diff --git a/.github/CODEOWNERS b/.github/CODEOWNERS index fdee6325d0f65c04fa76eec1cfa58ee90012c8c9..3d73ffc63ee4c719f751d19c9607e261acbabcc8 100644 --- a/.github/CODEOWNERS +++ b/.github/CODEOWNERS @@ -9,13 +9,37 @@ lib/kokkos/* @stanmoore1 lib/molfile/* @akohlmey lib/qmmm/* @akohlmey lib/vtk/* @rbberger +lib/kim/* @ellio167 -# packages -src/KOKKOS @stanmoore1 -src/USER-CGSDK @akohlmey -src/USER-COLVARS @giacomofiorin -src/USER-OMP @akohlmey -src/USER-QMMM @akohlmey +# whole packages +src/COMPRESS/* @akohlmey +src/GPU/* @ndtrung81 +src/KOKKOS/* @stanmoore1 +src/KIM/* @ellio167 +src/USER-CGDNA/* @ohenrich +src/USER-CGSDK/* @akohlmey +src/USER-COLVARS/* @giacomofiorin +src/USER-DPD/* @timattox +src/USER-INTEL/* @wmbrownintel +src/USER-MANIFOLD/* @Pakketeretet2 +src/USER-MEAMC/* @martok +src/USER-MOFFF/* @hheenen +src/USER-MOLFILE/* @akohlmey +src/USER-NETCDF/* @pastewka +src/USER-PHONON/* @lingtikong +src/USER-OMP/* @akohlmey +src/USER-QMMM/* @akohlmey +src/USER-REAXC/* @hasanmetin +src/USER-TALLY/* @akohlmey +src/USER-UEF/* @danicholson +src/USER-VTK/* @rbberger + +# individual files in packages +src/GPU/pair_vashishta_gpu.* @andeplane +src/KOKKOS/pair_vashishta_kokkos.* @andeplane +src/MANYBODY/pair_vashishta_table.* @andeplane +src/USER-MISC/fix_bond_react.* @jrgissing +src/USER-MISC/*_grem.* @dstelter92 # tools tools/msi2lmp/* @akohlmey diff --git a/cmake/CMakeLists.txt b/cmake/CMakeLists.txt index a4988611563ad8e681ae2ff39f3f7eeaad524ff6..8e750d222def5c8be4f7fcf17232bd8997e81b56 100644 --- a/cmake/CMakeLists.txt +++ b/cmake/CMakeLists.txt @@ -101,7 +101,7 @@ set(DEFAULT_PACKAGES ASPHERE BODY CLASS2 COLLOID COMPRESS CORESHELL DIPOLE GRANU KSPACE MANYBODY MC MEAM MISC MOLECULE PERI QEQ REAX REPLICA RIGID SHOCK SNAP SRD) set(OTHER_PACKAGES KIM PYTHON MSCG MPIIO VORONOI POEMS LATTE - USER-ATC USER-AWPMD USER-CGDNA USER-MESO + 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-NETCDF USER-PHONON USER-QTB USER-REAXC USER-SMD diff --git a/doc/src/PDF/colvars-refman-lammps.pdf b/doc/src/PDF/colvars-refman-lammps.pdf index 2d28758819a9a7a0dac700cd4a8239f51257b8e1..7f52367c82eec09a0465b356b326e996482a9bc3 100644 Binary files a/doc/src/PDF/colvars-refman-lammps.pdf and b/doc/src/PDF/colvars-refman-lammps.pdf differ diff --git a/doc/src/Section_commands.txt b/doc/src/Section_commands.txt index 76051490e401b9ff5b9ac3c4aeb292a1b86b66b3..cdbdec9ee3ef6e7a8d13cbb28b53d9d41034c487 100644 --- a/doc/src/Section_commands.txt +++ b/doc/src/Section_commands.txt @@ -684,6 +684,7 @@ package"_Section_start.html#start_3. "addtorque"_fix_addtorque.html, "atc"_fix_atc.html, "ave/correlate/long"_fix_ave_correlate_long.html, +"bond/react"_fix_bond_react.html, "colvars"_fix_colvars.html, "dpd/energy (k)"_fix_dpd_energy.html, "drude"_fix_drude.html, diff --git a/doc/src/Section_packages.txt b/doc/src/Section_packages.txt index ade75c588f071fc75fb85e35b9e28e304f693070..e9387fe35fb41758089081bed202e832029c25df 100644 --- a/doc/src/Section_packages.txt +++ b/doc/src/Section_packages.txt @@ -122,6 +122,7 @@ Package, Description, Doc page, Example, Library Package, Description, Doc page, Example, Library "USER-ATC"_#USER-ATC, atom-to-continuum coupling, "fix atc"_fix_atc.html, USER/atc, int "USER-AWPMD"_#USER-AWPMD, wave-packet MD, "pair_style awpmd/cut"_pair_awpmd.html, USER/awpmd, int +"USER-BOCS"_#USER-BOCS, BOCS bottom up coarse graining, "fix bocs"_fix_bocs.html, USER/bocs, - "USER-CGDNA"_#USER-CGDNA, coarse-grained DNA force fields, src/USER-CGDNA/README, USER/cgdna, - "USER-CGSDK"_#USER-CGSDK, SDK coarse-graining model, "pair_style lj/sdk"_pair_sdk.html, USER/cgsdk, - "USER-COLVARS"_#USER-COLVARS, collective variables library, "fix colvars"_fix_colvars.html, USER/colvars, int @@ -1625,6 +1626,43 @@ examples/USER/awpmd :ul :line +USER-BOCS package :link(USER-BOCS),h4 + +[Contents:] + +This package provides "fix bocs"_fix_bocs.html, a modified version +of "fix npt"_fix_nh.html 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). + +[Authors:] Nicholas J. H. Dunn and Michael R. DeLyser (The Pennsylvania State University) + +[Install or un-install:] + +make yes-user-bocs +make machine :pre + +make no-user-bocs +make machine :pre + +[Supporting info:] + +The USER-BOCS user package for LAMMPS is part of the BOCS software package: +"https://github.com/noid-group/BOCS"_https://github.com/noid-group/BOCS + +See the following reference for information about the entire package: + +Dunn, NJH; Lebold, KM; DeLyser, MR; Rudzinski, JF; Noid, WG. +"BOCS: Bottom-Up Open-Source Coarse-Graining Software." +J. Phys. Chem. B. 122, 13, 3363-3377 (2018). + +Example inputs are in the examples/USER/bocs folder. + +:line + USER-CGDNA package :link(USER-CGDNA),h4 [Contents:] diff --git a/doc/src/compute_ackland_atom.txt b/doc/src/compute_ackland_atom.txt index b75d100112b9f3a9a5e49d1ec282f275e56a9014..3fd838d95775ae9e97f7ad8da792112b9890d80d 100644 --- a/doc/src/compute_ackland_atom.txt +++ b/doc/src/compute_ackland_atom.txt @@ -10,19 +10,29 @@ compute ackland/atom command :h3 [Syntax:] -compute ID group-ID ackland/atom :pre +compute ID group-ID ackland/atom keyword/value :pre -ID, group-ID are documented in "compute"_compute.html command -ackland/atom = style name of this compute command :ul +ID, group-ID are documented in "compute"_compute.html command :ulb,l +ackland/atom = style name of this compute command :l + +zero or more keyword/value pairs may be appended :l +keyword = {legacy} :l + {legacy} yes/no = use ({yes}) or do not use ({no}) legacy ackland algorithm implementation :pre +:ule [Examples:] -compute 1 all ackland/atom :pre +compute 1 all ackland/atom +compute 1 all ackland/atom legacy yes :pre [Description:] Defines a computation that calculates the local lattice structure according to the formulation given in "(Ackland)"_#Ackland. +Historically, LAMMPS had two, slightly different implementations of +the algorithm from the paper. With the {legacy} keyword, it is +possible to switch between the pre-2015 ({legacy yes}) and post-2015 +implemention ({legacy no}). The post-2015 variant is the default. In contrast to the "centro-symmetry parameter"_compute_centro_atom.html this method is stable against @@ -66,7 +76,8 @@ integers defined above. "compute centro/atom"_compute_centro_atom.html -[Default:] none +[Default:] +The keyword {legacy} defaults to {no}. :line diff --git a/doc/src/compute_displace_atom.txt b/doc/src/compute_displace_atom.txt index 39c301cf911a159089189ee02cef15a5ffae4d1e..00e5f696c118029431bf5a36395bcd906fe432ee 100644 --- a/doc/src/compute_displace_atom.txt +++ b/doc/src/compute_displace_atom.txt @@ -15,7 +15,7 @@ compute ID group-ID displace/atom :pre ID, group-ID are documented in "compute"_compute.html command :ulb,l displace/atom = style name of this compute command :l zero or more keyword/arg pairs may be appended :l -keyword = {refresh} : +keyword = {refresh} :l {replace} arg = name of per-atom variable :pre :ule diff --git a/doc/src/compute_sna_atom.txt b/doc/src/compute_sna_atom.txt index 1c3787e696638191373d0b563f461c37d42dddad..268e23ac2808d82f8750b95bd652cd4d50f6b9d2 100644 --- a/doc/src/compute_sna_atom.txt +++ b/doc/src/compute_sna_atom.txt @@ -161,9 +161,9 @@ function. The keyword {bzeroflag} determines whether or not {B0}, the bispectrum components of an atom with no neighbors, are subtracted from -the calculated bispectrum components. This optional keyword is only -available for compute {sna/atom}, as {snad/atom} and {snav/atom} -are unaffected by the removal of constant terms. +the calculated bispectrum components. This optional keyword +normally only affects compute {sna/atom}. However, when +{quadraticflag} is on, it also affects {snad/atom} and {snav/atom}. The keyword {quadraticflag} determines whether or not the quadratic analogs to the bispectrum quantities are generated. @@ -230,13 +230,18 @@ are 30, 90, and 180, respectively. With {quadratic} value=1, the numbers of columns are 930, 2790, and 5580, respectively. If the {quadratic} keyword value is set to 1, then additional -columns are appended to each per-atom array, corresponding to +columns are generated, corresponding to the products of all distinct pairs of bispectrum components. If the number of bispectrum components is {K}, then the number of distinct pairs -is {K}({K}+1)/2. These are output in subblocks of {K}({K}+1)/2 columns, using the same -ordering of sub-blocks as was used for the bispectrum -components. Within each sub-block, the ordering is upper-triangular, -(1,1),(1,2)...(1,{K}),(2,1)...({K}-1,{K}-1),({K}-1,{K}),({K},{K}) +is {K}({K}+1)/2. +For compute {sna/atom} these columns are appended to existing {K} columns. +The ordering of quadratic terms is upper-triangular, +(1,1),(1,2)...(1,{K}),(2,1)...({K}-1,{K}-1),({K}-1,{K}),({K},{K}). +For computes {snad/atom} and {snav/atom} each set of {K}({K}+1)/2 +additional columns is inserted directly after each of sub-block +of linear terms i.e. linear and quadratic terms are contiguous. +So the nesting order from inside to outside is bispectrum component, +linear then quadratic, vector/tensor component, type. These values can be accessed by any command that uses per-atom values from a compute as input. See "Section diff --git a/doc/src/fix_bocs.txt b/doc/src/fix_bocs.txt new file mode 100644 index 0000000000000000000000000000000000000000..f53b7c785c251240a0d325b820545f342ce21c06 --- /dev/null +++ b/doc/src/fix_bocs.txt @@ -0,0 +1,112 @@ +<"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 + +fix bocs command :h3 + +[Syntax:] + +fix ID group-ID bocs keyword values ... :pre + +keyword = {temp} or {cgiso} or {analytic} or {linear_spline} or {cubic_spline} + {temp} values = Tstart Tstop Tdamp + {cgiso} values = Pstart Pstop Pdamp + {basis set} + {analytic} values = V_avg N_particles N_coeff Coeff_1 Coeff_2 ... Coeff_N + {linear_spline} values = input_filename + {cubic_spline} values = input_filename :pre +:ule + +[Examples:] + +fix 1 all bocs temp 300.0 300.0 100.0 cgiso 0.986 0.986 1000.0 analytic 66476.015 968 2 245030.10 8962.20 :pre + +fix 1 all bocs temp 300.0 300.0 100.0 cgiso 0.986 0.986 1000.0 cubic_spline input_Fv.dat :pre + +thermo_modify press 1_press :pre + + +[Description:] + +These commands incorporate a pressure correction as described by +Dunn and Noid in "(Dunn1)"_#bocs-Dunn1 to the standard MTTK +barostat by Martyna et. al. in "(Martyna)"_#bocs-Martyna . +The first half of the command mimics a standard fix npt command: + +fix 1 all bocs temp Tstart Tstop Tcoupl cgiso Pstart Pstop Pdamp :pre + +The two differences are replacing {npt} with {bocs}, and replacing +{iso}/{aniso}/{etc} with {cgiso}. +The rest of the command details what form you would like to use for +the pressure correction equation. The choices are: {analytic}, {linear_spline}, +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: + +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 +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 atomspheres. Furthermore, the table should start/end at a +volume considerably smaller/larger than you expect your system to sample +during the simulation. If the system ever reaches a volume outside of the +range provided, the simulation will stop. + +With the {analytic} option, the arguments are as follows: + +... analytic V_avg N_particles N_coeff Coeff_1 Coeff_2 ... Coeff_N :pre + +Note that {V_avg} and {Coeff_i} should all be in the proper units, e.g. if you +are using {units real}, {V_avg} should be in cubic angstroms, and the +coefficients should all be in atmospheres * cubic angstroms. + +[Restrictions:] + +As this is computing a (modified) pressure, group-ID should be {all}. + +The pressure correction has only been tested for use with an isotropic +pressure coupling in 3 dimensions. + +By default, LAMMPS will still report the normal value for the pressure +if the pressure is printed via a {thermo} command, or if the pressures +are written to a file every so often. In order to have LAMMPS report the +modified pressure, you must include the {thermo_modify} command given in +the examples. For the last argument in the command, you should put +XXXX_press, where XXXX is the ID given to the fix bocs command (in the +example, the ID of the fix bocs command is 1 ). + +This fix is part of the USER-BOCS package. It is only enabled if +LAMMPS was built with that package. See the "Making +LAMMPS"_Section_start.html#start_3 section for more info. + +[Related:] + +For more details about the pressure correction and the entire BOCS software +package, visit the "BOCS package on github"_bocsgithub and read the release +paper by Dunn et. al. "(Dunn2)"_#bocs-Dunn2 . + + +:link(bocsgithub,https://github.com/noid-group/BOCS) + +:line + +:link(bocs-Dunn1) +[(Dunn1)] Dunn and Noid, J Chem Phys, 143, 243148 (2015). + +:link(bocs-Martyna) +[(Martyna)] Martyna, Tobias, and Klein, J Chem Phys, 101, 4177 (1994). + +:link(bocs-Dunn2) +[(Dunn2)] Dunn, Lebold, DeLyser, Rudzinski, and Noid, J. Phys. Chem. B, 122, 3363 (2018). + + + diff --git a/doc/src/fix_bond_react.txt b/doc/src/fix_bond_react.txt new file mode 100644 index 0000000000000000000000000000000000000000..4a7c2428c16aa050a24f71d685960d9d952b65a4 --- /dev/null +++ b/doc/src/fix_bond_react.txt @@ -0,0 +1,363 @@ +"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 + +fix bond/react command :h3 + +[Syntax:] + +fix ID group-ID bond/react common_keyword values ... + react react-ID react-group-ID Nevery Rmin Rmax template-ID(pre-reacted) template-ID(post-reacted) map_file individual_keyword values ... + react react-ID react-group-ID Nevery Rmin Rmax template-ID(pre-reacted) template-ID(post-reacted) map_file individual_keyword values ... + react react-ID react-group-ID Nevery Rmin Rmax template-ID(pre-reacted) template-ID(post-reacted) map_file individual_keyword values ... + ... :pre + +ID, group-ID are documented in "fix"_fix.html command. Group-ID is ignored. :ulb,l +bond/react = style name of this fix command :l +zero or more common keyword/value pairs may be appended directly after 'bond/react' :l +these apply to all reaction specifications (below) :l +common_keyword = {stabilization} + {stabilization} values = group-ID xmax + group-ID = user-assigned ID of an internally-created dynamic group that excludes reacting atoms, and can be used by a subsequent time integration fix such as nvt, npt, or nve (cannot be 'all') + {xmax} value = distance + distance = xmax value that is used by an internally created "nve/limit"_fix_nve_limit.html integrator +react = mandatory argument indicating new reaction specification + react-ID = user-assigned name for the reaction + react-group-ID = only atoms in this group are available for the reaction + Nevery = attempt reaction every this many steps :l + Rmin = bonding pair atoms must be separated by more than Rmin to initiate reaction (distance units) :l + Rmax = bonding pair atoms must be separated by less than Rmax to initiate reaction (distance units) :l + template-ID(pre-reacted) = ID of a molecule template containing pre-reaction topology :l + template-ID(post-reacted) = ID of a molecule template containing post-reaction topology :l + map_file = name of file specifying corresponding atomIDs in the pre- and post-reacted templates :l + zero or more individual keyword/value pairs may be appended to each react argument :l + individual_keyword = {prob} or {stabilize_steps} :l + {prob} values = fraction seed + fraction = initiate reaction with this probability if otherwise eligible + seed = random number seed (positive integer) + {stabilize_steps} value = timesteps + timesteps = number of timesteps to apply internally created nve/limit.html :pre +:ule + +[Examples:] + +molecule mol1 pre_reacted_topology.txt +molecule mol2 post_reacted_topology.txt +fix 5 all bond/react stabilization no react myrxn1 all 1 0 3.25 mol1 mol2 map_file.txt + +molecule mol1 pre_reacted_rxn1.txt +molecule mol2 post_reacted_rxn1.txt +molecule mol3 pre_reacted_rxn2.txt +molecule mol4 post_reacted_rxn2.txt +fix 5 all bond/react stabilization yes nvt_grp .03 & + react myrxn1 all 1 0 3.25 mol1 mol2 map_file_rxn1.txt prob 0.50 12345 & + react myrxn2 all 1 0 2.75 mol3 mol4 map_file_rxn2.txt prob 0.25 12345 +fix 6 nvt_grp nvt temp 300 300 100 # system-wide thermostat must be defined after bond/react :pre + +[Description:] + +Initiate complex covalent bonding (topology) changes. These topology +changes will be referred to as "reactions" throughout this +documentation. Topology changes are defined in pre- and post-reaction +molecule templates and can include creation and deletion of bonds, +angles, dihedrals, impropers, bond-types, angle-types, dihedral-types, +atom-types, or atomic charges. + +Fix bond/react does not use quantum mechanical (eg. fix qmmm) or +pairwise bond-order potential (eg. Tersoff or AIREBO) methods to +determine bonding changes a priori. Rather, it uses a distance-based +probabilistic criteria to effect predetermined topology changes in +simulations using standard force fields. + +This fix was created to facilitate the dynamic creation of polymeric, +amorphous or highly-crosslinked systems. A suggested workflow for +using this fix is: 1) identify a reaction to be simulated 2) build a +molecule template of the reaction site before the reaction has +occurred 3) build a molecule template of the reaction site after the +reaction has occurred 4) create a map that relates the +template-atom-IDs of each atom between pre- and post-reaction molecule +templates 5) fill a simulation box with molecules and run a simulation +with fix/bond react. + +Only one 'fix bond/react' command can be used at a time. Multiple +reactions can be simultaneously applied by specifying multiple 'react' +arguments to a single 'fix bond/react' command. This syntax is +necessary because the 'common keywords' are applied to all reactions. + +The {stabilization} keyword enables reaction site stabilization. +Reaction site stabilization is performed by including reacting atoms +in an internally created fix "nve/limit"_fix_nve_limit.html time +integrator for a set number of timesteps given by the +{stabilize_steps} keyword. While reacting atoms are being time +integrated by the internal nve/limit, they are prevented from being +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. + +The group-ID set using the {stabilization} keyword should be a +previously unused group-ID. The fix bond/react command creates a +"dynamic group"_group.html of this name that excludes reacting atoms. +This dynamic group-ID should then be used by a subsequent system-wide +time integrator, as shown in the second example above. It is currently +necessary to place the time integration command after the fix +bond/react command due to the internal dynamic grouping performed by +fix bond/react. + +NOTE: The internally created group currently applies to all atoms in +the system, i.e. you should generally not have a separate thermostat +which acts on the 'all' group. + +The following comments pertain to each 'react' argument: + +A check for possible new reaction sites is performed every Nevery +timesteps. + +Two conditions must be met for a reaction to occur. First a bonding +atom pair must be identified. Second, the topology surrounding the +bonding atom pair must match the topology of the pre-reaction +template. If both these conditions are met, the reaction site is +modified to match the post-reaction template. + +A bonding atom pair will be identified if several conditions are met. +First, a pair of atoms within the specified react-group-ID of type +typei and typej must separated by a distance between Rmin and Rmax. It +is possible that multiple bonding atom pairs are identified: if the +bonding atoms in the pre-reacted template are not 1-2, 1-3, or 1-4 +neighbors, the closest bonding atom partner is set as its bonding +partner; otherwise, the farthest potential partner is chosen. Then, if +both an atomi and atomj have each other as their nearest bonding +partners, these two atoms are identified as the bonding atom pair of +the reaction site. Once this unique bonding atom pair is identified +for each reaction, there could two or more reactions that involve a +given atom on the same timestep. If this is the case, only one such +reaction is permitted to occur. This reaction is chosen randomly from +all potential reactions. This capability allows e.g. for different +reaction pathways to proceed from identical reaction sites with +user-specified probabilities. + +The pre-reacted molecule template is specified by a molecule command. +This molecule template file contains a sample reaction site and its +surrounding topology. As described below, the bonding atom pairs of +the pre-reacted template are specified by atom ID in the map file. The +pre-reacted molecule template should contain as few atoms as possible +while still completely describing the topology of all atoms affected +by the reaction. For example, if the force field contains dihedrals, +the pre-reacted template should contain any atom within three bonds of +reacting atoms. + +Some atoms in the pre-reacted template that are not reacting may have +missing topology with respect to the simulation. For example, the +pre-reacted template may contain an atom that would connect to the +rest of a long polymer chain. These are referred to as edge atoms, and +are also specified in the map file. + +Note that some care must be taken when a building a molecule template +for a given simulation. All atom types in the pre-reacted template +must be the same as those of a potential reaction site in the +simulation. A detailed discussion of matching molecule template atom +types with the simulation is provided on the "molecule"_molecule.html +command page. + +The post-reacted molecule template contains a sample of the reaction +site and its surrounding topology after the reaction has occurred. It +must contain the same number of atoms as the pre-reacted template. A +one-to-one correspondence between the atom IDs in the pre- and +post-reacted templates is specified in the map file as described +below. Note that during a reaction, an atom, bond, etc. type may +change to one that was previously not present in the simulation. These +new types must also be defined during the setup of a given simulation. +A discussion of correctly handling this is also provided on the +"molecule"_molecule.html command page. + +The map file is a text document with the following format: + +Format of the map file + +A map file has a header and a body. The header appears first. The +first line of the header is always skipped; it typically contains a +description of the file. Lines can have a trailing comment starting +with '#' that is ignored. If the line is blank (only whitespace after +comment is deleted), it is skipped. If the line contains a header +keyword, the corresponding value(s) is read from the line. If it +doesn't contain a header keyword, the line begins the body of the +file. + +The header contains one mandatory keyword and one optional keyword. +The mandatory keyword is 'equivalences' and the optional keyword is +'edgeIDs.' These specify the number of atoms in the pre- and +post-reacted templates and the number of edge atoms in pre-reacted +template, respectively. + +The body contains two mandatory sections and one optional section. The +first section begins with the keyword 'BondingIDs' and lists the atom +IDs of the bonding atom pair in the pre-reacted molecule template. The +second mandatory section begins with the keyword 'Equivalences' and +lists a one-to-one correspondence between atom IDs of the pre- and +post-reacted templates. The optional section begins with the keyword +'EdgeIDs' and list the atom IDs of edge atoms in the pre-reacted +molecule template. + +Format of the header of the map file + +These are the recognized header keywords. Header lines can come in any +order. The value(s) are read from the beginning of the line. Thus the +keyword 'equivalences' should be in a line like "25 equivalences." + +equivalences = # of atoms in the pre- and post-reacted molecule +templates edgeIDs = # of edge atoms in the pre-reacted molecule template :pre + +The edgeIDs keyword is optional. + +Format of the body of the map file + +These are the section keywords for the body of the file. + +BondingIDs, EdgeIDs = list of atom IDs of bonding and edge atoms in +the pre-reacted molecule template + +Equivalences = a two column list where the first column is an atom ID +of the pre-reacted molecule template, and the second column is the +corresponding atom ID of the post-reacted molecule template + +The bondingIDs section will always contain two atom IDs, corresponding +to the bonding atom pairs of the pre-reacted map file. The +Equivalences section will contain as many rows as there are atoms in +the pre- and post-reacted molecule templates. The edgeIDs section is +optional, but would contain an atom ID for each edge atom in the +pre-reacted molecule template. + +A sample map file is given below: + +:line + +# This is a map file :pre + +2 edgeIDs +7 equivalences :pre + +BondingIDs :pre + +3 5 :pre + +EdgeIDs :pre + +1 7 :pre + +Equivalences :pre + +1 1 +2 2 +3 3 +4 4 +5 5 +6 6 +7 7 :pre + +:line + +Once a reaction site has been successfully identified, data structures +within LAMMPS that store bond topology are updated to reflect the +post-reacted molecule template. All force fields with fixed bonds, +angles, dihedrals or impropers are supported. + +A few capabilities to note: 1) You may specify as many 'react' +arguments as desired. For example, you could break down a complicated +reaction mechanism into several reaction steps, each defined by its +own 'react' argument. 2) While typically a bond is formed or removed +between the bonding atom pairs specified in the pre-reacted molecule +template, this is not required. 3) By reversing the order of the pre- +and post- reacted molecule templates in another 'react' argument, you +can allow for the possibility of one or more reverse reactions. + +The optional keywords deal with the probability of a given reaction +occurring as well as the stable equilibration of each reaction site as +it occurs. + +The {prob} keyword can affect whether an eligible reaction actually +occurs. The fraction setting must be a value between 0.0 and 1.0. A +uniform random number between 0.0 and 1.0 is generated and the +eligible reaction only occurs if the random number is less than the +fraction. + +The {stabilize_steps} keyword allows for the specification of how many +timesteps a reaction site is stabilized before being returned to the +overall system thermostat. + +In order to produce the most physical behavior, this 'reaction site +equilibration time' should be tuned to be as small as possible while +retaining stability for a given system or reaction step. After a +limited number of case studies, this number has been set to a default +of 60 timesteps. Ideally, it should be individually tuned for each fix +reaction step. Note that in some situations, decreasing rather than +increasing this parameter will result in an increase in stability. + +A few other considerations: + +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: + +fix 1 bond_react_MASTER_group temp/rescale 1 300 300 10 1 + +NOTE: This command must be added after the fix bond/react command, and +will apply to all reactions. + +Computationally, each timestep this fix operates, it loops over +neighbor lists (for bond-forming reactions) and computes distances +between pairs of atoms in the list. It also communicates between +neighboring processors to coordinate which bonds are created and/or +removed. All of these operations increase the cost of a timestep. Thus +you should be cautious about invoking this fix too frequently. + +You can dump out snapshots of the current bond topology via the dump +local command. + +:line + +[Restart, fix_modify, output, run start/stop, minimize info:] + +No information about this fix is written to "binary restart +files"_restart.html. None of the "fix_modify"_fix_modify.html options +are relevant to this fix. + +This fix computes one statistic for each 'react' argument that it +stores in a global vector, of length 'number of react arguments', that +can be accessed by various "output +commands"_Section_howto.html#howto_15. The vector values calculated by +this fix are "intensive". + +These is 1 quantity for each react argument: + +(1) cumulative # of reactions occurred :ul + +No parameter of this fix can be used with the {start/stop} keywords of +the "run"_run.html command. This fix is not invoked during "energy +minimization"_minimize.html. + +[Restrictions:] + +This fix is part of the USER-MISC package. It is only enabled if +LAMMPS was built with that package. See the "Making +LAMMPS"_Section_start.html#start_3 section for more info. + +[Related commands:] + +"fix bond/create"_fix_bond_create.html, "fix +bond/break"_fix_bond_break.html, "fix bond/swap"_fix_bond_swap.html, +"dump local"_dump.html, "special_bonds"_special_bonds.html + +[Default:] + +The option defaults are stabilization = no, stabilize_steps = 60 + +:line + +:link(Gissinger) [(Gissinger)] Gissinger, Jensen and Wise, Polymer, +128, 211 (2017). diff --git a/doc/src/fix_langevin_drude.txt b/doc/src/fix_langevin_drude.txt index afc9c5f257523646906966d89464da26a070023e..c85ff24c96d2982439d67c4ac52fd3bea5083044 100644 --- a/doc/src/fix_langevin_drude.txt +++ b/doc/src/fix_langevin_drude.txt @@ -154,7 +154,7 @@ Note: The temperature thermostating the core-Drude particle pairs should be chosen low enough, so as to mimic as closely as possible the self-consistent minimization. It must however be high enough, so that the dipoles can follow the local electric field exerted by the -neighbouring atoms. The optimal value probably depends on the +neighboring atoms. The optimal value probably depends on the temperature of the centers of mass and on the mass of the Drude particles. diff --git a/doc/src/fix_reax_bonds.txt b/doc/src/fix_reax_bonds.txt index 54aa7faef802f3061f795c54a7449d6d93265d0b..3f8f237de1c7d574bfc214b9dfec2892e11b3793 100644 --- a/doc/src/fix_reax_bonds.txt +++ b/doc/src/fix_reax_bonds.txt @@ -34,6 +34,8 @@ written to {filename} on timesteps that are multiples of {Nevery}, including timestep 0. For time-averaged chemical species analysis, please see the "fix reaxc/c/species"_fix_reaxc_species.html command. +The specified group-ID is ignored by this fix. + The format of the output file should be reasonably self-explanatory. The meaning of the column header abbreviations is as follows: diff --git a/doc/src/fix_restrain.txt b/doc/src/fix_restrain.txt index c8ec20daaa4ae3953b2660a2770607b15610533e..1a7c7b6ba5df11d6c9331de0963e2bc562131e42 100644 --- a/doc/src/fix_restrain.txt +++ b/doc/src/fix_restrain.txt @@ -24,10 +24,12 @@ keyword = {bond} or {angle} or {dihedral} :l atom1,atom2,atom3 = IDs of 3 atoms in angle, atom2 = middle atom Kstart,Kstop = restraint coefficients at start/end of run (energy units) theta0 = equilibrium angle theta (degrees) - {dihedral} args = atom1 atom2 atom3 atom4 Kstart Kstop phi0 + {dihedral} args = atom1 atom2 atom3 atom4 Kstart Kstop phi0 keyword/value atom1,atom2,atom3,atom4 = IDs of 4 atoms in dihedral in linear order Kstart,Kstop = restraint coefficients at start/end of run (energy units) - phi0 = equilibrium dihedral angle phi (degrees) :pre + phi0 = equilibrium dihedral angle phi (degrees) + keyword/value = optional keyword value pairs. supported keyword/value pairs: + {mult} n = dihedral multiplicity n (integer >= 0, default = 1) :pre :ule [Examples:] @@ -155,11 +157,13 @@ associated with the restraint is with the following coefficients: K (energy) -n = 1 +n (multiplicity, >= 0) d (degrees) = phi0 + 180 :ul -K and phi0 are specified with the fix. Note that the value of n is -hard-wired to 1. Also note that the energy will be a minimum when the +K and phi0 are specified with the fix. Note that the value of the +dihedral multiplicity {n} is set by default to 1. You can use the +optional {mult} keyword to set it to a different positive integer. +Also note that the energy will be a minimum when the current dihedral angle phi is equal to phi0. :line diff --git a/doc/src/fixes.txt b/doc/src/fixes.txt index c3fcc06bf1c53e780b9b7bc3ce9885671fc9f690..79c2f75b8ba46f2924c2e34ed98c81edd6fe71b8 100644 --- a/doc/src/fixes.txt +++ b/doc/src/fixes.txt @@ -20,9 +20,11 @@ Fixes :h1 fix_ave_time fix_aveforce fix_balance + fix_bocs fix_bond_break fix_bond_create fix_bond_swap + fix_bond_react fix_box_relax fix_cmap fix_colvars diff --git a/doc/src/lammps.book b/doc/src/lammps.book index ec34f41872db2aa143628ce3f99c249a8641cda9..1f4bf157f4829df2446970b8c9550f7098b765f8 100644 --- a/doc/src/lammps.book +++ b/doc/src/lammps.book @@ -135,8 +135,10 @@ fix_ave_histo.html fix_ave_time.html fix_aveforce.html fix_balance.html +fix_bocs.html fix_bond_break.html fix_bond_create.html +fix_bond_react.html fix_bond_swap.html fix_box_relax.html fix_cmap.html diff --git a/doc/src/pair_kolmogorov_crespi_z.txt b/doc/src/pair_kolmogorov_crespi_z.txt index c7e005a591c04b712f0bb2ed3a640b1ea8e3e5e1..97f132eacd41e00cd4318cfde24b09e29b4a6ae1 100644 --- a/doc/src/pair_kolmogorov_crespi_z.txt +++ b/doc/src/pair_kolmogorov_crespi_z.txt @@ -38,7 +38,7 @@ This shift is achieved by the last term in the equation for {Vij} above. This potential is intended for interactions between two layers of graphene. Therefore, to avoid interaction between layers in multi-layered materials, each layer should have a separate atom type and interactions should only -be computed between atom types of neighbouring layers. +be computed between atom types of neighboring layers. The parameter file (e.g. CC.KC), is intended for use with metal "units"_units.html, with energies in meV. An additional parameter, {S}, diff --git a/examples/USER/bocs/README b/examples/USER/bocs/README new file mode 100644 index 0000000000000000000000000000000000000000..ae1739f8c0378256a7232290ecdd6a3a238bc7e9 --- /dev/null +++ b/examples/USER/bocs/README @@ -0,0 +1,6 @@ +This folder contains the files to run a NPT simulation of 1 site CG methanol +while employing a correction to the barostat. +The pair force was computed via the Multi-Scale Coarse-Graining method. +The resulting model was then iteratively pressure matched. +The model accurately reproduces both structural (RDF) and thermodynamic +(Pressure-Volume EoS) properties of the underlying OPLS-AA model of methanol. diff --git a/examples/USER/bocs/in.methanol b/examples/USER/bocs/in.methanol new file mode 100644 index 0000000000000000000000000000000000000000..e7c80e014d04de182615de67dd142c54034beccf --- /dev/null +++ b/examples/USER/bocs/in.methanol @@ -0,0 +1,69 @@ +units real +dimension 3 +boundary p p p +atom_style atomic + +newton on +timestep 1.0 + +read_data methanol.data + +velocity all create 300.0 16802 dist gaussian + +pair_style table spline 15000 + +pair_coeff 1 1 lammps_nb_MET-MET.table nb_METMET 12.0 + +neigh_modify delay 0 every 1 check yes one 10000 +neighbor 12.0 bin + +thermo 500 +thermo_style custom step temp pe etotal press vol + +variable STEP equal step +variable TEMP equal temp +## volume from cubic angstroms to cubic nm +variable VOL equal vol/1000.0 +## pressure from atm to bar +variable PRESS equal press*1.01325 +variable PXX equal pxx*1.01325 +variable PYY equal pyy*1.01325 +variable PZZ equal pzz*1.01325 +variable PXY equal pxy*1.01325 +variable PXZ equal pxz*1.01325 +variable PYZ equal pyz*1.01325 +## energy from kcal/mol to kJ/mol +variable KE equal ke*4.184 +variable PE equal pe*4.184 +variable UVDW equal evdwl*4.184 + + +##### SPECIAL COMMANDS FOR FIX_BOCS ##### +# ID group-ID style_name thermostat T_init T_end T_couple barostat P_start P_end P_couple pmatch_basis avg_vol N_sites N_coeffs coeff1 coeff2 +fix 1 all bocs temp 300.0 300.0 100.0 cgiso 0.986 0.986 1000.0 analytic 66476.015 968 2 245030.10 8962.20 + +# Report the modified pressure +thermo_modify press 1_press + + + +## Uncomment to save some data from simulation to files +#fix print_temp all print 500 "${STEP} ${TEMP}" file temp.dat screen no +#fix print_vol all print 500 "${STEP} ${VOL}" file vol.dat screen no +#fix print_press all print 500 "${STEP} ${PRESS}" file press.dat screen no +#fix print_ke all print 500 "${STEP} ${KE}" file kinetic_E.dat screen no +#fix print_pe all print 500 "${STEP} ${PE}" file potential_E.dat screen no +#fix print_ve all print 500 "${STEP} ${UVDW}" file vdw_E.dat screen no +#fix print_press_tens all print 500 "${STEP} ${PXX} ${PYY} ${PZZ} ${PXY} ${PXZ} ${PYZ}" file press_tens.dat screen no +#fix print_PV_eos all print 500 "${VOL} ${PRESS}" file pv_eos.dat screen no + +## Prints a configuration to dump.txt every 500 steps +#dump 1 all custom 500 dump.txt id type x y z fx fy fz + +# Write restart files to continue simulations +#restart 10000 state1.restart state2.restart + +## Run for this many steps +run_style verlet +run 10000 + diff --git a/examples/USER/bocs/lammps_nb_MET-MET.table b/examples/USER/bocs/lammps_nb_MET-MET.table new file mode 100644 index 0000000000000000000000000000000000000000..c6d9fc6ca251cd012c78f50b1e86bc03c72cc6be --- /dev/null +++ b/examples/USER/bocs/lammps_nb_MET-MET.table @@ -0,0 +1,2505 @@ +#Converted from table.xvg + +nb_METMET +N 2500 + +1 0.010000 573.151769 380.122371 +2 0.020000 569.356836 378.855163 +3 0.030000 565.574570 377.588193 +4 0.040000 561.805210 376.320985 +5 0.050000 558.048279 375.053776 +6 0.060000 554.304015 373.786807 +7 0.070000 550.572419 372.519598 +8 0.080000 546.853728 371.252390 +9 0.090000 543.147467 369.985421 +10 0.100000 539.453872 368.718212 +11 0.110000 535.773184 367.451004 +12 0.120000 532.104924 366.184034 +13 0.130000 528.449331 364.916826 +14 0.140000 524.806644 363.649618 +15 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0.000000 +2493 24.930000 0.000000 0.000000 +2494 24.940000 0.000000 0.000000 +2495 24.950000 0.000000 0.000000 +2496 24.960000 0.000000 0.000000 +2497 24.970000 0.000000 0.000000 +2498 24.980000 0.000000 0.000000 +2499 24.990000 0.000000 0.000000 +2500 25.000000 0.000000 0.000000 diff --git a/examples/USER/bocs/log.20Apr18.methanol.g++.1 b/examples/USER/bocs/log.20Apr18.methanol.g++.1 new file mode 100644 index 0000000000000000000000000000000000000000..a94bd959c816c3cb1faa1b03ee9dc176b5301950 --- /dev/null +++ b/examples/USER/bocs/log.20Apr18.methanol.g++.1 @@ -0,0 +1,143 @@ +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 +units real +dimension 3 +boundary p p p +atom_style atomic + +newton on +timestep 1.0 + +read_data methanol.data + orthogonal box = (0 0 0) to (40.4635 40.4635 40.4635) + 1 by 1 by 1 MPI processor grid + reading atoms ... + 968 atoms + +velocity all create 300.0 16802 dist gaussian + +pair_style table spline 15000 + +pair_coeff 1 1 lammps_nb_MET-MET.table nb_METMET 12.0 +WARNING: 78 of 2500 force values in table are inconsistent with -dE/dr. + Should only be flagged at inflection points (../pair_table.cpp:481) + +neigh_modify delay 0 every 1 check yes one 10000 +neighbor 12.0 bin + +thermo 500 +thermo_style custom step temp pe etotal press vol + +variable STEP equal step +variable TEMP equal temp +## volume from cubic angstroms to cubic nm +variable VOL equal vol/1000.0 +## pressure from atm to bar +variable PRESS equal press*1.01325 +variable PXX equal pxx*1.01325 +variable PYY equal pyy*1.01325 +variable PZZ equal pzz*1.01325 +variable PXY equal pxy*1.01325 +variable PXZ equal pxz*1.01325 +variable PYZ equal pyz*1.01325 +## energy from kcal/mol to kJ/mol +variable KE equal ke*4.184 +variable PE equal pe*4.184 +variable UVDW equal evdwl*4.184 + + +##### SPECIAL COMMANDS FOR FIX_BOCS ##### +# ID group-ID style_name thermostat T_init T_end T_couple barostat P_start P_end P_couple pmatch_basis avg_vol N_sites N_coeffs coeff1 coeff2 +fix 1 all bocs temp 300.0 300.0 100.0 cgiso 0.986 0.986 1000.0 analytic 66476.015 968 2 245030.10 8962.20 + +# Report the modified pressure +thermo_modify press 1_press + + + +## Uncomment to save some data from simulation to files +#fix print_temp all print 500 "${STEP} ${TEMP}" file temp.dat screen no +#fix print_vol all print 500 "${STEP} ${VOL}" file vol.dat screen no +#fix print_press all print 500 "${STEP} ${PRESS}" file press.dat screen no +#fix print_ke all print 500 "${STEP} ${KE}" file kinetic_E.dat screen no +#fix print_pe all print 500 "${STEP} ${PE}" file potential_E.dat screen no +#fix print_ve all print 500 "${STEP} ${UVDW}" file vdw_E.dat screen no +#fix print_press_tens all print 500 "${STEP} ${PXX} ${PYY} ${PZZ} ${PXY} ${PXZ} ${PYZ}" file press_tens.dat screen no +#fix print_PV_eos all print 500 "${VOL} ${PRESS}" file pv_eos.dat screen no + +## Prints a configuration to dump.txt every 500 steps +#dump 1 all custom 500 dump.txt id type x y z fx fy fz + +# Write restart files to continue simulations +#restart 10000 state1.restart state2.restart + +## Run for this many steps +run_style verlet +run 10000 +Neighbor list info ... + update every 1 steps, delay 0 steps, check yes + max neighbors/atom: 10000, page size: 100000 + master list distance cutoff = 24 + ghost atom cutoff = 24 + binsize = 12, bins = 4 4 4 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair table, perpetual + attributes: half, newton on + pair build: half/bin/atomonly/newton + stencil: half/bin/3d/newton + bin: standard +Per MPI rank memory allocation (min/avg/max) = 4.691 | 4.691 | 4.691 Mbytes +Step Temp PotEng TotEng Press Volume + 0 300 1061.5961 1926.3291 107.006 66250.679 + 500 314.54728 1034.1091 1940.7738 194.42689 65660.282 + 1000 301.41603 1030.7027 1899.5173 -91.966709 66262.543 + 1500 298.8308 1014.8276 1876.1905 -80.178606 67053.605 + 2000 294.78476 1046.8207 1896.521 50.592942 66316.735 + 2500 301.18564 1033.9214 1902.0719 40.48255 66607.667 + 3000 301.06632 1022.0381 1889.8447 47.582344 66341.947 + 3500 297.98361 989.80983 1848.7307 -204.69879 67462.078 + 4000 299.03493 1034.6571 1896.6083 89.188888 66457.385 + 4500 306.03351 985.4121 1867.5363 -51.102407 67519.446 + 5000 305.6903 1013.8613 1894.9963 -141.13704 67240.467 + 5500 292.23444 1029.5558 1871.905 20.764579 66683.876 + 6000 287.87735 1017.7325 1847.5226 -35.288049 66630.031 + 6500 305.26461 960.08118 1839.9891 -352.42596 67612.317 + 7000 300.34449 1055.0664 1920.7923 22.04027 66187.27 + 7500 305.48612 1038.6651 1919.2115 17.807254 66324.168 + 8000 316.03232 1034.6809 1945.6262 27.482857 66502.198 + 8500 294.28636 1038.8213 1887.085 -72.840559 66851.661 + 9000 316.69029 1065.7481 1978.5899 245.61677 65678.385 + 9500 297.46127 1034.5547 1891.97 54.23428 66892.627 + 10000 301.24799 1036.5432 1904.8735 7.7134029 66150.506 +Loop time of 34.426 on 1 procs for 10000 steps with 968 atoms + +Performance: 25.097 ns/day, 0.956 hours/ns, 290.478 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 | 33.324 | 33.324 | 33.324 | 0.0 | 96.80 +Neigh | 0.12198 | 0.12198 | 0.12198 | 0.0 | 0.35 +Comm | 0.42865 | 0.42865 | 0.42865 | 0.0 | 1.25 +Output | 0.00059938 | 0.00059938 | 0.00059938 | 0.0 | 0.00 +Modify | 0.42553 | 0.42553 | 0.42553 | 0.0 | 1.24 +Other | | 0.1252 | | | 0.36 + +Nlocal: 968 ave 968 max 968 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 9112 ave 9112 max 9112 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 404392 ave 404392 max 404392 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 404392 +Ave neighs/atom = 417.76 +Neighbor list builds = 13 +Dangerous builds = 0 + + +Please see the log.cite file for references relevant to this simulation + +Total wall time: 0:00:34 diff --git a/examples/USER/bocs/log.20Apr18.methanol.g++.4 b/examples/USER/bocs/log.20Apr18.methanol.g++.4 new file mode 100644 index 0000000000000000000000000000000000000000..cf5891f97cbf6fee1cc998fb40fb4e8e7cb04a24 --- /dev/null +++ b/examples/USER/bocs/log.20Apr18.methanol.g++.4 @@ -0,0 +1,143 @@ +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 +units real +dimension 3 +boundary p p p +atom_style atomic + +newton on +timestep 1.0 + +read_data methanol.data + orthogonal box = (0 0 0) to (40.4635 40.4635 40.4635) + 1 by 2 by 2 MPI processor grid + reading atoms ... + 968 atoms + +velocity all create 300.0 16802 dist gaussian + +pair_style table spline 15000 + +pair_coeff 1 1 lammps_nb_MET-MET.table nb_METMET 12.0 +WARNING: 78 of 2500 force values in table are inconsistent with -dE/dr. + Should only be flagged at inflection points (../pair_table.cpp:481) + +neigh_modify delay 0 every 1 check yes one 10000 +neighbor 12.0 bin + +thermo 500 +thermo_style custom step temp pe etotal press vol + +variable STEP equal step +variable TEMP equal temp +## volume from cubic angstroms to cubic nm +variable VOL equal vol/1000.0 +## pressure from atm to bar +variable PRESS equal press*1.01325 +variable PXX equal pxx*1.01325 +variable PYY equal pyy*1.01325 +variable PZZ equal pzz*1.01325 +variable PXY equal pxy*1.01325 +variable PXZ equal pxz*1.01325 +variable PYZ equal pyz*1.01325 +## energy from kcal/mol to kJ/mol +variable KE equal ke*4.184 +variable PE equal pe*4.184 +variable UVDW equal evdwl*4.184 + + +##### SPECIAL COMMANDS FOR FIX_BOCS ##### +# ID group-ID style_name thermostat T_init T_end T_couple barostat P_start P_end P_couple pmatch_basis avg_vol N_sites N_coeffs coeff1 coeff2 +fix 1 all bocs temp 300.0 300.0 100.0 cgiso 0.986 0.986 1000.0 analytic 66476.015 968 2 245030.10 8962.20 + +# Report the modified pressure +thermo_modify press 1_press + + + +## Uncomment to save some data from simulation to files +#fix print_temp all print 500 "${STEP} ${TEMP}" file temp.dat screen no +#fix print_vol all print 500 "${STEP} ${VOL}" file vol.dat screen no +#fix print_press all print 500 "${STEP} ${PRESS}" file press.dat screen no +#fix print_ke all print 500 "${STEP} ${KE}" file kinetic_E.dat screen no +#fix print_pe all print 500 "${STEP} ${PE}" file potential_E.dat screen no +#fix print_ve all print 500 "${STEP} ${UVDW}" file vdw_E.dat screen no +#fix print_press_tens all print 500 "${STEP} ${PXX} ${PYY} ${PZZ} ${PXY} ${PXZ} ${PYZ}" file press_tens.dat screen no +#fix print_PV_eos all print 500 "${VOL} ${PRESS}" file pv_eos.dat screen no + +## Prints a configuration to dump.txt every 500 steps +#dump 1 all custom 500 dump.txt id type x y z fx fy fz + +# Write restart files to continue simulations +#restart 10000 state1.restart state2.restart + +## Run for this many steps +run_style verlet +run 10000 +Neighbor list info ... + update every 1 steps, delay 0 steps, check yes + max neighbors/atom: 10000, page size: 100000 + master list distance cutoff = 24 + ghost atom cutoff = 24 + binsize = 12, bins = 4 4 4 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair table, perpetual + attributes: half, newton on + pair build: half/bin/atomonly/newton + stencil: half/bin/3d/newton + bin: standard +Per MPI rank memory allocation (min/avg/max) = 3.37 | 3.37 | 3.371 Mbytes +Step Temp PotEng TotEng Press Volume + 0 300 1061.5961 1926.3291 107.006 66250.679 + 500 314.54728 1034.1091 1940.7738 194.42689 65660.282 + 1000 301.41603 1030.7027 1899.5173 -91.966709 66262.543 + 1500 298.8308 1014.8276 1876.1905 -80.178606 67053.605 + 2000 294.78476 1046.8207 1896.521 50.592942 66316.735 + 2500 301.18564 1033.9214 1902.0719 40.482557 66607.667 + 3000 301.06631 1022.0381 1889.8447 47.582403 66341.947 + 3500 297.98353 989.81011 1848.7308 -204.69823 67462.076 + 4000 299.03465 1034.6603 1896.6108 89.196235 66457.338 + 4500 306.04532 985.37017 1867.5285 -51.094929 67519.735 + 5000 304.72903 1014.9543 1893.3184 -127.04402 67238.517 + 5500 292.52622 1025.6599 1868.8502 -19.753932 66716.551 + 6000 296.82719 1031.5184 1887.1059 -1.2609328 66368.611 + 6500 298.63312 1018.4299 1879.2229 -24.75835 66524.898 + 7000 303.25389 1005.9283 1880.0404 -96.273504 67349.674 + 7500 292.45089 1068.2863 1911.2595 103.23295 65778.08 + 8000 301.22765 1040.6294 1908.9011 -0.83635353 66831.038 + 8500 300.19765 1047.5856 1912.8883 -31.582343 66316.305 + 9000 295.1108 1023.8234 1874.4635 -88.165532 67192.344 + 9500 302.1087 1003.6348 1874.4459 -18.707065 66369.361 + 10000 296.3083 1004.126 1858.2178 -28.293045 66862.576 +Loop time of 28.8053 on 4 procs for 10000 steps with 968 atoms + +Performance: 29.994 ns/day, 0.800 hours/ns, 347.159 timesteps/s +95.2% CPU use with 4 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 19.929 | 21.765 | 23.391 | 27.8 | 75.56 +Neigh | 0.067397 | 0.071231 | 0.077313 | 1.5 | 0.25 +Comm | 3.9226 | 5.5183 | 7.3214 | 53.7 | 19.16 +Output | 0.00069928 | 0.0016099 | 0.0043275 | 3.9 | 0.01 +Modify | 1.0874 | 1.1376 | 1.1888 | 4.2 | 3.95 +Other | | 0.3112 | | | 1.08 + +Nlocal: 242 ave 244 max 239 min +Histogram: 1 0 0 0 0 0 1 0 1 1 +Nghost: 5718.5 ave 5736 max 5702 min +Histogram: 1 0 0 0 1 1 0 0 0 1 +Neighs: 100703 ave 108064 max 93454 min +Histogram: 1 0 0 1 0 0 1 0 0 1 + +Total # of neighbors = 402813 +Ave neighs/atom = 416.129 +Neighbor list builds = 14 +Dangerous builds = 0 + + +Please see the log.cite file for references relevant to this simulation + +Total wall time: 0:00:28 diff --git a/examples/USER/bocs/methanol.data b/examples/USER/bocs/methanol.data new file mode 100644 index 0000000000000000000000000000000000000000..01f66de6f62294929f87497522ae541b567596a0 --- /dev/null +++ b/examples/USER/bocs/methanol.data @@ -0,0 +1,991 @@ +LAMMPS Description + + 968 atoms + 0 bonds + 0 angles + 0 dihedrals + 0 impropers + + 1 atom types + 0 bond types + 0 angle types + 0 dihedral types + + 0 40.4635 xlo xhi + 0 40.4635 ylo yhi + 0 40.4635 zlo zhi + +Masses + + 1 32.0424 + +Atoms + +1 1 36.39 8.05 27.55 +2 1 18.38 15.72 26.03 +3 1 3.52 1.77 23.57 +4 1 31.09 11.38 12.17 +5 1 13.3 34.8 2.89 +6 1 1.72 38.55 10.36 +7 1 38.6 23.16 6.19 +8 1 0.74 33.21 0.17 +9 1 26.97 9.53 11.24 +10 1 31.68 12.19 17.04 +11 1 15.19 9.06 0.2 +12 1 34.39 20.63 35.71 +13 1 21.79 4.93 6.49 +14 1 28.08 33.01 24.51 +15 1 37.03 20.52 32.9 +16 1 32.69 20 30.11 +17 1 23.77 38.59 18.79 +18 1 16.01 2.31 20.15 +19 1 5.65 15.5 28.5 +20 1 8.35 17.35 20.48 +21 1 31.24 24.68 27.4 +22 1 29.41 16.64 19.79 +23 1 37.42 31.93 26.68 +24 1 18.76 39.06 30.68 +25 1 22.97 35 20.81 +26 1 39.47 18.28 29.6 +27 1 34.37 19.4 0.17 +28 1 5.94 9.53 10.95 +29 1 11.45 38.44 14.64 +30 1 39.57 11.04 1.57 +31 1 25.91 20.97 12.79 +32 1 36.3 22.1 1.68 +33 1 21.87 22.49 3.43 +34 1 5.77 18.66 3.97 +35 1 7 7.59 18.42 +36 1 39.76 27.63 17.98 +37 1 10.26 23.18 5.11 +38 1 23.23 21.37 17.38 +39 1 7.47 37.37 5.57 +40 1 0.73 21.6 14.78 +41 1 2.27 30.22 14.93 +42 1 7.39 28.22 14.88 +43 1 27.48 1.11 25.02 +44 1 8.37 13.19 14.64 +45 1 7.11 33.57 0.65 +46 1 34.19 35.11 3.17 +47 1 7.52 3.2 20.33 +48 1 1.02 17.69 37.85 +49 1 8.59 6.21 10.26 +50 1 2.89 16.81 30.02 +51 1 27.05 9.07 32.8 +52 1 12.32 14.79 21.11 +53 1 26.63 22.69 16.75 +54 1 31.6 2.79 20.45 +55 1 35.11 0.74 12.16 +56 1 29.71 31.23 37.63 +57 1 38.22 19.02 18.12 +58 1 10.95 17.4 0.39 +59 1 1.65 19.87 6.67 +60 1 5.15 1.94 14.61 +61 1 8.2 31.43 15.72 +62 1 0.55 20.85 2.45 +63 1 15.27 31.74 0.33 +64 1 17.9 9.84 23.87 +65 1 1.46 8.39 19.24 +66 1 37.79 25.11 12.24 +67 1 14.11 27.19 30.7 +68 1 29.39 24.12 38.92 +69 1 39.15 20.32 39.86 +70 1 11.79 11.38 30.6 +71 1 29.87 30.18 32.5 +72 1 11.06 37.8 30.18 +73 1 20.11 4.59 35.57 +74 1 37.19 27.23 1.44 +75 1 18.83 26.13 35.26 +76 1 29.27 7.86 36.75 +77 1 34.83 29.59 37.82 +78 1 22.16 34.68 25.27 +79 1 5.95 14.65 25.55 +80 1 -0.04 3.48 29.91 +81 1 14.69 6.75 38.06 +82 1 16.8 23.69 3.14 +83 1 14.52 38.72 21.61 +84 1 37.36 15.13 27.98 +85 1 29.79 17.03 27.55 +86 1 21.01 0.39 0.9 +87 1 35.3 6.45 14.41 +88 1 13.74 34.69 10.01 +89 1 13.83 7.92 31.88 +90 1 26.88 37.81 22.36 +91 1 31.76 7.34 10.03 +92 1 11.98 37.49 19.61 +93 1 29.19 31.74 20.69 +94 1 39.15 10.97 21.06 +95 1 1.47 5 22.21 +96 1 -0.1 1.33 16.26 +97 1 34.74 34.78 30.66 +98 1 22.09 26.78 2.27 +99 1 36.58 34.8 16.19 +100 1 19.09 24.88 15.75 +101 1 2.21 31.42 38.32 +102 1 28.02 8.18 29.77 +103 1 15.99 16.78 17.61 +104 1 32.43 12.2 35.3 +105 1 26.54 38.8 30.88 +106 1 35.58 22.23 18.31 +107 1 28.3 30.81 2.96 +108 1 8.95 32.9 9.02 +109 1 28.51 30.02 29.39 +110 1 13 5.35 34.26 +111 1 37.9 36.79 1.37 +112 1 12.78 1.99 40.66 +113 1 21.19 34.55 17.45 +114 1 10.5 20 5.07 +115 1 16.19 21.64 18.49 +116 1 14.62 26.41 19.88 +117 1 27.97 2.89 28.03 +118 1 29.44 14.35 39.04 +119 1 2.29 24.16 33.8 +120 1 39.22 15.81 32.02 +121 1 7.31 19.66 18.18 +122 1 27.67 7.98 15.53 +123 1 31.23 4.04 33 +124 1 29.52 39.44 28.71 +125 1 30.86 20.28 15.84 +126 1 32.25 7.44 19.79 +127 1 34.68 15.68 1.18 +128 1 16.58 27.98 27.97 +129 1 32.27 24.24 15.82 +130 1 3.86 6.57 39.8 +131 1 9.1 2.88 13.12 +132 1 17.84 27.8 11.79 +133 1 4.77 10.88 6.75 +134 1 16.58 24.21 24.5 +135 1 10.17 19.31 38.32 +136 1 6.27 7.81 36.44 +137 1 34.76 37.89 29.76 +138 1 40.99 38.22 35.21 +139 1 25.04 21.79 36.88 +140 1 4.78 15.35 16.44 +141 1 19.24 5.77 40.18 +142 1 13.59 11.27 37.14 +143 1 1.61 23.83 39.61 +144 1 6.02 33.07 3.77 +145 1 0.85 7.4 35.42 +146 1 6.47 40.34 4.65 +147 1 16.45 36.52 15.44 +148 1 19.58 9.5 1.64 +149 1 1.36 1.72 35.53 +150 1 11.74 5.48 4.98 +151 1 25.45 40.36 15.44 +152 1 19.09 0.74 36.18 +153 1 31.78 37.98 1.84 +154 1 23.26 18.47 38.56 +155 1 7.29 22.87 25.86 +156 1 2.36 7.83 8.78 +157 1 39.61 25.94 21.12 +158 1 7.78 18.97 25.29 +159 1 36.56 19.61 26.7 +160 1 4.64 12.06 19.9 +161 1 21.05 33.08 0.87 +162 1 33.93 22.87 39.71 +163 1 33.62 29.48 20.83 +164 1 0.64 18.79 9.52 +165 1 27.53 16.7 22.51 +166 1 17.66 9.84 14.61 +167 1 31.23 22.44 24.98 +168 1 39.3 34.88 11.03 +169 1 24.01 10.56 0.09 +170 1 15.81 33.44 18.52 +171 1 19.92 30.61 19.25 +172 1 16.49 3.95 38.28 +173 1 18.6 38.87 24.98 +174 1 33.04 25.55 8.57 +175 1 16.9 35.09 22.94 +176 1 15.18 6.74 2.33 +177 1 40.54 12.58 31.65 +178 1 21.21 37.62 14.35 +179 1 33.52 38.19 14.89 +180 1 22.06 12.49 29.81 +181 1 19.49 29.03 2.52 +182 1 26.97 18.55 38.45 +183 1 24.1 11.86 17.22 +184 1 12.02 0.55 10.39 +185 1 3.8 35.94 19.94 +186 1 8.31 14.31 37.4 +187 1 29.03 8.28 22.92 +188 1 18.92 0.22 27.87 +189 1 26.79 24.9 24.62 +190 1 36.59 18.86 21.13 +191 1 33.06 13.58 30.17 +192 1 32.37 2.02 39.69 +193 1 22.65 25.97 32.59 +194 1 21.81 38.04 33.85 +195 1 36.82 37.68 19.22 +196 1 32.48 31.43 33.66 +197 1 8.75 36.66 20.34 +198 1 14.88 15.11 28.76 +199 1 22.83 28.55 29.5 +200 1 2.98 12.06 2.88 +201 1 3.01 37 6.91 +202 1 14.79 16.69 3.66 +203 1 12.62 38.28 0.97 +204 1 40.07 21.27 25.25 +205 1 34.58 6.14 39.48 +206 1 11.51 30.52 33.53 +207 1 32.22 9.28 30.52 +208 1 0.7 4.01 38.87 +209 1 32.66 39.86 36.84 +210 1 27.34 34.57 21.76 +211 1 13.7 23.12 8.34 +212 1 28 9.71 6.29 +213 1 31.69 26.39 38.19 +214 1 2.04 20.93 36.95 +215 1 30.31 26.61 12.31 +216 1 25.37 20.63 9.4 +217 1 16.29 5.62 14.04 +218 1 1.36 1.95 4.97 +219 1 38.75 26.8 5.62 +220 1 40.28 29.89 12.27 +221 1 0.52 31.22 7.58 +222 1 15.64 21.64 14.71 +223 1 10.11 28.8 9.67 +224 1 19.03 37.3 38.87 +225 1 12.07 6.46 19.25 +226 1 36.22 21.11 15.02 +227 1 12.49 15.69 7.21 +228 1 25.2 30.8 19.71 +229 1 8.24 35.22 23.02 +230 1 9.94 4.1 1.86 +231 1 4.31 19.07 26.23 +232 1 22.03 19.99 14.19 +233 1 30.84 5.24 2.75 +234 1 35.51 30.52 32.3 +235 1 3.88 20.41 39.48 +236 1 30.86 0.39 31.56 +237 1 25.91 27.12 39.04 +238 1 33.39 5.37 4.51 +239 1 20.58 28.33 37.53 +240 1 11.83 21.81 39.11 +241 1 39.94 5.2 5.73 +242 1 29.89 33.21 15.44 +243 1 23.42 15.38 30.98 +244 1 28.66 11.56 16.13 +245 1 16.74 20.43 21.72 +246 1 9.31 0.26 22.42 +247 1 4.38 37.78 14.12 +248 1 13.86 4.65 16.99 +249 1 6.72 27.43 8.14 +250 1 33.45 18.74 19.98 +251 1 17.34 14.55 35.57 +252 1 14.21 37.39 28.76 +253 1 26.29 29.06 22.26 +254 1 36.52 26.18 15.62 +255 1 17.6 8.81 10.14 +256 1 21.95 25.19 17.69 +257 1 17.4 7.46 18.59 +258 1 6.15 29.7 35.99 +259 1 9.73 37.39 24.96 +260 1 28.58 28.21 36.19 +261 1 8.24 13.72 32.2 +262 1 13.25 34.6 22.71 +263 1 38.58 7.98 10.3 +264 1 18.29 29.75 23.51 +265 1 3.74 13.22 31.05 +266 1 30.78 0.7 24.57 +267 1 24.5 12.94 10.81 +268 1 33.88 26.44 1.96 +269 1 29.92 22.6 9.59 +270 1 15.87 21.94 33.44 +271 1 23.63 8.41 10.95 +272 1 26.53 0.01 7.58 +273 1 33.88 8.73 2.52 +274 1 39.74 31.46 36.87 +275 1 13.28 39.54 37 +276 1 24.74 35.41 32.14 +277 1 17.3 34.32 6.85 +278 1 24.43 13.36 5.63 +279 1 31.23 17.12 7.11 +280 1 15.58 37.85 34.06 +281 1 25.93 38.17 3.13 +282 1 31.84 34.34 39.67 +283 1 14.41 17.74 14.43 +284 1 9.4 1.78 29.53 +285 1 8.29 29.61 6.81 +286 1 7.13 17.36 -0.19 +287 1 38.04 19.52 11.25 +288 1 34.87 32.77 38.75 +289 1 27.18 22.49 5.69 +290 1 29.69 27.11 20.29 +291 1 25.23 2.22 39.75 +292 1 35.8 17.1 36.09 +293 1 20.53 17.67 35.47 +294 1 23.41 31.36 2.24 +295 1 25.17 20.09 29.2 +296 1 0.32 9.28 39.74 +297 1 22.49 18.77 29.89 +298 1 38.64 0.85 39.43 +299 1 18.55 5.87 9.15 +300 1 35.21 28.69 25.76 +301 1 39.24 15.68 6.36 +302 1 5.91 13.29 3.92 +303 1 0.5 21.25 21.62 +304 1 34.39 9.43 18.59 +305 1 22.7 1.03 8.79 +306 1 40.15 16.25 24.87 +307 1 16.52 13.69 10.25 +308 1 6.88 36.77 39.57 +309 1 11.95 37.1 7.59 +310 1 19.49 26.66 9.76 +311 1 36.34 29.89 29.31 +312 1 18.76 35.75 12.72 +313 1 23.15 38.68 4.96 +314 1 10.78 17.11 34.38 +315 1 13.58 14.89 0.34 +316 1 4.73 33.88 32.41 +317 1 12.68 29.51 17.07 +318 1 9.45 27 4.98 +319 1 29.02 19.27 6.45 +320 1 19.09 36.35 19.84 +321 1 23.13 6.75 19.78 +322 1 8.02 34.1 26.95 +323 1 26.03 14.18 1.57 +324 1 15.01 34.16 28.32 +325 1 28.71 36.53 15.08 +326 1 9.64 13.94 24.05 +327 1 1.24 36.96 30.41 +328 1 15.44 31.39 4.77 +329 1 25.72 14.42 38.01 +330 1 7.35 31.84 12.61 +331 1 32.33 16.79 3.07 +332 1 15.86 0.39 8.39 +333 1 27.69 7.32 25.74 +334 1 27.77 1.17 4.96 +335 1 29.38 26.68 23.48 +336 1 14.95 3.41 2.13 +337 1 2.45 38.8 17.54 +338 1 9.18 27.58 31.12 +339 1 36.62 15.23 23.66 +340 1 12.23 30.74 10.85 +341 1 12.87 0.23 24.05 +342 1 33.85 35.75 19.95 +343 1 36.36 30.35 13.94 +344 1 38.11 8.15 5.49 +345 1 15.58 1.29 29.89 +346 1 25.95 30.47 39.19 +347 1 27.69 15.5 13.37 +348 1 25.48 13.7 25.29 +349 1 0.72 39.53 4.41 +350 1 8.75 15.21 5.79 +351 1 10.49 26.46 27.25 +352 1 16.9 20.08 26.58 +353 1 3.95 4.33 20.25 +354 1 18.03 7.66 31.87 +355 1 21.35 2.88 17.26 +356 1 32.92 22.68 6.56 +357 1 21.72 4.62 12.02 +358 1 37.6 6.04 25.2 +359 1 22.22 23.78 7.36 +360 1 12.53 19.53 10.6 +361 1 17.87 26.05 19.32 +362 1 20.94 30.75 31.23 +363 1 22.33 11.87 35.79 +364 1 28.54 6.88 10.52 +365 1 29.58 26.13 8.56 +366 1 19.06 24.2 21.73 +367 1 25.05 38.41 26.91 +368 1 18.66 40.35 4.69 +369 1 11.87 6.75 12.72 +370 1 17.99 11.82 37.79 +371 1 8.97 24.7 0.61 +372 1 26.89 1.52 31.33 +373 1 6.88 22.51 14.06 +374 1 29.51 3.87 13.35 +375 1 0.95 14.53 10 +376 1 26.43 31.54 11.63 +377 1 6.1 35.16 11.28 +378 1 10.2 15.91 28.7 +379 1 13.24 25.67 24.3 +380 1 34.5 3.91 20.22 +381 1 22.48 2.17 5.2 +382 1 24.26 16.15 11.3 +383 1 20.63 32.57 27.3 +384 1 39.95 6.81 1.05 +385 1 24.38 34.78 38.27 +386 1 4.63 23.56 0.55 +387 1 33.5 8.38 36.97 +388 1 5.76 27.14 12.06 +389 1 37.45 26.58 32.25 +390 1 2.8 8.96 32.35 +391 1 5.29 39.84 30.1 +392 1 29.2 26.49 31.18 +393 1 33.91 27.39 12.89 +394 1 3.37 14.19 39.34 +395 1 30.68 28.7 27 +396 1 2.59 18.45 19.38 +397 1 13.55 0.75 27.35 +398 1 3.82 20.12 16.1 +399 1 37.72 0.72 34.29 +400 1 23.85 3.32 19.46 +401 1 4.78 0.67 38.23 +402 1 22.78 23.26 38.6 +403 1 11.56 39.29 4.23 +404 1 21.38 32.45 5.39 +405 1 8.32 19.42 9.52 +406 1 28.43 31.07 17.8 +407 1 11.02 5.75 39.84 +408 1 27.36 36.71 7.62 +409 1 34.22 16.74 27.88 +410 1 3.22 22.01 27.42 +411 1 29.2 15.76 32.33 +412 1 25.29 23.44 2.2 +413 1 10.8 32.43 39.96 +414 1 32.2 1.41 4.44 +415 1 32.94 15.59 37.21 +416 1 6.8 8.08 0.84 +417 1 10.42 9.91 37.73 +418 1 1.18 31.39 3.93 +419 1 10.1 36.38 38.57 +420 1 32.89 26.96 35.07 +421 1 28.12 11.93 25.96 +422 1 4.9 29.15 -0.25 +423 1 2.21 27.99 3.72 +424 1 11.33 3.94 25.55 +425 1 3.3 30.26 10.78 +426 1 11.57 27.26 19.31 +427 1 21.79 32.67 13.3 +428 1 4.96 26.53 33.78 +429 1 33.41 32.87 18.46 +430 1 13.92 30.37 20.3 +431 1 16.91 3.5 11.57 +432 1 -0.06 4.42 34.05 +433 1 7.04 24.33 16.85 +434 1 28.66 11.93 19.73 +435 1 30.21 1.75 36.36 +436 1 3.91 6.2 6.26 +437 1 7.01 25.6 27.34 +438 1 34 1.06 18.12 +439 1 29.14 8.5 3.09 +440 1 40.13 23.52 16.94 +441 1 21.69 22.38 26.78 +442 1 18.44 32.85 39.84 +443 1 38.87 1.99 27.63 +444 1 10.47 12.02 33.68 +445 1 9.65 19.94 21.88 +446 1 25.04 8.12 27.89 +447 1 12.18 16.78 31.09 +448 1 38.31 8.2 30.6 +449 1 0.11 5.21 18.12 +450 1 23.48 7.88 38.7 +451 1 7.9 11.99 7.04 +452 1 2.09 34.5 8.64 +453 1 19 18.3 0.42 +454 1 37.94 18.06 15.21 +455 1 25.05 33.33 29.55 +456 1 33.74 37.88 34.54 +457 1 36.07 29.5 17.47 +458 1 27.7 13.54 10.46 +459 1 27.18 23.18 21.06 +460 1 17.49 2.04 23.22 +461 1 23.84 26.31 36.76 +462 1 31.08 32.24 24.92 +463 1 17.7 28.73 16.66 +464 1 1.59 15.5 18.04 +465 1 33.49 18.99 8.75 +466 1 1.19 8.43 28.01 +467 1 5.43 20.26 22.25 +468 1 23.3 5.31 15.05 +469 1 27.09 4.47 21.96 +470 1 26.61 27.48 28.83 +471 1 13 3.18 13.4 +472 1 36.09 34.56 10.58 +473 1 19.09 15.33 7.48 +474 1 12.94 18.16 22.07 +475 1 38.8 16.16 36.73 +476 1 16.73 39.94 -0.46 +477 1 3.64 12.56 9.42 +478 1 27.64 3.31 18.29 +479 1 15.58 12.36 4.52 +480 1 15.37 11.18 18.19 +481 1 37.52 11.23 14.94 +482 1 37.16 2.3 10.01 +483 1 36.19 9.86 21.99 +484 1 36.38 21.09 4.76 +485 1 38.15 12.94 25.35 +486 1 15.1 29.65 24.64 +487 1 16.54 29.12 38.85 +488 1 33.86 11.39 14.4 +489 1 27.99 18.55 9.87 +490 1 0.66 1.26 8.28 +491 1 29.89 33.84 29.75 +492 1 6.64 33.3 6.74 +493 1 31.47 0.39 11.25 +494 1 8.76 15.96 10.74 +495 1 39.6 15.8 21.04 +496 1 22.38 28.55 19.85 +497 1 25.87 6.23 5.4 +498 1 36.24 26.67 38.61 +499 1 23.05 8.79 7.01 +500 1 32.05 4.16 8.87 +501 1 35.3 13.36 38.03 +502 1 39.91 25.91 36.45 +503 1 32.17 17.27 31.82 +504 1 29.99 21.54 20.57 +505 1 9.39 0.57 34.17 +506 1 22.12 17.22 13.03 +507 1 15.23 16.27 24.39 +508 1 26.32 25.89 13.26 +509 1 39.25 3.46 1.34 +510 1 32.56 10.28 7.96 +511 1 25.76 14.8 34.79 +512 1 32.12 5.38 36.94 +513 1 17.74 15.37 14.87 +514 1 21.93 3.26 25.26 +515 1 24.05 0.48 36.27 +516 1 8.2 19.02 33.92 +517 1 33.07 25.88 24.79 +518 1 12.54 0.52 32.8 +519 1 18.5 6.34 23.21 +520 1 35.93 10.26 34.79 +521 1 19.33 11.86 6.94 +522 1 1.63 5.31 25.43 +523 1 30.62 36.78 30.77 +524 1 12.25 26.79 13.74 +525 1 21 1.47 13.99 +526 1 22.24 29.36 34.11 +527 1 29.05 1.74 0.24 +528 1 19.34 25.14 39.77 +529 1 12.9 25.42 35.42 +530 1 4.1 20.69 33.31 +531 1 35.38 5.64 9.17 +532 1 5.01 34.03 23.36 +533 1 15.7 10.01 7.1 +534 1 25.95 19.48 24.73 +535 1 11.15 4.16 21.43 +536 1 1.47 3.23 13.72 +537 1 26.54 36.76 17.48 +538 1 7.65 30.6 27.73 +539 1 18.59 3.05 3.32 +540 1 6.92 36.14 15.67 +541 1 12.72 36.21 32.72 +542 1 16.33 26.24 14.35 +543 1 21.66 12.61 26.18 +544 1 15.72 32.37 10.71 +545 1 27.57 15.75 4.97 +546 1 20.18 39.13 18.44 +547 1 18.77 17.09 4.74 +548 1 12.75 14.08 17.89 +549 1 10.71 37.26 35.13 +550 1 20.88 32.12 9.94 +551 1 8.69 0.06 9.54 +552 1 1.58 12.61 26.42 +553 1 10.29 22.73 13.14 +554 1 23.31 25.7 4.97 +555 1 36.7 30.78 5.26 +556 1 5.6 28.71 23.76 +557 1 13.04 7.91 15.46 +558 1 40.24 33.53 34.5 +559 1 39.7 18.36 34.25 +560 1 23.52 22.84 21.14 +561 1 32.82 27.9 5.02 +562 1 1.52 33.77 27.04 +563 1 31.48 18.68 13.1 +564 1 34 24.07 34.55 +565 1 34.72 25.03 30.45 +566 1 18.92 5.7 16.54 +567 1 15.26 40.2 16.97 +568 1 24.55 16.8 26.26 +569 1 17.59 18.03 31.75 +570 1 12.08 27.38 38.42 +571 1 31.42 21.91 35.27 +572 1 9.68 6.93 36.96 +573 1 22.93 15.19 2.53 +574 1 11.83 24.38 2.24 +575 1 16.02 12.44 31.42 +576 1 20.24 10.7 20.15 +577 1 37.38 17.37 40.63 +578 1 3.74 17.41 22.49 +579 1 23.21 9.86 23.99 +580 1 2.49 36.56 38 +581 1 20.51 1.54 22.62 +582 1 8.23 33.44 33.15 +583 1 30.93 8.12 14.85 +584 1 36.35 3.92 37.65 +585 1 5.57 10.63 28.64 +586 1 30.24 22.84 4.6 +587 1 3.24 15.97 7.43 +588 1 22.64 0.7 27.09 +589 1 1.64 40.37 27.74 +590 1 30.53 35.28 3.5 +591 1 25.55 4.7 2.53 +592 1 22.04 29.56 12.29 +593 1 3.42 8.76 2.28 +594 1 16.37 37.65 7.87 +595 1 20.65 12.75 2.9 +596 1 8.07 20.49 2.6 +597 1 20.04 24.72 28.2 +598 1 29.75 0.33 16.1 +599 1 31.36 33.09 8.02 +600 1 8.6 10.56 2.65 +601 1 20.55 33.93 33.71 +602 1 23.11 -0.42 31.7 +603 1 27.07 6.69 18.5 +604 1 15.65 23.71 11.8 +605 1 23.88 24.17 30.1 +606 1 0.79 32.46 16.99 +607 1 25.96 20.19 2.43 +608 1 35.16 12.33 4.73 +609 1 16.53 17.12 10.45 +610 1 19.74 35.94 8.62 +611 1 -0.24 28.29 28.3 +612 1 33.15 4.39 12.64 +613 1 24.27 18.59 33.59 +614 1 0.3 9.61 23.54 +615 1 5.52 10.89 34.71 +616 1 9.85 26.26 34.42 +617 1 25.54 37.74 39.13 +618 1 4.11 29.65 5.81 +619 1 30.86 22.72 31.07 +620 1 39.54 34.54 23.24 +621 1 15.03 9.34 12.11 +622 1 21.93 38.49 9.53 +623 1 18.21 19.2 16.65 +624 1 38.71 32.83 14.49 +625 1 37.74 36.38 31.43 +626 1 7.57 2.2 1.07 +627 1 12.27 10.05 1.53 +628 1 18.32 19.55 12.51 +629 1 12.49 24.81 16.57 +630 1 35.07 31.62 22.85 +631 1 4.91 19.68 30.45 +632 1 11.36 2.92 36.19 +633 1 26.76 35.53 1.29 +634 1 1.13 14.55 14.77 +635 1 8.2 25.14 37.83 +636 1 -0.5 0.85 23.08 +637 1 17.95 18.01 37.61 +638 1 2.44 37.75 0.71 +639 1 3.77 23.41 17.91 +640 1 3.34 14.41 35.96 +641 1 14.89 31.42 31.76 +642 1 15.72 22.91 30.66 +643 1 37.42 3.13 5.51 +644 1 1.51 38.14 20.78 +645 1 12.55 18.16 25.81 +646 1 18.98 15.88 29.21 +647 1 17.33 32.04 27.87 +648 1 31.21 37.38 22.84 +649 1 11.88 32.4 31 +650 1 25.1 2.19 12.69 +651 1 38.85 39.1 27.87 +652 1 5.9 16.14 33.34 +653 1 6.3 17.5 36.46 +654 1 2.28 25.02 12.53 +655 1 19.33 25.49 6.78 +656 1 8.57 37.22 8.4 +657 1 22 38.61 24.14 +658 1 35.63 3.23 2.15 +659 1 37.35 22.64 9.99 +660 1 25.46 28.22 33.18 +661 1 13.99 4.21 9.07 +662 1 9.04 40.64 37.59 +663 1 17.46 6.49 27.93 +664 1 1.42 6.14 30.2 +665 1 25.82 28.28 10.33 +666 1 30.71 30.2 -0.02 +667 1 8.05 29.32 0.62 +668 1 6.49 3.17 6.65 +669 1 7.77 39.88 26.03 +670 1 28.53 12.14 30.96 +671 1 6.25 12.64 39.55 +672 1 3.78 7.96 25.83 +673 1 28.69 29.58 6.61 +674 1 5.32 18.55 8.6 +675 1 5.3 11.44 14.19 +676 1 39 12.03 36.99 +677 1 11.08 32.51 19.12 +678 1 38.48 1.03 20.34 +679 1 38.47 11.31 10.12 +680 1 3.65 20.3 11.99 +681 1 27.18 11.39 3.4 +682 1 29.61 20.72 38.86 +683 1 31.88 4.82 24.75 +684 1 14.52 36.61 25.66 +685 1 21.68 19.96 24.58 +686 1 1.2 13.59 23.16 +687 1 37.71 5.97 35.28 +688 1 19.81 22.04 37.54 +689 1 40.67 27.07 10.14 +690 1 38.57 13.96 13.75 +691 1 18.15 17.19 21.63 +692 1 3.76 27.51 30.32 +693 1 11.39 25.09 7.96 +694 1 28.95 22.02 13.33 +695 1 31.72 35.46 35.33 +696 1 15.17 6.03 23.94 +697 1 9.63 9.42 22.18 +698 1 27.76 4.1 38.61 +699 1 27.37 37.46 11.07 +700 1 35.69 15.24 6.39 +701 1 21.92 33.09 36.84 +702 1 4.79 15.51 13.28 +703 1 9.31 26.44 22.8 +704 1 30.14 38.31 6.98 +705 1 4.33 6.66 13.77 +706 1 3.66 27.15 37.83 +707 1 0.44 24.06 29.62 +708 1 35.4 9.59 9.8 +709 1 33.77 39.44 21.41 +710 1 29.2 18.74 24.38 +711 1 34.14 30 7.36 +712 1 16.02 4.37 6.43 +713 1 35.75 39.41 40.58 +714 1 15.32 11.84 23.24 +715 1 32.52 24.39 20.97 +716 1 11.45 2.9 7.16 +717 1 7.07 34.28 36.04 +718 1 11.41 8.83 7.57 +719 1 29.29 27.79 16.55 +720 1 2.41 9.16 16.14 +721 1 13.14 38.07 12.01 +722 1 37.45 14.26 18.3 +723 1 34.64 18.37 16.65 +724 1 29.26 34.28 33.46 +725 1 13.67 19.83 3.04 +726 1 19.64 2.6 32.95 +727 1 23.61 23.55 11.34 +728 1 6.87 22.5 36.5 +729 1 36.78 28.34 22.96 +730 1 11.3 13.98 9.84 +731 1 20.82 19.73 9.16 +732 1 12.65 12.61 6.16 +733 1 9.25 7.81 25.28 +734 1 25.4 29.36 5.84 +735 1 17.86 9.06 4.45 +736 1 35.84 40.51 26.06 +737 1 26.97 21.28 31.59 +738 1 39.94 38.14 24.86 +739 1 3.16 17.07 2.49 +740 1 14.08 15.4 36.99 +741 1 26.1 13.88 29.68 +742 1 26.36 20 20.56 +743 1 12.02 6.35 27.65 +744 1 11.21 19.14 15.27 +745 1 35.86 22.93 26.81 +746 1 32.26 12.62 2.68 +747 1 29.36 4.91 6.86 +748 1 20.14 7.97 29.32 +749 1 25.53 11.2 36.18 +750 1 30.36 14.25 24.79 +751 1 29.84 38.37 39.29 +752 1 15.79 36.4 4.26 +753 1 32.59 14.17 10.29 +754 1 13.89 34.54 15.42 +755 1 12.13 33.62 7.27 +756 1 25.86 23.81 33.97 +757 1 18.4 31.27 34.96 +758 1 6.58 40.49 17.57 +759 1 5.64 39.86 23.05 +760 1 25.32 33 16.24 +761 1 0.98 10.99 12.21 +762 1 32.86 23.75 12.41 +763 1 32.91 1.3 26.94 +764 1 9.46 8.66 31.47 +765 1 17.49 15.53 1.82 +766 1 8.17 18.16 15.3 +767 1 4.84 30.63 26.32 +768 1 6.75 37.1 30.8 +769 1 7.16 5.72 15.74 +770 1 20.09 17.82 19.18 +771 1 1.02 27.99 32.54 +772 1 21.44 1.28 38.4 +773 1 21.06 14.62 37.08 +774 1 27.82 18.99 15.96 +775 1 33.51 21.46 22.82 +776 1 8.29 2.79 17.09 +777 1 18.14 11.41 28.62 +778 1 17.94 28.54 32.73 +779 1 36.1 9.54 40.1 +780 1 36.55 2.62 22.97 +781 1 27.29 10.41 39.35 +782 1 22.04 37.76 2.02 +783 1 23.01 30.08 16.58 +784 1 6.34 15.31 21.61 +785 1 7.3 22.39 7.74 +786 1 38 5.77 21.04 +787 1 32.93 12.85 26.58 +788 1 22.43 15.36 16.72 +789 1 18.54 2.38 8.35 +790 1 0.62 31.88 23.84 +791 1 39.56 30.3 21.7 +792 1 7.56 11.78 25.2 +793 1 16.05 3.98 26.72 +794 1 24.33 36.16 13.16 +795 1 26.38 31.24 35.77 +796 1 14.94 26.46 -0.44 +797 1 3.53 28 19.79 +798 1 11.94 32.27 25.88 +799 1 34.59 15.06 19.23 +800 1 3.51 10.62 24.22 +801 1 13.18 21.59 35.52 +802 1 19.95 13.15 16.23 +803 1 24.48 9.63 19.58 +804 1 37.7 34.42 19.19 +805 1 22.84 19.59 5.52 +806 1 34.62 36.75 12.26 +807 1 10.33 21.85 25.15 +808 1 21.51 29.7 7.23 +809 1 34.05 3 30.58 +810 1 12.43 29.67 5.59 +811 1 18.94 21.82 29.31 +812 1 39.21 17.7 4 +813 1 7.04 2.97 37.09 +814 1 30.87 10.8 22.09 +815 1 33.54 7.16 23.15 +816 1 32.82 32.27 11.47 +817 1 21.8 14.54 21.61 +818 1 38.83 6.69 13.68 +819 1 30.37 39.05 18.66 +820 1 31.21 15.08 13.79 +821 1 1.07 11.97 35.04 +822 1 26.02 35.8 35.47 +823 1 27.64 33.32 8.04 +824 1 39.57 36.88 4.39 +825 1 14.48 30.97 36.87 +826 1 36.86 27.04 8.96 +827 1 34.73 26.27 19.55 +828 1 29.24 29.12 10.86 +829 1 8.35 39.9 13.92 +830 1 5.43 5.1 31.85 +831 1 18.36 22.31 5.89 +832 1 2.46 27.35 16.36 +833 1 21.76 37.05 27.45 +834 1 29.32 17.11 2.28 +835 1 3.58 21.98 3.09 +836 1 10.61 9.17 10.69 +837 1 25.15 17.54 6.05 +838 1 3.4 22.81 7.03 +839 1 16.12 23.66 38.29 +840 1 8.67 4.79 31.8 +841 1 27.82 0.02 20.45 +842 1 4.46 2.44 29.46 +843 1 39.11 22.69 36.33 +844 1 4.26 2.45 34.43 +845 1 13.47 3.5 30.9 +846 1 26.92 22.55 26.54 +847 1 5.66 30.07 30.65 +848 1 31.58 35.68 25.46 +849 1 31.23 5.65 27.78 +850 1 8.76 19.49 28.61 +851 1 24.13 8.02 2.3 +852 1 8.27 6.8 4.93 +853 1 15.31 34.36 37.63 +854 1 3.96 35.82 26.97 +855 1 24.95 4.01 29.96 +856 1 26.54 25.95 19.15 +857 1 17.76 29.23 5.35 +858 1 16.95 21.79 0.78 +859 1 17.52 39.02 13.01 +860 1 20.5 22.86 10.41 +861 1 27.67 27.07 2.78 +862 1 37.1 31.02 2.03 +863 1 37.17 2.24 16.34 +864 1 24.51 34.69 10.28 +865 1 17.38 13.41 21.4 +866 1 38 9.37 17.94 +867 1 35.67 25.27 5.3 +868 1 22.66 4.47 0.97 +869 1 20.06 28.17 27.42 +870 1 27.33 2.38 9.79 +871 1 36.4 10.73 31.42 +872 1 0.53 9.45 6.96 +873 1 12.89 9.03 25.13 +874 1 37.5 23.54 21.33 +875 1 7.19 28.87 19.11 +876 1 21.45 32.81 22.71 +877 1 8.76 8.3 13.51 +878 1 10.24 31.46 3.73 +879 1 15.93 9.7 35.82 +880 1 14.92 19.46 39.91 +881 1 13.02 22.03 27.3 +882 1 34.57 1.59 34.73 +883 1 0.5 21.04 30.77 +884 1 24.84 32.67 4.97 +885 1 30.96 4.24 17.34 +886 1 23.63 8.84 32.7 +887 1 6.84 3.83 26.13 +888 1 31.57 9.23 27.06 +889 1 14.99 35.15 0.07 +890 1 36.29 40.01 8.22 +891 1 18 36.86 35.66 +892 1 11.5 29.22 0.37 +893 1 35.18 36.03 24.88 +894 1 14.49 9.41 27.73 +895 1 10.12 12.91 0.99 +896 1 11.91 29.4 27.3 +897 1 25.51 28.68 14.56 +898 1 29.32 12.95 35.59 +899 1 2.96 0.59 0.53 +900 1 5.47 5.35 9.88 +901 1 8.93 39.33 1.78 +902 1 39.68 38.49 12.33 +903 1 3.78 1.24 11.85 +904 1 29.54 33.76 11.99 +905 1 7.48 6.16 28.8 +906 1 10.83 33.63 36.96 +907 1 22.03 19.06 21.39 +908 1 31.68 31 3.71 +909 1 35.32 0.3 30.88 +910 1 9.93 35.42 14.85 +911 1 21.01 10.66 12.97 +912 1 22.54 21.62 33.81 +913 1 12.48 12.46 25.15 +914 1 0.64 27.93 39.01 +915 1 13.88 27.29 3.8 +916 1 13.03 20.93 19.25 +917 1 5.7 37.48 34.09 +918 1 2.27 35.08 14.29 +919 1 21.75 26.44 13.48 +920 1 10.66 11.35 17.49 +921 1 36.67 34.72 27.69 +922 1 8.23 22.8 33.36 +923 1 4.79 4.05 3.48 +924 1 35.61 35 35.21 +925 1 31.38 37.67 10.06 +926 1 26.44 35.58 27.52 +927 1 25.53 4.47 8.03 +928 1 38.81 33.08 31.55 +929 1 29.62 39.68 34.32 +930 1 0.76 3.88 10.61 +931 1 24.06 30.13 24.84 +932 1 18.77 8.38 37.02 +933 1 2.81 24.14 24.45 +934 1 11.33 1.25 19.69 +935 1 1.61 26.53 6.48 +936 1 9.52 29.81 35.98 +937 1 7.83 31.75 20.77 +938 1 9.67 23.93 20.57 +939 1 33.96 16.95 24.79 +940 1 37.55 37.31 37.17 +941 1 6.2 24.19 31.13 +942 1 17.79 4.35 30.56 +943 1 13.51 20.25 30.45 +944 1 14.76 12.48 13.13 +945 1 32.56 27.52 30.41 +946 1 35.81 40.1 4.85 +947 1 39.01 25.43 27.07 +948 1 22.8 5.53 32.22 +949 1 2.35 39.55 32.5 +950 1 3.31 31.51 34.19 +951 1 40.63 37.01 15.9 +952 1 18.43 35.86 30.77 +953 1 37.01 39.18 15.57 +954 1 6.74 6.26 21.64 +955 1 5.22 24.94 22.53 +956 1 25.2 11.08 13.98 +957 1 14.66 -0.14 5 +958 1 14.96 8.38 20.32 +959 1 1.89 23.03 10.1 +960 1 33.01 11.23 39.32 +961 1 32.68 6.79 32.04 +962 1 6.25 25.81 3.82 +963 1 18.37 31.97 14.57 +964 1 9.74 30.21 22.71 +965 1 3.09 1.52 19.38 +966 1 33.98 37.34 5.63 +967 1 32.19 28.35 15.8 +968 1 24.4 15.49 19.39 diff --git a/examples/USER/misc/bond_react/nylon,6-6_melt/in.large_nylon_melt b/examples/USER/misc/bond_react/nylon,6-6_melt/in.large_nylon_melt new file mode 100644 index 0000000000000000000000000000000000000000..f2dc506ddef28d978d48eb90569302e0de27124b --- /dev/null +++ b/examples/USER/misc/bond_react/nylon,6-6_melt/in.large_nylon_melt @@ -0,0 +1,52 @@ +# 35,000 atom nylon melt example + +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 large_nylon_melt.data.gz + +velocity all create 800.0 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 100 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 + +# stable at 800K +fix 1 statted_grp nvt temp 800 800 100 + +# in order to customize behavior of reacting atoms, +# you can use the internally created 'bond_react_MASTER_group', like so: +# fix 2 bond_react_MASTER_group temp/rescale 1 800 800 10 1 + +thermo_style custom step temp press density f_myrxns[1] f_myrxns[2] # cumulative reaction counts + +# restart 100 restart1 restart2 + +run 200 + +# write_restart restart_longrun +# write_data restart_longrun.data diff --git a/examples/USER/misc/bond_react/nylon,6-6_melt/large_nylon_melt.data.gz b/examples/USER/misc/bond_react/nylon,6-6_melt/large_nylon_melt.data.gz new file mode 100644 index 0000000000000000000000000000000000000000..c620b879a883817b8eb7abe4495e585ecacfaf02 Binary files /dev/null and b/examples/USER/misc/bond_react/nylon,6-6_melt/large_nylon_melt.data.gz differ diff --git a/examples/USER/misc/bond_react/nylon,6-6_melt/log.20Apr18.large_nylon_melt.g++.1 b/examples/USER/misc/bond_react/nylon,6-6_melt/log.20Apr18.large_nylon_melt.g++.1 new file mode 100644 index 0000000000000000000000000000000000000000..653c7582f8d7aba4c8800e5fcfff5ebb22d44a15 --- /dev/null +++ b/examples/USER/misc/bond_react/nylon,6-6_melt/log.20Apr18.large_nylon_melt.g++.1 @@ -0,0 +1,175 @@ +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 +# 35,000 atom nylon melt example + +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 large_nylon_melt.data.gz + orthogonal box = (-2.68344 -2.06791 -2.21988) to (73.4552 73.2448 73.4065) + 1 by 1 by 1 MPI processor grid + reading atoms ... + 35200 atoms + reading velocities ... + 35200 velocities + scanning bonds ... + 9 = max bonds/atom + scanning angles ... + 21 = max angles/atom + scanning dihedrals ... + 31 = max dihedrals/atom + scanning impropers ... + 29 = max impropers/atom + reading bonds ... + 33600 bonds + reading angles ... + 59200 angles + reading dihedrals ... + 80000 dihedrals + reading impropers ... + 35200 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 800.0 4928459 dist gaussian + +molecule mol1 rxn1_stp1_unreacted.data_template +Read molecule mol1: + 18 atoms with max type 8 + 16 bonds with max type 12 + 25 angles with max type 24 + 23 dihedrals with max type 33 + 14 impropers with max type 9 +molecule mol2 rxn1_stp1_reacted.data_template +Read molecule mol2: + 18 atoms with max type 9 + 17 bonds with max type 11 + 31 angles with max type 23 + 39 dihedrals with max type 30 + 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 11 + 25 angles with max type 23 + 30 dihedrals with max type 30 + 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 13 + 19 angles with max type 25 + 16 dihedrals with max type 29 + 10 impropers with max type 11 + +thermo 50 + +# dump 1 all xyz 100 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 + +# stable at 800K +fix 1 statted_grp nvt temp 800 800 100 + +# in order to customize behavior of reacting atoms, +# you can use the internally created 'bond_react_MASTER_group', like so: +# fix 2 bond_react_MASTER_group temp/rescale 1 800 800 10 1 + +thermo_style custom step temp press density f_myrxns[1] f_myrxns[2] # cumulative reaction counts + +# restart 100 restart1 restart2 + +run 200 +PPPM initialization ... + using 12-bit tables for long-range coulomb (../kspace.cpp:321) + G vector (1/distance) = 0.20765 + grid = 18 18 18 + stencil order = 5 + estimated absolute RMS force accuracy = 0.0333156 + estimated relative force accuracy = 0.000100329 + using double precision FFTs + 3d grid and FFT values/proc = 12167 5832 +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 = 15 15 15 + 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 +Per MPI rank memory allocation (min/avg/max) = 209.1 | 209.1 | 209.1 Mbytes +Step Temp Press Density f_myrxns[1] f_myrxns[2] + 0 800 3666.3948 0.80366765 0 0 + 50 673.95238 -9670.9169 0.80366765 31 0 + 100 697.22819 -4624.0512 0.80366765 57 22 + 150 723.60507 -17175.571 0.80366765 76 48 + 200 736.71277 -12961.963 0.80366765 84 64 +Loop time of 102.825 on 1 procs for 200 steps with 35200 atoms + +Performance: 0.168 ns/day, 142.812 hours/ns, 1.945 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 | 27.193 | 27.193 | 27.193 | 0.0 | 26.45 +Bond | 11.324 | 11.324 | 11.324 | 0.0 | 11.01 +Kspace | 4.1878 | 4.1878 | 4.1878 | 0.0 | 4.07 +Neigh | 54.724 | 54.724 | 54.724 | 0.0 | 53.22 +Comm | 0.40662 | 0.40662 | 0.40662 | 0.0 | 0.40 +Output | 0.0011101 | 0.0011101 | 0.0011101 | 0.0 | 0.00 +Modify | 4.9422 | 4.9422 | 4.9422 | 0.0 | 4.81 +Other | | 0.04545 | | | 0.04 + +Nlocal: 35200 ave 35200 max 35200 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 38403 ave 38403 max 38403 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 6.9281e+06 ave 6.9281e+06 max 6.9281e+06 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 6928101 +Ave neighs/atom = 196.821 +Ave special neighs/atom = 9.83727 +Neighbor list builds = 200 +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: 0:01:43 diff --git a/examples/USER/misc/bond_react/nylon,6-6_melt/log.20Apr18.large_nylon_melt.g++.4 b/examples/USER/misc/bond_react/nylon,6-6_melt/log.20Apr18.large_nylon_melt.g++.4 new file mode 100644 index 0000000000000000000000000000000000000000..cc0dda60c7dcec4b775d0d5cd6cdad4f6b751124 --- /dev/null +++ b/examples/USER/misc/bond_react/nylon,6-6_melt/log.20Apr18.large_nylon_melt.g++.4 @@ -0,0 +1,175 @@ +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 +# 35,000 atom nylon melt example + +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 large_nylon_melt.data.gz + orthogonal box = (-2.68344 -2.06791 -2.21988) to (73.4552 73.2448 73.4065) + 2 by 1 by 2 MPI processor grid + reading atoms ... + 35200 atoms + reading velocities ... + 35200 velocities + scanning bonds ... + 9 = max bonds/atom + scanning angles ... + 21 = max angles/atom + scanning dihedrals ... + 31 = max dihedrals/atom + scanning impropers ... + 29 = max impropers/atom + reading bonds ... + 33600 bonds + reading angles ... + 59200 angles + reading dihedrals ... + 80000 dihedrals + reading impropers ... + 35200 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 800.0 4928459 dist gaussian + +molecule mol1 rxn1_stp1_unreacted.data_template +Read molecule mol1: + 18 atoms with max type 8 + 16 bonds with max type 12 + 25 angles with max type 24 + 23 dihedrals with max type 33 + 14 impropers with max type 9 +molecule mol2 rxn1_stp1_reacted.data_template +Read molecule mol2: + 18 atoms with max type 9 + 17 bonds with max type 11 + 31 angles with max type 23 + 39 dihedrals with max type 30 + 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 11 + 25 angles with max type 23 + 30 dihedrals with max type 30 + 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 13 + 19 angles with max type 25 + 16 dihedrals with max type 29 + 10 impropers with max type 11 + +thermo 50 + +# dump 1 all xyz 100 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 + +# stable at 800K +fix 1 statted_grp nvt temp 800 800 100 + +# in order to customize behavior of reacting atoms, +# you can use the internally created 'bond_react_MASTER_group', like so: +# fix 2 bond_react_MASTER_group temp/rescale 1 800 800 10 1 + +thermo_style custom step temp press density f_myrxns[1] f_myrxns[2] # cumulative reaction counts + +# restart 100 restart1 restart2 + +run 200 +PPPM initialization ... + using 12-bit tables for long-range coulomb (../kspace.cpp:321) + G vector (1/distance) = 0.20765 + grid = 18 18 18 + stencil order = 5 + estimated absolute RMS force accuracy = 0.0333156 + estimated relative force accuracy = 0.000100329 + using double precision FFTs + 3d grid and FFT values/proc = 4508 1620 +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 = 15 15 15 + 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 +Per MPI rank memory allocation (min/avg/max) = 81.11 | 81.13 | 81.15 Mbytes +Step Temp Press Density f_myrxns[1] f_myrxns[2] + 0 800 3666.3948 0.80366765 0 0 + 50 673.95238 -9670.9169 0.80366765 31 0 + 100 697.22819 -4624.0512 0.80366765 57 22 + 150 724.40407 -17166.729 0.80366765 76 49 + 200 737.28582 -12968.224 0.80366765 84 65 +Loop time of 51.171 on 4 procs for 200 steps with 35200 atoms + +Performance: 0.338 ns/day, 71.071 hours/ns, 3.908 timesteps/s +98.4% CPU use with 4 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 12.926 | 13.247 | 13.493 | 6.7 | 25.89 +Bond | 5.2132 | 5.2733 | 5.3367 | 1.9 | 10.31 +Kspace | 2.3601 | 2.6534 | 3.0067 | 16.0 | 5.19 +Neigh | 25.93 | 25.934 | 25.937 | 0.1 | 50.68 +Comm | 0.73273 | 0.75464 | 0.78505 | 2.3 | 1.47 +Output | 0.00045228 | 0.00067407 | 0.0013323 | 0.0 | 0.00 +Modify | 3.2682 | 3.2686 | 3.2692 | 0.0 | 6.39 +Other | | 0.03995 | | | 0.08 + +Nlocal: 8800 ave 8913 max 8652 min +Histogram: 1 0 0 0 1 0 0 0 1 1 +Nghost: 18366 ave 18461 max 18190 min +Histogram: 1 0 0 0 0 0 0 1 1 1 +Neighs: 1.73203e+06 ave 1.77261e+06 max 1.68165e+06 min +Histogram: 1 0 1 0 0 0 0 0 0 2 + +Total # of neighbors = 6928132 +Ave neighs/atom = 196.822 +Ave special neighs/atom = 9.83608 +Neighbor list builds = 200 +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: 0:00:52 diff --git a/examples/USER/misc/bond_react/nylon,6-6_melt/rxn1_stp1_map b/examples/USER/misc/bond_react/nylon,6-6_melt/rxn1_stp1_map new file mode 100644 index 0000000000000000000000000000000000000000..44f7ad8137549eaa375046e114c59a7aa09c0c65 --- /dev/null +++ b/examples/USER/misc/bond_react/nylon,6-6_melt/rxn1_stp1_map @@ -0,0 +1,35 @@ +this is a nominal superimpose file + +2 edgeIDs +18 equivalences + +BondingIDs + +10 +1 + +EdgeIDs + +16 +8 + +Equivalences + +1 1 +2 2 +3 3 +4 4 +5 5 +6 6 +7 7 +8 8 +9 9 +10 10 +11 11 +12 12 +13 13 +14 14 +15 15 +16 16 +17 17 +18 18 diff --git a/examples/USER/misc/bond_react/nylon,6-6_melt/rxn1_stp1_reacted.data_template b/examples/USER/misc/bond_react/nylon,6-6_melt/rxn1_stp1_reacted.data_template new file mode 100644 index 0000000000000000000000000000000000000000..61c0408ce3e57955e736d15e77736b95dccf240b --- /dev/null +++ b/examples/USER/misc/bond_react/nylon,6-6_melt/rxn1_stp1_reacted.data_template @@ -0,0 +1,189 @@ +this is a molecule template for: initial nylon crosslink, post-reacting + +18 atoms +17 bonds +31 angles +39 dihedrals +20 impropers + +Types + +1 9 +2 1 +3 1 +4 4 +5 4 +6 3 +7 3 +8 1 +9 1 +10 5 +11 8 +12 6 +13 3 +14 3 +15 7 +16 1 +17 3 +18 3 + +Charges + +1 -0.300000 +2 0.000000 +3 0.000000 +4 0.000000 +5 0.000000 +6 0.000000 +7 0.000000 +8 0.000000 +9 0.000000 +10 0.300000 +11 0.000000 +12 0.000000 +13 0.000000 +14 0.000000 +15 0.000000 +16 0.000000 +17 0.000000 +18 0.000000 + +Coords + +1 -5.522237 -0.752722 1.631158 +2 -5.170398 -0.545733 0.178130 +3 -6.469695 -0.553072 -0.648889 +4 -6.052076 -1.721152 1.744648 +5 -6.183059 0.071387 1.971497 +6 -4.489340 -1.389197 -0.173156 +7 -4.637591 0.453703 0.051252 +8 -5.618658 0.138919 4.386107 +9 -4.669492 -0.989819 3.943591 +10 -4.270194 -0.766405 2.474102 +11 -3.348470 -1.875393 2.024289 +12 -3.569794 0.564183 2.345995 +13 -5.201079 -1.993301 4.044219 +14 -3.736682 -0.984819 4.598305 +15 -4.255402 1.370923 2.679069 +16 -6.136394 -0.339866 -2.136775 +17 -6.996331 -1.555519 -0.517408 +18 -7.153308 0.284949 -0.289930 + +Bonds + +1 9 1 2 +2 10 1 4 +3 10 1 5 +4 11 1 10 +5 1 2 3 +6 2 2 6 +7 2 2 7 +8 1 3 16 +9 2 3 17 +10 2 3 18 +11 1 8 9 +12 6 9 10 +13 2 9 13 +14 2 9 14 +15 7 10 11 +16 5 10 12 +17 8 12 15 + +Angles + +1 14 2 1 4 +2 14 2 1 5 +3 15 2 1 10 +4 16 4 1 5 +5 17 4 1 10 +6 17 5 1 10 +7 18 1 2 3 +8 19 1 2 6 +9 19 1 2 7 +10 1 3 2 6 +11 1 3 2 7 +12 3 6 2 7 +13 2 2 3 16 +14 1 2 3 17 +15 1 2 3 18 +16 1 16 3 17 +17 1 16 3 18 +18 3 17 3 18 +19 12 8 9 10 +20 1 8 9 13 +21 1 8 9 14 +22 13 13 9 10 +23 13 14 9 10 +24 3 13 9 14 +25 10 9 10 11 +26 8 9 10 12 +27 20 1 10 9 +28 21 11 10 12 +29 22 1 10 11 +30 23 1 10 12 +31 11 10 12 15 + +Dihedrals + +1 16 4 1 2 3 +2 17 4 1 2 6 +3 17 4 1 2 7 +4 16 5 1 2 3 +5 17 5 1 2 6 +6 17 5 1 2 7 +7 18 10 1 2 3 +8 19 10 1 2 6 +9 19 10 1 2 7 +10 20 2 1 10 9 +11 21 2 1 10 11 +12 22 2 1 10 12 +13 23 4 1 10 9 +14 24 4 1 10 11 +15 25 4 1 10 12 +16 23 5 1 10 9 +17 24 5 1 10 11 +18 25 5 1 10 12 +19 26 1 2 3 16 +20 27 1 2 3 17 +21 27 1 2 3 18 +22 4 16 3 2 6 +23 2 6 2 3 17 +24 2 6 2 3 18 +25 4 16 3 2 7 +26 2 7 2 3 17 +27 2 7 2 3 18 +28 14 8 9 10 11 +29 12 8 9 10 12 +30 28 8 9 10 1 +31 15 13 9 10 11 +32 13 13 9 10 12 +33 29 13 9 10 1 +34 15 14 9 10 11 +35 13 14 9 10 12 +36 29 14 9 10 1 +37 10 9 10 12 15 +38 11 11 10 12 15 +39 30 1 10 12 15 + +Impropers + +1 1 2 1 4 5 +2 1 2 1 4 10 +3 1 2 1 5 10 +4 1 4 1 5 10 +5 1 1 2 3 6 +6 1 1 2 3 7 +7 1 1 2 6 7 +8 1 3 2 6 7 +9 1 2 3 16 17 +10 1 2 3 16 18 +11 1 2 3 17 18 +12 1 16 3 17 18 +13 1 8 9 13 10 +14 1 8 9 14 10 +15 1 8 9 13 14 +16 1 13 9 14 10 +17 1 9 10 11 12 +18 1 1 10 9 11 +19 1 1 10 9 12 +20 1 1 10 11 12 diff --git a/examples/USER/misc/bond_react/nylon,6-6_melt/rxn1_stp1_unreacted.data_template b/examples/USER/misc/bond_react/nylon,6-6_melt/rxn1_stp1_unreacted.data_template new file mode 100644 index 0000000000000000000000000000000000000000..944d6918c57e77d2d96b3a949efac38cfce1c5f6 --- /dev/null +++ b/examples/USER/misc/bond_react/nylon,6-6_melt/rxn1_stp1_unreacted.data_template @@ -0,0 +1,160 @@ +this is a molecule template for: initial nylon crosslink, pre-reacting + +18 atoms +16 bonds +25 angles +23 dihedrals +14 impropers + +Types + +1 2 +2 1 +3 1 +4 4 +5 4 +6 3 +7 3 +8 1 +9 1 +10 5 +11 8 +12 6 +13 3 +14 3 +15 7 +16 1 +17 3 +18 3 + +Charges + +1 -0.300000 +2 0.000000 +3 0.000000 +4 0.000000 +5 0.000000 +6 0.000000 +7 0.000000 +8 0.000000 +9 0.000000 +10 0.300000 +11 0.000000 +12 0.000000 +13 0.000000 +14 0.000000 +15 0.000000 +16 0.000000 +17 0.000000 +18 0.000000 + +Coords + +1 -4.922858 -0.946982 1.146055 +2 -5.047195 -0.935267 -0.358173 +3 -6.526281 -0.755366 -0.743523 +4 -5.282604 0.020447 1.552710 +5 -3.860697 -1.095850 1.428305 +6 -4.662382 -1.920900 -0.781524 +7 -4.433977 -0.072765 -0.784071 +8 -5.506279 0.202610 4.825816 +9 -4.449177 -0.844592 4.423366 +10 -4.103916 -0.749629 2.925195 +11 -3.376249 -1.886171 2.245643 +12 -4.493235 0.477214 2.137199 +13 -4.849053 -1.888877 4.663994 +14 -3.491823 -0.662913 5.018510 +15 -5.020777 1.189745 2.805427 +16 -3.964987 2.900602 -1.551341 +17 -4.460694 2.836102 0.668882 +18 -4.828494 3.219656 -0.122111 + +Bonds + +1 12 1 2 +2 4 1 4 +3 4 1 5 +4 1 2 3 +5 2 2 6 +6 2 2 7 +7 1 3 16 +8 2 3 17 +9 2 3 18 +10 1 8 9 +11 6 9 10 +12 2 9 13 +13 2 9 14 +14 7 10 11 +15 5 10 12 +16 8 12 15 + +Angles + +1 6 2 1 4 +2 6 2 1 5 +3 7 4 1 5 +4 24 1 2 3 +5 5 1 2 6 +6 5 1 2 7 +7 1 3 2 6 +8 1 3 2 7 +9 3 6 2 7 +10 2 2 3 16 +11 1 2 3 17 +12 1 2 3 18 +13 1 16 3 17 +14 1 16 3 18 +15 3 17 3 18 +16 12 8 9 10 +17 1 8 9 13 +18 1 8 9 14 +19 13 13 9 10 +20 13 14 9 10 +21 3 13 9 14 +22 10 9 10 11 +23 8 9 10 12 +24 21 11 10 12 +25 11 10 12 15 + +Dihedrals + +1 31 4 1 2 3 +2 32 4 1 2 6 +3 32 4 1 2 7 +4 31 5 1 2 3 +5 32 5 1 2 6 +6 32 5 1 2 7 +7 33 1 2 3 16 +8 1 1 2 3 17 +9 1 1 2 3 18 +10 4 16 3 2 6 +11 2 6 2 3 17 +12 2 6 2 3 18 +13 4 16 3 2 7 +14 2 7 2 3 17 +15 2 7 2 3 18 +16 14 8 9 10 11 +17 12 8 9 10 12 +18 15 13 9 10 11 +19 13 13 9 10 12 +20 15 14 9 10 11 +21 13 14 9 10 12 +22 10 9 10 12 15 +23 11 11 10 12 15 + +Impropers + +1 1 2 1 4 5 +2 9 9 10 11 12 +3 1 1 2 3 6 +4 1 1 2 3 7 +5 1 1 2 6 7 +6 1 3 2 6 7 +7 1 2 3 16 17 +8 1 2 3 16 18 +9 1 2 3 17 18 +10 1 16 3 17 18 +11 1 8 9 13 10 +12 1 8 9 14 10 +13 1 8 9 13 14 +14 1 13 9 14 10 diff --git a/examples/USER/misc/bond_react/nylon,6-6_melt/rxn1_stp2_map b/examples/USER/misc/bond_react/nylon,6-6_melt/rxn1_stp2_map new file mode 100644 index 0000000000000000000000000000000000000000..35fe47fdb3bdb0386d65b950d45cbfb39fbe6f7f --- /dev/null +++ b/examples/USER/misc/bond_react/nylon,6-6_melt/rxn1_stp2_map @@ -0,0 +1,32 @@ +this is a nominal superimpose file + +2 edgeIDs +15 equivalences + +BondingIDs + +4 +12 + +EdgeIDs + +8 +3 + +Equivalences + +1 1 +2 2 +3 3 +4 4 +5 5 +6 6 +7 7 +8 8 +9 9 +10 10 +11 11 +12 12 +13 13 +14 14 +15 15 diff --git a/examples/USER/misc/bond_react/nylon,6-6_melt/rxn1_stp2_reacted.data_template b/examples/USER/misc/bond_react/nylon,6-6_melt/rxn1_stp2_reacted.data_template new file mode 100644 index 0000000000000000000000000000000000000000..ffd3ef733c0ff4eb28c59ba4d8c657a2710dd8ad --- /dev/null +++ b/examples/USER/misc/bond_react/nylon,6-6_melt/rxn1_stp2_reacted.data_template @@ -0,0 +1,131 @@ +this is a molecule template for: water condensation, post-reacting + +15 atoms +13 bonds +19 angles +16 dihedrals +10 impropers + +Types + +1 9 +2 1 +3 1 +4 10 +5 4 +6 3 +7 3 +8 1 +9 1 +10 5 +11 8 +12 11 +13 3 +14 3 +15 10 + +Charges + +1 -0.300000 +2 0.000000 +3 0.000000 +4 0.410000 +5 0.000000 +6 0.000000 +7 0.000000 +8 0.000000 +9 0.000000 +10 0.300000 +11 0.000000 +12 -0.820000 +13 0.000000 +14 0.000000 +15 0.410000 + +Coords + +1 -4.856280 -1.050468 1.432625 +2 -5.047195 -0.935267 -0.358173 +3 -6.526281 -0.755366 -0.743523 +4 -5.282604 0.020447 1.552710 +5 -3.860697 -1.095850 1.428305 +6 -4.662382 -1.920900 -0.781524 +7 -4.433977 -0.072765 -0.784071 +8 -5.506279 0.202610 4.825816 +9 -4.449177 -0.844592 4.423366 +10 -4.103916 -0.749629 2.925195 +11 -3.376249 -1.886171 2.245643 +12 -4.493235 0.477214 2.137199 +13 -4.849053 -1.888877 4.663994 +14 -3.491823 -0.662913 5.018510 +15 -5.020777 1.189745 2.805427 + +Bonds + +1 9 1 2 +2 10 1 5 +3 11 1 10 +4 1 2 3 +5 2 2 6 +6 2 2 7 +7 13 4 12 +8 1 8 9 +9 6 9 10 +10 2 9 13 +11 2 9 14 +12 7 10 11 +13 13 15 12 + +Angles + +1 14 2 1 5 +2 15 2 1 10 +3 17 5 1 10 +4 18 1 2 3 +5 19 1 2 6 +6 19 1 2 7 +7 1 3 2 6 +8 1 3 2 7 +9 3 6 2 7 +10 12 8 9 10 +11 1 8 9 13 +12 1 8 9 14 +13 13 13 9 10 +14 13 14 9 10 +15 3 13 9 14 +16 10 9 10 11 +17 20 1 10 9 +18 22 1 10 11 +19 25 15 12 4 + +Dihedrals + +1 16 5 1 2 3 +2 17 5 1 2 6 +3 17 5 1 2 7 +4 18 10 1 2 3 +5 19 10 1 2 6 +6 19 10 1 2 7 +7 20 2 1 10 9 +8 21 2 1 10 11 +9 23 5 1 10 9 +10 24 5 1 10 11 +11 14 8 9 10 11 +12 28 8 9 10 1 +13 15 13 9 10 11 +14 29 13 9 10 1 +15 15 14 9 10 11 +16 29 14 9 10 1 + +Impropers + +1 10 2 1 5 10 +2 11 1 10 9 11 +3 1 1 2 3 6 +4 1 1 2 3 7 +5 1 1 2 6 7 +6 1 3 2 6 7 +7 1 8 9 13 10 +8 1 8 9 14 10 +9 1 8 9 13 14 +10 1 13 9 14 10 diff --git a/examples/USER/misc/bond_react/nylon,6-6_melt/rxn1_stp2_unreacted.data_template b/examples/USER/misc/bond_react/nylon,6-6_melt/rxn1_stp2_unreacted.data_template new file mode 100644 index 0000000000000000000000000000000000000000..7abe15ada8d2372e4435ef82b5e60b7417865790 --- /dev/null +++ b/examples/USER/misc/bond_react/nylon,6-6_melt/rxn1_stp2_unreacted.data_template @@ -0,0 +1,158 @@ +this is a molecule template for: water condensation, pre-reacting + +15 atoms +14 bonds +25 angles +30 dihedrals +16 impropers + +Types + +1 9 +2 1 +3 1 +4 4 +5 4 +6 3 +7 3 +8 1 +9 1 +10 5 +11 8 +12 6 +13 3 +14 3 +15 7 + +Charges + +1 -0.300000 +2 0.000000 +3 0.000000 +4 0.000000 +5 0.000000 +6 0.000000 +7 0.000000 +8 0.000000 +9 0.000000 +10 0.300000 +11 0.000000 +12 0.000000 +13 0.000000 +14 0.000000 +15 0.000000 + +Coords + +1 -4.922858 -0.946982 1.146055 +2 -5.047195 -0.935267 -0.358173 +3 -6.526281 -0.755366 -0.743523 +4 -5.282604 0.020447 1.552710 +5 -3.860697 -1.095850 1.428305 +6 -4.662382 -1.920900 -0.781524 +7 -4.433977 -0.072765 -0.784071 +8 -5.506279 0.202610 4.825816 +9 -4.449177 -0.844592 4.423366 +10 -4.103916 -0.749629 2.925195 +11 -3.376249 -1.886171 2.245643 +12 -4.493235 0.477214 2.137199 +13 -4.849053 -1.888877 4.663994 +14 -3.491823 -0.662913 5.018510 +15 -5.020777 1.189745 2.805427 + +Bonds + +1 9 1 2 +2 10 1 4 +3 10 1 5 +4 11 1 10 +5 1 2 3 +6 2 2 6 +7 2 2 7 +8 1 8 9 +9 6 9 10 +10 2 9 13 +11 2 9 14 +12 7 10 11 +13 5 10 12 +14 8 12 15 + +Angles + +1 14 2 1 4 +2 14 2 1 5 +3 15 2 1 10 +4 16 4 1 5 +5 17 4 1 10 +6 17 5 1 10 +7 18 1 2 3 +8 19 1 2 6 +9 19 1 2 7 +10 1 3 2 6 +11 1 3 2 7 +12 3 6 2 7 +13 12 8 9 10 +14 1 8 9 13 +15 1 8 9 14 +16 13 13 9 10 +17 13 14 9 10 +18 3 13 9 14 +19 10 9 10 11 +20 8 9 10 12 +21 20 1 10 9 +22 21 11 10 12 +23 22 1 10 11 +24 23 1 10 12 +25 11 10 12 15 + +Dihedrals + +1 16 4 1 2 3 +2 17 4 1 2 6 +3 17 4 1 2 7 +4 16 5 1 2 3 +5 17 5 1 2 6 +6 17 5 1 2 7 +7 18 10 1 2 3 +8 19 10 1 2 6 +9 19 10 1 2 7 +10 20 2 1 10 9 +11 21 2 1 10 11 +12 22 2 1 10 12 +13 23 4 1 10 9 +14 24 4 1 10 11 +15 25 4 1 10 12 +16 23 5 1 10 9 +17 24 5 1 10 11 +18 25 5 1 10 12 +19 14 8 9 10 11 +20 12 8 9 10 12 +21 28 8 9 10 1 +22 15 13 9 10 11 +23 13 13 9 10 12 +24 29 13 9 10 1 +25 15 14 9 10 11 +26 13 14 9 10 12 +27 29 14 9 10 1 +28 10 9 10 12 15 +29 11 11 10 12 15 +30 30 1 10 12 15 + +Impropers + +1 1 2 1 4 5 +2 1 2 1 4 10 +3 1 2 1 5 10 +4 1 4 1 5 10 +5 1 1 2 3 6 +6 1 1 2 3 7 +7 1 1 2 6 7 +8 1 3 2 6 7 +9 1 8 9 13 10 +10 1 8 9 14 10 +11 1 8 9 13 14 +12 1 13 9 14 10 +13 1 9 10 11 12 +14 1 1 10 9 11 +15 1 1 10 9 12 +16 1 1 10 11 12 diff --git a/examples/USER/misc/bond_react/tiny_nylon/in.tiny_nylon b/examples/USER/misc/bond_react/tiny_nylon/in.tiny_nylon new file mode 100644 index 0000000000000000000000000000000000000000..1f7e9c42b7b4098fd355dec8afc696e42631321c --- /dev/null +++ b/examples/USER/misc/bond_react/tiny_nylon/in.tiny_nylon @@ -0,0 +1,50 @@ +# 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 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 + +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 + +# 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 new file mode 100644 index 0000000000000000000000000000000000000000..344439f94c5906e1fc7417921b89434ae0a7b8b5 --- /dev/null +++ b/examples/USER/misc/bond_react/tiny_nylon/log.20Apr18.tiny_nylon.g++.1 @@ -0,0 +1,370 @@ +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 new file mode 100644 index 0000000000000000000000000000000000000000..377781f48f7091dbc910d9ce1ab0f98723abb7bb --- /dev/null +++ b/examples/USER/misc/bond_react/tiny_nylon/log.20Apr18.tiny_nylon.g++.4 @@ -0,0 +1,370 @@ +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/rxn1_stp1_map b/examples/USER/misc/bond_react/tiny_nylon/rxn1_stp1_map new file mode 100644 index 0000000000000000000000000000000000000000..44f7ad8137549eaa375046e114c59a7aa09c0c65 --- /dev/null +++ b/examples/USER/misc/bond_react/tiny_nylon/rxn1_stp1_map @@ -0,0 +1,35 @@ +this is a nominal superimpose file + +2 edgeIDs +18 equivalences + +BondingIDs + +10 +1 + +EdgeIDs + +16 +8 + +Equivalences + +1 1 +2 2 +3 3 +4 4 +5 5 +6 6 +7 7 +8 8 +9 9 +10 10 +11 11 +12 12 +13 13 +14 14 +15 15 +16 16 +17 17 +18 18 diff --git a/examples/USER/misc/bond_react/tiny_nylon/rxn1_stp1_reacted.data_template b/examples/USER/misc/bond_react/tiny_nylon/rxn1_stp1_reacted.data_template new file mode 100644 index 0000000000000000000000000000000000000000..d7256f43d2b3c659159ef23e3169dc6123d193ec --- /dev/null +++ b/examples/USER/misc/bond_react/tiny_nylon/rxn1_stp1_reacted.data_template @@ -0,0 +1,189 @@ +this is a molecule template for: initial nylon crosslink, post-reacting + +18 atoms +17 bonds +31 angles +39 dihedrals +20 impropers + +Types + +1 9 +2 1 +3 1 +4 8 +5 8 +6 4 +7 4 +8 1 +9 1 +10 2 +11 6 +12 3 +13 4 +14 4 +15 5 +16 1 +17 4 +18 4 + +Charges + +1 -0.300000 +2 0.000000 +3 0.000000 +4 0.000000 +5 0.000000 +6 0.000000 +7 0.000000 +8 0.000000 +9 0.000000 +10 0.300000 +11 0.000000 +12 0.000000 +13 0.000000 +14 0.000000 +15 0.000000 +16 0.000000 +17 0.000000 +18 0.000000 + +Coords + +1 -5.522237 -0.752722 1.631158 +2 -5.170398 -0.545733 0.178130 +3 -6.469695 -0.553072 -0.648889 +4 -6.052076 -1.721152 1.744648 +5 -6.183059 0.071387 1.971497 +6 -4.489340 -1.389197 -0.173156 +7 -4.637591 0.453703 0.051252 +8 -5.618658 0.138919 4.386107 +9 -4.669492 -0.989819 3.943591 +10 -4.270194 -0.766405 2.474102 +11 -3.348470 -1.875393 2.024289 +12 -3.569794 0.564183 2.345995 +13 -5.201079 -1.993301 4.044219 +14 -3.736682 -0.984819 4.598305 +15 -4.255402 1.370923 2.679069 +16 -6.136394 -0.339866 -2.136775 +17 -6.996331 -1.555519 -0.517408 +18 -7.153308 0.284949 -0.289930 + +Bonds + +1 11 1 2 +2 12 1 4 +3 12 1 5 +4 13 1 10 +5 2 2 3 +6 1 2 6 +7 1 2 7 +8 2 3 16 +9 1 3 17 +10 1 3 18 +11 2 8 9 +12 4 9 10 +13 1 9 13 +14 1 9 14 +15 5 10 11 +16 3 10 12 +17 6 12 15 + +Angles + +1 17 2 1 4 +2 17 2 1 5 +3 18 2 1 10 +4 19 4 1 5 +5 20 4 1 10 +6 20 5 1 10 +7 21 1 2 3 +8 22 1 2 6 +9 22 1 2 7 +10 2 3 2 6 +11 2 3 2 7 +12 1 6 2 7 +13 3 2 3 16 +14 2 2 3 17 +15 2 2 3 18 +16 2 16 3 17 +17 2 16 3 18 +18 1 17 3 18 +19 8 8 9 10 +20 2 8 9 13 +21 2 8 9 14 +22 23 13 9 10 +23 23 14 9 10 +24 1 13 9 14 +25 6 9 10 11 +26 4 9 10 12 +27 24 1 10 9 +28 25 11 10 12 +29 26 1 10 11 +30 27 1 10 12 +31 7 10 12 15 + +Dihedrals + +1 19 4 1 2 3 +2 20 4 1 2 6 +3 20 4 1 2 7 +4 19 5 1 2 3 +5 20 5 1 2 6 +6 20 5 1 2 7 +7 21 10 1 2 3 +8 22 10 1 2 6 +9 22 10 1 2 7 +10 23 2 1 10 9 +11 24 2 1 10 11 +12 25 2 1 10 12 +13 26 4 1 10 9 +14 27 4 1 10 11 +15 28 4 1 10 12 +16 26 5 1 10 9 +17 27 5 1 10 11 +18 28 5 1 10 12 +19 29 1 2 3 16 +20 30 1 2 3 17 +21 30 1 2 3 18 +22 4 16 3 2 6 +23 2 6 2 3 17 +24 2 6 2 3 18 +25 4 16 3 2 7 +26 2 7 2 3 17 +27 2 7 2 3 18 +28 10 8 9 10 11 +29 8 8 9 10 12 +30 31 8 9 10 1 +31 11 13 9 10 11 +32 9 13 9 10 12 +33 32 13 9 10 1 +34 11 14 9 10 11 +35 9 14 9 10 12 +36 32 14 9 10 1 +37 6 9 10 12 15 +38 7 11 10 12 15 +39 33 1 10 12 15 + +Impropers + +1 1 2 1 4 5 +2 1 2 1 4 10 +3 1 2 1 5 10 +4 1 4 1 5 10 +5 1 1 2 3 6 +6 1 1 2 3 7 +7 1 1 2 6 7 +8 1 3 2 6 7 +9 1 2 3 16 17 +10 1 2 3 16 18 +11 1 2 3 17 18 +12 1 16 3 17 18 +13 1 8 9 13 10 +14 1 8 9 14 10 +15 1 8 9 13 14 +16 1 13 9 14 10 +17 1 9 10 11 12 +18 1 1 10 9 11 +19 1 1 10 9 12 +20 1 1 10 11 12 diff --git a/examples/USER/misc/bond_react/tiny_nylon/rxn1_stp1_unreacted.data_template b/examples/USER/misc/bond_react/tiny_nylon/rxn1_stp1_unreacted.data_template new file mode 100644 index 0000000000000000000000000000000000000000..ec3f109d7b50c06c642635693f77257c4ce68c7e --- /dev/null +++ b/examples/USER/misc/bond_react/tiny_nylon/rxn1_stp1_unreacted.data_template @@ -0,0 +1,160 @@ +this is a molecule template for: initial nylon crosslink, pre-reacting + +18 atoms +16 bonds +25 angles +23 dihedrals +14 impropers + +Types + +1 7 +2 1 +3 1 +4 8 +5 8 +6 4 +7 4 +8 1 +9 1 +10 2 +11 6 +12 3 +13 4 +14 4 +15 5 +16 1 +17 4 +18 4 + +Charges + +1 -0.300000 +2 0.000000 +3 0.000000 +4 0.000000 +5 0.000000 +6 0.000000 +7 0.000000 +8 0.000000 +9 0.000000 +10 0.300000 +11 0.000000 +12 0.000000 +13 0.000000 +14 0.000000 +15 0.000000 +16 0.000000 +17 0.000000 +18 0.000000 + +Coords + +1 -4.922858 -0.946982 1.146055 +2 -5.047195 -0.935267 -0.358173 +3 -6.526281 -0.755366 -0.743523 +4 -5.282604 0.020447 1.552710 +5 -3.860697 -1.095850 1.428305 +6 -4.662382 -1.920900 -0.781524 +7 -4.433977 -0.072765 -0.784071 +8 -5.506279 0.202610 4.825816 +9 -4.449177 -0.844592 4.423366 +10 -4.103916 -0.749629 2.925195 +11 -3.376249 -1.886171 2.245643 +12 -4.493235 0.477214 2.137199 +13 -4.849053 -1.888877 4.663994 +14 -3.491823 -0.662913 5.018510 +15 -5.020777 1.189745 2.805427 +16 -3.964987 2.900602 -1.551341 +17 -4.460694 2.836102 0.668882 +18 -4.828494 3.219656 -0.122111 + +Bonds + +1 14 1 2 +2 10 1 4 +3 10 1 5 +4 2 2 3 +5 1 2 6 +6 1 2 7 +7 2 3 16 +8 1 3 17 +9 1 3 18 +10 2 8 9 +11 4 9 10 +12 1 9 13 +13 1 9 14 +14 5 10 11 +15 3 10 12 +16 6 12 15 + +Angles + +1 15 2 1 4 +2 15 2 1 5 +3 16 4 1 5 +4 28 1 2 3 +5 14 1 2 6 +6 14 1 2 7 +7 2 3 2 6 +8 2 3 2 7 +9 1 6 2 7 +10 3 2 3 16 +11 2 2 3 17 +12 2 2 3 18 +13 2 16 3 17 +14 2 16 3 18 +15 1 17 3 18 +16 8 8 9 10 +17 2 8 9 13 +18 2 8 9 14 +19 23 13 9 10 +20 23 14 9 10 +21 1 13 9 14 +22 6 9 10 11 +23 4 9 10 12 +24 25 11 10 12 +25 7 10 12 15 + +Dihedrals + +1 34 4 1 2 3 +2 35 4 1 2 6 +3 35 4 1 2 7 +4 34 5 1 2 3 +5 35 5 1 2 6 +6 35 5 1 2 7 +7 36 1 2 3 16 +8 12 1 2 3 17 +9 12 1 2 3 18 +10 4 16 3 2 6 +11 2 6 2 3 17 +12 2 6 2 3 18 +13 4 16 3 2 7 +14 2 7 2 3 17 +15 2 7 2 3 18 +16 10 8 9 10 11 +17 8 8 9 10 12 +18 11 13 9 10 11 +19 9 13 9 10 12 +20 11 14 9 10 11 +21 9 14 9 10 12 +22 6 9 10 12 15 +23 7 11 10 12 15 + +Impropers + +1 6 2 1 4 5 +2 11 9 10 11 12 +3 1 1 2 3 6 +4 1 1 2 3 7 +5 1 1 2 6 7 +6 1 3 2 6 7 +7 1 2 3 16 17 +8 1 2 3 16 18 +9 1 2 3 17 18 +10 1 16 3 17 18 +11 1 8 9 13 10 +12 1 8 9 14 10 +13 1 8 9 13 14 +14 1 13 9 14 10 diff --git a/examples/USER/misc/bond_react/tiny_nylon/rxn1_stp2_map b/examples/USER/misc/bond_react/tiny_nylon/rxn1_stp2_map new file mode 100644 index 0000000000000000000000000000000000000000..35fe47fdb3bdb0386d65b950d45cbfb39fbe6f7f --- /dev/null +++ b/examples/USER/misc/bond_react/tiny_nylon/rxn1_stp2_map @@ -0,0 +1,32 @@ +this is a nominal superimpose file + +2 edgeIDs +15 equivalences + +BondingIDs + +4 +12 + +EdgeIDs + +8 +3 + +Equivalences + +1 1 +2 2 +3 3 +4 4 +5 5 +6 6 +7 7 +8 8 +9 9 +10 10 +11 11 +12 12 +13 13 +14 14 +15 15 diff --git a/examples/USER/misc/bond_react/tiny_nylon/rxn1_stp2_reacted.data_template b/examples/USER/misc/bond_react/tiny_nylon/rxn1_stp2_reacted.data_template new file mode 100644 index 0000000000000000000000000000000000000000..785363464696967b7938c142043868792546e3cf --- /dev/null +++ b/examples/USER/misc/bond_react/tiny_nylon/rxn1_stp2_reacted.data_template @@ -0,0 +1,131 @@ +this is a molecule template for: water condensation, post-reacting + +15 atoms +13 bonds +19 angles +16 dihedrals +10 impropers + +Types + +1 9 +2 1 +3 1 +4 10 +5 8 +6 4 +7 4 +8 1 +9 1 +10 2 +11 6 +12 11 +13 4 +14 4 +15 10 + +Charges + +1 -0.300000 +2 0.000000 +3 0.000000 +4 0.410000 +5 0.000000 +6 0.000000 +7 0.000000 +8 0.000000 +9 0.000000 +10 0.300000 +11 0.000000 +12 -0.820000 +13 0.000000 +14 0.000000 +15 0.410000 + +Coords + +1 -4.856280 -1.050468 1.432625 +2 -5.047195 -0.935267 -0.358173 +3 -6.526281 -0.755366 -0.743523 +4 -5.282604 0.020447 1.552710 +5 -3.860697 -1.095850 1.428305 +6 -4.662382 -1.920900 -0.781524 +7 -4.433977 -0.072765 -0.784071 +8 -5.506279 0.202610 4.825816 +9 -4.449177 -0.844592 4.423366 +10 -4.103916 -0.749629 2.925195 +11 -3.376249 -1.886171 2.245643 +12 -4.493235 0.477214 2.137199 +13 -4.849053 -1.888877 4.663994 +14 -3.491823 -0.662913 5.018510 +15 -5.020777 1.189745 2.805427 + +Bonds + +1 11 1 2 +2 12 1 5 +3 13 1 10 +4 2 2 3 +5 1 2 6 +6 1 2 7 +7 15 4 12 +8 2 8 9 +9 4 9 10 +10 1 9 13 +11 1 9 14 +12 5 10 11 +13 15 15 12 + +Angles + +1 17 2 1 5 +2 18 2 1 10 +3 20 5 1 10 +4 21 1 2 3 +5 22 1 2 6 +6 22 1 2 7 +7 2 3 2 6 +8 2 3 2 7 +9 1 6 2 7 +10 8 8 9 10 +11 2 8 9 13 +12 2 8 9 14 +13 23 13 9 10 +14 23 14 9 10 +15 1 13 9 14 +16 6 9 10 11 +17 24 1 10 9 +18 26 1 10 11 +19 29 15 12 4 + +Dihedrals + +1 19 5 1 2 3 +2 20 5 1 2 6 +3 20 5 1 2 7 +4 21 10 1 2 3 +5 22 10 1 2 6 +6 22 10 1 2 7 +7 23 2 1 10 9 +8 24 2 1 10 11 +9 26 5 1 10 9 +10 27 5 1 10 11 +11 10 8 9 10 11 +12 31 8 9 10 1 +13 11 13 9 10 11 +14 32 13 9 10 1 +15 11 14 9 10 11 +16 32 14 9 10 1 + +Impropers + +1 12 2 1 5 10 +2 13 1 10 9 11 +3 1 1 2 3 6 +4 1 1 2 3 7 +5 1 1 2 6 7 +6 1 3 2 6 7 +7 1 8 9 13 10 +8 1 8 9 14 10 +9 1 8 9 13 14 +10 1 13 9 14 10 diff --git a/examples/USER/misc/bond_react/tiny_nylon/rxn1_stp2_unreacted.data_template b/examples/USER/misc/bond_react/tiny_nylon/rxn1_stp2_unreacted.data_template new file mode 100644 index 0000000000000000000000000000000000000000..847f0622e506865117fbe542f89de35fb20ccede --- /dev/null +++ b/examples/USER/misc/bond_react/tiny_nylon/rxn1_stp2_unreacted.data_template @@ -0,0 +1,158 @@ +this is a molecule template for: water condensation, pre-reacting + +15 atoms +14 bonds +25 angles +30 dihedrals +16 impropers + +Types + +1 9 +2 1 +3 1 +4 8 +5 8 +6 4 +7 4 +8 1 +9 1 +10 2 +11 6 +12 3 +13 4 +14 4 +15 5 + +Charges + +1 -0.300000 +2 0.000000 +3 0.000000 +4 0.000000 +5 0.000000 +6 0.000000 +7 0.000000 +8 0.000000 +9 0.000000 +10 0.300000 +11 0.000000 +12 0.000000 +13 0.000000 +14 0.000000 +15 0.000000 + +Coords + +1 -4.922858 -0.946982 1.146055 +2 -5.047195 -0.935267 -0.358173 +3 -6.526281 -0.755366 -0.743523 +4 -5.282604 0.020447 1.552710 +5 -3.860697 -1.095850 1.428305 +6 -4.662382 -1.920900 -0.781524 +7 -4.433977 -0.072765 -0.784071 +8 -5.506279 0.202610 4.825816 +9 -4.449177 -0.844592 4.423366 +10 -4.103916 -0.749629 2.925195 +11 -3.376249 -1.886171 2.245643 +12 -4.493235 0.477214 2.137199 +13 -4.849053 -1.888877 4.663994 +14 -3.491823 -0.662913 5.018510 +15 -5.020777 1.189745 2.805427 + +Bonds + +1 11 1 2 +2 12 1 4 +3 12 1 5 +4 13 1 10 +5 2 2 3 +6 1 2 6 +7 1 2 7 +8 2 8 9 +9 4 9 10 +10 1 9 13 +11 1 9 14 +12 5 10 11 +13 3 10 12 +14 6 12 15 + +Angles + +1 17 2 1 4 +2 17 2 1 5 +3 18 2 1 10 +4 19 4 1 5 +5 20 4 1 10 +6 20 5 1 10 +7 21 1 2 3 +8 22 1 2 6 +9 22 1 2 7 +10 2 3 2 6 +11 2 3 2 7 +12 1 6 2 7 +13 8 8 9 10 +14 2 8 9 13 +15 2 8 9 14 +16 23 13 9 10 +17 23 14 9 10 +18 1 13 9 14 +19 6 9 10 11 +20 4 9 10 12 +21 24 1 10 9 +22 25 11 10 12 +23 26 1 10 11 +24 27 1 10 12 +25 7 10 12 15 + +Dihedrals + +1 19 4 1 2 3 +2 20 4 1 2 6 +3 20 4 1 2 7 +4 19 5 1 2 3 +5 20 5 1 2 6 +6 20 5 1 2 7 +7 21 10 1 2 3 +8 22 10 1 2 6 +9 22 10 1 2 7 +10 23 2 1 10 9 +11 24 2 1 10 11 +12 25 2 1 10 12 +13 26 4 1 10 9 +14 27 4 1 10 11 +15 28 4 1 10 12 +16 26 5 1 10 9 +17 27 5 1 10 11 +18 28 5 1 10 12 +19 10 8 9 10 11 +20 8 8 9 10 12 +21 31 8 9 10 1 +22 11 13 9 10 11 +23 9 13 9 10 12 +24 32 13 9 10 1 +25 11 14 9 10 11 +26 9 14 9 10 12 +27 32 14 9 10 1 +28 6 9 10 12 15 +29 7 11 10 12 15 +30 33 1 10 12 15 + +Impropers + +1 1 2 1 4 5 +2 1 2 1 4 10 +3 1 2 1 5 10 +4 1 4 1 5 10 +5 1 1 2 3 6 +6 1 1 2 3 7 +7 1 1 2 6 7 +8 1 3 2 6 7 +9 1 8 9 13 10 +10 1 8 9 14 10 +11 1 8 9 13 14 +12 1 13 9 14 10 +13 1 9 10 11 12 +14 1 1 10 9 11 +15 1 1 10 9 12 +16 1 1 10 11 12 diff --git a/examples/USER/misc/bond_react/tiny_nylon/tiny_nylon.data b/examples/USER/misc/bond_react/tiny_nylon/tiny_nylon.data new file mode 100644 index 0000000000000000000000000000000000000000..8466e68ea57fed2ddca9851724e4ea1509049435 --- /dev/null +++ b/examples/USER/misc/bond_react/tiny_nylon/tiny_nylon.data @@ -0,0 +1,795 @@ +this is LAMMPS data file containing two nylon monomers + +44 atoms +11 atom types +42 bonds +15 bond types +74 angles +29 angle types +100 dihedrals +36 dihedral types +44 impropers +13 improper types +5 extra bond per atom +15 extra angle per atom +15 extra dihedral per atom +25 extra improper per atom +25 extra special per atom + +-25 25 xlo xhi +-25 25 ylo yhi +-25 25 zlo zhi + +Masses + +1 12.0112 +2 12.0112 +3 15.9994 +4 1.00797 +5 1.00797 +6 15.9994 +7 14.0067 +8 1.00797 +9 14.0067 +10 1.00797 +11 15.9994 + +Pair Coeffs # lj/class2/coul/cut + +1 0.054 4.01 +2 0.12 3.81 +3 0.24 3.535 +4 0.02 2.7 +5 0.013 1.098 +6 0.267 3.3 +7 0.065 4.07 +8 0.013 1.098 +9 0.106 4.07 +10 0.013 1.098 +11 0.26 3.61 + +Bond Coeffs # class2 + +1 1.101 345 -691.89 844.6 +2 1.53 299.67 -501.77 679.81 +3 1.3649 368.731 -832.478 1274.02 +4 1.5202 253.707 -423.037 396.9 +5 1.202 851.14 -1918.49 2160.77 +6 0.965 532.506 -1282.9 2004.77 +7 1.53 299.67 -501.77 679.81 +8 1.101 345 -691.89 844.6 +9 1.457 365.805 -699.637 998.484 +10 1.006 466.74 -1073.6 1251.11 +11 1.452 327.166 -547.899 526.5 +12 1.01 462.75 -1053.63 1545.76 +13 1.416 359.159 -558.473 1146.38 +14 1.457 365.805 -699.637 998.484 +15 0.97 563.28 -1428.22 1902.12 + +Angle Coeffs # class2 + +1 107.66 39.641 -12.921 -2.4318 +2 110.77 41.453 -10.604 5.129 +3 112.67 39.516 -7.443 -9.5583 +4 123.145 55.5431 -17.2123 0.1348 +5 118.986 98.6813 -22.2485 10.3673 +6 123.145 55.5431 -17.2123 0.1348 +7 111.254 53.5303 -11.8454 -11.5405 +8 108.53 51.9747 -9.4851 -10.9985 +9 107.734 40.6099 -28.8121 0 +10 110.77 41.453 -10.604 5.129 +11 112.67 39.516 -7.443 -9.5583 +12 107.66 39.641 -12.921 -2.4318 +13 111.91 60.7147 -13.3366 -13.0785 +14 110.62 51.3137 -6.7198 -2.6003 +15 110.954 50.8652 -4.4522 -10.0298 +16 107.067 45.252 -7.5558 -9.512 +17 113.868 45.9271 -20.0824 0 +18 111.037 31.8958 -6.6942 -6.837 +19 116.94 37.5749 -8.6676 0 +20 117.961 37.4964 -8.1837 0 +21 114.302 42.6589 -10.5464 -9.3243 +22 108.937 57.401 2.9374 0 +23 107.734 40.6099 -28.8121 0 +24 116.926 39.4193 -10.9945 -8.7733 +25 118.986 98.6813 -22.2485 10.3673 +26 125.542 92.572 -34.48 -11.1871 +27 0 0 0 0 +28 111.91 60.7147 -13.3366 -13.0785 +29 103.7 49.84 -11.6 -8 + +BondBond Coeffs + +1 5.3316 1.101 1.101 +2 3.3872 1.53 1.101 +3 0 1.53 1.53 +4 0 1.5202 1.3649 +5 0 1.3649 1.202 +6 46.0685 1.5202 1.202 +7 0 1.3649 0.965 +8 5.4199 1.53 1.5202 +9 0.7115 1.5202 1.101 +10 3.3872 1.53 1.101 +11 0 1.53 1.53 +12 5.3316 1.101 1.101 +13 4.6217 1.53 1.457 +14 12.426 1.457 1.101 +15 -6.4168 1.457 1.006 +16 -1.8749 1.006 1.006 +17 -3.471 1.452 1.01 +18 12.1186 1.452 1.416 +19 -0.5655 1.01 1.01 +20 -4.3126 1.01 1.416 +21 3.5446 1.452 1.53 +22 15.2994 1.452 1.101 +23 0.7115 1.101 1.5202 +24 0 1.416 1.5202 +25 0 1.202 1.3649 +26 138.495 1.416 1.202 +27 0 1.416 1.3649 +28 4.6217 1.457 1.53 +29 -9.5 0.97 0.97 + +BondAngle Coeffs + +1 18.103 18.103 1.101 1.101 +2 20.754 11.421 1.53 1.101 +3 8.016 8.016 1.53 1.53 +4 0 0 1.5202 1.3649 +5 0 0 1.3649 1.202 +6 34.9982 37.1298 1.5202 1.202 +7 0 0 1.3649 0.965 +8 18.1678 15.8758 1.53 1.5202 +9 12.4632 9.1765 1.5202 1.101 +10 20.754 11.421 1.53 1.101 +11 8.016 8.016 1.53 1.53 +12 18.103 18.103 1.101 1.101 +13 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39 44 +43 7 26 42 43 44 +44 7 39 42 43 44 diff --git a/examples/snap/log.20Apr18.snap.Mo_Chen.g++.1 b/examples/snap/log.20Apr18.snap.Mo_Chen.g++.1 new file mode 100644 index 0000000000000000000000000000000000000000..c5e0f6abab7b7eb657e529096265fa9d3a9bfcff --- /dev/null +++ b/examples/snap/log.20Apr18.snap.Mo_Chen.g++.1 @@ -0,0 +1,127 @@ +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 +# Demonstrate SNAP Ta potential + +# Initialize simulation + +variable nsteps index 100 +variable nrep equal 4 +variable a equal 3.160 +units metal + +# generate the box and atom positions using a BCC lattice + +variable nx equal ${nrep} +variable nx equal 4 +variable ny equal ${nrep} +variable ny equal 4 +variable nz equal ${nrep} +variable nz equal 4 + +boundary p p p + +lattice bcc $a +lattice bcc 3.16 +Lattice spacing in x,y,z = 3.16 3.16 3.16 +region box block 0 ${nx} 0 ${ny} 0 ${nz} +region box block 0 4 0 ${ny} 0 ${nz} +region box block 0 4 0 4 0 ${nz} +region box block 0 4 0 4 0 4 +create_box 1 box +Created orthogonal box = (0 0 0) to (12.64 12.64 12.64) + 1 by 1 by 1 MPI processor grid +create_atoms 1 box +Created 128 atoms + Time spent = 0.000223637 secs + +mass 1 183.84 + +# choose potential + +include Mo_Chen_PRM2017.snap + +# DATE: 2017-09-18 CONTRIBUTOR: Chi Chen CITATION: C. Chen, Z. Deng, R. Tran, H. Tang, I.