------------------------// + for(int i=0;imass=mass[mapping[i]-1]; + IM(1,1)=inertia[mapping[i]-1][0]; + IM(2,2)=inertia[mapping[i]-1][1]; + IM(3,3)=inertia[mapping[i]-1][2]; + IM(1,2)=0.0; + IM(1,3)=0.0; + IM(2,3)=0.0; + IM(2,1)=IM(1,2); + IM(3,1)=IM(1,3); + IM(3,2)=IM(2,3); + body->inertia = IM; + + //-------------------------------------------------------// + + for (int k=0;k<3;k++){ + r1(k+1)=xh1[i][k]-xcm[mapping[i]-1][k]; + r3(k+1)=xh2[i][k]-xcm[mapping[i]-1][k]; + } + r2.Zeros(); + + for (int k=1;k<=3;k++){ + N(k,1)=ex_space[mapping[i]-1][k-1]; + N(k,2)=ey_space[mapping[i]-1][k-1]; + N(k,3)=ez_space[mapping[i]-1][k-1]; + } + + + if (i==0){ + PKCK=T(N); + PKCN=T(N); + + q.Zeros(); + EP_FromTransformation(q,N); + + r1=PKCN*r1; + r3=PKCN*r3; + + for (int k=1;k<=3;k++){ + w(k)=omega[mappings[i]-1][k-1]; + } + + for (int k=1;k<=3;k++){ + cart_r(k)=xcm[mappings[i]-1][k-1]; + cart_v(k)=vcm[mappings[i]-1][k-1]; + } + w=PKCN*w; + EP_Derivatives(q,w,qdot); + + } + else{ + PKCK=PKCN*N; + PKCN=T(N); + + q.Zeros(); + EP_FromTransformation(q,PKCK); + + r1=PKCN*r1; + r3=PKCN*r3; + + for (int k=1;k<=3;k++){ + w(k)=omega[mapping[i]-1][k-1]-omega[mapping[i-1]-1][k-1]; + } + + w=PKCN*w; + EP_Derivatives(q, w, qdot); + } + + + //-------------------------------------------------------------------------// // Create bodies and joints with associated properties for POEMS - //-------------------------------------------------------------------------// - - point_CM = new FixedPoint(r2); - point_k = new FixedPoint(r1); - point_ch = new FixedPoint(r3); - body->AddPoint(point_CM); - body->AddPoint(point_k); - body->AddPoint(point_ch); - AddBody(body); - - Mat3x3 One; - One.Identity(); - if (i==0){ - ColMatrix qq=Stack(q,cart_r); - ColMatrix vv=Stack(qdot,cart_v); - joint=new FreeBodyJoint; - AddJoint(joint); - joint->SetBodies(prev,body); - body->AddJoint(joint); - prev->AddJoint(joint); - joint->SetPoints(point_p,point_k); - joint->SetZeroOrientation(One); - joint->DimQandU(7,6); - joint->SetInitialState(qq,vv); - joint->ForwardKinematics(); - } - else{ - joint= new SphericalJoint; - AddJoint(joint); - joint->SetBodies(prev,body); - body->AddJoint(joint); - prev->AddJoint(joint); - joint->SetPoints(point_p,point_k); - joint->SetZeroOrientation(One); - joint->DimQandU(4,3); - joint->SetInitialState(q,qdot); - joint->ForwardKinematics(); - } - } - for(int i = 0; i < b; i++) - { - delete [] xh1[i]; - delete [] xh2[i]; - } - delete [] xh1; - delete [] xh2; - + //-------------------------------------------------------------------------// + + point_CM = new FixedPoint(r2); + point_k = new FixedPoint(r1); + point_ch = new FixedPoint(r3); + body->AddPoint(point_CM); + body->AddPoint(point_k); + body->AddPoint(point_ch); + AddBody(body); + + Mat3x3 One; + One.Identity(); + if (i==0){ + ColMatrix qq=Stack(q,cart_r); + ColMatrix vv=Stack(qdot,cart_v); + joint=new FreeBodyJoint; + AddJoint(joint); + joint->SetBodies(prev,body); + body->AddJoint(joint); + prev->AddJoint(joint); + joint->SetPoints(point_p,point_k); + joint->SetZeroOrientation(One); + joint->DimQandU(7,6); + joint->SetInitialState(qq,vv); + joint->ForwardKinematics(); + } + else{ + joint= new SphericalJoint; + AddJoint(joint); + joint->SetBodies(prev,body); + body->AddJoint(joint); + prev->AddJoint(joint); + joint->SetPoints(point_p,point_k); + joint->SetZeroOrientation(One); + joint->DimQandU(4,3); + joint->SetInitialState(q,qdot); + joint->ForwardKinematics(); + } + } + for(int i = 0; i < b; i++) + { + delete [] xh1[i]; + delete [] xh2[i]; + } + delete [] xh1; + delete [] xh2; + } diff --git a/lib/poems/system.h b/lib/poems/system.h index 2402e5852f..1b59395de7 100644 --- a/lib/poems/system.h +++ b/lib/poems/system.h @@ -3,7 +3,7 @@ * POEMS: PARALLELIZABLE OPEN SOURCE EFFICIENT MULTIBODY SOFTWARE * * DESCRIPTION: SEE READ-ME * * FILE NAME: system.h * - * AUTHORS: See Author List * + * AUTHORS: See Author List * * GRANTS: See Grants List * * COPYRIGHT: (C) 2005 by Authors as listed in Author's List * * LICENSE: Please see License Agreement * @@ -11,18 +11,40 @@ * ADMINISTRATOR: Prof. Kurt Anderson * * Computational Dynamics Lab * * Rensselaer Polytechnic Institute * - * 110 8th St. Troy NY 12180 * + * 110 8th St. Troy NY 12180 * * CONTACT: anderk5@rpi.edu * *_________________________________________________________________________*/ - + #ifndef SYSTEM_H #define SYSTEM_H + #include +#include +#include +#include +#include + #include "poemslist.h" +#include "matrices.h" +#include "workspace.h" +#include "matrixfun.h" +#include "onsolver.h" +#include "system.h" +#include "inertialframe.h" +#include "rigidbody.h" +#include "revolutejoint.h" +#include "fixedpoint.h" +#include "freebodyjoint.h" +#include "sphericaljoint.h" +#include "body23joint.h" +#include "mixedjoint.h" +#include "eulerparameters.h" +#include "matrices.h" +#include "norm.h" + -namespace POEMS { class Body; class Joint; @@ -34,37 +56,37 @@ namespace POEMS { double time; List bodies; List joints; - + System(); ~System(); void Delete(); - + int GetNumBodies(); - + int * GetMappings(); void AddBody(Body* body); - + void AddJoint(Joint* joint); - + void SetTime(double t); - + double GetTime(); - + void ComputeForces(); - + bool ReadIn(std::istream& in); - + void WriteOut(std::ostream& out); - + void ClearBodyIDs(); - - void ClearJointIDs(); + + void ClearJointIDs(); void Create_System_LAMMPS(int numbodies, double *mass,double **inertia, double ** xcm, double ** xjoint,double **vh1,double **omega,double **ex_space, double **ey_space, double **ez_space, int b, int * mapping, int count); - + void Create_DegenerateSystem(int& nfree, int*freelist, double *&masstotal, double **&inertia, double **&xcm, double **&vcm, double **&omega, double **&ex_space, double **&ey_space, double **&ez_space); }; -} + #endif diff --git a/lib/poems/vect3.cpp b/lib/poems/vect3.cpp index 66c2f902d5..03c5d7bc00 100644 --- a/lib/poems/vect3.cpp +++ b/lib/poems/vect3.cpp @@ -16,13 +16,9 @@ *_________________________________________________________________________*/ #include "vect3.h" - #include -#include using namespace std; -using namespace POEMS; - Vect3::Vect3(){ numrows = 3; numcols = 1; @@ -145,13 +141,6 @@ Vect3& Vect3::operator+=(const Vect3& A){ return *this; } -Vect3& Vect3::operator-(){ - elements[0] = -elements[0]; - elements[1] = -elements[1]; - elements[2] = -elements[2]; - return *this; -} - Vect3& Vect3::operator-=(const Vect3& A){ elements[0] -= A.elements[0]; elements[1] -= A.elements[1]; diff --git a/lib/poems/vect3.h b/lib/poems/vect3.h index 6b0efc371a..ababe18e51 100644 --- a/lib/poems/vect3.h +++ b/lib/poems/vect3.h @@ -3,7 +3,7 @@ * POEMS: PARALLELIZABLE OPEN SOURCE EFFICIENT MULTIBODY SOFTWARE * * DESCRIPTION: SEE READ-ME * * FILE NAME: vect3.h * - * AUTHORS: See Author List * + * AUTHORS: See Author List * * GRANTS: See Grants List * * COPYRIGHT: (C) 2005 by Authors as listed in Author's List * * LICENSE: Please see License Agreement * @@ -11,19 +11,15 @@ * ADMINISTRATOR: Prof. Kurt Anderson * * Computational Dynamics Lab * * Rensselaer Polytechnic Institute * - * 110 8th St. Troy NY 12180 * + * 110 8th St. Troy NY 12180 * * CONTACT: anderk5@rpi.edu * *_________________________________________________________________________*/ #ifndef VECT3_H #define VECT3_H -#include - #include "virtualcolmatrix.h" -#include "virtualmatrix.h" -namespace POEMS { class Matrix; class Mat3x3; class Mat6x6; @@ -56,7 +52,6 @@ public: Vect3& operator*=(double b); Vect3& operator+=(const Vect3& A); Vect3& operator-=(const Vect3& A); - Vect3& operator-(); friend Matrix T(const Vect3& A); // a wasteful transpose friend Mat3x3 CrossMat(Vect3& a); // a wasteful cross matrix implementation @@ -83,6 +78,7 @@ public: friend void FastMult(Mat3x3& A, ColMatrix& B, Vect3& C); friend void FastAssign(ColMatrix&A, Vect3& C); friend void FastMult(Mat3x3& A, Vect3& B, ColMatrix& C); + }; -} + #endif diff --git a/lib/poems/vect4.cpp b/lib/poems/vect4.cpp index 8e903d57bd..3b5afddc50 100644 --- a/lib/poems/vect4.cpp +++ b/lib/poems/vect4.cpp @@ -16,13 +16,9 @@ *_________________________________________________________________________*/ #include "vect4.h" - #include -#include using namespace std; -using namespace POEMS; - Vect4::Vect4(){ numrows = 4; numcols = 1; diff --git a/lib/poems/vect4.h b/lib/poems/vect4.h index 754706f10a..695f5e158a 100644 --- a/lib/poems/vect4.h +++ b/lib/poems/vect4.h @@ -3,7 +3,7 @@ * POEMS: PARALLELIZABLE OPEN SOURCE EFFICIENT MULTIBODY SOFTWARE * * DESCRIPTION: SEE READ-ME * * FILE NAME: vect4.h * - * AUTHORS: See Author List * + * AUTHORS: See Author List * * GRANTS: See Grants List * * COPYRIGHT: (C) 2005 by Authors as listed in Author's List * * LICENSE: Please see License Agreement * @@ -11,19 +11,16 @@ * ADMINISTRATOR: Prof. Kurt Anderson * * Computational Dynamics Lab * * Rensselaer Polytechnic Institute * - * 110 8th St. Troy NY 12180 * + * 110 8th St. Troy NY 12180 * * CONTACT: anderk5@rpi.edu * *_________________________________________________________________________*/ #ifndef VECT4_H #define VECT4_H -#include - #include "virtualcolmatrix.h" -#include "virtualmatrix.h" -namespace POEMS { + class Matrix; class Mat4x4; @@ -42,7 +39,7 @@ public: void BasicSet_1int(int i, double value); void BasicIncrement_1int(int i, double value); - + void Const(double value); MatrixType GetType() const; std::ostream& WriteData(std::ostream& c) const; @@ -70,5 +67,5 @@ public: friend void FastAdd(Vect4& A, Vect4& B, Vect4& C); friend void FastSubt(Vect4& A, Vect4& B, Vect4& C); }; -} + #endif diff --git a/lib/poems/vect6.cpp b/lib/poems/vect6.cpp index 5aabe520e1..eb65d24f16 100644 --- a/lib/poems/vect6.cpp +++ b/lib/poems/vect6.cpp @@ -16,13 +16,9 @@ *_________________________________________________________________________*/ #include "vect6.h" - #include -#include using namespace std; -using namespace POEMS; - Vect6::Vect6(){ numrows = 6; numcols = 1; diff --git a/lib/poems/vect6.h b/lib/poems/vect6.h index 5def4c6b1b..c346c852ef 100644 --- a/lib/poems/vect6.h +++ b/lib/poems/vect6.h @@ -18,12 +18,8 @@ #ifndef VECT6_H #define VECT6_H -#include - #include "virtualcolmatrix.h" -#include "virtualmatrix.h" -namespace POEMS { class Matrix; class Mat6x6; class ColMatrix; @@ -70,5 +66,5 @@ public: friend void OnPopulateSVect(Vect3& angular, Vect3& linear, Vect6& sV); }; -} + #endif diff --git a/lib/poems/virtualcolmatrix.cpp b/lib/poems/virtualcolmatrix.cpp index fa430b81f7..3a6c6e22cd 100644 --- a/lib/poems/virtualcolmatrix.cpp +++ b/lib/poems/virtualcolmatrix.cpp @@ -20,8 +20,6 @@ #include using namespace std; -using namespace POEMS; - VirtualColMatrix::VirtualColMatrix(){ numcols = 1; diff --git a/lib/poems/virtualcolmatrix.h b/lib/poems/virtualcolmatrix.h index 040fce051e..1548794ca0 100644 --- a/lib/poems/virtualcolmatrix.h +++ b/lib/poems/virtualcolmatrix.h @@ -3,7 +3,7 @@ * POEMS: PARALLELIZABLE OPEN SOURCE EFFICIENT MULTIBODY SOFTWARE * * DESCRIPTION: SEE READ-ME * * FILE NAME: virtualcolmatrix.h * - * AUTHORS: See Author List * + * AUTHORS: See Author List * * GRANTS: See Grants List * * COPYRIGHT: (C) 2005 by Authors as listed in Author's List * * LICENSE: Please see License Agreement * @@ -11,7 +11,7 @@ * ADMINISTRATOR: Prof. Kurt Anderson * * Computational Dynamics Lab * * Rensselaer Polytechnic Institute * - * 110 8th St. Troy NY 12180 * + * 110 8th St. Troy NY 12180 * * CONTACT: anderk5@rpi.edu * *_________________________________________________________________________*/ @@ -21,25 +21,25 @@ #include "virtualmatrix.h" -namespace POEMS { + class VirtualColMatrix : public VirtualMatrix { -public: - VirtualColMatrix(); - ~VirtualColMatrix(); - double& operator_2int (int i, int j); // array access - double Get_2int (int i, int j) const; - void Set_2int (int i, int j, double value); - double BasicGet_2int(int i, int j) const; - void BasicSet_2int(int i, int j, double value); - void BasicIncrement_2int(int i, int j, double value); - - virtual double& operator_1int (int i) = 0; // array access - virtual double Get_1int(int i) const = 0; - virtual void Set_1int(int i, double value) = 0; - virtual double BasicGet_1int(int i) const = 0; - virtual void BasicSet_1int(int i, double value) = 0; - virtual void BasicIncrement_1int(int i, double value) = 0; +public: + VirtualColMatrix(); + ~VirtualColMatrix(); + double& operator_2int (int i, int j); // array access + double Get_2int (int i, int j) const; + void Set_2int (int i, int j, double value); + double BasicGet_2int(int i, int j) const; + void BasicSet_2int(int i, int j, double value); + void BasicIncrement_2int(int i, int j, double value); + + virtual double& operator_1int (int i) = 0; // array access + virtual double Get_1int(int i) const = 0; + virtual void Set_1int(int i, double value) = 0; + virtual double BasicGet_1int(int i) const = 0; + virtual void BasicSet_1int(int i, double value) = 0; + virtual void BasicIncrement_1int(int i, double value) = 0; }; -} + #endif diff --git a/lib/poems/virtualmatrix.cpp b/lib/poems/virtualmatrix.cpp index bfffeb3d74..19d5946961 100644 --- a/lib/poems/virtualmatrix.cpp +++ b/lib/poems/virtualmatrix.cpp @@ -21,8 +21,6 @@ #include using namespace std; -using namespace POEMS; - VirtualMatrix::VirtualMatrix(){ numrows = numcols = 0; @@ -142,14 +140,14 @@ istream& VirtualMatrix::ReadData(istream& c){ // operators and functions // -ostream& POEMS::operator<< (ostream& c, const VirtualMatrix& A){ //output +ostream& operator<< (ostream& c, const VirtualMatrix& A){ //output c << A.GetType() << ' '; A.WriteData(c); c << endl; return c; } -istream& POEMS::operator>> (istream& c, VirtualMatrix& A){ //input +istream& operator>> (istream& c, VirtualMatrix& A){ //input VirtualMatrix* vm; int matrixtype; c >> matrixtype; diff --git a/lib/poems/virtualmatrix.h b/lib/poems/virtualmatrix.h index 706b943d66..a27c7de047 100644 --- a/lib/poems/virtualmatrix.h +++ b/lib/poems/virtualmatrix.h @@ -20,7 +20,6 @@ #define VIRTUALMATRIX_H #include -namespace POEMS { enum MatrixType { MATRIX = 0, COLMATRIX = 1, @@ -84,5 +83,5 @@ protected: // overloaded operators std::ostream& operator<< (std::ostream& c, const VirtualMatrix& A); // output std::istream& operator>> (std::istream& c, VirtualMatrix& A); // input -} + #endif diff --git a/lib/poems/virtualrowmatrix.cpp b/lib/poems/virtualrowmatrix.cpp index 740c747407..1a12cfbfd9 100644 --- a/lib/poems/virtualrowmatrix.cpp +++ b/lib/poems/virtualrowmatrix.cpp @@ -21,8 +21,6 @@ #include using namespace std; -using namespace POEMS; - VirtualRowMatrix::VirtualRowMatrix(){ numrows = 1; diff --git a/lib/poems/virtualrowmatrix.h b/lib/poems/virtualrowmatrix.h index 0a3c877f64..68b39f137d 100644 --- a/lib/poems/virtualrowmatrix.h +++ b/lib/poems/virtualrowmatrix.h @@ -3,7 +3,7 @@ * POEMS: PARALLELIZABLE OPEN SOURCE EFFICIENT MULTIBODY SOFTWARE * * DESCRIPTION: SEE READ-ME * * FILE NAME: virtualrowmatrix.h * - * AUTHORS: See Author List * + * AUTHORS: See Author List * * GRANTS: See Grants List * * COPYRIGHT: (C) 2005 by Authors as listed in Author's List * * LICENSE: Please see License Agreement * @@ -11,7 +11,7 @@ * ADMINISTRATOR: Prof. Kurt Anderson * * Computational Dynamics Lab * * Rensselaer Polytechnic Institute * - * 110 8th St. Troy NY 12180 * + * 110 8th St. Troy NY 12180 * * CONTACT: anderk5@rpi.edu * *_________________________________________________________________________*/ @@ -21,9 +21,8 @@ #include "virtualmatrix.h" -namespace POEMS { class VirtualRowMatrix : public VirtualMatrix { -public: +public: VirtualRowMatrix(); ~VirtualRowMatrix(); double& operator_2int (int i, int j); // array access @@ -32,7 +31,7 @@ public: double BasicGet_2int(int i, int j) const; void BasicSet_2int(int i, int j, double value); void BasicIncrement_2int(int i, int j, double value); - + virtual double& operator_1int (int i) = 0; // array access virtual double Get_1int(int i) const = 0; virtual void Set_1int(int i, double value) = 0; @@ -40,5 +39,5 @@ public: virtual void BasicSet_1int(int i, double value) = 0; virtual void BasicIncrement_1int(int i, double value) = 0; }; -} + #endif diff --git a/lib/poems/workspace.cpp b/lib/poems/workspace.cpp index 03f18a7895..2b3257b0dd 100644 --- a/lib/poems/workspace.cpp +++ b/lib/poems/workspace.cpp @@ -15,31 +15,18 @@ * CONTACT: anderk5@rpi.edu * *_________________________________________________________________________*/ -#include -#include // IWYU pragma: keep -#include #include "workspace.h" #include "system.h" #include "solver.h" #include "SystemProcessor.h" -#include "POEMSChain.h" -#include "body.h" -#include "colmatmap.h" -#include "colmatrix.h" -#include "defines.h" -#include "joint.h" -#include "mat3x3.h" -#include "matrix.h" -#include "matrixfun.h" -#include "poemslist.h" -#include "vect3.h" -#include "virtualmatrix.h" +#include +#include +#include +#include using namespace std; -using namespace POEMS; - void Workspace::allocateNewSystem() { currentIndex++; diff --git a/lib/poems/workspace.h b/lib/poems/workspace.h index 2510b2fc3a..5faaf904dc 100644 --- a/lib/poems/workspace.h +++ b/lib/poems/workspace.h @@ -3,7 +3,7 @@ * POEMS: PARALLELIZABLE OPEN SOURCE EFFICIENT MULTIBODY SOFTWARE * * DESCRIPTION: SEE READ-ME * * FILE NAME: workspace.h * - * AUTHORS: See Author List * + * AUTHORS: See Author List * * GRANTS: See Grants List * * COPYRIGHT: (C) 2005 by Authors as listed in Author's List * * LICENSE: Please see License Agreement * @@ -11,7 +11,7 @@ * ADMINISTRATOR: Prof. Kurt Anderson * * Computational Dynamics Lab * * Rensselaer Polytechnic Institute * - * 110 8th St. Troy NY 12180 * + * 110 8th St. Troy NY 12180 * * CONTACT: anderk5@rpi.edu * *_________________________________________________________________________*/ @@ -19,62 +19,70 @@ #ifndef WORKSPACE_H #define WORKSPACE_H -namespace POEMS { +#include "matrices.h" +#include +#include +#include +#include +#include +#include + + class System; class Solver; struct SysData{ - System * system; - int solver; - int integrator; + System * system; + int solver; + int integrator; }; class Workspace { - SysData * system; // the multibody systems data - int currentIndex; - int maxAlloc; - + SysData * system; // the multibody systems data + int currentIndex; + int maxAlloc; + public: Workspace(); ~Workspace(); - + double Thalf; double Tfull; double ConFac; double KE_val; - int FirstTime; - + int FirstTime; + bool LoadFile(char* filename); - + bool SaveFile(char* filename, int index = -1); System* GetSystem(int index = -1); - - void AddSolver(Solver* s, int index = -1); - - - void LobattoOne(double **&xcm, double **&vcm,double **&omega,double **&torque, double **&fcm, double **&ex_space, double **&ey_space, double **&ez_space); - - void LobattoTwo(double **&vcm,double **&omega,double **&torque, double **&fcm); - - + + void AddSolver(Solver* s, int index = -1); + + + void LobattoOne(double **&xcm, double **&vcm,double **&omega,double **&torque, double **&fcm, double **&ex_space, double **&ey_space, double **&ez_space); + + void LobattoTwo(double **&vcm,double **&omega,double **&torque, double **&fcm); + + bool MakeSystem(int& nbody, double *&masstotal, double **&inertia, double **&xcm, double **&vcm, double **&omega, double **&ex_space, double **&ey_space, double **&ez_space, int &njoint, int **&jointbody, double **&xjoint, int& nfree, int*freelist, double dthalf, double dtv, double tempcon, double KE); - - - bool SaveSystem(int& nbody, double *&masstotal, double **&inertia, double **&xcm, double **&xjoint, double **&vcm, double **&omega, double **&ex_space, double **&ey_space, double **&ez_space, double **&acm, double **&alpha, double **&torque, double **&fcm, int **&jointbody, int &njoint); - - bool MakeDegenerateSystem(int& nfree, int*freelist, double *&masstotal, double **&inertia, double **&xcm, double **&vcm, double **&omega, double **&ex_space, double **&ey_space, double **&ez_space); + + + bool SaveSystem(int& nbody, double *&masstotal, double **&inertia, double **&xcm, double **&xjoint, double **&vcm, double **&omega, double **&ex_space, double **&ey_space, double **&ez_space, double **&acm, double **&alpha, double **&torque, double **&fcm, int **&jointbody, int &njoint); + + bool MakeDegenerateSystem(int& nfree, int*freelist, double *&masstotal, double **&inertia, double **&xcm, double **&vcm, double **&omega, double **&ex_space, double **&ey_space, double **&ez_space); int getNumberOfSystems(); - + void SetLammpsValues(double dtv, double dthalf, double tempcon); void SetKE(int temp, double SysKE); - - void RKStep(double **&xcm, double **&vcm,double **&omega,double **&torque, double **&fcm, double **&ex_space, double **&ey_space, double **&ez_space); - - void WriteFile(char* filename); + + void RKStep(double **&xcm, double **&vcm,double **&omega,double **&torque, double **&fcm, double **&ex_space, double **&ey_space, double **&ez_space); + + void WriteFile(char* filename); private: - void allocateNewSystem(); //helper function to handle vector resizing and such for the array of system pointers + void allocateNewSystem(); //helper function to handle vector resizing and such for the array of system pointers }; -} + #endif diff --git a/src/POEMS/fix_poems.cpp b/src/POEMS/fix_poems.cpp index 21c12f700b..c8646f5b14 100644 --- a/src/POEMS/fix_poems.cpp +++ b/src/POEMS/fix_poems.cpp @@ -263,7 +263,7 @@ FixPOEMS::FixPOEMS(LAMMPS *lmp, int narg, char **arg) : // create POEMS instance - poems = new POEMS::Workspace; + poems = new Workspace; // compute per body forces and torques inside final_integrate() by default diff --git a/src/POEMS/fix_poems.h b/src/POEMS/fix_poems.h index 87f9557ac0..7b2c77a1bd 100644 --- a/src/POEMS/fix_poems.h +++ b/src/POEMS/fix_poems.h @@ -22,7 +22,6 @@ FixStyle(poems,FixPOEMS) #include "fix.h" -namespace POEMS { class Workspace; } namespace LAMMPS_NS { class FixPOEMS : public Fix { @@ -95,7 +94,7 @@ class FixPOEMS : public Fix { // POEMS object - POEMS::Workspace *poems; + class Workspace *poems; // internal class functions -- GitLab From b6b802d0b11d75f1dd5cd58f76f3392fcb8a04c2 Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Mon, 22 Jul 2019 14:36:09 -0400 Subject: [PATCH 288/469] correct forward declaration of POEMS workspace class --- src/POEMS/fix_poems.h | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/src/POEMS/fix_poems.h b/src/POEMS/fix_poems.h index 7b2c77a1bd..6892c51d7e 100644 --- a/src/POEMS/fix_poems.h +++ b/src/POEMS/fix_poems.h @@ -22,6 +22,8 @@ FixStyle(poems,FixPOEMS) #include "fix.h" +class Workspace; + namespace LAMMPS_NS { class FixPOEMS : public Fix { @@ -94,7 +96,7 @@ class FixPOEMS : public Fix { // POEMS object - class Workspace *poems; + Workspace *poems; // internal class functions -- GitLab From dd4368dd1b471134629486e590a6624a66265c8f Mon Sep 17 00:00:00 2001 From: "Ryan S. Elliott" Date: Tue, 23 Jul 2019 13:40:13 -0500 Subject: [PATCH 289/469] Fix bug in pair_kim.cpp for partialParticleVirial computation --- src/KIM/pair_kim.cpp | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/KIM/pair_kim.cpp b/src/KIM/pair_kim.cpp index 6251ebb6c7..50eef1de2b 100644 --- a/src/KIM/pair_kim.cpp +++ b/src/KIM/pair_kim.cpp @@ -826,7 +826,7 @@ void PairKIM::set_argument_pointers() } else if (KIM_SupportStatus_NotEqual(kim_model_support_for_particleVirial, KIM_SUPPORT_STATUS_notSupported)) { kimerror = kimerror || KIM_ComputeArguments_SetArgumentPointerDouble( - pargs, KIM_COMPUTE_ARGUMENT_NAME_partialParticleEnergy, &(vatom[0][0])); + pargs, KIM_COMPUTE_ARGUMENT_NAME_partialParticleVirial, &(vatom[0][0])); } if (kimerror) error->all(FLERR,"Unable to set KIM argument pointers"); -- GitLab From be86db9dd9cde416f0136b282c830e9bf231c59a Mon Sep 17 00:00:00 2001 From: "Ryan S. Elliott" Date: Tue, 23 Jul 2019 21:06:02 -0500 Subject: [PATCH 290/469] Update /lib/kim stuff --- lib/kim/Install.py | 11 ++++------- lib/kim/README | 22 ++++++++++------------ 2 files changed, 14 insertions(+), 19 deletions(-) diff --git a/lib/kim/Install.py b/lib/kim/Install.py index c3588241c4..de22950639 100644 --- a/lib/kim/Install.py +++ b/lib/kim/Install.py @@ -18,7 +18,7 @@ parser = ArgumentParser(prog='Install.py', # settings thisdir = fullpath('.') -version = "kim-api-2.0.2" +version = "kim-api-2.1.1" # help message @@ -39,11 +39,8 @@ make lib-kim args="-b -a EAM_ErcolessiAdams_1994_Al__MO_324507536345_002" # Ditt make lib-kim args="-b -a everything" # install KIM API lib with all models make lib-kim args="-n -a EAM_Dynamo_Ackland_2003_W__MO_141627196590_005" # only add one model or model driver -See the list of KIM model drivers here: -https://openkim.org/browse/model-drivers/alphabetical - See the list of all KIM models here: -https://openkim.org/browse/models/by-model-drivers +https://openkim.org/browse/models """ pgroup = parser.add_mutually_exclusive_group() @@ -132,7 +129,7 @@ if buildflag: # build kim-api print("Building kim-api ...") - cmd = 'cd "%s/%s/build" && make' % (thisdir, version) + cmd = 'cd "%s/%s/build" && make -j2' % (thisdir, version) txt = subprocess.check_output(cmd, stderr=subprocess.STDOUT, shell=True) if verboseflag: print(txt.decode("UTF-8")) @@ -140,7 +137,7 @@ if buildflag: # install kim-api print("Installing kim-api ...") - cmd = 'cd "%s/%s/build" && make install' % (thisdir, version) + cmd = 'cd "%s/%s/build" && make -j2 install' % (thisdir, version) txt = subprocess.check_output(cmd, stderr=subprocess.STDOUT, shell=True) if verboseflag: print(txt.decode("UTF-8")) diff --git a/lib/kim/README b/lib/kim/README index d3327537b6..3cba4a4597 100644 --- a/lib/kim/README +++ b/lib/kim/README @@ -1,11 +1,11 @@ -This directory contains build settings for the KIM API library which -is required to use the KIM package and its pair_style kim command in a -LAMMPS input script. +This directory contains build settings for the KIM API library which is +required to use the KIM package and its kim_init, kim_interactions, kim_query, +and pair_kim commands in a LAMMPS input script. Information about the KIM project can be found at https://openkim.org. The KIM project is lead by Ellad Tadmor and Ryan Elliott (U Minn). Ryan Elliott is the main developer for the KIM API and he also -maintains the code that implements the pair_style kim command. +maintains the code that implements the KIM commands. You can type "make lib-kim" from the src directory to see help on how to download and build this library via make commands, or you can @@ -13,11 +13,9 @@ do the same thing by typing "python Install.py" from within this directory, or you can do it manually by following the instructions below. -As of KIM API version 2, the KIM package also provides a LAMMPS command -to perform queries through the OpenKIM web API. This feature requires -that the CURL library (libcurl) development package and its configuration -query tool, curl-config, are installed. The provided Makefile.lammps -is set up to automatically detect this. +Use of the kim_query command requires that the CURL library (libcurl) +development package and its configuration query tool, curl-config, are +installed. The provided Makefile.lammps is set up to automatically detect this. ----------------- @@ -40,8 +38,8 @@ $ cmake .. -DCMAKE_INSTALL_PREFIX=${PWD}/../../installed-kim-api-X.Y.Z 3. Build and install the kim-api and model -$ make -$ make install +$ make -j2 +$ make -j2 install 4. Remove source and build files @@ -53,7 +51,7 @@ $ rm -rf kim-api-X.Y.Z.txz desired value) $ source ${PWD}/kim-api-X.Y.Z/bin/kim-api-activate -$ kim-api-collections-management install system Pair_Johnson_Fe__MO_857282754307_002 +$ kim-api-collections-management install system EAM_ErcolessiAdams_1994_Al__MO_324507536345_002 ----------------- -- GitLab From 3bc4a07c74aac582a9e74ce429abb4564e224cfd Mon Sep 17 00:00:00 2001 From: Ellad Tadmor Date: Wed, 24 Jul 2019 11:23:51 -0500 Subject: [PATCH 291/469] Corrections to kim_query in example --- doc/src/kim_commands.txt | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/doc/src/kim_commands.txt b/doc/src/kim_commands.txt index 01df0532b7..6fe7d7ba3e 100644 --- a/doc/src/kim_commands.txt +++ b/doc/src/kim_commands.txt @@ -433,7 +433,7 @@ the returned values is determined by the type of query performed. kim_init EAM_Dynamo_ErcolessiAdams_1994_Al__MO_123629422045_005 metal boundary p p p kim_query a0 get_lattice_constant_cubic crystal=\["fcc"\] species=\["Al"\] units=\["angstrom"\] -kim_query alpha get_linear_thermal_expansion_constant_cubic crystal=\["fcc"\] species=\["Al"\] units=\{"1/K"\} temperature=[293.15] temperature_units=["K"] +kim_query alpha get_linear_thermal_expansion_coefficient_cubic crystal=\["fcc"\] species=\["Al"\] units=\["1/K"\] temperature=\[293.15\] temperature_units=\["K"\] variable DeltaT equal 300 lattice fcc $\{a0\}*$\{alpha\}*$\{DeltaT\} ... :pre -- GitLab From 3887a7f3d79559eb47d82e989a71ed1abf6a0320 Mon Sep 17 00:00:00 2001 From: Ellad Tadmor Date: Wed, 24 Jul 2019 12:07:38 -0500 Subject: [PATCH 292/469] Updated KIM ID code for IFF SM --- doc/src/kim_commands.txt | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/doc/src/kim_commands.txt b/doc/src/kim_commands.txt index 6fe7d7ba3e..dd61f6f5cc 100644 --- a/doc/src/kim_commands.txt +++ b/doc/src/kim_commands.txt @@ -33,7 +33,7 @@ kim_interactions Si kim_init Sim_LAMMPS_ReaxFF_StrachanVanDuinChakraborty_2003_CHNO__SM_107643900657_000 real kim_init Sim_LAMMPS_ReaxFF_StrachanVanDuinChakraborty_2003_CHNO__SM_107643900657_000 metal unit_conversion_mode kim_interactions C H O -Sim_LAMMPS_IFF_PCFF_HeinzMishraLinEmami_2015Ver1v5_FccmetalsMineralsSolvents Polymers__SM_064312669787_000 real +Sim_LAMMPS_IFF_PCFF_HeinzMishraLinEmami_2015Ver1v5_FccmetalsMineralsSolvents Polymers__SM_039297821658_000 real kim_interactions fixed_types kim_query a0 get_lattice_constant_cubic crystal=\["fcc"\] species=\["Al"\] units=\["angstrom"\] :pre -- GitLab From 440025778388c97af44d0d023673f39deb8b2672 Mon Sep 17 00:00:00 2001 From: Stan Moore Date: Wed, 24 Jul 2019 12:10:57 -0600 Subject: [PATCH 293/469] Change GPU-direct to CUDA-aware MPI and add workaround for IBM Spectrum MPI --- src/KOKKOS/comm_kokkos.cpp | 4 +-- src/KOKKOS/gridcomm_kokkos.cpp | 8 ++--- src/KOKKOS/kokkos.cpp | 58 ++++++++++++++++++---------------- src/KOKKOS/kokkos.h | 2 +- 4 files changed, 37 insertions(+), 35 deletions(-) diff --git a/src/KOKKOS/comm_kokkos.cpp b/src/KOKKOS/comm_kokkos.cpp index 87986a9ca9..d0bd978ae7 100644 --- a/src/KOKKOS/comm_kokkos.cpp +++ b/src/KOKKOS/comm_kokkos.cpp @@ -418,7 +418,7 @@ void CommKokkos::forward_comm_pair_device(Pair *pair) if (sendproc[iswap] != me) { double* buf_send_pair; double* buf_recv_pair; - if (lmp->kokkos->gpu_direct_flag) { + if (lmp->kokkos->cuda_aware_flag) { buf_send_pair = k_buf_send_pair.view().data(); buf_recv_pair = k_buf_recv_pair.view().data(); } else { @@ -436,7 +436,7 @@ void CommKokkos::forward_comm_pair_device(Pair *pair) MPI_Send(buf_send_pair,n,MPI_DOUBLE,sendproc[iswap],0,world); if (recvnum[iswap]) MPI_Wait(&request,MPI_STATUS_IGNORE); - if (!lmp->kokkos->gpu_direct_flag) { + if (!lmp->kokkos->cuda_aware_flag) { k_buf_recv_pair.modify(); k_buf_recv_pair.sync(); } diff --git a/src/KOKKOS/gridcomm_kokkos.cpp b/src/KOKKOS/gridcomm_kokkos.cpp index 14b84a5733..348217634b 100644 --- a/src/KOKKOS/gridcomm_kokkos.cpp +++ b/src/KOKKOS/gridcomm_kokkos.cpp @@ -529,7 +529,7 @@ void GridCommKokkos::forward_comm(KSpace *kspace, int which) if (swap[m].sendproc != me) { FFT_SCALAR* buf1; FFT_SCALAR* buf2; - if (lmp->kokkos->gpu_direct_flag) { + if (lmp->kokkos->cuda_aware_flag) { buf1 = k_buf1.view().data(); buf2 = k_buf2.view().data(); } else { @@ -545,7 +545,7 @@ void GridCommKokkos::forward_comm(KSpace *kspace, int which) swap[m].sendproc,0,gridcomm); MPI_Wait(&request,MPI_STATUS_IGNORE); - if (!lmp->kokkos->gpu_direct_flag) { + if (!lmp->kokkos->cuda_aware_flag) { k_buf2.modify(); k_buf2.sync(); } @@ -579,7 +579,7 @@ void GridCommKokkos::reverse_comm(KSpace *kspace, int which) if (swap[m].recvproc != me) { FFT_SCALAR* buf1; FFT_SCALAR* buf2; - if (lmp->kokkos->gpu_direct_flag) { + if (lmp->kokkos->cuda_aware_flag) { buf1 = k_buf1.view().data(); buf2 = k_buf2.view().data(); } else { @@ -595,7 +595,7 @@ void GridCommKokkos::reverse_comm(KSpace *kspace, int which) swap[m].recvproc,0,gridcomm); MPI_Wait(&request,MPI_STATUS_IGNORE); - if (!lmp->kokkos->gpu_direct_flag) { + if (!lmp->kokkos->cuda_aware_flag) { k_buf2.modify(); k_buf2.sync(); } diff --git a/src/KOKKOS/kokkos.cpp b/src/KOKKOS/kokkos.cpp index 3fa84d98b2..7d2ef8e4d7 100644 --- a/src/KOKKOS/kokkos.cpp +++ b/src/KOKKOS/kokkos.cpp @@ -28,31 +28,33 @@ #ifdef KOKKOS_ENABLE_CUDA -// for detecting GPU-direct support: -// the function int have_gpu_direct() -// - returns -1 if GPU-direct support is unknown -// - returns 0 if no GPU-direct support available -// - returns 1 if GPU-direct support is available +// for detecting CUDA-aware MPI support: +// the variable int have_cuda_aware +// - is -1 if CUDA-aware MPI support is unknown +// - is 0 if no CUDA-aware MPI support available +// - is 1 if CUDA-aware MPI support is available -#define GPU_DIRECT_UNKNOWN static int have_gpu_direct() {return -1;} +#define CUDA_AWARE_UNKNOWN static int have_cuda_aware = -1; -// OpenMPI supports detecting GPU-direct as of version 2.0.0 +// OpenMPI supports detecting CUDA-aware MPI as of version 2.0.0 #if OPEN_MPI #if (OMPI_MAJOR_VERSION >= 2) #include -#if defined(MPIX_CUDA_AWARE_SUPPORT) -static int have_gpu_direct() { return MPIX_Query_cuda_support(); } +#if defined(MPIX_CUDA_AWARE_SUPPORT) && MPIX_CUDA_AWARE_SUPPORT +static int have_cuda_aware = 1; +#elif defined(MPIX_CUDA_AWARE_SUPPORT) && !MPIX_CUDA_AWARE_SUPPORT +static int have_cuda_aware = 0; #else -GPU_DIRECT_UNKNOWN +CUDA_AWARE_UNKNOWN #endif #else // old OpenMPI -GPU_DIRECT_UNKNOWN +CUDA_AWARE_UNKNOWN #endif #else // unknown MPI library -GPU_DIRECT_UNKNOWN +CUDA_AWARE_UNKNOWN #endif #endif // KOKKOS_ENABLE_CUDA @@ -146,20 +148,20 @@ KokkosLMP::KokkosLMP(LAMMPS *lmp, int narg, char **arg) : Pointers(lmp) if (ngpus <= 0) error->all(FLERR,"Kokkos has been compiled for CUDA but no GPUs are requested"); - // check and warn about GPU-direct availability when using multiple MPI tasks + // check and warn about CUDA-aware MPI availability when using multiple MPI tasks int nmpi = 0; MPI_Comm_size(world,&nmpi); if ((nmpi > 1) && (me == 0)) { - if ( 1 == have_gpu_direct() ) { + if ( 1 == have_cuda_aware ) { ; // all good, nothing to warn about - } else if (-1 == have_gpu_direct() ) { - error->warning(FLERR,"Kokkos with CUDA assumes GPU-direct is available," + } else if ( -1 == have_cuda_aware ) { + error->warning(FLERR,"Kokkos with CUDA assumes CUDA-aware MPI is available," " but cannot determine if this is the case\n try" - " '-pk kokkos gpu/direct off' when getting segmentation faults"); - } else if ( 0 == have_gpu_direct() ) { - error->warning(FLERR,"GPU-direct is NOT available, " - "using '-pk kokkos gpu/direct off' by default"); + " '-pk kokkos cuda/aware off' when getting segmentation faults"); + } else if ( 0 == have_cuda_aware ) { + error->warning(FLERR,"CUDA-aware MPI is NOT available, " + "using '-pk kokkos cuda/aware off' by default"); } else { ; // should never get here } @@ -183,7 +185,7 @@ KokkosLMP::KokkosLMP(LAMMPS *lmp, int narg, char **arg) : Pointers(lmp) // default settings for package kokkos command binsize = 0.0; - gpu_direct_flag = 1; + cuda_aware_flag = 1; neigh_thread = 0; neigh_thread_set = 0; neighflag_qeq_set = 0; @@ -207,8 +209,8 @@ KokkosLMP::KokkosLMP(LAMMPS *lmp, int narg, char **arg) : Pointers(lmp) } #if KOKKOS_USE_CUDA - // only if we can safely detect, that GPU-direct is not available, change default - if (0 == have_gpu_direct()) gpu_direct_flag = 0; + // change default only if we can safely detect that CUDA-aware MPI is not available + if (0 == have_cuda_aware()) cuda_aware_flag = 0; #endif #ifdef KILL_KOKKOS_ON_SIGSEGV @@ -313,10 +315,10 @@ void KokkosLMP::accelerator(int narg, char **arg) reverse_comm_on_host = 0; } else error->all(FLERR,"Illegal package kokkos command"); iarg += 2; - } else if (strcmp(arg[iarg],"gpu/direct") == 0) { + } else if (strcmp(arg[iarg],"cuda/aware") == 0) { if (iarg+2 > narg) error->all(FLERR,"Illegal package kokkos command"); - if (strcmp(arg[iarg+1],"off") == 0) gpu_direct_flag = 0; - else if (strcmp(arg[iarg+1],"on") == 0) gpu_direct_flag = 1; + if (strcmp(arg[iarg+1],"off") == 0) cuda_aware_flag = 0; + else if (strcmp(arg[iarg+1],"on") == 0) cuda_aware_flag = 1; else error->all(FLERR,"Illegal package kokkos command"); iarg += 2; } else if (strcmp(arg[iarg],"neigh/thread") == 0) { @@ -329,9 +331,9 @@ void KokkosLMP::accelerator(int narg, char **arg) } else error->all(FLERR,"Illegal package kokkos command"); } - // if "gpu/direct off" and "comm device", change to "comm host" + // if "cuda/aware off" and "comm device", change to "comm host" - if (!gpu_direct_flag) { + if (!cuda_aware_flag) { if (exchange_comm_classic == 0 && exchange_comm_on_host == 0) exchange_comm_on_host = 1; if (forward_comm_classic == 0 && forward_comm_on_host == 0) diff --git a/src/KOKKOS/kokkos.h b/src/KOKKOS/kokkos.h index 46044799c4..19e6297ea4 100644 --- a/src/KOKKOS/kokkos.h +++ b/src/KOKKOS/kokkos.h @@ -35,7 +35,7 @@ class KokkosLMP : protected Pointers { int nthreads,ngpus; int numa; int auto_sync; - int gpu_direct_flag; + int cuda_aware_flag; int neigh_thread; int neigh_thread_set; int newtonflag; -- GitLab From 4760cf868d7f5e0fe51f88ca83a14744a6c7c4ea Mon Sep 17 00:00:00 2001 From: Stan Moore Date: Wed, 24 Jul 2019 12:11:26 -0600 Subject: [PATCH 294/469] Update docs to change GPU-direct to CUDA-aware MPI --- doc/src/Speed_kokkos.txt | 24 +++++++++++------------- doc/src/package.txt | 28 +++++++++++++++------------- 2 files changed, 26 insertions(+), 26 deletions(-) diff --git a/doc/src/Speed_kokkos.txt b/doc/src/Speed_kokkos.txt index fd33491253..99d29864dc 100644 --- a/doc/src/Speed_kokkos.txt +++ b/doc/src/Speed_kokkos.txt @@ -46,16 +46,15 @@ software version 7.5 or later must be installed on your system. See the discussion for the "GPU package"_Speed_gpu.html for details of how to check and do this. -NOTE: Kokkos with CUDA currently implicitly assumes that the MPI -library is CUDA-aware and has support for GPU-direct. This is not -always the case, especially when using pre-compiled MPI libraries -provided by a Linux distribution. This is not a problem when using -only a single GPU and a single MPI rank on a desktop. When running -with multiple MPI ranks, you may see segmentation faults without -GPU-direct support. These can be avoided by adding the flags "-pk -kokkos gpu/direct off"_Run_options.html to the LAMMPS command line or -by using the command "package kokkos gpu/direct off"_package.html in -the input file. +NOTE: Kokkos with CUDA currently implicitly assumes that the MPI library +is CUDA-aware. This is not always the case, especially when using +pre-compiled MPI libraries provided by a Linux distribution. This is not +a problem when using only a single GPU with a single MPI rank. When +running with multiple MPI ranks, you may see segmentation faults without +CUDA-aware MPI support. These can be avoided by adding the flags "-pk +kokkos cuda/aware off"_Run_options.html to the LAMMPS command line or by +using the command "package kokkos cuda/aware off"_package.html in the +input file. [Building LAMMPS with the KOKKOS package:] @@ -217,9 +216,8 @@ case, also packing/unpacking communication buffers on the host may give speedup (see the KOKKOS "package"_package.html command). Using CUDA MPS is recommended in this scenario. -Using a CUDA-aware MPI library with -support for GPU-direct is highly recommended. GPU-direct use can be -avoided by using "-pk kokkos gpu/direct no"_package.html. As above for +Using a CUDA-aware MPI library is highly recommended. CUDA-aware MPI use can be +avoided by using "-pk kokkos cuda/aware no"_package.html. As above for multi-core CPUs (and no GPU), if N is the number of physical cores/node, then the number of MPI tasks/node should not exceed N. diff --git a/doc/src/package.txt b/doc/src/package.txt index 6a6d17bcbc..edd409a842 100644 --- a/doc/src/package.txt +++ b/doc/src/package.txt @@ -64,7 +64,7 @@ args = arguments specific to the style :l {no_affinity} values = none {kokkos} args = keyword value ... zero or more keyword/value pairs may be appended - keywords = {neigh} or {neigh/qeq} or {neigh/thread} or {newton} or {binsize} or {comm} or {comm/exchange} or {comm/forward} or {comm/reverse} or {gpu/direct} + keywords = {neigh} or {neigh/qeq} or {neigh/thread} or {newton} or {binsize} or {comm} or {comm/exchange} or {comm/forward} or {comm/reverse} or {cuda/aware} {neigh} value = {full} or {half} full = full neighbor list half = half neighbor list built in thread-safe manner @@ -87,9 +87,9 @@ args = arguments specific to the style :l no = perform communication pack/unpack in non-KOKKOS mode host = perform pack/unpack on host (e.g. with OpenMP threading) device = perform pack/unpack on device (e.g. on GPU) - {gpu/direct} = {off} or {on} - off = do not use GPU-direct - on = use GPU-direct (default) + {cuda/aware} = {off} or {on} + off = do not use CUDA-aware MPI + on = use CUDA-aware MPI (default) {omp} args = Nthreads keyword value ... Nthread = # of OpenMP threads to associate with each MPI process zero or more keyword/value pairs may be appended @@ -520,19 +520,21 @@ pack/unpack communicated data. When running small systems on a GPU, performing the exchange pack/unpack on the host CPU can give speedup since it reduces the number of CUDA kernel launches. -The {gpu/direct} keyword chooses whether GPU-direct will be used. When +The {cuda/aware} keyword chooses whether CUDA-aware MPI will be used. When this keyword is set to {on}, buffers in GPU memory are passed directly through MPI send/receive calls. This reduces overhead of first copying -the data to the host CPU. However GPU-direct is not supported on all +the data to the host CPU. However CUDA-aware MPI is not supported on all systems, which can lead to segmentation faults and would require using a -value of {off}. If LAMMPS can safely detect that GPU-direct is not +value of {off}. If LAMMPS can safely detect that CUDA-aware MPI is not available (currently only possible with OpenMPI v2.0.0 or later), then -the {gpu/direct} keyword is automatically set to {off} by default. When -the {gpu/direct} keyword is set to {off} while any of the {comm} +the {cuda/aware} keyword is automatically set to {off} by default. When +the {cuda/aware} keyword is set to {off} while any of the {comm} keywords are set to {device}, the value for these {comm} keywords will be automatically changed to {host}. This setting has no effect if not -running on GPUs. GPU-direct is available for OpenMPI 1.8 (or later -versions), Mvapich2 1.9 (or later), and CrayMPI. +running on GPUs. CUDA-aware MPI is available for OpenMPI 1.8 (or later +versions), Mvapich2 1.9 (or later) when the "MV2_USE_CUDA" environment +variable is set to "1", CrayMPI, and IBM Spectrum MPI when the "-gpu" +flag is used. :line @@ -641,8 +643,8 @@ switch"_Run_options.html. For the KOKKOS package, the option defaults for GPUs are neigh = full, neigh/qeq = full, newton = off, binsize for GPUs = 2x LAMMPS default -value, comm = device, gpu/direct = on. When LAMMPS can safely detect -that GPU-direct is not available, the default value of gpu/direct +value, comm = device, cuda/aware = on. When LAMMPS can safely detect +that CUDA-aware MPI is not available, the default value of cuda/aware becomes "off". For CPUs or Xeon Phis, the option defaults are neigh = half, neigh/qeq = half, newton = on, binsize = 0.0, and comm = no. The option neigh/thread = on when there are 16K atoms or less on an MPI -- GitLab From 985c959a91d5701da3f8292534c024721007b21b Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Wed, 24 Jul 2019 14:27:29 -0400 Subject: [PATCH 295/469] include the bond length in communication cutoff considerations --- src/neighbor.cpp | 25 ++++++++++++++++++++++++- 1 file changed, 24 insertions(+), 1 deletion(-) diff --git a/src/neighbor.cpp b/src/neighbor.cpp index 0382624198..1cae719df1 100644 --- a/src/neighbor.cpp +++ b/src/neighbor.cpp @@ -35,6 +35,7 @@ #include "comm.h" #include "force.h" #include "pair.h" +#include "bond.h" #include "domain.h" #include "group.h" #include "modify.h" @@ -276,6 +277,28 @@ void Neighbor::init() // cutneigh = force cutoff + skin if cutforce > 0, else cutneigh = 0 // cutneighghost = pair cutghost if it requests it, else same as cutneigh + // also consider bonded interactions for estimating the the neighborlist + // and communication cutoff. we use the bond equilibrium distance as + // cutoff, if only a bond style exists. if also an angle style exists we + // multiply by 2, for dihedral or improper we multiply by 3. + // this plus "skin" will become the default communication cutoff, if no + // pair style is defined. otherwise the maximum of the largest pairwise + // cutoff of this is used. + + double maxbondcutoff = 0.0; + if (force->bond) { + n = atom->nbondtypes; + for (i = 1; i <= n; ++i) { + double bondcutoff = force->bond->equilibrium_distance(i); + maxbondcutoff = MAX(bondcutoff,maxbondcutoff); + } + if (force->dihedral || force->improper) { + maxbondcutoff *= 3.0; + } else if (force->angle) { + maxbondcutoff *=2.0; + } + } + triggersq = 0.25*skin*skin; boxcheck = 0; if (domain->box_change && (domain->xperiodic || domain->yperiodic || @@ -293,7 +316,7 @@ void Neighbor::init() double cutoff,delta,cut; cutneighmin = BIG; - cutneighmax = 0.0; + cutneighmax = maxbondcutoff; for (i = 1; i <= n; i++) { cuttype[i] = cuttypesq[i] = 0.0; -- GitLab From be1522d16d8ce58711537a7fdb33884f887c3f96 Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Wed, 24 Jul 2019 14:42:17 -0400 Subject: [PATCH 296/469] add warning to Comm class against zero communication cutoff --- src/comm_brick.cpp | 3 +++ src/comm_tiled.cpp | 4 ++++ 2 files changed, 7 insertions(+) diff --git a/src/comm_brick.cpp b/src/comm_brick.cpp index 330551aaed..eb53f89746 100644 --- a/src/comm_brick.cpp +++ b/src/comm_brick.cpp @@ -176,6 +176,9 @@ void CommBrick::setup() double *prd,*sublo,*subhi; double cut = MAX(neighbor->cutneighmax,cutghostuser); + if ((cut == 0.0) && (me == 0)) + error->warning(FLERR,"Communication cutoff is 0.0. No ghost atoms " + "will be generated. Atoms may get lost."); if (triclinic == 0) { prd = domain->prd; diff --git a/src/comm_tiled.cpp b/src/comm_tiled.cpp index d1d625445a..9d4c446057 100644 --- a/src/comm_tiled.cpp +++ b/src/comm_tiled.cpp @@ -158,6 +158,10 @@ void CommTiled::setup() // check that cutoff < any periodic box length double cut = MAX(neighbor->cutneighmax,cutghostuser); + if ((cut == 0.0) && (me == 0)) + error->warning(FLERR,"Communication cutoff is 0.0. No ghost atoms " + "will be generated. Atoms may get lost."); + cutghost[0] = cutghost[1] = cutghost[2] = cut; if ((periodicity[0] && cut > prd[0]) || -- GitLab From 20843f7476e28a37e7933b2ebc920f0a41eb2983 Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Wed, 24 Jul 2019 14:52:07 -0400 Subject: [PATCH 297/469] add documentation for warning added to comm styles --- doc/src/Errors_warnings.txt | 10 ++++++++++ src/comm.h | 9 +++++++++ 2 files changed, 19 insertions(+) diff --git a/doc/src/Errors_warnings.txt b/doc/src/Errors_warnings.txt index 1507d6b22c..9f346ba8c1 100644 --- a/doc/src/Errors_warnings.txt +++ b/doc/src/Errors_warnings.txt @@ -129,6 +129,16 @@ Self-explanatory. :dd Self-explanatory. :dd +{Communication cutoff is 0.0. No ghost atoms will be generated. Atoms may get lost} :dt + +The communication cutoff defaults to the maximum of what is inferred from +pair and bond styles (will be zero, if none are defined) and what is specified +via "comm_modify cutoff"_comm_modify.html (defaults to 0.0). If this results +to 0.0, no ghost atoms will be generated and LAMMPS may lose atoms or use +incorrect periodic images of atoms in interaction lists. To avoid, either use +"pair style zero"_pair_zero.html with a suitable cutoff or use "comm_modify +cutoff"_comm_modify.html. :dd + {Communication cutoff is too small for SNAP micro load balancing, increased to %lf} :dt Self-explanatory. :dd diff --git a/src/comm.h b/src/comm.h index 30360b1059..90a215b4a6 100644 --- a/src/comm.h +++ b/src/comm.h @@ -237,6 +237,15 @@ Self-explanatory. E: Cannot put data on ring from NULL pointer +W: Communication cutoff is 0.0. No ghost atoms will be generated. Atoms may get lost. + +The communication cutoff defaults to the maximum of what is inferred from pair and +bond styles (will be zero, if none are defined) and what is specified via +"comm_modify cutoff" (defaults to 0.0). If this results to 0.0, no ghost atoms will +be generated and LAMMPS may lose atoms or use incorrect periodic images of atoms in +interaction lists. To avoid, either define pair style zero with a suitable cutoff +or use comm_modify cutoff. + UNDOCUMENTED U: OMP_NUM_THREADS environment is not set. -- GitLab From 1d310ad73e80f220cbfc90153758b43af7700032 Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Wed, 24 Jul 2019 14:52:37 -0400 Subject: [PATCH 298/469] add half a bond length safety margin to bond length based cutoff estimates --- src/neighbor.cpp | 13 ++++++++----- 1 file changed, 8 insertions(+), 5 deletions(-) diff --git a/src/neighbor.cpp b/src/neighbor.cpp index 1cae719df1..9964b23b60 100644 --- a/src/neighbor.cpp +++ b/src/neighbor.cpp @@ -278,9 +278,10 @@ void Neighbor::init() // cutneighghost = pair cutghost if it requests it, else same as cutneigh // also consider bonded interactions for estimating the the neighborlist - // and communication cutoff. we use the bond equilibrium distance as - // cutoff, if only a bond style exists. if also an angle style exists we - // multiply by 2, for dihedral or improper we multiply by 3. + // and communication cutoff. we use the 1.5x the bond equilibrium distance + // as cutoff, if only a bond style exists. if also an angle style exists we + // multiply by 2.5, for dihedral or improper we multiply by 3.5. (1,2, or 3 + // bonds plus half a bond length total stretch). // this plus "skin" will become the default communication cutoff, if no // pair style is defined. otherwise the maximum of the largest pairwise // cutoff of this is used. @@ -293,9 +294,11 @@ void Neighbor::init() maxbondcutoff = MAX(bondcutoff,maxbondcutoff); } if (force->dihedral || force->improper) { - maxbondcutoff *= 3.0; + maxbondcutoff *= 3.5; } else if (force->angle) { - maxbondcutoff *=2.0; + maxbondcutoff *=2.5; + } else { + maxbondcutoff *=1.5; } } -- GitLab From afab7d99c1ea2488763f6770723b574b9e78a5b0 Mon Sep 17 00:00:00 2001 From: Stan Moore Date: Wed, 24 Jul 2019 13:10:37 -0600 Subject: [PATCH 299/469] Fix variable name --- src/KOKKOS/kokkos.cpp | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/src/KOKKOS/kokkos.cpp b/src/KOKKOS/kokkos.cpp index 7d2ef8e4d7..3d1cb419d6 100644 --- a/src/KOKKOS/kokkos.cpp +++ b/src/KOKKOS/kokkos.cpp @@ -208,9 +208,9 @@ KokkosLMP::KokkosLMP(LAMMPS *lmp, int narg, char **arg) : Pointers(lmp) exchange_comm_on_host = forward_comm_on_host = reverse_comm_on_host = 0; } -#if KOKKOS_USE_CUDA +#ifdef KOKKOS_ENABLE_CUDA // change default only if we can safely detect that CUDA-aware MPI is not available - if (0 == have_cuda_aware()) cuda_aware_flag = 0; + if (0 == have_cuda_aware) cuda_aware_flag = 0; #endif #ifdef KILL_KOKKOS_ON_SIGSEGV -- GitLab From cb9facea8b3643de95b4b41df11f4b998b335828 Mon Sep 17 00:00:00 2001 From: Steve Plimpton Date: Wed, 24 Jul 2019 13:43:12 -0600 Subject: [PATCH 300/469] add reset of dotmark --- src/rcb.cpp | 50 ++++++++++++++++++-------------------------------- 1 file changed, 18 insertions(+), 32 deletions(-) diff --git a/src/rcb.cpp b/src/rcb.cpp index ac7ac60b1f..5cb3b697e2 100644 --- a/src/rcb.cpp +++ b/src/rcb.cpp @@ -467,44 +467,30 @@ void RCB::compute(int dimension, int n, double **x, double *wt, } } - //check if zero box width is the result due to dots being on box vertices - //select half of the box in this case along the best dim - //the best dim is chosen according to the optimum volume (to minimize surface area) - - if(largest==0.0){ - double best_volume=0; - double current_volume; - int dim1o,dim2o; - for (dim = 0; dim < dimension; dim++){ - if(dim==0){ - dim1o=1; - dim2o=2; - } - if(dim==1){ - dim1o=0; - dim2o=2; - } - if(dim==2){ - dim1o=0; - dim2o=1; - } - valuehalf = 0.5*(lo[dim] + hi[dim]); - current_volume = (hi[dim1o]-lo[dim1o]) - *(hi[dim2o]-lo[dim2o])*(valuehalf-lo[dim]); - //chose cut that minimizes surface area by maximizing volume; - if(current_volume>best_volume){ best_volume = current_volume; - valuehalf_select = valuehalf; - dim_select = dim; - } - } - } - // copy results for best dim cut into dim,valuehalf,dotmark dim = dim_select; valuehalf = valuehalf_select; if (ndot > 0) memcpy(dotmark,dotmark_select,ndot*sizeof(int)); + // special case for zero box width + // can occur when all dots are on corner vertices of this sub-box + // split box on longest dimension + // reset dotmark for that cut + + if (largest == 0.0) { + dim = 0; + if (hi[1]-lo[1] > hi[0]-lo[0]) dim = 1; + if (dimension == 3 && hi[2]-lo[2] > hi[dim]-lo[dim]) dim = 2; + valuehalf = 0.5* (lo[dim] + hi[dim]); + + for (j = 0; j < nlist; j++) { + i = dotlist[j]; + if (dots[i].x[dim] <= valuehalf) dotmark[i] = 0; + else dotmark[i] = 1; + } + } + // found median // store cut info only if I am procmid -- GitLab From 24d9c537c0d589cfd1b46f9ccf65d765d93ff953 Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Wed, 24 Jul 2019 16:01:46 -0400 Subject: [PATCH 301/469] only search for LAPACK when building in static mode and when it is not needed for something else --- cmake/CMakeLists.txt | 3 +-- cmake/Modules/Packages/USER-PLUMED.cmake | 6 ++++++ 2 files changed, 7 insertions(+), 2 deletions(-) diff --git a/cmake/CMakeLists.txt b/cmake/CMakeLists.txt index 0f99cc6274..2fa3170415 100644 --- a/cmake/CMakeLists.txt +++ b/cmake/CMakeLists.txt @@ -219,8 +219,7 @@ if(BUILD_OMP) set (CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} ${OpenMP_CXX_FLAGS}") endif() - -if(PKG_MSCG OR PKG_USER-ATC OR PKG_USER-AWPMD OR PKG_USER-PLUMED OR PKG_USER-QUIP OR PKG_LATTE) +if(PKG_MSCG OR PKG_USER-ATC OR PKG_USER-AWPMD OR PKG_USER-QUIP OR PKG_LATTE) find_package(LAPACK) find_package(BLAS) if(NOT LAPACK_FOUND OR NOT BLAS_FOUND) diff --git a/cmake/Modules/Packages/USER-PLUMED.cmake b/cmake/Modules/Packages/USER-PLUMED.cmake index 500558fc72..f71d59901d 100644 --- a/cmake/Modules/Packages/USER-PLUMED.cmake +++ b/cmake/Modules/Packages/USER-PLUMED.cmake @@ -6,6 +6,12 @@ if(PKG_USER-PLUMED) validate_option(PLUMED_MODE PLUMED_MODE_VALUES) string(TOUPPER ${PLUMED_MODE} PLUMED_MODE) + if((PLUMED_MODE STREQUAL "STATIC") AND NOT LAPACK_LIBRARIES) + find_package(LAPACK REQUIRED) + find_package(BLAS REQUIRED) + list(APPEND LAPACK_LIBRARIES ${BLAS_LIBRARIES}) + endif() + find_package(PkgConfig QUIET) set(DOWNLOAD_PLUMED_DEFAULT ON) if(PKG_CONFIG_FOUND) -- GitLab From 6ee38d4887719368f6b89265b4656ce7a0ab4558 Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Wed, 24 Jul 2019 16:02:36 -0400 Subject: [PATCH 302/469] use ${CMAKE_SHARED_LIBRARY_SUFFIX) for better portability --- cmake/Modules/Packages/USER-PLUMED.cmake | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/cmake/Modules/Packages/USER-PLUMED.cmake b/cmake/Modules/Packages/USER-PLUMED.cmake index f71d59901d..35533f01ef 100644 --- a/cmake/Modules/Packages/USER-PLUMED.cmake +++ b/cmake/Modules/Packages/USER-PLUMED.cmake @@ -61,9 +61,9 @@ if(PKG_USER-PLUMED) add_definitions(-D__PLUMED_WRAPPER_CXX=1) list(APPEND LAMMPS_LINK_LIBS ${PLUMED_INSTALL_DIR}/lib/libplumed.a ${GSL_LIBRARIES} ${LAPACK_LIBRARIES} ${CMAKE_DL_LIBS}) elseif(PLUMED_MODE STREQUAL "SHARED") - list(APPEND LAMMPS_LINK_LIBS ${PLUMED_INSTALL_DIR}/lib/libplumed.so ${PLUMED_INSTALL_DIR}/lib/libplumedKernel.so ${CMAKE_DL_LIBS}) + list(APPEND LAMMPS_LINK_LIBS ${PLUMED_INSTALL_DIR}/lib/libplumed${CMAKE_SHARED_LIBRARY_SUFFIX} ${PLUMED_INSTALL_DIR}/lib/libplumedKernel${CMAKE_SHARED_LIBRARY_SUFFIX} ${CMAKE_DL_LIBS}) elseif(PLUMED_MODE STREQUAL "RUNTIME") - add_definitions(-D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_DEFAULT_KERNEL=${PLUMED_INSTALL_DIR}/lib/libplumedKernel.so) + add_definitions(-D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_DEFAULT_KERNEL=${PLUMED_INSTALL_DIR}/lib/libplumedKernel${CMAKE_SHARED_LIBRARY_SUFFIX}) list(APPEND LAMMPS_LINK_LIBS ${PLUMED_INSTALL_DIR}/lib/libplumedWrapper.a -rdynamic ${CMAKE_DL_LIBS}) endif() set(PLUMED_INCLUDE_DIRS "${PLUMED_INSTALL_DIR}/include") @@ -76,7 +76,7 @@ if(PKG_USER-PLUMED) elseif(PLUMED_MODE STREQUAL "SHARED") include(${PLUMED_LIBDIR}/plumed/src/lib/Plumed.cmake.shared) elseif(PLUMED_MODE STREQUAL "RUNTIME") - add_definitions(-D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_DEFAULT_KERNEL=${PLUMED_LIBDIR}/libplumedKernel.so) + add_definitions(-D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_DEFAULT_KERNEL=${PLUMED_LIBDIR}/libplumedKernel${CMAKE_SHARED_LIBRARY_SUFFIX}) include(${PLUMED_LIBDIR}/plumed/src/lib/Plumed.cmake.runtime) endif() list(APPEND LAMMPS_LINK_LIBS ${PLUMED_LOAD}) -- GitLab From d59737299cde717e88731c6324206a47b371679d Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Wed, 24 Jul 2019 16:02:49 -0400 Subject: [PATCH 303/469] whitespace cleanup --- lib/plumed/README | 16 ++++++++-------- 1 file changed, 8 insertions(+), 8 deletions(-) diff --git a/lib/plumed/README b/lib/plumed/README index fb8ef29ff3..0d5f52f6b2 100644 --- a/lib/plumed/README +++ b/lib/plumed/README @@ -1,7 +1,7 @@ This directory contains links to the PLUMED library which is required to use the PLUMED package and its fix plumed command in a -LAMMPS input script. PLUMED should only be downloaded into this directory if -you wish to statically link the library. If you wish to link PLUMED as +LAMMPS input script. PLUMED should only be downloaded into this directory if +you wish to statically link the library. If you wish to link PLUMED as a dynamic library (as we recommend) then you can compile and build PLUMED separately to LAMMPS. To use PLUMED in conjuction with LAMMPS you then simply need to ensure that the PLUMED library is in your path at runtime. @@ -18,15 +18,15 @@ below. Instructions: -1. Download PLUMED either as a tarball from +1. Download PLUMED either as a tarball from http://www.plumed.org/get-it - or clone it using git clone https://github.com/plumed/plumed2.git. + or clone it using git clone https://github.com/plumed/plumed2.git. If you download the tarball unpack it in unpack it in this /lib/plumed directory. Similarly if you clone it clone it to the /lib/plumed directory. -2. Compile PLUMED from within its home directory. In the +2. Compile PLUMED from within its home directory. In the simplest cases this be done by issuing the commands % ./configure % make @@ -34,14 +34,14 @@ Instructions: http://plumed.github.io/doc-master/user-doc/html/_installation.html 3. There is no need to install PLUMED if you only wish - to use it from LAMMPS. You should thus only run + to use it from LAMMPS. You should thus only run make install if you want to use PLUMED as a stand-alone - code or from some other code. To install it you can + code or from some other code. To install it you can run the following commands: a) install under the default /usr/local % sudo make install b) install under a user-writeable location by first - changing the PREFIX variable when running the + changing the PREFIX variable when running the configure command file, then % make install -- GitLab From 3c53efb1ca132c1cf9671ccb0877bf762d6a61f4 Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Wed, 24 Jul 2019 16:03:11 -0400 Subject: [PATCH 304/469] don't set MPI communicator when compiling in serial with MPI stubs --- src/USER-PLUMED/fix_plumed.cpp | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/src/USER-PLUMED/fix_plumed.cpp b/src/USER-PLUMED/fix_plumed.cpp index 8bd0ecca05..c75a48f9b4 100644 --- a/src/USER-PLUMED/fix_plumed.cpp +++ b/src/USER-PLUMED/fix_plumed.cpp @@ -107,7 +107,11 @@ FixPlumed::FixPlumed(LAMMPS *lmp, int narg, char **arg) : // whereas if partitions are not defined then world is equal to // MPI_COMM_WORLD. +#if !defined(MPI_STUBS) + // plumed does not know about LAMMPS using the MPI STUBS library and will + // fail if this is called under these circumstances p->cmd("setMPIComm",&world); +#endif // Set up units // LAMMPS units wrt kj/mol - nm - ps -- GitLab From eaf2b59b1b4b586f279d4a958293a343e1cea906 Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Wed, 24 Jul 2019 16:53:03 -0400 Subject: [PATCH 305/469] adapt fix neigh/history/omp to changes for dynamic exchange buffer size --- src/USER-OMP/fix_neigh_history_omp.cpp | 11 ++++++++--- src/fix.h | 2 +- 2 files changed, 9 insertions(+), 4 deletions(-) diff --git a/src/USER-OMP/fix_neigh_history_omp.cpp b/src/USER-OMP/fix_neigh_history_omp.cpp index efa7f5a3f1..c44d122981 100644 --- a/src/USER-OMP/fix_neigh_history_omp.cpp +++ b/src/USER-OMP/fix_neigh_history_omp.cpp @@ -175,6 +175,8 @@ void FixNeighHistoryOMP::pre_exchange_onesided() } // set maxpartner = max # of partners of any owned atom + // maxexchange = max # of values for any Comm::exchange() atom + maxpartner = m = 0; for (i = lfrom; i < lto; i++) m = MAX(m,npartner[i]); @@ -184,7 +186,7 @@ void FixNeighHistoryOMP::pre_exchange_onesided() #endif { maxpartner = MAX(m,maxpartner); - comm->maxexchange_fix =MAX(comm->maxexchange_fix,(dnum+1)*maxpartner+1); + maxexchange = (dnum+1)*maxpartner+1; } } @@ -347,6 +349,7 @@ void FixNeighHistoryOMP::pre_exchange_newton() } // set maxpartner = max # of partners of any owned atom + // maxexchange = max # of values for any Comm::exchange() atom m = 0; for (i = lfrom; i < lto; i++) m = MAX(m,npartner[i]); @@ -356,7 +359,7 @@ void FixNeighHistoryOMP::pre_exchange_newton() #endif { maxpartner = MAX(m,maxpartner); - comm->maxexchange_fix = MAX(comm->maxexchange_fix,(dnum+1)*maxpartner+1); + maxexchange = (dnum+1)*maxpartner+1; } } @@ -485,6 +488,8 @@ void FixNeighHistoryOMP::pre_exchange_no_newton() } // set maxpartner = max # of partners of any owned atom + // maxexchange = max # of values for any Comm::exchange() atom + m = 0; for (i = lfrom; i < lto; i++) m = MAX(m,npartner[i]); @@ -494,7 +499,7 @@ void FixNeighHistoryOMP::pre_exchange_no_newton() #endif { maxpartner = MAX(m,maxpartner); - comm->maxexchange_fix = MAX(comm->maxexchange_fix,(dnum+1)*maxpartner+1); + maxexchange = (dnum+1)*maxpartner+1; } } } diff --git a/src/fix.h b/src/fix.h index f4bf7f9c01..be99fe7cff 100644 --- a/src/fix.h +++ b/src/fix.h @@ -57,7 +57,7 @@ class Fix : protected Pointers { int respa_level_support; // 1 if fix supports fix_modify respa int respa_level; // which respa level to apply fix (1-Nrespa) int maxexchange; // max # of per-atom values for Comm::exchange() - int maxexchange_dynamic; // 1 if fix sets maxexchange dynamically + int maxexchange_dynamic; // 1 if fix sets maxexchange dynamically int scalar_flag; // 0/1 if compute_scalar() function exists int vector_flag; // 0/1 if compute_vector() function exists -- GitLab From c098582df81520e55d63621845bcada8cdbfded1 Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Wed, 24 Jul 2019 17:27:35 -0400 Subject: [PATCH 306/469] refactor communication cutoff estimator. move it to Comm class. and adjust heuristics. --- src/comm.cpp | 41 ++++++++++++++++++++++++++++++++++++----- src/comm.h | 2 ++ src/comm_brick.cpp | 2 +- src/comm_tiled.cpp | 2 +- src/info.cpp | 2 +- src/neighbor.cpp | 28 +--------------------------- 6 files changed, 42 insertions(+), 35 deletions(-) diff --git a/src/comm.cpp b/src/comm.cpp index 052de93793..3b4029e7d3 100644 --- a/src/comm.cpp +++ b/src/comm.cpp @@ -20,6 +20,7 @@ #include "atom_vec.h" #include "force.h" #include "pair.h" +#include "bond.h" #include "modify.h" #include "fix.h" #include "compute.h" @@ -585,6 +586,41 @@ void Comm::set_proc_grid(int outflag) } } +/* ---------------------------------------------------------------------- + determine suitable communication cutoff. + it is the maximum of the user specified value and estimates based on + the maximum neighbor list cutoff and largest bond equilibrium length. + we use the 1.5x the bond equilibrium distance as cutoff, if only a + bond style exists or only bond and angle styles exists. If dihedrals + or impropers are present we multiply by 2.0. This plus the + "neighbor list skin" will become the default communication cutoff, if + no pair style is defined and thus avoids all kinds of unexpected behavior + for such systems. If a pair style exists, the result is the maximum of + the bond based cutoff and the largest pair cutoff and the user + specified communication cutoff. +------------------------------------------------------------------------- */ + +double Comm::get_comm_cutoff() +{ + double maxcommcutoff = 0.0; + if (force->bond) { + int n = atom->nbondtypes; + for (int i = 1; i <= n; ++i) + maxcommcutoff = MAX(maxcommcutoff,force->bond->equilibrium_distance(i)); + + if (force->dihedral || force->improper) { + maxcommcutoff *= 2.0; + } else { + maxcommcutoff *=1.5; + } + maxcommcutoff += neighbor->skin; + } + maxcommcutoff = MAX(maxcommcutoff,neighbor->cutneighmax); + maxcommcutoff = MAX(maxcommcutoff,cutghostuser); + + return maxcommcutoff; +} + /* ---------------------------------------------------------------------- determine which proc owns atom with coord x[3] based on current decomp x will be in box (orthogonal) or lamda coords (triclinic) @@ -963,11 +999,6 @@ rendezvous_all2all(int n, char *inbuf, int insize, int inorder, int *procs, return 0; // all nout_rvous are 0, no 2nd irregular } - - - - - // create procs and outbuf for All2all if necesary if (!outorder) { diff --git a/src/comm.h b/src/comm.h index 90a215b4a6..860912a7d2 100644 --- a/src/comm.h +++ b/src/comm.h @@ -70,6 +70,8 @@ class Comm : protected Pointers { void set_processors(int, char **); // set 3d processor grid attributes virtual void set_proc_grid(int outflag = 1); // setup 3d grid of procs + double get_comm_cutoff(); // determine communication cutoff + virtual void setup() = 0; // setup 3d comm pattern virtual void forward_comm(int dummy = 0) = 0; // forward comm of atom coords virtual void reverse_comm() = 0; // reverse comm of forces diff --git a/src/comm_brick.cpp b/src/comm_brick.cpp index eb53f89746..a9ce64399f 100644 --- a/src/comm_brick.cpp +++ b/src/comm_brick.cpp @@ -175,7 +175,7 @@ void CommBrick::setup() int ntypes = atom->ntypes; double *prd,*sublo,*subhi; - double cut = MAX(neighbor->cutneighmax,cutghostuser); + double cut = get_comm_cutoff(); if ((cut == 0.0) && (me == 0)) error->warning(FLERR,"Communication cutoff is 0.0. No ghost atoms " "will be generated. Atoms may get lost."); diff --git a/src/comm_tiled.cpp b/src/comm_tiled.cpp index 9d4c446057..2558559cf7 100644 --- a/src/comm_tiled.cpp +++ b/src/comm_tiled.cpp @@ -157,7 +157,7 @@ void CommTiled::setup() // set cutoff for comm forward and comm reverse // check that cutoff < any periodic box length - double cut = MAX(neighbor->cutneighmax,cutghostuser); + double cut = get_comm_cutoff(); if ((cut == 0.0) && (me == 0)) error->warning(FLERR,"Communication cutoff is 0.0. No ghost atoms " "will be generated. Atoms may get lost."); diff --git a/src/info.cpp b/src/info.cpp index 25b9879408..74cbe6556f 100644 --- a/src/info.cpp +++ b/src/info.cpp @@ -366,7 +366,7 @@ void Info::command(int narg, char **arg) if (comm->mode == 0) { fprintf(out,"Communication mode = single\n"); fprintf(out,"Communication cutoff = %g\n", - MAX(comm->cutghostuser,neighbor->cutneighmax)); + comm->get_comm_cutoff()); } if (comm->mode == 1) { diff --git a/src/neighbor.cpp b/src/neighbor.cpp index 9964b23b60..0382624198 100644 --- a/src/neighbor.cpp +++ b/src/neighbor.cpp @@ -35,7 +35,6 @@ #include "comm.h" #include "force.h" #include "pair.h" -#include "bond.h" #include "domain.h" #include "group.h" #include "modify.h" @@ -277,31 +276,6 @@ void Neighbor::init() // cutneigh = force cutoff + skin if cutforce > 0, else cutneigh = 0 // cutneighghost = pair cutghost if it requests it, else same as cutneigh - // also consider bonded interactions for estimating the the neighborlist - // and communication cutoff. we use the 1.5x the bond equilibrium distance - // as cutoff, if only a bond style exists. if also an angle style exists we - // multiply by 2.5, for dihedral or improper we multiply by 3.5. (1,2, or 3 - // bonds plus half a bond length total stretch). - // this plus "skin" will become the default communication cutoff, if no - // pair style is defined. otherwise the maximum of the largest pairwise - // cutoff of this is used. - - double maxbondcutoff = 0.0; - if (force->bond) { - n = atom->nbondtypes; - for (i = 1; i <= n; ++i) { - double bondcutoff = force->bond->equilibrium_distance(i); - maxbondcutoff = MAX(bondcutoff,maxbondcutoff); - } - if (force->dihedral || force->improper) { - maxbondcutoff *= 3.5; - } else if (force->angle) { - maxbondcutoff *=2.5; - } else { - maxbondcutoff *=1.5; - } - } - triggersq = 0.25*skin*skin; boxcheck = 0; if (domain->box_change && (domain->xperiodic || domain->yperiodic || @@ -319,7 +293,7 @@ void Neighbor::init() double cutoff,delta,cut; cutneighmin = BIG; - cutneighmax = maxbondcutoff; + cutneighmax = 0.0; for (i = 1; i <= n; i++) { cuttype[i] = cuttypesq[i] = 0.0; -- GitLab From d08477cc5f152f9fe8e2d916a9548aac798b75c9 Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Wed, 24 Jul 2019 17:49:00 -0400 Subject: [PATCH 307/469] print warning, when explicitly specified communication cutoff is increased --- src/comm.cpp | 5 +++++ 1 file changed, 5 insertions(+) diff --git a/src/comm.cpp b/src/comm.cpp index 3b4029e7d3..4e605808af 100644 --- a/src/comm.cpp +++ b/src/comm.cpp @@ -617,6 +617,11 @@ double Comm::get_comm_cutoff() } maxcommcutoff = MAX(maxcommcutoff,neighbor->cutneighmax); maxcommcutoff = MAX(maxcommcutoff,cutghostuser); + if ((me == 0) && (cutghostuser > 0.0) && (maxcommcutoff > cutghostuser)) { + char mesg[128]; + snprintf(mesg,128,"Communication cutoff is changed to %g",maxcommcutoff); + error->warning(FLERR,mesg); + } return maxcommcutoff; } -- GitLab From b5a066ecd023495b252f3dfab7a8aedce0ac77bc Mon Sep 17 00:00:00 2001 From: "Ryan S. Elliott" Date: Wed, 24 Jul 2019 21:08:08 -0500 Subject: [PATCH 308/469] Better error checking for kim_init log.cite behavior --- src/KIM/kim_init.cpp | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/KIM/kim_init.cpp b/src/KIM/kim_init.cpp index 5fb6748427..83638f3428 100644 --- a/src/KIM/kim_init.cpp +++ b/src/KIM/kim_init.cpp @@ -486,7 +486,7 @@ void KimInit::write_log_cite(char * model_name) if (0 == strncmp("kimcite",fileName,7)) { - if (lmp->citeme) lmp->citeme->add(fileString); + if ((lmp->citeme) && (availableAsString)) lmp->citeme->add(fileString); } } -- GitLab From aec43304f4b71efba11471450b078d6ccff65573 Mon Sep 17 00:00:00 2001 From: Evangelos Voyiatzis Date: Thu, 25 Jul 2019 11:02:51 +0200 Subject: [PATCH 309/469] Add files via upload tex file with the equations for the shape parameters --- doc/src/Eqs/compute_shape_parameters.tex | 12 ++++++++++++ 1 file changed, 12 insertions(+) create mode 100644 doc/src/Eqs/compute_shape_parameters.tex diff --git a/doc/src/Eqs/compute_shape_parameters.tex b/doc/src/Eqs/compute_shape_parameters.tex new file mode 100644 index 0000000000..af7a6777f6 --- /dev/null +++ b/doc/src/Eqs/compute_shape_parameters.tex @@ -0,0 +1,12 @@ +\documentstyle[12pt]{article} + +\begin{document} + +\begin{eqnarray*} + c = l_z - 0.5(l_y+l_x) \\ + b = l_y - l_x \\ + k = \frac{3}{2} \frac{l_x^2+l_y^2+l_z^2}{(l_x+l_y+l_z)^2} - \frac{1}{2} +\end{eqnarray*} + +\end{document} + -- GitLab From 0be034ea46cb1013fcb04d23c343d50eb887a649 Mon Sep 17 00:00:00 2001 From: Evangelos Voyiatzis Date: Thu, 25 Jul 2019 11:03:41 +0200 Subject: [PATCH 310/469] Add files via upload txt file with the documentation of the new compute style --- doc/src/compute_gyration_shape.txt | 86 ++++++++++++++++++++++++++++++ 1 file changed, 86 insertions(+) create mode 100644 doc/src/compute_gyration_shape.txt diff --git a/doc/src/compute_gyration_shape.txt b/doc/src/compute_gyration_shape.txt new file mode 100644 index 0000000000..b9b62cfaa7 --- /dev/null +++ b/doc/src/compute_gyration_shape.txt @@ -0,0 +1,86 @@ +"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c + +:link(lws,http://lammps.sandia.gov) +:link(ld,Manual.html) +:link(lc,Commands_all.html) + +:line + +compute gyration/shape command :h3 + +[Syntax:] + +compute ID group-ID gyration computeID :pre + +ID, group-ID are documented in "compute"_compute.html command +gyration/shape = style name of this compute command +computeID = ID of "compute gyration"_compute_gyration.html command :ul + +[Examples:] + +compute 1 molecule gyration/shape pe :pre + +[Description:] + +Define a computation that calculates the eigenvalues of the gyration tensor of a +group of atoms and three shape parameters. The computation includes all effects +due to atoms passing thru periodic boundaries. + +The three computed shape parameters are the asphericity, b, the acylindricity, c, +and the relative shape anisotropy, k: + +:c,image(Eqs/compute_shape_parameters.jpg) + +where lx ≤ ly ≤ lz are the three eigenvalues of the gyration tensor. +The asphericity is always non-negative and zero only when the three principal +moments are equal. This zero condition is met when the distribution of particles +is spherically symmetric (hence the name asphericity) but also whenever the particle + distribution is symmetric with respect to the three coordinate axes, e.g., +when the particles are distributed uniformly on a cube, tetrahedron or other Platonic +solid. The acylindricity is always non-negative and zero only when the two principal +moments are equal. This zero condition is met when the distribution of particles is +cylindrically symmetric (hence the name, acylindricity), but also whenever the particle +distribution is symmetric with respect to the two coordinate axes, e.g., when the +particles are distributed uniformly on a regular prism. the relative shape anisotropy +is bounded between zero (if all points are spherically symmetric) and one +(if all points lie on a line). + +NOTE: The coordinates of an atom contribute to the gyration tensor in +"unwrapped" form, by using the image flags associated with each atom. +See the "dump custom"_dump.html command for a discussion of "unwrapped" +coordinates. See the Atoms section of the "read_data"_read_data.html +command for a discussion of image flags and how they are set for each +atom. You can reset the image flags (e.g. to 0) before invoking this +compute by using the "set image"_set.html command. + +[Output info:] + +This compute calculates a global vector of +length 6, which can be accessed by indices 1-6. The first three values are the +eigenvalues of the gyration tensor followed by the asphericity, the acylindricity +and the relative shape anisotropy. The computed values can be used by any command +that uses global vector values from a compute as input. See the "Howto +output"_Howto_output.html doc page for an overview of LAMMPS output +options. + +The vector values calculated by this compute are +"intensive". The first five vector values will be in +distance^2 "units"_units.html while the sixth one is dimensionless. + +[Restrictions:] + +This compute is part of the USER-MISC package. It is only enabled if +LAMMPS was built with that package. See the "Build +package"_Build_package.html doc page for more info. + +[Related commands:] + +"compute gyration"_compute_gyration.html + +[Default:] none + +:line + +:link(Theodorou) +[(Theodorou)] Theodorou, Suter, Macromolecules, 18, 1206 (1985). + -- GitLab From 1cebc5516e1093f21f7f87e345a27c51cf2b4355 Mon Sep 17 00:00:00 2001 From: Evangelos Voyiatzis Date: Thu, 25 Jul 2019 11:05:35 +0200 Subject: [PATCH 311/469] Update README Adding my e-mail to README --- src/USER-MISC/README | 1 + 1 file changed, 1 insertion(+) diff --git a/src/USER-MISC/README b/src/USER-MISC/README index 219e19673d..c5b9353415 100644 --- a/src/USER-MISC/README +++ b/src/USER-MISC/README @@ -30,6 +30,7 @@ compute ackland/atom, Gerolf Ziegenhain, gerolf at ziegenhain.com, 4 Oct 2007 compute basal/atom, Christopher Barrett, cdb333 at cavs.msstate.edu, 3 Mar 2013 compute cnp/atom, Paulo Branicio (USC), branicio at usc.edu, 31 May 2017 compute entropy/atom, Pablo Piaggi (EPFL), pablo.piaggi at epfl.ch, 15 June 2018 +compute gyration/shape, Evangelos Voyiatzis, evoyiatzis at gmail.com, 25 July 2019 compute pressure/cylinder, Cody K. Addington (NCSU), , 2 Oct 2018 compute stress/mop, Romain Vermorel (U Pau) & Laurent Joly (U Lyon), romain.vermorel at univ-pau.fr & ljoly.ulyon at gmail.com, 5 Sep 18 compute stress/mop/profile, Romain Vermorel (U Pau) & Laurent Joly (U Lyon), romain.vermorel at univ-pau.fr & ljoly.ulyon at gmail.com, 5 Sep 18 -- GitLab From 6e9252c8475f3c328e6df45a19f45dd7d0daae35 Mon Sep 17 00:00:00 2001 From: Evangelos Voyiatzis Date: Thu, 25 Jul 2019 11:10:36 +0200 Subject: [PATCH 312/469] Add files via upload The actual source code for the new compute --- src/USER-MISC/compute_gyration.cpp | 115 +++++++++++++++++++++++++ src/USER-MISC/compute_gyration_shape.h | 53 ++++++++++++ 2 files changed, 168 insertions(+) create mode 100644 src/USER-MISC/compute_gyration.cpp create mode 100644 src/USER-MISC/compute_gyration_shape.h diff --git a/src/USER-MISC/compute_gyration.cpp b/src/USER-MISC/compute_gyration.cpp new file mode 100644 index 0000000000..f8d19853e0 --- /dev/null +++ b/src/USER-MISC/compute_gyration.cpp @@ -0,0 +1,115 @@ +/* ---------------------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + http://lammps.sandia.gov, Sandia National Laboratories + Steve Plimpton, sjplimp@sandia.gov + + Copyright (2003) Sandia Corporation. Under the terms of Contract + DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains + certain rights in this software. This software is distributed under + the GNU General Public License. + + See the README file in the top-level LAMMPS directory. +------------------------------------------------------------------------- */ + +#include +#include "compute_gyration.h" +#include "update.h" +#include "atom.h" +#include "group.h" +#include "domain.h" +#include "error.h" + +using namespace LAMMPS_NS; + +/* ---------------------------------------------------------------------- */ + +ComputeGyration::ComputeGyration(LAMMPS *lmp, int narg, char **arg) : + Compute(lmp, narg, arg) +{ + if (narg != 3) error->all(FLERR,"Illegal compute gyration command"); + + scalar_flag = vector_flag = 1; + size_vector = 6; + extscalar = 0; + extvector = 0; + + vector = new double[6]; +} + +/* ---------------------------------------------------------------------- */ + +ComputeGyration::~ComputeGyration() +{ + delete [] vector; +} + +/* ---------------------------------------------------------------------- */ + +void ComputeGyration::init() +{ + masstotal = group->mass(igroup); +} + +/* ---------------------------------------------------------------------- */ + +double ComputeGyration::compute_scalar() +{ + invoked_scalar = update->ntimestep; + + double xcm[3]; + if (group->dynamic[igroup]) masstotal = group->mass(igroup); + group->xcm(igroup,masstotal,xcm); + scalar = group->gyration(igroup,masstotal,xcm); + return scalar; +} + +/* ---------------------------------------------------------------------- + compute the radius-of-gyration tensor of group of atoms + around center-of-mass cm + must unwrap atoms to compute Rg tensor correctly +------------------------------------------------------------------------- */ + +void ComputeGyration::compute_vector() +{ + invoked_vector = update->ntimestep; + + double xcm[3]; + group->xcm(igroup,masstotal,xcm); + + double **x = atom->x; + int *mask = atom->mask; + int *type = atom->type; + imageint *image = atom->image; + double *mass = atom->mass; + double *rmass = atom->rmass; + int nlocal = atom->nlocal; + + double dx,dy,dz,massone; + double unwrap[3]; + + double rg[6]; + rg[0] = rg[1] = rg[2] = rg[3] = rg[4] = rg[5] = 0.0; + + for (int i = 0; i < nlocal; i++) + if (mask[i] & groupbit) { + if (rmass) massone = rmass[i]; + else massone = mass[type[i]]; + + domain->unmap(x[i],image[i],unwrap); + dx = unwrap[0] - xcm[0]; + dy = unwrap[1] - xcm[1]; + dz = unwrap[2] - xcm[2]; + + rg[0] += dx*dx * massone; + rg[1] += dy*dy * massone; + rg[2] += dz*dz * massone; + rg[3] += dx*dy * massone; + rg[4] += dx*dz * massone; + rg[5] += dy*dz * massone; + } + MPI_Allreduce(rg,vector,6,MPI_DOUBLE,MPI_SUM,world); + + if (masstotal > 0.0) + for (int i = 0; i < 6; i++) + vector[i] /= masstotal; +} diff --git a/src/USER-MISC/compute_gyration_shape.h b/src/USER-MISC/compute_gyration_shape.h new file mode 100644 index 0000000000..1b39dd2e38 --- /dev/null +++ b/src/USER-MISC/compute_gyration_shape.h @@ -0,0 +1,53 @@ +/* -*- c++ -*- ---------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + http://lammps.sandia.gov, Sandia National Laboratories + Steve Plimpton, sjplimp@sandia.gov + + Copyright (2003) Sandia Corporation. Under the terms of Contract + DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains + certain rights in this software. This software is distributed under + the GNU General Public License. + + See the README file in the top-level LAMMPS directory. +------------------------------------------------------------------------- */ + +#ifdef COMPUTE_CLASS + +ComputeStyle(gyration/shape,ComputeGyrationShape) + +#else + +#ifndef LMP_COMPUTE_GYRATION_SHAPE_H +#define LMP_COMPUTE_GYRATION_SHAPE_H + +#include "compute.h" + +namespace LAMMPS_NS { + +class ComputeGyrationShape : public Compute { + public: + char *id_gyration; // fields accessed by other classes + + ComputeGyrationShape(class LAMMPS *, int, char **); + ~ComputeGyrationShape(); + void init(); + void compute_vector(); + + private: + class Compute *c_gyration; +}; + +} + +#endif +#endif + +/* ERROR/WARNING messages: + +E: Illegal ... command + +Self-explanatory. Check the input script syntax and compare to the +documentation for the command. You can use -echo screen as a +command-line option when running LAMMPS to see the offending line. + +*/ -- GitLab From 6710cc40527519efae40c349ec468cb4cc133dd3 Mon Sep 17 00:00:00 2001 From: Evangelos Voyiatzis Date: Thu, 25 Jul 2019 11:44:43 +0200 Subject: [PATCH 313/469] cpp file for the compute command The right file with the cpp code --- src/USER-MISC/compute_gyration_shape.cpp | 133 +++++++++++++++++++++++ 1 file changed, 133 insertions(+) create mode 100644 src/USER-MISC/compute_gyration_shape.cpp diff --git a/src/USER-MISC/compute_gyration_shape.cpp b/src/USER-MISC/compute_gyration_shape.cpp new file mode 100644 index 0000000000..0e566e671f --- /dev/null +++ b/src/USER-MISC/compute_gyration_shape.cpp @@ -0,0 +1,133 @@ +/* ---------------------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + http://lammps.sandia.gov, Sandia National Laboratories + Steve Plimpton, sjplimp@sandia.gov + + Copyright (2003) Sandia Corporation. Under the terms of Contract + DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains + certain rights in this software. This software is distributed under + the GNU General Public License. + + See the README file in the top-level LAMMPS directory. +------------------------------------------------------------------------- */ + +/* ---------------------------------------------------------------------- + * Contributing author: Evangelos Voyiatzis (Royal DSM) + * ------------------------------------------------------------------------- */ + + +#include +#include +#include "compute_gyration_shape.h" +#include "math_extra.h" +#include "update.h" +#include "atom.h" +#include "group.h" +#include "domain.h" +#include "error.h" +#include "modify.h" +#include "compute.h" + +using namespace LAMMPS_NS; + +/* ---------------------------------------------------------------------- */ + +ComputeGyrationShape::ComputeGyrationShape(LAMMPS *lmp, int narg, char **arg) : + Compute(lmp, narg, arg), id_gyration(NULL) +{ + if (narg != 4) error->all(FLERR,"Illegal compute gyration/shape command"); + + vector_flag = 1; + size_vector = 6; + extscalar = 0; + extvector = 0; + + // ID of compute gyration + int n = strlen(arg[3]) + 1; + id_gyration = new char[n]; + strcpy(id_gyration,arg[3]); + + init(); + + vector = new double[6]; +} + +/* ---------------------------------------------------------------------- */ + +ComputeGyrationShape::~ComputeGyrationShape() +{ + delete [] id_gyration; + delete [] vector; +} + +/* ---------------------------------------------------------------------- */ + +void ComputeGyrationShape::init() +{ + // check that the compute gyration command exist + int icompute = modify->find_compute(id_gyration); + if (icompute < 0) + error->all(FLERR,"Compute gyration does not exist for compute gyration/shape"); + + // check the id_gyration corresponds really to a compute gyration command + c_gyration = (Compute *) modify->compute[icompute]; + if (strcmp(c_gyration->style,"gyration") != 0) + error->all(FLERR,"Compute gyration/shape does not use gyration compute"); +} + +/* ---------------------------------------------------------------------- + compute shape parameters based on the eigenvalues of the gyration tensor of group of atoms +------------------------------------------------------------------------- */ + +void ComputeGyrationShape::compute_vector() +{ + invoked_vector = update->ntimestep; + + // get the gyration tensor from the compute gyration + int icompute = modify->find_compute(id_gyration); + Compute *compute = modify->compute[icompute]; + compute->compute_vector(); + double *gyration_tensor = compute->vector; + + // call the function for the calculation of the eigenvalues + double ione[3][3], evalues[3], evectors[3][3]; + + ione[0][0] = gyration_tensor[0]; + ione[1][1] = gyration_tensor[1]; + ione[2][2] = gyration_tensor[2]; + ione[0][1] = ione[1][0] = gyration_tensor[3]; + ione[1][2] = ione[2][1] = gyration_tensor[4]; + ione[0][2] = ione[2][0] = gyration_tensor[5]; + + int ierror = MathExtra::jacobi(ione,evalues,evectors); + if (ierror) error->all(FLERR, "Insufficient Jacobi rotations for gyration/shape"); + + // sort the eigenvalues according to their size with bubble sort + double t; + for (int i = 0; i < 3; i++) { + for (int j = 0; j < 2-i; j++) { + if (fabs(evalues[j]) < fabs(evalues[j+1])) { + t = evalues[j]; + evalues[j] = evalues[j+1]; + evalues[j+1] = t; + } + } + } + + // compute the shape parameters of the gyration tensor + double sq_eigen_x = pow(evalues[0], 2); + double sq_eigen_y = pow(evalues[1], 2); + double sq_eigen_z = pow(evalues[2], 2); + + double nominator = pow(sq_eigen_x, 2) + pow(sq_eigen_y, 2) + pow(sq_eigen_z, 2); + double denominator = pow(sq_eigen_x+sq_eigen_y+sq_eigen_z, 2); + + vector[0] = evalues[0]; + vector[1] = evalues[1]; + vector[2] = evalues[2]; + vector[3] = sq_eigen_z - 0.5*(sq_eigen_x + sq_eigen_y); + vector[4] = sq_eigen_y - sq_eigen_x; + vector[5] = 0.5*(3*nominator/denominator -1); + +} + -- GitLab From 114a754a72b19eec8e3aa28ce328018263530577 Mon Sep 17 00:00:00 2001 From: Evangelos Voyiatzis Date: Thu, 25 Jul 2019 11:48:04 +0200 Subject: [PATCH 314/469] Delete compute_gyration.cpp It is not part of the new compute style --- src/USER-MISC/compute_gyration.cpp | 115 ----------------------------- 1 file changed, 115 deletions(-) delete mode 100644 src/USER-MISC/compute_gyration.cpp diff --git a/src/USER-MISC/compute_gyration.cpp b/src/USER-MISC/compute_gyration.cpp deleted file mode 100644 index f8d19853e0..0000000000 --- a/src/USER-MISC/compute_gyration.cpp +++ /dev/null @@ -1,115 +0,0 @@ -/* ---------------------------------------------------------------------- - LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov - - Copyright (2003) Sandia Corporation. Under the terms of Contract - DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains - certain rights in this software. This software is distributed under - the GNU General Public License. - - See the README file in the top-level LAMMPS directory. -------------------------------------------------------------------------- */ - -#include -#include "compute_gyration.h" -#include "update.h" -#include "atom.h" -#include "group.h" -#include "domain.h" -#include "error.h" - -using namespace LAMMPS_NS; - -/* ---------------------------------------------------------------------- */ - -ComputeGyration::ComputeGyration(LAMMPS *lmp, int narg, char **arg) : - Compute(lmp, narg, arg) -{ - if (narg != 3) error->all(FLERR,"Illegal compute gyration command"); - - scalar_flag = vector_flag = 1; - size_vector = 6; - extscalar = 0; - extvector = 0; - - vector = new double[6]; -} - -/* ---------------------------------------------------------------------- */ - -ComputeGyration::~ComputeGyration() -{ - delete [] vector; -} - -/* ---------------------------------------------------------------------- */ - -void ComputeGyration::init() -{ - masstotal = group->mass(igroup); -} - -/* ---------------------------------------------------------------------- */ - -double ComputeGyration::compute_scalar() -{ - invoked_scalar = update->ntimestep; - - double xcm[3]; - if (group->dynamic[igroup]) masstotal = group->mass(igroup); - group->xcm(igroup,masstotal,xcm); - scalar = group->gyration(igroup,masstotal,xcm); - return scalar; -} - -/* ---------------------------------------------------------------------- - compute the radius-of-gyration tensor of group of atoms - around center-of-mass cm - must unwrap atoms to compute Rg tensor correctly -------------------------------------------------------------------------- */ - -void ComputeGyration::compute_vector() -{ - invoked_vector = update->ntimestep; - - double xcm[3]; - group->xcm(igroup,masstotal,xcm); - - double **x = atom->x; - int *mask = atom->mask; - int *type = atom->type; - imageint *image = atom->image; - double *mass = atom->mass; - double *rmass = atom->rmass; - int nlocal = atom->nlocal; - - double dx,dy,dz,massone; - double unwrap[3]; - - double rg[6]; - rg[0] = rg[1] = rg[2] = rg[3] = rg[4] = rg[5] = 0.0; - - for (int i = 0; i < nlocal; i++) - if (mask[i] & groupbit) { - if (rmass) massone = rmass[i]; - else massone = mass[type[i]]; - - domain->unmap(x[i],image[i],unwrap); - dx = unwrap[0] - xcm[0]; - dy = unwrap[1] - xcm[1]; - dz = unwrap[2] - xcm[2]; - - rg[0] += dx*dx * massone; - rg[1] += dy*dy * massone; - rg[2] += dz*dz * massone; - rg[3] += dx*dy * massone; - rg[4] += dx*dz * massone; - rg[5] += dy*dz * massone; - } - MPI_Allreduce(rg,vector,6,MPI_DOUBLE,MPI_SUM,world); - - if (masstotal > 0.0) - for (int i = 0; i < 6; i++) - vector[i] /= masstotal; -} -- GitLab From b1a5444815925197b05a51362c336a61fbd59aaf Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Thu, 25 Jul 2019 07:32:15 -0400 Subject: [PATCH 315/469] add (empty) read/write_restart_settings() functions to bond/angle/dihedral/improper base classes --- src/angle.h | 2 ++ src/bond.h | 2 ++ src/dihedral.h | 2 ++ src/improper.h | 2 ++ 4 files changed, 8 insertions(+) diff --git a/src/angle.h b/src/angle.h index 3d8371242e..ddd12ab7b8 100644 --- a/src/angle.h +++ b/src/angle.h @@ -46,6 +46,8 @@ class Angle : protected Pointers { virtual double equilibrium_angle(int) = 0; virtual void write_restart(FILE *) = 0; virtual void read_restart(FILE *) = 0; + virtual void write_restart_settings(FILE *) {}; + virtual void read_restart_settings(FILE *) {}; virtual void write_data(FILE *) {} virtual double single(int, int, int, int) = 0; virtual double memory_usage(); diff --git a/src/bond.h b/src/bond.h index 8fb7040832..cce94e33a0 100644 --- a/src/bond.h +++ b/src/bond.h @@ -48,6 +48,8 @@ class Bond : protected Pointers { virtual double equilibrium_distance(int) = 0; virtual void write_restart(FILE *) = 0; virtual void read_restart(FILE *) = 0; + virtual void write_restart_settings(FILE *) {}; + virtual void read_restart_settings(FILE *) {}; virtual void write_data(FILE *) {} virtual double single(int, double, int, int, double &) = 0; virtual double memory_usage(); diff --git a/src/dihedral.h b/src/dihedral.h index f1b42008bf..ac3786c40e 100644 --- a/src/dihedral.h +++ b/src/dihedral.h @@ -45,6 +45,8 @@ class Dihedral : protected Pointers { virtual void coeff(int, char **) = 0; virtual void write_restart(FILE *) = 0; virtual void read_restart(FILE *) = 0; + virtual void write_restart_settings(FILE *) {}; + virtual void read_restart_settings(FILE *) {}; virtual void write_data(FILE *) {} virtual double memory_usage(); diff --git a/src/improper.h b/src/improper.h index d940b43a13..876c928d7e 100644 --- a/src/improper.h +++ b/src/improper.h @@ -45,6 +45,8 @@ class Improper : protected Pointers { virtual void coeff(int, char **) = 0; virtual void write_restart(FILE *) = 0; virtual void read_restart(FILE *) = 0; + virtual void write_restart_settings(FILE *) {}; + virtual void read_restart_settings(FILE *) {}; virtual void write_data(FILE *) {} virtual double memory_usage(); -- GitLab From 5ca93e3651661bc25514fcdf046a22d88d88549c Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Thu, 25 Jul 2019 07:54:21 -0400 Subject: [PATCH 316/469] move global settings in restart files for table styles to restart settings functions --- src/MOLECULE/angle_table.cpp | 23 ++++++++++++++++++++--- src/MOLECULE/angle_table.h | 2 ++ src/MOLECULE/bond_table.cpp | 23 ++++++++++++++++++++--- src/MOLECULE/bond_table.h | 2 ++ src/USER-MISC/dihedral_table.cpp | 24 +++++++++++++++++++++--- src/USER-MISC/dihedral_table.h | 2 ++ src/USER-MISC/dihedral_table_cut.cpp | 21 +++++++++++++++++++-- src/USER-MISC/dihedral_table_cut.h | 2 ++ 8 files changed, 88 insertions(+), 11 deletions(-) diff --git a/src/MOLECULE/angle_table.cpp b/src/MOLECULE/angle_table.cpp index c18b4c43b0..898ce49be7 100644 --- a/src/MOLECULE/angle_table.cpp +++ b/src/MOLECULE/angle_table.cpp @@ -277,6 +277,25 @@ double AngleTable::equilibrium_angle(int i) ------------------------------------------------------------------------- */ void AngleTable::write_restart(FILE *fp) +{ + write_restart_settings(fp); +} + +/* ---------------------------------------------------------------------- + proc 0 reads from restart file, bcasts + ------------------------------------------------------------------------- */ + +void AngleTable::read_restart(FILE *fp) +{ + read_restart_settings(fp); + allocate(); +} + +/* ---------------------------------------------------------------------- + proc 0 writes to restart file + ------------------------------------------------------------------------- */ + +void AngleTable::write_restart_settings(FILE *fp) { fwrite(&tabstyle,sizeof(int),1,fp); fwrite(&tablength,sizeof(int),1,fp); @@ -286,7 +305,7 @@ void AngleTable::write_restart(FILE *fp) proc 0 reads from restart file, bcasts ------------------------------------------------------------------------- */ -void AngleTable::read_restart(FILE *fp) +void AngleTable::read_restart_settings(FILE *fp) { if (comm->me == 0) { fread(&tabstyle,sizeof(int),1,fp); @@ -294,8 +313,6 @@ void AngleTable::read_restart(FILE *fp) } MPI_Bcast(&tabstyle,1,MPI_INT,0,world); MPI_Bcast(&tablength,1,MPI_INT,0,world); - - allocate(); } /* ---------------------------------------------------------------------- */ diff --git a/src/MOLECULE/angle_table.h b/src/MOLECULE/angle_table.h index 0088ace39b..81e6c2ed89 100644 --- a/src/MOLECULE/angle_table.h +++ b/src/MOLECULE/angle_table.h @@ -35,6 +35,8 @@ class AngleTable : public Angle { double equilibrium_angle(int); void write_restart(FILE *); void read_restart(FILE *); + void write_restart_settings(FILE *); + void read_restart_settings(FILE *); double single(int, int, int, int); protected: diff --git a/src/MOLECULE/bond_table.cpp b/src/MOLECULE/bond_table.cpp index 10851774d7..170afc27f0 100644 --- a/src/MOLECULE/bond_table.cpp +++ b/src/MOLECULE/bond_table.cpp @@ -221,6 +221,25 @@ double BondTable::equilibrium_distance(int i) ------------------------------------------------------------------------- */ void BondTable::write_restart(FILE *fp) +{ + write_restart_settings(fp); +} + +/* ---------------------------------------------------------------------- + proc 0 reads from restart file, bcasts + ------------------------------------------------------------------------- */ + +void BondTable::read_restart(FILE *fp) +{ + read_restart_settings(fp); + allocate(); +} + +/* ---------------------------------------------------------------------- + proc 0 writes to restart file + ------------------------------------------------------------------------- */ + +void BondTable::write_restart_settings(FILE *fp) { fwrite(&tabstyle,sizeof(int),1,fp); fwrite(&tablength,sizeof(int),1,fp); @@ -230,7 +249,7 @@ void BondTable::write_restart(FILE *fp) proc 0 reads from restart file, bcasts ------------------------------------------------------------------------- */ -void BondTable::read_restart(FILE *fp) +void BondTable::read_restart_settings(FILE *fp) { if (comm->me == 0) { fread(&tabstyle,sizeof(int),1,fp); @@ -238,8 +257,6 @@ void BondTable::read_restart(FILE *fp) } MPI_Bcast(&tabstyle,1,MPI_INT,0,world); MPI_Bcast(&tablength,1,MPI_INT,0,world); - - allocate(); } /* ---------------------------------------------------------------------- */ diff --git a/src/MOLECULE/bond_table.h b/src/MOLECULE/bond_table.h index 5766239167..5d4f2e8493 100644 --- a/src/MOLECULE/bond_table.h +++ b/src/MOLECULE/bond_table.h @@ -35,6 +35,8 @@ class BondTable : public Bond { double equilibrium_distance(int); void write_restart(FILE *); void read_restart(FILE *); + void write_restart_settings(FILE *); + void read_restart_settings(FILE *); double single(int, double, int, int, double &); protected: diff --git a/src/USER-MISC/dihedral_table.cpp b/src/USER-MISC/dihedral_table.cpp index a97ae3649f..ce5a32b603 100644 --- a/src/USER-MISC/dihedral_table.cpp +++ b/src/USER-MISC/dihedral_table.cpp @@ -1011,6 +1011,26 @@ void DihedralTable::coeff(int narg, char **arg) ------------------------------------------------------------------------- */ void DihedralTable::write_restart(FILE *fp) +{ + write_restart_settings(fp); +} + +/* ---------------------------------------------------------------------- + proc 0 reads from restart file, bcasts + ------------------------------------------------------------------------- */ + +void DihedralTable::read_restart(FILE *fp) +{ + read_restart_settings(fp); + allocate(); +} + + +/* ---------------------------------------------------------------------- + proc 0 writes to restart file + ------------------------------------------------------------------------- */ + +void DihedralTable::write_restart_settings(FILE *fp) { fwrite(&tabstyle,sizeof(int),1,fp); fwrite(&tablength,sizeof(int),1,fp); @@ -1020,7 +1040,7 @@ void DihedralTable::write_restart(FILE *fp) proc 0 reads from restart file, bcasts ------------------------------------------------------------------------- */ -void DihedralTable::read_restart(FILE *fp) +void DihedralTable::read_restart_settings(FILE *fp) { if (comm->me == 0) { fread(&tabstyle,sizeof(int),1,fp); @@ -1029,8 +1049,6 @@ void DihedralTable::read_restart(FILE *fp) MPI_Bcast(&tabstyle,1,MPI_INT,0,world); MPI_Bcast(&tablength,1,MPI_INT,0,world); - - allocate(); } diff --git a/src/USER-MISC/dihedral_table.h b/src/USER-MISC/dihedral_table.h index 08bd21ba83..a7b8417b48 100644 --- a/src/USER-MISC/dihedral_table.h +++ b/src/USER-MISC/dihedral_table.h @@ -36,6 +36,8 @@ class DihedralTable : public Dihedral { void coeff(int, char **); void write_restart(FILE *); void read_restart(FILE *); + void write_restart_settings(FILE *); + void read_restart_settings(FILE *); double single(int type, int i1, int i2, int i3, int i4); protected: diff --git a/src/USER-MISC/dihedral_table_cut.cpp b/src/USER-MISC/dihedral_table_cut.cpp index 18a645cd75..f5c85cc52b 100644 --- a/src/USER-MISC/dihedral_table_cut.cpp +++ b/src/USER-MISC/dihedral_table_cut.cpp @@ -1003,8 +1003,7 @@ void DihedralTableCut::coeff(int narg, char **arg) void DihedralTableCut::write_restart(FILE *fp) { - fwrite(&tabstyle,sizeof(int),1,fp); - fwrite(&tablength,sizeof(int),1,fp); + write_restart_settings(fp); } /* ---------------------------------------------------------------------- @@ -1013,8 +1012,26 @@ void DihedralTableCut::write_restart(FILE *fp) void DihedralTableCut::read_restart(FILE *fp) { + read_restart_settings(fp); allocate(); +} +/* ---------------------------------------------------------------------- + proc 0 writes out coeffs to restart file +------------------------------------------------------------------------- */ + +void DihedralTableCut::write_restart_settings(FILE *fp) +{ + fwrite(&tabstyle,sizeof(int),1,fp); + fwrite(&tablength,sizeof(int),1,fp); +} + +/* ---------------------------------------------------------------------- + proc 0 reads coeffs from restart file, bcasts them +------------------------------------------------------------------------- */ + +void DihedralTableCut::read_restart_settings(FILE *fp) +{ if (comm->me == 0) { fread(&tabstyle,sizeof(int),1,fp); fread(&tablength,sizeof(int),1,fp); diff --git a/src/USER-MISC/dihedral_table_cut.h b/src/USER-MISC/dihedral_table_cut.h index dd645bedda..b07e925f08 100644 --- a/src/USER-MISC/dihedral_table_cut.h +++ b/src/USER-MISC/dihedral_table_cut.h @@ -33,6 +33,8 @@ class DihedralTableCut : public Dihedral { void coeff(int, char **); void write_restart(FILE *); void read_restart(FILE *); + void write_restart_settings(FILE *); + void read_restart_settings(FILE *); protected: double *aat_k,*aat_theta0_1,*aat_theta0_2; -- GitLab From f86d2c99346b66f27a036e694251ac77b40d0796 Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Thu, 25 Jul 2019 07:55:39 -0400 Subject: [PATCH 317/469] read/write settings in restart files for bonded hybrid styles this allows to properly restart table styles, which require additional settings unlike all other bonded styles. --- src/angle_hybrid.cpp | 2 ++ src/bond_hybrid.cpp | 2 ++ src/dihedral_hybrid.cpp | 2 ++ src/improper_hybrid.cpp | 2 ++ src/pair.h | 2 +- 5 files changed, 9 insertions(+), 1 deletion(-) diff --git a/src/angle_hybrid.cpp b/src/angle_hybrid.cpp index 6afa7413b2..d6c616fae4 100644 --- a/src/angle_hybrid.cpp +++ b/src/angle_hybrid.cpp @@ -324,6 +324,7 @@ void AngleHybrid::write_restart(FILE *fp) n = strlen(keywords[m]) + 1; fwrite(&n,sizeof(int),1,fp); fwrite(keywords[m],sizeof(char),n,fp); + styles[m]->write_restart_settings(fp); } } @@ -349,6 +350,7 @@ void AngleHybrid::read_restart(FILE *fp) if (me == 0) fread(keywords[m],sizeof(char),n,fp); MPI_Bcast(keywords[m],n,MPI_CHAR,0,world); styles[m] = force->new_angle(keywords[m],0,dummy); + styles[m]->read_restart_settings(fp); } } diff --git a/src/bond_hybrid.cpp b/src/bond_hybrid.cpp index 65609b4b6e..1527943dc7 100644 --- a/src/bond_hybrid.cpp +++ b/src/bond_hybrid.cpp @@ -325,6 +325,7 @@ void BondHybrid::write_restart(FILE *fp) n = strlen(keywords[m]) + 1; fwrite(&n,sizeof(int),1,fp); fwrite(keywords[m],sizeof(char),n,fp); + styles[m]->write_restart_settings(fp); } } @@ -350,6 +351,7 @@ void BondHybrid::read_restart(FILE *fp) if (me == 0) fread(keywords[m],sizeof(char),n,fp); MPI_Bcast(keywords[m],n,MPI_CHAR,0,world); styles[m] = force->new_bond(keywords[m],0,dummy); + styles[m]->read_restart_settings(fp); } } diff --git a/src/dihedral_hybrid.cpp b/src/dihedral_hybrid.cpp index f3e4823d53..8908139bdc 100644 --- a/src/dihedral_hybrid.cpp +++ b/src/dihedral_hybrid.cpp @@ -309,6 +309,7 @@ void DihedralHybrid::write_restart(FILE *fp) n = strlen(keywords[m]) + 1; fwrite(&n,sizeof(int),1,fp); fwrite(keywords[m],sizeof(char),n,fp); + styles[m]->write_restart_settings(fp); } } @@ -334,6 +335,7 @@ void DihedralHybrid::read_restart(FILE *fp) if (me == 0) fread(keywords[m],sizeof(char),n,fp); MPI_Bcast(keywords[m],n,MPI_CHAR,0,world); styles[m] = force->new_dihedral(keywords[m],0,dummy); + styles[m]->read_restart_settings(fp); } } diff --git a/src/improper_hybrid.cpp b/src/improper_hybrid.cpp index 5fdcb42a96..174f54907e 100644 --- a/src/improper_hybrid.cpp +++ b/src/improper_hybrid.cpp @@ -306,6 +306,7 @@ void ImproperHybrid::write_restart(FILE *fp) n = strlen(keywords[m]) + 1; fwrite(&n,sizeof(int),1,fp); fwrite(keywords[m],sizeof(char),n,fp); + styles[m]->write_restart_settings(fp); } } @@ -331,6 +332,7 @@ void ImproperHybrid::read_restart(FILE *fp) if (me == 0) fread(keywords[m],sizeof(char),n,fp); MPI_Bcast(keywords[m],n,MPI_CHAR,0,world); styles[m] = force->new_improper(keywords[m],0,dummy); + styles[m]->read_restart_settings(fp); } } diff --git a/src/pair.h b/src/pair.h index 7481514dae..bad2b83c74 100644 --- a/src/pair.h +++ b/src/pair.h @@ -61,7 +61,7 @@ class Pair : protected Pointers { int dispersionflag; // 1 if compatible with LJ/dispersion solver int tip4pflag; // 1 if compatible with TIP4P solver int dipoleflag; // 1 if compatible with dipole solver - int spinflag; // 1 if compatible with spin solver + int spinflag; // 1 if compatible with spin solver int reinitflag; // 1 if compatible with fix adapt and alike int tail_flag; // pair_modify flag for LJ tail correction -- GitLab From 18730e0f923813ebc5f0a6266e4996bd25408eb0 Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Thu, 25 Jul 2019 08:15:18 -0400 Subject: [PATCH 318/469] add documentation for the need to respecify coeff commands for bonded table styles --- doc/src/angle_table.txt | 10 ++++++++++ doc/src/bond_table.txt | 10 ++++++++++ doc/src/dihedral_table.txt | 10 ++++++++++ doc/src/dihedral_table_cut.txt | 10 ++++++++++ 4 files changed, 40 insertions(+) diff --git a/doc/src/angle_table.txt b/doc/src/angle_table.txt index 6b9187e512..61c987f587 100644 --- a/doc/src/angle_table.txt +++ b/doc/src/angle_table.txt @@ -143,6 +143,16 @@ instructions on how to use the accelerated styles effectively. :line +[Restart info:] + +This angle style writes the settings for the "angle_style table" +command to "binary restart files"_restart.html, so a angle_style +command does not need to specified in an input script that reads a +restart file. However, the coefficient information is not stored in +the restart file, since it is tabulated in the potential files. Thus, +angle_coeff commands do need to be specified in the restart input +script. + [Restrictions:] This angle style can only be used if LAMMPS was built with the diff --git a/doc/src/bond_table.txt b/doc/src/bond_table.txt index fbf6eb5815..7235214af0 100644 --- a/doc/src/bond_table.txt +++ b/doc/src/bond_table.txt @@ -140,6 +140,16 @@ instructions on how to use the accelerated styles effectively. :line +[Restart info:] + +This bond style writes the settings for the "bond_style table" +command to "binary restart files"_restart.html, so a bond_style +command does not need to specified in an input script that reads a +restart file. However, the coefficient information is not stored in +the restart file, since it is tabulated in the potential files. Thus, +bond_coeff commands do need to be specified in the restart input +script. + [Restrictions:] This bond style can only be used if LAMMPS was built with the MOLECULE diff --git a/doc/src/dihedral_table.txt b/doc/src/dihedral_table.txt index 3f679f5709..b3cfd37570 100644 --- a/doc/src/dihedral_table.txt +++ b/doc/src/dihedral_table.txt @@ -191,6 +191,16 @@ switch"_Run_options.html when you invoke LAMMPS, or you can use the See the "Speed packages"_Speed_packages.html doc page for more instructions on how to use the accelerated styles effectively. +[Restart info:] + +This dihedral style writes the settings for the "dihedral_style table" +command to "binary restart files"_restart.html, so a dihedral_style +command does not need to specified in an input script that reads a +restart file. However, the coefficient information is not stored in +the restart file, since it is tabulated in the potential files. Thus, +dihedral_coeff commands do need to be specified in the restart input +script. + [Restrictions:] This dihedral style can only be used if LAMMPS was built with the diff --git a/doc/src/dihedral_table_cut.txt b/doc/src/dihedral_table_cut.txt index b72f34e36e..560f5375a7 100644 --- a/doc/src/dihedral_table_cut.txt +++ b/doc/src/dihedral_table_cut.txt @@ -189,6 +189,16 @@ Note that one file can contain many sections, each with a tabulated potential. LAMMPS reads the file section by section until it finds one that matches the specified keyword. +[Restart info:] + +This dihedral style writes the settings for the "dihedral_style table/cut" +command to "binary restart files"_restart.html, so a dihedral_style +command does not need to specified in an input script that reads a +restart file. However, the coefficient information is not stored in +the restart file, since it is tabulated in the potential files. Thus, +dihedral_coeff commands do need to be specified in the restart input +script. + [Restrictions:] This dihedral style can only be used if LAMMPS was built with the -- GitLab From 4586fd50af7143b7349399ceee2ac7629af7a0ec Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Thu, 25 Jul 2019 08:33:21 -0400 Subject: [PATCH 319/469] adjust logic for choosing the communication cutoff to requests from @sjplimp limit cases where warning about adjusting the comm cutoff is printed. --- src/comm.cpp | 53 ++++++++++++++++++++++++++++++++-------------------- 1 file changed, 33 insertions(+), 20 deletions(-) diff --git a/src/comm.cpp b/src/comm.cpp index 4e605808af..ae2715f0fd 100644 --- a/src/comm.cpp +++ b/src/comm.cpp @@ -588,39 +588,52 @@ void Comm::set_proc_grid(int outflag) /* ---------------------------------------------------------------------- determine suitable communication cutoff. - it is the maximum of the user specified value and estimates based on - the maximum neighbor list cutoff and largest bond equilibrium length. - we use the 1.5x the bond equilibrium distance as cutoff, if only a - bond style exists or only bond and angle styles exists. If dihedrals - or impropers are present we multiply by 2.0. This plus the - "neighbor list skin" will become the default communication cutoff, if - no pair style is defined and thus avoids all kinds of unexpected behavior - for such systems. If a pair style exists, the result is the maximum of - the bond based cutoff and the largest pair cutoff and the user - specified communication cutoff. + use the larger of the user specified value and the cutoff required + by the neighborlist build for pair styles. + if bonded interactions exist, apply a heuristic based on the equilibrium + bond length (use 1.5x r_bond if no dihedral or improper style exists + otherwise 2x r_bond) plus neighbor list skin. + if no user specified communication cutoff is given include this + heuristic, otherwise ignore it. + print a warning, if a user specified communication cutoff is overridden. ------------------------------------------------------------------------- */ double Comm::get_comm_cutoff() { double maxcommcutoff = 0.0; + double maxbondcutoff = 0.0; + if (force->bond) { int n = atom->nbondtypes; for (int i = 1; i <= n; ++i) - maxcommcutoff = MAX(maxcommcutoff,force->bond->equilibrium_distance(i)); + maxbondcutoff = MAX(maxbondcutoff,force->bond->equilibrium_distance(i)); if (force->dihedral || force->improper) { - maxcommcutoff *= 2.0; + maxbondcutoff *= 2.0; } else { - maxcommcutoff *=1.5; + maxbondcutoff *=1.5; } - maxcommcutoff += neighbor->skin; + maxbondcutoff += neighbor->skin; } - maxcommcutoff = MAX(maxcommcutoff,neighbor->cutneighmax); - maxcommcutoff = MAX(maxcommcutoff,cutghostuser); - if ((me == 0) && (cutghostuser > 0.0) && (maxcommcutoff > cutghostuser)) { - char mesg[128]; - snprintf(mesg,128,"Communication cutoff is changed to %g",maxcommcutoff); - error->warning(FLERR,mesg); + + // always take the larger of max neighbor list and user specified cutoff + + maxcommcutoff = MAX(cutghostuser,neighbor->cutneighmax); + + // consider cutoff estimate from bond length only if no user specified cutoff + + if (cutghostuser == 0.0) maxcommcutoff = MAX(maxcommcutoff,maxbondcutoff); + + // print warning if neighborlist cutoff overrides user cutoff or + // applied bond based cutoff is larger than neighbor cutoff. + + if (me == 0) { + if ( ((cutghostuser > 0.0) && (maxcommcutoff > cutghostuser)) + || ((cutghostuser == 0.0) && (maxcommcutoff == maxbondcutoff)) ) { + char mesg[128]; + snprintf(mesg,128,"Communication cutoff adjusted to %g",maxcommcutoff); + error->warning(FLERR,mesg); + } } return maxcommcutoff; -- GitLab From 183d92cad777efd998981b0b1f3c36752fa9c256 Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Thu, 25 Jul 2019 08:42:48 -0400 Subject: [PATCH 320/469] update comm_modify documentation --- doc/src/comm_modify.txt | 9 +++++++++ 1 file changed, 9 insertions(+) diff --git a/doc/src/comm_modify.txt b/doc/src/comm_modify.txt index 482259142b..d5f5aecf54 100644 --- a/doc/src/comm_modify.txt +++ b/doc/src/comm_modify.txt @@ -72,6 +72,15 @@ greater than the neighbor cutoff, then extra ghost atoms will be acquired. If the provided cutoff is smaller, the provided value will be ignored and the ghost cutoff is set to the neighbor cutoff. Specifying a cutoff value of 0.0 will reset any previous value to the default. +If bonded interactions exist and equilibrium bond length information is +available, then also a heuristic based on that bond length (2.0x {r_eq} +for systems with dihedrals or improper, 1.5x {r_eq} without) plus +neighbor skin is applied if the communication cutoff is set to its +default value of 0.0. This avoids problems for systems without a pair +style or where the non-bonded cutoff is (much) shorter than the largest +bond lengths. A warning message is printed, if a specified +communication cutoff > 0.0 is overridden or the bond length heuristics +lead to a larger communication cutoff. The {cutoff/multi} option is equivalent to {cutoff}, but applies to communication mode {multi} instead. Since in this case the communication -- GitLab From ca291f1015a1606c3f529ad69f42b98697ae9fb7 Mon Sep 17 00:00:00 2001 From: "Ryan S. Elliott" Date: Thu, 25 Jul 2019 11:47:56 -0500 Subject: [PATCH 321/469] Update to kim-api-2.1.1 --- cmake/Modules/Packages/KIM.cmake | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/cmake/Modules/Packages/KIM.cmake b/cmake/Modules/Packages/KIM.cmake index 5c0b8e2ee8..1a9dcf83a4 100644 --- a/cmake/Modules/Packages/KIM.cmake +++ b/cmake/Modules/Packages/KIM.cmake @@ -21,8 +21,8 @@ if(PKG_KIM) enable_language(Fortran) include(ExternalProject) ExternalProject_Add(kim_build - URL https://s3.openkim.org/kim-api/kim-api-2.1.0.txz - URL_MD5 9ada58e677a545a1987b1ecb98e39d7e + URL https://s3.openkim.org/kim-api/kim-api-2.1.1.txz + URL_MD5 ae0ee413e026c6e93d35692db5966fb4 BINARY_DIR build CMAKE_ARGS -DCMAKE_C_COMPILER=${CMAKE_C_COMPILER} -DCMAKE_CXX_COMPILER=${CMAKE_CXX_COMPILER} -- GitLab From df139bf32bdcaeddb6a0675167781dd5fc802204 Mon Sep 17 00:00:00 2001 From: Stan Moore Date: Thu, 25 Jul 2019 11:17:45 -0600 Subject: [PATCH 322/469] Merge in suggestions from PR #1582 --- src/KOKKOS/kokkos.cpp | 84 +++++++++++++------- src/MAKE/MACHINES/Makefile.lassen | 125 ++++++++++++++++++++++++++++++ 2 files changed, 181 insertions(+), 28 deletions(-) create mode 100644 src/MAKE/MACHINES/Makefile.lassen diff --git a/src/KOKKOS/kokkos.cpp b/src/KOKKOS/kokkos.cpp index 3d1cb419d6..c0a74ca3b0 100644 --- a/src/KOKKOS/kokkos.cpp +++ b/src/KOKKOS/kokkos.cpp @@ -30,32 +30,38 @@ // for detecting CUDA-aware MPI support: // the variable int have_cuda_aware -// - is -1 if CUDA-aware MPI support is unknown -// - is 0 if no CUDA-aware MPI support available // - is 1 if CUDA-aware MPI support is available +// - is 0 if CUDA-aware MPI support is unavailable +// - is -1 if CUDA-aware MPI support is unknown #define CUDA_AWARE_UNKNOWN static int have_cuda_aware = -1; // OpenMPI supports detecting CUDA-aware MPI as of version 2.0.0 -#if OPEN_MPI +// IBM Spectrum MPI looks like OpenMPI but defines MPIX_CUDA_AWARE_SUPPORT=0 +// even when CUDA-aware MPI is available, and also has a runtime option +// to turn CUDA-aware MPI on/off, so support is unknown + +#if (defined OPEN_MPI) && !(defined SPECTRUM_MPI) #if (OMPI_MAJOR_VERSION >= 2) + #include + #if defined(MPIX_CUDA_AWARE_SUPPORT) && MPIX_CUDA_AWARE_SUPPORT static int have_cuda_aware = 1; #elif defined(MPIX_CUDA_AWARE_SUPPORT) && !MPIX_CUDA_AWARE_SUPPORT static int have_cuda_aware = 0; #else CUDA_AWARE_UNKNOWN -#endif +#endif // defined(MPIX_CUDA_AWARE_SUPPORT) #else // old OpenMPI CUDA_AWARE_UNKNOWN -#endif +#endif // (OMPI_MAJOR_VERSION >=2) #else // unknown MPI library CUDA_AWARE_UNKNOWN -#endif +#endif // OPEN_MPI #endif // KOKKOS_ENABLE_CUDA @@ -147,29 +153,10 @@ KokkosLMP::KokkosLMP(LAMMPS *lmp, int narg, char **arg) : Pointers(lmp) #ifdef KOKKOS_ENABLE_CUDA if (ngpus <= 0) error->all(FLERR,"Kokkos has been compiled for CUDA but no GPUs are requested"); - - // check and warn about CUDA-aware MPI availability when using multiple MPI tasks - - int nmpi = 0; - MPI_Comm_size(world,&nmpi); - if ((nmpi > 1) && (me == 0)) { - if ( 1 == have_cuda_aware ) { - ; // all good, nothing to warn about - } else if ( -1 == have_cuda_aware ) { - error->warning(FLERR,"Kokkos with CUDA assumes CUDA-aware MPI is available," - " but cannot determine if this is the case\n try" - " '-pk kokkos cuda/aware off' when getting segmentation faults"); - } else if ( 0 == have_cuda_aware ) { - error->warning(FLERR,"CUDA-aware MPI is NOT available, " - "using '-pk kokkos cuda/aware off' by default"); - } else { - ; // should never get here - } - } #endif #ifndef KOKKOS_ENABLE_SERIAL - if (nthreads == 1) + if (nthreads == 1 && me == 0) error->warning(FLERR,"When using a single thread, the Kokkos Serial backend " "(i.e. Makefile.kokkos_mpi_only) gives better performance " "than the OpenMP backend"); @@ -185,7 +172,11 @@ KokkosLMP::KokkosLMP(LAMMPS *lmp, int narg, char **arg) : Pointers(lmp) // default settings for package kokkos command binsize = 0.0; - cuda_aware_flag = 1; +#if KOKKOS_USE_CUDA + cuda_aware_flag = 1; +#else + cuda_aware_flag = 0; +#endif neigh_thread = 0; neigh_thread_set = 0; neighflag_qeq_set = 0; @@ -209,9 +200,46 @@ KokkosLMP::KokkosLMP(LAMMPS *lmp, int narg, char **arg) : Pointers(lmp) } #ifdef KOKKOS_ENABLE_CUDA + + // check and warn about CUDA-aware MPI availability when using multiple MPI tasks // change default only if we can safely detect that CUDA-aware MPI is not available - if (0 == have_cuda_aware) cuda_aware_flag = 0; + + int nmpi = 0; + MPI_Comm_size(world,&nmpi); + if (nmpi > 0) { + if (have_cuda_aware == 0) { + if (me == 0) + error->warning(FLERR,"CUDA-aware MPI is NOT available, " + "using '-pk kokkos cuda/aware off'"); + cuda_aware_flag = 0; + } else if (have_cuda_aware == -1) { // maybe we are dealing with MPICH, MVAPICH2 or some derivative? + // MVAPICH2 +#if (defined MPICH) && (defined MVAPICH2_VERSION) + char* str; + if (!(str = getenv("MV2_ENABLE_CUDA") && (!(strcmp(str,"1") == 0))) { + if (me == 0) + error->warning(FLERR,"MVAPICH2 'MV2_ENABLE_CUDA' environment variable is not set. Disabling CUDA-aware MPI"); + cuda_aware_flag = 0; + } + // pure MPICH or some unsupported MPICH derivative +#elif (defined MPICH) && !(defined MVAPICH2_VERSION) + if (me == 0) + error->warning(FLERR,"Detected MPICH. Disabling CUDA-aware MPI"); + cuda_aware_flag = 0; +#elif (defined SPECTRUM_MPI) + if (me == 0) + error->warning(FLERR,"Must use the '-gpu' flag with Spectrum MPI to enable " + "CUDA-aware MPI support"); +#else + if (me == 0) + error->warning(FLERR,"Kokkos with CUDA assumes CUDA-aware MPI is available," + " but cannot determine if this is the case\n try" + " '-pk kokkos cuda/aware off' if getting segmentation faults"); + #endif + } // if (-1 == have_cuda_aware) + } // nmpi > 0 +#endif // KOKKOS_USE_CUDA #ifdef KILL_KOKKOS_ON_SIGSEGV signal(SIGSEGV, my_signal_handler); diff --git a/src/MAKE/MACHINES/Makefile.lassen b/src/MAKE/MACHINES/Makefile.lassen new file mode 100644 index 0000000000..669e599e3c --- /dev/null +++ b/src/MAKE/MACHINES/Makefile.lassen @@ -0,0 +1,125 @@ +# lassen_kokkos = KOKKOS/CUDA, V100 GPU and Power9, IBM Spectrum MPI, nvcc compiler with gcc 7.3.1 + +SHELL = /bin/sh + +# --------------------------------------------------------------------- +# compiler/linker settings +# specify flags and libraries needed for your compiler + +KOKKOS_ABSOLUTE_PATH = $(shell cd $(KOKKOS_PATH); pwd) +export MPICH_CXX = $(KOKKOS_ABSOLUTE_PATH)/bin/nvcc_wrapper +export OMPI_CXX = $(KOKKOS_ABSOLUTE_PATH)/bin/nvcc_wrapper +CC = $(KOKKOS_ABSOLUTE_PATH)/bin/nvcc_wrapper +CCFLAGS = -g -O3 +SHFLAGS = -fPIC +DEPFLAGS = -M + +LINK = $(KOKKOS_ABSOLUTE_PATH)/bin/nvcc_wrapper +LINKFLAGS = -g -O3 +LIB = +SIZE = size + +ARCHIVE = ar +ARFLAGS = -rc +SHLIBFLAGS = -shared +KOKKOS_DEVICES = Cuda +KOKKOS_ARCH = Power9,Volta70 + +# --------------------------------------------------------------------- +# LAMMPS-specific settings, all OPTIONAL +# specify settings for LAMMPS features you will use +# if you change any -D setting, do full re-compile after "make clean" + +# LAMMPS ifdef settings +# see possible settings in Section 2.2 (step 4) of manual + +LMP_INC = -DLAMMPS_GZIP + +# MPI library +# see discussion in Section 2.2 (step 5) of manual +# MPI wrapper compiler/linker can provide this info +# can point to dummy MPI library in src/STUBS as in Makefile.serial +# use -D MPICH and OMPI settings in INC to avoid C++ lib conflicts +# INC = path for mpi.h, MPI compiler settings +# PATH = path for MPI library +# LIB = name of MPI library + +MPI_INC = -DSPECTRUM_MPI -DMPICH_SKIP_MPICXX -DOMPI_SKIP_MPICXX=1 -I/usr/tce/packages/spectrum-mpi/spectrum-mpi-rolling-release-gcc-7.3.1/include +MPI_PATH = +MPI_LIB = -L/usr/tce/packages/spectrum-mpi/spectrum-mpi-rolling-release-gcc-7.3.1/lib -lmpi_ibm + +# FFT library +# see discussion in Section 2.2 (step 6) of manaul +# can be left blank to use provided KISS FFT library +# INC = -DFFT setting, e.g. -DFFT_FFTW, FFT compiler settings +# PATH = path for FFT library +# LIB = name of FFT library + +FFT_INC = +FFT_PATH = +FFT_LIB = + +# JPEG and/or PNG library +# see discussion in Section 2.2 (step 7) of manual +# only needed if -DLAMMPS_JPEG or -DLAMMPS_PNG listed with LMP_INC +# INC = path(s) for jpeglib.h and/or png.h +# PATH = path(s) for JPEG library and/or PNG library +# LIB = name(s) of JPEG library and/or PNG library + +JPG_INC = +JPG_PATH = +JPG_LIB = + +# --------------------------------------------------------------------- +# build rules and dependencies +# do not edit this section + +include Makefile.package.settings +include Makefile.package + +EXTRA_INC = $(LMP_INC) $(PKG_INC) $(MPI_INC) $(FFT_INC) $(JPG_INC) $(PKG_SYSINC) +EXTRA_PATH = $(PKG_PATH) $(MPI_PATH) $(FFT_PATH) $(JPG_PATH) $(PKG_SYSPATH) +EXTRA_LIB = $(PKG_LIB) $(MPI_LIB) $(FFT_LIB) $(JPG_LIB) $(PKG_SYSLIB) +EXTRA_CPP_DEPENDS = $(PKG_CPP_DEPENDS) +EXTRA_LINK_DEPENDS = $(PKG_LINK_DEPENDS) + +# Path to src files + +vpath %.cpp .. +vpath %.h .. + +# Link target + +$(EXE): $(OBJ) $(EXTRA_LINK_DEPENDS) + $(LINK) $(LINKFLAGS) $(EXTRA_PATH) $(OBJ) $(EXTRA_LIB) $(LIB) -o $(EXE) + $(SIZE) $(EXE) + +# Library targets + +lib: $(OBJ) $(EXTRA_LINK_DEPENDS) + $(ARCHIVE) $(ARFLAGS) $(EXE) $(OBJ) + +shlib: $(OBJ) $(EXTRA_LINK_DEPENDS) + $(CC) $(CCFLAGS) $(SHFLAGS) $(SHLIBFLAGS) $(EXTRA_PATH) -o $(EXE) \ + $(OBJ) $(EXTRA_LIB) $(LIB) + +# Compilation rules + +%.o:%.cpp $(EXTRA_CPP_DEPENDS) + $(CC) $(CCFLAGS) $(SHFLAGS) $(EXTRA_INC) -c $< + +%.d:%.cpp $(EXTRA_CPP_DEPENDS) + $(CC) $(CCFLAGS) $(EXTRA_INC) $(DEPFLAGS) $< > $@ + +%.o:%.cu $(EXTRA_CPP_DEPENDS) + $(CC) $(CCFLAGS) $(SHFLAGS) $(EXTRA_INC) -c $< + +# Individual dependencies + +depend : fastdep.exe $(SRC) + @./fastdep.exe $(EXTRA_INC) -- $^ > .depend || exit 1 + +fastdep.exe: ../DEPEND/fastdep.c + cc -O -o $@ $< + +sinclude .depend -- GitLab From d0b442aca1ca95ed7de518cd79981b153a1fbe23 Mon Sep 17 00:00:00 2001 From: Stan Moore Date: Thu, 25 Jul 2019 11:25:32 -0600 Subject: [PATCH 323/469] Rename file --- src/MAKE/MACHINES/{Makefile.lassen => Makefile.lassen_kokkos} | 0 1 file changed, 0 insertions(+), 0 deletions(-) rename src/MAKE/MACHINES/{Makefile.lassen => Makefile.lassen_kokkos} (100%) diff --git a/src/MAKE/MACHINES/Makefile.lassen b/src/MAKE/MACHINES/Makefile.lassen_kokkos similarity index 100% rename from src/MAKE/MACHINES/Makefile.lassen rename to src/MAKE/MACHINES/Makefile.lassen_kokkos -- GitLab From 081780706c45560e8f83798ded0c1abd37676e7a Mon Sep 17 00:00:00 2001 From: Stan Moore Date: Thu, 25 Jul 2019 12:15:29 -0600 Subject: [PATCH 324/469] Store if comm flags are changed by turning off CUDA-aware MPI so they can be restored if using cuda/aware on --- src/KOKKOS/kokkos.cpp | 46 +++++++++++++++++++++++++++++++++++-------- src/KOKKOS/kokkos.h | 3 +++ 2 files changed, 41 insertions(+), 8 deletions(-) diff --git a/src/KOKKOS/kokkos.cpp b/src/KOKKOS/kokkos.cpp index c0a74ca3b0..5e8b63936b 100644 --- a/src/KOKKOS/kokkos.cpp +++ b/src/KOKKOS/kokkos.cpp @@ -74,6 +74,10 @@ KokkosLMP::KokkosLMP(LAMMPS *lmp, int narg, char **arg) : Pointers(lmp) kokkos_exists = 1; lmp->kokkos = this; + exchange_comm_changed = 0; + forward_comm_changed = 0; + reverse_comm_changed = 0; + delete memory; memory = new MemoryKokkos(lmp); memoryKK = (MemoryKokkos*) memory; @@ -209,8 +213,8 @@ KokkosLMP::KokkosLMP(LAMMPS *lmp, int narg, char **arg) : Pointers(lmp) if (nmpi > 0) { if (have_cuda_aware == 0) { if (me == 0) - error->warning(FLERR,"CUDA-aware MPI is NOT available, " - "using '-pk kokkos cuda/aware off'"); + error->warning(FLERR,"Turning off CUDA-aware MPI since it is not detected, " + "use '-pk kokkos cuda/aware on' to override"); cuda_aware_flag = 0; } else if (have_cuda_aware == -1) { // maybe we are dealing with MPICH, MVAPICH2 or some derivative? // MVAPICH2 @@ -320,6 +324,7 @@ void KokkosLMP::accelerator(int narg, char **arg) exchange_comm_classic = 0; exchange_comm_on_host = 0; } else error->all(FLERR,"Illegal package kokkos command"); + exchange_comm_changed = 0; iarg += 2; } else if (strcmp(arg[iarg],"comm/forward") == 0) { if (iarg+2 > narg) error->all(FLERR,"Illegal package kokkos command"); @@ -331,6 +336,7 @@ void KokkosLMP::accelerator(int narg, char **arg) forward_comm_classic = 0; forward_comm_on_host = 0; } else error->all(FLERR,"Illegal package kokkos command"); + forward_comm_changed = 0; iarg += 2; } else if (strcmp(arg[iarg],"comm/reverse") == 0) { if (iarg+2 > narg) error->all(FLERR,"Illegal package kokkos command"); @@ -342,6 +348,7 @@ void KokkosLMP::accelerator(int narg, char **arg) reverse_comm_classic = 0; reverse_comm_on_host = 0; } else error->all(FLERR,"Illegal package kokkos command"); + reverse_comm_changed = 0; iarg += 2; } else if (strcmp(arg[iarg],"cuda/aware") == 0) { if (iarg+2 > narg) error->all(FLERR,"Illegal package kokkos command"); @@ -362,12 +369,35 @@ void KokkosLMP::accelerator(int narg, char **arg) // if "cuda/aware off" and "comm device", change to "comm host" if (!cuda_aware_flag) { - if (exchange_comm_classic == 0 && exchange_comm_on_host == 0) - exchange_comm_on_host = 1; - if (forward_comm_classic == 0 && forward_comm_on_host == 0) - forward_comm_on_host = 1; - if (reverse_comm_classic == 0 && reverse_comm_on_host == 0) - reverse_comm_on_host = 1; + if (exchange_comm_classic == 0 && exchange_comm_on_host == 0) { + exchange_comm_on_host = 1; + exchange_comm_changed = 1; + } + if (forward_comm_classic == 0 && forward_comm_on_host == 0) { + forward_comm_on_host = 1; + forward_comm_changed = 1; + } + if (reverse_comm_classic == 0 && reverse_comm_on_host == 0) { + reverse_comm_on_host = 1; + reverse_comm_changed = 1; + } + } + + // if "cuda/aware on" and comm flags were changed previously, change them back + + if (cuda_aware_flag) { + if (exchange_comm_changed) { + exchange_comm_on_host = 0; + exchange_comm_changed = 0; + } + if (forward_comm_changed) { + forward_comm_on_host = 0; + forward_comm_changed = 0; + } + if (reverse_comm_changed) { + reverse_comm_on_host = 0; + reverse_comm_changed = 0; + } } // set newton flags diff --git a/src/KOKKOS/kokkos.h b/src/KOKKOS/kokkos.h index 19e6297ea4..b9f1e66c68 100644 --- a/src/KOKKOS/kokkos.h +++ b/src/KOKKOS/kokkos.h @@ -32,6 +32,9 @@ class KokkosLMP : protected Pointers { int exchange_comm_on_host; int forward_comm_on_host; int reverse_comm_on_host; + int exchange_comm_changed; + int forward_comm_changed; + int reverse_comm_changed; int nthreads,ngpus; int numa; int auto_sync; -- GitLab From 7c1fedff1887951068d82cb4930cab3afc0e2b48 Mon Sep 17 00:00:00 2001 From: Stan Moore Date: Thu, 25 Jul 2019 12:30:45 -0600 Subject: [PATCH 325/469] Fix var name --- src/KOKKOS/kokkos.cpp | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/src/KOKKOS/kokkos.cpp b/src/KOKKOS/kokkos.cpp index 5e8b63936b..c90e702d7d 100644 --- a/src/KOKKOS/kokkos.cpp +++ b/src/KOKKOS/kokkos.cpp @@ -176,7 +176,7 @@ KokkosLMP::KokkosLMP(LAMMPS *lmp, int narg, char **arg) : Pointers(lmp) // default settings for package kokkos command binsize = 0.0; -#if KOKKOS_USE_CUDA +#ifdef KOKKOS_ENABLE_CUDA cuda_aware_flag = 1; #else cuda_aware_flag = 0; @@ -243,7 +243,7 @@ KokkosLMP::KokkosLMP(LAMMPS *lmp, int narg, char **arg) : Pointers(lmp) #endif } // if (-1 == have_cuda_aware) } // nmpi > 0 -#endif // KOKKOS_USE_CUDA +#endif // KOKKOS_ENABLE_CUDA #ifdef KILL_KOKKOS_ON_SIGSEGV signal(SIGSEGV, my_signal_handler); -- GitLab From ab74bfef20844f81707362224ee990712119f17c Mon Sep 17 00:00:00 2001 From: Stan Moore Date: Thu, 25 Jul 2019 12:52:16 -0600 Subject: [PATCH 326/469] Small logic tweak --- src/KOKKOS/kokkos.cpp | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/KOKKOS/kokkos.cpp b/src/KOKKOS/kokkos.cpp index c90e702d7d..f6ab8f5916 100644 --- a/src/KOKKOS/kokkos.cpp +++ b/src/KOKKOS/kokkos.cpp @@ -42,7 +42,7 @@ // even when CUDA-aware MPI is available, and also has a runtime option // to turn CUDA-aware MPI on/off, so support is unknown -#if (defined OPEN_MPI) && !(defined SPECTRUM_MPI) +#if (OPEN_MPI) && !(defined SPECTRUM_MPI) #if (OMPI_MAJOR_VERSION >= 2) #include -- GitLab From fadb40051ba753d6534d7f6d128dc3eb1e00fe69 Mon Sep 17 00:00:00 2001 From: "Ryan S. Elliott" Date: Thu, 25 Jul 2019 14:03:35 -0500 Subject: [PATCH 327/469] Update kim_query & clear and update examples/kim --- ....kim.lj.simulator_model => in.kim-ex.melt} | 6 +- examples/kim/in.kim-pm-query.melt | 37 +++++ .../{in.kim.lj.newton-off => in.kim-pm.melt} | 19 +-- examples/kim/in.kim-sm.melt | 36 +++++ examples/kim/in.kim.lj.lmp.newton-off | 35 ----- examples/kim/in.kim.lj.newton-on | 41 ------ ...in.kim.lj.lmp.newton-on => in.lammps.melt} | 4 +- examples/kim/in.query | 12 -- .../log.06Feb2019.in.kim.lj.lmp.newton-off.1 | 55 -------- .../log.06Feb2019.in.kim.lj.lmp.newton-off.4 | 55 -------- .../log.06Feb2019.in.kim.lj.lmp.newton-on.1 | 55 -------- .../log.06Feb2019.in.kim.lj.lmp.newton-on.4 | 55 -------- .../kim/log.06Feb2019.in.kim.lj.newton-off.1 | 59 -------- .../kim/log.06Feb2019.in.kim.lj.newton-off.4 | 65 --------- .../kim/log.06Feb2019.in.kim.lj.newton-on.1 | 59 -------- .../kim/log.06Feb2019.in.kim.lj.newton-on.4 | 65 --------- examples/kim/log.22Mar2019.query.g++.1 | 34 ----- ...og.30Apr2019.kim.VOH.simulator_model.g++.1 | 92 ------------ ....30Apr2019.kim.ex_si.simulator_model.g++.1 | 132 ------------------ ....30Apr2019.kim.ex_si.simulator_model.g++.4 | 132 ------------------ ...log.30Apr2019.kim.lj.simulator_model.g++.1 | 104 -------------- ...log.30Apr2019.kim.lj.simulator_model.g++.4 | 104 -------------- src/KIM/kim_query.cpp | 3 +- 23 files changed, 86 insertions(+), 1173 deletions(-) rename examples/kim/{in.kim.lj.simulator_model => in.kim-ex.melt} (82%) create mode 100644 examples/kim/in.kim-pm-query.melt rename examples/kim/{in.kim.lj.newton-off => in.kim-pm.melt} (52%) create mode 100644 examples/kim/in.kim-sm.melt delete mode 100644 examples/kim/in.kim.lj.lmp.newton-off delete mode 100644 examples/kim/in.kim.lj.newton-on rename examples/kim/{in.kim.lj.lmp.newton-on => in.lammps.melt} (91%) delete mode 100644 examples/kim/in.query delete mode 100644 examples/kim/log.06Feb2019.in.kim.lj.lmp.newton-off.1 delete mode 100644 examples/kim/log.06Feb2019.in.kim.lj.lmp.newton-off.4 delete mode 100644 examples/kim/log.06Feb2019.in.kim.lj.lmp.newton-on.1 delete mode 100644 examples/kim/log.06Feb2019.in.kim.lj.lmp.newton-on.4 delete mode 100644 examples/kim/log.06Feb2019.in.kim.lj.newton-off.1 delete mode 100644 examples/kim/log.06Feb2019.in.kim.lj.newton-off.4 delete mode 100644 examples/kim/log.06Feb2019.in.kim.lj.newton-on.1 delete mode 100644 examples/kim/log.06Feb2019.in.kim.lj.newton-on.4 delete mode 100644 examples/kim/log.22Mar2019.query.g++.1 delete mode 100644 examples/kim/log.30Apr2019.kim.VOH.simulator_model.g++.1 delete mode 100644 examples/kim/log.30Apr2019.kim.ex_si.simulator_model.g++.1 delete mode 100644 examples/kim/log.30Apr2019.kim.ex_si.simulator_model.g++.4 delete mode 100644 examples/kim/log.30Apr2019.kim.lj.simulator_model.g++.1 delete mode 100644 examples/kim/log.30Apr2019.kim.lj.simulator_model.g++.4 diff --git a/examples/kim/in.kim.lj.simulator_model b/examples/kim/in.kim-ex.melt similarity index 82% rename from examples/kim/in.kim.lj.simulator_model rename to examples/kim/in.kim-ex.melt index cb7a2e14ed..5cc3dbc61b 100644 --- a/examples/kim/in.kim.lj.simulator_model +++ b/examples/kim/in.kim-ex.melt @@ -14,15 +14,14 @@ variable xx equal 20*$x variable yy equal 20*$y variable zz equal 20*$z -kim_init Sim_LAMMPS_LJcut_AkersonElliott_Alchemy_PbAu real unit_conversion_mode -newton on +kim_init LennardJones_Ar real lattice fcc 4.4300 region box block 0 ${xx} 0 ${yy} 0 ${zz} create_box 1 box create_atoms 1 box -kim_interactions Au +kim_interactions Ar mass 1 39.95 velocity all create 200.0 232345 loop geom @@ -31,5 +30,6 @@ neighbor 0.3 bin neigh_modify delay 0 every 1 check yes fix 1 all nve +#fix 1 all npt temp 1.0 1.0 1.0 iso 1.0 1.0 3.0 run 100 diff --git a/examples/kim/in.kim-pm-query.melt b/examples/kim/in.kim-pm-query.melt new file mode 100644 index 0000000000..d39dd2d464 --- /dev/null +++ b/examples/kim/in.kim-pm-query.melt @@ -0,0 +1,37 @@ +# 3d Lennard-Jones melt +# +# This example requires that the KIM Portable Model (PM) +# SW_StillingerWeber_1985_Si__MO_405512056662_005 +# is installed. This can be done with the command +# kim-api-collections-management install user SW_StillingerWeber_1985_Si__MO_405512056662_005 +# Or, see https://openkim.org/doc/obtaining-models for alternative options. +# + +variable x index 1 +variable y index 1 +variable z index 1 + +variable xx equal 20*$x +variable yy equal 20*$y +variable zz equal 20*$z + +kim_init SW_StillingerWeber_1985_Si__MO_405512056662_005 real +kim_query a0 get_lattice_constant_cubic crystal=["fcc"] species=["Si"] units=["angstrom"] + +lattice fcc ${a0} +region box block 0 ${xx} 0 ${yy} 0 ${zz} +create_box 1 box +create_atoms 1 box + +kim_interactions Si + +mass 1 39.95 +velocity all create 200.0 232345 loop geom + +neighbor 0.3 bin +neigh_modify delay 0 every 1 check yes + +fix 1 all nve +#fix 1 all npt temp 1.0 1.0 1.0 iso 1.0 1.0 3.0 + +run 100 diff --git a/examples/kim/in.kim.lj.newton-off b/examples/kim/in.kim-pm.melt similarity index 52% rename from examples/kim/in.kim.lj.newton-off rename to examples/kim/in.kim-pm.melt index 82cf5ba602..999cf77180 100644 --- a/examples/kim/in.kim.lj.newton-off +++ b/examples/kim/in.kim-pm.melt @@ -1,9 +1,10 @@ # 3d Lennard-Jones melt # -# This example requires that the example models provided with -# the kim-api package are installed. see the ./lib/kim/README or -# ./lib/kim/Install.py files for details on how to install these -# example models. +# This example requires that the KIM Portable Model (PM) +# SW_StillingerWeber_1985_Si__MO_405512056662_005 +# is installed. This can be done with the command +# kim-api-collections-management install user SW_StillingerWeber_1985_Si__MO_405512056662_005 +# Or, see https://openkim.org/doc/obtaining-models for alternative options. # variable x index 1 @@ -14,20 +15,14 @@ variable xx equal 20*$x variable yy equal 20*$y variable zz equal 20*$z -units metal -atom_style atomic -newton off +kim_init SW_StillingerWeber_1985_Si__MO_405512056662_005 real lattice fcc 4.4300 region box block 0 ${xx} 0 ${yy} 0 ${zz} create_box 1 box create_atoms 1 box -#pair_style lj/cut 8.1500 -#pair_coeff 1 1 0.0104 3.4000 - -pair_style kim LennardJones_Ar -pair_coeff * * Ar +kim_interactions Si mass 1 39.95 velocity all create 200.0 232345 loop geom diff --git a/examples/kim/in.kim-sm.melt b/examples/kim/in.kim-sm.melt new file mode 100644 index 0000000000..32f8c6170f --- /dev/null +++ b/examples/kim/in.kim-sm.melt @@ -0,0 +1,36 @@ +# 3d Lennard-Jones melt +# +# This example requires that the KIM Simulator Model (PM) +# Sim_LAMMPS_ReaxFF_StrachanVanDuinChakraborty_2003_CHNO__SM_107643900657_000 +# is installed. This can be done with the command +# kim-api-collections-management install user Sim_LAMMPS_ReaxFF_StrachanVanDuinChakraborty_2003_CHNO__SM_107643900657_000 +# Or, see https://openkim.org/doc/obtaining-models for alternative options. +# + +variable x index 1 +variable y index 1 +variable z index 1 + +variable xx equal 20*$x +variable yy equal 20*$y +variable zz equal 20*$z + +kim_init Sim_LAMMPS_ReaxFF_StrachanVanDuinChakraborty_2003_CHNO__SM_107643900657_000 real + +lattice fcc 4.4300 +region box block 0 ${xx} 0 ${yy} 0 ${zz} +create_box 1 box +create_atoms 1 box + +kim_interactions O + +mass 1 39.95 +velocity all create 200.0 232345 loop geom + +neighbor 0.3 bin +neigh_modify delay 0 every 1 check yes + +fix 1 all nve +#fix 1 all npt temp 1.0 1.0 1.0 iso 1.0 1.0 3.0 + +run 100 diff --git a/examples/kim/in.kim.lj.lmp.newton-off b/examples/kim/in.kim.lj.lmp.newton-off deleted file mode 100644 index 197755294a..0000000000 --- a/examples/kim/in.kim.lj.lmp.newton-off +++ /dev/null @@ -1,35 +0,0 @@ -# 3d Lennard-Jones melt - -variable x index 1 -variable y index 1 -variable z index 1 - -variable xx equal 20*$x -variable yy equal 20*$y -variable zz equal 20*$z - -units metal -atom_style atomic -newton off - -lattice fcc 4.4300 -region box block 0 ${xx} 0 ${yy} 0 ${zz} -create_box 1 box -create_atoms 1 box - -pair_style lj/cut 8.1500 -pair_coeff 1 1 0.0104 3.4000 - -#pair_style kim LennardJones_Ar -#pair_coeff * * Ar - -mass 1 39.95 -velocity all create 200.0 232345 loop geom - -neighbor 0.3 bin -neigh_modify delay 0 every 1 check yes - -fix 1 all nve -#fix 1 all npt temp 1.0 1.0 1.0 iso 1.0 1.0 3.0 - -run 100 diff --git a/examples/kim/in.kim.lj.newton-on b/examples/kim/in.kim.lj.newton-on deleted file mode 100644 index 3a95f1dbb0..0000000000 --- a/examples/kim/in.kim.lj.newton-on +++ /dev/null @@ -1,41 +0,0 @@ -# 3d Lennard-Jones melt -# -# This example requires that the example models provided with -# the kim-api package are installed. see the ./lib/kim/README or -# ./lib/kim/Install.py files for details on how to install these -# example models. -# - -variable x index 1 -variable y index 1 -variable z index 1 - -variable xx equal 20*$x -variable yy equal 20*$y -variable zz equal 20*$z - -units metal -atom_style atomic -newton on - -lattice fcc 4.4300 -region box block 0 ${xx} 0 ${yy} 0 ${zz} -create_box 1 box -create_atoms 1 box - -#pair_style lj/cut 8.1500 -#pair_coeff 1 1 0.0104 3.4000 - -pair_style kim LennardJones_Ar -pair_coeff * * Ar - -mass 1 39.95 -velocity all create 200.0 232345 loop geom - -neighbor 0.3 bin -neigh_modify delay 0 every 1 check yes - -fix 1 all nve -#fix 1 all npt temp 1.0 1.0 1.0 iso 1.0 1.0 3.0 - -run 100 diff --git a/examples/kim/in.kim.lj.lmp.newton-on b/examples/kim/in.lammps.melt similarity index 91% rename from examples/kim/in.kim.lj.lmp.newton-on rename to examples/kim/in.lammps.melt index f9f79e2bb2..5792f3a5db 100644 --- a/examples/kim/in.kim.lj.lmp.newton-on +++ b/examples/kim/in.lammps.melt @@ -8,9 +8,7 @@ variable xx equal 20*$x variable yy equal 20*$y variable zz equal 20*$z -units metal -atom_style atomic -newton on +units real lattice fcc 4.4300 region box block 0 ${xx} 0 ${yy} 0 ${zz} diff --git a/examples/kim/in.query b/examples/kim/in.query deleted file mode 100644 index 72e739fb52..0000000000 --- a/examples/kim/in.query +++ /dev/null @@ -1,12 +0,0 @@ - -# example for performing a query to the OpenKIM test database to retrieve -# a parameter to be used in the input. here it requests the aluminium -# lattice constant for a specific test used for a specific model and then -# assigns it to the variable 'latconst' - -kim_init EAM_CubicNaturalSpline_ErcolessiAdams_1994_Al__MO_800509458712_002 metal -info variables out log -kim_query latconst split get_test_result test=TE_156715955670 species=["Al"] prop=structure-cubic-crystal-npt keys=["a","a"] units=["angstrom","angstrom"] -info variables out log -lattice fcc ${latconst_1} -lattice fcc ${latconst_2} diff --git a/examples/kim/log.06Feb2019.in.kim.lj.lmp.newton-off.1 b/examples/kim/log.06Feb2019.in.kim.lj.lmp.newton-off.1 deleted file mode 100644 index 5925fd750d..0000000000 --- a/examples/kim/log.06Feb2019.in.kim.lj.lmp.newton-off.1 +++ /dev/null @@ -1,55 +0,0 @@ -LAMMPS (1 Feb 2019) -OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:87) - using 1 OpenMP thread(s) per MPI task -Lattice spacing in x,y,z = 4.43 4.43 4.43 -Created orthogonal box = (0 0 0) to (88.6 88.6 88.6) - 1 by 1 by 1 MPI processor grid -Created 32000 atoms - Time spent = 0.004499 secs -Neighbor list info ... - update every 1 steps, delay 0 steps, check yes - max neighbors/atom: 2000, page size: 100000 - master list distance cutoff = 8.45 - ghost atom cutoff = 8.45 - binsize = 4.225, bins = 21 21 21 - 1 neighbor lists, perpetual/occasional/extra = 1 0 0 - (1) pair lj/cut, perpetual - attributes: half, newton off - pair build: half/bin/newtoff - stencil: half/bin/3d/newtoff - bin: standard -Setting up Verlet run ... - Unit style : metal - Current step : 0 - Time step : 0.001 -Per MPI rank memory allocation (min/avg/max) = 20.37 | 20.37 | 20.37 Mbytes -Step Temp E_pair E_mol TotEng Press - 0 200 6290.8194 0 7118.0584 129712.25 - 100 95.179725 6718.814 0 7112.496 133346.59 -Loop time of 2.92885 on 1 procs for 100 steps with 32000 atoms - -Performance: 2.950 ns/day, 8.136 hours/ns, 34.143 timesteps/s -99.1% CPU use with 1 MPI tasks x 1 OpenMP threads - -MPI task timing breakdown: -Section | min time | avg time | max time |%varavg| %total ---------------------------------------------------------------- -Pair | 2.5638 | 2.5638 | 2.5638 | 0.0 | 87.54 -Neigh | 0.31935 | 0.31935 | 0.31935 | 0.0 | 10.90 -Comm | 0.006833 | 0.006833 | 0.006833 | 0.0 | 0.23 -Output | 0.000107 | 0.000107 | 0.000107 | 0.0 | 0.00 -Modify | 0.027806 | 0.027806 | 0.027806 | 0.0 | 0.95 -Other | | 0.01091 | | | 0.37 - -Nlocal: 32000 ave 32000 max 32000 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Nghost: 19911 ave 19911 max 19911 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Neighs: 2.3705e+06 ave 2.3705e+06 max 2.3705e+06 min -Histogram: 1 0 0 0 0 0 0 0 0 0 - -Total # of neighbors = 2370499 -Ave neighs/atom = 74.0781 -Neighbor list builds = 3 -Dangerous builds = 0 -Total wall time: 0:00:03 diff --git a/examples/kim/log.06Feb2019.in.kim.lj.lmp.newton-off.4 b/examples/kim/log.06Feb2019.in.kim.lj.lmp.newton-off.4 deleted file mode 100644 index c1ca108c7b..0000000000 --- a/examples/kim/log.06Feb2019.in.kim.lj.lmp.newton-off.4 +++ /dev/null @@ -1,55 +0,0 @@ -LAMMPS (1 Feb 2019) -OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:87) - using 1 OpenMP thread(s) per MPI task -Lattice spacing in x,y,z = 4.43 4.43 4.43 -Created orthogonal box = (0 0 0) to (88.6 88.6 88.6) - 1 by 2 by 2 MPI processor grid -Created 32000 atoms - Time spent = 0.001039 secs -Neighbor list info ... - update every 1 steps, delay 0 steps, check yes - max neighbors/atom: 2000, page size: 100000 - master list distance cutoff = 8.45 - ghost atom cutoff = 8.45 - binsize = 4.225, bins = 21 21 21 - 1 neighbor lists, perpetual/occasional/extra = 1 0 0 - (1) pair lj/cut, perpetual - attributes: half, newton off - pair build: half/bin/newtoff - stencil: half/bin/3d/newtoff - bin: standard -Setting up Verlet run ... - Unit style : metal - Current step : 0 - Time step : 0.001 -Per MPI rank memory allocation (min/avg/max) = 8.013 | 8.013 | 8.013 Mbytes -Step Temp E_pair E_mol TotEng Press - 0 200 6290.8194 0 7118.0584 129712.25 - 100 95.179725 6718.814 0 7112.496 133346.59 -Loop time of 0.778581 on 4 procs for 100 steps with 32000 atoms - -Performance: 11.097 ns/day, 2.163 hours/ns, 128.439 timesteps/s -99.8% CPU use with 4 MPI tasks x 1 OpenMP threads - -MPI task timing breakdown: -Section | min time | avg time | max time |%varavg| %total ---------------------------------------------------------------- -Pair | 0.65171 | 0.65891 | 0.67656 | 1.3 | 84.63 -Neigh | 0.07924 | 0.079548 | 0.07997 | 0.1 | 10.22 -Comm | 0.006755 | 0.0069015 | 0.007072 | 0.2 | 0.89 -Output | 4.6e-05 | 9.725e-05 | 0.000203 | 0.0 | 0.01 -Modify | 0.006841 | 0.006941 | 0.007015 | 0.1 | 0.89 -Other | | 0.02618 | | | 3.36 - -Nlocal: 8000 ave 8018 max 7967 min -Histogram: 1 0 0 0 0 0 1 0 0 2 -Nghost: 9131 ave 9164 max 9113 min -Histogram: 2 0 0 1 0 0 0 0 0 1 -Neighs: 630904 ave 632094 max 628209 min -Histogram: 1 0 0 0 0 0 0 1 0 2 - -Total # of neighbors = 2523614 -Ave neighs/atom = 78.8629 -Neighbor list builds = 3 -Dangerous builds = 0 -Total wall time: 0:00:00 diff --git a/examples/kim/log.06Feb2019.in.kim.lj.lmp.newton-on.1 b/examples/kim/log.06Feb2019.in.kim.lj.lmp.newton-on.1 deleted file mode 100644 index 53555743d7..0000000000 --- a/examples/kim/log.06Feb2019.in.kim.lj.lmp.newton-on.1 +++ /dev/null @@ -1,55 +0,0 @@ -LAMMPS (1 Feb 2019) -OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:87) - using 1 OpenMP thread(s) per MPI task -Lattice spacing in x,y,z = 4.43 4.43 4.43 -Created orthogonal box = (0 0 0) to (88.6 88.6 88.6) - 1 by 1 by 1 MPI processor grid -Created 32000 atoms - Time spent = 0.003479 secs -Neighbor list info ... - update every 1 steps, delay 0 steps, check yes - max neighbors/atom: 2000, page size: 100000 - master list distance cutoff = 8.45 - ghost atom cutoff = 8.45 - binsize = 4.225, bins = 21 21 21 - 1 neighbor lists, perpetual/occasional/extra = 1 0 0 - (1) pair lj/cut, perpetual - attributes: half, newton on - pair build: half/bin/atomonly/newton - stencil: half/bin/3d/newton - bin: standard -Setting up Verlet run ... - Unit style : metal - Current step : 0 - Time step : 0.001 -Per MPI rank memory allocation (min/avg/max) = 19.23 | 19.23 | 19.23 Mbytes -Step Temp E_pair E_mol TotEng Press - 0 200 6290.8194 0 7118.0584 129712.25 - 100 95.179725 6718.814 0 7112.496 133346.59 -Loop time of 2.17978 on 1 procs for 100 steps with 32000 atoms - -Performance: 3.964 ns/day, 6.055 hours/ns, 45.876 timesteps/s -99.9% CPU use with 1 MPI tasks x 1 OpenMP threads - -MPI task timing breakdown: -Section | min time | avg time | max time |%varavg| %total ---------------------------------------------------------------- -Pair | 1.9892 | 1.9892 | 1.9892 | 0.0 | 91.26 -Neigh | 0.14506 | 0.14506 | 0.14506 | 0.0 | 6.65 -Comm | 0.011049 | 0.011049 | 0.011049 | 0.0 | 0.51 -Output | 9.1e-05 | 9.1e-05 | 9.1e-05 | 0.0 | 0.00 -Modify | 0.02347 | 0.02347 | 0.02347 | 0.0 | 1.08 -Other | | 0.01094 | | | 0.50 - -Nlocal: 32000 ave 32000 max 32000 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Nghost: 19911 ave 19911 max 19911 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Neighs: 2.12688e+06 ave 2.12688e+06 max 2.12688e+06 min -Histogram: 1 0 0 0 0 0 0 0 0 0 - -Total # of neighbors = 2126875 -Ave neighs/atom = 66.4648 -Neighbor list builds = 3 -Dangerous builds = 0 -Total wall time: 0:00:02 diff --git a/examples/kim/log.06Feb2019.in.kim.lj.lmp.newton-on.4 b/examples/kim/log.06Feb2019.in.kim.lj.lmp.newton-on.4 deleted file mode 100644 index f0fdf66193..0000000000 --- a/examples/kim/log.06Feb2019.in.kim.lj.lmp.newton-on.4 +++ /dev/null @@ -1,55 +0,0 @@ -LAMMPS (1 Feb 2019) -OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:87) - using 1 OpenMP thread(s) per MPI task -Lattice spacing in x,y,z = 4.43 4.43 4.43 -Created orthogonal box = (0 0 0) to (88.6 88.6 88.6) - 1 by 2 by 2 MPI processor grid -Created 32000 atoms - Time spent = 0.000919 secs -Neighbor list info ... - update every 1 steps, delay 0 steps, check yes - max neighbors/atom: 2000, page size: 100000 - master list distance cutoff = 8.45 - ghost atom cutoff = 8.45 - binsize = 4.225, bins = 21 21 21 - 1 neighbor lists, perpetual/occasional/extra = 1 0 0 - (1) pair lj/cut, perpetual - attributes: half, newton on - pair build: half/bin/atomonly/newton - stencil: half/bin/3d/newton - bin: standard -Setting up Verlet run ... - Unit style : metal - Current step : 0 - Time step : 0.001 -Per MPI rank memory allocation (min/avg/max) = 7.632 | 7.632 | 7.632 Mbytes -Step Temp E_pair E_mol TotEng Press - 0 200 6290.8194 0 7118.0584 129712.25 - 100 95.179725 6718.814 0 7112.496 133346.59 -Loop time of 0.63515 on 4 procs for 100 steps with 32000 atoms - -Performance: 13.603 ns/day, 1.764 hours/ns, 157.443 timesteps/s -99.8% CPU use with 4 MPI tasks x 1 OpenMP threads - -MPI task timing breakdown: -Section | min time | avg time | max time |%varavg| %total ---------------------------------------------------------------- -Pair | 0.55365 | 0.5566 | 0.55868 | 0.2 | 87.63 -Neigh | 0.041495 | 0.0418 | 0.04211 | 0.1 | 6.58 -Comm | 0.019086 | 0.021075 | 0.023898 | 1.2 | 3.32 -Output | 4.4e-05 | 5.025e-05 | 6e-05 | 0.0 | 0.01 -Modify | 0.009315 | 0.0093595 | 0.009422 | 0.0 | 1.47 -Other | | 0.006263 | | | 0.99 - -Nlocal: 8000 ave 8018 max 7967 min -Histogram: 1 0 0 0 0 0 1 0 0 2 -Nghost: 9131 ave 9164 max 9113 min -Histogram: 2 0 0 1 0 0 0 0 0 1 -Neighs: 531719 ave 533273 max 529395 min -Histogram: 1 0 0 0 1 0 0 0 0 2 - -Total # of neighbors = 2126875 -Ave neighs/atom = 66.4648 -Neighbor list builds = 3 -Dangerous builds = 0 -Total wall time: 0:00:00 diff --git a/examples/kim/log.06Feb2019.in.kim.lj.newton-off.1 b/examples/kim/log.06Feb2019.in.kim.lj.newton-off.1 deleted file mode 100644 index 0ab258fe0d..0000000000 --- a/examples/kim/log.06Feb2019.in.kim.lj.newton-off.1 +++ /dev/null @@ -1,59 +0,0 @@ -LAMMPS (1 Feb 2019) -OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:87) - using 1 OpenMP thread(s) per MPI task -Lattice spacing in x,y,z = 4.43 4.43 4.43 -Created orthogonal box = (0 0 0) to (88.6 88.6 88.6) - 1 by 1 by 1 MPI processor grid -Created 32000 atoms - Time spent = 0.003446 secs -WARNING: KIM Model does not provide `partialParticleEnergy'; energy per atom will be zero (src/KIM/pair_kim.cpp:1097) -WARNING: KIM Model does not provide `partialParticleVirial'; virial per atom will be zero (src/KIM/pair_kim.cpp:1102) -Neighbor list info ... - update every 1 steps, delay 0 steps, check yes - max neighbors/atom: 2000, page size: 100000 - master list distance cutoff = 8.45 - ghost atom cutoff = 8.45 - binsize = 4.225, bins = 21 21 21 - 1 neighbor lists, perpetual/occasional/extra = 1 0 0 - (1) pair kim, perpetual - attributes: full, newton off, cut 8.45 - pair build: full/bin/atomonly - stencil: full/bin/3d - bin: standard -Setting up Verlet run ... - Unit style : metal - Current step : 0 - Time step : 0.001 -Per MPI rank memory allocation (min/avg/max) = 28.51 | 28.51 | 28.51 Mbytes -Step Temp E_pair E_mol TotEng Press - 0 200 6290.8194 0 7118.0584 129712.25 - 100 95.179725 6718.814 0 7112.496 133346.59 -Loop time of 3.01669 on 1 procs for 100 steps with 32000 atoms - -Performance: 2.864 ns/day, 8.380 hours/ns, 33.149 timesteps/s -99.8% CPU use with 1 MPI tasks x 1 OpenMP threads - -MPI task timing breakdown: -Section | min time | avg time | max time |%varavg| %total ---------------------------------------------------------------- -Pair | 2.6562 | 2.6562 | 2.6562 | 0.0 | 88.05 -Neigh | 0.31903 | 0.31903 | 0.31903 | 0.0 | 10.58 -Comm | 0.00634 | 0.00634 | 0.00634 | 0.0 | 0.21 -Output | 9.1e-05 | 9.1e-05 | 9.1e-05 | 0.0 | 0.00 -Modify | 0.024723 | 0.024723 | 0.024723 | 0.0 | 0.82 -Other | | 0.01032 | | | 0.34 - -Nlocal: 32000 ave 32000 max 32000 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Nghost: 19911 ave 19911 max 19911 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Neighs: 0 ave 0 max 0 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -FullNghs: 4.25375e+06 ave 4.25375e+06 max 4.25375e+06 min -Histogram: 1 0 0 0 0 0 0 0 0 0 - -Total # of neighbors = 4253750 -Ave neighs/atom = 132.93 -Neighbor list builds = 3 -Dangerous builds = 0 -Total wall time: 0:00:03 diff --git a/examples/kim/log.06Feb2019.in.kim.lj.newton-off.4 b/examples/kim/log.06Feb2019.in.kim.lj.newton-off.4 deleted file mode 100644 index c17ea6afb7..0000000000 --- a/examples/kim/log.06Feb2019.in.kim.lj.newton-off.4 +++ /dev/null @@ -1,65 +0,0 @@ -LAMMPS (1 Feb 2019) -OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:87) - using 1 OpenMP thread(s) per MPI task -Lattice spacing in x,y,z = 4.43 4.43 4.43 -Created orthogonal box = (0 0 0) to (88.6 88.6 88.6) - 1 by 2 by 2 MPI processor grid -Created 32000 atoms - Time spent = 0.000921 secs -WARNING: KIM Model does not provide `partialParticleEnergy'; energy per atom will be zero (src/KIM/pair_kim.cpp:1097) -WARNING: KIM Model does not provide `partialParticleVirial'; virial per atom will be zero (src/KIM/pair_kim.cpp:1102) -WARNING: KIM Model does not provide `partialParticleEnergy'; energy per atom will be zero (src/KIM/pair_kim.cpp:1097) -WARNING: KIM Model does not provide `partialParticleVirial'; virial per atom will be zero (src/KIM/pair_kim.cpp:1102) -WARNING: KIM Model does not provide `partialParticleEnergy'; energy per atom will be zero (src/KIM/pair_kim.cpp:1097) -WARNING: KIM Model does not provide `partialParticleVirial'; virial per atom will be zero (src/KIM/pair_kim.cpp:1102) -WARNING: KIM Model does not provide `partialParticleEnergy'; energy per atom will be zero (src/KIM/pair_kim.cpp:1097) -WARNING: KIM Model does not provide `partialParticleVirial'; virial per atom will be zero (src/KIM/pair_kim.cpp:1102) -Neighbor list info ... - update every 1 steps, delay 0 steps, check yes - max neighbors/atom: 2000, page size: 100000 - master list distance cutoff = 8.45 - ghost atom cutoff = 8.45 - binsize = 4.225, bins = 21 21 21 - 1 neighbor lists, perpetual/occasional/extra = 1 0 0 - (1) pair kim, perpetual - attributes: full, newton off, cut 8.45 - pair build: full/bin/atomonly - stencil: full/bin/3d - bin: standard -Setting up Verlet run ... - Unit style : metal - Current step : 0 - Time step : 0.001 -Per MPI rank memory allocation (min/avg/max) = 10.05 | 10.05 | 10.05 Mbytes -Step Temp E_pair E_mol TotEng Press - 0 200 6290.8194 0 7118.0584 129712.25 - 100 95.179725 6718.814 0 7112.496 133346.59 -Loop time of 0.890192 on 4 procs for 100 steps with 32000 atoms - -Performance: 9.706 ns/day, 2.473 hours/ns, 112.335 timesteps/s -99.7% CPU use with 4 MPI tasks x 1 OpenMP threads - -MPI task timing breakdown: -Section | min time | avg time | max time |%varavg| %total ---------------------------------------------------------------- -Pair | 0.77867 | 0.77906 | 0.7794 | 0.0 | 87.52 -Neigh | 0.087831 | 0.088176 | 0.088805 | 0.1 | 9.91 -Comm | 0.006358 | 0.0065898 | 0.006815 | 0.3 | 0.74 -Output | 4.9e-05 | 5.975e-05 | 6.8e-05 | 0.0 | 0.01 -Modify | 0.010265 | 0.010429 | 0.010678 | 0.2 | 1.17 -Other | | 0.005874 | | | 0.66 - -Nlocal: 8000 ave 8018 max 7967 min -Histogram: 1 0 0 0 0 0 1 0 0 2 -Nghost: 9131 ave 9164 max 9113 min -Histogram: 2 0 0 1 0 0 0 0 0 1 -Neighs: 0 ave 0 max 0 min -Histogram: 4 0 0 0 0 0 0 0 0 0 -FullNghs: 1.06344e+06 ave 1.06594e+06 max 1.05881e+06 min -Histogram: 1 0 0 0 0 0 1 0 0 2 - -Total # of neighbors = 4253750 -Ave neighs/atom = 132.93 -Neighbor list builds = 3 -Dangerous builds = 0 -Total wall time: 0:00:00 diff --git a/examples/kim/log.06Feb2019.in.kim.lj.newton-on.1 b/examples/kim/log.06Feb2019.in.kim.lj.newton-on.1 deleted file mode 100644 index 59d018e12a..0000000000 --- a/examples/kim/log.06Feb2019.in.kim.lj.newton-on.1 +++ /dev/null @@ -1,59 +0,0 @@ -LAMMPS (1 Feb 2019) -OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:87) - using 1 OpenMP thread(s) per MPI task -Lattice spacing in x,y,z = 4.43 4.43 4.43 -Created orthogonal box = (0 0 0) to (88.6 88.6 88.6) - 1 by 1 by 1 MPI processor grid -Created 32000 atoms - Time spent = 0.003089 secs -WARNING: KIM Model does not provide `partialParticleEnergy'; energy per atom will be zero (src/KIM/pair_kim.cpp:1097) -WARNING: KIM Model does not provide `partialParticleVirial'; virial per atom will be zero (src/KIM/pair_kim.cpp:1102) -Neighbor list info ... - update every 1 steps, delay 0 steps, check yes - max neighbors/atom: 2000, page size: 100000 - master list distance cutoff = 8.45 - ghost atom cutoff = 8.45 - binsize = 4.225, bins = 21 21 21 - 1 neighbor lists, perpetual/occasional/extra = 1 0 0 - (1) pair kim, perpetual - attributes: full, newton off, cut 8.45 - pair build: full/bin/atomonly - stencil: full/bin/3d - bin: standard -Setting up Verlet run ... - Unit style : metal - Current step : 0 - Time step : 0.001 -Per MPI rank memory allocation (min/avg/max) = 28.12 | 28.12 | 28.12 Mbytes -Step Temp E_pair E_mol TotEng Press - 0 200 6290.8194 0 7118.0584 129712.25 - 100 95.179725 6718.814 0 7112.496 133346.59 -Loop time of 3.05849 on 1 procs for 100 steps with 32000 atoms - -Performance: 2.825 ns/day, 8.496 hours/ns, 32.696 timesteps/s -99.6% CPU use with 1 MPI tasks x 1 OpenMP threads - -MPI task timing breakdown: -Section | min time | avg time | max time |%varavg| %total ---------------------------------------------------------------- -Pair | 2.6786 | 2.6786 | 2.6786 | 0.0 | 87.58 -Neigh | 0.33105 | 0.33105 | 0.33105 | 0.0 | 10.82 -Comm | 0.012602 | 0.012602 | 0.012602 | 0.0 | 0.41 -Output | 9.5e-05 | 9.5e-05 | 9.5e-05 | 0.0 | 0.00 -Modify | 0.024858 | 0.024858 | 0.024858 | 0.0 | 0.81 -Other | | 0.01132 | | | 0.37 - -Nlocal: 32000 ave 32000 max 32000 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Nghost: 19911 ave 19911 max 19911 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Neighs: 0 ave 0 max 0 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -FullNghs: 4.25375e+06 ave 4.25375e+06 max 4.25375e+06 min -Histogram: 1 0 0 0 0 0 0 0 0 0 - -Total # of neighbors = 4253750 -Ave neighs/atom = 132.93 -Neighbor list builds = 3 -Dangerous builds = 0 -Total wall time: 0:00:03 diff --git a/examples/kim/log.06Feb2019.in.kim.lj.newton-on.4 b/examples/kim/log.06Feb2019.in.kim.lj.newton-on.4 deleted file mode 100644 index da8c9f0faa..0000000000 --- a/examples/kim/log.06Feb2019.in.kim.lj.newton-on.4 +++ /dev/null @@ -1,65 +0,0 @@ -LAMMPS (1 Feb 2019) -OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:87) - using 1 OpenMP thread(s) per MPI task -Lattice spacing in x,y,z = 4.43 4.43 4.43 -Created orthogonal box = (0 0 0) to (88.6 88.6 88.6) - 1 by 2 by 2 MPI processor grid -Created 32000 atoms - Time spent = 0.000893 secs -WARNING: KIM Model does not provide `partialParticleEnergy'; energy per atom will be zero (src/KIM/pair_kim.cpp:1097) -WARNING: KIM Model does not provide `partialParticleVirial'; virial per atom will be zero (src/KIM/pair_kim.cpp:1102) -WARNING: KIM Model does not provide `partialParticleEnergy'; energy per atom will be zero (src/KIM/pair_kim.cpp:1097) -WARNING: KIM Model does not provide `partialParticleVirial'; virial per atom will be zero (src/KIM/pair_kim.cpp:1102) -WARNING: KIM Model does not provide `partialParticleEnergy'; energy per atom will be zero (src/KIM/pair_kim.cpp:1097) -WARNING: KIM Model does not provide `partialParticleVirial'; virial per atom will be zero (src/KIM/pair_kim.cpp:1102) -WARNING: KIM Model does not provide `partialParticleEnergy'; energy per atom will be zero (src/KIM/pair_kim.cpp:1097) -WARNING: KIM Model does not provide `partialParticleVirial'; virial per atom will be zero (src/KIM/pair_kim.cpp:1102) -Neighbor list info ... - update every 1 steps, delay 0 steps, check yes - max neighbors/atom: 2000, page size: 100000 - master list distance cutoff = 8.45 - ghost atom cutoff = 8.45 - binsize = 4.225, bins = 21 21 21 - 1 neighbor lists, perpetual/occasional/extra = 1 0 0 - (1) pair kim, perpetual - attributes: full, newton off, cut 8.45 - pair build: full/bin/atomonly - stencil: full/bin/3d - bin: standard -Setting up Verlet run ... - Unit style : metal - Current step : 0 - Time step : 0.001 -Per MPI rank memory allocation (min/avg/max) = 9.789 | 9.789 | 9.789 Mbytes -Step Temp E_pair E_mol TotEng Press - 0 200 6290.8194 0 7118.0584 129712.25 - 100 95.179725 6718.814 0 7112.496 133346.59 -Loop time of 0.903182 on 4 procs for 100 steps with 32000 atoms - -Performance: 9.566 ns/day, 2.509 hours/ns, 110.720 timesteps/s -99.6% CPU use with 4 MPI tasks x 1 OpenMP threads - -MPI task timing breakdown: -Section | min time | avg time | max time |%varavg| %total ---------------------------------------------------------------- -Pair | 0.76173 | 0.76349 | 0.76597 | 0.2 | 84.53 -Neigh | 0.088773 | 0.088938 | 0.089074 | 0.0 | 9.85 -Comm | 0.032018 | 0.03452 | 0.03638 | 0.9 | 3.82 -Output | 4e-05 | 4.425e-05 | 5.2e-05 | 0.0 | 0.00 -Modify | 0.009278 | 0.0093917 | 0.009528 | 0.1 | 1.04 -Other | | 0.006797 | | | 0.75 - -Nlocal: 8000 ave 8018 max 7967 min -Histogram: 1 0 0 0 0 0 1 0 0 2 -Nghost: 9131 ave 9164 max 9113 min -Histogram: 2 0 0 1 0 0 0 0 0 1 -Neighs: 0 ave 0 max 0 min -Histogram: 4 0 0 0 0 0 0 0 0 0 -FullNghs: 1.06344e+06 ave 1.06594e+06 max 1.05881e+06 min -Histogram: 1 0 0 0 0 0 1 0 0 2 - -Total # of neighbors = 4253750 -Ave neighs/atom = 132.93 -Neighbor list builds = 3 -Dangerous builds = 0 -Total wall time: 0:00:00 diff --git a/examples/kim/log.22Mar2019.query.g++.1 b/examples/kim/log.22Mar2019.query.g++.1 deleted file mode 100644 index 034bb13bba..0000000000 --- a/examples/kim/log.22Mar2019.query.g++.1 +++ /dev/null @@ -1,34 +0,0 @@ -LAMMPS (28 Feb 2019) - -# example for performing a query to the OpenKIM test database to retrieve -# a parameter to be used in the input. here it requests the aluminium -# lattice constant for a specific test used for a specific model and then -# assigns it to the variable 'latconst' - -units metal -info variables out log - -Info-Info-Info-Info-Info-Info-Info-Info-Info-Info-Info -Printed on Fri Mar 22 20:00:56 2019 - - -Variable information: - -Info-Info-Info-Info-Info-Info-Info-Info-Info-Info-Info - -kim_query latconst get_test_result test=TE_156715955670 species=["Al"] model=MO_800509458712 prop=structure-cubic-crystal-npt keys=["a"] units=["angstrom"] -info variables out log - -Info-Info-Info-Info-Info-Info-Info-Info-Info-Info-Info -Printed on Fri Mar 22 20:00:57 2019 - - -Variable information: -Variable[ 0]: latconst , style = string , def = 4.03208274841 - -Info-Info-Info-Info-Info-Info-Info-Info-Info-Info-Info - -lattice fcc ${latconst} -lattice fcc 4.03208274841 -Lattice spacing in x,y,z = 4.03208 4.03208 4.03208 -Total wall time: 0:00:00 diff --git a/examples/kim/log.30Apr2019.kim.VOH.simulator_model.g++.1 b/examples/kim/log.30Apr2019.kim.VOH.simulator_model.g++.1 deleted file mode 100644 index e9d1f17d76..0000000000 --- a/examples/kim/log.30Apr2019.kim.VOH.simulator_model.g++.1 +++ /dev/null @@ -1,92 +0,0 @@ -LAMMPS (30 Apr 2019) - using 1 OpenMP thread(s) per MPI task -# REAX potential for VOH system -# ..... - -units real -atom_style charge - -kim_style init Sim_LAMMPS_ReaxFF_ChenowethVanDuinPersson_2008_CHOV__SM_429148913211_000 -units real -atom_style charge -neigh_modify one 4000 - -read_data data.VOH - orthogonal box = (0 0 0) to (25 25 25) - 1 by 1 by 1 MPI processor grid - reading atoms ... - 100 atoms - read_data CPU = 0.000217199 secs - -kim_style define H C O V -Using KIM Simulator Model : Sim_LAMMPS_ReaxFF_ChenowethVanDuinPersson_2008_CHOV__SM_429148913211_000 -For Simulator : LAMMPS 28-Feb-2019 -Running on : LAMMPS 30 Apr 2019 -pair_style reax/c /tmp/kim-simulator-model-parameter-file-XXXXXXFRmlac safezone 2.0 mincap 100 -pair_coeff * * /tmp/kim-simulator-model-parameter-file-XXXXXX363kge H C O V -Reading potential file /tmp/kim-simulator-model-parameter-file-XXXXXX363kge with DATE: 2011-02-18 -WARNING: Changed valency_val to valency_boc for X (src/USER-REAXC/reaxc_ffield.cpp:311) -fix reaxqeq all qeq/reax 1 0.0 10.0 1.0e-6 /tmp/kim-simulator-model-parameter-file-XXXXXXzgDl49 - -neighbor 2 bin -neigh_modify every 10 delay 0 check no - -fix 1 all nve -fix 3 all temp/berendsen 500.0 500.0 100.0 - -timestep 0.25 - -#dump 1 all atom 30 dump.reax.voh - -run 300 -Neighbor list info ... - update every 10 steps, delay 0 steps, check no - max neighbors/atom: 4000, page size: 100000 - master list distance cutoff = 12 - ghost atom cutoff = 12 - binsize = 6, bins = 5 5 5 - 2 neighbor lists, perpetual/occasional/extra = 2 0 0 - (1) pair reax/c, perpetual - attributes: half, newton off, ghost - pair build: half/bin/newtoff/ghost - stencil: half/ghost/bin/3d/newtoff - bin: standard - (2) fix qeq/reax, perpetual, copy from (1) - attributes: half, newton off, ghost - pair build: copy - stencil: none - bin: none -Per MPI rank memory allocation (min/avg/max) = 25.97 | 25.97 | 25.97 Mbytes -Step Temp E_pair E_mol TotEng Press - 0 0 -10246.825 0 -10246.825 42.256089 - 300 199.45773 -10218.342 0 -10159.482 -66.730725 -Loop time of 1.06721 on 1 procs for 300 steps with 100 atoms - -Performance: 6.072 ns/day, 3.953 hours/ns, 281.107 timesteps/s -98.8% CPU use with 1 MPI tasks x 1 OpenMP threads - -MPI task timing breakdown: -Section | min time | avg time | max time |%varavg| %total ---------------------------------------------------------------- -Pair | 0.93954 | 0.93954 | 0.93954 | 0.0 | 88.04 -Neigh | 0.029087 | 0.029087 | 0.029087 | 0.0 | 2.73 -Comm | 0.0018935 | 0.0018935 | 0.0018935 | 0.0 | 0.18 -Output | 1.8358e-05 | 1.8358e-05 | 1.8358e-05 | 0.0 | 0.00 -Modify | 0.096112 | 0.096112 | 0.096112 | 0.0 | 9.01 -Other | | 0.0005522 | | | 0.05 - -Nlocal: 100 ave 100 max 100 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Nghost: 608 ave 608 max 608 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Neighs: 3441 ave 3441 max 3441 min -Histogram: 1 0 0 0 0 0 0 0 0 0 - -Total # of neighbors = 3441 -Ave neighs/atom = 34.41 -Neighbor list builds = 30 -Dangerous builds not checked - -Please see the log.cite file for references relevant to this simulation - -Total wall time: 0:00:01 diff --git a/examples/kim/log.30Apr2019.kim.ex_si.simulator_model.g++.1 b/examples/kim/log.30Apr2019.kim.ex_si.simulator_model.g++.1 deleted file mode 100644 index a6d1c4a955..0000000000 --- a/examples/kim/log.30Apr2019.kim.ex_si.simulator_model.g++.1 +++ /dev/null @@ -1,132 +0,0 @@ -LAMMPS (30 Apr 2019) - using 1 OpenMP thread(s) per MPI task - -units metal -kim_style init ex_sim_model_Si_mod_tersoff -units metal -newton on - -atom_style atomic -atom_modify map array -boundary p p p - -# temperatures -variable tlo equal 1800.0 -variable thi equal 2400.0 - -# coordination number cutoff - -variable r equal 2.835 - -# minimization parameters - -variable etol equal 1.0e-5 -variable ftol equal 1.0e-5 -variable maxiter equal 100 -variable maxeval equal 100 -variable dmax equal 1.0e-1 - -# diamond unit cell - -variable a equal 5.431 -lattice custom $a a1 1.0 0.0 0.0 a2 0.0 1.0 0.0 a3 0.0 0.0 1.0 basis 0.0 0.0 0.0 basis 0.0 0.5 0.5 basis 0.5 0.0 0.5 basis 0.5 0.5 0.0 basis 0.25 0.25 0.25 basis 0.25 0.75 0.75 basis 0.75 0.25 0.75 basis 0.75 0.75 0.25 -lattice custom 5.431 a1 1.0 0.0 0.0 a2 0.0 1.0 0.0 a3 0.0 0.0 1.0 basis 0.0 0.0 0.0 basis 0.0 0.5 0.5 basis 0.5 0.0 0.5 basis 0.5 0.5 0.0 basis 0.25 0.25 0.25 basis 0.25 0.75 0.75 basis 0.75 0.25 0.75 basis 0.75 0.75 0.25 -Lattice spacing in x,y,z = 5.431 5.431 5.431 - -region myreg block 0 4 0 4 0 4 -create_box 1 myreg -Created orthogonal box = (0 0 0) to (21.724 21.724 21.724) - 1 by 1 by 1 MPI processor grid -create_atoms 1 region myreg -Created 512 atoms - create_atoms CPU = 0.000393867 secs - -mass 1 28.06 - -group Si type 1 -512 atoms in group Si - -velocity all create ${thi} 5287286 mom yes rot yes dist gaussian -velocity all create 2400 5287286 mom yes rot yes dist gaussian - -# make a vacancy - -group del id 300 -1 atoms in group del -delete_atoms group del -Deleted 1 atoms, new total = 511 -kim_style define Si -Using KIM Simulator Model : ex_sim_model_Si_mod_tersoff -For Simulator : LAMMPS 12-Dec-2018 -Running on : LAMMPS 30 Apr 2019 -pair_style tersoff/mod -pair_coeff * * /tmp/kim-simulator-model-parameter-file-XXXXXXVWG8uV Si -Reading potential file /tmp/kim-simulator-model-parameter-file-XXXXXXVWG8uV with DATE: 2013-07-26 - -thermo 10 - -fix 1 all nve -fix 2 all langevin ${thi} ${thi} 0.1 48278 -fix 2 all langevin 2400 ${thi} 0.1 48278 -fix 2 all langevin 2400 2400 0.1 48278 - -timestep 1.0e-3 -neighbor 1.0 bin -neigh_modify every 1 delay 10 check yes - -run 100 -Neighbor list info ... - update every 1 steps, delay 10 steps, check yes - max neighbors/atom: 2000, page size: 100000 - master list distance cutoff = 4.3 - ghost atom cutoff = 4.3 - binsize = 2.15, bins = 11 11 11 - 1 neighbor lists, perpetual/occasional/extra = 1 0 0 - (1) pair tersoff/mod, perpetual - attributes: full, newton on - pair build: full/bin/atomonly - stencil: full/bin/3d - bin: standard -Per MPI rank memory allocation (min/avg/max) = 3.11 | 3.11 | 3.11 Mbytes -Step Temp E_pair E_mol TotEng Press - 0 2397.3877 -2363.0694 0 -2205.0272 15086.224 - 10 1328.4035 -2289.1682 0 -2201.5963 29164.666 - 20 1086.1557 -2254.4447 0 -2182.8424 31906.878 - 30 1528.8439 -2270.2968 0 -2169.5113 21610.528 - 40 1345.227 -2250.3915 0 -2161.7105 22146.886 - 50 1300.3329 -2235.8593 0 -2150.1379 23557.875 - 60 1546.1664 -2241.3019 0 -2139.3744 21648.774 - 70 1662.2896 -2236.2369 0 -2126.6543 23958.738 - 80 1631.7284 -2223.45 0 -2115.8821 28842.194 - 90 1795.3629 -2225.2998 0 -2106.9447 29522.37 - 100 1830.156 -2224.3733 0 -2103.7245 28805.09 -Loop time of 0.201725 on 1 procs for 100 steps with 511 atoms - -Performance: 42.831 ns/day, 0.560 hours/ns, 495.724 timesteps/s -99.3% CPU use with 1 MPI tasks x 1 OpenMP threads - -MPI task timing breakdown: -Section | min time | avg time | max time |%varavg| %total ---------------------------------------------------------------- -Pair | 0.19292 | 0.19292 | 0.19292 | 0.0 | 95.63 -Neigh | 0.0037313 | 0.0037313 | 0.0037313 | 0.0 | 1.85 -Comm | 0.00074744 | 0.00074744 | 0.00074744 | 0.0 | 0.37 -Output | 0.00026727 | 0.00026727 | 0.00026727 | 0.0 | 0.13 -Modify | 0.0036564 | 0.0036564 | 0.0036564 | 0.0 | 1.81 -Other | | 0.0004075 | | | 0.20 - -Nlocal: 511 ave 511 max 511 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Nghost: 970 ave 970 max 970 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Neighs: 0 ave 0 max 0 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -FullNghs: 9174 ave 9174 max 9174 min -Histogram: 1 0 0 0 0 0 0 0 0 0 - -Total # of neighbors = 9174 -Ave neighs/atom = 17.953 -Neighbor list builds = 4 -Dangerous builds = 0 - -Total wall time: 0:00:00 diff --git a/examples/kim/log.30Apr2019.kim.ex_si.simulator_model.g++.4 b/examples/kim/log.30Apr2019.kim.ex_si.simulator_model.g++.4 deleted file mode 100644 index dcb170aeb6..0000000000 --- a/examples/kim/log.30Apr2019.kim.ex_si.simulator_model.g++.4 +++ /dev/null @@ -1,132 +0,0 @@ -LAMMPS (30 Apr 2019) - using 1 OpenMP thread(s) per MPI task - -units metal -kim_style init ex_sim_model_Si_mod_tersoff -units metal -newton on - -atom_style atomic -atom_modify map array -boundary p p p - -# temperatures -variable tlo equal 1800.0 -variable thi equal 2400.0 - -# coordination number cutoff - -variable r equal 2.835 - -# minimization parameters - -variable etol equal 1.0e-5 -variable ftol equal 1.0e-5 -variable maxiter equal 100 -variable maxeval equal 100 -variable dmax equal 1.0e-1 - -# diamond unit cell - -variable a equal 5.431 -lattice custom $a a1 1.0 0.0 0.0 a2 0.0 1.0 0.0 a3 0.0 0.0 1.0 basis 0.0 0.0 0.0 basis 0.0 0.5 0.5 basis 0.5 0.0 0.5 basis 0.5 0.5 0.0 basis 0.25 0.25 0.25 basis 0.25 0.75 0.75 basis 0.75 0.25 0.75 basis 0.75 0.75 0.25 -lattice custom 5.431 a1 1.0 0.0 0.0 a2 0.0 1.0 0.0 a3 0.0 0.0 1.0 basis 0.0 0.0 0.0 basis 0.0 0.5 0.5 basis 0.5 0.0 0.5 basis 0.5 0.5 0.0 basis 0.25 0.25 0.25 basis 0.25 0.75 0.75 basis 0.75 0.25 0.75 basis 0.75 0.75 0.25 -Lattice spacing in x,y,z = 5.431 5.431 5.431 - -region myreg block 0 4 0 4 0 4 -create_box 1 myreg -Created orthogonal box = (0 0 0) to (21.724 21.724 21.724) - 1 by 2 by 2 MPI processor grid -create_atoms 1 region myreg -Created 512 atoms - create_atoms CPU = 0.102434 secs - -mass 1 28.06 - -group Si type 1 -512 atoms in group Si - -velocity all create ${thi} 5287286 mom yes rot yes dist gaussian -velocity all create 2400 5287286 mom yes rot yes dist gaussian - -# make a vacancy - -group del id 300 -1 atoms in group del -delete_atoms group del -Deleted 1 atoms, new total = 511 -kim_style define Si -Using KIM Simulator Model : ex_sim_model_Si_mod_tersoff -For Simulator : LAMMPS 12-Dec-2018 -Running on : LAMMPS 30 Apr 2019 -pair_style tersoff/mod -pair_coeff * * /tmp/kim-simulator-model-parameter-file-XXXXXXqDlERL Si -Reading potential file /tmp/kim-simulator-model-parameter-file-XXXXXXqDlERL with DATE: 2013-07-26 - -thermo 10 - -fix 1 all nve -fix 2 all langevin ${thi} ${thi} 0.1 48278 -fix 2 all langevin 2400 ${thi} 0.1 48278 -fix 2 all langevin 2400 2400 0.1 48278 - -timestep 1.0e-3 -neighbor 1.0 bin -neigh_modify every 1 delay 10 check yes - -run 100 -Neighbor list info ... - update every 1 steps, delay 10 steps, check yes - max neighbors/atom: 2000, page size: 100000 - master list distance cutoff = 4.3 - ghost atom cutoff = 4.3 - binsize = 2.15, bins = 11 11 11 - 1 neighbor lists, perpetual/occasional/extra = 1 0 0 - (1) pair tersoff/mod, perpetual - attributes: full, newton on - pair build: full/bin/atomonly - stencil: full/bin/3d - bin: standard -Per MPI rank memory allocation (min/avg/max) = 3.082 | 3.082 | 3.082 Mbytes -Step Temp E_pair E_mol TotEng Press - 0 2397.5824 -2363.0694 0 -2205.0143 15087.562 - 10 1298.5003 -2292.5456 0 -2206.945 28361.893 - 20 1114.7065 -2260.7006 0 -2187.2161 30574.077 - 30 1504.9472 -2271.8639 0 -2172.6537 20395.651 - 40 1357.5949 -2248.6066 0 -2159.1103 21779.773 - 50 1351.7212 -2235.0803 0 -2145.9713 23404.844 - 60 1582.4191 -2238.3233 0 -2134.006 21711.26 - 70 1654.3988 -2230.0965 0 -2121.0341 24276.504 - 80 1654.9629 -2218.6654 0 -2109.5658 27571.472 - 90 1815.7206 -2219.2065 0 -2099.5093 28475.757 - 100 1901.1544 -2216.5428 0 -2091.2137 28962.04 -Loop time of 4.36959 on 4 procs for 100 steps with 511 atoms - -Performance: 1.977 ns/day, 12.138 hours/ns, 22.885 timesteps/s -47.8% CPU use with 4 MPI tasks x 1 OpenMP threads - -MPI task timing breakdown: -Section | min time | avg time | max time |%varavg| %total ---------------------------------------------------------------- -Pair | 0.051784 | 0.056551 | 0.064825 | 2.1 | 1.29 -Neigh | 0.00093389 | 0.001028 | 0.0011392 | 0.3 | 0.02 -Comm | 2.8964 | 2.9342 | 3.016 | 2.8 | 67.15 -Output | 0.673 | 0.68159 | 0.69707 | 1.1 | 15.60 -Modify | 0.0011303 | 0.0029655 | 0.0081694 | 5.5 | 0.07 -Other | | 0.6933 | | | 15.87 - -Nlocal: 127.75 ave 134 max 123 min -Histogram: 1 0 0 2 0 0 0 0 0 1 -Nghost: 495 ave 498 max 489 min -Histogram: 1 0 0 0 0 0 0 1 1 1 -Neighs: 0 ave 0 max 0 min -Histogram: 4 0 0 0 0 0 0 0 0 0 -FullNghs: 2302 ave 2443 max 2194 min -Histogram: 1 0 0 2 0 0 0 0 0 1 - -Total # of neighbors = 9208 -Ave neighs/atom = 18.0196 -Neighbor list builds = 4 -Dangerous builds = 0 - -Total wall time: 0:00:05 diff --git a/examples/kim/log.30Apr2019.kim.lj.simulator_model.g++.1 b/examples/kim/log.30Apr2019.kim.lj.simulator_model.g++.1 deleted file mode 100644 index 94aaf1aaef..0000000000 --- a/examples/kim/log.30Apr2019.kim.lj.simulator_model.g++.1 +++ /dev/null @@ -1,104 +0,0 @@ -LAMMPS (30 Apr 2019) - using 1 OpenMP thread(s) per MPI task -# 3d Lennard-Jones melt -# -# This example requires that the example models provided with -# the kim-api package are installed. see the ./lib/kim/README or -# ./lib/kim/Install.py files for details on how to install these -# example models. -# - -variable x index 1 -variable y index 1 -variable z index 1 - -variable xx equal 20*$x -variable xx equal 20*1 -variable yy equal 20*$y -variable yy equal 20*1 -variable zz equal 20*$z -variable zz equal 20*1 - -units metal -atom_style atomic -newton on - -kim_style init LennardJones_Ar - -lattice fcc 4.4300 -Lattice spacing in x,y,z = 4.43 4.43 4.43 -region box block 0 ${xx} 0 ${yy} 0 ${zz} -region box block 0 20 0 ${yy} 0 ${zz} -region box block 0 20 0 20 0 ${zz} -region box block 0 20 0 20 0 20 -create_box 1 box -Created orthogonal box = (0 0 0) to (88.6 88.6 88.6) - 1 by 1 by 1 MPI processor grid -create_atoms 1 box -Created 32000 atoms - create_atoms CPU = 0.00314307 secs - -#pair_style lj/cut 8.1500 -#pair_coeff 1 1 0.0104 3.4000 - -kim_style define Ar -pair_style kim LennardJones_Ar -WARNING: KIM Model does not provide `partialParticleEnergy'; energy per atom will be zero (src/KIM/pair_kim.cpp:980) -WARNING: KIM Model does not provide `partialParticleVirial'; virial per atom will be zero (src/KIM/pair_kim.cpp:985) -pair_coeff * * Ar - -mass 1 39.95 -velocity all create 200.0 232345 loop geom - -neighbor 0.3 bin -neigh_modify delay 0 every 1 check yes - -fix 1 all nve -#fix 1 all npt temp 1.0 1.0 1.0 iso 1.0 1.0 3.0 - -run 100 -Neighbor list info ... - update every 1 steps, delay 0 steps, check yes - max neighbors/atom: 2000, page size: 100000 - master list distance cutoff = 8.45 - ghost atom cutoff = 8.45 - binsize = 4.225, bins = 21 21 21 - 1 neighbor lists, perpetual/occasional/extra = 1 0 0 - (1) pair kim, perpetual - attributes: full, newton off, cut 8.45 - pair build: full/bin/atomonly - stencil: full/bin/3d - bin: standard -Per MPI rank memory allocation (min/avg/max) = 28.12 | 28.12 | 28.12 Mbytes -Step Temp E_pair E_mol TotEng Press - 0 200 6290.8194 0 7118.0584 129712.25 - 100 95.179725 6718.814 0 7112.496 133346.59 -Loop time of 4.91804 on 1 procs for 100 steps with 32000 atoms - -Performance: 1.757 ns/day, 13.661 hours/ns, 20.333 timesteps/s -99.7% CPU use with 1 MPI tasks x 1 OpenMP threads - -MPI task timing breakdown: -Section | min time | avg time | max time |%varavg| %total ---------------------------------------------------------------- -Pair | 4.3033 | 4.3033 | 4.3033 | 0.0 | 87.50 -Neigh | 0.53176 | 0.53176 | 0.53176 | 0.0 | 10.81 -Comm | 0.024606 | 0.024606 | 0.024606 | 0.0 | 0.50 -Output | 0.00016403 | 0.00016403 | 0.00016403 | 0.0 | 0.00 -Modify | 0.038671 | 0.038671 | 0.038671 | 0.0 | 0.79 -Other | | 0.01951 | | | 0.40 - -Nlocal: 32000 ave 32000 max 32000 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Nghost: 19911 ave 19911 max 19911 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Neighs: 0 ave 0 max 0 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -FullNghs: 4.25375e+06 ave 4.25375e+06 max 4.25375e+06 min -Histogram: 1 0 0 0 0 0 0 0 0 0 - -Total # of neighbors = 4253750 -Ave neighs/atom = 132.93 -Neighbor list builds = 3 -Dangerous builds = 0 -Total wall time: 0:00:05 diff --git a/examples/kim/log.30Apr2019.kim.lj.simulator_model.g++.4 b/examples/kim/log.30Apr2019.kim.lj.simulator_model.g++.4 deleted file mode 100644 index 3377f22d02..0000000000 --- a/examples/kim/log.30Apr2019.kim.lj.simulator_model.g++.4 +++ /dev/null @@ -1,104 +0,0 @@ -LAMMPS (30 Apr 2019) - using 1 OpenMP thread(s) per MPI task -# 3d Lennard-Jones melt -# -# This example requires that the example models provided with -# the kim-api package are installed. see the ./lib/kim/README or -# ./lib/kim/Install.py files for details on how to install these -# example models. -# - -variable x index 1 -variable y index 1 -variable z index 1 - -variable xx equal 20*$x -variable xx equal 20*1 -variable yy equal 20*$y -variable yy equal 20*1 -variable zz equal 20*$z -variable zz equal 20*1 - -units metal -atom_style atomic -newton on - -kim_style init LennardJones_Ar - -lattice fcc 4.4300 -Lattice spacing in x,y,z = 4.43 4.43 4.43 -region box block 0 ${xx} 0 ${yy} 0 ${zz} -region box block 0 20 0 ${yy} 0 ${zz} -region box block 0 20 0 20 0 ${zz} -region box block 0 20 0 20 0 20 -create_box 1 box -Created orthogonal box = (0 0 0) to (88.6 88.6 88.6) - 1 by 2 by 2 MPI processor grid -create_atoms 1 box -Created 32000 atoms - create_atoms CPU = 0.0979962 secs - -#pair_style lj/cut 8.1500 -#pair_coeff 1 1 0.0104 3.4000 - -kim_style define Ar -pair_style kim LennardJones_Ar -WARNING: KIM Model does not provide `partialParticleEnergy'; energy per atom will be zero (src/KIM/pair_kim.cpp:980) -WARNING: KIM Model does not provide `partialParticleVirial'; virial per atom will be zero (src/KIM/pair_kim.cpp:985) -pair_coeff * * Ar - -mass 1 39.95 -velocity all create 200.0 232345 loop geom - -neighbor 0.3 bin -neigh_modify delay 0 every 1 check yes - -fix 1 all nve -#fix 1 all npt temp 1.0 1.0 1.0 iso 1.0 1.0 3.0 - -run 100 -Neighbor list info ... - update every 1 steps, delay 0 steps, check yes - max neighbors/atom: 2000, page size: 100000 - master list distance cutoff = 8.45 - ghost atom cutoff = 8.45 - binsize = 4.225, bins = 21 21 21 - 1 neighbor lists, perpetual/occasional/extra = 1 0 0 - (1) pair kim, perpetual - attributes: full, newton off, cut 8.45 - pair build: full/bin/atomonly - stencil: full/bin/3d - bin: standard -Per MPI rank memory allocation (min/avg/max) = 9.789 | 9.789 | 9.789 Mbytes -Step Temp E_pair E_mol TotEng Press - 0 200 6290.8194 0 7118.0584 129712.25 - 100 95.179725 6718.814 0 7112.496 133346.59 -Loop time of 6.29539 on 4 procs for 100 steps with 32000 atoms - -Performance: 1.372 ns/day, 17.487 hours/ns, 15.885 timesteps/s -48.4% CPU use with 4 MPI tasks x 1 OpenMP threads - -MPI task timing breakdown: -Section | min time | avg time | max time |%varavg| %total ---------------------------------------------------------------- -Pair | 1.9399 | 2.079 | 2.2181 | 9.1 | 33.02 -Neigh | 0.25924 | 0.26632 | 0.2692 | 0.8 | 4.23 -Comm | 2.5011 | 2.6605 | 2.751 | 5.9 | 42.26 -Output | 0.069904 | 0.07097 | 0.071545 | 0.3 | 1.13 -Modify | 0.011383 | 0.012206 | 0.01419 | 1.0 | 0.19 -Other | | 1.206 | | | 19.16 - -Nlocal: 8000 ave 8018 max 7967 min -Histogram: 1 0 0 0 0 0 1 0 0 2 -Nghost: 9131 ave 9164 max 9113 min -Histogram: 2 0 0 1 0 0 0 0 0 1 -Neighs: 0 ave 0 max 0 min -Histogram: 4 0 0 0 0 0 0 0 0 0 -FullNghs: 1.06344e+06 ave 1.06594e+06 max 1.05881e+06 min -Histogram: 1 0 0 0 0 0 1 0 0 2 - -Total # of neighbors = 4253750 -Ave neighs/atom = 132.93 -Neighbor list builds = 3 -Dangerous builds = 0 -Total wall time: 0:00:07 diff --git a/src/KIM/kim_query.cpp b/src/KIM/kim_query.cpp index dc8d0544f6..85b865d03f 100644 --- a/src/KIM/kim_query.cpp +++ b/src/KIM/kim_query.cpp @@ -220,8 +220,9 @@ char *do_query(char *qfunction, char * model_name, int narg, char **arg, url += qfunction; std::string query(arg[0]); - query += "&model="; + query += "&model=[\""; query += model_name; + query += "\"]"; for (int i=1; i < narg; ++i) { query += '&'; query += arg[i]; -- GitLab From fe83e4de2ec4acc6e5a190bac6dd597e52a1aab5 Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Thu, 25 Jul 2019 16:00:01 -0400 Subject: [PATCH 328/469] revise logic and documentation of communication cutoff selection one more time --- doc/src/comm_modify.txt | 21 +++++++-------- src/comm.cpp | 59 ++++++++++++++++++++++++++++------------- 2 files changed, 50 insertions(+), 30 deletions(-) diff --git a/doc/src/comm_modify.txt b/doc/src/comm_modify.txt index d5f5aecf54..5f03636c1d 100644 --- a/doc/src/comm_modify.txt +++ b/doc/src/comm_modify.txt @@ -69,18 +69,15 @@ processors. By default the ghost cutoff = neighbor cutoff = pairwise force cutoff + neighbor skin. See the "neighbor"_neighbor.html command for more information about the skin distance. If the specified Rcut is greater than the neighbor cutoff, then extra ghost atoms will be acquired. -If the provided cutoff is smaller, the provided value will be ignored -and the ghost cutoff is set to the neighbor cutoff. Specifying a -cutoff value of 0.0 will reset any previous value to the default. -If bonded interactions exist and equilibrium bond length information is -available, then also a heuristic based on that bond length (2.0x {r_eq} -for systems with dihedrals or improper, 1.5x {r_eq} without) plus -neighbor skin is applied if the communication cutoff is set to its -default value of 0.0. This avoids problems for systems without a pair -style or where the non-bonded cutoff is (much) shorter than the largest -bond lengths. A warning message is printed, if a specified -communication cutoff > 0.0 is overridden or the bond length heuristics -lead to a larger communication cutoff. +If the provided cutoff is smaller, the provided value will be ignored, +the ghost cutoff is set to the neighbor cutoff and a warning will be +printed. Specifying a cutoff value of 0.0 will reset any previous value +to the default. If bonded interactions exist and equilibrium bond length +information is available, then also a heuristic based on that bond length +is computed. It is used as communication cutoff, if there is no pair +style present and no {comm_modify cutoff} command used. Otherwise a +warning is printed, if this bond based estimate is larger than the +communication cutoff used. A The {cutoff/multi} option is equivalent to {cutoff}, but applies to communication mode {multi} instead. Since in this case the communication diff --git a/src/comm.cpp b/src/comm.cpp index ae2715f0fd..303bd6a8cb 100644 --- a/src/comm.cpp +++ b/src/comm.cpp @@ -588,30 +588,42 @@ void Comm::set_proc_grid(int outflag) /* ---------------------------------------------------------------------- determine suitable communication cutoff. - use the larger of the user specified value and the cutoff required - by the neighborlist build for pair styles. - if bonded interactions exist, apply a heuristic based on the equilibrium - bond length (use 1.5x r_bond if no dihedral or improper style exists - otherwise 2x r_bond) plus neighbor list skin. - if no user specified communication cutoff is given include this - heuristic, otherwise ignore it. + this uses three inputs: 1) maximum neighborlist cutoff, 2) an estimate + based on bond lengths and bonded interaction styles present, and 3) a + user supplied communication cutoff. + the neighbor list cutoff (1) is *always* used, since it is a requirement + for neighborlists working correctly. the bond length based cutoff is + *only* used, if no pair style is defined and no user cutoff is provided. + otherwise, a warning is printed. if the bond length based estimate is + larger than what is used. print a warning, if a user specified communication cutoff is overridden. ------------------------------------------------------------------------- */ double Comm::get_comm_cutoff() { - double maxcommcutoff = 0.0; - double maxbondcutoff = 0.0; + double maxcommcutoff, maxbondcutoff = 0.0; if (force->bond) { int n = atom->nbondtypes; for (int i = 1; i <= n; ++i) maxbondcutoff = MAX(maxbondcutoff,force->bond->equilibrium_distance(i)); - if (force->dihedral || force->improper) { - maxbondcutoff *= 2.0; + // apply bond length based heuristics. + + if (force->newton_bond) { + if (force->dihedral || force->improper) { + maxbondcutoff *= 2.25; + } else { + maxbondcutoff *=1.5; + } } else { - maxbondcutoff *=1.5; + if (force->dihedral || force->improper) { + maxbondcutoff *= 3.125; + } else if (force->angle) { + maxbondcutoff *= 2.25; + } else { + maxbondcutoff *=1.5; + } } maxbondcutoff += neighbor->skin; } @@ -620,16 +632,27 @@ double Comm::get_comm_cutoff() maxcommcutoff = MAX(cutghostuser,neighbor->cutneighmax); - // consider cutoff estimate from bond length only if no user specified cutoff + // use cutoff estimate from bond length only if no user specified + // cutoff was given and no pair style present. Otherwise print a + // warning, if the estimated bond based cutoff is larger than what + // is currently used. - if (cutghostuser == 0.0) maxcommcutoff = MAX(maxcommcutoff,maxbondcutoff); + if (!force->pair && (cutghostuser == 0.0)) { + maxcommcutoff = MAX(maxcommcutoff,maxbondcutoff); + } else { + if ((me == 0) && (maxbondcutoff > maxcommcutoff)) { + char mesg[256]; + snprintf(mesg,256,"Communication cutoff %g is shorter than a bond " + "length based estimate of %g. This may lead to errors.", + maxcommcutoff,maxbondcutoff); + error->warning(FLERR,mesg); + } + } - // print warning if neighborlist cutoff overrides user cutoff or - // applied bond based cutoff is larger than neighbor cutoff. + // print warning if neighborlist cutoff overrides user cutoff if (me == 0) { - if ( ((cutghostuser > 0.0) && (maxcommcutoff > cutghostuser)) - || ((cutghostuser == 0.0) && (maxcommcutoff == maxbondcutoff)) ) { + if ((cutghostuser > 0.0) && (maxcommcutoff > cutghostuser)) { char mesg[128]; snprintf(mesg,128,"Communication cutoff adjusted to %g",maxcommcutoff); error->warning(FLERR,mesg); -- GitLab From 60dfa7daf81e056a126dc52e131295aafe97a3d1 Mon Sep 17 00:00:00 2001 From: "Ryan S. Elliott" Date: Thu, 25 Jul 2019 18:31:40 -0500 Subject: [PATCH 329/469] doc spelling update --- doc/src/Install_mac.txt | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/doc/src/Install_mac.txt b/doc/src/Install_mac.txt index e277f7e0e4..773c9ec93a 100644 --- a/doc/src/Install_mac.txt +++ b/doc/src/Install_mac.txt @@ -28,7 +28,7 @@ Lennard-Jones benchmark file: % brew test lammps -v :pre The LAMMPS binary is built with the "KIM package"_Build_extras#kim which -results in homebrew also installing the `kim-api` binaries when LAMMPS is +results in Homebrew also installing the `kim-api` binaries when LAMMPS is installed. In order to use potentials from "openkim.org"_openkim, you can install the `openkim-models` package -- GitLab From 52e175546420c04705ac101f58806a94f5705aba Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Thu, 25 Jul 2019 21:20:42 -0400 Subject: [PATCH 330/469] fix spelling errors and false positives --- doc/src/kim_commands.txt | 4 ++-- doc/utils/sphinx-config/false_positives.txt | 1 + 2 files changed, 3 insertions(+), 2 deletions(-) diff --git a/doc/src/kim_commands.txt b/doc/src/kim_commands.txt index dd61f6f5cc..0bb7de03d6 100644 --- a/doc/src/kim_commands.txt +++ b/doc/src/kim_commands.txt @@ -282,7 +282,7 @@ keyword {fixed_types} for models that have a preset fixed mapping (i.e. the mapping between LAMMPS atom types and chemical species is defined by the model and cannot be changed). In the latter case, the user must consult the model documentation to see how many atom types there are and how they -map to the chemcial species. +map to the chemical species. For example, consider an OpenKIM IM that supports Si and C species. If the LAMMPS simulation has four atom types, where the first three are Si, @@ -488,7 +488,7 @@ The citation format for an IM is displayed on its page on "OpenKIM"_https://openkim.org along with the corresponding BibTex file, and is automatically added to the LAMMPS {log.cite} file. -Citing the IM software (KIM infrastucture and specific PM or SM codes) +Citing the IM software (KIM infrastructure and specific PM or SM codes) used in the simulation gives credit to the researchers who developed them and enables open source efforts like OpenKIM to function. diff --git a/doc/utils/sphinx-config/false_positives.txt b/doc/utils/sphinx-config/false_positives.txt index e383fddfa9..cf9b823ba3 100644 --- a/doc/utils/sphinx-config/false_positives.txt +++ b/doc/utils/sphinx-config/false_positives.txt @@ -884,6 +884,7 @@ Fogarty Foiles fopenmp forestgreen +formatarg formulae Forschungszentrum Fortran -- GitLab From 179b507107ce774f89e3b116697d974264013f1c Mon Sep 17 00:00:00 2001 From: Denis Taniguchi Date: Fri, 26 Jul 2019 10:55:27 +0100 Subject: [PATCH 331/469] Fixing bug in nve/kk when using rmass. --- src/KOKKOS/fix_nve_kokkos.cpp | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/KOKKOS/fix_nve_kokkos.cpp b/src/KOKKOS/fix_nve_kokkos.cpp index 6db8ff8c0f..740e6ff54b 100644 --- a/src/KOKKOS/fix_nve_kokkos.cpp +++ b/src/KOKKOS/fix_nve_kokkos.cpp @@ -98,7 +98,7 @@ KOKKOS_INLINE_FUNCTION void FixNVEKokkos::initial_integrate_rmass_item(int i) const { if (mask[i] & groupbit) { - const double dtfm = dtf / rmass[type[i]]; + const double dtfm = dtf / rmass[i]; v(i,0) += dtfm * f(i,0); v(i,1) += dtfm * f(i,1); v(i,2) += dtfm * f(i,2); -- GitLab From 47689b4ad36198e7501d5bbd37419d658dce3c3f Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Fri, 26 Jul 2019 06:03:21 -0400 Subject: [PATCH 332/469] make include files independent of previously included headers. include them first in implementation files. this is to be compliant with upcoming definition of include file policy --- src/KIM/fix_store_kim.cpp | 2 +- src/KIM/fix_store_kim.h | 1 - src/KIM/kim_init.cpp | 2 +- src/KIM/kim_init.h | 1 + src/KIM/kim_interactions.cpp | 2 +- src/KIM/kim_interactions.h | 1 + src/KIM/kim_query.cpp | 2 +- src/KIM/pair_kim.cpp | 2 +- 8 files changed, 7 insertions(+), 6 deletions(-) diff --git a/src/KIM/fix_store_kim.cpp b/src/KIM/fix_store_kim.cpp index 1bd924bcfb..16d606d2ed 100644 --- a/src/KIM/fix_store_kim.cpp +++ b/src/KIM/fix_store_kim.cpp @@ -54,8 +54,8 @@ Designed for use with the kim-api-2.0.2 (and newer) package ------------------------------------------------------------------------- */ -#include #include "fix_store_kim.h" +#include extern "C" { #include "KIM_SimulatorModel.h" } diff --git a/src/KIM/fix_store_kim.h b/src/KIM/fix_store_kim.h index 655be83ad0..6baf480993 100644 --- a/src/KIM/fix_store_kim.h +++ b/src/KIM/fix_store_kim.h @@ -63,7 +63,6 @@ FixStyle(STORE/KIM,FixStoreKIM) #ifndef LMP_FIX_STORE_KIM_H #define LMP_FIX_STORE_KIM_H -#include #include "fix.h" namespace LAMMPS_NS { diff --git a/src/KIM/kim_init.cpp b/src/KIM/kim_init.cpp index 83638f3428..bae286aff6 100644 --- a/src/KIM/kim_init.cpp +++ b/src/KIM/kim_init.cpp @@ -55,11 +55,11 @@ Designed for use with the kim-api-2.1.0 (and newer) package ------------------------------------------------------------------------- */ +#include "kim_init.h" #include #include #include #include -#include "kim_init.h" #include "error.h" #include "atom.h" #include "comm.h" diff --git a/src/KIM/kim_init.h b/src/KIM/kim_init.h index 7c7a24615b..2b5dc520c7 100644 --- a/src/KIM/kim_init.h +++ b/src/KIM/kim_init.h @@ -65,6 +65,7 @@ CommandStyle(kim_init,KimInit) #define LMP_KIM_INIT_H #include "pointers.h" +#include namespace LAMMPS_NS { diff --git a/src/KIM/kim_interactions.cpp b/src/KIM/kim_interactions.cpp index d0fbb809d2..449b6bcb13 100644 --- a/src/KIM/kim_interactions.cpp +++ b/src/KIM/kim_interactions.cpp @@ -55,10 +55,10 @@ Designed for use with the kim-api-2.1.0 (and newer) package ------------------------------------------------------------------------- */ +#include "kim_interactions.h" #include #include #include -#include "kim_interactions.h" #include "error.h" #include "atom.h" #include "comm.h" diff --git a/src/KIM/kim_interactions.h b/src/KIM/kim_interactions.h index 6da1880f84..8172004d53 100644 --- a/src/KIM/kim_interactions.h +++ b/src/KIM/kim_interactions.h @@ -65,6 +65,7 @@ CommandStyle(kim_interactions,KimInteractions) #define LMP_KIM_INTERACTIONS_H #include "pointers.h" +#include namespace LAMMPS_NS { diff --git a/src/KIM/kim_query.cpp b/src/KIM/kim_query.cpp index 85b865d03f..6688ed6690 100644 --- a/src/KIM/kim_query.cpp +++ b/src/KIM/kim_query.cpp @@ -54,11 +54,11 @@ Designed for use with the kim-api-2.1.0 (and newer) package ------------------------------------------------------------------------- */ +#include "kim_query.h" #include #include #include #include -#include "kim_query.h" #include "comm.h" #include "error.h" #include "input.h" diff --git a/src/KIM/pair_kim.cpp b/src/KIM/pair_kim.cpp index 50eef1de2b..74b92a3e2b 100644 --- a/src/KIM/pair_kim.cpp +++ b/src/KIM/pair_kim.cpp @@ -53,13 +53,13 @@ /* ---------------------------------------------------------------------- Designed for use with the kim-api-2.0.2 (and newer) package ------------------------------------------------------------------------- */ +#include "pair_kim.h" #include #include #include // includes from LAMMPS -#include "pair_kim.h" #include "atom.h" #include "comm.h" #include "universe.h" -- GitLab From e8d891c0ddb78c5be220fb9ccdcdbba1fa24509f Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Fri, 26 Jul 2019 06:06:03 -0400 Subject: [PATCH 333/469] simplify installation of data folders and make it consistent fixes #1586 --- cmake/CMakeLists.txt | 8 +++----- 1 file changed, 3 insertions(+), 5 deletions(-) diff --git a/cmake/CMakeLists.txt b/cmake/CMakeLists.txt index 0f99cc6274..7cd7b62c91 100644 --- a/cmake/CMakeLists.txt +++ b/cmake/CMakeLists.txt @@ -551,11 +551,9 @@ include(Documentation) ############################################################################### # Install potential and force field files in data directory ############################################################################### -set(LAMMPS_INSTALL_POTENTIALS_DIR ${CMAKE_INSTALL_FULL_DATADIR}/lammps/potentials) -install(DIRECTORY ${LAMMPS_POTENTIALS_DIR} DESTINATION ${LAMMPS_INSTALL_POTENTIALS_DIR}) - -set(LAMMPS_INSTALL_FRC_FILES_DIR ${CMAKE_INSTALL_FULL_DATADIR}/lammps/frc_files) -install(DIRECTORY ${LAMMPS_TOOLS_DIR}/msi2lmp/frc_files/ DESTINATION ${LAMMPS_INSTALL_FRC_FILES_DIR}) +set(LAMMPS_INSTALL_DATADIR ${CMAKE_INSTALL_FULL_DATADIR}/lammps) +install(DIRECTORY ${LAMMPS_POTENTIALS_DIR} DESTINATION ${LAMMPS_INSTALL_DATADIR}) +install(DIRECTORY ${LAMMPS_TOOLS_DIR}/msi2lmp/frc_files DESTINATION ${LAMMPS_INSTALL_DATADIR}) configure_file(etc/profile.d/lammps.sh.in ${CMAKE_BINARY_DIR}/etc/profile.d/lammps.sh @ONLY) configure_file(etc/profile.d/lammps.csh.in ${CMAKE_BINARY_DIR}/etc/profile.d/lammps.csh @ONLY) -- GitLab From ca1fece850217324c5566f96dbd54d3d8ab66dca Mon Sep 17 00:00:00 2001 From: Denis Taniguchi Date: Fri, 26 Jul 2019 12:46:04 +0100 Subject: [PATCH 334/469] Fixing remaining wrong indexing of rmass in nve/kk. --- src/KOKKOS/fix_nve_kokkos.cpp | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/KOKKOS/fix_nve_kokkos.cpp b/src/KOKKOS/fix_nve_kokkos.cpp index 740e6ff54b..ca7f728370 100644 --- a/src/KOKKOS/fix_nve_kokkos.cpp +++ b/src/KOKKOS/fix_nve_kokkos.cpp @@ -154,7 +154,7 @@ KOKKOS_INLINE_FUNCTION void FixNVEKokkos::final_integrate_rmass_item(int i) const { if (mask[i] & groupbit) { - const double dtfm = dtf / rmass[type[i]]; + const double dtfm = dtf / rmass[i]; v(i,0) += dtfm * f(i,0); v(i,1) += dtfm * f(i,1); v(i,2) += dtfm * f(i,2); -- GitLab From 8d4f1896994e50d7f66ab1f66a7bf8bd306f48e0 Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Fri, 26 Jul 2019 09:38:32 -0400 Subject: [PATCH 335/469] Revert "new versions of jacobi() method" This reverts commit 39315268e885fba886a0ff30eccc619ffaa64c5f. --- src/math_extra.cpp | 229 ++++++++++++--------------------------------- src/math_extra.h | 9 +- 2 files changed, 63 insertions(+), 175 deletions(-) diff --git a/src/math_extra.cpp b/src/math_extra.cpp index 4184e84b59..797d210d0e 100644 --- a/src/math_extra.cpp +++ b/src/math_extra.cpp @@ -13,7 +13,6 @@ /* ---------------------------------------------------------------------- Contributing author: Mike Brown (SNL) - Arno Mayrhofer (DCS Computing), jacobi() functions ------------------------------------------------------------------------- */ #include "math_extra.h" @@ -96,189 +95,83 @@ int mldivide3(const double m[3][3], const double *v, double *ans) /* ---------------------------------------------------------------------- compute evalues and evectors of 3x3 real symmetric matrix based on Jacobi rotations - two variants for passing in matrix - - procedure jacobi(S ∈ Rn×n; out e ∈ Rn; out E ∈ Rn×n) - var - i, k, l, m, state ∈ N - s, c, t, p, y, d, r ∈ R - ind ∈ Nn - changed ∈ Ln - ! init e, E, and arrays ind, changed - E := I; state := n - for k := 1 to n do indk := maxind(k); ek := Skk; changedk := true endfor - while state≠0 do ! next rotation - m := 1 ! find index (k,l) of pivot p - for k := 2 to n−1 do - if │Sk indk│ > │Sm indm│ then m := k endif - endfor - k := m; l := indm; p := Skl - ! calculate c = cos φ, s = sin φ - y := (el−ek)/2; d := │y│+√(p2+y2) - r := √(p2+d2); c := d/r; s := p/r; t := p2/d - if y<0 then s := −s; t := −t endif - Skl := 0.0; update(k,−t); update(l,t) - ! rotate rows and columns k and l - for i := 1 to k−1 do rotate(i,k,i,l) endfor - for i := k+1 to l−1 do rotate(k,i,i,l) endfor - for i := l+1 to n do rotate(k,i,l,i) endfor - ! rotate eigenvectors - for i := 1 to n do - ┌ ┐ ┌ ┐┌ ┐ - │Eik│ │c −s││Eik│ - │ │ := │ ││ │ - │Eil│ │s c││Eil│ - └ ┘ └ ┘└ ┘ - endfor - ! rows k, l have changed, update rows indk, indl - indk := maxind(k); indl := maxind(l) - loop - endproc + adapted from Numerical Recipes jacobi() function ------------------------------------------------------------------------- */ int jacobi(double matrix[3][3], double *evalues, double evectors[3][3]) { - evectors[0][0] = 1.0; evectors[0][1] = 0.0; evectors[0][2] = 0.0; - evectors[1][0] = 0.0; evectors[1][1] = 1.0; evectors[1][2] = 0.0; - evectors[2][0] = 0.0; evectors[2][1] = 0.0; evectors[2][2] = 1.0; - evalues[0] = 0.0; evalues[1] = 0.0; evalues[2] = 0.0; - double threshold = 0.0; - - for (int i = 0; i < 3; i++) - for (int j = i; j < 3; j++) - threshold += fabs(matrix[i][j]); - - if (threshold < 1.0e-200) return 0; - threshold *= 1.0e-12; - int state = 2; - bool changed[3] = {true, true, true}; - - int iteration = 0; - while (state > 0 && iteration < MAXJACOBI) { - for (int k = 0; k < 2; k++) { - for (int l = k+1; l < 3; l++) { - const double p = matrix[k][l]; - const double y = (matrix[l][l]-matrix[k][k])*0.5; - const double d = fabs(y)+sqrt(p*p + y*y); - const double r = sqrt(p*p + d*d); - const double c = r > threshold ? d/r : 1.0; - double s = r > threshold ? p/r : 0.0; - double t = d > threshold ? p*p/d : 0.0; - if (y < 0.0) { - s *= -1.0; - t *= -1.0; - } - matrix[k][l] = 0.0; - update_eigenvalue(matrix[k][k], changed[k], state, -t, threshold); - update_eigenvalue(matrix[l][l], changed[l], state, t, threshold); - for (int i = 0; i < k; i++) - rotate(matrix[i][k], matrix[i][l],c,s); - for (int i = k+1; i < l; i++) - rotate(matrix[k][i], matrix[i][l],c,s); - for (int i = l+1; i < 3; i++) - rotate(matrix[k][i], matrix[l][i],c,s); - for (int i = 0; i < 3; i++) - rotate(evectors[i][k], evectors[i][l],c,s); - } - } - iteration++; - } - - for (int i = 0; i < 3; i++) - evalues[i] = matrix[i][i]; + int i,j,k; + double tresh,theta,tau,t,sm,s,h,g,c,b[3],z[3]; - if (iteration == MAXJACOBI) return 1; - return 0; -} + for (i = 0; i < 3; i++) { + for (j = 0; j < 3; j++) evectors[i][j] = 0.0; + evectors[i][i] = 1.0; + } + for (i = 0; i < 3; i++) { + b[i] = evalues[i] = matrix[i][i]; + z[i] = 0.0; + } -int jacobi(double **matrix, double *evalues, double **evectors) -{ - evectors[0][0] = 1.0; evectors[0][1] = 0.0; evectors[0][2] = 0.0; - evectors[1][0] = 0.0; evectors[1][1] = 1.0; evectors[1][2] = 0.0; - evectors[2][0] = 0.0; evectors[2][1] = 0.0; evectors[2][2] = 1.0; - evalues[0] = 0.0; evalues[1] = 0.0; evalues[2] = 0.0; - double threshold = 0.0; - - for (int i = 0; i < 3; i++) - for (int j = i; j < 3; j++) - threshold += fabs(matrix[i][j]); - - if (threshold < 1.0e-200) return 0; - threshold *= 1.0e-12; - int state = 2; - bool changed[3] = {true, true, true}; - - int iteration = 0; - while (state > 0 && iteration < MAXJACOBI) { - for (int k = 0; k < 2; k++) { - for (int l = k+1; l < 3; l++) { - const double p = matrix[k][l]; - const double y = (matrix[l][l]-matrix[k][k])*0.5; - const double d = fabs(y)+sqrt(p*p + y*y); - const double r = sqrt(p*p + d*d); - const double c = r > threshold ? d/r : 1.0; - double s = r > threshold ? p/r : 0.0; - double t = d > threshold ? p*p/d : 0.0; - if (y < 0.0) { - s *= -1.0; - t *= -1.0; + for (int iter = 1; iter <= MAXJACOBI; iter++) { + sm = 0.0; + for (i = 0; i < 2; i++) + for (j = i+1; j < 3; j++) + sm += fabs(matrix[i][j]); + if (sm == 0.0) return 0; + + if (iter < 4) tresh = 0.2*sm/(3*3); + else tresh = 0.0; + + for (i = 0; i < 2; i++) { + for (j = i+1; j < 3; j++) { + g = 100.0*fabs(matrix[i][j]); + if (iter > 4 && fabs(evalues[i])+g == fabs(evalues[i]) + && fabs(evalues[j])+g == fabs(evalues[j])) + matrix[i][j] = 0.0; + else if (fabs(matrix[i][j]) > tresh) { + h = evalues[j]-evalues[i]; + if (fabs(h)+g == fabs(h)) t = (matrix[i][j])/h; + else { + theta = 0.5*h/(matrix[i][j]); + t = 1.0/(fabs(theta)+sqrt(1.0+theta*theta)); + if (theta < 0.0) t = -t; + } + c = 1.0/sqrt(1.0+t*t); + s = t*c; + tau = s/(1.0+c); + h = t*matrix[i][j]; + z[i] -= h; + z[j] += h; + evalues[i] -= h; + evalues[j] += h; + matrix[i][j] = 0.0; + for (k = 0; k < i; k++) rotate(matrix,k,i,k,j,s,tau); + for (k = i+1; k < j; k++) rotate(matrix,i,k,k,j,s,tau); + for (k = j+1; k < 3; k++) rotate(matrix,i,k,j,k,s,tau); + for (k = 0; k < 3; k++) rotate(evectors,k,i,k,j,s,tau); } - matrix[k][l] = 0.0; - update_eigenvalue(matrix[k][k], changed[k], state, -t, threshold); - update_eigenvalue(matrix[l][l], changed[l], state, t, threshold); - for (int i = 0; i < k; i++) - rotate(matrix[i][k], matrix[i][l],c,s); - for (int i = k+1; i < l; i++) - rotate(matrix[k][i], matrix[i][l],c,s); - for (int i = l+1; i < 3; i++) - rotate(matrix[k][i], matrix[l][i],c,s); - for (int i = 0; i < 3; i++) - rotate(evectors[i][k], evectors[i][l],c,s); } } - iteration++; - } - for (int i = 0; i < 3; i++) - evalues[i] = matrix[i][i]; - - if (iteration == MAXJACOBI) return 1; - return 0; -} - -/* ---------------------------------------------------------------------- - perform a single Jacobi rotation of Sij, Skl - ┌ ┐ ┌ ┐┌ ┐ - │Skl│ │c −s││Skl│ - │ │ := │ ││ │ - │Sij│ │s c││Sij│ - └ ┘ └ ┘└ ┘ -------------------------------------------------------------------------- */ - -void rotate(double &matrix_kl, double &matrix_ij, - const double c, const double s) -{ - const double tmp_kl = matrix_kl; - matrix_kl = c*matrix_kl - s*matrix_ij; - matrix_ij = s*tmp_kl + c*matrix_ij; + for (i = 0; i < 3; i++) { + evalues[i] = b[i] += z[i]; + z[i] = 0.0; + } + } + return 1; } /* ---------------------------------------------------------------------- - update eigenvalue and its status + perform a single Jacobi rotation ------------------------------------------------------------------------- */ -void update_eigenvalue(double &eigenvalue, bool &changed, int &state, - const double t, const double threshold) +void rotate(double matrix[3][3], int i, int j, int k, int l, + double s, double tau) { - eigenvalue += t; - - if (changed && fabs(t) < threshold) { - changed = false; - state--; - } else if (!changed && fabs(t) > threshold) { - changed = true; - state++; - } + double g = matrix[i][j]; + double h = matrix[k][l]; + matrix[i][j] = g-s*(h+g*tau); + matrix[k][l] = h+s*(g-h*tau); } /* ---------------------------------------------------------------------- diff --git a/src/math_extra.h b/src/math_extra.h index ad8105d271..09b135c641 100644 --- a/src/math_extra.h +++ b/src/math_extra.h @@ -74,14 +74,9 @@ namespace MathExtra { void write3(const double mat[3][3]); int mldivide3(const double mat[3][3], const double *vec, double *ans); - int jacobi(double matrix[3][3], double *evalues, double evectors[3][3]); - int jacobi(double **matrix, double *evalues, double **evectors); - void rotate(double &matrix_kl, double &matrix_ij, - const double c, const double s); - void update_eigenvalue(double &eigenvalue, bool &changed, int &state, - const double t, const double threshold); - + void rotate(double matrix[3][3], int i, int j, int k, int l, + double s, double tau); void richardson(double *q, double *m, double *w, double *moments, double dtq); void no_squish_rotate(int k, double *p, double *q, double *inertia, double dt); -- GitLab From 0bb9df76c2d132e66e79f482432ac2f33ec9781e Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Fri, 26 Jul 2019 09:58:18 -0400 Subject: [PATCH 336/469] correct shell profile variables to point to the installation directory --- cmake/etc/profile.d/lammps.csh.in | 4 ++-- cmake/etc/profile.d/lammps.sh.in | 4 ++-- 2 files changed, 4 insertions(+), 4 deletions(-) diff --git a/cmake/etc/profile.d/lammps.csh.in b/cmake/etc/profile.d/lammps.csh.in index 42f222d67c..1c13583914 100644 --- a/cmake/etc/profile.d/lammps.csh.in +++ b/cmake/etc/profile.d/lammps.csh.in @@ -1,4 +1,4 @@ # set environment for LAMMPS and msi2lmp executables # to find potential and force field files -if ( "$?LAMMPS_POTENTIALS" == 0 ) setenv LAMMPS_POTENTIALS @LAMMPS_POTENTIALS_DIR@ -if ( "$?MSI2LMP_LIBRARY" == 0 ) setenv MSI2LMP_LIBRARY @LAMMPS_FRC_FILES_DIR@ +if ( "$?LAMMPS_POTENTIALS" == 0 ) setenv LAMMPS_POTENTIALS @LAMMPS_INSTALL_DATADIR@/potentials +if ( "$?MSI2LMP_LIBRARY" == 0 ) setenv MSI2LMP_LIBRARY @LAMMPS_INSTALL_DATADIR@/frc_files diff --git a/cmake/etc/profile.d/lammps.sh.in b/cmake/etc/profile.d/lammps.sh.in index c1967cb5b2..1542a8982f 100644 --- a/cmake/etc/profile.d/lammps.sh.in +++ b/cmake/etc/profile.d/lammps.sh.in @@ -1,5 +1,5 @@ # set environment for LAMMPS and msi2lmp executables # to find potential and force field files -LAMMPS_POTENTIALS=${LAMMPS_POTENTIALS-@LAMMPS_POTENTIALS_DIR@} -MSI2LMP_LIBRARY=${MSI2LMP_LIBRARY-@LAMMPS_FRC_FILES_DIR@} +LAMMPS_POTENTIALS=${LAMMPS_POTENTIALS-@LAMMPS_INSTALL_DATADIR@/potentials} +MSI2LMP_LIBRARY=${MSI2LMP_LIBRARY-@LAMMPS_INSTALL_DATADIR@/frc_files} export LAMMPS_POTENTIALS MSI2LMP_LIBRARY -- GitLab From 010cb0edf304035fafd16b7870dce1a4b05fc7b9 Mon Sep 17 00:00:00 2001 From: "Ryan S. Elliott" Date: Fri, 26 Jul 2019 11:10:54 -0500 Subject: [PATCH 337/469] Add warning to cmake if PKG_KIM=ON but DOWNLOAD_KIM not set & KIM is not found This can be a scenario where the user has KIM installed but does not have the environment setup correctly to be found. The config. step should provide some warning of this. Otherwise, it is easy to miss the fact that KIM is being downloaded and built. --- cmake/Modules/Packages/KIM.cmake | 1 + 1 file changed, 1 insertion(+) diff --git a/cmake/Modules/Packages/KIM.cmake b/cmake/Modules/Packages/KIM.cmake index 1a9dcf83a4..5987ebbf0a 100644 --- a/cmake/Modules/Packages/KIM.cmake +++ b/cmake/Modules/Packages/KIM.cmake @@ -9,6 +9,7 @@ if(PKG_KIM) if(KIM-API_FOUND) set(DOWNLOAD_KIM_DEFAULT OFF) else() + message(WARNING "KIM-API package not found. We will download and build our own") set(DOWNLOAD_KIM_DEFAULT ON) endif() option(DOWNLOAD_KIM "Download KIM-API from OpenKIM instead of using an already installed one" ${DOWNLOAD_KIM_DEFAULT}) -- GitLab From 6a5902ec489b49386cf21b9d6fdc5487baa00f33 Mon Sep 17 00:00:00 2001 From: "Ryan S. Elliott" Date: Fri, 26 Jul 2019 11:14:46 -0500 Subject: [PATCH 338/469] Update kim_init to use KIM::Collections::GetItemType() A bit of a cleaner solution. Should be no visible change for users. --- src/KIM/kim_init.cpp | 106 +++++++++++++++++++++++++------------------ 1 file changed, 63 insertions(+), 43 deletions(-) diff --git a/src/KIM/kim_init.cpp b/src/KIM/kim_init.cpp index bae286aff6..954a4b0f2c 100644 --- a/src/KIM/kim_init.cpp +++ b/src/KIM/kim_init.cpp @@ -164,21 +164,39 @@ void KimInit::determine_model_type_and_units(char * model_name, KIM_TemperatureUnit temperatureUnit; KIM_TimeUnit timeUnit; int units_accepted; - KIM_Model * kim_MO; - - get_kim_unit_names(user_units, lengthUnit, energyUnit, - chargeUnit, temperatureUnit, timeUnit, error); - int kim_error = KIM_Model_Create(KIM_NUMBERING_zeroBased, - lengthUnit, - energyUnit, - chargeUnit, - temperatureUnit, - timeUnit, - model_name, - &units_accepted, - &kim_MO); - - if (!kim_error) { // model is an MO + KIM_Collections * kim_Coll; + KIM_CollectionItemType itemType; + + int kim_error = KIM_Collections_Create(&kim_Coll); + if (kim_error) { + error->all(FLERR,"Unable to access KIM Collections to find Model."); + } + + kim_error = KIM_Collections_GetItemType(kim_Coll, model_name, &itemType); + if (kim_error) { + error->all(FLERR,"KIM Model name not found."); + } + KIM_Collections_Destroy(&kim_Coll); + + if (KIM_CollectionItemType_Equal(itemType, + KIM_COLLECTION_ITEM_TYPE_portableModel)) + { + get_kim_unit_names(user_units, lengthUnit, energyUnit, + chargeUnit, temperatureUnit, timeUnit, error); + KIM_Model * kim_MO; + int kim_error = KIM_Model_Create(KIM_NUMBERING_zeroBased, + lengthUnit, + energyUnit, + chargeUnit, + temperatureUnit, + timeUnit, + model_name, + &units_accepted, + &kim_MO); + + if (kim_error) + error->all(FLERR,"Unable to load KIM Simulator Model."); + model_type = MO; KIM_Model_Destroy(&kim_MO); @@ -213,37 +231,39 @@ void KimInit::determine_model_type_and_units(char * model_name, error->all(FLERR,"KIM Model does not support the requested unit system"); } } + else if (KIM_CollectionItemType_Equal( + itemType, KIM_COLLECTION_ITEM_TYPE_simulatorModel)) { + KIM_SimulatorModel * kim_SM; + kim_error = KIM_SimulatorModel_Create(model_name, &kim_SM); + if (kim_error) + error->all(FLERR,"Unable to load KIM Simulator Model."); + model_type = SM; + + int sim_fields; + int sim_lines; + char const * sim_field; + char const * sim_value; + KIM_SimulatorModel_GetNumberOfSimulatorFields(kim_SM, &sim_fields); + KIM_SimulatorModel_CloseTemplateMap(kim_SM); + for (int i=0; i < sim_fields; ++i) { + KIM_SimulatorModel_GetSimulatorFieldMetadata( + kim_SM,i,&sim_lines,&sim_field); - KIM_SimulatorModel * kim_SM; - kim_error = KIM_SimulatorModel_Create(model_name, &kim_SM); - if (kim_error) - error->all(FLERR,"KIM model name not found"); - model_type = SM; - - int sim_fields; - int sim_lines; - char const * sim_field; - char const * sim_value; - KIM_SimulatorModel_GetNumberOfSimulatorFields(kim_SM, &sim_fields); - KIM_SimulatorModel_CloseTemplateMap(kim_SM); - for (int i=0; i < sim_fields; ++i) { - KIM_SimulatorModel_GetSimulatorFieldMetadata( - kim_SM,i,&sim_lines,&sim_field); - - if (0 == strcmp(sim_field,"units")) { - KIM_SimulatorModel_GetSimulatorFieldLine(kim_SM,i,0,&sim_value); - int len=strlen(sim_value)+1; - *model_units = new char[len]; strcpy(*model_units,sim_value); - break; + if (0 == strcmp(sim_field,"units")) { + KIM_SimulatorModel_GetSimulatorFieldLine(kim_SM,i,0,&sim_value); + int len=strlen(sim_value)+1; + *model_units = new char[len]; strcpy(*model_units,sim_value); + break; + } } - } - KIM_SimulatorModel_Destroy(&kim_SM); + KIM_SimulatorModel_Destroy(&kim_SM); - if ((! unit_conversion_mode) && (strcmp(*model_units, user_units)!