-H. Chu, S. P. Ong, "Accurate force field for molybdenum by machine learning large materials data" Physical Review Materials 1, 04 3603 (2017) +# Generated by Materials Virtual Lab +# Definition of SNAP potential. +pair_style snap +pair_coeff * * Mo_Chen_PRM2017.snapcoeff Mo Mo_Chen_PRM2017.snapparam Mo +Reading potential file Mo_Chen_PRM2017.snapcoeff with DATE: 2017-09-18 +SNAP Element = Mo, Radius 0.5, Weight 1 +Reading potential file Mo_Chen_PRM2017.snapparam with DATE: 2017-09-18 +SNAP keyword rcutfac 4.615858 +SNAP keyword twojmax 6 + + +# Setup output + +thermo 10 +thermo_modify norm yes + +# Set up NVE run + +timestep 0.5e-3 +neighbor 1.0 bin +neigh_modify once no every 1 delay 0 check yes + +# Run MD + +velocity all create 300.0 4928459 +fix 1 all nve +run ${nsteps} +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 = 5.61586 + ghost atom cutoff = 5.61586 + binsize = 2.80793, bins = 5 5 5 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair snap, perpetual + attributes: full, newton on + pair build: full/bin/atomonly + stencil: full/bin/3d + bin: standard +Per MPI rank memory allocation (min/avg/max) = 3.507 | 3.507 | 3.507 Mbytes +Step Temp E_pair E_mol TotEng Press + 0 300 -22.405975 0 -22.3675 2575.7657 + 10 294.77555 -22.405305 0 -22.3675 2756.6894 + 20 279.53011 -22.40335 0 -22.3675 3285.8272 + 30 255.52174 -22.40027 0 -22.3675 4122.8933 + 40 224.7299 -22.396321 0 -22.367499 5204.3499 + 50 189.67529 -22.391825 0 -22.367499 6449.1308 + 60 153.18862 -22.387145 0 -22.367499 7765.911 + 70 118.14998 -22.382652 0 -22.367499 9061.1616 + 80 87.224916 -22.378685 0 -22.367499 10247.68 + 90 62.623892 -22.37553 0 -22.367498 11250.067 + 100 45.9103 -22.373386 0 -22.367498 12011.726 +Loop time of 3.3917 on 1 procs for 100 steps with 128 atoms + +Performance: 1.274 ns/day, 18.843 hours/ns, 29.484 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 | 3.3906 | 3.3906 | 3.3906 | 0.0 | 99.97 +Neigh | 0 | 0 | 0 | 0.0 | 0.00 +Comm | 0.00039721 | 0.00039721 | 0.00039721 | 0.0 | 0.01 +Output | 0.00023007 | 0.00023007 | 0.00023007 | 0.0 | 0.01 +Modify | 0.00021887 | 0.00021887 | 0.00021887 | 0.0 | 0.01 +Other | | 0.0002868 | | | 0.01 + +Nlocal: 128 ave 128 max 128 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 727 ave 727 max 727 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: 7424 ave 7424 max 7424 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 7424 +Ave neighs/atom = 58 +Neighbor list builds = 0 +Dangerous builds = 0 + +Total wall time: 0:00:03 diff --git a/examples/snap/log.20Apr18.snap.Mo_Chen.g++.4 b/examples/snap/log.20Apr18.snap.Mo_Chen.g++.4 new file mode 100644 index 0000000000000000000000000000000000000000..c25f1f5530856ab7dc5492526aa168c9dafd6fad --- /dev/null +++ b/examples/snap/log.20Apr18.snap.Mo_Chen.g++.4 @@ -0,0 +1,127 @@ +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 +# Demonstrate SNAP Ta potential + +# Initialize simulation + +variable nsteps index 100 +variable nrep equal 4 +variable a equal 3.160 +units metal + +# generate the box and atom positions using a BCC lattice + +variable nx equal ${nrep} +variable nx equal 4 +variable ny equal ${nrep} +variable ny equal 4 +variable nz equal ${nrep} +variable nz equal 4 + +boundary p p p + +lattice bcc $a +lattice bcc 3.16 +Lattice spacing in x,y,z = 3.16 3.16 3.16 +region box block 0 ${nx} 0 ${ny} 0 ${nz} +region box block 0 4 0 ${ny} 0 ${nz} +region box block 0 4 0 4 0 ${nz} +region box block 0 4 0 4 0 4 +create_box 1 box +Created orthogonal box = (0 0 0) to (12.64 12.64 12.64) + 1 by 2 by 2 MPI processor grid +create_atoms 1 box +Created 128 atoms + Time spent = 0.000277281 secs + +mass 1 183.84 + +# choose potential + +include Mo_Chen_PRM2017.snap + +# DATE: 2017-09-18 CONTRIBUTOR: Chi Chen CITATION: C. Chen, Z. Deng, R. Tran, H. Tang, I.-H. Chu, S. P. Ong, "Accurate force field for molybdenum by machine learning large materials data" Physical Review Materials 1, 04 3603 (2017) +# Generated by Materials Virtual Lab +# Definition of SNAP potential. +pair_style snap +pair_coeff * * Mo_Chen_PRM2017.snapcoeff Mo Mo_Chen_PRM2017.snapparam Mo +Reading potential file Mo_Chen_PRM2017.snapcoeff with DATE: 2017-09-18 +SNAP Element = Mo, Radius 0.5, Weight 1 +Reading potential file Mo_Chen_PRM2017.snapparam with DATE: 2017-09-18 +SNAP keyword rcutfac 4.615858 +SNAP keyword twojmax 6 + + +# Setup output + +thermo 10 +thermo_modify norm yes + +# Set up NVE run + +timestep 0.5e-3 +neighbor 1.0 bin +neigh_modify once no every 1 delay 0 check yes + +# Run MD + +velocity all create 300.0 4928459 +fix 1 all nve +run ${nsteps} +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 = 5.61586 + ghost atom cutoff = 5.61586 + binsize = 2.80793, bins = 5 5 5 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair snap, perpetual + attributes: full, newton on + pair build: full/bin/atomonly + stencil: full/bin/3d + bin: standard +Per MPI rank memory allocation (min/avg/max) = 3.486 | 3.486 | 3.486 Mbytes +Step Temp E_pair E_mol TotEng Press + 0 300 -22.405975 0 -22.3675 2575.7657 + 10 294.63153 -22.405286 0 -22.3675 2753.4662 + 20 278.98535 -22.40328 0 -22.3675 3272.416 + 30 254.38916 -22.400125 0 -22.3675 4091.8933 + 40 222.91191 -22.396088 0 -22.367499 5148.5505 + 50 187.16984 -22.391504 0 -22.367499 6362.2454 + 60 150.08253 -22.386747 0 -22.367499 7643.2732 + 70 114.60307 -22.382197 0 -22.367499 8900.2448 + 80 83.449257 -22.378201 0 -22.367499 10047.619 + 90 58.862643 -22.375048 0 -22.367498 11012.233 + 100 42.41931 -22.372939 0 -22.367498 11740.641 +Loop time of 1.91636 on 4 procs for 100 steps with 128 atoms + +Performance: 2.254 ns/day, 10.646 hours/ns, 52.182 timesteps/s +97.9% CPU use with 4 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 1.8147 | 1.8411 | 1.8875 | 2.1 | 96.07 +Neigh | 0 | 0 | 0 | 0.0 | 0.00 +Comm | 0.022276 | 0.069629 | 0.095057 | 10.7 | 3.63 +Output | 0.00032496 | 0.00065821 | 0.0016179 | 0.0 | 0.03 +Modify | 0.00019503 | 0.00020915 | 0.00023341 | 0.0 | 0.01 +Other | | 0.00481 | | | 0.25 + +Nlocal: 32 ave 32 max 32 min +Histogram: 4 0 0 0 0 0 0 0 0 0 +Nghost: 431 ave 431 max 431 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: 1856 ave 1856 max 1856 min +Histogram: 4 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 7424 +Ave neighs/atom = 58 +Neighbor list builds = 0 +Dangerous builds = 0 + +Total wall time: 0:00:01 diff --git a/examples/snap/log.5Oct16.snap.Ta06A.g++.1 b/examples/snap/log.20Apr18.snap.Ta06A.g++.1 similarity index 71% rename from examples/snap/log.5Oct16.snap.Ta06A.g++.1 rename to examples/snap/log.20Apr18.snap.Ta06A.g++.1 index 647ffac8b4326efa8ce7f6fca6b4ee9e577d32f5..d2296852a051bc6d12c58924a802357574a47d6e 100644 --- a/examples/snap/log.5Oct16.snap.Ta06A.g++.1 +++ b/examples/snap/log.20Apr18.snap.Ta06A.g++.1 @@ -1,4 +1,6 @@ -LAMMPS (5 Oct 2016) +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 # Demonstrate SNAP Ta potential # Initialize simulation @@ -31,12 +33,13 @@ Created orthogonal box = (0 0 0) to (13.264 13.264 13.264) 1 by 1 by 1 MPI processor grid create_atoms 1 box Created 128 atoms + Time spent = 0.000328064 secs mass 1 180.88 # choose potential -include Ta06A_pot.snap +include Ta06A.snap # DATE: 2014-09-05 CONTRIBUTOR: Aidan Thompson athomps@sandia.gov CITATION: Thompson, Swiler, Trott, Foiles and Tucker, arxiv.org, 1409.3880 (2014) # Definition of SNAP potential Ta_Cand06A @@ -48,10 +51,9 @@ variable zblz equal 73 # Specify hybrid with SNAP, ZBL -pair_style hybrid/overlay snap zbl ${zblcutinner} ${zblcutouter} -pair_style hybrid/overlay snap zbl 4 ${zblcutouter} -pair_style hybrid/overlay snap zbl 4 4.8 - +pair_style hybrid/overlay zbl ${zblcutinner} ${zblcutouter} snap +pair_style hybrid/overlay zbl 4 ${zblcutouter} snap +pair_style hybrid/overlay zbl 4 4.8 snap pair_coeff 1 1 zbl ${zblz} ${zblz} pair_coeff 1 1 zbl 73 ${zblz} pair_coeff 1 1 zbl 73 73 @@ -61,10 +63,11 @@ SNAP Element = Ta, Radius 0.5, Weight 1 Reading potential file Ta06A.snapparam with DATE: 2014-09-05 SNAP keyword rcutfac 4.67637 SNAP keyword twojmax 6 -SNAP keyword gamma 1 SNAP keyword rfac0 0.99363 SNAP keyword rmin0 0 SNAP keyword diagonalstyle 3 +SNAP keyword bzeroflag 0 +SNAP keyword quadraticflag 0 # Setup output @@ -85,13 +88,23 @@ fix 1 all nve run ${nsteps} run 100 Neighbor list info ... - 2 neighbor list requests update every 1 steps, delay 0 steps, check yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 5.8 ghost atom cutoff = 5.8 - binsize = 2.9 -> bins = 5 5 5 -Memory usage per processor = 2.92823 Mbytes + binsize = 2.9, bins = 5 5 5 + 2 neighbor lists, perpetual/occasional/extra = 2 0 0 + (1) pair zbl, perpetual, half/full from (2) + attributes: half, newton on + pair build: halffull/newton + stencil: none + bin: none + (2) pair snap, perpetual + attributes: full, newton on + pair build: full/bin/atomonly + stencil: full/bin/3d + bin: standard +Per MPI rank memory allocation (min/avg/max) = 4.138 | 4.138 | 4.138 Mbytes Step Temp E_pair E_mol TotEng Press 0 300 -11.85157 0 -11.813095 2717.1661 10 295.96579 -11.851053 0 -11.813095 2696.1559 @@ -104,20 +117,20 @@ Step Temp E_pair E_mol TotEng Press 80 124.04276 -11.829003 0 -11.813094 1537.703 90 97.37622 -11.825582 0 -11.813094 1734.9662 100 75.007873 -11.822714 0 -11.813094 1930.8005 -Loop time of 3.43062 on 1 procs for 100 steps with 128 atoms +Loop time of 2.53266 on 1 procs for 100 steps with 128 atoms -Performance: 1.259 ns/day, 19.059 hours/ns, 29.149 timesteps/s -99.9% CPU use with 1 MPI tasks x no OpenMP threads +Performance: 1.706 ns/day, 14.070 hours/ns, 39.484 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 | 3.4295 | 3.4295 | 3.4295 | 0.0 | 99.97 +Pair | 2.5313 | 2.5313 | 2.5313 | 0.0 | 99.95 Neigh | 0 | 0 | 0 | 0.0 | 0.00 -Comm | 0.00043988 | 0.00043988 | 0.00043988 | 0.0 | 0.01 -Output | 0.00010014 | 0.00010014 | 0.00010014 | 0.0 | 0.00 -Modify | 0.00024533 | 0.00024533 | 0.00024533 | 0.0 | 0.01 -Other | | 0.0002978 | | | 0.01 +Comm | 0.00051379 | 0.00051379 | 0.00051379 | 0.0 | 0.02 +Output | 0.00023317 | 0.00023317 | 0.00023317 | 0.0 | 0.01 +Modify | 0.00023675 | 0.00023675 | 0.00023675 | 0.0 | 0.01 +Other | | 0.0003583 | | | 0.01 Nlocal: 128 ave 128 max 128 min Histogram: 1 0 0 0 0 0 0 0 0 0 @@ -133,4 +146,4 @@ Ave neighs/atom = 58 Neighbor list builds = 0 Dangerous builds = 0 -Total wall time: 0:00:03 +Total wall time: 0:00:02 diff --git a/examples/snap/log.5Oct16.snap.Ta06A.g++.4 b/examples/snap/log.20Apr18.snap.Ta06A.g++.4 similarity index 71% rename from examples/snap/log.5Oct16.snap.Ta06A.g++.4 rename to examples/snap/log.20Apr18.snap.Ta06A.g++.4 index 19d64c557c33538c702da0ddfb4fa1b30c336f8e..4d26481d5de2ccb00bbc364d70af786f458ec2e2 100644 --- a/examples/snap/log.5Oct16.snap.Ta06A.g++.4 +++ b/examples/snap/log.20Apr18.snap.Ta06A.g++.4 @@ -1,4 +1,6 @@ -LAMMPS (5 Oct 2016) +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 # Demonstrate SNAP Ta potential # Initialize simulation @@ -31,12 +33,13 @@ Created orthogonal box = (0 0 0) to (13.264 13.264 13.264) 1 by 2 by 2 MPI processor grid create_atoms 1 box Created 128 atoms + Time spent = 0.000288486 secs mass 1 180.88 # choose potential -include Ta06A_pot.snap +include Ta06A.snap # DATE: 2014-09-05 CONTRIBUTOR: Aidan Thompson athomps@sandia.gov CITATION: Thompson, Swiler, Trott, Foiles and Tucker, arxiv.org, 1409.3880 (2014) # Definition of SNAP potential Ta_Cand06A @@ -48,10 +51,9 @@ variable zblz equal 73 # Specify hybrid with SNAP, ZBL -pair_style hybrid/overlay snap zbl ${zblcutinner} ${zblcutouter} -pair_style hybrid/overlay snap zbl 4 ${zblcutouter} -pair_style hybrid/overlay snap zbl 4 4.8 - +pair_style hybrid/overlay zbl ${zblcutinner} ${zblcutouter} snap +pair_style hybrid/overlay zbl 4 ${zblcutouter} snap +pair_style hybrid/overlay zbl 4 4.8 snap pair_coeff 1 1 zbl ${zblz} ${zblz} pair_coeff 1 1 zbl 73 ${zblz} pair_coeff 1 1 zbl 73 73 @@ -61,10 +63,11 @@ SNAP Element = Ta, Radius 0.5, Weight 1 Reading potential file Ta06A.snapparam with DATE: 2014-09-05 SNAP keyword rcutfac 4.67637 SNAP keyword twojmax 6 -SNAP keyword gamma 1 SNAP keyword rfac0 0.99363 SNAP keyword rmin0 0 SNAP keyword diagonalstyle 3 +SNAP keyword bzeroflag 0 +SNAP keyword quadraticflag 0 # Setup output @@ -85,13 +88,23 @@ fix 1 all nve run ${nsteps} run 100 Neighbor list info ... - 2 neighbor list requests update every 1 steps, delay 0 steps, check yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 5.8 ghost atom cutoff = 5.8 - binsize = 2.9 -> bins = 5 5 5 -Memory usage per processor = 2.91109 Mbytes + binsize = 2.9, bins = 5 5 5 + 2 neighbor lists, perpetual/occasional/extra = 2 0 0 + (1) pair zbl, perpetual, half/full from (2) + attributes: half, newton on + pair build: halffull/newton + stencil: none + bin: none + (2) pair snap, perpetual + attributes: full, newton on + pair build: full/bin/atomonly + stencil: full/bin/3d + bin: standard +Per MPI rank memory allocation (min/avg/max) = 4.118 | 4.118 | 4.118 Mbytes Step Temp E_pair E_mol TotEng Press 0 300 -11.85157 0 -11.813095 2717.1661 10 295.8664 -11.85104 0 -11.813095 2702.935 @@ -104,20 +117,20 @@ Step Temp E_pair E_mol TotEng Press 80 121.80051 -11.828715 0 -11.813094 1627.6911 90 95.262635 -11.825311 0 -11.813094 1812.9327 100 73.194645 -11.822481 0 -11.813094 1995.2199 -Loop time of 0.89193 on 4 procs for 100 steps with 128 atoms +Loop time of 1.3621 on 4 procs for 100 steps with 128 atoms -Performance: 4.843 ns/day, 4.955 hours/ns, 112.116 timesteps/s -99.9% CPU use with 4 MPI tasks x no OpenMP threads +Performance: 3.172 ns/day, 7.567 hours/ns, 73.416 timesteps/s +98.7% CPU use with 4 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- -Pair | 0.84444 | 0.86772 | 0.88108 | 1.6 | 97.29 +Pair | 1.2867 | 1.309 | 1.35 | 2.1 | 96.10 Neigh | 0 | 0 | 0 | 0.0 | 0.00 -Comm | 0.009577 | 0.023049 | 0.046417 | 9.8 | 2.58 -Output | 0.00024009 | 0.00026137 | 0.00027895 | 0.1 | 0.03 -Modify | 8.2493e-05 | 9.352e-05 | 0.00010061 | 0.1 | 0.01 -Other | | 0.0008071 | | | 0.09 +Comm | 0.0096083 | 0.050652 | 0.072999 | 10.9 | 3.72 +Output | 0.00031447 | 0.00060236 | 0.0014303 | 0.0 | 0.04 +Modify | 0.00014234 | 0.00016212 | 0.00018811 | 0.0 | 0.01 +Other | | 0.001728 | | | 0.13 Nlocal: 32 ave 32 max 32 min Histogram: 4 0 0 0 0 0 0 0 0 0 @@ -133,4 +146,4 @@ Ave neighs/atom = 58 Neighbor list builds = 0 Dangerous builds = 0 -Total wall time: 0:00:00 +Total wall time: 0:00:01 diff --git a/examples/snap/log.21Feb17.snap.W.2940.g++.1 b/examples/snap/log.20Apr18.snap.W.2940.g++.1 similarity index 79% rename from examples/snap/log.21Feb17.snap.W.2940.g++.1 rename to examples/snap/log.20Apr18.snap.W.2940.g++.1 index 8c74380b8b7246dad9bf1079f17ad1ef8e56f7b8..19b2bfb40d88b1fd6dd62ab892dba1f463a48b03 100644 --- a/examples/snap/log.21Feb17.snap.W.2940.g++.1 +++ b/examples/snap/log.20Apr18.snap.W.2940.g++.1 @@ -1,4 +1,6 @@ -LAMMPS (13 Feb 2017) +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 # Demonstrate SNAP Ta potential # Initialize simulation @@ -31,20 +33,21 @@ Created orthogonal box = (0 0 0) to (12.7212 12.7212 12.7212) 1 by 1 by 1 MPI processor grid create_atoms 1 box Created 128 atoms + Time spent = 0.000190258 secs mass 1 183.84 # choose potential -include W_2940_2017_2.pot.snap -# DATE: 2017-02-20 CONTRIBUTOR: Mitchell Wood mitwood@sandia.gov CITATION: Wood, M. A. and Thompson, A. P. to appear in arxiv Feb2017 +include W_2940_2017_2.snap +# DATE: 2017-02-20 CONTRIBUTOR: Mitchell Wood mitwood@sandia.gov CITATION: Wood, M. A. and Thompson, A. P. "Quantum-Accurate Molecular Dynamics Potential for Tungsten" arXiv:1702.07042 [physics.comp-ph] # # Definition of SNAP+ZBL potential. variable zblcutinner equal 4 variable zblcutouter equal 4.8 variable zblz equal 74 -# Specify hybrid with SNAP, ZBL, and long-range Coulomb +# Specify hybrid with SNAP and ZBL pair_style hybrid/overlay zbl ${zblcutinner} ${zblcutouter} snap pair_style hybrid/overlay zbl 4 ${zblcutouter} snap @@ -58,10 +61,11 @@ SNAP Element = W, Radius 0.5, Weight 1 Reading potential file W_2940_2017_2.snapparam with DATE: 2017-02-20 SNAP keyword rcutfac 4.73442 SNAP keyword twojmax 8 -SNAP keyword gamma 1 SNAP keyword rfac0 0.99363 SNAP keyword rmin0 0 SNAP keyword diagonalstyle 3 +SNAP keyword bzeroflag 0 +SNAP keyword quadraticflag 0 #Nomenclature on the snap files are Element_DakotaID_Year_Month @@ -99,7 +103,7 @@ Neighbor list info ... pair build: full/bin/atomonly stencil: full/bin/3d bin: standard -Memory usage per processor = 5.14696 Mbytes +Per MPI rank memory allocation (min/avg/max) = 5.15 | 5.15 | 5.15 Mbytes Step Temp E_pair E_mol TotEng Press 0 300 -11.028325 0 -10.98985 3010.497 10 293.40666 -11.027479 0 -10.989849 3246.0559 @@ -112,20 +116,20 @@ Step Temp E_pair E_mol TotEng Press 80 58.605244 -10.997364 0 -10.989848 11289.914 90 39.754503 -10.994946 0 -10.989848 11824.945 100 32.524085 -10.994019 0 -10.989848 11932.118 -Loop time of 11.8271 on 1 procs for 100 steps with 128 atoms +Loop time of 9.69738 on 1 procs for 100 steps with 128 atoms -Performance: 0.365 ns/day, 65.706 hours/ns, 8.455 timesteps/s -99.9% CPU use with 1 MPI tasks x no OpenMP threads +Performance: 0.445 ns/day, 53.874 hours/ns, 10.312 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 | 11.826 | 11.826 | 11.826 | 0.0 | 99.99 +Pair | 9.6961 | 9.6961 | 9.6961 | 0.0 | 99.99 Neigh | 0 | 0 | 0 | 0.0 | 0.00 -Comm | 0.00044084 | 0.00044084 | 0.00044084 | 0.0 | 0.00 -Output | 0.00013232 | 0.00013232 | 0.00013232 | 0.0 | 0.00 -Modify | 0.00021887 | 0.00021887 | 0.00021887 | 0.0 | 0.00 -Other | | 0.0002718 | | | 0.00 +Comm | 0.00044036 | 0.00044036 | 0.00044036 | 0.0 | 0.00 +Output | 0.00024843 | 0.00024843 | 0.00024843 | 0.0 | 0.00 +Modify | 0.00023937 | 0.00023937 | 0.00023937 | 0.0 | 0.00 +Other | | 0.0003347 | | | 0.00 Nlocal: 128 ave 128 max 128 min Histogram: 1 0 0 0 0 0 0 0 0 0 @@ -141,4 +145,4 @@ Ave neighs/atom = 58 Neighbor list builds = 0 Dangerous builds = 0 -Total wall time: 0:00:11 +Total wall time: 0:00:09 diff --git a/examples/snap/log.21Feb17.snap.W.2940.g++.4 b/examples/snap/log.20Apr18.snap.W.2940.g++.4 similarity index 79% rename from examples/snap/log.21Feb17.snap.W.2940.g++.4 rename to examples/snap/log.20Apr18.snap.W.2940.g++.4 index 97ed5cc8d12728a0e1d9fb2bc79729188ad7c569..dfa63fc6ea208d4552b8533a1a32fd73bc88d4fe 100644 --- a/examples/snap/log.21Feb17.snap.W.2940.g++.4 +++ b/examples/snap/log.20Apr18.snap.W.2940.g++.4 @@ -1,4 +1,6 @@ -LAMMPS (13 Feb 2017) +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 # Demonstrate SNAP Ta potential # Initialize simulation @@ -31,20 +33,21 @@ Created orthogonal box = (0 0 0) to (12.7212 12.7212 12.7212) 1 by 2 by 2 MPI processor grid create_atoms 1 box Created 128 atoms + Time spent = 0.000309944 secs mass 1 183.84 # choose potential -include W_2940_2017_2.pot.snap -# DATE: 2017-02-20 CONTRIBUTOR: Mitchell Wood mitwood@sandia.gov CITATION: Wood, M. A. and Thompson, A. P. to appear in arxiv Feb2017 +include W_2940_2017_2.snap +# DATE: 2017-02-20 CONTRIBUTOR: Mitchell Wood mitwood@sandia.gov CITATION: Wood, M. A. and Thompson, A. P. "Quantum-Accurate Molecular Dynamics Potential for Tungsten" arXiv:1702.07042 [physics.comp-ph] # # Definition of SNAP+ZBL potential. variable zblcutinner equal 4 variable zblcutouter equal 4.8 variable zblz equal 74 -# Specify hybrid with SNAP, ZBL, and long-range Coulomb +# Specify hybrid with SNAP and ZBL pair_style hybrid/overlay zbl ${zblcutinner} ${zblcutouter} snap pair_style hybrid/overlay zbl 4 ${zblcutouter} snap @@ -58,10 +61,11 @@ SNAP Element = W, Radius 0.5, Weight 1 Reading potential file W_2940_2017_2.snapparam with DATE: 2017-02-20 SNAP keyword rcutfac 4.73442 SNAP keyword twojmax 8 -SNAP keyword gamma 1 SNAP keyword rfac0 0.99363 SNAP keyword rmin0 0 SNAP keyword diagonalstyle 3 +SNAP keyword bzeroflag 0 +SNAP keyword quadraticflag 0 #Nomenclature on the snap files are Element_DakotaID_Year_Month @@ -99,7 +103,7 @@ Neighbor list info ... pair build: full/bin/atomonly stencil: full/bin/3d bin: standard -Memory usage per processor = 5.12833 Mbytes +Per MPI rank memory allocation (min/avg/max) = 5.13 | 5.13 | 5.13 Mbytes Step Temp E_pair E_mol TotEng Press 0 300 -11.028325 0 -10.98985 3010.497 10 293.22504 -11.027456 0 -10.989849 3258.275 @@ -112,20 +116,20 @@ Step Temp E_pair E_mol TotEng Press 80 56.127265 -10.997046 0 -10.989848 11551.687 90 38.025013 -10.994724 0 -10.989847 12069.936 100 31.768127 -10.993922 0 -10.989847 12145.648 -Loop time of 3.03545 on 4 procs for 100 steps with 128 atoms +Loop time of 5.15615 on 4 procs for 100 steps with 128 atoms -Performance: 1.423 ns/day, 16.864 hours/ns, 32.944 timesteps/s -99.9% CPU use with 4 MPI tasks x no OpenMP threads +Performance: 0.838 ns/day, 28.645 hours/ns, 19.394 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 | 2.9594 | 2.9866 | 3.0319 | 1.6 | 98.39 +Pair | 5.0497 | 5.0762 | 5.092 | 0.8 | 98.45 Neigh | 0 | 0 | 0 | 0.0 | 0.00 -Comm | 0.0024238 | 0.047825 | 0.075032 | 12.5 | 1.58 -Output | 0.00021601 | 0.00024045 | 0.00027442 | 0.0 | 0.01 -Modify | 9.6798e-05 | 0.00011188 | 0.00011802 | 0.0 | 0.00 -Other | | 0.000698 | | | 0.02 +Comm | 0.060802 | 0.07661 | 0.10305 | 6.1 | 1.49 +Output | 0.00040722 | 0.00078458 | 0.0018959 | 0.0 | 0.02 +Modify | 0.0002389 | 0.00024962 | 0.00027442 | 0.0 | 0.00 +Other | | 0.002315 | | | 0.04 Nlocal: 32 ave 32 max 32 min Histogram: 4 0 0 0 0 0 0 0 0 0 @@ -141,4 +145,4 @@ Ave neighs/atom = 58 Neighbor list builds = 0 Dangerous builds = 0 -Total wall time: 0:00:03 +Total wall time: 0:00:05 diff --git a/examples/snap/log.21Feb17.snap.hybrid.WSNAP.HePair.g++.1 b/examples/snap/log.20Apr18.snap.hybrid.WSNAP.HePair.g++.1 similarity index 83% rename from examples/snap/log.21Feb17.snap.hybrid.WSNAP.HePair.g++.1 rename to examples/snap/log.20Apr18.snap.hybrid.WSNAP.HePair.g++.1 index 846eef269ce580ca63d730be0fb1ced38da1bf58..3f40936308b21d4e3d0ed1e8e83145c5cfd9d0f7 100644 --- a/examples/snap/log.21Feb17.snap.hybrid.WSNAP.HePair.g++.1 +++ b/examples/snap/log.20Apr18.snap.hybrid.WSNAP.HePair.g++.1 @@ -1,4 +1,6 @@ -LAMMPS (13 Feb 2017) +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 # Demonstrate SNAP Ta potential # Initialize simulation @@ -31,6 +33,7 @@ Created orthogonal box = (0 0 0) to (12.7212 12.7212 12.7212) 1 by 1 by 1 MPI processor grid create_atoms 1 box Created 128 atoms + Time spent = 0.000431538 secs mass 1 183.84 mass 2 4.0026 @@ -42,15 +45,15 @@ group helium type 2 5 atoms in group helium # choose potential -include W.SNAP_HePair.pot -# DATE: 2017-02-20 CONTRIBUTOR: Mitchell Wood mitwood@sandia.gov CITATION: Wood, M. A. and Thompson, A. P. to appear in arxiv Feb2017, W-He and He-He from Juslin, N. and Wirth, B. D. Journal of Nuclear Materials, 423, (2013) p61-63 +include W_2940_2017_2_He_JW2013.snap +# DATE: 2017-02-20 CONTRIBUTOR: Mitchell Wood mitwood@sandia.gov CITATION: Wood, M. A. and Thompson, A. P. "Quantum-Accurate Molecular Dynamics Potential for Tungsten" arXiv:1702.07042 [physics.comp-ph] # # Definition of SNAP+ZBL+Tabulated potential. variable zblcutinner equal 4 variable zblcutouter equal 4.8 variable zblz equal 74 -# Specify hybrid with SNAP, ZBL, and long-range Coulomb +# Specify hybrid with SNAP and ZBL pair_style hybrid/overlay zbl ${zblcutinner} ${zblcutouter} snap table spline 10000 table spline 10000 pair_style hybrid/overlay zbl 4 ${zblcutouter} snap table spline 10000 table spline 10000 @@ -64,18 +67,19 @@ SNAP Element = W, Radius 0.5, Weight 1 Reading potential file W_2940_2017_2.snapparam with DATE: 2017-02-20 SNAP keyword rcutfac 4.73442 SNAP keyword twojmax 8 -SNAP keyword gamma 1 SNAP keyword rfac0 0.99363 SNAP keyword rmin0 0 SNAP keyword diagonalstyle 3 +SNAP keyword bzeroflag 0 +SNAP keyword quadraticflag 0 pair_coeff 2 2 table 1 He_He_JW2013.table HeHe Reading potential file He_He_JW2013.table with DATE: 2017-02-20 WARNING: 1 of 4999 force values in table are inconsistent with -dE/dr. - Should only be flagged at inflection points (../pair_table.cpp:476) + Should only be flagged at inflection points (../pair_table.cpp:481) pair_coeff 1 2 table 2 W_He_JW2013.table WHe Reading potential file W_He_JW2013.table with DATE: 2017-02-20 WARNING: 3 of 325 force values in table are inconsistent with -dE/dr. - Should only be flagged at inflection points (../pair_table.cpp:476) + Should only be flagged at inflection points (../pair_table.cpp:481) #Hybrid/overlay will take all pair styles and add their contributions equally, order of pair_coeff doesnt matter here #This is not the case for pair_style hybrid ... where only one pair_coeff is read for each type combination, order matters here. @@ -134,7 +138,7 @@ Neighbor list info ... pair build: full/bin/atomonly stencil: full/bin/3d bin: standard -Memory usage per processor = 7.6729 Mbytes +Per MPI rank memory allocation (min/avg/max) = 7.676 | 7.676 | 7.676 Mbytes Step Temp E_pair E_mol TotEng Press 0 300 -10.438105 0 -10.39963 -5445.2808 10 290.48923 -10.436885 0 -10.399629 -5646.4813 @@ -147,20 +151,20 @@ Step Temp E_pair E_mol TotEng Press 80 85.903126 -10.410645 0 -10.399628 857.74986 90 65.223651 -10.407993 0 -10.399628 1494.2746 100 59.833542 -10.407302 0 -10.399628 1938.9164 -Loop time of 11.0736 on 1 procs for 100 steps with 128 atoms +Loop time of 8.902 on 1 procs for 100 steps with 128 atoms -Performance: 0.390 ns/day, 61.520 hours/ns, 9.030 timesteps/s -99.9% CPU use with 1 MPI tasks x no OpenMP threads +Performance: 0.485 ns/day, 49.456 hours/ns, 11.233 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 | 11.072 | 11.072 | 11.072 | 0.0 | 99.99 -Neigh | 0.00041604 | 0.00041604 | 0.00041604 | 0.0 | 0.00 -Comm | 0.00046253 | 0.00046253 | 0.00046253 | 0.0 | 0.00 -Output | 0.0001657 | 0.0001657 | 0.0001657 | 0.0 | 0.00 -Modify | 0.0002265 | 0.0002265 | 0.0002265 | 0.0 | 0.00 -Other | | 0.0003119 | | | 0.00 +Pair | 8.9002 | 8.9002 | 8.9002 | 0.0 | 99.98 +Neigh | 0.00043058 | 0.00043058 | 0.00043058 | 0.0 | 0.00 +Comm | 0.00045776 | 0.00045776 | 0.00045776 | 0.0 | 0.01 +Output | 0.00025344 | 0.00025344 | 0.00025344 | 0.0 | 0.00 +Modify | 0.00022483 | 0.00022483 | 0.00022483 | 0.0 | 0.00 +Other | | 0.0003953 | | | 0.00 Nlocal: 128 ave 128 max 128 min Histogram: 1 0 0 0 0 0 0 0 0 0 @@ -176,4 +180,4 @@ Ave neighs/atom = 53.5156 Neighbor list builds = 1 Dangerous builds = 0 -Total wall time: 0:00:11 +Total wall time: 0:00:09 diff --git a/examples/snap/log.21Feb17.snap.hybrid.WSNAP.HePair.g++.4 b/examples/snap/log.20Apr18.snap.hybrid.WSNAP.HePair.g++.4 similarity index 84% rename from examples/snap/log.21Feb17.snap.hybrid.WSNAP.HePair.g++.4 rename to examples/snap/log.20Apr18.snap.hybrid.WSNAP.HePair.g++.4 index 9bcbd288aa664cf29025090e8c0937e2580d905a..4ec85a63d014085449367848dbfd2c6f787a41e4 100644 --- a/examples/snap/log.21Feb17.snap.hybrid.WSNAP.HePair.g++.4 +++ b/examples/snap/log.20Apr18.snap.hybrid.WSNAP.HePair.g++.4 @@ -1,4 +1,6 @@ -LAMMPS (13 Feb 2017) +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 # Demonstrate SNAP Ta potential # Initialize simulation @@ -31,6 +33,7 @@ Created orthogonal box = (0 0 0) to (12.7212 12.7212 12.7212) 1 by 2 by 2 MPI processor grid create_atoms 1 box Created 128 atoms + Time spent = 0.000274658 secs mass 1 183.84 mass 2 4.0026 @@ -42,15 +45,15 @@ group helium type 2 5 atoms in group helium # choose potential -include W.SNAP_HePair.pot -# DATE: 2017-02-20 CONTRIBUTOR: Mitchell Wood mitwood@sandia.gov CITATION: Wood, M. A. and Thompson, A. P. to appear in arxiv Feb2017, W-He and He-He from Juslin, N. and Wirth, B. D. Journal of Nuclear Materials, 423, (2013) p61-63 +include W_2940_2017_2_He_JW2013.snap +# DATE: 2017-02-20 CONTRIBUTOR: Mitchell Wood mitwood@sandia.gov CITATION: Wood, M. A. and Thompson, A. P. "Quantum-Accurate Molecular Dynamics Potential for Tungsten" arXiv:1702.07042 [physics.comp-ph] # # Definition of SNAP+ZBL+Tabulated potential. variable zblcutinner equal 4 variable zblcutouter equal 4.8 variable zblz equal 74 -# Specify hybrid with SNAP, ZBL, and long-range Coulomb +# Specify hybrid with SNAP and ZBL pair_style hybrid/overlay zbl ${zblcutinner} ${zblcutouter} snap table spline 10000 table spline 10000 pair_style hybrid/overlay zbl 4 ${zblcutouter} snap table spline 10000 table spline 10000 @@ -64,18 +67,19 @@ SNAP Element = W, Radius 0.5, Weight 1 Reading potential file W_2940_2017_2.snapparam with DATE: 2017-02-20 SNAP keyword rcutfac 4.73442 SNAP keyword twojmax 8 -SNAP keyword gamma 1 SNAP keyword rfac0 0.99363 SNAP keyword rmin0 0 SNAP keyword diagonalstyle 3 +SNAP keyword bzeroflag 0 +SNAP keyword quadraticflag 0 pair_coeff 2 2 table 1 He_He_JW2013.table HeHe Reading potential file He_He_JW2013.table with DATE: 2017-02-20 WARNING: 1 of 4999 force values in table are inconsistent with -dE/dr. - Should only be flagged at inflection points (../pair_table.cpp:476) + Should only be flagged at inflection points (../pair_table.cpp:481) pair_coeff 1 2 table 2 W_He_JW2013.table WHe Reading potential file W_He_JW2013.table with DATE: 2017-02-20 WARNING: 3 of 325 force values in table are inconsistent with -dE/dr. - Should only be flagged at inflection points (../pair_table.cpp:476) + Should only be flagged at inflection points (../pair_table.cpp:481) #Hybrid/overlay will take all pair styles and add their contributions equally, order of pair_coeff doesnt matter here #This is not the case for pair_style hybrid ... where only one pair_coeff is read for each type combination, order matters here. @@ -134,7 +138,7 @@ Neighbor list info ... pair build: full/bin/atomonly stencil: full/bin/3d bin: standard -Memory usage per processor = 7.65426 Mbytes +Per MPI rank memory allocation (min/avg/max) = 7.656 | 7.656 | 7.656 Mbytes Step Temp E_pair E_mol TotEng Press 0 300 -10.438105 0 -10.39963 -5445.2808 10 292.13979 -10.437097 0 -10.39963 -5516.3963 @@ -147,20 +151,20 @@ Step Temp E_pair E_mol TotEng Press 80 79.985938 -10.409886 0 -10.399628 2392.1106 90 62.568933 -10.407652 0 -10.399628 3141.7027 100 56.697933 -10.406899 0 -10.399628 3583.9538 -Loop time of 2.8757 on 4 procs for 100 steps with 128 atoms +Loop time of 4.82103 on 4 procs for 100 steps with 128 atoms -Performance: 1.502 ns/day, 15.976 hours/ns, 34.774 timesteps/s -99.9% CPU use with 4 MPI tasks x no OpenMP threads +Performance: 0.896 ns/day, 26.783 hours/ns, 20.742 timesteps/s +99.0% CPU use with 4 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- -Pair | 2.7363 | 2.8122 | 2.8636 | 2.9 | 97.79 +Pair | 4.4837 | 4.6734 | 4.7605 | 5.2 | 96.94 Neigh | 0 | 0 | 0 | 0.0 | 0.00 -Comm | 0.011014 | 0.062439 | 0.13842 | 19.3 | 2.17 -Output | 0.00023842 | 0.00025076 | 0.0002861 | 0.0 | 0.01 -Modify | 9.2506e-05 | 9.9301e-05 | 0.00010395 | 0.0 | 0.00 -Other | | 0.0006654 | | | 0.02 +Comm | 0.057389 | 0.14453 | 0.33421 | 29.4 | 3.00 +Output | 0.00038719 | 0.00073916 | 0.0017841 | 0.0 | 0.02 +Modify | 0.00018716 | 0.00022203 | 0.00026417 | 0.0 | 0.00 +Other | | 0.002119 | | | 0.04 Nlocal: 32 ave 32 max 32 min Histogram: 4 0 0 0 0 0 0 0 0 0 @@ -176,4 +180,4 @@ Ave neighs/atom = 53.5156 Neighbor list builds = 0 Dangerous builds = 0 -Total wall time: 0:00:02 +Total wall time: 0:00:04 diff --git a/lib/colvars/Makefile.deps b/lib/colvars/Makefile.deps index 9a7de0647db57eeb3d62ee866e71f6e363b6c802..a0d8515bc104f985584d18726c79914c67227cdf 100644 --- a/lib/colvars/Makefile.deps +++ b/lib/colvars/Makefile.deps @@ -1,9 +1,9 @@ $(COLVARS_OBJ_DIR)colvaratoms.o: colvaratoms.cpp colvarmodule.h \ - colvars_version.h colvarproxy.h colvarvalue.h colvartypes.h \ + colvars_version.h colvarproxy.h colvartypes.h colvarvalue.h \ colvarparse.h colvaratoms.h colvardeps.h $(COLVARS_OBJ_DIR)colvarbias_abf.o: colvarbias_abf.cpp colvarmodule.h \ - colvars_version.h colvarproxy.h colvarvalue.h colvartypes.h colvar.h \ + colvars_version.h colvarproxy.h colvartypes.h colvarvalue.h colvar.h \ colvarparse.h colvardeps.h lepton/include/Lepton.h \ lepton/include/lepton/CompiledExpression.h \ lepton/include/lepton/ExpressionTreeNode.h \ @@ -29,7 +29,7 @@ $(COLVARS_OBJ_DIR)colvarbias_alb.o: colvarbias_alb.cpp colvarmodule.h \ lepton/include/lepton/ParsedExpression.h lepton/include/lepton/Parser.h \ colvarbias_alb.h $(COLVARS_OBJ_DIR)colvarbias.o: colvarbias.cpp colvarmodule.h \ - colvars_version.h colvarproxy.h colvarvalue.h colvartypes.h colvarbias.h \ + colvars_version.h colvarproxy.h colvartypes.h colvarvalue.h colvarbias.h \ colvar.h colvarparse.h colvardeps.h lepton/include/Lepton.h \ lepton/include/lepton/CompiledExpression.h \ lepton/include/lepton/ExpressionTreeNode.h \ @@ -42,8 +42,8 @@ $(COLVARS_OBJ_DIR)colvarbias.o: colvarbias.cpp colvarmodule.h \ lepton/include/lepton/ParsedExpression.h lepton/include/lepton/Parser.h \ colvargrid.h $(COLVARS_OBJ_DIR)colvarbias_histogram.o: colvarbias_histogram.cpp \ - colvarmodule.h colvars_version.h colvarproxy.h colvarvalue.h \ - colvartypes.h colvar.h colvarparse.h colvardeps.h \ + colvarmodule.h colvars_version.h colvarproxy.h colvartypes.h \ + colvarvalue.h colvar.h colvarparse.h colvardeps.h \ lepton/include/Lepton.h lepton/include/lepton/CompiledExpression.h \ lepton/include/lepton/ExpressionTreeNode.h \ lepton/include/lepton/windowsIncludes.h \ @@ -55,7 +55,7 @@ $(COLVARS_OBJ_DIR)colvarbias_histogram.o: colvarbias_histogram.cpp \ lepton/include/lepton/ParsedExpression.h lepton/include/lepton/Parser.h \ colvarbias_histogram.h colvarbias.h colvargrid.h $(COLVARS_OBJ_DIR)colvarbias_meta.o: colvarbias_meta.cpp colvarmodule.h \ - colvars_version.h colvarproxy.h colvarvalue.h colvartypes.h colvar.h \ + colvars_version.h colvarproxy.h colvartypes.h colvarvalue.h colvar.h \ colvarparse.h colvardeps.h lepton/include/Lepton.h \ lepton/include/lepton/CompiledExpression.h \ lepton/include/lepton/ExpressionTreeNode.h \ @@ -68,8 +68,8 @@ $(COLVARS_OBJ_DIR)colvarbias_meta.o: colvarbias_meta.cpp colvarmodule.h \ lepton/include/lepton/ParsedExpression.h lepton/include/lepton/Parser.h \ colvarbias_meta.h colvarbias.h colvargrid.h $(COLVARS_OBJ_DIR)colvarbias_restraint.o: colvarbias_restraint.cpp \ - colvarmodule.h colvars_version.h colvarproxy.h colvarvalue.h \ - colvartypes.h colvarbias_restraint.h colvarbias.h colvar.h colvarparse.h \ + colvarmodule.h colvars_version.h colvarproxy.h colvartypes.h \ + colvarvalue.h colvarbias_restraint.h colvarbias.h colvar.h colvarparse.h \ colvardeps.h lepton/include/Lepton.h \ lepton/include/lepton/CompiledExpression.h \ lepton/include/lepton/ExpressionTreeNode.h \ @@ -171,7 +171,7 @@ $(COLVARS_OBJ_DIR)colvar.o: colvar.cpp colvarmodule.h colvars_version.h \ lepton/include/lepton/ParsedExpression.h lepton/include/lepton/Parser.h \ colvarcomp.h colvaratoms.h colvarproxy.h colvarscript.h colvarbias.h $(COLVARS_OBJ_DIR)colvardeps.o: colvardeps.cpp colvarmodule.h \ - colvars_version.h colvarproxy.h colvarvalue.h colvartypes.h colvardeps.h \ + colvars_version.h colvarproxy.h colvartypes.h colvarvalue.h colvardeps.h \ colvarparse.h $(COLVARS_OBJ_DIR)colvargrid.o: colvargrid.cpp colvarmodule.h \ colvars_version.h colvarvalue.h colvartypes.h colvarparse.h colvar.h \ @@ -204,7 +204,7 @@ $(COLVARS_OBJ_DIR)colvarmodule.o: colvarmodule.cpp colvarmodule.h \ $(COLVARS_OBJ_DIR)colvarparse.o: colvarparse.cpp colvarmodule.h \ colvars_version.h colvarvalue.h colvartypes.h colvarparse.h $(COLVARS_OBJ_DIR)colvarproxy.o: colvarproxy.cpp colvarmodule.h \ - colvars_version.h colvarproxy.h colvarvalue.h colvartypes.h \ + colvars_version.h colvarproxy.h colvartypes.h colvarvalue.h \ colvarscript.h colvarbias.h colvar.h colvarparse.h colvardeps.h \ lepton/include/Lepton.h lepton/include/lepton/CompiledExpression.h \ lepton/include/lepton/ExpressionTreeNode.h \ diff --git a/lib/colvars/colvar.cpp b/lib/colvars/colvar.cpp index 5a4e8b617a9007fff02e87233b8f8dfebb1e7a25..c5b6d906c1ec063fac7ee5e48b39a41c4e841e96 100644 --- a/lib/colvars/colvar.cpp +++ b/lib/colvars/colvar.cpp @@ -7,6 +7,10 @@ // If you wish to distribute your changes, please submit them to the // Colvars repository at GitHub. +#include +#include +#include + #include "colvarmodule.h" #include "colvarvalue.h" #include "colvarparse.h" @@ -14,15 +18,6 @@ #include "colvarcomp.h" #include "colvarscript.h" -// used in build_atom_list() -#include - - -/// Compare two cvcs using their names -/// Used to sort CVC array in scripted coordinates -bool compare(colvar::cvc *i, colvar::cvc *j) { - return i->name < j->name; -} colvar::colvar() @@ -34,6 +29,15 @@ colvar::colvar() } +namespace { + /// Compare two cvcs using their names + /// Used to sort CVC array in scripted coordinates + bool compare(colvar::cvc *i, colvar::cvc *j) + { + return i->name < j->name; + } +} + int colvar::init(std::string const &conf) { cvm::log("Initializing a new collective variable.\n"); @@ -143,6 +147,9 @@ int colvar::init(std::string const &conf) x.type(cvc_value); x_reported.type(cvc_value); } + + set_enabled(f_cv_scalar, (value().type() == colvarvalue::type_scalar)); + // If using scripted biases, any colvar may receive bias forces // and will need its gradient if (cvm::scripted_forces()) { @@ -198,6 +205,7 @@ int colvar::init(std::string const &conf) if (is_enabled(f_cv_homogeneous) && cvcs[0]->b_periodic) { // TODO make this a CVC feature bool b_periodic = true; period = cvcs[0]->period; + wrap_center = cvcs[0]->wrap_center; for (i = 1; i < cvcs.size(); i++) { if (!cvcs[i]->b_periodic || cvcs[i]->period != period) { b_periodic = false; @@ -211,6 +219,14 @@ int colvar::init(std::string const &conf) set_enabled(f_cv_periodic, b_periodic); } + // Allow scripted/custom functions to be defined as periodic + if ( (is_enabled(f_cv_scripted) || is_enabled(f_cv_custom_function)) && is_enabled(f_cv_scalar) ) { + if (get_keyval(conf, "period", period, 0.)) { + set_enabled(f_cv_periodic, true); + get_keyval(conf, "wrapAround", wrap_center, 0.); + } + } + // check that cvcs are compatible for (i = 0; i < cvcs.size(); i++) { @@ -443,8 +459,6 @@ int colvar::init_grid_parameters(std::string const &conf) upper_boundary.type(value()); upper_wall.type(value()); - set_enabled(f_cv_scalar, (value().type() == colvarvalue::type_scalar)); - if (is_enabled(f_cv_scalar)) { if (get_keyval(conf, "lowerBoundary", lower_boundary, lower_boundary)) { @@ -1503,7 +1517,7 @@ cvm::real colvar::update_forces_energy() vr += (0.5 * dt) * f_ext / ext_mass; xr += dt * vr; xr.apply_constraints(); - if (this->is_enabled(f_cv_periodic)) this->wrap(xr); + this->wrap(xr); } // Now adding the force on the actual colvar (for those biases that @@ -1714,9 +1728,18 @@ colvarvalue colvar::dist2_rgrad(colvarvalue const &x1, void colvar::wrap(colvarvalue &x) const { - if (is_enabled(f_cv_homogeneous)) { - (cvcs[0])->wrap(x); + if ( !is_enabled(f_cv_periodic) ) { + return; + } + + if ( is_enabled(f_cv_scripted) || is_enabled(f_cv_custom_function) ) { + // Scripted functions do their own wrapping, as cvcs might not be periodic + cvm::real shift = std::floor((x.real_value - wrap_center) / period + 0.5); + x.real_value -= shift * period; + } else { + cvcs[0]->wrap(x); } + return; } @@ -2244,7 +2267,7 @@ void colvar::calc_runave() runave.type(value().type()); runave.reset(); - // first-step operations + // first-step operationsf if (cvm::debug()) cvm::log("Colvar \""+this->name+ diff --git a/lib/colvars/colvar.h b/lib/colvars/colvar.h index 32c329460d06cfa5ceba43e245aa08a0d0810100..271231fb2aa2c6c6404c2f19f752cb80edfc66bf 100644 --- a/lib/colvars/colvar.h +++ b/lib/colvars/colvar.h @@ -216,6 +216,7 @@ public: /// Period, if this variable is periodic cvm::real period; + cvm::real wrap_center; /// \brief Expand the boundaries of multiples of width, to keep the diff --git a/lib/colvars/colvaratoms.cpp b/lib/colvars/colvaratoms.cpp index 1be6f42e594f86adf16a5b4702a631a6bef9c1e7..c8dcfc076619f881a3a217d4e794d52a9838c44e 100644 --- a/lib/colvars/colvaratoms.cpp +++ b/lib/colvars/colvaratoms.cpp @@ -7,6 +7,10 @@ // If you wish to distribute your changes, please submit them to the // Colvars repository at GitHub. +#include +#include +#include + #include "colvarmodule.h" #include "colvarproxy.h" #include "colvarparse.h" @@ -436,7 +440,7 @@ int cvm::atom_group::parse(std::string const &group_conf) } bool b_print_atom_ids = false; - get_keyval(group_conf, "printAtomIDs", b_print_atom_ids, false, colvarparse::parse_silent); + get_keyval(group_conf, "printAtomIDs", b_print_atom_ids, false); // Calculate all required properties (such as total mass) setup(); @@ -715,13 +719,10 @@ int cvm::atom_group::parse_fitting_options(std::string const &group_conf) "if provided, must be non-zero.\n", INPUT_ERROR); return COLVARS_ERROR; } - } else { - // if not, rely on existing atom indices for the group - group_for_fit->create_sorted_ids(); - ref_pos.resize(group_for_fit->size()); } - cvm::load_coords(ref_pos_file.c_str(), ref_pos, group_for_fit->sorted_ids, + ref_pos.resize(group_for_fit->size()); + cvm::load_coords(ref_pos_file.c_str(), &ref_pos, group_for_fit, ref_pos_col, ref_pos_col_value); } @@ -789,33 +790,39 @@ void cvm::atom_group::do_feature_side_effects(int id) } -int cvm::atom_group::create_sorted_ids(void) +int cvm::atom_group::create_sorted_ids() { // Only do the work if the vector is not yet populated - if (sorted_ids.size()) + if (sorted_atoms_ids.size()) return COLVARS_OK; - std::list temp_id_list; - for (cvm::atom_iter ai = this->begin(); ai != this->end(); ai++) { - temp_id_list.push_back(ai->id); - } - temp_id_list.sort(); - temp_id_list.unique(); - if (temp_id_list.size() != this->size()) { - cvm::error("Error: duplicate atom IDs in atom group? (found " + - cvm::to_str(temp_id_list.size()) + - " unique atom IDs instead of" + - cvm::to_str(this->size()) + ").\n"); - return COLVARS_ERROR; + // Sort the internal IDs + std::list sorted_atoms_ids_list; + for (size_t i = 0; i < this->size(); i++) { + sorted_atoms_ids_list.push_back(atoms_ids[i]); } - sorted_ids = std::vector (temp_id_list.size()); - unsigned int id_i = 0; - std::list::iterator li; - for (li = temp_id_list.begin(); li != temp_id_list.end(); ++li) { - sorted_ids[id_i] = *li; - id_i++; + sorted_atoms_ids_list.sort(); + sorted_atoms_ids_list.unique(); + if (sorted_atoms_ids_list.size() != this->size()) { + return cvm::error("Error: duplicate atom IDs in atom group? (found " + + cvm::to_str(sorted_atoms_ids_list.size()) + + " unique atom IDs instead of " + + cvm::to_str(this->size()) + ").\n", BUG_ERROR); } - return (cvm::get_error() ? COLVARS_ERROR : COLVARS_OK); + + // Compute map between sorted and unsorted elements + sorted_atoms_ids.resize(this->size()); + sorted_atoms_ids_map.resize(this->size()); + std::list::iterator lsii = sorted_atoms_ids_list.begin(); + size_t ii = 0; + for ( ; ii < this->size(); lsii++, ii++) { + sorted_atoms_ids[ii] = *lsii; + size_t const pos = std::find(atoms_ids.begin(), atoms_ids.end(), *lsii) - + atoms_ids.begin(); + sorted_atoms_ids_map[ii] = pos; + } + + return COLVARS_OK; } diff --git a/lib/colvars/colvaratoms.h b/lib/colvars/colvaratoms.h index 0dda6ab792d8ae20afcf6a9aeaa615675f332d1b..93ae594aae893e303fff493487c6b49e7cf09ae8 100644 --- a/lib/colvars/colvaratoms.h +++ b/lib/colvars/colvaratoms.h @@ -227,9 +227,16 @@ protected: /// \brief Array of atom objects std::vector atoms; - /// \brief Array of atom identifiers for the MD program (0-based) + /// \brief Internal atom IDs for host code std::vector atoms_ids; + /// Sorted list of internal atom IDs (populated on-demand by + /// create_sorted_ids); used to read coordinate files + std::vector sorted_atoms_ids; + + /// Map entries of sorted_atoms_ids onto the original positions in the group + std::vector sorted_atoms_ids_map; + /// \brief Dummy atom position cvm::atom_pos dummy_atom_pos; @@ -273,19 +280,34 @@ public: return atoms.size(); } - std::string const print_atom_ids() const; - /// \brief If this option is on, this group merely acts as a wrapper /// for a fixed position; any calls to atoms within or to /// functions that return disaggregated data will fail bool b_dummy; - /// Sorted list of zero-based (internal) atom ids - /// (populated on-demand by create_sorted_ids) - std::vector sorted_ids; + /// Internal atom IDs (populated during initialization) + inline std::vector const &ids() const + { + return atoms_ids; + } + + std::string const print_atom_ids() const; + + /// Allocates and populates sorted_ids and sorted_ids_map + int create_sorted_ids(); - /// Allocates and populates the sorted list of atom ids - int create_sorted_ids(void); + /// Sorted internal atom IDs (populated on-demand by create_sorted_ids); + /// used to read coordinate files + inline std::vector const &sorted_ids() const + { + return sorted_atoms_ids; + } + + /// Map entries of sorted_atoms_ids onto the original positions in the group + inline std::vector const &sorted_ids_map() const + { + return sorted_atoms_ids_map; + } /// Detect whether two groups share atoms /// If yes, returns 1-based number of a common atom; else, returns 0 diff --git a/lib/colvars/colvarbias_abf.cpp b/lib/colvars/colvarbias_abf.cpp index b3b5b3eb1654df12992b2fafb206d82851d3788b..771955a4fa354222b300b2e3cefcfb71c81c2c12 100644 --- a/lib/colvars/colvarbias_abf.cpp +++ b/lib/colvars/colvarbias_abf.cpp @@ -17,17 +17,17 @@ colvarbias_abf::colvarbias_abf(char const *key) : colvarbias(key), b_UI_estimator(false), b_CZAR_estimator(false), + pabf_freq(0), system_force(NULL), gradients(NULL), - pmf(NULL), samples(NULL), + pmf(NULL), z_gradients(NULL), z_samples(NULL), czar_gradients(NULL), czar_pmf(NULL), last_gradients(NULL), - last_samples(NULL), - pabf_freq(0) + last_samples(NULL) { } @@ -315,8 +315,6 @@ colvarbias_abf::~colvarbias_abf() int colvarbias_abf::update() { - int iter; - if (cvm::debug()) cvm::log("Updating ABF bias " + this->name); size_t i; @@ -368,7 +366,12 @@ int colvarbias_abf::update() if ( b_integrate ) { if ( pabf_freq && cvm::step_relative() % pabf_freq == 0 ) { cvm::real err; - iter = pmf->integrate(integrate_steps, integrate_tol, err); + int iter = pmf->integrate(integrate_steps, integrate_tol, err); + if ( iter == integrate_steps ) { + cvm::log("Warning: PMF integration did not converge to " + cvm::to_str(integrate_tol) + + " in " + cvm::to_str(integrate_steps) + + " steps. Residual error: " + cvm::to_str(err)); + } pmf->set_zero_minimum(); // TODO: do this only when necessary } } @@ -485,7 +488,6 @@ int colvarbias_abf::update() int colvarbias_abf::replica_share() { - int p; if ( !cvm::replica_enabled() ) { cvm::error("Error: shared ABF: No replicas.\n"); @@ -507,6 +509,7 @@ int colvarbias_abf::replica_share() { char* msg_data = new char[msg_total]; if (cvm::replica_index() == 0) { + int p; // Replica 0 collects the delta gradient and count from the others. for (p = 1; p < cvm::replica_num(); p++) { // Receive the deltas. diff --git a/lib/colvars/colvarcomp.cpp b/lib/colvars/colvarcomp.cpp index 589de1d32af44a82d8b6beb78e8ee3d5f5ec8fc3..39b84b26d195dc59eae8bbced3ef40ef14f4cbb9 100644 --- a/lib/colvars/colvarcomp.cpp +++ b/lib/colvars/colvarcomp.cpp @@ -21,6 +21,9 @@ colvar::cvc::cvc() b_try_scalable(true) { init_cvc_requires(); + sup_coeff = 1.0; + period = 0.0; + wrap_center = 0.0; } @@ -30,43 +33,52 @@ colvar::cvc::cvc(std::string const &conf) b_periodic(false), b_try_scalable(true) { + init_cvc_requires(); + sup_coeff = 1.0; + period = 0.0; + wrap_center = 0.0; + init(conf); +} + + +int colvar::cvc::init(std::string const &conf) +{ + int error_code = COLVARS_OK; if (cvm::debug()) cvm::log("Initializing cvc base object.\n"); - init_cvc_requires(); - - if (get_keyval(conf, "name", this->name, std::string(""), parse_silent)) { + get_keyval(conf, "name", this->name, this->name); + if (name.size() > 0) { // Temporary description until child object is initialized description = "cvc " + name; } else { description = "uninitialized cvc"; } - get_keyval(conf, "componentCoeff", sup_coeff, 1.0); - get_keyval(conf, "componentExp", sup_np, 1); + get_keyval(conf, "componentCoeff", sup_coeff, sup_coeff); + get_keyval(conf, "componentExp", sup_np, sup_np); - get_keyval(conf, "period", period, 0.0); - get_keyval(conf, "wrapAround", wrap_center, 0.0); + get_keyval(conf, "period", period, period); + get_keyval(conf, "wrapAround", wrap_center, wrap_center); - get_keyval_feature((colvarparse *)this, conf, "debugGradients", + get_keyval_feature(dynamic_cast(this), conf, "debugGradients", f_cvc_debug_gradient, false, parse_silent); - { - bool b_no_PBC = false; - get_keyval(conf, "forceNoPBC", b_no_PBC, false); - if (b_no_PBC) { - disable(f_cvc_pbc_minimum_image); - } else { - enable(f_cvc_pbc_minimum_image); - } - // this does not use get_keyval_feature() only for backward compatibility + bool b_no_PBC = !is_enabled(f_cvc_pbc_minimum_image); // Enabled by default + get_keyval(conf, "forceNoPBC", b_no_PBC, b_no_PBC); + if (b_no_PBC) { + disable(f_cvc_pbc_minimum_image); + } else { + enable(f_cvc_pbc_minimum_image); } // Attempt scalable calculations when in parallel? (By default yes, if available) - get_keyval(conf, "scalable", b_try_scalable, true); + get_keyval(conf, "scalable", b_try_scalable, b_try_scalable); if (cvm::debug()) cvm::log("Done initializing cvc base object.\n"); + + return error_code; } diff --git a/lib/colvars/colvarcomp.h b/lib/colvars/colvarcomp.h index 52078a3a3059cb91315ac9f52e62b2f06e1e55f3..b5c3b16098c94f3fa94140b1259f016ef6581187 100644 --- a/lib/colvars/colvarcomp.h +++ b/lib/colvars/colvarcomp.h @@ -98,12 +98,14 @@ public: /// \brief Constructor /// - /// At least one constructor which reads a string should be defined - /// for every class inheriting from cvc \param conf Contents - /// of the configuration file pertaining to this \link cvc - /// \endlink + /// Calls the init() function of the class cvc(std::string const &conf); + /// An init function should be defined for every class inheriting from cvc + /// \param conf Contents of the configuration file pertaining to this \link + /// cvc \endlink + virtual int init(std::string const &conf); + /// \brief Within the constructor, make a group parse its own /// options from the provided configuration string /// Returns reference to new group @@ -231,7 +233,7 @@ public: virtual colvarvalue dist2_rgrad(colvarvalue const &x1, colvarvalue const &x2) const; - /// \brief Wrapp value (for periodic/symmetric cvcs) + /// \brief Wrap value (for periodic/symmetric cvcs) virtual void wrap(colvarvalue &x) const; /// \brief Pointers to all atom groups, to let colvars collect info diff --git a/lib/colvars/colvarcomp_distances.cpp b/lib/colvars/colvarcomp_distances.cpp index 9911f4c87edef9c17605403f21a0ffc1a45826e9..57b2a9a625fa01c49a8301b34b7e5f688096f8b4 100644 --- a/lib/colvars/colvarcomp_distances.cpp +++ b/lib/colvars/colvarcomp_distances.cpp @@ -148,7 +148,7 @@ void colvar::distance_vec::apply_force(colvarvalue const &force) cvm::real colvar::distance_vec::dist2(colvarvalue const &x1, colvarvalue const &x2) const { - return cvm::position_dist2(x1.rvector_value, x2.rvector_value); + return (cvm::position_distance(x1.rvector_value, x2.rvector_value)).norm2(); } @@ -192,7 +192,7 @@ colvar::distance_z::distance_z(std::string const &conf) // this group is optional ref2 = parse_group(conf, "ref2", true); - if (ref2 && ref2->size()) { + if ( ref2 ) { cvm::log("Using axis joining the centers of mass of groups \"ref\" and \"ref2\""); fixed_axis = false; if (key_lookup(conf, "axis")) @@ -306,7 +306,7 @@ void colvar::distance_z::apply_force(colvarvalue const &force) if (!ref1->noforce) ref1->apply_colvar_force(force.real_value); - if (ref2 && ref2->size() && !ref2->noforce) + if (ref2 && !ref2->noforce) ref2->apply_colvar_force(force.real_value); if (!main->noforce) @@ -464,7 +464,7 @@ void colvar::distance_xy::apply_force(colvarvalue const &force) if (!ref1->noforce) ref1->apply_colvar_force(force.real_value); - if (ref2 && ref2->size() && !ref2->noforce) + if (ref2 && !ref2->noforce) ref2->apply_colvar_force(force.real_value); if (!main->noforce) @@ -979,14 +979,12 @@ colvar::rmsd::rmsd(std::string const &conf) "if provided, must be non-zero.\n"); return; } - } else { - // if not, rely on existing atom indices for the group - atoms->create_sorted_ids(); - ref_pos.resize(atoms->size()); } - cvm::load_coords(ref_pos_file.c_str(), ref_pos, atoms->sorted_ids, - ref_pos_col, ref_pos_col_value); + ref_pos.resize(atoms->size()); + + cvm::load_coords(ref_pos_file.c_str(), &ref_pos, atoms, + ref_pos_col, ref_pos_col_value); } } @@ -1172,13 +1170,11 @@ colvar::eigenvector::eigenvector(std::string const &conf) "if provided, must be non-zero.\n"); return; } - } else { - // if not, use atom indices - atoms->create_sorted_ids(); } ref_pos.resize(atoms->size()); - cvm::load_coords(file_name.c_str(), ref_pos, atoms->sorted_ids, file_col, file_col_value); + cvm::load_coords(file_name.c_str(), &ref_pos, atoms, + file_col, file_col_value); } } @@ -1249,13 +1245,11 @@ colvar::eigenvector::eigenvector(std::string const &conf) cvm::error("Error: vectorColValue, if provided, must be non-zero.\n"); return; } - } else { - // if not, use atom indices - atoms->create_sorted_ids(); } eigenvec.resize(atoms->size()); - cvm::load_coords(file_name.c_str(), eigenvec, atoms->sorted_ids, file_col, file_col_value); + cvm::load_coords(file_name.c_str(), &eigenvec, atoms, + file_col, file_col_value); } } diff --git a/lib/colvars/colvarcomp_rotations.cpp b/lib/colvars/colvarcomp_rotations.cpp index 2650a9fe18efaaff66e6711d73be99a715d17ec1..498ef7c2f548f0cc6593725c52fb24d341c72822 100644 --- a/lib/colvars/colvarcomp_rotations.cpp +++ b/lib/colvars/colvarcomp_rotations.cpp @@ -50,12 +50,11 @@ colvar::orientation::orientation(std::string const &conf) "if provided, must be non-zero.\n"); return; } - } else { - // if not, use atom indices - atoms->create_sorted_ids(); } + ref_pos.resize(atoms->size()); - cvm::load_coords(file_name.c_str(), ref_pos, atoms->sorted_ids, file_col, file_col_value); + cvm::load_coords(file_name.c_str(), &ref_pos, atoms, + file_col, file_col_value); } } diff --git a/lib/colvars/colvardeps.cpp b/lib/colvars/colvardeps.cpp index a058ad55c2a4911324c9cd07b4ea7bb1e1afb147..80bd6670d3f13317bdf10da43a48cee5b482ec61 100644 --- a/lib/colvars/colvardeps.cpp +++ b/lib/colvars/colvardeps.cpp @@ -549,7 +549,7 @@ void colvardeps::init_cv_requires() { f_req_exclude(f_cv_custom_function, f_cv_scripted); init_feature(f_cv_periodic, "periodic", f_type_static); - f_req_self(f_cv_periodic, f_cv_homogeneous); + f_req_self(f_cv_periodic, f_cv_scalar); init_feature(f_cv_scalar, "scalar", f_type_static); init_feature(f_cv_linear, "linear", f_type_static); init_feature(f_cv_homogeneous, "homogeneous", f_type_static); diff --git a/lib/colvars/colvargrid.cpp b/lib/colvars/colvargrid.cpp index 1ac4aae133c3a225aa8d4a8bb2dbdd1c3ac381cb..407b336afd7b09e49a05c1550096bf318f4f06f3 100644 --- a/lib/colvars/colvargrid.cpp +++ b/lib/colvars/colvargrid.cpp @@ -329,7 +329,6 @@ void integrate_potential::update_div_local(const std::vector &ix0) const int linear_index = address(ix0); int i, j, k; std::vector ix = ix0; - const cvm::real * g; if (nd == 2) { // gradients at grid points surrounding the current scalar grid point @@ -783,7 +782,7 @@ void integrate_potential::atimes(const std::vector &A, std::vector &b, std::vector &x) { - for (size_t i=0; i &b, std::ve iter=0; atimes(x,r); - for (j=0;j &b, std::ve bkden = 1.0; while (iter < itmax) { ++iter; - for (bknum=0.0,j=0;jget_version_from_string(COLVARS_VERSION); } else { // TODO relax this error to handle multiple molecules in VMD // once the module is not static anymore @@ -58,22 +58,24 @@ colvarmodule::colvarmodule(colvarproxy *proxy_in) // "it_restart" will be set by the input state file, if any; // "it" should be updated by the proxy colvarmodule::it = colvarmodule::it_restart = 0; - colvarmodule::it_restart_from_state_file = true; - colvarmodule::use_scripted_forces = false; + use_scripted_forces = false; + scripting_after_biases = false; - colvarmodule::b_analysis = false; + b_analysis = false; colvarmodule::debug_gradients_step_size = 1.0e-07; colvarmodule::rotation::monitor_crossings = false; colvarmodule::rotation::crossing_threshold = 1.0e-02; - colvarmodule::cv_traj_freq = 100; - colvarmodule::restart_out_freq = proxy->restart_frequency(); + cv_traj_freq = 100; + restart_out_freq = proxy->restart_frequency(); // by default overwrite the existing trajectory file - colvarmodule::cv_traj_append = false; + cv_traj_append = false; + + cv_traj_write_labels = true; } @@ -189,26 +191,27 @@ int colvarmodule::parse_config(std::string &conf) { extra_conf.clear(); - // parse global options + // Parse global options if (catch_input_errors(parse_global_params(conf))) { return get_error(); } - // parse the options for collective variables + // Parse the options for collective variables if (catch_input_errors(parse_colvars(conf))) { return get_error(); } - // parse the options for biases + // Parse the options for biases if (catch_input_errors(parse_biases(conf))) { return get_error(); } - // done parsing known keywords, check that all keywords found were valid ones + // Done parsing known keywords, check that all keywords found were valid ones if (catch_input_errors(parse->check_keywords(conf, "colvarmodule"))) { return get_error(); } + // Parse auto-generated configuration (e.g. for back-compatibility) if (extra_conf.size()) { catch_input_errors(parse_global_params(extra_conf)); catch_input_errors(parse_colvars(extra_conf)); @@ -222,13 +225,11 @@ int colvarmodule::parse_config(std::string &conf) cvm::log("Collective variables module (re)initialized.\n"); cvm::log(cvm::line_marker); - // update any necessary proxy data + // Update any necessary proxy data proxy->setup(); - if (cv_traj_os != NULL) { - // configuration might have changed, better redo the labels - write_traj_label(*cv_traj_os); - } + // configuration might have changed, better redo the labels + cv_traj_write_labels = true; return get_error(); } @@ -279,15 +280,18 @@ int colvarmodule::parse_global_params(std::string const &conf) parse->get_keyval(conf, "colvarsTrajAppend", cv_traj_append, cv_traj_append, colvarparse::parse_silent); - parse->get_keyval(conf, "scriptedColvarForces", use_scripted_forces, false); + parse->get_keyval(conf, "scriptedColvarForces", + use_scripted_forces, use_scripted_forces); - parse->get_keyval(conf, "scriptingAfterBiases", scripting_after_biases, true); + parse->get_keyval(conf, "scriptingAfterBiases", + scripting_after_biases, scripting_after_biases); if (use_scripted_forces && !proxy->force_script_defined) { - cvm::error("User script for scripted colvar forces not found.", INPUT_ERROR); + return cvm::error("User script for scripted colvar forces not found.", + INPUT_ERROR); } - return (cvm::get_error() ? COLVARS_ERROR : COLVARS_OK); + return cvm::get_error(); } @@ -432,13 +436,13 @@ int colvarmodule::parse_biases(std::string const &conf) } -int colvarmodule::num_variables() const +size_t colvarmodule::num_variables() const { return colvars.size(); } -int colvarmodule::num_variables_feature(int feature_id) const +size_t colvarmodule::num_variables_feature(int feature_id) const { size_t n = 0; for (std::vector::const_iterator cvi = colvars.begin(); @@ -452,13 +456,13 @@ int colvarmodule::num_variables_feature(int feature_id) const } -int colvarmodule::num_biases() const +size_t colvarmodule::num_biases() const { return biases.size(); } -int colvarmodule::num_biases_feature(int feature_id) const +size_t colvarmodule::num_biases_feature(int feature_id) const { size_t n = 0; for (std::vector::const_iterator bi = biases.begin(); @@ -472,7 +476,7 @@ int colvarmodule::num_biases_feature(int feature_id) const } -int colvarmodule::num_biases_type(std::string const &type) const +size_t colvarmodule::num_biases_type(std::string const &type) const { size_t n = 0; for (std::vector::const_iterator bi = biases.begin(); @@ -971,13 +975,20 @@ int colvarmodule::write_restart_file(std::string const &out_name) int colvarmodule::write_traj_files() { if (cv_traj_os == NULL) { - open_traj_file(cv_traj_name); + if (open_traj_file(cv_traj_name) != COLVARS_OK) { + return cvm::get_error(); + } else { + cv_traj_write_labels = true; + } } // write labels in the traj file every 1000 lines and at first timestep - if ((cvm::step_absolute() % (cv_traj_freq * 1000)) == 0 || cvm::step_relative() == 0) { + if ((cvm::step_absolute() % (cv_traj_freq * 1000)) == 0 || + cvm::step_relative() == 0 || + cv_traj_write_labels) { write_traj_label(*cv_traj_os); } + cv_traj_write_labels = false; if ((cvm::step_absolute() % cv_traj_freq) == 0) { write_traj(*cv_traj_os); @@ -1064,7 +1075,7 @@ int colvarmodule::reset() { parse->init(); - cvm::log("Resetting the Collective Variables Module.\n"); + cvm::log("Resetting the Collective Variables module.\n"); // Iterate backwards because we are deleting the elements as we go for (std::vector::reverse_iterator bi = biases.rbegin(); @@ -1073,6 +1084,7 @@ int colvarmodule::reset() delete *bi; // the bias destructor updates the biases array } biases.clear(); + biases_active_.clear(); // Iterate backwards because we are deleting the elements as we go for (std::vector::reverse_iterator cvi = colvars.rbegin(); @@ -1088,7 +1100,7 @@ int colvarmodule::reset() proxy->reset(); if (cv_traj_os != NULL) { - // Do not close file here, as we might not be done with it yet. + // Do not close traj file here, as we might not be done with it yet. proxy->flush_output_stream(cv_traj_os); } @@ -1188,12 +1200,10 @@ std::istream & colvarmodule::read_restart(std::istream &is) // read global restart information std::string restart_conf; if (is >> colvarparse::read_block("configuration", restart_conf)) { - if (it_restart_from_state_file) { - parse->get_keyval(restart_conf, "step", - it_restart, (size_t) 0, - colvarparse::parse_silent); + parse->get_keyval(restart_conf, "step", + it_restart, (size_t) 0, + colvarparse::parse_silent); it = it_restart; - } std::string restart_version; parse->get_keyval(restart_conf, "version", restart_version, std::string(""), @@ -1688,40 +1698,59 @@ int cvm::read_index_file(char const *filename) return (cvm::get_error() ? COLVARS_ERROR : COLVARS_OK); } + int cvm::load_atoms(char const *file_name, cvm::atom_group &atoms, std::string const &pdb_field, - double const pdb_field_value) + double pdb_field_value) { return proxy->load_atoms(file_name, atoms, pdb_field, pdb_field_value); } + int cvm::load_coords(char const *file_name, - std::vector &pos, - const std::vector &indices, + std::vector *pos, + cvm::atom_group *atoms, std::string const &pdb_field, - double const pdb_field_value) + double pdb_field_value) { - // Differentiate between PDB and XYZ files - // for XYZ files, use CVM internal parser - // otherwise call proxy function for PDB + int error_code = COLVARS_OK; + + std::string const ext(strlen(file_name) > 4 ? + (file_name + (strlen(file_name) - 4)) : + file_name); + + atoms->create_sorted_ids(); + + std::vector sorted_pos(atoms->size(), cvm::rvector(0.0)); - std::string const ext(strlen(file_name) > 4 ? (file_name + (strlen(file_name) - 4)) : file_name); + // Differentiate between PDB and XYZ files if (colvarparse::to_lower_cppstr(ext) == std::string(".xyz")) { - if ( pdb_field.size() > 0 ) { - cvm::error("Error: PDB column may not be specified for XYZ coordinate file.\n", INPUT_ERROR); - return COLVARS_ERROR; + if (pdb_field.size() > 0) { + return cvm::error("Error: PDB column may not be specified " + "for XYZ coordinate files.\n", INPUT_ERROR); } - return cvm::load_coords_xyz(file_name, pos, indices); + // For XYZ files, use internal parser + error_code |= cvm::load_coords_xyz(file_name, &sorted_pos, atoms); } else { - return proxy->load_coords(file_name, pos, indices, pdb_field, pdb_field_value); + // Otherwise, call proxy function for PDB + error_code |= proxy->load_coords(file_name, + sorted_pos, atoms->sorted_ids(), + pdb_field, pdb_field_value); } + + std::vector const &map = atoms->sorted_ids_map(); + for (size_t i = 0; i < atoms->size(); i++) { + (*pos)[map[i]] = sorted_pos[i]; + } + + return error_code; } int cvm::load_coords_xyz(char const *filename, - std::vector &pos, - const std::vector &indices) + std::vector *pos, + cvm::atom_group *atoms) { std::ifstream xyz_is(filename); unsigned int natoms; @@ -1736,12 +1765,12 @@ int cvm::load_coords_xyz(char const *filename, cvm::getline(xyz_is, line); cvm::getline(xyz_is, line); xyz_is.width(255); - std::vector::iterator pos_i = pos.begin(); + std::vector::iterator pos_i = pos->begin(); - if (pos.size() != natoms) { // Use specified indices + if (pos->size() != natoms) { // Use specified indices int next = 0; // indices are zero-based - std::vector::const_iterator index = indices.begin(); - for ( ; pos_i != pos.end() ; pos_i++, index++) { + std::vector::const_iterator index = atoms->sorted_ids().begin(); + for ( ; pos_i != pos->end() ; pos_i++, index++) { while ( next < *index ) { cvm::getline(xyz_is, line); @@ -1751,7 +1780,7 @@ int cvm::load_coords_xyz(char const *filename, xyz_is >> (*pos_i)[0] >> (*pos_i)[1] >> (*pos_i)[2]; } } else { // Use all positions - for ( ; pos_i != pos.end() ; pos_i++) { + for ( ; pos_i != pos->end() ; pos_i++) { xyz_is >> symbol; xyz_is >> (*pos_i)[0] >> (*pos_i)[1] >> (*pos_i)[2]; } @@ -1792,17 +1821,13 @@ void cvm::request_total_force() proxy->request_total_force(true); } -cvm::rvector cvm::position_distance(atom_pos const &pos1, - atom_pos const &pos2) + +cvm::rvector cvm::position_distance(cvm::atom_pos const &pos1, + cvm::atom_pos const &pos2) { return proxy->position_distance(pos1, pos2); } -cvm::real cvm::position_dist2(cvm::atom_pos const &pos1, - cvm::atom_pos const &pos2) -{ - return proxy->position_dist2(pos1, pos2); -} cvm::real cvm::rand_gaussian(void) { diff --git a/lib/colvars/colvarmodule.h b/lib/colvars/colvarmodule.h index 64a98b77a02d59eae598a3f223214fc103018263..f3d99a2b234baf4a72300b4c59c3c9595d318b12 100644 --- a/lib/colvars/colvarmodule.h +++ b/lib/colvars/colvarmodule.h @@ -73,8 +73,17 @@ private: /// Impossible to initialize the main object without arguments colvarmodule(); + /// Integer representing the version string (allows comparisons) + int version_int; + public: + /// Get the version number (higher = more recent) + int version_number() const + { + return version_int; + } + friend class colvarproxy; // TODO colvarscript should be unaware of colvarmodule's internals friend class colvarscript; @@ -158,10 +167,6 @@ public: return it; } - /// If true, get it_restart from the state file; if set to false, - /// the MD program is providing it - bool it_restart_from_state_file; - /// \brief Finite difference step size (if there is no dynamics, or /// if gradients need to be tested independently from the size of /// dt) @@ -306,19 +311,19 @@ private: public: /// Return how many variables are defined - int num_variables() const; + size_t num_variables() const; /// Return how many variables have this feature enabled - int num_variables_feature(int feature_id) const; + size_t num_variables_feature(int feature_id) const; /// Return how many biases are defined - int num_biases() const; + size_t num_biases() const; /// Return how many biases have this feature enabled - int num_biases_feature(int feature_id) const; + size_t num_biases_feature(int feature_id) const; /// Return how many biases of this type are defined - int num_biases_type(std::string const &type) const; + size_t num_biases_type(std::string const &type) const; /// Return the names of time-dependent biases with forces enabled (ABF, /// metadynamics, etc) @@ -479,9 +484,6 @@ public: /// Print a message to the main log and set global error code static int error(std::string const &message, int code = COLVARS_ERROR); - /// Print a message to the main log and exit normally - static void exit(std::string const &message); - // Replica exchange commands. static bool replica_enabled(); static int replica_index(); @@ -495,15 +497,6 @@ public: static rvector position_distance(atom_pos const &pos1, atom_pos const &pos2); - /// \brief Get the square distance between two positions (with - /// periodic boundary conditions handled transparently) - /// - /// Note: in the case of periodic boundary conditions, this provides - /// an analytical square distance (while taking the square of - /// position_distance() would produce leads to a cusp) - static real position_dist2(atom_pos const &pos1, - atom_pos const &pos2); - /// \brief Names of groups from a Gromacs .ndx file to be read at startup std::list index_group_names; @@ -513,29 +506,36 @@ public: /// \brief Read a Gromacs .ndx file int read_index_file(char const *filename); - - /// \brief Create atoms from a file \param filename name of the file - /// (usually a PDB) \param atoms array of the atoms to be allocated - /// \param pdb_field (optiona) if "filename" is a PDB file, use this - /// field to determine which are the atoms to be set + /// \brief Select atom IDs from a file (usually PDB) \param filename name of + /// the file \param atoms array into which atoms read from "filename" will be + /// appended \param pdb_field (optional) if the file is a PDB and this + /// string is non-empty, select atoms for which this field is non-zero + /// \param pdb_field_value (optional) if non-zero, select only atoms whose + /// pdb_field equals this static int load_atoms(char const *filename, atom_group &atoms, std::string const &pdb_field, - double const pdb_field_value = 0.0); - - /// \brief Load the coordinates for a group of atoms from a file - /// (PDB or XYZ) + double pdb_field_value = 0.0); + + /// \brief Load coordinates for a group of atoms from a file (PDB or XYZ); + /// if "pos" is already allocated, the number of its elements must match the + /// number of entries in "filename" \param filename name of the file \param + /// pos array of coordinates \param atoms group containing the atoms (used + /// to obtain internal IDs) \param pdb_field (optional) if the file is a PDB + /// and this string is non-empty, select atoms for which this field is + /// non-zero \param pdb_field_value (optional) if non-zero, select only + /// atoms whose pdb_field equals this static int load_coords(char const *filename, - std::vector &pos, - const std::vector &indices, + std::vector *pos, + atom_group *atoms, std::string const &pdb_field, - double const pdb_field_value = 0.0); + double pdb_field_value = 0.0); /// \brief Load the coordinates for a group of atoms from an /// XYZ file static int load_coords_xyz(char const *filename, - std::vector &pos, - const std::vector &indices); + std::vector *pos, + atom_group *atoms); /// Frequency for collective variables trajectory output static size_t cv_traj_freq; @@ -568,6 +568,9 @@ protected: /// Appending to the existing trajectory file? bool cv_traj_append; + /// Write labels at the next iteration + bool cv_traj_write_labels; + private: /// Counter for the current depth in the object hierarchy (useg e.g. in output) diff --git a/lib/colvars/colvarproxy.cpp b/lib/colvars/colvarproxy.cpp index 8767d5f459090854cf19ad011f579e752c6d2230..c2992c309c6340e237e332014e24a30f44a73c7d 100644 --- a/lib/colvars/colvarproxy.cpp +++ b/lib/colvars/colvarproxy.cpp @@ -26,7 +26,10 @@ -colvarproxy_system::colvarproxy_system() {} +colvarproxy_system::colvarproxy_system() +{ + reset_pbc_lattice(); +} colvarproxy_system::~colvarproxy_system() {} @@ -55,10 +58,73 @@ bool colvarproxy_system::total_forces_same_step() const } -cvm::real colvarproxy_system::position_dist2(cvm::atom_pos const &pos1, - cvm::atom_pos const &pos2) +inline int round_to_integer(cvm::real x) { - return (position_distance(pos1, pos2)).norm2(); + return std::floor(x+0.5); +} + + +void colvarproxy_system::update_pbc_lattice() +{ + // Periodicity is assumed in all directions + + if (boundaries_type == boundaries_unsupported || + boundaries_type == boundaries_non_periodic) { + cvm::error("Error: setting PBC lattice with unsupported boundaries.\n", + BUG_ERROR); + return; + } + + { + cvm::rvector const v = cvm::rvector::outer(unit_cell_y, unit_cell_z); + reciprocal_cell_x = v/(v*unit_cell_x); + } + { + cvm::rvector const v = cvm::rvector::outer(unit_cell_z, unit_cell_x); + reciprocal_cell_y = v/(v*unit_cell_y); + } + { + cvm::rvector const v = cvm::rvector::outer(unit_cell_x, unit_cell_y); + reciprocal_cell_z = v/(v*unit_cell_z); + } +} + + +void colvarproxy_system::reset_pbc_lattice() +{ + unit_cell_x.reset(); + unit_cell_y.reset(); + unit_cell_z.reset(); + reciprocal_cell_x.reset(); + reciprocal_cell_y.reset(); + reciprocal_cell_z.reset(); +} + + +cvm::rvector colvarproxy_system::position_distance(cvm::atom_pos const &pos1, + cvm::atom_pos const &pos2) + const +{ + if (boundaries_type == boundaries_unsupported) { + cvm::error("Error: unsupported boundary conditions.\n", INPUT_ERROR); + } + + cvm::rvector diff = (pos2 - pos1); + + if (boundaries_type == boundaries_non_periodic) return diff; + + cvm::real const x_shift = round_to_integer(reciprocal_cell_x*diff); + cvm::real const y_shift = round_to_integer(reciprocal_cell_y*diff); + cvm::real const z_shift = round_to_integer(reciprocal_cell_z*diff); + + diff.x -= x_shift*unit_cell_x.x + y_shift*unit_cell_y.x + + z_shift*unit_cell_z.x; + diff.y -= x_shift*unit_cell_x.y + y_shift*unit_cell_y.y + + z_shift*unit_cell_z.y; + diff.z -= x_shift*unit_cell_x.z + y_shift*unit_cell_y.z + + z_shift*unit_cell_z.z; + + return diff; } @@ -132,7 +198,7 @@ void colvarproxy_atoms::clear_atom(int index) int colvarproxy_atoms::load_atoms(char const *filename, cvm::atom_group &atoms, std::string const &pdb_field, - double const) + double) { return cvm::error("Error: loading atom identifiers from a file " "is currently not implemented.\n", @@ -142,9 +208,9 @@ int colvarproxy_atoms::load_atoms(char const *filename, int colvarproxy_atoms::load_coords(char const *filename, std::vector &pos, - const std::vector &indices, + std::vector const &sorted_ids, std::string const &pdb_field, - double const) + double) { return cvm::error("Error: loading atomic coordinates from a file " "is currently not implemented.\n", @@ -661,6 +727,7 @@ int colvarproxy_io::close_output_stream(std::string const &output_name) for ( ; osi != output_files.end(); osi++, osni++) { if (*osni == output_name) { ((std::ofstream *) (*osi))->close(); + delete *osi; output_files.erase(osi); output_stream_names.erase(osni); return COLVARS_OK; @@ -729,3 +796,13 @@ size_t colvarproxy::restart_frequency() return 0; } + +int colvarproxy::get_version_from_string(char const *version_string) +{ + std::string const v(version_string); + std::istringstream is(v.substr(0, 4) + v.substr(5, 2) + v.substr(8, 2)); + int newint; + is >> newint; + return newint; +} + diff --git a/lib/colvars/colvarproxy.h b/lib/colvars/colvarproxy.h index bf290482704af3204518c0ffae7daf5ad5d88c0b..845f93c9bcde6b2654b86fcc9b52baee998ec8a4 100644 --- a/lib/colvars/colvarproxy.h +++ b/lib/colvars/colvarproxy.h @@ -14,6 +14,7 @@ #include #include "colvarmodule.h" +#include "colvartypes.h" #include "colvarvalue.h" @@ -29,7 +30,7 @@ /// To interface to a new MD engine, the simplest solution is to derive a new /// class from \link colvarproxy \endlink. Currently implemented are: \link /// colvarproxy_lammps, \endlink, \link colvarproxy_namd, \endlink, \link -/// colvarproxy_vmd, \endlink. +/// colvarproxy_vmd \endlink. // forward declarations @@ -68,14 +69,16 @@ public: /// \brief Get the PBC-aware distance vector between two positions virtual cvm::rvector position_distance(cvm::atom_pos const &pos1, - cvm::atom_pos const &pos2) = 0; + cvm::atom_pos const &pos2) const; - /// \brief Get the PBC-aware square distance between two positions; - /// may need to be reimplemented independently from position_distance() for optimization purposes - virtual cvm::real position_dist2(cvm::atom_pos const &pos1, - cvm::atom_pos const &pos2); + /// Recompute PBC reciprocal lattice (assumes XYZ periodicity) + void update_pbc_lattice(); - /// Tell the proxy whether total forces are needed (may not always be available) + /// Set the lattice vectors to zero + void reset_pbc_lattice(); + + /// \brief Tell the proxy whether total forces are needed (they may not + /// always be available) virtual void request_total_force(bool yesno); /// Are total forces being used? @@ -83,6 +86,29 @@ public: /// Are total forces from the current step available? virtual bool total_forces_same_step() const; + +protected: + + /// \brief Type of boundary conditions + /// + /// Orthogonal and triclinic cells are made available to objects. + /// For any other conditions (mixed periodicity, triclinic cells in LAMMPS) + /// minimum-image distances are computed by the host engine regardless. + enum Boundaries_type { + boundaries_non_periodic, + boundaries_pbc_ortho, + boundaries_pbc_triclinic, + boundaries_unsupported + }; + + /// Type of boundary conditions + Boundaries_type boundaries_type; + + /// Bravais lattice vectors + cvm::rvector unit_cell_x, unit_cell_y, unit_cell_z; + + /// Reciprocal lattice vectors + cvm::rvector reciprocal_cell_x, reciprocal_cell_y, reciprocal_cell_z; }; @@ -121,24 +147,30 @@ public: /// (costly) set the corresponding atoms_ncopies to zero virtual void clear_atom(int index); - /// \brief Read atom identifiers from a file \param filename name of - /// the file (usually a PDB) \param atoms array to which atoms read - /// from "filename" will be appended \param pdb_field (optiona) if - /// "filename" is a PDB file, use this field to determine which are - /// the atoms to be set + /// \brief Select atom IDs from a file (usually PDB) \param filename name of + /// the file \param atoms array to which atoms read from "filename" will be + /// appended \param pdb_field (optional) if the file is a PDB and this + /// string is non-empty, select atoms for which this field is non-zero + /// \param pdb_field_value (optional) if non-zero, select only atoms whose + /// pdb_field equals this virtual int load_atoms(char const *filename, cvm::atom_group &atoms, std::string const &pdb_field, - double const pdb_field_value = 0.0); - - /// \brief Load the coordinates for a group of atoms from a file - /// (usually a PDB); if "pos" is already allocated, the number of its - /// elements must match the number of atoms in "filename" + double pdb_field_value = 0.0); + + /// \brief Load a set of coordinates from a file (usually PDB); if "pos" is + /// already allocated, the number of its elements must match the number of + /// entries in "filename" \param filename name of the file \param pos array + /// of coordinates \param sorted_ids array of sorted internal IDs, used to + /// loop through the file only once \param pdb_field (optional) if the file + /// is a PDB and this string is non-empty, select atoms for which this field + /// is non-zero \param pdb_field_value (optional) if non-zero, select only + /// atoms whose pdb_field equals this virtual int load_coords(char const *filename, std::vector &pos, - const std::vector &indices, + std::vector const &sorted_ids, std::string const &pdb_field, - double const pdb_field_value = 0.0); + double pdb_field_value = 0.0); /// Clear atomic data int reset(); @@ -636,6 +668,15 @@ public: return b_simulation_running; } + /// Convert a version string "YYYY-MM-DD" into an integer + int get_version_from_string(char const *version_string); + + /// Get the version number (higher = more recent) + int version_number() const + { + return version_int; + } + protected: /// Whether a simulation is running (warn against irrecovarable errors) @@ -644,6 +685,9 @@ protected: /// Whether the entire module should be deallocated by the host engine bool b_delete_requested; + /// Integer representing the version string (allows comparisons) + int version_int; + }; diff --git a/lib/colvars/colvars_version.h b/lib/colvars/colvars_version.h index dc4b8bd07e420d83289b99f458ed2bf935ab210e..68f5cd13ab14eae1d71a47eba46d8729167966cd 100644 --- a/lib/colvars/colvars_version.h +++ b/lib/colvars/colvars_version.h @@ -1,5 +1,5 @@ #ifndef COLVARS_VERSION -#define COLVARS_VERSION "2018-01-17" +#define COLVARS_VERSION "2018-04-29" // 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/lib/colvars/colvartypes.h b/lib/colvars/colvartypes.h index 97257d18ad66d1da99b0b74586190e735687850b..4ef9557dcbf400c2e7adfc846207874632b134ac 100644 --- a/lib/colvars/colvartypes.h +++ b/lib/colvars/colvartypes.h @@ -130,7 +130,7 @@ public: } } - inline void operator *= (cvm::real const &a) + inline void operator *= (cvm::real a) { size_t i; for (i = 0; i < this->size(); i++) { @@ -138,7 +138,7 @@ public: } } - inline void operator /= (cvm::real const &a) + inline void operator /= (cvm::real a) { size_t i; for (i = 0; i < this->size(); i++) { @@ -146,7 +146,8 @@ public: } } - inline friend vector1d operator + (vector1d const &v1, vector1d const &v2) + inline friend vector1d operator + (vector1d const &v1, + vector1d const &v2) { check_sizes(v1.size(), v2.size()); vector1d result(v1.size()); @@ -157,7 +158,8 @@ public: return result; } - inline friend vector1d operator - (vector1d const &v1, vector1d const &v2) + inline friend vector1d operator - (vector1d const &v1, + vector1d const &v2) { check_sizes(v1.size(), v2.size()); vector1d result(v1.size()); @@ -168,7 +170,7 @@ public: return result; } - inline friend vector1d operator * (vector1d const &v, cvm::real const &a) + inline friend vector1d operator * (vector1d const &v, cvm::real a) { vector1d result(v.size()); size_t i; @@ -178,12 +180,12 @@ public: return result; } - inline friend vector1d operator * (cvm::real const &a, vector1d const &v) + inline friend vector1d operator * (cvm::real a, vector1d const &v) { return v * a; } - inline friend vector1d operator / (vector1d const &v, cvm::real const &a) + inline friend vector1d operator / (vector1d const &v, cvm::real a) { vector1d result(v.size()); size_t i; @@ -246,7 +248,8 @@ public: } /// Assign a vector to a slice of this vector - inline void sliceassign(size_t const i1, size_t const i2, vector1d const &v) + inline void sliceassign(size_t const i1, size_t const i2, + vector1d const &v) { if ((i2 < i1) || (i2 >= this->size())) { cvm::error("Error: trying to slice a vector using incorrect boundaries.\n"); @@ -259,12 +262,13 @@ public: /// Formatted output - inline size_t output_width(size_t const &real_width) const + inline size_t output_width(size_t real_width) const { return real_width*(this->size()) + 3*(this->size()-1) + 4; } - inline friend std::istream & operator >> (std::istream &is, cvm::vector1d &v) + inline friend std::istream & operator >> (std::istream &is, + cvm::vector1d &v) { if (v.size() == 0) return is; size_t const start_pos = is.tellg(); @@ -288,7 +292,8 @@ public: return is; } - inline friend std::ostream & operator << (std::ostream &os, cvm::vector1d const &v) + inline friend std::ostream & operator << (std::ostream &os, + cvm::vector1d const &v) { std::streamsize const w = os.width(); std::streamsize const p = os.precision(); @@ -377,6 +382,15 @@ protected: { return vector1d(length, data); } + inline int set(cvm::vector1d const &v) const + { + if (v.size() != length) { + return cvm::error("Error: setting a matrix row from a vector of " + "incompatible size.\n", BUG_ERROR); + } + for (size_t i = 0; i < length; i++) data[i] = v[i]; + return COLVARS_OK; + } }; std::vector data; @@ -515,9 +529,12 @@ public: { if ((m1.outer_length != m2.outer_length) || (m1.inner_length != m2.inner_length)) { - cvm::error("Error: trying to perform an operation between matrices of different sizes, "+ - cvm::to_str(m1.outer_length)+"x"+cvm::to_str(m1.inner_length)+" and "+ - cvm::to_str(m2.outer_length)+"x"+cvm::to_str(m2.inner_length)+".\n"); + cvm::error("Error: trying to perform an operation between " + "matrices of different sizes, "+ + cvm::to_str(m1.outer_length)+"x"+ + cvm::to_str(m1.inner_length)+" and "+ + cvm::to_str(m2.outer_length)+"x"+ + cvm::to_str(m2.inner_length)+".\n"); } } @@ -539,7 +556,7 @@ public: } } - inline void operator *= (cvm::real const &a) + inline void operator *= (cvm::real a) { size_t i; for (i = 0; i < data.size(); i++) { @@ -547,7 +564,7 @@ public: } } - inline void operator /= (cvm::real const &a) + inline void operator /= (cvm::real a) { size_t i; for (i = 0; i < data.size(); i++) { @@ -555,7 +572,8 @@ public: } } - inline friend matrix2d operator + (matrix2d const &m1, matrix2d const &m2) + inline friend matrix2d operator + (matrix2d const &m1, + matrix2d const &m2) { check_sizes(m1, m2); matrix2d result(m1.outer_length, m1.inner_length); @@ -566,7 +584,8 @@ public: return result; } - inline friend matrix2d operator - (matrix2d const &m1, matrix2d const &m2) + inline friend matrix2d operator - (matrix2d const &m1, + matrix2d const &m2) { check_sizes(m1, m2); matrix2d result(m1.outer_length, m1.inner_length); @@ -577,7 +596,7 @@ public: return result; } - inline friend matrix2d operator * (matrix2d const &m, cvm::real const &a) + inline friend matrix2d operator * (matrix2d const &m, cvm::real a) { matrix2d result(m.outer_length, m.inner_length); size_t i; @@ -587,12 +606,12 @@ public: return result; } - inline friend matrix2d operator * (cvm::real const &a, matrix2d const &m) + inline friend matrix2d operator * (cvm::real a, matrix2d const &m) { return m * a; } - inline friend matrix2d operator / (matrix2d const &m, cvm::real const &a) + inline friend matrix2d operator / (matrix2d const &m, cvm::real a) { matrix2d result(m.outer_length, m.inner_length); size_t i; @@ -602,34 +621,17 @@ public: return result; } - /// Matrix multiplication -// inline friend matrix2d const & operator * (matrix2d const &m1, matrix2d const &m2) -// { -// matrix2d result(m1.outer_length, m2.inner_length); -// if (m1.inner_length != m2.outer_length) { -// cvm::error("Error: trying to multiply two matrices of incompatible sizes, "+ -// cvm::to_str(m1.outer_length)+"x"+cvm::to_str(m1.inner_length)+" and "+ -// cvm::to_str(m2.outer_length)+"x"+cvm::to_str(m2.inner_length)+".\n"); -// } else { -// size_t i, j, k; -// for (i = 0; i < m1.outer_length; i++) { -// for (j = 0; j < m2.inner_length; j++) { -// for (k = 0; k < m1.inner_length; k++) { -// result[i][j] += m1[i][k] * m2[k][j]; -// } -// } -// } -// } -// return result; -// } - /// vector-matrix multiplication - inline friend vector1d operator * (vector1d const &v, matrix2d const &m) + inline friend vector1d operator * (vector1d const &v, + matrix2d const &m) { vector1d result(m.inner_length); if (m.outer_length != v.size()) { - cvm::error("Error: trying to multiply a vector and a matrix of incompatible sizes, "+ - cvm::to_str(v.size()) + " and " + cvm::to_str(m.outer_length)+"x"+cvm::to_str(m.inner_length) + ".\n"); + cvm::error("Error: trying to multiply a vector and a matrix " + "of incompatible sizes, "+ + cvm::to_str(v.size()) + " and " + + cvm::to_str(m.outer_length)+"x"+cvm::to_str(m.inner_length) + + ".\n"); } else { size_t i, k; for (i = 0; i < m.inner_length; i++) { @@ -641,25 +643,6 @@ public: return result; } -// /// matrix-vector multiplication (unused for now) -// inline friend vector1d const & operator * (matrix2d const &m, vector1d const &v) -// { -// vector1d result(m.outer_length); -// if (m.inner_length != v.size()) { -// cvm::error("Error: trying to multiply a matrix and a vector of incompatible sizes, "+ -// cvm::to_str(m.outer_length)+"x"+cvm::to_str(m.inner_length) -// + " and " + cvm::to_str(v.length) + ".\n"); -// } else { -// size_t i, k; -// for (i = 0; i < m.outer_length; i++) { -// for (k = 0; k < m.inner_length; k++) { -// result[i] += m[i][k] * v[k]; -// } -// } -// } -// return result; -// } - /// Formatted output friend std::ostream & operator << (std::ostream &os, matrix2d const &m) @@ -725,49 +708,52 @@ public: cvm::real x, y, z; inline rvector() - : x(0.0), y(0.0), z(0.0) - {} + { + reset(); + } - inline rvector(cvm::real const &x_i, - cvm::real const &y_i, - cvm::real const &z_i) - : x(x_i), y(y_i), z(z_i) - {} + /// \brief Set all components to zero + inline void reset() + { + set(0.0); + } + + inline rvector(cvm::real x_i, cvm::real y_i, cvm::real z_i) + { + set(x_i, y_i, z_i); + } inline rvector(cvm::vector1d const &v) - : x(v[0]), y(v[1]), z(v[2]) - {} + { + set(v[0], v[1], v[2]); + } inline rvector(cvm::real t) - : x(t), y(t), z(t) - {} + { + set(t); + } - /// \brief Set all components to a scalar value - inline void set(cvm::real const &value) { + /// \brief Set all components to a scalar + inline void set(cvm::real value) + { x = y = z = value; } /// \brief Assign all components - inline void set(cvm::real const &x_i, - cvm::real const &y_i, - cvm::real const &z_i) { + inline void set(cvm::real x_i, cvm::real y_i, cvm::real z_i) + { x = x_i; y = y_i; z = z_i; } - /// \brief Set all components to zero - inline void reset() { - x = y = z = 0.0; - } - /// \brief Access cartesian components by index - inline cvm::real & operator [] (int const &i) { + inline cvm::real & operator [] (int i) { return (i == 0) ? x : (i == 1) ? y : (i == 2) ? z : x; } /// \brief Access cartesian components by index - inline cvm::real const & operator [] (int const &i) const { + inline cvm::real operator [] (int i) const { return (i == 0) ? x : (i == 1) ? y : (i == 2) ? z : x; } @@ -780,14 +766,6 @@ public: return result; } - inline cvm::rvector & operator = (cvm::real const &v) - { - x = v; - y = v; - z = v; - return *this; - } - inline void operator += (cvm::rvector const &v) { x += v.x; @@ -802,7 +780,7 @@ public: z -= v.z; } - inline void operator *= (cvm::real const &v) + inline void operator *= (cvm::real v) { x *= v; y *= v; @@ -832,13 +810,14 @@ public: return (n > 0. ? cvm::rvector(x, y, z)/n : cvm::rvector(1., 0., 0.)); } - static inline size_t output_width(size_t const &real_width) + static inline size_t output_width(size_t real_width) { return 3*real_width + 10; } - static inline cvm::rvector outer(cvm::rvector const &v1, cvm::rvector const &v2) + static inline cvm::rvector outer(cvm::rvector const &v1, + cvm::rvector const &v2) { return cvm::rvector( v1.y*v2.z - v2.y*v1.z, -v1.x*v2.z + v2.x*v1.z, @@ -850,41 +829,35 @@ public: return cvm::rvector(-v.x, -v.y, -v.z); } - friend inline int operator == (cvm::rvector const &v1, cvm::rvector const &v2) - { - return (v1.x == v2.x) && (v1.y == v2.y) && (v1.z == v2.z); - } - - friend inline int operator != (cvm::rvector const &v1, cvm::rvector const &v2) - { - return (v1.x != v2.x) || (v1.y != v2.y) || (v1.z != v2.z); - } - - friend inline cvm::rvector operator + (cvm::rvector const &v1, cvm::rvector const &v2) + friend inline cvm::rvector operator + (cvm::rvector const &v1, + cvm::rvector const &v2) { return cvm::rvector(v1.x + v2.x, v1.y + v2.y, v1.z + v2.z); } - friend inline cvm::rvector operator - (cvm::rvector const &v1, cvm::rvector const &v2) + friend inline cvm::rvector operator - (cvm::rvector const &v1, + cvm::rvector const &v2) { return cvm::rvector(v1.x - v2.x, v1.y - v2.y, v1.z - v2.z); } - friend inline cvm::real operator * (cvm::rvector const &v1, cvm::rvector const &v2) + /// Inner (dot) product + friend inline cvm::real operator * (cvm::rvector const &v1, + cvm::rvector const &v2) { return v1.x * v2.x + v1.y * v2.y + v1.z * v2.z; } - friend inline cvm::rvector operator * (cvm::real const &a, cvm::rvector const &v) + friend inline cvm::rvector operator * (cvm::real a, cvm::rvector const &v) { return cvm::rvector(a*v.x, a*v.y, a*v.z); } - friend inline cvm::rvector operator * (cvm::rvector const &v, cvm::real const &a) + friend inline cvm::rvector operator * (cvm::rvector const &v, cvm::real a) { return cvm::rvector(a*v.x, a*v.y, a*v.z); } - friend inline cvm::rvector operator / (cvm::rvector const &v, cvm::real const &a) + friend inline cvm::rvector operator / (cvm::rvector const &v, cvm::real a) { return cvm::rvector(v.x/a, v.y/a, v.z/a); } @@ -946,15 +919,9 @@ public: {} /// Constructor component by component - inline rmatrix(cvm::real const &xxi, - cvm::real const &xyi, - cvm::real const &xzi, - cvm::real const &yxi, - cvm::real const &yyi, - cvm::real const &yzi, - cvm::real const &zxi, - cvm::real const &zyi, - cvm::real const &zzi) + inline rmatrix(cvm::real xxi, cvm::real xyi, cvm::real xzi, + cvm::real yxi, cvm::real yyi, cvm::real yzi, + cvm::real zxi, cvm::real zyi, cvm::real zzi) : cvm::matrix2d(3, 3) { this->xx() = xxi; @@ -983,31 +950,13 @@ public: inline cvm::rmatrix transpose() const { - return cvm::rmatrix(this->xx(), - this->yx(), - this->zx(), - this->xy(), - this->yy(), - this->zy(), - this->xz(), - this->yz(), - this->zz()); + return cvm::rmatrix(this->xx(), this->yx(), this->zx(), + this->xy(), this->yy(), this->zy(), + this->xz(), this->yz(), this->zz()); } friend cvm::rvector operator * (cvm::rmatrix const &m, cvm::rvector const &r); - // friend inline cvm::rmatrix const operator * (cvm::rmatrix const &m1, cvm::rmatrix const &m2) { - // return cvm::rmatrix (m1.xx()*m2.xx() + m1.xy()*m2.yx() + m1.xz()*m2.yz(), - // m1.xx()*m2.xy() + m1.xy()*m2.yy() + m1.xz()*m2.zy(), - // m1.xx()*m2.xz() + m1.xy()*m2.yz() + m1.xz()*m2.zz(), - // m1.yx()*m2.xx() + m1.yy()*m2.yx() + m1.yz()*m2.yz(), - // m1.yx()*m2.xy() + m1.yy()*m2.yy() + m1.yz()*m2.yy(), - // m1.yx()*m2.xz() + m1.yy()*m2.yz() + m1.yz()*m2.yz(), - // m1.zx()*m2.xx() + m1.zy()*m2.yx() + m1.zz()*m2.yz(), - // m1.zx()*m2.xy() + m1.zy()*m2.yy() + m1.zz()*m2.yy(), - // m1.zx()*m2.xz() + m1.zy()*m2.yz() + m1.zz()*m2.yz()); - // } - }; @@ -1031,7 +980,7 @@ public: cvm::real q0, q1, q2, q3; /// Constructor from a 3-d vector - inline quaternion(cvm::real const &x, cvm::real const &y, cvm::real const &z) + inline quaternion(cvm::real x, cvm::real y, cvm::real z) : q0(0.0), q1(x), q2(y), q3(z) {} @@ -1041,10 +990,10 @@ public: {} /// Constructor component by component - inline quaternion(cvm::real const &q0i, - cvm::real const &q1i, - cvm::real const &q2i, - cvm::real const &q3i) + inline quaternion(cvm::real q0i, + cvm::real q1i, + cvm::real q2i, + cvm::real q3i) : q0(q0i), q1(q1i), q2(q2i), q3(q3i) {} @@ -1055,9 +1004,9 @@ public: /// "Constructor" after Euler angles (in radians) /// /// http://en.wikipedia.org/wiki/Conversion_between_quaternions_and_Euler_angles - inline void set_from_euler_angles(cvm::real const &phi_in, - cvm::real const &theta_in, - cvm::real const &psi_in) + inline void set_from_euler_angles(cvm::real phi_in, + cvm::real theta_in, + cvm::real psi_in) { q0 = ( (std::cos(phi_in/2.0)) * (std::cos(theta_in/2.0)) * (std::cos(psi_in/2.0)) + (std::sin(phi_in/2.0)) * (std::sin(theta_in/2.0)) * (std::sin(psi_in/2.0)) ); @@ -1079,7 +1028,7 @@ public: } /// \brief Set all components to a scalar - inline void set(cvm::real const &value = 0.0) + inline void set(cvm::real value) { q0 = q1 = q2 = q3 = value; } @@ -1087,7 +1036,7 @@ public: /// \brief Set all components to zero (null quaternion) inline void reset() { - q0 = q1 = q2 = q3 = 0.0; + set(0.0); } /// \brief Set the q0 component to 1 and the others to 0 (quaternion @@ -1099,7 +1048,7 @@ public: } /// Tell the number of characters required to print a quaternion, given that of a real number - static inline size_t output_width(size_t const &real_width) + static inline size_t output_width(size_t real_width) { return 4*real_width + 13; } @@ -1113,7 +1062,7 @@ public: friend std::istream & operator >> (std::istream &is, cvm::quaternion &q); /// Access the quaternion as a 4-d array (return a reference) - inline cvm::real & operator [] (int const &i) { + inline cvm::real & operator [] (int i) { switch (i) { case 0: return this->q0; @@ -1130,7 +1079,7 @@ public: } /// Access the quaternion as a 4-d array (return a value) - inline cvm::real operator [] (int const &i) const { + inline cvm::real operator [] (int i) const { switch (i) { case 0: return this->q0; @@ -1175,12 +1124,12 @@ public: return cvm::quaternion(q0, -q1, -q2, -q3); } - inline void operator *= (cvm::real const &a) + inline void operator *= (cvm::real a) { q0 *= a; q1 *= a; q2 *= a; q3 *= a; } - inline void operator /= (cvm::real const &a) + inline void operator /= (cvm::real a) { q0 /= a; q1 /= a; q2 /= a; q3 /= a; } @@ -1215,19 +1164,22 @@ public: } - friend inline cvm::quaternion operator + (cvm::quaternion const &h, cvm::quaternion const &q) + friend inline cvm::quaternion operator + (cvm::quaternion const &h, + cvm::quaternion const &q) { return cvm::quaternion(h.q0+q.q0, h.q1+q.q1, h.q2+q.q2, h.q3+q.q3); } - friend inline cvm::quaternion operator - (cvm::quaternion const &h, cvm::quaternion const &q) + friend inline cvm::quaternion operator - (cvm::quaternion const &h, + cvm::quaternion const &q) { return cvm::quaternion(h.q0-q.q0, h.q1-q.q1, h.q2-q.q2, h.q3-q.q3); } /// \brief Provides the quaternion product. \b NOTE: for the inner /// product use: \code h.inner (q); \endcode - friend inline cvm::quaternion operator * (cvm::quaternion const &h, cvm::quaternion const &q) + friend inline cvm::quaternion operator * (cvm::quaternion const &h, + cvm::quaternion const &q) { return cvm::quaternion(h.q0*q.q0 - h.q1*q.q1 - h.q2*q.q2 - h.q3*q.q3, h.q0*q.q1 + h.q1*q.q0 + h.q2*q.q3 - h.q3*q.q2, @@ -1235,18 +1187,18 @@ public: h.q0*q.q3 + h.q3*q.q0 + h.q1*q.q2 - h.q2*q.q1); } - friend inline cvm::quaternion operator * (cvm::real const &c, + friend inline cvm::quaternion operator * (cvm::real c, cvm::quaternion const &q) { return cvm::quaternion(c*q.q0, c*q.q1, c*q.q2, c*q.q3); } friend inline cvm::quaternion operator * (cvm::quaternion const &q, - cvm::real const &c) + cvm::real c) { return cvm::quaternion(q.q0*c, q.q1*c, q.q2*c, q.q3*c); } friend inline cvm::quaternion operator / (cvm::quaternion const &q, - cvm::real const &c) + cvm::real c) { return cvm::quaternion(q.q0/c, q.q1/c, q.q2/c, q.q3/c); } @@ -1407,7 +1359,7 @@ public: std::vector< cvm::vector1d > dQ0_1, dQ0_2; /// Allocate space for the derivatives of the rotation - inline void request_group1_gradients(size_t const &n) + inline void request_group1_gradients(size_t n) { dS_1.resize(n, cvm::matrix2d(4, 4)); dL0_1.resize(n, cvm::rvector(0.0, 0.0, 0.0)); @@ -1415,7 +1367,7 @@ public: } /// Allocate space for the derivatives of the rotation - inline void request_group2_gradients(size_t const &n) + inline void request_group2_gradients(size_t n) { dS_2.resize(n, cvm::matrix2d(4, 4)); dL0_2.resize(n, cvm::rvector(0.0, 0.0, 0.0)); @@ -1448,7 +1400,7 @@ public: } /// Constructor after an axis of rotation and an angle (in radians) - inline rotation(cvm::real const &angle, cvm::rvector const &axis) + inline rotation(cvm::real angle, cvm::rvector const &axis) : b_debug_gradients(false) { cvm::rvector const axis_n = axis.unit(); @@ -1500,20 +1452,18 @@ public: if (q.q0 != 0.0) { - // cvm::real const x = iprod/q.q0; - - cvm::real const dspindx = (180.0/PI) * 2.0 * (1.0 / (1.0 + (iprod*iprod)/(q.q0*q.q0))); + cvm::real const dspindx = + (180.0/PI) * 2.0 * (1.0 / (1.0 + (iprod*iprod)/(q.q0*q.q0))); - return - cvm::quaternion( dspindx * (iprod * (-1.0) / (q.q0*q.q0)), - dspindx * ((1.0/q.q0) * axis.x), - dspindx * ((1.0/q.q0) * axis.y), - dspindx * ((1.0/q.q0) * axis.z)); + return cvm::quaternion( dspindx * (iprod * (-1.0) / (q.q0*q.q0)), + dspindx * ((1.0/q.q0) * axis.x), + dspindx * ((1.0/q.q0) * axis.y), + dspindx * ((1.0/q.q0) * axis.z)); } else { // (1/(1+x^2)) ~ (1/x)^2 - return - cvm::quaternion((180.0/PI) * 2.0 * ((-1.0)/iprod), 0.0, 0.0, 0.0); - // XX TODO: What if iprod == 0? XX + // The documentation of spinAngle discourages its use when q_vec and + // axis are not close + return cvm::quaternion((180.0/PI) * 2.0 * ((-1.0)/iprod), 0.0, 0.0, 0.0); } } diff --git a/lib/latte/.gitignore b/lib/latte/.gitignore index a4c2a2362e959e7672e6289f0b9cbade4b6156a5..2c9ff6be9e655db4bf7c02b5b639e398ac8781ad 100644 --- a/lib/latte/.gitignore +++ b/lib/latte/.gitignore @@ -2,4 +2,4 @@ /filelink /liblink /includelink -/LATTE-master +/LATTE-* diff --git a/lib/vtk/Makefile.lammps.fedora28_vtk7 b/lib/vtk/Makefile.lammps.fedora28_vtk7 new file mode 100644 index 0000000000000000000000000000000000000000..6919dd36b96c37cedd912ba5b0dad1f88dba0ded --- /dev/null +++ b/lib/vtk/Makefile.lammps.fedora28_vtk7 @@ -0,0 +1,8 @@ +# Settings that the LAMMPS build will import when this package library is used + +# settings for VTK 7.1.1 on Fedora 28. This seems to work with Fedora versions going back to at least 23 and VTK version 6.x. +# You need to install vtk-devel and all its dependencies using "dnf install vtk-devel" +vtk_SYSINC = -I/usr/include/vtk +vtk_SYSLIB = -lvtkCommonCore -lvtkIOCore -lvtkCommonDataModel -lvtkIOXML -lvtkIOLegacy -lvtkIOParallelXML +vtk_SYSPATH = -L/usr/lib64/vtk + diff --git a/python/lammps.py b/python/lammps.py index e798ef60718d7cd9763641f799b0dd8330da1f53..417427eb4b715bb64cdabeceb65b93ae036f492c 100644 --- a/python/lammps.py +++ b/python/lammps.py @@ -5,7 +5,7 @@ # # 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 +# 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. @@ -37,7 +37,7 @@ def get_ctypes_int(size): return c_int32 elif size == 8: return c_int64 - return c_int + return c_int class MPIAbortException(Exception): def __init__(self, message): @@ -47,7 +47,7 @@ class MPIAbortException(Exception): return repr(self.message) class lammps(object): - + # detect if Python is using version of mpi4py that can pass a communicator has_mpi4py = False @@ -71,7 +71,7 @@ class lammps(object): # if a pointer to a LAMMPS object is handed in, # all symbols should already be available - + try: if ptr: self.lib = CDLL("",RTLD_GLOBAL) except: @@ -84,7 +84,7 @@ class lammps(object): # so that LD_LIBRARY_PATH does not need to be set for regular install # fall back to loading with a relative path, # typically requires LD_LIBRARY_PATH to be set appropriately - + if not self.lib: try: if not name: self.lib = CDLL(join(modpath,"liblammps.so"),RTLD_GLOBAL) @@ -110,15 +110,15 @@ class lammps(object): self.lib.lammps_gather_atoms.argtypes = \ [c_void_p,c_char_p,c_int,c_int,c_void_p] self.lib.lammps_gather_atoms.restype = None - + self.lib.lammps_gather_atoms_concat.argtypes = \ [c_void_p,c_char_p,c_int,c_int,c_void_p] self.lib.lammps_gather_atoms_concat.restype = None - + self.lib.lammps_gather_atoms_subset.argtypes = \ [c_void_p,c_char_p,c_int,c_int,c_int,POINTER(c_int),c_void_p] self.lib.lammps_gather_atoms_subset.restype = None - + self.lib.lammps_scatter_atoms.argtypes = \ [c_void_p,c_char_p,c_int,c_int,c_void_p] self.lib.lammps_scatter_atoms.restype = None @@ -137,7 +137,7 @@ class lammps(object): # just convert it to ctypes ptr and store in self.lmp if not ptr: - + # with mpi4py v2, can pass MPI communicator to LAMMPS # need to adjust for type of MPI communicator object # allow for int (like MPICH) or void* (like OpenMPI) @@ -211,7 +211,7 @@ class lammps(object): self.c_imageint = get_ctypes_int(self.extract_setting("imageint")) # shut-down LAMMPS instance - + def __del__(self): if self.lmp and self.opened: self.lib.lammps_close(self.lmp) @@ -230,7 +230,7 @@ class lammps(object): self.lib.lammps_file(self.lmp,file) # send a single command - + def command(self,cmd): if cmd: cmd = cmd.encode() self.lib.lammps_command(self.lmp,cmd) @@ -250,13 +250,13 @@ class lammps(object): cmds = [x.encode() for x in cmdlist if type(x) is str] args = (c_char_p * len(cmdlist))(*cmds) self.lib.lammps_commands_list(self.lmp,len(cmdlist),args) - + # send a string of commands def commands_string(self,multicmd): if type(multicmd) is str: multicmd = multicmd.encode() self.lib.lammps_commands_string(self.lmp,c_char_p(multicmd)) - + # extract lammps type byte sizes def extract_setting(self, name): @@ -265,7 +265,7 @@ class lammps(object): return int(self.lib.lammps_extract_setting(self.lmp,name)) # extract global info - + def extract_global(self,name,type): if name: name = name.encode() if type == 0: @@ -277,7 +277,7 @@ class lammps(object): return ptr[0] # extract global info - + def extract_box(self): boxlo = (3*c_double)() boxhi = (3*c_double)() @@ -286,11 +286,11 @@ class lammps(object): xz = c_double() periodicity = (3*c_int)() box_change = c_int() - + self.lib.lammps_extract_box(self.lmp,boxlo,boxhi, byref(xy),byref(yz),byref(xz), periodicity,byref(box_change)) - + boxlo = boxlo[:3] boxhi = boxhi[:3] xy = xy.value @@ -298,9 +298,9 @@ class lammps(object): xz = xz.value periodicity = periodicity[:3] box_change = box_change.value - + return boxlo,boxhi,xy,yz,xz,periodicity,box_change - + # extract per-atom info # NOTE: need to insure are converting to/from correct Python type # e.g. for Python list or NumPy or ctypes @@ -318,7 +318,7 @@ class lammps(object): else: return None ptr = self.lib.lammps_extract_atom(self.lmp,name) return ptr - + @property def numpy(self): if not self._numpy: @@ -371,7 +371,7 @@ class lammps(object): return self._numpy # extract compute info - + def extract_compute(self,id,style,type): if id: id = id.encode() if type == 0: @@ -384,9 +384,14 @@ class lammps(object): ptr = self.lib.lammps_extract_compute(self.lmp,id,style,type) return ptr if type == 2: - self.lib.lammps_extract_compute.restype = POINTER(POINTER(c_double)) - ptr = self.lib.lammps_extract_compute(self.lmp,id,style,type) - return ptr + if style == 0: + self.lib.lammps_extract_compute.restype = POINTER(c_int) + ptr = self.lib.lammps_extract_compute(self.lmp,id,style,type) + return ptr[0] + else: + self.lib.lammps_extract_compute.restype = POINTER(POINTER(c_double)) + ptr = self.lib.lammps_extract_compute(self.lmp,id,style,type) + return ptr return None # extract fix info @@ -466,7 +471,7 @@ class lammps(object): cboxlo = (3*c_double)(*boxlo) cboxhi = (3*c_double)(*boxhi) self.lib.lammps_reset_box(self.lmp,cboxlo,cboxhi,xy,yz,xz) - + # return vector of atom properties gathered across procs # 3 variants to match src/library.cpp # name = atom property recognized by LAMMPS in atom->extract() @@ -475,7 +480,7 @@ class lammps(object): # returned data is a 1d vector - doc how it is ordered? # NOTE: need to insure are converting to/from correct Python type # e.g. for Python list or NumPy or ctypes - + def gather_atoms(self,name,type,count): if name: name = name.encode() natoms = self.lib.lammps_get_natoms(self.lmp) @@ -487,7 +492,7 @@ class lammps(object): self.lib.lammps_gather_atoms(self.lmp,name,type,count,data) else: return None return data - + def gather_atoms_concat(self,name,type,count): if name: name = name.encode() natoms = self.lib.lammps_get_natoms(self.lmp) @@ -519,7 +524,7 @@ class lammps(object): # assume data is of correct type and length, as created by gather_atoms() # NOTE: need to insure are converting to/from correct Python type # e.g. for Python list or NumPy or ctypes - + def scatter_atoms(self,name,type,count,data): if name: name = name.encode() self.lib.lammps_scatter_atoms(self.lmp,name,type,count,data) diff --git a/src/.gitignore b/src/.gitignore index 94d55b87052fccae48f4d24b3db41695aa2f77a5..1ff66859e86cb6c1f920439aa4e2fa25e799c61d 100644 --- a/src/.gitignore +++ b/src/.gitignore @@ -374,6 +374,8 @@ /fix_bond_break.h /fix_bond_create.cpp /fix_bond_create.h +/fix_bond_react.cpp +/fix_bond_react.h /fix_bond_swap.cpp /fix_bond_swap.h /fix_cmap.cpp @@ -732,6 +734,8 @@ /pair_hbond_dreiding_morse.h /pair_ilp_graphene_hbn.cpp /pair_ilp_graphene_hbn.h +/pair_kim.cpp +/pair_kim.h /pair_kolmogorov_crespi_full.cpp /pair_kolmogorov_crespi_full.h /pair_kolmogorov_crespi_z.cpp diff --git a/src/ASPHERE/compute_temp_asphere.cpp b/src/ASPHERE/compute_temp_asphere.cpp index b6d37db6ce91693d9c4592b8e501f37b33546df2..011d8cae80f662d668223f7f43af71fc162df413 100644 --- a/src/ASPHERE/compute_temp_asphere.cpp +++ b/src/ASPHERE/compute_temp_asphere.cpp @@ -16,7 +16,7 @@ ------------------------------------------------------------------------- */ #include -#include +#include #include "compute_temp_asphere.h" #include "math_extra.h" #include "atom.h" diff --git a/src/ASPHERE/fix_nh_asphere.cpp b/src/ASPHERE/fix_nh_asphere.cpp index 2eee28dc1ce1ead9da818fb1e12832c06d8e5ef3..828c064a526cb3c8b0c3eb9c8e9341b7db3eed11 100644 --- a/src/ASPHERE/fix_nh_asphere.cpp +++ b/src/ASPHERE/fix_nh_asphere.cpp @@ -15,9 +15,9 @@ Contributing author: Mike Brown (SNL) ------------------------------------------------------------------------- */ -#include -#include -#include +#include +#include +#include #include "math_extra.h" #include "fix_nh_asphere.h" #include "atom.h" diff --git a/src/ASPHERE/fix_nph_asphere.cpp b/src/ASPHERE/fix_nph_asphere.cpp index e0558ef4f24cd29af20311b03cfaef7528fb540a..5f201a8463e325c2ff9bdeae85a1e6687907fd77 100644 --- a/src/ASPHERE/fix_nph_asphere.cpp +++ b/src/ASPHERE/fix_nph_asphere.cpp @@ -11,7 +11,7 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include +#include #include "fix_nph_asphere.h" #include "modify.h" #include "error.h" diff --git a/src/ASPHERE/fix_npt_asphere.cpp b/src/ASPHERE/fix_npt_asphere.cpp index 205630376af2d49b7ef5bf6d3a439f6f5ffd1e1a..5d528911698f2c045c763163ec2c8912ec1661c5 100644 --- a/src/ASPHERE/fix_npt_asphere.cpp +++ b/src/ASPHERE/fix_npt_asphere.cpp @@ -11,7 +11,7 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include +#include #include "fix_npt_asphere.h" #include "modify.h" #include "error.h" diff --git a/src/ASPHERE/fix_nve_asphere.cpp b/src/ASPHERE/fix_nve_asphere.cpp index 2ac3f95c5398220c1d981844a82fd5d0a4b5ab3a..a33848f1a1dac5c143c411414a8eba0c8a50c683 100644 --- a/src/ASPHERE/fix_nve_asphere.cpp +++ b/src/ASPHERE/fix_nve_asphere.cpp @@ -15,9 +15,9 @@ Contributing author: Mike Brown (SNL) ------------------------------------------------------------------------- */ -#include -#include -#include +#include +#include +#include #include "fix_nve_asphere.h" #include "math_extra.h" #include "atom.h" diff --git a/src/ASPHERE/fix_nve_asphere_noforce.cpp b/src/ASPHERE/fix_nve_asphere_noforce.cpp index 34fb57159c69612c19dacd5e1246f6a180532428..d944b68f35a425cceae1f6faec6ed3b5e70a68ac 100644 --- a/src/ASPHERE/fix_nve_asphere_noforce.cpp +++ b/src/ASPHERE/fix_nve_asphere_noforce.cpp @@ -11,9 +11,9 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include -#include -#include +#include +#include +#include #include "fix_nve_asphere_noforce.h" #include "math_extra.h" #include "atom.h" diff --git a/src/ASPHERE/fix_nve_line.cpp b/src/ASPHERE/fix_nve_line.cpp index 554242fb5b4209d797d91c0dbf1f61b6a0594e37..c145e99fcb1a608e540941eb2b6402a58e6a5a33 100644 --- a/src/ASPHERE/fix_nve_line.cpp +++ b/src/ASPHERE/fix_nve_line.cpp @@ -11,9 +11,9 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include -#include -#include +#include +#include +#include #include "fix_nve_line.h" #include "atom.h" #include "atom_vec_line.h" diff --git a/src/ASPHERE/fix_nve_tri.cpp b/src/ASPHERE/fix_nve_tri.cpp index f859ce08c81b75b29adc72ddba388edd406931b6..d06063d905940276941a14f1d3f46e1f95a0ff5d 100644 --- a/src/ASPHERE/fix_nve_tri.cpp +++ b/src/ASPHERE/fix_nve_tri.cpp @@ -11,9 +11,9 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include -#include -#include +#include +#include +#include #include "fix_nve_tri.h" #include "math_extra.h" #include "atom.h" diff --git a/src/ASPHERE/fix_nvt_asphere.cpp b/src/ASPHERE/fix_nvt_asphere.cpp index f43e731c23851520a03f4bd3775d410fff6660d8..5ef91923ebb396b008b07d274c90c625670713e7 100644 --- a/src/ASPHERE/fix_nvt_asphere.cpp +++ b/src/ASPHERE/fix_nvt_asphere.cpp @@ -11,7 +11,7 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include +#include #include "fix_nvt_asphere.h" #include "group.h" #include "modify.h" diff --git a/src/ASPHERE/pair_gayberne.cpp b/src/ASPHERE/pair_gayberne.cpp index 9ff87326ed7a0f88d156a99e1c0123b48fe89d8b..857541957e6512ffad74bdccfb351c3a6a8acd0d 100644 --- a/src/ASPHERE/pair_gayberne.cpp +++ b/src/ASPHERE/pair_gayberne.cpp @@ -15,10 +15,10 @@ Contributing author: Mike Brown (SNL) ------------------------------------------------------------------------- */ -#include -#include -#include -#include +#include +#include +#include +#include #include "pair_gayberne.h" #include "math_extra.h" #include "atom.h" diff --git a/src/ASPHERE/pair_line_lj.cpp b/src/ASPHERE/pair_line_lj.cpp index 83a6f4ea8c998ccef44ac408d3d7b523dc9be061..963ff985c478e3c29a2e11ed8bf3fc37dd5fe536 100644 --- a/src/ASPHERE/pair_line_lj.cpp +++ b/src/ASPHERE/pair_line_lj.cpp @@ -11,10 +11,10 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include -#include -#include -#include +#include +#include +#include +#include #include "pair_line_lj.h" #include "atom.h" #include "atom_vec_line.h" diff --git a/src/ASPHERE/pair_resquared.cpp b/src/ASPHERE/pair_resquared.cpp index caa031a1e83933f1e271216def61b81ee5355337..c477b1b8cfbfdf1a4faa721831874bcb009a7ae1 100644 --- a/src/ASPHERE/pair_resquared.cpp +++ b/src/ASPHERE/pair_resquared.cpp @@ -15,10 +15,10 @@ Contributing author: Mike Brown (SNL) ------------------------------------------------------------------------- */ -#include -#include -#include -#include +#include +#include +#include +#include #include "pair_resquared.h" #include "math_extra.h" #include "atom.h" diff --git a/src/ASPHERE/pair_tri_lj.cpp b/src/ASPHERE/pair_tri_lj.cpp index 4f30b40e9a8976d9abb98913c7d4b30c5ae78278..142caf376425b34bd5f0cad23b76a9436f4ea8be 100644 --- a/src/ASPHERE/pair_tri_lj.cpp +++ b/src/ASPHERE/pair_tri_lj.cpp @@ -11,10 +11,10 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include -#include -#include -#include +#include +#include +#include +#include #include "pair_tri_lj.h" #include "math_extra.h" #include "atom.h" diff --git a/src/BODY/body_nparticle.cpp b/src/BODY/body_nparticle.cpp index 7e3e6f463cd44d5cea74317a7842a5f1aa87ef39..684e5768dae00176fa05eaacf75cf43c1cb60468 100644 --- a/src/BODY/body_nparticle.cpp +++ b/src/BODY/body_nparticle.cpp @@ -11,7 +11,7 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include +#include #include "body_nparticle.h" #include "math_extra.h" #include "atom_vec_body.h" diff --git a/src/BODY/compute_body_local.cpp b/src/BODY/compute_body_local.cpp index e72dd59b25fb214cd6ae536333f2367dfdc1b3c4..df8a76d0fedc1f5951572999615ff9ae67ffbaf5 100644 --- a/src/BODY/compute_body_local.cpp +++ b/src/BODY/compute_body_local.cpp @@ -11,8 +11,8 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include -#include +#include +#include #include "compute_body_local.h" #include "atom.h" #include "atom_vec_body.h" diff --git a/src/BODY/compute_temp_body.cpp b/src/BODY/compute_temp_body.cpp index ec992cea22490b5b05b455980636e48696c16a47..5446fb6d644497a2e9331c745f21e58bc5487644 100644 --- a/src/BODY/compute_temp_body.cpp +++ b/src/BODY/compute_temp_body.cpp @@ -17,7 +17,7 @@ ------------------------------------------------------------------------- */ #include -#include +#include #include "compute_temp_body.h" #include "math_extra.h" #include "atom.h" diff --git a/src/BODY/fix_nh_body.cpp b/src/BODY/fix_nh_body.cpp index a1865dfd182af602bd63d26e778fa5c22f463869..97398424193f37d0b4f34e6268ec09b2ad5e60c4 100644 --- a/src/BODY/fix_nh_body.cpp +++ b/src/BODY/fix_nh_body.cpp @@ -16,9 +16,9 @@ based on FixNHAsphere ------------------------------------------------------------------------- */ -#include -#include -#include +#include +#include +#include #include "math_extra.h" #include "fix_nh_body.h" #include "atom.h" diff --git a/src/BODY/fix_nph_body.cpp b/src/BODY/fix_nph_body.cpp index 99e33a3d22e90d814f9e92415e63024ee04e45dc..e647488bce9ae3de2cc3e232aa7a5bbb8c796679 100644 --- a/src/BODY/fix_nph_body.cpp +++ b/src/BODY/fix_nph_body.cpp @@ -15,7 +15,7 @@ Contributing author: Trung Dac Nguyen (ndactrung@gmail.com) ------------------------------------------------------------------------- */ -#include +#include #include "fix_nph_body.h" #include "modify.h" #include "error.h" diff --git a/src/BODY/fix_npt_body.cpp b/src/BODY/fix_npt_body.cpp index 077a7babd4866ad99e060723ae4cb503d6bc8194..3c30e9e4e92f3825cd3d89da1a46a6f3798f9130 100644 --- a/src/BODY/fix_npt_body.cpp +++ b/src/BODY/fix_npt_body.cpp @@ -15,7 +15,7 @@ Contributing author: Trung Dac Nguyen (ndactrung@gmail.com) ------------------------------------------------------------------------- */ -#include +#include #include "fix_npt_body.h" #include "modify.h" #include "error.h" diff --git a/src/BODY/fix_nve_body.cpp b/src/BODY/fix_nve_body.cpp index edc88ed3b4213fb5eae64a1283e5b1bb88bf14fa..0606723cb77d558c8500c5469e16d64773f962fd 100644 --- a/src/BODY/fix_nve_body.cpp +++ b/src/BODY/fix_nve_body.cpp @@ -11,9 +11,9 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include -#include -#include +#include +#include +#include #include "fix_nve_body.h" #include "math_extra.h" #include "atom.h" diff --git a/src/BODY/fix_nvt_body.cpp b/src/BODY/fix_nvt_body.cpp index 464f42eae91d5cada1c2c0cf8c9b4f6eedce065b..273b5e7fffd2ac3bf0750ed6cfd2548b4f4f4465 100644 --- a/src/BODY/fix_nvt_body.cpp +++ b/src/BODY/fix_nvt_body.cpp @@ -15,7 +15,7 @@ Contributing author: Trung Dac Nguyen (ndactrung@gmail.com) ------------------------------------------------------------------------- */ -#include +#include #include "fix_nvt_body.h" #include "group.h" #include "modify.h" diff --git a/src/BODY/pair_body.cpp b/src/BODY/pair_body.cpp index b1be99731018e2f30ebaa4258a679abb93944472..8c12c0cf36aa0384c50e3745b45c969c8aa29cc2 100644 --- a/src/BODY/pair_body.cpp +++ b/src/BODY/pair_body.cpp @@ -11,10 +11,10 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include -#include -#include -#include +#include +#include +#include +#include #include "pair_body.h" #include "math_extra.h" #include "atom.h" diff --git a/src/CLASS2/angle_class2.cpp b/src/CLASS2/angle_class2.cpp index 7dfdaa17f48dbca47b0dfa17bd4eeddf4b06eb85..24f41bfd587e00d1ec3ae121a9511c0dcf712641 100644 --- a/src/CLASS2/angle_class2.cpp +++ b/src/CLASS2/angle_class2.cpp @@ -15,9 +15,9 @@ Contributing author: Eric Simon (Cray) ------------------------------------------------------------------------- */ -#include -#include -#include +#include +#include +#include #include "angle_class2.h" #include "atom.h" #include "neighbor.h" diff --git a/src/CLASS2/angle_class2.h b/src/CLASS2/angle_class2.h index 1d595d5f6ac8737d58def4dff9109a4d13a09b26..d18f71e1eb74b9a8c852cebc8895b05195e9c90a 100644 --- a/src/CLASS2/angle_class2.h +++ b/src/CLASS2/angle_class2.h @@ -20,7 +20,7 @@ AngleStyle(class2,AngleClass2) #ifndef LMP_ANGLE_CLASS2_H #define LMP_ANGLE_CLASS2_H -#include +#include #include "angle.h" namespace LAMMPS_NS { diff --git a/src/CLASS2/bond_class2.cpp b/src/CLASS2/bond_class2.cpp index b016de0206f5ae52ca61677512a44364d27e92e9..c3dc09715c9c341b57a73e274251cdc35bdeb0da 100644 --- a/src/CLASS2/bond_class2.cpp +++ b/src/CLASS2/bond_class2.cpp @@ -15,8 +15,8 @@ Contributing author: Eric Simon (Cray) ------------------------------------------------------------------------- */ -#include -#include +#include +#include #include "bond_class2.h" #include "atom.h" #include "neighbor.h" diff --git a/src/CLASS2/bond_class2.h b/src/CLASS2/bond_class2.h index 51e2c939a77432100f4833378d53e2dff652c826..f8e294e2b0dae71441151db5aa820db19e441c89 100644 --- a/src/CLASS2/bond_class2.h +++ b/src/CLASS2/bond_class2.h @@ -20,7 +20,7 @@ BondStyle(class2,BondClass2) #ifndef LMP_BOND_CLASS2_H #define LMP_BOND_CLASS2_H -#include +#include #include "bond.h" namespace LAMMPS_NS { diff --git a/src/CLASS2/dihedral_class2.cpp b/src/CLASS2/dihedral_class2.cpp index b79f574829e3c40d3e4f4f2abdbe56a462d22612..c6360dd84643b95fc1996e4cd10e8005b5d3c8b8 100644 --- a/src/CLASS2/dihedral_class2.cpp +++ b/src/CLASS2/dihedral_class2.cpp @@ -15,9 +15,9 @@ Contributing author: Eric Simon (Cray) ------------------------------------------------------------------------- */ -#include -#include -#include +#include +#include +#include #include "dihedral_class2.h" #include "atom.h" #include "neighbor.h" diff --git a/src/CLASS2/dihedral_class2.h b/src/CLASS2/dihedral_class2.h index e8309dad7a94d2b1ebc91c08291185445006297c..9ccf6623a06533c40f823d9cbbdf04b6eda576d0 100644 --- a/src/CLASS2/dihedral_class2.h +++ b/src/CLASS2/dihedral_class2.h @@ -20,7 +20,7 @@ DihedralStyle(class2,DihedralClass2) #ifndef LMP_DIHEDRAL_CLASS2_H #define LMP_DIHEDRAL_CLASS2_H -#include +#include #include "dihedral.h" namespace LAMMPS_NS { diff --git a/src/CLASS2/improper_class2.cpp b/src/CLASS2/improper_class2.cpp index e7c4aa94be8ae6c9fadf0b3938055234e0b694d3..3b3811584d07e4f71a53b986084cd735841decbd 100644 --- a/src/CLASS2/improper_class2.cpp +++ b/src/CLASS2/improper_class2.cpp @@ -15,9 +15,9 @@ Contributing author: Eric Simon (Cray) ------------------------------------------------------------------------- */ -#include -#include -#include +#include +#include +#include #include "improper_class2.h" #include "atom.h" #include "neighbor.h" diff --git a/src/CLASS2/improper_class2.h b/src/CLASS2/improper_class2.h index f814da96c545daee13babb3ca34f53bc03b235ca..f155f67c5c8169fa4125c3f6a19700a3e2ef2129 100644 --- a/src/CLASS2/improper_class2.h +++ b/src/CLASS2/improper_class2.h @@ -20,7 +20,7 @@ ImproperStyle(class2,ImproperClass2) #ifndef LMP_IMPROPER_CLASS2_H #define LMP_IMPROPER_CLASS2_H -#include +#include #include "improper.h" namespace LAMMPS_NS { diff --git a/src/CLASS2/pair_lj_class2.cpp b/src/CLASS2/pair_lj_class2.cpp index 0b90b2717e314cda29d441465214b2767dff152d..e255807ab6a5f217f076892d9a695d5d5d4cd787 100644 --- a/src/CLASS2/pair_lj_class2.cpp +++ b/src/CLASS2/pair_lj_class2.cpp @@ -11,9 +11,9 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include -#include -#include +#include +#include +#include #include "pair_lj_class2.h" #include "atom.h" #include "comm.h" diff --git a/src/CLASS2/pair_lj_class2_coul_cut.cpp b/src/CLASS2/pair_lj_class2_coul_cut.cpp index 395953e0a9c7a70fa9bb9d3cd8c4834c1923a714..5cd5ad0e32cc1ae4df4242144d4438c3f9996a7b 100644 --- a/src/CLASS2/pair_lj_class2_coul_cut.cpp +++ b/src/CLASS2/pair_lj_class2_coul_cut.cpp @@ -11,9 +11,9 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include -#include -#include +#include +#include +#include #include "pair_lj_class2_coul_cut.h" #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 9278703e2a4685898b97a4d0e1ebf3bca6a6b2ff..bf892bc894fd699a1d368a409b0c609bffef0134 100644 --- a/src/CLASS2/pair_lj_class2_coul_long.cpp +++ b/src/CLASS2/pair_lj_class2_coul_long.cpp @@ -11,10 +11,10 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include -#include -#include -#include +#include +#include +#include +#include #include "pair_lj_class2_coul_long.h" #include "atom.h" #include "comm.h" diff --git a/src/COLLOID/fix_wall_colloid.cpp b/src/COLLOID/fix_wall_colloid.cpp index 651e0da4f8e195f7f9abdec004acf44753ba2667..095d01eef3019b6a5735c93dfa5fb093feeca65d 100644 --- a/src/COLLOID/fix_wall_colloid.cpp +++ b/src/COLLOID/fix_wall_colloid.cpp @@ -15,8 +15,8 @@ Contributing authors: Jeremy Lechman (SNL) ------------------------------------------------------------------------- */ -#include -#include +#include +#include #include "fix_wall_colloid.h" #include "atom.h" #include "atom_vec.h" diff --git a/src/COLLOID/pair_brownian.cpp b/src/COLLOID/pair_brownian.cpp index 2bf01303b44aa1193d9e885fc3f49e8ec27f5463..e532c06c863f28eba94c5b93cd8a8ef01dd78a23 100644 --- a/src/COLLOID/pair_brownian.cpp +++ b/src/COLLOID/pair_brownian.cpp @@ -15,10 +15,10 @@ Contributing authors: Amit Kumar and Michael Bybee (UIUC) ------------------------------------------------------------------------- */ -#include -#include -#include -#include +#include +#include +#include +#include #include "pair_brownian.h" #include "atom.h" #include "atom_vec.h" diff --git a/src/COLLOID/pair_brownian_poly.cpp b/src/COLLOID/pair_brownian_poly.cpp index 84c56109d13cbb6f788cd65135a8ca9a268ca853..c6d5def2fafd80be6e70052159ef9b6803effd74 100644 --- a/src/COLLOID/pair_brownian_poly.cpp +++ b/src/COLLOID/pair_brownian_poly.cpp @@ -16,10 +16,10 @@ Dave Heine (Corning), polydispersity ------------------------------------------------------------------------- */ -#include -#include -#include -#include +#include +#include +#include +#include #include "pair_brownian_poly.h" #include "atom.h" #include "atom_vec.h" diff --git a/src/COLLOID/pair_colloid.cpp b/src/COLLOID/pair_colloid.cpp index 983b973e0e096e245d1b3eb9d3b1aae48888a165..4448d6e110ec8ca21840eab06258692e356ca650 100644 --- a/src/COLLOID/pair_colloid.cpp +++ b/src/COLLOID/pair_colloid.cpp @@ -15,10 +15,10 @@ Contributing author: Pieter in 't Veld (SNL) ------------------------------------------------------------------------- */ -#include -#include -#include -#include +#include +#include +#include +#include #include "pair_colloid.h" #include "atom.h" #include "comm.h" diff --git a/src/COLLOID/pair_lubricate.cpp b/src/COLLOID/pair_lubricate.cpp index 93cb48a15db6355f79d25264a9dd0bed35681101..5410a4c7731b493bd456f1a6e8658362a9ad6adf 100644 --- a/src/COLLOID/pair_lubricate.cpp +++ b/src/COLLOID/pair_lubricate.cpp @@ -16,10 +16,10 @@ Amit Kumar and Michael Bybee (UIUC) ------------------------------------------------------------------------- */ -#include -#include -#include -#include +#include +#include +#include +#include #include "pair_lubricate.h" #include "atom.h" #include "atom_vec.h" diff --git a/src/COLLOID/pair_lubricateU.cpp b/src/COLLOID/pair_lubricateU.cpp index 5d0a4243a7fbb59e021dea3c9179146730c264c8..11fb2131577c6f32a20358fc9a769038d20e0075 100644 --- a/src/COLLOID/pair_lubricateU.cpp +++ b/src/COLLOID/pair_lubricateU.cpp @@ -16,10 +16,10 @@ ------------------------------------------------------------------------- */ #include -#include -#include -#include -#include +#include +#include +#include +#include #include "pair_lubricateU.h" #include "atom.h" #include "atom_vec.h" diff --git a/src/COLLOID/pair_lubricateU_poly.cpp b/src/COLLOID/pair_lubricateU_poly.cpp index 428aa41cb6f9c2000549db290f45d813d6805d45..90ac848d2653479a34bcf2850d214fe8340b5a14 100644 --- a/src/COLLOID/pair_lubricateU_poly.cpp +++ b/src/COLLOID/pair_lubricateU_poly.cpp @@ -18,10 +18,10 @@ ------------------------------------------------------------------------- */ #include -#include -#include -#include -#include +#include +#include +#include +#include #include "pair_lubricateU_poly.h" #include "atom.h" #include "atom_vec.h" diff --git a/src/COLLOID/pair_lubricate_poly.cpp b/src/COLLOID/pair_lubricate_poly.cpp index 2561ca3637317cfe1b640d070b866ece285566cd..0ed87c37be8834d051163d8da2666d5a860fdc19 100644 --- a/src/COLLOID/pair_lubricate_poly.cpp +++ b/src/COLLOID/pair_lubricate_poly.cpp @@ -17,10 +17,10 @@ Dave Heine (Corning), polydispersity ------------------------------------------------------------------------- */ -#include -#include -#include -#include +#include +#include +#include +#include #include "pair_lubricate_poly.h" #include "atom.h" #include "atom_vec.h" diff --git a/src/COLLOID/pair_yukawa_colloid.cpp b/src/COLLOID/pair_yukawa_colloid.cpp index 87fa7f542285d4285e7229a0b61a893ea4d50eb8..5965fd3aa86913824e3a21be449d607a89f87e83 100644 --- a/src/COLLOID/pair_yukawa_colloid.cpp +++ b/src/COLLOID/pair_yukawa_colloid.cpp @@ -15,8 +15,8 @@ Contributing authors: Randy Schunk (Sandia) ------------------------------------------------------------------------- */ -#include -#include +#include +#include #include "pair_yukawa_colloid.h" #include "atom.h" #include "atom_vec.h" diff --git a/src/COMPRESS/dump_atom_gz.cpp b/src/COMPRESS/dump_atom_gz.cpp index dfd23e2b4a8bc17d859f62a276591ebd28cb925e..fb605b74cee56bae62e53ab4f0251f7e612d3aa1 100644 --- a/src/COMPRESS/dump_atom_gz.cpp +++ b/src/COMPRESS/dump_atom_gz.cpp @@ -16,7 +16,7 @@ #include "error.h" #include "update.h" -#include +#include using namespace LAMMPS_NS; diff --git a/src/COMPRESS/dump_cfg_gz.cpp b/src/COMPRESS/dump_cfg_gz.cpp index 6f653e73ee2dcf545994c4e95d72a72c48115dd8..a1ffa92ec859958c616a310c7705c088f35114c0 100644 --- a/src/COMPRESS/dump_cfg_gz.cpp +++ b/src/COMPRESS/dump_cfg_gz.cpp @@ -17,7 +17,7 @@ #include "error.h" #include "update.h" -#include +#include using namespace LAMMPS_NS; #define UNWRAPEXPAND 10.0 diff --git a/src/COMPRESS/dump_custom_gz.cpp b/src/COMPRESS/dump_custom_gz.cpp index 1905577a12bbc5ca50decffa659bb300d6068160..52d67445be0ca940fdafc3b08ef8ba9bb93c51ab 100644 --- a/src/COMPRESS/dump_custom_gz.cpp +++ b/src/COMPRESS/dump_custom_gz.cpp @@ -16,7 +16,7 @@ #include "error.h" #include "update.h" -#include +#include using namespace LAMMPS_NS; diff --git a/src/COMPRESS/dump_xyz_gz.cpp b/src/COMPRESS/dump_xyz_gz.cpp index 1a4474cba2929ff918777bf3de04c8326425befc..047ad8652f9587bdba8d306be030a357711ccc78 100644 --- a/src/COMPRESS/dump_xyz_gz.cpp +++ b/src/COMPRESS/dump_xyz_gz.cpp @@ -16,7 +16,7 @@ #include "error.h" #include "update.h" -#include +#include using namespace LAMMPS_NS; diff --git a/src/CORESHELL/compute_temp_cs.cpp b/src/CORESHELL/compute_temp_cs.cpp index d2345684dc61ff6dbb17c49286a77f9daf939a27..03ebfa154d5e2bf78dd6c0e731f5a6f4e2e92a8f 100644 --- a/src/CORESHELL/compute_temp_cs.cpp +++ b/src/CORESHELL/compute_temp_cs.cpp @@ -17,9 +17,9 @@ ------------------------------------------------------------------------- */ #include -#include -#include -#include +#include +#include +#include #include "compute_temp_cs.h" #include "atom.h" #include "atom_vec.h" diff --git a/src/CORESHELL/pair_born_coul_dsf_cs.cpp b/src/CORESHELL/pair_born_coul_dsf_cs.cpp index 4a5c9da07e0256f4c11ee44c7868b3785045e6a6..549c7c03481c6c4481085fe0a414780291687302 100644 --- a/src/CORESHELL/pair_born_coul_dsf_cs.cpp +++ b/src/CORESHELL/pair_born_coul_dsf_cs.cpp @@ -16,10 +16,10 @@ References: Fennell and Gezelter, JCP 124, 234104 (2006) ------------------------------------------------------------------------- */ -#include -#include -#include -#include +#include +#include +#include +#include #include "pair_born_coul_dsf_cs.h" #include "atom.h" #include "comm.h" diff --git a/src/CORESHELL/pair_born_coul_long_cs.cpp b/src/CORESHELL/pair_born_coul_long_cs.cpp index 7d0d9c9416a4ad46ded5be36dbbaadd6a474ab38..76f6eb387df5f2df2ca8e7b4f3c05afc3ae78574 100644 --- a/src/CORESHELL/pair_born_coul_long_cs.cpp +++ b/src/CORESHELL/pair_born_coul_long_cs.cpp @@ -15,10 +15,10 @@ Contributing author: Hendrik Heenen (hendrik.heenen@mytum.de) ------------------------------------------------------------------------- */ -#include -#include -#include -#include +#include +#include +#include +#include #include "pair_born_coul_long_cs.h" #include "atom.h" #include "comm.h" diff --git a/src/CORESHELL/pair_born_coul_wolf_cs.cpp b/src/CORESHELL/pair_born_coul_wolf_cs.cpp index f39e2ca81631b7ce85ce8b70b4649c1fcaf34f07..84179ce50ab7a8d20e27042480ccade65d331dd3 100644 --- a/src/CORESHELL/pair_born_coul_wolf_cs.cpp +++ b/src/CORESHELL/pair_born_coul_wolf_cs.cpp @@ -12,10 +12,10 @@ ------------------------------------------------------------------------- */ -#include -#include -#include -#include +#include +#include +#include +#include #include "pair_born_coul_wolf_cs.h" #include "atom.h" #include "comm.h" diff --git a/src/CORESHELL/pair_buck_coul_long_cs.cpp b/src/CORESHELL/pair_buck_coul_long_cs.cpp index 822ec1049725ac2d2470b653ec9e68adc178702a..ea072d44a13d8a88fbc80e31f6339fdbe37e538d 100644 --- a/src/CORESHELL/pair_buck_coul_long_cs.cpp +++ b/src/CORESHELL/pair_buck_coul_long_cs.cpp @@ -15,10 +15,10 @@ Contributing author: Hendrik Heenen (hendrik.heenen@mytum.de) ------------------------------------------------------------------------- */ -#include -#include -#include -#include +#include +#include +#include +#include #include "pair_buck_coul_long_cs.h" #include "atom.h" #include "comm.h" diff --git a/src/CORESHELL/pair_coul_long_cs.cpp b/src/CORESHELL/pair_coul_long_cs.cpp index 9177e9a0613ce7b61f3028fbad65d7076861664e..b21465384199c5a58a8fa3c03a700c29faadef17 100644 --- a/src/CORESHELL/pair_coul_long_cs.cpp +++ b/src/CORESHELL/pair_coul_long_cs.cpp @@ -15,10 +15,10 @@ Contributing author: Hendrik Heenen (hendrik.heenen@mytum.de) ------------------------------------------------------------------------- */ -#include -#include -#include -#include +#include +#include +#include +#include #include "pair_coul_long_cs.h" #include "atom.h" #include "comm.h" diff --git a/src/CORESHELL/pair_coul_wolf_cs.cpp b/src/CORESHELL/pair_coul_wolf_cs.cpp index 5f277dcdd2e49e8b8bb37b639c4c9109c624388e..b50f14833e9664552022c3d54d36c4e2f953cc28 100644 --- a/src/CORESHELL/pair_coul_wolf_cs.cpp +++ b/src/CORESHELL/pair_coul_wolf_cs.cpp @@ -12,10 +12,10 @@ ------------------------------------------------------------------------- */ -#include -#include -#include -#include +#include +#include +#include +#include #include "pair_coul_wolf_cs.h" #include "atom.h" #include "comm.h" diff --git a/src/CORESHELL/pair_lj_cut_coul_long_cs.cpp b/src/CORESHELL/pair_lj_cut_coul_long_cs.cpp index c660eee3bc19569578aae1aa5e661d2ca301d2cd..8caefc0e66096283ca363c207a6290bfcea5183d 100644 --- a/src/CORESHELL/pair_lj_cut_coul_long_cs.cpp +++ b/src/CORESHELL/pair_lj_cut_coul_long_cs.cpp @@ -15,10 +15,10 @@ Contributing author: Hendrik Heenen (hendrik.heenen@mytum.de) ------------------------------------------------------------------------- */ -#include -#include -#include -#include +#include +#include +#include +#include #include "pair_lj_cut_coul_long_cs.h" #include "atom.h" #include "comm.h" diff --git a/src/DIPOLE/atom_vec_dipole.cpp b/src/DIPOLE/atom_vec_dipole.cpp index 5d69f03376b976fee756534660b8510bbe03162c..c304ae3bc660598eb421e2d67c4af4400886ec55 100644 --- a/src/DIPOLE/atom_vec_dipole.cpp +++ b/src/DIPOLE/atom_vec_dipole.cpp @@ -11,8 +11,8 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include -#include +#include +#include #include "atom_vec_dipole.h" #include "atom.h" #include "comm.h" diff --git a/src/DIPOLE/pair_lj_cut_dipole_cut.cpp b/src/DIPOLE/pair_lj_cut_dipole_cut.cpp index af987bf2585f962d6c18f8fec4acd7306210cc8f..6af9b457246fb0bc446dfcc37ef1449806b745da 100644 --- a/src/DIPOLE/pair_lj_cut_dipole_cut.cpp +++ b/src/DIPOLE/pair_lj_cut_dipole_cut.cpp @@ -11,8 +11,9 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include -#include +#include +#include +#include #include "pair_lj_cut_dipole_cut.h" #include "atom.h" #include "neighbor.h" @@ -22,7 +23,6 @@ #include "memory.h" #include "error.h" #include "update.h" -#include using namespace LAMMPS_NS; diff --git a/src/DIPOLE/pair_lj_cut_dipole_long.cpp b/src/DIPOLE/pair_lj_cut_dipole_long.cpp index 63f48bea8116b026b29af9dee1d74d2726f21c08..817a120e3d084b9301095d2364e8402586a04b57 100644 --- a/src/DIPOLE/pair_lj_cut_dipole_long.cpp +++ b/src/DIPOLE/pair_lj_cut_dipole_long.cpp @@ -11,10 +11,10 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include -#include -#include -#include +#include +#include +#include +#include #include "pair_lj_cut_dipole_long.h" #include "atom.h" #include "comm.h" @@ -26,7 +26,6 @@ #include "memory.h" #include "error.h" #include "update.h" -#include using namespace LAMMPS_NS; diff --git a/src/DIPOLE/pair_lj_long_dipole_long.cpp b/src/DIPOLE/pair_lj_long_dipole_long.cpp index 262727c5b600de8d2554a4a3ab9e673bf6137f2b..1635bd4f636f33d3b4f678aef45a4d2b4727fe2f 100644 --- a/src/DIPOLE/pair_lj_long_dipole_long.cpp +++ b/src/DIPOLE/pair_lj_long_dipole_long.cpp @@ -15,10 +15,10 @@ Contributing author: Pieter J. in 't Veld and Stan Moore (Sandia) ------------------------------------------------------------------------- */ -#include -#include -#include -#include +#include +#include +#include +#include #include "math_const.h" #include "math_vector.h" #include "pair_lj_long_dipole_long.h" diff --git a/src/Depend.sh b/src/Depend.sh index a83a99ffb5da5bf320b8a28a151b33af4eb189f6..9fe30e658325bbbf385e33e543065a1ab32eff44 100644 --- a/src/Depend.sh +++ b/src/Depend.sh @@ -134,6 +134,7 @@ fi if (test $1 = "USER-MISC") then depend GPU depend USER-OMP + depend USER-INTEL fi if (test $1 = "USER-REAXC") then diff --git a/src/GPU/fix_gpu.cpp b/src/GPU/fix_gpu.cpp index 87db73bd12d64bd792d684d3903c9b713f642b48..268a7410329176672eee4a6e8ca8a3428b77aa50 100644 --- a/src/GPU/fix_gpu.cpp +++ b/src/GPU/fix_gpu.cpp @@ -11,8 +11,8 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include -#include +#include +#include #include "fix_gpu.h" #include "atom.h" #include "force.h" diff --git a/src/GPU/gpu_extra.h b/src/GPU/gpu_extra.h index ddb0b5ceaa51cf1bae036d014f6aa24220bdc98d..56a4f15f1bff5a18ee050badf8acfb420c97b28b 100644 --- a/src/GPU/gpu_extra.h +++ b/src/GPU/gpu_extra.h @@ -61,13 +61,13 @@ namespace GPU_EXTRA { else error->all(FLERR,"Unknown error in GPU library"); } - }; + } inline void gpu_ready(LAMMPS_NS::Modify *modify, LAMMPS_NS::Error *error) { int ifix = modify->find_fix("package_gpu"); if (ifix < 0) error->all(FLERR,"The package gpu command is required for gpu styles"); - }; + } } #endif diff --git a/src/GPU/pair_beck_gpu.cpp b/src/GPU/pair_beck_gpu.cpp index c81318664086f895c7665d7bece4e25cd0ec40f8..f929dd437f8b808f4551850446ba7027b3d55799 100644 --- a/src/GPU/pair_beck_gpu.cpp +++ b/src/GPU/pair_beck_gpu.cpp @@ -15,9 +15,10 @@ Contributing author: Trung Dac Nguyen (ORNL) ------------------------------------------------------------------------- */ -#include -#include -#include +#include +#include +#include +#include #include "pair_beck_gpu.h" #include "atom.h" #include "atom_vec.h" @@ -32,7 +33,6 @@ #include "universe.h" #include "update.h" #include "domain.h" -#include #include "gpu_extra.h" #include "math_special.h" diff --git a/src/GPU/pair_born_coul_long_gpu.cpp b/src/GPU/pair_born_coul_long_gpu.cpp index b6a7e57038f6c217233768c265b513c124539f65..c3c3fee40c804314cb982db435a86731f2cb03f2 100644 --- a/src/GPU/pair_born_coul_long_gpu.cpp +++ b/src/GPU/pair_born_coul_long_gpu.cpp @@ -15,9 +15,10 @@ Contributing author: Trung Dac Nguyen (ORNL) ------------------------------------------------------------------------- */ -#include -#include -#include +#include +#include +#include +#include #include "pair_born_coul_long_gpu.h" #include "atom.h" #include "atom_vec.h" @@ -33,7 +34,6 @@ #include "universe.h" #include "update.h" #include "domain.h" -#include #include "kspace.h" #include "gpu_extra.h" diff --git a/src/GPU/pair_born_coul_wolf_gpu.cpp b/src/GPU/pair_born_coul_wolf_gpu.cpp index 931252be6bf92693a548fc9bc73aefb37d9a2ad7..df1922d76a00968b83490a639489faefb127b665 100644 --- a/src/GPU/pair_born_coul_wolf_gpu.cpp +++ b/src/GPU/pair_born_coul_wolf_gpu.cpp @@ -15,9 +15,10 @@ Contributing authors: Trung Dac Nguyen (ORNL) ------------------------------------------------------------------------- */ -#include -#include -#include +#include +#include +#include +#include #include "pair_born_coul_wolf_gpu.h" #include "atom.h" #include "atom_vec.h" @@ -33,7 +34,6 @@ #include "universe.h" #include "update.h" #include "domain.h" -#include #include "gpu_extra.h" using namespace LAMMPS_NS; diff --git a/src/GPU/pair_born_gpu.cpp b/src/GPU/pair_born_gpu.cpp index 46729ab77c577059c256d4ce7200079d4bf7fb54..92a7a85997fcaa6609e1f40a553accd0361affb8 100644 --- a/src/GPU/pair_born_gpu.cpp +++ b/src/GPU/pair_born_gpu.cpp @@ -15,9 +15,10 @@ Contributing author: Trung Dac Nguyen (ORNL) ------------------------------------------------------------------------- */ -#include -#include -#include +#include +#include +#include +#include #include "pair_born_gpu.h" #include "atom.h" #include "atom_vec.h" @@ -32,7 +33,6 @@ #include "universe.h" #include "update.h" #include "domain.h" -#include #include "gpu_extra.h" using namespace LAMMPS_NS; diff --git a/src/GPU/pair_buck_coul_cut_gpu.cpp b/src/GPU/pair_buck_coul_cut_gpu.cpp index e74020dd3a61f653cdaf008987480f1033cf2da7..6396e301e3f56e0fddcd040a4520b345bd34098f 100644 --- a/src/GPU/pair_buck_coul_cut_gpu.cpp +++ b/src/GPU/pair_buck_coul_cut_gpu.cpp @@ -15,9 +15,10 @@ Contributing authors: Trung Dac Nguyen (ORNL) ------------------------------------------------------------------------- */ -#include -#include -#include +#include +#include +#include +#include #include "pair_buck_coul_cut_gpu.h" #include "atom.h" #include "atom_vec.h" @@ -32,7 +33,6 @@ #include "universe.h" #include "update.h" #include "domain.h" -#include #include "gpu_extra.h" using namespace LAMMPS_NS; diff --git a/src/GPU/pair_buck_coul_long_gpu.cpp b/src/GPU/pair_buck_coul_long_gpu.cpp index c2a37fc3dc5fef8859aab5f8f2e84db58afdde23..73821cee8aaf826ac341655a2c48518bf9b0507f 100644 --- a/src/GPU/pair_buck_coul_long_gpu.cpp +++ b/src/GPU/pair_buck_coul_long_gpu.cpp @@ -15,9 +15,10 @@ Contributing author: Trung Dac Nguyen (ORNL) ------------------------------------------------------------------------- */ -#include -#include -#include +#include +#include +#include +#include #include "pair_buck_coul_long_gpu.h" #include "atom.h" #include "atom_vec.h" @@ -32,7 +33,6 @@ #include "universe.h" #include "update.h" #include "domain.h" -#include #include "kspace.h" #include "gpu_extra.h" diff --git a/src/GPU/pair_buck_gpu.cpp b/src/GPU/pair_buck_gpu.cpp index 1e9b838ec805301151c0f7fa892fa6f0bf4aded4..20302e4f1a14246b4e76037af59791cd380bd5c2 100644 --- a/src/GPU/pair_buck_gpu.cpp +++ b/src/GPU/pair_buck_gpu.cpp @@ -15,9 +15,10 @@ Contributing author: Trung Dac Nguyen (ORNL) ------------------------------------------------------------------------- */ -#include -#include -#include +#include +#include +#include +#include #include "pair_buck_gpu.h" #include "atom.h" #include "atom_vec.h" @@ -32,7 +33,6 @@ #include "universe.h" #include "update.h" #include "domain.h" -#include #include "gpu_extra.h" using namespace LAMMPS_NS; diff --git a/src/GPU/pair_colloid_gpu.cpp b/src/GPU/pair_colloid_gpu.cpp index d4e8224238375a1fd0b432a522c57c9370d48b9e..7bbac32ed3c287c13785fa31db863d48b33285ba 100644 --- a/src/GPU/pair_colloid_gpu.cpp +++ b/src/GPU/pair_colloid_gpu.cpp @@ -15,9 +15,10 @@ Contributing author: Trung Dac Nguyen (ORNL) ------------------------------------------------------------------------- */ -#include -#include -#include +#include +#include +#include +#include #include "pair_colloid_gpu.h" #include "atom.h" #include "atom_vec.h" @@ -32,7 +33,6 @@ #include "universe.h" #include "update.h" #include "domain.h" -#include #include "gpu_extra.h" using namespace LAMMPS_NS; diff --git a/src/GPU/pair_coul_cut_gpu.cpp b/src/GPU/pair_coul_cut_gpu.cpp index c66a0a8ef4b3891f82e96ad867d0382b4684cd7e..d5d9b10abba4d1a676cfcb804d2aaadafc9c80cc 100644 --- a/src/GPU/pair_coul_cut_gpu.cpp +++ b/src/GPU/pair_coul_cut_gpu.cpp @@ -15,9 +15,10 @@ Contributing author: Trung Dac Nguyen ------------------------------------------------------------------------- */ -#include -#include -#include +#include +#include +#include +#include #include "pair_coul_cut_gpu.h" #include "atom.h" #include "atom_vec.h" @@ -32,7 +33,6 @@ #include "universe.h" #include "update.h" #include "domain.h" -#include #include "gpu_extra.h" using namespace LAMMPS_NS; diff --git a/src/GPU/pair_coul_debye_gpu.cpp b/src/GPU/pair_coul_debye_gpu.cpp index 2b5d608fc7f142d84270deae65e7cefc54e11f76..9fd28bf9c5f01863c6a6e28c999b5f4b9e2da97c 100644 --- a/src/GPU/pair_coul_debye_gpu.cpp +++ b/src/GPU/pair_coul_debye_gpu.cpp @@ -15,9 +15,10 @@ Contributing author: Trung Dac Nguyen (ndtrung@umich.edu) ------------------------------------------------------------------------- */ -#include -#include -#include +#include +#include +#include +#include #include "pair_coul_debye_gpu.h" #include "atom.h" #include "atom_vec.h" @@ -32,7 +33,6 @@ #include "universe.h" #include "update.h" #include "domain.h" -#include #include "gpu_extra.h" using namespace LAMMPS_NS; diff --git a/src/GPU/pair_coul_dsf_gpu.cpp b/src/GPU/pair_coul_dsf_gpu.cpp index d2d060281c23eeaf36f5fecae7ae5baecc7db906..75168c3cd96d3c2538d78e64de00d5a0dbb06206 100644 --- a/src/GPU/pair_coul_dsf_gpu.cpp +++ b/src/GPU/pair_coul_dsf_gpu.cpp @@ -15,9 +15,10 @@ Contributing author: Trung Dac Nguyen (ORNL) ------------------------------------------------------------------------- */ -#include -#include -#include +#include +#include +#include +#include #include "pair_coul_dsf_gpu.h" #include "atom.h" #include "atom_vec.h" @@ -32,7 +33,6 @@ #include "universe.h" #include "update.h" #include "domain.h" -#include #include "gpu_extra.h" #define MY_PIS 1.77245385090551602729 diff --git a/src/GPU/pair_coul_long_gpu.cpp b/src/GPU/pair_coul_long_gpu.cpp index 465d82232f54da2ad4b5687a2c548530652764d0..2f12e41b0cc6af68cfe0a792357c88b9c19c3b87 100644 --- a/src/GPU/pair_coul_long_gpu.cpp +++ b/src/GPU/pair_coul_long_gpu.cpp @@ -15,9 +15,10 @@ Contributing author: Axel Kohlmeyer (Temple) ------------------------------------------------------------------------- */ -#include -#include -#include +#include +#include +#include +#include #include "pair_coul_long_gpu.h" #include "atom.h" #include "atom_vec.h" @@ -32,7 +33,6 @@ #include "universe.h" #include "update.h" #include "domain.h" -#include #include "kspace.h" #include "gpu_extra.h" diff --git a/src/GPU/pair_dpd_gpu.cpp b/src/GPU/pair_dpd_gpu.cpp index c82ed97485851fada7d1f71ab12c21c880d44664..293a82ffa9eaddd5aaf0dde87e468f35bcea0531 100644 --- a/src/GPU/pair_dpd_gpu.cpp +++ b/src/GPU/pair_dpd_gpu.cpp @@ -15,9 +15,10 @@ Contributing author: Trung Dac Nguyen (ORNL) ------------------------------------------------------------------------- */ -#include -#include -#include +#include +#include +#include +#include #include "pair_dpd_gpu.h" #include "atom.h" #include "atom_vec.h" @@ -33,7 +34,6 @@ #include "universe.h" #include "update.h" #include "domain.h" -#include #include "gpu_extra.h" using namespace LAMMPS_NS; diff --git a/src/GPU/pair_dpd_tstat_gpu.cpp b/src/GPU/pair_dpd_tstat_gpu.cpp index e051a13a0b2f947570d803a25bb584d69a5bb3f0..bf02570f439dbd8f06b786d5b89d112f2dceac06 100644 --- a/src/GPU/pair_dpd_tstat_gpu.cpp +++ b/src/GPU/pair_dpd_tstat_gpu.cpp @@ -15,9 +15,10 @@ Contributing author: Trung Dac Nguyen (ORNL) ------------------------------------------------------------------------- */ -#include -#include -#include +#include +#include +#include +#include #include "pair_dpd_tstat_gpu.h" #include "atom.h" #include "atom_vec.h" @@ -33,7 +34,6 @@ #include "universe.h" #include "update.h" #include "domain.h" -#include #include "gpu_extra.h" using namespace LAMMPS_NS; diff --git a/src/GPU/pair_eam_alloy_gpu.cpp b/src/GPU/pair_eam_alloy_gpu.cpp index 9b42b0a14fab56b44652942973fd122a7fe113da..3a8e440bdc0c88164e3e3f8c3ea17def4659bb4e 100644 --- a/src/GPU/pair_eam_alloy_gpu.cpp +++ b/src/GPU/pair_eam_alloy_gpu.cpp @@ -15,9 +15,9 @@ Contributing authors: Trung Dac Nguyen (ORNL), W. Michael Brown (ORNL) ------------------------------------------------------------------------- */ -#include -#include -#include +#include +#include +#include #include "pair_eam_alloy_gpu.h" #include "atom.h" #include "force.h" diff --git a/src/GPU/pair_eam_fs_gpu.cpp b/src/GPU/pair_eam_fs_gpu.cpp index c29b49631ce210121df7479b3fc60867bca31438..51681d563bc94894015219bb7d3dd5a69fbc436a 100644 --- a/src/GPU/pair_eam_fs_gpu.cpp +++ b/src/GPU/pair_eam_fs_gpu.cpp @@ -15,9 +15,9 @@ Contributing authors: Trung Dac Nguyen (ORNL), W. Michael Brown (ORNL) ------------------------------------------------------------------------- */ -#include -#include -#include +#include +#include +#include #include "pair_eam_fs_gpu.h" #include "atom.h" #include "force.h" diff --git a/src/GPU/pair_eam_gpu.cpp b/src/GPU/pair_eam_gpu.cpp index ea75ff8ca843637285083729e015f637063a3784..e2eb9dacedd2c5d7c95e9cbe029b4bb14dc4bc74 100644 --- a/src/GPU/pair_eam_gpu.cpp +++ b/src/GPU/pair_eam_gpu.cpp @@ -15,10 +15,10 @@ Contributing authors: Trung Dac Nguyen (ORNL), W. Michael Brown (ORNL) ------------------------------------------------------------------------- */ -#include -#include -#include -#include +#include +#include +#include +#include #include "pair_eam_gpu.h" #include "atom.h" #include "force.h" diff --git a/src/GPU/pair_eam_gpu.h b/src/GPU/pair_eam_gpu.h index 2c4731d9cf105b93a118756c4b62ee9062391b03..099529f3df90c766d0385dcb0319294b6f28c4b4 100644 --- a/src/GPU/pair_eam_gpu.h +++ b/src/GPU/pair_eam_gpu.h @@ -20,7 +20,7 @@ PairStyle(eam/gpu,PairEAMGPU) #ifndef LMP_PAIR_EAM_GPU_H #define LMP_PAIR_EAM_GPU_H -#include +#include #include "pair_eam.h" namespace LAMMPS_NS { diff --git a/src/GPU/pair_gauss_gpu.cpp b/src/GPU/pair_gauss_gpu.cpp index 01cc63a9f9a49c378b7318cb36b9b6143269d853..f99a10a6809e5abbce5504dc2705650a3347ec7e 100644 --- a/src/GPU/pair_gauss_gpu.cpp +++ b/src/GPU/pair_gauss_gpu.cpp @@ -15,9 +15,10 @@ Contributing author: Trung Dac Nguyen (ORNL) ------------------------------------------------------------------------- */ -#include -#include -#include +#include +#include +#include +#include #include "pair_gauss_gpu.h" #include "atom.h" #include "atom_vec.h" @@ -32,7 +33,6 @@ #include "universe.h" #include "update.h" #include "domain.h" -#include #include "gpu_extra.h" using namespace LAMMPS_NS; diff --git a/src/GPU/pair_gayberne_gpu.cpp b/src/GPU/pair_gayberne_gpu.cpp index aae8fb2b7118e593edcf495e52229bfbfe5e4f8b..8bd5eb073fd6f18e9f6f4b4b7ce67539bf38fd53 100644 --- a/src/GPU/pair_gayberne_gpu.cpp +++ b/src/GPU/pair_gayberne_gpu.cpp @@ -15,9 +15,10 @@ Contributing author: Mike Brown (SNL) ------------------------------------------------------------------------- */ -#include -#include -#include +#include +#include +#include +#include #include "pair_gayberne_gpu.h" #include "math_extra.h" #include "atom.h" @@ -34,7 +35,6 @@ #include "universe.h" #include "domain.h" #include "update.h" -#include #include "gpu_extra.h" using namespace LAMMPS_NS; diff --git a/src/GPU/pair_lj96_cut_gpu.cpp b/src/GPU/pair_lj96_cut_gpu.cpp index 813daa4da24f33c4cf535146cd03a3d941fa866b..800f13ef60f3157eb55b08269f321abecce7228d 100644 --- a/src/GPU/pair_lj96_cut_gpu.cpp +++ b/src/GPU/pair_lj96_cut_gpu.cpp @@ -15,9 +15,10 @@ Contributing author: Mike Brown (SNL) ------------------------------------------------------------------------- */ -#include -#include -#include +#include +#include +#include +#include #include "pair_lj96_cut_gpu.h" #include "atom.h" #include "atom_vec.h" @@ -32,7 +33,6 @@ #include "universe.h" #include "update.h" #include "domain.h" -#include #include "gpu_extra.h" using namespace LAMMPS_NS; diff --git a/src/GPU/pair_lj_charmm_coul_long_gpu.cpp b/src/GPU/pair_lj_charmm_coul_long_gpu.cpp index b951567f45db68eb2a1699dfc4696bfcd6463e52..8c806053d4f2fb71a34047d1277c9bbd5956ec4b 100644 --- a/src/GPU/pair_lj_charmm_coul_long_gpu.cpp +++ b/src/GPU/pair_lj_charmm_coul_long_gpu.cpp @@ -15,9 +15,10 @@ Contributing author: Mike Brown (SNL) ------------------------------------------------------------------------- */ -#include -#include -#include +#include +#include +#include +#include #include "pair_lj_charmm_coul_long_gpu.h" #include "atom.h" #include "atom_vec.h" @@ -32,7 +33,6 @@ #include "universe.h" #include "update.h" #include "domain.h" -#include #include "kspace.h" #include "gpu_extra.h" diff --git a/src/GPU/pair_lj_class2_coul_long_gpu.cpp b/src/GPU/pair_lj_class2_coul_long_gpu.cpp index f7c874cb65e7ed50aa385be7da882e906acde79c..214ff306db0d8ac22903357f2bf20ac324963d6a 100644 --- a/src/GPU/pair_lj_class2_coul_long_gpu.cpp +++ b/src/GPU/pair_lj_class2_coul_long_gpu.cpp @@ -15,9 +15,10 @@ Contributing author: Mike Brown (SNL) ------------------------------------------------------------------------- */ -#include -#include -#include +#include +#include +#include +#include #include "pair_lj_class2_coul_long_gpu.h" #include "atom.h" #include "atom_vec.h" @@ -32,7 +33,6 @@ #include "universe.h" #include "update.h" #include "domain.h" -#include #include "kspace.h" #include "gpu_extra.h" diff --git a/src/GPU/pair_lj_class2_gpu.cpp b/src/GPU/pair_lj_class2_gpu.cpp index cc6866db1ca7a07bb79e05e1a5396db7211c5d97..61b0a8caf134695d96be363a4e90ed93396bfc5e 100644 --- a/src/GPU/pair_lj_class2_gpu.cpp +++ b/src/GPU/pair_lj_class2_gpu.cpp @@ -15,9 +15,10 @@ Contributing author: Mike Brown (SNL) ------------------------------------------------------------------------- */ -#include -#include -#include +#include +#include +#include +#include #include "pair_lj_class2_gpu.h" #include "atom.h" #include "atom_vec.h" @@ -32,7 +33,6 @@ #include "universe.h" #include "update.h" #include "domain.h" -#include #include "gpu_extra.h" using namespace LAMMPS_NS; diff --git a/src/GPU/pair_lj_cubic_gpu.cpp b/src/GPU/pair_lj_cubic_gpu.cpp index 516ac7d15432abfd7f3cd5d4fcb4bd774beb5153..366c33191b4f249afde0e133356783b3bac5d991 100644 --- a/src/GPU/pair_lj_cubic_gpu.cpp +++ b/src/GPU/pair_lj_cubic_gpu.cpp @@ -15,9 +15,10 @@ Contributing author: Trung Dac Nguyen (ndactrung@gmail.com) ------------------------------------------------------------------------- */ -#include -#include -#include +#include +#include +#include +#include #include "pair_lj_cubic_gpu.h" #include "atom.h" #include "atom_vec.h" @@ -32,7 +33,6 @@ #include "universe.h" #include "update.h" #include "domain.h" -#include #include "gpu_extra.h" using namespace LAMMPS_NS; diff --git a/src/GPU/pair_lj_cut_coul_cut_gpu.cpp b/src/GPU/pair_lj_cut_coul_cut_gpu.cpp index 840c07680f44a450a7beb240a1ec50223f64dfe2..baafcd2d62f936b8bc370ba96e99f8b1fd7ce4a3 100644 --- a/src/GPU/pair_lj_cut_coul_cut_gpu.cpp +++ b/src/GPU/pair_lj_cut_coul_cut_gpu.cpp @@ -15,9 +15,10 @@ Contributing author: Mike Brown (SNL) ------------------------------------------------------------------------- */ -#include -#include -#include +#include +#include +#include +#include #include "pair_lj_cut_coul_cut_gpu.h" #include "atom.h" #include "atom_vec.h" @@ -32,7 +33,6 @@ #include "universe.h" #include "update.h" #include "domain.h" -#include #include "gpu_extra.h" using namespace LAMMPS_NS; diff --git a/src/GPU/pair_lj_cut_coul_debye_gpu.cpp b/src/GPU/pair_lj_cut_coul_debye_gpu.cpp index 39108d8558f1bd5dca8549e1c7de5c979fc1ebd6..662375da2c6c6dc77872518f4a623e47133d2ec9 100644 --- a/src/GPU/pair_lj_cut_coul_debye_gpu.cpp +++ b/src/GPU/pair_lj_cut_coul_debye_gpu.cpp @@ -15,9 +15,10 @@ Contributing author: Trung Dac Nguyen (ORNL) ------------------------------------------------------------------------- */ -#include -#include -#include +#include +#include +#include +#include #include "pair_lj_cut_coul_debye_gpu.h" #include "atom.h" #include "atom_vec.h" @@ -32,7 +33,6 @@ #include "universe.h" #include "update.h" #include "domain.h" -#include #include "gpu_extra.h" using namespace LAMMPS_NS; diff --git a/src/GPU/pair_lj_cut_coul_dsf_gpu.cpp b/src/GPU/pair_lj_cut_coul_dsf_gpu.cpp index efca1a2c511d0ea45f521d2975a7337e603e7ec6..c8e68140a1a520c8efd3fe6b371d5833756faa04 100644 --- a/src/GPU/pair_lj_cut_coul_dsf_gpu.cpp +++ b/src/GPU/pair_lj_cut_coul_dsf_gpu.cpp @@ -15,9 +15,10 @@ Contributing author: Mike Brown (SNL) ------------------------------------------------------------------------- */ -#include -#include -#include +#include +#include +#include +#include #include "pair_lj_cut_coul_dsf_gpu.h" #include "atom.h" #include "atom_vec.h" @@ -32,7 +33,6 @@ #include "universe.h" #include "update.h" #include "domain.h" -#include #include "gpu_extra.h" #define MY_PIS 1.77245385090551602729 diff --git a/src/GPU/pair_lj_cut_coul_long_gpu.cpp b/src/GPU/pair_lj_cut_coul_long_gpu.cpp index 0c09cb1d51a39beb952f85c4a29950d077df56f6..3cccb898cc4d57e6c5b565ca47f6dcdd77e4486a 100644 --- a/src/GPU/pair_lj_cut_coul_long_gpu.cpp +++ b/src/GPU/pair_lj_cut_coul_long_gpu.cpp @@ -15,9 +15,10 @@ Contributing author: Mike Brown (SNL) ------------------------------------------------------------------------- */ -#include -#include -#include +#include +#include +#include +#include #include "pair_lj_cut_coul_long_gpu.h" #include "atom.h" #include "atom_vec.h" @@ -32,7 +33,6 @@ #include "universe.h" #include "update.h" #include "domain.h" -#include #include "kspace.h" #include "gpu_extra.h" diff --git a/src/GPU/pair_lj_cut_coul_msm_gpu.cpp b/src/GPU/pair_lj_cut_coul_msm_gpu.cpp index 7d8be01e814398c630b4564ae44c79d0d469812a..04ffe245b24756dba88990345c625fa09b23b2f3 100644 --- a/src/GPU/pair_lj_cut_coul_msm_gpu.cpp +++ b/src/GPU/pair_lj_cut_coul_msm_gpu.cpp @@ -15,9 +15,10 @@ Contributing author: Trung Dac Nguyen (ORNL) ------------------------------------------------------------------------- */ -#include -#include -#include +#include +#include +#include +#include #include "pair_lj_cut_coul_msm_gpu.h" #include "atom.h" #include "atom_vec.h" @@ -33,7 +34,6 @@ #include "update.h" #include "domain.h" #include "kspace.h" -#include #include "gpu_extra.h" using namespace LAMMPS_NS; diff --git a/src/GPU/pair_lj_cut_dipole_cut_gpu.cpp b/src/GPU/pair_lj_cut_dipole_cut_gpu.cpp index 3b5f0c12830543ffa77f8914d063b92d4aa55ab9..1f4528cb88e4a73864553ed57506960595f8697d 100644 --- a/src/GPU/pair_lj_cut_dipole_cut_gpu.cpp +++ b/src/GPU/pair_lj_cut_dipole_cut_gpu.cpp @@ -15,9 +15,10 @@ Contributing author: Trung Dac Nguyen (ORNL) ------------------------------------------------------------------------- */ -#include -#include -#include +#include +#include +#include +#include #include "pair_lj_cut_dipole_cut_gpu.h" #include "atom.h" #include "atom_vec.h" @@ -32,7 +33,6 @@ #include "universe.h" #include "update.h" #include "domain.h" -#include #include "gpu_extra.h" using namespace LAMMPS_NS; diff --git a/src/GPU/pair_lj_cut_gpu.cpp b/src/GPU/pair_lj_cut_gpu.cpp index feba9ed88bb20a81e7ff3b016c36b636d8c4b388..af654bcc5dd0b09c90b0ac126b534d0f76d83aad 100644 --- a/src/GPU/pair_lj_cut_gpu.cpp +++ b/src/GPU/pair_lj_cut_gpu.cpp @@ -15,9 +15,10 @@ Contributing author: Mike Brown (SNL) ------------------------------------------------------------------------- */ -#include -#include -#include +#include +#include +#include +#include #include "pair_lj_cut_gpu.h" #include "atom.h" #include "atom_vec.h" @@ -32,7 +33,6 @@ #include "universe.h" #include "update.h" #include "domain.h" -#include #include "gpu_extra.h" using namespace LAMMPS_NS; diff --git a/src/GPU/pair_lj_expand_gpu.cpp b/src/GPU/pair_lj_expand_gpu.cpp index 43ec1ec45a0dc2ba63ba8b2b49d5755aaf711bcc..f0a9f67b10f3d1b4ee85163f66781871d24b96c3 100644 --- a/src/GPU/pair_lj_expand_gpu.cpp +++ b/src/GPU/pair_lj_expand_gpu.cpp @@ -15,9 +15,10 @@ Contributing author: Inderaj Bains (NVIDIA), ibains@nvidia.com ------------------------------------------------------------------------- */ -#include -#include -#include +#include +#include +#include +#include #include "pair_lj_expand_gpu.h" #include "atom.h" #include "atom_vec.h" @@ -32,7 +33,6 @@ #include "universe.h" #include "update.h" #include "domain.h" -#include #include "gpu_extra.h" using namespace LAMMPS_NS; diff --git a/src/GPU/pair_lj_gromacs_gpu.cpp b/src/GPU/pair_lj_gromacs_gpu.cpp index d749eacba3301f07c8589d8968f586e625364e45..f2006798291751e5188406ec16e8e3f071844eac 100644 --- a/src/GPU/pair_lj_gromacs_gpu.cpp +++ b/src/GPU/pair_lj_gromacs_gpu.cpp @@ -15,9 +15,10 @@ Contributing author: Trung Dac Nguyen (ORNL) ------------------------------------------------------------------------- */ -#include -#include -#include +#include +#include +#include +#include #include "pair_lj_gromacs_gpu.h" #include "atom.h" #include "atom_vec.h" @@ -32,7 +33,6 @@ #include "universe.h" #include "update.h" #include "domain.h" -#include #include "kspace.h" #include "gpu_extra.h" diff --git a/src/GPU/pair_lj_sdk_coul_long_gpu.cpp b/src/GPU/pair_lj_sdk_coul_long_gpu.cpp index 77c0dc06601887f0d3451c9c3cd49480bb11e218..4dbd8874d65751c50da0398776f96389d7043860 100644 --- a/src/GPU/pair_lj_sdk_coul_long_gpu.cpp +++ b/src/GPU/pair_lj_sdk_coul_long_gpu.cpp @@ -15,9 +15,10 @@ Contributing author: Mike Brown (SNL) ------------------------------------------------------------------------- */ -#include -#include -#include +#include +#include +#include +#include #include "pair_lj_sdk_coul_long_gpu.h" #include "atom.h" #include "atom_vec.h" @@ -32,7 +33,6 @@ #include "universe.h" #include "update.h" #include "domain.h" -#include #include "kspace.h" #include "gpu_extra.h" diff --git a/src/GPU/pair_lj_sdk_gpu.cpp b/src/GPU/pair_lj_sdk_gpu.cpp index 67103181d53a852325a7c5ee8411fbb037695f52..84d224a8c4caca209b43828e2f9c8ab6ae4ddd03 100644 --- a/src/GPU/pair_lj_sdk_gpu.cpp +++ b/src/GPU/pair_lj_sdk_gpu.cpp @@ -15,9 +15,10 @@ Contributing author: Mike Brown (SNL) ------------------------------------------------------------------------- */ -#include -#include -#include +#include +#include +#include +#include #include "pair_lj_sdk_gpu.h" #include "atom.h" #include "atom_vec.h" @@ -32,7 +33,6 @@ #include "universe.h" #include "update.h" #include "domain.h" -#include #include "gpu_extra.h" using namespace LAMMPS_NS; diff --git a/src/GPU/pair_lj_sf_dipole_sf_gpu.cpp b/src/GPU/pair_lj_sf_dipole_sf_gpu.cpp index 5b22bebf7f357b0de570d8d15c29d821ddbab3a4..a5ebb1dbc1774234aacade666c565889b686f9ff 100644 --- a/src/GPU/pair_lj_sf_dipole_sf_gpu.cpp +++ b/src/GPU/pair_lj_sf_dipole_sf_gpu.cpp @@ -15,9 +15,10 @@ Contributing author: Trung Dac Nguyen (ORNL) ------------------------------------------------------------------------- */ -#include -#include -#include +#include +#include +#include +#include #include "pair_lj_sf_dipole_sf_gpu.h" #include "atom.h" #include "atom_vec.h" @@ -32,7 +33,6 @@ #include "universe.h" #include "update.h" #include "domain.h" -#include #include "gpu_extra.h" using namespace LAMMPS_NS; diff --git a/src/GPU/pair_mie_cut_gpu.cpp b/src/GPU/pair_mie_cut_gpu.cpp index 4857928a27c3d5b1d7aa23eb797669c341f81528..5919b054668e58b9c5dc497735207a0d4d335855 100644 --- a/src/GPU/pair_mie_cut_gpu.cpp +++ b/src/GPU/pair_mie_cut_gpu.cpp @@ -15,9 +15,10 @@ Contributing author: Trung Dac Nguyen (ORNL) ------------------------------------------------------------------------- */ -#include -#include -#include +#include +#include +#include +#include #include "pair_mie_cut_gpu.h" #include "atom.h" #include "atom_vec.h" @@ -32,7 +33,6 @@ #include "universe.h" #include "update.h" #include "domain.h" -#include #include "gpu_extra.h" using namespace LAMMPS_NS; diff --git a/src/GPU/pair_morse_gpu.cpp b/src/GPU/pair_morse_gpu.cpp index b72a6afaf4c72fcdf98b0dab1759e8bbe2cf2760..81ea7c818ae9fbfa625d5538e8e2860c14c30f70 100644 --- a/src/GPU/pair_morse_gpu.cpp +++ b/src/GPU/pair_morse_gpu.cpp @@ -15,9 +15,10 @@ Contributing author: Mike Brown (SNL) ------------------------------------------------------------------------- */ -#include -#include -#include +#include +#include +#include +#include #include "pair_morse_gpu.h" #include "atom.h" #include "atom_vec.h" @@ -32,7 +33,6 @@ #include "universe.h" #include "update.h" #include "domain.h" -#include #include "gpu_extra.h" using namespace LAMMPS_NS; diff --git a/src/GPU/pair_resquared_gpu.cpp b/src/GPU/pair_resquared_gpu.cpp index d83a63c467115af4b1df7427c5430715b85c98b1..34bd0ec22feb2f03c904330f50a5194ff7157ce2 100644 --- a/src/GPU/pair_resquared_gpu.cpp +++ b/src/GPU/pair_resquared_gpu.cpp @@ -15,9 +15,10 @@ Contributing author: Mike Brown (SNL) ------------------------------------------------------------------------- */ -#include -#include -#include +#include +#include +#include +#include #include "pair_resquared_gpu.h" #include "math_extra.h" #include "atom.h" @@ -34,7 +35,6 @@ #include "universe.h" #include "domain.h" #include "update.h" -#include #include "gpu_extra.h" using namespace LAMMPS_NS; diff --git a/src/GPU/pair_soft_gpu.cpp b/src/GPU/pair_soft_gpu.cpp index aa0268025c186100f0c6255e8a9efb336965c7a3..cc0ea7263353de6d62918d7ed3bb35657143a0d9 100644 --- a/src/GPU/pair_soft_gpu.cpp +++ b/src/GPU/pair_soft_gpu.cpp @@ -15,9 +15,10 @@ Contributing author: Trung Dac Nguyen (ORNL) ------------------------------------------------------------------------- */ -#include -#include -#include +#include +#include +#include +#include #include "pair_soft_gpu.h" #include "atom.h" #include "atom_vec.h" @@ -32,7 +33,6 @@ #include "universe.h" #include "update.h" #include "domain.h" -#include #include "gpu_extra.h" #include "math_const.h" diff --git a/src/GPU/pair_sw_gpu.cpp b/src/GPU/pair_sw_gpu.cpp index d2d21a131a2659d62a9336076e97ade12b318d78..5368bee95904ffd1cf805bfcc5936d4846b028f9 100644 --- a/src/GPU/pair_sw_gpu.cpp +++ b/src/GPU/pair_sw_gpu.cpp @@ -15,10 +15,10 @@ Contributing author: Mike Brown (ORNL) ------------------------------------------------------------------------- */ -#include -#include -#include -#include +#include +#include +#include +#include #include "pair_sw_gpu.h" #include "atom.h" #include "neighbor.h" diff --git a/src/GPU/pair_table_gpu.cpp b/src/GPU/pair_table_gpu.cpp index b0a38eb461e1a2826ada524a7ea70aaaf59b9567..c5aef996db4bbee0af580e9348fa1b4b0e69b20c 100644 --- a/src/GPU/pair_table_gpu.cpp +++ b/src/GPU/pair_table_gpu.cpp @@ -15,9 +15,10 @@ Contributing authors: Trung Dac Nguyen (ORNL) ------------------------------------------------------------------------- */ -#include -#include -#include +#include +#include +#include +#include #include "pair_table_gpu.h" #include "atom.h" #include "atom_vec.h" @@ -32,7 +33,6 @@ #include "universe.h" #include "update.h" #include "domain.h" -#include #include "gpu_extra.h" #define LOOKUP 0 diff --git a/src/GPU/pair_tersoff_gpu.cpp b/src/GPU/pair_tersoff_gpu.cpp index 41d8e6b75145390a1e115fe844131393240a6054..535b56163ea2036e326f453cfcac254f139bad0d 100644 --- a/src/GPU/pair_tersoff_gpu.cpp +++ b/src/GPU/pair_tersoff_gpu.cpp @@ -15,10 +15,10 @@ Contributing author: Trung Dac Nguyen (ndactrung@gmail.com) ------------------------------------------------------------------------- */ -#include -#include -#include -#include +#include +#include +#include +#include #include "pair_tersoff_gpu.h" #include "atom.h" #include "neighbor.h" diff --git a/src/GPU/pair_tersoff_mod_gpu.cpp b/src/GPU/pair_tersoff_mod_gpu.cpp index 25ea2cb99f95f6514da5d721cdae9777ea5912ba..f8b6c50db5620853641d9bce6caad90df3b4f6b2 100644 --- a/src/GPU/pair_tersoff_mod_gpu.cpp +++ b/src/GPU/pair_tersoff_mod_gpu.cpp @@ -15,10 +15,10 @@ Contributing author: Trung Dac Nguyen (ndactrung@gmail.com) ------------------------------------------------------------------------- */ -#include -#include -#include -#include +#include +#include +#include +#include #include "pair_tersoff_mod_gpu.h" #include "atom.h" #include "neighbor.h" diff --git a/src/GPU/pair_tersoff_zbl_gpu.cpp b/src/GPU/pair_tersoff_zbl_gpu.cpp index b4b679b7d03e5a28722bab02180d8c981b9421aa..b45503d759e47931137e5892352c279d902fa197 100644 --- a/src/GPU/pair_tersoff_zbl_gpu.cpp +++ b/src/GPU/pair_tersoff_zbl_gpu.cpp @@ -15,10 +15,10 @@ Contributing author: Trung Dac Nguyen (ndactrung@gmail.com) ------------------------------------------------------------------------- */ -#include -#include -#include -#include +#include +#include +#include +#include #include "pair_tersoff_zbl_gpu.h" #include "atom.h" #include "neighbor.h" diff --git a/src/GPU/pair_ufm_gpu.cpp b/src/GPU/pair_ufm_gpu.cpp index ad66c3871fa5a2a03820ce60e344f1c222294655..40e8df33239bfeaeb2db9be4f7b63e416001971d 100644 --- a/src/GPU/pair_ufm_gpu.cpp +++ b/src/GPU/pair_ufm_gpu.cpp @@ -17,9 +17,10 @@ Maurice de Koning (Unicamp/Brazil) - dekoning@ifi.unicamp.br ------------------------------------------------------------------------- */ -#include -#include -#include +#include +#include +#include +#include #include "pair_ufm_gpu.h" #include "atom.h" #include "atom_vec.h" @@ -34,7 +35,6 @@ #include "universe.h" #include "update.h" #include "domain.h" -#include #include "gpu_extra.h" using namespace LAMMPS_NS; diff --git a/src/GPU/pair_vashishta_gpu.cpp b/src/GPU/pair_vashishta_gpu.cpp index 7d21aaa581763d7da631cebf1dbb42cfbce8f098..00dbac5f1eac4942e9ccc4624047dd138c04dc3e 100644 --- a/src/GPU/pair_vashishta_gpu.cpp +++ b/src/GPU/pair_vashishta_gpu.cpp @@ -15,10 +15,10 @@ Contributing author: Anders Hafreager (UiO) ------------------------------------------------------------------------- */ #include -#include -#include -#include -#include +#include +#include +#include +#include #include "pair_vashishta_gpu.h" #include "atom.h" #include "neighbor.h" diff --git a/src/GPU/pair_yukawa_colloid_gpu.cpp b/src/GPU/pair_yukawa_colloid_gpu.cpp index 4041bd2ebfb19e53343535e02a5f460f4862f5d7..0332e5f755f491bc34de0645d22994907306d8a3 100644 --- a/src/GPU/pair_yukawa_colloid_gpu.cpp +++ b/src/GPU/pair_yukawa_colloid_gpu.cpp @@ -15,9 +15,10 @@ Contributing author: Trung Dac Nguyen (ORNL) ------------------------------------------------------------------------- */ -#include -#include -#include +#include +#include +#include +#include #include "pair_yukawa_colloid_gpu.h" #include "atom.h" #include "atom_vec.h" @@ -32,7 +33,6 @@ #include "universe.h" #include "update.h" #include "domain.h" -#include #include "gpu_extra.h" using namespace LAMMPS_NS; diff --git a/src/GPU/pair_yukawa_gpu.cpp b/src/GPU/pair_yukawa_gpu.cpp index fcb0ae56bcc6376e62b77d9f80b1137ac4f5dd19..dda4250f0702ca71daba67519ad5dd22fcb3dec4 100644 --- a/src/GPU/pair_yukawa_gpu.cpp +++ b/src/GPU/pair_yukawa_gpu.cpp @@ -15,9 +15,10 @@ Contributing author: Trung Dac Nguyen (ORNL) ------------------------------------------------------------------------- */ -#include -#include -#include +#include +#include +#include +#include #include "pair_yukawa_gpu.h" #include "atom.h" #include "atom_vec.h" @@ -32,7 +33,6 @@ #include "universe.h" #include "update.h" #include "domain.h" -#include #include "gpu_extra.h" using namespace LAMMPS_NS; diff --git a/src/GPU/pair_zbl_gpu.cpp b/src/GPU/pair_zbl_gpu.cpp index f1f6bdd44bcdb2e8ad12a03ca21c5c3fe273de48..daca79c8e3454d812cf684365bd18db79b22387e 100644 --- a/src/GPU/pair_zbl_gpu.cpp +++ b/src/GPU/pair_zbl_gpu.cpp @@ -16,9 +16,10 @@ ------------------------------------------------------------------------- */ #include "lmptype.h" -#include -#include -#include +#include +#include +#include +#include #include "pair_zbl_gpu.h" #include "atom.h" #include "atom_vec.h" @@ -33,7 +34,6 @@ #include "universe.h" #include "update.h" #include "domain.h" -#include #include "gpu_extra.h" using namespace LAMMPS_NS; diff --git a/src/GPU/pppm_gpu.cpp b/src/GPU/pppm_gpu.cpp index b2b529f7ef1183494439c23c0c932ee11105bd2e..1f7c4239f8d5fff7793663440d460d536493d3bd 100644 --- a/src/GPU/pppm_gpu.cpp +++ b/src/GPU/pppm_gpu.cpp @@ -16,10 +16,10 @@ ------------------------------------------------------------------------- */ #include -#include -#include -#include -#include +#include +#include +#include +#include #include "pppm_gpu.h" #include "atom.h" #include "comm.h" diff --git a/src/GRANULAR/fix_freeze.cpp b/src/GRANULAR/fix_freeze.cpp index 3cfee675b26ec51f07d01f6e2a87f86f499a70ea..0f581be01c4718b52e6fa9b686329c2c26fc34b4 100644 --- a/src/GRANULAR/fix_freeze.cpp +++ b/src/GRANULAR/fix_freeze.cpp @@ -11,7 +11,7 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include +#include #include "fix_freeze.h" #include "atom.h" #include "update.h" diff --git a/src/GRANULAR/fix_pour.cpp b/src/GRANULAR/fix_pour.cpp index c4e03a24a97609d6dffd22e43a72f3aea8b5b0f9..835d6c42ddd49aff7d3d24c07b9729ac3b6060ac 100644 --- a/src/GRANULAR/fix_pour.cpp +++ b/src/GRANULAR/fix_pour.cpp @@ -11,9 +11,9 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include -#include -#include +#include +#include +#include #include "fix_pour.h" #include "atom.h" #include "atom_vec.h" diff --git a/src/GRANULAR/fix_wall_gran.cpp b/src/GRANULAR/fix_wall_gran.cpp index 033c35dbacc0e96bb910cd1c3e6b2fa261eb815a..368ff99fb75929303f85b7a2bf8ffaaacc3a37ed 100644 --- a/src/GRANULAR/fix_wall_gran.cpp +++ b/src/GRANULAR/fix_wall_gran.cpp @@ -16,9 +16,9 @@ Dan Bolintineanu (SNL) ------------------------------------------------------------------------- */ -#include -#include -#include +#include +#include +#include #include "fix_wall_gran.h" #include "atom.h" #include "domain.h" diff --git a/src/GRANULAR/fix_wall_gran_region.cpp b/src/GRANULAR/fix_wall_gran_region.cpp index d1c5d4c9c771f8a73bd0d95165ee362976f50509..12fa25714ccbbf8447cbda043ee8ba00d0d66c14 100644 --- a/src/GRANULAR/fix_wall_gran_region.cpp +++ b/src/GRANULAR/fix_wall_gran_region.cpp @@ -15,9 +15,9 @@ Contributing authors: Dan Bolintineanu (SNL) ------------------------------------------------------------------------- */ -#include -#include -#include +#include +#include +#include #include "fix_wall_gran_region.h" #include "region.h" #include "atom.h" diff --git a/src/GRANULAR/pair_gran_hertz_history.cpp b/src/GRANULAR/pair_gran_hertz_history.cpp index 9723531625fdf44b81fa727538a394f9f24a157e..9d4f5c1a9b8a703d4dd83600e84186a6f140f5fe 100644 --- a/src/GRANULAR/pair_gran_hertz_history.cpp +++ b/src/GRANULAR/pair_gran_hertz_history.cpp @@ -15,10 +15,10 @@ Contributing authors: Leo Silbert (SNL), Gary Grest (SNL) ------------------------------------------------------------------------- */ -#include -#include -#include -#include +#include +#include +#include +#include #include "pair_gran_hertz_history.h" #include "atom.h" #include "update.h" diff --git a/src/GRANULAR/pair_gran_hooke.cpp b/src/GRANULAR/pair_gran_hooke.cpp index 66e1c3dd7a8bc09a2b8649e388fce6ff832b0cdd..4937c2fe8b1142816d20c03f8548b208b594a860 100644 --- a/src/GRANULAR/pair_gran_hooke.cpp +++ b/src/GRANULAR/pair_gran_hooke.cpp @@ -15,9 +15,9 @@ Contributing authors: Leo Silbert (SNL), Gary Grest (SNL) ------------------------------------------------------------------------- */ -#include -#include -#include +#include +#include +#include #include "pair_gran_hooke.h" #include "atom.h" #include "force.h" diff --git a/src/GRANULAR/pair_gran_hooke_history.cpp b/src/GRANULAR/pair_gran_hooke_history.cpp index 4f120150ded77ccfdaf5e839f2b5cc68a39ddfd7..d70c7391e2ba896961640895ce98e07acc6a0cd5 100644 --- a/src/GRANULAR/pair_gran_hooke_history.cpp +++ b/src/GRANULAR/pair_gran_hooke_history.cpp @@ -15,10 +15,10 @@ Contributing authors: Leo Silbert (SNL), Gary Grest (SNL) ------------------------------------------------------------------------- */ -#include -#include -#include -#include +#include +#include +#include +#include #include "pair_gran_hooke_history.h" #include "atom.h" #include "atom_vec.h" diff --git a/src/KIM/pair_kim.cpp b/src/KIM/pair_kim.cpp index 46e843158abe6649ba751b7480bba01e4ba94ebe..fe638214baabe8205172d78d898bd21ee75096e5 100644 --- a/src/KIM/pair_kim.cpp +++ b/src/KIM/pair_kim.cpp @@ -1264,15 +1264,15 @@ void *PairKIM::extract(const char *str, int &dim) int ier; int dummyint; int isIndexed = 0; - int maxLine = 1024; + const int MAXLINE = 1024; int rank; int validParam = 0; int numParams; - int *speciesIndex = new int[maxLine]; - char *paramStr = new char[maxLine]; + int *speciesIndex = new int[MAXLINE]; + char *paramStr = new char[MAXLINE]; char *paramName; char *indexStr; - char message[maxLine]; + char message[MAXLINE]; int offset; double* paramPtr; @@ -1354,7 +1354,7 @@ void *PairKIM::extract(const char *str, int &dim) } kim_error(__LINE__,"get_rank",kimerror); - int *shape = new int[maxLine]; + int *shape = new int[MAXLINE]; dummyint = (*pkim).get_shape(paramName, shape, &kimerror); if (kimerror == KIM_STATUS_FAIL) { diff --git a/src/KOKKOS/angle_charmm_kokkos.cpp b/src/KOKKOS/angle_charmm_kokkos.cpp index f048738489ea8efd7ce749c5477fdf1a391b3f6f..4a81f4f49436817027af36c6be411749d6a57a75 100644 --- a/src/KOKKOS/angle_charmm_kokkos.cpp +++ b/src/KOKKOS/angle_charmm_kokkos.cpp @@ -15,8 +15,8 @@ Contributing author: Stan Moore (SNL) ------------------------------------------------------------------------- */ -#include -#include +#include +#include #include "angle_charmm_kokkos.h" #include "atom_kokkos.h" #include "neighbor_kokkos.h" diff --git a/src/KOKKOS/angle_class2_kokkos.cpp b/src/KOKKOS/angle_class2_kokkos.cpp index 670cfa152d44ac7fe3b8e1e121d42354bf1bcd8b..870603791bd657d5d6e7157ae77bdd1002705c79 100644 --- a/src/KOKKOS/angle_class2_kokkos.cpp +++ b/src/KOKKOS/angle_class2_kokkos.cpp @@ -15,8 +15,8 @@ Contributing author: Ray Shan (Materials Design) ------------------------------------------------------------------------- */ -#include -#include +#include +#include #include "angle_class2_kokkos.h" #include "atom_kokkos.h" #include "neighbor_kokkos.h" diff --git a/src/KOKKOS/angle_harmonic_kokkos.cpp b/src/KOKKOS/angle_harmonic_kokkos.cpp index dd5a1e26c7c55d135a5e37a0619dace64b49dbb1..d8e5659e1efd9103c512163d9cd3c88868c84238 100644 --- a/src/KOKKOS/angle_harmonic_kokkos.cpp +++ b/src/KOKKOS/angle_harmonic_kokkos.cpp @@ -15,8 +15,8 @@ Contributing author: Stan Moore (SNL) ------------------------------------------------------------------------- */ -#include -#include +#include +#include #include "angle_harmonic_kokkos.h" #include "atom_kokkos.h" #include "neighbor_kokkos.h" diff --git a/src/KOKKOS/atom_vec_angle_kokkos.cpp b/src/KOKKOS/atom_vec_angle_kokkos.cpp index 8ff6d721a8a7b1fd4a8b06fdd7f534d0720530eb..352fec57fbbbff1c2510cabb0dda4aed7dc5082c 100644 --- a/src/KOKKOS/atom_vec_angle_kokkos.cpp +++ b/src/KOKKOS/atom_vec_angle_kokkos.cpp @@ -11,7 +11,7 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include +#include #include "atom_vec_angle_kokkos.h" #include "atom_kokkos.h" #include "comm_kokkos.h" diff --git a/src/KOKKOS/atom_vec_atomic_kokkos.cpp b/src/KOKKOS/atom_vec_atomic_kokkos.cpp index 0b96d8dbadc98f8fcf3559e21464d6102b8af088..6aba49e5f3a5b9689b19ce109c5a2534d44c8fd8 100644 --- a/src/KOKKOS/atom_vec_atomic_kokkos.cpp +++ b/src/KOKKOS/atom_vec_atomic_kokkos.cpp @@ -11,7 +11,7 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include +#include #include "atom_vec_atomic_kokkos.h" #include "atom_kokkos.h" #include "comm_kokkos.h" diff --git a/src/KOKKOS/atom_vec_bond_kokkos.cpp b/src/KOKKOS/atom_vec_bond_kokkos.cpp index adad4f767bb1d2e9a55021c32a71c3bb0b450d24..c884d23880504c533d7b9d545898a6a319c93149 100644 --- a/src/KOKKOS/atom_vec_bond_kokkos.cpp +++ b/src/KOKKOS/atom_vec_bond_kokkos.cpp @@ -11,7 +11,7 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include +#include #include "atom_vec_bond_kokkos.h" #include "atom_kokkos.h" #include "comm_kokkos.h" diff --git a/src/KOKKOS/atom_vec_charge_kokkos.cpp b/src/KOKKOS/atom_vec_charge_kokkos.cpp index 3e50870c8f9db9a399355ef60724d6ac85f41ee2..11e46d1274165b4b58e509deb545dfc7848bf42a 100644 --- a/src/KOKKOS/atom_vec_charge_kokkos.cpp +++ b/src/KOKKOS/atom_vec_charge_kokkos.cpp @@ -11,7 +11,7 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include +#include #include "atom_vec_charge_kokkos.h" #include "atom_kokkos.h" #include "comm_kokkos.h" diff --git a/src/KOKKOS/atom_vec_dpd_kokkos.cpp b/src/KOKKOS/atom_vec_dpd_kokkos.cpp index 06ca2083dce28372a6d9a05235ef224766420208..539f8e673698b67b570bad160ff45648c01c2567 100644 --- a/src/KOKKOS/atom_vec_dpd_kokkos.cpp +++ b/src/KOKKOS/atom_vec_dpd_kokkos.cpp @@ -11,7 +11,7 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include +#include #include "atom_vec_dpd_kokkos.h" #include "atom_kokkos.h" #include "comm_kokkos.h" diff --git a/src/KOKKOS/atom_vec_full_kokkos.cpp b/src/KOKKOS/atom_vec_full_kokkos.cpp index 6492a264ac153d330c2d1670b67c790c7b163aa6..a6ae1e0cccebd8e87b9af5213e1583756c48347a 100644 --- a/src/KOKKOS/atom_vec_full_kokkos.cpp +++ b/src/KOKKOS/atom_vec_full_kokkos.cpp @@ -11,7 +11,7 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include +#include #include "atom_vec_full_kokkos.h" #include "atom_kokkos.h" #include "comm_kokkos.h" diff --git a/src/KOKKOS/atom_vec_hybrid_kokkos.cpp b/src/KOKKOS/atom_vec_hybrid_kokkos.cpp index 67dce07b80d79323c0a822e64fcdc9847cb5bcac..7e1cc200d36bec7d4c9571fb403ca8f4dbd0c242 100644 --- a/src/KOKKOS/atom_vec_hybrid_kokkos.cpp +++ b/src/KOKKOS/atom_vec_hybrid_kokkos.cpp @@ -11,8 +11,8 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include -#include +#include +#include #include "atom_vec_hybrid_kokkos.h" #include "atom_kokkos.h" #include "domain.h" diff --git a/src/KOKKOS/atom_vec_hybrid_kokkos.h b/src/KOKKOS/atom_vec_hybrid_kokkos.h index 988de7fa2124e452d8db4bafae5a3db3c6457317..1bbbd26319af9da9a7c90de4600d78fefe63f6c6 100644 --- a/src/KOKKOS/atom_vec_hybrid_kokkos.h +++ b/src/KOKKOS/atom_vec_hybrid_kokkos.h @@ -20,7 +20,7 @@ AtomStyle(hybrid/kk,AtomVecHybridKokkos) #ifndef LMP_ATOM_VEC_HYBRID_KOKKOS_H #define LMP_ATOM_VEC_HYBRID_KOKKOS_H -#include +#include #include "atom_vec_kokkos.h" #include "kokkos_type.h" diff --git a/src/KOKKOS/atom_vec_molecular_kokkos.cpp b/src/KOKKOS/atom_vec_molecular_kokkos.cpp index 1a0c03cca5631ce58a86321757d5610323319336..9537320976298f4bf2a17cc0bd3bb6e93b703a76 100644 --- a/src/KOKKOS/atom_vec_molecular_kokkos.cpp +++ b/src/KOKKOS/atom_vec_molecular_kokkos.cpp @@ -11,7 +11,7 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include +#include #include "atom_vec_molecular_kokkos.h" #include "atom_kokkos.h" #include "comm_kokkos.h" diff --git a/src/KOKKOS/bond_class2_kokkos.cpp b/src/KOKKOS/bond_class2_kokkos.cpp index 80f2a6dfbbe8b6e423d0b5fd7174f53f7eeb2da1..f5af93a22aaa666ae8ac03ec4c09d3f3a6530d92 100644 --- a/src/KOKKOS/bond_class2_kokkos.cpp +++ b/src/KOKKOS/bond_class2_kokkos.cpp @@ -15,8 +15,8 @@ Contributing author: Ray Shan (Materials Design) ------------------------------------------------------------------------- */ -#include -#include +#include +#include #include "bond_class2_kokkos.h" #include "atom_kokkos.h" #include "neighbor_kokkos.h" diff --git a/src/KOKKOS/bond_fene_kokkos.cpp b/src/KOKKOS/bond_fene_kokkos.cpp index 20c20542083b35c289d8efdab2f3dce5adc95077..30faf4cee03589161158e3bc9a58a09a6ea2d574 100644 --- a/src/KOKKOS/bond_fene_kokkos.cpp +++ b/src/KOKKOS/bond_fene_kokkos.cpp @@ -15,8 +15,8 @@ Contributing author: Stan Moore (SNL) ------------------------------------------------------------------------- */ -#include -#include +#include +#include #include "bond_fene_kokkos.h" #include "atom_kokkos.h" #include "neighbor_kokkos.h" diff --git a/src/KOKKOS/bond_harmonic_kokkos.cpp b/src/KOKKOS/bond_harmonic_kokkos.cpp index e277104ddb317217dfd5dcddeef9bac584b4dd6f..8aa71b9eb3ec2491ef6c710be6a6763fc776f218 100644 --- a/src/KOKKOS/bond_harmonic_kokkos.cpp +++ b/src/KOKKOS/bond_harmonic_kokkos.cpp @@ -15,8 +15,8 @@ Contributing author: Stan Moore (SNL) ------------------------------------------------------------------------- */ -#include -#include +#include +#include #include "bond_harmonic_kokkos.h" #include "atom_kokkos.h" #include "neighbor_kokkos.h" diff --git a/src/KOKKOS/comm_tiled_kokkos.cpp b/src/KOKKOS/comm_tiled_kokkos.cpp index 33cd8eaa6e9eabc518a163d1ffbe68bbe0cffc30..4809f4cff2eebae63bcd002d0199d8e2fba1c0bc 100644 --- a/src/KOKKOS/comm_tiled_kokkos.cpp +++ b/src/KOKKOS/comm_tiled_kokkos.cpp @@ -11,7 +11,7 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include +#include #include "comm_tiled_kokkos.h" #include "comm_brick.h" #include "atom_kokkos.h" diff --git a/src/KOKKOS/compute_temp_kokkos.cpp b/src/KOKKOS/compute_temp_kokkos.cpp index 2ea67a1fb135a695a1e37b3c5d3e0de2ae82762e..fec3d89fffa8169e975373c3f20f258af3ee0b47 100644 --- a/src/KOKKOS/compute_temp_kokkos.cpp +++ b/src/KOKKOS/compute_temp_kokkos.cpp @@ -12,7 +12,7 @@ ------------------------------------------------------------------------- */ #include -#include +#include #include "compute_temp_kokkos.h" #include "atom_kokkos.h" #include "update.h" diff --git a/src/KOKKOS/dihedral_charmm_kokkos.cpp b/src/KOKKOS/dihedral_charmm_kokkos.cpp index 13e3a6d2d1c600d62fd6cbeb56efa0f88b5553c1..41593ffbda6bebe72e4bf7d68bc250760c757d0c 100644 --- a/src/KOKKOS/dihedral_charmm_kokkos.cpp +++ b/src/KOKKOS/dihedral_charmm_kokkos.cpp @@ -15,8 +15,8 @@ Contributing author: Stan Moore (SNL) ------------------------------------------------------------------------- */ -#include -#include +#include +#include #include "dihedral_charmm_kokkos.h" #include "atom_kokkos.h" #include "comm.h" diff --git a/src/KOKKOS/dihedral_class2_kokkos.cpp b/src/KOKKOS/dihedral_class2_kokkos.cpp index b96e4c99af9893f644459e79b36b0bd87e90f865..f656fcf756ad5611985fb0739ff31136ef681971 100644 --- a/src/KOKKOS/dihedral_class2_kokkos.cpp +++ b/src/KOKKOS/dihedral_class2_kokkos.cpp @@ -15,8 +15,8 @@ Contributing author: Ray Shan (Materials Design) ------------------------------------------------------------------------- */ -#include -#include +#include +#include #include "dihedral_class2_kokkos.h" #include "atom_kokkos.h" #include "comm.h" diff --git a/src/KOKKOS/dihedral_opls_kokkos.cpp b/src/KOKKOS/dihedral_opls_kokkos.cpp index 4349aff48df93848f097bd1130c758ec6be91951..62c481fa9c3ee17ac92fbc17ec70fa6c1e833079 100644 --- a/src/KOKKOS/dihedral_opls_kokkos.cpp +++ b/src/KOKKOS/dihedral_opls_kokkos.cpp @@ -15,8 +15,8 @@ Contributing author: Stan Moore (SNL) ------------------------------------------------------------------------- */ -#include -#include +#include +#include #include "dihedral_opls_kokkos.h" #include "atom_kokkos.h" #include "comm.h" diff --git a/src/KOKKOS/fix_deform_kokkos.cpp b/src/KOKKOS/fix_deform_kokkos.cpp index 52953207340546890af19b6470f91f4b4b4c1f82..050364979550f25b74be0961ce5930ba4aa62f1d 100644 --- a/src/KOKKOS/fix_deform_kokkos.cpp +++ b/src/KOKKOS/fix_deform_kokkos.cpp @@ -15,9 +15,9 @@ Contributing author: Pieter in 't Veld (SNL) ------------------------------------------------------------------------- */ -#include -#include -#include +#include +#include +#include #include "fix_deform_kokkos.h" #include "atom_kokkos.h" #include "update.h" diff --git a/src/KOKKOS/fix_dpd_energy_kokkos.cpp b/src/KOKKOS/fix_dpd_energy_kokkos.cpp index e6878afed4ba44287e1efecb138b7f7c95272314..b12c6a476e0939d26da6c4d20a37cb56fe072e0c 100644 --- a/src/KOKKOS/fix_dpd_energy_kokkos.cpp +++ b/src/KOKKOS/fix_dpd_energy_kokkos.cpp @@ -11,8 +11,8 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include -#include +#include +#include #include "fix_dpd_energy_kokkos.h" #include "atom_masks.h" #include "atom_kokkos.h" diff --git a/src/KOKKOS/fix_eos_table_rx_kokkos.cpp b/src/KOKKOS/fix_eos_table_rx_kokkos.cpp index fb4ca443a9dac49a9566733a0db474e2022b2fc7..39f612ec46e002fbaaab31ae42221b5b6fdf9e72 100644 --- a/src/KOKKOS/fix_eos_table_rx_kokkos.cpp +++ b/src/KOKKOS/fix_eos_table_rx_kokkos.cpp @@ -15,15 +15,15 @@ Contributing author: Stan Moore (Sandia) ------------------------------------------------------------------------- */ -#include -#include +#include +#include #include "fix_eos_table_rx_kokkos.h" #include "atom_kokkos.h" #include "error.h" #include "force.h" #include "memory_kokkos.h" #include "comm.h" -#include +#include #include "modify.h" #include "atom_masks.h" @@ -387,7 +387,7 @@ void FixEOStableRXKokkos::temperature_lookup(int id, double ui, doub // Apply the Secant Method for(it=0; it()() = 2; + if(std::isnan(f1) || std::isnan(f2)) k_error_flag.template view()() = 2; temp = t1; temp = MAX(temp,lo); temp = MIN(temp,hi); @@ -403,7 +403,7 @@ void FixEOStableRXKokkos::temperature_lookup(int id, double ui, doub f2 = u2 - ui; } if(it==maxit){ - if(isnan(f1) || isnan(f2) || isnan(ui) || isnan(thetai) || isnan(t1) || isnan(t2)) + if(std::isnan(f1) || std::isnan(f2) || std::isnan(ui) || std::isnan(thetai) || std::isnan(t1) || std::isnan(t2)) k_error_flag.template view()() = 2; else k_error_flag.template view()() = 3; diff --git a/src/KOKKOS/fix_langevin_kokkos.cpp b/src/KOKKOS/fix_langevin_kokkos.cpp index 108c3b692ad7f4fcb176a407a558c5dca3685ca8..24d505e08d46854b3b72660436070ef1f9688a78 100644 --- a/src/KOKKOS/fix_langevin_kokkos.cpp +++ b/src/KOKKOS/fix_langevin_kokkos.cpp @@ -11,9 +11,9 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include -#include -#include +#include +#include +#include #include "fix_langevin_kokkos.h" #include "atom_masks.h" #include "atom_kokkos.h" diff --git a/src/KOKKOS/fix_momentum_kokkos.cpp b/src/KOKKOS/fix_momentum_kokkos.cpp index 9ffe67a46ba7615efd9255f6a95500bcbe69af6e..9af7e79da88663490c30c31c494f0ca4ef49b86e 100644 --- a/src/KOKKOS/fix_momentum_kokkos.cpp +++ b/src/KOKKOS/fix_momentum_kokkos.cpp @@ -11,8 +11,8 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include -#include +#include +#include #include "fix_momentum_kokkos.h" #include "atom_kokkos.h" #include "atom_masks.h" diff --git a/src/KOKKOS/fix_nh_kokkos.cpp b/src/KOKKOS/fix_nh_kokkos.cpp index 345259e35519b24a6b6b669c175fc9e5bdeaf746..679690ea82215c9a389ff9b417c74385a35a163e 100644 --- a/src/KOKKOS/fix_nh_kokkos.cpp +++ b/src/KOKKOS/fix_nh_kokkos.cpp @@ -15,9 +15,9 @@ Contributing author: Stan Moore (SNL) ------------------------------------------------------------------------- */ -#include -#include -#include +#include +#include +#include #include "fix_nh_kokkos.h" #include "math_extra.h" #include "atom.h" diff --git a/src/KOKKOS/fix_nph_kokkos.cpp b/src/KOKKOS/fix_nph_kokkos.cpp index 34fc212c0f996adbed0597d479e63bcc929722f1..ed825ad9ee448a156ecf5e91b1fd329c94a79fa5 100644 --- a/src/KOKKOS/fix_nph_kokkos.cpp +++ b/src/KOKKOS/fix_nph_kokkos.cpp @@ -11,7 +11,7 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include +#include #include "fix_nph_kokkos.h" #include "modify.h" #include "error.h" diff --git a/src/KOKKOS/fix_npt_kokkos.cpp b/src/KOKKOS/fix_npt_kokkos.cpp index c99a322a01679f0667c1de85d51c1d3afacc8ab3..b33e733aee707b8c4f572cc3ae93a14d09fc7eab 100644 --- a/src/KOKKOS/fix_npt_kokkos.cpp +++ b/src/KOKKOS/fix_npt_kokkos.cpp @@ -11,7 +11,7 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include +#include #include "fix_npt_kokkos.h" #include "modify.h" #include "error.h" diff --git a/src/KOKKOS/fix_nve_kokkos.cpp b/src/KOKKOS/fix_nve_kokkos.cpp index c071447eb7872e72f51055e8ab5232a574f29545..cb3eadcd9009f8e7a4426dae6a2bc0c459592111 100644 --- a/src/KOKKOS/fix_nve_kokkos.cpp +++ b/src/KOKKOS/fix_nve_kokkos.cpp @@ -11,8 +11,8 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include -#include +#include +#include #include "fix_nve_kokkos.h" #include "atom_masks.h" #include "atom_kokkos.h" diff --git a/src/KOKKOS/fix_nvt_kokkos.cpp b/src/KOKKOS/fix_nvt_kokkos.cpp index 9628ff023126b13286d3c5594050bf501c5e322d..8b2d9362745c98812b367b9df82054ac883158bf 100644 --- a/src/KOKKOS/fix_nvt_kokkos.cpp +++ b/src/KOKKOS/fix_nvt_kokkos.cpp @@ -11,7 +11,7 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include +#include #include "fix_nvt_kokkos.h" #include "group.h" #include "modify.h" diff --git a/src/KOKKOS/fix_property_atom_kokkos.cpp b/src/KOKKOS/fix_property_atom_kokkos.cpp index fb3f5a3f341fbcf4f51ab555c1686a0f7de2d147..12f27f99322aaa863da3b77243715183dd951db6 100644 --- a/src/KOKKOS/fix_property_atom_kokkos.cpp +++ b/src/KOKKOS/fix_property_atom_kokkos.cpp @@ -11,8 +11,8 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include -#include +#include +#include #include "fix_property_atom_kokkos.h" #include "atom_kokkos.h" #include "comm.h" diff --git a/src/KOKKOS/fix_qeq_reax_kokkos.cpp b/src/KOKKOS/fix_qeq_reax_kokkos.cpp index ca2525d4f0783f14851fe4c9c69b5fbd57fac32e..52822856ee014cbb5b13b09ef87e3f54186a4a53 100644 --- a/src/KOKKOS/fix_qeq_reax_kokkos.cpp +++ b/src/KOKKOS/fix_qeq_reax_kokkos.cpp @@ -15,10 +15,10 @@ Contributing author: Ray Shan (SNL), Stan Moore (SNL) ------------------------------------------------------------------------- */ -#include -#include -#include -#include +#include +#include +#include +#include #include "fix_qeq_reax_kokkos.h" #include "kokkos.h" #include "atom.h" diff --git a/src/KOKKOS/fix_reaxc_bonds_kokkos.cpp b/src/KOKKOS/fix_reaxc_bonds_kokkos.cpp index 586daadd55e64c3922f52ee16faa454f7b723da5..9aed0b9ae4052490b798aad062c3856b0d225b81 100644 --- a/src/KOKKOS/fix_reaxc_bonds_kokkos.cpp +++ b/src/KOKKOS/fix_reaxc_bonds_kokkos.cpp @@ -15,8 +15,8 @@ Contributing author: Stan Moore (Sandia) ------------------------------------------------------------------------- */ -#include -#include +#include +#include #include "fix_ave_atom.h" #include "fix_reaxc_bonds_kokkos.h" #include "atom.h" diff --git a/src/KOKKOS/fix_reaxc_species_kokkos.cpp b/src/KOKKOS/fix_reaxc_species_kokkos.cpp index a676c7ef27ae81cf7ec39e8467e7ecdceb816e06..bd92251960608a2bdfa6cb47c8a3180ae2356cec 100644 --- a/src/KOKKOS/fix_reaxc_species_kokkos.cpp +++ b/src/KOKKOS/fix_reaxc_species_kokkos.cpp @@ -15,10 +15,10 @@ Contributing authors: Stan Moore (Sandia) ------------------------------------------------------------------------- */ -#include -#include +#include +#include #include "atom.h" -#include +#include #include "fix_ave_atom.h" #include "fix_reaxc_species_kokkos.h" #include "domain.h" diff --git a/src/KOKKOS/fix_rx_kokkos.cpp b/src/KOKKOS/fix_rx_kokkos.cpp index 22450e19d948ac53a64837c021bf6c32c879968a..f636f6454d17874737a9e951bb271da0755328b9 100644 --- a/src/KOKKOS/fix_rx_kokkos.cpp +++ b/src/KOKKOS/fix_rx_kokkos.cpp @@ -11,8 +11,8 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include -#include +#include +#include #include "fix_rx_kokkos.h" #include "atom_masks.h" #include "atom_kokkos.h" @@ -30,7 +30,7 @@ #include "domain.h" #include "kokkos.h" -#include // DBL_EPSILON +#include // DBL_EPSILON using namespace LAMMPS_NS; using namespace FixConst; diff --git a/src/KOKKOS/fix_setforce_kokkos.cpp b/src/KOKKOS/fix_setforce_kokkos.cpp index e99160989497381ef63985fad512ec3e2d3af664..5150c71249dd7611e006241ba735de2176329ef9 100644 --- a/src/KOKKOS/fix_setforce_kokkos.cpp +++ b/src/KOKKOS/fix_setforce_kokkos.cpp @@ -11,8 +11,8 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include -#include +#include +#include #include "fix_setforce_kokkos.h" #include "atom_kokkos.h" #include "update.h" diff --git a/src/KOKKOS/fix_shardlow_kokkos.cpp b/src/KOKKOS/fix_shardlow_kokkos.cpp index e973e5c99f5d4035207689c297c0ba1bb4f92cd3..70055bf8c9df4fd0f70f32b83e012e9eec0132c9 100644 --- a/src/KOKKOS/fix_shardlow_kokkos.cpp +++ b/src/KOKKOS/fix_shardlow_kokkos.cpp @@ -33,9 +33,9 @@ 135, 204105. ------------------------------------------------------------------------- */ -#include -#include -#include +#include +#include +#include #include "fix_shardlow_kokkos.h" #include "atom.h" #include "atom_masks.h" @@ -44,7 +44,7 @@ #include "update.h" #include "respa.h" #include "error.h" -#include +#include #include "atom_vec.h" #include "comm.h" #include "neighbor.h" diff --git a/src/KOKKOS/fix_shardlow_kokkos.h b/src/KOKKOS/fix_shardlow_kokkos.h index 4e87de6910d7724a0bc1a736cb15b2b5d56c1049..0469f6033d33ad49d14282a61b9a16f008d55742 100644 --- a/src/KOKKOS/fix_shardlow_kokkos.h +++ b/src/KOKKOS/fix_shardlow_kokkos.h @@ -22,7 +22,6 @@ FixStyle(shardlow/kk/host,FixShardlowKokkos) #ifndef LMP_FIX_SHARDLOW_KOKKOS_H #define LMP_FIX_SHARDLOW_KOKKOS_H -#include "float.h" #include "fix_shardlow.h" #include "kokkos_type.h" #include "neigh_list_kokkos.h" diff --git a/src/KOKKOS/fix_wall_lj93_kokkos.cpp b/src/KOKKOS/fix_wall_lj93_kokkos.cpp index 602922d0ecae3426ba666dadf375ad26fd6adc99..3aaa45f8a8d0237be4cad83bd12d4f0ecfa81b8a 100644 --- a/src/KOKKOS/fix_wall_lj93_kokkos.cpp +++ b/src/KOKKOS/fix_wall_lj93_kokkos.cpp @@ -11,7 +11,7 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include +#include #include "fix_wall_lj93_kokkos.h" #include "atom_kokkos.h" #include "error.h" diff --git a/src/KOKKOS/fix_wall_reflect_kokkos.cpp b/src/KOKKOS/fix_wall_reflect_kokkos.cpp index cd7a2c59b78ae84c3c0ae58f34c3998705b442d1..2516ac6577000b6f0c0de347b5e5dc60f0868b92 100644 --- a/src/KOKKOS/fix_wall_reflect_kokkos.cpp +++ b/src/KOKKOS/fix_wall_reflect_kokkos.cpp @@ -11,8 +11,8 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include -#include +#include +#include #include "fix_wall_reflect_kokkos.h" #include "atom_kokkos.h" #include "comm.h" diff --git a/src/KOKKOS/improper_class2_kokkos.cpp b/src/KOKKOS/improper_class2_kokkos.cpp index 28f57608bbce990793b47b5f66f95d28dbec6ec5..fdb890be5481969c48b885b3f99f0b54d97e4f38 100644 --- a/src/KOKKOS/improper_class2_kokkos.cpp +++ b/src/KOKKOS/improper_class2_kokkos.cpp @@ -16,8 +16,8 @@ ------------------------------------------------------------------------- */ #include -#include -#include +#include +#include #include "improper_class2_kokkos.h" #include "atom_kokkos.h" #include "comm.h" diff --git a/src/KOKKOS/improper_harmonic_kokkos.cpp b/src/KOKKOS/improper_harmonic_kokkos.cpp index f1a0ac3631c1a862dab0172b4f58dadcfeff8038..9f4e8b9440f52cbfa10262623544ac25bce78c4b 100644 --- a/src/KOKKOS/improper_harmonic_kokkos.cpp +++ b/src/KOKKOS/improper_harmonic_kokkos.cpp @@ -16,8 +16,8 @@ ------------------------------------------------------------------------- */ #include -#include -#include +#include +#include #include "improper_harmonic_kokkos.h" #include "atom_kokkos.h" #include "comm.h" diff --git a/src/KOKKOS/kokkos.cpp b/src/KOKKOS/kokkos.cpp index 65942fbeaf9144407ada297ac3b036c6de7fa846..3bbff6be7e77c93930b23b1bf937c28c1a2afd04 100644 --- a/src/KOKKOS/kokkos.cpp +++ b/src/KOKKOS/kokkos.cpp @@ -11,11 +11,11 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include -#include -#include -#include -#include +#include +#include +#include +#include +#include #include #include "kokkos.h" #include "lammps.h" diff --git a/src/KOKKOS/math_special_kokkos.cpp b/src/KOKKOS/math_special_kokkos.cpp index a8c35b12b8838ca3a83fe42c646851532523af89..127168ef8bae1bce35a2031fce6077e9d0020e1e 100644 --- a/src/KOKKOS/math_special_kokkos.cpp +++ b/src/KOKKOS/math_special_kokkos.cpp @@ -1,6 +1,6 @@ -#include -#include +#include +#include #include "math_special_kokkos.h" using namespace LAMMPS_NS; diff --git a/src/KOKKOS/math_special_kokkos.h b/src/KOKKOS/math_special_kokkos.h index 254b452eab786bc7dcac5255d7f98fec27bc31a7..d10d164bcfbc510cbe17c3f091c9ca1fb8d7b5f1 100644 --- a/src/KOKKOS/math_special_kokkos.h +++ b/src/KOKKOS/math_special_kokkos.h @@ -14,7 +14,7 @@ #ifndef LMP_MATH_SPECIAL_KOKKOS_H #define LMP_MATH_SPECIAL_KOKKOS_H -#include +#include #include "kokkos_type.h" namespace LAMMPS_NS { diff --git a/src/KOKKOS/neigh_bond_kokkos.cpp b/src/KOKKOS/neigh_bond_kokkos.cpp index 3ecc8b5e516c8243a36a668fcdceb7b434e7145c..4dd39a1d383cb5da9063a5c439ca725d511d7c48 100644 --- a/src/KOKKOS/neigh_bond_kokkos.cpp +++ b/src/KOKKOS/neigh_bond_kokkos.cpp @@ -28,7 +28,7 @@ #include "error.h" #include "modify.h" #include "fix.h" -#include +#include #include "atom_masks.h" #include "domain.h" diff --git a/src/KOKKOS/neighbor_kokkos.h b/src/KOKKOS/neighbor_kokkos.h index 137c071e87a7f078647f34ca43c73254c9ab916b..5c98c4d26db2d74b70747f705f0e9f755bae8edd 100644 --- a/src/KOKKOS/neighbor_kokkos.h +++ b/src/KOKKOS/neighbor_kokkos.h @@ -18,7 +18,7 @@ #include "neigh_list_kokkos.h" #include "neigh_bond_kokkos.h" #include "kokkos_type.h" -#include +#include namespace LAMMPS_NS { diff --git a/src/KOKKOS/pair_buck_coul_cut_kokkos.cpp b/src/KOKKOS/pair_buck_coul_cut_kokkos.cpp index ba3eda64ddee4e389b771f5e47168c98c5a6fa08..9c12d2c978f7a385dfb11f82e34b55984cc0ec76 100644 --- a/src/KOKKOS/pair_buck_coul_cut_kokkos.cpp +++ b/src/KOKKOS/pair_buck_coul_cut_kokkos.cpp @@ -15,10 +15,10 @@ Contributing author: Ray Shan (SNL) ------------------------------------------------------------------------- */ -#include -#include -#include -#include +#include +#include +#include +#include #include "pair_buck_coul_cut_kokkos.h" #include "kokkos.h" #include "atom_kokkos.h" diff --git a/src/KOKKOS/pair_buck_coul_long_kokkos.cpp b/src/KOKKOS/pair_buck_coul_long_kokkos.cpp index 19af349a63588a464f4e1785be291510fd91acfa..4978d3d7fc3b210ecb98dbd55413014aff67ae8a 100644 --- a/src/KOKKOS/pair_buck_coul_long_kokkos.cpp +++ b/src/KOKKOS/pair_buck_coul_long_kokkos.cpp @@ -15,10 +15,10 @@ Contributing author: Ray Shan (SNL) ------------------------------------------------------------------------- */ -#include -#include -#include -#include +#include +#include +#include +#include #include "pair_buck_coul_long_kokkos.h" #include "kokkos.h" #include "atom_kokkos.h" diff --git a/src/KOKKOS/pair_buck_kokkos.cpp b/src/KOKKOS/pair_buck_kokkos.cpp index fcf14533dc991d469ad1c0e65951ca80d515b0b2..8785700186a94aa2a081873348c69b9712715e6c 100644 --- a/src/KOKKOS/pair_buck_kokkos.cpp +++ b/src/KOKKOS/pair_buck_kokkos.cpp @@ -15,10 +15,10 @@ Contributing author: Stan Moore (SNL) ------------------------------------------------------------------------- */ -#include -#include -#include -#include +#include +#include +#include +#include #include "pair_buck_kokkos.h" #include "kokkos.h" #include "atom_kokkos.h" diff --git a/src/KOKKOS/pair_coul_cut_kokkos.cpp b/src/KOKKOS/pair_coul_cut_kokkos.cpp index e20e243c09aefb7313cbe13ce50a498356ea405d..b6e36d4f0ddaae5d9db211607c0493623d0b76b7 100644 --- a/src/KOKKOS/pair_coul_cut_kokkos.cpp +++ b/src/KOKKOS/pair_coul_cut_kokkos.cpp @@ -11,10 +11,10 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include -#include -#include -#include +#include +#include +#include +#include #include "pair_coul_cut_kokkos.h" #include "kokkos.h" #include "atom_kokkos.h" diff --git a/src/KOKKOS/pair_coul_debye_kokkos.cpp b/src/KOKKOS/pair_coul_debye_kokkos.cpp index 729b24ff29d2a8ca40e54ed0ad9c95d17ec8873a..5d15be7d769a16ff4185a8db0acb7c76d562538f 100644 --- a/src/KOKKOS/pair_coul_debye_kokkos.cpp +++ b/src/KOKKOS/pair_coul_debye_kokkos.cpp @@ -15,10 +15,10 @@ Contributing author: Ray Shan (SNL) ------------------------------------------------------------------------- */ -#include -#include -#include -#include +#include +#include +#include +#include #include "pair_coul_debye_kokkos.h" #include "kokkos.h" #include "atom_kokkos.h" diff --git a/src/KOKKOS/pair_coul_dsf_kokkos.cpp b/src/KOKKOS/pair_coul_dsf_kokkos.cpp index f77e63bbf0551b0412b21e0b7631c098ff082f78..a714f665f7f14e3424c66f5aadaf5b6c355a4c54 100644 --- a/src/KOKKOS/pair_coul_dsf_kokkos.cpp +++ b/src/KOKKOS/pair_coul_dsf_kokkos.cpp @@ -15,10 +15,10 @@ Contributing author: Stan Moore (SNL) ------------------------------------------------------------------------- */ -#include -#include -#include -#include +#include +#include +#include +#include #include "pair_coul_dsf_kokkos.h" #include "kokkos.h" #include "atom_kokkos.h" diff --git a/src/KOKKOS/pair_coul_long_kokkos.cpp b/src/KOKKOS/pair_coul_long_kokkos.cpp index f2ade3f367c0e01b8118d454a3d0259618cffddf..1e8c6c5f4e69f7f0f78ff927f9757c35b2046195 100644 --- a/src/KOKKOS/pair_coul_long_kokkos.cpp +++ b/src/KOKKOS/pair_coul_long_kokkos.cpp @@ -15,10 +15,10 @@ Contributing author: Ray Shan (SNL) ------------------------------------------------------------------------- */ -#include -#include -#include -#include +#include +#include +#include +#include #include "pair_coul_long_kokkos.h" #include "kokkos.h" #include "atom_kokkos.h" diff --git a/src/KOKKOS/pair_coul_wolf_kokkos.cpp b/src/KOKKOS/pair_coul_wolf_kokkos.cpp index 0f3e9b94290918dd78cb8940cc762d5e82494977..2bff824c3dd395e602d08243da7a5426805e9303 100644 --- a/src/KOKKOS/pair_coul_wolf_kokkos.cpp +++ b/src/KOKKOS/pair_coul_wolf_kokkos.cpp @@ -15,10 +15,10 @@ Contributing author: Stan Moore (SNL) ------------------------------------------------------------------------- */ -#include -#include -#include -#include +#include +#include +#include +#include #include "pair_coul_wolf_kokkos.h" #include "kokkos.h" #include "atom_kokkos.h" diff --git a/src/KOKKOS/pair_dpd_fdt_energy_kokkos.cpp b/src/KOKKOS/pair_dpd_fdt_energy_kokkos.cpp index f45da3a131de15aa1a0113ec27c3b2032a2654c4..7ff536f8dd792c77515ec0e0f55a569d1f4763ef 100644 --- a/src/KOKKOS/pair_dpd_fdt_energy_kokkos.cpp +++ b/src/KOKKOS/pair_dpd_fdt_energy_kokkos.cpp @@ -15,10 +15,10 @@ Contributing author: Stan Moore (Sandia) ------------------------------------------------------------------------- */ -#include -#include -#include -#include +#include +#include +#include +#include #include "atom_kokkos.h" #include "atom_vec.h" #include "comm.h" diff --git a/src/KOKKOS/pair_eam_alloy_kokkos.cpp b/src/KOKKOS/pair_eam_alloy_kokkos.cpp index f263cbb6d90be1cd34d5f0f9abab2b4e04174794..f21ea2335dd36c00429064fd3924dd78055ce88f 100644 --- a/src/KOKKOS/pair_eam_alloy_kokkos.cpp +++ b/src/KOKKOS/pair_eam_alloy_kokkos.cpp @@ -15,10 +15,10 @@ Contributing authors: Stan Moore (SNL) ------------------------------------------------------------------------- */ -#include -#include -#include -#include +#include +#include +#include +#include #include "kokkos.h" #include "pair_kokkos.h" #include "pair_eam_alloy_kokkos.h" diff --git a/src/KOKKOS/pair_eam_alloy_kokkos.h b/src/KOKKOS/pair_eam_alloy_kokkos.h index a962f559085d767f10c1b347a83b9d006c68a548..584839967218b3d8ea1079c9cbf7a2ea597436e4 100644 --- a/src/KOKKOS/pair_eam_alloy_kokkos.h +++ b/src/KOKKOS/pair_eam_alloy_kokkos.h @@ -23,7 +23,7 @@ PairStyle(eam/alloy/kk/host,PairEAMAlloyKokkos) #ifndef LMP_PAIR_EAM_ALLOY_KOKKOS_H #define LMP_PAIR_EAM_ALLOY_KOKKOS_H -#include +#include #include "kokkos_base.h" #include "pair_kokkos.h" #include "pair_eam.h" diff --git a/src/KOKKOS/pair_eam_fs_kokkos.cpp b/src/KOKKOS/pair_eam_fs_kokkos.cpp index 05ec1a644b829cc587ca30a4f99148d78dbeeb11..627b56b84ac10e76e9c189d80abde07fe2b8678f 100644 --- a/src/KOKKOS/pair_eam_fs_kokkos.cpp +++ b/src/KOKKOS/pair_eam_fs_kokkos.cpp @@ -15,10 +15,10 @@ Contributing authors: Stan Moore (SNL) ------------------------------------------------------------------------- */ -#include -#include -#include -#include +#include +#include +#include +#include #include "kokkos.h" #include "pair_kokkos.h" #include "pair_eam_fs_kokkos.h" diff --git a/src/KOKKOS/pair_eam_fs_kokkos.h b/src/KOKKOS/pair_eam_fs_kokkos.h index ec87e44ece248f93f0193684311f3587be8ec5d3..ce0b572ea2054113b32064e748a970027b66ab35 100644 --- a/src/KOKKOS/pair_eam_fs_kokkos.h +++ b/src/KOKKOS/pair_eam_fs_kokkos.h @@ -23,7 +23,7 @@ PairStyle(eam/fs/kk/host,PairEAMFSKokkos) #ifndef LMP_PAIR_EAM_FS_KOKKOS_H #define LMP_PAIR_EAM_FS_KOKKOS_H -#include +#include #include "kokkos_base.h" #include "pair_kokkos.h" #include "pair_eam.h" diff --git a/src/KOKKOS/pair_eam_kokkos.cpp b/src/KOKKOS/pair_eam_kokkos.cpp index ffa65acb87db22116d32361ea1c049ae38c69e0a..1bfb8255dc68b089bc7362501691a577970d4af4 100644 --- a/src/KOKKOS/pair_eam_kokkos.cpp +++ b/src/KOKKOS/pair_eam_kokkos.cpp @@ -15,10 +15,10 @@ Contributing authors: Stan Moore (SNL), Christian Trott (SNL) ------------------------------------------------------------------------- */ -#include -#include -#include -#include +#include +#include +#include +#include #include "kokkos.h" #include "pair_kokkos.h" #include "pair_eam_kokkos.h" diff --git a/src/KOKKOS/pair_eam_kokkos.h b/src/KOKKOS/pair_eam_kokkos.h index 34a4795ec54e97986b9cd39e0e79e7932d5d6bd4..c821750da54a0c2faf2eeb49ad0689f016bf1e41 100644 --- a/src/KOKKOS/pair_eam_kokkos.h +++ b/src/KOKKOS/pair_eam_kokkos.h @@ -23,7 +23,7 @@ PairStyle(eam/kk/host,PairEAMKokkos) #ifndef LMP_PAIR_EAM_KOKKOS_H #define LMP_PAIR_EAM_KOKKOS_H -#include +#include #include "kokkos_base.h" #include "pair_kokkos.h" #include "pair_eam.h" diff --git a/src/KOKKOS/pair_exp6_rx_kokkos.cpp b/src/KOKKOS/pair_exp6_rx_kokkos.cpp index 427561d868218dde728e671cf213af6661a94cf0..6ff787b67b82d199867a4d25773d182db5814a69 100644 --- a/src/KOKKOS/pair_exp6_rx_kokkos.cpp +++ b/src/KOKKOS/pair_exp6_rx_kokkos.cpp @@ -15,10 +15,10 @@ Contributing author: Stan Moore (Sandia) ------------------------------------------------------------------------- */ -#include -#include -#include -#include +#include +#include +#include +#include #include "pair_exp6_rx_kokkos.h" #include "atom.h" #include "comm.h" @@ -30,7 +30,7 @@ #include "error.h" #include "modify.h" #include "fix.h" -#include +#include #include "atom_masks.h" #include "neigh_request.h" #include "atom_kokkos.h" diff --git a/src/KOKKOS/pair_hybrid_kokkos.cpp b/src/KOKKOS/pair_hybrid_kokkos.cpp index db757f6ce1847806d266de13037d99b6489732a3..03ad77c34af8d0cc2b7760224ba7eac6814a9043 100644 --- a/src/KOKKOS/pair_hybrid_kokkos.cpp +++ b/src/KOKKOS/pair_hybrid_kokkos.cpp @@ -11,10 +11,10 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include -#include -#include -#include +#include +#include +#include +#include #include "pair_hybrid_kokkos.h" #include "atom_kokkos.h" #include "force.h" diff --git a/src/KOKKOS/pair_hybrid_kokkos.h b/src/KOKKOS/pair_hybrid_kokkos.h index 62d325925b87e188245feb813279c26871769caa..94e034f8757618105b8b64cf37af7ec2d0b13dd6 100644 --- a/src/KOKKOS/pair_hybrid_kokkos.h +++ b/src/KOKKOS/pair_hybrid_kokkos.h @@ -20,7 +20,7 @@ PairStyle(hybrid/kk,PairHybridKokkos) #ifndef LMP_PAIR_HYBRID_KOKKOS_H #define LMP_PAIR_HYBRID_KOKKOS_H -#include +#include #include "pair_hybrid.h" #include "pair_kokkos.h" #include "kokkos_type.h" diff --git a/src/KOKKOS/pair_hybrid_overlay_kokkos.cpp b/src/KOKKOS/pair_hybrid_overlay_kokkos.cpp index aa5d8951552889d492dba8405924d495eb2d63c4..a2c3edab6596061f39cda2e3fb4e1527e36dcd9c 100644 --- a/src/KOKKOS/pair_hybrid_overlay_kokkos.cpp +++ b/src/KOKKOS/pair_hybrid_overlay_kokkos.cpp @@ -11,9 +11,9 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include -#include -#include +#include +#include +#include #include "pair_hybrid_overlay_kokkos.h" #include "atom.h" #include "force.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 70f0c3e00a639b532c236e62f9072e6e3c60e16a..d0d290d1f1c437df18718504e150b6a39f8fdf4c 100644 --- a/src/KOKKOS/pair_lj_charmm_coul_charmm_implicit_kokkos.cpp +++ b/src/KOKKOS/pair_lj_charmm_coul_charmm_implicit_kokkos.cpp @@ -15,10 +15,10 @@ Contributing author: Ray Shan (SNL) ------------------------------------------------------------------------- */ -#include -#include -#include -#include +#include +#include +#include +#include #include "pair_lj_charmm_coul_charmm_implicit_kokkos.h" #include "kokkos.h" #include "atom_kokkos.h" diff --git a/src/KOKKOS/pair_lj_charmm_coul_charmm_kokkos.cpp b/src/KOKKOS/pair_lj_charmm_coul_charmm_kokkos.cpp index 0316b65aedd6754dee21ace6cbc406a5c4ae00a7..2203dfa2a01821771943a3afa7c19ff32cb2ece2 100644 --- a/src/KOKKOS/pair_lj_charmm_coul_charmm_kokkos.cpp +++ b/src/KOKKOS/pair_lj_charmm_coul_charmm_kokkos.cpp @@ -15,10 +15,10 @@ Contributing author: Ray Shan (SNL) ------------------------------------------------------------------------- */ -#include -#include -#include -#include +#include +#include +#include +#include #include "pair_lj_charmm_coul_charmm_kokkos.h" #include "kokkos.h" #include "atom_kokkos.h" diff --git a/src/KOKKOS/pair_lj_charmm_coul_long_kokkos.cpp b/src/KOKKOS/pair_lj_charmm_coul_long_kokkos.cpp index 4d27373824b3ce4b778d54f31b9eb6ad3214f3db..e1ecfbac3c14ce9fe31151077a0ff99a58d8195b 100644 --- a/src/KOKKOS/pair_lj_charmm_coul_long_kokkos.cpp +++ b/src/KOKKOS/pair_lj_charmm_coul_long_kokkos.cpp @@ -15,10 +15,10 @@ Contributing author: Ray Shan (SNL) ------------------------------------------------------------------------- */ -#include -#include -#include -#include +#include +#include +#include +#include #include "pair_lj_charmm_coul_long_kokkos.h" #include "kokkos.h" #include "atom_kokkos.h" diff --git a/src/KOKKOS/pair_lj_class2_coul_cut_kokkos.cpp b/src/KOKKOS/pair_lj_class2_coul_cut_kokkos.cpp index 3f355b1b160bf34df464b833cf1c938e76f5a17e..abd0183e213b679560f8ea685b5da048d9c5580f 100644 --- a/src/KOKKOS/pair_lj_class2_coul_cut_kokkos.cpp +++ b/src/KOKKOS/pair_lj_class2_coul_cut_kokkos.cpp @@ -11,10 +11,10 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include -#include -#include -#include +#include +#include +#include +#include #include "pair_lj_class2_coul_cut_kokkos.h" #include "kokkos.h" #include "atom_kokkos.h" diff --git a/src/KOKKOS/pair_lj_class2_coul_long_kokkos.cpp b/src/KOKKOS/pair_lj_class2_coul_long_kokkos.cpp index 47976ec610aecdef5d6c41bd9d612533e6bc16aa..5f850689d427154ddaeed02d0f23ae6650ca2cdb 100644 --- a/src/KOKKOS/pair_lj_class2_coul_long_kokkos.cpp +++ b/src/KOKKOS/pair_lj_class2_coul_long_kokkos.cpp @@ -11,10 +11,10 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include -#include -#include -#include +#include +#include +#include +#include #include "pair_lj_class2_coul_long_kokkos.h" #include "kokkos.h" #include "atom_kokkos.h" diff --git a/src/KOKKOS/pair_lj_class2_kokkos.cpp b/src/KOKKOS/pair_lj_class2_kokkos.cpp index 5beb520c00feb1971f5248e4ab31a7442133faa7..063753f1f8ccba97326bb580cdd74dd83aab66df 100644 --- a/src/KOKKOS/pair_lj_class2_kokkos.cpp +++ b/src/KOKKOS/pair_lj_class2_kokkos.cpp @@ -15,10 +15,10 @@ Contributing author: Ray Shan (SNL) ------------------------------------------------------------------------- */ -#include -#include -#include -#include +#include +#include +#include +#include #include "pair_lj_class2_kokkos.h" #include "kokkos.h" #include "atom_kokkos.h" diff --git a/src/KOKKOS/pair_lj_cut_coul_cut_kokkos.cpp b/src/KOKKOS/pair_lj_cut_coul_cut_kokkos.cpp index 86e37bea77a6ffadf9ab082a36005ebca6da8aba..a2067f8cf90f4dac64a3d3dadd4be69ff8e51323 100644 --- a/src/KOKKOS/pair_lj_cut_coul_cut_kokkos.cpp +++ b/src/KOKKOS/pair_lj_cut_coul_cut_kokkos.cpp @@ -11,10 +11,10 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include -#include -#include -#include +#include +#include +#include +#include #include "pair_lj_cut_coul_cut_kokkos.h" #include "kokkos.h" #include "atom_kokkos.h" diff --git a/src/KOKKOS/pair_lj_cut_coul_debye_kokkos.cpp b/src/KOKKOS/pair_lj_cut_coul_debye_kokkos.cpp index 76e488c68667e4ac7b19150ba70e876ebc81fe7e..277f1f658c2feabbdcff1ab678f4c8e08dc19d20 100644 --- a/src/KOKKOS/pair_lj_cut_coul_debye_kokkos.cpp +++ b/src/KOKKOS/pair_lj_cut_coul_debye_kokkos.cpp @@ -15,10 +15,10 @@ Contributing author: Ray Shan (SNL) ------------------------------------------------------------------------- */ -#include -#include -#include -#include +#include +#include +#include +#include #include "pair_lj_cut_coul_debye_kokkos.h" #include "kokkos.h" #include "atom_kokkos.h" diff --git a/src/KOKKOS/pair_lj_cut_coul_dsf_kokkos.cpp b/src/KOKKOS/pair_lj_cut_coul_dsf_kokkos.cpp index b64d9fa31a9101425b3b995c9ec711126b0e422f..165bd972763ef52019096ed66566af34ebb552fd 100644 --- a/src/KOKKOS/pair_lj_cut_coul_dsf_kokkos.cpp +++ b/src/KOKKOS/pair_lj_cut_coul_dsf_kokkos.cpp @@ -15,10 +15,10 @@ Contributing author: Ray Shan (SNL) ------------------------------------------------------------------------- */ -#include -#include -#include -#include +#include +#include +#include +#include #include "pair_lj_cut_coul_dsf_kokkos.h" #include "kokkos.h" #include "atom_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 77a604534e2ae907a16db82ed013c26af2ec1042..d02e83eb116060f95ed7177a29e9424e8865d3e1 100644 --- a/src/KOKKOS/pair_lj_cut_coul_long_kokkos.cpp +++ b/src/KOKKOS/pair_lj_cut_coul_long_kokkos.cpp @@ -11,10 +11,10 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include -#include -#include -#include +#include +#include +#include +#include #include "pair_lj_cut_coul_long_kokkos.h" #include "kokkos.h" #include "atom_kokkos.h" diff --git a/src/KOKKOS/pair_lj_cut_kokkos.cpp b/src/KOKKOS/pair_lj_cut_kokkos.cpp index 2a228fb168be97184fda12d80b012745b286fa80..daaab8d29ea45cc19c73f8c8b26a5ed8826684f6 100644 --- a/src/KOKKOS/pair_lj_cut_kokkos.cpp +++ b/src/KOKKOS/pair_lj_cut_kokkos.cpp @@ -11,10 +11,10 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include -#include -#include -#include +#include +#include +#include +#include #include "pair_lj_cut_kokkos.h" #include "kokkos.h" #include "atom_kokkos.h" diff --git a/src/KOKKOS/pair_lj_expand_kokkos.cpp b/src/KOKKOS/pair_lj_expand_kokkos.cpp index aca7202b78be66a04ce7443e7eb4f34c34a6a6e0..55c8b200efc4c411b629503b47836b227ce9860e 100644 --- a/src/KOKKOS/pair_lj_expand_kokkos.cpp +++ b/src/KOKKOS/pair_lj_expand_kokkos.cpp @@ -15,10 +15,10 @@ Contributing author: Ray Shan (SNL) ------------------------------------------------------------------------- */ -#include -#include -#include -#include +#include +#include +#include +#include #include "pair_lj_expand_kokkos.h" #include "kokkos.h" #include "atom_kokkos.h" diff --git a/src/KOKKOS/pair_lj_gromacs_coul_gromacs_kokkos.cpp b/src/KOKKOS/pair_lj_gromacs_coul_gromacs_kokkos.cpp index 1cc8d9b3e2f042cd468afe8b4f151872e97215c7..b7fb5acccb7d147bc04e8498ae3a1808d9c2a169 100644 --- a/src/KOKKOS/pair_lj_gromacs_coul_gromacs_kokkos.cpp +++ b/src/KOKKOS/pair_lj_gromacs_coul_gromacs_kokkos.cpp @@ -15,10 +15,10 @@ Contributing author: Ray Shan (SNL) ------------------------------------------------------------------------- */ -#include -#include -#include -#include +#include +#include +#include +#include #include "pair_lj_gromacs_coul_gromacs_kokkos.h" #include "kokkos.h" #include "atom_kokkos.h" diff --git a/src/KOKKOS/pair_lj_gromacs_kokkos.cpp b/src/KOKKOS/pair_lj_gromacs_kokkos.cpp index f0ad9357694dc64b163f6a5d9c3307159a43ee48..5d2725ccddf7dd778271d7155b08b50a88af8754 100644 --- a/src/KOKKOS/pair_lj_gromacs_kokkos.cpp +++ b/src/KOKKOS/pair_lj_gromacs_kokkos.cpp @@ -15,10 +15,10 @@ Contributing author: Ray Shan (SNL) ------------------------------------------------------------------------- */ -#include -#include -#include -#include +#include +#include +#include +#include #include "pair_lj_gromacs_kokkos.h" #include "kokkos.h" #include "atom_kokkos.h" diff --git a/src/KOKKOS/pair_lj_sdk_kokkos.cpp b/src/KOKKOS/pair_lj_sdk_kokkos.cpp index aa579d5dc12995475731589da686ee4271867db9..8f719582fa981d4d856cabc4cc8b19740531a22f 100644 --- a/src/KOKKOS/pair_lj_sdk_kokkos.cpp +++ b/src/KOKKOS/pair_lj_sdk_kokkos.cpp @@ -11,10 +11,10 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include -#include -#include -#include +#include +#include +#include +#include #include "pair_lj_sdk_kokkos.h" #include "kokkos.h" #include "atom_kokkos.h" diff --git a/src/KOKKOS/pair_morse_kokkos.cpp b/src/KOKKOS/pair_morse_kokkos.cpp index dd555b6eb9cf937be79a1377096a4687b026ca92..97c5f9be84ae10ecf3a1c98a8880701da08556d9 100644 --- a/src/KOKKOS/pair_morse_kokkos.cpp +++ b/src/KOKKOS/pair_morse_kokkos.cpp @@ -15,10 +15,10 @@ Contributing authors: Stefan Paquay (Eindhoven University of Technology) ------------------------------------------------------------------------- */ -#include -#include -#include -#include +#include +#include +#include +#include #include "pair_morse_kokkos.h" #include "kokkos.h" #include "atom_kokkos.h" diff --git a/src/KOKKOS/pair_multi_lucy_rx_kokkos.cpp b/src/KOKKOS/pair_multi_lucy_rx_kokkos.cpp index 7cb869a8a558bc524d172bf31b529554cfd0866d..a6af26cb0ffa891584ad622d2c6510e190f03b09 100644 --- a/src/KOKKOS/pair_multi_lucy_rx_kokkos.cpp +++ b/src/KOKKOS/pair_multi_lucy_rx_kokkos.cpp @@ -22,10 +22,10 @@ ------------------------------------------------------------------------------------------- */ #include -#include +#include #include "math_const.h" -#include -#include +#include +#include #include "pair_multi_lucy_rx_kokkos.h" #include "atom_kokkos.h" #include "force.h" diff --git a/src/KOKKOS/pair_reaxc_kokkos.cpp b/src/KOKKOS/pair_reaxc_kokkos.cpp index 9352d8367c441919accde7f5a2c286f739ac26cb..bb9f8ab417fab2f659f17f18b58ad38b51861279 100644 --- a/src/KOKKOS/pair_reaxc_kokkos.cpp +++ b/src/KOKKOS/pair_reaxc_kokkos.cpp @@ -15,10 +15,10 @@ Contributing author: Ray Shan (SNL), Stan Moore (SNL) ------------------------------------------------------------------------- */ -#include -#include -#include -#include +#include +#include +#include +#include #include "pair_reaxc_kokkos.h" #include "kokkos.h" #include "atom_kokkos.h" diff --git a/src/KOKKOS/pair_reaxc_kokkos.h b/src/KOKKOS/pair_reaxc_kokkos.h index e69b80c2a7f5bcabdc982c2e133952def3910e1b..5175e274a8998f45ee6d8f40116f1bf47f671af3 100644 --- a/src/KOKKOS/pair_reaxc_kokkos.h +++ b/src/KOKKOS/pair_reaxc_kokkos.h @@ -23,7 +23,7 @@ PairStyle(reax/c/kk/host,PairReaxCKokkos) #ifndef LMP_PAIR_REAXC_KOKKOS_H #define LMP_PAIR_REAXC_KOKKOS_H -#include +#include #include "pair_kokkos.h" #include "pair_reaxc.h" #include "neigh_list_kokkos.h" diff --git a/src/KOKKOS/pair_snap_kokkos_impl.h b/src/KOKKOS/pair_snap_kokkos_impl.h index d79cfef24b599a2d347b17aeed9e2512b4249679..a024e5cbd19238a739663870c8e21fcabaea0a41 100644 --- a/src/KOKKOS/pair_snap_kokkos_impl.h +++ b/src/KOKKOS/pair_snap_kokkos_impl.h @@ -15,9 +15,9 @@ Contributing authors: Christian Trott (SNL), Stan Moore (SNL) ------------------------------------------------------------------------- */ -#include -#include -#include +#include +#include +#include #include "pair_snap_kokkos.h" #include "atom_kokkos.h" #include "error.h" diff --git a/src/KOKKOS/pair_sw_kokkos.cpp b/src/KOKKOS/pair_sw_kokkos.cpp index a19e2fc271d0292e6e6c2d9d487c29a82c886135..8f4903c76794a4c7a1d38b5bbbf1b53894788bda 100644 --- a/src/KOKKOS/pair_sw_kokkos.cpp +++ b/src/KOKKOS/pair_sw_kokkos.cpp @@ -15,10 +15,10 @@ Contributing author: Stan Moore (SNL) ------------------------------------------------------------------------- */ -#include -#include -#include -#include +#include +#include +#include +#include #include "pair_sw_kokkos.h" #include "kokkos.h" #include "pair_kokkos.h" diff --git a/src/KOKKOS/pair_table_kokkos.cpp b/src/KOKKOS/pair_table_kokkos.cpp index e3e4ee01f397c750636fde67868fc7bf17f9555d..7b06f814bb4624874ca16f313f9faeda83cea9db 100644 --- a/src/KOKKOS/pair_table_kokkos.cpp +++ b/src/KOKKOS/pair_table_kokkos.cpp @@ -16,9 +16,9 @@ ------------------------------------------------------------------------- */ #include -#include -#include -#include +#include +#include +#include #include "pair_table_kokkos.h" #include "kokkos.h" #include "atom.h" diff --git a/src/KOKKOS/pair_table_rx_kokkos.cpp b/src/KOKKOS/pair_table_rx_kokkos.cpp index 0b1e0ee9e6f6adbaaef11d5011287269d8f4ed64..30ca54986b7d378d1ed88e26cf86597f8a775709 100644 --- a/src/KOKKOS/pair_table_rx_kokkos.cpp +++ b/src/KOKKOS/pair_table_rx_kokkos.cpp @@ -16,9 +16,9 @@ ------------------------------------------------------------------------- */ #include -#include -#include -#include +#include +#include +#include #include "pair_table_rx_kokkos.h" #include "kokkos.h" #include "atom.h" diff --git a/src/KOKKOS/pair_tersoff_kokkos.cpp b/src/KOKKOS/pair_tersoff_kokkos.cpp index 1fb97f913f8d560d7c9c3605fe577d08efffe711..cb4def2d373b4d3950334997b98ab09ffe0efe14 100644 --- a/src/KOKKOS/pair_tersoff_kokkos.cpp +++ b/src/KOKKOS/pair_tersoff_kokkos.cpp @@ -15,10 +15,10 @@ Contributing author: Ray Shan (SNL) and Christian Trott (SNL) ------------------------------------------------------------------------- */ -#include -#include -#include -#include +#include +#include +#include +#include #include "pair_tersoff_kokkos.h" #include "kokkos.h" #include "atom_kokkos.h" diff --git a/src/KOKKOS/pair_tersoff_kokkos.h b/src/KOKKOS/pair_tersoff_kokkos.h index f40d28b72bd96549f2fd53cd6ac191acda55d0fa..2dac2c5991fe1ba733b7ae1bedb7c9e640c1b645 100644 --- a/src/KOKKOS/pair_tersoff_kokkos.h +++ b/src/KOKKOS/pair_tersoff_kokkos.h @@ -23,7 +23,7 @@ PairStyle(tersoff/kk/host,PairTersoffKokkos) #ifndef LMP_PAIR_TERSOFF_KOKKOS_H #define LMP_PAIR_TERSOFF_KOKKOS_H -#include +#include #include "pair_kokkos.h" #include "pair_tersoff.h" #include "neigh_list_kokkos.h" diff --git a/src/KOKKOS/pair_tersoff_mod_kokkos.cpp b/src/KOKKOS/pair_tersoff_mod_kokkos.cpp index a30e1229f2a6959d35d462ff006e8ceabb07747b..0d150f83e4a084a8d92a24a79f806aecea3e34c3 100644 --- a/src/KOKKOS/pair_tersoff_mod_kokkos.cpp +++ b/src/KOKKOS/pair_tersoff_mod_kokkos.cpp @@ -15,10 +15,10 @@ Contributing author: Ray Shan (SNL) ------------------------------------------------------------------------- */ -#include -#include -#include -#include +#include +#include +#include +#include #include "pair_tersoff_mod_kokkos.h" #include "kokkos.h" #include "atom_kokkos.h" diff --git a/src/KOKKOS/pair_tersoff_mod_kokkos.h b/src/KOKKOS/pair_tersoff_mod_kokkos.h index c9995b2904349a03dffbe32bd7f234c2bf4f5225..dd5efb50f1da33e7743f6c8c4d51c5e1e9086dee 100644 --- a/src/KOKKOS/pair_tersoff_mod_kokkos.h +++ b/src/KOKKOS/pair_tersoff_mod_kokkos.h @@ -23,7 +23,7 @@ PairStyle(tersoff/mod/kk/host,PairTersoffMODKokkos) #ifndef LMP_PAIR_TERSOFF_MOD_KOKKOS_H #define LMP_PAIR_TERSOFF_MOD_KOKKOS_H -#include +#include #include "pair_kokkos.h" #include "pair_tersoff_mod.h" #include "neigh_list_kokkos.h" diff --git a/src/KOKKOS/pair_tersoff_zbl_kokkos.cpp b/src/KOKKOS/pair_tersoff_zbl_kokkos.cpp index aeefbf67f688caf403ca4e6a10d9a49ffc3e08cf..2fb9675db60efa9b5ebda7e81dee5e1271d021fd 100644 --- a/src/KOKKOS/pair_tersoff_zbl_kokkos.cpp +++ b/src/KOKKOS/pair_tersoff_zbl_kokkos.cpp @@ -15,10 +15,10 @@ Contributing author: Ray Shan (SNL) ------------------------------------------------------------------------- */ -#include -#include -#include -#include +#include +#include +#include +#include #include "pair_tersoff_zbl_kokkos.h" #include "kokkos.h" #include "atom_kokkos.h" diff --git a/src/KOKKOS/pair_tersoff_zbl_kokkos.h b/src/KOKKOS/pair_tersoff_zbl_kokkos.h index 92239532be72bae61ab223999f29a45d6ccab54d..45982bd420b5b860291a54e29ecf0f9f79581063 100644 --- a/src/KOKKOS/pair_tersoff_zbl_kokkos.h +++ b/src/KOKKOS/pair_tersoff_zbl_kokkos.h @@ -23,7 +23,7 @@ PairStyle(tersoff/zbl/kk/host,PairTersoffZBLKokkos) #ifndef LMP_PAIR_TERSOFF_ZBL_KOKKOS_H #define LMP_PAIR_TERSOFF_ZBL_KOKKOS_H -#include +#include #include "pair_kokkos.h" #include "pair_tersoff_zbl.h" #include "neigh_list_kokkos.h" diff --git a/src/KOKKOS/pair_vashishta_kokkos.cpp b/src/KOKKOS/pair_vashishta_kokkos.cpp index 2e4989356eab8b296f8ff87e882907101e82ae91..3d4bd22a3cb33913e7b8e96eb4bff020e7a27627 100644 --- a/src/KOKKOS/pair_vashishta_kokkos.cpp +++ b/src/KOKKOS/pair_vashishta_kokkos.cpp @@ -15,10 +15,10 @@ Contributing author: Anders Hafreager (UiO), andershaf@gmail.com ------------------------------------------------------------------------- */ -#include -#include -#include -#include +#include +#include +#include +#include #include "pair_vashishta_kokkos.h" #include "kokkos.h" #include "pair_kokkos.h" diff --git a/src/KOKKOS/pair_yukawa_kokkos.cpp b/src/KOKKOS/pair_yukawa_kokkos.cpp index 6560ec9684b3f88abb0143aeb39ca791de02affb..8fc2fda1207a74c21ebda02a136348a796142b28 100644 --- a/src/KOKKOS/pair_yukawa_kokkos.cpp +++ b/src/KOKKOS/pair_yukawa_kokkos.cpp @@ -14,8 +14,8 @@ /* ---------------------------------------------------------------------- Contributing authors: Stefan Paquay (Brandeis University) ------------------------------------------------------------------------- */ -#include -#include +#include +#include #include "pair_yukawa_kokkos.h" #include "kokkos.h" #include "atom_kokkos.h" diff --git a/src/KOKKOS/pair_zbl_kokkos.cpp b/src/KOKKOS/pair_zbl_kokkos.cpp index 0ed9e62dfff2d496dde2d9cac65ab31423cb0982..f57d5eaad0cccf6751a839a96e3926270cfcb7a3 100644 --- a/src/KOKKOS/pair_zbl_kokkos.cpp +++ b/src/KOKKOS/pair_zbl_kokkos.cpp @@ -15,10 +15,10 @@ Contributing authors: Stan Moore (SNL) ------------------------------------------------------------------------- */ -#include -#include -#include -#include +#include +#include +#include +#include #include "pair_zbl_kokkos.h" #include "atom_kokkos.h" #include "comm.h" diff --git a/src/KOKKOS/pppm_kokkos.cpp b/src/KOKKOS/pppm_kokkos.cpp index a28e462044ac7a4f1b674b620c7c3102a846c9aa..13683d148f91d351dfe166da79925ebd20be9a35 100644 --- a/src/KOKKOS/pppm_kokkos.cpp +++ b/src/KOKKOS/pppm_kokkos.cpp @@ -16,10 +16,10 @@ ------------------------------------------------------------------------- */ #include -#include -#include -#include -#include +#include +#include +#include +#include #include "pppm_kokkos.h" #include "atom_kokkos.h" #include "comm.h" @@ -1579,7 +1579,7 @@ void PPPMKokkos::particle_map() k_flag.template modify(); k_flag.template sync(); - if (!ISFINITE(boxlo[0]) || !ISFINITE(boxlo[1]) || !ISFINITE(boxlo[2])) + if (!std::isfinite(boxlo[0]) || !std::isfinite(boxlo[1]) || !std::isfinite(boxlo[2])) error->one(FLERR,"Non-numeric box dimensions - simulation unstable"); copymode = 1; diff --git a/src/KOKKOS/region_block_kokkos.cpp b/src/KOKKOS/region_block_kokkos.cpp index eed4272f2302b7244be637409054ddac7a4d59f9..8ff6e8937d0919f905599c7b95bb6c01a9f7c0d6 100644 --- a/src/KOKKOS/region_block_kokkos.cpp +++ b/src/KOKKOS/region_block_kokkos.cpp @@ -11,8 +11,8 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include -#include +#include +#include #include "region_block_kokkos.h" #include "domain.h" #include "force.h" diff --git a/src/KOKKOS/sna_kokkos_impl.h b/src/KOKKOS/sna_kokkos_impl.h index ccc4010f68af839e39f59a0277231e618b1d6d0e..25561fef5d0decf60f4ab6d74d3e8cf20693c9ff 100644 --- a/src/KOKKOS/sna_kokkos_impl.h +++ b/src/KOKKOS/sna_kokkos_impl.h @@ -16,9 +16,9 @@ ------------------------------------------------------------------------- */ #include "sna_kokkos.h" -#include -#include -#include +#include +#include +#include using namespace LAMMPS_NS; diff --git a/src/KOKKOS/verlet_kokkos.cpp b/src/KOKKOS/verlet_kokkos.cpp index fe11e6b3fa4986459ad9847ec3f41b6d72ccd72e..136e543a2cd708501004d2f94290b21454dabe0a 100644 --- a/src/KOKKOS/verlet_kokkos.cpp +++ b/src/KOKKOS/verlet_kokkos.cpp @@ -11,7 +11,7 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include +#include #include "verlet_kokkos.h" #include "neighbor.h" #include "domain.h" diff --git a/src/KSPACE/ewald.cpp b/src/KSPACE/ewald.cpp index 766520172b46e0c5103c7821bad3dc70c612ff3a..0ced09eb93610c42a13bdabe19f5067081735f25 100644 --- a/src/KSPACE/ewald.cpp +++ b/src/KSPACE/ewald.cpp @@ -19,10 +19,10 @@ ------------------------------------------------------------------------- */ #include -#include -#include -#include -#include +#include +#include +#include +#include #include "ewald.h" #include "atom.h" #include "comm.h" diff --git a/src/KSPACE/ewald_disp.cpp b/src/KSPACE/ewald_disp.cpp index e0424b0d932b7d4adbd50a5272695abe08da1fb9..fb48edc117ae48ce986ba9f794bcc58bfe0b062f 100644 --- a/src/KSPACE/ewald_disp.cpp +++ b/src/KSPACE/ewald_disp.cpp @@ -16,10 +16,10 @@ ------------------------------------------------------------------------- */ #include -#include -#include -#include -#include +#include +#include +#include +#include #include "ewald_disp.h" #include "math_vector.h" #include "math_const.h" diff --git a/src/KSPACE/fft3d.cpp b/src/KSPACE/fft3d.cpp index 2a0d85bac655ff24000fb8755c4b531a47358763..6da7f197ee7024bb3a6457f33a21138ad24d0a73 100644 --- a/src/KSPACE/fft3d.cpp +++ b/src/KSPACE/fft3d.cpp @@ -20,9 +20,9 @@ ------------------------------------------------------------------------- */ #include -#include -#include -#include +#include +#include +#include #include "fft3d.h" #include "remap.h" diff --git a/src/KSPACE/fix_tune_kspace.cpp b/src/KSPACE/fix_tune_kspace.cpp index 5ce867778d838eab52147a2edd55c76fd809048e..399e551b57dff8afea6a128bb88f6713572168a5 100644 --- a/src/KSPACE/fix_tune_kspace.cpp +++ b/src/KSPACE/fix_tune_kspace.cpp @@ -15,8 +15,8 @@ Contributing author: Paul Crozier (SNL) ------------------------------------------------------------------------- */ -#include -#include +#include +#include #include "fix_tune_kspace.h" #include "update.h" #include "domain.h" diff --git a/src/KSPACE/fix_tune_kspace.h b/src/KSPACE/fix_tune_kspace.h index 3311bd1d430ee35c12c9c20aaa090d975efc8611..6f40fc8711e32f501237ef8f629dc3065beaea60 100644 --- a/src/KSPACE/fix_tune_kspace.h +++ b/src/KSPACE/fix_tune_kspace.h @@ -20,7 +20,7 @@ FixStyle(tune/kspace,FixTuneKspace) #ifndef LMP_FIX_TUNE_KSPACE_H #define LMP_FIX_TUNE_KSPACE_H -#include +#include #include "fix.h" namespace LAMMPS_NS { diff --git a/src/KSPACE/kissfft.h b/src/KSPACE/kissfft.h index ec6ef97feab0eb3017fa15eae33c0a4d5a58a49d..4e15f494a972f817a23208d53b6d5c80e1f121ad 100644 --- a/src/KSPACE/kissfft.h +++ b/src/KSPACE/kissfft.h @@ -16,9 +16,9 @@ #ifndef LMP_FFT_KISSFFT #define LMP_FFT_KISSFFT -#include -#include -#include +#include +#include +#include #if defined(_OPENMP) #include diff --git a/src/KSPACE/msm.cpp b/src/KSPACE/msm.cpp index c151095a6724e827f101b057be6de2b9420517cb..9f3221449bb2329923cfa9ed987beb6f26e58e3f 100644 --- a/src/KSPACE/msm.cpp +++ b/src/KSPACE/msm.cpp @@ -16,10 +16,10 @@ ------------------------------------------------------------------------- */ #include -#include -#include -#include -#include +#include +#include +#include +#include #include "msm.h" #include "atom.h" #include "comm.h" @@ -1442,7 +1442,7 @@ void MSM::particle_map() int flag = 0; - if (!ISFINITE(boxlo[0]) || !ISFINITE(boxlo[1]) || !ISFINITE(boxlo[2])) + if (!std::isfinite(boxlo[0]) || !std::isfinite(boxlo[1]) || !std::isfinite(boxlo[2])) error->one(FLERR,"Non-numeric box dimensions - simulation unstable"); for (int i = 0; i < nlocal; i++) { @@ -2261,7 +2261,7 @@ void MSM::restriction(int n) double ***qgrid2 = qgrid[n+1]; int k = 0; - int index[p+2]; + int *index = new int[p+2]; for (int nu=-p; nu<=p; nu++) { if (nu%2 == 0 && nu != 0) continue; phi1d[0][k] = compute_phi(nu*delxinv[n+1]/delxinv[n]); @@ -2317,7 +2317,7 @@ void MSM::restriction(int n) } qgrid2[kp][jp][ip] += q2sum; } - + delete[] index; } /* ---------------------------------------------------------------------- @@ -2348,7 +2348,7 @@ void MSM::prolongation(int n) double ***v5grid2 = v5grid[n+1]; int k = 0; - int index[p+2]; + int *index = new int[p+2]; for (int nu=-p; nu<=p; nu++) { if (nu%2 == 0 && nu != 0) continue; phi1d[0][k] = compute_phi(nu*delxinv[n+1]/delxinv[n]); @@ -2420,7 +2420,7 @@ void MSM::prolongation(int n) } } - + delete[] index; } /* ---------------------------------------------------------------------- diff --git a/src/KSPACE/msm_cg.cpp b/src/KSPACE/msm_cg.cpp index 3354593ec86f58ad533427bf336ee2bd3df58b2f..3ae3d627251c02951bdf62c6653c535c87e6814f 100644 --- a/src/KSPACE/msm_cg.cpp +++ b/src/KSPACE/msm_cg.cpp @@ -16,10 +16,10 @@ ------------------------------------------------------------------------- */ #include -#include -#include -#include -#include +#include +#include +#include +#include #include "atom.h" #include "gridcomm.h" #include "domain.h" @@ -314,7 +314,7 @@ void MSMCG::particle_map() int flag = 0; int i; - if (!ISFINITE(boxlo[0]) || !ISFINITE(boxlo[1]) || !ISFINITE(boxlo[2])) + if (!std::isfinite(boxlo[0]) || !std::isfinite(boxlo[1]) || !std::isfinite(boxlo[2])) error->one(FLERR,"Non-numeric box dimensions - simulation unstable"); for (int j = 0; j < num_charged; j++) { diff --git a/src/KSPACE/pair_born_coul_long.cpp b/src/KSPACE/pair_born_coul_long.cpp index 479128ef2b4ad070a5b567543652c6b93762d881..d55a5a3afe7e239480daa22f17712a020c44cc2f 100644 --- a/src/KSPACE/pair_born_coul_long.cpp +++ b/src/KSPACE/pair_born_coul_long.cpp @@ -15,10 +15,10 @@ Contributing author: Ahmed Ismail (SNL) ------------------------------------------------------------------------- */ -#include -#include -#include -#include +#include +#include +#include +#include #include "pair_born_coul_long.h" #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 6ed120cdc575341614e92e9d82ea2f2c654383a8..775d26df95e131fe812069c8124555739cee2f70 100644 --- a/src/KSPACE/pair_born_coul_msm.cpp +++ b/src/KSPACE/pair_born_coul_msm.cpp @@ -15,10 +15,10 @@ Contributing author: Stan Moore (SNL), Paul Crozier (SNL) ------------------------------------------------------------------------- */ -#include -#include -#include -#include +#include +#include +#include +#include #include "pair_born_coul_msm.h" #include "atom.h" #include "comm.h" diff --git a/src/KSPACE/pair_buck_coul_long.cpp b/src/KSPACE/pair_buck_coul_long.cpp index 95496409b98fb21387c939da1dca06104445c3af..a37e4ab4e9429180b786d6d110512355ae3f4095 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 -#include -#include -#include +#include +#include +#include +#include #include "pair_buck_coul_long.h" #include "atom.h" #include "comm.h" diff --git a/src/KSPACE/pair_buck_coul_msm.cpp b/src/KSPACE/pair_buck_coul_msm.cpp index e33bdc839c3dfaf4e97223381ba5121450170566..fc72f1a4d6886b275a8b195a162364f85ae50ddf 100644 --- a/src/KSPACE/pair_buck_coul_msm.cpp +++ b/src/KSPACE/pair_buck_coul_msm.cpp @@ -11,10 +11,10 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include -#include -#include -#include +#include +#include +#include +#include #include "pair_buck_coul_msm.h" #include "atom.h" #include "comm.h" diff --git a/src/KSPACE/pair_buck_long_coul_long.cpp b/src/KSPACE/pair_buck_long_coul_long.cpp index 7781e24a5ee8febd641a3af783bf9ede7ad47582..55825b56571c492eca8c3262a75916e29f82ae60 100644 --- a/src/KSPACE/pair_buck_long_coul_long.cpp +++ b/src/KSPACE/pair_buck_long_coul_long.cpp @@ -15,10 +15,10 @@ Contributing author: Pieter J. in 't Veld (SNL) ------------------------------------------------------------------------- */ -#include -#include -#include -#include +#include +#include +#include +#include #include "math_vector.h" #include "pair_buck_long_coul_long.h" #include "atom.h" diff --git a/src/KSPACE/pair_coul_long.cpp b/src/KSPACE/pair_coul_long.cpp index 988694153afa952e71a403f859a0106860496a5a..4b10782ee646c23268fb5603cacb3f730336f1ba 100644 --- a/src/KSPACE/pair_coul_long.cpp +++ b/src/KSPACE/pair_coul_long.cpp @@ -15,10 +15,10 @@ Contributing author: Paul Crozier (SNL) ------------------------------------------------------------------------- */ -#include -#include -#include -#include +#include +#include +#include +#include #include "pair_coul_long.h" #include "atom.h" #include "comm.h" diff --git a/src/KSPACE/pair_coul_msm.cpp b/src/KSPACE/pair_coul_msm.cpp index 62daee9a13695636aa3f10153bf7e4a2603f143d..f5cd9a04452a2a6c16a03e15527c47c331d11913 100644 --- a/src/KSPACE/pair_coul_msm.cpp +++ b/src/KSPACE/pair_coul_msm.cpp @@ -15,10 +15,10 @@ Contributing authors: Stan Moore (SNL), Paul Crozier (SNL) ------------------------------------------------------------------------- */ -#include -#include -#include -#include +#include +#include +#include +#include #include "pair_coul_msm.h" #include "atom.h" #include "comm.h" diff --git a/src/KSPACE/pair_lj_charmm_coul_long.cpp b/src/KSPACE/pair_lj_charmm_coul_long.cpp index daa493cef06e6327966c9dfb490a33c071ff8a22..749d9657aacc6c0418ed04b059a737a031e3dfc0 100644 --- a/src/KSPACE/pair_lj_charmm_coul_long.cpp +++ b/src/KSPACE/pair_lj_charmm_coul_long.cpp @@ -15,10 +15,10 @@ Contributing author: Paul Crozier (SNL) ------------------------------------------------------------------------- */ -#include -#include -#include -#include +#include +#include +#include +#include #include "pair_lj_charmm_coul_long.h" #include "atom.h" #include "comm.h" diff --git a/src/KSPACE/pair_lj_charmm_coul_msm.cpp b/src/KSPACE/pair_lj_charmm_coul_msm.cpp index 00617c0bf2331a51ba721cc9a8ba05ba5209f2ec..aecadcf127394e0b89dcbf56605e5e34ad7cfc81 100644 --- a/src/KSPACE/pair_lj_charmm_coul_msm.cpp +++ b/src/KSPACE/pair_lj_charmm_coul_msm.cpp @@ -15,10 +15,10 @@ Contributing authors: Paul Crozier (SNL), Stan Moore (SNL) ------------------------------------------------------------------------- */ -#include -#include -#include -#include +#include +#include +#include +#include #include "pair_lj_charmm_coul_msm.h" #include "atom.h" #include "comm.h" diff --git a/src/KSPACE/pair_lj_charmmfsw_coul_long.cpp b/src/KSPACE/pair_lj_charmmfsw_coul_long.cpp index 4a37ddb81fa29989b06eb0934637ed77cf7931ff..614980117e4e8b9c45de65a80b8547a6b42f9d0b 100644 --- a/src/KSPACE/pair_lj_charmmfsw_coul_long.cpp +++ b/src/KSPACE/pair_lj_charmmfsw_coul_long.cpp @@ -19,10 +19,10 @@ additional assistance from Robert A. Latour, Clemson University ------------------------------------------------------------------------- */ -#include -#include -#include -#include +#include +#include +#include +#include #include "pair_lj_charmmfsw_coul_long.h" #include "atom.h" #include "update.h" diff --git a/src/KSPACE/pair_lj_cut_coul_long.cpp b/src/KSPACE/pair_lj_cut_coul_long.cpp index 3096df2b01626e1fbfd255c176ed0803bf07817c..c9530fe157f5fcfa012b8fdb7ea49a9d2dc4c0aa 100644 --- a/src/KSPACE/pair_lj_cut_coul_long.cpp +++ b/src/KSPACE/pair_lj_cut_coul_long.cpp @@ -15,10 +15,10 @@ Contributing author: Paul Crozier (SNL) ------------------------------------------------------------------------- */ -#include -#include -#include -#include +#include +#include +#include +#include #include "pair_lj_cut_coul_long.h" #include "atom.h" #include "comm.h" diff --git a/src/KSPACE/pair_lj_cut_coul_msm.cpp b/src/KSPACE/pair_lj_cut_coul_msm.cpp index 9f901db9fcfbb2375734877b0a918368cd49d5cb..78c364bd6aae4a416945e22e207bc28985ba0471 100644 --- a/src/KSPACE/pair_lj_cut_coul_msm.cpp +++ b/src/KSPACE/pair_lj_cut_coul_msm.cpp @@ -15,10 +15,10 @@ Contributing authors: Stan Moore (SNL), Paul Crozier (SNL) ------------------------------------------------------------------------- */ -#include -#include -#include -#include +#include +#include +#include +#include #include "pair_lj_cut_coul_msm.h" #include "atom.h" #include "comm.h" diff --git a/src/KSPACE/pair_lj_cut_tip4p_long.cpp b/src/KSPACE/pair_lj_cut_tip4p_long.cpp index 588d21ac66be082e4bb9c8412bddd39261fc54fa..d622a83b394e95e48195cb037ba35ab67536e3b6 100644 --- a/src/KSPACE/pair_lj_cut_tip4p_long.cpp +++ b/src/KSPACE/pair_lj_cut_tip4p_long.cpp @@ -16,10 +16,10 @@ simpler force assignment added by Rolf Isele-Holder (Aachen University) ------------------------------------------------------------------------- */ -#include -#include -#include -#include +#include +#include +#include +#include #include "pair_lj_cut_tip4p_long.h" #include "angle.h" #include "atom.h" diff --git a/src/KSPACE/pair_lj_long_coul_long.cpp b/src/KSPACE/pair_lj_long_coul_long.cpp index f6f6ebd6a2988e1faa00495d348818d2579aea47..32d6d9e0a3e82e602d838beade4b656496e689b3 100644 --- a/src/KSPACE/pair_lj_long_coul_long.cpp +++ b/src/KSPACE/pair_lj_long_coul_long.cpp @@ -17,10 +17,10 @@ University New Orleans) ------------------------------------------------------------------------- */ -#include -#include -#include -#include +#include +#include +#include +#include #include "math_vector.h" #include "pair_lj_long_coul_long.h" #include "atom.h" diff --git a/src/KSPACE/pair_lj_long_tip4p_long.cpp b/src/KSPACE/pair_lj_long_tip4p_long.cpp index 6dd552c819d2bbd918508240ae5fe2a03c2f7015..78316b9daad147c3fb7b236760c13a99a08c89dd 100644 --- a/src/KSPACE/pair_lj_long_tip4p_long.cpp +++ b/src/KSPACE/pair_lj_long_tip4p_long.cpp @@ -16,10 +16,10 @@ Rolf Isele-Holder (Aachen University) ------------------------------------------------------------------------- */ -#include -#include -#include -#include +#include +#include +#include +#include #include "pair_lj_long_tip4p_long.h" #include "angle.h" #include "atom.h" diff --git a/src/KSPACE/pair_tip4p_long.cpp b/src/KSPACE/pair_tip4p_long.cpp index 1dd57ce822c90751b523397f29ec636eaaffa49b..ac428d483af745221d89146d9de6f576c0923c8d 100644 --- a/src/KSPACE/pair_tip4p_long.cpp +++ b/src/KSPACE/pair_tip4p_long.cpp @@ -16,10 +16,10 @@ simpler force assignment added by Rolf Isele-Holder (Aachen University) ------------------------------------------------------------------------- */ -#include -#include -#include -#include +#include +#include +#include +#include #include "pair_tip4p_long.h" #include "angle.h" #include "atom.h" diff --git a/src/KSPACE/pppm.cpp b/src/KSPACE/pppm.cpp index bc82dce5320a7e8ea87d75dc6d29b18a86561263..132389b7d619b22d8f71cb0caf696e12498ab10c 100644 --- a/src/KSPACE/pppm.cpp +++ b/src/KSPACE/pppm.cpp @@ -19,10 +19,10 @@ ------------------------------------------------------------------------- */ #include -#include -#include -#include -#include +#include +#include +#include +#include #include "pppm.h" #include "atom.h" #include "comm.h" @@ -1913,7 +1913,7 @@ void PPPM::particle_map() int flag = 0; - if (!ISFINITE(boxlo[0]) || !ISFINITE(boxlo[1]) || !ISFINITE(boxlo[2])) + if (!std::isfinite(boxlo[0]) || !std::isfinite(boxlo[1]) || !std::isfinite(boxlo[2])) error->one(FLERR,"Non-numeric box dimensions - simulation unstable"); for (int i = 0; i < nlocal; i++) { diff --git a/src/KSPACE/pppm_cg.cpp b/src/KSPACE/pppm_cg.cpp index 9489224e03031b8c279e05a5365a3ad9a58bb572..ca7abc9b5adc60454c4f7e4a24d501980005d679 100644 --- a/src/KSPACE/pppm_cg.cpp +++ b/src/KSPACE/pppm_cg.cpp @@ -16,9 +16,9 @@ ------------------------------------------------------------------------- */ #include -#include -#include -#include +#include +#include +#include #include "atom.h" #include "gridcomm.h" @@ -284,7 +284,7 @@ void PPPMCG::particle_map() double **x = atom->x; - if (!ISFINITE(boxlo[0]) || !ISFINITE(boxlo[1]) || !ISFINITE(boxlo[2])) + if (!std::isfinite(boxlo[0]) || !std::isfinite(boxlo[1]) || !std::isfinite(boxlo[2])) error->one(FLERR,"Non-numeric box dimensions - simulation unstable"); int flag = 0; diff --git a/src/KSPACE/pppm_disp.cpp b/src/KSPACE/pppm_disp.cpp index 3e764cc3e7f6f3104f2d0a0722a4e72b5399ebe5..4fbc20c0fc80d8d338308c22724a49a5ff3fbdb9 100644 --- a/src/KSPACE/pppm_disp.cpp +++ b/src/KSPACE/pppm_disp.cpp @@ -17,10 +17,10 @@ ------------------------------------------------------------------------- */ #include -#include -#include -#include -#include +#include +#include +#include +#include #include "pppm_disp.h" #include "math_const.h" #include "atom.h" @@ -4278,7 +4278,7 @@ void PPPMDisp::particle_map(double delx, double dely, double delz, double **x = atom->x; int nlocal = atom->nlocal; - if (!ISFINITE(boxlo[0]) || !ISFINITE(boxlo[1]) || !ISFINITE(boxlo[2])) + if (!std::isfinite(boxlo[0]) || !std::isfinite(boxlo[1]) || !std::isfinite(boxlo[2])) error->one(FLERR,"Non-numeric box dimensions - simulation unstable"); int flag = 0; diff --git a/src/KSPACE/pppm_disp_tip4p.cpp b/src/KSPACE/pppm_disp_tip4p.cpp index 686ed3df8ea0903979b2ef8e49289b46072d2507..1a25b300fc34b3db42bc5fb66342d2282704cb55 100644 --- a/src/KSPACE/pppm_disp_tip4p.cpp +++ b/src/KSPACE/pppm_disp_tip4p.cpp @@ -16,7 +16,7 @@ Rolf Isele-Holder (Aachen University) ------------------------------------------------------------------------- */ -#include +#include #include "pppm_disp_tip4p.h" #include "pppm_disp.h" #include "atom.h" @@ -78,7 +78,7 @@ void PPPMDispTIP4P::particle_map_c(double delx, double dely, double delz, double **x = atom->x; int nlocal = atom->nlocal; - if (!ISFINITE(boxlo[0]) || !ISFINITE(boxlo[1]) || !ISFINITE(boxlo[2])) + if (!std::isfinite(boxlo[0]) || !std::isfinite(boxlo[1]) || !std::isfinite(boxlo[2])) error->one(FLERR,"Non-numeric box dimensions - simulation unstable"); int flag = 0; diff --git a/src/KSPACE/pppm_stagger.cpp b/src/KSPACE/pppm_stagger.cpp index 49c84e58c0b4f36c8be56d758fa2759a0c478c2b..6d3308a05b1d02d1db2344075577676f59d21fd6 100644 --- a/src/KSPACE/pppm_stagger.cpp +++ b/src/KSPACE/pppm_stagger.cpp @@ -16,10 +16,10 @@ ------------------------------------------------------------------------- */ #include -#include -#include -#include -#include +#include +#include +#include +#include #include "pppm_stagger.h" #include "atom.h" #include "gridcomm.h" @@ -680,7 +680,7 @@ void PPPMStagger::particle_map() double **x = atom->x; int nlocal = atom->nlocal; - if (!ISFINITE(boxlo[0]) || !ISFINITE(boxlo[1]) || !ISFINITE(boxlo[2])) + if (!std::isfinite(boxlo[0]) || !std::isfinite(boxlo[1]) || !std::isfinite(boxlo[2])) error->one(FLERR,"Non-numeric box dimensions - simulation unstable"); int flag = 0; diff --git a/src/KSPACE/pppm_tip4p.cpp b/src/KSPACE/pppm_tip4p.cpp index e807f7e2e98a8ecbddca91fdc6ddb0d29c3ff46d..08fc8c711cdb869e45dffefe6da6cae176d2ad69 100644 --- a/src/KSPACE/pppm_tip4p.cpp +++ b/src/KSPACE/pppm_tip4p.cpp @@ -15,7 +15,7 @@ Contributing authors: Amalie Frischknecht and Ahmed Ismail (SNL) ------------------------------------------------------------------------- */ -#include +#include #include "pppm_tip4p.h" #include "atom.h" #include "domain.h" @@ -73,7 +73,7 @@ void PPPMTIP4P::particle_map() double **x = atom->x; int nlocal = atom->nlocal; - if (!ISFINITE(boxlo[0]) || !ISFINITE(boxlo[1]) || !ISFINITE(boxlo[2])) + if (!std::isfinite(boxlo[0]) || !std::isfinite(boxlo[1]) || !std::isfinite(boxlo[2])) error->one(FLERR,"Non-numeric box dimensions - simulation unstable"); int flag = 0; diff --git a/src/KSPACE/remap.cpp b/src/KSPACE/remap.cpp index 86522f3f2f7f166c6e34e6043047998d0178cc37..81dd692f4f91a44cebfdf68ab2ca79d8d37f0973 100644 --- a/src/KSPACE/remap.cpp +++ b/src/KSPACE/remap.cpp @@ -11,8 +11,8 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include -#include +#include +#include #include "remap.h" #define PACK_DATA FFT_SCALAR diff --git a/src/LATTE/fix_latte.cpp b/src/LATTE/fix_latte.cpp index 4594f26f8f8c182901ed564895e5814d77cb5e06..c2bfa1a5a1f1ba6500b4da5baa4633833abb6d1b 100644 --- a/src/LATTE/fix_latte.cpp +++ b/src/LATTE/fix_latte.cpp @@ -15,8 +15,8 @@ Contributing author: Christian Negre (LANL) ------------------------------------------------------------------------- */ -#include -#include +#include +#include #include "fix_latte.h" #include "atom.h" #include "comm.h" diff --git a/src/MANYBODY/fix_qeq_comb.cpp b/src/MANYBODY/fix_qeq_comb.cpp index c0d36d8fac60f3df808ab251ac409c9c52457d44..b8d9c7e6dfb7b0c739f5195e538f7c4c399625db 100644 --- a/src/MANYBODY/fix_qeq_comb.cpp +++ b/src/MANYBODY/fix_qeq_comb.cpp @@ -16,9 +16,9 @@ ------------------------------------------------------------------------- */ #include -#include -#include -#include +#include +#include +#include #include "pair_comb.h" #include "pair_comb3.h" #include "fix_qeq_comb.h" diff --git a/src/MANYBODY/fix_qeq_comb.h b/src/MANYBODY/fix_qeq_comb.h index 384ea4bbccacd267300b1e8d36620f722affd0a5..dd4c9f729085ad8bc107b748036c57b57cc8c515 100644 --- a/src/MANYBODY/fix_qeq_comb.h +++ b/src/MANYBODY/fix_qeq_comb.h @@ -20,7 +20,7 @@ FixStyle(qeq/comb,FixQEQComb) #ifndef LMP_FIX_QEQ_COMB_H #define LMP_FIX_QEQ_COMB_H -#include +#include #include "fix.h" namespace LAMMPS_NS { diff --git a/src/MANYBODY/pair_adp.cpp b/src/MANYBODY/pair_adp.cpp index 579675c4a020a1d08c60bb39b785a250e3edd8e8..d0b4d197583d260ccf42592dbb7b5921b0384d9d 100644 --- a/src/MANYBODY/pair_adp.cpp +++ b/src/MANYBODY/pair_adp.cpp @@ -16,10 +16,10 @@ Chandra Veer Singh (Cornell) ------------------------------------------------------------------------- */ -#include -#include -#include -#include +#include +#include +#include +#include #include "pair_adp.h" #include "atom.h" #include "force.h" diff --git a/src/MANYBODY/pair_airebo.cpp b/src/MANYBODY/pair_airebo.cpp index fd5691fecbc508cb7456e7885cac98db39f3a184..3be27354c15c46929e4700e8f453f2f1cce45c5e 100644 --- a/src/MANYBODY/pair_airebo.cpp +++ b/src/MANYBODY/pair_airebo.cpp @@ -20,10 +20,10 @@ Thomas C. O'Connor (JHU) 2014 ------------------------------------------------------------------------- */ -#include -#include -#include -#include +#include +#include +#include +#include #include #include "pair_airebo.h" #include "atom.h" diff --git a/src/MANYBODY/pair_airebo.h b/src/MANYBODY/pair_airebo.h index d9628f3bb30893590c26d6260d1cb1e2da10acc7..c7c9b07357c2ae11bbd6a48ac427d6e435f1257e 100644 --- a/src/MANYBODY/pair_airebo.h +++ b/src/MANYBODY/pair_airebo.h @@ -22,7 +22,7 @@ PairStyle(airebo,PairAIREBO) #include "pair.h" #include "my_page.h" -#include +#include #include "math_const.h" namespace LAMMPS_NS { diff --git a/src/MANYBODY/pair_bop.cpp b/src/MANYBODY/pair_bop.cpp index 04d7cd41531a87dc4505a969dd14c69f9e974302..87a23dff99c4c16bd88fd68101f0b0103f08ab39 100644 --- a/src/MANYBODY/pair_bop.cpp +++ b/src/MANYBODY/pair_bop.cpp @@ -32,10 +32,10 @@ Rules"_http://lammps.sandia.gov/open_source.html ------------------------------------------------------------------------- */ -#include -#include -#include -#include +#include +#include +#include +#include #include #include "pair_bop.h" #include "atom.h" @@ -49,7 +49,7 @@ #include "neigh_request.h" #include "memory.h" #include "error.h" -#include +#include using namespace LAMMPS_NS; diff --git a/src/MANYBODY/pair_bop.h b/src/MANYBODY/pair_bop.h index ec6448db47c19cc53616a1945ecd74fff619c267..3bd9b8cea970da0ea9ede32c54c3290cf10c4644 100644 --- a/src/MANYBODY/pair_bop.h +++ b/src/MANYBODY/pair_bop.h @@ -26,7 +26,7 @@ PairStyle(bop,PairBOP) #define LMP_PAIR_BOP_H #include "pair.h" -#include +#include #include "update.h" namespace LAMMPS_NS { diff --git a/src/MANYBODY/pair_comb.cpp b/src/MANYBODY/pair_comb.cpp index 5a2b4c25403bb99d85c579640c663a312493c4e1..de686d4bcf5e68ebf9dedaf9aacc72dd3a3e8c65 100644 --- a/src/MANYBODY/pair_comb.cpp +++ b/src/MANYBODY/pair_comb.cpp @@ -18,10 +18,10 @@ and Aidan Thompson's Tersoff code in LAMMPS ------------------------------------------------------------------------- */ -#include -#include -#include -#include +#include +#include +#include +#include #include "pair_comb.h" #include "atom.h" #include "comm.h" diff --git a/src/MANYBODY/pair_comb3.cpp b/src/MANYBODY/pair_comb3.cpp index 743511e753201a7c7ee0afdd5e7b6f535ab05277..b4f9c02206f926d39307b19317bd7e00b9cd16eb 100644 --- a/src/MANYBODY/pair_comb3.cpp +++ b/src/MANYBODY/pair_comb3.cpp @@ -17,10 +17,10 @@ Dundar Yilmaz (dundar.yilmaz@zirve.edu.tr) ------------------------------------------------------------------------- */ -#include -#include -#include -#include +#include +#include +#include +#include #include "pair_comb3.h" #include "atom.h" #include "comm.h" @@ -310,10 +310,10 @@ double PairComb3::init_one(int i, int j) void PairComb3::read_lib() { - unsigned int maxlib = 1024; + const unsigned int MAXLIB = 1024; int i,j,k,l,nwords,m; int ii,jj,kk,ll,mm,iii; - char s[maxlib]; + char s[MAXLIB]; char **words = new char*[80]; // open libraray file on proc 0 @@ -327,8 +327,8 @@ void PairComb3::read_lib() } // read and store at the same time - fgets(s,maxlib,fp); - fgets(s,maxlib,fp); + fgets(s,MAXLIB,fp); + fgets(s,MAXLIB,fp); nwords = 0; words[nwords++] = strtok(s," \t\n\r\f"); while ((words[nwords++] = strtok(NULL," \t\n\r\f")))continue; @@ -339,7 +339,7 @@ void PairComb3::read_lib() ccutoff[4] = atof(words[4]); ccutoff[5] = atof(words[5]); - fgets(s,maxlib,fp); + fgets(s,MAXLIB,fp); nwords = 0; words[nwords++] = strtok(s," \t\n\r\f"); while ((words[nwords++] = strtok(NULL," \t\n\r\f")))continue; @@ -351,7 +351,7 @@ void PairComb3::read_lib() ch_a[5] = atof(words[5]); ch_a[6] = atof(words[6]); - fgets(s,maxlib,fp); + fgets(s,MAXLIB,fp); nwords = 0; words[nwords++] = strtok(s," \t\n\r\f"); while ((words[nwords++] = strtok(NULL," \t\n\r\f")))continue; @@ -359,7 +359,7 @@ void PairComb3::read_lib() nsplrad = atoi(words[1]); nspltor = atoi(words[2]); - fgets(s,maxlib,fp); + fgets(s,MAXLIB,fp); nwords = 0; words[nwords++] = strtok(s," \t\n\r\f"); while ((words[nwords++] = strtok(NULL," \t\n\r\f")))continue; @@ -367,7 +367,7 @@ void PairComb3::read_lib() maxy = atoi(words[1]); maxz = atoi(words[2]); - fgets(s,maxlib,fp); + fgets(s,MAXLIB,fp); nwords = 0; words[nwords++] = strtok(s," \t\n\r\f"); while ((words[nwords++] = strtok(NULL," \t\n\r\f")))continue; @@ -376,7 +376,7 @@ void PairComb3::read_lib() maxconj = atoi(words[2]); for (l=0; l -#include -#include -#include +#include +#include +#include +#include #include "pair_eam.h" #include "atom.h" #include "force.h" diff --git a/src/MANYBODY/pair_eam.h b/src/MANYBODY/pair_eam.h index 63fdde9fc5a7a060e00ec704c2522fad0526a79a..234552157b305e7c439d0b04bf529c5c07a62934 100644 --- a/src/MANYBODY/pair_eam.h +++ b/src/MANYBODY/pair_eam.h @@ -20,7 +20,7 @@ PairStyle(eam,PairEAM) #ifndef LMP_PAIR_EAM_H #define LMP_PAIR_EAM_H -#include +#include #include "pair.h" namespace LAMMPS_NS { diff --git a/src/MANYBODY/pair_eam_alloy.cpp b/src/MANYBODY/pair_eam_alloy.cpp index e22b4642a82d5609710c287fbabda4fe67792fd1..eed38f79e9f75c9a258dec18edff32307dbdfaf9 100644 --- a/src/MANYBODY/pair_eam_alloy.cpp +++ b/src/MANYBODY/pair_eam_alloy.cpp @@ -15,9 +15,9 @@ Contributing authors: Stephen Foiles (SNL), Murray Daw (SNL) ------------------------------------------------------------------------- */ -#include -#include -#include +#include +#include +#include #include "pair_eam_alloy.h" #include "atom.h" #include "comm.h" diff --git a/src/MANYBODY/pair_eam_fs.cpp b/src/MANYBODY/pair_eam_fs.cpp index 2817e13f8a3b96d9121983e3710e0e29f64cb0eb..2b5d530d3a962e2c15b3e8dbc3d05ba2d59ac3f4 100644 --- a/src/MANYBODY/pair_eam_fs.cpp +++ b/src/MANYBODY/pair_eam_fs.cpp @@ -15,9 +15,9 @@ Contributing authors: Tim Lau (MIT) ------------------------------------------------------------------------- */ -#include -#include -#include +#include +#include +#include #include "pair_eam_fs.h" #include "atom.h" #include "comm.h" diff --git a/src/MANYBODY/pair_eim.cpp b/src/MANYBODY/pair_eim.cpp index e2d8a88aee67c9ddb852865d29b095097145f14a..b810d444fc6483cde6a87733b9376557efce7739 100644 --- a/src/MANYBODY/pair_eim.cpp +++ b/src/MANYBODY/pair_eim.cpp @@ -15,10 +15,10 @@ Contributing author: Xiaowang Zhou (SNL) ------------------------------------------------------------------------- */ -#include -#include -#include -#include +#include +#include +#include +#include #include "pair_eim.h" #include "atom.h" #include "force.h" diff --git a/src/MANYBODY/pair_eim.h b/src/MANYBODY/pair_eim.h index 9b2d518a2a20d97af6ed3cc25cdb56c2ea10198f..50f9934c44b94ad6c74533bba1e9684ddfe15ade 100644 --- a/src/MANYBODY/pair_eim.h +++ b/src/MANYBODY/pair_eim.h @@ -20,7 +20,7 @@ PairStyle(eim,PairEIM) #ifndef LMP_PAIR_EIM_H #define LMP_PAIR_EIM_H -#include +#include #include "pair.h" namespace LAMMPS_NS { diff --git a/src/MANYBODY/pair_gw.cpp b/src/MANYBODY/pair_gw.cpp index 8befa42d1c6ec5f022eb18ddf7c435253e9a0a1e..35f092b580e4693e45db8bbda6b0a12d20a094ac 100644 --- a/src/MANYBODY/pair_gw.cpp +++ b/src/MANYBODY/pair_gw.cpp @@ -16,10 +16,10 @@ based on PairTersoff by Aidan Thompson (SNL) ------------------------------------------------------------------------- */ -#include -#include -#include -#include +#include +#include +#include +#include #include "pair_gw.h" #include "atom.h" #include "neighbor.h" diff --git a/src/MANYBODY/pair_gw_zbl.cpp b/src/MANYBODY/pair_gw_zbl.cpp index a4e1ccb1f994b4a612b2eba8e9baf737891d6edb..81d4866e84f6a654dd057b9ea892ae9f6ce12505 100644 --- a/src/MANYBODY/pair_gw_zbl.cpp +++ b/src/MANYBODY/pair_gw_zbl.cpp @@ -16,10 +16,10 @@ Based on PairTersoffZBL by Aidan Thompson (SNL) and David Farrell (NWU) ------------------------------------------------------------------------- */ -#include -#include -#include -#include +#include +#include +#include +#include #include "pair_gw_zbl.h" #include "atom.h" #include "update.h" diff --git a/src/MANYBODY/pair_lcbop.cpp b/src/MANYBODY/pair_lcbop.cpp index 414f2adb741f4cbef4338eb2cbbec7eaee21bd4f..d334defcc607447a357b6a2da1d215d6dcd6cba5 100644 --- a/src/MANYBODY/pair_lcbop.cpp +++ b/src/MANYBODY/pair_lcbop.cpp @@ -16,10 +16,10 @@ based on pair_airebo by Ase Henry (MIT) ------------------------------------------------------------------------- */ -#include -#include -#include -#include +#include +#include +#include +#include #include #include "pair_lcbop.h" #include "atom.h" diff --git a/src/MANYBODY/pair_lcbop.h b/src/MANYBODY/pair_lcbop.h index c099c7c4a1be2e64f5a664551b05c77fcaf718bf..0d7c7a51b17e220abc290d9d348398894c2dc08c 100644 --- a/src/MANYBODY/pair_lcbop.h +++ b/src/MANYBODY/pair_lcbop.h @@ -22,7 +22,7 @@ PairStyle(lcbop,PairLCBOP) #include "pair.h" #include "my_page.h" -#include +#include #include "math_const.h" namespace LAMMPS_NS { diff --git a/src/MANYBODY/pair_nb3b_harmonic.cpp b/src/MANYBODY/pair_nb3b_harmonic.cpp index 0b930c73608c1996a9e58f279332a19ac5f50bf9..36be9c2b90758b075a7566f6c469d038049c2f5d 100644 --- a/src/MANYBODY/pair_nb3b_harmonic.cpp +++ b/src/MANYBODY/pair_nb3b_harmonic.cpp @@ -16,10 +16,10 @@ (based on Stillinger-Weber pair style) ------------------------------------------------------------------------- */ -#include -#include -#include -#include +#include +#include +#include +#include #include "pair_nb3b_harmonic.h" #include "atom.h" #include "neighbor.h" diff --git a/src/MANYBODY/pair_polymorphic.cpp b/src/MANYBODY/pair_polymorphic.cpp index 9ceceed076825d4d81c4a90c85c9a40969a8def1..2afb08b7a1e6e56059a44c3e862d047bb95566be 100644 --- a/src/MANYBODY/pair_polymorphic.cpp +++ b/src/MANYBODY/pair_polymorphic.cpp @@ -16,10 +16,10 @@ This modifies from pair_tersoff.cpp by Aidan Thompson (SNL) ------------------------------------------------------------------------- */ -#include -#include -#include -#include +#include +#include +#include +#include #include "pair_polymorphic.h" #include "atom.h" #include "neighbor.h" diff --git a/src/MANYBODY/pair_polymorphic.h b/src/MANYBODY/pair_polymorphic.h index 3b5407f802938e4e78cf42e9a5669278ea92a402..32f1c5414a6714847f2877a643224d50544cf89f 100644 --- a/src/MANYBODY/pair_polymorphic.h +++ b/src/MANYBODY/pair_polymorphic.h @@ -21,7 +21,7 @@ PairStyle(polymorphic,PairPolymorphic) #define LMP_PAIR_POLYMORPHIC_H #include "pair.h" -#include +#include namespace LAMMPS_NS { diff --git a/src/MANYBODY/pair_sw.cpp b/src/MANYBODY/pair_sw.cpp index da2f5da37e003119d2f77521f883bbb28630bc20..6fbc00204c3ba8e046262799357281d8730e4d22 100644 --- a/src/MANYBODY/pair_sw.cpp +++ b/src/MANYBODY/pair_sw.cpp @@ -15,10 +15,10 @@ Contributing author: Aidan Thompson (SNL) ------------------------------------------------------------------------- */ -#include -#include -#include -#include +#include +#include +#include +#include #include "pair_sw.h" #include "atom.h" #include "neighbor.h" diff --git a/src/MANYBODY/pair_tersoff.cpp b/src/MANYBODY/pair_tersoff.cpp index 047c59fc87797802531951c2f6abf81ca5c6e716..507b07e29a21fc1031b1c25269f35da942d19715 100644 --- a/src/MANYBODY/pair_tersoff.cpp +++ b/src/MANYBODY/pair_tersoff.cpp @@ -15,10 +15,10 @@ Contributing author: Aidan Thompson (SNL) ------------------------------------------------------------------------- */ -#include -#include -#include -#include +#include +#include +#include +#include #include "pair_tersoff.h" #include "atom.h" #include "neighbor.h" diff --git a/src/MANYBODY/pair_tersoff_mod.cpp b/src/MANYBODY/pair_tersoff_mod.cpp index a90cf3bb77fbcbce5f9609aa507ec3e44ffb023b..73297fb53451640d9cf105de3367d49b5cb78c82 100644 --- a/src/MANYBODY/pair_tersoff_mod.cpp +++ b/src/MANYBODY/pair_tersoff_mod.cpp @@ -16,10 +16,10 @@ Vitaly Dozhdikov (JIHT of RAS) - MOD addition ------------------------------------------------------------------------- */ -#include -#include -#include -#include +#include +#include +#include +#include #include "pair_tersoff_mod.h" #include "atom.h" #include "neighbor.h" diff --git a/src/MANYBODY/pair_tersoff_mod.h b/src/MANYBODY/pair_tersoff_mod.h index 42a3a2b26c96ca2511ef0968b70177234bc88860..162603bc5ca42d16fe513e949b609583d74c83bd 100644 --- a/src/MANYBODY/pair_tersoff_mod.h +++ b/src/MANYBODY/pair_tersoff_mod.h @@ -21,7 +21,7 @@ PairStyle(tersoff/mod,PairTersoffMOD) #define LMP_PAIR_TERSOFF_MOD_H #include "pair_tersoff.h" -#include +#include namespace LAMMPS_NS { diff --git a/src/MANYBODY/pair_tersoff_mod_c.cpp b/src/MANYBODY/pair_tersoff_mod_c.cpp index c0d6cb164a2d98dc13449c591e7e7e96cddaad7e..0d0016664a1dd93c1a981ae95af29958ef012c1f 100644 --- a/src/MANYBODY/pair_tersoff_mod_c.cpp +++ b/src/MANYBODY/pair_tersoff_mod_c.cpp @@ -15,10 +15,10 @@ Contributing author: Ganga P Purja Pun (George Mason University, Fairfax) ------------------------------------------------------------------------- */ -#include -#include -#include -#include +#include +#include +#include +#include #include "pair_tersoff_mod_c.h" #include "atom.h" #include "neighbor.h" diff --git a/src/MANYBODY/pair_tersoff_zbl.cpp b/src/MANYBODY/pair_tersoff_zbl.cpp index 15163c2bf9843607dde1f65d8e78d0abdef78957..1692c88a5087b1f970a63a3b4dce00705a5358f6 100644 --- a/src/MANYBODY/pair_tersoff_zbl.cpp +++ b/src/MANYBODY/pair_tersoff_zbl.cpp @@ -16,10 +16,10 @@ David Farrell (NWU) - ZBL addition ------------------------------------------------------------------------- */ -#include -#include -#include -#include +#include +#include +#include +#include #include "pair_tersoff_zbl.h" #include "atom.h" #include "update.h" diff --git a/src/MANYBODY/pair_vashishta.cpp b/src/MANYBODY/pair_vashishta.cpp index bc594d9b4daf614bc0bc3afe835bb86bd0dfcd82..8506c9a69fd79f35f362f5f24f65854cf34e5537 100644 --- a/src/MANYBODY/pair_vashishta.cpp +++ b/src/MANYBODY/pair_vashishta.cpp @@ -16,10 +16,10 @@ Aidan Thompson (SNL) ------------------------------------------------------------------------- */ -#include -#include -#include -#include +#include +#include +#include +#include #include "pair_vashishta.h" #include "atom.h" #include "neighbor.h" diff --git a/src/MANYBODY/pair_vashishta_table.cpp b/src/MANYBODY/pair_vashishta_table.cpp index 88a7040d761d6127bd2f08a3e727dcbfd9b7f169..1055db99fa8b06df3e880280d839aafd19ef1650 100644 --- a/src/MANYBODY/pair_vashishta_table.cpp +++ b/src/MANYBODY/pair_vashishta_table.cpp @@ -15,10 +15,10 @@ Contributing author: Anders Hafreager (UiO), andershaf@gmail.com ------------------------------------------------------------------------- */ -#include -#include -#include -#include +#include +#include +#include +#include #include "pair_vashishta_table.h" #include "atom.h" #include "neighbor.h" diff --git a/src/MC/fix_atom_swap.cpp b/src/MC/fix_atom_swap.cpp index 100600c0daeb2c169b6ed0a9ed66243315603e1e..4d9377022b265fe1488bf241e4ac69f3c1185252 100644 --- a/src/MC/fix_atom_swap.cpp +++ b/src/MC/fix_atom_swap.cpp @@ -16,10 +16,10 @@ Alexander Stukowski ------------------------------------------------------------------------- */ -#include -#include -#include -#include +#include +#include +#include +#include #include "fix_atom_swap.h" #include "atom.h" #include "atom_vec.h" diff --git a/src/MC/fix_atom_swap.h b/src/MC/fix_atom_swap.h index 74720d6222e1dcdf9cfc3a4d054c60a609cd9c43..19895704f186dd87325acfcefc56d6ad902863ff 100644 --- a/src/MC/fix_atom_swap.h +++ b/src/MC/fix_atom_swap.h @@ -20,7 +20,7 @@ FixStyle(atom/swap,FixAtomSwap) #ifndef LMP_FIX_MCSWAP_H #define LMP_FIX_MCSWAP_H -#include +#include #include "fix.h" namespace LAMMPS_NS { diff --git a/src/MC/fix_bond_break.cpp b/src/MC/fix_bond_break.cpp index 711f764282b92737b6b98fda94c9cbd4ffe16fd2..9a5b59b60188b89d2cf671a1a3fbf1db1e265daa 100644 --- a/src/MC/fix_bond_break.cpp +++ b/src/MC/fix_bond_break.cpp @@ -11,10 +11,10 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include +#include #include -#include -#include +#include +#include #include "fix_bond_break.h" #include "update.h" #include "respa.h" diff --git a/src/MC/fix_bond_create.cpp b/src/MC/fix_bond_create.cpp index 789f1794f1864f1823def41669bb5250b452ce08..8e9db6a18b130819adbbf280fdbdae9ce2c9fea4 100644 --- a/src/MC/fix_bond_create.cpp +++ b/src/MC/fix_bond_create.cpp @@ -11,10 +11,10 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include +#include #include -#include -#include +#include +#include #include "fix_bond_create.h" #include "update.h" #include "respa.h" diff --git a/src/MC/fix_bond_swap.cpp b/src/MC/fix_bond_swap.cpp index d5b7394dd1e799ea32299f82233b29d641baf7df..d6df4d9a960343520e610280e5941600584b6050 100644 --- a/src/MC/fix_bond_swap.cpp +++ b/src/MC/fix_bond_swap.cpp @@ -11,9 +11,9 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include -#include -#include +#include +#include +#include #include "fix_bond_swap.h" #include "atom.h" #include "force.h" diff --git a/src/MC/fix_gcmc.cpp b/src/MC/fix_gcmc.cpp index f2c41c9ccf0559ee3103c99d62994d95e2af907d..6221e6d52c26b359d9efd7d87460a1ed3ceacaf3 100644 --- a/src/MC/fix_gcmc.cpp +++ b/src/MC/fix_gcmc.cpp @@ -15,9 +15,9 @@ Contributing author: Paul Crozier, Aidan Thompson (SNL) ------------------------------------------------------------------------- */ -#include -#include -#include +#include +#include +#include #include "fix_gcmc.h" #include "atom.h" #include "atom_vec.h" @@ -1349,7 +1349,7 @@ void FixGCMC::attempt_molecule_insertion() MathExtra::quat_to_mat(quat,rotmat); double insertion_energy = 0.0; - bool procflag[natoms_per_molecule]; + bool *procflag = new bool[natoms_per_molecule]; for (int i = 0; i < natoms_per_molecule; i++) { MathExtra::matvec(rotmat,onemols[imol]->x[i],molcoords[i]); @@ -1472,6 +1472,7 @@ void FixGCMC::attempt_molecule_insertion() update_gas_atoms_list(); ninsertion_successes += 1.0; } + delete[] procflag; } /* ---------------------------------------------------------------------- @@ -1934,7 +1935,7 @@ void FixGCMC::attempt_molecule_deletion_full() grow_molecule_arrays(nmolq); int m = 0; - int tmpmask[atom->nlocal]; + int *tmpmask = new int[atom->nlocal]; for (int i = 0; i < atom->nlocal; i++) { if (atom->molecule[i] == deletion_molecule) { tmpmask[i] = atom->mask[i]; @@ -1982,6 +1983,7 @@ void FixGCMC::attempt_molecule_deletion_full() if (force->kspace) force->kspace->qsum_qsq(); } update_gas_atoms_list(); + delete[] tmpmask; } /* ---------------------------------------------------------------------- @@ -2426,9 +2428,9 @@ void FixGCMC::update_gas_atoms_list() for (int i = 0; i < nlocal; i++) maxmol = MAX(maxmol,molecule[i]); tagint maxmol_all; MPI_Allreduce(&maxmol,&maxmol_all,1,MPI_LMP_TAGINT,MPI_MAX,world); - double comx[maxmol_all]; - double comy[maxmol_all]; - double comz[maxmol_all]; + double *comx = new double[maxmol_all]; + double *comy = new double[maxmol_all]; + double *comz = new double[maxmol_all]; for (int imolecule = 0; imolecule < maxmol_all; imolecule++) { for (int i = 0; i < nlocal; i++) { if (molecule[i] == imolecule) { @@ -2458,7 +2460,9 @@ void FixGCMC::update_gas_atoms_list() } } } - + delete[] comx; + delete[] comy; + delete[] comz; } else { for (int i = 0; i < nlocal; i++) { if (mask[i] & groupbit) { diff --git a/src/MC/fix_gcmc.h b/src/MC/fix_gcmc.h index e8de53215fcd319bb0ecc62fb42c2ec11071c150..5d0b7aab8fab5377f2ec065110b76fce99816851 100644 --- a/src/MC/fix_gcmc.h +++ b/src/MC/fix_gcmc.h @@ -20,7 +20,7 @@ FixStyle(gcmc,FixGCMC) #ifndef LMP_FIX_GCMC_H #define LMP_FIX_GCMC_H -#include +#include #include "fix.h" namespace LAMMPS_NS { diff --git a/src/MC/fix_tfmc.cpp b/src/MC/fix_tfmc.cpp index 60ded5fd4470edab95493552700d820111323b9c..b8217103535a2e08826fffa134c831e3856bdffe 100644 --- a/src/MC/fix_tfmc.cpp +++ b/src/MC/fix_tfmc.cpp @@ -17,9 +17,9 @@ #include "fix_tfmc.h" #include -#include -#include -#include +#include +#include +#include #include "atom.h" #include "force.h" #include "update.h" diff --git a/src/MC/pair_dsmc.cpp b/src/MC/pair_dsmc.cpp index d3327eea296b943a8c49e0bf57d270b6a7917944..02f9754c2a2fdd1a78565931d607010ca66e1a49 100644 --- a/src/MC/pair_dsmc.cpp +++ b/src/MC/pair_dsmc.cpp @@ -15,10 +15,11 @@ Contributing authors: Paul Crozier (SNL) ------------------------------------------------------------------------- */ -#include -#include -#include -#include +#include +#include +#include +#include +#include #include "pair_dsmc.h" #include "atom.h" #include "comm.h" @@ -28,7 +29,6 @@ #include "domain.h" #include "update.h" #include "random_mars.h" -#include using namespace LAMMPS_NS; diff --git a/src/MEAM/pair_meam.cpp b/src/MEAM/pair_meam.cpp index fa47944cd50944c4e5c631b8088c42a51c519f86..687055aa6a6735fceb1749c4124ae73797dc8d9f 100644 --- a/src/MEAM/pair_meam.cpp +++ b/src/MEAM/pair_meam.cpp @@ -15,10 +15,10 @@ Contributing author: Greg Wagner (SNL) ------------------------------------------------------------------------- */ -#include -#include -#include -#include +#include +#include +#include +#include #include "pair_meam.h" #include "atom.h" #include "force.h" diff --git a/src/MISC/compute_msd_nongauss.cpp b/src/MISC/compute_msd_nongauss.cpp index 4639fa7916c116ef0f4786819c716b0cf91474b3..f6291f4204e0633921c69f63c3f0709922e7fe24 100644 --- a/src/MISC/compute_msd_nongauss.cpp +++ b/src/MISC/compute_msd_nongauss.cpp @@ -15,7 +15,7 @@ Contributing authors: Rob Hoy ------------------------------------------------------------------------- */ -#include +#include #include "compute_msd_nongauss.h" #include "atom.h" #include "update.h" diff --git a/src/MISC/compute_ti.cpp b/src/MISC/compute_ti.cpp index 9f1b2898bbe67ea3d3fc1f73bef1db7c46bd42bc..d2e43a9f69ffd417afd1668b983b2225960816b1 100644 --- a/src/MISC/compute_ti.cpp +++ b/src/MISC/compute_ti.cpp @@ -17,7 +17,7 @@ #include #include "atom.h" -#include +#include #include "compute_ti.h" #include "update.h" #include "modify.h" diff --git a/src/MISC/dump_xtc.cpp b/src/MISC/dump_xtc.cpp index 674e480f9e697fd0b2049d208fa79094e2b99ff8..a82cba20bde3fd4e1c05bac4525abe898d61fbae 100644 --- a/src/MISC/dump_xtc.cpp +++ b/src/MISC/dump_xtc.cpp @@ -22,11 +22,11 @@ support for groups ------------------------------------------------------------------------- */ -#include -#include -#include -#include -#include +#include +#include +#include +#include +#include #include "dump_xtc.h" #include "domain.h" #include "atom.h" diff --git a/src/MISC/fix_deposit.cpp b/src/MISC/fix_deposit.cpp index 023ec797df0099d3724beac106ebfdb5f8f39497..4215df07a62c3ef7d1f8e276ef9a8015bf581d41 100644 --- a/src/MISC/fix_deposit.cpp +++ b/src/MISC/fix_deposit.cpp @@ -11,9 +11,9 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include -#include -#include +#include +#include +#include #include "fix_deposit.h" #include "atom.h" #include "atom_vec.h" diff --git a/src/MISC/fix_deposit.h b/src/MISC/fix_deposit.h index 46de781d8998f4c47a4bc0f75c8ff83afcee27ac..38958b80e7a2af9f0d2d088d5b716f4b575ebe19 100644 --- a/src/MISC/fix_deposit.h +++ b/src/MISC/fix_deposit.h @@ -20,7 +20,7 @@ FixStyle(deposit,FixDeposit) #ifndef LMP_FIX_DEPOSIT_H #define LMP_FIX_DEPOSIT_H -#include +#include #include "fix.h" namespace LAMMPS_NS { diff --git a/src/MISC/fix_efield.cpp b/src/MISC/fix_efield.cpp index c0384adc410e64d6c8b337ca9e551bb5bcb5e753..1fa141e2bf3c9ea821436fc46a105dbbf034dd6b 100644 --- a/src/MISC/fix_efield.cpp +++ b/src/MISC/fix_efield.cpp @@ -16,9 +16,9 @@ Stan Moore (Sandia) for dipole terms ------------------------------------------------------------------------- */ -#include -#include -#include +#include +#include +#include #include "fix_efield.h" #include "atom.h" #include "update.h" diff --git a/src/MISC/fix_evaporate.cpp b/src/MISC/fix_evaporate.cpp index 54d1090892eeb75cc84dd704e987489d14ba7c6e..1bf7a15f1fe02372998cad59e425529e7470a822 100644 --- a/src/MISC/fix_evaporate.cpp +++ b/src/MISC/fix_evaporate.cpp @@ -11,9 +11,9 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include -#include -#include +#include +#include +#include #include "fix_evaporate.h" #include "atom.h" #include "atom_vec.h" diff --git a/src/MISC/fix_gld.cpp b/src/MISC/fix_gld.cpp index 90579388cc9cb953d6447d40cf2a95ea6514ef45..370730133ee1cc77eaa9dde98bb91ebb5e8bc01c 100644 --- a/src/MISC/fix_gld.cpp +++ b/src/MISC/fix_gld.cpp @@ -16,9 +16,9 @@ Andrew Baczewski (Michigan State/SNL) ------------------------------------------------------------------------- */ -#include -#include -#include +#include +#include +#include #include "fix_gld.h" #include "math_extra.h" #include "atom.h" diff --git a/src/MISC/fix_oneway.cpp b/src/MISC/fix_oneway.cpp index 758beed5536f273e331a2b814e2cc81b606d4593..73853775a30c2d8db9710101c366a6e714bd3903 100644 --- a/src/MISC/fix_oneway.cpp +++ b/src/MISC/fix_oneway.cpp @@ -15,7 +15,7 @@ Contributing author: Axel Kohlmeyer (ICTP, Italy) ------------------------------------------------------------------------- */ -#include +#include #include "fix_oneway.h" #include "atom.h" #include "domain.h" diff --git a/src/MISC/fix_orient_bcc.cpp b/src/MISC/fix_orient_bcc.cpp index 0cb0f96aa8d722bffed2edb04999cb7a36c41217..c5ba6514a90c566688e530f85d65415039586b22 100644 --- a/src/MISC/fix_orient_bcc.cpp +++ b/src/MISC/fix_orient_bcc.cpp @@ -18,9 +18,9 @@ (https://dx.doi.org/10.6084/m9.figshare.1488628.v1 ------------------------------------------------------------------------- */ -#include -#include -#include +#include +#include +#include #include #include "fix_orient_bcc.h" #include "atom.h" diff --git a/src/MISC/fix_orient_fcc.cpp b/src/MISC/fix_orient_fcc.cpp index 6743132cfa2e0f1d862626e4b4a1de040f9d45b7..5786571a89e9a9ccb8445ee2bc4c5582af8c22f6 100644 --- a/src/MISC/fix_orient_fcc.cpp +++ b/src/MISC/fix_orient_fcc.cpp @@ -15,9 +15,9 @@ Contributing authors: Koenraad Janssens and David Olmsted (SNL) ------------------------------------------------------------------------- */ -#include -#include -#include +#include +#include +#include #include #include "fix_orient_fcc.h" #include "atom.h" diff --git a/src/MISC/fix_thermal_conductivity.cpp b/src/MISC/fix_thermal_conductivity.cpp index b9e70e9c009cb4bdb57146a953ecaa43abfa8138..f1aec3ff6991a1adb129c54d90b0198dbee2831d 100644 --- a/src/MISC/fix_thermal_conductivity.cpp +++ b/src/MISC/fix_thermal_conductivity.cpp @@ -16,10 +16,10 @@ for swapping atoms of different masses ------------------------------------------------------------------------- */ -#include +#include #include -#include -#include +#include +#include #include "fix_thermal_conductivity.h" #include "atom.h" #include "force.h" diff --git a/src/MISC/fix_ttm.cpp b/src/MISC/fix_ttm.cpp index bb13b166fbcf4ceb7ea645a55e709067e5c2c075..7ffd979e5089ca391990427693276bc30c74b5a4 100644 --- a/src/MISC/fix_ttm.cpp +++ b/src/MISC/fix_ttm.cpp @@ -17,9 +17,9 @@ ------------------------------------------------------------------------- */ #include -#include -#include -#include +#include +#include +#include #include "fix_ttm.h" #include "atom.h" #include "force.h" diff --git a/src/MISC/fix_viscosity.cpp b/src/MISC/fix_viscosity.cpp index 3f6d5e33d1ac6eb3dea29b23ca693d7056a51fd3..8e33c1c6148ec4ca20fab9219cf7348722b65ddb 100644 --- a/src/MISC/fix_viscosity.cpp +++ b/src/MISC/fix_viscosity.cpp @@ -16,10 +16,10 @@ for swapping atoms of different masses ------------------------------------------------------------------------- */ -#include +#include #include -#include -#include +#include +#include #include "fix_viscosity.h" #include "atom.h" #include "domain.h" diff --git a/src/MISC/pair_nm_cut.cpp b/src/MISC/pair_nm_cut.cpp index b9bf6ac477052d400a1340620465d731ee3c5774..83d734de0f4e492f8ffdadf2c771aaaaf250b248 100644 --- a/src/MISC/pair_nm_cut.cpp +++ b/src/MISC/pair_nm_cut.cpp @@ -15,10 +15,10 @@ Contributing Author: Julien Devemy (ICCF) ------------------------------------------------------------------------- */ -#include -#include -#include -#include +#include +#include +#include +#include #include "pair_nm_cut.h" #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 78c77a648f906da56b38848436e0ec45aa485eb5..0c9a43f4dc94fc5b4a8e9d2c705be0bad3cc2438 100644 --- a/src/MISC/pair_nm_cut_coul_cut.cpp +++ b/src/MISC/pair_nm_cut_coul_cut.cpp @@ -15,10 +15,10 @@ Contributing Author: Julien Devemy (ICCF) ------------------------------------------------------------------------- */ -#include -#include -#include -#include +#include +#include +#include +#include #include "pair_nm_cut_coul_cut.h" #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 8e0da40eac78d4689e666325a27da008d4667b3e..3296f8fd92b62ae567c7790ffbf0d98c62cd021a 100644 --- a/src/MISC/pair_nm_cut_coul_long.cpp +++ b/src/MISC/pair_nm_cut_coul_long.cpp @@ -15,10 +15,10 @@ Contributing Author: Julien Devemy (ICCF) ------------------------------------------------------------------------- */ -#include -#include -#include -#include +#include +#include +#include +#include #include "pair_nm_cut_coul_long.h" #include "atom.h" #include "comm.h" diff --git a/src/MISC/xdr_compat.cpp b/src/MISC/xdr_compat.cpp index 9483070fee919f50b14e1b2dd1f0b8384988bbda..3987aa02fc2e0252cdd1eff3ceaf0b2113cd72c1 100644 --- a/src/MISC/xdr_compat.cpp +++ b/src/MISC/xdr_compat.cpp @@ -1,6 +1,6 @@ -#include -#include -#include +#include +#include +#include #include "xdr_compat.h" /* 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 605374c47fc7172f42dad2a89137628e2b8bc236..30622350807b7d871a9870e17b45cc4890e38646 100644 --- a/src/MISC/xdr_compat.h +++ b/src/MISC/xdr_compat.h @@ -1,9 +1,9 @@ #ifndef LMP_XDR_COMPAT_H #define LMP_XDR_COMPAT_H -#include -#include -#include +#include +#include +#include #ifdef __cplusplus extern "C" { diff --git a/src/MOLECULE/angle_charmm.cpp b/src/MOLECULE/angle_charmm.cpp index c7284add8ccfa765b96a70e27d861b454de67cc2..3608601c1fdb73ccf0c20b9910ee3101c32bdbfe 100644 --- a/src/MOLECULE/angle_charmm.cpp +++ b/src/MOLECULE/angle_charmm.cpp @@ -15,8 +15,8 @@ Contributing author: Paul Crozier (SNL) ------------------------------------------------------------------------- */ -#include -#include +#include +#include #include "angle_charmm.h" #include "atom.h" #include "neighbor.h" diff --git a/src/MOLECULE/angle_charmm.h b/src/MOLECULE/angle_charmm.h index fa27866be38750ae04cf08ddaab0d6fed5ab479e..82c9e42fbabc92f6a1a4be186aeccfa095e5bcc2 100644 --- a/src/MOLECULE/angle_charmm.h +++ b/src/MOLECULE/angle_charmm.h @@ -20,7 +20,7 @@ AngleStyle(charmm,AngleCharmm) #ifndef LMP_ANGLE_CHARMM_H #define LMP_ANGLE_CHARMM_H -#include +#include #include "angle.h" namespace LAMMPS_NS { diff --git a/src/MOLECULE/angle_cosine.cpp b/src/MOLECULE/angle_cosine.cpp index f064a34f20d17aa02f07c90ef152ab87246d8357..e3472dfd7a6b3050a0ab2690764efb8ffaece032 100644 --- a/src/MOLECULE/angle_cosine.cpp +++ b/src/MOLECULE/angle_cosine.cpp @@ -11,8 +11,8 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include -#include +#include +#include #include "angle_cosine.h" #include "atom.h" #include "neighbor.h" diff --git a/src/MOLECULE/angle_cosine.h b/src/MOLECULE/angle_cosine.h index a6581f11bde0bd01e2c5459000df9495c146a9da..ac50a67468ea875df965388fc1a52be35c8db2b7 100644 --- a/src/MOLECULE/angle_cosine.h +++ b/src/MOLECULE/angle_cosine.h @@ -20,7 +20,7 @@ AngleStyle(cosine,AngleCosine) #ifndef LMP_ANGLE_COSINE_H #define LMP_ANGLE_COSINE_H -#include +#include #include "angle.h" namespace LAMMPS_NS { diff --git a/src/MOLECULE/angle_cosine_delta.cpp b/src/MOLECULE/angle_cosine_delta.cpp index fe482eb3ebef6fe18160c602c143ed3712747700..6f4f5c20d71198cb00b2b5469e43c0fefee0fe2f 100644 --- a/src/MOLECULE/angle_cosine_delta.cpp +++ b/src/MOLECULE/angle_cosine_delta.cpp @@ -15,8 +15,8 @@ Contributing author: Axel Kohlmeyer (Temple U), akohlmey at gmail.com ------------------------------------------------------------------------- */ -#include -#include +#include +#include #include "angle_cosine_delta.h" #include "atom.h" #include "neighbor.h" diff --git a/src/MOLECULE/angle_cosine_delta.h b/src/MOLECULE/angle_cosine_delta.h index b29064e35eadbcb2d4fd6ad8efc6b4994fef5995..1e19ecaf7962e4883403a51e34d3707df5e1693e 100644 --- a/src/MOLECULE/angle_cosine_delta.h +++ b/src/MOLECULE/angle_cosine_delta.h @@ -20,7 +20,7 @@ AngleStyle(cosine/delta,AngleCosineDelta) #ifndef LMP_ANGLE_COSINE_DELTA_H #define LMP_ANGLE_COSINE_DELTA_H -#include +#include #include "angle_cosine_squared.h" namespace LAMMPS_NS { diff --git a/src/MOLECULE/angle_cosine_periodic.cpp b/src/MOLECULE/angle_cosine_periodic.cpp index 77fb335b785c769c6494012e2e5798b29ca44555..4e620b436e4f0a3a505d683e792e1ea8fc5cc3a0 100644 --- a/src/MOLECULE/angle_cosine_periodic.cpp +++ b/src/MOLECULE/angle_cosine_periodic.cpp @@ -15,8 +15,8 @@ Contributing author: Tod A Pascal (Caltech) ------------------------------------------------------------------------- */ -#include -#include +#include +#include #include "angle_cosine_periodic.h" #include "atom.h" #include "neighbor.h" diff --git a/src/MOLECULE/angle_cosine_periodic.h b/src/MOLECULE/angle_cosine_periodic.h index 9b7f06227241f929095e0b00f153c413f98e05e3..e131e85101e8d452bca29cc4389bd268baf5a8d2 100644 --- a/src/MOLECULE/angle_cosine_periodic.h +++ b/src/MOLECULE/angle_cosine_periodic.h @@ -20,7 +20,7 @@ AngleStyle(cosine/periodic, AngleCosinePeriodic) #ifndef LMP_ANGLE_PERIODIC_H #define LMP_ANGLE_PERIODIC_H -#include +#include #include "angle.h" namespace LAMMPS_NS { diff --git a/src/MOLECULE/angle_cosine_squared.cpp b/src/MOLECULE/angle_cosine_squared.cpp index bc38d76dcdb4fded224f9994d08f756c8532255b..c83ba90a60f35b1db16fde1c3a2cb53c31eafa82 100644 --- a/src/MOLECULE/angle_cosine_squared.cpp +++ b/src/MOLECULE/angle_cosine_squared.cpp @@ -15,8 +15,8 @@ Contributing author: Naveen Michaud-Agrawal (Johns Hopkins U) ------------------------------------------------------------------------- */ -#include -#include +#include +#include #include "angle_cosine_squared.h" #include "atom.h" #include "neighbor.h" @@ -34,7 +34,11 @@ using namespace MathConst; /* ---------------------------------------------------------------------- */ -AngleCosineSquared::AngleCosineSquared(LAMMPS *lmp) : Angle(lmp) {} +AngleCosineSquared::AngleCosineSquared(LAMMPS *lmp) : Angle(lmp) +{ + k = NULL; + theta0 = NULL; +} /* ---------------------------------------------------------------------- */ diff --git a/src/MOLECULE/angle_cosine_squared.h b/src/MOLECULE/angle_cosine_squared.h index b9f79f923fb794e5c4c0842c2da44023d9db18ec..8e8c84c0f99c98a107d8072cdfac53badf04c3b7 100644 --- a/src/MOLECULE/angle_cosine_squared.h +++ b/src/MOLECULE/angle_cosine_squared.h @@ -20,7 +20,7 @@ AngleStyle(cosine/squared,AngleCosineSquared) #ifndef LMP_ANGLE_COSINE_SQUARED_H #define LMP_ANGLE_COSINE_SQUARED_H -#include +#include #include "angle.h" namespace LAMMPS_NS { diff --git a/src/MOLECULE/angle_harmonic.cpp b/src/MOLECULE/angle_harmonic.cpp index 7e8b57b04fad7748eeaf0ce0f1ee75a743992425..d28afd76d688ca2a0a1a8d39d0724dc84a5210b9 100644 --- a/src/MOLECULE/angle_harmonic.cpp +++ b/src/MOLECULE/angle_harmonic.cpp @@ -11,8 +11,8 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include -#include +#include +#include #include "angle_harmonic.h" #include "atom.h" #include "neighbor.h" @@ -30,7 +30,11 @@ using namespace MathConst; /* ---------------------------------------------------------------------- */ -AngleHarmonic::AngleHarmonic(LAMMPS *lmp) : Angle(lmp) {} +AngleHarmonic::AngleHarmonic(LAMMPS *lmp) : Angle(lmp) +{ + k = NULL; + theta0 = NULL; +} /* ---------------------------------------------------------------------- */ diff --git a/src/MOLECULE/angle_harmonic.h b/src/MOLECULE/angle_harmonic.h index 177e7cbadb7b404167bbdf91484a342c8ae6c211..ff8bd55fc00f217009ae3e606de45c18873cb796 100644 --- a/src/MOLECULE/angle_harmonic.h +++ b/src/MOLECULE/angle_harmonic.h @@ -20,7 +20,7 @@ AngleStyle(harmonic,AngleHarmonic) #ifndef LMP_ANGLE_HARMONIC_H #define LMP_ANGLE_HARMONIC_H -#include +#include #include "angle.h" namespace LAMMPS_NS { diff --git a/src/MOLECULE/angle_table.cpp b/src/MOLECULE/angle_table.cpp index 6e145efa10850909b288d8e0941ecc27c641a979..235e9b4d5b379c480026b052e0fb63d7a175810a 100644 --- a/src/MOLECULE/angle_table.cpp +++ b/src/MOLECULE/angle_table.cpp @@ -15,9 +15,9 @@ Contributing author: Chuanfu Luo (luochuanfu@gmail.com) ------------------------------------------------------------------------- */ -#include -#include -#include +#include +#include +#include #include "angle_table.h" #include "atom.h" #include "neighbor.h" @@ -609,7 +609,7 @@ double AngleTable::splint(double *xa, double *ya, double *y2a, int n, double x) void AngleTable::uf_lookup(int type, double x, double &u, double &f) { - if (!ISFINITE(x)) { + if (!std::isfinite(x)) { error->one(FLERR,"Illegal angle in angle style table"); } @@ -644,7 +644,7 @@ void AngleTable::uf_lookup(int type, double x, double &u, double &f) void AngleTable::u_lookup(int type, double x, double &u) { - if (!ISFINITE(x)) { + if (!std::isfinite(x)) { error->one(FLERR,"Illegal angle in angle style table"); } diff --git a/src/MOLECULE/angle_table.h b/src/MOLECULE/angle_table.h index 984c5dc640eafb82eacdcc85ef1e3842f2754c89..0088ace39b7a709a4da82d1a069c6a73d923956b 100644 --- a/src/MOLECULE/angle_table.h +++ b/src/MOLECULE/angle_table.h @@ -20,7 +20,7 @@ AngleStyle(table,AngleTable) #ifndef LMP_ANGLE_TABLE_H #define LMP_ANGLE_TABLE_H -#include +#include #include "angle.h" namespace LAMMPS_NS { diff --git a/src/MOLECULE/atom_vec_angle.cpp b/src/MOLECULE/atom_vec_angle.cpp index 7053f0eb30b7b1976282bf16f49f5c87d0ae35a5..6eb5b50fd2265e0559b68637f2dafd58d1b0eae0 100644 --- a/src/MOLECULE/atom_vec_angle.cpp +++ b/src/MOLECULE/atom_vec_angle.cpp @@ -11,7 +11,7 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include +#include #include "atom_vec_angle.h" #include "atom.h" #include "comm.h" diff --git a/src/MOLECULE/atom_vec_bond.cpp b/src/MOLECULE/atom_vec_bond.cpp index bae924c28add23da39dc550f7c3ea1427607e1b6..6a7b3585b4a17d07bcd45a68a174f98ede2c486d 100644 --- a/src/MOLECULE/atom_vec_bond.cpp +++ b/src/MOLECULE/atom_vec_bond.cpp @@ -11,7 +11,7 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include +#include #include "atom_vec_bond.h" #include "atom.h" #include "comm.h" diff --git a/src/MOLECULE/atom_vec_full.cpp b/src/MOLECULE/atom_vec_full.cpp index ba85a1280b46545963ab5f700508ae433cd38621..d682abf7994705eb2ff93d4eeb25c170842d0f1e 100644 --- a/src/MOLECULE/atom_vec_full.cpp +++ b/src/MOLECULE/atom_vec_full.cpp @@ -11,7 +11,7 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include +#include #include "atom_vec_full.h" #include "atom.h" #include "comm.h" diff --git a/src/MOLECULE/atom_vec_molecular.cpp b/src/MOLECULE/atom_vec_molecular.cpp index 23786d7641a7464f63ddd93a910fa110fc50ee5a..6e903a936eb8177db81606880bd23655739f64dc 100644 --- a/src/MOLECULE/atom_vec_molecular.cpp +++ b/src/MOLECULE/atom_vec_molecular.cpp @@ -11,7 +11,7 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include +#include #include "atom_vec_molecular.h" #include "atom.h" #include "comm.h" diff --git a/src/MOLECULE/atom_vec_template.cpp b/src/MOLECULE/atom_vec_template.cpp index 5d3b0a326492fe1ca1aef37be2d20b2e2a762c1a..3172804b95b1009c2349192d10ffe2233744bfc3 100644 --- a/src/MOLECULE/atom_vec_template.cpp +++ b/src/MOLECULE/atom_vec_template.cpp @@ -11,8 +11,8 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include -#include +#include +#include #include "atom_vec_template.h" #include "atom.h" #include "molecule.h" diff --git a/src/MOLECULE/bond_fene.cpp b/src/MOLECULE/bond_fene.cpp index 5d58f2683a0a4969663776323761d101d50bb31b..b6da72bfaf6b6968609ed1670a14149b66cd5be3 100644 --- a/src/MOLECULE/bond_fene.cpp +++ b/src/MOLECULE/bond_fene.cpp @@ -11,8 +11,8 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include -#include +#include +#include #include "bond_fene.h" #include "atom.h" #include "neighbor.h" diff --git a/src/MOLECULE/bond_fene.h b/src/MOLECULE/bond_fene.h index 6124478567e8bfd550c1a90af645b800a2572660..678ae165d66ffd59347e8451d8f95fd8f1465e39 100644 --- a/src/MOLECULE/bond_fene.h +++ b/src/MOLECULE/bond_fene.h @@ -20,7 +20,7 @@ BondStyle(fene,BondFENE) #ifndef LMP_BOND_FENE_H #define LMP_BOND_FENE_H -#include +#include #include "bond.h" namespace LAMMPS_NS { diff --git a/src/MOLECULE/bond_fene_expand.cpp b/src/MOLECULE/bond_fene_expand.cpp index 033f8d6502ef91d2fcb53b9b25a972bfa01eb391..26b699d7bfdcca6cdd8d1ecb2d87e0d610c4ac38 100644 --- a/src/MOLECULE/bond_fene_expand.cpp +++ b/src/MOLECULE/bond_fene_expand.cpp @@ -11,8 +11,8 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include -#include +#include +#include #include "bond_fene_expand.h" #include "atom.h" #include "neighbor.h" diff --git a/src/MOLECULE/bond_fene_expand.h b/src/MOLECULE/bond_fene_expand.h index 1971c6f428037558dace9aa741f85dcc0ad06d89..cb316ac5f2b366cd534e1429088eaffe6cce15e9 100644 --- a/src/MOLECULE/bond_fene_expand.h +++ b/src/MOLECULE/bond_fene_expand.h @@ -20,7 +20,7 @@ BondStyle(fene/expand,BondFENEExpand) #ifndef LMP_BOND_FENE_EXPAND_H #define LMP_BOND_FENE_EXPAND_H -#include +#include #include "bond.h" namespace LAMMPS_NS { diff --git a/src/MOLECULE/bond_gromos.cpp b/src/MOLECULE/bond_gromos.cpp index 4e409b7a72d686a7c573801a7bdaba608548ffd7..8e989259afa750eabdf5f44ac2ef91ab8f943b58 100644 --- a/src/MOLECULE/bond_gromos.cpp +++ b/src/MOLECULE/bond_gromos.cpp @@ -15,9 +15,9 @@ Contributing author: Axel Kohlmeyer (Temple U) ------------------------------------------------------------------------- */ -#include -#include -#include +#include +#include +#include #include "bond_gromos.h" #include "atom.h" #include "neighbor.h" diff --git a/src/MOLECULE/bond_gromos.h b/src/MOLECULE/bond_gromos.h index dafe85e92b2e671427d3c1e8e8e68e6ab38b0202..c26ad64b3d6ad5bcdeaaa3b8f94303299e7b0e82 100644 --- a/src/MOLECULE/bond_gromos.h +++ b/src/MOLECULE/bond_gromos.h @@ -20,7 +20,7 @@ BondStyle(gromos,BondGromos) #ifndef LMP_BOND_GROMOS_H #define LMP_BOND_GROMOS_H -#include +#include #include "bond.h" namespace LAMMPS_NS { diff --git a/src/MOLECULE/bond_harmonic.cpp b/src/MOLECULE/bond_harmonic.cpp index 0763d7d3e24667be3c3d81adbd236c16c3a54c7b..e7f510d2de9c59607351eba0b80ac51ce19a7831 100644 --- a/src/MOLECULE/bond_harmonic.cpp +++ b/src/MOLECULE/bond_harmonic.cpp @@ -11,9 +11,9 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include -#include -#include +#include +#include +#include #include "bond_harmonic.h" #include "atom.h" #include "neighbor.h" diff --git a/src/MOLECULE/bond_harmonic.h b/src/MOLECULE/bond_harmonic.h index a0fd24577a8988e18fcb7a676a0041c353c52191..73f6a9f774cbb373fa9161701cf6680822b23c29 100644 --- a/src/MOLECULE/bond_harmonic.h +++ b/src/MOLECULE/bond_harmonic.h @@ -20,7 +20,7 @@ BondStyle(harmonic,BondHarmonic) #ifndef LMP_BOND_HARMONIC_H #define LMP_BOND_HARMONIC_H -#include +#include #include "bond.h" namespace LAMMPS_NS { diff --git a/src/MOLECULE/bond_morse.cpp b/src/MOLECULE/bond_morse.cpp index 3204a0ca6183b003e0ec012083a8cd817f6e6f2c..35be50e8df9b6eebd071933953b1298c9d6e8ad3 100644 --- a/src/MOLECULE/bond_morse.cpp +++ b/src/MOLECULE/bond_morse.cpp @@ -15,8 +15,8 @@ Contributing author: Jeff Greathouse (SNL) ------------------------------------------------------------------------- */ -#include -#include +#include +#include #include "bond_morse.h" #include "atom.h" #include "neighbor.h" diff --git a/src/MOLECULE/bond_morse.h b/src/MOLECULE/bond_morse.h index 74379c91ee766b50996ad32d97219bfbb7d31ecd..c4d60bc21768c1ffe3ddf806d26dfea6dd475a95 100644 --- a/src/MOLECULE/bond_morse.h +++ b/src/MOLECULE/bond_morse.h @@ -20,7 +20,7 @@ BondStyle(morse,BondMorse) #ifndef LMP_BOND_MORSE_H #define LMP_BOND_MORSE_H -#include +#include #include "bond.h" namespace LAMMPS_NS { diff --git a/src/MOLECULE/bond_nonlinear.cpp b/src/MOLECULE/bond_nonlinear.cpp index edd9dcd4e5c9e8e8be20a2ea85c1ee5b3fb13a3a..3926c3494b3666e0a30af5b5c51bd00bc92476ca 100644 --- a/src/MOLECULE/bond_nonlinear.cpp +++ b/src/MOLECULE/bond_nonlinear.cpp @@ -11,8 +11,8 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include -#include +#include +#include #include "bond_nonlinear.h" #include "atom.h" #include "neighbor.h" diff --git a/src/MOLECULE/bond_nonlinear.h b/src/MOLECULE/bond_nonlinear.h index 5d2448b112b45d24229f5e1768911fe211b82f18..175421264b91e11b0f71453716bb11c774f00d34 100644 --- a/src/MOLECULE/bond_nonlinear.h +++ b/src/MOLECULE/bond_nonlinear.h @@ -20,7 +20,7 @@ BondStyle(nonlinear,BondNonlinear) #ifndef LMP_BOND_NONLINEAR_H #define LMP_BOND_NONLINEAR_H -#include +#include #include "bond.h" namespace LAMMPS_NS { diff --git a/src/MOLECULE/bond_quartic.cpp b/src/MOLECULE/bond_quartic.cpp index 2a3e395a77f81f9c92b59f6137d0cfbdc6c13a26..f581c7f33155e6d0059d0925e6be5524680e2574 100644 --- a/src/MOLECULE/bond_quartic.cpp +++ b/src/MOLECULE/bond_quartic.cpp @@ -15,8 +15,8 @@ Contributing authors: Chris Lorenz and Mark Stevens (SNL) ------------------------------------------------------------------------- */ -#include -#include +#include +#include #include "bond_quartic.h" #include "atom.h" #include "neighbor.h" diff --git a/src/MOLECULE/bond_quartic.h b/src/MOLECULE/bond_quartic.h index 21bd7f00b4055a92e407fb0e4429b9de778f2e26..2aaa76e2c374e531637455f612af56ab30bcc3d8 100644 --- a/src/MOLECULE/bond_quartic.h +++ b/src/MOLECULE/bond_quartic.h @@ -20,7 +20,7 @@ BondStyle(quartic,BondQuartic) #ifndef LMP_BOND_QUARTIC_H #define LMP_BOND_QUARTIC_H -#include +#include #include "bond.h" namespace LAMMPS_NS { diff --git a/src/MOLECULE/bond_table.cpp b/src/MOLECULE/bond_table.cpp index 4f8db66757c5b71fa392e3c84ee5d5d6f76ec946..7515f713df7db4d3e07fe0019f4fec10e93303a0 100644 --- a/src/MOLECULE/bond_table.cpp +++ b/src/MOLECULE/bond_table.cpp @@ -15,9 +15,9 @@ Contributing author: Chuanfu Luo (luochuanfu@gmail.com) ------------------------------------------------------------------------- */ -#include -#include -#include +#include +#include +#include #include "bond_table.h" #include "atom.h" #include "neighbor.h" @@ -590,7 +590,7 @@ double BondTable::splint(double *xa, double *ya, double *y2a, int n, double x) void BondTable::uf_lookup(int type, double x, double &u, double &f) { - if (!ISFINITE(x)) { + if (!std::isfinite(x)) { error->one(FLERR,"Illegal bond in bond style table"); } @@ -633,7 +633,7 @@ void BondTable::uf_lookup(int type, double x, double &u, double &f) void BondTable::u_lookup(int type, double x, double &u) { - if (!ISFINITE(x)) { + if (!std::isfinite(x)) { error->one(FLERR,"Illegal bond in bond style table"); } diff --git a/src/MOLECULE/bond_table.h b/src/MOLECULE/bond_table.h index ee053d497bb4b2960b1ec174e86ae90b152aa05c..5766239167c26dbc80ef62e08d52da29b26bb50f 100644 --- a/src/MOLECULE/bond_table.h +++ b/src/MOLECULE/bond_table.h @@ -20,7 +20,7 @@ BondStyle(table,BondTable) #ifndef LMP_BOND_TABLE_H #define LMP_BOND_TABLE_H -#include +#include #include "bond.h" namespace LAMMPS_NS { diff --git a/src/MOLECULE/dihedral_charmm.cpp b/src/MOLECULE/dihedral_charmm.cpp index 35953a6ac456185b8b87a49b5b7c5be772e2d3e5..2372fae38b696a01b61cdce87cc83c62e60ee50c 100644 --- a/src/MOLECULE/dihedral_charmm.cpp +++ b/src/MOLECULE/dihedral_charmm.cpp @@ -16,9 +16,9 @@ ------------------------------------------------------------------------- */ #include -#include -#include -#include +#include +#include +#include #include "dihedral_charmm.h" #include "atom.h" #include "comm.h" diff --git a/src/MOLECULE/dihedral_charmm.h b/src/MOLECULE/dihedral_charmm.h index 2f8a6a667924473d0b8ecd0e3ec19f426355c13d..349bee73d8ae938f70a31ad13ff327ab25c95928 100644 --- a/src/MOLECULE/dihedral_charmm.h +++ b/src/MOLECULE/dihedral_charmm.h @@ -20,7 +20,7 @@ DihedralStyle(charmm,DihedralCharmm) #ifndef LMP_DIHEDRAL_CHARMM_H #define LMP_DIHEDRAL_CHARMM_H -#include +#include #include "dihedral.h" namespace LAMMPS_NS { diff --git a/src/MOLECULE/dihedral_charmmfsw.cpp b/src/MOLECULE/dihedral_charmmfsw.cpp index d33db36fda302c9d01c88c9a3bcf23cc17322915..99a53336205f3b5f20623320dd8fa8b092a40073 100644 --- a/src/MOLECULE/dihedral_charmmfsw.cpp +++ b/src/MOLECULE/dihedral_charmmfsw.cpp @@ -19,9 +19,9 @@ ------------------------------------------------------------------------- */ #include -#include -#include -#include +#include +#include +#include #include "dihedral_charmmfsw.h" #include "atom.h" #include "comm.h" diff --git a/src/MOLECULE/dihedral_charmmfsw.h b/src/MOLECULE/dihedral_charmmfsw.h index 3c93f8abcf127edc56cb8d8ba16b6374ed94a961..dd31067a8dba9bd39b01373fba5b3dc29da842d4 100644 --- a/src/MOLECULE/dihedral_charmmfsw.h +++ b/src/MOLECULE/dihedral_charmmfsw.h @@ -20,7 +20,7 @@ DihedralStyle(charmmfsw,DihedralCharmmfsw) #ifndef LMP_DIHEDRAL_CHARMMFSW_H #define LMP_DIHEDRAL_CHARMMFSW_H -#include +#include #include "dihedral.h" namespace LAMMPS_NS { diff --git a/src/MOLECULE/dihedral_harmonic.cpp b/src/MOLECULE/dihedral_harmonic.cpp index 82c5fe31507d667359a208a00bb43056af1eef6a..cb122f4bc2b7166ae84a70f3199c0a042dfddcbd 100644 --- a/src/MOLECULE/dihedral_harmonic.cpp +++ b/src/MOLECULE/dihedral_harmonic.cpp @@ -16,8 +16,8 @@ ------------------------------------------------------------------------- */ #include -#include -#include +#include +#include #include "dihedral_harmonic.h" #include "atom.h" #include "comm.h" diff --git a/src/MOLECULE/dihedral_harmonic.h b/src/MOLECULE/dihedral_harmonic.h index db8789675d8c87f3e076ed9284d6c8cea69025ce..20312612568ae92681d8a79649069e9496028896 100644 --- a/src/MOLECULE/dihedral_harmonic.h +++ b/src/MOLECULE/dihedral_harmonic.h @@ -20,7 +20,7 @@ DihedralStyle(harmonic,DihedralHarmonic) #ifndef LMP_DIHEDRAL_HARMONIC_H #define LMP_DIHEDRAL_HARMONIC_H -#include +#include #include "dihedral.h" namespace LAMMPS_NS { diff --git a/src/MOLECULE/dihedral_helix.cpp b/src/MOLECULE/dihedral_helix.cpp index 43794bd6aabfacca837f8b9a57e10452b46f2a70..ae23b77951dda47600972f86df05636db8757001 100644 --- a/src/MOLECULE/dihedral_helix.cpp +++ b/src/MOLECULE/dihedral_helix.cpp @@ -17,8 +17,8 @@ ------------------------------------------------------------------------- */ #include -#include -#include +#include +#include #include "dihedral_helix.h" #include "atom.h" #include "neighbor.h" @@ -332,3 +332,13 @@ void DihedralHelix::read_restart(FILE *fp) for (int i = 1; i <= atom->ndihedraltypes; i++) setflag[i] = 1; } + +/* ---------------------------------------------------------------------- + proc 0 writes to data file +------------------------------------------------------------------------- */ + +void DihedralHelix::write_data(FILE *fp) +{ + for (int i = 1; i <= atom->ndihedraltypes; i++) + fprintf(fp,"%d %g %g %g\n",i,aphi[i],bphi[i],cphi[i]); +} diff --git a/src/MOLECULE/dihedral_helix.h b/src/MOLECULE/dihedral_helix.h index 61aef1d2ecadeb27b892797b774847650ccb6e06..745ab841156164e095c0ffbc55f93705d83f7662 100644 --- a/src/MOLECULE/dihedral_helix.h +++ b/src/MOLECULE/dihedral_helix.h @@ -20,7 +20,7 @@ DihedralStyle(helix,DihedralHelix) #ifndef LMP_DIHEDRAL_HELIX_H #define LMP_DIHEDRAL_HELIX_H -#include +#include #include "dihedral.h" namespace LAMMPS_NS { @@ -33,6 +33,7 @@ class DihedralHelix : public Dihedral { void coeff(int, char **); void write_restart(FILE *); void read_restart(FILE *); + void write_data(FILE *); protected: double *aphi,*bphi,*cphi; diff --git a/src/MOLECULE/dihedral_multi_harmonic.cpp b/src/MOLECULE/dihedral_multi_harmonic.cpp index 3a4be46fc7876360636365724968ca6fc007a710..f6461abb6e9fbf3ef84fbb82935755d73639c751 100644 --- a/src/MOLECULE/dihedral_multi_harmonic.cpp +++ b/src/MOLECULE/dihedral_multi_harmonic.cpp @@ -15,8 +15,8 @@ Contributing author: Mathias Puetz (SNL) and friends ------------------------------------------------------------------------- */ -#include -#include +#include +#include #include "dihedral_multi_harmonic.h" #include "atom.h" #include "neighbor.h" @@ -331,3 +331,13 @@ void DihedralMultiHarmonic::read_restart(FILE *fp) for (int i = 1; i <= atom->ndihedraltypes; i++) setflag[i] = 1; } + +/* ---------------------------------------------------------------------- + proc 0 writes to data file +------------------------------------------------------------------------- */ + +void DihedralMultiHarmonic::write_data(FILE *fp) +{ + for (int i = 1; i <= atom->ndihedraltypes; i++) + fprintf(fp,"%d %g %g %g %g %g\n",i,a1[i],a2[i],a3[i],a4[i],a5[i]); +} diff --git a/src/MOLECULE/dihedral_multi_harmonic.h b/src/MOLECULE/dihedral_multi_harmonic.h index 8f40b56a5ffb80ae428c8f059246173abb4b9d66..32f17e75ae4a79571a6cdca27e199405d25069c8 100644 --- a/src/MOLECULE/dihedral_multi_harmonic.h +++ b/src/MOLECULE/dihedral_multi_harmonic.h @@ -20,7 +20,7 @@ DihedralStyle(multi/harmonic,DihedralMultiHarmonic) #ifndef LMP_DIHEDRAL_MULTI_HARMONIC_H #define LMP_DIHEDRAL_MULTI_HARMONIC_H -#include +#include #include "dihedral.h" namespace LAMMPS_NS { @@ -33,6 +33,7 @@ class DihedralMultiHarmonic : public Dihedral { void coeff(int, char **); void write_restart(FILE *); void read_restart(FILE *); + void write_data(FILE *); protected: double *a1,*a2,*a3,*a4,*a5; diff --git a/src/MOLECULE/dihedral_opls.cpp b/src/MOLECULE/dihedral_opls.cpp index c3a7ee6aa7f9a4388f058b39587b4e695702020b..b5103413b227d2402f4e9e3f563632ac2b914f9a 100644 --- a/src/MOLECULE/dihedral_opls.cpp +++ b/src/MOLECULE/dihedral_opls.cpp @@ -15,8 +15,8 @@ Contributing author: Mark Stevens (SNL) ------------------------------------------------------------------------- */ -#include -#include +#include +#include #include "dihedral_opls.h" #include "atom.h" #include "comm.h" diff --git a/src/MOLECULE/dihedral_opls.h b/src/MOLECULE/dihedral_opls.h index 0a127d3ac178ebffb97a616dc64acb19abea91df..378dec1a6a930db5733fe20ee444f318fba81dfe 100644 --- a/src/MOLECULE/dihedral_opls.h +++ b/src/MOLECULE/dihedral_opls.h @@ -20,7 +20,7 @@ DihedralStyle(opls,DihedralOPLS) #ifndef LMP_DIHEDRAL_OPLS_H #define LMP_DIHEDRAL_OPLS_H -#include +#include #include "dihedral.h" namespace LAMMPS_NS { diff --git a/src/MOLECULE/fix_cmap.cpp b/src/MOLECULE/fix_cmap.cpp index f4bc6c1ee645ee98fa9b77b680dc5c7fefe32b07..5ef2e662abfb6cc618cb8c377fef940385410b38 100644 --- a/src/MOLECULE/fix_cmap.cpp +++ b/src/MOLECULE/fix_cmap.cpp @@ -28,10 +28,10 @@ ------------------------------------------------------------------------- */ #include -#include -#include -#include -#include +#include +#include +#include +#include #include "fix_cmap.h" #include "atom.h" #include "atom_vec.h" diff --git a/src/MOLECULE/improper_cvff.cpp b/src/MOLECULE/improper_cvff.cpp index 45740d7880f0b57409d8de9c73872d7176861cf7..641eea74a88f63aa40084d3d38b08f90c5a9c1c9 100644 --- a/src/MOLECULE/improper_cvff.cpp +++ b/src/MOLECULE/improper_cvff.cpp @@ -12,8 +12,8 @@ ------------------------------------------------------------------------- */ #include -#include -#include +#include +#include #include "improper_cvff.h" #include "atom.h" #include "comm.h" diff --git a/src/MOLECULE/improper_cvff.h b/src/MOLECULE/improper_cvff.h index 8e997e3ff4a5f8caf9f1ca75ed1661055f4ed9fc..d4c30cc2eead856bc70d8215add5d9a58b9942df 100644 --- a/src/MOLECULE/improper_cvff.h +++ b/src/MOLECULE/improper_cvff.h @@ -20,7 +20,7 @@ ImproperStyle(cvff,ImproperCvff) #ifndef LMP_IMPROPER_CVFF_H #define LMP_IMPROPER_CVFF_H -#include +#include #include "improper.h" namespace LAMMPS_NS { diff --git a/src/MOLECULE/improper_harmonic.cpp b/src/MOLECULE/improper_harmonic.cpp index c482055c76f8c57b4acb7e1dee7af71066663d11..091bd463163488cba7a36dac2e114e1e272e6a0e 100644 --- a/src/MOLECULE/improper_harmonic.cpp +++ b/src/MOLECULE/improper_harmonic.cpp @@ -12,8 +12,8 @@ ------------------------------------------------------------------------- */ #include -#include -#include +#include +#include #include "improper_harmonic.h" #include "atom.h" #include "comm.h" diff --git a/src/MOLECULE/improper_harmonic.h b/src/MOLECULE/improper_harmonic.h index b5132ab7ffc636f6f0f0d411ab0a951ebd4c048c..be9b25f3b6929ced0877a647a2d561f9e864453c 100644 --- a/src/MOLECULE/improper_harmonic.h +++ b/src/MOLECULE/improper_harmonic.h @@ -20,7 +20,7 @@ ImproperStyle(harmonic,ImproperHarmonic) #ifndef LMP_IMPROPER_HARMONIC_H #define LMP_IMPROPER_HARMONIC_H -#include +#include #include "improper.h" namespace LAMMPS_NS { diff --git a/src/MOLECULE/improper_umbrella.cpp b/src/MOLECULE/improper_umbrella.cpp index 8a9b0b44345711174b26c84799ac13b7793c5081..31d7cba54dca313ae2016fe477b9882e0787f515 100644 --- a/src/MOLECULE/improper_umbrella.cpp +++ b/src/MOLECULE/improper_umbrella.cpp @@ -16,8 +16,8 @@ ------------------------------------------------------------------------- */ #include -#include -#include +#include +#include #include "improper_umbrella.h" #include "atom.h" #include "comm.h" diff --git a/src/MOLECULE/improper_umbrella.h b/src/MOLECULE/improper_umbrella.h index f590a63c3277f7e2b4fe63988e0c06391eabb9bc..dc2262d01c31d48713c74bdcd1d347c7f8c98d15 100644 --- a/src/MOLECULE/improper_umbrella.h +++ b/src/MOLECULE/improper_umbrella.h @@ -20,7 +20,7 @@ ImproperStyle(umbrella,ImproperUmbrella) #ifndef LMP_IMPROPER_UMBRELLA_H #define LMP_IMPROPER_UMBRELLA_H -#include +#include #include "improper.h" namespace LAMMPS_NS { diff --git a/src/MOLECULE/pair_hbond_dreiding_lj.cpp b/src/MOLECULE/pair_hbond_dreiding_lj.cpp index ecb4883cb364b07afbb56208e62c73afe91c50b2..26ff499dec6cd0dd2b6b8bb6ad15c95fb97032ca 100644 --- a/src/MOLECULE/pair_hbond_dreiding_lj.cpp +++ b/src/MOLECULE/pair_hbond_dreiding_lj.cpp @@ -15,10 +15,10 @@ Contributing author: Tod A Pascal (Caltech) ------------------------------------------------------------------------- */ -#include -#include -#include -#include +#include +#include +#include +#include #include "pair_hbond_dreiding_lj.h" #include "atom.h" #include "atom_vec.h" diff --git a/src/MOLECULE/pair_hbond_dreiding_morse.cpp b/src/MOLECULE/pair_hbond_dreiding_morse.cpp index 83b03f9a2fb9c6565c4cac14a685ea7e270d9a27..749053164cf5746602ac31e933ac533659e51609 100644 --- a/src/MOLECULE/pair_hbond_dreiding_morse.cpp +++ b/src/MOLECULE/pair_hbond_dreiding_morse.cpp @@ -15,10 +15,10 @@ Contributing author: Tod A Pascal (Caltech) ------------------------------------------------------------------------- */ -#include -#include -#include -#include +#include +#include +#include +#include #include "pair_hbond_dreiding_morse.h" #include "atom.h" #include "atom_vec.h" diff --git a/src/MOLECULE/pair_lj_charmm_coul_charmm.cpp b/src/MOLECULE/pair_lj_charmm_coul_charmm.cpp index 3700de00b0fe380a96abaf358ab0e06f0416ab5a..688c675815ad7efa3fa4bd6fec4e08a7e79108ca 100644 --- a/src/MOLECULE/pair_lj_charmm_coul_charmm.cpp +++ b/src/MOLECULE/pair_lj_charmm_coul_charmm.cpp @@ -15,10 +15,10 @@ Contributing author: Paul Crozier (SNL) ------------------------------------------------------------------------- */ -#include -#include -#include -#include +#include +#include +#include +#include #include "pair_lj_charmm_coul_charmm.h" #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 3421f88eb3c1edc1217f53da2f093ccde2aaa4e5..6c083a49b09ac84ca950abe8c4ca83d6f7e2123c 100644 --- a/src/MOLECULE/pair_lj_charmm_coul_charmm_implicit.cpp +++ b/src/MOLECULE/pair_lj_charmm_coul_charmm_implicit.cpp @@ -11,8 +11,8 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include -#include +#include +#include #include "pair_lj_charmm_coul_charmm_implicit.h" #include "atom.h" #include "force.h" diff --git a/src/MOLECULE/pair_lj_charmmfsw_coul_charmmfsh.cpp b/src/MOLECULE/pair_lj_charmmfsw_coul_charmmfsh.cpp index 7da6d59d32f5ef2a1ae49b59226312968a6f080e..4b9147c1698a3a3eaab1ede1a648380ceb180dac 100644 --- a/src/MOLECULE/pair_lj_charmmfsw_coul_charmmfsh.cpp +++ b/src/MOLECULE/pair_lj_charmmfsw_coul_charmmfsh.cpp @@ -19,10 +19,10 @@ with additional assistance from Robert A. Latour, Clemson University ------------------------------------------------------------------------- */ -#include -#include -#include -#include +#include +#include +#include +#include #include "pair_lj_charmmfsw_coul_charmmfsh.h" #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 c616a9fa83af793eb095daff37b8e69ce20da915..92dead8435237b593d154d0f8337d8f1d6207240 100644 --- a/src/MOLECULE/pair_lj_cut_tip4p_cut.cpp +++ b/src/MOLECULE/pair_lj_cut_tip4p_cut.cpp @@ -15,9 +15,9 @@ Contributing author: Pavel Elkind (Gothenburg University) ------------------------------------------------------------------------- */ -#include -#include -#include +#include +#include +#include #include "pair_lj_cut_tip4p_cut.h" #include "atom.h" #include "force.h" diff --git a/src/MOLECULE/pair_tip4p_cut.cpp b/src/MOLECULE/pair_tip4p_cut.cpp index 954bd35435604f118a77d05b70f25100cfa887a7..e9f52b87246c3ef076818253b160893d019c44b6 100644 --- a/src/MOLECULE/pair_tip4p_cut.cpp +++ b/src/MOLECULE/pair_tip4p_cut.cpp @@ -15,8 +15,8 @@ Contributing author: Pavel Elkind (Gothenburg University) ------------------------------------------------------------------------- */ -#include -#include +#include +#include #include "pair_tip4p_cut.h" #include "atom.h" #include "force.h" diff --git a/src/MPIIO/dump_atom_mpiio.cpp b/src/MPIIO/dump_atom_mpiio.cpp index 75702ed9b0d7179aa1e9ee075d087be0b3ad9dc5..4422ef1cdfb5c16df75cdd8ff745d67a212d889d 100644 --- a/src/MPIIO/dump_atom_mpiio.cpp +++ b/src/MPIIO/dump_atom_mpiio.cpp @@ -15,7 +15,7 @@ Contributing author: Paul Coffman (IBM) ------------------------------------------------------------------------- */ -#include +#include #include "dump_atom_mpiio.h" #include "domain.h" #include "atom.h" diff --git a/src/MPIIO/dump_atom_mpiio.h b/src/MPIIO/dump_atom_mpiio.h index 265f9a3b0200c48249f0cdd0494453b7fe359d78..ad49fa11823a21354c0340b335a01129e20fd97b 100644 --- a/src/MPIIO/dump_atom_mpiio.h +++ b/src/MPIIO/dump_atom_mpiio.h @@ -21,7 +21,7 @@ DumpStyle(atom/mpiio,DumpAtomMPIIO) #define LMP_DUMP_ATOM_MPIIO_H #include "dump_atom.h" -#include +#include namespace LAMMPS_NS { diff --git a/src/MPIIO/dump_cfg_mpiio.cpp b/src/MPIIO/dump_cfg_mpiio.cpp index 1cca047bb2aaa3f055fcdf2257efc5eb7e73e8ac..5086d1dc6cdf70cd93ad2f44760ca3c8795fc64b 100644 --- a/src/MPIIO/dump_cfg_mpiio.cpp +++ b/src/MPIIO/dump_cfg_mpiio.cpp @@ -15,9 +15,9 @@ Contributing author: Paul Coffman (IBM) ------------------------------------------------------------------------- */ -#include -#include -#include +#include +#include +#include #include "dump_cfg_mpiio.h" #include "atom.h" #include "domain.h" @@ -34,7 +34,6 @@ #ifdef LMP_USER_IO_TIMER #include #include -#include long dumpCFGTimestamps[10]; #endif diff --git a/src/MPIIO/dump_custom_mpiio.cpp b/src/MPIIO/dump_custom_mpiio.cpp index 0b282b77efad41a25da336c34483ef51e098665e..2da6dd700d1348a15a96f68c14d6363b0a04ce14 100644 --- a/src/MPIIO/dump_custom_mpiio.cpp +++ b/src/MPIIO/dump_custom_mpiio.cpp @@ -15,9 +15,9 @@ Contributing author: Paul Coffman (IBM) ------------------------------------------------------------------------- */ -#include -#include -#include +#include +#include +#include #include "dump_custom_mpiio.h" #include "atom.h" #include "force.h" @@ -32,7 +32,6 @@ #include "fix.h" #include "memory.h" #include "error.h" -#include #if defined(_OPENMP) #include diff --git a/src/MPIIO/dump_xyz_mpiio.cpp b/src/MPIIO/dump_xyz_mpiio.cpp index cc87fe881c468ffbc84269558e96abd1b8c4d426..4725efccd14b990d28ea7afe6991c40117f5d688 100644 --- a/src/MPIIO/dump_xyz_mpiio.cpp +++ b/src/MPIIO/dump_xyz_mpiio.cpp @@ -15,9 +15,9 @@ Contributing author: Paul Coffman (IBM) ------------------------------------------------------------------------- */ -#include -#include -#include +#include +#include +#include #include "dump_xyz_mpiio.h" #include "atom.h" #include "force.h" @@ -32,7 +32,6 @@ #include "fix.h" #include "memory.h" #include "error.h" -#include #if defined(_OPENMP) #include diff --git a/src/MPIIO/restart_mpiio.cpp b/src/MPIIO/restart_mpiio.cpp index 8ad1dccdca9fe60fb5a29fdb2f5cf20d328eb4d2..804df211dc4579957b14fa1b3e94b0bcf36c73f6 100644 --- a/src/MPIIO/restart_mpiio.cpp +++ b/src/MPIIO/restart_mpiio.cpp @@ -16,9 +16,9 @@ ------------------------------------------------------------------------- */ #include +#include #include "restart_mpiio.h" #include "error.h" -#include using namespace LAMMPS_NS; diff --git a/src/MSCG/fix_mscg.cpp b/src/MSCG/fix_mscg.cpp index fba198c814c77b2cf5585fd7e73f8311a271b4ae..b28259524071672463f17051e5a388e0d89d133d 100644 --- a/src/MSCG/fix_mscg.cpp +++ b/src/MSCG/fix_mscg.cpp @@ -16,11 +16,12 @@ ------------------------------------------------------------------------- */ #include -#include -#include +#include +#include #include "fix_mscg.h" #include "mscg.h" #include "atom.h" +#include "comm.h" #include "domain.h" #include "error.h" #include "force.h" @@ -284,11 +285,9 @@ void FixMSCG::end_of_step() if (domain->triclinic == 1) error->all(FLERR,"Fix mscg does not yet support triclinic geometries"); - int natoms = atom->natoms; int nlocal = atom->nlocal; tagint *tag = atom->tag; double **x = atom->x; - double *prd_half = domain->prd_half; int i,ii,j; // trajectory information diff --git a/src/Makefile b/src/Makefile index 03f40721324e8d1712d967481f7611484be0c558..d17a2ccbd99ecf0ff2c29b1626ebe1bdd3da39dc 100644 --- a/src/Makefile +++ b/src/Makefile @@ -57,10 +57,10 @@ PACKAGE = asphere body class2 colloid compress coreshell dipole gpu \ molecule mpiio mscg opt peri poems \ python qeq reax replica rigid shock snap srd voronoi -PACKUSER = user-atc user-awpmd user-cgdna user-cgsdk user-colvars \ +PACKUSER = user-atc user-awpmd user-bocs user-cgdna user-cgsdk user-colvars \ user-diffraction user-dpd user-drude user-eff user-fep user-h5md \ user-intel user-lb user-manifold user-meamc user-meso \ - user-mgpt user-misc user-molfile \ + user-mgpt user-misc user-mofff user-molfile \ user-netcdf user-omp user-phonon user-qmmm user-qtb \ user-quip user-reaxc user-smd user-smtbq user-sph user-tally \ user-uef user-vtk @@ -267,7 +267,7 @@ package: @echo 'make yes-all install all pgks in src dir' @echo 'make no-all remove all pkgs from src dir' @echo 'make yes-standard (yes-std) install all standard pkgs' - @echo 'make no-standard (no-srd) remove all standard pkgs' + @echo 'make no-standard (no-std) remove all standard pkgs' @echo 'make yes-user install all user pkgs' @echo 'make no-user remove all user pkgs' @echo 'make yes-lib install all pkgs with libs (included or ext)' diff --git a/src/OPT/pair_eam_opt.cpp b/src/OPT/pair_eam_opt.cpp index 3afec5644a70bb12497163d8fd8174202f2d11b1..5345d7f8d6c40c41f56f1cc0b8df81a997a6c18e 100644 --- a/src/OPT/pair_eam_opt.cpp +++ b/src/OPT/pair_eam_opt.cpp @@ -19,8 +19,8 @@ Vincent Natoli, Stone Ridge Technology ------------------------------------------------------------------------- */ -#include -#include +#include +#include #include "pair_eam_opt.h" #include "atom.h" #include "comm.h" diff --git a/src/OPT/pair_lj_charmm_coul_long_opt.cpp b/src/OPT/pair_lj_charmm_coul_long_opt.cpp index b98dd36dd138fe7f93a60c2445decb3bd3f3736b..43f4ba7f5a9ae9fa29ae1d7c9c20220160cf96d1 100644 --- a/src/OPT/pair_lj_charmm_coul_long_opt.cpp +++ b/src/OPT/pair_lj_charmm_coul_long_opt.cpp @@ -18,8 +18,8 @@ Vincent Natoli, Stone Ridge Technology ------------------------------------------------------------------------- */ -#include -#include +#include +#include #include "pair_lj_charmm_coul_long_opt.h" #include "atom.h" #include "force.h" diff --git a/src/OPT/pair_lj_cut_coul_long_opt.cpp b/src/OPT/pair_lj_cut_coul_long_opt.cpp index 140d4d023a688e52a2b65386442525a63d26570f..98683a67a4ccbfc537393c2aa55dcb758f1b0ee6 100644 --- a/src/OPT/pair_lj_cut_coul_long_opt.cpp +++ b/src/OPT/pair_lj_cut_coul_long_opt.cpp @@ -11,7 +11,7 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include +#include #include "pair_lj_cut_coul_long_opt.h" #include "atom.h" #include "force.h" diff --git a/src/OPT/pair_lj_cut_opt.cpp b/src/OPT/pair_lj_cut_opt.cpp index 0812a56f015cd1f888c1eee840f00484a645ce61..ed35178c1f9e60d6fd40cada3e5452f2b318a224 100644 --- a/src/OPT/pair_lj_cut_opt.cpp +++ b/src/OPT/pair_lj_cut_opt.cpp @@ -18,7 +18,7 @@ Vincent Natoli, Stone Ridge Technology ------------------------------------------------------------------------- */ -#include +#include #include "pair_lj_cut_opt.h" #include "atom.h" #include "force.h" diff --git a/src/OPT/pair_lj_cut_tip4p_long_opt.cpp b/src/OPT/pair_lj_cut_tip4p_long_opt.cpp index db9402b521c902119e57fbe4dbdca27bb11e0a87..4842cc4fc00ea6725c5f683e010b1e58f55c5b21 100644 --- a/src/OPT/pair_lj_cut_tip4p_long_opt.cpp +++ b/src/OPT/pair_lj_cut_tip4p_long_opt.cpp @@ -15,7 +15,7 @@ OPT version: Axel Kohlmeyer (Temple U) ------------------------------------------------------------------------- */ -#include +#include #include "pair_lj_cut_tip4p_long_opt.h" #include "atom.h" #include "domain.h" diff --git a/src/OPT/pair_lj_long_coul_long_opt.cpp b/src/OPT/pair_lj_long_coul_long_opt.cpp index c5756cbecc6de1613222e7163e43db7bf0885232..91ffc2c01ed20e96f317cf82cd48d778cb1233a0 100644 --- a/src/OPT/pair_lj_long_coul_long_opt.cpp +++ b/src/OPT/pair_lj_long_coul_long_opt.cpp @@ -15,7 +15,7 @@ OPT version: Wayne Mitchell (Loyola University New Orleans) ------------------------------------------------------------------------- */ -#include +#include #include "pair_lj_long_coul_long_opt.h" #include "atom.h" #include "force.h" diff --git a/src/OPT/pair_morse_opt.cpp b/src/OPT/pair_morse_opt.cpp index e63fbd0938c5cb235b22d10d92d86d84797513e9..6299136f46af21f358079429b8ed3981d4562589 100644 --- a/src/OPT/pair_morse_opt.cpp +++ b/src/OPT/pair_morse_opt.cpp @@ -18,8 +18,8 @@ Vincent Natoli, Stone Ridge Technology ------------------------------------------------------------------------- */ -#include -#include +#include +#include #include "pair_morse_opt.h" #include "atom.h" #include "force.h" diff --git a/src/OPT/pair_ufm_opt.cpp b/src/OPT/pair_ufm_opt.cpp index f6f4c4ce3e7bc2a7a04a97db049c2a239e863288..85c76d624d7eaad82a27d319134642a0aee6724e 100644 --- a/src/OPT/pair_ufm_opt.cpp +++ b/src/OPT/pair_ufm_opt.cpp @@ -17,8 +17,8 @@ Maurice de Koning (Unicamp/Brazil) - dekoning@ifi.unicamp.br ------------------------------------------------------------------------- */ -#include -#include +#include +#include #include "pair_ufm_opt.h" #include "atom.h" #include "force.h" diff --git a/src/PERI/atom_vec_peri.cpp b/src/PERI/atom_vec_peri.cpp index 3e6a72289a6d3afa7e6c4ccb7105f0f64d342221..d78fe27c94b62fa8d313b968cbc2fe55f54fb315 100644 --- a/src/PERI/atom_vec_peri.cpp +++ b/src/PERI/atom_vec_peri.cpp @@ -15,9 +15,9 @@ Contributing author: Mike Parks (SNL) ------------------------------------------------------------------------- */ -#include -#include -#include +#include +#include +#include #include "atom_vec_peri.h" #include "atom.h" #include "comm.h" diff --git a/src/PERI/compute_damage_atom.cpp b/src/PERI/compute_damage_atom.cpp index a3bc580f7ab72d0ddf7562eea2d858345578b803..4bf8fa17a57fd7ff034a46a15f64c713d741fc01 100644 --- a/src/PERI/compute_damage_atom.cpp +++ b/src/PERI/compute_damage_atom.cpp @@ -15,7 +15,7 @@ Contributing author: Mike Parks (SNL) ------------------------------------------------------------------------- */ -#include +#include #include "compute_damage_atom.h" #include "atom.h" #include "update.h" diff --git a/src/PERI/compute_dilatation_atom.cpp b/src/PERI/compute_dilatation_atom.cpp index d79b80f4d459ad3d60ee43d9795f898860024633..990731a227d30865c2dbba4a2566217cd94913d7 100644 --- a/src/PERI/compute_dilatation_atom.cpp +++ b/src/PERI/compute_dilatation_atom.cpp @@ -15,7 +15,7 @@ Contributing author: Rezwanur Rahman, John Foster (UTSA) ------------------------------------------------------------------------- */ -#include +#include #include "compute_dilatation_atom.h" #include "atom.h" #include "update.h" diff --git a/src/PERI/compute_plasticity_atom.cpp b/src/PERI/compute_plasticity_atom.cpp index 34fd23fe6a663bccb36257724ff09a4f46b146ab..d08fb98e07b84d1c893c5d05588cb1db4e4622a6 100644 --- a/src/PERI/compute_plasticity_atom.cpp +++ b/src/PERI/compute_plasticity_atom.cpp @@ -15,7 +15,7 @@ Contributing author: Rezwanur Rahman, John Foster (UTSA) ------------------------------------------------------------------------- */ -#include +#include #include "compute_plasticity_atom.h" #include "atom.h" #include "update.h" diff --git a/src/PERI/fix_peri_neigh.cpp b/src/PERI/fix_peri_neigh.cpp index d92f355c53866bf8e2f13d4e020b054a598e80a0..42d86e14b2b4eec17c78d95457c48647af0f7b86 100644 --- a/src/PERI/fix_peri_neigh.cpp +++ b/src/PERI/fix_peri_neigh.cpp @@ -15,7 +15,7 @@ Contributing authors: Mike Parks (SNL), Ezwanur Rahman, J.T. Foster (UTSA) ------------------------------------------------------------------------- */ -#include +#include #include "fix_peri_neigh.h" #include "pair_peri_pmb.h" #include "pair_peri_lps.h" diff --git a/src/PERI/pair_peri_eps.cpp b/src/PERI/pair_peri_eps.cpp index 670e1d6937aaafce5962ca6f7a24bc2fb945f6fc..9950c36f41446ca28adbeb0162dd188adf0eb6e6 100644 --- a/src/PERI/pair_peri_eps.cpp +++ b/src/PERI/pair_peri_eps.cpp @@ -15,9 +15,9 @@ Contributing author: Rezwanur Rahman, John Foster (UTSA) ------------------------------------------------------------------------- */ -#include -#include -#include +#include +#include +#include #include "pair_peri_eps.h" #include "atom.h" #include "domain.h" diff --git a/src/PERI/pair_peri_lps.cpp b/src/PERI/pair_peri_lps.cpp index 0fe8f29f387fee4513cb9dd1ad60305561b7f012..4c48223b0749e9ebc7b4cbe4e4d1345854da21b9 100644 --- a/src/PERI/pair_peri_lps.cpp +++ b/src/PERI/pair_peri_lps.cpp @@ -15,9 +15,9 @@ Contributing author: Mike Parks (SNL) ------------------------------------------------------------------------- */ -#include -#include -#include +#include +#include +#include #include "pair_peri_lps.h" #include "atom.h" #include "domain.h" diff --git a/src/PERI/pair_peri_pmb.cpp b/src/PERI/pair_peri_pmb.cpp index 9e598289bd01842bb255a5501f5163fad9488d0e..81461f0b83f0c7c12df432046036a6003199397f 100644 --- a/src/PERI/pair_peri_pmb.cpp +++ b/src/PERI/pair_peri_pmb.cpp @@ -15,10 +15,10 @@ Contributing author: Mike Parks (SNL) ------------------------------------------------------------------------- */ -#include -#include -#include -#include +#include +#include +#include +#include #include "pair_peri_pmb.h" #include "atom.h" #include "domain.h" diff --git a/src/PERI/pair_peri_ves.cpp b/src/PERI/pair_peri_ves.cpp index 87213b5b59c10de830ae0e131335f5f99779b0f9..a9f620ef4b7bcbc4b92b7881a6ebaf8e8ea0e8fc 100644 --- a/src/PERI/pair_peri_ves.cpp +++ b/src/PERI/pair_peri_ves.cpp @@ -15,9 +15,9 @@ Contributing authors: Rezwanur Rahman, J.T. Foster (UTSA) ------------------------------------------------------------------------- */ -#include -#include -#include +#include +#include +#include #include "pair_peri_ves.h" #include "atom.h" #include "domain.h" diff --git a/src/POEMS/fix_poems.cpp b/src/POEMS/fix_poems.cpp index 7ff9e91af8127ad76b0b7e661a00cbe47f1fbce1..ebd1729b6e02521299517a54aa68650c1da65856 100644 --- a/src/POEMS/fix_poems.cpp +++ b/src/POEMS/fix_poems.cpp @@ -18,10 +18,10 @@ ------------------------------------------------------------------------- */ #include -#include -#include -#include -#include +#include +#include +#include +#include #include "workspace.h" #include "fix_poems.h" #include "atom.h" diff --git a/src/PYTHON/fix_python_invoke.cpp b/src/PYTHON/fix_python_invoke.cpp index 9a4db51d99251a2e44d7101aeaa3530254b18a72..199dd94f3d1cd87cf9cc1fbbbdf15e161c2813fa 100644 --- a/src/PYTHON/fix_python_invoke.cpp +++ b/src/PYTHON/fix_python_invoke.cpp @@ -16,8 +16,8 @@ ------------------------------------------------------------------------- */ #include -#include -#include +#include +#include #include "fix_python_invoke.h" #include "atom.h" #include "force.h" diff --git a/src/PYTHON/fix_python_move.cpp b/src/PYTHON/fix_python_move.cpp index 22d3bd065f5bc899eb89f2fc6359e399f6412306..b330ab79450b805e595e6b5d52710722d962ee32 100644 --- a/src/PYTHON/fix_python_move.cpp +++ b/src/PYTHON/fix_python_move.cpp @@ -16,9 +16,9 @@ ------------------------------------------------------------------------- */ #include -#include -#include -#include +#include +#include +#include #include "fix_python_move.h" #include "atom.h" #include "comm.h" @@ -47,7 +47,7 @@ FixPythonMove::FixPythonMove(LAMMPS *lmp, int narg, char **arg) : PyGILState_STATE gstate = PyGILState_Ensure(); // add current directory to PYTHONPATH - PyObject * py_path = PySys_GetObject("path"); + PyObject * py_path = PySys_GetObject((char *)"path"); PyList_Append(py_path, PY_STRING_FROM_STRING(".")); @@ -136,7 +136,7 @@ void FixPythonMove::init() { PyGILState_STATE gstate = PyGILState_Ensure(); PyObject *py_move_obj = (PyObject *) py_move; - PyObject *py_init = PyObject_GetAttrString(py_move_obj,"init"); + PyObject *py_init = PyObject_GetAttrString(py_move_obj,(char *)"init"); if (!py_init) { PyErr_Print(); PyErr_Clear(); diff --git a/src/PYTHON/pair_python.cpp b/src/PYTHON/pair_python.cpp index 0db987bb63d01c932f8e895218b1279ba01ceaf7..223129f7d662111de1f31573f3bf9f6a4945acb6 100644 --- a/src/PYTHON/pair_python.cpp +++ b/src/PYTHON/pair_python.cpp @@ -16,9 +16,9 @@ ------------------------------------------------------------------------- */ #include -#include -#include -#include +#include +#include +#include #include "pair_python.h" #include "atom.h" #include "comm.h" diff --git a/src/QEQ/fix_qeq.cpp b/src/QEQ/fix_qeq.cpp index afa2801831f0c677a979d4c49df7af2fe63bee75..8acf4498f5c6f67db6a1640d4872ff34efe2b746 100644 --- a/src/QEQ/fix_qeq.cpp +++ b/src/QEQ/fix_qeq.cpp @@ -16,10 +16,10 @@ Based on fix qeq/reax by H. Metin Aktulga ------------------------------------------------------------------------- */ -#include -#include -#include -#include +#include +#include +#include +#include #include "fix_qeq.h" #include "atom.h" #include "comm.h" diff --git a/src/QEQ/fix_qeq_dynamic.cpp b/src/QEQ/fix_qeq_dynamic.cpp index 43e9a9c874c44c0ce1a421029992f7f1297f5417..aeb8dd2c59043d1c1852e8cd678074d19e51785c 100644 --- a/src/QEQ/fix_qeq_dynamic.cpp +++ b/src/QEQ/fix_qeq_dynamic.cpp @@ -15,10 +15,10 @@ Contributing author: Ray Shan (Sandia) ------------------------------------------------------------------------- */ -#include -#include -#include -#include +#include +#include +#include +#include #include "fix_qeq_dynamic.h" #include "atom.h" #include "comm.h" diff --git a/src/QEQ/fix_qeq_fire.cpp b/src/QEQ/fix_qeq_fire.cpp index 763a39e82e9d961d253c6085750270c891779245..db63bec2063f98de16b963be899e72b920d06023 100644 --- a/src/QEQ/fix_qeq_fire.cpp +++ b/src/QEQ/fix_qeq_fire.cpp @@ -15,10 +15,10 @@ Contributing author: Ray Shan (Sandia) ------------------------------------------------------------------------- */ -#include -#include -#include -#include +#include +#include +#include +#include #include "fix_qeq_fire.h" #include "atom.h" #include "comm.h" diff --git a/src/QEQ/fix_qeq_point.cpp b/src/QEQ/fix_qeq_point.cpp index 906f73799142fd0295b6096da6b2e0f6dc845169..bf7130c1d6704b334f05c227245082e61f107fd9 100644 --- a/src/QEQ/fix_qeq_point.cpp +++ b/src/QEQ/fix_qeq_point.cpp @@ -15,10 +15,10 @@ Contributing author: Ray Shan (Sandia) ------------------------------------------------------------------------- */ -#include -#include -#include -#include +#include +#include +#include +#include #include "fix_qeq_point.h" #include "atom.h" #include "comm.h" diff --git a/src/QEQ/fix_qeq_shielded.cpp b/src/QEQ/fix_qeq_shielded.cpp index e23384b1c92cdd1f945b93723b571245d4fa7e8d..70898fd96c68908ca4c74203a72c577883710ff0 100644 --- a/src/QEQ/fix_qeq_shielded.cpp +++ b/src/QEQ/fix_qeq_shielded.cpp @@ -15,10 +15,10 @@ Contributing author: Ray Shan (Sandia) ------------------------------------------------------------------------- */ -#include -#include -#include -#include +#include +#include +#include +#include #include "fix_qeq_shielded.h" #include "atom.h" #include "comm.h" diff --git a/src/QEQ/fix_qeq_slater.cpp b/src/QEQ/fix_qeq_slater.cpp index 544b9f037aeb9268d97603021078fe07372021ba..4ddcf06357b3e5c42e010a47c16f1fd8177a0a16 100644 --- a/src/QEQ/fix_qeq_slater.cpp +++ b/src/QEQ/fix_qeq_slater.cpp @@ -15,10 +15,10 @@ Contributing author: Ray Shan (Sandia) ------------------------------------------------------------------------- */ -#include -#include -#include -#include +#include +#include +#include +#include #include "fix_qeq_slater.h" #include "atom.h" #include "comm.h" diff --git a/src/REAX/fix_reax_bonds.cpp b/src/REAX/fix_reax_bonds.cpp index 00cfb0937b93b1c03c8e23f9f258d80a54737df1..84e4a66e6cede6db5d347281df036486cc2efec9 100644 --- a/src/REAX/fix_reax_bonds.cpp +++ b/src/REAX/fix_reax_bonds.cpp @@ -19,8 +19,8 @@ #error LAMMPS_BIGBIG is not supported by the REAX package #endif -#include -#include +#include +#include #include "fix_reax_bonds.h" #include "pair_reax_fortran.h" #include "atom.h" diff --git a/src/REAX/fix_reax_bonds.h b/src/REAX/fix_reax_bonds.h index 7246b836c1a2c693db3f0e8bf0b800503baf7688..03bad1ef16b3b0f45842ee709adef4e9be12868f 100644 --- a/src/REAX/fix_reax_bonds.h +++ b/src/REAX/fix_reax_bonds.h @@ -20,7 +20,7 @@ FixStyle(reax/bonds,FixReaxBonds) #ifndef LMP_FIX_REAX_BONDS_H #define LMP_FIX_REAX_BONDS_H -#include +#include #include "fix.h" namespace LAMMPS_NS { diff --git a/src/REAX/pair_reax.cpp b/src/REAX/pair_reax.cpp index f6217c69a4aa7169d816e317cc508d75bae6761a..24083a288ab6ec3b5b66a771ca3a48a6b86d9cc2 100644 --- a/src/REAX/pair_reax.cpp +++ b/src/REAX/pair_reax.cpp @@ -21,10 +21,10 @@ ------------------------------------------------------------------------- */ #include -#include -#include -#include -#include +#include +#include +#include +#include #include "pair_reax.h" #include "pair_reax_fortran.h" #include "atom.h" diff --git a/src/REPLICA/compute_event_displace.cpp b/src/REPLICA/compute_event_displace.cpp index 330e2ebca33a522267581e434a81b86cb627ba28..df142215863e73e13ab3448d95ef29f95c427bc6 100644 --- a/src/REPLICA/compute_event_displace.cpp +++ b/src/REPLICA/compute_event_displace.cpp @@ -16,9 +16,9 @@ ------------------------------------------------------------------------- */ #include -#include -#include -#include +#include +#include +#include #include "compute_event_displace.h" #include "atom.h" #include "domain.h" diff --git a/src/REPLICA/fix_event.cpp b/src/REPLICA/fix_event.cpp index f688550a6554c679432191817da5dd098254f26a..3b9b49ac57a24977766a144388a99b52cf3d8103 100644 --- a/src/REPLICA/fix_event.cpp +++ b/src/REPLICA/fix_event.cpp @@ -15,8 +15,8 @@ Contributing author: Mike Brown (SNL), Aidan Thompson (SNL) ------------------------------------------------------------------------- */ -#include -#include +#include +#include #include "fix_event.h" #include "atom.h" #include "update.h" diff --git a/src/REPLICA/fix_event_prd.cpp b/src/REPLICA/fix_event_prd.cpp index 863caa64f240f999b920bf11ebe9bf7cf0e17ccd..a311a6444aad250d5b25454afabcf215a8be7fcc 100644 --- a/src/REPLICA/fix_event_prd.cpp +++ b/src/REPLICA/fix_event_prd.cpp @@ -15,8 +15,8 @@ Contributing author: Mike Brown (SNL) ------------------------------------------------------------------------- */ -#include -#include +#include +#include #include "fix_event_prd.h" #include "atom.h" #include "update.h" diff --git a/src/REPLICA/fix_event_tad.cpp b/src/REPLICA/fix_event_tad.cpp index b2d74855faf08cb6001256be13e9a1caf894ce84..0916fdf493748a842a6ad84783d5dfa0f9960075 100644 --- a/src/REPLICA/fix_event_tad.cpp +++ b/src/REPLICA/fix_event_tad.cpp @@ -15,8 +15,8 @@ Contributing author: Mike Brown (SNL) ------------------------------------------------------------------------- */ -#include -#include +#include +#include #include "fix_event_tad.h" #include "atom.h" #include "update.h" diff --git a/src/REPLICA/fix_neb.cpp b/src/REPLICA/fix_neb.cpp index 33f834a14069b42d4fa56379c35db41a2e102379..e5d24da392649fe1f8cecbd9bc20fea0e17194b9 100644 --- a/src/REPLICA/fix_neb.cpp +++ b/src/REPLICA/fix_neb.cpp @@ -17,9 +17,9 @@ ------------------------------------------------------------------------- */ #include -#include -#include -#include +#include +#include +#include #include "fix_neb.h" #include "universe.h" #include "update.h" diff --git a/src/REPLICA/neb.cpp b/src/REPLICA/neb.cpp index 692f9361258a847e51775cb1f451e1f04895ce11..c9aedf74018409a5913ed1055d554775e4704746 100644 --- a/src/REPLICA/neb.cpp +++ b/src/REPLICA/neb.cpp @@ -17,9 +17,9 @@ #include "lmptype.h" #include -#include -#include -#include +#include +#include +#include #include "neb.h" #include "universe.h" #include "atom.h" @@ -303,7 +303,7 @@ void NEB::run() update->minimize->setup(); if (me_universe == 0) { - if (uscreen) + if (uscreen) { if (verbose) { fprintf(uscreen,"Step MaxReplicaForce MaxAtomForce " "GradV0 GradV1 GradVc EBF EBR RDT " @@ -317,7 +317,8 @@ void NEB::run() "EBF EBR RDT " "RD1 PE1 RD2 PE2 ... RDN PEN\n"); } - if (ulogfile) + } + if (ulogfile) { if (verbose) { fprintf(ulogfile,"Step MaxReplicaForce MaxAtomForce " "GradV0 GradV1 GradVc EBF EBR RDT " @@ -331,6 +332,7 @@ void NEB::run() "EBF EBR RDT " "RD1 PE1 RD2 PE2 ... RDN PEN\n"); } + } } print_status(); @@ -588,7 +590,7 @@ void NEB::print_status() MPI_Allgather(&fnorminf,1,MPI_DOUBLE,&fmaxatomInRepl[0],1,MPI_DOUBLE,roots); } - double one[numall]; + double one[7]; one[0] = fneb->veng; one[1] = fneb->plen; one[2] = fneb->nlen; diff --git a/src/REPLICA/neb.h b/src/REPLICA/neb.h index 556ea22bbeb6ea0e25dd20ee16ee5927ffc432b7..9453c3c43bfb3786276094cf5dafc839daf8c0a1 100644 --- a/src/REPLICA/neb.h +++ b/src/REPLICA/neb.h @@ -20,7 +20,7 @@ CommandStyle(neb,NEB) #ifndef LMP_NEB_H #define LMP_NEB_H -#include +#include #include "pointers.h" namespace LAMMPS_NS { diff --git a/src/REPLICA/prd.cpp b/src/REPLICA/prd.cpp index 684277a698b265f778864f5290325dffb232c21a..6d450f48e3ed6bac08bcef47f5666e4e06a3f283 100644 --- a/src/REPLICA/prd.cpp +++ b/src/REPLICA/prd.cpp @@ -21,9 +21,9 @@ #include "lmptype.h" #include -#include -#include -#include +#include +#include +#include #include "prd.h" #include "universe.h" #include "update.h" diff --git a/src/REPLICA/tad.cpp b/src/REPLICA/tad.cpp index 958a57e4e8936e895621fd4ec6fb5cf89baf153e..46073952fc6fe341f797364507b6d83fa392b59e 100644 --- a/src/REPLICA/tad.cpp +++ b/src/REPLICA/tad.cpp @@ -21,9 +21,9 @@ #include "lmptype.h" #include -#include -#include -#include +#include +#include +#include #include "tad.h" #include "universe.h" #include "update.h" diff --git a/src/REPLICA/temper.cpp b/src/REPLICA/temper.cpp index d7e8c981bb51a729595aeee17ae8c2c4b43fd71d..fe3e3fb993d43e0d88c8eb2dcc777ea621a482ef 100644 --- a/src/REPLICA/temper.cpp +++ b/src/REPLICA/temper.cpp @@ -15,9 +15,9 @@ Contributing author: Mark Sears (SNL) ------------------------------------------------------------------------- */ -#include -#include -#include +#include +#include +#include #include "temper.h" #include "universe.h" #include "domain.h" diff --git a/src/REPLICA/verlet_split.cpp b/src/REPLICA/verlet_split.cpp index e47965d1c3c02a28f00351c5a8139caf4514915c..05ea0877ab1e84bd618ec125e1e287063344e5f3 100644 --- a/src/REPLICA/verlet_split.cpp +++ b/src/REPLICA/verlet_split.cpp @@ -15,7 +15,7 @@ Contributing authors: Yuxing Peng and Chris Knight (U Chicago) ------------------------------------------------------------------------- */ -#include +#include #include "verlet_split.h" #include "universe.h" #include "neighbor.h" diff --git a/src/RIGID/compute_erotate_rigid.cpp b/src/RIGID/compute_erotate_rigid.cpp index e31565cb6070844d8be629e49d4cd0b6ba99c3f1..a3ddffd9abed86427c1d06da997e7d5344676795 100644 --- a/src/RIGID/compute_erotate_rigid.cpp +++ b/src/RIGID/compute_erotate_rigid.cpp @@ -12,7 +12,7 @@ ------------------------------------------------------------------------- */ #include -#include +#include #include "compute_erotate_rigid.h" #include "update.h" #include "force.h" diff --git a/src/RIGID/compute_ke_rigid.cpp b/src/RIGID/compute_ke_rigid.cpp index 2db756140fb7b35a2934ad9fb7d63aacfc4a21a2..4de13532b29856d7381f358d194d6554515983c6 100644 --- a/src/RIGID/compute_ke_rigid.cpp +++ b/src/RIGID/compute_ke_rigid.cpp @@ -12,7 +12,7 @@ ------------------------------------------------------------------------- */ #include -#include +#include #include "compute_ke_rigid.h" #include "update.h" #include "force.h" diff --git a/src/RIGID/compute_rigid_local.cpp b/src/RIGID/compute_rigid_local.cpp index deca01f2aea749fa9cc82c075659fba711f13807..bcb778ab86b993c5391549b4040330bd424b651c 100644 --- a/src/RIGID/compute_rigid_local.cpp +++ b/src/RIGID/compute_rigid_local.cpp @@ -11,8 +11,8 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include -#include +#include +#include #include "compute_rigid_local.h" #include "atom.h" #include "update.h" diff --git a/src/RIGID/fix_ehex.cpp b/src/RIGID/fix_ehex.cpp index 61b76b513f57f654268936711bfe535b2250b751..1476c71d3fa080912fbaa98ed44b09f410e43385 100644 --- a/src/RIGID/fix_ehex.cpp +++ b/src/RIGID/fix_ehex.cpp @@ -22,9 +22,9 @@ which implements the heat exchange (HEX) algorithm. ------------------------------------------------------------------------- */ -#include -#include -#include +#include +#include +#include #include "fix_ehex.h" #include "atom.h" #include "domain.h" diff --git a/src/RIGID/fix_rattle.cpp b/src/RIGID/fix_rattle.cpp index 666561b462bb7011378e02e2d3bba776f723ff97..7ade8d6848f176e64456dd875c53768a69fe2fab 100644 --- a/src/RIGID/fix_rattle.cpp +++ b/src/RIGID/fix_rattle.cpp @@ -16,10 +16,10 @@ ------------------------------------------------------------------------- */ #include -#include -#include -#include -#include +#include +#include +#include +#include #include "fix_rattle.h" #include "atom.h" #include "atom_vec.h" diff --git a/src/RIGID/fix_rigid.cpp b/src/RIGID/fix_rigid.cpp index e9f668dafdd4873d5c81f3ecd4275e0d470dd8a6..3d9e24ced96d2a274f782177508b93fedfe99aeb 100644 --- a/src/RIGID/fix_rigid.cpp +++ b/src/RIGID/fix_rigid.cpp @@ -11,10 +11,10 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include -#include -#include -#include +#include +#include +#include +#include #include "fix_rigid.h" #include "math_extra.h" #include "atom.h" @@ -2342,7 +2342,7 @@ void FixRigid::write_restart_file(char *file) sprintf(outfile,"%s.rigid",file); FILE *fp = fopen(outfile,"w"); if (fp == NULL) { - char str[128]; + char str[192]; sprintf(str,"Cannot open fix rigid restart file %s",outfile); error->one(FLERR,str); } diff --git a/src/RIGID/fix_rigid_nh.cpp b/src/RIGID/fix_rigid_nh.cpp index 0e05685dba4ac546c5e3d6b1f63844921309eddb..7007ba1930252740ceb7491f859ee65da9b9036b 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 -#include -#include +#include +#include +#include #include "fix_rigid_nh.h" #include "math_extra.h" #include "atom.h" diff --git a/src/RIGID/fix_rigid_nh_small.cpp b/src/RIGID/fix_rigid_nh_small.cpp index 50777766fe33b2e6a38a13ea2fbb42b037785e58..874812cc69d5ed964e58271f040662493c1e84b5 100644 --- a/src/RIGID/fix_rigid_nh_small.cpp +++ b/src/RIGID/fix_rigid_nh_small.cpp @@ -17,9 +17,9 @@ Miller et al., J Chem Phys. 116, 8649-8659 (2002) ------------------------------------------------------------------------- */ -#include -#include -#include +#include +#include +#include #include "fix_rigid_nh_small.h" #include "math_extra.h" #include "atom.h" diff --git a/src/RIGID/fix_rigid_nph.cpp b/src/RIGID/fix_rigid_nph.cpp index c0aa3b7040e0224a495af26dd7e934d2ab4b018f..45a4a8d09cd00dfa14abf23db64652a0ca5d4a12 100644 --- a/src/RIGID/fix_rigid_nph.cpp +++ b/src/RIGID/fix_rigid_nph.cpp @@ -17,7 +17,7 @@ Miller et al., J Chem Phys. 116, 8649-8659 (2002) ------------------------------------------------------------------------- */ -#include +#include #include "fix_rigid_nph.h" #include "domain.h" #include "modify.h" diff --git a/src/RIGID/fix_rigid_nph_small.cpp b/src/RIGID/fix_rigid_nph_small.cpp index 4e3e54766f7cbc8e7b179d63e0c5da394d51f956..d32e3043f45451b7ef9a07856f918b5b3deb2bf8 100644 --- a/src/RIGID/fix_rigid_nph_small.cpp +++ b/src/RIGID/fix_rigid_nph_small.cpp @@ -17,7 +17,7 @@ Miller et al., J Chem Phys. 116, 8649-8659 (2002) ------------------------------------------------------------------------- */ -#include +#include #include "fix_rigid_nph_small.h" #include "domain.h" #include "modify.h" diff --git a/src/RIGID/fix_rigid_npt.cpp b/src/RIGID/fix_rigid_npt.cpp index 24e12e41c235e37b26b9fa77b1f353d9c440223a..da5d5ffaa54837c0d54aa4830790ce98903a36cc 100644 --- a/src/RIGID/fix_rigid_npt.cpp +++ b/src/RIGID/fix_rigid_npt.cpp @@ -17,7 +17,7 @@ Miller et al., J Chem Phys. 116, 8649-8659 (2002) ------------------------------------------------------------------------- */ -#include +#include #include "fix_rigid_npt.h" #include "domain.h" #include "modify.h" diff --git a/src/RIGID/fix_rigid_npt_small.cpp b/src/RIGID/fix_rigid_npt_small.cpp index 551ef50ca91ce84b8d00dc1ed3e41c754bb18ad3..f1fd5470da68dfd80bdc15644952dcfd649dc160 100644 --- a/src/RIGID/fix_rigid_npt_small.cpp +++ b/src/RIGID/fix_rigid_npt_small.cpp @@ -17,7 +17,7 @@ Miller et al., J Chem Phys. 116, 8649-8659 (2002) ------------------------------------------------------------------------- */ -#include +#include #include "fix_rigid_npt_small.h" #include "domain.h" #include "modify.h" diff --git a/src/RIGID/fix_rigid_small.cpp b/src/RIGID/fix_rigid_small.cpp index 0cdec74fe86d3af2a675fd759badf913d2f95f3f..e5ccd5ec1591cca90b1a08274dd67480e980740c 100644 --- a/src/RIGID/fix_rigid_small.cpp +++ b/src/RIGID/fix_rigid_small.cpp @@ -11,10 +11,10 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include -#include -#include -#include +#include +#include +#include +#include #include "fix_rigid_small.h" #include "math_extra.h" #include "atom.h" diff --git a/src/RIGID/fix_shake.cpp b/src/RIGID/fix_shake.cpp index 35c8d7a91741432f04dd22ea46f3fa6939bd31c4..0beef3bfa24cec383ba2a5d29304aff1bb596366 100644 --- a/src/RIGID/fix_shake.cpp +++ b/src/RIGID/fix_shake.cpp @@ -12,10 +12,10 @@ ------------------------------------------------------------------------- */ #include -#include -#include -#include -#include +#include +#include +#include +#include #include "fix_shake.h" #include "fix_rattle.h" #include "atom.h" diff --git a/src/SHOCK/fix_append_atoms.cpp b/src/SHOCK/fix_append_atoms.cpp index 80be74bee1634a0665c0a08fffde6b1197cd885e..27a7f5514abcfe821ddc88a416dbc6d2037f2c90 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 +#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 d7e5723980c647714836c561812f008d5daa561e..a7890c3afa4ab8825c585c06faae9cd4ef5135de 100644 --- a/src/SHOCK/fix_msst.cpp +++ b/src/SHOCK/fix_msst.cpp @@ -17,9 +17,9 @@ see Reed, Fried, Joannopoulos, Phys Rev Lett, 90, 235503 (2003) ------------------------------------------------------------------------- */ -#include -#include -#include +#include +#include +#include #include "fix_msst.h" #include "atom.h" #include "force.h" diff --git a/src/SHOCK/fix_nphug.cpp b/src/SHOCK/fix_nphug.cpp index d28e9daf775e7bf85e8f20b52413f0e4ab7feeba..c6df6646cf44a436bc7f2622034add37c76d728e 100644 --- a/src/SHOCK/fix_nphug.cpp +++ b/src/SHOCK/fix_nphug.cpp @@ -11,8 +11,9 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include -#include +#include +#include +#include #include "fix_nphug.h" #include "modify.h" #include "error.h" @@ -21,10 +22,8 @@ #include "force.h" #include "domain.h" #include "group.h" -#include #include "memory.h" #include "comm.h" -#include using namespace LAMMPS_NS; using namespace FixConst; diff --git a/src/SHOCK/fix_wall_piston.cpp b/src/SHOCK/fix_wall_piston.cpp index 7dff3d986ff136083566df2ab6988e904bf8fe9a..7146b46c1e12f4a021a71b9d4c1f0dd963975cd3 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 -#include -#include +#include +#include +#include #include "fix_wall_piston.h" #include "atom.h" #include "modify.h" diff --git a/src/SNAP/compute_sna_atom.cpp b/src/SNAP/compute_sna_atom.cpp index 4b114d9ce777714ee305311398421979b99f69b7..0d8b0bae14c3f82ccac058b88c9e37757c8f1e12 100644 --- a/src/SNAP/compute_sna_atom.cpp +++ b/src/SNAP/compute_sna_atom.cpp @@ -11,8 +11,8 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ #include "sna.h" -#include -#include +#include +#include #include "compute_sna_atom.h" #include "atom.h" #include "update.h" @@ -276,9 +276,13 @@ void ComputeSNAAtom::compute_peratom() for (int icoeff = 0; icoeff < ncoeff; icoeff++) { double bi = snaptr[tid]->bvec[icoeff]; + // diagonal element of quadratic matrix + + sna[i][ncount++] = 0.5*bi*bi; + // upper-triangular elements of quadratic matrix - for (int jcoeff = icoeff; jcoeff < ncoeff; jcoeff++) + for (int jcoeff = icoeff+1; jcoeff < ncoeff; jcoeff++) sna[i][ncount++] = bi*snaptr[tid]->bvec[jcoeff]; } } diff --git a/src/SNAP/compute_snad_atom.cpp b/src/SNAP/compute_snad_atom.cpp index 54a6ce761248c3ee6fcb2c4ab14fce16e5520e00..b0fef8e1e3fe5203f8c8d978b0f356671acbd97b 100644 --- a/src/SNAP/compute_snad_atom.cpp +++ b/src/SNAP/compute_snad_atom.cpp @@ -11,8 +11,8 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ #include "sna.h" -#include -#include +#include +#include #include "compute_snad_atom.h" #include "atom.h" #include "update.h" @@ -95,6 +95,11 @@ ComputeSNADAtom::ComputeSNADAtom(LAMMPS *lmp, int narg, char **arg) : error->all(FLERR,"Illegal compute snad/atom command"); rmin0 = atof(arg[iarg+1]); iarg += 2; + } else if (strcmp(arg[iarg],"bzeroflag") == 0) { + if (iarg+2 > narg) + error->all(FLERR,"Illegal compute snad/atom command"); + bzeroflag = atoi(arg[iarg+1]); + iarg += 2; } else if (strcmp(arg[iarg],"switchflag") == 0) { if (iarg+2 > narg) error->all(FLERR,"Illegal compute snad/atom command"); @@ -121,16 +126,11 @@ ComputeSNADAtom::ComputeSNADAtom(LAMMPS *lmp, int narg, char **arg) : } ncoeff = snaptr[0]->ncoeff; - twoncoeff = 2*ncoeff; - threencoeff = 3*ncoeff; - size_peratom_cols = threencoeff*atom->ntypes; - if (quadraticflag) { - ncoeffq = (ncoeff*(ncoeff+1))/2; - twoncoeffq = 2*ncoeffq; - threencoeffq = 3*ncoeffq; - size_peratom_cols += - threencoeffq*atom->ntypes; - } + nperdim = ncoeff; + if (quadraticflag) nperdim += (ncoeff*(ncoeff+1))/2; + yoffset = nperdim; + zoffset = 2*nperdim; + size_peratom_cols = 3*nperdim*atom->ntypes; comm_reverse = size_peratom_cols; peratom_flag = 1; @@ -248,9 +248,10 @@ void ComputeSNADAtom::compute_peratom() const int* const jlist = firstneigh[i]; const int jnum = numneigh[i]; - const int typeoffset = threencoeff*(atom->type[i]-1); - const int quadraticoffset = threencoeff*atom->ntypes + - threencoeffq*(atom->type[i]-1); + // const int typeoffset = threencoeff*(atom->type[i]-1); + // const int quadraticoffset = threencoeff*atom->ntypes + + // threencoeffq*(atom->type[i]-1); + const int typeoffset = 3*nperdim*(atom->type[i]-1); // insure rij, inside, and typej are of size jnum @@ -304,16 +305,17 @@ void ComputeSNADAtom::compute_peratom() for (int icoeff = 0; icoeff < ncoeff; icoeff++) { snadi[icoeff] += snaptr[tid]->dbvec[icoeff][0]; - snadi[icoeff+ncoeff] += snaptr[tid]->dbvec[icoeff][1]; - snadi[icoeff+twoncoeff] += snaptr[tid]->dbvec[icoeff][2]; + snadi[icoeff+yoffset] += snaptr[tid]->dbvec[icoeff][1]; + snadi[icoeff+zoffset] += snaptr[tid]->dbvec[icoeff][2]; snadj[icoeff] -= snaptr[tid]->dbvec[icoeff][0]; - snadj[icoeff+ncoeff] -= snaptr[tid]->dbvec[icoeff][1]; - snadj[icoeff+twoncoeff] -= snaptr[tid]->dbvec[icoeff][2]; + snadj[icoeff+yoffset] -= snaptr[tid]->dbvec[icoeff][1]; + snadj[icoeff+zoffset] -= snaptr[tid]->dbvec[icoeff][2]; } if (quadraticflag) { - double *snadi = snad[i]+quadraticoffset; - double *snadj = snad[j]+quadraticoffset; + const int quadraticoffset = ncoeff; + snadi += quadraticoffset; + snadj += quadraticoffset; int ncount = 0; for (int icoeff = 0; icoeff < ncoeff; icoeff++) { double bi = snaptr[tid]->bvec[icoeff]; @@ -321,21 +323,36 @@ void ComputeSNADAtom::compute_peratom() double biy = snaptr[tid]->dbvec[icoeff][1]; double biz = snaptr[tid]->dbvec[icoeff][2]; + // diagonal elements of quadratic matrix + + double dbxtmp = bi*bix; + double dbytmp = bi*biy; + double dbztmp = bi*biz; + + snadi[ncount] += dbxtmp; + snadi[ncount+yoffset] += dbytmp; + snadi[ncount+zoffset] += dbztmp; + snadj[ncount] -= dbxtmp; + snadj[ncount+yoffset] -= dbytmp; + snadj[ncount+zoffset] -= dbztmp; + ncount++; + // upper-triangular elements of quadratic matrix - for (int jcoeff = icoeff; jcoeff < ncoeff; jcoeff++) { + for (int jcoeff = icoeff+1; jcoeff < ncoeff; jcoeff++) { double dbxtmp = bi*snaptr[tid]->dbvec[jcoeff][0] + bix*snaptr[tid]->bvec[jcoeff]; double dbytmp = bi*snaptr[tid]->dbvec[jcoeff][1] + biy*snaptr[tid]->bvec[jcoeff]; double dbztmp = bi*snaptr[tid]->dbvec[jcoeff][2] + biz*snaptr[tid]->bvec[jcoeff]; - snadi[ncount] += dbxtmp; - snadi[ncount+ncoeffq] += dbytmp; - snadi[ncount+twoncoeffq] += dbztmp; - snadj[ncount] -= dbxtmp; - snadj[ncount+ncoeffq] -= dbytmp; - snadj[ncount+twoncoeffq] -= dbztmp; + + snadi[ncount] += dbxtmp; + snadi[ncount+yoffset] += dbytmp; + snadi[ncount+zoffset] += dbztmp; + snadj[ncount] -= dbxtmp; + snadj[ncount+yoffset] -= dbytmp; + snadj[ncount+zoffset] -= dbztmp; ncount++; } } @@ -361,7 +378,7 @@ int ComputeSNADAtom::pack_reverse_comm(int n, int first, double *buf) for (i = first; i < last; i++) for (icoeff = 0; icoeff < size_peratom_cols; icoeff++) buf[m++] = snad[i][icoeff]; - return comm_reverse; + return m; } /* ---------------------------------------------------------------------- */ @@ -387,8 +404,7 @@ double ComputeSNADAtom::memory_usage() double bytes = nmax*size_peratom_cols * sizeof(double); bytes += 3*njmax*sizeof(double); bytes += njmax*sizeof(int); - bytes += threencoeff*atom->ntypes; - if (quadraticflag) bytes += threencoeffq*atom->ntypes; + bytes += 3*nperdim*atom->ntypes; bytes += snaptr[0]->memory_usage()*comm->nthreads; return bytes; } diff --git a/src/SNAP/compute_snad_atom.h b/src/SNAP/compute_snad_atom.h index 5e40632d8c5c61f7970428ce79ed1241c794c54c..a33e6047c2c2bd0fca6d25d8a2b948fef9f7d4f9 100644 --- a/src/SNAP/compute_snad_atom.h +++ b/src/SNAP/compute_snad_atom.h @@ -37,7 +37,7 @@ class ComputeSNADAtom : public Compute { private: int nmax, njmax, diagonalstyle; - int ncoeff, twoncoeff, threencoeff, ncoeffq, twoncoeffq, threencoeffq; + int ncoeff, nperdim, yoffset, zoffset; double **cutsq; class NeighList *list; double **snad; diff --git a/src/SNAP/compute_snav_atom.cpp b/src/SNAP/compute_snav_atom.cpp index 0278be5a97414f8dd9fb9ba681edd33255ecfbed..cf66b1c136ae8cbe32f1014005c49ce32f8d9d77 100644 --- a/src/SNAP/compute_snav_atom.cpp +++ b/src/SNAP/compute_snav_atom.cpp @@ -11,8 +11,8 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ #include "sna.h" -#include -#include +#include +#include #include "compute_snav_atom.h" #include "atom.h" #include "update.h" @@ -96,6 +96,11 @@ ComputeSNAVAtom::ComputeSNAVAtom(LAMMPS *lmp, int narg, char **arg) : error->all(FLERR,"Illegal compute snav/atom command"); switchflag = atoi(arg[iarg+1]); iarg += 2; + } else if (strcmp(arg[iarg],"bzeroflag") == 0) { + if (iarg+2 > narg) + error->all(FLERR,"Illegal compute snav/atom command"); + bzeroflag = atoi(arg[iarg+1]); + iarg += 2; } else if (strcmp(arg[iarg],"quadraticflag") == 0) { if (iarg+2 > narg) error->all(FLERR,"Illegal compute snav/atom command"); @@ -117,22 +122,9 @@ ComputeSNAVAtom::ComputeSNAVAtom(LAMMPS *lmp, int narg, char **arg) : } ncoeff = snaptr[0]->ncoeff; - twoncoeff = 2*ncoeff; - threencoeff = 3*ncoeff; - fourncoeff = 4*ncoeff; - fivencoeff = 5*ncoeff; - sixncoeff = 6*ncoeff; - size_peratom_cols = sixncoeff*atom->ntypes; - if (quadraticflag) { - ncoeffq = ncoeff*ncoeff; - twoncoeffq = 2*ncoeffq; - threencoeffq = 3*ncoeffq; - fourncoeffq = 4*ncoeffq; - fivencoeffq = 5*ncoeffq; - sixncoeffq = 6*ncoeffq; - size_peratom_cols += - sixncoeffq*atom->ntypes; - } + nperdim = ncoeff; + if (quadraticflag) nperdim += (ncoeff*(ncoeff+1))/2; + size_peratom_cols = 6*nperdim*atom->ntypes; comm_reverse = size_peratom_cols; peratom_flag = 1; @@ -251,9 +243,7 @@ void ComputeSNAVAtom::compute_peratom() const int* const jlist = firstneigh[i]; const int jnum = numneigh[i]; - const int typeoffset = sixncoeff*(atom->type[i]-1); - const int quadraticoffset = sixncoeff*atom->ntypes + - sixncoeffq*(atom->type[i]-1); + const int typeoffset = 6*nperdim*(atom->type[i]-1); // insure rij, inside, and typej are of size jnum @@ -307,23 +297,24 @@ void ComputeSNAVAtom::compute_peratom() double *snavj = snav[j]+typeoffset; for (int icoeff = 0; icoeff < ncoeff; icoeff++) { - snavi[icoeff] += snaptr[tid]->dbvec[icoeff][0]*xtmp; - snavi[icoeff+ncoeff] += snaptr[tid]->dbvec[icoeff][1]*ytmp; - snavi[icoeff+twoncoeff] += snaptr[tid]->dbvec[icoeff][2]*ztmp; - snavi[icoeff+threencoeff] += snaptr[tid]->dbvec[icoeff][1]*ztmp; - snavi[icoeff+fourncoeff] += snaptr[tid]->dbvec[icoeff][0]*ztmp; - snavi[icoeff+fivencoeff] += snaptr[tid]->dbvec[icoeff][0]*ytmp; - snavj[icoeff] -= snaptr[tid]->dbvec[icoeff][0]*x[j][0]; - snavj[icoeff+ncoeff] -= snaptr[tid]->dbvec[icoeff][1]*x[j][1]; - snavj[icoeff+twoncoeff] -= snaptr[tid]->dbvec[icoeff][2]*x[j][2]; - snavj[icoeff+threencoeff] -= snaptr[tid]->dbvec[icoeff][1]*x[j][2]; - snavj[icoeff+fourncoeff] -= snaptr[tid]->dbvec[icoeff][0]*x[j][2]; - snavj[icoeff+fivencoeff] -= snaptr[tid]->dbvec[icoeff][0]*x[j][1]; + snavi[icoeff] += snaptr[tid]->dbvec[icoeff][0]*xtmp; + snavi[icoeff+nperdim] += snaptr[tid]->dbvec[icoeff][1]*ytmp; + snavi[icoeff+2*nperdim] += snaptr[tid]->dbvec[icoeff][2]*ztmp; + snavi[icoeff+3*nperdim] += snaptr[tid]->dbvec[icoeff][1]*ztmp; + snavi[icoeff+4*nperdim] += snaptr[tid]->dbvec[icoeff][0]*ztmp; + snavi[icoeff+5*nperdim] += snaptr[tid]->dbvec[icoeff][0]*ytmp; + snavj[icoeff] -= snaptr[tid]->dbvec[icoeff][0]*x[j][0]; + snavj[icoeff+nperdim] -= snaptr[tid]->dbvec[icoeff][1]*x[j][1]; + snavj[icoeff+2*nperdim] -= snaptr[tid]->dbvec[icoeff][2]*x[j][2]; + snavj[icoeff+3*nperdim] -= snaptr[tid]->dbvec[icoeff][1]*x[j][2]; + snavj[icoeff+4*nperdim] -= snaptr[tid]->dbvec[icoeff][0]*x[j][2]; + snavj[icoeff+5*nperdim] -= snaptr[tid]->dbvec[icoeff][0]*x[j][1]; } if (quadraticflag) { - double *snavi = snav[i]+quadraticoffset; - double *snavj = snav[j]+quadraticoffset; + const int quadraticoffset = ncoeff; + snavi += quadraticoffset; + snavj += quadraticoffset; int ncount = 0; for (int icoeff = 0; icoeff < ncoeff; icoeff++) { double bi = snaptr[tid]->bvec[icoeff]; @@ -331,27 +322,46 @@ void ComputeSNAVAtom::compute_peratom() double biy = snaptr[tid]->dbvec[icoeff][1]; double biz = snaptr[tid]->dbvec[icoeff][2]; + // diagonal element of quadratic matrix + + double dbxtmp = bi*bix; + double dbytmp = bi*biy; + double dbztmp = bi*biz; + snavi[ncount] += dbxtmp*xtmp; + snavi[ncount+nperdim] += dbytmp*ytmp; + snavi[ncount+2*nperdim] += dbztmp*ztmp; + snavi[ncount+3*nperdim] += dbytmp*ztmp; + snavi[ncount+4*nperdim] += dbxtmp*ztmp; + snavi[ncount+5*nperdim] += dbxtmp*ytmp; + snavj[ncount] -= dbxtmp*x[j][0]; + snavj[ncount+nperdim] -= dbytmp*x[j][1]; + snavj[ncount+2*nperdim] -= dbztmp*x[j][2]; + snavj[ncount+3*nperdim] -= dbytmp*x[j][2]; + snavj[ncount+4*nperdim] -= dbxtmp*x[j][2]; + snavj[ncount+5*nperdim] -= dbxtmp*x[j][1]; + ncount++; + // upper-triangular elements of quadratic matrix - for (int jcoeff = icoeff; jcoeff < ncoeff; jcoeff++) { + for (int jcoeff = icoeff+1; jcoeff < ncoeff; jcoeff++) { double dbxtmp = bi*snaptr[tid]->dbvec[jcoeff][0] + bix*snaptr[tid]->bvec[jcoeff]; double dbytmp = bi*snaptr[tid]->dbvec[jcoeff][1] + biy*snaptr[tid]->bvec[jcoeff]; double dbztmp = bi*snaptr[tid]->dbvec[jcoeff][2] + biz*snaptr[tid]->bvec[jcoeff]; - snavi[ncount] += dbxtmp*xtmp; - snavi[ncount+ncoeffq] += dbytmp*ytmp; - snavi[ncount+twoncoeffq] += dbztmp*ztmp; - snavi[ncount+threencoeffq] += dbytmp*ztmp; - snavi[ncount+fourncoeffq] += dbxtmp*ztmp; - snavi[ncount+fivencoeffq] += dbxtmp*ytmp; - snavj[ncount] -= dbxtmp*x[j][0]; - snavj[ncount+ncoeffq] -= dbytmp*x[j][1]; - snavj[ncount+twoncoeffq] -= dbztmp*x[j][2]; - snavj[ncount+threencoeffq] -= dbytmp*x[j][2]; - snavj[ncount+fourncoeffq] -= dbxtmp*x[j][2]; - snavj[ncount+fivencoeffq] -= dbxtmp*x[j][1]; + snavi[ncount] += dbxtmp*xtmp; + snavi[ncount+nperdim] += dbytmp*ytmp; + snavi[ncount+2*nperdim] += dbztmp*ztmp; + snavi[ncount+3*nperdim] += dbytmp*ztmp; + snavi[ncount+4*nperdim] += dbxtmp*ztmp; + snavi[ncount+5*nperdim] += dbxtmp*ytmp; + snavj[ncount] -= dbxtmp*x[j][0]; + snavj[ncount+nperdim] -= dbytmp*x[j][1]; + snavj[ncount+2*nperdim] -= dbztmp*x[j][2]; + snavj[ncount+3*nperdim] -= dbytmp*x[j][2]; + snavj[ncount+4*nperdim] -= dbxtmp*x[j][2]; + snavj[ncount+5*nperdim] -= dbxtmp*x[j][1]; ncount++; } } @@ -377,7 +387,7 @@ int ComputeSNAVAtom::pack_reverse_comm(int n, int first, double *buf) for (i = first; i < last; i++) for (icoeff = 0; icoeff < size_peratom_cols; icoeff++) buf[m++] = snav[i][icoeff]; - return comm_reverse; + return m; } /* ---------------------------------------------------------------------- */ @@ -403,8 +413,8 @@ double ComputeSNAVAtom::memory_usage() double bytes = nmax*size_peratom_cols * sizeof(double); bytes += 3*njmax*sizeof(double); bytes += njmax*sizeof(int); - bytes += sixncoeff*atom->ntypes; - if (quadraticflag) bytes += sixncoeffq*atom->ntypes; + bytes += 6*nperdim*atom->ntypes; + if (quadraticflag) bytes += 6*nperdim*atom->ntypes; bytes += snaptr[0]->memory_usage()*comm->nthreads; return bytes; } diff --git a/src/SNAP/compute_snav_atom.h b/src/SNAP/compute_snav_atom.h index 35f1478393520dc9f2a687a0db86201b0ca5e52c..2eb9fb804f7420aab541b5995b81e39a2ca83766 100644 --- a/src/SNAP/compute_snav_atom.h +++ b/src/SNAP/compute_snav_atom.h @@ -37,8 +37,7 @@ class ComputeSNAVAtom : public Compute { private: int nmax, njmax, diagonalstyle; - int ncoeff, twoncoeff, threencoeff, fourncoeff, fivencoeff, sixncoeff; - int ncoeffq, twoncoeffq, threencoeffq, fourncoeffq, fivencoeffq, sixncoeffq; + int ncoeff, nperdim; double **cutsq; class NeighList *list; double **snav; diff --git a/src/SNAP/pair_snap.cpp b/src/SNAP/pair_snap.cpp index 377235685cd0f052d2f51ab01967a63f6679707c..2b1816950c28c11c3b23c288aacb4fd33be5348f 100644 --- a/src/SNAP/pair_snap.cpp +++ b/src/SNAP/pair_snap.cpp @@ -11,9 +11,9 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include -#include -#include +#include +#include +#include #include "pair_snap.h" #include "atom.h" #include "atom_vec.h" @@ -278,14 +278,15 @@ void PairSNAP::compute_regular(int eflag, int vflag) double bveci = snaptr->bvec[icoeff]; double fack = coeffi[k]*bveci; double* dbveci = snaptr->dbvec[icoeff]; - fij[0] += fack*snaptr->dbvec[icoeff][0]; - fij[1] += fack*snaptr->dbvec[icoeff][1]; - fij[2] += fack*snaptr->dbvec[icoeff][2]; + fij[0] += fack*dbveci[0]; + fij[1] += fack*dbveci[1]; + fij[2] += fack*dbveci[2]; k++; for (int jcoeff = icoeff+1; jcoeff < ncoeff; jcoeff++) { double facki = coeffi[k]*bveci; double fackj = coeffi[k]*snaptr->bvec[jcoeff]; double* dbvecj = snaptr->dbvec[jcoeff]; + fij[0] += facki*dbvecj[0]+fackj*dbveci[0]; fij[1] += facki*dbvecj[1]+fackj*dbveci[1]; fij[2] += facki*dbvecj[2]+fackj*dbveci[2]; @@ -1529,10 +1530,10 @@ void PairSNAP::coeff(int narg, char **arg) } if (comm->me == 0) - printf("ncoeff = %d snancoeff = %d \n",ncoeff,sna[0]->ncoeff); - if (ncoeff != sna[0]->ncoeff) { - error->all(FLERR,"Incorrect SNAP parameter file"); - } + if (ncoeff != sna[0]->ncoeff) { + printf("ncoeff = %d snancoeff = %d \n",ncoeff,sna[0]->ncoeff); + error->all(FLERR,"Incorrect SNAP parameter file"); + } // Calculate maximum cutoff for all elements diff --git a/src/SNAP/pair_snap.h b/src/SNAP/pair_snap.h index d39cb0f8d44a73b37ff5c4688b4c3f690e52f232..b60ab3c3e42657fba6fff2f316aa6e93aa5056a5 100644 --- a/src/SNAP/pair_snap.h +++ b/src/SNAP/pair_snap.h @@ -37,11 +37,8 @@ public: virtual double init_one(int, int); virtual double memory_usage(); - double rcutfac, quadraticflag; // declared public to workaround gcc 4.9 - int ncoeff; // compiler bug, manifest in KOKKOS package - protected: - int ncoeffq, ncoeffall; + int ncoeff, ncoeffq, ncoeffall; double **bvec, ***dbvec; class SNA** sna; int nmax; @@ -100,8 +97,8 @@ protected: double *wjelem; // elements weights double **coeffelem; // element bispectrum coefficients int *map; // mapping from atom types to elements - int twojmax, diagonalstyle, switchflag, bzeroflag; - double rfac0, rmin0, wj1, wj2; + int twojmax, diagonalstyle, switchflag, bzeroflag, quadraticflag; + double rcutfac, rfac0, rmin0, wj1, wj2; int rcutfacflag, twojmaxflag; // flags for required parameters }; diff --git a/src/SNAP/sna.cpp b/src/SNAP/sna.cpp index 16c382cc4ce34949e463d4b1bb8fae52512290ee..31505730433a4b00b2956c10afb5a272e94a0f55 100644 --- a/src/SNAP/sna.cpp +++ b/src/SNAP/sna.cpp @@ -16,11 +16,11 @@ ------------------------------------------------------------------------- */ #include "sna.h" -#include +#include #include "math_const.h" #include "math_extra.h" -#include -#include +#include +#include #include "openmp_snap.h" #include "memory.h" diff --git a/src/SRD/fix_srd.cpp b/src/SRD/fix_srd.cpp index 81ef2024203c0b858500466ecaab0500e828c955..6bc72dca4bd72974cd39a054263364b51bab9dc8 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 +#include #include "fix_srd.h" #include "math_extra.h" #include "atom.h" diff --git a/src/SRD/fix_wall_srd.cpp b/src/SRD/fix_wall_srd.cpp index dbca9c5fc88adf49e47a024415bf3b1d9eb07ccb..24b0c3cec5c2d5210ed21a39450649ac16464485 100644 --- a/src/SRD/fix_wall_srd.cpp +++ b/src/SRD/fix_wall_srd.cpp @@ -11,8 +11,8 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include -#include +#include +#include #include "fix_wall_srd.h" #include "atom.h" #include "modify.h" diff --git a/src/USER-ATC/fix_atc.cpp b/src/USER-ATC/fix_atc.cpp index 96ad93481d1aa4675eeb362cb6809ab35ad48b80..f53343ced1380ce59fe9a6b273e14fda3035335f 100644 --- a/src/USER-ATC/fix_atc.cpp +++ b/src/USER-ATC/fix_atc.cpp @@ -35,8 +35,8 @@ #include "ATC_CouplingMomentumEnergy.h" #include "LammpsInterface.h" // other -#include -#include +#include +#include #include using namespace LAMMPS_NS; diff --git a/src/USER-AWPMD/atom_vec_wavepacket.cpp b/src/USER-AWPMD/atom_vec_wavepacket.cpp index 33048efba6d8c24f112dc36bc288179679165ff3..7556dd2c8e3ed968aa750620b58ce885debff2a5 100644 --- a/src/USER-AWPMD/atom_vec_wavepacket.cpp +++ b/src/USER-AWPMD/atom_vec_wavepacket.cpp @@ -15,9 +15,9 @@ Contributing author: Ilya Valuev (JIHT, Moscow, Russia) ------------------------------------------------------------------------- */ -#include -#include -#include +#include +#include +#include #include "atom_vec_wavepacket.h" #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 3ad425030d3d2ebfc81531f73e63e43b92dc68f6..7722c931218f3cc56c1a8acbf6fd0d4bcec97e78 100644 --- a/src/USER-AWPMD/fix_nve_awpmd.cpp +++ b/src/USER-AWPMD/fix_nve_awpmd.cpp @@ -15,16 +15,15 @@ Contributing author: Ilya Valuev (JIHT, Moscow, Russia) ------------------------------------------------------------------------- */ -#include -#include -#include +#include +#include +#include #include "fix_nve_awpmd.h" #include "atom.h" #include "force.h" #include "update.h" #include "respa.h" #include "error.h" -#include #include "TCP/wpmd_split.h" diff --git a/src/USER-AWPMD/pair_awpmd_cut.cpp b/src/USER-AWPMD/pair_awpmd_cut.cpp index 2ce1a926845721c8fc10fe001585f99de5dae2b7..2dcb3e62962f43f6a1e9fc35aa75ffaa969557dc 100644 --- a/src/USER-AWPMD/pair_awpmd_cut.cpp +++ b/src/USER-AWPMD/pair_awpmd_cut.cpp @@ -15,10 +15,10 @@ Contributing author: Ilya Valuev (JIHT, Moscow, Russia) ------------------------------------------------------------------------- */ -#include -#include -#include -#include +#include +#include +#include +#include #include "pair_awpmd_cut.h" #include "atom.h" #include "update.h" diff --git a/src/USER-BOCS/README b/src/USER-BOCS/README new file mode 100644 index 0000000000000000000000000000000000000000..adeb34c38729a3614df738333bb64c6565c3dec7 --- /dev/null +++ b/src/USER-BOCS/README @@ -0,0 +1,19 @@ +This user package implements 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). + +doi: 10.1063/1.4937383 + +The USER-BOCS user package for LAMMPS is part of the BOCS software package: +https://github.com/noid-group/BOCS + +See the following reference for information about the entire package: + +Dunn, NJH; Lebold, KM; DeLyser, MR; Rudzinski, JF; Noid, WG. +"BOCS: Bottom-Up Open-Source Coarse-Graining Software." +J. Phys. Chem. B. 122, 13, 3363-3377 (2018). + +Example inputs are in the examples/USER/bocs folder. diff --git a/src/USER-BOCS/compute_pressure_bocs.cpp b/src/USER-BOCS/compute_pressure_bocs.cpp new file mode 100644 index 0000000000000000000000000000000000000000..fc24efab4c52e27529b225c67f37393d7c500b01 --- /dev/null +++ b/src/USER-BOCS/compute_pressure_bocs.cpp @@ -0,0 +1,444 @@ +/* ---------------------------------------------------------------------- + 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. +------------------------------------------------------------------------- + USER-BOCS written by: Nicholas J. H. Dunn and Michael R. DeLyser + from The Pennsylvania State University +------------------------------------------------------------------------- */ + +#include +#include +#include +#include "compute_pressure_bocs.h" +#include "atom.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" + + +using namespace LAMMPS_NS; + +/* ---------------------------------------------------------------------- */ + +ComputePressureBocs::ComputePressureBocs(LAMMPS *lmp, int narg, char **arg) : + Compute(lmp, narg, arg), + vptr(NULL), id_temp(NULL) +{ + if (narg < 4) error->all(FLERR,"Illegal compute pressure/bocs command"); + if (igroup) error->all(FLERR,"Compute pressure/bocs must use group all"); + + scalar_flag = vector_flag = 1; + size_vector = 6; + extscalar = 0; + extvector = 0; + pressflag = 1; + timeflag = 1; + + p_match_flag = 0; + phi_coeff = NULL; + + // store temperature ID used by pressure computation + // insure it is valid for temperature computation + + if (strcmp(arg[3],"NULL") == 0) id_temp = NULL; + else { + int n = strlen(arg[3]) + 1; + id_temp = new char[n]; + strcpy(id_temp,arg[3]); + + int icompute = modify->find_compute(id_temp); + if (icompute < 0) + error->all(FLERR,"Could not find compute pressure/bocs temperature ID"); + if (modify->compute[icompute]->tempflag == 0) + error->all(FLERR,"Compute pressure/bocs temperature ID does not " + "compute temperature"); + } + + // process optional args + + if (narg == 4) { + keflag = 1; + pairflag = 1; + bondflag = angleflag = dihedralflag = improperflag = 1; + kspaceflag = fixflag = 1; + } else { + keflag = 0; + pairflag = 0; + bondflag = angleflag = dihedralflag = improperflag = 0; + kspaceflag = fixflag = 0; + int iarg = 4; + while (iarg < narg) { + if (strcmp(arg[iarg],"ke") == 0) keflag = 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; + else if (strcmp(arg[iarg],"dihedral") == 0) dihedralflag = 1; + else if (strcmp(arg[iarg],"improper") == 0) improperflag = 1; + else if (strcmp(arg[iarg],"kspace") == 0) kspaceflag = 1; + else if (strcmp(arg[iarg],"fix") == 0) fixflag = 1; + else if (strcmp(arg[iarg],"virial") == 0) { + pairflag = 1; + bondflag = angleflag = dihedralflag = improperflag = 1; + kspaceflag = fixflag = 1; + } else error->all(FLERR,"Illegal compute pressure/bocs command"); + iarg++; + } + } + + // error check + + if (keflag && id_temp == NULL) + error->all(FLERR,"Compute pressure/bocs requires temperature ID " + "to include kinetic energy"); + + vector = new double[6]; + nvirial = 0; + vptr = NULL; +} + +/* ---------------------------------------------------------------------- */ + +ComputePressureBocs::~ComputePressureBocs() +{ + delete [] id_temp; + delete [] vector; + delete [] vptr; + if (phi_coeff) free(phi_coeff); +} + +/* ---------------------------------------------------------------------- */ + +void ComputePressureBocs::init() +{ + boltz = force->boltz; + nktv2p = force->nktv2p; + dimension = domain->dimension; + + // set temperature compute, must be done in init() + // fixes could have changed or compute_modify could have changed it + + if (keflag) { + int icompute = modify->find_compute(id_temp); + if (icompute < 0) + error->all(FLERR,"Could not find compute pressure/bocs temperature ID"); + temperature = modify->compute[icompute]; + } + + // detect contributions to virial + // vptr points to all virial[6] contributions + + delete [] vptr; + nvirial = 0; + vptr = NULL; + + if (pairflag && force->pair) nvirial++; + if (bondflag && atom->molecular && force->bond) nvirial++; + if (angleflag && atom->molecular && force->angle) nvirial++; + if (dihedralflag && atom->molecular && force->dihedral) nvirial++; + if (improperflag && atom->molecular && force->improper) nvirial++; + if (fixflag) + for (int i = 0; i < modify->nfix; i++) + if (modify->fix[i]->virial_flag) nvirial++; + + if (nvirial) { + vptr = new double*[nvirial]; + nvirial = 0; + 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; + if (dihedralflag && force->dihedral) + vptr[nvirial++] = force->dihedral->virial; + if (improperflag && force->improper) + vptr[nvirial++] = force->improper->virial; + if (fixflag) + for (int i = 0; i < modify->nfix; i++) + if (modify->fix[i]->virial_flag) + vptr[nvirial++] = modify->fix[i]->virial; + } + + // flag Kspace contribution separately, since not summed across procs + + if (kspaceflag && force->kspace) kspace_virial = force->kspace->virial; + else kspace_virial = NULL; +} + +/* Extra functions added for BOCS */ + +/* ---------------------------------------------------------------------- + Compute the pressure correction for the analytical basis set +------------------------------------------------------------------------- */ +double ComputePressureBocs::get_cg_p_corr(int N_basis, double *phi_coeff, + int N_mol, double vavg, double vCG) +{ + double correction = 0.0; + for (int i = 1; i <= N_basis; ++i) + { + correction -= phi_coeff[i-1] * ( N_mol * i / vavg ) * + pow( ( 1 / vavg ) * ( vCG - vavg ),i-1); + } + return correction; +} + +/* ---------------------------------------------------------------------- + Find the relevant index position if using a spline basis set +------------------------------------------------------------------------- */ +double ComputePressureBocs::find_index(double * grid, double value) +{ + int i; + double spacing = fabs(grid[1]-grid[0]); + int gridsize = spline_length; + for (i = 0; i < (gridsize-1); ++i) + { + if (value >= grid[i] && value <= grid[i+1]) { return i; } + } + + if (value >= grid[i] && value <= (grid[i] + spacing)) { return i; } + + for (int i = 0; i < gridsize; ++i) + { + fprintf(stderr, "grid %d: %f\n",i,grid[i]); + } + char * errmsg = (char *) calloc(100,sizeof(char)); + sprintf(errmsg,"Value %f does not fall within spline grid.\n",value); + error->all(FLERR,errmsg); + + exit(1); +} + +/* ---------------------------------------------------------------------- + Compute the pressure correction for a spline basis set +------------------------------------------------------------------------- */ + +double ComputePressureBocs::get_cg_p_corr(double ** grid, int basis_type, + double vCG) +{ + int i = find_index(grid[0],vCG); + double correction, deltax = vCG - grid[0][i]; + + if (basis_type == 1) + { + correction = grid[1][i] + (deltax) * + ( grid[1][i+1] - grid[1][i] ) / ( grid[0][i+1] - grid[0][i] ); + } + else if (basis_type == 2) + { + correction = grid[1][i] + (grid[2][i] * deltax) + + (grid[3][i] * pow(deltax,2)) + (grid[4][i] * pow(deltax,3)); + } + else + { + error->all(FLERR,"bad spline type passed to get_cg_p_corr()\n"); + } + return correction; +} + +/* ---------------------------------------------------------------------- + send cg info from fix_bocs to compute_pressure_bocs for the analytical + basis set +------------------------------------------------------------------------- */ +void ComputePressureBocs::send_cg_info(int basis_type, int sent_N_basis, + double *sent_phi_coeff, int sent_N_mol, double sent_vavg) +{ + if (basis_type == 0) { p_basis_type = 0; } + else + { + error->all(FLERR,"Incorrect basis type passed to ComputePressureBocs\n"); + } + + p_match_flag = 1; + + N_basis = sent_N_basis; + if (phi_coeff) free(phi_coeff); + phi_coeff = ((double *) calloc(N_basis, sizeof(double)) ); + for (int i=0; iall(FLERR,"Incorrect basis type passed to ComputePressureBocs\n"); + } + splines = in_splines; + spline_length = gridsize; + p_match_flag = 1; +} + +/* End of new functions for BOCS */ + +/* ---------------------------------------------------------------------- + compute total pressure, averaged over Pxx, Pyy, Pzz +------------------------------------------------------------------------- */ +double ComputePressureBocs::compute_scalar() +{ + invoked_scalar = update->ntimestep; + if (update->vflag_global != invoked_scalar) + error->all(FLERR,"Virial was not tallied on needed timestep"); + + // invoke temperature if it hasn't been already + + double t; + double volume, correction = 0; + if (keflag) { + if (temperature->invoked_scalar != update->ntimestep) + t = temperature->compute_scalar(); + else t = temperature->scalar; + } + + if (dimension == 3) { + inv_volume = 1.0 / (domain->xprd * domain->yprd * domain->zprd); + volume = (domain->xprd * domain->yprd * domain->zprd); + + /* MRD NJD if block */ + if ( p_basis_type == 0 ) + { + correction = get_cg_p_corr(N_basis,phi_coeff,N_mol,vavg,volume); + } + else if ( p_basis_type == 1 || p_basis_type == 2 ) + { + correction = get_cg_p_corr(splines, p_basis_type, volume); + } + + virial_compute(3,3); + if (keflag) + scalar = (temperature->dof * boltz * t + + virial[0] + virial[1] + virial[2]) / 3.0 * + inv_volume * nktv2p + (correction); + else + scalar = (virial[0] + virial[1] + virial[2]) / 3.0 * + inv_volume * nktv2p + (correction); + } else { + if (p_match_flag) + { + error->all(FLERR,"Pressure matching not implemented in 2-d.\n"); + exit(1); + } // The rest of this can probably be deleted. + inv_volume = 1.0 / (domain->xprd * domain->yprd); + virial_compute(2,2); + if (keflag) + scalar = (temperature->dof * boltz * t + + virial[0] + virial[1]) / 2.0 * inv_volume * nktv2p; + else + scalar = (virial[0] + virial[1]) / 2.0 * inv_volume * nktv2p; + } + + return scalar; +} + +/* ---------------------------------------------------------------------- + compute pressure tensor + assume KE tensor has already been computed +------------------------------------------------------------------------- */ + +void ComputePressureBocs::compute_vector() +{ + invoked_vector = update->ntimestep; + if (update->vflag_global != invoked_vector) + error->all(FLERR,"Virial was not tallied on needed timestep"); + + 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"); + + // invoke temperature if it hasn't been already + + double *ke_tensor; + if (keflag) { + if (temperature->invoked_vector != update->ntimestep) + temperature->compute_vector(); + ke_tensor = temperature->vector; + } + + if (dimension == 3) { + inv_volume = 1.0 / (domain->xprd * domain->yprd * domain->zprd); + virial_compute(6,3); + if (keflag) { + for (int i = 0; i < 6; i++) + vector[i] = (ke_tensor[i] + virial[i]) * inv_volume * nktv2p; + } else + for (int i = 0; i < 6; i++) + vector[i] = virial[i] * inv_volume * nktv2p; + } else { + inv_volume = 1.0 / (domain->xprd * domain->yprd); + virial_compute(4,2); + if (keflag) { + vector[0] = (ke_tensor[0] + virial[0]) * inv_volume * nktv2p; + vector[1] = (ke_tensor[1] + virial[1]) * inv_volume * nktv2p; + vector[3] = (ke_tensor[3] + virial[3]) * inv_volume * nktv2p; + vector[2] = vector[4] = vector[5] = 0.0; + } else { + vector[0] = virial[0] * inv_volume * nktv2p; + vector[1] = virial[1] * inv_volume * nktv2p; + vector[3] = virial[3] * inv_volume * nktv2p; + vector[2] = vector[4] = vector[5] = 0.0; + } + } +} + +/* ---------------------------------------------------------------------- */ + +void ComputePressureBocs::virial_compute(int n, int ndiag) +{ + int i,j; + double v[6],*vcomponent; + + for (i = 0; i < n; i++) v[i] = 0.0; + + // sum contributions to virial from forces and fixes + + for (j = 0; j < nvirial; j++) { + vcomponent = vptr[j]; + for (i = 0; i < n; i++) v[i] += vcomponent[i]; + } + + // sum virial across procs + + MPI_Allreduce(v,virial,n,MPI_DOUBLE,MPI_SUM,world); + + // KSpace virial contribution is already summed across procs + + if (kspace_virial) + for (i = 0; i < n; i++) virial[i] += kspace_virial[i]; + + // LJ long-range tail correction, only if pair contributions are included + + if (force->pair && pairflag && force->pair->tail_flag) + for (i = 0; i < ndiag; i++) virial[i] += force->pair->ptail * inv_volume; +} + +/* ---------------------------------------------------------------------- */ + +void ComputePressureBocs::reset_extra_compute_fix(const char *id_new) +{ + delete [] id_temp; + int n = strlen(id_new) + 1; + id_temp = new char[n]; + strcpy(id_temp,id_new); +} diff --git a/src/USER-BOCS/compute_pressure_bocs.h b/src/USER-BOCS/compute_pressure_bocs.h new file mode 100644 index 0000000000000000000000000000000000000000..4fb932c5082473e2b3c111774dd78c1675ad6ec4 --- /dev/null +++ b/src/USER-BOCS/compute_pressure_bocs.h @@ -0,0 +1,114 @@ +/* -*- 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. +------------------------------------------------------------------------- + USER-BOCS written by: Nicholas J. H. Dunn and Michael R. DeLyser + from The Pennsylvania State University +------------------------------------------------------------------------- */ + +#ifdef COMPUTE_CLASS + +ComputeStyle(PRESSURE/BOCS,ComputePressureBocs) + +#else + + +#ifndef LMP_COMPUTE_PRESSURE_BOCS_H +#define LMP_COMPUTE_PRESSURE_BOCS_H + +#include "compute.h" + +namespace LAMMPS_NS { +// ComputePressure -> ComputePressureBocs MRD NJD +class ComputePressureBocs : public Compute { + public: + ComputePressureBocs(class LAMMPS *, int, char **); + virtual ~ComputePressureBocs(); + virtual void init(); + virtual double compute_scalar(); + virtual void compute_vector(); + void reset_extra_compute_fix(const char *); + + double compute_cg_scalar(); + double get_cg_p_corr(int, double *, int, double, double); + double get_cg_fluct(double, double); + void send_cg_info(int, int, double*, int, double); + void send_cg_info(int, double **, int); + double get_cg_p_corr(double **, int, double); + double find_index(double* , double); + + protected: + double boltz,nktv2p,inv_volume; + int nvirial,dimension; + double **vptr; + double *kspace_virial; + Compute *temperature; + char *id_temp; + double virial[6]; + int keflag,pairflag,bondflag,angleflag,dihedralflag,improperflag; + int fixflag,kspaceflag; + +// NJD MRD + int p_basis_type; + int p_match_flag; + double vavg; + int N_mol; + int N_basis; + double *phi_coeff; + double ** splines; + int spline_length; + + void virial_compute(int, int); +}; + +} + +#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: Compute pressure must use group all + +Virial contributions computed by potentials (pair, bond, etc) are +computed on all atoms. + +E: Could not find compute pressure temperature ID + +The compute ID for calculating temperature does not exist. + +E: Compute pressure temperature ID does not compute temperature + +The compute ID assigned to a pressure computation must compute +temperature. + +E: Compute pressure requires temperature ID to include kinetic energy + +The keflag cannot be used unless a temperature compute is provided. + +E: Virial was not tallied on needed timestep + +You are using a thermo keyword that requires potentials to +have tallied the virial, but they didn't on this timestep. See the +variable doc page for ideas on how to make this work. + +E: Must use 'kspace_modify pressure/scalar no' for tensor components with kspace_style msm + +Otherwise MSM will compute only a scalar pressure. See the kspace_modify +command for details on this setting. + +*/ diff --git a/src/USER-BOCS/fix_bocs.cpp b/src/USER-BOCS/fix_bocs.cpp new file mode 100644 index 0000000000000000000000000000000000000000..37e128f55662a6e6c9152abb518d3233845604fd --- /dev/null +++ b/src/USER-BOCS/fix_bocs.cpp @@ -0,0 +1,2431 @@ +/* ---------------------------------------------------------------------- + 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. +------------------------------------------------------------------------- + USER-BOCS written by: Nicholas J. H. Dunn and Michael R. DeLyser + from The Pennsylvania State University +------------------------------------------------------------------------- */ + +#include +#include +#include +#include "fix_bocs.h" +#include "math_extra.h" +#include "atom.h" +#include "force.h" +#include "group.h" +#include "comm.h" +#include "neighbor.h" +#include "irregular.h" +#include "modify.h" +#include "fix_deform.h" +#include "compute.h" +#include "kspace.h" +#include "update.h" +#include "respa.h" +#include "domain.h" +#include "memory.h" +#include "error.h" +#include "citeme.h" + +#include "compute_pressure_bocs.h" + +using namespace LAMMPS_NS; +using namespace FixConst; + +static const char cite_user_bocs_package[] = + "USER-BOCS package:\n\n" + "@Article{Dunn2018,\n" + " author = {NJH Dunn, KM Lebold, MR DeLyser, JF Rudzinski, WG Noid},\n" + " title = {BOCS: Bottom-Up Open-Source Coarse-Graining Software},\n" + " journal = {J. Phys. Chem. B},\n" + " year = 2018,\n" + " volume = 122,\n" + " pages = {3363--3377}\n" + "}\n\n"; + + +#define DELTAFLIP 0.1 +#define TILTMAX 1.5 + +enum{NOBIAS,BIAS}; +enum{NONE,XYZ,XY,YZ,XZ}; +enum{ISO,ANISO,TRICLINIC}; + +/* ---------------------------------------------------------------------- + NVT,NPH,NPT integrators for improved Nose-Hoover equations of motion + ---------------------------------------------------------------------- */ + +FixBocs::FixBocs(LAMMPS *lmp, int narg, char **arg) : + Fix(lmp, narg, arg), + rfix(NULL), id_dilate(NULL), irregular(NULL), id_temp(NULL), id_press(NULL), + eta(NULL), eta_dot(NULL), eta_dotdot(NULL), + eta_mass(NULL), etap(NULL), etap_dot(NULL), etap_dotdot(NULL), + etap_mass(NULL) +{ + if (lmp->citeme) lmp->citeme->add(cite_user_bocs_package); + + if (narg < 4) error->all(FLERR,"Illegal fix bocs command"); + + restart_global = 1; + dynamic_group_allow = 1; + time_integrate = 1; + scalar_flag = 1; + vector_flag = 1; + global_freq = 1; + extscalar = 1; + extvector = 0; + + // default values + + pcouple = NONE; + drag = 0.0; + allremap = 1; + id_dilate = NULL; + mtchain = mpchain = 3; + nc_tchain = nc_pchain = 1; + mtk_flag = 1; + deviatoric_flag = 0; + nreset_h0 = 0; + eta_mass_flag = 1; + omega_mass_flag = 0; + etap_mass_flag = 0; + flipflag = 1; + dipole_flag = 0; + dlm_flag = 0; + + tcomputeflag = 0; + pcomputeflag = 0; + id_temp = NULL; + id_press = NULL; + + p_match_coeffs = NULL; + + // turn on tilt factor scaling, whenever applicable + + dimension = domain->dimension; + + scaleyz = scalexz = scalexy = 0; + if (domain->yperiodic && domain->xy != 0.0) scalexy = 1; + if (domain->zperiodic && dimension == 3) { + if (domain->yz != 0.0) scaleyz = 1; + if (domain->xz != 0.0) scalexz = 1; + } + + // set fixed-point to default = center of cell + + fixedpoint[0] = 0.5*(domain->boxlo[0]+domain->boxhi[0]); + fixedpoint[1] = 0.5*(domain->boxlo[1]+domain->boxhi[1]); + fixedpoint[2] = 0.5*(domain->boxlo[2]+domain->boxhi[2]); + + // used by FixNVTSllod to preserve non-default value + + mtchain_default_flag = 1; + + tstat_flag = 0; + double t_period = 0.0; + + double p_period[6]; + for (int i = 0; i < 6; i++) { + p_start[i] = p_stop[i] = p_period[i] = p_target[i] = 0.0; + p_flag[i] = 0; + } + + // process keywords + + int iarg = 3; + + while (iarg < narg) { + if (strcmp(arg[iarg],"temp") == 0) { + if (iarg+4 > narg) error->all(FLERR,"Illegal fix bocs command"); + tstat_flag = 1; + t_start = force->numeric(FLERR,arg[iarg+1]); + t_target = t_start; + t_stop = force->numeric(FLERR,arg[iarg+2]); + t_period = force->numeric(FLERR,arg[iarg+3]); + if (t_start <= 0.0 || t_stop <= 0.0) + error->all(FLERR, + "Target temperature for fix bocs cannot be 0.0"); + iarg += 4; + } else if (strcmp(arg[iarg],"iso") == 0) { + error->all(FLERR,"Illegal fix bocs command. Pressure fix must be " + "cgiso . Use regular fix bocs for iso"); // MRD NJD + } else if (strcmp(arg[iarg],"cgiso") == 0) { // MRD NJD the whole else if + if (iarg+4 > narg) + error->all(FLERR,"Illegal fix bocs command. cgiso must be " + "followed by: P_0 P_f P_coupl"); + p_match_flag = 1; + pcouple = XYZ; + p_start[0] = p_start[1] = p_start[2] = + force->numeric(FLERR,arg[iarg+1]); + p_stop[0] = p_stop[1] = p_stop[2] = + force->numeric(FLERR,arg[iarg+2]); + p_period[0] = p_period[1] = p_period[2] = + force->numeric(FLERR,arg[iarg+3]); + + p_flag[0] = p_flag[1] = p_flag[2] = 1; + p_flag[3] = p_flag[4] = p_flag[5] = 0; // MRD + if (dimension == 2) { // Later I force 3D... MRD + p_start[2] = p_stop[2] = p_period[2] = 0.0; + p_flag[2] = 0; + } + iarg += 4; + + if ( strcmp(arg[iarg], "analytic") == 0 ) { + if (iarg + 4 > narg) { + error->all(FLERR,"Illegal fix bocs command. basis type analytic" + " must be followed by: avg_vol n_mol n_pmatch_coeff"); + } + p_basis_type = 0; + vavg = force->numeric(FLERR,arg[iarg+1]); + N_mol = force->inumeric(FLERR,arg[iarg+2]); + N_p_match = force->inumeric(FLERR,arg[iarg+3]); + p_match_coeffs = (double *) (calloc(N_p_match, sizeof(double)) ); + iarg += 4; + if (iarg + N_p_match > narg) + error->all(FLERR,"Illegal fix bocs command. Missing coeffs."); + for (int pmatchi = 0; pmatchi < N_p_match; pmatchi++) + p_match_coeffs[pmatchi] = force->numeric(FLERR,arg[iarg+pmatchi]); + iarg += (N_p_match); + } else if (strcmp(arg[iarg], "linear_spline") == 0 ) { + if (iarg+2 > narg) error->all(FLERR,"Illegal fix bocs command. " + "Supply a file name after linear_spline."); + p_basis_type = 1; + spline_length = read_F_table( arg[iarg+1], p_basis_type ); + iarg += 2; + } else if (strcmp(arg[iarg], "cubic_spline") == 0 ) { + if (iarg+2 > narg) error->all(FLERR,"Illegal fix bocs command. " + "Supply a file name after cubic_spline."); + p_basis_type = 2; + spline_length = read_F_table( arg[iarg+1], p_basis_type ); + iarg += 2; + } else + { + char * errmsg = (char *) calloc(150,sizeof(char)); + sprintf(errmsg,"CG basis type %s is not recognized\nSupported " + "basis types: analytic linear_spline cubic_spline",arg[iarg]); + error->all(FLERR,errmsg); + } // END NJD MRD + } else if (strcmp(arg[iarg],"tchain") == 0) { + if (iarg+2 > narg) error->all(FLERR,"Illegal fix bocs command"); + mtchain = force->inumeric(FLERR,arg[iarg+1]); + // used by FixNVTSllod to preserve non-default value + mtchain_default_flag = 0; + if (mtchain < 1) error->all(FLERR,"Illegal fix bocs command"); + iarg += 2; + } else if (strcmp(arg[iarg],"pchain") == 0) { + if (iarg+2 > narg) error->all(FLERR,"Illegal fix bocs command"); + mpchain = force->inumeric(FLERR,arg[iarg+1]); + if (mpchain < 0) error->all(FLERR,"Illegal fix bocs command"); + iarg += 2; + } else if (strcmp(arg[iarg],"mtk") == 0) { + if (iarg+2 > narg) error->all(FLERR,"Illegal fix bocs command"); + if (strcmp(arg[iarg+1],"yes") == 0) mtk_flag = 1; + else if (strcmp(arg[iarg+1],"no") == 0) mtk_flag = 0; + else error->all(FLERR,"Illegal fix bocs command"); + iarg += 2; + } else if (strcmp(arg[iarg],"tloop") == 0) { + if (iarg+2 > narg) error->all(FLERR,"Illegal fix bocs command"); + nc_tchain = force->inumeric(FLERR,arg[iarg+1]); + if (nc_tchain < 0) error->all(FLERR,"Illegal fix bocs command"); + iarg += 2; + } else if (strcmp(arg[iarg],"ploop") == 0) { + if (iarg+2 > narg) error->all(FLERR,"Illegal fix bocs command"); + nc_pchain = force->inumeric(FLERR,arg[iarg+1]); + if (nc_pchain < 0) error->all(FLERR,"Illegal fix bocs command"); + iarg += 2; + } else { + char * errmsg = (char *) calloc(80,sizeof(char)); + sprintf(errmsg,"Illegal fix bocs command: unrecognized keyword %s" + ,arg[iarg]); + error->all(FLERR,errmsg); + } + } + // error checks + + if (dimension != 3) // MRD NJD + error->all(FLERR,"Invalid fix bocs command. Must use 3 dimensions"); + +// With cgiso, p_flag[0] = p_flag[1] = p_flag[2] = 1 + + // require periodicity in tensile dimension + + if (p_flag[0] && domain->xperiodic == 0) + error->all(FLERR,"Cannot use fix bocs on a non-periodic dimension"); + if (p_flag[1] && domain->yperiodic == 0) + error->all(FLERR,"Cannot use fix bocs on a non-periodic dimension"); + if (p_flag[2] && domain->zperiodic == 0) + error->all(FLERR,"Cannot use fix bocs on a non-periodic dimension"); + + if (dipole_flag) { + if (!atom->sphere_flag) + error->all(FLERR,"Using update dipole flag requires atom style sphere"); + if (!atom->mu_flag) + error->all(FLERR,"Using update dipole flag requires atom attribute mu"); + } + + if ((tstat_flag && t_period <= 0.0) || + (p_flag[0] && p_period[0] <= 0.0) || + (p_flag[1] && p_period[1] <= 0.0) || + (p_flag[2] && p_period[2] <= 0.0) || + (p_flag[3] && p_period[3] <= 0.0) || + (p_flag[4] && p_period[4] <= 0.0) || + (p_flag[5] && p_period[5] <= 0.0)) + error->all(FLERR,"Fix bocs damping parameters must be > 0.0"); + + // set pstat_flag and box change and restart_pbc variables + + pre_exchange_flag = 0; + pstat_flag = 0; + pstyle = ISO; + + for (int i = 0; i < 6; i++) + if (p_flag[i]) pstat_flag = 1; + + if (pstat_flag) { + if (p_flag[0] || p_flag[1] || p_flag[2]) box_change_size = 1; + if (p_flag[3] || p_flag[4] || p_flag[5]) box_change_shape = 1; + no_change_box = 1; + if (allremap == 0) restart_pbc = 1; + + pstyle = ISO; // MRD this is the only one that can happen + + // pre_exchange only required if flips can occur due to shape changes + + if (flipflag && (p_flag[3] || p_flag[4] || p_flag[5])) + pre_exchange_flag = 1; + if (flipflag && (domain->yz != 0.0 || domain->xz != 0.0 || + domain->xy != 0.0)) + pre_exchange_flag = 1; + } + + // convert input periods to frequencies + + t_freq = 0.0; + p_freq[0] = p_freq[1] = p_freq[2] = p_freq[3] = p_freq[4] = p_freq[5] = 0.0; + + if (tstat_flag) t_freq = 1.0 / t_period; + if (p_flag[0]) p_freq[0] = 1.0 / p_period[0]; + if (p_flag[1]) p_freq[1] = 1.0 / p_period[1]; + if (p_flag[2]) p_freq[2] = 1.0 / p_period[2]; + if (p_flag[3]) p_freq[3] = 1.0 / p_period[3]; + if (p_flag[4]) p_freq[4] = 1.0 / p_period[4]; + if (p_flag[5]) p_freq[5] = 1.0 / p_period[5]; + + // Nose/Hoover temp and pressure init + + size_vector = 0; + + if (tstat_flag) { + int ich; + eta = new double[mtchain]; + + // add one extra dummy thermostat, set to zero + + eta_dot = new double[mtchain+1]; + eta_dot[mtchain] = 0.0; + eta_dotdot = new double[mtchain]; + for (ich = 0; ich < mtchain; ich++) { + eta[ich] = eta_dot[ich] = eta_dotdot[ich] = 0.0; + } + eta_mass = new double[mtchain]; + size_vector += 2*2*mtchain; + } + + if (pstat_flag) { + omega[0] = omega[1] = omega[2] = 0.0; + omega_dot[0] = omega_dot[1] = omega_dot[2] = 0.0; + omega_mass[0] = omega_mass[1] = omega_mass[2] = 0.0; + omega[3] = omega[4] = omega[5] = 0.0; + omega_dot[3] = omega_dot[4] = omega_dot[5] = 0.0; + omega_mass[3] = omega_mass[4] = omega_mass[5] = 0.0; + if (pstyle == ISO) size_vector += 2*2*1; + else if (pstyle == ANISO) size_vector += 2*2*3; + else if (pstyle == TRICLINIC) size_vector += 2*2*6; + + if (mpchain) { + int ich; + etap = new double[mpchain]; + + // add one extra dummy thermostat, set to zero + + etap_dot = new double[mpchain+1]; + etap_dot[mpchain] = 0.0; + etap_dotdot = new double[mpchain]; + for (ich = 0; ich < mpchain; ich++) { + etap[ich] = etap_dot[ich] = + etap_dotdot[ich] = 0.0; + } + etap_mass = new double[mpchain]; + size_vector += 2*2*mpchain; + } + + if (deviatoric_flag) size_vector += 1; + } + + nrigid = 0; + rfix = NULL; + + if (pre_exchange_flag) irregular = new Irregular(lmp); + else irregular = NULL; + + // initialize vol0,t0 to zero to signal uninitialized + // values then assigned in init(), if necessary + + vol0 = t0 = 0.0; + + /*~ MRD I copied this from fix_npt.cpp 8/17/17 ~*/ + + if (!tstat_flag) + error->all(FLERR,"Temperature control must be used with fix bocs"); + if (!pstat_flag) + error->all(FLERR,"Pressure control must be used with fix bocs"); + + // create a new compute temp style + // id = fix-ID + temp + // compute group = all since pressure is always global (group all) + // and thus its KE/temperature contribution should use group all + + + int n = strlen(id) + 6; + id_temp = new char[n]; + strcpy(id_temp,id); + strcat(id_temp,"_temp"); + + char **newarg = new char*[3]; + newarg[0] = id_temp; + newarg[1] = (char *) "all"; + newarg[2] = (char *) "temp"; + + + modify->add_compute(3,newarg); + delete [] newarg; + tcomputeflag = 1; + + // create a new compute pressure style + // id = fix-ID + press, compute group = all + // pass id_temp as 4th arg to pressure constructor + + n = strlen(id) + 7; + id_press = new char[n]; + strcpy(id_press,id); + strcat(id_press,"_press"); + + newarg = new char*[4]; + newarg[0] = id_press; + newarg[1] = (char *) "all"; + newarg[2] = (char *) "PRESSURE/BOCS"; + newarg[3] = id_temp; + modify->add_compute(4,newarg); + delete [] newarg; + pcomputeflag = 1; + +/*~ MRD End of stuff copied from fix_npt.cpp~*/ + +} + +/* ---------------------------------------------------------------------- */ + +FixBocs::~FixBocs() +{ + if (copymode) return; + + delete [] id_dilate; + delete [] rfix; + + delete irregular; + + // delete temperature and pressure if fix created them + + if (tcomputeflag) modify->delete_compute(id_temp); + delete [] id_temp; + + if (tstat_flag) { + delete [] eta; + delete [] eta_dot; + delete [] eta_dotdot; + delete [] eta_mass; + } + + if (pstat_flag) { + if (pcomputeflag) modify->delete_compute(id_press); + delete [] id_press; + if (mpchain) { + delete [] etap; + delete [] etap_dot; + delete [] etap_dotdot; + delete [] etap_mass; + } + } + if (p_match_coeffs) free(p_match_coeffs); +} + +/* ---------------------------------------------------------------------- */ + +int FixBocs::setmask() +{ + int mask = 0; + mask |= INITIAL_INTEGRATE; + mask |= FINAL_INTEGRATE; + mask |= THERMO_ENERGY; + mask |= INITIAL_INTEGRATE_RESPA; + mask |= FINAL_INTEGRATE_RESPA; + if (pre_exchange_flag) mask |= PRE_EXCHANGE; + return mask; +} + +/* ---------------------------------------------------------------------- */ + +void FixBocs::init() +{ + // recheck that dilate group has not been deleted + if (allremap == 0) { + int idilate = group->find(id_dilate); + if (idilate == -1) + error->all(FLERR,"Fix bocs dilate group ID does not exist"); + dilate_group_bit = group->bitmask[idilate]; + } + + // ensure no conflict with fix deform + + if (pstat_flag) + { + for (int i = 0; i < modify->nfix; i++) + if (strcmp(modify->fix[i]->style,"deform") == 0) { + int *dimflag = ((FixDeform *) modify->fix[i])->dimflag; + if ((p_flag[0] && dimflag[0]) || (p_flag[1] && dimflag[1]) || + (p_flag[2] && dimflag[2]) || (p_flag[3] && dimflag[3]) || + (p_flag[4] && dimflag[4]) || (p_flag[5] && dimflag[5])) + error->all(FLERR,"Cannot use fix bocs and fix deform on " + "same component of stress tensor"); + } + } + + // set temperature and pressure ptrs + int icompute = modify->find_compute(id_temp); + if (icompute < 0) + error->all(FLERR,"Temperature ID for fix bocs does not exist"); + temperature = modify->compute[icompute]; + + if (temperature->tempbias) which = BIAS; + else which = NOBIAS; + + if (pstat_flag) { + icompute = modify->find_compute(id_press); + if (icompute < 0) + error->all(FLERR,"Pressure ID for fix bocs does not exist"); + pressure = modify->compute[icompute]; + } + + + if (pstat_flag) + { + if (p_match_flag) // MRD NJD + { + if (pressure) + { + if (p_basis_type == 0) + { + ((ComputePressureBocs *)pressure)->send_cg_info(p_basis_type, + N_p_match, p_match_coeffs, N_mol, vavg); + } + else if ( p_basis_type == 1 || p_basis_type == 2 ) + { + ((ComputePressureBocs *)pressure)->send_cg_info(p_basis_type, + splines, spline_length); + } + } + else + { + error->all(FLERR,"Unable to find pressure. Are you sure you included" + " the compute bocsPress and fix_modify commands?"); + } + } + } + + + // set timesteps and frequencies + + dtv = update->dt; + dtf = 0.5 * update->dt * force->ftm2v; + dthalf = 0.5 * update->dt; + dt4 = 0.25 * update->dt; + dt8 = 0.125 * update->dt; + dto = dthalf; + + p_freq_max = 0.0; + if (pstat_flag) { + p_freq_max = MAX(p_freq[0],p_freq[1]); + p_freq_max = MAX(p_freq_max,p_freq[2]); + if (pstyle == TRICLINIC) { + p_freq_max = MAX(p_freq_max,p_freq[3]); + p_freq_max = MAX(p_freq_max,p_freq[4]); + p_freq_max = MAX(p_freq_max,p_freq[5]); + } + pdrag_factor = 1.0 - (update->dt * p_freq_max * drag / nc_pchain); + } + + if (tstat_flag) + tdrag_factor = 1.0 - (update->dt * t_freq * drag / nc_tchain); + + // tally the number of dimensions that are barostatted + // set initial volume and reference cell, if not already done + + if (pstat_flag) { + pdim = p_flag[0] + p_flag[1] + p_flag[2]; + if (vol0 == 0.0) { + if (dimension == 3) vol0 = domain->xprd * domain->yprd * domain->zprd; + else vol0 = domain->xprd * domain->yprd; + h0_inv[0] = domain->h_inv[0]; + h0_inv[1] = domain->h_inv[1]; + h0_inv[2] = domain->h_inv[2]; + h0_inv[3] = domain->h_inv[3]; + h0_inv[4] = domain->h_inv[4]; + h0_inv[5] = domain->h_inv[5]; + } + } + + boltz = force->boltz; + nktv2p = force->nktv2p; + + if (force->kspace) kspace_flag = 1; + else kspace_flag = 0; + + if (strstr(update->integrate_style,"respa")) { + nlevels_respa = ((Respa *) update->integrate)->nlevels; + step_respa = ((Respa *) update->integrate)->step; + dto = 0.5*step_respa[0]; + } + + // detect if any rigid fixes exist so rigid bodies move when box is remapped + // rfix[] = indices to each fix rigid + + delete [] rfix; + nrigid = 0; + rfix = NULL; + + for (int i = 0; i < modify->nfix; i++) + if (modify->fix[i]->rigid_flag) nrigid++; + if (nrigid) { + rfix = new int[nrigid]; + nrigid = 0; + for (int i = 0; i < modify->nfix; i++) + if (modify->fix[i]->rigid_flag) rfix[nrigid++] = i; + } +} + +// NJD MRD 2 functions +int FixBocs::read_F_table( char *filename, int p_basis_type ) +{ + char separator = ','; + FILE *fpi; + int N_columns = 2, n_entries = 0, i; + float f1, f2; + double n1, n2; + int test_sscanf; + double **data = (double **) calloc(N_columns,sizeof(double *)); + char * line = (char *) calloc(200,sizeof(char)); + + 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 = (char *) calloc(50,sizeof(char)); + sprintf(errmsg,"Unable to open file: %s\n",filename); + error->all(FLERR,errmsg); + } + + n_entries = 0; + fpi = fopen(filename,"r"); + if (fpi) + { + while( fgets(line,199,fpi)) + { + ++n_entries; + test_sscanf = sscanf(line," %f , %f ",&f1, &f2); + if (test_sscanf == 2) + { + data[0][n_entries-1] = (double) f1; + data[1][n_entries-1] = (double) f2; + } + else + { + fprintf(stderr,"WARNING: did not find 2 comma separated values in " + "line %d of file %s\n\tline: %s",n_entries,filename,line); + } + } + } + else + { + char * errmsg = (char *) calloc(50,sizeof(char)); + sprintf(errmsg,"Unable to open file: %s\n",filename); + error->all(FLERR,errmsg); + } + fclose(fpi); + + if (p_basis_type == 1) + { + splines = (double **) calloc(2,sizeof(double *)); + splines[0] = (double *) calloc(n_entries,sizeof(double)); + splines[1] = (double *) calloc(n_entries,sizeof(double)); + int idxa, idxb; + for (idxa = 0; idxa < 2; ++idxa) + { + for (idxb = 0; idxb < n_entries; ++idxb) + { + splines[idxa][idxb] = data[idxa][idxb]; + } + } + } + else if (p_basis_type == 2) + { + spline_length = n_entries; + build_cubic_splines(data); + n_entries -= 1; + } + 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); + error->all(FLERR,errmsg); + } + return n_entries; +} + +void FixBocs::build_cubic_splines( double **data ) +{ + double *a, *b, *d, *h, *alpha, *c, *l, *mu, *z; + int n = spline_length; + double alpha_i; + a = (double *) calloc(n,sizeof(double)); + b = (double *) calloc(n+1,sizeof(double)); + d = (double *) calloc(n+1,sizeof(double)); + h = (double *) calloc(n,sizeof(double)); + alpha = (double *) calloc(n,sizeof(double)); + c = (double *) calloc(n+1,sizeof(double)); + l = (double *) calloc(n,sizeof(double)); + mu = (double *) calloc(n,sizeof(double)); + z = (double *) calloc(n,sizeof(double)); + int idx; + for (int i=0; i1 && i<(n-1)) + { + alpha_i = (3.0 / h[i]) * ( data[1][i+1] - data[1][i]) - (3.0 / h[i-1] ) + * ( data[1][i] - data[1][i-1] ); + alpha[i-1] = alpha_i; + } + } + l[0] = 1.0; + mu[0] = 0.0; + z[0] = 0.0; + + for (int i=1; i=0; j--) + { + c[j] = z[j] - mu[j]*c[j+1]; + + b[j] = (a[j+1]-a[j])/h[j] - h[j]*(c[j+1] + 2.0 * c[j])/3.0; + + d[j] = (c[j+1]-c[j])/(3.0 * h[j]); + } + splines = (double **) calloc(5,sizeof(double *)); + + for ( idx = 0; idx < 5; ++idx) + { + splines[idx] = (double *) calloc(n-1,sizeof(double)); + } + idx = 0; + for ( idx = 0; idx < n - 1; ++idx) + { + splines[1][idx] = a[idx]; + splines[2][idx] = b[idx]; + splines[3][idx] = c[idx]; + splines[4][idx] = d[idx]; + splines[0][idx] = data[0][idx]; + } +} +// END NJD MRD 2 functions + +/* ---------------------------------------------------------------------- + compute T,P before integrator starts +------------------------------------------------------------------------- */ + +void FixBocs::setup(int vflag) +{ + // tdof needed by compute_temp_target() + + t_current = temperature->compute_scalar(); + tdof = temperature->dof; + + // t_target is needed by NVT and NPT in compute_scalar() + // If no thermostat or using fix nphug, + // t_target must be defined by other means. + + if (tstat_flag && strstr(style,"nphug") == NULL) { + compute_temp_target(); + } else if (pstat_flag) { + + // t0 = reference temperature for masses + // cannot be done in init() b/c temperature cannot be called there + // is b/c Modify::init() inits computes after fixes due to dof dependence + // guesstimate a unit-dependent t0 if actual T = 0.0 + // if it was read in from a restart file, leave it be + + if (t0 == 0.0) { + t0 = temperature->compute_scalar(); + if (t0 == 0.0) { + if (strcmp(update->unit_style,"lj") == 0) t0 = 1.0; + else t0 = 300.0; + } + } + t_target = t0; + } + + if (pstat_flag) compute_press_target(); + + if (pstat_flag) { + if (pstyle == ISO) pressure->compute_scalar(); + else pressure->compute_vector(); + couple(); + pressure->addstep(update->ntimestep+1); + } + + // masses and initial forces on thermostat variables + + if (tstat_flag) { + eta_mass[0] = tdof * boltz * t_target / (t_freq*t_freq); + for (int ich = 1; ich < mtchain; ich++) + eta_mass[ich] = boltz * t_target / (t_freq*t_freq); + for (int ich = 1; ich < mtchain; ich++) { + eta_dotdot[ich] = (eta_mass[ich-1]*eta_dot[ich-1]*eta_dot[ich-1] - + boltz * t_target) / eta_mass[ich]; + } + } + + // masses and initial forces on barostat variables + + if (pstat_flag) { + double kt = boltz * t_target; + double nkt = atom->natoms * kt; + + for (int i = 0; i < 3; i++) + if (p_flag[i]) + omega_mass[i] = nkt/(p_freq[i]*p_freq[i]); + + if (pstyle == TRICLINIC) { + for (int i = 3; i < 6; i++) + if (p_flag[i]) omega_mass[i] = nkt/(p_freq[i]*p_freq[i]); + } + + // masses and initial forces on barostat thermostat variables + + if (mpchain) { + etap_mass[0] = boltz * t_target / (p_freq_max*p_freq_max); + for (int ich = 1; ich < mpchain; ich++) + etap_mass[ich] = boltz * t_target / (p_freq_max*p_freq_max); + for (int ich = 1; ich < mpchain; ich++) + etap_dotdot[ich] = + (etap_mass[ich-1]*etap_dot[ich-1]*etap_dot[ich-1] - + boltz * t_target) / etap_mass[ich]; + } + } +} + +/* ---------------------------------------------------------------------- + 1st half of Verlet update +------------------------------------------------------------------------- */ + +void FixBocs::initial_integrate(int vflag) +{ + // update eta_press_dot + + if (pstat_flag && mpchain) nhc_press_integrate(); + + // update eta_dot + + if (tstat_flag) { + compute_temp_target(); + nhc_temp_integrate(); + } + + // need to recompute pressure to account for change in KE + // t_current is up-to-date, but compute_temperature is not + // compute appropriately coupled elements of mvv_current + + if (pstat_flag) { + if (pstyle == ISO) { + temperature->compute_scalar(); + pressure->compute_scalar(); + } else { + temperature->compute_vector(); + pressure->compute_vector(); + } + couple(); + pressure->addstep(update->ntimestep+1); + } + + if (pstat_flag) { + compute_press_target(); + nh_omega_dot(); + nh_v_press(); + } + + nve_v(); + + // remap simulation box by 1/2 step + + if (pstat_flag) remap(); + + nve_x(); + + // remap simulation box by 1/2 step + // redo KSpace coeffs since volume has changed + + if (pstat_flag) { + remap(); + if (kspace_flag) force->kspace->setup(); + } +} + +/* ---------------------------------------------------------------------- + 2nd half of Verlet update +------------------------------------------------------------------------- */ + +void FixBocs::final_integrate() +{ + nve_v(); + + // re-compute temp before nh_v_press() + // only needed for temperature computes with BIAS on reneighboring steps: + // b/c some biases store per-atom values (e.g. temp/profile) + // per-atom values are invalid if reneigh/comm occurred + // since temp->compute() in initial_integrate() + + if (which == BIAS && neighbor->ago == 0) + t_current = temperature->compute_scalar(); + + if (pstat_flag) nh_v_press(); + + // compute new T,P after velocities rescaled by nh_v_press() + // compute appropriately coupled elements of mvv_current + + t_current = temperature->compute_scalar(); + tdof = temperature->dof; + + if (pstat_flag) { + if (pstyle == ISO) pressure->compute_scalar(); + else pressure->compute_vector(); + couple(); + pressure->addstep(update->ntimestep+1); + } + + if (pstat_flag) nh_omega_dot(); + + // update eta_dot + // update eta_press_dot + + if (tstat_flag) nhc_temp_integrate(); + if (pstat_flag && mpchain) nhc_press_integrate(); +} + +/* ---------------------------------------------------------------------- */ + +void FixBocs::initial_integrate_respa(int vflag, int ilevel, int iloop) +{ + // set timesteps by level + + dtv = step_respa[ilevel]; + dtf = 0.5 * step_respa[ilevel] * force->ftm2v; + dthalf = 0.5 * step_respa[ilevel]; + + // outermost level - update eta_dot and omega_dot, apply to v + // all other levels - NVE update of v + // x,v updates only performed for atoms in group + + if (ilevel == nlevels_respa-1) { + + // update eta_press_dot + + if (pstat_flag && mpchain) nhc_press_integrate(); + + // update eta_dot + + if (tstat_flag) { + compute_temp_target(); + nhc_temp_integrate(); + } + + // recompute pressure to account for change in KE + // t_current is up-to-date, but compute_temperature is not + // compute appropriately coupled elements of mvv_current + + if (pstat_flag) { + if (pstyle == ISO) { + temperature->compute_scalar(); + pressure->compute_scalar(); + } else { + temperature->compute_vector(); + pressure->compute_vector(); + } + couple(); + pressure->addstep(update->ntimestep+1); + } + + if (pstat_flag) { + compute_press_target(); + nh_omega_dot(); + nh_v_press(); + } + + nve_v(); + + } else nve_v(); + + // innermost level - also update x only for atoms in group + // if barostat, perform 1/2 step remap before and after + + if (ilevel == 0) { + if (pstat_flag) remap(); + nve_x(); + if (pstat_flag) remap(); + } + + // if barostat, redo KSpace coeffs at outermost level, + // since volume has changed + + if (ilevel == nlevels_respa-1 && kspace_flag && pstat_flag) + force->kspace->setup(); +} + +/* ---------------------------------------------------------------------- */ + +void FixBocs::final_integrate_respa(int ilevel, int iloop) +{ + // set timesteps by level + + dtf = 0.5 * step_respa[ilevel] * force->ftm2v; + dthalf = 0.5 * step_respa[ilevel]; + + // outermost level - update eta_dot and omega_dot, apply via final_integrate + // all other levels - NVE update of v + + if (ilevel == nlevels_respa-1) final_integrate(); + else nve_v(); +} + +/* ---------------------------------------------------------------------- */ + +void FixBocs::couple() +{ + double *tensor = pressure->vector; + + if (pstyle == ISO) + p_current[0] = p_current[1] = p_current[2] = pressure->scalar; + else if (pcouple == XYZ) { + double ave = 1.0/3.0 * (tensor[0] + tensor[1] + tensor[2]); + p_current[0] = p_current[1] = p_current[2] = ave; + } else if (pcouple == XY) { + double ave = 0.5 * (tensor[0] + tensor[1]); + p_current[0] = p_current[1] = ave; + p_current[2] = tensor[2]; + } else if (pcouple == YZ) { + double ave = 0.5 * (tensor[1] + tensor[2]); + p_current[1] = p_current[2] = ave; + p_current[0] = tensor[0]; + } else if (pcouple == XZ) { + double ave = 0.5 * (tensor[0] + tensor[2]); + p_current[0] = p_current[2] = ave; + p_current[1] = tensor[1]; + } else { + p_current[0] = tensor[0]; + p_current[1] = tensor[1]; + p_current[2] = tensor[2]; + } + + if (!std::isfinite(p_current[0]) || !std::isfinite(p_current[1]) || !std::isfinite(p_current[2])) + error->all(FLERR,"Non-numeric pressure - simulation unstable"); + + // switch order from xy-xz-yz to Voigt + + if (pstyle == TRICLINIC) { + p_current[3] = tensor[5]; + p_current[4] = tensor[4]; + p_current[5] = tensor[3]; + + if (!std::isfinite(p_current[3]) || !std::isfinite(p_current[4]) || !std::isfinite(p_current[5])) + error->all(FLERR,"Non-numeric pressure - simulation unstable"); + } +} + +/* ---------------------------------------------------------------------- + change box size + remap all atoms or dilate group atoms depending on allremap flag + if rigid bodies exist, scale rigid body centers-of-mass +------------------------------------------------------------------------- */ + +void FixBocs::remap() +{ + int i; + double oldlo,oldhi; + double expfac; + + double **x = atom->x; + int *mask = atom->mask; + int nlocal = atom->nlocal; + double *h = domain->h; + + // omega is not used, except for book-keeping + + for (int i = 0; i < 6; i++) omega[i] += dto*omega_dot[i]; + + // convert pertinent atoms and rigid bodies to lamda coords + + if (allremap) domain->x2lamda(nlocal); + else { + for (i = 0; i < nlocal; i++) + if (mask[i] & dilate_group_bit) + domain->x2lamda(x[i],x[i]); + } + + if (nrigid) + for (i = 0; i < nrigid; i++) + modify->fix[rfix[i]]->deform(0); + + // reset global and local box to new size/shape + + // this operation corresponds to applying the + // translate and scale operations + // corresponding to the solution of the following ODE: + // + // h_dot = omega_dot * h + // + // where h_dot, omega_dot and h are all upper-triangular + // 3x3 tensors. In Voigt notation, the elements of the + // RHS product tensor are: + // h_dot = [0*0, 1*1, 2*2, 1*3+3*2, 0*4+5*3+4*2, 0*5+5*1] + // + // Ordering of operations preserves time symmetry. + + double dto2 = dto/2.0; + double dto4 = dto/4.0; + double dto8 = dto/8.0; + + // off-diagonal components, first half + + if (pstyle == TRICLINIC) { + + if (p_flag[4]) { + expfac = exp(dto8*omega_dot[0]); + h[4] *= expfac; + h[4] += dto4*(omega_dot[5]*h[3]+omega_dot[4]*h[2]); + h[4] *= expfac; + } + + if (p_flag[3]) { + expfac = exp(dto4*omega_dot[1]); + h[3] *= expfac; + h[3] += dto2*(omega_dot[3]*h[2]); + h[3] *= expfac; + } + + if (p_flag[5]) { + expfac = exp(dto4*omega_dot[0]); + h[5] *= expfac; + h[5] += dto2*(omega_dot[5]*h[1]); + h[5] *= expfac; + } + + if (p_flag[4]) { + expfac = exp(dto8*omega_dot[0]); + h[4] *= expfac; + h[4] += dto4*(omega_dot[5]*h[3]+omega_dot[4]*h[2]); + h[4] *= expfac; + } + } + + // scale diagonal components + // scale tilt factors with cell, if set + + if (p_flag[0]) { + oldlo = domain->boxlo[0]; + oldhi = domain->boxhi[0]; + expfac = exp(dto*omega_dot[0]); + domain->boxlo[0] = (oldlo-fixedpoint[0])*expfac + fixedpoint[0]; + domain->boxhi[0] = (oldhi-fixedpoint[0])*expfac + fixedpoint[0]; + } + + if (p_flag[1]) { + oldlo = domain->boxlo[1]; + oldhi = domain->boxhi[1]; + expfac = exp(dto*omega_dot[1]); + domain->boxlo[1] = (oldlo-fixedpoint[1])*expfac + fixedpoint[1]; + domain->boxhi[1] = (oldhi-fixedpoint[1])*expfac + fixedpoint[1]; + if (scalexy) h[5] *= expfac; + } + + if (p_flag[2]) { + oldlo = domain->boxlo[2]; + oldhi = domain->boxhi[2]; + expfac = exp(dto*omega_dot[2]); + domain->boxlo[2] = (oldlo-fixedpoint[2])*expfac + fixedpoint[2]; + domain->boxhi[2] = (oldhi-fixedpoint[2])*expfac + fixedpoint[2]; + if (scalexz) h[4] *= expfac; + if (scaleyz) h[3] *= expfac; + } + + // off-diagonal components, second half + + if (pstyle == TRICLINIC) { + + if (p_flag[4]) { + expfac = exp(dto8*omega_dot[0]); + h[4] *= expfac; + h[4] += dto4*(omega_dot[5]*h[3]+omega_dot[4]*h[2]); + h[4] *= expfac; + } + + if (p_flag[3]) { + expfac = exp(dto4*omega_dot[1]); + h[3] *= expfac; + h[3] += dto2*(omega_dot[3]*h[2]); + h[3] *= expfac; + } + + if (p_flag[5]) { + expfac = exp(dto4*omega_dot[0]); + h[5] *= expfac; + h[5] += dto2*(omega_dot[5]*h[1]); + h[5] *= expfac; + } + + if (p_flag[4]) { + expfac = exp(dto8*omega_dot[0]); + h[4] *= expfac; + h[4] += dto4*(omega_dot[5]*h[3]+omega_dot[4]*h[2]); + h[4] *= expfac; + } + + } + + domain->yz = h[3]; + domain->xz = h[4]; + domain->xy = h[5]; + + // tilt factor to cell length ratio can not exceed TILTMAX in one step + + if (domain->yz < -TILTMAX*domain->yprd || + domain->yz > TILTMAX*domain->yprd || + domain->xz < -TILTMAX*domain->xprd || + domain->xz > TILTMAX*domain->xprd || + domain->xy < -TILTMAX*domain->xprd || + domain->xy > TILTMAX*domain->xprd) + error->all(FLERR,"Fix bocs has tilted box too far in one step - " + "periodic cell is too far from equilibrium state"); + + domain->set_global_box(); + domain->set_local_box(); + + // convert pertinent atoms and rigid bodies back to box coords + + if (allremap) domain->lamda2x(nlocal); + else { + for (i = 0; i < nlocal; i++) + if (mask[i] & dilate_group_bit) + domain->lamda2x(x[i],x[i]); + } + + if (nrigid) + for (i = 0; i < nrigid; i++) + modify->fix[rfix[i]]->deform(1); +} + +/* ---------------------------------------------------------------------- + pack entire state of Fix into one write +------------------------------------------------------------------------- */ + +void FixBocs::write_restart(FILE *fp) +{ + int nsize = size_restart_global(); + + double *list; + memory->create(list,nsize,"nh:list"); + + pack_restart_data(list); + + if (comm->me == 0) { + int size = nsize * sizeof(double); + fwrite(&size,sizeof(int),1,fp); + fwrite(list,sizeof(double),nsize,fp); + } + + memory->destroy(list); +} + +/* ---------------------------------------------------------------------- + calculate the number of data to be packed +------------------------------------------------------------------------- */ + +int FixBocs::size_restart_global() +{ + int nsize = 2; + if (tstat_flag) nsize += 1 + 2*mtchain; + if (pstat_flag) { + nsize += 16 + 2*mpchain; + if (deviatoric_flag) nsize += 6; + } + + return nsize; +} + +/* ---------------------------------------------------------------------- + pack restart data +------------------------------------------------------------------------- */ + +int FixBocs::pack_restart_data(double *list) +{ + int n = 0; + + list[n++] = tstat_flag; + if (tstat_flag) { + list[n++] = mtchain; + for (int ich = 0; ich < mtchain; ich++) + list[n++] = eta[ich]; + for (int ich = 0; ich < mtchain; ich++) + list[n++] = eta_dot[ich]; + } + + list[n++] = pstat_flag; + if (pstat_flag) { + list[n++] = omega[0]; + list[n++] = omega[1]; + list[n++] = omega[2]; + list[n++] = omega[3]; + list[n++] = omega[4]; + list[n++] = omega[5]; + list[n++] = omega_dot[0]; + list[n++] = omega_dot[1]; + list[n++] = omega_dot[2]; + list[n++] = omega_dot[3]; + list[n++] = omega_dot[4]; + list[n++] = omega_dot[5]; + list[n++] = vol0; + list[n++] = t0; + list[n++] = mpchain; + if (mpchain) { + for (int ich = 0; ich < mpchain; ich++) + list[n++] = etap[ich]; + for (int ich = 0; ich < mpchain; ich++) + list[n++] = etap_dot[ich]; + } + + list[n++] = deviatoric_flag; + if (deviatoric_flag) { + list[n++] = h0_inv[0]; + list[n++] = h0_inv[1]; + list[n++] = h0_inv[2]; + list[n++] = h0_inv[3]; + list[n++] = h0_inv[4]; + list[n++] = h0_inv[5]; + } + } + + return n; +} + +/* ---------------------------------------------------------------------- + use state info from restart file to restart the Fix +------------------------------------------------------------------------- */ + +void FixBocs::restart(char *buf) +{ + int n = 0; + double *list = (double *) buf; + int flag = static_cast (list[n++]); + if (flag) { + int m = static_cast (list[n++]); + if (tstat_flag && m == mtchain) { + for (int ich = 0; ich < mtchain; ich++) + eta[ich] = list[n++]; + for (int ich = 0; ich < mtchain; ich++) + eta_dot[ich] = list[n++]; + } else n += 2*m; + } + flag = static_cast (list[n++]); + if (flag) { + omega[0] = list[n++]; + omega[1] = list[n++]; + omega[2] = list[n++]; + omega[3] = list[n++]; + omega[4] = list[n++]; + omega[5] = list[n++]; + omega_dot[0] = list[n++]; + omega_dot[1] = list[n++]; + omega_dot[2] = list[n++]; + omega_dot[3] = list[n++]; + omega_dot[4] = list[n++]; + omega_dot[5] = list[n++]; + vol0 = list[n++]; + t0 = list[n++]; + int m = static_cast (list[n++]); + if (pstat_flag && m == mpchain) { + for (int ich = 0; ich < mpchain; ich++) + etap[ich] = list[n++]; + for (int ich = 0; ich < mpchain; ich++) + etap_dot[ich] = list[n++]; + } else n+=2*m; + flag = static_cast (list[n++]); + if (flag) { + h0_inv[0] = list[n++]; + h0_inv[1] = list[n++]; + h0_inv[2] = list[n++]; + h0_inv[3] = list[n++]; + h0_inv[4] = list[n++]; + h0_inv[5] = list[n++]; + } + } +} + +/* ---------------------------------------------------------------------- */ + +int FixBocs::modify_param(int narg, char **arg) +{ + if (strcmp(arg[0],"temp") == 0) { + if (narg < 2) error->all(FLERR,"Illegal fix_modify command"); + if (tcomputeflag) { + modify->delete_compute(id_temp); + tcomputeflag = 0; + } + delete [] id_temp; + int n = strlen(arg[1]) + 1; + id_temp = new char[n]; + strcpy(id_temp,arg[1]); + + int icompute = modify->find_compute(arg[1]); + if (icompute < 0) + error->all(FLERR,"Could not find fix_modify temperature ID"); + temperature = modify->compute[icompute]; + + if (temperature->tempflag == 0) + error->all(FLERR, + "Fix_modify temperature ID does not compute temperature"); + if (temperature->igroup != 0 && comm->me == 0) + error->warning(FLERR,"Temperature for fix modify is not for group all"); + + // reset id_temp of pressure to new temperature ID + + if (pstat_flag) { + icompute = modify->find_compute(id_press); + if (icompute < 0) + error->all(FLERR,"Pressure ID for fix modify does not exist"); + modify->compute[icompute]->reset_extra_compute_fix(id_temp); + } + + return 2; + + } else if (strcmp(arg[0],"press") == 0) { + if (narg < 2) error->all(FLERR,"Illegal fix_modify command"); + if (!pstat_flag) error->all(FLERR,"Illegal fix_modify command"); + if (pcomputeflag) { + modify->delete_compute(id_press); + pcomputeflag = 0; + } + delete [] id_press; + int n = strlen(arg[1]) + 1; + id_press = new char[n]; + strcpy(id_press,arg[1]); + + int icompute = modify->find_compute(arg[1]); + if (icompute < 0) error->all(FLERR,"Could not find fix_modify pressure ID"); + pressure = modify->compute[icompute]; + + if (p_match_flag) // NJD MRD + { + if ( p_basis_type == 0 ) + { + ((ComputePressureBocs *)pressure)->send_cg_info(p_basis_type, N_p_match, + p_match_coeffs, N_mol, vavg); + } + else if ( p_basis_type == 1 || p_basis_type == 2 ) + { + ((ComputePressureBocs *)pressure)->send_cg_info(p_basis_type, splines, + spline_length ); + } + } + + if (pressure->pressflag == 0) + error->all(FLERR,"Fix_modify pressure ID does not compute pressure"); + return 2; + } + + return 0; +} + +/* ---------------------------------------------------------------------- */ + +double FixBocs::compute_scalar() +{ + int i; + double volume; + double energy; + double kt = boltz * t_target; + double lkt_press = kt; + int ich; + if (dimension == 3) volume = domain->xprd * domain->yprd * domain->zprd; + else volume = domain->xprd * domain->yprd; + + energy = 0.0; + + // thermostat chain energy is equivalent to Eq. (2) in + // Martyna, Tuckerman, Tobias, Klein, Mol Phys, 87, 1117 + // Sum(0.5*p_eta_k^2/Q_k,k=1,M) + L*k*T*eta_1 + Sum(k*T*eta_k,k=2,M), + // where L = tdof + // M = mtchain + // p_eta_k = Q_k*eta_dot[k-1] + // Q_1 = L*k*T/t_freq^2 + // Q_k = k*T/t_freq^2, k > 1 + + if (tstat_flag) { + energy += ke_target * eta[0] + 0.5*eta_mass[0]*eta_dot[0]*eta_dot[0]; + for (ich = 1; ich < mtchain; ich++) + energy += kt * eta[ich] + 0.5*eta_mass[ich]*eta_dot[ich]*eta_dot[ich]; + } + + // barostat energy is equivalent to Eq. (8) in + // Martyna, Tuckerman, Tobias, Klein, Mol Phys, 87, 1117 + // Sum(0.5*p_omega^2/W + P*V), + // where N = natoms + // p_omega = W*omega_dot + // W = N*k*T/p_freq^2 + // sum is over barostatted dimensions + + if (pstat_flag) { + for (i = 0; i < 3; i++) + if (p_flag[i]) + energy += 0.5*omega_dot[i]*omega_dot[i]*omega_mass[i] + + p_hydro*(volume-vol0) / (pdim*nktv2p); + + if (pstyle == TRICLINIC) { + for (i = 3; i < 6; i++) + if (p_flag[i]) + energy += 0.5*omega_dot[i]*omega_dot[i]*omega_mass[i]; + } + + // extra contributions from thermostat chain for barostat + + if (mpchain) { + energy += lkt_press * etap[0] + 0.5*etap_mass[0]*etap_dot[0]*etap_dot[0]; + for (ich = 1; ich < mpchain; ich++) + energy += kt * etap[ich] + + 0.5*etap_mass[ich]*etap_dot[ich]*etap_dot[ich]; + } + + // extra contribution from strain energy + + if (deviatoric_flag) energy += compute_strain_energy(); + } + + return energy; +} + +/* ---------------------------------------------------------------------- + return a single element of the following vectors, in this order: + eta[tchain], eta_dot[tchain], omega[ndof], omega_dot[ndof] + etap[pchain], etap_dot[pchain], PE_eta[tchain], KE_eta_dot[tchain] + PE_omega[ndof], KE_omega_dot[ndof], PE_etap[pchain], KE_etap_dot[pchain] + PE_strain[1] + if no thermostat exists, related quantities are omitted from the list + if no barostat exists, related quantities are omitted from the list + ndof = 1,3,6 degrees of freedom for pstyle = ISO,ANISO,TRI +------------------------------------------------------------------------- */ + +double FixBocs::compute_vector(int n) +{ + int ilen; + + if (tstat_flag) { + ilen = mtchain; + if (n < ilen) return eta[n]; + n -= ilen; + ilen = mtchain; + if (n < ilen) return eta_dot[n]; + n -= ilen; + } + + if (pstat_flag) { + if (pstyle == ISO) { + ilen = 1; + if (n < ilen) return omega[n]; + n -= ilen; + } else if (pstyle == ANISO) { + ilen = 3; + if (n < ilen) return omega[n]; + n -= ilen; + } else { + ilen = 6; + if (n < ilen) return omega[n]; + n -= ilen; + } + + if (pstyle == ISO) { + ilen = 1; + if (n < ilen) return omega_dot[n]; + n -= ilen; + } else if (pstyle == ANISO) { + ilen = 3; + if (n < ilen) return omega_dot[n]; + n -= ilen; + } else { + ilen = 6; + if (n < ilen) return omega_dot[n]; + n -= ilen; + } + + if (mpchain) { + ilen = mpchain; + if (n < ilen) return etap[n]; + n -= ilen; + ilen = mpchain; + if (n < ilen) return etap_dot[n]; + n -= ilen; + } + } + + double volume; + double kt = boltz * t_target; + double lkt_press = kt; + int ich; + if (dimension == 3) volume = domain->xprd * domain->yprd * domain->zprd; + else volume = domain->xprd * domain->yprd; + + if (tstat_flag) { + ilen = mtchain; + if (n < ilen) { + ich = n; + if (ich == 0) + return ke_target * eta[0]; + else + return kt * eta[ich]; + } + n -= ilen; + ilen = mtchain; + if (n < ilen) { + ich = n; + if (ich == 0) + return 0.5*eta_mass[0]*eta_dot[0]*eta_dot[0]; + else + return 0.5*eta_mass[ich]*eta_dot[ich]*eta_dot[ich]; + } + n -= ilen; + } + + if (pstat_flag) { + if (pstyle == ISO) { + ilen = 1; + if (n < ilen) + return p_hydro*(volume-vol0) / nktv2p; + n -= ilen; + } else if (pstyle == ANISO) { + ilen = 3; + if (n < ilen) { + if (p_flag[n]) + return p_hydro*(volume-vol0) / (pdim*nktv2p); + else + return 0.0; + } + n -= ilen; + } else { + ilen = 6; + if (n < ilen) { + if (n > 2) return 0.0; + else if (p_flag[n]) + return p_hydro*(volume-vol0) / (pdim*nktv2p); + else + return 0.0; + } + n -= ilen; + } + + if (pstyle == ISO) { + ilen = 1; + if (n < ilen) + return pdim*0.5*omega_dot[n]*omega_dot[n]*omega_mass[n]; + n -= ilen; + } else if (pstyle == ANISO) { + ilen = 3; + if (n < ilen) { + if (p_flag[n]) + return 0.5*omega_dot[n]*omega_dot[n]*omega_mass[n]; + else return 0.0; + } + n -= ilen; + } else { + ilen = 6; + if (n < ilen) { + if (p_flag[n]) + return 0.5*omega_dot[n]*omega_dot[n]*omega_mass[n]; + else return 0.0; + } + n -= ilen; + } + + if (mpchain) { + ilen = mpchain; + if (n < ilen) { + ich = n; + if (ich == 0) return lkt_press * etap[0]; + else return kt * etap[ich]; + } + n -= ilen; + ilen = mpchain; + if (n < ilen) { + ich = n; + if (ich == 0) + return 0.5*etap_mass[0]*etap_dot[0]*etap_dot[0]; + else + return 0.5*etap_mass[ich]*etap_dot[ich]*etap_dot[ich]; + } + n -= ilen; + } + + if (deviatoric_flag) { + ilen = 1; + if (n < ilen) + return compute_strain_energy(); + n -= ilen; + } + } + + return 0.0; +} + +/* ---------------------------------------------------------------------- */ + +void FixBocs::reset_target(double t_new) +{ + t_target = t_start = t_stop = t_new; +} + +/* ---------------------------------------------------------------------- */ + +void FixBocs::reset_dt() +{ + dtv = update->dt; + dtf = 0.5 * update->dt * force->ftm2v; + dthalf = 0.5 * update->dt; + dt4 = 0.25 * update->dt; + dt8 = 0.125 * update->dt; + dto = dthalf; + + // If using respa, then remap is performed in innermost level + + if (strstr(update->integrate_style,"respa")) + dto = 0.5*step_respa[0]; + + if (pstat_flag) + pdrag_factor = 1.0 - (update->dt * p_freq_max * drag / nc_pchain); + + if (tstat_flag) + tdrag_factor = 1.0 - (update->dt * t_freq * drag / nc_tchain); +} + +/* ---------------------------------------------------------------------- + extract thermostat properties +------------------------------------------------------------------------- */ + +void *FixBocs::extract(const char *str, int &dim) +{ + dim=0; + if (tstat_flag && strcmp(str,"t_target") == 0) { + return &t_target; + } else if (tstat_flag && strcmp(str,"t_start") == 0) { + return &t_start; + } else if (tstat_flag && strcmp(str,"t_stop") == 0) { + return &t_stop; + } else if (tstat_flag && strcmp(str,"mtchain") == 0) { + return &mtchain; + } else if (pstat_flag && strcmp(str,"mpchain") == 0) { + return &mtchain; + } + dim=1; + if (tstat_flag && strcmp(str,"eta") == 0) { + return η + } else if (pstat_flag && strcmp(str,"etap") == 0) { + return η + } else if (pstat_flag && strcmp(str,"p_flag") == 0) { + return &p_flag; + } else if (pstat_flag && strcmp(str,"p_start") == 0) { + return &p_start; + } else if (pstat_flag && strcmp(str,"p_stop") == 0) { + return &p_stop; + } else if (pstat_flag && strcmp(str,"p_target") == 0) { + return &p_target; + } + return NULL; +} + +/* ---------------------------------------------------------------------- + perform half-step update of chain thermostat variables +------------------------------------------------------------------------- */ + +void FixBocs::nhc_temp_integrate() +{ + int ich; + double expfac; + double kecurrent = tdof * boltz * t_current; + + // Update masses, to preserve initial freq, if flag set + + if (eta_mass_flag) { + eta_mass[0] = tdof * boltz * t_target / (t_freq*t_freq); + for (int ich = 1; ich < mtchain; ich++) + eta_mass[ich] = boltz * t_target / (t_freq*t_freq); + } + + if (eta_mass[0] > 0.0) + eta_dotdot[0] = (kecurrent - ke_target)/eta_mass[0]; + else eta_dotdot[0] = 0.0; + + double ncfac = 1.0/nc_tchain; + for (int iloop = 0; iloop < nc_tchain; iloop++) { + + for (ich = mtchain-1; ich > 0; ich--) { + expfac = exp(-ncfac*dt8*eta_dot[ich+1]); + eta_dot[ich] *= expfac; + eta_dot[ich] += eta_dotdot[ich] * ncfac*dt4; + eta_dot[ich] *= tdrag_factor; + eta_dot[ich] *= expfac; + } + + expfac = exp(-ncfac*dt8*eta_dot[1]); + eta_dot[0] *= expfac; + eta_dot[0] += eta_dotdot[0] * ncfac*dt4; + eta_dot[0] *= tdrag_factor; + eta_dot[0] *= expfac; + + factor_eta = exp(-ncfac*dthalf*eta_dot[0]); + nh_v_temp(); + + // rescale temperature due to velocity scaling + // should not be necessary to explicitly recompute the temperature + + t_current *= factor_eta*factor_eta; + kecurrent = tdof * boltz * t_current; + + if (eta_mass[0] > 0.0) + eta_dotdot[0] = (kecurrent - ke_target)/eta_mass[0]; + else eta_dotdot[0] = 0.0; + + for (ich = 0; ich < mtchain; ich++) + eta[ich] += ncfac*dthalf*eta_dot[ich]; + + eta_dot[0] *= expfac; + eta_dot[0] += eta_dotdot[0] * ncfac*dt4; + eta_dot[0] *= expfac; + + for (ich = 1; ich < mtchain; ich++) { + expfac = exp(-ncfac*dt8*eta_dot[ich+1]); + eta_dot[ich] *= expfac; + eta_dotdot[ich] = (eta_mass[ich-1]*eta_dot[ich-1]*eta_dot[ich-1] + - boltz * t_target)/eta_mass[ich]; + eta_dot[ich] += eta_dotdot[ich] * ncfac*dt4; + eta_dot[ich] *= expfac; + } + } +} + +/* ---------------------------------------------------------------------- + perform half-step update of chain thermostat variables for barostat + scale barostat velocities +------------------------------------------------------------------------- */ + +void FixBocs::nhc_press_integrate() +{ + int ich,i; + double expfac,factor_etap,kecurrent; + double kt = boltz * t_target; + double lkt_press = kt; + + // Update masses, to preserve initial freq, if flag set + + if (omega_mass_flag) { + double nkt = atom->natoms * kt; + for (int i = 0; i < 3; i++) + if (p_flag[i]) + omega_mass[i] = nkt/(p_freq[i]*p_freq[i]); + + if (pstyle == TRICLINIC) { + for (int i = 3; i < 6; i++) + if (p_flag[i]) omega_mass[i] = nkt/(p_freq[i]*p_freq[i]); + } + } + + if (etap_mass_flag) { + if (mpchain) { + etap_mass[0] = boltz * t_target / (p_freq_max*p_freq_max); + for (int ich = 1; ich < mpchain; ich++) + etap_mass[ich] = boltz * t_target / (p_freq_max*p_freq_max); + for (int ich = 1; ich < mpchain; ich++) + etap_dotdot[ich] = + (etap_mass[ich-1]*etap_dot[ich-1]*etap_dot[ich-1] - + boltz * t_target) / etap_mass[ich]; + } + } + + kecurrent = 0.0; + for (i = 0; i < 3; i++) + if (p_flag[i]) kecurrent += omega_mass[i]*omega_dot[i]*omega_dot[i]; + + if (pstyle == TRICLINIC) { + for (i = 3; i < 6; i++) + if (p_flag[i]) kecurrent += omega_mass[i]*omega_dot[i]*omega_dot[i]; + } + + etap_dotdot[0] = (kecurrent - lkt_press)/etap_mass[0]; + + double ncfac = 1.0/nc_pchain; + for (int iloop = 0; iloop < nc_pchain; iloop++) { + + for (ich = mpchain-1; ich > 0; ich--) { + expfac = exp(-ncfac*dt8*etap_dot[ich+1]); + etap_dot[ich] *= expfac; + etap_dot[ich] += etap_dotdot[ich] * ncfac*dt4; + etap_dot[ich] *= pdrag_factor; + etap_dot[ich] *= expfac; + } + + expfac = exp(-ncfac*dt8*etap_dot[1]); + etap_dot[0] *= expfac; + etap_dot[0] += etap_dotdot[0] * ncfac*dt4; + etap_dot[0] *= pdrag_factor; + etap_dot[0] *= expfac; + + for (ich = 0; ich < mpchain; ich++) + etap[ich] += ncfac*dthalf*etap_dot[ich]; + + factor_etap = exp(-ncfac*dthalf*etap_dot[0]); + for (i = 0; i < 3; i++) + if (p_flag[i]) omega_dot[i] *= factor_etap; + + if (pstyle == TRICLINIC) { + for (i = 3; i < 6; i++) + if (p_flag[i]) omega_dot[i] *= factor_etap; + } + + kecurrent = 0.0; + for (i = 0; i < 3; i++) + if (p_flag[i]) kecurrent += omega_mass[i]*omega_dot[i]*omega_dot[i]; + + if (pstyle == TRICLINIC) { + for (i = 3; i < 6; i++) + if (p_flag[i]) kecurrent += omega_mass[i]*omega_dot[i]*omega_dot[i]; + } + + etap_dotdot[0] = (kecurrent - lkt_press)/etap_mass[0]; + + etap_dot[0] *= expfac; + etap_dot[0] += etap_dotdot[0] * ncfac*dt4; + etap_dot[0] *= expfac; + + for (ich = 1; ich < mpchain; ich++) { + expfac = exp(-ncfac*dt8*etap_dot[ich+1]); + etap_dot[ich] *= expfac; + etap_dotdot[ich] = + (etap_mass[ich-1]*etap_dot[ich-1]*etap_dot[ich-1] - boltz*t_target) / + etap_mass[ich]; + etap_dot[ich] += etap_dotdot[ich] * ncfac*dt4; + etap_dot[ich] *= expfac; + } + } +} + +/* ---------------------------------------------------------------------- + perform half-step barostat scaling of velocities +-----------------------------------------------------------------------*/ + +void FixBocs::nh_v_press() +{ + double factor[3]; + double **v = atom->v; + int *mask = atom->mask; + int nlocal = atom->nlocal; + if (igroup == atom->firstgroup) nlocal = atom->nfirst; + + factor[0] = exp(-dt4*(omega_dot[0]+mtk_term2)); + factor[1] = exp(-dt4*(omega_dot[1]+mtk_term2)); + factor[2] = exp(-dt4*(omega_dot[2]+mtk_term2)); + + if (which == NOBIAS) { + for (int i = 0; i < nlocal; i++) { + if (mask[i] & groupbit) { + v[i][0] *= factor[0]; + v[i][1] *= factor[1]; + v[i][2] *= factor[2]; + if (pstyle == TRICLINIC) { + v[i][0] += -dthalf*(v[i][1]*omega_dot[5] + v[i][2]*omega_dot[4]); + v[i][1] += -dthalf*v[i][2]*omega_dot[3]; + } + v[i][0] *= factor[0]; + v[i][1] *= factor[1]; + v[i][2] *= factor[2]; + } + } + } else if (which == BIAS) { + for (int i = 0; i < nlocal; i++) { + if (mask[i] & groupbit) { + temperature->remove_bias(i,v[i]); + v[i][0] *= factor[0]; + v[i][1] *= factor[1]; + v[i][2] *= factor[2]; + if (pstyle == TRICLINIC) { + v[i][0] += -dthalf*(v[i][1]*omega_dot[5] + v[i][2]*omega_dot[4]); + v[i][1] += -dthalf*v[i][2]*omega_dot[3]; + } + v[i][0] *= factor[0]; + v[i][1] *= factor[1]; + v[i][2] *= factor[2]; + temperature->restore_bias(i,v[i]); + } + } + } +} + +/* ---------------------------------------------------------------------- + perform half-step update of velocities +-----------------------------------------------------------------------*/ + +void FixBocs::nve_v() +{ + double dtfm; + double **v = atom->v; + double **f = atom->f; + double *rmass = atom->rmass; + double *mass = atom->mass; + int *type = atom->type; + int *mask = atom->mask; + int nlocal = atom->nlocal; + if (igroup == atom->firstgroup) nlocal = atom->nfirst; + + if (rmass) { + for (int i = 0; i < nlocal; i++) { + if (mask[i] & groupbit) { + 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]; + } + } + } else { + for (int i = 0; i < nlocal; i++) { + if (mask[i] & groupbit) { + dtfm = dtf / mass[type[i]]; + v[i][0] += dtfm*f[i][0]; + v[i][1] += dtfm*f[i][1]; + v[i][2] += dtfm*f[i][2]; + } + } + } +} + +/* ---------------------------------------------------------------------- + perform full-step update of positions +-----------------------------------------------------------------------*/ + +void FixBocs::nve_x() +{ + double **x = atom->x; + double **v = atom->v; + int *mask = atom->mask; + int nlocal = atom->nlocal; + if (igroup == atom->firstgroup) nlocal = atom->nfirst; + + // x update by full step only for atoms in group + + for (int i = 0; i < nlocal; i++) { + if (mask[i] & groupbit) { + x[i][0] += dtv * v[i][0]; + x[i][1] += dtv * v[i][1]; + x[i][2] += dtv * v[i][2]; + } + } +} + +/* ---------------------------------------------------------------------- + perform half-step thermostat scaling of velocities +-----------------------------------------------------------------------*/ + +void FixBocs::nh_v_temp() +{ + double **v = atom->v; + int *mask = atom->mask; + int nlocal = atom->nlocal; + if (igroup == atom->firstgroup) nlocal = atom->nfirst; + + if (which == NOBIAS) { + for (int i = 0; i < nlocal; i++) { + if (mask[i] & groupbit) { + v[i][0] *= factor_eta; + v[i][1] *= factor_eta; + v[i][2] *= factor_eta; + } + } + } else if (which == BIAS) { + for (int i = 0; i < nlocal; i++) { + if (mask[i] & groupbit) { + temperature->remove_bias(i,v[i]); + v[i][0] *= factor_eta; + v[i][1] *= factor_eta; + v[i][2] *= factor_eta; + temperature->restore_bias(i,v[i]); + } + } + } +} + +/* ---------------------------------------------------------------------- + compute sigma tensor + needed whenever p_target or h0_inv changes +-----------------------------------------------------------------------*/ + +void FixBocs::compute_sigma() +{ + // if nreset_h0 > 0, reset vol0 and h0_inv + // every nreset_h0 timesteps + + if (nreset_h0 > 0) { + int delta = update->ntimestep - update->beginstep; + if (delta % nreset_h0 == 0) { + if (dimension == 3) vol0 = domain->xprd * domain->yprd * domain->zprd; + else vol0 = domain->xprd * domain->yprd; + h0_inv[0] = domain->h_inv[0]; + h0_inv[1] = domain->h_inv[1]; + h0_inv[2] = domain->h_inv[2]; + h0_inv[3] = domain->h_inv[3]; + h0_inv[4] = domain->h_inv[4]; + h0_inv[5] = domain->h_inv[5]; + } + } + + // generate upper-triangular half of + // sigma = vol0*h0inv*(p_target-p_hydro)*h0inv^t + // units of sigma are are PV/L^2 e.g. atm.A + // + // [ 0 5 4 ] [ 0 5 4 ] [ 0 5 4 ] [ 0 - - ] + // [ 5 1 3 ] = [ - 1 3 ] [ 5 1 3 ] [ 5 1 - ] + // [ 4 3 2 ] [ - - 2 ] [ 4 3 2 ] [ 4 3 2 ] + + sigma[0] = + vol0*(h0_inv[0]*((p_target[0]-p_hydro)*h0_inv[0] + + p_target[5]*h0_inv[5]+p_target[4]*h0_inv[4]) + + h0_inv[5]*(p_target[5]*h0_inv[0] + + (p_target[1]-p_hydro)*h0_inv[5]+p_target[3]*h0_inv[4]) + + h0_inv[4]*(p_target[4]*h0_inv[0]+p_target[3]*h0_inv[5] + + (p_target[2]-p_hydro)*h0_inv[4])); + sigma[1] = + vol0*(h0_inv[1]*((p_target[1]-p_hydro)*h0_inv[1] + + p_target[3]*h0_inv[3]) + + h0_inv[3]*(p_target[3]*h0_inv[1] + + (p_target[2]-p_hydro)*h0_inv[3])); + sigma[2] = + vol0*(h0_inv[2]*((p_target[2]-p_hydro)*h0_inv[2])); + sigma[3] = + vol0*(h0_inv[1]*(p_target[3]*h0_inv[2]) + + h0_inv[3]*((p_target[2]-p_hydro)*h0_inv[2])); + sigma[4] = + vol0*(h0_inv[0]*(p_target[4]*h0_inv[2]) + + h0_inv[5]*(p_target[3]*h0_inv[2]) + + h0_inv[4]*((p_target[2]-p_hydro)*h0_inv[2])); + sigma[5] = + vol0*(h0_inv[0]*(p_target[5]*h0_inv[1]+p_target[4]*h0_inv[3]) + + h0_inv[5]*((p_target[1]-p_hydro)*h0_inv[1]+p_target[3]*h0_inv[3]) + + h0_inv[4]*(p_target[3]*h0_inv[1]+(p_target[2]-p_hydro)*h0_inv[3])); +} + +/* ---------------------------------------------------------------------- + compute strain energy +-----------------------------------------------------------------------*/ + +double FixBocs::compute_strain_energy() +{ + // compute strain energy = 0.5*Tr(sigma*h*h^t) in energy units + + double* h = domain->h; + double d0,d1,d2; + + d0 = + sigma[0]*(h[0]*h[0]+h[5]*h[5]+h[4]*h[4]) + + sigma[5]*( h[1]*h[5]+h[3]*h[4]) + + sigma[4]*( h[2]*h[4]); + d1 = + sigma[5]*( h[5]*h[1]+h[4]*h[3]) + + sigma[1]*( h[1]*h[1]+h[3]*h[3]) + + sigma[3]*( h[2]*h[3]); + d2 = + sigma[4]*( h[4]*h[2]) + + sigma[3]*( h[3]*h[2]) + + sigma[2]*( h[2]*h[2]); + + double energy = 0.5*(d0+d1+d2)/nktv2p; + return energy; +} + +/* ---------------------------------------------------------------------- + compute deviatoric barostat force = h*sigma*h^t +-----------------------------------------------------------------------*/ + +void FixBocs::compute_deviatoric() +{ + // generate upper-triangular part of h*sigma*h^t + // units of fdev are are PV, e.g. atm*A^3 + // [ 0 5 4 ] [ 0 5 4 ] [ 0 5 4 ] [ 0 - - ] + // [ 5 1 3 ] = [ - 1 3 ] [ 5 1 3 ] [ 5 1 - ] + // [ 4 3 2 ] [ - - 2 ] [ 4 3 2 ] [ 4 3 2 ] + + double* h = domain->h; + + fdev[0] = + h[0]*(sigma[0]*h[0]+sigma[5]*h[5]+sigma[4]*h[4]) + + h[5]*(sigma[5]*h[0]+sigma[1]*h[5]+sigma[3]*h[4]) + + h[4]*(sigma[4]*h[0]+sigma[3]*h[5]+sigma[2]*h[4]); + fdev[1] = + h[1]*( sigma[1]*h[1]+sigma[3]*h[3]) + + h[3]*( sigma[3]*h[1]+sigma[2]*h[3]); + fdev[2] = + h[2]*( sigma[2]*h[2]); + fdev[3] = + h[1]*( sigma[3]*h[2]) + + h[3]*( sigma[2]*h[2]); + fdev[4] = + h[0]*( sigma[4]*h[2]) + + h[5]*( sigma[3]*h[2]) + + h[4]*( sigma[2]*h[2]); + fdev[5] = + h[0]*( sigma[5]*h[1]+sigma[4]*h[3]) + + h[5]*( sigma[1]*h[1]+sigma[3]*h[3]) + + h[4]*( sigma[3]*h[1]+sigma[2]*h[3]); +} + +/* ---------------------------------------------------------------------- + compute target temperature and kinetic energy +-----------------------------------------------------------------------*/ + +void FixBocs::compute_temp_target() +{ + double delta = update->ntimestep - update->beginstep; + if (delta != 0.0) delta /= update->endstep - update->beginstep; + + t_target = t_start + delta * (t_stop-t_start); + ke_target = tdof * boltz * t_target; +} + +/* ---------------------------------------------------------------------- + compute hydrostatic target pressure +-----------------------------------------------------------------------*/ + +void FixBocs::compute_press_target() +{ + double delta = update->ntimestep - update->beginstep; + if (delta != 0.0) delta /= update->endstep - update->beginstep; + + p_hydro = 0.0; + for (int i = 0; i < 3; i++) + if (p_flag[i]) { + p_target[i] = p_start[i] + delta * (p_stop[i]-p_start[i]); + p_hydro += p_target[i]; + } + if (pdim > 0) p_hydro /= pdim; + + if (pstyle == TRICLINIC) + for (int i = 3; i < 6; i++) + p_target[i] = p_start[i] + delta * (p_stop[i]-p_start[i]); + + // if deviatoric, recompute sigma each time p_target changes + + if (deviatoric_flag) compute_sigma(); +} + +/* ---------------------------------------------------------------------- + update omega_dot, omega +-----------------------------------------------------------------------*/ + +void FixBocs::nh_omega_dot() +{ + double f_omega,volume; + + if (dimension == 3) volume = domain->xprd*domain->yprd*domain->zprd; + else volume = domain->xprd*domain->yprd; + + if (deviatoric_flag) compute_deviatoric(); + + mtk_term1 = 0.0; + if (mtk_flag) { + if (pstyle == ISO) { + mtk_term1 = tdof * boltz * t_current; + mtk_term1 /= pdim * atom->natoms; + } else { + double *mvv_current = temperature->vector; + for (int i = 0; i < 3; i++) + if (p_flag[i]) + mtk_term1 += mvv_current[i]; + mtk_term1 /= pdim * atom->natoms; + } + } + + for (int i = 0; i < 3; i++) + if (p_flag[i]) { + f_omega = (p_current[i]-p_hydro)*volume / + (omega_mass[i] * nktv2p) + mtk_term1 / omega_mass[i]; + if (deviatoric_flag) f_omega -= fdev[i]/(omega_mass[i] * nktv2p); + omega_dot[i] += f_omega*dthalf; + omega_dot[i] *= pdrag_factor; + } + + mtk_term2 = 0.0; + if (mtk_flag) { + for (int i = 0; i < 3; i++) + if (p_flag[i]) + mtk_term2 += omega_dot[i]; + if (pdim > 0) mtk_term2 /= pdim * atom->natoms; + } + + if (pstyle == TRICLINIC) { + for (int i = 3; i < 6; i++) { + if (p_flag[i]) { + f_omega = p_current[i]*volume/(omega_mass[i] * nktv2p); + if (deviatoric_flag) + f_omega -= fdev[i]/(omega_mass[i] * nktv2p); + omega_dot[i] += f_omega*dthalf; + omega_dot[i] *= pdrag_factor; + } + } + } +} + +/* ---------------------------------------------------------------------- + if any tilt ratios exceed limits, set flip = 1 and compute new tilt values + do not flip in x or y if non-periodic (can tilt but not flip) + this is b/c the box length would be changed (dramatically) by flip + if yz tilt exceeded, adjust C vector by one B vector + if xz tilt exceeded, adjust C vector by one A vector + if xy tilt exceeded, adjust B vector by one A vector + check yz first since it may change xz, then xz check comes after + if any flip occurs, create new box in domain + image_flip() adjusts image flags due to box shape change induced by flip + remap() puts atoms outside the new box back into the new box + perform irregular on atoms in lamda coords to migrate atoms to new procs + important that image_flip comes before remap, since remap may change + image flags to new values, making eqs in doc of Domain:image_flip incorrect +------------------------------------------------------------------------- */ + +void FixBocs::pre_exchange() +{ + double xprd = domain->xprd; + double yprd = domain->yprd; + + // flip is only triggered when tilt exceeds 0.5 by DELTAFLIP + // this avoids immediate re-flipping due to tilt oscillations + + double xtiltmax = (0.5+DELTAFLIP)*xprd; + double ytiltmax = (0.5+DELTAFLIP)*yprd; + + int flipxy,flipxz,flipyz; + flipxy = flipxz = flipyz = 0; + + if (domain->yperiodic) { + if (domain->yz < -ytiltmax) { + domain->yz += yprd; + domain->xz += domain->xy; + flipyz = 1; + } else if (domain->yz >= ytiltmax) { + domain->yz -= yprd; + domain->xz -= domain->xy; + flipyz = -1; + } + } + + if (domain->xperiodic) { + if (domain->xz < -xtiltmax) { + domain->xz += xprd; + flipxz = 1; + } else if (domain->xz >= xtiltmax) { + domain->xz -= xprd; + flipxz = -1; + } + if (domain->xy < -xtiltmax) { + domain->xy += xprd; + flipxy = 1; + } else if (domain->xy >= xtiltmax) { + domain->xy -= xprd; + flipxy = -1; + } + } + + int flip = 0; + if (flipxy || flipxz || flipyz) flip = 1; + + if (flip) { + domain->set_global_box(); + domain->set_local_box(); + + domain->image_flip(flipxy,flipxz,flipyz); + + double **x = atom->x; + imageint *image = atom->image; + int nlocal = atom->nlocal; + for (int i = 0; i < nlocal; i++) domain->remap(x[i],image[i]); + + domain->x2lamda(atom->nlocal); + irregular->migrate_atoms(); + domain->lamda2x(atom->nlocal); + } +} + +/* ---------------------------------------------------------------------- + memory usage of Irregular +------------------------------------------------------------------------- */ + +double FixBocs::memory_usage() +{ + double bytes = 0.0; + if (irregular) bytes += irregular->memory_usage(); + return bytes; +} diff --git a/src/USER-BOCS/fix_bocs.h b/src/USER-BOCS/fix_bocs.h new file mode 100644 index 0000000000000000000000000000000000000000..34090e4f3ac5cfc624dbc22e1ae77b905c4ee153 --- /dev/null +++ b/src/USER-BOCS/fix_bocs.h @@ -0,0 +1,302 @@ +/* -*- 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. +------------------------------------------------------------------------- + USER-BOCS written by: Nicholas J. H. Dunn and Michael R. DeLyser + from The Pennsylvania State University +------------------------------------------------------------------------- */ + + +#ifdef FIX_CLASS + +FixStyle(bocs,FixBocs) + +#else + +#ifndef LMP_FIX_BOCS_H +#define LMP_FIX_BOCS_H + +#include "fix.h" + + +namespace LAMMPS_NS { + +class FixBocs : public Fix { + public: + FixBocs(class LAMMPS *, int, char **); // MRD NJD + virtual ~FixBocs(); // MRD NJD + int setmask(); + virtual void init(); + virtual void setup(int); + virtual void initial_integrate(int); + virtual void final_integrate(); + void initial_integrate_respa(int, int, int); + void final_integrate_respa(int, int); + virtual void pre_exchange(); + double compute_scalar(); + virtual double compute_vector(int); + void write_restart(FILE *); + virtual int pack_restart_data(double *); // pack restart data + virtual void restart(char *); + int modify_param(int, char **); + void reset_target(double); + void reset_dt(); + virtual void *extract(const char*,int &); + double memory_usage(); + + + protected: + int dimension,which; + double dtv,dtf,dthalf,dt4,dt8,dto; + double boltz,nktv2p,tdof; + double vol0; // reference volume + double t0; // reference temperature + // used for barostat mass + double t_start,t_stop; + double t_current,t_target,ke_target; + double t_freq; + + int tstat_flag; // 1 if control T + int pstat_flag; // 1 if control P + + int pstyle,pcouple,allremap; + int p_flag[6]; // 1 if control P on this dim, 0 if not + double p_start[6],p_stop[6]; + double p_freq[6],p_target[6]; + double omega[6],omega_dot[6]; + double omega_mass[6]; + double p_current[6]; + double drag,tdrag_factor; // drag factor on particle thermostat + double pdrag_factor; // drag factor on barostat + int kspace_flag; // 1 if KSpace invoked, 0 if not + int nrigid; // number of rigid fixes + int dilate_group_bit; // mask for dilation group + int *rfix; // indices of rigid fixes + char *id_dilate; // group name to dilate + class Irregular *irregular; // for migrating atoms after box flips + +// MRD NJD + int p_basis_type; + int p_match_flag; + double vavg; + int N_mol; + int N_p_match; + double *p_match_coeffs; + double ** splines; + int spline_length; + + + int nlevels_respa; + double *step_respa; + + char *id_temp,*id_press; + class Compute *temperature,*pressure; + int tcomputeflag,pcomputeflag; // 1 = compute was created by fix + // 0 = created externally + + double *eta,*eta_dot; // chain thermostat for particles + double *eta_dotdot; + double *eta_mass; + int mtchain; // length of chain + int mtchain_default_flag; // 1 = mtchain is default + + double *etap; // chain thermostat for barostat + double *etap_dot; + double *etap_dotdot; + double *etap_mass; + int mpchain; // length of chain + + int mtk_flag; // 0 if using Hoover barostat + int pdim; // number of barostatted dims + double p_freq_max; // maximum barostat frequency + + double p_hydro; // hydrostatic target pressure + + int nc_tchain,nc_pchain; + double factor_eta; + double sigma[6]; // scaled target stress + double fdev[6]; // deviatoric force on barostat + int deviatoric_flag; // 0 if target stress tensor is hydrostatic + double h0_inv[6]; // h_inv of reference (zero strain) box + int nreset_h0; // interval for resetting h0 + + double mtk_term1,mtk_term2; // Martyna-Tobias-Klein corrections + + int eta_mass_flag; // 1 if eta_mass updated, 0 if not. + int omega_mass_flag; // 1 if omega_mass updated, 0 if not. + int etap_mass_flag; // 1 if etap_mass updated, 0 if not. + int dipole_flag; // 1 if dipole is updated, 0 if not. + int dlm_flag; // 1 if using the DLM rotational integrator, 0 if not + + int scaleyz; // 1 if yz scaled with lz + int scalexz; // 1 if xz scaled with lz + int scalexy; // 1 if xy scaled with ly + int flipflag; // 1 if box flips are invoked as needed + + int pre_exchange_flag; // set if pre_exchange needed for box flips + + double fixedpoint[3]; // location of dilation fixed-point + + void couple(); + virtual void remap(); + void nhc_temp_integrate(); + void nhc_press_integrate(); + + int read_F_table(char *, int); + void build_cubic_splines(double **); + + virtual void nve_x(); // may be overwritten by child classes + virtual void nve_v(); + virtual void nh_v_press(); + virtual void nh_v_temp(); + virtual void compute_temp_target(); + virtual int size_restart_global(); + + void compute_sigma(); + void compute_deviatoric(); + double compute_strain_energy(); + void compute_press_target(); + void nh_omega_dot(); +}; + +} + +#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: Target temperature for fix bocs cannot be 0.0 + +Self-explanatory. + +E: Invalid fix bocs command for a 2d simulation + +Cannot control z dimension in a 2d model. + +E: Fix bocs dilate group ID does not exist + +Self-explanatory. + +E: Invalid fix bocs command pressure settings + +If multiple dimensions are coupled, those dimensions must be +specified. + +E: Cannot use fix bocs on a non-periodic dimension + +When specifying a diagonal pressure component, the dimension