=0)) { - std::string mesg("Incompatible units for KIM Simulator Model, " - "required units = "); - mesg += *model_units; - error->all(FLERR,mesg.c_str()); + if ((! unit_conversion_mode) && (strcmp(*model_units, user_units)!=0)) { + std::string mesg("Incompatible units for KIM Simulator Model, " + "required units = "); + mesg += *model_units; + error->all(FLERR,mesg.c_str()); + } } } -- GitLab From 17d6b317a77033dddd21cc3e259738b9359515bf Mon Sep 17 00:00:00 2001 From: Stan Moore Date: Fri, 26 Jul 2019 10:37:22 -0600 Subject: [PATCH 339/469] Better workaround for Spectrum MPI --- src/KOKKOS/kokkos.cpp | 42 +++++++++++++++++++++++++++++++----------- 1 file changed, 31 insertions(+), 11 deletions(-) diff --git a/src/KOKKOS/kokkos.cpp b/src/KOKKOS/kokkos.cpp index f6ab8f5916..6f6602b947 100644 --- a/src/KOKKOS/kokkos.cpp +++ b/src/KOKKOS/kokkos.cpp @@ -38,11 +38,7 @@ // OpenMPI supports detecting CUDA-aware MPI as of version 2.0.0 -// IBM Spectrum MPI looks like OpenMPI but defines MPIX_CUDA_AWARE_SUPPORT=0 -// even when CUDA-aware MPI is available, and also has a runtime option -// to turn CUDA-aware MPI on/off, so support is unknown - -#if (OPEN_MPI) && !(defined SPECTRUM_MPI) +#if (OPEN_MPI) #if (OMPI_MAJOR_VERSION >= 2) #include @@ -211,7 +207,30 @@ KokkosLMP::KokkosLMP(LAMMPS *lmp, int narg, char **arg) : Pointers(lmp) int nmpi = 0; MPI_Comm_size(world,&nmpi); if (nmpi > 0) { - if (have_cuda_aware == 0) { + + // Check for IBM Spectrum MPI + + int len; + char mpi_version[MPI_MAX_LIBRARY_VERSION_STRING]; + MPI_Get_library_version(mpi_version, &len); + if (strstr(&mpi_version[0], "Spectrum") != NULL) { + int gpu_flag = 0; + char* str; + if (str = getenv("OMPI_MCA_pml_pami_enable_cuda")) { + if(!(strcmp(str,"1") == 0)) { + cuda_aware_flag = 1; + gpu_flag = 1; + } + } + + if (!gpu_flag) { + if (me == 0) + error->warning(FLERR,"The Spectrum MPI '-gpu' flag is not set. Disabling CUDA-aware MPI"); + cuda_aware_flag = 0; + } + } + + if (cuda_aware_flag == 1 && have_cuda_aware == 0) { if (me == 0) error->warning(FLERR,"Turning off CUDA-aware MPI since it is not detected, " "use '-pk kokkos cuda/aware on' to override"); @@ -220,7 +239,12 @@ KokkosLMP::KokkosLMP(LAMMPS *lmp, int narg, char **arg) : Pointers(lmp) // MVAPICH2 #if (defined MPICH) && (defined MVAPICH2_VERSION) char* str; - if (!(str = getenv("MV2_ENABLE_CUDA") && (!(strcmp(str,"1") == 0))) { + int gpu_flag = 0; + if (str = getenv("MV2_ENABLE_CUDA") + if (!(strcmp(str,"1") == 0)) + gpu_flag = 1; + + if (!gpu_flag) { if (me == 0) error->warning(FLERR,"MVAPICH2 'MV2_ENABLE_CUDA' environment variable is not set. Disabling CUDA-aware MPI"); cuda_aware_flag = 0; @@ -230,10 +254,6 @@ KokkosLMP::KokkosLMP(LAMMPS *lmp, int narg, char **arg) : Pointers(lmp) if (me == 0) error->warning(FLERR,"Detected MPICH. Disabling CUDA-aware MPI"); cuda_aware_flag = 0; -#elif (defined SPECTRUM_MPI) - if (me == 0) - error->warning(FLERR,"Must use the '-gpu' flag with Spectrum MPI to enable " - "CUDA-aware MPI support"); #else if (me == 0) error->warning(FLERR,"Kokkos with CUDA assumes CUDA-aware MPI is available," -- GitLab From 0ba854b4ab28866387977419134c6afaea57e36d Mon Sep 17 00:00:00 2001 From: Stan Moore Date: Fri, 26 Jul 2019 11:23:46 -0600 Subject: [PATCH 340/469] Add MPI_Get_library_version to STUBS library --- src/STUBS/mpi.c | 17 +++++++++++++++++ src/STUBS/mpi.h | 2 ++ 2 files changed, 19 insertions(+) diff --git a/src/STUBS/mpi.c b/src/STUBS/mpi.c index af7a489bb1..c104a0ad7c 100644 --- a/src/STUBS/mpi.c +++ b/src/STUBS/mpi.c @@ -76,6 +76,23 @@ int MPI_Finalized(int *flag) /* ---------------------------------------------------------------------- */ +/* return "LAMMPS MPI STUBS" as name of the library */ + +int MPI_Get_library_version(char *verison, int *resultlen) +{ + const char string[] = "LAMMPS MPI STUBS"; + int len; + + if (!version || !resultlen) return MPI_ERR_ARG; + + len = strlen(string); + memcpy(version,string,len+1); + *resultlen = len; + return MPI_SUCCESS; +} + +/* ---------------------------------------------------------------------- */ + /* return "localhost" as name of the processor */ int MPI_Get_processor_name(char *name, int *resultlen) diff --git a/src/STUBS/mpi.h b/src/STUBS/mpi.h index 1eca1ec527..063dc542be 100644 --- a/src/STUBS/mpi.h +++ b/src/STUBS/mpi.h @@ -63,6 +63,7 @@ extern "C" { #define MPI_IN_PLACE NULL #define MPI_MAX_PROCESSOR_NAME 128 +#define MPI_MAX_LIBRARY_VERSION_STRING 128 typedef void MPI_User_function(void *invec, void *inoutvec, int *len, MPI_Datatype *datatype); @@ -79,6 +80,7 @@ typedef struct _MPI_Status MPI_Status; int MPI_Init(int *argc, char ***argv); int MPI_Initialized(int *flag); int MPI_Finalized(int *flag); +int MPI_Get_library_version(char *version, int *resultlen); int MPI_Get_processor_name(char *name, int *resultlen); int MPI_Get_version(int *major, int *minor); -- GitLab From e816f0e7a6e74e828a7d8cb9be1d16d2f01b211b Mon Sep 17 00:00:00 2001 From: Stan Moore Date: Fri, 26 Jul 2019 11:24:15 -0600 Subject: [PATCH 341/469] Cleanup of CUDA-aware MPI code --- src/KOKKOS/kokkos.cpp | 23 +++++++++-------------- src/MAKE/MACHINES/Makefile.lassen_kokkos | 2 +- 2 files changed, 10 insertions(+), 15 deletions(-) diff --git a/src/KOKKOS/kokkos.cpp b/src/KOKKOS/kokkos.cpp index 6f6602b947..18a4a3168f 100644 --- a/src/KOKKOS/kokkos.cpp +++ b/src/KOKKOS/kokkos.cpp @@ -214,20 +214,17 @@ KokkosLMP::KokkosLMP(LAMMPS *lmp, int narg, char **arg) : Pointers(lmp) char mpi_version[MPI_MAX_LIBRARY_VERSION_STRING]; MPI_Get_library_version(mpi_version, &len); if (strstr(&mpi_version[0], "Spectrum") != NULL) { - int gpu_flag = 0; + cuda_aware_flag = 0; char* str; - if (str = getenv("OMPI_MCA_pml_pami_enable_cuda")) { - if(!(strcmp(str,"1") == 0)) { + if (str = getenv("OMPI_MCA_pml_pami_enable_cuda")) + if((strcmp(str,"1") == 0)) { + have_cuda_aware = 1; cuda_aware_flag = 1; - gpu_flag = 1; } - } - if (!gpu_flag) { + if (!cuda_aware_flag) if (me == 0) error->warning(FLERR,"The Spectrum MPI '-gpu' flag is not set. Disabling CUDA-aware MPI"); - cuda_aware_flag = 0; - } } if (cuda_aware_flag == 1 && have_cuda_aware == 0) { @@ -239,16 +236,14 @@ KokkosLMP::KokkosLMP(LAMMPS *lmp, int narg, char **arg) : Pointers(lmp) // MVAPICH2 #if (defined MPICH) && (defined MVAPICH2_VERSION) char* str; - int gpu_flag = 0; + cuda_aware_flag = 0; if (str = getenv("MV2_ENABLE_CUDA") - if (!(strcmp(str,"1") == 0)) - gpu_flag = 1; + if ((strcmp(str,"1") == 0)) + cuda_aware_flag = 1; - if (!gpu_flag) { + if (!cuda_aware_flag) if (me == 0) error->warning(FLERR,"MVAPICH2 'MV2_ENABLE_CUDA' environment variable is not set. Disabling CUDA-aware MPI"); - cuda_aware_flag = 0; - } // pure MPICH or some unsupported MPICH derivative #elif (defined MPICH) && !(defined MVAPICH2_VERSION) if (me == 0) diff --git a/src/MAKE/MACHINES/Makefile.lassen_kokkos b/src/MAKE/MACHINES/Makefile.lassen_kokkos index 669e599e3c..23697bfea2 100644 --- a/src/MAKE/MACHINES/Makefile.lassen_kokkos +++ b/src/MAKE/MACHINES/Makefile.lassen_kokkos @@ -44,7 +44,7 @@ LMP_INC = -DLAMMPS_GZIP # PATH = path for MPI library # LIB = name of MPI library -MPI_INC = -DSPECTRUM_MPI -DMPICH_SKIP_MPICXX -DOMPI_SKIP_MPICXX=1 -I/usr/tce/packages/spectrum-mpi/spectrum-mpi-rolling-release-gcc-7.3.1/include +MPI_INC = -DMPICH_SKIP_MPICXX -DOMPI_SKIP_MPICXX=1 -I/usr/tce/packages/spectrum-mpi/spectrum-mpi-rolling-release-gcc-7.3.1/include MPI_PATH = MPI_LIB = -L/usr/tce/packages/spectrum-mpi/spectrum-mpi-rolling-release-gcc-7.3.1/lib -lmpi_ibm -- GitLab From f2dbe186ca2ce3846a8e7a9abc3c533acf791e1a Mon Sep 17 00:00:00 2001 From: Stan Moore Date: Fri, 26 Jul 2019 11:45:50 -0600 Subject: [PATCH 342/469] Fix typo --- src/STUBS/mpi.c | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/STUBS/mpi.c b/src/STUBS/mpi.c index c104a0ad7c..cd92750b9a 100644 --- a/src/STUBS/mpi.c +++ b/src/STUBS/mpi.c @@ -78,7 +78,7 @@ int MPI_Finalized(int *flag) /* return "LAMMPS MPI STUBS" as name of the library */ -int MPI_Get_library_version(char *verison, int *resultlen) +int MPI_Get_library_version(char *version, int *resultlen) { const char string[] = "LAMMPS MPI STUBS"; int len; -- GitLab From a5a1e27fb1d0692dcb7bf8b4a5bc25810a943719 Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Fri, 26 Jul 2019 15:42:34 -0400 Subject: [PATCH 343/469] refactor commands in the STUBS folder for 'make serial' and 'make clean-serial' make so that for the "serial" make target we not only automatically build the STUBS library, if it is missing, but also update its compilation when there are changes and remove it on the "clean-serial" target. --- src/Makefile | 7 +++++-- src/STUBS/Makefile | 4 ++-- 2 files changed, 7 insertions(+), 4 deletions(-) diff --git a/src/Makefile b/src/Makefile index d611adc404..5db09db65a 100644 --- a/src/Makefile +++ b/src/Makefile @@ -198,8 +198,8 @@ gitversion: # shlib = shared lib in Obj_shared_machine .DEFAULT: - @if [ $@ = "serial" -a ! -f STUBS/libmpi_stubs.a ]; \ - then $(MAKE) mpi-stubs; fi + @if [ $@ = "serial" ]; \ + then cd STUBS; $(MAKE); cd ..; fi @test -f MAKE/Makefile.$@ -o -f MAKE/OPTIONS/Makefile.$@ -o \ -f MAKE/MACHINES/Makefile.$@ -o -f MAKE/MINE/Makefile.$@ @if [ ! -d $(objdir) ]; then mkdir $(objdir); fi @@ -256,7 +256,10 @@ clean: clean-all: rm -rf Obj_* + clean-%: + @if [ $@ = "clean-serial" ]; \ + then cd STUBS; $(MAKE) clean; cd ..; fi rm -rf Obj_$(@:clean-%=%) Obj_shared_$(@:clean-%=%) # Create Makefile.list diff --git a/src/STUBS/Makefile b/src/STUBS/Makefile index 3649ddb383..3c3c3b46d9 100644 --- a/src/STUBS/Makefile +++ b/src/STUBS/Makefile @@ -28,7 +28,7 @@ ARCHFLAG = rs # Targets -lib: $(OBJ) +$(EXE): $(OBJ) $(ARCHIVE) $(ARCHFLAG) $(EXE) $(OBJ) clean: @@ -41,4 +41,4 @@ clean: # Individual dependencies -$(OBJ): $(INC) +$(OBJ): $(INC) ../version.h -- GitLab From a0e005f93c290ae12076546a2739bafee34d9e20 Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Fri, 26 Jul 2019 15:43:01 -0400 Subject: [PATCH 344/469] include LAMMPS version in STUBS library version string. --- src/STUBS/mpi.c | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/src/STUBS/mpi.c b/src/STUBS/mpi.c index cd92750b9a..f56d3616c8 100644 --- a/src/STUBS/mpi.c +++ b/src/STUBS/mpi.c @@ -20,6 +20,7 @@ #include #include #include +#include "../version.h" /* data structure for double/int */ @@ -80,7 +81,7 @@ int MPI_Finalized(int *flag) int MPI_Get_library_version(char *version, int *resultlen) { - const char string[] = "LAMMPS MPI STUBS"; + const char string[] = "LAMMPS MPI STUBS for LAMMPS version " LAMMPS_VERSION; int len; if (!version || !resultlen) return MPI_ERR_ARG; -- GitLab From 94126e5424a2516b1b6e448c8c9c4195fc38e629 Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Fri, 26 Jul 2019 15:44:10 -0400 Subject: [PATCH 345/469] use MPI_Get_library_version() API to provide a more detailed version info, not just the MPI standard level very chatty output (e.g. from MPICH) is truncated to the next line after 80 characters. --- src/info.cpp | 10 +++++++++- 1 file changed, 9 insertions(+), 1 deletion(-) diff --git a/src/info.cpp b/src/info.cpp index 25b9879408..6241877c82 100644 --- a/src/info.cpp +++ b/src/info.cpp @@ -353,11 +353,19 @@ void Info::command(int narg, char **arg) } if (flags & COMM) { - int major,minor; + int major,minor,len; + char version[MPI_MAX_LIBRARY_VERSION_STRING]; + MPI_Get_version(&major,&minor); + MPI_Get_library_version(version,&len); + if (len > 80) { + char *ptr = strchr(version+80,'\n'); + if (ptr) *ptr = '\0'; + } fprintf(out,"\nCommunication information:\n"); fprintf(out,"MPI library level: MPI v%d.%d\n",major,minor); + fprintf(out,"MPI version: %s\n",version); fprintf(out,"Comm style = %s, Comm layout = %s\n", commstyles[comm->style], commlayout[comm->layout]); fprintf(out,"Communicate velocities for ghost atoms = %s\n", -- GitLab From 0f10c55c1cbc693491c6d180807a7ca40f61b18a Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Fri, 26 Jul 2019 17:26:59 -0400 Subject: [PATCH 346/469] avoid recursive header inclusion --- lib/poems/system.h | 2 -- 1 file changed, 2 deletions(-) diff --git a/lib/poems/system.h b/lib/poems/system.h index 1b59395de7..573044ce33 100644 --- a/lib/poems/system.h +++ b/lib/poems/system.h @@ -15,7 +15,6 @@ * CONTACT: anderk5@rpi.edu * *_________________________________________________________________________*/ - #ifndef SYSTEM_H #define SYSTEM_H @@ -31,7 +30,6 @@ #include "workspace.h" #include "matrixfun.h" #include "onsolver.h" -#include "system.h" #include "inertialframe.h" #include "rigidbody.h" #include "revolutejoint.h" -- GitLab From 2fba3d027a6a41866890acfe2b1975aac822d2bc Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Sun, 28 Jul 2019 14:44:47 -0400 Subject: [PATCH 347/469] fix small formatting issue --- doc/src/compute_hexorder_atom.txt | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/doc/src/compute_hexorder_atom.txt b/doc/src/compute_hexorder_atom.txt index 082a3cad7a..3c58c3f4dd 100644 --- a/doc/src/compute_hexorder_atom.txt +++ b/doc/src/compute_hexorder_atom.txt @@ -65,7 +65,7 @@ In an isotropic liquid, local neighborhoods may still exhibit weak hexagonal symmetry, but because the orientational correlation decays quickly with distance, the value of phi will be different for different atoms, and so when {q}6 is averaged over all the atoms -in the system, \|<{q}6>\| << 1. +in the system, |<{q}6>| << 1. The value of {qn} is set to zero for atoms not in the specified compute group, as well as for atoms that have less than -- GitLab From a0abd270b53f58dd99b702ee1fa2691960ee3738 Mon Sep 17 00:00:00 2001 From: "Ryan S. Elliott" Date: Mon, 29 Jul 2019 11:41:01 -0500 Subject: [PATCH 348/469] kim_query check for empty query result --- src/KIM/kim_query.cpp | 14 ++++++++++---- 1 file changed, 10 insertions(+), 4 deletions(-) diff --git a/src/KIM/kim_query.cpp b/src/KIM/kim_query.cpp index 6688ed6690..e81e8c5d18 100644 --- a/src/KIM/kim_query.cpp +++ b/src/KIM/kim_query.cpp @@ -130,11 +130,13 @@ void KimQuery::command(int narg, char **arg) // as the first element, and then the error message // that was returned by the web server + char errmsg[1024]; if (0 == strlen(value)) { - char errmsg[1024]; - sprintf(errmsg,"OpenKIM query failed: %s",value+1); - error->all(FLERR,errmsg); + error->all(FLERR,errmsg); + } else if (0 == strcmp(value,"EMPTY")) { + sprintf(errmsg,"OpenKIM query returned no results"); + error->all(FLERR,errmsg); } char **varcmd = new char*[3]; @@ -269,7 +271,11 @@ char *do_query(char *qfunction, char * model_name, int narg, char **arg, if (value[len] == ']') { retval = new char[len]; value[len] = '\0'; - strcpy(retval,value+1); + if (0 == strcmp(value+1, "")) { + strcpy(retval,"EMPTY"); + } + else + strcpy(retval,value+1); } else { retval = new char[len+2]; retval[0] = '\0'; -- GitLab From 5307558727d3b7ea07a3a664aa9e550713547239 Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Mon, 29 Jul 2019 13:34:04 -0400 Subject: [PATCH 349/469] need to install some base C++ headers for C++ library use --- cmake/CMakeLists.txt | 34 ++++++++++++++++++++++++++++++++++ 1 file changed, 34 insertions(+) diff --git a/cmake/CMakeLists.txt b/cmake/CMakeLists.txt index 7cd7b62c91..eee595df7e 100644 --- a/cmake/CMakeLists.txt +++ b/cmake/CMakeLists.txt @@ -497,10 +497,44 @@ if(BUILD_LIB) if(LAMMPS_DEPS) add_dependencies(lammps ${LAMMPS_DEPS}) endif() + set(LAMMPS_CXX_HEADERS + angle.h + atom.h + bond.h + citeme.h + comm.h + compute.h + dihedral.h + domain.h + error.h + fix.h + force.h + group.h + improper.h + input.h + kspace.h + lammps.h + lattice.h + lmppython.h + memory.h + modify.h + neighbor.h + neigh_list.h + output.h + pair.h + pointers.h + region.h + timer.h + universe.h + update.h + variable.h) + list(TRANSFORM LAMMPS_CXX_HEADERS PREPEND ${LAMMPS_SOURCE_DIR}/) + set_target_properties(lammps PROPERTIES OUTPUT_NAME lammps${LAMMPS_LIB_SUFFIX}) set_target_properties(lammps PROPERTIES SOVERSION ${SOVERSION}) install(TARGETS lammps LIBRARY DESTINATION ${CMAKE_INSTALL_LIBDIR} ARCHIVE DESTINATION ${CMAKE_INSTALL_LIBDIR}) install(FILES ${LAMMPS_SOURCE_DIR}/library.h DESTINATION ${CMAKE_INSTALL_INCLUDEDIR}/lammps) + install(FILES ${LAMMPS_CXX_HEADERS} DESTINATION ${CMAKE_INSTALL_INCLUDEDIR}/lammps) configure_file(pkgconfig/liblammps.pc.in ${CMAKE_CURRENT_BINARY_DIR}/liblammps${LAMMPS_LIB_SUFFIX}.pc @ONLY) install(FILES ${CMAKE_CURRENT_BINARY_DIR}/liblammps${LAMMPS_LIB_SUFFIX}.pc DESTINATION ${CMAKE_INSTALL_LIBDIR}/pkgconfig) configure_file(FindLAMMPS.cmake.in ${CMAKE_CURRENT_BINARY_DIR}/FindLAMMPS${LAMMPS_LIB_SUFFIX}.cmake @ONLY) -- GitLab From 96e0b03ede16ae551fde9fce4c2657e9d972181f Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Mon, 29 Jul 2019 13:38:38 -0400 Subject: [PATCH 350/469] .frc files only need to be installed if msi2lmp is built --- cmake/CMakeLists.txt | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/cmake/CMakeLists.txt b/cmake/CMakeLists.txt index eee595df7e..eaa699106c 100644 --- a/cmake/CMakeLists.txt +++ b/cmake/CMakeLists.txt @@ -587,7 +587,9 @@ include(Documentation) ############################################################################### set(LAMMPS_INSTALL_DATADIR ${CMAKE_INSTALL_FULL_DATADIR}/lammps) install(DIRECTORY ${LAMMPS_POTENTIALS_DIR} DESTINATION ${LAMMPS_INSTALL_DATADIR}) -install(DIRECTORY ${LAMMPS_TOOLS_DIR}/msi2lmp/frc_files DESTINATION ${LAMMPS_INSTALL_DATADIR}) +if(BUILD_TOOLS) + install(DIRECTORY ${LAMMPS_TOOLS_DIR}/msi2lmp/frc_files DESTINATION ${LAMMPS_INSTALL_DATADIR}) +endif() configure_file(etc/profile.d/lammps.sh.in ${CMAKE_BINARY_DIR}/etc/profile.d/lammps.sh @ONLY) configure_file(etc/profile.d/lammps.csh.in ${CMAKE_BINARY_DIR}/etc/profile.d/lammps.csh @ONLY) -- GitLab From 6a1b61637bb7eaded180ef01167c7e3295af1ce6 Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Mon, 29 Jul 2019 13:43:06 -0400 Subject: [PATCH 351/469] provide some more details about 'make install' with CMake --- doc/src/Build_cmake.txt | 9 +++++++-- 1 file changed, 7 insertions(+), 2 deletions(-) diff --git a/doc/src/Build_cmake.txt b/doc/src/Build_cmake.txt index a16ba995a8..8106b008bb 100644 --- a/doc/src/Build_cmake.txt +++ b/doc/src/Build_cmake.txt @@ -52,11 +52,16 @@ LAMMPS or need to re-compile LAMMPS repeatedly, installation of the ccache (= Compiler Cache) software may speed up repeated compilation even more. -After compilation, you can optionally copy the LAMMPS executable and -library into your system folders (by default under $HOME/.local) with: +After compilation, you may optionally install the LAMMPS executable into +your system with: make install # optional, copy LAMMPS executable & library elsewhere :pre +This will install the lammps executable and library (if requested), some +tools (if configured) and additional files like library API headers, manpages, +potential files. The location of the installation tree is set by the CMake +variable "CMAKE_INSTALL_PREFIX" which defaults to $\{HOME\}/.local + :line There are 3 variants of CMake: a command-line version (cmake), a text mode -- GitLab From e0b20c4fd404cff90e2a6335862b1dcca69e22b3 Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Mon, 29 Jul 2019 15:23:23 -0400 Subject: [PATCH 352/469] add false positive --- doc/src/Build_cmake.txt | 7 ++++--- doc/utils/sphinx-config/false_positives.txt | 1 + 2 files changed, 5 insertions(+), 3 deletions(-) diff --git a/doc/src/Build_cmake.txt b/doc/src/Build_cmake.txt index 8106b008bb..6eb23b2bb5 100644 --- a/doc/src/Build_cmake.txt +++ b/doc/src/Build_cmake.txt @@ -58,9 +58,10 @@ your system with: make install # optional, copy LAMMPS executable & library elsewhere :pre This will install the lammps executable and library (if requested), some -tools (if configured) and additional files like library API headers, manpages, -potential files. The location of the installation tree is set by the CMake -variable "CMAKE_INSTALL_PREFIX" which defaults to $\{HOME\}/.local +tools (if configured) and additional files like library API headers, +manpages, potential and force field files. The location of the installation +tree is set by the CMake variable "CMAKE_INSTALL_PREFIX" which defaults +to $\{HOME\}/.local :line diff --git a/doc/utils/sphinx-config/false_positives.txt b/doc/utils/sphinx-config/false_positives.txt index da5c869075..e6fdaf826b 100644 --- a/doc/utils/sphinx-config/false_positives.txt +++ b/doc/utils/sphinx-config/false_positives.txt @@ -1539,6 +1539,7 @@ Mandelli Manh manifoldforce Manolopoulos +manpages manybody MANYBODY Maras -- GitLab From 2afc498a2b595157ef63c50894c03e5106b57dbc Mon Sep 17 00:00:00 2001 From: "Ryan S. Elliott" Date: Mon, 29 Jul 2019 15:04:15 -0500 Subject: [PATCH 353/469] Add logging to kim_query (compile error at moment) --- src/KIM/kim_query.cpp | 15 ++++++++++++++- src/KIM/kim_query.h | 4 ++++ 2 files changed, 18 insertions(+), 1 deletion(-) diff --git a/src/KIM/kim_query.cpp b/src/KIM/kim_query.cpp index e81e8c5d18..e2bee158ed 100644 --- a/src/KIM/kim_query.cpp +++ b/src/KIM/kim_query.cpp @@ -154,14 +154,16 @@ void KimQuery::command(int narg, char **arg) varcmd[0] = const_cast(splitname.str().c_str()); varcmd[2] = const_cast(token.c_str()); input->variable->set(3,varcmd); + echo_var_assign(splitname.str(), varcmd[2]); } } else { varcmd[0] = varname; varcmd[1] = (char *) "string"; varcmd[2] = value; - input->variable->set(3,varcmd); + + echo_var_assign(varname, value); } delete[] varcmd; @@ -297,3 +299,14 @@ char *do_query(char *qfunction, char * model_name, int narg, char **arg, return retval; } #endif + +void KimQuery::echo_var_assign(std::string const & name, + std::string const & value) const +{ + if (comm->me == 0) { + std::string mesg; + mesg = name + " = " + value + "\n"; + if ((screen) && (input->echo_screen)) fputs(mesg.c_str(),screen); + if ((logfile) && (input->echo_log)) fputs(mesg.c_str(),logfile); + } +} diff --git a/src/KIM/kim_query.h b/src/KIM/kim_query.h index b5433def79..9cffc9ad28 100644 --- a/src/KIM/kim_query.h +++ b/src/KIM/kim_query.h @@ -64,6 +64,7 @@ CommandStyle(kim_query,KimQuery) #define LMP_KIM_QUERY_H #include "pointers.h" +#include namespace LAMMPS_NS { @@ -71,6 +72,9 @@ class KimQuery : protected Pointers { public: KimQuery(class LAMMPS *lmp) : Pointers(lmp) {}; void command(int, char **); + private: + void echo_var_assign(std::string const & name, std::string const & value) + const; }; } -- GitLab From 0beb39c1af9cf93979452cdd84722c3118cbebfb Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Mon, 29 Jul 2019 15:59:42 -0400 Subject: [PATCH 354/469] fully integrate compute gyration/shape into doc build system --- doc/src/Commands_compute.txt | 1 + doc/src/Eqs/compute_shape_parameters.jpg | Bin 0 -> 7007 bytes doc/src/Eqs/compute_shape_parameters.tex | 3 +- doc/src/Errors_messages.txt | 8 ++++ doc/src/compute.txt | 1 + doc/src/compute_gyration.txt | 3 +- doc/src/compute_gyration_shape.txt | 48 ++++++++++---------- doc/src/computes.txt | 1 + doc/src/lammps.book | 1 + doc/utils/sphinx-config/false_positives.txt | 6 +++ 10 files changed, 46 insertions(+), 26 deletions(-) create mode 100644 doc/src/Eqs/compute_shape_parameters.jpg diff --git a/doc/src/Commands_compute.txt b/doc/src/Commands_compute.txt index f566702609..3413116e80 100644 --- a/doc/src/Commands_compute.txt +++ b/doc/src/Commands_compute.txt @@ -66,6 +66,7 @@ KOKKOS, o = USER-OMP, t = OPT. 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zyIroV)jjgz#_hWt#~zr)c&u7+hErbe?w_9dX9CzGU5l?*ty`G?=&iO_|H%ryph(qI zbN_{87^^uRuuDF+AbHv2m)&yWSC?NealNw4lb0 ztd(ou@4ziv%cQ5K&kdOPiqZ63#E*XGc!_Kyv#rZHZr!?~ExqKR!s$6Ozx&VaI;s0` zMzfCLPFZdZ)5gT){QnG`eOqToZ2LRwx@1rCnw<-HSKB(B4(wgBanJT$y?)m+RQVXc zoG?9IfVRy-B~r_wAkRcjel@N2ccH<=29uwHoR?lK9v{ zQaj(z^S}4#eWOzT54U}{4zmaD-myRM-;qn3m;bW}+Z6>K=K^)FPS1CZ{NtIvwszYq z^KDHYcIWz7g4h(Ewpl96gzGOpsJ8iIa?nTB723<9G7ozRecL(1d+(`VEx&huJ;%?s zYW6{8s+(P6>fMbJjc0nHcm+%BOr+(96R8H{YBP^q8o}*}@}n r Date: Mon, 29 Jul 2019 16:16:24 -0400 Subject: [PATCH 355/469] cleanup of compute gyration/shape code. - use MathSpecial::square(x) instead of pow(x,2) for improved precision and handling of small and negative numbers - remove unused include statements - no need to refetch the compute in every step. during init() is sufficient --- src/USER-MISC/compute_gyration_shape.cpp | 47 +++++++++++------------- src/USER-MISC/compute_gyration_shape.h | 7 ++++ 2 files changed, 29 insertions(+), 25 deletions(-) diff --git a/src/USER-MISC/compute_gyration_shape.cpp b/src/USER-MISC/compute_gyration_shape.cpp index 0e566e671f..a0ee6089b7 100644 --- a/src/USER-MISC/compute_gyration_shape.cpp +++ b/src/USER-MISC/compute_gyration_shape.cpp @@ -16,17 +16,14 @@ * ------------------------------------------------------------------------- */ +#include "compute_gyration_shape.h" #include #include -#include "compute_gyration_shape.h" -#include "math_extra.h" -#include "update.h" -#include "atom.h" -#include "group.h" -#include "domain.h" #include "error.h" +#include "math_extra.h" +#include "math_special.h" #include "modify.h" -#include "compute.h" +#include "update.h" using namespace LAMMPS_NS; @@ -67,27 +64,26 @@ void ComputeGyrationShape::init() // check that the compute gyration command exist int icompute = modify->find_compute(id_gyration); if (icompute < 0) - error->all(FLERR,"Compute gyration does not exist for compute gyration/shape"); + error->all(FLERR,"Compute gyration ID does not exist for " + "compute gyration/shape"); // check the id_gyration corresponds really to a compute gyration command c_gyration = (Compute *) modify->compute[icompute]; if (strcmp(c_gyration->style,"gyration") != 0) - error->all(FLERR,"Compute gyration/shape does not use gyration compute"); + error->all(FLERR,"Compute gyration compute ID does not point to " + "gyration compute for compute gyration/shape"); } /* ---------------------------------------------------------------------- - compute shape parameters based on the eigenvalues of the gyration tensor of group of atoms + compute shape parameters based on the eigenvalues of the + gyration tensor of group of atoms ------------------------------------------------------------------------- */ void ComputeGyrationShape::compute_vector() { invoked_vector = update->ntimestep; - - // get the gyration tensor from the compute gyration - int icompute = modify->find_compute(id_gyration); - Compute *compute = modify->compute[icompute]; - compute->compute_vector(); - double *gyration_tensor = compute->vector; + c_gyration->compute_vector(); + double *gyration_tensor = c_gyration->vector; // call the function for the calculation of the eigenvalues double ione[3][3], evalues[3], evectors[3][3]; @@ -100,7 +96,8 @@ void ComputeGyrationShape::compute_vector() ione[0][2] = ione[2][0] = gyration_tensor[5]; int ierror = MathExtra::jacobi(ione,evalues,evectors); - if (ierror) error->all(FLERR, "Insufficient Jacobi rotations for gyration/shape"); + if (ierror) error->all(FLERR, "Insufficient Jacobi rotations " + "for gyration/shape"); // sort the eigenvalues according to their size with bubble sort double t; @@ -115,19 +112,19 @@ void ComputeGyrationShape::compute_vector() } // compute the shape parameters of the gyration tensor - double sq_eigen_x = pow(evalues[0], 2); - double sq_eigen_y = pow(evalues[1], 2); - double sq_eigen_z = pow(evalues[2], 2); + double sq_eigen_x = MathSpecial::square(evalues[0]); + double sq_eigen_y = MathSpecial::square(evalues[1]); + double sq_eigen_z = MathSpecial::square(evalues[2]); - double nominator = pow(sq_eigen_x, 2) + pow(sq_eigen_y, 2) + pow(sq_eigen_z, 2); - double denominator = pow(sq_eigen_x+sq_eigen_y+sq_eigen_z, 2); + double nominator = MathSpecial::square(sq_eigen_x) + + MathSpecial::square(sq_eigen_y) + + MathSpecial::square(sq_eigen_z); + double denominator = MathSpecial::square(sq_eigen_x+sq_eigen_y+sq_eigen_z); vector[0] = evalues[0]; vector[1] = evalues[1]; vector[2] = evalues[2]; vector[3] = sq_eigen_z - 0.5*(sq_eigen_x + sq_eigen_y); vector[4] = sq_eigen_y - sq_eigen_x; - vector[5] = 0.5*(3*nominator/denominator -1); - + vector[5] = 0.5*(3*nominator/denominator - 1.0); } - diff --git a/src/USER-MISC/compute_gyration_shape.h b/src/USER-MISC/compute_gyration_shape.h index 1b39dd2e38..1d58f000dd 100644 --- a/src/USER-MISC/compute_gyration_shape.h +++ b/src/USER-MISC/compute_gyration_shape.h @@ -50,4 +50,11 @@ Self-explanatory. Check the input script syntax and compare to the documentation for the command. You can use -echo screen as a command-line option when running LAMMPS to see the offending line. +E: Compute gyration ID does not exist for compute gyration/shape + +Self-explanatory. Provide a valid compute ID + +E: Compute gyration/shape compute ID does not point to a gyration compute + +Self-explanatory. Provide an ID of a compute gyration command. */ -- GitLab From 0f059c56f946b9de88a869401370e6e874fd808c Mon Sep 17 00:00:00 2001 From: "Ryan S. Elliott" Date: Mon, 29 Jul 2019 15:30:46 -0500 Subject: [PATCH 356/469] Add details about installing models to KIM example input --- examples/kim/in.kim-pm-query.melt | 9 +++++++++ examples/kim/in.kim-pm.melt | 9 +++++++++ examples/kim/in.kim-sm.melt | 11 ++++++++++- 3 files changed, 28 insertions(+), 1 deletion(-) diff --git a/examples/kim/in.kim-pm-query.melt b/examples/kim/in.kim-pm-query.melt index d39dd2d464..fa04d90436 100644 --- a/examples/kim/in.kim-pm-query.melt +++ b/examples/kim/in.kim-pm-query.melt @@ -4,6 +4,15 @@ # SW_StillingerWeber_1985_Si__MO_405512056662_005 # is installed. This can be done with the command # kim-api-collections-management install user SW_StillingerWeber_1985_Si__MO_405512056662_005 +# If this command does not work, you may need to setup your PATH to find the utility. +# If you installed the kim-api using the LAMMPS CMake build, you can do the following +# (where the current working directory is assumed to be the LAMMPS build directory) +# source ./kim_build-prefix/bin/kim-api-activate +# If you installed the kim-api using the LAMMPS Make build, you can do the following +# (where the current working directory is assumed to be the LAMMPS src directory) +# source ../lib/kim/installed-kim-api-X.Y.Z/bin/kim-api-activate +# (where you should relplace X.Y.Z with the appropriate kim-api version number). +# # Or, see https://openkim.org/doc/obtaining-models for alternative options. # diff --git a/examples/kim/in.kim-pm.melt b/examples/kim/in.kim-pm.melt index 999cf77180..9959a66793 100644 --- a/examples/kim/in.kim-pm.melt +++ b/examples/kim/in.kim-pm.melt @@ -4,6 +4,15 @@ # SW_StillingerWeber_1985_Si__MO_405512056662_005 # is installed. This can be done with the command # kim-api-collections-management install user SW_StillingerWeber_1985_Si__MO_405512056662_005 +# If this command does not work, you may need to setup your PATH to find the utility. +# If you installed the kim-api using the LAMMPS CMake build, you can do the following +# (where the current working directory is assumed to be the LAMMPS build directory) +# source ./kim_build-prefix/bin/kim-api-activate +# If you installed the kim-api using the LAMMPS Make build, you can do the following +# (where the current working directory is assumed to be the LAMMPS src directory) +# source ../lib/kim/installed-kim-api-X.Y.Z/bin/kim-api-activate +# (where you should relplace X.Y.Z with the appropriate kim-api version number). +# # Or, see https://openkim.org/doc/obtaining-models for alternative options. # diff --git a/examples/kim/in.kim-sm.melt b/examples/kim/in.kim-sm.melt index 32f8c6170f..0ee8e9a857 100644 --- a/examples/kim/in.kim-sm.melt +++ b/examples/kim/in.kim-sm.melt @@ -4,7 +4,16 @@ # Sim_LAMMPS_ReaxFF_StrachanVanDuinChakraborty_2003_CHNO__SM_107643900657_000 # is installed. This can be done with the command # kim-api-collections-management install user Sim_LAMMPS_ReaxFF_StrachanVanDuinChakraborty_2003_CHNO__SM_107643900657_000 -# Or, see https://openkim.org/doc/obtaining-models for alternative options. +# If this command does not work, you may need to setup your PATH to find the utility. +# If you installed the kim-api using the LAMMPS CMake build, you can do the following +# (where the current working directory is assumed to be the LAMMPS build directory) +# source ./kim_build-prefix/bin/kim-api-activate +# If you installed the kim-api using the LAMMPS Make build, you can do the following +# (where the current working directory is assumed to be the LAMMPS src directory) +# source ../lib/kim/installed-kim-api-X.Y.Z/bin/kim-api-activate +# (where you should relplace X.Y.Z with the appropriate kim-api version number). +# +# See https://openkim.org/doc/obtaining-models for alternative options. # variable x index 1 -- GitLab From ea4107c4b433082aad60b811588e8e53fc1c1651 Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Mon, 29 Jul 2019 16:36:57 -0400 Subject: [PATCH 357/469] add write_echo() method to Input class for logging implicit commands where the echo command would send explicit ones --- src/KIM/kim_init.cpp | 14 ++++---------- src/KIM/kim_interactions.cpp | 3 +-- src/KIM/kim_query.cpp | 3 +-- src/input.cpp | 11 +++++++++++ src/input.h | 5 ++--- 5 files changed, 19 insertions(+), 17 deletions(-) diff --git a/src/KIM/kim_init.cpp b/src/KIM/kim_init.cpp index 954a4b0f2c..a4272caa01 100644 --- a/src/KIM/kim_init.cpp +++ b/src/KIM/kim_init.cpp @@ -377,8 +377,7 @@ void KimInit::kim_init_log_delimiter(std::string const begin_end) const mesg = "#=== END kim-init ============================================\n\n"; - if ((screen) && (input->echo_screen)) fputs(mesg.c_str(),screen); - if ((logfile) && (input->echo_log)) fputs(mesg.c_str(),logfile); + input->write_echo(mesg.c_str()); } } @@ -425,8 +424,7 @@ void KimInit::do_variables(char *user_units, char *model_units) mesg += " to "; mesg += to; mesg += ":\n"; - if ((screen) && (input->echo_screen)) fputs(mesg.c_str(),screen); - if ((logfile) && (input->echo_log)) fputs(mesg.c_str(),logfile); + input->write_echo(mesg.c_str()); } for (int i = 0; i < nunits; i++) { @@ -455,14 +453,10 @@ void KimInit::do_variables(char *user_units, char *model_units) << " internal " << std::setprecision(12) << std::scientific << conversion_factor << std::endl; - if ((screen) && (input->echo_screen)) fputs(mesg.str().c_str(),screen); - if ((logfile) && (input->echo_log)) fputs(mesg.str().c_str(),logfile); + input->write_echo(mesg.str().c_str()); } } - if (comm->me == 0) { - if ((screen) && (input->echo_screen)) fputs("#\n",screen); - if ((logfile) && (input->echo_log)) fputs("#\n",logfile); - } + if (comm->me == 0) input->write_echo("#\n"); } /* ---------------------------------------------------------------------- */ diff --git a/src/KIM/kim_interactions.cpp b/src/KIM/kim_interactions.cpp index 449b6bcb13..7dbe523033 100644 --- a/src/KIM/kim_interactions.cpp +++ b/src/KIM/kim_interactions.cpp @@ -106,8 +106,7 @@ void KimInteractions::kim_interactions_log_delimiter( mesg = "#=== END kim_interactions ====================================\n\n"; - if ((screen) && (input->echo_screen)) fputs(mesg.c_str(),screen); - if ((logfile) && (input->echo_log)) fputs(mesg.c_str(),logfile); + input->write_echo(mesg.c_str()); } } diff --git a/src/KIM/kim_query.cpp b/src/KIM/kim_query.cpp index e2bee158ed..1e699e74b0 100644 --- a/src/KIM/kim_query.cpp +++ b/src/KIM/kim_query.cpp @@ -306,7 +306,6 @@ void KimQuery::echo_var_assign(std::string const & name, if (comm->me == 0) { std::string mesg; mesg = name + " = " + value + "\n"; - if ((screen) && (input->echo_screen)) fputs(mesg.c_str(),screen); - if ((logfile) && (input->echo_log)) fputs(mesg.c_str(),logfile); + input->write_echo(mesg.c_str()); } } diff --git a/src/input.cpp b/src/input.cpp index 08e3655437..8bf4fc12e1 100644 --- a/src/input.cpp +++ b/src/input.cpp @@ -314,6 +314,17 @@ char *Input::one(const char *single) return command; } +/* ---------------------------------------------------------------------- + Send text to active echo file pointers +------------------------------------------------------------------------- */ +void Input::write_echo(const char *txt) +{ + if (me == 0) { + if (echo_screen && screen) fputs(txt,screen); + if (echo_log && logfile) fputs(txt,logfile); + } +} + /* ---------------------------------------------------------------------- parse copy of command line by inserting string terminators strip comment = all chars from # on diff --git a/src/input.h b/src/input.h index dc5a2670d4..b86982cb39 100644 --- a/src/input.h +++ b/src/input.h @@ -25,8 +25,6 @@ class Input : protected Pointers { friend class Info; friend class Error; friend class Deprecated; - friend class KimInit; - friend class KimInteractions; public: int narg; // # of command args @@ -41,7 +39,8 @@ class Input : protected Pointers { void substitute(char *&, char *&, int &, int &, int); // substitute for variables in a string int expand_args(int, char **, int, char **&); // expand args due to wildcard - + void write_echo(const char *); // send text to active echo file pointers + protected: char *command; // ptr to current command int echo_screen; // 0 = no, 1 = yes -- GitLab From 2ffc35297bfc7904051cbc18ec4c6ea7d6599d86 Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Mon, 29 Jul 2019 16:57:34 -0400 Subject: [PATCH 358/469] make kim_query log of variable setting look more like other KIM log messages this adds BEGIN/END marker comments and echoes the actual command line that the kim_query command implicitly executes --- src/KIM/kim_query.cpp | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/src/KIM/kim_query.cpp b/src/KIM/kim_query.cpp index 1e699e74b0..cfb26c4d5e 100644 --- a/src/KIM/kim_query.cpp +++ b/src/KIM/kim_query.cpp @@ -305,7 +305,9 @@ void KimQuery::echo_var_assign(std::string const & name, { if (comm->me == 0) { std::string mesg; - mesg = name + " = " + value + "\n"; + mesg = "#=== BEGIN kim_query =========================================\n"; + mesg += "variable " + name + " string " + value + "\n"; + mesg += "#=== END kim_query ===========================================\n"; input->write_echo(mesg.c_str()); } } -- GitLab From c03e9c9711b5eed9ba3e2c589c18af4b5728e7e7 Mon Sep 17 00:00:00 2001 From: "Ryan S. Elliott" Date: Mon, 29 Jul 2019 16:11:08 -0500 Subject: [PATCH 359/469] Adjust write_echo() within kim_query --- src/KIM/kim_query.cpp | 23 +++++++++++++++++++++-- src/KIM/kim_query.h | 1 + 2 files changed, 22 insertions(+), 2 deletions(-) diff --git a/src/KIM/kim_query.cpp b/src/KIM/kim_query.cpp index cfb26c4d5e..e35afa9a8b 100644 --- a/src/KIM/kim_query.cpp +++ b/src/KIM/kim_query.cpp @@ -139,6 +139,7 @@ void KimQuery::command(int narg, char **arg) error->all(FLERR,errmsg); } + kim_query_log_delimiter("begin"); char **varcmd = new char*[3]; if (split) { int counter = 1; @@ -165,6 +166,7 @@ void KimQuery::command(int narg, char **arg) echo_var_assign(varname, value); } + kim_query_log_delimiter("end"); delete[] varcmd; delete[] value; @@ -300,14 +302,31 @@ char *do_query(char *qfunction, char * model_name, int narg, char **arg, } #endif +/* ---------------------------------------------------------------------- */ + +void KimQuery::kim_query_log_delimiter(std::string const begin_end) const +{ + if (comm->me == 0) { + std::string mesg; + if (begin_end == "begin") + mesg = + "#=== BEGIN kim-query =========================================\n"; + else if (begin_end == "end") + mesg = + "#=== END kim-query ===========================================\n\n"; + + input->write_echo(mesg.c_str()); + } +} + +/* ---------------------------------------------------------------------- */ + void KimQuery::echo_var_assign(std::string const & name, std::string const & value) const { if (comm->me == 0) { std::string mesg; - mesg = "#=== BEGIN kim_query =========================================\n"; mesg += "variable " + name + " string " + value + "\n"; - mesg += "#=== END kim_query ===========================================\n"; input->write_echo(mesg.c_str()); } } diff --git a/src/KIM/kim_query.h b/src/KIM/kim_query.h index 9cffc9ad28..33a37f5131 100644 --- a/src/KIM/kim_query.h +++ b/src/KIM/kim_query.h @@ -73,6 +73,7 @@ class KimQuery : protected Pointers { KimQuery(class LAMMPS *lmp) : Pointers(lmp) {}; void command(int, char **); private: + void kim_query_log_delimiter(std::string const begin_end) const; void echo_var_assign(std::string const & name, std::string const & value) const; }; -- GitLab From 180c90acfbf412e7e2156f533d08441055daa129 Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Mon, 29 Jul 2019 20:21:31 -0400 Subject: [PATCH 360/469] use utils::strmatch() to more safely detect gravity fix --- src/GRANULAR/fix_pour.cpp | 9 ++++----- 1 file changed, 4 insertions(+), 5 deletions(-) diff --git a/src/GRANULAR/fix_pour.cpp b/src/GRANULAR/fix_pour.cpp index 3ffca8db9d..4972d8f3f4 100644 --- a/src/GRANULAR/fix_pour.cpp +++ b/src/GRANULAR/fix_pour.cpp @@ -32,6 +32,7 @@ #include "math_const.h" #include "memory.h" #include "error.h" +#include "utils.h" using namespace LAMMPS_NS; using namespace FixConst; @@ -180,11 +181,9 @@ FixPour::FixPour(LAMMPS *lmp, int narg, char **arg) : // assume grav = -magnitude at this point, enforce in init() int ifix; - for (ifix = 0; ifix < modify->nfix; ifix++) { - if (strcmp(modify->fix[ifix]->style,"gravity") == 0) break; - if (strcmp(modify->fix[ifix]->style,"gravity/omp") == 0) break; - if (strstr(modify->fix[ifix]->style,"gravity/kk") != NULL) break; - } + for (ifix = 0; ifix < modify->nfix; ifix++) + if (utils:strmatch(modify->fix[ifix]->style,"^gravity")) break; + if (ifix == modify->nfix) error->all(FLERR,"No fix gravity defined for fix pour"); grav = - ((FixGravity *) modify->fix[ifix])->magnitude * force->ftm2v; -- GitLab From 5cb02781c24d48071d4c45d9b637c41e5abb5842 Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Mon, 29 Jul 2019 20:35:24 -0400 Subject: [PATCH 361/469] simplify checking for per chunk compute --- src/compute_chunk_spread_atom.cpp | 5 ++--- 1 file changed, 2 insertions(+), 3 deletions(-) diff --git a/src/compute_chunk_spread_atom.cpp b/src/compute_chunk_spread_atom.cpp index 3d0cea1add..4beeb2b010 100644 --- a/src/compute_chunk_spread_atom.cpp +++ b/src/compute_chunk_spread_atom.cpp @@ -23,6 +23,7 @@ #include "input.h" #include "memory.h" #include "error.h" +#include "utils.h" using namespace LAMMPS_NS; @@ -116,9 +117,7 @@ ComputeChunkSpreadAtom(LAMMPS *lmp, int narg, char **arg) : error->all(FLERR,"Compute ID for compute chunk/spread/atom " "does not exist"); - char *ptr = strstr(modify->compute[icompute]->style,"/chunk"); - if (!ptr || (ptr != modify->compute[icompute]->style + - strlen(modify->compute[icompute]->style) - strlen("/chunk"))) + if (!utils::strmatch(modify->compute[icompute]->style,"/chunk$") error->all(FLERR,"Compute for compute chunk/spread/atom " "does not calculate per-chunk values"); -- GitLab From 9f276be0e532cee13031b807303cb8ffb5b0d43f Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Mon, 29 Jul 2019 20:48:47 -0400 Subject: [PATCH 362/469] fix up legacy doc building for final kim doc files --- doc/src/lammps.book | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/doc/src/lammps.book b/doc/src/lammps.book index 79b410c783..a3ec9c568b 100644 --- a/doc/src/lammps.book +++ b/doc/src/lammps.book @@ -168,7 +168,7 @@ include.html info.html jump.html kim_query.html -kim_style.html +kim_commands.html label.html lattice.html log.html -- GitLab From 90c678849ade82a139852971a5040039485ecfbf Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Mon, 29 Jul 2019 21:10:49 -0400 Subject: [PATCH 363/469] replace non-ascii characters with ASCII equivalents --- doc/src/compute.txt | 2 +- doc/src/kim_commands.txt | 12 ++++++------ 2 files changed, 7 insertions(+), 7 deletions(-) diff --git a/doc/src/compute.txt b/doc/src/compute.txt index 53ed373aa5..0741699e61 100644 --- a/doc/src/compute.txt +++ b/doc/src/compute.txt @@ -177,7 +177,7 @@ compute"_Commands_compute.html doc page are followed by one or more of "angle"_compute_angle.html - energy of each angle sub-style "angle/local"_compute_angle_local.html - theta and energy of each angle "angmom/chunk"_compute_angmom_chunk.html - angular momentum for each chunk -"basal/atom"_compute_basal_atom.html - calculates the hexagonal close-packed “c” lattice vector of each atom +"basal/atom"_compute_basal_atom.html - calculates the hexagonal close-packed "c" lattice vector of each atom "body/local"_compute_body_local.html - attributes of body sub-particles "bond"_compute_bond.html - energy of each bond sub-style "bond/local"_compute_bond_local.html - distance and energy of each bond diff --git a/doc/src/kim_commands.txt b/doc/src/kim_commands.txt index 0bb7de03d6..93c4e8c4a8 100644 --- a/doc/src/kim_commands.txt +++ b/doc/src/kim_commands.txt @@ -258,12 +258,12 @@ variable xyfinal equal xy*$\{_u_distance\} variable xzfinal equal xz*$\{_u_distance\} variable yzfinal equal yz*$\{_u_distance\} change_box all x scale $\{_u_distance\} & -               y scale $\{_u_distance\} & -               z scale $\{_u_distance\} & -               xy final $\{xyfinal\} & -               xz final $\{xzfinal\} & -               yz final $\{yzfinal\} & -               remap :pre + y scale $\{_u_distance\} & + z scale $\{_u_distance\} & + xy final $\{xyfinal\} & + xz final $\{xzfinal\} & + yz final $\{yzfinal\} & + remap :pre NOTE: Unit conversion will only work if the conversion factors are placed in all appropriate places in the input script. It is up to the user to do this -- GitLab From 9004ebc3fe8ebb38b1b64236eb7e95b144a6882e Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Mon, 29 Jul 2019 21:11:13 -0400 Subject: [PATCH 364/469] one more fixup for compatibility for old PDF build scheme --- doc/src/lammps.book | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/doc/src/lammps.book b/doc/src/lammps.book index a3ec9c568b..b3808e18dc 100644 --- a/doc/src/lammps.book +++ b/doc/src/lammps.book @@ -42,6 +42,7 @@ Commands_compute.html Commands_pair.html Commands_bond.html Commands_kspace.html +Commands_removed.html Packages.html Packages_standard.html Packages_user.html @@ -167,7 +168,6 @@ if.html include.html info.html jump.html -kim_query.html kim_commands.html label.html lattice.html -- GitLab From 4289dbb78d3fe8267e2a91881e30a92c6dbbd461 Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Mon, 29 Jul 2019 22:28:29 -0400 Subject: [PATCH 365/469] clean up includes and whitespace --- src/USER-MISC/compute_momentum.cpp | 15 ++++++--------- 1 file changed, 6 insertions(+), 9 deletions(-) diff --git a/src/USER-MISC/compute_momentum.cpp b/src/USER-MISC/compute_momentum.cpp index f8fc0ec6ab..541b52d9c0 100644 --- a/src/USER-MISC/compute_momentum.cpp +++ b/src/USER-MISC/compute_momentum.cpp @@ -1,12 +1,9 @@ -#include #include "compute_momentum.h" +#include #include "atom.h" -#include "update.h" -#include "force.h" -#include "domain.h" -#include "group.h" #include "error.h" +#include "update.h" using namespace LAMMPS_NS; @@ -45,14 +42,14 @@ void ComputeMomentum::compute_vector() if (rmass) { for (int i = 0; i < nlocal; i++) if (mask[i] & groupbit) { - for(int j = 0; j < 3; ++j) - mom[j] += rmass[i] * v[i][j]; + for(int j = 0; j < 3; ++j) + mom[j] += rmass[i] * v[i][j]; } } else { for (int i = 0; i < nlocal; i++) if (mask[i] & groupbit) - for(int j = 0; j < 3; ++j) - mom[j] += mass[type[i]] * v[i][j]; + for(int j = 0; j < 3; ++j) + mom[j] += mass[type[i]] * v[i][j]; } MPI_Allreduce(&mom, vector, 3, MPI_DOUBLE, MPI_SUM, world); -- GitLab From c9f3f99ee84f2136acf5cb16c590289de41c4a14 Mon Sep 17 00:00:00 2001 From: "Ryan S. Elliott" Date: Mon, 29 Jul 2019 21:48:12 -0500 Subject: [PATCH 366/469] Update to kim-api-2.1.2 --- cmake/Modules/Packages/KIM.cmake | 8 +++++--- 1 file changed, 5 insertions(+), 3 deletions(-) diff --git a/cmake/Modules/Packages/KIM.cmake b/cmake/Modules/Packages/KIM.cmake index 5987ebbf0a..d9d028f6dc 100644 --- a/cmake/Modules/Packages/KIM.cmake +++ b/cmake/Modules/Packages/KIM.cmake @@ -9,7 +9,9 @@ if(PKG_KIM) if(KIM-API_FOUND) set(DOWNLOAD_KIM_DEFAULT OFF) else() - message(WARNING "KIM-API package not found. We will download and build our own") + if (NOT DOWNLOAD_KIM) + message(WARNING "KIM-API package not found. We will download and build our own") + endif() set(DOWNLOAD_KIM_DEFAULT ON) endif() option(DOWNLOAD_KIM "Download KIM-API from OpenKIM instead of using an already installed one" ${DOWNLOAD_KIM_DEFAULT}) @@ -22,8 +24,8 @@ if(PKG_KIM) enable_language(Fortran) include(ExternalProject) ExternalProject_Add(kim_build - URL https://s3.openkim.org/kim-api/kim-api-2.1.1.txz - URL_MD5 ae0ee413e026c6e93d35692db5966fb4 + URL https://s3.openkim.org/kim-api/kim-api-2.1.2.txz + URL_MD5 6ac52e14ef52967fc7858220b208cba5 BINARY_DIR build CMAKE_ARGS -DCMAKE_C_COMPILER=${CMAKE_C_COMPILER} -DCMAKE_CXX_COMPILER=${CMAKE_CXX_COMPILER} -- GitLab From d201d6c2d11f8150d11e74ad58498fd1fc678d9e Mon Sep 17 00:00:00 2001 From: mkanski Date: Tue, 30 Jul 2019 10:18:53 +0200 Subject: [PATCH 367/469] fix grammar error --- doc/src/create_atoms.txt | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/doc/src/create_atoms.txt b/doc/src/create_atoms.txt index e673849793..2c97194cba 100644 --- a/doc/src/create_atoms.txt +++ b/doc/src/create_atoms.txt @@ -242,7 +242,7 @@ write_dump all atom sinusoid.lammpstrj :pre :c,image(JPG/sinusoid_small.jpg,JPG/sinusoid.jpg) -The {rotate} keyword allows to specify the orientation +The {rotate} keyword allows specification of the orientation at which molecules are inserted. The axis of rotation is determined by the rotation vector (Rx,Ry,Rz) that goes through the insertion point. The specified {theta} determines the angle of -- GitLab From 3ee86470bbb2cd93cca8c9d7b90d3937d7518c51 Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Tue, 30 Jul 2019 05:53:28 -0400 Subject: [PATCH 368/469] correct documentation URL for PLUMED --- doc/src/fix_plumed.txt | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/doc/src/fix_plumed.txt b/doc/src/fix_plumed.txt index 97b3150a0b..86807f531d 100644 --- a/doc/src/fix_plumed.txt +++ b/doc/src/fix_plumed.txt @@ -114,5 +114,5 @@ The default options are plumedfile = NULL and outfile = NULL :link(PLUMED) [(PLUMED)] G.A. Tribello, M. Bonomi, D. Branduardi, C. Camilloni and G. Bussi, Comp. Phys. Comm 185, 604 (2014) -:link(plumeddocs,http://www.plumed.org/documentation) +:link(plumeddocs,http://www.plumed.org/doc.html) :link(plumedhome,http://www.plumed.org/) -- GitLab From 7ab7691c5122f5fc33c0b60bfa02b696d7ccb65d Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Tue, 30 Jul 2019 05:57:57 -0400 Subject: [PATCH 369/469] update PLUMED support to version 2.5.2 --- cmake/Modules/Packages/USER-PLUMED.cmake | 4 ++-- lib/plumed/Install.py | 3 ++- 2 files changed, 4 insertions(+), 3 deletions(-) diff --git a/cmake/Modules/Packages/USER-PLUMED.cmake b/cmake/Modules/Packages/USER-PLUMED.cmake index 35533f01ef..a9c5a59338 100644 --- a/cmake/Modules/Packages/USER-PLUMED.cmake +++ b/cmake/Modules/Packages/USER-PLUMED.cmake @@ -43,8 +43,8 @@ if(PKG_USER-PLUMED) message(STATUS "PLUMED download requested - we will build our own") include(ExternalProject) ExternalProject_Add(plumed_build - URL https://github.com/plumed/plumed2/releases/download/v2.5.1/plumed-src-2.5.1.tgz - URL_MD5 c2a7b519e32197a120cdf47e0f194f81 + URL https://github.com/plumed/plumed2/releases/download/v2.5.2/plumed-src-2.5.2.tgz + URL_MD5 bd2f18346c788eb54e1e52f4f6acf41a BUILD_IN_SOURCE 1 CONFIGURE_COMMAND /configure --prefix= ${CONFIGURE_REQUEST_PIC} diff --git a/lib/plumed/Install.py b/lib/plumed/Install.py index 3623a8cff0..a59200d1f8 100644 --- a/lib/plumed/Install.py +++ b/lib/plumed/Install.py @@ -17,7 +17,7 @@ parser = ArgumentParser(prog='Install.py', # settings -version = "2.5.1" +version = "2.5.2" mode = "static" # help message @@ -44,6 +44,7 @@ checksums = { \ '2.4.4' : '71ed465bdc7c2059e282dbda8d564e71', \ '2.5.0' : '6224cd089493661e19ceacccd35cf911', \ '2.5.1' : 'c2a7b519e32197a120cdf47e0f194f81', \ + '2.5.2' : 'bd2f18346c788eb54e1e52f4f6acf41a', \ } # parse and process arguments -- GitLab From 3fdadb587554308e1db82e5d3ac4838850f61f58 Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Tue, 30 Jul 2019 06:02:47 -0400 Subject: [PATCH 370/469] add configuration for linking VTK 7.1 on Ubuntu 18.04 --- lib/vtk/Makefile.lammps.ubuntu18.04_vtk7 | 12 ++++++++++++ 1 file changed, 12 insertions(+) create mode 100644 lib/vtk/Makefile.lammps.ubuntu18.04_vtk7 diff --git a/lib/vtk/Makefile.lammps.ubuntu18.04_vtk7 b/lib/vtk/Makefile.lammps.ubuntu18.04_vtk7 new file mode 100644 index 0000000000..c833a5f67c --- /dev/null +++ b/lib/vtk/Makefile.lammps.ubuntu18.04_vtk7 @@ -0,0 +1,12 @@ +# Settings that the LAMMPS build will import when this package library is used +# +# Ubuntu 18.04 installation of VTK7 library: +# ------------------------------------------ +# +# Execute the following installation command: +# +# $ sudo apt-get install libvtk7-dev +# +vtk_SYSINC = -I/usr/include/vtk7.1 +vtk_SYSLIB = -lvtkCommonCore-7.1 -lvtkIOCore-7.1 -lvtkIOXML-7.1 -lvtkIOLegacy-7.1 -lvtkCommonDataModel-7.1 -lvtkIOParallelXML-7.1 +vtk_SYSPATH = -L/usr/lib/x86_64-linux-gnu -- GitLab From 3559c25bd9d91167e4dcec040dcda6348cdc349c Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Tue, 30 Jul 2019 06:35:35 -0400 Subject: [PATCH 371/469] add missing parenthesis --- src/compute_chunk_spread_atom.cpp | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/compute_chunk_spread_atom.cpp b/src/compute_chunk_spread_atom.cpp index 4beeb2b010..a58c52d8e8 100644 --- a/src/compute_chunk_spread_atom.cpp +++ b/src/compute_chunk_spread_atom.cpp @@ -117,7 +117,7 @@ ComputeChunkSpreadAtom(LAMMPS *lmp, int narg, char **arg) : error->all(FLERR,"Compute ID for compute chunk/spread/atom " "does not exist"); - if (!utils::strmatch(modify->compute[icompute]->style,"/chunk$") + if (!utils::strmatch(modify->compute[icompute]->style,"/chunk$")) error->all(FLERR,"Compute for compute chunk/spread/atom " "does not calculate per-chunk values"); -- GitLab From b0bccfd8a10b8418da9490c54c5e5ae83864b837 Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Tue, 30 Jul 2019 06:55:47 -0400 Subject: [PATCH 372/469] fix typo --- src/GRANULAR/fix_pour.cpp | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/GRANULAR/fix_pour.cpp b/src/GRANULAR/fix_pour.cpp index 4972d8f3f4..f7cf408e78 100644 --- a/src/GRANULAR/fix_pour.cpp +++ b/src/GRANULAR/fix_pour.cpp @@ -182,7 +182,7 @@ FixPour::FixPour(LAMMPS *lmp, int narg, char **arg) : int ifix; for (ifix = 0; ifix < modify->nfix; ifix++) - if (utils:strmatch(modify->fix[ifix]->style,"^gravity")) break; + if (utils::strmatch(modify->fix[ifix]->style,"^gravity")) break; if (ifix == modify->nfix) error->all(FLERR,"No fix gravity defined for fix pour"); -- GitLab From d1e8d7cbf88f102af94715f1cd65ec9936c2217f Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Tue, 30 Jul 2019 08:26:11 -0400 Subject: [PATCH 373/469] Step version string for next patch release --- doc/lammps.1 | 2 +- doc/src/Manual.txt | 4 ++-- src/version.h | 2 +- 3 files changed, 4 insertions(+), 4 deletions(-) diff --git a/doc/lammps.1 b/doc/lammps.1 index 4685ad22a3..9a3d7e78c8 100644 --- a/doc/lammps.1 +++ b/doc/lammps.1 @@ -1,4 +1,4 @@ -.TH LAMMPS "19 July 2019" "2019-07-19" +.TH LAMMPS "31 July 2019" "2019-07-31" .SH NAME .B LAMMPS \- Molecular Dynamics Simulator. diff --git a/doc/src/Manual.txt b/doc/src/Manual.txt index 80d72aac57..927ee780e4 100644 --- a/doc/src/Manual.txt +++ b/doc/src/Manual.txt @@ -1,7 +1,7 @@ LAMMPS Users Manual - + @@ -21,7 +21,7 @@ :line LAMMPS Documentation :c,h1 -19 Jul 2019 version :c,h2 +31 Jul 2019 version :c,h2 "What is a LAMMPS version?"_Manual_version.html diff --git a/src/version.h b/src/version.h index 8a8cbec57e..9007966450 100644 --- a/src/version.h +++ b/src/version.h @@ -1 +1 @@ -#define LAMMPS_VERSION "19 Jul 2019" +#define LAMMPS_VERSION "31 Jul 2019" -- GitLab From 354855147983862c1830af93970db678e3c2dc09 Mon Sep 17 00:00:00 2001 From: Stan Moore Date: Tue, 30 Jul 2019 08:49:58 -0600 Subject: [PATCH 374/469] Fix Kokkos package compile error --- src/KOKKOS/fix_neigh_history_kokkos.cpp | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/KOKKOS/fix_neigh_history_kokkos.cpp b/src/KOKKOS/fix_neigh_history_kokkos.cpp index 5f53950fe6..8cfe7111dd 100644 --- a/src/KOKKOS/fix_neigh_history_kokkos.cpp +++ b/src/KOKKOS/fix_neigh_history_kokkos.cpp @@ -99,7 +99,7 @@ void FixNeighHistoryKokkos::pre_exchange() copymode = 0; - comm->maxexchange_fix = MAX(comm->maxexchange_fix,(dnum+1)*maxpartner+1); + maxexchange = (dnum+1)*maxpartner+1; } /* ---------------------------------------------------------------------- */ -- GitLab From 602b4a47c0dad33501990a0601b89ec29e8abfbb Mon Sep 17 00:00:00 2001 From: Stan Moore Date: Tue, 30 Jul 2019 10:37:27 -0600 Subject: [PATCH 375/469] Fix failing regression test --- examples/USER/eff/Be-solid/data.Be-solid | 2016 +++++++++++----------- 1 file changed, 1008 insertions(+), 1008 deletions(-) diff --git a/examples/USER/eff/Be-solid/data.Be-solid b/examples/USER/eff/Be-solid/data.Be-solid index e13aebf738..aa2e0a00aa 100644 --- a/examples/USER/eff/Be-solid/data.Be-solid +++ b/examples/USER/eff/Be-solid/data.Be-solid @@ -12115,7 +12115,7 @@ Atoms 12099 2 0.000000 1 2.500000 5.740000 7.290779 1.756250 12100 2 0.000000 -1 2.500000 5.740000 7.290779 1.756250 12101 2 0.000000 1 2.500000 63.140000 5.965183 5.268750 -12102 2 0.000000 -1.000000 2.500000 63.140000 5.965183 5.268750 +12102 2 0.000000 -1 2.500000 63.140000 5.965183 5.268750 12103 2 0.000000 1 2.500000 1.148000 1.988394 5.268750 12104 2 0.000000 -1 2.500000 1.148000 1.988394 5.268750 12105 2 0.000000 1 2.500000 3.444000 3.313991 8.781250 @@ -12123,7 +12123,7 @@ Atoms 12107 2 0.000000 1 2.500000 5.740000 7.290779 8.781250 12108 2 0.000000 -1 2.500000 5.740000 7.290779 8.781250 12109 2 0.000000 1 2.500000 63.140000 5.965183 12.293750 -12110 2 0.000000 -1.000000 2.500000 63.140000 5.965183 12.293750 +12110 2 0.000000 -1 2.500000 63.140000 5.965183 12.293750 12111 2 0.000000 1 2.500000 1.148000 1.988394 12.293750 12112 2 0.000000 -1 2.500000 1.148000 1.988394 12.293750 12113 2 0.000000 1 2.500000 3.444000 3.313991 15.806250 @@ -12131,7 +12131,7 @@ Atoms 12115 2 0.000000 1 2.500000 5.740000 7.290779 15.806250 12116 2 0.000000 -1 2.500000 5.740000 7.290779 15.806250 12117 2 0.000000 1 2.500000 63.140000 5.965183 19.318750 -12118 2 0.000000 -1.000000 2.500000 63.140000 5.965183 19.318750 +12118 2 0.000000 -1 2.500000 63.140000 5.965183 19.318750 12119 2 0.000000 1 2.500000 1.148000 1.988394 19.318750 12120 2 0.000000 -1 2.500000 1.148000 1.988394 19.318750 12121 2 0.000000 1 2.500000 3.444000 3.313991 22.831250 @@ -12139,7 +12139,7 @@ Atoms 12123 2 0.000000 1 2.500000 5.740000 7.290779 22.831250 12124 2 0.000000 -1 2.500000 5.740000 7.290779 22.831250 12125 2 0.000000 1 2.500000 63.140000 5.965183 26.343750 -12126 2 0.000000 -1.000000 2.500000 63.140000 5.965183 26.343750 +12126 2 0.000000 -1 2.500000 63.140000 5.965183 26.343750 12127 2 0.000000 1 2.500000 1.148000 1.988394 26.343750 12128 2 0.000000 -1 2.500000 1.148000 1.988394 26.343750 12129 2 0.000000 1 2.500000 3.444000 3.313991 29.856250 @@ -12147,7 +12147,7 @@ Atoms 12131 2 0.000000 1 2.500000 5.740000 7.290779 29.856250 12132 2 0.000000 -1 2.500000 5.740000 7.290779 29.856250 12133 2 0.000000 1 2.500000 63.140000 5.965183 33.368750 -12134 2 0.000000 -1.000000 2.500000 63.140000 5.965183 33.368750 +12134 2 0.000000 -1 2.500000 63.140000 5.965183 33.368750 12135 2 0.000000 1 2.500000 1.148000 1.988394 33.368750 12136 2 0.000000 -1 2.500000 1.148000 1.988394 33.368750 12137 2 0.000000 1 2.500000 3.444000 3.313991 36.881250 @@ -12155,7 +12155,7 @@ Atoms 12139 2 0.000000 1 2.500000 5.740000 7.290779 36.881250 12140 2 0.000000 -1 2.500000 5.740000 7.290779 36.881250 12141 2 0.000000 1 2.500000 63.140000 5.965183 40.393750 -12142 2 0.000000 -1.000000 2.500000 63.140000 5.965183 40.393750 +12142 2 0.000000 -1 2.500000 63.140000 5.965183 40.393750 12143 2 0.000000 1 2.500000 1.148000 1.988394 40.393750 12144 2 0.000000 -1 2.500000 1.148000 1.988394 40.393750 12145 2 0.000000 1 2.500000 3.444000 3.313991 43.906250 @@ -12163,7 +12163,7 @@ Atoms 12147 2 0.000000 1 2.500000 5.740000 7.290779 43.906250 12148 2 0.000000 -1 2.500000 5.740000 7.290779 43.906250 12149 2 0.000000 1 2.500000 63.140000 5.965183 47.418750 -12150 2 0.000000 -1.000000 2.500000 63.140000 5.965183 47.418750 +12150 2 0.000000 -1 2.500000 63.140000 5.965183 47.418750 12151 2 0.000000 1 2.500000 1.148000 1.988394 47.418750 12152 2 0.000000 -1 2.500000 1.148000 1.988394 47.418750 12153 2 0.000000 1 2.500000 3.444000 3.313991 50.931250 @@ -12171,7 +12171,7 @@ Atoms 12155 2 0.000000 1 2.500000 5.740000 7.290779 50.931250 12156 2 0.000000 -1 2.500000 5.740000 7.290779 50.931250 12157 2 0.000000 1 2.500000 63.140000 5.965183 54.443750 -12158 2 0.000000 -1.000000 2.500000 63.140000 5.965183 54.443750 +12158 2 0.000000 -1 2.500000 63.140000 5.965183 54.443750 12159 2 0.000000 1 2.500000 1.148000 1.988394 54.443750 12160 2 0.000000 -1 2.500000 1.148000 1.988394 54.443750 12161 2 0.000000 1 2.500000 3.444000 3.313991 57.956250 @@ -12179,7 +12179,7 @@ Atoms 12163 2 0.000000 1 2.500000 5.740000 7.290779 57.956250 12164 2 0.000000 -1 2.500000 5.740000 7.290779 57.956250 12165 2 0.000000 1 2.500000 63.140000 5.965183 61.468750 -12166 2 0.000000 -1.000000 2.500000 63.140000 5.965183 61.468750 +12166 2 0.000000 -1 2.500000 63.140000 5.965183 61.468750 12167 2 0.000000 1 2.500000 1.148000 1.988394 61.468750 12168 2 0.000000 -1 2.500000 1.148000 1.988394 61.468750 12169 2 0.000000 1 2.500000 3.444000 11.267568 1.756250 @@ -12187,7 +12187,7 @@ Atoms 12171 2 0.000000 1 2.500000 5.740000 15.244357 1.756250 12172 2 0.000000 -1 2.500000 5.740000 15.244357 1.756250 12173 2 0.000000 1 2.500000 63.140000 13.918760 5.268750 -12174 2 0.000000 -1.000000 2.500000 63.140000 13.918760 5.268750 +12174 2 0.000000 -1 2.500000 63.140000 13.918760 5.268750 12175 2 0.000000 1 2.500000 1.148000 9.941972 5.268750 12176 2 0.000000 -1 2.500000 1.148000 9.941972 5.268750 12177 2 0.000000 1 2.500000 3.444000 11.267568 8.781250 @@ -12195,7 +12195,7 @@ Atoms 12179 2 0.000000 1 2.500000 5.740000 15.244357 8.781250 12180 2 0.000000 -1 2.500000 5.740000 15.244357 8.781250 12181 2 0.000000 1 2.500000 63.140000 13.918760 12.293750 -12182 2 0.000000 -1.000000 2.500000 63.140000 13.918760 12.293750 +12182 2 0.000000 -1 2.500000 63.140000 13.918760 12.293750 12183 2 0.000000 1 2.500000 1.148000 9.941972 12.293750 12184 2 0.000000 -1 2.500000 1.148000 9.941972 12.293750 12185 2 0.000000 1 2.500000 3.444000 11.267568 15.806250 @@ -12203,7 +12203,7 @@ Atoms 12187 2 0.000000 1 2.500000 5.740000 15.244357 15.806250 12188 2 0.000000 -1 2.500000 5.740000 15.244357 15.806250 12189 2 0.000000 1 2.500000 63.140000 13.918760 19.318750 -12190 2 0.000000 -1.000000 2.500000 63.140000 13.918760 19.318750 +12190 2 0.000000 -1 2.500000 63.140000 13.918760 19.318750 12191 2 0.000000 1 2.500000 1.148000 9.941972 19.318750 12192 2 0.000000 -1 2.500000 1.148000 9.941972 19.318750 12193 2 0.000000 1 2.500000 3.444000 11.267568 22.831250 @@ -12211,7 +12211,7 @@ Atoms 12195 2 0.000000 1 2.500000 5.740000 15.244357 22.831250 12196 2 0.000000 -1 2.500000 5.740000 15.244357 22.831250 12197 2 0.000000 1 2.500000 63.140000 13.918760 26.343750 -12198 2 0.000000 -1.000000 2.500000 63.140000 13.918760 26.343750 +12198 2 0.000000 -1 2.500000 63.140000 13.918760 26.343750 12199 2 0.000000 1 2.500000 1.148000 9.941972 26.343750 12200 2 0.000000 -1 2.500000 1.148000 9.941972 26.343750 12201 2 0.000000 1 2.500000 3.444000 11.267568 29.856250 @@ -12219,7 +12219,7 @@ Atoms 12203 2 0.000000 1 2.500000 5.740000 15.244357 29.856250 12204 2 0.000000 -1 2.500000 5.740000 15.244357 29.856250 12205 2 0.000000 1 2.500000 63.140000 13.918760 33.368750 -12206 2 0.000000 -1.000000 2.500000 63.140000 13.918760 33.368750 +12206 2 0.000000 -1 2.500000 63.140000 13.918760 33.368750 12207 2 0.000000 1 2.500000 1.148000 9.941972 33.368750 12208 2 0.000000 -1 2.500000 1.148000 9.941972 33.368750 12209 2 0.000000 1 2.500000 3.444000 11.267568 36.881250 @@ -12227,7 +12227,7 @@ Atoms 12211 2 0.000000 1 2.500000 5.740000 15.244357 36.881250 12212 2 0.000000 -1 2.500000 5.740000 15.244357 36.881250 12213 2 0.000000 1 2.500000 63.140000 13.918760 40.393750 -12214 2 0.000000 -1.000000 2.500000 63.140000 13.918760 40.393750 +12214 2 0.000000 -1 2.500000 63.140000 13.918760 40.393750 12215 2 0.000000 1 2.500000 1.148000 9.941972 40.393750 12216 2 0.000000 -1 2.500000 1.148000 9.941972 40.393750 12217 2 0.000000 1 2.500000 3.444000 11.267568 43.906250 @@ -12235,7 +12235,7 @@ Atoms 12219 2 0.000000 1 2.500000 5.740000 15.244357 43.906250 12220 2 0.000000 -1 2.500000 5.740000 15.244357 43.906250 12221 2 0.000000 1 2.500000 63.140000 13.918760 47.418750 -12222 2 0.000000 -1.000000 2.500000 63.140000 13.918760 47.418750 +12222 2 0.000000 -1 2.500000 63.140000 13.918760 47.418750 12223 2 0.000000 1 2.500000 1.148000 9.941972 47.418750 12224 2 0.000000 -1 2.500000 1.148000 9.941972 47.418750 12225 2 0.000000 1 2.500000 3.444000 11.267568 50.931250 @@ -12243,7 +12243,7 @@ Atoms 12227 2 0.000000 1 2.500000 5.740000 15.244357 50.931250 12228 2 0.000000 -1 2.500000 5.740000 15.244357 50.931250 12229 2 0.000000 1 2.500000 63.140000 13.918760 54.443750 -12230 2 0.000000 -1.000000 2.500000 63.140000 13.918760 54.443750 +12230 2 0.000000 -1 2.500000 63.140000 13.918760 54.443750 12231 2 0.000000 1 2.500000 1.148000 9.941972 54.443750 12232 2 0.000000 -1 2.500000 1.148000 9.941972 54.443750 12233 2 0.000000 1 2.500000 3.444000 11.267568 57.956250 @@ -12251,7 +12251,7 @@ Atoms 12235 2 0.000000 1 2.500000 5.740000 15.244357 57.956250 12236 2 0.000000 -1 2.500000 5.740000 15.244357 57.956250 12237 2 0.000000 1 2.500000 63.140000 13.918760 61.468750 -12238 2 0.000000 -1.000000 2.500000 63.140000 13.918760 61.468750 +12238 2 0.000000 -1 2.500000 63.140000 13.918760 61.468750 12239 2 0.000000 1 2.500000 1.148000 9.941972 61.468750 12240 2 0.000000 -1 2.500000 1.148000 9.941972 61.468750 12241 2 0.000000 1 2.500000 3.444000 19.221145 1.756250 @@ -12259,7 +12259,7 @@ Atoms 12243 2 0.000000 1 2.500000 5.740000 23.197934 1.756250 12244 2 0.000000 -1 2.500000 5.740000 23.197934 1.756250 12245 2 0.000000 1 2.500000 63.140000 21.872338 5.268750 -12246 2 0.000000 -1.000000 2.500000 63.140000 21.872338 5.268750 +12246 2 0.000000 -1 2.500000 63.140000 21.872338 5.268750 12247 2 0.000000 1 2.500000 1.148000 17.895549 5.268750 12248 2 0.000000 -1 2.500000 1.148000 17.895549 5.268750 12249 2 0.000000 1 2.500000 3.444000 19.221145 8.781250 @@ -12267,7 +12267,7 @@ Atoms 12251 2 0.000000 1 2.500000 5.740000 23.197934 8.781250 12252 2 0.000000 -1 2.500000 5.740000 23.197934 8.781250 12253 2 0.000000 1 2.500000 63.140000 21.872338 12.293750 -12254 2 0.000000 -1.000000 2.500000 63.140000 21.872338 12.293750 +12254 2 0.000000 -1 2.500000 63.140000 21.872338 12.293750 12255 2 0.000000 1 2.500000 1.148000 17.895549 12.293750 12256 2 0.000000 -1 2.500000 1.148000 17.895549 12.293750 12257 2 0.000000 1 2.500000 3.444000 19.221145 15.806250 @@ -12275,7 +12275,7 @@ Atoms 12259 2 0.000000 1 2.500000 5.740000 23.197934 15.806250 12260 2 0.000000 -1 2.500000 5.740000 23.197934 15.806250 12261 2 0.000000 1 2.500000 63.140000 21.872338 19.318750 -12262 2 0.000000 -1.000000 2.500000 63.140000 21.872338 19.318750 +12262 2 0.000000 -1 2.500000 63.140000 21.872338 19.318750 12263 2 0.000000 1 2.500000 1.148000 17.895549 19.318750 12264 2 0.000000 -1 2.500000 1.148000 17.895549 19.318750 12265 2 0.000000 1 2.500000 3.444000 19.221145 22.831250 @@ -12283,7 +12283,7 @@ Atoms 12267 2 0.000000 1 2.500000 5.740000 23.197934 22.831250 12268 2 0.000000 -1 2.500000 5.740000 23.197934 22.831250 12269 2 0.000000 1 2.500000 63.140000 21.872338 26.343750 -12270 2 0.000000 -1.000000 2.500000 63.140000 21.872338 26.343750 +12270 2 0.000000 -1 2.500000 63.140000 21.872338 26.343750 12271 2 0.000000 1 2.500000 1.148000 17.895549 26.343750 12272 2 0.000000 -1 2.500000 1.148000 17.895549 26.343750 12273 2 0.000000 1 2.500000 3.444000 19.221145 29.856250 @@ -12291,7 +12291,7 @@ Atoms 12275 2 0.000000 1 2.500000 5.740000 23.197934 29.856250 12276 2 0.000000 -1 2.500000 5.740000 23.197934 29.856250 12277 2 0.000000 1 2.500000 63.140000 21.872338 33.368750 -12278 2 0.000000 -1.000000 2.500000 63.140000 21.872338 33.368750 +12278 2 0.000000 -1 2.500000 63.140000 21.872338 33.368750 12279 2 0.000000 1 2.500000 1.148000 17.895549 33.368750 12280 2 0.000000 -1 2.500000 1.148000 17.895549 33.368750 12281 2 0.000000 1 2.500000 3.444000 19.221145 36.881250 @@ -12299,7 +12299,7 @@ Atoms 12283 2 0.000000 1 2.500000 5.740000 23.197934 36.881250 12284 2 0.000000 -1 2.500000 5.740000 23.197934 36.881250 12285 2 0.000000 1 2.500000 63.140000 21.872338 40.393750 -12286 2 0.000000 -1.000000 2.500000 63.140000 21.872338 40.393750 +12286 2 0.000000 -1 2.500000 63.140000 21.872338 40.393750 12287 2 0.000000 1 2.500000 1.148000 17.895549 40.393750 12288 2 0.000000 -1 2.500000 1.148000 17.895549 40.393750 12289 2 0.000000 1 2.500000 3.444000 19.221145 43.906250 @@ -12307,7 +12307,7 @@ Atoms 12291 2 0.000000 1 2.500000 5.740000 23.197934 43.906250 12292 2 0.000000 -1 2.500000 5.740000 23.197934 43.906250 12293 2 0.000000 1 2.500000 63.140000 21.872338 47.418750 -12294 2 0.000000 -1.000000 2.500000 63.140000 21.872338 47.418750 +12294 2 0.000000 -1 2.500000 63.140000 21.872338 47.418750 12295 2 0.000000 1 2.500000 1.148000 17.895549 47.418750 12296 2 0.000000 -1 2.500000 1.148000 17.895549 47.418750 12297 2 0.000000 1 2.500000 3.444000 19.221145 50.931250 @@ -12315,7 +12315,7 @@ Atoms 12299 2 0.000000 1 2.500000 5.740000 23.197934 50.931250 12300 2 0.000000 -1 2.500000 5.740000 23.197934 50.931250 12301 2 0.000000 1 2.500000 63.140000 21.872338 54.443750 -12302 2 0.000000 -1.000000 2.500000 63.140000 21.872338 54.443750 +12302 2 0.000000 -1 2.500000 63.140000 21.872338 54.443750 12303 2 0.000000 1 2.500000 1.148000 17.895549 54.443750 12304 2 0.000000 -1 2.500000 1.148000 17.895549 54.443750 12305 2 0.000000 1 2.500000 3.444000 19.221145 57.956250 @@ -12323,7 +12323,7 @@ Atoms 12307 2 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0.000000 1 2.500000 5.740000 31.151511 8.781250 12324 2 0.000000 -1 2.500000 5.740000 31.151511 8.781250 12325 2 0.000000 1 2.500000 63.140000 29.825915 12.293750 -12326 2 0.000000 -1.000000 2.500000 63.140000 29.825915 12.293750 +12326 2 0.000000 -1 2.500000 63.140000 29.825915 12.293750 12327 2 0.000000 1 2.500000 1.148000 25.849126 12.293750 12328 2 0.000000 -1 2.500000 1.148000 25.849126 12.293750 12329 2 0.000000 1 2.500000 3.444000 27.174722 15.806250 @@ -12347,7 +12347,7 @@ Atoms 12331 2 0.000000 1 2.500000 5.740000 31.151511 15.806250 12332 2 0.000000 -1 2.500000 5.740000 31.151511 15.806250 12333 2 0.000000 1 2.500000 63.140000 29.825915 19.318750 -12334 2 0.000000 -1.000000 2.500000 63.140000 29.825915 19.318750 +12334 2 0.000000 -1 2.500000 63.140000 29.825915 19.318750 12335 2 0.000000 1 2.500000 1.148000 25.849126 19.318750 12336 2 0.000000 -1 2.500000 1.148000 25.849126 19.318750 12337 2 0.000000 1 2.500000 3.444000 27.174722 22.831250 @@ -12355,7 +12355,7 @@ Atoms 12339 2 0.000000 1 2.500000 5.740000 31.151511 22.831250 12340 2 0.000000 -1 2.500000 5.740000 31.151511 22.831250 12341 2 0.000000 1 2.500000 63.140000 29.825915 26.343750 -12342 2 0.000000 -1.000000 2.500000 63.140000 29.825915 26.343750 +12342 2 0.000000 -1 2.500000 63.140000 29.825915 26.343750 12343 2 0.000000 1 2.500000 1.148000 25.849126 26.343750 12344 2 0.000000 -1 2.500000 1.148000 25.849126 26.343750 12345 2 0.000000 1 2.500000 3.444000 27.174722 29.856250 @@ -12363,7 +12363,7 @@ Atoms 12347 2 0.000000 1 2.500000 5.740000 31.151511 29.856250 12348 2 0.000000 -1 2.500000 5.740000 31.151511 29.856250 12349 2 0.000000 1 2.500000 63.140000 29.825915 33.368750 -12350 2 0.000000 -1.000000 2.500000 63.140000 29.825915 33.368750 +12350 2 0.000000 -1 2.500000 63.140000 29.825915 33.368750 12351 2 0.000000 1 2.500000 1.148000 25.849126 33.368750 12352 2 0.000000 -1 2.500000 1.148000 25.849126 33.368750 12353 2 0.000000 1 2.500000 3.444000 27.174722 36.881250 @@ -12371,7 +12371,7 @@ Atoms 12355 2 0.000000 1 2.500000 5.740000 31.151511 36.881250 12356 2 0.000000 -1 2.500000 5.740000 31.151511 36.881250 12357 2 0.000000 1 2.500000 63.140000 29.825915 40.393750 -12358 2 0.000000 -1.000000 2.500000 63.140000 29.825915 40.393750 +12358 2 0.000000 -1 2.500000 63.140000 29.825915 40.393750 12359 2 0.000000 1 2.500000 1.148000 25.849126 40.393750 12360 2 0.000000 -1 2.500000 1.148000 25.849126 40.393750 12361 2 0.000000 1 2.500000 3.444000 27.174722 43.906250 @@ -12379,7 +12379,7 @@ Atoms 12363 2 0.000000 1 2.500000 5.740000 31.151511 43.906250 12364 2 0.000000 -1 2.500000 5.740000 31.151511 43.906250 12365 2 0.000000 1 2.500000 63.140000 29.825915 47.418750 -12366 2 0.000000 -1.000000 2.500000 63.140000 29.825915 47.418750 +12366 2 0.000000 -1 2.500000 63.140000 29.825915 47.418750 12367 2 0.000000 1 2.500000 1.148000 25.849126 47.418750 12368 2 0.000000 -1 2.500000 1.148000 25.849126 47.418750 12369 2 0.000000 1 2.500000 3.444000 27.174722 50.931250 @@ -12387,7 +12387,7 @@ Atoms 12371 2 0.000000 1 2.500000 5.740000 31.151511 50.931250 12372 2 0.000000 -1 2.500000 5.740000 31.151511 50.931250 12373 2 0.000000 1 2.500000 63.140000 29.825915 54.443750 -12374 2 0.000000 -1.000000 2.500000 63.140000 29.825915 54.443750 +12374 2 0.000000 -1 2.500000 63.140000 29.825915 54.443750 12375 2 0.000000 1 2.500000 1.148000 25.849126 54.443750 12376 2 0.000000 -1 2.500000 1.148000 25.849126 54.443750 12377 2 0.000000 1 2.500000 3.444000 27.174722 57.956250 @@ -12395,7 +12395,7 @@ Atoms 12379 2 0.000000 1 2.500000 5.740000 31.151511 57.956250 12380 2 0.000000 -1 2.500000 5.740000 31.151511 57.956250 12381 2 0.000000 1 2.500000 63.140000 29.825915 61.468750 -12382 2 0.000000 -1.000000 2.500000 63.140000 29.825915 61.468750 +12382 2 0.000000 -1 2.500000 63.140000 29.825915 61.468750 12383 2 0.000000 1 2.500000 1.148000 25.849126 61.468750 12384 2 0.000000 -1 2.500000 1.148000 25.849126 61.468750 12385 2 0.000000 1 2.500000 3.444000 35.128300 1.756250 @@ -12403,7 +12403,7 @@ Atoms 12387 2 0.000000 1 2.500000 5.740000 39.105088 1.756250 12388 2 0.000000 -1 2.500000 5.740000 39.105088 1.756250 12389 2 0.000000 1 2.500000 63.140000 37.779492 5.268750 -12390 2 0.000000 -1.000000 2.500000 63.140000 37.779492 5.268750 +12390 2 0.000000 -1 2.500000 63.140000 37.779492 5.268750 12391 2 0.000000 1 2.500000 1.148000 33.802704 5.268750 12392 2 0.000000 -1 2.500000 1.148000 33.802704 5.268750 12393 2 0.000000 1 2.500000 3.444000 35.128300 8.781250 @@ -12411,7 +12411,7 @@ Atoms 12395 2 0.000000 1 2.500000 5.740000 39.105088 8.781250 12396 2 0.000000 -1 2.500000 5.740000 39.105088 8.781250 12397 2 0.000000 1 2.500000 63.140000 37.779492 12.293750 -12398 2 0.000000 -1.000000 2.500000 63.140000 37.779492 12.293750 +12398 2 0.000000 -1 2.500000 63.140000 37.779492 12.293750 12399 2 0.000000 1 2.500000 1.148000 33.802704 12.293750 12400 2 0.000000 -1 2.500000 1.148000 33.802704 12.293750 12401 2 0.000000 1 2.500000 3.444000 35.128300 15.806250 @@ -12419,7 +12419,7 @@ Atoms 12403 2 0.000000 1 2.500000 5.740000 39.105088 15.806250 12404 2 0.000000 -1 2.500000 5.740000 39.105088 15.806250 12405 2 0.000000 1 2.500000 63.140000 37.779492 19.318750 -12406 2 0.000000 -1.000000 2.500000 63.140000 37.779492 19.318750 +12406 2 0.000000 -1 2.500000 63.140000 37.779492 19.318750 12407 2 0.000000 1 2.500000 1.148000 33.802704 19.318750 12408 2 0.000000 -1 2.500000 1.148000 33.802704 19.318750 12409 2 0.000000 1 2.500000 3.444000 35.128300 22.831250 @@ -12427,7 +12427,7 @@ Atoms 12411 2 0.000000 1 2.500000 5.740000 39.105088 22.831250 12412 2 0.000000 -1 2.500000 5.740000 39.105088 22.831250 12413 2 0.000000 1 2.500000 63.140000 37.779492 26.343750 -12414 2 0.000000 -1.000000 2.500000 63.140000 37.779492 26.343750 +12414 2 0.000000 -1 2.500000 63.140000 37.779492 26.343750 12415 2 0.000000 1 2.500000 1.148000 33.802704 26.343750 12416 2 0.000000 -1 2.500000 1.148000 33.802704 26.343750 12417 2 0.000000 1 2.500000 3.444000 35.128300 29.856250 @@ -12435,7 +12435,7 @@ Atoms 12419 2 0.000000 1 2.500000 5.740000 39.105088 29.856250 12420 2 0.000000 -1 2.500000 5.740000 39.105088 29.856250 12421 2 0.000000 1 2.500000 63.140000 37.779492 33.368750 -12422 2 0.000000 -1.000000 2.500000 63.140000 37.779492 33.368750 +12422 2 0.000000 -1 2.500000 63.140000 37.779492 33.368750 12423 2 0.000000 1 2.500000 1.148000 33.802704 33.368750 12424 2 0.000000 -1 2.500000 1.148000 33.802704 33.368750 12425 2 0.000000 1 2.500000 3.444000 35.128300 36.881250 @@ -12443,7 +12443,7 @@ Atoms 12427 2 0.000000 1 2.500000 5.740000 39.105088 36.881250 12428 2 0.000000 -1 2.500000 5.740000 39.105088 36.881250 12429 2 0.000000 1 2.500000 63.140000 37.779492 40.393750 -12430 2 0.000000 -1.000000 2.500000 63.140000 37.779492 40.393750 +12430 2 0.000000 -1 2.500000 63.140000 37.779492 40.393750 12431 2 0.000000 1 2.500000 1.148000 33.802704 40.393750 12432 2 0.000000 -1 2.500000 1.148000 33.802704 40.393750 12433 2 0.000000 1 2.500000 3.444000 35.128300 43.906250 @@ -12451,7 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-12467,7 +12467,7 @@ Atoms 12451 2 0.000000 1 2.500000 5.740000 39.105088 57.956250 12452 2 0.000000 -1 2.500000 5.740000 39.105088 57.956250 12453 2 0.000000 1 2.500000 63.140000 37.779492 61.468750 -12454 2 0.000000 -1.000000 2.500000 63.140000 37.779492 61.468750 +12454 2 0.000000 -1 2.500000 63.140000 37.779492 61.468750 12455 2 0.000000 1 2.500000 1.148000 33.802704 61.468750 12456 2 0.000000 -1 2.500000 1.148000 33.802704 61.468750 12457 2 0.000000 1 2.500000 3.444000 43.081877 1.756250 @@ -12475,7 +12475,7 @@ Atoms 12459 2 0.000000 1 2.500000 5.740000 47.058666 1.756250 12460 2 0.000000 -1 2.500000 5.740000 47.058666 1.756250 12461 2 0.000000 1 2.500000 63.140000 45.733070 5.268750 -12462 2 0.000000 -1.000000 2.500000 63.140000 45.733070 5.268750 +12462 2 0.000000 -1 2.500000 63.140000 45.733070 5.268750 12463 2 0.000000 1 2.500000 1.148000 41.756281 5.268750 12464 2 0.000000 -1 2.500000 1.148000 41.756281 5.268750 12465 2 0.000000 1 2.500000 3.444000 43.081877 8.781250 @@ -12483,7 +12483,7 @@ Atoms 12467 2 0.000000 1 2.500000 5.740000 47.058666 8.781250 12468 2 0.000000 -1 2.500000 5.740000 47.058666 8.781250 12469 2 0.000000 1 2.500000 63.140000 45.733070 12.293750 -12470 2 0.000000 -1.000000 2.500000 63.140000 45.733070 12.293750 +12470 2 0.000000 -1 2.500000 63.140000 45.733070 12.293750 12471 2 0.000000 1 2.500000 1.148000 41.756281 12.293750 12472 2 0.000000 -1 2.500000 1.148000 41.756281 12.293750 12473 2 0.000000 1 2.500000 3.444000 43.081877 15.806250 @@ -12491,7 +12491,7 @@ Atoms 12475 2 0.000000 1 2.500000 5.740000 47.058666 15.806250 12476 2 0.000000 -1 2.500000 5.740000 47.058666 15.806250 12477 2 0.000000 1 2.500000 63.140000 45.733070 19.318750 -12478 2 0.000000 -1.000000 2.500000 63.140000 45.733070 19.318750 +12478 2 0.000000 -1 2.500000 63.140000 45.733070 19.318750 12479 2 0.000000 1 2.500000 1.148000 41.756281 19.318750 12480 2 0.000000 -1 2.500000 1.148000 41.756281 19.318750 12481 2 0.000000 1 2.500000 3.444000 43.081877 22.831250 @@ -12499,7 +12499,7 @@ Atoms 12483 2 0.000000 1 2.500000 5.740000 47.058666 22.831250 12484 2 0.000000 -1 2.500000 5.740000 47.058666 22.831250 12485 2 0.000000 1 2.500000 63.140000 45.733070 26.343750 -12486 2 0.000000 -1.000000 2.500000 63.140000 45.733070 26.343750 +12486 2 0.000000 -1 2.500000 63.140000 45.733070 26.343750 12487 2 0.000000 1 2.500000 1.148000 41.756281 26.343750 12488 2 0.000000 -1 2.500000 1.148000 41.756281 26.343750 12489 2 0.000000 1 2.500000 3.444000 43.081877 29.856250 @@ -12507,7 +12507,7 @@ Atoms 12491 2 0.000000 1 2.500000 5.740000 47.058666 29.856250 12492 2 0.000000 -1 2.500000 5.740000 47.058666 29.856250 12493 2 0.000000 1 2.500000 63.140000 45.733070 33.368750 -12494 2 0.000000 -1.000000 2.500000 63.140000 45.733070 33.368750 +12494 2 0.000000 -1 2.500000 63.140000 45.733070 33.368750 12495 2 0.000000 1 2.500000 1.148000 41.756281 33.368750 12496 2 0.000000 -1 2.500000 1.148000 41.756281 33.368750 12497 2 0.000000 1 2.500000 3.444000 43.081877 36.881250 @@ -12515,7 +12515,7 @@ Atoms 12499 2 0.000000 1 2.500000 5.740000 47.058666 36.881250 12500 2 0.000000 -1 2.500000 5.740000 47.058666 36.881250 12501 2 0.000000 1 2.500000 63.140000 45.733070 40.393750 -12502 2 0.000000 -1.000000 2.500000 63.140000 45.733070 40.393750 +12502 2 0.000000 -1 2.500000 63.140000 45.733070 40.393750 12503 2 0.000000 1 2.500000 1.148000 41.756281 40.393750 12504 2 0.000000 -1 2.500000 1.148000 41.756281 40.393750 12505 2 0.000000 1 2.500000 3.444000 43.081877 43.906250 @@ -12523,7 +12523,7 @@ Atoms 12507 2 0.000000 1 2.500000 5.740000 47.058666 43.906250 12508 2 0.000000 -1 2.500000 5.740000 47.058666 43.906250 12509 2 0.000000 1 2.500000 63.140000 45.733070 47.418750 -12510 2 0.000000 -1.000000 2.500000 63.140000 45.733070 47.418750 +12510 2 0.000000 -1 2.500000 63.140000 45.733070 47.418750 12511 2 0.000000 1 2.500000 1.148000 41.756281 47.418750 12512 2 0.000000 -1 2.500000 1.148000 41.756281 47.418750 12513 2 0.000000 1 2.500000 3.444000 43.081877 50.931250 @@ -12531,7 +12531,7 @@ Atoms 12515 2 0.000000 1 2.500000 5.740000 47.058666 50.931250 12516 2 0.000000 -1 2.500000 5.740000 47.058666 50.931250 12517 2 0.000000 1 2.500000 63.140000 45.733070 54.443750 -12518 2 0.000000 -1.000000 2.500000 63.140000 45.733070 54.443750 +12518 2 0.000000 -1 2.500000 63.140000 45.733070 54.443750 12519 2 0.000000 1 2.500000 1.148000 41.756281 54.443750 12520 2 0.000000 -1 2.500000 1.148000 41.756281 54.443750 12521 2 0.000000 1 2.500000 3.444000 43.081877 57.956250 @@ -12539,7 +12539,7 @@ Atoms 12523 2 0.000000 1 2.500000 5.740000 47.058666 57.956250 12524 2 0.000000 -1 2.500000 5.740000 47.058666 57.956250 12525 2 0.000000 1 2.500000 63.140000 45.733070 61.468750 -12526 2 0.000000 -1.000000 2.500000 63.140000 45.733070 61.468750 +12526 2 0.000000 -1 2.500000 63.140000 45.733070 61.468750 12527 2 0.000000 1 2.500000 1.148000 41.756281 61.468750 12528 2 0.000000 -1 2.500000 1.148000 41.756281 61.468750 12529 2 0.000000 1 2.500000 3.444000 51.035454 1.756250 @@ -12547,7 +12547,7 @@ Atoms 12531 2 0.000000 1 2.500000 5.740000 55.012243 1.756250 12532 2 0.000000 -1 2.500000 5.740000 55.012243 1.756250 12533 2 0.000000 1 2.500000 63.140000 53.686647 5.268750 -12534 2 0.000000 -1.000000 2.500000 63.140000 53.686647 5.268750 +12534 2 0.000000 -1 2.500000 63.140000 53.686647 5.268750 12535 2 0.000000 1 2.500000 1.148000 49.709858 5.268750 12536 2 0.000000 -1 2.500000 1.148000 49.709858 5.268750 12537 2 0.000000 1 2.500000 3.444000 51.035454 8.781250 @@ -12555,7 +12555,7 @@ Atoms 12539 2 0.000000 1 2.500000 5.740000 55.012243 8.781250 12540 2 0.000000 -1 2.500000 5.740000 55.012243 8.781250 12541 2 0.000000 1 2.500000 63.140000 53.686647 12.293750 -12542 2 0.000000 -1.000000 2.500000 63.140000 53.686647 12.293750 +12542 2 0.000000 -1 2.500000 63.140000 53.686647 12.293750 12543 2 0.000000 1 2.500000 1.148000 49.709858 12.293750 12544 2 0.000000 -1 2.500000 1.148000 49.709858 12.293750 12545 2 0.000000 1 2.500000 3.444000 51.035454 15.806250 @@ -12563,7 +12563,7 @@ Atoms 12547 2 0.000000 1 2.500000 5.740000 55.012243 15.806250 12548 2 0.000000 -1 2.500000 5.740000 55.012243 15.806250 12549 2 0.000000 1 2.500000 63.140000 53.686647 19.318750 -12550 2 0.000000 -1.000000 2.500000 63.140000 53.686647 19.318750 +12550 2 0.000000 -1 2.500000 63.140000 53.686647 19.318750 12551 2 0.000000 1 2.500000 1.148000 49.709858 19.318750 12552 2 0.000000 -1 2.500000 1.148000 49.709858 19.318750 12553 2 0.000000 1 2.500000 3.444000 51.035454 22.831250 @@ -12571,7 +12571,7 @@ Atoms 12555 2 0.000000 1 2.500000 5.740000 55.012243 22.831250 12556 2 0.000000 -1 2.500000 5.740000 55.012243 22.831250 12557 2 0.000000 1 2.500000 63.140000 53.686647 26.343750 -12558 2 0.000000 -1.000000 2.500000 63.140000 53.686647 26.343750 +12558 2 0.000000 -1 2.500000 63.140000 53.686647 26.343750 12559 2 0.000000 1 2.500000 1.148000 49.709858 26.343750 12560 2 0.000000 -1 2.500000 1.148000 49.709858 26.343750 12561 2 0.000000 1 2.500000 3.444000 51.035454 29.856250 @@ -12579,7 +12579,7 @@ Atoms 12563 2 0.000000 1 2.500000 5.740000 55.012243 29.856250 12564 2 0.000000 -1 2.500000 5.740000 55.012243 29.856250 12565 2 0.000000 1 2.500000 63.140000 53.686647 33.368750 -12566 2 0.000000 -1.000000 2.500000 63.140000 53.686647 33.368750 +12566 2 0.000000 -1 2.500000 63.140000 53.686647 33.368750 12567 2 0.000000 1 2.500000 1.148000 49.709858 33.368750 12568 2 0.000000 -1 2.500000 1.148000 49.709858 33.368750 12569 2 0.000000 1 2.500000 3.444000 51.035454 36.881250 @@ -12587,7 +12587,7 @@ Atoms 12571 2 0.000000 1 2.500000 5.740000 55.012243 36.881250 12572 2 0.000000 -1 2.500000 5.740000 55.012243 36.881250 12573 2 0.000000 1 2.500000 63.140000 53.686647 40.393750 -12574 2 0.000000 -1.000000 2.500000 63.140000 53.686647 40.393750 +12574 2 0.000000 -1 2.500000 63.140000 53.686647 40.393750 12575 2 0.000000 1 2.500000 1.148000 49.709858 40.393750 12576 2 0.000000 -1 2.500000 1.148000 49.709858 40.393750 12577 2 0.000000 1 2.500000 3.444000 51.035454 43.906250 @@ -12595,7 +12595,7 @@ Atoms 12579 2 0.000000 1 2.500000 5.740000 55.012243 43.906250 12580 2 0.000000 -1 2.500000 5.740000 55.012243 43.906250 12581 2 0.000000 1 2.500000 63.140000 53.686647 47.418750 -12582 2 0.000000 -1.000000 2.500000 63.140000 53.686647 47.418750 +12582 2 0.000000 -1 2.500000 63.140000 53.686647 47.418750 12583 2 0.000000 1 2.500000 1.148000 49.709858 47.418750 12584 2 0.000000 -1 2.500000 1.148000 49.709858 47.418750 12585 2 0.000000 1 2.500000 3.444000 51.035454 50.931250 @@ -12603,7 +12603,7 @@ Atoms 12587 2 0.000000 1 2.500000 5.740000 55.012243 50.931250 12588 2 0.000000 -1 2.500000 5.740000 55.012243 50.931250 12589 2 0.000000 1 2.500000 63.140000 53.686647 54.443750 -12590 2 0.000000 -1.000000 2.500000 63.140000 53.686647 54.443750 +12590 2 0.000000 -1 2.500000 63.140000 53.686647 54.443750 12591 2 0.000000 1 2.500000 1.148000 49.709858 54.443750 12592 2 0.000000 -1 2.500000 1.148000 49.709858 54.443750 12593 2 0.000000 1 2.500000 3.444000 51.035454 57.956250 @@ -12611,7 +12611,7 @@ Atoms 12595 2 0.000000 1 2.500000 5.740000 55.012243 57.956250 12596 2 0.000000 -1 2.500000 5.740000 55.012243 57.956250 12597 2 0.000000 1 2.500000 63.140000 53.686647 61.468750 -12598 2 0.000000 -1.000000 2.500000 63.140000 53.686647 61.468750 +12598 2 0.000000 -1 2.500000 63.140000 53.686647 61.468750 12599 2 0.000000 1 2.500000 1.148000 49.709858 61.468750 12600 2 0.000000 -1 2.500000 1.148000 49.709858 61.468750 12601 2 0.000000 1 2.500000 3.444000 58.989032 1.756250 @@ -12619,7 +12619,7 @@ Atoms 12603 2 0.000000 1 2.500000 5.740000 62.965820 1.756250 12604 2 0.000000 -1 2.500000 5.740000 62.965820 1.756250 12605 2 0.000000 1 2.500000 63.140000 61.640224 5.268750 -12606 2 0.000000 -1.000000 2.500000 63.140000 61.640224 5.268750 +12606 2 0.000000 -1 2.500000 63.140000 61.640224 5.268750 12607 2 0.000000 1 2.500000 1.148000 57.663435 5.268750 12608 2 0.000000 -1 2.500000 1.148000 57.663435 5.268750 12609 2 0.000000 1 2.500000 3.444000 58.989032 8.781250 @@ -12627,7 +12627,7 @@ Atoms 12611 2 0.000000 1 2.500000 5.740000 62.965820 8.781250 12612 2 0.000000 -1 2.500000 5.740000 62.965820 8.781250 12613 2 0.000000 1 2.500000 63.140000 61.640224 12.293750 -12614 2 0.000000 -1.000000 2.500000 63.140000 61.640224 12.293750 +12614 2 0.000000 -1 2.500000 63.140000 61.640224 12.293750 12615 2 0.000000 1 2.500000 1.148000 57.663435 12.293750 12616 2 0.000000 -1 2.500000 1.148000 57.663435 12.293750 12617 2 0.000000 1 2.500000 3.444000 58.989032 15.806250 @@ -12635,7 +12635,7 @@ Atoms 12619 2 0.000000 1 2.500000 5.740000 62.965820 15.806250 12620 2 0.000000 -1 2.500000 5.740000 62.965820 15.806250 12621 2 0.000000 1 2.500000 63.140000 61.640224 19.318750 -12622 2 0.000000 -1.000000 2.500000 63.140000 61.640224 19.318750 +12622 2 0.000000 -1 2.500000 63.140000 61.640224 19.318750 12623 2 0.000000 1 2.500000 1.148000 57.663435 19.318750 12624 2 0.000000 -1 2.500000 1.148000 57.663435 19.318750 12625 2 0.000000 1 2.500000 3.444000 58.989032 22.831250 @@ -12643,7 +12643,7 @@ Atoms 12627 2 0.000000 1 2.500000 5.740000 62.965820 22.831250 12628 2 0.000000 -1 2.500000 5.740000 62.965820 22.831250 12629 2 0.000000 1 2.500000 63.140000 61.640224 26.343750 -12630 2 0.000000 -1.000000 2.500000 63.140000 61.640224 26.343750 +12630 2 0.000000 -1 2.500000 63.140000 61.640224 26.343750 12631 2 0.000000 1 2.500000 1.148000 57.663435 26.343750 12632 2 0.000000 -1 2.500000 1.148000 57.663435 26.343750 12633 2 0.000000 1 2.500000 3.444000 58.989032 29.856250 @@ -12651,7 +12651,7 @@ Atoms 12635 2 0.000000 1 2.500000 5.740000 62.965820 29.856250 12636 2 0.000000 -1 2.500000 5.740000 62.965820 29.856250 12637 2 0.000000 1 2.500000 63.140000 61.640224 33.368750 -12638 2 0.000000 -1.000000 2.500000 63.140000 61.640224 33.368750 +12638 2 0.000000 -1 2.500000 63.140000 61.640224 33.368750 12639 2 0.000000 1 2.500000 1.148000 57.663435 33.368750 12640 2 0.000000 -1 2.500000 1.148000 57.663435 33.368750 12641 2 0.000000 1 2.500000 3.444000 58.989032 36.881250 @@ -12659,7 +12659,7 @@ Atoms 12643 2 0.000000 1 2.500000 5.740000 62.965820 36.881250 12644 2 0.000000 -1 2.500000 5.740000 62.965820 36.881250 12645 2 0.000000 1 2.500000 63.140000 61.640224 40.393750 -12646 2 0.000000 -1.000000 2.500000 63.140000 61.640224 40.393750 +12646 2 0.000000 -1 2.500000 63.140000 61.640224 40.393750 12647 2 0.000000 1 2.500000 1.148000 57.663435 40.393750 12648 2 0.000000 -1 2.500000 1.148000 57.663435 40.393750 12649 2 0.000000 1 2.500000 3.444000 58.989032 43.906250 @@ -12667,7 +12667,7 @@ Atoms 12651 2 0.000000 1 2.500000 5.740000 62.965820 43.906250 12652 2 0.000000 -1 2.500000 5.740000 62.965820 43.906250 12653 2 0.000000 1 2.500000 63.140000 61.640224 47.418750 -12654 2 0.000000 -1.000000 2.500000 63.140000 61.640224 47.418750 +12654 2 0.000000 -1 2.500000 63.140000 61.640224 47.418750 12655 2 0.000000 1 2.500000 1.148000 57.663435 47.418750 12656 2 0.000000 -1 2.500000 1.148000 57.663435 47.418750 12657 2 0.000000 1 2.500000 3.444000 58.989032 50.931250 @@ -12675,7 +12675,7 @@ Atoms 12659 2 0.000000 1 2.500000 5.740000 62.965820 50.931250 12660 2 0.000000 -1 2.500000 5.740000 62.965820 50.931250 12661 2 0.000000 1 2.500000 63.140000 61.640224 54.443750 -12662 2 0.000000 -1.000000 2.500000 63.140000 61.640224 54.443750 +12662 2 0.000000 -1 2.500000 63.140000 61.640224 54.443750 12663 2 0.000000 1 2.500000 1.148000 57.663435 54.443750 12664 2 0.000000 -1 2.500000 1.148000 57.663435 54.443750 12665 2 0.000000 1 2.500000 3.444000 58.989032 57.956250 @@ -12683,7 +12683,7 @@ Atoms 12667 2 0.000000 1 2.500000 5.740000 62.965820 57.956250 12668 2 0.000000 -1 2.500000 5.740000 62.965820 57.956250 12669 2 0.000000 1 2.500000 63.140000 61.640224 61.468750 -12670 2 0.000000 -1.000000 2.500000 63.140000 61.640224 61.468750 +12670 2 0.000000 -1 2.500000 63.140000 61.640224 61.468750 12671 2 0.000000 1 2.500000 1.148000 57.663435 61.468750 12672 2 0.000000 -1 2.500000 1.148000 57.663435 61.468750 12673 2 0.000000 1 2.500000 8.036000 3.313991 1.756250 @@ -12691,7 +12691,7 @@ Atoms 12675 2 0.000000 1 2.500000 10.332000 7.290779 1.756250 12676 2 0.000000 -1 2.500000 10.332000 7.290779 1.756250 12677 2 0.000000 1 2.500000 3.444000 5.965183 5.268750 -12678 2 0.000000 -1.000000 2.500000 3.444000 5.965183 5.268750 +12678 2 0.000000 -1 2.500000 3.444000 5.965183 5.268750 12679 2 0.000000 1 2.500000 5.740000 1.988394 5.268750 12680 2 0.000000 -1 2.500000 5.740000 1.988394 5.268750 12681 2 0.000000 1 2.500000 8.036000 3.313991 8.781250 @@ -12699,7 +12699,7 @@ Atoms 12683 2 0.000000 1 2.500000 10.332000 7.290779 8.781250 12684 2 0.000000 -1 2.500000 10.332000 7.290779 8.781250 12685 2 0.000000 1 2.500000 3.444000 5.965183 12.293750 -12686 2 0.000000 -1.000000 2.500000 3.444000 5.965183 12.293750 +12686 2 0.000000 -1 2.500000 3.444000 5.965183 12.293750 12687 2 0.000000 1 2.500000 5.740000 1.988394 12.293750 12688 2 0.000000 -1 2.500000 5.740000 1.988394 12.293750 12689 2 0.000000 1 2.500000 8.036000 3.313991 15.806250 @@ -12707,7 +12707,7 @@ Atoms 12691 2 0.000000 1 2.500000 10.332000 7.290779 15.806250 12692 2 0.000000 -1 2.500000 10.332000 7.290779 15.806250 12693 2 0.000000 1 2.500000 3.444000 5.965183 19.318750 -12694 2 0.000000 -1.000000 2.500000 3.444000 5.965183 19.318750 +12694 2 0.000000 -1 2.500000 3.444000 5.965183 19.318750 12695 2 0.000000 1 2.500000 5.740000 1.988394 19.318750 12696 2 0.000000 -1 2.500000 5.740000 1.988394 19.318750 12697 2 0.000000 1 2.500000 8.036000 3.313991 22.831250 @@ -12715,7 +12715,7 @@ Atoms 12699 2 0.000000 1 2.500000 10.332000 7.290779 22.831250 12700 2 0.000000 -1 2.500000 10.332000 7.290779 22.831250 12701 2 0.000000 1 2.500000 3.444000 5.965183 26.343750 -12702 2 0.000000 -1.000000 2.500000 3.444000 5.965183 26.343750 +12702 2 0.000000 -1 2.500000 3.444000 5.965183 26.343750 12703 2 0.000000 1 2.500000 5.740000 1.988394 26.343750 12704 2 0.000000 -1 2.500000 5.740000 1.988394 26.343750 12705 2 0.000000 1 2.500000 8.036000 3.313991 29.856250 @@ -12723,7 +12723,7 @@ Atoms 12707 2 0.000000 1 2.500000 10.332000 7.290779 29.856250 12708 2 0.000000 -1 2.500000 10.332000 7.290779 29.856250 12709 2 0.000000 1 2.500000 3.444000 5.965183 33.368750 -12710 2 0.000000 -1.000000 2.500000 3.444000 5.965183 33.368750 +12710 2 0.000000 -1 2.500000 3.444000 5.965183 33.368750 12711 2 0.000000 1 2.500000 5.740000 1.988394 33.368750 12712 2 0.000000 -1 2.500000 5.740000 1.988394 33.368750 12713 2 0.000000 1 2.500000 8.036000 3.313991 36.881250 @@ -12731,7 +12731,7 @@ Atoms 12715 2 0.000000 1 2.500000 10.332000 7.290779 36.881250 12716 2 0.000000 -1 2.500000 10.332000 7.290779 36.881250 12717 2 0.000000 1 2.500000 3.444000 5.965183 40.393750 -12718 2 0.000000 -1.000000 2.500000 3.444000 5.965183 40.393750 +12718 2 0.000000 -1 2.500000 3.444000 5.965183 40.393750 12719 2 0.000000 1 2.500000 5.740000 1.988394 40.393750 12720 2 0.000000 -1 2.500000 5.740000 1.988394 40.393750 12721 2 0.000000 1 2.500000 8.036000 3.313991 43.906250 @@ -12739,7 +12739,7 @@ Atoms 12723 2 0.000000 1 2.500000 10.332000 7.290779 43.906250 12724 2 0.000000 -1 2.500000 10.332000 7.290779 43.906250 12725 2 0.000000 1 2.500000 3.444000 5.965183 47.418750 -12726 2 0.000000 -1.000000 2.500000 3.444000 5.965183 47.418750 +12726 2 0.000000 -1 2.500000 3.444000 5.965183 47.418750 12727 2 0.000000 1 2.500000 5.740000 1.988394 47.418750 12728 2 0.000000 -1 2.500000 5.740000 1.988394 47.418750 12729 2 0.000000 1 2.500000 8.036000 3.313991 50.931250 @@ -12747,7 +12747,7 @@ Atoms 12731 2 0.000000 1 2.500000 10.332000 7.290779 50.931250 12732 2 0.000000 -1 2.500000 10.332000 7.290779 50.931250 12733 2 0.000000 1 2.500000 3.444000 5.965183 54.443750 -12734 2 0.000000 -1.000000 2.500000 3.444000 5.965183 54.443750 +12734 2 0.000000 -1 2.500000 3.444000 5.965183 54.443750 12735 2 0.000000 1 2.500000 5.740000 1.988394 54.443750 12736 2 0.000000 -1 2.500000 5.740000 1.988394 54.443750 12737 2 0.000000 1 2.500000 8.036000 3.313991 57.956250 @@ -12755,7 +12755,7 @@ Atoms 12739 2 0.000000 1 2.500000 10.332000 7.290779 57.956250 12740 2 0.000000 -1 2.500000 10.332000 7.290779 57.956250 12741 2 0.000000 1 2.500000 3.444000 5.965183 61.468750 -12742 2 0.000000 -1.000000 2.500000 3.444000 5.965183 61.468750 +12742 2 0.000000 -1 2.500000 3.444000 5.965183 61.468750 12743 2 0.000000 1 2.500000 5.740000 1.988394 61.468750 12744 2 0.000000 -1 2.500000 5.740000 1.988394 61.468750 12745 2 0.000000 1 2.500000 8.036000 11.267568 1.756250 @@ -12763,7 +12763,7 @@ Atoms 12747 2 0.000000 1 2.500000 10.332000 15.244357 1.756250 12748 2 0.000000 -1 2.500000 10.332000 15.244357 1.756250 12749 2 0.000000 1 2.500000 3.444000 13.918760 5.268750 -12750 2 0.000000 -1.000000 2.500000 3.444000 13.918760 5.268750 +12750 2 0.000000 -1 2.500000 3.444000 13.918760 5.268750 12751 2 0.000000 1 2.500000 5.740000 9.941972 5.268750 12752 2 0.000000 -1 2.500000 5.740000 9.941972 5.268750 12753 2 0.000000 1 2.500000 8.036000 11.267568 8.781250 @@ -12771,7 +12771,7 @@ Atoms 12755 2 0.000000 1 2.500000 10.332000 15.244357 8.781250 12756 2 0.000000 -1 2.500000 10.332000 15.244357 8.781250 12757 2 0.000000 1 2.500000 3.444000 13.918760 12.293750 -12758 2 0.000000 -1.000000 2.500000 3.444000 13.918760 12.293750 +12758 2 0.000000 -1 2.500000 3.444000 13.918760 12.293750 12759 2 0.000000 1 2.500000 5.740000 9.941972 12.293750 12760 2 0.000000 -1 2.500000 5.740000 9.941972 12.293750 12761 2 0.000000 1 2.500000 8.036000 11.267568 15.806250 @@ -12779,7 +12779,7 @@ Atoms 12763 2 0.000000 1 2.500000 10.332000 15.244357 15.806250 12764 2 0.000000 -1 2.500000 10.332000 15.244357 15.806250 12765 2 0.000000 1 2.500000 3.444000 13.918760 19.318750 -12766 2 0.000000 -1.000000 2.500000 3.444000 13.918760 19.318750 +12766 2 0.000000 -1 2.500000 3.444000 13.918760 19.318750 12767 2 0.000000 1 2.500000 5.740000 9.941972 19.318750 12768 2 0.000000 -1 2.500000 5.740000 9.941972 19.318750 12769 2 0.000000 1 2.500000 8.036000 11.267568 22.831250 @@ -12787,7 +12787,7 @@ Atoms 12771 2 0.000000 1 2.500000 10.332000 15.244357 22.831250 12772 2 0.000000 -1 2.500000 10.332000 15.244357 22.831250 12773 2 0.000000 1 2.500000 3.444000 13.918760 26.343750 -12774 2 0.000000 -1.000000 2.500000 3.444000 13.918760 26.343750 +12774 2 0.000000 -1 2.500000 3.444000 13.918760 26.343750 12775 2 0.000000 1 2.500000 5.740000 9.941972 26.343750 12776 2 0.000000 -1 2.500000 5.740000 9.941972 26.343750 12777 2 0.000000 1 2.500000 8.036000 11.267568 29.856250 @@ -12795,7 +12795,7 @@ Atoms 12779 2 0.000000 1 2.500000 10.332000 15.244357 29.856250 12780 2 0.000000 -1 2.500000 10.332000 15.244357 29.856250 12781 2 0.000000 1 2.500000 3.444000 13.918760 33.368750 -12782 2 0.000000 -1.000000 2.500000 3.444000 13.918760 33.368750 +12782 2 0.000000 -1 2.500000 3.444000 13.918760 33.368750 12783 2 0.000000 1 2.500000 5.740000 9.941972 33.368750 12784 2 0.000000 -1 2.500000 5.740000 9.941972 33.368750 12785 2 0.000000 1 2.500000 8.036000 11.267568 36.881250 @@ -12803,7 +12803,7 @@ Atoms 12787 2 0.000000 1 2.500000 10.332000 15.244357 36.881250 12788 2 0.000000 -1 2.500000 10.332000 15.244357 36.881250 12789 2 0.000000 1 2.500000 3.444000 13.918760 40.393750 -12790 2 0.000000 -1.000000 2.500000 3.444000 13.918760 40.393750 +12790 2 0.000000 -1 2.500000 3.444000 13.918760 40.393750 12791 2 0.000000 1 2.500000 5.740000 9.941972 40.393750 12792 2 0.000000 -1 2.500000 5.740000 9.941972 40.393750 12793 2 0.000000 1 2.500000 8.036000 11.267568 43.906250 @@ -12811,7 +12811,7 @@ Atoms 12795 2 0.000000 1 2.500000 10.332000 15.244357 43.906250 12796 2 0.000000 -1 2.500000 10.332000 15.244357 43.906250 12797 2 0.000000 1 2.500000 3.444000 13.918760 47.418750 -12798 2 0.000000 -1.000000 2.500000 3.444000 13.918760 47.418750 +12798 2 0.000000 -1 2.500000 3.444000 13.918760 47.418750 12799 2 0.000000 1 2.500000 5.740000 9.941972 47.418750 12800 2 0.000000 -1 2.500000 5.740000 9.941972 47.418750 12801 2 0.000000 1 2.500000 8.036000 11.267568 50.931250 @@ -12819,7 +12819,7 @@ Atoms 12803 2 0.000000 1 2.500000 10.332000 15.244357 50.931250 12804 2 0.000000 -1 2.500000 10.332000 15.244357 50.931250 12805 2 0.000000 1 2.500000 3.444000 13.918760 54.443750 -12806 2 0.000000 -1.000000 2.500000 3.444000 13.918760 54.443750 +12806 2 0.000000 -1 2.500000 3.444000 13.918760 54.443750 12807 2 0.000000 1 2.500000 5.740000 9.941972 54.443750 12808 2 0.000000 -1 2.500000 5.740000 9.941972 54.443750 12809 2 0.000000 1 2.500000 8.036000 11.267568 57.956250 @@ -12827,7 +12827,7 @@ Atoms 12811 2 0.000000 1 2.500000 10.332000 15.244357 57.956250 12812 2 0.000000 -1 2.500000 10.332000 15.244357 57.956250 12813 2 0.000000 1 2.500000 3.444000 13.918760 61.468750 -12814 2 0.000000 -1.000000 2.500000 3.444000 13.918760 61.468750 +12814 2 0.000000 -1 2.500000 3.444000 13.918760 61.468750 12815 2 0.000000 1 2.500000 5.740000 9.941972 61.468750 12816 2 0.000000 -1 2.500000 5.740000 9.941972 61.468750 12817 2 0.000000 1 2.500000 8.036000 19.221145 1.756250 @@ -12835,7 +12835,7 @@ Atoms 12819 2 0.000000 1 2.500000 10.332000 23.197934 1.756250 12820 2 0.000000 -1 2.500000 10.332000 23.197934 1.756250 12821 2 0.000000 1 2.500000 3.444000 21.872338 5.268750 -12822 2 0.000000 -1.000000 2.500000 3.444000 21.872338 5.268750 +12822 2 0.000000 -1 2.500000 3.444000 21.872338 5.268750 12823 2 0.000000 1 2.500000 5.740000 17.895549 5.268750 12824 2 0.000000 -1 2.500000 5.740000 17.895549 5.268750 12825 2 0.000000 1 2.500000 8.036000 19.221145 8.781250 @@ -12843,7 +12843,7 @@ Atoms 12827 2 0.000000 1 2.500000 10.332000 23.197934 8.781250 12828 2 0.000000 -1 2.500000 10.332000 23.197934 8.781250 12829 2 0.000000 1 2.500000 3.444000 21.872338 12.293750 -12830 2 0.000000 -1.000000 2.500000 3.444000 21.872338 12.293750 +12830 2 0.000000 -1 2.500000 3.444000 21.872338 12.293750 12831 2 0.000000 1 2.500000 5.740000 17.895549 12.293750 12832 2 0.000000 -1 2.500000 5.740000 17.895549 12.293750 12833 2 0.000000 1 2.500000 8.036000 19.221145 15.806250 @@ -12851,7 +12851,7 @@ Atoms 12835 2 0.000000 1 2.500000 10.332000 23.197934 15.806250 12836 2 0.000000 -1 2.500000 10.332000 23.197934 15.806250 12837 2 0.000000 1 2.500000 3.444000 21.872338 19.318750 -12838 2 0.000000 -1.000000 2.500000 3.444000 21.872338 19.318750 +12838 2 0.000000 -1 2.500000 3.444000 21.872338 19.318750 12839 2 0.000000 1 2.500000 5.740000 17.895549 19.318750 12840 2 0.000000 -1 2.500000 5.740000 17.895549 19.318750 12841 2 0.000000 1 2.500000 8.036000 19.221145 22.831250 @@ -12859,7 +12859,7 @@ Atoms 12843 2 0.000000 1 2.500000 10.332000 23.197934 22.831250 12844 2 0.000000 -1 2.500000 10.332000 23.197934 22.831250 12845 2 0.000000 1 2.500000 3.444000 21.872338 26.343750 -12846 2 0.000000 -1.000000 2.500000 3.444000 21.872338 26.343750 +12846 2 0.000000 -1 2.500000 3.444000 21.872338 26.343750 12847 2 0.000000 1 2.500000 5.740000 17.895549 26.343750 12848 2 0.000000 -1 2.500000 5.740000 17.895549 26.343750 12849 2 0.000000 1 2.500000 8.036000 19.221145 29.856250 @@ -12867,7 +12867,7 @@ Atoms 12851 2 0.000000 1 2.500000 10.332000 23.197934 29.856250 12852 2 0.000000 -1 2.500000 10.332000 23.197934 29.856250 12853 2 0.000000 1 2.500000 3.444000 21.872338 33.368750 -12854 2 0.000000 -1.000000 2.500000 3.444000 21.872338 33.368750 +12854 2 0.000000 -1 2.500000 3.444000 21.872338 33.368750 12855 2 0.000000 1 2.500000 5.740000 17.895549 33.368750 12856 2 0.000000 -1 2.500000 5.740000 17.895549 33.368750 12857 2 0.000000 1 2.500000 8.036000 19.221145 36.881250 @@ -12875,7 +12875,7 @@ Atoms 12859 2 0.000000 1 2.500000 10.332000 23.197934 36.881250 12860 2 0.000000 -1 2.500000 10.332000 23.197934 36.881250 12861 2 0.000000 1 2.500000 3.444000 21.872338 40.393750 -12862 2 0.000000 -1.000000 2.500000 3.444000 21.872338 40.393750 +12862 2 0.000000 -1 2.500000 3.444000 21.872338 40.393750 12863 2 0.000000 1 2.500000 5.740000 17.895549 40.393750 12864 2 0.000000 -1 2.500000 5.740000 17.895549 40.393750 12865 2 0.000000 1 2.500000 8.036000 19.221145 43.906250 @@ -12883,7 +12883,7 @@ Atoms 12867 2 0.000000 1 2.500000 10.332000 23.197934 43.906250 12868 2 0.000000 -1 2.500000 10.332000 23.197934 43.906250 12869 2 0.000000 1 2.500000 3.444000 21.872338 47.418750 -12870 2 0.000000 -1.000000 2.500000 3.444000 21.872338 47.418750 +12870 2 0.000000 -1 2.500000 3.444000 21.872338 47.418750 12871 2 0.000000 1 2.500000 5.740000 17.895549 47.418750 12872 2 0.000000 -1 2.500000 5.740000 17.895549 47.418750 12873 2 0.000000 1 2.500000 8.036000 19.221145 50.931250 @@ -12891,7 +12891,7 @@ Atoms 12875 2 0.000000 1 2.500000 10.332000 23.197934 50.931250 12876 2 0.000000 -1 2.500000 10.332000 23.197934 50.931250 12877 2 0.000000 1 2.500000 3.444000 21.872338 54.443750 -12878 2 0.000000 -1.000000 2.500000 3.444000 21.872338 54.443750 +12878 2 0.000000 -1 2.500000 3.444000 21.872338 54.443750 12879 2 0.000000 1 2.500000 5.740000 17.895549 54.443750 12880 2 0.000000 -1 2.500000 5.740000 17.895549 54.443750 12881 2 0.000000 1 2.500000 8.036000 19.221145 57.956250 @@ -12899,7 +12899,7 @@ Atoms 12883 2 0.000000 1 2.500000 10.332000 23.197934 57.956250 12884 2 0.000000 -1 2.500000 10.332000 23.197934 57.956250 12885 2 0.000000 1 2.500000 3.444000 21.872338 61.468750 -12886 2 0.000000 -1.000000 2.500000 3.444000 21.872338 61.468750 +12886 2 0.000000 -1 2.500000 3.444000 21.872338 61.468750 12887 2 0.000000 1 2.500000 5.740000 17.895549 61.468750 12888 2 0.000000 -1 2.500000 5.740000 17.895549 61.468750 12889 2 0.000000 1 2.500000 8.036000 27.174722 1.756250 @@ -12907,7 +12907,7 @@ Atoms 12891 2 0.000000 1 2.500000 10.332000 31.151511 1.756250 12892 2 0.000000 -1 2.500000 10.332000 31.151511 1.756250 12893 2 0.000000 1 2.500000 3.444000 29.825915 5.268750 -12894 2 0.000000 -1.000000 2.500000 3.444000 29.825915 5.268750 +12894 2 0.000000 -1 2.500000 3.444000 29.825915 5.268750 12895 2 0.000000 1 2.500000 5.740000 25.849126 5.268750 12896 2 0.000000 -1 2.500000 5.740000 25.849126 5.268750 12897 2 0.000000 1 2.500000 8.036000 27.174722 8.781250 @@ -12915,7 +12915,7 @@ Atoms 12899 2 0.000000 1 2.500000 10.332000 31.151511 8.781250 12900 2 0.000000 -1 2.500000 10.332000 31.151511 8.781250 12901 2 0.000000 1 2.500000 3.444000 29.825915 12.293750 -12902 2 0.000000 -1.000000 2.500000 3.444000 29.825915 12.293750 +12902 2 0.000000 -1 2.500000 3.444000 29.825915 12.293750 12903 2 0.000000 1 2.500000 5.740000 25.849126 12.293750 12904 2 0.000000 -1 2.500000 5.740000 25.849126 12.293750 12905 2 0.000000 1 2.500000 8.036000 27.174722 15.806250 @@ -12923,7 +12923,7 @@ Atoms 12907 2 0.000000 1 2.500000 10.332000 31.151511 15.806250 12908 2 0.000000 -1 2.500000 10.332000 31.151511 15.806250 12909 2 0.000000 1 2.500000 3.444000 29.825915 19.318750 -12910 2 0.000000 -1.000000 2.500000 3.444000 29.825915 19.318750 +12910 2 0.000000 -1 2.500000 3.444000 29.825915 19.318750 12911 2 0.000000 1 2.500000 5.740000 25.849126 19.318750 12912 2 0.000000 -1 2.500000 5.740000 25.849126 19.318750 12913 2 0.000000 1 2.500000 8.036000 27.174722 22.831250 @@ -12931,7 +12931,7 @@ Atoms 12915 2 0.000000 1 2.500000 10.332000 31.151511 22.831250 12916 2 0.000000 -1 2.500000 10.332000 31.151511 22.831250 12917 2 0.000000 1 2.500000 3.444000 29.825915 26.343750 -12918 2 0.000000 -1.000000 2.500000 3.444000 29.825915 26.343750 +12918 2 0.000000 -1 2.500000 3.444000 29.825915 26.343750 12919 2 0.000000 1 2.500000 5.740000 25.849126 26.343750 12920 2 0.000000 -1 2.500000 5.740000 25.849126 26.343750 12921 2 0.000000 1 2.500000 8.036000 27.174722 29.856250 @@ -12939,7 +12939,7 @@ Atoms 12923 2 0.000000 1 2.500000 10.332000 31.151511 29.856250 12924 2 0.000000 -1 2.500000 10.332000 31.151511 29.856250 12925 2 0.000000 1 2.500000 3.444000 29.825915 33.368750 -12926 2 0.000000 -1.000000 2.500000 3.444000 29.825915 33.368750 +12926 2 0.000000 -1 2.500000 3.444000 29.825915 33.368750 12927 2 0.000000 1 2.500000 5.740000 25.849126 33.368750 12928 2 0.000000 -1 2.500000 5.740000 25.849126 33.368750 12929 2 0.000000 1 2.500000 8.036000 27.174722 36.881250 @@ -12947,7 +12947,7 @@ Atoms 12931 2 0.000000 1 2.500000 10.332000 31.151511 36.881250 12932 2 0.000000 -1 2.500000 10.332000 31.151511 36.881250 12933 2 0.000000 1 2.500000 3.444000 29.825915 40.393750 -12934 2 0.000000 -1.000000 2.500000 3.444000 29.825915 40.393750 +12934 2 0.000000 -1 2.500000 3.444000 29.825915 40.393750 12935 2 0.000000 1 2.500000 5.740000 25.849126 40.393750 12936 2 0.000000 -1 2.500000 5.740000 25.849126 40.393750 12937 2 0.000000 1 2.500000 8.036000 27.174722 43.906250 @@ -12955,7 +12955,7 @@ Atoms 12939 2 0.000000 1 2.500000 10.332000 31.151511 43.906250 12940 2 0.000000 -1 2.500000 10.332000 31.151511 43.906250 12941 2 0.000000 1 2.500000 3.444000 29.825915 47.418750 -12942 2 0.000000 -1.000000 2.500000 3.444000 29.825915 47.418750 +12942 2 0.000000 -1 2.500000 3.444000 29.825915 47.418750 12943 2 0.000000 1 2.500000 5.740000 25.849126 47.418750 12944 2 0.000000 -1 2.500000 5.740000 25.849126 47.418750 12945 2 0.000000 1 2.500000 8.036000 27.174722 50.931250 @@ -12963,7 +12963,7 @@ Atoms 12947 2 0.000000 1 2.500000 10.332000 31.151511 50.931250 12948 2 0.000000 -1 2.500000 10.332000 31.151511 50.931250 12949 2 0.000000 1 2.500000 3.444000 29.825915 54.443750 -12950 2 0.000000 -1.000000 2.500000 3.444000 29.825915 54.443750 +12950 2 0.000000 -1 2.500000 3.444000 29.825915 54.443750 12951 2 0.000000 1 2.500000 5.740000 25.849126 54.443750 12952 2 0.000000 -1 2.500000 5.740000 25.849126 54.443750 12953 2 0.000000 1 2.500000 8.036000 27.174722 57.956250 @@ -12971,7 +12971,7 @@ Atoms 12955 2 0.000000 1 2.500000 10.332000 31.151511 57.956250 12956 2 0.000000 -1 2.500000 10.332000 31.151511 57.956250 12957 2 0.000000 1 2.500000 3.444000 29.825915 61.468750 -12958 2 0.000000 -1.000000 2.500000 3.444000 29.825915 61.468750 +12958 2 0.000000 -1 2.500000 3.444000 29.825915 61.468750 12959 2 0.000000 1 2.500000 5.740000 25.849126 61.468750 12960 2 0.000000 -1 2.500000 5.740000 25.849126 61.468750 12961 2 0.000000 1 2.500000 8.036000 35.128300 1.756250 @@ -12979,7 +12979,7 @@ Atoms 12963 2 0.000000 1 2.500000 10.332000 39.105088 1.756250 12964 2 0.000000 -1 2.500000 10.332000 39.105088 1.756250 12965 2 0.000000 1 2.500000 3.444000 37.779492 5.268750 -12966 2 0.000000 -1.000000 2.500000 3.444000 37.779492 5.268750 +12966 2 0.000000 -1 2.500000 3.444000 37.779492 5.268750 12967 2 0.000000 1 2.500000 5.740000 33.802704 5.268750 12968 2 0.000000 -1 2.500000 5.740000 33.802704 5.268750 12969 2 0.000000 1 2.500000 8.036000 35.128300 8.781250 @@ -12987,7 +12987,7 @@ Atoms 12971 2 0.000000 1 2.500000 10.332000 39.105088 8.781250 12972 2 0.000000 -1 2.500000 10.332000 39.105088 8.781250 12973 2 0.000000 1 2.500000 3.444000 37.779492 12.293750 -12974 2 0.000000 -1.000000 2.500000 3.444000 37.779492 12.293750 +12974 2 0.000000 -1 2.500000 3.444000 37.779492 12.293750 12975 2 0.000000 1 2.500000 5.740000 33.802704 12.293750 12976 2 0.000000 -1 2.500000 5.740000 33.802704 12.293750 12977 2 0.000000 1 2.500000 8.036000 35.128300 15.806250 @@ -12995,7 +12995,7 @@ Atoms 12979 2 0.000000 1 2.500000 10.332000 39.105088 15.806250 12980 2 0.000000 -1 2.500000 10.332000 39.105088 15.806250 12981 2 0.000000 1 2.500000 3.444000 37.779492 19.318750 -12982 2 0.000000 -1.000000 2.500000 3.444000 37.779492 19.318750 +12982 2 0.000000 -1 2.500000 3.444000 37.779492 19.318750 12983 2 0.000000 1 2.500000 5.740000 33.802704 19.318750 12984 2 0.000000 -1 2.500000 5.740000 33.802704 19.318750 12985 2 0.000000 1 2.500000 8.036000 35.128300 22.831250 @@ -13003,7 +13003,7 @@ Atoms 12987 2 0.000000 1 2.500000 10.332000 39.105088 22.831250 12988 2 0.000000 -1 2.500000 10.332000 39.105088 22.831250 12989 2 0.000000 1 2.500000 3.444000 37.779492 26.343750 -12990 2 0.000000 -1.000000 2.500000 3.444000 37.779492 26.343750 +12990 2 0.000000 -1 2.500000 3.444000 37.779492 26.343750 12991 2 0.000000 1 2.500000 5.740000 33.802704 26.343750 12992 2 0.000000 -1 2.500000 5.740000 33.802704 26.343750 12993 2 0.000000 1 2.500000 8.036000 35.128300 29.856250 @@ -13011,7 +13011,7 @@ Atoms 12995 2 0.000000 1 2.500000 10.332000 39.105088 29.856250 12996 2 0.000000 -1 2.500000 10.332000 39.105088 29.856250 12997 2 0.000000 1 2.500000 3.444000 37.779492 33.368750 -12998 2 0.000000 -1.000000 2.500000 3.444000 37.779492 33.368750 +12998 2 0.000000 -1 2.500000 3.444000 37.779492 33.368750 12999 2 0.000000 1 2.500000 5.740000 33.802704 33.368750 13000 2 0.000000 -1 2.500000 5.740000 33.802704 33.368750 13001 2 0.000000 1 2.500000 8.036000 35.128300 36.881250 @@ -13019,7 +13019,7 @@ Atoms 13003 2 0.000000 1 2.500000 10.332000 39.105088 36.881250 13004 2 0.000000 -1 2.500000 10.332000 39.105088 36.881250 13005 2 0.000000 1 2.500000 3.444000 37.779492 40.393750 -13006 2 0.000000 -1.000000 2.500000 3.444000 37.779492 40.393750 +13006 2 0.000000 -1 2.500000 3.444000 37.779492 40.393750 13007 2 0.000000 1 2.500000 5.740000 33.802704 40.393750 13008 2 0.000000 -1 2.500000 5.740000 33.802704 40.393750 13009 2 0.000000 1 2.500000 8.036000 35.128300 43.906250 @@ -13027,7 +13027,7 @@ Atoms 13011 2 0.000000 1 2.500000 10.332000 39.105088 43.906250 13012 2 0.000000 -1 2.500000 10.332000 39.105088 43.906250 13013 2 0.000000 1 2.500000 3.444000 37.779492 47.418750 -13014 2 0.000000 -1.000000 2.500000 3.444000 37.779492 47.418750 +13014 2 0.000000 -1 2.500000 3.444000 37.779492 47.418750 13015 2 0.000000 1 2.500000 5.740000 33.802704 47.418750 13016 2 0.000000 -1 2.500000 5.740000 33.802704 47.418750 13017 2 0.000000 1 2.500000 8.036000 35.128300 50.931250 @@ -13035,7 +13035,7 @@ Atoms 13019 2 0.000000 1 2.500000 10.332000 39.105088 50.931250 13020 2 0.000000 -1 2.500000 10.332000 39.105088 50.931250 13021 2 0.000000 1 2.500000 3.444000 37.779492 54.443750 -13022 2 0.000000 -1.000000 2.500000 3.444000 37.779492 54.443750 +13022 2 0.000000 -1 2.500000 3.444000 37.779492 54.443750 13023 2 0.000000 1 2.500000 5.740000 33.802704 54.443750 13024 2 0.000000 -1 2.500000 5.740000 33.802704 54.443750 13025 2 0.000000 1 2.500000 8.036000 35.128300 57.956250 @@ -13043,7 +13043,7 @@ Atoms 13027 2 0.000000 1 2.500000 10.332000 39.105088 57.956250 13028 2 0.000000 -1 2.500000 10.332000 39.105088 57.956250 13029 2 0.000000 1 2.500000 3.444000 37.779492 61.468750 -13030 2 0.000000 -1.000000 2.500000 3.444000 37.779492 61.468750 +13030 2 0.000000 -1 2.500000 3.444000 37.779492 61.468750 13031 2 0.000000 1 2.500000 5.740000 33.802704 61.468750 13032 2 0.000000 -1 2.500000 5.740000 33.802704 61.468750 13033 2 0.000000 1 2.500000 8.036000 43.081877 1.756250 @@ -13051,7 +13051,7 @@ Atoms 13035 2 0.000000 1 2.500000 10.332000 47.058666 1.756250 13036 2 0.000000 -1 2.500000 10.332000 47.058666 1.756250 13037 2 0.000000 1 2.500000 3.444000 45.733070 5.268750 -13038 2 0.000000 -1.000000 2.500000 3.444000 45.733070 5.268750 +13038 2 0.000000 -1 2.500000 3.444000 45.733070 5.268750 13039 2 0.000000 1 2.500000 5.740000 41.756281 5.268750 13040 2 0.000000 -1 2.500000 5.740000 41.756281 5.268750 13041 2 0.000000 1 2.500000 8.036000 43.081877 8.781250 @@ -13059,7 +13059,7 @@ Atoms 13043 2 0.000000 1 2.500000 10.332000 47.058666 8.781250 13044 2 0.000000 -1 2.500000 10.332000 47.058666 8.781250 13045 2 0.000000 1 2.500000 3.444000 45.733070 12.293750 -13046 2 0.000000 -1.000000 2.500000 3.444000 45.733070 12.293750 +13046 2 0.000000 -1 2.500000 3.444000 45.733070 12.293750 13047 2 0.000000 1 2.500000 5.740000 41.756281 12.293750 13048 2 0.000000 -1 2.500000 5.740000 41.756281 12.293750 13049 2 0.000000 1 2.500000 8.036000 43.081877 15.806250 @@ -13067,7 +13067,7 @@ Atoms 13051 2 0.000000 1 2.500000 10.332000 47.058666 15.806250 13052 2 0.000000 -1 2.500000 10.332000 47.058666 15.806250 13053 2 0.000000 1 2.500000 3.444000 45.733070 19.318750 -13054 2 0.000000 -1.000000 2.500000 3.444000 45.733070 19.318750 +13054 2 0.000000 -1 2.500000 3.444000 45.733070 19.318750 13055 2 0.000000 1 2.500000 5.740000 41.756281 19.318750 13056 2 0.000000 -1 2.500000 5.740000 41.756281 19.318750 13057 2 0.000000 1 2.500000 8.036000 43.081877 22.831250 @@ -13075,7 +13075,7 @@ Atoms 13059 2 0.000000 1 2.500000 10.332000 47.058666 22.831250 13060 2 0.000000 -1 2.500000 10.332000 47.058666 22.831250 13061 2 0.000000 1 2.500000 3.444000 45.733070 26.343750 -13062 2 0.000000 -1.000000 2.500000 3.444000 45.733070 26.343750 +13062 2 0.000000 -1 2.500000 3.444000 45.733070 26.343750 13063 2 0.000000 1 2.500000 5.740000 41.756281 26.343750 13064 2 0.000000 -1 2.500000 5.740000 41.756281 26.343750 13065 2 0.000000 1 2.500000 8.036000 43.081877 29.856250 @@ -13083,7 +13083,7 @@ Atoms 13067 2 0.000000 1 2.500000 10.332000 47.058666 29.856250 13068 2 0.000000 -1 2.500000 10.332000 47.058666 29.856250 13069 2 0.000000 1 2.500000 3.444000 45.733070 33.368750 -13070 2 0.000000 -1.000000 2.500000 3.444000 45.733070 33.368750 +13070 2 0.000000 -1 2.500000 3.444000 45.733070 33.368750 13071 2 0.000000 1 2.500000 5.740000 41.756281 33.368750 13072 2 0.000000 -1 2.500000 5.740000 41.756281 33.368750 13073 2 0.000000 1 2.500000 8.036000 43.081877 36.881250 @@ -13091,7 +13091,7 @@ Atoms 13075 2 0.000000 1 2.500000 10.332000 47.058666 36.881250 13076 2 0.000000 -1 2.500000 10.332000 47.058666 36.881250 13077 2 0.000000 1 2.500000 3.444000 45.733070 40.393750 -13078 2 0.000000 -1.000000 2.500000 3.444000 45.733070 40.393750 +13078 2 0.000000 -1 2.500000 3.444000 45.733070 40.393750 13079 2 0.000000 1 2.500000 5.740000 41.756281 40.393750 13080 2 0.000000 -1 2.500000 5.740000 41.756281 40.393750 13081 2 0.000000 1 2.500000 8.036000 43.081877 43.906250 @@ -13099,7 +13099,7 @@ Atoms 13083 2 0.000000 1 2.500000 10.332000 47.058666 43.906250 13084 2 0.000000 -1 2.500000 10.332000 47.058666 43.906250 13085 2 0.000000 1 2.500000 3.444000 45.733070 47.418750 -13086 2 0.000000 -1.000000 2.500000 3.444000 45.733070 47.418750 +13086 2 0.000000 -1 2.500000 3.444000 45.733070 47.418750 13087 2 0.000000 1 2.500000 5.740000 41.756281 47.418750 13088 2 0.000000 -1 2.500000 5.740000 41.756281 47.418750 13089 2 0.000000 1 2.500000 8.036000 43.081877 50.931250 @@ -13107,7 +13107,7 @@ Atoms 13091 2 0.000000 1 2.500000 10.332000 47.058666 50.931250 13092 2 0.000000 -1 2.500000 10.332000 47.058666 50.931250 13093 2 0.000000 1 2.500000 3.444000 45.733070 54.443750 -13094 2 0.000000 -1.000000 2.500000 3.444000 45.733070 54.443750 +13094 2 0.000000 -1 2.500000 3.444000 45.733070 54.443750 13095 2 0.000000 1 2.500000 5.740000 41.756281 54.443750 13096 2 0.000000 -1 2.500000 5.740000 41.756281 54.443750 13097 2 0.000000 1 2.500000 8.036000 43.081877 57.956250 @@ -13115,7 +13115,7 @@ Atoms 13099 2 0.000000 1 2.500000 10.332000 47.058666 57.956250 13100 2 0.000000 -1 2.500000 10.332000 47.058666 57.956250 13101 2 0.000000 1 2.500000 3.444000 45.733070 61.468750 -13102 2 0.000000 -1.000000 2.500000 3.444000 45.733070 61.468750 +13102 2 0.000000 -1 2.500000 3.444000 45.733070 61.468750 13103 2 0.000000 1 2.500000 5.740000 41.756281 61.468750 13104 2 0.000000 -1 2.500000 5.740000 41.756281 61.468750 13105 2 0.000000 1 2.500000 8.036000 51.035454 1.756250 @@ -13123,7 +13123,7 @@ Atoms 13107 2 0.000000 1 2.500000 10.332000 55.012243 1.756250 13108 2 0.000000 -1 2.500000 10.332000 55.012243 1.756250 13109 2 0.000000 1 2.500000 3.444000 53.686647 5.268750 -13110 2 0.000000 -1.000000 2.500000 3.444000 53.686647 5.268750 +13110 2 0.000000 -1 2.500000 3.444000 53.686647 5.268750 13111 2 0.000000 1 2.500000 5.740000 49.709858 5.268750 13112 2 0.000000 -1 2.500000 5.740000 49.709858 5.268750 13113 2 0.000000 1 2.500000 8.036000 51.035454 8.781250 @@ -13131,7 +13131,7 @@ Atoms 13115 2 0.000000 1 2.500000 10.332000 55.012243 8.781250 13116 2 0.000000 -1 2.500000 10.332000 55.012243 8.781250 13117 2 0.000000 1 2.500000 3.444000 53.686647 12.293750 -13118 2 0.000000 -1.000000 2.500000 3.444000 53.686647 12.293750 +13118 2 0.000000 -1 2.500000 3.444000 53.686647 12.293750 13119 2 0.000000 1 2.500000 5.740000 49.709858 12.293750 13120 2 0.000000 -1 2.500000 5.740000 49.709858 12.293750 13121 2 0.000000 1 2.500000 8.036000 51.035454 15.806250 @@ -13139,7 +13139,7 @@ Atoms 13123 2 0.000000 1 2.500000 10.332000 55.012243 15.806250 13124 2 0.000000 -1 2.500000 10.332000 55.012243 15.806250 13125 2 0.000000 1 2.500000 3.444000 53.686647 19.318750 -13126 2 0.000000 -1.000000 2.500000 3.444000 53.686647 19.318750 +13126 2 0.000000 -1 2.500000 3.444000 53.686647 19.318750 13127 2 0.000000 1 2.500000 5.740000 49.709858 19.318750 13128 2 0.000000 -1 2.500000 5.740000 49.709858 19.318750 13129 2 0.000000 1 2.500000 8.036000 51.035454 22.831250 @@ -13147,7 +13147,7 @@ Atoms 13131 2 0.000000 1 2.500000 10.332000 55.012243 22.831250 13132 2 0.000000 -1 2.500000 10.332000 55.012243 22.831250 13133 2 0.000000 1 2.500000 3.444000 53.686647 26.343750 -13134 2 0.000000 -1.000000 2.500000 3.444000 53.686647 26.343750 +13134 2 0.000000 -1 2.500000 3.444000 53.686647 26.343750 13135 2 0.000000 1 2.500000 5.740000 49.709858 26.343750 13136 2 0.000000 -1 2.500000 5.740000 49.709858 26.343750 13137 2 0.000000 1 2.500000 8.036000 51.035454 29.856250 @@ -13155,7 +13155,7 @@ Atoms 13139 2 0.000000 1 2.500000 10.332000 55.012243 29.856250 13140 2 0.000000 -1 2.500000 10.332000 55.012243 29.856250 13141 2 0.000000 1 2.500000 3.444000 53.686647 33.368750 -13142 2 0.000000 -1.000000 2.500000 3.444000 53.686647 33.368750 +13142 2 0.000000 -1 2.500000 3.444000 53.686647 33.368750 13143 2 0.000000 1 2.500000 5.740000 49.709858 33.368750 13144 2 0.000000 -1 2.500000 5.740000 49.709858 33.368750 13145 2 0.000000 1 2.500000 8.036000 51.035454 36.881250 @@ -13163,7 +13163,7 @@ Atoms 13147 2 0.000000 1 2.500000 10.332000 55.012243 36.881250 13148 2 0.000000 -1 2.500000 10.332000 55.012243 36.881250 13149 2 0.000000 1 2.500000 3.444000 53.686647 40.393750 -13150 2 0.000000 -1.000000 2.500000 3.444000 53.686647 40.393750 +13150 2 0.000000 -1 2.500000 3.444000 53.686647 40.393750 13151 2 0.000000 1 2.500000 5.740000 49.709858 40.393750 13152 2 0.000000 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0.000000 -1 2.500000 5.740000 49.709858 54.443750 13169 2 0.000000 1 2.500000 8.036000 51.035454 57.956250 @@ -13187,7 +13187,7 @@ Atoms 13171 2 0.000000 1 2.500000 10.332000 55.012243 57.956250 13172 2 0.000000 -1 2.500000 10.332000 55.012243 57.956250 13173 2 0.000000 1 2.500000 3.444000 53.686647 61.468750 -13174 2 0.000000 -1.000000 2.500000 3.444000 53.686647 61.468750 +13174 2 0.000000 -1 2.500000 3.444000 53.686647 61.468750 13175 2 0.000000 1 2.500000 5.740000 49.709858 61.468750 13176 2 0.000000 -1 2.500000 5.740000 49.709858 61.468750 13177 2 0.000000 1 2.500000 8.036000 58.989032 1.756250 @@ -13195,7 +13195,7 @@ Atoms 13179 2 0.000000 1 2.500000 10.332000 62.965820 1.756250 13180 2 0.000000 -1 2.500000 10.332000 62.965820 1.756250 13181 2 0.000000 1 2.500000 3.444000 61.640224 5.268750 -13182 2 0.000000 -1.000000 2.500000 3.444000 61.640224 5.268750 +13182 2 0.000000 -1 2.500000 3.444000 61.640224 5.268750 13183 2 0.000000 1 2.500000 5.740000 57.663435 5.268750 13184 2 0.000000 -1 2.500000 5.740000 57.663435 5.268750 13185 2 0.000000 1 2.500000 8.036000 58.989032 8.781250 @@ -13203,7 +13203,7 @@ Atoms 13187 2 0.000000 1 2.500000 10.332000 62.965820 8.781250 13188 2 0.000000 -1 2.500000 10.332000 62.965820 8.781250 13189 2 0.000000 1 2.500000 3.444000 61.640224 12.293750 -13190 2 0.000000 -1.000000 2.500000 3.444000 61.640224 12.293750 +13190 2 0.000000 -1 2.500000 3.444000 61.640224 12.293750 13191 2 0.000000 1 2.500000 5.740000 57.663435 12.293750 13192 2 0.000000 -1 2.500000 5.740000 57.663435 12.293750 13193 2 0.000000 1 2.500000 8.036000 58.989032 15.806250 @@ -13211,7 +13211,7 @@ Atoms 13195 2 0.000000 1 2.500000 10.332000 62.965820 15.806250 13196 2 0.000000 -1 2.500000 10.332000 62.965820 15.806250 13197 2 0.000000 1 2.500000 3.444000 61.640224 19.318750 -13198 2 0.000000 -1.000000 2.500000 3.444000 61.640224 19.318750 +13198 2 0.000000 -1 2.500000 3.444000 61.640224 19.318750 13199 2 0.000000 1 2.500000 5.740000 57.663435 19.318750 13200 2 0.000000 -1 2.500000 5.740000 57.663435 19.318750 13201 2 0.000000 1 2.500000 8.036000 58.989032 22.831250 @@ -13219,7 +13219,7 @@ Atoms 13203 2 0.000000 1 2.500000 10.332000 62.965820 22.831250 13204 2 0.000000 -1 2.500000 10.332000 62.965820 22.831250 13205 2 0.000000 1 2.500000 3.444000 61.640224 26.343750 -13206 2 0.000000 -1.000000 2.500000 3.444000 61.640224 26.343750 +13206 2 0.000000 -1 2.500000 3.444000 61.640224 26.343750 13207 2 0.000000 1 2.500000 5.740000 57.663435 26.343750 13208 2 0.000000 -1 2.500000 5.740000 57.663435 26.343750 13209 2 0.000000 1 2.500000 8.036000 58.989032 29.856250 @@ -13227,7 +13227,7 @@ Atoms 13211 2 0.000000 1 2.500000 10.332000 62.965820 29.856250 13212 2 0.000000 -1 2.500000 10.332000 62.965820 29.856250 13213 2 0.000000 1 2.500000 3.444000 61.640224 33.368750 -13214 2 0.000000 -1.000000 2.500000 3.444000 61.640224 33.368750 +13214 2 0.000000 -1 2.500000 3.444000 61.640224 33.368750 13215 2 0.000000 1 2.500000 5.740000 57.663435 33.368750 13216 2 0.000000 -1 2.500000 5.740000 57.663435 33.368750 13217 2 0.000000 1 2.500000 8.036000 58.989032 36.881250 @@ -13235,7 +13235,7 @@ Atoms 13219 2 0.000000 1 2.500000 10.332000 62.965820 36.881250 13220 2 0.000000 -1 2.500000 10.332000 62.965820 36.881250 13221 2 0.000000 1 2.500000 3.444000 61.640224 40.393750 -13222 2 0.000000 -1.000000 2.500000 3.444000 61.640224 40.393750 +13222 2 0.000000 -1 2.500000 3.444000 61.640224 40.393750 13223 2 0.000000 1 2.500000 5.740000 57.663435 40.393750 13224 2 0.000000 -1 2.500000 5.740000 57.663435 40.393750 13225 2 0.000000 1 2.500000 8.036000 58.989032 43.906250 @@ -13243,7 +13243,7 @@ Atoms 13227 2 0.000000 1 2.500000 10.332000 62.965820 43.906250 13228 2 0.000000 -1 2.500000 10.332000 62.965820 43.906250 13229 2 0.000000 1 2.500000 3.444000 61.640224 47.418750 -13230 2 0.000000 -1.000000 2.500000 3.444000 61.640224 47.418750 +13230 2 0.000000 -1 2.500000 3.444000 61.640224 47.418750 13231 2 0.000000 1 2.500000 5.740000 57.663435 47.418750 13232 2 0.000000 -1 2.500000 5.740000 57.663435 47.418750 13233 2 0.000000 1 2.500000 8.036000 58.989032 50.931250 @@ -13251,7 +13251,7 @@ Atoms 13235 2 0.000000 1 2.500000 10.332000 62.965820 50.931250 13236 2 0.000000 -1 2.500000 10.332000 62.965820 50.931250 13237 2 0.000000 1 2.500000 3.444000 61.640224 54.443750 -13238 2 0.000000 -1.000000 2.500000 3.444000 61.640224 54.443750 +13238 2 0.000000 -1 2.500000 3.444000 61.640224 54.443750 13239 2 0.000000 1 2.500000 5.740000 57.663435 54.443750 13240 2 0.000000 -1 2.500000 5.740000 57.663435 54.443750 13241 2 0.000000 1 2.500000 8.036000 58.989032 57.956250 @@ -13259,7 +13259,7 @@ Atoms 13243 2 0.000000 1 2.500000 10.332000 62.965820 57.956250 13244 2 0.000000 -1 2.500000 10.332000 62.965820 57.956250 13245 2 0.000000 1 2.500000 3.444000 61.640224 61.468750 -13246 2 0.000000 -1.000000 2.500000 3.444000 61.640224 61.468750 +13246 2 0.000000 -1 2.500000 3.444000 61.640224 61.468750 13247 2 0.000000 1 2.500000 5.740000 57.663435 61.468750 13248 2 0.000000 -1 2.500000 5.740000 57.663435 61.468750 13249 2 0.000000 1 2.500000 12.628000 3.313991 1.756250 @@ -13267,7 +13267,7 @@ Atoms 13251 2 0.000000 1 2.500000 14.924000 7.290779 1.756250 13252 2 0.000000 -1 2.500000 14.924000 7.290779 1.756250 13253 2 0.000000 1 2.500000 8.036000 5.965183 5.268750 -13254 2 0.000000 -1.000000 2.500000 8.036000 5.965183 5.268750 +13254 2 0.000000 -1 2.500000 8.036000 5.965183 5.268750 13255 2 0.000000 1 2.500000 10.332000 1.988394 5.268750 13256 2 0.000000 -1 2.500000 10.332000 1.988394 5.268750 13257 2 0.000000 1 2.500000 12.628000 3.313991 8.781250 @@ -13275,7 +13275,7 @@ Atoms 13259 2 0.000000 1 2.500000 14.924000 7.290779 8.781250 13260 2 0.000000 -1 2.500000 14.924000 7.290779 8.781250 13261 2 0.000000 1 2.500000 8.036000 5.965183 12.293750 -13262 2 0.000000 -1.000000 2.500000 8.036000 5.965183 12.293750 +13262 2 0.000000 -1 2.500000 8.036000 5.965183 12.293750 13263 2 0.000000 1 2.500000 10.332000 1.988394 12.293750 13264 2 0.000000 -1 2.500000 10.332000 1.988394 12.293750 13265 2 0.000000 1 2.500000 12.628000 3.313991 15.806250 @@ -13283,7 +13283,7 @@ Atoms 13267 2 0.000000 1 2.500000 14.924000 7.290779 15.806250 13268 2 0.000000 -1 2.500000 14.924000 7.290779 15.806250 13269 2 0.000000 1 2.500000 8.036000 5.965183 19.318750 -13270 2 0.000000 -1.000000 2.500000 8.036000 5.965183 19.318750 +13270 2 0.000000 -1 2.500000 8.036000 5.965183 19.318750 13271 2 0.000000 1 2.500000 10.332000 1.988394 19.318750 13272 2 0.000000 -1 2.500000 10.332000 1.988394 19.318750 13273 2 0.000000 1 2.500000 12.628000 3.313991 22.831250 @@ -13291,7 +13291,7 @@ Atoms 13275 2 0.000000 1 2.500000 14.924000 7.290779 22.831250 13276 2 0.000000 -1 2.500000 14.924000 7.290779 22.831250 13277 2 0.000000 1 2.500000 8.036000 5.965183 26.343750 -13278 2 0.000000 -1.000000 2.500000 8.036000 5.965183 26.343750 +13278 2 0.000000 -1 2.500000 8.036000 5.965183 26.343750 13279 2 0.000000 1 2.500000 10.332000 1.988394 26.343750 13280 2 0.000000 -1 2.500000 10.332000 1.988394 26.343750 13281 2 0.000000 1 2.500000 12.628000 3.313991 29.856250 @@ -13299,7 +13299,7 @@ Atoms 13283 2 0.000000 1 2.500000 14.924000 7.290779 29.856250 13284 2 0.000000 -1 2.500000 14.924000 7.290779 29.856250 13285 2 0.000000 1 2.500000 8.036000 5.965183 33.368750 -13286 2 0.000000 -1.000000 2.500000 8.036000 5.965183 33.368750 +13286 2 0.000000 -1 2.500000 8.036000 5.965183 33.368750 13287 2 0.000000 1 2.500000 10.332000 1.988394 33.368750 13288 2 0.000000 -1 2.500000 10.332000 1.988394 33.368750 13289 2 0.000000 1 2.500000 12.628000 3.313991 36.881250 @@ -13307,7 +13307,7 @@ Atoms 13291 2 0.000000 1 2.500000 14.924000 7.290779 36.881250 13292 2 0.000000 -1 2.500000 14.924000 7.290779 36.881250 13293 2 0.000000 1 2.500000 8.036000 5.965183 40.393750 -13294 2 0.000000 -1.000000 2.500000 8.036000 5.965183 40.393750 +13294 2 0.000000 -1 2.500000 8.036000 5.965183 40.393750 13295 2 0.000000 1 2.500000 10.332000 1.988394 40.393750 13296 2 0.000000 -1 2.500000 10.332000 1.988394 40.393750 13297 2 0.000000 1 2.500000 12.628000 3.313991 43.906250 @@ -13315,7 +13315,7 @@ Atoms 13299 2 0.000000 1 2.500000 14.924000 7.290779 43.906250 13300 2 0.000000 -1 2.500000 14.924000 7.290779 43.906250 13301 2 0.000000 1 2.500000 8.036000 5.965183 47.418750 -13302 2 0.000000 -1.000000 2.500000 8.036000 5.965183 47.418750 +13302 2 0.000000 -1 2.500000 8.036000 5.965183 47.418750 13303 2 0.000000 1 2.500000 10.332000 1.988394 47.418750 13304 2 0.000000 -1 2.500000 10.332000 1.988394 47.418750 13305 2 0.000000 1 2.500000 12.628000 3.313991 50.931250 @@ -13323,7 +13323,7 @@ Atoms 13307 2 0.000000 1 2.500000 14.924000 7.290779 50.931250 13308 2 0.000000 -1 2.500000 14.924000 7.290779 50.931250 13309 2 0.000000 1 2.500000 8.036000 5.965183 54.443750 -13310 2 0.000000 -1.000000 2.500000 8.036000 5.965183 54.443750 +13310 2 0.000000 -1 2.500000 8.036000 5.965183 54.443750 13311 2 0.000000 1 2.500000 10.332000 1.988394 54.443750 13312 2 0.000000 -1 2.500000 10.332000 1.988394 54.443750 13313 2 0.000000 1 2.500000 12.628000 3.313991 57.956250 @@ -13331,7 +13331,7 @@ Atoms 13315 2 0.000000 1 2.500000 14.924000 7.290779 57.956250 13316 2 0.000000 -1 2.500000 14.924000 7.290779 57.956250 13317 2 0.000000 1 2.500000 8.036000 5.965183 61.468750 -13318 2 0.000000 -1.000000 2.500000 8.036000 5.965183 61.468750 +13318 2 0.000000 -1 2.500000 8.036000 5.965183 61.468750 13319 2 0.000000 1 2.500000 10.332000 1.988394 61.468750 13320 2 0.000000 -1 2.500000 10.332000 1.988394 61.468750 13321 2 0.000000 1 2.500000 12.628000 11.267568 1.756250 @@ -13339,7 +13339,7 @@ Atoms 13323 2 0.000000 1 2.500000 14.924000 15.244357 1.756250 13324 2 0.000000 -1 2.500000 14.924000 15.244357 1.756250 13325 2 0.000000 1 2.500000 8.036000 13.918760 5.268750 -13326 2 0.000000 -1.000000 2.500000 8.036000 13.918760 5.268750 +13326 2 0.000000 -1 2.500000 8.036000 13.918760 5.268750 13327 2 0.000000 1 2.500000 10.332000 9.941972 5.268750 13328 2 0.000000 -1 2.500000 10.332000 9.941972 5.268750 13329 2 0.000000 1 2.500000 12.628000 11.267568 8.781250 @@ -13347,7 +13347,7 @@ Atoms 13331 2 0.000000 1 2.500000 14.924000 15.244357 8.781250 13332 2 0.000000 -1 2.500000 14.924000 15.244357 8.781250 13333 2 0.000000 1 2.500000 8.036000 13.918760 12.293750 -13334 2 0.000000 -1.000000 2.500000 8.036000 13.918760 12.293750 +13334 2 0.000000 -1 2.500000 8.036000 13.918760 12.293750 13335 2 0.000000 1 2.500000 10.332000 9.941972 12.293750 13336 2 0.000000 -1 2.500000 10.332000 9.941972 12.293750 13337 2 0.000000 1 2.500000 12.628000 11.267568 15.806250 @@ -13355,7 +13355,7 @@ Atoms 13339 2 0.000000 1 2.500000 14.924000 15.244357 15.806250 13340 2 0.000000 -1 2.500000 14.924000 15.244357 15.806250 13341 2 0.000000 1 2.500000 8.036000 13.918760 19.318750 -13342 2 0.000000 -1.000000 2.500000 8.036000 13.918760 19.318750 +13342 2 0.000000 -1 2.500000 8.036000 13.918760 19.318750 13343 2 0.000000 1 2.500000 10.332000 9.941972 19.318750 13344 2 0.000000 -1 2.500000 10.332000 9.941972 19.318750 13345 2 0.000000 1 2.500000 12.628000 11.267568 22.831250 @@ -13363,7 +13363,7 @@ Atoms 13347 2 0.000000 1 2.500000 14.924000 15.244357 22.831250 13348 2 0.000000 -1 2.500000 14.924000 15.244357 22.831250 13349 2 0.000000 1 2.500000 8.036000 13.918760 26.343750 -13350 2 0.000000 -1.000000 2.500000 8.036000 13.918760 26.343750 +13350 2 0.000000 -1 2.500000 8.036000 13.918760 26.343750 13351 2 0.000000 1 2.500000 10.332000 9.941972 26.343750 13352 2 0.000000 -1 2.500000 10.332000 9.941972 26.343750 13353 2 0.000000 1 2.500000 12.628000 11.267568 29.856250 @@ -13371,7 +13371,7 @@ Atoms 13355 2 0.000000 1 2.500000 14.924000 15.244357 29.856250 13356 2 0.000000 -1 2.500000 14.924000 15.244357 29.856250 13357 2 0.000000 1 2.500000 8.036000 13.918760 33.368750 -13358 2 0.000000 -1.000000 2.500000 8.036000 13.918760 33.368750 +13358 2 0.000000 -1 2.500000 8.036000 13.918760 33.368750 13359 2 0.000000 1 2.500000 10.332000 9.941972 33.368750 13360 2 0.000000 -1 2.500000 10.332000 9.941972 33.368750 13361 2 0.000000 1 2.500000 12.628000 11.267568 36.881250 @@ -13379,7 +13379,7 @@ Atoms 13363 2 0.000000 1 2.500000 14.924000 15.244357 36.881250 13364 2 0.000000 -1 2.500000 14.924000 15.244357 36.881250 13365 2 0.000000 1 2.500000 8.036000 13.918760 40.393750 -13366 2 0.000000 -1.000000 2.500000 8.036000 13.918760 40.393750 +13366 2 0.000000 -1 2.500000 8.036000 13.918760 40.393750 13367 2 0.000000 1 2.500000 10.332000 9.941972 40.393750 13368 2 0.000000 -1 2.500000 10.332000 9.941972 40.393750 13369 2 0.000000 1 2.500000 12.628000 11.267568 43.906250 @@ -13387,7 +13387,7 @@ Atoms 13371 2 0.000000 1 2.500000 14.924000 15.244357 43.906250 13372 2 0.000000 -1 2.500000 14.924000 15.244357 43.906250 13373 2 0.000000 1 2.500000 8.036000 13.918760 47.418750 -13374 2 0.000000 -1.000000 2.500000 8.036000 13.918760 47.418750 +13374 2 0.000000 -1 2.500000 8.036000 13.918760 47.418750 13375 2 0.000000 1 2.500000 10.332000 9.941972 47.418750 13376 2 0.000000 -1 2.500000 10.332000 9.941972 47.418750 13377 2 0.000000 1 2.500000 12.628000 11.267568 50.931250 @@ -13395,7 +13395,7 @@ Atoms 13379 2 0.000000 1 2.500000 14.924000 15.244357 50.931250 13380 2 0.000000 -1 2.500000 14.924000 15.244357 50.931250 13381 2 0.000000 1 2.500000 8.036000 13.918760 54.443750 -13382 2 0.000000 -1.000000 2.500000 8.036000 13.918760 54.443750 +13382 2 0.000000 -1 2.500000 8.036000 13.918760 54.443750 13383 2 0.000000 1 2.500000 10.332000 9.941972 54.443750 13384 2 0.000000 -1 2.500000 10.332000 9.941972 54.443750 13385 2 0.000000 1 2.500000 12.628000 11.267568 57.956250 @@ -13403,7 +13403,7 @@ Atoms 13387 2 0.000000 1 2.500000 14.924000 15.244357 57.956250 13388 2 0.000000 -1 2.500000 14.924000 15.244357 57.956250 13389 2 0.000000 1 2.500000 8.036000 13.918760 61.468750 -13390 2 0.000000 -1.000000 2.500000 8.036000 13.918760 61.468750 +13390 2 0.000000 -1 2.500000 8.036000 13.918760 61.468750 13391 2 0.000000 1 2.500000 10.332000 9.941972 61.468750 13392 2 0.000000 -1 2.500000 10.332000 9.941972 61.468750 13393 2 0.000000 1 2.500000 12.628000 19.221145 1.756250 @@ -13411,7 +13411,7 @@ Atoms 13395 2 0.000000 1 2.500000 14.924000 23.197934 1.756250 13396 2 0.000000 -1 2.500000 14.924000 23.197934 1.756250 13397 2 0.000000 1 2.500000 8.036000 21.872338 5.268750 -13398 2 0.000000 -1.000000 2.500000 8.036000 21.872338 5.268750 +13398 2 0.000000 -1 2.500000 8.036000 21.872338 5.268750 13399 2 0.000000 1 2.500000 10.332000 17.895549 5.268750 13400 2 0.000000 -1 2.500000 10.332000 17.895549 5.268750 13401 2 0.000000 1 2.500000 12.628000 19.221145 8.781250 @@ -13419,7 +13419,7 @@ Atoms 13403 2 0.000000 1 2.500000 14.924000 23.197934 8.781250 13404 2 0.000000 -1 2.500000 14.924000 23.197934 8.781250 13405 2 0.000000 1 2.500000 8.036000 21.872338 12.293750 -13406 2 0.000000 -1.000000 2.500000 8.036000 21.872338 12.293750 +13406 2 0.000000 -1 2.500000 8.036000 21.872338 12.293750 13407 2 0.000000 1 2.500000 10.332000 17.895549 12.293750 13408 2 0.000000 -1 2.500000 10.332000 17.895549 12.293750 13409 2 0.000000 1 2.500000 12.628000 19.221145 15.806250 @@ -13427,7 +13427,7 @@ Atoms 13411 2 0.000000 1 2.500000 14.924000 23.197934 15.806250 13412 2 0.000000 -1 2.500000 14.924000 23.197934 15.806250 13413 2 0.000000 1 2.500000 8.036000 21.872338 19.318750 -13414 2 0.000000 -1.000000 2.500000 8.036000 21.872338 19.318750 +13414 2 0.000000 -1 2.500000 8.036000 21.872338 19.318750 13415 2 0.000000 1 2.500000 10.332000 17.895549 19.318750 13416 2 0.000000 -1 2.500000 10.332000 17.895549 19.318750 13417 2 0.000000 1 2.500000 12.628000 19.221145 22.831250 @@ -13435,7 +13435,7 @@ Atoms 13419 2 0.000000 1 2.500000 14.924000 23.197934 22.831250 13420 2 0.000000 -1 2.500000 14.924000 23.197934 22.831250 13421 2 0.000000 1 2.500000 8.036000 21.872338 26.343750 -13422 2 0.000000 -1.000000 2.500000 8.036000 21.872338 26.343750 +13422 2 0.000000 -1 2.500000 8.036000 21.872338 26.343750 13423 2 0.000000 1 2.500000 10.332000 17.895549 26.343750 13424 2 0.000000 -1 2.500000 10.332000 17.895549 26.343750 13425 2 0.000000 1 2.500000 12.628000 19.221145 29.856250 @@ -13443,7 +13443,7 @@ Atoms 13427 2 0.000000 1 2.500000 14.924000 23.197934 29.856250 13428 2 0.000000 -1 2.500000 14.924000 23.197934 29.856250 13429 2 0.000000 1 2.500000 8.036000 21.872338 33.368750 -13430 2 0.000000 -1.000000 2.500000 8.036000 21.872338 33.368750 +13430 2 0.000000 -1 2.500000 8.036000 21.872338 33.368750 13431 2 0.000000 1 2.500000 10.332000 17.895549 33.368750 13432 2 0.000000 -1 2.500000 10.332000 17.895549 33.368750 13433 2 0.000000 1 2.500000 12.628000 19.221145 36.881250 @@ -13451,7 +13451,7 @@ Atoms 13435 2 0.000000 1 2.500000 14.924000 23.197934 36.881250 13436 2 0.000000 -1 2.500000 14.924000 23.197934 36.881250 13437 2 0.000000 1 2.500000 8.036000 21.872338 40.393750 -13438 2 0.000000 -1.000000 2.500000 8.036000 21.872338 40.393750 +13438 2 0.000000 -1 2.500000 8.036000 21.872338 40.393750 13439 2 0.000000 1 2.500000 10.332000 17.895549 40.393750 13440 2 0.000000 -1 2.500000 10.332000 17.895549 40.393750 13441 2 0.000000 1 2.500000 12.628000 19.221145 43.906250 @@ -13459,7 +13459,7 @@ Atoms 13443 2 0.000000 1 2.500000 14.924000 23.197934 43.906250 13444 2 0.000000 -1 2.500000 14.924000 23.197934 43.906250 13445 2 0.000000 1 2.500000 8.036000 21.872338 47.418750 -13446 2 0.000000 -1.000000 2.500000 8.036000 21.872338 47.418750 +13446 2 0.000000 -1 2.500000 8.036000 21.872338 47.418750 13447 2 0.000000 1 2.500000 10.332000 17.895549 47.418750 13448 2 0.000000 -1 2.500000 10.332000 17.895549 47.418750 13449 2 0.000000 1 2.500000 12.628000 19.221145 50.931250 @@ -13467,7 +13467,7 @@ Atoms 13451 2 0.000000 1 2.500000 14.924000 23.197934 50.931250 13452 2 0.000000 -1 2.500000 14.924000 23.197934 50.931250 13453 2 0.000000 1 2.500000 8.036000 21.872338 54.443750 -13454 2 0.000000 -1.000000 2.500000 8.036000 21.872338 54.443750 +13454 2 0.000000 -1 2.500000 8.036000 21.872338 54.443750 13455 2 0.000000 1 2.500000 10.332000 17.895549 54.443750 13456 2 0.000000 -1 2.500000 10.332000 17.895549 54.443750 13457 2 0.000000 1 2.500000 12.628000 19.221145 57.956250 @@ -13475,7 +13475,7 @@ Atoms 13459 2 0.000000 1 2.500000 14.924000 23.197934 57.956250 13460 2 0.000000 -1 2.500000 14.924000 23.197934 57.956250 13461 2 0.000000 1 2.500000 8.036000 21.872338 61.468750 -13462 2 0.000000 -1.000000 2.500000 8.036000 21.872338 61.468750 +13462 2 0.000000 -1 2.500000 8.036000 21.872338 61.468750 13463 2 0.000000 1 2.500000 10.332000 17.895549 61.468750 13464 2 0.000000 -1 2.500000 10.332000 17.895549 61.468750 13465 2 0.000000 1 2.500000 12.628000 27.174722 1.756250 @@ -13483,7 +13483,7 @@ Atoms 13467 2 0.000000 1 2.500000 14.924000 31.151511 1.756250 13468 2 0.000000 -1 2.500000 14.924000 31.151511 1.756250 13469 2 0.000000 1 2.500000 8.036000 29.825915 5.268750 -13470 2 0.000000 -1.000000 2.500000 8.036000 29.825915 5.268750 +13470 2 0.000000 -1 2.500000 8.036000 29.825915 5.268750 13471 2 0.000000 1 2.500000 10.332000 25.849126 5.268750 13472 2 0.000000 -1 2.500000 10.332000 25.849126 5.268750 13473 2 0.000000 1 2.500000 12.628000 27.174722 8.781250 @@ -13491,7 +13491,7 @@ Atoms 13475 2 0.000000 1 2.500000 14.924000 31.151511 8.781250 13476 2 0.000000 -1 2.500000 14.924000 31.151511 8.781250 13477 2 0.000000 1 2.500000 8.036000 29.825915 12.293750 -13478 2 0.000000 -1.000000 2.500000 8.036000 29.825915 12.293750 +13478 2 0.000000 -1 2.500000 8.036000 29.825915 12.293750 13479 2 0.000000 1 2.500000 10.332000 25.849126 12.293750 13480 2 0.000000 -1 2.500000 10.332000 25.849126 12.293750 13481 2 0.000000 1 2.500000 12.628000 27.174722 15.806250 @@ -13499,7 +13499,7 @@ Atoms 13483 2 0.000000 1 2.500000 14.924000 31.151511 15.806250 13484 2 0.000000 -1 2.500000 14.924000 31.151511 15.806250 13485 2 0.000000 1 2.500000 8.036000 29.825915 19.318750 -13486 2 0.000000 -1.000000 2.500000 8.036000 29.825915 19.318750 +13486 2 0.000000 -1 2.500000 8.036000 29.825915 19.318750 13487 2 0.000000 1 2.500000 10.332000 25.849126 19.318750 13488 2 0.000000 -1 2.500000 10.332000 25.849126 19.318750 13489 2 0.000000 1 2.500000 12.628000 27.174722 22.831250 @@ -13507,7 +13507,7 @@ Atoms 13491 2 0.000000 1 2.500000 14.924000 31.151511 22.831250 13492 2 0.000000 -1 2.500000 14.924000 31.151511 22.831250 13493 2 0.000000 1 2.500000 8.036000 29.825915 26.343750 -13494 2 0.000000 -1.000000 2.500000 8.036000 29.825915 26.343750 +13494 2 0.000000 -1 2.500000 8.036000 29.825915 26.343750 13495 2 0.000000 1 2.500000 10.332000 25.849126 26.343750 13496 2 0.000000 -1 2.500000 10.332000 25.849126 26.343750 13497 2 0.000000 1 2.500000 12.628000 27.174722 29.856250 @@ -13515,7 +13515,7 @@ Atoms 13499 2 0.000000 1 2.500000 14.924000 31.151511 29.856250 13500 2 0.000000 -1 2.500000 14.924000 31.151511 29.856250 13501 2 0.000000 1 2.500000 8.036000 29.825915 33.368750 -13502 2 0.000000 -1.000000 2.500000 8.036000 29.825915 33.368750 +13502 2 0.000000 -1 2.500000 8.036000 29.825915 33.368750 13503 2 0.000000 1 2.500000 10.332000 25.849126 33.368750 13504 2 0.000000 -1 2.500000 10.332000 25.849126 33.368750 13505 2 0.000000 1 2.500000 12.628000 27.174722 36.881250 @@ -13523,7 +13523,7 @@ Atoms 13507 2 0.000000 1 2.500000 14.924000 31.151511 36.881250 13508 2 0.000000 -1 2.500000 14.924000 31.151511 36.881250 13509 2 0.000000 1 2.500000 8.036000 29.825915 40.393750 -13510 2 0.000000 -1.000000 2.500000 8.036000 29.825915 40.393750 +13510 2 0.000000 -1 2.500000 8.036000 29.825915 40.393750 13511 2 0.000000 1 2.500000 10.332000 25.849126 40.393750 13512 2 0.000000 -1 2.500000 10.332000 25.849126 40.393750 13513 2 0.000000 1 2.500000 12.628000 27.174722 43.906250 @@ -13531,7 +13531,7 @@ Atoms 13515 2 0.000000 1 2.500000 14.924000 31.151511 43.906250 13516 2 0.000000 -1 2.500000 14.924000 31.151511 43.906250 13517 2 0.000000 1 2.500000 8.036000 29.825915 47.418750 -13518 2 0.000000 -1.000000 2.500000 8.036000 29.825915 47.418750 +13518 2 0.000000 -1 2.500000 8.036000 29.825915 47.418750 13519 2 0.000000 1 2.500000 10.332000 25.849126 47.418750 13520 2 0.000000 -1 2.500000 10.332000 25.849126 47.418750 13521 2 0.000000 1 2.500000 12.628000 27.174722 50.931250 @@ -13539,7 +13539,7 @@ Atoms 13523 2 0.000000 1 2.500000 14.924000 31.151511 50.931250 13524 2 0.000000 -1 2.500000 14.924000 31.151511 50.931250 13525 2 0.000000 1 2.500000 8.036000 29.825915 54.443750 -13526 2 0.000000 -1.000000 2.500000 8.036000 29.825915 54.443750 +13526 2 0.000000 -1 2.500000 8.036000 29.825915 54.443750 13527 2 0.000000 1 2.500000 10.332000 25.849126 54.443750 13528 2 0.000000 -1 2.500000 10.332000 25.849126 54.443750 13529 2 0.000000 1 2.500000 12.628000 27.174722 57.956250 @@ -13547,7 +13547,7 @@ Atoms 13531 2 0.000000 1 2.500000 14.924000 31.151511 57.956250 13532 2 0.000000 -1 2.500000 14.924000 31.151511 57.956250 13533 2 0.000000 1 2.500000 8.036000 29.825915 61.468750 -13534 2 0.000000 -1.000000 2.500000 8.036000 29.825915 61.468750 +13534 2 0.000000 -1 2.500000 8.036000 29.825915 61.468750 13535 2 0.000000 1 2.500000 10.332000 25.849126 61.468750 13536 2 0.000000 -1 2.500000 10.332000 25.849126 61.468750 13537 2 0.000000 1 2.500000 12.628000 35.128300 1.756250 @@ -13555,7 +13555,7 @@ Atoms 13539 2 0.000000 1 2.500000 14.924000 39.105088 1.756250 13540 2 0.000000 -1 2.500000 14.924000 39.105088 1.756250 13541 2 0.000000 1 2.500000 8.036000 37.779492 5.268750 -13542 2 0.000000 -1.000000 2.500000 8.036000 37.779492 5.268750 +13542 2 0.000000 -1 2.500000 8.036000 37.779492 5.268750 13543 2 0.000000 1 2.500000 10.332000 33.802704 5.268750 13544 2 0.000000 -1 2.500000 10.332000 33.802704 5.268750 13545 2 0.000000 1 2.500000 12.628000 35.128300 8.781250 @@ -13563,7 +13563,7 @@ Atoms 13547 2 0.000000 1 2.500000 14.924000 39.105088 8.781250 13548 2 0.000000 -1 2.500000 14.924000 39.105088 8.781250 13549 2 0.000000 1 2.500000 8.036000 37.779492 12.293750 -13550 2 0.000000 -1.000000 2.500000 8.036000 37.779492 12.293750 +13550 2 0.000000 -1 2.500000 8.036000 37.779492 12.293750 13551 2 0.000000 1 2.500000 10.332000 33.802704 12.293750 13552 2 0.000000 -1 2.500000 10.332000 33.802704 12.293750 13553 2 0.000000 1 2.500000 12.628000 35.128300 15.806250 @@ -13571,7 +13571,7 @@ Atoms 13555 2 0.000000 1 2.500000 14.924000 39.105088 15.806250 13556 2 0.000000 -1 2.500000 14.924000 39.105088 15.806250 13557 2 0.000000 1 2.500000 8.036000 37.779492 19.318750 -13558 2 0.000000 -1.000000 2.500000 8.036000 37.779492 19.318750 +13558 2 0.000000 -1 2.500000 8.036000 37.779492 19.318750 13559 2 0.000000 1 2.500000 10.332000 33.802704 19.318750 13560 2 0.000000 -1 2.500000 10.332000 33.802704 19.318750 13561 2 0.000000 1 2.500000 12.628000 35.128300 22.831250 @@ -13579,7 +13579,7 @@ Atoms 13563 2 0.000000 1 2.500000 14.924000 39.105088 22.831250 13564 2 0.000000 -1 2.500000 14.924000 39.105088 22.831250 13565 2 0.000000 1 2.500000 8.036000 37.779492 26.343750 -13566 2 0.000000 -1.000000 2.500000 8.036000 37.779492 26.343750 +13566 2 0.000000 -1 2.500000 8.036000 37.779492 26.343750 13567 2 0.000000 1 2.500000 10.332000 33.802704 26.343750 13568 2 0.000000 -1 2.500000 10.332000 33.802704 26.343750 13569 2 0.000000 1 2.500000 12.628000 35.128300 29.856250 @@ -13587,7 +13587,7 @@ Atoms 13571 2 0.000000 1 2.500000 14.924000 39.105088 29.856250 13572 2 0.000000 -1 2.500000 14.924000 39.105088 29.856250 13573 2 0.000000 1 2.500000 8.036000 37.779492 33.368750 -13574 2 0.000000 -1.000000 2.500000 8.036000 37.779492 33.368750 +13574 2 0.000000 -1 2.500000 8.036000 37.779492 33.368750 13575 2 0.000000 1 2.500000 10.332000 33.802704 33.368750 13576 2 0.000000 -1 2.500000 10.332000 33.802704 33.368750 13577 2 0.000000 1 2.500000 12.628000 35.128300 36.881250 @@ -13595,7 +13595,7 @@ Atoms 13579 2 0.000000 1 2.500000 14.924000 39.105088 36.881250 13580 2 0.000000 -1 2.500000 14.924000 39.105088 36.881250 13581 2 0.000000 1 2.500000 8.036000 37.779492 40.393750 -13582 2 0.000000 -1.000000 2.500000 8.036000 37.779492 40.393750 +13582 2 0.000000 -1 2.500000 8.036000 37.779492 40.393750 13583 2 0.000000 1 2.500000 10.332000 33.802704 40.393750 13584 2 0.000000 -1 2.500000 10.332000 33.802704 40.393750 13585 2 0.000000 1 2.500000 12.628000 35.128300 43.906250 @@ -13603,7 +13603,7 @@ Atoms 13587 2 0.000000 1 2.500000 14.924000 39.105088 43.906250 13588 2 0.000000 -1 2.500000 14.924000 39.105088 43.906250 13589 2 0.000000 1 2.500000 8.036000 37.779492 47.418750 -13590 2 0.000000 -1.000000 2.500000 8.036000 37.779492 47.418750 +13590 2 0.000000 -1 2.500000 8.036000 37.779492 47.418750 13591 2 0.000000 1 2.500000 10.332000 33.802704 47.418750 13592 2 0.000000 -1 2.500000 10.332000 33.802704 47.418750 13593 2 0.000000 1 2.500000 12.628000 35.128300 50.931250 @@ -13611,7 +13611,7 @@ Atoms 13595 2 0.000000 1 2.500000 14.924000 39.105088 50.931250 13596 2 0.000000 -1 2.500000 14.924000 39.105088 50.931250 13597 2 0.000000 1 2.500000 8.036000 37.779492 54.443750 -13598 2 0.000000 -1.000000 2.500000 8.036000 37.779492 54.443750 +13598 2 0.000000 -1 2.500000 8.036000 37.779492 54.443750 13599 2 0.000000 1 2.500000 10.332000 33.802704 54.443750 13600 2 0.000000 -1 2.500000 10.332000 33.802704 54.443750 13601 2 0.000000 1 2.500000 12.628000 35.128300 57.956250 @@ -13619,7 +13619,7 @@ Atoms 13603 2 0.000000 1 2.500000 14.924000 39.105088 57.956250 13604 2 0.000000 -1 2.500000 14.924000 39.105088 57.956250 13605 2 0.000000 1 2.500000 8.036000 37.779492 61.468750 -13606 2 0.000000 -1.000000 2.500000 8.036000 37.779492 61.468750 +13606 2 0.000000 -1 2.500000 8.036000 37.779492 61.468750 13607 2 0.000000 1 2.500000 10.332000 33.802704 61.468750 13608 2 0.000000 -1 2.500000 10.332000 33.802704 61.468750 13609 2 0.000000 1 2.500000 12.628000 43.081877 1.756250 @@ -13627,7 +13627,7 @@ Atoms 13611 2 0.000000 1 2.500000 14.924000 47.058666 1.756250 13612 2 0.000000 -1 2.500000 14.924000 47.058666 1.756250 13613 2 0.000000 1 2.500000 8.036000 45.733070 5.268750 -13614 2 0.000000 -1.000000 2.500000 8.036000 45.733070 5.268750 +13614 2 0.000000 -1 2.500000 8.036000 45.733070 5.268750 13615 2 0.000000 1 2.500000 10.332000 41.756281 5.268750 13616 2 0.000000 -1 2.500000 10.332000 41.756281 5.268750 13617 2 0.000000 1 2.500000 12.628000 43.081877 8.781250 @@ -13635,7 +13635,7 @@ Atoms 13619 2 0.000000 1 2.500000 14.924000 47.058666 8.781250 13620 2 0.000000 -1 2.500000 14.924000 47.058666 8.781250 13621 2 0.000000 1 2.500000 8.036000 45.733070 12.293750 -13622 2 0.000000 -1.000000 2.500000 8.036000 45.733070 12.293750 +13622 2 0.000000 -1 2.500000 8.036000 45.733070 12.293750 13623 2 0.000000 1 2.500000 10.332000 41.756281 12.293750 13624 2 0.000000 -1 2.500000 10.332000 41.756281 12.293750 13625 2 0.000000 1 2.500000 12.628000 43.081877 15.806250 @@ -13643,7 +13643,7 @@ Atoms 13627 2 0.000000 1 2.500000 14.924000 47.058666 15.806250 13628 2 0.000000 -1 2.500000 14.924000 47.058666 15.806250 13629 2 0.000000 1 2.500000 8.036000 45.733070 19.318750 -13630 2 0.000000 -1.000000 2.500000 8.036000 45.733070 19.318750 +13630 2 0.000000 -1 2.500000 8.036000 45.733070 19.318750 13631 2 0.000000 1 2.500000 10.332000 41.756281 19.318750 13632 2 0.000000 -1 2.500000 10.332000 41.756281 19.318750 13633 2 0.000000 1 2.500000 12.628000 43.081877 22.831250 @@ -13651,7 +13651,7 @@ Atoms 13635 2 0.000000 1 2.500000 14.924000 47.058666 22.831250 13636 2 0.000000 -1 2.500000 14.924000 47.058666 22.831250 13637 2 0.000000 1 2.500000 8.036000 45.733070 26.343750 -13638 2 0.000000 -1.000000 2.500000 8.036000 45.733070 26.343750 +13638 2 0.000000 -1 2.500000 8.036000 45.733070 26.343750 13639 2 0.000000 1 2.500000 10.332000 41.756281 26.343750 13640 2 0.000000 -1 2.500000 10.332000 41.756281 26.343750 13641 2 0.000000 1 2.500000 12.628000 43.081877 29.856250 @@ -13659,7 +13659,7 @@ Atoms 13643 2 0.000000 1 2.500000 14.924000 47.058666 29.856250 13644 2 0.000000 -1 2.500000 14.924000 47.058666 29.856250 13645 2 0.000000 1 2.500000 8.036000 45.733070 33.368750 -13646 2 0.000000 -1.000000 2.500000 8.036000 45.733070 33.368750 +13646 2 0.000000 -1 2.500000 8.036000 45.733070 33.368750 13647 2 0.000000 1 2.500000 10.332000 41.756281 33.368750 13648 2 0.000000 -1 2.500000 10.332000 41.756281 33.368750 13649 2 0.000000 1 2.500000 12.628000 43.081877 36.881250 @@ -13667,7 +13667,7 @@ Atoms 13651 2 0.000000 1 2.500000 14.924000 47.058666 36.881250 13652 2 0.000000 -1 2.500000 14.924000 47.058666 36.881250 13653 2 0.000000 1 2.500000 8.036000 45.733070 40.393750 -13654 2 0.000000 -1.000000 2.500000 8.036000 45.733070 40.393750 +13654 2 0.000000 -1 2.500000 8.036000 45.733070 40.393750 13655 2 0.000000 1 2.500000 10.332000 41.756281 40.393750 13656 2 0.000000 -1 2.500000 10.332000 41.756281 40.393750 13657 2 0.000000 1 2.500000 12.628000 43.081877 43.906250 @@ -13675,7 +13675,7 @@ Atoms 13659 2 0.000000 1 2.500000 14.924000 47.058666 43.906250 13660 2 0.000000 -1 2.500000 14.924000 47.058666 43.906250 13661 2 0.000000 1 2.500000 8.036000 45.733070 47.418750 -13662 2 0.000000 -1.000000 2.500000 8.036000 45.733070 47.418750 +13662 2 0.000000 -1 2.500000 8.036000 45.733070 47.418750 13663 2 0.000000 1 2.500000 10.332000 41.756281 47.418750 13664 2 0.000000 -1 2.500000 10.332000 41.756281 47.418750 13665 2 0.000000 1 2.500000 12.628000 43.081877 50.931250 @@ -13683,7 +13683,7 @@ Atoms 13667 2 0.000000 1 2.500000 14.924000 47.058666 50.931250 13668 2 0.000000 -1 2.500000 14.924000 47.058666 50.931250 13669 2 0.000000 1 2.500000 8.036000 45.733070 54.443750 -13670 2 0.000000 -1.000000 2.500000 8.036000 45.733070 54.443750 +13670 2 0.000000 -1 2.500000 8.036000 45.733070 54.443750 13671 2 0.000000 1 2.500000 10.332000 41.756281 54.443750 13672 2 0.000000 -1 2.500000 10.332000 41.756281 54.443750 13673 2 0.000000 1 2.500000 12.628000 43.081877 57.956250 @@ -13691,7 +13691,7 @@ Atoms 13675 2 0.000000 1 2.500000 14.924000 47.058666 57.956250 13676 2 0.000000 -1 2.500000 14.924000 47.058666 57.956250 13677 2 0.000000 1 2.500000 8.036000 45.733070 61.468750 -13678 2 0.000000 -1.000000 2.500000 8.036000 45.733070 61.468750 +13678 2 0.000000 -1 2.500000 8.036000 45.733070 61.468750 13679 2 0.000000 1 2.500000 10.332000 41.756281 61.468750 13680 2 0.000000 -1 2.500000 10.332000 41.756281 61.468750 13681 2 0.000000 1 2.500000 12.628000 51.035454 1.756250 @@ -13699,7 +13699,7 @@ Atoms 13683 2 0.000000 1 2.500000 14.924000 55.012243 1.756250 13684 2 0.000000 -1 2.500000 14.924000 55.012243 1.756250 13685 2 0.000000 1 2.500000 8.036000 53.686647 5.268750 -13686 2 0.000000 -1.000000 2.500000 8.036000 53.686647 5.268750 +13686 2 0.000000 -1 2.500000 8.036000 53.686647 5.268750 13687 2 0.000000 1 2.500000 10.332000 49.709858 5.268750 13688 2 0.000000 -1 2.500000 10.332000 49.709858 5.268750 13689 2 0.000000 1 2.500000 12.628000 51.035454 8.781250 @@ -13707,7 +13707,7 @@ Atoms 13691 2 0.000000 1 2.500000 14.924000 55.012243 8.781250 13692 2 0.000000 -1 2.500000 14.924000 55.012243 8.781250 13693 2 0.000000 1 2.500000 8.036000 53.686647 12.293750 -13694 2 0.000000 -1.000000 2.500000 8.036000 53.686647 12.293750 +13694 2 0.000000 -1 2.500000 8.036000 53.686647 12.293750 13695 2 0.000000 1 2.500000 10.332000 49.709858 12.293750 13696 2 0.000000 -1 2.500000 10.332000 49.709858 12.293750 13697 2 0.000000 1 2.500000 12.628000 51.035454 15.806250 @@ -13715,7 +13715,7 @@ Atoms 13699 2 0.000000 1 2.500000 14.924000 55.012243 15.806250 13700 2 0.000000 -1 2.500000 14.924000 55.012243 15.806250 13701 2 0.000000 1 2.500000 8.036000 53.686647 19.318750 -13702 2 0.000000 -1.000000 2.500000 8.036000 53.686647 19.318750 +13702 2 0.000000 -1 2.500000 8.036000 53.686647 19.318750 13703 2 0.000000 1 2.500000 10.332000 49.709858 19.318750 13704 2 0.000000 -1 2.500000 10.332000 49.709858 19.318750 13705 2 0.000000 1 2.500000 12.628000 51.035454 22.831250 @@ -13723,7 +13723,7 @@ Atoms 13707 2 0.000000 1 2.500000 14.924000 55.012243 22.831250 13708 2 0.000000 -1 2.500000 14.924000 55.012243 22.831250 13709 2 0.000000 1 2.500000 8.036000 53.686647 26.343750 -13710 2 0.000000 -1.000000 2.500000 8.036000 53.686647 26.343750 +13710 2 0.000000 -1 2.500000 8.036000 53.686647 26.343750 13711 2 0.000000 1 2.500000 10.332000 49.709858 26.343750 13712 2 0.000000 -1 2.500000 10.332000 49.709858 26.343750 13713 2 0.000000 1 2.500000 12.628000 51.035454 29.856250 @@ -13731,7 +13731,7 @@ Atoms 13715 2 0.000000 1 2.500000 14.924000 55.012243 29.856250 13716 2 0.000000 -1 2.500000 14.924000 55.012243 29.856250 13717 2 0.000000 1 2.500000 8.036000 53.686647 33.368750 -13718 2 0.000000 -1.000000 2.500000 8.036000 53.686647 33.368750 +13718 2 0.000000 -1 2.500000 8.036000 53.686647 33.368750 13719 2 0.000000 1 2.500000 10.332000 49.709858 33.368750 13720 2 0.000000 -1 2.500000 10.332000 49.709858 33.368750 13721 2 0.000000 1 2.500000 12.628000 51.035454 36.881250 @@ -13739,7 +13739,7 @@ Atoms 13723 2 0.000000 1 2.500000 14.924000 55.012243 36.881250 13724 2 0.000000 -1 2.500000 14.924000 55.012243 36.881250 13725 2 0.000000 1 2.500000 8.036000 53.686647 40.393750 -13726 2 0.000000 -1.000000 2.500000 8.036000 53.686647 40.393750 +13726 2 0.000000 -1 2.500000 8.036000 53.686647 40.393750 13727 2 0.000000 1 2.500000 10.332000 49.709858 40.393750 13728 2 0.000000 -1 2.500000 10.332000 49.709858 40.393750 13729 2 0.000000 1 2.500000 12.628000 51.035454 43.906250 @@ -13747,7 +13747,7 @@ Atoms 13731 2 0.000000 1 2.500000 14.924000 55.012243 43.906250 13732 2 0.000000 -1 2.500000 14.924000 55.012243 43.906250 13733 2 0.000000 1 2.500000 8.036000 53.686647 47.418750 -13734 2 0.000000 -1.000000 2.500000 8.036000 53.686647 47.418750 +13734 2 0.000000 -1 2.500000 8.036000 53.686647 47.418750 13735 2 0.000000 1 2.500000 10.332000 49.709858 47.418750 13736 2 0.000000 -1 2.500000 10.332000 49.709858 47.418750 13737 2 0.000000 1 2.500000 12.628000 51.035454 50.931250 @@ -13755,7 +13755,7 @@ Atoms 13739 2 0.000000 1 2.500000 14.924000 55.012243 50.931250 13740 2 0.000000 -1 2.500000 14.924000 55.012243 50.931250 13741 2 0.000000 1 2.500000 8.036000 53.686647 54.443750 -13742 2 0.000000 -1.000000 2.500000 8.036000 53.686647 54.443750 +13742 2 0.000000 -1 2.500000 8.036000 53.686647 54.443750 13743 2 0.000000 1 2.500000 10.332000 49.709858 54.443750 13744 2 0.000000 -1 2.500000 10.332000 49.709858 54.443750 13745 2 0.000000 1 2.500000 12.628000 51.035454 57.956250 @@ -13763,7 +13763,7 @@ Atoms 13747 2 0.000000 1 2.500000 14.924000 55.012243 57.956250 13748 2 0.000000 -1 2.500000 14.924000 55.012243 57.956250 13749 2 0.000000 1 2.500000 8.036000 53.686647 61.468750 -13750 2 0.000000 -1.000000 2.500000 8.036000 53.686647 61.468750 +13750 2 0.000000 -1 2.500000 8.036000 53.686647 61.468750 13751 2 0.000000 1 2.500000 10.332000 49.709858 61.468750 13752 2 0.000000 -1 2.500000 10.332000 49.709858 61.468750 13753 2 0.000000 1 2.500000 12.628000 58.989032 1.756250 @@ -13771,7 +13771,7 @@ Atoms 13755 2 0.000000 1 2.500000 14.924000 62.965820 1.756250 13756 2 0.000000 -1 2.500000 14.924000 62.965820 1.756250 13757 2 0.000000 1 2.500000 8.036000 61.640224 5.268750 -13758 2 0.000000 -1.000000 2.500000 8.036000 61.640224 5.268750 +13758 2 0.000000 -1 2.500000 8.036000 61.640224 5.268750 13759 2 0.000000 1 2.500000 10.332000 57.663435 5.268750 13760 2 0.000000 -1 2.500000 10.332000 57.663435 5.268750 13761 2 0.000000 1 2.500000 12.628000 58.989032 8.781250 @@ -13779,7 +13779,7 @@ Atoms 13763 2 0.000000 1 2.500000 14.924000 62.965820 8.781250 13764 2 0.000000 -1 2.500000 14.924000 62.965820 8.781250 13765 2 0.000000 1 2.500000 8.036000 61.640224 12.293750 -13766 2 0.000000 -1.000000 2.500000 8.036000 61.640224 12.293750 +13766 2 0.000000 -1 2.500000 8.036000 61.640224 12.293750 13767 2 0.000000 1 2.500000 10.332000 57.663435 12.293750 13768 2 0.000000 -1 2.500000 10.332000 57.663435 12.293750 13769 2 0.000000 1 2.500000 12.628000 58.989032 15.806250 @@ -13787,7 +13787,7 @@ Atoms 13771 2 0.000000 1 2.500000 14.924000 62.965820 15.806250 13772 2 0.000000 -1 2.500000 14.924000 62.965820 15.806250 13773 2 0.000000 1 2.500000 8.036000 61.640224 19.318750 -13774 2 0.000000 -1.000000 2.500000 8.036000 61.640224 19.318750 +13774 2 0.000000 -1 2.500000 8.036000 61.640224 19.318750 13775 2 0.000000 1 2.500000 10.332000 57.663435 19.318750 13776 2 0.000000 -1 2.500000 10.332000 57.663435 19.318750 13777 2 0.000000 1 2.500000 12.628000 58.989032 22.831250 @@ -13795,7 +13795,7 @@ Atoms 13779 2 0.000000 1 2.500000 14.924000 62.965820 22.831250 13780 2 0.000000 -1 2.500000 14.924000 62.965820 22.831250 13781 2 0.000000 1 2.500000 8.036000 61.640224 26.343750 -13782 2 0.000000 -1.000000 2.500000 8.036000 61.640224 26.343750 +13782 2 0.000000 -1 2.500000 8.036000 61.640224 26.343750 13783 2 0.000000 1 2.500000 10.332000 57.663435 26.343750 13784 2 0.000000 -1 2.500000 10.332000 57.663435 26.343750 13785 2 0.000000 1 2.500000 12.628000 58.989032 29.856250 @@ -13803,7 +13803,7 @@ Atoms 13787 2 0.000000 1 2.500000 14.924000 62.965820 29.856250 13788 2 0.000000 -1 2.500000 14.924000 62.965820 29.856250 13789 2 0.000000 1 2.500000 8.036000 61.640224 33.368750 -13790 2 0.000000 -1.000000 2.500000 8.036000 61.640224 33.368750 +13790 2 0.000000 -1 2.500000 8.036000 61.640224 33.368750 13791 2 0.000000 1 2.500000 10.332000 57.663435 33.368750 13792 2 0.000000 -1 2.500000 10.332000 57.663435 33.368750 13793 2 0.000000 1 2.500000 12.628000 58.989032 36.881250 @@ -13811,7 +13811,7 @@ Atoms 13795 2 0.000000 1 2.500000 14.924000 62.965820 36.881250 13796 2 0.000000 -1 2.500000 14.924000 62.965820 36.881250 13797 2 0.000000 1 2.500000 8.036000 61.640224 40.393750 -13798 2 0.000000 -1.000000 2.500000 8.036000 61.640224 40.393750 +13798 2 0.000000 -1 2.500000 8.036000 61.640224 40.393750 13799 2 0.000000 1 2.500000 10.332000 57.663435 40.393750 13800 2 0.000000 -1 2.500000 10.332000 57.663435 40.393750 13801 2 0.000000 1 2.500000 12.628000 58.989032 43.906250 @@ -13819,7 +13819,7 @@ Atoms 13803 2 0.000000 1 2.500000 14.924000 62.965820 43.906250 13804 2 0.000000 -1 2.500000 14.924000 62.965820 43.906250 13805 2 0.000000 1 2.500000 8.036000 61.640224 47.418750 -13806 2 0.000000 -1.000000 2.500000 8.036000 61.640224 47.418750 +13806 2 0.000000 -1 2.500000 8.036000 61.640224 47.418750 13807 2 0.000000 1 2.500000 10.332000 57.663435 47.418750 13808 2 0.000000 -1 2.500000 10.332000 57.663435 47.418750 13809 2 0.000000 1 2.500000 12.628000 58.989032 50.931250 @@ -13827,7 +13827,7 @@ Atoms 13811 2 0.000000 1 2.500000 14.924000 62.965820 50.931250 13812 2 0.000000 -1 2.500000 14.924000 62.965820 50.931250 13813 2 0.000000 1 2.500000 8.036000 61.640224 54.443750 -13814 2 0.000000 -1.000000 2.500000 8.036000 61.640224 54.443750 +13814 2 0.000000 -1 2.500000 8.036000 61.640224 54.443750 13815 2 0.000000 1 2.500000 10.332000 57.663435 54.443750 13816 2 0.000000 -1 2.500000 10.332000 57.663435 54.443750 13817 2 0.000000 1 2.500000 12.628000 58.989032 57.956250 @@ -13835,7 +13835,7 @@ Atoms 13819 2 0.000000 1 2.500000 14.924000 62.965820 57.956250 13820 2 0.000000 -1 2.500000 14.924000 62.965820 57.956250 13821 2 0.000000 1 2.500000 8.036000 61.640224 61.468750 -13822 2 0.000000 -1.000000 2.500000 8.036000 61.640224 61.468750 +13822 2 0.000000 -1 2.500000 8.036000 61.640224 61.468750 13823 2 0.000000 1 2.500000 10.332000 57.663435 61.468750 13824 2 0.000000 -1 2.500000 10.332000 57.663435 61.468750 13825 2 0.000000 1 2.500000 17.220000 3.313991 1.756250 @@ -13843,7 +13843,7 @@ Atoms 13827 2 0.000000 1 2.500000 19.516000 7.290779 1.756250 13828 2 0.000000 -1 2.500000 19.516000 7.290779 1.756250 13829 2 0.000000 1 2.500000 12.628000 5.965183 5.268750 -13830 2 0.000000 -1.000000 2.500000 12.628000 5.965183 5.268750 +13830 2 0.000000 -1 2.500000 12.628000 5.965183 5.268750 13831 2 0.000000 1 2.500000 14.924000 1.988394 5.268750 13832 2 0.000000 -1 2.500000 14.924000 1.988394 5.268750 13833 2 0.000000 1 2.500000 17.220000 3.313991 8.781250 @@ -13851,7 +13851,7 @@ Atoms 13835 2 0.000000 1 2.500000 19.516000 7.290779 8.781250 13836 2 0.000000 -1 2.500000 19.516000 7.290779 8.781250 13837 2 0.000000 1 2.500000 12.628000 5.965183 12.293750 -13838 2 0.000000 -1.000000 2.500000 12.628000 5.965183 12.293750 +13838 2 0.000000 -1 2.500000 12.628000 5.965183 12.293750 13839 2 0.000000 1 2.500000 14.924000 1.988394 12.293750 13840 2 0.000000 -1 2.500000 14.924000 1.988394 12.293750 13841 2 0.000000 1 2.500000 17.220000 3.313991 15.806250 @@ -13859,7 +13859,7 @@ Atoms 13843 2 0.000000 1 2.500000 19.516000 7.290779 15.806250 13844 2 0.000000 -1 2.500000 19.516000 7.290779 15.806250 13845 2 0.000000 1 2.500000 12.628000 5.965183 19.318750 -13846 2 0.000000 -1.000000 2.500000 12.628000 5.965183 19.318750 +13846 2 0.000000 -1 2.500000 12.628000 5.965183 19.318750 13847 2 0.000000 1 2.500000 14.924000 1.988394 19.318750 13848 2 0.000000 -1 2.500000 14.924000 1.988394 19.318750 13849 2 0.000000 1 2.500000 17.220000 3.313991 22.831250 @@ -13867,7 +13867,7 @@ Atoms 13851 2 0.000000 1 2.500000 19.516000 7.290779 22.831250 13852 2 0.000000 -1 2.500000 19.516000 7.290779 22.831250 13853 2 0.000000 1 2.500000 12.628000 5.965183 26.343750 -13854 2 0.000000 -1.000000 2.500000 12.628000 5.965183 26.343750 +13854 2 0.000000 -1 2.500000 12.628000 5.965183 26.343750 13855 2 0.000000 1 2.500000 14.924000 1.988394 26.343750 13856 2 0.000000 -1 2.500000 14.924000 1.988394 26.343750 13857 2 0.000000 1 2.500000 17.220000 3.313991 29.856250 @@ -13875,7 +13875,7 @@ Atoms 13859 2 0.000000 1 2.500000 19.516000 7.290779 29.856250 13860 2 0.000000 -1 2.500000 19.516000 7.290779 29.856250 13861 2 0.000000 1 2.500000 12.628000 5.965183 33.368750 -13862 2 0.000000 -1.000000 2.500000 12.628000 5.965183 33.368750 +13862 2 0.000000 -1 2.500000 12.628000 5.965183 33.368750 13863 2 0.000000 1 2.500000 14.924000 1.988394 33.368750 13864 2 0.000000 -1 2.500000 14.924000 1.988394 33.368750 13865 2 0.000000 1 2.500000 17.220000 3.313991 36.881250 @@ -13883,7 +13883,7 @@ Atoms 13867 2 0.000000 1 2.500000 19.516000 7.290779 36.881250 13868 2 0.000000 -1 2.500000 19.516000 7.290779 36.881250 13869 2 0.000000 1 2.500000 12.628000 5.965183 40.393750 -13870 2 0.000000 -1.000000 2.500000 12.628000 5.965183 40.393750 +13870 2 0.000000 -1 2.500000 12.628000 5.965183 40.393750 13871 2 0.000000 1 2.500000 14.924000 1.988394 40.393750 13872 2 0.000000 -1 2.500000 14.924000 1.988394 40.393750 13873 2 0.000000 1 2.500000 17.220000 3.313991 43.906250 @@ -13891,7 +13891,7 @@ Atoms 13875 2 0.000000 1 2.500000 19.516000 7.290779 43.906250 13876 2 0.000000 -1 2.500000 19.516000 7.290779 43.906250 13877 2 0.000000 1 2.500000 12.628000 5.965183 47.418750 -13878 2 0.000000 -1.000000 2.500000 12.628000 5.965183 47.418750 +13878 2 0.000000 -1 2.500000 12.628000 5.965183 47.418750 13879 2 0.000000 1 2.500000 14.924000 1.988394 47.418750 13880 2 0.000000 -1 2.500000 14.924000 1.988394 47.418750 13881 2 0.000000 1 2.500000 17.220000 3.313991 50.931250 @@ -13899,7 +13899,7 @@ Atoms 13883 2 0.000000 1 2.500000 19.516000 7.290779 50.931250 13884 2 0.000000 -1 2.500000 19.516000 7.290779 50.931250 13885 2 0.000000 1 2.500000 12.628000 5.965183 54.443750 -13886 2 0.000000 -1.000000 2.500000 12.628000 5.965183 54.443750 +13886 2 0.000000 -1 2.500000 12.628000 5.965183 54.443750 13887 2 0.000000 1 2.500000 14.924000 1.988394 54.443750 13888 2 0.000000 -1 2.500000 14.924000 1.988394 54.443750 13889 2 0.000000 1 2.500000 17.220000 3.313991 57.956250 @@ -13907,7 +13907,7 @@ Atoms 13891 2 0.000000 1 2.500000 19.516000 7.290779 57.956250 13892 2 0.000000 -1 2.500000 19.516000 7.290779 57.956250 13893 2 0.000000 1 2.500000 12.628000 5.965183 61.468750 -13894 2 0.000000 -1.000000 2.500000 12.628000 5.965183 61.468750 +13894 2 0.000000 -1 2.500000 12.628000 5.965183 61.468750 13895 2 0.000000 1 2.500000 14.924000 1.988394 61.468750 13896 2 0.000000 -1 2.500000 14.924000 1.988394 61.468750 13897 2 0.000000 1 2.500000 17.220000 11.267568 1.756250 @@ -13915,7 +13915,7 @@ Atoms 13899 2 0.000000 1 2.500000 19.516000 15.244357 1.756250 13900 2 0.000000 -1 2.500000 19.516000 15.244357 1.756250 13901 2 0.000000 1 2.500000 12.628000 13.918760 5.268750 -13902 2 0.000000 -1.000000 2.500000 12.628000 13.918760 5.268750 +13902 2 0.000000 -1 2.500000 12.628000 13.918760 5.268750 13903 2 0.000000 1 2.500000 14.924000 9.941972 5.268750 13904 2 0.000000 -1 2.500000 14.924000 9.941972 5.268750 13905 2 0.000000 1 2.500000 17.220000 11.267568 8.781250 @@ -13923,7 +13923,7 @@ Atoms 13907 2 0.000000 1 2.500000 19.516000 15.244357 8.781250 13908 2 0.000000 -1 2.500000 19.516000 15.244357 8.781250 13909 2 0.000000 1 2.500000 12.628000 13.918760 12.293750 -13910 2 0.000000 -1.000000 2.500000 12.628000 13.918760 12.293750 +13910 2 0.000000 -1 2.500000 12.628000 13.918760 12.293750 13911 2 0.000000 1 2.500000 14.924000 9.941972 12.293750 13912 2 0.000000 -1 2.500000 14.924000 9.941972 12.293750 13913 2 0.000000 1 2.500000 17.220000 11.267568 15.806250 @@ -13931,7 +13931,7 @@ Atoms 13915 2 0.000000 1 2.500000 19.516000 15.244357 15.806250 13916 2 0.000000 -1 2.500000 19.516000 15.244357 15.806250 13917 2 0.000000 1 2.500000 12.628000 13.918760 19.318750 -13918 2 0.000000 -1.000000 2.500000 12.628000 13.918760 19.318750 +13918 2 0.000000 -1 2.500000 12.628000 13.918760 19.318750 13919 2 0.000000 1 2.500000 14.924000 9.941972 19.318750 13920 2 0.000000 -1 2.500000 14.924000 9.941972 19.318750 13921 2 0.000000 1 2.500000 17.220000 11.267568 22.831250 @@ -13939,7 +13939,7 @@ Atoms 13923 2 0.000000 1 2.500000 19.516000 15.244357 22.831250 13924 2 0.000000 -1 2.500000 19.516000 15.244357 22.831250 13925 2 0.000000 1 2.500000 12.628000 13.918760 26.343750 -13926 2 0.000000 -1.000000 2.500000 12.628000 13.918760 26.343750 +13926 2 0.000000 -1 2.500000 12.628000 13.918760 26.343750 13927 2 0.000000 1 2.500000 14.924000 9.941972 26.343750 13928 2 0.000000 -1 2.500000 14.924000 9.941972 26.343750 13929 2 0.000000 1 2.500000 17.220000 11.267568 29.856250 @@ -13947,7 +13947,7 @@ Atoms 13931 2 0.000000 1 2.500000 19.516000 15.244357 29.856250 13932 2 0.000000 -1 2.500000 19.516000 15.244357 29.856250 13933 2 0.000000 1 2.500000 12.628000 13.918760 33.368750 -13934 2 0.000000 -1.000000 2.500000 12.628000 13.918760 33.368750 +13934 2 0.000000 -1 2.500000 12.628000 13.918760 33.368750 13935 2 0.000000 1 2.500000 14.924000 9.941972 33.368750 13936 2 0.000000 -1 2.500000 14.924000 9.941972 33.368750 13937 2 0.000000 1 2.500000 17.220000 11.267568 36.881250 @@ -13955,7 +13955,7 @@ Atoms 13939 2 0.000000 1 2.500000 19.516000 15.244357 36.881250 13940 2 0.000000 -1 2.500000 19.516000 15.244357 36.881250 13941 2 0.000000 1 2.500000 12.628000 13.918760 40.393750 -13942 2 0.000000 -1.000000 2.500000 12.628000 13.918760 40.393750 +13942 2 0.000000 -1 2.500000 12.628000 13.918760 40.393750 13943 2 0.000000 1 2.500000 14.924000 9.941972 40.393750 13944 2 0.000000 -1 2.500000 14.924000 9.941972 40.393750 13945 2 0.000000 1 2.500000 17.220000 11.267568 43.906250 @@ -13963,7 +13963,7 @@ Atoms 13947 2 0.000000 1 2.500000 19.516000 15.244357 43.906250 13948 2 0.000000 -1 2.500000 19.516000 15.244357 43.906250 13949 2 0.000000 1 2.500000 12.628000 13.918760 47.418750 -13950 2 0.000000 -1.000000 2.500000 12.628000 13.918760 47.418750 +13950 2 0.000000 -1 2.500000 12.628000 13.918760 47.418750 13951 2 0.000000 1 2.500000 14.924000 9.941972 47.418750 13952 2 0.000000 -1 2.500000 14.924000 9.941972 47.418750 13953 2 0.000000 1 2.500000 17.220000 11.267568 50.931250 @@ -13971,7 +13971,7 @@ Atoms 13955 2 0.000000 1 2.500000 19.516000 15.244357 50.931250 13956 2 0.000000 -1 2.500000 19.516000 15.244357 50.931250 13957 2 0.000000 1 2.500000 12.628000 13.918760 54.443750 -13958 2 0.000000 -1.000000 2.500000 12.628000 13.918760 54.443750 +13958 2 0.000000 -1 2.500000 12.628000 13.918760 54.443750 13959 2 0.000000 1 2.500000 14.924000 9.941972 54.443750 13960 2 0.000000 -1 2.500000 14.924000 9.941972 54.443750 13961 2 0.000000 1 2.500000 17.220000 11.267568 57.956250 @@ -13979,7 +13979,7 @@ Atoms 13963 2 0.000000 1 2.500000 19.516000 15.244357 57.956250 13964 2 0.000000 -1 2.500000 19.516000 15.244357 57.956250 13965 2 0.000000 1 2.500000 12.628000 13.918760 61.468750 -13966 2 0.000000 -1.000000 2.500000 12.628000 13.918760 61.468750 +13966 2 0.000000 -1 2.500000 12.628000 13.918760 61.468750 13967 2 0.000000 1 2.500000 14.924000 9.941972 61.468750 13968 2 0.000000 -1 2.500000 14.924000 9.941972 61.468750 13969 2 0.000000 1 2.500000 17.220000 19.221145 1.756250 @@ -13987,7 +13987,7 @@ Atoms 13971 2 0.000000 1 2.500000 19.516000 23.197934 1.756250 13972 2 0.000000 -1 2.500000 19.516000 23.197934 1.756250 13973 2 0.000000 1 2.500000 12.628000 21.872338 5.268750 -13974 2 0.000000 -1.000000 2.500000 12.628000 21.872338 5.268750 +13974 2 0.000000 -1 2.500000 12.628000 21.872338 5.268750 13975 2 0.000000 1 2.500000 14.924000 17.895549 5.268750 13976 2 0.000000 -1 2.500000 14.924000 17.895549 5.268750 13977 2 0.000000 1 2.500000 17.220000 19.221145 8.781250 @@ -13995,7 +13995,7 @@ Atoms 13979 2 0.000000 1 2.500000 19.516000 23.197934 8.781250 13980 2 0.000000 -1 2.500000 19.516000 23.197934 8.781250 13981 2 0.000000 1 2.500000 12.628000 21.872338 12.293750 -13982 2 0.000000 -1.000000 2.500000 12.628000 21.872338 12.293750 +13982 2 0.000000 -1 2.500000 12.628000 21.872338 12.293750 13983 2 0.000000 1 2.500000 14.924000 17.895549 12.293750 13984 2 0.000000 -1 2.500000 14.924000 17.895549 12.293750 13985 2 0.000000 1 2.500000 17.220000 19.221145 15.806250 @@ -14003,7 +14003,7 @@ Atoms 13987 2 0.000000 1 2.500000 19.516000 23.197934 15.806250 13988 2 0.000000 -1 2.500000 19.516000 23.197934 15.806250 13989 2 0.000000 1 2.500000 12.628000 21.872338 19.318750 -13990 2 0.000000 -1.000000 2.500000 12.628000 21.872338 19.318750 +13990 2 0.000000 -1 2.500000 12.628000 21.872338 19.318750 13991 2 0.000000 1 2.500000 14.924000 17.895549 19.318750 13992 2 0.000000 -1 2.500000 14.924000 17.895549 19.318750 13993 2 0.000000 1 2.500000 17.220000 19.221145 22.831250 @@ -14011,7 +14011,7 @@ Atoms 13995 2 0.000000 1 2.500000 19.516000 23.197934 22.831250 13996 2 0.000000 -1 2.500000 19.516000 23.197934 22.831250 13997 2 0.000000 1 2.500000 12.628000 21.872338 26.343750 -13998 2 0.000000 -1.000000 2.500000 12.628000 21.872338 26.343750 +13998 2 0.000000 -1 2.500000 12.628000 21.872338 26.343750 13999 2 0.000000 1 2.500000 14.924000 17.895549 26.343750 14000 2 0.000000 -1 2.500000 14.924000 17.895549 26.343750 14001 2 0.000000 1 2.500000 17.220000 19.221145 29.856250 @@ -14019,7 +14019,7 @@ Atoms 14003 2 0.000000 1 2.500000 19.516000 23.197934 29.856250 14004 2 0.000000 -1 2.500000 19.516000 23.197934 29.856250 14005 2 0.000000 1 2.500000 12.628000 21.872338 33.368750 -14006 2 0.000000 -1.000000 2.500000 12.628000 21.872338 33.368750 +14006 2 0.000000 -1 2.500000 12.628000 21.872338 33.368750 14007 2 0.000000 1 2.500000 14.924000 17.895549 33.368750 14008 2 0.000000 -1 2.500000 14.924000 17.895549 33.368750 14009 2 0.000000 1 2.500000 17.220000 19.221145 36.881250 @@ -14027,7 +14027,7 @@ Atoms 14011 2 0.000000 1 2.500000 19.516000 23.197934 36.881250 14012 2 0.000000 -1 2.500000 19.516000 23.197934 36.881250 14013 2 0.000000 1 2.500000 12.628000 21.872338 40.393750 -14014 2 0.000000 -1.000000 2.500000 12.628000 21.872338 40.393750 +14014 2 0.000000 -1 2.500000 12.628000 21.872338 40.393750 14015 2 0.000000 1 2.500000 14.924000 17.895549 40.393750 14016 2 0.000000 -1 2.500000 14.924000 17.895549 40.393750 14017 2 0.000000 1 2.500000 17.220000 19.221145 43.906250 @@ -14035,7 +14035,7 @@ Atoms 14019 2 0.000000 1 2.500000 19.516000 23.197934 43.906250 14020 2 0.000000 -1 2.500000 19.516000 23.197934 43.906250 14021 2 0.000000 1 2.500000 12.628000 21.872338 47.418750 -14022 2 0.000000 -1.000000 2.500000 12.628000 21.872338 47.418750 +14022 2 0.000000 -1 2.500000 12.628000 21.872338 47.418750 14023 2 0.000000 1 2.500000 14.924000 17.895549 47.418750 14024 2 0.000000 -1 2.500000 14.924000 17.895549 47.418750 14025 2 0.000000 1 2.500000 17.220000 19.221145 50.931250 @@ -14043,7 +14043,7 @@ Atoms 14027 2 0.000000 1 2.500000 19.516000 23.197934 50.931250 14028 2 0.000000 -1 2.500000 19.516000 23.197934 50.931250 14029 2 0.000000 1 2.500000 12.628000 21.872338 54.443750 -14030 2 0.000000 -1.000000 2.500000 12.628000 21.872338 54.443750 +14030 2 0.000000 -1 2.500000 12.628000 21.872338 54.443750 14031 2 0.000000 1 2.500000 14.924000 17.895549 54.443750 14032 2 0.000000 -1 2.500000 14.924000 17.895549 54.443750 14033 2 0.000000 1 2.500000 17.220000 19.221145 57.956250 @@ -14051,7 +14051,7 @@ Atoms 14035 2 0.000000 1 2.500000 19.516000 23.197934 57.956250 14036 2 0.000000 -1 2.500000 19.516000 23.197934 57.956250 14037 2 0.000000 1 2.500000 12.628000 21.872338 61.468750 -14038 2 0.000000 -1.000000 2.500000 12.628000 21.872338 61.468750 +14038 2 0.000000 -1 2.500000 12.628000 21.872338 61.468750 14039 2 0.000000 1 2.500000 14.924000 17.895549 61.468750 14040 2 0.000000 -1 2.500000 14.924000 17.895549 61.468750 14041 2 0.000000 1 2.500000 17.220000 27.174722 1.756250 @@ -14059,7 +14059,7 @@ Atoms 14043 2 0.000000 1 2.500000 19.516000 31.151511 1.756250 14044 2 0.000000 -1 2.500000 19.516000 31.151511 1.756250 14045 2 0.000000 1 2.500000 12.628000 29.825915 5.268750 -14046 2 0.000000 -1.000000 2.500000 12.628000 29.825915 5.268750 +14046 2 0.000000 -1 2.500000 12.628000 29.825915 5.268750 14047 2 0.000000 1 2.500000 14.924000 25.849126 5.268750 14048 2 0.000000 -1 2.500000 14.924000 25.849126 5.268750 14049 2 0.000000 1 2.500000 17.220000 27.174722 8.781250 @@ -14067,7 +14067,7 @@ Atoms 14051 2 0.000000 1 2.500000 19.516000 31.151511 8.781250 14052 2 0.000000 -1 2.500000 19.516000 31.151511 8.781250 14053 2 0.000000 1 2.500000 12.628000 29.825915 12.293750 -14054 2 0.000000 -1.000000 2.500000 12.628000 29.825915 12.293750 +14054 2 0.000000 -1 2.500000 12.628000 29.825915 12.293750 14055 2 0.000000 1 2.500000 14.924000 25.849126 12.293750 14056 2 0.000000 -1 2.500000 14.924000 25.849126 12.293750 14057 2 0.000000 1 2.500000 17.220000 27.174722 15.806250 @@ -14075,7 +14075,7 @@ Atoms 14059 2 0.000000 1 2.500000 19.516000 31.151511 15.806250 14060 2 0.000000 -1 2.500000 19.516000 31.151511 15.806250 14061 2 0.000000 1 2.500000 12.628000 29.825915 19.318750 -14062 2 0.000000 -1.000000 2.500000 12.628000 29.825915 19.318750 +14062 2 0.000000 -1 2.500000 12.628000 29.825915 19.318750 14063 2 0.000000 1 2.500000 14.924000 25.849126 19.318750 14064 2 0.000000 -1 2.500000 14.924000 25.849126 19.318750 14065 2 0.000000 1 2.500000 17.220000 27.174722 22.831250 @@ -14083,7 +14083,7 @@ Atoms 14067 2 0.000000 1 2.500000 19.516000 31.151511 22.831250 14068 2 0.000000 -1 2.500000 19.516000 31.151511 22.831250 14069 2 0.000000 1 2.500000 12.628000 29.825915 26.343750 -14070 2 0.000000 -1.000000 2.500000 12.628000 29.825915 26.343750 +14070 2 0.000000 -1 2.500000 12.628000 29.825915 26.343750 14071 2 0.000000 1 2.500000 14.924000 25.849126 26.343750 14072 2 0.000000 -1 2.500000 14.924000 25.849126 26.343750 14073 2 0.000000 1 2.500000 17.220000 27.174722 29.856250 @@ -14091,7 +14091,7 @@ Atoms 14075 2 0.000000 1 2.500000 19.516000 31.151511 29.856250 14076 2 0.000000 -1 2.500000 19.516000 31.151511 29.856250 14077 2 0.000000 1 2.500000 12.628000 29.825915 33.368750 -14078 2 0.000000 -1.000000 2.500000 12.628000 29.825915 33.368750 +14078 2 0.000000 -1 2.500000 12.628000 29.825915 33.368750 14079 2 0.000000 1 2.500000 14.924000 25.849126 33.368750 14080 2 0.000000 -1 2.500000 14.924000 25.849126 33.368750 14081 2 0.000000 1 2.500000 17.220000 27.174722 36.881250 @@ -14099,7 +14099,7 @@ Atoms 14083 2 0.000000 1 2.500000 19.516000 31.151511 36.881250 14084 2 0.000000 -1 2.500000 19.516000 31.151511 36.881250 14085 2 0.000000 1 2.500000 12.628000 29.825915 40.393750 -14086 2 0.000000 -1.000000 2.500000 12.628000 29.825915 40.393750 +14086 2 0.000000 -1 2.500000 12.628000 29.825915 40.393750 14087 2 0.000000 1 2.500000 14.924000 25.849126 40.393750 14088 2 0.000000 -1 2.500000 14.924000 25.849126 40.393750 14089 2 0.000000 1 2.500000 17.220000 27.174722 43.906250 @@ -14107,7 +14107,7 @@ Atoms 14091 2 0.000000 1 2.500000 19.516000 31.151511 43.906250 14092 2 0.000000 -1 2.500000 19.516000 31.151511 43.906250 14093 2 0.000000 1 2.500000 12.628000 29.825915 47.418750 -14094 2 0.000000 -1.000000 2.500000 12.628000 29.825915 47.418750 +14094 2 0.000000 -1 2.500000 12.628000 29.825915 47.418750 14095 2 0.000000 1 2.500000 14.924000 25.849126 47.418750 14096 2 0.000000 -1 2.500000 14.924000 25.849126 47.418750 14097 2 0.000000 1 2.500000 17.220000 27.174722 50.931250 @@ -14115,7 +14115,7 @@ Atoms 14099 2 0.000000 1 2.500000 19.516000 31.151511 50.931250 14100 2 0.000000 -1 2.500000 19.516000 31.151511 50.931250 14101 2 0.000000 1 2.500000 12.628000 29.825915 54.443750 -14102 2 0.000000 -1.000000 2.500000 12.628000 29.825915 54.443750 +14102 2 0.000000 -1 2.500000 12.628000 29.825915 54.443750 14103 2 0.000000 1 2.500000 14.924000 25.849126 54.443750 14104 2 0.000000 -1 2.500000 14.924000 25.849126 54.443750 14105 2 0.000000 1 2.500000 17.220000 27.174722 57.956250 @@ -14123,7 +14123,7 @@ Atoms 14107 2 0.000000 1 2.500000 19.516000 31.151511 57.956250 14108 2 0.000000 -1 2.500000 19.516000 31.151511 57.956250 14109 2 0.000000 1 2.500000 12.628000 29.825915 61.468750 -14110 2 0.000000 -1.000000 2.500000 12.628000 29.825915 61.468750 +14110 2 0.000000 -1 2.500000 12.628000 29.825915 61.468750 14111 2 0.000000 1 2.500000 14.924000 25.849126 61.468750 14112 2 0.000000 -1 2.500000 14.924000 25.849126 61.468750 14113 2 0.000000 1 2.500000 17.220000 35.128300 1.756250 @@ -14131,7 +14131,7 @@ Atoms 14115 2 0.000000 1 2.500000 19.516000 39.105088 1.756250 14116 2 0.000000 -1 2.500000 19.516000 39.105088 1.756250 14117 2 0.000000 1 2.500000 12.628000 37.779492 5.268750 -14118 2 0.000000 -1.000000 2.500000 12.628000 37.779492 5.268750 +14118 2 0.000000 -1 2.500000 12.628000 37.779492 5.268750 14119 2 0.000000 1 2.500000 14.924000 33.802704 5.268750 14120 2 0.000000 -1 2.500000 14.924000 33.802704 5.268750 14121 2 0.000000 1 2.500000 17.220000 35.128300 8.781250 @@ -14139,7 +14139,7 @@ Atoms 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2 0.000000 1 2.500000 17.220000 43.081877 15.806250 @@ -14219,7 +14219,7 @@ Atoms 14203 2 0.000000 1 2.500000 19.516000 47.058666 15.806250 14204 2 0.000000 -1 2.500000 19.516000 47.058666 15.806250 14205 2 0.000000 1 2.500000 12.628000 45.733070 19.318750 -14206 2 0.000000 -1.000000 2.500000 12.628000 45.733070 19.318750 +14206 2 0.000000 -1 2.500000 12.628000 45.733070 19.318750 14207 2 0.000000 1 2.500000 14.924000 41.756281 19.318750 14208 2 0.000000 -1 2.500000 14.924000 41.756281 19.318750 14209 2 0.000000 1 2.500000 17.220000 43.081877 22.831250 @@ -14227,7 +14227,7 @@ Atoms 14211 2 0.000000 1 2.500000 19.516000 47.058666 22.831250 14212 2 0.000000 -1 2.500000 19.516000 47.058666 22.831250 14213 2 0.000000 1 2.500000 12.628000 45.733070 26.343750 -14214 2 0.000000 -1.000000 2.500000 12.628000 45.733070 26.343750 +14214 2 0.000000 -1 2.500000 12.628000 45.733070 26.343750 14215 2 0.000000 1 2.500000 14.924000 41.756281 26.343750 14216 2 0.000000 -1 2.500000 14.924000 41.756281 26.343750 14217 2 0.000000 1 2.500000 17.220000 43.081877 29.856250 @@ -14235,7 +14235,7 @@ Atoms 14219 2 0.000000 1 2.500000 19.516000 47.058666 29.856250 14220 2 0.000000 -1 2.500000 19.516000 47.058666 29.856250 14221 2 0.000000 1 2.500000 12.628000 45.733070 33.368750 -14222 2 0.000000 -1.000000 2.500000 12.628000 45.733070 33.368750 +14222 2 0.000000 -1 2.500000 12.628000 45.733070 33.368750 14223 2 0.000000 1 2.500000 14.924000 41.756281 33.368750 14224 2 0.000000 -1 2.500000 14.924000 41.756281 33.368750 14225 2 0.000000 1 2.500000 17.220000 43.081877 36.881250 @@ -14243,7 +14243,7 @@ Atoms 14227 2 0.000000 1 2.500000 19.516000 47.058666 36.881250 14228 2 0.000000 -1 2.500000 19.516000 47.058666 36.881250 14229 2 0.000000 1 2.500000 12.628000 45.733070 40.393750 -14230 2 0.000000 -1.000000 2.500000 12.628000 45.733070 40.393750 +14230 2 0.000000 -1 2.500000 12.628000 45.733070 40.393750 14231 2 0.000000 1 2.500000 14.924000 41.756281 40.393750 14232 2 0.000000 -1 2.500000 14.924000 41.756281 40.393750 14233 2 0.000000 1 2.500000 17.220000 43.081877 43.906250 @@ -14251,7 +14251,7 @@ Atoms 14235 2 0.000000 1 2.500000 19.516000 47.058666 43.906250 14236 2 0.000000 -1 2.500000 19.516000 47.058666 43.906250 14237 2 0.000000 1 2.500000 12.628000 45.733070 47.418750 -14238 2 0.000000 -1.000000 2.500000 12.628000 45.733070 47.418750 +14238 2 0.000000 -1 2.500000 12.628000 45.733070 47.418750 14239 2 0.000000 1 2.500000 14.924000 41.756281 47.418750 14240 2 0.000000 -1 2.500000 14.924000 41.756281 47.418750 14241 2 0.000000 1 2.500000 17.220000 43.081877 50.931250 @@ -14259,7 +14259,7 @@ Atoms 14243 2 0.000000 1 2.500000 19.516000 47.058666 50.931250 14244 2 0.000000 -1 2.500000 19.516000 47.058666 50.931250 14245 2 0.000000 1 2.500000 12.628000 45.733070 54.443750 -14246 2 0.000000 -1.000000 2.500000 12.628000 45.733070 54.443750 +14246 2 0.000000 -1 2.500000 12.628000 45.733070 54.443750 14247 2 0.000000 1 2.500000 14.924000 41.756281 54.443750 14248 2 0.000000 -1 2.500000 14.924000 41.756281 54.443750 14249 2 0.000000 1 2.500000 17.220000 43.081877 57.956250 @@ -14267,7 +14267,7 @@ Atoms 14251 2 0.000000 1 2.500000 19.516000 47.058666 57.956250 14252 2 0.000000 -1 2.500000 19.516000 47.058666 57.956250 14253 2 0.000000 1 2.500000 12.628000 45.733070 61.468750 -14254 2 0.000000 -1.000000 2.500000 12.628000 45.733070 61.468750 +14254 2 0.000000 -1 2.500000 12.628000 45.733070 61.468750 14255 2 0.000000 1 2.500000 14.924000 41.756281 61.468750 14256 2 0.000000 -1 2.500000 14.924000 41.756281 61.468750 14257 2 0.000000 1 2.500000 17.220000 51.035454 1.756250 @@ -14275,7 +14275,7 @@ Atoms 14259 2 0.000000 1 2.500000 19.516000 55.012243 1.756250 14260 2 0.000000 -1 2.500000 19.516000 55.012243 1.756250 14261 2 0.000000 1 2.500000 12.628000 53.686647 5.268750 -14262 2 0.000000 -1.000000 2.500000 12.628000 53.686647 5.268750 +14262 2 0.000000 -1 2.500000 12.628000 53.686647 5.268750 14263 2 0.000000 1 2.500000 14.924000 49.709858 5.268750 14264 2 0.000000 -1 2.500000 14.924000 49.709858 5.268750 14265 2 0.000000 1 2.500000 17.220000 51.035454 8.781250 @@ -14283,7 +14283,7 @@ Atoms 14267 2 0.000000 1 2.500000 19.516000 55.012243 8.781250 14268 2 0.000000 -1 2.500000 19.516000 55.012243 8.781250 14269 2 0.000000 1 2.500000 12.628000 53.686647 12.293750 -14270 2 0.000000 -1.000000 2.500000 12.628000 53.686647 12.293750 +14270 2 0.000000 -1 2.500000 12.628000 53.686647 12.293750 14271 2 0.000000 1 2.500000 14.924000 49.709858 12.293750 14272 2 0.000000 -1 2.500000 14.924000 49.709858 12.293750 14273 2 0.000000 1 2.500000 17.220000 51.035454 15.806250 @@ -14291,7 +14291,7 @@ Atoms 14275 2 0.000000 1 2.500000 19.516000 55.012243 15.806250 14276 2 0.000000 -1 2.500000 19.516000 55.012243 15.806250 14277 2 0.000000 1 2.500000 12.628000 53.686647 19.318750 -14278 2 0.000000 -1.000000 2.500000 12.628000 53.686647 19.318750 +14278 2 0.000000 -1 2.500000 12.628000 53.686647 19.318750 14279 2 0.000000 1 2.500000 14.924000 49.709858 19.318750 14280 2 0.000000 -1 2.500000 14.924000 49.709858 19.318750 14281 2 0.000000 1 2.500000 17.220000 51.035454 22.831250 @@ -14299,7 +14299,7 @@ Atoms 14283 2 0.000000 1 2.500000 19.516000 55.012243 22.831250 14284 2 0.000000 -1 2.500000 19.516000 55.012243 22.831250 14285 2 0.000000 1 2.500000 12.628000 53.686647 26.343750 -14286 2 0.000000 -1.000000 2.500000 12.628000 53.686647 26.343750 +14286 2 0.000000 -1 2.500000 12.628000 53.686647 26.343750 14287 2 0.000000 1 2.500000 14.924000 49.709858 26.343750 14288 2 0.000000 -1 2.500000 14.924000 49.709858 26.343750 14289 2 0.000000 1 2.500000 17.220000 51.035454 29.856250 @@ -14307,7 +14307,7 @@ Atoms 14291 2 0.000000 1 2.500000 19.516000 55.012243 29.856250 14292 2 0.000000 -1 2.500000 19.516000 55.012243 29.856250 14293 2 0.000000 1 2.500000 12.628000 53.686647 33.368750 -14294 2 0.000000 -1.000000 2.500000 12.628000 53.686647 33.368750 +14294 2 0.000000 -1 2.500000 12.628000 53.686647 33.368750 14295 2 0.000000 1 2.500000 14.924000 49.709858 33.368750 14296 2 0.000000 -1 2.500000 14.924000 49.709858 33.368750 14297 2 0.000000 1 2.500000 17.220000 51.035454 36.881250 @@ -14315,7 +14315,7 @@ Atoms 14299 2 0.000000 1 2.500000 19.516000 55.012243 36.881250 14300 2 0.000000 -1 2.500000 19.516000 55.012243 36.881250 14301 2 0.000000 1 2.500000 12.628000 53.686647 40.393750 -14302 2 0.000000 -1.000000 2.500000 12.628000 53.686647 40.393750 +14302 2 0.000000 -1 2.500000 12.628000 53.686647 40.393750 14303 2 0.000000 1 2.500000 14.924000 49.709858 40.393750 14304 2 0.000000 -1 2.500000 14.924000 49.709858 40.393750 14305 2 0.000000 1 2.500000 17.220000 51.035454 43.906250 @@ -14323,7 +14323,7 @@ Atoms 14307 2 0.000000 1 2.500000 19.516000 55.012243 43.906250 14308 2 0.000000 -1 2.500000 19.516000 55.012243 43.906250 14309 2 0.000000 1 2.500000 12.628000 53.686647 47.418750 -14310 2 0.000000 -1.000000 2.500000 12.628000 53.686647 47.418750 +14310 2 0.000000 -1 2.500000 12.628000 53.686647 47.418750 14311 2 0.000000 1 2.500000 14.924000 49.709858 47.418750 14312 2 0.000000 -1 2.500000 14.924000 49.709858 47.418750 14313 2 0.000000 1 2.500000 17.220000 51.035454 50.931250 @@ -14331,7 +14331,7 @@ Atoms 14315 2 0.000000 1 2.500000 19.516000 55.012243 50.931250 14316 2 0.000000 -1 2.500000 19.516000 55.012243 50.931250 14317 2 0.000000 1 2.500000 12.628000 53.686647 54.443750 -14318 2 0.000000 -1.000000 2.500000 12.628000 53.686647 54.443750 +14318 2 0.000000 -1 2.500000 12.628000 53.686647 54.443750 14319 2 0.000000 1 2.500000 14.924000 49.709858 54.443750 14320 2 0.000000 -1 2.500000 14.924000 49.709858 54.443750 14321 2 0.000000 1 2.500000 17.220000 51.035454 57.956250 @@ -14339,7 +14339,7 @@ Atoms 14323 2 0.000000 1 2.500000 19.516000 55.012243 57.956250 14324 2 0.000000 -1 2.500000 19.516000 55.012243 57.956250 14325 2 0.000000 1 2.500000 12.628000 53.686647 61.468750 -14326 2 0.000000 -1.000000 2.500000 12.628000 53.686647 61.468750 +14326 2 0.000000 -1 2.500000 12.628000 53.686647 61.468750 14327 2 0.000000 1 2.500000 14.924000 49.709858 61.468750 14328 2 0.000000 -1 2.500000 14.924000 49.709858 61.468750 14329 2 0.000000 1 2.500000 17.220000 58.989032 1.756250 @@ -14347,7 +14347,7 @@ Atoms 14331 2 0.000000 1 2.500000 19.516000 62.965820 1.756250 14332 2 0.000000 -1 2.500000 19.516000 62.965820 1.756250 14333 2 0.000000 1 2.500000 12.628000 61.640224 5.268750 -14334 2 0.000000 -1.000000 2.500000 12.628000 61.640224 5.268750 +14334 2 0.000000 -1 2.500000 12.628000 61.640224 5.268750 14335 2 0.000000 1 2.500000 14.924000 57.663435 5.268750 14336 2 0.000000 -1 2.500000 14.924000 57.663435 5.268750 14337 2 0.000000 1 2.500000 17.220000 58.989032 8.781250 @@ -14355,7 +14355,7 @@ Atoms 14339 2 0.000000 1 2.500000 19.516000 62.965820 8.781250 14340 2 0.000000 -1 2.500000 19.516000 62.965820 8.781250 14341 2 0.000000 1 2.500000 12.628000 61.640224 12.293750 -14342 2 0.000000 -1.000000 2.500000 12.628000 61.640224 12.293750 +14342 2 0.000000 -1 2.500000 12.628000 61.640224 12.293750 14343 2 0.000000 1 2.500000 14.924000 57.663435 12.293750 14344 2 0.000000 -1 2.500000 14.924000 57.663435 12.293750 14345 2 0.000000 1 2.500000 17.220000 58.989032 15.806250 @@ -14363,7 +14363,7 @@ Atoms 14347 2 0.000000 1 2.500000 19.516000 62.965820 15.806250 14348 2 0.000000 -1 2.500000 19.516000 62.965820 15.806250 14349 2 0.000000 1 2.500000 12.628000 61.640224 19.318750 -14350 2 0.000000 -1.000000 2.500000 12.628000 61.640224 19.318750 +14350 2 0.000000 -1 2.500000 12.628000 61.640224 19.318750 14351 2 0.000000 1 2.500000 14.924000 57.663435 19.318750 14352 2 0.000000 -1 2.500000 14.924000 57.663435 19.318750 14353 2 0.000000 1 2.500000 17.220000 58.989032 22.831250 @@ -14371,7 +14371,7 @@ Atoms 14355 2 0.000000 1 2.500000 19.516000 62.965820 22.831250 14356 2 0.000000 -1 2.500000 19.516000 62.965820 22.831250 14357 2 0.000000 1 2.500000 12.628000 61.640224 26.343750 -14358 2 0.000000 -1.000000 2.500000 12.628000 61.640224 26.343750 +14358 2 0.000000 -1 2.500000 12.628000 61.640224 26.343750 14359 2 0.000000 1 2.500000 14.924000 57.663435 26.343750 14360 2 0.000000 -1 2.500000 14.924000 57.663435 26.343750 14361 2 0.000000 1 2.500000 17.220000 58.989032 29.856250 @@ -14379,7 +14379,7 @@ Atoms 14363 2 0.000000 1 2.500000 19.516000 62.965820 29.856250 14364 2 0.000000 -1 2.500000 19.516000 62.965820 29.856250 14365 2 0.000000 1 2.500000 12.628000 61.640224 33.368750 -14366 2 0.000000 -1.000000 2.500000 12.628000 61.640224 33.368750 +14366 2 0.000000 -1 2.500000 12.628000 61.640224 33.368750 14367 2 0.000000 1 2.500000 14.924000 57.663435 33.368750 14368 2 0.000000 -1 2.500000 14.924000 57.663435 33.368750 14369 2 0.000000 1 2.500000 17.220000 58.989032 36.881250 @@ -14387,7 +14387,7 @@ Atoms 14371 2 0.000000 1 2.500000 19.516000 62.965820 36.881250 14372 2 0.000000 -1 2.500000 19.516000 62.965820 36.881250 14373 2 0.000000 1 2.500000 12.628000 61.640224 40.393750 -14374 2 0.000000 -1.000000 2.500000 12.628000 61.640224 40.393750 +14374 2 0.000000 -1 2.500000 12.628000 61.640224 40.393750 14375 2 0.000000 1 2.500000 14.924000 57.663435 40.393750 14376 2 0.000000 -1 2.500000 14.924000 57.663435 40.393750 14377 2 0.000000 1 2.500000 17.220000 58.989032 43.906250 @@ -14395,7 +14395,7 @@ Atoms 14379 2 0.000000 1 2.500000 19.516000 62.965820 43.906250 14380 2 0.000000 -1 2.500000 19.516000 62.965820 43.906250 14381 2 0.000000 1 2.500000 12.628000 61.640224 47.418750 -14382 2 0.000000 -1.000000 2.500000 12.628000 61.640224 47.418750 +14382 2 0.000000 -1 2.500000 12.628000 61.640224 47.418750 14383 2 0.000000 1 2.500000 14.924000 57.663435 47.418750 14384 2 0.000000 -1 2.500000 14.924000 57.663435 47.418750 14385 2 0.000000 1 2.500000 17.220000 58.989032 50.931250 @@ -14403,7 +14403,7 @@ Atoms 14387 2 0.000000 1 2.500000 19.516000 62.965820 50.931250 14388 2 0.000000 -1 2.500000 19.516000 62.965820 50.931250 14389 2 0.000000 1 2.500000 12.628000 61.640224 54.443750 -14390 2 0.000000 -1.000000 2.500000 12.628000 61.640224 54.443750 +14390 2 0.000000 -1 2.500000 12.628000 61.640224 54.443750 14391 2 0.000000 1 2.500000 14.924000 57.663435 54.443750 14392 2 0.000000 -1 2.500000 14.924000 57.663435 54.443750 14393 2 0.000000 1 2.500000 17.220000 58.989032 57.956250 @@ -14411,7 +14411,7 @@ Atoms 14395 2 0.000000 1 2.500000 19.516000 62.965820 57.956250 14396 2 0.000000 -1 2.500000 19.516000 62.965820 57.956250 14397 2 0.000000 1 2.500000 12.628000 61.640224 61.468750 -14398 2 0.000000 -1.000000 2.500000 12.628000 61.640224 61.468750 +14398 2 0.000000 -1 2.500000 12.628000 61.640224 61.468750 14399 2 0.000000 1 2.500000 14.924000 57.663435 61.468750 14400 2 0.000000 -1 2.500000 14.924000 57.663435 61.468750 14401 2 0.000000 1 2.500000 21.812000 3.313991 1.756250 @@ -14419,7 +14419,7 @@ Atoms 14403 2 0.000000 1 2.500000 24.108000 7.290779 1.756250 14404 2 0.000000 -1 2.500000 24.108000 7.290779 1.756250 14405 2 0.000000 1 2.500000 17.220000 5.965183 5.268750 -14406 2 0.000000 -1.000000 2.500000 17.220000 5.965183 5.268750 +14406 2 0.000000 -1 2.500000 17.220000 5.965183 5.268750 14407 2 0.000000 1 2.500000 19.516000 1.988394 5.268750 14408 2 0.000000 -1 2.500000 19.516000 1.988394 5.268750 14409 2 0.000000 1 2.500000 21.812000 3.313991 8.781250 @@ -14427,7 +14427,7 @@ Atoms 14411 2 0.000000 1 2.500000 24.108000 7.290779 8.781250 14412 2 0.000000 -1 2.500000 24.108000 7.290779 8.781250 14413 2 0.000000 1 2.500000 17.220000 5.965183 12.293750 -14414 2 0.000000 -1.000000 2.500000 17.220000 5.965183 12.293750 +14414 2 0.000000 -1 2.500000 17.220000 5.965183 12.293750 14415 2 0.000000 1 2.500000 19.516000 1.988394 12.293750 14416 2 0.000000 -1 2.500000 19.516000 1.988394 12.293750 14417 2 0.000000 1 2.500000 21.812000 3.313991 15.806250 @@ -14435,7 +14435,7 @@ Atoms 14419 2 0.000000 1 2.500000 24.108000 7.290779 15.806250 14420 2 0.000000 -1 2.500000 24.108000 7.290779 15.806250 14421 2 0.000000 1 2.500000 17.220000 5.965183 19.318750 -14422 2 0.000000 -1.000000 2.500000 17.220000 5.965183 19.318750 +14422 2 0.000000 -1 2.500000 17.220000 5.965183 19.318750 14423 2 0.000000 1 2.500000 19.516000 1.988394 19.318750 14424 2 0.000000 -1 2.500000 19.516000 1.988394 19.318750 14425 2 0.000000 1 2.500000 21.812000 3.313991 22.831250 @@ -14443,7 +14443,7 @@ Atoms 14427 2 0.000000 1 2.500000 24.108000 7.290779 22.831250 14428 2 0.000000 -1 2.500000 24.108000 7.290779 22.831250 14429 2 0.000000 1 2.500000 17.220000 5.965183 26.343750 -14430 2 0.000000 -1.000000 2.500000 17.220000 5.965183 26.343750 +14430 2 0.000000 -1 2.500000 17.220000 5.965183 26.343750 14431 2 0.000000 1 2.500000 19.516000 1.988394 26.343750 14432 2 0.000000 -1 2.500000 19.516000 1.988394 26.343750 14433 2 0.000000 1 2.500000 21.812000 3.313991 29.856250 @@ -14451,7 +14451,7 @@ Atoms 14435 2 0.000000 1 2.500000 24.108000 7.290779 29.856250 14436 2 0.000000 -1 2.500000 24.108000 7.290779 29.856250 14437 2 0.000000 1 2.500000 17.220000 5.965183 33.368750 -14438 2 0.000000 -1.000000 2.500000 17.220000 5.965183 33.368750 +14438 2 0.000000 -1 2.500000 17.220000 5.965183 33.368750 14439 2 0.000000 1 2.500000 19.516000 1.988394 33.368750 14440 2 0.000000 -1 2.500000 19.516000 1.988394 33.368750 14441 2 0.000000 1 2.500000 21.812000 3.313991 36.881250 @@ -14459,7 +14459,7 @@ Atoms 14443 2 0.000000 1 2.500000 24.108000 7.290779 36.881250 14444 2 0.000000 -1 2.500000 24.108000 7.290779 36.881250 14445 2 0.000000 1 2.500000 17.220000 5.965183 40.393750 -14446 2 0.000000 -1.000000 2.500000 17.220000 5.965183 40.393750 +14446 2 0.000000 -1 2.500000 17.220000 5.965183 40.393750 14447 2 0.000000 1 2.500000 19.516000 1.988394 40.393750 14448 2 0.000000 -1 2.500000 19.516000 1.988394 40.393750 14449 2 0.000000 1 2.500000 21.812000 3.313991 43.906250 @@ -14467,7 +14467,7 @@ Atoms 14451 2 0.000000 1 2.500000 24.108000 7.290779 43.906250 14452 2 0.000000 -1 2.500000 24.108000 7.290779 43.906250 14453 2 0.000000 1 2.500000 17.220000 5.965183 47.418750 -14454 2 0.000000 -1.000000 2.500000 17.220000 5.965183 47.418750 +14454 2 0.000000 -1 2.500000 17.220000 5.965183 47.418750 14455 2 0.000000 1 2.500000 19.516000 1.988394 47.418750 14456 2 0.000000 -1 2.500000 19.516000 1.988394 47.418750 14457 2 0.000000 1 2.500000 21.812000 3.313991 50.931250 @@ -14475,7 +14475,7 @@ Atoms 14459 2 0.000000 1 2.500000 24.108000 7.290779 50.931250 14460 2 0.000000 -1 2.500000 24.108000 7.290779 50.931250 14461 2 0.000000 1 2.500000 17.220000 5.965183 54.443750 -14462 2 0.000000 -1.000000 2.500000 17.220000 5.965183 54.443750 +14462 2 0.000000 -1 2.500000 17.220000 5.965183 54.443750 14463 2 0.000000 1 2.500000 19.516000 1.988394 54.443750 14464 2 0.000000 -1 2.500000 19.516000 1.988394 54.443750 14465 2 0.000000 1 2.500000 21.812000 3.313991 57.956250 @@ -14483,7 +14483,7 @@ Atoms 14467 2 0.000000 1 2.500000 24.108000 7.290779 57.956250 14468 2 0.000000 -1 2.500000 24.108000 7.290779 57.956250 14469 2 0.000000 1 2.500000 17.220000 5.965183 61.468750 -14470 2 0.000000 -1.000000 2.500000 17.220000 5.965183 61.468750 +14470 2 0.000000 -1 2.500000 17.220000 5.965183 61.468750 14471 2 0.000000 1 2.500000 19.516000 1.988394 61.468750 14472 2 0.000000 -1 2.500000 19.516000 1.988394 61.468750 14473 2 0.000000 1 2.500000 21.812000 11.267568 1.756250 @@ -14491,7 +14491,7 @@ Atoms 14475 2 0.000000 1 2.500000 24.108000 15.244357 1.756250 14476 2 0.000000 -1 2.500000 24.108000 15.244357 1.756250 14477 2 0.000000 1 2.500000 17.220000 13.918760 5.268750 -14478 2 0.000000 -1.000000 2.500000 17.220000 13.918760 5.268750 +14478 2 0.000000 -1 2.500000 17.220000 13.918760 5.268750 14479 2 0.000000 1 2.500000 19.516000 9.941972 5.268750 14480 2 0.000000 -1 2.500000 19.516000 9.941972 5.268750 14481 2 0.000000 1 2.500000 21.812000 11.267568 8.781250 @@ -14499,7 +14499,7 @@ Atoms 14483 2 0.000000 1 2.500000 24.108000 15.244357 8.781250 14484 2 0.000000 -1 2.500000 24.108000 15.244357 8.781250 14485 2 0.000000 1 2.500000 17.220000 13.918760 12.293750 -14486 2 0.000000 -1.000000 2.500000 17.220000 13.918760 12.293750 +14486 2 0.000000 -1 2.500000 17.220000 13.918760 12.293750 14487 2 0.000000 1 2.500000 19.516000 9.941972 12.293750 14488 2 0.000000 -1 2.500000 19.516000 9.941972 12.293750 14489 2 0.000000 1 2.500000 21.812000 11.267568 15.806250 @@ -14507,7 +14507,7 @@ Atoms 14491 2 0.000000 1 2.500000 24.108000 15.244357 15.806250 14492 2 0.000000 -1 2.500000 24.108000 15.244357 15.806250 14493 2 0.000000 1 2.500000 17.220000 13.918760 19.318750 -14494 2 0.000000 -1.000000 2.500000 17.220000 13.918760 19.318750 +14494 2 0.000000 -1 2.500000 17.220000 13.918760 19.318750 14495 2 0.000000 1 2.500000 19.516000 9.941972 19.318750 14496 2 0.000000 -1 2.500000 19.516000 9.941972 19.318750 14497 2 0.000000 1 2.500000 21.812000 11.267568 22.831250 @@ -14515,7 +14515,7 @@ Atoms 14499 2 0.000000 1 2.500000 24.108000 15.244357 22.831250 14500 2 0.000000 -1 2.500000 24.108000 15.244357 22.831250 14501 2 0.000000 1 2.500000 17.220000 13.918760 26.343750 -14502 2 0.000000 -1.000000 2.500000 17.220000 13.918760 26.343750 +14502 2 0.000000 -1 2.500000 17.220000 13.918760 26.343750 14503 2 0.000000 1 2.500000 19.516000 9.941972 26.343750 14504 2 0.000000 -1 2.500000 19.516000 9.941972 26.343750 14505 2 0.000000 1 2.500000 21.812000 11.267568 29.856250 @@ -14523,7 +14523,7 @@ Atoms 14507 2 0.000000 1 2.500000 24.108000 15.244357 29.856250 14508 2 0.000000 -1 2.500000 24.108000 15.244357 29.856250 14509 2 0.000000 1 2.500000 17.220000 13.918760 33.368750 -14510 2 0.000000 -1.000000 2.500000 17.220000 13.918760 33.368750 +14510 2 0.000000 -1 2.500000 17.220000 13.918760 33.368750 14511 2 0.000000 1 2.500000 19.516000 9.941972 33.368750 14512 2 0.000000 -1 2.500000 19.516000 9.941972 33.368750 14513 2 0.000000 1 2.500000 21.812000 11.267568 36.881250 @@ -14531,7 +14531,7 @@ Atoms 14515 2 0.000000 1 2.500000 24.108000 15.244357 36.881250 14516 2 0.000000 -1 2.500000 24.108000 15.244357 36.881250 14517 2 0.000000 1 2.500000 17.220000 13.918760 40.393750 -14518 2 0.000000 -1.000000 2.500000 17.220000 13.918760 40.393750 +14518 2 0.000000 -1 2.500000 17.220000 13.918760 40.393750 14519 2 0.000000 1 2.500000 19.516000 9.941972 40.393750 14520 2 0.000000 -1 2.500000 19.516000 9.941972 40.393750 14521 2 0.000000 1 2.500000 21.812000 11.267568 43.906250 @@ -14539,7 +14539,7 @@ Atoms 14523 2 0.000000 1 2.500000 24.108000 15.244357 43.906250 14524 2 0.000000 -1 2.500000 24.108000 15.244357 43.906250 14525 2 0.000000 1 2.500000 17.220000 13.918760 47.418750 -14526 2 0.000000 -1.000000 2.500000 17.220000 13.918760 47.418750 +14526 2 0.000000 -1 2.500000 17.220000 13.918760 47.418750 14527 2 0.000000 1 2.500000 19.516000 9.941972 47.418750 14528 2 0.000000 -1 2.500000 19.516000 9.941972 47.418750 14529 2 0.000000 1 2.500000 21.812000 11.267568 50.931250 @@ -14547,7 +14547,7 @@ Atoms 14531 2 0.000000 1 2.500000 24.108000 15.244357 50.931250 14532 2 0.000000 -1 2.500000 24.108000 15.244357 50.931250 14533 2 0.000000 1 2.500000 17.220000 13.918760 54.443750 -14534 2 0.000000 -1.000000 2.500000 17.220000 13.918760 54.443750 +14534 2 0.000000 -1 2.500000 17.220000 13.918760 54.443750 14535 2 0.000000 1 2.500000 19.516000 9.941972 54.443750 14536 2 0.000000 -1 2.500000 19.516000 9.941972 54.443750 14537 2 0.000000 1 2.500000 21.812000 11.267568 57.956250 @@ -14555,7 +14555,7 @@ Atoms 14539 2 0.000000 1 2.500000 24.108000 15.244357 57.956250 14540 2 0.000000 -1 2.500000 24.108000 15.244357 57.956250 14541 2 0.000000 1 2.500000 17.220000 13.918760 61.468750 -14542 2 0.000000 -1.000000 2.500000 17.220000 13.918760 61.468750 +14542 2 0.000000 -1 2.500000 17.220000 13.918760 61.468750 14543 2 0.000000 1 2.500000 19.516000 9.941972 61.468750 14544 2 0.000000 -1 2.500000 19.516000 9.941972 61.468750 14545 2 0.000000 1 2.500000 21.812000 19.221145 1.756250 @@ -14563,7 +14563,7 @@ Atoms 14547 2 0.000000 1 2.500000 24.108000 23.197934 1.756250 14548 2 0.000000 -1 2.500000 24.108000 23.197934 1.756250 14549 2 0.000000 1 2.500000 17.220000 21.872338 5.268750 -14550 2 0.000000 -1.000000 2.500000 17.220000 