must be +periodic. + +E: Cannot use fix bocs on a 2nd non-periodic dimension + +When specifying an off-diagonal pressure component, the 2nd of the two +dimensions must be periodic. E.g. if the xy component is specified, +then the y dimension must be periodic. + +E: Cannot use fix bocs with yz scaling when z is non-periodic dimension + +The 2nd dimension in the barostatted tilt factor must be periodic. + +E: Cannot use fix bocs with xz scaling when z is non-periodic dimension + +The 2nd dimension in the barostatted tilt factor must be periodic. + +E: Cannot use fix bocs with xy scaling when y is non-periodic dimension + +The 2nd dimension in the barostatted tilt factor must be periodic. + +E: Cannot use fix bocs with both yz dynamics and yz scaling + +Self-explanatory. + +E: Cannot use fix bocs with both xz dynamics and xz scaling + +Self-explanatory. + +E: Cannot use fix bocs with both xy dynamics and xy scaling + +Self-explanatory. + +E: Can not specify Pxy/Pxz/Pyz in fix bocs with non-triclinic box + +Only triclinic boxes can be used with off-diagonal pressure components. +See the region prism command for details. + +E: Invalid fix bocs pressure settings + +Settings for coupled dimensions must be the same. + +E: Using update dipole flag requires atom style sphere + +Self-explanatory. + +E: Using update dipole flag requires atom attribute mu + +Self-explanatory. + +E: The dlm flag must be used with update dipole + +Self-explanatory. + +E: Fix bocs damping parameters must be > 0.0 + +Self-explanatory. + +E: Cannot use fix npt and fix deform on same component of stress tensor + +This would be changing the same box dimension twice. + +E: Temperature ID for fix bocs does not exist + +Self-explanatory. + +E: Pressure ID for fix bocs does not exist + +Self-explanatory. + +E: Fix bocs has tilted box too far in one step - periodic cell is too far from equilibrium state + +Self-explanatory. The change in the box tilt is too extreme +on a short timescale. + +E: Could not find fix_modify temperature ID + +The compute ID for computing temperature does not exist. + +E: Fix_modify temperature ID does not compute temperature + +The compute ID assigned to the fix must compute temperature. + +W: Temperature for fix modify is not for group all + +The temperature compute is being used with a pressure calculation +which does operate on group all, so this may be inconsistent. + +E: Pressure ID for fix modify does not exist + +Self-explanatory. + +E: Could not find fix_modify pressure ID + +The compute ID for computing pressure does not exist. + +E: Fix_modify pressure ID does not compute pressure + +The compute ID assigned to the fix must compute pressure. + +*/ diff --git a/src/USER-CGDNA/bond_oxdna2_fene.cpp b/src/USER-CGDNA/bond_oxdna2_fene.cpp index b2e1afb073d5af6a71a61428a2b64249d4af3166..39cbb04f88e1aad84a1b181757bf1b1b83d92f19 100644 --- a/src/USER-CGDNA/bond_oxdna2_fene.cpp +++ b/src/USER-CGDNA/bond_oxdna2_fene.cpp @@ -14,8 +14,8 @@ Contributing author: Oliver Henrich (University of Strathclyde, Glasgow) ------------------------------------------------------------------------- */ -#include -#include +#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 e5d3a3e45242d29b21ba2c5683082d82f0e98f08..47d8d8f60b3854632e13bdf7358200f596fef98c 100644 --- a/src/USER-CGDNA/bond_oxdna_fene.cpp +++ b/src/USER-CGDNA/bond_oxdna_fene.cpp @@ -14,8 +14,8 @@ Contributing author: Oliver Henrich (University of Strathclyde, Glasgow) ------------------------------------------------------------------------- */ -#include -#include +#include +#include #include "bond_oxdna_fene.h" #include "atom.h" #include "neighbor.h" @@ -242,7 +242,7 @@ void BondOxdnaFene::coeff(int narg, char **arg) void BondOxdnaFene::init_style() { /* special bonds have to be lj = 0 1 1 and coul = 1 1 1 to exclude - the ss excluded volume interaction between nearest neighbours */ + the ss excluded volume interaction between nearest neighbors */ force->special_lj[1] = 0.0; force->special_lj[2] = 1.0; diff --git a/src/USER-CGDNA/fix_nve_dot.cpp b/src/USER-CGDNA/fix_nve_dot.cpp index 5cdda597037e238de9da6d234d799728f04baf64..63f38a4e12af727939cb5848153315f44f43b662 100644 --- a/src/USER-CGDNA/fix_nve_dot.cpp +++ b/src/USER-CGDNA/fix_nve_dot.cpp @@ -14,9 +14,9 @@ Contributing author: Oliver Henrich (University of Strathclyde, Glasgow) ------------------------------------------------------------------------- */ -#include -#include -#include +#include +#include +#include #include "fix_nve_dot.h" #include "math_extra.h" #include "atom.h" diff --git a/src/USER-CGDNA/fix_nve_dotc_langevin.cpp b/src/USER-CGDNA/fix_nve_dotc_langevin.cpp index fae515897c0ad4c07d019cf8c80284eec1d46f44..90f7b1caebbc56e5849e47b72895128b22afcbbb 100644 --- a/src/USER-CGDNA/fix_nve_dotc_langevin.cpp +++ b/src/USER-CGDNA/fix_nve_dotc_langevin.cpp @@ -15,9 +15,9 @@ Contributing author: Oliver Henrich (University of Strathclyde, Glasgow) ------------------------------------------------------------------------- */ -#include -#include -#include +#include +#include +#include #include "fix_nve_dotc_langevin.h" #include "math_extra.h" #include "atom.h" diff --git a/src/USER-CGDNA/mf_oxdna.h b/src/USER-CGDNA/mf_oxdna.h index 56055d5facab082760d899473fec3cbe667b5f8f..c63a37cde2ab4b8a9fa07e6b556181e947e4c997 100644 --- a/src/USER-CGDNA/mf_oxdna.h +++ b/src/USER-CGDNA/mf_oxdna.h @@ -14,7 +14,7 @@ #ifndef MF_OXDNA_H #define MF_OXDNA_H -#include +#include #include "math_extra.h" namespace MFOxdna { diff --git a/src/USER-CGDNA/pair_oxdna2_coaxstk.cpp b/src/USER-CGDNA/pair_oxdna2_coaxstk.cpp index 8312d92bc06f788c8c87d76bb063fd6ad4ef1e67..151e7526924f508677c0c4648203b1091db9a4a0 100644 --- a/src/USER-CGDNA/pair_oxdna2_coaxstk.cpp +++ b/src/USER-CGDNA/pair_oxdna2_coaxstk.cpp @@ -14,10 +14,10 @@ Contributing author: Oliver Henrich (University of Strathclyde, Glasgow) ------------------------------------------------------------------------- */ -#include -#include -#include -#include +#include +#include +#include +#include #include "pair_oxdna2_coaxstk.h" #include "mf_oxdna.h" #include "atom.h" @@ -157,7 +157,7 @@ void PairOxdna2Coaxstk::compute(int eflag, int vflag) numneigh = list->numneigh; firstneigh = list->firstneigh; - // loop over pair interaction neighbours of my atoms + // loop over pair interaction neighbors of my atoms for (ia = 0; ia < anum; ia++) { @@ -183,7 +183,7 @@ void PairOxdna2Coaxstk::compute(int eflag, int vflag) for (ib = 0; ib < bnum; ib++) { b = blist[ib]; - factor_lj = special_lj[sbmask(b)]; // = 0 for nearest neighbours + factor_lj = special_lj[sbmask(b)]; // = 0 for nearest neighbors b &= NEIGHMASK; btype = type[b]; diff --git a/src/USER-CGDNA/pair_oxdna2_dh.cpp b/src/USER-CGDNA/pair_oxdna2_dh.cpp index 48914239251e282239e8510a4355b31148e05dae..974ade89c1230b3e6fff154855cdf8c7d13513f3 100644 --- a/src/USER-CGDNA/pair_oxdna2_dh.cpp +++ b/src/USER-CGDNA/pair_oxdna2_dh.cpp @@ -14,10 +14,10 @@ Contributing author: Oliver Henrich (University of Strathclyde, Glasgow) ------------------------------------------------------------------------- */ -#include -#include -#include -#include +#include +#include +#include +#include #include "pair_oxdna2_dh.h" #include "mf_oxdna.h" #include "atom.h" @@ -122,7 +122,7 @@ void PairOxdna2Dh::compute(int eflag, int vflag) numneigh = list->numneigh; firstneigh = list->firstneigh; - // loop over pair interaction neighbours of my atoms + // loop over pair interaction neighbors of my atoms for (ia = 0; ia < anum; ia++) { @@ -145,7 +145,7 @@ void PairOxdna2Dh::compute(int eflag, int vflag) for (ib = 0; ib < bnum; ib++) { b = blist[ib]; - factor_lj = special_lj[sbmask(b)]; // = 0 for nearest neighbours + factor_lj = special_lj[sbmask(b)]; // = 0 for nearest neighbors b &= NEIGHMASK; btype = type[b]; @@ -186,7 +186,7 @@ void PairOxdna2Dh::compute(int eflag, int vflag) } - // knock out nearest-neighbour interaction between adjacent backbone sites + // knock out nearest-neighbor interaction between adjacent backbone sites fpair *= factor_lj; evdwl *= factor_lj; diff --git a/src/USER-CGDNA/pair_oxdna2_excv.cpp b/src/USER-CGDNA/pair_oxdna2_excv.cpp index e1b18e1487a0d41e079e4dc50fbaf1d1a2bf13aa..4329fbe0715a2e10d22302aa0b2b2e462047a299 100644 --- a/src/USER-CGDNA/pair_oxdna2_excv.cpp +++ b/src/USER-CGDNA/pair_oxdna2_excv.cpp @@ -14,10 +14,10 @@ Contributing author: Oliver Henrich (University of Strathclyde, Glasgow) ------------------------------------------------------------------------- */ -#include -#include -#include -#include +#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 3b98db32012d2cf4a99eafa3ef2a8545b8f7cbf7..f479572aa6ed5a070150cf2516a9012fbb96c471 100644 --- a/src/USER-CGDNA/pair_oxdna2_stk.cpp +++ b/src/USER-CGDNA/pair_oxdna2_stk.cpp @@ -14,10 +14,10 @@ Contributing author: Oliver Henrich (University of Strathclyde, Glasgow) ------------------------------------------------------------------------- */ -#include -#include -#include -#include +#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 4a1af83884d3a19fa10a82d905ae395b26a23639..0eb75fbb43b39b6bf29c460e2ebc0680d1cb66cb 100644 --- a/src/USER-CGDNA/pair_oxdna_coaxstk.cpp +++ b/src/USER-CGDNA/pair_oxdna_coaxstk.cpp @@ -14,10 +14,10 @@ Contributing author: Oliver Henrich (University of Strathclyde, Glasgow) ------------------------------------------------------------------------- */ -#include -#include -#include -#include +#include +#include +#include +#include #include "pair_oxdna_coaxstk.h" #include "mf_oxdna.h" #include "atom.h" @@ -163,7 +163,7 @@ void PairOxdnaCoaxstk::compute(int eflag, int vflag) numneigh = list->numneigh; firstneigh = list->firstneigh; - // loop over pair interaction neighbours of my atoms + // loop over pair interaction neighbors of my atoms for (ia = 0; ia < anum; ia++) { @@ -189,7 +189,7 @@ void PairOxdnaCoaxstk::compute(int eflag, int vflag) for (ib = 0; ib < bnum; ib++) { b = blist[ib]; - factor_lj = special_lj[sbmask(b)]; // = 0 for nearest neighbours + factor_lj = special_lj[sbmask(b)]; // = 0 for nearest neighbors b &= NEIGHMASK; btype = type[b]; diff --git a/src/USER-CGDNA/pair_oxdna_excv.cpp b/src/USER-CGDNA/pair_oxdna_excv.cpp index 09ae13f1b2618fadf28b2f48bf6f7775ec56eea5..e2b8334078cc4c0fae3dc34dcceb6bdefc662657 100644 --- a/src/USER-CGDNA/pair_oxdna_excv.cpp +++ b/src/USER-CGDNA/pair_oxdna_excv.cpp @@ -14,10 +14,10 @@ Contributing author: Oliver Henrich (University of Strathclyde, Glasgow) ------------------------------------------------------------------------- */ -#include -#include -#include -#include +#include +#include +#include +#include #include "pair_oxdna_excv.h" #include "mf_oxdna.h" #include "atom.h" @@ -152,7 +152,7 @@ void PairOxdnaExcv::compute(int eflag, int vflag) numneigh = list->numneigh; firstneigh = list->firstneigh; - // loop over pair interaction neighbours of my atoms + // loop over pair interaction neighbors of my atoms for (ia = 0; ia < anum; ia++) { @@ -179,7 +179,7 @@ void PairOxdnaExcv::compute(int eflag, int vflag) for (ib = 0; ib < bnum; ib++) { b = blist[ib]; - factor_lj = special_lj[sbmask(b)]; // = 0 for nearest neighbours + factor_lj = special_lj[sbmask(b)]; // = 0 for nearest neighbors b &= NEIGHMASK; btype = type[b]; @@ -222,7 +222,7 @@ void PairOxdnaExcv::compute(int eflag, int vflag) evdwl = F3(rsq_ss,cutsq_ss_ast[atype][btype],cut_ss_c[atype][btype],lj1_ss[atype][btype], lj2_ss[atype][btype],epsilon_ss[atype][btype],b_ss[atype][btype],fpair); - // knock out nearest-neighbour interaction between ss + // knock out nearest-neighbor interaction between ss fpair *= factor_lj; evdwl *= factor_lj; diff --git a/src/USER-CGDNA/pair_oxdna_hbond.cpp b/src/USER-CGDNA/pair_oxdna_hbond.cpp index 1caf320ef1b0105cc336cfa8c2125203bb4c3337..ce1bfe036a3842ae07ceb2baf3b42eef63bd3c7b 100644 --- a/src/USER-CGDNA/pair_oxdna_hbond.cpp +++ b/src/USER-CGDNA/pair_oxdna_hbond.cpp @@ -14,10 +14,10 @@ Contributing author: Oliver Henrich (University of Strathclyde, Glasgow) ------------------------------------------------------------------------- */ -#include -#include -#include -#include +#include +#include +#include +#include #include "pair_oxdna_hbond.h" #include "mf_oxdna.h" #include "atom.h" @@ -168,7 +168,7 @@ void PairOxdnaHbond::compute(int eflag, int vflag) numneigh = list->numneigh; firstneigh = list->firstneigh; - // loop over pair interaction neighbours of my atoms + // loop over pair interaction neighbors of my atoms for (ia = 0; ia < anum; ia++) { @@ -188,7 +188,7 @@ void PairOxdnaHbond::compute(int eflag, int vflag) for (ib = 0; ib < bnum; ib++) { b = blist[ib]; - factor_lj = special_lj[sbmask(b)]; // = 0 for nearest neighbours + factor_lj = special_lj[sbmask(b)]; // = 0 for nearest neighbors b &= NEIGHMASK; btype = type[b]; diff --git a/src/USER-CGDNA/pair_oxdna_stk.cpp b/src/USER-CGDNA/pair_oxdna_stk.cpp index 9c3a11b9b712eef4dbaecf71c709fd0e9766d255..8c4498e627cfecb185289cf1834e74fab1f484a8 100644 --- a/src/USER-CGDNA/pair_oxdna_stk.cpp +++ b/src/USER-CGDNA/pair_oxdna_stk.cpp @@ -14,10 +14,10 @@ Contributing author: Oliver Henrich (University of Strathclyde, Glasgow) ------------------------------------------------------------------------- */ -#include -#include -#include -#include +#include +#include +#include +#include #include "pair_oxdna_stk.h" #include "mf_oxdna.h" #include "atom.h" diff --git a/src/USER-CGDNA/pair_oxdna_xstk.cpp b/src/USER-CGDNA/pair_oxdna_xstk.cpp index c14993dc36a4e8186e93d6f841b1697489edf386..e5b9de81c09c4450584434a8dfa006c826675c0a 100644 --- a/src/USER-CGDNA/pair_oxdna_xstk.cpp +++ b/src/USER-CGDNA/pair_oxdna_xstk.cpp @@ -14,10 +14,10 @@ Contributing author: Oliver Henrich (University of Strathclyde, Glasgow) ------------------------------------------------------------------------- */ -#include -#include -#include -#include +#include +#include +#include +#include #include "pair_oxdna_xstk.h" #include "mf_oxdna.h" #include "atom.h" @@ -160,7 +160,7 @@ void PairOxdnaXstk::compute(int eflag, int vflag) numneigh = list->numneigh; firstneigh = list->firstneigh; - // loop over pair interaction neighbours of my atoms + // loop over pair interaction neighbors of my atoms for (ia = 0; ia < anum; ia++) { @@ -180,7 +180,7 @@ void PairOxdnaXstk::compute(int eflag, int vflag) for (ib = 0; ib < bnum; ib++) { b = blist[ib]; - factor_lj = special_lj[sbmask(b)]; // = 0 for nearest neighbours + factor_lj = special_lj[sbmask(b)]; // = 0 for nearest neighbors b &= NEIGHMASK; btype = type[b]; diff --git a/src/USER-CGSDK/angle_sdk.cpp b/src/USER-CGSDK/angle_sdk.cpp index a4f979961f2e3cdc6b91a9b42103427a088a4ec9..6b8245b4914447cab0426d9a3a95633105c119b2 100644 --- a/src/USER-CGSDK/angle_sdk.cpp +++ b/src/USER-CGSDK/angle_sdk.cpp @@ -18,8 +18,8 @@ lj/sdk potential for coarse grained MD simulations. ------------------------------------------------------------------------- */ -#include -#include +#include +#include #include "angle_sdk.h" #include "atom.h" #include "neighbor.h" diff --git a/src/USER-CGSDK/angle_sdk.h b/src/USER-CGSDK/angle_sdk.h index a5d917e57cfcc0e281d05b86335db9eb017709c8..293004ad4d51b4e159dce696cd8d7aea89caf063 100644 --- a/src/USER-CGSDK/angle_sdk.h +++ b/src/USER-CGSDK/angle_sdk.h @@ -20,7 +20,7 @@ AngleStyle(sdk,AngleSDK) #ifndef LMP_ANGLE_SDK_H #define LMP_ANGLE_SDK_H -#include +#include #include "angle.h" namespace LAMMPS_NS { diff --git a/src/USER-CGSDK/lj_sdk_common.h b/src/USER-CGSDK/lj_sdk_common.h index f8f7a66ce9bd9570af5528b29aab1d4e627dbfef..c1f2cf215a68966884b90778bcd09319fe5e935b 100644 --- a/src/USER-CGSDK/lj_sdk_common.h +++ b/src/USER-CGSDK/lj_sdk_common.h @@ -19,7 +19,7 @@ #ifndef LMP_LJ_SDK_COMMON_H #define LMP_LJ_SDK_COMMON_H -#include +#include namespace LAMMPS_NS { namespace LJSDKParms { diff --git a/src/USER-CGSDK/pair_lj_sdk.cpp b/src/USER-CGSDK/pair_lj_sdk.cpp index 56e56c9605cc82b3e20352dfc2303b948b486771..cbcba7f6b260dc777bd40433aaa5610d33be0800 100644 --- a/src/USER-CGSDK/pair_lj_sdk.cpp +++ b/src/USER-CGSDK/pair_lj_sdk.cpp @@ -16,10 +16,10 @@ This style is a simplified re-implementation of the CG/CMM pair style ------------------------------------------------------------------------- */ -#include -#include -#include -#include +#include +#include +#include +#include #include "pair_lj_sdk.h" #include "atom.h" #include "comm.h" diff --git a/src/USER-CGSDK/pair_lj_sdk_coul_long.cpp b/src/USER-CGSDK/pair_lj_sdk_coul_long.cpp index 4c9e42f778431810a2c78af21ed4a7b702484c2d..1d93363e207f185d7460b3f038fb1042a82eb2b4 100644 --- a/src/USER-CGSDK/pair_lj_sdk_coul_long.cpp +++ b/src/USER-CGSDK/pair_lj_sdk_coul_long.cpp @@ -16,10 +16,10 @@ This style is a simplified re-implementation of the CG/CMM pair style ------------------------------------------------------------------------- */ -#include -#include -#include -#include +#include +#include +#include +#include #include "pair_lj_sdk_coul_long.h" #include "atom.h" #include "comm.h" diff --git a/src/USER-CGSDK/pair_lj_sdk_coul_msm.cpp b/src/USER-CGSDK/pair_lj_sdk_coul_msm.cpp index ddca927a681bf94752825621698f0949bbd8112a..c4882fdbdb9e13b2ae953b5f666a8c95c92d4d63 100644 --- a/src/USER-CGSDK/pair_lj_sdk_coul_msm.cpp +++ b/src/USER-CGSDK/pair_lj_sdk_coul_msm.cpp @@ -16,10 +16,10 @@ This style is a simplified re-implementation of the CG/CMM pair style ------------------------------------------------------------------------- */ -#include -#include -#include -#include +#include +#include +#include +#include #include "pair_lj_sdk_coul_msm.h" #include "atom.h" #include "comm.h" diff --git a/src/USER-COLVARS/colvarproxy_lammps.cpp b/src/USER-COLVARS/colvarproxy_lammps.cpp index c5b9e5a60c860355a4a5960089b8f288b9566841..ff74602b418e0bce8cfdfbc3f60692f4a8aeeebc 100644 --- a/src/USER-COLVARS/colvarproxy_lammps.cpp +++ b/src/USER-COLVARS/colvarproxy_lammps.cpp @@ -133,6 +133,8 @@ colvarproxy_lammps::colvarproxy_lammps(LAMMPS_NS::LAMMPS *lmp, void colvarproxy_lammps::init(const char *conf_file) { + version_int = get_version_from_string(COLVARPROXY_VERSION); + // create the colvarmodule instance colvars = new colvarmodule(this); @@ -203,6 +205,25 @@ double colvarproxy_lammps::compute() } previous_step = _lmp->update->ntimestep; + unit_cell_x.set(_lmp->domain->xprd, 0.0, 0.0); + unit_cell_y.set(0.0, _lmp->domain->yprd, 0.0); + unit_cell_z.set(0.0, 0.0, _lmp->domain->zprd); + + if (_lmp->domain->xperiodic == 0 && _lmp->domain->yperiodic == 0 && + _lmp->domain->zperiodic == 0) { + boundaries_type = boundaries_non_periodic; + reset_pbc_lattice(); + } else if ((_lmp->domain->nonperiodic == 0) && + (_lmp->domain->dimension == 3) && + (_lmp->domain->triclinic == 0)) { + // Orthogonal unit cell + boundaries_type = boundaries_pbc_ortho; + colvarproxy_system::update_pbc_lattice(); + // It is safer to let LAMMPS deal with high-tilt triclinic boxes + } else { + boundaries_type = boundaries_unsupported; + } + if (cvm::debug()) { cvm::log(std::string(cvm::line_marker)+ "colvarproxy_lammps, step no. "+cvm::to_str(colvars->it)+"\n"+ @@ -263,8 +284,10 @@ bool colvarproxy_lammps::deserialize_status(std::string &rst) } } + cvm::rvector colvarproxy_lammps::position_distance(cvm::atom_pos const &pos1, cvm::atom_pos const &pos2) + const { double xtmp = pos2.x - pos1.x; double ytmp = pos2.y - pos1.y; @@ -273,28 +296,6 @@ cvm::rvector colvarproxy_lammps::position_distance(cvm::atom_pos const &pos1, return cvm::rvector(xtmp, ytmp, ztmp); } -cvm::real colvarproxy_lammps::position_dist2(cvm::atom_pos const &pos1, - cvm::atom_pos const &pos2) -{ - double xtmp = pos2.x - pos1.x; - double ytmp = pos2.y - pos1.y; - double ztmp = pos2.z - pos1.z; - _lmp->domain->minimum_image(xtmp,ytmp,ztmp); - return cvm::real(xtmp*xtmp + ytmp*ytmp + ztmp*ztmp); -} - - -void colvarproxy_lammps::select_closest_image(cvm::atom_pos &pos, - cvm::atom_pos const &ref) -{ - double xtmp = pos.x - ref.x; - double ytmp = pos.y - ref.y; - double ztmp = pos.z - ref.z; - _lmp->domain->minimum_image(xtmp,ytmp,ztmp); - pos.x = ref.x + xtmp; - pos.y = ref.y + ytmp; - pos.z = ref.z + ztmp; -} void colvarproxy_lammps::log(std::string const &message) { @@ -308,12 +309,14 @@ void colvarproxy_lammps::log(std::string const &message) } } + void colvarproxy_lammps::error(std::string const &message) { // In LAMMPS, all errors are fatal fatal_error(message); } + void colvarproxy_lammps::fatal_error(std::string const &message) { log(message); @@ -321,13 +324,6 @@ void colvarproxy_lammps::fatal_error(std::string const &message) "Fatal error in the collective variables module.\n"); } -void colvarproxy_lammps::exit(std::string const &message) -{ - log(message); - log("Request to exit the simulation made.\n"); - do_exit=true; -} - int colvarproxy_lammps::backup_file(char const *filename) { @@ -342,10 +338,12 @@ int colvarproxy_lammps::backup_file(char const *filename) // multi-replica support -void colvarproxy_lammps::replica_comm_barrier() { +void colvarproxy_lammps::replica_comm_barrier() +{ MPI_Barrier(inter_comm); } + int colvarproxy_lammps::replica_comm_recv(char* msg_data, int buf_len, int src_rep) { @@ -359,6 +357,7 @@ int colvarproxy_lammps::replica_comm_recv(char* msg_data, return retval; } + int colvarproxy_lammps::replica_comm_send(char* msg_data, int msg_len, int dest_rep) { diff --git a/src/USER-COLVARS/colvarproxy_lammps.h b/src/USER-COLVARS/colvarproxy_lammps.h index af2aa04dfc890a55443588435206279280581b6c..cdd86cbd16a04c50d176b720e676b36b0615d2a6 100644 --- a/src/USER-COLVARS/colvarproxy_lammps.h +++ b/src/USER-COLVARS/colvarproxy_lammps.h @@ -120,14 +120,9 @@ class colvarproxy_lammps : public colvarproxy { void log(std::string const &message); void error(std::string const &message); void fatal_error(std::string const &message); - void exit(std::string const &message); cvm::rvector position_distance(cvm::atom_pos const &pos1, - cvm::atom_pos const &pos2); - cvm::real position_dist2(cvm::atom_pos const &pos1, - cvm::atom_pos const &pos2); - void select_closest_image(cvm::atom_pos &pos, - cvm::atom_pos const &ref_pos); + cvm::atom_pos const &pos2) const; int backup_file(char const *filename); diff --git a/src/USER-COLVARS/colvarproxy_lammps_version.h b/src/USER-COLVARS/colvarproxy_lammps_version.h index 79f77dad4e8284d4a7c0c771f0e464626a8f828d..0d451212b261cb07bb9aa2a66f9c8ad7e0918ce5 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 "2017-12-01" +#define COLVARPROXY_VERSION "2018-04-29" // 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/fix_colvars.cpp b/src/USER-COLVARS/fix_colvars.cpp index 84b3ee07d62533c07c6cbc7cb68bb675a5b07d3a..0e4e151c3dcca2bc43e4033df9127480f46a1318 100644 --- a/src/USER-COLVARS/fix_colvars.cpp +++ b/src/USER-COLVARS/fix_colvars.cpp @@ -24,10 +24,10 @@ Contributing author: Axel Kohlmeyer (Temple U) ------------------------------------------------------------------------- */ -#include -#include -#include -#include +#include +#include +#include +#include #include #include "fix_colvars.h" diff --git a/src/USER-COLVARS/group_ndx.cpp b/src/USER-COLVARS/group_ndx.cpp index 50769180390cec50f8f693444393506ca990522c..450c250ffa4fcbe23aef74fd10cda0887ecfb3dd 100644 --- a/src/USER-COLVARS/group_ndx.cpp +++ b/src/USER-COLVARS/group_ndx.cpp @@ -23,8 +23,8 @@ #include "memory.h" #include "error.h" -#include -#include +#include +#include using namespace LAMMPS_NS; diff --git a/src/USER-COLVARS/ndx_group.cpp b/src/USER-COLVARS/ndx_group.cpp index c7972e372ec940989ec58d2c727cf2ce4aba5a78..7b46364f189cc1e9ebef74bb965c8670affadbd2 100644 --- a/src/USER-COLVARS/ndx_group.cpp +++ b/src/USER-COLVARS/ndx_group.cpp @@ -24,9 +24,9 @@ #include "force.h" #include "error.h" -#include -#include -#include +#include +#include +#include using namespace LAMMPS_NS; #define BUFLEN 4096 diff --git a/src/USER-DIFFRACTION/compute_saed.cpp b/src/USER-DIFFRACTION/compute_saed.cpp index cc1dec96fa14872b1d792a5fab15847c796e825f..3d09955275c1b2de3aa7219b0a162151ce49de29 100644 --- a/src/USER-DIFFRACTION/compute_saed.cpp +++ b/src/USER-DIFFRACTION/compute_saed.cpp @@ -16,8 +16,10 @@ ------------------------------------------------------------------------- */ #include -#include -#include +#include +#include +#include +#include #include "math_const.h" #include "compute_saed.h" #include "compute_saed_consts.h" @@ -29,8 +31,6 @@ #include "citeme.h" #include "memory.h" #include "error.h" -#include -#include using namespace LAMMPS_NS; using namespace MathConst; diff --git a/src/USER-DIFFRACTION/compute_xrd.cpp b/src/USER-DIFFRACTION/compute_xrd.cpp index 380629ffb9ea6c48f9c8113af305ea30b182a8ab..4d5cccdc504433afa39802bbd9d1a1ef1f5fd48b 100644 --- a/src/USER-DIFFRACTION/compute_xrd.cpp +++ b/src/USER-DIFFRACTION/compute_xrd.cpp @@ -17,8 +17,10 @@ ------------------------------------------------------------------------- */ #include -#include -#include +#include +#include +#include +#include #include "math_const.h" #include "compute_xrd.h" #include "compute_xrd_consts.h" @@ -30,8 +32,6 @@ #include "citeme.h" #include "memory.h" #include "error.h" -#include -#include using namespace LAMMPS_NS; using namespace MathConst; diff --git a/src/USER-DIFFRACTION/fix_saed_vtk.cpp b/src/USER-DIFFRACTION/fix_saed_vtk.cpp index dfa63f630ad5537b7700a25b330d9e17af1d1185..45bfeca48bd2269d0579672994fca283d8495ae1 100644 --- a/src/USER-DIFFRACTION/fix_saed_vtk.cpp +++ b/src/USER-DIFFRACTION/fix_saed_vtk.cpp @@ -16,8 +16,9 @@ Incorporating SAED: Shawn Coleman (Arkansas) ------------------------------------------------------------------------- */ -#include -#include +#include +#include +#include #include "fix_saed_vtk.h" #include "update.h" #include "modify.h" @@ -29,7 +30,6 @@ #include "memory.h" #include "error.h" #include "force.h" -#include #include "domain.h" using namespace LAMMPS_NS; diff --git a/src/USER-DIFFRACTION/fix_saed_vtk.h b/src/USER-DIFFRACTION/fix_saed_vtk.h index fa379e7216ca9dfdb366969e3aca3c481559d3b4..2fc09c781c8da9644959fd5ddba30588556cf162 100644 --- a/src/USER-DIFFRACTION/fix_saed_vtk.h +++ b/src/USER-DIFFRACTION/fix_saed_vtk.h @@ -20,7 +20,7 @@ FixStyle(saed/vtk,FixSAEDVTK) #ifndef LMP_FIX_SAED_VTK_H #define LMP_FIX_SAED_VTK_H -#include +#include #include "fix.h" namespace LAMMPS_NS { diff --git a/src/USER-DPD/atom_vec_dpd.cpp b/src/USER-DPD/atom_vec_dpd.cpp index 477ed05e3f04c85cd0ba864bb56b0bd76200df5b..6c8e6f91a9b4ea16b778228731be2eb3d2639f94 100644 --- a/src/USER-DPD/atom_vec_dpd.cpp +++ b/src/USER-DPD/atom_vec_dpd.cpp @@ -15,7 +15,7 @@ Contributing author: James Larentzos (U.S. Army Research Laboratory) ------------------------------------------------------------------------- */ -#include +#include #include "atom_vec_dpd.h" #include "atom.h" #include "comm.h" diff --git a/src/USER-DPD/compute_dpd_atom.cpp b/src/USER-DPD/compute_dpd_atom.cpp index c8231ddabc231cb806c7af2289168a8486826a1a..78f842a68f2f2b351c672ba68bf4dbd6f4628057 100644 --- a/src/USER-DPD/compute_dpd_atom.cpp +++ b/src/USER-DPD/compute_dpd_atom.cpp @@ -15,9 +15,9 @@ Contributing author: James Larentzos (U.S. Army Research Laboratory) ------------------------------------------------------------------------- */ -#include -#include -#include +#include +#include +#include #include "compute_dpd_atom.h" #include "atom.h" #include "update.h" diff --git a/src/USER-DPD/fix_dpd_energy.cpp b/src/USER-DPD/fix_dpd_energy.cpp index 475e12f02fb10a30acf23e5ed27ed4605b5995fc..d89ea7759a8fbae547aeb4d724b3b8c82ca73472 100644 --- a/src/USER-DPD/fix_dpd_energy.cpp +++ b/src/USER-DPD/fix_dpd_energy.cpp @@ -11,8 +11,8 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include -#include +#include +#include #include "fix_dpd_energy.h" #include "atom.h" #include "force.h" diff --git a/src/USER-DPD/fix_eos_cv.cpp b/src/USER-DPD/fix_eos_cv.cpp index 7a2d278fe4766d73e20163704d3ffbcd23632fad..919e6829f30fd91d5a8d2580ac64c0b276f44ea0 100644 --- a/src/USER-DPD/fix_eos_cv.cpp +++ b/src/USER-DPD/fix_eos_cv.cpp @@ -15,8 +15,8 @@ Contributing author: James Larentzos (U.S. Army Research Laboratory) ------------------------------------------------------------------------- */ -#include -#include +#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 c17a9721084d11968b5ae7ae9771fb1789c9fc97..e57a3788bf733f8f57ec12a54ea5b501eb0c0e4f 100644 --- a/src/USER-DPD/fix_eos_table.cpp +++ b/src/USER-DPD/fix_eos_table.cpp @@ -15,8 +15,8 @@ Contributing author: James Larentzos (U.S. Army Research Laboratory) ------------------------------------------------------------------------- */ -#include -#include +#include +#include #include "fix_eos_table.h" #include "atom.h" #include "error.h" diff --git a/src/USER-DPD/fix_eos_table_rx.cpp b/src/USER-DPD/fix_eos_table_rx.cpp index c9a705446a0f6b54d2870590366a350b1a70ed04..73144c0a0f9423196b106ba67ebd917f56bf8c77 100644 --- a/src/USER-DPD/fix_eos_table_rx.cpp +++ b/src/USER-DPD/fix_eos_table_rx.cpp @@ -15,15 +15,15 @@ Contributing author: James Larentzos (U.S. Army Research Laboratory) ------------------------------------------------------------------------- */ -#include -#include +#include +#include +#include #include "fix_eos_table_rx.h" #include "atom.h" #include "error.h" #include "force.h" #include "memory.h" #include "comm.h" -#include #include "modify.h" #define MAXLINE 1024 @@ -774,7 +774,7 @@ void FixEOStableRX::temperature_lookup(int id, double ui, double &thetai) // Apply the Secant Method for(it=0; itone(FLERR,"NaN detected in secant solver."); + if(std::isnan(f1) || std::isnan(f2)) error->one(FLERR,"NaN detected in secant solver."); temp = t1; temp = MAX(temp,tb->lo); temp = MIN(temp,tb->hi); @@ -794,7 +794,7 @@ void FixEOStableRX::temperature_lookup(int id, double ui, double &thetai) if(it==maxit){ char str[256]; sprintf(str,"Maxit exceeded in secant solver: id=%d ui=%lf thetai=%lf t1=%lf t2=%lf f1=%lf f2=%lf\n",id,ui,thetai,t1,t2,f1,f2); - if(isnan(f1) || isnan(f2) || isnan(ui) || isnan(thetai) || isnan(t1) || isnan(t2)) + if(std::isnan(f1) || std::isnan(f2) || std::isnan(ui) || std::isnan(thetai) || std::isnan(t1) || std::isnan(t2)) error->one(FLERR,"NaN detected in secant solver."); error->one(FLERR,str); } diff --git a/src/USER-DPD/fix_rx.cpp b/src/USER-DPD/fix_rx.cpp index 0d0ec2a75b0ebba55b74162ac39fbcc71a517356..c370f8abe6ebe0fb35fae63730a909ae44dcf335 100644 --- a/src/USER-DPD/fix_rx.cpp +++ b/src/USER-DPD/fix_rx.cpp @@ -11,10 +11,11 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include -#include -#include -#include +#include +#include +#include +#include +#include // DBL_EPSILON #include "fix_rx.h" #include "atom.h" #include "error.h" @@ -31,10 +32,8 @@ #include "math_special.h" #include "pair_dpd_fdt_energy.h" -#include // DBL_EPSILON #include // std::vector<> #include // std::max -#include // std::fmod using namespace LAMMPS_NS; using namespace FixConst; @@ -261,6 +260,7 @@ void FixRX::post_constructor() error->all(FLERR,"fix rx cannot be combined with fix property/atom"); char **tmpspecies = new char*[maxspecies]; + int tmpmaxstrlen = 0; for(int jj=0; jj < maxspecies; jj++) tmpspecies[jj] = NULL; @@ -321,6 +321,7 @@ void FixRX::post_constructor() error->all(FLERR,"Exceeded the maximum number of species permitted in fix rx."); tmpspecies[nUniqueSpecies] = new char[strlen(word)+1]; strcpy(tmpspecies[nUniqueSpecies],word); + tmpmaxstrlen = MAX(tmpmaxstrlen,strlen(word)); nUniqueSpecies++; } word = strtok(NULL, " \t\n\r\f"); @@ -355,9 +356,9 @@ void FixRX::post_constructor() newarg2[0] = id_fix_species_old; newarg2[1] = group->names[igroup]; newarg2[2] = (char *) "property/atom"; + char *str1 = new char[tmpmaxstrlen+3]; + char *str2 = new char[tmpmaxstrlen+6]; for(int ii=0; ii -#include -#include +#include +#include +#include +#include #include "fix_shardlow.h" #include "atom.h" #include "force.h" #include "update.h" #include "respa.h" #include "error.h" -#include #include "atom_vec.h" #include "comm.h" #include "neighbor.h" diff --git a/src/USER-DPD/fix_shardlow.h b/src/USER-DPD/fix_shardlow.h index 21f7569a233de12032311d80b0144ef7fa8acf1e..67e4b8f32e8383ada4448c87434edaf5ea3a0b7a 100644 --- a/src/USER-DPD/fix_shardlow.h +++ b/src/USER-DPD/fix_shardlow.h @@ -22,7 +22,6 @@ FixStyle(shardlow,FixShardlow) #include "fix.h" #include "random_external_state.h" -#include namespace LAMMPS_NS { diff --git a/src/USER-DPD/nbin_ssa.h b/src/USER-DPD/nbin_ssa.h index 12a572b94caab73125eb01887b89849189c11826..c738391d67f3cc0980b80dd8e275e1cb24c2ace4 100644 --- a/src/USER-DPD/nbin_ssa.h +++ b/src/USER-DPD/nbin_ssa.h @@ -22,8 +22,8 @@ NBinStyle(ssa, #ifndef LMP_NBIN_SSA_H #define LMP_NBIN_SSA_H +#include #include "nbin_standard.h" -#include "math.h" #include "error.h" namespace LAMMPS_NS { @@ -54,7 +54,7 @@ class NBinSSA : public NBinStandard { { int ix,iy,iz; - if (!ISFINITE(x) || !ISFINITE(y) || !ISFINITE(z)) + if (!std::isfinite(x) || !std::isfinite(y) || !std::isfinite(z)) error->one(FLERR,"Non-numeric positions - simulation unstable"); if (x >= bboxhi_[0]) diff --git a/src/USER-DPD/pair_dpd_fdt.cpp b/src/USER-DPD/pair_dpd_fdt.cpp index 95908c556d12156e3e8e0d14e8f672be66655890..aeade16e7cb0525a5e1ce75dba723832646b7ad4 100644 --- a/src/USER-DPD/pair_dpd_fdt.cpp +++ b/src/USER-DPD/pair_dpd_fdt.cpp @@ -15,10 +15,10 @@ Contributing author: James Larentzos (U.S. Army Research Laboratory) ------------------------------------------------------------------------- */ -#include -#include -#include -#include +#include +#include +#include +#include #include "atom.h" #include "atom_vec.h" #include "comm.h" diff --git a/src/USER-DPD/pair_dpd_fdt_energy.cpp b/src/USER-DPD/pair_dpd_fdt_energy.cpp index 32ac456b0fffede0ea5b4551877f6d1e001bb511..d1f3cceed4ca14db73014d7e252770b007d8db95 100644 --- a/src/USER-DPD/pair_dpd_fdt_energy.cpp +++ b/src/USER-DPD/pair_dpd_fdt_energy.cpp @@ -15,10 +15,10 @@ Contributing author: James Larentzos (U.S. Army Research Laboratory) ------------------------------------------------------------------------- */ -#include -#include -#include -#include +#include +#include +#include +#include #include "atom.h" #include "atom_vec.h" #include "comm.h" diff --git a/src/USER-DPD/pair_exp6_rx.cpp b/src/USER-DPD/pair_exp6_rx.cpp index 8b6fc9beed8e65836bb26350d1ecf8c48c02ed1d..057c8fa1190e00e61b718edc0f4d66f865cb43f0 100644 --- a/src/USER-DPD/pair_exp6_rx.cpp +++ b/src/USER-DPD/pair_exp6_rx.cpp @@ -11,10 +11,11 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include -#include -#include -#include +#include +#include +#include +#include +#include #include "pair_exp6_rx.h" #include "atom.h" #include "comm.h" @@ -26,7 +27,6 @@ #include "error.h" #include "modify.h" #include "fix.h" -#include using namespace LAMMPS_NS; using namespace MathConst; diff --git a/src/USER-DPD/pair_multi_lucy.cpp b/src/USER-DPD/pair_multi_lucy.cpp index 6f4104e93d0d45705891ccbc09667e7fbc8c40c7..3d204a849e3bfe1d70497f0c2c2340f48b3dab47 100644 --- a/src/USER-DPD/pair_multi_lucy.cpp +++ b/src/USER-DPD/pair_multi_lucy.cpp @@ -22,10 +22,10 @@ ------------------------------------------------------------------------------------------- */ #include -#include +#include #include "math_const.h" -#include -#include +#include +#include #include "pair_multi_lucy.h" #include "atom.h" #include "force.h" diff --git a/src/USER-DPD/pair_multi_lucy_rx.cpp b/src/USER-DPD/pair_multi_lucy_rx.cpp index 4628edbc127c41187ea750a5545b55f192c9592f..0070ca82d9c5eed5f07fa16defbf4b0da7944829 100644 --- a/src/USER-DPD/pair_multi_lucy_rx.cpp +++ b/src/USER-DPD/pair_multi_lucy_rx.cpp @@ -22,10 +22,10 @@ ------------------------------------------------------------------------------------------- */ #include -#include +#include #include "math_const.h" -#include -#include +#include +#include #include "pair_multi_lucy_rx.h" #include "atom.h" #include "force.h" diff --git a/src/USER-DPD/pair_table_rx.cpp b/src/USER-DPD/pair_table_rx.cpp index 89d09e73227bd3ed0c6d9f3e86714237fc98ae3d..221944edc5170612b0ae7a246f3dd7bc61e6a26d 100644 --- a/src/USER-DPD/pair_table_rx.cpp +++ b/src/USER-DPD/pair_table_rx.cpp @@ -16,9 +16,9 @@ ------------------------------------------------------------------------- */ #include -#include -#include -#include +#include +#include +#include #include "pair_table_rx.h" #include "atom.h" #include "force.h" diff --git a/src/USER-DPD/random_external_state.h b/src/USER-DPD/random_external_state.h index 47288d77fd86ed4a13f8f3ff717903b6adecde29..de017ee8bdbe0e3ddb7e8ec714920ace97f2c49f 100644 --- a/src/USER-DPD/random_external_state.h +++ b/src/USER-DPD/random_external_state.h @@ -63,7 +63,7 @@ #ifndef LMP_RANDOM_EXTERNALSTATE_H #define LMP_RANDOM_EXTERNALSTATE_H -#include +#include #include "accelerator_kokkos.h" diff --git a/src/USER-DRUDE/compute_temp_drude.cpp b/src/USER-DRUDE/compute_temp_drude.cpp index 44b727f6b7b95660abc4cba3a0812edffe5ccecc..27b525c07d4393fc9cb4709b3a1c67f8d6351c97 100644 --- a/src/USER-DRUDE/compute_temp_drude.cpp +++ b/src/USER-DRUDE/compute_temp_drude.cpp @@ -12,8 +12,8 @@ ------------------------------------------------------------------------- */ #include -#include -#include +#include +#include #include "compute_temp_drude.h" #include "atom.h" #include "update.h" diff --git a/src/USER-DRUDE/fix_drude.cpp b/src/USER-DRUDE/fix_drude.cpp index a38f9f1e669716981174f6035089ff93eef571a5..19fd775715822d040edf8b3bf4621902fbafb71d 100644 --- a/src/USER-DRUDE/fix_drude.cpp +++ b/src/USER-DRUDE/fix_drude.cpp @@ -11,8 +11,8 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include -#include +#include +#include #include "fix_drude.h" #include "atom.h" #include "comm.h" diff --git a/src/USER-DRUDE/fix_drude_transform.cpp b/src/USER-DRUDE/fix_drude_transform.cpp index adbfd324df302a244189c7ea38495824d38ba4fc..34742a0683311a8e1286b4e122897434d845209b 100644 --- a/src/USER-DRUDE/fix_drude_transform.cpp +++ b/src/USER-DRUDE/fix_drude_transform.cpp @@ -12,7 +12,8 @@ ------------------------------------------------------------------------- */ /** Fix Drude Transform ******************************************************/ -#include +#include +#include #include "fix_drude_transform.h" #include "atom.h" #include "domain.h" @@ -21,8 +22,6 @@ #include "modify.h" #include "force.h" -#include - using namespace LAMMPS_NS; using namespace FixConst; @@ -76,7 +75,7 @@ void FixDrudeTransform::setup(int) { if (!rmass) { if (!mcoeff) mcoeff = new double[ntypes+1]; - double mcoeff_loc[ntypes+1]; + double *mcoeff_loc = new double[ntypes+1]; for (int itype=0; itype<=ntypes; itype++) mcoeff_loc[itype] = 2.; // an impossible value: mcoeff is at most 1. for (int i=0; i::setup(int) { // mcoeff is 2 for non polarizable // 0 < mcoeff < 1 for drude // mcoeff < 0 for core + delete[] mcoeff_loc; } } @@ -314,6 +314,6 @@ void FixDrudeTransform::unpack_forward_comm(int n, int first, double *b } /* ---------------------------------------------------------------------- */ -template class FixDrudeTransform; -template class FixDrudeTransform; +template class LAMMPS_NS::FixDrudeTransform; +template class LAMMPS_NS::FixDrudeTransform; diff --git a/src/USER-DRUDE/fix_langevin_drude.cpp b/src/USER-DRUDE/fix_langevin_drude.cpp index d04adb022327de0e3822f47b246e37c73d870513..235c5d224ba8e1914e201b95055cf072d3c9b64b 100644 --- a/src/USER-DRUDE/fix_langevin_drude.cpp +++ b/src/USER-DRUDE/fix_langevin_drude.cpp @@ -11,9 +11,9 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include -#include -#include +#include +#include +#include #include "fix_langevin_drude.h" #include "atom.h" #include "force.h" diff --git a/src/USER-DRUDE/pair_lj_cut_thole_long.cpp b/src/USER-DRUDE/pair_lj_cut_thole_long.cpp index f78ced3d8bd96caaa35798db21f1bce5f19a05e2..ce5d3a92a9002af04c1e3cbae013bc0c605424a9 100644 --- a/src/USER-DRUDE/pair_lj_cut_thole_long.cpp +++ b/src/USER-DRUDE/pair_lj_cut_thole_long.cpp @@ -15,10 +15,10 @@ Contributing author: Paul Crozier (SNL) ------------------------------------------------------------------------- */ -#include -#include -#include -#include +#include +#include +#include +#include #include "pair_lj_cut_thole_long.h" #include "atom.h" #include "comm.h" diff --git a/src/USER-DRUDE/pair_thole.cpp b/src/USER-DRUDE/pair_thole.cpp index ace119ce523892b0ad7a8d52c0288f0bc0f725b4..8c20ee8c4208e7cd59377d184b99662444bf35bd 100644 --- a/src/USER-DRUDE/pair_thole.cpp +++ b/src/USER-DRUDE/pair_thole.cpp @@ -11,10 +11,10 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include -#include -#include -#include +#include +#include +#include +#include #include "pair_thole.h" #include "atom.h" #include "comm.h" diff --git a/src/USER-EFF/atom_vec_electron.cpp b/src/USER-EFF/atom_vec_electron.cpp index 56d61fd74f99ffb6c237ecfc2c0487bcd0d37569..1bc5387c9e20800a6c35809ed29a2587da6b2ed8 100644 --- a/src/USER-EFF/atom_vec_electron.cpp +++ b/src/USER-EFF/atom_vec_electron.cpp @@ -15,9 +15,9 @@ Contributing author: Andres Jaramillo-Botero (Caltech) ------------------------------------------------------------------------- */ -#include -#include -#include +#include +#include +#include #include "atom_vec_electron.h" #include "atom.h" #include "comm.h" diff --git a/src/USER-EFF/compute_ke_atom_eff.cpp b/src/USER-EFF/compute_ke_atom_eff.cpp index 8d03e97b0af4d653d3d1d4809009d60b868c664a..b1b87cd3df18d10d9dd1e366d1ed8fc849fd7909 100644 --- a/src/USER-EFF/compute_ke_atom_eff.cpp +++ b/src/USER-EFF/compute_ke_atom_eff.cpp @@ -15,9 +15,9 @@ Contributing author: Andres Jaramillo-Botero ------------------------------------------------------------------------- */ -#include -#include -#include +#include +#include +#include #include "compute_ke_atom_eff.h" #include "atom.h" #include "update.h" diff --git a/src/USER-EFF/compute_ke_eff.cpp b/src/USER-EFF/compute_ke_eff.cpp index 80c7192708fab9c6aebb39181cf4b27829ddd1e4..b4f571cb63718e8e425820961fb1ae62c4bea93c 100644 --- a/src/USER-EFF/compute_ke_eff.cpp +++ b/src/USER-EFF/compute_ke_eff.cpp @@ -16,8 +16,8 @@ ------------------------------------------------------------------------- */ #include -#include -#include +#include +#include #include "compute_ke_eff.h" #include "atom.h" #include "update.h" diff --git a/src/USER-EFF/compute_temp_deform_eff.cpp b/src/USER-EFF/compute_temp_deform_eff.cpp index 40e8e529c0ea2baf1a0ada81edd5b0cbe06356bb..53fb7683a76bcde71ecf5dcfd32270c48c877844 100644 --- a/src/USER-EFF/compute_temp_deform_eff.cpp +++ b/src/USER-EFF/compute_temp_deform_eff.cpp @@ -16,9 +16,9 @@ ------------------------------------------------------------------------- */ #include -#include -#include -#include +#include +#include +#include #include "compute_temp_deform_eff.h" #include "domain.h" #include "atom.h" diff --git a/src/USER-EFF/compute_temp_eff.cpp b/src/USER-EFF/compute_temp_eff.cpp index 251cdccaca7a83dc4cf2b866d075823d92b6892d..956461adf19489df4ad25c3c56812726c5a0a111 100644 --- a/src/USER-EFF/compute_temp_eff.cpp +++ b/src/USER-EFF/compute_temp_eff.cpp @@ -16,9 +16,9 @@ ------------------------------------------------------------------------- */ #include -#include -#include -#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 c0cd56f3a8d65c5b55d30108446cb3c58566e702..4548914ce13f5a349c0a6b00db726e5160c6cef3 100644 --- a/src/USER-EFF/compute_temp_region_eff.cpp +++ b/src/USER-EFF/compute_temp_region_eff.cpp @@ -16,9 +16,9 @@ ------------------------------------------------------------------------- */ #include -#include -#include -#include +#include +#include +#include #include "compute_temp_region_eff.h" #include "atom.h" #include "update.h" diff --git a/src/USER-EFF/fix_langevin_eff.cpp b/src/USER-EFF/fix_langevin_eff.cpp index 9584623fc3970e055ae9113d76b12e62cfccb1b9..2d0eef8e8573293af0ae480abb86898273d92a4a 100644 --- a/src/USER-EFF/fix_langevin_eff.cpp +++ b/src/USER-EFF/fix_langevin_eff.cpp @@ -16,9 +16,9 @@ ------------------------------------------------------------------------- */ #include -#include -#include -#include +#include +#include +#include #include "fix_langevin_eff.h" #include "math_extra.h" #include "atom.h" diff --git a/src/USER-EFF/fix_nh_eff.cpp b/src/USER-EFF/fix_nh_eff.cpp index 464498969ebf6ff0a23ba335e9f0842e1dc4f364..3e0a59612c2d0ccf4af8e64dd98f76e4dbfaa82c 100644 --- a/src/USER-EFF/fix_nh_eff.cpp +++ b/src/USER-EFF/fix_nh_eff.cpp @@ -15,8 +15,8 @@ Contributing author: Andres Jaramillo-Botero (Caltech) ------------------------------------------------------------------------- */ -#include -#include +#include +#include #include "fix_nh_eff.h" #include "atom.h" #include "atom_vec.h" diff --git a/src/USER-EFF/fix_nph_eff.cpp b/src/USER-EFF/fix_nph_eff.cpp index 0fe8c8e6dbd12116cbf5972e53c325de23aa00f9..28ebc620f9fe7aaf2c7425172385ae3c621fb97a 100644 --- a/src/USER-EFF/fix_nph_eff.cpp +++ b/src/USER-EFF/fix_nph_eff.cpp @@ -11,7 +11,7 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include +#include #include "fix_nph_eff.h" #include "modify.h" #include "error.h" diff --git a/src/USER-EFF/fix_npt_eff.cpp b/src/USER-EFF/fix_npt_eff.cpp index 02f09839b182a7b7891d3f53f8e20619883c1b88..6aac7f373462daa1d290ed22b2b70a6dc6f944ee 100644 --- a/src/USER-EFF/fix_npt_eff.cpp +++ b/src/USER-EFF/fix_npt_eff.cpp @@ -11,7 +11,7 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include +#include #include "fix_npt_eff.h" #include "modify.h" #include "error.h" diff --git a/src/USER-EFF/fix_nve_eff.cpp b/src/USER-EFF/fix_nve_eff.cpp index 09cd81a722165dfb9e9c7bacf39576f8707563bb..584714a44e7413e0eed09fedb95994a853b37811 100644 --- a/src/USER-EFF/fix_nve_eff.cpp +++ b/src/USER-EFF/fix_nve_eff.cpp @@ -15,17 +15,16 @@ Contributing author: Andres Jaramillo-Botero (Caltech) ------------------------------------------------------------------------- */ -#include -#include -#include -#include +#include +#include +#include +#include #include "fix_nve_eff.h" #include "atom.h" #include "force.h" #include "update.h" #include "respa.h" #include "error.h" -#include #include "domain.h" using namespace LAMMPS_NS; diff --git a/src/USER-EFF/fix_nvt_eff.cpp b/src/USER-EFF/fix_nvt_eff.cpp index ab82f9e0f8296f4008c44087f6ce0e5ad1a0b97b..9e23ee023be8702180190bae0bdf3d9e9f0e5ac2 100644 --- a/src/USER-EFF/fix_nvt_eff.cpp +++ b/src/USER-EFF/fix_nvt_eff.cpp @@ -11,8 +11,8 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include -#include +#include +#include #include "fix_nvt_eff.h" #include "group.h" #include "modify.h" diff --git a/src/USER-EFF/fix_nvt_sllod_eff.cpp b/src/USER-EFF/fix_nvt_sllod_eff.cpp index 1b4ec1f3fbb25ecf565d19e4eed2ddbee72a1ab4..f7b1a4ab2b162925999df9797050993902491772 100644 --- a/src/USER-EFF/fix_nvt_sllod_eff.cpp +++ b/src/USER-EFF/fix_nvt_sllod_eff.cpp @@ -11,8 +11,8 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include -#include +#include +#include #include "fix_nvt_sllod_eff.h" #include "math_extra.h" #include "atom.h" diff --git a/src/USER-EFF/fix_temp_rescale_eff.cpp b/src/USER-EFF/fix_temp_rescale_eff.cpp index 774cd1f2e303782236613686a10d5eca3146a2bc..37f45b3c28ad45142262121a957787b5e8e43a8c 100644 --- a/src/USER-EFF/fix_temp_rescale_eff.cpp +++ b/src/USER-EFF/fix_temp_rescale_eff.cpp @@ -15,9 +15,9 @@ Contributing author: Andres Jaramillo-Botero ------------------------------------------------------------------------- */ -#include -#include -#include +#include +#include +#include #include "fix_temp_rescale_eff.h" #include "atom.h" #include "force.h" diff --git a/src/USER-EFF/pair_eff_cut.cpp b/src/USER-EFF/pair_eff_cut.cpp index 850c52362967721bf00248aa0474d4a7d67efd18..0379c0264b5570f18ab1f8d401078c1abe700de9 100644 --- a/src/USER-EFF/pair_eff_cut.cpp +++ b/src/USER-EFF/pair_eff_cut.cpp @@ -15,10 +15,10 @@ Contributing author: Andres Jaramillo-Botero ------------------------------------------------------------------------- */ -#include -#include -#include -#include +#include +#include +#include +#include #include "pair_eff_cut.h" #include "pair_eff_inline.h" #include "atom.h" diff --git a/src/USER-FEP/compute_fep.cpp b/src/USER-FEP/compute_fep.cpp index bfa3bf7e2c91648cb08b74cca10e394da9a4a9e9..0e5f164f88d861b9614cd9e0bad8b93a3c4890e6 100644 --- a/src/USER-FEP/compute_fep.cpp +++ b/src/USER-FEP/compute_fep.cpp @@ -15,9 +15,9 @@ Contributing author: Agilio Padua (Univ Blaise Pascal & CNRS) ------------------------------------------------------------------------- */ -#include -#include -#include +#include +#include +#include #include #include "comm.h" #include "update.h" diff --git a/src/USER-FEP/fix_adapt_fep.cpp b/src/USER-FEP/fix_adapt_fep.cpp index 1b7fc559420f2ee6bd932d872c50524cebe208d9..3b8c9d4201f592343dff8d9e43c6a6b7ae9f1407 100644 --- a/src/USER-FEP/fix_adapt_fep.cpp +++ b/src/USER-FEP/fix_adapt_fep.cpp @@ -15,9 +15,9 @@ Charges by type and after option: Agilio Padua (Univ Blaise Pascal & CNRS) ------------------------------------------------------------------------- */ -#include -#include -#include +#include +#include +#include #include "fix_adapt_fep.h" #include "atom.h" #include "update.h" diff --git a/src/USER-FEP/pair_coul_cut_soft.cpp b/src/USER-FEP/pair_coul_cut_soft.cpp index a7ac8004fe631c576d9e5cc3b58106dd6d997356..5bcb5a752256a07ac83d4d74c2d044681b891b40 100644 --- a/src/USER-FEP/pair_coul_cut_soft.cpp +++ b/src/USER-FEP/pair_coul_cut_soft.cpp @@ -15,10 +15,10 @@ Soft-core version: Agilio Padua (Univ Blaise Pascal & CNRS) ------------------------------------------------------------------------- */ -#include -#include -#include -#include +#include +#include +#include +#include #include "pair_coul_cut_soft.h" #include "atom.h" #include "comm.h" diff --git a/src/USER-FEP/pair_coul_long_soft.cpp b/src/USER-FEP/pair_coul_long_soft.cpp index 3d24a997ddf0162af51b1a89a93dc0e525d4cf30..94bb3659fa3beea5a4025ace13b876ad6405375b 100644 --- a/src/USER-FEP/pair_coul_long_soft.cpp +++ b/src/USER-FEP/pair_coul_long_soft.cpp @@ -16,10 +16,10 @@ Soft-core version: Agilio Padua (Univ Blaise Pascal & CNRS) ------------------------------------------------------------------------- */ -#include -#include -#include -#include +#include +#include +#include +#include #include "pair_coul_long_soft.h" #include "atom.h" #include "comm.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 06285a58d3c3009e8ddb94fa7eb8402dc1ff8c3c..34758b159b34bcbf546b76add6e8329f28caaff1 100644 --- a/src/USER-FEP/pair_lj_charmm_coul_long_soft.cpp +++ b/src/USER-FEP/pair_lj_charmm_coul_long_soft.cpp @@ -16,10 +16,10 @@ Soft-core version: Agilio Padua (Univ Blaise Pascal & CNRS) ------------------------------------------------------------------------- */ -#include -#include -#include -#include +#include +#include +#include +#include #include "pair_lj_charmm_coul_long_soft.h" #include "atom.h" #include "comm.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 9e52a16a025d103a1c2ca95c60aac239e7b8c471..fc887fbec5cf2b8729bd6dc5f1cb433ed632209f 100644 --- a/src/USER-FEP/pair_lj_cut_coul_cut_soft.cpp +++ b/src/USER-FEP/pair_lj_cut_coul_cut_soft.cpp @@ -15,10 +15,10 @@ Soft-core version: Agilio Padua (Univ Blaise Pascal & CNRS) ------------------------------------------------------------------------- */ -#include -#include -#include -#include +#include +#include +#include +#include #include "pair_lj_cut_coul_cut_soft.h" #include "atom.h" #include "comm.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 7be2ebabea1fc434f5db0e920adc9f26fa70a875..a9032ab4d723d7e595b585f5ae910367107f7078 100644 --- a/src/USER-FEP/pair_lj_cut_coul_long_soft.cpp +++ b/src/USER-FEP/pair_lj_cut_coul_long_soft.cpp @@ -16,10 +16,10 @@ Soft-core version: Agilio Padua (Univ Blaise Pascal & CNRS) ------------------------------------------------------------------------- */ -#include -#include -#include -#include +#include +#include +#include +#include #include "pair_lj_cut_coul_long_soft.h" #include "atom.h" #include "comm.h" diff --git a/src/USER-FEP/pair_lj_cut_soft.cpp b/src/USER-FEP/pair_lj_cut_soft.cpp index 9ae108fa338849a37704e58b66e039fff49d09ee..4aaa5c292531f7cc0aee51712576de220fe56909 100644 --- a/src/USER-FEP/pair_lj_cut_soft.cpp +++ b/src/USER-FEP/pair_lj_cut_soft.cpp @@ -16,10 +16,10 @@ Soft-core version: Agilio Padua (Univ Blaise Pascal & CNRS) ------------------------------------------------------------------------- */ -#include -#include -#include -#include +#include +#include +#include +#include #include "pair_lj_cut_soft.h" #include "atom.h" #include "comm.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 8d9162e564097a44c68960ee2d28eb7746b856fc..8653800ee67f5f210e7a44db4789c571089cca08 100644 --- a/src/USER-FEP/pair_lj_cut_tip4p_long_soft.cpp +++ b/src/USER-FEP/pair_lj_cut_tip4p_long_soft.cpp @@ -17,10 +17,10 @@ Soft-core version: Agilio Padua (Univ Blaise Pascal & CNRS) ------------------------------------------------------------------------- */ -#include -#include -#include -#include +#include +#include +#include +#include #include "pair_lj_cut_tip4p_long_soft.h" #include "angle.h" #include "atom.h" diff --git a/src/USER-FEP/pair_morse_soft.cpp b/src/USER-FEP/pair_morse_soft.cpp index 1333bc28ca947075eeb439458db0870f53c5809a..7a897e1870ed96a0aad08671b5d031e7764557d7 100644 --- a/src/USER-FEP/pair_morse_soft.cpp +++ b/src/USER-FEP/pair_morse_soft.cpp @@ -11,10 +11,10 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include -#include -#include -#include +#include +#include +#include +#include #include "pair_morse_soft.h" #include "atom.h" #include "comm.h" diff --git a/src/USER-FEP/pair_tip4p_long_soft.cpp b/src/USER-FEP/pair_tip4p_long_soft.cpp index 7ad654d95c3988e562d44829f5231f730b7e8303..5e8c5000f88e894bfc5ffd60224f26605a038dc6 100644 --- a/src/USER-FEP/pair_tip4p_long_soft.cpp +++ b/src/USER-FEP/pair_tip4p_long_soft.cpp @@ -17,10 +17,10 @@ Soft-core version: Agilio Padua (Univ Blaise Pascal & CNRS) ------------------------------------------------------------------------- */ -#include -#include -#include -#include +#include +#include +#include +#include #include "pair_tip4p_long_soft.h" #include "angle.h" #include "atom.h" diff --git a/src/USER-H5MD/dump_h5md.cpp b/src/USER-H5MD/dump_h5md.cpp index 4e85b5c8b69175e98b374f53fc228ced6ab88998..393871ae0b9a7325d435f9a4f7f03f1fb2489090 100644 --- a/src/USER-H5MD/dump_h5md.cpp +++ b/src/USER-H5MD/dump_h5md.cpp @@ -15,11 +15,11 @@ Contributing author: Pierre de Buyl (KU Leuven) ------------------------------------------------------------------------- */ -#include -#include -#include -#include -#include +#include +#include +#include +#include +#include #include "ch5md.h" #include "dump_h5md.h" #include "domain.h" diff --git a/src/USER-INTEL/Install.sh b/src/USER-INTEL/Install.sh index da553d158ac24ff88ec9f86fd4e5b88ad7750191..8c291f0ae28da6090db92191e1ca48df7cebb8fd 100644 --- a/src/USER-INTEL/Install.sh +++ b/src/USER-INTEL/Install.sh @@ -38,6 +38,8 @@ for file in *_intel.h; do action $file $dep done +# step 2: handle cases and tasks not handled in step 1. + action intel_preprocess.h action intel_buffers.h action intel_buffers.cpp @@ -50,8 +52,6 @@ action intel_simd.h action intel_intrinsics.h pair_tersoff_intel.cpp action intel_intrinsics_airebo.h pair_airebo_intel.cpp -# step 2: handle cases and tasks not handled in step 1. - if (test $mode = 1) then if (test -e ../Makefile.package) then diff --git a/src/USER-INTEL/angle_charmm_intel.cpp b/src/USER-INTEL/angle_charmm_intel.cpp index bcaecb4696fa1d93e277d473e931b268298c5153..672b70b6f68785256c67b694b58b8d8e741dce87 100644 --- a/src/USER-INTEL/angle_charmm_intel.cpp +++ b/src/USER-INTEL/angle_charmm_intel.cpp @@ -15,8 +15,8 @@ Contributing author: W. Michael Brown (Intel) ------------------------------------------------------------------------- */ -#include -#include +#include +#include #include "angle_charmm_intel.h" #include "atom.h" #include "neighbor.h" diff --git a/src/USER-INTEL/angle_charmm_intel.h b/src/USER-INTEL/angle_charmm_intel.h index 342af31b8c122a937ab156e71c5ef12a7290bd11..5d173ee6a982e834587d5d7bc908854ec3a538d8 100644 --- a/src/USER-INTEL/angle_charmm_intel.h +++ b/src/USER-INTEL/angle_charmm_intel.h @@ -24,7 +24,7 @@ AngleStyle(charmm/intel,AngleCharmmIntel) #ifndef LMP_ANGLE_CHARMM_INTEL_H #define LMP_ANGLE_CHARMM_INTEL_H -#include +#include #include "angle_charmm.h" #include "fix_intel.h" diff --git a/src/USER-INTEL/angle_harmonic_intel.cpp b/src/USER-INTEL/angle_harmonic_intel.cpp index ffc81c496d77c654f35d6f0e1ad71a39a06844ee..74639f3aebddd8c705f622c2165edcf033617ea0 100644 --- a/src/USER-INTEL/angle_harmonic_intel.cpp +++ b/src/USER-INTEL/angle_harmonic_intel.cpp @@ -15,8 +15,8 @@ Contributing author: W. Michael Brown (Intel) ------------------------------------------------------------------------- */ -#include -#include +#include +#include #include "angle_harmonic_intel.h" #include "atom.h" #include "neighbor.h" diff --git a/src/USER-INTEL/angle_harmonic_intel.h b/src/USER-INTEL/angle_harmonic_intel.h index 301fc7cc066aabbb484f0c55b5065acbb93fd9b8..e7768542a1f1fbcb90692cf7f8afbad7f31d4ded 100644 --- a/src/USER-INTEL/angle_harmonic_intel.h +++ b/src/USER-INTEL/angle_harmonic_intel.h @@ -24,7 +24,7 @@ AngleStyle(harmonic/intel,AngleHarmonicIntel) #ifndef LMP_ANGLE_HARMONIC_INTEL_H #define LMP_ANGLE_HARMONIC_INTEL_H -#include +#include #include "angle_harmonic.h" #include "fix_intel.h" diff --git a/src/USER-INTEL/bond_fene_intel.cpp b/src/USER-INTEL/bond_fene_intel.cpp index 004a2e5413d6d566cb536b9d4290e80540315e81..2d70049a89b705918589f6402e987f6eb3edff34 100644 --- a/src/USER-INTEL/bond_fene_intel.cpp +++ b/src/USER-INTEL/bond_fene_intel.cpp @@ -15,8 +15,8 @@ Contributing author: Stan Moore (Sandia) ------------------------------------------------------------------------- */ -#include -#include +#include +#include #include "bond_fene_intel.h" #include "atom.h" #include "modify.h" diff --git a/src/USER-INTEL/bond_fene_intel.h b/src/USER-INTEL/bond_fene_intel.h index 89c3033096e43eba27065220e2b77769cc831591..afe3b85470d6d81b0639a57a3ce7ade9a1ff0467 100644 --- a/src/USER-INTEL/bond_fene_intel.h +++ b/src/USER-INTEL/bond_fene_intel.h @@ -24,7 +24,7 @@ BondStyle(fene/intel,BondFENEIntel) #ifndef LMP_BOND_FENE_INTEL_H #define LMP_BOND_FENE_INTEL_H -#include +#include #include "bond_fene.h" #include "fix_intel.h" diff --git a/src/USER-INTEL/bond_harmonic_intel.cpp b/src/USER-INTEL/bond_harmonic_intel.cpp index 0c714edc0959519621b624d19dd6e79b5b081977..ed9cab082ed5553c9afd38ddf12f2aabf98861fe 100644 --- a/src/USER-INTEL/bond_harmonic_intel.cpp +++ b/src/USER-INTEL/bond_harmonic_intel.cpp @@ -15,8 +15,8 @@ Contributing author: W. Michael Brown (Intel) ------------------------------------------------------------------------- */ -#include -#include +#include +#include #include "bond_harmonic_intel.h" #include "atom.h" #include "modify.h" diff --git a/src/USER-INTEL/bond_harmonic_intel.h b/src/USER-INTEL/bond_harmonic_intel.h index 8fc04f432a2a5994b08e9807f42161d36b933e62..b86a560d6e167e592aaee3cdfdc97b13fe906879 100644 --- a/src/USER-INTEL/bond_harmonic_intel.h +++ b/src/USER-INTEL/bond_harmonic_intel.h @@ -24,7 +24,7 @@ BondStyle(harmonic/intel,BondHarmonicIntel) #ifndef LMP_BOND_HARMONIC_INTEL_H #define LMP_BOND_HARMONIC_INTEL_H -#include +#include #include "bond_harmonic.h" #include "fix_intel.h" diff --git a/src/USER-INTEL/dihedral_charmm_intel.cpp b/src/USER-INTEL/dihedral_charmm_intel.cpp index c8429dc8ff7079930f00459c33ad85674ebaf222..c9237e7309ea7b5f51a34fe86bcc13559119b7c7 100644 --- a/src/USER-INTEL/dihedral_charmm_intel.cpp +++ b/src/USER-INTEL/dihedral_charmm_intel.cpp @@ -16,7 +16,7 @@ ------------------------------------------------------------------------- */ #include -#include +#include #include "dihedral_charmm_intel.h" #include "atom.h" #include "comm.h" diff --git a/src/USER-INTEL/dihedral_fourier_intel.cpp b/src/USER-INTEL/dihedral_fourier_intel.cpp index c46617bbc253ac9ac2bf3290d5a047ff456c0b95..6ad25f1ce49228f5f719cc21277b01a9bcfd26d8 100644 --- a/src/USER-INTEL/dihedral_fourier_intel.cpp +++ b/src/USER-INTEL/dihedral_fourier_intel.cpp @@ -16,7 +16,7 @@ ------------------------------------------------------------------------- */ #include -#include +#include #include "dihedral_fourier_intel.h" #include "atom.h" #include "comm.h" diff --git a/src/USER-INTEL/dihedral_harmonic_intel.cpp b/src/USER-INTEL/dihedral_harmonic_intel.cpp index b35ea4e03a9b67a3b619028c0c559b304cbbaf07..b2bf54102c4b8cfb05d8cfbe949d4cca4261ead9 100644 --- a/src/USER-INTEL/dihedral_harmonic_intel.cpp +++ b/src/USER-INTEL/dihedral_harmonic_intel.cpp @@ -16,7 +16,7 @@ ------------------------------------------------------------------------- */ #include -#include +#include #include "dihedral_harmonic_intel.h" #include "atom.h" #include "comm.h" diff --git a/src/USER-INTEL/dihedral_opls_intel.cpp b/src/USER-INTEL/dihedral_opls_intel.cpp index 6b7b2c81ebd75bace530cbde5dd9bee1f0981c57..832ce7ed50e482c787bd4e14e22d225b7b3be721 100644 --- a/src/USER-INTEL/dihedral_opls_intel.cpp +++ b/src/USER-INTEL/dihedral_opls_intel.cpp @@ -16,7 +16,7 @@ ------------------------------------------------------------------------- */ #include -#include +#include #include "dihedral_opls_intel.h" #include "atom.h" #include "comm.h" @@ -185,13 +185,6 @@ void DihedralOPLSIntel::eval(const int vflag, const flt_t vb3y = x[i4].y - x[i3].y; const flt_t vb3z = x[i4].z - x[i3].z; - // 1-4 - - const flt_t delx = x[i1].x - x[i4].x; - const flt_t dely = x[i1].y - x[i4].y; - const flt_t delz = x[i1].z - x[i4].z; - - // c0 calculation // 1st and 2nd angle diff --git a/src/USER-INTEL/fix_intel.cpp b/src/USER-INTEL/fix_intel.cpp index d05e05957844d37e1b100d04415632ffbbd0e05e..124c7a9c76f403ea29dcee43a368e1ad97e3774f 100644 --- a/src/USER-INTEL/fix_intel.cpp +++ b/src/USER-INTEL/fix_intel.cpp @@ -29,10 +29,10 @@ #include "update.h" #include "fix_intel.h" -#include -#include -#include -#include +#include +#include +#include +#include #ifdef LAMMPS_BIGBIG #error "The USER-INTEL package is not compatible with -DLAMMPS_BIGBIG" diff --git a/src/USER-INTEL/fix_nh_intel.cpp b/src/USER-INTEL/fix_nh_intel.cpp index 6e44b38ef17439d6c7080ad30c497e8efca6cd56..44253e8bb0b9c3b5750c6e0a46e2f3c3cf25a7ab 100644 --- a/src/USER-INTEL/fix_nh_intel.cpp +++ b/src/USER-INTEL/fix_nh_intel.cpp @@ -28,8 +28,8 @@ #include "update.h" #include -#include -#include +#include +#include using namespace LAMMPS_NS; using namespace FixConst; diff --git a/src/USER-INTEL/fix_npt_intel.cpp b/src/USER-INTEL/fix_npt_intel.cpp index 56df3bba4bb3e999e12d49696c4f8e5dd162c2ce..bc0d297078a57adc0bfdf64a6431d2e6d20a1ade 100644 --- a/src/USER-INTEL/fix_npt_intel.cpp +++ b/src/USER-INTEL/fix_npt_intel.cpp @@ -11,7 +11,7 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include +#include #include "fix_npt_intel.h" #include "modify.h" #include "error.h" diff --git a/src/USER-INTEL/fix_nve_asphere_intel.cpp b/src/USER-INTEL/fix_nve_asphere_intel.cpp index 8ad63f7326dfac6df7fa5f4e1e2cb36bb2368ee6..17bbcff77140de04b60b4cfdf8f79867d11f87d8 100644 --- a/src/USER-INTEL/fix_nve_asphere_intel.cpp +++ b/src/USER-INTEL/fix_nve_asphere_intel.cpp @@ -15,9 +15,9 @@ Contributing author: W. Michael Brown (Intel) ------------------------------------------------------------------------- */ -#include -#include -#include +#include +#include +#include #include "fix_nve_asphere_intel.h" #include "math_extra_intel.h" #include "atom.h" diff --git a/src/USER-INTEL/fix_nvt_intel.cpp b/src/USER-INTEL/fix_nvt_intel.cpp index 3fe712c9ab812cf55bfbfab57d07e78c545a0559..547039ff23a10342a35c381e8ae6ef285d0e8d04 100644 --- a/src/USER-INTEL/fix_nvt_intel.cpp +++ b/src/USER-INTEL/fix_nvt_intel.cpp @@ -11,7 +11,7 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include +#include #include "fix_nvt_intel.h" #include "group.h" #include "modify.h" diff --git a/src/USER-INTEL/fix_nvt_sllod_intel.cpp b/src/USER-INTEL/fix_nvt_sllod_intel.cpp index bab748ad748c72fdabbe11bf922731e595d5c95e..5684f469038d023d71cbc4dd95f79cd1b9907601 100644 --- a/src/USER-INTEL/fix_nvt_sllod_intel.cpp +++ b/src/USER-INTEL/fix_nvt_sllod_intel.cpp @@ -11,8 +11,8 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include -#include +#include +#include #include "fix_nvt_sllod_intel.h" #include "math_extra.h" #include "atom.h" diff --git a/src/USER-INTEL/improper_cvff_intel.cpp b/src/USER-INTEL/improper_cvff_intel.cpp index 39090e5a7420b3fd32598cbab2aca8a802e497b1..e0ef2162d1e72ce865cf080e5de9192c51247d6c 100644 --- a/src/USER-INTEL/improper_cvff_intel.cpp +++ b/src/USER-INTEL/improper_cvff_intel.cpp @@ -16,8 +16,8 @@ ------------------------------------------------------------------------- */ #include -#include -#include +#include +#include #include "improper_cvff_intel.h" #include "atom.h" #include "comm.h" diff --git a/src/USER-INTEL/improper_cvff_intel.h b/src/USER-INTEL/improper_cvff_intel.h index cb5da25f992d26f95f365918f1a5691c0e3f0fe0..e815fa75c904e678f375af053c82ed2ea5a2a2b4 100644 --- a/src/USER-INTEL/improper_cvff_intel.h +++ b/src/USER-INTEL/improper_cvff_intel.h @@ -24,7 +24,7 @@ ImproperStyle(cvff/intel,ImproperCvffIntel) #ifndef LMP_IMPROPER_CVFF_INTEL_H #define LMP_IMPROPER_CVFF_INTEL_H -#include +#include #include "improper_cvff.h" #include "fix_intel.h" diff --git a/src/USER-INTEL/improper_harmonic_intel.cpp b/src/USER-INTEL/improper_harmonic_intel.cpp index 3547061672cff079b53761f928761e746d637d8a..60cbe163586da454d9dd7d70710ad6551f0c89ff 100644 --- a/src/USER-INTEL/improper_harmonic_intel.cpp +++ b/src/USER-INTEL/improper_harmonic_intel.cpp @@ -16,8 +16,8 @@ ------------------------------------------------------------------------- */ #include -#include -#include +#include +#include #include "improper_harmonic_intel.h" #include "atom.h" #include "comm.h" diff --git a/src/USER-INTEL/improper_harmonic_intel.h b/src/USER-INTEL/improper_harmonic_intel.h index 0b759b4e43e894d30d5a9ec5390b4259302a69a4..ce38e8fc317ed5dc996de47387baec910c40f71c 100644 --- a/src/USER-INTEL/improper_harmonic_intel.h +++ b/src/USER-INTEL/improper_harmonic_intel.h @@ -24,7 +24,7 @@ ImproperStyle(harmonic/intel,ImproperHarmonicIntel) #ifndef LMP_IMPROPER_HARMONIC_INTEL_H #define LMP_IMPROPER_HARMONIC_INTEL_H -#include +#include #include "improper_harmonic.h" #include "fix_intel.h" diff --git a/src/USER-INTEL/intel_buffers.cpp b/src/USER-INTEL/intel_buffers.cpp index 8948abe1725ebe2547301591748523f021d81c5f..1b31ec7fc2f6216497104a6edb64e64c238975b8 100644 --- a/src/USER-INTEL/intel_buffers.cpp +++ b/src/USER-INTEL/intel_buffers.cpp @@ -12,7 +12,7 @@ Contributing author: W. Michael Brown (Intel) ------------------------------------------------------------------------- */ -#include +#include #include "intel_buffers.h" #include "force.h" #include "memory.h" diff --git a/src/USER-INTEL/intel_intrinsics_airebo.h b/src/USER-INTEL/intel_intrinsics_airebo.h index f17fd6985608307183aa7b69a36714a59be74dc5..4a86d8db290d096dff9ae1e16809176a6ce18930 100644 --- a/src/USER-INTEL/intel_intrinsics_airebo.h +++ b/src/USER-INTEL/intel_intrinsics_airebo.h @@ -744,7 +744,7 @@ struct intr_types { #include #include -#include +#include // requires C++-11 #define VEC_INLINE __attribute__((always_inline)) diff --git a/src/USER-INTEL/intel_simd.h b/src/USER-INTEL/intel_simd.h index 4616f628e73a969b3aee3ba2e036d91ffa5f97f6..e9d5d929953682276884274fe6d90285a88bf5eb 100644 --- a/src/USER-INTEL/intel_simd.h +++ b/src/USER-INTEL/intel_simd.h @@ -29,7 +29,7 @@ authors for more details. #ifndef INTEL_SIMD_H #define INTEL_SIMD_H -#include +#include #include "intel_preprocess.h" #include "immintrin.h" diff --git a/src/USER-INTEL/pair_airebo_intel.cpp b/src/USER-INTEL/pair_airebo_intel.cpp index 43e0bb7eedc9e64888d3e3ebbd5d4ecfab5ccc68..07f33f7ebe10bdfb1fac0511b768a9eba1fa3148 100644 --- a/src/USER-INTEL/pair_airebo_intel.cpp +++ b/src/USER-INTEL/pair_airebo_intel.cpp @@ -19,12 +19,13 @@ #pragma offload_attribute(push, target(mic)) #endif #include -#include -#include -#include -#include -#include -#include +#include +#include +#include +#include +#include // requires C++-11 +#include +#include #include "lmptype.h" #include "intel_preprocess.h" #include "intel_intrinsics_airebo.h" @@ -35,7 +36,6 @@ #if defined(_OPENMP) #include #endif -#include #include "pair_airebo_intel.h" #include "atom.h" #include "neighbor.h" diff --git a/src/USER-INTEL/pair_buck_coul_cut_intel.cpp b/src/USER-INTEL/pair_buck_coul_cut_intel.cpp index e32fd066607fff224be9bcf2d606c4472864220e..71aad95bc51016543352997c0ccba9e4b595ced3 100644 --- a/src/USER-INTEL/pair_buck_coul_cut_intel.cpp +++ b/src/USER-INTEL/pair_buck_coul_cut_intel.cpp @@ -15,10 +15,10 @@ Contributing author: Rodrigo Canales (RWTH Aachen University) ------------------------------------------------------------------------- */ -#include -#include -#include -#include +#include +#include +#include +#include #include "pair_buck_coul_cut_intel.h" #include "atom.h" #include "comm.h" diff --git a/src/USER-INTEL/pair_buck_coul_long_intel.cpp b/src/USER-INTEL/pair_buck_coul_long_intel.cpp index 2b9fea7a50f80c0298069d976c3211d47bffc12e..bba8a7b5e7e6a7f30133a0064bc5f102e7e5ea29 100644 --- a/src/USER-INTEL/pair_buck_coul_long_intel.cpp +++ b/src/USER-INTEL/pair_buck_coul_long_intel.cpp @@ -15,10 +15,10 @@ Contributing author: Rodrigo Canales (RWTH Aachen University) ------------------------------------------------------------------------- */ -#include -#include -#include -#include +#include +#include +#include +#include #include "pair_buck_coul_long_intel.h" #include "atom.h" #include "comm.h" diff --git a/src/USER-INTEL/pair_buck_intel.cpp b/src/USER-INTEL/pair_buck_intel.cpp index 05a28eb7f05b71e3df46b4403ae6971b70351295..f5dde26393d5878207df9b8775e2329cb19f272a 100644 --- a/src/USER-INTEL/pair_buck_intel.cpp +++ b/src/USER-INTEL/pair_buck_intel.cpp @@ -15,7 +15,7 @@ Contributing author: Rodrigo Canales (RWTH Aachen University) ------------------------------------------------------------------------- */ -#include +#include #include "pair_buck_intel.h" #include "atom.h" #include "comm.h" diff --git a/src/USER-INTEL/pair_dpd_intel.cpp b/src/USER-INTEL/pair_dpd_intel.cpp index 60361cac7953c17db45cde6683948499fb23dba2..cb8c06cacc258778ba944b02ccc4096600033ea1 100644 --- a/src/USER-INTEL/pair_dpd_intel.cpp +++ b/src/USER-INTEL/pair_dpd_intel.cpp @@ -13,7 +13,7 @@ Shun Xu (Computer Network Information Center, CAS) ------------------------------------------------------------------------- */ -#include +#include #include "pair_dpd_intel.h" #include "atom.h" #include "comm.h" diff --git a/src/USER-INTEL/pair_eam_alloy_intel.cpp b/src/USER-INTEL/pair_eam_alloy_intel.cpp index 4f47c7ee23967fd11c5042316b583b8157b3b19f..192b39b2e8c27ffd8a8cd3cffeee1de9969552e3 100644 --- a/src/USER-INTEL/pair_eam_alloy_intel.cpp +++ b/src/USER-INTEL/pair_eam_alloy_intel.cpp @@ -15,9 +15,9 @@ Contributing authors: Stephen Foiles (SNL), Murray Daw (SNL) ------------------------------------------------------------------------- */ -#include -#include -#include +#include +#include +#include #include "pair_eam_alloy_intel.h" #include "atom.h" #include "comm.h" diff --git a/src/USER-INTEL/pair_eam_fs_intel.cpp b/src/USER-INTEL/pair_eam_fs_intel.cpp index cfcc8200cc751a8f3aafde06e79d4a6827a59900..61bb6e0b4d17674a2602f7eddea08cc4b82fa0ce 100644 --- a/src/USER-INTEL/pair_eam_fs_intel.cpp +++ b/src/USER-INTEL/pair_eam_fs_intel.cpp @@ -15,9 +15,9 @@ Contributing authors: Tim Lau (MIT) ------------------------------------------------------------------------- */ -#include -#include -#include +#include +#include +#include #include "pair_eam_fs_intel.h" #include "atom.h" #include "comm.h" diff --git a/src/USER-INTEL/pair_eam_intel.cpp b/src/USER-INTEL/pair_eam_intel.cpp index ea4ee30d52602440b06b81603a3d93897b72cba3..94799cdba26b5b609aa2eb28e9966e03a23509f3 100644 --- a/src/USER-INTEL/pair_eam_intel.cpp +++ b/src/USER-INTEL/pair_eam_intel.cpp @@ -15,10 +15,10 @@ Contributing authors: W. Michael Brown (Intel) ------------------------------------------------------------------------- */ -#include -#include -#include -#include +#include +#include +#include +#include #include "pair_eam_intel.h" #include "atom.h" #include "force.h" diff --git a/src/USER-INTEL/pair_eam_intel.h b/src/USER-INTEL/pair_eam_intel.h index f34e740bdaaf83c9229239339d755dd0588dab55..83b1fbf6a13e76cffcd55e574cac81d4c4ac1d8a 100644 --- a/src/USER-INTEL/pair_eam_intel.h +++ b/src/USER-INTEL/pair_eam_intel.h @@ -20,7 +20,7 @@ PairStyle(eam/intel,PairEAMIntel) #ifndef LMP_PAIR_EAM_INTEL_H #define LMP_PAIR_EAM_INTEL_H -#include +#include #include "pair_eam.h" #include "fix_intel.h" diff --git a/src/USER-INTEL/pair_lj_charmm_coul_charmm_intel.cpp b/src/USER-INTEL/pair_lj_charmm_coul_charmm_intel.cpp index b36e594f54e8ddb81a28ff0ea96671c99ba12ad1..7485395bef089c57338097d03145a5e3f435d2e3 100644 --- a/src/USER-INTEL/pair_lj_charmm_coul_charmm_intel.cpp +++ b/src/USER-INTEL/pair_lj_charmm_coul_charmm_intel.cpp @@ -12,7 +12,7 @@ Contributing author: W. Michael Brown (Intel) ------------------------------------------------------------------------- */ -#include +#include #include "pair_lj_charmm_coul_charmm_intel.h" #include "atom.h" #include "comm.h" diff --git a/src/USER-INTEL/pair_lj_charmm_coul_long_intel.cpp b/src/USER-INTEL/pair_lj_charmm_coul_long_intel.cpp index a2680cdff41bb964cf39e42f85c140837e08fca8..25cca59714c9f5bdadfbf19bd5cd8b64279afb25 100644 --- a/src/USER-INTEL/pair_lj_charmm_coul_long_intel.cpp +++ b/src/USER-INTEL/pair_lj_charmm_coul_long_intel.cpp @@ -12,7 +12,7 @@ Contributing author: W. Michael Brown (Intel) ------------------------------------------------------------------------- */ -#include +#include #include "pair_lj_charmm_coul_long_intel.h" #include "atom.h" #include "comm.h" diff --git a/src/USER-INTEL/pair_lj_cut_coul_long_intel.cpp b/src/USER-INTEL/pair_lj_cut_coul_long_intel.cpp index c0bf6f35c6e6b220f33d6d6bbb00232d8fcce3bd..cb7381270dd72d9dad1476645e901e13bc1998cb 100644 --- a/src/USER-INTEL/pair_lj_cut_coul_long_intel.cpp +++ b/src/USER-INTEL/pair_lj_cut_coul_long_intel.cpp @@ -12,7 +12,7 @@ Contributing author: W. Michael Brown (Intel) ------------------------------------------------------------------------- */ -#include +#include #include "pair_lj_cut_coul_long_intel.h" #include "atom.h" #include "comm.h" diff --git a/src/USER-INTEL/pair_lj_cut_intel.cpp b/src/USER-INTEL/pair_lj_cut_intel.cpp index f5a7999ee2e9cf13280167af8eecb008dbca59fe..b16f6230ccd5d30a6fc55eb239d8a5cc9f8c2cd2 100644 --- a/src/USER-INTEL/pair_lj_cut_intel.cpp +++ b/src/USER-INTEL/pair_lj_cut_intel.cpp @@ -12,7 +12,7 @@ Contributing author: W. Michael Brown (Intel) ------------------------------------------------------------------------- */ -#include +#include #include "pair_lj_cut_intel.h" #include "atom.h" #include "comm.h" diff --git a/src/USER-INTEL/pair_lj_long_coul_long_intel.cpp b/src/USER-INTEL/pair_lj_long_coul_long_intel.cpp index 86929d41ea3332db08e1a1295762b63884ac561d..8b9670f41917df66487a1b53dad343f96f59e9dc 100644 --- a/src/USER-INTEL/pair_lj_long_coul_long_intel.cpp +++ b/src/USER-INTEL/pair_lj_long_coul_long_intel.cpp @@ -15,7 +15,7 @@ Contributing authors: William McDoniel (RWTH Aachen University) ------------------------------------------------------------------------- */ -#include +#include #include "pair_lj_long_coul_long_intel.h" #include "atom.h" #include "comm.h" diff --git a/src/USER-INTEL/pair_sw_intel.cpp b/src/USER-INTEL/pair_sw_intel.cpp index 2c28fcfd94d2793b4338abb80024ec19722e261b..421de91ee938b1137ae546b0df36422c1b9ac5cb 100644 --- a/src/USER-INTEL/pair_sw_intel.cpp +++ b/src/USER-INTEL/pair_sw_intel.cpp @@ -25,9 +25,9 @@ #pragma offload_attribute(pop) #endif -#include -#include -#include +#include +#include +#include #include "atom.h" #include "neighbor.h" #include "neigh_request.h" diff --git a/src/USER-INTEL/pair_tersoff_intel.cpp b/src/USER-INTEL/pair_tersoff_intel.cpp index a59fe12f5ba0ffcd9ee96145f37337cd4231e21a..c772546928dff386b5272d12a428553abe50f5eb 100644 --- a/src/USER-INTEL/pair_tersoff_intel.cpp +++ b/src/USER-INTEL/pair_tersoff_intel.cpp @@ -15,10 +15,10 @@ Contributing author: Markus Höhnerbach (RWTH) ------------------------------------------------------------------------- */ -#include -#include -#include -#include +#include +#include +#include +#include #include "pair_tersoff_intel.h" #include "atom.h" #include "neighbor.h" diff --git a/src/USER-INTEL/pppm_disp_intel.cpp b/src/USER-INTEL/pppm_disp_intel.cpp index 52e418c7138e1131919e90c0b434883982637233..0a41e5d8a5341c635853a2125ea2603ba6a9e64e 100644 --- a/src/USER-INTEL/pppm_disp_intel.cpp +++ b/src/USER-INTEL/pppm_disp_intel.cpp @@ -16,8 +16,8 @@ ------------------------------------------------------------------------- */ #include -#include -#include +#include +#include #include "pppm_disp_intel.h" #include "atom.h" #include "comm.h" @@ -728,7 +728,7 @@ void PPPMDispIntel::particle_map(double delx, double dely, double delz, int nlocal = atom->nlocal; int nthr = comm->nthreads; - if (!ISFINITE(boxlo[0]) || !ISFINITE(boxlo[1]) || !ISFINITE(boxlo[2])) + if (!std::isfinite(boxlo[0]) || !std::isfinite(boxlo[1]) || !std::isfinite(boxlo[2])) error->one(FLERR,"Non-numeric box dimensions - simulation unstable"); int flag = 0; diff --git a/src/USER-INTEL/pppm_intel.cpp b/src/USER-INTEL/pppm_intel.cpp index 1fd267be51900d9c61d1112fb648f52491101ee6..46a55e558afbad5e408be10b24077430b53b65cc 100644 --- a/src/USER-INTEL/pppm_intel.cpp +++ b/src/USER-INTEL/pppm_intel.cpp @@ -19,8 +19,8 @@ ------------------------------------------------------------------------- */ #include -#include -#include +#include +#include #include "pppm_intel.h" #include "atom.h" #include "comm.h" @@ -358,7 +358,7 @@ void PPPMIntel::particle_map(IntelBuffers *buffers) int flag = 0; - if (!ISFINITE(boxlo[0]) || !ISFINITE(boxlo[1]) || !ISFINITE(boxlo[2])) + if (!std::isfinite(boxlo[0]) || !std::isfinite(boxlo[1]) || !std::isfinite(boxlo[2])) error->one(FLERR,"Non-numeric box dimensions - simulation unstable"); #if defined(_OPENMP) diff --git a/src/USER-INTEL/verlet_lrt_intel.cpp b/src/USER-INTEL/verlet_lrt_intel.cpp index 1b9c305e9c69377906b0346de8b6803c37b307b9..962202e228f74bce7e9b8486c33d50b0a04d4da3 100644 --- a/src/USER-INTEL/verlet_lrt_intel.cpp +++ b/src/USER-INTEL/verlet_lrt_intel.cpp @@ -11,7 +11,7 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include +#include #include "verlet_lrt_intel.h" #include "neighbor.h" #include "domain.h" diff --git a/src/USER-LB/fix_lb_fluid.cpp b/src/USER-LB/fix_lb_fluid.cpp index 638901d6b3d06199b56edc97ddf73624c84b01eb..7a0bd0572ed63f1df5cd51eb8bead57d5ec05349 100644 --- a/src/USER-LB/fix_lb_fluid.cpp +++ b/src/USER-LB/fix_lb_fluid.cpp @@ -17,11 +17,11 @@ ------------------------------------------------------------------------- */ #include "fix_lb_fluid.h" -#include +#include #include -#include -#include -#include +#include +#include +#include #include "comm.h" #include "memory.h" #include "error.h" diff --git a/src/USER-LB/fix_lb_momentum.cpp b/src/USER-LB/fix_lb_momentum.cpp index d604d8fed414240cedd96972d8b9ee08f882778d..490b95ef719a132448c2925ba2879c9f1874f163 100644 --- a/src/USER-LB/fix_lb_momentum.cpp +++ b/src/USER-LB/fix_lb_momentum.cpp @@ -18,8 +18,8 @@ Contributing author: Naveen Michaud-Agrawal (Johns Hopkins U) ------------------------------------------------------------------------- */ -#include -#include +#include +#include #include "fix_lb_momentum.h" #include "atom.h" #include "domain.h" @@ -102,8 +102,8 @@ void FixLbMomentum::end_of_step() double masslb,masslbloc; double momentumlbloc[3],momentumlb[3]; double vcmtotal[3]; - int numvel = fix_lb_fluid->numvel; - double etacov[numvel]; + const int numvel = fix_lb_fluid->numvel; + double etacov[19]; // = double etacov[numvel]; i.e. 15 or 19 double rho; if (linear) { diff --git a/src/USER-LB/fix_lb_pc.cpp b/src/USER-LB/fix_lb_pc.cpp index c4d7cf70d3ae504f34a17418466533fdf7815396..9fd0dab51de39ec708cad06ac94202321d3bb59c 100644 --- a/src/USER-LB/fix_lb_pc.cpp +++ b/src/USER-LB/fix_lb_pc.cpp @@ -15,9 +15,9 @@ Contributing authors: Frances Mackay, Santtu Ollila, Colin Denniston (UWO) ------------------------------------------------------------------------- */ -#include -#include -#include +#include +#include +#include #include "fix_lb_pc.h" #include "atom.h" #include "force.h" diff --git a/src/USER-LB/fix_lb_rigid_pc_sphere.cpp b/src/USER-LB/fix_lb_rigid_pc_sphere.cpp index 42e8eae3d225c36972d36a97c09b5d4c291a9b3c..dddd060fa4cd416bb3e97a77bfffedcb0a05da03 100644 --- a/src/USER-LB/fix_lb_rigid_pc_sphere.cpp +++ b/src/USER-LB/fix_lb_rigid_pc_sphere.cpp @@ -16,10 +16,10 @@ Based on fix_rigid (version from 2008). ------------------------------------------------------------------------- */ -#include -#include -#include -#include +#include +#include +#include +#include #include "fix_lb_rigid_pc_sphere.h" #include "atom.h" #include "atom_vec.h" diff --git a/src/USER-LB/fix_lb_viscous.cpp b/src/USER-LB/fix_lb_viscous.cpp index 0e156bc46ce957153bcbca2d2e68b5cbab4ebfd7..8ee4d8419e73e5a377fa65b2c8e40b13baef6b5a 100644 --- a/src/USER-LB/fix_lb_viscous.cpp +++ b/src/USER-LB/fix_lb_viscous.cpp @@ -15,9 +15,9 @@ Contributing authors: Frances Mackay, Santtu Ollila, Colin Denniston (UWO) ------------------------------------------------------------------------- */ -#include -#include -#include +#include +#include +#include #include "fix_lb_viscous.h" #include "atom.h" #include "update.h" diff --git a/src/USER-MANIFOLD/fix_manifoldforce.cpp b/src/USER-MANIFOLD/fix_manifoldforce.cpp index e66b7c9fc2ac34bf80e197461b8ea9314c7320c4..ab33b5bc972627e1611bbc80bbbaa3f1e3c660b3 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 -#include +#include +#include +#include #include "atom.h" #include "update.h" #include "respa.h" diff --git a/src/USER-MANIFOLD/fix_nve_manifold_rattle.cpp b/src/USER-MANIFOLD/fix_nve_manifold_rattle.cpp index a8ce87ef111256b4eeb4c5bfa3c50c56c5ade443..4dcc3f9704aa3543aeaa62ed7a9202135218c801 100644 --- a/src/USER-MANIFOLD/fix_nve_manifold_rattle.cpp +++ b/src/USER-MANIFOLD/fix_nve_manifold_rattle.cpp @@ -32,16 +32,16 @@ ------------------------------------------------------------------------- */ -#include -#include -#include +#include +#include +#include #include "atom.h" #include "force.h" #include "update.h" #include "respa.h" #include "error.h" #include "group.h" -#include +#include #include "input.h" #include "variable.h" #include "citeme.h" diff --git a/src/USER-MANIFOLD/fix_nvt_manifold_rattle.cpp b/src/USER-MANIFOLD/fix_nvt_manifold_rattle.cpp index 38e8c6a26506b33c075a757e64ea29574fb09c64..973a5bcf43875d12af45655be1ff97f54c17e139 100644 --- a/src/USER-MANIFOLD/fix_nvt_manifold_rattle.cpp +++ b/src/USER-MANIFOLD/fix_nvt_manifold_rattle.cpp @@ -32,16 +32,16 @@ ------------------------------------------------------------------------- */ -#include -#include -#include +#include +#include +#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" diff --git a/src/USER-MANIFOLD/manifold.h b/src/USER-MANIFOLD/manifold.h index f0d56ffd82efd240526bbe204181206cbf2d2400..6eb09010efbb3022bed71c282744db7792140ba8 100644 --- a/src/USER-MANIFOLD/manifold.h +++ b/src/USER-MANIFOLD/manifold.h @@ -38,7 +38,7 @@ #define LMP_MANIFOLD_H #include "pointers.h" -#include +#include namespace LAMMPS_NS { namespace user_manifold { diff --git a/src/USER-MANIFOLD/manifold_cylinder_dent.cpp b/src/USER-MANIFOLD/manifold_cylinder_dent.cpp index 687e311c9cd61d87fddf846e2af04f9418ed1cb1..21d4087d7c240722162b0eb556aa0b873c1a8896 100644 --- a/src/USER-MANIFOLD/manifold_cylinder_dent.cpp +++ b/src/USER-MANIFOLD/manifold_cylinder_dent.cpp @@ -1,7 +1,7 @@ #include "manifold_cylinder_dent.h" #include "math_const.h" -#include +#include using namespace LAMMPS_NS; diff --git a/src/USER-MANIFOLD/manifold_dumbbell.cpp b/src/USER-MANIFOLD/manifold_dumbbell.cpp index ed1583ac9af5cc0c74f73f7f558194a657d5909d..fa7edc6e4afa4fa345c283187d073365a05dedb7 100644 --- a/src/USER-MANIFOLD/manifold_dumbbell.cpp +++ b/src/USER-MANIFOLD/manifold_dumbbell.cpp @@ -1,6 +1,6 @@ #include "manifold_dumbbell.h" -#include +#include using namespace LAMMPS_NS; diff --git a/src/USER-MANIFOLD/manifold_factory.h b/src/USER-MANIFOLD/manifold_factory.h index 7fdd0a6de555f23c146849d67909a9367d74c5ea..cc3e1245bfd11f0a4c46cdb55948f40c3810bffd 100644 --- a/src/USER-MANIFOLD/manifold_factory.h +++ b/src/USER-MANIFOLD/manifold_factory.h @@ -37,7 +37,7 @@ #include "manifold.h" -#include +#include /* * Defining USE_PHONY_LAMMPS makes sure that none of the LAMMPS classes are diff --git a/src/USER-MANIFOLD/manifold_plane_wiggle.cpp b/src/USER-MANIFOLD/manifold_plane_wiggle.cpp index 136c52ab361a2023ee2442fc038039a8d2c1a7d0..ccf0a794dadc28900dcee2a01cee1a6343d39b68 100644 --- a/src/USER-MANIFOLD/manifold_plane_wiggle.cpp +++ b/src/USER-MANIFOLD/manifold_plane_wiggle.cpp @@ -1,6 +1,6 @@ #include "manifold_plane_wiggle.h" -#include +#include using namespace LAMMPS_NS; using namespace user_manifold; diff --git a/src/USER-MANIFOLD/manifold_spine.cpp b/src/USER-MANIFOLD/manifold_spine.cpp index 1081ab673e2e493e8da40c8c1a1c41d2de58949c..308190c5288ea41ad9ceb689b9df1f849ffb8c08 100644 --- a/src/USER-MANIFOLD/manifold_spine.cpp +++ b/src/USER-MANIFOLD/manifold_spine.cpp @@ -1,6 +1,6 @@ #include "manifold_spine.h" -#include +#include #include "math_special.h" using namespace LAMMPS_NS; diff --git a/src/USER-MANIFOLD/manifold_thylakoid.cpp b/src/USER-MANIFOLD/manifold_thylakoid.cpp index 4bb2b71331ead05bc3a70c58d58a0f3378d36bf7..b7eb155ba27b5b40c4f4d1dafc87942839b887d4 100644 --- a/src/USER-MANIFOLD/manifold_thylakoid.cpp +++ b/src/USER-MANIFOLD/manifold_thylakoid.cpp @@ -1,5 +1,5 @@ #include "manifold_thylakoid.h" -#include +#include #include "comm.h" #include "domain.h" // For some checks regarding the simulation box. @@ -85,7 +85,7 @@ double manifold_thylakoid::g( const double *x ) error->one(FLERR,msg); } double con_val = p->g(x); - if( ISFINITE(con_val) ){ + if( std::isfinite(con_val) ){ return con_val; }else{ char msg[2048]; @@ -107,7 +107,7 @@ void manifold_thylakoid::n( const double *x, double *n ) error->one(FLERR,msg); } p->n(x,n); - if( ISFINITE(n[0]) && ISFINITE(n[1]) && ISFINITE(n[2]) ){ + if( std::isfinite(n[0]) && std::isfinite(n[1]) && std::isfinite(n[2]) ){ return; }else{ char msg[2048]; diff --git a/src/USER-MANIFOLD/manifold_thylakoid.h b/src/USER-MANIFOLD/manifold_thylakoid.h index 231525950d3324086f17b40508a77c35ebb8c7b4..5e5d3b9c4192a9c622c06da6daeee0722bf3cdff 100644 --- a/src/USER-MANIFOLD/manifold_thylakoid.h +++ b/src/USER-MANIFOLD/manifold_thylakoid.h @@ -3,7 +3,7 @@ #include "manifold.h" #include -#include +#include #include "manifold_thylakoid_shared.h" diff --git a/src/USER-MANIFOLD/manifold_thylakoid_shared.cpp b/src/USER-MANIFOLD/manifold_thylakoid_shared.cpp index 5b87ba7c2b9eec67bff54e044450bcbfa2b3523f..4c4297f822ef2cfa7eb4113f4e61bb234dac6bf8 100644 --- a/src/USER-MANIFOLD/manifold_thylakoid_shared.cpp +++ b/src/USER-MANIFOLD/manifold_thylakoid_shared.cpp @@ -1,5 +1,5 @@ #include "manifold_thylakoid_shared.h" -#include +#include using namespace LAMMPS_NS; using namespace user_manifold; diff --git a/src/USER-MANIFOLD/manifold_torus.cpp b/src/USER-MANIFOLD/manifold_torus.cpp index b46998b28d7f04b61a8fee406d266a0d4d03ad43..44a17725b5e2230e4cbc2e2fb5809ef693d99c0a 100644 --- a/src/USER-MANIFOLD/manifold_torus.cpp +++ b/src/USER-MANIFOLD/manifold_torus.cpp @@ -1,4 +1,4 @@ -#include +#include #include "manifold_torus.h" #include "error.h" diff --git a/src/USER-MEAMC/meam.h b/src/USER-MEAMC/meam.h index 4e86df62d5bad0b762db67a0e2cbf13a9a2ebebe..42fd722e016ce4dce882599cb1ff37fe24dd7422 100644 --- a/src/USER-MEAMC/meam.h +++ b/src/USER-MEAMC/meam.h @@ -2,8 +2,8 @@ #define LMP_MEAM_H #include "memory.h" -#include -#include +#include +#include #define maxelt 5 @@ -255,5 +255,5 @@ static inline double fdiv_zero(const double n, const double d) { return n / d; } -}; +} #endif diff --git a/src/USER-MEAMC/meam_funcs.cpp b/src/USER-MEAMC/meam_funcs.cpp index 3b7c114d5cc7e1e60baef248a9d220fc0a8200a7..599e9019d930aedac8a7c84ba45bfb8496f7a639 100644 --- a/src/USER-MEAMC/meam_funcs.cpp +++ b/src/USER-MEAMC/meam_funcs.cpp @@ -17,7 +17,7 @@ #include "meam.h" #include "math_special.h" -#include +#include using namespace LAMMPS_NS; diff --git a/src/USER-MEAMC/meam_setup_global.cpp b/src/USER-MEAMC/meam_setup_global.cpp index 7062d5ebca972c1a095222420926a189c335834e..7f8ad3d81f5f09fbff2224c28ee866ddf234686f 100644 --- a/src/USER-MEAMC/meam_setup_global.cpp +++ b/src/USER-MEAMC/meam_setup_global.cpp @@ -1,5 +1,5 @@ #include "meam.h" -#include +#include using namespace LAMMPS_NS; void diff --git a/src/USER-MEAMC/pair_meamc.cpp b/src/USER-MEAMC/pair_meamc.cpp index 2404005fdf695e9387b1a6d7a9ed5bc65262a23a..027e4c27a79ca000dd10a3b6383a97152f0a1bd1 100644 --- a/src/USER-MEAMC/pair_meamc.cpp +++ b/src/USER-MEAMC/pair_meamc.cpp @@ -15,10 +15,10 @@ Contributing author: Greg Wagner (SNL) ------------------------------------------------------------------------- */ -#include -#include -#include -#include +#include +#include +#include +#include #include "meam.h" #include "pair_meamc.h" #include "atom.h" diff --git a/src/USER-MESO/atom_vec_edpd.cpp b/src/USER-MESO/atom_vec_edpd.cpp index c8f1421512f5e74211e5e768f0cc89e9a6f58f61..d956e914b5d851108a01f07019ffb606e82e9d0c 100644 --- a/src/USER-MESO/atom_vec_edpd.cpp +++ b/src/USER-MESO/atom_vec_edpd.cpp @@ -10,8 +10,8 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include -#include +#include +#include #include "atom_vec_edpd.h" #include "atom.h" #include "comm.h" diff --git a/src/USER-MESO/atom_vec_mdpd.cpp b/src/USER-MESO/atom_vec_mdpd.cpp index 1d81bd2c39a0693d0becbf634800d1db32ec899f..5bc5e212ff62e5630da12864462ab901fbfca889 100644 --- a/src/USER-MESO/atom_vec_mdpd.cpp +++ b/src/USER-MESO/atom_vec_mdpd.cpp @@ -11,8 +11,8 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include -#include +#include +#include #include "atom_vec_mdpd.h" #include "atom.h" #include "comm.h" diff --git a/src/USER-MESO/atom_vec_tdpd.cpp b/src/USER-MESO/atom_vec_tdpd.cpp index 6733e3e4df51b3d1dddf7ee0691ba771929754f8..aa0dc93809f8d9b51065dfccc91306fac160a56b 100644 --- a/src/USER-MESO/atom_vec_tdpd.cpp +++ b/src/USER-MESO/atom_vec_tdpd.cpp @@ -11,8 +11,8 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include -#include +#include +#include #include "atom_vec_tdpd.h" #include "atom.h" #include "comm.h" diff --git a/src/USER-MESO/compute_edpd_temp_atom.cpp b/src/USER-MESO/compute_edpd_temp_atom.cpp index 15fdab2a69720102075f0c0b13c7ae1e11bc0345..119e0079d133dc50ba146952967cd99eb3dd3876 100644 --- a/src/USER-MESO/compute_edpd_temp_atom.cpp +++ b/src/USER-MESO/compute_edpd_temp_atom.cpp @@ -11,7 +11,7 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include +#include #include "compute_edpd_temp_atom.h" #include "atom.h" #include "update.h" diff --git a/src/USER-MESO/compute_tdpd_cc_atom.cpp b/src/USER-MESO/compute_tdpd_cc_atom.cpp index b33550f5c164075a373fb1c4dce29de126d4da7d..6378ed5ef674eada4fea33594ffde53559fdc4a6 100644 --- a/src/USER-MESO/compute_tdpd_cc_atom.cpp +++ b/src/USER-MESO/compute_tdpd_cc_atom.cpp @@ -11,7 +11,7 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include +#include #include "compute_tdpd_cc_atom.h" #include "atom.h" #include "update.h" diff --git a/src/USER-MESO/fix_edpd_source.cpp b/src/USER-MESO/fix_edpd_source.cpp index fb8fecdcdf470c3beb7edde514b2e2c187088b8e..56e855ad0c80fa7a0fec7d381976a39d685d85e3 100644 --- a/src/USER-MESO/fix_edpd_source.cpp +++ b/src/USER-MESO/fix_edpd_source.cpp @@ -11,8 +11,8 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include -#include +#include +#include #include "fix_edpd_source.h" #include "atom.h" #include "comm.h" diff --git a/src/USER-MESO/fix_mvv_dpd.cpp b/src/USER-MESO/fix_mvv_dpd.cpp index c1c4f203f1cc0547fd87b4c46d7b822b0308e435..c97a2d779c0de1595e13a5e09f2a3809d4057fa1 100644 --- a/src/USER-MESO/fix_mvv_dpd.cpp +++ b/src/USER-MESO/fix_mvv_dpd.cpp @@ -20,8 +20,8 @@ Email: zhen_li@brown.edu ------------------------------------------------------------------------- */ -#include -#include +#include +#include #include "fix_mvv_dpd.h" #include "atom.h" #include "force.h" diff --git a/src/USER-MESO/fix_mvv_edpd.cpp b/src/USER-MESO/fix_mvv_edpd.cpp index 12c8bbcafbbe0cb9e465ffc5cc9b5c50474023ea..89a831e121b9a37fbdb8271f9db554b2fa6d2d07 100644 --- a/src/USER-MESO/fix_mvv_edpd.cpp +++ b/src/USER-MESO/fix_mvv_edpd.cpp @@ -29,8 +29,8 @@ Communications, 2015, 51: 11038-11040. ------------------------------------------------------------------------- */ -#include -#include +#include +#include #include "fix_mvv_edpd.h" #include "atom.h" #include "force.h" diff --git a/src/USER-MESO/fix_mvv_tdpd.cpp b/src/USER-MESO/fix_mvv_tdpd.cpp index 58832e084654f8b938350f0819389c0876bf067d..e16171800b1b61bc44899fc0895adff7a52637a3 100644 --- a/src/USER-MESO/fix_mvv_tdpd.cpp +++ b/src/USER-MESO/fix_mvv_tdpd.cpp @@ -25,8 +25,8 @@ -reaction problems". The Journal of Chemical Physics, 2015, 143: 014101. ------------------------------------------------------------------------- */ -#include -#include +#include +#include #include "fix_mvv_tdpd.h" #include "atom.h" #include "force.h" diff --git a/src/USER-MESO/fix_tdpd_source.cpp b/src/USER-MESO/fix_tdpd_source.cpp index c58dff76be3915b8a5c313cf6e144cf351715bd5..21fecdf49d8c03848cbd45a89e77140c1c843468 100644 --- a/src/USER-MESO/fix_tdpd_source.cpp +++ b/src/USER-MESO/fix_tdpd_source.cpp @@ -11,8 +11,8 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include -#include +#include +#include #include "fix_tdpd_source.h" #include "atom.h" #include "comm.h" diff --git a/src/USER-MESO/pair_edpd.cpp b/src/USER-MESO/pair_edpd.cpp index 64d29cb65df27be31a658d5a4aeb5241090b9acf..351637a842018c6469c09a1929e5552487c20695 100644 --- a/src/USER-MESO/pair_edpd.cpp +++ b/src/USER-MESO/pair_edpd.cpp @@ -16,9 +16,11 @@ Email: zhen_li@brown.edu ------------------------------------------------------------------------- */ -#include -#include -#include +#include +#include +#include +#include +#include #include "pair_edpd.h" #include "atom.h" #include "atom_vec.h" @@ -31,8 +33,6 @@ #include "citeme.h" #include "memory.h" #include "error.h" -#include -#include using namespace LAMMPS_NS; @@ -59,7 +59,6 @@ static const char cite_pair_edpd[] = " volume = {51},\n" " pages = {11038--11040}\n" "}\n\n"; -; /* ---------------------------------------------------------------------- */ diff --git a/src/USER-MESO/pair_mdpd.cpp b/src/USER-MESO/pair_mdpd.cpp index 1b8cd45be98d06900975243bf4aad62eaf2791f7..f9acd3dbe1eb3c74fa2d0f1af87e8ce4ae42e80f 100644 --- a/src/USER-MESO/pair_mdpd.cpp +++ b/src/USER-MESO/pair_mdpd.cpp @@ -16,9 +16,10 @@ Email: zhen_li@brown.edu ------------------------------------------------------------------------- */ -#include -#include -#include +#include +#include +#include +#include #include "pair_mdpd.h" #include "atom.h" #include "atom_vec.h" @@ -31,7 +32,6 @@ #include "citeme.h" #include "memory.h" #include "error.h" -#include using namespace LAMMPS_NS; diff --git a/src/USER-MESO/pair_mdpd_rhosum.cpp b/src/USER-MESO/pair_mdpd_rhosum.cpp index ecfc9d5c00eb3d4f7ba4c86848d631b0805262f4..1264d03ed3b5dd9404fef9ba6a5eac0acb28b16d 100644 --- a/src/USER-MESO/pair_mdpd_rhosum.cpp +++ b/src/USER-MESO/pair_mdpd_rhosum.cpp @@ -19,8 +19,8 @@ Contributing author: Zhen Li (Brown University) ------------------------------------------------------------------------- */ -#include -#include +#include +#include #include "pair_mdpd_rhosum.h" #include "atom.h" #include "force.h" diff --git a/src/USER-MESO/pair_tdpd.cpp b/src/USER-MESO/pair_tdpd.cpp index 71dbaaba83e23bbe91f1404fb0422599adbb6851..b8bbf6d622f51e16f15813cbeb1af08a692adceb 100644 --- a/src/USER-MESO/pair_tdpd.cpp +++ b/src/USER-MESO/pair_tdpd.cpp @@ -16,9 +16,10 @@ Email: zhen_li@brown.edu ------------------------------------------------------------------------- */ -#include -#include -#include +#include +#include +#include +#include #include "pair_tdpd.h" #include "atom.h" #include "atom_vec.h" @@ -31,7 +32,6 @@ #include "citeme.h" #include "memory.h" #include "error.h" -#include using namespace LAMMPS_NS; @@ -280,7 +280,9 @@ void PairTDPD::coeff(int narg, char **arg) double power_one = force->numeric(FLERR,arg[4]); double cut_one = force->numeric(FLERR,arg[5]); double cutcc_one = force->numeric(FLERR,arg[6]); - double kappa_one[cc_species],epsilon_one[cc_species],powercc_one[cc_species]; + double *kappa_one = new double[cc_species]; + double *epsilon_one = new double[cc_species]; + double *powercc_one = new double[cc_species]; for(int k=0; knumeric(FLERR,arg[7+3*k]); epsilon_one[k] = force->numeric(FLERR,arg[8+3*k]); @@ -304,6 +306,9 @@ void PairTDPD::coeff(int narg, char **arg) setflag[i][j] = 1; count++; } + delete[] kappa_one; + delete[] epsilon_one; + delete[] powercc_one; if (count == 0) error->all(FLERR,"Incorrect args for pair coefficients"); } diff --git a/src/USER-MISC/README b/src/USER-MISC/README index a8c33fa38056454194ff2346c9bd2d4822019200..7fc931b9625ed9fa6884bb5b1564692cf77564dd 100644 --- a/src/USER-MISC/README +++ b/src/USER-MISC/README @@ -39,6 +39,7 @@ dihedral_style spherical, Andrew Jewett, jewett.aij@gmail.com, 15 Jul 16 dihedral_style table, Andrew Jewett, jewett.aij@gmail.com, 10 Jan 12 fix addtorque, Laurent Joly (U Lyon), ljoly.ulyon at gmail.com, 8 Aug 11 fix ave/correlate/long, Jorge Ramirez (UPM Madrid), jorge.ramirez at upm.es, 21 Oct 2015 +fix bond/react, Jacob Gissinger (CU Boulder), info at disarmmd.org, 24 Feb 2018 fix filter/corotate, Lukas Fath (KIT), lukas.fath at kit.edu, 15 Mar 2017 fix flow/gauss, Joel Eaves (CU Boulder), Joel.Eaves@Colorado.edu, 23 Aug 2016 fix gle, Michele Ceriotti (EPFL Lausanne), michele.ceriotti at gmail.com, 24 Nov 2014 diff --git a/src/USER-MISC/angle_cosine_shift.cpp b/src/USER-MISC/angle_cosine_shift.cpp index 66f5c82c8445185b07e618d77fcace93f03cba32..a361db497081441da026375482b8dcaef575bd4e 100644 --- a/src/USER-MISC/angle_cosine_shift.cpp +++ b/src/USER-MISC/angle_cosine_shift.cpp @@ -15,8 +15,8 @@ Contributing author: Carsten Svaneborg, science@zqex.dk ------------------------------------------------------------------------- */ -#include -#include +#include +#include #include "angle_cosine_shift.h" #include "atom.h" #include "neighbor.h" @@ -34,7 +34,10 @@ using namespace MathConst; /* ---------------------------------------------------------------------- */ -AngleCosineShift::AngleCosineShift(LAMMPS *lmp) : Angle(lmp) {} +AngleCosineShift::AngleCosineShift(LAMMPS *lmp) : Angle(lmp) +{ + kcost = NULL; +} /* ---------------------------------------------------------------------- */ diff --git a/src/USER-MISC/angle_cosine_shift.h b/src/USER-MISC/angle_cosine_shift.h index b8ab74ee43d886a452ce542ba77c07244b4e529e..030709a0e20ba90a8a168fe11fcd1b53a33f72da 100644 --- a/src/USER-MISC/angle_cosine_shift.h +++ b/src/USER-MISC/angle_cosine_shift.h @@ -20,7 +20,7 @@ AngleStyle(cosine/shift,AngleCosineShift) #ifndef LMP_ANGLE_COSINE_SHIFT_H #define LMP_ANGLE_COSINE_SHIFT_H -#include +#include #include "angle.h" namespace LAMMPS_NS { diff --git a/src/USER-MISC/angle_cosine_shift_exp.cpp b/src/USER-MISC/angle_cosine_shift_exp.cpp index 6d11c6894e0b7d1734b6393b582b8373c82f2c2d..c87c73171a9509fc8895ab9ac1caaa58f0b64dde 100644 --- a/src/USER-MISC/angle_cosine_shift_exp.cpp +++ b/src/USER-MISC/angle_cosine_shift_exp.cpp @@ -15,8 +15,8 @@ Contributing author: Carsten Svaneborg, science@zqex.dk ------------------------------------------------------------------------- */ -#include -#include +#include +#include #include "angle_cosine_shift_exp.h" #include "atom.h" #include "neighbor.h" @@ -34,7 +34,16 @@ using namespace MathConst; /* ---------------------------------------------------------------------- */ -AngleCosineShiftExp::AngleCosineShiftExp(LAMMPS *lmp) : Angle(lmp) {} +AngleCosineShiftExp::AngleCosineShiftExp(LAMMPS *lmp) : Angle(lmp) +{ + doExpansion = NULL; + umin = NULL; + a = NULL; + opt1 = NULL; + theta0 = NULL; + sint = NULL; + cost = NULL; +} /* ---------------------------------------------------------------------- */ diff --git a/src/USER-MISC/angle_cosine_shift_exp.h b/src/USER-MISC/angle_cosine_shift_exp.h index 4db9e1f6960067df88249bc1ea5539594cf30f73..8b8e389380b7af7be8f1a2ce4816827c19000d29 100644 --- a/src/USER-MISC/angle_cosine_shift_exp.h +++ b/src/USER-MISC/angle_cosine_shift_exp.h @@ -18,7 +18,7 @@ AngleStyle(cosine/shift/exp,AngleCosineShiftExp) #ifndef LMP_ANGLE_COSINE_SHIFT_EXP_H #define LMP_ANGLE_COSINE_SHIFT_EXP_H -#include +#include #include "angle.h" namespace LAMMPS_NS { diff --git a/src/USER-MISC/angle_dipole.cpp b/src/USER-MISC/angle_dipole.cpp index 1e8c0e18fb1ba99594e9ac19231364540dad6a6c..bcb631c61f065353cbb60761a4e693c28800693a 100644 --- a/src/USER-MISC/angle_dipole.cpp +++ b/src/USER-MISC/angle_dipole.cpp @@ -15,8 +15,8 @@ Contributing authors: Mario Orsi & Wei Ding (QMUL), m.orsi@qmul.ac.uk ------------------------------------------------------------------------- */ -#include -#include +#include +#include #include "angle_dipole.h" #include "atom.h" #include "neighbor.h" @@ -32,7 +32,11 @@ using namespace MathConst; /* ---------------------------------------------------------------------- */ -AngleDipole::AngleDipole(LAMMPS *lmp) : Angle(lmp) {} +AngleDipole::AngleDipole(LAMMPS *lmp) : Angle(lmp) +{ + k = NULL; + gamma0 = NULL; +} /* ---------------------------------------------------------------------- */ diff --git a/src/USER-MISC/angle_dipole.h b/src/USER-MISC/angle_dipole.h index 347eecfca4a098477bf9a419a8fd6285fe51cdda..6c5dccb803677b274c7cd903549389b80befb986 100644 --- a/src/USER-MISC/angle_dipole.h +++ b/src/USER-MISC/angle_dipole.h @@ -20,7 +20,7 @@ AngleStyle(dipole,AngleDipole) #ifndef LMP_ANGLE_DIPOLE_H #define LMP_ANGLE_DIPOLE_H -#include +#include #include "angle.h" namespace LAMMPS_NS { diff --git a/src/USER-MISC/angle_fourier.cpp b/src/USER-MISC/angle_fourier.cpp index 689caeaa5f457b6b3d6dcf4a6c1fe760aec2c47d..e6cc1f1a7e9945a55091002529051649f78186a9 100644 --- a/src/USER-MISC/angle_fourier.cpp +++ b/src/USER-MISC/angle_fourier.cpp @@ -16,8 +16,8 @@ [ based on angle_cosine_squared.cpp Naveen Michaud-Agrawal (Johns Hopkins U)] ------------------------------------------------------------------------- */ -#include -#include +#include +#include #include "angle_fourier.h" #include "atom.h" #include "neighbor.h" @@ -35,7 +35,13 @@ using namespace MathConst; /* ---------------------------------------------------------------------- */ -AngleFourier::AngleFourier(LAMMPS *lmp) : Angle(lmp) {} +AngleFourier::AngleFourier(LAMMPS *lmp) : Angle(lmp) +{ + k = NULL; + C0 = NULL; + C1 = NULL; + C2 = NULL; +} /* ---------------------------------------------------------------------- */ diff --git a/src/USER-MISC/angle_fourier.h b/src/USER-MISC/angle_fourier.h index da5c96479f2febf30a9ca0f9f945980c216f69e6..14b4eedf57be4bee470b70243a9b30a5ec7e6554 100644 --- a/src/USER-MISC/angle_fourier.h +++ b/src/USER-MISC/angle_fourier.h @@ -20,7 +20,7 @@ AngleStyle(fourier,AngleFourier) #ifndef ANGLE_FOURIER_H #define ANGLE_FOURIER_H -#include +#include #include "angle.h" namespace LAMMPS_NS { diff --git a/src/USER-MISC/angle_fourier_simple.cpp b/src/USER-MISC/angle_fourier_simple.cpp index bd4322fe78ca77e385d4c3668b1594408f9a55b9..8464fe815c9db0e9948ec9a0c7185a4409edf6e3 100644 --- a/src/USER-MISC/angle_fourier_simple.cpp +++ b/src/USER-MISC/angle_fourier_simple.cpp @@ -16,8 +16,8 @@ [ based on angle_cosine_squared.cpp Naveen Michaud-Agrawal (Johns Hopkins U)] ------------------------------------------------------------------------- */ -#include -#include +#include +#include #include "angle_fourier_simple.h" #include "atom.h" #include "neighbor.h" @@ -35,7 +35,12 @@ using namespace MathConst; /* ---------------------------------------------------------------------- */ -AngleFourierSimple::AngleFourierSimple(LAMMPS *lmp) : Angle(lmp) {} +AngleFourierSimple::AngleFourierSimple(LAMMPS *lmp) : Angle(lmp) +{ + k = NULL; + C = NULL; + N = NULL; +} /* ---------------------------------------------------------------------- */ diff --git a/src/USER-MISC/angle_fourier_simple.h b/src/USER-MISC/angle_fourier_simple.h index ca160f185da7f393f9926a6f84a2e1aca232d6a5..3a7bd37750a93b029f0917a95dd5a7374c2a2e12 100644 --- a/src/USER-MISC/angle_fourier_simple.h +++ b/src/USER-MISC/angle_fourier_simple.h @@ -20,7 +20,7 @@ AngleStyle(fourier/simple,AngleFourierSimple) #ifndef ANGLE_FOURIER_SIMPLE_H #define ANGLE_FOURIER_SIMPLE_H -#include +#include #include "angle.h" namespace LAMMPS_NS { diff --git a/src/USER-MISC/angle_quartic.cpp b/src/USER-MISC/angle_quartic.cpp index 5d990003a88ac063d1a6c108402a55fd5c3ecd9e..356f2df5d478683e4c0be128ff589f0de0a54047 100644 --- a/src/USER-MISC/angle_quartic.cpp +++ b/src/USER-MISC/angle_quartic.cpp @@ -16,8 +16,8 @@ [ based on angle_harmonic.cpp] ------------------------------------------------------------------------- */ -#include -#include +#include +#include #include "angle_quartic.h" #include "atom.h" #include "neighbor.h" diff --git a/src/USER-MISC/angle_quartic.h b/src/USER-MISC/angle_quartic.h index 8844ad111de54d44d8f1c59828fc9cc9b056bfaa..7043cab06413dda4da43caa8baac0aa3a762cf6c 100644 --- a/src/USER-MISC/angle_quartic.h +++ b/src/USER-MISC/angle_quartic.h @@ -20,7 +20,7 @@ AngleStyle(quartic,AngleQuartic) #ifndef LMP_ANGLE_QUARTIC_H #define LMP_ANGLE_QUARTIC_H -#include +#include #include "angle.h" namespace LAMMPS_NS { diff --git a/src/USER-MISC/bond_harmonic_shift.cpp b/src/USER-MISC/bond_harmonic_shift.cpp index 70db2cc2bd690f73ec687b9aeb9e616867853a33..7148c5438d1d4ff200915edbb5c1fda345bd3d01 100644 --- a/src/USER-MISC/bond_harmonic_shift.cpp +++ b/src/USER-MISC/bond_harmonic_shift.cpp @@ -15,8 +15,8 @@ Contributing author: Carsten Svaneborg, science@zqex.dk ------------------------------------------------------------------------- */ -#include -#include +#include +#include #include "bond_harmonic_shift.h" #include "atom.h" #include "neighbor.h" diff --git a/src/USER-MISC/bond_harmonic_shift.h b/src/USER-MISC/bond_harmonic_shift.h index 95dc091a62926894c99417895050c7743a2c2b6f..ff0d358243a832c36e43333ce5707a4321fa9fcc 100644 --- a/src/USER-MISC/bond_harmonic_shift.h +++ b/src/USER-MISC/bond_harmonic_shift.h @@ -20,7 +20,7 @@ BondStyle(harmonic/shift,BondHarmonicShift) #ifndef LMP_BOND_HARMONIC_SHIFT_H #define LMP_BOND_HARMONIC_SHIFT_H -#include +#include #include "bond.h" namespace LAMMPS_NS { diff --git a/src/USER-MISC/bond_harmonic_shift_cut.cpp b/src/USER-MISC/bond_harmonic_shift_cut.cpp index aa0091019dbc2509e83c86732c02c901ff66df85..20c8a1a30019fb5cb3bdb99b597e91c6fd116778 100644 --- a/src/USER-MISC/bond_harmonic_shift_cut.cpp +++ b/src/USER-MISC/bond_harmonic_shift_cut.cpp @@ -15,8 +15,8 @@ Contributing author: Carsten Svaneborg, science@zqex.dk ------------------------------------------------------------------------- */ -#include -#include +#include +#include #include "bond_harmonic_shift_cut.h" #include "atom.h" #include "neighbor.h" diff --git a/src/USER-MISC/bond_harmonic_shift_cut.h b/src/USER-MISC/bond_harmonic_shift_cut.h index 9b2587936ec7012dfef6af00b715cc1a459bb4a2..5db76d51aa5fbde88bc2061a4b34c506bcd239c3 100644 --- a/src/USER-MISC/bond_harmonic_shift_cut.h +++ b/src/USER-MISC/bond_harmonic_shift_cut.h @@ -20,7 +20,7 @@ BondStyle(harmonic/shift/cut,BondHarmonicShiftCut) #ifndef LMP_BOND_HARMONIC_SHIFT_CUT_H #define LMP_BOND_HARMONIC_SHIFT_CUT_H -#include +#include #include "bond.h" namespace LAMMPS_NS { diff --git a/src/USER-MISC/compute_ackland_atom.cpp b/src/USER-MISC/compute_ackland_atom.cpp index 285f64a5e94bec9678fcd9d57493fdf4d90902e0..a17aefe71b46b0dd435473c9d917eb6a74561365 100644 --- a/src/USER-MISC/compute_ackland_atom.cpp +++ b/src/USER-MISC/compute_ackland_atom.cpp @@ -12,11 +12,13 @@ ------------------------------------------------------------------------- */ /* ---------------------------------------------------------------------- - Contributing author: G. Ziegenhain, gerolf@ziegenhain.com - Copyright (C) 2007 + Contributing author: G. Ziegenhain, gerolf@ziegenhain.com + Copyright (C) 2007 + Updated algorithm by: Brian Barnes, brian.c.barnes11.civ@mail.mil ------------------------------------------------------------------------- */ -#include +#include +#include #include "compute_ackland_atom.h" #include "atom.h" #include "update.h" @@ -29,7 +31,6 @@ #include "comm.h" #include "memory.h" #include "error.h" -#include using namespace LAMMPS_NS; @@ -40,7 +41,8 @@ enum{UNKNOWN,BCC,FCC,HCP,ICO}; ComputeAcklandAtom::ComputeAcklandAtom(LAMMPS *lmp, int narg, char **arg) : Compute(lmp, narg, arg) { - if (narg != 3) error->all(FLERR,"Illegal compute ackland/atom command"); + if ((narg < 3) || (narg > 5)) + error->all(FLERR,"Illegal compute ackland/atom command"); peratom_flag = 1; size_peratom_cols = 0; @@ -48,10 +50,26 @@ ComputeAcklandAtom::ComputeAcklandAtom(LAMMPS *lmp, int narg, char **arg) : nmax = 0; structure = NULL; maxneigh = 0; + legacy = 0; distsq = NULL; nearest = NULL; nearest_n0 = NULL; nearest_n1 = NULL; + + int iarg = 3; + while (narg > iarg) { + if (strcmp("legacy",arg[iarg]) == 0) { + ++iarg; + if (iarg >= narg) + error->all(FLERR,"Invalid compute ackland/atom command"); + if (strcmp("yes",arg[iarg]) == 0) + legacy = 1; + else if (strcmp("no",arg[iarg]) == 0) + legacy = 0; + else error->all(FLERR,"Invalid compute ackland/atom command"); + } + ++iarg; + } } /* ---------------------------------------------------------------------- */ @@ -140,13 +158,13 @@ void ComputeAcklandAtom::compute_peratom() // ensure distsq and nearest arrays are long enough if (jnum > maxneigh) { - memory->destroy(distsq); - memory->destroy(nearest); + memory->destroy(distsq); + memory->destroy(nearest); memory->destroy(nearest_n0); memory->destroy(nearest_n1); - maxneigh = jnum; - memory->create(distsq,maxneigh,"compute/ackland/atom:distsq"); - memory->create(nearest,maxneigh,"compute/ackland/atom:nearest"); + maxneigh = jnum; + memory->create(distsq,maxneigh,"compute/ackland/atom:distsq"); + memory->create(nearest,maxneigh,"compute/ackland/atom:nearest"); memory->create(nearest_n0,maxneigh,"compute/ackland/atom:nearest_n0"); memory->create(nearest_n1,maxneigh,"compute/ackland/atom:nearest_n1"); } @@ -157,14 +175,14 @@ void ComputeAcklandAtom::compute_peratom() n = 0; for (jj = 0; jj < jnum; jj++) { - j = jlist[jj]; + j = jlist[jj]; j &= NEIGHMASK; - delx = xtmp - x[j][0]; - dely = ytmp - x[j][1]; - delz = ztmp - x[j][2]; - rsq = delx*delx + dely*dely + delz*delz; - if (rsq < cutsq) { + delx = xtmp - x[j][0]; + dely = ytmp - x[j][1]; + delz = ztmp - x[j][2]; + rsq = delx*delx + dely*dely + delz*delz; + if (rsq < cutsq) { distsq[n] = rsq; nearest[n++] = j; } @@ -188,12 +206,12 @@ void ComputeAcklandAtom::compute_peratom() n1_dist_sq = 1.55*r0_sq; int n0 = 0, n1 = 0; for (j = 0; j < n; j++) { - if (distsq[j] < n1_dist_sq) { - nearest_n1[n1++] = nearest[j]; - if (distsq[j] < n0_dist_sq) { - nearest_n0[n0++] = nearest[j]; - } - } + if (distsq[j] < n1_dist_sq) { + nearest_n1[n1++] = nearest[j]; + if (distsq[j] < n0_dist_sq) { + nearest_n0[n0++] = nearest[j]; + } + } } // Evaluate all angles <(r_ij,rik) forall n0 particles with: @@ -231,47 +249,98 @@ void ComputeAcklandAtom::compute_peratom() else chi[7]++; } } + if (legacy) { - if (chi[7] > 0 || n0 < 11) structure[i] = UNKNOWN; - else if (chi[0] == 7) structure[i] = BCC; - else if (chi[0] == 6) structure[i] = FCC; - else if (chi[0] == 3) structure[i] = HCP; - else { + // This is the original implementation by Gerolf Ziegenhain // Deviations from the different lattice structures + double delta_bcc = 0.35*chi[4]/(double)(chi[5]+chi[6]-chi[4]); double delta_cp = fabs(1.-(double)chi[6]/24.); + double delta_fcc = 0.61*(fabs((double)(chi[0]+chi[1]-6.))+ + (double)chi[2])/6.0; + double delta_hcp = (fabs((double)chi[0]-3.)+ + fabs((double)chi[0]+(double)chi[1]+ + (double)chi[2]+(double)chi[3]-9.0))/12.0; + + // Identification of the local structure according to the reference + + if (chi[0] == 7) { delta_bcc = 0.; } + else if (chi[0] == 6) { delta_fcc = 0.; } + else if (chi[0] <= 3) { delta_hcp = 0.; } + + if (chi[7] > 0.) + structure[i] = UNKNOWN; + else + if (chi[4] < 3.) + { + if (n1 > 13 || n1 < 11) + structure[i] = UNKNOWN; + else + structure[i] = ICO; + } else + if (delta_bcc <= delta_cp) + { + if (n1 < 11) + structure[i] = UNKNOWN; + else + structure[i] = BCC; + } else + if (n1 > 12 || n1 < 11) + structure[i] = UNKNOWN; + else + if (delta_fcc < delta_hcp) + structure[i] = FCC; + else + structure[i] = HCP; - // ensure we do not get divide by zero - // and if we will, make delta_bcc irrelevant - double delta_bcc = delta_cp + 1.0; - int chi56m4 = chi[5]+chi[6]-chi[4]; + } else { - // note that chi[7] presumed zero - if (chi56m4 != 0) delta_bcc = 0.35*chi[4]/(double)chi56m4; + // This is the updated implementation by Brian Barnes - double delta_fcc = 0.61*(fabs((double)(chi[0]+chi[1]-6)) - +(double)chi[2])/6.0; + if (chi[7] > 0 || n0 < 11) structure[i] = UNKNOWN; + else if (chi[0] == 7) structure[i] = BCC; + else if (chi[0] == 6) structure[i] = FCC; + else if (chi[0] == 3) structure[i] = HCP; + else { + // Deviations from the different lattice structures - double delta_hcp = (fabs((double)chi[0]-3.)