21.872338 5.268750 +14550 2 0.000000 -1 2.500000 17.220000 21.872338 5.268750 14551 2 0.000000 1 2.500000 19.516000 17.895549 5.268750 14552 2 0.000000 -1 2.500000 19.516000 17.895549 5.268750 14553 2 0.000000 1 2.500000 21.812000 19.221145 8.781250 @@ -14571,7 +14571,7 @@ Atoms 14555 2 0.000000 1 2.500000 24.108000 23.197934 8.781250 14556 2 0.000000 -1 2.500000 24.108000 23.197934 8.781250 14557 2 0.000000 1 2.500000 17.220000 21.872338 12.293750 -14558 2 0.000000 -1.000000 2.500000 17.220000 21.872338 12.293750 +14558 2 0.000000 -1 2.500000 17.220000 21.872338 12.293750 14559 2 0.000000 1 2.500000 19.516000 17.895549 12.293750 14560 2 0.000000 -1 2.500000 19.516000 17.895549 12.293750 14561 2 0.000000 1 2.500000 21.812000 19.221145 15.806250 @@ -14579,7 +14579,7 @@ Atoms 14563 2 0.000000 1 2.500000 24.108000 23.197934 15.806250 14564 2 0.000000 -1 2.500000 24.108000 23.197934 15.806250 14565 2 0.000000 1 2.500000 17.220000 21.872338 19.318750 -14566 2 0.000000 -1.000000 2.500000 17.220000 21.872338 19.318750 +14566 2 0.000000 -1 2.500000 17.220000 21.872338 19.318750 14567 2 0.000000 1 2.500000 19.516000 17.895549 19.318750 14568 2 0.000000 -1 2.500000 19.516000 17.895549 19.318750 14569 2 0.000000 1 2.500000 21.812000 19.221145 22.831250 @@ -14587,7 +14587,7 @@ Atoms 14571 2 0.000000 1 2.500000 24.108000 23.197934 22.831250 14572 2 0.000000 -1 2.500000 24.108000 23.197934 22.831250 14573 2 0.000000 1 2.500000 17.220000 21.872338 26.343750 -14574 2 0.000000 -1.000000 2.500000 17.220000 21.872338 26.343750 +14574 2 0.000000 -1 2.500000 17.220000 21.872338 26.343750 14575 2 0.000000 1 2.500000 19.516000 17.895549 26.343750 14576 2 0.000000 -1 2.500000 19.516000 17.895549 26.343750 14577 2 0.000000 1 2.500000 21.812000 19.221145 29.856250 @@ -14595,7 +14595,7 @@ Atoms 14579 2 0.000000 1 2.500000 24.108000 23.197934 29.856250 14580 2 0.000000 -1 2.500000 24.108000 23.197934 29.856250 14581 2 0.000000 1 2.500000 17.220000 21.872338 33.368750 -14582 2 0.000000 -1.000000 2.500000 17.220000 21.872338 33.368750 +14582 2 0.000000 -1 2.500000 17.220000 21.872338 33.368750 14583 2 0.000000 1 2.500000 19.516000 17.895549 33.368750 14584 2 0.000000 -1 2.500000 19.516000 17.895549 33.368750 14585 2 0.000000 1 2.500000 21.812000 19.221145 36.881250 @@ -14603,7 +14603,7 @@ Atoms 14587 2 0.000000 1 2.500000 24.108000 23.197934 36.881250 14588 2 0.000000 -1 2.500000 24.108000 23.197934 36.881250 14589 2 0.000000 1 2.500000 17.220000 21.872338 40.393750 -14590 2 0.000000 -1.000000 2.500000 17.220000 21.872338 40.393750 +14590 2 0.000000 -1 2.500000 17.220000 21.872338 40.393750 14591 2 0.000000 1 2.500000 19.516000 17.895549 40.393750 14592 2 0.000000 -1 2.500000 19.516000 17.895549 40.393750 14593 2 0.000000 1 2.500000 21.812000 19.221145 43.906250 @@ -14611,7 +14611,7 @@ Atoms 14595 2 0.000000 1 2.500000 24.108000 23.197934 43.906250 14596 2 0.000000 -1 2.500000 24.108000 23.197934 43.906250 14597 2 0.000000 1 2.500000 17.220000 21.872338 47.418750 -14598 2 0.000000 -1.000000 2.500000 17.220000 21.872338 47.418750 +14598 2 0.000000 -1 2.500000 17.220000 21.872338 47.418750 14599 2 0.000000 1 2.500000 19.516000 17.895549 47.418750 14600 2 0.000000 -1 2.500000 19.516000 17.895549 47.418750 14601 2 0.000000 1 2.500000 21.812000 19.221145 50.931250 @@ -14619,7 +14619,7 @@ Atoms 14603 2 0.000000 1 2.500000 24.108000 23.197934 50.931250 14604 2 0.000000 -1 2.500000 24.108000 23.197934 50.931250 14605 2 0.000000 1 2.500000 17.220000 21.872338 54.443750 -14606 2 0.000000 -1.000000 2.500000 17.220000 21.872338 54.443750 +14606 2 0.000000 -1 2.500000 17.220000 21.872338 54.443750 14607 2 0.000000 1 2.500000 19.516000 17.895549 54.443750 14608 2 0.000000 -1 2.500000 19.516000 17.895549 54.443750 14609 2 0.000000 1 2.500000 21.812000 19.221145 57.956250 @@ -14627,7 +14627,7 @@ Atoms 14611 2 0.000000 1 2.500000 24.108000 23.197934 57.956250 14612 2 0.000000 -1 2.500000 24.108000 23.197934 57.956250 14613 2 0.000000 1 2.500000 17.220000 21.872338 61.468750 -14614 2 0.000000 -1.000000 2.500000 17.220000 21.872338 61.468750 +14614 2 0.000000 -1 2.500000 17.220000 21.872338 61.468750 14615 2 0.000000 1 2.500000 19.516000 17.895549 61.468750 14616 2 0.000000 -1 2.500000 19.516000 17.895549 61.468750 14617 2 0.000000 1 2.500000 21.812000 27.174722 1.756250 @@ -14635,7 +14635,7 @@ Atoms 14619 2 0.000000 1 2.500000 24.108000 31.151511 1.756250 14620 2 0.000000 -1 2.500000 24.108000 31.151511 1.756250 14621 2 0.000000 1 2.500000 17.220000 29.825915 5.268750 -14622 2 0.000000 -1.000000 2.500000 17.220000 29.825915 5.268750 +14622 2 0.000000 -1 2.500000 17.220000 29.825915 5.268750 14623 2 0.000000 1 2.500000 19.516000 25.849126 5.268750 14624 2 0.000000 -1 2.500000 19.516000 25.849126 5.268750 14625 2 0.000000 1 2.500000 21.812000 27.174722 8.781250 @@ -14643,7 +14643,7 @@ Atoms 14627 2 0.000000 1 2.500000 24.108000 31.151511 8.781250 14628 2 0.000000 -1 2.500000 24.108000 31.151511 8.781250 14629 2 0.000000 1 2.500000 17.220000 29.825915 12.293750 -14630 2 0.000000 -1.000000 2.500000 17.220000 29.825915 12.293750 +14630 2 0.000000 -1 2.500000 17.220000 29.825915 12.293750 14631 2 0.000000 1 2.500000 19.516000 25.849126 12.293750 14632 2 0.000000 -1 2.500000 19.516000 25.849126 12.293750 14633 2 0.000000 1 2.500000 21.812000 27.174722 15.806250 @@ -14651,7 +14651,7 @@ Atoms 14635 2 0.000000 1 2.500000 24.108000 31.151511 15.806250 14636 2 0.000000 -1 2.500000 24.108000 31.151511 15.806250 14637 2 0.000000 1 2.500000 17.220000 29.825915 19.318750 -14638 2 0.000000 -1.000000 2.500000 17.220000 29.825915 19.318750 +14638 2 0.000000 -1 2.500000 17.220000 29.825915 19.318750 14639 2 0.000000 1 2.500000 19.516000 25.849126 19.318750 14640 2 0.000000 -1 2.500000 19.516000 25.849126 19.318750 14641 2 0.000000 1 2.500000 21.812000 27.174722 22.831250 @@ -14659,7 +14659,7 @@ Atoms 14643 2 0.000000 1 2.500000 24.108000 31.151511 22.831250 14644 2 0.000000 -1 2.500000 24.108000 31.151511 22.831250 14645 2 0.000000 1 2.500000 17.220000 29.825915 26.343750 -14646 2 0.000000 -1.000000 2.500000 17.220000 29.825915 26.343750 +14646 2 0.000000 -1 2.500000 17.220000 29.825915 26.343750 14647 2 0.000000 1 2.500000 19.516000 25.849126 26.343750 14648 2 0.000000 -1 2.500000 19.516000 25.849126 26.343750 14649 2 0.000000 1 2.500000 21.812000 27.174722 29.856250 @@ -14667,7 +14667,7 @@ Atoms 14651 2 0.000000 1 2.500000 24.108000 31.151511 29.856250 14652 2 0.000000 -1 2.500000 24.108000 31.151511 29.856250 14653 2 0.000000 1 2.500000 17.220000 29.825915 33.368750 -14654 2 0.000000 -1.000000 2.500000 17.220000 29.825915 33.368750 +14654 2 0.000000 -1 2.500000 17.220000 29.825915 33.368750 14655 2 0.000000 1 2.500000 19.516000 25.849126 33.368750 14656 2 0.000000 -1 2.500000 19.516000 25.849126 33.368750 14657 2 0.000000 1 2.500000 21.812000 27.174722 36.881250 @@ -14675,7 +14675,7 @@ Atoms 14659 2 0.000000 1 2.500000 24.108000 31.151511 36.881250 14660 2 0.000000 -1 2.500000 24.108000 31.151511 36.881250 14661 2 0.000000 1 2.500000 17.220000 29.825915 40.393750 -14662 2 0.000000 -1.000000 2.500000 17.220000 29.825915 40.393750 +14662 2 0.000000 -1 2.500000 17.220000 29.825915 40.393750 14663 2 0.000000 1 2.500000 19.516000 25.849126 40.393750 14664 2 0.000000 -1 2.500000 19.516000 25.849126 40.393750 14665 2 0.000000 1 2.500000 21.812000 27.174722 43.906250 @@ -14683,7 +14683,7 @@ Atoms 14667 2 0.000000 1 2.500000 24.108000 31.151511 43.906250 14668 2 0.000000 -1 2.500000 24.108000 31.151511 43.906250 14669 2 0.000000 1 2.500000 17.220000 29.825915 47.418750 -14670 2 0.000000 -1.000000 2.500000 17.220000 29.825915 47.418750 +14670 2 0.000000 -1 2.500000 17.220000 29.825915 47.418750 14671 2 0.000000 1 2.500000 19.516000 25.849126 47.418750 14672 2 0.000000 -1 2.500000 19.516000 25.849126 47.418750 14673 2 0.000000 1 2.500000 21.812000 27.174722 50.931250 @@ -14691,7 +14691,7 @@ Atoms 14675 2 0.000000 1 2.500000 24.108000 31.151511 50.931250 14676 2 0.000000 -1 2.500000 24.108000 31.151511 50.931250 14677 2 0.000000 1 2.500000 17.220000 29.825915 54.443750 -14678 2 0.000000 -1.000000 2.500000 17.220000 29.825915 54.443750 +14678 2 0.000000 -1 2.500000 17.220000 29.825915 54.443750 14679 2 0.000000 1 2.500000 19.516000 25.849126 54.443750 14680 2 0.000000 -1 2.500000 19.516000 25.849126 54.443750 14681 2 0.000000 1 2.500000 21.812000 27.174722 57.956250 @@ -14699,7 +14699,7 @@ Atoms 14683 2 0.000000 1 2.500000 24.108000 31.151511 57.956250 14684 2 0.000000 -1 2.500000 24.108000 31.151511 57.956250 14685 2 0.000000 1 2.500000 17.220000 29.825915 61.468750 -14686 2 0.000000 -1.000000 2.500000 17.220000 29.825915 61.468750 +14686 2 0.000000 -1 2.500000 17.220000 29.825915 61.468750 14687 2 0.000000 1 2.500000 19.516000 25.849126 61.468750 14688 2 0.000000 -1 2.500000 19.516000 25.849126 61.468750 14689 2 0.000000 1 2.500000 21.812000 35.128300 1.756250 @@ -14707,7 +14707,7 @@ Atoms 14691 2 0.000000 1 2.500000 24.108000 39.105088 1.756250 14692 2 0.000000 -1 2.500000 24.108000 39.105088 1.756250 14693 2 0.000000 1 2.500000 17.220000 37.779492 5.268750 -14694 2 0.000000 -1.000000 2.500000 17.220000 37.779492 5.268750 +14694 2 0.000000 -1 2.500000 17.220000 37.779492 5.268750 14695 2 0.000000 1 2.500000 19.516000 33.802704 5.268750 14696 2 0.000000 -1 2.500000 19.516000 33.802704 5.268750 14697 2 0.000000 1 2.500000 21.812000 35.128300 8.781250 @@ -14715,7 +14715,7 @@ Atoms 14699 2 0.000000 1 2.500000 24.108000 39.105088 8.781250 14700 2 0.000000 -1 2.500000 24.108000 39.105088 8.781250 14701 2 0.000000 1 2.500000 17.220000 37.779492 12.293750 -14702 2 0.000000 -1.000000 2.500000 17.220000 37.779492 12.293750 +14702 2 0.000000 -1 2.500000 17.220000 37.779492 12.293750 14703 2 0.000000 1 2.500000 19.516000 33.802704 12.293750 14704 2 0.000000 -1 2.500000 19.516000 33.802704 12.293750 14705 2 0.000000 1 2.500000 21.812000 35.128300 15.806250 @@ -14723,7 +14723,7 @@ Atoms 14707 2 0.000000 1 2.500000 24.108000 39.105088 15.806250 14708 2 0.000000 -1 2.500000 24.108000 39.105088 15.806250 14709 2 0.000000 1 2.500000 17.220000 37.779492 19.318750 -14710 2 0.000000 -1.000000 2.500000 17.220000 37.779492 19.318750 +14710 2 0.000000 -1 2.500000 17.220000 37.779492 19.318750 14711 2 0.000000 1 2.500000 19.516000 33.802704 19.318750 14712 2 0.000000 -1 2.500000 19.516000 33.802704 19.318750 14713 2 0.000000 1 2.500000 21.812000 35.128300 22.831250 @@ -14731,7 +14731,7 @@ Atoms 14715 2 0.000000 1 2.500000 24.108000 39.105088 22.831250 14716 2 0.000000 -1 2.500000 24.108000 39.105088 22.831250 14717 2 0.000000 1 2.500000 17.220000 37.779492 26.343750 -14718 2 0.000000 -1.000000 2.500000 17.220000 37.779492 26.343750 +14718 2 0.000000 -1 2.500000 17.220000 37.779492 26.343750 14719 2 0.000000 1 2.500000 19.516000 33.802704 26.343750 14720 2 0.000000 -1 2.500000 19.516000 33.802704 26.343750 14721 2 0.000000 1 2.500000 21.812000 35.128300 29.856250 @@ -14739,7 +14739,7 @@ Atoms 14723 2 0.000000 1 2.500000 24.108000 39.105088 29.856250 14724 2 0.000000 -1 2.500000 24.108000 39.105088 29.856250 14725 2 0.000000 1 2.500000 17.220000 37.779492 33.368750 -14726 2 0.000000 -1.000000 2.500000 17.220000 37.779492 33.368750 +14726 2 0.000000 -1 2.500000 17.220000 37.779492 33.368750 14727 2 0.000000 1 2.500000 19.516000 33.802704 33.368750 14728 2 0.000000 -1 2.500000 19.516000 33.802704 33.368750 14729 2 0.000000 1 2.500000 21.812000 35.128300 36.881250 @@ -14747,7 +14747,7 @@ Atoms 14731 2 0.000000 1 2.500000 24.108000 39.105088 36.881250 14732 2 0.000000 -1 2.500000 24.108000 39.105088 36.881250 14733 2 0.000000 1 2.500000 17.220000 37.779492 40.393750 -14734 2 0.000000 -1.000000 2.500000 17.220000 37.779492 40.393750 +14734 2 0.000000 -1 2.500000 17.220000 37.779492 40.393750 14735 2 0.000000 1 2.500000 19.516000 33.802704 40.393750 14736 2 0.000000 -1 2.500000 19.516000 33.802704 40.393750 14737 2 0.000000 1 2.500000 21.812000 35.128300 43.906250 @@ -14755,7 +14755,7 @@ Atoms 14739 2 0.000000 1 2.500000 24.108000 39.105088 43.906250 14740 2 0.000000 -1 2.500000 24.108000 39.105088 43.906250 14741 2 0.000000 1 2.500000 17.220000 37.779492 47.418750 -14742 2 0.000000 -1.000000 2.500000 17.220000 37.779492 47.418750 +14742 2 0.000000 -1 2.500000 17.220000 37.779492 47.418750 14743 2 0.000000 1 2.500000 19.516000 33.802704 47.418750 14744 2 0.000000 -1 2.500000 19.516000 33.802704 47.418750 14745 2 0.000000 1 2.500000 21.812000 35.128300 50.931250 @@ -14763,7 +14763,7 @@ Atoms 14747 2 0.000000 1 2.500000 24.108000 39.105088 50.931250 14748 2 0.000000 -1 2.500000 24.108000 39.105088 50.931250 14749 2 0.000000 1 2.500000 17.220000 37.779492 54.443750 -14750 2 0.000000 -1.000000 2.500000 17.220000 37.779492 54.443750 +14750 2 0.000000 -1 2.500000 17.220000 37.779492 54.443750 14751 2 0.000000 1 2.500000 19.516000 33.802704 54.443750 14752 2 0.000000 -1 2.500000 19.516000 33.802704 54.443750 14753 2 0.000000 1 2.500000 21.812000 35.128300 57.956250 @@ -14771,7 +14771,7 @@ Atoms 14755 2 0.000000 1 2.500000 24.108000 39.105088 57.956250 14756 2 0.000000 -1 2.500000 24.108000 39.105088 57.956250 14757 2 0.000000 1 2.500000 17.220000 37.779492 61.468750 -14758 2 0.000000 -1.000000 2.500000 17.220000 37.779492 61.468750 +14758 2 0.000000 -1 2.500000 17.220000 37.779492 61.468750 14759 2 0.000000 1 2.500000 19.516000 33.802704 61.468750 14760 2 0.000000 -1 2.500000 19.516000 33.802704 61.468750 14761 2 0.000000 1 2.500000 21.812000 43.081877 1.756250 @@ -14779,7 +14779,7 @@ Atoms 14763 2 0.000000 1 2.500000 24.108000 47.058666 1.756250 14764 2 0.000000 -1 2.500000 24.108000 47.058666 1.756250 14765 2 0.000000 1 2.500000 17.220000 45.733070 5.268750 -14766 2 0.000000 -1.000000 2.500000 17.220000 45.733070 5.268750 +14766 2 0.000000 -1 2.500000 17.220000 45.733070 5.268750 14767 2 0.000000 1 2.500000 19.516000 41.756281 5.268750 14768 2 0.000000 -1 2.500000 19.516000 41.756281 5.268750 14769 2 0.000000 1 2.500000 21.812000 43.081877 8.781250 @@ -14787,7 +14787,7 @@ Atoms 14771 2 0.000000 1 2.500000 24.108000 47.058666 8.781250 14772 2 0.000000 -1 2.500000 24.108000 47.058666 8.781250 14773 2 0.000000 1 2.500000 17.220000 45.733070 12.293750 -14774 2 0.000000 -1.000000 2.500000 17.220000 45.733070 12.293750 +14774 2 0.000000 -1 2.500000 17.220000 45.733070 12.293750 14775 2 0.000000 1 2.500000 19.516000 41.756281 12.293750 14776 2 0.000000 -1 2.500000 19.516000 41.756281 12.293750 14777 2 0.000000 1 2.500000 21.812000 43.081877 15.806250 @@ -14795,7 +14795,7 @@ Atoms 14779 2 0.000000 1 2.500000 24.108000 47.058666 15.806250 14780 2 0.000000 -1 2.500000 24.108000 47.058666 15.806250 14781 2 0.000000 1 2.500000 17.220000 45.733070 19.318750 -14782 2 0.000000 -1.000000 2.500000 17.220000 45.733070 19.318750 +14782 2 0.000000 -1 2.500000 17.220000 45.733070 19.318750 14783 2 0.000000 1 2.500000 19.516000 41.756281 19.318750 14784 2 0.000000 -1 2.500000 19.516000 41.756281 19.318750 14785 2 0.000000 1 2.500000 21.812000 43.081877 22.831250 @@ -14803,7 +14803,7 @@ Atoms 14787 2 0.000000 1 2.500000 24.108000 47.058666 22.831250 14788 2 0.000000 -1 2.500000 24.108000 47.058666 22.831250 14789 2 0.000000 1 2.500000 17.220000 45.733070 26.343750 -14790 2 0.000000 -1.000000 2.500000 17.220000 45.733070 26.343750 +14790 2 0.000000 -1 2.500000 17.220000 45.733070 26.343750 14791 2 0.000000 1 2.500000 19.516000 41.756281 26.343750 14792 2 0.000000 -1 2.500000 19.516000 41.756281 26.343750 14793 2 0.000000 1 2.500000 21.812000 43.081877 29.856250 @@ -14811,7 +14811,7 @@ Atoms 14795 2 0.000000 1 2.500000 24.108000 47.058666 29.856250 14796 2 0.000000 -1 2.500000 24.108000 47.058666 29.856250 14797 2 0.000000 1 2.500000 17.220000 45.733070 33.368750 -14798 2 0.000000 -1.000000 2.500000 17.220000 45.733070 33.368750 +14798 2 0.000000 -1 2.500000 17.220000 45.733070 33.368750 14799 2 0.000000 1 2.500000 19.516000 41.756281 33.368750 14800 2 0.000000 -1 2.500000 19.516000 41.756281 33.368750 14801 2 0.000000 1 2.500000 21.812000 43.081877 36.881250 @@ -14819,7 +14819,7 @@ Atoms 14803 2 0.000000 1 2.500000 24.108000 47.058666 36.881250 14804 2 0.000000 -1 2.500000 24.108000 47.058666 36.881250 14805 2 0.000000 1 2.500000 17.220000 45.733070 40.393750 -14806 2 0.000000 -1.000000 2.500000 17.220000 45.733070 40.393750 +14806 2 0.000000 -1 2.500000 17.220000 45.733070 40.393750 14807 2 0.000000 1 2.500000 19.516000 41.756281 40.393750 14808 2 0.000000 -1 2.500000 19.516000 41.756281 40.393750 14809 2 0.000000 1 2.500000 21.812000 43.081877 43.906250 @@ -14827,7 +14827,7 @@ Atoms 14811 2 0.000000 1 2.500000 24.108000 47.058666 43.906250 14812 2 0.000000 -1 2.500000 24.108000 47.058666 43.906250 14813 2 0.000000 1 2.500000 17.220000 45.733070 47.418750 -14814 2 0.000000 -1.000000 2.500000 17.220000 45.733070 47.418750 +14814 2 0.000000 -1 2.500000 17.220000 45.733070 47.418750 14815 2 0.000000 1 2.500000 19.516000 41.756281 47.418750 14816 2 0.000000 -1 2.500000 19.516000 41.756281 47.418750 14817 2 0.000000 1 2.500000 21.812000 43.081877 50.931250 @@ -14835,7 +14835,7 @@ Atoms 14819 2 0.000000 1 2.500000 24.108000 47.058666 50.931250 14820 2 0.000000 -1 2.500000 24.108000 47.058666 50.931250 14821 2 0.000000 1 2.500000 17.220000 45.733070 54.443750 -14822 2 0.000000 -1.000000 2.500000 17.220000 45.733070 54.443750 +14822 2 0.000000 -1 2.500000 17.220000 45.733070 54.443750 14823 2 0.000000 1 2.500000 19.516000 41.756281 54.443750 14824 2 0.000000 -1 2.500000 19.516000 41.756281 54.443750 14825 2 0.000000 1 2.500000 21.812000 43.081877 57.956250 @@ -14843,7 +14843,7 @@ Atoms 14827 2 0.000000 1 2.500000 24.108000 47.058666 57.956250 14828 2 0.000000 -1 2.500000 24.108000 47.058666 57.956250 14829 2 0.000000 1 2.500000 17.220000 45.733070 61.468750 -14830 2 0.000000 -1.000000 2.500000 17.220000 45.733070 61.468750 +14830 2 0.000000 -1 2.500000 17.220000 45.733070 61.468750 14831 2 0.000000 1 2.500000 19.516000 41.756281 61.468750 14832 2 0.000000 -1 2.500000 19.516000 41.756281 61.468750 14833 2 0.000000 1 2.500000 21.812000 51.035454 1.756250 @@ -14851,7 +14851,7 @@ Atoms 14835 2 0.000000 1 2.500000 24.108000 55.012243 1.756250 14836 2 0.000000 -1 2.500000 24.108000 55.012243 1.756250 14837 2 0.000000 1 2.500000 17.220000 53.686647 5.268750 -14838 2 0.000000 -1.000000 2.500000 17.220000 53.686647 5.268750 +14838 2 0.000000 -1 2.500000 17.220000 53.686647 5.268750 14839 2 0.000000 1 2.500000 19.516000 49.709858 5.268750 14840 2 0.000000 -1 2.500000 19.516000 49.709858 5.268750 14841 2 0.000000 1 2.500000 21.812000 51.035454 8.781250 @@ -14859,7 +14859,7 @@ Atoms 14843 2 0.000000 1 2.500000 24.108000 55.012243 8.781250 14844 2 0.000000 -1 2.500000 24.108000 55.012243 8.781250 14845 2 0.000000 1 2.500000 17.220000 53.686647 12.293750 -14846 2 0.000000 -1.000000 2.500000 17.220000 53.686647 12.293750 +14846 2 0.000000 -1 2.500000 17.220000 53.686647 12.293750 14847 2 0.000000 1 2.500000 19.516000 49.709858 12.293750 14848 2 0.000000 -1 2.500000 19.516000 49.709858 12.293750 14849 2 0.000000 1 2.500000 21.812000 51.035454 15.806250 @@ -14867,7 +14867,7 @@ Atoms 14851 2 0.000000 1 2.500000 24.108000 55.012243 15.806250 14852 2 0.000000 -1 2.500000 24.108000 55.012243 15.806250 14853 2 0.000000 1 2.500000 17.220000 53.686647 19.318750 -14854 2 0.000000 -1.000000 2.500000 17.220000 53.686647 19.318750 +14854 2 0.000000 -1 2.500000 17.220000 53.686647 19.318750 14855 2 0.000000 1 2.500000 19.516000 49.709858 19.318750 14856 2 0.000000 -1 2.500000 19.516000 49.709858 19.318750 14857 2 0.000000 1 2.500000 21.812000 51.035454 22.831250 @@ -14875,7 +14875,7 @@ Atoms 14859 2 0.000000 1 2.500000 24.108000 55.012243 22.831250 14860 2 0.000000 -1 2.500000 24.108000 55.012243 22.831250 14861 2 0.000000 1 2.500000 17.220000 53.686647 26.343750 -14862 2 0.000000 -1.000000 2.500000 17.220000 53.686647 26.343750 +14862 2 0.000000 -1 2.500000 17.220000 53.686647 26.343750 14863 2 0.000000 1 2.500000 19.516000 49.709858 26.343750 14864 2 0.000000 -1 2.500000 19.516000 49.709858 26.343750 14865 2 0.000000 1 2.500000 21.812000 51.035454 29.856250 @@ -14883,7 +14883,7 @@ Atoms 14867 2 0.000000 1 2.500000 24.108000 55.012243 29.856250 14868 2 0.000000 -1 2.500000 24.108000 55.012243 29.856250 14869 2 0.000000 1 2.500000 17.220000 53.686647 33.368750 -14870 2 0.000000 -1.000000 2.500000 17.220000 53.686647 33.368750 +14870 2 0.000000 -1 2.500000 17.220000 53.686647 33.368750 14871 2 0.000000 1 2.500000 19.516000 49.709858 33.368750 14872 2 0.000000 -1 2.500000 19.516000 49.709858 33.368750 14873 2 0.000000 1 2.500000 21.812000 51.035454 36.881250 @@ -14891,7 +14891,7 @@ Atoms 14875 2 0.000000 1 2.500000 24.108000 55.012243 36.881250 14876 2 0.000000 -1 2.500000 24.108000 55.012243 36.881250 14877 2 0.000000 1 2.500000 17.220000 53.686647 40.393750 -14878 2 0.000000 -1.000000 2.500000 17.220000 53.686647 40.393750 +14878 2 0.000000 -1 2.500000 17.220000 53.686647 40.393750 14879 2 0.000000 1 2.500000 19.516000 49.709858 40.393750 14880 2 0.000000 -1 2.500000 19.516000 49.709858 40.393750 14881 2 0.000000 1 2.500000 21.812000 51.035454 43.906250 @@ -14899,7 +14899,7 @@ Atoms 14883 2 0.000000 1 2.500000 24.108000 55.012243 43.906250 14884 2 0.000000 -1 2.500000 24.108000 55.012243 43.906250 14885 2 0.000000 1 2.500000 17.220000 53.686647 47.418750 -14886 2 0.000000 -1.000000 2.500000 17.220000 53.686647 47.418750 +14886 2 0.000000 -1 2.500000 17.220000 53.686647 47.418750 14887 2 0.000000 1 2.500000 19.516000 49.709858 47.418750 14888 2 0.000000 -1 2.500000 19.516000 49.709858 47.418750 14889 2 0.000000 1 2.500000 21.812000 51.035454 50.931250 @@ -14907,7 +14907,7 @@ Atoms 14891 2 0.000000 1 2.500000 24.108000 55.012243 50.931250 14892 2 0.000000 -1 2.500000 24.108000 55.012243 50.931250 14893 2 0.000000 1 2.500000 17.220000 53.686647 54.443750 -14894 2 0.000000 -1.000000 2.500000 17.220000 53.686647 54.443750 +14894 2 0.000000 -1 2.500000 17.220000 53.686647 54.443750 14895 2 0.000000 1 2.500000 19.516000 49.709858 54.443750 14896 2 0.000000 -1 2.500000 19.516000 49.709858 54.443750 14897 2 0.000000 1 2.500000 21.812000 51.035454 57.956250 @@ -14915,7 +14915,7 @@ Atoms 14899 2 0.000000 1 2.500000 24.108000 55.012243 57.956250 14900 2 0.000000 -1 2.500000 24.108000 55.012243 57.956250 14901 2 0.000000 1 2.500000 17.220000 53.686647 61.468750 -14902 2 0.000000 -1.000000 2.500000 17.220000 53.686647 61.468750 +14902 2 0.000000 -1 2.500000 17.220000 53.686647 61.468750 14903 2 0.000000 1 2.500000 19.516000 49.709858 61.468750 14904 2 0.000000 -1 2.500000 19.516000 49.709858 61.468750 14905 2 0.000000 1 2.500000 21.812000 58.989032 1.756250 @@ -14923,7 +14923,7 @@ Atoms 14907 2 0.000000 1 2.500000 24.108000 62.965820 1.756250 14908 2 0.000000 -1 2.500000 24.108000 62.965820 1.756250 14909 2 0.000000 1 2.500000 17.220000 61.640224 5.268750 -14910 2 0.000000 -1.000000 2.500000 17.220000 61.640224 5.268750 +14910 2 0.000000 -1 2.500000 17.220000 61.640224 5.268750 14911 2 0.000000 1 2.500000 19.516000 57.663435 5.268750 14912 2 0.000000 -1 2.500000 19.516000 57.663435 5.268750 14913 2 0.000000 1 2.500000 21.812000 58.989032 8.781250 @@ -14931,7 +14931,7 @@ Atoms 14915 2 0.000000 1 2.500000 24.108000 62.965820 8.781250 14916 2 0.000000 -1 2.500000 24.108000 62.965820 8.781250 14917 2 0.000000 1 2.500000 17.220000 61.640224 12.293750 -14918 2 0.000000 -1.000000 2.500000 17.220000 61.640224 12.293750 +14918 2 0.000000 -1 2.500000 17.220000 61.640224 12.293750 14919 2 0.000000 1 2.500000 19.516000 57.663435 12.293750 14920 2 0.000000 -1 2.500000 19.516000 57.663435 12.293750 14921 2 0.000000 1 2.500000 21.812000 58.989032 15.806250 @@ -14939,7 +14939,7 @@ Atoms 14923 2 0.000000 1 2.500000 24.108000 62.965820 15.806250 14924 2 0.000000 -1 2.500000 24.108000 62.965820 15.806250 14925 2 0.000000 1 2.500000 17.220000 61.640224 19.318750 -14926 2 0.000000 -1.000000 2.500000 17.220000 61.640224 19.318750 +14926 2 0.000000 -1 2.500000 17.220000 61.640224 19.318750 14927 2 0.000000 1 2.500000 19.516000 57.663435 19.318750 14928 2 0.000000 -1 2.500000 19.516000 57.663435 19.318750 14929 2 0.000000 1 2.500000 21.812000 58.989032 22.831250 @@ -14947,7 +14947,7 @@ Atoms 14931 2 0.000000 1 2.500000 24.108000 62.965820 22.831250 14932 2 0.000000 -1 2.500000 24.108000 62.965820 22.831250 14933 2 0.000000 1 2.500000 17.220000 61.640224 26.343750 -14934 2 0.000000 -1.000000 2.500000 17.220000 61.640224 26.343750 +14934 2 0.000000 -1 2.500000 17.220000 61.640224 26.343750 14935 2 0.000000 1 2.500000 19.516000 57.663435 26.343750 14936 2 0.000000 -1 2.500000 19.516000 57.663435 26.343750 14937 2 0.000000 1 2.500000 21.812000 58.989032 29.856250 @@ -14955,7 +14955,7 @@ Atoms 14939 2 0.000000 1 2.500000 24.108000 62.965820 29.856250 14940 2 0.000000 -1 2.500000 24.108000 62.965820 29.856250 14941 2 0.000000 1 2.500000 17.220000 61.640224 33.368750 -14942 2 0.000000 -1.000000 2.500000 17.220000 61.640224 33.368750 +14942 2 0.000000 -1 2.500000 17.220000 61.640224 33.368750 14943 2 0.000000 1 2.500000 19.516000 57.663435 33.368750 14944 2 0.000000 -1 2.500000 19.516000 57.663435 33.368750 14945 2 0.000000 1 2.500000 21.812000 58.989032 36.881250 @@ -14963,7 +14963,7 @@ Atoms 14947 2 0.000000 1 2.500000 24.108000 62.965820 36.881250 14948 2 0.000000 -1 2.500000 24.108000 62.965820 36.881250 14949 2 0.000000 1 2.500000 17.220000 61.640224 40.393750 -14950 2 0.000000 -1.000000 2.500000 17.220000 61.640224 40.393750 +14950 2 0.000000 -1 2.500000 17.220000 61.640224 40.393750 14951 2 0.000000 1 2.500000 19.516000 57.663435 40.393750 14952 2 0.000000 -1 2.500000 19.516000 57.663435 40.393750 14953 2 0.000000 1 2.500000 21.812000 58.989032 43.906250 @@ -14971,7 +14971,7 @@ Atoms 14955 2 0.000000 1 2.500000 24.108000 62.965820 43.906250 14956 2 0.000000 -1 2.500000 24.108000 62.965820 43.906250 14957 2 0.000000 1 2.500000 17.220000 61.640224 47.418750 -14958 2 0.000000 -1.000000 2.500000 17.220000 61.640224 47.418750 +14958 2 0.000000 -1 2.500000 17.220000 61.640224 47.418750 14959 2 0.000000 1 2.500000 19.516000 57.663435 47.418750 14960 2 0.000000 -1 2.500000 19.516000 57.663435 47.418750 14961 2 0.000000 1 2.500000 21.812000 58.989032 50.931250 @@ -14979,7 +14979,7 @@ Atoms 14963 2 0.000000 1 2.500000 24.108000 62.965820 50.931250 14964 2 0.000000 -1 2.500000 24.108000 62.965820 50.931250 14965 2 0.000000 1 2.500000 17.220000 61.640224 54.443750 -14966 2 0.000000 -1.000000 2.500000 17.220000 61.640224 54.443750 +14966 2 0.000000 -1 2.500000 17.220000 61.640224 54.443750 14967 2 0.000000 1 2.500000 19.516000 57.663435 54.443750 14968 2 0.000000 -1 2.500000 19.516000 57.663435 54.443750 14969 2 0.000000 1 2.500000 21.812000 58.989032 57.956250 @@ -14987,7 +14987,7 @@ Atoms 14971 2 0.000000 1 2.500000 24.108000 62.965820 57.956250 14972 2 0.000000 -1 2.500000 24.108000 62.965820 57.956250 14973 2 0.000000 1 2.500000 17.220000 61.640224 61.468750 -14974 2 0.000000 -1.000000 2.500000 17.220000 61.640224 61.468750 +14974 2 0.000000 -1 2.500000 17.220000 61.640224 61.468750 14975 2 0.000000 1 2.500000 19.516000 57.663435 61.468750 14976 2 0.000000 -1 2.500000 19.516000 57.663435 61.468750 14977 2 0.000000 1 2.500000 26.404000 3.313991 1.756250 @@ -14995,7 +14995,7 @@ Atoms 14979 2 0.000000 1 2.500000 28.700000 7.290779 1.756250 14980 2 0.000000 -1 2.500000 28.700000 7.290779 1.756250 14981 2 0.000000 1 2.500000 21.812000 5.965183 5.268750 -14982 2 0.000000 -1.000000 2.500000 21.812000 5.965183 5.268750 +14982 2 0.000000 -1 2.500000 21.812000 5.965183 5.268750 14983 2 0.000000 1 2.500000 24.108000 1.988394 5.268750 14984 2 0.000000 -1 2.500000 24.108000 1.988394 5.268750 14985 2 0.000000 1 2.500000 26.404000 3.313991 8.781250 @@ -15003,7 +15003,7 @@ Atoms 14987 2 0.000000 1 2.500000 28.700000 7.290779 8.781250 14988 2 0.000000 -1 2.500000 28.700000 7.290779 8.781250 14989 2 0.000000 1 2.500000 21.812000 5.965183 12.293750 -14990 2 0.000000 -1.000000 2.500000 21.812000 5.965183 12.293750 +14990 2 0.000000 -1 2.500000 21.812000 5.965183 12.293750 14991 2 0.000000 1 2.500000 24.108000 1.988394 12.293750 14992 2 0.000000 -1 2.500000 24.108000 1.988394 12.293750 14993 2 0.000000 1 2.500000 26.404000 3.313991 15.806250 @@ -15011,7 +15011,7 @@ Atoms 14995 2 0.000000 1 2.500000 28.700000 7.290779 15.806250 14996 2 0.000000 -1 2.500000 28.700000 7.290779 15.806250 14997 2 0.000000 1 2.500000 21.812000 5.965183 19.318750 -14998 2 0.000000 -1.000000 2.500000 21.812000 5.965183 19.318750 +14998 2 0.000000 -1 2.500000 21.812000 5.965183 19.318750 14999 2 0.000000 1 2.500000 24.108000 1.988394 19.318750 15000 2 0.000000 -1 2.500000 24.108000 1.988394 19.318750 15001 2 0.000000 1 2.500000 26.404000 3.313991 22.831250 @@ -15019,7 +15019,7 @@ Atoms 15003 2 0.000000 1 2.500000 28.700000 7.290779 22.831250 15004 2 0.000000 -1 2.500000 28.700000 7.290779 22.831250 15005 2 0.000000 1 2.500000 21.812000 5.965183 26.343750 -15006 2 0.000000 -1.000000 2.500000 21.812000 5.965183 26.343750 +15006 2 0.000000 -1 2.500000 21.812000 5.965183 26.343750 15007 2 0.000000 1 2.500000 24.108000 1.988394 26.343750 15008 2 0.000000 -1 2.500000 24.108000 1.988394 26.343750 15009 2 0.000000 1 2.500000 26.404000 3.313991 29.856250 @@ -15027,7 +15027,7 @@ Atoms 15011 2 0.000000 1 2.500000 28.700000 7.290779 29.856250 15012 2 0.000000 -1 2.500000 28.700000 7.290779 29.856250 15013 2 0.000000 1 2.500000 21.812000 5.965183 33.368750 -15014 2 0.000000 -1.000000 2.500000 21.812000 5.965183 33.368750 +15014 2 0.000000 -1 2.500000 21.812000 5.965183 33.368750 15015 2 0.000000 1 2.500000 24.108000 1.988394 33.368750 15016 2 0.000000 -1 2.500000 24.108000 1.988394 33.368750 15017 2 0.000000 1 2.500000 26.404000 3.313991 36.881250 @@ -15035,7 +15035,7 @@ Atoms 15019 2 0.000000 1 2.500000 28.700000 7.290779 36.881250 15020 2 0.000000 -1 2.500000 28.700000 7.290779 36.881250 15021 2 0.000000 1 2.500000 21.812000 5.965183 40.393750 -15022 2 0.000000 -1.000000 2.500000 21.812000 5.965183 40.393750 +15022 2 0.000000 -1 2.500000 21.812000 5.965183 40.393750 15023 2 0.000000 1 2.500000 24.108000 1.988394 40.393750 15024 2 0.000000 -1 2.500000 24.108000 1.988394 40.393750 15025 2 0.000000 1 2.500000 26.404000 3.313991 43.906250 @@ -15043,7 +15043,7 @@ Atoms 15027 2 0.000000 1 2.500000 28.700000 7.290779 43.906250 15028 2 0.000000 -1 2.500000 28.700000 7.290779 43.906250 15029 2 0.000000 1 2.500000 21.812000 5.965183 47.418750 -15030 2 0.000000 -1.000000 2.500000 21.812000 5.965183 47.418750 +15030 2 0.000000 -1 2.500000 21.812000 5.965183 47.418750 15031 2 0.000000 1 2.500000 24.108000 1.988394 47.418750 15032 2 0.000000 -1 2.500000 24.108000 1.988394 47.418750 15033 2 0.000000 1 2.500000 26.404000 3.313991 50.931250 @@ -15051,7 +15051,7 @@ Atoms 15035 2 0.000000 1 2.500000 28.700000 7.290779 50.931250 15036 2 0.000000 -1 2.500000 28.700000 7.290779 50.931250 15037 2 0.000000 1 2.500000 21.812000 5.965183 54.443750 -15038 2 0.000000 -1.000000 2.500000 21.812000 5.965183 54.443750 +15038 2 0.000000 -1 2.500000 21.812000 5.965183 54.443750 15039 2 0.000000 1 2.500000 24.108000 1.988394 54.443750 15040 2 0.000000 -1 2.500000 24.108000 1.988394 54.443750 15041 2 0.000000 1 2.500000 26.404000 3.313991 57.956250 @@ -15059,7 +15059,7 @@ Atoms 15043 2 0.000000 1 2.500000 28.700000 7.290779 57.956250 15044 2 0.000000 -1 2.500000 28.700000 7.290779 57.956250 15045 2 0.000000 1 2.500000 21.812000 5.965183 61.468750 -15046 2 0.000000 -1.000000 2.500000 21.812000 5.965183 61.468750 +15046 2 0.000000 -1 2.500000 21.812000 5.965183 61.468750 15047 2 0.000000 1 2.500000 24.108000 1.988394 61.468750 15048 2 0.000000 -1 2.500000 24.108000 1.988394 61.468750 15049 2 0.000000 1 2.500000 26.404000 11.267568 1.756250 @@ -15067,7 +15067,7 @@ Atoms 15051 2 0.000000 1 2.500000 28.700000 15.244357 1.756250 15052 2 0.000000 -1 2.500000 28.700000 15.244357 1.756250 15053 2 0.000000 1 2.500000 21.812000 13.918760 5.268750 -15054 2 0.000000 -1.000000 2.500000 21.812000 13.918760 5.268750 +15054 2 0.000000 -1 2.500000 21.812000 13.918760 5.268750 15055 2 0.000000 1 2.500000 24.108000 9.941972 5.268750 15056 2 0.000000 -1 2.500000 24.108000 9.941972 5.268750 15057 2 0.000000 1 2.500000 26.404000 11.267568 8.781250 @@ -15075,7 +15075,7 @@ Atoms 15059 2 0.000000 1 2.500000 28.700000 15.244357 8.781250 15060 2 0.000000 -1 2.500000 28.700000 15.244357 8.781250 15061 2 0.000000 1 2.500000 21.812000 13.918760 12.293750 -15062 2 0.000000 -1.000000 2.500000 21.812000 13.918760 12.293750 +15062 2 0.000000 -1 2.500000 21.812000 13.918760 12.293750 15063 2 0.000000 1 2.500000 24.108000 9.941972 12.293750 15064 2 0.000000 -1 2.500000 24.108000 9.941972 12.293750 15065 2 0.000000 1 2.500000 26.404000 11.267568 15.806250 @@ -15083,7 +15083,7 @@ Atoms 15067 2 0.000000 1 2.500000 28.700000 15.244357 15.806250 15068 2 0.000000 -1 2.500000 28.700000 15.244357 15.806250 15069 2 0.000000 1 2.500000 21.812000 13.918760 19.318750 -15070 2 0.000000 -1.000000 2.500000 21.812000 13.918760 19.318750 +15070 2 0.000000 -1 2.500000 21.812000 13.918760 19.318750 15071 2 0.000000 1 2.500000 24.108000 9.941972 19.318750 15072 2 0.000000 -1 2.500000 24.108000 9.941972 19.318750 15073 2 0.000000 1 2.500000 26.404000 11.267568 22.831250 @@ -15091,7 +15091,7 @@ Atoms 15075 2 0.000000 1 2.500000 28.700000 15.244357 22.831250 15076 2 0.000000 -1 2.500000 28.700000 15.244357 22.831250 15077 2 0.000000 1 2.500000 21.812000 13.918760 26.343750 -15078 2 0.000000 -1.000000 2.500000 21.812000 13.918760 26.343750 +15078 2 0.000000 -1 2.500000 21.812000 13.918760 26.343750 15079 2 0.000000 1 2.500000 24.108000 9.941972 26.343750 15080 2 0.000000 -1 2.500000 24.108000 9.941972 26.343750 15081 2 0.000000 1 2.500000 26.404000 11.267568 29.856250 @@ -15099,7 +15099,7 @@ Atoms 15083 2 0.000000 1 2.500000 28.700000 15.244357 29.856250 15084 2 0.000000 -1 2.500000 28.700000 15.244357 29.856250 15085 2 0.000000 1 2.500000 21.812000 13.918760 33.368750 -15086 2 0.000000 -1.000000 2.500000 21.812000 13.918760 33.368750 +15086 2 0.000000 -1 2.500000 21.812000 13.918760 33.368750 15087 2 0.000000 1 2.500000 24.108000 9.941972 33.368750 15088 2 0.000000 -1 2.500000 24.108000 9.941972 33.368750 15089 2 0.000000 1 2.500000 26.404000 11.267568 36.881250 @@ -15107,7 +15107,7 @@ Atoms 15091 2 0.000000 1 2.500000 28.700000 15.244357 36.881250 15092 2 0.000000 -1 2.500000 28.700000 15.244357 36.881250 15093 2 0.000000 1 2.500000 21.812000 13.918760 40.393750 -15094 2 0.000000 -1.000000 2.500000 21.812000 13.918760 40.393750 +15094 2 0.000000 -1 2.500000 21.812000 13.918760 40.393750 15095 2 0.000000 1 2.500000 24.108000 9.941972 40.393750 15096 2 0.000000 -1 2.500000 24.108000 9.941972 40.393750 15097 2 0.000000 1 2.500000 26.404000 11.267568 43.906250 @@ -15115,7 +15115,7 @@ Atoms 15099 2 0.000000 1 2.500000 28.700000 15.244357 43.906250 15100 2 0.000000 -1 2.500000 28.700000 15.244357 43.906250 15101 2 0.000000 1 2.500000 21.812000 13.918760 47.418750 -15102 2 0.000000 -1.000000 2.500000 21.812000 13.918760 47.418750 +15102 2 0.000000 -1 2.500000 21.812000 13.918760 47.418750 15103 2 0.000000 1 2.500000 24.108000 9.941972 47.418750 15104 2 0.000000 -1 2.500000 24.108000 9.941972 47.418750 15105 2 0.000000 1 2.500000 26.404000 11.267568 50.931250 @@ -15123,7 +15123,7 @@ Atoms 15107 2 0.000000 1 2.500000 28.700000 15.244357 50.931250 15108 2 0.000000 -1 2.500000 28.700000 15.244357 50.931250 15109 2 0.000000 1 2.500000 21.812000 13.918760 54.443750 -15110 2 0.000000 -1.000000 2.500000 21.812000 13.918760 54.443750 +15110 2 0.000000 -1 2.500000 21.812000 13.918760 54.443750 15111 2 0.000000 1 2.500000 24.108000 9.941972 54.443750 15112 2 0.000000 -1 2.500000 24.108000 9.941972 54.443750 15113 2 0.000000 1 2.500000 26.404000 11.267568 57.956250 @@ -15131,7 +15131,7 @@ Atoms 15115 2 0.000000 1 2.500000 28.700000 15.244357 57.956250 15116 2 0.000000 -1 2.500000 28.700000 15.244357 57.956250 15117 2 0.000000 1 2.500000 21.812000 13.918760 61.468750 -15118 2 0.000000 -1.000000 2.500000 21.812000 13.918760 61.468750 +15118 2 0.000000 -1 2.500000 21.812000 13.918760 61.468750 15119 2 0.000000 1 2.500000 24.108000 9.941972 61.468750 15120 2 0.000000 -1 2.500000 24.108000 9.941972 61.468750 15121 2 0.000000 1 2.500000 26.404000 19.221145 1.756250 @@ -15139,7 +15139,7 @@ Atoms 15123 2 0.000000 1 2.500000 28.700000 23.197934 1.756250 15124 2 0.000000 -1 2.500000 28.700000 23.197934 1.756250 15125 2 0.000000 1 2.500000 21.812000 21.872338 5.268750 -15126 2 0.000000 -1.000000 2.500000 21.812000 21.872338 5.268750 +15126 2 0.000000 -1 2.500000 21.812000 21.872338 5.268750 15127 2 0.000000 1 2.500000 24.108000 17.895549 5.268750 15128 2 0.000000 -1 2.500000 24.108000 17.895549 5.268750 15129 2 0.000000 1 2.500000 26.404000 19.221145 8.781250 @@ -15147,7 +15147,7 @@ Atoms 15131 2 0.000000 1 2.500000 28.700000 23.197934 8.781250 15132 2 0.000000 -1 2.500000 28.700000 23.197934 8.781250 15133 2 0.000000 1 2.500000 21.812000 21.872338 12.293750 -15134 2 0.000000 -1.000000 2.500000 21.812000 21.872338 12.293750 +15134 2 0.000000 -1 2.500000 21.812000 21.872338 12.293750 15135 2 0.000000 1 2.500000 24.108000 17.895549 12.293750 15136 2 0.000000 -1 2.500000 24.108000 17.895549 12.293750 15137 2 0.000000 1 2.500000 26.404000 19.221145 15.806250 @@ -15155,7 +15155,7 @@ Atoms 15139 2 0.000000 1 2.500000 28.700000 23.197934 15.806250 15140 2 0.000000 -1 2.500000 28.700000 23.197934 15.806250 15141 2 0.000000 1 2.500000 21.812000 21.872338 19.318750 -15142 2 0.000000 -1.000000 2.500000 21.812000 21.872338 19.318750 +15142 2 0.000000 -1 2.500000 21.812000 21.872338 19.318750 15143 2 0.000000 1 2.500000 24.108000 17.895549 19.318750 15144 2 0.000000 -1 2.500000 24.108000 17.895549 19.318750 15145 2 0.000000 1 2.500000 26.404000 19.221145 22.831250 @@ -15163,7 +15163,7 @@ Atoms 15147 2 0.000000 1 2.500000 28.700000 23.197934 22.831250 15148 2 0.000000 -1 2.500000 28.700000 23.197934 22.831250 15149 2 0.000000 1 2.500000 21.812000 21.872338 26.343750 -15150 2 0.000000 -1.000000 2.500000 21.812000 21.872338 26.343750 +15150 2 0.000000 -1 2.500000 21.812000 21.872338 26.343750 15151 2 0.000000 1 2.500000 24.108000 17.895549 26.343750 15152 2 0.000000 -1 2.500000 24.108000 17.895549 26.343750 15153 2 0.000000 1 2.500000 26.404000 19.221145 29.856250 @@ -15171,7 +15171,7 @@ Atoms 15155 2 0.000000 1 2.500000 28.700000 23.197934 29.856250 15156 2 0.000000 -1 2.500000 28.700000 23.197934 29.856250 15157 2 0.000000 1 2.500000 21.812000 21.872338 33.368750 -15158 2 0.000000 -1.000000 2.500000 21.812000 21.872338 33.368750 +15158 2 0.000000 -1 2.500000 21.812000 21.872338 33.368750 15159 2 0.000000 1 2.500000 24.108000 17.895549 33.368750 15160 2 0.000000 -1 2.500000 24.108000 17.895549 33.368750 15161 2 0.000000 1 2.500000 26.404000 19.221145 36.881250 @@ -15179,7 +15179,7 @@ Atoms 15163 2 0.000000 1 2.500000 28.700000 23.197934 36.881250 15164 2 0.000000 -1 2.500000 28.700000 23.197934 36.881250 15165 2 0.000000 1 2.500000 21.812000 21.872338 40.393750 -15166 2 0.000000 -1.000000 2.500000 21.812000 21.872338 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21.812000 21.872338 54.443750 +15182 2 0.000000 -1 2.500000 21.812000 21.872338 54.443750 15183 2 0.000000 1 2.500000 24.108000 17.895549 54.443750 15184 2 0.000000 -1 2.500000 24.108000 17.895549 54.443750 15185 2 0.000000 1 2.500000 26.404000 19.221145 57.956250 @@ -15203,7 +15203,7 @@ Atoms 15187 2 0.000000 1 2.500000 28.700000 23.197934 57.956250 15188 2 0.000000 -1 2.500000 28.700000 23.197934 57.956250 15189 2 0.000000 1 2.500000 21.812000 21.872338 61.468750 -15190 2 0.000000 -1.000000 2.500000 21.812000 21.872338 61.468750 +15190 2 0.000000 -1 2.500000 21.812000 21.872338 61.468750 15191 2 0.000000 1 2.500000 24.108000 17.895549 61.468750 15192 2 0.000000 -1 2.500000 24.108000 17.895549 61.468750 15193 2 0.000000 1 2.500000 26.404000 27.174722 1.756250 @@ -15211,7 +15211,7 @@ Atoms 15195 2 0.000000 1 2.500000 28.700000 31.151511 1.756250 15196 2 0.000000 -1 2.500000 28.700000 31.151511 1.756250 15197 2 0.000000 1 2.500000 21.812000 29.825915 5.268750 -15198 2 0.000000 -1.000000 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29.825915 47.418750 -15246 2 0.000000 -1.000000 2.500000 21.812000 29.825915 47.418750 +15246 2 0.000000 -1 2.500000 21.812000 29.825915 47.418750 15247 2 0.000000 1 2.500000 24.108000 25.849126 47.418750 15248 2 0.000000 -1 2.500000 24.108000 25.849126 47.418750 15249 2 0.000000 1 2.500000 26.404000 27.174722 50.931250 @@ -15267,7 +15267,7 @@ Atoms 15251 2 0.000000 1 2.500000 28.700000 31.151511 50.931250 15252 2 0.000000 -1 2.500000 28.700000 31.151511 50.931250 15253 2 0.000000 1 2.500000 21.812000 29.825915 54.443750 -15254 2 0.000000 -1.000000 2.500000 21.812000 29.825915 54.443750 +15254 2 0.000000 -1 2.500000 21.812000 29.825915 54.443750 15255 2 0.000000 1 2.500000 24.108000 25.849126 54.443750 15256 2 0.000000 -1 2.500000 24.108000 25.849126 54.443750 15257 2 0.000000 1 2.500000 26.404000 27.174722 57.956250 @@ -15275,7 +15275,7 @@ Atoms 15259 2 0.000000 1 2.500000 28.700000 31.151511 57.956250 15260 2 0.000000 -1 2.500000 28.700000 31.151511 57.956250 15261 2 0.000000 1 2.500000 21.812000 29.825915 61.468750 -15262 2 0.000000 -1.000000 2.500000 21.812000 29.825915 61.468750 +15262 2 0.000000 -1 2.500000 21.812000 29.825915 61.468750 15263 2 0.000000 1 2.500000 24.108000 25.849126 61.468750 15264 2 0.000000 -1 2.500000 24.108000 25.849126 61.468750 15265 2 0.000000 1 2.500000 26.404000 35.128300 1.756250 @@ -15283,7 +15283,7 @@ Atoms 15267 2 0.000000 1 2.500000 28.700000 39.105088 1.756250 15268 2 0.000000 -1 2.500000 28.700000 39.105088 1.756250 15269 2 0.000000 1 2.500000 21.812000 37.779492 5.268750 -15270 2 0.000000 -1.000000 2.500000 21.812000 37.779492 5.268750 +15270 2 0.000000 -1 2.500000 21.812000 37.779492 5.268750 15271 2 0.000000 1 2.500000 24.108000 33.802704 5.268750 15272 2 0.000000 -1 2.500000 24.108000 33.802704 5.268750 15273 2 0.000000 1 2.500000 26.404000 35.128300 8.781250 @@ -15291,7 +15291,7 @@ Atoms 15275 2 0.000000 1 2.500000 28.700000 39.105088 8.781250 15276 2 0.000000 -1 2.500000 28.700000 39.105088 8.781250 15277 2 0.000000 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15293 2 0.000000 1 2.500000 21.812000 37.779492 26.343750 -15294 2 0.000000 -1.000000 2.500000 21.812000 37.779492 26.343750 +15294 2 0.000000 -1 2.500000 21.812000 37.779492 26.343750 15295 2 0.000000 1 2.500000 24.108000 33.802704 26.343750 15296 2 0.000000 -1 2.500000 24.108000 33.802704 26.343750 15297 2 0.000000 1 2.500000 26.404000 35.128300 29.856250 @@ -15315,7 +15315,7 @@ Atoms 15299 2 0.000000 1 2.500000 28.700000 39.105088 29.856250 15300 2 0.000000 -1 2.500000 28.700000 39.105088 29.856250 15301 2 0.000000 1 2.500000 21.812000 37.779492 33.368750 -15302 2 0.000000 -1.000000 2.500000 21.812000 37.779492 33.368750 +15302 2 0.000000 -1 2.500000 21.812000 37.779492 33.368750 15303 2 0.000000 1 2.500000 24.108000 33.802704 33.368750 15304 2 0.000000 -1 2.500000 24.108000 33.802704 33.368750 15305 2 0.000000 1 2.500000 26.404000 35.128300 36.881250 @@ -15323,7 +15323,7 @@ Atoms 15307 2 0.000000 1 2.500000 28.700000 39.105088 36.881250 15308 2 0.000000 -1 2.500000 28.700000 39.105088 36.881250 15309 2 0.000000 1 2.500000 21.812000 37.779492 40.393750 -15310 2 0.000000 -1.000000 2.500000 21.812000 37.779492 40.393750 +15310 2 0.000000 -1 2.500000 21.812000 37.779492 40.393750 15311 2 0.000000 1 2.500000 24.108000 33.802704 40.393750 15312 2 0.000000 -1 2.500000 24.108000 33.802704 40.393750 15313 2 0.000000 1 2.500000 26.404000 35.128300 43.906250 @@ -15331,7 +15331,7 @@ Atoms 15315 2 0.000000 1 2.500000 28.700000 39.105088 43.906250 15316 2 0.000000 -1 2.500000 28.700000 39.105088 43.906250 15317 2 0.000000 1 2.500000 21.812000 37.779492 47.418750 -15318 2 0.000000 -1.000000 2.500000 21.812000 37.779492 47.418750 +15318 2 0.000000 -1 2.500000 21.812000 37.779492 47.418750 15319 2 0.000000 1 2.500000 24.108000 33.802704 47.418750 15320 2 0.000000 -1 2.500000 24.108000 33.802704 47.418750 15321 2 0.000000 1 2.500000 26.404000 35.128300 50.931250 @@ -15339,7 +15339,7 @@ Atoms 15323 2 0.000000 1 2.500000 28.700000 39.105088 50.931250 15324 2 0.000000 -1 2.500000 28.700000 39.105088 50.931250 15325 2 0.000000 1 2.500000 21.812000 37.779492 54.443750 -15326 2 0.000000 -1.000000 2.500000 21.812000 37.779492 54.443750 +15326 2 0.000000 -1 2.500000 21.812000 37.779492 54.443750 15327 2 0.000000 1 2.500000 24.108000 33.802704 54.443750 15328 2 0.000000 -1 2.500000 24.108000 33.802704 54.443750 15329 2 0.000000 1 2.500000 26.404000 35.128300 57.956250 @@ -15347,7 +15347,7 @@ Atoms 15331 2 0.000000 1 2.500000 28.700000 39.105088 57.956250 15332 2 0.000000 -1 2.500000 28.700000 39.105088 57.956250 15333 2 0.000000 1 2.500000 21.812000 37.779492 61.468750 -15334 2 0.000000 -1.000000 2.500000 21.812000 37.779492 61.468750 +15334 2 0.000000 -1 2.500000 21.812000 37.779492 61.468750 15335 2 0.000000 1 2.500000 24.108000 33.802704 61.468750 15336 2 0.000000 -1 2.500000 24.108000 33.802704 61.468750 15337 2 0.000000 1 2.500000 26.404000 43.081877 1.756250 @@ -15355,7 +15355,7 @@ Atoms 15339 2 0.000000 1 2.500000 28.700000 47.058666 1.756250 15340 2 0.000000 -1 2.500000 28.700000 47.058666 1.756250 15341 2 0.000000 1 2.500000 21.812000 45.733070 5.268750 -15342 2 0.000000 -1.000000 2.500000 21.812000 45.733070 5.268750 +15342 2 0.000000 -1 2.500000 21.812000 45.733070 5.268750 15343 2 0.000000 1 2.500000 24.108000 41.756281 5.268750 15344 2 0.000000 -1 2.500000 24.108000 41.756281 5.268750 15345 2 0.000000 1 2.500000 26.404000 43.081877 8.781250 @@ -15363,7 +15363,7 @@ Atoms 15347 2 0.000000 1 2.500000 28.700000 47.058666 8.781250 15348 2 0.000000 -1 2.500000 28.700000 47.058666 8.781250 15349 2 0.000000 1 2.500000 21.812000 45.733070 12.293750 -15350 2 0.000000 -1.000000 2.500000 21.812000 45.733070 12.293750 +15350 2 0.000000 -1 2.500000 21.812000 45.733070 12.293750 15351 2 0.000000 1 2.500000 24.108000 41.756281 12.293750 15352 2 0.000000 -1 2.500000 24.108000 41.756281 12.293750 15353 2 0.000000 1 2.500000 26.404000 43.081877 15.806250 @@ -15371,7 +15371,7 @@ Atoms 15355 2 0.000000 1 2.500000 28.700000 47.058666 15.806250 15356 2 0.000000 -1 2.500000 28.700000 47.058666 15.806250 15357 2 0.000000 1 2.500000 21.812000 45.733070 19.318750 -15358 2 0.000000 -1.000000 2.500000 21.812000 45.733070 19.318750 +15358 2 0.000000 -1 2.500000 21.812000 45.733070 19.318750 15359 2 0.000000 1 2.500000 24.108000 41.756281 19.318750 15360 2 0.000000 -1 2.500000 24.108000 41.756281 19.318750 15361 2 0.000000 1 2.500000 26.404000 43.081877 22.831250 @@ -15379,7 +15379,7 @@ Atoms 15363 2 0.000000 1 2.500000 28.700000 47.058666 22.831250 15364 2 0.000000 -1 2.500000 28.700000 47.058666 22.831250 15365 2 0.000000 1 2.500000 21.812000 45.733070 26.343750 -15366 2 0.000000 -1.000000 2.500000 21.812000 45.733070 26.343750 +15366 2 0.000000 -1 2.500000 21.812000 45.733070 26.343750 15367 2 0.000000 1 2.500000 24.108000 41.756281 26.343750 15368 2 0.000000 -1 2.500000 24.108000 41.756281 26.343750 15369 2 0.000000 1 2.500000 26.404000 43.081877 29.856250 @@ -15387,7 +15387,7 @@ Atoms 15371 2 0.000000 1 2.500000 28.700000 47.058666 29.856250 15372 2 0.000000 -1 2.500000 28.700000 47.058666 29.856250 15373 2 0.000000 1 2.500000 21.812000 45.733070 33.368750 -15374 2 0.000000 -1.000000 2.500000 21.812000 45.733070 33.368750 +15374 2 0.000000 -1 2.500000 21.812000 45.733070 33.368750 15375 2 0.000000 1 2.500000 24.108000 41.756281 33.368750 15376 2 0.000000 -1 2.500000 24.108000 41.756281 33.368750 15377 2 0.000000 1 2.500000 26.404000 43.081877 36.881250 @@ -15395,7 +15395,7 @@ Atoms 15379 2 0.000000 1 2.500000 28.700000 47.058666 36.881250 15380 2 0.000000 -1 2.500000 28.700000 47.058666 36.881250 15381 2 0.000000 1 2.500000 21.812000 45.733070 40.393750 -15382 2 0.000000 -1.000000 2.500000 21.812000 45.733070 40.393750 +15382 2 0.000000 -1 2.500000 21.812000 45.733070 40.393750 15383 2 0.000000 1 2.500000 24.108000 41.756281 40.393750 15384 2 0.000000 -1 2.500000 24.108000 41.756281 40.393750 15385 2 0.000000 1 2.500000 26.404000 43.081877 43.906250 @@ -15403,7 +15403,7 @@ Atoms 15387 2 0.000000 1 2.500000 28.700000 47.058666 43.906250 15388 2 0.000000 -1 2.500000 28.700000 47.058666 43.906250 15389 2 0.000000 1 2.500000 21.812000 45.733070 47.418750 -15390 2 0.000000 -1.000000 2.500000 21.812000 45.733070 47.418750 +15390 2 0.000000 -1 2.500000 21.812000 45.733070 47.418750 15391 2 0.000000 1 2.500000 24.108000 41.756281 47.418750 15392 2 0.000000 -1 2.500000 24.108000 41.756281 47.418750 15393 2 0.000000 1 2.500000 26.404000 43.081877 50.931250 @@ -15411,7 +15411,7 @@ Atoms 15395 2 0.000000 1 2.500000 28.700000 47.058666 50.931250 15396 2 0.000000 -1 2.500000 28.700000 47.058666 50.931250 15397 2 0.000000 1 2.500000 21.812000 45.733070 54.443750 -15398 2 0.000000 -1.000000 2.500000 21.812000 45.733070 54.443750 +15398 2 0.000000 -1 2.500000 21.812000 45.733070 54.443750 15399 2 0.000000 1 2.500000 24.108000 41.756281 54.443750 15400 2 0.000000 -1 2.500000 24.108000 41.756281 54.443750 15401 2 0.000000 1 2.500000 26.404000 43.081877 57.956250 @@ -15419,7 +15419,7 @@ Atoms 15403 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26.404000 51.035454 50.931250 @@ -15483,7 +15483,7 @@ Atoms 15467 2 0.000000 1 2.500000 28.700000 55.012243 50.931250 15468 2 0.000000 -1 2.500000 28.700000 55.012243 50.931250 15469 2 0.000000 1 2.500000 21.812000 53.686647 54.443750 -15470 2 0.000000 -1.000000 2.500000 21.812000 53.686647 54.443750 +15470 2 0.000000 -1 2.500000 21.812000 53.686647 54.443750 15471 2 0.000000 1 2.500000 24.108000 49.709858 54.443750 15472 2 0.000000 -1 2.500000 24.108000 49.709858 54.443750 15473 2 0.000000 1 2.500000 26.404000 51.035454 57.956250 @@ -15491,7 +15491,7 @@ Atoms 15475 2 0.000000 1 2.500000 28.700000 55.012243 57.956250 15476 2 0.000000 -1 2.500000 28.700000 55.012243 57.956250 15477 2 0.000000 1 2.500000 21.812000 53.686647 61.468750 -15478 2 0.000000 -1.000000 2.500000 21.812000 53.686647 61.468750 +15478 2 0.000000 -1 2.500000 21.812000 53.686647 61.468750 15479 2 0.000000 1 2.500000 24.108000 49.709858 61.468750 15480 2 0.000000 -1 2.500000 24.108000 49.709858 61.468750 15481 2 0.000000 1 2.500000 26.404000 58.989032 1.756250 @@ -15499,7 +15499,7 @@ Atoms 15483 2 0.000000 1 2.500000 28.700000 62.965820 1.756250 15484 2 0.000000 -1 2.500000 28.700000 62.965820 1.756250 15485 2 0.000000 1 2.500000 21.812000 61.640224 5.268750 -15486 2 0.000000 -1.000000 2.500000 21.812000 61.640224 5.268750 +15486 2 0.000000 -1 2.500000 21.812000 61.640224 5.268750 15487 2 0.000000 1 2.500000 24.108000 57.663435 5.268750 15488 2 0.000000 -1 2.500000 24.108000 57.663435 5.268750 15489 2 0.000000 1 2.500000 26.404000 58.989032 8.781250 @@ -15507,7 +15507,7 @@ Atoms 15491 2 0.000000 1 2.500000 28.700000 62.965820 8.781250 15492 2 0.000000 -1 2.500000 28.700000 62.965820 8.781250 15493 2 0.000000 1 2.500000 21.812000 61.640224 12.293750 -15494 2 0.000000 -1.000000 2.500000 21.812000 61.640224 12.293750 +15494 2 0.000000 -1 2.500000 21.812000 61.640224 12.293750 15495 2 0.000000 1 2.500000 24.108000 57.663435 12.293750 15496 2 0.000000 -1 2.500000 24.108000 57.663435 12.293750 15497 2 0.000000 1 2.500000 26.404000 58.989032 15.806250 @@ -15515,7 +15515,7 @@ Atoms 15499 2 0.000000 1 2.500000 28.700000 62.965820 15.806250 15500 2 0.000000 -1 2.500000 28.700000 62.965820 15.806250 15501 2 0.000000 1 2.500000 21.812000 61.640224 19.318750 -15502 2 0.000000 -1.000000 2.500000 21.812000 61.640224 19.318750 +15502 2 0.000000 -1 2.500000 21.812000 61.640224 19.318750 15503 2 0.000000 1 2.500000 24.108000 57.663435 19.318750 15504 2 0.000000 -1 2.500000 24.108000 57.663435 19.318750 15505 2 0.000000 1 2.500000 26.404000 58.989032 22.831250 @@ -15523,7 +15523,7 @@ Atoms 15507 2 0.000000 1 2.500000 28.700000 62.965820 22.831250 15508 2 0.000000 -1 2.500000 28.700000 62.965820 22.831250 15509 2 0.000000 1 2.500000 21.812000 61.640224 26.343750 -15510 2 0.000000 -1.000000 2.500000 21.812000 61.640224 26.343750 +15510 2 0.000000 -1 2.500000 21.812000 61.640224 26.343750 15511 2 0.000000 1 2.500000 24.108000 57.663435 26.343750 15512 2 0.000000 -1 2.500000 24.108000 57.663435 26.343750 15513 2 0.000000 1 2.500000 26.404000 58.989032 29.856250 @@ -15531,7 +15531,7 @@ Atoms 15515 2 0.000000 1 2.500000 28.700000 62.965820 29.856250 15516 2 0.000000 -1 2.500000 28.700000 62.965820 29.856250 15517 2 0.000000 1 2.500000 21.812000 61.640224 33.368750 -15518 2 0.000000 -1.000000 2.500000 21.812000 61.640224 33.368750 +15518 2 0.000000 -1 2.500000 21.812000 61.640224 33.368750 15519 2 0.000000 1 2.500000 24.108000 57.663435 33.368750 15520 2 0.000000 -1 2.500000 24.108000 57.663435 33.368750 15521 2 0.000000 1 2.500000 26.404000 58.989032 36.881250 @@ -15539,7 +15539,7 @@ Atoms 15523 2 0.000000 1 2.500000 28.700000 62.965820 36.881250 15524 2 0.000000 -1 2.500000 28.700000 62.965820 36.881250 15525 2 0.000000 1 2.500000 21.812000 61.640224 40.393750 -15526 2 0.000000 -1.000000 2.500000 21.812000 61.640224 40.393750 +15526 2 0.000000 -1 2.500000 21.812000 61.640224 40.393750 15527 2 0.000000 1 2.500000 24.108000 57.663435 40.393750 15528 2 0.000000 -1 2.500000 24.108000 57.663435 40.393750 15529 2 0.000000 1 2.500000 26.404000 58.989032 43.906250 @@ -15547,7 +15547,7 @@ Atoms 15531 2 0.000000 1 2.500000 28.700000 62.965820 43.906250 15532 2 0.000000 -1 2.500000 28.700000 62.965820 43.906250 15533 2 0.000000 1 2.500000 21.812000 61.640224 47.418750 -15534 2 0.000000 -1.000000 2.500000 21.812000 61.640224 47.418750 +15534 2 0.000000 -1 2.500000 21.812000 61.640224 47.418750 15535 2 0.000000 1 2.500000 24.108000 57.663435 47.418750 15536 2 0.000000 -1 2.500000 24.108000 57.663435 47.418750 15537 2 0.000000 1 2.500000 26.404000 58.989032 50.931250 @@ -15555,7 +15555,7 @@ Atoms 15539 2 0.000000 1 2.500000 28.700000 62.965820 50.931250 15540 2 0.000000 -1 2.500000 28.700000 62.965820 50.931250 15541 2 0.000000 1 2.500000 21.812000 61.640224 54.443750 -15542 2 0.000000 -1.000000 2.500000 21.812000 61.640224 54.443750 +15542 2 0.000000 -1 2.500000 21.812000 61.640224 54.443750 15543 2 0.000000 1 2.500000 24.108000 57.663435 54.443750 15544 2 0.000000 -1 2.500000 24.108000 57.663435 54.443750 15545 2 0.000000 1 2.500000 26.404000 58.989032 57.956250 @@ -15563,7 +15563,7 @@ Atoms 15547 2 0.000000 1 2.500000 28.700000 62.965820 57.956250 15548 2 0.000000 -1 2.500000 28.700000 62.965820 57.956250 15549 2 0.000000 1 2.500000 21.812000 61.640224 61.468750 -15550 2 0.000000 -1.000000 2.500000 21.812000 61.640224 61.468750 +15550 2 0.000000 -1 2.500000 21.812000 61.640224 61.468750 15551 2 0.000000 1 2.500000 24.108000 57.663435 61.468750 15552 2 0.000000 -1 2.500000 24.108000 57.663435 61.468750 15553 2 0.000000 1 2.500000 30.996000 3.313991 1.756250 @@ -15571,7 +15571,7 @@ Atoms 15555 2 0.000000 1 2.500000 33.292000 7.290779 1.756250 15556 2 0.000000 -1 2.500000 33.292000 7.290779 1.756250 15557 2 0.000000 1 2.500000 26.404000 5.965183 5.268750 -15558 2 0.000000 -1.000000 2.500000 26.404000 5.965183 5.268750 +15558 2 0.000000 -1 2.500000 26.404000 5.965183 5.268750 15559 2 0.000000 1 2.500000 28.700000 1.988394 5.268750 15560 2 0.000000 -1 2.500000 28.700000 1.988394 5.268750 15561 2 0.000000 1 2.500000 30.996000 3.313991 8.781250 @@ -15579,7 +15579,7 @@ Atoms 15563 2 0.000000 1 2.500000 33.292000 7.290779 8.781250 15564 2 0.000000 -1 2.500000 33.292000 7.290779 8.781250 15565 2 0.000000 1 2.500000 26.404000 5.965183 12.293750 -15566 2 0.000000 -1.000000 2.500000 26.404000 5.965183 12.293750 +15566 2 0.000000 -1 2.500000 26.404000 5.965183 12.293750 15567 2 0.000000 1 2.500000 28.700000 1.988394 12.293750 15568 2 0.000000 -1 2.500000 28.700000 1.988394 12.293750 15569 2 0.000000 1 2.500000 30.996000 3.313991 15.806250 @@ -15587,7 +15587,7 @@ Atoms 15571 2 0.000000 1 2.500000 33.292000 7.290779 15.806250 15572 2 0.000000 -1 2.500000 33.292000 7.290779 15.806250 15573 2 0.000000 1 2.500000 26.404000 5.965183 19.318750 -15574 2 0.000000 -1.000000 2.500000 26.404000 5.965183 19.318750 +15574 2 0.000000 -1 2.500000 26.404000 5.965183 19.318750 15575 2 0.000000 1 2.500000 28.700000 1.988394 19.318750 15576 2 0.000000 -1 2.500000 28.700000 1.988394 19.318750 15577 2 0.000000 1 2.500000 30.996000 3.313991 22.831250 @@ -15595,7 +15595,7 @@ Atoms 15579 2 0.000000 1 2.500000 33.292000 7.290779 22.831250 15580 2 0.000000 -1 2.500000 33.292000 7.290779 22.831250 15581 2 0.000000 1 2.500000 26.404000 5.965183 26.343750 -15582 2 0.000000 -1.000000 2.500000 26.404000 5.965183 26.343750 +15582 2 0.000000 -1 2.500000 26.404000 5.965183 26.343750 15583 2 0.000000 1 2.500000 28.700000 1.988394 26.343750 15584 2 0.000000 -1 2.500000 28.700000 1.988394 26.343750 15585 2 0.000000 1 2.500000 30.996000 3.313991 29.856250 @@ -15603,7 +15603,7 @@ Atoms 15587 2 0.000000 1 2.500000 33.292000 7.290779 29.856250 15588 2 0.000000 -1 2.500000 33.292000 7.290779 29.856250 15589 2 0.000000 1 2.500000 26.404000 5.965183 33.368750 -15590 2 0.000000 -1.000000 2.500000 26.404000 5.965183 33.368750 +15590 2 0.000000 -1 2.500000 26.404000 5.965183 33.368750 15591 2 0.000000 1 2.500000 28.700000 1.988394 33.368750 15592 2 0.000000 -1 2.500000 28.700000 1.988394 33.368750 15593 2 0.000000 1 2.500000 30.996000 3.313991 36.881250 @@ -15611,7 +15611,7 @@ Atoms 15595 2 0.000000 1 2.500000 33.292000 7.290779 36.881250 15596 2 0.000000 -1 2.500000 33.292000 7.290779 36.881250 15597 2 0.000000 1 2.500000 26.404000 5.965183 40.393750 -15598 2 0.000000 -1.000000 2.500000 26.404000 5.965183 40.393750 +15598 2 0.000000 -1 2.500000 26.404000 5.965183 40.393750 15599 2 0.000000 1 2.500000 28.700000 1.988394 40.393750 15600 2 0.000000 -1 2.500000 28.700000 1.988394 40.393750 15601 2 0.000000 1 2.500000 30.996000 3.313991 43.906250 @@ -15619,7 +15619,7 @@ Atoms 15603 2 0.000000 1 2.500000 33.292000 7.290779 43.906250 15604 2 0.000000 -1 2.500000 33.292000 7.290779 43.906250 15605 2 0.000000 1 2.500000 26.404000 5.965183 47.418750 -15606 2 0.000000 -1.000000 2.500000 26.404000 5.965183 47.418750 +15606 2 0.000000 -1 2.500000 26.404000 5.965183 47.418750 15607 2 0.000000 1 2.500000 28.700000 1.988394 47.418750 15608 2 0.000000 -1 2.500000 28.700000 1.988394 47.418750 15609 2 0.000000 1 2.500000 30.996000 3.313991 50.931250 @@ -15627,7 +15627,7 @@ Atoms 15611 2 0.000000 1 2.500000 33.292000 7.290779 50.931250 15612 2 0.000000 -1 2.500000 33.292000 7.290779 50.931250 15613 2 0.000000 1 2.500000 26.404000 5.965183 54.443750 -15614 2 0.000000 -1.000000 2.500000 26.404000 5.965183 54.443750 +15614 2 0.000000 -1 2.500000 26.404000 5.965183 54.443750 15615 2 0.000000 1 2.500000 28.700000 1.988394 54.443750 15616 2 0.000000 -1 2.500000 28.700000 1.988394 54.443750 15617 2 0.000000 1 2.500000 30.996000 3.313991 57.956250 @@ -15635,7 +15635,7 @@ Atoms 15619 2 0.000000 1 2.500000 33.292000 7.290779 57.956250 15620 2 0.000000 -1 2.500000 33.292000 7.290779 57.956250 15621 2 0.000000 1 2.500000 26.404000 5.965183 61.468750 -15622 2 0.000000 -1.000000 2.500000 26.404000 5.965183 61.468750 +15622 2 0.000000 -1 2.500000 26.404000 5.965183 61.468750 15623 2 0.000000 1 2.500000 28.700000 1.988394 61.468750 15624 2 0.000000 -1 2.500000 28.700000 1.988394 61.468750 15625 2 0.000000 1 2.500000 30.996000 11.267568 1.756250 @@ -15643,7 +15643,7 @@ Atoms 15627 2 0.000000 1 2.500000 33.292000 15.244357 1.756250 15628 2 0.000000 -1 2.500000 33.292000 15.244357 1.756250 15629 2 0.000000 1 2.500000 26.404000 13.918760 5.268750 -15630 2 0.000000 -1.000000 2.500000 26.404000 13.918760 5.268750 +15630 2 0.000000 -1 2.500000 26.404000 13.918760 5.268750 15631 2 0.000000 1 2.500000 28.700000 9.941972 5.268750 15632 2 0.000000 -1 2.500000 28.700000 9.941972 5.268750 15633 2 0.000000 1 2.500000 30.996000 11.267568 8.781250 @@ -15651,7 +15651,7 @@ Atoms 15635 2 0.000000 1 2.500000 33.292000 15.244357 8.781250 15636 2 0.000000 -1 2.500000 33.292000 15.244357 8.781250 15637 2 0.000000 1 2.500000 26.404000 13.918760 12.293750 -15638 2 0.000000 -1.000000 2.500000 26.404000 13.918760 12.293750 +15638 2 0.000000 -1 2.500000 26.404000 13.918760 12.293750 15639 2 0.000000 1 2.500000 28.700000 9.941972 12.293750 15640 2 0.000000 -1 2.500000 28.700000 9.941972 12.293750 15641 2 0.000000 1 2.500000 30.996000 11.267568 15.806250 @@ -15659,7 +15659,7 @@ Atoms 15643 2 0.000000 1 2.500000 33.292000 15.244357 15.806250 15644 2 0.000000 -1 2.500000 33.292000 15.244357 15.806250 15645 2 0.000000 1 2.500000 26.404000 13.918760 19.318750 -15646 2 0.000000 -1.000000 2.500000 26.404000 13.918760 19.318750 +15646 2 0.000000 -1 2.500000 26.404000 13.918760 19.318750 15647 2 0.000000 1 2.500000 28.700000 9.941972 19.318750 15648 2 0.000000 -1 2.500000 28.700000 9.941972 19.318750 15649 2 0.000000 1 2.500000 30.996000 11.267568 22.831250 @@ -15667,7 +15667,7 @@ Atoms 15651 2 0.000000 1 2.500000 33.292000 15.244357 22.831250 15652 2 0.000000 -1 2.500000 33.292000 15.244357 22.831250 15653 2 0.000000 1 2.500000 26.404000 13.918760 26.343750 -15654 2 0.000000 -1.000000 2.500000 26.404000 13.918760 26.343750 +15654 2 0.000000 -1 2.500000 26.404000 13.918760 26.343750 15655 2 0.000000 1 2.500000 28.700000 9.941972 26.343750 15656 2 0.000000 -1 2.500000 28.700000 9.941972 26.343750 15657 2 0.000000 1 2.500000 30.996000 11.267568 29.856250 @@ -15675,7 +15675,7 @@ Atoms 15659 2 0.000000 1 2.500000 33.292000 15.244357 29.856250 15660 2 0.000000 -1 2.500000 33.292000 15.244357 29.856250 15661 2 0.000000 1 2.500000 26.404000 13.918760 33.368750 -15662 2 0.000000 -1.000000 2.500000 26.404000 13.918760 33.368750 +15662 2 0.000000 -1 2.500000 26.404000 13.918760 33.368750 15663 2 0.000000 1 2.500000 28.700000 9.941972 33.368750 15664 2 0.000000 -1 2.500000 28.700000 9.941972 33.368750 15665 2 0.000000 1 2.500000 30.996000 11.267568 36.881250 @@ -15683,7 +15683,7 @@ Atoms 15667 2 0.000000 1 2.500000 33.292000 15.244357 36.881250 15668 2 0.000000 -1 2.500000 33.292000 15.244357 36.881250 15669 2 0.000000 1 2.500000 26.404000 13.918760 40.393750 -15670 2 0.000000 -1.000000 2.500000 26.404000 13.918760 40.393750 +15670 2 0.000000 -1 2.500000 26.404000 13.918760 40.393750 15671 2 0.000000 1 2.500000 28.700000 9.941972 40.393750 15672 2 0.000000 -1 2.500000 28.700000 9.941972 40.393750 15673 2 0.000000 1 2.500000 30.996000 11.267568 43.906250 @@ -15691,7 +15691,7 @@ Atoms 15675 2 0.000000 1 2.500000 33.292000 15.244357 43.906250 15676 2 0.000000 -1 2.500000 33.292000 15.244357 43.906250 15677 2 0.000000 1 2.500000 26.404000 13.918760 47.418750 -15678 2 0.000000 -1.000000 2.500000 26.404000 13.918760 47.418750 +15678 2 0.000000 -1 2.500000 26.404000 13.918760 47.418750 15679 2 0.000000 1 2.500000 28.700000 9.941972 47.418750 15680 2 0.000000 -1 2.500000 28.700000 9.941972 47.418750 15681 2 0.000000 1 2.500000 30.996000 11.267568 50.931250 @@ -15699,7 +15699,7 @@ Atoms 15683 2 0.000000 1 2.500000 33.292000 15.244357 50.931250 15684 2 0.000000 -1 2.500000 33.292000 15.244357 50.931250 15685 2 0.000000 1 2.500000 26.404000 13.918760 54.443750 -15686 2 0.000000 -1.000000 2.500000 26.404000 13.918760 54.443750 +15686 2 0.000000 -1 2.500000 26.404000 13.918760 54.443750 15687 2 0.000000 1 2.500000 28.700000 9.941972 54.443750 15688 2 0.000000 -1 2.500000 28.700000 9.941972 54.443750 15689 2 0.000000 1 2.500000 30.996000 11.267568 57.956250 @@ -15707,7 +15707,7 @@ Atoms 15691 2 0.000000 1 2.500000 33.292000 15.244357 57.956250 15692 2 0.000000 -1 2.500000 33.292000 15.244357 57.956250 15693 2 0.000000 1 2.500000 26.404000 13.918760 61.468750 -15694 2 0.000000 -1.000000 2.500000 26.404000 13.918760 61.468750 +15694 2 0.000000 -1 2.500000 26.404000 13.918760 61.468750 15695 2 0.000000 1 2.500000 28.700000 9.941972 61.468750 15696 2 0.000000 -1 2.500000 28.700000 9.941972 61.468750 15697 2 0.000000 1 2.500000 30.996000 19.221145 1.756250 @@ -15715,7 +15715,7 @@ Atoms 15699 2 0.000000 1 2.500000 33.292000 23.197934 1.756250 15700 2 0.000000 -1 2.500000 33.292000 23.197934 1.756250 15701 2 0.000000 1 2.500000 26.404000 21.872338 5.268750 -15702 2 0.000000 -1.000000 2.500000 26.404000 21.872338 5.268750 +15702 2 0.000000 -1 2.500000 26.404000 21.872338 5.268750 15703 2 0.000000 1 2.500000 28.700000 17.895549 5.268750 15704 2 0.000000 -1 2.500000 28.700000 17.895549 5.268750 15705 2 0.000000 1 2.500000 30.996000 19.221145 8.781250 @@ -15723,7 +15723,7 @@ Atoms 15707 2 0.000000 1 2.500000 33.292000 23.197934 8.781250 15708 2 0.000000 -1 2.500000 33.292000 23.197934 8.781250 15709 2 0.000000 1 2.500000 26.404000 21.872338 12.293750 -15710 2 0.000000 -1.000000 2.500000 26.404000 21.872338 12.293750 +15710 2 0.000000 -1 2.500000 26.404000 21.872338 12.293750 15711 2 0.000000 1 2.500000 28.700000 17.895549 12.293750 15712 2 0.000000 -1 2.500000 28.700000 17.895549 12.293750 15713 2 0.000000 1 2.500000 30.996000 19.221145 15.806250 @@ -15731,7 +15731,7 @@ Atoms 15715 2 0.000000 1 2.500000 33.292000 23.197934 15.806250 15716 2 0.000000 -1 2.500000 33.292000 23.197934 15.806250 15717 2 0.000000 1 2.500000 26.404000 21.872338 19.318750 -15718 2 0.000000 -1.000000 2.500000 26.404000 21.872338 19.318750 +15718 2 0.000000 -1 2.500000 26.404000 21.872338 19.318750 15719 2 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33.368750 15735 2 0.000000 1 2.500000 28.700000 17.895549 33.368750 15736 2 0.000000 -1 2.500000 28.700000 17.895549 33.368750 15737 2 0.000000 1 2.500000 30.996000 19.221145 36.881250 @@ -15755,7 +15755,7 @@ Atoms 15739 2 0.000000 1 2.500000 33.292000 23.197934 36.881250 15740 2 0.000000 -1 2.500000 33.292000 23.197934 36.881250 15741 2 0.000000 1 2.500000 26.404000 21.872338 40.393750 -15742 2 0.000000 -1.000000 2.500000 26.404000 21.872338 40.393750 +15742 2 0.000000 -1 2.500000 26.404000 21.872338 40.393750 15743 2 0.000000 1 2.500000 28.700000 17.895549 40.393750 15744 2 0.000000 -1 2.500000 28.700000 17.895549 40.393750 15745 2 0.000000 1 2.500000 30.996000 19.221145 43.906250 @@ -15763,7 +15763,7 @@ Atoms 15747 2 0.000000 1 2.500000 33.292000 23.197934 43.906250 15748 2 0.000000 -1 2.500000 33.292000 23.197934 43.906250 15749 2 0.000000 1 2.500000 26.404000 21.872338 47.418750 -15750 2 0.000000 -1.000000 2.500000 26.404000 21.872338 47.418750 +15750 2 0.000000 -1 2.500000 26.404000 21.872338 47.418750 15751 2 0.000000 1 2.500000 28.700000 17.895549 47.418750 15752 2 0.000000 -1 2.500000 28.700000 17.895549 47.418750 15753 2 0.000000 1 2.500000 30.996000 19.221145 50.931250 @@ -15771,7 +15771,7 @@ Atoms 15755 2 0.000000 1 2.500000 33.292000 23.197934 50.931250 15756 2 0.000000 -1 2.500000 33.292000 23.197934 50.931250 15757 2 0.000000 1 2.500000 26.404000 21.872338 54.443750 -15758 2 0.000000 -1.000000 2.500000 26.404000 21.872338 54.443750 +15758 2 0.000000 -1 2.500000 26.404000 21.872338 54.443750 15759 2 0.000000 1 2.500000 28.700000 17.895549 54.443750 15760 2 0.000000 -1 2.500000 28.700000 17.895549 54.443750 15761 2 0.000000 1 2.500000 30.996000 19.221145 57.956250 @@ -15779,7 +15779,7 @@ Atoms 15763 2 0.000000 1 2.500000 33.292000 23.197934 57.956250 15764 2 0.000000 -1 2.500000 33.292000 23.197934 57.956250 15765 2 0.000000 1 2.500000 26.404000 21.872338 61.468750 -15766 2 0.000000 -1.000000 2.500000 26.404000 21.872338 61.468750 +15766 2 0.000000 -1 2.500000 26.404000 21.872338 61.468750 15767 2 0.000000 1 2.500000 28.700000 17.895549 61.468750 15768 2 0.000000 -1 2.500000 28.700000 17.895549 61.468750 15769 2 0.000000 1 2.500000 30.996000 27.174722 1.756250 @@ -15787,7 +15787,7 @@ Atoms 15771 2 0.000000 1 2.500000 33.292000 31.151511 1.756250 15772 2 0.000000 -1 2.500000 33.292000 31.151511 1.756250 15773 2 0.000000 1 2.500000 26.404000 29.825915 5.268750 -15774 2 0.000000 -1.000000 2.500000 26.404000 29.825915 5.268750 +15774 2 0.000000 -1 2.500000 26.404000 29.825915 5.268750 15775 2 0.000000 1 2.500000 28.700000 25.849126 5.268750 15776 2 0.000000 -1 2.500000 28.700000 25.849126 5.268750 15777 2 0.000000 1 2.500000 30.996000 27.174722 8.781250 @@ -15795,7 +15795,7 @@ Atoms 15779 2 0.000000 1 2.500000 33.292000 31.151511 8.781250 15780 2 0.000000 -1 2.500000 33.292000 31.151511 8.781250 15781 2 0.000000 1 2.500000 26.404000 29.825915 12.293750 -15782 2 0.000000 -1.000000 2.500000 26.404000 29.825915 12.293750 +15782 2 0.000000 -1 2.500000 26.404000 29.825915 12.293750 15783 2 0.000000 1 2.500000 28.700000 25.849126 12.293750 15784 2 0.000000 -1 2.500000 28.700000 25.849126 12.293750 15785 2 0.000000 1 2.500000 30.996000 27.174722 15.806250 @@ -15803,7 +15803,7 @@ Atoms 15787 2 0.000000 1 2.500000 33.292000 31.151511 15.806250 15788 2 0.000000 -1 2.500000 33.292000 31.151511 15.806250 15789 2 0.000000 1 2.500000 26.404000 29.825915 19.318750 -15790 2 0.000000 -1.000000 2.500000 26.404000 29.825915 19.318750 +15790 2 0.000000 -1 2.500000 26.404000 29.825915 19.318750 15791 2 0.000000 1 2.500000 28.700000 25.849126 19.318750 15792 2 0.000000 -1 2.500000 28.700000 25.849126 19.318750 15793 2 0.000000 1 2.500000 30.996000 27.174722 22.831250 @@ -15811,7 +15811,7 @@ Atoms 15795 2 0.000000 1 2.500000 33.292000 31.151511 22.831250 15796 2 0.000000 -1 2.500000 33.292000 31.151511 22.831250 15797 2 0.000000 1 2.500000 26.404000 29.825915 26.343750 -15798 2 0.000000 -1.000000 2.500000 26.404000 29.825915 26.343750 +15798 2 0.000000 -1 2.500000 26.404000 29.825915 26.343750 15799 2 0.000000 1 2.500000 28.700000 25.849126 26.343750 15800 2 0.000000 -1 2.500000 28.700000 25.849126 26.343750 15801 2 0.000000 1 2.500000 30.996000 27.174722 29.856250 @@ -15819,7 +15819,7 @@ Atoms 15803 2 0.000000 1 2.500000 33.292000 31.151511 29.856250 15804 2 0.000000 -1 2.500000 33.292000 31.151511 29.856250 15805 2 0.000000 1 2.500000 26.404000 29.825915 33.368750 -15806 2 0.000000 -1.000000 2.500000 26.404000 29.825915 33.368750 +15806 2 0.000000 -1 2.500000 26.404000 29.825915 33.368750 15807 2 0.000000 1 2.500000 28.700000 25.849126 33.368750 15808 2 0.000000 -1 2.500000 28.700000 25.849126 33.368750 15809 2 0.000000 1 2.500000 30.996000 27.174722 36.881250 @@ -15827,7 +15827,7 @@ Atoms 15811 2 0.000000 1 2.500000 33.292000 31.151511 36.881250 15812 2 0.000000 -1 2.500000 33.292000 31.151511 36.881250 15813 2 0.000000 1 2.500000 26.404000 29.825915 40.393750 -15814 2 0.000000 -1.000000 2.500000 26.404000 29.825915 40.393750 +15814 2 0.000000 -1 2.500000 26.404000 29.825915 40.393750 15815 2 0.000000 1 2.500000 28.700000 25.849126 40.393750 15816 2 0.000000 -1 2.500000 28.700000 25.849126 40.393750 15817 2 0.000000 1 2.500000 30.996000 27.174722 43.906250 @@ -15835,7 +15835,7 @@ Atoms 15819 2 0.000000 1 2.500000 33.292000 31.151511 43.906250 15820 2 0.000000 -1 2.500000 33.292000 31.151511 43.906250 15821 2 0.000000 1 2.500000 26.404000 29.825915 47.418750 -15822 2 0.000000 -1.000000 2.500000 26.404000 29.825915 47.418750 +15822 2 0.000000 -1 2.500000 26.404000 29.825915 47.418750 15823 2 0.000000 1 2.500000 28.700000 25.849126 47.418750 15824 2 0.000000 -1 2.500000 28.700000 25.849126 47.418750 15825 2 0.000000 1 2.500000 30.996000 27.174722 50.931250 @@ -15843,7 +15843,7 @@ Atoms 15827 2 0.000000 1 2.500000 33.292000 31.151511 50.931250 15828 2 0.000000 -1 2.500000 33.292000 31.151511 50.931250 15829 2 0.000000 1 2.500000 26.404000 29.825915 54.443750 -15830 2 0.000000 -1.000000 2.500000 26.404000 29.825915 54.443750 +15830 2 0.000000 -1 2.500000 26.404000 29.825915 54.443750 15831 2 0.000000 1 2.500000 28.700000 25.849126 54.443750 15832 2 0.000000 -1 2.500000 28.700000 25.849126 54.443750 15833 2 0.000000 1 2.500000 30.996000 27.174722 57.956250 @@ -15851,7 +15851,7 @@ Atoms 15835 2 0.000000 1 2.500000 33.292000 31.151511 57.956250 15836 2 0.000000 -1 2.500000 33.292000 31.151511 57.956250 15837 2 0.000000 1 2.500000 26.404000 29.825915 61.468750 -15838 2 0.000000 -1.000000 2.500000 26.404000 29.825915 61.468750 +15838 2 0.000000 -1 2.500000 26.404000 29.825915 61.468750 15839 2 0.000000 1 2.500000 28.700000 25.849126 61.468750 15840 2 0.000000 -1 2.500000 28.700000 25.849126 61.468750 15841 2 0.000000 1 2.500000 30.996000 35.128300 1.756250 @@ -15859,7 +15859,7 @@ Atoms 15843 2 0.000000 1 2.500000 33.292000 39.105088 1.756250 15844 2 0.000000 -1 2.500000 33.292000 39.105088 1.756250 15845 2 0.000000 1 2.500000 26.404000 37.779492 5.268750 -15846 2 0.000000 -1.000000 2.500000 26.404000 37.779492 5.268750 +15846 2 0.000000 -1 2.500000 26.404000 37.779492 5.268750 15847 2 0.000000 1 2.500000 28.700000 33.802704 5.268750 15848 2 0.000000 -1 2.500000 28.700000 33.802704 5.268750 15849 2 0.000000 1 2.500000 30.996000 35.128300 8.781250 @@ -15867,7 +15867,7 @@ Atoms 15851 2 0.000000 1 2.500000 33.292000 39.105088 8.781250 15852 2 0.000000 -1 2.500000 33.292000 39.105088 8.781250 15853 2 0.000000 1 2.500000 26.404000 37.779492 12.293750 -15854 2 0.000000 -1.000000 2.500000 26.404000 37.779492 12.293750 +15854 2 0.000000 -1 2.500000 26.404000 37.779492 12.293750 15855 2 0.000000 1 2.500000 28.700000 33.802704 12.293750 15856 2 0.000000 -1 2.500000 28.700000 33.802704 12.293750 15857 2 0.000000 1 2.500000 30.996000 35.128300 15.806250 @@ -15875,7 +15875,7 @@ Atoms 15859 2 0.000000 1 2.500000 33.292000 39.105088 15.806250 15860 2 0.000000 -1 2.500000 33.292000 39.105088 15.806250 15861 2 0.000000 1 2.500000 26.404000 37.779492 19.318750 -15862 2 0.000000 -1.000000 2.500000 26.404000 37.779492 19.318750 +15862 2 0.000000 -1 2.500000 26.404000 37.779492 19.318750 15863 2 0.000000 1 2.500000 28.700000 33.802704 19.318750 15864 2 0.000000 -1 2.500000 28.700000 33.802704 19.318750 15865 2 0.000000 1 2.500000 30.996000 35.128300 22.831250 @@ -15883,7 +15883,7 @@ Atoms 15867 2 0.000000 1 2.500000 33.292000 39.105088 22.831250 15868 2 0.000000 -1 2.500000 33.292000 39.105088 22.831250 15869 2 0.000000 1 2.500000 26.404000 37.779492 26.343750 -15870 2 0.000000 -1.000000 2.500000 26.404000 37.779492 26.343750 +15870 2 0.000000 -1 2.500000 26.404000 37.779492 26.343750 15871 2 0.000000 1 2.500000 28.700000 33.802704 26.343750 15872 2 0.000000 -1 2.500000 28.700000 33.802704 26.343750 15873 2 0.000000 1 2.500000 30.996000 35.128300 29.856250 @@ -15891,7 +15891,7 @@ Atoms 15875 2 0.000000 1 2.500000 33.292000 39.105088 29.856250 15876 2 0.000000 -1 2.500000 33.292000 39.105088 29.856250 15877 2 0.000000 1 2.500000 26.404000 37.779492 33.368750 -15878 2 0.000000 -1.000000 2.500000 26.404000 37.779492 33.368750 +15878 2 0.000000 -1 2.500000 26.404000 37.779492 33.368750 15879 2 0.000000 1 2.500000 28.700000 33.802704 33.368750 15880 2 0.000000 -1 2.500000 28.700000 33.802704 33.368750 15881 2 0.000000 1 2.500000 30.996000 35.128300 36.881250 @@ -15899,7 +15899,7 @@ Atoms 15883 2 0.000000 1 2.500000 33.292000 39.105088 36.881250 15884 2 0.000000 -1 2.500000 33.292000 39.105088 36.881250 15885 2 0.000000 1 2.500000 26.404000 37.779492 40.393750 -15886 2 0.000000 -1.000000 2.500000 26.404000 37.779492 40.393750 +15886 2 0.000000 -1 2.500000 26.404000 37.779492 40.393750 15887 2 0.000000 1 2.500000 28.700000 33.802704 40.393750 15888 2 0.000000 -1 2.500000 28.700000 33.802704 40.393750 15889 2 0.000000 1 2.500000 30.996000 35.128300 43.906250 @@ -15907,7 +15907,7 @@ Atoms 15891 2 0.000000 1 2.500000 33.292000 39.105088 43.906250 15892 2 0.000000 -1 2.500000 33.292000 39.105088 43.906250 15893 2 0.000000 1 2.500000 26.404000 37.779492 47.418750 -15894 2 0.000000 -1.000000 2.500000 26.404000 37.779492 47.418750 +15894 2 0.000000 -1 2.500000 26.404000 37.779492 47.418750 15895 2 0.000000 1 2.500000 28.700000 33.802704 47.418750 15896 2 0.000000 -1 2.500000 28.700000 33.802704 47.418750 15897 2 0.000000 1 2.500000 30.996000 35.128300 50.931250 @@ -15915,7 +15915,7 @@ Atoms 15899 2 0.000000 1 2.500000 33.292000 39.105088 50.931250 15900 2 0.000000 -1 2.500000 33.292000 39.105088 50.931250 15901 2 0.000000 1 2.500000 26.404000 37.779492 54.443750 -15902 2 0.000000 -1.000000 2.500000 26.404000 37.779492 54.443750 +15902 2 0.000000 -1 2.500000 26.404000 37.779492 54.443750 15903 2 0.000000 1 2.500000 28.700000 33.802704 54.443750 15904 2 0.000000 -1 2.500000 28.700000 33.802704 54.443750 15905 2 0.000000 1 2.500000 30.996000 35.128300 57.956250 @@ -15923,7 +15923,7 @@ Atoms 15907 2 0.000000 1 2.500000 33.292000 39.105088 57.956250 15908 2 0.000000 -1 2.500000 33.292000 39.105088 57.956250 15909 2 0.000000 1 2.500000 26.404000 37.779492 61.468750 -15910 2 0.000000 -1.000000 2.500000 26.404000 37.779492 61.468750 +15910 2 0.000000 -1 2.500000 26.404000 37.779492 61.468750 15911 2 0.000000 1 2.500000 28.700000 33.802704 61.468750 15912 2 0.000000 -1 2.500000 28.700000 33.802704 61.468750 15913 2 0.000000 1 2.500000 30.996000 43.081877 1.756250 @@ -15931,7 +15931,7 @@ Atoms 15915 2 0.000000 1 2.500000 33.292000 47.058666 1.756250 15916 2 0.000000 -1 2.500000 33.292000 47.058666 1.756250 15917 2 0.000000 1 2.500000 26.404000 45.733070 5.268750 -15918 2 0.000000 -1.000000 2.500000 26.404000 45.733070 5.268750 +15918 2 0.000000 -1 2.500000 26.404000 45.733070 5.268750 15919 2 0.000000 1 2.500000 28.700000 41.756281 5.268750 15920 2 0.000000 -1 2.500000 28.700000 41.756281 5.268750 15921 2 0.000000 1 2.500000 30.996000 43.081877 8.781250 @@ -15939,7 +15939,7 @@ Atoms 15923 2 0.000000 1 2.500000 33.292000 47.058666 8.781250 15924 2 0.000000 -1 2.500000 33.292000 47.058666 8.781250 15925 2 0.000000 1 2.500000 26.404000 45.733070 12.293750 -15926 2 0.000000 -1.000000 2.500000 26.404000 45.733070 12.293750 +15926 2 0.000000 -1 2.500000 26.404000 45.733070 12.293750 15927 2 0.000000 1 2.500000 28.700000 41.756281 12.293750 15928 2 0.000000 -1 2.500000 28.700000 41.756281 12.293750 15929 2 0.000000 1 2.500000 30.996000 43.081877 15.806250 @@ -15947,7 +15947,7 @@ Atoms 15931 2 0.000000 1 2.500000 33.292000 47.058666 15.806250 15932 2 0.000000 -1 2.500000 33.292000 47.058666 15.806250 15933 2 0.000000 1 2.500000 26.404000 45.733070 19.318750 -15934 2 0.000000 -1.000000 2.500000 26.404000 45.733070 19.318750 +15934 2 0.000000 -1 2.500000 26.404000 45.733070 19.318750 15935 2 0.000000 1 2.500000 28.700000 41.756281 19.318750 15936 2 0.000000 -1 2.500000 28.700000 41.756281 19.318750 15937 2 0.000000 1 2.500000 30.996000 43.081877 22.831250 @@ -15955,7 +15955,7 @@ Atoms 15939 2 0.000000 1 2.500000 33.292000 47.058666 22.831250 15940 2 0.000000 -1 2.500000 33.292000 47.058666 22.831250 15941 2 0.000000 1 2.500000 26.404000 45.733070 26.343750 -15942 2 0.000000 -1.000000 2.500000 26.404000 45.733070 26.343750 +15942 2 0.000000 -1 2.500000 26.404000 45.733070 26.343750 15943 2 0.000000 1 2.500000 28.700000 41.756281 26.343750 15944 2 0.000000 -1 2.500000 28.700000 41.756281 26.343750 15945 2 0.000000 1 2.500000 30.996000 43.081877 29.856250 @@ -15963,7 +15963,7 @@ Atoms 15947 2 0.000000 1 2.500000 33.292000 47.058666 29.856250 15948 2 0.000000 -1 2.500000 33.292000 47.058666 29.856250 15949 2 0.000000 1 2.500000 26.404000 45.733070 33.368750 -15950 2 0.000000 -1.000000 2.500000 26.404000 45.733070 33.368750 +15950 2 0.000000 -1 2.500000 26.404000 45.733070 33.368750 15951 2 0.000000 1 2.500000 28.700000 41.756281 33.368750 15952 2 0.000000 -1 2.500000 28.700000 41.756281 33.368750 15953 2 0.000000 1 2.500000 30.996000 43.081877 36.881250 @@ -15971,7 +15971,7 @@ Atoms 15955 2 0.000000 1 2.500000 33.292000 47.058666 36.881250 15956 2 0.000000 -1 2.500000 33.292000 47.058666 36.881250 15957 2 0.000000 1 2.500000 26.404000 45.733070 40.393750 -15958 2 0.000000 -1.000000 2.500000 26.404000 45.733070 40.393750 +15958 2 0.000000 -1 2.500000 26.404000 45.733070 40.393750 15959 2 0.000000 1 2.500000 28.700000 41.756281 40.393750 15960 2 0.000000 -1 2.500000 28.700000 41.756281 40.393750 15961 2 0.000000 1 2.500000 30.996000 43.081877 43.906250 @@ -15979,7 +15979,7 @@ Atoms 15963 2 0.000000 1 2.500000 33.292000 47.058666 43.906250 15964 2 0.000000 -1 2.500000 33.292000 47.058666 43.906250 15965 2 0.000000 1 2.500000 26.404000 45.733070 47.418750 -15966 2 0.000000 -1.000000 2.500000 26.404000 45.733070 47.418750 +15966 2 0.000000 -1 2.500000 26.404000 45.733070 47.418750 15967 2 0.000000 1 2.500000 28.700000 41.756281 47.418750 15968 2 0.000000 -1 2.500000 28.700000 41.756281 47.418750 15969 2 0.000000 1 2.500000 30.996000 43.081877 50.931250 @@ -15987,7 +15987,7 @@ Atoms 15971 2 0.000000 1 2.500000 33.292000 47.058666 50.931250 15972 2 0.000000 -1 2.500000 33.292000 47.058666 50.931250 15973 2 0.000000 1 2.500000 26.404000 45.733070 54.443750 -15974 2 0.000000 -1.000000 2.500000 26.404000 45.733070 54.443750 +15974 2 0.000000 -1 2.500000 26.404000 45.733070 54.443750 15975 2 0.000000 1 2.500000 28.700000 41.756281 54.443750 15976 2 0.000000 -1 2.500000 28.700000 41.756281 54.443750 15977 2 0.000000 1 2.500000 30.996000 43.081877 57.956250 @@ -15995,7 +15995,7 @@ Atoms 15979 2 0.000000 1 2.500000 33.292000 47.058666 57.956250 15980 2 0.000000 -1 2.500000 33.292000 47.058666 57.956250 15981 2 0.000000 1 2.500000 26.404000 45.733070 61.468750 -15982 2 0.000000 -1.000000 2.500000 26.404000 45.733070 61.468750 +15982 2 0.000000 -1 2.500000 26.404000 45.733070 61.468750 15983 2 0.000000 1 2.500000 28.700000 41.756281 61.468750 15984 2 0.000000 -1 2.500000 28.700000 41.756281 61.468750 15985 2 0.000000 1 2.500000 30.996000 51.035454 1.756250 @@ -16003,7 +16003,7 @@ Atoms 15987 2 0.000000 1 2.500000 33.292000 55.012243 1.756250 15988 2 0.000000 -1 2.500000 33.292000 55.012243 1.756250 15989 2 0.000000 1 2.500000 26.404000 53.686647 5.268750 -15990 2 0.000000 -1.000000 2.500000 26.404000 53.686647 5.268750 +15990 2 0.000000 -1 2.500000 26.404000 53.686647 5.268750 15991 2 0.000000 1 2.500000 28.700000 49.709858 5.268750 15992 2 0.000000 -1 2.500000 28.700000 49.709858 5.268750 15993 2 0.000000 1 2.500000 30.996000 51.035454 8.781250 @@ -16011,7 +16011,7 @@ Atoms 15995 2 0.000000 1 2.500000 33.292000 55.012243 8.781250 15996 2 0.000000 -1 2.500000 33.292000 55.012243 8.781250 15997 2 0.000000 1 2.500000 26.404000 53.686647 12.293750 -15998 2 0.000000 -1.000000 2.500000 26.404000 53.686647 12.293750 +15998 2 0.000000 -1 2.500000 26.404000 53.686647 12.293750 15999 2 0.000000 1 2.500000 28.700000 49.709858 12.293750 16000 2 0.000000 -1 2.500000 28.700000 49.709858 12.293750 16001 2 0.000000 1 2.500000 30.996000 51.035454 15.806250 @@ -16019,7 +16019,7 @@ Atoms 16003 2 0.000000 1 2.500000 33.292000 55.012243 15.806250 16004 2 0.000000 -1 2.500000 33.292000 55.012243 15.806250 16005 2 0.000000 1 2.500000 26.404000 53.686647 19.318750 -16006 2 0.000000 -1.000000 2.500000 26.404000 53.686647 19.318750 +16006 2 0.000000 -1 2.500000 26.404000 53.686647 19.318750 16007 2 0.000000 1 2.500000 28.700000 49.709858 19.318750 16008 2 0.000000 -1 2.500000 28.700000 49.709858 19.318750 16009 2 0.000000 1 2.500000 30.996000 51.035454 22.831250 @@ -16027,7 +16027,7 @@ Atoms 16011 2 0.000000 1 2.500000 33.292000 55.012243 22.831250 16012 2 0.000000 -1 2.500000 33.292000 55.012243 22.831250 16013 2 0.000000 1 2.500000 26.404000 53.686647 26.343750 -16014 2 0.000000 -1.000000 2.500000 26.404000 53.686647 26.343750 +16014 2 0.000000 -1 2.500000 26.404000 53.686647 26.343750 16015 2 0.000000 1 2.500000 28.700000 49.709858 26.343750 16016 2 0.000000 -1 2.500000 28.700000 49.709858 26.343750 16017 2 0.000000 1 2.500000 30.996000 51.035454 29.856250 @@ -16035,7 +16035,7 @@ Atoms 16019 2 0.000000 1 2.500000 33.292000 55.012243 29.856250 16020 2 0.000000 -1 2.500000 33.292000 55.012243 29.856250 16021 2 0.000000 1 2.500000 26.404000 53.686647 33.368750 -16022 2 0.000000 -1.000000 2.500000 26.404000 53.686647 33.368750 +16022 2 0.000000 -1 2.500000 26.404000 53.686647 33.368750 16023 2 0.000000 1 2.500000 28.700000 49.709858 33.368750 16024 2 0.000000 -1 2.500000 28.700000 49.709858 33.368750 16025 2 0.000000 1 2.500000 30.996000 51.035454 36.881250 @@ -16043,7 +16043,7 @@ Atoms 16027 2 0.000000 1 2.500000 33.292000 55.012243 36.881250 16028 2 0.000000 -1 2.500000 33.292000 55.012243 36.881250 16029 2 0.000000 1 2.500000 26.404000 53.686647 40.393750 -16030 2 0.000000 -1.000000 2.500000 26.404000 53.686647 40.393750 +16030 2 0.000000 -1 2.500000 26.404000 53.686647 40.393750 16031 2 0.000000 1 2.500000 28.700000 49.709858 40.393750 16032 2 0.000000 -1 2.500000 28.700000 49.709858 40.393750 16033 2 0.000000 1 2.500000 30.996000 51.035454 43.906250 @@ -16051,7 +16051,7 @@ Atoms 16035 2 0.000000 1 2.500000 33.292000 55.012243 43.906250 16036 2 0.000000 -1 2.500000 33.292000 55.012243 43.906250 16037 2 0.000000 1 2.500000 26.404000 53.686647 47.418750 -16038 2 0.000000 -1.000000 2.500000 26.404000 53.686647 47.418750 +16038 2 0.000000 -1 2.500000 26.404000 53.686647 47.418750 16039 2 0.000000 1 2.500000 28.700000 49.709858 47.418750 16040 2 0.000000 -1 2.500000 28.700000 49.709858 47.418750 16041 2 0.000000 1 2.500000 30.996000 51.035454 50.931250 @@ -16059,7 +16059,7 @@ Atoms 16043 2 0.000000 1 2.500000 33.292000 55.012243 50.931250 16044 2 0.000000 -1 2.500000 33.292000 55.012243 50.931250 16045 2 0.000000 1 2.500000 26.404000 53.686647 54.443750 -16046 2 0.000000 -1.000000 2.500000 26.404000 53.686647 54.443750 +16046 2 0.000000 -1 2.500000 26.404000 53.686647 54.443750 16047 2 0.000000 1 2.500000 28.700000 49.709858 54.443750 16048 2 0.000000 -1 2.500000 28.700000 49.709858 54.443750 16049 2 0.000000 1 2.500000 30.996000 51.035454 57.956250 @@ -16067,7 +16067,7 @@ Atoms 16051 2 0.000000 1 2.500000 33.292000 55.012243 57.956250 16052 2 0.000000 -1 2.500000 33.292000 55.012243 57.956250 16053 2 0.000000 1 2.500000 26.404000 53.686647 61.468750 -16054 2 0.000000 -1.000000 2.500000 26.404000 53.686647 61.468750 +16054 2 0.000000 -1 2.500000 26.404000 53.686647 61.468750 16055 2 0.000000 1 2.500000 28.700000 49.709858 61.468750 16056 2 0.000000 -1 2.500000 28.700000 49.709858 61.468750 16057 2 0.000000 1 2.500000 30.996000 58.989032 1.756250 @@ -16075,7 +16075,7 @@ Atoms 16059 2 0.000000 1 2.500000 33.292000 62.965820 1.756250 16060 2 0.000000 -1 2.500000 33.292000 62.965820 1.756250 16061 2 0.000000 1 2.500000 26.404000 61.640224 5.268750 -16062 2 0.000000 -1.000000 2.500000 26.404000 61.640224 5.268750 +16062 2 0.000000 -1 2.500000 26.404000 61.640224 5.268750 16063 2 0.000000 1 2.500000 28.700000 57.663435 5.268750 16064 2 0.000000 -1 2.500000 28.700000 57.663435 5.268750 16065 2 0.000000 1 2.500000 30.996000 58.989032 8.781250 @@ -16083,7 +16083,7 @@ Atoms 16067 2 0.000000 1 2.500000 33.292000 62.965820 8.781250 16068 2 0.000000 -1 2.500000 33.292000 62.965820 8.781250 16069 2 0.000000 1 2.500000 26.404000 61.640224 12.293750 -16070 2 0.000000 -1.000000 2.500000 26.404000 61.640224 12.293750 +16070 2 0.000000 -1 2.500000 26.404000 61.640224 12.293750 16071 2 0.000000 1 2.500000 28.700000 57.663435 12.293750 16072 2 0.000000 -1 2.500000 28.700000 57.663435 12.293750 16073 2 0.000000 1 2.500000 30.996000 58.989032 15.806250 @@ -16091,7 +16091,7 @@ Atoms 16075 2 0.000000 1 2.500000 33.292000 62.965820 15.806250 16076 2 0.000000 -1 2.500000 33.292000 62.965820 15.806250 16077 2 0.000000 1 2.500000 26.404000 61.640224 19.318750 -16078 2 0.000000 -1.000000 2.500000 26.404000 61.640224 19.318750 +16078 2 0.000000 -1 2.500000 26.404000 61.640224 19.318750 16079 2 0.000000 1 2.500000 28.700000 57.663435 19.318750 16080 2 0.000000 -1 2.500000 28.700000 57.663435 19.318750 16081 2 0.000000 1 2.500000 30.996000 58.989032 22.831250 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58.989032 36.881250 @@ -16115,7 +16115,7 @@ Atoms 16099 2 0.000000 1 2.500000 33.292000 62.965820 36.881250 16100 2 0.000000 -1 2.500000 33.292000 62.965820 36.881250 16101 2 0.000000 1 2.500000 26.404000 61.640224 40.393750 -16102 2 0.000000 -1.000000 2.500000 26.404000 61.640224 40.393750 +16102 2 0.000000 -1 2.500000 26.404000 61.640224 40.393750 16103 2 0.000000 1 2.500000 28.700000 57.663435 40.393750 16104 2 0.000000 -1 2.500000 28.700000 57.663435 40.393750 16105 2 0.000000 1 2.500000 30.996000 58.989032 43.906250 @@ -16123,7 +16123,7 @@ Atoms 16107 2 0.000000 1 2.500000 33.292000 62.965820 43.906250 16108 2 0.000000 -1 2.500000 33.292000 62.965820 43.906250 16109 2 0.000000 1 2.500000 26.404000 61.640224 47.418750 -16110 2 0.000000 -1.000000 2.500000 26.404000 61.640224 47.418750 +16110 2 0.000000 -1 2.500000 26.404000 61.640224 47.418750 16111 2 0.000000 1 2.500000 28.700000 57.663435 47.418750 16112 2 0.000000 -1 2.500000 28.700000 57.663435 47.418750 16113 2 0.000000 1 2.500000 30.996000 58.989032 50.931250 @@ -16131,7 +16131,7 @@ Atoms 16115 2 0.000000 1 2.500000 33.292000 62.965820 50.931250 16116 2 0.000000 -1 2.500000 33.292000 62.965820 50.931250 16117 2 0.000000 1 2.500000 26.404000 61.640224 54.443750 -16118 2 0.000000 -1.000000 2.500000 26.404000 61.640224 54.443750 +16118 2 0.000000 -1 2.500000 26.404000 61.640224 54.443750 16119 2 0.000000 1 2.500000 28.700000 57.663435 54.443750 16120 2 0.000000 -1 2.500000 28.700000 57.663435 54.443750 16121 2 0.000000 1 2.500000 30.996000 58.989032 57.956250 @@ -16139,7 +16139,7 @@ Atoms 16123 2 0.000000 1 2.500000 33.292000 62.965820 57.956250 16124 2 0.000000 -1 2.500000 33.292000 62.965820 57.956250 16125 2 0.000000 1 2.500000 26.404000 61.640224 61.468750 -16126 2 0.000000 -1.000000 2.500000 26.404000 61.640224 61.468750 +16126 2 0.000000 -1 2.500000 26.404000 61.640224 61.468750 16127 2 0.000000 1 2.500000 28.700000 57.663435 61.468750 16128 2 0.000000 -1 2.500000 28.700000 57.663435 61.468750 16129 2 0.000000 1 2.500000 35.588000 3.313991 1.756250 @@ -16147,7 +16147,7 @@ Atoms 16131 2 0.000000 1 2.500000 37.884000 7.290779 1.756250 16132 2 0.000000 -1 2.500000 37.884000 7.290779 1.756250 16133 2 0.000000 1 2.500000 30.996000 5.965183 5.268750 -16134 2 0.000000 -1.000000 2.500000 30.996000 5.965183 5.268750 +16134 2 0.000000 -1 2.500000 30.996000 5.965183 5.268750 16135 2 0.000000 1 2.500000 33.292000 1.988394 5.268750 16136 2 0.000000 -1 2.500000 33.292000 1.988394 5.268750 16137 2 0.000000 1 2.500000 35.588000 3.313991 8.781250 @@ -16155,7 +16155,7 @@ Atoms 16139 2 0.000000 1 2.500000 37.884000 7.290779 8.781250 16140 2 0.000000 -1 2.500000 37.884000 7.290779 8.781250 16141 2 0.000000 1 2.500000 30.996000 5.965183 12.293750 -16142 2 0.000000 -1.000000 2.500000 30.996000 5.965183 12.293750 +16142 2 0.000000 -1 2.500000 30.996000 5.965183 12.293750 16143 2 0.000000 1 2.500000 33.292000 1.988394 12.293750 16144 2 0.000000 -1 2.500000 33.292000 1.988394 12.293750 16145 2 0.000000 1 2.500000 35.588000 3.313991 15.806250 @@ -16163,7 +16163,7 @@ Atoms 16147 2 0.000000 1 2.500000 37.884000 7.290779 15.806250 16148 2 0.000000 -1 2.500000 37.884000 7.290779 15.806250 16149 2 0.000000 1 2.500000 30.996000 5.965183 19.318750 -16150 2 0.000000 -1.000000 2.500000 30.996000 5.965183 19.318750 +16150 2 0.000000 -1 2.500000 30.996000 5.965183 19.318750 16151 2 0.000000 1 2.500000 33.292000 1.988394 19.318750 16152 2 0.000000 -1 2.500000 33.292000 1.988394 19.318750 16153 2 0.000000 1 2.500000 35.588000 3.313991 22.831250 @@ -16171,7 +16171,7 @@ Atoms 16155 2 0.000000 1 2.500000 37.884000 7.290779 22.831250 16156 2 0.000000 -1 2.500000 37.884000 7.290779 22.831250 16157 2 0.000000 1 2.500000 30.996000 5.965183 26.343750 -16158 2 0.000000 -1.000000 2.500000 30.996000 5.965183 26.343750 +16158 2 0.000000 -1 2.500000 30.996000 5.965183 26.343750 16159 2 0.000000 1 2.500000 33.292000 1.988394 26.343750 16160 2 0.000000 -1 2.500000 33.292000 1.988394 26.343750 16161 2 0.000000 1 2.500000 35.588000 3.313991 29.856250 @@ -16179,7 +16179,7 @@ Atoms 16163 2 0.000000 1 2.500000 37.884000 7.290779 29.856250 16164 2 0.000000 -1 2.500000 37.884000 7.290779 29.856250 16165 2 0.000000 1 2.500000 30.996000 5.965183 33.368750 -16166 2 0.000000 -1.000000 2.500000 30.996000 5.965183 33.368750 +16166 2 0.000000 -1 2.500000 30.996000 5.965183 33.368750 16167 2 0.000000 1 2.500000 33.292000 1.988394 33.368750 16168 2 0.000000 -1 2.500000 33.292000 1.988394 33.368750 16169 2 0.000000 1 2.500000 35.588000 3.313991 36.881250 @@ -16187,7 +16187,7 @@ Atoms 16171 2 0.000000 1 2.500000 37.884000 7.290779 36.881250 16172 2 0.000000 -1 2.500000 37.884000 7.290779 36.881250 16173 2 0.000000 1 2.500000 30.996000 5.965183 40.393750 -16174 2 0.000000 -1.000000 2.500000 30.996000 5.965183 40.393750 +16174 2 0.000000 -1 2.500000 30.996000 5.965183 40.393750 16175 2 0.000000 1 2.500000 33.292000 1.988394 40.393750 16176 2 0.000000 -1 2.500000 33.292000 1.988394 40.393750 16177 2 0.000000 1 2.500000 35.588000 3.313991 43.906250 @@ -16195,7 +16195,7 @@ Atoms 16179 2 0.000000 1 2.500000 37.884000 7.290779 43.906250 16180 2 0.000000 -1 2.500000 37.884000 7.290779 43.906250 16181 2 0.000000 1 2.500000 30.996000 5.965183 47.418750 -16182 2 0.000000 -1.000000 2.500000 30.996000 5.965183 47.418750 +16182 2 0.000000 -1 2.500000 30.996000 5.965183 47.418750 16183 2 0.000000 1 2.500000 33.292000 1.988394 47.418750 16184 2 0.000000 -1 2.500000 33.292000 1.988394 47.418750 16185 2 0.000000 1 2.500000 35.588000 3.313991 50.931250 @@ -16203,7 +16203,7 @@ Atoms 16187 2 0.000000 1 2.500000 37.884000 7.290779 50.931250 16188 2 0.000000 -1 2.500000 37.884000 7.290779 50.931250 16189 2 0.000000 1 2.500000 30.996000 5.965183 54.443750 -16190 2 0.000000 -1.000000 2.500000 30.996000 5.965183 54.443750 +16190 2 0.000000 -1 2.500000 30.996000 5.965183 54.443750 16191 2 0.000000 1 2.500000 33.292000 1.988394 54.443750 16192 2 0.000000 -1 2.500000 33.292000 1.988394 54.443750 16193 2 0.000000 1 2.500000 35.588000 3.313991 57.956250 @@ -16211,7 +16211,7 @@ Atoms 16195 2 0.000000 1 2.500000 37.884000 7.290779 57.956250 16196 2 0.000000 -1 2.500000 37.884000 7.290779 57.956250 16197 2 0.000000 1 2.500000 30.996000 5.965183 61.468750 -16198 2 0.000000 -1.000000 2.500000 30.996000 5.965183 61.468750 +16198 2 0.000000 -1 2.500000 30.996000 5.965183 61.468750 16199 2 0.000000 1 2.500000 33.292000 1.988394 61.468750 16200 2 0.000000 -1 2.500000 33.292000 1.988394 61.468750 16201 2 0.000000 1 2.500000 35.588000 11.267568 1.756250 @@ -16219,7 +16219,7 @@ Atoms 16203 2 0.000000 1 2.500000 37.884000 15.244357 1.756250 16204 2 0.000000 -1 2.500000 37.884000 15.244357 1.756250 16205 2 0.000000 1 2.500000 30.996000 13.918760 5.268750 -16206 2 0.000000 -1.000000 2.500000 30.996000 13.918760 5.268750 +16206 2 0.000000 -1 2.500000 30.996000 13.918760 5.268750 16207 2 0.000000 1 2.500000 33.292000 9.941972 5.268750 16208 2 0.000000 -1 2.500000 33.292000 9.941972 5.268750 16209 2 0.000000 1 2.500000 35.588000 11.267568 8.781250 @@ -16227,7 +16227,7 @@ Atoms 16211 2 0.000000 1 2.500000 37.884000 15.244357 8.781250 16212 2 0.000000 -1 2.500000 37.884000 15.244357 8.781250 16213 2 0.000000 1 2.500000 30.996000 13.918760 12.293750 -16214 2 0.000000 -1.000000 2.500000 30.996000 13.918760 12.293750 +16214 2 0.000000 -1 2.500000 30.996000 13.918760 12.293750 16215 2 0.000000 1 2.500000 33.292000 9.941972 12.293750 16216 2 0.000000 -1 2.500000 33.292000 9.941972 12.293750 16217 2 0.000000 1 2.500000 35.588000 11.267568 15.806250 @@ -16235,7 +16235,7 @@ Atoms 16219 2 0.000000 1 2.500000 37.884000 15.244357 15.806250 16220 2 0.000000 -1 2.500000 37.884000 15.244357 15.806250 16221 2 0.000000 1 2.500000 30.996000 13.918760 19.318750 -16222 2 0.000000 -1.000000 2.500000 30.996000 13.918760 19.318750 +16222 2 0.000000 -1 2.500000 30.996000 13.918760 19.318750 16223 2 0.000000 1 2.500000 33.292000 9.941972 19.318750 16224 2 0.000000 -1 2.500000 33.292000 9.941972 19.318750 16225 2 0.000000 1 2.500000 35.588000 11.267568 22.831250 @@ -16243,7 +16243,7 @@ Atoms 16227 2 0.000000 1 2.500000 37.884000 15.244357 22.831250 16228 2 0.000000 -1 2.500000 37.884000 15.244357 22.831250 16229 2 0.000000 1 2.500000 30.996000 13.918760 26.343750 -16230 2 0.000000 -1.000000 2.500000 30.996000 13.918760 26.343750 +16230 2 0.000000 -1 2.500000 30.996000 13.918760 26.343750 16231 2 0.000000 1 2.500000 33.292000 9.941972 26.343750 16232 2 0.000000 -1 2.500000 33.292000 9.941972 26.343750 16233 2 0.000000 1 2.500000 35.588000 11.267568 29.856250 @@ -16251,7 +16251,7 @@ Atoms 16235 2 0.000000 1 2.500000 37.884000 15.244357 29.856250 16236 2 0.000000 -1 2.500000 37.884000 15.244357 29.856250 16237 2 0.000000 1 2.500000 30.996000 13.918760 33.368750 -16238 2 0.000000 -1.000000 2.500000 30.996000 13.918760 33.368750 +16238 2 0.000000 -1 2.500000 30.996000 13.918760 33.368750 16239 2 0.000000 1 2.500000 33.292000 9.941972 33.368750 16240 2 0.000000 -1 2.500000 33.292000 9.941972 33.368750 16241 2 0.000000 1 2.500000 35.588000 11.267568 36.881250 @@ -16259,7 +16259,7 @@ Atoms 16243 2 0.000000 1 2.500000 37.884000 15.244357 36.881250 16244 2 0.000000 -1 2.500000 37.884000 15.244357 36.881250 16245 2 0.000000 1 2.500000 30.996000 13.918760 40.393750 -16246 2 0.000000 -1.000000 2.500000 30.996000 13.918760 40.393750 +16246 2 0.000000 -1 2.500000 30.996000 13.918760 40.393750 16247 2 0.000000 1 2.500000 33.292000 9.941972 40.393750 16248 2 0.000000 -1 2.500000 33.292000 9.941972 40.393750 16249 2 0.000000 1 2.500000 35.588000 11.267568 43.906250 @@ -16267,7 +16267,7 @@ Atoms 16251 2 0.000000 1 2.500000 37.884000 15.244357 43.906250 16252 2 0.000000 -1 2.500000 37.884000 15.244357 43.906250 16253 2 0.000000 1 2.500000 30.996000 13.918760 47.418750 -16254 2 0.000000 -1.000000 2.500000 30.996000 13.918760 47.418750 +16254 2 0.000000 -1 2.500000 30.996000 13.918760 47.418750 16255 2 0.000000 1 2.500000 33.292000 9.941972 47.418750 16256 2 0.000000 -1 2.500000 33.292000 9.941972 47.418750 16257 2 0.000000 1 2.500000 35.588000 11.267568 50.931250 @@ -16275,7 +16275,7 @@ Atoms 16259 2 0.000000 1 2.500000 37.884000 15.244357 50.931250 16260 2 0.000000 -1 2.500000 37.884000 15.244357 50.931250 16261 2 0.000000 1 2.500000 30.996000 13.918760 54.443750 -16262 2 0.000000 -1.000000 2.500000 30.996000 13.918760 54.443750 +16262 2 0.000000 -1 2.500000 30.996000 13.918760 54.443750 16263 2 0.000000 1 2.500000 33.292000 9.941972 54.443750 16264 2 0.000000 -1 2.500000 33.292000 9.941972 54.443750 16265 2 0.000000 1 2.500000 35.588000 11.267568 57.956250 @@ -16283,7 +16283,7 @@ Atoms 16267 2 0.000000 1 2.500000 37.884000 15.244357 57.956250 16268 2 0.000000 -1 2.500000 37.884000 15.244357 57.956250 16269 2 0.000000 1 2.500000 30.996000 13.918760 61.468750 -16270 2 0.000000 -1.000000 2.500000 30.996000 13.918760 61.468750 +16270 2 0.000000 -1 2.500000 30.996000 13.918760 61.468750 16271 2 0.000000 1 2.500000 33.292000 9.941972 61.468750 16272 2 0.000000 -1 2.500000 33.292000 9.941972 61.468750 16273 2 0.000000 1 2.500000 35.588000 19.221145 1.756250 @@ -16291,7 +16291,7 @@ Atoms 16275 2 0.000000 1 2.500000 37.884000 23.197934 1.756250 16276 2 0.000000 -1 2.500000 37.884000 23.197934 1.756250 16277 2 0.000000 1 2.500000 30.996000 21.872338 5.268750 -16278 2 0.000000 -1.000000 2.500000 30.996000 21.872338 5.268750 +16278 2 0.000000 -1 2.500000 30.996000 21.872338 5.268750 16279 2 0.000000 1 2.500000 33.292000 17.895549 5.268750 16280 2 0.000000 -1 2.500000 33.292000 17.895549 5.268750 16281 2 0.000000 1 2.500000 35.588000 19.221145 8.781250 @@ -16299,7 +16299,7 @@ Atoms 16283 2 0.000000 1 2.500000 37.884000 23.197934 8.781250 16284 2 0.000000 -1 2.500000 37.884000 23.197934 8.781250 16285 2 0.000000 1 2.500000 30.996000 21.872338 12.293750 -16286 2 0.000000 -1.000000 2.500000 30.996000 21.872338 12.293750 +16286 2 0.000000 -1 2.500000 30.996000 21.872338 12.293750 16287 2 0.000000 1 2.500000 33.292000 17.895549 12.293750 16288 2 0.000000 -1 2.500000 33.292000 17.895549 12.293750 16289 2 0.000000 1 2.500000 35.588000 19.221145 15.806250 @@ -16307,7 +16307,7 @@ Atoms 16291 2 0.000000 1 2.500000 37.884000 23.197934 15.806250 16292 2 0.000000 -1 2.500000 37.884000 23.197934 15.806250 16293 2 0.000000 1 2.500000 30.996000 21.872338 19.318750 -16294 2 0.000000 -1.000000 2.500000 30.996000 21.872338 19.318750 +16294 2 0.000000 -1 2.500000 30.996000 21.872338 19.318750 16295 2 0.000000 1 2.500000 33.292000 17.895549 19.318750 16296 2 0.000000 -1 2.500000 33.292000 17.895549 19.318750 16297 2 0.000000 1 2.500000 35.588000 19.221145 22.831250 @@ -16315,7 +16315,7 @@ Atoms 16299 2 0.000000 1 2.500000 37.884000 23.197934 22.831250 16300 2 0.000000 -1 2.500000 37.884000 23.197934 22.831250 16301 2 0.000000 1 2.500000 30.996000 21.872338 26.343750 -16302 2 0.000000 -1.000000 2.500000 30.996000 21.872338 26.343750 +16302 2 0.000000 -1 2.500000 30.996000 21.872338 26.343750 16303 2 0.000000 1 2.500000 33.292000 17.895549 26.343750 16304 2 0.000000 -1 2.500000 33.292000 17.895549 26.343750 16305 2 0.000000 1 2.500000 35.588000 19.221145 29.856250 @@ -16323,7 +16323,7 @@ Atoms 16307 2 0.000000 1 2.500000 37.884000 23.197934 29.856250 16308 2 0.000000 -1 2.500000 37.884000 23.197934 29.856250 16309 2 0.000000 1 2.500000 30.996000 21.872338 33.368750 -16310 2 0.000000 -1.000000 2.500000 30.996000 21.872338 33.368750 +16310 2 0.000000 -1 2.500000 30.996000 21.872338 33.368750 16311 2 0.000000 1 2.500000 33.292000 17.895549 33.368750 16312 2 0.000000 -1 2.500000 33.292000 17.895549 33.368750 16313 2 0.000000 1 2.500000 35.588000 19.221145 36.881250 @@ -16331,7 +16331,7 @@ Atoms 16315 2 0.000000 1 2.500000 37.884000 23.197934 36.881250 16316 2 0.000000 -1 2.500000 37.884000 23.197934 36.881250 16317 2 0.000000 1 2.500000 30.996000 21.872338 40.393750 -16318 2 0.000000 -1.000000 2.500000 30.996000 21.872338 40.393750 +16318 2 0.000000 -1 2.500000 30.996000 21.872338 40.393750 16319 2 0.000000 1 2.500000 33.292000 17.895549 40.393750 16320 2 0.000000 -1 2.500000 33.292000 17.895549 40.393750 16321 2 0.000000 1 2.500000 35.588000 19.221145 43.906250 @@ -16339,7 +16339,7 @@ Atoms 16323 2 0.000000 1 2.500000 37.884000 23.197934 43.906250 16324 2 0.000000 -1 2.500000 37.884000 23.197934 43.906250 16325 2 0.000000 1 2.500000 30.996000 21.872338 47.418750 -16326 2 0.000000 -1.000000 2.500000 30.996000 21.872338 47.418750 +16326 2 0.000000 -1 2.500000 30.996000 21.872338 47.418750 16327 2 0.000000 1 2.500000 33.292000 17.895549 47.418750 16328 2 0.000000 -1 2.500000 33.292000 17.895549 47.418750 16329 2 0.000000 1 2.500000 35.588000 19.221145 50.931250 @@ -16347,7 +16347,7 @@ Atoms 16331 2 0.000000 1 2.500000 37.884000 23.197934 50.931250 16332 2 0.000000 -1 2.500000 37.884000 23.197934 50.931250 16333 2 0.000000 1 2.500000 30.996000 21.872338 54.443750 -16334 2 0.000000 -1.000000 2.500000 30.996000 21.872338 54.443750 +16334 2 0.000000 -1 2.500000 30.996000 21.872338 54.443750 16335 2 0.000000 1 2.500000 33.292000 17.895549 54.443750 16336 2 0.000000 -1 2.500000 33.292000 17.895549 54.443750 16337 2 0.000000 1 2.500000 35.588000 19.221145 57.956250 @@ -16355,7 +16355,7 @@ Atoms 16339 2 0.000000 1 2.500000 37.884000 23.197934 57.956250 16340 2 0.000000 -1 2.500000 37.884000 23.197934 57.956250 16341 2 0.000000 1 2.500000 30.996000 21.872338 61.468750 -16342 2 0.000000 -1.000000 2.500000 30.996000 21.872338 61.468750 +16342 2 0.000000 -1 2.500000 30.996000 21.872338 61.468750 16343 2 0.000000 1 2.500000 33.292000 17.895549 61.468750 16344 2 0.000000 -1 2.500000 33.292000 17.895549 61.468750 16345 2 0.000000 1 2.500000 35.588000 27.174722 1.756250 @@ -16363,7 +16363,7 @@ Atoms 16347 2 0.000000 1 2.500000 37.884000 31.151511 1.756250 16348 2 0.000000 -1 2.500000 37.884000 31.151511 1.756250 16349 2 0.000000 1 2.500000 30.996000 29.825915 5.268750 -16350 2 0.000000 -1.000000 2.500000 30.996000 29.825915 5.268750 +16350 2 0.000000 -1 2.500000 30.996000 29.825915 5.268750 16351 2 0.000000 1 2.500000 33.292000 25.849126 5.268750 16352 2 0.000000 -1 2.500000 33.292000 25.849126 5.268750 16353 2 0.000000 1 2.500000 35.588000 27.174722 8.781250 @@ -16371,7 +16371,7 @@ Atoms 16355 2 0.000000 1 2.500000 37.884000 31.151511 8.781250 16356 2 0.000000 -1 2.500000 37.884000 31.151511 8.781250 16357 2 0.000000 1 2.500000 30.996000 29.825915 12.293750 -16358 2 0.000000 -1.000000 2.500000 30.996000 29.825915 12.293750 +16358 2 0.000000 -1 2.500000 30.996000 29.825915 12.293750 16359 2 0.000000 1 2.500000 33.292000 25.849126 12.293750 16360 2 0.000000 -1 2.500000 33.292000 25.849126 12.293750 16361 2 0.000000 1 2.500000 35.588000 27.174722 15.806250 @@ -16379,7 +16379,7 @@ Atoms 16363 2 0.000000 1 2.500000 37.884000 31.151511 15.806250 16364 2 0.000000 -1 2.500000 37.884000 31.151511 15.806250 16365 2 0.000000 1 2.500000 30.996000 29.825915 19.318750 -16366 2 0.000000 -1.000000 2.500000 30.996000 29.825915 19.318750 +16366 2 0.000000 -1 2.500000 30.996000 29.825915 19.318750 16367 2 0.000000 1 2.500000 33.292000 25.849126 19.318750 16368 2 0.000000 -1 2.500000 33.292000 25.849126 19.318750 16369 2 0.000000 1 2.500000 35.588000 27.174722 22.831250 @@ -16387,7 +16387,7 @@ Atoms 16371 2 0.000000 1 2.500000 37.884000 31.151511 22.831250 16372 2 0.000000 -1 2.500000 37.884000 31.151511 22.831250 16373 2 0.000000 1 2.500000 30.996000 29.825915 26.343750 -16374 2 0.000000 -1.000000 2.500000 30.996000 29.825915 26.343750 +16374 2 0.000000 -1 2.500000 30.996000 29.825915 26.343750 16375 2 0.000000 1 2.500000 33.292000 25.849126 26.343750 16376 2 0.000000 -1 2.500000 33.292000 25.849126 26.343750 16377 2 0.000000 1 2.500000 35.588000 27.174722 29.856250 @@ -16395,7 +16395,7 @@ Atoms 16379 2 0.000000 1 2.500000 37.884000 31.151511 29.856250 16380 2 0.000000 -1 2.500000 37.884000 31.151511 29.856250 16381 2 0.000000 1 2.500000 30.996000 29.825915 33.368750 -16382 2 0.000000 -1.000000 2.500000 30.996000 29.825915 33.368750 +16382 2 0.000000 -1 2.500000 30.996000 29.825915 33.368750 16383 2 0.000000 1 2.500000 33.292000 25.849126 33.368750 16384 2 0.000000 -1 2.500000 33.292000 25.849126 33.368750 16385 2 0.000000 1 2.500000 35.588000 27.174722 36.881250 @@ -16403,7 +16403,7 @@ Atoms 16387 2 0.000000 1 2.500000 37.884000 31.151511 36.881250 16388 2 0.000000 -1 2.500000 37.884000 31.151511 36.881250 16389 2 0.000000 1 2.500000 30.996000 29.825915 40.393750 -16390 2 0.000000 -1.000000 2.500000 30.996000 29.825915 40.393750 +16390 2 0.000000 -1 2.500000 30.996000 29.825915 40.393750 16391 2 0.000000 1 2.500000 33.292000 25.849126 40.393750 16392 2 0.000000 -1 2.500000 33.292000 25.849126 40.393750 16393 2 0.000000 1 2.500000 35.588000 27.174722 43.906250 @@ -16411,7 +16411,7 @@ Atoms 16395 2 0.000000 1 2.500000 37.884000 31.151511 43.906250 16396 2 0.000000 -1 2.500000 37.884000 31.151511 43.906250 16397 2 0.000000 1 2.500000 30.996000 29.825915 47.418750 -16398 2 0.000000 -1.000000 2.500000 30.996000 29.825915 47.418750 +16398 2 0.000000 -1 2.500000 30.996000 29.825915 47.418750 16399 2 0.000000 1 2.500000 33.292000 25.849126 47.418750 16400 2 0.000000 -1 2.500000 33.292000 25.849126 47.418750 16401 2 0.000000 1 2.500000 35.588000 27.174722 50.931250 @@ -16419,7 +16419,7 @@ Atoms 16403 2 0.000000 1 2.500000 37.884000 31.151511 50.931250 16404 2 0.000000 -1 2.500000 37.884000 31.151511 50.931250 16405 2 0.000000 1 2.500000 30.996000 29.825915 54.443750 -16406 2 0.000000 -1.000000 2.500000 30.996000 29.825915 54.443750 +16406 2 0.000000 -1 2.500000 30.996000 29.825915 54.443750 16407 2 0.000000 1 2.500000 33.292000 25.849126 54.443750 16408 2 0.000000 -1 2.500000 33.292000 25.849126 54.443750 16409 2 0.000000 1 2.500000 35.588000 27.174722 57.956250 @@ -16427,7 +16427,7 @@ Atoms 16411 2 0.000000 1 2.500000 37.884000 31.151511 57.956250 16412 2 0.000000 -1 2.500000 37.884000 31.151511 57.956250 16413 2 0.000000 1 2.500000 30.996000 29.825915 61.468750 -16414 2 0.000000 -1.000000 2.500000 30.996000 29.825915 61.468750 +16414 2 0.000000 -1 2.500000 30.996000 29.825915 61.468750 16415 2 0.000000 1 2.500000 33.292000 25.849126 61.468750 16416 2 0.000000 -1 2.500000 33.292000 25.849126 61.468750 16417 2 0.000000 1 2.500000 35.588000 35.128300 1.756250 @@ -16435,7 +16435,7 @@ Atoms 16419 2 0.000000 1 2.500000 37.884000 39.105088 1.756250 16420 2 0.000000 -1 2.500000 37.884000 39.105088 1.756250 16421 2 0.000000 1 2.500000 30.996000 37.779492 5.268750 -16422 2 0.000000 -1.000000 2.500000 30.996000 37.779492 5.268750 +16422 2 0.000000 -1 2.500000 30.996000 37.779492 5.268750 16423 2 0.000000 1 2.500000 33.292000 33.802704 5.268750 16424 2 0.000000 -1 2.500000 33.292000 33.802704 5.268750 16425 2 0.000000 1 2.500000 35.588000 35.128300 8.781250 @@ -16443,7 +16443,7 @@ Atoms 16427 2 0.000000 1 2.500000 37.884000 39.105088 8.781250 16428 2 0.000000 -1 2.500000 37.884000 39.105088 8.781250 16429 2 0.000000 1 2.500000 30.996000 37.779492 12.293750 -16430 2 0.000000 -1.000000 2.500000 30.996000 37.779492 12.293750 +16430 2 0.000000 -1 2.500000 30.996000 37.779492 12.293750 16431 2 0.000000 1 2.500000 33.292000 33.802704 12.293750 16432 2 0.000000 -1 2.500000 33.292000 33.802704 12.293750 16433 2 0.000000 1 2.500000 35.588000 35.128300 15.806250 @@ -16451,7 +16451,7 @@ Atoms 16435 2 0.000000 1 2.500000 37.884000 39.105088 15.806250 16436 2 0.000000 -1 2.500000 37.884000 39.105088 15.806250 16437 2 0.000000 1 2.500000 30.996000 37.779492 19.318750 -16438 2 0.000000 -1.000000 2.500000 30.996000 37.779492 19.318750 +16438 2 0.000000 -1 2.500000 30.996000 37.779492 19.318750 16439 2 0.000000 1 2.500000 33.292000 33.802704 19.318750 16440 2 0.000000 -1 2.500000 33.292000 33.802704 19.318750 16441 2 0.000000 1 2.500000 35.588000 35.128300 22.831250 @@ -16459,7 +16459,7 @@ Atoms 16443 2 0.000000 1 2.500000 37.884000 39.105088 22.831250 16444 2 0.000000 -1 2.500000 37.884000 39.105088 22.831250 16445 2 0.000000 1 2.500000 30.996000 37.779492 26.343750 -16446 2 0.000000 -1.000000 2.500000 30.996000 37.779492 26.343750 +16446 2 0.000000 -1 2.500000 30.996000 37.779492 26.343750 16447 2 0.000000 1 2.500000 33.292000 33.802704 26.343750 16448 2 0.000000 -1 2.500000 33.292000 33.802704 26.343750 16449 2 0.000000 1 2.500000 35.588000 35.128300 29.856250 @@ -16467,7 +16467,7 @@ Atoms 16451 2 0.000000 1 2.500000 37.884000 39.105088 29.856250 16452 2 0.000000 -1 2.500000 37.884000 39.105088 29.856250 16453 2 0.000000 1 2.500000 30.996000 37.779492 33.368750 -16454 2 0.000000 -1.000000 2.500000 30.996000 37.779492 33.368750 +16454 2 0.000000 -1 2.500000 30.996000 37.779492 33.368750 16455 2 0.000000 1 2.500000 33.292000 33.802704 33.368750 16456 2 0.000000 -1 2.500000 33.292000 33.802704 33.368750 16457 2 0.000000 1 2.500000 35.588000 35.128300 36.881250 @@ -16475,7 +16475,7 @@ Atoms 16459 2 0.000000 1 2.500000 37.884000 39.105088 36.881250 16460 2 0.000000 -1 2.500000 37.884000 39.105088 36.881250 16461 2 0.000000 1 2.500000 30.996000 37.779492 40.393750 -16462 2 0.000000 -1.000000 2.500000 30.996000 37.779492 40.393750 +16462 2 0.000000 -1 2.500000 30.996000 37.779492 40.393750 16463 2 0.000000 1 2.500000 33.292000 33.802704 40.393750 16464 2 0.000000 -1 2.500000 33.292000 33.802704 40.393750 16465 2 0.000000 1 2.500000 35.588000 35.128300 43.906250 @@ -16483,7 +16483,7 @@ Atoms 16467 2 0.000000 1 2.500000 37.884000 39.105088 43.906250 16468 2 0.000000 -1 2.500000 37.884000 39.105088 43.906250 16469 2 0.000000 1 2.500000 30.996000 37.779492 47.418750 -16470 2 0.000000 -1.000000 2.500000 30.996000 37.779492 47.418750 +16470 2 0.000000 -1 2.500000 30.996000 37.779492 47.418750 16471 2 0.000000 1 2.500000 33.292000 33.802704 47.418750 16472 2 0.000000 -1 2.500000 33.292000 33.802704 47.418750 16473 2 0.000000 1 2.500000 35.588000 35.128300 50.931250 @@ -16491,7 +16491,7 @@ Atoms 16475 2 0.000000 1 2.500000 37.884000 39.105088 50.931250 16476 2 0.000000 -1 2.500000 37.884000 39.105088 50.931250 16477 2 0.000000 1 2.500000 30.996000 37.779492 54.443750 -16478 2 0.000000 -1.000000 2.500000 30.996000 37.779492 54.443750 +16478 2 0.000000 -1 2.500000 30.996000 37.779492 54.443750 16479 2 0.000000 1 2.500000 33.292000 33.802704 54.443750 16480 2 0.000000 -1 2.500000 33.292000 33.802704 54.443750 16481 2 0.000000 1 2.500000 35.588000 35.128300 57.956250 @@ -16499,7 +16499,7 @@ Atoms 16483 2 0.000000 1 2.500000 37.884000 39.105088 57.956250 16484 2 0.000000 -1 2.500000 37.884000 39.105088 57.956250 16485 2 0.000000 1 2.500000 30.996000 37.779492 61.468750 -16486 2 0.000000 -1.000000 2.500000 30.996000 37.779492 61.468750 +16486 2 0.000000 -1 2.500000 30.996000 37.779492 61.468750 16487 2 0.000000 1 2.500000 33.292000 33.802704 61.468750 16488 2 0.000000 -1 2.500000 33.292000 33.802704 61.468750 16489 2 0.000000 1 2.500000 35.588000 43.081877 1.756250 @@ -16507,7 +16507,7 @@ Atoms 16491 2 0.000000 1 2.500000 37.884000 47.058666 1.756250 16492 2 0.000000 -1 2.500000 37.884000 47.058666 1.756250 16493 2 0.000000 1 2.500000 30.996000 45.733070 5.268750 -16494 2 0.000000 -1.000000 2.500000 30.996000 45.733070 5.268750 +16494 2 0.000000 -1 2.500000 30.996000 45.733070 5.268750 16495 2 0.000000 1 2.500000 33.292000 41.756281 5.268750 16496 2 0.000000 -1 2.500000 33.292000 41.756281 5.268750 16497 2 0.000000 1 2.500000 35.588000 43.081877 8.781250 @@ -16515,7 +16515,7 @@ Atoms 16499 2 0.000000 1 2.500000 37.884000 47.058666 8.781250 16500 2 0.000000 -1 2.500000 37.884000 47.058666 8.781250 16501 2 0.000000 1 2.500000 30.996000 45.733070 12.293750 -16502 2 0.000000 -1.000000 2.500000 30.996000 45.733070 12.293750 +16502 2 0.000000 -1 2.500000 30.996000 45.733070 12.293750 16503 2 0.000000 1 2.500000 33.292000 41.756281 12.293750 16504 2 0.000000 -1 2.500000 33.292000 41.756281 12.293750 16505 2 0.000000 1 2.500000 35.588000 43.081877 15.806250 @@ -16523,7 +16523,7 @@ Atoms 16507 2 0.000000 1 2.500000 37.884000 47.058666 15.806250 16508 2 0.000000 -1 2.500000 37.884000 47.058666 15.806250 16509 2 0.000000 1 2.500000 30.996000 45.733070 19.318750 -16510 2 0.000000 -1.000000 2.500000 30.996000 45.733070 19.318750 +16510 2 0.000000 -1 2.500000 30.996000 45.733070 19.318750 16511 2 0.000000 1 2.500000 33.292000 41.756281 19.318750 16512 2 0.000000 -1 2.500000 33.292000 41.756281 19.318750 16513 2 0.000000 1 2.500000 35.588000 43.081877 22.831250 @@ -16531,7 +16531,7 @@ Atoms 16515 2 0.000000 1 2.500000 37.884000 47.058666 22.831250 16516 2 0.000000 -1 2.500000 37.884000 47.058666 22.831250 16517 2 0.000000 1 2.500000 30.996000 45.733070 26.343750 -16518 2 0.000000 -1.000000 2.500000 30.996000 45.733070 26.343750 +16518 2 0.000000 -1 2.500000 30.996000 45.733070 26.343750 16519 2 0.000000 1 2.500000 33.292000 41.756281 26.343750 16520 2 0.000000 -1 2.500000 33.292000 41.756281 26.343750 16521 2 0.000000 1 2.500000 35.588000 43.081877 29.856250 @@ -16539,7 +16539,7 @@ Atoms 16523 2 0.000000 1 2.500000 37.884000 47.058666 29.856250 16524 2 0.000000 -1 2.500000 37.884000 47.058666 29.856250 16525 2 0.000000 1 2.500000 30.996000 45.733070 33.368750 -16526 2 0.000000 -1.000000 2.500000 30.996000 45.733070 33.368750 +16526 2 0.000000 -1 2.500000 30.996000 45.733070 33.368750 16527 2 0.000000 1 2.500000 33.292000 41.756281 33.368750 16528 2 0.000000 -1 2.500000 33.292000 41.756281 33.368750 16529 2 0.000000 1 2.500000 35.588000 43.081877 36.881250 @@ -16547,7 +16547,7 @@ Atoms 16531 2 0.000000 1 2.500000 37.884000 47.058666 36.881250 16532 2 0.000000 -1 2.500000 37.884000 47.058666 36.881250 16533 2 0.000000 1 2.500000 30.996000 45.733070 40.393750 -16534 2 0.000000 -1.000000 2.500000 30.996000 45.733070 40.393750 +16534 2 0.000000 -1 2.500000 30.996000 45.733070 40.393750 16535 2 0.000000 1 2.500000 33.292000 41.756281 40.393750 16536 2 0.000000 -1 2.500000 33.292000 41.756281 40.393750 16537 2 0.000000 1 2.500000 35.588000 43.081877 43.906250 @@ -16555,7 +16555,7 @@ Atoms 16539 2 0.000000 1 2.500000 37.884000 47.058666 43.906250 16540 2 0.000000 -1 2.500000 37.884000 47.058666 43.906250 16541 2 0.000000 1 2.500000 30.996000 45.733070 47.418750 -16542 2 0.000000 -1.000000 2.500000 30.996000 45.733070 47.418750 +16542 2 0.000000 -1 2.500000 30.996000 45.733070 47.418750 16543 2 0.000000 1 2.500000 33.292000 41.756281 47.418750 16544 2 0.000000 -1 2.500000 33.292000 41.756281 47.418750 16545 2 0.000000 1 2.500000 35.588000 43.081877 50.931250 @@ -16563,7 +16563,7 @@ Atoms 16547 2 0.000000 1 2.500000 37.884000 47.058666 50.931250 16548 2 0.000000 -1 2.500000 37.884000 47.058666 50.931250 16549 2 0.000000 1 2.500000 30.996000 45.733070 54.443750 -16550 2 0.000000 -1.000000 2.500000 30.996000 45.733070 54.443750 +16550 2 0.000000 -1 2.500000 30.996000 45.733070 54.443750 16551 2 0.000000 1 2.500000 33.292000 41.756281 54.443750 16552 2 0.000000 -1 2.500000 33.292000 41.756281 54.443750 16553 2 0.000000 1 2.500000 35.588000 43.081877 57.956250 @@ -16571,7 +16571,7 @@ Atoms 16555 2 0.000000 1 2.500000 37.884000 47.058666 57.956250 16556 2 0.000000 -1 2.500000 37.884000 47.058666 57.956250 16557 2 0.000000 1 2.500000 30.996000 45.733070 61.468750 -16558 2 0.000000 -1.000000 2.500000 30.996000 45.733070 61.468750 +16558 2 0.000000 -1 2.500000 30.996000 45.733070 61.468750 16559 2 0.000000 1 2.500000 33.292000 41.756281 61.468750 16560 2 0.000000 -1 2.500000 33.292000 41.756281 61.468750 16561 2 0.000000 1 2.500000 35.588000 51.035454 1.756250 @@ -16579,7 +16579,7 @@ Atoms 16563 2 0.000000 1 2.500000 37.884000 55.012243 1.756250 16564 2 0.000000 -1 2.500000 37.884000 55.012243 1.756250 16565 2 0.000000 1 2.500000 30.996000 53.686647 5.268750 -16566 2 0.000000 -1.000000 2.500000 30.996000 53.686647 5.268750 +16566 2 0.000000 -1 2.500000 30.996000 53.686647 5.268750 16567 2 0.000000 1 2.500000 33.292000 49.709858 5.268750 16568 2 0.000000 -1 2.500000 33.292000 49.709858 5.268750 16569 2 0.000000 1 2.500000 35.588000 51.035454 8.781250 @@ -16587,7 +16587,7 @@ Atoms 16571 2 0.000000 1 2.500000 37.884000 55.012243 8.781250 16572 2 0.000000 -1 2.500000 37.884000 55.012243 8.781250 16573 2 0.000000 1 2.500000 30.996000 53.686647 12.293750 -16574 2 0.000000 -1.000000 2.500000 30.996000 53.686647 12.293750 +16574 2 0.000000 -1 2.500000 30.996000 53.686647 12.293750 16575 2 0.000000 1 2.500000 33.292000 49.709858 12.293750 16576 2 0.000000 -1 2.500000 33.292000 49.709858 12.293750 16577 2 0.000000 1 2.500000 35.588000 51.035454 15.806250 @@ -16595,7 +16595,7 @@ Atoms 16579 2 0.000000 1 2.500000 37.884000 55.012243 15.806250 16580 2 0.000000 -1 2.500000 37.884000 55.012243 15.806250 16581 2 0.000000 1 2.500000 30.996000 53.686647 19.318750 -16582 2 0.000000 -1.000000 2.500000 30.996000 53.686647 19.318750 +16582 2 0.000000 -1 2.500000 30.996000 53.686647 19.318750 16583 2 0.000000 1 2.500000 33.292000 49.709858 19.318750 16584 2 0.000000 -1 2.500000 33.292000 49.709858 19.318750 16585 2 0.000000 1 2.500000 35.588000 51.035454 22.831250 @@ -16603,7 +16603,7 @@ Atoms 16587 2 0.000000 1 2.500000 37.884000 55.012243 22.831250 16588 2 0.000000 -1 2.500000 37.884000 55.012243 22.831250 16589 2 0.000000 1 2.500000 30.996000 53.686647 26.343750 -16590 2 0.000000 -1.000000 2.500000 30.996000 53.686647 26.343750 +16590 2 0.000000 -1 2.500000 30.996000 53.686647 26.343750 16591 2 0.000000 1 2.500000 33.292000 49.709858 26.343750 16592 2 0.000000 -1 2.500000 33.292000 49.709858 26.343750 16593 2 0.000000 1 2.500000 35.588000 51.035454 29.856250 @@ -16611,7 +16611,7 @@ Atoms 16595 2 0.000000 1 2.500000 37.884000 55.012243 29.856250 16596 2 0.000000 -1 2.500000 37.884000 55.012243 29.856250 16597 2 0.000000 1 2.500000 30.996000 53.686647 33.368750 -16598 2 0.000000 -1.000000 2.500000 30.996000 53.686647 33.368750 +16598 2 0.000000 -1 2.500000 30.996000 53.686647 33.368750 16599 2 0.000000 1 2.500000 33.292000 49.709858 33.368750 16600 2 0.000000 -1 2.500000 33.292000 49.709858 33.368750 16601 2 0.000000 1 2.500000 35.588000 51.035454 36.881250 @@ -16619,7 +16619,7 @@ Atoms 16603 2 0.000000 1 2.500000 37.884000 55.012243 36.881250 16604 2 0.000000 -1 2.500000 37.884000 55.012243 36.881250 16605 2 0.000000 1 2.500000 30.996000 53.686647 40.393750 -16606 2 0.000000 -1.000000 2.500000 30.996000 53.686647 40.393750 +16606 2 0.000000 -1 2.500000 30.996000 53.686647 40.393750 16607 2 0.000000 1 2.500000 33.292000 49.709858 40.393750 16608 2 0.000000 -1 2.500000 33.292000 49.709858 40.393750 16609 2 0.000000 1 2.500000 35.588000 51.035454 43.906250 @@ -16627,7 +16627,7 @@ Atoms 16611 2 0.000000 1 2.500000 37.884000 55.012243 43.906250 16612 2 0.000000 -1 2.500000 37.884000 55.012243 43.906250 16613 2 0.000000 1 2.500000 30.996000 53.686647 47.418750 -16614 2 0.000000 -1.000000 2.500000 30.996000 53.686647 47.418750 +16614 2 0.000000 -1 2.500000 30.996000 53.686647 47.418750 16615 2 0.000000 1 2.500000 33.292000 49.709858 47.418750 16616 2 0.000000 -1 2.500000 33.292000 49.709858 47.418750 16617 2 0.000000 1 2.500000 35.588000 51.035454 50.931250 @@ -16635,7 +16635,7 @@ Atoms 16619 2 0.000000 1 2.500000 37.884000 55.012243 50.931250 16620 2 0.000000 -1 2.500000 37.884000 55.012243 50.931250 16621 2 0.000000 1 2.500000 30.996000 53.686647 54.443750 -16622 2 0.000000 -1.000000 2.500000 30.996000 53.686647 54.443750 +16622 2 0.000000 -1 2.500000 30.996000 53.686647 54.443750 16623 2 0.000000 1 2.500000 33.292000 49.709858 54.443750 16624 2 0.000000 -1 2.500000 33.292000 49.709858 54.443750 16625 2 0.000000 1 2.500000 35.588000 51.035454 57.956250 @@ -16643,7 +16643,7 @@ Atoms 16627 2 0.000000 1 2.500000 37.884000 55.012243 57.956250 16628 2 0.000000 -1 2.500000 37.884000 55.012243 57.956250 16629 2 0.000000 1 2.500000 30.996000 53.686647 61.468750 -16630 2 0.000000 -1.000000 2.500000 30.996000 53.686647 61.468750 +16630 2 0.000000 -1 2.500000 30.996000 53.686647 61.468750 16631 2 0.000000 1 2.500000 33.292000 49.709858 61.468750 16632 2 0.000000 -1 2.500000 33.292000 49.709858 61.468750 16633 2 0.000000 1 2.500000 35.588000 58.989032 1.756250 @@ -16651,7 +16651,7 @@ Atoms 16635 2 0.000000 1 2.500000 37.884000 62.965820 1.756250 16636 2 0.000000 -1 2.500000 37.884000 62.965820 1.756250 16637 2 0.000000 1 2.500000 30.996000 61.640224 5.268750 -16638 2 0.000000 -1.000000 2.500000 30.996000 61.640224 5.268750 +16638 2 0.000000 -1 2.500000 30.996000 61.640224 5.268750 16639 2 0.000000 1 2.500000 33.292000 57.663435 5.268750 16640 2 0.000000 -1 2.500000 33.292000 57.663435 5.268750 16641 2 0.000000 1 2.500000 35.588000 58.989032 8.781250 @@ -16659,7 +16659,7 @@ Atoms 16643 2 0.000000 1 2.500000 37.884000 62.965820 8.781250 16644 2 0.000000 -1 2.500000 37.884000 62.965820 8.781250 16645 2 0.000000 1 2.500000 30.996000 61.640224 12.293750 -16646 2 0.000000 -1.000000 2.500000 30.996000 61.640224 12.293750 +16646 2 0.000000 -1 2.500000 30.996000 61.640224 12.293750 16647 2 0.000000 1 2.500000 33.292000 57.663435 12.293750 16648 2 0.000000 -1 2.500000 33.292000 57.663435 12.293750 16649 2 0.000000 1 2.500000 35.588000 58.989032 15.806250 @@ -16667,7 +16667,7 @@ Atoms 16651 2 0.000000 1 2.500000 37.884000 62.965820 15.806250 16652 2 0.000000 -1 2.500000 37.884000 62.965820 15.806250 16653 2 0.000000 1 2.500000 30.996000 61.640224 19.318750 -16654 2 0.000000 -1.000000 2.500000 30.996000 61.640224 19.318750 +16654 2 0.000000 -1 2.500000 30.996000 61.640224 19.318750 16655 2 0.000000 1 2.500000 33.292000 57.663435 19.318750 16656 2 0.000000 -1 2.500000 33.292000 57.663435 19.318750 16657 2 0.000000 1 2.500000 35.588000 58.989032 22.831250 @@ -16675,7 +16675,7 @@ Atoms 16659 2 0.000000 1 2.500000 37.884000 62.965820 22.831250 16660 2 0.000000 -1 2.500000 37.884000 62.965820 22.831250 16661 2 0.000000 1 2.500000 30.996000 61.640224 26.343750 -16662 2 0.000000 -1.000000 2.500000 30.996000 61.640224 26.343750 +16662 2 0.000000 -1 2.500000 30.996000 61.640224 26.343750 16663 2 0.000000 1 2.500000 33.292000 57.663435 26.343750 16664 2 0.000000 -1 2.500000 33.292000 57.663435 26.343750 16665 2 0.000000 1 2.500000 35.588000 58.989032 29.856250 @@ -16683,7 +16683,7 @@ Atoms 16667 2 0.000000 1 2.500000 37.884000 62.965820 29.856250 16668 2 0.000000 -1 2.500000 37.884000 62.965820 29.856250 16669 2 0.000000 1 2.500000 30.996000 61.640224 33.368750 -16670 2 0.000000 -1.000000 2.500000 30.996000 61.640224 33.368750 +16670 2 0.000000 -1 2.500000 30.996000 61.640224 33.368750 16671 2 0.000000 1 2.500000 33.292000 57.663435 33.368750 16672 2 0.000000 -1 2.500000 33.292000 57.663435 33.368750 16673 2 0.000000 1 2.500000 35.588000 58.989032 36.881250 @@ -16691,7 +16691,7 @@ Atoms 16675 2 0.000000 1 2.500000 37.884000 62.965820 36.881250 16676 2 0.000000 -1 2.500000 37.884000 62.965820 36.881250 16677 2 0.000000 1 2.500000 30.996000 61.640224 40.393750 -16678 2 0.000000 -1.000000 2.500000 30.996000 61.640224 40.393750 +16678 2 0.000000 -1 2.500000 30.996000 61.640224 40.393750 16679 2 0.000000 1 2.500000 33.292000 57.663435 40.393750 16680 2 0.000000 -1 2.500000 33.292000 57.663435 40.393750 16681 2 0.000000 1 2.500000 35.588000 58.989032 43.906250 @@ -16699,7 +16699,7 @@ Atoms 16683 2 0.000000 1 2.500000 37.884000 62.965820 43.906250 16684 2 0.000000 -1 2.500000 37.884000 62.965820 43.906250 16685 2 0.000000 1 2.500000 30.996000 61.640224 47.418750 -16686 2 0.000000 -1.000000 2.500000 30.996000 61.640224 47.418750 +16686 2 0.000000 -1 2.500000 30.996000 61.640224 47.418750 16687 2 0.000000 1 2.500000 33.292000 57.663435 47.418750 16688 2 0.000000 -1 2.500000 33.292000 57.663435 47.418750 16689 2 0.000000 1 2.500000 35.588000 58.989032 50.931250 @@ -16707,7 +16707,7 @@ Atoms 16691 2 0.000000 1 2.500000 37.884000 62.965820 50.931250 16692 2 0.000000 -1 2.500000 37.884000 62.965820 50.931250 16693 2 0.000000 1 2.500000 30.996000 61.640224 54.443750 -16694 2 0.000000 -1.000000 2.500000 30.996000 61.640224 54.443750 +16694 2 0.000000 -1 2.500000 30.996000 61.640224 54.443750 16695 2 0.000000 1 2.500000 33.292000 57.663435 54.443750 16696 2 0.000000 -1 2.500000 33.292000 57.663435 54.443750 16697 2 0.000000 1 2.500000 35.588000 58.989032 57.956250 @@ -16715,7 +16715,7 @@ Atoms 16699 2 0.000000 1 2.500000 37.884000 62.965820 57.956250 16700 2 0.000000 -1 2.500000 37.884000 62.965820 57.956250 16701 2 0.000000 1 2.500000 30.996000 61.640224 61.468750 -16702 2 0.000000 -1.000000 2.500000 30.996000 61.640224 61.468750 +16702 2 0.000000 -1 2.500000 30.996000 61.640224 61.468750 16703 2 0.000000 1 2.500000 33.292000 57.663435 61.468750 16704 2 0.000000 -1 2.500000 33.292000 57.663435 61.468750 16705 2 0.000000 1 2.500000 40.180000 3.313991 1.756250 @@ -16723,7 +16723,7 @@ Atoms 16707 2 0.000000 1 2.500000 42.476000 7.290779 1.756250 16708 2 0.000000 -1 2.500000 42.476000 7.290779 1.756250 16709 2 0.000000 1 2.500000 35.588000 5.965183 5.268750 -16710 2 0.000000 -1.000000 2.500000 35.588000 5.965183 5.268750 +16710 2 0.000000 -1 2.500000 35.588000 5.965183 5.268750 16711 2 0.000000 1 2.500000 37.884000 1.988394 5.268750 16712 2 0.000000 -1 2.500000 37.884000 1.988394 5.268750 16713 2 0.000000 1 2.500000 40.180000 3.313991 8.781250 @@ -16731,7 +16731,7 @@ Atoms 16715 2 0.000000 1 2.500000 42.476000 7.290779 8.781250 16716 2 0.000000 -1 2.500000 42.476000 7.290779 8.781250 16717 2 0.000000 1 2.500000 35.588000 5.965183 12.293750 -16718 2 0.000000 -1.000000 2.500000 35.588000 5.965183 12.293750 +16718 2 0.000000 -1 2.500000 35.588000 5.965183 12.293750 16719 2 0.000000 1 2.500000 37.884000 1.988394 12.293750 16720 2 0.000000 -1 2.500000 37.884000 1.988394 12.293750 16721 2 0.000000 1 2.500000 40.180000 3.313991 15.806250 @@ -16739,7 +16739,7 @@ Atoms 16723 2 0.000000 1 2.500000 42.476000 7.290779 15.806250 16724 2 0.000000 -1 2.500000 42.476000 7.290779 15.806250 16725 2 0.000000 1 2.500000 35.588000 5.965183 19.318750 -16726 2 0.000000 -1.000000 2.500000 35.588000 5.965183 19.318750 +16726 2 0.000000 -1 2.500000 35.588000 5.965183 19.318750 16727 2 0.000000 1 2.500000 37.884000 1.988394 19.318750 16728 2 0.000000 -1 2.500000 37.884000 1.988394 19.318750 16729 2 0.000000 1 2.500000 40.180000 3.313991 22.831250 @@ -16747,7 +16747,7 @@ Atoms 16731 2 0.000000 1 2.500000 42.476000 7.290779 22.831250 16732 2 0.000000 -1 2.500000 42.476000 7.290779 22.831250 16733 2 0.000000 1 2.500000 35.588000 5.965183 26.343750 -16734 2 0.000000 -1.000000 2.500000 35.588000 5.965183 26.343750 +16734 2 0.000000 -1 2.500000 35.588000 5.965183 26.343750 16735 2 0.000000 1 2.500000 37.884000 1.988394 26.343750 16736 2 0.000000 -1 2.500000 37.884000 1.988394 26.343750 16737 2 0.000000 1 2.500000 40.180000 3.313991 29.856250 @@ -16755,7 +16755,7 @@ Atoms 16739 2 0.000000 1 2.500000 42.476000 7.290779 29.856250 16740 2 0.000000 -1 2.500000 42.476000 7.290779 29.856250 16741 2 0.000000 1 2.500000 35.588000 5.965183 33.368750 -16742 2 0.000000 -1.000000 2.500000 35.588000 5.965183 33.368750 +16742 2 0.000000 -1 2.500000 35.588000 5.965183 33.368750 16743 2 0.000000 1 2.500000 37.884000 1.988394 33.368750 16744 2 0.000000 -1 2.500000 37.884000 1.988394 33.368750 16745 2 0.000000 1 2.500000 40.180000 3.313991 36.881250 @@ -16763,7 +16763,7 @@ Atoms 16747 2 0.000000 1 2.500000 42.476000 7.290779 36.881250 16748 2 0.000000 -1 2.500000 42.476000 7.290779 36.881250 16749 2 0.000000 1 2.500000 35.588000 5.965183 40.393750 -16750 2 0.000000 -1.000000 2.500000 35.588000 5.965183 40.393750 +16750 2 0.000000 -1 2.500000 35.588000 5.965183 40.393750 16751 2 0.000000 1 2.500000 37.884000 1.988394 40.393750 16752 2 0.000000 -1 2.500000 37.884000 1.988394 40.393750 16753 2 0.000000 1 2.500000 40.180000 3.313991 43.906250 @@ -16771,7 +16771,7 @@ Atoms 16755 2 0.000000 1 2.500000 42.476000 7.290779 43.906250 16756 2 0.000000 -1 2.500000 42.476000 7.290779 43.906250 16757 2 0.000000 1 2.500000 35.588000 5.965183 47.418750 -16758 2 0.000000 -1.000000 2.500000 35.588000 5.965183 47.418750 +16758 2 0.000000 -1 2.500000 35.588000 5.965183 47.418750 16759 2 0.000000 1 2.500000 37.884000 1.988394 47.418750 16760 2 0.000000 -1 2.500000 37.884000 1.988394 47.418750 16761 2 0.000000 1 2.500000 40.180000 3.313991 50.931250 @@ -16779,7 +16779,7 @@ Atoms 16763 2 0.000000 1 2.500000 42.476000 7.290779 50.931250 16764 2 0.000000 -1 2.500000 42.476000 7.290779 50.931250 16765 2 0.000000 1 2.500000 35.588000 5.965183 54.443750 -16766 2 0.000000 -1.000000 2.500000 35.588000 5.965183 54.443750 +16766 2 0.000000 -1 2.500000 35.588000 5.965183 54.443750 16767 2 0.000000 1 2.500000 37.884000 1.988394 54.443750 16768 2 0.000000 -1 2.500000 37.884000 1.988394 54.443750 16769 2 0.000000 1 2.500000 40.180000 3.313991 57.956250 @@ -16787,7 +16787,7 @@ Atoms 16771 2 0.000000 1 2.500000 42.476000 7.290779 57.956250 16772 2 0.000000 -1 2.500000 42.476000 7.290779 57.956250 16773 2 0.000000 1 2.500000 35.588000 5.965183 61.468750 -16774 2 0.000000 -1.000000 2.500000 35.588000 5.965183 61.468750 +16774 2 0.000000 -1 2.500000 35.588000 5.965183 61.468750 16775 2 0.000000 1 2.500000 37.884000 1.988394 61.468750 16776 2 0.000000 -1 2.500000 37.884000 1.988394 61.468750 16777 2 0.000000 1 2.500000 40.180000 11.267568 1.756250 @@ -16795,7 +16795,7 @@ Atoms 16779 2 0.000000 1 2.500000 42.476000 15.244357 1.756250 16780 2 0.000000 -1 2.500000 42.476000 15.244357 1.756250 16781 2 0.000000 1 2.500000 35.588000 13.918760 5.268750 -16782 2 0.000000 -1.000000 2.500000 35.588000 13.918760 5.268750 +16782 2 0.000000 -1 2.500000 35.588000 13.918760 5.268750 16783 2 0.000000 1 2.500000 37.884000 9.941972 5.268750 16784 2 0.000000 -1 2.500000 37.884000 9.941972 5.268750 16785 2 0.000000 1 2.500000 40.180000 11.267568 8.781250 @@ -16803,7 +16803,7 @@ Atoms 16787 2 0.000000 1 2.500000 42.476000 15.244357 8.781250 16788 2 0.000000 -1 2.500000 42.476000 15.244357 8.781250 16789 2 0.000000 1 2.500000 35.588000 13.918760 12.293750 -16790 2 0.000000 -1.000000 2.500000 35.588000 13.918760 12.293750 +16790 2 0.000000 -1 2.500000 35.588000 13.918760 12.293750 16791 2 0.000000 1 2.500000 37.884000 9.941972 12.293750 16792 2 0.000000 -1 2.500000 37.884000 9.941972 12.293750 16793 2 0.000000 1 2.500000 40.180000 11.267568 15.806250 @@ -16811,7 +16811,7 @@ Atoms 16795 2 0.000000 1 2.500000 42.476000 15.244357 15.806250 16796 2 0.000000 -1 2.500000 42.476000 15.244357 15.806250 16797 2 0.000000 1 2.500000 35.588000 13.918760 19.318750 -16798 2 0.000000 -1.000000 2.500000 35.588000 13.918760 19.318750 +16798 2 0.000000 -1 2.500000 35.588000 13.918760 19.318750 16799 2 0.000000 1 2.500000 37.884000 9.941972 19.318750 16800 2 0.000000 -1 2.500000 37.884000 9.941972 19.318750 16801 2 0.000000 1 2.500000 40.180000 11.267568 22.831250 @@ -16819,7 +16819,7 @@ Atoms 16803 2 0.000000 1 2.500000 42.476000 15.244357 22.831250 16804 2 0.000000 -1 2.500000 42.476000 15.244357 22.831250 16805 2 0.000000 1 2.500000 35.588000 13.918760 26.343750 -16806 2 0.000000 -1.000000 2.500000 35.588000 13.918760 26.343750 +16806 2 0.000000 -1 2.500000 35.588000 13.918760 26.343750 16807 2 0.000000 1 2.500000 37.884000 9.941972 26.343750 16808 2 0.000000 -1 2.500000 37.884000 9.941972 26.343750 16809 2 0.000000 1 2.500000 40.180000 11.267568 29.856250 @@ -16827,7 +16827,7 @@ Atoms 16811 2 0.000000 1 2.500000 42.476000 15.244357 29.856250 16812 2 0.000000 -1 2.500000 42.476000 15.244357 29.856250 16813 2 0.000000 1 2.500000 35.588000 13.918760 33.368750 -16814 2 0.000000 -1.000000 2.500000 35.588000 13.918760 33.368750 +16814 2 0.000000 -1 2.500000 35.588000 13.918760 33.368750 16815 2 0.000000 1 2.500000 37.884000 9.941972 33.368750 16816 2 0.000000 -1 2.500000 37.884000 9.941972 33.368750 16817 2 0.000000 1 2.500000 40.180000 11.267568 36.881250 @@ -16835,7 +16835,7 @@ Atoms 16819 2 0.000000 1 2.500000 42.476000 15.244357 36.881250 16820 2 0.000000 -1 2.500000 42.476000 15.244357 36.881250 16821 2 0.000000 1 2.500000 35.588000 13.918760 40.393750 -16822 2 0.000000 -1.000000 2.500000 35.588000 13.918760 40.393750 +16822 2 0.000000 -1 2.500000 35.588000 13.918760 40.393750 16823 2 0.000000 1 2.500000 37.884000 9.941972 40.393750 16824 2 0.000000 -1 2.500000 37.884000 9.941972 40.393750 16825 2 0.000000 1 2.500000 40.180000 11.267568 43.906250 @@ -16843,7 +16843,7 @@ Atoms 16827 2 0.000000 1 2.500000 42.476000 15.244357 43.906250 16828 2 0.000000 -1 2.500000 42.476000 15.244357 43.906250 16829 2 0.000000 1 2.500000 35.588000 13.918760 47.418750 -16830 2 0.000000 -1.000000 2.500000 35.588000 13.918760 47.418750 +16830 2 0.000000 -1 2.500000 35.588000 13.918760 47.418750 16831 2 0.000000 1 2.500000 37.884000 9.941972 47.418750 16832 2 0.000000 -1 2.500000 37.884000 9.941972 47.418750 16833 2 0.000000 1 2.500000 40.180000 11.267568 50.931250 @@ -16851,7 +16851,7 @@ Atoms 16835 2 0.000000 1 2.500000 42.476000 15.244357 50.931250 16836 2 0.000000 -1 2.500000 42.476000 15.244357 50.931250 16837 2 0.000000 1 2.500000 35.588000 13.918760 54.443750 -16838 2 0.000000 -1.000000 2.500000 35.588000 13.918760 54.443750 +16838 2 0.000000 -1 2.500000 35.588000 13.918760 54.443750 16839 2 0.000000 1 2.500000 37.884000 9.941972 54.443750 16840 2 0.000000 -1 2.500000 37.884000 9.941972 54.443750 16841 2 0.000000 1 2.500000 40.180000 11.267568 57.956250 @@ -16859,7 +16859,7 @@ Atoms 16843 2 0.000000 1 2.500000 42.476000 15.244357 57.956250 16844 2 0.000000 -1 2.500000 42.476000 15.244357 57.956250 16845 2 0.000000 1 2.500000 35.588000 13.918760 61.468750 -16846 2 0.000000 -1.000000 2.500000 35.588000 13.918760 61.468750 +16846 2 0.000000 -1 2.500000 35.588000 13.918760 61.468750 16847 2 0.000000 1 2.500000 37.884000 9.941972 61.468750 16848 2 0.000000 -1 2.500000 37.884000 9.941972 61.468750 16849 2 0.000000 1 2.500000 40.180000 19.221145 1.756250 @@ -16867,7 +16867,7 @@ Atoms 16851 2 0.000000 1 2.500000 42.476000 23.197934 1.756250 16852 2 0.000000 -1 2.500000 42.476000 23.197934 1.756250 16853 2 0.000000 1 2.500000 35.588000 21.872338 5.268750 -16854 2 0.000000 -1.000000 2.500000 35.588000 21.872338 5.268750 +16854 2 0.000000 -1 2.500000 35.588000 21.872338 5.268750 16855 2 0.000000 1 2.500000 37.884000 17.895549 5.268750 16856 2 0.000000 -1 2.500000 37.884000 17.895549 5.268750 16857 2 0.000000 1 2.500000 40.180000 19.221145 8.781250 @@ -16875,7 +16875,7 @@ Atoms 16859 2 0.000000 1 2.500000 42.476000 23.197934 8.781250 16860 2 0.000000 -1 2.500000 42.476000 23.197934 8.781250 16861 2 0.000000 1 2.500000 35.588000 21.872338 12.293750 -16862 2 0.000000 -1.000000 2.500000 35.588000 21.872338 12.293750 +16862 2 0.000000 -1 2.500000 35.588000 21.872338 12.293750 16863 2 0.000000 1 2.500000 37.884000 17.895549 12.293750 16864 2 0.000000 -1 2.500000 37.884000 17.895549 12.293750 16865 2 0.000000 1 2.500000 40.180000 19.221145 15.806250 @@ -16883,7 +16883,7 @@ Atoms 16867 2 0.000000 1 2.500000 42.476000 23.197934 15.806250 16868 2 0.000000 -1 2.500000 42.476000 23.197934 15.806250 16869 2 0.000000 1 2.500000 35.588000 21.872338 19.318750 -16870 2 0.000000 -1.000000 2.500000 35.588000 21.872338 19.318750 +16870 2 0.000000 -1 2.500000 35.588000 21.872338 19.318750 16871 2 0.000000 1 2.500000 37.884000 17.895549 19.318750 16872 2 0.000000 -1 2.500000 37.884000 17.895549 19.318750 16873 2 0.000000 1 2.500000 40.180000 19.221145 22.831250 @@ -16891,7 +16891,7 @@ Atoms 16875 2 0.000000 1 2.500000 42.476000 23.197934 22.831250 16876 2 0.000000 -1 2.500000 42.476000 23.197934 22.831250 16877 2 0.000000 1 2.500000 35.588000 21.872338 26.343750 -16878 2 0.000000 -1.000000 2.500000 35.588000 21.872338 26.343750 +16878 2 0.000000 -1 2.500000 35.588000 21.872338 26.343750 16879 2 0.000000 1 2.500000 37.884000 17.895549 26.343750 16880 2 0.000000 -1 2.500000 37.884000 17.895549 26.343750 16881 2 0.000000 1 2.500000 40.180000 19.221145 29.856250 @@ -16899,7 +16899,7 @@ Atoms 16883 2 0.000000 1 2.500000 42.476000 23.197934 29.856250 16884 2 0.000000 -1 2.500000 42.476000 23.197934 29.856250 16885 2 0.000000 1 2.500000 35.588000 21.872338 33.368750 -16886 2 0.000000 -1.000000 2.500000 35.588000 21.872338 33.368750 +16886 2 0.000000 -1 2.500000 35.588000 21.872338 33.368750 16887 2 0.000000 1 2.500000 37.884000 17.895549 33.368750 16888 2 0.000000 -1 2.500000 37.884000 17.895549 33.368750 16889 2 0.000000 1 2.500000 40.180000 19.221145 36.881250 @@ -16907,7 +16907,7 @@ Atoms 16891 2 0.000000 1 2.500000 42.476000 23.197934 36.881250 16892 2 0.000000 -1 2.500000 42.476000 23.197934 36.881250 16893 2 0.000000 1 2.500000 35.588000 21.872338 40.393750 -16894 2 0.000000 -1.000000 2.500000 35.588000 21.872338 40.393750 +16894 2 0.000000 -1 2.500000 35.588000 21.872338 40.393750 16895 2 0.000000 1 2.500000 37.884000 17.895549 40.393750 16896 2 0.000000 -1 2.500000 37.884000 17.895549 40.393750 16897 2 0.000000 1 2.500000 40.180000 19.221145 43.906250 @@ -16915,7 +16915,7 @@ Atoms 16899 2 0.000000 1 2.500000 42.476000 23.197934 43.906250 16900 2 0.000000 -1 2.500000 42.476000 23.197934 43.906250 16901 2 0.000000 1 2.500000 35.588000 21.872338 47.418750 -16902 2 0.000000 -1.000000 2.500000 35.588000 21.872338 47.418750 +16902 2 0.000000 -1 2.500000 35.588000 21.872338 47.418750 16903 2 0.000000 1 2.500000 37.884000 17.895549 47.418750 16904 2 0.000000 -1 2.500000 37.884000 17.895549 47.418750 16905 2 0.000000 1 2.500000 40.180000 19.221145 50.931250 @@ -16923,7 +16923,7 @@ Atoms 16907 2 0.000000 1 2.500000 42.476000 23.197934 50.931250 16908 2 0.000000 -1 2.500000 42.476000 23.197934 50.931250 16909 2 0.000000 1 2.500000 35.588000 21.872338 54.443750 -16910 2 0.000000 -1.000000 2.500000 35.588000 21.872338 54.443750 +16910 2 0.000000 -1 2.500000 35.588000 21.872338 54.443750 16911 2 0.000000 1 2.500000 37.884000 17.895549 54.443750 16912 2 0.000000 -1 2.500000 37.884000 17.895549 54.443750 16913 2 0.000000 1 2.500000 40.180000 19.221145 57.956250 @@ -16931,7 +16931,7 @@ Atoms 16915 2 0.000000 1 2.500000 42.476000 23.197934 57.956250 16916 2 0.000000 -1 2.500000 42.476000 23.197934 57.956250 16917 2 0.000000 1 2.500000 35.588000 21.872338 61.468750 -16918 2 0.000000 -1.000000 2.500000 35.588000 21.872338 61.468750 +16918 2 0.000000 -1 2.500000 35.588000 21.872338 61.468750 16919 2 0.000000 1 2.500000 37.884000 17.895549 61.468750 16920 2 0.000000 -1 2.500000 37.884000 17.895549 61.468750 16921 2 0.000000 1 2.500000 40.180000 27.174722 1.756250 @@ -16939,7 +16939,7 @@ Atoms 16923 2 0.000000 1 2.500000 42.476000 31.151511 1.756250 16924 2 0.000000 -1 2.500000 42.476000 31.151511 1.756250 16925 2 0.000000 1 2.500000 35.588000 29.825915 5.268750 -16926 2 0.000000 -1.000000 2.500000 35.588000 29.825915 5.268750 +16926 2 0.000000 -1 2.500000 35.588000 29.825915 5.268750 16927 2 0.000000 1 2.500000 37.884000 25.849126 5.268750 16928 2 0.000000 -1 2.500000 37.884000 25.849126 5.268750 16929 2 0.000000 1 2.500000 40.180000 27.174722 8.781250 @@ -16947,7 +16947,7 @@ Atoms 16931 2 0.000000 1 2.500000 42.476000 31.151511 8.781250 16932 2 0.000000 -1 2.500000 42.476000 31.151511 8.781250 16933 2 0.000000 1 2.500000 35.588000 29.825915 12.293750 -16934 2 0.000000 -1.000000 2.500000 35.588000 29.825915 12.293750 +16934 2 0.000000 -1 2.500000 35.588000 29.825915 12.293750 16935 2 0.000000 1 2.500000 37.884000 25.849126 12.293750 16936 2 0.000000 -1 2.500000 37.884000 25.849126 12.293750 16937 2 0.000000 1 2.500000 40.180000 27.174722 15.806250 @@ -16955,7 +16955,7 @@ Atoms 16939 2 0.000000 1 2.500000 42.476000 31.151511 15.806250 16940 2 0.000000 -1 2.500000 42.476000 31.151511 15.806250 16941 2 0.000000 1 2.500000 35.588000 29.825915 19.318750 -16942 2 0.000000 -1.000000 2.500000 35.588000 29.825915 19.318750 +16942 2 0.000000 -1 2.500000 35.588000 29.825915 19.318750 16943 2 0.000000 1 2.500000 37.884000 25.849126 19.318750 16944 2 0.000000 -1 2.500000 37.884000 25.849126 19.318750 16945 2 0.000000 1 2.500000 40.180000 27.174722 22.831250 @@ -16963,7 +16963,7 @@ Atoms 16947 2 0.000000 1 2.500000 42.476000 31.151511 22.831250 16948 2 0.000000 -1 2.500000 42.476000 31.151511 22.831250 16949 2 0.000000 1 2.500000 35.588000 29.825915 26.343750 -16950 2 0.000000 -1.000000 2.500000 35.588000 29.825915 26.343750 +16950 2 0.000000 -1 2.500000 35.588000 29.825915 26.343750 16951 2 0.000000 1 2.500000 37.884000 25.849126 26.343750 16952 2 0.000000 -1 2.500000 37.884000 25.849126 26.343750 16953 2 0.000000 1 2.500000 40.180000 27.174722 29.856250 @@ -16971,7 +16971,7 @@ Atoms 16955 2 0.000000 1 2.500000 42.476000 31.151511 29.856250 16956 2 0.000000 -1 2.500000 42.476000 31.151511 29.856250 16957 2 0.000000 1 2.500000 35.588000 29.825915 33.368750 -16958 2 0.000000 -1.000000 2.500000 35.588000 29.825915 33.368750 +16958 2 0.000000 -1 2.500000 35.588000 29.825915 33.368750 16959 2 0.000000 1 2.500000 37.884000 25.849126 33.368750 16960 2 0.000000 -1 2.500000 37.884000 25.849126 33.368750 16961 2 0.000000 1 2.500000 40.180000 27.174722 36.881250 @@ -16979,7 +16979,7 @@ Atoms 16963 2 0.000000 1 2.500000 42.476000 31.151511 36.881250 16964 2 0.000000 -1 2.500000 42.476000 31.151511 36.881250 16965 2 0.000000 1 2.500000 35.588000 29.825915 40.393750 -16966 2 0.000000 -1.000000 2.500000 35.588000 29.825915 40.393750 +16966 2 0.000000 -1 2.500000 35.588000 29.825915 40.393750 16967 2 0.000000 1 2.500000 37.884000 25.849126 40.393750 16968 2 0.000000 -1 2.500000 37.884000 25.849126 40.393750 16969 2 0.000000 1 2.500000 40.180000 27.174722 43.906250 @@ -16987,7 +16987,7 @@ Atoms 16971 2 0.000000 1 2.500000 42.476000 31.151511 43.906250 16972 2 0.000000 -1 2.500000 42.476000 31.151511 43.906250 16973 2 0.000000 1 2.500000 35.588000 29.825915 47.418750 -16974 2 0.000000 -1.000000 2.500000 35.588000 29.825915 47.418750 +16974 2 0.000000 -1 2.500000 35.588000 29.825915 47.418750 16975 2 0.000000 1 2.500000 37.884000 25.849126 47.418750 16976 2 0.000000 -1 2.500000 37.884000 25.849126 47.418750 16977 2 0.000000 1 2.500000 40.180000 27.174722 50.931250 @@ -16995,7 +16995,7 @@ Atoms 16979 2 0.000000 1 2.500000 42.476000 31.151511 50.931250 16980 2 0.000000 -1 2.500000 42.476000 31.151511 50.931250 16981 2 0.000000 1 2.500000 35.588000 29.825915 54.443750 -16982 2 0.000000 -1.000000 2.500000 35.588000 29.825915 54.443750 +16982 2 0.000000 -1 2.500000 35.588000 29.825915 54.443750 16983 2 0.000000 1 2.500000 37.884000 25.849126 54.443750 16984 2 0.000000 -1 2.500000 37.884000 25.849126 54.443750 16985 2 0.000000 1 2.500000 40.180000 27.174722 57.956250 @@ -17003,7 +17003,7 @@ Atoms 16987 2 0.000000 1 2.500000 42.476000 31.151511 57.956250 16988 2 0.000000 -1 2.500000 42.476000 31.151511 57.956250 16989 2 0.000000 1 2.500000 35.588000 29.825915 61.468750 -16990 2 0.000000 -1.000000 2.500000 35.588000 29.825915 61.468750 +16990 2 0.000000 -1 2.500000 35.588000 29.825915 61.468750 16991 2 0.000000 1 2.500000 37.884000 25.849126 61.468750 16992 2 0.000000 -1 2.500000 37.884000 25.849126 61.468750 16993 2 0.000000 1 2.500000 40.180000 35.128300 1.756250 @@ -17011,7 +17011,7 @@ Atoms 16995 2 0.000000 1 2.500000 42.476000 39.105088 1.756250 16996 2 0.000000 -1 2.500000 42.476000 39.105088 1.756250 16997 2 0.000000 1 2.500000 35.588000 37.779492 5.268750 -16998 2 0.000000 -1.000000 2.500000 35.588000 37.779492 5.268750 +16998 2 0.000000 -1 2.500000 35.588000 37.779492 5.268750 16999 2 0.000000 1 2.500000 37.884000 33.802704 5.268750 17000 2 0.000000 -1 2.500000 37.884000 33.802704 5.268750 17001 2 0.000000 1 2.500000 40.180000 35.128300 8.781250 @@ -17019,7 +17019,7 @@ Atoms 17003 2 0.000000 1 2.500000 42.476000 39.105088 8.781250 17004 2 0.000000 -1 2.500000 42.476000 39.105088 8.781250 17005 2 0.000000 1 2.500000 35.588000 37.779492 12.293750 -17006 2 0.000000 -1.000000 2.500000 35.588000 37.779492 12.293750 +17006 2 0.000000 -1 2.500000 35.588000 37.779492 12.293750 17007 2 0.000000 1 2.500000 37.884000 33.802704 12.293750 17008 2 0.000000 -1 2.500000 37.884000 33.802704 12.293750 17009 2 0.000000 1 2.500000 40.180000 35.128300 15.806250 @@ -17027,7 +17027,7 @@ Atoms 17011 2 0.000000 1 2.500000 42.476000 39.105088 15.806250 17012 2 0.000000 -1 2.500000 42.476000 39.105088 15.806250 17013 2 0.000000 1 2.500000 35.588000 37.779492 19.318750 -17014 2 0.000000 -1.000000 2.500000 35.588000 37.779492 19.318750 +17014 2 0.000000 -1 2.500000 35.588000 37.779492 19.318750 17015 2 0.000000 1 2.500000 37.884000 33.802704 19.318750 17016 2 0.000000 -1 2.500000 37.884000 33.802704 19.318750 17017 2 0.000000 1 2.500000 40.180000 35.128300 22.831250 @@ -17035,7 +17035,7 @@ Atoms 17019 2 0.000000 1 2.500000 42.476000 39.105088 22.831250 17020 2 0.000000 -1 2.500000 42.476000 39.105088 22.831250 17021 2 0.000000 1 2.500000 35.588000 37.779492 26.343750 -17022 2 0.000000 -1.000000 2.500000 35.588000 37.779492 26.343750 +17022 2 0.000000 -1 2.500000 35.588000 37.779492 26.343750 17023 2 0.000000 1 2.500000 37.884000 33.802704 26.343750 17024 2 0.000000 -1 2.500000 37.884000 33.802704 26.343750 17025 2 0.000000 1 2.500000 40.180000 35.128300 29.856250 @@ -17043,7 +17043,7 @@ Atoms 17027 2 0.000000 1 2.500000 42.476000 39.105088 29.856250 17028 2 0.000000 -1 2.500000 42.476000 39.105088 29.856250 17029 2 0.000000 1 2.500000 35.588000 37.779492 33.368750 -17030 2 0.000000 -1.000000 2.500000 35.588000 37.779492 33.368750 +17030 2 0.000000 -1 2.500000 35.588000 37.779492 33.368750 17031 2 0.000000 1 2.500000 37.884000 33.802704 33.368750 17032 2 0.000000 -1 2.500000 37.884000 33.802704 33.368750 17033 2 0.000000 1 2.500000 40.180000 35.128300 36.881250 @@ -17051,7 +17051,7 @@ Atoms 17035 2 0.000000 1 2.500000 42.476000 39.105088 36.881250 17036 2 0.000000 -1 2.500000 42.476000 39.105088 36.881250 17037 2 0.000000 1 2.500000 35.588000 37.779492 40.393750 -17038 2 0.000000 -1.000000 2.500000 35.588000 37.779492 40.393750 +17038 2 0.000000 -1 2.500000 35.588000 37.779492 40.393750 17039 2 0.000000 1 2.500000 37.884000 33.802704 40.393750 17040 2 0.000000 -1 2.500000 37.884000 33.802704 40.393750 17041 2 0.000000 1 2.500000 40.180000 35.128300 43.906250 @@ -17059,7 +17059,7 @@ Atoms 17043 2 0.000000 1 2.500000 42.476000 39.105088 43.906250 17044 2 0.000000 -1 2.500000 42.476000 39.105088 43.906250 17045 2 0.000000 1 2.500000 35.588000 37.779492 47.418750 -17046 2 0.000000 -1.000000 2.500000 35.588000 37.779492 47.418750 +17046 2 0.000000 -1 2.500000 35.588000 37.779492 47.418750 17047 2 0.000000 1 2.500000 37.884000 33.802704 47.418750 17048 2 0.000000 -1 2.500000 37.884000 33.802704 47.418750 17049 2 0.000000 1 2.500000 40.180000 35.128300 50.931250 @@ -17067,7 +17067,7 @@ Atoms 17051 2 0.000000 1 2.500000 42.476000 39.105088 50.931250 17052 2 0.000000 -1 2.500000 42.476000 39.105088 50.931250 17053 2 0.000000 1 2.500000 35.588000 37.779492 54.443750 -17054 2 0.000000 -1.000000 2.500000 35.588000 37.779492 54.443750 +17054 2 0.000000 -1 2.500000 35.588000 37.779492 54.443750 17055 2 0.000000 1 2.500000 37.884000 33.802704 54.443750 17056 2 0.000000 -1 2.500000 37.884000 33.802704 54.443750 17057 2 0.000000 1 2.500000 40.180000 35.128300 57.956250 @@ -17075,7 +17075,7 @@ Atoms 17059 2 0.000000 1 2.500000 42.476000 39.105088 57.956250 17060 2 0.000000 -1 2.500000 42.476000 39.105088 57.956250 17061 2 0.000000 1 2.500000 35.588000 37.779492 61.468750 -17062 2 0.000000 -1.000000 2.500000 35.588000 37.779492 61.468750 +17062 2 0.000000 -1 2.500000 35.588000 37.779492 61.468750 17063 2 0.000000 1 2.500000 37.884000 33.802704 61.468750 17064 2 0.000000 -1 2.500000 37.884000 33.802704 61.468750 17065 2 0.000000 1 2.500000 40.180000 43.081877 1.756250 @@ -17083,7 +17083,7 @@ Atoms 17067 2 0.000000 1 2.500000 42.476000 47.058666 1.756250 17068 2 0.000000 -1 2.500000 42.476000 47.058666 1.756250 17069 2 0.000000 1 2.500000 35.588000 45.733070 5.268750 -17070 2 0.000000 -1.000000 2.500000 35.588000 45.733070 5.268750 +17070 2 0.000000 -1 2.500000 35.588000 45.733070 5.268750 17071 2 0.000000 1 2.500000 37.884000 41.756281 5.268750 17072 2 0.000000 -1 2.500000 37.884000 41.756281 5.268750 17073 2 0.000000 1 2.500000 40.180000 43.081877 8.781250 @@ -17091,7 +17091,7 @@ Atoms 17075 2 0.000000 1 2.500000 42.476000 47.058666 8.781250 17076 2 0.000000 -1 2.500000 42.476000 47.058666 8.781250 17077 2 0.000000 1 2.500000 35.588000 45.733070 12.293750 -17078 2 0.000000 -1.000000 2.500000 35.588000 45.733070 12.293750 +17078 2 0.000000 -1 2.500000 35.588000 45.733070 12.293750 17079 2 0.000000 1 2.500000 37.884000 41.756281 12.293750 17080 2 0.000000 -1 2.500000 37.884000 41.756281 12.293750 17081 2 0.000000 1 2.500000 40.180000 43.081877 15.806250 @@ -17099,7 +17099,7 @@ Atoms 17083 2 0.000000 1 2.500000 42.476000 47.058666 15.806250 17084 2 0.000000 -1 2.500000 42.476000 47.058666 15.806250 17085 2 0.000000 1 2.500000 35.588000 45.733070 19.318750 -17086 2 0.000000 -1.000000 2.500000 35.588000 45.733070 19.318750 +17086 2 0.000000 -1 2.500000 35.588000 45.733070 19.318750 17087 2 0.000000 1 2.500000 37.884000 41.756281 19.318750 17088 2 0.000000 -1 2.500000 37.884000 41.756281 19.318750 17089 2 0.000000 1 2.500000 40.180000 43.081877 22.831250 @@ -17107,7 +17107,7 @@ Atoms 17091 2 0.000000 1 2.500000 42.476000 47.058666 22.831250 17092 2 0.000000 -1 2.500000 42.476000 47.058666 22.831250 17093 2 0.000000 1 2.500000 35.588000 45.733070 26.343750 -17094 2 0.000000 -1.000000 2.500000 35.588000 45.733070 26.343750 +17094 2 0.000000 -1 2.500000 35.588000 45.733070 26.343750 17095 2 0.000000 1 2.500000 37.884000 41.756281 26.343750 17096 2 0.000000 -1 2.500000 37.884000 41.756281 26.343750 17097 2 0.000000 1 2.500000 40.180000 43.081877 29.856250 @@ -17115,7 +17115,7 @@ Atoms 17099 2 0.000000 1 2.500000 42.476000 47.058666 29.856250 17100 2 0.000000 -1 2.500000 42.476000 47.058666 29.856250 17101 2 0.000000 1 2.500000 35.588000 45.733070 33.368750 -17102 2 0.000000 -1.000000 2.500000 35.588000 45.733070 33.368750 +17102 2 0.000000 -1 2.500000 35.588000 45.733070 33.368750 17103 2 0.000000 1 2.500000 37.884000 41.756281 33.368750 17104 2 0.000000 -1 2.500000 37.884000 41.756281 33.368750 17105 2 0.000000 1 2.500000 40.180000 43.081877 36.881250 @@ -17123,7 +17123,7 @@ Atoms 17107 2 0.000000 1 2.500000 42.476000 47.058666 36.881250 17108 2 0.000000 -1 2.500000 42.476000 47.058666 36.881250 17109 2 0.000000 1 2.500000 35.588000 45.733070 40.393750 -17110 2 0.000000 -1.000000 2.500000 35.588000 45.733070 40.393750 +17110 2 0.000000 -1 2.500000 35.588000 45.733070 40.393750 17111 2 0.000000 1 2.500000 37.884000 41.756281 40.393750 17112 2 0.000000 -1 2.500000 37.884000 41.756281 40.393750 17113 2 0.000000 1 2.500000 40.180000 43.081877 43.906250 @@ -17131,7 +17131,7 @@ Atoms 17115 2 0.000000 1 2.500000 42.476000 47.058666 43.906250 17116 2 0.000000 -1 2.500000 42.476000 47.058666 43.906250 17117 2 0.000000 1 2.500000 35.588000 45.733070 47.418750 -17118 2 0.000000 -1.000000 2.500000 35.588000 45.733070 47.418750 +17118 2 0.000000 -1 2.500000 35.588000 45.733070 47.418750 17119 2 0.000000 1 2.500000 37.884000 41.756281 47.418750 17120 2 0.000000 -1 2.500000 37.884000 41.756281 47.418750 17121 2 0.000000 1 2.500000 40.180000 43.081877 50.931250 @@ -17139,7 +17139,7 @@ Atoms 17123 2 0.000000 1 2.500000 42.476000 47.058666 50.931250 17124 2 0.000000 -1 2.500000 42.476000 47.058666 50.931250 17125 2 0.000000 1 2.500000 35.588000 45.733070 54.443750 -17126 2 0.000000 -1.000000 2.500000 35.588000 45.733070 54.443750 +17126 2 0.000000 -1 2.500000 35.588000 45.733070 54.443750 17127 2 0.000000 1 2.500000 37.884000 41.756281 54.443750 17128 2 0.000000 -1 2.500000 37.884000 41.756281 54.443750 17129 2 0.000000 1 2.500000 40.180000 43.081877 57.956250 @@ -17147,7 +17147,7 @@ Atoms 17131 2 0.000000 1 2.500000 42.476000 47.058666 57.956250 17132 2 0.000000 -1 2.500000 42.476000 47.058666 57.956250 17133 2 0.000000 1 2.500000 35.588000 45.733070 61.468750 -17134 2 0.000000 -1.000000 2.500000 35.588000 45.733070 61.468750 +17134 2 0.000000 -1 2.500000 35.588000 45.733070 61.468750 17135 2 0.000000 1 2.500000 37.884000 41.756281 61.468750 17136 2 0.000000 -1 2.500000 37.884000 41.756281 61.468750 17137 2 0.000000 1 2.500000 40.180000 51.035454 1.756250 @@ -17155,7 +17155,7 @@ Atoms 17139 2 0.000000 1 2.500000 42.476000 55.012243 1.756250 17140 2 0.000000 -1 2.500000 42.476000 55.012243 1.756250 17141 2 0.000000 1 2.500000 35.588000 53.686647 5.268750 -17142 2 0.000000 -1.000000 2.500000 35.588000 53.686647 5.268750 +17142 2 0.000000 -1 2.500000 35.588000 53.686647 5.268750 17143 2 0.000000 1 2.500000 37.884000 49.709858 5.268750 17144 2 0.000000 -1 2.500000 37.884000 49.709858 5.268750 17145 2 0.000000 1 2.500000 40.180000 51.035454 8.781250 @@ -17163,7 +17163,7 @@ Atoms 17147 2 0.000000 1 2.500000 42.476000 55.012243 8.781250 17148 2 0.000000 -1 2.500000 42.476000 55.012243 8.781250 17149 2 0.000000 1 2.500000 35.588000 53.686647 12.293750 -17150 2 0.000000 -1.000000 2.500000 35.588000 53.686647 12.293750 +17150 2 0.000000 -1 2.500000 35.588000 53.686647 12.293750 17151 2 0.000000 1 2.500000 37.884000 49.709858 12.293750 17152 2 0.000000 -1 2.500000 37.884000 49.709858 12.293750 17153 2 0.000000 1 2.500000 40.180000 51.035454 15.806250 @@ -17171,7 +17171,7 @@ Atoms 17155 2 0.000000 1 2.500000 42.476000 55.012243 15.806250 17156 2 0.000000 -1 2.500000 42.476000 55.012243 15.806250 17157 2 0.000000 1 2.500000 35.588000 53.686647 19.318750 -17158 2 0.000000 -1.000000 2.500000 35.588000 53.686647 19.318750 +17158 2 0.000000 -1 2.500000 35.588000 53.686647 19.318750 17159 2 0.000000 1 2.500000 37.884000 49.709858 19.318750 17160 2 0.000000 -1 2.500000 37.884000 49.709858 19.318750 17161 2 0.000000 1 2.500000 40.180000 51.035454 22.831250 @@ -17179,7 +17179,7 @@ Atoms 17163 2 0.000000 1 2.500000 42.476000 55.012243 22.831250 17164 2 0.000000 -1 2.500000 42.476000 55.012243 22.831250 17165 2 0.000000 1 2.500000 35.588000 53.686647 26.343750 -17166 2 0.000000 -1.000000 2.500000 35.588000 53.686647 26.343750 +17166 2 0.000000 -1 2.500000 35.588000 53.686647 26.343750 17167 2 0.000000 1 2.500000 37.884000 49.709858 26.343750 17168 2 0.000000 -1 2.500000 37.884000 49.709858 26.343750 17169 2 0.000000 1 2.500000 40.180000 51.035454 29.856250 @@ -17187,7 +17187,7 @@ Atoms 17171 2 0.000000 1 2.500000 42.476000 55.012243 29.856250 17172 2 0.000000 -1 2.500000 42.476000 55.012243 29.856250 17173 2 0.000000 1 2.500000 35.588000 53.686647 33.368750 -17174 2 0.000000 -1.000000 2.500000 35.588000 53.686647 33.368750 +17174 2 0.000000 -1 2.500000 35.588000 53.686647 33.368750 17175 2 0.000000 1 2.500000 37.884000 49.709858 33.368750 17176 2 0.000000 -1 2.500000 37.884000 49.709858 33.368750 17177 2 0.000000 1 2.500000 40.180000 51.035454 36.881250 @@ -17195,7 +17195,7 @@ Atoms 17179 2 0.000000 1 2.500000 42.476000 55.012243 36.881250 17180 2 0.000000 -1 2.500000 42.476000 55.012243 36.881250 17181 2 0.000000 1 2.500000 35.588000 53.686647 40.393750 -17182 2 0.000000 -1.000000 2.500000 35.588000 53.686647 40.393750 +17182 2 0.000000 -1 2.500000 35.588000 53.686647 40.393750 17183 2 0.000000 1 2.500000 37.884000 49.709858 40.393750 17184 2 0.000000 -1 2.500000 37.884000 49.709858 40.393750 17185 2 0.000000 1 2.500000 40.180000 51.035454 43.906250 @@ -17203,7 +17203,7 @@ Atoms 17187 2 0.000000 1 2.500000 42.476000 55.012243 43.906250 17188 2 0.000000 -1 2.500000 42.476000 55.012243 43.906250 17189 2 0.000000 1 2.500000 35.588000 53.686647 47.418750 -17190 2 0.000000 -1.000000 2.500000 35.588000 53.686647 47.418750 +17190 2 0.000000 -1 2.500000 35.588000 53.686647 47.418750 17191 2 0.000000 1 2.500000 37.884000 49.709858 47.418750 17192 2 0.000000 -1 2.500000 37.884000 49.709858 47.418750 17193 2 0.000000 1 2.500000 40.180000 51.035454 50.931250 @@ -17211,7 +17211,7 @@ Atoms 17195 2 0.000000 1 2.500000 42.476000 55.012243 50.931250 17196 2 0.000000 -1 2.500000 42.476000 55.012243 50.931250 17197 2 0.000000 1 2.500000 35.588000 53.686647 54.443750 -17198 2 0.000000 -1.000000 2.500000 35.588000 53.686647 54.443750 +17198 2 0.000000 -1 2.500000 35.588000 53.686647 54.443750 17199 2 0.000000 1 2.500000 37.884000 49.709858 54.443750 17200 2 0.000000 -1 2.500000 37.884000 49.709858 54.443750 17201 2 0.000000 1 2.500000 40.180000 51.035454 57.956250 @@ -17219,7 +17219,7 @@ Atoms 17203 2 0.000000 1 2.500000 42.476000 55.012243 57.956250 17204 2 0.000000 -1 2.500000 42.476000 55.012243 57.956250 17205 2 0.000000 1 2.500000 35.588000 53.686647 61.468750 -17206 2 0.000000 -1.000000 2.500000 35.588000 53.686647 61.468750 +17206 2 0.000000 -1 2.500000 35.588000 53.686647 61.468750 17207 2 0.000000 1 2.500000 37.884000 49.709858 61.468750 17208 2 0.000000 -1 2.500000 37.884000 49.709858 61.468750 17209 2 0.000000 1 2.500000 40.180000 58.989032 1.756250 @@ -17227,7 +17227,7 @@ Atoms 17211 2 0.000000 1 2.500000 42.476000 62.965820 1.756250 17212 2 0.000000 -1 2.500000 42.476000 62.965820 1.756250 17213 2 0.000000 1 2.500000 35.588000 61.640224 5.268750 -17214 2 0.000000 -1.000000 2.500000 35.588000 61.640224 5.268750 +17214 2 0.000000 -1 2.500000 35.588000 61.640224 5.268750 17215 2 0.000000 1 2.500000 37.884000 57.663435 5.268750 17216 2 0.000000 -1 2.500000 37.884000 57.663435 5.268750 17217 2 0.000000 1 2.500000 40.180000 58.989032 8.781250 @@ -17235,7 +17235,7 @@ Atoms 17219 2 0.000000 1 2.500000 42.476000 62.965820 8.781250 17220 2 0.000000 -1 2.500000 42.476000 62.965820 8.781250 17221 2 0.000000 1 2.500000 35.588000 61.640224 12.293750 -17222 2 0.000000 -1.000000 2.500000 35.588000 61.640224 12.293750 +17222 2 0.000000 -1 2.500000 35.588000 61.640224 12.293750 17223 2 0.000000 1 2.500000 37.884000 57.663435 12.293750 17224 2 0.000000 -1 2.500000 37.884000 57.663435 12.293750 17225 2 0.000000 1 2.500000 40.180000 58.989032 15.806250 @@ -17243,7 +17243,7 @@ Atoms 17227 2 0.000000 1 2.500000 42.476000 62.965820 15.806250 17228 2 0.000000 -1 2.500000 42.476000 62.965820 15.806250 17229 2 0.000000 1 2.500000 35.588000 61.640224 19.318750 -17230 2 0.000000 -1.000000 2.500000 35.588000 61.640224 19.318750 +17230 2 0.000000 -1 2.500000 35.588000 61.640224 19.318750 17231 2 0.000000 1 2.500000 37.884000 57.663435 19.318750 17232 2 0.000000 -1 2.500000 37.884000 57.663435 19.318750 17233 2 0.000000 1 2.500000 40.180000 58.989032 22.831250 @@ -17251,7 +17251,7 @@ Atoms 17235 2 0.000000 1 2.500000 42.476000 62.965820 22.831250 17236 2 0.000000 -1 2.500000 42.476000 62.965820 22.831250 17237 2 0.000000 1 2.500000 35.588000 61.640224 26.343750 -17238 2 0.000000 -1.000000 2.500000 35.588000 61.640224 26.343750 +17238 2 0.000000 -1 2.500000 35.588000 61.640224 26.343750 17239 2 0.000000 1 2.500000 37.884000 57.663435 26.343750 17240 2 0.000000 -1 2.500000 37.884000 57.663435 26.343750 17241 2 0.000000 1 2.500000 40.180000 58.989032 29.856250 @@ -17259,7 +17259,7 @@ Atoms 17243 2 0.000000 1 2.500000 42.476000 62.965820 29.856250 17244 2 0.000000 -1 2.500000 42.476000 62.965820 29.856250 17245 2 0.000000 1 2.500000 35.588000 61.640224 33.368750 -17246 2 0.000000 -1.000000 2.500000 35.588000 61.640224 33.368750 +17246 2 0.000000 -1 2.500000 35.588000 61.640224 33.368750 17247 2 0.000000 1 2.500000 37.884000 57.663435 33.368750 17248 2 0.000000 -1 2.500000 37.884000 57.663435 33.368750 17249 2 0.000000 1 2.500000 40.180000 58.989032 36.881250 @@ -17267,7 +17267,7 @@ Atoms 17251 2 0.000000 1 2.500000 42.476000 62.965820 36.881250 17252 2 0.000000 -1 2.500000 42.476000 62.965820 36.881250 17253 2 0.000000 1 2.500000 35.588000 61.640224 40.393750 -17254 2 0.000000 -1.000000 2.500000 35.588000 61.640224 40.393750 +17254 2 0.000000 -1 2.500000 35.588000 61.640224 40.393750 17255 2 0.000000 1 2.500000 37.884000 57.663435 40.393750 17256 2 0.000000 -1 2.500000 37.884000 57.663435 40.393750 17257 2 0.000000 1 2.500000 40.180000 58.989032 43.906250 @@ -17275,7 +17275,7 @@ Atoms 17259 2 0.000000 1 2.500000 42.476000 62.965820 43.906250 17260 2 0.000000 -1 2.500000 42.476000 62.965820 43.906250 17261 2 0.000000 1 2.500000 35.588000 61.640224 47.418750 -17262 2 0.000000 -1.000000 2.500000 35.588000 61.640224 47.418750 +17262 2 0.000000 -1 2.500000 35.588000 61.640224 47.418750 17263 2 0.000000 1 2.500000 37.884000 57.663435 47.418750 17264 2 0.000000 -1 2.500000 37.884000 57.663435 47.418750 17265 2 0.000000 1 2.500000 40.180000 58.989032 50.931250 @@ -17283,7 +17283,7 @@ Atoms 17267 2 0.000000 1 2.500000 42.476000 62.965820 50.931250 17268 2 0.000000 -1 2.500000 42.476000 62.965820 50.931250 17269 2 0.000000 1 2.500000 35.588000 61.640224 54.443750 -17270 2 0.000000 -1.000000 2.500000 35.588000 61.640224 54.443750 +17270 2 0.000000 -1 2.500000 35.588000 61.640224 54.443750 17271 2 0.000000 1 2.500000 37.884000 57.663435 54.443750 17272 2 0.000000 -1 2.500000 37.884000 57.663435 54.443750 17273 2 0.000000 1 2.500000 40.180000 58.989032 57.956250 @@ -17291,7 +17291,7 @@ Atoms 17275 2 0.000000 1 2.500000 42.476000 62.965820 57.956250 17276 2 0.000000 -1 2.500000 42.476000 62.965820 57.956250 17277 2 0.000000 1 2.500000 35.588000 61.640224 61.468750 -17278 2 0.000000 -1.000000 2.500000 35.588000 61.640224 61.468750 +17278 2 0.000000 -1 2.500000 35.588000 61.640224 61.468750 17279 2 0.000000 1 2.500000 37.884000 57.663435 61.468750 17280 2 0.000000 -1 2.500000 37.884000 57.663435 61.468750 17281 2 0.000000 1 2.500000 44.772000 3.313991 1.756250 @@ -17299,7 +17299,7 @@ Atoms 17283 2 0.000000 1 2.500000 47.068000 7.290779 1.756250 17284 2 0.000000 -1 2.500000 47.068000 7.290779 1.756250 17285 2 0.000000 1 2.500000 40.180000 5.965183 5.268750 -17286 2 0.000000 -1.000000 2.500000 40.180000 5.965183 5.268750 +17286 2 0.000000 -1 2.500000 40.180000 5.965183 5.268750 17287 2 0.000000 1 2.500000 42.476000 1.988394 5.268750 17288 2 0.000000 -1 2.500000 42.476000 1.988394 5.268750 17289 2 0.000000 1 2.500000 44.772000 3.313991 8.781250 @@ -17307,7 +17307,7 @@ Atoms 17291 2 0.000000 1 2.500000 47.068000 7.290779 8.781250 17292 2 0.000000 -1 2.500000 47.068000 7.290779 8.781250 17293 2 0.000000 1 2.500000 40.180000 5.965183 12.293750 -17294 2 0.000000 -1.000000 2.500000 40.180000 5.965183 12.293750 +17294 2 0.000000 -1 2.500000 40.180000 5.965183 12.293750 17295 2 0.000000 1 2.500000 42.476000 1.988394 12.293750 17296 2 0.000000 -1 2.500000 42.476000 1.988394 12.293750 17297 2 0.000000 1 2.500000 44.772000 3.313991 15.806250 @@ -17315,7 +17315,7 @@ Atoms 17299 2 0.000000 1 2.500000 47.068000 7.290779 15.806250 17300 2 0.000000 -1 2.500000 47.068000 7.290779 15.806250 17301 2 0.000000 1 2.500000 40.180000 5.965183 19.318750 -17302 2 0.000000 -1.000000 2.500000 40.180000 5.965183 19.318750 +17302 2 0.000000 -1 2.500000 40.180000 5.965183 19.318750 17303 2 0.000000 1 2.500000 42.476000 1.988394 19.318750 17304 2 0.000000 -1 2.500000 42.476000 1.988394 19.318750 17305 2 0.000000 1 2.500000 44.772000 3.313991 22.831250 @@ -17323,7 +17323,7 @@ Atoms 17307 2 0.000000 1 2.500000 47.068000 7.290779 22.831250 17308 2 0.000000 -1 2.500000 47.068000 7.290779 22.831250 17309 2 0.000000 1 2.500000 40.180000 5.965183 26.343750 -17310 2 0.000000 -1.000000 2.500000 40.180000 5.965183 26.343750 +17310 2 0.000000 -1 2.500000 40.180000 5.965183 26.343750 17311 2 0.000000 1 2.500000 42.476000 1.988394 26.343750 17312 2 0.000000 -1 2.500000 42.476000 1.988394 26.343750 17313 2 0.000000 1 2.500000 44.772000 3.313991 29.856250 @@ -17331,7 +17331,7 @@ Atoms 17315 2 0.000000 1 2.500000 47.068000 7.290779 29.856250 17316 2 0.000000 -1 2.500000 47.068000 7.290779 29.856250 17317 2 0.000000 1 2.500000 40.180000 5.965183 33.368750 -17318 2 0.000000 -1.000000 2.500000 40.180000 5.965183 33.368750 +17318 2 0.000000 -1 2.500000 40.180000 5.965183 33.368750 17319 2 0.000000 1 2.500000 42.476000 1.988394 33.368750 17320 2 0.000000 -1 2.500000 42.476000 1.988394 33.368750 17321 2 0.000000 1 2.500000 44.772000 3.313991 36.881250 @@ -17339,7 +17339,7 @@ Atoms 17323 2 0.000000 1 2.500000 47.068000 7.290779 36.881250 17324 2 0.000000 -1 2.500000 47.068000 7.290779 36.881250 17325 2 0.000000 1 2.500000 40.180000 5.965183 40.393750 -17326 2 0.000000 -1.000000 2.500000 40.180000 5.965183 40.393750 +17326 2 0.000000 -1 2.500000 40.180000 5.965183 40.393750 17327 2 0.000000 1 2.500000 42.476000 1.988394 40.393750 17328 2 0.000000 -1 2.500000 42.476000 1.988394 40.393750 17329 2 0.000000 1 2.500000 44.772000 3.313991 43.906250 @@ -17347,7 +17347,7 @@ Atoms 17331 2 0.000000 1 2.500000 47.068000 7.290779 43.906250 17332 2 0.000000 -1 2.500000 47.068000 7.290779 43.906250 17333 2 0.000000 1 2.500000 40.180000 5.965183 47.418750 -17334 2 0.000000 -1.000000 2.500000 40.180000 5.965183 47.418750 +17334 2 0.000000 -1 2.500000 40.180000 5.965183 47.418750 17335 2 0.000000 1 2.500000 42.476000 1.988394 47.418750 17336 2 0.000000 -1 2.500000 42.476000 1.988394 47.418750 17337 2 0.000000 1 2.500000 44.772000 3.313991 50.931250 @@ -17355,7 +17355,7 @@ Atoms 17339 2 0.000000 1 2.500000 47.068000 7.290779 50.931250 17340 2 0.000000 -1 2.500000 47.068000 7.290779 50.931250 17341 2 0.000000 1 2.500000 40.180000 5.965183 54.443750 -17342 2 0.000000 -1.000000 2.500000 40.180000 5.965183 54.443750 +17342 2 0.000000 -1 2.500000 40.180000 5.965183 54.443750 17343 2 0.000000 1 2.500000 42.476000 1.988394 54.443750 17344 2 0.000000 -1 2.500000 42.476000 1.988394 54.443750 17345 2 0.000000 1 2.500000 44.772000 3.313991 57.956250 @@ -17363,7 +17363,7 @@ Atoms 17347 2 0.000000 1 2.500000 47.068000 7.290779 57.956250 17348 2 0.000000 -1 2.500000 47.068000 7.290779 57.956250 17349 2 0.000000 1 2.500000 40.180000 5.965183 61.468750 -17350 2 0.000000 -1.000000 2.500000 40.180000 5.965183 61.468750 +17350 2 0.000000 -1 2.500000 40.180000 5.965183 61.468750 17351 2 0.000000 1 2.500000 42.476000 1.988394 61.468750 17352 2 0.000000 -1 2.500000 42.476000 1.988394 61.468750 17353 2 0.000000 1 2.500000 44.772000 11.267568 1.756250 @@ -17371,7 +17371,7 @@ Atoms 17355 2 0.000000 1 2.500000 47.068000 15.244357 1.756250 17356 2 0.000000 -1 2.500000 47.068000 15.244357 1.756250 17357 2 0.000000 1 2.500000 40.180000 13.918760 5.268750 -17358 2 0.000000 -1.000000 2.500000 40.180000 13.918760 5.268750 +17358 2 0.000000 -1 2.500000 40.180000 13.918760 5.268750 17359 2 0.000000 1 2.500000 42.476000 9.941972 5.268750 17360 2 0.000000 -1 2.500000 42.476000 9.941972 5.268750 17361 2 0.000000 1 2.500000 44.772000 11.267568 8.781250 @@ -17379,7 +17379,7 @@ Atoms 17363 2 0.000000 1 2.500000 47.068000 15.244357 8.781250 17364 2 0.000000 -1 2.500000 47.068000 15.244357 8.781250 17365 2 0.000000 1 2.500000 40.180000 13.918760 12.293750 -17366 2 0.000000 -1.000000 2.500000 40.180000 13.918760 12.293750 +17366 2 0.000000 -1 2.500000 40.180000 13.918760 12.293750 17367 2 0.000000 1 2.500000 42.476000 9.941972 12.293750 17368 2 0.000000 -1 2.500000 42.476000 9.941972 12.293750 17369 2 0.000000 1 2.500000 44.772000 11.267568 15.806250 @@ -17387,7 +17387,7 @@ Atoms 17371 2 0.000000 1 2.500000 47.068000 15.244357 15.806250 17372 2 0.000000 -1 2.500000 47.068000 15.244357 15.806250 17373 2 0.000000 1 2.500000 40.180000 13.918760 19.318750 -17374 2 0.000000 -1.000000 2.500000 40.180000 13.918760 19.318750 +17374 2 0.000000 -1 2.500000 40.180000 13.918760 19.318750 17375 2 0.000000 1 2.500000 42.476000 9.941972 19.318750 17376 2 0.000000 -1 2.500000 42.476000 9.941972 19.318750 17377 2 0.000000 1 2.500000 44.772000 11.267568 22.831250 @@ -17395,7 +17395,7 @@ Atoms 17379 2 0.000000 1 2.500000 47.068000 15.244357 22.831250 17380 2 0.000000 -1 2.500000 47.068000 15.244357 22.831250 17381 2 0.000000 1 2.500000 40.180000 13.918760 26.343750 -17382 2 0.000000 -1.000000 2.500000 40.180000 13.918760 26.343750 +17382 2 0.000000 -1 2.500000 40.180000 13.918760 26.343750 17383 2 0.000000 1 2.500000 42.476000 9.941972 26.343750 17384 2 0.000000 -1 2.500000 42.476000 9.941972 26.343750 17385 2 0.000000 1 2.500000 44.772000 11.267568 29.856250 @@ -17403,7 +17403,7 @@ Atoms 17387 2 0.000000 1 2.500000 47.068000 15.244357 29.856250 17388 2 0.000000 -1 2.500000 47.068000 15.244357 29.856250 17389 2 0.000000 1 2.500000 40.180000 13.918760 33.368750 -17390 2 0.000000 -1.000000 2.500000 40.180000 13.918760 33.368750 +17390 2 0.000000 -1 2.500000 40.180000 13.918760 33.368750 17391 2 0.000000 1 2.500000 42.476000 9.941972 33.368750 17392 2 0.000000 -1 2.500000 42.476000 9.941972 33.368750 17393 2 0.000000 1 2.500000 44.772000 11.267568 36.881250 @@ -17411,7 +17411,7 @@ Atoms 17395 2 0.000000 1 2.500000 47.068000 15.244357 36.881250 17396 2 0.000000 -1 2.500000 47.068000 15.244357 36.881250 17397 2 0.000000 1 2.500000 40.180000 13.918760 40.393750 -17398 2 0.000000 -1.000000 2.500000 40.180000 13.918760 40.393750 +17398 2 0.000000 -1 2.500000 40.180000 13.918760 40.393750 17399 2 0.000000 1 2.500000 42.476000 9.941972 40.393750 17400 2 0.000000 -1 2.500000 42.476000 9.941972 40.393750 17401 2 0.000000 1 2.500000 44.772000 11.267568 43.906250 @@ -17419,7 +17419,7 @@ Atoms 17403 2 0.000000 1 2.500000 47.068000 15.244357 43.906250 17404 2 0.000000 -1 2.500000 47.068000 15.244357 43.906250 17405 2 0.000000 1 2.500000 40.180000 13.918760 47.418750 -17406 2 0.000000 -1.000000 2.500000 40.180000 13.918760 47.418750 +17406 2 0.000000 -1 2.500000 40.180000 13.918760 47.418750 17407 2 0.000000 1 2.500000 42.476000 9.941972 47.418750 17408 2 0.000000 -1 2.500000 42.476000 9.941972 47.418750 17409 2 0.000000 1 2.500000 44.772000 11.267568 50.931250 @@ -17427,7 +17427,7 @@ Atoms 17411 2 0.000000 1 2.500000 47.068000 15.244357 50.931250 17412 2 0.000000 -1 2.500000 47.068000 15.244357 50.931250 17413 2 0.000000 1 2.500000 40.180000 13.918760 54.443750 -17414 2 0.000000 -1.000000 2.500000 40.180000 13.918760 54.443750 +17414 2 0.000000 -1 2.500000 40.180000 13.918760 54.443750 17415 2 0.000000 1 2.500000 42.476000 9.941972 54.443750 17416 2 0.000000 -1 2.500000 42.476000 9.941972 54.443750 17417 2 0.000000 1 2.500000 44.772000 11.267568 57.956250 @@ -17435,7 +17435,7 @@ Atoms 17419 2 0.000000 1 2.500000 47.068000 15.244357 57.956250 17420 2 0.000000 -1 2.500000 47.068000 15.244357 57.956250 17421 2 0.000000 1 2.500000 40.180000 13.918760 61.468750 -17422 2 0.000000 -1.000000 2.500000 40.180000 13.918760 61.468750 +17422 2 0.000000 -1 2.500000 40.180000 13.918760 61.468750 17423 2 0.000000 1 2.500000 42.476000 9.941972 61.468750 17424 2 0.000000 -1 2.500000 42.476000 9.941972 61.468750 17425 2 0.000000 1 2.500000 44.772000 19.221145 1.756250 @@ -17443,7 +17443,7 @@ Atoms 17427 2 0.000000 1 2.500000 47.068000 23.197934 1.756250 17428 2 0.000000 -1 2.500000 47.068000 23.197934 1.756250 17429 2 0.000000 1 2.500000 40.180000 21.872338 5.268750 -17430 2 0.000000 -1.000000 2.500000 40.180000 21.872338 5.268750 +17430 2 0.000000 -1 2.500000 40.180000 21.872338 5.268750 17431 2 0.000000 1 2.500000 42.476000 17.895549 5.268750 17432 2 0.000000 -1 2.500000 42.476000 17.895549 5.268750 17433 2 0.000000 1 2.500000 44.772000 19.221145 8.781250 @@ -17451,7 +17451,7 @@ Atoms 17435 2 0.000000 1 2.500000 47.068000 23.197934 8.781250 17436 2 0.000000 -1 2.500000 47.068000 23.197934 8.781250 17437 2 0.000000 1 2.500000 40.180000 21.872338 12.293750 -17438 2 0.000000 -1.000000 2.500000 40.180000 21.872338 12.293750 +17438 2 0.000000 -1 2.500000 40.180000 21.872338 12.293750 17439 2 0.000000 1 2.500000 42.476000 17.895549 12.293750 17440 2 0.000000 -1 2.500000 42.476000 17.895549 12.293750 17441 2 0.000000 1 2.500000 44.772000 19.221145 15.806250 @@ -17459,7 +17459,7 @@ Atoms 17443 2 0.000000 1 2.500000 47.068000 23.197934 15.806250 17444 2 0.000000 -1 2.500000 47.068000 23.197934 15.806250 17445 2 0.000000 1 2.500000 40.180000 21.872338 19.318750 -17446 2 0.000000 -1.000000 2.500000 40.180000 21.872338 19.318750 +17446 2 0.000000 -1 2.500000 40.180000 21.872338 19.318750 17447 2 0.000000 1 2.500000 42.476000 17.895549 19.318750 17448 2 0.000000 -1 2.500000 42.476000 17.895549 19.318750 17449 2 0.000000 1 2.500000 44.772000 19.221145 22.831250 @@ -17467,7 +17467,7 @@ Atoms 17451 2 0.000000 1 2.500000 47.068000 23.197934 22.831250 17452 2 0.000000 -1 2.500000 47.068000 23.197934 22.831250 17453 2 0.000000 1 2.500000 40.180000 21.872338 26.343750 -17454 2 0.000000 -1.000000 2.500000 40.180000 21.872338 26.343750 +17454 2 0.000000 -1 2.500000 40.180000 21.872338 26.343750 17455 2 0.000000 1 2.500000 42.476000 17.895549 26.343750 17456 2 0.000000 -1 2.500000 42.476000 17.895549 26.343750 17457 2 0.000000 1 2.500000 44.772000 19.221145 29.856250 @@ -17475,7 +17475,7 @@ Atoms 17459 2 0.000000 1 2.500000 47.068000 23.197934 29.856250 17460 2 0.000000 -1 2.500000 47.068000 23.197934 29.856250 17461 2 0.000000 1 2.500000 40.180000 21.872338 33.368750 -17462 2 0.000000 -1.000000 2.500000 40.180000 21.872338 33.368750 +17462 2 0.000000 -1 2.500000 40.180000 21.872338 33.368750 17463 2 0.000000 1 2.500000 42.476000 17.895549 33.368750 17464 2 0.000000 -1 2.500000 42.476000 17.895549 33.368750 17465 2 0.000000 1 2.500000 44.772000 19.221145 36.881250 @@ -17483,7 +17483,7 @@ Atoms 17467 2 0.000000 1 2.500000 47.068000 23.197934 36.881250 17468 2 0.000000 -1 2.500000 47.068000 23.197934 36.881250 17469 2 0.000000 1 2.500000 40.180000 21.872338 40.393750 -17470 2 0.000000 -1.000000 2.500000 40.180000 21.872338 40.393750 +17470 2 0.000000 -1 2.500000 40.180000 21.872338 40.393750 17471 2 0.000000 1 2.500000 42.476000 17.895549 40.393750 17472 2 0.000000 -1 2.500000 42.476000 17.895549 40.393750 17473 2 0.000000 1 2.500000 44.772000 19.221145 43.906250 @@ -17491,7 +17491,7 @@ Atoms 17475 2 0.000000 1 2.500000 47.068000 23.197934 43.906250 17476 2 0.000000 -1 2.500000 47.068000 23.197934 43.906250 17477 2 0.000000 1 2.500000 40.180000 21.872338 47.418750 -17478 2 0.000000 -1.000000 2.500000 40.180000 21.872338 47.418750 +17478 2 0.000000 -1 2.500000 40.180000 21.872338 47.418750 17479 2 0.000000 1 2.500000 42.476000 17.895549 47.418750 17480 2 0.000000 -1 2.500000 42.476000 17.895549 47.418750 17481 2 0.000000 1 2.500000 44.772000 19.221145 50.931250 @@ -17499,7 +17499,7 @@ Atoms 17483 2 0.000000 1 2.500000 47.068000 23.197934 50.931250 17484 2 0.000000 -1 2.500000 47.068000 23.197934 50.931250 17485 2 0.000000 1 2.500000 40.180000 21.872338 54.443750 -17486 2 0.000000 -1.000000 2.500000 40.180000 21.872338 54.443750 +17486 2 0.000000 -1 2.500000 40.180000 21.872338 54.443750 17487 2 0.000000 1 2.500000 42.476000 17.895549 54.443750 17488 2 0.000000 -1 2.500000 42.476000 17.895549 54.443750 17489 2 0.000000 1 2.500000 44.772000 19.221145 57.956250 @@ -17507,7 +17507,7 @@ Atoms 17491 2 0.000000 1 2.500000 47.068000 23.197934 57.956250 17492 2 0.000000 -1 2.500000 47.068000 23.197934 57.956250 17493 2 0.000000 1 2.500000 40.180000 21.872338 61.468750 -17494 2 0.000000 -1.000000 2.500000 40.180000 21.872338 61.468750 +17494 2 0.000000 -1 2.500000 40.180000 21.872338 61.468750 17495 2 0.000000 1 2.500000 42.476000 17.895549 61.468750 17496 2 0.000000 -1 2.500000 42.476000 17.895549 61.468750 17497 2 0.000000 1 2.500000 44.772000 27.174722 1.756250 @@ -17515,7 +17515,7 @@ Atoms 17499 2 0.000000 1 2.500000 47.068000 31.151511 1.756250 17500 2 0.000000 -1 2.500000 47.068000 31.151511 1.756250 17501 2 0.000000 1 2.500000 40.180000 29.825915 5.268750 -17502 2 0.000000 -1.000000 2.500000 40.180000 29.825915 5.268750 +17502 2 0.000000 -1 2.500000 40.180000 29.825915 5.268750 17503 2 0.000000 1 2.500000 42.476000 25.849126 5.268750 17504 2 0.000000 -1 2.500000 42.476000 25.849126 5.268750 17505 2 0.000000 1 2.500000 44.772000 27.174722 8.781250 @@ -17523,7 +17523,7 @@ Atoms 17507 2 0.000000 1 2.500000 47.068000 31.151511 8.781250 17508 2 0.000000 -1 2.500000 47.068000 31.151511 8.781250 17509 2 0.000000 1 2.500000 40.180000 29.825915 12.293750 -17510 2 0.000000 -1.000000 2.500000 40.180000 29.825915 12.293750 +17510 2 0.000000 -1 2.500000 40.180000 29.825915 12.293750 17511 2 0.000000 1 2.500000 42.476000 25.849126 12.293750 17512 2 0.000000 -1 2.500000 42.476000 25.849126 12.293750 17513 2 0.000000 1 2.500000 44.772000 27.174722 15.806250 @@ -17531,7 +17531,7 @@ Atoms 17515 2 0.000000 1 2.500000 47.068000 31.151511 15.806250 17516 2 0.000000 -1 2.500000 47.068000 31.151511 15.806250 17517 2 0.000000 1 2.500000 40.180000 29.825915 19.318750 -17518 2 0.000000 -1.000000 2.500000 40.180000 29.825915 19.318750 +17518 2 0.000000 -1 2.500000 40.180000 29.825915 19.318750 17519 2 0.000000 1 2.500000 42.476000 25.849126 19.318750 17520 2 0.000000 -1 2.500000 42.476000 25.849126 19.318750 17521 2 0.000000 1 2.500000 44.772000 27.174722 22.831250 @@ -17539,7 +17539,7 @@ Atoms 17523 2 0.000000 1 2.500000 47.068000 31.151511 22.831250 17524 2 0.000000 -1 2.500000 47.068000 31.151511 22.831250 17525 2 0.000000 1 2.500000 40.180000 29.825915 26.343750 -17526 2 0.000000 -1.000000 2.500000 40.180000 29.825915 26.343750 +17526 2 0.000000 -1 2.500000 40.180000 29.825915 26.343750 17527 2 0.000000 1 2.500000 42.476000 25.849126 26.343750 17528 2 0.000000 -1 2.500000 42.476000 25.849126 26.343750 17529 2 0.000000 1 2.500000 44.772000 27.174722 29.856250 @@ -17547,7 +17547,7 @@ Atoms 17531 2 0.000000 1 2.500000 47.068000 31.151511 29.856250 17532 2 0.000000 -1 2.500000 47.068000 31.151511 29.856250 17533 2 0.000000 1 2.500000 40.180000 29.825915 33.368750 -17534 2 0.000000 -1.000000 2.500000 40.180000 29.825915 33.368750 +17534 2 0.000000 -1 2.500000 40.180000 29.825915 33.368750 17535 2 0.000000 1 2.500000 42.476000 25.849126 33.368750 17536 2 0.000000 -1 2.500000 42.476000 25.849126 33.368750 17537 2 0.000000 1 2.500000 44.772000 27.174722 36.881250 @@ -17555,7 +17555,7 @@ Atoms 17539 2 0.000000 1 2.500000 47.068000 31.151511 36.881250 17540 2 0.000000 -1 2.500000 47.068000 31.151511 36.881250 17541 2 0.000000 1 2.500000 40.180000 29.825915 40.393750 -17542 2 0.000000 -1.000000 2.500000 40.180000 29.825915 40.393750 +17542 2 0.000000 -1 2.500000 40.180000 29.825915 40.393750 17543 2 0.000000 1 2.500000 42.476000 25.849126 40.393750 17544 2 0.000000 -1 2.500000 42.476000 25.849126 40.393750 17545 2 0.000000 1 2.500000 44.772000 27.174722 43.906250 @@ -17563,7 +17563,7 @@ Atoms 17547 2 0.000000 1 2.500000 47.068000 31.151511 43.906250 17548 2 0.000000 -1 2.500000 47.068000 31.151511 43.906250 17549 2 0.000000 1 2.500000 40.180000 29.825915 47.418750 -17550 2 0.000000 -1.000000 2.500000 40.180000 29.825915 47.418750 +17550 2 0.000000 -1 2.500000 40.180000 29.825915 47.418750 17551 2 0.000000 1 2.500000 42.476000 25.849126 47.418750 17552 2 0.000000 -1 2.500000 42.476000 25.849126 47.418750 17553 2 0.000000 1 2.500000 44.772000 27.174722 50.931250 @@ -17571,7 +17571,7 @@ Atoms 17555 2 0.000000 1 2.500000 47.068000 31.151511 50.931250 17556 2 0.000000 -1 2.500000 47.068000 31.151511 50.931250 17557 2 0.000000 1 2.500000 40.180000 29.825915 54.443750 -17558 2 0.000000 -1.000000 2.500000 40.180000 29.825915 54.443750 +17558 2 0.000000 -1 2.500000 40.180000 29.825915 54.443750 17559 2 0.000000 1 2.500000 42.476000 25.849126 54.443750 17560 2 0.000000 -1 2.500000 42.476000 25.849126 54.443750 17561 2 0.000000 1 2.500000 44.772000 27.174722 57.956250 @@ -17579,7 +17579,7 @@ Atoms 17563 2 0.000000 1 2.500000 47.068000 31.151511 57.956250 17564 2 0.000000 -1 2.500000 47.068000 31.151511 57.956250 17565 2 0.000000 1 2.500000 40.180000 29.825915 61.468750 -17566 2 0.000000 -1.000000 2.500000 40.180000 29.825915 61.468750 +17566 2 0.000000 -1 2.500000 40.180000 29.825915 61.468750 17567 2 0.000000 1 2.500000 42.476000 25.849126 61.468750 17568 2 0.000000 -1 2.500000 42.476000 25.849126 61.468750 17569 2 0.000000 1 2.500000 44.772000 35.128300 1.756250 @@ -17587,7 +17587,7 @@ Atoms 17571 2 0.000000 1 2.500000 47.068000 39.105088 1.756250 17572 2 0.000000 -1 2.500000 47.068000 39.105088 1.756250 17573 2 0.000000 1 2.500000 40.180000 37.779492 5.268750 -17574 2 0.000000 -1.000000 2.500000 40.180000 37.779492 5.268750 +17574 2 0.000000 -1 2.500000 40.180000 37.779492 5.268750 17575 2 0.000000 1 2.500000 42.476000 33.802704 5.268750 17576 2 0.000000 -1 2.500000 42.476000 33.802704 5.268750 17577 2 0.000000 1 2.500000 44.772000 35.128300 8.781250 @@ -17595,7 +17595,7 @@ Atoms 17579 2 0.000000 1 2.500000 47.068000 39.105088 8.781250 17580 2 0.000000 -1 2.500000 47.068000 39.105088 8.781250 17581 2 0.000000 1 2.500000 40.180000 37.779492 12.293750 -17582 2 0.000000 -1.000000 2.500000 40.180000 37.779492 12.293750 +17582 2 0.000000 -1 2.500000 40.180000 37.779492 12.293750 17583 2 0.000000 1 2.500000 42.476000 33.802704 12.293750 17584 2 0.000000 -1 2.500000 42.476000 33.802704 12.293750 17585 2 0.000000 1 2.500000 44.772000 35.128300 15.806250 @@ -17603,7 +17603,7 @@ Atoms 17587 2 0.000000 1 2.500000 47.068000 39.105088 15.806250 17588 2 0.000000 -1 2.500000 47.068000 39.105088 15.806250 17589 2 0.000000 1 2.500000 40.180000 37.779492 19.318750 -17590 2 0.000000 -1.000000 2.500000 40.180000 37.779492 19.318750 +17590 2 0.000000 -1 2.500000 40.180000 37.779492 19.318750 17591 2 0.000000 1 2.500000 42.476000 33.802704 19.318750 17592 2 0.000000 -1 2.500000 42.476000 33.802704 19.318750 17593 2 0.000000 1 2.500000 44.772000 35.128300 22.831250 @@ -17611,7 +17611,7 @@ Atoms 17595 2 0.000000 1 2.500000 47.068000 39.105088 22.831250 17596 2 0.000000 -1 2.500000 47.068000 39.105088 22.831250 17597 2 0.000000 1 2.500000 40.180000 37.779492 26.343750 -17598 2 0.000000 -1.000000 2.500000 40.180000 37.779492 26.343750 +17598 2 0.000000 -1 2.500000 40.180000 37.779492 26.343750 17599 2 0.000000 1 2.500000 42.476000 33.802704 26.343750 17600 2 0.000000 -1 2.500000 42.476000 33.802704 26.343750 17601 2 0.000000 1 2.500000 44.772000 35.128300 29.856250 @@ -17619,7 +17619,7 @@ Atoms 17603 2 0.000000 1 2.500000 47.068000 39.105088 29.856250 17604 2 0.000000 -1 2.500000 47.068000 39.105088 29.856250 17605 2 0.000000 1 2.500000 40.180000 37.779492 33.368750 -17606 2 0.000000 -1.000000 2.500000 40.180000 37.779492 33.368750 +17606 2 0.000000 -1 2.500000 40.180000 37.779492 33.368750 17607 2 0.000000 1 2.500000 42.476000 33.802704 33.368750 17608 2 0.000000 -1 2.500000 42.476000 33.802704 33.368750 17609 2 0.000000 1 2.500000 44.772000 35.128300 36.881250 @@ -17627,7 +17627,7 @@ Atoms 17611 2 0.000000 1 2.500000 47.068000 39.105088 36.881250 17612 2 0.000000 -1 2.500000 47.068000 39.105088 36.881250 17613 2 0.000000 1 2.500000 40.180000 37.779492 40.393750 -17614 2 0.000000 -1.000000 2.500000 40.180000 37.779492 40.393750 +17614 2 0.000000 -1 2.500000 40.180000 37.779492 40.393750 17615 2 0.000000 1 2.500000 42.476000 33.802704 40.393750 17616 2 0.000000 -1 2.500000 42.476000 33.802704 40.393750 17617 2 0.000000 1 2.500000 44.772000 35.128300 43.906250 @@ -17635,7 +17635,7 @@ Atoms 17619 2 0.000000 1 2.500000 47.068000 39.105088 43.906250 17620 2 0.000000 -1 2.500000 47.068000 39.105088 43.906250 17621 2 0.000000 1 2.500000 40.180000 37.779492 47.418750 -17622 2 0.000000 -1.000000 2.500000 40.180000 37.779492 47.418750 +17622 2 0.000000 -1 2.500000 40.180000 37.779492 47.418750 17623 2 0.000000 1 2.500000 42.476000 33.802704 47.418750 17624 2 0.000000 -1 2.500000 42.476000 33.802704 47.418750 17625 2 0.000000 1 2.500000 44.772000 35.128300 50.931250 @@ -17643,7 +17643,7 @@ Atoms 17627 2 0.000000 1 2.500000 47.068000 39.105088 50.931250 17628 2 0.000000 -1 2.500000 47.068000 39.105088 50.931250 17629 2 0.000000 1 2.500000 40.180000 37.779492 54.443750 -17630 2 0.000000 -1.000000 2.500000 40.180000 37.779492 54.443750 +17630 2 0.000000 -1 2.500000 40.180000 37.779492 54.443750 17631 2 0.000000 1 2.500000 42.476000 33.802704 54.443750 17632 2 0.000000 -1 2.500000 42.476000 33.802704 54.443750 17633 2 0.000000 1 2.500000 44.772000 35.128300 57.956250 @@ -17651,7 +17651,7 @@ Atoms 17635 2 0.000000 1 2.500000 47.068000 39.105088 57.956250 17636 2 0.000000 -1 2.500000 47.068000 39.105088 57.956250 17637 2 0.000000 1 2.500000 40.180000 37.779492 61.468750 -17638 2 0.000000 -1.000000 2.500000 40.180000 37.779492 61.468750 +17638 2 0.000000 -1 2.500000 40.180000 37.779492 61.468750 17639 2 0.000000 1 2.500000 42.476000 33.802704 61.468750 17640 2 0.000000 -1 2.500000 42.476000 33.802704 61.468750 17641 2 0.000000 1 2.500000 44.772000 43.081877 1.756250 @@ -17659,7 +17659,7 @@ Atoms 17643 2 0.000000 1 2.500000 47.068000 47.058666 1.756250 17644 2 0.000000 -1 2.500000 47.068000 47.058666 1.756250 17645 2 0.000000 1 2.500000 40.180000 45.733070 5.268750 -17646 2 0.000000 -1.000000 2.500000 40.180000 45.733070 5.268750 +17646 2 0.000000 -1 2.500000 40.180000 45.733070 5.268750 17647 2 0.000000 1 2.500000 42.476000 41.756281 5.268750 17648 2 0.000000 -1 2.500000 42.476000 41.756281 5.268750 17649 2 0.000000 1 2.500000 44.772000 43.081877 8.781250 @@ -17667,7 +17667,7 @@ Atoms 17651 2 0.000000 1 2.500000 47.068000 47.058666 8.781250 17652 2 0.000000 -1 2.500000 47.068000 47.058666 8.781250 17653 2 0.000000 1 2.500000 40.180000 45.733070 12.293750 -17654 2 0.000000 -1.000000 2.500000 40.180000 45.733070 12.293750 +17654 2 0.000000 -1 2.500000 40.180000 45.733070 12.293750 17655 2 0.000000 1 2.500000 42.476000 41.756281 12.293750 17656 2 0.000000 -1 2.500000 42.476000 41.756281 12.293750 17657 2 0.000000 1 2.500000 44.772000 43.081877 15.806250 @@ -17675,7 +17675,7 @@ Atoms 17659 2 0.000000 1 2.500000 47.068000 47.058666 15.806250 17660 2 0.000000 -1 2.500000 47.068000 47.058666 15.806250 17661 2 0.000000 1 2.500000 40.180000 45.733070 19.318750 -17662 2 0.000000 -1.000000 2.500000 40.180000 45.733070 19.318750 +17662 2 0.000000 -1 2.500000 40.180000 45.733070 19.318750 17663 2 0.000000 1 2.500000 42.476000 41.756281 19.318750 17664 2 0.000000 -1 2.500000 42.476000 41.756281 19.318750 17665 2 0.000000 1 2.500000 44.772000 43.081877 22.831250 @@ -17683,7 +17683,7 @@ Atoms 17667 2 0.000000 1 2.500000 47.068000 47.058666 22.831250 17668 2 0.000000 -1 2.500000 47.068000 47.058666 22.831250 17669 2 0.000000 1 2.500000 40.180000 45.733070 26.343750 -17670 2 0.000000 -1.000000 2.500000 40.180000 45.733070 26.343750 +17670 2 0.000000 -1 2.500000 40.180000 45.733070 26.343750 17671 2 0.000000 1 2.500000 42.476000 41.756281 26.343750 17672 2 0.000000 -1 2.500000 42.476000 41.756281 26.343750 17673 2 0.000000 1 2.500000 44.772000 43.081877 29.856250 @@ -17691,7 +17691,7 @@ Atoms 17675 2 0.000000 1 2.500000 47.068000 47.058666 29.856250 17676 2 0.000000 -1 2.500000 47.068000 47.058666 29.856250 17677 2 0.000000 1 2.500000 40.180000 45.733070 33.368750 -17678 2 0.000000 -1.000000 2.500000 40.180000 45.733070 33.368750 +17678 2 0.000000 -1 2.500000 40.180000 45.733070 33.368750 17679 2 0.000000 1 2.500000 42.476000 41.756281 33.368750 17680 2 0.000000 -1 2.500000 42.476000 41.756281 33.368750 17681 2 0.000000 1 2.500000 44.772000 43.081877 36.881250 @@ -17699,7 +17699,7 @@ Atoms 17683 2 0.000000 1 2.500000 47.068000 47.058666 36.881250 17684 2 0.000000 -1 2.500000 47.068000 47.058666 36.881250 17685 2 0.000000 1 2.500000 40.180000 45.733070 40.393750 -17686 2 0.000000 -1.000000 2.500000 40.180000 45.733070 40.393750 +17686 2 0.000000 -1 2.500000 40.180000 45.733070 40.393750 17687 2 0.000000 1 2.500000 42.476000 41.756281 40.393750 17688 2 0.000000 -1 2.500000 42.476000 41.756281 40.393750 17689 2 0.000000 1 2.500000 44.772000 43.081877 43.906250 @@ -17707,7 +17707,7 @@ Atoms 17691 2 0.000000 1 2.500000 47.068000 47.058666 43.906250 17692 2 0.000000 -1 2.500000 47.068000 47.058666 43.906250 17693 2 0.000000 1 2.500000 40.180000 45.733070 47.418750 -17694 2 0.000000 -1.000000 2.500000 40.180000 45.733070 47.418750 +17694 2 0.000000 -1 2.500000 40.180000 45.733070 47.418750 17695 2 0.000000 1 2.500000 42.476000 41.756281 47.418750 17696 2 0.000000 -1 2.500000 42.476000 41.756281 47.418750 17697 2 0.000000 1 2.500000 44.772000 43.081877 50.931250 @@ -17715,7 +17715,7 @@ Atoms 17699 2 0.000000 1 2.500000 47.068000 47.058666 50.931250 17700 2 0.000000 -1 2.500000 47.068000 47.058666 50.931250 17701 2 0.000000 1 2.500000 40.180000 45.733070 54.443750 -17702 2 0.000000 -1.000000 2.500000 40.180000 45.733070 54.443750 +17702 2 0.000000 -1 2.500000 40.180000 45.733070 54.443750 17703 2 0.000000 1 2.500000 42.476000 41.756281 54.443750 17704 2 0.000000 -1 2.500000 42.476000 41.756281 54.443750 17705 2 0.000000 1 2.500000 44.772000 43.081877 57.956250 @@ -17723,7 +17723,7 @@ Atoms 17707 2 0.000000 1 2.500000 47.068000 47.058666 57.956250 17708 2 0.000000 -1 2.500000 47.068000 47.058666 57.956250 17709 2 0.000000 1 2.500000 40.180000 45.733070 61.468750 -17710 2 0.000000 -1.000000 2.500000 40.180000 45.733070 61.468750 +17710 2 0.000000 -1 2.500000 40.180000 45.733070 61.468750 17711 2 0.000000 1 2.500000 42.476000 41.756281 61.468750 17712 2 0.000000 -1 2.500000 42.476000 41.756281 61.468750 17713 2 0.000000 1 2.500000 44.772000 51.035454 1.756250 @@ -17731,7 +17731,7 @@ Atoms 17715 2 0.000000 1 2.500000 47.068000 55.012243 1.756250 17716 2 0.000000 -1 2.500000 47.068000 55.012243 1.756250 17717 2 0.000000 1 2.500000 40.180000 53.686647 5.268750 -17718 2 0.000000 -1.000000 2.500000 40.180000 53.686647 5.268750 +17718 2 0.000000 -1 2.500000 40.180000 53.686647 5.268750 17719 2 0.000000 1 2.500000 42.476000 49.709858 5.268750 17720 2 0.000000 -1 2.500000 42.476000 49.709858 5.268750 17721 2 0.000000 1 2.500000 44.772000 51.035454 8.781250 @@ -17739,7 +17739,7 @@ Atoms 17723 2 0.000000 1 2.500000 47.068000 55.012243 8.781250 17724 2 0.000000 -1 2.500000 47.068000 55.012243 8.781250 17725 2 0.000000 1 2.500000 40.180000 53.686647 12.293750 -17726 2 0.000000 -1.000000 2.500000 40.180000 53.686647 12.293750 +17726 2 0.000000 -1 2.500000 40.180000 53.686647 12.293750 17727 2 0.000000 1 2.500000 42.476000 49.709858 12.293750 17728 2 0.000000 -1 2.500000 42.476000 49.709858 12.293750 17729 2 0.000000 1 2.500000 44.772000 51.035454 15.806250 @@ -17747,7 +17747,7 @@ Atoms 17731 2 0.000000 1 2.500000 47.068000 55.012243 15.806250 17732 2 0.000000 -1 2.500000 47.068000 55.012243 15.806250 17733 2 0.000000 1 2.500000 40.180000 53.686647 19.318750 -17734 2 0.000000 -1.000000 2.500000 40.180000 53.686647 19.318750 +17734 2 0.000000 -1 2.500000 40.180000 53.686647 19.318750 17735 2 0.000000 1 2.500000 42.476000 49.709858 19.318750 17736 2 0.000000 -1 2.500000 42.476000 49.709858 19.318750 17737 2 0.000000 1 2.500000 44.772000 51.035454 22.831250 @@ -17755,7 +17755,7 @@ Atoms 17739 2 0.000000 1 2.500000 47.068000 55.012243 22.831250 17740 2 0.000000 -1 2.500000 47.068000 55.012243 22.831250 17741 2 0.000000 1 2.500000 40.180000 53.686647 26.343750 -17742 2 0.000000 -1.000000 2.500000 40.180000 53.686647 26.343750 +17742 2 0.000000 -1 2.500000 40.180000 53.686647 26.343750 17743 2 0.000000 1 2.500000 42.476000 49.709858 26.343750 17744 2 0.000000 -1 2.500000 42.476000 49.709858 26.343750 17745 2 0.000000 1 2.500000 44.772000 51.035454 29.856250 @@ -17763,7 +17763,7 @@ Atoms 17747 2 0.000000 1 2.500000 47.068000 55.012243 29.856250 17748 2 0.000000 -1 2.500000 47.068000 55.012243 29.856250 17749 2 0.000000 1 2.500000 40.180000 53.686647 33.368750 -17750 2 0.000000 -1.000000 2.500000 40.180000 53.686647 33.368750 +17750 2 0.000000 -1 2.500000 40.180000 53.686647 33.368750 17751 2 0.000000 1 2.500000 42.476000 49.709858 33.368750 17752 2 0.000000 -1 2.500000 42.476000 49.709858 33.368750 17753 2 0.000000 1 2.500000 44.772000 51.035454 36.881250 @@ -17771,7 +17771,7 @@ Atoms 17755 2 0.000000 1 2.500000 47.068000 55.012243 36.881250 17756 2 0.000000 -1 2.500000 47.068000 55.012243 36.881250 17757 2 0.000000 1 2.500000 40.180000 53.686647 40.393750 -17758 2 0.000000 -1.000000 2.500000 40.180000 53.686647 40.393750 +17758 2 0.000000 -1 2.500000 40.180000 53.686647 40.393750 17759 2 0.000000 1 2.500000 42.476000 49.709858 40.393750 17760 2 0.000000 -1 2.500000 42.476000 49.709858 40.393750 17761 2 0.000000 1 2.500000 44.772000 51.035454 43.906250 @@ -17779,7 +17779,7 @@ Atoms 17763 2 0.000000 1 2.500000 47.068000 55.012243 43.906250 17764 2 0.000000 -1 2.500000 47.068000 55.012243 43.906250 17765 2 0.000000 1 2.500000 40.180000 53.686647 47.418750 -17766 2 0.000000 -1.000000 2.500000 40.180000 53.686647 47.418750 +17766 2 0.000000 -1 2.500000 40.180000 53.686647 47.418750 17767 2 0.000000 1 2.500000 42.476000 49.709858 47.418750 17768 2 0.000000 -1 2.500000 42.476000 49.709858 47.418750 17769 2 0.000000 1 2.500000 44.772000 51.035454 50.931250 @@ -17787,7 +17787,7 @@ Atoms 17771 2 0.000000 1 2.500000 47.068000 55.012243 50.931250 17772 2 0.000000 -1 2.500000 47.068000 55.012243 50.931250 17773 2 0.000000 1 2.500000 40.180000 53.686647 54.443750 -17774 2 0.000000 -1.000000 2.500000 40.180000 53.686647 54.443750 +17774 2 0.000000 -1 2.500000 40.180000 53.686647 54.443750 17775 2 0.000000 1 2.500000 42.476000 49.709858 54.443750 17776 2 0.000000 -1 2.500000 42.476000 49.709858 54.443750 17777 2 0.000000 1 2.500000 44.772000 51.035454 57.956250 @@ -17795,7 +17795,7 @@ Atoms 17779 2 0.000000 1 2.500000 47.068000 55.012243 57.956250 17780 2 0.000000 -1 2.500000 47.068000 55.012243 57.956250 17781 2 0.000000 1 2.500000 40.180000 53.686647 61.468750 -17782 2 0.000000 -1.000000 2.500000 40.180000 53.686647 61.468750 +17782 2 0.000000 -1 2.500000 40.180000 53.686647 61.468750 17783 2 0.000000 1 2.500000 42.476000 49.709858 61.468750 17784 2 0.000000 -1 2.500000 42.476000 49.709858 61.468750 17785 2 0.000000 1 2.500000 44.772000 58.989032 1.756250 @@ -17803,7 +17803,7 @@ Atoms 17787 2 0.000000 1 2.500000 47.068000 62.965820 1.756250 17788 2 0.000000 -1 2.500000 47.068000 62.965820 1.756250 17789 2 0.000000 1 2.500000 40.180000 61.640224 5.268750 -17790 2 0.000000 -1.000000 2.500000 40.180000 61.640224 5.268750 +17790 2 0.000000 -1 2.500000 40.180000 61.640224 5.268750 17791 2 0.000000 1 2.500000 42.476000 57.663435 5.268750 17792 2 0.000000 -1 2.500000 42.476000 57.663435 5.268750 17793 2 0.000000 1 2.500000 44.772000 58.989032 8.781250 @@ -17811,7 +17811,7 @@ Atoms 17795 2 0.000000 1 2.500000 47.068000 62.965820 8.781250 17796 2 0.000000 -1 2.500000 47.068000 62.965820 8.781250 17797 2 0.000000 1 2.500000 40.180000 61.640224 12.293750 -17798 2 0.000000 -1.000000 2.500000 40.180000 61.640224 12.293750 +17798 2 0.000000 -1 2.500000 40.180000 61.640224 12.293750 17799 2 0.000000 1 2.500000 42.476000 57.663435 12.293750 17800 2 0.000000 -1 2.500000 42.476000 57.663435 12.293750 17801 2 0.000000 1 2.500000 44.772000 58.989032 15.806250 @@ -17819,7 +17819,7 @@ Atoms 17803 2 0.000000 1 2.500000 47.068000 62.965820 15.806250 17804 2 0.000000 -1 2.500000 47.068000 62.965820 15.806250 17805 2 0.000000 1 2.500000 40.180000 61.640224 19.318750 -17806 2 0.000000 -1.000000 2.500000 40.180000 61.640224 19.318750 +17806 2 0.000000 -1 2.500000 40.180000 61.640224 19.318750 17807 2 0.000000 1 2.500000 42.476000 57.663435 19.318750 17808 2 0.000000 -1 2.500000 42.476000 57.663435 19.318750 17809 2 0.000000 1 2.500000 44.772000 58.989032 22.831250 @@ -17827,7 +17827,7 @@ Atoms 17811 2 0.000000 1 2.500000 47.068000 62.965820 22.831250 17812 2 0.000000 -1 2.500000 47.068000 62.965820 22.831250 17813 2 0.000000 1 2.500000 40.180000 61.640224 26.343750 -17814 2 0.000000 -1.000000 2.500000 40.180000 61.640224 26.343750 +17814 2 0.000000 -1 2.500000 40.180000 61.640224 26.343750 17815 2 0.000000 1 2.500000 42.476000 57.663435 26.343750 17816 2 0.000000 -1 2.500000 42.476000 57.663435 26.343750 17817 2 0.000000 1 2.500000 44.772000 58.989032 29.856250 @@ -17835,7 +17835,7 @@ Atoms 17819 2 0.000000 1 2.500000 47.068000 62.965820 29.856250 17820 2 0.000000 -1 2.500000 47.068000 62.965820 29.856250 17821 2 0.000000 1 2.500000 40.180000 61.640224 33.368750 -17822 2 0.000000 -1.000000 2.500000 40.180000 61.640224 33.368750 +17822 2 0.000000 -1 2.500000 40.180000 61.640224 33.368750 17823 2 0.000000 1 2.500000 42.476000 57.663435 33.368750 17824 2 0.000000 -1 2.500000 42.476000 57.663435 33.368750 17825 2 0.000000 1 2.500000 44.772000 58.989032 36.881250 @@ -17843,7 +17843,7 @@ Atoms 17827 2 0.000000 1 2.500000 47.068000 62.965820 36.881250 17828 2 0.000000 -1 2.500000 47.068000 62.965820 36.881250 17829 2 0.000000 1 2.500000 40.180000 61.640224 40.393750 -17830 2 0.000000 -1.000000 2.500000 40.180000 61.640224 40.393750 +17830 2 0.000000 -1 2.500000 40.180000 61.640224 40.393750 17831 2 0.000000 1 2.500000 42.476000 57.663435 40.393750 17832 2 0.000000 -1 2.500000 42.476000 57.663435 40.393750 17833 2 0.000000 1 2.500000 44.772000 58.989032 43.906250 @@ -17851,7 +17851,7 @@ Atoms 17835 2 0.000000 1 2.500000 47.068000 62.965820 43.906250 17836 2 0.000000 -1 2.500000 47.068000 62.965820 43.906250 17837 2 0.000000 1 2.500000 40.180000 61.640224 47.418750 -17838 2 0.000000 -1.000000 2.500000 40.180000 61.640224 47.418750 +17838 2 0.000000 -1 2.500000 40.180000 61.640224 47.418750 17839 2 0.000000 1 2.500000 42.476000 57.663435 47.418750 17840 2 0.000000 -1 2.500000 42.476000 57.663435 47.418750 17841 2 0.000000 1 2.500000 44.772000 58.989032 50.931250 @@ -17859,7 +17859,7 @@ Atoms 17843 2 0.000000 1 2.500000 47.068000 62.965820 50.931250 17844 2 0.000000 -1 2.500000 47.068000 62.965820 50.931250 17845 2 0.000000 1 2.500000 40.180000 61.640224 54.443750 -17846 2 0.000000 -1.000000 2.500000 40.180000 61.640224 54.443750 +17846 2 0.000000 -1 2.500000 40.180000 61.640224 54.443750 17847 2 0.000000 1 2.500000 42.476000 57.663435 54.443750 17848 2 0.000000 -1 2.500000 42.476000 57.663435 54.443750 17849 2 0.000000 1 2.500000 44.772000 58.989032 57.956250 @@ -17867,7 +17867,7 @@ Atoms 17851 2 0.000000 1 2.500000 47.068000 62.965820 57.956250 17852 2 0.000000 -1 2.500000 47.068000 62.965820 57.956250 17853 2 0.000000 1 2.500000 40.180000 61.640224 61.468750 -17854 2 0.000000 -1.000000 2.500000 40.180000 61.640224 61.468750 +17854 2 0.000000 -1 2.500000 40.180000 61.640224 61.468750 17855 2 0.000000 1 2.500000 42.476000 57.663435 61.468750 17856 2 0.000000 -1 2.500000 42.476000 57.663435 61.468750 17857 2 0.000000 1 2.500000 49.364000 3.313991 1.756250 @@ -17875,7 +17875,7 @@ Atoms 17859 2 0.000000 1 2.500000 51.660000 7.290779 1.756250 17860 2 0.000000 -1 2.500000 51.660000 7.290779 1.756250 17861 2 0.000000 1 2.500000 44.772000 5.965183 5.268750 -17862 2 0.000000 -1.000000 2.500000 44.772000 5.965183 5.268750 +17862 2 0.000000 -1 2.500000 44.772000 5.965183 5.268750 17863 2 0.000000 1 2.500000 47.068000 1.988394 5.268750 17864 2 0.000000 -1 2.500000 47.068000 1.988394 5.268750 17865 2 0.000000 1 2.500000 49.364000 3.313991 8.781250 @@ -17883,7 +17883,7 @@ Atoms 17867 2 0.000000 1 2.500000 51.660000 7.290779 8.781250 17868 2 0.000000 -1 2.500000 51.660000 7.290779 8.781250 17869 2 0.000000 1 2.500000 44.772000 5.965183 12.293750 -17870 2 0.000000 -1.000000 2.500000 44.772000 5.965183 12.293750 +17870 2 0.000000 -1 2.500000 44.772000 5.965183 12.293750 17871 2 0.000000 1 2.500000 47.068000 1.988394 12.293750 17872 2 0.000000 -1 2.500000 47.068000 1.988394 12.293750 17873 2 0.000000 1 2.500000 49.364000 3.313991 15.806250 @@ -17891,7 +17891,7 @@ Atoms 17875 2 0.000000 1 2.500000 51.660000 7.290779 15.806250 17876 2 0.000000 -1 2.500000 51.660000 7.290779 15.806250 17877 2 0.000000 1 2.500000 44.772000 5.965183 19.318750 -17878 2 0.000000 -1.000000 2.500000 44.772000 5.965183 19.318750 +17878 2 0.000000 -1 2.500000 44.772000 5.965183 19.318750 17879 2 0.000000 1 2.500000 47.068000 1.988394 19.318750 17880 2 0.000000 -1 2.500000 47.068000 1.988394 19.318750 17881 2 0.000000 1 2.500000 49.364000 3.313991 22.831250 @@ -17899,7 +17899,7 @@ Atoms 17883 2 0.000000 1 2.500000 51.660000 7.290779 22.831250 17884 2 0.000000 -1 2.500000 51.660000 7.290779 22.831250 17885 2 0.000000 1 2.500000 44.772000 5.965183 26.343750 -17886 2 0.000000 -1.000000 2.500000 44.772000 5.965183 26.343750 +17886 2 0.000000 -1 2.500000 44.772000 5.965183 26.343750 17887 2 0.000000 1 2.500000 47.068000 1.988394 26.343750 17888 2 0.000000 -1 2.500000 47.068000 1.988394 26.343750 17889 2 0.000000 1 2.500000 49.364000 3.313991 29.856250 @@ -17907,7 +17907,7 @@ Atoms 17891 2 0.000000 1 2.500000 51.660000 7.290779 29.856250 17892 2 0.000000 -1 2.500000 51.660000 7.290779 29.856250 17893 2 0.000000 1 2.500000 44.772000 5.965183 33.368750 -17894 2 0.000000 -1.000000 2.500000 44.772000 5.965183 33.368750 +17894 2 0.000000 -1 2.500000 44.772000 5.965183 33.368750 17895 2 0.000000 1 2.500000 47.068000 1.988394 33.368750 17896 2 0.000000 -1 2.500000 47.068000 1.988394 33.368750 17897 2 0.000000 1 2.500000 49.364000 3.313991 36.881250 @@ -17915,7 +17915,7 @@ Atoms 17899 2 0.000000 1 2.500000 51.660000 7.290779 36.881250 17900 2 0.000000 -1 2.500000 51.660000 7.290779 36.881250 17901 2 0.000000 1 2.500000 44.772000 5.965183 40.393750 -17902 2 0.000000 -1.000000 2.500000 44.772000 5.965183 40.393750 +17902 2 0.000000 -1 2.500000 44.772000 5.965183 40.393750 17903 2 0.000000 1 2.500000 47.068000 1.988394 40.393750 17904 2 0.000000 -1 2.500000 47.068000 1.988394 40.393750 17905 2 0.000000 1 2.500000 49.364000 3.313991 43.906250 @@ -17923,7 +17923,7 @@ Atoms 17907 2 0.000000 1 2.500000 51.660000 7.290779 43.906250 17908 2 0.000000 -1 2.500000 51.660000 7.290779 43.906250 17909 2 0.000000 1 2.500000 44.772000 5.965183 47.418750 -17910 2 0.000000 -1.000000 2.500000 44.772000 5.965183 47.418750 +17910 2 0.000000 -1 2.500000 44.772000 5.965183 47.418750 17911 2 0.000000 1 2.500000 47.068000 1.988394 47.418750 17912 2 0.000000 -1 2.500000 47.068000 1.988394 47.418750 17913 2 0.000000 1 2.500000 49.364000 3.313991 50.931250 @@ -17931,7 +17931,7 @@ Atoms 17915 2 0.000000 1 2.500000 51.660000 7.290779 50.931250 17916 2 0.000000 -1 2.500000 51.660000 7.290779 50.931250 17917 2 0.000000 1 2.500000 44.772000 5.965183 54.443750 -17918 2 0.000000 -1.000000 2.500000 44.772000 5.965183 54.443750 +17918 2 0.000000 -1 2.500000 44.772000 5.965183 54.443750 17919 2 0.000000 1 2.500000 47.068000 1.988394 54.443750 17920 2 0.000000 -1 2.500000 47.068000 1.988394 54.443750 17921 2 0.000000 1 2.500000 49.364000 3.313991 57.956250 @@ -17939,7 +17939,7 @@ Atoms 17923 2 0.000000 1 2.500000 51.660000 7.290779 57.956250 17924 2 0.000000 -1 2.500000 51.660000 7.290779 57.956250 17925 2 0.000000 1 2.500000 44.772000 5.965183 61.468750 -17926 2 0.000000 -1.000000 2.500000 44.772000 5.965183 61.468750 +17926 2 0.000000 -1 2.500000 44.772000 5.965183 61.468750 17927 2 0.000000 1 2.500000 47.068000 1.988394 61.468750 17928 2 0.000000 -1 2.500000 47.068000 1.988394 61.468750 17929 2 0.000000 1 2.500000 49.364000 11.267568 1.756250 @@ -17947,7 +17947,7 @@ Atoms 17931 2 0.000000 1 2.500000 51.660000 15.244357 1.756250 17932 2 0.000000 -1 2.500000 51.660000 15.244357 1.756250 17933 2 0.000000 1 2.500000 44.772000 13.918760 5.268750 -17934 2 0.000000 -1.000000 2.500000 44.772000 13.918760 5.268750 +17934 2 0.000000 -1 2.500000 44.772000 13.918760 5.268750 17935 2 0.000000 1 2.500000 47.068000 9.941972 5.268750 17936 2 0.000000 -1 2.500000 47.068000 9.941972 5.268750 17937 2 0.000000 1 2.500000 49.364000 11.267568 8.781250 @@ -17955,7 +17955,7 @@ Atoms 17939 2 0.000000 1 2.500000 51.660000 15.244357 8.781250 17940 2 0.000000 -1 2.500000 51.660000 15.244357 8.781250 17941 2 0.000000 1 2.500000 44.772000 13.918760 12.293750 -17942 2 0.000000 -1.000000 2.500000 44.772000 13.918760 12.293750 +17942 2 0.000000 -1 2.500000 44.772000 13.918760 12.293750 17943 2 0.000000 1 2.500000 47.068000 9.941972 12.293750 17944 2 0.000000 -1 2.500000 47.068000 9.941972 12.293750 17945 2 0.000000 1 2.500000 49.364000 11.267568 15.806250 @@ -17963,7 +17963,7 @@ Atoms 17947 2 0.000000 1 2.500000 51.660000 15.244357 15.806250 17948 2 0.000000 -1 2.500000 51.660000 15.244357 15.806250 17949 2 0.000000 1 2.500000 44.772000 13.918760 19.318750 -17950 2 0.000000 -1.000000 2.500000 44.772000 13.918760 19.318750 +17950 2 0.000000 -1 2.500000 44.772000 13.918760 19.318750 17951 2 0.000000 1 2.500000 47.068000 9.941972 19.318750 17952 2 0.000000 -1 2.500000 47.068000 9.941972 19.318750 17953 2 0.000000 1 2.500000 49.364000 11.267568 22.831250 @@ -17971,7 +17971,7 @@ Atoms 17955 2 0.000000 1 2.500000 51.660000 15.244357 22.831250 17956 2 0.000000 -1 2.500000 51.660000 15.244357 22.831250 17957 2 0.000000 1 2.500000 44.772000 13.918760 26.343750 -17958 2 0.000000 -1.000000 2.500000 44.772000 13.918760 26.343750 +17958 2 0.000000 -1 2.500000 44.772000 13.918760 26.343750 17959 2 0.000000 1 2.500000 47.068000 9.941972 26.343750 17960 2 0.000000 -1 2.500000 47.068000 9.941972 26.343750 17961 2 0.000000 1 2.500000 49.364000 11.267568 29.856250 @@ -17979,7 +17979,7 @@ Atoms 17963 2 0.000000 1 2.500000 51.660000 15.244357 29.856250 17964 2 0.000000 -1 2.500000 51.660000 15.244357 29.856250 17965 2 0.000000 1 2.500000 44.772000 13.918760 33.368750 -17966 2 0.000000 -1.000000 2.500000 44.772000 13.918760 33.368750 +17966 2 0.000000 -1 2.500000 44.772000 13.918760 33.368750 17967 2 0.000000 1 2.500000 47.068000 9.941972 33.368750 17968 2 0.000000 -1 2.500000 47.068000 9.941972 33.368750 17969 2 0.000000 1 2.500000 49.364000 11.267568 36.881250 @@ -17987,7 +17987,7 @@ Atoms 17971 2 0.000000 1 2.500000 51.660000 15.244357 36.881250 17972 2 0.000000 -1 2.500000 51.660000 15.244357 36.881250 17973 2 0.000000 1 2.500000 44.772000 13.918760 40.393750 -17974 2 0.000000 -1.000000 2.500000 44.772000 13.918760 40.393750 +17974 2 0.000000 -1 2.500000 44.772000 13.918760 40.393750 17975 2 0.000000 1 2.500000 47.068000 9.941972 40.393750 17976 2 0.000000 -1 2.500000 47.068000 9.941972 40.393750 17977 2 0.000000 1 2.500000 49.364000 11.267568 43.906250 @@ -17995,7 +17995,7 @@ Atoms 17979 2 0.000000 1 2.500000 51.660000 15.244357 43.906250 17980 2 0.000000 -1 2.500000 51.660000 15.244357 43.906250 17981 2 0.000000 1 2.500000 44.772000 13.918760 47.418750 -17982 2 0.000000 -1.000000 2.500000 44.772000 13.918760 47.418750 +17982 2 0.000000 -1 2.500000 44.772000 13.918760 47.418750 17983 2 0.000000 1 2.500000 47.068000 9.941972 47.418750 17984 2 0.000000 -1 2.500000 47.068000 9.941972 47.418750 17985 2 0.000000 1 2.500000 49.364000 11.267568 50.931250 @@ -18003,7 +18003,7 @@ Atoms 17987 2 0.000000 1 2.500000 51.660000 15.244357 50.931250 17988 2 0.000000 -1 2.500000 51.660000 15.244357 50.931250 17989 2 0.000000 1 2.500000 44.772000 13.918760 54.443750 -17990 2 0.000000 -1.000000 2.500000 44.772000 13.918760 54.443750 +17990 2 0.000000 -1 2.500000 44.772000 13.918760 54.443750 17991 2 0.000000 1 2.500000 47.068000 9.941972 54.443750 17992 2 0.000000 -1 2.500000 47.068000 9.941972 54.443750 17993 2 0.000000 1 2.500000 49.364000 11.267568 57.956250 @@ -18011,7 +18011,7 @@ Atoms 17995 2 0.000000 1 2.500000 51.660000 15.244357 57.956250 17996 2 0.000000 -1 2.500000 51.660000 15.244357 57.956250 17997 2 0.000000 1 2.500000 44.772000 13.918760 61.468750 -17998 2 0.000000 -1.000000 2.500000 44.772000 13.918760 61.468750 +17998 2 0.000000 -1 2.500000 44.772000 13.918760 61.468750 17999 2 0.000000 1 2.500000 47.068000 9.941972 61.468750 18000 2 0.000000 -1 2.500000 47.068000 9.941972 61.468750 18001 2 0.000000 1 2.500000 49.364000 19.221145 1.756250 @@ -18019,7 +18019,7 @@ Atoms 18003 2 0.000000 1 2.500000 51.660000 23.197934 1.756250 18004 2 0.000000 -1 2.500000 51.660000 23.197934 1.756250 18005 2 0.000000 1 2.500000 44.772000 21.872338 5.268750 -18006 2 0.000000 -1.000000 2.500000 44.772000 21.872338 5.268750 +18006 2 0.000000 -1 2.500000 44.772000 21.872338 5.268750 18007 2 0.000000 1 2.500000 47.068000 17.895549 5.268750 18008 2 0.000000 -1 2.500000 47.068000 17.895549 5.268750 18009 2 0.000000 1 2.500000 49.364000 19.221145 8.781250 @@ -18027,7 +18027,7 @@ Atoms 18011 2 0.000000 1 2.500000 51.660000 23.197934 8.781250 18012 2 0.000000 -1 2.500000 51.660000 23.197934 8.781250 18013 2 0.000000 1 2.500000 44.772000 21.872338 12.293750 -18014 2 0.000000 -1.000000 2.500000 44.772000 21.872338 12.293750 +18014 2 0.000000 -1 2.500000 44.772000 21.872338 12.293750 18015 2 0.000000 1 2.500000 47.068000 17.895549 12.293750 18016 2 0.000000 -1 2.500000 47.068000 17.895549 12.293750 18017 2 0.000000 1 2.500000 49.364000 19.221145 15.806250 @@ -18035,7 +18035,7 @@ Atoms 18019 2 0.000000 1 2.500000 51.660000 23.197934 15.806250 18020 2 0.000000 -1 2.500000 51.660000 23.197934 15.806250 18021 2 0.000000 1 2.500000 44.772000 21.872338 19.318750 -18022 2 0.000000 -1.000000 2.500000 44.772000 21.872338 19.318750 +18022 2 0.000000 -1 2.500000 44.772000 21.872338 19.318750 18023 2 0.000000 1 2.500000 47.068000 17.895549 19.318750 18024 2 0.000000 -1 2.500000 47.068000 17.895549 19.318750 18025 2 0.000000 1 2.500000 49.364000 19.221145 22.831250 @@ -18043,7 +18043,7 @@ Atoms 18027 2 0.000000 1 2.500000 51.660000 23.197934 22.831250 18028 2 0.000000 -1 2.500000 51.660000 23.197934 22.831250 18029 2 0.000000 1 2.500000 44.772000 21.872338 26.343750 -18030 2 0.000000 -1.000000 2.500000 44.772000 21.872338 26.343750 +18030 2 0.000000 -1 2.500000 44.772000 21.872338 26.343750 18031 2 0.000000 1 2.500000 47.068000 17.895549 26.343750 18032 2 0.000000 -1 2.500000 47.068000 17.895549 26.343750 18033 2 0.000000 1 2.500000 49.364000 19.221145 29.856250 @@ -18051,7 +18051,7 @@ Atoms 18035 2 0.000000 1 2.500000 51.660000 23.197934 29.856250 18036 2 0.000000 -1 2.500000 51.660000 23.197934 29.856250 18037 2 0.000000 1 2.500000 44.772000 21.872338 33.368750 -18038 2 0.000000 -1.000000 2.500000 44.772000 21.872338 33.368750 +18038 2 0.000000 -1 2.500000 44.772000 21.872338 33.368750 18039 2 0.000000 1 2.500000 47.068000 17.895549 33.368750 18040 2 0.000000 -1 2.500000 47.068000 17.895549 33.368750 18041 2 0.000000 1 2.500000 49.364000 19.221145 36.881250 @@ -18059,7 +18059,7 @@ Atoms 18043 2 0.000000 1 2.500000 51.660000 23.197934 36.881250 18044 2 0.000000 -1 2.500000 51.660000 23.197934 36.881250 18045 2 0.000000 1 2.500000 44.772000 21.872338 40.393750 -18046 2 0.000000 -1.000000 2.500000 44.772000 21.872338 40.393750 +18046 2 0.000000 -1 2.500000 44.772000 21.872338 40.393750 18047 2 0.000000 1 2.500000 47.068000 17.895549 40.393750 18048 2 0.000000 -1 2.500000 47.068000 17.895549 40.393750 18049 2 0.000000 1 2.500000 49.364000 19.221145 43.906250 @@ -18067,7 +18067,7 @@ Atoms 18051 2 0.000000 1 2.500000 51.660000 23.197934 43.906250 18052 2 0.000000 -1 2.500000 51.660000 23.197934 43.906250 18053 2 0.000000 1 2.500000 44.772000 21.872338 47.418750 -18054 2 0.000000 -1.000000 2.500000 44.772000 21.872338 47.418750 +18054 2 0.000000 -1 2.500000 44.772000 21.872338 47.418750 18055 2 0.000000 1 2.500000 47.068000 17.895549 47.418750 18056 2 0.000000 -1 2.500000 47.068000 17.895549 47.418750 18057 2 0.000000 1 2.500000 49.364000 19.221145 50.931250 @@ -18075,7 +18075,7 @@ Atoms 18059 2 0.000000 1 2.500000 51.660000 23.197934 50.931250 18060 2 0.000000 -1 2.500000 51.660000 23.197934 50.931250 18061 2 0.000000 1 2.500000 44.772000 21.872338 54.443750 -18062 2 0.000000 -1.000000 2.500000 44.772000 21.872338 54.443750 +18062 2 0.000000 -1 2.500000 44.772000 21.872338 54.443750 18063 2 0.000000 1 2.500000 47.068000 17.895549 54.443750 18064 2 0.000000 -1 2.500000 47.068000 17.895549 54.443750 18065 2 0.000000 1 2.500000 49.364000 19.221145 57.956250 @@ -18083,7 +18083,7 @@ Atoms 18067 2 0.000000 1 2.500000 51.660000 23.197934 57.956250 18068 2 0.000000 -1 2.500000 51.660000 23.197934 57.956250 18069 2 0.000000 1 2.500000 44.772000 21.872338 61.468750 -18070 2 0.000000 -1.000000 2.500000 44.772000 21.872338 61.468750 +18070 2 0.000000 -1 2.500000 44.772000 21.872338 61.468750 18071 2 0.000000 1 2.500000 47.068000 17.895549 61.468750 18072 2 0.000000 -1 2.500000 47.068000 17.895549 61.468750 18073 2 0.000000 1 2.500000 49.364000 27.174722 1.756250 @@ -18091,7 +18091,7 @@ Atoms 18075 2 0.000000 1 2.500000 51.660000 31.151511 1.756250 18076 2 0.000000 -1 2.500000 51.660000 31.151511 1.756250 18077 2 0.000000 1 2.500000 44.772000 29.825915 5.268750 -18078 2 0.000000 -1.000000 2.500000 44.772000 29.825915 5.268750 +18078 2 0.000000 -1 2.500000 44.772000 29.825915 5.268750 18079 2 0.000000 1 2.500000 47.068000 25.849126 5.268750 18080 2 0.000000 -1 2.500000 47.068000 25.849126 5.268750 18081 2 0.000000 1 2.500000 49.364000 27.174722 8.781250 @@ -18099,7 +18099,7 @@ Atoms 18083 2 0.000000 1 2.500000 51.660000 31.151511 8.781250 18084 2 0.000000 -1 2.500000 51.660000 31.151511 8.781250 18085 2 0.000000 1 2.500000 44.772000 29.825915 12.293750 -18086 2 0.000000 -1.000000 2.500000 44.772000 29.825915 12.293750 +18086 2 0.000000 -1 2.500000 44.772000 29.825915 12.293750 18087 2 0.000000 1 2.500000 47.068000 25.849126 12.293750 18088 2 0.000000 -1 2.500000 47.068000 25.849126 12.293750 18089 2 0.000000 1 2.500000 49.364000 27.174722 15.806250 @@ -18107,7 +18107,7 @@ Atoms 18091 2 0.000000 1 2.500000 51.660000 31.151511 15.806250 18092 2 0.000000 -1 2.500000 51.660000 31.151511 15.806250 18093 2 0.000000 1 2.500000 44.772000 29.825915 19.318750 -18094 2 0.000000 -1.000000 2.500000 44.772000 29.825915 19.318750 +18094 2 0.000000 -1 2.500000 44.772000 29.825915 19.318750 18095 2 0.000000 1 2.500000 47.068000 25.849126 19.318750 18096 2 0.000000 -1 2.500000 47.068000 25.849126 19.318750 18097 2 0.000000 1 2.500000 49.364000 27.174722 22.831250 @@ -18115,7 +18115,7 @@ Atoms 18099 2 0.000000 1 2.500000 51.660000 31.151511 22.831250 18100 2 0.000000 -1 2.500000 51.660000 31.151511 22.831250 18101 2 0.000000 1 2.500000 44.772000 29.825915 26.343750 -18102 2 0.000000 -1.000000 2.500000 44.772000 29.825915 26.343750 +18102 2 0.000000 -1 2.500000 44.772000 29.825915 26.343750 18103 2 0.000000 1 2.500000 47.068000 25.849126 26.343750 18104 2 0.000000 -1 2.500000 47.068000 25.849126 26.343750 18105 2 0.000000 1 2.500000 49.364000 27.174722 29.856250 @@ -18123,7 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43.906250 @@ -18139,7 +18139,7 @@ Atoms 18123 2 0.000000 1 2.500000 51.660000 31.151511 43.906250 18124 2 0.000000 -1 2.500000 51.660000 31.151511 43.906250 18125 2 0.000000 1 2.500000 44.772000 29.825915 47.418750 -18126 2 0.000000 -1.000000 2.500000 44.772000 29.825915 47.418750 +18126 2 0.000000 -1 2.500000 44.772000 29.825915 47.418750 18127 2 0.000000 1 2.500000 47.068000 25.849126 47.418750 18128 2 0.000000 -1 2.500000 47.068000 25.849126 47.418750 18129 2 0.000000 1 2.500000 49.364000 27.174722 50.931250 @@ -18147,7 +18147,7 @@ Atoms 18131 2 0.000000 1 2.500000 51.660000 31.151511 50.931250 18132 2 0.000000 -1 2.500000 51.660000 31.151511 50.931250 18133 2 0.000000 1 2.500000 44.772000 29.825915 54.443750 -18134 2 0.000000 -1.000000 2.500000 44.772000 29.825915 54.443750 +18134 2 0.000000 -1 2.500000 44.772000 29.825915 54.443750 18135 2 0.000000 1 2.500000 47.068000 25.849126 54.443750 18136 2 0.000000 -1 2.500000 47.068000 25.849126 54.443750 18137 2 0.000000 1 2.500000 49.364000 27.174722 57.956250 @@ -18155,7 +18155,7 @@ Atoms 18139 2 0.000000 1 2.500000 51.660000 31.151511 57.956250 18140 2 0.000000 -1 2.500000 51.660000 31.151511 57.956250 18141 2 0.000000 1 2.500000 44.772000 29.825915 61.468750 -18142 2 0.000000 -1.000000 2.500000 44.772000 29.825915 61.468750 +18142 2 0.000000 -1 2.500000 44.772000 29.825915 61.468750 18143 2 0.000000 1 2.500000 47.068000 25.849126 61.468750 18144 2 0.000000 -1 2.500000 47.068000 25.849126 61.468750 18145 2 0.000000 1 2.500000 49.364000 35.128300 1.756250 @@ -18163,7 +18163,7 @@ Atoms 18147 2 0.000000 1 2.500000 51.660000 39.105088 1.756250 18148 2 0.000000 -1 2.500000 51.660000 39.105088 1.756250 18149 2 0.000000 1 2.500000 44.772000 37.779492 5.268750 -18150 2 0.000000 -1.000000 2.500000 44.772000 37.779492 5.268750 +18150 2 0.000000 -1 2.500000 44.772000 37.779492 5.268750 18151 2 0.000000 1 2.500000 47.068000 33.802704 5.268750 18152 2 0.000000 -1 2.500000 47.068000 33.802704 5.268750 18153 2 0.000000 1 2.500000 49.364000 35.128300 8.781250 @@ -18171,7 +18171,7 @@ Atoms 18155 2 0.000000 1 2.500000 51.660000 39.105088 8.781250 18156 2 0.000000 -1 2.500000 51.660000 39.105088 8.781250 18157 2 0.000000 1 2.500000 44.772000 37.779492 12.293750 -18158 2 0.000000 -1.000000 2.500000 44.772000 37.779492 12.293750 +18158 2 0.000000 -1 2.500000 44.772000 37.779492 12.293750 18159 2 0.000000 1 2.500000 47.068000 33.802704 12.293750 18160 2 0.000000 -1 2.500000 47.068000 33.802704 12.293750 18161 2 0.000000 1 2.500000 49.364000 35.128300 15.806250 @@ -18179,7 +18179,7 @@ Atoms 18163 2 0.000000 1 2.500000 51.660000 39.105088 15.806250 18164 2 0.000000 -1 2.500000 51.660000 39.105088 15.806250 18165 2 0.000000 1 2.500000 44.772000 37.779492 19.318750 -18166 2 0.000000 -1.000000 2.500000 44.772000 37.779492 19.318750 +18166 2 0.000000 -1 2.500000 44.772000 37.779492 19.318750 18167 2 0.000000 1 2.500000 47.068000 33.802704 19.318750 18168 2 0.000000 -1 2.500000 47.068000 33.802704 19.318750 18169 2 0.000000 1 2.500000 49.364000 35.128300 22.831250 @@ -18187,7 +18187,7 @@ Atoms 18171 2 0.000000 1 2.500000 51.660000 39.105088 22.831250 18172 2 0.000000 -1 2.500000 51.660000 39.105088 22.831250 18173 2 0.000000 1 2.500000 44.772000 37.779492 26.343750 -18174 2 0.000000 -1.000000 2.500000 44.772000 37.779492 26.343750 +18174 2 0.000000 -1 2.500000 44.772000 37.779492 26.343750 18175 2 0.000000 1 2.500000 47.068000 33.802704 26.343750 18176 2 0.000000 -1 2.500000 47.068000 33.802704 26.343750 18177 2 0.000000 1 2.500000 49.364000 35.128300 29.856250 @@ -18195,7 +18195,7 @@ Atoms 18179 2 0.000000 1 2.500000 51.660000 39.105088 29.856250 18180 2 0.000000 -1 2.500000 51.660000 39.105088 29.856250 18181 2 0.000000 1 2.500000 44.772000 37.779492 33.368750 -18182 2 0.000000 -1.000000 2.500000 44.772000 37.779492 33.368750 +18182 2 0.000000 -1 2.500000 44.772000 37.779492 33.368750 18183 2 0.000000 1 2.500000 47.068000 33.802704 33.368750 18184 2 0.000000 -1 2.500000 47.068000 33.802704 33.368750 18185 2 0.000000 1 2.500000 49.364000 35.128300 36.881250 @@ -18203,7 +18203,7 @@ Atoms 18187 2 0.000000 1 2.500000 51.660000 39.105088 36.881250 18188 2 0.000000 -1 2.500000 51.660000 39.105088 36.881250 18189 2 0.000000 1 2.500000 44.772000 37.779492 40.393750 -18190 2 0.000000 -1.000000 2.500000 44.772000 37.779492 40.393750 +18190 2 0.000000 -1 2.500000 44.772000 37.779492 40.393750 18191 2 0.000000 1 2.500000 47.068000 33.802704 40.393750 18192 2 0.000000 -1 2.500000 47.068000 33.802704 40.393750 18193 2 0.000000 1 2.500000 49.364000 35.128300 43.906250 @@ -18211,7 +18211,7 @@ Atoms 18195 2 0.000000 1 2.500000 51.660000 39.105088 43.906250 18196 2 0.000000 -1 2.500000 51.660000 39.105088 43.906250 18197 2 0.000000 1 2.500000 44.772000 37.779492 47.418750 -18198 2 0.000000 -1.000000 2.500000 44.772000 37.779492 47.418750 +18198 2 0.000000 -1 2.500000 44.772000 37.779492 47.418750 18199 2 0.000000 1 2.500000 47.068000 33.802704 47.418750 18200 2 0.000000 -1 2.500000 47.068000 33.802704 47.418750 18201 2 0.000000 1 2.500000 49.364000 35.128300 50.931250 @@ -18219,7 +18219,7 @@ Atoms 18203 2 0.000000 1 2.500000 51.660000 39.105088 50.931250 18204 2 0.000000 -1 2.500000 51.660000 39.105088 50.931250 18205 2 0.000000 1 2.500000 44.772000 37.779492 54.443750 -18206 2 0.000000 -1.000000 2.500000 44.772000 37.779492 54.443750 +18206 2 0.000000 -1 2.500000 44.772000 37.779492 54.443750 18207 2 0.000000 1 2.500000 47.068000 33.802704 54.443750 18208 2 0.000000 -1 2.500000 47.068000 33.802704 54.443750 18209 2 0.000000 1 2.500000 49.364000 35.128300 57.956250 @@ -18227,7 +18227,7 @@ Atoms 18211 2 0.000000 1 2.500000 51.660000 39.105088 57.956250 18212 2 0.000000 -1 2.500000 51.660000 39.105088 57.956250 18213 2 0.000000 1 2.500000 44.772000 37.779492 61.468750 -18214 2 0.000000 -1.000000 2.500000 44.772000 37.779492 61.468750 +18214 2 0.000000 -1 2.500000 44.772000 37.779492 61.468750 18215 2 0.000000 1 2.500000 47.068000 33.802704 61.468750 18216 2 0.000000 -1 2.500000 47.068000 33.802704 61.468750 18217 2 0.000000 1 2.500000 49.364000 43.081877 1.756250 @@ -18235,7 +18235,7 @@ Atoms 18219 2 0.000000 1 2.500000 51.660000 47.058666 1.756250 18220 2 0.000000 -1 2.500000 51.660000 47.058666 1.756250 18221 2 0.000000 1 2.500000 44.772000 45.733070 5.268750 -18222 2 0.000000 -1.000000 2.500000 44.772000 45.733070 5.268750 +18222 2 0.000000 -1 2.500000 44.772000 45.733070 5.268750 18223 2 0.000000 1 2.500000 47.068000 41.756281 5.268750 18224 2 0.000000 -1 2.500000 47.068000 41.756281 5.268750 18225 2 0.000000 1 2.500000 49.364000 43.081877 8.781250 @@ -18243,7 +18243,7 @@ Atoms 18227 2 0.000000 1 2.500000 51.660000 47.058666 8.781250 18228 2 0.000000 -1 2.500000 51.660000 47.058666 8.781250 18229 2 0.000000 1 2.500000 44.772000 45.733070 12.293750 -18230 2 0.000000 -1.000000 2.500000 44.772000 45.733070 12.293750 +18230 2 0.000000 -1 2.500000 44.772000 45.733070 12.293750 18231 2 0.000000 1 2.500000 47.068000 41.756281 12.293750 18232 2 0.000000 -1 2.500000 47.068000 41.756281 12.293750 18233 2 0.000000 1 2.500000 49.364000 43.081877 15.806250 @@ -18251,7 +18251,7 @@ Atoms 18235 2 0.000000 1 2.500000 51.660000 47.058666 15.806250 18236 2 0.000000 -1 2.500000 51.660000 47.058666 15.806250 18237 2 0.000000 1 2.500000 44.772000 45.733070 19.318750 -18238 2 0.000000 -1.000000 2.500000 44.772000 45.733070 19.318750 +18238 2 0.000000 -1 2.500000 44.772000 45.733070 19.318750 18239 2 0.000000 1 2.500000 47.068000 41.756281 19.318750 18240 2 0.000000 -1 2.500000 47.068000 41.756281 19.318750 18241 2 0.000000 1 2.500000 49.364000 43.081877 22.831250 @@ -18259,7 +18259,7 @@ Atoms 18243 2 0.000000 1 2.500000 51.660000 47.058666 22.831250 18244 2 0.000000 -1 2.500000 51.660000 47.058666 22.831250 18245 2 0.000000 1 2.500000 44.772000 45.733070 26.343750 -18246 2 0.000000 -1.000000 2.500000 44.772000 45.733070 26.343750 +18246 2 0.000000 -1 2.500000 44.772000 45.733070 26.343750 18247 2 0.000000 1 2.500000 47.068000 41.756281 26.343750 18248 2 0.000000 -1 2.500000 47.068000 41.756281 26.343750 18249 2 0.000000 1 2.500000 49.364000 43.081877 29.856250 @@ -18267,7 +18267,7 @@ Atoms 18251 2 0.000000 1 2.500000 51.660000 47.058666 29.856250 18252 2 0.000000 -1 2.500000 51.660000 47.058666 29.856250 18253 2 0.000000 1 2.500000 44.772000 45.733070 33.368750 -18254 2 0.000000 -1.000000 2.500000 44.772000 45.733070 33.368750 +18254 2 0.000000 -1 2.500000 44.772000 45.733070 33.368750 18255 2 0.000000 1 2.500000 47.068000 41.756281 33.368750 18256 2 0.000000 -1 2.500000 47.068000 41.756281 33.368750 18257 2 0.000000 1 2.500000 49.364000 43.081877 36.881250 @@ -18275,7 +18275,7 @@ Atoms 18259 2 0.000000 1 2.500000 51.660000 47.058666 36.881250 18260 2 0.000000 -1 2.500000 51.660000 47.058666 36.881250 18261 2 0.000000 1 2.500000 44.772000 45.733070 40.393750 -18262 2 0.000000 -1.000000 2.500000 44.772000 45.733070 40.393750 +18262 2 0.000000 -1 2.500000 44.772000 45.733070 40.393750 18263 2 0.000000 1 2.500000 47.068000 41.756281 40.393750 18264 2 0.000000 -1 2.500000 47.068000 41.756281 40.393750 18265 2 0.000000 1 2.500000 49.364000 43.081877 43.906250 @@ -18283,7 +18283,7 @@ Atoms 18267 2 0.000000 1 2.500000 51.660000 47.058666 43.906250 18268 2 0.000000 -1 2.500000 51.660000 47.058666 43.906250 18269 2 0.000000 1 2.500000 44.772000 45.733070 47.418750 -18270 2 0.000000 -1.000000 2.500000 44.772000 45.733070 47.418750 +18270 2 0.000000 -1 2.500000 44.772000 45.733070 47.418750 18271 2 0.000000 1 2.500000 47.068000 41.756281 47.418750 18272 2 0.000000 -1 2.500000 47.068000 41.756281 47.418750 18273 2 0.000000 1 2.500000 49.364000 43.081877 50.931250 @@ -18291,7 +18291,7 @@ Atoms 18275 2 0.000000 1 2.500000 51.660000 47.058666 50.931250 18276 2 0.000000 -1 2.500000 51.660000 47.058666 50.931250 18277 2 0.000000 1 2.500000 44.772000 45.733070 54.443750 -18278 2 0.000000 -1.000000 2.500000 44.772000 45.733070 54.443750 +18278 2 0.000000 -1 2.500000 44.772000 45.733070 54.443750 18279 2 0.000000 1 2.500000 47.068000 41.756281 54.443750 18280 2 0.000000 -1 2.500000 47.068000 41.756281 54.443750 18281 2 0.000000 1 2.500000 49.364000 43.081877 57.956250 @@ -18299,7 +18299,7 @@ Atoms 18283 2 0.000000 1 2.500000 51.660000 47.058666 57.956250 18284 2 0.000000 -1 2.500000 51.660000 47.058666 57.956250 18285 2 0.000000 1 2.500000 44.772000 45.733070 61.468750 -18286 2 0.000000 -1.000000 2.500000 44.772000 45.733070 61.468750 +18286 2 0.000000 -1 2.500000 44.772000 45.733070 61.468750 18287 2 0.000000 1 2.500000 47.068000 41.756281 61.468750 18288 2 0.000000 -1 2.500000 47.068000 41.756281 61.468750 18289 2 0.000000 1 2.500000 49.364000 51.035454 1.756250 @@ -18307,7 +18307,7 @@ Atoms 18291 2 0.000000 1 2.500000 51.660000 55.012243 1.756250 18292 2 0.000000 -1 2.500000 51.660000 55.012243 1.756250 18293 2 0.000000 1 2.500000 44.772000 53.686647 5.268750 -18294 2 0.000000 -1.000000 2.500000 44.772000 53.686647 5.268750 +18294 2 0.000000 -1 2.500000 44.772000 53.686647 5.268750 18295 2 0.000000 1 2.500000 47.068000 49.709858 5.268750 18296 2 0.000000 -1 2.500000 47.068000 49.709858 5.268750 18297 2 0.000000 1 2.500000 49.364000 51.035454 8.781250 @@ -18315,7 +18315,7 @@ Atoms 18299 2 0.000000 1 2.500000 51.660000 55.012243 8.781250 18300 2 0.000000 -1 2.500000 51.660000 55.012243 8.781250 18301 2 0.000000 1 2.500000 44.772000 53.686647 12.293750 -18302 2 0.000000 -1.000000 2.500000 44.772000 53.686647 12.293750 +18302 2 0.000000 -1 2.500000 44.772000 53.686647 12.293750 18303 2 0.000000 1 2.500000 47.068000 49.709858 12.293750 18304 2 0.000000 -1 2.500000 47.068000 49.709858 12.293750 18305 2 0.000000 1 2.500000 49.364000 51.035454 15.806250 @@ -18323,7 +18323,7 @@ Atoms 18307 2 0.000000 1 2.500000 51.660000 55.012243 15.806250 18308 2 0.000000 -1 2.500000 51.660000 55.012243 15.806250 18309 2 0.000000 1 2.500000 44.772000 53.686647 19.318750 -18310 2 0.000000 -1.000000 2.500000 44.772000 53.686647 19.318750 +18310 2 0.000000 -1 2.500000 44.772000 53.686647 19.318750 18311 2 0.000000 1 2.500000 47.068000 49.709858 19.318750 18312 2 0.000000 -1 2.500000 47.068000 49.709858 19.318750 18313 2 0.000000 1 2.500000 49.364000 51.035454 22.831250 @@ -18331,7 +18331,7 @@ Atoms 18315 2 0.000000 1 2.500000 51.660000 55.012243 22.831250 18316 2 0.000000 -1 2.500000 51.660000 55.012243 22.831250 18317 2 0.000000 1 2.500000 44.772000 53.686647 26.343750 -18318 2 0.000000 -1.000000 2.500000 44.772000 53.686647 26.343750 +18318 2 0.000000 -1 2.500000 44.772000 53.686647 26.343750 18319 2 0.000000 1 2.500000 47.068000 49.709858 26.343750 18320 2 0.000000 -1 2.500000 47.068000 49.709858 26.343750 18321 2 0.000000 1 2.500000 49.364000 51.035454 29.856250 @@ -18339,7 +18339,7 @@ Atoms 18323 2 0.000000 1 2.500000 51.660000 55.012243 29.856250 18324 2 0.000000 -1 2.500000 51.660000 55.012243 29.856250 18325 2 0.000000 1 2.500000 44.772000 53.686647 33.368750 -18326 2 0.000000 -1.000000 2.500000 44.772000 53.686647 33.368750 +18326 2 0.000000 -1 2.500000 44.772000 53.686647 33.368750 18327 2 0.000000 1 2.500000 47.068000 49.709858 33.368750 18328 2 0.000000 -1 2.500000 47.068000 49.709858 33.368750 18329 2 0.000000 1 2.500000 49.364000 51.035454 36.881250 @@ -18347,7 +18347,7 @@ Atoms 18331 2 0.000000 1 2.500000 51.660000 55.012243 36.881250 18332 2 0.000000 -1 2.500000 51.660000 55.012243 36.881250 18333 2 0.000000 1 2.500000 44.772000 53.686647 40.393750 -18334 2 0.000000 -1.000000 2.500000 44.772000 53.686647 40.393750 +18334 2 0.000000 -1 2.500000 44.772000 53.686647 40.393750 18335 2 0.000000 1 2.500000 47.068000 49.709858 40.393750 18336 2 0.000000 -1 2.500000 47.068000 49.709858 40.393750 18337 2 0.000000 1 2.500000 49.364000 51.035454 43.906250 @@ -18355,7 +18355,7 @@ Atoms 18339 2 0.000000 1 2.500000 51.660000 55.012243 43.906250 18340 2 0.000000 -1 2.500000 51.660000 55.012243 43.906250 18341 2 0.000000 1 2.500000 44.772000 53.686647 47.418750 -18342 2 0.000000 -1.000000 2.500000 44.772000 53.686647 47.418750 +18342 2 0.000000 -1 2.500000 44.772000 53.686647 47.418750 18343 2 0.000000 1 2.500000 47.068000 49.709858 47.418750 18344 2 0.000000 -1 2.500000 47.068000 49.709858 47.418750 18345 2 0.000000 1 2.500000 49.364000 51.035454 50.931250 @@ -18363,7 +18363,7 @@ Atoms 18347 2 0.000000 1 2.500000 51.660000 55.012243 50.931250 18348 2 0.000000 -1 2.500000 51.660000 55.012243 50.931250 18349 2 0.000000 1 2.500000 44.772000 53.686647 54.443750 -18350 2 0.000000 -1.000000 2.500000 44.772000 53.686647 54.443750 +18350 2 0.000000 -1 2.500000 44.772000 53.686647 54.443750 18351 2 0.000000 1 2.500000 47.068000 49.709858 54.443750 18352 2 0.000000 -1 2.500000 47.068000 49.709858 54.443750 18353 2 0.000000 1 2.500000 49.364000 51.035454 57.956250 @@ -18371,7 +18371,7 @@ Atoms 18355 2 0.000000 1 2.500000 51.660000 55.012243 57.956250 18356 2 0.000000 -1 2.500000 51.660000 55.012243 57.956250 18357 2 0.000000 1 2.500000 44.772000 53.686647 61.468750 -18358 2 0.000000 -1.000000 2.500000 44.772000 53.686647 61.468750 +18358 2 0.000000 -1 2.500000 44.772000 53.686647 61.468750 18359 2 0.000000 1 2.500000 47.068000 49.709858 61.468750 18360 2 0.000000 -1 2.500000 47.068000 49.709858 61.468750 18361 2 0.000000 1 2.500000 49.364000 58.989032 1.756250 @@ -18379,7 +18379,7 @@ Atoms 18363 2 0.000000 1 2.500000 51.660000 62.965820 1.756250 18364 2 0.000000 -1 2.500000 51.660000 62.965820 1.756250 18365 2 0.000000 1 2.500000 44.772000 61.640224 5.268750 -18366 2 0.000000 -1.000000 2.500000 44.772000 61.640224 5.268750 +18366 2 0.000000 -1 2.500000 44.772000 61.640224 5.268750 18367 2 0.000000 1 2.500000 47.068000 57.663435 5.268750 18368 2 0.000000 -1 2.500000 47.068000 57.663435 5.268750 18369 2 0.000000 1 2.500000 49.364000 58.989032 8.781250 @@ -18387,7 +18387,7 @@ Atoms 18371 2 0.000000 1 2.500000 51.660000 62.965820 8.781250 18372 2 0.000000 -1 2.500000 51.660000 62.965820 8.781250 18373 2 0.000000 1 2.500000 44.772000 61.640224 12.293750 -18374 2 0.000000 -1.000000 2.500000 44.772000 61.640224 12.293750 +18374 2 0.000000 -1 2.500000 44.772000 61.640224 12.293750 18375 2 0.000000 1 2.500000 47.068000 57.663435 12.293750 18376 2 0.000000 -1 2.500000 47.068000 57.663435 12.293750 18377 2 0.000000 1 2.500000 49.364000 58.989032 15.806250 @@ -18395,7 +18395,7 @@ Atoms 18379 2 0.000000 1 2.500000 51.660000 62.965820 15.806250 18380 2 0.000000 -1 2.500000 51.660000 62.965820 15.806250 18381 2 0.000000 1 2.500000 44.772000 61.640224 19.318750 -18382 2 0.000000 -1.000000 2.500000 44.772000 61.640224 19.318750 +18382 2 0.000000 -1 2.500000 44.772000 61.640224 19.318750 18383 2 0.000000 1 2.500000 47.068000 57.663435 19.318750 18384 2 0.000000 -1 2.500000 47.068000 57.663435 19.318750 18385 2 0.000000 1 2.500000 49.364000 58.989032 22.831250 @@ -18403,7 +18403,7 @@ Atoms 18387 2 0.000000 1 2.500000 51.660000 62.965820 22.831250 18388 2 0.000000 -1 2.500000 51.660000 62.965820 22.831250 18389 2 0.000000 1 2.500000 44.772000 61.640224 26.343750 -18390 2 0.000000 -1.000000 2.500000 44.772000 61.640224 26.343750 +18390 2 0.000000 -1 2.500000 44.772000 61.640224 26.343750 18391 2 0.000000 1 2.500000 47.068000 57.663435 26.343750 18392 2 0.000000 -1 2.500000 47.068000 57.663435 26.343750 18393 2 0.000000 1 2.500000 49.364000 58.989032 29.856250 @@ -18411,7 +18411,7 @@ Atoms 18395 2 0.000000 1 2.500000 51.660000 62.965820 29.856250 18396 2 0.000000 -1 2.500000 51.660000 62.965820 29.856250 18397 2 0.000000 1 2.500000 44.772000 61.640224 33.368750 -18398 2 0.000000 -1.000000 2.500000 44.772000 61.640224 33.368750 +18398 2 0.000000 -1 2.500000 44.772000 61.640224 33.368750 18399 2 0.000000 1 2.500000 47.068000 57.663435 33.368750 18400 2 0.000000 -1 2.500000 47.068000 57.663435 33.368750 18401 2 0.000000 1 2.500000 49.364000 58.989032 36.881250 @@ -18419,7 +18419,7 @@ Atoms 18403 2 0.000000 1 2.500000 51.660000 62.965820 36.881250 18404 2 0.000000 -1 2.500000 51.660000 62.965820 36.881250 18405 2 0.000000 1 2.500000 44.772000 61.640224 40.393750 -18406 2 0.000000 -1.000000 2.500000 44.772000 61.640224 40.393750 +18406 2 0.000000 -1 2.500000 44.772000 61.640224 40.393750 18407 2 0.000000 1 2.500000 47.068000 57.663435 40.393750 18408 2 0.000000 -1 2.500000 47.068000 57.663435 40.393750 18409 2 0.000000 1 2.500000 49.364000 58.989032 43.906250 @@ -18427,7 +18427,7 @@ Atoms 18411 2 0.000000 1 2.500000 51.660000 62.965820 43.906250 18412 2 0.000000 -1 2.500000 51.660000 62.965820 43.906250 18413 2 0.000000 1 2.500000 44.772000 61.640224 47.418750 -18414 2 0.000000 -1.000000 2.500000 44.772000 61.640224 47.418750 +18414 2 0.000000 -1 2.500000 44.772000 61.640224 47.418750 18415 2 0.000000 1 2.500000 47.068000 57.663435 47.418750 18416 2 0.000000 -1 2.500000 47.068000 57.663435 47.418750 18417 2 0.000000 1 2.500000 49.364000 58.989032 50.931250 @@ -18435,7 +18435,7 @@ Atoms 18419 2 0.000000 1 2.500000 51.660000 62.965820 50.931250 18420 2 0.000000 -1 2.500000 51.660000 62.965820 50.931250 18421 2 0.000000 1 2.500000 44.772000 61.640224 54.443750 -18422 2 0.000000 -1.000000 2.500000 44.772000 61.640224 54.443750 +18422 2 0.000000 -1 2.500000 44.772000 61.640224 54.443750 18423 2 0.000000 1 2.500000 47.068000 57.663435 54.443750 18424 2 0.000000 -1 2.500000 47.068000 57.663435 54.443750 18425 2 0.000000 1 2.500000 49.364000 58.989032 57.956250 @@ -18443,7 +18443,7 @@ Atoms 18427 2 0.000000 1 2.500000 51.660000 62.965820 57.956250 18428 2 0.000000 -1 2.500000 51.660000 62.965820 57.956250 18429 2 0.000000 1 2.500000 44.772000 61.640224 61.468750 -18430 2 0.000000 -1.000000 2.500000 44.772000 61.640224 61.468750 +18430 2 0.000000 -1 2.500000 44.772000 61.640224 61.468750 18431 2 0.000000 1 2.500000 47.068000 57.663435 61.468750 18432 2 0.000000 -1 2.500000 47.068000 57.663435 61.468750 18433 2 0.000000 1 2.500000 53.956000 3.313991 1.756250 @@ -18451,7 +18451,7 @@ Atoms 18435 2 0.000000 1 2.500000 56.252000 7.290779 1.756250 18436 2 0.000000 -1 2.500000 56.252000 7.290779 1.756250 18437 2 0.000000 1 2.500000 49.364000 5.965183 5.268750 -18438 2 0.000000 -1.000000 2.500000 49.364000 5.965183 5.268750 +18438 2 0.000000 -1 2.500000 49.364000 5.965183 5.268750 18439 2 0.000000 1 2.500000 51.660000 1.988394 5.268750 18440 2 0.000000 -1 2.500000 51.660000 1.988394 5.268750 18441 2 0.000000 1 2.500000 53.956000 3.313991 8.781250 @@ -18459,7 +18459,7 @@ Atoms 18443 2 0.000000 1 2.500000 56.252000 7.290779 8.781250 18444 2 0.000000 -1 2.500000 56.252000 7.290779 8.781250 18445 2 0.000000 1 2.500000 49.364000 5.965183 12.293750 -18446 2 0.000000 -1.000000 2.500000 49.364000 5.965183 12.293750 +18446 2 0.000000 -1 2.500000 49.364000 5.965183 12.293750 18447 2 0.000000 1 2.500000 51.660000 1.988394 12.293750 18448 2 0.000000 -1 2.500000 51.660000 1.988394 12.293750 18449 2 0.000000 1 2.500000 53.956000 3.313991 15.806250 @@ -18467,7 +18467,7 @@ Atoms 18451 2 0.000000 1 2.500000 56.252000 7.290779 15.806250 18452 2 0.000000 -1 2.500000 56.252000 7.290779 15.806250 18453 2 0.000000 1 2.500000 49.364000 5.965183 19.318750 -18454 2 0.000000 -1.000000 2.500000 49.364000 5.965183 19.318750 +18454 2 0.000000 -1 2.500000 49.364000 5.965183 19.318750 18455 2 0.000000 1 2.500000 51.660000 1.988394 19.318750 18456 2 0.000000 -1 2.500000 51.660000 1.988394 19.318750 18457 2 0.000000 1 2.500000 53.956000 3.313991 22.831250 @@ -18475,7 +18475,7 @@ Atoms 18459 2 0.000000 1 2.500000 56.252000 7.290779 22.831250 18460 2 0.000000 -1 2.500000 56.252000 7.290779 22.831250 18461 2 0.000000 1 2.500000 49.364000 5.965183 26.343750 -18462 2 0.000000 -1.000000 2.500000 49.364000 5.965183 26.343750 +18462 2 0.000000 -1 2.500000 49.364000 5.965183 26.343750 18463 2 0.000000 1 2.500000 51.660000 1.988394 26.343750 18464 2 0.000000 -1 2.500000 51.660000 1.988394 26.343750 18465 2 0.000000 1 2.500000 53.956000 3.313991 29.856250 @@ -18483,7 +18483,7 @@ Atoms 18467 2 0.000000 1 2.500000 56.252000 7.290779 29.856250 18468 2 0.000000 -1 2.500000 56.252000 7.290779 29.856250 18469 2 0.000000 1 2.500000 49.364000 5.965183 33.368750 -18470 2 0.000000 -1.000000 2.500000 49.364000 5.965183 33.368750 +18470 2 0.000000 -1 2.500000 49.364000 5.965183 33.368750 18471 2 0.000000 1 2.500000 51.660000 1.988394 33.368750 18472 2 0.000000 -1 2.500000 51.660000 1.988394 33.368750 18473 2 0.000000 1 2.500000 53.956000 3.313991 36.881250 @@ -18491,7 +18491,7 @@ Atoms 18475 2 0.000000 1 2.500000 56.252000 7.290779 36.881250 18476 2 0.000000 -1 2.500000 56.252000 7.290779 36.881250 18477 2 0.000000 1 2.500000 49.364000 5.965183 40.393750 -18478 2 0.000000 -1.000000 2.500000 49.364000 5.965183 40.393750 +18478 2 0.000000 -1 2.500000 49.364000 5.965183 40.393750 18479 2 0.000000 1 2.500000 51.660000 1.988394 40.393750 18480 2 0.000000 -1 2.500000 51.660000 1.988394 40.393750 18481 2 0.000000 1 2.500000 53.956000 3.313991 43.906250 @@ -18499,7 +18499,7 @@ Atoms 18483 2 0.000000 1 2.500000 56.252000 7.290779 43.906250 18484 2 0.000000 -1 2.500000 56.252000 7.290779 43.906250 18485 2 0.000000 1 2.500000 49.364000 5.965183 47.418750 -18486 2 0.000000 -1.000000 2.500000 49.364000 5.965183 47.418750 +18486 2 0.000000 -1 2.500000 49.364000 5.965183 47.418750 18487 2 0.000000 1 2.500000 51.660000 1.988394 47.418750 18488 2 0.000000 -1 2.500000 51.660000 1.988394 47.418750 18489 2 0.000000 1 2.500000 53.956000 3.313991 50.931250 @@ -18507,7 +18507,7 @@ Atoms 18491 2 0.000000 1 2.500000 56.252000 7.290779 50.931250 18492 2 0.000000 -1 2.500000 56.252000 7.290779 50.931250 18493 2 0.000000 1 2.500000 49.364000 5.965183 54.443750 -18494 2 0.000000 -1.000000 2.500000 49.364000 5.965183 54.443750 +18494 2 0.000000 -1 2.500000 49.364000 5.965183 54.443750 18495 2 0.000000 1 2.500000 51.660000 1.988394 54.443750 18496 2 0.000000 -1 2.500000 51.660000 1.988394 54.443750 18497 2 0.000000 1 2.500000 53.956000 3.313991 57.956250 @@ -18515,7 +18515,7 @@ Atoms 18499 2 0.000000 1 2.500000 56.252000 7.290779 57.956250 18500 2 0.000000 -1 2.500000 56.252000 7.290779 57.956250 18501 2 0.000000 1 2.500000 49.364000 5.965183 61.468750 -18502 2 0.000000 -1.000000 2.500000 49.364000 5.965183 61.468750 +18502 2 0.000000 -1 2.500000 49.364000 5.965183 61.468750 18503 2 0.000000 1 2.500000 51.660000 1.988394 61.468750 18504 2 0.000000 -1 2.500000 51.660000 1.988394 61.468750 18505 2 0.000000 1 2.500000 53.956000 11.267568 1.756250 @@ -18523,7 +18523,7 @@ Atoms 18507 2 0.000000 1 2.500000 56.252000 15.244357 1.756250 18508 2 0.000000 -1 2.500000 56.252000 15.244357 1.756250 18509 2 0.000000 1 2.500000 49.364000 13.918760 5.268750 -18510 2 0.000000 -1.000000 2.500000 49.364000 13.918760 5.268750 +18510 2 0.000000 -1 2.500000 49.364000 13.918760 5.268750 18511 2 0.000000 1 2.500000 51.660000 9.941972 5.268750 18512 2 0.000000 -1 2.500000 51.660000 9.941972 5.268750 18513 2 0.000000 1 2.500000 53.956000 11.267568 8.781250 @@ -18531,7 +18531,7 @@ Atoms 18515 2 0.000000 1 2.500000 56.252000 15.244357 8.781250 18516 2 0.000000 -1 2.500000 56.252000 15.244357 8.781250 18517 2 0.000000 1 2.500000 49.364000 13.918760 12.293750 -18518 2 0.000000 -1.000000 2.500000 49.364000 13.918760 12.293750 +18518 2 0.000000 -1 2.500000 49.364000 13.918760 12.293750 18519 2 0.000000 1 2.500000 51.660000 9.941972 12.293750 18520 2 0.000000 -1 2.500000 51.660000 9.941972 12.293750 18521 2 0.000000 1 2.500000 53.956000 11.267568 15.806250 @@ -18539,7 +18539,7 @@ Atoms 18523 2 0.000000 1 2.500000 56.252000 15.244357 15.806250 18524 2 0.000000 -1 2.500000 56.252000 15.244357 15.806250 18525 2 0.000000 1 2.500000 49.364000 13.918760 19.318750 -18526 2 0.000000 -1.000000 2.500000 49.364000 13.918760 19.318750 +18526 2 0.000000 -1 2.500000 49.364000 13.918760 19.318750 18527 2 0.000000 1 2.500000 51.660000 9.941972 19.318750 18528 2 0.000000 -1 2.500000 51.660000 9.941972 19.318750 18529 2 0.000000 1 2.500000 53.956000 11.267568 22.831250 @@ -18547,7 +18547,7 @@ Atoms 18531 2 0.000000 1 2.500000 56.252000 15.244357 22.831250 18532 2 0.000000 -1 2.500000 56.252000 15.244357 22.831250 18533 2 0.000000 1 2.500000 49.364000 13.918760 26.343750 -18534 2 0.000000 -1.000000 2.500000 49.364000 13.918760 26.343750 +18534 2 0.000000 -1 2.500000 49.364000 13.918760 26.343750 18535 2 0.000000 1 2.500000 51.660000 9.941972 26.343750 18536 2 0.000000 -1 2.500000 51.660000 9.941972 26.343750 18537 2 0.000000 1 2.500000 53.956000 11.267568 29.856250 @@ -18555,7 +18555,7 @@ Atoms 18539 2 0.000000 1 2.500000 56.252000 15.244357 29.856250 18540 2 0.000000 -1 2.500000 56.252000 15.244357 29.856250 18541 2 0.000000 1 2.500000 49.364000 13.918760 33.368750 -18542 2 0.000000 -1.000000 2.500000 49.364000 13.918760 33.368750 +18542 2 0.000000 -1 2.500000 49.364000 13.918760 33.368750 18543 2 0.000000 1 2.500000 51.660000 9.941972 33.368750 18544 2 0.000000 -1 2.500000 51.660000 9.941972 33.368750 18545 2 0.000000 1 2.500000 53.956000 11.267568 36.881250 @@ -18563,7 +18563,7 @@ Atoms 18547 2 0.000000 1 2.500000 56.252000 15.244357 36.881250 18548 2 0.000000 -1 2.500000 56.252000 15.244357 36.881250 18549 2 0.000000 1 2.500000 49.364000 13.918760 40.393750 -18550 2 0.000000 -1.000000 2.500000 49.364000 13.918760 40.393750 +18550 2 0.000000 -1 2.500000 49.364000 13.918760 40.393750 18551 2 0.000000 1 2.500000 51.660000 9.941972 40.393750 18552 2 0.000000 -1 2.500000 51.660000 9.941972 40.393750 18553 2 0.000000 1 2.500000 53.956000 11.267568 43.906250 @@ -18571,7 +18571,7 @@ Atoms 18555 2 0.000000 1 2.500000 56.252000 15.244357 43.906250 18556 2 0.000000 -1 2.500000 56.252000 15.244357 43.906250 18557 2 0.000000 1 2.500000 49.364000 13.918760 47.418750 -18558 2 0.000000 -1.000000 2.500000 49.364000 13.918760 47.418750 +18558 2 0.000000 -1 2.500000 49.364000 13.918760 47.418750 18559 2 0.000000 1 2.500000 51.660000 9.941972 47.418750 18560 2 0.000000 -1 2.500000 51.660000 9.941972 47.418750 18561 2 0.000000 1 2.500000 53.956000 11.267568 50.931250 @@ -18579,7 +18579,7 @@ Atoms 18563 2 0.000000 1 2.500000 56.252000 15.244357 50.931250 18564 2 0.000000 -1 2.500000 56.252000 15.244357 50.931250 18565 2 0.000000 1 2.500000 49.364000 13.918760 54.443750 -18566 2 0.000000 -1.000000 2.500000 49.364000 13.918760 54.443750 +18566 2 0.000000 -1 2.500000 49.364000 13.918760 54.443750 18567 2 0.000000 1 2.500000 51.660000 9.941972 54.443750 18568 2 0.000000 -1 2.500000 51.660000 9.941972 54.443750 18569 2 0.000000 1 2.500000 53.956000 11.267568 57.956250 @@ -18587,7 +18587,7 @@ Atoms 18571 2 0.000000 1 2.500000 56.252000 15.244357 57.956250 18572 2 0.000000 -1 2.500000 56.252000 15.244357 57.956250 18573 2 0.000000 1 2.500000 49.364000 13.918760 61.468750 -18574 2 0.000000 -1.000000 2.500000 49.364000 13.918760 61.468750 +18574 2 0.000000 -1 2.500000 49.364000 13.918760 61.468750 18575 2 0.000000 1 2.500000 51.660000 9.941972 61.468750 18576 2 0.000000 -1 2.500000 51.660000 9.941972 61.468750 18577 2 0.000000 1 2.500000 53.956000 19.221145 1.756250 @@ -18595,7 +18595,7 @@ Atoms 18579 2 0.000000 1 2.500000 56.252000 23.197934 1.756250 18580 2 0.000000 -1 2.500000 56.252000 23.197934 1.756250 18581 2 0.000000 1 2.500000 49.364000 21.872338 5.268750 -18582 2 0.000000 -1.000000 2.500000 49.364000 21.872338 5.268750 +18582 2 0.000000 -1 2.500000 49.364000 21.872338 5.268750 18583 2 0.000000 1 2.500000 51.660000 17.895549 5.268750 18584 2 0.000000 -1 2.500000 51.660000 17.895549 5.268750 18585 2 0.000000 1 2.500000 53.956000 19.221145 8.781250 @@ -18603,7 +18603,7 @@ Atoms 18587 2 0.000000 1 2.500000 56.252000 23.197934 8.781250 18588 2 0.000000 -1 2.500000 56.252000 23.197934 8.781250 18589 2 0.000000 1 2.500000 49.364000 21.872338 12.293750 -18590 2 0.000000 -1.000000 2.500000 49.364000 21.872338 12.293750 +18590 2 0.000000 -1 2.500000 49.364000 21.872338 12.293750 18591 2 0.000000 1 2.500000 51.660000 17.895549 12.293750 18592 2 0.000000 -1 2.500000 51.660000 17.895549 12.293750 18593 2 0.000000 1 2.500000 53.956000 19.221145 15.806250 @@ -18611,7 +18611,7 @@ Atoms 18595 2 0.000000 1 2.500000 56.252000 23.197934 15.806250 18596 2 0.000000 -1 2.500000 56.252000 23.197934 15.806250 18597 2 0.000000 1 2.500000 49.364000 21.872338 19.318750 -18598 2 0.000000 -1.000000 2.500000 49.364000 21.872338 19.318750 +18598 2 0.000000 -1 2.500000 49.364000 21.872338 19.318750 18599 2 0.000000 1 2.500000 51.660000 17.895549 19.318750 18600 2 0.000000 -1 2.500000 51.660000 17.895549 19.318750 18601 2 0.000000 1 2.500000 53.956000 19.221145 22.831250 @@ -18619,7 +18619,7 @@ Atoms 18603 2 0.000000 1 2.500000 56.252000 23.197934 22.831250 18604 2 0.000000 -1 2.500000 56.252000 23.197934 22.831250 18605 2 0.000000 1 2.500000 49.364000 21.872338 26.343750 -18606 2 0.000000 -1.000000 2.500000 49.364000 21.872338 26.343750 +18606 2 0.000000 -1 2.500000 49.364000 21.872338 26.343750 18607 2 0.000000 1 2.500000 51.660000 17.895549 26.343750 18608 2 0.000000 -1 2.500000 51.660000 17.895549 26.343750 18609 2 0.000000 1 2.500000 53.956000 19.221145 29.856250 @@ -18627,7 +18627,7 @@ Atoms 18611 2 0.000000 1 2.500000 56.252000 23.197934 29.856250 18612 2 0.000000 -1 2.500000 56.252000 23.197934 29.856250 18613 2 0.000000 1 2.500000 49.364000 21.872338 33.368750 -18614 2 0.000000 -1.000000 2.500000 49.364000 21.872338 33.368750 +18614 2 0.000000 -1 2.500000 49.364000 21.872338 33.368750 18615 2 0.000000 1 2.500000 51.660000 17.895549 33.368750 18616 2 0.000000 -1 2.500000 51.660000 17.895549 33.368750 18617 2 0.000000 1 2.500000 53.956000 19.221145 36.881250 @@ -18635,7 +18635,7 @@ Atoms 18619 2 0.000000 1 2.500000 56.252000 23.197934 36.881250 18620 2 0.000000 -1 2.500000 56.252000 23.197934 36.881250 18621 2 0.000000 1 2.500000 49.364000 21.872338 40.393750 -18622 2 0.000000 -1.000000 2.500000 49.364000 21.872338 40.393750 +18622 2 0.000000 -1 2.500000 49.364000 21.872338 40.393750 18623 2 0.000000 1 2.500000 51.660000 17.895549 40.393750 18624 2 0.000000 -1 2.500000 51.660000 17.895549 40.393750 18625 2 0.000000 1 2.500000 53.956000 19.221145 43.906250 @@ -18643,7 +18643,7 @@ Atoms 18627 2 0.000000 1 2.500000 56.252000 23.197934 43.906250 18628 2 0.000000 -1 2.500000 56.252000 23.197934 43.906250 18629 2 0.000000 1 2.500000 49.364000 21.872338 47.418750 -18630 2 0.000000 -1.000000 2.500000 49.364000 21.872338 47.418750 +18630 2 0.000000 -1 2.500000 49.364000 21.872338 47.418750 18631 2 0.000000 1 2.500000 51.660000 17.895549 47.418750 18632 2 0.000000 -1 2.500000 51.660000 17.895549 47.418750 18633 2 0.000000 1 2.500000 53.956000 19.221145 50.931250 @@ -18651,7 +18651,7 @@ Atoms 18635 2 0.000000 1 2.500000 56.252000 23.197934 50.931250 18636 2 0.000000 -1 2.500000 56.252000 23.197934 50.931250 18637 2 0.000000 1 2.500000 49.364000 21.872338 54.443750 -18638 2 0.000000 -1.000000 2.500000 49.364000 21.872338 54.443750 +18638 2 0.000000 -1 2.500000 49.364000 21.872338 54.443750 18639 2 0.000000 1 2.500000 51.660000 17.895549 54.443750 18640 2 0.000000 -1 2.500000 51.660000 17.895549 54.443750 18641 2 0.000000 1 2.500000 53.956000 19.221145 57.956250 @@ -18659,7 +18659,7 @@ Atoms 18643 2 0.000000 1 2.500000 56.252000 23.197934 57.956250 18644 2 0.000000 -1 2.500000 56.252000 23.197934 57.956250 18645 2 0.000000 1 2.500000 49.364000 21.872338 61.468750 -18646 2 0.000000 -1.000000 2.500000 49.364000 21.872338 61.468750 +18646 2 0.000000 -1 2.500000 49.364000 21.872338 61.468750 18647 2 0.000000 1 2.500000 51.660000 17.895549 61.468750 18648 2 0.000000 -1 2.500000 51.660000 17.895549 61.468750 18649 2 0.000000 1 2.500000 53.956000 27.174722 1.756250 @@ -18667,7 +18667,7 @@ Atoms 18651 2 0.000000 1 2.500000 56.252000 31.151511 1.756250 18652 2 0.000000 -1 2.500000 56.252000 31.151511 1.756250 18653 2 0.000000 1 2.500000 49.364000 29.825915 5.268750 -18654 2 0.000000 -1.000000 2.500000 49.364000 29.825915 5.268750 +18654 2 0.000000 -1 2.500000 49.364000 29.825915 5.268750 18655 2 0.000000 1 2.500000 51.660000 25.849126 5.268750 18656 2 0.000000 -1 2.500000 51.660000 25.849126 5.268750 18657 2 0.000000 1 2.500000 53.956000 27.174722 8.781250 @@ -18675,7 +18675,7 @@ Atoms 18659 2 0.000000 1 2.500000 56.252000 31.151511 8.781250 18660 2 0.000000 -1 2.500000 56.252000 31.151511 8.781250 18661 2 0.000000 1 2.500000 49.364000 29.825915 12.293750 -18662 2 0.000000 -1.000000 2.500000 49.364000 29.825915 12.293750 +18662 2 0.000000 -1 2.500000 49.364000 29.825915 12.293750 18663 2 0.000000 1 2.500000 51.660000 25.849126 12.293750 18664 2 0.000000 -1 2.500000 51.660000 25.849126 12.293750 18665 2 0.000000 1 2.500000 53.956000 27.174722 15.806250 @@ -18683,7 +18683,7 @@ Atoms 18667 2 0.000000 1 2.500000 56.252000 31.151511 15.806250 18668 2 0.000000 -1 2.500000 56.252000 31.151511 15.806250 18669 2 0.000000 1 2.500000 49.364000 29.825915 19.318750 -18670 2 0.000000 -1.000000 2.500000 49.364000 29.825915 19.318750 +18670 2 0.000000 -1 2.500000 49.364000 29.825915 19.318750 18671 2 0.000000 1 2.500000 51.660000 25.849126 19.318750 18672 2 0.000000 -1 2.500000 51.660000 25.849126 19.318750 18673 2 0.000000 1 2.500000 53.956000 27.174722 22.831250 @@ -18691,7 +18691,7 @@ Atoms 18675 2 0.000000 1 2.500000 56.252000 31.151511 22.831250 18676 2 0.000000 -1 2.500000 56.252000 31.151511 22.831250 18677 2 0.000000 1 2.500000 49.364000 29.825915 26.343750 -18678 2 0.000000 -1.000000 2.500000 49.364000 29.825915 26.343750 +18678 2 0.000000 -1 2.500000 49.364000 29.825915 26.343750 18679 2 0.000000 1 2.500000 51.660000 25.849126 26.343750 18680 2 0.000000 -1 2.500000 51.660000 25.849126 26.343750 18681 2 0.000000 1 2.500000 53.956000 27.174722 29.856250 @@ -18699,7 +18699,7 @@ Atoms 18683 2 0.000000 1 2.500000 56.252000 31.151511 29.856250 18684 2 0.000000 -1 2.500000 56.252000 31.151511 29.856250 18685 2 0.000000 1 2.500000 49.364000 29.825915 33.368750 -18686 2 0.000000 -1.000000 2.500000 49.364000 29.825915 33.368750 +18686 2 0.000000 -1 2.500000 49.364000 29.825915 33.368750 18687 2 0.000000 1 2.500000 51.660000 25.849126 33.368750 18688 2 0.000000 -1 2.500000 51.660000 25.849126 33.368750 18689 2 0.000000 1 2.500000 53.956000 27.174722 36.881250 @@ -18707,7 +18707,7 @@ Atoms 18691 2 0.000000 1 2.500000 56.252000 31.151511 36.881250 18692 2 0.000000 -1 2.500000 56.252000 31.151511 36.881250 18693 2 0.000000 1 2.500000 49.364000 29.825915 40.393750 -18694 2 0.000000 -1.000000 2.500000 49.364000 29.825915 40.393750 +18694 2 0.000000 -1 2.500000 49.364000 29.825915 40.393750 18695 2 0.000000 1 2.500000 51.660000 25.849126 40.393750 18696 2 0.000000 -1 2.500000 51.660000 25.849126 40.393750 18697 2 0.000000 1 2.500000 53.956000 27.174722 43.906250 @@ -18715,7 +18715,7 @@ Atoms 18699 2 0.000000 1 2.500000 56.252000 31.151511 43.906250 18700 2 0.000000 -1 2.500000 56.252000 31.151511 43.906250 18701 2 0.000000 1 2.500000 49.364000 29.825915 47.418750 -18702 2 0.000000 -1.000000 2.500000 49.364000 29.825915 47.418750 +18702 2 0.000000 -1 2.500000 49.364000 29.825915 47.418750 18703 2 0.000000 1 2.500000 51.660000 25.849126 47.418750 18704 2 0.000000 -1 2.500000 51.660000 25.849126 47.418750 18705 2 0.000000 1 2.500000 53.956000 27.174722 50.931250 @@ -18723,7 +18723,7 @@ Atoms 18707 2 0.000000 1 2.500000 56.252000 31.151511 50.931250 18708 2 0.000000 -1 2.500000 56.252000 31.151511 50.931250 18709 2 0.000000 1 2.500000 49.364000 29.825915 54.443750 -18710 2 0.000000 -1.000000 2.500000 49.364000 29.825915 54.443750 +18710 2 0.000000 -1 2.500000 49.364000 29.825915 54.443750 18711 2 0.000000 1 2.500000 51.660000 25.849126 54.443750 18712 2 0.000000 -1 2.500000 51.660000 25.849126 54.443750 18713 2 0.000000 1 2.500000 53.956000 27.174722 57.956250 @@ -18731,7 +18731,7 @@ Atoms 18715 2 0.000000 1 2.500000 56.252000 31.151511 57.956250 18716 2 0.000000 -1 2.500000 56.252000 31.151511 57.956250 18717 2 0.000000 1 2.500000 49.364000 29.825915 61.468750 -18718 2 0.000000 -1.000000 2.500000 49.364000 29.825915 61.468750 +18718 2 0.000000 -1 2.500000 49.364000 29.825915 61.468750 18719 2 0.000000 1 2.500000 51.660000 25.849126 61.468750 18720 2 0.000000 -1 2.500000 51.660000 25.849126 61.468750 18721 2 0.000000 1 2.500000 53.956000 35.128300 1.756250 @@ -18739,7 +18739,7 @@ Atoms 18723 2 0.000000 1 2.500000 56.252000 39.105088 1.756250 18724 2 0.000000 -1 2.500000 56.252000 39.105088 1.756250 18725 2 0.000000 1 2.500000 49.364000 37.779492 5.268750 -18726 2 0.000000 -1.000000 2.500000 49.364000 37.779492 5.268750 +18726 2 0.000000 -1 2.500000 49.364000 37.779492 5.268750 18727 2 0.000000 1 2.500000 51.660000 33.802704 5.268750 18728 2 0.000000 -1 2.500000 51.660000 33.802704 5.268750 18729 2 0.000000 1 2.500000 53.956000 35.128300 8.781250 @@ -18747,7 +18747,7 @@ Atoms 18731 2 0.000000 1 2.500000 56.252000 39.105088 8.781250 18732 2 0.000000 -1 2.500000 56.252000 39.105088 8.781250 18733 2 0.000000 1 2.500000 49.364000 37.779492 12.293750 -18734 2 0.000000 -1.000000 2.500000 49.364000 37.779492 12.293750 +18734 2 0.000000 -1 2.500000 49.364000 37.779492 12.293750 18735 2 0.000000 1 2.500000 51.660000 33.802704 12.293750 18736 2 0.000000 -1 2.500000 51.660000 33.802704 12.293750 18737 2 0.000000 1 2.500000 53.956000 35.128300 15.806250 @@ -18755,7 +18755,7 @@ Atoms 18739 2 0.000000 1 2.500000 56.252000 39.105088 15.806250 18740 2 0.000000 -1 2.500000 56.252000 39.105088 15.806250 18741 2 0.000000 1 2.500000 49.364000 37.779492 19.318750 -18742 2 0.000000 -1.000000 2.500000 49.364000 37.779492 19.318750 +18742 2 0.000000 -1 2.500000 49.364000 37.779492 19.318750 18743 2 0.000000 1 2.500000 51.660000 33.802704 19.318750 18744 2 0.000000 -1 2.500000 51.660000 33.802704 19.318750 18745 2 0.000000 1 2.500000 53.956000 35.128300 22.831250 @@ -18763,7 +18763,7 @@ Atoms 18747 2 0.000000 1 2.500000 56.252000 39.105088 22.831250 18748 2 0.000000 -1 2.500000 56.252000 39.105088 22.831250 18749 2 0.000000 1 2.500000 49.364000 37.779492 26.343750 -18750 2 0.000000 -1.000000 2.500000 49.364000 37.779492 26.343750 +18750 2 0.000000 -1 2.500000 49.364000 37.779492 26.343750 18751 2 0.000000 1 2.500000 51.660000 33.802704 26.343750 18752 2 0.000000 -1 2.500000 51.660000 33.802704 26.343750 18753 2 0.000000 1 2.500000 53.956000 35.128300 29.856250 @@ -18771,7 +18771,7 @@ Atoms 18755 2 0.000000 1 2.500000 56.252000 39.105088 29.856250 18756 2 0.000000 -1 2.500000 56.252000 39.105088 29.856250 18757 2 0.000000 1 2.500000 49.364000 37.779492 33.368750 -18758 2 0.000000 -1.000000 2.500000 49.364000 37.779492 33.368750 +18758 2 0.000000 -1 2.500000 49.364000 37.779492 33.368750 18759 2 0.000000 1 2.500000 51.660000 33.802704 33.368750 18760 2 0.000000 -1 2.500000 51.660000 33.802704 33.368750 18761 2 0.000000 1 2.500000 53.956000 35.128300 36.881250 @@ -18779,7 +18779,7 @@ Atoms 18763 2 0.000000 1 2.500000 56.252000 39.105088 36.881250 18764 2 0.000000 -1 2.500000 56.252000 39.105088 36.881250 18765 2 0.000000 1 2.500000 49.364000 37.779492 40.393750 -18766 2 0.000000 -1.000000 2.500000 49.364000 37.779492 40.393750 +18766 2 0.000000 -1 2.500000 49.364000 37.779492 40.393750 18767 2 0.000000 1 2.500000 51.660000 33.802704 40.393750 18768 2 0.000000 -1 2.500000 51.660000 33.802704 40.393750 18769 2 0.000000 1 2.500000 53.956000 35.128300 43.906250 @@ -18787,7 +18787,7 @@ Atoms 18771 2 0.000000 1 2.500000 56.252000 39.105088 43.906250 18772 2 0.000000 -1 2.500000 56.252000 39.105088 43.906250 18773 2 0.000000 1 2.500000 49.364000 37.779492 47.418750 -18774 2 0.000000 -1.000000 2.500000 49.364000 37.779492 47.418750 +18774 2 0.000000 -1 2.500000 49.364000 37.779492 47.418750 18775 2 0.000000 1 2.500000 51.660000 33.802704 47.418750 18776 2 0.000000 -1 2.500000 51.660000 33.802704 47.418750 18777 2 0.000000 1 2.500000 53.956000 35.128300 50.931250 @@ -18795,7 +18795,7 @@ Atoms 18779 2 0.000000 1 2.500000 56.252000 39.105088 50.931250 18780 2 0.000000 -1 2.500000 56.252000 39.105088 50.931250 18781 2 0.000000 1 2.500000 49.364000 37.779492 54.443750 -18782 2 0.000000 -1.000000 2.500000 49.364000 37.779492 54.443750 +18782 2 0.000000 -1 2.500000 49.364000 37.779492 54.443750 18783 2 0.000000 1 2.500000 51.660000 33.802704 54.443750 18784 2 0.000000 -1 2.500000 51.660000 33.802704 54.443750 18785 2 0.000000 1 2.500000 53.956000 35.128300 57.956250 @@ -18803,7 +18803,7 @@ Atoms 18787 2 0.000000 1 2.500000 56.252000 39.105088 57.956250 18788 2 0.000000 -1 2.500000 56.252000 39.105088 57.956250 18789 2 0.000000 1 2.500000 49.364000 37.779492 61.468750 -18790 2 0.000000 -1.000000 2.500000 49.364000 37.779492 61.468750 +18790 2 0.000000 -1 2.500000 49.364000 37.779492 61.468750 18791 2 0.000000 1 2.500000 51.660000 33.802704 61.468750 18792 2 0.000000 -1 2.500000 51.660000 33.802704 61.468750 18793 2 0.000000 1 2.500000 53.956000 43.081877 1.756250 @@ -18811,7 +18811,7 @@ Atoms 18795 2 0.000000 1 2.500000 56.252000 47.058666 1.756250 18796 2 0.000000 -1 2.500000 56.252000 47.058666 1.756250 18797 2 0.000000 1 2.500000 49.364000 45.733070 5.268750 -18798 2 0.000000 -1.000000 2.500000 49.364000 45.733070 5.268750 +18798 2 0.000000 -1 2.500000 49.364000 45.733070 5.268750 18799 2 0.000000 1 2.500000 51.660000 41.756281 5.268750 18800 2 0.000000 -1 2.500000 51.660000 41.756281 5.268750 18801 2 0.000000 1 2.500000 53.956000 43.081877 8.781250 @@ -18819,7 +18819,7 @@ Atoms 18803 2 0.000000 1 2.500000 56.252000 47.058666 8.781250 18804 2 0.000000 -1 2.500000 56.252000 47.058666 8.781250 18805 2 0.000000 1 2.500000 49.364000 45.733070 12.293750 -18806 2 0.000000 -1.000000 2.500000 49.364000 45.733070 12.293750 +18806 2 0.000000 -1 2.500000 49.364000 45.733070 12.293750 18807 2 0.000000 1 2.500000 51.660000 41.756281 12.293750 18808 2 0.000000 -1 2.500000 51.660000 41.756281 12.293750 18809 2 0.000000 1 2.500000 53.956000 43.081877 15.806250 @@ -18827,7 +18827,7 @@ Atoms 18811 2 0.000000 1 2.500000 56.252000 47.058666 15.806250 18812 2 0.000000 -1 2.500000 56.252000 47.058666 15.806250 18813 2 0.000000 1 2.500000 49.364000 45.733070 19.318750 -18814 2 0.000000 -1.000000 2.500000 49.364000 45.733070 19.318750 +18814 2 0.000000 -1 2.500000 49.364000 45.733070 19.318750 18815 2 0.000000 1 2.500000 51.660000 41.756281 19.318750 18816 2 0.000000 -1 2.500000 51.660000 41.756281 19.318750 18817 2 0.000000 1 2.500000 53.956000 43.081877 22.831250 @@ -18835,7 +18835,7 @@ Atoms 18819 2 0.000000 1 2.500000 56.252000 47.058666 22.831250 18820 2 0.000000 -1 2.500000 56.252000 47.058666 22.831250 18821 2 0.000000 1 2.500000 49.364000 45.733070 26.343750 -18822 2 0.000000 -1.000000 2.500000 49.364000 45.733070 26.343750 +18822 2 0.000000 -1 2.500000 49.364000 45.733070 26.343750 18823 2 0.000000 1 2.500000 51.660000 41.756281 26.343750 18824 2 0.000000 -1 2.500000 51.660000 41.756281 26.343750 18825 2 0.000000 1 2.500000 53.956000 43.081877 29.856250 @@ -18843,7 +18843,7 @@ Atoms 18827 2 0.000000 1 2.500000 56.252000 47.058666 29.856250 18828 2 0.000000 -1 2.500000 56.252000 47.058666 29.856250 18829 2 0.000000 1 2.500000 49.364000 45.733070 33.368750 -18830 2 0.000000 -1.000000 2.500000 49.364000 45.733070 33.368750 +18830 2 0.000000 -1 2.500000 49.364000 45.733070 33.368750 18831 2 0.000000 1 2.500000 51.660000 41.756281 33.368750 18832 2 0.000000 -1 2.500000 51.660000 41.756281 33.368750 18833 2 0.000000 1 2.500000 53.956000 43.081877 36.881250 @@ -18851,7 +18851,7 @@ Atoms 18835 2 0.000000 1 2.500000 56.252000 47.058666 36.881250 18836 2 0.000000 -1 2.500000 56.252000 47.058666 36.881250 18837 2 0.000000 1 2.500000 49.364000 45.733070 40.393750 -18838 2 0.000000 -1.000000 2.500000 49.364000 45.733070 40.393750 +18838 2 0.000000 -1 2.500000 49.364000 45.733070 40.393750 18839 2 0.000000 1 2.500000 51.660000 41.756281 40.393750 18840 2 0.000000 -1 2.500000 51.660000 41.756281 40.393750 18841 2 0.000000 1 2.500000 53.956000 43.081877 43.906250 @@ -18859,7 +18859,7 @@ Atoms 18843 2 0.000000 1 2.500000 56.252000 47.058666 43.906250 18844 2 0.000000 -1 2.500000 56.252000 47.058666 43.906250 18845 2 0.000000 1 2.500000 49.364000 45.733070 47.418750 -18846 2 0.000000 -1.000000 2.500000 49.364000 45.733070 47.418750 +18846 2 0.000000 -1 2.500000 49.364000 45.733070 47.418750 18847 2 0.000000 1 2.500000 51.660000 41.756281 47.418750 18848 2 0.000000 -1 2.500000 51.660000 41.756281 47.418750 18849 2 0.000000 1 2.500000 53.956000 43.081877 50.931250 @@ -18867,7 +18867,7 @@ Atoms 18851 2 0.000000 1 2.500000 56.252000 47.058666 50.931250 18852 2 0.000000 -1 2.500000 56.252000 47.058666 50.931250 18853 2 0.000000 1 2.500000 49.364000 45.733070 54.443750 -18854 2 0.000000 -1.000000 2.500000 49.364000 45.733070 54.443750 +18854 2 0.000000 -1 2.500000 49.364000 45.733070 54.443750 18855 2 0.000000 1 2.500000 51.660000 41.756281 54.443750 18856 2 0.000000 -1 2.500000 51.660000 41.756281 54.443750 18857 2 0.000000 1 2.500000 53.956000 43.081877 57.956250 @@ -18875,7 +18875,7 @@ Atoms 18859 2 0.000000 1 2.500000 56.252000 47.058666 57.956250 18860 2 0.000000 -1 2.500000 56.252000 47.058666 57.956250 18861 2 0.000000 1 2.500000 49.364000 45.733070 61.468750 -18862 2 0.000000 -1.000000 2.500000 49.364000 45.733070 61.468750 +18862 2 0.000000 -1 2.500000 49.364000 45.733070 61.468750 18863 2 0.000000 1 2.500000 51.660000 41.756281 61.468750 18864 2 0.000000 -1 2.500000 51.660000 41.756281 61.468750 18865 2 0.000000 1 2.500000 53.956000 51.035454 1.756250 @@ -18883,7 +18883,7 @@ Atoms 18867 2 0.000000 1 2.500000 56.252000 55.012243 1.756250 18868 2 0.000000 -1 2.500000 56.252000 55.012243 1.756250 18869 2 0.000000 1 2.500000 49.364000 53.686647 5.268750 -18870 2 0.000000 -1.000000 2.500000 49.364000 53.686647 5.268750 +18870 2 0.000000 -1 2.500000 49.364000 53.686647 5.268750 18871 2 0.000000 1 2.500000 51.660000 49.709858 5.268750 18872 2 0.000000 -1 2.500000 51.660000 49.709858 5.268750 18873 2 0.000000 1 2.500000 53.956000 51.035454 8.781250 @@ -18891,7 +18891,7 @@ Atoms 18875 2 0.000000 1 2.500000 56.252000 55.012243 8.781250 18876 2 0.000000 -1 2.500000 56.252000 55.012243 8.781250 18877 2 0.000000 1 2.500000 49.364000 53.686647 12.293750 -18878 2 0.000000 -1.000000 2.500000 49.364000 53.686647 12.293750 +18878 2 0.000000 -1 2.500000 49.364000 53.686647 12.293750 18879 2 0.000000 1 2.500000 51.660000 49.709858 12.293750 18880 2 0.000000 -1 2.500000 51.660000 49.709858 12.293750 18881 2 0.000000 1 2.500000 53.956000 51.035454 15.806250 @@ -18899,7 +18899,7 @@ Atoms 18883 2 0.000000 1 2.500000 56.252000 55.012243 15.806250 18884 2 0.000000 -1 2.500000 56.252000 55.012243 15.806250 18885 2 0.000000 1 2.500000 49.364000 53.686647 19.318750 -18886 2 0.000000 -1.000000 2.500000 49.364000 53.686647 19.318750 +18886 2 0.000000 -1 2.500000 49.364000 53.686647 19.318750 18887 2 0.000000 1 2.500000 51.660000 49.709858 19.318750 18888 2 0.000000 -1 2.500000 51.660000 49.709858 19.318750 18889 2 0.000000 1 2.500000 53.956000 51.035454 22.831250 @@ -18907,7 +18907,7 @@ Atoms 18891 2 0.000000 1 2.500000 56.252000 55.012243 22.831250 18892 2 0.000000 -1 2.500000 56.252000 55.012243 22.831250 18893 2 0.000000 1 2.500000 49.364000 53.686647 26.343750 -18894 2 0.000000 -1.000000 2.500000 49.364000 53.686647 26.343750 +18894 2 0.000000 -1 2.500000 49.364000 53.686647 26.343750 18895 2 0.000000 1 2.500000 51.660000 49.709858 26.343750 18896 2 0.000000 -1 2.500000 51.660000 49.709858 26.343750 18897 2 0.000000 1 2.500000 53.956000 51.035454 29.856250 @@ -18915,7 +18915,7 @@ Atoms 18899 2 0.000000 1 2.500000 56.252000 55.012243 29.856250 18900 2 0.000000 -1 2.500000 56.252000 55.012243 29.856250 18901 2 0.000000 1 2.500000 49.364000 53.686647 33.368750 -18902 2 0.000000 -1.000000 2.500000 49.364000 53.686647 33.368750 +18902 2 0.000000 -1 2.500000 49.364000 53.686647 33.368750 18903 2 0.000000 1 2.500000 51.660000 49.709858 33.368750 18904 2 0.000000 -1 2.500000 51.660000 49.709858 33.368750 18905 2 0.000000 1 2.500000 53.956000 51.035454 36.881250 @@ -18923,7 +18923,7 @@ Atoms 18907 2 0.000000 1 2.500000 56.252000 55.012243 36.881250 18908 2 0.000000 -1 2.500000 56.252000 55.012243 36.881250 18909 2 0.000000 1 2.500000 49.364000 53.686647 40.393750 -18910 2 0.000000 -1.000000 2.500000 49.364000 53.686647 40.393750 +18910 2 0.000000 -1 2.500000 49.364000 53.686647 40.393750 18911 2 0.000000 1 2.500000 51.660000 49.709858 40.393750 18912 2 0.000000 -1 2.500000 51.660000 49.709858 40.393750 18913 2 0.000000 1 2.500000 53.956000 51.035454 43.906250 @@ -18931,7 +18931,7 @@ Atoms 18915 2 0.000000 1 2.500000 56.252000 55.012243 43.906250 18916 2 0.000000 -1 2.500000 56.252000 55.012243 43.906250 18917 2 0.000000 1 2.500000 49.364000 53.686647 47.418750 -18918 2 0.000000 -1.000000 2.500000 49.364000 53.686647 47.418750 +18918 2 0.000000 -1 2.500000 49.364000 53.686647 47.418750 18919 2 0.000000 1 2.500000 51.660000 49.709858 47.418750 18920 2 0.000000 -1 2.500000 51.660000 49.709858 47.418750 18921 2 0.000000 1 2.500000 53.956000 51.035454 50.931250 @@ -18939,7 +18939,7 @@ Atoms 18923 2 0.000000 1 2.500000 56.252000 55.012243 50.931250 18924 2 0.000000 -1 2.500000 56.252000 55.012243 50.931250 18925 2 0.000000 1 2.500000 49.364000 53.686647 54.443750 -18926 2 0.000000 -1.000000 2.500000 49.364000 53.686647 54.443750 +18926 2 0.000000 -1 2.500000 49.364000 53.686647 54.443750 18927 2 0.000000 1 2.500000 51.660000 49.709858 54.443750 18928 2 0.000000 -1 2.500000 51.660000 49.709858 54.443750 18929 2 0.000000 1 2.500000 53.956000 51.035454 57.956250 @@ -18947,7 +18947,7 @@ Atoms 18931 2 0.000000 1 2.500000 56.252000 55.012243 57.956250 18932 2 0.000000 -1 2.500000 56.252000 55.012243 57.956250 18933 2 0.000000 1 2.500000 49.364000 53.686647 61.468750 -18934 2 0.000000 -1.000000 2.500000 49.364000 53.686647 61.468750 +18934 2 0.000000 -1 2.500000 49.364000 53.686647 61.468750 18935 2 0.000000 1 2.500000 51.660000 49.709858 61.468750 18936 2 0.000000 -1 2.500000 51.660000 49.709858 61.468750 18937 2 0.000000 1 2.500000 53.956000 58.989032 1.756250 @@ -18955,7 +18955,7 @@ Atoms 18939 2 0.000000 1 2.500000 56.252000 62.965820 1.756250 18940 2 0.000000 -1 2.500000 56.252000 62.965820 1.756250 18941 2 0.000000 1 2.500000 49.364000 61.640224 5.268750 -18942 2 0.000000 -1.000000 2.500000 49.364000 61.640224 5.268750 +18942 2 0.000000 -1 2.500000 49.364000 61.640224 5.268750 18943 2 0.000000 1 2.500000 51.660000 57.663435 5.268750 18944 2 0.000000 -1 2.500000 51.660000 57.663435 5.268750 18945 2 0.000000 1 2.500000 53.956000 58.989032 8.781250 @@ -18963,7 +18963,7 @@ Atoms 18947 2 0.000000 1 2.500000 56.252000 62.965820 8.781250 18948 2 0.000000 -1 2.500000 56.252000 62.965820 8.781250 18949 2 0.000000 1 2.500000 49.364000 61.640224 12.293750 -18950 2 0.000000 -1.000000 2.500000 49.364000 61.640224 12.293750 +18950 2 0.000000 -1 2.500000 49.364000 61.640224 12.293750 18951 2 0.000000 1 2.500000 51.660000 57.663435 12.293750 18952 2 0.000000 -1 2.500000 51.660000 57.663435 12.293750 18953 2 0.000000 1 2.500000 53.956000 58.989032 15.806250 @@ -18971,7 +18971,7 @@ Atoms 18955 2 0.000000 1 2.500000 56.252000 62.965820 15.806250 18956 2 0.000000 -1 2.500000 56.252000 62.965820 15.806250 18957 2 0.000000 1 2.500000 49.364000 61.640224 19.318750 -18958 2 0.000000 -1.000000 2.500000 49.364000 61.640224 19.318750 +18958 2 0.000000 -1 2.500000 49.364000 61.640224 19.318750 18959 2 0.000000 1 2.500000 51.660000 57.663435 19.318750 18960 2 0.000000 -1 2.500000 51.660000 57.663435 19.318750 18961 2 0.000000 1 2.500000 53.956000 58.989032 22.831250 @@ -18979,7 +18979,7 @@ Atoms 18963 2 0.000000 1 2.500000 56.252000 62.965820 22.831250 18964 2 0.000000 -1 2.500000 56.252000 62.965820 22.831250 18965 2 0.000000 1 2.500000 49.364000 61.640224 26.343750 -18966 2 0.000000 -1.000000 2.500000 49.364000 61.640224 26.343750 +18966 2 0.000000 -1 2.500000 49.364000 61.640224 26.343750 18967 2 0.000000 1 2.500000 51.660000 57.663435 26.343750 18968 2 0.000000 -1 2.500000 51.660000 57.663435 26.343750 18969 2 0.000000 1 2.500000 53.956000 58.989032 29.856250 @@ -18987,7 +18987,7 @@ Atoms 18971 2 0.000000 1 2.500000 56.252000 62.965820 29.856250 18972 2 0.000000 -1 2.500000 56.252000 62.965820 29.856250 18973 2 0.000000 1 2.500000 49.364000 61.640224 33.368750 -18974 2 0.000000 -1.000000 2.500000 49.364000 61.640224 33.368750 +18974 2 0.000000 -1 2.500000 49.364000 61.640224 33.368750 18975 2 0.000000 1 2.500000 51.660000 57.663435 33.368750 18976 2 0.000000 -1 2.500000 51.660000 57.663435 33.368750 18977 2 0.000000 1 2.500000 53.956000 58.989032 36.881250 @@ -18995,7 +18995,7 @@ Atoms 18979 2 0.000000 1 2.500000 56.252000 62.965820 36.881250 18980 2 0.000000 -1 2.500000 56.252000 62.965820 36.881250 18981 2 0.000000 1 2.500000 49.364000 61.640224 40.393750 -18982 2 0.000000 -1.000000 2.500000 49.364000 61.640224 40.393750 +18982 2 0.000000 -1 2.500000 49.364000 61.640224 40.393750 18983 2 0.000000 1 2.500000 51.660000 57.663435 40.393750 18984 2 0.000000 -1 2.500000 51.660000 57.663435 40.393750 18985 2 0.000000 1 2.500000 53.956000 58.989032 43.906250 @@ -19003,7 +19003,7 @@ Atoms 18987 2 0.000000 1 2.500000 56.252000 62.965820 43.906250 18988 2 0.000000 -1 2.500000 56.252000 62.965820 43.906250 18989 2 0.000000 1 2.500000 49.364000 61.640224 47.418750 -18990 2 0.000000 -1.000000 2.500000 49.364000 61.640224 47.418750 +18990 2 0.000000 -1 2.500000 49.364000 61.640224 47.418750 18991 2 0.000000 1 2.500000 51.660000 57.663435 47.418750 18992 2 0.000000 -1 2.500000 51.660000 57.663435 47.418750 18993 2 0.000000 1 2.500000 53.956000 58.989032 50.931250 @@ -19011,7 +19011,7 @@ Atoms 18995 2 0.000000 1 2.500000 56.252000 62.965820 50.931250 18996 2 0.000000 -1 2.500000 56.252000 62.965820 50.931250 18997 2 0.000000 1 2.500000 49.364000 61.640224 54.443750 -18998 2 0.000000 -1.000000 2.500000 49.364000 61.640224 54.443750 +18998 2 0.000000 -1 2.500000 49.364000 61.640224 54.443750 18999 2 0.000000 1 2.500000 51.660000 57.663435 54.443750 19000 2 0.000000 -1 2.500000 51.660000 57.663435 54.443750 19001 2 0.000000 1 2.500000 53.956000 58.989032 57.956250 @@ -19019,7 +19019,7 @@ Atoms 19003 2 0.000000 1 2.500000 56.252000 62.965820 57.956250 19004 2 0.000000 -1 2.500000 56.252000 62.965820 57.956250 19005 2 0.000000 1 2.500000 49.364000 61.640224 61.468750 -19006 2 0.000000 -1.000000 2.500000 49.364000 61.640224 61.468750 +19006 2 0.000000 -1 2.500000 49.364000 61.640224 61.468750 19007 2 0.000000 1 2.500000 51.660000 57.663435 61.468750 19008 2 0.000000 -1 2.500000 51.660000 57.663435 61.468750 19009 2 0.000000 1 2.500000 58.548000 3.313991 1.756250 @@ -19027,7 +19027,7 @@ Atoms 19011 2 0.000000 1 2.500000 60.844000 7.290779 1.756250 19012 2 0.000000 -1 2.500000 60.844000 7.290779 1.756250 19013 2 0.000000 1 2.500000 53.956000 5.965183 5.268750 -19014 2 0.000000 -1.000000 2.500000 53.956000 5.965183 5.268750 +19014 2 0.000000 -1 2.500000 53.956000 5.965183 5.268750 19015 2 0.000000 1 2.500000 56.252000 1.988394 5.268750 19016 2 0.000000 -1 2.500000 56.252000 1.988394 5.268750 19017 2 0.000000 1 2.500000 58.548000 3.313991 8.781250 @@ -19035,7 +19035,7 @@ Atoms 19019 2 0.000000 1 2.500000 60.844000 7.290779 8.781250 19020 2 0.000000 -1 2.500000 60.844000 7.290779 8.781250 19021 2 0.000000 1 2.500000 53.956000 5.965183 12.293750 -19022 2 0.000000 -1.000000 2.500000 53.956000 5.965183 12.293750 +19022 2 0.000000 -1 2.500000 53.956000 5.965183 12.293750 19023 2 0.000000 1 2.500000 56.252000 1.988394 12.293750 19024 2 0.000000 -1 2.500000 56.252000 1.988394 12.293750 19025 2 0.000000 1 2.500000 58.548000 3.313991 15.806250 @@ -19043,7 +19043,7 @@ Atoms 19027 2 0.000000 1 2.500000 60.844000 7.290779 15.806250 19028 2 0.000000 -1 2.500000 60.844000 7.290779 15.806250 19029 2 0.000000 1 2.500000 53.956000 5.965183 19.318750 -19030 2 0.000000 -1.000000 2.500000 53.956000 5.965183 19.318750 +19030 2 0.000000 -1 2.500000 53.956000 5.965183 19.318750 19031 2 0.000000 1 2.500000 56.252000 1.988394 19.318750 19032 2 0.000000 -1 2.500000 56.252000 1.988394 19.318750 19033 2 0.000000 1 2.500000 58.548000 3.313991 22.831250 @@ -19051,7 +19051,7 @@ Atoms 19035 2 0.000000 1 2.500000 60.844000 7.290779 22.831250 19036 2 0.000000 -1 2.500000 60.844000 7.290779 22.831250 19037 2 0.000000 1 2.500000 53.956000 5.965183 26.343750 -19038 2 0.000000 -1.000000 2.500000 53.956000 5.965183 26.343750 +19038 2 0.000000 -1 2.500000 53.956000 5.965183 26.343750 19039 2 0.000000 1 2.500000 56.252000 1.988394 26.343750 19040 2 0.000000 -1 2.500000 56.252000 1.988394 26.343750 19041 2 0.000000 1 2.500000 58.548000 3.313991 29.856250 @@ -19059,7 +19059,7 @@ Atoms 19043 2 0.000000 1 2.500000 60.844000 7.290779 29.856250 19044 2 0.000000 -1 2.500000 60.844000 7.290779 29.856250 19045 2 0.000000 1 2.500000 53.956000 5.965183 33.368750 -19046 2 0.000000 -1.000000 2.500000 53.956000 5.965183 33.368750 +19046 2 0.000000 -1 2.500000 53.956000 5.965183 33.368750 19047 2 0.000000 1 2.500000 56.252000 1.988394 33.368750 19048 2 0.000000 -1 2.500000 56.252000 1.988394 33.368750 19049 2 0.000000 1 2.500000 58.548000 3.313991 36.881250 @@ -19067,7 +19067,7 @@ Atoms 19051 2 0.000000 1 2.500000 60.844000 7.290779 36.881250 19052 2 0.000000 -1 2.500000 60.844000 7.290779 36.881250 19053 2 0.000000 1 2.500000 53.956000 5.965183 40.393750 -19054 2 0.000000 -1.000000 2.500000 53.956000 5.965183 40.393750 +19054 2 0.000000 -1 2.500000 53.956000 5.965183 40.393750 19055 2 0.000000 1 2.500000 56.252000 1.988394 40.393750 19056 2 0.000000 -1 2.500000 56.252000 1.988394 40.393750 19057 2 0.000000 1 2.500000 58.548000 3.313991 43.906250 @@ -19075,7 +19075,7 @@ Atoms 19059 2 0.000000 1 2.500000 60.844000 7.290779 43.906250 19060 2 0.000000 -1 2.500000 60.844000 7.290779 43.906250 19061 2 0.000000 1 2.500000 53.956000 5.965183 47.418750 -19062 2 0.000000 -1.000000 2.500000 53.956000 5.965183 47.418750 +19062 2 0.000000 -1 2.500000 53.956000 5.965183 47.418750 19063 2 0.000000 1 2.500000 56.252000 1.988394 47.418750 19064 2 0.000000 -1 2.500000 56.252000 1.988394 47.418750 19065 2 0.000000 1 2.500000 58.548000 3.313991 50.931250 @@ -19083,7 +19083,7 @@ Atoms 19067 2 0.000000 1 2.500000 60.844000 7.290779 50.931250 19068 2 0.000000 -1 2.500000 60.844000 7.290779 50.931250 19069 2 0.000000 1 2.500000 53.956000 5.965183 54.443750 -19070 2 0.000000 -1.000000 2.500000 53.956000 5.965183 54.443750 +19070 2 0.000000 -1 2.500000 53.956000 5.965183 54.443750 19071 2 0.000000 1 2.500000 56.252000 1.988394 54.443750 19072 2 0.000000 -1 2.500000 56.252000 1.988394 54.443750 19073 2 0.000000 1 2.500000 58.548000 3.313991 57.956250 @@ -19091,7 +19091,7 @@ Atoms 19075 2 0.000000 1 2.500000 60.844000 7.290779 57.956250 19076 2 0.000000 -1 2.500000 60.844000 7.290779 57.956250 19077 2 0.000000 1 2.500000 53.956000 5.965183 61.468750 -19078 2 0.000000 -1.000000 2.500000 53.956000 5.965183 61.468750 +19078 2 0.000000 -1 2.500000 53.956000 5.965183 61.468750 19079 2 0.000000 1 2.500000 56.252000 1.988394 61.468750 19080 2 0.000000 -1 2.500000 56.252000 1.988394 61.468750 19081 2 0.000000 1 2.500000 58.548000 11.267568 1.756250 @@ -19099,7 +19099,7 @@ Atoms 19083 2 0.000000 1 2.500000 60.844000 15.244357 1.756250 19084 2 0.000000 -1 2.500000 60.844000 15.244357 1.756250 19085 2 0.000000 1 2.500000 53.956000 13.918760 5.268750 -19086 2 0.000000 -1.000000 2.500000 53.956000 13.918760 5.268750 +19086 2 0.000000 -1 2.500000 53.956000 13.918760 5.268750 19087 2 0.000000 1 2.500000 56.252000 9.941972 5.268750 19088 2 0.000000 -1 2.500000 56.252000 9.941972 5.268750 19089 2 0.000000 1 2.500000 58.548000 11.267568 8.781250 @@ -19107,7 +19107,7 @@ Atoms 19091 2 0.000000 1 2.500000 60.844000 15.244357 8.781250 19092 2 0.000000 -1 2.500000 60.844000 15.244357 8.781250 19093 2 0.000000 1 2.500000 53.956000 13.918760 12.293750 -19094 2 0.000000 -1.000000 2.500000 53.956000 13.918760 12.293750 +19094 2 0.000000 -1 2.500000 53.956000 13.918760 12.293750 19095 2 0.000000 1 2.500000 56.252000 9.941972 12.293750 19096 2 0.000000 -1 2.500000 56.252000 9.941972 12.293750 19097 2 0.000000 1 2.500000 58.548000 11.267568 15.806250 @@ -19115,7 +19115,7 @@ Atoms 19099 2 0.000000 1 2.500000 60.844000 15.244357 15.806250 19100 2 0.000000 -1 2.500000 60.844000 15.244357 15.806250 19101 2 0.000000 1 2.500000 53.956000 13.918760 19.318750 -19102 2 0.000000 -1.000000 2.500000 53.956000 13.918760 19.318750 +19102 2 0.000000 -1 2.500000 53.956000 13.918760 19.318750 19103 2 0.000000 1 2.500000 56.252000 9.941972 19.318750 19104 2 0.000000 -1 2.500000 56.252000 9.941972 19.318750 19105 2 0.000000 1 2.500000 58.548000 11.267568 22.831250 @@ -19123,7 +19123,7 @@ Atoms 19107 2 0.000000 1 2.500000 60.844000 15.244357 22.831250 19108 2 0.000000 -1 2.500000 60.844000 15.244357 22.831250 19109 2 0.000000 1 2.500000 53.956000 13.918760 26.343750 -19110 2 0.000000 -1.000000 2.500000 53.956000 13.918760 26.343750 +19110 2 0.000000 -1 2.500000 53.956000 13.918760 26.343750 19111 2 0.000000 1 2.500000 56.252000 9.941972 26.343750 19112 2 0.000000 -1 2.500000 56.252000 9.941972 26.343750 19113 2 0.000000 1 2.500000 58.548000 11.267568 29.856250 @@ -19131,7 +19131,7 @@ Atoms 19115 2 0.000000 1 2.500000 60.844000 15.244357 29.856250 19116 2 0.000000 -1 2.500000 60.844000 15.244357 29.856250 19117 2 0.000000 1 2.500000 53.956000 13.918760 33.368750 -19118 2 0.000000 -1.000000 2.500000 53.956000 13.918760 33.368750 +19118 2 0.000000 -1 2.500000 53.956000 13.918760 33.368750 19119 2 0.000000 1 2.500000 56.252000 9.941972 33.368750 19120 2 0.000000 -1 2.500000 56.252000 9.941972 33.368750 19121 2 0.000000 1 2.500000 58.548000 11.267568 36.881250 @@ -19139,7 +19139,7 @@ Atoms 19123 2 0.000000 1 2.500000 60.844000 15.244357 36.881250 19124 2 0.000000 -1 2.500000 60.844000 15.244357 36.881250 19125 2 0.000000 1 2.500000 53.956000 13.918760 40.393750 -19126 2 0.000000 -1.000000 2.500000 53.956000 13.918760 40.393750 +19126 2 0.000000 -1 2.500000 53.956000 13.918760 40.393750 19127 2 0.000000 1 2.500000 56.252000 9.941972 40.393750 19128 2 0.000000 -1 2.500000 56.252000 9.941972 40.393750 19129 2 0.000000 1 2.500000 58.548000 11.267568 43.906250 @@ -19147,7 +19147,7 @@ Atoms 19131 2 0.000000 1 2.500000 60.844000 15.244357 43.906250 19132 2 0.000000 -1 2.500000 60.844000 15.244357 43.906250 19133 2 0.000000 1 2.500000 53.956000 13.918760 47.418750 -19134 2 0.000000 -1.000000 2.500000 53.956000 13.918760 47.418750 +19134 2 0.000000 -1 2.500000 53.956000 13.918760 47.418750 19135 2 0.000000 1 2.500000 56.252000 9.941972 47.418750 19136 2 0.000000 -1 2.500000 56.252000 9.941972 47.418750 19137 2 0.000000 1 2.500000 58.548000 11.267568 50.931250 @@ -19155,7 +19155,7 @@ Atoms 19139 2 0.000000 1 2.500000 60.844000 15.244357 50.931250 19140 2 0.000000 -1 2.500000 60.844000 15.244357 50.931250 19141 2 0.000000 1 2.500000 53.956000 13.918760 54.443750 -19142 2 0.000000 -1.000000 2.500000 53.956000 13.918760 54.443750 +19142 2 0.000000 -1 2.500000 53.956000 13.918760 54.443750 19143 2 0.000000 1 2.500000 56.252000 9.941972 54.443750 19144 2 0.000000 -1 2.500000 56.252000 9.941972 54.443750 19145 2 0.000000 1 2.500000 58.548000 11.267568 57.956250 @@ -19163,7 +19163,7 @@ Atoms 19147 2 0.000000 1 2.500000 60.844000 15.244357 57.956250 19148 2 0.000000 -1 2.500000 60.844000 15.244357 57.956250 19149 2 0.000000 1 2.500000 53.956000 13.918760 61.468750 -19150 2 0.000000 -1.000000 2.500000 53.956000 13.918760 61.468750 +19150 2 0.000000 -1 2.500000 53.956000 13.918760 61.468750 19151 2 0.000000 1 2.500000 56.252000 9.941972 61.468750 19152 2 0.000000 -1 2.500000 56.252000 9.941972 61.468750 19153 2 0.000000 1 2.500000 58.548000 19.221145 1.756250 @@ -19171,7 +19171,7 @@ Atoms 19155 2 0.000000 1 2.500000 60.844000 23.197934 1.756250 19156 2 0.000000 -1 2.500000 60.844000 23.197934 1.756250 19157 2 0.000000 1 2.500000 53.956000 21.872338 5.268750 -19158 2 0.000000 -1.000000 2.500000 53.956000 21.872338 5.268750 +19158 2 0.000000 -1 2.500000 53.956000 21.872338 5.268750 19159 2 0.000000 1 2.500000 56.252000 17.895549 5.268750 19160 2 0.000000 -1 2.500000 56.252000 17.895549 5.268750 19161 2 0.000000 1 2.500000 58.548000 19.221145 8.781250 @@ -19179,7 +19179,7 @@ Atoms 19163 2 0.000000 1 2.500000 60.844000 23.197934 8.781250 19164 2 0.000000 -1 2.500000 60.844000 23.197934 8.781250 19165 2 0.000000 1 2.500000 53.956000 21.872338 12.293750 -19166 2 0.000000 -1.000000 2.500000 53.956000 21.872338 12.293750 +19166 2 0.000000 -1 2.500000 53.956000 21.872338 12.293750 19167 2 0.000000 1 2.500000 56.252000 17.895549 12.293750 19168 2 0.000000 -1 2.500000 56.252000 17.895549 12.293750 19169 2 0.000000 1 2.500000 58.548000 19.221145 15.806250 @@ -19187,7 +19187,7 @@ Atoms 19171 2 0.000000 1 2.500000 60.844000 23.197934 15.806250 19172 2 0.000000 -1 2.500000 60.844000 23.197934 15.806250 19173 2 0.000000 1 2.500000 53.956000 21.872338 19.318750 -19174 2 0.000000 -1.000000 2.500000 53.956000 21.872338 19.318750 +19174 2 0.000000 -1 2.500000 53.956000 21.872338 19.318750 19175 2 0.000000 1 2.500000 56.252000 17.895549 19.318750 19176 2 0.000000 -1 2.500000 56.252000 17.895549 19.318750 19177 2 0.000000 1 2.500000 58.548000 19.221145 22.831250 @@ -19195,7 +19195,7 @@ Atoms 19179 2 0.000000 1 2.500000 60.844000 23.197934 22.831250 19180 2 0.000000 -1 2.500000 60.844000 23.197934 22.831250 19181 2 0.000000 1 2.500000 53.956000 21.872338 26.343750 -19182 2 0.000000 -1.000000 2.500000 53.956000 21.872338 26.343750 +19182 2 0.000000 -1 2.500000 53.956000 21.872338 26.343750 19183 2 0.000000 1 2.500000 56.252000 17.895549 26.343750 19184 2 0.000000 -1 2.500000 56.252000 17.895549 26.343750 19185 2 0.000000 1 2.500000 58.548000 19.221145 29.856250 @@ -19203,7 +19203,7 @@ Atoms 19187 2 0.000000 1 2.500000 60.844000 23.197934 29.856250 19188 2 0.000000 -1 2.500000 60.844000 23.197934 29.856250 19189 2 0.000000 1 2.500000 53.956000 21.872338 33.368750 -19190 2 0.000000 -1.000000 2.500000 53.956000 21.872338 33.368750 +19190 2 0.000000 -1 2.500000 53.956000 21.872338 33.368750 19191 2 0.000000 1 2.500000 56.252000 17.895549 33.368750 19192 2 0.000000 -1 2.500000 56.252000 17.895549 33.368750 19193 2 0.000000 1 2.500000 58.548000 19.221145 36.881250 @@ -19211,7 +19211,7 @@ Atoms 19195 2 0.000000 1 2.500000 60.844000 23.197934 36.881250 19196 2 0.000000 -1 2.500000 60.844000 23.197934 36.881250 19197 2 0.000000 1 2.500000 53.956000 21.872338 40.393750 -19198 2 0.000000 -1.000000 2.500000 53.956000 21.872338 40.393750 +19198 2 0.000000 -1 2.500000 53.956000 21.872338 40.393750 19199 2 0.000000 1 2.500000 56.252000 17.895549 40.393750 19200 2 0.000000 -1 2.500000 56.252000 17.895549 40.393750 19201 2 0.000000 1 2.500000 58.548000 19.221145 43.906250 @@ -19219,7 +19219,7 @@ Atoms 19203 2 0.000000 1 2.500000 60.844000 23.197934 43.906250 19204 2 0.000000 -1 2.500000 60.844000 23.197934 43.906250 19205 2 0.000000 1 2.500000 53.956000 21.872338 47.418750 -19206 2 0.000000 -1.000000 2.500000 53.956000 21.872338 47.418750 +19206 2 0.000000 -1 2.500000 53.956000 21.872338 47.418750 19207 2 0.000000 1 2.500000 56.252000 17.895549 47.418750 19208 2 0.000000 -1 2.500000 56.252000 17.895549 47.418750 19209 2 0.000000 1 2.500000 58.548000 19.221145 50.931250 @@ -19227,7 +19227,7 @@ Atoms 19211 2 0.000000 1 2.500000 60.844000 23.197934 50.931250 19212 2 0.000000 -1 2.500000 60.844000 23.197934 50.931250 19213 2 0.000000 1 2.500000 53.956000 21.872338 54.443750 -19214 2 0.000000 -1.000000 2.500000 53.956000 21.872338 54.443750 +19214 2 0.000000 -1 2.500000 53.956000 21.872338 54.443750 19215 2 0.000000 1 2.500000 56.252000 17.895549 54.443750 19216 2 0.000000 -1 2.500000 56.252000 17.895549 54.443750 19217 2 0.000000 1 2.500000 58.548000 19.221145 57.956250 @@ -19235,7 +19235,7 @@ Atoms 19219 2 0.000000 1 2.500000 60.844000 23.197934 57.956250 19220 2 0.000000 -1 2.500000 60.844000 23.197934 57.956250 19221 2 0.000000 1 2.500000 53.956000 21.872338 61.468750 -19222 2 0.000000 -1.000000 2.500000 53.956000 21.872338 61.468750 +19222 2 0.000000 -1 2.500000 53.956000 21.872338 61.468750 19223 2 0.000000 1 2.500000 56.252000 17.895549 61.468750 19224 2 0.000000 -1 2.500000 56.252000 17.895549 61.468750 19225 2 0.000000 1 2.500000 58.548000 27.174722 1.756250 @@ -19243,7 +19243,7 @@ Atoms 19227 2 0.000000 1 2.500000 60.844000 31.151511 1.756250 19228 2 0.000000 -1 2.500000 60.844000 31.151511 1.756250 19229 2 0.000000 1 2.500000 53.956000 29.825915 5.268750 -19230 2 0.000000 -1.000000 2.500000 53.956000 29.825915 5.268750 +19230 2 0.000000 -1 2.500000 53.956000 29.825915 5.268750 19231 2 0.000000 1 2.500000 56.252000 25.849126 5.268750 19232 2 0.000000 -1 2.500000 56.252000 25.849126 5.268750 19233 2 0.000000 1 2.500000 58.548000 27.174722 8.781250 @@ -19251,7 +19251,7 @@ Atoms 19235 2 0.000000 1 2.500000 60.844000 31.151511 8.781250 19236 2 0.000000 -1 2.500000 60.844000 31.151511 8.781250 19237 2 0.000000 1 2.500000 53.956000 29.825915 12.293750 -19238 2 0.000000 -1.000000 2.500000 53.956000 29.825915 12.293750 +19238 2 0.000000 -1 2.500000 53.956000 29.825915 12.293750 19239 2 0.000000 1 2.500000 56.252000 25.849126 12.293750 19240 2 0.000000 -1 2.500000 56.252000 25.849126 12.293750 19241 2 0.000000 1 2.500000 58.548000 27.174722 15.806250 @@ -19259,7 +19259,7 @@ Atoms 19243 2 0.000000 1 2.500000 60.844000 31.151511 15.806250 19244 2 0.000000 -1 2.500000 60.844000 31.151511 15.806250 19245 2 0.000000 1 2.500000 53.956000 29.825915 19.318750 -19246 2 0.000000 -1.000000 2.500000 53.956000 29.825915 19.318750 +19246 2 0.000000 -1 2.500000 53.956000 29.825915 19.318750 19247 2 0.000000 1 2.500000 56.252000 25.849126 19.318750 19248 2 0.000000 -1 2.500000 56.252000 25.849126 19.318750 19249 2 0.000000 1 2.500000 58.548000 27.174722 22.831250 @@ -19267,7 +19267,7 @@ Atoms 19251 2 0.000000 1 2.500000 60.844000 31.151511 22.831250 19252 2 0.000000 -1 2.500000 60.844000 31.151511 22.831250 19253 2 0.000000 1 2.500000 53.956000 29.825915 26.343750 -19254 2 0.000000 -1.000000 2.500000 53.956000 29.825915 26.343750 +19254 2 0.000000 -1 2.500000 53.956000 29.825915 26.343750 19255 2 0.000000 1 2.500000 56.252000 25.849126 26.343750 19256 2 0.000000 -1 2.500000 56.252000 25.849126 26.343750 19257 2 0.000000 1 2.500000 58.548000 27.174722 29.856250 @@ -19275,7 +19275,7 @@ Atoms 19259 2 0.000000 1 2.500000 60.844000 31.151511 29.856250 19260 2 0.000000 -1 2.500000 60.844000 31.151511 29.856250 19261 2 0.000000 1 2.500000 53.956000 29.825915 33.368750 -19262 2 0.000000 -1.000000 2.500000 53.956000 29.825915 33.368750 +19262 2 0.000000 -1 2.500000 53.956000 29.825915 33.368750 19263 2 0.000000 1 2.500000 56.252000 25.849126 33.368750 19264 2 0.000000 -1 2.500000 56.252000 25.849126 33.368750 19265 2 0.000000 1 2.500000 58.548000 27.174722 36.881250 @@ -19283,7 +19283,7 @@ Atoms 19267 2 0.000000 1 2.500000 60.844000 31.151511 36.881250 19268 2 0.000000 -1 2.500000 60.844000 31.151511 36.881250 19269 2 0.000000 1 2.500000 53.956000 29.825915 40.393750 -19270 2 0.000000 -1.000000 2.500000 53.956000 29.825915 40.393750 +19270 2 0.000000 -1 2.500000 53.956000 29.825915 40.393750 19271 2 0.000000 1 2.500000 56.252000 25.849126 40.393750 19272 2 0.000000 -1 2.500000 56.252000 25.849126 40.393750 19273 2 0.000000 1 2.500000 58.548000 27.174722 43.906250 @@ -19291,7 +19291,7 @@ Atoms 19275 2 0.000000 1 2.500000 60.844000 31.151511 43.906250 19276 2 0.000000 -1 2.500000 60.844000 31.151511 43.906250 19277 2 0.000000 1 2.500000 53.956000 29.825915 47.418750 -19278 2 0.000000 -1.000000 2.500000 53.956000 29.825915 47.418750 +19278 2 0.000000 -1 2.500000 53.956000 29.825915 47.418750 19279 2 0.000000 1 2.500000 56.252000 25.849126 47.418750 19280 2 0.000000 -1 2.500000 56.252000 25.849126 47.418750 19281 2 0.000000 1 2.500000 58.548000 27.174722 50.931250 @@ -19299,7 +19299,7 @@ Atoms 19283 2 0.000000 1 2.500000 60.844000 31.151511 50.931250 19284 2 0.000000 -1 2.500000 60.844000 31.151511 50.931250 19285 2 0.000000 1 2.500000 53.956000 29.825915 54.443750 -19286 2 0.000000 -1.000000 2.500000 53.956000 29.825915 54.443750 +19286 2 0.000000 -1 2.500000 53.956000 29.825915 54.443750 19287 2 0.000000 1 2.500000 56.252000 25.849126 54.443750 19288 2 0.000000 -1 2.500000 56.252000 25.849126 54.443750 19289 2 0.000000 1 2.500000 58.548000 27.174722 57.956250 @@ -19307,7 +19307,7 @@ Atoms 19291 2 0.000000 1 2.500000 60.844000 31.151511 57.956250 19292 2 0.000000 -1 2.500000 60.844000 31.151511 57.956250 19293 2 0.000000 1 2.500000 53.956000 29.825915 61.468750 -19294 2 0.000000 -1.000000 2.500000 53.956000 29.825915 61.468750 +19294 2 0.000000 -1 2.500000 53.956000 29.825915 61.468750 19295 2 0.000000 1 2.500000 56.252000 25.849126 61.468750 19296 2 0.000000 -1 2.500000 56.252000 25.849126 61.468750 19297 2 0.000000 1 2.500000 58.548000 35.128300 1.756250 @@ -19315,7 +19315,7 @@ Atoms 19299 2 0.000000 1 2.500000 60.844000 39.105088 1.756250 19300 2 0.000000 -1 2.500000 60.844000 39.105088 1.756250 19301 2 0.000000 1 2.500000 53.956000 37.779492 5.268750 -19302 2 0.000000 -1.000000 2.500000 53.956000 37.779492 5.268750 +19302 2 0.000000 -1 2.500000 53.956000 37.779492 5.268750 19303 2 0.000000 1 2.500000 56.252000 33.802704 5.268750 19304 2 0.000000 -1 2.500000 56.252000 33.802704 5.268750 19305 2 0.000000 1 2.500000 58.548000 35.128300 8.781250 @@ -19323,7 +19323,7 @@ Atoms 19307 2 0.000000 1 2.500000 60.844000 39.105088 8.781250 19308 2 0.000000 -1 2.500000 60.844000 39.105088 8.781250 19309 2 0.000000 1 2.500000 53.956000 37.779492 12.293750 -19310 2 0.000000 -1.000000 2.500000 53.956000 37.779492 12.293750 +19310 2 0.000000 -1 2.500000 53.956000 37.779492 12.293750 19311 2 0.000000 1 2.500000 56.252000 33.802704 12.293750 19312 2 0.000000 -1 2.500000 56.252000 33.802704 12.293750 19313 2 0.000000 1 2.500000 58.548000 35.128300 15.806250 @@ -19331,7 +19331,7 @@ Atoms 19315 2 0.000000 1 2.500000 60.844000 39.105088 15.806250 19316 2 0.000000 -1 2.500000 60.844000 39.105088 15.806250 19317 2 0.000000 1 2.500000 53.956000 37.779492 19.318750 -19318 2 0.000000 -1.000000 2.500000 53.956000 37.779492 19.318750 +19318 2 0.000000 -1 2.500000 53.956000 37.779492 19.318750 19319 2 0.000000 1 2.500000 56.252000 33.802704 19.318750 19320 2 0.000000 -1 2.500000 56.252000 33.802704 19.318750 19321 2 0.000000 1 2.500000 58.548000 35.128300 22.831250 @@ -19339,7 +19339,7 @@ Atoms 19323 2 0.000000 1 2.500000 60.844000 39.105088 22.831250 19324 2 0.000000 -1 2.500000 60.844000 39.105088 22.831250 19325 2 0.000000 1 2.500000 53.956000 37.779492 26.343750 -19326 2 0.000000 -1.000000 2.500000 53.956000 37.779492 26.343750 +19326 2 0.000000 -1 2.500000 53.956000 37.779492 26.343750 19327 2 0.000000 1 2.500000 56.252000 33.802704 26.343750 19328 2 0.000000 -1 2.500000 56.252000 33.802704 26.343750 19329 2 0.000000 1 2.500000 58.548000 35.128300 29.856250 @@ -19347,7 +19347,7 @@ Atoms 19331 2 0.000000 1 2.500000 60.844000 39.105088 29.856250 19332 2 0.000000 -1 2.500000 60.844000 39.105088 29.856250 19333 2 0.000000 1 2.500000 53.956000 37.779492 33.368750 -19334 2 0.000000 -1.000000 2.500000 53.956000 37.779492 33.368750 +19334 2 0.000000 -1 2.500000 53.956000 37.779492 33.368750 19335 2 0.000000 1 2.500000 56.252000 33.802704 33.368750 19336 2 0.000000 -1 2.500000 56.252000 33.802704 33.368750 19337 2 0.000000 1 2.500000 58.548000 35.128300 36.881250 @@ -19355,7 +19355,7 @@ Atoms 19339 2 0.000000 1 2.500000 60.844000 39.105088 36.881250 19340 2 0.000000 -1 2.500000 60.844000 39.105088 36.881250 19341 2 0.000000 1 2.500000 53.956000 37.779492 40.393750 -19342 2 0.000000 -1.000000 2.500000 53.956000 37.779492 40.393750 +19342 2 0.000000 -1 2.500000 53.956000 37.779492 40.393750 19343 2 0.000000 1 2.500000 56.252000 33.802704 40.393750 19344 2 0.000000 -1 2.500000 56.252000 33.802704 40.393750 19345 2 0.000000 1 2.500000 58.548000 35.128300 43.906250 @@ -19363,7 +19363,7 @@ Atoms 19347 2 0.000000 1 2.500000 60.844000 39.105088 43.906250 19348 2 0.000000 -1 2.500000 60.844000 39.105088 43.906250 19349 2 0.000000 1 2.500000 53.956000 37.779492 47.418750 -19350 2 0.000000 -1.000000 2.500000 53.956000 37.779492 47.418750 +19350 2 0.000000 -1 2.500000 53.956000 37.779492 47.418750 19351 2 0.000000 1 2.500000 56.252000 33.802704 47.418750 19352 2 0.000000 -1 2.500000 56.252000 33.802704 47.418750 19353 2 0.000000 1 2.500000 58.548000 35.128300 50.931250 @@ -19371,7 +19371,7 @@ Atoms 19355 2 0.000000 1 2.500000 60.844000 39.105088 50.931250 19356 2 0.000000 -1 2.500000 60.844000 39.105088 50.931250 19357 2 0.000000 1 2.500000 53.956000 37.779492 54.443750 -19358 2 0.000000 -1.000000 2.500000 53.956000 37.779492 54.443750 +19358 2 0.000000 -1 2.500000 53.956000 37.779492 54.443750 19359 2 0.000000 1 2.500000 56.252000 33.802704 54.443750 19360 2 0.000000 -1 2.500000 56.252000 33.802704 54.443750 19361 2 0.000000 1 2.500000 58.548000 35.128300 57.956250 @@ -19379,7 +19379,7 @@ Atoms 19363 2 0.000000 1 2.500000 60.844000 39.105088 57.956250 19364 2 0.000000 -1 2.500000 60.844000 39.105088 57.956250 19365 2 0.000000 1 2.500000 53.956000 37.779492 61.468750 -19366 2 0.000000 -1.000000 2.500000 53.956000 37.779492 61.468750 +19366 2 0.000000 -1 2.500000 53.956000 37.779492 61.468750 19367 2 0.000000 1 2.500000 56.252000 33.802704 61.468750 19368 2 0.000000 -1 2.500000 56.252000 33.802704 61.468750 19369 2 0.000000 1 2.500000 58.548000 43.081877 1.756250 @@ -19387,7 +19387,7 @@ Atoms 19371 2 0.000000 1 2.500000 60.844000 47.058666 1.756250 19372 2 0.000000 -1 2.500000 60.844000 47.058666 1.756250 19373 2 0.000000 1 2.500000 53.956000 45.733070 5.268750 -19374 2 0.000000 -1.000000 2.500000 53.956000 45.733070 5.268750 +19374 2 0.000000 -1 2.500000 53.956000 45.733070 5.268750 19375 2 0.000000 1 2.500000 56.252000 41.756281 5.268750 19376 2 0.000000 -1 2.500000 56.252000 41.756281 5.268750 19377 2 0.000000 1 2.500000 58.548000 43.081877 8.781250 @@ -19395,7 +19395,7 @@ Atoms 19379 2 0.000000 1 2.500000 60.844000 47.058666 8.781250 19380 2 0.000000 -1 2.500000 60.844000 47.058666 8.781250 19381 2 0.000000 1 2.500000 53.956000 45.733070 12.293750 -19382 2 0.000000 -1.000000 2.500000 53.956000 45.733070 12.293750 +19382 2 0.000000 -1 2.500000 53.956000 45.733070 12.293750 19383 2 0.000000 1 2.500000 56.252000 41.756281 12.293750 19384 2 0.000000 -1 2.500000 56.252000 41.756281 12.293750 19385 2 0.000000 1 2.500000 58.548000 43.081877 15.806250 @@ -19403,7 +19403,7 @@ Atoms 19387 2 0.000000 1 2.500000 60.844000 47.058666 15.806250 19388 2 0.000000 -1 2.500000 60.844000 47.058666 15.806250 19389 2 0.000000 1 2.500000 53.956000 45.733070 19.318750 -19390 2 0.000000 -1.000000 2.500000 53.956000 45.733070 19.318750 +19390 2 0.000000 -1 2.500000 53.956000 45.733070 19.318750 19391 2 0.000000 1 2.500000 56.252000 41.756281 19.318750 19392 2 0.000000 -1 2.500000 56.252000 41.756281 19.318750 19393 2 0.000000 1 2.500000 58.548000 43.081877 22.831250 @@ -19411,7 +19411,7 @@ Atoms 19395 2 0.000000 1 2.500000 60.844000 47.058666 22.831250 19396 2 0.000000 -1 2.500000 60.844000 47.058666 22.831250 19397 2 0.000000 1 2.500000 53.956000 45.733070 26.343750 -19398 2 0.000000 -1.000000 2.500000 53.956000 45.733070 26.343750 +19398 2 0.000000 -1 2.500000 53.956000 45.733070 26.343750 19399 2 0.000000 1 2.500000 56.252000 41.756281 26.343750 19400 2 0.000000 -1 2.500000 56.252000 41.756281 26.343750 19401 2 0.000000 1 2.500000 58.548000 43.081877 29.856250 @@ -19419,7 +19419,7 @@ Atoms 19403 2 0.000000 1 2.500000 60.844000 47.058666 29.856250 19404 2 0.000000 -1 2.500000 60.844000 47.058666 29.856250 19405 2 0.000000 1 2.500000 53.956000 45.733070 33.368750 -19406 2 0.000000 -1.000000 2.500000 53.956000 45.733070 33.368750 +19406 2 0.000000 -1 2.500000 53.956000 45.733070 33.368750 19407 2 0.000000 1 2.500000 56.252000 41.756281 33.368750 19408 2 0.000000 -1 2.500000 56.252000 41.756281 33.368750 19409 2 0.000000 1 2.500000 58.548000 43.081877 36.881250 @@ -19427,7 +19427,7 @@ Atoms 19411 2 0.000000 1 2.500000 60.844000 47.058666 36.881250 19412 2 0.000000 -1 2.500000 60.844000 47.058666 36.881250 19413 2 0.000000 1 2.500000 53.956000 45.733070 40.393750 -19414 2 0.000000 -1.000000 2.500000 53.956000 45.733070 40.393750 +19414 2 0.000000 -1 2.500000 53.956000 45.733070 40.393750 19415 2 0.000000 1 2.500000 56.252000 41.756281 40.393750 19416 2 0.000000 -1 2.500000 56.252000 41.756281 40.393750 19417 2 0.000000 1 2.500000 58.548000 43.081877 43.906250 @@ -19435,7 +19435,7 @@ Atoms 19419 2 0.000000 1 2.500000 60.844000 47.058666 43.906250 19420 2 0.000000 -1 2.500000 60.844000 47.058666 43.906250 19421 2 0.000000 1 2.500000 53.956000 45.733070 47.418750 -19422 2 0.000000 -1.000000 2.500000 53.956000 45.733070 47.418750 +19422 2 0.000000 -1 2.500000 53.956000 45.733070 47.418750 19423 2 0.000000 1 2.500000 56.252000 41.756281 47.418750 19424 2 0.000000 -1 2.500000 56.252000 41.756281 47.418750 19425 2 0.000000 1 2.500000 58.548000 43.081877 50.931250 @@ -19443,7 +19443,7 @@ Atoms 19427 2 0.000000 1 2.500000 60.844000 47.058666 50.931250 19428 2 0.000000 -1 2.500000 60.844000 47.058666 50.931250 19429 2 0.000000 1 2.500000 53.956000 45.733070 54.443750 -19430 2 0.000000 -1.000000 2.500000 53.956000 45.733070 54.443750 +19430 2 0.000000 -1 2.500000 53.956000 45.733070 54.443750 19431 2 0.000000 1 2.500000 56.252000 41.756281 54.443750 19432 2 0.000000 -1 2.500000 56.252000 41.756281 54.443750 19433 2 0.000000 1 2.500000 58.548000 43.081877 57.956250 @@ -19451,7 +19451,7 @@ Atoms 19435 2 0.000000 1 2.500000 60.844000 47.058666 57.956250 19436 2 0.000000 -1 2.500000 60.844000 47.058666 57.956250 19437 2 0.000000 1 2.500000 53.956000 45.733070 61.468750 -19438 2 0.000000 -1.000000 2.500000 53.956000 45.733070 61.468750 +19438 2 0.000000 -1 2.500000 53.956000 45.733070 61.468750 19439 2 0.000000 1 2.500000 56.252000 41.756281 61.468750 19440 2 0.000000 -1 2.500000 56.252000 41.756281 61.468750 19441 2 0.000000 1 2.500000 58.548000 51.035454 1.756250 @@ -19459,7 +19459,7 @@ Atoms 19443 2 0.000000 1 2.500000 60.844000 55.012243 1.756250 19444 2 0.000000 -1 2.500000 60.844000 55.012243 1.756250 19445 2 0.000000 1 2.500000 53.956000 53.686647 5.268750 -19446 2 0.000000 -1.000000 2.500000 53.956000 53.686647 5.268750 +19446 2 0.000000 -1 2.500000 53.956000 53.686647 5.268750 19447 2 0.000000 1 2.500000 56.252000 49.709858 5.268750 19448 2 0.000000 -1 2.500000 56.252000 49.709858 5.268750 19449 2 0.000000 1 2.500000 58.548000 51.035454 8.781250 @@ -19467,7 +19467,7 @@ Atoms 19451 2 0.000000 1 2.500000 60.844000 55.012243 8.781250 19452 2 0.000000 -1 2.500000 60.844000 55.012243 8.781250 19453 2 0.000000 1 2.500000 53.956000 53.686647 12.293750 -19454 2 0.000000 -1.000000 2.500000 53.956000 53.686647 12.293750 +19454 2 0.000000 -1 2.500000 53.956000 53.686647 12.293750 19455 2 0.000000 1 2.500000 56.252000 49.709858 12.293750 19456 2 0.000000 -1 2.500000 56.252000 49.709858 12.293750 19457 2 0.000000 1 2.500000 58.548000 51.035454 15.806250 @@ -19475,7 +19475,7 @@ Atoms 19459 2 0.000000 1 2.500000 60.844000 55.012243 15.806250 19460 2 0.000000 -1 2.500000 60.844000 55.012243 15.806250 19461 2 0.000000 1 2.500000 53.956000 53.686647 19.318750 -19462 2 0.000000 -1.000000 2.500000 53.956000 53.686647 19.318750 +19462 2 0.000000 -1 2.500000 53.956000 53.686647 19.318750 19463 2 0.000000 1 2.500000 56.252000 49.709858 19.318750 19464 2 0.000000 -1 2.500000 56.252000 49.709858 19.318750 19465 2 0.000000 1 2.500000 58.548000 51.035454 22.831250 @@ -19483,7 +19483,7 @@ Atoms 19467 2 0.000000 1 2.500000 60.844000 55.012243 22.831250 19468 2 0.000000 -1 2.500000 60.844000 55.012243 22.831250 19469 2 0.000000 1 2.500000 53.956000 53.686647 26.343750 -19470 2 0.000000 -1.000000 2.500000 53.956000 53.686647 26.343750 +19470 2 0.000000 -1 2.500000 53.956000 53.686647 26.343750 19471 2 0.000000 1 2.500000 56.252000 49.709858 26.343750 19472 2 0.000000 -1 2.500000 56.252000 49.709858 26.343750 19473 2 0.000000 1 2.500000 58.548000 51.035454 29.856250 @@ -19491,7 +19491,7 @@ Atoms 19475 2 0.000000 1 2.500000 60.844000 55.012243 29.856250 19476 2 0.000000 -1 2.500000 60.844000 55.012243 29.856250 19477 2 0.000000 1 2.500000 53.956000 53.686647 33.368750 -19478 2 0.000000 -1.000000 2.500000 53.956000 53.686647 33.368750 +19478 2 0.000000 -1 2.500000 53.956000 53.686647 33.368750 19479 2 0.000000 1 2.500000 56.252000 49.709858 33.368750 19480 2 0.000000 -1 2.500000 56.252000 49.709858 33.368750 19481 2 0.000000 1 2.500000 58.548000 51.035454 36.881250 @@ -19499,7 +19499,7 @@ Atoms 19483 2 0.000000 1 2.500000 60.844000 55.012243 36.881250 19484 2 0.000000 -1 2.500000 60.844000 55.012243 36.881250 19485 2 0.000000 1 2.500000 53.956000 53.686647 40.393750 -19486 2 0.000000 -1.000000 2.500000 53.956000 53.686647 40.393750 +19486 2 0.000000 -1 2.500000 53.956000 53.686647 40.393750 19487 2 0.000000 1 2.500000 56.252000 49.709858 40.393750 19488 2 0.000000 -1 2.500000 56.252000 49.709858 40.393750 19489 2 0.000000 1 2.500000 58.548000 51.035454 43.906250 @@ -19507,7 +19507,7 @@ Atoms 19491 2 0.000000 1 2.500000 60.844000 55.012243 43.906250 19492 2 0.000000 -1 2.500000 60.844000 55.012243 43.906250 19493 2 0.000000 1 2.500000 53.956000 53.686647 47.418750 -19494 2 0.000000 -1.000000 2.500000 53.956000 53.686647 47.418750 +19494 2 0.000000 -1 2.500000 53.956000 53.686647 47.418750 19495 2 0.000000 1 2.500000 56.252000 49.709858 47.418750 19496 2 0.000000 -1 2.500000 56.252000 49.709858 47.418750 19497 2 0.000000 1 2.500000 58.548000 51.035454 50.931250 @@ -19515,7 +19515,7 @@ Atoms 19499 2 0.000000 1 2.500000 60.844000 55.012243 50.931250 19500 2 0.000000 -1 2.500000 60.844000 55.012243 50.931250 19501 2 0.000000 1 2.500000 53.956000 53.686647 54.443750 -19502 2 0.000000 -1.000000 2.500000 53.956000 53.686647 54.443750 +19502 2 0.000000 -1 2.500000 53.956000 53.686647 54.443750 19503 2 0.000000 1 2.500000 56.252000 49.709858 54.443750 19504 2 0.000000 -1 2.500000 56.252000 49.709858 54.443750 19505 2 0.000000 1 2.500000 58.548000 51.035454 57.956250 @@ -19523,7 +19523,7 @@ Atoms 19507 2 0.000000 1 2.500000 60.844000 55.012243 57.956250 19508 2 0.000000 -1 2.500000 60.844000 55.012243 57.956250 19509 2 0.000000 1 2.500000 53.956000 53.686647 61.468750 -19510 2 0.000000 -1.000000 2.500000 53.956000 53.686647 61.468750 +19510 2 0.000000 -1 2.500000 53.956000 53.686647 61.468750 19511 2 0.000000 1 2.500000 56.252000 49.709858 61.468750 19512 2 0.000000 -1 2.500000 56.252000 49.709858 61.468750 19513 2 0.000000 1 2.500000 58.548000 58.989032 1.756250 @@ -19531,7 +19531,7 @@ Atoms 19515 2 0.000000 1 2.500000 60.844000 62.965820 1.756250 19516 2 0.000000 -1 2.500000 60.844000 62.965820 1.756250 19517 2 0.000000 1 2.500000 53.956000 61.640224 5.268750 -19518 2 0.000000 -1.000000 2.500000 53.956000 61.640224 5.268750 +19518 2 0.000000 -1 2.500000 53.956000 61.640224 5.268750 19519 2 0.000000 1 2.500000 56.252000 57.663435 5.268750 19520 2 0.000000 -1 2.500000 56.252000 57.663435 5.268750 19521 2 0.000000 1 2.500000 58.548000 58.989032 8.781250 @@ -19539,7 +19539,7 @@ Atoms 19523 2 0.000000 1 2.500000 60.844000 62.965820 8.781250 19524 2 0.000000 -1 2.500000 60.844000 62.965820 8.781250 19525 2 0.000000 1 2.500000 53.956000 61.640224 12.293750 -19526 2 0.000000 -1.000000 2.500000 53.956000 61.640224 12.293750 +19526 2 0.000000 -1 2.500000 53.956000 61.640224 12.293750 19527 2 0.000000 1 2.500000 56.252000 57.663435 12.293750 19528 2 0.000000 -1 2.500000 56.252000 57.663435 12.293750 19529 2 0.000000 1 2.500000 58.548000 58.989032 15.806250 @@ -19547,7 +19547,7 @@ Atoms 19531 2 0.000000 1 2.500000 60.844000 62.965820 15.806250 19532 2 0.000000 -1 2.500000 60.844000 62.965820 15.806250 19533 2 0.000000 1 2.500000 53.956000 61.640224 19.318750 -19534 2 0.000000 -1.000000 2.500000 53.956000 61.640224 19.318750 +19534 2 0.000000 -1 2.500000 53.956000 61.640224 19.318750 19535 2 0.000000 1 2.500000 56.252000 57.663435 19.318750 19536 2 0.000000 -1 2.500000 56.252000 57.663435 19.318750 19537 2 0.000000 1 2.500000 58.548000 58.989032 22.831250 @@ -19555,7 +19555,7 @@ Atoms 19539 2 0.000000 1 2.500000 60.844000 62.965820 22.831250 19540 2 0.000000 -1 2.500000 60.844000 62.965820 22.831250 19541 2 0.000000 1 2.500000 53.956000 61.640224 26.343750 -19542 2 0.000000 -1.000000 2.500000 53.956000 61.640224 26.343750 +19542 2 0.000000 -1 2.500000 53.956000 61.640224 26.343750 19543 2 0.000000 1 2.500000 56.252000 57.663435 26.343750 19544 2 0.000000 -1 2.500000 56.252000 57.663435 26.343750 19545 2 0.000000 1 2.500000 58.548000 58.989032 29.856250 @@ -19563,7 +19563,7 @@ Atoms 19547 2 0.000000 1 2.500000 60.844000 62.965820 29.856250 19548 2 0.000000 -1 2.500000 60.844000 62.965820 29.856250 19549 2 0.000000 1 2.500000 53.956000 61.640224 33.368750 -19550 2 0.000000 -1.000000 2.500000 53.956000 61.640224 33.368750 +19550 2 0.000000 -1 2.500000 53.956000 61.640224 33.368750 19551 2 0.000000 1 2.500000 56.252000 57.663435 33.368750 19552 2 0.000000 -1 2.500000 56.252000 57.663435 33.368750 19553 2 0.000000 1 2.500000 58.548000 58.989032 36.881250 @@ -19571,7 +19571,7 @@ Atoms 19555 2 0.000000 1 2.500000 60.844000 62.965820 36.881250 19556 2 0.000000 -1 2.500000 60.844000 62.965820 36.881250 19557 2 0.000000 1 2.500000 53.956000 61.640224 40.393750 -19558 2 0.000000 -1.000000 2.500000 53.956000 61.640224 40.393750 +19558 2 0.000000 -1 2.500000 53.956000 61.640224 40.393750 19559 2 0.000000 1 2.500000 56.252000 57.663435 40.393750 19560 2 0.000000 -1 2.500000 56.252000 57.663435 40.393750 19561 2 0.000000 1 2.500000 58.548000 58.989032 43.906250 @@ -19579,7 +19579,7 @@ Atoms 19563 2 0.000000 1 2.500000 60.844000 62.965820 43.906250 19564 2 0.000000 -1 2.500000 60.844000 62.965820 43.906250 19565 2 0.000000 1 2.500000 53.956000 61.640224 47.418750 -19566 2 0.000000 -1.000000 2.500000 53.956000 61.640224 47.418750 +19566 2 0.000000 -1 2.500000 53.956000 61.640224 47.418750 19567 2 0.000000 1 2.500000 56.252000 57.663435 47.418750 19568 2 0.000000 -1 2.500000 56.252000 57.663435 47.418750 19569 2 0.000000 1 2.500000 58.548000 58.989032 50.931250 @@ -19587,7 +19587,7 @@ Atoms 19571 2 0.000000 1 2.500000 60.844000 62.965820 50.931250 19572 2 0.000000 -1 2.500000 60.844000 62.965820 50.931250 19573 2 0.000000 1 2.500000 53.956000 61.640224 54.443750 -19574 2 0.000000 -1.000000 2.500000 53.956000 61.640224 54.443750 +19574 2 0.000000 -1 2.500000 53.956000 61.640224 54.443750 19575 2 0.000000 1 2.500000 56.252000 57.663435 54.443750 19576 2 0.000000 -1 2.500000 56.252000 57.663435 54.443750 19577 2 0.000000 1 2.500000 58.548000 58.989032 57.956250 @@ -19595,7 +19595,7 @@ Atoms 19579 2 0.000000 1 2.500000 60.844000 62.965820 57.956250 19580 2 0.000000 -1 2.500000 60.844000 62.965820 57.956250 19581 2 0.000000 1 2.500000 53.956000 61.640224 61.468750 -19582 2 0.000000 -1.000000 2.500000 53.956000 61.640224 61.468750 +19582 2 0.000000 -1 2.500000 53.956000 61.640224 61.468750 19583 2 0.000000 1 2.500000 56.252000 57.663435 61.468750 19584 2 0.000000 -1 2.500000 56.252000 57.663435 61.468750 19585 2 0.000000 1 2.500000 63.140000 3.313991 1.756250 @@ -19603,7 +19603,7 @@ Atoms 19587 2 0.000000 1 2.500000 1.148000 7.290779 1.756250 19588 2 0.000000 -1 2.500000 1.148000 7.290779 1.756250 19589 2 0.000000 1 2.500000 58.548000 5.965183 5.268750 -19590 2 0.000000 -1.000000 2.500000 58.548000 5.965183 5.268750 +19590 2 0.000000 -1 2.500000 58.548000 5.965183 5.268750 19591 2 0.000000 1 2.500000 60.844000 1.988394 5.268750 19592 2 0.000000 -1 2.500000 60.844000 1.988394 5.268750 19593 2 0.000000 1 2.500000 63.140000 3.313991 8.781250 @@ -19611,7 +19611,7 @@ Atoms 19595 2 0.000000 1 2.500000 1.148000 7.290779 8.781250 19596 2 0.000000 -1 2.500000 1.148000 7.290779 8.781250 19597 2 0.000000 1 2.500000 58.548000 5.965183 12.293750 -19598 2 0.000000 -1.000000 2.500000 58.548000 5.965183 12.293750 +19598 2 0.000000 -1 2.500000 58.548000 5.965183 12.293750 19599 2 0.000000 1 2.500000 60.844000 1.988394 12.293750 19600 2 0.000000 -1 2.500000 60.844000 1.988394 12.293750 19601 2 0.000000 1 2.500000 63.140000 3.313991 15.806250 @@ -19619,7 +19619,7 @@ Atoms 19603 2 0.000000 1 2.500000 1.148000 7.290779 15.806250 19604 2 0.000000 -1 2.500000 1.148000 7.290779 15.806250 19605 2 0.000000 1 2.500000 58.548000 5.965183 19.318750 -19606 2 0.000000 -1.000000 2.500000 58.548000 5.965183 19.318750 +19606 2 0.000000 -1 2.500000 58.548000 5.965183 19.318750 19607 2 0.000000 1 2.500000 60.844000 1.988394 19.318750 19608 2 0.000000 -1 2.500000 60.844000 1.988394 19.318750 19609 2 0.000000 1 2.500000 63.140000 3.313991 22.831250 @@ -19627,7 +19627,7 @@ Atoms 19611 2 0.000000 1 2.500000 1.148000 7.290779 22.831250 19612 2 0.000000 -1 2.500000 1.148000 7.290779 22.831250 19613 2 0.000000 1 2.500000 58.548000 5.965183 26.343750 -19614 2 0.000000 -1.000000 2.500000 58.548000 5.965183 26.343750 +19614 2 0.000000 -1 2.500000 58.548000 5.965183 26.343750 19615 2 0.000000 1 2.500000 60.844000 1.988394 26.343750 19616 2 0.000000 -1 2.500000 60.844000 1.988394 26.343750 19617 2 0.000000 1 2.500000 63.140000 3.313991 29.856250 @@ -19635,7 +19635,7 @@ Atoms 19619 2 0.000000 1 2.500000 1.148000 7.290779 29.856250 19620 2 0.000000 -1 2.500000 1.148000 7.290779 29.856250 19621 2 0.000000 1 2.500000 58.548000 5.965183 33.368750 -19622 2 0.000000 -1.000000 2.500000 58.548000 5.965183 33.368750 +19622 2 0.000000 -1 2.500000 58.548000 5.965183 33.368750 19623 2 0.000000 1 2.500000 60.844000 1.988394 33.368750 19624 2 0.000000 -1 2.500000 60.844000 1.988394 33.368750 19625 2 0.000000 1 2.500000 63.140000 3.313991 36.881250 @@ -19643,7 +19643,7 @@ Atoms 19627 2 0.000000 1 2.500000 1.148000 7.290779 36.881250 19628 2 0.000000 -1 2.500000 1.148000 7.290779 36.881250 19629 2 0.000000 1 2.500000 58.548000 5.965183 40.393750 -19630 2 0.000000 -1.000000 2.500000 58.548000 5.965183 40.393750 +19630 2 0.000000 -1 2.500000 58.548000 5.965183 40.393750 19631 2 0.000000 1 2.500000 60.844000 1.988394 40.393750 19632 2 0.000000 -1 2.500000 60.844000 1.988394 40.393750 19633 2 0.000000 1 2.500000 63.140000 3.313991 43.906250 @@ -19651,7 +19651,7 @@ Atoms 19635 2 0.000000 1 2.500000 1.148000 7.290779 43.906250 19636 2 0.000000 -1 2.500000 1.148000 7.290779 43.906250 19637 2 0.000000 1 2.500000 58.548000 5.965183 47.418750 -19638 2 0.000000 -1.000000 2.500000 58.548000 5.965183 47.418750 +19638 2 0.000000 -1 2.500000 58.548000 5.965183 47.418750 19639 2 0.000000 1 2.500000 60.844000 1.988394 47.418750 19640 2 0.000000 -1 2.500000 60.844000 1.988394 47.418750 19641 2 0.000000 1 2.500000 63.140000 3.313991 50.931250 @@ -19659,7 +19659,7 @@ Atoms 19643 2 0.000000 1 2.500000 1.148000 7.290779 50.931250 19644 2 0.000000 -1 2.500000 1.148000 7.290779 50.931250 19645 2 0.000000 1 2.500000 58.548000 5.965183 54.443750 -19646 2 0.000000 -1.000000 2.500000 58.548000 5.965183 54.443750 +19646 2 0.000000 -1 2.500000 58.548000 5.965183 54.443750 19647 2 0.000000 1 2.500000 60.844000 1.988394 54.443750 19648 2 0.000000 -1 2.500000 60.844000 1.988394 54.443750 19649 2 0.000000 1 2.500000 63.140000 3.313991 57.956250 @@ -19667,7 +19667,7 @@ Atoms 19651 2 0.000000 1 2.500000 1.148000 7.290779 57.956250 19652 2 0.000000 -1 2.500000 1.148000 7.290779 57.956250 19653 2 0.000000 1 2.500000 58.548000 5.965183 61.468750 -19654 2 0.000000 -1.000000 2.500000 58.548000 5.965183 61.468750 +19654 2 0.000000 -1 2.500000 58.548000 5.965183 61.468750 19655 2 0.000000 1 2.500000 60.844000 1.988394 61.468750 19656 2 0.000000 -1 2.500000 60.844000 1.988394 61.468750 19657 2 0.000000 1 2.500000 63.140000 11.267568 1.756250 @@ -19675,7 +19675,7 @@ Atoms 19659 2 0.000000 1 2.500000 1.148000 15.244357 1.756250 19660 2 0.000000 -1 2.500000 1.148000 15.244357 1.756250 19661 2 0.000000 1 2.500000 58.548000 13.918760 5.268750 -19662 2 0.000000 -1.000000 2.500000 58.548000 13.918760 5.268750 +19662 2 0.000000 -1 2.500000 58.548000 13.918760 5.268750 19663 2 0.000000 1 2.500000 60.844000 9.941972 5.268750 19664 2 0.000000 -1 2.500000 60.844000 9.941972 5.268750 19665 2 0.000000 1 2.500000 63.140000 11.267568 8.781250 @@ -19683,7 +19683,7 @@ Atoms 19667 2 0.000000 1 2.500000 1.148000 15.244357 8.781250 19668 2 0.000000 -1 2.500000 1.148000 15.244357 8.781250 19669 2 0.000000 1 2.500000 58.548000 13.918760 12.293750 -19670 2 0.000000 -1.000000 2.500000 58.548000 13.918760 12.293750 +19670 2 0.000000 -1 2.500000 58.548000 13.918760 12.293750 19671 2 0.000000 1 2.500000 60.844000 9.941972 12.293750 19672 2 0.000000 -1 2.500000 60.844000 9.941972 12.293750 19673 2 0.000000 1 2.500000 63.140000 11.267568 15.806250 @@ -19691,7 +19691,7 @@ Atoms 19675 2 0.000000 1 2.500000 1.148000 15.244357 15.806250 19676 2 0.000000 -1 2.500000 1.148000 15.244357 15.806250 19677 2 0.000000 1 2.500000 58.548000 13.918760 19.318750 -19678 2 0.000000 -1.000000 2.500000 58.548000 13.918760 19.318750 +19678 2 0.000000 -1 2.500000 58.548000 13.918760 19.318750 19679 2 0.000000 1 2.500000 60.844000 9.941972 19.318750 19680 2 0.000000 -1 2.500000 60.844000 9.941972 19.318750 19681 2 0.000000 1 2.500000 63.140000 11.267568 22.831250 @@ -19699,7 +19699,7 @@ Atoms 19683 2 0.000000 1 2.500000 1.148000 15.244357 22.831250 19684 2 0.000000 -1 2.500000 1.148000 15.244357 22.831250 19685 2 0.000000 1 2.500000 58.548000 13.918760 26.343750 -19686 2 0.000000 -1.000000 2.500000 58.548000 13.918760 26.343750 +19686 2 0.000000 -1 2.500000 58.548000 13.918760 26.343750 19687 2 0.000000 1 2.500000 60.844000 9.941972 26.343750 19688 2 0.000000 -1 2.500000 60.844000 9.941972 26.343750 19689 2 0.000000 1 2.500000 63.140000 11.267568 29.856250 @@ -19707,7 +19707,7 @@ Atoms 19691 2 0.000000 1 2.500000 1.148000 15.244357 29.856250 19692 2 0.000000 -1 2.500000 1.148000 15.244357 29.856250 19693 2 0.000000 1 2.500000 58.548000 13.918760 33.368750 -19694 2 0.000000 -1.000000 2.500000 58.548000 13.918760 33.368750 +19694 2 0.000000 -1 2.500000 58.548000 13.918760 33.368750 19695 2 0.000000 1 2.500000 60.844000 9.941972 33.368750 19696 2 0.000000 -1 2.500000 60.844000 9.941972 33.368750 19697 2 0.000000 1 2.500000 63.140000 11.267568 36.881250 @@ -19715,7 +19715,7 @@ Atoms 19699 2 0.000000 1 2.500000 1.148000 15.244357 36.881250 19700 2 0.000000 -1 2.500000 1.148000 15.244357 36.881250 19701 2 0.000000 1 2.500000 58.548000 13.918760 40.393750 -19702 2 0.000000 -1.000000 2.500000 58.548000 13.918760 40.393750 +19702 2 0.000000 -1 2.500000 58.548000 13.918760 40.393750 19703 2 0.000000 1 2.500000 60.844000 9.941972 40.393750 19704 2 0.000000 -1 2.500000 60.844000 9.941972 40.393750 19705 2 0.000000 1 2.500000 63.140000 11.267568 43.906250 @@ -19723,7 +19723,7 @@ Atoms 19707 2 0.000000 1 2.500000 1.148000 15.244357 43.906250 19708 2 0.000000 -1 2.500000 1.148000 15.244357 43.906250 19709 2 0.000000 1 2.500000 58.548000 13.918760 47.418750 -19710 2 0.000000 -1.000000 2.500000 58.548000 13.918760 47.418750 +19710 2 0.000000 -1 2.500000 58.548000 13.918760 47.418750 19711 2 0.000000 1 2.500000 60.844000 9.941972 47.418750 19712 2 0.000000 -1 2.500000 60.844000 9.941972 47.418750 19713 2 0.000000 1 2.500000 63.140000 11.267568 50.931250 @@ -19731,7 +19731,7 @@ Atoms 19715 2 0.000000 1 2.500000 1.148000 15.244357 50.931250 19716 2 0.000000 -1 2.500000 1.148000 15.244357 50.931250 19717 2 0.000000 1 2.500000 58.548000 13.918760 54.443750 -19718 2 0.000000 -1.000000 2.500000 58.548000 13.918760 54.443750 +19718 2 0.000000 -1 2.500000 58.548000 13.918760 54.443750 19719 2 0.000000 1 2.500000 60.844000 9.941972 54.443750 19720 2 0.000000 -1 2.500000 60.844000 9.941972 54.443750 19721 2 0.000000 1 2.500000 63.140000 11.267568 57.956250 @@ -19739,7 +19739,7 @@ Atoms 19723 2 0.000000 1 2.500000 1.148000 15.244357 57.956250 19724 2 0.000000 -1 2.500000 1.148000 15.244357 57.956250 19725 2 0.000000 1 2.500000 58.548000 13.918760 61.468750 -19726 2 0.000000 -1.000000 2.500000 58.548000 13.918760 61.468750 +19726 2 0.000000 -1 2.500000 58.548000 13.918760 61.468750 19727 2 0.000000 1 2.500000 60.844000 9.941972 61.468750 19728 2 0.000000 -1 2.500000 60.844000 9.941972 61.468750 19729 2 0.000000 1 2.500000 63.140000 19.221145 1.756250 @@ -19747,7 +19747,7 @@ Atoms 19731 2 0.000000 1 2.500000 1.148000 23.197934 1.756250 19732 2 0.000000 -1 2.500000 1.148000 23.197934 1.756250 19733 2 0.000000 1 2.500000 58.548000 21.872338 5.268750 -19734 2 0.000000 -1.000000 2.500000 58.548000 21.872338 5.268750 +19734 2 0.000000 -1 2.500000 58.548000 21.872338 5.268750 19735 2 0.000000 1 2.500000 60.844000 17.895549 5.268750 19736 2 0.000000 -1 2.500000 60.844000 17.895549 5.268750 19737 2 0.000000 1 2.500000 63.140000 19.221145 8.781250 @@ -19755,7 +19755,7 @@ Atoms 19739 2 0.000000 1 2.500000 1.148000 23.197934 8.781250 19740 2 0.000000 -1 2.500000 1.148000 23.197934 8.781250 19741 2 0.000000 1 2.500000 58.548000 21.872338 12.293750 -19742 2 0.000000 -1.000000 2.500000 58.548000 21.872338 12.293750 +19742 2 0.000000 -1 2.500000 58.548000 21.872338 12.293750 19743 2 0.000000 1 2.500000 60.844000 17.895549 12.293750 19744 2 0.000000 -1 2.500000 60.844000 17.895549 12.293750 19745 2 0.000000 1 2.500000 63.140000 19.221145 15.806250 @@ -19763,7 +19763,7 @@ Atoms 19747 2 0.000000 1 2.500000 1.148000 23.197934 15.806250 19748 2 0.000000 -1 2.500000 1.148000 23.197934 15.806250 19749 2 0.000000 1 2.500000 58.548000 21.872338 19.318750 -19750 2 0.000000 -1.000000 2.500000 58.548000 21.872338 19.318750 +19750 2 0.000000 -1 2.500000 58.548000 21.872338 19.318750 19751 2 0.000000 1 2.500000 60.844000 17.895549 19.318750 19752 2 0.000000 -1 2.500000 60.844000 17.895549 19.318750 19753 2 0.000000 1 2.500000 63.140000 19.221145 22.831250 @@ -19771,7 +19771,7 @@ Atoms 19755 2 0.000000 1 2.500000 1.148000 23.197934 22.831250 19756 2 0.000000 -1 2.500000 1.148000 23.197934 22.831250 19757 2 0.000000 1 2.500000 58.548000 21.872338 26.343750 -19758 2 0.000000 -1.000000 2.500000 58.548000 21.872338 26.343750 +19758 2 0.000000 -1 2.500000 58.548000 21.872338 26.343750 19759 2 0.000000 1 2.500000 60.844000 17.895549 26.343750 19760 2 0.000000 -1 2.500000 60.844000 17.895549 26.343750 19761 2 0.000000 1 2.500000 63.140000 19.221145 29.856250 @@ -19779,7 +19779,7 @@ Atoms 19763 2 0.000000 1 2.500000 1.148000 23.197934 29.856250 19764 2 0.000000 -1 2.500000 1.148000 23.197934 29.856250 19765 2 0.000000 1 2.500000 58.548000 21.872338 33.368750 -19766 2 0.000000 -1.000000 2.500000 58.548000 21.872338 33.368750 +19766 2 0.000000 -1 2.500000 58.548000 21.872338 33.368750 19767 2 0.000000 1 2.500000 60.844000 17.895549 33.368750 19768 2 0.000000 -1 2.500000 60.844000 17.895549 33.368750 19769 2 0.000000 1 2.500000 63.140000 19.221145 36.881250 @@ -19787,7 +19787,7 @@ Atoms 19771 2 0.000000 1 2.500000 1.148000 23.197934 36.881250 19772 2 0.000000 -1 2.500000 1.148000 23.197934 36.881250 19773 2 0.000000 1 2.500000 58.548000 21.872338 40.393750 -19774 2 0.000000 -1.000000 2.500000 58.548000 21.872338 40.393750 +19774 2 0.000000 -1 2.500000 58.548000 21.872338 40.393750 19775 2 0.000000 1 2.500000 60.844000 17.895549 40.393750 19776 2 0.000000 -1 2.500000 60.844000 17.895549 40.393750 19777 2 0.000000 1 2.500000 63.140000 19.221145 43.906250 @@ -19795,7 +19795,7 @@ Atoms 19779 2 0.000000 1 2.500000 1.148000 23.197934 43.906250 19780 2 0.000000 -1 2.500000 1.148000 23.197934 43.906250 19781 2 0.000000 1 2.500000 58.548000 21.872338 47.418750 -19782 2 0.000000 -1.000000 2.500000 58.548000 21.872338 47.418750 +19782 2 0.000000 -1 2.500000 58.548000 21.872338 47.418750 19783 2 0.000000 1 2.500000 60.844000 17.895549 47.418750 19784 2 0.000000 -1 2.500000 60.844000 17.895549 47.418750 19785 2 0.000000 1 2.500000 63.140000 19.221145 50.931250 @@ -19803,7 +19803,7 @@ Atoms 19787 2 0.000000 1 2.500000 1.148000 23.197934 50.931250 19788 2 0.000000 -1 2.500000 1.148000 23.197934 50.931250 19789 2 0.000000 1 2.500000 58.548000 21.872338 54.443750 -19790 2 0.000000 -1.000000 2.500000 58.548000 21.872338 54.443750 +19790 2 0.000000 -1 2.500000 58.548000 21.872338 54.443750 19791 2 0.000000 1 2.500000 60.844000 17.895549 54.443750 19792 2 0.000000 -1 2.500000 60.844000 17.895549 54.443750 19793 2 0.000000 1 2.500000 63.140000 19.221145 57.956250 @@ -19811,7 +19811,7 @@ Atoms 19795 2 0.000000 1 2.500000 1.148000 23.197934 57.956250 19796 2 0.000000 -1 2.500000 1.148000 23.197934 57.956250 19797 2 0.000000 1 2.500000 58.548000 21.872338 61.468750 -19798 2 0.000000 -1.000000 2.500000 58.548000 21.872338 61.468750 +19798 2 0.000000 -1 2.500000 58.548000 21.872338 61.468750 19799 2 0.000000 1 2.500000 60.844000 17.895549 61.468750 19800 2 0.000000 -1 2.500000 60.844000 17.895549 61.468750 19801 2 0.000000 1 2.500000 63.140000 27.174722 1.756250 @@ -19819,7 +19819,7 @@ Atoms 19803 2 0.000000 1 2.500000 1.148000 31.151511 1.756250 19804 2 0.000000 -1 2.500000 1.148000 31.151511 1.756250 19805 2 0.000000 1 2.500000 58.548000 29.825915 5.268750 -19806 2 0.000000 -1.000000 2.500000 58.548000 29.825915 5.268750 +19806 2 0.000000 -1 2.500000 58.548000 29.825915 5.268750 19807 2 0.000000 1 2.500000 60.844000 25.849126 5.268750 19808 2 0.000000 -1 2.500000 60.844000 25.849126 5.268750 19809 2 0.000000 1 2.500000 63.140000 27.174722 8.781250 @@ -19827,7 +19827,7 @@ Atoms 19811 2 0.000000 1 2.500000 1.148000 31.151511 8.781250 19812 2 0.000000 -1 2.500000 1.148000 31.151511 8.781250 19813 2 0.000000 1 2.500000 58.548000 29.825915 12.293750 -19814 2 0.000000 -1.000000 2.500000 58.548000 29.825915 12.293750 +19814 2 0.000000 -1 2.500000 58.548000 29.825915 12.293750 19815 2 0.000000 1 2.500000 60.844000 25.849126 12.293750 19816 2 0.000000 -1 2.500000 60.844000 25.849126 12.293750 19817 2 0.000000 1 2.500000 63.140000 27.174722 15.806250 @@ -19835,7 +19835,7 @@ Atoms 19819 2 0.000000 1 2.500000 1.148000 31.151511 15.806250 19820 2 0.000000 -1 2.500000 1.148000 31.151511 15.806250 19821 2 0.000000 1 2.500000 58.548000 29.825915 19.318750 -19822 2 0.000000 -1.000000 2.500000 58.548000 29.825915 19.318750 +19822 2 0.000000 -1 2.500000 58.548000 29.825915 19.318750 19823 2 0.000000 1 2.500000 60.844000 25.849126 19.318750 19824 2 0.000000 -1 2.500000 60.844000 25.849126 19.318750 19825 2 0.000000 1 2.500000 63.140000 27.174722 22.831250 @@ -19843,7 +19843,7 @@ Atoms 19827 2 0.000000 1 2.500000 1.148000 31.151511 22.831250 19828 2 0.000000 -1 2.500000 1.148000 31.151511 22.831250 19829 2 0.000000 1 2.500000 58.548000 29.825915 26.343750 -19830 2 0.000000 -1.000000 2.500000 58.548000 29.825915 26.343750 +19830 2 0.000000 -1 2.500000 58.548000 29.825915 26.343750 19831 2 0.000000 1 2.500000 60.844000 25.849126 26.343750 19832 2 0.000000 -1 2.500000 60.844000 25.849126 26.343750 19833 2 0.000000 1 2.500000 63.140000 27.174722 29.856250 @@ -19851,7 +19851,7 @@ Atoms 19835 2 0.000000 1 2.500000 1.148000 31.151511 29.856250 19836 2 0.000000 -1 2.500000 1.148000 31.151511 29.856250 19837 2 0.000000 1 2.500000 58.548000 29.825915 33.368750 -19838 2 0.000000 -1.000000 2.500000 58.548000 29.825915 33.368750 +19838 2 0.000000 -1 2.500000 58.548000 29.825915 33.368750 19839 2 0.000000 1 2.500000 60.844000 25.849126 33.368750 19840 2 0.000000 -1 2.500000 60.844000 25.849126 33.368750 19841 2 0.000000 1 2.500000 63.140000 27.174722 36.881250 @@ -19859,7 +19859,7 @@ Atoms 19843 2 0.000000 1 2.500000 1.148000 31.151511 36.881250 19844 2 0.000000 -1 2.500000 1.148000 31.151511 36.881250 19845 2 0.000000 1 2.500000 58.548000 29.825915 40.393750 -19846 2 0.000000 -1.000000 2.500000 58.548000 29.825915 40.393750 +19846 2 0.000000 -1 2.500000 58.548000 29.825915 40.393750 19847 2 0.000000 1 2.500000 60.844000 25.849126 40.393750 19848 2 0.000000 -1 2.500000 60.844000 25.849126 40.393750 19849 2 0.000000 1 2.500000 63.140000 27.174722 43.906250 @@ -19867,7 +19867,7 @@ Atoms 19851 2 0.000000 1 2.500000 1.148000 31.151511 43.906250 19852 2 0.000000 -1 2.500000 1.148000 31.151511 43.906250 19853 2 0.000000 1 2.500000 58.548000 29.825915 47.418750 -19854 2 0.000000 -1.000000 2.500000 58.548000 29.825915 47.418750 +19854 2 0.000000 -1 2.500000 58.548000 29.825915 47.418750 19855 2 0.000000 1 2.500000 60.844000 25.849126 47.418750 19856 2 0.000000 -1 2.500000 60.844000 25.849126 47.418750 19857 2 0.000000 1 2.500000 63.140000 27.174722 50.931250 @@ -19875,7 +19875,7 @@ Atoms 19859 2 0.000000 1 2.500000 1.148000 31.151511 50.931250 19860 2 0.000000 -1 2.500000 1.148000 31.151511 50.931250 19861 2 0.000000 1 2.500000 58.548000 29.825915 54.443750 -19862 2 0.000000 -1.000000 2.500000 58.548000 29.825915 54.443750 +19862 2 0.000000 -1 2.500000 58.548000 29.825915 54.443750 19863 2 0.000000 1 2.500000 60.844000 25.849126 54.443750 19864 2 0.000000 -1 2.500000 60.844000 25.849126 54.443750 19865 2 0.000000 1 2.500000 63.140000 27.174722 57.956250 @@ -19883,7 +19883,7 @@ Atoms 19867 2 0.000000 1 2.500000 1.148000 31.151511 57.956250 19868 2 0.000000 -1 2.500000 1.148000 31.151511 57.956250 19869 2 0.000000 1 2.500000 58.548000 29.825915 61.468750 -19870 2 0.000000 -1.000000 2.500000 58.548000 29.825915 61.468750 +19870 2 0.000000 -1 2.500000 58.548000 29.825915 61.468750 19871 2 0.000000 1 2.500000 60.844000 25.849126 61.468750 19872 2 0.000000 -1 2.500000 60.844000 25.849126 61.468750 19873 2 0.000000 1 2.500000 63.140000 35.128300 1.756250 @@ -19891,7 +19891,7 @@ Atoms 19875 2 0.000000 1 2.500000 1.148000 39.105088 1.756250 19876 2 0.000000 -1 2.500000 1.148000 39.105088 1.756250 19877 2 0.000000 1 2.500000 58.548000 37.779492 5.268750 -19878 2 0.000000 -1.000000 2.500000 58.548000 37.779492 5.268750 +19878 2 0.000000 -1 2.500000 58.548000 37.779492 5.268750 19879 2 0.000000 1 2.500000 60.844000 33.802704 5.268750 19880 2 0.000000 -1 2.500000 60.844000 33.802704 5.268750 19881 2 0.000000 1 2.500000 63.140000 35.128300 8.781250 @@ -19899,7 +19899,7 @@ Atoms 19883 2 0.000000 1 2.500000 1.148000 39.105088 8.781250 19884 2 0.000000 -1 2.500000 1.148000 39.105088 8.781250 19885 2 0.000000 1 2.500000 58.548000 37.779492 12.293750 -19886 2 0.000000 -1.000000 2.500000 58.548000 37.779492 12.293750 +19886 2 0.000000 -1 2.500000 58.548000 37.779492 12.293750 19887 2 0.000000 1 2.500000 60.844000 33.802704 12.293750 19888 2 0.000000 -1 2.500000 60.844000 33.802704 12.293750 19889 2 0.000000 1 2.500000 63.140000 35.128300 15.806250 @@ -19907,7 +19907,7 @@ Atoms 19891 2 0.000000 1 2.500000 1.148000 39.105088 15.806250 19892 2 0.000000 -1 2.500000 1.148000 39.105088 15.806250 19893 2 0.000000 1 2.500000 58.548000 37.779492 19.318750 -19894 2 0.000000 -1.000000 2.500000 58.548000 37.779492 19.318750 +19894 2 0.000000 -1 2.500000 58.548000 37.779492 19.318750 19895 2 0.000000 1 2.500000 60.844000 33.802704 19.318750 19896 2 0.000000 -1 2.500000 60.844000 33.802704 19.318750 19897 2 0.000000 1 2.500000 63.140000 35.128300 22.831250 @@ -19915,7 +19915,7 @@ Atoms 19899 2 0.000000 1 2.500000 1.148000 39.105088 22.831250 19900 2 0.000000 -1 2.500000 1.148000 39.105088 22.831250 19901 2 0.000000 1 2.500000 58.548000 37.779492 26.343750 -19902 2 0.000000 -1.000000 2.500000 58.548000 37.779492 26.343750 +19902 2 0.000000 -1 2.500000 58.548000 37.779492 26.343750 19903 2 0.000000 1 2.500000 60.844000 33.802704 26.343750 19904 2 0.000000 -1 2.500000 60.844000 33.802704 26.343750 19905 2 0.000000 1 2.500000 63.140000 35.128300 29.856250 @@ -19923,7 +19923,7 @@ Atoms 19907 2 0.000000 1 2.500000 1.148000 39.105088 29.856250 19908 2 0.000000 -1 2.500000 1.148000 39.105088 29.856250 19909 2 0.000000 1 2.500000 58.548000 37.779492 33.368750 -19910 2 0.000000 -1.000000 2.500000 58.548000 37.779492 33.368750 +19910 2 0.000000 -1 2.500000 58.548000 37.779492 33.368750 19911 2 0.000000 1 2.500000 60.844000 33.802704 33.368750 19912 2 0.000000 -1 2.500000 60.844000 33.802704 33.368750 19913 2 0.000000 1 2.500000 63.140000 35.128300 36.881250 @@ -19931,7 +19931,7 @@ Atoms 19915 2 0.000000 1 2.500000 1.148000 39.105088 36.881250 19916 2 0.000000 -1 2.500000 1.148000 39.105088 36.881250 19917 2 0.000000 1 2.500000 58.548000 37.779492 40.393750 -19918 2 0.000000 -1.000000 2.500000 58.548000 37.779492 40.393750 +19918 2 0.000000 -1 2.500000 58.548000 37.779492 40.393750 19919 2 0.000000 1 2.500000 60.844000 33.802704 40.393750 19920 2 0.000000 -1 2.500000 60.844000 33.802704 40.393750 19921 2 0.000000 1 2.500000 63.140000 35.128300 43.906250 @@ -19939,7 +19939,7 @@ Atoms 19923 2 0.000000 1 2.500000 1.148000 39.105088 43.906250 19924 2 0.000000 -1 2.500000 1.148000 39.105088 43.906250 19925 2 0.000000 1 2.500000 58.548000 37.779492 47.418750 -19926 2 0.000000 -1.000000 2.500000 58.548000 37.779492 47.418750 +19926 2 0.000000 -1 2.500000 58.548000 37.779492 47.418750 19927 2 0.000000 1 2.500000 60.844000 33.802704 47.418750 19928 2 0.000000 -1 2.500000 60.844000 33.802704 47.418750 19929 2 0.000000 1 2.500000 63.140000 35.128300 50.931250 @@ -19947,7 +19947,7 @@ Atoms 19931 2 0.000000 1 2.500000 1.148000 39.105088 50.931250 19932 2 0.000000 -1 2.500000 1.148000 39.105088 50.931250 19933 2 0.000000 1 2.500000 58.548000 37.779492 54.443750 -19934 2 0.000000 -1.000000 2.500000 58.548000 37.779492 54.443750 +19934 2 0.000000 -1 2.500000 58.548000 37.779492 54.443750 19935 2 0.000000 1 2.500000 60.844000 33.802704 54.443750 19936 2 0.000000 -1 2.500000 60.844000 33.802704 54.443750 19937 2 0.000000 1 2.500000 63.140000 35.128300 57.956250 @@ -19955,7 +19955,7 @@ Atoms 19939 2 0.000000 1 2.500000 1.148000 39.105088 57.956250 19940 2 0.000000 -1 2.500000 1.148000 39.105088 57.956250 19941 2 0.000000 1 2.500000 58.548000 37.779492 61.468750 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26.343750 -19974 2 0.000000 -1.000000 2.500000 58.548000 45.733070 26.343750 +19974 2 0.000000 -1 2.500000 58.548000 45.733070 26.343750 19975 2 0.000000 1 2.500000 60.844000 41.756281 26.343750 19976 2 0.000000 -1 2.500000 60.844000 41.756281 26.343750 19977 2 0.000000 1 2.500000 63.140000 43.081877 29.856250 @@ -19995,7 +19995,7 @@ Atoms 19979 2 0.000000 1 2.500000 1.148000 47.058666 29.856250 19980 2 0.000000 -1 2.500000 1.148000 47.058666 29.856250 19981 2 0.000000 1 2.500000 58.548000 45.733070 33.368750 -19982 2 0.000000 -1.000000 2.500000 58.548000 45.733070 33.368750 +19982 2 0.000000 -1 2.500000 58.548000 45.733070 33.368750 19983 2 0.000000 1 2.500000 60.844000 41.756281 33.368750 19984 2 0.000000 -1 2.500000 60.844000 41.756281 33.368750 19985 2 0.000000 1 2.500000 63.140000 43.081877 36.881250 @@ -20003,7 +20003,7 @@ Atoms 19987 2 0.000000 1 2.500000 1.148000 47.058666 36.881250 19988 2 0.000000 -1 2.500000 1.148000 47.058666 36.881250 19989 2 0.000000 1 2.500000 58.548000 45.733070 40.393750 -19990 2 0.000000 -1.000000 2.500000 58.548000 45.733070 40.393750 +19990 2 0.000000 -1 2.500000 58.548000 45.733070 40.393750 19991 2 0.000000 1 2.500000 60.844000 41.756281 40.393750 19992 2 0.000000 -1 2.500000 60.844000 41.756281 40.393750 19993 2 0.000000 1 2.500000 63.140000 43.081877 43.906250 @@ -20011,7 +20011,7 @@ Atoms 19995 2 0.000000 1 2.500000 1.148000 47.058666 43.906250 19996 2 0.000000 -1 2.500000 1.148000 47.058666 43.906250 19997 2 0.000000 1 2.500000 58.548000 45.733070 47.418750 -19998 2 0.000000 -1.000000 2.500000 58.548000 45.733070 47.418750 +19998 2 0.000000 -1 2.500000 58.548000 45.733070 47.418750 19999 2 0.000000 1 2.500000 60.844000 41.756281 47.418750 20000 2 0.000000 -1 2.500000 60.844000 41.756281 47.418750 20001 2 0.000000 1 2.500000 63.140000 43.081877 50.931250 @@ -20019,7 +20019,7 @@ Atoms 20003 2 0.000000 1 2.500000 1.148000 47.058666 50.931250 20004 2 0.000000 -1 2.500000 1.148000 47.058666 50.931250 20005 2 0.000000 1 2.500000 58.548000 45.733070 54.443750 -20006 2 0.000000 -1.000000 2.500000 58.548000 45.733070 54.443750 +20006 2 0.000000 -1 2.500000 58.548000 45.733070 54.443750 20007 2 0.000000 1 2.500000 60.844000 41.756281 54.443750 20008 2 0.000000 -1 2.500000 60.844000 41.756281 54.443750 20009 2 0.000000 1 2.500000 63.140000 43.081877 57.956250 @@ -20027,7 +20027,7 @@ Atoms 20011 2 0.000000 1 2.500000 1.148000 47.058666 57.956250 20012 2 0.000000 -1 2.500000 1.148000 47.058666 57.956250 20013 2 0.000000 1 2.500000 58.548000 45.733070 61.468750 -20014 2 0.000000 -1.000000 2.500000 58.548000 45.733070 61.468750 +20014 2 0.000000 -1 2.500000 58.548000 45.733070 61.468750 20015 2 0.000000 1 2.500000 60.844000 41.756281 61.468750 20016 2 0.000000 -1 2.500000 60.844000 41.756281 61.468750 20017 2 0.000000 1 2.500000 63.140000 51.035454 1.756250 @@ -20035,7 +20035,7 @@ Atoms 20019 2 0.000000 1 2.500000 1.148000 55.012243 1.756250 20020 2 0.000000 -1 2.500000 1.148000 55.012243 1.756250 20021 2 0.000000 1 2.500000 58.548000 53.686647 5.268750 -20022 2 0.000000 -1.000000 2.500000 58.548000 53.686647 5.268750 +20022 2 0.000000 -1 2.500000 58.548000 53.686647 5.268750 20023 2 0.000000 1 2.500000 60.844000 49.709858 5.268750 20024 2 0.000000 -1 2.500000 60.844000 49.709858 5.268750 20025 2 0.000000 1 2.500000 63.140000 51.035454 8.781250 @@ -20043,7 +20043,7 @@ Atoms 20027 2 0.000000 1 2.500000 1.148000 55.012243 8.781250 20028 2 0.000000 -1 2.500000 1.148000 55.012243 8.781250 20029 2 0.000000 1 2.500000 58.548000 53.686647 12.293750 -20030 2 0.000000 -1.000000 2.500000 58.548000 53.686647 12.293750 +20030 2 0.000000 -1 2.500000 58.548000 53.686647 12.293750 20031 2 0.000000 1 2.500000 60.844000 49.709858 12.293750 20032 2 0.000000 -1 2.500000 60.844000 49.709858 12.293750 20033 2 0.000000 1 2.500000 63.140000 51.035454 15.806250 @@ -20051,7 +20051,7 @@ Atoms 20035 2 0.000000 1 2.500000 1.148000 55.012243 15.806250 20036 2 0.000000 -1 2.500000 1.148000 55.012243 15.806250 20037 2 0.000000 1 2.500000 58.548000 53.686647 19.318750 -20038 2 0.000000 -1.000000 2.500000 58.548000 53.686647 19.318750 +20038 2 0.000000 -1 2.500000 58.548000 53.686647 19.318750 20039 2 0.000000 1 2.500000 60.844000 49.709858 19.318750 20040 2 0.000000 -1 2.500000 60.844000 49.709858 19.318750 20041 2 0.000000 1 2.500000 63.140000 51.035454 22.831250 @@ -20059,7 +20059,7 @@ Atoms 20043 2 0.000000 1 2.500000 1.148000 55.012243 22.831250 20044 2 0.000000 -1 2.500000 1.148000 55.012243 22.831250 20045 2 0.000000 1 2.500000 58.548000 53.686647 26.343750 -20046 2 0.000000 -1.000000 2.500000 58.548000 53.686647 26.343750 +20046 2 0.000000 -1 2.500000 58.548000 53.686647 26.343750 20047 2 0.000000 1 2.500000 60.844000 49.709858 26.343750 20048 2 0.000000 -1 2.500000 60.844000 49.709858 26.343750 20049 2 0.000000 1 2.500000 63.140000 51.035454 29.856250 @@ -20067,7 +20067,7 @@ Atoms 20051 2 0.000000 1 2.500000 1.148000 55.012243 29.856250 20052 2 0.000000 -1 2.500000 1.148000 55.012243 29.856250 20053 2 0.000000 1 2.500000 58.548000 53.686647 33.368750 -20054 2 0.000000 -1.000000 2.500000 58.548000 53.686647 33.368750 +20054 2 0.000000 -1 2.500000 58.548000 53.686647 33.368750 20055 2 0.000000 1 2.500000 60.844000 49.709858 33.368750 20056 2 0.000000 -1 2.500000 60.844000 49.709858 33.368750 20057 2 0.000000 1 2.500000 63.140000 51.035454 36.881250 @@ -20075,7 +20075,7 @@ Atoms 20059 2 0.000000 1 2.500000 1.148000 55.012243 36.881250 20060 2 0.000000 -1 2.500000 1.148000 55.012243 36.881250 20061 2 0.000000 1 2.500000 58.548000 53.686647 40.393750 -20062 2 0.000000 -1.000000 2.500000 58.548000 53.686647 40.393750 +20062 2 0.000000 -1 2.500000 58.548000 53.686647 40.393750 20063 2 0.000000 1 2.500000 60.844000 49.709858 40.393750 20064 2 0.000000 -1 2.500000 60.844000 49.709858 40.393750 20065 2 0.000000 1 2.500000 63.140000 51.035454 43.906250 @@ -20083,7 +20083,7 @@ Atoms 20067 2 0.000000 1 2.500000 1.148000 55.012243 43.906250 20068 2 0.000000 -1 2.500000 1.148000 55.012243 43.906250 20069 2 0.000000 1 2.500000 58.548000 53.686647 47.418750 -20070 2 0.000000 -1.000000 2.500000 58.548000 53.686647 47.418750 +20070 2 0.000000 -1 2.500000 58.548000 53.686647 47.418750 20071 2 0.000000 1 2.500000 60.844000 49.709858 47.418750 20072 2 0.000000 -1 2.500000 60.844000 49.709858 47.418750 20073 2 0.000000 1 2.500000 63.140000 51.035454 50.931250 @@ -20091,7 +20091,7 @@ Atoms 20075 2 0.000000 1 2.500000 1.148000 55.012243 50.931250 20076 2 0.000000 -1 2.500000 1.148000 55.012243 50.931250 20077 2 0.000000 1 2.500000 58.548000 53.686647 54.443750 -20078 2 0.000000 -1.000000 2.500000 58.548000 53.686647 54.443750 +20078 2 0.000000 -1 2.500000 58.548000 53.686647 54.443750 20079 2 0.000000 1 2.500000 60.844000 49.709858 54.443750 20080 2 0.000000 -1 2.500000 60.844000 49.709858 54.443750 20081 2 0.000000 1 2.500000 63.140000 51.035454 57.956250 @@ -20099,7 +20099,7 @@ Atoms 20083 2 0.000000 1 2.500000 1.148000 55.012243 57.956250 20084 2 0.000000 -1 2.500000 1.148000 55.012243 57.956250 20085 2 0.000000 1 2.500000 58.548000 53.686647 61.468750 -20086 2 0.000000 -1.000000 2.500000 58.548000 53.686647 61.468750 +20086 2 0.000000 -1 2.500000 58.548000 53.686647 61.468750 20087 2 0.000000 1 2.500000 60.844000 49.709858 61.468750 20088 2 0.000000 -1 2.500000 60.844000 49.709858 61.468750 20089 2 0.000000 1 2.500000 63.140000 58.989032 1.756250 @@ -20107,7 +20107,7 @@ Atoms 20091 2 0.000000 1 2.500000 1.148000 62.965820 1.756250 20092 2 0.000000 -1 2.500000 1.148000 62.965820 1.756250 20093 2 0.000000 1 2.500000 58.548000 61.640224 5.268750 -20094 2 0.000000 -1.000000 2.500000 58.548000 61.640224 5.268750 +20094 2 0.000000 -1 2.500000 58.548000 61.640224 5.268750 20095 2 0.000000 1 2.500000 60.844000 57.663435 5.268750 20096 2 0.000000 -1 2.500000 60.844000 57.663435 5.268750 20097 2 0.000000 1 2.500000 63.140000 58.989032 8.781250 @@ -20115,7 +20115,7 @@ Atoms 20099 2 0.000000 1 2.500000 1.148000 62.965820 8.781250 20100 2 0.000000 -1 2.500000 1.148000 62.965820 8.781250 20101 2 0.000000 1 2.500000 58.548000 61.640224 12.293750 -20102 2 0.000000 -1.000000 2.500000 58.548000 61.640224 12.293750 +20102 2 0.000000 -1 2.500000 58.548000 61.640224 12.293750 20103 2 0.000000 1 2.500000 60.844000 57.663435 12.293750 20104 2 0.000000 -1 2.500000 60.844000 57.663435 12.293750 20105 2 0.000000 1 2.500000 63.140000 58.989032 15.806250 @@ -20123,7 +20123,7 @@ Atoms 20107 2 0.000000 1 2.500000 1.148000 62.965820 15.806250 20108 2 0.000000 -1 2.500000 1.148000 62.965820 15.806250 20109 2 0.000000 1 2.500000 58.548000 61.640224 19.318750 -20110 2 0.000000 -1.000000 2.500000 58.548000 61.640224 19.318750 +20110 2 0.000000 -1 2.500000 58.548000 61.640224 19.318750 20111 2 0.000000 1 2.500000 60.844000 57.663435 19.318750 20112 2 0.000000 -1 2.500000 60.844000 57.663435 19.318750 20113 2 0.000000 1 2.500000 63.140000 58.989032 22.831250 @@ -20131,7 +20131,7 @@ Atoms 20115 2 0.000000 1 2.500000 1.148000 62.965820 22.831250 20116 2 0.000000 -1 2.500000 1.148000 62.965820 22.831250 20117 2 0.000000 1 2.500000 58.548000 61.640224 26.343750 -20118 2 0.000000 -1.000000 2.500000 58.548000 61.640224 26.343750 +20118 2 0.000000 -1 2.500000 58.548000 61.640224 26.343750 20119 2 0.000000 1 2.500000 60.844000 57.663435 26.343750 20120 2 0.000000 -1 2.500000 60.844000 57.663435 26.343750 20121 2 0.000000 1 2.500000 63.140000 58.989032 29.856250 @@ -20139,7 +20139,7 @@ Atoms 20123 2 0.000000 1 2.500000 1.148000 62.965820 29.856250 20124 2 0.000000 -1 2.500000 1.148000 62.965820 29.856250 20125 2 0.000000 1 2.500000 58.548000 61.640224 33.368750 -20126 2 0.000000 -1.000000 2.500000 58.548000 61.640224 33.368750 +20126 2 0.000000 -1 2.500000 58.548000 61.640224 33.368750 20127 2 0.000000 1 2.500000 60.844000 57.663435 33.368750 20128 2 0.000000 -1 2.500000 60.844000 57.663435 33.368750 20129 2 0.000000 1 2.500000 63.140000 58.989032 36.881250 @@ -20147,7 +20147,7 @@ Atoms 20131 2 0.000000 1 2.500000 1.148000 62.965820 36.881250 20132 2 0.000000 -1 2.500000 1.148000 62.965820 36.881250 20133 2 0.000000 1 2.500000 58.548000 61.640224 40.393750 -20134 2 0.000000 -1.000000 2.500000 58.548000 61.640224 40.393750 +20134 2 0.000000 -1 2.500000 58.548000 61.640224 40.393750 20135 2 0.000000 1 2.500000 60.844000 57.663435 40.393750 20136 2 0.000000 -1 2.500000 60.844000 57.663435 40.393750 20137 2 0.000000 1 2.500000 63.140000 58.989032 43.906250 @@ -20155,7 +20155,7 @@ Atoms 20139 2 0.000000 1 2.500000 1.148000 62.965820 43.906250 20140 2 0.000000 -1 2.500000 1.148000 62.965820 43.906250 20141 2 0.000000 1 2.500000 58.548000 61.640224 47.418750 -20142 2 0.000000 -1.000000 2.500000 58.548000 61.640224 47.418750 +20142 2 0.000000 -1 2.500000 58.548000 61.640224 47.418750 20143 2 0.000000 1 2.500000 60.844000 57.663435 47.418750 20144 2 0.000000 -1 2.500000 60.844000 57.663435 47.418750 20145 2 0.000000 1 2.500000 63.140000 58.989032 50.931250 @@ -20163,7 +20163,7 @@ Atoms 20147 2 0.000000 1 2.500000 1.148000 62.965820 50.931250 20148 2 0.000000 -1 2.500000 1.148000 62.965820 50.931250 20149 2 0.000000 1 2.500000 58.548000 61.640224 54.443750 -20150 2 0.000000 -1.000000 2.500000 58.548000 61.640224 54.443750 +20150 2 0.000000 -1 2.500000 58.548000 61.640224 54.443750 20151 2 0.000000 1 2.500000 60.844000 57.663435 54.443750 20152 2 0.000000 -1 2.500000 60.844000 57.663435 54.443750 20153 2 0.000000 1 2.500000 63.140000 58.989032 57.956250 @@ -20171,6 +20171,6 @@ Atoms 20155 2 0.000000 1 2.500000 1.148000 62.965820 57.956250 20156 2 0.000000 -1 2.500000 1.148000 62.965820 57.956250 20157 2 0.000000 1 2.500000 58.548000 61.640224 61.468750 -20158 2 0.000000 -1.000000 2.500000 58.548000 61.640224 61.468750 +20158 2 0.000000 -1 2.500000 58.548000 61.640224 61.468750 20159 2 0.000000 1 2.500000 60.844000 57.663435 61.468750 20160 2 0.000000 -1 2.500000 60.844000 57.663435 61.468750 -- GitLab From 6d94fc1b3d64ae95a15cacc4dadc3fd944638d08 Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Tue, 30 Jul 2019 14:07:30 -0400 Subject: [PATCH 376/469] include cstdlib in lmptype.h since we define ATOX() macros. --- src/lmptype.h | 1 + 1 file changed, 1 insertion(+) diff --git a/src/lmptype.h b/src/lmptype.h index 12fa6cc4fb..ad00df6c63 100644 --- a/src/lmptype.h +++ b/src/lmptype.h @@ -37,6 +37,7 @@ #endif #include +#include #include // requires C++-11 #include // requires C++-11 -- GitLab From 47fc31d00577e6299705ba64defe5ae7e6bbb00e Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Tue, 30 Jul 2019 14:21:53 -0400 Subject: [PATCH 377/469] move inline functions to the only place they are used. no need to use size_t for indices that are small --- src/USER-MEAMC/meam.h | 15 --------------- src/USER-MEAMC/meam_setup_global.cpp | 17 ++++++++++++++++- 2 files changed, 16 insertions(+), 16 deletions(-) diff --git a/src/USER-MEAMC/meam.h b/src/USER-MEAMC/meam.h index da55805790..4e5b298ffb 100644 --- a/src/USER-MEAMC/meam.h +++ b/src/USER-MEAMC/meam.h @@ -234,21 +234,6 @@ static inline bool iszero(const double f) { return fabs(f) < 1e-20; } -template -static inline void setall2d(TYPE (&arr)[maxi][maxj], const TYPE v) { - for (size_t i = 0; i < maxi; i++) - for (size_t j = 0; j < maxj; j++) - arr[i][j] = v; -} - -template -static inline void setall3d(TYPE (&arr)[maxi][maxj][maxk], const TYPE v) { - for (size_t i = 0; i < maxi; i++) - for (size_t j = 0; j < maxj; j++) - for (size_t k = 0; k < maxk; k++) - arr[i][j][k] = v; -} - // Helper functions static inline double fdiv_zero(const double n, const double d) { diff --git a/src/USER-MEAMC/meam_setup_global.cpp b/src/USER-MEAMC/meam_setup_global.cpp index 503ee65496..b66aafa06c 100644 --- a/src/USER-MEAMC/meam_setup_global.cpp +++ b/src/USER-MEAMC/meam_setup_global.cpp @@ -2,6 +2,21 @@ #include using namespace LAMMPS_NS; +template +static inline void setall2d(TYPE (&arr)[maxi][maxj], const TYPE v) { + for (int i = 0; i < maxi; i++) + for (int j = 0; j < maxj; j++) + arr[i][j] = v; +} + +template +static inline void setall3d(TYPE (&arr)[maxi][maxj][maxk], const TYPE v) { + for (int i = 0; i < maxi; i++) + for (int j = 0; j < maxj; j++) + for (int k = 0; k < maxk; k++) + arr[i][j][k] = v; +} + void MEAM::meam_setup_global(int nelt, lattice_t* lat, double* z, int* ielement, double* /*atwt*/, double* alpha, double* b0, double* b1, double* b2, double* b3, double* alat, double* esub, @@ -56,7 +71,7 @@ MEAM::meam_setup_global(int nelt, lattice_t* lat, double* z, int* ielement, doub setall2d(this->repuls_meam, 0.0); setall3d(this->Cmax_meam, 2.8); setall3d(this->Cmin_meam, 2.0); - setall2d(this->ebound_meam, pow(2.8, 2) / (4.0 * (2.8 - 1.0))); + setall2d(this->ebound_meam, (2.8*2.8) / (4.0 * (2.8 - 1.0))); setall2d(this->delta_meam, 0.0); setall2d(this->nn2_meam, 0); setall2d(this->zbl_meam, 1); -- GitLab From d4503a05a47b94e65eaaf47910234abe835bc47a Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Tue, 30 Jul 2019 14:22:33 -0400 Subject: [PATCH 378/469] mention that cstdlib is included in lmptype.h now, too. --- doc/include-file-conventions.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/doc/include-file-conventions.md b/doc/include-file-conventions.md index c9f8bd5cb1..132f2ec4eb 100644 --- a/doc/include-file-conventions.md +++ b/doc/include-file-conventions.md @@ -107,7 +107,7 @@ Include files should be included in this order: #### pointers.h The `pointer.h` header file also includes `cstdio` and `lmptype.h` -(and through it `stdint.h`, `intttypes.h`, and `climits`). +(and through it `stdint.h`, `intttypes.h`, cstdlib, and `climits`). This means any header including `pointers.h` can assume that `FILE`, `NULL`, `INT_MAX` are defined. -- GitLab From f5bf86b32d668d9fcbe1e5e80089f620ddcfab9e Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Tue, 30 Jul 2019 16:27:00 -0400 Subject: [PATCH 379/469] more improvements to CMake build for USER-PLUMED on MacOSX default to shared linkage on MacOSX to avoid linker issues from configure/cmake library detection differences link/depend on GSL and LAPACK explicitly only for static linkage --- cmake/Modules/Packages/USER-PLUMED.cmake | 18 ++++++++++++++---- 1 file changed, 14 insertions(+), 4 deletions(-) diff --git a/cmake/Modules/Packages/USER-PLUMED.cmake b/cmake/Modules/Packages/USER-PLUMED.cmake index a9c5a59338..0b3d13cd70 100644 --- a/cmake/Modules/Packages/USER-PLUMED.cmake +++ b/cmake/Modules/Packages/USER-PLUMED.cmake @@ -1,15 +1,25 @@ if(PKG_USER-PLUMED) - find_package(GSL REQUIRED) - set(PLUMED_MODE "static" CACHE STRING "Linkage mode for Plumed2 library") + if(APPLE) + set(PLUMED_MODE "shared" CACHE STRING "Linkage mode for Plumed2 library") + else() + set(PLUMED_MODE "static" CACHE STRING "Linkage mode for Plumed2 library") + endif() set(PLUMED_MODE_VALUES static shared runtime) set_property(CACHE PLUMED_MODE PROPERTY STRINGS ${PLUMED_MODE_VALUES}) validate_option(PLUMED_MODE PLUMED_MODE_VALUES) string(TOUPPER ${PLUMED_MODE} PLUMED_MODE) - if((PLUMED_MODE STREQUAL "STATIC") AND NOT LAPACK_LIBRARIES) + set(PLUMED_LINK_LIBS "") + if(PLUMED_MODE STREQUAL "STATIC") find_package(LAPACK REQUIRED) find_package(BLAS REQUIRED) + find_package(GSL REQUIRED) list(APPEND LAPACK_LIBRARIES ${BLAS_LIBRARIES}) + list(APPEND PLUMED_LINK_LIBS ${LAPACK_LIBRARIES} ${GSL_LIBRARIES}) + find_package(ZLIB QUIET) + if(ZLIB_FOUND) + list(APPEND PLUMED_LINK_LIBS ${ZLIB_LIBRARIES}) + endif() endif() find_package(PkgConfig QUIET) @@ -59,7 +69,7 @@ if(PKG_USER-PLUMED) list(APPEND LAMMPS_DEPS plumed_build) if(PLUMED_MODE STREQUAL "STATIC") add_definitions(-D__PLUMED_WRAPPER_CXX=1) - list(APPEND LAMMPS_LINK_LIBS ${PLUMED_INSTALL_DIR}/lib/libplumed.a ${GSL_LIBRARIES} ${LAPACK_LIBRARIES} ${CMAKE_DL_LIBS}) + list(APPEND LAMMPS_LINK_LIBS ${PLUMED_INSTALL_DIR}/lib/libplumed.a ${PLUMED_LINK_LIBS} ${CMAKE_DL_LIBS}) elseif(PLUMED_MODE STREQUAL "SHARED") list(APPEND LAMMPS_LINK_LIBS ${PLUMED_INSTALL_DIR}/lib/libplumed${CMAKE_SHARED_LIBRARY_SUFFIX} ${PLUMED_INSTALL_DIR}/lib/libplumedKernel${CMAKE_SHARED_LIBRARY_SUFFIX} ${CMAKE_DL_LIBS}) elseif(PLUMED_MODE STREQUAL "RUNTIME") -- GitLab From 528ec75f8879af135ce256b02bb4882d4c9e4768 Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Tue, 30 Jul 2019 16:38:40 -0400 Subject: [PATCH 380/469] special case for MacOSX not needed --- cmake/Modules/Packages/USER-PLUMED.cmake | 6 +----- 1 file changed, 1 insertion(+), 5 deletions(-) diff --git a/cmake/Modules/Packages/USER-PLUMED.cmake b/cmake/Modules/Packages/USER-PLUMED.cmake index 0b3d13cd70..5c35e13bda 100644 --- a/cmake/Modules/Packages/USER-PLUMED.cmake +++ b/cmake/Modules/Packages/USER-PLUMED.cmake @@ -1,9 +1,5 @@ if(PKG_USER-PLUMED) - if(APPLE) - set(PLUMED_MODE "shared" CACHE STRING "Linkage mode for Plumed2 library") - else() - set(PLUMED_MODE "static" CACHE STRING "Linkage mode for Plumed2 library") - endif() + set(PLUMED_MODE "static" CACHE STRING "Linkage mode for Plumed2 library") set(PLUMED_MODE_VALUES static shared runtime) set_property(CACHE PLUMED_MODE PROPERTY STRINGS ${PLUMED_MODE_VALUES}) validate_option(PLUMED_MODE PLUMED_MODE_VALUES) -- GitLab From 882b2301bb21413eb3d464c74a0e4b5cac5131a3 Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Tue, 30 Jul 2019 16:48:50 -0400 Subject: [PATCH 381/469] handle shared library extension on macosx for plumed runtime build --- lib/plumed/Install.py | 7 +++++-- lib/plumed/Makefile.lammps.runtime.macosx | 5 +++++ 2 files changed, 10 insertions(+), 2 deletions(-) create mode 100644 lib/plumed/Makefile.lammps.runtime.macosx diff --git a/lib/plumed/Install.py b/lib/plumed/Install.py index a59200d1f8..e34fc9236a 100644 --- a/lib/plumed/Install.py +++ b/lib/plumed/Install.py @@ -6,7 +6,7 @@ used to automate the steps described in the README file in this dir """ from __future__ import print_function -import sys, os, subprocess, shutil +import sys, os, platform, subprocess, shutil from argparse import ArgumentParser sys.path.append('..') @@ -130,7 +130,10 @@ if os.path.isfile("Makefile.lammps.%s" % mode): print("Creating Makefile.lammps") plumedinc = os.path.join('liblink', 'plumed', 'src', 'lib', 'Plumed.inc.' + mode) lines1 = open(plumedinc, 'r').readlines() - lines2 = open("Makefile.lammps.%s" % mode, 'r').readlines() + if (platform.system() == 'Darwin' and os.path.isfile("Makefile.lammps.%s.macosx")): + lines2 = open("Makefile.lammps.%s.macosx" % mode, 'r').readlines() + else: + lines2 = open("Makefile.lammps.%s" % mode, 'r').readlines() fp = open("Makefile.lammps", 'w') fp.write("PLUMED_LIBDIR=" + os.path.join(homedir, "lib\n")) for line in lines1: diff --git a/lib/plumed/Makefile.lammps.runtime.macosx b/lib/plumed/Makefile.lammps.runtime.macosx new file mode 100644 index 0000000000..d0ae6e82a5 --- /dev/null +++ b/lib/plumed/Makefile.lammps.runtime.macosx @@ -0,0 +1,5 @@ +# Settings that the LAMMPS build will import when this package library is used + +plumed_SYSINC = -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_DEFAULT_KERNEL=$(PLUMED_LIBDIR)/libplumedKernel.dylib +plumed_SYSLIB = $(PLUMED_LOAD) -rdynamic +plumed_SYSPATH = -- GitLab From 2b288bc9e05e39fd58c6709636451beccc0da20b Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Tue, 30 Jul 2019 16:53:27 -0400 Subject: [PATCH 382/469] add missing mode keyword for substitution --- lib/plumed/Install.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/lib/plumed/Install.py b/lib/plumed/Install.py index e34fc9236a..d56b68b877 100644 --- a/lib/plumed/Install.py +++ b/lib/plumed/Install.py @@ -130,7 +130,7 @@ if os.path.isfile("Makefile.lammps.%s" % mode): print("Creating Makefile.lammps") plumedinc = os.path.join('liblink', 'plumed', 'src', 'lib', 'Plumed.inc.' + mode) lines1 = open(plumedinc, 'r').readlines() - if (platform.system() == 'Darwin' and os.path.isfile("Makefile.lammps.%s.macosx")): + if (platform.system() == 'Darwin' and os.path.isfile("Makefile.lammps.%s.macosx" % mode)): lines2 = open("Makefile.lammps.%s.macosx" % mode, 'r').readlines() else: lines2 = open("Makefile.lammps.%s" % mode, 'r').readlines() -- GitLab From bc79412203448c480362c1583b37b4f1f2b7a3f3 Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Tue, 30 Jul 2019 22:54:02 -0400 Subject: [PATCH 383/469] list(TRANSFORM ...) is not portable to older versions of cmake. work around it. --- cmake/CMakeLists.txt | 61 ++++++++++++++++++++++---------------------- 1 file changed, 30 insertions(+), 31 deletions(-) diff --git a/cmake/CMakeLists.txt b/cmake/CMakeLists.txt index 2fc7fc8307..187b41e980 100644 --- a/cmake/CMakeLists.txt +++ b/cmake/CMakeLists.txt @@ -497,37 +497,36 @@ if(BUILD_LIB) add_dependencies(lammps ${LAMMPS_DEPS}) endif() set(LAMMPS_CXX_HEADERS - angle.h - atom.h - bond.h - citeme.h - comm.h - compute.h - dihedral.h - domain.h - error.h - fix.h - force.h - group.h - improper.h - input.h - kspace.h - lammps.h - lattice.h - lmppython.h - memory.h - modify.h - neighbor.h - neigh_list.h - output.h - pair.h - pointers.h - region.h - timer.h - universe.h - update.h - variable.h) - list(TRANSFORM LAMMPS_CXX_HEADERS PREPEND ${LAMMPS_SOURCE_DIR}/) + ${LAMMPS_SOURCE_DIR}/angle.h + ${LAMMPS_SOURCE_DIR}/atom.h + ${LAMMPS_SOURCE_DIR}/bond.h + ${LAMMPS_SOURCE_DIR}/citeme.h + ${LAMMPS_SOURCE_DIR}/comm.h + ${LAMMPS_SOURCE_DIR}/compute.h + ${LAMMPS_SOURCE_DIR}/dihedral.h + ${LAMMPS_SOURCE_DIR}/domain.h + ${LAMMPS_SOURCE_DIR}/error.h + ${LAMMPS_SOURCE_DIR}/fix.h + ${LAMMPS_SOURCE_DIR}/force.h + ${LAMMPS_SOURCE_DIR}/group.h + ${LAMMPS_SOURCE_DIR}/improper.h + ${LAMMPS_SOURCE_DIR}/input.h + ${LAMMPS_SOURCE_DIR}/kspace.h + ${LAMMPS_SOURCE_DIR}/lammps.h + ${LAMMPS_SOURCE_DIR}/lattice.h + ${LAMMPS_SOURCE_DIR}/lmppython.h + ${LAMMPS_SOURCE_DIR}/memory.h + ${LAMMPS_SOURCE_DIR}/modify.h + ${LAMMPS_SOURCE_DIR}/neighbor.h + ${LAMMPS_SOURCE_DIR}/neigh_list.h + ${LAMMPS_SOURCE_DIR}/output.h + ${LAMMPS_SOURCE_DIR}/pair.h + ${LAMMPS_SOURCE_DIR}/pointers.h + ${LAMMPS_SOURCE_DIR}/region.h + ${LAMMPS_SOURCE_DIR}/timer.h + ${LAMMPS_SOURCE_DIR}/universe.h + ${LAMMPS_SOURCE_DIR}/update.h + ${LAMMPS_SOURCE_DIR}/variable.h) set_target_properties(lammps PROPERTIES OUTPUT_NAME lammps${LAMMPS_LIB_SUFFIX}) set_target_properties(lammps PROPERTIES SOVERSION ${SOVERSION}) -- GitLab From da3b91a744731789f723a314fb41e68bf7cc92b1 Mon Sep 17 00:00:00 2001 From: Richard Berger Date: Wed, 31 Jul 2019 03:11:44 -0400 Subject: [PATCH 384/469] Remove not existing files from USER-PHONON Install.sh --- src/USER-PHONON/Install.sh | 2 -- 1 file changed, 2 deletions(-) diff --git a/src/USER-PHONON/Install.sh b/src/USER-PHONON/Install.sh index a73f529cfa..26104b45cf 100755 --- a/src/USER-PHONON/Install.sh +++ b/src/USER-PHONON/Install.sh @@ -42,5 +42,3 @@ action fix_phonon.cpp fft3d_wrap.h action fix_phonon.h fft3d_wrap.h action dynamical_matrix.cpp action dynamical_matrix.h -action third_order.cpp -action third_order.h -- GitLab From 3cc8508795fefedd4532d27dfeecc1957f6144bf Mon Sep 17 00:00:00 2001 From: Richard Berger Date: Wed, 31 Jul 2019 03:22:22 -0400 Subject: [PATCH 385/469] Add missing definition of NULL in USER-PTM header --- src/USER-PTM/ptm_initialize_data.h | 1 + 1 file changed, 1 insertion(+) diff --git a/src/USER-PTM/ptm_initialize_data.h b/src/USER-PTM/ptm_initialize_data.h index 4e7f3e8f0a..87111b1282 100644 --- a/src/USER-PTM/ptm_initialize_data.h +++ b/src/USER-PTM/ptm_initialize_data.h @@ -15,6 +15,7 @@ THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLI #include "ptm_deformation_gradient.h" #include "ptm_fundamental_mappings.h" #include "ptm_alt_templates.h" +#include namespace ptm { -- GitLab From 0fa9cd5004d35a50dd9943a1fec649dcb72f9c78 Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Wed, 31 Jul 2019 05:03:59 -0400 Subject: [PATCH 386/469] use utils::strmatch to simplify checks for compatible thermostat/barostat fixes --- src/REPLICA/temper.cpp | 34 ++++++---------------------------- src/USER-MISC/temper_npt.cpp | 5 +++-- 2 files changed, 9 insertions(+), 30 deletions(-) diff --git a/src/REPLICA/temper.cpp b/src/REPLICA/temper.cpp index 46fc3af649..2352a7de48 100644 --- a/src/REPLICA/temper.cpp +++ b/src/REPLICA/temper.cpp @@ -31,6 +31,7 @@ #include "finish.h" #include "timer.h" #include "error.h" +#include "utils.h" using namespace LAMMPS_NS; @@ -94,34 +95,11 @@ void Temper::command(int narg, char **arg) // fix style must be appropriate for temperature control, i.e. it needs // to provide a working Fix::reset_target() and must not change the volume. - if ((strcmp(modify->fix[whichfix]->style,"nvt") != 0) && - (strcmp(modify->fix[whichfix]->style,"nvt/asphere") != 0) && - (strcmp(modify->fix[whichfix]->style,"nvt/asphere/omp") != 0) && - (strcmp(modify->fix[whichfix]->style,"nvt/body") != 0) && - (strcmp(modify->fix[whichfix]->style,"nvt/eff") != 0) && - (strcmp(modify->fix[whichfix]->style,"nvt/intel") != 0) && - (strcmp(modify->fix[whichfix]->style,"nvt/kk") != 0) && - (strcmp(modify->fix[whichfix]->style,"nvt/kk/host") != 0) && - (strcmp(modify->fix[whichfix]->style,"nvt/kk/device") != 0) && - (strcmp(modify->fix[whichfix]->style,"nvt/omp") != 0) && - (strcmp(modify->fix[whichfix]->style,"nvt/sphere") != 0) && - (strcmp(modify->fix[whichfix]->style,"nvt/sphere/omp") != 0) && - (strcmp(modify->fix[whichfix]->style,"langevin") != 0) && - (strcmp(modify->fix[whichfix]->style,"langevin/drude") != 0) && - (strcmp(modify->fix[whichfix]->style,"langevin/eff") != 0) && - (strcmp(modify->fix[whichfix]->style,"gld") != 0) && - (strcmp(modify->fix[whichfix]->style,"gle") != 0) && - (strcmp(modify->fix[whichfix]->style,"rigid/nvt") != 0) && - (strcmp(modify->fix[whichfix]->style,"rigid/nvt/small") != 0) && - (strcmp(modify->fix[whichfix]->style,"rigid/nvt/omp") != 0) && - (strcmp(modify->fix[whichfix]->style,"rigid/nvt/small/omp") != 0) && - (strcmp(modify->fix[whichfix]->style,"temp/berendsen") != 0) && - (strcmp(modify->fix[whichfix]->style,"temp/berendsen/cuda") != 0) && - (strcmp(modify->fix[whichfix]->style,"temp/csvr") != 0) && - (strcmp(modify->fix[whichfix]->style,"temp/csld") != 0) && - (strcmp(modify->fix[whichfix]->style,"temp/rescale") != 0) && - (strcmp(modify->fix[whichfix]->style,"temp/rescale/cuda") != 0) && - (strcmp(modify->fix[whichfix]->style,"temp/rescale/eff") != 0)) + if ((!utils::strmatch(modify->fix[whichfix]->style,"^nvt")) && + (!utils::strmatch(modify->fix[whichfix]->style,"^langevin")) && + (!utils::strmatch(modify->fix[whichfix]->style,"^gl[de]$")) && + (!utils::strmatch(modify->fix[whichfix]->style,"^rigid/nvt")) && + (!utils::strcmp(modify->fix[whichfix]->style,"^temp/")) error->universe_all(FLERR,"Tempering temperature fix is not supported"); // setup for long tempering run diff --git a/src/USER-MISC/temper_npt.cpp b/src/USER-MISC/temper_npt.cpp index 9fd4bd6d06..1fff222835 100644 --- a/src/USER-MISC/temper_npt.cpp +++ b/src/USER-MISC/temper_npt.cpp @@ -33,6 +33,7 @@ #include "finish.h" #include "timer.h" #include "error.h" +#include "utils.h" using namespace LAMMPS_NS; @@ -97,8 +98,8 @@ void TemperNPT::command(int narg, char **arg) // change the volume. This currently only applies to fix npt and // fix rigid/npt variants - if ((strncmp(modify->fix[whichfix]->style,"npt",3) != 0) - && (strncmp(modify->fix[whichfix]->style,"rigid/npt",9) != 0)) + if ( (!utils::strmatch(modify->fix[whichfix]->style,"^npt")) && + (!utils::strmatch(modify->fix[whichfix]->style,"^rigid/npt")) ) error->universe_all(FLERR,"Tempering temperature and pressure fix is not supported"); // setup for long tempering run -- GitLab From 4011f6650de39065bcd616d19bc8cdf69e065e18 Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Wed, 31 Jul 2019 05:05:17 -0400 Subject: [PATCH 387/469] first step of adding timeout support to temper commands --- src/REPLICA/temper.cpp | 4 ++++ src/USER-MISC/temper_grem.cpp | 3 +++ src/USER-MISC/temper_npt.cpp | 4 ++++ 3 files changed, 11 insertions(+) diff --git a/src/REPLICA/temper.cpp b/src/REPLICA/temper.cpp index 2352a7de48..24c79c45bf 100644 --- a/src/REPLICA/temper.cpp +++ b/src/REPLICA/temper.cpp @@ -71,6 +71,10 @@ void Temper::command(int narg, char **arg) nevery = force->inumeric(FLERR,arg[1]); double temp = force->numeric(FLERR,arg[2]); + // ignore temper command, if walltime limit was already reached + + if (timer->is_timeout()) return; + for (whichfix = 0; whichfix < modify->nfix; whichfix++) if (strcmp(arg[3],modify->fix[whichfix]->id) == 0) break; if (whichfix == modify->nfix) diff --git a/src/USER-MISC/temper_grem.cpp b/src/USER-MISC/temper_grem.cpp index d0e2fa5606..abc18b2ddf 100644 --- a/src/USER-MISC/temper_grem.cpp +++ b/src/USER-MISC/temper_grem.cpp @@ -71,6 +71,9 @@ void TemperGrem::command(int narg, char **arg) nevery = force->inumeric(FLERR,arg[1]); double lambda = force->numeric(FLERR,arg[2]); + // ignore temper command, if walltime limit was already reached + if (timer->is_timeout()) return; + // Get and check if gREM fix exists for (whichfix = 0; whichfix < modify->nfix; whichfix++) if (strcmp(arg[3],modify->fix[whichfix]->id) == 0) break; diff --git a/src/USER-MISC/temper_npt.cpp b/src/USER-MISC/temper_npt.cpp index 1fff222835..ea8cc08369 100644 --- a/src/USER-MISC/temper_npt.cpp +++ b/src/USER-MISC/temper_npt.cpp @@ -74,6 +74,10 @@ void TemperNPT::command(int narg, char **arg) double temp = force->numeric(FLERR,arg[2]); double press_set = force->numeric(FLERR,arg[6]); + // ignore temper command, if walltime limit was already reached + + if (timer->is_timeout()) return; + for (whichfix = 0; whichfix < modify->nfix; whichfix++) if (strcmp(arg[3],modify->fix[whichfix]->id) == 0) break; if (whichfix == modify->nfix) -- GitLab From 58404946db5680811dbd6122d6e4fae84f1cf13b Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Wed, 31 Jul 2019 23:26:13 -0400 Subject: [PATCH 388/469] add timer timeout support to temper commands --- src/REPLICA/temper.cpp | 7 ++++++- src/USER-MISC/temper_grem.cpp | 5 +++++ src/USER-MISC/temper_npt.cpp | 5 +++++ 3 files changed, 16 insertions(+), 1 deletion(-) diff --git a/src/REPLICA/temper.cpp b/src/REPLICA/temper.cpp index 24c79c45bf..daa17c4cf4 100644 --- a/src/REPLICA/temper.cpp +++ b/src/REPLICA/temper.cpp @@ -103,12 +103,14 @@ void Temper::command(int narg, char **arg) (!utils::strmatch(modify->fix[whichfix]->style,"^langevin")) && (!utils::strmatch(modify->fix[whichfix]->style,"^gl[de]$")) && (!utils::strmatch(modify->fix[whichfix]->style,"^rigid/nvt")) && - (!utils::strcmp(modify->fix[whichfix]->style,"^temp/")) + (!utils::strcmp(modify->fix[whichfix]->style,"^temp/"))) error->universe_all(FLERR,"Tempering temperature fix is not supported"); // setup for long tempering run update->whichflag = 1; + timer->init_timeout(); + update->nsteps = nsteps; update->beginstep = update->firststep = update->ntimestep; update->endstep = update->laststep = update->firststep + nsteps; @@ -213,6 +215,9 @@ void Temper::command(int narg, char **arg) for (int iswap = 0; iswap < nswaps; iswap++) { + if (timer->is_timeout()) break; + timer->init_timeout(); + // run for nevery timesteps update->integrate->run(nevery); diff --git a/src/USER-MISC/temper_grem.cpp b/src/USER-MISC/temper_grem.cpp index abc18b2ddf..e05a27bb14 100644 --- a/src/USER-MISC/temper_grem.cpp +++ b/src/USER-MISC/temper_grem.cpp @@ -130,6 +130,8 @@ void TemperGrem::command(int narg, char **arg) // setup for long tempering run update->whichflag = 1; + timer->init_timeout(); + update->nsteps = nsteps; update->beginstep = update->firststep = update->ntimestep; update->endstep = update->laststep = update->firststep + nsteps; @@ -235,6 +237,9 @@ void TemperGrem::command(int narg, char **arg) for (int iswap = 0; iswap < nswaps; iswap++) { + if (timer->is_timeout()) break; + timer->init_timeout(); + // run for nevery timesteps update->integrate->run(nevery); diff --git a/src/USER-MISC/temper_npt.cpp b/src/USER-MISC/temper_npt.cpp index ea8cc08369..d40ca3b707 100644 --- a/src/USER-MISC/temper_npt.cpp +++ b/src/USER-MISC/temper_npt.cpp @@ -109,6 +109,8 @@ void TemperNPT::command(int narg, char **arg) // setup for long tempering run update->whichflag = 1; + timer->init_timeout(); + update->nsteps = nsteps; update->beginstep = update->firststep = update->ntimestep; update->endstep = update->laststep = update->firststep + nsteps; @@ -214,6 +216,9 @@ void TemperNPT::command(int narg, char **arg) for (int iswap = 0; iswap < nswaps; iswap++) { + if (timer->is_timeout()) break; + timer->init_timeout(); + // run for nevery timesteps update->integrate->run(nevery); -- GitLab From 75c1e2856600482807da4930775cff527cb53eb8 Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Wed, 31 Jul 2019 23:28:57 -0400 Subject: [PATCH 389/469] fix typo --- src/REPLICA/temper.cpp | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/REPLICA/temper.cpp b/src/REPLICA/temper.cpp index daa17c4cf4..cd14de9475 100644 --- a/src/REPLICA/temper.cpp +++ b/src/REPLICA/temper.cpp @@ -103,7 +103,7 @@ void Temper::command(int narg, char **arg) (!utils::strmatch(modify->fix[whichfix]->style,"^langevin")) && (!utils::strmatch(modify->fix[whichfix]->style,"^gl[de]$")) && (!utils::strmatch(modify->fix[whichfix]->style,"^rigid/nvt")) && - (!utils::strcmp(modify->fix[whichfix]->style,"^temp/"))) + (!utils::strmatch(modify->fix[whichfix]->style,"^temp/"))) error->universe_all(FLERR,"Tempering temperature fix is not supported"); // setup for long tempering run -- GitLab From 074ae06b36918819fc9d040afbf046a036e53164 Mon Sep 17 00:00:00 2001 From: Michael Brown Date: Thu, 1 Aug 2019 02:19:49 -0700 Subject: [PATCH 390/469] Bug fix for eam/intel per-atom energy calculation. --- src/USER-INTEL/pair_eam_intel.cpp | 1 - 1 file changed, 1 deletion(-) diff --git a/src/USER-INTEL/pair_eam_intel.cpp b/src/USER-INTEL/pair_eam_intel.cpp index 9d2629ef1c..32d7e74cbc 100644 --- a/src/USER-INTEL/pair_eam_intel.cpp +++ b/src/USER-INTEL/pair_eam_intel.cpp @@ -451,7 +451,6 @@ void PairEAMIntel::eval(const int offload, const int vflag, if (tid == 0) comm->forward_comm_pair(this); - if (NEWTON_PAIR) memset(f + minlocal, 0, f_stride * sizeof(FORCE_T)); #if defined(_OPENMP) #pragma omp barrier -- GitLab From 207976f4e9ddcb6a12bdfed741acdc808dd1d3eb Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Thu, 1 Aug 2019 06:11:05 -0400 Subject: [PATCH 391/469] avoid abort when timeout appears in temper commands --- src/REPLICA/temper.cpp | 5 ++--- src/USER-MISC/temper_grem.cpp | 6 ++---- src/USER-MISC/temper_npt.cpp | 5 ++--- 3 files changed, 6 insertions(+), 10 deletions(-) diff --git a/src/REPLICA/temper.cpp b/src/REPLICA/temper.cpp index cd14de9475..00ca062ecc 100644 --- a/src/REPLICA/temper.cpp +++ b/src/REPLICA/temper.cpp @@ -215,12 +215,11 @@ void Temper::command(int narg, char **arg) for (int iswap = 0; iswap < nswaps; iswap++) { - if (timer->is_timeout()) break; - timer->init_timeout(); - // run for nevery timesteps + timer->init_timeout(); update->integrate->run(nevery); + if (timer->is_timeout()) break; // compute PE // notify compute it will be called at next swap diff --git a/src/USER-MISC/temper_grem.cpp b/src/USER-MISC/temper_grem.cpp index e05a27bb14..692f78cf9f 100644 --- a/src/USER-MISC/temper_grem.cpp +++ b/src/USER-MISC/temper_grem.cpp @@ -237,12 +237,11 @@ void TemperGrem::command(int narg, char **arg) for (int iswap = 0; iswap < nswaps; iswap++) { - if (timer->is_timeout()) break; - timer->init_timeout(); - // run for nevery timesteps + timer->init_timeout(); update->integrate->run(nevery); + if (timer->is_timeout()) break; // compute PE // notify compute it will be called at next swap @@ -250,7 +249,6 @@ void TemperGrem::command(int narg, char **arg) pe = pe_compute->compute_scalar(); pe_compute->addstep(update->ntimestep + nevery); - // which = which of 2 kinds of swaps to do (0,1) if (!ranswap) which = iswap % 2; diff --git a/src/USER-MISC/temper_npt.cpp b/src/USER-MISC/temper_npt.cpp index d40ca3b707..55c9aadc6f 100644 --- a/src/USER-MISC/temper_npt.cpp +++ b/src/USER-MISC/temper_npt.cpp @@ -216,12 +216,11 @@ void TemperNPT::command(int narg, char **arg) for (int iswap = 0; iswap < nswaps; iswap++) { - if (timer->is_timeout()) break; - timer->init_timeout(); - // run for nevery timesteps + timer->init_timeout(); update->integrate->run(nevery); + if (timer->is_timeout()) break; // compute PE // notify compute it will be called at next swap -- GitLab From 892e4759df463d0439a44d4997fd277331cfb7d7 Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Thu, 1 Aug 2019 07:02:55 -0400 Subject: [PATCH 392/469] protect Spectrum MPI detection from failing to compile with MPI libraries implementing MPI version 2 or 1 --- src/KOKKOS/kokkos.cpp | 2 ++ 1 file changed, 2 insertions(+) diff --git a/src/KOKKOS/kokkos.cpp b/src/KOKKOS/kokkos.cpp index a353c3dd18..dd0aca2a9f 100644 --- a/src/KOKKOS/kokkos.cpp +++ b/src/KOKKOS/kokkos.cpp @@ -208,6 +208,7 @@ KokkosLMP::KokkosLMP(LAMMPS *lmp, int narg, char **arg) : Pointers(lmp) MPI_Comm_size(world,&nmpi); if (nmpi > 0) { +#if defined(MPI_VERSION) && (MPI_VERSION > 2) // Check for IBM Spectrum MPI int len; @@ -226,6 +227,7 @@ KokkosLMP::KokkosLMP(LAMMPS *lmp, int narg, char **arg) : Pointers(lmp) if (me == 0) error->warning(FLERR,"The Spectrum MPI '-gpu' flag is not set. Disabling CUDA-aware MPI"); } +#endif if (cuda_aware_flag == 1 && have_cuda_aware == 0) { if (me == 0) -- GitLab From 86e3740fb337bafb1a8c5ea77909361ef2da2235 Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Thu, 1 Aug 2019 07:03:51 -0400 Subject: [PATCH 393/469] use more common syntax for CPP's "defined" keyword --- src/KOKKOS/kokkos.cpp | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/src/KOKKOS/kokkos.cpp b/src/KOKKOS/kokkos.cpp index dd0aca2a9f..6fd8f46e43 100644 --- a/src/KOKKOS/kokkos.cpp +++ b/src/KOKKOS/kokkos.cpp @@ -236,7 +236,7 @@ KokkosLMP::KokkosLMP(LAMMPS *lmp, int narg, char **arg) : Pointers(lmp) cuda_aware_flag = 0; } else if (have_cuda_aware == -1) { // maybe we are dealing with MPICH, MVAPICH2 or some derivative? // MVAPICH2 -#if (defined MPICH) && (defined MVAPICH2_VERSION) +#if defined(MPICH) && defined(MVAPICH2_VERSION) char* str; cuda_aware_flag = 0; if (str = getenv("MV2_ENABLE_CUDA") @@ -247,7 +247,7 @@ KokkosLMP::KokkosLMP(LAMMPS *lmp, int narg, char **arg) : Pointers(lmp) if (me == 0) error->warning(FLERR,"MVAPICH2 'MV2_ENABLE_CUDA' environment variable is not set. Disabling CUDA-aware MPI"); // pure MPICH or some unsupported MPICH derivative -#elif (defined MPICH) && !(defined MVAPICH2_VERSION) +#elif defined(MPICH) && !defined(MVAPICH2_VERSION) if (me == 0) error->warning(FLERR,"Detected MPICH. Disabling CUDA-aware MPI"); cuda_aware_flag = 0; -- GitLab From 2a74832a1e662f8090562598b350b5b4fae80f0a Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Thu, 1 Aug 2019 07:04:24 -0400 Subject: [PATCH 394/469] protect MPI library version detection from incompatible MPI libraries --- src/info.cpp | 7 ++++++- 1 file changed, 6 insertions(+), 1 deletion(-) diff --git a/src/info.cpp b/src/info.cpp index 0d54c6d001..21297c52c6 100644 --- a/src/info.cpp +++ b/src/info.cpp @@ -354,10 +354,15 @@ void Info::command(int narg, char **arg) if (flags & COMM) { int major,minor,len; +#if (defined(MPI_VERSION) && (MPI_VERSION > 2)) || defined(MPI_STUBS) char version[MPI_MAX_LIBRARY_VERSION_STRING]; + MPI_Get_library_version(version,&len); +#else + char version[] = "Undetected MPI implementation"; + len = strlen(version); +#endif MPI_Get_version(&major,&minor); - MPI_Get_library_version(version,&len); if (len > 80) { char *ptr = strchr(version+80,'\n'); if (ptr) *ptr = '\0'; -- GitLab From e3c91626c841226e97f7f8784346a3bca315ec34 Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Thu, 1 Aug 2019 07:07:21 -0400 Subject: [PATCH 395/469] need to include update.h when exceptions are enabled --- src/error.cpp | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/src/error.cpp b/src/error.cpp index 656c957ee2..e5e9179fda 100644 --- a/src/error.cpp +++ b/src/error.cpp @@ -19,6 +19,10 @@ #include "output.h" #include "input.h" +#if defined(LAMMPS_EXCEPTIONS) +#include "update.h" +#endif + using namespace LAMMPS_NS; // helper function to truncate a string to a segment starting with "src/"; -- GitLab From a6bd86eb77da12f691165e7c8c4a9b4af81696e4 Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Thu, 1 Aug 2019 08:14:03 -0400 Subject: [PATCH 396/469] make USER-OMP code compatible with pre-c++ 11 compilers again --- src/USER-OMP/thr_data.h | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/src/USER-OMP/thr_data.h b/src/USER-OMP/thr_data.h index edff17cad3..68673e7503 100644 --- a/src/USER-OMP/thr_data.h +++ b/src/USER-OMP/thr_data.h @@ -31,7 +31,7 @@ class ThrData { public: ThrData(int tid, class Timer *t); - ~ThrData() { delete _timer; _timer = nullptr; }; + ~ThrData() { delete _timer; _timer = NULL; }; void check_tid(int); // thread id consistency check int get_tid() const { return _tid; }; // our thread id. @@ -136,7 +136,7 @@ class ThrData { // disabled default methods private: - ThrData() : _tid(-1), _timer(nullptr) {}; + ThrData() : _tid(-1), _timer(NULL) {}; }; //////////////////////////////////////////////////////////////////////// -- GitLab From c967c0956170b0b9e7fd8f1124f0a71b09d7f5fc Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Thu, 1 Aug 2019 08:14:27 -0400 Subject: [PATCH 397/469] correct compilation error with exceptions enabled in main.cpp --- src/main.cpp | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/src/main.cpp b/src/main.cpp index b7f6adbdda..85e25aa2e4 100644 --- a/src/main.cpp +++ b/src/main.cpp @@ -23,6 +23,10 @@ #include #endif +#if defined(LAMMPS_EXCEPTIONS) +#include "exceptions.h" +#endif + using namespace LAMMPS_NS; /* ---------------------------------------------------------------------- -- GitLab From e57c3c04d0261d61fdd12267b81d55d76289ba9d Mon Sep 17 00:00:00 2001 From: Michael Brown Date: Thu, 1 Aug 2019 05:32:18 -0700 Subject: [PATCH 398/469] Bug fixes for use of uninitialized variable and strict-aliasing in USER-INTEL. --- src/USER-INTEL/fix_intel.cpp | 6 +++--- src/USER-INTEL/intel_intrinsics_airebo.h | 4 +++- 2 files changed, 6 insertions(+), 4 deletions(-) diff --git a/src/USER-INTEL/fix_intel.cpp b/src/USER-INTEL/fix_intel.cpp index bdc47827ab..83a22f0562 100644 --- a/src/USER-INTEL/fix_intel.cpp +++ b/src/USER-INTEL/fix_intel.cpp @@ -352,15 +352,15 @@ void FixIntel::init() if (_offload_balance != 0.0) off_mode = 1; if (_precision_mode == PREC_MODE_SINGLE) { _single_buffers->zero_ev(); - _single_buffers->grow_ncache(off_mode,_nthreads); + _single_buffers->grow_ncache(off_mode, comm->nthreads); _single_buffers->free_list_ptrs(); } else if (_precision_mode == PREC_MODE_MIXED) { _mixed_buffers->zero_ev(); - _mixed_buffers->grow_ncache(off_mode,_nthreads); + _mixed_buffers->grow_ncache(off_mode, comm->nthreads); _mixed_buffers->free_list_ptrs(); } else { _double_buffers->zero_ev(); - _double_buffers->grow_ncache(off_mode,_nthreads); + _double_buffers->grow_ncache(off_mode, comm->nthreads); _double_buffers->free_list_ptrs(); } diff --git a/src/USER-INTEL/intel_intrinsics_airebo.h b/src/USER-INTEL/intel_intrinsics_airebo.h index 2b55b41ad1..cadf80bbe8 100644 --- a/src/USER-INTEL/intel_intrinsics_airebo.h +++ b/src/USER-INTEL/intel_intrinsics_airebo.h @@ -2223,7 +2223,9 @@ public: } VEC_INLINE static ivec unpackloepi32(const fvec &a) { - return reinterpret_cast(&a.val_)[0]; + union { int i; flt_t f; } atype; + atype.f = a.val_; + return ivec(atype.i); } VEC_INLINE static fvec mask_sincos( -- GitLab From 8f5cd8661f1fa5007faa72a3d3dae036b80b5524 Mon Sep 17 00:00:00 2001 From: oywg11 Date: Thu, 1 Aug 2019 16:38:19 +0300 Subject: [PATCH 399/469] Fix communication bug of ILP --- doc/src/Eqs/pair_kolmogorov_crespi_full.jpg | Bin 181806 -> 50604 bytes doc/src/Eqs/pair_kolmogorov_crespi_full.tex | 2 +- doc/src/pair_coul_shield.txt | 2 +- doc/src/pair_ilp_graphene_hbn.txt | 28 +- doc/src/pair_kolmogorov_crespi_full.txt | 24 +- .../bilayer-graphene/BNCH.ILP | 1 + .../Bi_gr_AB_stack_2L_noH.data | 1372 ++++++++++++++ .../ilp_graphene_hbn/bilayer-graphene/CH.rebo | 1 + .../bilayer-graphene/in.bilayer-graphene | 49 +- .../log.5Jun19.bilayer-graphene.icc.1 | 128 ++ .../log.5Jun19.bilayer-graphene.icc.4 | 128 ++ .../ilp_graphene_hbn/bilayer-hBN/BNC.tersoff | 1 + .../ilp_graphene_hbn/bilayer-hBN/BNCH.ILP | 1 + .../hBN_AA_prime_stack_2L_noH.data | 1372 ++++++++++++++ .../bilayer-hBN/in.bilayer-hBN | 57 + .../bilayer-hBN/log.5Jun19.bilayer_hBN.icc.1 | 144 ++ .../bilayer-hBN/log.5Jun19.bilayer_hBN.icc.4 | 144 ++ .../misc/ilp_graphene_hbn/gr-hBN/BNCH.ILP | 1 + .../USER/misc/ilp_graphene_hbn/gr-hBN/CH.rebo | 1 + .../misc/ilp_graphene_hbn/gr-hBN/in.grhBN | 64 +- .../gr-hBN/log.5Jun19.grhBN.icc.1 | 155 ++ .../gr-hBN/log.5Jun19.grhBN.icc.4 | 155 ++ src/USER-MISC/pair_ilp_graphene_hbn.cpp | 1675 ++++++++-------- src/USER-MISC/pair_ilp_graphene_hbn.h | 8 +- src/USER-MISC/pair_kolmogorov_crespi_full.cpp | 1685 +++++++++-------- src/USER-MISC/pair_kolmogorov_crespi_full.h | 8 +- 26 files changed, 5442 insertions(+), 1764 deletions(-) create mode 120000 examples/USER/misc/ilp_graphene_hbn/bilayer-graphene/BNCH.ILP create mode 100644 examples/USER/misc/ilp_graphene_hbn/bilayer-graphene/Bi_gr_AB_stack_2L_noH.data create mode 120000 examples/USER/misc/ilp_graphene_hbn/bilayer-graphene/CH.rebo create mode 100644 examples/USER/misc/ilp_graphene_hbn/bilayer-graphene/log.5Jun19.bilayer-graphene.icc.1 create mode 100644 examples/USER/misc/ilp_graphene_hbn/bilayer-graphene/log.5Jun19.bilayer-graphene.icc.4 create mode 120000 examples/USER/misc/ilp_graphene_hbn/bilayer-hBN/BNC.tersoff create mode 120000 examples/USER/misc/ilp_graphene_hbn/bilayer-hBN/BNCH.ILP create mode 100644 examples/USER/misc/ilp_graphene_hbn/bilayer-hBN/hBN_AA_prime_stack_2L_noH.data create mode 100644 examples/USER/misc/ilp_graphene_hbn/bilayer-hBN/in.bilayer-hBN create mode 100644 examples/USER/misc/ilp_graphene_hbn/bilayer-hBN/log.5Jun19.bilayer_hBN.icc.1 create mode 100644 examples/USER/misc/ilp_graphene_hbn/bilayer-hBN/log.5Jun19.bilayer_hBN.icc.4 create mode 120000 examples/USER/misc/ilp_graphene_hbn/gr-hBN/BNCH.ILP create mode 120000 examples/USER/misc/ilp_graphene_hbn/gr-hBN/CH.rebo create mode 100644 examples/USER/misc/ilp_graphene_hbn/gr-hBN/log.5Jun19.grhBN.icc.1 create mode 100644 examples/USER/misc/ilp_graphene_hbn/gr-hBN/log.5Jun19.grhBN.icc.4 diff --git a/doc/src/Eqs/pair_kolmogorov_crespi_full.jpg 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zYQMjd#O99=*Lc+U%vf{N_*!A6VWiyp(SE=|xfj!quJ03)-nIGQ&WDS` z+<5P{E`9F9{-a}Fi|x)W(wi?$TforrhJnT3%geImNcE4IVYyF~RV8=zO-%TxE1vPQ z`HFeY+u2J*j-6a{_jGB9Ys&WPRvPnuXKpj@dCsC$@%!Yx<{vYh*MD3mdPa3``orJ$ zPFuh36F;Y6_Ak}@i~oGpb?;3lZ!J=LQyqGG>ZiEYGvzaG9@*-2;`Qnfoe$EMrQ-VB z_N#k*Rm~Y5{h4&#(ly)GQlD?tDsEXz+gDe%TJ?CpmAbH2@|GOGGGiO%KNocvZLnCy0b`HdUc+!mC+9UlfJ=wdUQ{ox#F}v@FRc9Prk4FXYJm< ze&xqG*{AoJZ+d_A$MWehk*lwtn|}HCr;`eE+&$k1i##{3xwnz=T#$2Y<`*g5{R`6K ze9JEdUpw~koOwf3mV?gX59ju*7K{>mYqf`c_qOaC4pCbzPMz$#@X)WMTEg|!$?0+; zK^v1!&oxl|T$qs0Vxd^FDKI-oL|;6@YNNKbIW|8D{S+$kF% diff --git a/doc/src/Eqs/pair_kolmogorov_crespi_full.tex b/doc/src/Eqs/pair_kolmogorov_crespi_full.tex index 606aa8b5fe..16bbc25abf 100644 --- a/doc/src/Eqs/pair_kolmogorov_crespi_full.tex +++ b/doc/src/Eqs/pair_kolmogorov_crespi_full.tex @@ -27,7 +27,7 @@ V_{ij} & = & e^{-\lambda (r_{ij} -z_0)} \left [ C + f(\rho_{ij}) + f(\rho_{ji}) - A \left ( \frac{r_{ij}}{z_0}\right )^{-6} \right ] \\ \rho_{ij}^2 & = & r_{ij}^2 - ({\bf r}_{ij}\cdot {\bf n}_{i})^2 \\[15pt] \rho_{ji}^2 & = & r_{ij}^2 - ({\bf r}_{ij}\cdot {\bf n}_{j})^2 \\[15pt] - f(\rho) & = & e^{-(\rho/\delta)^2} \sum_{n=0}^2 C_{2n} { \rho/\delta }^{2n} + f(\rho) & = & e^{-(\rho/\delta)^2} \sum_{n=0}^2 C_{2n} { (\rho/\delta) }^{2n} \end{eqnarray*} \endgroup \end{document} diff --git a/doc/src/pair_coul_shield.txt b/doc/src/pair_coul_shield.txt index df04e76de9..8152a1a12e 100644 --- a/doc/src/pair_coul_shield.txt +++ b/doc/src/pair_coul_shield.txt @@ -13,7 +13,7 @@ pair_style coul/shield command :h3 pair_style coul/shield cutoff tap_flag :pre cutoff = global cutoff (distance units) -tap_flag = 0/1 to turn off/on the taper function +tap_flag = 0/1 to turn off/on the taper function :ul [Examples:] diff --git a/doc/src/pair_ilp_graphene_hbn.txt b/doc/src/pair_ilp_graphene_hbn.txt index 4dd244c17f..0e8ac5e9c5 100644 --- a/doc/src/pair_ilp_graphene_hbn.txt +++ b/doc/src/pair_ilp_graphene_hbn.txt @@ -13,17 +13,17 @@ pair_style ilp/graphene/hbn command :h3 pair_style \[hybrid/overlay ...\] ilp/graphene/hbn cutoff tap_flag :pre cutoff = global cutoff (distance units) -tap_flag = 0/1 to turn off/on the taper function +tap_flag = 0/1 to turn off/on the taper function :ul [Examples:] -pair_style hybrid/overlay ilp/graphene/hbn 16.0 1 -pair_coeff * * ilp/graphene/hbn BNCH.ILP B N C :pre +pair_style hybrid/overlay ilp/graphene/hbn 16.0 1 +pair_coeff * * ilp/graphene/hbn ../potentials/BNCH.ILP B N C :pre pair_style hybrid/overlay rebo tersoff ilp/graphene/hbn 16.0 coul/shield 16.0 -pair_coeff * * rebo CH.rebo NULL NULL C -pair_coeff * * tersoff BNC.tersoff B N NULL -pair_coeff * * ilp/graphene/hbn BNCH.ILP B N C +pair_coeff * * rebo ../potentials/CH.rebo NULL NULL C +pair_coeff * * tersoff ../potentials/BNC.tersoff B N NULL +pair_coeff * * ilp/graphene/hbn ../potentials/BNCH.ILP B N C pair_coeff 1 1 coul/shield 0.70 pair_coeff 1 2 coul/shield 0.695 pair_coeff 2 2 coul/shield 0.69 :pre @@ -85,6 +85,22 @@ be found in "(Ouyang)"_#Ouyang. This potential must be used in combination with hybrid/overlay. Other interactions can be set to zero using pair_style {none}. +This pair style tallies a breakdown of the total interlayer potential +energy into sub-categories, which can be accessed via the "compute +pair"_compute_pair.html command as a vector of values of length 2. +The 2 values correspond to the following sub-categories: + +{E_vdW} = vdW (attractive) energy +{E_Rep} = Repulsive energy :ol + +To print these quantities to the log file (with descriptive column +headings) the following commands could be included in an input script: + +compute 0 all pair ilp/graphene/hbn +variable Evdw equal c_0\[1\] +variable Erep equal c_0\[2\] +thermo_style custom step temp epair v_Erep v_Evdw :pre + :line [Mixing, shift, table, tail correction, restart, rRESPA info]: diff --git a/doc/src/pair_kolmogorov_crespi_full.txt b/doc/src/pair_kolmogorov_crespi_full.txt index 9ad5bfea84..bfadc33e30 100644 --- a/doc/src/pair_kolmogorov_crespi_full.txt +++ b/doc/src/pair_kolmogorov_crespi_full.txt @@ -13,17 +13,17 @@ pair_style kolmogorov/crespi/full command :h3 pair_style hybrid/overlay kolmogorov/crespi/full cutoff tap_flag :pre cutoff = global cutoff (distance units) -tap_flag = 0/1 to turn off/on the taper function +tap_flag = 0/1 to turn off/on the taper function :ul [Examples:] pair_style hybrid/overlay kolmogorov/crespi/full 20.0 0 pair_coeff * * none -pair_coeff * * kolmogorov/crespi/full CH.KC C C :pre +pair_coeff * * kolmogorov/crespi/full ../potentials/CH.KC C C :pre pair_style hybrid/overlay rebo kolmogorov/crespi/full 16.0 1 -pair_coeff * * rebo CH.rebo C H -pair_coeff * * kolmogorov/crespi/full CH_taper.KC C H :pre +pair_coeff * * rebo ../potentials/CH.rebo C H +pair_coeff * * kolmogorov/crespi/full ../potentials/CH_taper.KC C H :pre [Description:] @@ -74,6 +74,22 @@ comparison of these parameters can be found in "(Ouyang)"_#Ouyang1. This potential must be used in combination with hybrid/overlay. Other interactions can be set to zero using pair_style {none}. +This pair style tallies a breakdown of the total interlayer potential +energy into sub-categories, which can be accessed via the "compute +pair"_compute_pair.html command as a vector of values of length 2. +The 2 values correspond to the following sub-categories: + +{E_vdW} = vdW (attractive) energy +{E_Rep} = Repulsive energy :ol + +To print these quantities to the log file (with descriptive column +headings) the following commands could be included in an input script: + +compute 0 all pair kolmogorov/crespi/full +variable Evdw equal c_0\[1\] +variable Erep equal c_0\[2\] +thermo_style custom step temp epair v_Erep v_Evdw :pre + :line [Mixing, shift, table, tail correction, restart, rRESPA info]: diff --git a/examples/USER/misc/ilp_graphene_hbn/bilayer-graphene/BNCH.ILP b/examples/USER/misc/ilp_graphene_hbn/bilayer-graphene/BNCH.ILP new file mode 120000 index 0000000000..b970e23f95 --- /dev/null +++ b/examples/USER/misc/ilp_graphene_hbn/bilayer-graphene/BNCH.ILP @@ -0,0 +1 @@ +../../../../../potentials/BNCH.ILP \ No newline at end of file diff --git a/examples/USER/misc/ilp_graphene_hbn/bilayer-graphene/Bi_gr_AB_stack_2L_noH.data b/examples/USER/misc/ilp_graphene_hbn/bilayer-graphene/Bi_gr_AB_stack_2L_noH.data new file mode 100644 index 0000000000..756123a6f1 --- /dev/null +++ b/examples/USER/misc/ilp_graphene_hbn/bilayer-graphene/Bi_gr_AB_stack_2L_noH.data @@ -0,0 +1,1372 @@ + Generate Bi-layer graphene + + 1360 atoms + + 2 atom types + + 0.000000000000000 42.599999999999994 xlo xhi + 0.000000000000000 41.811706494712695 ylo yhi + 0.000000000000000 100.000000000000000 zlo zhi + + Atoms + + 1 1 1 0.000000000000000 0.000000000000000 1.229756073373903 0.000000000000000 + 2 1 1 0.000000000000000 0.710000000000000 0.000000000000000 0.000000000000000 + 3 1 1 0.000000000000000 2.130000000000000 0.000000000000000 0.000000000000000 + 4 1 1 0.000000000000000 2.840000000000000 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42.599999999999994 40.581950421338796 3.3000000000000000 diff --git a/examples/USER/misc/ilp_graphene_hbn/bilayer-graphene/CH.rebo b/examples/USER/misc/ilp_graphene_hbn/bilayer-graphene/CH.rebo new file mode 120000 index 0000000000..b98001a7fd --- /dev/null +++ b/examples/USER/misc/ilp_graphene_hbn/bilayer-graphene/CH.rebo @@ -0,0 +1 @@ +../../../../../potentials/CH.rebo \ No newline at end of file diff --git a/examples/USER/misc/ilp_graphene_hbn/bilayer-graphene/in.bilayer-graphene b/examples/USER/misc/ilp_graphene_hbn/bilayer-graphene/in.bilayer-graphene index 8674917af2..949de4b74c 100644 --- a/examples/USER/misc/ilp_graphene_hbn/bilayer-graphene/in.bilayer-graphene +++ b/examples/USER/misc/ilp_graphene_hbn/bilayer-graphene/in.bilayer-graphene @@ -5,21 +5,22 @@ atom_style full processors * * 1 # domain decomposition over x and y # System and atom definition -# we use 2 atom types so that inter- and intra-layer +# we use different molecule ids for each layer of hBN +# so that inter- and intra-layer # interactions can be specified separately -# read lammps data file -read_data Bi_gr_AB_stack_2L_noH_300K.data + +read_data Bi_gr_AB_stack_2L_noH.data mass 1 12.0107 # carbon mass (g/mole) | membrane mass 2 12.0107 # carbon mass (g/mole) | adsorbate # Separate atom groups -group membrane type 1 -group adsorbate type 2 +group layer1 molecule 1 +group layer2 molecule 2 ######################## Potential defition ######################## pair_style hybrid/overlay rebo ilp/graphene/hbn 16.0 #################################################################### -pair_coeff * * rebo CH.airebo NULL C # chemical -pair_coeff * * ilp/graphene/hbn BNCH-old.ILP C C # long range +pair_coeff * * rebo CH.rebo C C # chemical +pair_coeff * * ilp/graphene/hbn BNCH.ILP C C # long range #################################################################### # Neighbor update settings neighbor 2.0 bin @@ -27,35 +28,25 @@ neigh_modify every 1 neigh_modify delay 0 neigh_modify check yes -# calculate the COM -variable adsxcom equal xcm(adsorbate,x) -variable adsycom equal xcm(adsorbate,y) -variable adszcom equal xcm(adsorbate,z) -variable adsvxcom equal vcm(adsorbate,x) -variable adsvycom equal vcm(adsorbate,y) -variable adsvzcom equal vcm(adsorbate,z) - #### Simulation settings #### -timestep 0.001 -#velocity adsorbate create 300.0 12345 -fix subf membrane setforce 0.0 0.0 0.0 -fix thermostat all nve +timestep 0.001 +velocity all create 300.0 12345 -compute 0 all pair rebo -compute 1 all pair ilp/graphene/hbn -variable REBO equal c_0 -variable ILP equal c_1 +compute 0 all pair rebo +compute 1 all pair ilp/graphene/hbn +variable REBO equal c_0 # REBO energy +variable ILP equal c_1 # total interlayer energy +variable Evdw equal c_1[1] # attractive energy +variable Erep equal c_1[2] # repulsive energy ############################ # Output thermo 100 -thermo_style custom step etotal pe ke v_REBO v_ILP temp v_adsxcom v_adsycom v_adszcom v_adsvxcom v_adsvycom v_adsvzcom -thermo_modify line one format float %.10f +thermo_style custom step cpu etotal pe ke v_REBO v_ILP v_Erep v_Evdw temp +thermo_modify line one format float %.16f thermo_modify flush yes norm no lost warn -#dump 1 all custom 1000 traj.lammpstrj id mol type xu yu zu -#dump_modify 1 format line "%7d %3d %3d %15.10g %15.10g %15.10g" flush yes - ###### Run molecular dynamics ###### -run 1000 +fix thermostat all nve +run 1000 diff --git a/examples/USER/misc/ilp_graphene_hbn/bilayer-graphene/log.5Jun19.bilayer-graphene.icc.1 b/examples/USER/misc/ilp_graphene_hbn/bilayer-graphene/log.5Jun19.bilayer-graphene.icc.1 new file mode 100644 index 0000000000..bb36f22d81 --- /dev/null +++ b/examples/USER/misc/ilp_graphene_hbn/bilayer-graphene/log.5Jun19.bilayer-graphene.icc.1 @@ -0,0 +1,128 @@ +LAMMPS (5 Jun 2019) +OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (../comm.cpp:88) + using 1 OpenMP thread(s) per MPI task +# Initialization +units metal +boundary p p p +atom_style full +processors * * 1 # domain decomposition over x and y + +# System and atom definition +# we use 2 molecule ids so that inter- and intra-layer +# interactions can be specified separately +# read lammps data file +read_data Bi_gr_AB_stack_2L_noH.data + orthogonal box = (0 0 0) to (42.6 41.8117 100) + 1 by 1 by 1 MPI processor grid + reading atoms ... + 1360 atoms + 0 = max # of 1-2 neighbors + 0 = max # of 1-3 neighbors + 0 = max # of 1-4 neighbors + 1 = max # of special neighbors + special bonds CPU = 0.00018123 secs + read_data CPU = 0.00179349 secs +mass 1 12.0107 # carbon mass (g/mole) | membrane +mass 2 12.0107 # carbon mass (g/mole) | adsorbate +# Separate atom groups +group layer1 molecule 1 +680 atoms in group layer1 +group layer2 molecule 2 +680 atoms in group layer2 + +######################## Potential defition ######################## +pair_style hybrid/overlay rebo ilp/graphene/hbn 16.0 +#################################################################### +pair_coeff * * rebo CH.rebo C C # chemical +Reading potential file CH.rebo with DATE: 2018-7-3 +pair_coeff * * ilp/graphene/hbn BNCH.ILP C C # long range +#################################################################### +# Neighbor update settings +neighbor 2.0 bin +neigh_modify every 1 +neigh_modify delay 0 +neigh_modify check yes + +#### Simulation settings #### +timestep 0.001 +velocity all create 300.0 12345 + +compute 0 all pair rebo +compute 1 all pair ilp/graphene/hbn +variable REBO equal c_0 # REBO energy +variable ILP equal c_1 # total interlayer energy +variable Evdw equal c_1[1] # attractive energy +variable Erep equal c_1[2] # repulsive energy + +############################ + +# Output +thermo 100 +thermo_style custom step cpu etotal pe ke v_REBO v_ILP v_Erep v_Evdw temp +thermo_modify line one format float %.16f +thermo_modify flush yes norm no lost warn + +###### Run molecular dynamics ###### +fix thermostat all nve +run 1000 +Neighbor list info ... + update every 1 steps, delay 0 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 18 + ghost atom cutoff = 18 + binsize = 9, bins = 5 5 12 + 2 neighbor lists, perpetual/occasional/extra = 2 0 0 + (1) pair rebo, perpetual + attributes: full, newton on, ghost + pair build: full/bin/ghost + stencil: full/ghost/bin/3d + bin: standard + (2) pair ilp/graphene/hbn, perpetual, copy from (1) + attributes: full, newton on, ghost + pair build: copy + stencil: none + bin: none +Per MPI rank memory allocation (min/avg/max) = 20.52 | 20.52 | 20.52 Mbytes +Step CPU TotEng PotEng KinEng v_REBO v_ILP v_Erep v_Evdw Temp + 0 0.0000000000000000 -10037.2853168513975106 -10089.9846779678973689 52.6993611164999436 -10057.1894932863488066 -32.7951846815484842 43.6401037466550932 -76.4352884281863538 299.9999999999996589 + 100 5.4714687280356884 -10037.0338552868142870 -10064.7651651140276954 27.7313098272134866 -10032.1809546658514591 -32.5842104481769326 34.7308676709731401 -67.3150781191208409 157.8651576016785896 + 200 10.9391297820257023 -10036.9626863095945737 -10061.1437965401473775 24.1811102305520329 -10028.8556641958457476 -32.2881323443021699 28.1799358234288526 -60.4680681676962450 137.6550477173489071 + 300 16.5882020250428468 -10037.0034097789539373 -10063.5001355365984637 26.4967257576440751 -10030.8230306457862753 -32.6771048908121244 34.9238490632189666 -67.6009539540019659 150.8370795942042264 + 400 22.1194989730138332 -10037.0320901258455706 -10064.3886163746337843 27.3565262487876240 -10031.8532011416427849 -32.5354152329904451 44.2423469839209460 -76.7777622168925546 155.7316388806602561 + 500 27.6722563949879259 -10037.0233394483148004 -10064.1136184894730832 27.0902790411580163 -10031.4312007416901906 -32.6824177477829565 37.2292320482101289 -69.9116497959676906 154.2159817531989177 + 600 33.2032995349727571 -10037.0033561502987141 -10063.6570740290953836 26.6537178787960869 -10031.3274097829344100 -32.3296642461602843 28.5090732059975061 -60.8387374521216842 151.7307837178934449 + 700 38.6685221369843930 -10037.0041655805853225 -10063.3498627390818001 26.3456971584966979 -10030.8006321783104795 -32.5492305607709014 32.5646861904578486 -65.1139167511948074 149.9773238251721921 + 800 44.2185375869739801 -10037.0245724491269357 -10064.2193369538654224 27.1947645047377584 -10031.7656842933574808 -32.4536526605085243 43.3815569718683705 -75.8352096323569498 154.8107828743098082 + 900 49.6989215560024604 -10037.0283918584391358 -10064.6675188165245345 27.6391269580851500 -10032.1673975747289660 -32.5001212417962648 39.9934500237055133 -72.4935712654787778 157.3403910741040761 + 1000 55.1455117090372369 -10037.0033475406326033 -10063.6621727186211501 26.6588251779885006 -10031.3371200905367004 -32.3250526280852100 29.5735783776502288 -61.8986310057011480 151.7598578798047697 +Loop time of 55.1456 on 1 procs for 1000 steps with 1360 atoms + +Performance: 1.567 ns/day, 15.318 hours/ns, 18.134 timesteps/s +100.0% CPU use with 1 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 55.092 | 55.092 | 55.092 | 0.0 | 99.90 +Bond | 0.00050265 | 0.00050265 | 0.00050265 | 0.0 | 0.00 +Neigh | 0 | 0 | 0 | 0.0 | 0.00 +Comm | 0.032649 | 0.032649 | 0.032649 | 0.0 | 0.06 +Output | 0.00060948 | 0.00060948 | 0.00060948 | 0.0 | 0.00 +Modify | 0.0093351 | 0.0093351 | 0.0093351 | 0.0 | 0.02 +Other | | 0.01008 | | | 0.02 + +Nlocal: 1360 ave 1360 max 1360 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 7964 ave 7964 max 7964 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 0 ave 0 max 0 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +FullNghs: 1.037e+06 ave 1.037e+06 max 1.037e+06 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 1037000 +Ave neighs/atom = 762.5 +Ave special neighs/atom = 0 +Neighbor list builds = 0 +Dangerous builds = 0 +Total wall time: 0:00:55 diff --git a/examples/USER/misc/ilp_graphene_hbn/bilayer-graphene/log.5Jun19.bilayer-graphene.icc.4 b/examples/USER/misc/ilp_graphene_hbn/bilayer-graphene/log.5Jun19.bilayer-graphene.icc.4 new file mode 100644 index 0000000000..95c495b677 --- /dev/null +++ b/examples/USER/misc/ilp_graphene_hbn/bilayer-graphene/log.5Jun19.bilayer-graphene.icc.4 @@ -0,0 +1,128 @@ +LAMMPS (5 Jun 2019) +OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (../comm.cpp:88) + using 1 OpenMP thread(s) per MPI task +# Initialization +units metal +boundary p p p +atom_style full +processors * * 1 # domain decomposition over x and y + +# System and atom definition +# we use 2 molecule ids so that inter- and intra-layer +# interactions can be specified separately +# read lammps data file +read_data Bi_gr_AB_stack_2L_noH.data + orthogonal box = (0 0 0) to (42.6 41.8117 100) + 2 by 2 by 1 MPI processor grid + reading atoms ... + 1360 atoms + 0 = max # of 1-2 neighbors + 0 = max # of 1-3 neighbors + 0 = max # of 1-4 neighbors + 1 = max # of special neighbors + special bonds CPU = 0.000147377 secs + read_data CPU = 0.0025185 secs +mass 1 12.0107 # carbon mass (g/mole) | membrane +mass 2 12.0107 # carbon mass (g/mole) | adsorbate +# Separate atom groups +group layer1 molecule 1 +680 atoms in group layer1 +group layer2 molecule 2 +680 atoms in group layer2 + +######################## Potential defition ######################## +pair_style hybrid/overlay rebo ilp/graphene/hbn 16.0 +#################################################################### +pair_coeff * * rebo CH.rebo C C # chemical +Reading potential file CH.rebo with DATE: 2018-7-3 +pair_coeff * * ilp/graphene/hbn BNCH.ILP C C # long range +#################################################################### +# Neighbor update settings +neighbor 2.0 bin +neigh_modify every 1 +neigh_modify delay 0 +neigh_modify check yes + +#### Simulation settings #### +timestep 0.001 +velocity all create 300.0 12345 + +compute 0 all pair rebo +compute 1 all pair ilp/graphene/hbn +variable REBO equal c_0 # REBO energy +variable ILP equal c_1 # total interlayer energy +variable Evdw equal c_1[1] # attractive energy +variable Erep equal c_1[2] # repulsive energy + +############################ + +# Output +thermo 100 +thermo_style custom step cpu etotal pe ke v_REBO v_ILP v_Erep v_Evdw temp +thermo_modify line one format float %.16f +thermo_modify flush yes norm no lost warn + +###### Run molecular dynamics ###### +fix thermostat all nve +run 1000 +Neighbor list info ... + update every 1 steps, delay 0 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 18 + ghost atom cutoff = 18 + binsize = 9, bins = 5 5 12 + 2 neighbor lists, perpetual/occasional/extra = 2 0 0 + (1) pair rebo, perpetual + attributes: full, newton on, ghost + pair build: full/bin/ghost + stencil: full/ghost/bin/3d + bin: standard + (2) pair ilp/graphene/hbn, perpetual, copy from (1) + attributes: full, newton on, ghost + pair build: copy + stencil: none + bin: none +Per MPI rank memory allocation (min/avg/max) = 11.64 | 11.64 | 11.64 Mbytes +Step CPU TotEng PotEng KinEng v_REBO v_ILP v_Erep v_Evdw Temp + 0 0.0000000000000000 -10037.2853168516194273 -10089.9846779681192857 52.6993611164999933 -10057.1894932866325689 -32.7951846814872354 43.6401037466782640 -76.4352884281594527 299.9999999999999432 + 100 1.5180878639221191 -10037.0338552867851831 -10064.7651651139967726 27.7313098272123320 -10032.1809546658569161 -32.5842104481406381 34.7308676709827395 -67.3150781191209546 157.8651576016720242 + 200 3.0293023219564930 -10036.9626863095381850 -10061.1437965400909889 24.1811102305529495 -10028.8556641958311957 -32.2881323442601911 28.1799358234373614 -60.4680681676959750 137.6550477173541367 + 300 4.5289151089964435 -10037.0034097789121006 -10063.5001355365566269 26.4967257576439188 -10030.8230306457808183 -32.6771048907772084 34.9238490632284311 -67.6009539540031454 150.8370795942033453 + 400 6.0309539699228480 -10037.0320901258182857 -10064.3886163746046805 27.3565262487870413 -10031.8532011416427849 -32.5354152329611424 44.2423469839354624 -76.7777622168941747 155.7316388806569307 + 500 7.5873900629812852 -10037.0233394482729636 -10064.1136184894312464 27.0902790411581904 -10031.4312007416810957 -32.6824177477510176 37.2292320482201404 -69.9116497959683159 154.2159817531999124 + 600 9.1088078819448128 -10037.0033561502586963 -10063.6570740290553658 26.6537178787959803 -10031.3274097829398670 -32.3296642461160033 28.5090732060055281 -60.8387374521202773 151.7307837178928480 + 700 10.6168858460150659 -10037.0041655805125629 -10063.3498627390090405 26.3456971584962574 -10030.8006321782777377 -32.5492305607314165 32.5646861904650535 -65.1139167511946653 149.9773238251696910 + 800 12.1294107990106568 -10037.0245724491123838 -10064.2193369538508705 27.1947645047383304 -10031.7656842933720327 -32.4536526604775162 43.3815569718824179 -75.8352096323571629 154.8107828743130767 + 900 13.6509861790109426 -10037.0283918584264029 -10064.6675188165099826 27.6391269580827625 -10032.1673975747471559 -32.5001212417642336 39.9934500237184380 -72.4935712654798436 157.3403910740904905 + 1000 15.1634582940023392 -10037.0033475405834906 -10063.6621727185720374 26.6588251779879926 -10031.3371200905276055 -32.3250526280445740 29.5735783776581442 -61.8986310057012972 151.7598578798018707 +Loop time of 15.1635 on 4 procs for 1000 steps with 1360 atoms + +Performance: 5.698 ns/day, 4.212 hours/ns, 65.948 timesteps/s +99.9% CPU use with 4 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 13.997 | 14.363 | 14.741 | 9.0 | 94.72 +Bond | 0.00036359 | 0.00040186 | 0.00044586 | 0.0 | 0.00 +Neigh | 0 | 0 | 0 | 0.0 | 0.00 +Comm | 0.40664 | 0.78485 | 1.1509 | 38.6 | 5.18 +Output | 0.00027687 | 0.00036825 | 0.00063194 | 0.0 | 0.00 +Modify | 0.0043962 | 0.0045847 | 0.0047857 | 0.2 | 0.03 +Other | | 0.01055 | | | 0.07 + +Nlocal: 340 ave 340 max 340 min +Histogram: 4 0 0 0 0 0 0 0 0 0 +Nghost: 4628 ave 4628 max 4628 min +Histogram: 4 0 0 0 0 0 0 0 0 0 +Neighs: 0 ave 0 max 0 min +Histogram: 4 0 0 0 0 0 0 0 0 0 +FullNghs: 259250 ave 259250 max 259250 min +Histogram: 4 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 1037000 +Ave neighs/atom = 762.5 +Ave special neighs/atom = 0 +Neighbor list builds = 0 +Dangerous builds = 0 +Total wall time: 0:00:15 diff --git a/examples/USER/misc/ilp_graphene_hbn/bilayer-hBN/BNC.tersoff b/examples/USER/misc/ilp_graphene_hbn/bilayer-hBN/BNC.tersoff new file mode 120000 index 0000000000..0c35f80da1 --- /dev/null +++ b/examples/USER/misc/ilp_graphene_hbn/bilayer-hBN/BNC.tersoff @@ -0,0 +1 @@ +../../../../../potentials/BNC.tersoff \ No newline at end of file diff --git a/examples/USER/misc/ilp_graphene_hbn/bilayer-hBN/BNCH.ILP b/examples/USER/misc/ilp_graphene_hbn/bilayer-hBN/BNCH.ILP new file mode 120000 index 0000000000..b970e23f95 --- /dev/null +++ b/examples/USER/misc/ilp_graphene_hbn/bilayer-hBN/BNCH.ILP @@ -0,0 +1 @@ +../../../../../potentials/BNCH.ILP \ No newline at end of file diff --git a/examples/USER/misc/ilp_graphene_hbn/bilayer-hBN/hBN_AA_prime_stack_2L_noH.data b/examples/USER/misc/ilp_graphene_hbn/bilayer-hBN/hBN_AA_prime_stack_2L_noH.data new file mode 100644 index 0000000000..b965f74d30 --- /dev/null +++ b/examples/USER/misc/ilp_graphene_hbn/bilayer-hBN/hBN_AA_prime_stack_2L_noH.data @@ -0,0 +1,1372 @@ + Generate Bi-layer hBN + + 1360 atoms + + 4 atom types + + 0.000000000000000 43.379999999999995 xlo xhi + 0.000000000000000 42.577272951658138 ylo yhi + 0.000000000000000 100.000000000000000 zlo zhi + + Atoms + + 1 1 1 0.42000 0.000000000000000 1.252272733872298 0.000000000000000 + 2 1 2 -0.42000 0.723000000000000 0.000000000000000 0.000000000000000 + 3 1 1 0.42000 2.169000000000000 0.000000000000000 0.000000000000000 + 4 1 2 -0.42000 2.892000000000000 1.252272733872298 0.000000000000000 + 5 1 1 0.42000 4.338000000000000 1.252272733872298 0.000000000000000 + 6 1 2 -0.42000 5.061000000000000 0.000000000000000 0.000000000000000 + 7 1 1 0.42000 6.507000000000000 0.000000000000000 0.000000000000000 + 8 1 2 -0.42000 7.230000000000000 1.252272733872298 0.000000000000000 + 9 1 1 0.42000 8.676000000000000 1.252272733872298 0.000000000000000 + 10 1 2 -0.42000 9.399000000000001 0.000000000000000 0.000000000000000 + 11 1 1 0.42000 10.845000000000001 0.000000000000000 0.000000000000000 + 12 1 2 -0.42000 11.568000000000000 1.252272733872298 0.000000000000000 + 13 1 1 0.42000 13.013999999999999 1.252272733872298 0.000000000000000 + 14 1 2 -0.42000 13.737000000000000 0.000000000000000 0.000000000000000 + 15 1 1 0.42000 15.183000000000000 0.000000000000000 0.000000000000000 + 16 1 2 -0.42000 15.905999999999999 1.252272733872298 0.000000000000000 + 17 1 1 0.42000 17.352000000000000 1.252272733872298 0.000000000000000 + 18 1 2 -0.42000 18.074999999999999 0.000000000000000 0.000000000000000 + 19 1 1 0.42000 19.521000000000001 0.000000000000000 0.000000000000000 + 20 1 2 -0.42000 20.244000000000000 1.252272733872298 0.000000000000000 + 21 1 1 0.42000 21.690000000000001 1.252272733872298 0.000000000000000 + 22 1 2 -0.42000 22.413000000000000 0.000000000000000 0.000000000000000 + 23 1 1 0.42000 23.859000000000002 0.000000000000000 0.000000000000000 + 24 1 2 -0.42000 24.582000000000001 1.252272733872298 0.000000000000000 + 25 1 1 0.42000 26.027999999999999 1.252272733872298 0.000000000000000 + 26 1 2 -0.42000 26.750999999999998 0.000000000000000 0.000000000000000 + 27 1 1 0.42000 28.196999999999999 0.000000000000000 0.000000000000000 + 28 1 2 -0.42000 28.919999999999998 1.252272733872298 0.000000000000000 + 29 1 1 0.42000 30.366000000000000 1.252272733872298 0.000000000000000 + 30 1 2 -0.42000 31.088999999999999 0.000000000000000 0.000000000000000 + 31 1 1 0.42000 32.534999999999997 0.000000000000000 0.000000000000000 + 32 1 2 -0.42000 33.258000000000003 1.252272733872298 0.000000000000000 + 33 1 1 0.42000 34.704000000000001 1.252272733872298 0.000000000000000 + 34 1 2 -0.42000 35.427000000000000 0.000000000000000 0.000000000000000 + 35 1 1 0.42000 36.872999999999998 0.000000000000000 0.000000000000000 + 36 1 2 -0.42000 37.596000000000004 1.252272733872298 0.000000000000000 + 37 1 1 0.42000 39.042000000000002 1.252272733872298 0.000000000000000 + 38 1 2 -0.42000 39.765000000000001 0.000000000000000 0.000000000000000 + 39 1 1 0.42000 41.210999999999999 0.000000000000000 0.000000000000000 + 40 1 2 -0.42000 41.934000000000005 1.252272733872298 0.000000000000000 + 41 1 1 0.42000 0.000000000000000 3.756818201616894 0.000000000000000 + 42 1 2 -0.42000 0.723000000000000 2.504545467744596 0.000000000000000 + 43 1 1 0.42000 2.169000000000000 2.504545467744596 0.000000000000000 + 44 1 2 -0.42000 2.892000000000000 3.756818201616894 0.000000000000000 + 45 1 1 0.42000 4.338000000000000 3.756818201616894 0.000000000000000 + 46 1 2 -0.42000 5.061000000000000 2.504545467744596 0.000000000000000 + 47 1 1 0.42000 6.507000000000000 2.504545467744596 0.000000000000000 + 48 1 2 -0.42000 7.230000000000000 3.756818201616894 0.000000000000000 + 49 1 1 0.42000 8.676000000000000 3.756818201616894 0.000000000000000 + 50 1 2 -0.42000 9.399000000000001 2.504545467744596 0.000000000000000 + 51 1 1 0.42000 10.845000000000001 2.504545467744596 0.000000000000000 + 52 1 2 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+ 1348 2 3 0.42000 28.919999999999998 41.325000217785835 3.330000000000000 + 1349 2 4 -0.42000 30.366000000000000 41.325000217785835 3.330000000000000 + 1350 2 3 0.42000 31.088999999999999 40.072727483913539 3.330000000000000 + 1351 2 4 -0.42000 32.534999999999997 40.072727483913539 3.330000000000000 + 1352 2 3 0.42000 33.258000000000003 41.325000217785835 3.330000000000000 + 1353 2 4 -0.42000 34.704000000000001 41.325000217785835 3.330000000000000 + 1354 2 3 0.42000 35.427000000000000 40.072727483913539 3.330000000000000 + 1355 2 4 -0.42000 36.872999999999998 40.072727483913539 3.330000000000000 + 1356 2 3 0.42000 37.596000000000004 41.325000217785835 3.330000000000000 + 1357 2 4 -0.42000 39.042000000000002 41.325000217785835 3.330000000000000 + 1358 2 3 0.42000 39.765000000000001 40.072727483913539 3.330000000000000 + 1359 2 4 -0.42000 41.210999999999999 40.072727483913539 3.330000000000000 + 1360 2 3 0.42000 41.934000000000005 41.325000217785835 3.330000000000000 diff --git a/examples/USER/misc/ilp_graphene_hbn/bilayer-hBN/in.bilayer-hBN b/examples/USER/misc/ilp_graphene_hbn/bilayer-hBN/in.bilayer-hBN new file mode 100644 index 0000000000..0e02104d59 --- /dev/null +++ b/examples/USER/misc/ilp_graphene_hbn/bilayer-hBN/in.bilayer-hBN @@ -0,0 +1,57 @@ +# Initialization +units metal +boundary p p p +atom_style full +processors * * 1 # domain decomposition over x and y + +# System and atom definition +# we use different molecule ids for each layer of hBN +# so that inter- and intra-layer +# interactions can be specified separately +read_data hBN_AA_prime_stack_2L_noH.data +mass 1 10.8110 # boron mass (g/mole) | membrane +mass 2 14.0067 # nitrogen mass (g/mole) | adsorbate +mass 3 10.8110 # boron mass (g/mole) | membrane +mass 4 14.0067 # nitrogen mass (g/mole) | adsorbate +# Separate atom groups +group layer1 molecule 1 +group layer2 molecule 2 + +######################## Potential defition ######################## +pair_style hybrid/overlay tersoff ilp/graphene/hbn 16.0 coul/shield 16.0 1 +#################################################################### +pair_coeff * * tersoff BNC.tersoff B N B N # chemical +pair_coeff * * ilp/graphene/hbn BNCH.ILP B N B N # long range +pair_coeff 1 3 coul/shield 0.70 +pair_coeff 1 4 coul/shield 0.69498201415576216335 +pair_coeff 2 3 coul/shield 0.69498201415576216335 +pair_coeff 2 4 coul/shield 0.69 +#################################################################### +# Neighbor update settings +neighbor 2.0 bin +neigh_modify every 1 +neigh_modify delay 0 +neigh_modify check yes + +#### Simulation settings #### +timestep 0.001 +velocity all create 300.0 12345 dist gaussian mom yes rot yes +fix thermostat all nve + +compute 0 all pair tersoff +compute 1 all pair coul/shield ecoul +compute 2 all pair ilp/graphene/hbn +variable Tersoff equal c_0 # Tersoff energy +variable Ecoul equal c_1 # Coulomb energy +variable EILP equal c_2 # total interlayer energy +variable Evdw equal c_2[1] # attractive energy +variable Erep equal c_2[2] # repulsive energy + +############# Output ############### +thermo 100 +thermo_style custom step cpu etotal pe ke v_Evdw v_Tersoff v_EILP v_Erep v_Evdw v_Ecoul temp +thermo_modify line one format float %.10f +thermo_modify flush yes norm no lost error + +###### Run molecular dynamics ###### +run 1000 diff --git a/examples/USER/misc/ilp_graphene_hbn/bilayer-hBN/log.5Jun19.bilayer_hBN.icc.1 b/examples/USER/misc/ilp_graphene_hbn/bilayer-hBN/log.5Jun19.bilayer_hBN.icc.1 new file mode 100644 index 0000000000..abebb8df27 --- /dev/null +++ b/examples/USER/misc/ilp_graphene_hbn/bilayer-hBN/log.5Jun19.bilayer_hBN.icc.1 @@ -0,0 +1,144 @@ +LAMMPS (5 Jun 2019) +OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (../comm.cpp:88) + using 1 OpenMP thread(s) per MPI task +# Initialization +units metal +boundary p p p +atom_style full +processors * * 1 # domain decomposition over x and y + +# System and atom definition +# we use different molecule ids for each layer of hBN +# so that inter- and intra-layer +# interactions can be specified separately +read_data hBN_AA_prime_stack_2L_noH.data + orthogonal box = (0 0 0) to (43.38 42.5773 100) + 1 by 1 by 1 MPI processor grid + reading atoms ... + 1360 atoms + 0 = max # of 1-2 neighbors + 0 = max # of 1-3 neighbors + 0 = max # of 1-4 neighbors + 1 = max # of special neighbors + special bonds CPU = 0.000162885 secs + read_data CPU = 0.00152144 secs +mass 1 10.8110 # boron mass (g/mole) | membrane +mass 2 14.0067 # nitrogen mass (g/mole) | adsorbate +mass 3 10.8110 # boron mass (g/mole) | membrane +mass 4 14.0067 # nitrogen mass (g/mole) | adsorbate +# Separate atom groups +group layer1 molecule 1 +680 atoms in group layer1 +group layer2 molecule 2 +680 atoms in group layer2 + +######################## Potential defition ######################## +pair_style hybrid/overlay tersoff ilp/graphene/hbn 16.0 coul/shield 16.0 1 +#################################################################### +pair_coeff * * tersoff BNC.tersoff B N B N # chemical +Reading potential file BNC.tersoff with DATE: 2013-03-21 +pair_coeff * * ilp/graphene/hbn BNCH.ILP B N B N # long range +pair_coeff 1 3 coul/shield 0.70 +pair_coeff 1 4 coul/shield 0.69498201415576216335 +pair_coeff 2 3 coul/shield 0.69498201415576216335 +pair_coeff 2 4 coul/shield 0.69 +#################################################################### +# Neighbor update settings +neighbor 2.0 bin +neigh_modify every 1 +neigh_modify delay 0 +neigh_modify check yes + +#### Simulation settings #### +timestep 0.001 +velocity all create 300.0 12345 dist gaussian mom yes rot yes +fix thermostat all nve + +compute 0 all pair tersoff +compute 1 all pair coul/shield ecoul +compute 2 all pair ilp/graphene/hbn +variable Tersoff equal c_0 # Tersoff energy +variable Ecoul equal c_1 # Coulomb energy +variable EILP equal c_2 # total interlayer energy +variable Evdw equal c_2[1] # attractive energy +variable Erep equal c_2[2] # repulsive energy + +############# Output ############### +thermo 100 +thermo_style custom step cpu etotal pe ke v_Evdw v_Tersoff v_EILP v_Erep v_Evdw v_Ecoul temp +thermo_modify line one format float %.10f +thermo_modify flush yes norm no lost error + +###### Run molecular dynamics ###### +run 1000 +Neighbor list info ... + update every 1 steps, delay 0 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 18 + ghost atom cutoff = 18 + binsize = 9, bins = 5 5 12 + 4 neighbor lists, perpetual/occasional/extra = 4 0 0 + (1) pair tersoff, perpetual + attributes: full, newton on + pair build: full/bin + stencil: full/bin/3d + bin: standard + (2) pair ilp/graphene/hbn, perpetual + attributes: full, newton on, ghost + pair build: full/bin/ghost + stencil: full/ghost/bin/3d + bin: standard + (3) pair coul/shield, perpetual, skip from (4) + attributes: half, newton on + pair build: skip + stencil: none + bin: none + (4) neighbor class addition, perpetual, half/full from (1) + attributes: half, newton on + pair build: halffull/newton + stencil: none + bin: none +Per MPI rank memory allocation (min/avg/max) = 39.16 | 39.16 | 39.16 Mbytes +Step CPU TotEng PotEng KinEng v_Evdw v_Tersoff v_EILP v_Erep v_Evdw v_Ecoul Temp + 0 0.0000000000 -10193.1380848266 -10245.8374459431 52.6993611165 -77.5570687695 -10208.7302118650 -36.7764829084 40.7805858612 -77.5570687695 -0.3307511697 300.0000000000 + 100 6.7965245070 -10192.8138221665 -10215.1933919318 22.3795697653 -80.9976194405 -10177.8775571602 -36.9677356248 44.0298838157 -80.9976194405 -0.3480991468 127.3994748197 + 200 13.6121753111 -10192.9217984546 -10221.8066529747 28.8848545200 -86.3703194681 -10184.2512197444 -37.1689855905 49.2013338776 -86.3703194681 -0.3864476398 164.4319052911 + 300 20.4697002331 -10192.8780091121 -10219.0294731325 26.1514640204 -83.0639240055 -10182.3487520151 -36.3041195435 46.7598044620 -83.0639240055 -0.3766015739 148.8716189324 + 400 27.2477328760 -10192.8915023008 -10218.8337311224 25.9422288216 -78.3942416895 -10181.3978178066 -37.1109676261 41.2832740634 -78.3942416895 -0.3249456897 147.6805122794 + 500 34.0398510781 -10192.9091924320 -10221.3314056924 28.4222132604 -81.7685306349 -10184.0302799036 -36.9462261394 44.8223044955 -81.7685306349 -0.3548996493 161.7982419039 + 600 40.8147194131 -10192.8859685989 -10219.3709182378 26.4849496389 -86.2783346104 -10182.6694059460 -36.2951497597 49.9831848507 -86.2783346104 -0.4063625321 150.7700420526 + 700 47.6096971680 -10192.9015812429 -10220.9496893393 28.0481080963 -82.2887300963 -10183.2081700333 -37.3937397296 44.8949903667 -82.2887300963 -0.3477795764 159.6685851711 + 800 54.4165411390 -10192.8798040842 -10218.5099898620 25.6301857778 -78.0110194568 -10181.4267315419 -36.7542088970 41.2568105599 -78.0110194568 -0.3290494232 145.9041546318 + 900 61.2580328170 -10192.8940657565 -10220.5595028458 27.6654370893 -82.4743793723 -10183.8013123118 -36.3811572492 46.0932221231 -82.4743793723 -0.3770332848 157.4901659330 + 1000 68.0452993071 -10192.8973362869 -10219.0104657947 26.1131295079 -87.1256831340 -10181.2524878789 -37.3618984004 49.7637847337 -87.1256831340 -0.3960795154 148.6533932553 +Loop time of 68.0453 on 1 procs for 1000 steps with 1360 atoms + +Performance: 1.270 ns/day, 18.901 hours/ns, 14.696 timesteps/s +100.0% CPU use with 1 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 67.995 | 67.995 | 67.995 | 0.0 | 99.93 +Bond | 0.00047219 | 0.00047219 | 0.00047219 | 0.0 | 0.00 +Neigh | 0 | 0 | 0 | 0.0 | 0.00 +Comm | 0.030427 | 0.030427 | 0.030427 | 0.0 | 0.04 +Output | 0.000568 | 0.000568 | 0.000568 | 0.0 | 0.00 +Modify | 0.0089312 | 0.0089312 | 0.0089312 | 0.0 | 0.01 +Other | | 0.01005 | | | 0.01 + +Nlocal: 1360 ave 1360 max 1360 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 7836 ave 7836 max 7836 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 249560 ave 249560 max 249560 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +FullNghs: 1.00504e+06 ave 1.00504e+06 max 1.00504e+06 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 1005040 +Ave neighs/atom = 739 +Ave special neighs/atom = 0 +Neighbor list builds = 0 +Dangerous builds = 0 +Total wall time: 0:01:08 diff --git a/examples/USER/misc/ilp_graphene_hbn/bilayer-hBN/log.5Jun19.bilayer_hBN.icc.4 b/examples/USER/misc/ilp_graphene_hbn/bilayer-hBN/log.5Jun19.bilayer_hBN.icc.4 new file mode 100644 index 0000000000..8ad5875282 --- /dev/null +++ b/examples/USER/misc/ilp_graphene_hbn/bilayer-hBN/log.5Jun19.bilayer_hBN.icc.4 @@ -0,0 +1,144 @@ +LAMMPS (5 Jun 2019) +OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (../comm.cpp:88) + using 1 OpenMP thread(s) per MPI task +# Initialization +units metal +boundary p p p +atom_style full +processors * * 1 # domain decomposition over x and y + +# System and atom definition +# we use different molecule ids for each layer of hBN +# so that inter- and intra-layer +# interactions can be specified separately +read_data hBN_AA_prime_stack_2L_noH.data + orthogonal box = (0 0 0) to (43.38 42.5773 100) + 2 by 2 by 1 MPI processor grid + reading atoms ... + 1360 atoms + 0 = max # of 1-2 neighbors + 0 = max # of 1-3 neighbors + 0 = max # of 1-4 neighbors + 1 = max # of special neighbors + special bonds CPU = 0.00013403 secs + read_data CPU = 0.00236647 secs +mass 1 10.8110 # boron mass (g/mole) | membrane +mass 2 14.0067 # nitrogen mass (g/mole) | adsorbate +mass 3 10.8110 # boron mass (g/mole) | membrane +mass 4 14.0067 # nitrogen mass (g/mole) | adsorbate +# Separate atom groups +group layer1 molecule 1 +680 atoms in group layer1 +group layer2 molecule 2 +680 atoms in group layer2 + +######################## Potential defition ######################## +pair_style hybrid/overlay tersoff ilp/graphene/hbn 16.0 coul/shield 16.0 1 +#################################################################### +pair_coeff * * tersoff BNC.tersoff B N B N # chemical +Reading potential file BNC.tersoff with DATE: 2013-03-21 +pair_coeff * * ilp/graphene/hbn BNCH.ILP B N B N # long range +pair_coeff 1 3 coul/shield 0.70 +pair_coeff 1 4 coul/shield 0.69498201415576216335 +pair_coeff 2 3 coul/shield 0.69498201415576216335 +pair_coeff 2 4 coul/shield 0.69 +#################################################################### +# Neighbor update settings +neighbor 2.0 bin +neigh_modify every 1 +neigh_modify delay 0 +neigh_modify check yes + +#### Simulation settings #### +timestep 0.001 +velocity all create 300.0 12345 dist gaussian mom yes rot yes +fix thermostat all nve + +compute 0 all pair tersoff +compute 1 all pair coul/shield ecoul +compute 2 all pair ilp/graphene/hbn +variable Tersoff equal c_0 # Tersoff energy +variable Ecoul equal c_1 # Coulomb energy +variable EILP equal c_2 # total interlayer energy +variable Evdw equal c_2[1] # attractive energy +variable Erep equal c_2[2] # repulsive energy + +############# Output ############### +thermo 100 +thermo_style custom step cpu etotal pe ke v_Evdw v_Tersoff v_EILP v_Erep v_Evdw v_Ecoul temp +thermo_modify line one format float %.10f +thermo_modify flush yes norm no lost error + +###### Run molecular dynamics ###### +run 1000 +Neighbor list info ... + update every 1 steps, delay 0 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 18 + ghost atom cutoff = 18 + binsize = 9, bins = 5 5 12 + 4 neighbor lists, perpetual/occasional/extra = 4 0 0 + (1) pair tersoff, perpetual + attributes: full, newton on + pair build: full/bin + stencil: full/bin/3d + bin: standard + (2) pair ilp/graphene/hbn, perpetual + attributes: full, newton on, ghost + pair build: full/bin/ghost + stencil: full/ghost/bin/3d + bin: standard + (3) pair coul/shield, perpetual, skip from (4) + attributes: half, newton on + pair build: skip + stencil: none + bin: none + (4) neighbor class addition, perpetual, half/full from (1) + attributes: half, newton on + pair build: halffull/newton + stencil: none + bin: none +Per MPI rank memory allocation (min/avg/max) = 20.72 | 20.72 | 20.72 Mbytes +Step CPU TotEng PotEng KinEng v_Evdw v_Tersoff v_EILP v_Erep v_Evdw v_Ecoul Temp + 0 0.0000000000 -10193.1380848270 -10245.8374459435 52.6993611165 -77.5570687695 -10208.7302118654 -36.7764829083 40.7805858612 -77.5570687695 -0.3307511697 300.0000000000 + 100 2.1550989150 -10192.8138221665 -10215.1933919317 22.3795697653 -80.9976194405 -10177.8775571601 -36.9677356248 44.0298838158 -80.9976194405 -0.3480991468 127.3994748197 + 200 4.3479236889 -10192.9217984546 -10221.8066529746 28.8848545200 -86.3703194681 -10184.2512197444 -37.1689855904 49.2013338777 -86.3703194681 -0.3864476398 164.4319052911 + 300 6.5410459590 -10192.8780091121 -10219.0294731324 26.1514640204 -83.0639240055 -10182.3487520151 -36.3041195435 46.7598044620 -83.0639240055 -0.3766015739 148.8716189324 + 400 8.7036962360 -10192.8915023008 -10218.8337311224 25.9422288216 -78.3942416895 -10181.3978178066 -37.1109676261 41.2832740634 -78.3942416895 -0.3249456897 147.6805122794 + 500 10.8535934120 -10192.9091924320 -10221.3314056923 28.4222132604 -81.7685306349 -10184.0302799036 -36.9462261394 44.8223044955 -81.7685306349 -0.3548996493 161.7982419039 + 600 12.9922130840 -10192.8859685988 -10219.3709182377 26.4849496389 -86.2783346104 -10182.6694059459 -36.2951497597 49.9831848507 -86.2783346104 -0.4063625321 150.7700420526 + 700 15.1486390879 -10192.9015812430 -10220.9496893393 28.0481080963 -82.2887300963 -10183.2081700333 -37.3937397295 44.8949903668 -82.2887300963 -0.3477795764 159.6685851711 + 800 17.3069961029 -10192.8798040842 -10218.5099898620 25.6301857778 -78.0110194568 -10181.4267315419 -36.7542088969 41.2568105599 -78.0110194568 -0.3290494232 145.9041546318 + 900 19.4832645269 -10192.8940657564 -10220.5595028457 27.6654370893 -82.4743793723 -10183.8013123118 -36.3811572492 46.0932221231 -82.4743793723 -0.3770332848 157.4901659330 + 1000 21.6507079899 -10192.8973362868 -10219.0104657947 26.1131295079 -87.1256831340 -10181.2524878789 -37.3618984003 49.7637847337 -87.1256831340 -0.3960795154 148.6533932553 +Loop time of 21.6507 on 4 procs for 1000 steps with 1360 atoms + +Performance: 3.991 ns/day, 6.014 hours/ns, 46.188 timesteps/s +99.8% CPU use with 4 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 20.152 | 20.681 | 21.202 | 8.2 | 95.52 +Bond | 0.00039643 | 0.00043971 | 0.00048381 | 0.0 | 0.00 +Neigh | 0 | 0 | 0 | 0.0 | 0.00 +Comm | 0.43171 | 0.9526 | 1.482 | 38.2 | 4.40 +Output | 0.00028839 | 0.00037988 | 0.00064771 | 0.0 | 0.00 +Modify | 0.0046368 | 0.0047831 | 0.0050183 | 0.2 | 0.02 +Other | | 0.01106 | | | 0.05 + +Nlocal: 340 ave 340 max 340 min +Histogram: 4 0 0 0 0 0 0 0 0 0 +Nghost: 4536 ave 4536 max 4536 min +Histogram: 4 0 0 0 0 0 0 0 0 0 +Neighs: 62390 ave 62390 max 62390 min +Histogram: 4 0 0 0 0 0 0 0 0 0 +FullNghs: 251260 ave 251260 max 251260 min +Histogram: 4 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 1005040 +Ave neighs/atom = 739 +Ave special neighs/atom = 0 +Neighbor list builds = 0 +Dangerous builds = 0 +Total wall time: 0:00:21 diff --git a/examples/USER/misc/ilp_graphene_hbn/gr-hBN/BNCH.ILP b/examples/USER/misc/ilp_graphene_hbn/gr-hBN/BNCH.ILP new file mode 120000 index 0000000000..b970e23f95 --- /dev/null +++ b/examples/USER/misc/ilp_graphene_hbn/gr-hBN/BNCH.ILP @@ -0,0 +1 @@ +../../../../../potentials/BNCH.ILP \ No newline at end of file diff --git a/examples/USER/misc/ilp_graphene_hbn/gr-hBN/CH.rebo b/examples/USER/misc/ilp_graphene_hbn/gr-hBN/CH.rebo new file mode 120000 index 0000000000..b98001a7fd --- /dev/null +++ b/examples/USER/misc/ilp_graphene_hbn/gr-hBN/CH.rebo @@ -0,0 +1 @@ +../../../../../potentials/CH.rebo \ No newline at end of file diff --git a/examples/USER/misc/ilp_graphene_hbn/gr-hBN/in.grhBN b/examples/USER/misc/ilp_graphene_hbn/gr-hBN/in.grhBN index bad7b17fde..1ae1704dec 100644 --- a/examples/USER/misc/ilp_graphene_hbn/gr-hBN/in.grhBN +++ b/examples/USER/misc/ilp_graphene_hbn/gr-hBN/in.grhBN @@ -5,22 +5,23 @@ atom_style full processors * * 1 # domain decomposition over x and y # System and atom definition -# we use 2 atom types so that inter- and intra-layer +# we use different molecule ids for each layer +# so that inter- and intra-layer # interactions can be specified separately read_data gr_hBN_Cstack_2L_noH.data mass 1 10.8110 # boron mass (g/mole) | membrane mass 2 14.0067 # nitrogen mass (g/mole) | membrane mass 3 12.0107 # carbon mass (g/mole) | adsorbate # Separate atom groups -group membrane type 1 2 -group adsorbate type 3 +group hBN molecule 1 +group gr molecule 2 ######################## Potential defition ######################## pair_style hybrid/overlay rebo tersoff ilp/graphene/hbn 16.0 coul/shield 16.0 #################################################################### -pair_coeff * * rebo CH.airebo NULL NULL C # chemical -pair_coeff * * tersoff BNC.tersoff B N NULL # chemical -pair_coeff * * ilp/graphene/hbn BNCH-old.ILP B N C # long range +pair_coeff * * rebo CH.rebo NULL NULL C # chemical +pair_coeff * * tersoff BNC.tersoff B N NULL # chemical +pair_coeff * * ilp/graphene/hbn BNCH.ILP B N C # long range pair_coeff 1 1 coul/shield 0.70 pair_coeff 1 2 coul/shield 0.69498201415576216335 pair_coeff 2 2 coul/shield 0.69 @@ -31,41 +32,26 @@ neigh_modify every 1 neigh_modify delay 0 neigh_modify check yes -# calculate the COM -variable adsxcom equal xcm(adsorbate,x) -variable adsycom equal xcm(adsorbate,y) -variable adszcom equal xcm(adsorbate,z) -variable adsvxcom equal vcm(adsorbate,x) -variable adsvycom equal vcm(adsorbate,y) -variable adsvzcom equal vcm(adsorbate,z) - #### Simulation settings #### -timestep 0.001 -velocity all create 300.0 12345 -fix thermostat all nve - -compute 0 all pair rebo -compute 1 all pair tersoff -compute 2 all pair ilp/graphene/hbn -compute 3 all pair coul/shield -variable REBO equal c_0 -variable Tersoff equal c_1 -variable EILP equal c_2 -variable Ecoul equal c_3 - -# Calculate the pair potential between the substrate and slider -compute sldsub adsorbate group/group membrane -variable Evdw equal c_sldsub - -############################ - -# Output +timestep 0.001 +velocity all create 300.0 12345 dist gaussian mom yes rot yes +fix thermostat all nve + +compute 0 all pair rebo +compute 1 all pair tersoff +compute 2 all pair ilp/graphene/hbn +compute 3 all pair coul/shield +variable REBO equal c_0 +variable Tersoff equal c_1 +variable EILP equal c_2 # total interlayer energy +variable Evdw equal c_2[1] # attractive energy +variable Erep equal c_2[2] # repulsive energy +variable Ecoul equal c_3 + +############# Output ############## thermo 100 -thermo_style custom step etotal pe ke v_Evdw v_Tersoff v_REBO v_EILP v_Ecoul temp v_adsxcom v_adsycom v_adszcom v_adsvxcom v_adsvycom v_adsvzcom +thermo_style custom step etotal pe ke v_Evdw v_Tersoff v_REBO v_EILP v_Erep v_Evdw v_Ecoul temp thermo_modify line one format float %.10f -#dump 1 all custom 1000 traj.lammpstrj id mol type xu yu zu -#dump_modify 1 format line "%7d %3d %3d %15.10g %15.10g %15.10g" flush yes - ###### Run molecular dynamics ###### -run 1000 +run 1000 diff --git a/examples/USER/misc/ilp_graphene_hbn/gr-hBN/log.5Jun19.grhBN.icc.1 b/examples/USER/misc/ilp_graphene_hbn/gr-hBN/log.5Jun19.grhBN.icc.1 new file mode 100644 index 0000000000..65e32502f0 --- /dev/null +++ b/examples/USER/misc/ilp_graphene_hbn/gr-hBN/log.5Jun19.grhBN.icc.1 @@ -0,0 +1,155 @@ +LAMMPS (5 Jun 2019) +OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (../comm.cpp:88) + using 1 OpenMP thread(s) per MPI task +# Initialization +units metal +boundary p p p +atom_style full +processors * * 1 # domain decomposition over x and y + +# System and atom definition +# we use different molecule ids for each layer +# so that inter- and intra-layer +# interactions can be specified separately +read_data gr_hBN_Cstack_2L_noH.data + orthogonal box = (0 0 0) to (44.583 42.9 100) + 1 by 1 by 1 MPI processor grid + reading atoms ... + 1440 atoms + 0 = max # of 1-2 neighbors + 0 = max # of 1-3 neighbors + 0 = max # of 1-4 neighbors + 1 = max # of special neighbors + special bonds CPU = 0.000152684 secs + read_data CPU = 0.00139584 secs +mass 1 10.8110 # boron mass (g/mole) | membrane +mass 2 14.0067 # nitrogen mass (g/mole) | membrane +mass 3 12.0107 # carbon mass (g/mole) | adsorbate +# Separate atom groups +group hBN molecule 1 +720 atoms in group hBN +group gr molecule 2 +720 atoms in group gr + +######################## Potential defition ######################## +pair_style hybrid/overlay rebo tersoff ilp/graphene/hbn 16.0 coul/shield 16.0 +#################################################################### +pair_coeff * * rebo CH.rebo NULL NULL C # chemical +Reading potential file CH.rebo with DATE: 2018-7-3 +pair_coeff * * tersoff BNC.tersoff B N NULL # chemical +Reading potential file BNC.tersoff with DATE: 2013-03-21 +pair_coeff * * ilp/graphene/hbn BNCH.ILP B N C # long range +pair_coeff 1 1 coul/shield 0.70 +pair_coeff 1 2 coul/shield 0.69498201415576216335 +pair_coeff 2 2 coul/shield 0.69 +#################################################################### +# Neighbor update settings +neighbor 2.0 bin +neigh_modify every 1 +neigh_modify delay 0 +neigh_modify check yes + +#### Simulation settings #### +timestep 0.001 +velocity all create 300.0 12345 dist gaussian mom yes rot yes +fix thermostat all nve + +compute 0 all pair rebo +compute 1 all pair tersoff +compute 2 all pair ilp/graphene/hbn +compute 3 all pair coul/shield +variable REBO equal c_0 +variable Tersoff equal c_1 +variable EILP equal c_2 # total interlayer energy +variable Evdw equal c_2[1] # attractive energy +variable Erep equal c_2[2] # repulsive energy +variable Ecoul equal c_3 + +############# Output ############## +thermo 100 +thermo_style custom step etotal pe ke v_Evdw v_Tersoff v_REBO v_EILP v_Erep v_Evdw v_Ecoul temp +thermo_modify line one format float %.10f + +###### Run molecular dynamics ###### +run 1000 +Neighbor list info ... + update every 1 steps, delay 0 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 18 + ghost atom cutoff = 18 + binsize = 9, bins = 5 5 12 + 6 neighbor lists, perpetual/occasional/extra = 6 0 0 + (1) pair rebo, perpetual, skip from (3) + attributes: full, newton on, ghost + pair build: skip/ghost + stencil: none + bin: none + (2) pair tersoff, perpetual, skip from (5) + attributes: full, newton on + pair build: skip + stencil: none + bin: none + (3) pair ilp/graphene/hbn, perpetual + attributes: full, newton on, ghost + pair build: full/bin/ghost + stencil: full/ghost/bin/3d + bin: standard + (4) pair coul/shield, perpetual, half/full from (2) + attributes: half, newton on + pair build: halffull/newton/skip + stencil: none + bin: none + (5) neighbor class addition, perpetual, copy from (3) + attributes: full, newton on + pair build: copy + stencil: none + bin: none + (6) neighbor class addition, perpetual, half/full from (5) + attributes: half, newton on + pair build: halffull/newton + stencil: none + bin: none +Per MPI rank memory allocation (min/avg/max) = 25.93 | 25.93 | 25.93 Mbytes +Step TotEng PotEng KinEng v_Evdw v_Tersoff v_REBO v_EILP v_Erep v_Evdw v_Ecoul Temp + 0 -10707.2836653377 -10763.0852699342 55.8016045965 -75.2477261362 -5401.7347845703 -5322.2780768034 -39.0724085605 36.1753175757 -75.2477261362 0.0000000000 300.0000000000 + 100 -10707.0738132278 -10737.1273434298 30.0535302020 -73.2173218622 -5389.9568321958 -5309.2004092412 -37.9701019928 35.2472198694 -73.2173218622 0.0000000000 161.5734731251 + 200 -10707.0160305531 -10734.9317906949 27.9157601418 -71.6030968581 -5389.1293717071 -5307.7455440517 -38.0568749361 33.5462219220 -71.6030968581 0.0000000000 150.0804162013 + 300 -10707.0133459577 -10734.9870508108 27.9737048532 -75.0821335395 -5388.9196081501 -5308.1164952096 -37.9509474511 37.1311860884 -75.0821335395 0.0000000000 150.3919379493 + 400 -10707.0118845924 -10735.4980560195 28.4861714271 -76.3398711857 -5389.1656629670 -5308.1529507210 -38.1794423315 38.1604288542 -76.3398711857 0.0000000000 153.1470553564 + 500 -10707.0073064907 -10734.6814074933 27.6741010026 -73.3123544614 -5388.7261058688 -5307.7383573628 -38.2169442617 35.0954101998 -73.3123544614 0.0000000000 148.7812108775 + 600 -10707.0179599067 -10735.8330915547 28.8151316481 -71.9277634955 -5389.0797599186 -5308.5959984739 -38.1573331622 33.7704303333 -71.9277634955 0.0000000000 154.9156078382 + 700 -10707.0202991119 -10735.6556762202 28.6353771083 -74.6793707186 -5389.2970704981 -5308.1866033124 -38.1720024097 36.5073683089 -74.6793707186 0.0000000000 153.9492133711 + 800 -10707.0042706783 -10734.3516957279 27.3474250495 -76.3712879764 -5388.5923210533 -5307.7206382682 -38.0387364064 38.3325515700 -76.3712879764 0.0000000000 147.0249390530 + 900 -10707.0144790011 -10735.8318835748 28.8174045738 -73.6993318112 -5388.9674133804 -5308.7963924816 -38.0680777128 35.6312540984 -73.6993318112 0.0000000000 154.9278275177 + 1000 -10706.9953891527 -10733.5615396283 26.5661504756 -71.4398677888 -5388.0186485439 -5307.4414386685 -38.1014524159 33.3384153730 -71.4398677888 0.0000000000 142.8246589021 +Loop time of 55.1175 on 1 procs for 1000 steps with 1440 atoms + +Performance: 1.568 ns/day, 15.310 hours/ns, 18.143 timesteps/s +100.0% CPU use with 1 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 55.062 | 55.062 | 55.062 | 0.0 | 99.90 +Bond | 0.00046717 | 0.00046717 | 0.00046717 | 0.0 | 0.00 +Neigh | 0 | 0 | 0 | 0.0 | 0.00 +Comm | 0.034313 | 0.034313 | 0.034313 | 0.0 | 0.06 +Output | 0.00034028 | 0.00034028 | 0.00034028 | 0.0 | 0.00 +Modify | 0.010012 | 0.010012 | 0.010012 | 0.0 | 0.02 +Other | | 0.01061 | | | 0.02 + +Nlocal: 1440 ave 1440 max 1440 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 8180 ave 8180 max 8180 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 140400 ave 140400 max 140400 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +FullNghs: 280800 ave 280800 max 280800 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 280800 +Ave neighs/atom = 195 +Ave special neighs/atom = 0 +Neighbor list builds = 0 +Dangerous builds = 0 +Total wall time: 0:00:55 diff --git a/examples/USER/misc/ilp_graphene_hbn/gr-hBN/log.5Jun19.grhBN.icc.4 b/examples/USER/misc/ilp_graphene_hbn/gr-hBN/log.5Jun19.grhBN.icc.4 new file mode 100644 index 0000000000..9ea23fb6e3 --- /dev/null +++ b/examples/USER/misc/ilp_graphene_hbn/gr-hBN/log.5Jun19.grhBN.icc.4 @@ -0,0 +1,155 @@ +LAMMPS (5 Jun 2019) +OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (../comm.cpp:88) + using 1 OpenMP thread(s) per MPI task +# Initialization +units metal +boundary p p p +atom_style full +processors * * 1 # domain decomposition over x and y + +# System and atom definition +# we use different molecule ids for each layer +# so that inter- and intra-layer +# interactions can be specified separately +read_data gr_hBN_Cstack_2L_noH.data + orthogonal box = (0 0 0) to (44.583 42.9 100) + 2 by 2 by 1 MPI processor grid + reading atoms ... + 1440 atoms + 0 = max # of 1-2 neighbors + 0 = max # of 1-3 neighbors + 0 = max # of 1-4 neighbors + 1 = max # of special neighbors + special bonds CPU = 0.000148868 secs + read_data CPU = 0.00332732 secs +mass 1 10.8110 # boron mass (g/mole) | membrane +mass 2 14.0067 # nitrogen mass (g/mole) | membrane +mass 3 12.0107 # carbon mass (g/mole) | adsorbate +# Separate atom groups +group hBN molecule 1 +720 atoms in group hBN +group gr molecule 2 +720 atoms in group gr + +######################## Potential defition ######################## +pair_style hybrid/overlay rebo tersoff ilp/graphene/hbn 16.0 coul/shield 16.0 +#################################################################### +pair_coeff * * rebo CH.rebo NULL NULL C # chemical +Reading potential file CH.rebo with DATE: 2018-7-3 +pair_coeff * * tersoff BNC.tersoff B N NULL # chemical +Reading potential file BNC.tersoff with DATE: 2013-03-21 +pair_coeff * * ilp/graphene/hbn BNCH.ILP B N C # long range +pair_coeff 1 1 coul/shield 0.70 +pair_coeff 1 2 coul/shield 0.69498201415576216335 +pair_coeff 2 2 coul/shield 0.69 +#################################################################### +# Neighbor update settings +neighbor 2.0 bin +neigh_modify every 1 +neigh_modify delay 0 +neigh_modify check yes + +#### Simulation settings #### +timestep 0.001 +velocity all create 300.0 12345 dist gaussian mom yes rot yes +fix thermostat all nve + +compute 0 all pair rebo +compute 1 all pair tersoff +compute 2 all pair ilp/graphene/hbn +compute 3 all pair coul/shield +variable REBO equal c_0 +variable Tersoff equal c_1 +variable EILP equal c_2 # total interlayer energy +variable Evdw equal c_2[1] # attractive energy +variable Erep equal c_2[2] # repulsive energy +variable Ecoul equal c_3 + +############# Output ############## +thermo 100 +thermo_style custom step etotal pe ke v_Evdw v_Tersoff v_REBO v_EILP v_Erep v_Evdw v_Ecoul temp +thermo_modify line one format float %.10f + +###### Run molecular dynamics ###### +run 1000 +Neighbor list info ... + update every 1 steps, delay 0 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 18 + ghost atom cutoff = 18 + binsize = 9, bins = 5 5 12 + 6 neighbor lists, perpetual/occasional/extra = 6 0 0 + (1) pair rebo, perpetual, skip from (3) + attributes: full, newton on, ghost + pair build: skip/ghost + stencil: none + bin: none + (2) pair tersoff, perpetual, skip from (5) + attributes: full, newton on + pair build: skip + stencil: none + bin: none + (3) pair ilp/graphene/hbn, perpetual + attributes: full, newton on, ghost + pair build: full/bin/ghost + stencil: full/ghost/bin/3d + bin: standard + (4) pair coul/shield, perpetual, half/full from (2) + attributes: half, newton on + pair build: halffull/newton/skip + stencil: none + bin: none + (5) neighbor class addition, perpetual, copy from (3) + attributes: full, newton on + pair build: copy + stencil: none + bin: none + (6) neighbor class addition, perpetual, half/full from (5) + attributes: half, newton on + pair build: halffull/newton + stencil: none + bin: none +Per MPI rank memory allocation (min/avg/max) = 14.25 | 14.25 | 14.25 Mbytes +Step TotEng PotEng KinEng v_Evdw v_Tersoff v_REBO v_EILP v_Erep v_Evdw v_Ecoul Temp + 0 -10707.2836653376 -10763.0852699341 55.8016045965 -75.2477261361 -5401.7347845703 -5322.2780768034 -39.0724085604 36.1753175757 -75.2477261361 0.0000000000 300.0000000000 + 100 -10707.0738132277 -10737.1273434298 30.0535302020 -73.2173218622 -5389.9568321958 -5309.2004092412 -37.9701019928 35.2472198694 -73.2173218622 0.0000000000 161.5734731251 + 200 -10707.0160305531 -10734.9317906949 27.9157601418 -71.6030968581 -5389.1293717071 -5307.7455440517 -38.0568749361 33.5462219220 -71.6030968581 0.0000000000 150.0804162013 + 300 -10707.0133459576 -10734.9870508108 27.9737048532 -75.0821335395 -5388.9196081501 -5308.1164952096 -37.9509474511 37.1311860885 -75.0821335395 0.0000000000 150.3919379493 + 400 -10707.0118845923 -10735.4980560194 28.4861714271 -76.3398711857 -5389.1656629669 -5308.1529507210 -38.1794423315 38.1604288542 -76.3398711857 0.0000000000 153.1470553564 + 500 -10707.0073064907 -10734.6814074932 27.6741010026 -73.3123544614 -5388.7261058688 -5307.7383573628 -38.2169442616 35.0954101998 -73.3123544614 0.0000000000 148.7812108775 + 600 -10707.0179599066 -10735.8330915547 28.8151316481 -71.9277634955 -5389.0797599186 -5308.5959984739 -38.1573331622 33.7704303333 -71.9277634955 0.0000000000 154.9156078382 + 700 -10707.0202991119 -10735.6556762202 28.6353771083 -74.6793707186 -5389.2970704981 -5308.1866033124 -38.1720024097 36.5073683089 -74.6793707186 0.0000000000 153.9492133711 + 800 -10707.0042706783 -10734.3516957278 27.3474250495 -76.3712879764 -5388.5923210533 -5307.7206382682 -38.0387364063 38.3325515701 -76.3712879764 0.0000000000 147.0249390530 + 900 -10707.0144790010 -10735.8318835748 28.8174045738 -73.6993318112 -5388.9674133804 -5308.7963924816 -38.0680777128 35.6312540984 -73.6993318112 0.0000000000 154.9278275177 + 1000 -10706.9953891527 -10733.5615396283 26.5661504756 -71.4398677888 -5388.0186485439 -5307.4414386685 -38.1014524158 33.3384153730 -71.4398677888 0.0000000000 142.8246589021 +Loop time of 15.7325 on 4 procs for 1000 steps with 1440 atoms + +Performance: 5.492 ns/day, 4.370 hours/ns, 63.563 timesteps/s +99.8% CPU use with 4 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 13.905 | 14.645 | 15.391 | 14.5 | 93.08 +Bond | 0.00029796 | 0.00040495 | 0.00046212 | 0.0 | 0.00 +Neigh | 0 | 0 | 0 | 0.0 | 0.00 +Comm | 0.3261 | 1.0722 | 1.8116 | 53.4 | 6.82 +Output | 0.00028242 | 0.00030932 | 0.00037515 | 0.0 | 0.00 +Modify | 0.0046079 | 0.0047365 | 0.0048651 | 0.2 | 0.03 +Other | | 0.01031 | | | 0.07 + +Nlocal: 360 ave 380 max 340 min +Histogram: 2 0 0 0 0 0 0 0 0 2 +Nghost: 4716 ave 4736 max 4696 min +Histogram: 2 0 0 0 0 0 0 0 0 2 +Neighs: 35100 ave 37050 max 33150 min +Histogram: 2 0 0 0 0 0 0 0 0 2 +FullNghs: 70200 ave 74100 max 66300 min +Histogram: 2 0 0 0 0 0 0 0 0 2 + +Total # of neighbors = 280800 +Ave neighs/atom = 195 +Ave special neighs/atom = 0 +Neighbor list builds = 0 +Dangerous builds = 0 +Total wall time: 0:00:15 diff --git a/src/USER-MISC/pair_ilp_graphene_hbn.cpp b/src/USER-MISC/pair_ilp_graphene_hbn.cpp index b94db6a871..a050f1f613 100644 --- a/src/USER-MISC/pair_ilp_graphene_hbn.cpp +++ b/src/USER-MISC/pair_ilp_graphene_hbn.cpp @@ -20,11 +20,12 @@ [Kolmogorov & Crespi, Phys. Rev. B 71, 235415 (2005)] ------------------------------------------------------------------------- */ -#include "pair_ilp_graphene_hbn.h" #include #include +#include #include #include +#include "pair_ilp_graphene_hbn.h" #include "atom.h" #include "comm.h" #include "force.h" @@ -48,6 +49,9 @@ PairILPGrapheneHBN::PairILPGrapheneHBN(LAMMPS *lmp) : Pair(lmp) restartinfo = 0; one_coeff = 1; + nextra = 2; + pvector = new double[nextra]; + // initialize element to parameter maps nelements = 0; elements = NULL; @@ -70,9 +74,7 @@ PairILPGrapheneHBN::PairILPGrapheneHBN(LAMMPS *lmp) : Pair(lmp) // always compute energy offset offset_flag = 1; - - // set comm size needed by this pair style - comm_forward = 39; + // turn on the taper function tap_flag = 1; } @@ -83,6 +85,7 @@ PairILPGrapheneHBN::~PairILPGrapheneHBN() memory->destroy(ILP_numneigh); memory->sfree(ILP_firstneigh); delete [] ipage; + delete [] pvector; memory->destroy(normal); memory->destroy(dnormal); memory->destroy(dnormdri); @@ -103,928 +106,991 @@ PairILPGrapheneHBN::~PairILPGrapheneHBN() if (allocated) delete [] map; } -/* ---------------------------------------------------------------------- */ +/* ---------------------------------------------------------------------- + allocate all arrays +------------------------------------------------------------------------- */ -void PairILPGrapheneHBN::compute(int eflag, int vflag) +void PairILPGrapheneHBN::allocate() { - int i,j,ii,jj,inum,jnum,itype,jtype,k,l,kk,ll; - tagint itag,jtag; - double prodnorm1,prodnorm2,fkcx,fkcy,fkcz; - double xtmp,ytmp,ztmp,delx,dely,delz,evdwl,fpair,fpair1,fpair2; - double rsq,r,Rcut,rhosq1,rhosq2,exp0,exp1,exp2,r2inv,r6inv,r8inv,Tap,dTap,Vilp; - double frho1,frho2,TSvdw,TSvdw2inv,Erep,fsum,rdsq1,rdsq2; - int *ilist,*jlist,*numneigh,**firstneigh; - int *ILP_neighs_i,*ILP_neighs_j; + allocated = 1; + int n = atom->ntypes; - evdwl = 0.0; - ev_init(eflag,vflag); + memory->create(setflag,n+1,n+1,"pair:setflag"); + for (int i = 1; i <= n; i++) + for (int j = i; j <= n; j++) + setflag[i][j] = 0; - double **x = atom->x; - double **f = atom->f; - int *type = atom->type; - tagint *tag = atom->tag; - int nlocal = atom->nlocal; - int newton_pair = force->newton_pair; - double dprodnorm1[3] = {0.0, 0.0, 0.0}; - double dprodnorm2[3] = {0.0, 0.0, 0.0}; - double fp1[3] = {0.0, 0.0, 0.0}; - double fp2[3] = {0.0, 0.0, 0.0}; - double fprod1[3] = {0.0, 0.0, 0.0}; - double fprod2[3] = {0.0, 0.0, 0.0}; - double fk[3] = {0.0, 0.0, 0.0}; - double fl[3] = {0.0, 0.0, 0.0}; - double delkj[3] = {0.0, 0.0, 0.0}; - double delli[3] = {0.0, 0.0, 0.0}; + memory->create(cutsq,n+1,n+1,"pair:cutsq"); + memory->create(cut,n+1,n+1,"pair:cut"); + memory->create(offset,n+1,n+1,"pair:offset"); + map = new int[atom->ntypes+1]; +} - inum = list->inum; - ilist = list->ilist; - numneigh = list->numneigh; - firstneigh = list->firstneigh; - // Build full neighbor list - ILP_neigh(); - // Calculate the normals - calc_normal(); +/* ---------------------------------------------------------------------- + global settings +------------------------------------------------------------------------- */ - // communicate the normal vector and its derivatives - comm->forward_comm_pair(this); +void PairILPGrapheneHBN::settings(int narg, char **arg) +{ + if (narg < 1 || narg > 2) error->all(FLERR,"Illegal pair_style command"); + if (strcmp(force->pair_style,"hybrid/overlay")!