+fabs((double)chi[0] - +(double)chi[1]+(double)chi[2]+(double)chi[3] - -9.0))/12.0; + double delta_cp = fabs(1.-(double)chi[6]/24.); - // Identification of the local structure according to the reference + // ensure we do not get divide by zero + // and if we will, make delta_bcc irrelevant + double delta_bcc = delta_cp + 1.0; + int chi56m4 = chi[5]+chi[6]-chi[4]; - if (delta_bcc >= 0.1 && delta_cp >= 0.1 && delta_fcc >= 0.1 - && delta_hcp >= 0.1) structure[i] = UNKNOWN; + // note that chi[7] presumed zero + if (chi56m4 != 0) delta_bcc = 0.35*chi[4]/(double)chi56m4; - // not part of Ackland-Jones 2006; included for backward compatibility - if (chi[4] < 3. && n1 == 12) structure[i] = ICO; + double delta_fcc = 0.61*(fabs((double)(chi[0]+chi[1]-6)) + +(double)chi[2])/6.0; + + double delta_hcp = (fabs((double)chi[0]-3.) + +fabs((double)chi[0] + +(double)chi[1] + +(double)chi[2] + +(double)chi[3] + -9.0))/12.0; + + // Identification of the local structure according to the reference + + if (delta_bcc >= 0.1 && delta_cp >= 0.1 && delta_fcc >= 0.1 + && delta_hcp >= 0.1) structure[i] = UNKNOWN; + + // not part of Ackland-Jones 2006; included for backward compatibility + if (chi[4] < 3. && n1 == 12) structure[i] = ICO; - else { - if (delta_bcc <= delta_cp && n1 > 10 && n1 < 13) structure[i] = BCC; else { - if (n0 > 12) structure[i] = UNKNOWN; + if (delta_bcc <= delta_cp && n1 > 10 && n1 < 13) structure[i] = BCC; else { - if (delta_fcc < delta_hcp) structure[i] = FCC; - else - structure[i] = HCP; + if (n0 > 12) structure[i] = UNKNOWN; + else { + if (delta_fcc < delta_hcp) structure[i] = FCC; + else + structure[i] = HCP; + } } } } diff --git a/src/USER-MISC/compute_ackland_atom.h b/src/USER-MISC/compute_ackland_atom.h index 5464a10f872101fc5b07a85dab118d091ab2980e..dd70762627646080dace0fd75dfc94a11d98feaf 100644 --- a/src/USER-MISC/compute_ackland_atom.h +++ b/src/USER-MISC/compute_ackland_atom.h @@ -34,7 +34,7 @@ class ComputeAcklandAtom : public Compute { double memory_usage(); private: - int nmax,maxneigh; + int nmax,maxneigh,legacy; double *distsq; int *nearest, *nearest_n0, *nearest_n1; double *structure; diff --git a/src/USER-MISC/compute_basal_atom.cpp b/src/USER-MISC/compute_basal_atom.cpp index cd393eb2acf81c6d2f14cc3516e87c24d6a3a906..4d8627a11fb66534b0e982413790156d4efaf524 100644 --- a/src/USER-MISC/compute_basal_atom.cpp +++ b/src/USER-MISC/compute_basal_atom.cpp @@ -16,7 +16,8 @@ Copyright (C) 2013 ------------------------------------------------------------------------- */ -#include +#include +#include #include "compute_basal_atom.h" #include "atom.h" #include "update.h" @@ -29,7 +30,6 @@ #include "comm.h" #include "memory.h" #include "error.h" -#include using namespace LAMMPS_NS; @@ -204,8 +204,11 @@ void ComputeBasalAtom::compute_peratom() double bond_angle; double norm_j, norm_k; chi[0] = chi[1] = chi[2] = chi[3] = chi[4] = chi[5] = chi[6] = chi[7] = 0; - double x_ij, y_ij, z_ij, x_ik, y_ik, z_ik,x3[n0],y3[n0],z3[n0], - xmean5, ymean5, zmean5, xmean6, ymean6, zmean6, xmean7, ymean7, zmean7; + double x_ij, y_ij, z_ij, x_ik, y_ik, z_ik, xmean5, ymean5, zmean5, + xmean6, ymean6, zmean6, xmean7, ymean7, zmean7; + double *x3 = new double[n0]; + double *y3 = new double[n0]; + double *z3 = new double[n0]; for (j = 0; j < n0; j++) { x_ij = x[i][0]-x[nearest_n0[j]][0]; y_ij = x[i][1]-x[nearest_n0[j]][1]; @@ -411,9 +414,12 @@ void ComputeBasalAtom::compute_peratom() } } } - } - //if there are less than two ~180 degree bond angles, the algorithm returns null - else BPV[i][0] = BPV[i][1] = BPV[i][2] = 0.0; + //if there are less than two ~180 degree bond angles, the algorithm returns null + } else BPV[i][0] = BPV[i][1] = BPV[i][2] = 0.0; + + delete[] x3; + delete[] y3; + delete[] z3; //normalize BPV: double Mag = sqrt(BPV[i][0]*BPV[i][0] + diff --git a/src/USER-MISC/compute_cnp_atom.cpp b/src/USER-MISC/compute_cnp_atom.cpp index f479486b79cc18f48fe7032f0c15ba3e9509f2df..51cf3ab07a43628ba454f708400d386bdffdb54f 100644 --- a/src/USER-MISC/compute_cnp_atom.cpp +++ b/src/USER-MISC/compute_cnp_atom.cpp @@ -21,9 +21,9 @@ branicio@usc.edu ------------------------------------------------------------------------- */ -#include -#include -#include +#include +#include +#include #include "compute_cnp_atom.h" #include "atom.h" diff --git a/src/USER-MISC/compute_pressure_grem.cpp b/src/USER-MISC/compute_pressure_grem.cpp index ae9179cc4313745ea248d606f1c4768e4fa86e82..087c01bd8e2ad8da526bf213609c8f7241377b0d 100644 --- a/src/USER-MISC/compute_pressure_grem.cpp +++ b/src/USER-MISC/compute_pressure_grem.cpp @@ -12,8 +12,8 @@ ------------------------------------------------------------------------- */ #include -#include -#include +#include +#include #include "compute_pressure_grem.h" #include "atom.h" #include "update.h" diff --git a/src/USER-MISC/compute_temp_rotate.cpp b/src/USER-MISC/compute_temp_rotate.cpp index b948738e0054dca0de40bde7481d678eb2bac198..66f1b8f5f75939d02092f5c1b9a7bf50a404c059 100644 --- a/src/USER-MISC/compute_temp_rotate.cpp +++ b/src/USER-MISC/compute_temp_rotate.cpp @@ -16,8 +16,8 @@ ------------------------------------------------------------------------- */ #include -#include -#include +#include +#include #include "compute_temp_rotate.h" #include "atom.h" #include "update.h" diff --git a/src/USER-MISC/dihedral_cosine_shift_exp.cpp b/src/USER-MISC/dihedral_cosine_shift_exp.cpp index 85ff4b27191e3b6d19bce335781f7bd715fbfff1..82da173f8e2c3d14bce6344f0f9d8080effd9594 100644 --- a/src/USER-MISC/dihedral_cosine_shift_exp.cpp +++ b/src/USER-MISC/dihedral_cosine_shift_exp.cpp @@ -16,8 +16,8 @@ ------------------------------------------------------------------------- */ #include -#include -#include +#include +#include #include "dihedral_cosine_shift_exp.h" #include "atom.h" #include "comm.h" @@ -26,6 +26,7 @@ #include "force.h" #include "update.h" #include "memory.h" +#include "math_const.h" #include "error.h" using namespace LAMMPS_NS; @@ -285,9 +286,9 @@ void DihedralCosineShiftExp::coeff(int narg, char **arg) doExpansion[i]=(fabs(a_)<0.001); umin[i] = umin_; a[i] = a_; - cost[i] = cos(theta0_*3.14159265/180); - sint[i] = sin(theta0_*3.14159265/180); - theta[i] = theta0_*3.14159265/180; + cost[i] = cos(theta0_*MathConst::MY_PI/180.0); + sint[i] = sin(theta0_*MathConst::MY_PI/180.0); + theta[i] = theta0_*MathConst::MY_PI/180.0; if (!doExpansion[i]) opt1[i]=umin_/(exp(a_)-1); @@ -338,3 +339,14 @@ void DihedralCosineShiftExp::read_restart(FILE *fp) if (!doExpansion[i]) opt1[i]=umin[i]/(exp(a[i])-1); } } + +/* ---------------------------------------------------------------------- + proc 0 writes to data file +------------------------------------------------------------------------- */ + +void DihedralCosineShiftExp::write_data(FILE *fp) +{ + for (int i = 1; i <= atom->ndihedraltypes; i++) + fprintf(fp,"%d %g %g %g\n",i,umin[i], + theta[i]*180.0/MathConst::MY_PI,a[i]); +} diff --git a/src/USER-MISC/dihedral_cosine_shift_exp.h b/src/USER-MISC/dihedral_cosine_shift_exp.h index 819fd769cb13cb3fad446b9e4fd9faa9f79b93af..fc4be5049b49c920d40d4fe83995a3b89f2b87db 100644 --- a/src/USER-MISC/dihedral_cosine_shift_exp.h +++ b/src/USER-MISC/dihedral_cosine_shift_exp.h @@ -20,7 +20,7 @@ DihedralStyle(cosine/shift/exp,DihedralCosineShiftExp) #ifndef LMP_DIHEDRAL_COSINE_SHIFT_EXP_H #define LMP_DIHEDRAL_COSINE_SHIFT_EXP_H -#include +#include #include "dihedral.h" namespace LAMMPS_NS { @@ -33,6 +33,7 @@ class DihedralCosineShiftExp : public Dihedral { void coeff(int, char **); void write_restart(FILE *); void read_restart(FILE *); + void write_data(FILE *); protected: bool *doExpansion; diff --git a/src/USER-MISC/dihedral_fourier.cpp b/src/USER-MISC/dihedral_fourier.cpp index fff10fde11b3c10b4c69294e9b0579869ff807a3..7c405ee28c3378c12a4ba6d28b44b366a1b2abb5 100644 --- a/src/USER-MISC/dihedral_fourier.cpp +++ b/src/USER-MISC/dihedral_fourier.cpp @@ -17,8 +17,8 @@ ------------------------------------------------------------------------- */ #include -#include -#include +#include +#include #include "dihedral_fourier.h" #include "atom.h" #include "comm.h" diff --git a/src/USER-MISC/dihedral_fourier.h b/src/USER-MISC/dihedral_fourier.h index 4cdb7f222621666624816bcc89ab65d0562a3d58..c1ed843c3486348cd90d364f2d46453838f6d1fc 100644 --- a/src/USER-MISC/dihedral_fourier.h +++ b/src/USER-MISC/dihedral_fourier.h @@ -20,7 +20,7 @@ DihedralStyle(fourier,DihedralFourier) #ifndef LMP_DIHEDRAL_FOURIER_H #define LMP_DIHEDRAL_FOURIER_H -#include +#include #include "dihedral.h" namespace LAMMPS_NS { diff --git a/src/USER-MISC/dihedral_nharmonic.cpp b/src/USER-MISC/dihedral_nharmonic.cpp index abb5904b6af55773b43a505263a457c2e92c0a6b..f8e885068070e3d7bbbf1601a7654e7331b5aa70 100644 --- a/src/USER-MISC/dihedral_nharmonic.cpp +++ b/src/USER-MISC/dihedral_nharmonic.cpp @@ -16,8 +16,8 @@ [ based on dihedral_multi_harmonic.cpp Mathias Puetz (SNL) and friends ] ------------------------------------------------------------------------- */ -#include -#include +#include +#include #include "dihedral_nharmonic.h" #include "atom.h" #include "neighbor.h" diff --git a/src/USER-MISC/dihedral_nharmonic.h b/src/USER-MISC/dihedral_nharmonic.h index 2e8050feb9348307b0c21edaf5aa3a10aeaf44f1..7c6a35b200a3a6a8bb91cb21b9a5d9babc3cdfd8 100644 --- a/src/USER-MISC/dihedral_nharmonic.h +++ b/src/USER-MISC/dihedral_nharmonic.h @@ -20,7 +20,7 @@ DihedralStyle(nharmonic,DihedralNHarmonic) #ifndef DIHEDRAL_NHARMONIC_H #define DIHEDRAL_NHARMONIC_H -#include +#include #include "dihedral.h" namespace LAMMPS_NS { diff --git a/src/USER-MISC/dihedral_quadratic.cpp b/src/USER-MISC/dihedral_quadratic.cpp index 6841492b2f077f5b2e875810b96c1a21a3761dd1..1b64b52faf34e50792105314277727edeb9efb1b 100644 --- a/src/USER-MISC/dihedral_quadratic.cpp +++ b/src/USER-MISC/dihedral_quadratic.cpp @@ -16,8 +16,8 @@ [ based on dihedral_helix.cpp Paul Crozier (SNL) ] ------------------------------------------------------------------------- */ -#include -#include +#include +#include #include "dihedral_quadratic.h" #include "atom.h" #include "neighbor.h" @@ -333,3 +333,12 @@ void DihedralQuadratic::read_restart(FILE *fp) for (int i = 1; i <= atom->ndihedraltypes; i++) setflag[i] = 1; } +/* ---------------------------------------------------------------------- + proc 0 writes to data file +------------------------------------------------------------------------- */ + +void DihedralQuadratic::write_data(FILE *fp) +{ + for (int i = 1; i <= atom->ndihedraltypes; i++) + fprintf(fp,"%d %g %g \n",i,k[i],phi0[i]*180.0/MY_PI); +} diff --git a/src/USER-MISC/dihedral_quadratic.h b/src/USER-MISC/dihedral_quadratic.h index 638efac6687dc7f83754384d41c4cff0208a14b7..edc29c3cf8b5b87a84d291450dacdeb359d05ac1 100644 --- a/src/USER-MISC/dihedral_quadratic.h +++ b/src/USER-MISC/dihedral_quadratic.h @@ -20,7 +20,7 @@ DihedralStyle(quadratic,DihedralQuadratic) #ifndef LMP_DIHEDRAL_QUADRATIC_H #define LMP_DIHEDRAL_QUADRATIC_H -#include +#include #include "dihedral.h" namespace LAMMPS_NS { @@ -33,6 +33,7 @@ class DihedralQuadratic : public Dihedral { void coeff(int, char **); void write_restart(FILE *); void read_restart(FILE *); + void write_data(FILE *); protected: double *k,*phi0; diff --git a/src/USER-MISC/dihedral_spherical.h b/src/USER-MISC/dihedral_spherical.h index 0067e5eca85058dc86d20b98cab2f5f716cd872b..ae0ece189a69118853c35b54ba74a00d7800a634 100644 --- a/src/USER-MISC/dihedral_spherical.h +++ b/src/USER-MISC/dihedral_spherical.h @@ -20,7 +20,7 @@ DihedralStyle(spherical,DihedralSpherical) #ifndef LMP_DIHEDRAL_SPHERICAL_H #define LMP_DIHEDRAL_SPHERICAL_H -#include +#include #include "dihedral.h" namespace LAMMPS_NS { diff --git a/src/USER-MISC/fix_addtorque.cpp b/src/USER-MISC/fix_addtorque.cpp index 6c3bb5738d8daec03fa1e1dc9a1801d2b8a65297..654911769c271bce9c23c7488d5fa35ca88370e0 100644 --- a/src/USER-MISC/fix_addtorque.cpp +++ b/src/USER-MISC/fix_addtorque.cpp @@ -15,8 +15,8 @@ Contributing author: Laurent Joly (U Lyon, France), ljoly.ulyon@gmail.com ------------------------------------------------------------------------- */ -#include -#include +#include +#include #include "fix_addtorque.h" #include "atom.h" #include "update.h" diff --git a/src/USER-MISC/fix_ave_correlate_long.cpp b/src/USER-MISC/fix_ave_correlate_long.cpp index e40447d859caf5cc890ccba60dec02dee30be9ba..da6d041287df6904548cd4fa0070ca2a58b7a86e 100644 --- a/src/USER-MISC/fix_ave_correlate_long.cpp +++ b/src/USER-MISC/fix_ave_correlate_long.cpp @@ -21,9 +21,9 @@ see J. Chem. Phys. 133, 154103 (2010) ------------------------------------------------------------------------- */ -#include -#include -#include +#include +#include +#include #include #include "fix_ave_correlate_long.h" #include "update.h" diff --git a/src/USER-MISC/fix_ave_correlate_long.h b/src/USER-MISC/fix_ave_correlate_long.h index 2823a5beb398de0f2b680db01b5093a87b70e602..5b38f454eaebcab5a81bb7a23278ee8f63c099f1 100644 --- a/src/USER-MISC/fix_ave_correlate_long.h +++ b/src/USER-MISC/fix_ave_correlate_long.h @@ -20,7 +20,7 @@ FixStyle(ave/correlate/long,FixAveCorrelateLong) #ifndef LMP_FIX_AVE_CORRELATE_LONG_H #define LMP_FIX_AVE_CORRELATE_LONG_H -#include +#include #include "fix.h" namespace LAMMPS_NS { diff --git a/src/USER-MISC/fix_bond_react.cpp b/src/USER-MISC/fix_bond_react.cpp new file mode 100644 index 0000000000000000000000000000000000000000..86da8a0c4fb306297f2cbdac9575e3cd32ec1dc9 --- /dev/null +++ b/src/USER-MISC/fix_bond_react.cpp @@ -0,0 +1,2695 @@ +/* ---------------------------------------------------------------------- +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: Jacob Gissinger (jacob.gissinger@colorado.edu) +------------------------------------------------------------------------- */ + +#include +#include +#include +#include +#include "fix_bond_react.h" +#include "update.h" +#include "modify.h" +#include "respa.h" +#include "atom.h" +#include "atom_vec.h" +#include "force.h" +#include "pair.h" +#include "comm.h" +#include "neighbor.h" +#include "neigh_list.h" +#include "neigh_request.h" +#include "random_mars.h" +#include "molecule.h" +#include "group.h" +#include "citeme.h" +#include "memory.h" +#include "error.h" + +#include + +using namespace LAMMPS_NS; +using namespace FixConst; + +static const char cite_fix_bond_react[] = + "fix bond/react:\n\n" + "@Article{Gissinger17,\n" + " author = {J. R. Gissinger, B. D. Jensen, K. E. Wise},\n" + " title = {Modeling chemical reactions in classical molecular dynamics simulations},\n" + " journal = {Polymer},\n" + " year = 2017,\n" + " volume = 128,\n" + " pages = {211--217}\n" + "}\n\n"; + +#define BIG 1.0e20 +#define DELTA 16 +#define MAXLINE 256 +#define MAXGUESS 20 + +// various statuses of superimpose algorithm: +// ACCEPT: site successfully matched to pre-reacted template +// REJECT: site does not match pre-reacted template +// PROCEED: normal execution (non-guessing mode) +// CONTINUE: a neighbor has been assigned, skip to next neighbor +// GUESSFAIL: a guess has failed (if no more restore points, status = 'REJECT') +// RESTORE: restore mode, load most recent restore point +enum{ACCEPT,REJECT,PROCEED,CONTINUE,GUESSFAIL,RESTORE}; + +/* ---------------------------------------------------------------------- */ + +FixBondReact::FixBondReact(LAMMPS *lmp, int narg, char **arg) : + Fix(lmp, narg, arg) +{ + if (lmp->citeme) lmp->citeme->add(cite_fix_bond_react); + + fix1 = NULL; + fix2 = NULL; + + if (narg < 8) error->all(FLERR,"Illegal fix bond/react command 0.0"); + + MPI_Comm_rank(world,&me); + MPI_Comm_size(world,&nprocs); + + attempted_rxn = 0; + force_reneighbor = 1; + next_reneighbor = -1; + vector_flag = 1; + global_freq = 1; + extvector = 0; + rxnID = 0; + status = PROCEED; + + // these group names are reserved for use exclusively by bond/react + master_group = (char *) "bond_react_MASTER_group"; + + // by using fixed group names, only one instance of fix bond/react is allowed. + if (modify->find_fix_by_style("bond/react") != -1) + error->all(FLERR,"Only one instance of fix bond/react allowed at a time"); + + // let's find number of reactions specified + nreacts = 0; + for (int i = 3; i < narg; i++) { + if (strcmp(arg[i],"react") == 0) { + nreacts++; + i = i + 6; // skip past mandatory arguments + if (i > narg) error->all(FLERR,"Illegal fix bond/react command 0.1"); + } + } + + if (nreacts == 0) error->all(FLERR,"Illegal fix bond/react command: missing mandatory 'react' argument"); + + size_vector = nreacts; + + int iarg = 3; + stabilization_flag = 0; + while (strcmp(arg[iarg],"react") != 0) { + if (strcmp(arg[iarg],"stabilization") == 0) { + if (strcmp(arg[iarg+1],"no") == 0) { + if (iarg+2 > narg) error->all(FLERR,"Illegal fix bond/react command 0.2"); + iarg += 2; + } + if (strcmp(arg[iarg+1],"yes") == 0) { + if (iarg+4 > narg) error->all(FLERR,"Illegal fix bond/react command 0.21"); + int n = strlen(arg[iarg+2]) + 1; + exclude_group = new char[n]; + strcpy(exclude_group,arg[iarg+2]); + stabilization_flag = 1; + nve_limit_xmax = arg[iarg+3]; + iarg += 4; + } + } + } + + // set up common variables as vectors of length 'nreacts' + // nevery, cutoff, onemol, twomol, superimpose file + + // this looks excessive + // the price of vectorization (all reactions in one command)? + memory->create(nevery,nreacts,"bond/react:nevery"); + memory->create(cutsq,nreacts,2,"bond/react:cutsq"); + memory->create(unreacted_mol,nreacts,"bond/react:unreacted_mol"); + memory->create(reacted_mol,nreacts,"bond/react:reacted_mol"); + memory->create(fraction,nreacts,"bond/react:fraction"); + memory->create(seed,nreacts,"bond/react:seed"); + memory->create(limit_duration,nreacts,"bond/react:limit_duration"); + memory->create(stabilize_steps_flag,nreacts,"bond/react:stabilize_steps_flag"); + memory->create(iatomtype,nreacts,"bond/react:iatomtype"); + memory->create(jatomtype,nreacts,"bond/react:jatomtype"); + memory->create(ibonding,nreacts,"bond/react:ibonding"); + memory->create(jbonding,nreacts,"bond/react:jbonding"); + memory->create(closeneigh,nreacts,"bond/react:closeneigh"); + memory->create(groupbits,nreacts,"bond/react:groupbits"); + memory->create(reaction_count,nreacts,"bond/react:reaction_count"); + memory->create(local_rxn_count,nreacts,"bond/react:local_rxn_count"); + memory->create(ghostly_rxn_count,nreacts,"bond/react:ghostly_rxn_count"); + memory->create(reaction_count_total,nreacts,"bond/react:reaction_count_total"); + + for (int i = 0; i < nreacts; i++) { + fraction[i] = 1; + seed[i] = 12345; + stabilize_steps_flag[i] = 0; + // set default limit duration to 60 timesteps + limit_duration[i] = 60; + reaction_count[i] = 0; + local_rxn_count[i] = 0; + ghostly_rxn_count[i] = 0; + reaction_count_total[i] = 0; + } + + char **files; + files = new char*[nreacts]; + + int rxn = 0; + while (iarg < narg && strcmp(arg[iarg],"react") == 0) { + + iarg++; + + iarg++; // read in reaction name here + //for example, rxn_name[rxn] = ... + + int igroup = group->find(arg[iarg++]); + if (igroup == -1) error->all(FLERR,"Could not find fix group ID"); + groupbits[rxn] = group->bitmask[igroup]; + + nevery[rxn] = force->inumeric(FLERR,arg[iarg++]); + if (nevery[rxn] <= 0) error->all(FLERR,"Illegal fix bond/react command 0.4"); + + double cutoff = force->numeric(FLERR,arg[iarg++]); + if (cutoff < 0.0) error->all(FLERR,"Illegal fix bond/react command 0.5"); + cutsq[rxn][0] = cutoff*cutoff; + + cutoff = force->numeric(FLERR,arg[iarg++]); + if (cutoff < 0.0) error->all(FLERR,"Illegal fix bond/react command 0.55"); + cutsq[rxn][1] = cutoff*cutoff; + + unreacted_mol[rxn] = atom->find_molecule(arg[iarg++]); + if (unreacted_mol[rxn] == -1) error->all(FLERR,"Unreacted molecule template ID for " + "fix bond/react does not exist"); + reacted_mol[rxn] = atom->find_molecule(arg[iarg++]); + if (reacted_mol[rxn] == -1) error->all(FLERR,"Reacted molecule template ID for " + "fix bond/react does not exist"); + + //read superimpose file + files[rxn] = new char[strlen(arg[iarg])+1]; + strcpy(files[rxn],arg[iarg]); + iarg++; + + while (iarg < narg && strcmp(arg[iarg],"react") != 0 ) { + if (strcmp(arg[iarg],"prob") == 0) { + if (iarg+3 > narg) error->all(FLERR,"Illegal fix bond/react command 0.6"); + fraction[rxn] = force->numeric(FLERR,arg[iarg+1]); + seed[rxn] = force->inumeric(FLERR,arg[iarg+2]); + if (fraction[rxn] < 0.0 || fraction[rxn] > 1.0) + error->all(FLERR,"Illegal fix bond/react command"); + if (seed[rxn] <= 0) error->all(FLERR,"Illegal fix bond/react command 0.7"); + iarg += 3; + } else if (strcmp(arg[iarg],"stabilize_steps") == 0) { + if (stabilization_flag == 0) error->all(FLERR,"Stabilize_steps keyword used without stabilization keyword"); + if (iarg+2 > narg) error->all(FLERR,"Illegal fix bond/react command 0.8"); + limit_duration[rxn] = force->numeric(FLERR,arg[iarg+1]); + stabilize_steps_flag[rxn] = 1; + iarg += 2; + } else error->all(FLERR,"Illegal fix bond/react command 0.9"); + } + rxn++; + } + + max_natoms = 0; // the number of atoms in largest molecule template + for (int myrxn = 0; myrxn < nreacts; myrxn++) { + twomol = atom->molecules[reacted_mol[myrxn]]; + max_natoms = MAX(max_natoms,twomol->natoms); + } + + memory->create(equivalences,max_natoms,2,nreacts,"bond/react:equivalences"); + memory->create(reverse_equiv,max_natoms,2,nreacts,"bond/react:reverse_equiv"); + memory->create(edge,max_natoms,nreacts,"bond/react:edge"); + memory->create(landlocked_atoms,max_natoms,nreacts,"bond/react:landlocked_atoms"); + + // read all superimpose files afterward + for (int i = 0; i < nreacts; i++) { + open(files[i]); + onemol = atom->molecules[unreacted_mol[i]]; + twomol = atom->molecules[reacted_mol[i]]; + read(i); + fclose(fp); + iatomtype[i] = onemol->type[ibonding[i]-1]; + jatomtype[i] = onemol->type[jbonding[i]-1]; + find_landlocked_atoms(i); + } + + for (int i = 0; i < nreacts; i++) { + delete [] files[i]; + } + delete [] files; + + if (atom->molecular != 1) + error->all(FLERR,"Cannot use fix bond/react with non-molecular systems"); + + // check if bonding atoms are 1-2, 1-3, or 1-4 bonded neighbors + // if so, we don't need non-bonded neighbor list + for (int myrxn = 0; myrxn < nreacts; myrxn++) { + closeneigh[myrxn] = -1; // indicates will search non-bonded neighbors + onemol = atom->molecules[unreacted_mol[myrxn]]; + for (int k = 0; k < onemol->nspecial[ibonding[myrxn]-1][2]; k++) { + if (onemol->special[ibonding[myrxn]-1][k] == jbonding[myrxn]) { + closeneigh[myrxn] = 2; // index for 1-4 neighbor + if (k < onemol->nspecial[ibonding[myrxn]-1][1]) + closeneigh[myrxn] = 1; // index for 1-3 neighbor + if (k < onemol->nspecial[ibonding[myrxn]-1][0]) + closeneigh[myrxn] = 0; // index for 1-2 neighbor + break; + } + } + } + + // initialize Marsaglia RNG with processor-unique seed + + random = new class RanMars*[nreacts]; + for (int i = 0; i < nreacts; i++) { + random[i] = new RanMars(lmp,seed[i] + me); + } + + // set comm sizes needed by this fix + // forward is big due to comm of broken bonds and 1-2 neighbors + + comm_forward = MAX(2,2+atom->maxspecial); + comm_reverse = 2; + + // allocate arrays local to this fix + + nmax = 0; + partner = finalpartner = NULL; + distsq = NULL; + probability = NULL; + maxcreate = 0; + created = NULL; + local_ncreate = NULL; + ncreate = NULL; + allncreate = 0; + local_num_mega = 0; + ghostly_num_mega = 0; + restore = NULL; + + // zero out stats + global_megasize = 0; + avail_guesses = 0; + glove_counter = 0; + guess_branch = new int[MAXGUESS](); + pioneer_count = new int[max_natoms]; + local_mega_glove = NULL; + ghostly_mega_glove = NULL; + global_mega_glove = NULL; + + // these are merely loop indices that became important + pion = neigh = trace = 0; + + id_fix1 = NULL; + id_fix2 = NULL; +} + +/* ---------------------------------------------------------------------- */ + +FixBondReact::~FixBondReact() +{ + // unregister callbacks to this fix from Atom class + atom->delete_callback(id,0); + + for (int i = 0; i < nreacts; i++) { + delete random[i]; + } + delete [] random; + + memory->destroy(partner); + memory->destroy(finalpartner); + memory->destroy(local_ncreate); + memory->destroy(ncreate); + memory->destroy(distsq); + memory->destroy(probability); + memory->destroy(created); + memory->destroy(edge); + memory->destroy(equivalences); + memory->destroy(reverse_equiv); + + memory->destroy(nevery); + memory->destroy(cutsq); + memory->destroy(unreacted_mol); + memory->destroy(reacted_mol); + memory->destroy(fraction); + memory->destroy(seed); + memory->destroy(limit_duration); + memory->destroy(stabilize_steps_flag); + + memory->destroy(iatomtype); + memory->destroy(jatomtype); + memory->destroy(ibonding); + memory->destroy(jbonding); + memory->destroy(closeneigh); + memory->destroy(groupbits); + memory->destroy(reaction_count); + memory->destroy(local_rxn_count); + memory->destroy(ghostly_rxn_count); + memory->destroy(reaction_count_total); + + if (attempted_rxn == 1) { + memory->destroy(restore_pt); + memory->destroy(restore); + memory->destroy(glove); + memory->destroy(pioneers); + memory->destroy(landlocked_atoms); + memory->destroy(local_mega_glove); + memory->destroy(ghostly_mega_glove); + } + + memory->destroy(global_mega_glove); + + if (stabilization_flag == 1) { + delete [] exclude_group; + + // check nfix in case all fixes have already been deleted + if (id_fix1 == NULL && modify->nfix) modify->delete_fix(id_fix1); + delete [] id_fix1; + } + + if (id_fix2 == NULL && modify->nfix) modify->delete_fix(id_fix2); + delete [] id_fix2; + + delete [] guess_branch; + delete [] pioneer_count; +} + +/* ---------------------------------------------------------------------- */ + +int FixBondReact::setmask() +{ + int mask = 0; + mask |= POST_INTEGRATE; + mask |= POST_INTEGRATE_RESPA; + return mask; +} + +/* ---------------------------------------------------------------------- +let's add an internal nve/limit fix for relaxation of reaction sites +also let's add our per-atom property fix here! +this per-atom property will state the timestep an atom was 'limited' +it will have the name 'i_limit_tags' and will be intitialized to 0 (not in group) +------------------------------------------------------------------------- */ + +void FixBondReact::post_constructor() +{ + // let's add the limit_tags per-atom property fix + int len = strlen("per_atom_props") + 1; + id_fix2 = new char[len]; + strcpy(id_fix2,"per_atom_props"); + + int ifix = modify->find_fix(id_fix2); + if (ifix == -1) { + char **newarg = new char*[8]; + newarg[0] = (char *) "per_atom_props"; + newarg[1] = (char *) "all"; // group ID is ignored + newarg[2] = (char *) "property/atom"; + newarg[3] = (char *) "i_limit_tags"; + newarg[4] = (char *) "i_statted_tags"; + newarg[5] = (char *) "i_react_tags"; + newarg[6] = (char *) "ghost"; + newarg[7] = (char *) "yes"; + modify->add_fix(8,newarg); + fix2 = modify->fix[modify->nfix-1]; + delete [] newarg; + } + + // limit_tags: these are recently reacted atoms being relaxed + // per-atom properties already initialized to zero (not in group) + // let's do it anyway for clarity + int flag; + int index = atom->find_custom("limit_tags",flag); //here's where error would happen + int *i_limit_tags = atom->ivector[index]; + + for (int i = 0; i < atom->nlocal; i++) + i_limit_tags[i] = 0; + + // create master_group if not already existing + if (group->find(master_group) == -1) { + group->find_or_create(master_group); + char **newarg; + newarg = new char*[5]; + newarg[0] = master_group; + newarg[1] = (char *) "dynamic"; + newarg[2] = (char *) "all"; + newarg[3] = (char *) "property"; + newarg[4] = (char *) "limit_tags"; + group->assign(5,newarg); + delete [] newarg; + } + + // on to statted_tags (system-wide thermostat) + // intialize per-atom statted_flags to 1 + index = atom->find_custom("statted_tags",flag); + int *i_statted_tags = atom->ivector[index]; + + for (int i = 0; i < atom->nlocal; i++) + i_statted_tags[i] = 1; + + if (stabilization_flag == 1) { + // create exclude_group if not already existing + if (group->find(exclude_group) == -1) { + group->find_or_create(exclude_group); + char **newarg; + newarg = new char*[5]; + newarg[0] = exclude_group; + newarg[1] = (char *) "dynamic"; + newarg[2] = (char *) "all"; + newarg[3] = (char *) "property"; + newarg[4] = (char *) "statted_tags"; + group->assign(5,newarg); + delete [] newarg; + } + + // let's create a new nve/limit fix to limit newly reacted atoms + len = strlen("bond_react_MASTER_nve_limit") + 1; + id_fix1 = new char[len]; + strcpy(id_fix1,"bond_react_MASTER_nve_limit"); + + ifix = modify->find_fix(id_fix1); + + if (ifix == -1) { + char **newarg = new char*[4]; + newarg[0] = id_fix1; + newarg[1] = master_group; + newarg[2] = (char *) "nve/limit"; + newarg[3] = nve_limit_xmax; + modify->add_fix(4,newarg); + fix1 = modify->fix[modify->nfix-1]; + delete [] newarg; + } + + } + + //react_tags: this per-atom property is the ID of the 'react' argument which recently caused atom to react + //so that atoms which wander between processors may be released to global thermostat at the proper time + + //per-atom values initalized to 0 + index = atom->find_custom("react_tags",flag); + int *i_react_tags = atom->ivector[index]; + + for (int i = 0; i < atom->nlocal; i++) + i_react_tags[i] = 0; + + // currently must redefine dynamic groups so they are updated at proper time + // -> should double check as to why + + int must_redefine_groups = 1; + + if (must_redefine_groups) { + group->find_or_create(master_group); + char **newarg; + newarg = new char*[5]; + newarg[0] = master_group; + newarg[1] = (char *) "dynamic"; + newarg[2] = (char *) "all"; + newarg[3] = (char *) "property"; + newarg[4] = (char *) "limit_tags"; + group->assign(5,newarg); + delete [] newarg; + } + + if (stabilization_flag == 1) { + if (must_redefine_groups) { + group->find_or_create(exclude_group); + char **newarg; + newarg = new char*[5]; + newarg[0] = exclude_group; + newarg[1] = (char *) "dynamic"; + newarg[2] = (char *) "all"; + newarg[3] = (char *) "property"; + newarg[4] = (char *) "statted_tags"; + group->assign(5,newarg); + delete [] newarg; + } + } +} + +/* ---------------------------------------------------------------------- */ + +void FixBondReact::init() +{ + + // warn if more than one bond/react fix + + int count = 0; + for (int i = 0; i < modify->nfix; i++) + if (strcmp(modify->fix[i]->style,"bond/react") == 0) count++; + if (count > 1 && comm->me == 0) error->warning(FLERR,"More than one fix bond/react"); + + if (strstr(update->integrate_style,"respa")) + nlevels_respa = ((Respa *) update->integrate)->nlevels; + + // check cutoff for iatomtype,jatomtype + for (int i = 0; i < nreacts; i++) { + if (force->pair == NULL || cutsq[i][1] > force->pair->cutsq[iatomtype[i]][jatomtype[i]]) + error->all(FLERR,"Fix bond/react cutoff is longer than pairwise cutoff"); + } + + // need a half neighbor list, built every Nevery steps + int irequest = neighbor->request(this,instance_me); + neighbor->requests[irequest]->pair = 0; + neighbor->requests[irequest]->fix = 1; + neighbor->requests[irequest]->occasional = 1; + + lastcheck = -1; +} + +/* ---------------------------------------------------------------------- */ + +void FixBondReact::init_list(int id, NeighList *ptr) +{ + list = ptr; +} + +/* ---------------------------------------------------------------------- + Identify all pairs of potentially reactive atoms for this time step. + This function is modified from LAMMPS’ fix bond/create. +---------------------------------------------------------------------- */ + +void FixBondReact::post_integrate() +{ + // check if any reactions could occur on this timestep + int nevery_check = 1; + for (int i = 0; i < nreacts; i++) { + if (!(update->ntimestep % nevery[i])) { + nevery_check = 0; + break; + } + } + + for (int i = 0; i < nreacts; i++) { + reaction_count[i] = 0; + local_rxn_count[i] = 0; + ghostly_rxn_count[i] = 0; + } + + if (nevery_check) { + unlimit_bond(); + return; + } + + // acquire updated ghost atom positions + // necessary b/c are calling this after integrate, but before Verlet comm + + comm->forward_comm(); + + // resize bond partner list and initialize it + // needs to be atom->nmax in length + + if (atom->nmax > nmax) { + memory->destroy(partner); + memory->destroy(finalpartner); + memory->destroy(distsq); + memory->destroy(local_ncreate); + memory->destroy(ncreate); + memory->destroy(probability); + nmax = atom->nmax; + memory->create(partner,nmax,"bond/react:partner"); + memory->create(finalpartner,nmax,"bond/react:finalpartner"); + memory->create(distsq,nmax,2,"bond/react:distsq"); + memory->create(local_ncreate,nreacts,"bond/react:local_ncreate"); + memory->create(ncreate,nreacts,"bond/react:ncreate"); + memory->create(probability,nmax,"bond/react:probability"); + } + + // reset create counts + for (int i = 0; i < nreacts; i++) { + local_ncreate[i] = 0; + ncreate[i] = 0; + } + + int nlocal = atom->nlocal; + int nall = atom->nlocal + atom->nghost; + + // loop over neighbors of my atoms + // each atom sets one closest eligible partner atom ID to bond with + + tagint *tag = atom->tag; + int *type = atom->type; + + neighbor->build_one(list,1); + + int j; + + for (rxnID = 0; rxnID < nreacts; rxnID++) { + + for (int ii = 0; ii < nall; ii++) { + partner[ii] = 0; + finalpartner[ii] = 0; + distsq[ii][0] = 0.0; + distsq[ii][1] = BIG; + } + + // fork between far and close_partner here + if (closeneigh[rxnID] < 0) far_partner(); + else close_partner(); + + // reverse comm of distsq and partner + // not needed if newton_pair off since I,J pair was seen by both procs + + commflag = 2; + if (force->newton_pair) comm->reverse_comm_fix(this); + + // each atom now knows its winning partner + // for prob check, generate random value for each atom with a bond partner + // forward comm of partner and random value, so ghosts have it + + if (fraction[rxnID] < 1.0) { + for (int i = 0; i < nlocal; i++) + if (partner[i]) probability[i] = random[rxnID]->uniform(); + } + + commflag = 2; + comm->forward_comm_fix(this,2); + + // consider for reaction: + // only if both atoms list each other as winning bond partner + // and probability constraint is satisfied + // if other atom is owned by another proc, it should do same thing + + int temp_ncreate = 0; + for (int i = 0; i < nlocal; i++) { + if (partner[i] == 0) { + continue; + } + j = atom->map(partner[i]); + if (partner[j] != tag[i]) { + continue; + } + + // apply probability constraint using RN for atom with smallest ID + + if (fraction[rxnID] < 1.0) { + if (tag[i] < tag[j]) { + if (probability[i] >= fraction[rxnID]) continue; + } else { + if (probability[j] >= fraction[rxnID]) continue; + } + } + + // store final created bond partners and count the rxn possibility once + + finalpartner[i] = tag[j]; + finalpartner[j] = tag[i]; + + if (tag[i] < tag[j]) temp_ncreate++; + } + + local_ncreate[rxnID] = temp_ncreate; + // break loop if no even eligible bonding atoms were found (on any proc) + int some_chance; + MPI_Allreduce(&temp_ncreate,&some_chance,1,MPI_INT,MPI_SUM,world); + if (!some_chance) continue; + + // communicate final partner + + commflag = 3; + comm->forward_comm_fix(this); + + // add instance to 'created' only if this processor + // owns the atoms with smaller global ID + // NOTE: we no longer care about ghost-ghost instances as bond/create did + // this is because we take care of updating topology later (and differently) + for (int i = 0; i < nlocal; i++) { + + if (finalpartner[i] == 0) continue; + + j = atom->map(finalpartner[i]); + // if (j < 0 || tag[i] < tag[j]) { + if (tag[i] < tag[j]) { //atom->map(std::min(tag[i],tag[j])) <= nlocal && + if (ncreate[rxnID] == maxcreate) { + maxcreate += DELTA; + // third column of 'created': bond/react integer ID + memory->grow(created,maxcreate,2,nreacts,"bond/react:created"); + } + // to ensure types remain in same order + // unnecessary now taken from reaction map file + if (iatomtype[rxnID] == type[i]) { + created[ncreate[rxnID]][0][rxnID] = tag[i]; + created[ncreate[rxnID]][1][rxnID] = finalpartner[i]; + } else { + created[ncreate[rxnID]][0][rxnID] = finalpartner[i]; + created[ncreate[rxnID]][1][rxnID] = tag[i]; + } + ncreate[rxnID]++; + } + } + unlimit_bond(); //free atoms that have been relaxed + } + + // break loop if no even eligible bonding atoms were found (on any proc) + int some_chance; + + allncreate = 0; + for (int i = 0; i < nreacts; i++) + allncreate += ncreate[i]; + + MPI_Allreduce(&allncreate,&some_chance,1,MPI_INT,MPI_SUM,world); + if (!some_chance) { + unlimit_bond(); + return; + } + + // run through the superimpose algorithm + // this checks if simulation topology matches unreacted mol template + superimpose_algorithm(); + // free atoms that have been limited after reacting + unlimit_bond(); +} + +/* ---------------------------------------------------------------------- + Search non-bonded neighbor lists if bonding atoms are not in special list +------------------------------------------------------------------------- */ + +void FixBondReact::far_partner() +{ + int inum,jnum,itype,jtype,possible; + double xtmp,ytmp,ztmp,delx,dely,delz,rsq; + int *ilist,*jlist,*numneigh,**firstneigh; + + // loop over neighbors of my atoms + // each atom sets one closest eligible partner atom ID to bond with + + double **x = atom->x; + tagint *tag = atom->tag; + int **nspecial = atom->nspecial; + tagint **special = atom->special; + int *mask = atom->mask; + int *type = atom->type; + + inum = list->inum; + ilist = list->ilist; + numneigh = list->numneigh; + firstneigh = list->firstneigh; + + // per-atom property indicating if in bond/react master group + int flag; + int index1 = atom->find_custom("limit_tags",flag); + int *i_limit_tags = atom->ivector[index1]; + + int i,j; + + for (int ii = 0; ii < inum; ii++) { + i = ilist[ii]; + if (!(mask[i] & groupbits[rxnID])) continue; + if (i_limit_tags[i] != 0) continue; + itype = type[i]; + xtmp = x[i][0]; + ytmp = x[i][1]; + ztmp = x[i][2]; + jlist = firstneigh[i]; + jnum = numneigh[i]; + + for (int jj = 0; jj < jnum; jj++) { + j = jlist[jj]; + j &= NEIGHMASK; + + if (!(mask[j] & groupbits[rxnID])) { + continue; +} + + if (i_limit_tags[j] != 0) { + continue; + } + + jtype = type[j]; + possible = 0; + + if (itype == iatomtype[rxnID] && jtype == jatomtype[rxnID]) { + possible = 1; + } else if (itype == jatomtype[rxnID] && jtype == iatomtype[rxnID]) { + possible = 1; + } + + if (possible == 0) continue; + + // do not allow bonding atoms within special list + for (int k = 0; k < nspecial[i][2]; k++) + if (special[i][k] == tag[j]) possible = 0; + if (!possible) continue; + + delx = xtmp - x[j][0]; + dely = ytmp - x[j][1]; + delz = ztmp - x[j][2]; + rsq = delx*delx + dely*dely + delz*delz; + + if (rsq >= cutsq[rxnID][1] || rsq <= cutsq[rxnID][0]) { + continue; + } + if (rsq < distsq[i][1]) { + partner[i] = tag[j]; + distsq[i][1] = rsq; + } + if (rsq < distsq[j][1]) { + partner[j] = tag[i]; + distsq[j][1] = rsq; + } + } + } +} + +/* ---------------------------------------------------------------------- + Slightly simpler to find bonding partner when a close neighbor +------------------------------------------------------------------------- */ + +void FixBondReact::close_partner() +{ + int n,i1,i2,itype,jtype; + double delx,dely,delz,rsq; + + double **x = atom->x; + tagint *tag = atom->tag; + int *type = atom->type; + int *mask = atom->mask; + int **nspecial = atom->nspecial; + tagint **special = atom->special; + + // per-atom property indicating if in bond/react master group + int flag; + int index1 = atom->find_custom("limit_tags",flag); + int *i_limit_tags = atom->ivector[index1]; + + // loop over special list + for (int ii = 0; ii < atom->nlocal; ii++) { + itype = type[ii]; + n = 0; + if (closeneigh[rxnID] != 0) + n = nspecial[ii][closeneigh[rxnID]-1]; + for (; n < nspecial[ii][closeneigh[rxnID]]; n++) { + i1 = ii; + i2 = atom->map(special[ii][n]); + jtype = type[i2]; + if (!(mask[i1] & groupbits[rxnID])) continue; + if (!(mask[i2] & groupbits[rxnID])) continue; + if (i_limit_tags[i1] != 0) continue; + if (i_limit_tags[i2] != 0) continue; + if (itype != iatomtype[rxnID] || jtype != jatomtype[rxnID]) continue; + + delx = x[i1][0] - x[i2][0]; + dely = x[i1][1] - x[i2][1]; + delz = x[i1][2] - x[i2][2]; + rsq = delx*delx + dely*dely + delz*delz; + if (rsq >= cutsq[rxnID][1] || rsq <= cutsq[rxnID][0]) continue; + + if (rsq > distsq[i1][0]) { + partner[i1] = tag[i2]; + distsq[i1][0] = rsq; + } + if (rsq > distsq[i2][0]) { + partner[i2] = tag[i1]; + distsq[i2][0] = rsq; + } + } + } +} + +/* ---------------------------------------------------------------------- + Set up global variables. Loop through all pairs; loop through Pioneers + until Superimpose Algorithm is completed for each pair. +------------------------------------------------------------------------- */ + +void FixBondReact::superimpose_algorithm() +{ + local_num_mega = 0; + ghostly_num_mega = 0; + + // quick description of important global indices you'll see floating about: + // 'pion' is the pioneer loop index + // 'neigh' in the first neighbor index + // 'trace' retraces the first nieghbors + // trace: once you choose a first neighbor, you then check for other nieghbors of same type + + if (attempted_rxn == 1) { + memory->destroy(restore_pt); + memory->destroy(restore); + memory->destroy(glove); + memory->destroy(pioneers); + memory->destroy(local_mega_glove); + memory->destroy(ghostly_mega_glove); + } + + memory->create(glove,max_natoms,2,"bond/react:glove"); + memory->create(restore_pt,MAXGUESS,4,"bond/react:restore_pt"); + memory->create(pioneers,max_natoms,"bond/react:pioneers"); + memory->create(restore,max_natoms,MAXGUESS,"bond/react:restore"); + memory->create(local_mega_glove,max_natoms+1,allncreate,"bond/react:local_mega_glove"); + memory->create(ghostly_mega_glove,max_natoms+1,allncreate,"bond/react:ghostly_mega_glove"); + + attempted_rxn = 1; + + for (int i = 0; i < max_natoms+1; i++) { + for (int j = 0; j < allncreate; j++) { + local_mega_glove[i][j] = 0; + ghostly_mega_glove[i][j] = 0; + } + } + + //let's finally begin the superimpose loop + for (rxnID = 0; rxnID < nreacts; rxnID++) { + for (lcl_inst = 0; lcl_inst < ncreate[rxnID]; lcl_inst++) { + + onemol = atom->molecules[unreacted_mol[rxnID]]; + twomol = atom->molecules[reacted_mol[rxnID]]; + + status = PROCEED; + + glove_counter = 0; + for (int i = 0; i < max_natoms; i++) { + for (int j = 0; j < 2; j++) { + glove[i][j] = 0; + } + } + + for (int i = 0; i < MAXGUESS; i++) { + guess_branch[i] = 0; + } + + int myibonding = ibonding[rxnID]; + int myjbonding = jbonding[rxnID]; + + glove[myibonding-1][0] = myibonding; + glove[myibonding-1][1] = created[lcl_inst][0][rxnID]; + glove_counter++; + glove[myjbonding-1][0] = myjbonding; + glove[myjbonding-1][1] = created[lcl_inst][1][rxnID]; + glove_counter++; + + avail_guesses = 0; + + for (int i = 0; i < max_natoms; i++) + pioneer_count[i] = 0; + + for (int i = 0; i < onemol->nspecial[myibonding-1][0]; i++) + pioneer_count[onemol->special[myibonding-1][i]-1]++; + + for (int i = 0; i < onemol->nspecial[myjbonding-1][0]; i++) + pioneer_count[onemol->special[myjbonding-1][i]-1]++; + + + int hang_catch = 0; + while (!(status == ACCEPT || status == REJECT)) { + + for (int i = 0; i < max_natoms; i++) { + pioneers[i] = 0; + } + + for (int i = 0; i < onemol->natoms; i++) { + if (glove[i][0] !=0 && pioneer_count[i] < onemol->nspecial[i][0] && edge[i][rxnID] == 0) { + pioneers[i] = 1; + } + } + + // run through the pioneers + // due to use of restore points, 'pion' index can change in loop + for (pion = 0; pion < onemol->natoms; pion++) { + if (pioneers[pion] || status == GUESSFAIL) { + make_a_guess(); + if (status == ACCEPT || status == REJECT) break; + } + } + + if (status == ACCEPT) { // reaction site found successfully! + glove_ghostcheck(); + } + hang_catch++; + // let's go ahead and catch the simplest of hangs + //if (hang_catch > onemol->natoms*4) + if (hang_catch > atom->nlocal*3) { + error->all(FLERR,"Excessive iteration of superimpose algorithm"); + } + } + } + } + + global_megasize = 0; + + ghost_glovecast(); // consolidate all mega_gloves to all processors + dedup_mega_gloves(0); // make sure atoms aren't added to more than one reaction + + MPI_Allreduce(&local_rxn_count[0],&reaction_count[0],nreacts,MPI_INT,MPI_SUM,world); + + for (int i = 0; i < nreacts; i++) + reaction_count_total[i] += reaction_count[i]; + + // this assumes compute_vector is called from process 0 + // ...so doesn't bother to bcast ghostly_rxn_count + if (me == 0) + for (int i = 0; i < nreacts; i++) + reaction_count_total[i] += ghostly_rxn_count[i]; + + // this updates topology next step + next_reneighbor = update->ntimestep; + + // call limit_bond in 'global_mega_glove mode.' oh, and local mode + limit_bond(0); // add reacting atoms to nve/limit + limit_bond(1); + update_everything(); // change topology +} + +/* ---------------------------------------------------------------------- + Screen for obvious algorithm fails. This is the return point when a guess + has failed: check for available restore points. +------------------------------------------------------------------------- */ + +void FixBondReact::make_a_guess() +{ + int **nspecial = atom->nspecial; + tagint **special = atom->special; + int *type = atom->type; + int nfirst_neighs = onemol->nspecial[pion][0]; + + // per-atom property indicating if in bond/react master group + int flag; + int index1 = atom->find_custom("limit_tags",flag); + int *i_limit_tags = atom->ivector[index1]; + + if (status == GUESSFAIL && avail_guesses == 0) { + status = REJECT; + return; + } + + if (status == GUESSFAIL && avail_guesses > 0) { + // load restore point + for (int i = 0; i < onemol->natoms; i++) { + glove[i][0] = restore[i][(avail_guesses*4)-4]; + glove[i][1] = restore[i][(avail_guesses*4)-3]; + pioneer_count[i] = restore[i][(avail_guesses*4)-2]; + pioneers[i] = restore[i][(avail_guesses*4)-1]; + } + pion = restore_pt[avail_guesses-1][0]; + neigh = restore_pt[avail_guesses-1][1]; + trace = restore_pt[avail_guesses-1][2]; + glove_counter = restore_pt[avail_guesses-1][3]; + status = RESTORE; + neighbor_loop(); + if (status != PROCEED) return; + } + + nfirst_neighs = onemol->nspecial[pion][0]; + + // check if any of first neighbors are in bond_react_MASTER_group + // if so, this constitutes a fail + // because still undergoing a previous reaction! + // could technically fail unnecessarily during a wrong guess if near edge atoms + // we accept this temporary and infrequent decrease in reaction occurences + + for (int i = 0; i < nspecial[atom->map(glove[pion][1])][0]; i++) { + if (atom->map(special[atom->map(glove[pion][1])][i]) < 0) { + error->all(FLERR,"Fix bond/react needs ghost atoms from further away1"); // parallel issues. + } + if (i_limit_tags[(int)atom->map(special[atom->map(glove[pion][1])][i])] != 0) { + status = GUESSFAIL; + return; + } + } + + // check for same number of neighbors between unreacted mol and simulation + if (nfirst_neighs != nspecial[atom->map(glove[pion][1])][0]) { + status = GUESSFAIL; + return; + } + + // make sure all neighbors aren't already assigned + // an issue discovered for coarse-grained example + int assigned_count = 0; + for (int i = 0; i < nfirst_neighs; i++) + for (int j = 0; j < onemol->natoms; j++) + if (special[atom->map(glove[pion][1])][i] == glove[j][1]) { + assigned_count++; + break; + } + + if (assigned_count == nfirst_neighs) status = GUESSFAIL; + + // check if all neigh atom types are the same between simulation and unreacted mol + int *mol_ntypes = new int[atom->ntypes]; + int *lcl_ntypes = new int[atom->ntypes]; + + for (int i = 0; i < atom->ntypes; i++) { + mol_ntypes[i] = 0; + lcl_ntypes[i] = 0; + } + + for (int i = 0; i < nfirst_neighs; i++) { + mol_ntypes[(int)onemol->type[(int)onemol->special[pion][i]-1]-1]++; + lcl_ntypes[(int)type[(int)atom->map(special[atom->map(glove[pion][1])][i])]-1]++; //added -1 + } + + for (int i = 0; i < atom->ntypes; i++) { + if (mol_ntypes[i] != lcl_ntypes[i]) { + status = GUESSFAIL; + return; + } + } + + delete [] mol_ntypes; + delete [] lcl_ntypes; + + // okay everything seems to be in order. let's assign some ID pairs!!! + neighbor_loop(); +} + +/* ---------------------------------------------------------------------- + Loop through all First Bonded Neighbors of the current Pioneer. + Prepare appropriately if we are in Restore Mode. +------------------------------------------------------------------------- */ + +void FixBondReact::neighbor_loop() +{ + int nfirst_neighs = onemol->nspecial[pion][0]; + + if (status == RESTORE) { + check_a_neighbor(); + return; + } + + for (neigh = 0; neigh < nfirst_neighs; neigh++) { + if (glove[(int)onemol->special[pion][neigh]-1][0] == 0) { + check_a_neighbor(); + } + } + // status should still = PROCEED +} + +/* ---------------------------------------------------------------------- + Check if we can assign this First Neighbor to pre-reacted template + without guessing. If so, do it! If not, call crosscheck_the_nieghbor(). +------------------------------------------------------------------------- */ + +void FixBondReact::check_a_neighbor() +{ + int **nspecial = atom->nspecial; + tagint **special = atom->special; + int *type = atom->type; + int nfirst_neighs = onemol->nspecial[pion][0]; + + if (status != RESTORE) { + // special consideration for hydrogen atoms (and all first neighbors bonded to no other atoms) (and aren't edge atoms) + if (onemol->nspecial[(int)onemol->special[pion][neigh]-1][0] == 1 && edge[(int)onemol->special[pion][neigh]-1][rxnID] == 0) { + + for (int i = 0; i < nfirst_neighs; i++) { + + if (type[(int)atom->map(special[(int)atom->map(glove[pion][1])][i])] == onemol->type[(int)onemol->special[pion][neigh]-1] && + nspecial[(int)atom->map(special[(int)atom->map(glove[pion][1])][i])][0] == 1) { + + int already_assigned = 0; + for (int j = 0; j < onemol->natoms; j++) { + if (glove[j][1] == special[atom->map(glove[pion][1])][i]) { + already_assigned = 1; + break; + } + } + + if (already_assigned == 0) { + glove[(int)onemol->special[pion][neigh]-1][0] = onemol->special[pion][neigh]; + glove[(int)onemol->special[pion][neigh]-1][1] = special[(int)atom->map(glove[pion][1])][i]; + + //another check for ghost atoms. perhaps remove the one in make_a_guess + if (atom->map(glove[(int)onemol->special[pion][neigh]-1][1]) < 0) { + error->all(FLERR,"Fix bond/react needs ghost atoms from further away2"); + } + + for (int j = 0; j < onemol->nspecial[onemol->special[pion][neigh]-1][0]; j++) { + pioneer_count[onemol->special[onemol->special[pion][neigh]-1][j]-1]++; + } + + glove_counter++; + if (glove_counter == onemol->natoms) { + status = ACCEPT; + ring_check(); + return; + } + // status should still == PROCEED + return; + } + } + } + // we are here if no matching atom found + status = GUESSFAIL; + return; + } + } + + crosscheck_the_neighbor(); + if (status != PROCEED) { + if (status == CONTINUE) + status = PROCEED; + return; + } + + // finally ready to match non-duplicate, non-edge atom IDs!! + + for (int i = 0; i < nfirst_neighs; i++) { + + if (type[atom->map((int)special[(int)atom->map(glove[pion][1])][i])] == onemol->type[(int)onemol->special[pion][neigh]-1]) { + int already_assigned = 0; + + //check if a first neighbor of the pioneer is already assigned to pre-reacted template + for (int j = 0; j < onemol->natoms; j++) { + if (glove[j][1] == special[atom->map(glove[pion][1])][i]) { + already_assigned = 1; + break; + } + } + + if (already_assigned == 0) { + glove[(int)onemol->special[pion][neigh]-1][0] = onemol->special[pion][neigh]; + glove[(int)onemol->special[pion][neigh]-1][1] = special[(int)atom->map(glove[pion][1])][i]; + + //another check for ghost atoms. perhaps remove the one in make_a_guess + if (atom->map(glove[(int)onemol->special[pion][neigh]-1][1]) < 0) { + error->all(FLERR,"Fix bond/react needs ghost atoms from further away3"); + } + + for (int ii = 0; ii < onemol->nspecial[onemol->special[pion][neigh]-1][0]; ii++) { + pioneer_count[onemol->special[onemol->special[pion][neigh]-1][ii]-1]++; + } + + glove_counter++; + if (glove_counter == onemol->natoms) { + status = ACCEPT; + ring_check(); + return; + // will never complete here when there are edge atoms + // ...actually that could be wrong if people get creative...shouldn't affect anything + } + // status should still = PROCEED + return; + } + } + } + // status is still 'PROCEED' if we are here! +} + +/* ---------------------------------------------------------------------- + Check if there a viable guess to be made. If so, prepare to make a + guess by recording a restore point. +------------------------------------------------------------------------- */ + +void FixBondReact::crosscheck_the_neighbor() +{ + int nfirst_neighs = onemol->nspecial[pion][0]; + + if (status == RESTORE) { + inner_crosscheck_loop(); + return; + } + + for (trace = 0; trace < nfirst_neighs; trace++) { + if (neigh!=trace && onemol->type[(int)onemol->special[pion][neigh]-1] == onemol->type[(int)onemol->special[pion][trace]-1] && + glove[onemol->special[pion][trace]-1][0] == 0) { + + if (avail_guesses == MAXGUESS) { + error->warning(FLERR,"Fix bond/react failed because MAXGUESS set too small. ask developer for info"); + status = GUESSFAIL; + return; + } + avail_guesses++; + for (int i = 0; i < onemol->natoms; i++) { + restore[i][(avail_guesses*4)-4] = glove[i][0]; + restore[i][(avail_guesses*4)-3] = glove[i][1]; + restore[i][(avail_guesses*4)-2] = pioneer_count[i]; + restore[i][(avail_guesses*4)-1] = pioneers[i]; + restore_pt[avail_guesses-1][0] = pion; + restore_pt[avail_guesses-1][1] = neigh; + restore_pt[avail_guesses-1][2] = trace; + restore_pt[avail_guesses-1][3] = glove_counter; + } + + inner_crosscheck_loop(); + return; + } + } + // status is still 'PROCEED' if we are here! +} + +/* ---------------------------------------------------------------------- + We are ready to make a guess. If there are multiple possible choices + for this guess, keep track of these. +------------------------------------------------------------------------- */ + +void FixBondReact::inner_crosscheck_loop() +{ + tagint **special = atom->special; + int *type = atom->type; + // arbitrarily limited to 5 identical first neighbors + tagint tag_choices[5]; + int nfirst_neighs = onemol->nspecial[pion][0]; + + int num_choices = 0; + for (int i = 0; i < nfirst_neighs; i++) { + + int already_assigned = 0; + for (int j = 0; j < onemol->natoms; j++) { + if (glove[j][1] == special[atom->map(glove[pion][1])][i]) { + already_assigned = 1; + break; + } + } + + if (already_assigned == 0 && + type[(int)atom->map(special[atom->map(glove[pion][1])][i])] == onemol->type[(int)onemol->special[pion][neigh]-1]) { + if (num_choices > 5) { // here failed because too many identical first neighbors. but really no limit if situation arises + status = GUESSFAIL; + return; + } + tag_choices[num_choices++] = special[atom->map(glove[pion][1])][i]; + } + } + + // guess branch is for when multiple identical neighbors. then we guess each one in turn + // guess_branch must work even when avail_guesses = 0. so index accordingly! + // ...actually, avail_guesses should never be zero here anyway + if (guess_branch[avail_guesses-1] == 0) guess_branch[avail_guesses-1] = num_choices; + + //std::size_t size = sizeof(tag_choices) / sizeof(tag_choices[0]); + std::sort(tag_choices, tag_choices + num_choices); //, std::greater()); + glove[onemol->special[pion][neigh]-1][0] = onemol->special[pion][neigh]; + glove[onemol->special[pion][neigh]-1][1] = tag_choices[guess_branch[avail_guesses-1]-1]; + guess_branch[avail_guesses-1]--; + + //another check for ghost atoms. perhaps remove the one in make_a_guess + if (atom->map(glove[(int)onemol->special[pion][neigh]-1][1]) < 0) { + error->all(FLERR,"Fix bond/react needs ghost atoms from further away4"); + } + + if (guess_branch[avail_guesses-1] == 0) avail_guesses--; + + for (int i = 0; i < onemol->nspecial[onemol->special[pion][neigh]-1][0]; i++) { + pioneer_count[onemol->special[onemol->special[pion][neigh]-1][i]-1]++; + } + glove_counter++; + if (glove_counter == onemol->natoms) { + status = ACCEPT; + ring_check(); + return; + } + status = CONTINUE; +} + +/* ---------------------------------------------------------------------- + Check that newly assigned atoms have correct bonds + Necessary for certain ringed structures +------------------------------------------------------------------------- */ + +void FixBondReact::ring_check() +{ + // ring_check can be made more efficient by re-introducing 'frozen' atoms + // 'frozen' atoms have been assigned and also are no longer pioneers + int **nspecial = atom->nspecial; + tagint **special = atom->special; + + for (int i = 0; i < onemol->natoms; i++) { + for (int j = 0; j < onemol->nspecial[i][0]; j++) { + int ring_fail = 1; + int ispecial = onemol->special[i][j]; + for (int k = 0; k < nspecial[atom->map(glove[i][1])][0]; k++) { + if (special[atom->map(glove[i][1])][k] == glove[ispecial-1][1]) { + ring_fail = 0; + break; + } + } + if (ring_fail == 1) { + status = GUESSFAIL; + return; + } + } + } +} + +/* ---------------------------------------------------------------------- + Determine which pre-reacted template atoms are at least three bonds + away from edge atoms. +------------------------------------------------------------------------- */ + +void FixBondReact::find_landlocked_atoms(int myrxn) +{ + // landlocked_atoms are atoms for which all topology is contained in reacted template + // if dihedrals/impropers exist: this means that edge atoms are not in their 1-3 neighbor list + // note: due to various usage/defintions of impropers, treated same as dihedrals + // if angles exist: this means edge atoms not in their 1-2 neighbors list + // if just bonds: this just means that edge atoms are not landlocked + // Note: landlocked defined in terms of reacted template + // if no edge atoms (small reacting molecule), all atoms are landlocked + // we can delete all current topology of landlocked atoms and replace + + // always remove edge atoms from landlocked list + for (int i = 0; i < twomol->natoms; i++) { + if (edge[equivalences[i][1][myrxn]-1][myrxn] == 1) landlocked_atoms[i][myrxn] = 0; + else landlocked_atoms[i][myrxn] = 1; + } + int nspecial_limit = -1; + if (force->angle && twomol->angleflag) nspecial_limit = 0; + + if ((force->dihedral && twomol->dihedralflag) || + (force->improper && twomol->improperflag)) nspecial_limit = 1; + + if (nspecial_limit != -1) { + for (int i = 0; i < twomol->natoms; i++) { + for (int j = 0; j < twomol->nspecial[i][nspecial_limit]; j++) { + for (int k = 0; k < onemol->natoms; k++) { + if (equivalences[twomol->special[i][j]-1][1][myrxn] == k+1 && edge[k][myrxn] == 1) { + landlocked_atoms[i][myrxn] = 0; + } + } + } + } + } + + // bad molecule templates check + // if atoms change types, but aren't landlocked, that's bad + for (int i = 0; i < twomol->natoms; i++) { + if (twomol->type[i] != onemol->type[equivalences[i][1][myrxn]-1] && landlocked_atoms[i][myrxn] == 0) + error->one(FLERR,"Atom affected by reaction too close to template edge"); + } + + // also, if atoms change number of bonds, but aren't landlocked, that could be bad + if (me == 0) + for (int i = 0; i < twomol->natoms; i++) { + if (twomol->nspecial[i][0] != onemol->nspecial[equivalences[i][1][myrxn]-1][0] && landlocked_atoms[i][myrxn] == 0) { + char str[128]; + sprintf(str,"An atom in 'react #%d' changes bond connectivity but not atom type",myrxn+1); + error->warning(FLERR,str); + break; + } + } +} + +/* ---------------------------------------------------------------------- +let's dedup global_mega_glove +allows for same site undergoing different pathways, in parallel +------------------------------------------------------------------------- */ + +void FixBondReact::dedup_mega_gloves(int dedup_mode) +{ + // dedup_mode == 0 for local_dedup + // dedup_mode == 1 for global_mega_glove + for (int i = 0; i < nreacts; i++) { + if (dedup_mode == 0) local_rxn_count[i] = 0; + if (dedup_mode == 1) ghostly_rxn_count[i] = 0; + } + + int dedup_size; + if (dedup_mode == 0) { + dedup_size = local_num_mega; + } else if (dedup_mode == 1) { + dedup_size = global_megasize; + } + + tagint **dedup_glove; + memory->create(dedup_glove,max_natoms+1,dedup_size,"bond/react:dedup_glove"); + + if (dedup_mode == 0) { + for (int i = 0; i < dedup_size; i++) { + for (int j = 0; j < max_natoms+1; j++) { + dedup_glove[j][i] = local_mega_glove[j][i]; + } + } + } else if (dedup_mode == 1) { + for (int i = 0; i < dedup_size; i++) { + for (int j = 0; j < max_natoms+1; j++) { + dedup_glove[j][i] = global_mega_glove[j][i]; + } + } + } + + // dedup_mask is size dedup_size and filters reactions that have been deleted + // a value of 1 means this reaction instance has been deleted + int *dedup_mask = new int[dedup_size]; + int *dup_list = new int[dedup_size]; + + for (int i = 0; i < dedup_size; i++) { + dedup_mask[i] = 0; + dup_list[i] = 0; + } + + // let's randomly mix up our reaction instances first + // then we can feel okay about ignoring ones we've already deleted (or accepted) + // based off std::shuffle + int *temp_rxn = new int[max_natoms+1]; + for (int i = dedup_size-1; i > 0; --i) { //dedup_size + // choose random entry to swap current one with + int k = floor(random[0]->uniform()*(i+1)); + + // swap entries + for (int j = 0; j < max_natoms+1; j++) + temp_rxn[j] = dedup_glove[j][i]; + + for (int j = 0; j < max_natoms+1; j++) { + dedup_glove[j][i] = dedup_glove[j][k]; + dedup_glove[j][k] = temp_rxn[j]; + } + } + delete [] temp_rxn; + + for (int i = 0; i < dedup_size; i++) { + if (dedup_mask[i] == 0) { + int num_dups = 0; + int myrxnid1 = dedup_glove[0][i]; + onemol = atom->molecules[unreacted_mol[myrxnid1]]; + for (int j = 0; j < onemol->natoms; j++) { + int check1 = dedup_glove[j+1][i]; + for (int ii = i + 1; ii < dedup_size; ii++) { + int already_listed = 0; + for (int jj = 0; jj < num_dups; jj++) { + if (dup_list[jj] == ii) { + already_listed = 1; + break; + } + } + if (dedup_mask[ii] == 0 && already_listed == 0) { + int myrxnid2 = dedup_glove[0][ii]; + twomol = atom->molecules[unreacted_mol[myrxnid2]]; + for (int jj = 0; jj < twomol->natoms; jj++) { + int check2 = dedup_glove[jj+1][ii]; + if (check2 == check1) { + // add this rxn instance as well + if (num_dups == 0) dup_list[num_dups++] = i; + dup_list[num_dups++] = ii; + break; + } + } + } + } + } + // here we choose random number and therefore reaction instance + int myrand = 1; + if (num_dups > 0) { + myrand = floor(random[0]->uniform()*num_dups); + for (int iii = 0; iii < num_dups; iii++) { + if (iii != myrand) dedup_mask[dup_list[iii]] = 1; + } + } + } + } + + // we must update local_mega_glove and local_megasize + // we can simply overwrite local_mega_glove column by column + if (dedup_mode == 0) { + int new_local_megasize = 0; + for (int i = 0; i < local_num_mega; i++) { + if (dedup_mask[i] == 0) { + local_rxn_count[(int) dedup_glove[0][i]]++; + for (int j = 0; j < max_natoms+1; j++) { + local_mega_glove[j][new_local_megasize] = dedup_glove[j][i]; + } + new_local_megasize++; + } + } + + local_num_mega = new_local_megasize; + } + + // we must update global_mega_glove and global_megasize + // we can simply overwrite global_mega_glove column by column + if (dedup_mode == 1) { + int new_global_megasize = 0; + for (int i = 0; i < global_megasize; i++) { + if (dedup_mask[i] == 0) { + ghostly_rxn_count[dedup_glove[0][i]]++; + for (int j = 0; j < max_natoms + 1; j++) { + global_mega_glove[j][new_global_megasize] = dedup_glove[j][i]; + } + new_global_megasize++; + } + } + global_megasize = new_global_megasize; + } + + memory->destroy(dedup_glove); + delete [] dedup_mask; + delete [] dup_list; +} + +/* ---------------------------------------------------------------------- +let's limit movement of newly bonded atoms +and exclude them from other thermostats via exclude_group +------------------------------------------------------------------------- */ + +void FixBondReact::limit_bond(int limit_bond_mode) +{ + //two types of passes: 1) while superimpose algorithm is iterating (only local atoms) + // 2) once more for global_mega_glove [after de-duplicating rxn instances] + //in second case, only add local atoms to group + //as with update_everything, we can pre-prepare these arrays, then run generic limit_bond code + + //create local, generic variables for onemol->natoms and glove + //to be filled differently on respective passes + + int nlocal = atom->nlocal; + int temp_limit_num = 0; + tagint *temp_limit_glove; + if (limit_bond_mode == 0) { + int max_temp = local_num_mega * (max_natoms + 1); + temp_limit_glove = new tagint[max_temp]; + for (int j = 0; j < local_num_mega; j++) { + rxnID = local_mega_glove[0][j]; + onemol = atom->molecules[unreacted_mol[rxnID]]; + for (int i = 0; i < onemol->natoms; i++) { + temp_limit_glove[temp_limit_num++] = local_mega_glove[i+1][j]; + } + } + + } else if (limit_bond_mode == 1) { + int max_temp = global_megasize * (max_natoms + 1); + temp_limit_glove = new tagint[max_temp]; + for (int j = 0; j < global_megasize; j++) { + rxnID = global_mega_glove[0][j]; + onemol = atom->molecules[unreacted_mol[rxnID]]; + for (int i = 0; i < onemol->natoms; i++) { + if (atom->map(global_mega_glove[i+1][j]) >= 0 && + atom->map(global_mega_glove[i+1][j]) < nlocal) + temp_limit_glove[temp_limit_num++] = global_mega_glove[i+1][j]; + } + } + } + + if (temp_limit_num == 0) { + delete [] temp_limit_glove; + return; + } + + // we must keep our own list of limited atoms + // this will be a new per-atom property! + + int flag; + int index1 = atom->find_custom("limit_tags",flag); + int *i_limit_tags = atom->ivector[index1]; + + int index2 = atom->find_custom("statted_tags",flag); + int *i_statted_tags = atom->ivector[index2]; + + int index3 = atom->find_custom("react_tags",flag); + int *i_react_tags = atom->ivector[index3]; + + for (int i = 0; i < temp_limit_num; i++) { + // update->ntimestep could be 0. so add 1 throughout + i_limit_tags[atom->map(temp_limit_glove[i])] = update->ntimestep + 1; + i_statted_tags[atom->map(temp_limit_glove[i])] = 0; + i_react_tags[atom->map(temp_limit_glove[i])] = rxnID; + } + + delete [] temp_limit_glove; +} + +/* ---------------------------------------------------------------------- +let's unlimit movement of newly bonded atoms after n timesteps. +we give them back to the system thermostat +------------------------------------------------------------------------- */ + +void FixBondReact::unlimit_bond() +{ + //let's now unlimit in terms of i_limit_tags + //we just run through all nlocal, looking for > limit_duration + //then we return i_limit_tag to 0 (which removes from dynamic group) + int flag; + int index1 = atom->find_custom("limit_tags",flag); + int *i_limit_tags = atom->ivector[index1]; + + int index2 = atom->find_custom("statted_tags",flag); + int *i_statted_tags = atom->ivector[index2]; + + int index3 = atom->find_custom("react_tags",flag); + int *i_react_tags = atom->ivector[index3]; + + for (int i = 0; i < atom->nlocal; i++) { + if (i_limit_tags[i] != 0 && (update->ntimestep + 1 - i_limit_tags[i]) > limit_duration[i_react_tags[i]]) { + i_limit_tags[i] = 0; + i_statted_tags[i] = 1; + i_react_tags[i] = 0; + } + } + + //really should only communicate this per-atom property, not entire reneighboring + next_reneighbor = update->ntimestep; +} + +/* ---------------------------------------------------------------------- +check mega_glove for ghosts +if so, flag for broadcasting for perusal by all processors +------------------------------------------------------------------------- */ + +void FixBondReact::glove_ghostcheck() +{ + // it appears this little loop was deemed important enough for its own function! + // noteworthy: it's only relevant for parallel + + // here we add glove to either local_mega_glove or ghostly_mega_glove + int ghostly = 0; + for (int i = 0; i < onemol->natoms; i++) { + if (atom->map(glove[i][1]) >= atom->nlocal) { + ghostly = 1; + break; + } + } + + if (ghostly == 1) { + ghostly_mega_glove[0][ghostly_num_mega] = rxnID; + ghostly_rxn_count[rxnID]++; //for debuginng + for (int i = 0; i < onemol->natoms; i++) { + ghostly_mega_glove[i+1][ghostly_num_mega] = glove[i][1]; + } + ghostly_num_mega++; + } else { + local_mega_glove[0][local_num_mega] = rxnID; + local_rxn_count[rxnID]++; //for debuginng + for (int i = 0; i < onemol->natoms; i++) { + local_mega_glove[i+1][local_num_mega] = glove[i][1]; + } + local_num_mega++; + } +} + +/* ---------------------------------------------------------------------- +broadcast entries of mega_glove which contain nonlocal atoms for perusal by all processors +------------------------------------------------------------------------- */ + +void FixBondReact::ghost_glovecast() +{ +#if !defined(MPI_STUBS) + + global_megasize = 0; + + int *allncols = new int[nprocs]; + for (int i = 0; i < nprocs; i++) + allncols[i] = 0; + MPI_Allgather(&ghostly_num_mega, 1, MPI_INT, allncols, 1, MPI_INT, world); + for (int i = 0; i < nprocs; i++) + global_megasize = global_megasize + allncols[i]; + + if (global_megasize == 0) { + delete [] allncols; + return; + } + + int *allstarts = new int[nprocs]; + + int start = 0; + for (int i = 0; i < me; i++) { + start += allncols[i]; + } + MPI_Allgather(&start, 1, MPI_INT, allstarts, 1, MPI_INT, world); + MPI_Datatype columnunsized, column; + int sizes[2] = {max_natoms+1, global_megasize}; + int subsizes[2] = {max_natoms+1, 1}; + int starts[2] = {0,0}; + MPI_Type_create_subarray (2, sizes, subsizes, starts, MPI_ORDER_C, + MPI_LMP_TAGINT, &columnunsized); + MPI_Type_create_resized (columnunsized, 0, sizeof(tagint), &column); + MPI_Type_commit(&column); + + memory->destroy(global_mega_glove); + memory->create(global_mega_glove,max_natoms+1,global_megasize,"bond/react:global_mega_glove"); + + for (int i = 0; i < max_natoms+1; i++) + for (int j = 0; j < global_megasize; j++) + global_mega_glove[i][j] = 0; + + if (ghostly_num_mega > 0) { + for (int i = 0; i < max_natoms+1; i++) { + for (int j = 0; j < ghostly_num_mega; j++) { + global_mega_glove[i][j+start] = ghostly_mega_glove[i][j]; + } + } + } + // let's send to root, dedup, then broadcast + if (me == 0) { + MPI_Gatherv(MPI_IN_PLACE, ghostly_num_mega, column, // Note: some values ignored for MPI_IN_PLACE + &(global_mega_glove[0][0]), allncols, allstarts, + column, 0, world); + } else { + MPI_Gatherv(&(global_mega_glove[0][start]), ghostly_num_mega, column, + &(global_mega_glove[0][0]), allncols, allstarts, + column, 0, world); + } + + if (me == 0) dedup_mega_gloves(1); // global_mega_glove mode + MPI_Bcast(&global_megasize,1,MPI_INT,0,world); + MPI_Bcast(&(global_mega_glove[0][0]), global_megasize, column, 0, world); + + delete [] allstarts; + delete [] allncols; + + MPI_Type_free(&column); + MPI_Type_free(&columnunsized); +#endif +} + +/* ---------------------------------------------------------------------- +update charges, types, special lists and all topology +------------------------------------------------------------------------- */ + +void FixBondReact::update_everything() +{ + int *type = atom->type; + + int nlocal = atom->nlocal; + int **nspecial = atom->nspecial; + tagint **special = atom->special; + + int **bond_type = atom->bond_type; + tagint **bond_atom = atom->bond_atom; + int *num_bond = atom->num_bond; + + // update atom->nbonds, etc. + // TODO: correctly tally with 'newton off' + int delta_bonds = 0; + int delta_angle = 0; + int delta_dihed = 0; + int delta_imprp = 0; + + // pass through twice + // redefining 'update_num_mega' and 'update_mega_glove' each time + // first pass: when glove is all local atoms + // second pass: search for local atoms in global_mega_glove + // add check for local atoms as well + + int update_num_mega; + tagint **update_mega_glove; + memory->create(update_mega_glove,max_natoms+1,MAX(local_num_mega,global_megasize),"bond/react:update_mega_glove"); + + for (int pass = 0; pass < 2; pass++) { + + if (pass == 0) { + update_num_mega = local_num_mega; + for (int i = 0; i < update_num_mega; i++) { + for (int j = 0; j < max_natoms+1; j++) + update_mega_glove[j][i] = local_mega_glove[j][i]; + } + } else if (pass == 1) { + update_num_mega = global_megasize; + for (int i = 0; i < global_megasize; i++) { + for (int j = 0; j < max_natoms+1; j++) + update_mega_glove[j][i] = global_mega_glove[j][i]; + } + } + + // update charges and types of landlocked atoms + // here, add check for charge instead of requiring it + for (int i = 0; i < update_num_mega; i++) { + rxnID = update_mega_glove[0][i]; + twomol = atom->molecules[reacted_mol[rxnID]]; + for (int j = 0; j < twomol->natoms; j++) { + int jj = equivalences[j][1][rxnID]-1; + if (landlocked_atoms[j][rxnID] == 1 && atom->map(update_mega_glove[jj+1][i]) >= 0 && + atom->map(update_mega_glove[jj+1][i]) < nlocal) { + type[atom->map(update_mega_glove[jj+1][i])] = twomol->type[j]; + if (twomol->qflag && atom->q_flag) { + double *q = atom->q; + q[atom->map(update_mega_glove[jj+1][i])] = twomol->q[j]; + } + } + } + } + + //maybe add check that all 1-3 neighbors of a local atoms are at least ghosts -> unneeded --jg + //okay, here goes: + for (int i = 0; i < update_num_mega; i++) { + rxnID = update_mega_glove[0][i]; + twomol = atom->molecules[reacted_mol[rxnID]]; + for (int j = 0; j < twomol->natoms; j++) { + int jj = equivalences[j][1][rxnID]-1; + if (atom->map(update_mega_glove[jj+1][i]) < nlocal && atom->map(update_mega_glove[jj+1][i]) >= 0) { + if (landlocked_atoms[j][rxnID] == 1) { + for (int k = 0; k < nspecial[atom->map(update_mega_glove[jj+1][i])][2]; k++) { + if (atom->map(special[atom->map(update_mega_glove[jj+1][i])][k]) < 0) { + error->all(FLERR,"Fix bond/react needs ghost atoms from further away - most likely too many processors"); + } + } + } + } + } + } + + int insert_num; + // very nice and easy to completely overwrite special bond info for landlocked atoms + for (int i = 0; i < update_num_mega; i++) { + rxnID = update_mega_glove[0][i]; + twomol = atom->molecules[reacted_mol[rxnID]]; + for (int j = 0; j < twomol->natoms; j++) { + int jj = equivalences[j][1][rxnID]-1; + if (atom->map(update_mega_glove[jj+1][i]) < nlocal && atom->map(update_mega_glove[jj+1][i]) >= 0) { + if (landlocked_atoms[j][rxnID] == 1) { + for (int k = 0; k < 3; k++) { + nspecial[atom->map(update_mega_glove[jj+1][i])][k] = twomol->nspecial[j][k]; + } + for (int p = 0; p < twomol->nspecial[j][2]; p++) { + special[atom->map(update_mega_glove[jj+1][i])][p] = update_mega_glove[equivalences[twomol->special[j][p]-1][1][rxnID]][i]; + } + } + // now delete and replace landlocked atoms from non-landlocked atoms' special info + if (landlocked_atoms[j][rxnID] == 0) { + for (int k = nspecial[atom->map(update_mega_glove[jj+1][i])][2]-1; k > -1; k--) { + for (int p = 0; p < twomol->natoms; p++) { + int pp = equivalences[p][1][rxnID]-1; + if (p!=j && special[atom->map(update_mega_glove[jj+1][i])][k] == update_mega_glove[pp+1][i] + && landlocked_atoms[p][rxnID] == 1 ) { + for (int n = k; n < nspecial[atom->map(update_mega_glove[jj+1][i])][2]-1; n++) { + special[atom->map(update_mega_glove[jj+1][i])][n] = special[atom->map(update_mega_glove[jj+1][i])][n+1]; + } + if (k+1 > nspecial[atom->map(update_mega_glove[jj+1][i])][1]) { + nspecial[atom->map(update_mega_glove[jj+1][i])][2]--; + } else if (k+1 > nspecial[atom->map(update_mega_glove[jj+1][i])][0]) { + nspecial[atom->map(update_mega_glove[jj+1][i])][1]--; + nspecial[atom->map(update_mega_glove[jj+1][i])][2]--; + } else { + nspecial[atom->map(update_mega_glove[jj+1][i])][0]--; + nspecial[atom->map(update_mega_glove[jj+1][i])][1]--; + nspecial[atom->map(update_mega_glove[jj+1][i])][2]--; + } + break; + } + } + } + // now reassign from reacted template + for (int k = 0; k < twomol->nspecial[j][2]; k++) { + if (landlocked_atoms[twomol->special[j][k]-1][rxnID] == 1) { + if (k > twomol->nspecial[j][1] - 1) { + insert_num = nspecial[atom->map(update_mega_glove[jj+1][i])][2]++; + } else if (k > twomol->nspecial[j][0] - 1) { + insert_num = nspecial[atom->map(update_mega_glove[jj+1][i])][1]++; + nspecial[atom->map(update_mega_glove[jj+1][i])][2]++; + } else { + insert_num = nspecial[atom->map(update_mega_glove[jj+1][i])][0]++; + nspecial[atom->map(update_mega_glove[jj+1][i])][1]++; + nspecial[atom->map(update_mega_glove[jj+1][i])][2]++; + } + for (int n = nspecial[atom->map(update_mega_glove[jj+1][i])][2]; n > insert_num; n--) { + special[atom->map(update_mega_glove[jj+1][i])][n] = special[atom->map(update_mega_glove[jj+1][i])][n-1]; + } + special[atom->map(update_mega_glove[jj+1][i])][insert_num] = update_mega_glove[equivalences[twomol->special[j][k]-1][1][rxnID]][i]; + } + } + } + } + } + } + + // next let's update bond info + // cool thing is, newton_bond issues are already taken care of in templates + // same with class2 improper issues, which is why this fix started in the first place + for (int i = 0; i < update_num_mega; i++) { + rxnID = update_mega_glove[0][i]; + twomol = atom->molecules[reacted_mol[rxnID]]; + // let's first delete all bond info about landlocked atoms + for (int j = 0; j < twomol->natoms; j++) { + int jj = equivalences[j][1][rxnID]-1; + if (atom->map(update_mega_glove[jj+1][i]) < nlocal && atom->map(update_mega_glove[jj+1][i]) >= 0) { + if (landlocked_atoms[j][rxnID] == 1) { + delta_bonds -= num_bond[atom->map(update_mega_glove[jj+1][i])]; + num_bond[atom->map(update_mega_glove[jj+1][i])] = 0; + } + if (landlocked_atoms[j][rxnID] == 0) { + for (int p = num_bond[atom->map(update_mega_glove[jj+1][i])]-1; p > -1 ; p--) { + for (int n = 0; n < twomol->natoms; n++) { + int nn = equivalences[n][1][rxnID]-1; + if (n!=j && bond_atom[atom->map(update_mega_glove[jj+1][i])][p] == update_mega_glove[nn+1][i] && landlocked_atoms[n][rxnID] == 1) { + for (int m = p; m < num_bond[atom->map(update_mega_glove[jj+1][i])]-1; m++) { + bond_atom[atom->map(update_mega_glove[jj+1][i])][m] = bond_atom[atom->map(update_mega_glove[jj+1][i])][m+1]; + } + num_bond[atom->map(update_mega_glove[jj+1][i])]--; + delta_bonds--; + } + } + } + } + } + } + // now let's add the new bond info. + for (int j = 0; j < twomol->natoms; j++) { + int jj = equivalences[j][1][rxnID]-1; + if (atom->map(update_mega_glove[jj+1][i]) < nlocal && atom->map(update_mega_glove[jj+1][i]) >= 0) { + if (landlocked_atoms[j][rxnID] == 1) { + num_bond[atom->map(update_mega_glove[jj+1][i])] = twomol->num_bond[j]; + delta_bonds += twomol->num_bond[j]; + for (int p = 0; p < twomol->num_bond[j]; p++) { + bond_type[atom->map(update_mega_glove[jj+1][i])][p] = twomol->bond_type[j][p]; + bond_atom[atom->map(update_mega_glove[jj+1][i])][p] = update_mega_glove[equivalences[twomol->bond_atom[j][p]-1][1][rxnID]][i]; + } + } + if (landlocked_atoms[j][rxnID] == 0) { + for (int p = 0; p < twomol->num_bond[j]; p++) { + if (landlocked_atoms[twomol->bond_atom[j][p]-1][rxnID] == 1) { + insert_num = num_bond[atom->map(update_mega_glove[jj+1][i])]; + bond_type[atom->map(update_mega_glove[jj+1][i])][insert_num] = twomol->bond_type[j][p]; + bond_atom[atom->map(update_mega_glove[jj+1][i])][insert_num] = update_mega_glove[equivalences[twomol->bond_atom[j][p]-1][1][rxnID]][i]; + num_bond[atom->map(update_mega_glove[jj+1][i])]++; + delta_bonds++; + } + } + } + } + } + } + + if (force->angle && twomol->angleflag) { + int *num_angle = atom->num_angle; + int **angle_type = atom->angle_type; + tagint **angle_atom1 = atom->angle_atom1; + tagint **angle_atom2 = atom->angle_atom2; + tagint **angle_atom3 = atom->angle_atom3; + + for (int i = 0; i < update_num_mega; i++) { + rxnID = update_mega_glove[0][i]; + twomol = atom->molecules[reacted_mol[rxnID]]; + // Angles! First let's delete all angle info: + for (int j = 0; j < twomol->natoms; j++) { + int jj = equivalences[j][1][rxnID]-1; + if (atom->map(update_mega_glove[jj+1][i]) < nlocal && atom->map(update_mega_glove[jj+1][i]) >= 0) { + if (landlocked_atoms[j][rxnID] == 1) { + delta_angle -= num_angle[atom->map(update_mega_glove[jj+1][i])]; + num_angle[atom->map(update_mega_glove[jj+1][i])] = 0; + } + if (landlocked_atoms[j][rxnID] == 0) { + for (int p = num_angle[atom->map(update_mega_glove[jj+1][i])]-1; p > -1; p--) { + for (int n = 0; n < twomol->natoms; n++) { + int nn = equivalences[n][1][rxnID]-1; + if (n!=j && landlocked_atoms[n][rxnID] == 1 && + (angle_atom1[atom->map(update_mega_glove[jj+1][i])][p] == update_mega_glove[nn+1][i] || + angle_atom2[atom->map(update_mega_glove[jj+1][i])][p] == update_mega_glove[nn+1][i] || + angle_atom3[atom->map(update_mega_glove[jj+1][i])][p] == update_mega_glove[nn+1][i])) { + for (int m = p; m < num_angle[atom->map(update_mega_glove[jj+1][i])]-1; m++) { + angle_atom1[atom->map(update_mega_glove[jj+1][i])][m] = angle_atom1[atom->map(update_mega_glove[jj+1][i])][m+1]; + angle_atom2[atom->map(update_mega_glove[jj+1][i])][m] = angle_atom2[atom->map(update_mega_glove[jj+1][i])][m+1]; + angle_atom3[atom->map(update_mega_glove[jj+1][i])][m] = angle_atom3[atom->map(update_mega_glove[jj+1][i])][m+1]; + } + num_angle[atom->map(update_mega_glove[jj+1][i])]--; + delta_angle--; + break; + } + } + } + } + } + } + // now let's add the new angle info. + for (int j = 0; j < twomol->natoms; j++) { + int jj = equivalences[j][1][rxnID]-1; + if (atom->map(update_mega_glove[jj+1][i]) < nlocal && atom->map(update_mega_glove[jj+1][i]) >= 0) { + if (landlocked_atoms[j][rxnID] == 1) { + num_angle[atom->map(update_mega_glove[jj+1][i])] = twomol->num_angle[j]; + delta_angle += twomol->num_angle[j]; + for (int p = 0; p < twomol->num_angle[j]; p++) { + angle_type[atom->map(update_mega_glove[jj+1][i])][p] = twomol->angle_type[j][p]; + angle_atom1[atom->map(update_mega_glove[jj+1][i])][p] = update_mega_glove[equivalences[twomol->angle_atom1[j][p]-1][1][rxnID]][i]; + angle_atom2[atom->map(update_mega_glove[jj+1][i])][p] = update_mega_glove[equivalences[twomol->angle_atom2[j][p]-1][1][rxnID]][i]; + angle_atom3[atom->map(update_mega_glove[jj+1][i])][p] = update_mega_glove[equivalences[twomol->angle_atom3[j][p]-1][1][rxnID]][i]; + } + } + if (landlocked_atoms[j][rxnID] == 0) { + for (int p = 0; p < twomol->num_angle[j]; p++) { + if (landlocked_atoms[twomol->angle_atom1[j][p]-1][rxnID] == 1 || + landlocked_atoms[twomol->angle_atom2[j][p]-1][rxnID] == 1 || + landlocked_atoms[twomol->angle_atom3[j][p]-1][rxnID] == 1) { + insert_num = num_angle[atom->map(update_mega_glove[jj+1][i])]; + angle_type[atom->map(update_mega_glove[jj+1][i])][insert_num] = twomol->angle_type[j][p]; + angle_atom1[atom->map(update_mega_glove[jj+1][i])][insert_num] = update_mega_glove[equivalences[twomol->angle_atom1[j][p]-1][1][rxnID]][i]; + angle_atom2[atom->map(update_mega_glove[jj+1][i])][insert_num] = update_mega_glove[equivalences[twomol->angle_atom2[j][p]-1][1][rxnID]][i]; + angle_atom3[atom->map(update_mega_glove[jj+1][i])][insert_num] = update_mega_glove[equivalences[twomol->angle_atom3[j][p]-1][1][rxnID]][i]; + num_angle[atom->map(update_mega_glove[jj+1][i])]++; + delta_angle++; + } + } + } + } + } + } + } + + // Dihedrals! first let's delete all dihedral info for landlocked atoms + if (force->dihedral && twomol->dihedralflag) { + int *num_dihedral = atom->num_dihedral; + int **dihedral_type = atom->dihedral_type; + tagint **dihedral_atom1 = atom->dihedral_atom1; + tagint **dihedral_atom2 = atom->dihedral_atom2; + tagint **dihedral_atom3 = atom->dihedral_atom3; + tagint **dihedral_atom4 = atom->dihedral_atom4; + + for (int i = 0; i < update_num_mega; i++) { + rxnID = update_mega_glove[0][i]; + twomol = atom->molecules[reacted_mol[rxnID]]; + for (int j = 0; j < twomol->natoms; j++) { + int jj = equivalences[j][1][rxnID]-1; + if (atom->map(update_mega_glove[jj+1][i]) < nlocal && atom->map(update_mega_glove[jj+1][i]) >= 0) { + if (landlocked_atoms[j][rxnID] == 1) { + delta_dihed -= num_dihedral[atom->map(update_mega_glove[jj+1][i])]; + num_dihedral[atom->map(update_mega_glove[jj+1][i])] = 0; + } + if (landlocked_atoms[j][rxnID] == 0) { + for (int p = num_dihedral[atom->map(update_mega_glove[jj+1][i])]-1; p > -1; p--) { + for (int n = 0; n < twomol->natoms; n++) { + int nn = equivalences[n][1][rxnID]-1; + if (n!=j && landlocked_atoms[n][rxnID] == 1 && + (dihedral_atom1[atom->map(update_mega_glove[jj+1][i])][p] == update_mega_glove[nn+1][i] || + dihedral_atom2[atom->map(update_mega_glove[jj+1][i])][p] == update_mega_glove[nn+1][i] || + dihedral_atom3[atom->map(update_mega_glove[jj+1][i])][p] == update_mega_glove[nn+1][i] || + dihedral_atom4[atom->map(update_mega_glove[jj+1][i])][p] == update_mega_glove[nn+1][i])) { + for (int m = p; m < num_dihedral[atom->map(update_mega_glove[jj+1][i])]-1; m++) { + dihedral_atom1[atom->map(update_mega_glove[jj+1][i])][m] = dihedral_atom1[atom->map(update_mega_glove[jj+1][i])][m+1]; + dihedral_atom2[atom->map(update_mega_glove[jj+1][i])][m] = dihedral_atom2[atom->map(update_mega_glove[jj+1][i])][m+1]; + dihedral_atom3[atom->map(update_mega_glove[jj+1][i])][m] = dihedral_atom3[atom->map(update_mega_glove[jj+1][i])][m+1]; + dihedral_atom4[atom->map(update_mega_glove[jj+1][i])][m] = dihedral_atom4[atom->map(update_mega_glove[jj+1][i])][m+1]; + } + num_dihedral[atom->map(update_mega_glove[jj+1][i])]--; + delta_dihed--; + break; + } + } + } + } + } + } + // now let's add new dihedral info + for (int j = 0; j < twomol->natoms; j++) { + int jj = equivalences[j][1][rxnID]-1; + if (atom->map(update_mega_glove[jj+1][i]) < nlocal && atom->map(update_mega_glove[jj+1][i]) >= 0) { + if (landlocked_atoms[j][rxnID] == 1) { + num_dihedral[atom->map(update_mega_glove[jj+1][i])] = twomol->num_dihedral[j]; + delta_dihed += twomol->num_dihedral[j]; + for (int p = 0; p < twomol->num_dihedral[j]; p++) { + dihedral_type[atom->map(update_mega_glove[jj+1][i])][p] = twomol->dihedral_type[j][p]; + dihedral_atom1[atom->map(update_mega_glove[jj+1][i])][p] = update_mega_glove[equivalences[twomol->dihedral_atom1[j][p]-1][1][rxnID]][i]; + dihedral_atom2[atom->map(update_mega_glove[jj+1][i])][p] = update_mega_glove[equivalences[twomol->dihedral_atom2[j][p]-1][1][rxnID]][i]; + dihedral_atom3[atom->map(update_mega_glove[jj+1][i])][p] = update_mega_glove[equivalences[twomol->dihedral_atom3[j][p]-1][1][rxnID]][i]; + dihedral_atom4[atom->map(update_mega_glove[jj+1][i])][p] = update_mega_glove[equivalences[twomol->dihedral_atom4[j][p]-1][1][rxnID]][i]; + } + } + if (landlocked_atoms[j][rxnID] == 0) { + for (int p = 0; p < twomol->num_dihedral[j]; p++) { + if (landlocked_atoms[twomol->dihedral_atom1[j][p]-1][rxnID] == 1 || + landlocked_atoms[twomol->dihedral_atom2[j][p]-1][rxnID] == 1 || + landlocked_atoms[twomol->dihedral_atom3[j][p]-1][rxnID] == 1 || + landlocked_atoms[twomol->dihedral_atom4[j][p]-1][rxnID] == 1) { + insert_num = num_dihedral[atom->map(update_mega_glove[jj+1][i])]; + dihedral_type[atom->map(update_mega_glove[jj+1][i])][insert_num] = twomol->dihedral_type[j][p]; + dihedral_atom1[atom->map(update_mega_glove[jj+1][i])][insert_num] = update_mega_glove[equivalences[twomol->dihedral_atom1[j][p]-1][1][rxnID]][i]; + dihedral_atom2[atom->map(update_mega_glove[jj+1][i])][insert_num] = update_mega_glove[equivalences[twomol->dihedral_atom2[j][p]-1][1][rxnID]][i]; + dihedral_atom3[atom->map(update_mega_glove[jj+1][i])][insert_num] = update_mega_glove[equivalences[twomol->dihedral_atom3[j][p]-1][1][rxnID]][i]; + dihedral_atom4[atom->map(update_mega_glove[jj+1][i])][insert_num] = update_mega_glove[equivalences[twomol->dihedral_atom4[j][p]-1][1][rxnID]][i]; + num_dihedral[atom->map(update_mega_glove[jj+1][i])]++; + delta_dihed++; + } + } + } + } + } + } + } + + // finally IMPROPERS!!!! first let's delete all improper info for landlocked atoms + if (force->improper && twomol->improperflag) { + int *num_improper = atom->num_improper; + int **improper_type = atom->improper_type; + tagint **improper_atom1 = atom->improper_atom1; + tagint **improper_atom2 = atom->improper_atom2; + tagint **improper_atom3 = atom->improper_atom3; + tagint **improper_atom4 = atom->improper_atom4; + + for (int i = 0; i < update_num_mega; i++) { + rxnID = update_mega_glove[0][i]; + twomol = atom->molecules[reacted_mol[rxnID]]; + for (int j = 0; j < twomol->natoms; j++) { + int jj = equivalences[j][1][rxnID]-1; + if (atom->map(update_mega_glove[jj+1][i]) < nlocal && atom->map(update_mega_glove[jj+1][i]) >= 0) { + if (landlocked_atoms[j][rxnID] == 1) { + delta_imprp -= num_improper[atom->map(update_mega_glove[jj+1][i])]; + num_improper[atom->map(update_mega_glove[jj+1][i])] = 0; + } + if (landlocked_atoms[j][rxnID] == 0) { + for (int p = num_improper[atom->map(update_mega_glove[jj+1][i])]-1; p > -1; p--) { + for (int n = 0; n < twomol->natoms; n++) { + int nn = equivalences[n][1][rxnID]-1; + if (n!=j && landlocked_atoms[n][rxnID] == 1 && + (improper_atom1[atom->map(update_mega_glove[jj+1][i])][p] == update_mega_glove[nn+1][i] || + improper_atom2[atom->map(update_mega_glove[jj+1][i])][p] == update_mega_glove[nn+1][i] || + improper_atom3[atom->map(update_mega_glove[jj+1][i])][p] == update_mega_glove[nn+1][i] || + improper_atom4[atom->map(update_mega_glove[jj+1][i])][p] == update_mega_glove[nn+1][i])) { + for (int m = p; m < num_improper[atom->map(update_mega_glove[jj+1][i])]-1; m++) { + improper_atom1[atom->map(update_mega_glove[jj+1][i])][m] = improper_atom1[atom->map(update_mega_glove[jj+1][i])][m+1]; + improper_atom2[atom->map(update_mega_glove[jj+1][i])][m] = improper_atom2[atom->map(update_mega_glove[jj+1][i])][m+1]; + improper_atom3[atom->map(update_mega_glove[jj+1][i])][m] = improper_atom3[atom->map(update_mega_glove[jj+1][i])][m+1]; + improper_atom4[atom->map(update_mega_glove[jj+1][i])][m] = improper_atom4[atom->map(update_mega_glove[jj+1][i])][m+1]; + } + num_improper[atom->map(update_mega_glove[jj+1][i])]--; + delta_imprp--; + break; + } + } + } + } + } + } + // now let's add new improper info + for (int j = 0; j < twomol->natoms; j++) { + int jj = equivalences[j][1][rxnID]-1; + if (atom->map(update_mega_glove[jj+1][i]) < nlocal && atom->map(update_mega_glove[jj+1][i]) >= 0) { + if (landlocked_atoms[j][rxnID] == 1) { + num_improper[atom->map(update_mega_glove[jj+1][i])] = twomol->num_improper[j]; + delta_imprp += twomol->num_improper[j]; + for (int p = 0; p < twomol->num_improper[j]; p++) { + improper_type[atom->map(update_mega_glove[jj+1][i])][p] = twomol->improper_type[j][p]; + improper_atom1[atom->map(update_mega_glove[jj+1][i])][p] = update_mega_glove[equivalences[twomol->improper_atom1[j][p]-1][1][rxnID]][i]; + improper_atom2[atom->map(update_mega_glove[jj+1][i])][p] = update_mega_glove[equivalences[twomol->improper_atom2[j][p]-1][1][rxnID]][i]; + improper_atom3[atom->map(update_mega_glove[jj+1][i])][p] = update_mega_glove[equivalences[twomol->improper_atom3[j][p]-1][1][rxnID]][i]; + improper_atom4[atom->map(update_mega_glove[jj+1][i])][p] = update_mega_glove[equivalences[twomol->improper_atom4[j][p]-1][1][rxnID]][i]; + } + } + if (landlocked_atoms[j][rxnID] == 0) { + for (int p = 0; p < twomol->num_improper[j]; p++) { + if (landlocked_atoms[twomol->improper_atom1[j][p]-1][rxnID] == 1 || + landlocked_atoms[twomol->improper_atom2[j][p]-1][rxnID] == 1 || + landlocked_atoms[twomol->improper_atom3[j][p]-1][rxnID] == 1 || + landlocked_atoms[twomol->improper_atom4[j][p]-1][rxnID] == 1) { + insert_num = num_improper[atom->map(update_mega_glove[jj+1][i])]; + improper_type[atom->map(update_mega_glove[jj+1][i])][insert_num] = twomol->improper_type[j][p]; + improper_atom1[atom->map(update_mega_glove[jj+1][i])][insert_num] = update_mega_glove[equivalences[twomol->improper_atom1[j][p]-1][1][rxnID]][i]; + improper_atom2[atom->map(update_mega_glove[jj+1][i])][insert_num] = update_mega_glove[equivalences[twomol->improper_atom2[j][p]-1][1][rxnID]][i]; + improper_atom3[atom->map(update_mega_glove[jj+1][i])][insert_num] = update_mega_glove[equivalences[twomol->improper_atom3[j][p]-1][1][rxnID]][i]; + improper_atom4[atom->map(update_mega_glove[jj+1][i])][insert_num] = update_mega_glove[equivalences[twomol->improper_atom4[j][p]-1][1][rxnID]][i]; + num_improper[atom->map(update_mega_glove[jj+1][i])]++; + delta_imprp++; + } + } + } + } + } + } + } + + } + + memory->destroy(update_mega_glove); + + // something to think about: this could done much more concisely if + // all atom-level info (bond,angles, etc...) were kinda inherited from a common data struct --JG + + int Tdelta_bonds; + MPI_Allreduce(&delta_bonds,&Tdelta_bonds,1,MPI_INT,MPI_SUM,world); + atom->nbonds += Tdelta_bonds; + + int Tdelta_angle; + MPI_Allreduce(&delta_angle,&Tdelta_angle,1,MPI_INT,MPI_SUM,world); + atom->nangles += Tdelta_angle; + + int Tdelta_dihed; + MPI_Allreduce(&delta_dihed,&Tdelta_dihed,1,MPI_INT,MPI_SUM,world); + atom->ndihedrals += Tdelta_dihed; + + int Tdelta_imprp; + MPI_Allreduce(&delta_imprp,&Tdelta_imprp,1,MPI_INT,MPI_SUM,world); + atom->nimpropers += Tdelta_imprp; +} + +/* ---------------------------------------------------------------------- +read superimpose file +------------------------------------------------------------------------- */ + +void FixBondReact::read(int myrxn) +{ + char line[MAXLINE],keyword[MAXLINE]; + char *eof,*ptr; + + // skip 1st line of file + eof = fgets(line,MAXLINE,fp); + if (eof == NULL) error->one(FLERR,"Unexpected end of superimpose file"); + + // read header lines + // skip blank lines or lines that start with "#" + // stop when read an unrecognized line + + while (1) { + + readline(line); + + // trim anything from '#' onward + // if line is blank, continue + + if ((ptr = strchr(line,'#'))) *ptr = '\0'; + if (strspn(line," \t\n\r") == strlen(line)) continue; + + if (strstr(line,"edgeIDs")) sscanf(line,"%d",&nedge); + else if (strstr(line,"equivalences")) sscanf(line,"%d",&nequivalent); + else break; + } + + //count = NULL; + + // grab keyword and skip next line + + parse_keyword(0,line,keyword); + readline(line); + + // loop over sections of superimpose file + + int equivflag = 0, edgeflag = 0, bondflag = 0; + while (strlen(keyword)) { + if (strcmp(keyword,"BondingIDs") == 0) { + bondflag = 1; + readline(line); + sscanf(line,"%d",&ibonding[myrxn]); + readline(line); + sscanf(line,"%d",&jbonding[myrxn]); + } else if (strcmp(keyword,"EdgeIDs") == 0) { + edgeflag = 1; + for (int i = 0; i < onemol->natoms; i++) edge[i][myrxn] = 0; + EdgeIDs(line, myrxn); + } else if (strcmp(keyword,"Equivalences") == 0) { + equivflag = 1; + Equivalences(line, myrxn); + } else error->one(FLERR,"Unknown section in superimpose file"); + + parse_keyword(1,line,keyword); + + } + + // error check + if (bondflag == 0 || equivflag == 0 || edgeflag == 0) + error->all(FLERR,"Superimpose file missing BondingIDs, EdgeIDs, or Equivalences section\n"); +} + +void FixBondReact::EdgeIDs(char *line, int myrxn) +{ + // puts a 1 at edge(edgeID) + + int tmp; + for (int i = 0; i < nedge; i++) { + readline(line); + sscanf(line,"%d",&tmp); + edge[tmp-1][myrxn] = 1; + } +} + +void FixBondReact::Equivalences(char *line, int myrxn) +{ + int tmp1; + int tmp2; + for (int i = 0; i < nequivalent; i++) { + readline(line); + sscanf(line,"%d %d",&tmp1,&tmp2); + //equivalences is-> clmn 1: post-reacted, clmn 2: pre-reacted + equivalences[tmp2-1][0][myrxn] = tmp2; + equivalences[tmp2-1][1][myrxn] = tmp1; + //reverse_equiv is-> clmn 1: pre-reacted, clmn 2: post-reacted + reverse_equiv[tmp1-1][0][myrxn] = tmp1; + reverse_equiv[tmp1-1][1][myrxn] = tmp2; + } +} + +void FixBondReact::open(char *file) +{ + fp = fopen(file,"r"); + if (fp == NULL) { + char str[128]; + sprintf(str,"Cannot open superimpose file %s",file); + error->one(FLERR,str); + } +} + +void FixBondReact::readline(char *line) +{ + int n; + if (me == 0) { + if (fgets(line,MAXLINE,fp) == NULL) n = 0; + else n = strlen(line) + 1; + } + MPI_Bcast(&n,1,MPI_INT,0,world); + if (n == 0) error->all(FLERR,"Unexpected end of superimpose file"); + MPI_Bcast(line,n,MPI_CHAR,0,world); +} + +void FixBondReact::parse_keyword(int flag, char *line, char *keyword) +{ + if (flag) { + + // read upto non-blank line plus 1 following line + // eof is set to 1 if any read hits end-of-file + + int eof = 0; + if (me == 0) { + if (fgets(line,MAXLINE,fp) == NULL) eof = 1; + while (eof == 0 && strspn(line," \t\n\r") == strlen(line)) { + if (fgets(line,MAXLINE,fp) == NULL) eof = 1; + } + if (fgets(keyword,MAXLINE,fp) == NULL) eof = 1; + } + + // if eof, set keyword empty and return + + MPI_Bcast(&eof,1,MPI_INT,0,world); + if (eof) { + keyword[0] = '\0'; + return; + } + + // bcast keyword line to all procs + + int n; + if (me == 0) n = strlen(line) + 1; + MPI_Bcast(&n,1,MPI_INT,0,world); + MPI_Bcast(line,n,MPI_CHAR,0,world); + } + + // copy non-whitespace portion of line into keyword + + int start = strspn(line," \t\n\r"); + int stop = strlen(line) - 1; + while (line[stop] == ' ' || line[stop] == '\t' + || line[stop] == '\n' || line[stop] == '\r') stop--; + line[stop+1] = '\0'; + strcpy(keyword,&line[start]); +} + + +void FixBondReact::skip_lines(int n, char *line) +{ + for (int i = 0; i < n; i++) readline(line); +} + +int FixBondReact::parse(char *line, char **words, int max) +{ + char *ptr; + + int nwords = 0; + words[nwords++] = strtok(line," \t\n\r\f"); + + while ((ptr = strtok(NULL," \t\n\r\f"))) { + if (nwords < max) words[nwords] = ptr; + nwords++; + } + + return nwords; +} + +/* ---------------------------------------------------------------------- */ + +double FixBondReact::compute_vector(int n) +{ + // now we print just the totals for each reaction instance + return (double) reaction_count_total[n]; + +} + +/* ---------------------------------------------------------------------- */ + +void FixBondReact::post_integrate_respa(int ilevel, int iloop) +{ + if (ilevel == nlevels_respa-1) post_integrate(); +} + +/* ---------------------------------------------------------------------- */ + +int FixBondReact::pack_forward_comm(int n, int *list, double *buf, + int pbc_flag, int *pbc) +{ + int i,j,k,m,ns; + + m = 0; + + if (commflag == 1) { + for (i = 0; i < n; i++) { + j = list[i]; + printf("hello you shouldn't be here\n"); + //buf[m++] = ubuf(bondcount[j]).d; + } + return m; + } + + if (commflag == 2) { + for (i = 0; i < n; i++) { + j = list[i]; + buf[m++] = ubuf(partner[j]).d; + buf[m++] = probability[j]; + } + return m; + } + + int **nspecial = atom->nspecial; + tagint **special = atom->special; + + m = 0; + for (i = 0; i < n; i++) { + j = list[i]; + buf[m++] = ubuf(finalpartner[j]).d; + ns = nspecial[j][0]; + buf[m++] = ubuf(ns).d; + for (k = 0; k < ns; k++) + buf[m++] = ubuf(special[j][k]).d; + } + return m; +} + +/* ---------------------------------------------------------------------- */ + +void FixBondReact::unpack_forward_comm(int n, int first, double *buf) +{ + int i,j,m,ns,last; + + m = 0; + last = first + n; + + if (commflag == 1) { + for (i = first; i < last; i++) + printf("hello you shouldn't be here\n"); + // bondcount[i] = (int) ubuf(buf[m++]).i; + + } else if (commflag == 2) { + for (i = first; i < last; i++) { + partner[i] = (tagint) ubuf(buf[m++]).i; + probability[i] = buf[m++]; + } + + } else { + int **nspecial = atom->nspecial; + tagint **special = atom->special; + + m = 0; + last = first + n; + for (i = first; i < last; i++) { + finalpartner[i] = (tagint) ubuf(buf[m++]).i; + ns = (int) ubuf(buf[m++]).i; + nspecial[i][0] = ns; + for (j = 0; j < ns; j++) + special[i][j] = (tagint) ubuf(buf[m++]).i; + } + } +} + +/* ---------------------------------------------------------------------- */ + +int FixBondReact::pack_reverse_comm(int n, int first, double *buf) +{ + int i,m,last; + + m = 0; + last = first + n; + + for (i = first; i < last; i++) { + buf[m++] = ubuf(partner[i]).d; + if (closeneigh[rxnID] < 0) + buf[m++] = distsq[i][1]; + else + buf[m++] = distsq[i][0]; + } + return m; +} + +/* ---------------------------------------------------------------------- */ + +void FixBondReact::unpack_reverse_comm(int n, int *list, double *buf) +{ + int i,j,m; + + m = 0; + + if (commflag != 1) { + for (i = 0; i < n; i++) { + j = list[i]; + if (closeneigh[rxnID] < 0) + if (buf[m+1] < distsq[j][1]) { + partner[j] = (tagint) ubuf(buf[m++]).i; + distsq[j][1] = buf[m++]; + } else m += 2; + else + if (buf[m+1] > distsq[j][0]) { + partner[j] = (tagint) ubuf(buf[m++]).i; + distsq[j][0] = buf[m++]; + } else m += 2; + } + } +} + +/* ---------------------------------------------------------------------- +memory usage of local atom-based arrays +------------------------------------------------------------------------- */ + +double FixBondReact::memory_usage() +{ + int nmax = atom->nmax; + double bytes = nmax * sizeof(int); + bytes = 2*nmax * sizeof(tagint); + bytes += nmax * sizeof(double); + return bytes; +} + +/* ---------------------------------------------------------------------- */ + +void FixBondReact::print_bb() +{ + + //fix bond/create cargo code. eg nbonds needs to be added + /* +for (int i = 0; i < atom->nlocal; i++) { + // printf("TAG " TAGINT_FORMAT ": %d nbonds: ",atom->tag[i],atom->num_bond[i]); + for (int j = 0; j < atom->num_bond[i]; j++) { + // printf(" " TAGINT_FORMAT,atom->bond_atom[i][j]); + } + // printf("\n"); + // printf("TAG " TAGINT_FORMAT ": %d nangles: ",atom->tag[i],atom->num_angle[i]); + for (int j = 0; j < atom->num_angle[i]; j++) { + // printf(" " TAGINT_FORMAT " " TAGINT_FORMAT " " TAGINT_FORMAT ",", + atom->angle_atom1[i][j], atom->angle_atom2[i][j], + atom->angle_atom3[i][j]); + } + // printf("\n"); + // printf("TAG " TAGINT_FORMAT ": %d ndihedrals: ",atom->tag[i],atom->num_dihedral[i]); + for (int j = 0; j < atom->num_dihedral[i]; j++) { + // printf(" " TAGINT_FORMAT " " TAGINT_FORMAT " " TAGINT_FORMAT " " + TAGINT_FORMAT ",", atom->dihedral_atom1[i][j], + atom->dihedral_atom2[i][j],atom->dihedral_atom3[i][j], + atom->dihedral_atom4[i][j]); + } + // printf("\n"); + // printf("TAG " TAGINT_FORMAT ": %d nimpropers: ",atom->tag[i],atom->num_improper[i]); + for (int j = 0; j < atom->num_improper[i]; j++) { + // printf(" " TAGINT_FORMAT " " TAGINT_FORMAT " " TAGINT_FORMAT " " + TAGINT_FORMAT ",",atom->improper_atom1[i][j], + atom->improper_atom2[i][j],atom->improper_atom3[i][j], + atom->improper_atom4[i][j]); + } + // printf("\n"); + // printf("TAG " TAGINT_FORMAT ": %d %d %d nspecial: ",atom->tag[i], + atom->nspecial[i][0],atom->nspecial[i][1],atom->nspecial[i][2]); + for (int j = 0; j < atom->nspecial[i][2]; j++) { + // printf(" " TAGINT_FORMAT,atom->special[i][j]); + } + // printf("\n"); +} +*/ +} diff --git a/src/USER-MISC/fix_bond_react.h b/src/USER-MISC/fix_bond_react.h new file mode 100644 index 0000000000000000000000000000000000000000..e60fff37fbaa93f6e4e09136a57282cd883d9fe3 --- /dev/null +++ b/src/USER-MISC/fix_bond_react.h @@ -0,0 +1,217 @@ +/* -*- 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 Author: Jacob Gissinger (jacob.gissinger@colorado.edu) +------------------------------------------------------------------------- */ + +#ifdef FIX_CLASS + +FixStyle(bond/react,FixBondReact) + +#else + +#ifndef LMP_FIX_BOND_REACT_H +#define LMP_FIX_BOND_REACT_H + +#include "fix.h" + +namespace LAMMPS_NS { + +class FixBondReact : public Fix { + public: + FixBondReact(class LAMMPS *, int, char **); + ~FixBondReact(); + int setmask(); + void post_constructor(); + void init(); + void init_list(int, class NeighList *); + void post_integrate(); + void post_integrate_respa(int, int); + + int pack_forward_comm(int, int *, double *, int, int *); + void unpack_forward_comm(int, int, double *); + int pack_reverse_comm(int, int, double *); + void unpack_reverse_comm(int, int *, double *); + double compute_vector(int); + double memory_usage(); + + private: + int me,nprocs; + int nreacts; + int *nevery; + FILE *fp; + int *iatomtype,*jatomtype; + int *seed; + double **cutsq,*fraction; + tagint lastcheck; + int stabilization_flag; + int *stabilize_steps_flag; + int status; + int *groupbits; + + int rxnID; // integer ID for identifying current bond/react + int *reaction_count; + int *reaction_count_total; + int nmax; // max num local atoms + int max_natoms; // max natoms in a molecule template + tagint *partner,*finalpartner; + double **distsq,*probability; + int *ncreate; + int maxcreate; + int allncreate; + tagint ***created; + int *local_ncreate; + + class Molecule *onemol; // pre-reacted molecule template + class Molecule *twomol; // post-reacted molecule template + Fix *fix1; // nve/limit used to relax reaction sites + Fix *fix2; // properties/atom used to indicate 1) indicate relaxing atoms + // 2) system-wide thermostat + // 3) to which 'react' atom belongs + class RanMars **random; + class NeighList *list; + + int *reacted_mol,*unreacted_mol; + int *limit_duration; // indicates how long to relax + char *nve_limit_xmax; // indicates max distance allowed to move when relaxing + char *id_fix1; // id of internally created fix nve/limit + char *id_fix2; // id of internally created fix per-atom properties + char *master_group; // group containing relaxing atoms from all fix rxns + char *exclude_group; // group for system-wide thermostat + + int countflag,commflag; + int nlevels_respa; + + void superimpose_algorithm(); // main function of the superimpose algorithm + + int *ibonding,*jbonding; + int *closeneigh; // indicates if bonding atoms of a rxn are 1-2, 1-3, or 1-4 neighbors + int nedge,nequivalent; // number of edge, equivalent atoms in mapping file + int attempted_rxn; // there was an attempt! + int *local_rxn_count; + int *ghostly_rxn_count; + int avail_guesses; // num of restore points available + int *guess_branch; // used when there is more than two choices when guessing + int **restore_pt; // contains info about restore points + tagint **restore; // contaings info about restore points + int *pioneer_count; // counts pioneers + + int **edge; // atoms in molecule templates with incorrect valences + int ***equivalences; // relation between pre- and post-reacted templates + int ***reverse_equiv; // re-ordered equivalences + int **landlocked_atoms; // all atoms at least three bonds away from edge atoms + + int pion,neigh,trace; // important indices for various loops. required for restore points + int lcl_inst; // reaction instance + tagint **glove; // 1st colmn: pre-reacted template, 2nd colmn: global IDs + // for all mega_gloves and global_mega_glove: first row is the ID of bond/react + tagint **local_mega_glove; // consolidation local of reaction instances + tagint **ghostly_mega_glove; // consolidation nonlocal of reaction instances + tagint **global_mega_glove; // consolidation (inter-processor) of gloves containing nonlocal atoms + int local_num_mega; // num of local reaction instances + int ghostly_num_mega; // num of ghostly reaction instances + int global_megasize; // num of reaction instances in global_mega_glove + int *pioneers; // during Superimpose Algorithm, atoms which have been assigned, but whose first neighbors haven't + int glove_counter; // used to determine when to terminate Superimpose Algorithm + + void read(int); + void EdgeIDs(char *,int); + void Equivalences(char *,int); + + void make_a_guess (); + void neighbor_loop(); + void check_a_neighbor(); + void crosscheck_the_neighbor(); + void inner_crosscheck_loop(); + void ring_check(); + + void open(char *); + void readline(char *); + void parse_keyword(int, char *, char *); + void skip_lines(int, char *); + int parse(char *, char **, int); + + void far_partner(); + void close_partner(); + void find_landlocked_atoms(int); + void glove_ghostcheck(); + void ghost_glovecast(); + void update_everything(); + void unlimit_bond(); + void limit_bond(int); + void dedup_mega_gloves(int); //dedup global mega_glove + + // DEBUG (currently obsolete) + + void print_bb(); + +}; + +} + +#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: Invalid exclude group name + +Exclude group name should not previously be defined. + +E: Cannot use fix bond/react with non-molecular systems + +Only systems with bonds that can be changed can be used. Atom_style +template does not qualify. + +E: Fix bond/react cutoff is longer than pairwise cutoff + +This is not allowed because bond creation is done using the +pairwise neighbor list. + +E: Molecule template ID for fix bond/react does not exist + +A valid molecule template must have been created with the molecule command. + +E: Superimpose file errors: + +Please ensure superimpose file is properly formatted. + +E: Atom affected by reaction too close to template edge + +This means an atom which changes type during the reaction is too close +to an 'edge' atom defined in the superimpose file. This could cause incorrect +assignment of bonds, angle, etc. Generally, this means you must include +more atoms in your templates, such that there are at least two atoms +between each atom involved in the reaction and an edge atom. + +E: Fix bond/react needs ghost atoms from farther away + +This is because a processor needs to superimpose the entire unreacted +molecule template onto simulation atoms it can 'see.' The comm_modify cutoff +command can be used to extend the communication range. + +E: Excessive iteration of superimpose algorithm + +You may have discovered a bug! But first, please double check that your +molecule template atom types, bond types, etc. are consistent with your simulation, +and that all atoms affected by a reaction are sufficently separated from edge atoms. +If this issue persists, please contact the developer. + +*/ diff --git a/src/USER-MISC/fix_filter_corotate.cpp b/src/USER-MISC/fix_filter_corotate.cpp index 7ada3aeb99e0d582bda2048e4dddb576ba53fc4e..91c70335133e4fdf6a37c0ec212d5d38dc9501fb 100644 --- a/src/USER-MISC/fix_filter_corotate.cpp +++ b/src/USER-MISC/fix_filter_corotate.cpp @@ -17,8 +17,8 @@ ------------------------------------------------------------------------- */ #include -#include -#include +#include +#include #include "fix_filter_corotate.h" #include "atom.h" #include "atom_vec.h" @@ -1527,7 +1527,10 @@ void FixFilterCorotate::general_cluster(int index, int index_in_list) //derivative: //dn1dx: - double sum1[3][3*N]; + + double **sum1; + memory->create(sum1,3,3*N,"filter_corotate:sum1"); + for (int i=0; i<3; i++) for (int j=0; j<3*N; j++) sum1[i][j] = 0; @@ -1564,10 +1567,12 @@ void FixFilterCorotate::general_cluster(int index, int index_in_list) dn1dx[i][j] = norm1*sum; } } + memory->destroy(sum1); //dn2dx: norm2 * I3mn2n2T * (I3mn1n1T*sum2 - rkn1pn1rk*dn1dx) - double sum2[3][3*N]; + double **sum2; + memory->create(sum2,3,3*N,"filter_corotate:sum2"); for (int i=0; i<3; i++) for (int j=0; j<3*N; j++) sum2[i][j] = 0; @@ -1618,7 +1623,8 @@ void FixFilterCorotate::general_cluster(int index, int index_in_list) //dn2dx: norm2 * I3mn2n2T * (I3mn1n1T*sum2 - rkn1pn1rk*dn1dx) //sum3 = (I3mn1n1T*sum2 - rkn1pn1rk*dn1dx) - double sum3[3][3*N]; + double **sum3; + memory->create(sum3,3,3*N,"filter_corotate:sum3"); for (int i=0; i<3; i++) for (int j=0; j<3*N; j++) { double sum = 0; @@ -1627,6 +1633,7 @@ void FixFilterCorotate::general_cluster(int index, int index_in_list) sum3[i][j] = sum; } + memory->destroy(sum2); //dn2dx = norm2 * I3mn2n2T * sum3 for (int i=0; i<3; i++) for (int j=0; j<3*N; j++) { @@ -1636,6 +1643,7 @@ void FixFilterCorotate::general_cluster(int index, int index_in_list) dn2dx[i][j] = norm2*sum; } + memory->destroy(sum3); //dn3dx = norm3 * I3mn3n3T * cross double I3mn3n3T[3][3]; //(I_3 - n3n3T) for (int i=0; i<3; i++) { @@ -1644,7 +1652,8 @@ void FixFilterCorotate::general_cluster(int index, int