=0) + error->all(FLERR,"ERROR: requires hybrid/overlay pair_style"); - // loop over neighbors of my atoms - for (ii = 0; ii < inum; ii++) { - i = ilist[ii]; - itag = tag[i]; - xtmp = x[i][0]; - ytmp = x[i][1]; - ztmp = x[i][2]; - itype = type[i]; - jlist = firstneigh[i]; - jnum = numneigh[i]; + cut_global = force->numeric(FLERR,arg[0]); + if (narg == 2) tap_flag = force->numeric(FLERR,arg[1]); - for (jj = 0; jj < jnum; jj++) { - j = jlist[jj]; - j &= NEIGHMASK; - jtype = type[j]; - jtag = tag[j]; + // reset cutoffs that have been explicitly set - // two-body interactions from full neighbor list, skip half of them - if (itag > jtag) { - if ((itag+jtag) % 2 == 0) continue; - } else if (itag < jtag) { - if ((itag+jtag) % 2 == 1) continue; - } else { - if (x[j][2] < ztmp) continue; - if (x[j][2] == ztmp && x[j][1] < ytmp) continue; - if (x[j][2] == ztmp && x[j][1] == ytmp && x[j][0] < xtmp) continue; - } + if (allocated) { + int i,j; + for (i = 1; i <= atom->ntypes; i++) + for (j = i; j <= atom->ntypes; j++) + if (setflag[i][j]) cut[i][j] = cut_global; + } +} - delx = xtmp - x[j][0]; - dely = ytmp - x[j][1]; - delz = ztmp - x[j][2]; - rsq = delx*delx + dely*dely + delz*delz; +/* ---------------------------------------------------------------------- + set coeffs for one or more type pairs +------------------------------------------------------------------------- */ - // only include the interation between different layers - if (rsq < cutsq[itype][jtype] && atom->molecule[i] != atom->molecule[j]) { +void PairILPGrapheneHBN::coeff(int narg, char **arg) +{ + int i,j,n; - int iparam_ij = elem2param[map[itype]][map[jtype]]; - Param& p = params[iparam_ij]; + if (narg != 3 + atom->ntypes) + error->all(FLERR,"Incorrect args for pair coefficients"); + if (!allocated) allocate(); - r = sqrt(rsq); - r2inv = 1.0/rsq; - r6inv = r2inv*r2inv*r2inv; - r8inv = r6inv*r2inv; - // turn on/off taper function - if (tap_flag) { - Rcut = sqrt(cutsq[itype][jtype]); - Tap = calc_Tap(r,Rcut); - dTap = calc_dTap(r,Rcut); - } else {Tap = 1.0; dTap = 0.0;} + // insure I,J args are * * - // Calculate the transverse distance - // note that rho_ij does not equal to rho_ji except when normals are all along z - prodnorm1 = normal[i][0]*delx + normal[i][1]*dely + normal[i][2]*delz; - prodnorm2 = normal[j][0]*delx + normal[j][1]*dely + normal[j][2]*delz; - rhosq1 = rsq - prodnorm1*prodnorm1; // rho_ij - rhosq2 = rsq - prodnorm2*prodnorm2; // rho_ji - rdsq1 = rhosq1*p.delta2inv; // (rho_ij/delta)^2 - rdsq2 = rhosq2*p.delta2inv; // (rho_ji/delta)^2 + if (strcmp(arg[0],"*") != 0 || strcmp(arg[1],"*") != 0) + error->all(FLERR,"Incorrect args for pair coefficients"); - // store exponents - exp0 = exp(-p.lambda*(r-p.z0)); - exp1 = exp(-rdsq1); - exp2 = exp(-rdsq2); + // read args that map atom types to elements in potential file + // map[i] = which element the Ith atom type is, -1 if NULL + // nelements = # of unique elements + // elements = list of element names - TSvdw = 1.0 + exp(-p.d*(r/p.seff - 1.0)); - TSvdw2inv = 1.0/pow(TSvdw,2.0); - frho1 = exp1*p.C; - frho2 = exp2*p.C; - Erep = p.epsilon + frho1 + frho2; - Vilp = -p.C6*r6inv/TSvdw + exp0*Erep; + if (elements) { + for (i = 0; i < nelements; i++) delete [] elements[i]; + delete [] elements; + } + elements = new char*[atom->ntypes]; + for (i = 0; i < atom->ntypes; i++) elements[i] = NULL; - // derivatives - fpair = -6.0*p.C6*r8inv/TSvdw + p.d/p.seff*p.C6*(TSvdw-1.0)*TSvdw2inv*r8inv*r + p.lambda*exp0/r*Erep; - fpair1 = 2.0*exp0*frho1*p.delta2inv; - fpair2 = 2.0*exp0*frho2*p.delta2inv; - fsum = fpair + fpair1 + fpair2; - // derivatives of the product of rij and ni, the result is a vector - dprodnorm1[0] = dnormdri[0][0][i]*delx + dnormdri[1][0][i]*dely + dnormdri[2][0][i]*delz; - dprodnorm1[1] = dnormdri[0][1][i]*delx + dnormdri[1][1][i]*dely + dnormdri[2][1][i]*delz; - dprodnorm1[2] = dnormdri[0][2][i]*delx + dnormdri[1][2][i]*dely + dnormdri[2][2][i]*delz; - // derivatives of the product of rji and nj, the result is a vector - dprodnorm2[0] = dnormdri[0][0][j]*delx + dnormdri[1][0][j]*dely + dnormdri[2][0][j]*delz; - dprodnorm2[1] = dnormdri[0][1][j]*delx + dnormdri[1][1][j]*dely + dnormdri[2][1][j]*delz; - dprodnorm2[2] = dnormdri[0][2][j]*delx + dnormdri[1][2][j]*dely + dnormdri[2][2][j]*delz; - fp1[0] = prodnorm1*normal[i][0]*fpair1; - fp1[1] = prodnorm1*normal[i][1]*fpair1; - fp1[2] = prodnorm1*normal[i][2]*fpair1; - fp2[0] = prodnorm2*normal[j][0]*fpair2; - fp2[1] = prodnorm2*normal[j][1]*fpair2; - fp2[2] = prodnorm2*normal[j][2]*fpair2; - fprod1[0] = prodnorm1*dprodnorm1[0]*fpair1; - fprod1[1] = prodnorm1*dprodnorm1[1]*fpair1; - fprod1[2] = prodnorm1*dprodnorm1[2]*fpair1; - fprod2[0] = prodnorm2*dprodnorm2[0]*fpair2; - fprod2[1] = prodnorm2*dprodnorm2[1]*fpair2; - fprod2[2] = prodnorm2*dprodnorm2[2]*fpair2; - fkcx = (delx*fsum - fp1[0] - fp2[0])*Tap - Vilp*dTap*delx/r; - fkcy = (dely*fsum - fp1[1] - fp2[1])*Tap - Vilp*dTap*dely/r; - fkcz = (delz*fsum - fp1[2] - fp2[2])*Tap - Vilp*dTap*delz/r; + nelements = 0; + for (i = 3; i < narg; i++) { + if (strcmp(arg[i],"NULL") == 0) { + map[i-2] = -1; + continue; + } + for (j = 0; j < nelements; j++) + if (strcmp(arg[i],elements[j]) == 0) break; + map[i-2] = j; + if (j == nelements) { + n = strlen(arg[i]) + 1; + elements[j] = new char[n]; + strcpy(elements[j],arg[i]); + nelements++; + } + } - f[i][0] += fkcx - fprod1[0]*Tap; - f[i][1] += fkcy - fprod1[1]*Tap; - f[i][2] += fkcz - fprod1[2]*Tap; - f[j][0] -= fkcx + fprod2[0]*Tap; - f[j][1] -= fkcy + fprod2[1]*Tap; - f[j][2] -= fkcz + fprod2[2]*Tap; - // calculate the forces acted on the neighbors of atom i from atom j - ILP_neighs_i = ILP_firstneigh[i]; - for (kk = 0; kk < ILP_numneigh[i]; kk++) { - k = ILP_neighs_i[kk]; - if (k == i) continue; - // derivatives of the product of rij and ni respect to rk, k=0,1,2, where atom k is the neighbors of atom i - dprodnorm1[0] = dnormal[0][0][kk][i]*delx + dnormal[1][0][kk][i]*dely + dnormal[2][0][kk][i]*delz; - dprodnorm1[1] = dnormal[0][1][kk][i]*delx + dnormal[1][1][kk][i]*dely + dnormal[2][1][kk][i]*delz; - dprodnorm1[2] = dnormal[0][2][kk][i]*delx + dnormal[1][2][kk][i]*dely + dnormal[2][2][kk][i]*delz; - fk[0] = (-prodnorm1*dprodnorm1[0]*fpair1)*Tap; - fk[1] = (-prodnorm1*dprodnorm1[1]*fpair1)*Tap; - fk[2] = (-prodnorm1*dprodnorm1[2]*fpair1)*Tap; - f[k][0] += fk[0]; - f[k][1] += fk[1]; - f[k][2] += fk[2]; - delkj[0] = x[k][0] - x[j][0]; - delkj[1] = x[k][1] - x[j][1]; - delkj[2] = x[k][2] - x[j][2]; - if (evflag) ev_tally_xyz(k,j,nlocal,newton_pair,0.0,0.0,fk[0],fk[1],fk[2],delkj[0],delkj[1],delkj[2]); - } + read_file(arg[2]); - // calculate the forces acted on the neighbors of atom j from atom i - ILP_neighs_j = ILP_firstneigh[j]; - for (ll = 0; ll < ILP_numneigh[j]; ll++) { - l = ILP_neighs_j[ll]; - if (l == j) continue; - // derivatives of the product of rji and nj respect to rl, l=0,1,2, where atom l is the neighbors of atom j - dprodnorm2[0] = dnormal[0][0][ll][j]*delx + dnormal[1][0][ll][j]*dely + dnormal[2][0][ll][j]*delz; - dprodnorm2[1] = dnormal[0][1][ll][j]*delx + dnormal[1][1][ll][j]*dely + dnormal[2][1][ll][j]*delz; - dprodnorm2[2] = dnormal[0][2][ll][j]*delx + dnormal[1][2][ll][j]*dely + dnormal[2][2][ll][j]*delz; - fl[0] = (-prodnorm2*dprodnorm2[0]*fpair2)*Tap; - fl[1] = (-prodnorm2*dprodnorm2[1]*fpair2)*Tap; - fl[2] = (-prodnorm2*dprodnorm2[2]*fpair2)*Tap; - f[l][0] += fl[0]; - f[l][1] += fl[1]; - f[l][2] += fl[2]; - delli[0] = x[l][0] - x[i][0]; - delli[1] = x[l][1] - x[i][1]; - delli[2] = x[l][2] - x[i][2]; - if (evflag) ev_tally_xyz(l,i,nlocal,newton_pair,0.0,0.0,fl[0],fl[1],fl[2],delli[0],delli[1],delli[2]); - } + // clear setflag since coeff() called once with I,J = * * - if (eflag) { - if (tap_flag) evdwl = Tap*Vilp; - else evdwl = Vilp - offset[itype][jtype]; - } + n = atom->ntypes; + for (int i = 1; i <= n; i++) + for (int j = i; j <= n; j++) + setflag[i][j] = 0; - if (evflag) ev_tally_xyz(i,j,nlocal,newton_pair,evdwl,0.0,fkcx,fkcy,fkcz,delx,dely,delz); + // set setflag i,j for type pairs where both are mapped to elements + + int count = 0; + for (int i = 1; i <= n; i++) + for (int j = i; j <= n; j++) + if (map[i] >= 0 && map[j] >= 0) { + setflag[i][j] = 1; + cut[i][j] = cut_global; + count++; } - } - } - if (vflag_fdotr) virial_fdotr_compute(); + + if (count == 0) error->all(FLERR,"Incorrect args for pair coefficients"); } + /* ---------------------------------------------------------------------- - Calculate the normals for each atom + init for one type pair i,j and corresponding j,i ------------------------------------------------------------------------- */ -void PairILPGrapheneHBN::calc_normal() -{ - int i,j,ii,jj,inum,jnum; - int cont,id,ip,m; - double nn,xtp,ytp,ztp,delx,dely,delz,nn2; - int *ilist,*jlist; - double pv12[3],pv31[3],pv23[3],n1[3],dni[3],dnn[3][3],vet[3][3],dpvdri[3][3]; - double dn1[3][3][3],dpv12[3][3][3],dpv23[3][3][3],dpv31[3][3][3]; - double **x = atom->x; +double PairILPGrapheneHBN::init_one(int i, int j) +{ + if (setflag[i][j] == 0) error->all(FLERR,"All pair coeffs are not set"); + if (!offset_flag) + error->all(FLERR,"Must use 'pair_modify shift yes' with this pair style"); - // grow normal array if necessary + if (offset_flag && (cut[i][j] > 0.0)) { + int iparam_ij = elem2param[map[i]][map[j]]; + Param& p = params[iparam_ij]; + offset[i][j] = -p.C6*pow(1.0/cut[i][j],6)/(1.0 + exp(-p.d*(cut[i][j]/p.seff - 1.0))); + } else offset[i][j] = 0.0; + offset[j][i] = offset[i][j]; - if (atom->nmax > nmax) { - memory->destroy(normal); - memory->destroy(dnormal); - memory->destroy(dnormdri); - nmax = atom->nmax; - memory->create(normal,nmax,3,"ILPGrapheneHBN:normal"); - memory->create(dnormdri,3,3,nmax,"ILPGrapheneHBN:dnormdri"); - memory->create(dnormal,3,3,3,nmax,"ILPGrapheneHBN:dnormal"); - } + return cut[i][j]; +} - inum = list->inum; - ilist = list->ilist; - //Calculate normals - for (ii = 0; ii < inum; ii++) { - i = ilist[ii]; - xtp = x[i][0]; - ytp = x[i][1]; - ztp = x[i][2]; +/* ---------------------------------------------------------------------- + read Interlayer potential file +------------------------------------------------------------------------- */ - // Initialize the arrays - for (id = 0; id < 3; id++){ - pv12[id] = 0.0; - pv31[id] = 0.0; - pv23[id] = 0.0; - n1[id] = 0.0; - dni[id] = 0.0; - normal[i][id] = 0.0; - for (ip = 0; ip < 3; ip++){ - vet[ip][id] = 0.0; - dnn[ip][id] = 0.0; - dpvdri[ip][id] = 0.0; - dnormdri[ip][id][i] = 0.0; - for (m = 0; m < 3; m++){ - dpv12[ip][id][m] = 0.0; - dpv31[ip][id][m] = 0.0; - dpv23[ip][id][m] = 0.0; - dn1[ip][id][m] = 0.0; - dnormal[ip][id][m][i] = 0.0; - } - } - } +void PairILPGrapheneHBN::read_file(char *filename) +{ + int params_per_line = 13; + char **words = new char*[params_per_line+1]; + memory->sfree(params); + params = NULL; + nparams = maxparam = 0; - cont = 0; - jlist = ILP_firstneigh[i]; - jnum = ILP_numneigh[i]; - for (jj = 0; jj < jnum; jj++) { - j = jlist[jj]; - j &= NEIGHMASK; + // open file on proc 0 - delx = x[j][0] - xtp; - dely = x[j][1] - ytp; - delz = x[j][2] - ztp; - vet[cont][0] = delx; - vet[cont][1] = dely; - vet[cont][2] = delz; - cont++; + FILE *fp; + if (comm->me == 0) { + fp = force->open_potential(filename); + if (fp == NULL) { + char str[128]; + snprintf(str,128,"Cannot open ILP potential file %s",filename); + error->one(FLERR,str); } + } - if (cont <= 1) { - normal[i][0] = 0.0; - normal[i][1] = 0.0; - normal[i][2] = 1.0; - for (id = 0; id < 3; id++){ - for (ip = 0; ip < 3; ip++){ - dnormdri[id][ip][i] = 0.0; - for (m = 0; m < 3; m++){ - dnormal[id][ip][m][i] = 0.0; - } - } - } + // read each line out of file, skipping blank lines or leading '#' + // store line of params if all 3 element tags are in element list + + int i,j,n,m,nwords,ielement,jelement; + char line[MAXLINE],*ptr; + int eof = 0; + + while (1) { + if (comm->me == 0) { + ptr = fgets(line,MAXLINE,fp); + if (ptr == NULL) { + eof = 1; + fclose(fp); + } else n = strlen(line) + 1; } - else if (cont == 2) { - pv12[0] = vet[0][1]*vet[1][2] - vet[1][1]*vet[0][2]; - pv12[1] = vet[0][2]*vet[1][0] - vet[1][2]*vet[0][0]; - pv12[2] = vet[0][0]*vet[1][1] - vet[1][0]*vet[0][1]; - // derivatives of pv12[0] to ri - dpvdri[0][0] = 0.0; - dpvdri[0][1] = vet[0][2]-vet[1][2]; - dpvdri[0][2] = vet[1][1]-vet[0][1]; - // derivatives of pv12[1] to ri - dpvdri[1][0] = vet[1][2]-vet[0][2]; - dpvdri[1][1] = 0.0; - dpvdri[1][2] = vet[0][0]-vet[1][0]; - // derivatives of pv12[2] to ri - dpvdri[2][0] = vet[0][1]-vet[1][1]; - dpvdri[2][1] = vet[1][0]-vet[0][0]; - dpvdri[2][2] = 0.0; + MPI_Bcast(&eof,1,MPI_INT,0,world); + if (eof) break; + MPI_Bcast(&n,1,MPI_INT,0,world); + MPI_Bcast(line,n,MPI_CHAR,0,world); - dpv12[0][0][0] = 0.0; - dpv12[0][1][0] = vet[1][2]; - dpv12[0][2][0] = -vet[1][1]; - dpv12[1][0][0] = -vet[1][2]; - dpv12[1][1][0] = 0.0; - dpv12[1][2][0] = vet[1][0]; - dpv12[2][0][0] = vet[1][1]; - dpv12[2][1][0] = -vet[1][0]; - dpv12[2][2][0] = 0.0; + // strip comment, skip line if blank - // derivatives respect to the second neighbor, atom l - dpv12[0][0][1] = 0.0; - dpv12[0][1][1] = -vet[0][2]; - dpv12[0][2][1] = vet[0][1]; - dpv12[1][0][1] = vet[0][2]; - dpv12[1][1][1] = 0.0; - dpv12[1][2][1] = -vet[0][0]; - dpv12[2][0][1] = -vet[0][1]; - dpv12[2][1][1] = vet[0][0]; - dpv12[2][2][1] = 0.0; + if ((ptr = strchr(line,'#'))) *ptr = '\0'; + nwords = atom->count_words(line); + if (nwords == 0) continue; - // derivatives respect to the third neighbor, atom n - // derivatives of pv12 to rn is zero - for (id = 0; id < 3; id++){ - for (ip = 0; ip < 3; ip++){ - dpv12[id][ip][2] = 0.0; - } - } + // concatenate additional lines until have params_per_line words - n1[0] = pv12[0]; - n1[1] = pv12[1]; - n1[2] = pv12[2]; - // the magnitude of the normal vector - nn2 = n1[0]*n1[0] + n1[1]*n1[1] + n1[2]*n1[2]; - nn = sqrt(nn2); - if (nn == 0) error->one(FLERR,"The magnitude of the normal vector is zero"); - // the unit normal vector - normal[i][0] = n1[0]/nn; - normal[i][1] = n1[1]/nn; - normal[i][2] = n1[2]/nn; - // derivatives of nn, dnn:3x1 vector - dni[0] = (n1[0]*dpvdri[0][0] + n1[1]*dpvdri[1][0] + n1[2]*dpvdri[2][0])/nn; - dni[1] = (n1[0]*dpvdri[0][1] + n1[1]*dpvdri[1][1] + n1[2]*dpvdri[2][1])/nn; - dni[2] = (n1[0]*dpvdri[0][2] + n1[1]*dpvdri[1][2] + n1[2]*dpvdri[2][2])/nn; - // derivatives of unit vector ni respect to ri, the result is 3x3 matrix - for (id = 0; id < 3; id++){ - for (ip = 0; ip < 3; ip++){ - dnormdri[id][ip][i] = dpvdri[id][ip]/nn - n1[id]*dni[ip]/nn2; - } - } - // derivatives of non-normalized normal vector, dn1:3x3x3 array - for (id = 0; id < 3; id++){ - for (ip = 0; ip < 3; ip++){ - for (m = 0; m < 3; m++){ - dn1[id][ip][m] = dpv12[id][ip][m]; - } - } - } - // derivatives of nn, dnn:3x3 vector - // dnn[id][m]: the derivative of nn respect to r[id][m], id,m=0,1,2 - // r[id][m]: the id's component of atom m - for (m = 0; m < 3; m++){ - for (id = 0; id < 3; id++){ - dnn[id][m] = (n1[0]*dn1[0][id][m] + n1[1]*dn1[1][id][m] + n1[2]*dn1[2][id][m])/nn; - } - } - // dnormal[id][ip][m][i]: the derivative of normal[id] respect to r[ip][m], id,ip=0,1,2 - // for atom m, which is a neighbor atom of atom i, m=0,jnum-1 - for (m = 0; m < 3; m++){ - for (id = 0; id < 3; id++){ - for (ip = 0; ip < 3; ip++){ - dnormal[id][ip][m][i] = dn1[id][ip][m]/nn - n1[id]*dnn[ip][m]/nn2; - } - } + while (nwords < params_per_line) { + n = strlen(line); + if (comm->me == 0) { + ptr = fgets(&line[n],MAXLINE-n,fp); + if (ptr == NULL) { + eof = 1; + fclose(fp); + } else n = strlen(line) + 1; } + MPI_Bcast(&eof,1,MPI_INT,0,world); + if (eof) break; + MPI_Bcast(&n,1,MPI_INT,0,world); + MPI_Bcast(line,n,MPI_CHAR,0,world); + if ((ptr = strchr(line,'#'))) *ptr = '\0'; + nwords = atom->count_words(line); } -//############################################################################################## - else if(cont == 3) { - pv12[0] = vet[0][1]*vet[1][2] - vet[1][1]*vet[0][2]; - pv12[1] = vet[0][2]*vet[1][0] - vet[1][2]*vet[0][0]; - pv12[2] = vet[0][0]*vet[1][1] - vet[1][0]*vet[0][1]; - // derivatives respect to the first neighbor, atom k - dpv12[0][0][0] = 0.0; - dpv12[0][1][0] = vet[1][2]; - dpv12[0][2][0] = -vet[1][1]; - dpv12[1][0][0] = -vet[1][2]; - dpv12[1][1][0] = 0.0; - dpv12[1][2][0] = vet[1][0]; - dpv12[2][0][0] = vet[1][1]; - dpv12[2][1][0] = -vet[1][0]; - dpv12[2][2][0] = 0.0; - // derivatives respect to the second neighbor, atom l - dpv12[0][0][1] = 0.0; - dpv12[0][1][1] = -vet[0][2]; - dpv12[0][2][1] = vet[0][1]; - dpv12[1][0][1] = vet[0][2]; - dpv12[1][1][1] = 0.0; - dpv12[1][2][1] = -vet[0][0]; - dpv12[2][0][1] = -vet[0][1]; - dpv12[2][1][1] = vet[0][0]; - dpv12[2][2][1] = 0.0; + if (nwords != params_per_line) + error->all(FLERR,"Insufficient format in ILP potential file"); - // derivatives respect to the third neighbor, atom n - for (id = 0; id < 3; id++){ - for (ip = 0; ip < 3; ip++){ - dpv12[id][ip][2] = 0.0; - } - } + // words = ptrs to all words in line - pv31[0] = vet[2][1]*vet[0][2] - vet[0][1]*vet[2][2]; - pv31[1] = vet[2][2]*vet[0][0] - vet[0][2]*vet[2][0]; - pv31[2] = vet[2][0]*vet[0][1] - vet[0][0]*vet[2][1]; - // derivatives respect to the first neighbor, atom k - dpv31[0][0][0] = 0.0; - dpv31[0][1][0] = -vet[2][2]; - dpv31[0][2][0] = vet[2][1]; - dpv31[1][0][0] = vet[2][2]; - dpv31[1][1][0] = 0.0; - dpv31[1][2][0] = -vet[2][0]; - dpv31[2][0][0] = -vet[2][1]; - dpv31[2][1][0] = vet[2][0]; - dpv31[2][2][0] = 0.0; - // derivatives respect to the third neighbor, atom n - dpv31[0][0][2] = 0.0; - dpv31[0][1][2] = vet[0][2]; - dpv31[0][2][2] = -vet[0][1]; - dpv31[1][0][2] = -vet[0][2]; - dpv31[1][1][2] = 0.0; - dpv31[1][2][2] = vet[0][0]; - dpv31[2][0][2] = vet[0][1]; - dpv31[2][1][2] = -vet[0][0]; - dpv31[2][2][2] = 0.0; - // derivatives respect to the second neighbor, atom l - for (id = 0; id < 3; id++){ - for (ip = 0; ip < 3; ip++){ - dpv31[id][ip][1] = 0.0; - } - } + nwords = 0; + words[nwords++] = strtok(line," \t\n\r\f"); + while ((words[nwords++] = strtok(NULL," \t\n\r\f"))) continue; - pv23[0] = vet[1][1]*vet[2][2] - vet[2][1]*vet[1][2]; - pv23[1] = vet[1][2]*vet[2][0] - vet[2][2]*vet[1][0]; - pv23[2] = vet[1][0]*vet[2][1] - vet[2][0]*vet[1][1]; - // derivatives respect to the second neighbor, atom k - for (id = 0; id < 3; id++){ - for (ip = 0; ip < 3; ip++){ - dpv23[id][ip][0] = 0.0; - } - } - // derivatives respect to the second neighbor, atom l - dpv23[0][0][1] = 0.0; - dpv23[0][1][1] = vet[2][2]; - dpv23[0][2][1] = -vet[2][1]; - dpv23[1][0][1] = -vet[2][2]; - dpv23[1][1][1] = 0.0; - dpv23[1][2][1] = vet[2][0]; - dpv23[2][0][1] = vet[2][1]; - dpv23[2][1][1] = -vet[2][0]; - dpv23[2][2][1] = 0.0; - // derivatives respect to the third neighbor, atom n - dpv23[0][0][2] = 0.0; - dpv23[0][1][2] = -vet[1][2]; - dpv23[0][2][2] = vet[1][1]; - dpv23[1][0][2] = vet[1][2]; - dpv23[1][1][2] = 0.0; - dpv23[1][2][2] = -vet[1][0]; - dpv23[2][0][2] = -vet[1][1]; - dpv23[2][1][2] = vet[1][0]; - dpv23[2][2][2] = 0.0; + // ielement,jelement = 1st args + // if these 2 args are in element list, then parse this line + // else skip to next line (continue) -//############################################################################################ - // average the normal vectors by using the 3 neighboring planes - n1[0] = (pv12[0] + pv31[0] + pv23[0])/cont; - n1[1] = (pv12[1] + pv31[1] + pv23[1])/cont; - n1[2] = (pv12[2] + pv31[2] + pv23[2])/cont; - // the magnitude of the normal vector - nn2 = n1[0]*n1[0] + n1[1]*n1[1] + n1[2]*n1[2]; - nn = sqrt(nn2); - if (nn == 0) error->one(FLERR,"The magnitude of the normal vector is zero"); - // the unit normal vector - normal[i][0] = n1[0]/nn; - normal[i][1] = n1[1]/nn; - normal[i][2] = n1[2]/nn; + for (ielement = 0; ielement < nelements; ielement++) + if (strcmp(words[0],elements[ielement]) == 0) break; + if (ielement == nelements) continue; + for (jelement = 0; jelement < nelements; jelement++) + if (strcmp(words[1],elements[jelement]) == 0) break; + if (jelement == nelements) continue; - // for the central atoms, dnormdri is always zero - for (id = 0; id < 3; id++){ - for (ip = 0; ip < 3; ip++){ - dnormdri[id][ip][i] = 0.0; - } - } + // load up parameter settings and error check their values - // derivatives of non-normalized normal vector, dn1:3x3x3 array - for (id = 0; id < 3; id++){ - for (ip = 0; ip < 3; ip++){ - for (m = 0; m < 3; m++){ - dn1[id][ip][m] = (dpv12[id][ip][m] + dpv23[id][ip][m] + dpv31[id][ip][m])/cont; - } - } - } - // derivatives of nn, dnn:3x3 vector - // dnn[id][m]: the derivative of nn respect to r[id][m], id,m=0,1,2 - // r[id][m]: the id's component of atom m - for (m = 0; m < 3; m++){ - for (id = 0; id < 3; id++){ - dnn[id][m] = (n1[0]*dn1[0][id][m] + n1[1]*dn1[1][id][m] + n1[2]*dn1[2][id][m])/nn; - } - } - // dnormal[id][ip][m][i]: the derivative of normal[id] respect to r[ip][m], id,ip=0,1,2 - // for atom m, which is a neighbor atom of atom i, m=0,jnum-1 - for (m = 0; m < 3; m++){ - for (id = 0; id < 3; id++){ - for (ip = 0; ip < 3; ip++){ - dnormal[id][ip][m][i] = dn1[id][ip][m]/nn - n1[id]*dnn[ip][m]/nn2; - } + if (nparams == maxparam) { + maxparam += DELTA; + params = (Param *) memory->srealloc(params,maxparam*sizeof(Param), + "pair:params"); + } + + params[nparams].ielement = ielement; + params[nparams].jelement = jelement; + params[nparams].z0 = atof(words[2]); + params[nparams].alpha = atof(words[3]); + params[nparams].delta = atof(words[4]); + params[nparams].epsilon = atof(words[5]); + params[nparams].C = atof(words[6]); + params[nparams].d = atof(words[7]); + params[nparams].sR = atof(words[8]); + params[nparams].reff = atof(words[9]); + params[nparams].C6 = atof(words[10]); + // S provides a convenient scaling of all energies + params[nparams].S = atof(words[11]); + params[nparams].rcut = atof(words[12]); + + // energies in meV further scaled by S + // S = 43.3634 meV = 1 kcal/mol + double meV = 1e-3*params[nparams].S; + params[nparams].C *= meV; + params[nparams].C6 *= meV; + params[nparams].epsilon *= meV; + + // precompute some quantities + params[nparams].delta2inv = pow(params[nparams].delta,-2.0); + params[nparams].lambda = params[nparams].alpha/params[nparams].z0; + params[nparams].seff = params[nparams].sR * params[nparams].reff; + + nparams++; + } + memory->destroy(elem2param); + memory->destroy(cutILPsq); + memory->create(elem2param,nelements,nelements,"pair:elem2param"); + memory->create(cutILPsq,nelements,nelements,"pair:cutILPsq"); + for (i = 0; i < nelements; i++) { + for (j = 0; j < nelements; j++) { + n = -1; + for (m = 0; m < nparams; m++) { + if (i == params[m].ielement && j == params[m].jelement) { + if (n >= 0) error->all(FLERR,"Potential file has duplicate entry"); + n = m; } } + if (n < 0) error->all(FLERR,"Potential file is missing an entry"); + elem2param[i][j] = n; + cutILPsq[i][j] = params[n].rcut*params[n].rcut; } - else { - error->one(FLERR,"There are too many neighbors for calculating normals"); - } + } + delete [] words; +} -//############################################################################################## +/* ---------------------------------------------------------------------- + init specific to this pair style +------------------------------------------------------------------------- */ + +void PairILPGrapheneHBN::init_style() +{ + if (force->newton_pair == 0) + error->all(FLERR,"Pair style ilp/graphene/hbn requires newton pair on"); + if (!atom->molecule_flag) + error->all(FLERR,"Pair style ilp/graphene/hbn requires atom attribute molecule"); + + // need a full neighbor list, including neighbors of ghosts + + int irequest = neighbor->request(this,instance_me); + neighbor->requests[irequest]->half = 0; + neighbor->requests[irequest]->full = 1; + neighbor->requests[irequest]->ghost = 1; + + // local ILP neighbor list + // create pages if first time or if neighbor pgsize/oneatom has changed + + int create = 0; + if (ipage == NULL) create = 1; + if (pgsize != neighbor->pgsize) create = 1; + if (oneatom != neighbor->oneatom) create = 1; + + if (create) { + delete [] ipage; + pgsize = neighbor->pgsize; + oneatom = neighbor->oneatom; + + int nmypage= comm->nthreads; + ipage = new MyPage[nmypage]; + for (int i = 0; i < nmypage; i++) + ipage[i].init(oneatom,pgsize,PGDELTA); } } -/* ---------------------------------------------------------------------- - init specific to this pair style -------------------------------------------------------------------------- */ +/* ---------------------------------------------------------------------- */ +void PairILPGrapheneHBN::compute(int eflag, int vflag) +{ + ev_init(eflag,vflag); + pvector[0] = pvector[1] = 0.0; + + // Build full neighbor list + ILP_neigh(); + // Calculate the normals and its derivatives + calc_normal(); + // Calculate the van der Waals force and energy + calc_FvdW(eflag,vflag); + // Calculate the repulsive force and energy + calc_FRep(eflag,vflag); + + if (vflag_fdotr) virial_fdotr_compute(); +} + +/* ---------------------------------------------------------------------- + van der Waals forces and energy +------------------------------------------------------------------------- */ + +void PairILPGrapheneHBN::calc_FvdW(int eflag, int vflag) +{ + int i,j,ii,jj,inum,jnum,itype,jtype,k,l,kk,ll; + tagint itag,jtag; + double xtmp,ytmp,ztmp,delx,dely,delz,evdwl,fpair; + double rsq,r,Rcut,r2inv,r6inv,r8inv,Tap,dTap,Vilp,TSvdw,TSvdw2inv,fsum; + int *ilist,*jlist,*numneigh,**firstneigh; + + evdwl = 0.0; + double **x = atom->x; + double **f = atom->f; + int *type = atom->type; + tagint *tag = atom->tag; + int nlocal = atom->nlocal; + int newton_pair = force->newton_pair; + + inum = list->inum; + ilist = list->ilist; + numneigh = list->numneigh; + firstneigh = list->firstneigh; + + // loop over neighbors of my atoms + for (ii = 0; ii < inum; ii++) { + i = ilist[ii]; + xtmp = x[i][0]; + ytmp = x[i][1]; + ztmp = x[i][2]; + itype = type[i]; + itag = tag[i]; + jlist = firstneigh[i]; + jnum = numneigh[i]; + + for (jj = 0; jj < jnum; jj++) { + j = jlist[jj]; + j &= NEIGHMASK; + jtype = type[j]; + jtag = tag[j]; -void PairILPGrapheneHBN::init_style() -{ - if (force->newton_pair == 0) - error->all(FLERR,"Pair style ilp/graphene/hbn requires newton pair on"); - if (!atom->molecule_flag) - error->all(FLERR,"Pair style ilp/graphene/hbn requires atom attribute molecule"); + // two-body interactions from full neighbor list, skip half of them + if (itag > jtag) { + if ((itag+jtag) % 2 == 0) continue; + } else if (itag < jtag) { + if ((itag+jtag) % 2 == 1) continue; + } else { + if (x[j][2] < ztmp) continue; + if (x[j][2] == ztmp && x[j][1] < ytmp) continue; + if (x[j][2] == ztmp && x[j][1] == ytmp && x[j][0] < xtmp) continue; + } - // need a full neighbor list, including neighbors of ghosts + delx = xtmp - x[j][0]; + dely = ytmp - x[j][1]; + delz = ztmp - x[j][2]; + rsq = delx*delx + dely*dely + delz*delz; - int irequest = neighbor->request(this,instance_me); - neighbor->requests[irequest]->half = 0; - neighbor->requests[irequest]->full = 1; - neighbor->requests[irequest]->ghost = 1; + // only include the interation between different layers + if (rsq < cutsq[itype][jtype] && atom->molecule[i] != atom->molecule[j]) { - // local ILP neighbor list - // create pages if first time or if neighbor pgsize/oneatom has changed + int iparam_ij = elem2param[map[itype]][map[jtype]]; + Param& p = params[iparam_ij]; - int create = 0; - if (ipage == NULL) create = 1; - if (pgsize != neighbor->pgsize) create = 1; - if (oneatom != neighbor->oneatom) create = 1; + r = sqrt(rsq); + r2inv = 1.0/rsq; + r6inv = r2inv*r2inv*r2inv; + r8inv = r6inv*r2inv; + // turn on/off taper function + if (tap_flag) { + Rcut = sqrt(cutsq[itype][jtype]); + Tap = calc_Tap(r,Rcut); + dTap = calc_dTap(r,Rcut); + } else {Tap = 1.0; dTap = 0.0;} - if (create) { - delete [] ipage; - pgsize = neighbor->pgsize; - oneatom = neighbor->oneatom; + TSvdw = 1.0 + exp(-p.d*(r/p.seff - 1.0)); + TSvdw2inv = pow(TSvdw,-2.0); + Vilp = -p.C6*r6inv/TSvdw; - int nmypage= comm->nthreads; - ipage = new MyPage[nmypage]; - for (int i = 0; i < nmypage; i++) - ipage[i].init(oneatom,pgsize,PGDELTA); + // derivatives + fpair = -6.0*p.C6*r8inv/TSvdw + p.C6*p.d/p.seff*(TSvdw-1.0)*TSvdw2inv*r8inv*r; + fsum = fpair*Tap - Vilp*dTap/r; + + f[i][0] += fsum*delx; + f[i][1] += fsum*dely; + f[i][2] += fsum*delz; + f[j][0] -= fsum*delx; + f[j][1] -= fsum*dely; + f[j][2] -= fsum*delz; + + if (eflag) pvector[0] += evdwl = Vilp*Tap; + if (evflag) ev_tally(i,j,nlocal,newton_pair, + evdwl,0.0,fsum,delx,dely,delz); + } + } } } - -/* ---------------------------------------------------------------------- - create ILP neighbor list from main neighbor list to calcualte normals +/* ---------------------------------------------------------------------- + Repulsive forces and energy ------------------------------------------------------------------------- */ -void PairILPGrapheneHBN::ILP_neigh() +void PairILPGrapheneHBN::calc_FRep(int eflag, int vflag) { - int i,j,ii,jj,n,allnum,jnum,itype,jtype; - double xtmp,ytmp,ztmp,delx,dely,delz,rsq; + int i,j,ii,jj,inum,jnum,itype,jtype,k,kk; + double prodnorm1,fkcx,fkcy,fkcz; + double xtmp,ytmp,ztmp,delx,dely,delz,evdwl,fpair,fpair1; + double rsq,r,Rcut,rhosq1,exp0,exp1,r2inv,r6inv,r8inv,Tap,dTap,Vilp; + double frho1,TSvdw,TSvdw2inv,Erep,fsum,rdsq1; int *ilist,*jlist,*numneigh,**firstneigh; - int *neighptr; + int *ILP_neighs_i,*ILP_neighs_j; + + evdwl = 0.0; double **x = atom->x; + double **f = atom->f; int *type = atom->type; + int nlocal = atom->nlocal; + int newton_pair = force->newton_pair; + double dprodnorm1[3] = {0.0, 0.0, 0.0}; + double fp1[3] = {0.0, 0.0, 0.0}; + double fprod1[3] = {0.0, 0.0, 0.0}; + double delkj[3] = {0.0, 0.0, 0.0}; + double fk[3] = {0.0, 0.0, 0.0}; - if (atom->nmax > maxlocal) { - maxlocal = atom->nmax; - memory->destroy(ILP_numneigh); - memory->sfree(ILP_firstneigh); - memory->create(ILP_numneigh,maxlocal,"ILPGrapheneHBN:numneigh"); - ILP_firstneigh = (int **) memory->smalloc(maxlocal*sizeof(int *),"ILPGrapheneHBN:firstneigh"); - } - - allnum = list->inum + list->gnum; + inum = list->inum; ilist = list->ilist; numneigh = list->numneigh; firstneigh = list->firstneigh; - // store all ILP neighs of owned and ghost atoms - // scan full neighbor list of I - - ipage->reset(); - - for (ii = 0; ii < allnum; ii++) { + //calculate exp(-lambda*(r-z0))*[epsilon/2 + f(rho_ij)] + // loop over neighbors of owned atoms + for (ii = 0; ii < inum; ii++) { i = ilist[ii]; - - n = 0; - neighptr = ipage->vget(); - + if (ILP_numneigh[i] == -1) { + continue; + } xtmp = x[i][0]; ytmp = x[i][1]; ztmp = x[i][2]; - itype = map[type[i]]; + itype = type[i]; jlist = firstneigh[i]; jnum = numneigh[i]; for (jj = 0; jj < jnum; jj++) { j = jlist[jj]; j &= NEIGHMASK; - jtype = map[type[j]]; + if (ILP_numneigh[j] == -1) { + continue; + } + jtype = type[j]; + delx = xtmp - x[j][0]; dely = ytmp - x[j][1]; delz = ztmp - x[j][2]; rsq = delx*delx + dely*dely + delz*delz; - if (rsq != 0 && rsq < cutILPsq[itype][jtype] && atom->molecule[i] == atom->molecule[j]) { - neighptr[n++] = j; - } - } - - ILP_firstneigh[i] = neighptr; - ILP_numneigh[i] = n; - if (n > 3) error->one(FLERR,"There are too many neighbors for some atoms, please check your configuration"); - ipage->vgot(n); - if (ipage->status()) - error->one(FLERR,"Neighbor list overflow, boost neigh_modify one"); - } -} + // only include the interation between different layers + if (rsq < cutsq[itype][jtype] && atom->molecule[i] != atom->molecule[j]) { + int iparam_ij = elem2param[map[itype]][map[jtype]]; + Param& p = params[iparam_ij]; -/* ---------------------------------------------------------------------- - allocate all arrays -------------------------------------------------------------------------- */ + r = sqrt(rsq); + // turn on/off taper function + if (tap_flag) { + Rcut = sqrt(cutsq[itype][jtype]); + Tap = calc_Tap(r,Rcut); + dTap = calc_dTap(r,Rcut); + } else {Tap = 1.0; dTap = 0.0;} -void PairILPGrapheneHBN::allocate() -{ - allocated = 1; - int n = atom->ntypes; + // Calculate the transverse distance + prodnorm1 = normal[i][0]*delx + normal[i][1]*dely + normal[i][2]*delz; + rhosq1 = rsq - prodnorm1*prodnorm1; // rho_ij + rdsq1 = rhosq1*p.delta2inv; // (rho_ij/delta)^2 - memory->create(setflag,n+1,n+1,"pair:setflag"); - for (int i = 1; i <= n; i++) - for (int j = i; j <= n; j++) - setflag[i][j] = 0; + // store exponents + exp0 = exp(-p.lambda*(r-p.z0)); + exp1 = exp(-rdsq1); - memory->create(cutsq,n+1,n+1,"pair:cutsq"); - memory->create(cut,n+1,n+1,"pair:cut"); - memory->create(offset,n+1,n+1,"pair:offset"); - map = new int[atom->ntypes+1]; -} + frho1 = exp1*p.C; + Erep = 0.5*p.epsilon + frho1; + Vilp = exp0*Erep; -/* ---------------------------------------------------------------------- - global settings -------------------------------------------------------------------------- */ + // derivatives + fpair = p.lambda*exp0/r*Erep; + fpair1 = 2.0*exp0*frho1*p.delta2inv; + fsum = fpair + fpair1; + // derivatives of the product of rij and ni, the result is a vector + dprodnorm1[0] = dnormdri[0][0][i]*delx + dnormdri[1][0][i]*dely + dnormdri[2][0][i]*delz; + dprodnorm1[1] = dnormdri[0][1][i]*delx + dnormdri[1][1][i]*dely + dnormdri[2][1][i]*delz; + dprodnorm1[2] = dnormdri[0][2][i]*delx + dnormdri[1][2][i]*dely + dnormdri[2][2][i]*delz; + fp1[0] = prodnorm1*normal[i][0]*fpair1; + fp1[1] = prodnorm1*normal[i][1]*fpair1; + fp1[2] = prodnorm1*normal[i][2]*fpair1; + fprod1[0] = prodnorm1*dprodnorm1[0]*fpair1; + fprod1[1] = prodnorm1*dprodnorm1[1]*fpair1; + fprod1[2] = prodnorm1*dprodnorm1[2]*fpair1; -void PairILPGrapheneHBN::settings(int narg, char **arg) -{ - if (narg < 1 || narg > 2) error->all(FLERR,"Illegal pair_style command"); - if (strcmp(force->pair_style,"hybrid/overlay")!=0) - error->all(FLERR,"ERROR: requires hybrid/overlay pair_style"); + fkcx = (delx*fsum - fp1[0])*Tap - Vilp*dTap*delx/r; + fkcy = (dely*fsum - fp1[1])*Tap - Vilp*dTap*dely/r; + fkcz = (delz*fsum - fp1[2])*Tap - Vilp*dTap*delz/r; - cut_global = force->numeric(FLERR,arg[0]); - if (narg == 2) tap_flag = force->numeric(FLERR,arg[1]); + f[i][0] += fkcx - fprod1[0]*Tap; + f[i][1] += fkcy - fprod1[1]*Tap; + f[i][2] += fkcz - fprod1[2]*Tap; + f[j][0] -= fkcx; + f[j][1] -= fkcy; + f[j][2] -= fkcz; - // reset cutoffs that have been explicitly set + // calculate the forces acted on the neighbors of atom i from atom j + ILP_neighs_i = ILP_firstneigh[i]; + for (kk = 0; kk < ILP_numneigh[i]; kk++) { + k = ILP_neighs_i[kk]; + if (k == i) continue; + // derivatives of the product of rij and ni respect to rk, k=0,1,2, where atom k is the neighbors of atom i + dprodnorm1[0] = dnormal[0][0][kk][i]*delx + dnormal[1][0][kk][i]*dely + dnormal[2][0][kk][i]*delz; + dprodnorm1[1] = dnormal[0][1][kk][i]*delx + dnormal[1][1][kk][i]*dely + dnormal[2][1][kk][i]*delz; + dprodnorm1[2] = dnormal[0][2][kk][i]*delx + dnormal[1][2][kk][i]*dely + dnormal[2][2][kk][i]*delz; + fk[0] = (-prodnorm1*dprodnorm1[0]*fpair1)*Tap; + fk[1] = (-prodnorm1*dprodnorm1[1]*fpair1)*Tap; + fk[2] = (-prodnorm1*dprodnorm1[2]*fpair1)*Tap; + f[k][0] += fk[0]; + f[k][1] += fk[1]; + f[k][2] += fk[2]; + delkj[0] = x[k][0] - x[j][0]; + delkj[1] = x[k][1] - x[j][1]; + delkj[2] = x[k][2] - x[j][2]; + if (evflag) ev_tally_xyz(k,j,nlocal,newton_pair,0.0,0.0,fk[0],fk[1],fk[2],delkj[0],delkj[1],delkj[2]); + } - if (allocated) { - int i,j; - for (i = 1; i <= atom->ntypes; i++) - for (j = i; j <= atom->ntypes; j++) - if (setflag[i][j]) cut[i][j] = cut_global; - } + if (eflag) pvector[1] += evdwl = Tap*Vilp; + if (evflag) ev_tally_xyz(i,j,nlocal,newton_pair,evdwl,0.0,fkcx,fkcy,fkcz,delx,dely,delz); + } + } // loop over jj + } // loop over ii } /* ---------------------------------------------------------------------- - set coeffs for one or more type pairs + create ILP neighbor list from main neighbor list to calcualte normals ------------------------------------------------------------------------- */ -void PairILPGrapheneHBN::coeff(int narg, char **arg) +void PairILPGrapheneHBN::ILP_neigh() { - int i,j,n; - - if (narg != 3 + atom->ntypes) - error->all(FLERR,"Incorrect args for pair coefficients"); - if (!allocated) allocate(); - - // insure I,J args are * * - - if (strcmp(arg[0],"*") != 0 || strcmp(arg[1],"*") != 0) - error->all(FLERR,"Incorrect args for pair coefficients"); + int i,j,ii,jj,n,allnum,inum,jnum,itype,jtype; + double xtmp,ytmp,ztmp,delx,dely,delz,rsq; + int *ilist,*jlist,*numneigh,**firstneigh; + int *neighptr; - // read args that map atom types to elements in potential file - // map[i] = which element the Ith atom type is, -1 if NULL - // nelements = # of unique elements - // elements = list of element names + double **x = atom->x; + int *type = atom->type; - if (elements) { - for (i = 0; i < nelements; i++) delete [] elements[i]; - delete [] elements; + if (atom->nmax > maxlocal) { + maxlocal = atom->nmax; + memory->destroy(ILP_numneigh); + memory->sfree(ILP_firstneigh); + memory->create(ILP_numneigh,maxlocal,"ILPGrapheneHBN:numneigh"); + ILP_firstneigh = (int **) memory->smalloc(maxlocal*sizeof(int *),"ILPGrapheneHBN:firstneigh"); } - elements = new char*[atom->ntypes]; - for (i = 0; i < atom->ntypes; i++) elements[i] = NULL; - nelements = 0; - for (i = 3; i < narg; i++) { - if (strcmp(arg[i],"NULL") == 0) { - map[i-2] = -1; - continue; - } - for (j = 0; j < nelements; j++) - if (strcmp(arg[i],elements[j]) == 0) break; - map[i-2] = j; - if (j == nelements) { - n = strlen(arg[i]) + 1; - elements[j] = new char[n]; - strcpy(elements[j],arg[i]); - nelements++; - } - } + inum = list->inum; + allnum = list->inum + list->gnum; + ilist = list->ilist; + numneigh = list->numneigh; + firstneigh = list->firstneigh; + // store all ILP neighs of owned and ghost atoms + // scan full neighbor list of I - read_file(arg[2]); + ipage->reset(); - // clear setflag since coeff() called once with I,J = * * + for (ii = 0; ii < allnum; ii++) { + i = ilist[ii]; - n = atom->ntypes; - for (int i = 1; i <= n; i++) - for (int j = i; j <= n; j++) - setflag[i][j] = 0; + n = 0; + neighptr = ipage->vget(); - // set setflag i,j for type pairs where both are mapped to elements + xtmp = x[i][0]; + ytmp = x[i][1]; + ztmp = x[i][2]; + itype = map[type[i]]; + jlist = firstneigh[i]; + jnum = numneigh[i]; - int count = 0; - for (int i = 1; i <= n; i++) - for (int j = i; j <= n; j++) - if (map[i] >= 0 && map[j] >= 0) { - setflag[i][j] = 1; - cut[i][j] = cut_global; - count++; + for (jj = 0; jj < jnum; jj++) { + j = jlist[jj]; + j &= NEIGHMASK; + jtype = map[type[j]]; + delx = xtmp - x[j][0]; + dely = ytmp - x[j][1]; + delz = ztmp - x[j][2]; + rsq = delx*delx + dely*dely + delz*delz; + + if (rsq != 0 && rsq < cutILPsq[itype][jtype] && atom->molecule[i] == atom->molecule[j]) { + neighptr[n++] = j; } + } // loop over jj - if (count == 0) error->all(FLERR,"Incorrect args for pair coefficients"); -} + ILP_firstneigh[i] = neighptr; + if (n == 3) { + ILP_numneigh[i] = n; + } + else if (n < 3) { + if (i < inum) { + ILP_numneigh[i] = n; + } else { + ILP_numneigh[i] = -1; + } + } + else if (n > 3) error->one(FLERR,"There are too many neighbors for some atoms, please check your configuration"); + ipage->vgot(n); + if (ipage->status()) + error->one(FLERR,"Neighbor list overflow, boost neigh_modify one"); + } +} /* ---------------------------------------------------------------------- - init for one type pair i,j and corresponding j,i + Calculate the normals for each atom ------------------------------------------------------------------------- */ - -double PairILPGrapheneHBN::init_one(int i, int j) +void PairILPGrapheneHBN::calc_normal() { - if (setflag[i][j] == 0) error->all(FLERR,"All pair coeffs are not set"); - if (!offset_flag) - error->all(FLERR,"Must use 'pair_modify shift yes' with this pair style"); + int i,j,ii,jj,inum,jnum; + int cont,id,ip,m; + double nn,xtp,ytp,ztp,delx,dely,delz,nn2; + int *ilist,*jlist; + double pv12[3],pv31[3],pv23[3],n1[3],dni[3],dnn[3][3],vet[3][3],dpvdri[3][3]; + double dn1[3][3][3],dpv12[3][3][3],dpv23[3][3][3],dpv31[3][3][3]; - if (offset_flag && (cut[i][j] > 0.0)) { - int iparam_ij = elem2param[map[i]][map[j]]; - Param& p = params[iparam_ij]; - offset[i][j] = -p.C6*pow(1.0/cut[i][j],6)/(1.0 + exp(-p.d*(cut[i][j]/p.seff - 1.0))); - } else offset[i][j] = 0.0; - offset[j][i] = offset[i][j]; + double **x = atom->x; - return cut[i][j]; -} + // grow normal array if necessary -/* ---------------------------------------------------------------------- - read Interlayer potential file -------------------------------------------------------------------------- */ + if (atom->nmax > nmax) { + memory->destroy(normal); + memory->destroy(dnormal); + memory->destroy(dnormdri); + nmax = atom->nmax; + memory->create(normal,nmax,3,"ILPGrapheneHBN:normal"); + memory->create(dnormdri,3,3,nmax,"ILPGrapheneHBN:dnormdri"); + memory->create(dnormal,3,3,3,nmax,"ILPGrapheneHBN:dnormal"); + } -void PairILPGrapheneHBN::read_file(char *filename) -{ - int params_per_line = 13; - char **words = new char*[params_per_line+1]; - memory->sfree(params); - params = NULL; - nparams = maxparam = 0; + inum = list->inum; + ilist = list->ilist; + //Calculate normals + for (ii = 0; ii < inum; ii++) { + i = ilist[ii]; - // open file on proc 0 + // Initialize the arrays + for (id = 0; id < 3; id++){ + pv12[id] = 0.0; + pv31[id] = 0.0; + pv23[id] = 0.0; + n1[id] = 0.0; + dni[id] = 0.0; + normal[i][id] = 0.0; + for (ip = 0; ip < 3; ip++){ + vet[ip][id] = 0.0; + dnn[ip][id] = 0.0; + dpvdri[ip][id] = 0.0; + dnormdri[ip][id][i] = 0.0; + for (m = 0; m < 3; m++){ + dpv12[ip][id][m] = 0.0; + dpv31[ip][id][m] = 0.0; + dpv23[ip][id][m] = 0.0; + dn1[ip][id][m] = 0.0; + dnormal[ip][id][m][i] = 0.0; + } + } + } - FILE *fp; - if (comm->me == 0) { - fp = force->open_potential(filename); - if (fp == NULL) { - char str[128]; - snprintf(str,128,"Cannot open ILP potential file %s",filename); - error->one(FLERR,str); + if (ILP_numneigh[i] == -1) { + continue; } - } + xtp = x[i][0]; + ytp = x[i][1]; + ztp = x[i][2]; - // read each line out of file, skipping blank lines or leading '#' - // store line of params if all 3 element tags are in element list + cont = 0; + jlist = ILP_firstneigh[i]; + jnum = ILP_numneigh[i]; + for (jj = 0; jj < jnum; jj++) { + j = jlist[jj]; + j &= NEIGHMASK; - int i,j,n,m,nwords,ielement,jelement; - char line[MAXLINE],*ptr; - int eof = 0; + delx = x[j][0] - xtp; + dely = x[j][1] - ytp; + delz = x[j][2] - ztp; + vet[cont][0] = delx; + vet[cont][1] = dely; + vet[cont][2] = delz; + cont++; + } - while (1) { - if (comm->me == 0) { - ptr = fgets(line,MAXLINE,fp); - if (ptr == NULL) { - eof = 1; - fclose(fp); - } else n = strlen(line) + 1; + if (cont <= 1) { + normal[i][0] = 0.0; + normal[i][1] = 0.0; + normal[i][2] = 1.0; + for (id = 0; id < 3; id++){ + for (ip = 0; ip < 3; ip++){ + dnormdri[id][ip][i] = 0.0; + for (m = 0; m < 3; m++){ + dnormal[id][ip][m][i] = 0.0; + } + } + } } - MPI_Bcast(&eof,1,MPI_INT,0,world); - if (eof) break; - MPI_Bcast(&n,1,MPI_INT,0,world); - MPI_Bcast(line,n,MPI_CHAR,0,world); + else if (cont == 2) { + pv12[0] = vet[0][1]*vet[1][2] - vet[1][1]*vet[0][2]; + pv12[1] = vet[0][2]*vet[1][0] - vet[1][2]*vet[0][0]; + pv12[2] = vet[0][0]*vet[1][1] - vet[1][0]*vet[0][1]; + // derivatives of pv12[0] to ri + dpvdri[0][0] = 0.0; + dpvdri[0][1] = vet[0][2]-vet[1][2]; + dpvdri[0][2] = vet[1][1]-vet[0][1]; + // derivatives of pv12[1] to ri + dpvdri[1][0] = vet[1][2]-vet[0][2]; + dpvdri[1][1] = 0.0; + dpvdri[1][2] = vet[0][0]-vet[1][0]; + // derivatives of pv12[2] to ri + dpvdri[2][0] = vet[0][1]-vet[1][1]; + dpvdri[2][1] = vet[1][0]-vet[0][0]; + dpvdri[2][2] = 0.0; - // strip comment, skip line if blank + dpv12[0][0][0] = 0.0; + dpv12[0][1][0] = vet[1][2]; + dpv12[0][2][0] = -vet[1][1]; + dpv12[1][0][0] = -vet[1][2]; + dpv12[1][1][0] = 0.0; + dpv12[1][2][0] = vet[1][0]; + dpv12[2][0][0] = vet[1][1]; + dpv12[2][1][0] = -vet[1][0]; + dpv12[2][2][0] = 0.0; - if ((ptr = strchr(line,'#'))) *ptr = '\0'; - nwords = atom->count_words(line); - if (nwords == 0) continue; + // derivatives respect to the second neighbor, atom l + dpv12[0][0][1] = 0.0; + dpv12[0][1][1] = -vet[0][2]; + dpv12[0][2][1] = vet[0][1]; + dpv12[1][0][1] = vet[0][2]; + dpv12[1][1][1] = 0.0; + dpv12[1][2][1] = -vet[0][0]; + dpv12[2][0][1] = -vet[0][1]; + dpv12[2][1][1] = vet[0][0]; + dpv12[2][2][1] = 0.0; - // concatenate additional lines until have params_per_line words + // derivatives respect to the third neighbor, atom n + // derivatives of pv12 to rn is zero + for (id = 0; id < 3; id++){ + for (ip = 0; ip < 3; ip++){ + dpv12[id][ip][2] = 0.0; + } + } - while (nwords < params_per_line) { - n = strlen(line); - if (comm->me == 0) { - ptr = fgets(&line[n],MAXLINE-n,fp); - if (ptr == NULL) { - eof = 1; - fclose(fp); - } else n = strlen(line) + 1; + n1[0] = pv12[0]; + n1[1] = pv12[1]; + n1[2] = pv12[2]; + // the magnitude of the normal vector + nn2 = n1[0]*n1[0] + n1[1]*n1[1] + n1[2]*n1[2]; + nn = sqrt(nn2); + if (nn == 0) error->one(FLERR,"The magnitude of the normal vector is zero"); + // the unit normal vector + normal[i][0] = n1[0]/nn; + normal[i][1] = n1[1]/nn; + normal[i][2] = n1[2]/nn; + // derivatives of nn, dnn:3x1 vector + dni[0] = (n1[0]*dpvdri[0][0] + n1[1]*dpvdri[1][0] + n1[2]*dpvdri[2][0])/nn; + dni[1] = (n1[0]*dpvdri[0][1] + n1[1]*dpvdri[1][1] + n1[2]*dpvdri[2][1])/nn; + dni[2] = (n1[0]*dpvdri[0][2] + n1[1]*dpvdri[1][2] + n1[2]*dpvdri[2][2])/nn; + // derivatives of unit vector ni respect to ri, the result is 3x3 matrix + for (id = 0; id < 3; id++){ + for (ip = 0; ip < 3; ip++){ + dnormdri[id][ip][i] = dpvdri[id][ip]/nn - n1[id]*dni[ip]/nn2; + } + } + // derivatives of non-normalized normal vector, dn1:3x3x3 array + for (id = 0; id < 3; id++){ + for (ip = 0; ip < 3; ip++){ + for (m = 0; m < 3; m++){ + dn1[id][ip][m] = dpv12[id][ip][m]; + } + } + } + // derivatives of nn, dnn:3x3 vector + // dnn[id][m]: the derivative of nn respect to r[id][m], id,m=0,1,2 + // r[id][m]: the id's component of atom m + for (m = 0; m < 3; m++){ + for (id = 0; id < 3; id++){ + dnn[id][m] = (n1[0]*dn1[0][id][m] + n1[1]*dn1[1][id][m] + n1[2]*dn1[2][id][m])/nn; + } + } + // dnormal[id][ip][m][i]: the derivative of normal[id] respect to r[ip][m], id,ip=0,1,2 + // for atom m, which is a neighbor atom of atom i, m=0,jnum-1 + for (m = 0; m < 3; m++){ + for (id = 0; id < 3; id++){ + for (ip = 0; ip < 3; ip++){ + dnormal[id][ip][m][i] = dn1[id][ip][m]/nn - n1[id]*dnn[ip][m]/nn2; + } + } } - MPI_Bcast(&eof,1,MPI_INT,0,world); - if (eof) break; - MPI_Bcast(&n,1,MPI_INT,0,world); - MPI_Bcast(line,n,MPI_CHAR,0,world); - if ((ptr = strchr(line,'#'))) *ptr = '\0'; - nwords = atom->count_words(line); } +//############################################################################################## - if (nwords != params_per_line) - error->all(FLERR,"Insufficient format in ILP potential file"); - - // words = ptrs to all words in line - - nwords = 0; - words[nwords++] = strtok(line," \t\n\r\f"); - while ((words[nwords++] = strtok(NULL," \t\n\r\f"))) continue; - - // ielement,jelement = 1st args - // if these 2 args are in element list, then parse this line - // else skip to next line (continue) - - for (ielement = 0; ielement < nelements; ielement++) - if (strcmp(words[0],elements[ielement]) == 0) break; - if (ielement == nelements) continue; - for (jelement = 0; jelement < nelements; jelement++) - if (strcmp(words[1],elements[jelement]) == 0) break; - if (jelement == nelements) continue; + else if(cont == 3) { + pv12[0] = vet[0][1]*vet[1][2] - vet[1][1]*vet[0][2]; + pv12[1] = vet[0][2]*vet[1][0] - vet[1][2]*vet[0][0]; + pv12[2] = vet[0][0]*vet[1][1] - vet[1][0]*vet[0][1]; + // derivatives respect to the first neighbor, atom k + dpv12[0][0][0] = 0.0; + dpv12[0][1][0] = vet[1][2]; + dpv12[0][2][0] = -vet[1][1]; + dpv12[1][0][0] = -vet[1][2]; + dpv12[1][1][0] = 0.0; + dpv12[1][2][0] = vet[1][0]; + dpv12[2][0][0] = vet[1][1]; + dpv12[2][1][0] = -vet[1][0]; + dpv12[2][2][0] = 0.0; + // derivatives respect to the second neighbor, atom l + dpv12[0][0][1] = 0.0; + dpv12[0][1][1] = -vet[0][2]; + dpv12[0][2][1] = vet[0][1]; + dpv12[1][0][1] = vet[0][2]; + dpv12[1][1][1] = 0.0; + dpv12[1][2][1] = -vet[0][0]; + dpv12[2][0][1] = -vet[0][1]; + dpv12[2][1][1] = vet[0][0]; + dpv12[2][2][1] = 0.0; - // load up parameter settings and error check their values + // derivatives respect to the third neighbor, atom n + for (id = 0; id < 3; id++){ + for (ip = 0; ip < 3; ip++){ + dpv12[id][ip][2] = 0.0; + } + } - if (nparams == maxparam) { - maxparam += DELTA; - params = (Param *) memory->srealloc(params,maxparam*sizeof(Param), - "pair:params"); - } + pv31[0] = vet[2][1]*vet[0][2] - vet[0][1]*vet[2][2]; + pv31[1] = vet[2][2]*vet[0][0] - vet[0][2]*vet[2][0]; + pv31[2] = vet[2][0]*vet[0][1] - vet[0][0]*vet[2][1]; + // derivatives respect to the first neighbor, atom k + dpv31[0][0][0] = 0.0; + dpv31[0][1][0] = -vet[2][2]; + dpv31[0][2][0] = vet[2][1]; + dpv31[1][0][0] = vet[2][2]; + dpv31[1][1][0] = 0.0; + dpv31[1][2][0] = -vet[2][0]; + dpv31[2][0][0] = -vet[2][1]; + dpv31[2][1][0] = vet[2][0]; + dpv31[2][2][0] = 0.0; + // derivatives respect to the third neighbor, atom n + dpv31[0][0][2] = 0.0; + dpv31[0][1][2] = vet[0][2]; + dpv31[0][2][2] = -vet[0][1]; + dpv31[1][0][2] = -vet[0][2]; + dpv31[1][1][2] = 0.0; + dpv31[1][2][2] = vet[0][0]; + dpv31[2][0][2] = vet[0][1]; + dpv31[2][1][2] = -vet[0][0]; + dpv31[2][2][2] = 0.0; + // derivatives respect to the second neighbor, atom l + for (id = 0; id < 3; id++){ + for (ip = 0; ip < 3; ip++){ + dpv31[id][ip][1] = 0.0; + } + } - params[nparams].ielement = ielement; - params[nparams].jelement = jelement; - params[nparams].z0 = atof(words[2]); - params[nparams].alpha = atof(words[3]); - params[nparams].delta = atof(words[4]); - params[nparams].epsilon = atof(words[5]); - params[nparams].C = atof(words[6]); - params[nparams].d = atof(words[7]); - params[nparams].sR = atof(words[8]); - params[nparams].reff = atof(words[9]); - params[nparams].C6 = atof(words[10]); - // S provides a convenient scaling of all energies - params[nparams].S = atof(words[11]); - params[nparams].rcut = atof(words[12]); + pv23[0] = vet[1][1]*vet[2][2] - vet[2][1]*vet[1][2]; + pv23[1] = vet[1][2]*vet[2][0] - vet[2][2]*vet[1][0]; + pv23[2] = vet[1][0]*vet[2][1] - vet[2][0]*vet[1][1]; + // derivatives respect to the second neighbor, atom k + for (id = 0; id < 3; id++){ + for (ip = 0; ip < 3; ip++){ + dpv23[id][ip][0] = 0.0; + } + } + // derivatives respect to the second neighbor, atom l + dpv23[0][0][1] = 0.0; + dpv23[0][1][1] = vet[2][2]; + dpv23[0][2][1] = -vet[2][1]; + dpv23[1][0][1] = -vet[2][2]; + dpv23[1][1][1] = 0.0; + dpv23[1][2][1] = vet[2][0]; + dpv23[2][0][1] = vet[2][1]; + dpv23[2][1][1] = -vet[2][0]; + dpv23[2][2][1] = 0.0; + // derivatives respect to the third neighbor, atom n + dpv23[0][0][2] = 0.0; + dpv23[0][1][2] = -vet[1][2]; + dpv23[0][2][2] = vet[1][1]; + dpv23[1][0][2] = vet[1][2]; + dpv23[1][1][2] = 0.0; + dpv23[1][2][2] = -vet[1][0]; + dpv23[2][0][2] = -vet[1][1]; + dpv23[2][1][2] = vet[1][0]; + dpv23[2][2][2] = 0.0; - // energies in meV further scaled by S - // S = 43.3634 meV = 1 kcal/mol - double meV = 1e-3*params[nparams].S; - params[nparams].C *= meV; - params[nparams].C6 *= meV; - params[nparams].epsilon *= meV; +//############################################################################################ + // average the normal vectors by using the 3 neighboring planes + n1[0] = (pv12[0] + pv31[0] + pv23[0])/cont; + n1[1] = (pv12[1] + pv31[1] + pv23[1])/cont; + n1[2] = (pv12[2] + pv31[2] + pv23[2])/cont; + // the magnitude of the normal vector + nn2 = n1[0]*n1[0] + n1[1]*n1[1] + n1[2]*n1[2]; + nn = sqrt(nn2); + if (nn == 0) error->one(FLERR,"The magnitude of the normal vector is zero"); + // the unit normal vector + normal[i][0] = n1[0]/nn; + normal[i][1] = n1[1]/nn; + normal[i][2] = n1[2]/nn; - // precompute some quantities - params[nparams].delta2inv = pow(params[nparams].delta,-2.0); - params[nparams].lambda = params[nparams].alpha/params[nparams].z0; - params[nparams].seff = params[nparams].sR * params[nparams].reff; + // for the central atoms, dnormdri is always zero + for (id = 0; id < 3; id++){ + for (ip = 0; ip < 3; ip++){ + dnormdri[id][ip][i] = 0.0; + } + } - nparams++; - } - memory->destroy(elem2param); - memory->destroy(cutILPsq); - memory->create(elem2param,nelements,nelements,"pair:elem2param"); - memory->create(cutILPsq,nelements,nelements,"pair:cutILPsq"); - for (i = 0; i < nelements; i++) { - for (j = 0; j < nelements; j++) { - n = -1; - for (m = 0; m < nparams; m++) { - if (i == params[m].ielement && j == params[m].jelement) { - if (n >= 0) error->all(FLERR,"Potential file has duplicate entry"); - n = m; + // derivatives of non-normalized normal vector, dn1:3x3x3 array + for (id = 0; id < 3; id++){ + for (ip = 0; ip < 3; ip++){ + for (m = 0; m < 3; m++){ + dn1[id][ip][m] = (dpv12[id][ip][m] + dpv23[id][ip][m] + dpv31[id][ip][m])/cont; + } } } - if (n < 0) error->all(FLERR,"Potential file is missing an entry"); - elem2param[i][j] = n; - cutILPsq[i][j] = params[n].rcut*params[n].rcut; + // derivatives of nn, dnn:3x3 vector + // dnn[id][m]: the derivative of nn respect to r[id][m], id,m=0,1,2 + // r[id][m]: the id's component of atom m + for (m = 0; m < 3; m++){ + for (id = 0; id < 3; id++){ + dnn[id][m] = (n1[0]*dn1[0][id][m] + n1[1]*dn1[1][id][m] + n1[2]*dn1[2][id][m])/nn; + } + } + // dnormal[id][ip][m][i]: the derivative of normal[id] respect to r[ip][m], id,ip=0,1,2 + // for atom m, which is a neighbor atom of atom i, m=0,jnum-1 + for (m = 0; m < 3; m++){ + for (id = 0; id < 3; id++){ + for (ip = 0; ip < 3; ip++){ + dnormal[id][ip][m][i] = dn1[id][ip][m]/nn - n1[id]*dnn[ip][m]/nn2; + } + } + } + } + else { + error->one(FLERR,"There are too many neighbors for calculating normals"); } + +//############################################################################################## } - delete [] words; } /* ---------------------------------------------------------------------- */ @@ -1061,70 +1127,3 @@ double PairILPGrapheneHBN::single(int /*i*/, int /*j*/, int itype, int jtype, do philj = Vilp*Tap; return factor_lj*philj; } - - -/* ---------------------------------------------------------------------- */ - -int PairILPGrapheneHBN::pack_forward_comm(int n, int *list, double *buf, - int /*pbc_flag*/, int * /*pbc*/) -{ - int i,j,m,id,ip,l; - - m = 0; - for (i = 0; i < n; i++) { - j = list[i]; - buf[m++] = normal[j][0]; - buf[m++] = normal[j][1]; - buf[m++] = normal[j][2]; - buf[m++] = dnormdri[0][0][j]; - buf[m++] = dnormdri[0][1][j]; - buf[m++] = dnormdri[0][2][j]; - buf[m++] = dnormdri[1][0][j]; - buf[m++] = dnormdri[1][1][j]; - buf[m++] = dnormdri[1][2][j]; - buf[m++] = dnormdri[2][0][j]; - buf[m++] = dnormdri[2][1][j]; - buf[m++] = dnormdri[2][2][j]; - for (l = 0; l < 3; l++){ - for (id = 0; id < 3; id++){ - for (ip = 0; ip < 3; ip++){ - buf[m++] = dnormal[id][ip][l][j]; - } - } - } - } - return m; -} - -/* ---------------------------------------------------------------------- */ - -void PairILPGrapheneHBN::unpack_forward_comm(int n, int first, double *buf) -{ - int i,m,last,id,ip,l; - - m = 0; - last = first + n; - for (i = first; i < last; i++) { - normal[i][0] = buf[m++]; - normal[i][1] = buf[m++]; - normal[i][2] = buf[m++]; - dnormdri[0][0][i] = buf[m++]; - dnormdri[0][1][i] = buf[m++]; - dnormdri[0][2][i] = buf[m++]; - dnormdri[1][0][i] = buf[m++]; - dnormdri[1][1][i] = buf[m++]; - dnormdri[1][2][i] = buf[m++]; - dnormdri[2][0][i] = buf[m++]; - dnormdri[2][1][i] = buf[m++]; - dnormdri[2][2][i] = buf[m++]; - for (l = 0; l < 3; l++){ - for (id = 0; id < 3; id++){ - for (ip = 0; ip < 3; ip++){ - dnormal[id][ip][l][i] = buf[m++]; - } - } - } - } -} - -/* ---------------------------------------------------------------------- */ diff --git a/src/USER-MISC/pair_ilp_graphene_hbn.h b/src/USER-MISC/pair_ilp_graphene_hbn.h index ae4662cdc5..32bee4a10f 100644 --- a/src/USER-MISC/pair_ilp_graphene_hbn.h +++ b/src/USER-MISC/pair_ilp_graphene_hbn.h @@ -21,6 +21,8 @@ PairStyle(ilp/graphene/hbn,PairILPGrapheneHBN) #define LMP_PAIR_ILP_GRAPHENE_HBN_H #include "pair.h" +#include "my_page.h" +#include namespace LAMMPS_NS { @@ -34,9 +36,10 @@ class PairILPGrapheneHBN : public Pair { void coeff(int, char **); double init_one(int, int); void init_style(); + void ILP_neigh(); void calc_normal(); - int pack_forward_comm(int, int *, double *, int, int *); - void unpack_forward_comm(int, int, double *); + void calc_FRep(int, int); + void calc_FvdW(int, int); double single(int, int, int, int, double, double, double, double &); protected: @@ -74,7 +77,6 @@ class PairILPGrapheneHBN : public Pair { void read_file( char * ); void allocate(); - void ILP_neigh(); /* ----Calculate the long-range cutoff term */ inline double calc_Tap(double r_ij, double Rcut) { diff --git a/src/USER-MISC/pair_kolmogorov_crespi_full.cpp b/src/USER-MISC/pair_kolmogorov_crespi_full.cpp index 0009531ca8..bfebb0c553 100644 --- a/src/USER-MISC/pair_kolmogorov_crespi_full.cpp +++ b/src/USER-MISC/pair_kolmogorov_crespi_full.cpp @@ -20,11 +20,12 @@ [Kolmogorov & Crespi, Phys. Rev. B 71, 235415 (2005)] ------------------------------------------------------------------------- */ -#include "pair_kolmogorov_crespi_full.h" #include +#include #include #include #include +#include "pair_kolmogorov_crespi_full.h" #include "atom.h" #include "comm.h" #include "force.h" @@ -48,6 +49,9 @@ PairKolmogorovCrespiFull::PairKolmogorovCrespiFull(LAMMPS *lmp) : Pair(lmp) restartinfo = 0; one_coeff = 1; + nextra = 2; + pvector = new double[nextra]; + // initialize element to parameter maps nelements = 0; elements = NULL; @@ -71,8 +75,7 @@ PairKolmogorovCrespiFull::PairKolmogorovCrespiFull(LAMMPS *lmp) : Pair(lmp) // always compute energy offset offset_flag = 1; - // set comm size needed by this Pair - comm_forward = 39; + // turn on the taper function tap_flag = 0; } @@ -83,6 +86,7 @@ PairKolmogorovCrespiFull::~PairKolmogorovCrespiFull() memory->destroy(KC_numneigh); memory->sfree(KC_firstneigh); delete [] ipage; + delete [] pvector; memory->destroy(normal); memory->destroy(dnormal); memory->destroy(dnormdri); @@ -103,934 +107,1001 @@ PairKolmogorovCrespiFull::~PairKolmogorovCrespiFull() if (allocated) delete [] map; } -/* ---------------------------------------------------------------------- */ +/* ---------------------------------------------------------------------- + allocate all arrays +------------------------------------------------------------------------- */ -void PairKolmogorovCrespiFull::compute(int eflag, int vflag) +void PairKolmogorovCrespiFull::allocate() { - int i,j,ii,jj,inum,jnum,itype,jtype,k,l,kk,ll; - tagint itag,jtag; - double prodnorm1,prodnorm2,fkcx,fkcy,fkcz; - double xtmp,ytmp,ztmp,delx,dely,delz,evdwl,fpair,fpair1,fpair2; - double rsq,r,rhosq1,rhosq2,exp0,exp1,exp2,r2inv,r6inv,r8inv,Tap,dTap,Vkc; - double frho1,frho2,sumC1,sumC2,sumC11,sumC22,sumCff,fsum,rdsq1,rdsq2; - int *ilist,*jlist,*numneigh,**firstneigh; - int *KC_neighs_i,*KC_neighs_j; + allocated = 1; + int n = atom->ntypes; - evdwl = 0.0; - ev_init(eflag,vflag); + memory->create(setflag,n+1,n+1,"pair:setflag"); + for (int i = 1; i <= n; i++) + for (int j = i; j <= n; j++) + setflag[i][j] = 0; - double **x = atom->x; - double **f = atom->f; - int *type = atom->type; - tagint *tag = atom->tag; - int nlocal = atom->nlocal; - int newton_pair = force->newton_pair; - double dprodnorm1[3] = {0.0, 0.0, 0.0}; - double dprodnorm2[3] = {0.0, 0.0, 0.0}; - double fp1[3] = {0.0, 0.0, 0.0}; - double fp2[3] = {0.0, 0.0, 0.0}; - double fprod1[3] = {0.0, 0.0, 0.0}; - double fprod2[3] = {0.0, 0.0, 0.0}; - double fk[3] = {0.0, 0.0, 0.0}; - double fl[3] = {0.0, 0.0, 0.0}; - double delkj[3] = {0.0, 0.0, 0.0}; - double delli[3] = {0.0, 0.0, 0.0}; + memory->create(cutsq,n+1,n+1,"pair:cutsq"); + memory->create(cut,n+1,n+1,"pair:cut"); + memory->create(offset,n+1,n+1,"pair:offset"); + map = new int[atom->ntypes+1]; +} - inum = list->inum; - ilist = list->ilist; - numneigh = list->numneigh; - firstneigh = list->firstneigh; - // Build full neighbor list - KC_neigh(); - // Calculate the normals - calc_normal(); +/* ---------------------------------------------------------------------- + global settings +------------------------------------------------------------------------- */ - // communicate the normal vector and its derivatives - comm->forward_comm_pair(this); +void PairKolmogorovCrespiFull::settings(int narg, char **arg) +{ + if (narg < 1 || narg > 2) error->all(FLERR,"Illegal pair_style command"); + if (strcmp(force->pair_style,"hybrid/overlay")!=0) + error->all(FLERR,"ERROR: requires hybrid/overlay pair_style"); - // loop over neighbors of my atoms - for (ii = 0; ii < inum; ii++) { - i = ilist[ii]; - itag = tag[i]; - xtmp = x[i][0]; - ytmp = x[i][1]; - ztmp = x[i][2]; - itype = type[i]; - jlist = firstneigh[i]; - jnum = numneigh[i]; + cut_global = force->numeric(FLERR,arg[0]); + if (narg == 2) tap_flag = force->numeric(FLERR,arg[1]); - for (jj = 0; jj < jnum; jj++) { - j = jlist[jj]; - j &= NEIGHMASK; - jtype = type[j]; - jtag = tag[j]; + // reset cutoffs that have been explicitly set - // two-body interactions from full neighbor list, skip half of them - if (itag > jtag) { - if ((itag+jtag) % 2 == 0) continue; - } else if (itag < jtag) { - if ((itag+jtag) % 2 == 1) continue; - } else { - if (x[j][2] < ztmp) continue; - if (x[j][2] == ztmp && x[j][1] < ytmp) continue; - if (x[j][2] == ztmp && x[j][1] == ytmp && x[j][0] < xtmp) continue; - } + if (allocated) { + int i,j; + for (i = 1; i <= atom->ntypes; i++) + for (j = i; j <= atom->ntypes; j++) + if (setflag[i][j]) cut[i][j] = cut_global; + } +} - delx = xtmp - x[j][0]; - dely = ytmp - x[j][1]; - delz = ztmp - x[j][2]; - rsq = delx*delx + dely*dely + delz*delz; +/* ---------------------------------------------------------------------- + set coeffs for one or more type pairs +------------------------------------------------------------------------- */ - // only include the interation between different layers - if (rsq < cutsq[itype][jtype] && atom->molecule[i] != atom->molecule[j]) { +void PairKolmogorovCrespiFull::coeff(int narg, char **arg) +{ + int i,j,n; - int iparam_ij = elem2param[map[itype]][map[jtype]]; - Param& p = params[iparam_ij]; + if (narg != 3 + atom->ntypes) + error->all(FLERR,"Incorrect args for pair coefficients"); + if (!allocated) allocate(); - r = sqrt(rsq); - r2inv = 1.0/rsq; - r6inv = r2inv*r2inv*r2inv; - r8inv = r2inv*r6inv; - // turn on/off taper function - if (tap_flag) { - Tap = calc_Tap(r,sqrt(cutsq[itype][jtype])); - dTap = calc_dTap(r,sqrt(cutsq[itype][jtype])); - } else {Tap = 1.0; dTap = 0.0;} + // insure I,J args are * * - // Calculate the transverse distance - // note that rho_ij does not equal to rho_ji except when normals are all along z - prodnorm1 = normal[i][0]*delx + normal[i][1]*dely + normal[i][2]*delz; - prodnorm2 = normal[j][0]*delx + normal[j][1]*dely + normal[j][2]*delz; - rhosq1 = rsq - prodnorm1*prodnorm1; // rho_ij - rhosq2 = rsq - prodnorm2*prodnorm2; // rho_ji - rdsq1 = rhosq1*p.delta2inv; // (rho_ij/delta)^2 - rdsq2 = rhosq2*p.delta2inv; // (rho_ji/delta)^2 + if (strcmp(arg[0],"*") != 0 || strcmp(arg[1],"*") != 0) + error->all(FLERR,"Incorrect args for pair coefficients"); - // store exponents - exp0 = exp(-p.lambda*(r-p.z0)); - exp1 = exp(-rdsq1); - exp2 = exp(-rdsq2); - - sumC1 = p.C0 + p.C2*rdsq1 + p.C4*rdsq1*rdsq1; - sumC2 = p.C0 + p.C2*rdsq2 + p.C4*rdsq2*rdsq2; - sumC11 = (p.C2 + 2.0*p.C4*rdsq1)*p.delta2inv; - sumC22 = (p.C2 + 2.0*p.C4*rdsq2)*p.delta2inv; - frho1 = exp1*sumC1; - frho2 = exp2*sumC2; - sumCff = p.C + frho1 + frho2; - Vkc = -p.A*p.z06*r6inv + exp0*sumCff; + // read args that map atom types to elements in potential file + // map[i] = which element the Ith atom type is, -1 if NULL + // nelements = # of unique elements + // elements = list of element names - // derivatives - fpair = -6.0*p.A*p.z06*r8inv + p.lambda*exp0/r*sumCff; - fpair1 = 2.0*exp0*exp1*(p.delta2inv*sumC1 - sumC11); - fpair2 = 2.0*exp0*exp2*(p.delta2inv*sumC2 - sumC22); - fsum = fpair + fpair1 + fpair2; - // derivatives of the product of rij and ni, the result is a vector - dprodnorm1[0] = dnormdri[0][0][i]*delx + dnormdri[1][0][i]*dely + dnormdri[2][0][i]*delz; - dprodnorm1[1] = dnormdri[0][1][i]*delx + dnormdri[1][1][i]*dely + dnormdri[2][1][i]*delz; - dprodnorm1[2] = dnormdri[0][2][i]*delx + dnormdri[1][2][i]*dely + dnormdri[2][2][i]*delz; - // derivatives of the product of rji and nj, the result is a vector - dprodnorm2[0] = dnormdri[0][0][j]*delx + dnormdri[1][0][j]*dely + dnormdri[2][0][j]*delz; - dprodnorm2[1] = dnormdri[0][1][j]*delx + dnormdri[1][1][j]*dely + dnormdri[2][1][j]*delz; - dprodnorm2[2] = dnormdri[0][2][j]*delx + dnormdri[1][2][j]*dely + dnormdri[2][2][j]*delz; - fp1[0] = prodnorm1*normal[i][0]*fpair1; - fp1[1] = prodnorm1*normal[i][1]*fpair1; - fp1[2] = prodnorm1*normal[i][2]*fpair1; - fp2[0] = prodnorm2*normal[j][0]*fpair2; - fp2[1] = prodnorm2*normal[j][1]*fpair2; - fp2[2] = prodnorm2*normal[j][2]*fpair2; - fprod1[0] = prodnorm1*dprodnorm1[0]*fpair1; - fprod1[1] = prodnorm1*dprodnorm1[1]*fpair1; - fprod1[2] = prodnorm1*dprodnorm1[2]*fpair1; - fprod2[0] = prodnorm2*dprodnorm2[0]*fpair2; - fprod2[1] = prodnorm2*dprodnorm2[1]*fpair2; - fprod2[2] = prodnorm2*dprodnorm2[2]*fpair2; - fkcx = (delx*fsum - fp1[0] - fp2[0])*Tap - Vkc*dTap*delx/r; - fkcy = (dely*fsum - fp1[1] - fp2[1])*Tap - Vkc*dTap*dely/r; - fkcz = (delz*fsum - fp1[2] - fp2[2])*Tap - Vkc*dTap*delz/r; + if (elements) { + for (i = 0; i < nelements; i++) delete [] elements[i]; + delete [] elements; + } + elements = new char*[atom->ntypes]; + for (i = 0; i < atom->ntypes; i++) elements[i] = NULL; - f[i][0] += fkcx - fprod1[0]*Tap; - f[i][1] += fkcy - fprod1[1]*Tap; - f[i][2] += fkcz - fprod1[2]*Tap; - f[j][0] -= fkcx + fprod2[0]*Tap; - f[j][1] -= fkcy + fprod2[1]*Tap; - f[j][2] -= fkcz + fprod2[2]*Tap; + nelements = 0; + for (i = 3; i < narg; i++) { + if (strcmp(arg[i],"NULL") == 0) { + map[i-2] = -1; + continue; + } + for (j = 0; j < nelements; j++) + if (strcmp(arg[i],elements[j]) == 0) break; + map[i-2] = j; + if (j == nelements) { + n = strlen(arg[i]) + 1; + elements[j] = new char[n]; + strcpy(elements[j],arg[i]); + nelements++; + } + } - // calculate the forces acted on the neighbors of atom i from atom j - KC_neighs_i = KC_firstneigh[i]; - for (kk = 0; kk < KC_numneigh[i]; kk++) { - k = KC_neighs_i[kk]; - if (k == i) continue; - // derivatives of the product of rij and ni respect to rk, k=0,1,2, where atom k is the neighbors of atom i - dprodnorm1[0] = dnormal[0][0][kk][i]*delx + dnormal[1][0][kk][i]*dely + dnormal[2][0][kk][i]*delz; - dprodnorm1[1] = dnormal[0][1][kk][i]*delx + dnormal[1][1][kk][i]*dely + dnormal[2][1][kk][i]*delz; - dprodnorm1[2] = dnormal[0][2][kk][i]*delx + dnormal[1][2][kk][i]*dely + dnormal[2][2][kk][i]*delz; - fk[0] = (-prodnorm1*dprodnorm1[0]*fpair1)*Tap; - fk[1] = (-prodnorm1*dprodnorm1[1]*fpair1)*Tap; - fk[2] = (-prodnorm1*dprodnorm1[2]*fpair1)*Tap; - f[k][0] += fk[0]; - f[k][1] += fk[1]; - f[k][2] += fk[2]; - delkj[0] = x[k][0] - x[j][0]; - delkj[1] = x[k][1] - x[j][1]; - delkj[2] = x[k][2] - x[j][2]; - if (evflag) ev_tally_xyz(k,j,nlocal,newton_pair,0.0,0.0,fk[0],fk[1],fk[2],delkj[0],delkj[1],delkj[2]); - } - // calculate the forces acted on the neighbors of atom j from atom i - KC_neighs_j = KC_firstneigh[j]; - for (ll = 0; ll < KC_numneigh[j]; ll++) { - l = KC_neighs_j[ll]; - if (l == j) continue; - // derivatives of the product of rji and nj respect to rl, l=0,1,2, where atom l is the neighbors of atom j - dprodnorm2[0] = dnormal[0][0][ll][j]*delx + dnormal[1][0][ll][j]*dely + dnormal[2][0][ll][j]*delz; - dprodnorm2[1] = dnormal[0][1][ll][j]*delx + dnormal[1][1][ll][j]*dely + dnormal[2][1][ll][j]*delz; - dprodnorm2[2] = dnormal[0][2][ll][j]*delx + dnormal[1][2][ll][j]*dely + dnormal[2][2][ll][j]*delz; - fl[0] = (-prodnorm2*dprodnorm2[0]*fpair2)*Tap; - fl[1] = (-prodnorm2*dprodnorm2[1]*fpair2)*Tap; - fl[2] = (-prodnorm2*dprodnorm2[2]*fpair2)*Tap; - f[l][0] += fl[0]; - f[l][1] += fl[1]; - f[l][2] += fl[2]; - delli[0] = x[l][0] - x[i][0]; - delli[1] = x[l][1] - x[i][1]; - delli[2] = x[l][2] - x[i][2]; - if (evflag) ev_tally_xyz(l,i,nlocal,newton_pair,0.0,0.0,fl[0],fl[1],fl[2],delli[0],delli[1],delli[2]); - } + read_file(arg[2]); - if (eflag) { - if (tap_flag) evdwl = Tap*Vkc; - else evdwl = Vkc - offset[itype][jtype]; - } + // clear setflag since coeff() called once with I,J = * * + + n = atom->ntypes; + for (int i = 1; i <= n; i++) + for (int j = i; j <= n; j++) + setflag[i][j] = 0; - if (evflag) ev_tally_xyz(i,j,nlocal,newton_pair,evdwl,0,fkcx,fkcy,fkcz,delx,dely,delz); + // set setflag i,j for type pairs where both are mapped to elements + + int count = 0; + for (int i = 1; i <= n; i++) + for (int j = i; j <= n; j++) + if (map[i] >= 0 && map[j] >= 0) { + setflag[i][j] = 1; + cut[i][j] = cut_global; + count++; } - } - } - if (vflag_fdotr) virial_fdotr_compute(); + + if (count == 0) error->all(FLERR,"Incorrect args for pair coefficients"); } + /* ---------------------------------------------------------------------- - Calculate the normals for each atom + init for one type pair i,j and corresponding j,i ------------------------------------------------------------------------- */ -void PairKolmogorovCrespiFull::calc_normal() -{ - int i,j,ii,jj,inum,jnum; - int cont,id,ip,m; - double nn,xtp,ytp,ztp,delx,dely,delz,nn2; - int *ilist,*jlist; - double pv12[3],pv31[3],pv23[3],n1[3],dni[3],dnn[3][3],vet[3][3],dpvdri[3][3]; - double dn1[3][3][3],dpv12[3][3][3],dpv23[3][3][3],dpv31[3][3][3]; - double **x = atom->x; +double PairKolmogorovCrespiFull::init_one(int i, int j) +{ + if (setflag[i][j] == 0) error->all(FLERR,"All pair coeffs are not set"); + if (!offset_flag) + error->all(FLERR,"Must use 'pair_modify shift yes' with this pair style"); - // grow normal array if necessary + if (offset_flag && (cut[i][j] > 0.0)) { + int iparam_ij = elem2param[map[i]][map[j]]; + Param& p = params[iparam_ij]; + offset[i][j] = -p.A*pow(p.z0/cut[i][j],6); + } else offset[i][j] = 0.0; + offset[j][i] = offset[i][j]; - if (atom->nmax > nmax) { - memory->destroy(normal); - memory->destroy(dnormal); - memory->destroy(dnormdri); - nmax = atom->nmax; - memory->create(normal,nmax,3,"KolmogorovCrespiFull:normal"); - memory->create(dnormdri,3,3,nmax,"KolmogorovCrespiFull:dnormdri"); - memory->create(dnormal,3,3,3,nmax,"KolmogorovCrespiFull:dnormal"); - } + return cut[i][j]; +} - inum = list->inum; - ilist = list->ilist; - //Calculate normals - for (ii = 0; ii < inum; ii++) { - i = ilist[ii]; - xtp = x[i][0]; - ytp = x[i][1]; - ztp = x[i][2]; +/* ---------------------------------------------------------------------- + read Kolmogorov-Crespi potential file +------------------------------------------------------------------------- */ - // Initialize the arrays - for (id = 0; id < 3; id++){ - pv12[id] = 0.0; - pv31[id] = 0.0; - pv23[id] = 0.0; - n1[id] = 0.0; - dni[id] = 0.0; - normal[i][id] = 0.0; - for (ip = 0; ip < 3; ip++){ - vet[ip][id] = 0.0; - dnn[ip][id] = 0.0; - dpvdri[ip][id] = 0.0; - dnormdri[ip][id][i] = 0.0; - for (m = 0; m < 3; m++){ - dpv12[ip][id][m] = 0.0; - dpv31[ip][id][m] = 0.0; - dpv23[ip][id][m] = 0.0; - dn1[ip][id][m] = 0.0; - dnormal[ip][id][m][i] = 0.0; - } - } - } +void PairKolmogorovCrespiFull::read_file(char *filename) +{ + int params_per_line = 12; + char **words = new char*[params_per_line+1]; + memory->sfree(params); + params = NULL; + nparams = maxparam = 0; - cont = 0; - jlist = KC_firstneigh[i]; - jnum = KC_numneigh[i]; - for (jj = 0; jj < jnum; jj++) { - j = jlist[jj]; - j &= NEIGHMASK; + // open file on proc 0 - delx = x[j][0] - xtp; - dely = x[j][1] - ytp; - delz = x[j][2] - ztp; - vet[cont][0] = delx; - vet[cont][1] = dely; - vet[cont][2] = delz; - cont++; + FILE *fp; + if (comm->me == 0) { + fp = force->open_potential(filename); + if (fp == NULL) { + char str[128]; + snprintf(str,128,"Cannot open KC potential file %s",filename); + error->one(FLERR,str); } + } - if (cont <= 1) { - normal[i][0] = 0.0; - normal[i][1] = 0.0; - normal[i][2] = 1.0; - // derivatives of normal vector is zero - for (id = 0; id < 3; id++){ - for (ip = 0; ip < 3; ip++){ - dnormdri[id][ip][i] = 0.0; - for (m = 0; m < 3; m++){ - dnormal[id][ip][m][i] = 0.0; - } - } - } - } - else if (cont == 2) { - // for the atoms at the edge who has only two neighbor atoms - pv12[0] = vet[0][1]*vet[1][2] - vet[1][1]*vet[0][2]; - pv12[1] = vet[0][2]*vet[1][0] - vet[1][2]*vet[0][0]; - pv12[2] = vet[0][0]*vet[1][1] - vet[1][0]*vet[0][1]; - dpvdri[0][0] = 0.0; - dpvdri[0][1] = vet[0][2]-vet[1][2]; - dpvdri[0][2] = vet[1][1]-vet[0][1]; - dpvdri[1][0] = vet[1][2]-vet[0][2]; - dpvdri[1][1] = 0.0; - dpvdri[1][2] = vet[0][0]-vet[1][0]; - dpvdri[2][0] = vet[0][1]-vet[1][1]; - dpvdri[2][1] = vet[1][0]-vet[0][0]; - dpvdri[2][2] = 0.0; + // read each line out of file, skipping blank lines or leading '#' + // store line of params if all 3 element tags are in element list - // derivatives respect to the first neighbor, atom k - dpv12[0][0][0] = 0.0; - dpv12[0][1][0] = vet[1][2]; - dpv12[0][2][0] = -vet[1][1]; - dpv12[1][0][0] = -vet[1][2]; - dpv12[1][1][0] = 0.0; - dpv12[1][2][0] = vet[1][0]; - dpv12[2][0][0] = vet[1][1]; - dpv12[2][1][0] = -vet[1][0]; - dpv12[2][2][0] = 0.0; + int i,j,n,m,nwords,ielement,jelement; + char line[MAXLINE],*ptr; + int eof = 0; - // derivatives respect to the second neighbor, atom l - dpv12[0][0][1] = 0.0; - dpv12[0][1][1] = -vet[0][2]; - dpv12[0][2][1] = vet[0][1]; - dpv12[1][0][1] = vet[0][2]; - dpv12[1][1][1] = 0.0; - dpv12[1][2][1] = -vet[0][0]; - dpv12[2][0][1] = -vet[0][1]; - dpv12[2][1][1] = vet[0][0]; - dpv12[2][2][1] = 0.0; + while (1) { + if (comm->me == 0) { + ptr = fgets(line,MAXLINE,fp); + if (ptr == NULL) { + eof = 1; + fclose(fp); + } else n = strlen(line) + 1; + } + MPI_Bcast(&eof,1,MPI_INT,0,world); + if (eof) break; + MPI_Bcast(&n,1,MPI_INT,0,world); + MPI_Bcast(line,n,MPI_CHAR,0,world); - // derivatives respect to the third neighbor, atom n - for (id = 0; id < 3; id++){ - for (ip = 0; ip < 3; ip++){ - dpv12[id][ip][2] = 0.0; - } - } + // strip comment, skip line if blank - n1[0] = pv12[0]; - n1[1] = pv12[1]; - n1[2] = pv12[2]; - // the magnitude of the normal vector - nn2 = n1[0]*n1[0] + n1[1]*n1[1] + n1[2]*n1[2]; - nn = sqrt(nn2); - if (nn == 0) error->one(FLERR,"The magnitude of the normal vector is zero"); - // the unit normal vector - normal[i][0] = n1[0]/nn; - normal[i][1] = n1[1]/nn; - normal[i][2] = n1[2]/nn; - // derivatives of nn, dnn:3x1 vector - dni[0] = (n1[0]*dpvdri[0][0] + n1[1]*dpvdri[1][0] + n1[2]*dpvdri[2][0])/nn; - dni[1] = (n1[0]*dpvdri[0][1] + n1[1]*dpvdri[1][1] + n1[2]*dpvdri[2][1])/nn; - dni[2] = (n1[0]*dpvdri[0][2] + n1[1]*dpvdri[1][2] + n1[2]*dpvdri[2][2])/nn; - // derivatives of unit vector ni respect to ri, the result is 3x3 matrix - for (id = 0; id < 3; id++){ - for (ip = 0; ip < 3; ip++){ - dnormdri[id][ip][i] = dpvdri[id][ip]/nn - n1[id]*dni[ip]/nn2; - } - } + if ((ptr = strchr(line,'#'))) *ptr = '\0'; + nwords = atom->count_words(line); + if (nwords == 0) continue; - // derivatives of non-normalized normal vector, dn1:3x3x3 array - for (id = 0; id < 3; id++){ - for (ip = 0; ip < 3; ip++){ - for (m = 0; m < 3; m++){ - dn1[id][ip][m] = dpv12[id][ip][m]; - } - } - } - // derivatives of nn, dnn:3x3 vector - // dnn[id][m]: the derivative of nn respect to r[id][m], id,m=0,1,2 - // r[id][m]: the id's component of atom m - for (m = 0; m < 3; m++){ - for (id = 0; id < 3; id++){ - dnn[id][m] = (n1[0]*dn1[0][id][m] + n1[1]*dn1[1][id][m] + n1[2]*dn1[2][id][m])/nn; - } - } - // dnormal[id][ip][m][i]: the derivative of normal[id] respect to r[ip][m], id,ip=0,1,2 - // for atom m, which is a neighbor atom of atom i, m=0,jnum-1 - for (m = 0; m < 3; m++){ - for (id = 0; id < 3; id++){ - for (ip = 0; ip < 3; ip++){ - dnormal[id][ip][m][i] = dn1[id][ip][m]/nn - n1[id]*dnn[ip][m]/nn2; - } - } + // concatenate additional lines until have params_per_line words + + while (nwords < params_per_line) { + n = strlen(line); + if (comm->me == 0) { + ptr = fgets(&line[n],MAXLINE-n,fp); + if (ptr == NULL) { + eof = 1; + fclose(fp); + } else n = strlen(line) + 1; } + MPI_Bcast(&eof,1,MPI_INT,0,world); + if (eof) break; + MPI_Bcast(&n,1,MPI_INT,0,world); + MPI_Bcast(line,n,MPI_CHAR,0,world); + if ((ptr = strchr(line,'#'))) *ptr = '\0'; + nwords = atom->count_words(line); } -//############################################################################################## - else if(cont == 3) { - // for the atoms at the edge who has only two neighbor atoms - pv12[0] = vet[0][1]*vet[1][2] - vet[1][1]*vet[0][2]; - pv12[1] = vet[0][2]*vet[1][0] - vet[1][2]*vet[0][0]; - pv12[2] = vet[0][0]*vet[1][1] - vet[1][0]*vet[0][1]; - // derivatives respect to the first neighbor, atom k - dpv12[0][0][0] = 0.0; - dpv12[0][1][0] = vet[1][2]; - dpv12[0][2][0] = -vet[1][1]; - dpv12[1][0][0] = -vet[1][2]; - dpv12[1][1][0] = 0.0; - dpv12[1][2][0] = vet[1][0]; - dpv12[2][0][0] = vet[1][1]; - dpv12[2][1][0] = -vet[1][0]; - dpv12[2][2][0] = 0.0; - // derivatives respect to the second neighbor, atom l - dpv12[0][0][1] = 0.0; - dpv12[0][1][1] = -vet[0][2]; - dpv12[0][2][1] = vet[0][1]; - dpv12[1][0][1] = vet[0][2]; - dpv12[1][1][1] = 0.0; - dpv12[1][2][1] = -vet[0][0]; - dpv12[2][0][1] = -vet[0][1]; - dpv12[2][1][1] = vet[0][0]; - dpv12[2][2][1] = 0.0; + if (nwords != params_per_line) + error->all(FLERR,"Insufficient format in KC potential file"); - // derivatives respect to the third neighbor, atom n - for (id = 0; id < 3; id++){ - for (ip = 0; ip < 3; ip++){ - dpv12[id][ip][2] = 0.0; - } - } + // words = ptrs to all words in line - pv31[0] = vet[2][1]*vet[0][2] - vet[0][1]*vet[2][2]; - pv31[1] = vet[2][2]*vet[0][0] - vet[0][2]*vet[2][0]; - pv31[2] = vet[2][0]*vet[0][1] - vet[0][0]*vet[2][1]; - // derivatives respect to the first neighbor, atom k - dpv31[0][0][0] = 0.0; - dpv31[0][1][0] = -vet[2][2]; - dpv31[0][2][0] = vet[2][1]; - dpv31[1][0][0] = vet[2][2]; - dpv31[1][1][0] = 0.0; - dpv31[1][2][0] = -vet[2][0]; - dpv31[2][0][0] = -vet[2][1]; - dpv31[2][1][0] = vet[2][0]; - dpv31[2][2][0] = 0.0; - // derivatives respect to the third neighbor, atom n - dpv31[0][0][2] = 0.0; - dpv31[0][1][2] = vet[0][2]; - dpv31[0][2][2] = -vet[0][1]; - // derivatives of pv13[1] to rn - dpv31[1][0][2] = -vet[0][2]; - dpv31[1][1][2] = 0.0; - dpv31[1][2][2] = vet[0][0]; - // derivatives of pv13[2] to rn - dpv31[2][0][2] = vet[0][1]; - dpv31[2][1][2] = -vet[0][0]; - dpv31[2][2][2] = 0.0; + nwords = 0; + words[nwords++] = strtok(line," \t\n\r\f"); + while ((words[nwords++] = strtok(NULL," \t\n\r\f"))) continue; - // derivatives respect to the second neighbor, atom l - for (id = 0; id < 3; id++){ - for (ip = 0; ip < 3; ip++){ - dpv31[id][ip][1] = 0.0; - } - } + // ielement,jelement = 1st args + // if these 2 args are in element list, then parse this line + // else skip to next line (continue) - pv23[0] = vet[1][1]*vet[2][2] - vet[2][1]*vet[1][2]; - pv23[1] = vet[1][2]*vet[2][0] - vet[2][2]*vet[1][0]; - pv23[2] = vet[1][0]*vet[2][1] - vet[2][0]*vet[1][1]; - // derivatives respect to the second neighbor, atom k - for (id = 0; id < 3; id++){ - for (ip = 0; ip < 3; ip++){ - dpv23[id][ip][0] = 0.0; - } - } - // derivatives respect to the second neighbor, atom l - dpv23[0][0][1] = 0.0; - dpv23[0][1][1] = vet[2][2]; - dpv23[0][2][1] = -vet[2][1]; - dpv23[1][0][1] = -vet[2][2]; - dpv23[1][1][1] = 0.0; - dpv23[1][2][1] = vet[2][0]; - dpv23[2][0][1] = vet[2][1]; - dpv23[2][1][1] = -vet[2][0]; - dpv23[2][2][1] = 0.0; - // derivatives respect to the third neighbor, atom n - dpv23[0][0][2] = 0.0; - dpv23[0][1][2] = -vet[1][2]; - dpv23[0][2][2] = vet[1][1]; - dpv23[1][0][2] = vet[1][2]; - dpv23[1][1][2] = 0.0; - dpv23[1][2][2] = -vet[1][0]; - dpv23[2][0][2] = -vet[1][1]; - dpv23[2][1][2] = vet[1][0]; - dpv23[2][2][2] = 0.0; + for (ielement = 0; ielement < nelements; ielement++) + if (strcmp(words[0],elements[ielement]) == 0) break; + if (ielement == nelements) continue; + for (jelement = 0; jelement < nelements; jelement++) + if (strcmp(words[1],elements[jelement]) == 0) break; + if (jelement == nelements) continue; -//############################################################################################ - // average the normal vectors by using the 3 neighboring planes - n1[0] = (pv12[0] + pv31[0] + pv23[0])/cont; - n1[1] = (pv12[1] + pv31[1] + pv23[1])/cont; - n1[2] = (pv12[2] + pv31[2] + pv23[2])/cont; - // the magnitude of the normal vector - nn2 = n1[0]*n1[0] + n1[1]*n1[1] + n1[2]*n1[2]; - nn = sqrt(nn2); - if (nn == 0) error->one(FLERR,"The magnitude of the normal vector is zero"); - // the unit normal vector - normal[i][0] = n1[0]/nn; - normal[i][1] = n1[1]/nn; - normal[i][2] = n1[2]/nn; + // load up parameter settings and error check their values - // for the central atoms, dnormdri is always zero - for (id = 0; id < 3; id++){ - for (ip = 0; ip < 3; ip++){ - dnormdri[id][ip][i] = 0.0; - } - } // end of derivatives of normals respect to atom i + if (nparams == maxparam) { + maxparam += DELTA; + params = (Param *) memory->srealloc(params,maxparam*sizeof(Param), + "pair:params"); + } - // derivatives of non-normalized normal vector, dn1:3x3x3 array - for (id = 0; id < 3; id++){ - for (ip = 0; ip < 3; ip++){ - for (m = 0; m < 3; m++){ - dn1[id][ip][m] = (dpv12[id][ip][m] + dpv23[id][ip][m] + dpv31[id][ip][m])/cont; - } - } - } - // derivatives of nn, dnn:3x3 vector - // dnn[id][m]: the derivative of nn respect to r[id][m], id,m=0,1,2 - // r[id][m]: the id's component of atom m - for (m = 0; m < 3; m++){ - for (id = 0; id < 3; id++){ - dnn[id][m] = (n1[0]*dn1[0][id][m] + n1[1]*dn1[1][id][m] + n1[2]*dn1[2][id][m])/nn; - } - } - // dnormal[id][ip][m][i]: the derivative of normal[id] respect to r[ip][m], id,ip=0,1,2 - // for atom m, which is a neighbor atom of atom i, m=0,jnum-1 - for (m = 0; m < 3; m++){ - for (id = 0; id < 3; id++){ - for (ip = 0; ip < 3; ip++){ - dnormal[id][ip][m][i] = dn1[id][ip][m]/nn - n1[id]*dnn[ip][m]/nn2; - } + params[nparams].ielement = ielement; + params[nparams].jelement = jelement; + params[nparams].z0 = atof(words[2]); + params[nparams].C0 = atof(words[3]); + params[nparams].C2 = atof(words[4]); + params[nparams].C4 = atof(words[5]); + params[nparams].C = atof(words[6]); + params[nparams].delta = atof(words[7]); + params[nparams].lambda = atof(words[8]); + params[nparams].A = atof(words[9]); + // S provides a convenient scaling of all energies + params[nparams].S = atof(words[10]); + params[nparams].rcut = atof(words[11]); + + // energies in meV further scaled by S + double meV = 1.0e-3*params[nparams].S; + params[nparams].C *= meV; + params[nparams].A *= meV; + params[nparams].C0 *= meV; + params[nparams].C2 *= meV; + params[nparams].C4 *= meV; + + // precompute some quantities + params[nparams].delta2inv = pow(params[nparams].delta,-2); + params[nparams].z06 = pow(params[nparams].z0,6); + + nparams++; + //if(nparams >= pow(atom->ntypes,3)) break; + } + memory->destroy(elem2param); + memory->destroy(cutKCsq); + memory->create(elem2param,nelements,nelements,"pair:elem2param"); + memory->create(cutKCsq,nelements,nelements,"pair:cutKCsq"); + for (i = 0; i < nelements; i++) { + for (j = 0; j < nelements; j++) { + n = -1; + for (m = 0; m < nparams; m++) { + if (i == params[m].ielement && j == params[m].jelement) { + if (n >= 0) error->all(FLERR,"Potential file has duplicate entry"); + n = m; } } + if (n < 0) error->all(FLERR,"Potential file is missing an entry"); + elem2param[i][j] = n; + cutKCsq[i][j] = params[n].rcut*params[n].rcut; } - else { - error->one(FLERR,"There are too many neighbors for calculating normals"); - } - -//############################################################################################## } + delete [] words; } /* ---------------------------------------------------------------------- init specific to this pair style ------------------------------------------------------------------------- */ -void PairKolmogorovCrespiFull::init_style() -{ - if (force->newton_pair == 0) - error->all(FLERR,"Pair style kolmolgorov/crespi/full requires newton pair on"); - if (!atom->molecule_flag) - error->all(FLERR,"Pair style kolmolgorov/crespi/full requires atom attribute molecule"); +void PairKolmogorovCrespiFull::init_style() +{ + if (force->newton_pair == 0) + error->all(FLERR,"Pair style kolmolgorov/crespi/full requires newton pair on"); + if (!atom->molecule_flag) + error->all(FLERR,"Pair style kolmolgorov/crespi/full requires atom attribute molecule"); + + // need a full neighbor list, including neighbors of ghosts + + int irequest = neighbor->request(this,instance_me); + neighbor->requests[irequest]->half = 0; + neighbor->requests[irequest]->full = 1; + neighbor->requests[irequest]->ghost = 1; + + // local KC neighbor list + // create pages if first time or if neighbor pgsize/oneatom has changed + + int create = 0; + if (ipage == NULL) create = 1; + if (pgsize != neighbor->pgsize) create = 1; + if (oneatom != neighbor->oneatom) create = 1; + + if (create) { + delete [] ipage; + pgsize = neighbor->pgsize; + oneatom = neighbor->oneatom; + + int nmypage= comm->nthreads; + ipage = new MyPage[nmypage]; + for (int i = 0; i < nmypage; i++) + ipage[i].init(oneatom,pgsize,PGDELTA); + } +} + +/* ---------------------------------------------------------------------- */ + +void PairKolmogorovCrespiFull::compute(int eflag, int vflag) +{ + ev_init(eflag,vflag); + pvector[0] = pvector[1] = 0.0; + + // Build full neighbor list + KC_neigh(); + // Calculate the normals and its derivatives + calc_normal(); + // Calculate the van der Waals force and energy + calc_FvdW(eflag,vflag); + // Calculate the repulsive force and energy + calc_FRep(eflag,vflag); + + if (vflag_fdotr) virial_fdotr_compute(); +} + +/* ---------------------------------------------------------------------- + van der Waals forces and energy +------------------------------------------------------------------------- */ + +void PairKolmogorovCrespiFull::calc_FvdW(int eflag, int vflag) +{ + int i,j,ii,jj,inum,jnum,itype,jtype,k,l,kk,ll; + tagint itag,jtag; + double xtmp,ytmp,ztmp,delx,dely,delz,evdwl,fpair; + double rsq,r,Rcut,r2inv,r6inv,r8inv,Tap,dTap,Vkc,fsum; + int *ilist,*jlist,*numneigh,**firstneigh; + + evdwl = 0.0; + double **x = atom->x; + double **f = atom->f; + int *type = atom->type; + tagint *tag = atom->tag; + int nlocal = atom->nlocal; + int newton_pair = force->newton_pair; + + inum = list->inum; + ilist = list->ilist; + numneigh = list->numneigh; + firstneigh = list->firstneigh; + + // loop over neighbors of my atoms + for (ii = 0; ii < inum; ii++) { + i = ilist[ii]; + xtmp = x[i][0]; + ytmp = x[i][1]; + ztmp = x[i][2]; + itype = type[i]; + itag = tag[i]; + jlist = firstneigh[i]; + jnum = numneigh[i]; + + for (jj = 0; jj < jnum; jj++) { + j = jlist[jj]; + j &= NEIGHMASK; + jtype = type[j]; + jtag = tag[j]; - // need a full neighbor list, including neighbors of ghosts + // two-body interactions from full neighbor list, skip half of them + if (itag > jtag) { + if ((itag+jtag) % 2 == 0) continue; + } else if (itag < jtag) { + if ((itag+jtag) % 2 == 1) continue; + } else { + if (x[j][2] < ztmp) continue; + if (x[j][2] == ztmp && x[j][1] < ytmp) continue; + if (x[j][2] == ztmp && x[j][1] == ytmp && x[j][0] < xtmp) continue; + } - int irequest = neighbor->request(this,instance_me); - neighbor->requests[irequest]->half = 0; - neighbor->requests[irequest]->full = 1; - neighbor->requests[irequest]->ghost = 1; + delx = xtmp - x[j][0]; + dely = ytmp - x[j][1]; + delz = ztmp - x[j][2]; + rsq = delx*delx + dely*dely + delz*delz; - // local KC neighbor list - // create pages if first time or if neighbor pgsize/oneatom has changed + // only include the interation between different layers + if (rsq < cutsq[itype][jtype] && atom->molecule[i] != atom->molecule[j]) { - int create = 0; - if (ipage == NULL) create = 1; - if (pgsize != neighbor->pgsize) create = 1; - if (oneatom != neighbor->oneatom) create = 1; + int iparam_ij = elem2param[map[itype]][map[jtype]]; + Param& p = params[iparam_ij]; - if (create) { - delete [] ipage; - pgsize = neighbor->pgsize; - oneatom = neighbor->oneatom; + r = sqrt(rsq); + r2inv = 1.0/rsq; + r6inv = r2inv*r2inv*r2inv; + r8inv = r6inv*r2inv; + // turn on/off taper function + if (tap_flag) { + Rcut = sqrt(cutsq[itype][jtype]); + Tap = calc_Tap(r,Rcut); + dTap = calc_dTap(r,Rcut); + } else {Tap = 1.0; dTap = 0.0;} - int nmypage= comm->nthreads; - ipage = new MyPage[nmypage]; - for (int i = 0; i < nmypage; i++) - ipage[i].init(oneatom,pgsize,PGDELTA); + Vkc = -p.A*p.z06*r6inv; + + // derivatives + fpair = -6.0*p.A*p.z06*r8inv; + fsum = fpair*Tap - Vkc*dTap/r; + + f[i][0] += fsum*delx; + f[i][1] += fsum*dely; + f[i][2] += fsum*delz; + f[j][0] -= fsum*delx; + f[j][1] -= fsum*dely; + f[j][2] -= fsum*delz; + + if (eflag) pvector[0] += evdwl = Vkc*Tap; + if (evflag) ev_tally(i,j,nlocal,newton_pair, + evdwl,0.0,fsum,delx,dely,delz); + } + } } } - -/* ---------------------------------------------------------------------- - create neighbor list from main neighbor list for calculating the normals +/* ---------------------------------------------------------------------- + Repulsive forces and energy ------------------------------------------------------------------------- */ -void PairKolmogorovCrespiFull::KC_neigh() +void PairKolmogorovCrespiFull::calc_FRep(int eflag, int vflag) { - int i,j,ii,jj,n,allnum,jnum,itype,jtype; - double xtmp,ytmp,ztmp,delx,dely,delz,rsq; + int i,j,ii,jj,inum,jnum,itype,jtype,k,kk; + double prodnorm1,fkcx,fkcy,fkcz; + double xtmp,ytmp,ztmp,delx,dely,delz,evdwl,fpair,fpair1; + double rsq,r,rhosq1,exp0,exp1,r2inv,r6inv,r8inv,Tap,dTap,Vkc; + double frho_ij,sumC1,sumC11,sumCff,fsum,rho_ij; int *ilist,*jlist,*numneigh,**firstneigh; - int *neighptr; + int *KC_neighs_i,*KC_neighs_j; + + evdwl = 0.0; double **x = atom->x; + double **f = atom->f; int *type = atom->type; + int nlocal = atom->nlocal; + int newton_pair = force->newton_pair; + double dprodnorm1[3] = {0.0, 0.0, 0.0}; + double fp1[3] = {0.0, 0.0, 0.0}; + double fprod1[3] = {0.0, 0.0, 0.0}; + double delkj[3] = {0.0, 0.0, 0.0}; + double fk[3] = {0.0, 0.0, 0.0}; - if (atom->nmax > maxlocal) { - maxlocal = atom->nmax; - memory->destroy(KC_numneigh); - memory->sfree(KC_firstneigh); - memory->create(KC_numneigh,maxlocal,"KolmogorovCrespiFull:numneigh"); - KC_firstneigh = (int **) memory->smalloc(maxlocal*sizeof(int *), - "KolmogorovCrespiFull:firstneigh"); - } - - allnum = list->inum + list->gnum; + inum = list->inum; ilist = list->ilist; numneigh = list->numneigh; firstneigh = list->firstneigh; - // store all KC neighs of owned and ghost atoms - // scan full neighbor list of I - - ipage->reset(); - - for (ii = 0; ii < allnum; ii++) { + //calculate exp(-lambda*(r-z0))*[epsilon/2 + f(rho_ij)] + // loop over neighbors of owned atoms + for (ii = 0; ii < inum; ii++) { i = ilist[ii]; - - n = 0; - neighptr = ipage->vget(); - + if (KC_numneigh[i] == -1) { + continue; + } xtmp = x[i][0]; ytmp = x[i][1]; ztmp = x[i][2]; - itype = map[type[i]]; + itype = type[i]; jlist = firstneigh[i]; jnum = numneigh[i]; for (jj = 0; jj < jnum; jj++) { j = jlist[jj]; j &= NEIGHMASK; - jtype = map[type[j]]; + if (KC_numneigh[j] == -1) { + continue; + } + jtype = type[j]; + delx = xtmp - x[j][0]; dely = ytmp - x[j][1]; delz = ztmp - x[j][2]; rsq = delx*delx + dely*dely + delz*delz; - if (rsq != 0 && rsq < cutKCsq[itype][jtype] && atom->molecule[i] == atom->molecule[j]) { - neighptr[n++] = j; - } - } - - KC_firstneigh[i] = neighptr; - KC_numneigh[i] = n; - if (n > 3) error->one(FLERR,"There are too many neighbors for some atoms, please check your configuration"); - ipage->vgot(n); - if (ipage->status()) - error->one(FLERR,"Neighbor list overflow, boost neigh_modify one"); - } -} - + // only include the interation between different layers + if (rsq < cutsq[itype][jtype] && atom->molecule[i] != atom->molecule[j]) { -/* ---------------------------------------------------------------------- - allocate all arrays -------------------------------------------------------------------------- */ + int iparam_ij = elem2param[map[itype]][map[jtype]]; + Param& p = params[iparam_ij]; -void PairKolmogorovCrespiFull::allocate() -{ - allocated = 1; - int n = atom->ntypes; + r = sqrt(rsq); + r2inv = 1.0/rsq; + r6inv = r2inv*r2inv*r2inv; + r8inv = r2inv*r6inv; + // turn on/off taper function + if (tap_flag) { + Tap = calc_Tap(r,sqrt(cutsq[itype][jtype])); + dTap = calc_dTap(r,sqrt(cutsq[itype][jtype])); + } else {Tap = 1.0; dTap = 0.0;} - memory->create(setflag,n+1,n+1,"pair:setflag"); - for (int i = 1; i <= n; i++) - for (int j = i; j <= n; j++) - setflag[i][j] = 0; + // Calculate the transverse distance + prodnorm1 = normal[i][0]*delx + normal[i][1]*dely + normal[i][2]*delz; + rhosq1 = rsq - prodnorm1*prodnorm1; // rho_ij + rho_ij = rhosq1*p.delta2inv; // (rho_ij/delta)^2 - memory->create(cutsq,n+1,n+1,"pair:cutsq"); - memory->create(cut,n+1,n+1,"pair:cut"); - memory->create(offset,n+1,n+1,"pair:offset"); - map = new int[atom->ntypes+1]; -} + // store exponents + exp0 = exp(-p.lambda*(r-p.z0)); + exp1 = exp(-rho_ij); -/* ---------------------------------------------------------------------- - global settings -------------------------------------------------------------------------- */ + sumC1 = p.C0 + p.C2*rho_ij + p.C4*rho_ij*rho_ij; + sumC11 = (p.C2 + 2.0*p.C4*rho_ij)*p.delta2inv; + frho_ij = exp1*sumC1; + sumCff = 0.5*p.C + frho_ij; + Vkc = exp0*sumCff; -void PairKolmogorovCrespiFull::settings(int narg, char **arg) -{ - if (narg < 1 || narg > 2) error->all(FLERR,"Illegal pair_style command"); - if (strcmp(force->pair_style,"hybrid/overlay")!=0) - error->all(FLERR,"ERROR: requires hybrid/overlay pair_style"); + // derivatives + fpair = p.lambda*exp0/r*sumCff; + fpair1 = 2.0*exp0*exp1*(p.delta2inv*sumC1 - sumC11); + fsum = fpair + fpair1; + // derivatives of the product of rij and ni, the result is a vector + dprodnorm1[0] = dnormdri[0][0][i]*delx + dnormdri[1][0][i]*dely + dnormdri[2][0][i]*delz; + dprodnorm1[1] = dnormdri[0][1][i]*delx + dnormdri[1][1][i]*dely + dnormdri[2][1][i]*delz; + dprodnorm1[2] = dnormdri[0][2][i]*delx + dnormdri[1][2][i]*dely + dnormdri[2][2][i]*delz; + fp1[0] = prodnorm1*normal[i][0]*fpair1; + fp1[1] = prodnorm1*normal[i][1]*fpair1; + fp1[2] = prodnorm1*normal[i][2]*fpair1; + fprod1[0] = prodnorm1*dprodnorm1[0]*fpair1; + fprod1[1] = prodnorm1*dprodnorm1[1]*fpair1; + fprod1[2] = prodnorm1*dprodnorm1[2]*fpair1; + fkcx = (delx*fsum - fp1[0])*Tap - Vkc*dTap*delx/r; + fkcy = (dely*fsum - fp1[1])*Tap - Vkc*dTap*dely/r; + fkcz = (delz*fsum - fp1[2])*Tap - Vkc*dTap*delz/r; - cut_global = force->numeric(FLERR,arg[0]); - if (narg == 2) tap_flag = force->numeric(FLERR,arg[1]); + f[i][0] += fkcx - fprod1[0]*Tap; + f[i][1] += fkcy - fprod1[1]*Tap; + f[i][2] += fkcz - fprod1[2]*Tap; + f[j][0] -= fkcx; + f[j][1] -= fkcy; + f[j][2] -= fkcz; - // reset cutoffs that have been explicitly set + // calculate the forces acted on the neighbors of atom i from atom j + KC_neighs_i = KC_firstneigh[i]; + for (kk = 0; kk < KC_numneigh[i]; kk++) { + k = KC_neighs_i[kk]; + if (k == i) continue; + // derivatives of the product of rij and ni respect to rk, k=0,1,2, where atom k is the neighbors of atom i + dprodnorm1[0] = dnormal[0][0][kk][i]*delx + dnormal[1][0][kk][i]*dely + dnormal[2][0][kk][i]*delz; + dprodnorm1[1] = dnormal[0][1][kk][i]*delx + dnormal[1][1][kk][i]*dely + dnormal[2][1][kk][i]*delz; + dprodnorm1[2] = dnormal[0][2][kk][i]*delx + dnormal[1][2][kk][i]*dely + dnormal[2][2][kk][i]*delz; + fk[0] = (-prodnorm1*dprodnorm1[0]*fpair1)*Tap; + fk[1] = (-prodnorm1*dprodnorm1[1]*fpair1)*Tap; + fk[2] = (-prodnorm1*dprodnorm1[2]*fpair1)*Tap; + f[k][0] += fk[0]; + f[k][1] += fk[1]; + f[k][2] += fk[2]; + delkj[0] = x[k][0] - x[j][0]; + delkj[1] = x[k][1] - x[j][1]; + delkj[2] = x[k][2] - x[j][2]; + if (evflag) ev_tally_xyz(k,j,nlocal,newton_pair,0.0,0.0,fk[0],fk[1],fk[2],delkj[0],delkj[1],delkj[2]); + } - if (allocated) { - int i,j; - for (i = 1; i <= atom->ntypes; i++) - for (j = i; j <= atom->ntypes; j++) - if (setflag[i][j]) cut[i][j] = cut_global; - } + if (eflag) { + if (tap_flag) pvector[1] += evdwl = Tap*Vkc; + else pvector[1] += evdwl = Vkc - offset[itype][jtype]; + } + if (evflag) ev_tally_xyz(i,j,nlocal,newton_pair,evdwl,0.0,fkcx,fkcy,fkcz,delx,dely,delz); + } + } // loop over jj + } // loop over ii } /* ---------------------------------------------------------------------- - set coeffs for one or more type pairs + create neighbor list from main neighbor list for calculating the normals ------------------------------------------------------------------------- */ -void PairKolmogorovCrespiFull::coeff(int narg, char **arg) +void PairKolmogorovCrespiFull::KC_neigh() { - int i,j,n; - - if (narg != 3 + atom->ntypes) - error->all(FLERR,"Incorrect args for pair coefficients"); - if (!allocated) allocate(); - - // insure I,J args are * * - - if (strcmp(arg[0],"*") != 0 || strcmp(arg[1],"*") != 0) - error->all(FLERR,"Incorrect args for pair coefficients"); + int i,j,ii,jj,n,allnum,inum,jnum,itype,jtype; + double xtmp,ytmp,ztmp,delx,dely,delz,rsq; + int *ilist,*jlist,*numneigh,**firstneigh; + int *neighptr; - // read args that map atom types to elements in potential file - // map[i] = which element the Ith atom type is, -1 if NULL - // nelements = # of unique elements - // elements = list of element names + double **x = atom->x; + int *type = atom->type; - if (elements) { - for (i = 0; i < nelements; i++) delete [] elements[i]; - delete [] elements; + if (atom->nmax > maxlocal) { + maxlocal = atom->nmax; + memory->destroy(KC_numneigh); + memory->sfree(KC_firstneigh); + memory->create(KC_numneigh,maxlocal,"KolmogorovCrespiFull:numneigh"); + KC_firstneigh = (int **) memory->smalloc(maxlocal*sizeof(int *), + "KolmogorovCrespiFull:firstneigh"); } - elements = new char*[atom->ntypes]; - for (i = 0; i < atom->ntypes; i++) elements[i] = NULL; - nelements = 0; - for (i = 3; i < narg; i++) { - if (strcmp(arg[i],"NULL") == 0) { - map[i-2] = -1; - continue; - } - for (j = 0; j < nelements; j++) - if (strcmp(arg[i],elements[j]) == 0) break; - map[i-2] = j; - if (j == nelements) { - n = strlen(arg[i]) + 1; - elements[j] = new char[n]; - strcpy(elements[j],arg[i]); - nelements++; - } - } + inum = list->inum; + allnum = list->inum + list->gnum; + ilist = list->ilist; + numneigh = list->numneigh; + firstneigh = list->firstneigh; + // store all KC neighs of owned and ghost atoms + // scan full neighbor list of I - read_file(arg[2]); + ipage->reset(); - // clear setflag since coeff() called once with I,J = * * + for (ii = 0; ii < allnum; ii++) { + i = ilist[ii]; - n = atom->ntypes; - for (int i = 1; i <= n; i++) - for (int j = i; j <= n; j++) - setflag[i][j] = 0; + n = 0; + neighptr = ipage->vget(); - // set setflag i,j for type pairs where both are mapped to elements + xtmp = x[i][0]; + ytmp = x[i][1]; + ztmp = x[i][2]; + itype = map[type[i]]; + jlist = firstneigh[i]; + jnum = numneigh[i]; - int count = 0; - for (int i = 1; i <= n; i++) - for (int j = i; j <= n; j++) - if (map[i] >= 0 && map[j] >= 0) { - setflag[i][j] = 1; - cut[i][j] = cut_global; - count++; + for (jj = 0; jj < jnum; jj++) { + j = jlist[jj]; + j &= NEIGHMASK; + jtype = map[type[j]]; + delx = xtmp - x[j][0]; + dely = ytmp - x[j][1]; + delz = ztmp - x[j][2]; + rsq = delx*delx + dely*dely + delz*delz; + + if (rsq != 0 && rsq < cutKCsq[itype][jtype] && atom->molecule[i] == atom->molecule[j]) { + neighptr[n++] = j; } + } - if (count == 0) error->all(FLERR,"Incorrect args for pair coefficients"); -} + KC_firstneigh[i] = neighptr; + if (n == 3) { + KC_numneigh[i] = n; + } + else if (n < 3) { + if (i < inum) { + KC_numneigh[i] = n; + } else { + KC_numneigh[i] = -1; + } + } + else if (n > 3) error->one(FLERR,"There are too many neighbors for some atoms, please check your configuration"); + ipage->vgot(n); + if (ipage->status()) + error->one(FLERR,"Neighbor list overflow, boost neigh_modify one"); + } +} /* ---------------------------------------------------------------------- - init for one type pair i,j and corresponding j,i + Calculate the normals for each atom ------------------------------------------------------------------------- */ - -double PairKolmogorovCrespiFull::init_one(int i, int j) +void PairKolmogorovCrespiFull::calc_normal() { - if (setflag[i][j] == 0) error->all(FLERR,"All pair coeffs are not set"); - if (!offset_flag) - error->all(FLERR,"Must use 'pair_modify shift yes' with this pair style"); + int i,j,ii,jj,inum,jnum; + int cont,id,ip,m; + double nn,xtp,ytp,ztp,delx,dely,delz,nn2; + int *ilist,*jlist; + double pv12[3],pv31[3],pv23[3],n1[3],dni[3],dnn[3][3],vet[3][3],dpvdri[3][3]; + double dn1[3][3][3],dpv12[3][3][3],dpv23[3][3][3],dpv31[3][3][3]; - if (offset_flag && (cut[i][j] > 0.0)) { - int iparam_ij = elem2param[map[i]][map[j]]; - Param& p = params[iparam_ij]; - offset[i][j] = -p.A*pow(p.z0/cut[i][j],6); - } else offset[i][j] = 0.0; - offset[j][i] = offset[i][j]; + double **x = atom->x; - return cut[i][j]; -} + // grow normal array if necessary -/* ---------------------------------------------------------------------- - read Kolmogorov-Crespi potential file -------------------------------------------------------------------------- */ + if (atom->nmax > nmax) { + memory->destroy(normal); + memory->destroy(dnormal); + memory->destroy(dnormdri); + nmax = atom->nmax; + memory->create(normal,nmax,3,"KolmogorovCrespiFull:normal"); + memory->create(dnormdri,3,3,nmax,"KolmogorovCrespiFull:dnormdri"); + memory->create(dnormal,3,3,3,nmax,"KolmogorovCrespiFull:dnormal"); + } -void PairKolmogorovCrespiFull::read_file(char *filename) -{ - int params_per_line = 12; - char **words = new char*[params_per_line+1]; - memory->sfree(params); - params = NULL; - nparams = maxparam = 0; + inum = list->inum; + ilist = list->ilist; + //Calculate normals + for (ii = 0; ii < inum; ii++) { + i = ilist[ii]; - // open file on proc 0 + // Initialize the arrays + for (id = 0; id < 3; id++){ + pv12[id] = 0.0; + pv31[id] = 0.0; + pv23[id] = 0.0; + n1[id] = 0.0; + dni[id] = 0.0; + normal[i][id] = 0.0; + for (ip = 0; ip < 3; ip++){ + vet[ip][id] = 0.0; + dnn[ip][id] = 0.0; + dpvdri[ip][id] = 0.0; + dnormdri[ip][id][i] = 0.0; + for (m = 0; m < 3; m++){ + dpv12[ip][id][m] = 0.0; + dpv31[ip][id][m] = 0.0; + dpv23[ip][id][m] = 0.0; + dn1[ip][id][m] = 0.0; + dnormal[ip][id][m][i] = 0.0; + } + } + } - FILE *fp; - if (comm->me == 0) { - fp = force->open_potential(filename); - if (fp == NULL) { - char str[128]; - snprintf(str,128,"Cannot open KC potential file %s",filename); - error->one(FLERR,str); + if (KC_numneigh[i] == -1) { + continue; } - } + xtp = x[i][0]; + ytp = x[i][1]; + ztp = x[i][2]; - // read each line out of file, skipping blank lines or leading '#' - // store line of params if all 3 element tags are in element list + cont = 0; + jlist = KC_firstneigh[i]; + jnum = KC_numneigh[i]; + for (jj = 0; jj < jnum; jj++) { + j = jlist[jj]; + j &= NEIGHMASK; - int i,j,n,m,nwords,ielement,jelement; - char line[MAXLINE],*ptr; - int eof = 0; + delx = x[j][0] - xtp; + dely = x[j][1] - ytp; + delz = x[j][2] - ztp; + vet[cont][0] = delx; + vet[cont][1] = dely; + vet[cont][2] = delz; + cont++; + } - while (1) { - if (comm->me == 0) { - ptr = fgets(line,MAXLINE,fp); - if (ptr == NULL) { - eof = 1; - fclose(fp); - } else n = strlen(line) + 1; + if (cont <= 1) { + normal[i][0] = 0.0; + normal[i][1] = 0.0; + normal[i][2] = 1.0; + // derivatives of normal vector is zero + for (id = 0; id < 3; id++){ + for (ip = 0; ip < 3; ip++){ + dnormdri[id][ip][i] = 0.0; + for (m = 0; m < 3; m++){ + dnormal[id][ip][m][i] = 0.0; + } + } + } } - MPI_Bcast(&eof,1,MPI_INT,0,world); - if (eof) break; - MPI_Bcast(&n,1,MPI_INT,0,world); - MPI_Bcast(line,n,MPI_CHAR,0,world); + else if (cont == 2) { + // for the atoms at the edge who has only two neighbor atoms + pv12[0] = vet[0][1]*vet[1][2] - vet[1][1]*vet[0][2]; + pv12[1] = vet[0][2]*vet[1][0] - vet[1][2]*vet[0][0]; + pv12[2] = vet[0][0]*vet[1][1] - vet[1][0]*vet[0][1]; + dpvdri[0][0] = 0.0; + dpvdri[0][1] = vet[0][2]-vet[1][2]; + dpvdri[0][2] = vet[1][1]-vet[0][1]; + dpvdri[1][0] = vet[1][2]-vet[0][2]; + dpvdri[1][1] = 0.0; + dpvdri[1][2] = vet[0][0]-vet[1][0]; + dpvdri[2][0] = vet[0][1]-vet[1][1]; + dpvdri[2][1] = vet[1][0]-vet[0][0]; + dpvdri[2][2] = 0.0; - // strip comment, skip line if blank + // derivatives respect to the first neighbor, atom k + dpv12[0][0][0] = 0.0; + dpv12[0][1][0] = vet[1][2]; + dpv12[0][2][0] = -vet[1][1]; + dpv12[1][0][0] = -vet[1][2]; + dpv12[1][1][0] = 0.0; + dpv12[1][2][0] = vet[1][0]; + dpv12[2][0][0] = vet[1][1]; + dpv12[2][1][0] = -vet[1][0]; + dpv12[2][2][0] = 0.0; - if ((ptr = strchr(line,'#'))) *ptr = '\0'; - nwords = atom->count_words(line); - if (nwords == 0) continue; + // derivatives respect to the second neighbor, atom l + dpv12[0][0][1] = 0.0; + dpv12[0][1][1] = -vet[0][2]; + dpv12[0][2][1] = vet[0][1]; + dpv12[1][0][1] = vet[0][2]; + dpv12[1][1][1] = 0.0; + dpv12[1][2][1] = -vet[0][0]; + dpv12[2][0][1] = -vet[0][1]; + dpv12[2][1][1] = vet[0][0]; + dpv12[2][2][1] = 0.0; - // concatenate additional lines until have params_per_line words + // derivatives respect to the third neighbor, atom n + for (id = 0; id < 3; id++){ + for (ip = 0; ip < 3; ip++){ + dpv12[id][ip][2] = 0.0; + } + } - while (nwords < params_per_line) { - n = strlen(line); - if (comm->me == 0) { - ptr = fgets(&line[n],MAXLINE-n,fp); - if (ptr == NULL) { - eof = 1; - fclose(fp); - } else n = strlen(line) + 1; + n1[0] = pv12[0]; + n1[1] = pv12[1]; + n1[2] = pv12[2]; + // the magnitude of the normal vector + nn2 = n1[0]*n1[0] + n1[1]*n1[1] + n1[2]*n1[2]; + nn = sqrt(nn2); + if (nn == 0) error->one(FLERR,"The magnitude of the normal vector is zero"); + // the unit normal vector + normal[i][0] = n1[0]/nn; + normal[i][1] = n1[1]/nn; + normal[i][2] = n1[2]/nn; + // derivatives of nn, dnn:3x1 vector + dni[0] = (n1[0]*dpvdri[0][0] + n1[1]*dpvdri[1][0] + n1[2]*dpvdri[2][0])/nn; + dni[1] = (n1[0]*dpvdri[0][1] + n1[1]*dpvdri[1][1] + n1[2]*dpvdri[2][1])/nn; + dni[2] = (n1[0]*dpvdri[0][2] + n1[1]*dpvdri[1][2] + n1[2]*dpvdri[2][2])/nn; + // derivatives of unit vector ni respect to ri, the result is 3x3 matrix + for (id = 0; id < 3; id++){ + for (ip = 0; ip < 3; ip++){ + dnormdri[id][ip][i] = dpvdri[id][ip]/nn - n1[id]*dni[ip]/nn2; + } + } + + // derivatives of non-normalized normal vector, dn1:3x3x3 array + for (id = 0; id < 3; id++){ + for (ip = 0; ip < 3; ip++){ + for (m = 0; m < 3; m++){ + dn1[id][ip][m] = dpv12[id][ip][m]; + } + } + } + // derivatives of nn, dnn:3x3 vector + // dnn[id][m]: the derivative of nn respect to r[id][m], id,m=0,1,2 + // r[id][m]: the id's component of atom m + for (m = 0; m < 3; m++){ + for (id = 0; id < 3; id++){ + dnn[id][m] = (n1[0]*dn1[0][id][m] + n1[1]*dn1[1][id][m] + n1[2]*dn1[2][id][m])/nn; + } + } + // dnormal[id][ip][m][i]: the derivative of normal[id] respect to r[ip][m], id,ip=0,1,2 + // for atom m, which is a neighbor atom of atom i, m=0,jnum-1 + for (m = 0; m < 3; m++){ + for (id = 0; id < 3; id++){ + for (ip = 0; ip < 3; ip++){ + dnormal[id][ip][m][i] = dn1[id][ip][m]/nn - n1[id]*dnn[ip][m]/nn2; + } + } } - MPI_Bcast(&eof,1,MPI_INT,0,world); - if (eof) break; - MPI_Bcast(&n,1,MPI_INT,0,world); - MPI_Bcast(line,n,MPI_CHAR,0,world); - if ((ptr = strchr(line,'#'))) *ptr = '\0'; - nwords = atom->count_words(line); } +//############################################################################################## - if (nwords != params_per_line) - error->all(FLERR,"Insufficient format in KC potential file"); - - // words = ptrs to all words in line - - nwords = 0; - words[nwords++] = strtok(line," \t\n\r\f"); - while ((words[nwords++] = strtok(NULL," \t\n\r\f"))) continue; - - // ielement,jelement = 1st args - // if these 2 args are in element list, then parse this line - // else skip to next line (continue) + else if(cont == 3) { + // for the atoms at the edge who has only two neighbor atoms + pv12[0] = vet[0][1]*vet[1][2] - vet[1][1]*vet[0][2]; + pv12[1] = vet[0][2]*vet[1][0] - vet[1][2]*vet[0][0]; + pv12[2] = vet[0][0]*vet[1][1] - vet[1][0]*vet[0][1]; + // derivatives respect to the first neighbor, atom k + dpv12[0][0][0] = 0.0; + dpv12[0][1][0] = vet[1][2]; + dpv12[0][2][0] = -vet[1][1]; + dpv12[1][0][0] = -vet[1][2]; + dpv12[1][1][0] = 0.0; + dpv12[1][2][0] = vet[1][0]; + dpv12[2][0][0] = vet[1][1]; + dpv12[2][1][0] = -vet[1][0]; + dpv12[2][2][0] = 0.0; + // derivatives respect to the second neighbor, atom l + dpv12[0][0][1] = 0.0; + dpv12[0][1][1] = -vet[0][2]; + dpv12[0][2][1] = vet[0][1]; + dpv12[1][0][1] = vet[0][2]; + dpv12[1][1][1] = 0.0; + dpv12[1][2][1] = -vet[0][0]; + dpv12[2][0][1] = -vet[0][1]; + dpv12[2][1][1] = vet[0][0]; + dpv12[2][2][1] = 0.0; - for (ielement = 0; ielement < nelements; ielement++) - if (strcmp(words[0],elements[ielement]) == 0) break; - if (ielement == nelements) continue; - for (jelement = 0; jelement < nelements; jelement++) - if (strcmp(words[1],elements[jelement]) == 0) break; - if (jelement == nelements) continue; + // derivatives respect to the third neighbor, atom n + for (id = 0; id < 3; id++){ + for (ip = 0; ip < 3; ip++){ + dpv12[id][ip][2] = 0.0; + } + } - // load up parameter settings and error check their values + pv31[0] = vet[2][1]*vet[0][2] - vet[0][1]*vet[2][2]; + pv31[1] = vet[2][2]*vet[0][0] - vet[0][2]*vet[2][0]; + pv31[2] = vet[2][0]*vet[0][1] - vet[0][0]*vet[2][1]; + // derivatives respect to the first neighbor, atom k + dpv31[0][0][0] = 0.0; + dpv31[0][1][0] = -vet[2][2]; + dpv31[0][2][0] = vet[2][1]; + dpv31[1][0][0] = vet[2][2]; + dpv31[1][1][0] = 0.0; + dpv31[1][2][0] = -vet[2][0]; + dpv31[2][0][0] = -vet[2][1]; + dpv31[2][1][0] = vet[2][0]; + dpv31[2][2][0] = 0.0; + // derivatives respect to the third neighbor, atom n + dpv31[0][0][2] = 0.0; + dpv31[0][1][2] = vet[0][2]; + dpv31[0][2][2] = -vet[0][1]; + // derivatives of pv13[1] to rn + dpv31[1][0][2] = -vet[0][2]; + dpv31[1][1][2] = 0.0; + dpv31[1][2][2] = vet[0][0]; + // derivatives of pv13[2] to rn + dpv31[2][0][2] = vet[0][1]; + dpv31[2][1][2] = -vet[0][0]; + dpv31[2][2][2] = 0.0; - if (nparams == maxparam) { - maxparam += DELTA; - params = (Param *) memory->srealloc(params,maxparam*sizeof(Param), - "pair:params"); - } + // derivatives respect to the second neighbor, atom l + for (id = 0; id < 3; id++){ + for (ip = 0; ip < 3; ip++){ + dpv31[id][ip][1] = 0.0; + } + } - params[nparams].ielement = ielement; - params[nparams].jelement = jelement; - params[nparams].z0 = atof(words[2]); - params[nparams].C0 = atof(words[3]); - params[nparams].C2 = atof(words[4]); - params[nparams].C4 = atof(words[5]); - params[nparams].C = atof(words[6]); - params[nparams].delta = atof(words[7]); - params[nparams].lambda = atof(words[8]); - params[nparams].A = atof(words[9]); - // S provides a convenient scaling of all energies - params[nparams].S = atof(words[10]); - params[nparams].rcut = atof(words[11]); + pv23[0] = vet[1][1]*vet[2][2] - vet[2][1]*vet[1][2]; + pv23[1] = vet[1][2]*vet[2][0] - vet[2][2]*vet[1][0]; + pv23[2] = vet[1][0]*vet[2][1] - vet[2][0]*vet[1][1]; + // derivatives respect to the second neighbor, atom k + for (id = 0; id < 3; id++){ + for (ip = 0; ip < 3; ip++){ + dpv23[id][ip][0] = 0.0; + } + } + // derivatives respect to the second neighbor, atom l + dpv23[0][0][1] = 0.0; + dpv23[0][1][1] = vet[2][2]; + dpv23[0][2][1] = -vet[2][1]; + dpv23[1][0][1] = -vet[2][2]; + dpv23[1][1][1] = 0.0; + dpv23[1][2][1] = vet[2][0]; + dpv23[2][0][1] = vet[2][1]; + dpv23[2][1][1] = -vet[2][0]; + dpv23[2][2][1] = 0.0; + // derivatives respect to the third neighbor, atom n + dpv23[0][0][2] = 0.0; + dpv23[0][1][2] = -vet[1][2]; + dpv23[0][2][2] = vet[1][1]; + dpv23[1][0][2] = vet[1][2]; + dpv23[1][1][2] = 0.0; + dpv23[1][2][2] = -vet[1][0]; + dpv23[2][0][2] = -vet[1][1]; + dpv23[2][1][2] = vet[1][0]; + dpv23[2][2][2] = 0.0; - // energies in meV further scaled by S - double meV = 1.0e-3*params[nparams].S; - params[nparams].C *= meV; - params[nparams].A *= meV; - params[nparams].C0 *= meV; - params[nparams].C2 *= meV; - params[nparams].C4 *= meV; +//############################################################################################ + // average the normal vectors by using the 3 neighboring planes + n1[0] = (pv12[0] + pv31[0] + pv23[0])/cont; + n1[1] = (pv12[1] + pv31[1] + pv23[1])/cont; + n1[2] = (pv12[2] + pv31[2] + pv23[2])/cont; + // the magnitude of the normal vector + nn2 = n1[0]*n1[0] + n1[1]*n1[1] + n1[2]*n1[2]; + nn = sqrt(nn2); + if (nn == 0) error->one(FLERR,"The magnitude of the normal vector is zero"); + // the unit normal vector + normal[i][0] = n1[0]/nn; + normal[i][1] = n1[1]/nn; + normal[i][2] = n1[2]/nn; - // precompute some quantities - params[nparams].delta2inv = pow(params[nparams].delta,-2); - params[nparams].z06 = pow(params[nparams].z0,6); + // for the central atoms, dnormdri is always zero + for (id = 0; id < 3; id++){ + for (ip = 0; ip < 3; ip++){ + dnormdri[id][ip][i] = 0.0; + } + } // end of derivatives of normals respect to atom i - nparams++; - //if(nparams >= pow(atom->ntypes,3)) break; - } - memory->destroy(elem2param); - memory->destroy(cutKCsq); - memory->create(elem2param,nelements,nelements,"pair:elem2param"); - memory->create(cutKCsq,nelements,nelements,"pair:cutKCsq"); - for (i = 0; i < nelements; i++) { - for (j = 0; j < nelements; j++) { - n = -1; - for (m = 0; m < nparams; m++) { - if (i == params[m].ielement && j == params[m].jelement) { - if (n >= 0) error->all(FLERR,"Potential file has duplicate entry"); - n = m; + // derivatives of non-normalized normal vector, dn1:3x3x3 array + for (id = 0; id < 3; id++){ + for (ip = 0; ip < 3; ip++){ + for (m = 0; m < 3; m++){ + dn1[id][ip][m] = (dpv12[id][ip][m] + dpv23[id][ip][m] + dpv31[id][ip][m])/cont; + } } } - if (n < 0) error->all(FLERR,"Potential file is missing an entry"); - elem2param[i][j] = n; - cutKCsq[i][j] = params[n].rcut*params[n].rcut; + // derivatives of nn, dnn:3x3 vector + // dnn[id][m]: the derivative of nn respect to r[id][m], id,m=0,1,2 + // r[id][m]: the id's component of atom m + for (m = 0; m < 3; m++){ + for (id = 0; id < 3; id++){ + dnn[id][m] = (n1[0]*dn1[0][id][m] + n1[1]*dn1[1][id][m] + n1[2]*dn1[2][id][m])/nn; + } + } + // dnormal[id][ip][m][i]: the derivative of normal[id] respect to r[ip][m], id,ip=0,1,2 + // for atom m, which is a neighbor atom of atom i, m=0,jnum-1 + for (m = 0; m < 3; m++){ + for (id = 0; id < 3; id++){ + for (ip = 0; ip < 3; ip++){ + dnormal[id][ip][m][i] = dn1[id][ip][m]/nn - n1[id]*dnn[ip][m]/nn2; + } + } + } + } + else { + error->one(FLERR,"There are too many neighbors for calculating normals"); } + +//############################################################################################## } - delete [] words; } /* ---------------------------------------------------------------------- */ @@ -1066,69 +1137,3 @@ double PairKolmogorovCrespiFull::single(int /*i*/, int /*j*/, int itype, int jty else philj = Vkc - offset[itype][jtype]; return factor_lj*philj; } - -/* ---------------------------------------------------------------------- */ - -int PairKolmogorovCrespiFull::pack_forward_comm(int n, int *list, double *buf, - int /*pbc_flag*/, int * /*pbc*/) -{ - int i,j,m,l,ip,id; - - m = 0; - for (i = 0; i < n; i++) { - j = list[i]; - buf[m++] = normal[j][0]; - buf[m++] = normal[j][1]; - buf[m++] = normal[j][2]; - buf[m++] = dnormdri[0][0][j]; - buf[m++] = dnormdri[0][1][j]; - buf[m++] = dnormdri[0][2][j]; - buf[m++] = dnormdri[1][0][j]; - buf[m++] = dnormdri[1][1][j]; - buf[m++] = dnormdri[1][2][j]; - buf[m++] = dnormdri[2][0][j]; - buf[m++] = dnormdri[2][1][j]; - buf[m++] = dnormdri[2][2][j]; - for (l = 0; l < 3; l++){ - for (id = 0; id < 3; id++){ - for (ip = 0; ip < 3; ip++){ - buf[m++] = dnormal[id][ip][l][j]; - } - } - } - } - return m; -} - -/* ---------------------------------------------------------------------- */ - -void PairKolmogorovCrespiFull::unpack_forward_comm(int n, int first, double *buf) -{ - int i,m,last,l,ip,id; - - m = 0; - last = first + n; - for (i = first; i < last; i++) { - normal[i][0] = buf[m++]; - normal[i][1] = buf[m++]; - normal[i][2] = buf[m++]; - dnormdri[0][0][i] = buf[m++]; - dnormdri[0][1][i] = buf[m++]; - dnormdri[0][2][i] = buf[m++]; - dnormdri[1][0][i] = buf[m++]; - dnormdri[1][1][i] = buf[m++]; - dnormdri[1][2][i] = buf[m++]; - dnormdri[2][0][i] = buf[m++]; - dnormdri[2][1][i] = buf[m++]; - dnormdri[2][2][i] = buf[m++]; - for (l = 0; l < 3; l++){ - for (id = 0; id < 3; id++){ - for (ip = 0; ip < 3; ip++){ - dnormal[id][ip][l][i] = buf[m++]; - } - } - } - } -} - -/* ---------------------------------------------------------------------- */ diff --git a/src/USER-MISC/pair_kolmogorov_crespi_full.h b/src/USER-MISC/pair_kolmogorov_crespi_full.h index 68dede0dd5..81ab1984da 100644 --- a/src/USER-MISC/pair_kolmogorov_crespi_full.h +++ b/src/USER-MISC/pair_kolmogorov_crespi_full.h @@ -21,6 +21,8 @@ PairStyle(kolmogorov/crespi/full,PairKolmogorovCrespiFull) #define LMP_PAIR_KolmogorovCrespi_FULL_H #include "pair.h" +#include "my_page.h" +#include namespace LAMMPS_NS { @@ -34,9 +36,10 @@ class PairKolmogorovCrespiFull : public Pair { void coeff(int, char **); double init_one(int, int); void init_style(); + void KC_neigh(); void calc_normal(); - int pack_forward_comm(int, int *, double *, int, int *); - void unpack_forward_comm(int, int, double *); + void calc_FRep(int, int); + void calc_FvdW(int, int); double single(int, int, int, int, double, double, double, double &); protected: @@ -75,7 +78,6 @@ class PairKolmogorovCrespiFull : public Pair { void read_file( char * ); void allocate(); - void KC_neigh(); /* ----Calculate the long-range cutoff term */ -- GitLab From 76bac4cedce4d8021781636d33425716b01d6dc8 Mon Sep 17 00:00:00 2001 From: oywg11 Date: Thu, 1 Aug 2019 16:39:42 +0300 Subject: [PATCH 400/469] Fix communication bug of ILP --- .../Bi_gr_AB_stack_2L_noH.data | 1372 +++++++++++++++++ .../USER/misc/kolmogorov_crespi_full/CH.KC | 1 + .../misc/kolmogorov_crespi_full/CH_taper.KC | 1 + .../in.bilayer-graphene | 52 +- .../log.5Jun19.bilayer-graphene.icc.1 | 129 ++ .../log.5Jun19.bilayer-graphene.icc.4 | 129 ++ 6 files changed, 1654 insertions(+), 30 deletions(-) create mode 100644 examples/USER/misc/kolmogorov_crespi_full/Bi_gr_AB_stack_2L_noH.data create mode 120000 examples/USER/misc/kolmogorov_crespi_full/CH.KC create mode 120000 examples/USER/misc/kolmogorov_crespi_full/CH_taper.KC create mode 100644 examples/USER/misc/kolmogorov_crespi_full/log.5Jun19.bilayer-graphene.icc.1 create mode 100644 examples/USER/misc/kolmogorov_crespi_full/log.5Jun19.bilayer-graphene.icc.4 diff --git a/examples/USER/misc/kolmogorov_crespi_full/Bi_gr_AB_stack_2L_noH.data b/examples/USER/misc/kolmogorov_crespi_full/Bi_gr_AB_stack_2L_noH.data new file mode 100644 index 0000000000..756123a6f1 --- /dev/null +++ b/examples/USER/misc/kolmogorov_crespi_full/Bi_gr_AB_stack_2L_noH.data @@ -0,0 +1,1372 @@ + Generate Bi-layer graphene + + 1360 atoms + + 2 atom types + + 0.000000000000000 42.599999999999994 xlo xhi + 0.000000000000000 41.811706494712695 ylo yhi + 0.000000000000000 100.000000000000000 zlo zhi + + Atoms + + 1 1 1 0.000000000000000 0.000000000000000 1.229756073373903 0.000000000000000 + 2 1 1 0.000000000000000 0.710000000000000 0.000000000000000 0.000000000000000 + 3 1 1 0.000000000000000 2.130000000000000 0.000000000000000 0.000000000000000 + 4 1 1 0.000000000000000 2.840000000000000 1.229756073373903 0.000000000000000 + 5 1 1 0.000000000000000 4.260000000000000 1.229756073373903 0.000000000000000 + 6 1 1 0.000000000000000 4.970000000000000 0.000000000000000 0.000000000000000 + 7 1 1 0.000000000000000 6.390000000000000 0.000000000000000 0.000000000000000 + 8 1 1 0.000000000000000 7.100000000000000 1.229756073373903 0.000000000000000 + 9 1 1 0.000000000000000 8.520000000000000 1.229756073373903 0.000000000000000 + 10 1 1 0.000000000000000 9.230000000000000 0.000000000000000 0.000000000000000 + 11 1 1 0.000000000000000 10.649999999999999 0.000000000000000 0.000000000000000 + 12 1 1 0.000000000000000 11.359999999999999 1.229756073373903 0.000000000000000 + 13 1 1 0.000000000000000 12.779999999999999 1.229756073373903 0.000000000000000 + 14 1 1 0.000000000000000 13.489999999999998 0.000000000000000 0.000000000000000 + 15 1 1 0.000000000000000 14.910000000000000 0.000000000000000 0.000000000000000 + 16 1 1 0.000000000000000 15.619999999999999 1.229756073373903 0.000000000000000 + 17 1 1 0.000000000000000 17.039999999999999 1.229756073373903 0.000000000000000 + 18 1 1 0.000000000000000 17.750000000000000 0.000000000000000 0.000000000000000 + 19 1 1 0.000000000000000 19.169999999999998 0.000000000000000 0.000000000000000 + 20 1 1 0.000000000000000 19.879999999999999 1.229756073373903 0.000000000000000 + 21 1 1 0.000000000000000 21.299999999999997 1.229756073373903 0.000000000000000 + 22 1 1 0.000000000000000 22.009999999999998 0.000000000000000 0.000000000000000 + 23 1 1 0.000000000000000 23.429999999999996 0.000000000000000 0.000000000000000 + 24 1 1 0.000000000000000 24.139999999999997 1.229756073373903 0.000000000000000 + 25 1 1 0.000000000000000 25.559999999999999 1.229756073373903 0.000000000000000 + 26 1 1 0.000000000000000 26.270000000000000 0.000000000000000 0.000000000000000 + 27 1 1 0.000000000000000 27.689999999999998 0.000000000000000 0.000000000000000 + 28 1 1 0.000000000000000 28.399999999999999 1.229756073373903 0.000000000000000 + 29 1 1 0.000000000000000 29.820000000000000 1.229756073373903 0.000000000000000 + 30 1 1 0.000000000000000 30.530000000000001 0.000000000000000 0.000000000000000 + 31 1 1 0.000000000000000 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b/examples/USER/misc/kolmogorov_crespi_full/CH.KC @@ -0,0 +1 @@ +../../../../potentials/CH.KC \ No newline at end of file diff --git a/examples/USER/misc/kolmogorov_crespi_full/CH_taper.KC b/examples/USER/misc/kolmogorov_crespi_full/CH_taper.KC new file mode 120000 index 0000000000..2693646814 --- /dev/null +++ b/examples/USER/misc/kolmogorov_crespi_full/CH_taper.KC @@ -0,0 +1 @@ +../../../../potentials/CH_taper.KC \ No newline at end of file diff --git a/examples/USER/misc/kolmogorov_crespi_full/in.bilayer-graphene b/examples/USER/misc/kolmogorov_crespi_full/in.bilayer-graphene index c3e59337de..259604d953 100644 --- a/examples/USER/misc/kolmogorov_crespi_full/in.bilayer-graphene +++ b/examples/USER/misc/kolmogorov_crespi_full/in.bilayer-graphene @@ -5,21 +5,22 @@ atom_style full processors * * 1 # domain decomposition over x and y # System and atom definition -# we use 2 atom types so that inter- and intra-layer +# we use different molecule ids for each layer of hBN +# so that inter- and intra-layer # interactions can be specified separately -# read lammps data file -read_data Bi_gr_AB_stack_2L_noH_300K.data + +read_data Bi_gr_AB_stack_2L_noH.data mass 1 12.0107 # carbon mass (g/mole) | membrane mass 2 12.0107 # carbon mass (g/mole) | adsorbate # Separate atom groups -group membrane type 1 -group adsorbate type 2 +group layer1 molecule 1 +group layer2 molecule 2 ######################## Potential defition ######################## -pair_style hybrid/overlay rebo kolmogorov/crespi/full 16.0 +pair_style hybrid/overlay rebo kolmogorov/crespi/full 16.0 1 #################################################################### -pair_coeff * * rebo CH.rebo NULL C # chemical -pair_coeff * * kolmogorov/crespi/full CC.KC-full C C # long range +pair_coeff * * rebo CH.rebo C C # chemical +pair_coeff * * kolmogorov/crespi/full CH_taper.KC C C # long range #################################################################### # Neighbor update settings neighbor 2.0 bin @@ -27,34 +28,25 @@ neigh_modify every 1 neigh_modify delay 0 neigh_modify check yes -# calculate the COM -variable adsxcom equal xcm(adsorbate,x) -variable adsycom equal xcm(adsorbate,y) -variable adszcom equal xcm(adsorbate,z) -variable adsvxcom equal vcm(adsorbate,x) -variable adsvycom equal vcm(adsorbate,y) -variable adsvzcom equal vcm(adsorbate,z) - #### Simulation settings #### -timestep 0.001 -fix subf membrane setforce 0.0 0.0 0.0 -fix thermostat all nve +timestep 0.001 +velocity all create 300.0 12345 -compute 0 all pair rebo -compute 1 all pair kolmogorov/crespi/full -variable REBO equal c_0 -variable KC equal c_1 +compute 0 all pair rebo +compute 1 all pair kolmogorov/crespi/full +variable REBO equal c_0 # REBO energy +variable KC equal c_1 # total interlayer energy +variable Evdw equal c_1[1] # attractive energy +variable Erep equal c_1[2] # repulsive energy ############################ # Output thermo 100 -thermo_style custom step etotal pe ke v_REBO v_KC temp v_adsxcom v_adsycom v_adszcom v_adsvxcom v_adsvycom v_adsvzcom -thermo_modify line one format float %.10f -thermo_modify flush yes norm no lost warn #ignore - -#dump 1 all custom 1000 traj.lammpstrj id mol type xu yu zu -#dump_modify 1 format line "%7d %3d %3d %15.10g %15.10g %15.10g" flush yes +thermo_style custom step cpu etotal pe ke v_REBO v_KC v_Erep v_Evdw temp +thermo_modify line one format float %.16f +thermo_modify flush yes norm no lost warn ###### Run molecular dynamics ###### -run 1000 +fix thermostat all nve +run 1000 diff --git a/examples/USER/misc/kolmogorov_crespi_full/log.5Jun19.bilayer-graphene.icc.1 b/examples/USER/misc/kolmogorov_crespi_full/log.5Jun19.bilayer-graphene.icc.1 new file mode 100644 index 0000000000..f400df565c --- /dev/null +++ b/examples/USER/misc/kolmogorov_crespi_full/log.5Jun19.bilayer-graphene.icc.1 @@ -0,0 +1,129 @@ +LAMMPS (5 Jun 2019) +OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (../comm.cpp:88) + using 1 OpenMP thread(s) per MPI task +# Initialization +units metal +boundary p p p +atom_style full +processors * * 1 # domain decomposition over x and y + +# System and atom definition +# we use different molecule ids for each layer of hBN +# so that inter- and intra-layer +# interactions can be specified separately + +read_data Bi_gr_AB_stack_2L_noH.data + orthogonal box = (0 0 0) to (42.6 41.8117 100) + 1 by 1 by 1 MPI processor grid + reading atoms ... + 1360 atoms + 0 = max # of 1-2 neighbors + 0 = max # of 1-3 neighbors + 0 = max # of 1-4 neighbors + 1 = max # of special neighbors + special bonds CPU = 0.000143357 secs + read_data CPU = 0.00128686 secs +mass 1 12.0107 # carbon mass (g/mole) | membrane +mass 2 12.0107 # carbon mass (g/mole) | adsorbate +# Separate atom groups +group layer1 molecule 1 +680 atoms in group layer1 +group layer2 molecule 2 +680 atoms in group layer2 + +######################## Potential defition ######################## +pair_style hybrid/overlay rebo kolmogorov/crespi/full 16.0 1 +#################################################################### +pair_coeff * * rebo CH.rebo C C # chemical +Reading potential file CH.rebo with DATE: 2018-7-3 +pair_coeff * * kolmogorov/crespi/full CH_taper.KC C C # long range +#################################################################### +# Neighbor update settings +neighbor 2.0 bin +neigh_modify every 1 +neigh_modify delay 0 +neigh_modify check yes + +#### Simulation settings #### +timestep 0.001 +velocity all create 300.0 12345 + +compute 0 all pair rebo +compute 1 all pair kolmogorov/crespi/full +variable REBO equal c_0 # REBO energy +variable KC equal c_1 # total interlayer energy +variable Evdw equal c_1[1] # attractive energy +variable Erep equal c_1[2] # repulsive energy + +############################ + +# Output +thermo 100 +thermo_style custom step cpu etotal pe ke v_REBO v_KC v_Erep v_Evdw temp +thermo_modify line one format float %.16f +thermo_modify flush yes norm no lost warn + +###### Run molecular dynamics ###### +fix thermostat all nve +run 1000 +Neighbor list info ... + update every 1 steps, delay 0 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 18 + ghost atom cutoff = 18 + binsize = 9, bins = 5 5 12 + 2 neighbor lists, perpetual/occasional/extra = 2 0 0 + (1) pair rebo, perpetual + attributes: full, newton on, ghost + pair build: full/bin/ghost + stencil: full/ghost/bin/3d + bin: standard + (2) pair kolmogorov/crespi/full, perpetual, copy from (1) + attributes: full, newton on, ghost + pair build: copy + stencil: none + bin: none +Per MPI rank memory allocation (min/avg/max) = 17.21 | 17.21 | 17.21 Mbytes +Step CPU TotEng PotEng KinEng v_REBO v_KC v_Erep v_Evdw Temp + 0 0.0000000000000000 -10037.7640583248121402 -10090.4634194413119985 52.6993611164999436 -10057.1894932863488066 -33.2739261549639664 35.9559834316876348 -69.2299095866357561 299.9999999999996589 + 100 5.3877589240437374 -10037.5122858156355505 -10065.4637593850693520 27.9514735694345475 -10032.2132655062632693 -33.2504938788055995 25.2100699045900747 -58.4605637833913789 159.1184768311149185 + 200 10.7755050340201706 -10037.4414086674350983 -10061.6271012692632212 24.1856926018286202 -10028.9093252939674130 -32.7177759752951403 18.5366534598604176 -51.2544294351563394 137.6811336385792970 + 300 16.1665089030284435 -10037.4824653300311184 -10064.2845326005663082 26.8020672705344225 -10030.9195389405322203 -33.3649936600345924 26.3639208740001152 -59.7289145340284122 152.5752876469470891 + 400 21.5454839280573651 -10037.5105626329259394 -10064.8769084956420556 27.3663458627154164 -10031.8478821022799821 -33.0290263933626349 36.6142885774199272 -69.6433149707719963 155.7875386888538571 + 500 26.9370588400634006 -10037.5010433785082569 -10064.8363209936451312 27.3352776151367571 -10031.4417172103931080 -33.3946037832518243 26.2980262321670750 -59.6926300154142595 155.6106774503846850 + 600 32.4204196080099791 -10037.4817772372425679 -10064.1925798287738871 26.7108025915316247 -10031.4376178099264507 -32.7549620188478201 18.5745873777024606 -51.3295493965519327 152.0557480714992380 + 700 37.8001567909959704 -10037.4834430268438155 -10064.1291975032218033 26.6457544763788299 -10030.8722888097800023 -33.2569086934421492 25.2322818106646771 -58.4891905041015008 151.6854507067418467 + 800 43.1622281169984490 -10037.5047888097760733 -10064.8671187128948077 27.3623299031188978 -10031.9815058608437539 -32.8856128520517217 36.5236695083771536 -69.4092823604148350 155.7646771616279011 + 900 48.5261204120470211 -10037.5068323940176924 -10065.3998155271074211 27.8929831330889542 -10032.1734374829957233 -33.2263780441125931 27.7314849391008309 -60.9578629832065317 158.7855101588076820 + 1000 53.8888844919856638 -10037.4811494880468672 -10064.0099109142265661 26.5287614261789670 -10031.3325267421259923 -32.6773841721003464 18.9005970229871600 -51.5779811950879434 151.0194480396057202 +Loop time of 53.8889 on 1 procs for 1000 steps with 1360 atoms + +Performance: 1.603 ns/day, 14.969 hours/ns, 18.557 timesteps/s +100.0% CPU use with 1 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 53.836 | 53.836 | 53.836 | 0.0 | 99.90 +Bond | 0.00043479 | 0.00043479 | 0.00043479 | 0.0 | 0.00 +Neigh | 0 | 0 | 0 | 0.0 | 0.00 +Comm | 0.032452 | 0.032452 | 0.032452 | 0.0 | 0.06 +Output | 0.00058326 | 0.00058326 | 0.00058326 | 0.0 | 0.00 +Modify | 0.0094135 | 0.0094135 | 0.0094135 | 0.0 | 0.02 +Other | | 0.009815 | | | 0.02 + +Nlocal: 1360 ave 1360 max 1360 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 7964 ave 7964 max 7964 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 0 ave 0 max 0 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +FullNghs: 1.037e+06 ave 1.037e+06 max 1.037e+06 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 1037000 +Ave neighs/atom = 762.5 +Ave special neighs/atom = 0 +Neighbor list builds = 0 +Dangerous builds = 0 +Total wall time: 0:00:54 diff --git a/examples/USER/misc/kolmogorov_crespi_full/log.5Jun19.bilayer-graphene.icc.4 b/examples/USER/misc/kolmogorov_crespi_full/log.5Jun19.bilayer-graphene.icc.4 new file mode 100644 index 0000000000..ebb2c8c3fa --- /dev/null +++ b/examples/USER/misc/kolmogorov_crespi_full/log.5Jun19.bilayer-graphene.icc.4 @@ -0,0 +1,129 @@ +LAMMPS (5 Jun 2019) +OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (../comm.cpp:88) + using 1 OpenMP thread(s) per MPI task +# Initialization +units metal +boundary p p p +atom_style full +processors * * 1 # domain decomposition over x and y + +# System and atom definition +# we use different molecule ids for each layer of hBN +# so that inter- and intra-layer +# interactions can be specified separately + +read_data Bi_gr_AB_stack_2L_noH.data + orthogonal box = (0 0 0) to (42.6 41.8117 100) + 2 by 2 by 1 MPI processor grid + reading atoms ... + 1360 atoms + 0 = max # of 1-2 neighbors + 0 = max # of 1-3 neighbors + 0 = max # of 1-4 neighbors + 1 = max # of special neighbors + special bonds CPU = 0.000245051 secs + read_data CPU = 0.00257704 secs +mass 1 12.0107 # carbon mass (g/mole) | membrane +mass 2 12.0107 # carbon mass (g/mole) | adsorbate +# Separate atom groups +group layer1 molecule 1 +680 atoms in group layer1 +group layer2 molecule 2 +680 atoms in group layer2 + +######################## Potential defition ######################## +pair_style hybrid/overlay rebo kolmogorov/crespi/full 16.0 1 +#################################################################### +pair_coeff * * rebo CH.rebo C C # chemical +Reading potential file CH.rebo with DATE: 2018-7-3 +pair_coeff * * kolmogorov/crespi/full CH_taper.KC C C # long range +#################################################################### +# Neighbor update settings +neighbor 2.0 bin +neigh_modify every 1 +neigh_modify delay 0 +neigh_modify check yes + +#### Simulation settings #### +timestep 0.001 +velocity all create 300.0 12345 + +compute 0 all pair rebo +compute 1 all pair kolmogorov/crespi/full +variable REBO equal c_0 # REBO energy +variable KC equal c_1 # total interlayer energy +variable Evdw equal c_1[1] # attractive energy +variable Erep equal c_1[2] # repulsive energy + +############################ + +# Output +thermo 100 +thermo_style custom step cpu etotal pe ke v_REBO v_KC v_Erep v_Evdw temp +thermo_modify line one format float %.16f +thermo_modify flush yes norm no lost warn + +###### Run molecular dynamics ###### +fix thermostat all nve +run 1000 +Neighbor list info ... + update every 1 steps, delay 0 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 18 + ghost atom cutoff = 18 + binsize = 9, bins = 5 5 12 + 2 neighbor lists, perpetual/occasional/extra = 2 0 0 + (1) pair rebo, perpetual + attributes: full, newton on, ghost + pair build: full/bin/ghost + stencil: full/ghost/bin/3d + bin: standard + (2) pair kolmogorov/crespi/full, perpetual, copy from (1) + attributes: full, newton on, ghost + pair build: copy + stencil: none + bin: none +Per MPI rank memory allocation (min/avg/max) = 9.878 | 9.878 | 9.878 Mbytes +Step CPU TotEng PotEng KinEng v_REBO v_KC v_Erep v_Evdw Temp + 0 0.0000000000000000 -10037.7640583250176860 -10090.4634194415175443 52.6993611164999933 -10057.1894932866325689 -33.2739261548851388 35.9559834317043467 -69.2299095866038954 299.9999999999999432 + 100 1.5180600649910048 -10037.5122858156355505 -10065.4637593850711710 27.9514735694348637 -10032.2132655062741833 -33.2504938787968172 25.2100699046001573 -58.4605637833912795 159.1184768311167090 + 200 3.0089348420733586 -10037.4414086674296414 -10061.6271012692577642 24.1856926018279914 -10028.9093252939601371 -32.7177759752976272 18.5366534598677504 -51.2544294351567515 137.6811336385757158 + 300 4.5315427089808509 -10037.4824653300020145 -10064.2845326005372044 26.8020672705348311 -10030.9195389405158494 -33.3649936600211205 26.3639208740115549 -59.7289145340278722 152.5752876469494197 + 400 6.0353655620710924 -10037.5105626329095685 -10064.8769084956238657 27.3663458627148124 -10031.8478821022818011 -33.0290263933414394 36.6142885774347562 -69.6433149707726074 155.7875386888504181 + 500 7.5396006110822782 -10037.5010433784900670 -10064.8363209936269413 27.3352776151361780 -10031.4417172103858320 -33.3946037832416351 26.2980262321774489 -59.6926300154146787 155.6106774503813881 + 600 9.2617433650884777 -10037.4817772372534819 -10064.1925798287848011 26.7108025915320830 -10031.4376178099319077 -32.7549620188514226 18.5745873777100208 -51.3295493965524017 152.0557480715018528 + 700 10.7484918619738892 -10037.4834430268347205 -10064.1291975032127084 26.6457544763787268 -10030.8722888097836403 -33.2569086934306739 25.2322818106757047 -58.4891905041008613 151.6854507067412499 + 800 12.2509897360578179 -10037.5047888097869873 -10064.8671187129039026 27.3623299031166667 -10031.9815058608728577 -32.8856128520297801 36.5236695083899718 -69.4092823604150908 155.7646771616151966 + 900 13.7584852169966325 -10037.5068323939758557 -10065.3998155270637653 27.8929831330881477 -10032.1734374829648004 -33.2263780440982259 27.7314849391120788 -60.9578629832060841 158.7855101588031062 + 1000 15.2755981830414385 -10037.4811494880432292 -10064.0099109142211091 26.5287614261777058 -10031.3325267421205353 -32.6773841721017888 18.9005970229946634 -51.5779811950868776 151.0194480395985295 +Loop time of 15.2757 on 4 procs for 1000 steps with 1360 atoms + +Performance: 5.656 ns/day, 4.243 hours/ns, 65.464 timesteps/s +99.9% CPU use with 4 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 13.985 | 14.446 | 14.823 | 7.9 | 94.57 +Bond | 0.00040979 | 0.00042456 | 0.00046059 | 0.0 | 0.00 +Neigh | 0 | 0 | 0 | 0.0 | 0.00 +Comm | 0.43692 | 0.81428 | 1.2749 | 33.2 | 5.33 +Output | 0.00028016 | 0.00037143 | 0.00063561 | 0.0 | 0.00 +Modify | 0.0045586 | 0.0046468 | 0.0047903 | 0.1 | 0.03 +Other | | 0.01041 | | | 0.07 + +Nlocal: 340 ave 340 max 340 min +Histogram: 4 0 0 0 0 0 0 0 0 0 +Nghost: 4628 ave 4628 max 4628 min +Histogram: 4 0 0 0 0 0 0 0 0 0 +Neighs: 0 ave 0 max 0 min +Histogram: 4 0 0 0 0 0 0 0 0 0 +FullNghs: 259250 ave 259250 max 259250 min +Histogram: 4 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 1037000 +Ave neighs/atom = 762.5 +Ave special neighs/atom = 0 +Neighbor list builds = 0 +Dangerous builds = 0 +Total wall time: 0:00:15 -- GitLab From 5fe457667e31f52b772609f58e981ffff5adb93b Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Thu, 1 Aug 2019 11:19:39 -0400 Subject: [PATCH 401/469] restore showing references to potential files without pathnames --- doc/src/pair_ilp_graphene_hbn.txt | 8 ++++---- doc/src/pair_kolmogorov_crespi_full.txt | 6 +++--- 2 files changed, 7 insertions(+), 7 deletions(-) diff --git a/doc/src/pair_ilp_graphene_hbn.txt b/doc/src/pair_ilp_graphene_hbn.txt index 0e8ac5e9c5..6d922e20f9 100644 --- a/doc/src/pair_ilp_graphene_hbn.txt +++ b/doc/src/pair_ilp_graphene_hbn.txt @@ -18,12 +18,12 @@ tap_flag = 0/1 to turn off/on the taper function :ul [Examples:] pair_style hybrid/overlay ilp/graphene/hbn 16.0 1 -pair_coeff * * ilp/graphene/hbn ../potentials/BNCH.ILP B N C :pre +pair_coeff * * ilp/graphene/hbn BNCH.ILP B N C :pre pair_style hybrid/overlay rebo tersoff ilp/graphene/hbn 16.0 coul/shield 16.0 -pair_coeff * * rebo ../potentials/CH.rebo NULL NULL C -pair_coeff * * tersoff ../potentials/BNC.tersoff B N NULL -pair_coeff * * ilp/graphene/hbn ../potentials/BNCH.ILP B N C +pair_coeff * * rebo CH.rebo NULL NULL C +pair_coeff * * tersoff BNC.tersoff B N NULL +pair_coeff * * ilp/graphene/hbn BNCH.ILP B N C pair_coeff 1 1 coul/shield 0.70 pair_coeff 1 2 coul/shield 0.695 pair_coeff 2 2 coul/shield 0.69 :pre diff --git a/doc/src/pair_kolmogorov_crespi_full.txt b/doc/src/pair_kolmogorov_crespi_full.txt index bfadc33e30..5a2623ed89 100644 --- a/doc/src/pair_kolmogorov_crespi_full.txt +++ b/doc/src/pair_kolmogorov_crespi_full.txt @@ -19,11 +19,11 @@ tap_flag = 0/1 to turn off/on the taper function :ul pair_style hybrid/overlay kolmogorov/crespi/full 20.0 0 pair_coeff * * none -pair_coeff * * kolmogorov/crespi/full ../potentials/CH.KC C C :pre +pair_coeff * * kolmogorov/crespi/full CH.KC C C :pre pair_style hybrid/overlay rebo kolmogorov/crespi/full 16.0 1 -pair_coeff * * rebo ../potentials/CH.rebo C H -pair_coeff * * kolmogorov/crespi/full ../potentials/CH_taper.KC C H :pre +pair_coeff * * rebo CH.rebo C H +pair_coeff * * kolmogorov/crespi/full CH_taper.KC C H :pre [Description:] -- GitLab From 2fe4a6490c771ca44c1973854241591236f976cc Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Thu, 1 Aug 2019 11:20:06 -0400 Subject: [PATCH 402/469] restore include file cleanup changes --- src/USER-MISC/pair_ilp_graphene_hbn.cpp | 3 +-- src/USER-MISC/pair_ilp_graphene_hbn.h | 2 -- src/USER-MISC/pair_kolmogorov_crespi_full.cpp | 3 +-- src/USER-MISC/pair_kolmogorov_crespi_full.h | 2 -- 4 files changed, 2 insertions(+), 8 deletions(-) diff --git a/src/USER-MISC/pair_ilp_graphene_hbn.cpp b/src/USER-MISC/pair_ilp_graphene_hbn.cpp index a050f1f613..4741263603 100644 --- a/src/USER-MISC/pair_ilp_graphene_hbn.cpp +++ b/src/USER-MISC/pair_ilp_graphene_hbn.cpp @@ -20,12 +20,11 @@ [Kolmogorov & Crespi, Phys. Rev. B 71, 235415 (2005)] ------------------------------------------------------------------------- */ +#include "pair_ilp_graphene_hbn.h" #include #include -#include #include #include -#include "pair_ilp_graphene_hbn.h" #include "atom.h" #include "comm.h" #include "force.h" diff --git a/src/USER-MISC/pair_ilp_graphene_hbn.h b/src/USER-MISC/pair_ilp_graphene_hbn.h index 32bee4a10f..ec6146fa33 100644 --- a/src/USER-MISC/pair_ilp_graphene_hbn.h +++ b/src/USER-MISC/pair_ilp_graphene_hbn.h @@ -21,8 +21,6 @@ PairStyle(ilp/graphene/hbn,PairILPGrapheneHBN) #define LMP_PAIR_ILP_GRAPHENE_HBN_H #include "pair.h" -#include "my_page.h" -#include namespace LAMMPS_NS { diff --git a/src/USER-MISC/pair_kolmogorov_crespi_full.cpp b/src/USER-MISC/pair_kolmogorov_crespi_full.cpp index bfebb0c553..7bfbedfa1c 100644 --- a/src/USER-MISC/pair_kolmogorov_crespi_full.cpp +++ b/src/USER-MISC/pair_kolmogorov_crespi_full.cpp @@ -20,12 +20,11 @@ [Kolmogorov & Crespi, Phys. Rev. B 71, 235415 (2005)] ------------------------------------------------------------------------- */ +#include "pair_kolmogorov_crespi_full.h" #include -#include #include #include #include -#include "pair_kolmogorov_crespi_full.h" #include "atom.h" #include "comm.h" #include "force.h" diff --git a/src/USER-MISC/pair_kolmogorov_crespi_full.h b/src/USER-MISC/pair_kolmogorov_crespi_full.h index 81ab1984da..d2971e3fbc 100644 --- a/src/USER-MISC/pair_kolmogorov_crespi_full.h +++ b/src/USER-MISC/pair_kolmogorov_crespi_full.h @@ -21,8 +21,6 @@ PairStyle(kolmogorov/crespi/full,PairKolmogorovCrespiFull) #define LMP_PAIR_KolmogorovCrespi_FULL_H #include "pair.h" -#include "my_page.h" -#include namespace LAMMPS_NS { -- GitLab From 73d2b824bdb4826f000527d133ebf204d8fde30a Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Thu, 1 Aug 2019 13:31:13 -0400 Subject: [PATCH 403/469] fix compilation issue of library.cpp with exceptions enabled --- src/library.cpp | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/src/library.cpp b/src/library.cpp index eabe5fd179..c8c2c24146 100644 --- a/src/library.cpp +++ b/src/library.cpp @@ -38,6 +38,10 @@ #include "force.h" #include "info.h" +#if defined(LAMMPS_EXCEPTIONS) +#include "exceptions.h" +#endif + using namespace LAMMPS_NS; // ---------------------------------------------------------------------- -- GitLab From fa6a990536b8d3098f9699059ca5935ab66042bd Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Thu, 1 Aug 2019 13:31:52 -0400 Subject: [PATCH 404/469] reduce output precision to default and don't output per-step cpu time --- .../ilp_graphene_hbn/bilayer-graphene/in.bilayer-graphene | 5 ++--- 1 file changed, 2 insertions(+), 3 deletions(-) diff --git a/examples/USER/misc/ilp_graphene_hbn/bilayer-graphene/in.bilayer-graphene b/examples/USER/misc/ilp_graphene_hbn/bilayer-graphene/in.bilayer-graphene index 949de4b74c..0ef2787744 100644 --- a/examples/USER/misc/ilp_graphene_hbn/bilayer-graphene/in.bilayer-graphene +++ b/examples/USER/misc/ilp_graphene_hbn/bilayer-graphene/in.bilayer-graphene @@ -43,9 +43,8 @@ variable Erep equal c_1[2] # repulsive energy # Output thermo 100 -thermo_style custom step cpu etotal pe ke v_REBO v_ILP v_Erep v_Evdw temp -thermo_modify line one format float %.16f -thermo_modify flush yes norm no lost warn +thermo_style custom step etotal pe ke v_REBO v_ILP v_Erep v_Evdw temp +thermo_modify lost warn ###### Run molecular dynamics ###### fix thermostat all nve -- GitLab From 083841ab2a8b4acc5610e7b43202512ca3e0633f Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Thu, 1 Aug 2019 13:34:05 -0400 Subject: [PATCH 405/469] another compilation fix --- src/library.cpp | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/src/library.cpp b/src/library.cpp index c8c2c24146..6e7a104270 100644 --- a/src/library.cpp +++ b/src/library.cpp @@ -810,7 +810,9 @@ void lammps_gather_atoms(void *ptr, char * /*name */, LAMMPS *lmp = (LAMMPS *) ptr; BEGIN_CAPTURE - lmp->error->all(FLERR,"Library function lammps_gather_atoms() not compatible with -DLAMMPS_BIGBIG"); + { + lmp->error->all(FLERR,"Library function lammps_gather_atoms() not compatible with -DLAMMPS_BIGBIG"); + } END_CAPTURE } #else -- GitLab From 64b682b9f9f39a5c50aced907a5e8ff3880b8397 Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Thu, 1 Aug 2019 13:40:50 -0400 Subject: [PATCH 406/469] library compilation fix for clang with exceptions and -DLAMMPS_BIGBIG --- src/library.cpp | 23 ++++++++++++++++++----- 1 file changed, 18 insertions(+), 5 deletions(-) diff --git a/src/library.cpp b/src/library.cpp index 6e7a104270..30b7c7c7ce 100644 --- a/src/library.cpp +++ b/src/library.cpp @@ -811,7 +811,8 @@ void lammps_gather_atoms(void *ptr, char * /*name */, BEGIN_CAPTURE { - lmp->error->all(FLERR,"Library function lammps_gather_atoms() not compatible with -DLAMMPS_BIGBIG"); + lmp->error->all(FLERR,"Library function lammps_gather_atoms() " + "is not compatible with -DLAMMPS_BIGBIG"); } END_CAPTURE } @@ -950,7 +951,10 @@ void lammps_gather_atoms_concat(void *ptr, char * /*name */, LAMMPS *lmp = (LAMMPS *) ptr; BEGIN_CAPTURE - lmp->error->all(FLERR,"Library function lammps_gather_atoms_concat() not compatible with -DLAMMPS_BIGBIG"); + { + lmp->error->all(FLERR,"Library function lammps_gather_atoms_concat() " + "is not compatible with -DLAMMPS_BIGBIG"); + } END_CAPTURE } #else @@ -1107,7 +1111,10 @@ void lammps_gather_atoms_subset(void *ptr, char * /*name */, LAMMPS *lmp = (LAMMPS *) ptr; BEGIN_CAPTURE - lmp->error->all(FLERR,"Library function lammps_gather_atoms_subset() not compatible with -DLAMMPS_BIGBIG"); + { + lmp->error->all(FLERR,"Library function lammps_gather_atoms_subset() " + "is not compatible with -DLAMMPS_BIGBIG"); + } END_CAPTURE } #else @@ -1253,7 +1260,10 @@ void lammps_scatter_atoms(void *ptr, char * /*name */, LAMMPS *lmp = (LAMMPS *) ptr; BEGIN_CAPTURE - lmp->error->all(FLERR,"Library function lammps_scatter_atoms() not compatible with -DLAMMPS_BIGBIG"); + { + lmp->error->all(FLERR,"Library function lammps_scatter_atoms() " + "is not compatible with -DLAMMPS_BIGBIG"); + } END_CAPTURE } #else @@ -1379,7 +1389,10 @@ void lammps_scatter_atoms_subset(void *ptr, char * /*name */, LAMMPS *lmp = (LAMMPS *) ptr; BEGIN_CAPTURE - lmp->error->all(FLERR,"Library function lammps_scatter_atoms_subset() not compatible with -DLAMMPS_BIGBIG"); + { + lmp->error->all(FLERR,"Library function lammps_scatter_atoms_subset() " + "is not compatible with -DLAMMPS_BIGBIG"); + } END_CAPTURE } #else -- GitLab From 5fd323fe32b7c3a108879bd971818a48e366c49b Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Thu, 1 Aug 2019 14:24:47 -0400 Subject: [PATCH 407/469] simplify example folder for ilp/graphene/hbn potential - flatten directory structure - remove CPU time and reduce excess precision from output - delete redundant and unused files - regenerate reference outputs --- .../Bi_gr_AB_stack_2L_noH.data | 0 .../bilayer-graphene/BNCH-old.ILP | 1 - .../bilayer-graphene/BNCH.ILP | 1 - .../Bi_gr_AB_stack_2L_noH_300K.data | 2739 ----------------- .../bilayer-graphene/CH.airebo | 1 - .../ilp_graphene_hbn/bilayer-graphene/CH.rebo | 1 - .../log.16Mar18.bilayer-graphene.g++.1 | 137 - .../log.16Mar18.bilayer-graphene.g++.4 | 137 - .../log.5Jun19.bilayer-graphene.icc.1 | 128 - .../log.5Jun19.bilayer-graphene.icc.4 | 128 - .../ilp_graphene_hbn/bilayer-hBN/BNC.tersoff | 1 - .../ilp_graphene_hbn/bilayer-hBN/BNCH.ILP | 1 - .../misc/ilp_graphene_hbn/gr-hBN/BNC.tersoff | 1 - .../misc/ilp_graphene_hbn/gr-hBN/BNCH-old.ILP | 1 - .../misc/ilp_graphene_hbn/gr-hBN/BNCH.ILP | 1 - .../misc/ilp_graphene_hbn/gr-hBN/CH.airebo | 1 - .../USER/misc/ilp_graphene_hbn/gr-hBN/CH.rebo | 1 - .../gr-hBN/log.16Mar18.grhBN.g++.1 | 171 - .../gr-hBN/log.16Mar18.grhBN.g++.4 | 171 - .../{gr-hBN => }/gr_hBN_Cstack_2L_noH.data | 0 .../hBN_AA_prime_stack_2L_noH.data | 0 .../in.bilayer-graphene | 0 .../{bilayer-hBN => }/in.bilayer-hBN | 5 +- .../ilp_graphene_hbn/{gr-hBN => }/in.grhBN | 3 +- .../misc/ilp_graphene_hbn/in.ilp_graphene_hbn | 21 +- .../log.16Mar18.ilp_gr_hBN.g++.1 | 168 - .../log.16Mar18.ilp_gr_hBN.g++.4 | 168 - .../log.31Jul19.bilayer-graphene.g++.1 | 127 + .../log.31Jul19.bilayer-graphene.g++.4 | 127 + ...BN.icc.1 => log.31Jul19.bilayer-hBN.g++.1} | 58 +- ...BN.icc.4 => log.31Jul19.bilayer-hBN.g++.4} | 58 +- ...19.grhBN.icc.1 => log.31Jul19.grhBN.g++.1} | 52 +- ...19.grhBN.icc.4 => log.31Jul19.grhBN.g++.4} | 52 +- .../log.31Jul19.ilp_graphene_hbn.g++.1 | 154 + .../log.31Jul19.ilp_graphene_hbn.g++.4 | 154 + 35 files changed, 676 insertions(+), 4093 deletions(-) rename examples/USER/misc/ilp_graphene_hbn/{bilayer-graphene => }/Bi_gr_AB_stack_2L_noH.data (100%) delete mode 120000 examples/USER/misc/ilp_graphene_hbn/bilayer-graphene/BNCH-old.ILP delete mode 120000 examples/USER/misc/ilp_graphene_hbn/bilayer-graphene/BNCH.ILP delete mode 100644 examples/USER/misc/ilp_graphene_hbn/bilayer-graphene/Bi_gr_AB_stack_2L_noH_300K.data delete mode 120000 examples/USER/misc/ilp_graphene_hbn/bilayer-graphene/CH.airebo delete mode 120000 examples/USER/misc/ilp_graphene_hbn/bilayer-graphene/CH.rebo delete mode 100644 examples/USER/misc/ilp_graphene_hbn/bilayer-graphene/log.16Mar18.bilayer-graphene.g++.1 delete mode 100644 examples/USER/misc/ilp_graphene_hbn/bilayer-graphene/log.16Mar18.bilayer-graphene.g++.4 delete mode 100644 examples/USER/misc/ilp_graphene_hbn/bilayer-graphene/log.5Jun19.bilayer-graphene.icc.1 delete mode 100644 examples/USER/misc/ilp_graphene_hbn/bilayer-graphene/log.5Jun19.bilayer-graphene.icc.4 delete mode 120000 examples/USER/misc/ilp_graphene_hbn/bilayer-hBN/BNC.tersoff delete mode 120000 examples/USER/misc/ilp_graphene_hbn/bilayer-hBN/BNCH.ILP delete mode 120000 examples/USER/misc/ilp_graphene_hbn/gr-hBN/BNC.tersoff delete mode 120000 examples/USER/misc/ilp_graphene_hbn/gr-hBN/BNCH-old.ILP delete mode 120000 examples/USER/misc/ilp_graphene_hbn/gr-hBN/BNCH.ILP delete mode 120000 examples/USER/misc/ilp_graphene_hbn/gr-hBN/CH.airebo delete mode 120000 examples/USER/misc/ilp_graphene_hbn/gr-hBN/CH.rebo delete mode 100644 examples/USER/misc/ilp_graphene_hbn/gr-hBN/log.16Mar18.grhBN.g++.1 delete mode 100644 examples/USER/misc/ilp_graphene_hbn/gr-hBN/log.16Mar18.grhBN.g++.4 rename examples/USER/misc/ilp_graphene_hbn/{gr-hBN => }/gr_hBN_Cstack_2L_noH.data (100%) rename examples/USER/misc/ilp_graphene_hbn/{bilayer-hBN => }/hBN_AA_prime_stack_2L_noH.data (100%) rename examples/USER/misc/ilp_graphene_hbn/{bilayer-graphene => }/in.bilayer-graphene (100%) rename examples/USER/misc/ilp_graphene_hbn/{bilayer-hBN => }/in.bilayer-hBN (91%) rename examples/USER/misc/ilp_graphene_hbn/{gr-hBN => }/in.grhBN (96%) delete mode 100644 examples/USER/misc/ilp_graphene_hbn/log.16Mar18.ilp_gr_hBN.g++.1 delete mode 100644 examples/USER/misc/ilp_graphene_hbn/log.16Mar18.ilp_gr_hBN.g++.4 create mode 100644 examples/USER/misc/ilp_graphene_hbn/log.31Jul19.bilayer-graphene.g++.1 create mode 100644 examples/USER/misc/ilp_graphene_hbn/log.31Jul19.bilayer-graphene.g++.4 rename examples/USER/misc/ilp_graphene_hbn/{bilayer-hBN/log.5Jun19.bilayer_hBN.icc.1 => log.31Jul19.bilayer-hBN.g++.1} (56%) rename examples/USER/misc/ilp_graphene_hbn/{bilayer-hBN/log.5Jun19.bilayer_hBN.icc.4 => log.31Jul19.bilayer-hBN.g++.4} (56%) rename examples/USER/misc/ilp_graphene_hbn/{gr-hBN/log.5Jun19.grhBN.icc.1 => log.31Jul19.grhBN.g++.1} (60%) rename examples/USER/misc/ilp_graphene_hbn/{gr-hBN/log.5Jun19.grhBN.icc.4 => log.31Jul19.grhBN.g++.4} (60%) create mode 100644 examples/USER/misc/ilp_graphene_hbn/log.31Jul19.ilp_graphene_hbn.g++.1 create mode 100644 examples/USER/misc/ilp_graphene_hbn/log.31Jul19.ilp_graphene_hbn.g++.4 diff --git a/examples/USER/misc/ilp_graphene_hbn/bilayer-graphene/Bi_gr_AB_stack_2L_noH.data b/examples/USER/misc/ilp_graphene_hbn/Bi_gr_AB_stack_2L_noH.data similarity index 100% rename from examples/USER/misc/ilp_graphene_hbn/bilayer-graphene/Bi_gr_AB_stack_2L_noH.data rename to examples/USER/misc/ilp_graphene_hbn/Bi_gr_AB_stack_2L_noH.data diff --git a/examples/USER/misc/ilp_graphene_hbn/bilayer-graphene/BNCH-old.ILP b/examples/USER/misc/ilp_graphene_hbn/bilayer-graphene/BNCH-old.ILP deleted file mode 120000 index 9a3bc96225..0000000000 --- a/examples/USER/misc/ilp_graphene_hbn/bilayer-graphene/BNCH-old.ILP +++ /dev/null @@ -1 +0,0 @@ -../../../../../potentials/BNCH-old.ILP \ No newline at end of file diff --git a/examples/USER/misc/ilp_graphene_hbn/bilayer-graphene/BNCH.ILP b/examples/USER/misc/ilp_graphene_hbn/bilayer-graphene/BNCH.ILP deleted file mode 120000 index b970e23f95..0000000000 --- a/examples/USER/misc/ilp_graphene_hbn/bilayer-graphene/BNCH.ILP +++ /dev/null @@ -1 +0,0 @@ -../../../../../potentials/BNCH.ILP \ No newline at end of file diff --git a/examples/USER/misc/ilp_graphene_hbn/bilayer-graphene/Bi_gr_AB_stack_2L_noH_300K.data b/examples/USER/misc/ilp_graphene_hbn/bilayer-graphene/Bi_gr_AB_stack_2L_noH_300K.data deleted file mode 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b/examples/USER/misc/ilp_graphene_hbn/bilayer-graphene/CH.rebo deleted file mode 120000 index b98001a7fd..0000000000 --- a/examples/USER/misc/ilp_graphene_hbn/bilayer-graphene/CH.rebo +++ /dev/null @@ -1 +0,0 @@ -../../../../../potentials/CH.rebo \ No newline at end of file diff --git a/examples/USER/misc/ilp_graphene_hbn/bilayer-graphene/log.16Mar18.bilayer-graphene.g++.1 b/examples/USER/misc/ilp_graphene_hbn/bilayer-graphene/log.16Mar18.bilayer-graphene.g++.1 deleted file mode 100644 index b93108646e..0000000000 --- a/examples/USER/misc/ilp_graphene_hbn/bilayer-graphene/log.16Mar18.bilayer-graphene.g++.1 +++ /dev/null @@ -1,137 +0,0 @@ -LAMMPS (8 Mar 2018) - using 1 OpenMP thread(s) per MPI task -# Initialization -units metal -boundary p p p -atom_style full -processors * * 1 # domain decomposition over x and y - -# System and atom definition -# we use 2 atom types so that inter- and intra-layer -# interactions can be specified separately -# read lammps data file -read_data Bi_gr_AB_stack_2L_noH_300K.data - orthogonal box = (0 0 0) to (42.6 41.8117 100) - 1 by 1 by 1 MPI processor grid - reading atoms ... - 1360 atoms - reading velocities ... - 1360 velocities - 0 = max # of 1-2 neighbors - 0 = max # of 1-3 neighbors - 0 = max # of 1-4 neighbors - 1 = max # of special neighbors -mass 1 12.0107 # carbon mass (g/mole) | membrane -mass 2 12.0107 # carbon mass (g/mole) | adsorbate -# Separate atom groups -group membrane type 1 -680 atoms in group membrane -group adsorbate type 2 -680 atoms in group adsorbate - -######################## Potential defition ######################## -pair_style hybrid/overlay rebo ilp/graphene/hbn 16.0 -#################################################################### -pair_coeff * * rebo CH.airebo NULL C # chemical -Reading potential file CH.airebo with DATE: 2011-10-25 -pair_coeff * * ilp/graphene/hbn BNCH-old.ILP C C # long range -#################################################################### -# Neighbor update settings -neighbor 2.0 bin -neigh_modify every 1 -neigh_modify delay 0 -neigh_modify check yes - -# calculate the COM -variable adsxcom equal xcm(adsorbate,x) -variable adsycom equal xcm(adsorbate,y) -variable adszcom equal xcm(adsorbate,z) -variable adsvxcom equal vcm(adsorbate,x) -variable adsvycom equal vcm(adsorbate,y) -variable adsvzcom equal vcm(adsorbate,z) - -#### Simulation settings #### -timestep 0.001 -#velocity adsorbate create 300.0 12345 -fix subf membrane setforce 0.0 0.0 0.0 -fix thermostat all nve - -compute 0 all pair rebo -compute 1 all pair ilp/graphene/hbn -variable REBO equal c_0 -variable ILP equal c_1 - -############################ - -# Output -thermo 100 -thermo_style custom step etotal pe ke v_REBO v_ILP temp v_adsxcom v_adsycom v_adszcom v_adsvxcom v_adsvycom v_adsvzcom -thermo_modify line one format float %.10f -thermo_modify flush yes norm no lost warn - -#dump 1 all custom 1000 traj.lammpstrj id mol type xu yu zu -#dump_modify 1 format line "%7d %3d %3d %15.10g %15.10g %15.10g" flush yes - -###### Run molecular dynamics ###### -run 1000 -Neighbor list info ... - update every 1 steps, delay 0 steps, check yes - max neighbors/atom: 2000, page size: 100000 - master list distance cutoff = 18 - ghost atom cutoff = 18 - binsize = 9, bins = 5 5 12 - 2 neighbor lists, perpetual/occasional/extra = 2 0 0 - (1) pair rebo, perpetual, skip from (2) - attributes: full, newton on, ghost - pair build: skip/ghost - stencil: none - bin: none - (2) pair ilp/graphene/hbn, perpetual - attributes: full, newton on, ghost - pair build: full/bin/ghost - stencil: full/ghost/bin/3d - bin: standard -Per MPI rank memory allocation (min/avg/max) = 16.96 | 16.96 | 16.96 Mbytes -Step TotEng PotEng KinEng v_REBO v_ILP Temp v_adsxcom v_adsycom v_adszcom v_adsvxcom v_adsvycom v_adsvzcom - 0 -5029.3801131277 -5044.0700799791 14.6899668514 -5011.2636297759 -32.8064502032 83.6251135127 22.0155657205 20.2812150219 3.4623630945 0.0282287195 0.0535565745 0.2193320108 - 100 -5029.3895815657 -5045.3201249690 15.9305434033 -5012.4897058028 -32.8304191662 90.6873047362 22.0181751545 20.2867946176 3.4502536831 0.0239131349 0.0576557373 -0.4387830564 - 200 -5029.3874064119 -5045.8119502228 16.4245438109 -5012.7276250747 -33.0843251481 93.4994853617 22.0202931358 20.2926890775 3.3883512918 0.0180268639 0.0596894423 -0.6964675465 - 300 -5029.3851410393 -5044.9928147367 15.6076736974 -5012.1131531405 -32.8796615962 88.8493144891 22.0216852689 20.2985091183 3.3368274018 0.0093519893 0.0546775051 -0.2110676539 - 400 -5029.3900102082 -5045.6706717598 16.2806615516 -5012.7330095297 -32.9376622301 92.6804113372 22.0220931529 20.3035219616 3.3560233852 -0.0015365116 0.0454268927 0.5478139709 - 500 -5029.3985510533 -5046.0433160610 16.6447650078 -5013.0924334585 -32.9508826025 94.7531316612 22.0214795944 20.3074656871 3.4232399722 -0.0107212024 0.0332249366 0.6595923534 - 600 -5029.3929936746 -5045.4367231195 16.0437294449 -5012.7046931021 -32.7320300174 91.3316353653 22.0200027176 20.3101652565 3.4651727438 -0.0178110391 0.0210056002 0.1144372537 - 700 -5029.3934435811 -5045.6074608403 16.2140172592 -5012.7886962164 -32.8187646239 92.3010274644 22.0178838793 20.3116257077 3.4432436715 -0.0242636237 0.0078323424 -0.5162836955 - 800 -5029.3892931255 -5046.2270462380 16.8377531124 -5013.2383770824 -32.9886691555 95.8517489911 22.0151485191 20.3116305041 3.3780520461 -0.0302821178 -0.0083184719 -0.6710801515 - 900 -5029.3930414672 -5046.0272003818 16.6341589146 -5013.2317798384 -32.7954205434 94.6927546874 22.0119224940 20.3099187654 3.3350551183 -0.0341747588 -0.0256858066 -0.0799872839 - 1000 -5029.3908907831 -5045.6437703691 16.2528795861 -5012.6800867885 -32.9636835807 92.5222578135 22.0084902521 20.3065746721 3.3658243730 -0.0336536245 -0.0406018547 0.6191660974 -Loop time of 137.46 on 1 procs for 1000 steps with 1360 atoms - -Performance: 0.629 ns/day, 38.183 hours/ns, 7.275 timesteps/s -95.1% CPU use with 1 MPI tasks x 1 OpenMP threads - -MPI task timing breakdown: -Section | min time | avg time | max time |%varavg| %total ---------------------------------------------------------------- -Pair | 137.33 | 137.33 | 137.33 | 0.0 | 99.90 -Bond | 0.00071788 | 0.00071788 | 0.00071788 | 0.0 | 0.00 -Neigh | 0 | 0 | 0 | 0.0 | 0.00 -Comm | 0.067907 | 0.067907 | 0.067907 | 0.0 | 0.05 -Output | 0.0016029 | 0.0016029 | 0.0016029 | 0.0 | 0.00 -Modify | 0.036542 | 0.036542 | 0.036542 | 0.0 | 0.03 -Other | | 0.02574 | | | 0.02 - -Nlocal: 1360 ave 1360 max 1360 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Nghost: 7964 ave 7964 max 7964 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Neighs: 0 ave 0 max 0 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -FullNghs: 265206 ave 265206 max 265206 min -Histogram: 1 0 0 0 0 0 0 0 0 0 - -Total # of neighbors = 265206 -Ave neighs/atom = 195.004 -Ave special neighs/atom = 0 -Neighbor list builds = 0 -Dangerous builds = 0 -Total wall time: 0:02:17 diff --git a/examples/USER/misc/ilp_graphene_hbn/bilayer-graphene/log.16Mar18.bilayer-graphene.g++.4 b/examples/USER/misc/ilp_graphene_hbn/bilayer-graphene/log.16Mar18.bilayer-graphene.g++.4 deleted file mode 100644 index 6e28672714..0000000000 --- a/examples/USER/misc/ilp_graphene_hbn/bilayer-graphene/log.16Mar18.bilayer-graphene.g++.4 +++ /dev/null @@ -1,137 +0,0 @@ -LAMMPS (8 Mar 2018) - using 1 OpenMP thread(s) per MPI task -# Initialization -units metal -boundary p p p -atom_style full -processors * * 1 # domain decomposition over x and y - -# System and atom definition -# we use 2 atom types so that inter- and intra-layer -# interactions can be specified separately -# read lammps data file -read_data Bi_gr_AB_stack_2L_noH_300K.data - orthogonal box = (0 0 0) to (42.6 41.8117 100) - 2 by 2 by 1 MPI processor grid - reading atoms ... - 1360 atoms - reading velocities ... - 1360 velocities - 0 = max # of 1-2 neighbors - 0 = max # of 1-3 neighbors - 0 = max # of 1-4 neighbors - 1 = max # of special neighbors -mass 1 12.0107 # carbon mass (g/mole) | membrane -mass 2 12.0107 # carbon mass (g/mole) | adsorbate -# Separate atom groups -group membrane type 1 -680 atoms in group membrane -group adsorbate type 2 -680 atoms in group adsorbate - -######################## Potential defition ######################## -pair_style hybrid/overlay rebo ilp/graphene/hbn 16.0 -#################################################################### -pair_coeff * * rebo CH.airebo NULL C # chemical -Reading potential file CH.airebo with DATE: 2011-10-25 -pair_coeff * * ilp/graphene/hbn BNCH-old.ILP C C # long range -#################################################################### -# Neighbor update settings -neighbor 2.0 bin -neigh_modify every 1 -neigh_modify delay 0 -neigh_modify check yes - -# calculate the COM -variable adsxcom equal xcm(adsorbate,x) -variable adsycom equal xcm(adsorbate,y) -variable adszcom equal xcm(adsorbate,z) -variable adsvxcom equal vcm(adsorbate,x) -variable adsvycom equal vcm(adsorbate,y) -variable adsvzcom equal vcm(adsorbate,z) - -#### Simulation settings #### -timestep 0.001 -#velocity adsorbate create 300.0 12345 -fix subf membrane setforce 0.0 0.0 0.0 -fix thermostat all nve - -compute 0 all pair rebo -compute 1 all pair ilp/graphene/hbn -variable REBO equal c_0 -variable ILP equal c_1 - -############################ - -# Output -thermo 100 -thermo_style custom step etotal pe ke v_REBO v_ILP temp v_adsxcom v_adsycom v_adszcom v_adsvxcom v_adsvycom v_adsvzcom -thermo_modify line one format float %.10f -thermo_modify flush yes norm no lost warn - -#dump 1 all custom 1000 traj.lammpstrj id mol type xu yu zu -#dump_modify 1 format line "%7d %3d %3d %15.10g %15.10g %15.10g" flush yes - -###### Run molecular dynamics ###### -run 1000 -Neighbor list info ... - update every 1 steps, delay 0 steps, check yes - max neighbors/atom: 2000, page size: 100000 - master list distance cutoff = 18 - ghost atom cutoff = 18 - binsize = 9, bins = 5 5 12 - 2 neighbor lists, perpetual/occasional/extra = 2 0 0 - (1) pair rebo, perpetual, skip from (2) - attributes: full, newton on, ghost - pair build: skip/ghost - stencil: none - bin: none - (2) pair ilp/graphene/hbn, perpetual - attributes: full, newton on, ghost - pair build: full/bin/ghost - stencil: full/ghost/bin/3d - bin: standard -Per MPI rank memory allocation (min/avg/max) = 11.13 | 11.13 | 11.13 Mbytes -Step TotEng PotEng KinEng v_REBO v_ILP Temp v_adsxcom v_adsycom v_adszcom v_adsvxcom v_adsvycom v_adsvzcom - 0 -5029.3801131277 -5044.0700799791 14.6899668514 -5011.2636297759 -32.8064502032 83.6251135127 22.0155657205 20.2812150219 3.4623630945 0.0282287195 0.0535565745 0.2193320108 - 100 -5029.3895815657 -5045.3201249690 15.9305434033 -5012.4897058028 -32.8304191662 90.6873047362 22.0181751545 20.2867946176 3.4502536831 0.0239131349 0.0576557373 -0.4387830564 - 200 -5029.3874064119 -5045.8119502228 16.4245438109 -5012.7276250747 -33.0843251481 93.4994853617 22.0202931358 20.2926890775 3.3883512918 0.0180268639 0.0596894423 -0.6964675465 - 300 -5029.3851410393 -5044.9928147367 15.6076736974 -5012.1131531405 -32.8796615962 88.8493144891 22.0216852689 20.2985091183 3.3368274018 0.0093519893 0.0546775051 -0.2110676539 - 400 -5029.3900102082 -5045.6706717598 16.2806615516 -5012.7330095297 -32.9376622301 92.6804113371 22.0220931529 20.3035219616 3.3560233852 -0.0015365116 0.0454268927 0.5478139709 - 500 -5029.3985510533 -5046.0433160611 16.6447650078 -5013.0924334585 -32.9508826025 94.7531316612 22.0214795944 20.3074656871 3.4232399722 -0.0107212024 0.0332249366 0.6595923534 - 600 -5029.3929936746 -5045.4367231195 16.0437294449 -5012.7046931021 -32.7320300174 91.3316353653 22.0200027176 20.3101652565 3.4651727438 -0.0178110391 0.0210056002 0.1144372537 - 700 -5029.3934435811 -5045.6074608403 16.2140172592 -5012.7886962164 -32.8187646239 92.3010274643 22.0178838793 20.3116257077 3.4432436715 -0.0242636237 0.0078323424 -0.5162836955 - 800 -5029.3892931255 -5046.2270462380 16.8377531124 -5013.2383770824 -32.9886691555 95.8517489911 22.0151485191 20.3116305041 3.3780520461 -0.0302821178 -0.0083184719 -0.6710801515 - 900 -5029.3930414671 -5046.0272003818 16.6341589146 -5013.2317798384 -32.7954205434 94.6927546874 22.0119224940 20.3099187654 3.3350551183 -0.0341747588 -0.0256858066 -0.0799872839 - 1000 -5029.3908907831 -5045.6437703692 16.2528795861 -5012.6800867885 -32.9636835807 92.5222578135 22.0084902521 20.3065746721 3.3658243730 -0.0336536245 -0.0406018547 0.6191660974 -Loop time of 36.0917 on 4 procs for 1000 steps with 1360 atoms - -Performance: 2.394 ns/day, 10.025 hours/ns, 27.707 timesteps/s -97.6% CPU use with 4 MPI tasks x 1 OpenMP threads - -MPI task timing breakdown: -Section | min time | avg time | max time |%varavg| %total ---------------------------------------------------------------- -Pair | 33.204 | 34.289 | 35.893 | 17.3 | 95.01 -Bond | 0.00038719 | 0.00065947 | 0.00097609 | 0.0 | 0.00 -Neigh | 0 | 0 | 0 | 0.0 | 0.00 -Comm | 0.1539 | 1.7595 | 2.8464 | 76.7 | 4.88 -Output | 0.0013447 | 0.0014529 | 0.0016887 | 0.4 | 0.00 -Modify | 0.010811 | 0.012037 | 0.013764 | 1.0 | 0.03 -Other | | 0.0287 | | | 0.08 - -Nlocal: 340 ave 344 max 334 min -Histogram: 1 0 0 0 0 0 1 0 1 1 -Nghost: 4628 ave 4634 max 4624 min -Histogram: 1 0 1 0 1 0 0 0 0 1 -Neighs: 0 ave 0 max 0 min -Histogram: 4 0 0 0 0 0 0 0 0 0 -FullNghs: 66301.5 ave 67860 max 63963 min -Histogram: 1 0 0 0 0 0 1 0 1 1 - -Total # of neighbors = 265206 -Ave neighs/atom = 195.004 -Ave special neighs/atom = 0 -Neighbor list builds = 0 -Dangerous builds = 0 -Total wall time: 0:00:36 diff --git a/examples/USER/misc/ilp_graphene_hbn/bilayer-graphene/log.5Jun19.bilayer-graphene.icc.1 b/examples/USER/misc/ilp_graphene_hbn/bilayer-graphene/log.5Jun19.bilayer-graphene.icc.1 deleted file mode 100644 index bb36f22d81..0000000000 --- a/examples/USER/misc/ilp_graphene_hbn/bilayer-graphene/log.5Jun19.bilayer-graphene.icc.1 +++ /dev/null @@ -1,128 +0,0 @@ -LAMMPS (5 Jun 2019) -OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (../comm.cpp:88) - using 1 OpenMP thread(s) per MPI task -# Initialization -units metal -boundary p p p -atom_style full -processors * * 1 # domain decomposition over x and y - -# System and atom definition -# we use 2 molecule ids so that inter- and intra-layer -# interactions can be specified separately -# read lammps data file -read_data Bi_gr_AB_stack_2L_noH.data - orthogonal box = (0 0 0) to (42.6 41.8117 100) - 1 by 1 by 1 MPI processor grid - reading atoms ... - 1360 atoms - 0 = max # of 1-2 neighbors - 0 = max # of 1-3 neighbors - 0 = max # of 1-4 neighbors - 1 = max # of special neighbors - special bonds CPU = 0.00018123 secs - read_data CPU = 0.00179349 secs -mass 1 12.0107 # carbon mass (g/mole) | membrane -mass 2 12.0107 # carbon mass (g/mole) | adsorbate -# Separate atom groups -group layer1 molecule 1 -680 atoms in group layer1 -group layer2 molecule 2 -680 atoms in group layer2 - -######################## Potential defition ######################## -pair_style hybrid/overlay rebo ilp/graphene/hbn 16.0 -#################################################################### -pair_coeff * * rebo CH.rebo C C # chemical -Reading potential file CH.rebo with DATE: 2018-7-3 -pair_coeff * * ilp/graphene/hbn BNCH.ILP C C # long range -#################################################################### -# Neighbor update settings -neighbor 2.0 bin -neigh_modify every 1 -neigh_modify delay 0 -neigh_modify check yes - -#### Simulation settings #### -timestep 0.001 -velocity all create 300.0 12345 - -compute 0 all pair rebo -compute 1 all pair ilp/graphene/hbn -variable REBO equal c_0 # REBO energy -variable ILP equal c_1 # total interlayer energy -variable Evdw equal c_1[1] # attractive energy -variable Erep equal c_1[2] # repulsive energy - -############################ - -# Output -thermo 100 -thermo_style custom step cpu etotal pe ke v_REBO v_ILP v_Erep v_Evdw temp -thermo_modify line one format float %.16f -thermo_modify flush yes norm no lost warn - -###### Run molecular dynamics ###### -fix thermostat all nve -run 1000 -Neighbor list info ... - update every 1 steps, delay 0 steps, check yes - max neighbors/atom: 2000, page size: 100000 - master list distance cutoff = 18 - ghost atom cutoff = 18 - binsize = 9, bins = 5 5 12 - 2 neighbor lists, perpetual/occasional/extra = 2 0 0 - (1) pair rebo, perpetual - attributes: full, newton on, ghost - pair build: full/bin/ghost - stencil: full/ghost/bin/3d - bin: standard - (2) pair ilp/graphene/hbn, perpetual, copy from (1) - attributes: full, newton on, ghost - pair build: copy - stencil: none - bin: none -Per MPI rank memory allocation (min/avg/max) = 20.52 | 20.52 | 20.52 Mbytes -Step CPU TotEng PotEng KinEng v_REBO v_ILP v_Erep v_Evdw Temp - 0 0.0000000000000000 -10037.2853168513975106 -10089.9846779678973689 52.6993611164999436 -10057.1894932863488066 -32.7951846815484842 43.6401037466550932 -76.4352884281863538 299.9999999999996589 - 100 5.4714687280356884 -10037.0338552868142870 -10064.7651651140276954 27.7313098272134866 -10032.1809546658514591 -32.5842104481769326 34.7308676709731401 -67.3150781191208409 157.8651576016785896 - 200 10.9391297820257023 -10036.9626863095945737 -10061.1437965401473775 24.1811102305520329 -10028.8556641958457476 -32.2881323443021699 28.1799358234288526 -60.4680681676962450 137.6550477173489071 - 300 16.5882020250428468 -10037.0034097789539373 -10063.5001355365984637 26.4967257576440751 -10030.8230306457862753 -32.6771048908121244 34.9238490632189666 -67.6009539540019659 150.8370795942042264 - 400 22.1194989730138332 -10037.0320901258455706 -10064.3886163746337843 27.3565262487876240 -10031.8532011416427849 -32.5354152329904451 44.2423469839209460 -76.7777622168925546 155.7316388806602561 - 500 27.6722563949879259 -10037.0233394483148004 -10064.1136184894730832 27.0902790411580163 -10031.4312007416901906 -32.6824177477829565 37.2292320482101289 -69.9116497959676906 154.2159817531989177 - 600 33.2032995349727571 -10037.0033561502987141 -10063.6570740290953836 26.6537178787960869 -10031.3274097829344100 -32.3296642461602843 28.5090732059975061 -60.8387374521216842 151.7307837178934449 - 700 38.6685221369843930 -10037.0041655805853225 -10063.3498627390818001 26.3456971584966979 -10030.8006321783104795 -32.5492305607709014 32.5646861904578486 -65.1139167511948074 149.9773238251721921 - 800 44.2185375869739801 -10037.0245724491269357 -10064.2193369538654224 27.1947645047377584 -10031.7656842933574808 -32.4536526605085243 43.3815569718683705 -75.8352096323569498 154.8107828743098082 - 900 49.6989215560024604 -10037.0283918584391358 -10064.6675188165245345 27.6391269580851500 -10032.1673975747289660 -32.5001212417962648 39.9934500237055133 -72.4935712654787778 157.3403910741040761 - 1000 55.1455117090372369 -10037.0033475406326033 -10063.6621727186211501 26.6588251779885006 -10031.3371200905367004 -32.3250526280852100 29.5735783776502288 -61.8986310057011480 151.7598578798047697 -Loop time of 55.1456 on 1 procs for 1000 steps with 1360 atoms - -Performance: 1.567 ns/day, 15.318 hours/ns, 18.134 timesteps/s -100.0% CPU use with 1 MPI tasks x 1 OpenMP threads - -MPI task timing breakdown: -Section | min time | avg time | max time |%varavg| %total ---------------------------------------------------------------- -Pair | 55.092 | 55.092 | 55.092 | 0.0 | 99.90 -Bond | 0.00050265 | 0.00050265 | 0.00050265 | 0.0 | 0.00 -Neigh | 0 | 0 | 0 | 0.0 | 0.00 -Comm | 0.032649 | 0.032649 | 0.032649 | 0.0 | 0.06 -Output | 0.00060948 | 0.00060948 | 0.00060948 | 0.0 | 0.00 -Modify | 0.0093351 | 0.0093351 | 0.0093351 | 0.0 | 0.02 -Other | | 0.01008 | | | 0.02 - -Nlocal: 1360 ave 1360 max 1360 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Nghost: 7964 ave 7964 max 7964 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Neighs: 0 ave 0 max 0 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -FullNghs: 1.037e+06 ave 1.037e+06 max 1.037e+06 min -Histogram: 1 0 0 0 0 0 0 0 0 0 - -Total # of neighbors = 1037000 -Ave neighs/atom = 762.5 -Ave special neighs/atom = 0 -Neighbor list builds = 0 -Dangerous builds = 0 -Total wall time: 0:00:55 diff --git a/examples/USER/misc/ilp_graphene_hbn/bilayer-graphene/log.5Jun19.bilayer-graphene.icc.4 b/examples/USER/misc/ilp_graphene_hbn/bilayer-graphene/log.5Jun19.bilayer-graphene.icc.4 deleted file mode 100644 index 95c495b677..0000000000 --- a/examples/USER/misc/ilp_graphene_hbn/bilayer-graphene/log.5Jun19.bilayer-graphene.icc.4 +++ /dev/null @@ -1,128 +0,0 @@ -LAMMPS (5 Jun 2019) -OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (../comm.cpp:88) - using 1 OpenMP thread(s) per MPI task -# Initialization -units metal -boundary p p p -atom_style full -processors * * 1 # domain decomposition over x and y - -# System and atom definition -# we use 2 molecule ids so that inter- and intra-layer -# interactions can be specified separately -# read lammps data file -read_data Bi_gr_AB_stack_2L_noH.data - orthogonal box = (0 0 0) to (42.6 41.8117 100) - 2 by 2 by 1 MPI processor grid - reading atoms ... - 1360 atoms - 0 = max # of 1-2 neighbors - 0 = max # of 1-3 neighbors - 0 = max # of 1-4 neighbors - 1 = max # of special neighbors - special bonds CPU = 0.000147377 secs - read_data CPU = 0.0025185 secs -mass 1 12.0107 # carbon mass (g/mole) | membrane -mass 2 12.0107 # carbon mass (g/mole) | adsorbate -# Separate atom groups -group layer1 molecule 1 -680 atoms in group layer1 -group layer2 molecule 2 -680 atoms in group layer2 - -######################## Potential defition ######################## -pair_style hybrid/overlay rebo ilp/graphene/hbn 16.0 -#################################################################### -pair_coeff * * rebo CH.rebo C C # chemical -Reading potential file CH.rebo with DATE: 2018-7-3 -pair_coeff * * ilp/graphene/hbn BNCH.ILP C C # long range -#################################################################### -# Neighbor update settings -neighbor 2.0 bin -neigh_modify every 1 -neigh_modify delay 0 -neigh_modify check yes - -#### Simulation settings #### -timestep 0.001 -velocity all create 300.0 12345 - -compute 0 all pair rebo -compute 1 all pair ilp/graphene/hbn -variable REBO equal c_0 # REBO energy -variable ILP equal c_1 # total interlayer energy -variable Evdw equal c_1[1] # attractive energy -variable Erep equal c_1[2] # repulsive energy - -############################ - -# Output -thermo 100 -thermo_style custom step cpu etotal pe ke v_REBO v_ILP v_Erep v_Evdw temp -thermo_modify line one format float %.16f -thermo_modify flush yes norm no lost warn - -###### Run molecular dynamics ###### -fix thermostat all nve -run 1000 -Neighbor list info ... - update every 1 steps, delay 0 steps, check yes - max neighbors/atom: 2000, page size: 100000 - master list distance cutoff = 18 - ghost atom cutoff = 18 - binsize = 9, bins = 5 5 12 - 2 neighbor lists, perpetual/occasional/extra = 2 0 0 - (1) pair rebo, perpetual - attributes: full, newton on, ghost - pair build: full/bin/ghost - stencil: full/ghost/bin/3d - bin: standard - (2) pair ilp/graphene/hbn, perpetual, copy from (1) - attributes: full, newton on, ghost - pair build: copy - stencil: none - bin: none -Per MPI rank memory allocation (min/avg/max) = 11.64 | 11.64 | 11.64 Mbytes -Step CPU TotEng PotEng KinEng v_REBO v_ILP v_Erep v_Evdw Temp - 0 0.0000000000000000 -10037.2853168516194273 -10089.9846779681192857 52.6993611164999933 -10057.1894932866325689 -32.7951846814872354 43.6401037466782640 -76.4352884281594527 299.9999999999999432 - 100 1.5180878639221191 -10037.0338552867851831 -10064.7651651139967726 27.7313098272123320 -10032.1809546658569161 -32.5842104481406381 34.7308676709827395 -67.3150781191209546 157.8651576016720242 - 200 3.0293023219564930 -10036.9626863095381850 -10061.1437965400909889 24.1811102305529495 -10028.8556641958311957 -32.2881323442601911 28.1799358234373614 -60.4680681676959750 137.6550477173541367 - 300 4.5289151089964435 -10037.0034097789121006 -10063.5001355365566269 26.4967257576439188 -10030.8230306457808183 -32.6771048907772084 34.9238490632284311 -67.6009539540031454 150.8370795942033453 - 400 6.0309539699228480 -10037.0320901258182857 -10064.3886163746046805 27.3565262487870413 -10031.8532011416427849 -32.5354152329611424 44.2423469839354624 -76.7777622168941747 155.7316388806569307 - 500 7.5873900629812852 -10037.0233394482729636 -10064.1136184894312464 27.0902790411581904 -10031.4312007416810957 -32.6824177477510176 37.2292320482201404 -69.9116497959683159 154.2159817531999124 - 600 9.1088078819448128 -10037.0033561502586963 -10063.6570740290553658 26.6537178787959803 -10031.3274097829398670 -32.3296642461160033 28.5090732060055281 -60.8387374521202773 151.7307837178928480 - 700 10.6168858460150659 -10037.0041655805125629 -10063.3498627390090405 26.3456971584962574 -10030.8006321782777377 -32.5492305607314165 32.5646861904650535 -65.1139167511946653 149.9773238251696910 - 800 12.1294107990106568 -10037.0245724491123838 -10064.2193369538508705 27.1947645047383304 -10031.7656842933720327 -32.4536526604775162 43.3815569718824179 -75.8352096323571629 154.8107828743130767 - 900 13.6509861790109426 -10037.0283918584264029 -10064.6675188165099826 27.6391269580827625 -10032.1673975747471559 -32.5001212417642336 39.9934500237184380 -72.4935712654798436 157.3403910740904905 - 1000 15.1634582940023392 -10037.0033475405834906 -10063.6621727185720374 26.6588251779879926 -10031.3371200905276055 -32.3250526280445740 29.5735783776581442 -61.8986310057012972 151.7598578798018707 -Loop time of 15.1635 on 4 procs for 1000 steps with 1360 atoms - -Performance: 5.698 ns/day, 4.212 hours/ns, 65.948 timesteps/s -99.9% CPU use with 4 MPI tasks x 1 OpenMP threads - -MPI task timing breakdown: -Section | min time | avg time | max time |%varavg| %total ---------------------------------------------------------------- -Pair | 13.997 | 14.363 | 14.741 | 9.0 | 94.72 -Bond | 0.00036359 | 0.00040186 | 0.00044586 | 0.0 | 0.00 -Neigh | 0 | 0 | 0 | 0.0 | 0.00 -Comm | 0.40664 | 0.78485 | 1.1509 | 38.6 | 5.18 -Output | 0.00027687 | 0.00036825 | 0.00063194 | 0.0 | 0.00 -Modify | 0.0043962 | 0.0045847 | 0.0047857 | 0.2 | 0.03 -Other | | 0.01055 | | | 0.07 - -Nlocal: 340 ave 340 max 340 min -Histogram: 4 0 0 0 0 0 0 0 0 0 -Nghost: 4628 ave 4628 max 4628 min -Histogram: 4 0 0 0 0 0 0 0 0 0 -Neighs: 0 ave 0 max 0 min -Histogram: 4 0 0 0 0 0 0 0 0 0 -FullNghs: 259250 ave 259250 max 259250 min -Histogram: 4 0 0 0 0 0 0 0 0 0 - -Total # of neighbors = 1037000 -Ave neighs/atom = 762.5 -Ave special neighs/atom = 0 -Neighbor list builds = 0 -Dangerous builds = 0 -Total wall time: 0:00:15 diff --git a/examples/USER/misc/ilp_graphene_hbn/bilayer-hBN/BNC.tersoff b/examples/USER/misc/ilp_graphene_hbn/bilayer-hBN/BNC.tersoff deleted file mode 120000 index 0c35f80da1..0000000000 --- a/examples/USER/misc/ilp_graphene_hbn/bilayer-hBN/BNC.tersoff +++ /dev/null @@ -1 +0,0 @@ -../../../../../potentials/BNC.tersoff \ No newline at end of file diff --git a/examples/USER/misc/ilp_graphene_hbn/bilayer-hBN/BNCH.ILP b/examples/USER/misc/ilp_graphene_hbn/bilayer-hBN/BNCH.ILP deleted file mode 120000 index b970e23f95..0000000000 --- a/examples/USER/misc/ilp_graphene_hbn/bilayer-hBN/BNCH.ILP +++ /dev/null @@ -1 +0,0 @@ -../../../../../potentials/BNCH.ILP \ No newline at end of file diff --git a/examples/USER/misc/ilp_graphene_hbn/gr-hBN/BNC.tersoff b/examples/USER/misc/ilp_graphene_hbn/gr-hBN/BNC.tersoff deleted file mode 120000 index 0c35f80da1..0000000000 --- a/examples/USER/misc/ilp_graphene_hbn/gr-hBN/BNC.tersoff +++ /dev/null @@ -1 +0,0 @@ -../../../../../potentials/BNC.tersoff \ No newline at end of file diff --git a/examples/USER/misc/ilp_graphene_hbn/gr-hBN/BNCH-old.ILP b/examples/USER/misc/ilp_graphene_hbn/gr-hBN/BNCH-old.ILP deleted file mode 120000 index 9a3bc96225..0000000000 --- a/examples/USER/misc/ilp_graphene_hbn/gr-hBN/BNCH-old.ILP +++ /dev/null @@ -1 +0,0 @@ -../../../../../potentials/BNCH-old.ILP \ No newline at end of file diff --git a/examples/USER/misc/ilp_graphene_hbn/gr-hBN/BNCH.ILP b/examples/USER/misc/ilp_graphene_hbn/gr-hBN/BNCH.ILP deleted file mode 120000 index b970e23f95..0000000000 --- a/examples/USER/misc/ilp_graphene_hbn/gr-hBN/BNCH.ILP +++ /dev/null @@ -1 +0,0 @@ -../../../../../potentials/BNCH.ILP \ No newline at end of file diff --git a/examples/USER/misc/ilp_graphene_hbn/gr-hBN/CH.airebo b/examples/USER/misc/ilp_graphene_hbn/gr-hBN/CH.airebo deleted file mode 120000 index 5d070dd3a4..0000000000 --- a/examples/USER/misc/ilp_graphene_hbn/gr-hBN/CH.airebo +++ /dev/null @@ -1 +0,0 @@ -../../../../../potentials/CH.airebo \ No newline at end of file diff --git a/examples/USER/misc/ilp_graphene_hbn/gr-hBN/CH.rebo b/examples/USER/misc/ilp_graphene_hbn/gr-hBN/CH.rebo deleted file mode 120000 index b98001a7fd..0000000000 --- a/examples/USER/misc/ilp_graphene_hbn/gr-hBN/CH.rebo +++ /dev/null @@ -1 +0,0 @@ -../../../../../potentials/CH.rebo \ No newline at end of file diff --git a/examples/USER/misc/ilp_graphene_hbn/gr-hBN/log.16Mar18.grhBN.g++.1 b/examples/USER/misc/ilp_graphene_hbn/gr-hBN/log.16Mar18.grhBN.g++.1 deleted file mode 100644 index e5bce94ef4..0000000000 --- a/examples/USER/misc/ilp_graphene_hbn/gr-hBN/log.16Mar18.grhBN.g++.1 +++ /dev/null @@ -1,171 +0,0 @@ -LAMMPS (8 Mar 2018) - using 1 OpenMP thread(s) per MPI task -# Initialization -units metal -boundary p p p -atom_style full -processors * * 1 # domain decomposition over x and y - -# System and atom definition -# we use 2 atom types so that inter- and intra-layer -# interactions can be specified separately -read_data gr_hBN_Cstack_2L_noH.data - orthogonal box = (0 0 0) to (44.583 42.9 100) - 1 by 1 by 1 MPI processor grid - reading atoms ... - 1440 atoms - 0 = max # of 1-2 neighbors - 0 = max # of 1-3 neighbors - 0 = max # of 1-4 neighbors - 1 = max # of special neighbors -mass 1 10.8110 # boron mass (g/mole) | membrane -mass 2 14.0067 # nitrogen mass (g/mole) | membrane -mass 3 12.0107 # carbon mass (g/mole) | adsorbate -# Separate atom groups -group membrane type 1 2 -720 atoms in group membrane -group adsorbate type 3 -720 atoms in group adsorbate - -######################## Potential defition ######################## -pair_style hybrid/overlay rebo tersoff ilp/graphene/hbn 16.0 coul/shield 16.0 -#################################################################### -pair_coeff * * rebo CH.airebo NULL NULL C # chemical -Reading potential file CH.airebo with DATE: 2011-10-25 -pair_coeff * * tersoff BNC.tersoff B N NULL # chemical -Reading potential file BNC.tersoff with DATE: 2013-03-21 -pair_coeff * * ilp/graphene/hbn BNCH-old.ILP B N C # long range -pair_coeff 1 1 coul/shield 0.70 -pair_coeff 1 2 coul/shield 0.69498201415576216335 -pair_coeff 2 2 coul/shield 0.69 -#################################################################### -# Neighbor update settings -neighbor 2.0 bin -neigh_modify every 1 -neigh_modify delay 0 -neigh_modify check yes - -# calculate the COM -variable adsxcom equal xcm(adsorbate,x) -variable adsycom equal xcm(adsorbate,y) -variable adszcom equal xcm(adsorbate,z) -variable adsvxcom equal vcm(adsorbate,x) -variable adsvycom equal vcm(adsorbate,y) -variable adsvzcom equal vcm(adsorbate,z) - -#### Simulation settings #### -timestep 0.001 -velocity all create 300.0 12345 -fix thermostat all nve - -compute 0 all pair rebo -compute 1 all pair tersoff -compute 2 all pair ilp/graphene/hbn -compute 3 all pair coul/shield -variable REBO equal c_0 -variable Tersoff equal c_1 -variable EILP equal c_2 -variable Ecoul equal c_3 - -# Calculate the pair potential between the substrate and slider -compute sldsub adsorbate group/group membrane -variable Evdw equal c_sldsub - -############################ - -# Output -thermo 100 -thermo_style custom step etotal pe ke v_Evdw v_Tersoff v_REBO v_EILP v_Ecoul temp v_adsxcom v_adsycom v_adszcom v_adsvxcom v_adsvycom v_adsvzcom -thermo_modify line one format float %.10f - -#dump 1 all custom 1000 traj.lammpstrj id mol type xu yu zu -#dump_modify 1 format line "%7d %3d %3d %15.10g %15.10g %15.10g" flush yes - -###### Run molecular dynamics ###### -run 1000 -Neighbor list info ... - update every 1 steps, delay 0 steps, check yes - max neighbors/atom: 2000, page size: 100000 - master list distance cutoff = 18 - ghost atom cutoff = 18 - binsize = 9, bins = 5 5 12 - 7 neighbor lists, perpetual/occasional/extra = 6 1 0 - (1) pair rebo, perpetual, skip from (3) - attributes: full, newton on, ghost - pair build: skip/ghost - stencil: none - bin: none - (2) pair tersoff, perpetual, skip from (6) - attributes: full, newton on - pair build: skip - stencil: none - bin: none - (3) pair ilp/graphene/hbn, perpetual - attributes: full, newton on, ghost - pair build: full/bin/ghost - stencil: full/ghost/bin/3d - bin: standard - (4) pair coul/shield, perpetual, half/full from (2) - attributes: half, newton on - pair build: halffull/newton/skip - stencil: none - bin: none - (5) compute group/group, occasional, copy from (7) - attributes: half, newton on - pair build: copy - stencil: none - bin: none - (6) neighbor class addition, perpetual, copy from (3) - attributes: full, newton on - pair build: copy - stencil: none - bin: none - (7) neighbor class addition, perpetual, half/full from (6) - attributes: half, newton on - pair build: halffull/newton - stencil: none - bin: none -Per MPI rank memory allocation (min/avg/max) = 25.93 | 25.93 | 25.93 Mbytes -Step TotEng PotEng KinEng v_Evdw v_Tersoff v_REBO v_EILP v_Ecoul Temp v_adsxcom v_adsycom v_adszcom v_adsvxcom v_adsvycom v_adsvzcom - 0 -10708.4531746010 -10764.2547791975 55.8016045965 -66.8250335416 -5401.7347845703 -5322.2780762734 -40.2419183538 0.0000000000 300.0000000000 21.6722857297 22.1650000000 3.3300000000 0.1682661410 -0.0842226772 0.1056563755 - 100 -10708.2491256387 -10738.4532793285 30.2041536898 -68.8603937785 -5389.4304136167 -5309.6361134033 -39.3867523085 0.0000000000 162.3832535368 21.6879886706 22.1574778199 3.3223279482 0.1346509596 -0.0580689194 -0.1274433614 - 200 -10708.1985754490 -10736.7142682477 28.5156927987 -70.0276479251 -5388.8677096501 -5308.3263464524 -39.5202121452 0.0000000000 153.3057678444 21.6968427596 22.1541506320 3.3143666142 0.0334706445 -0.0081639882 -0.0055006321 - 300 -10708.1878214116 -10736.9033486636 28.7155272520 -68.2422175765 -5388.5952548022 -5308.9505338445 -39.3575600169 0.0000000000 154.3801157314 21.6939171741 22.1551483321 3.3251666346 -0.0896064591 0.0248921781 0.1717740196 - 400 -10708.2036103906 -10738.2295882994 30.0259779088 -67.4993928655 -5389.4510311345 -5309.1985887571 -39.5799684078 0.0000000000 161.4253467759 21.6806789605 22.1589742804 3.3300374170 -0.1615300496 0.0532638209 -0.1185426799 - 500 -10708.1853082161 -10736.0245173060 27.8392090900 -69.9737746636 -5387.9379921501 -5308.5551693329 -39.5313558230 0.0000000000 149.6688632411 21.6641276776 22.1655659011 3.3143210751 -0.1579504334 0.0766822604 -0.1154029266 - 600 -10708.1781001285 -10736.4254568396 28.2473567110 -69.9368770273 -5388.3515507737 -5308.6700567475 -39.4038493184 0.0000000000 151.8631421907 21.6516789999 22.1733266592 3.3149997184 -0.0805825343 0.0684349609 0.1419617624 - 700 -10708.1867253590 -10736.6143955088 28.4276701498 -67.1597096579 -5387.8570063253 -5309.0676141640 -39.6897750195 0.0000000000 152.8325414049 21.6489884054 22.1774523945 3.3315351816 0.0259900263 0.0094570835 0.0707953688 - 800 -10708.1733385055 -10736.0277775931 27.8544390876 -68.6354557276 -5388.1933954711 -5308.5094712719 -39.3249108500 0.0000000000 149.7507425941 21.6565725156 22.1751617515 3.3227650180 0.1222442823 -0.0531420670 -0.1677749693 - 900 -10708.1827888042 -10737.2646739167 29.0818851126 -70.2218493216 -5387.9824857335 -5309.6527953488 -39.6293928345 0.0000000000 156.3497250098 21.6716950833 22.1680989334 3.3131455846 0.1650154385 -0.0820901425 0.0072049300 - 1000 -10708.1804322657 -10736.1966428009 28.0162105352 -68.3753745517 -5388.2611029662 -5308.4521913187 -39.4833485160 0.0000000000 150.6204565501 21.6865468141 22.1602434319 3.3246621699 0.1213363701 -0.0688593023 0.1701174943 -Loop time of 149.449 on 1 procs for 1000 steps with 1440 atoms - -Performance: 0.578 ns/day, 41.514 hours/ns, 6.691 timesteps/s -96.7% CPU use with 1 MPI tasks x 1 OpenMP threads - -MPI task timing breakdown: -Section | min time | avg time | max time |%varavg| %total ---------------------------------------------------------------- -Pair | 149.06 | 149.06 | 149.06 | 0.0 | 99.74 -Bond | 0.00082946 | 0.00082946 | 0.00082946 | 0.0 | 0.00 -Neigh | 0 | 0 | 0 | 0.0 | 0.00 -Comm | 0.068351 | 0.068351 | 0.068351 | 0.0 | 0.05 -Output | 0.25935 | 0.25935 | 0.25935 | 0.0 | 0.17 -Modify | 0.030915 | 0.030915 | 0.030915 | 0.0 | 0.02 -Other | | 0.02702 | | | 0.02 - -Nlocal: 1440 ave 1440 max 1440 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Nghost: 8180 ave 8180 max 8180 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Neighs: 140400 ave 140400 max 140400 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -FullNghs: 280800 ave 280800 max 280800 min -Histogram: 1 0 0 0 0 0 0 0 0 0 - -Total # of neighbors = 280800 -Ave neighs/atom = 195 -Ave special neighs/atom = 0 -Neighbor list builds = 0 -Dangerous builds = 0 -Total wall time: 0:02:29 diff --git a/examples/USER/misc/ilp_graphene_hbn/gr-hBN/log.16Mar18.grhBN.g++.4 b/examples/USER/misc/ilp_graphene_hbn/gr-hBN/log.16Mar18.grhBN.g++.4 deleted file mode 100644 index 86e93369ff..0000000000 --- a/examples/USER/misc/ilp_graphene_hbn/gr-hBN/log.16Mar18.grhBN.g++.4 +++ /dev/null @@ -1,171 +0,0 @@ -LAMMPS (8 Mar 2018) - using 1 OpenMP thread(s) per MPI task -# Initialization -units metal -boundary p p p -atom_style full -processors * * 1 # domain decomposition over x and y - -# System and atom definition -# we use 2 atom types so that inter- and intra-layer -# interactions can be specified separately -read_data gr_hBN_Cstack_2L_noH.data - orthogonal box = (0 0 0) to (44.583 42.9 100) - 2 by 2 by 1 MPI processor grid - reading atoms ... - 1440 atoms - 0 = max # of 1-2 neighbors - 0 = max # of 1-3 neighbors - 0 = max # of 1-4 neighbors - 1 = max # of special neighbors -mass 1 10.8110 # boron mass (g/mole) | membrane -mass 2 14.0067 # nitrogen mass (g/mole) | membrane -mass 3 12.0107 # carbon mass (g/mole) | adsorbate -# Separate atom groups -group membrane type 1 2 -720 atoms in group membrane -group adsorbate type 3 -720 atoms in group adsorbate - -######################## Potential defition ######################## -pair_style hybrid/overlay rebo tersoff ilp/graphene/hbn 16.0 coul/shield 16.0 -#################################################################### -pair_coeff * * rebo CH.airebo NULL NULL C # chemical -Reading potential file CH.airebo with DATE: 2011-10-25 -pair_coeff * * tersoff BNC.tersoff B N NULL # chemical -Reading potential file BNC.tersoff with DATE: 2013-03-21 -pair_coeff * * ilp/graphene/hbn BNCH-old.ILP B N C # long range -pair_coeff 1 1 coul/shield 0.70 -pair_coeff 1 2 coul/shield 0.69498201415576216335 -pair_coeff 2 2 coul/shield 0.69 -#################################################################### -# Neighbor update settings -neighbor 2.0 bin -neigh_modify every 1 -neigh_modify delay 0 -neigh_modify check yes - -# calculate the COM -variable adsxcom equal xcm(adsorbate,x) -variable adsycom equal xcm(adsorbate,y) -variable adszcom equal xcm(adsorbate,z) -variable adsvxcom equal vcm(adsorbate,x) -variable adsvycom equal vcm(adsorbate,y) -variable adsvzcom equal vcm(adsorbate,z) - -#### Simulation settings #### -timestep 0.001 -velocity all create 300.0 12345 -fix thermostat all nve - -compute 0 all pair rebo -compute 1 all pair tersoff -compute 2 all pair ilp/graphene/hbn -compute 3 all pair coul/shield -variable REBO equal c_0 -variable Tersoff equal c_1 -variable EILP equal c_2 -variable Ecoul equal c_3 - -# Calculate the pair potential between the substrate and slider -compute sldsub adsorbate group/group membrane -variable Evdw equal c_sldsub - -############################ - -# Output -thermo 100 -thermo_style custom step etotal pe ke v_Evdw v_Tersoff v_REBO v_EILP v_Ecoul temp v_adsxcom v_adsycom v_adszcom v_adsvxcom v_adsvycom v_adsvzcom -thermo_modify line one format float %.10f - -#dump 1 all custom 1000 traj.lammpstrj id mol type xu yu zu -#dump_modify 1 format line "%7d %3d %3d %15.10g %15.10g %15.10g" flush yes - -###### Run molecular dynamics ###### -run 1000 -Neighbor list info ... - update every 1 steps, delay 0 steps, check yes - max neighbors/atom: 2000, page size: 100000 - master list distance cutoff = 18 - ghost atom cutoff = 18 - binsize = 9, bins = 5 5 12 - 7 neighbor lists, perpetual/occasional/extra = 6 1 0 - (1) pair rebo, perpetual, skip from (3) - attributes: full, newton on, ghost - pair build: skip/ghost - stencil: none - bin: none - (2) pair tersoff, perpetual, skip from (6) - attributes: full, newton on - pair build: skip - stencil: none - bin: none - (3) pair ilp/graphene/hbn, perpetual - attributes: full, newton on, ghost - pair build: full/bin/ghost - stencil: full/ghost/bin/3d - bin: standard - (4) pair coul/shield, perpetual, half/full from (2) - attributes: half, newton on - pair build: halffull/newton/skip - stencil: none - bin: none - (5) compute group/group, occasional, copy from (7) - attributes: half, newton on - pair build: copy - stencil: none - bin: none - (6) neighbor class addition, perpetual, copy from (3) - attributes: full, newton on - pair build: copy - stencil: none - bin: none - (7) neighbor class addition, perpetual, half/full from (6) - attributes: half, newton on - pair build: halffull/newton - stencil: none - bin: none -Per MPI rank memory allocation (min/avg/max) = 14.25 | 14.25 | 14.25 Mbytes -Step TotEng PotEng KinEng v_Evdw v_Tersoff v_REBO v_EILP v_Ecoul Temp v_adsxcom v_adsycom v_adszcom v_adsvxcom v_adsvycom v_adsvzcom - 0 -10708.4531746011 -10764.2547791976 55.8016045965 -66.8250335415 -5401.7347845703 -5322.2780762735 -40.2419183538 0.0000000000 300.0000000000 21.6722857297 22.1650000000 3.3300000000 0.1682661410 -0.0842226772 0.1056563755 - 100 -10708.2491256387 -10738.4532793285 30.2041536898 -68.8603937785 -5389.4304136167 -5309.6361134033 -39.3867523085 0.0000000000 162.3832535368 21.6879886706 22.1574778199 3.3223279482 0.1346509596 -0.0580689194 -0.1274433614 - 200 -10708.1985754490 -10736.7142682477 28.5156927987 -70.0276479251 -5388.8677096501 -5308.3263464524 -39.5202121452 0.0000000000 153.3057678444 21.6968427596 22.1541506320 3.3143666142 0.0334706445 -0.0081639882 -0.0055006321 - 300 -10708.1878214116 -10736.9033486636 28.7155272520 -68.2422175765 -5388.5952548022 -5308.9505338445 -39.3575600169 0.0000000000 154.3801157314 21.6939171741 22.1551483321 3.3251666346 -0.0896064591 0.0248921781 0.1717740196 - 400 -10708.2036103906 -10738.2295882994 30.0259779088 -67.4993928655 -5389.4510311345 -5309.1985887571 -39.5799684078 0.0000000000 161.4253467759 21.6806789605 22.1589742804 3.3300374170 -0.1615300496 0.0532638209 -0.1185426799 - 500 -10708.1853082161 -10736.0245173060 27.8392090900 -69.9737746636 -5387.9379921501 -5308.5551693329 -39.5313558230 0.0000000000 149.6688632411 21.6641276776 22.1655659011 3.3143210751 -0.1579504334 0.0766822604 -0.1154029266 - 600 -10708.1781001285 -10736.4254568396 28.2473567110 -69.9368770273 -5388.3515507736 -5308.6700567475 -39.4038493184 0.0000000000 151.8631421907 21.6516789999 22.1733266592 3.3149997184 -0.0805825343 0.0684349609 0.1419617624 - 700 -10708.1867253590 -10736.6143955089 28.4276701498 -67.1597096579 -5387.8570063253 -5309.0676141640 -39.6897750195 0.0000000000 152.8325414049 21.6489884054 22.1774523945 3.3315351816 0.0259900263 0.0094570835 0.0707953688 - 800 -10708.1733385055 -10736.0277775930 27.8544390876 -68.6354557276 -5388.1933954711 -5308.5094712719 -39.3249108500 0.0000000000 149.7507425941 21.6565725156 22.1751617515 3.3227650180 0.1222442823 -0.0531420670 -0.1677749693 - 900 -10708.1827888042 -10737.2646739167 29.0818851126 -70.2218493216 -5387.9824857335 -5309.6527953488 -39.6293928345 0.0000000000 156.3497250098 21.6716950833 22.1680989334 3.3131455846 0.1650154385 -0.0820901425 0.0072049300 - 1000 -10708.1804322657 -10736.1966428009 28.0162105352 -68.3753745517 -5388.2611029662 -5308.4521913187 -39.4833485160 0.0000000000 150.6204565501 21.6865468141 22.1602434319 3.3246621699 0.1213363701 -0.0688593023 0.1701174943 -Loop time of 39.6206 on 4 procs for 1000 steps with 1440 atoms - -Performance: 2.181 ns/day, 11.006 hours/ns, 25.239 timesteps/s -98.9% CPU use with 4 MPI tasks x 1 OpenMP threads - -MPI task timing breakdown: -Section | min time | avg time | max time |%varavg| %total ---------------------------------------------------------------- -Pair | 34.948 | 37.122 | 39.309 | 31.6 | 93.69 -Bond | 0.00046444 | 0.0005914 | 0.00089121 | 0.0 | 0.00 -Neigh | 0 | 0 | 0 | 0.0 | 0.00 -Comm | 0.20131 | 2.3895 | 4.565 | 124.7 | 6.03 -Output | 0.069107 | 0.069157 | 0.069264 | 0.0 | 0.17 -Modify | 0.010056 | 0.010403 | 0.010688 | 0.3 | 0.03 -Other | | 0.02875 | | | 0.07 - -Nlocal: 360 ave 380 max 340 min -Histogram: 2 0 0 0 0 0 0 0 0 2 -Nghost: 4716 ave 4736 max 4696 min -Histogram: 2 0 0 0 0 0 0 0 0 2 -Neighs: 35100 ave 37050 max 33150 min -Histogram: 2 0 0 0 0 0 0 0 0 2 -FullNghs: 70200 ave 74100 max 66300 min -Histogram: 2 0 0 0 0 0 0 0 0 2 - -Total # of neighbors = 280800 -Ave neighs/atom = 195 -Ave special neighs/atom = 0 -Neighbor list builds = 0 -Dangerous builds = 0 -Total wall time: 0:00:39 diff --git a/examples/USER/misc/ilp_graphene_hbn/gr-hBN/gr_hBN_Cstack_2L_noH.data b/examples/USER/misc/ilp_graphene_hbn/gr_hBN_Cstack_2L_noH.data similarity index 100% rename from examples/USER/misc/ilp_graphene_hbn/gr-hBN/gr_hBN_Cstack_2L_noH.data rename to examples/USER/misc/ilp_graphene_hbn/gr_hBN_Cstack_2L_noH.data diff --git a/examples/USER/misc/ilp_graphene_hbn/bilayer-hBN/hBN_AA_prime_stack_2L_noH.data b/examples/USER/misc/ilp_graphene_hbn/hBN_AA_prime_stack_2L_noH.data similarity index 100% rename from examples/USER/misc/ilp_graphene_hbn/bilayer-hBN/hBN_AA_prime_stack_2L_noH.data rename to examples/USER/misc/ilp_graphene_hbn/hBN_AA_prime_stack_2L_noH.data diff --git a/examples/USER/misc/ilp_graphene_hbn/bilayer-graphene/in.bilayer-graphene b/examples/USER/misc/ilp_graphene_hbn/in.bilayer-graphene similarity index 100% rename from examples/USER/misc/ilp_graphene_hbn/bilayer-graphene/in.bilayer-graphene rename to examples/USER/misc/ilp_graphene_hbn/in.bilayer-graphene diff --git a/examples/USER/misc/ilp_graphene_hbn/bilayer-hBN/in.bilayer-hBN b/examples/USER/misc/ilp_graphene_hbn/in.bilayer-hBN similarity index 91% rename from examples/USER/misc/ilp_graphene_hbn/bilayer-hBN/in.bilayer-hBN rename to examples/USER/misc/ilp_graphene_hbn/in.bilayer-hBN index 0e02104d59..1cf982d8dc 100644 --- a/examples/USER/misc/ilp_graphene_hbn/bilayer-hBN/in.bilayer-hBN +++ b/examples/USER/misc/ilp_graphene_hbn/in.bilayer-hBN @@ -49,9 +49,8 @@ variable Erep equal c_2[2] # repulsive energy ############# Output ############### thermo 100 -thermo_style custom step cpu etotal pe ke v_Evdw v_Tersoff v_EILP v_Erep v_Evdw v_Ecoul temp -thermo_modify line one format float %.10f -thermo_modify flush yes norm no lost error +thermo_style custom step etotal pe ke v_Evdw v_Tersoff v_EILP v_Erep v_Evdw v_Ecoul temp +thermo_modify lost warn ###### Run molecular dynamics ###### run 1000 diff --git a/examples/USER/misc/ilp_graphene_hbn/gr-hBN/in.grhBN b/examples/USER/misc/ilp_graphene_hbn/in.grhBN similarity index 96% rename from examples/USER/misc/ilp_graphene_hbn/gr-hBN/in.grhBN rename to examples/USER/misc/ilp_graphene_hbn/in.grhBN index 1ae1704dec..46c42e0d6d 100644 --- a/examples/USER/misc/ilp_graphene_hbn/gr-hBN/in.grhBN +++ b/examples/USER/misc/ilp_graphene_hbn/in.grhBN @@ -50,8 +50,7 @@ variable Ecoul equal c_3 ############# Output ############## thermo 100 -thermo_style custom step etotal pe ke v_Evdw v_Tersoff v_REBO v_EILP v_Erep v_Evdw v_Ecoul temp -thermo_modify line one format float %.10f +thermo_style custom step etotal pe ke v_Evdw v_Tersoff v_REBO v_EILP v_Erep v_Evdw v_Ecoul temp ###### Run molecular dynamics ###### run 1000 diff --git a/examples/USER/misc/ilp_graphene_hbn/in.ilp_graphene_hbn b/examples/USER/misc/ilp_graphene_hbn/in.ilp_graphene_hbn index da813b3d10..9b122e194e 100644 --- a/examples/USER/misc/ilp_graphene_hbn/in.ilp_graphene_hbn +++ b/examples/USER/misc/ilp_graphene_hbn/in.ilp_graphene_hbn @@ -32,14 +32,6 @@ neigh_modify every 1 neigh_modify delay 0 neigh_modify check yes -# calculate the COM -variable adsxcom equal xcm(adsorbate,x) -variable adsycom equal xcm(adsorbate,y) -variable adszcom equal xcm(adsorbate,z) -variable adsvxcom equal vcm(adsorbate,x) -variable adsvycom equal vcm(adsorbate,y) -variable adsvzcom equal vcm(adsorbate,z) - #### Simulation settings #### timestep 0.001 #velocity adsorbate create 300.0 12345 @@ -51,19 +43,16 @@ compute 1 all pair coul/shield ecoul compute 2 all pair ilp/graphene/hbn variable Tersoff equal c_0 variable Ecoul equal c_1 -variable EILP equal c_2 - -# Calculate the pair potential between the substrate and slider -compute sldsub adsorbate group/group membrane -variable Evdw equal c_sldsub +variable ILP equal c_2 +variable Evdw equal c_2[1] +variable Erep equal c_2[2] ############################ # Output thermo 100 -thermo_style custom step etotal pe ke v_Evdw v_Tersoff v_EILP v_Ecoul temp v_adsxcom v_adsycom v_adszcom v_adsvxcom v_adsvycom v_adsvzcom f_subf[1] f_subf[2] f_subf[3] -thermo_modify line one format float %.10f -thermo_modify flush yes norm no lost warn #ignore +thermo_style custom step etotal pe ke v_Tersoff v_ILP v_Ecoul v_Erep v_Evdw temp +thermo_modify lost warn #ignore #dump 1 all custom 1000 traj.lammpstrj id mol type xu yu zu #dump_modify 1 format line "%7d %3d %3d %15.10g %15.10g %15.10g" flush yes diff --git a/examples/USER/misc/ilp_graphene_hbn/log.16Mar18.ilp_gr_hBN.g++.1 b/examples/USER/misc/ilp_graphene_hbn/log.16Mar18.ilp_gr_hBN.g++.1 deleted file mode 100644 index fc10948f9a..0000000000 --- a/examples/USER/misc/ilp_graphene_hbn/log.16Mar18.ilp_gr_hBN.g++.1 +++ /dev/null @@ -1,168 +0,0 @@ -LAMMPS (8 Mar 2018) - using 1 OpenMP thread(s) per MPI task -# Initialization -units metal -boundary p p p -atom_style full -processors * * 1 # domain decomposition over x and y - -# System and atom definition -# we use 2 atom types so that inter- and intra-layer -# interactions can be specified separately -read_data hBN_AB_stack_2L_noH_equi_300K.data - orthogonal box = (0 0 0) to (43.38 42.5773 100) - 1 by 1 by 1 MPI processor grid - reading atoms ... - 1360 atoms - reading velocities ... - 1360 velocities - 0 = max # of 1-2 neighbors - 0 = max # of 1-3 neighbors - 0 = max # of 1-4 neighbors - 1 = max # of special neighbors -mass 1 10.8110 # boron mass (g/mole) | membrane -mass 2 14.0067 # nitrogen mass (g/mole) | adsorbate -mass 3 10.8110 # boron mass (g/mole) | membrane -mass 4 14.0067 # nitrogen mass (g/mole) | adsorbate -# Separate atom groups -group membrane type 1 2 -680 atoms in group membrane -group adsorbate type 3 4 -680 atoms in group adsorbate - -######################## Potential defition ######################## -pair_style hybrid/overlay tersoff ilp/graphene/hbn 16.0 coul/shield 16.0 1 -#################################################################### -pair_coeff * * tersoff BNC.tersoff NULL NULL B N # chemical -Reading potential file BNC.tersoff with DATE: 2013-03-21 -pair_coeff * * ilp/graphene/hbn BNCH-old.ILP B N B N # long range -pair_coeff 1 3 coul/shield 0.70 -pair_coeff 1 4 coul/shield 0.69498201415576216335 -pair_coeff 2 3 coul/shield 0.69498201415576216335 -pair_coeff 2 4 coul/shield 0.69 -#################################################################### -# Neighbor update settings -neighbor 2.0 bin -neigh_modify every 1 -neigh_modify delay 0 -neigh_modify check yes - -# calculate the COM -variable adsxcom equal xcm(adsorbate,x) -variable adsycom equal xcm(adsorbate,y) -variable adszcom equal xcm(adsorbate,z) -variable adsvxcom equal vcm(adsorbate,x) -variable adsvycom equal vcm(adsorbate,y) -variable adsvzcom equal vcm(adsorbate,z) - -#### Simulation settings #### -timestep 0.001 -#velocity adsorbate create 300.0 12345 -fix subf membrane setforce 0.0 0.0 0.0 -fix thermostat all nve - -compute 0 all pair tersoff -compute 1 all pair coul/shield ecoul -compute 2 all pair ilp/graphene/hbn -variable Tersoff equal c_0 -variable Ecoul equal c_1 -variable EILP equal c_2 - -# Calculate the pair potential between the substrate and slider -compute sldsub adsorbate group/group membrane -variable Evdw equal c_sldsub - -############################ - -# Output -thermo 100 -thermo_style custom step etotal pe ke v_Evdw v_Tersoff v_EILP v_Ecoul temp v_adsxcom v_adsycom v_adszcom v_adsvxcom v_adsvycom v_adsvzcom f_subf[1] f_subf[2] f_subf[3] -thermo_modify line one format float %.10f -thermo_modify flush yes norm no lost warn #ignore - -#dump 1 all custom 1000 traj.lammpstrj id mol type xu yu zu -#dump_modify 1 format line "%7d %3d %3d %15.10g %15.10g %15.10g" flush yes - -###### Run molecular dynamics ###### -run 1000 -Neighbor list info ... - update every 1 steps, delay 0 steps, check yes - max neighbors/atom: 2000, page size: 100000 - master list distance cutoff = 18 - ghost atom cutoff = 18 - binsize = 9, bins = 5 5 12 - 6 neighbor lists, perpetual/occasional/extra = 5 1 0 - (1) pair tersoff, perpetual, skip from (5) - attributes: full, newton on - pair build: skip - stencil: none - bin: none - (2) pair ilp/graphene/hbn, perpetual - attributes: full, newton on, ghost - pair build: full/bin/ghost - stencil: full/ghost/bin/3d - bin: standard - (3) pair coul/shield, perpetual, skip from (6) - attributes: half, newton on - pair build: skip - stencil: none - bin: none - (4) compute group/group, occasional, copy from (6) - attributes: half, newton on - pair build: copy - stencil: none - bin: none - (5) neighbor class addition, perpetual, copy from (2) - attributes: full, newton on - pair build: copy - stencil: none - bin: none - (6) neighbor class addition, perpetual, half/full from (5) - attributes: half, newton on - pair build: halffull/newton - stencil: none - bin: none -Per MPI rank memory allocation (min/avg/max) = 57.85 | 57.85 | 57.85 Mbytes -Step TotEng PotEng KinEng v_Evdw v_Tersoff v_EILP v_Ecoul Temp v_adsxcom v_adsycom v_adszcom v_adsvxcom v_adsvycom v_adsvzcom f_subf[1] f_subf[2] f_subf[3] - 0 -5114.6628078598 -5127.8586355055 13.1958276458 -75.3652234209 -5091.4120857465 -36.0831137829 -0.3634359761 75.1194741238 20.9113202537 20.6582215878 3.2895976612 -0.0495147937 -0.0552233516 -0.0166592619 -0.1742790202 -0.0884665936 -0.8010816801 - 100 -5114.6620580583 -5127.6958349342 13.0337768758 -75.2249487778 -5091.2407919311 -36.0927601416 -0.3622828614 74.1969727889 20.9076129631 20.6534162972 3.2908118318 -0.0234802196 -0.0397832410 0.0332404745 -0.2430042439 -0.1598109185 -0.5351246275 - 200 -5114.6630637865 -5127.5945140906 12.9314503041 -74.6445167393 -5091.1507571912 -36.0866688941 -0.3570880053 73.6144615235 20.9067696105 20.6505240051 3.2976575241 0.0078967872 -0.0170385302 0.0850447973 -0.2934041648 -0.2405295165 0.2309200807 - 300 -5114.6693830121 -5128.3286231421 13.6592401300 -74.2223518942 -5091.8645555419 -36.1107860098 -0.3532815904 77.7575278367 20.9090146500 20.6502445717 3.3024525026 0.0352437329 0.0112279015 -0.0021399216 -0.2166516175 -0.2410661267 0.9007458614 - 400 -5114.6614035404 -5127.6423784754 12.9809749350 -74.6548295432 -5091.2348011465 -36.0496340516 -0.3579432773 73.8963888364 20.9136276183 20.6526810045 3.2977225951 0.0556629502 0.0358324354 -0.0738287296 -0.1431221016 -0.1626739623 0.0673046122 - 500 -5114.6599876234 -5127.4097813122 12.7497936887 -75.2268687829 -5090.9284608504 -36.1195707042 -0.3617497575 72.5803506074 20.9197050770 20.6571510311 3.2909058903 0.0631939085 0.0530269602 -0.0516940297 -0.0112976844 -0.1217009147 -0.4713422319 - 600 -5114.6672773464 -5128.0912983829 13.4240210364 -75.3848112535 -5091.6338883189 -36.0938401510 -0.3635699131 76.4185034811 20.9258252862 20.6628322031 3.2892805234 0.0573396226 0.0579085440 0.0291853982 0.1059950758 0.0102266125 -0.7683214794 - 700 -5114.6609647250 -5127.7466720637 13.0857073388 -74.7981789470 -5091.2811095008 -36.1066385732 -0.3589239897 74.4925957063 20.9307092134 20.6683554324 3.2957959411 0.0396744013 0.0503347378 0.0818267711 0.1737903706 0.1258761156 0.1307185989 - 800 -5114.6622627667 -5128.0130406264 13.3507778597 -74.2952448854 -5091.5693975625 -36.0897180314 -0.3539250325 76.0015543464 20.9334441079 20.6725125240 3.3019570181 0.0142277646 0.0313116646 0.0291673132 0.2457478793 0.1912082770 0.7239823553 - 900 -5114.6675469561 -5128.1496933801 13.4821464240 -74.3644898573 -5091.6703861750 -36.1246785145 -0.3546286905 76.7493920516 20.9334403558 20.6744181494 3.3005582394 -0.0141399355 0.0063543986 -0.0561206619 0.2370151923 0.2115707560 0.7822017606 - 1000 -5114.6683146144 -5128.3364609113 13.6681462969 -75.1091579020 -5091.9370210069 -36.0375964349 -0.3618434694 77.8082276935 20.9306643096 20.6737238853 3.2922181699 -0.0411219854 -0.0200694204 -0.0788193565 0.2225175431 0.2377413412 -0.5875288557 -Loop time of 202.063 on 1 procs for 1000 steps with 1360 atoms - -Performance: 0.428 ns/day, 56.129 hours/ns, 4.949 timesteps/s -91.0% CPU use with 1 MPI tasks x 1 OpenMP threads - -MPI task timing breakdown: -Section | min time | avg time | max time |%varavg| %total ---------------------------------------------------------------- -Pair | 201.4 | 201.4 | 201.4 | 0.0 | 99.67 -Bond | 0.00092697 | 0.00092697 | 0.00092697 | 0.0 | 0.00 -Neigh | 0 | 0 | 0 | 0.0 | 0.00 -Comm | 0.086005 | 0.086005 | 0.086005 | 0.0 | 0.04 -Output | 0.50438 | 0.50438 | 0.50438 | 0.0 | 0.25 -Modify | 0.038846 | 0.038846 | 0.038846 | 0.0 | 0.02 -Other | | 0.03093 | | | 0.02 - -Nlocal: 1360 ave 1360 max 1360 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Nghost: 7840 ave 7840 max 7840 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Neighs: 249628 ave 249628 max 249628 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -FullNghs: 253390 ave 253390 max 253390 min -Histogram: 1 0 0 0 0 0 0 0 0 0 - -Total # of neighbors = 253390 -Ave neighs/atom = 186.316 -Ave special neighs/atom = 0 -Neighbor list builds = 0 -Dangerous builds = 0 -Total wall time: 0:03:22 diff --git a/examples/USER/misc/ilp_graphene_hbn/log.16Mar18.ilp_gr_hBN.g++.4 b/examples/USER/misc/ilp_graphene_hbn/log.16Mar18.ilp_gr_hBN.g++.4 deleted file mode 100644 index 5cd3518918..0000000000 --- a/examples/USER/misc/ilp_graphene_hbn/log.16Mar18.ilp_gr_hBN.g++.4 +++ /dev/null @@ -1,168 +0,0 @@ -LAMMPS (8 Mar 2018) - using 1 OpenMP thread(s) per MPI task -# Initialization -units metal -boundary p p p -atom_style full -processors * * 1 # domain decomposition over x and y - -# System and atom definition -# we use 2 atom types so that inter- and intra-layer -# interactions can be specified separately -read_data hBN_AB_stack_2L_noH_equi_300K.data - orthogonal box = (0 0 0) to (43.38 42.5773 100) - 2 by 2 by 1 MPI processor grid - reading atoms ... - 1360 atoms - reading velocities ... - 1360 velocities - 0 = max # of 1-2 neighbors - 0 = max # of 1-3 neighbors - 0 = max # of 1-4 neighbors - 1 = max # of special neighbors -mass 1 10.8110 # boron mass (g/mole) | membrane -mass 2 14.0067 # nitrogen mass (g/mole) | adsorbate -mass 3 10.8110 # boron mass (g/mole) | membrane -mass 4 14.0067 # nitrogen mass (g/mole) | adsorbate -# Separate atom groups -group membrane type 1 2 -680 atoms in group membrane -group adsorbate type 3 4 -680 atoms in group adsorbate - -######################## Potential defition ######################## -pair_style hybrid/overlay tersoff ilp/graphene/hbn 16.0 coul/shield 16.0 1 -#################################################################### -pair_coeff * * tersoff BNC.tersoff NULL NULL B N # chemical -Reading potential file BNC.tersoff with DATE: 2013-03-21 -pair_coeff * * ilp/graphene/hbn BNCH-old.ILP B N B N # long range -pair_coeff 1 3 coul/shield 0.70 -pair_coeff 1 4 coul/shield 0.69498201415576216335 -pair_coeff 2 3 coul/shield 0.69498201415576216335 -pair_coeff 2 4 coul/shield 0.69 -#################################################################### -# Neighbor update settings -neighbor 2.0 bin -neigh_modify every 1 -neigh_modify delay 0 -neigh_modify check yes - -# calculate the COM -variable adsxcom equal xcm(adsorbate,x) -variable adsycom equal xcm(adsorbate,y) -variable adszcom equal xcm(adsorbate,z) -variable adsvxcom equal vcm(adsorbate,x) -variable adsvycom equal vcm(adsorbate,y) -variable adsvzcom equal vcm(adsorbate,z) - -#### Simulation settings #### -timestep 0.001 -#velocity adsorbate create 300.0 12345 -fix subf membrane setforce 0.0 0.0 0.0 -fix thermostat all nve - -compute 0 all pair tersoff -compute 1 all pair coul/shield ecoul -compute 2 all pair ilp/graphene/hbn -variable Tersoff equal c_0 -variable Ecoul equal c_1 -variable EILP equal c_2 - -# Calculate the pair potential between the substrate and slider -compute sldsub adsorbate group/group membrane -variable Evdw equal c_sldsub - -############################ - -# Output -thermo 100 -thermo_style custom step etotal pe ke v_Evdw v_Tersoff v_EILP v_Ecoul temp v_adsxcom v_adsycom v_adszcom v_adsvxcom v_adsvycom v_adsvzcom f_subf[1] f_subf[2] f_subf[3] -thermo_modify line one format float %.10f -thermo_modify flush yes norm no lost warn #ignore - -#dump 1 all custom 1000 traj.lammpstrj id mol type xu yu zu -#dump_modify 1 format line "%7d %3d %3d %15.10g %15.10g %15.10g" flush yes - -###### Run molecular dynamics ###### -run 1000 -Neighbor list info ... - update every 1 steps, delay 0 steps, check yes - max neighbors/atom: 2000, page size: 100000 - master list distance cutoff = 18 - ghost atom cutoff = 18 - binsize = 9, bins = 5 5 12 - 6 neighbor lists, perpetual/occasional/extra = 5 1 0 - (1) pair tersoff, perpetual, skip from (5) - attributes: full, newton on - pair build: skip - stencil: none - bin: none - (2) pair ilp/graphene/hbn, perpetual - attributes: full, newton on, ghost - pair build: full/bin/ghost - stencil: full/ghost/bin/3d - bin: standard - (3) pair coul/shield, perpetual, skip from (6) - attributes: half, newton on - pair build: skip - stencil: none - bin: none - (4) compute group/group, occasional, copy from (6) - attributes: half, newton on - pair build: copy - stencil: none - bin: none - (5) neighbor class addition, perpetual, copy from (2) - attributes: full, newton on - pair build: copy - stencil: none - bin: none - (6) neighbor class addition, perpetual, half/full from (5) - attributes: half, newton on - pair build: halffull/newton - stencil: none - bin: none -Per MPI rank memory allocation (min/avg/max) = 30.63 | 30.63 | 30.64 Mbytes -Step TotEng PotEng KinEng v_Evdw v_Tersoff v_EILP v_Ecoul Temp v_adsxcom v_adsycom v_adszcom v_adsvxcom v_adsvycom v_adsvzcom f_subf[1] f_subf[2] f_subf[3] - 0 -5114.6628078598 -5127.8586355055 13.1958276458 -75.3652234209 -5091.4120857465 -36.0831137829 -0.3634359761 75.1194741238 20.9113202537 20.6582215878 3.2895976612 -0.0495147937 -0.0552233516 -0.0166592619 -0.1742790202 -0.0884665936 -0.8010816801 - 100 -5114.6620580583 -5127.6958349342 13.0337768758 -75.2249487778 -5091.2407919311 -36.0927601416 -0.3622828614 74.1969727889 20.9076129631 20.6534162972 3.2908118318 -0.0234802196 -0.0397832410 0.0332404745 -0.2430042439 -0.1598109185 -0.5351246275 - 200 -5114.6630637865 -5127.5945140906 12.9314503041 -74.6445167393 -5091.1507571912 -36.0866688941 -0.3570880053 73.6144615235 20.9067696105 20.6505240051 3.2976575241 0.0078967872 -0.0170385302 0.0850447973 -0.2934041648 -0.2405295165 0.2309200807 - 300 -5114.6693830121 -5128.3286231421 13.6592401300 -74.2223518942 -5091.8645555419 -36.1107860098 -0.3532815904 77.7575278367 20.9090146500 20.6502445717 3.3024525026 0.0352437329 0.0112279015 -0.0021399216 -0.2166516175 -0.2410661267 0.9007458614 - 400 -5114.6614035404 -5127.6423784754 12.9809749350 -74.6548295432 -5091.2348011465 -36.0496340516 -0.3579432773 73.8963888364 20.9136276183 20.6526810045 3.2977225951 0.0556629502 0.0358324354 -0.0738287296 -0.1431221016 -0.1626739623 0.0673046122 - 500 -5114.6599876234 -5127.4097813122 12.7497936887 -75.2268687829 -5090.9284608504 -36.1195707042 -0.3617497575 72.5803506074 20.9197050770 20.6571510311 3.2909058903 0.0631939085 0.0530269602 -0.0516940297 -0.0112976844 -0.1217009147 -0.4713422319 - 600 -5114.6672773464 -5128.0912983829 13.4240210364 -75.3848112535 -5091.6338883189 -36.0938401510 -0.3635699131 76.4185034811 20.9258252862 20.6628322031 3.2892805234 0.0573396226 0.0579085440 0.0291853982 0.1059950758 0.0102266125 -0.7683214794 - 700 -5114.6609647250 -5127.7466720637 13.0857073388 -74.7981789470 -5091.2811095008 -36.1066385732 -0.3589239897 74.4925957063 20.9307092134 20.6683554324 3.2957959411 0.0396744013 0.0503347378 0.0818267711 0.1737903706 0.1258761156 0.1307185989 - 800 -5114.6622627667 -5128.0130406264 13.3507778597 -74.2952448854 -5091.5693975625 -36.0897180314 -0.3539250325 76.0015543464 20.9334441079 20.6725125240 3.3019570181 0.0142277646 0.0313116646 0.0291673132 0.2457478793 0.1912082770 0.7239823553 - 900 -5114.6675469561 -5128.1496933801 13.4821464240 -74.3644898573 -5091.6703861750 -36.1246785145 -0.3546286905 76.7493920516 20.9334403558 20.6744181494 3.3005582394 -0.0141399355 0.0063543986 -0.0561206619 0.2370151923 0.2115707560 0.7822017606 - 1000 -5114.6683146144 -5128.3364609113 13.6681462969 -75.1091579020 -5091.9370210069 -36.0375964349 -0.3618434694 77.8082276935 20.9306643096 20.6737238853 3.2922181699 -0.0411219854 -0.0200694204 -0.0788193565 0.2225175431 0.2377413412 -0.5875288557 -Loop time of 53.3155 on 4 procs for 1000 steps with 1360 atoms - -Performance: 1.621 ns/day, 14.810 hours/ns, 18.756 timesteps/s -97.6% CPU use with 4 MPI tasks x 1 OpenMP threads - -MPI task timing breakdown: -Section | min time | avg time | max time |%varavg| %total ---------------------------------------------------------------- -Pair | 49.475 | 50.978 | 52.988 | 18.0 | 95.62 -Bond | 0.00045061 | 0.00066602 | 0.00086665 | 0.0 | 0.00 -Neigh | 0 | 0 | 0 | 0.0 | 0.00 -Comm | 0.16491 | 2.1759 | 3.679 | 87.0 | 4.08 -Output | 0.11871 | 0.11882 | 0.11911 | 0.0 | 0.22 -Modify | 0.012956 | 0.013504 | 0.01387 | 0.3 | 0.03 -Other | | 0.02828 | | | 0.05 - -Nlocal: 340 ave 346 max 336 min -Histogram: 1 0 1 0 1 0 0 0 0 1 -Nghost: 4537.5 ave 4540 max 4534 min -Histogram: 1 0 0 0 0 0 2 0 0 1 -Neighs: 62407 ave 62413 max 62402 min -Histogram: 1 0 0 1 1 0 0 0 0 1 -FullNghs: 63347.5 ave 65585 max 61866 min -Histogram: 1 1 0 1 0 0 0 0 0 1 - -Total # of neighbors = 253926 -Ave neighs/atom = 186.71 -Ave special neighs/atom = 0 -Neighbor list builds = 0 -Dangerous builds = 0 -Total wall time: 0:00:53 diff --git a/examples/USER/misc/ilp_graphene_hbn/log.31Jul19.bilayer-graphene.g++.1 b/examples/USER/misc/ilp_graphene_hbn/log.31Jul19.bilayer-graphene.g++.1 new file mode 100644 index 0000000000..df3a7b70ab --- /dev/null +++ b/examples/USER/misc/ilp_graphene_hbn/log.31Jul19.bilayer-graphene.g++.1 @@ -0,0 +1,127 @@ +LAMMPS (31 Jul 2019) + using 1 OpenMP thread(s) per MPI task +# Initialization +units metal +boundary p p p +atom_style full +processors * * 1 # domain decomposition over x and y + +# System and atom definition +# we use different molecule ids for each layer of hBN +# so that inter- and intra-layer +# interactions can be specified separately + +read_data Bi_gr_AB_stack_2L_noH.data + orthogonal box = (0 0 0) to (42.6 41.8117 100) + 1 by 1 by 1 MPI processor grid + reading atoms ... + 1360 atoms + 0 = max # of 1-2 neighbors + 0 = max # of 1-3 neighbors + 0 = max # of 1-4 neighbors + 1 = max # of special neighbors + special bonds CPU = 0.000290871 secs + read_data CPU = 0.00159073 secs +mass 1 12.0107 # carbon mass (g/mole) | membrane +mass 2 12.0107 # carbon mass (g/mole) | adsorbate +# Separate atom groups +group layer1 molecule 1 +680 atoms in group layer1 +group layer2 molecule 2 +680 atoms in group layer2 + +######################## Potential defition ######################## +pair_style hybrid/overlay rebo ilp/graphene/hbn 16.0 +#################################################################### +pair_coeff * * rebo CH.rebo C C # chemical +Reading potential file CH.rebo with DATE: 2018-7-3 +pair_coeff * * ilp/graphene/hbn BNCH.ILP C C # long range +#################################################################### +# Neighbor update settings +neighbor 2.0 bin +neigh_modify every 1 +neigh_modify delay 0 +neigh_modify check yes + +#### Simulation settings #### +timestep 0.001 +velocity all create 300.0 12345 + +compute 0 all pair rebo +compute 1 all pair ilp/graphene/hbn +variable REBO equal c_0 # REBO energy +variable ILP equal c_1 # total interlayer energy +variable Evdw equal c_1[1] # attractive energy +variable Erep equal c_1[2] # repulsive energy + +############################ + +# Output +thermo 100 +thermo_style custom step etotal pe ke v_REBO v_ILP v_Erep v_Evdw temp +thermo_modify lost warn + +###### Run molecular dynamics ###### +fix thermostat all nve +run 1000 +Neighbor list info ... + update every 1 steps, delay 0 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 18 + ghost atom cutoff = 18 + binsize = 9, bins = 5 5 12 + 2 neighbor lists, perpetual/occasional/extra = 2 0 0 + (1) pair rebo, perpetual + attributes: full, newton on, ghost + pair build: full/bin/ghost + stencil: full/ghost/bin/3d + bin: standard + (2) pair ilp/graphene/hbn, perpetual, copy from (1) + attributes: full, newton on, ghost + pair build: copy + stencil: none + bin: none +Per MPI rank memory allocation (min/avg/max) = 17.21 | 17.21 | 17.21 Mbytes +Step TotEng PotEng KinEng v_REBO v_ILP v_Erep v_Evdw Temp + 0 -10037.285 -10089.985 52.699361 -10057.189 -32.795185 43.640104 -76.435288 300 + 100 -10037.034 -10064.765 27.73131 -10032.181 -32.58421 34.730868 -67.315078 157.86516 + 200 -10036.963 -10061.144 24.18111 -10028.856 -32.288132 28.179936 -60.468068 137.65505 + 300 -10037.003 -10063.5 26.496726 -10030.823 -32.677105 34.923849 -67.600954 150.83708 + 400 -10037.032 -10064.389 27.356526 -10031.853 -32.535415 44.242347 -76.777762 155.73164 + 500 -10037.023 -10064.114 27.090279 -10031.431 -32.682418 37.229232 -69.91165 154.21598 + 600 -10037.003 -10063.657 26.653718 -10031.327 -32.329664 28.509073 -60.838737 151.73078 + 700 -10037.004 -10063.35 26.345697 -10030.801 -32.549231 32.564686 -65.113917 149.97732 + 800 -10037.025 -10064.219 27.194765 -10031.766 -32.453653 43.381557 -75.83521 154.81078 + 900 -10037.028 -10064.668 27.639127 -10032.167 -32.500121 39.99345 -72.493571 157.34039 + 1000 -10037.003 -10063.662 26.658825 -10031.337 -32.325053 29.573578 -61.898631 151.75986 +Loop time of 149.887 on 1 procs for 1000 steps with 1360 atoms + +Performance: 0.576 ns/day, 41.635 hours/ns, 6.672 timesteps/s +99.8% CPU use with 1 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 149.75 | 149.75 | 149.75 | 0.0 | 99.91 +Bond | 0.00024772 | 0.00024772 | 0.00024772 | 0.0 | 0.00 +Neigh | 0 | 0 | 0 | 0.0 | 0.00 +Comm | 0.086328 | 0.086328 | 0.086328 | 0.0 | 0.06 +Output | 0.00036383 | 0.00036383 | 0.00036383 | 0.0 | 0.00 +Modify | 0.028636 | 0.028636 | 0.028636 | 0.0 | 0.02 +Other | | 0.01708 | | | 0.01 + +Nlocal: 1360 ave 1360 max 1360 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 7964 ave 7964 max 7964 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 0 ave 0 max 0 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +FullNghs: 1.037e+06 ave 1.037e+06 max 1.037e+06 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 1037000 +Ave neighs/atom = 762.5 +Ave special neighs/atom = 0 +Neighbor list builds = 0 +Dangerous builds = 0 +Total wall time: 0:02:30 diff --git a/examples/USER/misc/ilp_graphene_hbn/log.31Jul19.bilayer-graphene.g++.4 b/examples/USER/misc/ilp_graphene_hbn/log.31Jul19.bilayer-graphene.g++.4 new file mode 100644 index 0000000000..9ecc05ce6d --- /dev/null +++ b/examples/USER/misc/ilp_graphene_hbn/log.31Jul19.bilayer-graphene.g++.4 @@ -0,0 +1,127 @@ +LAMMPS (31 Jul 2019) + using 1 OpenMP thread(s) per MPI task +# Initialization +units metal +boundary p p p +atom_style full +processors * * 1 # domain decomposition over x and y + +# System and atom definition +# we use different molecule ids for each layer of hBN +# so that inter- and intra-layer +# interactions can be specified separately + +read_data Bi_gr_AB_stack_2L_noH.data + orthogonal box = (0 0 0) to (42.6 41.8117 100) + 2 by 2 by 1 MPI processor grid + reading atoms ... + 1360 atoms + 0 = max # of 1-2 neighbors + 0 = max # of 1-3 neighbors + 0 = max # of 1-4 neighbors + 1 = max # of special neighbors + special bonds CPU = 0.000157118 secs + read_data CPU = 0.00145698 secs +mass 1 12.0107 # carbon mass (g/mole) | membrane +mass 2 12.0107 # carbon mass (g/mole) | adsorbate +# Separate atom groups +group layer1 molecule 1 +680 atoms in group layer1 +group layer2 molecule 2 +680 atoms in group layer2 + +######################## Potential defition ######################## +pair_style hybrid/overlay rebo ilp/graphene/hbn 16.0 +#################################################################### +pair_coeff * * rebo CH.rebo C C # chemical +Reading potential file CH.rebo with DATE: 2018-7-3 +pair_coeff * * ilp/graphene/hbn BNCH.ILP C C # long range +#################################################################### +# Neighbor update settings +neighbor 2.0 bin +neigh_modify every 1 +neigh_modify delay 0 +neigh_modify check yes + +#### Simulation settings #### +timestep 0.001 +velocity all create 300.0 12345 + +compute 0 all pair rebo +compute 1 all pair ilp/graphene/hbn +variable REBO equal c_0 # REBO energy +variable ILP equal c_1 # total interlayer energy +variable Evdw equal c_1[1] # attractive energy +variable Erep equal c_1[2] # repulsive energy + +############################ + +# Output +thermo 100 +thermo_style custom step etotal pe ke v_REBO v_ILP v_Erep v_Evdw temp +thermo_modify lost warn + +###### Run molecular dynamics ###### +fix thermostat all nve +run 1000 +Neighbor list info ... + update every 1 steps, delay 0 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 18 + ghost atom cutoff = 18 + binsize = 9, bins = 5 5 12 + 2 neighbor lists, perpetual/occasional/extra = 2 0 0 + (1) pair rebo, perpetual + attributes: full, newton on, ghost + pair build: full/bin/ghost + stencil: full/ghost/bin/3d + bin: standard + (2) pair ilp/graphene/hbn, perpetual, copy from (1) + attributes: full, newton on, ghost + pair build: copy + stencil: none + bin: none +Per MPI rank memory allocation (min/avg/max) = 9.879 | 9.879 | 9.879 Mbytes +Step TotEng PotEng KinEng v_REBO v_ILP v_Erep v_Evdw Temp + 0 -10037.285 -10089.985 52.699361 -10057.189 -32.795185 43.640104 -76.435288 300 + 100 -10037.034 -10064.765 27.73131 -10032.181 -32.58421 34.730868 -67.315078 157.86516 + 200 -10036.963 -10061.144 24.18111 -10028.856 -32.288132 28.179936 -60.468068 137.65505 + 300 -10037.003 -10063.5 26.496726 -10030.823 -32.677105 34.923849 -67.600954 150.83708 + 400 -10037.032 -10064.389 27.356526 -10031.853 -32.535415 44.242347 -76.777762 155.73164 + 500 -10037.023 -10064.114 27.090279 -10031.431 -32.682418 37.229232 -69.91165 154.21598 + 600 -10037.003 -10063.657 26.653718 -10031.327 -32.329664 28.509073 -60.838737 151.73078 + 700 -10037.004 -10063.35 26.345697 -10030.801 -32.549231 32.564686 -65.113917 149.97732 + 800 -10037.025 -10064.219 27.194765 -10031.766 -32.453653 43.381557 -75.83521 154.81078 + 900 -10037.028 -10064.668 27.639127 -10032.167 -32.500121 39.99345 -72.493571 157.34039 + 1000 -10037.003 -10063.662 26.658825 -10031.337 -32.325053 29.573578 -61.898631 151.75986 +Loop time of 44.6551 on 4 procs for 1000 steps with 1360 atoms + +Performance: 1.935 ns/day, 12.404 hours/ns, 22.394 timesteps/s +93.9% CPU use with 4 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 40.304 | 41.221 | 41.998 | 9.5 | 92.31 +Bond | 0.00027633 | 0.00029379 | 0.00031424 | 0.0 | 0.00 +Neigh | 0 | 0 | 0 | 0.0 | 0.00 +Comm | 2.5678 | 3.3334 | 4.2403 | 32.9 | 7.46 +Output | 0.0051446 | 0.0054518 | 0.0059683 | 0.4 | 0.01 +Modify | 0.0088317 | 0.009002 | 0.0090654 | 0.1 | 0.02 +Other | | 0.08586 | | | 0.19 + +Nlocal: 340 ave 340 max 340 min +Histogram: 4 0 0 0 0 0 0 0 0 0 +Nghost: 4628 ave 4628 max 4628 min +Histogram: 4 0 0 0 0 0 0 0 0 0 +Neighs: 0 ave 0 max 0 min +Histogram: 4 0 0 0 0 0 0 0 0 0 +FullNghs: 259250 ave 259250 max 259250 min +Histogram: 4 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 1037000 +Ave neighs/atom = 762.5 +Ave special neighs/atom = 0 +Neighbor list builds = 0 +Dangerous builds = 0 +Total wall time: 0:00:44 diff --git a/examples/USER/misc/ilp_graphene_hbn/bilayer-hBN/log.5Jun19.bilayer_hBN.icc.1 b/examples/USER/misc/ilp_graphene_hbn/log.31Jul19.bilayer-hBN.g++.1 similarity index 56% rename from examples/USER/misc/ilp_graphene_hbn/bilayer-hBN/log.5Jun19.bilayer_hBN.icc.1 rename to examples/USER/misc/ilp_graphene_hbn/log.31Jul19.bilayer-hBN.g++.1 index abebb8df27..c5c6e94f15 100644 --- a/examples/USER/misc/ilp_graphene_hbn/bilayer-hBN/log.5Jun19.bilayer_hBN.icc.1 +++ b/examples/USER/misc/ilp_graphene_hbn/log.31Jul19.bilayer-hBN.g++.1 @@ -1,5 +1,4 @@ -LAMMPS (5 Jun 2019) -OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (../comm.cpp:88) +LAMMPS (31 Jul 2019) using 1 OpenMP thread(s) per MPI task # Initialization units metal @@ -20,8 +19,8 @@ read_data hBN_AA_prime_stack_2L_noH.data 0 = max # of 1-3 neighbors 0 = max # of 1-4 neighbors 1 = max # of special neighbors - special bonds CPU = 0.000162885 secs - read_data CPU = 0.00152144 secs + special bonds CPU = 0.000375509 secs + read_data CPU = 0.00181293 secs mass 1 10.8110 # boron mass (g/mole) | membrane mass 2 14.0067 # nitrogen mass (g/mole) | adsorbate mass 3 10.8110 # boron mass (g/mole) | membrane @@ -65,9 +64,8 @@ variable Erep equal c_2[2] # repulsive energy ############# Output ############### thermo 100 -thermo_style custom step cpu etotal pe ke v_Evdw v_Tersoff v_EILP v_Erep v_Evdw v_Ecoul temp -thermo_modify line one format float %.10f -thermo_modify flush yes norm no lost error +thermo_style custom step etotal pe ke v_Evdw v_Tersoff v_EILP v_Erep v_Evdw v_Ecoul temp +thermo_modify lost warn ###### Run molecular dynamics ###### run 1000 @@ -98,34 +96,34 @@ Neighbor list info ... pair build: halffull/newton stencil: none bin: none -Per MPI rank memory allocation (min/avg/max) = 39.16 | 39.16 | 39.16 Mbytes -Step CPU TotEng PotEng KinEng v_Evdw v_Tersoff v_EILP v_Erep v_Evdw v_Ecoul Temp - 0 0.0000000000 -10193.1380848266 -10245.8374459431 52.6993611165 -77.5570687695 -10208.7302118650 -36.7764829084 40.7805858612 -77.5570687695 -0.3307511697 300.0000000000 - 100 6.7965245070 -10192.8138221665 -10215.1933919318 22.3795697653 -80.9976194405 -10177.8775571602 -36.9677356248 44.0298838157 -80.9976194405 -0.3480991468 127.3994748197 - 200 13.6121753111 -10192.9217984546 -10221.8066529747 28.8848545200 -86.3703194681 -10184.2512197444 -37.1689855905 49.2013338776 -86.3703194681 -0.3864476398 164.4319052911 - 300 20.4697002331 -10192.8780091121 -10219.0294731325 26.1514640204 -83.0639240055 -10182.3487520151 -36.3041195435 46.7598044620 -83.0639240055 -0.3766015739 148.8716189324 - 400 27.2477328760 -10192.8915023008 -10218.8337311224 25.9422288216 -78.3942416895 -10181.3978178066 -37.1109676261 41.2832740634 -78.3942416895 -0.3249456897 147.6805122794 - 500 34.0398510781 -10192.9091924320 -10221.3314056924 28.4222132604 -81.7685306349 -10184.0302799036 -36.9462261394 44.8223044955 -81.7685306349 -0.3548996493 161.7982419039 - 600 40.8147194131 -10192.8859685989 -10219.3709182378 26.4849496389 -86.2783346104 -10182.6694059460 -36.2951497597 49.9831848507 -86.2783346104 -0.4063625321 150.7700420526 - 700 47.6096971680 -10192.9015812429 -10220.9496893393 28.0481080963 -82.2887300963 -10183.2081700333 -37.3937397296 44.8949903667 -82.2887300963 -0.3477795764 159.6685851711 - 800 54.4165411390 -10192.8798040842 -10218.5099898620 25.6301857778 -78.0110194568 -10181.4267315419 -36.7542088970 41.2568105599 -78.0110194568 -0.3290494232 145.9041546318 - 900 61.2580328170 -10192.8940657565 -10220.5595028458 27.6654370893 -82.4743793723 -10183.8013123118 -36.3811572492 46.0932221231 -82.4743793723 -0.3770332848 157.4901659330 - 1000 68.0452993071 -10192.8973362869 -10219.0104657947 26.1131295079 -87.1256831340 -10181.2524878789 -37.3618984004 49.7637847337 -87.1256831340 -0.3960795154 148.6533932553 -Loop time of 68.0453 on 1 procs for 1000 steps with 1360 atoms +Per MPI rank memory allocation (min/avg/max) = 35.9 | 35.9 | 35.9 Mbytes +Step TotEng PotEng KinEng v_Evdw v_Tersoff v_EILP v_Erep v_Evdw v_Ecoul Temp + 0 -10193.138 -10245.837 52.699361 -77.557069 -10208.73 -36.776483 40.780586 -77.557069 -0.33075117 300 + 100 -10192.814 -10215.193 22.37957 -80.997619 -10177.878 -36.967736 44.029884 -80.997619 -0.34809915 127.39947 + 200 -10192.922 -10221.807 28.884855 -86.370319 -10184.251 -37.168986 49.201334 -86.370319 -0.38644764 164.43191 + 300 -10192.878 -10219.029 26.151464 -83.063924 -10182.349 -36.30412 46.759804 -83.063924 -0.37660157 148.87162 + 400 -10192.892 -10218.834 25.942229 -78.394242 -10181.398 -37.110968 41.283274 -78.394242 -0.32494569 147.68051 + 500 -10192.909 -10221.331 28.422213 -81.768531 -10184.03 -36.946226 44.822304 -81.768531 -0.35489965 161.79824 + 600 -10192.886 -10219.371 26.48495 -86.278335 -10182.669 -36.29515 49.983185 -86.278335 -0.40636253 150.77004 + 700 -10192.902 -10220.95 28.048108 -82.28873 -10183.208 -37.39374 44.89499 -82.28873 -0.34777958 159.66859 + 800 -10192.88 -10218.51 25.630186 -78.011019 -10181.427 -36.754209 41.256811 -78.011019 -0.32904942 145.90415 + 900 -10192.894 -10220.56 27.665437 -82.474379 -10183.801 -36.381157 46.093222 -82.474379 -0.37703328 157.49017 + 1000 -10192.897 -10219.01 26.11313 -87.125683 -10181.252 -37.361898 49.763785 -87.125683 -0.39607952 148.65339 +Loop time of 211.527 on 1 procs for 1000 steps with 1360 atoms -Performance: 1.270 ns/day, 18.901 hours/ns, 14.696 timesteps/s -100.0% CPU use with 1 MPI tasks x 1 OpenMP threads +Performance: 0.408 ns/day, 58.757 hours/ns, 4.728 timesteps/s +99.9% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- -Pair | 67.995 | 67.995 | 67.995 | 0.0 | 99.93 -Bond | 0.00047219 | 0.00047219 | 0.00047219 | 0.0 | 0.00 +Pair | 211.4 | 211.4 | 211.4 | 0.0 | 99.94 +Bond | 0.00018859 | 0.00018859 | 0.00018859 | 0.0 | 0.00 Neigh | 0 | 0 | 0 | 0.0 | 0.00 -Comm | 0.030427 | 0.030427 | 0.030427 | 0.0 | 0.04 -Output | 0.000568 | 0.000568 | 0.000568 | 0.0 | 0.00 -Modify | 0.0089312 | 0.0089312 | 0.0089312 | 0.0 | 0.01 -Other | | 0.01005 | | | 0.01 +Comm | 0.082034 | 0.082034 | 0.082034 | 0.0 | 0.04 +Output | 0.00037289 | 0.00037289 | 0.00037289 | 0.0 | 0.00 +Modify | 0.027928 | 0.027928 | 0.027928 | 0.0 | 0.01 +Other | | 0.0159 | | | 0.01 Nlocal: 1360 ave 1360 max 1360 min Histogram: 1 0 0 0 0 0 0 0 0 0 @@ -141,4 +139,4 @@ Ave neighs/atom = 739 Ave special neighs/atom = 0 Neighbor list builds = 0 Dangerous builds = 0 -Total wall time: 0:01:08 +Total wall time: 0:03:31 diff --git a/examples/USER/misc/ilp_graphene_hbn/bilayer-hBN/log.5Jun19.bilayer_hBN.icc.4 b/examples/USER/misc/ilp_graphene_hbn/log.31Jul19.bilayer-hBN.g++.4 similarity index 56% rename from examples/USER/misc/ilp_graphene_hbn/bilayer-hBN/log.5Jun19.bilayer_hBN.icc.4 rename to examples/USER/misc/ilp_graphene_hbn/log.31Jul19.bilayer-hBN.g++.4 index 8ad5875282..7a0b7a269b 100644 --- a/examples/USER/misc/ilp_graphene_hbn/bilayer-hBN/log.5Jun19.bilayer_hBN.icc.4 +++ b/examples/USER/misc/ilp_graphene_hbn/log.31Jul19.bilayer-hBN.g++.4 @@ -1,5 +1,4 @@ -LAMMPS (5 Jun 2019) -OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (../comm.cpp:88) +LAMMPS (31 Jul 2019) using 1 OpenMP thread(s) per MPI task # Initialization units metal @@ -20,8 +19,8 @@ read_data hBN_AA_prime_stack_2L_noH.data 0 = max # of 1-3 neighbors 0 = max # of 1-4 neighbors 1 = max # of special neighbors - special bonds CPU = 0.00013403 secs - read_data CPU = 0.00236647 secs + special bonds CPU = 0.000224352 secs + read_data CPU = 0.00160909 secs mass 1 10.8110 # boron mass (g/mole) | membrane mass 2 14.0067 # nitrogen mass (g/mole) | adsorbate mass 3 10.8110 # boron mass (g/mole) | membrane @@ -65,9 +64,8 @@ variable Erep equal c_2[2] # repulsive energy ############# Output ############### thermo 100 -thermo_style custom step cpu etotal pe ke v_Evdw v_Tersoff v_EILP v_Erep v_Evdw v_Ecoul temp -thermo_modify line one format float %.10f -thermo_modify flush yes norm no lost error +thermo_style custom step etotal pe ke v_Evdw v_Tersoff v_EILP v_Erep v_Evdw v_Ecoul temp +thermo_modify lost warn ###### Run molecular dynamics ###### run 1000 @@ -98,34 +96,34 @@ Neighbor list info ... pair build: halffull/newton stencil: none bin: none -Per MPI rank memory allocation (min/avg/max) = 20.72 | 20.72 | 20.72 Mbytes -Step CPU TotEng PotEng KinEng v_Evdw v_Tersoff v_EILP v_Erep v_Evdw v_Ecoul Temp - 0 0.0000000000 -10193.1380848270 -10245.8374459435 52.6993611165 -77.5570687695 -10208.7302118654 -36.7764829083 40.7805858612 -77.5570687695 -0.3307511697 300.0000000000 - 100 2.1550989150 -10192.8138221665 -10215.1933919317 22.3795697653 -80.9976194405 -10177.8775571601 -36.9677356248 44.0298838158 -80.9976194405 -0.3480991468 127.3994748197 - 200 4.3479236889 -10192.9217984546 -10221.8066529746 28.8848545200 -86.3703194681 -10184.2512197444 -37.1689855904 49.2013338777 -86.3703194681 -0.3864476398 164.4319052911 - 300 6.5410459590 -10192.8780091121 -10219.0294731324 26.1514640204 -83.0639240055 -10182.3487520151 -36.3041195435 46.7598044620 -83.0639240055 -0.3766015739 148.8716189324 - 400 8.7036962360 -10192.8915023008 -10218.8337311224 25.9422288216 -78.3942416895 -10181.3978178066 -37.1109676261 41.2832740634 -78.3942416895 -0.3249456897 147.6805122794 - 500 10.8535934120 -10192.9091924320 -10221.3314056923 28.4222132604 -81.7685306349 -10184.0302799036 -36.9462261394 44.8223044955 -81.7685306349 -0.3548996493 161.7982419039 - 600 12.9922130840 -10192.8859685988 -10219.3709182377 26.4849496389 -86.2783346104 -10182.6694059459 -36.2951497597 49.9831848507 -86.2783346104 -0.4063625321 150.7700420526 - 700 15.1486390879 -10192.9015812430 -10220.9496893393 28.0481080963 -82.2887300963 -10183.2081700333 -37.3937397295 44.8949903668 -82.2887300963 -0.3477795764 159.6685851711 - 800 17.3069961029 -10192.8798040842 -10218.5099898620 25.6301857778 -78.0110194568 -10181.4267315419 -36.7542088969 41.2568105599 -78.0110194568 -0.3290494232 145.9041546318 - 900 19.4832645269 -10192.8940657564 -10220.5595028457 27.6654370893 -82.4743793723 -10183.8013123118 -36.3811572492 46.0932221231 -82.4743793723 -0.3770332848 157.4901659330 - 1000 21.6507079899 -10192.8973362868 -10219.0104657947 26.1131295079 -87.1256831340 -10181.2524878789 -37.3618984003 49.7637847337 -87.1256831340 -0.3960795154 148.6533932553 -Loop time of 21.6507 on 4 procs for 1000 steps with 1360 atoms +Per MPI rank memory allocation (min/avg/max) = 18.99 | 18.99 | 18.99 Mbytes +Step TotEng PotEng KinEng v_Evdw v_Tersoff v_EILP v_Erep v_Evdw v_Ecoul Temp + 0 -10193.138 -10245.837 52.699361 -77.557069 -10208.73 -36.776483 40.780586 -77.557069 -0.33075117 300 + 100 -10192.814 -10215.193 22.37957 -80.997619 -10177.878 -36.967736 44.029884 -80.997619 -0.34809915 127.39947 + 200 -10192.922 -10221.807 28.884855 -86.370319 -10184.251 -37.168986 49.201334 -86.370319 -0.38644764 164.43191 + 300 -10192.878 -10219.029 26.151464 -83.063924 -10182.349 -36.30412 46.759804 -83.063924 -0.37660157 148.87162 + 400 -10192.892 -10218.834 25.942229 -78.394242 -10181.398 -37.110968 41.283274 -78.394242 -0.32494569 147.68051 + 500 -10192.909 -10221.331 28.422213 -81.768531 -10184.03 -36.946226 44.822304 -81.768531 -0.35489965 161.79824 + 600 -10192.886 -10219.371 26.48495 -86.278335 -10182.669 -36.29515 49.983185 -86.278335 -0.40636253 150.77004 + 700 -10192.902 -10220.95 28.048108 -82.28873 -10183.208 -37.39374 44.89499 -82.28873 -0.34777958 159.66859 + 800 -10192.88 -10218.51 25.630186 -78.011019 -10181.427 -36.754209 41.256811 -78.011019 -0.32904942 145.90415 + 900 -10192.894 -10220.56 27.665437 -82.474379 -10183.801 -36.381157 46.093222 -82.474379 -0.37703328 157.49017 + 1000 -10192.897 -10219.01 26.11313 -87.125683 -10181.252 -37.361898 49.763785 -87.125683 -0.39607952 148.65339 +Loop time of 68.3631 on 4 procs for 1000 steps with 1360 atoms -Performance: 3.991 ns/day, 6.014 hours/ns, 46.188 timesteps/s -99.8% CPU use with 4 MPI tasks x 1 OpenMP threads +Performance: 1.264 ns/day, 18.990 hours/ns, 14.628 timesteps/s +98.5% CPU use with 4 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- -Pair | 20.152 | 20.681 | 21.202 | 8.2 | 95.52 -Bond | 0.00039643 | 0.00043971 | 0.00048381 | 0.0 | 0.00 +Pair | 64.58 | 66.38 | 67.402 | 13.2 | 97.10 +Bond | 0.0001719 | 0.00021869 | 0.00024033 | 0.0 | 0.00 Neigh | 0 | 0 | 0 | 0.0 | 0.00 -Comm | 0.43171 | 0.9526 | 1.482 | 38.2 | 4.40 -Output | 0.00028839 | 0.00037988 | 0.00064771 | 0.0 | 0.00 -Modify | 0.0046368 | 0.0047831 | 0.0050183 | 0.2 | 0.02 -Other | | 0.01106 | | | 0.05 +Comm | 0.93767 | 1.9601 | 3.76 | 77.0 | 2.87 +Output | 0.00033593 | 0.00061601 | 0.0014501 | 0.0 | 0.00 +Modify | 0.0085733 | 0.0089303 | 0.0093236 | 0.4 | 0.01 +Other | | 0.01285 | | | 0.02 Nlocal: 340 ave 340 max 340 min Histogram: 4 0 0 0 0 0 0 0 0 0 @@ -141,4 +139,4 @@ Ave neighs/atom = 739 Ave special neighs/atom = 0 Neighbor list builds = 0 Dangerous builds = 0 -Total wall time: 0:00:21 +Total wall time: 0:01:08 diff --git a/examples/USER/misc/ilp_graphene_hbn/gr-hBN/log.5Jun19.grhBN.icc.1 b/examples/USER/misc/ilp_graphene_hbn/log.31Jul19.grhBN.g++.1 similarity index 60% rename from examples/USER/misc/ilp_graphene_hbn/gr-hBN/log.5Jun19.grhBN.icc.1 rename to examples/USER/misc/ilp_graphene_hbn/log.31Jul19.grhBN.g++.1 index 65e32502f0..f9f1dedff6 100644 --- a/examples/USER/misc/ilp_graphene_hbn/gr-hBN/log.5Jun19.grhBN.icc.1 +++ b/examples/USER/misc/ilp_graphene_hbn/log.31Jul19.grhBN.g++.1 @@ -1,5 +1,4 @@ -LAMMPS (5 Jun 2019) -OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (../comm.cpp:88) +LAMMPS (31 Jul 2019) using 1 OpenMP thread(s) per MPI task # Initialization units metal @@ -20,8 +19,8 @@ read_data gr_hBN_Cstack_2L_noH.data 0 = max # of 1-3 neighbors 0 = max # of 1-4 neighbors 1 = max # of special neighbors - special bonds CPU = 0.000152684 secs - read_data CPU = 0.00139584 secs + special bonds CPU = 0.000282049 secs + read_data CPU = 0.00159025 secs mass 1 10.8110 # boron mass (g/mole) | membrane mass 2 14.0067 # nitrogen mass (g/mole) | membrane mass 3 12.0107 # carbon mass (g/mole) | adsorbate @@ -68,7 +67,6 @@ variable Ecoul equal c_3 ############# Output ############## thermo 100 thermo_style custom step etotal pe ke v_Evdw v_Tersoff v_REBO v_EILP v_Erep v_Evdw v_Ecoul temp -thermo_modify line one format float %.10f ###### Run molecular dynamics ###### run 1000 @@ -109,34 +107,34 @@ Neighbor list info ... pair build: halffull/newton stencil: none bin: none -Per MPI rank memory allocation (min/avg/max) = 25.93 | 25.93 | 25.93 Mbytes +Per MPI rank memory allocation (min/avg/max) = 22.52 | 22.52 | 22.52 Mbytes Step TotEng PotEng KinEng v_Evdw v_Tersoff v_REBO v_EILP v_Erep v_Evdw v_Ecoul Temp - 0 -10707.2836653377 -10763.0852699342 55.8016045965 -75.2477261362 -5401.7347845703 -5322.2780768034 -39.0724085605 36.1753175757 -75.2477261362 0.0000000000 300.0000000000 - 100 -10707.0738132278 -10737.1273434298 30.0535302020 -73.2173218622 -5389.9568321958 -5309.2004092412 -37.9701019928 35.2472198694 -73.2173218622 0.0000000000 161.5734731251 - 200 -10707.0160305531 -10734.9317906949 27.9157601418 -71.6030968581 -5389.1293717071 -5307.7455440517 -38.0568749361 33.5462219220 -71.6030968581 0.0000000000 150.0804162013 - 300 -10707.0133459577 -10734.9870508108 27.9737048532 -75.0821335395 -5388.9196081501 -5308.1164952096 -37.9509474511 37.1311860884 -75.0821335395 0.0000000000 150.3919379493 - 400 -10707.0118845924 -10735.4980560195 28.4861714271 -76.3398711857 -5389.1656629670 -5308.1529507210 -38.1794423315 38.1604288542 -76.3398711857 0.0000000000 153.1470553564 - 500 -10707.0073064907 -10734.6814074933 27.6741010026 -73.3123544614 -5388.7261058688 -5307.7383573628 -38.2169442617 35.0954101998 -73.3123544614 0.0000000000 148.7812108775 - 600 -10707.0179599067 -10735.8330915547 28.8151316481 -71.9277634955 -5389.0797599186 -5308.5959984739 -38.1573331622 33.7704303333 -71.9277634955 0.0000000000 154.9156078382 - 700 -10707.0202991119 -10735.6556762202 28.6353771083 -74.6793707186 -5389.2970704981 -5308.1866033124 -38.1720024097 36.5073683089 -74.6793707186 0.0000000000 153.9492133711 - 800 -10707.0042706783 -10734.3516957279 27.3474250495 -76.3712879764 -5388.5923210533 -5307.7206382682 -38.0387364064 38.3325515700 -76.3712879764 0.0000000000 147.0249390530 - 900 -10707.0144790011 -10735.8318835748 28.8174045738 -73.6993318112 -5388.9674133804 -5308.7963924816 -38.0680777128 35.6312540984 -73.6993318112 0.0000000000 154.9278275177 - 1000 -10706.9953891527 -10733.5615396283 26.5661504756 -71.4398677888 -5388.0186485439 -5307.4414386685 -38.1014524159 33.3384153730 -71.4398677888 0.0000000000 142.8246589021 -Loop time of 55.1175 on 1 procs for 1000 steps with 1440 atoms + 0 -10707.284 -10763.085 55.801605 -75.247726 -5401.7348 -5322.2781 -39.072409 36.175318 -75.247726 0 300 + 100 -10707.074 -10737.127 30.05353 -73.217322 -5389.9568 -5309.2004 -37.970102 35.24722 -73.217322 0 161.57347 + 200 -10707.016 -10734.932 27.91576 -71.603097 -5389.1294 -5307.7455 -38.056875 33.546222 -71.603097 0 150.08042 + 300 -10707.013 -10734.987 27.973705 -75.082134 -5388.9196 -5308.1165 -37.950947 37.131186 -75.082134 0 150.39194 + 400 -10707.012 -10735.498 28.486171 -76.339871 -5389.1657 -5308.153 -38.179442 38.160429 -76.339871 0 153.14706 + 500 -10707.007 -10734.681 27.674101 -73.312354 -5388.7261 -5307.7384 -38.216944 35.09541 -73.312354 0 148.78121 + 600 -10707.018 -10735.833 28.815132 -71.927763 -5389.0798 -5308.596 -38.157333 33.77043 -71.927763 0 154.91561 + 700 -10707.02 -10735.656 28.635377 -74.679371 -5389.2971 -5308.1866 -38.172002 36.507368 -74.679371 0 153.94921 + 800 -10707.004 -10734.352 27.347425 -76.371288 -5388.5923 -5307.7206 -38.038736 38.332552 -76.371288 0 147.02494 + 900 -10707.014 -10735.832 28.817405 -73.699332 -5388.9674 -5308.7964 -38.068078 35.631254 -73.699332 0 154.92783 + 1000 -10706.995 -10733.562 26.56615 -71.439868 -5388.0186 -5307.4414 -38.101452 33.338415 -71.439868 0 142.82466 +Loop time of 152.66 on 1 procs for 1000 steps with 1440 atoms -Performance: 1.568 ns/day, 15.310 hours/ns, 18.143 timesteps/s -100.0% CPU use with 1 MPI tasks x 1 OpenMP threads +Performance: 0.566 ns/day, 42.406 hours/ns, 6.550 timesteps/s +99.8% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- -Pair | 55.062 | 55.062 | 55.062 | 0.0 | 99.90 -Bond | 0.00046717 | 0.00046717 | 0.00046717 | 0.0 | 0.00 +Pair | 152.52 | 152.52 | 152.52 | 0.0 | 99.91 +Bond | 0.00023174 | 0.00023174 | 0.00023174 | 0.0 | 0.00 Neigh | 0 | 0 | 0 | 0.0 | 0.00 -Comm | 0.034313 | 0.034313 | 0.034313 | 0.0 | 0.06 -Output | 0.00034028 | 0.00034028 | 0.00034028 | 0.0 | 0.00 -Modify | 0.010012 | 0.010012 | 0.010012 | 0.0 | 0.02 -Other | | 0.01061 | | | 0.02 +Comm | 0.087147 | 0.087147 | 0.087147 | 0.0 | 0.06 +Output | 0.0004189 | 0.0004189 | 0.0004189 | 0.0 | 0.00 +Modify | 0.029972 | 0.029972 | 0.029972 | 0.0 | 0.02 +Other | | 0.02057 | | | 0.01 Nlocal: 1440 ave 1440 max 1440 min Histogram: 1 0 0 0 0 0 0 0 0 0 @@ -152,4 +150,4 @@ Ave neighs/atom = 195 Ave special neighs/atom = 0 Neighbor list builds = 0 Dangerous builds = 0 -Total wall time: 0:00:55 +Total wall time: 0:02:32 diff --git a/examples/USER/misc/ilp_graphene_hbn/gr-hBN/log.5Jun19.grhBN.icc.4 b/examples/USER/misc/ilp_graphene_hbn/log.31Jul19.grhBN.g++.4 similarity index 60% rename from examples/USER/misc/ilp_graphene_hbn/gr-hBN/log.5Jun19.grhBN.icc.4 rename to examples/USER/misc/ilp_graphene_hbn/log.31Jul19.grhBN.g++.4 index 9ea23fb6e3..a7b97a81b7 100644 --- a/examples/USER/misc/ilp_graphene_hbn/gr-hBN/log.5Jun19.grhBN.icc.4 +++ b/examples/USER/misc/ilp_graphene_hbn/log.31Jul19.grhBN.g++.4 @@ -1,5 +1,4 @@ -LAMMPS (5 Jun 2019) -OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (../comm.cpp:88) +LAMMPS (31 Jul 2019) using 1 OpenMP thread(s) per MPI task # Initialization units metal @@ -20,8 +19,8 @@ read_data gr_hBN_Cstack_2L_noH.data 0 = max # of 1-3 neighbors 0 = max # of 1-4 neighbors 1 = max # of special neighbors - special bonds CPU = 0.000148868 secs - read_data CPU = 0.00332732 secs + special bonds CPU = 0.00012207 secs + read_data CPU = 0.00357461 secs mass 1 10.8110 # boron mass (g/mole) | membrane mass 2 14.0067 # nitrogen mass (g/mole) | membrane mass 3 12.0107 # carbon mass (g/mole) | adsorbate @@ -68,7 +67,6 @@ variable Ecoul equal c_3 ############# Output ############## thermo 100 thermo_style custom step etotal pe ke v_Evdw v_Tersoff v_REBO v_EILP v_Erep v_Evdw v_Ecoul temp -thermo_modify line one format float %.10f ###### Run molecular dynamics ###### run 1000 @@ -109,34 +107,34 @@ Neighbor list info ... pair build: halffull/newton stencil: none bin: none -Per MPI rank memory allocation (min/avg/max) = 14.25 | 14.25 | 14.25 Mbytes +Per MPI rank memory allocation (min/avg/max) = 12.45 | 12.45 | 12.45 Mbytes Step TotEng PotEng KinEng v_Evdw v_Tersoff v_REBO v_EILP v_Erep v_Evdw v_Ecoul Temp - 0 -10707.2836653376 -10763.0852699341 55.8016045965 -75.2477261361 -5401.7347845703 -5322.2780768034 -39.0724085604 36.1753175757 -75.2477261361 0.0000000000 300.0000000000 - 100 -10707.0738132277 -10737.1273434298 30.0535302020 -73.2173218622 -5389.9568321958 -5309.2004092412 -37.9701019928 35.2472198694 -73.2173218622 0.0000000000 161.5734731251 - 200 -10707.0160305531 -10734.9317906949 27.9157601418 -71.6030968581 -5389.1293717071 -5307.7455440517 -38.0568749361 33.5462219220 -71.6030968581 0.0000000000 150.0804162013 - 300 -10707.0133459576 -10734.9870508108 27.9737048532 -75.0821335395 -5388.9196081501 -5308.1164952096 -37.9509474511 37.1311860885 -75.0821335395 0.0000000000 150.3919379493 - 400 -10707.0118845923 -10735.4980560194 28.4861714271 -76.3398711857 -5389.1656629669 -5308.1529507210 -38.1794423315 38.1604288542 -76.3398711857 0.0000000000 153.1470553564 - 500 -10707.0073064907 -10734.6814074932 27.6741010026 -73.3123544614 -5388.7261058688 -5307.7383573628 -38.2169442616 35.0954101998 -73.3123544614 0.0000000000 148.7812108775 - 600 -10707.0179599066 -10735.8330915547 28.8151316481 -71.9277634955 -5389.0797599186 -5308.5959984739 -38.1573331622 33.7704303333 -71.9277634955 0.0000000000 154.9156078382 - 700 -10707.0202991119 -10735.6556762202 28.6353771083 -74.6793707186 -5389.2970704981 -5308.1866033124 -38.1720024097 36.5073683089 -74.6793707186 0.0000000000 153.9492133711 - 800 -10707.0042706783 -10734.3516957278 27.3474250495 -76.3712879764 -5388.5923210533 -5307.7206382682 -38.0387364063 38.3325515701 -76.3712879764 0.0000000000 147.0249390530 - 900 -10707.0144790010 -10735.8318835748 28.8174045738 -73.6993318112 -5388.9674133804 -5308.7963924816 -38.0680777128 35.6312540984 -73.6993318112 0.0000000000 154.9278275177 - 1000 -10706.9953891527 -10733.5615396283 26.5661504756 -71.4398677888 -5388.0186485439 -5307.4414386685 -38.1014524158 33.3384153730 -71.4398677888 0.0000000000 142.8246589021 -Loop time of 15.7325 on 4 procs for 1000 steps with 1440 atoms + 0 -10707.284 -10763.085 55.801605 -75.247726 -5401.7348 -5322.2781 -39.072409 36.175318 -75.247726 0 300 + 100 -10707.074 -10737.127 30.05353 -73.217322 -5389.9568 -5309.2004 -37.970102 35.24722 -73.217322 0 161.57347 + 200 -10707.016 -10734.932 27.91576 -71.603097 -5389.1294 -5307.7455 -38.056875 33.546222 -71.603097 0 150.08042 + 300 -10707.013 -10734.987 27.973705 -75.082134 -5388.9196 -5308.1165 -37.950947 37.131186 -75.082134 0 150.39194 + 400 -10707.012 -10735.498 28.486171 -76.339871 -5389.1657 -5308.153 -38.179442 38.160429 -76.339871 0 153.14706 + 500 -10707.007 -10734.681 27.674101 -73.312354 -5388.7261 -5307.7384 -38.216944 35.09541 -73.312354 0 148.78121 + 600 -10707.018 -10735.833 28.815132 -71.927763 -5389.0798 -5308.596 -38.157333 33.77043 -71.927763 0 154.91561 + 700 -10707.02 -10735.656 28.635377 -74.679371 -5389.2971 -5308.1866 -38.172002 36.507368 -74.679371 0 153.94921 + 800 -10707.004 -10734.352 27.347425 -76.371288 -5388.5923 -5307.7206 -38.038736 38.332552 -76.371288 0 147.02494 + 900 -10707.014 -10735.832 28.817405 -73.699332 -5388.9674 -5308.7964 -38.068078 35.631254 -73.699332 0 154.92783 + 1000 -10706.995 -10733.562 26.56615 -71.439868 -5388.0186 -5307.4414 -38.101452 33.338415 -71.439868 0 142.82466 +Loop time of 54.095 on 4 procs for 1000 steps with 1440 atoms -Performance: 5.492 ns/day, 4.370 hours/ns, 63.563 timesteps/s -99.8% CPU use with 4 MPI tasks x 1 OpenMP threads +Performance: 1.597 ns/day, 15.026 hours/ns, 18.486 timesteps/s +84.8% CPU use with 4 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- -Pair | 13.905 | 14.645 | 15.391 | 14.5 | 93.08 -Bond | 0.00029796 | 0.00040495 | 0.00046212 | 0.0 | 0.00 +Pair | 42.138 | 45.531 | 49.106 | 42.0 | 84.17 +Bond | 0.0003159 | 0.00037384 | 0.000489 | 0.0 | 0.00 Neigh | 0 | 0 | 0 | 0.0 | 0.00 -Comm | 0.3261 | 1.0722 | 1.8116 | 53.4 | 6.82 -Output | 0.00028242 | 0.00030932 | 0.00037515 | 0.0 | 0.00 -Modify | 0.0046079 | 0.0047365 | 0.0048651 | 0.2 | 0.03 -Other | | 0.01031 | | | 0.07 +Comm | 4.71 | 8.2803 | 11.682 | 98.3 | 15.31 +Output | 0.0021999 | 0.0055975 | 0.013382 | 6.0 | 0.01 +Modify | 0.0092845 | 0.010981 | 0.012538 | 1.3 | 0.02 +Other | | 0.2673 | | | 0.49 Nlocal: 360 ave 380 max 340 min Histogram: 2 0 0 0 0 0 0 0 0 2 @@ -152,4 +150,4 @@ Ave neighs/atom = 195 Ave special neighs/atom = 0 Neighbor list builds = 0 Dangerous builds = 0 -Total wall time: 0:00:15 +Total wall time: 0:00:54 diff --git a/examples/USER/misc/ilp_graphene_hbn/log.31Jul19.ilp_graphene_hbn.g++.1 b/examples/USER/misc/ilp_graphene_hbn/log.31Jul19.ilp_graphene_hbn.g++.1 new file mode 100644 index 0000000000..1845c2e54d --- /dev/null +++ b/examples/USER/misc/ilp_graphene_hbn/log.31Jul19.ilp_graphene_hbn.g++.1 @@ -0,0 +1,154 @@ +LAMMPS (31 Jul 2019) + using 1 OpenMP thread(s) per MPI task +# Initialization +units metal +boundary p p p +atom_style full +processors * * 1 # domain decomposition over x and y + +# System and atom definition +# we use 2 atom types so that inter- and intra-layer +# interactions can be specified separately +read_data hBN_AB_stack_2L_noH_equi_300K.data + orthogonal box = (0 0 0) to (43.38 42.5773 100) + 1 by 1 by 1 MPI processor grid + reading atoms ... + 1360 atoms + reading velocities ... + 1360 velocities + 0 = max # of 1-2 neighbors + 0 = max # of 1-3 neighbors + 0 = max # of 1-4 neighbors + 1 = max # of special neighbors + special bonds CPU = 0.000251532 secs + read_data CPU = 0.00451231 secs +mass 1 10.8110 # boron mass (g/mole) | membrane +mass 2 14.0067 # nitrogen mass (g/mole) | adsorbate +mass 3 10.8110 # boron mass (g/mole) | membrane +mass 4 14.0067 # nitrogen mass (g/mole) | adsorbate +# Separate atom groups +group membrane type 1 2 +680 atoms in group membrane +group adsorbate type 3 4 +680 atoms in group adsorbate + +######################## Potential defition ######################## +pair_style hybrid/overlay tersoff ilp/graphene/hbn 16.0 coul/shield 16.0 1 +#################################################################### +pair_coeff * * tersoff BNC.tersoff NULL NULL B N # chemical +Reading potential file BNC.tersoff with DATE: 2013-03-21 +pair_coeff * * ilp/graphene/hbn BNCH-old.ILP B N B N # long range +pair_coeff 1 3 coul/shield 0.70 +pair_coeff 1 4 coul/shield 0.69498201415576216335 +pair_coeff 2 3 coul/shield 0.69498201415576216335 +pair_coeff 2 4 coul/shield 0.69 +#################################################################### +# Neighbor update settings +neighbor 2.0 bin +neigh_modify every 1 +neigh_modify delay 0 +neigh_modify check yes + +#### Simulation settings #### +timestep 0.001 +#velocity adsorbate create 300.0 12345 +fix subf membrane setforce 0.0 0.0 0.0 +fix thermostat all nve + +compute 0 all pair tersoff +compute 1 all pair coul/shield ecoul +compute 2 all pair ilp/graphene/hbn +variable Tersoff equal c_0 +variable Ecoul equal c_1 +variable ILP equal c_2 +variable Evdw equal c_2[1] +variable Erep equal c_2[2] + +############################ + +# Output +thermo 100 +thermo_style custom step etotal pe ke v_Tersoff v_ILP v_Ecoul v_Erep v_Evdw temp +thermo_modify lost warn #ignore + +#dump 1 all custom 1000 traj.lammpstrj id mol type xu yu zu +#dump_modify 1 format line "%7d %3d %3d %15.10g %15.10g %15.10g" flush yes + +###### Run molecular dynamics ###### +run 1000 +Neighbor list info ... + update every 1 steps, delay 0 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 18 + ghost atom cutoff = 18 + binsize = 9, bins = 5 5 12 + 5 neighbor lists, perpetual/occasional/extra = 5 0 0 + (1) pair tersoff, perpetual, skip from (4) + attributes: full, newton on + pair build: skip + stencil: none + bin: none + (2) pair ilp/graphene/hbn, perpetual + attributes: full, newton on, ghost + pair build: full/bin/ghost + stencil: full/ghost/bin/3d + bin: standard + (3) pair coul/shield, perpetual, skip from (5) + attributes: half, newton on + pair build: skip + stencil: none + bin: none + (4) neighbor class addition, perpetual, copy from (2) + attributes: full, newton on + pair build: copy + stencil: none + bin: none + (5) neighbor class addition, perpetual, half/full from (4) + attributes: half, newton on + pair build: halffull/newton + stencil: none + bin: none +Per MPI rank memory allocation (min/avg/max) = 54.59 | 54.59 | 54.59 Mbytes +Step TotEng PotEng KinEng v_Tersoff v_ILP v_Ecoul v_Erep v_Evdw Temp + 0 -5114.6628 -5127.8586 13.195828 -5091.4121 -36.083114 -0.36343598 38.918674 -75.001787 75.119474 + 100 -5114.6621 -5127.6958 13.033777 -5091.2408 -36.09276 -0.36228286 38.769906 -74.862666 74.196973 + 200 -5114.6631 -5127.5945 12.93145 -5091.1508 -36.086669 -0.35708801 38.20076 -74.287429 73.614462 + 300 -5114.6694 -5128.3286 13.65924 -5091.8646 -36.110786 -0.35328159 37.758284 -73.86907 77.757528 + 400 -5114.6614 -5127.6424 12.980975 -5091.2348 -36.049634 -0.35794328 38.247252 -74.296886 73.896389 + 500 -5114.66 -5127.4098 12.749794 -5090.9285 -36.119571 -0.36174976 38.745548 -74.865119 72.580351 + 600 -5114.6673 -5128.0913 13.424021 -5091.6339 -36.09384 -0.36356991 38.927401 -75.021241 76.418503 + 700 -5114.661 -5127.7467 13.085707 -5091.2811 -36.106639 -0.35892399 38.332616 -74.439255 74.492596 + 800 -5114.6623 -5128.013 13.350778 -5091.5694 -36.089718 -0.35392503 37.851602 -73.94132 76.001554 + 900 -5114.6675 -5128.1497 13.482146 -5091.6704 -36.124679 -0.35462869 37.885183 -74.009861 76.749392 + 1000 -5114.6683 -5128.3365 13.668146 -5091.937 -36.037596 -0.36184347 38.709718 -74.747314 77.808228 +Loop time of 207.028 on 1 procs for 1000 steps with 1360 atoms + +Performance: 0.417 ns/day, 57.508 hours/ns, 4.830 timesteps/s +99.9% CPU use with 1 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 206.9 | 206.9 | 206.9 | 0.0 | 99.94 +Bond | 0.00019169 | 0.00019169 | 0.00019169 | 0.0 | 0.00 +Neigh | 0 | 0 | 0 | 0.0 | 0.00 +Comm | 0.081397 | 0.081397 | 0.081397 | 0.0 | 0.04 +Output | 0.00036597 | 0.00036597 | 0.00036597 | 0.0 | 0.00 +Modify | 0.033408 | 0.033408 | 0.033408 | 0.0 | 0.02 +Other | | 0.01615 | | | 0.01 + +Nlocal: 1360 ave 1360 max 1360 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 7840 ave 7840 max 7840 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 249628 ave 249628 max 249628 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +FullNghs: 253390 ave 253390 max 253390 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 253390 +Ave neighs/atom = 186.316 +Ave special neighs/atom = 0 +Neighbor list builds = 0 +Dangerous builds = 0 +Total wall time: 0:03:27 diff --git a/examples/USER/misc/ilp_graphene_hbn/log.31Jul19.ilp_graphene_hbn.g++.4 b/examples/USER/misc/ilp_graphene_hbn/log.31Jul19.ilp_graphene_hbn.g++.4 new file mode 100644 index 0000000000..ec2a8443a4 --- /dev/null +++ b/examples/USER/misc/ilp_graphene_hbn/log.31Jul19.ilp_graphene_hbn.g++.4 @@ -0,0 +1,154 @@ +LAMMPS (31 Jul 2019) + using 1 OpenMP thread(s) per MPI task +# Initialization +units metal +boundary p p p +atom_style full +processors * * 1 # domain decomposition over x and y + +# System and atom definition +# we use 2 atom types so that inter- and intra-layer +# interactions can be specified separately +read_data hBN_AB_stack_2L_noH_equi_300K.data + orthogonal box = (0 0 0) to (43.38 42.5773 100) + 2 by 2 by 1 MPI processor grid + reading atoms ... + 1360 atoms + reading velocities ... + 1360 velocities + 0 = max # of 1-2 neighbors + 0 = max # of 1-3 neighbors + 0 = max # of 1-4 neighbors + 1 = max # of special neighbors + special bonds CPU = 0.000332117 secs + read_data CPU = 0.00270581 secs +mass 1 10.8110 # boron mass (g/mole) | membrane +mass 2 14.0067 # nitrogen mass (g/mole) | adsorbate +mass 3 10.8110 # boron mass (g/mole) | membrane +mass 4 14.0067 # nitrogen mass (g/mole) | adsorbate +# Separate atom groups +group membrane type 1 2 +680 atoms in group membrane +group adsorbate type 3 4 +680 atoms in group adsorbate + +######################## Potential defition ######################## +pair_style hybrid/overlay tersoff ilp/graphene/hbn 16.0 coul/shield 16.0 1 +#################################################################### +pair_coeff * * tersoff BNC.tersoff NULL NULL B N # chemical +Reading potential file BNC.tersoff with DATE: 2013-03-21 +pair_coeff * * ilp/graphene/hbn BNCH-old.ILP B N B N # long range +pair_coeff 1 3 coul/shield 0.70 +pair_coeff 1 4 coul/shield 0.69498201415576216335 +pair_coeff 2 3 coul/shield 0.69498201415576216335 +pair_coeff 2 4 coul/shield 0.69 +#################################################################### +# Neighbor update settings +neighbor 2.0 bin +neigh_modify every 1 +neigh_modify delay 0 +neigh_modify check yes + +#### Simulation settings #### +timestep 0.001 +#velocity adsorbate create 300.0 12345 +fix subf membrane setforce 0.0 0.0 0.0 +fix thermostat all nve + +compute 0 all pair tersoff +compute 1 all pair coul/shield ecoul +compute 2 all pair ilp/graphene/hbn +variable Tersoff equal c_0 +variable Ecoul equal c_1 +variable ILP equal c_2 +variable Evdw equal c_2[1] +variable Erep equal c_2[2] + +############################ + +# Output +thermo 100 +thermo_style custom step etotal pe ke v_Tersoff v_ILP v_Ecoul v_Erep v_Evdw temp +thermo_modify lost warn #ignore + +#dump 1 all custom 1000 traj.lammpstrj id mol type xu yu zu +#dump_modify 1 format line "%7d %3d %3d %15.10g %15.10g %15.10g" flush yes + +###### Run molecular dynamics ###### +run 1000 +Neighbor list info ... + update every 1 steps, delay 0 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 18 + ghost atom cutoff = 18 + binsize = 9, bins = 5 5 12 + 5 neighbor lists, perpetual/occasional/extra = 5 0 0 + (1) pair tersoff, perpetual, skip from (4) + attributes: full, newton on + pair build: skip + stencil: none + bin: none + (2) pair ilp/graphene/hbn, perpetual + attributes: full, newton on, ghost + pair build: full/bin/ghost + stencil: full/ghost/bin/3d + bin: standard + (3) pair coul/shield, perpetual, skip from (5) + attributes: half, newton on + pair build: skip + stencil: none + bin: none + (4) neighbor class addition, perpetual, copy from (2) + attributes: full, newton on + pair build: copy + stencil: none + bin: none + (5) neighbor class addition, perpetual, half/full from (4) + attributes: half, newton on + pair build: halffull/newton + stencil: none + bin: none +Per MPI rank memory allocation (min/avg/max) = 28.9 | 28.9 | 28.9 Mbytes +Step TotEng PotEng KinEng v_Tersoff v_ILP v_Ecoul v_Erep v_Evdw Temp + 0 -5114.6628 -5127.8586 13.195828 -5091.4121 -36.083114 -0.36343598 38.918674 -75.001787 75.119474 + 100 -5114.6621 -5127.6958 13.033777 -5091.2408 -36.09276 -0.36228286 38.769906 -74.862666 74.196973 + 200 -5114.6631 -5127.5945 12.93145 -5091.1508 -36.086669 -0.35708801 38.20076 -74.287429 73.614462 + 300 -5114.6694 -5128.3286 13.65924 -5091.8646 -36.110786 -0.35328159 37.758284 -73.86907 77.757528 + 400 -5114.6614 -5127.6424 12.980975 -5091.2348 -36.049634 -0.35794328 38.247252 -74.296886 73.896389 + 500 -5114.66 -5127.4098 12.749794 -5090.9285 -36.119571 -0.36174976 38.745548 -74.865119 72.580351 + 600 -5114.6673 -5128.0913 13.424021 -5091.6339 -36.09384 -0.36356991 38.927401 -75.021241 76.418503 + 700 -5114.661 -5127.7467 13.085707 -5091.2811 -36.106639 -0.35892399 38.332616 -74.439255 74.492596 + 800 -5114.6623 -5128.013 13.350778 -5091.5694 -36.089718 -0.35392503 37.851602 -73.94132 76.001554 + 900 -5114.6675 -5128.1497 13.482146 -5091.6704 -36.124679 -0.35462869 37.885183 -74.009861 76.749392 + 1000 -5114.6683 -5128.3365 13.668146 -5091.937 -36.037596 -0.36184347 38.709718 -74.747314 77.808228 +Loop time of 65.9005 on 4 procs for 1000 steps with 1360 atoms + +Performance: 1.311 ns/day, 18.306 hours/ns, 15.174 timesteps/s +98.9% CPU use with 4 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 63.244 | 64.208 | 65.281 | 10.1 | 97.43 +Bond | 0.00013971 | 0.00017679 | 0.00022101 | 0.0 | 0.00 +Neigh | 0 | 0 | 0 | 0.0 | 0.00 +Comm | 0.58237 | 1.6612 | 2.6292 | 63.1 | 2.52 +Output | 0.0003171 | 0.00062358 | 0.0015192 | 0.0 | 0.00 +Modify | 0.010251 | 0.010509 | 0.01075 | 0.2 | 0.02 +Other | | 0.02025 | | | 0.03 + +Nlocal: 340 ave 346 max 336 min +Histogram: 1 0 1 0 1 0 0 0 0 1 +Nghost: 4537.5 ave 4540 max 4534 min +Histogram: 1 0 0 0 0 0 2 0 0 1 +Neighs: 62407 ave 62413 max 62402 min +Histogram: 1 0 0 1 1 0 0 0 0 1 +FullNghs: 63347.5 ave 65585 max 61866 min +Histogram: 1 1 0 1 0 0 0 0 0 1 + +Total # of neighbors = 253926 +Ave neighs/atom = 186.71 +Ave special neighs/atom = 0 +Neighbor list builds = 0 +Dangerous builds = 0 +Total wall time: 0:01:06 -- GitLab From 52e2db44a1c3f1c30cdc99580078251d61b80962 Mon Sep 17 00:00:00 2001 From: Giacomo Fiorin Date: Thu, 1 Aug 2019 15:12:42 -0400 Subject: [PATCH 408/469] Update Colvars to version 2019-08-01 One new feature (geometric path variables) and bugfixes. Minimize occurrence of file-read errors in multiple-walker metadynamics https://github.com/Colvars/colvars/pull/276 Better error messages for RMSD https://github.com/Colvars/colvars/pull/272 Ensemble-biased metadynamics documentation https://github.com/Colvars/colvars/pull/261 Fix bug on multiple walkers metadynamics, pmf included twice https://github.com/Colvars/colvars/pull/259 Implementation of the geometric path collective variables (C++11-only feature) https://github.com/Colvars/colvars/pull/249 --- doc/src/PDF/colvars-refman-lammps.pdf | Bin 628031 -> 665730 bytes lib/colvars/Makefile.common | 1 + lib/colvars/colvar.cpp | 20 +- lib/colvars/colvar.h | 8 + lib/colvars/colvar_geometricpath.h | 270 ++++++ lib/colvars/colvarbias_meta.cpp | 208 ++-- lib/colvars/colvarbias_meta.h | 8 +- lib/colvars/colvarbias_restraint.cpp | 3 +- lib/colvars/colvarcomp.cpp | 2 + lib/colvars/colvarcomp.h | 226 ++++- lib/colvars/colvarcomp_distances.cpp | 8 +- lib/colvars/colvarcomp_gpath.cpp | 910 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z?Yl+yw7<<`&fmHF_Q7_}SpDSP_s*2>ZF*ZJfB!DG-Q^eW*yZ1q@Hd&?kG=nW%)gYW$gX+s+gK diff --git a/lib/colvars/Makefile.common b/lib/colvars/Makefile.common index e3fa4662e6..5958765077 100644 --- a/lib/colvars/Makefile.common +++ b/lib/colvars/Makefile.common @@ -34,6 +34,7 @@ COLVARS_SRCS = \ colvarcomp_coordnums.cpp \ colvarcomp.cpp \ colvarcomp_distances.cpp \ + colvarcomp_gpath.cpp \ colvarcomp_protein.cpp \ colvarcomp_rotations.cpp \ colvar.cpp \ diff --git a/lib/colvars/colvar.cpp b/lib/colvars/colvar.cpp index 723a54ad39..e3676084ac 100644 --- a/lib/colvars/colvar.cpp +++ b/lib/colvars/colvar.cpp @@ -791,6 +791,11 @@ int colvar::init_components(std::string const &conf) "inertia", "inertia"); error_code |= init_components_type(conf, "moment of inertia around an axis", "inertiaZ"); error_code |= init_components_type(conf, "eigenvector", "eigenvector"); + error_code |= init_components_type(conf, "geometrical path collective variables (s)", "gspath"); + error_code |= init_components_type(conf, "geometrical path collective variables (z)", "gzpath"); + error_code |= init_components_type(conf, "linear combination of other collective variables", "subColvar"); + error_code |= init_components_type(conf, "geometrical path collective variables (s) for other CVs", "gspathCV"); + error_code |= init_components_type(conf, "geometrical path collective variables (z) for other CVs", "gzpathCV"); if (!cvcs.size() || (error_code != COLVARS_OK)) { cvm::error("Error: no valid components were provided " @@ -1495,6 +1500,8 @@ int colvar::calc_colvar_properties() // calculate the velocity by finite differences if (cvm::step_relative() == 0) { x_old = x; + v_fdiff.reset(); // Do not pretend we know anything about the actual velocity + // eg. upon restarting. That would require saving v_fdiff or x_old to the state file } else { v_fdiff = fdiff_velocity(x_old, x); v_reported = v_fdiff; @@ -1516,8 +1523,9 @@ int colvar::calc_colvar_properties() x_ext = prev_x_ext; v_ext = prev_v_ext; } - // report the restraint center as "value" + // These position and velocities come from integration at the _previous timestep_ in update_forces_energy() + // But we report values at the beginning of the timestep (value at t=0 on the first timestep) x_reported = x_ext; v_reported = v_ext; // the "total force" with the extended Lagrangian is @@ -1651,8 +1659,6 @@ cvm::real colvar::update_forces_energy() // is equal to the actual coordinate x_ext = x; } - // Report extended value - x_reported = x_ext; } // Now adding the force on the actual colvar (for those biases that @@ -1975,9 +1981,8 @@ std::istream & colvar::read_restart(std::istream &is) } if (is_enabled(f_cv_extended_Lagrangian)) { - if ( !(get_keyval(conf, "extended_x", x_ext, - colvarvalue(x.type()), colvarparse::parse_silent)) && + colvarvalue(x.type()), colvarparse::parse_silent)) || !(get_keyval(conf, "extended_v", v_ext, colvarvalue(x.type()), colvarparse::parse_silent)) ) { cvm::log("Error: restart file does not contain " @@ -2079,11 +2084,11 @@ std::ostream & colvar::write_restart(std::ostream &os) { os << " extended_x " << std::setprecision(cvm::cv_prec) << std::setw(cvm::cv_width) - << x_ext << "\n" + << x_reported << "\n" << " extended_v " << std::setprecision(cvm::cv_prec) << std::setw(cvm::cv_width) - << v_ext << "\n"; + << v_reported << "\n"; } os << "}\n\n"; @@ -2150,7 +2155,6 @@ std::ostream & colvar::write_traj_label(std::ostream & os) std::ostream & colvar::write_traj(std::ostream &os) { os << " "; - if (is_enabled(f_cv_output_value)) { if (is_enabled(f_cv_extended_Lagrangian)) { diff --git a/lib/colvars/colvar.h b/lib/colvars/colvar.h index 74f7fdee51..e2ab0f3c1d 100644 --- a/lib/colvars/colvar.h +++ b/lib/colvars/colvar.h @@ -569,6 +569,14 @@ public: class alpha_dihedrals; class alpha_angles; class dihedPC; + class componentDisabled; + class CartesianBasedPath; + class gspath; + class gzpath; + class linearCombination; + class CVBasedPath; + class gspathCV; + class gzpathCV; // non-scalar components class distance_vec; diff --git a/lib/colvars/colvar_geometricpath.h b/lib/colvars/colvar_geometricpath.h new file mode 100644 index 0000000000..a7ef7f337c --- /dev/null +++ b/lib/colvars/colvar_geometricpath.h @@ -0,0 +1,270 @@ +#ifndef GEOMETRICPATHCV_H +#define GEOMETRICPATHCV_H +// This file is part of the Collective Variables module (Colvars). +// The original version of Colvars and its updates are located at: +// https://github.com/colvars/colvars +// Please update all Colvars source files before making any changes. +// If you wish to distribute your changes, please submit them to the +// Colvars repository at GitHub. + + +#include +#include +#include +#include +#include +#include + +namespace GeometricPathCV { + +enum path_sz {S, Z}; + +template +class GeometricPathBase { +private: + struct doCompareFrameDistance { + doCompareFrameDistance(const GeometricPathBase& obj): m_obj(obj) {} + const GeometricPathBase& m_obj; + bool operator()(const size_t& i1, const size_t& i2) { + return m_obj.frame_distances[i1] < m_obj.frame_distances[i2]; + } + }; +protected: + scalar_type v1v1; + scalar_type v2v2; + scalar_type v3v3; + scalar_type v4v4; + scalar_type v1v3; + scalar_type v1v4; + scalar_type f; + scalar_type dx; + scalar_type s; + scalar_type z; + scalar_type zz; + std::vector v1; + std::vector v2; + std::vector v3; + std::vector v4; + std::vector dfdv1; + std::vector dfdv2; + std::vector dzdv1; + std::vector dzdv2; + std::vector frame_distances; + std::vector frame_index; + bool use_second_closest_frame; + bool use_third_closest_frame; + bool use_z_square; + long min_frame_index_1; + long min_frame_index_2; + long min_frame_index_3; + long sign; + double M; + double m; +public: + GeometricPathBase(size_t vector_size, const element_type& element = element_type(), size_t total_frames = 1, bool p_use_second_closest_frame = true, bool p_use_third_closest_frame = false, bool p_use_z_square = false); + GeometricPathBase(size_t vector_size, const std::vector& elements, size_t total_frames = 1, bool p_use_second_closest_frame = true, bool p_use_third_closest_frame = false, bool p_use_z_square = false); + GeometricPathBase() {} + virtual ~GeometricPathBase() {} + virtual void initialize(size_t vector_size, const element_type& element = element_type(), size_t total_frames = 1, bool p_use_second_closest_frame = true, bool p_use_third_closest_frame = false, bool p_use_z_square = false); + virtual void initialize(size_t vector_size, const std::vector& elements, size_t total_frames = 1, bool p_use_second_closest_frame = true, bool p_use_third_closest_frame = false, bool p_use_z_square = false); + virtual void prepareVectors(); + virtual void updateReferenceDistances(); + virtual void compute(); + virtual void determineClosestFrames(); + virtual void computeValue(); + virtual void computeDerivatives(); +}; + +template +GeometricPathBase::GeometricPathBase(size_t vector_size, const element_type& element, size_t total_frames, bool p_use_second_closest_frame, bool p_use_third_closest_frame, bool p_use_z_square) { + initialize(vector_size, element, total_frames, p_use_second_closest_frame, p_use_third_closest_frame, p_use_z_square); +} + +template +GeometricPathBase::GeometricPathBase(size_t vector_size, const std::vector& elements, size_t total_frames, bool p_use_second_closest_frame, bool p_use_third_closest_frame, bool p_use_z_square) { + initialize(vector_size, elements, total_frames, p_use_second_closest_frame, p_use_third_closest_frame, p_use_z_square); +} + +template +void GeometricPathBase::initialize(size_t vector_size, const element_type& element, size_t total_frames, bool p_use_second_closest_frame, bool p_use_third_closest_frame, bool p_use_z_square) { + v1v1 = scalar_type(); + v2v2 = scalar_type(); + v3v3 = scalar_type(); + v4v4 = scalar_type(); + v1v3 = scalar_type(); + v1v4 = scalar_type(); + f = scalar_type(); + dx = scalar_type(); + z = scalar_type(); + zz = scalar_type(); + sign = 0; + v1.resize(vector_size, element); + v2.resize(vector_size, element); + v3.resize(vector_size, element); + v4.resize(vector_size, element); + dfdv1.resize(vector_size, element); + dfdv2.resize(vector_size, element); + dzdv1.resize(vector_size, element); + dzdv2.resize(vector_size, element); + frame_distances.resize(total_frames); + frame_index.resize(total_frames); + for (size_t i_frame = 0; i_frame < frame_index.size(); ++i_frame) { + frame_index[i_frame] = i_frame; + } + use_second_closest_frame = p_use_second_closest_frame; + use_third_closest_frame = p_use_third_closest_frame; + use_z_square = p_use_z_square; + M = static_cast(total_frames - 1); + m = static_cast(1.0); +} + +template +void GeometricPathBase::initialize(size_t vector_size, const std::vector& elements, size_t total_frames, bool p_use_second_closest_frame, bool p_use_third_closest_frame, bool p_use_z_square) { + v1v1 = scalar_type(); + v2v2 = scalar_type(); + v3v3 = scalar_type(); + v4v4 = scalar_type(); + v1v3 = scalar_type(); + v1v4 = scalar_type(); + f = scalar_type(); + dx = scalar_type(); + z = scalar_type(); + zz = scalar_type(); + sign = 0; + v1 = elements; + v2 = elements; + v3 = elements; + v4 = elements; + dfdv1 = elements; + dfdv2 = elements; + dzdv1 = elements; + dzdv2 = elements; + frame_distances.resize(total_frames); + frame_index.resize(total_frames); + for (size_t i_frame = 0; i_frame < frame_index.size(); ++i_frame) { + frame_index[i_frame] = i_frame; + } + use_second_closest_frame = p_use_second_closest_frame; + use_third_closest_frame = p_use_third_closest_frame; + use_z_square = p_use_z_square; + M = static_cast(total_frames - 1); + m = static_cast(1.0); +} + +template +void GeometricPathBase::prepareVectors() { + std::cout << "Warning: you should not call the prepareVectors() in base class!\n"; + std::cout << std::flush; +} + +template +void GeometricPathBase::updateReferenceDistances() { + std::cout << "Warning: you should not call the updateReferenceDistances() in base class!\n"; + std::cout << std::flush; +} + +template +void GeometricPathBase::compute() { + computeValue(); + computeDerivatives(); +} + +template +void GeometricPathBase::determineClosestFrames() { + // Find the closest and the second closest frames + std::sort(frame_index.begin(), frame_index.end(), doCompareFrameDistance(*this)); + // Determine the sign + sign = static_cast(frame_index[0]) - static_cast(frame_index[1]); + if (sign > 1) { + // sigma(z) is on the left side of the closest frame + sign = 1; + } else if (sign < -1) { + // sigma(z) is on the right side of the closest frame + sign = -1; + } + if (std::abs(static_cast(frame_index[0]) - static_cast(frame_index[1])) > 1) { + std::cout << "Warning: Geometrical pathCV relies on the assumption that the second closest frame is the neighbouring frame\n"; + std::cout << " Please check your configuration or increase restraint on z(σ)\n"; + for (size_t i_frame = 0; i_frame < frame_index.size(); ++i_frame) { + std::cout << "Frame index: " << frame_index[i_frame] << " ; optimal RMSD = " << frame_distances[frame_index[i_frame]] << "\n"; + } + } + min_frame_index_1 = frame_index[0]; // s_m + min_frame_index_2 = use_second_closest_frame ? frame_index[1] : min_frame_index_1 - sign; // s_(m-1) + min_frame_index_3 = use_third_closest_frame ? frame_index[2] : min_frame_index_1 + sign; // s_(m+1) + m = static_cast(frame_index[0]); +} + +template +void GeometricPathBase::computeValue() { + updateReferenceDistances(); + determineClosestFrames(); + prepareVectors(); + v1v1 = scalar_type(); + v2v2 = scalar_type(); + v3v3 = scalar_type(); + v1v3 = scalar_type(); + if (path_type == Z) { + v1v4 = scalar_type(); + v4v4 = scalar_type(); + } + for (size_t i_elem = 0; i_elem < v1.size(); ++i_elem) { + v1v1 += v1[i_elem] * v1[i_elem]; + v2v2 += v2[i_elem] * v2[i_elem]; + v3v3 += v3[i_elem] * v3[i_elem]; + v1v3 += v1[i_elem] * v3[i_elem]; + if (path_type == Z) { + v1v4 += v1[i_elem] * v4[i_elem]; + v4v4 += v4[i_elem] * v4[i_elem]; + } + } + f = (std::sqrt(v1v3 * v1v3 - v3v3 * (v1v1 - v2v2)) - v1v3) / v3v3; + if (path_type == Z) { + dx = 0.5 * (f - 1); + zz = v1v1 + 2 * dx * v1v4 + dx * dx * v4v4; + if (use_z_square) { + z = zz; + } else { + z = std::sqrt(std::fabs(zz)); + } + } + if (path_type == S) { + s = m/M + static_cast(sign) * ((f - 1) / (2 * M)); + } +} + +template +void GeometricPathBase::computeDerivatives() { + const scalar_type factor1 = 1.0 / (2.0 * v3v3 * std::sqrt(v1v3 * v1v3 - v3v3 * (v1v1 - v2v2))); + const scalar_type factor2 = 1.0 / v3v3; + for (size_t i_elem = 0; i_elem < v1.size(); ++i_elem) { + // Compute the derivative of f with vector v1 + dfdv1[i_elem] = factor1 * (2.0 * v1v3 * v3[i_elem] - 2.0 * v3v3 * v1[i_elem]) - factor2 * v3[i_elem]; + // Compute the derivative of f with respect to vector v2 + dfdv2[i_elem] = factor1 * (2.0 * v3v3 * v2[i_elem]); + // dZ(v1(r), v2(r), v3) / dr = ∂Z/∂v1 * dv1/dr + ∂Z/∂v2 * dv2/dr + // dv1/dr = [fitting matrix 1][-1, ..., -1] + // dv2/dr = [fitting matrix 2][1, ..., 1] + // ∂Z/∂v1 = 1/(2*z) * (2v1 + (f-1)v4 + (v1⋅v4)∂f/∂v1 + v4^2 * 1/4 * 2(f-1) * ∂f/∂v1) + // ∂Z/∂v2 = 1/(2*z) * ((v1⋅v4)∂f/∂v2 + v4^2 * 1/4 * 2(f-1) * ∂f/∂v2) + if (path_type == Z) { + if (use_z_square) { + dzdv1[i_elem] = 2.0 * v1[i_elem] + (f-1) * v4[i_elem] + v1v4 * dfdv1[i_elem] + v4v4 * 0.25 * 2.0 * (f-1) * dfdv1[i_elem]; + dzdv2[i_elem] = v1v4 * dfdv2[i_elem] + v4v4 * 0.25 * 2.0 * (f-1) * dfdv2[i_elem]; + } else { + if (z > static_cast(0)) { + dzdv1[i_elem] = (1.0 / (2.0 * z)) * (2.0 * v1[i_elem] + (f-1) * v4[i_elem] + v1v4 * dfdv1[i_elem] + v4v4 * 0.25 * 2.0 * (f-1) * dfdv1[i_elem]); + dzdv2[i_elem] = (1.0 / (2.0 * z)) * (v1v4 * dfdv2[i_elem] + v4v4 * 0.25 * 2.0 * (f-1) * dfdv2[i_elem]); + } else { + // workaround at z = 0 + dzdv1[i_elem] = 0; + dzdv2[i_elem] = 0; + } + } + } + } +} + +} + +#endif // GEOMETRICPATHCV_H diff --git a/lib/colvars/colvarbias_meta.cpp b/lib/colvars/colvarbias_meta.cpp index 27781ec733..8540e4a945 100644 --- a/lib/colvars/colvarbias_meta.cpp +++ b/lib/colvars/colvarbias_meta.cpp @@ -37,7 +37,6 @@ colvarbias_meta::colvarbias_meta(char const *key) { new_hills_begin = hills.end(); hills_traj_os = NULL; - replica_hills_os = NULL; ebmeta_equil_steps = 0L; } @@ -203,23 +202,37 @@ int colvarbias_meta::init_ebmeta_params(std::string const &conf) target_dist = new colvar_grid_scalar(); target_dist->init_from_colvars(colvars); std::string target_dist_file; - get_keyval(conf, "targetdistfile", target_dist_file); + get_keyval(conf, "targetDistFile", target_dist_file); std::ifstream targetdiststream(target_dist_file.c_str()); target_dist->read_multicol(targetdiststream); cvm::real min_val = target_dist->minimum_value(); + cvm::real max_val = target_dist->maximum_value(); if(min_val<0){ - cvm::error("Error: Target distribution of ebMeta " + cvm::error("Error: Target distribution of EBMetaD " "has negative values!.\n", INPUT_ERROR); } - cvm::real min_pos_val = target_dist->minimum_pos_value(); - if(min_pos_val<=0){ - cvm::error("Error: Target distribution of ebMeta has negative " - "or zero minimum positive value!.\n", INPUT_ERROR); - } - if(min_val==0){ - cvm::log("WARNING: Target distribution has zero values.\n"); - cvm::log("Zeros will be converted to the minimum positive value.\n"); - target_dist->remove_zeros(min_pos_val); + cvm::real target_dist_min_val; + get_keyval(conf, "targetDistMinVal", target_dist_min_val, 1/1000000.0); + if(target_dist_min_val>0 && target_dist_min_val<1){ + target_dist_min_val=max_val*target_dist_min_val; + target_dist->remove_small_values(target_dist_min_val); + } else { + if (target_dist_min_val==0) { + cvm::log("NOTE: targetDistMinVal is set to zero, the minimum value of the target \n"); + cvm::log(" distribution will be set as the minimum positive value.\n"); + cvm::real min_pos_val = target_dist->minimum_pos_value(); + if(min_pos_val<=0){ + cvm::error("Error: Target distribution of EBMetaD has negative " + "or zero minimum positive value!.\n", INPUT_ERROR); + } + if(min_val==0){ + cvm::log("WARNING: Target distribution has zero values.\n"); + cvm::log("Zeros will be converted to the minimum positive value.\n"); + target_dist->remove_small_values(min_pos_val); + } + } else { + cvm::error("Error: targetDistMinVal must be a value between 0 and 1!.\n", INPUT_ERROR); + } } // normalize target distribution and multiply by effective volume = exp(differential entropy) target_dist->multiply_constant(1.0/target_dist->integral()); @@ -235,14 +248,14 @@ int colvarbias_meta::init_ebmeta_params(std::string const &conf) colvarbias_meta::~colvarbias_meta() { colvarbias_meta::clear_state_data(); + colvarproxy *proxy = cvm::proxy; - if (replica_hills_os) { - cvm::proxy->close_output_stream(replica_hills_file); - replica_hills_os = NULL; + if (proxy->get_output_stream(replica_hills_file)) { + proxy->close_output_stream(replica_hills_file); } if (hills_traj_os) { - cvm::proxy->close_output_stream(hills_traj_file_name()); + proxy->close_output_stream(hills_traj_file_name()); hills_traj_os = NULL; } @@ -523,6 +536,8 @@ int colvarbias_meta::update_bias() case multiple_replicas: create_hill(hill(hill_weight*hills_scale, colvars, hill_width, replica_id)); + std::ostream *replica_hills_os = + cvm::proxy->get_output_stream(replica_hills_file); if (replica_hills_os) { *replica_hills_os << hills.back(); } else { @@ -921,13 +936,16 @@ void colvarbias_meta::recount_hills_off_grid(colvarbias_meta::hill_iter h_first int colvarbias_meta::replica_share() { + colvarproxy *proxy = cvm::proxy; // sync with the other replicas (if needed) if (comm == multiple_replicas) { // reread the replicas registry update_replicas_registry(); // empty the output buffer + std::ostream *replica_hills_os = + proxy->get_output_stream(replica_hills_file); if (replica_hills_os) { - cvm::proxy->flush_output_stream(replica_hills_os); + proxy->flush_output_stream(replica_hills_os); } read_replica_files(); } @@ -1089,11 +1107,7 @@ void colvarbias_meta::read_replica_files() (replicas[ir])->replica_state_file+"\".\n"); std::ifstream is((replicas[ir])->replica_state_file.c_str()); - if (! (replicas[ir])->read_state(is)) { - cvm::log("Reading from file \""+(replicas[ir])->replica_state_file+ - "\" failed or incomplete: will try again in "+ - cvm::to_str(replica_update_freq)+" steps.\n"); - } else { + if ((replicas[ir])->read_state(is)) { // state file has been read successfully (replicas[ir])->replica_state_file_in_sync = true; (replicas[ir])->update_status = 0; @@ -1550,15 +1564,11 @@ int colvarbias_meta::setup_output() // for the others to read // open the "hills" buffer file - if (!replica_hills_os) { - cvm::proxy->backup_file(replica_hills_file); - replica_hills_os = cvm::proxy->output_stream(replica_hills_file); - if (!replica_hills_os) return cvm::get_error(); - replica_hills_os->setf(std::ios::scientific, std::ios::floatfield); - } + reopen_replica_buffer_file(); // write the state file (so that there is always one available) write_replica_state_file(); + // schedule to read the state files of the other replicas for (size_t ir = 0; ir < replicas.size(); ir++) { (replicas[ir])->replica_state_file_in_sync = false; @@ -1661,15 +1671,16 @@ std::ostream & colvarbias_meta::write_state_data(std::ostream& os) int colvarbias_meta::write_state_to_replicas() { + int error_code = COLVARS_OK; if (comm != single_replica) { - write_replica_state_file(); - // schedule to reread the state files of the other replicas (they - // have also rewritten them) + error_code |= write_replica_state_file(); + error_code |= reopen_replica_buffer_file(); + // schedule to reread the state files of the other replicas for (size_t ir = 0; ir < replicas.size(); ir++) { (replicas[ir])->replica_state_file_in_sync = false; } } - return COLVARS_OK; + return error_code; } @@ -1693,6 +1704,20 @@ void colvarbias_meta::write_pmf() // output the PMF from this instance or replica pmf->reset(); pmf->add_grid(*hills_energy); + + if (ebmeta) { + int nt_points=pmf->number_of_points(); + for (int i = 0; i < nt_points; i++) { + cvm:: real pmf_val=0.0; + cvm:: real target_val=target_dist->value(i); + if (target_val>0) { + pmf_val=pmf->value(i); + pmf_val=pmf_val+cvm::temperature() * cvm::boltzmann() * std::log(target_val); + } + pmf->set_value(i,pmf_val); + } + } + cvm::real const max = pmf->maximum_value(); pmf->add_constant(-1.0 * max); pmf->multiply_constant(-1.0); @@ -1716,10 +1741,24 @@ void colvarbias_meta::write_pmf() if (comm != single_replica) { // output the combined PMF from all replicas pmf->reset(); - pmf->add_grid(*hills_energy); + // current replica already included in the pools of replicas for (size_t ir = 0; ir < replicas.size(); ir++) { pmf->add_grid(*(replicas[ir]->hills_energy)); } + + if (ebmeta) { + int nt_points=pmf->number_of_points(); + for (int i = 0; i < nt_points; i++) { + cvm:: real pmf_val=0.0; + cvm:: real target_val=target_dist->value(i); + if (target_val>0) { + pmf_val=pmf->value(i); + pmf_val=pmf_val+cvm::temperature() * cvm::boltzmann() * std::log(target_val); + } + pmf->set_value(i,pmf_val); + } + } + cvm::real const max = pmf->maximum_value(); pmf->add_constant(-1.0 * max); pmf->multiply_constant(-1.0); @@ -1744,74 +1783,47 @@ void colvarbias_meta::write_pmf() int colvarbias_meta::write_replica_state_file() { + colvarproxy *proxy = cvm::proxy; + if (cvm::debug()) { cvm::log("Writing replica state file for bias \""+name+"\"\n"); } - // write down also the restart for the other replicas - cvm::backup_file(replica_state_file.c_str()); - std::ostream *rep_state_os = cvm::proxy->output_stream(replica_state_file); - if (rep_state_os == NULL) { - cvm::error("Error: in opening file \""+ - replica_state_file+"\" for writing.\n", FILE_ERROR); - return FILE_ERROR; - } - - rep_state_os->setf(std::ios::scientific, std::ios::floatfield); - - if (!write_state(*rep_state_os)) { - cvm::error("Error: in writing to file \""+ - replica_state_file+"\".\n", FILE_ERROR); - cvm::proxy->close_output_stream(replica_state_file); - return FILE_ERROR; - } - - cvm::proxy->close_output_stream(replica_state_file); - - // rep_state_os.setf(std::ios::scientific, std::ios::floatfield); - // rep_state_os << "\n" - // << "metadynamics {\n" - // << " configuration {\n" - // << " name " << this->name << "\n" - // << " step " << cvm::step_absolute() << "\n"; - // if (this->comm != single_replica) { - // rep_state_os << " replicaID " << this->replica_id << "\n"; - // } - // rep_state_os << " }\n\n"; - // rep_state_os << " hills_energy\n"; - // rep_state_os << std::setprecision(cvm::cv_prec) - // << std::setw(cvm::cv_width); - // hills_energy->write_restart(rep_state_os); - // rep_state_os << " hills_energy_gradients\n"; - // rep_state_os << std::setprecision(cvm::cv_prec) - // << std::setw(cvm::cv_width); - // hills_energy_gradients->write_restart(rep_state_os); - - // if ( (!use_grids) || keep_hills ) { - // // write all hills currently in memory - // for (std::list::const_iterator h = this->hills.begin(); - // h != this->hills.end(); - // h++) { - // rep_state_os << *h; - // } - // } else { - // // write just those that are near the grid boundaries - // for (std::list::const_iterator h = this->hills_off_grid.begin(); - // h != this->hills_off_grid.end(); - // h++) { - // rep_state_os << *h; - // } - // } - // rep_state_os << "}\n\n"; - // rep_state_os.close(); - - // reopen the hills file - cvm::proxy->close_output_stream(replica_hills_file); - cvm::proxy->backup_file(replica_hills_file); - replica_hills_os = cvm::proxy->output_stream(replica_hills_file); - if (!replica_hills_os) return cvm::get_error(); - replica_hills_os->setf(std::ios::scientific, std::ios::floatfield); - return COLVARS_OK; + int error_code = COLVARS_OK; + + // Write to temporary state file + std::string const tmp_state_file(replica_state_file+".tmp"); + error_code |= proxy->remove_file(tmp_state_file); + std::ostream *rep_state_os = cvm::proxy->output_stream(tmp_state_file); + if (rep_state_os) { + if (!write_state(*rep_state_os)) { + error_code |= cvm::error("Error: in writing to temporary file \""+ + tmp_state_file+"\".\n", FILE_ERROR); + } + } + error_code |= proxy->close_output_stream(tmp_state_file); + + error_code |= proxy->rename_file(tmp_state_file, replica_state_file); + + return error_code; +} + + +int colvarbias_meta::reopen_replica_buffer_file() +{ + int error_code = COLVARS_OK; + colvarproxy *proxy = cvm::proxy; + if (proxy->get_output_stream(replica_hills_file) != NULL) { + error_code |= proxy->close_output_stream(replica_hills_file); + } + error_code |= proxy->remove_file(replica_hills_file); + std::ostream *replica_hills_os = proxy->output_stream(replica_hills_file); + if (replica_hills_os) { + replica_hills_os->setf(std::ios::scientific, std::ios::floatfield); + } else { + error_code |= FILE_ERROR; + } + return error_code; } @@ -1883,5 +1895,3 @@ std::ostream & operator << (std::ostream &os, colvarbias_meta::hill const &h) return os; } - - diff --git a/lib/colvars/colvarbias_meta.h b/lib/colvars/colvarbias_meta.h index 0ba2bef1c3..8e98274b2d 100644 --- a/lib/colvars/colvarbias_meta.h +++ b/lib/colvars/colvarbias_meta.h @@ -215,9 +215,12 @@ protected: /// \brief Read new data from replicas' files virtual void read_replica_files(); - /// \brief Write data to other replicas + /// Write full state information to be read by other replicas virtual int write_replica_state_file(); + /// Call this after write_replica_state_file() + virtual int reopen_replica_buffer_file(); + /// \brief Additional, "mirror" metadynamics biases, to collect info /// from the other replicas /// @@ -251,9 +254,6 @@ protected: /// This file becomes empty after replica_state_file is rewritten std::string replica_hills_file; - /// \brief Output stream corresponding to replica_hills_file - std::ostream *replica_hills_os; - /// Position within replica_hills_file (when reading it) int replica_hills_file_pos; diff --git a/lib/colvars/colvarbias_restraint.cpp b/lib/colvars/colvarbias_restraint.cpp index 90588f5a1f..ab02820cf0 100644 --- a/lib/colvars/colvarbias_restraint.cpp +++ b/lib/colvars/colvarbias_restraint.cpp @@ -1295,7 +1295,8 @@ colvarvalue const colvarbias_restraint_linear::restraint_force(size_t i) const cvm::real colvarbias_restraint_linear::d_restraint_potential_dk(size_t i) const { - return 1.0 / variables(i)->width * (variables(i)->value() - colvar_centers[i]); + return 1.0 / variables(i)->width * (variables(i)->value() - + colvar_centers[i]).sum(); } diff --git a/lib/colvars/colvarcomp.cpp b/lib/colvars/colvarcomp.cpp index 3075ed82ca..431884a877 100644 --- a/lib/colvars/colvarcomp.cpp +++ b/lib/colvars/colvarcomp.cpp @@ -7,6 +7,8 @@ // If you wish to distribute your changes, please submit them to the // Colvars repository at GitHub. +#include + #include "colvarmodule.h" #include "colvarvalue.h" #include "colvar.h" diff --git a/lib/colvars/colvarcomp.h b/lib/colvars/colvarcomp.h index f615680ba6..5e7a91e872 100644 --- a/lib/colvars/colvarcomp.h +++ b/lib/colvars/colvarcomp.h @@ -24,6 +24,13 @@ #include "colvar.h" #include "colvaratoms.h" +#if (__cplusplus >= 201103L) +#include "colvar_geometricpath.h" +#include +#endif // C++11 checking + +#include + /// \brief Colvar component (base class for collective variables) /// @@ -688,9 +695,6 @@ protected: /// Reference coordinates std::vector ref_pos; - /// Geometric center of the reference coordinates - cvm::atom_pos ref_pos_center; - /// Eigenvector (of a normal or essential mode): will always have zero center std::vector eigenvec; @@ -1383,6 +1387,222 @@ public: }; + +class colvar::componentDisabled + : public colvar::cvc +{ +public: + componentDisabled(std::string const &conf) { + cvm::error("Error: this component is not enabled in the current build; please see https://colvars.github.io/README-c++11.html"); + } + virtual ~componentDisabled() {} + virtual void calc_value() {} + virtual void calc_gradients() {} + virtual void apply_force(colvarvalue const &force) {} +}; + + + +#if (__cplusplus >= 201103L) +class colvar::CartesianBasedPath + : public colvar::cvc +{ +protected: + virtual void computeReferenceDistance(std::vector& result); + /// Selected atoms + cvm::atom_group *atoms; + /// Fitting options + bool has_user_defined_fitting; + /// Reference frames + std::vector> reference_frames; + std::vector> reference_fitting_frames; + /// Atom groups for RMSD calculation together with reference frames + std::vector comp_atoms; + /// Total number of reference frames + size_t total_reference_frames; +public: + CartesianBasedPath(std::string const &conf); + virtual ~CartesianBasedPath(); + virtual void calc_value() = 0; + virtual void apply_force(colvarvalue const &force) = 0; +}; + +/// \brief Colvar component: alternative path collective variable using geometry, variable s +/// For more information see https://plumed.github.io/doc-v2.5/user-doc/html/_p_a_t_h.html +/// Díaz Leines, G.; Ensing, B. Path Finding on High-Dimensional Free Energy Landscapes. Phys. Rev. Lett. 2012, 109 (2), 020601. https://doi.org/10.1103/PhysRevLett.109.020601. +class colvar::gspath + : public colvar::CartesianBasedPath, public GeometricPathCV::GeometricPathBase +{ +private: + // Optimal rotation for compute v3 + cvm::rotation rot_v3; +protected: + virtual void prepareVectors(); + virtual void updateReferenceDistances(); +public: + gspath(std::string const &conf); + virtual ~gspath() {} + virtual void calc_value(); + virtual void calc_gradients(); + virtual void apply_force(colvarvalue const &force); +}; + + + +/// \brief Colvar component: alternative path collective variable using geometry, variable z +/// This should be merged with gspath in the same class by class inheritance or something else +class colvar::gzpath + : public colvar::CartesianBasedPath, public GeometricPathCV::GeometricPathBase +{ +private: + // Optimal rotation for compute v3, v4 + cvm::rotation rot_v3; + cvm::rotation rot_v4; +protected: + virtual void prepareVectors(); + virtual void updateReferenceDistances(); +public: + gzpath(std::string const &conf); + virtual ~gzpath() {} + virtual void calc_value(); + virtual void calc_gradients(); + virtual void apply_force(colvarvalue const &force); +}; + +/// Current only linear combination of sub-CVCs is available +class colvar::linearCombination + : public colvar::cvc +{ +protected: + /// Map from string to the types of colvar components + std::map> string_cv_map; + /// Sub-colvar components + std::vector cv; + /// If all sub-cvs use explicit gradients then we also use it + bool use_explicit_gradients; +protected: + cvm::real getPolynomialFactorOfCVGradient(size_t i_cv) const; +public: + linearCombination(std::string const &conf); + virtual ~linearCombination(); + virtual void calc_value(); + virtual void calc_gradients(); + virtual void apply_force(colvarvalue const &force); +}; + + +class colvar::CVBasedPath + : public colvar::cvc +{ +protected: + /// Map from string to the types of colvar components + std::map> string_cv_map; + /// Sub-colvar components + std::vector cv; + /// Refernce colvar values from path + std::vector> ref_cv; + /// If all sub-cvs use explicit gradients then we also use it + bool use_explicit_gradients; + /// Total number of reference frames + size_t total_reference_frames; +protected: + virtual void computeReferenceDistance(std::vector& result); + cvm::real getPolynomialFactorOfCVGradient(size_t i_cv) const; +public: + CVBasedPath(std::string const &conf); + virtual ~CVBasedPath(); + virtual void calc_value() = 0; + virtual void apply_force(colvarvalue const &force) = 0; +}; + + +/// \brief Colvar component: alternative path collective variable using geometry, variable s +/// Allow any combination of existing (scalar) CVs +/// For more information see https://plumed.github.io/doc-v2.5/user-doc/html/_p_a_t_h.html +/// Díaz Leines, G.; Ensing, B. Path Finding on High-Dimensional Free Energy Landscapes. Phys. Rev. Lett. 2012, 109 (2), 020601. https://doi.org/10.1103/PhysRevLett.109.020601. +class colvar::gspathCV + : public colvar::CVBasedPath, public GeometricPathCV::GeometricPathBase +{ +protected: + virtual void updateReferenceDistances(); + virtual void prepareVectors(); +public: + gspathCV(std::string const &conf); + virtual ~gspathCV(); + virtual void calc_value(); + virtual void calc_gradients(); + virtual void apply_force(colvarvalue const &force); +}; + + + +class colvar::gzpathCV + : public colvar::CVBasedPath, public GeometricPathCV::GeometricPathBase +{ +protected: + virtual void updateReferenceDistances(); + virtual void prepareVectors(); +public: + gzpathCV(std::string const &conf); + virtual ~gzpathCV(); + virtual void calc_value(); + virtual void calc_gradients(); + virtual void apply_force(colvarvalue const &force); +}; + +#else // if the compiler doesn't support C++11 + +class colvar::linearCombination + : public colvar::componentDisabled +{ +public: + linearCombination(std::string const &conf) : componentDisabled(conf) {} +}; + +class colvar::CartesianBasedPath + : public colvar::componentDisabled +{ +public: + CartesianBasedPath(std::string const &conf) : componentDisabled(conf) {} +}; + +class colvar::CVBasedPath + : public colvar::componentDisabled +{ +public: + CVBasedPath(std::string const &conf) : componentDisabled(conf) {} +}; + +class colvar::gspath + : public colvar::componentDisabled +{ +public: + gspath(std::string const &conf) : componentDisabled(conf) {} +}; + +class colvar::gzpath + : public colvar::componentDisabled +{ +public: + gzpath(std::string const &conf) : componentDisabled(conf) {} +}; + +class colvar::gspathCV + : public colvar::componentDisabled +{ +public: + gspathCV(std::string const &conf) : componentDisabled(conf) {} +}; + +class colvar::gzpathCV + : public colvar::componentDisabled +{ +public: + gzpathCV(std::string const &conf) : componentDisabled(conf) {} +}; + +#endif // C++11 checking + // metrics functions for cvc implementations // simple definitions of the distance functions; these are useful only diff --git a/lib/colvars/colvarcomp_distances.cpp b/lib/colvars/colvarcomp_distances.cpp index d9cd9d55e4..7cb4c30c31 100644 --- a/lib/colvars/colvarcomp_distances.cpp +++ b/lib/colvars/colvarcomp_distances.cpp @@ -1013,8 +1013,7 @@ colvar::rmsd::rmsd(std::string const &conf) cvm::to_str(atoms->size())+").\n"); return; } - } - { + } else { // Only look for ref pos file if ref positions not already provided std::string ref_pos_file; if (get_keyval(conf, "refPositionsFile", ref_pos_file, std::string(""))) { @@ -1041,12 +1040,15 @@ colvar::rmsd::rmsd(std::string const &conf) cvm::load_coords(ref_pos_file.c_str(), &ref_pos, atoms, ref_pos_col, ref_pos_col_value); + } else { + cvm::error("Error: no reference positions for RMSD; use either refPositions of refPositionsFile."); + return; } } if (ref_pos.size() != atoms->size()) { cvm::error("Error: found " + cvm::to_str(ref_pos.size()) + - " reference positions; expected " + cvm::to_str(atoms->size())); + " reference positions for RMSD; expected " + cvm::to_str(atoms->size())); return; } diff --git a/lib/colvars/colvarcomp_gpath.cpp b/lib/colvars/colvarcomp_gpath.cpp new file mode 100644 index 0000000000..530aaf3284 --- /dev/null +++ b/lib/colvars/colvarcomp_gpath.cpp @@ -0,0 +1,910 @@ +#if (__cplusplus >= 201103L) + +// This file is part of the Collective Variables module (Colvars). +// The original version of Colvars and its updates are located at: +// https://github.com/colvars/colvars +// Please update all Colvars source files before making any changes. +// If you wish to distribute your changes, please submit them to the +// Colvars repository at GitHub. + +#include +#include +#include +#include +#include + +#include "colvarmodule.h" +#include "colvarvalue.h" +#include "colvarparse.h" +#include "colvar.h" +#include "colvarcomp.h" + +namespace GeometricPathCV { +void init_string_cv_map(std::map>& string_cv_map); +} + +bool compareColvarComponent(colvar::cvc *i, colvar::cvc *j) +{ + return i->name < j->name; +} + +colvar::CartesianBasedPath::CartesianBasedPath(std::string const &conf): cvc(conf), atoms(nullptr), reference_frames(0) { + // Parse selected atoms + atoms = parse_group(conf, "atoms"); + has_user_defined_fitting = false; + std::string fitting_conf; + if (key_lookup(conf, "fittingAtoms", &fitting_conf)) { + has_user_defined_fitting = true; + } + // Lookup reference column of PDB + // Copied from the RMSD class + std::string reference_column; + double reference_column_value; + if (get_keyval(conf, "refPositionsCol", reference_column, std::string(""))) { + bool found = get_keyval(conf, "refPositionsColValue", reference_column_value, 0.0); + if (found && reference_column_value == 0.0) { + cvm::error("Error: refPositionsColValue, " + "if provided, must be non-zero.\n"); + return; + } + } + // Lookup all reference frames + bool has_frames = true; + total_reference_frames = 0; + while (has_frames) { + std::string reference_position_file_lookup = "refPositionsFile" + cvm::to_str(total_reference_frames + 1); + if (key_lookup(conf, reference_position_file_lookup.c_str())) { + std::string reference_position_filename; + get_keyval(conf, reference_position_file_lookup.c_str(), reference_position_filename, std::string("")); + std::vector reference_position(atoms->size()); + cvm::load_coords(reference_position_filename.c_str(), &reference_position, atoms, reference_column, reference_column_value); + reference_frames.push_back(reference_position); + ++total_reference_frames; + } else { + has_frames = false; + } + } + // Setup alignment to compute RMSD with respect to reference frames + for (size_t i_frame = 0; i_frame < reference_frames.size(); ++i_frame) { + cvm::atom_group* tmp_atoms = parse_group(conf, "atoms"); + if (!has_user_defined_fitting) { + // Swipe from the rmsd class + tmp_atoms->b_center = true; + tmp_atoms->b_rotate = true; + tmp_atoms->ref_pos = reference_frames[i_frame]; + tmp_atoms->center_ref_pos(); + tmp_atoms->enable(f_ag_fit_gradients); + tmp_atoms->rot.request_group1_gradients(tmp_atoms->size()); + tmp_atoms->rot.request_group2_gradients(tmp_atoms->size()); + comp_atoms.push_back(tmp_atoms); + } else { + // parse a group of atoms for fitting + std::string fitting_group_name = std::string("fittingAtoms") + cvm::to_str(i_frame); + cvm::atom_group* tmp_fitting_atoms = new cvm::atom_group(fitting_group_name.c_str()); + tmp_fitting_atoms->parse(fitting_conf); + tmp_fitting_atoms->disable(f_ag_scalable); + tmp_fitting_atoms->disable(f_ag_scalable_com); + tmp_fitting_atoms->fit_gradients.assign(tmp_fitting_atoms->size(), cvm::atom_pos(0.0, 0.0, 0.0)); + std::string reference_position_file_lookup = "refPositionsFile" + cvm::to_str(i_frame + 1); + std::string reference_position_filename; + get_keyval(conf, reference_position_file_lookup.c_str(), reference_position_filename, std::string("")); + std::vector reference_fitting_position(tmp_fitting_atoms->size()); + cvm::load_coords(reference_position_filename.c_str(), &reference_fitting_position, tmp_fitting_atoms, reference_column, reference_column_value); + // setup the atom group for calculating + tmp_atoms->b_center = true; + tmp_atoms->b_rotate = true; + tmp_atoms->b_user_defined_fit = true; + tmp_atoms->disable(f_ag_scalable); + tmp_atoms->disable(f_ag_scalable_com); + tmp_atoms->ref_pos = reference_fitting_position; + tmp_atoms->center_ref_pos(); + tmp_atoms->enable(f_ag_fit_gradients); + tmp_atoms->enable(f_ag_fitting_group); + tmp_atoms->fitting_group = tmp_fitting_atoms; + tmp_atoms->rot.request_group1_gradients(tmp_fitting_atoms->size()); + tmp_atoms->rot.request_group2_gradients(tmp_fitting_atoms->size()); + reference_fitting_frames.push_back(reference_fitting_position); + comp_atoms.push_back(tmp_atoms); + } + } + x.type(colvarvalue::type_scalar); + // Don't use implicit gradient + enable(f_cvc_explicit_gradient); +} + +colvar::CartesianBasedPath::~CartesianBasedPath() { + for (auto it_comp_atoms = comp_atoms.begin(); it_comp_atoms != comp_atoms.end(); ++it_comp_atoms) { + if (*it_comp_atoms != nullptr) { + delete (*it_comp_atoms); + (*it_comp_atoms) = nullptr; + } + } +} + +void colvar::CartesianBasedPath::computeReferenceDistance(std::vector& result) { + for (size_t i_frame = 0; i_frame < reference_frames.size(); ++i_frame) { + cvm::real frame_rmsd = 0.0; + for (size_t i_atom = 0; i_atom < atoms->size(); ++i_atom) { + frame_rmsd += ((*(comp_atoms[i_frame]))[i_atom].pos - reference_frames[i_frame][i_atom]).norm2(); + } + frame_rmsd /= cvm::real(atoms->size()); + frame_rmsd = cvm::sqrt(frame_rmsd); + result[i_frame] = frame_rmsd; + } +} + +colvar::gspath::gspath(std::string const &conf): CartesianBasedPath(conf) { + function_type = "gspath"; + get_keyval(conf, "useSecondClosestFrame", use_second_closest_frame, true); + if (use_second_closest_frame == true) { + cvm::log(std::string("Geometric path s(σ) will use the second closest frame to compute s_(m-1)\n")); + } else { + cvm::log(std::string("Geometric path s(σ) will use the neighbouring frame to compute s_(m-1)\n")); + } + get_keyval(conf, "useThirdClosestFrame", use_third_closest_frame, false); + if (use_third_closest_frame == true) { + cvm::log(std::string("Geometric path s(σ) will use the third closest frame to compute s_(m+1)\n")); + } else { + cvm::log(std::string("Geometric path s(σ) will use the neighbouring frame to compute s_(m+1)\n")); + } + GeometricPathCV::GeometricPathBase::initialize(atoms->size(), cvm::atom_pos(), total_reference_frames, use_second_closest_frame, use_third_closest_frame); + cvm::log(std::string("Geometric pathCV(s) is initialized.\n")); + cvm::log(std::string("Geometric pathCV(s) loaded ") + cvm::to_str(reference_frames.size()) + std::string(" frames.\n")); +} + +void colvar::gspath::updateReferenceDistances() { + computeReferenceDistance(frame_distances); +} + +void colvar::gspath::prepareVectors() { + size_t i_atom; + for (i_atom = 0; i_atom < atoms->size(); ++i_atom) { + // v1 = s_m - z + v1[i_atom] = reference_frames[min_frame_index_1][i_atom] - (*(comp_atoms[min_frame_index_1]))[i_atom].pos; + // v2 = z - s_(m-1) + v2[i_atom] = (*(comp_atoms[min_frame_index_2]))[i_atom].pos - reference_frames[min_frame_index_2][i_atom]; + } + if (min_frame_index_3 < 0 || min_frame_index_3 > M) { + cvm::atom_pos reference_cog_1, reference_cog_2; + for (i_atom = 0; i_atom < atoms->size(); ++i_atom) { + reference_cog_1 += reference_frames[min_frame_index_1][i_atom]; + reference_cog_2 += reference_frames[min_frame_index_2][i_atom]; + } + reference_cog_1 /= reference_frames[min_frame_index_1].size(); + reference_cog_2 /= reference_frames[min_frame_index_2].size(); + std::vector tmp_reference_frame_1(reference_frames[min_frame_index_1].size()); + std::vector tmp_reference_frame_2(reference_frames[min_frame_index_2].size()); + for (i_atom = 0; i_atom < atoms->size(); ++i_atom) { + tmp_reference_frame_1[i_atom] = reference_frames[min_frame_index_1][i_atom] - reference_cog_1; + tmp_reference_frame_2[i_atom] = reference_frames[min_frame_index_2][i_atom] - reference_cog_2; + } + if (has_user_defined_fitting) { + cvm::atom_pos reference_fitting_cog_1, reference_fitting_cog_2; + for (i_atom = 0; i_atom < reference_fitting_frames[min_frame_index_1].size(); ++i_atom) { + reference_fitting_cog_1 += reference_fitting_frames[min_frame_index_1][i_atom]; + reference_fitting_cog_2 += reference_fitting_frames[min_frame_index_2][i_atom]; + } + reference_fitting_cog_1 /= reference_fitting_frames[min_frame_index_1].size(); + reference_fitting_cog_2 /= reference_fitting_frames[min_frame_index_2].size(); + std::vector tmp_reference_fitting_frame_1(reference_fitting_frames[min_frame_index_1].size()); + std::vector tmp_reference_fitting_frame_2(reference_fitting_frames[min_frame_index_2].size()); + for (i_atom = 0; i_atom < reference_fitting_frames[min_frame_index_1].size(); ++i_atom) { + tmp_reference_fitting_frame_1[i_atom] = reference_fitting_frames[min_frame_index_1][i_atom] - reference_fitting_cog_1; + tmp_reference_fitting_frame_2[i_atom] = reference_fitting_frames[min_frame_index_2][i_atom] - reference_fitting_cog_2; + } + rot_v3.calc_optimal_rotation(tmp_reference_fitting_frame_1, tmp_reference_fitting_frame_2); + } else { + rot_v3.calc_optimal_rotation(tmp_reference_frame_1, tmp_reference_frame_2); + } + for (i_atom = 0; i_atom < atoms->size(); ++i_atom) { + v3[i_atom] = rot_v3.q.rotate(tmp_reference_frame_1[i_atom]) - tmp_reference_frame_2[i_atom]; + } + } else { + cvm::atom_pos reference_cog_1, reference_cog_3; + for (i_atom = 0; i_atom < atoms->size(); ++i_atom) { + reference_cog_1 += reference_frames[min_frame_index_1][i_atom]; + reference_cog_3 += reference_frames[min_frame_index_3][i_atom]; + } + reference_cog_1 /= reference_frames[min_frame_index_1].size(); + reference_cog_3 /= reference_frames[min_frame_index_3].size(); + std::vector tmp_reference_frame_1(reference_frames[min_frame_index_1].size()); + std::vector tmp_reference_frame_3(reference_frames[min_frame_index_3].size()); + for (i_atom = 0; i_atom < atoms->size(); ++i_atom) { + tmp_reference_frame_1[i_atom] = reference_frames[min_frame_index_1][i_atom] - reference_cog_1; + tmp_reference_frame_3[i_atom] = reference_frames[min_frame_index_3][i_atom] - reference_cog_3; + } + if (has_user_defined_fitting) { + cvm::atom_pos reference_fitting_cog_1, reference_fitting_cog_3; + for (i_atom = 0; i_atom < reference_fitting_frames[min_frame_index_1].size(); ++i_atom) { + reference_fitting_cog_1 += reference_fitting_frames[min_frame_index_1][i_atom]; + reference_fitting_cog_3 += reference_fitting_frames[min_frame_index_3][i_atom]; + } + reference_fitting_cog_1 /= reference_fitting_frames[min_frame_index_1].size(); + reference_fitting_cog_3 /= reference_fitting_frames[min_frame_index_3].size(); + std::vector tmp_reference_fitting_frame_1(reference_fitting_frames[min_frame_index_1].size()); + std::vector tmp_reference_fitting_frame_3(reference_fitting_frames[min_frame_index_3].size()); + for (i_atom = 0; i_atom < reference_fitting_frames[min_frame_index_1].size(); ++i_atom) { + tmp_reference_fitting_frame_1[i_atom] = reference_fitting_frames[min_frame_index_1][i_atom] - reference_fitting_cog_1; + tmp_reference_fitting_frame_3[i_atom] = reference_fitting_frames[min_frame_index_3][i_atom] - reference_fitting_cog_3; + } + rot_v3.calc_optimal_rotation(tmp_reference_fitting_frame_1, tmp_reference_fitting_frame_3); + } else { + rot_v3.calc_optimal_rotation(tmp_reference_frame_1, tmp_reference_frame_3); + } + for (i_atom = 0; i_atom < atoms->size(); ++i_atom) { + // v3 = s_(m+1) - s_m + v3[i_atom] = tmp_reference_frame_3[i_atom] - rot_v3.q.rotate(tmp_reference_frame_1[i_atom]); + } + } +} + +void colvar::gspath::calc_value() { + computeValue(); + x = s; +} + +void colvar::gspath::calc_gradients() { + computeDerivatives(); + cvm::rvector tmp_atom_grad_v1, tmp_atom_grad_v2; + // dS(v1, v2(r), v3) / dr = ∂S/∂v1 * dv1/dr + ∂S/∂v2 * dv2/dr + // dv1/dr = [fitting matrix 1][-1, ..., -1] + // dv2/dr = [fitting matrix 2][1, ..., 1] + // ∂S/∂v1 = ± (∂f/∂v1) / (2M) + // ∂S/∂v2 = ± (∂f/∂v2) / (2M) + // dS(v1, v2(r), v3) / dr = -1.0 * ± (∂f/∂v1) / (2M) + ± (∂f/∂v2) / (2M) + for (size_t i_atom = 0; i_atom < atoms->size(); ++i_atom) { + tmp_atom_grad_v1[0] = -1.0 * sign * 0.5 * dfdv1[i_atom][0] / M; + tmp_atom_grad_v1[1] = -1.0 * sign * 0.5 * dfdv1[i_atom][1] / M; + tmp_atom_grad_v1[2] = -1.0 * sign * 0.5 * dfdv1[i_atom][2] / M; + tmp_atom_grad_v2[0] = sign * 0.5 * dfdv2[i_atom][0] / M; + tmp_atom_grad_v2[1] = sign * 0.5 * dfdv2[i_atom][1] / M; + tmp_atom_grad_v2[2] = sign * 0.5 * dfdv2[i_atom][2] / M; + (*(comp_atoms[min_frame_index_1]))[i_atom].grad += tmp_atom_grad_v1; + (*(comp_atoms[min_frame_index_2]))[i_atom].grad += tmp_atom_grad_v2; + } +} + +void colvar::gspath::apply_force(colvarvalue const &force) { + // The force applied to this CV is scalar type + cvm::real const &F = force.real_value; + (*(comp_atoms[min_frame_index_1])).apply_colvar_force(F); + (*(comp_atoms[min_frame_index_2])).apply_colvar_force(F); +} + +colvar::gzpath::gzpath(std::string const &conf): CartesianBasedPath(conf) { + function_type = "gzpath"; + get_keyval(conf, "useSecondClosestFrame", use_second_closest_frame, true); + if (use_second_closest_frame == true) { + cvm::log(std::string("Geometric path z(σ) will use the second closest frame to compute s_(m-1)\n")); + } else { + cvm::log(std::string("Geometric path z(σ) will use the neighbouring frame to compute s_(m-1)\n")); + } + get_keyval(conf, "useThirdClosestFrame", use_third_closest_frame, false); + if (use_third_closest_frame == true) { + cvm::log(std::string("Geometric path z(σ) will use the third closest frame to compute s_(m+1)\n")); + } else { + cvm::log(std::string("Geometric path z(σ) will use the neighbouring frame to compute s_(m+1)\n")); + } + bool b_use_z_square = false; + get_keyval(conf, "useZsquare", b_use_z_square, false); + if (b_use_z_square == true) { + cvm::log(std::string("Geometric path z(σ) will use the square of distance from current frame to path compute z\n")); + } + GeometricPathCV::GeometricPathBase::initialize(atoms->size(), cvm::atom_pos(), total_reference_frames, use_second_closest_frame, use_third_closest_frame, b_use_z_square); + // Logging + cvm::log(std::string("Geometric pathCV(z) is initialized.\n")); + cvm::log(std::string("Geometric pathCV(z) loaded ") + cvm::to_str(reference_frames.size()) + std::string(" frames.\n")); +} + +void colvar::gzpath::updateReferenceDistances() { + computeReferenceDistance(frame_distances); +} + +void colvar::gzpath::prepareVectors() { + cvm::atom_pos reference_cog_1, reference_cog_2; + size_t i_atom; + for (i_atom = 0; i_atom < atoms->size(); ++i_atom) { + reference_cog_1 += reference_frames[min_frame_index_1][i_atom]; + reference_cog_2 += reference_frames[min_frame_index_2][i_atom]; + } + reference_cog_1 /= reference_frames[min_frame_index_1].size(); + reference_cog_2 /= reference_frames[min_frame_index_2].size(); + std::vector tmp_reference_frame_1(reference_frames[min_frame_index_1].size()); + std::vector tmp_reference_frame_2(reference_frames[min_frame_index_2].size()); + for (i_atom = 0; i_atom < atoms->size(); ++i_atom) { + tmp_reference_frame_1[i_atom] = reference_frames[min_frame_index_1][i_atom] - reference_cog_1; + tmp_reference_frame_2[i_atom] = reference_frames[min_frame_index_2][i_atom] - reference_cog_2; + } + std::vector tmp_reference_fitting_frame_1; + std::vector tmp_reference_fitting_frame_2; + if (has_user_defined_fitting) { + cvm::atom_pos reference_fitting_cog_1, reference_fitting_cog_2; + for (i_atom = 0; i_atom < reference_fitting_frames[min_frame_index_1].size(); ++i_atom) { + reference_fitting_cog_1 += reference_fitting_frames[min_frame_index_1][i_atom]; + reference_fitting_cog_2 += reference_fitting_frames[min_frame_index_2][i_atom]; + } + reference_fitting_cog_1 /= reference_fitting_frames[min_frame_index_1].size(); + reference_fitting_cog_2 /= reference_fitting_frames[min_frame_index_2].size(); + tmp_reference_fitting_frame_1.resize(reference_fitting_frames[min_frame_index_1].size()); + tmp_reference_fitting_frame_2.resize(reference_fitting_frames[min_frame_index_2].size()); + for (i_atom = 0; i_atom < reference_fitting_frames[min_frame_index_1].size(); ++i_atom) { + tmp_reference_fitting_frame_1[i_atom] = reference_fitting_frames[min_frame_index_1][i_atom] - reference_fitting_cog_1; + tmp_reference_fitting_frame_2[i_atom] = reference_fitting_frames[min_frame_index_2][i_atom] - reference_fitting_cog_2; + } + rot_v4.calc_optimal_rotation(tmp_reference_fitting_frame_1, tmp_reference_fitting_frame_2); + } else { + rot_v4.calc_optimal_rotation(tmp_reference_frame_1, tmp_reference_frame_2); + } + for (i_atom = 0; i_atom < atoms->size(); ++i_atom) { + v1[i_atom] = reference_frames[min_frame_index_1][i_atom] - (*(comp_atoms[min_frame_index_1]))[i_atom].pos; + v2[i_atom] = (*(comp_atoms[min_frame_index_2]))[i_atom].pos - reference_frames[min_frame_index_2][i_atom]; + // v4 only computes in gzpath + // v4 = s_m - s_(m-1) + v4[i_atom] = rot_v4.q.rotate(tmp_reference_frame_1[i_atom]) - tmp_reference_frame_2[i_atom]; + } + if (min_frame_index_3 < 0 || min_frame_index_3 > M) { + v3 = v4; + } else { + cvm::atom_pos reference_cog_3; + for (i_atom = 0; i_atom < atoms->size(); ++i_atom) { + reference_cog_3 += reference_frames[min_frame_index_3][i_atom]; + } + reference_cog_3 /= reference_frames[min_frame_index_3].size(); + std::vector tmp_reference_frame_3(reference_frames[min_frame_index_3].size()); + for (i_atom = 0; i_atom < atoms->size(); ++i_atom) { + tmp_reference_frame_3[i_atom] = reference_frames[min_frame_index_3][i_atom] - reference_cog_3; + } + if (has_user_defined_fitting) { + cvm::atom_pos reference_fitting_cog_3; + for (i_atom = 0; i_atom < reference_fitting_frames[min_frame_index_3].size(); ++i_atom) { + reference_fitting_cog_3 += reference_fitting_frames[min_frame_index_3][i_atom]; + } + reference_fitting_cog_3 /= reference_fitting_frames[min_frame_index_3].size(); + std::vector tmp_reference_fitting_frame_3(reference_fitting_frames[min_frame_index_3].size()); + for (i_atom = 0; i_atom < reference_fitting_frames[min_frame_index_3].size(); ++i_atom) { + tmp_reference_fitting_frame_3[i_atom] = reference_fitting_frames[min_frame_index_3][i_atom] - reference_fitting_cog_3; + } + rot_v3.calc_optimal_rotation(tmp_reference_fitting_frame_1, tmp_reference_fitting_frame_3); + } else { + rot_v3.calc_optimal_rotation(tmp_reference_frame_1, tmp_reference_frame_3); + } + for (i_atom = 0; i_atom < atoms->size(); ++i_atom) { + // v3 = s_(m+1) - s_m + v3[i_atom] = tmp_reference_frame_3[i_atom] - rot_v3.q.rotate(tmp_reference_frame_1[i_atom]); + } + } +} + +void colvar::gzpath::calc_value() { + computeValue(); + x = z; +} + +void colvar::gzpath::calc_gradients() { + computeDerivatives(); + cvm::rvector tmp_atom_grad_v1, tmp_atom_grad_v2; + for (size_t i_atom = 0; i_atom < atoms->size(); ++i_atom) { + tmp_atom_grad_v1 = -1.0 * dzdv1[i_atom]; + tmp_atom_grad_v2 = dzdv2[i_atom]; + (*(comp_atoms[min_frame_index_1]))[i_atom].grad += tmp_atom_grad_v1; + (*(comp_atoms[min_frame_index_2]))[i_atom].grad += tmp_atom_grad_v2; + } +} + +void colvar::gzpath::apply_force(colvarvalue const &force) { + // The force applied to this CV is scalar type + cvm::real const &F = force.real_value; + (*(comp_atoms[min_frame_index_1])).apply_colvar_force(F); + (*(comp_atoms[min_frame_index_2])).apply_colvar_force(F); +} + +colvar::linearCombination::linearCombination(std::string const &conf): cvc(conf) { + GeometricPathCV::init_string_cv_map(string_cv_map); + // Lookup all available sub-cvcs + for (auto it_cv_map = string_cv_map.begin(); it_cv_map != string_cv_map.end(); ++it_cv_map) { + if (key_lookup(conf, it_cv_map->first.c_str())) { + std::vector sub_cvc_confs; + get_key_string_multi_value(conf, it_cv_map->first.c_str(), sub_cvc_confs); + for (auto it_sub_cvc_conf = sub_cvc_confs.begin(); it_sub_cvc_conf != sub_cvc_confs.end(); ++it_sub_cvc_conf) { + cv.push_back((it_cv_map->second)(*(it_sub_cvc_conf))); + } + } + } + // Sort all sub CVs by their names + std::sort(cv.begin(), cv.end(), compareColvarComponent); + for (auto it_sub_cv = cv.begin(); it_sub_cv != cv.end(); ++it_sub_cv) { + for (auto it_atom_group = (*it_sub_cv)->atom_groups.begin(); it_atom_group != (*it_sub_cv)->atom_groups.end(); ++it_atom_group) { + register_atom_group(*it_atom_group); + } + } + x.type(cv[0]->value()); + x.reset(); + use_explicit_gradients = true; + for (size_t i_cv = 0; i_cv < cv.size(); ++i_cv) { + if (!cv[i_cv]->is_enabled(f_cvc_explicit_gradient)) { + use_explicit_gradients = false; + } + } + if (!use_explicit_gradients) { + disable(f_cvc_explicit_gradient); + } +} + +cvm::real colvar::linearCombination::getPolynomialFactorOfCVGradient(size_t i_cv) const { + cvm::real factor_polynomial = 1.0; + if (cv[i_cv]->value().type() == colvarvalue::type_scalar) { + factor_polynomial = cv[i_cv]->sup_coeff * cv[i_cv]->sup_np * cvm::pow(cv[i_cv]->value().real_value, cv[i_cv]->sup_np - 1); + } else { + factor_polynomial = cv[i_cv]->sup_coeff; + } + return factor_polynomial; +} + +colvar::linearCombination::~linearCombination() { + for (auto it = cv.begin(); it != cv.end(); ++it) { + delete (*it); + } +} + +void colvar::linearCombination::calc_value() { + x.reset(); + for (size_t i_cv = 0; i_cv < cv.size(); ++i_cv) { + cv[i_cv]->calc_value(); + colvarvalue current_cv_value(cv[i_cv]->value()); + // polynomial combination allowed + if (current_cv_value.type() == colvarvalue::type_scalar) { + x += cv[i_cv]->sup_coeff * (cvm::pow(current_cv_value.real_value, cv[i_cv]->sup_np)); + } else { + x += cv[i_cv]->sup_coeff * current_cv_value; + } + } +} + +void colvar::linearCombination::calc_gradients() { + for (size_t i_cv = 0; i_cv < cv.size(); ++i_cv) { + cv[i_cv]->calc_gradients(); + if ( cv[i_cv]->is_enabled(f_cvc_explicit_gradient) && + !cv[i_cv]->is_enabled(f_cvc_scalable) && + !cv[i_cv]->is_enabled(f_cvc_scalable_com)) { + cvm::real factor_polynomial = getPolynomialFactorOfCVGradient(i_cv); + for (size_t j_elem = 0; j_elem < cv[i_cv]->value().size(); ++j_elem) { + for (size_t k_ag = 0 ; k_ag < cv[i_cv]->atom_groups.size(); ++k_ag) { + for (size_t l_atom = 0; l_atom < (cv[i_cv]->atom_groups)[k_ag]->size(); ++l_atom) { + (*(cv[i_cv]->atom_groups)[k_ag])[l_atom].grad = factor_polynomial * (*(cv[i_cv]->atom_groups)[k_ag])[l_atom].grad; + } + } + } + } + } +} + +void colvar::linearCombination::apply_force(colvarvalue const &force) { + for (size_t i_cv = 0; i_cv < cv.size(); ++i_cv) { + // If this CV us explicit gradients, then atomic gradients is already calculated + // We can apply the force to atom groups directly + if ( cv[i_cv]->is_enabled(f_cvc_explicit_gradient) && + !cv[i_cv]->is_enabled(f_cvc_scalable) && + !cv[i_cv]->is_enabled(f_cvc_scalable_com) + ) { + for (size_t k_ag = 0 ; k_ag < cv[i_cv]->atom_groups.size(); ++k_ag) { + (cv[i_cv]->atom_groups)[k_ag]->apply_colvar_force(force.real_value); + } + } else { + // Compute factors for polynomial combinations + cvm::real factor_polynomial = getPolynomialFactorOfCVGradient(i_cv); + colvarvalue cv_force = force.real_value * factor_polynomial; + cv[i_cv]->apply_force(cv_force); + } + } +} + +colvar::CVBasedPath::CVBasedPath(std::string const &conf): cvc(conf) { + GeometricPathCV::init_string_cv_map(string_cv_map); + // Lookup all available sub-cvcs + for (auto it_cv_map = string_cv_map.begin(); it_cv_map != string_cv_map.end(); ++it_cv_map) { + if (key_lookup(conf, it_cv_map->first.c_str())) { + std::vector sub_cvc_confs; + get_key_string_multi_value(conf, it_cv_map->first.c_str(), sub_cvc_confs); + for (auto it_sub_cvc_conf = sub_cvc_confs.begin(); it_sub_cvc_conf != sub_cvc_confs.end(); ++it_sub_cvc_conf) { + cv.push_back((it_cv_map->second)(*(it_sub_cvc_conf))); + } + } + } + // Sort all sub CVs by their names + std::sort(cv.begin(), cv.end(), compareColvarComponent); + // Register atom groups and determine the colvar type for reference + std::vector tmp_cv; + for (auto it_sub_cv = cv.begin(); it_sub_cv != cv.end(); ++it_sub_cv) { + for (auto it_atom_group = (*it_sub_cv)->atom_groups.begin(); it_atom_group != (*it_sub_cv)->atom_groups.end(); ++it_atom_group) { + register_atom_group(*it_atom_group); + } + colvarvalue tmp_i_cv((*it_sub_cv)->value()); + tmp_i_cv.reset(); + tmp_cv.push_back(tmp_i_cv); + } + // Read path file + // Lookup all reference CV values + std::string path_filename; + get_keyval(conf, "pathFile", path_filename); + cvm::log(std::string("Reading path file: ") + path_filename + std::string("\n")); + std::ifstream ifs_path(path_filename); + if (!ifs_path.is_open()) { + cvm::error("Error: failed to open path file.\n"); + } + std::string line; + const std::string token(" "); + total_reference_frames = 0; + while (std::getline(ifs_path, line)) { + std::vector fields; + split_string(line, token, fields); + size_t num_value_required = 0; + for (size_t i_cv = 0; i_cv < tmp_cv.size(); ++i_cv) { + const size_t value_size = tmp_cv[i_cv].size(); + num_value_required += value_size; + cvm::log(std::string("Reading CV ") + cv[i_cv]->name + std::string(" with ") + cvm::to_str(value_size) + std::string(" value(s)\n")); + if (num_value_required <= fields.size()) { + size_t start_index = num_value_required - value_size; + for (size_t i = start_index; i < num_value_required; ++i) { + tmp_cv[i_cv][i] = std::atof(fields[i].c_str()); + cvm::log(fields[i] + std::string(" ")); + } + cvm::log(std::string("\n")); + } else { + cvm::error("Error: incorrect format of path file.\n"); + } + } + if (!fields.empty()) { + ref_cv.push_back(tmp_cv); + ++total_reference_frames; + } + } + x.type(colvarvalue::type_scalar); + use_explicit_gradients = true; + for (size_t i_cv = 0; i_cv < cv.size(); ++i_cv) { + if (!cv[i_cv]->is_enabled(f_cvc_explicit_gradient)) { + use_explicit_gradients = false; + } + } + if (!use_explicit_gradients) { + disable(f_cvc_explicit_gradient); + } +} + +void colvar::CVBasedPath::computeReferenceDistance(std::vector& result) { + for (size_t i_cv = 0; i_cv < cv.size(); ++i_cv) { + cv[i_cv]->calc_value(); + } + for (size_t i_frame = 0; i_frame < ref_cv.size(); ++i_frame) { + cvm::real rmsd_i = 0.0; + for (size_t i_cv = 0; i_cv < cv.size(); ++i_cv) { + colvarvalue ref_cv_value(ref_cv[i_frame][i_cv]); + colvarvalue current_cv_value(cv[i_cv]->value()); + // polynomial combination allowed + if (current_cv_value.type() == colvarvalue::type_scalar) { + // wrapping is already in dist2 + rmsd_i += cv[i_cv]->dist2(cv[i_cv]->sup_coeff * (cvm::pow(current_cv_value.real_value, cv[i_cv]->sup_np)), ref_cv_value.real_value); + } else { + rmsd_i += cv[i_cv]->dist2(cv[i_cv]->sup_coeff * current_cv_value, ref_cv_value); + } + } + rmsd_i /= cvm::real(cv.size()); + rmsd_i = cvm::sqrt(rmsd_i); + result[i_frame] = rmsd_i; + } +} + +cvm::real colvar::CVBasedPath::getPolynomialFactorOfCVGradient(size_t i_cv) const { + cvm::real factor_polynomial = 1.0; + if (cv[i_cv]->value().type() == colvarvalue::type_scalar) { + factor_polynomial = cv[i_cv]->sup_coeff * cv[i_cv]->sup_np * cvm::pow(cv[i_cv]->value().real_value, cv[i_cv]->sup_np - 1); + } else { + factor_polynomial = cv[i_cv]->sup_coeff; + } + return factor_polynomial; +} + +colvar::CVBasedPath::~CVBasedPath() { + for (auto it = cv.begin(); it != cv.end(); ++it) { + delete (*it); + } +} + +colvar::gspathCV::gspathCV(std::string const &conf): CVBasedPath(conf) { + function_type = "gspathCV"; + cvm::log(std::string("Total number of frames: ") + cvm::to_str(total_reference_frames) + std::string("\n")); + // Initialize variables for future calculation + get_keyval(conf, "useSecondClosestFrame", use_second_closest_frame, true); + if (use_second_closest_frame == true) { + cvm::log(std::string("Geometric path s(σ) will use the second closest frame to compute s_(m-1)\n")); + } else { + cvm::log(std::string("Geometric path s(σ) will use the neighbouring frame to compute s_(m-1)\n")); + } + get_keyval(conf, "useThirdClosestFrame", use_third_closest_frame, false); + if (use_third_closest_frame == true) { + cvm::log(std::string("Geometric path s(σ) will use the third closest frame to compute s_(m+1)\n")); + } else { + cvm::log(std::string("Geometric path s(σ) will use the neighbouring frame to compute s_(m+1)\n")); + } + GeometricPathCV::GeometricPathBase::initialize(cv.size(), ref_cv[0], total_reference_frames, use_second_closest_frame, use_third_closest_frame); + x.type(colvarvalue::type_scalar); + use_explicit_gradients = true; + for (size_t i_cv = 0; i_cv < cv.size(); ++i_cv) { + if (!cv[i_cv]->is_enabled(f_cvc_explicit_gradient)) { + use_explicit_gradients = false; + } + } + if (!use_explicit_gradients) { + cvm::log("Geometric path s(σ) will use implicit gradients.\n"); + disable(f_cvc_explicit_gradient); + } +} + +colvar::gspathCV::~gspathCV() {} + +void colvar::gspathCV::updateReferenceDistances() { + computeReferenceDistance(frame_distances); +} + +void colvar::gspathCV::prepareVectors() { + // Compute v1, v2 and v3 + for (size_t i_cv = 0; i_cv < cv.size(); ++i_cv) { + // values of sub-cvc are computed in update_distances + // cv[i_cv]->calc_value(); + colvarvalue f1_ref_cv_i_value(ref_cv[min_frame_index_1][i_cv]); + colvarvalue f2_ref_cv_i_value(ref_cv[min_frame_index_2][i_cv]); + colvarvalue current_cv_value(cv[i_cv]->value()); + // polynomial combination allowed + if (current_cv_value.type() == colvarvalue::type_scalar) { + v1[i_cv] = f1_ref_cv_i_value.real_value - cv[i_cv]->sup_coeff * (cvm::pow(current_cv_value.real_value, cv[i_cv]->sup_np)); + v2[i_cv] = cv[i_cv]->sup_coeff * (cvm::pow(current_cv_value.real_value, cv[i_cv]->sup_np)) - f2_ref_cv_i_value.real_value; + } else { + v1[i_cv] = f1_ref_cv_i_value - cv[i_cv]->sup_coeff * current_cv_value; + v2[i_cv] = cv[i_cv]->sup_coeff * current_cv_value - f2_ref_cv_i_value; + } + cv[i_cv]->wrap(v1[i_cv]); + cv[i_cv]->wrap(v2[i_cv]); + } + if (min_frame_index_3 < 0 || min_frame_index_3 > M) { + for (size_t i_cv = 0; i_cv < cv.size(); ++i_cv) { + v3[i_cv] = ref_cv[min_frame_index_1][i_cv] - ref_cv[min_frame_index_2][i_cv]; + cv[i_cv]->wrap(v3[i_cv]); + } + } else { + for (size_t i_cv = 0; i_cv < cv.size(); ++i_cv) { + v3[i_cv] = ref_cv[min_frame_index_3][i_cv] - ref_cv[min_frame_index_1][i_cv]; + cv[i_cv]->wrap(v3[i_cv]); + } + } +} + +void colvar::gspathCV::calc_value() { + computeValue(); + x = s; +} + +void colvar::gspathCV::calc_gradients() { + computeDerivatives(); + for (size_t i_cv = 0; i_cv < cv.size(); ++i_cv) { + // No matter whether the i-th cv uses implicit gradient, compute it first. + cv[i_cv]->calc_gradients(); + // If the gradient is not implicit, then add the gradients to its atom groups + if ( cv[i_cv]->is_enabled(f_cvc_explicit_gradient) && + !cv[i_cv]->is_enabled(f_cvc_scalable) && + !cv[i_cv]->is_enabled(f_cvc_scalable_com)) { + // Temporary variables storing gradients + colvarvalue tmp_cv_grad_v1(cv[i_cv]->value()); + colvarvalue tmp_cv_grad_v2(cv[i_cv]->value()); + // Compute factors for polynomial combinations + cvm::real factor_polynomial = getPolynomialFactorOfCVGradient(i_cv); + // Loop over all elements of the corresponding colvar value + for (size_t j_elem = 0; j_elem < cv[i_cv]->value().size(); ++j_elem) { + // ds/dz, z = vector of CVs + tmp_cv_grad_v1[j_elem] = -1.0 * sign * 0.5 * dfdv1[i_cv][j_elem] / M; + tmp_cv_grad_v2[j_elem] = sign * 0.5 * dfdv2[i_cv][j_elem] / M; + // Apply the gradients to the atom groups in i-th cv + // Loop over all atom groups + for (size_t k_ag = 0 ; k_ag < cv[i_cv]->atom_groups.size(); ++k_ag) { + // Loop over all atoms in the k-th atom group + for (size_t l_atom = 0; l_atom < (cv[i_cv]->atom_groups)[k_ag]->size(); ++l_atom) { + // Chain rule + (*(cv[i_cv]->atom_groups)[k_ag])[l_atom].grad = factor_polynomial * ((*(cv[i_cv]->atom_groups)[k_ag])[l_atom].grad * tmp_cv_grad_v1[j_elem] + (*(cv[i_cv]->atom_groups)[k_ag])[l_atom].grad * tmp_cv_grad_v2[j_elem]); + } + } + } + } + } +} + +void colvar::gspathCV::apply_force(colvarvalue const &force) { + for (size_t i_cv = 0; i_cv < cv.size(); ++i_cv) { + // If this CV us explicit gradients, then atomic gradients is already calculated + // We can apply the force to atom groups directly + if ( cv[i_cv]->is_enabled(f_cvc_explicit_gradient) && + !cv[i_cv]->is_enabled(f_cvc_scalable) && + !cv[i_cv]->is_enabled(f_cvc_scalable_com) + ) { + for (size_t k_ag = 0 ; k_ag < cv[i_cv]->atom_groups.size(); ++k_ag) { + (cv[i_cv]->atom_groups)[k_ag]->apply_colvar_force(force.real_value); + } + } else { + // Temporary variables storing gradients + colvarvalue tmp_cv_grad_v1(cv[i_cv]->value()); + colvarvalue tmp_cv_grad_v2(cv[i_cv]->value()); + // Compute factors for polynomial combinations + cvm::real factor_polynomial = getPolynomialFactorOfCVGradient(i_cv); + for (size_t j_elem = 0; j_elem < cv[i_cv]->value().size(); ++j_elem) { + // ds/dz, z = vector of CVs + tmp_cv_grad_v1[j_elem] = -1.0 * sign * 0.5 * dfdv1[i_cv][j_elem] / M; + tmp_cv_grad_v2[j_elem] = sign * 0.5 * dfdv2[i_cv][j_elem] / M; + } + colvarvalue cv_force = force.real_value * factor_polynomial * (tmp_cv_grad_v1 + tmp_cv_grad_v2); + cv[i_cv]->apply_force(cv_force); + } + } +} + +colvar::gzpathCV::gzpathCV(std::string const &conf): CVBasedPath(conf) { + function_type = "gzpathCV"; + cvm::log(std::string("Total number of frames: ") + cvm::to_str(total_reference_frames) + std::string("\n")); + // Initialize variables for future calculation + M = cvm::real(total_reference_frames - 1); + m = 1.0; + get_keyval(conf, "useSecondClosestFrame", use_second_closest_frame, true); + if (use_second_closest_frame == true) { + cvm::log(std::string("Geometric path z(σ) will use the second closest frame to compute s_(m-1)\n")); + } else { + cvm::log(std::string("Geometric path z(σ) will use the neighbouring frame to compute s_(m-1)\n")); + } + get_keyval(conf, "useThirdClosestFrame", use_third_closest_frame, false); + if (use_third_closest_frame == true) { + cvm::log(std::string("Geometric path z(σ) will use the third closest frame to compute s_(m+1)\n")); + } else { + cvm::log(std::string("Geometric path z(σ) will use the neighbouring frame to compute s_(m+1)\n")); + } + bool b_use_z_square = false; + get_keyval(conf, "useZsquare", b_use_z_square, false); + if (b_use_z_square == true) { + cvm::log(std::string("Geometric path z(σ) will use the square of distance from current frame to path compute z\n")); + } + GeometricPathCV::GeometricPathBase::initialize(cv.size(), ref_cv[0], total_reference_frames, use_second_closest_frame, use_third_closest_frame, b_use_z_square); + x.type(colvarvalue::type_scalar); + use_explicit_gradients = true; + for (size_t i_cv = 0; i_cv < cv.size(); ++i_cv) { + if (!cv[i_cv]->is_enabled(f_cvc_explicit_gradient)) { + use_explicit_gradients = false; + } + } + if (!use_explicit_gradients) { + cvm::log("Geometric path z(σ) will use implicit gradients.\n"); + disable(f_cvc_explicit_gradient); + } +} + +colvar::gzpathCV::~gzpathCV() { +} + +void colvar::gzpathCV::updateReferenceDistances() { + computeReferenceDistance(frame_distances); +} + +void colvar::gzpathCV::prepareVectors() { + // Compute v1, v2 and v3 + for (size_t i_cv = 0; i_cv < cv.size(); ++i_cv) { + // values of sub-cvc are computed in update_distances + // cv[i_cv]->calc_value(); + colvarvalue f1_ref_cv_i_value(ref_cv[min_frame_index_1][i_cv]); + colvarvalue f2_ref_cv_i_value(ref_cv[min_frame_index_2][i_cv]); + colvarvalue current_cv_value(cv[i_cv]->value()); + // polynomial combination allowed + if (current_cv_value.type() == colvarvalue::type_scalar) { + v1[i_cv] = f1_ref_cv_i_value.real_value - cv[i_cv]->sup_coeff * (cvm::pow(current_cv_value.real_value, cv[i_cv]->sup_np)); + v2[i_cv] = cv[i_cv]->sup_coeff * (cvm::pow(current_cv_value.real_value, cv[i_cv]->sup_np)) - f2_ref_cv_i_value.real_value; + } else { + v1[i_cv] = f1_ref_cv_i_value - cv[i_cv]->sup_coeff * current_cv_value; + v2[i_cv] = cv[i_cv]->sup_coeff * current_cv_value - f2_ref_cv_i_value; + } + v4[i_cv] = f1_ref_cv_i_value - f2_ref_cv_i_value; + cv[i_cv]->wrap(v1[i_cv]); + cv[i_cv]->wrap(v2[i_cv]); + cv[i_cv]->wrap(v4[i_cv]); + } + if (min_frame_index_3 < 0 || min_frame_index_3 > M) { + for (size_t i_cv = 0; i_cv < cv.size(); ++i_cv) { + v3[i_cv] = ref_cv[min_frame_index_1][i_cv] - ref_cv[min_frame_index_2][i_cv]; + cv[i_cv]->wrap(v3[i_cv]); + } + } else { + for (size_t i_cv = 0; i_cv < cv.size(); ++i_cv) { + v3[i_cv] = ref_cv[min_frame_index_3][i_cv] - ref_cv[min_frame_index_1][i_cv]; + cv[i_cv]->wrap(v3[i_cv]); + } + } +} + +void colvar::gzpathCV::calc_value() { + computeValue(); + x = z; +} + +void colvar::gzpathCV::calc_gradients() { + computeDerivatives(); + for (size_t i_cv = 0; i_cv < cv.size(); ++i_cv) { + // No matter whether the i-th cv uses implicit gradient, compute it first. + cv[i_cv]->calc_gradients(); + // If the gradient is not implicit, then add the gradients to its atom groups + if ( cv[i_cv]->is_enabled(f_cvc_explicit_gradient) && + !cv[i_cv]->is_enabled(f_cvc_scalable) && + !cv[i_cv]->is_enabled(f_cvc_scalable_com)) { + // Temporary variables storing gradients + colvarvalue tmp_cv_grad_v1 = -1.0 * dzdv1[i_cv]; + colvarvalue tmp_cv_grad_v2 = 1.0 * dzdv2[i_cv]; + // Compute factors for polynomial combinations + cvm::real factor_polynomial = getPolynomialFactorOfCVGradient(i_cv); + for (size_t j_elem = 0; j_elem < cv[i_cv]->value().size(); ++j_elem) { + // Apply the gradients to the atom groups in i-th cv + // Loop over all atom groups + for (size_t k_ag = 0 ; k_ag < cv[i_cv]->atom_groups.size(); ++k_ag) { + // Loop over all atoms in the k-th atom group + for (size_t l_atom = 0; l_atom < (cv[i_cv]->atom_groups)[k_ag]->size(); ++l_atom) { + // Chain rule + (*(cv[i_cv]->atom_groups)[k_ag])[l_atom].grad = factor_polynomial * ((*(cv[i_cv]->atom_groups)[k_ag])[l_atom].grad * tmp_cv_grad_v1[j_elem] + (*(cv[i_cv]->atom_groups)[k_ag])[l_atom].grad * tmp_cv_grad_v2[j_elem]); + } + } + } + } + } +} + +void colvar::gzpathCV::apply_force(colvarvalue const &force) { + for (size_t i_cv = 0; i_cv < cv.size(); ++i_cv) { + // If this CV us explicit gradients, then atomic gradients is already calculated + // We can apply the force to atom groups directly + if ( cv[i_cv]->is_enabled(f_cvc_explicit_gradient) && + !cv[i_cv]->is_enabled(f_cvc_scalable) && + !cv[i_cv]->is_enabled(f_cvc_scalable_com)) { + for (size_t k_ag = 0 ; k_ag < cv[i_cv]->atom_groups.size(); ++k_ag) { + (cv[i_cv]->atom_groups)[k_ag]->apply_colvar_force(force.real_value); + } + } + else { + colvarvalue tmp_cv_grad_v1 = -1.0 * dzdv1[i_cv]; + colvarvalue tmp_cv_grad_v2 = 1.0 * dzdv2[i_cv]; + // Temporary variables storing gradients + // Compute factors for polynomial combinations + cvm::real factor_polynomial = getPolynomialFactorOfCVGradient(i_cv); + colvarvalue cv_force = force.real_value * factor_polynomial * (tmp_cv_grad_v1 + tmp_cv_grad_v2); + cv[i_cv]->apply_force(cv_force); + } + } +} + +void GeometricPathCV::init_string_cv_map(std::map>& string_cv_map) { + string_cv_map["distance"] = [](const std::string& conf){return new colvar::distance(conf);}; + string_cv_map["dihedral"] = [](const std::string& conf){return new colvar::dihedral(conf);}; + string_cv_map["angle"] = [](const std::string& conf){return new colvar::angle(conf);}; + string_cv_map["rmsd"] = [](const std::string& conf){return new colvar::rmsd(conf);}; + string_cv_map["gyration"] = [](const std::string& conf){return new colvar::gyration(conf);}; + string_cv_map["inertia"] = [](const std::string& conf){return new colvar::inertia(conf);}; + string_cv_map["inertiaZ"] = [](const std::string& conf){return new colvar::inertia_z(conf);}; + string_cv_map["tilt"] = [](const std::string& conf){return new colvar::tilt(conf);}; + string_cv_map["distanceZ"] = [](const std::string& conf){return new colvar::distance_z(conf);}; + string_cv_map["distanceXY"] = [](const std::string& conf){return new colvar::distance_xy(conf);}; + string_cv_map["polarTheta"] = [](const std::string& conf){return new colvar::polar_theta(conf);}; + string_cv_map["polarPhi"] = [](const std::string& conf){return new colvar::polar_phi(conf);}; + string_cv_map["distanceVec"] = [](const std::string& conf){return new colvar::distance_vec(conf);}; + string_cv_map["orientationAngle"] = [](const std::string& conf){return new colvar::orientation_angle(conf);}; + string_cv_map["distancePairs"] = [](const std::string& conf){return new colvar::distance_pairs(conf);}; + string_cv_map["dipoleMagnitude"] = [](const std::string& conf){return new colvar::dipole_magnitude(conf);}; + string_cv_map["coordNum"] = [](const std::string& conf){return new colvar::coordnum(conf);}; + string_cv_map["selfCoordNum"] = [](const std::string& conf){return new colvar::selfcoordnum(conf);}; + string_cv_map["dipoleAngle"] = [](const std::string& conf){return new colvar::dipole_angle(conf);}; + string_cv_map["orientation"] = [](const std::string& conf){return new colvar::orientation(conf);}; + string_cv_map["orientationProj"] = [](const std::string& conf){return new colvar::orientation_proj(conf);}; + string_cv_map["eigenvector"] = [](const std::string& conf){return new colvar::eigenvector(conf);}; + string_cv_map["cartesian"] = [](const std::string& conf){return new colvar::cartesian(conf);}; + string_cv_map["alpha"] = [](const std::string& conf){return new colvar::alpha_angles(conf);}; + string_cv_map["dihedralPC"] = [](const std::string& conf){return new colvar::dihedPC(conf);}; + string_cv_map["linearCombination"] = [](const std::string& conf){return new colvar::linearCombination(conf);}; +} + +#endif diff --git a/lib/colvars/colvarcomp_protein.cpp b/lib/colvars/colvarcomp_protein.cpp index b9f9c60cdb..aa61cdf1dc 100644 --- a/lib/colvars/colvarcomp_protein.cpp +++ b/lib/colvars/colvarcomp_protein.cpp @@ -7,6 +7,8 @@ // If you wish to distribute your changes, please submit them to the // Colvars repository at GitHub. +#include + #include "colvarmodule.h" #include "colvarvalue.h" #include "colvarparse.h" diff --git a/lib/colvars/colvargrid.cpp b/lib/colvars/colvargrid.cpp index dc1a709edb..bc5ac3c57c 100644 --- a/lib/colvars/colvargrid.cpp +++ b/lib/colvars/colvargrid.cpp @@ -109,7 +109,9 @@ cvm::real colvar_grid_scalar::entropy() const { cvm::real sum = 0.0; for (size_t i = 0; i < nt; i++) { - sum += -1.0 * data[i] * cvm::logn(data[i]); + if (data[i] >0) { + sum += -1.0 * data[i] * cvm::logn(data[i]); + } } cvm::real bin_volume = 1.0; for (size_t id = 0; id < widths.size(); id++) { diff --git a/lib/colvars/colvargrid.h b/lib/colvars/colvargrid.h index 2ba0566e49..7792b7d0df 100644 --- a/lib/colvars/colvargrid.h +++ b/lib/colvars/colvargrid.h @@ -557,11 +557,11 @@ public: data[i] *= a; } - /// \brief Assign all zero elements a scalar constant (fast loop) - inline void remove_zeros(cvm::real const &a) + /// \brief Assign values that are smaller than scalar constant the latter value (fast loop) + inline void remove_small_values(cvm::real const &a) { for (size_t i = 0; i < nt; i++) - if(data[i]==0) data[i] = a; + if(data[i] #include #include @@ -58,6 +57,28 @@ bool colvarparse::get_key_string_value(std::string const &conf, return b_found_any; } +bool colvarparse::get_key_string_multi_value(std::string const &conf, + char const *key, std::vector& data) +{ + bool b_found = false, b_found_any = false; + size_t save_pos = 0, found_count = 0; + + data.clear(); + + do { + std::string data_this = ""; + b_found = key_lookup(conf, key, &data_this, &save_pos); + if (b_found) { + if (!b_found_any) + b_found_any = true; + found_count++; + data.push_back(data_this); + } + } while (b_found); + + return b_found_any; +} + template void colvarparse::mark_key_set_user(std::string const &key_str, @@ -843,3 +864,18 @@ int colvarparse::check_braces(std::string const &conf, } return (brace_count != 0) ? INPUT_ERROR : COLVARS_OK; } + +void colvarparse::split_string(const std::string& data, const std::string& delim, std::vector& dest) { + size_t index = 0, new_index = 0; + std::string tmpstr; + while (index != data.length()) { + new_index = data.find(delim, index); + if (new_index != std::string::npos) tmpstr = data.substr(index, new_index - index); + else tmpstr = data.substr(index, data.length()); + if (!tmpstr.empty()) { + dest.push_back(tmpstr); + } + if (new_index == std::string::npos) break; + index = new_index + 1; + } +} diff --git a/lib/colvars/colvarparse.h b/lib/colvars/colvarparse.h index 8501ee8c14..f4ead26601 100644 --- a/lib/colvars/colvarparse.h +++ b/lib/colvars/colvarparse.h @@ -212,6 +212,10 @@ protected: bool get_key_string_value(std::string const &conf, char const *key, std::string &data); + /// Get multiple strings from repeated instances of a same keyword + bool get_key_string_multi_value(std::string const &conf, + char const *key, std::vector& data); + /// Template for single-value keyword parsers template bool _get_keyval_scalar_(std::string const &conf, @@ -322,6 +326,12 @@ public: /// from this position static int check_braces(std::string const &conf, size_t const start_pos); + /// \brief Split a string with a specified delimiter into a vector + /// \param data The string to be splitted + /// \param delim A delimiter + /// \param dest A destination vector to store the splitted results + static void split_string(const std::string& data, const std::string& delim, std::vector& dest); + protected: /// \brief List of legal keywords for this object: this is updated diff --git a/lib/colvars/colvarproxy.cpp b/lib/colvars/colvarproxy.cpp index 5f8e82d30a..f077984556 100644 --- a/lib/colvars/colvarproxy.cpp +++ b/lib/colvars/colvarproxy.cpp @@ -7,8 +7,14 @@ // If you wish to distribute your changes, please submit them to the // Colvars repository at GitHub. +#if !defined(WIN32) || defined(__CYGWIN__) +#include +#endif +#include + #include #include +#include #if defined(_OPENMP) #include @@ -704,28 +710,39 @@ std::ostream * colvarproxy_io::output_stream(std::string const &output_name, if (cvm::debug()) { cvm::log("Using colvarproxy::output_stream()\n"); } - std::list::iterator osi = output_files.begin(); - std::list::iterator osni = output_stream_names.begin(); - for ( ; osi != output_files.end(); osi++, osni++) { - if (*osni == output_name) { - return *osi; - } - } + + std::ostream *os = get_output_stream(output_name); + if (os != NULL) return os; + if (!(mode & (std::ios_base::app | std::ios_base::ate))) { backup_file(output_name); } - std::ofstream *os = new std::ofstream(output_name.c_str(), mode); - if (!os->is_open()) { + std::ofstream *osf = new std::ofstream(output_name.c_str(), mode); + if (!osf->is_open()) { cvm::error("Error: cannot write to file/channel \""+output_name+"\".\n", FILE_ERROR); return NULL; } output_stream_names.push_back(output_name); - output_files.push_back(os); - return os; + output_files.push_back(osf); + return osf; } +std::ostream *colvarproxy_io::get_output_stream(std::string const &output_name) +{ + std::list::iterator osi = output_files.begin(); + std::list::iterator osni = output_stream_names.begin(); + for ( ; osi != output_files.end(); osi++, osni++) { + if (*osni == output_name) { + return *osi; + } + } + return NULL; +} + + + int colvarproxy_io::flush_output_stream(std::ostream *os) { std::list::iterator osi = output_files.begin(); @@ -761,10 +778,45 @@ int colvarproxy_io::close_output_stream(std::string const &output_name) int colvarproxy_io::backup_file(char const *filename) { + // TODO implement this using rename_file() return COLVARS_NOT_IMPLEMENTED; } +int colvarproxy_io::remove_file(char const *filename) +{ + if (std::remove(filename)) { + if (errno != ENOENT) { + return cvm::error("Error: in removing file \""+std::string(filename)+ + "\".\n.", + FILE_ERROR); + } + } + return COLVARS_OK; +} + + +int colvarproxy_io::rename_file(char const *filename, char const *newfilename) +{ + int error_code = COLVARS_OK; +#if defined(WIN32) && !defined(__CYGWIN__) + // On straight Windows, must remove the destination before renaming it + error_code |= remove_file(newfilename); +#endif + int rename_exit_code = 0; + while ((rename_exit_code = std::rename(filename, newfilename)) != 0) { + if (errno == EINTR) continue; + // Call log() instead of error to allow the next try + cvm::log("Error: in renaming file \""+std::string(filename)+"\" to \""+ + std::string(newfilename)+"\".\n."); + error_code |= FILE_ERROR; + if (errno == EXDEV) continue; + break; + } + return rename_exit_code ? error_code : COLVARS_OK; +} + + colvarproxy::colvarproxy() { @@ -826,4 +878,3 @@ int colvarproxy::get_version_from_string(char const *version_string) is >> newint; return newint; } - diff --git a/lib/colvars/colvarproxy.h b/lib/colvars/colvarproxy.h index 3bbdfe522e..21944106f1 100644 --- a/lib/colvars/colvarproxy.h +++ b/lib/colvars/colvarproxy.h @@ -571,7 +571,10 @@ public: /// if this is not open already, then open it virtual std::ostream *output_stream(std::string const &output_name, std::ios_base::openmode mode = - std::ios_base::out); + std::ios_base::out); + + /// Returns a reference to output_name if it exists, NULL otherwise + virtual std::ostream *get_output_stream(std::string const &output_name); /// \brief Flushes the given output channel virtual int flush_output_stream(std::ostream *os); @@ -588,6 +591,25 @@ public: return backup_file(filename.c_str()); } + /// Remove the given file + int remove_file(char const *filename); + + /// Remove the given file + inline int remove_file(std::string const &filename) + { + return remove_file(filename.c_str()); + } + + /// Rename the given file + int rename_file(char const *filename, char const *newfilename); + + /// Rename the given file + inline int rename_file(std::string const &filename, + std::string const &newfilename) + { + return rename_file(filename.c_str(), newfilename.c_str()); + } + /// \brief Prefix of the input state file inline std::string & input_prefix() { diff --git a/lib/colvars/colvars_version.h b/lib/colvars/colvars_version.h index 2521fdf872..0f1ee9a0a0 100644 --- a/lib/colvars/colvars_version.h +++ b/lib/colvars/colvars_version.h @@ -1,5 +1,5 @@ #ifndef COLVARS_VERSION -#define COLVARS_VERSION "2019-04-26" +#define COLVARS_VERSION "2019-08-01" // This file is part of the Collective Variables module (Colvars). // The original version of Colvars and its updates are located at: // https://github.com/colvars/colvars diff --git a/src/USER-COLVARS/colvarproxy_lammps_version.h b/src/USER-COLVARS/colvarproxy_lammps_version.h index 0a4f9fdf4f..d976f40510 100644 --- a/src/USER-COLVARS/colvarproxy_lammps_version.h +++ b/src/USER-COLVARS/colvarproxy_lammps_version.h @@ -1,5 +1,5 @@ #ifndef COLVARPROXY_VERSION -#define COLVARPROXY_VERSION "2019-04-09" +#define COLVARPROXY_VERSION "2019-08-01" // This file is part of the Collective Variables module (Colvars). // The original version of Colvars and its updates are located at: // https://github.com/colvars/colvars -- GitLab From f9e34825f0f07ac60c97a593b363ee518e83ad56 Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Thu, 1 Aug 2019 16:42:52 -0400 Subject: [PATCH 409/469] workaround for xcode oddity with compiling voro++ --- cmake/Modules/Packages/VORONOI.cmake | 8 ++++++-- 1 file changed, 6 insertions(+), 2 deletions(-) diff --git a/cmake/Modules/Packages/VORONOI.cmake b/cmake/Modules/Packages/VORONOI.cmake index 5ce974a7ae..89fa70bf98 100644 --- a/cmake/Modules/Packages/VORONOI.cmake +++ b/cmake/Modules/Packages/VORONOI.cmake @@ -18,8 +18,12 @@ if(PKG_VORONOI) else() set(VORO_BUILD_CFLAGS "${CMAKE_CXX_FLAGS} ${CMAKE_CXX_FLAGS_${BTYPE}}") endif() - string(APPEND VORO_BUILD_CFLAGS ${CMAKE_CXX_FLAGS}) - set(VORO_BUILD_OPTIONS CXX=${CMAKE_CXX_COMPILER} CFLAGS=${VORO_BUILD_CFLAGS}) + if(APPLE) + get_filename_component(VORO_CXX ${CMAKE_CXX_COMPILER} NAME_WE) + set(VORO_BUILD_OPTIONS CXX=${VORO_CXX} CFLAGS=${VORO_BUILD_CFLAGS}) + else() + set(VORO_BUILD_OPTIONS CXX=${CMAKE_CXX_COMPILER} CFLAGS=${VORO_BUILD_CFLAGS}) + endif() ExternalProject_Add(voro_build URL https://download.lammps.org/thirdparty/voro++-0.4.6.tar.gz -- GitLab From 5b4b418289c86fbed8a4fc93b72633e1cce304b9 Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Thu, 1 Aug 2019 18:24:14 -0400 Subject: [PATCH 410/469] use check_language() instead of enable_language() to get fortran compiler name --- cmake/Modules/Packages/KIM.cmake | 8 ++++++-- 1 file changed, 6 insertions(+), 2 deletions(-) diff --git a/cmake/Modules/Packages/KIM.cmake b/cmake/Modules/Packages/KIM.cmake index d9d028f6dc..31586bfbe0 100644 --- a/cmake/Modules/Packages/KIM.cmake +++ b/cmake/Modules/Packages/KIM.cmake @@ -20,9 +20,13 @@ if(PKG_KIM) message(FATAL_ERROR "Cannot build downloaded KIM-API library with Ninja build tool") endif() message(STATUS "KIM-API download requested - we will build our own") - enable_language(C) - enable_language(Fortran) + include(CheckLanguage) include(ExternalProject) + enable_language(C) + check_language(Fortran) + if(NOT CMAKE_Fortran_COMPILER) + message(FATAL_ERROR "Compiling the KIM-API library requires a Fortran compiler") + endif() ExternalProject_Add(kim_build URL https://s3.openkim.org/kim-api/kim-api-2.1.2.txz URL_MD5 6ac52e14ef52967fc7858220b208cba5 -- GitLab From f61cd68ca47aff365b76248d95e816b8b3aac687 Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Thu, 1 Aug 2019 20:43:33 -0400 Subject: [PATCH 411/469] add missing parenthesis --- src/KOKKOS/kokkos.cpp | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/KOKKOS/kokkos.cpp b/src/KOKKOS/kokkos.cpp index 6fd8f46e43..32550e8285 100644 --- a/src/KOKKOS/kokkos.cpp +++ b/src/KOKKOS/kokkos.cpp @@ -239,7 +239,7 @@ KokkosLMP::KokkosLMP(LAMMPS *lmp, int narg, char **arg) : Pointers(lmp) #if defined(MPICH) && defined(MVAPICH2_VERSION) char* str; cuda_aware_flag = 0; - if (str = getenv("MV2_ENABLE_CUDA") + if ((str = getenv("MV2_ENABLE_CUDA"))) if ((strcmp(str,"1") == 0)) cuda_aware_flag = 1; -- GitLab From 5076f1a36c2d2ccbff93e621fa0460ebe6ca947c Mon Sep 17 00:00:00 2001 From: Evangelos Voyiatzis Date: Fri, 2 Aug 2019 10:55:18 +0200 Subject: [PATCH 412/469] small clean-up of fix.txt --- doc/src/fix.txt | 77 +++++++++++++++++++++++-------------------------- 1 file changed, 36 insertions(+), 41 deletions(-) diff --git a/doc/src/fix.txt b/doc/src/fix.txt index 294802c4fa..c64d61d949 100644 --- a/doc/src/fix.txt +++ b/doc/src/fix.txt @@ -169,7 +169,7 @@ accelerated styles exist. "addforce"_fix_addforce.html - add a force to each atom "addtorque"_fix_addtorque.html - "append/atoms"_fix_append_atoms.html - append atoms to a running simulation -"atc"_fix_atc.html - +"atc"_fix_atc.html - initiates a coupled MD/FE simulation "atom/swap"_fix_atom_swap.html - Monte Carlo atom type swapping "ave/atom"_fix_ave_atom.html - compute per-atom time-averaged quantities "ave/chunk"_fix_ave_chunk.html - compute per-chunk time-averaged quantities @@ -187,12 +187,12 @@ accelerated styles exist. "bond/swap"_fix_bond_swap.html - Monte Carlo bond swapping "box/relax"_fix_box_relax.html - relax box size during energy minimization "client/md"_fix_client_md.html - -"cmap"_fix_cmap.html - -"colvars"_fix_colvars.html - -"controller"_fix_controller.html - +"cmap"_fix_cmap.html - enables CMAP cross-terms of the CHARMM force field +"colvars"_fix_colvars.html - interface to the collective variables “Colvars” library +"controller"_fix_controller.html - "deform"_fix_deform.html - change the simulation box size/shape "deposit"_fix_deposit.html - add new atoms above a surface -"dpd/energy"_fix_dpd_energy.html - +"dpd/energy"_fix_dpd_energy.html - constant energy dissipative particle dynamics "drag"_fix_drag.html - drag atoms towards a defined coordinate "drude"_fix_drude.html - "drude/transform/direct"_fix_drude_transform.html - @@ -208,27 +208,26 @@ accelerated styles exist. "eos/table/rx"_fix_eos_table_rx.html - "evaporate"_fix_evaporate.html - remove atoms from simulation periodically "external"_fix_external.html - callback to an external driver program -"ffl"_fix_ffl.html - +"ffl"_fix_ffl.html - apply a Fast-Forward Langevin equation thermostat "filter/corotate"_fix_filter_corotate.html - "flow/gauss"_fix_flow_gauss.html - "freeze"_fix_freeze.html - freeze atoms in a granular simulation "gcmc"_fix_gcmc.html - grand canonical insertions/deletions -"gld"_fix_gcmc.html - generalized Langevin dynamics integrator -"gld"_fix_gld.html - -"gle"_fix_gle.html - +"gld"_fix_gld.html - generalized Langevin dynamics integrator +"gle"_fix_gle.html - generalized Langevin equation thermostat "gravity"_fix_gravity.html - add gravity to atoms in a granular simulation -"grem"_fix_grem.html - +"grem"_fix_grem.html - implements the generalized replica exchange method "halt"_fix_halt.html - terminate a dynamics run or minimization "heat"_fix_heat.html - add/subtract momentum-conserving heat "hyper/global"_fix_hyper_global.html - global hyperdynamics "hyper/local"_fix_hyper_local.html - local hyperdynamics -"imd"_fix_imd.html - +"imd"_fix_imd.html - implements the “Interactive MD” (IMD) protocol "indent"_fix_indent.html - impose force due to an indenter "ipi"_fix_ipi.html - "langevin"_fix_langevin.html - Langevin temperature control -"langevin/drude"_fix_langevin_drude.html - -"langevin/eff"_fix_langevin_eff.html - -"langevin/spin"_fix_langevin_spin.html - +"langevin/drude"_fix_langevin_drude.html - Langevin temperature control of Drude oscillators +"langevin/eff"_fix_langevin_eff.html - Langevin temperature control for the electron force field model +"langevin/spin"_fix_langevin_spin.html - Langevin temperature control for a spin or spin-lattice system "latte"_fix_latte.html - wrapper on LATTE density-functional tight-binding code "lb/fluid"_fix_lb_fluid.html - "lb/momentum"_fix_lb_momentum.html - @@ -238,62 +237,58 @@ accelerated styles exist. "lineforce"_fix_lineforce.html - constrain atoms to move in a line "manifoldforce"_fix_manifoldforce.html - "meso"_fix_meso.html - -"meso"_fix_meso_move.html - move mesoscopic SPH/SDPD particles in a prescribed fashion -"meso/move"_fix_meso_move.html - +"meso/move"_fix_meso_move.html - move mesoscopic SPH/SDPD particles in a prescribed fashion "meso/stationary"_fix_meso_stationary.html - "momentum"_fix_momentum.html - zero the linear and/or angular momentum of a group of atoms "move"_fix_move.html - move atoms in a prescribed fashion "mscg"_fix_mscg.html - "msst"_fix_msst.html - multi-scale shock technique (MSST) integration -"mvv/dpd"_fix_mvv_dpd.html - -"mvv/edpd"_fix_mvv_dpd.html - -"mvv/tdpd"_fix_mvv_dpd.html - +"mvv/dpd"_fix_mvv_dpd.html - DPD using the modified velocity-Verlet integration algorithm +"mvv/edpd"_fix_mvv_dpd.html - constant energy DPD using the modified velocity-Verlet algrithm +"mvv/tdpd"_fix_mvv_dpd.html - constant temperature DPD using the modified velocity-Verlet algorithm "neb"_fix_neb.html - nudged elastic band (NEB) spring forces "nph"_fix_nh.html - constant NPH time integration via Nose/Hoover "nph/asphere"_fix_nph_asphere.html - NPH for aspherical particles -"nph/body"_fix_nph_body.html - -"nph/body"_fix_nve_body.html - NPH for body particles -"nph/eff"_fix_nh_eff.html - +"nph/body"_fix_nph_body.html - NPH for body particles +"nph/eff"_fix_nh_eff.html - NPH for nuclei and electrons in the electron force field model "nph/sphere"_fix_nph_sphere.html - NPH for spherical particles "nphug"_fix_nphug.html - constant-stress Hugoniostat integration "npt"_fix_nh.html - constant NPT time integration via Nose/Hoover "npt/asphere"_fix_npt_asphere.html - NPT for aspherical particles -"npt/body"_fix_npt_body.html - -"npt/body"_fix_nve_body.html - NPT for body particles -"npt/eff"_fix_nh_eff.html - +"npt/body"_fix_npt_body.html - NPT for body particles +"npt/eff"_fix_nh_eff.html - NPT for nuclei and electrons in the electron force field model "npt/sphere"_fix_npt_sphere.html - NPT for spherical particles "npt/uef"_fix_nh_uef.html - "nve"_fix_nve.html - constant NVE time integration "nve/asphere"_fix_nve_asphere.html - NVE for aspherical particles -"nve/asphere/noforce"_fix_nve_asphere_noforce.html - NVE for aspherical particles without forces" -"nve/awpmd"_fix_nve_awpmd.html - +"nve/asphere/noforce"_fix_nve_asphere_noforce.html - NVE for aspherical particles without forces +"nve/awpmd"_fix_nve_awpmd.html - NVE for the Antisymmetrized Wave Packet Molecular Dynamics model "nve/body"_fix_nve_body.html - NVE for body particles "nve/dot"_fix_nve_dot.html - "nve/dotc/langevin"_fix_nve_dotc_langevin.html - -"nve/eff"_fix_nve_eff.html - +"nve/eff"_fix_nve_eff.html - NVE for nuclei and electrons in the electron force field model "nve/limit"_fix_nve_limit.html - NVE with limited step length "nve/line"_fix_nve_line.html - NVE for line segments "nve/manifold/rattle"_fix_nve_manifold_rattle.html - "nve/noforce"_fix_nve_noforce.html - NVE without forces (v only) "nve/sphere"_fix_nve_sphere.html - NVE for spherical particles -"nve/spin"_fix_nve_spin.html - +"nve/spin"_fix_nve_spin.html - NVE for a spin or spin-lattice system "nve/tri"_fix_nve_tri.html - NVE for triangles -"nvk"_fix_nvk.html - -"nvt"_fix_nh.html - constant NVT time integration via Nose/Hoover +"nvk"_fix_nvk.html - constant kinetic energy time integration +"nvt"_fix_nh.html - NVT time integration via Nose/Hoover "nvt/asphere"_fix_nvt_asphere.html - NVT for aspherical particles -"nvt/body"_fix_nve_body.html - NVT for body particles -"nvt/body"_fix_nvt_body.html - -"nvt/eff"_fix_nh_eff.html - +"nvt/body"_fix_nvt_body.html - NVT for body particles +"nvt/eff"_fix_nh_eff.html - NVE for nuclei and electrons in the electron force field model "nvt/manifold/rattle"_fix_nvt_manifold_rattle.html - "nvt/sllod"_fix_nvt_sllod.html - NVT for NEMD with SLLOD equations -"nvt/sllod/eff"_fix_nvt_sllod_eff.html - +"nvt/sllod/eff"_fix_nvt_sllod_eff.html - NVT for NEMD with SLLOD equations for the electron force field model "nvt/sphere"_fix_nvt_sphere.html - NVT for spherical particles "nvt/uef"_fix_nh_uef.html - "oneway"_fix_oneway.html - constrain particles on move in one direction "orient/bcc"_fix_orient.html - add grain boundary migration force for BCC "orient/fcc"_fix_orient.html - add grain boundary migration force for FCC "phonon"_fix_phonon.html - -"pimd"_fix_pimd.html - +"pimd"_fix_pimd.html - Feynman path integral molecular dynamics "planeforce"_fix_planeforce.html - constrain atoms to move in a plane "plumed"_fix_plumed.html - wrapper on PLUMED free energy library "poems"_fix_poems.html - constrain clusters of atoms to move as coupled rigid bodies @@ -303,16 +298,16 @@ accelerated styles exist. "print"_fix_print.html - print text and variables during a simulation "property/atom"_fix_property_atom.html - add customized per-atom values "python/invoke"_fix_python_invoke.html - -"python/move"_fix_python_move.html - +"python/move"_fix_python_move.html - call a Python function during a simulation run "qbmsst"_fix_qbmsst.html - "qeq/comb"_fix_qeq_comb.html - charge equilibration for COMB potential "qeq/dynamic"_fix_qeq.html - charge equilibration via dynamic method "qeq/fire"_fix_qeq.html - charge equilibration via FIRE minimizer "qeq/point"_fix_qeq.html - charge equilibration via point method -"qeq/reax"_fix_qeq_reax.html - +"qeq/reax"_fix_qeq_reax.html - charge equilibration for ReaxFF potential "qeq/shielded"_fix_qeq.html - charge equilibration via shielded method "qeq/slater"_fix_qeq.html - charge equilibration via Slater method -"qmmm"_fix_qmmm.html - +"qmmm"_fix_qmmm.html - functionality to enable a quantum mechanics/molecular mechanics coupling "qtb"_fix_qtb.html - "rattle"_fix_shake.html - RATTLE constraints on bonds and/or angles "reax/c/bonds"_fix_reaxc_bonds.html - write out ReaxFF bond information @@ -335,7 +330,7 @@ accelerated styles exist. "saed/vtk"_fix_saed_vtk.html - "setforce"_fix_setforce.html - set the force on each atom "shake"_fix_shake.html - SHAKE constraints on bonds and/or angles -"shardlow"_fix_shardlow.html - +"shardlow"_fix_shardlow.html - integration of DPD equations of motion using the Shardlow splitting "smd"_fix_smd.html - "smd/adjust_dt"_fix_smd_adjust_dt.html - "smd/integrate_tlsph"_fix_smd_integrate_tlsph.html - @@ -355,7 +350,7 @@ accelerated styles exist. "temp/csld"_fix_temp_csvr.html - canonical sampling thermostat with Langevin dynamics "temp/csvr"_fix_temp_csvr.html - canonical sampling thermostat with Hamiltonian dynamics "temp/rescale"_fix_temp_rescale.html - temperature control by velocity rescaling -"temp/rescale/eff"_fix_temp_rescale_eff.html - +"temp/rescale/eff"_fix_temp_rescale_eff.html - temperature control by velocity rescaling in the electron force field model "tfmc"_fix_tfmc.html - perform force-bias Monte Carlo with time-stamped method "thermal/conductivity"_fix_thermal_conductivity.html - Muller-Plathe kinetic energy exchange for thermal conductivity calculation "ti/spring"_fix_ti_spring.html - -- GitLab From b5f19b93c24d27f90096c03e27877e57f53c5eab Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Fri, 2 Aug 2019 05:15:29 -0400 Subject: [PATCH 413/469] Step version string for next patch release --- doc/lammps.1 | 2 +- doc/src/Manual.txt | 4 ++-- src/version.h | 2 +- 3 files changed, 4 insertions(+), 4 deletions(-) diff --git a/doc/lammps.1 b/doc/lammps.1 index 9a3d7e78c8..6539b85af9 100644 --- a/doc/lammps.1 +++ b/doc/lammps.1 @@ -1,4 +1,4 @@ -.TH LAMMPS "31 July 2019" "2019-07-31" +.TH LAMMPS "2 August 2019" "2019-08-02" .SH NAME .B LAMMPS \- Molecular Dynamics Simulator. diff --git a/doc/src/Manual.txt b/doc/src/Manual.txt index 927ee780e4..85828f1d90 100644 --- a/doc/src/Manual.txt +++ b/doc/src/Manual.txt @@ -1,7 +1,7 @@ LAMMPS Users Manual - + @@ -21,7 +21,7 @@ :line LAMMPS Documentation :c,h1 -31 Jul 2019 version :c,h2 +2 Aug 2019 version :c,h2 "What is a LAMMPS version?"_Manual_version.html diff --git a/src/version.h b/src/version.h index 9007966450..b74aa30172 100644 --- a/src/version.h +++ b/src/version.h @@ -1 +1 @@ -#define LAMMPS_VERSION "31 Jul 2019" +#define LAMMPS_VERSION "2 Aug 2019" -- GitLab From 8fd28cd78d24bb2a3e7a126ad0614e03f1f42cfa Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Fri, 2 Aug 2019 08:40:59 -0400 Subject: [PATCH 414/469] fix typo --- doc/src/fix_rhok.txt | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/doc/src/fix_rhok.txt b/doc/src/fix_rhok.txt index f013ebfae1..7f0a72d1b3 100644 --- a/doc/src/fix_rhok.txt +++ b/doc/src/fix_rhok.txt @@ -39,8 +39,8 @@ An example of using the interface pinning method is located in the [Restrictions:] -This fix is part of the MISC package. It is only enabled if LAMMPS -was built with that package. See the "Build +This fix is part of the USER-MISC package. It is only enabled if +LAMMPS was built with that package. See the "Build package"_Build_package.html doc page for more info. [Related commands:] -- GitLab From 9ed43e55f090ffef11cd71ea45f88cda2b57b371 Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Fri, 2 Aug 2019 08:41:34 -0400 Subject: [PATCH 415/469] add some more descriptions for fixes to list of style in fix command docs --- doc/src/fix.txt | 62 ++++++++++++++++++++++++------------------------- 1 file changed, 31 insertions(+), 31 deletions(-) diff --git a/doc/src/fix.txt b/doc/src/fix.txt index c64d61d949..409fde3503 100644 --- a/doc/src/fix.txt +++ b/doc/src/fix.txt @@ -165,9 +165,9 @@ page are followed by one or more of (g,i,k,o,t) to indicate which accelerated styles exist. "adapt"_fix_adapt.html - change a simulation parameter over time -"adapt/fep"_fix_adapt_fep.html - +"adapt/fep"_fix_adapt_fep.html - enhanced version of fix adapt "addforce"_fix_addforce.html - add a force to each atom -"addtorque"_fix_addtorque.html - +"addtorque"_fix_addtorque.html - add a torque to a group of atoms "append/atoms"_fix_append_atoms.html - append atoms to a running simulation "atc"_fix_atc.html - initiates a coupled MD/FE simulation "atom/swap"_fix_atom_swap.html - Monte Carlo atom type swapping @@ -176,29 +176,29 @@ accelerated styles exist. "ave/correlate"_fix_ave_correlate.html - compute/output time correlations "ave/correlate/long"_fix_ave_correlate_long.html - "ave/histo"_fix_ave_histo.html - compute/output time-averaged histograms -"ave/histo/weight"_fix_ave_histo.html - +"ave/histo/weight"_fix_ave_histo.html - weighted version of fix ave/histo "ave/time"_fix_ave_time.html - compute/output global time-averaged quantities "aveforce"_fix_aveforce.html - add an averaged force to each atom "balance"_fix_balance.html - perform dynamic load-balancing -"bocs"_fix_bocs.html - +"bocs"_fix_bocs.html - NPT style time integration with pressure correction "bond/break"_fix_bond_break.html - break bonds on the fly "bond/create"_fix_bond_create.html - create bonds on the fly -"bond/react"_fix_bond_react.html - +"bond/react"_fix_bond_react.html - apply topology changes to model reactions "bond/swap"_fix_bond_swap.html - Monte Carlo bond swapping "box/relax"_fix_box_relax.html - relax box size during energy minimization -"client/md"_fix_client_md.html - +"client/md"_fix_client_md.html - MD client for client/server simulations "cmap"_fix_cmap.html - enables CMAP cross-terms of the CHARMM force field "colvars"_fix_colvars.html - interface to the collective variables “Colvars” library -"controller"_fix_controller.html - +"controller"_fix_controller.html - apply control loop feedback mechanism "deform"_fix_deform.html - change the simulation box size/shape "deposit"_fix_deposit.html - add new atoms above a surface "dpd/energy"_fix_dpd_energy.html - constant energy dissipative particle dynamics "drag"_fix_drag.html - drag atoms towards a defined coordinate -"drude"_fix_drude.html - -"drude/transform/direct"_fix_drude_transform.html - -"drude/transform/inverse"_fix_drude_transform.html - +"drude"_fix_drude.html - part of Drude oscillator polarization model +"drude/transform/direct"_fix_drude_transform.html - part of Drude oscillator polarization model +"drude/transform/inverse"_fix_drude_transform.html - part of Drude oscillator polarization model "dt/reset"_fix_dt_reset.html - reset the timestep based on velocity, forces -"edpd/source"_fix_dpd_source.html - +"edpd/source"_fix_dpd_source.html - add heat source to eDPD simulations "efield"_fix_efield.html - impose electric field on system "ehex"_fix_ehex.html - enhanced heat exchange algorithm "electron/stopping"_fix_electron_stopping.html - electronic stopping power as a friction force @@ -209,8 +209,8 @@ accelerated styles exist. "evaporate"_fix_evaporate.html - remove atoms from simulation periodically "external"_fix_external.html - callback to an external driver program "ffl"_fix_ffl.html - apply a Fast-Forward Langevin equation thermostat -"filter/corotate"_fix_filter_corotate.html - -"flow/gauss"_fix_flow_gauss.html - +"filter/corotate"_fix_filter_corotate.html - implement corotation filter to allow larger timesteps with r-RESPA +"flow/gauss"_fix_flow_gauss.html - Gaussian dynamics for constant mass flux "freeze"_fix_freeze.html - freeze atoms in a granular simulation "gcmc"_fix_gcmc.html - grand canonical insertions/deletions "gld"_fix_gld.html - generalized Langevin dynamics integrator @@ -223,7 +223,7 @@ accelerated styles exist. "hyper/local"_fix_hyper_local.html - local hyperdynamics "imd"_fix_imd.html - implements the “Interactive MD” (IMD) protocol "indent"_fix_indent.html - impose force due to an indenter -"ipi"_fix_ipi.html - +"ipi"_fix_ipi.html - enable LAMMPS to run as a client for i-PI path-integral simulations "langevin"_fix_langevin.html - Langevin temperature control "langevin/drude"_fix_langevin_drude.html - Langevin temperature control of Drude oscillators "langevin/eff"_fix_langevin_eff.html - Langevin temperature control for the electron force field model @@ -235,13 +235,13 @@ accelerated styles exist. "lb/rigid/pc/sphere"_fix_lb_rigid_pc_sphere.html - "lb/viscous"_fix_lb_viscous.html - "lineforce"_fix_lineforce.html - constrain atoms to move in a line -"manifoldforce"_fix_manifoldforce.html - -"meso"_fix_meso.html - +"manifoldforce"_fix_manifoldforce.html - restrain atoms to a manifold during minimization +"meso"_fix_meso.html - time integration for SPH/DPDE particles "meso/move"_fix_meso_move.html - move mesoscopic SPH/SDPD particles in a prescribed fashion "meso/stationary"_fix_meso_stationary.html - "momentum"_fix_momentum.html - zero the linear and/or angular momentum of a group of atoms "move"_fix_move.html - move atoms in a prescribed fashion -"mscg"_fix_mscg.html - +"mscg"_fix_mscg.html - apply MSCG method for force-matching to generate coarse grain models "msst"_fix_msst.html - multi-scale shock technique (MSST) integration "mvv/dpd"_fix_mvv_dpd.html - DPD using the modified velocity-Verlet integration algorithm "mvv/edpd"_fix_mvv_dpd.html - constant energy DPD using the modified velocity-Verlet algrithm @@ -258,14 +258,14 @@ accelerated styles exist. "npt/body"_fix_npt_body.html - NPT for body particles "npt/eff"_fix_nh_eff.html - NPT for nuclei and electrons in the electron force field model "npt/sphere"_fix_npt_sphere.html - NPT for spherical particles -"npt/uef"_fix_nh_uef.html - +"npt/uef"_fix_nh_uef.html - NPT style time integration with diagonal flow "nve"_fix_nve.html - constant NVE time integration "nve/asphere"_fix_nve_asphere.html - NVE for aspherical particles "nve/asphere/noforce"_fix_nve_asphere_noforce.html - NVE for aspherical particles without forces "nve/awpmd"_fix_nve_awpmd.html - NVE for the Antisymmetrized Wave Packet Molecular Dynamics model "nve/body"_fix_nve_body.html - NVE for body particles -"nve/dot"_fix_nve_dot.html - -"nve/dotc/langevin"_fix_nve_dotc_langevin.html - +"nve/dot"_fix_nve_dot.html - rigid body constant energy time integrator for coarse grain models +"nve/dotc/langevin"_fix_nve_dotc_langevin.html - Langevin style rigid body time integrator for coarse grain models "nve/eff"_fix_nve_eff.html - NVE for nuclei and electrons in the electron force field model "nve/limit"_fix_nve_limit.html - NVE with limited step length "nve/line"_fix_nve_line.html - NVE for line segments @@ -283,11 +283,11 @@ accelerated styles exist. "nvt/sllod"_fix_nvt_sllod.html - NVT for NEMD with SLLOD equations "nvt/sllod/eff"_fix_nvt_sllod_eff.html - NVT for NEMD with SLLOD equations for the electron force field model "nvt/sphere"_fix_nvt_sphere.html - NVT for spherical particles -"nvt/uef"_fix_nh_uef.html - +"nvt/uef"_fix_nh_uef.html - NVT style time integration with diagonal flow "oneway"_fix_oneway.html - constrain particles on move in one direction "orient/bcc"_fix_orient.html - add grain boundary migration force for BCC "orient/fcc"_fix_orient.html - add grain boundary migration force for FCC -"phonon"_fix_phonon.html - +"phonon"_fix_phonon.html - calculate dynamical matrix from MD simulations "pimd"_fix_pimd.html - Feynman path integral molecular dynamics "planeforce"_fix_planeforce.html - constrain atoms to move in a plane "plumed"_fix_plumed.html - wrapper on PLUMED free energy library @@ -297,9 +297,9 @@ accelerated styles exist. "press/berendsen"_fix_press_berendsen.html - pressure control by Berendsen barostat "print"_fix_print.html - print text and variables during a simulation "property/atom"_fix_property_atom.html - add customized per-atom values -"python/invoke"_fix_python_invoke.html - +"python/invoke"_fix_python_invoke.html - call a Python function during a simulation "python/move"_fix_python_move.html - call a Python function during a simulation run -"qbmsst"_fix_qbmsst.html - +"qbmsst"_fix_qbmsst.html - quantum bath multi-scale shock technique time integrator "qeq/comb"_fix_qeq_comb.html - charge equilibration for COMB potential "qeq/dynamic"_fix_qeq.html - charge equilibration via dynamic method "qeq/fire"_fix_qeq.html - charge equilibration via FIRE minimizer @@ -308,13 +308,13 @@ accelerated styles exist. "qeq/shielded"_fix_qeq.html - charge equilibration via shielded method "qeq/slater"_fix_qeq.html - charge equilibration via Slater method "qmmm"_fix_qmmm.html - functionality to enable a quantum mechanics/molecular mechanics coupling -"qtb"_fix_qtb.html - +"qtb"_fix_qtb.html - implement quantum thermal bath scheme "rattle"_fix_shake.html - RATTLE constraints on bonds and/or angles "reax/c/bonds"_fix_reaxc_bonds.html - write out ReaxFF bond information "reax/c/species"_fix_reaxc_species.html - write out ReaxFF molecule information "recenter"_fix_recenter.html - constrain the center-of-mass position of a group of atoms "restrain"_fix_restrain.html - constrain a bond, angle, dihedral -"rhok"_fix_rhok.html - +"rhok"_fix_rhok.html - add bias potential for long-range ordered systems "rigid"_fix_rigid.html - constrain one or more clusters of atoms to move as a rigid body with NVE integration "rigid/meso"_fix_rigid_meso.html - constrain clusters of mesoscopic SPH/SDPD particles to move as a rigid body "rigid/nph"_fix_rigid.html - constrain one or more clusters of atoms to move as a rigid body with NPH integration @@ -327,11 +327,11 @@ accelerated styles exist. "rigid/nvt/small"_fix_rigid.html - constrain many small clusters of atoms to move as a rigid body with NVT integration "rigid/small"_fix_rigid.html - constrain many small clusters of atoms to move as a rigid body with NVE integration "rx"_fix_rx.html - -"saed/vtk"_fix_saed_vtk.html - +"saed/vtk"_fix_saed_vtk.html - "setforce"_fix_setforce.html - set the force on each atom "shake"_fix_shake.html - SHAKE constraints on bonds and/or angles "shardlow"_fix_shardlow.html - integration of DPD equations of motion using the Shardlow splitting -"smd"_fix_smd.html - +"smd"_fix_smd.html - applied a steered MD force to a group "smd/adjust_dt"_fix_smd_adjust_dt.html - "smd/integrate_tlsph"_fix_smd_integrate_tlsph.html - "smd/integrate_ulsph"_fix_smd_integrate_ulsph.html - @@ -356,7 +356,7 @@ accelerated styles exist. "ti/spring"_fix_ti_spring.html - "tmd"_fix_tmd.html - guide a group of atoms to a new configuration "ttm"_fix_ttm.html - two-temperature model for electronic/atomic coupling -"ttm/mod"_fix_ttm.html - +"ttm/mod"_fix_ttm.html - enhanced two-temperature model with additional options "tune/kspace"_fix_tune_kspace.html - auto-tune KSpace parameters "vector"_fix_vector.html - accumulate a global vector every N timesteps "viscosity"_fix_viscosity.html - Muller-Plathe momentum exchange for viscosity calculation @@ -364,7 +364,7 @@ accelerated styles exist. "wall/body/polygon"_fix_wall_body_polygon.html - "wall/body/polyhedron"_fix_wall_body_polyhedron.html - "wall/colloid"_fix_wall.html - Lennard-Jones wall interacting with finite-size particles -"wall/ees"_fix_wall_ees.html - +"wall/ees"_fix_wall_ees.html - wall for ellipsoidal particles "wall/gran"_fix_wall_gran.html - frictional wall(s) for granular simulations "wall/gran/region"_fix_wall_gran_region.html - "wall/harmonic"_fix_wall.html - harmonic spring wall @@ -374,7 +374,7 @@ accelerated styles exist. "wall/piston"_fix_wall_piston.html - moving reflective piston wall "wall/reflect"_fix_wall_reflect.html - reflecting wall(s) "wall/region"_fix_wall_region.html - use region surface as wall -"wall/region/ees"_fix_wall_ees.html - +"wall/region/ees"_fix_wall_ees.html - use region surface as wall for ellipsoidal particles "wall/srd"_fix_wall_srd.html - slip/no-slip wall for SRD particles :ul [Restrictions:] -- GitLab From d750cc02c0518739bc2f2ad4c1c4552d644cfe63 Mon Sep 17 00:00:00 2001 From: Anne Gunn Date: Wed, 31 Jul 2019 14:26:21 -0600 Subject: [PATCH 416/469] Changed the code in the read_F_table function to conform to the "expected behavior" description in #1572. Adopted a best-of-both-worlds approach, though, and processed the whole input file all the way through, emitting a message for each problem found, before issuing a final error message to stop processing. Updated doc to clarify requirement for uniform spacing of pressure correction points. --- doc/src/fix_bocs.txt | 4 +- src/USER-BOCS/fix_bocs.cpp | 76 +++++++++++++++++++++++++++++--------- 2 files changed, 60 insertions(+), 20 deletions(-) diff --git a/doc/src/fix_bocs.txt b/doc/src/fix_bocs.txt index db9c35069c..bb7ac3713c 100644 --- a/doc/src/fix_bocs.txt +++ b/doc/src/fix_bocs.txt @@ -47,13 +47,13 @@ or {cubic_spline}. With either spline method, the only argument that needs to follow it is the name of a file that contains the desired pressure correction -as a function of volume. The file should be formatted so each line has: +as a function of volume. The file must be formatted so each line has: Volume_i, PressureCorrection_i :pre Note both the COMMA and the SPACE separating the volume's value and its corresponding pressure correction. The volumes in the file -should be uniformly spaced. Both the volumes and the pressure corrections +must be uniformly spaced. Both the volumes and the pressure corrections should be provided in the proper units, e.g. if you are using {units real}, the volumes should all be in cubic angstroms, and the pressure corrections should all be in atmospheres. Furthermore, the table should start/end at a diff --git a/src/USER-BOCS/fix_bocs.cpp b/src/USER-BOCS/fix_bocs.cpp index 936e5ff58e..adce231bf1 100644 --- a/src/USER-BOCS/fix_bocs.cpp +++ b/src/USER-BOCS/fix_bocs.cpp @@ -59,6 +59,9 @@ enum{NOBIAS,BIAS}; enum{NONE,XYZ,XY,YZ,XZ}; enum{ISO,ANISO,TRICLINIC}; +// NB: Keep error and warning messages less than 255 chars long. +const int MAX_MESSAGE_LENGTH = 256; + /* ---------------------------------------------------------------------- NVT,NPH,NPT integrators for improved Nose-Hoover equations of motion ---------------------------------------------------------------------- */ @@ -630,24 +633,32 @@ int FixBocs::read_F_table( char *filename, int p_basis_type ) double **data = (double **) calloc(N_columns,sizeof(double *)); char * line = (char *) calloc(200,sizeof(char)); + bool badInput = false; + char badDataMsg[MAX_MESSAGE_LENGTH]; fpi = fopen(filename,"r"); if (fpi) { while (fgets(line,199,fpi)) { ++n_entries; } - fclose(fpi); + for (i = 0; i < N_columns; ++i) { data[i] = (double *) calloc(n_entries,sizeof(double)); } - } else { - char errmsg[128]; - snprintf(errmsg,128,"Unable to open file: %s\n",filename); - error->all(FLERR,errmsg); - } - n_entries = 0; - fpi = fopen(filename,"r"); - if (fpi) { + // Don't need to re-open the file to make a second pass through it + // simply rewind to beginning + rewind(fpi); + + double stdVolumeInterval = 0.0; + double currVolumeInterval = 0.0; + // When comparing doubles/floats, we need an Epsilon. + // The literature indicates getting this value right in the + // general case can be pretty complicated. I don't think it + // needs to be complicated here, though. At least based on the + // sample data I've seen where the volume values are fairly + // large. + const double volumeIntervalTolerance = 0.001; + n_entries = 0; while( fgets(line,199,fpi)) { ++n_entries; test_sscanf = sscanf(line," %f , %f ",&f1, &f2); @@ -655,19 +666,47 @@ int FixBocs::read_F_table( char *filename, int p_basis_type ) { data[0][n_entries-1] = (double) f1; data[1][n_entries-1] = (double) f2; + if (n_entries == 2) { + stdVolumeInterval = data[0][n_entries-1] - data[0][n_entries-2]; + } + else if (n_entries > 2) { + currVolumeInterval = data[0][n_entries-1] - data[0][n_entries-2]; + if (fabs(currVolumeInterval - stdVolumeInterval) > volumeIntervalTolerance) { + snprintf(badDataMsg,MAX_MESSAGE_LENGTH, + "BAD VOLUME INTERVAL: spline analysis requires uniform" + " volume distribution, found inconsistent volume" + " differential, line %d of file %s\n\tline: %s", + n_entries,filename,line); + error->message(FLERR,badDataMsg); + badInput = true; + } + } + // no else -- first entry is simply ignored } else { - fprintf(stderr,"WARNING: did not find 2 comma separated values in " - "line %d of file %s\n\tline: %s",n_entries,filename,line); + snprintf(badDataMsg,MAX_MESSAGE_LENGTH, + "BAD INPUT FORMAT: did not find 2 comma separated numeric" + " values in line %d of file %s\n\tline: %s", + n_entries,filename,line); + error->message(FLERR,badDataMsg); + badInput = true; } } - } else { - char errmsg[128]; - snprintf(errmsg,128,"Unable to open file: %s\n",filename); + fclose(fpi); + } + else { + char errmsg[MAX_MESSAGE_LENGTH]; + snprintf(errmsg,MAX_MESSAGE_LENGTH,"Unable to open file: %s\n",filename); + error->all(FLERR,errmsg); + } + + if (badInput) { + char errmsg[MAX_MESSAGE_LENGTH]; + snprintf(errmsg,MAX_MESSAGE_LENGTH, + "Bad volume / pressure-correction data: %s\nSee details above",filename); error->all(FLERR,errmsg); } - fclose(fpi); if (p_basis_type == 1) { @@ -691,9 +730,10 @@ int FixBocs::read_F_table( char *filename, int p_basis_type ) } else { - char * errmsg = (char *) calloc(70,sizeof(char)); - sprintf(errmsg,"ERROR: invalid p_basis_type value " - "of %d in read_F_table",p_basis_type); + char errmsg[MAX_MESSAGE_LENGTH]; + snprintf(errmsg, MAX_MESSAGE_LENGTH, + "ERROR: invalid p_basis_type value of %d in read_F_table", + p_basis_type); error->all(FLERR,errmsg); } // cleanup -- GitLab From eb7fa1b6cb6a545fc80a2f84c10b751d75bb5823 Mon Sep 17 00:00:00 2001 From: Richard Berger Date: Fri, 2 Aug 2019 17:04:59 -0400 Subject: [PATCH 417/469] Update CMake documentation --- cmake/README.md | 654 +++++++++++++++++++++++++++++----- doc/src/Build.txt | 1 + doc/src/Build_basics.txt | 24 ++ doc/src/Build_cmake.txt | 2 +- doc/src/Build_development.txt | 86 +++++ doc/src/Build_extras.txt | 6 +- doc/src/Packages_details.txt | 4 +- 7 files changed, 691 insertions(+), 86 deletions(-) create mode 100644 doc/src/Build_development.txt diff --git a/cmake/README.md b/cmake/README.md index c11326f9d5..95b2dd7447 100644 --- a/cmake/README.md +++ b/cmake/README.md @@ -33,12 +33,17 @@ tasks, act as a reference and provide examples of typical use cases. * [Package-Specific Configuration Options](#package-specific-configuration-options) * [KSPACE Package](#kspace-package) * [MKL](#mkl) - * [FFTW2](#fftw2) * [FFTW3](#fftw3) + * [BLAS](#blas) * [LAPACK](#lapack) * [PYTHON Package](#python-package) * [GPU Package](#gpu-package) + * [MESSAGE Package](#message-package) + * [MSCG Package](#mscg-package) * [VORONOI Package](#voronoi-package) + * [USER-LATTE Package](#user-latte-package) + * [USER-PLUMED Package](#user-plumed-package) + * [USER-SCAFACOS Package](#user-scafacos-package) * [USER-SMD Package](#user-smd-package) * [Optional Features](#optional-features) * [zlib support](#zlib-support) @@ -50,8 +55,6 @@ tasks, act as a reference and provide examples of typical use cases. * [Building with GNU Compilers](#building-with-gnu-compilers) * [Building with Intel Compilers](#building-with-intel-compilers) * [Building with LLVM/Clang Compilers](#building-with-llvmclang-compilers) - * [Examples](#examples) - ## Quick Start for the Impatient If you want to skip ahead and just run the compilation using `cmake`, please @@ -205,8 +208,10 @@ cmake -C ../cmake/presets/all_on.cmake -C ../cmake/presets/nolib.cmake -D PKG_GP Controls if debugging symbols are added to the generated binaries

-
Release (default)
+
RelWithDebInfo (default)
+
Release
Debug
+
MinSizeRel
@@ -249,6 +254,16 @@ cmake -C ../cmake/presets/all_on.cmake -C ../cmake/presets/nolib.cmake -D PKG_GP + + LAMMPS_LONGLONG_TO_LONG + Workaround if your system or MPI version does not recognize long long data types + +
+
off (default)
+
on
+
+ + LAMMPS_MEMALIGN controls the alignment of blocks of memory allocated by LAMMPS @@ -319,8 +334,8 @@ cmake -C ../cmake/presets/all_on.cmake -C ../cmake/presets/nolib.cmake -D PKG_GP - LAMMPS_LONGLONG_TO_LONG - Workaround if your system or MPI version does not recognize long long data types + BUILD_TOOLS + control whether to build LAMMPS tools
off (default)
@@ -561,23 +576,6 @@ cmake -C ../cmake/presets/all_on.cmake -C ../cmake/presets/nolib.cmake -D PKG_GP
- - PKG_MEAM - -

A pair style for the modified embedded atom (MEAM) potential.

- -

Please note that the MEAM package has been superseded by the USER-MEAMC package, -which is a direct translation of the MEAM package to C++. USER-MEAMC contains -additional optimizations making it run faster than MEAM on most machines, while -providing the identical features and USER interface.

- - -
-
off (default)
-
on
-
- - PKG_MISC @@ -634,21 +632,6 @@ providing the identical features and USER interface.

- - PKG_REAX - - A pair style which wraps a Fortran library which implements the ReaxFF - potential, which is a universal reactive force field. See the USER-REAXC - package for an alternate implementation in C/C++. Also a fix reax/bonds - command for monitoring molecules as bonds are created and destroyed. - - -
-
off (default)
-
on
-
- - PKG_REPLICA @@ -695,6 +678,16 @@ providing the identical features and USER interface.

+ + PKG_SPIN + Model atomic magnetic spins classically, coupled to atoms moving in the usual manner via MD. Various pair, fix, and compute styles. + +
+
off (default)
+
on
+
+ + PKG_SNAP @@ -757,6 +750,16 @@ providing the identical features and USER interface.

+ + PKG_MESSAGE + Commands to use LAMMPS as either a client or server and couple it to another application. + +
+
off (default)
+
on
+
+ + PKG_MSCG @@ -811,6 +814,18 @@ providing the identical features and USER interface.

+ + PKG_VORONOI + + A compute command which calculates the Voronoi tesselation of a collection of atoms by wrapping the Voro++ library. This can be used to calculate the local volume or each atoms or its near neighbors. + + +
+
off (default)
+
on
+
+ + @@ -825,6 +840,16 @@ providing the identical features and USER interface.

+ + PKG_USER-ADIOS + ADIOS is a high-performance I/O library. This package implements the dump “atom/adios” and dump “custom/adios” commands to write data using the ADIOS library. + +
+
off (default)
+
on
+
+ + PKG_USER-ATC @@ -853,6 +878,18 @@ providing the identical features and USER interface.

+ + PKG_USER-BOCS + + This package provides fix bocs, a modified version of fix npt which includes the pressure correction to the barostat as outlined in: N. J. H. Dunn and W. G. Noid, “Bottom-up coarse-grained models that accurately describe the structure, pressure, and compressibility of molecular liquids,” J. Chem. Phys. 143, 243148 (2015). + + +
+
off (default)
+
on
+
+ + PKG_USER-CGDNA @@ -1142,6 +1179,30 @@ providing the identical features and USER interface.

+ + PKG_USER-PLUMED + + The fix plumed command allows you to use the PLUMED free energy plugin for molecular dynamics to analyze and bias your LAMMPS trajectory on the fly. The PLUMED library is called from within the LAMMPS input script by using the fix plumed command. + + +
+
off (default)
+
on
+
+ + + + PKG_USER-PTM + + A compute ptm/atom command that calculates local structure characterization using the Polyhedral Template Matching methodology. + + +
+
off (default)
+
on
+
+ + PKG_USER-QTB @@ -1197,6 +1258,33 @@ providing the identical features and USER interface.

+ + PKG_USER-SCAFACOS + + A KSpace style which wraps the ScaFaCoS Coulomb solver library to compute long-range Coulombic interactions. + + +
+
off (default)
+
on
+
+ + + + PKG_USER-SDPD + + A pair style for smoothed dissipative particle dynamics (SDPD), which is an + extension of smoothed particle hydrodynamics (SPH) to mesoscale where thermal + fluctuations are important (see the USER-SPH package). Also two fixes for + moving and rigid body integration of SPH/SDPD particles (particles of + atom_style meso). + +
+
off (default)
+
on
+
+ + PKG_USER-SMD @@ -1280,6 +1368,23 @@ providing the identical features and USER interface.

+ + PKG_USER-YAFF + + Some potentials that are also implemented in the Yet Another Force Field (YAFF) code. + The expressions and their use are discussed in the following papers: + + + +
+
off (default)
+
on
+
+ + @@ -1300,14 +1405,27 @@ providing the identical features and USER interface.

FFT

FFT library for KSPACE package

-

If either MKL or FFTW is selected cmake will try to locate these libraries automatically. To control which one should be used please see the options below for each FFT library.

+

If either MKL or FFTW is selected cmake will try to locate + these libraries automatically. To control which one should be used please see + the options below for each FFT library. Otherwise it will default to KISS + FFT.

-
KISS
FFTW3
FFTW2
MKL
+
KISS (default)
+
+ + + + FFT_SINGLE + Use single-precision floating-point in FFT + +
+
off (default = double precision)
+
on
@@ -1325,7 +1443,7 @@ providing the identical features and USER interface.

-### MKL +### FFTW3 @@ -1337,23 +1455,21 @@ providing the identical features and USER interface.

- - + + - - + +
MKL_INCLUDE_DIRSFFTW3_INCLUDE_DIRSpath to FFTW3 include files
MKL_LIBRARIESFFTW3_LIBRARIESlist of paths to FFTW3 libraries
-TODO static vs dynamic linking - -### FFTW2 +### MKL @@ -1365,51 +1481,32 @@ TODO static vs dynamic linking - - + + - - + +
FFTW2_INCLUDE_DIRSMKL_INCLUDE_DIRSpath to MKL include files
FFTW2_LIBRARIESMKL_LIBRARIESlist of paths to MKL libraries
-### FFTW3 +### BLAS - - - - - - - - - - - - - - - - - - - - -
OptionDescriptionValues
FFTW3_INCLUDE_DIRS -
FFTW3_LIBRARIES -
+See [FindBLAS documentation](https://cmake.org/cmake/help/latest/module/FindBLAS.html) ### LAPACK -TODO + +See [FindLAPACK documentation](https://cmake.org/cmake/help/latest/module/FindLAPACK.html) ### PYTHON Package +See [FindPYTHON documentation](https://cmake.org/cmake/help/latest/module/FindPython.html) + ### USER-INTEL Package @@ -1499,10 +1596,11 @@ target API. @@ -1534,13 +1632,273 @@ target API.
sm_20 (Fermi)
-
sm_30 (Kepler)
+
sm_30 (Kepler) (default)
sm_50 (Maxwell)
sm_60 (Pascal)
sm_70 (Volta)
+
sm_75 (Turing)
+### KIM Package + +Requires installation of the KIM library with API v2 + +If `DOWNLOAD_KIM` is set, the KIM library will be downloaded and built inside +the CMake build directory. If the KIM library is already on your system (in a +location CMake cannot find it), set the `PKG_CONFIG_PATH` environment variable +so that `libkim-api` can be found. + + + + + + + + + + + + + + + + +
OptionDescriptionValues
DOWNLOAD_KIMDownload KIM API v2 and compile it as part of the build. +
+
off (default)
+
on
+
+
+ +### MESSAGE Package + +This package can optionally include support for messaging via sockets, using the open-source [ZeroMQ library](http://zeromq.org/), which must be installed on your system. + + + + + + + + + + + + + + + + + + + + + + + + + + +
OptionDescriptionValues
MESSAGE_ZMQBuild with ZeroMQ support +
+
off (default)
+
on
+
+
ZMQ_LIBRARY + ZMQ library file (only needed if at custom location) + +
ZMG_INCLUDE_DIR + Provide include directory of existing ZMQ installation (only needed if at custom location) + +
+ +### MSCG Package + +Requires installation of the MSCG library + + + + + + + + + + + + + + + + + + + + + + + + + + +
OptionDescriptionValues
DOWNLOAD_MSCGDownload MSCG and compile it as part of the build +
+
off (default)
+
on
+
+
MSCG_LIBRARY + MSCG library file (only needed if at custom location) + +
MSCG_INCLUDE_DIR + Provide include directory of existing MSCG installation (only needed if at custom location) + +
+ ### VORONOI Package -TODO +Requires installation of the Voro++ library + + + + + + + + + + + + + + + + + + + + + + + + + + +
OptionDescriptionValues
DOWNLOAD_VORODownload Voro++ and compile it as part of the build +
+
off (default)
+
on
+
+
VORO_LIBRARY + Voro++ library file (only needed if at custom location) + +
VORO_INCLUDE_DIR + Provide include directory of existing Voro++ installation (only needed if at custom location) + +
+ +### USER-LATTE Package + +Requires installation of the LATTE library + + + + + + + + + + + + + + + + + + + + + +
OptionDescriptionValues
DOWNLOAD_LATTEDownload LATTE and compile it as part of the build +
+
off (default)
+
on
+
+
LATTE_LIBRARY + LATTE library file (only needed if at custom location) + +
+ +### USER-PLUMED Package + +Requires installation of the PLUMED library + + + + + + + + + + + + + + + + + + + + + +
OptionDescriptionValues
DOWNLOAD_PLUMEDDownload PLUMED and compile it as part of the build +
+
off (default)
+
on
+
+
PLUMED_MODE + Determines the linkage mode for the PLUMED library. + +
+
static (default)
+
shared
+
runtime
+
+
+ +### USER-LATTE Package + +Requires installation of the LATTE library + + + + + + + + + + + + + + + + + + + + + +
OptionDescriptionValues
DOWNLOAD_LATTEDownload LATTE and compile it as part of the build +
+
off (default)
+
on
+
+
LATTE_LIBRARY + LATTE library file (only needed if at custom location) + +
### USER-SMD Package -Requires a Eigen3 installation +Requires installation of the Eigen3 library @@ -1551,9 +1909,64 @@ Requires a Eigen3 installation + + + + + - + + + + +
DOWNLOAD_EIGEN3Download Eigen3 and compile it as part of the build +
+
off (default)
+
on
+
+
EIGEN3_INCLUDE_DIR + Provide include directory of existing Eigen3 installation (only needed if at custom location) + +
+ + +### USER-SCAFACOS Package + +To build with this package, you must download and build the [ScaFaCoS Coulomb solver library](http://www.scafacos.de/) + + + + + + + + + + + + + + + + + + + + + + + @@ -1791,5 +2204,82 @@ cmake -D CMAKE_C_COMPILER=icc -D CMAKE_CXX_COMPILER=icpc -D CMAKE_Fortran_COMPIL cmake -D CMAKE_C_COMPILER=clang -D CMAKE_CXX_COMPILER=clang++ -D CMAKE_Fortran_COMPILER=flang ../cmake ``` +## LAMMPS Developer Options + -## Examples +
OptionDescriptionValues
DOWNLOAD_SCAFACOSDownload SCAFACOS and compile it as part of the build +
+
off (default)
+
on
+
+
SCAFACOS_LIBRARY + SCAFACOS library file (only needed if at custom location) + +
SCAFACOS_INCLUDE_DIR + SCAFACOS include directory (only needed if at custom location) +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
OptionDescriptionValues
ENABLE_TESTINGControl wheather to add tests via CTest +
+
off (default)
+
on
+
+
LAMMPS_TESTING_SOURCE_DIRCustom location of lammps-testing repository (optional). If not specified it will download it via Git +
LAMMPS_TESTING_GIT_TAGIf lammps-testing repository is cloned, this is the tag/commit that will be checked out +
+
master (default)
+
+
ENABLE_COVERAGEEnables code coverage support via gcov and adds a gcovr build target to generate a coverage report. +
+
off (default)
+
on
+
+
ENABLE_SANITIZE_ADDRESSEnables Address Sanitizer support when compiling using GCC or Clang for detecting memory leaks in binaries while running them. See https://clang.llvm.org/docs/AddressSanitizer.html +
+
off (default)
+
on
+
+
ENABLE_SANITIZE_UNDEFINEDEnables Undefined Behavior Sanitizer support when compiling using GCC or Clang for detecting code that is running into undefined behavior of the language. See https://clang.llvm.org/docs/UndefinedBehaviorSanitizer.html +
+
off (default)
+
on
+
+
ENABLE_SANITIZE_THREADEnables Thread Sanitizer support when compiling using GCC or Clang for detecting data races in binaries while running them. See https://clang.llvm.org/docs/ThreadSanitizer.html +
+
off (default)
+
on
+
+
diff --git a/doc/src/Build.txt b/doc/src/Build.txt index df30af36f5..50d62ac889 100644 --- a/doc/src/Build.txt +++ b/doc/src/Build.txt @@ -29,6 +29,7 @@ as described on the "Install"_Install.html doc page. Build_package Build_extras Build_windows + Build_development END_RST --> diff --git a/doc/src/Build_basics.txt b/doc/src/Build_basics.txt index fa4ef12586..411e7858ac 100644 --- a/doc/src/Build_basics.txt +++ b/doc/src/Build_basics.txt @@ -310,6 +310,30 @@ current LAMMPS version (HTML and PDF files), from the website :line +Build LAMMPS tools :h4,link(tools) + +Some tools described in "Auxiliary tools"_Tools.html can be built directly +using CMake or Make. + +[CMake variable]: + +-D BUILD_TOOLS=value # yes or no (default) :pre + +The generated binaries will also become part of the LAMMPS installation (see below) + +[Traditional make]: + +cd lammps/tools +make all # build all binaries of tools +make binary2txt # build only binary2txt tool +make chain # build only chain tool +make micelle2d # build only micelle2d tool +make thermo_extract # build only thermo_extract tool +:pre + +:line + + Install LAMMPS after a build :h4,link(install) After building LAMMPS, you may wish to copy the LAMMPS executable of diff --git a/doc/src/Build_cmake.txt b/doc/src/Build_cmake.txt index 6eb23b2bb5..b2411272eb 100644 --- a/doc/src/Build_cmake.txt +++ b/doc/src/Build_cmake.txt @@ -120,7 +120,7 @@ The argument can be preceeded or followed by various CMake command-line options. Several useful ones are: -D CMAKE_INSTALL_PREFIX=path # where to install LAMMPS executable/lib if desired --D CMAKE_BUILD_TYPE=type # type = Release or Debug +-D CMAKE_BUILD_TYPE=type # type = RelWithDebInfo (default), Release, MinSizeRel, or Debug -G output # style of output CMake generates -DVARIABLE=value # setting for a LAMMPS feature to enable -D VARIABLE=value # ditto, but cannot come after CMakeLists.txt dir diff --git a/doc/src/Build_development.txt b/doc/src/Build_development.txt new file mode 100644 index 0000000000..7ce4b0e8a6 --- /dev/null +++ b/doc/src/Build_development.txt @@ -0,0 +1,86 @@ +"Higher level section"_Build.html - "LAMMPS WWW Site"_lws - "LAMMPS +Documentation"_ld - "LAMMPS Commands"_lc :c + +:link(lws,http://lammps.sandia.gov) +:link(ld,Manual.html) +:link(lc,Commands_all.html) + +:line + +Development options (CMake only) :h3 + +The CMake build of LAMMPS has a few extra options which are useful during +development, testing or debugging. + +:line + +Verify compilation flags :h4,link(compilation) + +Sometimes it is necessary to verify the complete sequence of compilation flags +generated by the CMake build. To enable a more verbose output during +compilation you can use the following option. + +-D CMAKE_VERBOSE_MAKEFILE=value # value = no (default) or yes :pre + +Another way of doing this without reconfiguration is calling make with variable VERBOSE set to 1: + +make VERBOSE=1 :pre + +:line + +Address, Undefined Behavior, and Thread Sanitizer Support :h4,link(sanitizer) + +Compilers such as GCC and Clang support generating binaries which use different +sanitizers to detect problems in code during run-time. They can detect "memory leaks"_https://clang.llvm.org/docs/AddressSanitizer.html, +code that runs into "undefined behavior"_https://clang.llvm.org/docs/UndefinedBehaviorSanitizer.html of the +language and "data races"_https://clang.llvm.org/docs/ThreadSanitizer.html in threaded code. + +The following settings allow you enable these features if your compiler supports +it. Please note that they come with a performance hit. However, they are +usually faster than using tools like Valgrind. + +-D ENABLE_SANITIZE_ADDRESS=value # enable Address Sanitizer, value = no (default) or yes +-D ENABLE_SANITIZE_UNDEFINED=value # enable Undefined Behaviour Sanitizer, value = no (default) or yes +-D ENABLE_SANITIZE_THREAD=value # enable Thread Sanitizer, value = no (default) or yes +:pre + +:line + +Code Coverage and Testing :h4,link(testing) + +We do extensive regression testing of the LAMMPS code base on a continuous +basis. Some of the logic to do this has been added to the CMake build so +developers can run the tests directly on their workstation. + +NOTE: this is incomplete and only represents a small subset of tests that we run + +-D ENABLE_TESTING=value # enable simple run tests of LAMMPS, value = no (default) or yes +-D LAMMPS_TESTING_SOURCE_DIR=path # path to lammps-testing repository (option if in custom location) +-D LAMMPS_TESTING_GIT_TAG=value # version of lammps-testing repository that should be used, value = master (default) or custom git commit or tag +:pre + +If you enable testing in the CMake build it will create an additional target called "test". You can run them with: + +make test +:pre + +The test cases used come from the lammps-testing repository. They are +derivatives of the examples folder with some modifications to make the run +faster. + +You can also collect code coverage metrics while running the tests by enabling +coverage support during building. + +-D ENABLE_COVERAGE=value # enable coverage measurements, value = no (default) or yes :pre + +This will also add the following targets to generate coverage reports after running the LAMMPS executable: + +make test # run tests first! +make gen_coverage_html # generate coverage report in HTML format +make gen_coverage_xml # generate coverage report in XML format +:pre + +These reports require GCOVR to be installed. The easiest way to do this to install it via pip: + +pip install git+https://github.com/gcovr/gcovr.git :pre +:pre diff --git a/doc/src/Build_extras.txt b/doc/src/Build_extras.txt index e6791de21b..b0bf0c9cd6 100644 --- a/doc/src/Build_extras.txt +++ b/doc/src/Build_extras.txt @@ -88,7 +88,7 @@ which GPU hardware to build for. # generic (default) or intel (Intel CPU) or fermi, kepler, cypress (NVIDIA) -D GPU_ARCH=value # primary GPU hardware choice for GPU_API=cuda # value = sm_XX, see below - # default is Cuda-compiler dependent, but typically sm_20 + # default is sm_30 -D CUDPP_OPT=value # optimization setting for GPU_API=cuda # enables CUDA Performance Primitives Optimizations # value = yes (default) or no @@ -354,6 +354,9 @@ be installed on your system. [CMake build]: -D MESSAGE_ZMQ=value # build with ZeroMQ support, value = no (default) or yes +-D ZMQ_LIBRARY=path # ZMQ library file (only needed if a custom location) +-D ZMQ_INCLUDE_DIR=path # ZMQ include directory (only needed if a custom location) +:pre [Traditional make]: @@ -366,6 +369,7 @@ simply invoke the lib/message/Install.py script with the specified args: make lib-message # print help message make lib-message args="-m -z" # build with MPI and socket (ZMQ) support make lib-message args="-s" # build as serial lib with no ZMQ support +:pre The build should produce two files: lib/message/cslib/src/libmessage.a and lib/message/Makefile.lammps. The latter is copied from an diff --git a/doc/src/Packages_details.txt b/doc/src/Packages_details.txt index 43274a9606..47341239f7 100644 --- a/doc/src/Packages_details.txt +++ b/doc/src/Packages_details.txt @@ -1,4 +1,4 @@ -"Higher level section"_Packages.html - "LAMMPS WWW Site"_lws - "LAMMPS +tion"_Packages.html - "LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c :link(lws,http://lammps.sandia.gov) @@ -1191,7 +1191,7 @@ USER-PLUMED package :link(PKG-USER-PLUMED),h4 The fix plumed command allows you to use the PLUMED free energy plugin for molecular dynamics to analyze and bias your LAMMPS trajectory on the fly. The PLUMED library is called from within the LAMMPS input -script by using the "fix plumed _fix_plumed.html command. +script by using the "fix plumed"_fix_plumed.html command. [Authors:] The "PLUMED library"_#PLUMED is written and maintained by Massimilliano Bonomi, Giovanni Bussi, Carlo Camiloni and Gareth -- GitLab From bd87b672327e10c8e1eaa3a99c8628ab0e9091b3 Mon Sep 17 00:00:00 2001 From: Richard Berger Date: Fri, 2 Aug 2019 17:35:26 -0400 Subject: [PATCH 418/469] Update false_positives.txt --- doc/utils/sphinx-config/false_positives.txt | 2 ++ 1 file changed, 2 insertions(+) diff --git a/doc/utils/sphinx-config/false_positives.txt b/doc/utils/sphinx-config/false_positives.txt index 1dea229393..67252659bb 100644 --- a/doc/utils/sphinx-config/false_positives.txt +++ b/doc/utils/sphinx-config/false_positives.txt @@ -2443,6 +2443,8 @@ Salles sandia Sandia sandybrown +Sanitizer +sanitizers sc scafacos SCAFACOS -- GitLab From 91fdd98fbc35f2a078e69551236786610a5190a9 Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Fri, 2 Aug 2019 18:44:40 -0400 Subject: [PATCH 419/469] restore accidentally deleted text --- doc/src/Packages_details.txt | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/doc/src/Packages_details.txt b/doc/src/Packages_details.txt index 47341239f7..eead133add 100644 --- a/doc/src/Packages_details.txt +++ b/doc/src/Packages_details.txt @@ -1,4 +1,4 @@ -tion"_Packages.html - "LAMMPS WWW Site"_lws - "LAMMPS +"Higher level section"_Packages.html - "LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c :link(lws,http://lammps.sandia.gov) -- GitLab From 0774e92ecea9aeaed8a8f0ad1cea7cc635f44224 Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Sat, 3 Aug 2019 06:40:31 -0400 Subject: [PATCH 420/469] use KIM-API 2.1.2 consistently with CMake and conventional build system --- lib/kim/Install.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/lib/kim/Install.py b/lib/kim/Install.py index de22950639..836b5ba205 100644 --- a/lib/kim/Install.py +++ b/lib/kim/Install.py @@ -18,7 +18,7 @@ parser = ArgumentParser(prog='Install.py', # settings thisdir = fullpath('.') -version = "kim-api-2.1.1" +version = "kim-api-2.1.2" # help message -- GitLab From faefcc776a70b490ee70c2522c5c2d99c6322ec4 Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Sat, 3 Aug 2019 10:38:41 -0400 Subject: [PATCH 421/469] sched_getaffinity() is a Linux specific system call. add preprocessor guards --- src/USER-INTEL/verlet_lrt_intel.cpp | 6 ++++-- 1 file changed, 4 insertions(+), 2 deletions(-) diff --git a/src/USER-INTEL/verlet_lrt_intel.cpp b/src/USER-INTEL/verlet_lrt_intel.cpp index 2b28eea3a2..a3c05c46bc 100644 --- a/src/USER-INTEL/verlet_lrt_intel.cpp +++ b/src/USER-INTEL/verlet_lrt_intel.cpp @@ -102,18 +102,20 @@ void VerletLRTIntel::setup(int flag) } #if defined(_LMP_INTEL_LRT_PTHREAD) + #if defined(__linux) if (comm->me == 0) { cpu_set_t cpuset; sched_getaffinity(0, sizeof(cpuset), &cpuset); int my_cpu_count = CPU_COUNT(&cpuset); if (my_cpu_count < comm->nthreads + 1) { char str[128]; - sprintf(str,"Using %d threads per MPI, but only %d core(s) allocated" - " per MPI", + sprintf(str,"Using %d threads per MPI rank, but only %d core(s)" + " allocated for each MPI rank", comm->nthreads + 1, my_cpu_count); error->warning(FLERR, str); } } + #endif _kspace_ready = 0; _kspace_done = 0; -- GitLab From 5b3423c60eb48444f959fe63d5e03ec6b09c0571 Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Sat, 3 Aug 2019 11:16:14 -0400 Subject: [PATCH 422/469] tweaks for Linux to Windows cross-compilation --- cmake/CMakeLists.txt | 1 + cmake/presets/mingw-cross.cmake | 7 +++---- 2 files changed, 4 insertions(+), 4 deletions(-) diff --git a/cmake/CMakeLists.txt b/cmake/CMakeLists.txt index 187b41e980..fd4cd51662 100644 --- a/cmake/CMakeLists.txt +++ b/cmake/CMakeLists.txt @@ -229,6 +229,7 @@ if(PKG_MSCG OR PKG_USER-ATC OR PKG_USER-AWPMD OR PKG_USER-QUIP OR PKG_LATTE) enable_language(Fortran) file(GLOB LAPACK_SOURCES ${LAMMPS_LIB_SOURCE_DIR}/linalg/[^.]*.[fF]) add_library(linalg STATIC ${LAPACK_SOURCES}) + set(BLAS_LIBRARIES linalg) set(LAPACK_LIBRARIES linalg) else() list(APPEND LAPACK_LIBRARIES ${BLAS_LIBRARIES}) diff --git a/cmake/presets/mingw-cross.cmake b/cmake/presets/mingw-cross.cmake index b53e5a7b93..2ac24490bc 100644 --- a/cmake/presets/mingw-cross.cmake +++ b/cmake/presets/mingw-cross.cmake @@ -3,9 +3,9 @@ set(WIN_PACKAGES ASPHERE BODY CLASS2 COLLOID COMPRESS CORESHELL DIPOLE GPU REPLICA RIGID SHOCK SNAP SPIN SRD VORONOI USER-ATC USER-AWPMD USER-BOCS USER-CGDNA USER-CGSDK USER-COLVARS USER-DIFFRACTION USER-DPD USER-DRUDE USER-EFF USER-FEP USER-INTEL USER-MANIFOLD - USER-MEAMC USER-MESO USER-MISC USER-MOFFF USER-MOLFILE USER-OMP - USER-PHONON USER-PTM USER-QTB USER-REAXC USER-SDPD USER-SMD - USER-SMTBQ USER-SPH USER-TALLY USER-UEF USER-YAFF) + USER-MEAMC USER-MESO USER-MISC USER-MGPT USER-MOFFF USER-MOLFILE + USER-OMP USER-PHONON USER-PTM USER-QTB USER-REAXC USER-SDPD + USER-SMD USER-SMTBQ USER-SPH USER-TALLY USER-UEF USER-YAFF) foreach(PKG ${WIN_PACKAGES}) set(PKG_${PKG} ON CACHE BOOL "" FORCE) @@ -14,4 +14,3 @@ endforeach() set(DOWNLOAD_VORO ON CACHE BOOL "" FORCE) set(DOWNLOAD_EIGEN3 ON CACHE BOOL "" FORCE) set(LAMMPS_MEMALIGN "0" CACHE STRING "" FORCE) -set(INTEL_LRT_MODE "none" CACHE STRING "" FORCE) -- GitLab From d82ae64d16778523fb0460b4ac3894cf6ffd01dd Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Sat, 3 Aug 2019 11:16:55 -0400 Subject: [PATCH 423/469] minor tweak for consistency --- src/info.cpp | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/info.cpp b/src/info.cpp index 21297c52c6..caa2d6fdd0 100644 --- a/src/info.cpp +++ b/src/info.cpp @@ -60,7 +60,7 @@ #include #endif -#if defined __linux +#if defined(__linux) #include #endif -- GitLab From b65ae605e5d8f6ce7b6225ddbafafc2188f86421 Mon Sep 17 00:00:00 2001 From: Richard Berger Date: Sat, 3 Aug 2019 15:17:18 -0400 Subject: [PATCH 424/469] Added one-liner for HTML-only docs in Build.txt --- doc/src/Build.txt | 3 ++- doc/src/Build_development.txt | 2 +- 2 files changed, 3 insertions(+), 2 deletions(-) diff --git a/doc/src/Build.txt b/doc/src/Build.txt index 50d62ac889..8906549350 100644 --- a/doc/src/Build.txt +++ b/doc/src/Build.txt @@ -42,7 +42,8 @@ END_RST --> "Optional build settings"_Build_settings.html "Include packages in build"_Build_package.html "Packages with extra build options"_Build_extras.html -"Notes for building LAMMPS on Windows"_Build_windows.html :all(b) +"Notes for building LAMMPS on Windows"_Build_windows.html +"Development build options (CMake only)"_Build_development.html :all(b) If you have problems building LAMMPS, it is often due to software issues on your local machine. If you can, find a local expert to diff --git a/doc/src/Build_development.txt b/doc/src/Build_development.txt index 7ce4b0e8a6..16a3d3d20e 100644 --- a/doc/src/Build_development.txt +++ b/doc/src/Build_development.txt @@ -7,7 +7,7 @@ Documentation"_ld - "LAMMPS Commands"_lc :c :line -Development options (CMake only) :h3 +Development build options (CMake only) :h3 The CMake build of LAMMPS has a few extra options which are useful during development, testing or debugging. -- GitLab From 58d27403f15fc8e0e92bfa8f73f5665dd08a2753 Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Sun, 4 Aug 2019 18:28:26 -0400 Subject: [PATCH 425/469] CMake tweaks to improve building LAMMPS for windows with mingw on Linux --- cmake/CMakeLists.txt | 29 +++++++++++++++++++++++++---- cmake/presets/mingw-cross.cmake | 3 +++ 2 files changed, 28 insertions(+), 4 deletions(-) diff --git a/cmake/CMakeLists.txt b/cmake/CMakeLists.txt index fd4cd51662..e961fe25d3 100644 --- a/cmake/CMakeLists.txt +++ b/cmake/CMakeLists.txt @@ -133,6 +133,24 @@ foreach(PKG ${DEFAULT_PACKAGES} ${ACCEL_PACKAGES}) option(PKG_${PKG} "Build ${PKG} Package" OFF) endforeach() +###################################################### +# download and unpack support binaries for compilation +# of windows binaries. +###################################################### +if(${CMAKE_SYSTEM_NAME} STREQUAL "Windows") + set(LAMMPS_THIRDPARTY_URL "http://download.lammps.org/thirdparty") + file(DOWNLOAD "${LAMMPS_THIRDPARTY_URL}/opencl-win-devel.tar.gz" "${CMAKE_CURRENT_BINARY_DIR}/opencl-win-devel.tar.gz" + EXPECTED_MD5 2c00364888d5671195598b44c2e0d44d) + execute_process(COMMAND ${CMAKE_COMMAND} -E tar xzf opencl-win-devel.tar.gz WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}) + if(${CMAKE_SYSTEM_PROCESSOR} STREQUAL "x86") + set(OpenCL_LIBRARY "${CMAKE_CURRENT_BINARY_DIR}/OpenCL/lib_win32/libOpenCL.dll") + elseif(${CMAKE_SYSTEM_PROCESSOR} STREQUAL "x86_64") + set(OpenCL_LIBRARY "${CMAKE_CURRENT_BINARY_DIR}/OpenCL/lib_win64/libOpenCL.dll") + endif() + set(OpenCL_INCLUDE_DIR "${CMAKE_CURRENT_BINARY_DIR}/OpenCL/include") +endif() + +###################################################### ###################################################### # packages with special compiler needs or external libs ###################################################### @@ -148,6 +166,7 @@ if(PKG_USER-ADIOS) endif() # do MPI detection after language activation, if MPI for these language is required +set(MPI_CXX_SKIP_MPICXX TRUE) find_package(MPI QUIET) option(BUILD_MPI "Build MPI version" ${MPI_FOUND}) if(BUILD_MPI) @@ -175,11 +194,13 @@ add_definitions(-DLAMMPS_${LAMMPS_SIZES}) set(LAMMPS_API_DEFINES "${LAMMPS_API_DEFINES} -DLAMMPS_${LAMMPS_SIZES}") # posix_memalign is not available on Windows -if(NOT ${CMAKE_SYSTEM_NAME} STREQUAL "Windows") +if(${CMAKE_SYSTEM_NAME} STREQUAL "Windows") + set(LAMMPS_MEMALIGN "0" CACHE STRING "posix_memalign() is not available on Windows" FORCE) +else() set(LAMMPS_MEMALIGN "64" CACHE STRING "enables the use of the posix_memalign() call instead of malloc() when large chunks or memory are allocated by LAMMPS. Set to 0 to disable") - if(NOT ${LAMMPS_MEMALIGN} STREQUAL "0") - add_definitions(-DLAMMPS_MEMALIGN=${LAMMPS_MEMALIGN}) - endif() +endif() +if(NOT ${LAMMPS_MEMALIGN} STREQUAL "0") + add_definitions(-DLAMMPS_MEMALIGN=${LAMMPS_MEMALIGN}) endif() option(LAMMPS_EXCEPTIONS "enable the use of C++ exceptions for error messages (useful for library interface)" OFF) diff --git a/cmake/presets/mingw-cross.cmake b/cmake/presets/mingw-cross.cmake index 2ac24490bc..fbec42529f 100644 --- a/cmake/presets/mingw-cross.cmake +++ b/cmake/presets/mingw-cross.cmake @@ -13,4 +13,7 @@ endforeach() set(DOWNLOAD_VORO ON CACHE BOOL "" FORCE) set(DOWNLOAD_EIGEN3 ON CACHE BOOL "" FORCE) +set(WITH_GZIP ON CACHE BOOL "" FORCE) +set(WITH_FFMPEG ON CACHE BOOL "" FORCE) set(LAMMPS_MEMALIGN "0" CACHE STRING "" FORCE) +set(CMAKE_INSTALL_PREFIX "${CMAKE_CURRENT_BINARY_DIR}/lammps-installer") -- GitLab From f2757eaf4182a883583278295a8961b60b3aebd3 Mon Sep 17 00:00:00 2001 From: Richard Berger Date: Mon, 5 Aug 2019 13:58:11 -0400 Subject: [PATCH 426/469] Mention LAMMPS_LIB_SUFFIX in docs --- cmake/README.md | 11 ++++++++++- doc/src/Build_basics.txt | 8 ++++++-- 2 files changed, 16 insertions(+), 3 deletions(-) diff --git a/cmake/README.md b/cmake/README.md index 95b2dd7447..01b6f6a60e 100644 --- a/cmake/README.md +++ b/cmake/README.md @@ -286,7 +286,16 @@ cmake -C ../cmake/presets/all_on.cmake -C ../cmake/presets/nolib.cmake -D PKG_GP LAMMPS_MACHINE - allows appending a machine suffix to the generate LAMMPS binary + allows appending a machine suffix to the generated LAMMPS binary + +
+
*none* (default)
+
+ + + + LAMMPS_LIB_SUFFIX + allows appending a suffix to the generated LAMMPS library
*none* (default)
diff --git a/doc/src/Build_basics.txt b/doc/src/Build_basics.txt index 411e7858ac..04e11009af 100644 --- a/doc/src/Build_basics.txt +++ b/doc/src/Build_basics.txt @@ -235,12 +235,16 @@ running LAMMPS from Python via its library interface. -D BUILD_EXE=value # yes (default) or no -D BUILD_LIB=value # yes or no (default) --D BUILD_SHARED_LIBS=value # yes or no (default) :pre +-D BUILD_SHARED_LIBS=value # yes or no (default) +-D LAMMPS_LIB_SUFFIX=name # name = mpi, serial, mybox, titan, laptop, etc + # no default value :pre + Setting BUILD_EXE=no will not produce an executable. Setting BUILD_LIB=yes will produce a static library named liblammps.a. Setting both BUILD_LIB=yes and BUILD_SHARED_LIBS=yes will produce a -shared library named liblammps.so. +shared library named liblammps.so. If LAMMPS_LIB_SUFFIX is set the generated +libraries will be named liblammps_name.a or liblammps_name.so instead. [Traditional make]: -- GitLab From 51ba9bd52069f34d0c112a1182660192bc81192c Mon Sep 17 00:00:00 2001 From: Giacomo Fiorin Date: Mon, 5 Aug 2019 14:12:38 -0400 Subject: [PATCH 427/469] Bugfix for Colvars library (update to version 2019-08-05) Bugfix for group2CenterOnly (coordNum option): https://github.com/Colvars/colvars/pull/278 --- lib/colvars/colvaratoms.cpp | 42 +++++++--- lib/colvars/colvaratoms.h | 6 ++ lib/colvars/colvarcomp.h | 10 ++- lib/colvars/colvarcomp_coordnums.cpp | 117 +++++++++------------------ lib/colvars/colvars_version.h | 2 +- 5 files changed, 80 insertions(+), 97 deletions(-) diff --git a/lib/colvars/colvaratoms.cpp b/lib/colvars/colvaratoms.cpp index eeb7985fec..af17d8df66 100644 --- a/lib/colvars/colvaratoms.cpp +++ b/lib/colvars/colvaratoms.cpp @@ -178,6 +178,31 @@ int cvm::atom_group::remove_atom(cvm::atom_iter ai) } +int cvm::atom_group::set_dummy() +{ + if (atoms_ids.size() > 0) { + return cvm::error("Error: setting group with keyword \""+key+ + "\" and name \""+name+"\" as dummy, but it already " + "contains atoms.\n", INPUT_ERROR); + } + b_dummy = true; + return COLVARS_OK; +} + + +int cvm::atom_group::set_dummy_pos(cvm::atom_pos const &pos) +{ + if (b_dummy) { + dummy_atom_pos = pos; + } else { + return cvm::error("Error: setting dummy position for group with keyword \""+ + key+"\" and name \""+name+ + "\", but it is not dummy.\n", INPUT_ERROR); + } + return COLVARS_OK; +} + + int cvm::atom_group::init() { if (!key.size()) key = "unnamed"; @@ -469,20 +494,15 @@ int cvm::atom_group::parse(std::string const &group_conf) // checks of doubly-counted atoms have been handled by add_atom() already if (get_keyval(group_conf, "dummyAtom", dummy_atom_pos, cvm::atom_pos())) { - b_dummy = true; - // note: atoms_ids.size() is used here in lieu of atoms.size(), - // which can be empty for scalable groups - if (atoms_ids.size()) { - cvm::error("Error: cannot set up group \""+ - key+"\" as a dummy atom " - "and provide it with atom definitions.\n", INPUT_ERROR); - } + + parse_error |= set_dummy(); + parse_error |= set_dummy_pos(dummy_atom_pos); + } else { - b_dummy = false; if (!(atoms_ids.size())) { - cvm::error("Error: no atoms defined for atom group \""+ - key+"\".\n", INPUT_ERROR); + parse_error |= cvm::error("Error: no atoms defined for atom group \""+ + key+"\".\n", INPUT_ERROR); } // whether these atoms will ever receive forces or not diff --git a/lib/colvars/colvaratoms.h b/lib/colvars/colvaratoms.h index 9756e0e364..c8b6ac4541 100644 --- a/lib/colvars/colvaratoms.h +++ b/lib/colvars/colvaratoms.h @@ -207,6 +207,12 @@ public: /// \brief Remove an atom object from this group int remove_atom(cvm::atom_iter ai); + /// Set this group as a dummy group (no actual atoms) + int set_dummy(); + + /// If this group is dummy, set the corresponding position + int set_dummy_pos(cvm::atom_pos const &pos); + /// \brief Print the updated the total mass and charge of a group. /// This is needed in case the hosting MD code has an option to /// change atom masses after their initialization. diff --git a/lib/colvars/colvarcomp.h b/lib/colvars/colvarcomp.h index 5e7a91e872..c3c663e357 100644 --- a/lib/colvars/colvarcomp.h +++ b/lib/colvars/colvarcomp.h @@ -887,9 +887,8 @@ protected: /// Integer exponent of the function denominator int ed; - /// \brief If true, group2 will be treated as a single atom, stored in this - /// accessory group - cvm::atom_group *group2_center; + /// If true, group2 will be treated as a single atom + bool b_group2_center_only; /// Tolerance for the pair list cvm::real tolerance; @@ -941,9 +940,12 @@ public: bool **pairlist_elem, cvm::real tolerance); - /// Main workhorse function + /// Workhorse function template int compute_coordnum(); + /// Workhorse function + template void main_loop(bool *pairlist_elem); + }; diff --git a/lib/colvars/colvarcomp_coordnums.cpp b/lib/colvars/colvarcomp_coordnums.cpp index 059b0c825b..b6dd6535ef 100644 --- a/lib/colvars/colvarcomp_coordnums.cpp +++ b/lib/colvars/colvarcomp_coordnums.cpp @@ -91,7 +91,7 @@ cvm::real colvar::coordnum::switching_function(cvm::real const &r0, colvar::coordnum::coordnum(std::string const &conf) - : cvc(conf), b_anisotropic(false), group2_center(NULL), pairlist(NULL) + : cvc(conf), b_anisotropic(false), pairlist(NULL) { function_type = "coordnum"; @@ -156,14 +156,7 @@ colvar::coordnum::coordnum(std::string const &conf) cvm::log("Warning: only minimum-image distances are used by this variable.\n"); } - bool b_group2_center_only = false; get_keyval(conf, "group2CenterOnly", b_group2_center_only, group2->b_dummy); - if (b_group2_center_only) { - if (!group2_center) { - group2_center = new cvm::atom_group(); - group2_center->add_atom(cvm::atom()); - } - } get_keyval(conf, "tolerance", tolerance, 0.0); if (tolerance > 0) { @@ -185,7 +178,7 @@ colvar::coordnum::coordnum(std::string const &conf) colvar::coordnum::coordnum() - : b_anisotropic(false), group2_center(NULL), pairlist(NULL) + : b_anisotropic(false), pairlist(NULL) { function_type = "coordnum"; x.type(colvarvalue::type_scalar); @@ -197,69 +190,60 @@ colvar::coordnum::~coordnum() if (pairlist != NULL) { delete [] pairlist; } - if (group2_center != NULL) { - delete group2_center; - } } -template int colvar::coordnum::compute_coordnum() +template void colvar::coordnum::main_loop(bool **pairlist_elem) { - if (group2_center) { - (*group2_center)[0].pos = group2->center_of_mass(); - group2_center->calc_required_properties(); + if (b_group2_center_only) { + cvm::atom group2_com_atom; + group2_com_atom.pos = group2->center_of_mass(); + for (cvm::atom_iter ai1 = group1->begin(); ai1 != group1->end(); ai1++) { + x.real_value += switching_function(r0, r0_vec, en, ed, + *ai1, group2_com_atom, + pairlist_elem, + tolerance); + } + if (b_group2_center_only) { + group2->set_weighted_gradient(group2_com_atom.grad); + } + } else { + for (cvm::atom_iter ai1 = group1->begin(); ai1 != group1->end(); ai1++) { + for (cvm::atom_iter ai2 = group2->begin(); ai2 != group2->end(); ai2++) { + x.real_value += switching_function(r0, r0_vec, en, ed, + *ai1, *ai2, + pairlist_elem, + tolerance); + } + } } - cvm::atom_group *group2p = group2_center ? group2_center : group2; +} + +template int colvar::coordnum::compute_coordnum() +{ bool const use_pairlist = (pairlist != NULL); bool const rebuild_pairlist = (pairlist != NULL) && (cvm::step_relative() % pairlist_freq == 0); bool *pairlist_elem = use_pairlist ? pairlist : NULL; - cvm::atom_iter ai1 = group1->begin(), ai2 = group2p->begin(); - cvm::atom_iter const ai1_end = group1->end(); - cvm::atom_iter const ai2_end = group2p->end(); if (b_anisotropic) { if (use_pairlist) { - if (rebuild_pairlist) { - int const flags = compute_flags | ef_anisotropic | ef_use_pairlist | ef_rebuild_pairlist; - for (ai1 = group1->begin(); ai1 != ai1_end; ai1++) { - for (ai2 = group2->begin(); ai2 != ai2_end; ai2++) { - x.real_value += switching_function(r0, r0_vec, en, ed, - *ai1, *ai2, - &pairlist_elem, - tolerance); - } - } - + main_loop(&pairlist_elem); } else { - int const flags = compute_flags | ef_anisotropic | ef_use_pairlist; - for (ai1 = group1->begin(); ai1 != ai1_end; ai1++) { - for (ai2 = group2->begin(); ai2 != ai2_end; ai2++) { - x.real_value += switching_function(r0, r0_vec, en, ed, - *ai1, *ai2, - &pairlist_elem, - tolerance); - } - } + main_loop(&pairlist_elem); } - } else { // if (use_pairlist) { + } else { int const flags = compute_flags | ef_anisotropic; - for (ai1 = group1->begin(); ai1 != ai1_end; ai1++) { - for (ai2 = group2->begin(); ai2 != ai2_end; ai2++) { - x.real_value += switching_function(r0, r0_vec, en, ed, - *ai1, *ai2, - NULL, 0.0); - } - } + main_loop(NULL); } } else { @@ -267,46 +251,17 @@ template int colvar::coordnum::compute_coordnum() if (use_pairlist) { if (rebuild_pairlist) { - int const flags = compute_flags | ef_use_pairlist | ef_rebuild_pairlist; - for (ai1 = group1->begin(); ai1 != ai1_end; ai1++) { - for (ai2 = group2->begin(); ai2 != ai2_end; ai2++) { - x.real_value += switching_function(r0, r0_vec, en, ed, - *ai1, *ai2, - &pairlist_elem, - tolerance); - } - } - + main_loop(&pairlist_elem); } else { - int const flags = compute_flags | ef_use_pairlist; - for (ai1 = group1->begin(); ai1 != ai1_end; ai1++) { - for (ai2 = group2->begin(); ai2 != ai2_end; ai2++) { - x.real_value += switching_function(r0, r0_vec, en, ed, - *ai1, *ai2, - &pairlist_elem, - tolerance); - } - } + main_loop(&pairlist_elem); } - } else { // if (use_pairlist) { + } else { int const flags = compute_flags; - for (ai1 = group1->begin(); ai1 != ai1_end; ai1++) { - for (ai2 = group2->begin(); ai2 != ai2_end; ai2++) { - x.real_value += switching_function(r0, r0_vec, en, ed, - *ai1, *ai2, - NULL, 0.0); - } - } - } - } - - if (compute_flags & ef_gradients) { - if (group2_center) { - group2->set_weighted_gradient((*group2_center)[0].grad); + main_loop(NULL); } } diff --git a/lib/colvars/colvars_version.h b/lib/colvars/colvars_version.h index 0f1ee9a0a0..77b3bd7e38 100644 --- a/lib/colvars/colvars_version.h +++ b/lib/colvars/colvars_version.h @@ -1,5 +1,5 @@ #ifndef COLVARS_VERSION -#define COLVARS_VERSION "2019-08-01" +#define COLVARS_VERSION "2019-08-05" // This file is part of the Collective Variables module (Colvars). // The original version of Colvars and its updates are located at: // https://github.com/colvars/colvars -- GitLab From 97501f0946580b98d50e83b237544fdd7dc79b36 Mon Sep 17 00:00:00 2001 From: Giacomo Fiorin Date: Mon, 5 Aug 2019 14:59:40 -0400 Subject: [PATCH 428/469] Fix typo --- lib/colvars/colvarcomp.h | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/lib/colvars/colvarcomp.h b/lib/colvars/colvarcomp.h index c3c663e357..1d95cbe600 100644 --- a/lib/colvars/colvarcomp.h +++ b/lib/colvars/colvarcomp.h @@ -944,7 +944,7 @@ public: template int compute_coordnum(); /// Workhorse function - template void main_loop(bool *pairlist_elem); + template void main_loop(bool **pairlist_elem); }; -- GitLab From e39b85b62fd06f25e94ff4e51cf08e453b35ccf1 Mon Sep 17 00:00:00 2001 From: "Ryan S. Elliott" Date: Mon, 5 Aug 2019 15:23:57 -0500 Subject: [PATCH 429/469] Update kim query url in docs --- doc/src/kim_commands.txt | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/doc/src/kim_commands.txt b/doc/src/kim_commands.txt index 93c4e8c4a8..47beb776a1 100644 --- a/doc/src/kim_commands.txt +++ b/doc/src/kim_commands.txt @@ -365,7 +365,7 @@ an array of one or more comma-separated items in brackets. The list of supported keywords and the type and format of their values depend on the query function used. The current list of query functions is available on the OpenKIM webpage at -"https://openkim.org/doc/repository/kim-query"_https://openkim.org/doc/repository/kim-query. +"https://openkim.org/doc/usage/kim-query"_https://openkim.org/doc/usage/kim-query. NOTE: All query functions require the {model} keyword, which identifies the IM whose predictions are being queried. This keyword is automatically -- GitLab From 2092b2c010a8e2bc419e94a8d9b48befc6847852 Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Sat, 3 Aug 2019 06:47:27 -0400 Subject: [PATCH 430/469] Step version string for stable release --- doc/lammps.1 | 2 +- doc/src/Manual.txt | 4 ++-- src/version.h | 2 +- 3 files changed, 4 insertions(+), 4 deletions(-) diff --git a/doc/lammps.1 b/doc/lammps.1 index 6539b85af9..46f83698ec 100644 --- a/doc/lammps.1 +++ b/doc/lammps.1 @@ -1,4 +1,4 @@ -.TH LAMMPS "2 August 2019" "2019-08-02" +.TH LAMMPS "6 August 2019" "2019-08-06" .SH NAME .B LAMMPS \- Molecular Dynamics Simulator. diff --git a/doc/src/Manual.txt b/doc/src/Manual.txt index 85828f1d90..e461e585d9 100644 --- a/doc/src/Manual.txt +++ b/doc/src/Manual.txt @@ -1,7 +1,7 @@ LAMMPS Users Manual - + @@ -21,7 +21,7 @@ :line LAMMPS Documentation :c,h1 -2 Aug 2019 version :c,h2 +6 Aug 2019 version :c,h2 "What is a LAMMPS version?"_Manual_version.html diff --git a/src/version.h b/src/version.h index b74aa30172..2154f428c4 100644 --- a/src/version.h +++ b/src/version.h @@ -1 +1 @@ -#define LAMMPS_VERSION "2 Aug 2019" +#define LAMMPS_VERSION "6 Aug 2019" -- GitLab From 3ef93d6e1b97384a5d11b8e1b31ec0114f089974 Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Mon, 5 Aug 2019 16:59:18 -0400 Subject: [PATCH 431/469] cannot forced enable FFMpeg and gzip on windows yet. --- cmake/presets/mingw-cross.cmake | 2 -- 1 file changed, 2 deletions(-) diff --git a/cmake/presets/mingw-cross.cmake b/cmake/presets/mingw-cross.cmake index fbec42529f..920b377e48 100644 --- a/cmake/presets/mingw-cross.cmake +++ b/cmake/presets/mingw-cross.cmake @@ -13,7 +13,5 @@ endforeach() set(DOWNLOAD_VORO ON CACHE BOOL "" FORCE) set(DOWNLOAD_EIGEN3 ON CACHE BOOL "" FORCE) -set(WITH_GZIP ON CACHE BOOL "" FORCE) -set(WITH_FFMPEG ON CACHE BOOL "" FORCE) set(LAMMPS_MEMALIGN "0" CACHE STRING "" FORCE) set(CMAKE_INSTALL_PREFIX "${CMAKE_CURRENT_BINARY_DIR}/lammps-installer") -- GitLab From 2d643233549f83b7e4d49712ff8b864d39c163c7 Mon Sep 17 00:00:00 2001 From: Steve Plimpton Date: Mon, 5 Aug 2019 17:21:11 -0600 Subject: [PATCH 432/469] fix formatting and augment explanation for bbox option --- doc/src/replicate.txt | 15 +++++++++------ 1 file changed, 9 insertions(+), 6 deletions(-) diff --git a/doc/src/replicate.txt b/doc/src/replicate.txt index 79a481746e..50e6e4c6d2 100644 --- a/doc/src/replicate.txt +++ b/doc/src/replicate.txt @@ -14,7 +14,8 @@ replicate nx ny nz {keyword} :pre nx,ny,nz = replication factors in each dimension :ulb optional {keyword} = {bbox} :l - {bbox} = only check atoms in replicas that overlap with a processor's sub-domain :ule + {bbox} = only check atoms in replicas that overlap with a processor's sub-domain :pre +:ule [Examples:] @@ -45,11 +46,13 @@ file that crosses a periodic boundary should be between two atoms with image flags that differ by 1. This will allow the bond to be unwrapped appropriately. -The optional keyword {bbox} uses a bounding box to only check atoms -in replicas that overlap with a processor's sub-domain when assigning -atoms to processors, and thus can result in substantial speedups for -calculations using a large number of processors. It does require -temporarily using more memory. +The optional keyword {bbox} uses a bounding box to only check atoms in +replicas that overlap with a processor's sub-domain when assigning +atoms to processors. It typically results in a substantial speedup +when using the replicate command on a large number of processors. It +does require temporary use of more memory, specifically that each +processor can store all atoms in the entire system before it is +replicated. [Restrictions:] -- GitLab From 21f3f51ea2a719c9e57bdaf31c34b385c0c4efd4 Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Fri, 2 Aug 2019 10:13:52 -0400 Subject: [PATCH 433/469] better error messages on accessing invalid IDs in variable expressions --- src/variable.cpp | 65 +++++++++++++++++++++++++++++++++--------------- 1 file changed, 45 insertions(+), 20 deletions(-) diff --git a/src/variable.cpp b/src/variable.cpp index 3fffa11d5e..1093ce9066 100644 --- a/src/variable.cpp +++ b/src/variable.cpp @@ -18,6 +18,7 @@ #include #include #include +#include #include "universe.h" #include "atom.h" #include "update.h" @@ -1302,8 +1303,12 @@ double Variable::evaluate(char *str, Tree **tree, int ivar) if (word[0] == 'C') lowercase = 0; int icompute = modify->find_compute(word+2); - if (icompute < 0) - print_var_error(FLERR,"Invalid compute ID in variable formula",ivar); + if (icompute < 0) { + std::string mesg = "Invalid compute ID '"; + mesg += (word+2); + mesg += "' in variable formula"; + print_var_error(FLERR,mesg.c_str(),ivar); + } Compute *compute = modify->compute[icompute]; // parse zero or one or two trailing brackets @@ -1604,9 +1609,10 @@ double Variable::evaluate(char *str, Tree **tree, int ivar) int ifix = modify->find_fix(word+2); if (ifix < 0) { - char msg[128]; - snprintf(msg,128,"Invalid fix ID '%s' in variable formula",word+2); - print_var_error(FLERR,msg,ivar); + std::string mesg = "Invalid fix ID '"; + mesg += (word+2); + mesg += "' in variable formula"; + print_var_error(FLERR,mesg.c_str(),ivar); } Fix *fix = modify->fix[ifix]; @@ -3792,8 +3798,12 @@ int Variable::group_function(char *word, char *contents, Tree **tree, // group to operate on int igroup = group->find(args[0]); - if (igroup == -1) - print_var_error(FLERR,"Group ID in variable formula does not exist",ivar); + if (igroup == -1) { + std::string mesg = "Group ID '"; + mesg += args[0]; + mesg += "' in variable formula does not exist"; + print_var_error(FLERR,mesg.c_str(),ivar); + } // match word to group function @@ -4001,8 +4011,12 @@ int Variable::group_function(char *word, char *contents, Tree **tree, int Variable::region_function(char *id, int ivar) { int iregion = domain->find_region(id); - if (iregion == -1) - print_var_error(FLERR,"Region ID in variable formula does not exist",ivar); + if (iregion == -1) { + std::string mesg = "Region ID '"; + mesg += id; + mesg += "' in variable formula does not exist"; + print_var_error(FLERR,mesg.c_str(),ivar); + } // init region in case sub-regions have been deleted @@ -4080,9 +4094,10 @@ int Variable::special_function(char *word, char *contents, Tree **tree, int icompute = modify->find_compute(&args[0][2]); if (icompute < 0) { - char msg[128]; - snprintf(msg,128,"Invalid compute ID '%s' in variable formula",word+2); - print_var_error(FLERR,msg,ivar); + std::string mesg = "Invalid compute ID '"; + mesg += (args[0]+2); + mesg += "' in variable formula"; + print_var_error(FLERR,mesg.c_str(),ivar); } compute = modify->compute[icompute]; if (index == 0 && compute->vector_flag) { @@ -4123,13 +4138,20 @@ int Variable::special_function(char *word, char *contents, Tree **tree, } else index = 0; int ifix = modify->find_fix(&args[0][2]); - if (ifix < 0) - print_var_error(FLERR,"Invalid fix ID in variable formula",ivar); + if (ifix < 0) { + std::string mesg = "Invalid fix ID '"; + mesg += (args[0]+2); + mesg += "' in variable formula"; + print_var_error(FLERR,mesg.c_str(),ivar); + } fix = modify->fix[ifix]; if (index == 0 && fix->vector_flag) { - if (update->whichflag > 0 && update->ntimestep % fix->global_freq) - print_var_error(FLERR,"Fix in variable not computed at " - "compatible time",ivar); + if (update->whichflag > 0 && update->ntimestep % fix->global_freq) { + std::string mesg = "Fix with ID '"; + mesg += (args[0]+2); + mesg += "' in variable formula not computed at compatible time"; + print_var_error(FLERR,mesg.c_str(),ivar); + } nvec = fix->size_vector; nstride = 1; } else if (index && fix->array_flag) { @@ -4336,9 +4358,12 @@ int Variable::special_function(char *word, char *contents, Tree **tree, print_var_error(FLERR,"Invalid special function in variable formula",ivar); int ivar = find(args[0]); - if (ivar < 0) - print_var_error(FLERR,"Variable ID in " - "variable formula does not exist",ivar); + if (ivar < 0) { + std::string mesg = "Variable ID '"; + mesg += args[0]; + mesg += "' in variable formula does not exist"; + print_var_error(FLERR,mesg.c_str(),ivar); + } // SCALARFILE has single current value, read next one // save value in tree or on argstack -- GitLab From 71ce1c20274d373b4312171d8f4ef95921a16a7c Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Mon, 5 Aug 2019 23:25:06 -0400 Subject: [PATCH 434/469] use cube() and square() from math_special.h instead of pow(x,3.0) and pow(x,2.0) --- src/MANYBODY/pair_tersoff.cpp | 8 +++++--- src/MANYBODY/pair_tersoff_mod.cpp | 8 +++++--- src/MANYBODY/pair_tersoff_zbl.cpp | 6 ++++-- 3 files changed, 14 insertions(+), 8 deletions(-) diff --git a/src/MANYBODY/pair_tersoff.cpp b/src/MANYBODY/pair_tersoff.cpp index 62c74576e0..5f53760e71 100644 --- a/src/MANYBODY/pair_tersoff.cpp +++ b/src/MANYBODY/pair_tersoff.cpp @@ -30,9 +30,11 @@ #include "error.h" #include "math_const.h" +#include "math_special.h" using namespace LAMMPS_NS; using namespace MathConst; +using namespace MathSpecial; #define MAXLINE 1024 #define DELTA 4 @@ -604,7 +606,7 @@ double PairTersoff::zeta(Param *param, double rsqij, double rsqik, costheta = (delrij[0]*delrik[0] + delrij[1]*delrik[1] + delrij[2]*delrik[2]) / (rij*rik); - if (param->powermint == 3) arg = pow(param->lam3 * (rij-rik),3.0); + if (param->powermint == 3) arg = cube(param->lam3 * (rij-rik)); else arg = param->lam3 * (rij-rik); if (arg > 69.0776) ex_delr = 1.e30; @@ -744,7 +746,7 @@ void PairTersoff::ters_zetaterm_d(double prefactor, fc = ters_fc(rik,param); dfc = ters_fc_d(rik,param); - if (param->powermint == 3) tmp = pow(param->lam3 * (rij-rik),3.0); + if (param->powermint == 3) tmp = cube(param->lam3 * (rij-rik)); else tmp = param->lam3 * (rij-rik); if (tmp > 69.0776) ex_delr = 1.e30; @@ -752,7 +754,7 @@ void PairTersoff::ters_zetaterm_d(double prefactor, else ex_delr = exp(tmp); if (param->powermint == 3) - ex_delr_d = 3.0*pow(param->lam3,3.0) * pow(rij-rik,2.0)*ex_delr; + ex_delr_d = 3.0*cube(param->lam3) * square(rij-rik)*ex_delr; else ex_delr_d = param->lam3 * ex_delr; cos_theta = vec3_dot(rij_hat,rik_hat); diff --git a/src/MANYBODY/pair_tersoff_mod.cpp b/src/MANYBODY/pair_tersoff_mod.cpp index 698dd8fa03..9d4bdb7fd0 100644 --- a/src/MANYBODY/pair_tersoff_mod.cpp +++ b/src/MANYBODY/pair_tersoff_mod.cpp @@ -25,11 +25,13 @@ #include "force.h" #include "comm.h" #include "math_const.h" +#include "math_special.h" #include "memory.h" #include "error.h" using namespace LAMMPS_NS; using namespace MathConst; +using namespace MathSpecial; #define MAXLINE 1024 #define DELTA 4 @@ -241,7 +243,7 @@ double PairTersoffMOD::zeta(Param *param, double rsqij, double rsqik, costheta = (delrij[0]*delrik[0] + delrij[1]*delrik[1] + delrij[2]*delrik[2]) / (rij*rik); - if (param->powermint == 3) arg = pow(param->lam3 * (rij-rik),3.0); + if (param->powermint == 3) arg = cube(param->lam3 * (rij-rik)); else arg = param->lam3 * (rij-rik); if (arg > 69.0776) ex_delr = 1.e30; @@ -314,7 +316,7 @@ void PairTersoffMOD::ters_zetaterm_d(double prefactor, fc = ters_fc(rik,param); dfc = ters_fc_d(rik,param); - if (param->powermint == 3) tmp = pow(param->lam3 * (rij-rik),3.0); + if (param->powermint == 3) tmp = cube(param->lam3 * (rij-rik)); else tmp = param->lam3 * (rij-rik); if (tmp > 69.0776) ex_delr = 1.e30; @@ -322,7 +324,7 @@ void PairTersoffMOD::ters_zetaterm_d(double prefactor, else ex_delr = exp(tmp); if (param->powermint == 3) - ex_delr_d = 3.0*pow(param->lam3,3.0) * pow(rij-rik,2.0)*ex_delr; + ex_delr_d = 3.0*cube(param->lam3) * square(rij-rik)*ex_delr; else ex_delr_d = param->lam3 * ex_delr; cos_theta = vec3_dot(rij_hat,rik_hat); diff --git a/src/MANYBODY/pair_tersoff_zbl.cpp b/src/MANYBODY/pair_tersoff_zbl.cpp index ab06e6ec31..d5e3fb1b0f 100644 --- a/src/MANYBODY/pair_tersoff_zbl.cpp +++ b/src/MANYBODY/pair_tersoff_zbl.cpp @@ -28,9 +28,11 @@ #include "memory.h" #include "error.h" #include "math_const.h" +#include "math_special.h" using namespace LAMMPS_NS; using namespace MathConst; +using namespace MathSpecial; #define MAXLINE 1024 #define DELTA 4 @@ -226,7 +228,7 @@ void PairTersoffZBL::repulsive(Param *param, double rsq, double &fforce, // ZBL repulsive portion - double esq = pow(global_e,2.0); + double esq = square(global_e); double a_ij = (0.8854*global_a_0) / (pow(param->Z_i,0.23) + pow(param->Z_j,0.23)); double premult = (param->Z_i * param->Z_j * esq)/(4.0*MY_PI*global_epsilon_0); @@ -286,5 +288,5 @@ double PairTersoffZBL::F_fermi(double r, Param *param) double PairTersoffZBL::F_fermi_d(double r, Param *param) { return param->ZBLexpscale*exp(-param->ZBLexpscale*(r-param->ZBLcut)) / - pow(1.0 + exp(-param->ZBLexpscale*(r-param->ZBLcut)),2.0); + square(1.0 + exp(-param->ZBLexpscale*(r-param->ZBLcut))); } -- GitLab From 4a55e9dd0c860e8c1f420eb274ea3fc91d6ff498 Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Tue, 6 Aug 2019 07:28:00 -0400 Subject: [PATCH 435/469] fix inconsistent enumerator bug in fix ave/histo vs fix ave/histo/weight --- src/fix_ave_histo_weight.cpp | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/fix_ave_histo_weight.cpp b/src/fix_ave_histo_weight.cpp index 1f0d282e5d..f4ff0ae55f 100644 --- a/src/fix_ave_histo_weight.cpp +++ b/src/fix_ave_histo_weight.cpp @@ -33,7 +33,7 @@ using namespace FixConst; enum{X,V,F,COMPUTE,FIX,VARIABLE}; enum{ONE,RUNNING}; enum{SCALAR,VECTOR,WINDOW}; -enum{GLOBAL,PERATOM,LOCAL}; +enum{DEFAULT,GLOBAL,PERATOM,LOCAL}; enum{IGNORE,END,EXTRA}; enum{SINGLE,VALUE}; -- GitLab From 59046e7444d709b7bf8f70c1f1ca890c93162975 Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Tue, 6 Aug 2019 08:52:54 -0400 Subject: [PATCH 436/469] step version number for stable release --- doc/lammps.1 | 2 +- doc/src/Manual.txt | 4 ++-- src/version.h | 2 +- 3 files changed, 4 insertions(+), 4 deletions(-) diff --git a/doc/lammps.1 b/doc/lammps.1 index 46f83698ec..ac19749dd6 100644 --- a/doc/lammps.1 +++ b/doc/lammps.1 @@ -1,4 +1,4 @@ -.TH LAMMPS "6 August 2019" "2019-08-06" +.TH LAMMPS "7 August 2019" "2019-08-07" .SH NAME .B LAMMPS \- Molecular Dynamics Simulator. diff --git a/doc/src/Manual.txt b/doc/src/Manual.txt index e461e585d9..c63137ef6f 100644 --- a/doc/src/Manual.txt +++ b/doc/src/Manual.txt @@ -1,7 +1,7 @@ LAMMPS Users Manual - + @@ -21,7 +21,7 @@ :line LAMMPS Documentation :c,h1 -6 Aug 2019 version :c,h2 +7 Aug 2019 version :c,h2 "What is a LAMMPS version?"_Manual_version.html diff --git a/src/version.h b/src/version.h index 2154f428c4..7387a3a1a4 100644 --- a/src/version.h +++ b/src/version.h @@ -1 +1 @@ -#define LAMMPS_VERSION "6 Aug 2019" +#define LAMMPS_VERSION "7 Aug 2019" -- GitLab From 131c5aadd2d938d9ef1e541ff452169b9a315292 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Eugen=20Ro=C5=BEi=C4=87?= Date: Wed, 7 Aug 2019 19:16:54 +0200 Subject: [PATCH 437/469] Error/warning tweaks --- src/USER-MISC/pair_cosine_squared.cpp | 4 ++-- src/USER-MISC/pair_cosine_squared.h | 5 +++++ 2 files changed, 7 insertions(+), 2 deletions(-) diff --git a/src/USER-MISC/pair_cosine_squared.cpp b/src/USER-MISC/pair_cosine_squared.cpp index 67cefd894b..4c8d738cee 100644 --- a/src/USER-MISC/pair_cosine_squared.cpp +++ b/src/USER-MISC/pair_cosine_squared.cpp @@ -154,10 +154,10 @@ void PairCosineSquared::coeff(int narg, char **arg) } if (cut_one < sigma_one) { - error->all(FLERR, "Incorrect args for cosine/squared pair coeffs (cutoff < sigma)"); + error->all(FLERR, "Incorrect args for pair coefficients (cutoff < sigma)"); } else if (cut_one == sigma_one) { if (wca_one == 0) { - error->all(FLERR, "Incorrect args for cosine/squared pair coeffs (cutoff = sigma w/o wca)"); + error->all(FLERR, "Incorrect args for pair coefficients (cutoff = sigma w/o wca)"); } else { error->warning(FLERR, "Cosine/squared set to WCA only (cutoff = sigma)"); } diff --git a/src/USER-MISC/pair_cosine_squared.h b/src/USER-MISC/pair_cosine_squared.h index 8c294e0d36..a638270e68 100644 --- a/src/USER-MISC/pair_cosine_squared.h +++ b/src/USER-MISC/pair_cosine_squared.h @@ -91,5 +91,10 @@ W: pair_modify shift/tail is meaningless for pair_style cosine/squared This style by definition gets to zero at cutoff distance, so there is nothing to shift and there is no tail contribution +W: Cosine/squared set to WCA only (cutoff = sigma) + +If cutoff is equal to sigma (minimum) then this pair style basically +degenerates/reverts to only WCA. This is for convenience. + */ -- GitLab From 8619462b3b5e9f0ef7ea9917f318646703efda72 Mon Sep 17 00:00:00 2001 From: "Ryan S. Elliott" Date: Wed, 7 Aug 2019 16:14:22 -0500 Subject: [PATCH 438/469] Added logs for examples/kim --- .../kim/log.7Aug19.in.kim-ex.melt.clang.1 | 107 +++++++++++++++ .../kim/log.7Aug19.in.kim-ex.melt.clang.4 | 113 ++++++++++++++++ .../log.7Aug19.in.kim-pm-query.melt.clang.1 | 124 ++++++++++++++++++ .../log.7Aug19.in.kim-pm-query.melt.clang.4 | 124 ++++++++++++++++++ .../kim/log.7Aug19.in.kim-pm.melt.clang.1 | 118 +++++++++++++++++ .../kim/log.7Aug19.in.kim-pm.melt.clang.4 | 118 +++++++++++++++++ .../kim/log.7Aug19.in.kim-sm.melt.clang.1 | 71 ++++++++++ .../kim/log.7Aug19.in.kim-sm.melt.clang.4 | 60 +++++++++ .../kim/log.7Aug19.in.lammps.melt.clang.1 | 92 +++++++++++++ .../kim/log.7Aug19.in.lammps.melt.clang.4 | 92 +++++++++++++ 10 files changed, 1019 insertions(+) create mode 100644 examples/kim/log.7Aug19.in.kim-ex.melt.clang.1 create mode 100644 examples/kim/log.7Aug19.in.kim-ex.melt.clang.4 create mode 100644 examples/kim/log.7Aug19.in.kim-pm-query.melt.clang.1 create mode 100644 examples/kim/log.7Aug19.in.kim-pm-query.melt.clang.4 create mode 100644 examples/kim/log.7Aug19.in.kim-pm.melt.clang.1 create mode 100644 examples/kim/log.7Aug19.in.kim-pm.melt.clang.4 create mode 100644 examples/kim/log.7Aug19.in.kim-sm.melt.clang.1 create mode 100644 examples/kim/log.7Aug19.in.kim-sm.melt.clang.4 create mode 100644 examples/kim/log.7Aug19.in.lammps.melt.clang.1 create mode 100644 examples/kim/log.7Aug19.in.lammps.melt.clang.4 diff --git a/examples/kim/log.7Aug19.in.kim-ex.melt.clang.1 b/examples/kim/log.7Aug19.in.kim-ex.melt.clang.1 new file mode 100644 index 0000000000..17fa1bc534 --- /dev/null +++ b/examples/kim/log.7Aug19.in.kim-ex.melt.clang.1 @@ -0,0 +1,107 @@ +LAMMPS (7 Aug 2019) +# 3d Lennard-Jones melt +# +# This example requires that the example models provided with +# the kim-api package are installed. see the ./lib/kim/README or +# ./lib/kim/Install.py files for details on how to install these +# example models. +# + +variable x index 1 +variable y index 1 +variable z index 1 + +variable xx equal 20*$x +variable xx equal 20*1 +variable yy equal 20*$y +variable yy equal 20*1 +variable zz equal 20*$z +variable zz equal 20*1 + +kim_init LennardJones_Ar real +#=== BEGIN kim-init ========================================== +units real +#=== END kim-init ============================================ + + +lattice fcc 4.4300 +Lattice spacing in x,y,z = 4.43 4.43 4.43 +region box block 0 ${xx} 0 ${yy} 0 ${zz} +region box block 0 20 0 ${yy} 0 ${zz} +region box block 0 20 0 20 0 ${zz} +region box block 0 20 0 20 0 20 +create_box 1 box +Created orthogonal box = (0 0 0) to (88.6 88.6 88.6) + 1 by 1 by 1 MPI processor grid +create_atoms 1 box +Created 32000 atoms + create_atoms CPU = 0.004321 secs + +kim_interactions Ar +#=== BEGIN kim_interactions ================================== +pair_style kim LennardJones_Ar +WARNING: KIM Model does not provide `partialParticleEnergy'; energy per atom will be zero (../pair_kim.cpp:974) +WARNING: KIM Model does not provide `partialParticleVirial'; virial per atom will be zero (../pair_kim.cpp:979) +pair_coeff * * Ar +#=== END kim_interactions ==================================== + + +mass 1 39.95 +velocity all create 200.0 232345 loop geom + +neighbor 0.3 bin +neigh_modify delay 0 every 1 check yes + +fix 1 all nve +#fix 1 all npt temp 1.0 1.0 1.0 iso 1.0 1.0 3.0 + +run 100 +Neighbor list info ... + update every 1 steps, delay 0 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 8.45 + ghost atom cutoff = 8.45 + binsize = 4.225, bins = 21 21 21 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair kim, perpetual + attributes: full, newton off, cut 8.45 + pair build: full/bin/atomonly + stencil: full/bin/3d + bin: standard +Setting up Verlet run ... + Unit style : real + Current step : 0 + Time step : 1 +Per MPI rank memory allocation (min/avg/max) = 28.12 | 28.12 | 28.12 Mbytes +Step Temp E_pair E_mol TotEng Press + 0 200 145069.63 0 164146.22 128015.94 + 100 95.179703 154939.42 0 164017.94 131602.75 +Loop time of 3.48256 on 1 procs for 100 steps with 32000 atoms + +Performance: 2.481 ns/day, 9.674 hours/ns, 28.715 timesteps/s +98.3% CPU use with 1 MPI tasks x no OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 3.0502 | 3.0502 | 3.0502 | 0.0 | 87.59 +Neigh | 0.3646 | 0.3646 | 0.3646 | 0.0 | 10.47 +Comm | 0.01783 | 0.01783 | 0.01783 | 0.0 | 0.51 +Output | 6.8e-05 | 6.8e-05 | 6.8e-05 | 0.0 | 0.00 +Modify | 0.034349 | 0.034349 | 0.034349 | 0.0 | 0.99 +Other | | 0.01547 | | | 0.44 + +Nlocal: 32000 ave 32000 max 32000 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 19911 ave 19911 max 19911 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 0 ave 0 max 0 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +FullNghs: 4.25375e+06 ave 4.25375e+06 max 4.25375e+06 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 4253750 +Ave neighs/atom = 132.93 +Neighbor list builds = 3 +Dangerous builds = 0 +Total wall time: 0:00:03 diff --git a/examples/kim/log.7Aug19.in.kim-ex.melt.clang.4 b/examples/kim/log.7Aug19.in.kim-ex.melt.clang.4 new file mode 100644 index 0000000000..8e076815fc --- /dev/null +++ b/examples/kim/log.7Aug19.in.kim-ex.melt.clang.4 @@ -0,0 +1,113 @@ +LAMMPS (7 Aug 2019) +# 3d Lennard-Jones melt +# +# This example requires that the example models provided with +# the kim-api package are installed. see the ./lib/kim/README or +# ./lib/kim/Install.py files for details on how to install these +# example models. +# + +variable x index 1 +variable y index 1 +variable z index 1 + +variable xx equal 20*$x +variable xx equal 20*1 +variable yy equal 20*$y +variable yy equal 20*1 +variable zz equal 20*$z +variable zz equal 20*1 + +kim_init LennardJones_Ar real +#=== BEGIN kim-init ========================================== +units real +#=== END kim-init ============================================ + + +lattice fcc 4.4300 +Lattice spacing in x,y,z = 4.43 4.43 4.43 +region box block 0 ${xx} 0 ${yy} 0 ${zz} +region box block 0 20 0 ${yy} 0 ${zz} +region box block 0 20 0 20 0 ${zz} +region box block 0 20 0 20 0 20 +create_box 1 box +Created orthogonal box = (0 0 0) to (88.6 88.6 88.6) + 1 by 2 by 2 MPI processor grid +create_atoms 1 box +Created 32000 atoms + create_atoms CPU = 0.000989 secs + +kim_interactions Ar +#=== BEGIN kim_interactions ================================== +pair_style kim LennardJones_Ar +WARNING: KIM Model does not provide `partialParticleEnergy'; energy per atom will be zero (../pair_kim.cpp:974) +WARNING: KIM Model does not provide `partialParticleVirial'; virial per atom will be zero (../pair_kim.cpp:979) +pair_coeff * * Ar +WARNING: KIM Model does not provide `partialParticleEnergy'; energy per atom will be zero (../pair_kim.cpp:974) +WARNING: KIM Model does not provide `partialParticleVirial'; virial per atom will be zero (../pair_kim.cpp:979) +#=== END kim_interactions ==================================== + + +mass 1 39.95 +velocity all create 200.0 232345 loop geom +WARNING: KIM Model does not provide `partialParticleEnergy'; energy per atom will be zero (../pair_kim.cpp:974) +WARNING: KIM Model does not provide `partialParticleVirial'; virial per atom will be zero (../pair_kim.cpp:979) +WARNING: KIM Model does not provide `partialParticleEnergy'; energy per atom will be zero (../pair_kim.cpp:974) +WARNING: KIM Model does not provide `partialParticleVirial'; virial per atom will be zero (../pair_kim.cpp:979) + +neighbor 0.3 bin +neigh_modify delay 0 every 1 check yes + +fix 1 all nve +#fix 1 all npt temp 1.0 1.0 1.0 iso 1.0 1.0 3.0 + +run 100 +Neighbor list info ... + update every 1 steps, delay 0 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 8.45 + ghost atom cutoff = 8.45 + binsize = 4.225, bins = 21 21 21 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair kim, perpetual + attributes: full, newton off, cut 8.45 + pair build: full/bin/atomonly + stencil: full/bin/3d + bin: standard +Setting up Verlet run ... + Unit style : real + Current step : 0 + Time step : 1 +Per MPI rank memory allocation (min/avg/max) = 9.791 | 9.791 | 9.791 Mbytes +Step Temp E_pair E_mol TotEng Press + 0 200 145069.63 0 164146.22 128015.94 + 100 95.179703 154939.42 0 164017.94 131602.75 +Loop time of 0.924494 on 4 procs for 100 steps with 32000 atoms + +Performance: 9.346 ns/day, 2.568 hours/ns, 108.167 timesteps/s +99.6% CPU use with 4 MPI tasks x no OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0.76434 | 0.76847 | 0.77207 | 0.3 | 83.12 +Neigh | 0.09089 | 0.094446 | 0.099911 | 1.1 | 10.22 +Comm | 0.038599 | 0.044759 | 0.051381 | 2.1 | 4.84 +Output | 3.5e-05 | 4e-05 | 4.9e-05 | 0.0 | 0.00 +Modify | 0.009396 | 0.009685 | 0.009941 | 0.2 | 1.05 +Other | | 0.00709 | | | 0.77 + +Nlocal: 8000 ave 8018 max 7967 min +Histogram: 1 0 0 0 0 0 1 0 0 2 +Nghost: 9131 ave 9164 max 9113 min +Histogram: 2 0 0 1 0 0 0 0 0 1 +Neighs: 0 ave 0 max 0 min +Histogram: 4 0 0 0 0 0 0 0 0 0 +FullNghs: 1.06344e+06 ave 1.06594e+06 max 1.05881e+06 min +Histogram: 1 0 0 0 0 0 1 0 0 2 + +Total # of neighbors = 4253750 +Ave neighs/atom = 132.93 +Neighbor list builds = 3 +Dangerous builds = 0 +Total wall time: 0:00:00 diff --git a/examples/kim/log.7Aug19.in.kim-pm-query.melt.clang.1 b/examples/kim/log.7Aug19.in.kim-pm-query.melt.clang.1 new file mode 100644 index 0000000000..1ca44c98ef --- /dev/null +++ b/examples/kim/log.7Aug19.in.kim-pm-query.melt.clang.1 @@ -0,0 +1,124 @@ +LAMMPS (7 Aug 2019) +# 3d Lennard-Jones melt +# +# This example requires that the KIM Portable Model (PM) +# SW_StillingerWeber_1985_Si__MO_405512056662_005 +# is installed. This can be done with the command +# kim-api-collections-management install user SW_StillingerWeber_1985_Si__MO_405512056662_005 +# If this command does not work, you may need to setup your PATH to find the utility. +# If you installed the kim-api using the LAMMPS CMake build, you can do the following +# (where the current working directory is assumed to be the LAMMPS build directory) +# source ./kim_build-prefix/bin/kim-api-activate +# If you installed the kim-api using the LAMMPS Make build, you can do the following +# (where the current working directory is assumed to be the LAMMPS src directory) +# source ../lib/kim/installed-kim-api-X.Y.Z/bin/kim-api-activate +# (where you should relplace X.Y.Z with the appropriate kim-api version number). +# +# Or, see https://openkim.org/doc/obtaining-models for alternative options. +# + +variable x index 1 +variable y index 1 +variable z index 1 + +variable xx equal 20*$x +variable xx equal 20*1 +variable yy equal 20*$y +variable yy equal 20*1 +variable zz equal 20*$z +variable zz equal 20*1 + +kim_init SW_StillingerWeber_1985_Si__MO_405512056662_005 real +#=== BEGIN kim-init ========================================== +units real +#=== END kim-init ============================================ + +kim_query a0 get_lattice_constant_cubic crystal=["fcc"] species=["Si"] units=["angstrom"] +#=== BEGIN kim-query ========================================= +variable a0 string 4.146581932902336 +#=== END kim-query =========================================== + + +lattice fcc ${a0} +lattice fcc 4.146581932902336 +Lattice spacing in x,y,z = 4.14658 4.14658 4.14658 +region box block 0 ${xx} 0 ${yy} 0 ${zz} +region box block 0 20 0 ${yy} 0 ${zz} +region box block 0 20 0 20 0 ${zz} +region box block 0 20 0 20 0 20 +create_box 1 box +Created orthogonal box = (0 0 0) to (82.9316 82.9316 82.9316) + 1 by 1 by 1 MPI processor grid +create_atoms 1 box +Created 32000 atoms + create_atoms CPU = 0.005415 secs + +kim_interactions Si +#=== BEGIN kim_interactions ================================== +pair_style kim SW_StillingerWeber_1985_Si__MO_405512056662_005 +pair_coeff * * Si +#=== END kim_interactions ==================================== + + +mass 1 39.95 +velocity all create 200.0 232345 loop geom + +neighbor 0.3 bin +neigh_modify delay 0 every 1 check yes + +fix 1 all nve +#fix 1 all npt temp 1.0 1.0 1.0 iso 1.0 1.0 3.0 + +run 100 +Neighbor list info ... + update every 1 steps, delay 0 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 4.07118 + ghost atom cutoff = 4.07118 + binsize = 2.03559, bins = 41 41 41 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair kim, perpetual + attributes: full, newton off, cut 4.07118 + pair build: full/bin/atomonly + stencil: full/bin/3d + bin: standard +Setting up Verlet run ... + Unit style : real + Current step : 0 + Time step : 1 +Per MPI rank memory allocation (min/avg/max) = 10.36 | 10.36 | 10.36 Mbytes +Step Temp E_pair E_mol TotEng Press + 0 200 -126084.25 0 -107007.66 1528.8768 + 100 94.450495 -116016.03 0 -107007.07 2282.2685 +Loop time of 74.6055 on 1 procs for 100 steps with 32000 atoms + +Performance: 0.116 ns/day, 207.238 hours/ns, 1.340 timesteps/s +98.6% CPU use with 1 MPI tasks x no OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 74.446 | 74.446 | 74.446 | 0.0 | 99.79 +Neigh | 0.096611 | 0.096611 | 0.096611 | 0.0 | 0.13 +Comm | 0.014594 | 0.014594 | 0.014594 | 0.0 | 0.02 +Output | 7.9e-05 | 7.9e-05 | 7.9e-05 | 0.0 | 0.00 +Modify | 0.03454 | 0.03454 | 0.03454 | 0.0 | 0.05 +Other | | 0.01396 | | | 0.02 + +Nlocal: 32000 ave 32000 max 32000 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 9667 ave 9667 max 9667 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 0 ave 0 max 0 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +FullNghs: 450192 ave 450192 max 450192 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 450192 +Ave neighs/atom = 14.0685 +Neighbor list builds = 3 +Dangerous builds = 0 + +Please see the log.cite file for references relevant to this simulation + +Total wall time: 0:01:16 diff --git a/examples/kim/log.7Aug19.in.kim-pm-query.melt.clang.4 b/examples/kim/log.7Aug19.in.kim-pm-query.melt.clang.4 new file mode 100644 index 0000000000..8c4148ce15 --- /dev/null +++ b/examples/kim/log.7Aug19.in.kim-pm-query.melt.clang.4 @@ -0,0 +1,124 @@ +LAMMPS (7 Aug 2019) +# 3d Lennard-Jones melt +# +# This example requires that the KIM Portable Model (PM) +# SW_StillingerWeber_1985_Si__MO_405512056662_005 +# is installed. This can be done with the command +# kim-api-collections-management install user SW_StillingerWeber_1985_Si__MO_405512056662_005 +# If this command does not work, you may need to setup your PATH to find the utility. +# If you installed the kim-api using the LAMMPS CMake build, you can do the following +# (where the current working directory is assumed to be the LAMMPS build directory) +# source ./kim_build-prefix/bin/kim-api-activate +# If you installed the kim-api using the LAMMPS Make build, you can do the following +# (where the current working directory is assumed to be the LAMMPS src directory) +# source ../lib/kim/installed-kim-api-X.Y.Z/bin/kim-api-activate +# (where you should relplace X.Y.Z with the appropriate kim-api version number). +# +# Or, see https://openkim.org/doc/obtaining-models for alternative options. +# + +variable x index 1 +variable y index 1 +variable z index 1 + +variable xx equal 20*$x +variable xx equal 20*1 +variable yy equal 20*$y +variable yy equal 20*1 +variable zz equal 20*$z +variable zz equal 20*1 + +kim_init SW_StillingerWeber_1985_Si__MO_405512056662_005 real +#=== BEGIN kim-init ========================================== +units real +#=== END kim-init ============================================ + +kim_query a0 get_lattice_constant_cubic crystal=["fcc"] species=["Si"] units=["angstrom"] +#=== BEGIN kim-query ========================================= +variable a0 string 4.146581932902336 +#=== END kim-query =========================================== + + +lattice fcc ${a0} +lattice fcc 4.146581932902336 +Lattice spacing in x,y,z = 4.14658 4.14658 4.14658 +region box block 0 ${xx} 0 ${yy} 0 ${zz} +region box block 0 20 0 ${yy} 0 ${zz} +region box block 0 20 0 20 0 ${zz} +region box block 0 20 0 20 0 20 +create_box 1 box +Created orthogonal box = (0 0 0) to (82.9316 82.9316 82.9316) + 1 by 2 by 2 MPI processor grid +create_atoms 1 box +Created 32000 atoms + create_atoms CPU = 0.000946 secs + +kim_interactions Si +#=== BEGIN kim_interactions ================================== +pair_style kim SW_StillingerWeber_1985_Si__MO_405512056662_005 +pair_coeff * * Si +#=== END kim_interactions ==================================== + + +mass 1 39.95 +velocity all create 200.0 232345 loop geom + +neighbor 0.3 bin +neigh_modify delay 0 every 1 check yes + +fix 1 all nve +#fix 1 all npt temp 1.0 1.0 1.0 iso 1.0 1.0 3.0 + +run 100 +Neighbor list info ... + update every 1 steps, delay 0 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 4.07118 + ghost atom cutoff = 4.07118 + binsize = 2.03559, bins = 41 41 41 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair kim, perpetual + attributes: full, newton off, cut 4.07118 + pair build: full/bin/atomonly + stencil: full/bin/3d + bin: standard +Setting up Verlet run ... + Unit style : real + Current step : 0 + Time step : 1 +Per MPI rank memory allocation (min/avg/max) = 3.489 | 3.489 | 3.489 Mbytes +Step Temp E_pair E_mol TotEng Press + 0 200 -126084.25 0 -107007.66 1528.8768 + 100 94.450495 -116016.03 0 -107007.07 2282.2685 +Loop time of 19.0792 on 4 procs for 100 steps with 32000 atoms + +Performance: 0.453 ns/day, 52.998 hours/ns, 5.241 timesteps/s +99.4% CPU use with 4 MPI tasks x no OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 18.78 | 18.855 | 18.937 | 1.5 | 98.83 +Neigh | 0.026047 | 0.026274 | 0.0266 | 0.1 | 0.14 +Comm | 0.09039 | 0.17196 | 0.24675 | 15.9 | 0.90 +Output | 3.9e-05 | 4.975e-05 | 6.1e-05 | 0.0 | 0.00 +Modify | 0.015667 | 0.015819 | 0.016008 | 0.1 | 0.08 +Other | | 0.01008 | | | 0.05 + +Nlocal: 8000 ave 8029 max 7968 min +Histogram: 1 1 0 0 0 0 0 0 0 2 +Nghost: 4259 ave 4303 max 4202 min +Histogram: 1 0 0 0 0 0 2 0 0 1 +Neighs: 0 ave 0 max 0 min +Histogram: 4 0 0 0 0 0 0 0 0 0 +FullNghs: 112548 ave 113091 max 111995 min +Histogram: 1 0 0 1 0 0 0 1 0 1 + +Total # of neighbors = 450192 +Ave neighs/atom = 14.0685 +Neighbor list builds = 3 +Dangerous builds = 0 + +Please see the log.cite file for references relevant to this simulation + +Total wall time: 0:00:20 diff --git a/examples/kim/log.7Aug19.in.kim-pm.melt.clang.1 b/examples/kim/log.7Aug19.in.kim-pm.melt.clang.1 new file mode 100644 index 0000000000..f5845d7fc4 --- /dev/null +++ b/examples/kim/log.7Aug19.in.kim-pm.melt.clang.1 @@ -0,0 +1,118 @@ +LAMMPS (7 Aug 2019) +# 3d Lennard-Jones melt +# +# This example requires that the KIM Portable Model (PM) +# SW_StillingerWeber_1985_Si__MO_405512056662_005 +# is installed. This can be done with the command +# kim-api-collections-management install user SW_StillingerWeber_1985_Si__MO_405512056662_005 +# If this command does not work, you may need to setup your PATH to find the utility. +# If you installed the kim-api using the LAMMPS CMake build, you can do the following +# (where the current working directory is assumed to be the LAMMPS build directory) +# source ./kim_build-prefix/bin/kim-api-activate +# If you installed the kim-api using the LAMMPS Make build, you can do the following +# (where the current working directory is assumed to be the LAMMPS src directory) +# source ../lib/kim/installed-kim-api-X.Y.Z/bin/kim-api-activate +# (where you should relplace X.Y.Z with the appropriate kim-api version number). +# +# Or, see https://openkim.org/doc/obtaining-models for alternative options. +# + +variable x index 1 +variable y index 1 +variable z index 1 + +variable xx equal 20*$x +variable xx equal 20*1 +variable yy equal 20*$y +variable yy equal 20*1 +variable zz equal 20*$z +variable zz equal 20*1 + +kim_init SW_StillingerWeber_1985_Si__MO_405512056662_005 real +#=== BEGIN kim-init ========================================== +units real +#=== END kim-init ============================================ + + +lattice fcc 4.4300 +Lattice spacing in x,y,z = 4.43 4.43 4.43 +region box block 0 ${xx} 0 ${yy} 0 ${zz} +region box block 0 20 0 ${yy} 0 ${zz} +region box block 0 20 0 20 0 ${zz} +region box block 0 20 0 20 0 20 +create_box 1 box +Created orthogonal box = (0 0 0) to (88.6 88.6 88.6) + 1 by 1 by 1 MPI processor grid +create_atoms 1 box +Created 32000 atoms + create_atoms CPU = 0.003591 secs + +kim_interactions Si +#=== BEGIN kim_interactions ================================== +pair_style kim SW_StillingerWeber_1985_Si__MO_405512056662_005 +pair_coeff * * Si +#=== END kim_interactions ==================================== + + +mass 1 39.95 +velocity all create 200.0 232345 loop geom + +neighbor 0.3 bin +neigh_modify delay 0 every 1 check yes + +fix 1 all nve +#fix 1 all npt temp 1.0 1.0 1.0 iso 1.0 1.0 3.0 + +run 100 +Neighbor list info ... + update every 1 steps, delay 0 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 4.07118 + ghost atom cutoff = 4.07118 + binsize = 2.03559, bins = 44 44 44 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair kim, perpetual + attributes: full, newton off, cut 4.07118 + pair build: full/bin/atomonly + stencil: full/bin/3d + bin: standard +Setting up Verlet run ... + Unit style : real + Current step : 0 + Time step : 1 +Per MPI rank memory allocation (min/avg/max) = 10.44 | 10.44 | 10.44 Mbytes +Step Temp E_pair E_mol TotEng Press + 0 200 -85249.847 0 -66173.259 -33302.387 + 100 253.43357 -90346.68 0 -66173.441 -14888.698 +Loop time of 74.248 on 1 procs for 100 steps with 32000 atoms + +Performance: 0.116 ns/day, 206.244 hours/ns, 1.347 timesteps/s +98.8% CPU use with 1 MPI tasks x no OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 74.118 | 74.118 | 74.118 | 0.0 | 99.83 +Neigh | 0.069623 | 0.069623 | 0.069623 | 0.0 | 0.09 +Comm | 0.0137 | 0.0137 | 0.0137 | 0.0 | 0.02 +Output | 7.6e-05 | 7.6e-05 | 7.6e-05 | 0.0 | 0.00 +Modify | 0.031883 | 0.031883 | 0.031883 | 0.0 | 0.04 +Other | | 0.01433 | | | 0.02 + +Nlocal: 32000 ave 32000 max 32000 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 7760 ave 7760 max 7760 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 0 ave 0 max 0 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +FullNghs: 402352 ave 402352 max 402352 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 402352 +Ave neighs/atom = 12.5735 +Neighbor list builds = 4 +Dangerous builds = 0 + +Please see the log.cite file for references relevant to this simulation + +Total wall time: 0:01:14 diff --git a/examples/kim/log.7Aug19.in.kim-pm.melt.clang.4 b/examples/kim/log.7Aug19.in.kim-pm.melt.clang.4 new file mode 100644 index 0000000000..0b4632b999 --- /dev/null +++ b/examples/kim/log.7Aug19.in.kim-pm.melt.clang.4 @@ -0,0 +1,118 @@ +LAMMPS (7 Aug 2019) +# 3d Lennard-Jones melt +# +# This example requires that the KIM Portable Model (PM) +# SW_StillingerWeber_1985_Si__MO_405512056662_005 +# is installed. This can be done with the command +# kim-api-collections-management install user SW_StillingerWeber_1985_Si__MO_405512056662_005 +# If this command does not work, you may need to setup your PATH to find the utility. +# If you installed the kim-api using the LAMMPS CMake build, you can do the following +# (where the current working directory is assumed to be the LAMMPS build directory) +# source ./kim_build-prefix/bin/kim-api-activate +# If you installed the kim-api using the LAMMPS Make build, you can do the following +# (where the current working directory is assumed to be the LAMMPS src directory) +# source ../lib/kim/installed-kim-api-X.Y.Z/bin/kim-api-activate +# (where you should relplace X.Y.Z with the appropriate kim-api version number). +# +# Or, see https://openkim.org/doc/obtaining-models for alternative options. +# + +variable x index 1 +variable y index 1 +variable z index 1 + +variable xx equal 20*$x +variable xx equal 20*1 +variable yy equal 20*$y +variable yy equal 20*1 +variable zz equal 20*$z +variable zz equal 20*1 + +kim_init SW_StillingerWeber_1985_Si__MO_405512056662_005 real +#=== BEGIN kim-init ========================================== +units real +#=== END kim-init ============================================ + + +lattice fcc 4.4300 +Lattice spacing in x,y,z = 4.43 4.43 4.43 +region box block 0 ${xx} 0 ${yy} 0 ${zz} +region box block 0 20 0 ${yy} 0 ${zz} +region box block 0 20 0 20 0 ${zz} +region box block 0 20 0 20 0 20 +create_box 1 box +Created orthogonal box = (0 0 0) to (88.6 88.6 88.6) + 1 by 2 by 2 MPI processor grid +create_atoms 1 box +Created 32000 atoms + create_atoms CPU = 0.000997 secs + +kim_interactions Si +#=== BEGIN kim_interactions ================================== +pair_style kim SW_StillingerWeber_1985_Si__MO_405512056662_005 +pair_coeff * * Si +#=== END kim_interactions ==================================== + + +mass 1 39.95 +velocity all create 200.0 232345 loop geom + +neighbor 0.3 bin +neigh_modify delay 0 every 1 check yes + +fix 1 all nve +#fix 1 all npt temp 1.0 1.0 1.0 iso 1.0 1.0 3.0 + +run 100 +Neighbor list info ... + update every 1 steps, delay 0 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 4.07118 + ghost atom cutoff = 4.07118 + binsize = 2.03559, bins = 44 44 44 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair kim, perpetual + attributes: full, newton off, cut 4.07118 + pair build: full/bin/atomonly + stencil: full/bin/3d + bin: standard +Setting up Verlet run ... + Unit style : real + Current step : 0 + Time step : 1 +Per MPI rank memory allocation (min/avg/max) = 3.517 | 3.517 | 3.517 Mbytes +Step Temp E_pair E_mol TotEng Press + 0 200 -85249.847 0 -66173.259 -33302.387 + 100 253.43357 -90346.68 0 -66173.441 -14888.698 +Loop time of 19.0287 on 4 procs for 100 steps with 32000 atoms + +Performance: 0.454 ns/day, 52.857 hours/ns, 5.255 timesteps/s +99.1% CPU use with 4 MPI tasks x no OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 18.81 | 18.838 | 18.883 | 0.6 | 99.00 +Neigh | 0.018598 | 0.01914 | 0.020732 | 0.7 | 0.10 +Comm | 0.10341 | 0.1475 | 0.17393 | 7.1 | 0.78 +Output | 6e-05 | 6.225e-05 | 6.7e-05 | 0.0 | 0.00 +Modify | 0.014839 | 0.014925 | 0.015047 | 0.1 | 0.08 +Other | | 0.008997 | | | 0.05 + +Nlocal: 8000 ave 8014 max 7988 min +Histogram: 1 1 0 0 0 0 1 0 0 1 +Nghost: 3374.75 ave 3389 max 3361 min +Histogram: 1 0 1 0 0 0 0 1 0 1 +Neighs: 0 ave 0 max 0 min +Histogram: 4 0 0 0 0 0 0 0 0 0 +FullNghs: 100588 ave 100856 max 100392 min +Histogram: 1 0 1 0 1 0 0 0 0 1 + +Total # of neighbors = 402352 +Ave neighs/atom = 12.5735 +Neighbor list builds = 4 +Dangerous builds = 0 + +Please see the log.cite file for references relevant to this simulation + +Total wall time: 0:00:19 diff --git a/examples/kim/log.7Aug19.in.kim-sm.melt.clang.1 b/examples/kim/log.7Aug19.in.kim-sm.melt.clang.1 new file mode 100644 index 0000000000..1b77e58a3a --- /dev/null +++ b/examples/kim/log.7Aug19.in.kim-sm.melt.clang.1 @@ -0,0 +1,71 @@ +LAMMPS (7 Aug 2019) +# 3d Lennard-Jones melt +# +# This example requires that the KIM Simulator Model (PM) +# Sim_LAMMPS_ReaxFF_StrachanVanDuinChakraborty_2003_CHNO__SM_107643900657_000 +# is installed. This can be done with the command +# kim-api-collections-management install user Sim_LAMMPS_ReaxFF_StrachanVanDuinChakraborty_2003_CHNO__SM_107643900657_000 +# If this command does not work, you may need to setup your PATH to find the utility. +# If you installed the kim-api using the LAMMPS CMake build, you can do the following +# (where the current working directory is assumed to be the LAMMPS build directory) +# source ./kim_build-prefix/bin/kim-api-activate +# If you installed the kim-api using the LAMMPS Make build, you can do the following +# (where the current working directory is assumed to be the LAMMPS src directory) +# source ../lib/kim/installed-kim-api-X.Y.Z/bin/kim-api-activate +# (where you should relplace X.Y.Z with the appropriate kim-api version number). +# +# See https://openkim.org/doc/obtaining-models for alternative options. +# + +variable x index 1 +variable y index 1 +variable z index 1 + +variable xx equal 20*$x +variable xx equal 20*1 +variable yy equal 20*$y +variable yy equal 20*1 +variable zz equal 20*$z +variable zz equal 20*1 + +kim_init Sim_LAMMPS_ReaxFF_StrachanVanDuinChakraborty_2003_CHNO__SM_107643900657_000 real +#=== BEGIN kim-init ========================================== +# Using KIM Simulator Model : Sim_LAMMPS_ReaxFF_StrachanVanDuinChakraborty_2003_CHNO__SM_107643900657_000 +# For Simulator : LAMMPS 28 Feb 2019 +# Running on : LAMMPS 7 Aug 2019 +# +units real +atom_style charge +neigh_modify one 4000 +#=== END kim-init ============================================ + + +lattice fcc 4.4300 +Lattice spacing in x,y,z = 4.43 4.43 4.43 +region box block 0 ${xx} 0 ${yy} 0 ${zz} +region box block 0 20 0 ${yy} 0 ${zz} +region box block 0 20 0 20 0 ${zz} +region box block 0 20 0 20 0 20 +create_box 1 box +Created orthogonal box = (0 0 0) to (88.6 88.6 88.6) + 1 by 1 by 1 MPI processor grid +create_atoms 1 box +Created 32000 atoms + create_atoms CPU = 0.003447 secs + +kim_interactions O +#=== BEGIN kim_interactions ================================== +pair_style reax/c /var/tmp/kim-simulator-model-parameter-file-directory-6Acs1QDbXgBx/lmp_control safezone 2.0 mincap 100 +ERROR: Unrecognized pair style 'reax/c' is part of the USER-REAXC package which is not enabled in this LAMMPS binary. (../force.cpp:262) +Last command: pair_style reax/c /var/tmp/kim-simulator-model-parameter-file-directory-6Acs1QDbXgBx/lmp_control safezone 2.0 mincap 100 +-------------------------------------------------------------------------- +Primary job terminated normally, but 1 process returned +a non-zero exit code. Per user-direction, the job has been aborted. +-------------------------------------------------------------------------- +-------------------------------------------------------------------------- +mpirun detected that one or more processes exited with non-zero status, thus causing +the job to be terminated. The first process to do so was: + + Process name: [[33054,1],0] + Exit code: 1 +-------------------------------------------------------------------------- diff --git a/examples/kim/log.7Aug19.in.kim-sm.melt.clang.4 b/examples/kim/log.7Aug19.in.kim-sm.melt.clang.4 new file mode 100644 index 0000000000..72b62beffb --- /dev/null +++ b/examples/kim/log.7Aug19.in.kim-sm.melt.clang.4 @@ -0,0 +1,60 @@ +LAMMPS (7 Aug 2019) +# 3d Lennard-Jones melt +# +# This example requires that the KIM Simulator Model (PM) +# Sim_LAMMPS_ReaxFF_StrachanVanDuinChakraborty_2003_CHNO__SM_107643900657_000 +# is installed. This can be done with the command +# kim-api-collections-management install user Sim_LAMMPS_ReaxFF_StrachanVanDuinChakraborty_2003_CHNO__SM_107643900657_000 +# If this command does not work, you may need to setup your PATH to find the utility. +# If you installed the kim-api using the LAMMPS CMake build, you can do the following +# (where the current working directory is assumed to be the LAMMPS build directory) +# source ./kim_build-prefix/bin/kim-api-activate +# If you installed the kim-api using the LAMMPS Make build, you can do the following +# (where the current working directory is assumed to be the LAMMPS src directory) +# source ../lib/kim/installed-kim-api-X.Y.Z/bin/kim-api-activate +# (where you should relplace X.Y.Z with the appropriate kim-api version number). +# +# See https://openkim.org/doc/obtaining-models for alternative options. +# + +variable x index 1 +variable y index 1 +variable z index 1 + +variable xx equal 20*$x +variable xx equal 20*1 +variable yy equal 20*$y +variable yy equal 20*1 +variable zz equal 20*$z +variable zz equal 20*1 + +kim_init Sim_LAMMPS_ReaxFF_StrachanVanDuinChakraborty_2003_CHNO__SM_107643900657_000 real +#=== BEGIN kim-init ========================================== +# Using KIM Simulator Model : Sim_LAMMPS_ReaxFF_StrachanVanDuinChakraborty_2003_CHNO__SM_107643900657_000 +# For Simulator : LAMMPS 28 Feb 2019 +# Running on : LAMMPS 7 Aug 2019 +# +units real +atom_style charge +neigh_modify one 4000 +#=== END kim-init ============================================ + + +lattice fcc 4.4300 +Lattice spacing in x,y,z = 4.43 4.43 4.43 +region box block 0 ${xx} 0 ${yy} 0 ${zz} +region box block 0 20 0 ${yy} 0 ${zz} +region box block 0 20 0 20 0 ${zz} +region box block 0 20 0 20 0 20 +create_box 1 box +Created orthogonal box = (0 0 0) to (88.6 88.6 88.6) + 1 by 2 by 2 MPI processor grid +create_atoms 1 box +Created 32000 atoms + create_atoms CPU = 0.001307 secs + +kim_interactions O +#=== BEGIN kim_interactions ================================== +pair_style reax/c /var/tmp/kim-simulator-model-parameter-file-directory-6tmKtZEXzhgv/lmp_control safezone 2.0 mincap 100 +ERROR: Unrecognized pair style 'reax/c' is part of the USER-REAXC package which is not enabled in this LAMMPS binary. (../force.cpp:262) +Last command: pair_style reax/c /var/tmp/kim-simulator-model-parameter-file-directory-6tmKtZEXzhgv/lmp_control safezone 2.0 mincap 100 diff --git a/examples/kim/log.7Aug19.in.lammps.melt.clang.1 b/examples/kim/log.7Aug19.in.lammps.melt.clang.1 new file mode 100644 index 0000000000..f697504777 --- /dev/null +++ b/examples/kim/log.7Aug19.in.lammps.melt.clang.1 @@ -0,0 +1,92 @@ +LAMMPS (7 Aug 2019) +# 3d Lennard-Jones melt + +variable x index 1 +variable y index 1 +variable z index 1 + +variable xx equal 20*$x +variable xx equal 20*1 +variable yy equal 20*$y +variable yy equal 20*1 +variable zz equal 20*$z +variable zz equal 20*1 + +units real + +lattice fcc 4.4300 +Lattice spacing in x,y,z = 4.43 4.43 4.43 +region box block 0 ${xx} 0 ${yy} 0 ${zz} +region box block 0 20 0 ${yy} 0 ${zz} +region box block 0 20 0 20 0 ${zz} +region box block 0 20 0 20 0 20 +create_box 1 box +Created orthogonal box = (0 0 0) to (88.6 88.6 88.6) + 1 by 1 by 1 MPI processor grid +create_atoms 1 box +Created 32000 atoms + create_atoms CPU = 0.003037 secs + +pair_style lj/cut 8.1500 +pair_coeff 1 1 0.0104 3.4000 + +#pair_style kim LennardJones_Ar +#pair_coeff * * Ar + +mass 1 39.95 +velocity all create 200.0 232345 loop geom + +neighbor 0.3 bin +neigh_modify delay 0 every 1 check yes + +fix 1 all nve +#fix 1 all npt temp 1.0 1.0 1.0 iso 1.0 1.0 3.0 + +run 100 +Neighbor list info ... + update every 1 steps, delay 0 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 8.45 + ghost atom cutoff = 8.45 + binsize = 4.225, bins = 21 21 21 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair lj/cut, perpetual + attributes: half, newton on + pair build: half/bin/atomonly/newton + stencil: half/bin/3d/newton + bin: standard +Setting up Verlet run ... + Unit style : real + Current step : 0 + Time step : 1 +Per MPI rank memory allocation (min/avg/max) = 19.23 | 19.23 | 19.23 Mbytes +Step Temp E_pair E_mol TotEng Press + 0 200 6290.8194 0 25367.408 6750.7421 + 100 98.747096 15900.676 0 25319.465 10184.453 +Loop time of 2.43768 on 1 procs for 100 steps with 32000 atoms + +Performance: 3.544 ns/day, 6.771 hours/ns, 41.023 timesteps/s +97.8% CPU use with 1 MPI tasks x no OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 2.1895 | 2.1895 | 2.1895 | 0.0 | 89.82 +Neigh | 0.17546 | 0.17546 | 0.17546 | 0.0 | 7.20 +Comm | 0.021001 | 0.021001 | 0.021001 | 0.0 | 0.86 +Output | 7.9e-05 | 7.9e-05 | 7.9e-05 | 0.0 | 0.00 +Modify | 0.034253 | 0.034253 | 0.034253 | 0.0 | 1.41 +Other | | 0.01735 | | | 0.71 + +Nlocal: 32000 ave 32000 max 32000 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 19911 ave 19911 max 19911 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 1.96027e+06 ave 1.96027e+06 max 1.96027e+06 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 1960266 +Ave neighs/atom = 61.2583 +Neighbor list builds = 3 +Dangerous builds = 0 +Total wall time: 0:00:02 diff --git a/examples/kim/log.7Aug19.in.lammps.melt.clang.4 b/examples/kim/log.7Aug19.in.lammps.melt.clang.4 new file mode 100644 index 0000000000..2d25348b06 --- /dev/null +++ b/examples/kim/log.7Aug19.in.lammps.melt.clang.4 @@ -0,0 +1,92 @@ +LAMMPS (7 Aug 2019) +# 3d Lennard-Jones melt + +variable x index 1 +variable y index 1 +variable z index 1 + +variable xx equal 20*$x +variable xx equal 20*1 +variable yy equal 20*$y +variable yy equal 20*1 +variable zz equal 20*$z +variable zz equal 20*1 + +units real + +lattice fcc 4.4300 +Lattice spacing in x,y,z = 4.43 4.43 4.43 +region box block 0 ${xx} 0 ${yy} 0 ${zz} +region box block 0 20 0 ${yy} 0 ${zz} +region box block 0 20 0 20 0 ${zz} +region box block 0 20 0 20 0 20 +create_box 1 box +Created orthogonal box = (0 0 0) to (88.6 88.6 88.6) + 1 by 2 by 2 MPI processor grid +create_atoms 1 box +Created 32000 atoms + create_atoms CPU = 0.001194 secs + +pair_style lj/cut 8.1500 +pair_coeff 1 1 0.0104 3.4000 + +#pair_style kim LennardJones_Ar +#pair_coeff * * Ar + +mass 1 39.95 +velocity all create 200.0 232345 loop geom + +neighbor 0.3 bin +neigh_modify delay 0 every 1 check yes + +fix 1 all nve +#fix 1 all npt temp 1.0 1.0 1.0 iso 1.0 1.0 3.0 + +run 100 +Neighbor list info ... + update every 1 steps, delay 0 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 8.45 + ghost atom cutoff = 8.45 + binsize = 4.225, bins = 21 21 21 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair lj/cut, perpetual + attributes: half, newton on + pair build: half/bin/atomonly/newton + stencil: half/bin/3d/newton + bin: standard +Setting up Verlet run ... + Unit style : real + Current step : 0 + Time step : 1 +Per MPI rank memory allocation (min/avg/max) = 7.633 | 7.633 | 7.633 Mbytes +Step Temp E_pair E_mol TotEng Press + 0 200 6290.8194 0 25367.408 6750.7421 + 100 98.747096 15900.676 0 25319.465 10184.453 +Loop time of 0.726239 on 4 procs for 100 steps with 32000 atoms + +Performance: 11.897 ns/day, 2.017 hours/ns, 137.696 timesteps/s +98.7% CPU use with 4 MPI tasks x no OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0.57617 | 0.5835 | 0.59084 | 0.9 | 80.34 +Neigh | 0.046682 | 0.047783 | 0.048641 | 0.3 | 6.58 +Comm | 0.065469 | 0.071509 | 0.07899 | 2.3 | 9.85 +Output | 3.9e-05 | 4.6e-05 | 6.1e-05 | 0.0 | 0.01 +Modify | 0.013205 | 0.01363 | 0.014044 | 0.3 | 1.88 +Other | | 0.009775 | | | 1.35 + +Nlocal: 8000 ave 8012 max 7989 min +Histogram: 1 0 0 0 2 0 0 0 0 1 +Nghost: 9131 ave 9142 max 9119 min +Histogram: 1 0 0 0 0 2 0 0 0 1 +Neighs: 490066 ave 491443 max 489273 min +Histogram: 2 0 0 0 1 0 0 0 0 1 + +Total # of neighbors = 1960266 +Ave neighs/atom = 61.2583 +Neighbor list builds = 3 +Dangerous builds = 0 +Total wall time: 0:00:00 -- GitLab From 838238b1ca80f44ea8cfd90e30b39a888c5f2077 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Eugen=20Ro=C5=BEi=C4=87?= Date: Thu, 8 Aug 2019 00:38:41 +0200 Subject: [PATCH 439/469] documentation --- doc/src/Commands_pair.txt | 1 + doc/src/Eqs/pair_cosine_squared.jpg | Bin 0 -> 8949 bytes doc/src/Eqs/pair_cosine_squared.tex | 16 ++++ doc/src/Eqs/pair_cosine_squared_wca.jpg | Bin 0 -> 6780 bytes doc/src/Eqs/pair_cosine_squared_wca.tex | 11 +++ doc/src/JPG/pair_cosine_squared_graphs.jpg | Bin 0 -> 29869 bytes doc/src/lammps.book | 1 + doc/src/pair_cosine_squared.txt | 95 +++++++++++++++++++++ doc/src/pair_style.txt | 1 + doc/src/pairs.txt | 1 + 10 files changed, 126 insertions(+) create mode 100644 doc/src/Eqs/pair_cosine_squared.jpg create mode 100644 doc/src/Eqs/pair_cosine_squared.tex create mode 100644 doc/src/Eqs/pair_cosine_squared_wca.jpg create mode 100644 doc/src/Eqs/pair_cosine_squared_wca.tex create mode 100644 doc/src/JPG/pair_cosine_squared_graphs.jpg create mode 100644 doc/src/pair_cosine_squared.txt diff --git a/doc/src/Commands_pair.txt b/doc/src/Commands_pair.txt index 6077fad8ec..47d4c40d8e 100644 --- a/doc/src/Commands_pair.txt +++ b/doc/src/Commands_pair.txt @@ -65,6 +65,7 @@ OPT. 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\sigma\right)}\right)&\quad \sigma \leq r < r_c \\ +0& \quad r \geq r_c +\end{cases} +\end{align*} + +\end{document} diff --git a/doc/src/Eqs/pair_cosine_squared_wca.jpg b/doc/src/Eqs/pair_cosine_squared_wca.jpg new file mode 100644 index 0000000000000000000000000000000000000000..086bc6367399f13c1529d860102b13ee6130e5d6 GIT binary patch literal 6780 zcmex=9G120;#nB*rbwj7khlf{e_9jQ@`?$TKi7vND1J0~9baF|)9;v2$>8asNNU zuvLJ8iIJI^iG>;DY6b?zT1F;j1{Oh9Aw@$+HsQcTcBMiQqsEB~Ih36?9uy6__(8=u zsi=vQOH5osQc6`#T|-mL#MI2(!qUpw#nsK-!_zA`Bs45MA~GsDB{eNQBQvYGq_nKO zqOz*FrM0cSqqA$$M%wS)E2#Ckf{3Xc1#K^?L z!py?X%EH3H$W+e2$iytj!m4P(ZXWYowZ;xuvL#)F*7#z7xMlZq~KiK&=8 zRQ(9@8rWyVd8~;npTRwb@YgK{9%e=cCP8LF2789T!Hc>y7zP+KAGOcOtv`C9V*Nw+ z)<3F`X4)vKcbT4Et$o%_T0-wh#G=c2?;1j8Mpjk`q)Q$&eNoSEWB!PrJ7dzVipfX6 z+nMgqZkuY#y;{23&EwPx!8eVe9xR3@C4cU1tvr8R|EKPMhRyr`_WbJqH)E^Rw^s}r z>&<>_|HvJ9QU8lRdqs$=dG8;uPu$K%`Q83o`txt)KaG1SP{OrS`pG1f6D$*NL>|q2 zP|vwy|JC$qr+v2S7q80NF8xHKEArVi=f)cwZ5VGbFfd4)grA;g`*-7?@Q3?3qATvZ 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zBfsv@vZZ~0w3)Xj6@TvT{5gx?Ir$my={?**X6gz58TS5Lu$bk6lFmv|F2M%>OOs~s k&(7P*wA67LbN+t@J*Jk$OA7cG{QknjV9kE%Kg0i<0E?C$n*aa+ literal 0 HcmV?d00001 diff --git a/doc/src/lammps.book b/doc/src/lammps.book index ef5a4275df..3c856bde19 100644 --- a/doc/src/lammps.book +++ b/doc/src/lammps.book @@ -569,6 +569,7 @@ pair_charmm.html pair_class2.html pair_colloid.html pair_comb.html +pair_cosine_squared.html pair_coul.html pair_coul_diel.html pair_coul_shield.html diff --git a/doc/src/pair_cosine_squared.txt b/doc/src/pair_cosine_squared.txt new file mode 100644 index 0000000000..ee629d867f --- /dev/null +++ b/doc/src/pair_cosine_squared.txt @@ -0,0 +1,95 @@ +"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c + +:link(lws,http://lammps.sandia.gov) +:link(ld,Manual.html) +:link(lc,Commands_all.html) + +:line + +pair_style cosine/squared command :h3 + +[Syntax:] + +pair_style cosine/squared cutoff :pre + +cutoff = global cutoff for cosine-squared interactions (distance units) :ul + +pair_coeff i j eps sigma +pair_coeff i j eps sigma cutoff +pair_coeff i j eps sigma wca +pair_coeff i j eps sigma cutoff wca :pre + +i,j = a particle type +eps = interaction strength, i.e. the depth of the potential minimum (energy units) +sigma = distance of the potential minimum from 0 +cutoff = the cutoff distance for this pair type, if different from global (distance units) +wca = if specified a Weeks-Chandler-Andersen potential (with eps strength and minimum at sigma) is added, otherwise not :ul + +[Examples:] + +pair_style cosine/squared 3.0 +pair_coeff * * 1.0 1.3 +pair_coeff 1 3 1.0 1.3 2.0 +pair_coeff 1 3 1.0 1.3 wca +pair_coeff 1 3 1.0 1.3 2.0 wca :pre + +[Description:] + +Style {cosine/squared} computes a potential of the form + +:c,image(Eqs/pair_cosine_squared.jpg) + +between two point particles, where (sigma, -epsilon) is the location of the (rightmost) minimum of the potential, as explained in the syntax section above. + +This potential was first used in \[1\] for a coarse-grained lipid membrane model. +It is generally very useful as a non-specific interaction potential because it is fully adjustable in depth and width while joining the minimum at (sigma, -epsilon) and zero at (cutoff, 0) smoothly, requiring no shifting and causing no related artifacts, tail energy calculations etc. This evidently requires {cutoff} to be larger than {sigma}. + +If the {wca} option is used then a Weeks-Chandler-Andersen potential \[2\] is added to the above specified cosine-squared potential, specifically the following: + +:c,image(Eqs/pair_cosine_squared_wca.jpg) + +In this case, and this case only, the {sigma} parameter can be equal to {cutoff} (sigma = cutoff) which will result in ONLY the WCA potential being used (and print a warning), so the minimum will be attained at (sigma, 0). This is a convenience feature that enables a purely repulsive potential to be used without a need to define an additional pair style and use the hybrid styles. + +The energy and force of this pair style for parameters epsilon = 1.0, sigma = 1.0, cutoff = 2.5, with and without the WCA potential, are shown in the graphs below: + +:c,image(JPG/pair_cosine_squared_graphs.jpg) + +:line + +There are currently no accelerated versions of this potential, although this should be relatively easy to implement on the basis of the code for the accelerated versions of similar styles (e.g. lj/cut) and anyone needing them is encouraged to do so. + +:line + +[Mixing, shift, table, tail correction, restart, rRESPA info]: + +Mixing is not supported for this style. + +The {shift}, {table} and {tail} options are not relevant for this style. + +This pair style writes its information to "binary restart +files"_restart.html, so pair_style and pair_coeff commands do not need +to be specified in an input script that reads a restart file. + +These pair styles can only be used via the {pair} keyword of the +"run_style respa"_run_style.html command. They do not support the +{inner}, {middle}, {outer} keywords. + +:line + +[Restrictions:] + +The {cosine/squared} style is part of the "USER-MISC" package. It is only +enabled if LAMMPS is build with that package. See the "Build +package"_Build_package.html doc page for more info. + +[Related commands:] + +"pair_coeff"_pair_coeff.html, +"pair_style lj/cut"_pair_lj.html + +[Default:] none + +:link(CKD,http://doi.org/10.1103/PhysRevE.72.011506) +\[1\] "Cooke, Kremer and Deserno, Phys. Rev. E, 72, 011506 (2005)"_CKD +:link(WCA,http://doi.org/10.1063/1.1674820) +\[2\] "Weeks, Chandler and Andersen, J. Chem. Phys., 54, 5237 (1971)"_WCA diff --git a/doc/src/pair_style.txt b/doc/src/pair_style.txt index 8a35e5a467..1b8e6d46ec 100644 --- a/doc/src/pair_style.txt +++ b/doc/src/pair_style.txt @@ -129,6 +129,7 @@ accelerated styles exist. "colloid"_pair_colloid.html - integrated colloidal potential "comb"_pair_comb.html - charge-optimized many-body (COMB) potential "comb3"_pair_comb.html - charge-optimized many-body (COMB3) potential +"cosine/squared"_pair_cosine_squared.html - Cooke-Kremer-Deserno membrane model potential "coul/cut"_pair_coul.html - cutoff Coulombic potential "coul/cut/soft"_pair_fep_soft.html - Coulombic potential with a soft core "coul/debye"_pair_coul.html - cutoff Coulombic potential with Debye screening diff --git a/doc/src/pairs.txt b/doc/src/pairs.txt index 2f63f18bad..f36a87dea3 100644 --- a/doc/src/pairs.txt +++ b/doc/src/pairs.txt @@ -24,6 +24,7 @@ Pair Styles :h1 pair_class2 pair_colloid pair_comb + pair_cosine_squared pair_coul pair_coul_diel pair_coul_shield -- GitLab From d90d2316d1061230145b37ff61322b4b7f5945da Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Fri, 9 Aug 2019 11:11:48 -0400 Subject: [PATCH 440/469] small tweak on include file list --- src/USER-MISC/pair_cosine_squared.cpp | 3 +-- 1 file changed, 1 insertion(+), 2 deletions(-) diff --git a/src/USER-MISC/pair_cosine_squared.cpp b/src/USER-MISC/pair_cosine_squared.cpp index 4c8d738cee..8307f0715e 100644 --- a/src/USER-MISC/pair_cosine_squared.cpp +++ b/src/USER-MISC/pair_cosine_squared.cpp @@ -14,11 +14,10 @@ Contributing authors: Eugen Rozic (University College London) ------------------------------------------------------------------------- */ +#include "pair_cosine_squared.h" #include -#include #include #include -#include "pair_cosine_squared.h" #include "atom.h" #include "comm.h" #include "force.h" -- GitLab From 11f1ba220b9bb1fa33e4f125a8b0f8a1ae521670 Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Fri, 9 Aug 2019 15:30:55 -0400 Subject: [PATCH 441/469] fix typo --- doc/src/fix.txt | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/doc/src/fix.txt b/doc/src/fix.txt index 409fde3503..e5036d5a73 100644 --- a/doc/src/fix.txt +++ b/doc/src/fix.txt @@ -244,7 +244,7 @@ accelerated styles exist. "mscg"_fix_mscg.html - apply MSCG method for force-matching to generate coarse grain models "msst"_fix_msst.html - multi-scale shock technique (MSST) integration "mvv/dpd"_fix_mvv_dpd.html - DPD using the modified velocity-Verlet integration algorithm -"mvv/edpd"_fix_mvv_dpd.html - constant energy DPD using the modified velocity-Verlet algrithm +"mvv/edpd"_fix_mvv_dpd.html - constant energy DPD using the modified velocity-Verlet algorithm "mvv/tdpd"_fix_mvv_dpd.html - constant temperature DPD using the modified velocity-Verlet algorithm "neb"_fix_neb.html - nudged elastic band (NEB) spring forces "nph"_fix_nh.html - constant NPH time integration via Nose/Hoover -- GitLab From 5f442d7b641cb697681ce70751be905b0d481afb Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Fri, 9 Aug 2019 15:31:22 -0400 Subject: [PATCH 442/469] add a couple of false positives --- doc/utils/sphinx-config/false_positives.txt | 2 ++ 1 file changed, 2 insertions(+) diff --git a/doc/utils/sphinx-config/false_positives.txt b/doc/utils/sphinx-config/false_positives.txt index 67252659bb..1d836c9235 100644 --- a/doc/utils/sphinx-config/false_positives.txt +++ b/doc/utils/sphinx-config/false_positives.txt @@ -421,6 +421,7 @@ coreshell cornflowerblue cornsilk corotate +corotation corotational correlator cosineshifted @@ -2991,6 +2992,7 @@ Waltham wavepacket wB Wbody +wca webpage Weckner WeinanE -- GitLab From 18725ce060d122622f78e44e6f87070ac8f3d1ee Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Fri, 9 Aug 2019 15:42:32 -0400 Subject: [PATCH 443/469] reformat documentation to match typical LAMMPS conventions, change links --- doc/src/pair_cosine_squared.txt | 45 +++++++++++++-------- doc/utils/sphinx-config/false_positives.txt | 1 + 2 files changed, 30 insertions(+), 16 deletions(-) diff --git a/doc/src/pair_cosine_squared.txt b/doc/src/pair_cosine_squared.txt index ee629d867f..f60e33f70d 100644 --- a/doc/src/pair_cosine_squared.txt +++ b/doc/src/pair_cosine_squared.txt @@ -39,27 +39,39 @@ Style {cosine/squared} computes a potential of the form :c,image(Eqs/pair_cosine_squared.jpg) -between two point particles, where (sigma, -epsilon) is the location of the (rightmost) minimum of the potential, as explained in the syntax section above. - -This potential was first used in \[1\] for a coarse-grained lipid membrane model. -It is generally very useful as a non-specific interaction potential because it is fully adjustable in depth and width while joining the minimum at (sigma, -epsilon) and zero at (cutoff, 0) smoothly, requiring no shifting and causing no related artifacts, tail energy calculations etc. This evidently requires {cutoff} to be larger than {sigma}. - -If the {wca} option is used then a Weeks-Chandler-Andersen potential \[2\] is added to the above specified cosine-squared potential, specifically the following: +between two point particles, where (sigma, -epsilon) is the location of +the (rightmost) minimum of the potential, as explained in the syntax +section above. + +This potential was first used in (Cooke)_#CKD for a coarse-grained lipid +membrane model. It is generally very useful as a non-specific +interaction potential because it is fully adjustable in depth and width +while joining the minimum at (sigma, -epsilon) and zero at (cutoff, 0) +smoothly, requiring no shifting and causing no related artifacts, tail +energy calculations etc. This evidently requires {cutoff} to be larger +than {sigma}. + +If the {wca} option is used then a Weeks-Chandler-Andersen potential +(Weeks)_#WCA is added to the above specified cosine-squared potential, +specifically the following: :c,image(Eqs/pair_cosine_squared_wca.jpg) -In this case, and this case only, the {sigma} parameter can be equal to {cutoff} (sigma = cutoff) which will result in ONLY the WCA potential being used (and print a warning), so the minimum will be attained at (sigma, 0). This is a convenience feature that enables a purely repulsive potential to be used without a need to define an additional pair style and use the hybrid styles. +In this case, and this case only, the {sigma} parameter can be equal to +{cutoff} (sigma = cutoff) which will result in ONLY the WCA potential +being used (and print a warning), so the minimum will be attained at +(sigma, 0). This is a convenience feature that enables a purely +repulsive potential to be used without a need to define an additional +pair style and use the hybrid styles. -The energy and force of this pair style for parameters epsilon = 1.0, sigma = 1.0, cutoff = 2.5, with and without the WCA potential, are shown in the graphs below: +The energy and force of this pair style for parameters epsilon = 1.0, +sigma = 1.0, cutoff = 2.5, with and without the WCA potential, are shown +in the graphs below: :c,image(JPG/pair_cosine_squared_graphs.jpg) :line -There are currently no accelerated versions of this potential, although this should be relatively easy to implement on the basis of the code for the accelerated versions of similar styles (e.g. lj/cut) and anyone needing them is encouraged to do so. - -:line - [Mixing, shift, table, tail correction, restart, rRESPA info]: Mixing is not supported for this style. @@ -89,7 +101,8 @@ package"_Build_package.html doc page for more info. [Default:] none -:link(CKD,http://doi.org/10.1103/PhysRevE.72.011506) -\[1\] "Cooke, Kremer and Deserno, Phys. Rev. E, 72, 011506 (2005)"_CKD -:link(WCA,http://doi.org/10.1063/1.1674820) -\[2\] "Weeks, Chandler and Andersen, J. Chem. Phys., 54, 5237 (1971)"_WCA +:link(CKD) +[(Cooke)] "Cooke, Kremer and Deserno, Phys. Rev. E, 72, 011506 (2005)" + +:link(WCA) +[(Weeks)] "Weeks, Chandler and Andersen, J. Chem. Phys., 54, 5237 (1971)" diff --git a/doc/utils/sphinx-config/false_positives.txt b/doc/utils/sphinx-config/false_positives.txt index 1d836c9235..a829060bfe 100644 --- a/doc/utils/sphinx-config/false_positives.txt +++ b/doc/utils/sphinx-config/false_positives.txt @@ -356,6 +356,7 @@ Cii Cij cis civ +CKD Clang clearstore Cleary -- GitLab From 42239bf480fa02e3c173fb7298577883345d7368 Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Fri, 9 Aug 2019 15:51:49 -0400 Subject: [PATCH 444/469] update USER-MISC README --- src/USER-MISC/README | 1 + 1 file changed, 1 insertion(+) diff --git a/src/USER-MISC/README b/src/USER-MISC/README index 59ea453058..592e38697d 100644 --- a/src/USER-MISC/README +++ b/src/USER-MISC/README @@ -69,6 +69,7 @@ improper_style ring, Georgios Vogiatzis, gvog at chemeng.ntua.gr, 25 May 12 improper_style distance, Paolo Raiteri, p.raiteri at curtin.edu.au, 2 Dec 15 pair_style agni, Axel Kohlmeyer, akohlmey at gmail.com, 9 Nov 16 pair_style buck/mdf, Paolo Raiteri, p.raiteri at curtin.edu.au, 2 Dec 15 +pair_style cosine/squared, Eugen Rozic, eugen.rozic.17 at ucl.ac.uk, 9 Aug 19 pair_style coul/diel, Axel Kohlmeyer, akohlmey at gmail.com, 1 Dec 11 pair_style coul/shield, Wengen Ouyang (Tel Aviv University), w.g.ouyang at gmail dot com, 30 Mar 18 pair_style dipole/sf, Mario Orsi, orsimario at gmail.com, 8 Aug 11 -- GitLab From fa6cf0fa8fd93f0794463d7bd5e8066e7b6cfd40 Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Fri, 9 Aug 2019 16:00:02 -0400 Subject: [PATCH 445/469] reduce compiler warnings --- src/USER-MISC/pair_cosine_squared.cpp | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/src/USER-MISC/pair_cosine_squared.cpp b/src/USER-MISC/pair_cosine_squared.cpp index 8307f0715e..4544a6db43 100644 --- a/src/USER-MISC/pair_cosine_squared.cpp +++ b/src/USER-MISC/pair_cosine_squared.cpp @@ -453,8 +453,8 @@ void PairCosineSquared::compute(int eflag, int vflag) it is called only if rsq < cutsq[itype][jtype], no need to check that ------------------------------------------------------------------------- */ -double PairCosineSquared::single(int i, int j, int itype, int jtype, double rsq, - double factor_coul, double factor_lj, +double PairCosineSquared::single(int /* i */, int /* j */, int itype, int jtype, double rsq, + double /* factor_coul */, double factor_lj, double &fforce) { double r, r2inv, r6inv, cosone, force, energy; -- GitLab From ff09c191493a1ebd6ec87159c25d1ab64749c8e7 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Eugen=20Ro=C5=BEi=C4=87?= Date: Tue, 13 Aug 2019 00:10:50 +0200 Subject: [PATCH 446/469] documentation for fix_wall_region morse --- doc/src/fix_wall_region.txt | 32 ++++++++++++++++++++++---------- 1 file changed, 22 insertions(+), 10 deletions(-) diff --git a/doc/src/fix_wall_region.txt b/doc/src/fix_wall_region.txt index 559a2f0d89..2ae73e8217 100644 --- a/doc/src/fix_wall_region.txt +++ b/doc/src/fix_wall_region.txt @@ -10,19 +10,23 @@ fix wall/region command :h3 [Syntax:] -fix ID group-ID wall/region region-ID style epsilon sigma cutoff :pre - -ID, group-ID are documented in "fix"_fix.html command -wall/region = style name of this fix command -region-ID = region whose boundary will act as wall -style = {lj93} or {lj126} or {lj1043} or {colloid} or {harmonic} -epsilon = strength factor for wall-particle interaction (energy or energy/distance^2 units) -sigma = size factor for wall-particle interaction (distance units) -cutoff = distance from wall at which wall-particle interaction is cut off (distance units) :ul +fix ID group-ID wall/region region-ID style epsilon sigma cutoff args ... :pre + +ID, group-ID are documented in "fix"_fix.html command :ulb,l +wall/region = style name of this fix command :l +region-ID = region whose boundary will act as wall :l +style = {lj93} or {lj126} or {lj1043} or {morse} or {colloid} or {harmonic} :l +epsilon = strength factor for wall-particle interaction (energy or energy/distance^2 units) :l +sigma = size factor for wall-particle interaction (distance units) :l +cutoff = distance from wall at which wall-particle interaction is cut off (distance units) :l +args = :l + alpha (width parameter), if style = {morse} + {none}, if style = {lj93/lj126/lj1043/colloid/harmonic} :pre [Examples:] -fix wall all wall/region mySphere lj93 1.0 1.0 2.5 :pre +fix wall all wall/region mySphere lj93 1.0 1.0 2.5 +fix wall all wall/region box_top morse 1.0 1.0 3.0 1.5 :pre [Description:] @@ -116,6 +120,12 @@ For style {wall/lj1043}, the energy E is given by the 10/4/3 potential: :c,image(Eqs/fix_wall_lj1043.jpg) +for style {wall/morse}, the energy E is given by the Morse potential: + +:c,image(Eqs/pair_morse.jpg) + +where {r_0 = sigma} and {D_0 = epsilon}. + For style {colloid}, the energy E is given by an integrated form of the "pair_style colloid"_pair_colloid.html potential: @@ -179,7 +189,9 @@ option for this fix. "fix wall/lj93"_fix_wall.html, "fix wall/lj126"_fix_wall.html, +"fix wall/lj1043"_fix_wall.html, "fix wall/colloid"_fix_wall.html, +"fix wall/harmonic"_fix_wall.html, "fix wall/gran"_fix_wall_gran.html [Default:] none -- GitLab From 47533bc5260c7959c15393e0ec66d466ed0267a6 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Eugen=20Ro=C5=BEi=C4=87?= Date: Tue, 13 Aug 2019 00:31:03 +0200 Subject: [PATCH 447/469] Update fix_wall_region.txt --- doc/src/fix_wall_region.txt | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/doc/src/fix_wall_region.txt b/doc/src/fix_wall_region.txt index 2ae73e8217..8d3b6aebae 100644 --- a/doc/src/fix_wall_region.txt +++ b/doc/src/fix_wall_region.txt @@ -22,6 +22,7 @@ cutoff = distance from wall at which wall-particle interaction is cut off (dista args = :l alpha (width parameter), if style = {morse} {none}, if style = {lj93/lj126/lj1043/colloid/harmonic} :pre +:ule [Examples:] @@ -120,7 +121,7 @@ For style {wall/lj1043}, the energy E is given by the 10/4/3 potential: :c,image(Eqs/fix_wall_lj1043.jpg) -for style {wall/morse}, the energy E is given by the Morse potential: +For style {wall/morse}, the energy E is given by the Morse potential: :c,image(Eqs/pair_morse.jpg) -- GitLab From e4e2342641a42dea2eec7c941f8f3d45c4fff525 Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Tue, 13 Aug 2019 11:01:14 -0400 Subject: [PATCH 448/469] no need to include mpi.h in headers that include pointers.h (directly or indirectly) --- src/comm_tiled.h | 1 - src/irregular.h | 1 - src/rcb.h | 1 - src/read_dump.h | 1 - 4 files changed, 4 deletions(-) diff --git a/src/comm_tiled.h b/src/comm_tiled.h index 4ceba44d4c..679be195aa 100644 --- a/src/comm_tiled.h +++ b/src/comm_tiled.h @@ -14,7 +14,6 @@ #ifndef LMP_COMM_TILED_H #define LMP_COMM_TILED_H -#include #include "comm.h" namespace LAMMPS_NS { diff --git a/src/irregular.h b/src/irregular.h index 7a3613b4e1..01fe40c46b 100644 --- a/src/irregular.h +++ b/src/irregular.h @@ -14,7 +14,6 @@ #ifndef LMP_IRREGULAR_H #define LMP_IRREGULAR_H -#include #include "pointers.h" namespace LAMMPS_NS { diff --git a/src/rcb.h b/src/rcb.h index f65ee2388a..555c4142b5 100644 --- a/src/rcb.h +++ b/src/rcb.h @@ -14,7 +14,6 @@ #ifndef LAMMPS_RCB_H #define LAMMPS_RCB_H -#include #include "pointers.h" namespace LAMMPS_NS { diff --git a/src/read_dump.h b/src/read_dump.h index 6fb4f11ed1..66c05cc445 100644 --- a/src/read_dump.h +++ b/src/read_dump.h @@ -22,7 +22,6 @@ CommandStyle(read_dump,ReadDump) #ifndef LMP_READ_DUMP_H #define LMP_READ_DUMP_H -#include #include "pointers.h" namespace LAMMPS_NS { -- GitLab From 259176c590f241445d13ffe011143fed9f41f00a Mon Sep 17 00:00:00 2001 From: "Ryan S. Elliott" Date: Wed, 14 Aug 2019 17:16:10 -0600 Subject: [PATCH 449/469] Add user-agent setting to kim_query curl command --- src/KIM/kim_query.cpp | 6 ++++++ 1 file changed, 6 insertions(+) diff --git a/src/KIM/kim_query.cpp b/src/KIM/kim_query.cpp index cddc81c333..8ceefeceaf 100644 --- a/src/KIM/kim_query.cpp +++ b/src/KIM/kim_query.cpp @@ -64,6 +64,8 @@ #include "input.h" #include "modify.h" #include "variable.h" +#include "version.h" +#include "info.h" #include "fix_store_kim.h" #if defined(LMP_KIM_CURL) @@ -242,6 +244,10 @@ char *do_query(char *qfunction, char * model_name, int narg, char **arg, curl_easy_setopt(handle, CURLOPT_SSL_VERIFYPEER, 0L); curl_easy_setopt(handle, CURLOPT_SSL_VERIFYHOST, 0L); #endif + std::string user_agent = std::string("kim_query--LAMMPS/") + + LAMMPS_VERSION + + " (" + Info::get_os_info() + ")"; + curl_easy_setopt(handle, CURLOPT_USERAGENT, user_agent.c_str()); curl_easy_setopt(handle, CURLOPT_URL, url.c_str()); curl_easy_setopt(handle, CURLOPT_FOLLOWLOCATION, 1L); -- GitLab From edbd525bcb19ac1bce446eaf056ff4354268b2d2 Mon Sep 17 00:00:00 2001 From: Christoph Junghans Date: Wed, 14 Aug 2019 17:16:43 -0600 Subject: [PATCH 450/469] cmake: install chain.x as well --- cmake/CMakeLists.txt | 1 + 1 file changed, 1 insertion(+) diff --git a/cmake/CMakeLists.txt b/cmake/CMakeLists.txt index e961fe25d3..91fb930be2 100644 --- a/cmake/CMakeLists.txt +++ b/cmake/CMakeLists.txt @@ -589,6 +589,7 @@ if(BUILD_TOOLS) enable_language(Fortran) add_executable(chain.x ${LAMMPS_TOOLS_DIR}/chain.f) target_link_libraries(chain.x ${CMAKE_Fortran_IMPLICIT_LINK_LIBRARIES}) + install(TARGETS chain.x DESTINATION ${CMAKE_INSTALL_BINDIR}) endif() enable_language(C) -- GitLab From 578bcf0fb0d22842f360352acd0f2d696bde8822 Mon Sep 17 00:00:00 2001 From: "Dan S. Bolintineanu" Date: Fri, 16 Aug 2019 01:19:08 -0600 Subject: [PATCH 451/469] Fixes normal force calculation bug in fix wall granular, allows twisting to be used without rolling in fix/wall/gran --- src/GRANULAR/fix_wall_gran.cpp | 6 ++++-- 1 file changed, 4 insertions(+), 2 deletions(-) diff --git a/src/GRANULAR/fix_wall_gran.cpp b/src/GRANULAR/fix_wall_gran.cpp index 8513fc702b..15c8c7519c 100644 --- a/src/GRANULAR/fix_wall_gran.cpp +++ b/src/GRANULAR/fix_wall_gran.cpp @@ -1149,11 +1149,11 @@ void FixWallGran::granular(double rsq, double dx, double dy, double dz, else{ knfac = E; //Hooke a = sqrt(dR); + Fne = knfac*delta; if (normal_model != HOOKE) { Fne *= a; knfac *= a; } - Fne = knfac*delta; if (normal_model == DMT) Fne -= 4*MY_PI*normal_coeffs[3]*Reff; } @@ -1294,10 +1294,12 @@ void FixWallGran::granular(double rsq, double dx, double dy, double dz, // rolling resistance //**************************************** - if (roll_model != ROLL_NONE) { + if (roll_model != ROLL_NONE || twist_model != NONE) { relrot1 = omega[0]; relrot2 = omega[1]; relrot3 = omega[2]; + } + if (roll_model != ROLL_NONE){ // rolling velocity, see eq. 31 of Wang et al, Particuology v 23, p 49 (2015) // This is different from the Marshall papers, -- GitLab From 42711245a2a8601ed8efeb59b8be2e060992861f Mon Sep 17 00:00:00 2001 From: "Ryan S. Elliott" Date: Fri, 16 Aug 2019 10:08:23 -0600 Subject: [PATCH 452/469] bump kim-api to 2.1.3 --- cmake/Modules/Packages/KIM.cmake | 4 ++-- lib/kim/Install.py | 2 +- 2 files changed, 3 insertions(+), 3 deletions(-) diff --git a/cmake/Modules/Packages/KIM.cmake b/cmake/Modules/Packages/KIM.cmake index 31586bfbe0..43f95125c8 100644 --- a/cmake/Modules/Packages/KIM.cmake +++ b/cmake/Modules/Packages/KIM.cmake @@ -28,8 +28,8 @@ if(PKG_KIM) message(FATAL_ERROR "Compiling the KIM-API library requires a Fortran compiler") endif() ExternalProject_Add(kim_build - URL https://s3.openkim.org/kim-api/kim-api-2.1.2.txz - URL_MD5 6ac52e14ef52967fc7858220b208cba5 + URL https://s3.openkim.org/kim-api/kim-api-2.1.3.txz + URL_MD5 6ee829a1bbba5f8b9874c88c4c4ebff8 BINARY_DIR build CMAKE_ARGS -DCMAKE_C_COMPILER=${CMAKE_C_COMPILER} -DCMAKE_CXX_COMPILER=${CMAKE_CXX_COMPILER} diff --git a/lib/kim/Install.py b/lib/kim/Install.py index 836b5ba205..2a70a720af 100644 --- a/lib/kim/Install.py +++ b/lib/kim/Install.py @@ -18,7 +18,7 @@ parser = ArgumentParser(prog='Install.py', # settings thisdir = fullpath('.') -version = "kim-api-2.1.2" +version = "kim-api-2.1.3" # help message -- GitLab From b72215fe026ecf4944c161bda578f8323bca7c8f Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Fri, 16 Aug 2019 12:43:37 -0400 Subject: [PATCH 453/469] add support for automated checksumming of downloaded sources to kim api conventional build --- lib/kim/Install.py | 36 ++++++++++++++++++++++++++---------- 1 file changed, 26 insertions(+), 10 deletions(-) diff --git a/lib/kim/Install.py b/lib/kim/Install.py index 2a70a720af..33d0071dde 100644 --- a/lib/kim/Install.py +++ b/lib/kim/Install.py @@ -10,7 +10,7 @@ import sys, os, subprocess, shutil from argparse import ArgumentParser sys.path.append('..') -from install_helpers import fullpath, geturl +from install_helpers import fullpath, geturl, checkmd5sum parser = ArgumentParser(prog='Install.py', description="LAMMPS library build wrapper script") @@ -18,7 +18,15 @@ parser = ArgumentParser(prog='Install.py', # settings thisdir = fullpath('.') -version = "kim-api-2.1.3" +version = "2.1.3" + +# known checksums for different KIM-API versions. used to validate the download. +checksums = { \ + '2.1.2' : '6ac52e14ef52967fc7858220b208cba5', \ + '2.1.3' : '6ee829a1bbba5f8b9874c88c4c4ebff8', \ + } + + # help message @@ -50,7 +58,7 @@ pgroup.add_argument("-n", "--nobuild", action="store_true", help="use the previously downloaded and compiled base KIM API.") pgroup.add_argument("-p", "--path", help="specify location of existing KIM API installation.") -parser.add_argument("-v", "--version", default=version, +parser.add_argument("-v", "--version", default=version, choices=checksums.keys(), help="set version of KIM API library to download and build (default: %s)" % version) parser.add_argument("-a", "--add", help="add single KIM model or model driver. If adding 'everything', then all available OpenKIM models are added (may take a long time)") @@ -73,6 +81,7 @@ if addflag and addmodelname == "everything": everythingflag = True buildflag = True verboseflag = args.verbose +version = args.version if pathflag: buildflag = False @@ -81,7 +90,7 @@ if pathflag: sys.exit("KIM API path %s does not exist" % kimdir) kimdir = fullpath(kimdir) -url = "https://s3.openkim.org/kim-api/%s.txz" % version +url = "https://s3.openkim.org/kim-api/kim-api-%s.txz" % version # set KIM API directory @@ -115,21 +124,28 @@ if buildflag: # download entire kim-api tarball print("Downloading kim-api tarball ...") - geturl(url, "%s/%s.txz" % (thisdir, version)) + filename = "kim-api-%s.txz" % version + geturl(url, "%s/%s" % (thisdir, filename)) + + # verify downloaded archive integrity via md5 checksum, if known. + if version in checksums: + if not checkmd5sum(checksums[version], filename): + sys.exit("Checksum for KIM-API library does not match") + print("Unpacking kim-api tarball ...") - cmd = 'cd "%s"; rm -rf "%s"; tar -xJvf %s.txz' % (thisdir, version, version) + cmd = 'cd "%s"; rm -rf "kim-api-%s"; tar -xJvf %s' % (thisdir, version, filename) subprocess.check_output(cmd, stderr=subprocess.STDOUT, shell=True) # configure kim-api print("Configuring kim-api ...") - cmd = 'cd "%s/%s" && mkdir build && cd build && cmake .. -DCMAKE_INSTALL_PREFIX="%s" -DCMAKE_BUILD_TYPE=Release' % (thisdir,version,kimdir) + cmd = 'cd "%s/kim-api-%s" && mkdir build && cd build && cmake .. -DCMAKE_INSTALL_PREFIX="%s" -DCMAKE_BUILD_TYPE=Release' % (thisdir,version,kimdir) txt = subprocess.check_output(cmd,stderr=subprocess.STDOUT,shell=True) if verboseflag: print(txt.decode("UTF-8")) # build kim-api print("Building kim-api ...") - cmd = 'cd "%s/%s/build" && make -j2' % (thisdir, version) + cmd = 'cd "%s/kim-api-%s/build" && make -j2' % (thisdir, version) txt = subprocess.check_output(cmd, stderr=subprocess.STDOUT, shell=True) if verboseflag: print(txt.decode("UTF-8")) @@ -137,7 +153,7 @@ if buildflag: # install kim-api print("Installing kim-api ...") - cmd = 'cd "%s/%s/build" && make -j2 install' % (thisdir, version) + cmd = 'cd "%s/kim-api-%s/build" && make -j2 install' % (thisdir, version) txt = subprocess.check_output(cmd, stderr=subprocess.STDOUT, shell=True) if verboseflag: print(txt.decode("UTF-8")) @@ -145,7 +161,7 @@ if buildflag: # remove source files print("Removing kim-api source and build files ...") - cmd = 'cd "%s"; rm -rf %s; rm -rf %s.txz' % (thisdir, version, version) + cmd = 'cd "%s"; rm -rf kim-api-%s; rm -rf kim-api-%s.txz' % (thisdir, version, version) subprocess.check_output(cmd, stderr=subprocess.STDOUT, shell=True) # add all OpenKIM models, if desired -- GitLab From a0f49f27d9d7387a7df4a95c86250e53b4ec8eda Mon Sep 17 00:00:00 2001 From: Andrew Schultz Date: Mon, 19 Aug 2019 18:15:19 -0400 Subject: [PATCH 454/469] Final tweaks to HMA documentation --- doc/src/compute_hma.txt | 28 +++++++++++++++------------- 1 file changed, 15 insertions(+), 13 deletions(-) diff --git a/doc/src/compute_hma.txt b/doc/src/compute_hma.txt index 863ee86159..4ab355abd7 100644 --- a/doc/src/compute_hma.txt +++ b/doc/src/compute_hma.txt @@ -49,11 +49,11 @@ decorrelation time. HMA should not be used if atoms are expected to diffuse. It is also restricted to simulations in the NVT ensemble. While this compute may be -used with any potential in LAMMPS, it may not provide efficiency improvements -for potentials that do not go to 0 smoothly at the truncation distance; +used with any potential in LAMMPS, it will provide inaccurate results +for potentials that do not go to 0 at the truncation distance; "pair_lj_smooth_linear"_pair_lj_smooth_linear.html and Ewald summation should work fine, while "pair_lj"_pair_lj.html will perform poorly unless -the cutoff is very large. Furthermore, computation of the heat capacity with +the potential is shifted (via "pair_modify"_pair_modify.html shift) or the cutoff is large. Furthermore, computation of the heat capacity with this compute is restricted to those that implement the single_hessian method in Pair. Implementing single_hessian in additional pair styles is simple. Please contact Andrew Schultz (ajs42 at buffalo.edu) and David Kofke (kofke at @@ -69,10 +69,11 @@ by noise produced by the already-known harmonic behavior. A detailed description of this method can be found in ("Moustafa"_#hma-Moustafa). The potential energy is computed by the formula: \begin\{equation\} -\left< U\right>_\{HMA\} = \frac\{d(N-1)\}\{2\beta\} + \left< U + \frac\{1\}\{2\} F\bullet\Delta r \right> +\left< U\right>_\{HMA\} = \frac\{d\}\{2\} (N-1) k_B T + \left< U + \frac\{1\}\{2\} F\bullet\Delta r \right> \end\{equation\} -where \(N\) is the number of atoms in the system, \(\beta\) is the reciprocal of the thermodynamic temperature, \(d\) is the +where \(N\) is the number of atoms in the system, \(k_B\) is Boltzmann's +constant, \(T\) is the temperature, \(d\) is the dimensionality of the system (2 or 3 for 2d/3d), \(F\bullet\Delta r\) is the sum of dot products of the atomic force vectors and displacement (from lattice sites) vectors, and \(U\) is the sum of pair, bond, angle, dihedral, improper, kspace (long-range), and fix energies. @@ -84,18 +85,18 @@ The pressure is computed by the formula: \end\{equation\} where \(\rho\) is the number density of the system, \(\Delta \hat P\) is the -difference between the harmonic and lattice pressure, and \(P_\{vir\}\) is +difference between the harmonic and lattice pressure, \(P_\{vir\}\) is the virial pressure computed as the sum of pair, bond, angle, dihedral, improper, kspace (long-range), and fix contributions to the force on each -atom. Although the method will work for any value of \(\Delta \hat P\) +atom, and \(k_B=1/k_B T\). Although the method will work for any value of \(\Delta \hat P\) specified (use pressure "units"_units.html), the precision of the resultant pressure is sensitive to \(\Delta \hat P\); the precision tends to be best when \(\Delta \hat P\) is the actual the difference between the lattice pressure and harmonic pressure. \begin\{equation\} -\left_\{HMA\} = \frac\{d k_B (N-1)\}\{2\} + \beta \left( \left< -U_\{HMA\}^2 \right> - \left^2 \right)/T + \frac\{1\}\{4 T\} +\left_\{HMA\} = \frac\{d\}\{2\} (N-1) k_B + \frac\{1\}\{k_B T^2\} \left( \left< +U_\{HMA\}^2 \right> - \left^2 \right) + \frac\{1\}\{4 T\} \left< F\bullet\Delta r + \Delta r \bullet \Phi \bullet \Delta r \right> \end\{equation\} @@ -111,7 +112,8 @@ digits. thermo_modify format float '%22.15e' :pre The {anharmonic} keyword will instruct the compute to return anharmonic -properties rather than the full properties (lattice, harmonic and anharmonic). +properties rather than the full properties, which include lattice, harmonic +and anharmonic contributions. When using this keyword, the compute must be first active (it must be included via a "thermo_style custom"_thermo_style.html command) while the atoms are still at their lattice sites (before equilibration). @@ -149,7 +151,7 @@ properties fluctuate less than the corresponding conventional properties. [Output info:] This compute calculates a global vector that includes the n properties -requested as arguments to the command (the potential energy, pressure or heat +requested as arguments to the command (the potential energy, pressure and/or heat capacity). The elements of the vector can be accessed by indices 1-n by any command that uses global vector values as input. See the "Howto output"_Howto_output.html doc page for an overview of LAMMPS output options. @@ -159,8 +161,8 @@ scalar value will be in energy "units"_units.html. [Restrictions:] -This compute is part of the USER-MISC package. It is only -enabled if LAMMPS was built with that package. See the "Build +This compute is part of the USER-MISC package. It is enabled only +if LAMMPS was built with that package. See the "Build package"_Build_package.html doc page for more info. Usage restricted to canonical (NVT) ensemble simulation only. -- GitLab From 3d9e737a19e7829d8880cd2fb87850f873a15b54 Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Tue, 20 Aug 2019 11:27:29 -0400 Subject: [PATCH 455/469] change order of morse style wall potential parameters to be consistent with pair morse and bond morse --- doc/src/fix_wall_region.txt | 35 ++++++++++++++++++----------------- src/fix_wall_region.cpp | 26 ++++++++++++++++---------- 2 files changed, 34 insertions(+), 27 deletions(-) diff --git a/doc/src/fix_wall_region.txt b/doc/src/fix_wall_region.txt index 8d3b6aebae..9807f5717d 100644 --- a/doc/src/fix_wall_region.txt +++ b/doc/src/fix_wall_region.txt @@ -10,24 +10,24 @@ fix wall/region command :h3 [Syntax:] -fix ID group-ID wall/region region-ID style epsilon sigma cutoff args ... :pre +fix ID group-ID wall/region region-ID style args ... cutoff :pre ID, group-ID are documented in "fix"_fix.html command :ulb,l wall/region = style name of this fix command :l region-ID = region whose boundary will act as wall :l style = {lj93} or {lj126} or {lj1043} or {morse} or {colloid} or {harmonic} :l -epsilon = strength factor for wall-particle interaction (energy or energy/distance^2 units) :l -sigma = size factor for wall-particle interaction (distance units) :l -cutoff = distance from wall at which wall-particle interaction is cut off (distance units) :l args = :l - alpha (width parameter), if style = {morse} - {none}, if style = {lj93/lj126/lj1043/colloid/harmonic} :pre + epsilon = strength factor for wall-particle interaction (energy or energy/distance^2 units) + alpha (width parameter), only if style = {morse} + sigma = size factor for wall-particle interaction (distance units) :pre +cutoff = distance from wall at which wall-particle interaction is cut off (distance units) :l :ule [Examples:] fix wall all wall/region mySphere lj93 1.0 1.0 2.5 -fix wall all wall/region box_top morse 1.0 1.0 3.0 1.5 :pre +fix wall all wall/region mySphere harmonic 1.0 0.0 2.5 +fix wall all wall/region box_top morse 1.0 1.0 1.5 3.0 :pre [Description:] @@ -121,27 +121,28 @@ For style {wall/lj1043}, the energy E is given by the 10/4/3 potential: :c,image(Eqs/fix_wall_lj1043.jpg) -For style {wall/morse}, the energy E is given by the Morse potential: - -:c,image(Eqs/pair_morse.jpg) - -where {r_0 = sigma} and {D_0 = epsilon}. - For style {colloid}, the energy E is given by an integrated form of the "pair_style colloid"_pair_colloid.html potential: :c,image(Eqs/fix_wall_colloid.jpg) For style {wall/harmonic}, the energy E is given by a harmonic spring -potential: +potential (the distance parameter is ignored): :c,image(Eqs/fix_wall_harmonic.jpg) +For style {wall/morse}, the energy E is given by the Morse potential: + +:c,image(Eqs/pair_morse.jpg) + +Unlike other styles, this requires three parameters ({D_0}, {alpha}, {r_0} +in this order) instead of two like for the other wall styles. + In all cases, {r} is the distance from the particle to the region surface, and Rc is the {cutoff} distance at which the particle and -surface no longer interact. The energy of the wall potential is -shifted so that the wall-particle interaction energy is 0.0 at the -cutoff distance. +surface no longer interact. The cutoff is always the last argument. +The energy of the wall potential is shifted so that the wall-particle +interaction energy is 0.0 at the cutoff distance. For a full description of these wall styles, see fix_style "wall"_fix_wall.html diff --git a/src/fix_wall_region.cpp b/src/fix_wall_region.cpp index cab5c37a45..70bde90d2b 100644 --- a/src/fix_wall_region.cpp +++ b/src/fix_wall_region.cpp @@ -28,7 +28,7 @@ using namespace LAMMPS_NS; using namespace FixConst; using namespace MathConst; -enum{LJ93,LJ126,LJ1043,MORSE,COLLOID,HARMONIC}; +enum{LJ93,LJ126,LJ1043,COLLOID,HARMONIC,MORSE}; /* ---------------------------------------------------------------------- */ @@ -60,25 +60,31 @@ FixWallRegion::FixWallRegion(LAMMPS *lmp, int narg, char **arg) : if (strcmp(arg[4],"lj93") == 0) style = LJ93; else if (strcmp(arg[4],"lj126") == 0) style = LJ126; else if (strcmp(arg[4],"lj1043") == 0) style = LJ1043; - else if (strcmp(arg[4],"morse") == 0) style = MORSE; else if (strcmp(arg[4],"colloid") == 0) style = COLLOID; else if (strcmp(arg[4],"harmonic") == 0) style = HARMONIC; + else if (strcmp(arg[4],"morse") == 0) style = MORSE; else error->all(FLERR,"Illegal fix wall/region command"); if (style != COLLOID) dynamic_group_allow = 1; - epsilon = force->numeric(FLERR,arg[5]); - sigma = force->numeric(FLERR,arg[6]); - cutoff = force->numeric(FLERR,arg[7]); - if (style == MORSE) { if (narg != 9) error->all(FLERR,"Illegal fix wall/region command"); - else - alpha = force->numeric(FLERR,arg[8]); - } else if (narg != 8) + + epsilon = force->numeric(FLERR,arg[5]); + alpha = force->numeric(FLERR,arg[6]); + sigma = force->numeric(FLERR,arg[7]); + cutoff = force->numeric(FLERR,arg[8]); + + } else { + if (narg != 8) error->all(FLERR,"Illegal fix wall/region command"); + epsilon = force->numeric(FLERR,arg[5]); + sigma = force->numeric(FLERR,arg[6]); + cutoff = force->numeric(FLERR,arg[7]); + } + if (cutoff <= 0.0) error->all(FLERR,"Fix wall/region cutoff <= 0.0"); eflag = 0; @@ -297,7 +303,7 @@ void FixWallRegion::post_force(int vflag) /* ---------------------------------------------------------------------- */ -void FixWallRegion::post_force_respa(int vflag, int ilevel, int iloop) +void FixWallRegion::post_force_respa(int vflag, int ilevel, int /* iloop */) { if (ilevel == ilevel_respa) post_force(vflag); } -- GitLab From 88ff8ce2d7942ce9e01d934fbaed9f4ef4905548 Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Tue, 20 Aug 2019 12:05:14 -0400 Subject: [PATCH 456/469] fix spelling issues in docs --- doc/src/fix.txt | 2 +- doc/utils/sphinx-config/false_positives.txt | 1 + 2 files changed, 2 insertions(+), 1 deletion(-) diff --git a/doc/src/fix.txt b/doc/src/fix.txt index 409fde3503..e5036d5a73 100644 --- a/doc/src/fix.txt +++ b/doc/src/fix.txt @@ -244,7 +244,7 @@ accelerated styles exist. "mscg"_fix_mscg.html - apply MSCG method for force-matching to generate coarse grain models "msst"_fix_msst.html - multi-scale shock technique (MSST) integration "mvv/dpd"_fix_mvv_dpd.html - DPD using the modified velocity-Verlet integration algorithm -"mvv/edpd"_fix_mvv_dpd.html - constant energy DPD using the modified velocity-Verlet algrithm +"mvv/edpd"_fix_mvv_dpd.html - constant energy DPD using the modified velocity-Verlet algorithm "mvv/tdpd"_fix_mvv_dpd.html - constant temperature DPD using the modified velocity-Verlet algorithm "neb"_fix_neb.html - nudged elastic band (NEB) spring forces "nph"_fix_nh.html - constant NPH time integration via Nose/Hoover diff --git a/doc/utils/sphinx-config/false_positives.txt b/doc/utils/sphinx-config/false_positives.txt index 67252659bb..012c377ba5 100644 --- a/doc/utils/sphinx-config/false_positives.txt +++ b/doc/utils/sphinx-config/false_positives.txt @@ -421,6 +421,7 @@ coreshell cornflowerblue cornsilk corotate +corotation corotational correlator cosineshifted -- GitLab From 2b42428d28605f33ebea01acb1eade08006a5a44 Mon Sep 17 00:00:00 2001 From: Richard Berger Date: Tue, 20 Aug 2019 14:04:49 -0600 Subject: [PATCH 457/469] Extend lib interface to set fix external callback This allows creating a callback in Python and attaching it to a fix external instance. --- examples/COUPLE/python/example.py | 36 ++++++++++++++++++++ examples/COUPLE/python/in.fix_external | 23 +++++++++++++ python/lammps.py | 46 ++++++++++++++++++++++++-- src/library.cpp | 30 +++++++++++++++++ src/library.h | 8 +++++ 5 files changed, 141 insertions(+), 2 deletions(-) create mode 100644 examples/COUPLE/python/example.py create mode 100644 examples/COUPLE/python/in.fix_external diff --git a/examples/COUPLE/python/example.py b/examples/COUPLE/python/example.py new file mode 100644 index 0000000000..6a3c978822 --- /dev/null +++ b/examples/COUPLE/python/example.py @@ -0,0 +1,36 @@ +# this example requires the LAMMPS Python package (lammps.py) to be installed +# and LAMMPS to be loadable as shared library in LD_LIBRARY_PATH + +import lammps + +def callback(caller, ntimestep, nlocal, tag, x, fext): + """ + This callback receives a caller object that was setup when registering the callback + + In addition to timestep and number of local atoms, the tag and x arrays are passed as + NumPy arrays. The fext array is a force array allocated for fix external, which + can be used to apply forces to all atoms. Simply update the value in the array, + it will be directly written into the LAMMPS C arrays + """ + print("Data passed by caller (optional)", caller) + print("Timestep:", ntimestep) + print("Number of Atoms:", nlocal) + print("Atom Tags:", tag) + print("Atom Positions:", x) + print("Force Additions:", fext) + fext.fill(1.0) + print("Force additions after update:", fext) + print("="*40) + +L = lammps.lammps() +L.file("in.lammps") + +# you can pass an arbitrary Python object to the callback every time it is called +# this can be useful if you need more state information such as the LAMMPS ptr to +# make additional library calls +custom_object = ["Some data", L] + +L.set_fix_external_callback("2", callback, custom_object) +L.command("run 100") + + diff --git a/examples/COUPLE/python/in.fix_external b/examples/COUPLE/python/in.fix_external new file mode 100644 index 0000000000..f222717c1a --- /dev/null +++ b/examples/COUPLE/python/in.fix_external @@ -0,0 +1,23 @@ +# LAMMPS input for coupling LAMMPS with Python via fix external + +units metal +dimension 3 +atom_style atomic +atom_modify sort 0 0.0 + +lattice diamond 5.43 +region box block 0 1 0 1 0 1 +create_box 1 box +create_atoms 1 box +mass 1 28.08 + +velocity all create 300.0 87293 loop geom + +fix 1 all nve +fix 2 all external pf/callback 1 1 + +#dump 2 all image 25 image.*.jpg type type & +# axes yes 0.8 0.02 view 60 -30 +#dump_modify 2 pad 3 + +thermo 1 diff --git a/python/lammps.py b/python/lammps.py index 9b3790f2db..36cf2d2fdd 100644 --- a/python/lammps.py +++ b/python/lammps.py @@ -219,6 +219,12 @@ class lammps(object): self.c_imageint = get_ctypes_int(self.extract_setting("imageint")) self._installed_packages = None + # add way to insert Python callback for fix external + self.callback = {} + self.FIX_EXTERNAL_CALLBACK_FUNC = CFUNCTYPE(None, c_void_p, self.c_bigint, c_int, POINTER(self.c_tagint), POINTER(POINTER(c_double)), POINTER(POINTER(c_double))) + self.lib.lammps_set_fix_external_callback.argtypes = [c_void_p, c_char_p, self.FIX_EXTERNAL_CALLBACK_FUNC, c_void_p] + self.lib.lammps_set_fix_external_callback.restype = None + # shut-down LAMMPS instance def __del__(self): @@ -602,6 +608,42 @@ class lammps(object): self._installed_packages.append(sb.value.decode()) return self._installed_packages + def set_fix_external_callback(self, fix_name, callback, caller=None): + import numpy as np + def _ctype_to_numpy_int(ctype_int): + if ctype_int == c_int32: + return np.int32 + elif ctype_int == c_int64: + return np.int64 + return np.intc + + def callback_wrapper(caller_ptr, ntimestep, nlocal, tag_ptr, x_ptr, fext_ptr): + if cast(caller_ptr,POINTER(py_object)).contents: + pyCallerObj = cast(caller_ptr,POINTER(py_object)).contents.value + else: + pyCallerObj = None + + tptr = cast(tag_ptr, POINTER(self.c_tagint * nlocal)) + tag = np.frombuffer(tptr.contents, dtype=_ctype_to_numpy_int(self.c_tagint)) + tag.shape = (nlocal) + + xptr = cast(x_ptr[0], POINTER(c_double * nlocal * 3)) + x = np.frombuffer(xptr.contents) + x.shape = (nlocal, 3) + + fptr = cast(fext_ptr[0], POINTER(c_double * nlocal * 3)) + f = np.frombuffer(fptr.contents) + f.shape = (nlocal, 3) + + callback(pyCallerObj, ntimestep, nlocal, tag, x, f) + + cFunc = self.FIX_EXTERNAL_CALLBACK_FUNC(callback_wrapper) + cCaller = cast(pointer(py_object(caller)), c_void_p) + + self.callback[fix_name] = { 'function': cFunc, 'caller': caller } + + self.lib.lammps_set_fix_external_callback(self.lmp, fix_name.encode(), cFunc, cCaller) + # ------------------------------------------------------------------------- # ------------------------------------------------------------------------- # ------------------------------------------------------------------------- @@ -872,8 +914,8 @@ class PyLammps(object): output = self.__getattr__('run')(*args, **kwargs) if(lammps.has_mpi4py): - output = self.lmp.comm.bcast(output, root=0) - + output = self.lmp.comm.bcast(output, root=0) + self.runs += get_thermo_data(output) return output diff --git a/src/library.cpp b/src/library.cpp index 30b7c7c7ce..4e265f2cd2 100644 --- a/src/library.cpp +++ b/src/library.cpp @@ -37,6 +37,7 @@ #include "error.h" #include "force.h" #include "info.h" +#include "fix_external.h" #if defined(LAMMPS_EXCEPTIONS) #include "exceptions.h" @@ -1605,6 +1606,35 @@ void lammps_create_atoms(void *ptr, int n, tagint *id, int *type, END_CAPTURE } +void lammps_set_fix_external_callback(void *ptr, char *id, FixExternalFnPtr callback_ptr, void * caller) +{ + LAMMPS *lmp = (LAMMPS *) ptr; + FixExternal::FnPtr callback = (FixExternal::FnPtr) callback_ptr; + + BEGIN_CAPTURE + { + int ifix = lmp->modify->find_fix(id); + if (ifix < 0) { + char str[50]; + sprintf(str, "Can not find fix with ID '%s'!", id); + lmp->error->all(FLERR,str); + } + + Fix *fix = lmp->modify->fix[ifix]; + + if (strcmp("external",fix->style) != 0){ + char str[50]; + sprintf(str, "Fix '%s' is not of style external!", id); + lmp->error->all(FLERR,str); + } + + FixExternal * fext = (FixExternal*) fix; + fext->set_callback(callback, caller); + } + END_CAPTURE +} + + // ---------------------------------------------------------------------- // library API functions for accessing LAMMPS configuration // ---------------------------------------------------------------------- diff --git a/src/library.h b/src/library.h index 8b03bb3621..59b68b9502 100644 --- a/src/library.h +++ b/src/library.h @@ -58,6 +58,14 @@ void lammps_gather_atoms_subset(void *, char *, int, int, int, int *, void *); void lammps_scatter_atoms(void *, char *, int, int, void *); void lammps_scatter_atoms_subset(void *, char *, int, int, int, int *, void *); +#ifdef LAMMPS_BIGBIG +typedef void (*FixExternalFnPtr)(void *, int64_t, int, int64_t *, double **, double **); +void lammps_set_fix_external_callback(void *, char *, FixExternalFnPtr, void*); +#else +typedef void (*FixExternalFnPtr)(void *, int, int, int *, double **, double **); +void lammps_set_fix_external_callback(void *, char *, FixExternalFnPtr, void*); +#endif + int lammps_config_has_package(char * package_name); int lammps_config_package_count(); int lammps_config_package_name(int index, char * buffer, int max_size); -- GitLab From 7beb2a53f2c4142bc0bba00130fd7e76a56152d3 Mon Sep 17 00:00:00 2001 From: Richard Berger Date: Tue, 20 Aug 2019 14:12:14 -0600 Subject: [PATCH 458/469] Add missing comment --- src/library.cpp | 5 +++++ 1 file changed, 5 insertions(+) diff --git a/src/library.cpp b/src/library.cpp index 4e265f2cd2..7cf0e0f01f 100644 --- a/src/library.cpp +++ b/src/library.cpp @@ -1606,6 +1606,11 @@ void lammps_create_atoms(void *ptr, int n, tagint *id, int *type, END_CAPTURE } +/* ---------------------------------------------------------------------- + find fix external with given ID and set the callback function + and caller pointer +------------------------------------------------------------------------- */ + void lammps_set_fix_external_callback(void *ptr, char *id, FixExternalFnPtr callback_ptr, void * caller) { LAMMPS *lmp = (LAMMPS *) ptr; -- GitLab From b5a79f9616457a5257970388506ae53232e03841 Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Tue, 20 Aug 2019 16:50:49 -0400 Subject: [PATCH 459/469] update fix wall/region docs as requested by @sjplimp (i hope) --- doc/src/fix_wall_region.txt | 9 ++++++--- 1 file changed, 6 insertions(+), 3 deletions(-) diff --git a/doc/src/fix_wall_region.txt b/doc/src/fix_wall_region.txt index 9807f5717d..702ca8e694 100644 --- a/doc/src/fix_wall_region.txt +++ b/doc/src/fix_wall_region.txt @@ -15,11 +15,14 @@ fix ID group-ID wall/region region-ID style args ... cutoff :pre ID, group-ID are documented in "fix"_fix.html command :ulb,l wall/region = style name of this fix command :l region-ID = region whose boundary will act as wall :l -style = {lj93} or {lj126} or {lj1043} or {morse} or {colloid} or {harmonic} :l -args = :l +style = {lj93} or {lj126} or {lj1043} or {colloid} or {harmonic} or {morse} :l +args for styles {lj93} or {lj126} or {lj1043} or {colloid} or {harmonic} = :l epsilon = strength factor for wall-particle interaction (energy or energy/distance^2 units) - alpha (width parameter), only if style = {morse} sigma = size factor for wall-particle interaction (distance units) :pre +args for style {morse} = :l + D_0 = depth of the potential (energy units) + alpha = width parameter (1/distance units) + r_0 = distance of the potential minimum from wall position (distance units) :pre cutoff = distance from wall at which wall-particle interaction is cut off (distance units) :l :ule -- GitLab From f4254cba0986bb4dc65244e1c2d51df273e5e9ee Mon Sep 17 00:00:00 2001 From: Richard Berger Date: Tue, 20 Aug 2019 16:47:43 -0600 Subject: [PATCH 460/469] Use snprintf instead of sprintf --- src/library.cpp | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/src/library.cpp b/src/library.cpp index 7cf0e0f01f..54497970ad 100644 --- a/src/library.cpp +++ b/src/library.cpp @@ -1596,7 +1596,7 @@ void lammps_create_atoms(void *ptr, int n, tagint *id, int *type, if (lmp->atom->natoms != natoms_prev + n) { char str[128]; - sprintf(str,"Library warning in lammps_create_atoms, " + snprintf(str, 128, "Library warning in lammps_create_atoms, " "invalid total atoms " BIGINT_FORMAT " " BIGINT_FORMAT, lmp->atom->natoms,natoms_prev+n); if (lmp->comm->me == 0) @@ -1621,7 +1621,7 @@ void lammps_set_fix_external_callback(void *ptr, char *id, FixExternalFnPtr call int ifix = lmp->modify->find_fix(id); if (ifix < 0) { char str[50]; - sprintf(str, "Can not find fix with ID '%s'!", id); + snprintf(str, 50, "Can not find fix with ID '%s'!", id); lmp->error->all(FLERR,str); } @@ -1629,7 +1629,7 @@ void lammps_set_fix_external_callback(void *ptr, char *id, FixExternalFnPtr call if (strcmp("external",fix->style) != 0){ char str[50]; - sprintf(str, "Fix '%s' is not of style external!", id); + snprintf(str, 50, "Fix '%s' is not of style external!", id); lmp->error->all(FLERR,str); } -- GitLab From 9b703c66751dd5b3e170e4b97aac6d6aba544b3c Mon Sep 17 00:00:00 2001 From: Richard Berger Date: Tue, 20 Aug 2019 16:54:37 -0600 Subject: [PATCH 461/469] Fix file name --- examples/COUPLE/python/example.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/examples/COUPLE/python/example.py b/examples/COUPLE/python/example.py index 6a3c978822..ea268fe1ca 100644 --- a/examples/COUPLE/python/example.py +++ b/examples/COUPLE/python/example.py @@ -23,7 +23,7 @@ def callback(caller, ntimestep, nlocal, tag, x, fext): print("="*40) L = lammps.lammps() -L.file("in.lammps") +L.file("in.fix_external") # you can pass an arbitrary Python object to the callback every time it is called # this can be useful if you need more state information such as the LAMMPS ptr to -- GitLab From b79e5401d408805b04e183591ab95c2d26311740 Mon Sep 17 00:00:00 2001 From: Richard Berger Date: Tue, 20 Aug 2019 16:55:36 -0600 Subject: [PATCH 462/469] Increase string buffer size to 128 --- src/library.cpp | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/src/library.cpp b/src/library.cpp index 54497970ad..6f283ea4da 100644 --- a/src/library.cpp +++ b/src/library.cpp @@ -1620,16 +1620,16 @@ void lammps_set_fix_external_callback(void *ptr, char *id, FixExternalFnPtr call { int ifix = lmp->modify->find_fix(id); if (ifix < 0) { - char str[50]; - snprintf(str, 50, "Can not find fix with ID '%s'!", id); + char str[128]; + snprintf(str, 128, "Can not find fix with ID '%s'!", id); lmp->error->all(FLERR,str); } Fix *fix = lmp->modify->fix[ifix]; if (strcmp("external",fix->style) != 0){ - char str[50]; - snprintf(str, 50, "Fix '%s' is not of style external!", id); + char str[128]; + snprintf(str, 128, "Fix '%s' is not of style external!", id); lmp->error->all(FLERR,str); } -- GitLab From 6b1df0729870fdc7622146b27da8a8721790e5a4 Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Tue, 20 Aug 2019 19:24:22 -0400 Subject: [PATCH 463/469] compute HMA style name should be lowercase --- examples/USER/misc/hma/hma.in | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/examples/USER/misc/hma/hma.in b/examples/USER/misc/hma/hma.in index 50c6dd96fb..96f2ca1f2a 100644 --- a/examples/USER/misc/hma/hma.in +++ b/examples/USER/misc/hma/hma.in @@ -23,7 +23,7 @@ compute u all pe compute p all pressure NULL pair -compute hma all HMA settemp u p 9.579586686264458 cv +compute hma all hma settemp u p 9.579586686264458 cv timestep 0.005 -- GitLab From 14b93f91e2a739cce040d1d3d8e92c9938c9b805 Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Tue, 20 Aug 2019 19:25:19 -0400 Subject: [PATCH 464/469] Compute HMA style name should be lowercase (and match the docs) --- src/USER-MISC/compute_hma.h | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/USER-MISC/compute_hma.h b/src/USER-MISC/compute_hma.h index 44906b53a1..233e8bbe57 100644 --- a/src/USER-MISC/compute_hma.h +++ b/src/USER-MISC/compute_hma.h @@ -13,7 +13,7 @@ #ifdef COMPUTE_CLASS -ComputeStyle(HMA,ComputeHMA) +ComputeStyle(hma,ComputeHMA) #else -- GitLab From fffe2eb958d6da8acf99e554b82bc944b294d0c6 Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Tue, 20 Aug 2019 19:26:26 -0400 Subject: [PATCH 465/469] Silence compiler warning --- src/pair_lj_smooth_linear.cpp | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/pair_lj_smooth_linear.cpp b/src/pair_lj_smooth_linear.cpp index 9dcee2362e..b6dae6524a 100644 --- a/src/pair_lj_smooth_linear.cpp +++ b/src/pair_lj_smooth_linear.cpp @@ -349,7 +349,7 @@ double PairLJSmoothLinear::single(int /*i*/, int /*j*/, int itype, int jtype, } double PairLJSmoothLinear::single_hessian(int /*i*/, int /*j*/, int itype, int jtype, double rsq, - double delr[3], double factor_coul, double factor_lj, + double delr[3], double /*factor_coul*/, double factor_lj, double &fforce, double d2u[6]) { double r2inv,r6inv,forcelj,philj,r,rinv; -- GitLab From 91a80c3c213acfb526a79522dfdd2ee58fca600c Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Tue, 20 Aug 2019 19:28:03 -0400 Subject: [PATCH 466/469] Silence another compiler warning --- src/pair_lj_smooth_linear.cpp | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/pair_lj_smooth_linear.cpp b/src/pair_lj_smooth_linear.cpp index b6dae6524a..bc2904c262 100644 --- a/src/pair_lj_smooth_linear.cpp +++ b/src/pair_lj_smooth_linear.cpp @@ -328,7 +328,7 @@ void PairLJSmoothLinear::read_restart_settings(FILE *fp) double PairLJSmoothLinear::single(int /*i*/, int /*j*/, int itype, int jtype, double rsq, - double factor_coul, double factor_lj, + double /*factor_coul*/, double factor_lj, double &fforce) { double r2inv,r6inv,forcelj,philj,r,rinv; -- GitLab From 6a584672e853005bf7e2040343049dc835e9430f Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Tue, 20 Aug 2019 13:29:09 -0400 Subject: [PATCH 467/469] implement fix wall/morse based on fix wall/region and fix wall/harmonic --- doc/src/fix_wall.txt | 22 +++++++++-- src/fix_wall.cpp | 14 +++++++ src/fix_wall.h | 6 +-- src/fix_wall_morse.cpp | 87 ++++++++++++++++++++++++++++++++++++++++++ src/fix_wall_morse.h | 49 ++++++++++++++++++++++++ 5 files changed, 172 insertions(+), 6 deletions(-) create mode 100644 src/fix_wall_morse.cpp create mode 100644 src/fix_wall_morse.h diff --git a/doc/src/fix_wall.txt b/doc/src/fix_wall.txt index 162e32c68c..b8e380fb16 100644 --- a/doc/src/fix_wall.txt +++ b/doc/src/fix_wall.txt @@ -12,22 +12,25 @@ fix wall/lj126 command :h3 fix wall/lj1043 command :h3 fix wall/colloid command :h3 fix wall/harmonic command :h3 +fix wall/morse command :h3 [Syntax:] fix ID group-ID style face args ... keyword value ... :pre ID, group-ID are documented in "fix"_fix.html command :ulb,l -style = {wall/lj93} or {wall/lj126} or {wall/lj1043} or {wall/colloid} or {wall/harmonic} :l +style = {wall/lj93} or {wall/lj126} or {wall/lj1043} or {wall/colloid} or {wall/harmonic} or {wall/morse} :l one or more face/arg pairs may be appended :l face = {xlo} or {xhi} or {ylo} or {yhi} or {zlo} or {zhi} :l - args = coord epsilon sigma cutoff + args = coord epsilon \[alpha\] sigma cutoff coord = position of wall = EDGE or constant or variable EDGE = current lo or hi edge of simulation box constant = number like 0.0 or -30.0 (distance units) variable = "equal-style variable"_variable.html like v_x or v_wiggle epsilon = strength factor for wall-particle interaction (energy or energy/distance^2 units) epsilon can be a variable (see below) + alpha = width factor for wall-particle interaction (1/distance units) + [only] for {wall/morse}. alpha can be a variable (see below) sigma = size factor for wall-particle interaction (distance units) sigma can be a variable (see below) cutoff = distance from wall at which wall-particle interaction is cut off (distance units) :pre @@ -48,6 +51,7 @@ keyword = {units} or {fld} :l fix wallhi all wall/lj93 xlo -1.0 1.0 1.0 2.5 units box fix wallhi all wall/lj93 xhi EDGE 1.0 1.0 2.5 +fix wallhi all wall/morse xhi EDGE 1.0 1.0 1.0 2.5 units box fix wallhi all wall/lj126 v_wiggle 23.2 1.0 1.0 2.5 fix zwalls all wall/colloid zlo 0.0 1.0 1.0 0.858 zhi 40.0 1.0 1.0 0.858 :pre @@ -80,6 +84,10 @@ potential: :c,image(Eqs/fix_wall_harmonic.jpg) +For style {wall/morse}, the energy E is given by a Morse potential: + +:c,image(Eqs/pair_morse.jpg) + In all cases, {r} is the distance from the particle to the wall at position {coord}, and Rc is the {cutoff} distance at which the particle and wall no longer interact. The energy of the wall @@ -147,7 +155,15 @@ constant K, and has units (energy/distance^2). The input parameter spring is at the {cutoff}. This is a repulsive-only spring since the interaction is truncated at the {cutoff} -For any wall, the {epsilon} and/or {sigma} parameter can be specified +For the {wall/morse} style, one additional parameter {alpha} is required. +Thus the parameters are in this order: {epsilon} as the depth of the +Morse potential (D_0), {alpha} as the width parameter of the Morse +potential, and {sigma} the location of the minimum (r_0) +the wall. {D_0} has energy units, {alpha} inverse distance units, and +{r_0} distance units. + +For any wall, the {epsilon} and/or {sigma} and/or {alpha} parameter can +be specified as an "equal-style variable"_variable.html, in which case it should be specified as v_name, where name is the variable name. As with a variable wall position, the variable is evaluated each timestep and diff --git a/src/fix_wall.cpp b/src/fix_wall.cpp index 8ceafb4bfc..a30b14c231 100644 --- a/src/fix_wall.cpp +++ b/src/fix_wall.cpp @@ -23,6 +23,7 @@ #include "respa.h" #include "error.h" #include "force.h" +#include "utils.h" using namespace LAMMPS_NS; using namespace FixConst; @@ -99,6 +100,19 @@ FixWall::FixWall(LAMMPS *lmp, int narg, char **arg) : estyle[nwall] = CONSTANT; } + if (utils::strmatch(style,"^wall/morse")) { + if (strstr(arg[iarg+3],"v_") == arg[iarg+3]) { + int n = strlen(&arg[iarg+3][2]) + 1; + astr[nwall] = new char[n]; + strcpy(astr[nwall],&arg[iarg+3][2]); + astyle[nwall] = VARIABLE; + } else { + alpha[nwall] = force->numeric(FLERR,arg[iarg+3]); + astyle[nwall] = CONSTANT; + } + ++iarg; + } + if (strstr(arg[iarg+3],"v_") == arg[iarg+3]) { int n = strlen(&arg[iarg+3][2]) + 1; sstr[nwall] = new char[n]; diff --git a/src/fix_wall.h b/src/fix_wall.h index 82634c349f..b2bdc2e27c 100644 --- a/src/fix_wall.h +++ b/src/fix_wall.h @@ -45,12 +45,12 @@ class FixWall : public Fix { virtual void wall_particle(int, int, double) = 0; protected: - double epsilon[6],sigma[6],cutoff[6]; + double epsilon[6],sigma[6],alpha[6],cutoff[6]; double ewall[7],ewall_all[7]; double xscale,yscale,zscale; - int estyle[6],sstyle[6],wstyle[6]; + int estyle[6],sstyle[6],astyle[6],wstyle[6]; int eindex[6],sindex[6]; - char *estr[6],*sstr[6]; + char *estr[6],*sstr[6],*astr[6]; int varflag; // 1 if any wall position,epsilon,sigma is a var int eflag; // per-wall flag for energy summation int ilevel_respa; diff --git a/src/fix_wall_morse.cpp b/src/fix_wall_morse.cpp new file mode 100644 index 0000000000..f854341e11 --- /dev/null +++ b/src/fix_wall_morse.cpp @@ -0,0 +1,87 @@ +/* ---------------------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + http://lammps.sandia.gov, Sandia National Laboratories + Steve Plimpton, sjplimp@sandia.gov + + Copyright (2003) Sandia Corporation. Under the terms of Contract + DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains + certain rights in this software. This software is distributed under + the GNU General Public License. + + See the README file in the top-level LAMMPS directory. +------------------------------------------------------------------------- */ + +#include "fix_wall_morse.h" +#include +#include "atom.h" +#include "error.h" + +using namespace LAMMPS_NS; +using namespace FixConst; + +/* ---------------------------------------------------------------------- */ + +FixWallMorse::FixWallMorse(LAMMPS *lmp, int narg, char **arg) : + FixWall(lmp, narg, arg) +{ + dynamic_group_allow = 1; +} + +/* ---------------------------------------------------------------------- */ + +void FixWallMorse::precompute(int m) +{ + coeff1[m] = 2.0 * epsilon[m] * alpha[m]; + const double alpha_dr = -alpha[m] * (cutoff[m] - sigma[m]); + offset[m] = epsilon[m] * (exp(2.0*alpha_dr) - 2.0*exp(alpha_dr)); +} + +/* ---------------------------------------------------------------------- + interaction of all particles in group with a wall + m = index of wall coeffs + which = xlo,xhi,ylo,yhi,zlo,zhi + error if any particle is on or behind wall +------------------------------------------------------------------------- */ + +void FixWallMorse::wall_particle(int m, int which, double coord) +{ + double delta,fwall; + double vn; + + double **x = atom->x; + double **f = atom->f; + int *mask = atom->mask; + int nlocal = atom->nlocal; + + int dim = which / 2; + int side = which % 2; + if (side == 0) side = -1; + + int onflag = 0; + + for (int i = 0; i < nlocal; i++) { + if (mask[i] & groupbit) { + if (side < 0) delta = x[i][dim] - coord; + else delta = coord - x[i][dim]; + if (delta >= cutoff[m]) continue; + if (delta <= 0.0) { + onflag = 1; + continue; + } + double dr = delta - sigma[m]; + double dexp = exp(-alpha[m] * dr); + fwall = side * coeff1[m] * (dexp*dexp - dexp) / delta; + ewall[0] += epsilon[m] * (dexp*dexp - 2.0*dexp) - offset[m]; + f[i][dim] -= fwall; + ewall[m+1] += fwall; + + if (evflag) { + if (side < 0) vn = -fwall*delta; + else vn = fwall*delta; + v_tally(dim, i, vn); + } + } + } + + if (onflag) error->one(FLERR,"Particle on or inside fix wall surface"); +} diff --git a/src/fix_wall_morse.h b/src/fix_wall_morse.h new file mode 100644 index 0000000000..a7359e9cde --- /dev/null +++ b/src/fix_wall_morse.h @@ -0,0 +1,49 @@ +/* -*- c++ -*- ---------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + http://lammps.sandia.gov, Sandia National Laboratories + Steve Plimpton, sjplimp@sandia.gov + + Copyright (2003) Sandia Corporation. Under the terms of Contract + DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains + certain rights in this software. This software is distributed under + the GNU General Public License. + + See the README file in the top-level LAMMPS directory. +------------------------------------------------------------------------- */ + +#ifdef FIX_CLASS + +FixStyle(wall/morse,FixWallMorse) + +#else + +#ifndef LMP_FIX_WALL_MORSE_H +#define LMP_FIX_WALL_MORSE_H + +#include "fix_wall.h" + +namespace LAMMPS_NS { + +class FixWallMorse : public FixWall { + public: + FixWallMorse(class LAMMPS *, int, char **); + void precompute(int); + void wall_particle(int, int, double); + + private: + double coeff1[6],offset[6]; +}; + +} + +#endif +#endif + +/* ERROR/WARNING messages: + +E: Particle on or inside fix wall surface + +Particles must be "exterior" to the wall in order for energy/force to +be calculated. + +*/ -- GitLab From aac557a98f72d366695b19f5dd39264f6baa68b8 Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Tue, 20 Aug 2019 13:33:36 -0400 Subject: [PATCH 468/469] integrate fix wall/morse docs properly into manual --- doc/src/Commands_fix.txt | 1 + doc/src/Howto_walls.txt | 11 ++++++----- doc/src/fix.txt | 1 + 3 files changed, 8 insertions(+), 5 deletions(-) diff --git a/doc/src/Commands_fix.txt b/doc/src/Commands_fix.txt index d2d781d4b2..cfd2bcf2ef 100644 --- a/doc/src/Commands_fix.txt +++ b/doc/src/Commands_fix.txt @@ -232,6 +232,7 @@ OPT. "wall/lj1043"_fix_wall.html, "wall/lj126"_fix_wall.html, "wall/lj93 (k)"_fix_wall.html, +"wall/morse"_fix_wall.html, "wall/piston"_fix_wall_piston.html, "wall/reflect (k)"_fix_wall_reflect.html, "wall/region"_fix_wall_region.html, diff --git a/doc/src/Howto_walls.txt b/doc/src/Howto_walls.txt index 7522118582..4e4f0c5d6f 100644 --- a/doc/src/Howto_walls.txt +++ b/doc/src/Howto_walls.txt @@ -59,14 +59,15 @@ granular particles; all the other commands create smooth walls. "fix wall/lj126"_fix_wall.html - flat walls, with Lennard-Jones 12/6 potential "fix wall/colloid"_fix_wall.html - flat walls, with "pair_style colloid"_pair_colloid.html potential "fix wall/harmonic"_fix_wall.html - flat walls, with repulsive harmonic spring potential +"fix wall/morse"_fix_wall.html - flat walls, with Morse potential "fix wall/region"_fix_wall_region.html - use region surface as wall "fix wall/gran"_fix_wall_gran.html - flat or curved walls with "pair_style granular"_pair_gran.html potential :ul -The {lj93}, {lj126}, {colloid}, and {harmonic} styles all allow the -flat walls to move with a constant velocity, or oscillate in time. -The "fix wall/region"_fix_wall_region.html command offers the most -generality, since the region surface is treated as a wall, and the -geometry of the region can be a simple primitive volume (e.g. a +The {lj93}, {lj126}, {colloid}, {harmonic}, and {morse} styles all +allow the flat walls to move with a constant velocity, or oscillate in +time. The "fix wall/region"_fix_wall_region.html command offers the +most generality, since the region surface is treated as a wall, and +the geometry of the region can be a simple primitive volume (e.g. a sphere, or cube, or plane), or a complex volume made from the union and intersection of primitive volumes. "Regions"_region.html can also specify a volume "interior" or "exterior" to the specified primitive diff --git a/doc/src/fix.txt b/doc/src/fix.txt index e5036d5a73..1dd9cc9f1b 100644 --- a/doc/src/fix.txt +++ b/doc/src/fix.txt @@ -371,6 +371,7 @@ accelerated styles exist. "wall/lj1043"_fix_wall.html - Lennard-Jones 10-4-3 wall "wall/lj126"_fix_wall.html - Lennard-Jones 12-6 wall "wall/lj93"_fix_wall.html - Lennard-Jones 9-3 wall +"wall/morse"_fix_wall.html - Morse potential wall "wall/piston"_fix_wall_piston.html - moving reflective piston wall "wall/reflect"_fix_wall_reflect.html - reflecting wall(s) "wall/region"_fix_wall_region.html - use region surface as wall -- GitLab From ad83f0e2e36d6658bccc9524ca0c196efc6fe3e8 Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Wed, 21 Aug 2019 17:12:04 -0400 Subject: [PATCH 469/469] update docs to add morse in a similar style to fix wall/region --- doc/src/fix_wall.txt | 28 +++++++++++++++++++--------- 1 file changed, 19 insertions(+), 9 deletions(-) diff --git a/doc/src/fix_wall.txt b/doc/src/fix_wall.txt index b8e380fb16..7868bacf04 100644 --- a/doc/src/fix_wall.txt +++ b/doc/src/fix_wall.txt @@ -22,18 +22,30 @@ ID, group-ID are documented in "fix"_fix.html command :ulb,l style = {wall/lj93} or {wall/lj126} or {wall/lj1043} or {wall/colloid} or {wall/harmonic} or {wall/morse} :l one or more face/arg pairs may be appended :l face = {xlo} or {xhi} or {ylo} or {yhi} or {zlo} or {zhi} :l - args = coord epsilon \[alpha\] sigma cutoff + args for styles {lj93} or {lj126} or {lj1043} or {colloid} or {harmonic} :l + args = coord epsilon sigma cutoff coord = position of wall = EDGE or constant or variable EDGE = current lo or hi edge of simulation box constant = number like 0.0 or -30.0 (distance units) variable = "equal-style variable"_variable.html like v_x or v_wiggle epsilon = strength factor for wall-particle interaction (energy or energy/distance^2 units) epsilon can be a variable (see below) - alpha = width factor for wall-particle interaction (1/distance units) - [only] for {wall/morse}. alpha can be a variable (see below) sigma = size factor for wall-particle interaction (distance units) sigma can be a variable (see below) cutoff = distance from wall at which wall-particle interaction is cut off (distance units) :pre + args for style {morse} :l + args = coord D_0 alpha r_0 cutoff + coord = position of wall = EDGE or constant or variable + EDGE = current lo or hi edge of simulation box + constant = number like 0.0 or -30.0 (distance units) + variable = "equal-style variable"_variable.html like v_x or v_wiggle + D_0 = depth of the potential (energy units) + D_0 can be a variable (see below) + alpha = width factor for wall-particle interaction (1/distance units) + alpha can be a variable (see below) + r_0 = distance of the potential minimum from the face of region (distance units) + r_0 can be a variable (see below) + cutoff = distance from wall at which wall-particle interaction is cut off (distance units) :pre zero or more keyword/value pairs may be appended :l keyword = {units} or {fld} :l {units} value = {lattice} or {box} @@ -155,12 +167,10 @@ constant K, and has units (energy/distance^2). The input parameter spring is at the {cutoff}. This is a repulsive-only spring since the interaction is truncated at the {cutoff} -For the {wall/morse} style, one additional parameter {alpha} is required. -Thus the parameters are in this order: {epsilon} as the depth of the -Morse potential (D_0), {alpha} as the width parameter of the Morse -potential, and {sigma} the location of the minimum (r_0) -the wall. {D_0} has energy units, {alpha} inverse distance units, and -{r_0} distance units. +For the {wall/morse} style, the three parameters are in this order: +{D_0} the depth of the potential, {alpha} the width parameter, and +{r_0} the location of the minimum. {D_0} has energy units, {alpha} +inverse distance units, and {r_0} distance units. For any wall, the {epsilon} and/or {sigma} and/or {alpha} parameter can be specified -- GitLab

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