index_in_list) I3mn3n3T[i][i] += 1.0; } - double cross[3][3*N]; + double **cross; + memory->create(cross,3,3*N,"filter_corotate:cross"); for (int j=0; j<3*N; j++) { cross[0][j] = dn1dx[1][j]*n2[2] -dn1dx[2][j]*n2[1] + @@ -1663,6 +1672,7 @@ void FixFilterCorotate::general_cluster(int index, int index_in_list) dn3dx[i][j] = norm3*sum; } + memory->destroy(cross); for (int l=0; l -#include +#include +#include #include "fix_flow_gauss.h" #include "atom.h" #include "force.h" diff --git a/src/USER-MISC/fix_gle.cpp b/src/USER-MISC/fix_gle.cpp index ecb3390e5ee6ecce55f64f2d3ee22516ba2a219b..584b33bfe7da1bc93d041ee15388d7e72ebe36d5 100644 --- a/src/USER-MISC/fix_gle.cpp +++ b/src/USER-MISC/fix_gle.cpp @@ -17,9 +17,9 @@ ------------------------------------------------------------------------- */ #include -#include -#include -#include +#include +#include +#include #include "fix_gle.h" #include "math_extra.h" #include "atom.h" @@ -44,6 +44,7 @@ using namespace FixConst; enum{NOBIAS,BIAS}; enum{CONSTANT,EQUAL,ATOM}; + //#define GLE_DEBUG 1 #define MAXLINE 1024 @@ -62,35 +63,37 @@ namespace GLE { //"stabilized" cholesky decomposition. does a LDL^t decomposition, then sets to zero the negative diagonal elements and gets MM^t void StabCholesky(int n, const double* MMt, double* M) { - double L[n*n], D[n]; - - int i,j,k; - for(i=0; i0.?sqrt(D[i]):0.); - } + D[i]=(D[i]>0.0) ? sqrt(D[i]):0.0; + } + + for (i=0; i=0; p--) - { - MyMult(n, n, n, SM, EM, TMP); for (int i=0; i=0; p--) { + MyMult(n, n, n, SM, EM, TMP); for (int i=0; i -#include -#include +#include +#include +#include #include "comm.h" #include "fix_grem.h" #include "atom.h" diff --git a/src/USER-MISC/fix_imd.cpp b/src/USER-MISC/fix_imd.cpp index b5bd8caf0b2bc5b2668c8f2590fbcd48891922cc..abf9e7cb0ba59629d5d1f65524dbea82b2f0db74 100644 --- a/src/USER-MISC/fix_imd.cpp +++ b/src/USER-MISC/fix_imd.cpp @@ -58,10 +58,10 @@ negotiate an appropriate license for such distribution." #include "group.h" #include "memory.h" -#include -#include -#include -#include +#include +#include +#include +#include #if defined(_MSC_VER) || defined(__MINGW32__) #include @@ -350,7 +350,7 @@ static void id_sort(tagint *idmap, tagint left, tagint right) /* part 1: Interactive MD (IMD) API */ -#include +#include #if ( INT_MAX == 2147483647 ) typedef int int32; diff --git a/src/USER-MISC/fix_ipi.cpp b/src/USER-MISC/fix_ipi.cpp index bacce679019beca073158a3f6a215134b2d0dfaa..c4750ce49e211b22c6f3b1ddc8e8d812f1843402 100644 --- a/src/USER-MISC/fix_ipi.cpp +++ b/src/USER-MISC/fix_ipi.cpp @@ -16,9 +16,9 @@ ------------------------------------------------------------------------- */ #include -#include -#include -#include +#include +#include +#include #include "fix_ipi.h" #include "atom.h" #include "force.h" @@ -50,7 +50,7 @@ using namespace FixConst; // socket interface #ifndef _WIN32 -#include +#include #include #include #include @@ -428,7 +428,7 @@ void FixIPI::final_integrate() int nat=bsize/3; double **f= atom->f; - double lbuf[bsize]; + double *lbuf = new double[bsize]; // reassembles the force vector from the local arrays int nlocal = atom->nlocal; @@ -440,6 +440,7 @@ void FixIPI::final_integrate() lbuf[3*(atom->tag[i]-1)+2]=f[i][2]*forceconv; } MPI_Allreduce(lbuf,buffer,bsize,MPI_DOUBLE,MPI_SUM,world); + delete[] lbuf; for (int i = 0; i < 9; ++i) vir[i]=0.0; diff --git a/src/USER-MISC/fix_nvk.cpp b/src/USER-MISC/fix_nvk.cpp index 5dcfe53e788c5f23539cd7f4fbfb764933112e2a..dbf7b56fe22048745d10b71dad15e8def74fa30e 100644 --- a/src/USER-MISC/fix_nvk.cpp +++ b/src/USER-MISC/fix_nvk.cpp @@ -15,9 +15,9 @@ Contributing author: Efrem Braun (UC Berkeley) ------------------------------------------------------------------------- */ -#include -#include -#include +#include +#include +#include #include "fix_nvk.h" #include "atom.h" #include "force.h" diff --git a/src/USER-MISC/fix_pimd.cpp b/src/USER-MISC/fix_pimd.cpp index 2c89ddda57e9a0a5d9a0f77e05e53f6f09f5049b..e65ae6ae28168acf3a766798f4028f5c7fca700a 100644 --- a/src/USER-MISC/fix_pimd.cpp +++ b/src/USER-MISC/fix_pimd.cpp @@ -21,9 +21,9 @@ Version 1.0 ------------------------------------------------------------------------- */ -#include -#include -#include +#include +#include +#include #include "fix_pimd.h" #include "universe.h" #include "comm.h" diff --git a/src/USER-MISC/fix_rhok.cpp b/src/USER-MISC/fix_rhok.cpp index 58b0e95a97e0abe10ac7d48e1e93807a0c5a16ab..bbc4ce417a460d194bf3014b61cadc802c763a8d 100644 --- a/src/USER-MISC/fix_rhok.cpp +++ b/src/USER-MISC/fix_rhok.cpp @@ -13,10 +13,10 @@ Contributing author: Ulf R. Pedersen, ulf@urp.dk ------------------------------------------------------------------------- */ -#include -#include -#include -#include +#include +#include +#include +#include #include "fix_rhok.h" #include "atom.h" diff --git a/src/USER-MISC/fix_smd.cpp b/src/USER-MISC/fix_smd.cpp index b2d3ee0779ded92b42e020d9ba9794b6890981c5..fb22483a073d327e188c62ac9bc782c74000ae26 100644 --- a/src/USER-MISC/fix_smd.cpp +++ b/src/USER-MISC/fix_smd.cpp @@ -16,9 +16,9 @@ based on fix spring by: Paul Crozier (SNL) ------------------------------------------------------------------------- */ -#include -#include -#include +#include +#include +#include #include "fix_smd.h" #include "atom.h" #include "comm.h" diff --git a/src/USER-MISC/fix_srp.cpp b/src/USER-MISC/fix_srp.cpp index 90935e482af3715e585b2e4f1249aea7a0969b43..e4d85e867418b3d3173b1883d79aa567d7129278 100644 --- a/src/USER-MISC/fix_srp.cpp +++ b/src/USER-MISC/fix_srp.cpp @@ -15,8 +15,8 @@ Contributing authors: Timothy Sirk (ARL), Pieter in't Veld (BASF) ------------------------------------------------------------------------- */ -#include -#include +#include +#include #include "fix_srp.h" #include "atom.h" #include "force.h" diff --git a/src/USER-MISC/fix_srp.h b/src/USER-MISC/fix_srp.h index aaeea2f03a1ff9c7b1bc5ba10b5a6090a28b2c5b..7dbf044bdadcd14562d99ecd0b56d1f046cc9aed 100644 --- a/src/USER-MISC/fix_srp.h +++ b/src/USER-MISC/fix_srp.h @@ -20,7 +20,7 @@ FixStyle(SRP,FixSRP) #ifndef LMP_FIX_SRP_H #define LMP_FIX_SRP_H -#include +#include #include "fix.h" namespace LAMMPS_NS { diff --git a/src/USER-MISC/fix_ti_spring.cpp b/src/USER-MISC/fix_ti_spring.cpp index fbbc747c38c91a88efaa148b5e723707a5a6a994..5812142763f82c44e9b9cab16595d579e5483701 100644 --- a/src/USER-MISC/fix_ti_spring.cpp +++ b/src/USER-MISC/fix_ti_spring.cpp @@ -18,8 +18,8 @@ Maurice de Koning (Unicamp/Brazil) - dekoning@ifi.unicamp.br ------------------------------------------------------------------------- */ -#include -#include +#include +#include #include "fix_ti_spring.h" #include "atom.h" #include "update.h" diff --git a/src/USER-MISC/fix_ttm_mod.cpp b/src/USER-MISC/fix_ttm_mod.cpp index b7261b85d4103a63cbdf186f7d1d16d32b59c4ed..1e1e62b638595c9e2aabcb3e690c2d64517dab80 100644 --- a/src/USER-MISC/fix_ttm_mod.cpp +++ b/src/USER-MISC/fix_ttm_mod.cpp @@ -19,9 +19,9 @@ #include "lmptype.h" #include -#include -#include -#include +#include +#include +#include #include "fix_ttm_mod.h" #include "atom.h" #include "force.h" diff --git a/src/USER-MISC/fix_wall_ees.cpp b/src/USER-MISC/fix_wall_ees.cpp index 9b65d1e30f37b74dd226d19956ee1d7e57864a0d..5ca16ebdadd26706a3cdbcdb26d6ed3f4def9b0f 100644 --- a/src/USER-MISC/fix_wall_ees.cpp +++ b/src/USER-MISC/fix_wall_ees.cpp @@ -15,7 +15,7 @@ Contributing author: Abdoreza Ershadinia, a.ershadinia at gmail.com ------------------------------------------------------------------------- */ -#include +#include #include "math_extra.h" #include "fix_wall_ees.h" #include "atom.h" diff --git a/src/USER-MISC/fix_wall_region_ees.cpp b/src/USER-MISC/fix_wall_region_ees.cpp index e070e2a2216e81c63e897fc99bafc771ecadf1fb..82a78d3e73bc2d757ca2399c6a3ebc8726ad99af 100644 --- a/src/USER-MISC/fix_wall_region_ees.cpp +++ b/src/USER-MISC/fix_wall_region_ees.cpp @@ -15,9 +15,9 @@ Contributing author: Abdoreza Ershadinia, a.ershadinia at gmail.com ------------------------------------------------------------------------- */ -#include -#include -#include +#include +#include +#include #include "fix_wall_region_ees.h" #include "atom.h" #include "atom_vec.h" diff --git a/src/USER-MISC/improper_cossq.cpp b/src/USER-MISC/improper_cossq.cpp index 223df4a76d064abcfead348518d17f1034bbd1a9..2483840e4234f37c14636937e4d1efe4d0498ced 100644 --- a/src/USER-MISC/improper_cossq.cpp +++ b/src/USER-MISC/improper_cossq.cpp @@ -17,8 +17,8 @@ ------------------------------------------------------------------------- */ #include -#include -#include +#include +#include #include "improper_cossq.h" #include "atom.h" #include "comm.h" @@ -312,3 +312,13 @@ void ImproperCossq::read_restart(FILE *fp) for (int i = 1; i <= atom->nimpropertypes; i++) setflag[i] = 1; } + +/* ---------------------------------------------------------------------- + proc 0 writes to data file +------------------------------------------------------------------------- */ + +void ImproperCossq::write_data(FILE *fp) +{ + for (int i = 1; i <= atom->nimpropertypes; i++) + fprintf(fp,"%d %g %g\n",i,k[i],chi[i]/MY_PI*180.0); +} diff --git a/src/USER-MISC/improper_cossq.h b/src/USER-MISC/improper_cossq.h index 266e31797781ab10cc4cd4ba0f28f3dc7f25fab2..ea880adfaf40845d301893abeb63849fb13a93e6 100644 --- a/src/USER-MISC/improper_cossq.h +++ b/src/USER-MISC/improper_cossq.h @@ -20,7 +20,7 @@ ImproperStyle(cossq,ImproperCossq) #ifndef LMP_IMPROPER_COSSQ_H #define LMP_IMPROPER_COSSQ_H -#include +#include #include "improper.h" namespace LAMMPS_NS { @@ -33,6 +33,7 @@ class ImproperCossq : public Improper { void coeff(int, char **); void write_restart(FILE *); void read_restart(FILE *); + void write_data(FILE *); protected: double *k, *chi; diff --git a/src/USER-MISC/improper_distance.cpp b/src/USER-MISC/improper_distance.cpp index ce6441d6746e3d4946bb8e21eaff27c39844cbe5..2edf37ec5c7b712c3c46a3da330ed4482edcd91d 100644 --- a/src/USER-MISC/improper_distance.cpp +++ b/src/USER-MISC/improper_distance.cpp @@ -16,8 +16,8 @@ ------------------------------------------------------------------------- */ #include -#include -#include +#include +#include #include "improper_distance.h" #include "atom.h" #include "comm.h" @@ -223,7 +223,6 @@ void ImproperDistance::coeff(int narg, char **arg) int count = 0; for (int i = ilo; i <= ihi; i++) { k[i] = k_one; - //chi[i] = chi_one/180.0 * PI; chi[i] = chi_one; setflag[i] = 1; count++; @@ -259,3 +258,13 @@ void ImproperDistance::read_restart(FILE *fp) for (int i = 1; i <= atom->nimpropertypes; i++) setflag[i] = 1; } + +/* ---------------------------------------------------------------------- + proc 0 writes to data file +------------------------------------------------------------------------- */ + +void ImproperDistance::write_data(FILE *fp) +{ + for (int i = 1; i <= atom->nimpropertypes; i++) + fprintf(fp,"%d %g %g\n",i,k[i],chi[i]); +} diff --git a/src/USER-MISC/improper_distance.h b/src/USER-MISC/improper_distance.h index cff96c6d9d7b096f3481730d23e354ad31cd6190..57e4d671e94320503bd1497ed18849366cd983b3 100644 --- a/src/USER-MISC/improper_distance.h +++ b/src/USER-MISC/improper_distance.h @@ -20,7 +20,7 @@ ImproperStyle(distance,ImproperDistance) #ifndef LMP_IMPROPER_DISTANCE_H #define LMP_IMPROPER_DISTANCE_H -#include +#include #include "improper.h" namespace LAMMPS_NS { @@ -33,6 +33,7 @@ class ImproperDistance : public Improper { void coeff(int, char **); void write_restart(FILE *); void read_restart(FILE *); + void write_data(FILE *); private: double *k,*chi; diff --git a/src/USER-MISC/improper_fourier.cpp b/src/USER-MISC/improper_fourier.cpp index b139fdad569dc14d67560301c1550fb867204d16..11478d08eab135f70baa9ab6d69a762b4a302672 100644 --- a/src/USER-MISC/improper_fourier.cpp +++ b/src/USER-MISC/improper_fourier.cpp @@ -17,9 +17,9 @@ ------------------------------------------------------------------------- */ #include -#include -#include -#include +#include +#include +#include #include "improper_fourier.h" #include "atom.h" #include "comm.h" @@ -343,3 +343,13 @@ void ImproperFourier::read_restart(FILE *fp) for (int i = 1; i <= atom->nimpropertypes; i++) setflag[i] = 1; } + +/* ---------------------------------------------------------------------- + proc 0 writes to data file +------------------------------------------------------------------------- */ + +void ImproperFourier::write_data(FILE *fp) +{ + for (int i = 1; i <= atom->nimpropertypes; i++) + fprintf(fp,"%d %g %g %g %g %d\n",i,k[i],C0[i],C1[i],C2[i],all[i]); +} diff --git a/src/USER-MISC/improper_fourier.h b/src/USER-MISC/improper_fourier.h index 903b9a12b652f50d0a3163c02934bb3982ae044e..0525c45494b56741b100d2e545c21364f5e8955a 100644 --- a/src/USER-MISC/improper_fourier.h +++ b/src/USER-MISC/improper_fourier.h @@ -20,7 +20,7 @@ ImproperStyle(fourier,ImproperFourier) #ifndef LMP_IMPROPER_FOURIER_H #define LMP_IMPROPER_FOURIER_H -#include +#include #include "improper.h" namespace LAMMPS_NS { @@ -33,6 +33,7 @@ class ImproperFourier : public Improper { void coeff(int, char **); void write_restart(FILE *); void read_restart(FILE *); + void write_data(FILE *); protected: double *k, *C0, *C1, *C2; diff --git a/src/USER-MISC/improper_ring.cpp b/src/USER-MISC/improper_ring.cpp index adf17ed1d566e26dcd759914c9f46c8409c91552..70124b2ed1d91de9d900aacdea1c0c828303c7fc 100644 --- a/src/USER-MISC/improper_ring.cpp +++ b/src/USER-MISC/improper_ring.cpp @@ -37,8 +37,8 @@ ------------------------------------------------------------------------- */ #include -#include -#include +#include +#include #include "improper_ring.h" #include "atom.h" #include "comm.h" @@ -337,3 +337,13 @@ void ImproperRing::read_restart(FILE *fp) for (int i = 1; i <= atom->nimpropertypes; i++) setflag[i] = 1; } + +/* ---------------------------------------------------------------------- + proc 0 writes to data file +------------------------------------------------------------------------- */ + +void ImproperRing::write_data(FILE *fp) +{ + for (int i = 1; i <= atom->nimpropertypes; i++) + fprintf(fp,"%d %g %g\n",i,k[i],acos(chi[i])/MY_PI*180.0); +} diff --git a/src/USER-MISC/improper_ring.h b/src/USER-MISC/improper_ring.h index cdb2907c6578de27620e41a4d7107c8a709b0fb2..c31329816f806f573a044f77962eeab0c1cd418d 100644 --- a/src/USER-MISC/improper_ring.h +++ b/src/USER-MISC/improper_ring.h @@ -20,7 +20,7 @@ ImproperStyle(ring,ImproperRing) #ifndef LMP_IMPROPER_RING_H #define LMP_IMPROPER_RING_H -#include +#include #include "improper.h" namespace LAMMPS_NS { @@ -33,6 +33,7 @@ class ImproperRing : public Improper { void coeff(int, char **); void write_restart(FILE *); void read_restart(FILE *); + void write_data(FILE *); protected: double *k,*chi; diff --git a/src/USER-MISC/pair_agni.cpp b/src/USER-MISC/pair_agni.cpp index 9cd2cf57b883175f5f8b50a1439f8fbed7bd9b8e..11bf2ae01ed2790cc65b62afe79c7bb2f392ee44 100644 --- a/src/USER-MISC/pair_agni.cpp +++ b/src/USER-MISC/pair_agni.cpp @@ -15,10 +15,10 @@ Contributing authors: Axel Kohlmeyer (Temple U), Venkatesh Botu ------------------------------------------------------------------------- */ -#include -#include -#include -#include +#include +#include +#include +#include #include "pair_agni.h" #include "atom.h" #include "neighbor.h" diff --git a/src/USER-MISC/pair_buck_mdf.cpp b/src/USER-MISC/pair_buck_mdf.cpp index 372fbaf8c0f4d9eebec30238f9052009c6c560ab..457d75bc7712907bd06caab711216947e2bcc270 100644 --- a/src/USER-MISC/pair_buck_mdf.cpp +++ b/src/USER-MISC/pair_buck_mdf.cpp @@ -15,10 +15,10 @@ Contributing author: Paolo Raiteri (Curtin University) ------------------------------------------------------------------------- */ -#include -#include -#include -#include +#include +#include +#include +#include #include "pair_buck_mdf.h" #include "atom.h" #include "comm.h" diff --git a/src/USER-MISC/pair_cdeam.cpp b/src/USER-MISC/pair_cdeam.cpp index b5607012ce16789056b4afed345ffcfe54d1ca7e..53d9036a61d44da205f921c3272ccf41b9075cde 100644 --- a/src/USER-MISC/pair_cdeam.cpp +++ b/src/USER-MISC/pair_cdeam.cpp @@ -17,10 +17,10 @@ Germany Department of Materials Science ------------------------------------------------------------------------- */ -#include -#include -#include -#include +#include +#include +#include +#include #include "pair_cdeam.h" #include "atom.h" #include "force.h" diff --git a/src/USER-MISC/pair_coul_diel.cpp b/src/USER-MISC/pair_coul_diel.cpp index c653e9abb23c6bfbe410d78f1691cf63a173ad7e..3f07df3d9861dbc0cb5af1bf6a3766d5ccebb38d 100644 --- a/src/USER-MISC/pair_coul_diel.cpp +++ b/src/USER-MISC/pair_coul_diel.cpp @@ -14,10 +14,10 @@ Contributiong authors: Arben Jusufi, Axel Kohlmeyer (Temple U.) ------------------------------------------------------------------------- */ -#include -#include -#include -#include +#include +#include +#include +#include #include "pair_coul_diel.h" #include "atom.h" #include "comm.h" diff --git a/src/USER-MISC/pair_coul_shield.cpp b/src/USER-MISC/pair_coul_shield.cpp index 0f7852163c1cd696867699e4e6bd8fec38133928..deec7da81faaa4a2557f7e40bd21c1389c6aa0e2 100644 --- a/src/USER-MISC/pair_coul_shield.cpp +++ b/src/USER-MISC/pair_coul_shield.cpp @@ -18,10 +18,10 @@ [Maaravi et al, J. Phys. Chem. C 121, 22826-22835 (2017)] ------------------------------------------------------------------------- */ -#include -#include -#include -#include +#include +#include +#include +#include #include "pair_coul_shield.h" #include "atom.h" #include "comm.h" @@ -231,6 +231,8 @@ void PairCoulShield::init_style() { if (!atom->q_flag) error->all(FLERR,"Pair style coul/shield requires atom attribute q"); + if (!atom->molecule_flag) + error->all(FLERR,"Pair style coul/shield requires atom attribute molecule"); neighbor->request(this,instance_me); } diff --git a/src/USER-MISC/pair_edip.cpp b/src/USER-MISC/pair_edip.cpp index 5f83af7f497809fd18c686dbcd6fc38fde7a098f..f556a099c97370ddd350196a613e31f524d9087f 100644 --- a/src/USER-MISC/pair_edip.cpp +++ b/src/USER-MISC/pair_edip.cpp @@ -21,11 +21,11 @@ Phys. Rev. B 58, 2539 (1998) ------------------------------------------------------------------------- */ -#include -#include -#include -#include -#include +#include +#include +#include +#include +#include #include "pair_edip.h" #include "atom.h" #include "neighbor.h" diff --git a/src/USER-MISC/pair_edip_multi.cpp b/src/USER-MISC/pair_edip_multi.cpp index bcef1b013b67aae593ed44e7143c34335b0c2291..7a4193f55cbebb25944b8266a71444d3b265af0c 100644 --- a/src/USER-MISC/pair_edip_multi.cpp +++ b/src/USER-MISC/pair_edip_multi.cpp @@ -17,11 +17,11 @@ Contributing author: Chao Jiang ------------------------------------------------------------------------- */ -#include -#include -#include -#include -#include +#include +#include +#include +#include +#include #include "pair_edip_multi.h" #include "atom.h" #include "neighbor.h" diff --git a/src/USER-MISC/pair_extep.cpp b/src/USER-MISC/pair_extep.cpp index cf859a28f8380fbfb65dd2b72092486f7d5941f3..5a8cdf28841cf2f7fa61b4f184867a2f8465ff7f 100644 --- a/src/USER-MISC/pair_extep.cpp +++ b/src/USER-MISC/pair_extep.cpp @@ -15,10 +15,10 @@ Contributing author: Jan Los ------------------------------------------------------------------------- */ -#include -#include -#include -#include +#include +#include +#include +#include #include "pair_extep.h" #include "atom.h" #include "neighbor.h" diff --git a/src/USER-MISC/pair_gauss_cut.cpp b/src/USER-MISC/pair_gauss_cut.cpp index c1daf9c923f7b356f7a94ab330f1f353988ff7b1..85f7c02887a1d0c1a9a6841d69df6c17a754b5e6 100644 --- a/src/USER-MISC/pair_gauss_cut.cpp +++ b/src/USER-MISC/pair_gauss_cut.cpp @@ -15,10 +15,10 @@ Contributing authors: Arben Jusufi, Axel Kohlmeyer (Temple U.) ------------------------------------------------------------------------- */ -#include -#include -#include -#include +#include +#include +#include +#include #include "pair_gauss_cut.h" #include "atom.h" #include "comm.h" diff --git a/src/USER-MISC/pair_ilp_graphene_hbn.cpp b/src/USER-MISC/pair_ilp_graphene_hbn.cpp index 02c33c7e86926d8581a513a267d81bce278475c1..30ee2e7a5ae3c3aa42843f2ba07c1c8f36b7dbb9 100644 --- a/src/USER-MISC/pair_ilp_graphene_hbn.cpp +++ b/src/USER-MISC/pair_ilp_graphene_hbn.cpp @@ -21,10 +21,10 @@ ------------------------------------------------------------------------- */ #include -#include -#include -#include -#include +#include +#include +#include +#include #include "pair_ilp_graphene_hbn.h" #include "atom.h" #include "comm.h" @@ -636,7 +636,9 @@ void PairILPGrapheneHBN::calc_normal() void PairILPGrapheneHBN::init_style() { if (force->newton_pair == 0) - error->all(FLERR,"Pair style ILP requires newton pair on"); + 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 diff --git a/src/USER-MISC/pair_ilp_graphene_hbn.h b/src/USER-MISC/pair_ilp_graphene_hbn.h index 3ced305429ad647387721672010ef7df5b0d356a..07c3b2e97b12c39224656eca4fa69cad6cc9a3dc 100644 --- a/src/USER-MISC/pair_ilp_graphene_hbn.h +++ b/src/USER-MISC/pair_ilp_graphene_hbn.h @@ -22,7 +22,7 @@ PairStyle(ilp/graphene/hbn,PairILPGrapheneHBN) #include "pair.h" #include "my_page.h" -#include +#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 a7eebe0b3f3162a210b63ba4a11a6a9179749d55..be0e81d48d9e986e38247aae32bb60b0ac4fb377 100644 --- a/src/USER-MISC/pair_kolmogorov_crespi_full.cpp +++ b/src/USER-MISC/pair_kolmogorov_crespi_full.cpp @@ -20,10 +20,10 @@ [Kolmogorov & Crespi, Phys. Rev. B 71, 235415 (2005)] ------------------------------------------------------------------------- */ -#include -#include -#include -#include +#include +#include +#include +#include #include #include "pair_kolmogorov_crespi_full.h" #include "atom.h" @@ -640,7 +640,9 @@ void PairKolmogorovCrespiFull::calc_normal() void PairKolmogorovCrespiFull::init_style() { if (force->newton_pair == 0) - error->all(FLERR,"Pair style KC requires newton pair on"); + 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 diff --git a/src/USER-MISC/pair_kolmogorov_crespi_full.h b/src/USER-MISC/pair_kolmogorov_crespi_full.h index 3078a7601a4053f2428c16400dd88701e6589e24..9923b409a7de490ce2717bf80aebfe010d34110d 100644 --- a/src/USER-MISC/pair_kolmogorov_crespi_full.h +++ b/src/USER-MISC/pair_kolmogorov_crespi_full.h @@ -22,7 +22,7 @@ PairStyle(kolmogorov/crespi/full,PairKolmogorovCrespiFull) #include "pair.h" #include "my_page.h" -#include +#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 dc1f56a318602b4792118d16673e2369e97849f0..fb7d5ae40eda1bc857c5c29f6f9955973e358f43 100644 --- a/src/USER-MISC/pair_kolmogorov_crespi_z.cpp +++ b/src/USER-MISC/pair_kolmogorov_crespi_z.cpp @@ -21,10 +21,10 @@ The simplification is that all normals are taken along the z-direction ------------------------------------------------------------------------- */ -#include -#include -#include -#include +#include +#include +#include +#include #include "pair_kolmogorov_crespi_z.h" #include "atom.h" #include "comm.h" diff --git a/src/USER-MISC/pair_lennard_mdf.cpp b/src/USER-MISC/pair_lennard_mdf.cpp index b959f513c0cec33e496b4c324eacb85ad50c9501..f6e7f7f56b0084b8fe5115e0424fce3909bde8c4 100644 --- a/src/USER-MISC/pair_lennard_mdf.cpp +++ b/src/USER-MISC/pair_lennard_mdf.cpp @@ -16,10 +16,10 @@ Contributing author: Paolo Raiteri (Curtin University) ------------------------------------------------------------------------- */ -#include -#include -#include -#include +#include +#include +#include +#include #include "pair_lennard_mdf.h" #include "atom.h" #include "comm.h" diff --git a/src/USER-MISC/pair_list.cpp b/src/USER-MISC/pair_list.cpp index 6bb71d05c8cfb1239ce4e6d4ad66431c887d6e6b..aaeb586c1d544dca1916e9d1d0aceae7581c586c 100644 --- a/src/USER-MISC/pair_list.cpp +++ b/src/USER-MISC/pair_list.cpp @@ -24,10 +24,10 @@ #include "error.h" -#include -#include -#include -#include +#include +#include +#include +#include using namespace LAMMPS_NS; diff --git a/src/USER-MISC/pair_lj_mdf.cpp b/src/USER-MISC/pair_lj_mdf.cpp index ebec1f80e1f75dd827fc6a9fb2f5cf10238db084..d43a6c30862165ea7cd6d0a801e7e285902feb0c 100644 --- a/src/USER-MISC/pair_lj_mdf.cpp +++ b/src/USER-MISC/pair_lj_mdf.cpp @@ -16,10 +16,10 @@ Contributing author: Paolo Raiteri (Curtin University) ------------------------------------------------------------------------- */ -#include -#include -#include -#include +#include +#include +#include +#include #include "pair_lj_mdf.h" #include "atom.h" #include "comm.h" diff --git a/src/USER-MISC/pair_lj_sf_dipole_sf.cpp b/src/USER-MISC/pair_lj_sf_dipole_sf.cpp index ab342fd055c5a6f2291d2dad357483a7c0723079..523b2ca71a7b466f35939a67c7b5e9ac77501cac 100644 --- a/src/USER-MISC/pair_lj_sf_dipole_sf.cpp +++ b/src/USER-MISC/pair_lj_sf_dipole_sf.cpp @@ -16,8 +16,9 @@ Samuel Genheden (University of Southampton) ------------------------------------------------------------------------- */ -#include -#include +#include +#include +#include #include "pair_lj_sf_dipole_sf.h" #include "atom.h" #include "neighbor.h" @@ -27,7 +28,6 @@ #include "memory.h" #include "error.h" #include "update.h" -#include using namespace LAMMPS_NS; @@ -539,7 +539,7 @@ double PairLJSFDipoleSF::single(int i, int j, int itype, int jtype, double rsq, double &fforce) { double r2inv,r6inv; - double pdotp,pidotr,pjdotr,pre1,delx,dely,delz; + double pdotp,pidotr,pjdotr,delx,dely,delz; double rinv, r3inv,r5inv, rcutlj2inv, rcutcoul2inv,rcutlj6inv; double qtmp,xtmp,ytmp,ztmp,bfac,pqfac,qpfac, ecoul, evdwl; diff --git a/src/USER-MISC/pair_meam_spline.cpp b/src/USER-MISC/pair_meam_spline.cpp index 10659e86547e1de37b9a8eea241c0d546e43ca68..750f6ac5bbaee20ffcdffbaf8dccecf28576701b 100644 --- a/src/USER-MISC/pair_meam_spline.cpp +++ b/src/USER-MISC/pair_meam_spline.cpp @@ -31,10 +31,10 @@ conform with pairing, updated to LAMMPS style ------------------------------------------------------------------------- */ -#include -#include -#include -#include +#include +#include +#include +#include #include "pair_meam_spline.h" #include "atom.h" #include "force.h" diff --git a/src/USER-MISC/pair_meam_sw_spline.cpp b/src/USER-MISC/pair_meam_sw_spline.cpp index 3eda3ea45d65dba61a454541f3e41d34e5c30a45..f6b7212f9cfd9ee124eed653d2cf588b77d502a0 100644 --- a/src/USER-MISC/pair_meam_sw_spline.cpp +++ b/src/USER-MISC/pair_meam_sw_spline.cpp @@ -23,10 +23,10 @@ * 01-Aug-12 - RER: First code version. ------------------------------------------------------------------------- */ -#include -#include -#include -#include +#include +#include +#include +#include #include "pair_meam_sw_spline.h" #include "atom.h" #include "force.h" diff --git a/src/USER-MISC/pair_momb.cpp b/src/USER-MISC/pair_momb.cpp index b69b8b86ccd066359667a8a161319ddd7bcb7919..12a40bb08beb6ce981920f5dbba5dc041564deb8 100644 --- a/src/USER-MISC/pair_momb.cpp +++ b/src/USER-MISC/pair_momb.cpp @@ -16,9 +16,9 @@ Ya Zhou (Penn State University) ------------------------------------------------------------------------- */ -#include -#include -#include +#include +#include +#include #include "pair_momb.h" #include "atom.h" #include "comm.h" diff --git a/src/USER-MISC/pair_morse_smooth_linear.cpp b/src/USER-MISC/pair_morse_smooth_linear.cpp index 37a880762079eb71885fa4c1286812c923abf997..8a9c89cf6945afbba59a7509d936f0ecf526c4a8 100644 --- a/src/USER-MISC/pair_morse_smooth_linear.cpp +++ b/src/USER-MISC/pair_morse_smooth_linear.cpp @@ -11,10 +11,10 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include -#include -#include -#include +#include +#include +#include +#include #include "pair_morse_smooth_linear.h" #include "atom.h" #include "comm.h" diff --git a/src/USER-MISC/pair_srp.cpp b/src/USER-MISC/pair_srp.cpp index 69c7e6b0be377270492521515561c7985b669541..7297b545f967ca3901d5918327b3d69e3331e942 100644 --- a/src/USER-MISC/pair_srp.cpp +++ b/src/USER-MISC/pair_srp.cpp @@ -25,7 +25,8 @@ There is an example script for this package in examples/USER/srp. Please contact Timothy Sirk for questions (tim.sirk@us.army.mil). ------------------------------------------------------------------------- */ -#include +#include +#include #include "pair_srp.h" #include "atom.h" #include "comm.h" @@ -40,7 +41,6 @@ Please contact Timothy Sirk for questions (tim.sirk@us.army.mil). #include "fix_srp.h" #include "thermo.h" #include "output.h" -#include #include "citeme.h" using namespace LAMMPS_NS; diff --git a/src/USER-MISC/pair_tersoff_table.cpp b/src/USER-MISC/pair_tersoff_table.cpp index 1c96b3d002b2d3b57a84db51612825174a57b8b5..c2362b8de9ce0c186636d91d324f406b5bdadfd4 100644 --- a/src/USER-MISC/pair_tersoff_table.cpp +++ b/src/USER-MISC/pair_tersoff_table.cpp @@ -20,10 +20,10 @@ 1) Tersoff, Phys. Rev. B 39, 5566 (1988) ------------------------------------------------------------------------- */ -#include -#include -#include -#include +#include +#include +#include +#include #include "pair_tersoff_table.h" #include "atom.h" #include "neighbor.h" diff --git a/src/USER-MISC/temper_grem.cpp b/src/USER-MISC/temper_grem.cpp index 9e5a4c5c3b95aed6cec87ea62e88d000874d9cc8..031a449689150ffe24d6413213d2183dd5ac5521 100644 --- a/src/USER-MISC/temper_grem.cpp +++ b/src/USER-MISC/temper_grem.cpp @@ -15,9 +15,9 @@ Contributing author: David Stelter (BU) ------------------------------------------------------------------------- */ -#include -#include -#include +#include +#include +#include #include "temper_grem.h" #include "fix_grem.h" #include "universe.h" diff --git a/src/USER-MISC/temper_npt.cpp b/src/USER-MISC/temper_npt.cpp index 66ab92a43b6758497883accc4439d1b45d7339d2..7cf8fbab9b76d86e46c54ebfd9c17b77fc873d0e 100644 --- a/src/USER-MISC/temper_npt.cpp +++ b/src/USER-MISC/temper_npt.cpp @@ -17,9 +17,9 @@ Contact Email: amulyapervaje@gmail.com ------------------------------------------------------------------------- */ -#include -#include -#include +#include +#include +#include #include "temper_npt.h" #include "universe.h" #include "domain.h" diff --git a/src/USER-MOFFF/angle_class2_p6.cpp b/src/USER-MOFFF/angle_class2_p6.cpp index d173669771f4fbbdadd1b87732ccf2c5acc9cb61..c821c9d883ed611661dffb1ddeefea86c6d0ba77 100644 --- a/src/USER-MOFFF/angle_class2_p6.cpp +++ b/src/USER-MOFFF/angle_class2_p6.cpp @@ -16,9 +16,9 @@ and Rochus Schmid (Ruhr-Universitaet Bochum) ------------------------------------------------------------------------- */ -#include -#include -#include +#include +#include +#include #include "angle_class2_p6.h" #include "atom.h" #include "neighbor.h" diff --git a/src/USER-MOFFF/angle_class2_p6.h b/src/USER-MOFFF/angle_class2_p6.h index aa0bdea6d6d3f7643690dbfdcffb4966040b1168..b583a45b191d17b79f3f7537967331635c757c09 100644 --- a/src/USER-MOFFF/angle_class2_p6.h +++ b/src/USER-MOFFF/angle_class2_p6.h @@ -20,7 +20,7 @@ AngleStyle(class2/p6,AngleClass2P6) #ifndef LMP_ANGLE_CLASS2_P6_H #define LMP_ANGLE_CLASS2_P6_H -#include +#include #include "angle.h" namespace LAMMPS_NS { diff --git a/src/USER-MOFFF/angle_cosine_buck6d.cpp b/src/USER-MOFFF/angle_cosine_buck6d.cpp index 493807dbdca9f34a3eca831403b4e81e2ae5f521..b5800db2beb9a398eaa2fd8d314a8ae5566df1a9 100644 --- a/src/USER-MOFFF/angle_cosine_buck6d.cpp +++ b/src/USER-MOFFF/angle_cosine_buck6d.cpp @@ -16,8 +16,8 @@ and Rochus Schmid (Ruhr-Universitaet Bochum) ------------------------------------------------------------------------- */ -#include -#include +#include +#include #include "angle_cosine_buck6d.h" #include "atom.h" #include "neighbor.h" diff --git a/src/USER-MOFFF/angle_cosine_buck6d.h b/src/USER-MOFFF/angle_cosine_buck6d.h index e021992b94565e04e7dda5e0146df006b6677ad5..689b1634e02c935c126380682fcbcbea0f573633 100644 --- a/src/USER-MOFFF/angle_cosine_buck6d.h +++ b/src/USER-MOFFF/angle_cosine_buck6d.h @@ -20,7 +20,7 @@ AngleStyle(cosine/buck6d, AngleCosineBuck6d) #ifndef LMP_ANGLE_COSINE_BUCK6D_H #define LMP_ANGLE_COSINE_BUCK6D_H -#include +#include #include "angle.h" namespace LAMMPS_NS { diff --git a/src/USER-MOFFF/improper_inversion_harmonic.cpp b/src/USER-MOFFF/improper_inversion_harmonic.cpp index 3a7c0272aa31f21706f315646f29208ce3f6a148..53a7b4729a990c6adacf7b69c8a57558e586e465 100644 --- a/src/USER-MOFFF/improper_inversion_harmonic.cpp +++ b/src/USER-MOFFF/improper_inversion_harmonic.cpp @@ -20,9 +20,9 @@ ------------------------------------------------------------------------- */ #include -#include -#include -#include "string.h" +#include +#include +#include #include "improper_inversion_harmonic.h" #include "atom.h" #include "comm.h" diff --git a/src/USER-MOFFF/improper_inversion_harmonic.h b/src/USER-MOFFF/improper_inversion_harmonic.h index 1b46c7489a9dafba9a569ad2bd2c5f3dca86a8a0..201c9e358d3d2d392dd856c9468595d2c9d53090 100644 --- a/src/USER-MOFFF/improper_inversion_harmonic.h +++ b/src/USER-MOFFF/improper_inversion_harmonic.h @@ -20,7 +20,7 @@ ImproperStyle(inversion/harmonic,ImproperInversionHarmonic) #ifndef LMP_IMPROPER_INVERSION_HARMONIC_H #define LMP_IMPROPER_INVERSION_HARMONIC_H -#include +#include #include "improper.h" namespace LAMMPS_NS { diff --git a/src/USER-MOFFF/pair_buck6d_coul_gauss_dsf.cpp b/src/USER-MOFFF/pair_buck6d_coul_gauss_dsf.cpp index baa42a4bc0d7abf0b0e4efb85f50cdbc0de0673d..f434d03858b3d370c63e03a2b911e9554d9763e9 100644 --- a/src/USER-MOFFF/pair_buck6d_coul_gauss_dsf.cpp +++ b/src/USER-MOFFF/pair_buck6d_coul_gauss_dsf.cpp @@ -18,10 +18,10 @@ Fennell and Gezelter, JCP 124, 234104 (2006) ------------------------------------------------------------------------- */ -#include -#include -#include -#include +#include +#include +#include +#include #include "pair_buck6d_coul_gauss_dsf.h" #include "atom.h" #include "comm.h" diff --git a/src/USER-MOFFF/pair_buck6d_coul_gauss_long.cpp b/src/USER-MOFFF/pair_buck6d_coul_gauss_long.cpp index 36018613a2614d753564d403a5fc41ccf5c92493..9902896d18ece26a6e49f461e613182b4440b0b5 100644 --- a/src/USER-MOFFF/pair_buck6d_coul_gauss_long.cpp +++ b/src/USER-MOFFF/pair_buck6d_coul_gauss_long.cpp @@ -17,10 +17,10 @@ References: Bureekaew and Schmid, Phys. Status Solidi B 250, 1128 (2013) ------------------------------------------------------------------------- */ -#include -#include -#include -#include +#include +#include +#include +#include #include "pair_buck6d_coul_gauss_long.h" #include "atom.h" #include "comm.h" diff --git a/src/USER-MOLFILE/dump_molfile.cpp b/src/USER-MOLFILE/dump_molfile.cpp index 54e86f3bc577fdfcc3c942fb40351b9cc4a685ba..732fea74bde61ae3a3fd4ba5bd6779cbeb1711db 100644 --- a/src/USER-MOLFILE/dump_molfile.cpp +++ b/src/USER-MOLFILE/dump_molfile.cpp @@ -15,9 +15,9 @@ Contributing author: Axel Kohlmeyer (Temple U) ------------------------------------------------------------------------- */ -#include -#include -#include +#include +#include +#include #include "dump_molfile.h" #include "domain.h" #include "atom.h" diff --git a/src/USER-MOLFILE/molfile_interface.cpp b/src/USER-MOLFILE/molfile_interface.cpp index 9c0c15f1ee3d6524cfe1c01b3aaa3cf155c12c5d..798beaee096a68a0b4200219e81e7373532c3ba0 100644 --- a/src/USER-MOLFILE/molfile_interface.cpp +++ b/src/USER-MOLFILE/molfile_interface.cpp @@ -18,11 +18,11 @@ #include "molfile_interface.h" #include -#include +#include #include -#include -#include -#include +#include +#include +#include #if defined(_WIN32) #include diff --git a/src/USER-MOLFILE/reader_molfile.cpp b/src/USER-MOLFILE/reader_molfile.cpp index 15735ab92a25bc47937a3b1de64089364b525fb0..6348009d8fd9ca866909f0994920a42a1a997258 100644 --- a/src/USER-MOLFILE/reader_molfile.cpp +++ b/src/USER-MOLFILE/reader_molfile.cpp @@ -15,9 +15,9 @@ Contributing author: Axel Kohlmeyer (Temple U) ------------------------------------------------------------------------- */ -#include -#include -#include +#include +#include +#include #include "reader_molfile.h" #include "atom.h" #include "comm.h" diff --git a/src/USER-NETCDF/dump_netcdf.cpp b/src/USER-NETCDF/dump_netcdf.cpp index 4147b3897d26df8a13086f43197ee8988de01248..c08bc89d04fd86215be6ecce3f6355a504fbad4a 100644 --- a/src/USER-NETCDF/dump_netcdf.cpp +++ b/src/USER-NETCDF/dump_netcdf.cpp @@ -18,8 +18,8 @@ #if defined(LMP_HAS_NETCDF) #include -#include -#include +#include +#include #include #include "dump_netcdf.h" #include "atom.h" diff --git a/src/USER-NETCDF/dump_netcdf_mpiio.cpp b/src/USER-NETCDF/dump_netcdf_mpiio.cpp index 129f9cccbb9978dc77968b9c673bc4e7b639b6a0..0a292d4721b5e5c909375b3e56b7ac991ee01795 100644 --- a/src/USER-NETCDF/dump_netcdf_mpiio.cpp +++ b/src/USER-NETCDF/dump_netcdf_mpiio.cpp @@ -18,8 +18,8 @@ #if defined(LMP_HAS_PNETCDF) #include -#include -#include +#include +#include #include #include "dump_netcdf_mpiio.h" #include "atom.h" diff --git a/src/USER-OMP/angle_charmm_omp.cpp b/src/USER-OMP/angle_charmm_omp.cpp index 228ca94dee718796389e785f5388acfdb54eae0a..1f24438df3e44fb274f4e458fc4a873c96c5bdd6 100644 --- a/src/USER-OMP/angle_charmm_omp.cpp +++ b/src/USER-OMP/angle_charmm_omp.cpp @@ -24,7 +24,7 @@ #include "math_const.h" -#include +#include #include "suffix.h" using namespace LAMMPS_NS; diff --git a/src/USER-OMP/angle_class2_omp.cpp b/src/USER-OMP/angle_class2_omp.cpp index 8f958b477cb8443a9378b2ebe94668c947cd5c17..bd13e20bcc5827ef547370999b1654de4304942b 100644 --- a/src/USER-OMP/angle_class2_omp.cpp +++ b/src/USER-OMP/angle_class2_omp.cpp @@ -24,7 +24,7 @@ #include "math_const.h" -#include +#include #include "suffix.h" using namespace LAMMPS_NS; diff --git a/src/USER-OMP/angle_cosine_delta_omp.cpp b/src/USER-OMP/angle_cosine_delta_omp.cpp index f9891dbb3d7bbe0721509a67cb7d0b5ef3ffa5a4..b3bb3e1f8a7e0f42c792929f962d8be05fc8ef0d 100644 --- a/src/USER-OMP/angle_cosine_delta_omp.cpp +++ b/src/USER-OMP/angle_cosine_delta_omp.cpp @@ -24,7 +24,7 @@ #include "math_const.h" -#include +#include #include "suffix.h" using namespace LAMMPS_NS; diff --git a/src/USER-OMP/angle_cosine_omp.cpp b/src/USER-OMP/angle_cosine_omp.cpp index 39ae3ce698f9ab14705c775826d59d07cf04b0dd..04b3870bc4e0220f631511a0d48d0e483f9878a9 100644 --- a/src/USER-OMP/angle_cosine_omp.cpp +++ b/src/USER-OMP/angle_cosine_omp.cpp @@ -24,7 +24,7 @@ #include "math_const.h" -#include +#include #include "suffix.h" using namespace LAMMPS_NS; diff --git a/src/USER-OMP/angle_cosine_periodic_omp.cpp b/src/USER-OMP/angle_cosine_periodic_omp.cpp index 3bd4ef1212cc0edbf06ee7528490007ab7cb8033..8060ebec7b0ef1fbad1c3a896009ec8fdd9dc56c 100644 --- a/src/USER-OMP/angle_cosine_periodic_omp.cpp +++ b/src/USER-OMP/angle_cosine_periodic_omp.cpp @@ -25,7 +25,7 @@ #include "math_const.h" #include "math_special.h" -#include +#include #include "suffix.h" using namespace LAMMPS_NS; diff --git a/src/USER-OMP/angle_cosine_shift_exp_omp.cpp b/src/USER-OMP/angle_cosine_shift_exp_omp.cpp index 3a3c31d62582db4f81b170a858bc3c7bf67f2d22..3e00681ec930aef234a266d803bc3fb22ee95147 100644 --- a/src/USER-OMP/angle_cosine_shift_exp_omp.cpp +++ b/src/USER-OMP/angle_cosine_shift_exp_omp.cpp @@ -24,7 +24,7 @@ #include "math_const.h" -#include +#include #include "suffix.h" using namespace LAMMPS_NS; diff --git a/src/USER-OMP/angle_cosine_shift_omp.cpp b/src/USER-OMP/angle_cosine_shift_omp.cpp index f9f538e55388b03fe4388d3c859cf7cef1a8caf8..0ab3df43594cc5caceeb0b760651bdc2e064f415 100644 --- a/src/USER-OMP/angle_cosine_shift_omp.cpp +++ b/src/USER-OMP/angle_cosine_shift_omp.cpp @@ -24,7 +24,7 @@ #include "math_const.h" -#include +#include #include "suffix.h" using namespace LAMMPS_NS; diff --git a/src/USER-OMP/angle_cosine_squared_omp.cpp b/src/USER-OMP/angle_cosine_squared_omp.cpp index c7d14468f5addd2614b7caf7e39a084987dd0f34..a1b1ffdf1a9ee121f1aa3b0dce09a78bd5ded27c 100644 --- a/src/USER-OMP/angle_cosine_squared_omp.cpp +++ b/src/USER-OMP/angle_cosine_squared_omp.cpp @@ -24,7 +24,7 @@ #include "math_const.h" -#include +#include #include "suffix.h" using namespace LAMMPS_NS; diff --git a/src/USER-OMP/angle_dipole_omp.cpp b/src/USER-OMP/angle_dipole_omp.cpp index ee2af539183d514a7c38b8273e8bf12dbbde64f9..92a5ba092edf1d5ad3c0ce0e19b1ef033a12c246 100644 --- a/src/USER-OMP/angle_dipole_omp.cpp +++ b/src/USER-OMP/angle_dipole_omp.cpp @@ -25,7 +25,7 @@ #include "math_const.h" -#include +#include #include "suffix.h" using namespace LAMMPS_NS; diff --git a/src/USER-OMP/angle_fourier_omp.cpp b/src/USER-OMP/angle_fourier_omp.cpp index 275eab29f1d7778d9c4d3cef6fa9432a57c29b20..dfc713c3728be3795ca98576666c89e69cf0f29d 100644 --- a/src/USER-OMP/angle_fourier_omp.cpp +++ b/src/USER-OMP/angle_fourier_omp.cpp @@ -24,7 +24,7 @@ #include "math_const.h" -#include +#include #include "suffix.h" using namespace LAMMPS_NS; diff --git a/src/USER-OMP/angle_fourier_simple_omp.cpp b/src/USER-OMP/angle_fourier_simple_omp.cpp index 5bdbfce05d38a28d53cad0c8e8eaf0aaf1a35449..dea7a8872340a655c14929543ae39af665197b70 100644 --- a/src/USER-OMP/angle_fourier_simple_omp.cpp +++ b/src/USER-OMP/angle_fourier_simple_omp.cpp @@ -24,7 +24,7 @@ #include "math_const.h" -#include +#include #include "suffix.h" using namespace LAMMPS_NS; diff --git a/src/USER-OMP/angle_harmonic_omp.cpp b/src/USER-OMP/angle_harmonic_omp.cpp index 917bc2d5b0b61412cca6c39c923d841f3aad06e4..0a71e5c9dd2ca645c59bf8166bdd48055350440a 100644 --- a/src/USER-OMP/angle_harmonic_omp.cpp +++ b/src/USER-OMP/angle_harmonic_omp.cpp @@ -24,7 +24,7 @@ #include "math_const.h" -#include +#include #include "suffix.h" using namespace LAMMPS_NS; diff --git a/src/USER-OMP/angle_quartic_omp.cpp b/src/USER-OMP/angle_quartic_omp.cpp index 70383fd50a56cd62b057cf1f1bac8cdf19d7f0fa..97a9b14f1dac16c87ab681fac72fc0c4e8ef1037 100644 --- a/src/USER-OMP/angle_quartic_omp.cpp +++ b/src/USER-OMP/angle_quartic_omp.cpp @@ -24,7 +24,7 @@ #include "math_const.h" -#include +#include #include "suffix.h" using namespace LAMMPS_NS; diff --git a/src/USER-OMP/angle_sdk_omp.cpp b/src/USER-OMP/angle_sdk_omp.cpp index 9b4a967bf32644979d7f9fe5fbb49ffdfab4e635..9383a9af83cda57631cf88fe77434461c5802000 100644 --- a/src/USER-OMP/angle_sdk_omp.cpp +++ b/src/USER-OMP/angle_sdk_omp.cpp @@ -23,7 +23,7 @@ #include "force.h" #include "math_const.h" -#include +#include #include "lj_sdk_common.h" diff --git a/src/USER-OMP/angle_table_omp.cpp b/src/USER-OMP/angle_table_omp.cpp index 465f4370fcce2b40946f3ae8bba77e7b2254c398..c3d2307489087fd412e67c94a238122aeea0194c 100644 --- a/src/USER-OMP/angle_table_omp.cpp +++ b/src/USER-OMP/angle_table_omp.cpp @@ -24,7 +24,7 @@ #include "math_const.h" -#include +#include #include "suffix.h" using namespace LAMMPS_NS; diff --git a/src/USER-OMP/bond_class2_omp.cpp b/src/USER-OMP/bond_class2_omp.cpp index 69decfb32acfd8d60bfc8693363403996fc5db75..1f9bcaa3204b054595664a027ef477c920374adc 100644 --- a/src/USER-OMP/bond_class2_omp.cpp +++ b/src/USER-OMP/bond_class2_omp.cpp @@ -22,7 +22,7 @@ #include "neighbor.h" #include "domain.h" -#include +#include #include "suffix.h" using namespace LAMMPS_NS; diff --git a/src/USER-OMP/bond_fene_expand_omp.cpp b/src/USER-OMP/bond_fene_expand_omp.cpp index 37cb8b403e479e6b6402d1b869217731b5a666a0..d002d454dd912612cf777f680adede7547d95654 100644 --- a/src/USER-OMP/bond_fene_expand_omp.cpp +++ b/src/USER-OMP/bond_fene_expand_omp.cpp @@ -24,7 +24,7 @@ #include "error.h" #include "update.h" -#include +#include #include "suffix.h" using namespace LAMMPS_NS; diff --git a/src/USER-OMP/bond_fene_omp.cpp b/src/USER-OMP/bond_fene_omp.cpp index e92dae999c41ac5e90fc30ad89b7b3a168bab4e7..ba958e1d6f3fc52f97bf3ea2adb60fde9b19121b 100644 --- a/src/USER-OMP/bond_fene_omp.cpp +++ b/src/USER-OMP/bond_fene_omp.cpp @@ -24,7 +24,7 @@ #include "error.h" #include "update.h" -#include +#include #include "suffix.h" using namespace LAMMPS_NS; diff --git a/src/USER-OMP/bond_gromos_omp.cpp b/src/USER-OMP/bond_gromos_omp.cpp index 7904c4683b4c5526a99b2e4fa56049cc43be2dbf..bcfde436d5338e4d7e93fd20e2fc02b167f2989a 100644 --- a/src/USER-OMP/bond_gromos_omp.cpp +++ b/src/USER-OMP/bond_gromos_omp.cpp @@ -22,7 +22,7 @@ #include "neighbor.h" #include "domain.h" -#include +#include #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 b62fd531939bc572b820e3c668ad69aae9c2286e..46a93cbbdd60f089b2952acab2e395bf7a39c672 100644 --- a/src/USER-OMP/bond_harmonic_omp.cpp +++ b/src/USER-OMP/bond_harmonic_omp.cpp @@ -22,7 +22,7 @@ #include "neighbor.h" #include "domain.h" -#include +#include #include "suffix.h" using namespace LAMMPS_NS; diff --git a/src/USER-OMP/bond_harmonic_shift_cut_omp.cpp b/src/USER-OMP/bond_harmonic_shift_cut_omp.cpp index db2518e9a9ba23d768f56d6b9cbf89e36c699b9d..5f39bb1b64beeeb977689da7ab31884ae05f7793 100644 --- a/src/USER-OMP/bond_harmonic_shift_cut_omp.cpp +++ b/src/USER-OMP/bond_harmonic_shift_cut_omp.cpp @@ -22,7 +22,7 @@ #include "neighbor.h" #include "domain.h" -#include +#include #include "suffix.h" using namespace LAMMPS_NS; diff --git a/src/USER-OMP/bond_harmonic_shift_omp.cpp b/src/USER-OMP/bond_harmonic_shift_omp.cpp index 632db873012e45e5f8cd20b0fbbe6ac08fe01f70..8c260bfc9b12558670f1528f482ca8199da3ce7e 100644 --- a/src/USER-OMP/bond_harmonic_shift_omp.cpp +++ b/src/USER-OMP/bond_harmonic_shift_omp.cpp @@ -22,7 +22,7 @@ #include "neighbor.h" #include "domain.h" -#include +#include #include "suffix.h" using namespace LAMMPS_NS; diff --git a/src/USER-OMP/bond_morse_omp.cpp b/src/USER-OMP/bond_morse_omp.cpp index d03783920b230529a41023ac8079be9050c45487..0c3cded71aa2ec6fab7ea44e8e3c5aa33c92b8d7 100644 --- a/src/USER-OMP/bond_morse_omp.cpp +++ b/src/USER-OMP/bond_morse_omp.cpp @@ -22,7 +22,7 @@ #include "neighbor.h" #include "domain.h" -#include +#include #include "suffix.h" using namespace LAMMPS_NS; diff --git a/src/USER-OMP/bond_nonlinear_omp.cpp b/src/USER-OMP/bond_nonlinear_omp.cpp index 2bc77de85c0ea9a8062d8224b12c1c9bec55d6d6..cdc70eac8d18947f585902ee74dce696e0c3da57 100644 --- a/src/USER-OMP/bond_nonlinear_omp.cpp +++ b/src/USER-OMP/bond_nonlinear_omp.cpp @@ -22,7 +22,7 @@ #include "neighbor.h" #include "domain.h" -#include +#include #include "suffix.h" using namespace LAMMPS_NS; diff --git a/src/USER-OMP/bond_quartic_omp.cpp b/src/USER-OMP/bond_quartic_omp.cpp index c0ddfd0b9267d888fd8bd3c4e623cfd80c08d51d..b2b1696bb41853b1205e143effa55972aa5d6328 100644 --- a/src/USER-OMP/bond_quartic_omp.cpp +++ b/src/USER-OMP/bond_quartic_omp.cpp @@ -23,7 +23,7 @@ #include "domain.h" #include "pair.h" -#include +#include #include "suffix.h" using namespace LAMMPS_NS; diff --git a/src/USER-OMP/bond_table_omp.cpp b/src/USER-OMP/bond_table_omp.cpp index 53226df4f70368842a36310dc161f22b4e3ef4fc..71dc23749655e558a82ce2a0990518ecb994debb 100644 --- a/src/USER-OMP/bond_table_omp.cpp +++ b/src/USER-OMP/bond_table_omp.cpp @@ -22,7 +22,7 @@ #include "neighbor.h" #include "domain.h" -#include +#include #include "suffix.h" using namespace LAMMPS_NS; diff --git a/src/USER-OMP/dihedral_charmm_omp.cpp b/src/USER-OMP/dihedral_charmm_omp.cpp index 95cab754c3b7465671f1c9e77d71ad6b0d99e2e6..1bed4497740c111386ec027469c04204662528f0 100644 --- a/src/USER-OMP/dihedral_charmm_omp.cpp +++ b/src/USER-OMP/dihedral_charmm_omp.cpp @@ -16,7 +16,7 @@ ------------------------------------------------------------------------- */ #include -#include +#include #include "dihedral_charmm_omp.h" #include "atom.h" #include "comm.h" diff --git a/src/USER-OMP/dihedral_class2_omp.cpp b/src/USER-OMP/dihedral_class2_omp.cpp index edf3e972d296c546bb808a2beb9b93911eae8d14..c7ae1572c766c2aaf0ad2c0ac036628049f9fd4e 100644 --- a/src/USER-OMP/dihedral_class2_omp.cpp +++ b/src/USER-OMP/dihedral_class2_omp.cpp @@ -15,7 +15,7 @@ Contributing author: Axel Kohlmeyer (Temple U) ------------------------------------------------------------------------- */ -#include +#include #include "dihedral_class2_omp.h" #include "atom.h" #include "comm.h" diff --git a/src/USER-OMP/dihedral_cosine_shift_exp_omp.cpp b/src/USER-OMP/dihedral_cosine_shift_exp_omp.cpp index fe99d52cb7e7d274873b85584443d2658231d03f..c43b9900281e54009ddf790a7b0c5bf6a895d540 100644 --- a/src/USER-OMP/dihedral_cosine_shift_exp_omp.cpp +++ b/src/USER-OMP/dihedral_cosine_shift_exp_omp.cpp @@ -15,7 +15,7 @@ Contributing author: Axel Kohlmeyer (Temple U) ------------------------------------------------------------------------- */ -#include +#include #include "dihedral_cosine_shift_exp_omp.h" #include "atom.h" #include "comm.h" diff --git a/src/USER-OMP/dihedral_fourier_omp.cpp b/src/USER-OMP/dihedral_fourier_omp.cpp index 9c93f2ad30651b4d498df9bf53e8a52b11eb0a6f..319acb0beb038eddb13384dc0cad10c5108fc00d 100644 --- a/src/USER-OMP/dihedral_fourier_omp.cpp +++ b/src/USER-OMP/dihedral_fourier_omp.cpp @@ -15,7 +15,7 @@ Contributing author: Axel Kohlmeyer (Temple U) ------------------------------------------------------------------------- */ -#include +#include #include "dihedral_fourier_omp.h" #include "atom.h" #include "comm.h" diff --git a/src/USER-OMP/dihedral_harmonic_omp.cpp b/src/USER-OMP/dihedral_harmonic_omp.cpp index 2e0a1cf5545694f24de16699e82fc5ee6f68d5cd..bb659cf2621a2929692fb0bed6cd076dda68cf25 100644 --- a/src/USER-OMP/dihedral_harmonic_omp.cpp +++ b/src/USER-OMP/dihedral_harmonic_omp.cpp @@ -15,7 +15,7 @@ Contributing author: Axel Kohlmeyer (Temple U) ------------------------------------------------------------------------- */ -#include +#include #include "dihedral_harmonic_omp.h" #include "atom.h" #include "comm.h" diff --git a/src/USER-OMP/dihedral_helix_omp.cpp b/src/USER-OMP/dihedral_helix_omp.cpp index 7dd1e8f8a4c59d5266a50fef0ac7757723254ca5..e40f084e547be390b30136135da554ada43b9deb 100644 --- a/src/USER-OMP/dihedral_helix_omp.cpp +++ b/src/USER-OMP/dihedral_helix_omp.cpp @@ -15,7 +15,7 @@ Contributing author: Axel Kohlmeyer (Temple U) ------------------------------------------------------------------------- */ -#include +#include #include "dihedral_helix_omp.h" #include "atom.h" #include "comm.h" diff --git a/src/USER-OMP/dihedral_multi_harmonic_omp.cpp b/src/USER-OMP/dihedral_multi_harmonic_omp.cpp index 06565e7b502a09217381e0b4e690ea685d30e765..e10fc7b94a0bcac42abd3350f4dbe320aeed1b10 100644 --- a/src/USER-OMP/dihedral_multi_harmonic_omp.cpp +++ b/src/USER-OMP/dihedral_multi_harmonic_omp.cpp @@ -15,7 +15,7 @@ Contributing author: Axel Kohlmeyer (Temple U) ------------------------------------------------------------------------- */ -#include +#include #include "dihedral_multi_harmonic_omp.h" #include "atom.h" #include "comm.h" diff --git a/src/USER-OMP/dihedral_nharmonic_omp.cpp b/src/USER-OMP/dihedral_nharmonic_omp.cpp index c698f7c109d1d9e88b1aa6c15f9e27bdf19a661a..ad758fc89231cd71cb8797cfb069081acde252ff 100644 --- a/src/USER-OMP/dihedral_nharmonic_omp.cpp +++ b/src/USER-OMP/dihedral_nharmonic_omp.cpp @@ -15,7 +15,7 @@ Contributing author: Axel Kohlmeyer (Temple U) ------------------------------------------------------------------------- */ -#include +#include #include "dihedral_nharmonic_omp.h" #include "atom.h" #include "comm.h" diff --git a/src/USER-OMP/dihedral_opls_omp.cpp b/src/USER-OMP/dihedral_opls_omp.cpp index 069d6d2dd203482adb62e7f6002d68c6fabeb128..53fddf51cbd6fe01fc236812b7b4d0db80d4d3cb 100644 --- a/src/USER-OMP/dihedral_opls_omp.cpp +++ b/src/USER-OMP/dihedral_opls_omp.cpp @@ -15,7 +15,7 @@ Contributing author: Axel Kohlmeyer (Temple U) ------------------------------------------------------------------------- */ -#include +#include #include "dihedral_opls_omp.h" #include "atom.h" #include "comm.h" diff --git a/src/USER-OMP/dihedral_quadratic_omp.cpp b/src/USER-OMP/dihedral_quadratic_omp.cpp index 3fa580defc20cd1027833d63f0655738f790b7d3..f6110cd5050ec580749530da13d699d74307d5b8 100644 --- a/src/USER-OMP/dihedral_quadratic_omp.cpp +++ b/src/USER-OMP/dihedral_quadratic_omp.cpp @@ -15,7 +15,7 @@ Contributing author: Axel Kohlmeyer (Temple U) ------------------------------------------------------------------------- */ -#include +#include #include "dihedral_quadratic_omp.h" #include "atom.h" #include "comm.h" diff --git a/src/USER-OMP/ewald_omp.cpp b/src/USER-OMP/ewald_omp.cpp index ad6b0bf80573f990616b53f0195ae092fa4f7e70..a26d5cf27d9be4f2e08103f7f9e0d36ed3156009 100644 --- a/src/USER-OMP/ewald_omp.cpp +++ b/src/USER-OMP/ewald_omp.cpp @@ -22,7 +22,7 @@ #include "force.h" #include "memory.h" -#include +#include #include "math_const.h" diff --git a/src/USER-OMP/fix_gravity_omp.cpp b/src/USER-OMP/fix_gravity_omp.cpp index 1e65d1f7641abd558040f8cc27f74788ea2f435f..ef1a07aa5ad909f0017bf58d3d304d610d9557e9 100644 --- a/src/USER-OMP/fix_gravity_omp.cpp +++ b/src/USER-OMP/fix_gravity_omp.cpp @@ -15,10 +15,10 @@ Contributing author: Axel Kohlmeyer (Temple U) ------------------------------------------------------------------------- */ -#include -#include -#include -#include +#include +#include +#include +#include #include "fix_gravity_omp.h" #include "atom.h" #include "update.h" diff --git a/src/USER-OMP/fix_neigh_history_omp.cpp b/src/USER-OMP/fix_neigh_history_omp.cpp index a7ee18257f30ba43e90a137fa67808ba8940304d..efa7f5a3f1697499824d93a1b62a74b251b46bdc 100644 --- a/src/USER-OMP/fix_neigh_history_omp.cpp +++ b/src/USER-OMP/fix_neigh_history_omp.cpp @@ -11,8 +11,8 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include -#include +#include +#include #include "fix_neigh_history_omp.h" #include "atom.h" #include "comm.h" diff --git a/src/USER-OMP/fix_nh_asphere_omp.cpp b/src/USER-OMP/fix_nh_asphere_omp.cpp index e710e6f12e4d86c427c4df84a7a75fb6272c9ccb..b0967bf7f78c7a2ca8f883c92c7b3558ddc2936d 100644 --- a/src/USER-OMP/fix_nh_asphere_omp.cpp +++ b/src/USER-OMP/fix_nh_asphere_omp.cpp @@ -15,9 +15,9 @@ Contributing author: Axel Kohlmeyer (Temple U) ------------------------------------------------------------------------- */ -#include -#include -#include +#include +#include +#include #include "math_extra.h" #include "fix_nh_asphere_omp.h" #include "atom.h" diff --git a/src/USER-OMP/fix_nh_omp.cpp b/src/USER-OMP/fix_nh_omp.cpp index ccb6090378faf3da1990499b2ff87217c5338f52..76a47b71fdf7c86b0ead410c639e82050523ef44 100644 --- a/src/USER-OMP/fix_nh_omp.cpp +++ b/src/USER-OMP/fix_nh_omp.cpp @@ -22,8 +22,8 @@ #include "error.h" #include "modify.h" -#include -#include +#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 dd0530dcfa3c2da91e3ef566ecb6eaa97a38acf9..a32f0f8b51e3d4a91e3d866cd04afbe5e1520223 100644 --- a/src/USER-OMP/fix_nh_sphere_omp.cpp +++ b/src/USER-OMP/fix_nh_sphere_omp.cpp @@ -15,7 +15,7 @@ Contributing author: Axel Kohlmeyer (Temple U) ------------------------------------------------------------------------- */ -#include +#include #include "fix_nh_sphere_omp.h" #include "atom.h" #include "atom_vec.h" diff --git a/src/USER-OMP/fix_nph_asphere_omp.cpp b/src/USER-OMP/fix_nph_asphere_omp.cpp index dfcbc87e6f9df5b0afa524b8484f2ca5142cfac3..c012583fda2a8a922aa2b3bac145cbb1de6c9b51 100644 --- a/src/USER-OMP/fix_nph_asphere_omp.cpp +++ b/src/USER-OMP/fix_nph_asphere_omp.cpp @@ -11,7 +11,7 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include +#include #include "fix_nph_asphere_omp.h" #include "modify.h" #include "error.h" diff --git a/src/USER-OMP/fix_nph_omp.cpp b/src/USER-OMP/fix_nph_omp.cpp index f2a4e66f55a481ee4f371a3d621c989b46206ee9..c11a64cd47949009969c6bdb1e612888071b7947 100644 --- a/src/USER-OMP/fix_nph_omp.cpp +++ b/src/USER-OMP/fix_nph_omp.cpp @@ -11,7 +11,7 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include +#include #include "fix_nph_omp.h" #include "modify.h" #include "error.h" diff --git a/src/USER-OMP/fix_nph_sphere_omp.cpp b/src/USER-OMP/fix_nph_sphere_omp.cpp index 670009de2fd29e44d3ca893b9a270712976c1696..21db6a3aaa8fc673498ff375eba913a903422f20 100644 --- a/src/USER-OMP/fix_nph_sphere_omp.cpp +++ b/src/USER-OMP/fix_nph_sphere_omp.cpp @@ -11,7 +11,7 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include +#include #include "fix_nph_sphere_omp.h" #include "modify.h" #include "error.h" diff --git a/src/USER-OMP/fix_nphug_omp.cpp b/src/USER-OMP/fix_nphug_omp.cpp index 75ff393e288efb55863ed7354945bb4370bfc9f0..a2ed8eb7aae023ff0e74ca1e986932843076c696 100644 --- a/src/USER-OMP/fix_nphug_omp.cpp +++ b/src/USER-OMP/fix_nphug_omp.cpp @@ -11,8 +11,9 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include -#include +#include +#include +#include #include "fix_nphug_omp.h" #include "modify.h" #include "error.h" @@ -21,10 +22,8 @@ #include "force.h" #include "domain.h" #include "group.h" -#include #include "memory.h" #include "comm.h" -#include using namespace LAMMPS_NS; using namespace FixConst; diff --git a/src/USER-OMP/fix_npt_asphere_omp.cpp b/src/USER-OMP/fix_npt_asphere_omp.cpp index 1db62d40c091da4e1a2889e2f540a89bf74d51b4..f1fbe27d8397b4daa83cfa4c5bd924bc39bc2243 100644 --- a/src/USER-OMP/fix_npt_asphere_omp.cpp +++ b/src/USER-OMP/fix_npt_asphere_omp.cpp @@ -11,7 +11,7 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include +#include #include "fix_npt_asphere_omp.h" #include "modify.h" #include "error.h" diff --git a/src/USER-OMP/fix_npt_omp.cpp b/src/USER-OMP/fix_npt_omp.cpp index 5610f62f368978788b2b4dc913514f1b0575d2e9..9244aa16068e0d5bd40014968e89588c8e529a5d 100644 --- a/src/USER-OMP/fix_npt_omp.cpp +++ b/src/USER-OMP/fix_npt_omp.cpp @@ -11,7 +11,7 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include +#include #include "fix_npt_omp.h" #include "modify.h" #include "error.h" diff --git a/src/USER-OMP/fix_npt_sphere_omp.cpp b/src/USER-OMP/fix_npt_sphere_omp.cpp index d71d1380b9c73c370e1504215a91b7fd1d48779f..b12bafecdd50eac66bb1b19b38f217165812ba1a 100644 --- a/src/USER-OMP/fix_npt_sphere_omp.cpp +++ b/src/USER-OMP/fix_npt_sphere_omp.cpp @@ -11,7 +11,7 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include +#include #include "fix_npt_sphere_omp.h" #include "modify.h" #include "error.h" diff --git a/src/USER-OMP/fix_nve_sphere_omp.cpp b/src/USER-OMP/fix_nve_sphere_omp.cpp index 43ecc998681992e0c061b2d336db88c81d888e4c..dd13e58d7cc2d0b37fc58368a59f57b51a7d3c73 100644 --- a/src/USER-OMP/fix_nve_sphere_omp.cpp +++ b/src/USER-OMP/fix_nve_sphere_omp.cpp @@ -11,9 +11,9 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include -#include -#include +#include +#include +#include #include "fix_nve_sphere_omp.h" #include "atom.h" #include "atom_vec.h" diff --git a/src/USER-OMP/fix_nvt_asphere_omp.cpp b/src/USER-OMP/fix_nvt_asphere_omp.cpp index bb1e784a3799ce64813d14b5d69b50d8fe67a782..d0ef28f4deba8cf34272230c7be826a00df12139 100644 --- a/src/USER-OMP/fix_nvt_asphere_omp.cpp +++ b/src/USER-OMP/fix_nvt_asphere_omp.cpp @@ -11,7 +11,7 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include +#include #include "fix_nvt_asphere_omp.h" #include "group.h" #include "modify.h" diff --git a/src/USER-OMP/fix_nvt_omp.cpp b/src/USER-OMP/fix_nvt_omp.cpp index f8f3c15b761384cb45e6f429ed353cecc8a56521..d4dbd4c8f0521be2ab4bf137c641886da1fb1d25 100644 --- a/src/USER-OMP/fix_nvt_omp.cpp +++ b/src/USER-OMP/fix_nvt_omp.cpp @@ -11,7 +11,7 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include +#include #include "fix_nvt_omp.h" #include "group.h" #include "modify.h" diff --git a/src/USER-OMP/fix_nvt_sllod_omp.cpp b/src/USER-OMP/fix_nvt_sllod_omp.cpp index a829d49c0f9e126459d3d33755c4e4d9a67f774f..33445c68af1e8000b669ba2df38db8b26a6a7ee2 100644 --- a/src/USER-OMP/fix_nvt_sllod_omp.cpp +++ b/src/USER-OMP/fix_nvt_sllod_omp.cpp @@ -15,8 +15,8 @@ Contributing author: Axel Kohlmeyer (Temple U) ------------------------------------------------------------------------- */ -#include -#include +#include +#include #include "fix_nvt_sllod_omp.h" #include "math_extra.h" #include "atom.h" diff --git a/src/USER-OMP/fix_nvt_sphere_omp.cpp b/src/USER-OMP/fix_nvt_sphere_omp.cpp index 22eda99883a28a9d309f32bf54ceed9ccb7ecc96..33ea949fcb34e7135ef06e26397fb09fae55210a 100644 --- a/src/USER-OMP/fix_nvt_sphere_omp.cpp +++ b/src/USER-OMP/fix_nvt_sphere_omp.cpp @@ -11,7 +11,7 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include +#include #include "fix_nvt_sphere_omp.h" #include "group.h" #include "modify.h" diff --git a/src/USER-OMP/fix_omp.cpp b/src/USER-OMP/fix_omp.cpp index 2a3717da0dcfa49036e8669da30aaa2017d63ecc..8d54d5b4516f109c2202868d985ca47e62893ce2 100644 --- a/src/USER-OMP/fix_omp.cpp +++ b/src/USER-OMP/fix_omp.cpp @@ -39,9 +39,9 @@ #include "improper_hybrid.h" #include "kspace.h" -#include -#include -#include +#include +#include +#include #include "suffix.h" diff --git a/src/USER-OMP/fix_qeq_comb_omp.cpp b/src/USER-OMP/fix_qeq_comb_omp.cpp index 351003b6685098390cab8525b20eeaa31629d63d..b898fe3fe4e90d17eb0b9847d5a49beef22b4b92 100644 --- a/src/USER-OMP/fix_qeq_comb_omp.cpp +++ b/src/USER-OMP/fix_qeq_comb_omp.cpp @@ -16,7 +16,8 @@ ------------------------------------------------------------------------- */ #include -#include +#include +#include #include "fix_qeq_comb_omp.h" #include "fix_omp.h" #include "atom.h" @@ -33,8 +34,6 @@ #include "update.h" #include "pair_comb_omp.h" -#include - 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 d89c9627fe30a79d2b6d3ee2e3052fe322becf35..a9ffb32d9094277e2e7770c75ef0a129aa9f8042 100644 --- a/src/USER-OMP/fix_qeq_reax_omp.cpp +++ b/src/USER-OMP/fix_qeq_reax_omp.cpp @@ -31,10 +31,10 @@ High Performance Computing Applications, to appear. ------------------------------------------------------------------------- */ -#include -#include -#include -#include +#include +#include +#include +#include #include "fix_qeq_reax_omp.h" #include "pair_reaxc_omp.h" #include "atom.h" diff --git a/src/USER-OMP/fix_rigid_nh_omp.cpp b/src/USER-OMP/fix_rigid_nh_omp.cpp index 9341f83079f8ad9fb3efb8492fa8908f74e51d7b..9f25a1d0001868f58b4152b08ce3a1fd80960a5b 100644 --- a/src/USER-OMP/fix_rigid_nh_omp.cpp +++ b/src/USER-OMP/fix_rigid_nh_omp.cpp @@ -29,7 +29,7 @@ #include "modify.h" #include "update.h" -#include +#include #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 6aca84c30973566ef1b58e7954d667144277d7ef..7db45ed9bf414a4b0c417a47b08945c8f9ba1a91 100644 --- a/src/USER-OMP/fix_rigid_nph_omp.cpp +++ b/src/USER-OMP/fix_rigid_nph_omp.cpp @@ -17,7 +17,7 @@ Miller et al., J Chem Phys. 116, 8649-8659 (2002) ------------------------------------------------------------------------- */ -#include +#include #include "fix_rigid_nph_omp.h" #include "domain.h" #include "modify.h" diff --git a/src/USER-OMP/fix_rigid_npt_omp.cpp b/src/USER-OMP/fix_rigid_npt_omp.cpp index 23f16c61556034bd208dda6d20f941ba87045d23..a041706f388890decd8c834021553e9eb18ddec2 100644 --- a/src/USER-OMP/fix_rigid_npt_omp.cpp +++ b/src/USER-OMP/fix_rigid_npt_omp.cpp @@ -17,7 +17,7 @@ Miller et al., J Chem Phys. 116, 8649-8659 (2002) ------------------------------------------------------------------------- */ -#include +#include #include "fix_rigid_npt_omp.h" #include "domain.h" #include "modify.h" diff --git a/src/USER-OMP/fix_rigid_omp.cpp b/src/USER-OMP/fix_rigid_omp.cpp index 6f084c628cb7e6b3538b74d4d462e909b93b6440..15e5f91c320513173bd482d0810f046b2ee6bad8 100644 --- a/src/USER-OMP/fix_rigid_omp.cpp +++ b/src/USER-OMP/fix_rigid_omp.cpp @@ -24,7 +24,7 @@ #include "comm.h" #include "domain.h" -#include +#include #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 156ef8a2d7a04876fd186ae4ec70c2a00fad2a3a..7d82bd04e8d056141978c046c907a8557a339c54 100644 --- a/src/USER-OMP/fix_rigid_small_omp.cpp +++ b/src/USER-OMP/fix_rigid_small_omp.cpp @@ -24,7 +24,7 @@ #include "comm.h" #include "domain.h" -#include +#include #if defined(_OPENMP) #include diff --git a/src/USER-OMP/fix_wall_gran_omp.cpp b/src/USER-OMP/fix_wall_gran_omp.cpp index 55ae8593a761d62d3cbfc1c136bb4ed611d8d2d5..d45e748b6a1100691fc7e46f246c08330913a870 100644 --- a/src/USER-OMP/fix_wall_gran_omp.cpp +++ b/src/USER-OMP/fix_wall_gran_omp.cpp @@ -15,7 +15,7 @@ Contributing author: Axel Kohlmeyer (Temple U) ------------------------------------------------------------------------- */ -#include +#include #include "fix_wall_gran_omp.h" #include "atom.h" #include "memory.h" diff --git a/src/USER-OMP/improper_class2_omp.cpp b/src/USER-OMP/improper_class2_omp.cpp index 3beeb41a2626d5f9b52d52a348d69cda07111c90..7184cbeb69b7800cc7477803b29df83e2af5fc10 100644 --- a/src/USER-OMP/improper_class2_omp.cpp +++ b/src/USER-OMP/improper_class2_omp.cpp @@ -15,7 +15,7 @@ Contributing author: Axel Kohlmeyer (Temple U) ------------------------------------------------------------------------- */ -#include +#include #include "improper_class2_omp.h" #include "atom.h" #include "comm.h" diff --git a/src/USER-OMP/improper_cossq_omp.cpp b/src/USER-OMP/improper_cossq_omp.cpp index f34941d6245b28f94d34d151225115c6b37976ad..022cfa6adf8216c80ce8ffd78068241ae35061be 100644 --- a/src/USER-OMP/improper_cossq_omp.cpp +++ b/src/USER-OMP/improper_cossq_omp.cpp @@ -15,7 +15,7 @@ Contributing author: Axel Kohlmeyer (Temple U) ------------------------------------------------------------------------- */ -#include +#include #include "improper_cossq_omp.h" #include "atom.h" #include "comm.h" diff --git a/src/USER-OMP/improper_cvff_omp.cpp b/src/USER-OMP/improper_cvff_omp.cpp index cba14226ac870029c3e6971155b5a6250eef3ba7..78c5a55e054da887354dc8707a026c9ddc9cb0da 100644 --- a/src/USER-OMP/improper_cvff_omp.cpp +++ b/src/USER-OMP/improper_cvff_omp.cpp @@ -15,7 +15,7 @@ Contributing author: Axel Kohlmeyer (Temple U) ------------------------------------------------------------------------- */ -#include +#include #include "improper_cvff_omp.h" #include "atom.h" #include "comm.h" diff --git a/src/USER-OMP/improper_fourier_omp.cpp b/src/USER-OMP/improper_fourier_omp.cpp index c1699baf02a5429c83ba561ea996fe632429975e..aed04003a5eff70550f4d98830145a7557cc22b5 100644 --- a/src/USER-OMP/improper_fourier_omp.cpp +++ b/src/USER-OMP/improper_fourier_omp.cpp @@ -15,7 +15,7 @@ Contributing author: Axel Kohlmeyer (Temple U) ------------------------------------------------------------------------- */ -#include +#include #include "improper_fourier_omp.h" #include "atom.h" #include "comm.h" diff --git a/src/USER-OMP/improper_harmonic_omp.cpp b/src/USER-OMP/improper_harmonic_omp.cpp index 8c1f91ecabb6213fe884cccfb7ecde71bedd9ada..3f1895142df47ebc6a6cfd532ff53e12a2517cff 100644 --- a/src/USER-OMP/improper_harmonic_omp.cpp +++ b/src/USER-OMP/improper_harmonic_omp.cpp @@ -15,7 +15,7 @@ Contributing author: Axel Kohlmeyer (Temple U) ------------------------------------------------------------------------- */ -#include +#include #include "improper_harmonic_omp.h" #include "atom.h" #include "comm.h" diff --git a/src/USER-OMP/improper_ring_omp.cpp b/src/USER-OMP/improper_ring_omp.cpp index 4eadc831833b9f2b3f9e26fd24a545ecafa962c4..7970de3839a8c98b92a68f65b8655110c3eda320 100644 --- a/src/USER-OMP/improper_ring_omp.cpp +++ b/src/USER-OMP/improper_ring_omp.cpp @@ -15,7 +15,7 @@ Contributing author: Axel Kohlmeyer (Temple U) ------------------------------------------------------------------------- */ -#include +#include #include "improper_ring_omp.h" #include "atom.h" #include "comm.h" diff --git a/src/USER-OMP/improper_umbrella_omp.cpp b/src/USER-OMP/improper_umbrella_omp.cpp index 9ea94c57050e3ba15555df231aaf94095228f8e9..dc11f24a4de084b07b666c08b76271d135218115 100644 --- a/src/USER-OMP/improper_umbrella_omp.cpp +++ b/src/USER-OMP/improper_umbrella_omp.cpp @@ -15,7 +15,7 @@ Contributing author: Axel Kohlmeyer (Temple U) ------------------------------------------------------------------------- */ -#include +#include #include "improper_umbrella_omp.h" #include "atom.h" #include "comm.h" diff --git a/src/USER-OMP/msm_cg_omp.cpp b/src/USER-OMP/msm_cg_omp.cpp index fb64bc5644683f1490bd8e90b9d5f64cc91cb871..226083deb48489ecb5cd6bedc56265185c506630 100644 --- a/src/USER-OMP/msm_cg_omp.cpp +++ b/src/USER-OMP/msm_cg_omp.cpp @@ -17,10 +17,10 @@ ------------------------------------------------------------------------- */ #include -#include -#include -#include -#include +#include +#include +#include +#include #include "atom.h" #include "gridcomm.h" @@ -331,7 +331,7 @@ void MSMCGOMP::particle_map() int flag = 0; int i; - if (!ISFINITE(boxlo[0]) || !ISFINITE(boxlo[1]) || !ISFINITE(boxlo[2])) + if (!std::isfinite(boxlo[0]) || !std::isfinite(boxlo[1]) || !std::isfinite(boxlo[2])) error->one(FLERR,"Non-numeric box dimensions - simulation unstable"); // XXX: O(N). is it worth to add OpenMP here? diff --git a/src/USER-OMP/msm_omp.cpp b/src/USER-OMP/msm_omp.cpp index 7a79dc865b7d28f6110d62823f9f259465e7f5fa..3bc7ddb1cdc28fc9851d12432422db994b3cbff7 100644 --- a/src/USER-OMP/msm_omp.cpp +++ b/src/USER-OMP/msm_omp.cpp @@ -24,7 +24,7 @@ #include "memory.h" #include "math_const.h" -#include +#include #if defined(_OPENMP) #include 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 fc101a33d21ce88b683df8835b5d083af287cbd5..dff2a762d51dd71b96fc84d98aa26d618acd2750 100644 --- a/src/USER-OMP/npair_half_size_bin_newtoff_omp.cpp +++ b/src/USER-OMP/npair_half_size_bin_newtoff_omp.cpp @@ -11,7 +11,7 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include +#include #include "npair_half_size_bin_newtoff_omp.h" #include "npair_omp.h" #include "neighbor.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 1f0dca79ac1b072b05176254577b3954bcb390e3..3053b815946f59ffa07b2943da022374083f1c14 100644 --- a/src/USER-OMP/npair_half_size_bin_newton_omp.cpp +++ b/src/USER-OMP/npair_half_size_bin_newton_omp.cpp @@ -11,7 +11,7 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include +#include #include "npair_half_size_bin_newton_omp.h" #include "npair_omp.h" #include "neighbor.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 1615effad3864afbec6ee9633580bd754c44a834..717012b226e3dfb08292b40e029bdb65592450ce 100644 --- a/src/USER-OMP/npair_half_size_nsq_newtoff_omp.cpp +++ b/src/USER-OMP/npair_half_size_nsq_newtoff_omp.cpp @@ -11,7 +11,7 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include +#include #include "npair_half_size_nsq_newtoff_omp.h" #include "npair_omp.h" #include "neighbor.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 e5de57aa5112698f7bc069914eef8d5d9256401d..5a55029d30fd77e50349f2aa6214a38009588a86 100644 --- a/src/USER-OMP/npair_half_size_nsq_newton_omp.cpp +++ b/src/USER-OMP/npair_half_size_nsq_newton_omp.cpp @@ -11,7 +11,7 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include +#include #include "npair_half_size_nsq_newton_omp.h" #include "npair_omp.h" #include "neighbor.h" diff --git a/src/USER-OMP/pair_adp_omp.cpp b/src/USER-OMP/pair_adp_omp.cpp index 658ef365a37c7948d36f8aea27feaa3b1f1b680a..264169773b9af8cb988377ebef73b187583013d2 100644 --- a/src/USER-OMP/pair_adp_omp.cpp +++ b/src/USER-OMP/pair_adp_omp.cpp @@ -12,8 +12,8 @@ Contributing author: Axel Kohlmeyer (Temple U) ------------------------------------------------------------------------- */ -#include -#include +#include +#include #include "pair_adp_omp.h" #include "atom.h" diff --git a/src/USER-OMP/pair_agni_omp.cpp b/src/USER-OMP/pair_agni_omp.cpp index 72e8331718c3461c1d33a147a41b63b2a1636af0..e8f003ea881674165d42e15053c2766b9be8a27e 100644 --- a/src/USER-OMP/pair_agni_omp.cpp +++ b/src/USER-OMP/pair_agni_omp.cpp @@ -12,9 +12,9 @@ Contributing author: Axel Kohlmeyer (Temple U) ------------------------------------------------------------------------- */ -#include -#include -#include +#include +#include +#include // requires C++-11 #include "pair_agni_omp.h" #include "atom.h" #include "comm.h" diff --git a/src/USER-OMP/pair_airebo_omp.cpp b/src/USER-OMP/pair_airebo_omp.cpp index 3e8f6d6df3ba242bc5d47249d8563bdc5136e03b..8decda7cabc86ef3096d806d03b101b3891afefa 100644 --- a/src/USER-OMP/pair_airebo_omp.cpp +++ b/src/USER-OMP/pair_airebo_omp.cpp @@ -12,7 +12,7 @@ Contributing author: Axel Kohlmeyer (Temple U) ------------------------------------------------------------------------- */ -#include +#include #include "pair_airebo_omp.h" #include "atom.h" #include "comm.h" diff --git a/src/USER-OMP/pair_beck_omp.cpp b/src/USER-OMP/pair_beck_omp.cpp index e56a0dc7faf1ac4b3ae8fa5442142b56d998b336..1494ec2987e09864b7b69f01cec12b59197d5bd5 100644 --- a/src/USER-OMP/pair_beck_omp.cpp +++ b/src/USER-OMP/pair_beck_omp.cpp @@ -12,7 +12,7 @@ Contributing author: Axel Kohlmeyer (Temple U) ------------------------------------------------------------------------- */ -#include +#include #include "pair_beck_omp.h" #include "atom.h" #include "comm.h" diff --git a/src/USER-OMP/pair_born_coul_long_omp.cpp b/src/USER-OMP/pair_born_coul_long_omp.cpp index cbb71dfeb54e65c728d6f22b2f493c3186c03247..f1981844066c3eab95133ef67957a8b9786414a7 100644 --- a/src/USER-OMP/pair_born_coul_long_omp.cpp +++ b/src/USER-OMP/pair_born_coul_long_omp.cpp @@ -12,7 +12,7 @@ Contributing author: Axel Kohlmeyer (Temple U) ------------------------------------------------------------------------- */ -#include +#include #include "pair_born_coul_long_omp.h" #include "atom.h" #include "comm.h" diff --git a/src/USER-OMP/pair_born_coul_msm_omp.cpp b/src/USER-OMP/pair_born_coul_msm_omp.cpp index 8ce564ccfabd10c2f8c3be2748822f430728327f..1b4757359f6a84b027a7e18078b8d7576993c64d 100644 --- a/src/USER-OMP/pair_born_coul_msm_omp.cpp +++ b/src/USER-OMP/pair_born_coul_msm_omp.cpp @@ -12,7 +12,7 @@ Contributing author: Axel Kohlmeyer (Temple U) ------------------------------------------------------------------------- */ -#include +#include #include "pair_born_coul_msm_omp.h" #include "atom.h" #include "comm.h" diff --git a/src/USER-OMP/pair_born_coul_wolf_omp.cpp b/src/USER-OMP/pair_born_coul_wolf_omp.cpp index bd3e539dd65dd030858b590754eed655fd3c6165..7904181ba594994be359c77c72dcf0be97d77082 100644 --- a/src/USER-OMP/pair_born_coul_wolf_omp.cpp +++ b/src/USER-OMP/pair_born_coul_wolf_omp.cpp @@ -12,7 +12,7 @@ Contributing author: Axel Kohlmeyer (Temple U) ------------------------------------------------------------------------- */ -#include +#include #include "pair_born_coul_wolf_omp.h" #include "atom.h" #include "comm.h" diff --git a/src/USER-OMP/pair_born_omp.cpp b/src/USER-OMP/pair_born_omp.cpp index 35669cb53955f3f9aca601efbafcda37b501998a..f75d4b9f35a6ba81467c382f6ce43f9052e0d4c6 100644 --- a/src/USER-OMP/pair_born_omp.cpp +++ b/src/USER-OMP/pair_born_omp.cpp @@ -12,7 +12,7 @@ Contributing author: Axel Kohlmeyer (Temple U) ------------------------------------------------------------------------- */ -#include +#include #include "pair_born_omp.h" #include "atom.h" #include "comm.h" diff --git a/src/USER-OMP/pair_brownian_omp.cpp b/src/USER-OMP/pair_brownian_omp.cpp index 9ea6a9187b75c0422043e7161a5c8d909618d32a..b1af821bba876a95dd27919c5d4abef736aa4af0 100644 --- a/src/USER-OMP/pair_brownian_omp.cpp +++ b/src/USER-OMP/pair_brownian_omp.cpp @@ -12,7 +12,7 @@ Contributing author: Axel Kohlmeyer (Temple U) ------------------------------------------------------------------------- */ -#include +#include #include "pair_brownian_omp.h" #include "atom.h" #include "comm.h" diff --git a/src/USER-OMP/pair_brownian_poly_omp.cpp b/src/USER-OMP/pair_brownian_poly_omp.cpp index d8cb3bf06e158454212026bd6d980cbae1dadcdf..2e677ed535220e11bf13ccbe4068a5bffebb91f8 100644 --- a/src/USER-OMP/pair_brownian_poly_omp.cpp +++ b/src/USER-OMP/pair_brownian_poly_omp.cpp @@ -12,7 +12,7 @@ Contributing author: Axel Kohlmeyer (Temple U) ------------------------------------------------------------------------- */ -#include +#include #include "pair_brownian_poly_omp.h" #include "atom.h" #include "comm.h" diff --git a/src/USER-OMP/pair_buck_coul_cut_omp.cpp b/src/USER-OMP/pair_buck_coul_cut_omp.cpp index ead60d70acc76e2fb650aa840a4550a716d93ded..8fa6be06b2ef595fd6d029e101d07e98e298632e 100644 --- a/src/USER-OMP/pair_buck_coul_cut_omp.cpp +++ b/src/USER-OMP/pair_buck_coul_cut_omp.cpp @@ -12,7 +12,7 @@ Contributing author: Axel Kohlmeyer (Temple U) ------------------------------------------------------------------------- */ -#include +#include #include "pair_buck_coul_cut_omp.h" #include "atom.h" #include "comm.h" diff --git a/src/USER-OMP/pair_buck_coul_long_omp.cpp b/src/USER-OMP/pair_buck_coul_long_omp.cpp index 48750f83181049664dd52618bf4ebb8aff3a0393..4d30eb3e82d991be28bf00ba4fc7ec67b4216bc8 100644 --- a/src/USER-OMP/pair_buck_coul_long_omp.cpp +++ b/src/USER-OMP/pair_buck_coul_long_omp.cpp @@ -12,7 +12,7 @@ Contributing author: Axel Kohlmeyer (Temple U) ------------------------------------------------------------------------- */ -#include +#include #include "pair_buck_coul_long_omp.h" #include "atom.h" #include "comm.h" diff --git a/src/USER-OMP/pair_buck_coul_msm_omp.cpp b/src/USER-OMP/pair_buck_coul_msm_omp.cpp index df94efc81232cc9547d01f9fabadfb30d6fda81e..a8bca36394bd5b4415ce840a238cdaaa195ab8df 100644 --- a/src/USER-OMP/pair_buck_coul_msm_omp.cpp +++ b/src/USER-OMP/pair_buck_coul_msm_omp.cpp @@ -12,7 +12,7 @@ Contributing author: Axel Kohlmeyer (Temple U) ------------------------------------------------------------------------- */ -#include +#include #include "pair_buck_coul_msm_omp.h" #include "atom.h" #include "comm.h" diff --git a/src/USER-OMP/pair_buck_long_coul_long_omp.cpp b/src/USER-OMP/pair_buck_long_coul_long_omp.cpp index dbcef106d2571f3a439a635be5f8417e3d105937..4a67cf9544fda593f82862e976498f1537d3a3c5 100644 --- a/src/USER-OMP/pair_buck_long_coul_long_omp.cpp +++ b/src/USER-OMP/pair_buck_long_coul_long_omp.cpp @@ -12,7 +12,7 @@ ------------------------------------------------------------------------- */ -#include +#include #include "math_vector.h" #include "pair_buck_long_coul_long_omp.h" #include "atom.h" diff --git a/src/USER-OMP/pair_buck_omp.cpp b/src/USER-OMP/pair_buck_omp.cpp index 826fd78deb3368a0745b3f6ee2717c10e1376c58..f3fa32a5ea231fc772c3edd6596c43e85a644ded 100644 --- a/src/USER-OMP/pair_buck_omp.cpp +++ b/src/USER-OMP/pair_buck_omp.cpp @@ -12,7 +12,7 @@ Contributing author: Axel Kohlmeyer (Temple U) ------------------------------------------------------------------------- */ -#include +#include #include "pair_buck_omp.h" #include "atom.h" #include "comm.h" diff --git a/src/USER-OMP/pair_cdeam_omp.cpp b/src/USER-OMP/pair_cdeam_omp.cpp index 3bfe74e129d391af143d3301a06f1b1e6f91326c..c3a9454567cccc0cb0c075f635e61c247ef9c476 100644 --- a/src/USER-OMP/pair_cdeam_omp.cpp +++ b/src/USER-OMP/pair_cdeam_omp.cpp @@ -12,8 +12,8 @@ Contributing author: Axel Kohlmeyer (Temple U) ------------------------------------------------------------------------- */ -#include -#include +#include +#include #include "pair_cdeam_omp.h" #include "atom.h" diff --git a/src/USER-OMP/pair_colloid_omp.cpp b/src/USER-OMP/pair_colloid_omp.cpp index 4c6411f1509f86973731a699d241836571a14ea7..536b7644bd4f12efcd0818ae18f57cdf656b0b6d 100644 --- a/src/USER-OMP/pair_colloid_omp.cpp +++ b/src/USER-OMP/pair_colloid_omp.cpp @@ -12,7 +12,7 @@ Contributing author: Axel Kohlmeyer (Temple U) ------------------------------------------------------------------------- */ -#include +#include #include "pair_colloid_omp.h" #include "atom.h" #include "comm.h" diff --git a/src/USER-OMP/pair_comb_omp.cpp b/src/USER-OMP/pair_comb_omp.cpp index 2a0e6ceb2354ea0361a540b824c18f1cecbdbc9f..8a77ab955fdeba423203938e0bd50012b4228621 100644 --- a/src/USER-OMP/pair_comb_omp.cpp +++ b/src/USER-OMP/pair_comb_omp.cpp @@ -12,7 +12,7 @@ Contributing author: Axel Kohlmeyer (Temple U) ------------------------------------------------------------------------- */ -#include +#include #include "pair_comb_omp.h" #include "atom.h" #include "comm.h" diff --git a/src/USER-OMP/pair_coul_cut_omp.cpp b/src/USER-OMP/pair_coul_cut_omp.cpp index 381e7f83c208c97980f11c0fec8be31d2b7b5782..b9ac72421ef874728a22ad24279840210fdefb7a 100644 --- a/src/USER-OMP/pair_coul_cut_omp.cpp +++ b/src/USER-OMP/pair_coul_cut_omp.cpp @@ -12,7 +12,7 @@ Contributing author: Axel Kohlmeyer (Temple U) ------------------------------------------------------------------------- */ -#include +#include #include "pair_coul_cut_omp.h" #include "atom.h" #include "comm.h" diff --git a/src/USER-OMP/pair_coul_cut_soft_omp.cpp b/src/USER-OMP/pair_coul_cut_soft_omp.cpp index af9c9472fa788b827ac0eaf18f09d2db782e3d90..c7e8c5e5603a0765e4911f5d34357cd1181089e3 100644 --- a/src/USER-OMP/pair_coul_cut_soft_omp.cpp +++ b/src/USER-OMP/pair_coul_cut_soft_omp.cpp @@ -12,7 +12,7 @@ Contributing author: Axel Kohlmeyer (Temple U) ------------------------------------------------------------------------- */ -#include +#include #include "pair_coul_cut_soft_omp.h" #include "atom.h" #include "comm.h" diff --git a/src/USER-OMP/pair_coul_debye_omp.cpp b/src/USER-OMP/pair_coul_debye_omp.cpp index 0d9b1179674495710e42c4a8a578d71f8c0b44ea..cb7a9025ce718bf297bc83b1e718c20a32fd4a34 100644 --- a/src/USER-OMP/pair_coul_debye_omp.cpp +++ b/src/USER-OMP/pair_coul_debye_omp.cpp @@ -12,7 +12,7 @@ Contributing author: Axel Kohlmeyer (Temple U) ------------------------------------------------------------------------- */ -#include +#include #include "pair_coul_debye_omp.h" #include "atom.h" #include "comm.h" diff --git a/src/USER-OMP/pair_coul_diel_omp.cpp b/src/USER-OMP/pair_coul_diel_omp.cpp index 577ba6bf65a9b49e0a22e1dcd04257cc0bde947b..c75e36b55ee842c05c8f9ca8de58875fa8c08ae8 100644 --- a/src/USER-OMP/pair_coul_diel_omp.cpp +++ b/src/USER-OMP/pair_coul_diel_omp.cpp @@ -12,7 +12,7 @@ Contributing author: Axel Kohlmeyer (Temple U) ------------------------------------------------------------------------- */ -#include +#include #include "pair_coul_diel_omp.h" #include "atom.h" #include "comm.h" diff --git a/src/USER-OMP/pair_coul_dsf_omp.cpp b/src/USER-OMP/pair_coul_dsf_omp.cpp index 4707fad733520cca8fca7e02f87753e543f085c0..740e3242ad2bcf3c0db313f3f2989dac2e32867a 100644 --- a/src/USER-OMP/pair_coul_dsf_omp.cpp +++ b/src/USER-OMP/pair_coul_dsf_omp.cpp @@ -12,7 +12,7 @@ Contributing author: Axel Kohlmeyer (Temple U) ------------------------------------------------------------------------- */ -#include +#include #include "pair_coul_dsf_omp.h" #include "atom.h" #include "comm.h" diff --git a/src/USER-OMP/pair_coul_long_omp.cpp b/src/USER-OMP/pair_coul_long_omp.cpp index dc619913d6ef82c9c2e141ac5128617b7c25744c..eb74bb9615cf2a5ac2f9d1118f3b1fb6a7263d92 100644 --- a/src/USER-OMP/pair_coul_long_omp.cpp +++ b/src/USER-OMP/pair_coul_long_omp.cpp @@ -12,7 +12,7 @@ Contributing author: Axel Kohlmeyer (Temple U) ------------------------------------------------------------------------- */ -#include +#include #include "pair_coul_long_omp.h" #include "atom.h" #include "comm.h" diff --git a/src/USER-OMP/pair_coul_long_soft_omp.cpp b/src/USER-OMP/pair_coul_long_soft_omp.cpp index f44f95717d10e5fcef2f12dd32a94f6e492d17f2..4e65483a17c7f4a6b7d9759781df748dcdc89561 100644 --- a/src/USER-OMP/pair_coul_long_soft_omp.cpp +++ b/src/USER-OMP/pair_coul_long_soft_omp.cpp @@ -12,7 +12,7 @@ Contributing author: Axel Kohlmeyer (Temple U) ------------------------------------------------------------------------- */ -#include +#include #include "pair_coul_long_soft_omp.h" #include "atom.h" #include "comm.h" diff --git a/src/USER-OMP/pair_coul_msm_omp.cpp b/src/USER-OMP/pair_coul_msm_omp.cpp index baf9ceefb5b4957e83d7408243c791d0ff67b3cd..f4bc279532fe96386de8344d0797bd925e6104c9 100644 --- a/src/USER-OMP/pair_coul_msm_omp.cpp +++ b/src/USER-OMP/pair_coul_msm_omp.cpp @@ -12,7 +12,7 @@ Contributing author: Axel Kohlmeyer (Temple U) ------------------------------------------------------------------------- */ -#include +#include #include "pair_coul_msm_omp.h" #include "atom.h" #include "comm.h" diff --git a/src/USER-OMP/pair_coul_wolf_omp.cpp b/src/USER-OMP/pair_coul_wolf_omp.cpp index c5080bc7de2185f860530235e48f496da1a8dd34..bc86cdbf5dae8e5d3378458ec11df65117c94a20 100644 --- a/src/USER-OMP/pair_coul_wolf_omp.cpp +++ b/src/USER-OMP/pair_coul_wolf_omp.cpp @@ -12,7 +12,7 @@ Contributing author: Axel Kohlmeyer (Temple U) ------------------------------------------------------------------------- */ -#include +#include #include "pair_coul_wolf_omp.h" #include "atom.h" #include "comm.h" diff --git a/src/USER-OMP/pair_dpd_omp.cpp b/src/USER-OMP/pair_dpd_omp.cpp index 98e5af0d814cdeb429057ae23dc8837a6efec27b..29b5568defa983e9393358331dfb75fffc459b94 100644 --- a/src/USER-OMP/pair_dpd_omp.cpp +++ b/src/USER-OMP/pair_dpd_omp.cpp @@ -12,7 +12,7 @@ Contributing author: Axel Kohlmeyer (Temple U) ------------------------------------------------------------------------- */ -#include +#include #include "pair_dpd_omp.h" #include "atom.h" #include "comm.h" diff --git a/src/USER-OMP/pair_dpd_tstat_omp.cpp b/src/USER-OMP/pair_dpd_tstat_omp.cpp index ee697a2e96f687b404091b5055a3de4bc4e4d791..0a9e96fa0cca4478b5364528f3d0a16f1fefecc6 100644 --- a/src/USER-OMP/pair_dpd_tstat_omp.cpp +++ b/src/USER-OMP/pair_dpd_tstat_omp.cpp @@ -12,7 +12,7 @@ Contributing author: Axel Kohlmeyer (Temple U) ------------------------------------------------------------------------- */ -#include +#include #include "pair_dpd_tstat_omp.h" #include "atom.h" #include "comm.h" diff --git a/src/USER-OMP/pair_eam_alloy_omp.cpp b/src/USER-OMP/pair_eam_alloy_omp.cpp index eea7383eac3ee19edf12f32314c9866464bd0fee..bbb3b03b020cffdf39327c6b556b26e165983699 100644 --- a/src/USER-OMP/pair_eam_alloy_omp.cpp +++ b/src/USER-OMP/pair_eam_alloy_omp.cpp @@ -15,9 +15,9 @@ Contributing authors: Stephen Foiles (SNL), Murray Daw (SNL) ------------------------------------------------------------------------- */ -#include -#include -#include +#include +#include +#include #include "pair_eam_alloy_omp.h" #include "atom.h" #include "comm.h" diff --git a/src/USER-OMP/pair_eam_fs_omp.cpp b/src/USER-OMP/pair_eam_fs_omp.cpp index c646632224a213762eb50ae81868b65c5ebf217e..a678c887a0726ce23d3c5e9468cf8e77581ae5af 100644 --- a/src/USER-OMP/pair_eam_fs_omp.cpp +++ b/src/USER-OMP/pair_eam_fs_omp.cpp @@ -15,9 +15,9 @@ Contributing authors: Tim Lau (MIT) ------------------------------------------------------------------------- */ -#include -#include -#include +#include +#include +#include #include "pair_eam_fs_omp.h" #include "atom.h" #include "comm.h" diff --git a/src/USER-OMP/pair_eam_omp.cpp b/src/USER-OMP/pair_eam_omp.cpp index 9c28477af03053b28a4ecde21daab5f370bbae49..492ff797692d19fba1de48296b98f4450037fc00 100644 --- a/src/USER-OMP/pair_eam_omp.cpp +++ b/src/USER-OMP/pair_eam_omp.cpp @@ -12,8 +12,8 @@ Contributing author: Axel Kohlmeyer (Temple U) ------------------------------------------------------------------------- */ -#include -#include +#include +#include #include "pair_eam_omp.h" #include "atom.h" diff --git a/src/USER-OMP/pair_edip_omp.cpp b/src/USER-OMP/pair_edip_omp.cpp index 7c503ea8aa13057c9149a3116c92336c0b7aa0a0..5ad8c808ba5e39a0ce728f1375065f296b247048 100644 --- a/src/USER-OMP/pair_edip_omp.cpp +++ b/src/USER-OMP/pair_edip_omp.cpp @@ -12,7 +12,7 @@ Contributing author: Axel Kohlmeyer (Temple U) ------------------------------------------------------------------------- */ -#include +#include #include "pair_edip_omp.h" #include "atom.h" #include "comm.h" diff --git a/src/USER-OMP/pair_eim_omp.cpp b/src/USER-OMP/pair_eim_omp.cpp index e98c035860c74289548fbc2ee17333875093c5ad..6a3e0bc529d99f2201a6d0df25535acddffa08f5 100644 --- a/src/USER-OMP/pair_eim_omp.cpp +++ b/src/USER-OMP/pair_eim_omp.cpp @@ -12,8 +12,8 @@ Contributing author: Axel Kohlmeyer (Temple U) ------------------------------------------------------------------------- */ -#include -#include +#include +#include #include "pair_eim_omp.h" #include "atom.h" diff --git a/src/USER-OMP/pair_gauss_cut_omp.cpp b/src/USER-OMP/pair_gauss_cut_omp.cpp index ad0eb77963448d92a2a7e3c9c9b491c99b7c638c..9a41dcc87ef3a4024b1a4a1a19f6f87f8a6b41ca 100644 --- a/src/USER-OMP/pair_gauss_cut_omp.cpp +++ b/src/USER-OMP/pair_gauss_cut_omp.cpp @@ -12,7 +12,7 @@ Contributing author: Axel Kohlmeyer (Temple U) ------------------------------------------------------------------------- */ -#include +#include #include "pair_gauss_cut_omp.h" #include "atom.h" #include "comm.h" diff --git a/src/USER-OMP/pair_gauss_omp.cpp b/src/USER-OMP/pair_gauss_omp.cpp index 062da924e32b2f3b4f63560b093db792dac99caf..059c77c677aded43c3bfe1dcf4ca0cdedd15c851 100644 --- a/src/USER-OMP/pair_gauss_omp.cpp +++ b/src/USER-OMP/pair_gauss_omp.cpp @@ -12,7 +12,7 @@ Contributing author: Axel Kohlmeyer (Temple U) ------------------------------------------------------------------------- */ -#include +#include #include "pair_gauss_omp.h" #include "atom.h" #include "comm.h" diff --git a/src/USER-OMP/pair_gayberne_omp.cpp b/src/USER-OMP/pair_gayberne_omp.cpp index 54e4496f22efcb5954fdee9c83c91024e1d48a01..5b0ff67afed9a8d5e3dfbb858a68c4f4e08ec477 100644 --- a/src/USER-OMP/pair_gayberne_omp.cpp +++ b/src/USER-OMP/pair_gayberne_omp.cpp @@ -12,7 +12,7 @@ Contributing author: Axel Kohlmeyer (Temple U) ------------------------------------------------------------------------- */ -#include +#include #include "pair_gayberne_omp.h" #include "math_extra.h" #include "atom.h" diff --git a/src/USER-OMP/pair_gran_hertz_history_omp.cpp b/src/USER-OMP/pair_gran_hertz_history_omp.cpp index 046b71a73aee49f91222b0b787f1c1ea4551f434..9854b8f9ff5261cc5d2a2609a1e146971298a03d 100644 --- a/src/USER-OMP/pair_gran_hertz_history_omp.cpp +++ b/src/USER-OMP/pair_gran_hertz_history_omp.cpp @@ -12,7 +12,7 @@ Contributing author: Axel Kohlmeyer (Temple U) ------------------------------------------------------------------------- */ -#include +#include #include "pair_gran_hertz_history_omp.h" #include "fix_neigh_history.h" #include "atom.h" diff --git a/src/USER-OMP/pair_gran_hooke_history_omp.cpp b/src/USER-OMP/pair_gran_hooke_history_omp.cpp index 2e7d55aff059c1e7867cb35edd03bd3d19cf7eb6..2327fc815ac218709b28ad358c4d124f4393a3e5 100644 --- a/src/USER-OMP/pair_gran_hooke_history_omp.cpp +++ b/src/USER-OMP/pair_gran_hooke_history_omp.cpp @@ -12,7 +12,8 @@ Contributing author: Axel Kohlmeyer (Temple U) ------------------------------------------------------------------------- */ -#include +#include +#include #include "pair_gran_hooke_history_omp.h" #include "fix_neigh_history.h" #include "atom.h" @@ -24,8 +25,6 @@ #include "neigh_list.h" #include "update.h" -#include - #include "suffix.h" using namespace LAMMPS_NS; diff --git a/src/USER-OMP/pair_gran_hooke_omp.cpp b/src/USER-OMP/pair_gran_hooke_omp.cpp index 3197b7076e8c09740ea75d1bd84950b4d8a67777..876fe9c4de5eb997a4c58b892a99f16728f87c6b 100644 --- a/src/USER-OMP/pair_gran_hooke_omp.cpp +++ b/src/USER-OMP/pair_gran_hooke_omp.cpp @@ -12,7 +12,7 @@ Contributing author: Axel Kohlmeyer (Temple U) ------------------------------------------------------------------------- */ -#include +#include #include "pair_gran_hooke_omp.h" #include "atom.h" #include "comm.h" diff --git a/src/USER-OMP/pair_hbond_dreiding_lj_omp.cpp b/src/USER-OMP/pair_hbond_dreiding_lj_omp.cpp index c22efffb5a8edca99cdfb486de5cfaab76dbcd26..ec9da78b16dc06d14135ade0263f635ecc39f25e 100644 --- a/src/USER-OMP/pair_hbond_dreiding_lj_omp.cpp +++ b/src/USER-OMP/pair_hbond_dreiding_lj_omp.cpp @@ -12,7 +12,7 @@ Contributing author: Axel Kohlmeyer (Temple U) ------------------------------------------------------------------------- */ -#include +#include #include "pair_hbond_dreiding_lj_omp.h" #include "atom.h" #include "atom_vec.h" diff --git a/src/USER-OMP/pair_hbond_dreiding_morse_omp.cpp b/src/USER-OMP/pair_hbond_dreiding_morse_omp.cpp index 7debe5a68a6f41ecbce2680e9c6671178af43288..4965be43b84a6f1dd3809c2cd90a5816adf14124 100644 --- a/src/USER-OMP/pair_hbond_dreiding_morse_omp.cpp +++ b/src/USER-OMP/pair_hbond_dreiding_morse_omp.cpp @@ -12,7 +12,7 @@ Contributing author: Axel Kohlmeyer (Temple U) ------------------------------------------------------------------------- */ -#include +#include #include "pair_hbond_dreiding_morse_omp.h" #include "atom.h" #include "atom_vec.h" diff --git a/src/USER-OMP/pair_lj96_cut_omp.cpp b/src/USER-OMP/pair_lj96_cut_omp.cpp index e502a93acfb1d711426b0660c401cdd16413eeb3..1cca6743690756f4e5f7300f425b4718999356ec 100644 --- a/src/USER-OMP/pair_lj96_cut_omp.cpp +++ b/src/USER-OMP/pair_lj96_cut_omp.cpp @@ -12,7 +12,7 @@ Contributing author: Axel Kohlmeyer (Temple U) ------------------------------------------------------------------------- */ -#include +#include #include "pair_lj96_cut_omp.h" #include "atom.h" #include "comm.h" diff --git a/src/USER-OMP/pair_lj_charmm_coul_charmm_implicit_omp.cpp b/src/USER-OMP/pair_lj_charmm_coul_charmm_implicit_omp.cpp index 1333ae27613e15beead53eac127fed836b52e28e..2f72f3851e244552b8b465ef05e7aca23a731872 100644 --- a/src/USER-OMP/pair_lj_charmm_coul_charmm_implicit_omp.cpp +++ b/src/USER-OMP/pair_lj_charmm_coul_charmm_implicit_omp.cpp @@ -12,7 +12,7 @@ Contributing author: Axel Kohlmeyer (Temple U) ------------------------------------------------------------------------- */ -#include +#include #include "pair_lj_charmm_coul_charmm_implicit_omp.h" #include "atom.h" #include "comm.h" diff --git a/src/USER-OMP/pair_lj_charmm_coul_charmm_omp.cpp b/src/USER-OMP/pair_lj_charmm_coul_charmm_omp.cpp index 9fd41e61dd48f4c92e925b5aeebbd4f0dbd6c7a0..b61a80a178b77c0b56ee696b30141b45f5b3e6eb 100644 --- a/src/USER-OMP/pair_lj_charmm_coul_charmm_omp.cpp +++ b/src/USER-OMP/pair_lj_charmm_coul_charmm_omp.cpp @@ -12,7 +12,7 @@ Contributing author: Axel Kohlmeyer (Temple U) ------------------------------------------------------------------------- */ -#include +#include #include "pair_lj_charmm_coul_charmm_omp.h" #include "atom.h" #include "comm.h" diff --git a/src/USER-OMP/pair_lj_charmm_coul_long_omp.cpp b/src/USER-OMP/pair_lj_charmm_coul_long_omp.cpp index acbf61d9fd717dfc403c219e180ca01fe88983b2..5351ab9aeaa95571a0fbb59f057c7b5d27ad6a06 100644 --- a/src/USER-OMP/pair_lj_charmm_coul_long_omp.cpp +++ b/src/USER-OMP/pair_lj_charmm_coul_long_omp.cpp @@ -12,7 +12,7 @@ Contributing author: Axel Kohlmeyer (Temple U) ------------------------------------------------------------------------- */ -#include +#include #include "pair_lj_charmm_coul_long_omp.h" #include "atom.h" #include "comm.h" diff --git a/src/USER-OMP/pair_lj_charmm_coul_long_soft_omp.cpp b/src/USER-OMP/pair_lj_charmm_coul_long_soft_omp.cpp index 4953c89a4d55142adade87e72685e5380f2085a4..ea5d739e49d2614f003571bc6128bca2c75d785c 100644 --- a/src/USER-OMP/pair_lj_charmm_coul_long_soft_omp.cpp +++ b/src/USER-OMP/pair_lj_charmm_coul_long_soft_omp.cpp @@ -12,7 +12,7 @@ Contributing author: Axel Kohlmeyer (Temple U) ------------------------------------------------------------------------- */ -#include +#include #include "pair_lj_charmm_coul_long_soft_omp.h" #include "atom.h" #include "comm.h" diff --git a/src/USER-OMP/pair_lj_charmm_coul_msm_omp.cpp b/src/USER-OMP/pair_lj_charmm_coul_msm_omp.cpp index c603f0dd3a01aa78d2c8b9d5cb29e0d8f1393f6c..3baa9597a8e28c3619fe1184c6fe937f0fd2012a 100644 --- a/src/USER-OMP/pair_lj_charmm_coul_msm_omp.cpp +++ b/src/USER-OMP/pair_lj_charmm_coul_msm_omp.cpp @@ -12,7 +12,7 @@ Contributing author: Axel Kohlmeyer (Temple U) ------------------------------------------------------------------------- */ -#include +#include #include "pair_lj_charmm_coul_msm_omp.h" #include "atom.h" #include "comm.h" diff --git a/src/USER-OMP/pair_lj_class2_coul_cut_omp.cpp b/src/USER-OMP/pair_lj_class2_coul_cut_omp.cpp index 98c2b0d578eaf153ee44d271b4db4cd1c82e03a0..38390918c7da9644f10193d362300d7c34324a54 100644 --- a/src/USER-OMP/pair_lj_class2_coul_cut_omp.cpp +++ b/src/USER-OMP/pair_lj_class2_coul_cut_omp.cpp @@ -12,7 +12,7 @@ Contributing author: Axel Kohlmeyer (Temple U) ------------------------------------------------------------------------- */ -#include +#include #include "pair_lj_class2_coul_cut_omp.h" #include "atom.h" #include "comm.h" diff --git a/src/USER-OMP/pair_lj_class2_coul_long_omp.cpp b/src/USER-OMP/pair_lj_class2_coul_long_omp.cpp index 3038332c905e7e69b4730816b1457519e632d19d..f47672c9bc39d3f01f8af5733f923d38578359f4 100644 --- a/src/USER-OMP/pair_lj_class2_coul_long_omp.cpp +++ b/src/USER-OMP/pair_lj_class2_coul_long_omp.cpp @@ -12,7 +12,7 @@ Contributing author: Axel Kohlmeyer (Temple U) ------------------------------------------------------------------------- */ -#include +#include #include "pair_lj_class2_coul_long_omp.h" #include "atom.h" #include "comm.h" diff --git a/src/USER-OMP/pair_lj_class2_omp.cpp b/src/USER-OMP/pair_lj_class2_omp.cpp index ffb0ceaa0a0f762ee63d8384b015bd2c4a1400fc..7ab4626c3e420ddf0e6dd633b8b8ca704568ae0e 100644 --- a/src/USER-OMP/pair_lj_class2_omp.cpp +++ b/src/USER-OMP/pair_lj_class2_omp.cpp @@ -12,7 +12,7 @@ Contributing author: Axel Kohlmeyer (Temple U) ------------------------------------------------------------------------- */ -#include +#include #include "pair_lj_class2_omp.h" #include "atom.h" #include "comm.h" diff --git a/src/USER-OMP/pair_lj_cubic_omp.cpp b/src/USER-OMP/pair_lj_cubic_omp.cpp index 1cea0f454a7199fbe54e6193b4ed75285b7cc1b5..3e8adb33b85df9fda3fcee37f875971713166661 100644 --- a/src/USER-OMP/pair_lj_cubic_omp.cpp +++ b/src/USER-OMP/pair_lj_cubic_omp.cpp @@ -12,7 +12,7 @@ Contributing author: Axel Kohlmeyer (Temple U) ------------------------------------------------------------------------- */ -#include +#include #include "pair_lj_cubic_omp.h" #include "atom.h" #include "comm.h" diff --git a/src/USER-OMP/pair_lj_cut_coul_cut_omp.cpp b/src/USER-OMP/pair_lj_cut_coul_cut_omp.cpp index 1f48b4245ec7f53b73807fe5f9ad5481e15674fa..ea560a09bf30382158a22fa5fadb575677ceb407 100644 --- a/src/USER-OMP/pair_lj_cut_coul_cut_omp.cpp +++ b/src/USER-OMP/pair_lj_cut_coul_cut_omp.cpp @@ -12,7 +12,7 @@ Contributing author: Axel Kohlmeyer (Temple U) ------------------------------------------------------------------------- */ -#include +#include #include "pair_lj_cut_coul_cut_omp.h" #include "atom.h" #include "comm.h" diff --git a/src/USER-OMP/pair_lj_cut_coul_cut_soft_omp.cpp b/src/USER-OMP/pair_lj_cut_coul_cut_soft_omp.cpp index f6ba7236a03f1700836098f2fd7dd5c19155f903..4ef12bb1bbe198439a2033ff8c5b9b5fdbcd8300 100644 --- a/src/USER-OMP/pair_lj_cut_coul_cut_soft_omp.cpp +++ b/src/USER-OMP/pair_lj_cut_coul_cut_soft_omp.cpp @@ -12,7 +12,7 @@ Contributing author: Axel Kohlmeyer (Temple U) ------------------------------------------------------------------------- */ -#include +#include #include "pair_lj_cut_coul_cut_soft_omp.h" #include "atom.h" #include "comm.h" diff --git a/src/USER-OMP/pair_lj_cut_coul_debye_omp.cpp b/src/USER-OMP/pair_lj_cut_coul_debye_omp.cpp index 9fc64cf38cdd6ea40564e09779f2958118d92f68..9163e98eddeae433ca7d360518d4197d51cf5c80 100644 --- a/src/USER-OMP/pair_lj_cut_coul_debye_omp.cpp +++ b/src/USER-OMP/pair_lj_cut_coul_debye_omp.cpp @@ -12,7 +12,7 @@ Contributing author: Axel Kohlmeyer (Temple U) ------------------------------------------------------------------------- */ -#include +#include #include "pair_lj_cut_coul_debye_omp.h" #include "atom.h" #include "comm.h" diff --git a/src/USER-OMP/pair_lj_cut_coul_dsf_omp.cpp b/src/USER-OMP/pair_lj_cut_coul_dsf_omp.cpp index d0b6c1b2dc3d108d24de94d2a0ebc9680baed248..9d9c098f8744afa5817f91b2fce97aed0fb213f3 100644 --- a/src/USER-OMP/pair_lj_cut_coul_dsf_omp.cpp +++ b/src/USER-OMP/pair_lj_cut_coul_dsf_omp.cpp @@ -12,7 +12,7 @@ Contributing author: Axel Kohlmeyer (Temple U) ------------------------------------------------------------------------- */ -#include +#include #include "pair_lj_cut_coul_dsf_omp.h" #include "atom.h" #include "comm.h" diff --git a/src/USER-OMP/pair_lj_cut_coul_long_omp.cpp b/src/USER-OMP/pair_lj_cut_coul_long_omp.cpp index 6746cf97015500e894a6c0bbf7f5a362a0856452..d2eaae4ca4f640282ad2c6d6ef885db228fdf1f5 100644 --- a/src/USER-OMP/pair_lj_cut_coul_long_omp.cpp +++ b/src/USER-OMP/pair_lj_cut_coul_long_omp.cpp @@ -12,7 +12,7 @@ Contributing author: Axel Kohlmeyer (Temple U) ------------------------------------------------------------------------- */ -#include +#include #include "pair_lj_cut_coul_long_omp.h" #include "atom.h" #include "comm.h" diff --git a/src/USER-OMP/pair_lj_cut_coul_long_soft_omp.cpp b/src/USER-OMP/pair_lj_cut_coul_long_soft_omp.cpp index 5f0a3d57c4cd940d3bd3db8a408942e633a8d4c0..725bfe4724020e70298a9d7fe955f04ae624cd71 100644 --- a/src/USER-OMP/pair_lj_cut_coul_long_soft_omp.cpp +++ b/src/USER-OMP/pair_lj_cut_coul_long_soft_omp.cpp @@ -12,7 +12,7 @@ Contributing author: Axel Kohlmeyer (Temple U) ------------------------------------------------------------------------- */ -#include +#include #include "pair_lj_cut_coul_long_soft_omp.h" #include "atom.h" #include "comm.h" diff --git a/src/USER-OMP/pair_lj_cut_coul_msm_omp.cpp b/src/USER-OMP/pair_lj_cut_coul_msm_omp.cpp index fba8f552db565aa9df09c1e9eb176f31111ea5c1..234204af93f362a5d81ecbf888b9cffa587d0aab 100644 --- a/src/USER-OMP/pair_lj_cut_coul_msm_omp.cpp +++ b/src/USER-OMP/pair_lj_cut_coul_msm_omp.cpp @@ -12,7 +12,7 @@ Contributing author: Axel Kohlmeyer (Temple U) ------------------------------------------------------------------------- */ -#include +#include #include "pair_lj_cut_coul_msm_omp.h" #include "atom.h" #include "comm.h" diff --git a/src/USER-OMP/pair_lj_cut_coul_wolf_omp.cpp b/src/USER-OMP/pair_lj_cut_coul_wolf_omp.cpp index 51574b2ee7d884f768ddd8635116bd0df842829a..36ef9d54f970741f0ab6638ca6d5d57c5b19528f 100644 --- a/src/USER-OMP/pair_lj_cut_coul_wolf_omp.cpp +++ b/src/USER-OMP/pair_lj_cut_coul_wolf_omp.cpp @@ -12,7 +12,7 @@ Contributing author: Axel Kohlmeyer (Temple U) ------------------------------------------------------------------------- */ -#include +#include #include "pair_lj_cut_coul_wolf_omp.h" #include "atom.h" #include "comm.h" diff --git a/src/USER-OMP/pair_lj_cut_dipole_cut_omp.cpp b/src/USER-OMP/pair_lj_cut_dipole_cut_omp.cpp index d9fd7ac72e1473389642ae650a77a480d794e1a9..d4145d98350c1890ca15ff869a880062471eb3ca 100644 --- a/src/USER-OMP/pair_lj_cut_dipole_cut_omp.cpp +++ b/src/USER-OMP/pair_lj_cut_dipole_cut_omp.cpp @@ -12,7 +12,7 @@ Contributing author: Axel Kohlmeyer (Temple U) ------------------------------------------------------------------------- */ -#include +#include #include "pair_lj_cut_dipole_cut_omp.h" #include "atom.h" #include "comm.h" diff --git a/src/USER-OMP/pair_lj_cut_omp.cpp b/src/USER-OMP/pair_lj_cut_omp.cpp index 34754975fb53f14de1997ebabfe165c05f86425c..319257b56b7f1800fd32c3624468b8cbaa08cb45 100644 --- a/src/USER-OMP/pair_lj_cut_omp.cpp +++ b/src/USER-OMP/pair_lj_cut_omp.cpp @@ -12,7 +12,7 @@ Contributing author: Axel Kohlmeyer (Temple U) ------------------------------------------------------------------------- */ -#include +#include #include "pair_lj_cut_omp.h" #include "atom.h" #include "comm.h" diff --git a/src/USER-OMP/pair_lj_cut_soft_omp.cpp b/src/USER-OMP/pair_lj_cut_soft_omp.cpp index 9147b9aa1c9e811d7fae59dc6bcdd3af1d1950be..7698f19b9512400e06c726be454c62c7df58805f 100644 --- a/src/USER-OMP/pair_lj_cut_soft_omp.cpp +++ b/src/USER-OMP/pair_lj_cut_soft_omp.cpp @@ -12,7 +12,7 @@ Contributing author: Axel Kohlmeyer (Temple U) ------------------------------------------------------------------------- */ -#include +#include #include "pair_lj_cut_soft_omp.h" #include "atom.h" #include "comm.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 110b8917cf07366b02aa0eeda1b99daeaffbe99a..536d5bcb863d7a0bfe2413caa750c59b9f7129fd 100644 --- a/src/USER-OMP/pair_lj_cut_thole_long_omp.cpp +++ b/src/USER-OMP/pair_lj_cut_thole_long_omp.cpp @@ -15,10 +15,10 @@ Contributing author: Paul Crozier (SNL) ------------------------------------------------------------------------- */ -#include -#include -#include -#include +#include +#include +#include +#include #include "pair_lj_cut_thole_long_omp.h" #include "atom.h" #include "comm.h" diff --git a/src/USER-OMP/pair_lj_cut_tip4p_cut_omp.cpp b/src/USER-OMP/pair_lj_cut_tip4p_cut_omp.cpp index 45797b289742084081cc6c874450859c48f3c441..619e970bb0035231a8e7a02dab09dd74ad22d09d 100644 --- a/src/USER-OMP/pair_lj_cut_tip4p_cut_omp.cpp +++ b/src/USER-OMP/pair_lj_cut_tip4p_cut_omp.cpp @@ -12,7 +12,7 @@ Contributing author: Axel Kohlmeyer (Temple U) ------------------------------------------------------------------------- */ -#include +#include #include "pair_lj_cut_tip4p_cut_omp.h" #include "atom.h" #include "domain.h" 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 d05b13cd10765b977adfbeff070f42a8e0e8ba63..ca8f450dc6b4f8371ad6e24bf0504890869ae6bf 100644 --- a/src/USER-OMP/pair_lj_cut_tip4p_long_omp.cpp +++ b/src/USER-OMP/pair_lj_cut_tip4p_long_omp.cpp @@ -12,7 +12,7 @@ Contributing author: Axel Kohlmeyer (Temple U) ------------------------------------------------------------------------- */ -#include +#include #include "pair_lj_cut_tip4p_long_omp.h" #include "atom.h" #include "domain.h" diff --git a/src/USER-OMP/pair_lj_cut_tip4p_long_soft_omp.cpp b/src/USER-OMP/pair_lj_cut_tip4p_long_soft_omp.cpp index b31c1c109b632d45e4a572000cc41d97bd0d6007..80b17fba96e6e81e0ba9ba34cb1450c37b478efc 100644 --- a/src/USER-OMP/pair_lj_cut_tip4p_long_soft_omp.cpp +++ b/src/USER-OMP/pair_lj_cut_tip4p_long_soft_omp.cpp @@ -12,7 +12,7 @@ Contributing author: Axel Kohlmeyer (Temple U) ------------------------------------------------------------------------- */ -#include +#include #include "pair_lj_cut_tip4p_long_soft_omp.h" #include "atom.h" #include "domain.h" diff --git a/src/USER-OMP/pair_lj_expand_omp.cpp b/src/USER-OMP/pair_lj_expand_omp.cpp index e0f64e471e46285511b3ac403a64ec02c12a0b36..064ea97809a791ccf77089ee9dba75b63c18d226 100644 --- a/src/USER-OMP/pair_lj_expand_omp.cpp +++ b/src/USER-OMP/pair_lj_expand_omp.cpp @@ -12,7 +12,7 @@ Contributing author: Axel Kohlmeyer (Temple U) ------------------------------------------------------------------------- */ -#include +#include #include "pair_lj_expand_omp.h" #include "atom.h" #include "comm.h" diff --git a/src/USER-OMP/pair_lj_gromacs_coul_gromacs_omp.cpp b/src/USER-OMP/pair_lj_gromacs_coul_gromacs_omp.cpp index 954fbe7cce751ce4036b022ae18c9b2c35994077..c87f369d115b499565ba3efd32f05a79627510a9 100644 --- a/src/USER-OMP/pair_lj_gromacs_coul_gromacs_omp.cpp +++ b/src/USER-OMP/pair_lj_gromacs_coul_gromacs_omp.cpp @@ -12,7 +12,7 @@ Contributing author: Axel Kohlmeyer (Temple U) ------------------------------------------------------------------------- */ -#include +#include #include "pair_lj_gromacs_coul_gromacs_omp.h" #include "atom.h" #include "comm.h" diff --git a/src/USER-OMP/pair_lj_gromacs_omp.cpp b/src/USER-OMP/pair_lj_gromacs_omp.cpp index 84c46886e10ec43c4dba2e3ed10508dca5c1cdfc..1d7cec5eef768425ed4d44ffb8d45d4e52b84af6 100644 --- a/src/USER-OMP/pair_lj_gromacs_omp.cpp +++ b/src/USER-OMP/pair_lj_gromacs_omp.cpp @@ -12,7 +12,7 @@ Contributing author: Axel Kohlmeyer (Temple U) ------------------------------------------------------------------------- */ -#include +#include #include "pair_lj_gromacs_omp.h" #include "atom.h" #include "comm.h" diff --git a/src/USER-OMP/pair_lj_long_coul_long_omp.cpp b/src/USER-OMP/pair_lj_long_coul_long_omp.cpp index 8cc4c95fc24f2cbd8584b816e5f6cc061a8810b8..0afc230e92c54c40f1a7578353ee367a80ef82b2 100644 --- a/src/USER-OMP/pair_lj_long_coul_long_omp.cpp +++ b/src/USER-OMP/pair_lj_long_coul_long_omp.cpp @@ -12,7 +12,7 @@ Contributing author: Axel Kohlmeyer (Temple U) ------------------------------------------------------------------------- */ -#include +#include #include "pair_lj_long_coul_long_omp.h" #include "atom.h" #include "comm.h" diff --git a/src/USER-OMP/pair_lj_long_tip4p_long_omp.cpp b/src/USER-OMP/pair_lj_long_tip4p_long_omp.cpp index f4b5071afbfe8eaadad74691d2bc113023223e02..8c0d72c74180a5dc61a32f6da8576196c5ee825e 100644 --- a/src/USER-OMP/pair_lj_long_tip4p_long_omp.cpp +++ b/src/USER-OMP/pair_lj_long_tip4p_long_omp.cpp @@ -12,7 +12,7 @@ Contributing author: Axel Kohlmeyer (Temple U) ------------------------------------------------------------------------- */ -#include +#include #include "pair_lj_long_tip4p_long_omp.h" #include "atom.h" #include "domain.h" diff --git a/src/USER-OMP/pair_lj_sdk_coul_long_omp.cpp b/src/USER-OMP/pair_lj_sdk_coul_long_omp.cpp index f388009bd808d12d6c6243bd6862fa38f1ec2328..c87f26204e8610114d5c6221278ec437b0ced1cd 100644 --- a/src/USER-OMP/pair_lj_sdk_coul_long_omp.cpp +++ b/src/USER-OMP/pair_lj_sdk_coul_long_omp.cpp @@ -12,7 +12,7 @@ Contributing author: Axel Kohlmeyer (Temple U) ------------------------------------------------------------------------- */ -#include +#include #include "pair_lj_sdk_coul_long_omp.h" #include "atom.h" #include "comm.h" diff --git a/src/USER-OMP/pair_lj_sdk_coul_msm_omp.cpp b/src/USER-OMP/pair_lj_sdk_coul_msm_omp.cpp index 9d991d5812ea7a1f88d929be5d2ac3b03c9dbf64..8ff0cfe9211f0221c106715ed4d6e264b64c7f50 100644 --- a/src/USER-OMP/pair_lj_sdk_coul_msm_omp.cpp +++ b/src/USER-OMP/pair_lj_sdk_coul_msm_omp.cpp @@ -13,7 +13,7 @@ This style is a simplified re-implementation of the CG/CMM pair style ------------------------------------------------------------------------- */ -#include +#include #include "pair_lj_sdk_coul_msm_omp.h" #include "atom.h" #include "comm.h" diff --git a/src/USER-OMP/pair_lj_sdk_omp.cpp b/src/USER-OMP/pair_lj_sdk_omp.cpp index 36e170046dbe45512fc843b4ec0ae69b802391a2..e107399316bdc80b0288f96cdcc943c41f00395e 100644 --- a/src/USER-OMP/pair_lj_sdk_omp.cpp +++ b/src/USER-OMP/pair_lj_sdk_omp.cpp @@ -13,7 +13,7 @@ This style is a simplified re-implementation of the CG/CMM pair style ------------------------------------------------------------------------- */ -#include +#include #include "pair_lj_sdk_omp.h" #include "atom.h" #include "comm.h" diff --git a/src/USER-OMP/pair_lj_sf_dipole_sf_omp.cpp b/src/USER-OMP/pair_lj_sf_dipole_sf_omp.cpp index 29250b09f4682b04ebe07720f9e9d7a19406b61f..250f6ff27214b4412935af0579c532165a504484 100644 --- a/src/USER-OMP/pair_lj_sf_dipole_sf_omp.cpp +++ b/src/USER-OMP/pair_lj_sf_dipole_sf_omp.cpp @@ -12,7 +12,7 @@ Contributing author: Axel Kohlmeyer (Temple U) ------------------------------------------------------------------------- */ -#include +#include #include "pair_lj_sf_dipole_sf_omp.h" #include "atom.h" #include "comm.h" diff --git a/src/USER-OMP/pair_lj_smooth_linear_omp.cpp b/src/USER-OMP/pair_lj_smooth_linear_omp.cpp index 9017ac740fb8d6ac6070b6295089898643bf31ca..b06de641f5b58337ec5d3e41f05ff4d61cd241e4 100644 --- a/src/USER-OMP/pair_lj_smooth_linear_omp.cpp +++ b/src/USER-OMP/pair_lj_smooth_linear_omp.cpp @@ -12,7 +12,7 @@ Contributing author: Axel Kohlmeyer (Temple U) ------------------------------------------------------------------------- */ -#include +#include #include "pair_lj_smooth_linear_omp.h" #include "atom.h" #include "comm.h" diff --git a/src/USER-OMP/pair_lj_smooth_omp.cpp b/src/USER-OMP/pair_lj_smooth_omp.cpp index 9bf15035bdce3604c09739d3cd0a4c43de434cf9..36935616bfdc5952cc77ef36fbc0958d80705f82 100644 --- a/src/USER-OMP/pair_lj_smooth_omp.cpp +++ b/src/USER-OMP/pair_lj_smooth_omp.cpp @@ -12,7 +12,7 @@ Contributing author: Axel Kohlmeyer (Temple U) ------------------------------------------------------------------------- */ -#include +#include #include "pair_lj_smooth_omp.h" #include "atom.h" #include "comm.h" diff --git a/src/USER-OMP/pair_lubricate_omp.cpp b/src/USER-OMP/pair_lubricate_omp.cpp index 1c622f5641035b743b3be6c08f6b7cebf13ea160..fbfc24769b73dfddd3853ec77a42530d328a5384 100644 --- a/src/USER-OMP/pair_lubricate_omp.cpp +++ b/src/USER-OMP/pair_lubricate_omp.cpp @@ -12,7 +12,7 @@ Contributing author: Axel Kohlmeyer (Temple U) ------------------------------------------------------------------------- */ -#include +#include #include "pair_lubricate_omp.h" #include "atom.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 2e7140e32bc96eee7d92c579865eab434bb1c094..825b3e8d705286ed254078ceca8dcd4fddbea070 100644 --- a/src/USER-OMP/pair_lubricate_poly_omp.cpp +++ b/src/USER-OMP/pair_lubricate_poly_omp.cpp @@ -12,7 +12,7 @@ Contributing author: Axel Kohlmeyer (Temple U) ------------------------------------------------------------------------- */ -#include +#include #include "pair_lubricate_poly_omp.h" #include "atom.h" #include "comm.h" diff --git a/src/USER-OMP/pair_meam_spline_omp.cpp b/src/USER-OMP/pair_meam_spline_omp.cpp index 4333d3b2a94ef8bc30d2aa2abef069041c07f584..dfc3b978a29f0a06665cfe4bbbbd35ef64dc03be 100644 --- a/src/USER-OMP/pair_meam_spline_omp.cpp +++ b/src/USER-OMP/pair_meam_spline_omp.cpp @@ -12,8 +12,8 @@ Contributing author: Axel Kohlmeyer (Temple U) ------------------------------------------------------------------------- */ -#include -#include +#include +#include #include "pair_meam_spline_omp.h" #include "atom.h" diff --git a/src/USER-OMP/pair_morse_omp.cpp b/src/USER-OMP/pair_morse_omp.cpp index 8aca4ef98f6c1ba0f939e54e198ad66134523fa3..922b67b46344335df4daad06d332ab973da72fb2 100644 --- a/src/USER-OMP/pair_morse_omp.cpp +++ b/src/USER-OMP/pair_morse_omp.cpp @@ -12,7 +12,7 @@ Contributing author: Axel Kohlmeyer (Temple U) ------------------------------------------------------------------------- */ -#include +#include #include "pair_morse_omp.h" #include "atom.h" #include "comm.h" diff --git a/src/USER-OMP/pair_morse_smooth_linear_omp.cpp b/src/USER-OMP/pair_morse_smooth_linear_omp.cpp index 113f6f2a02d57d081a31c43dbd800c7c330394a4..61cef69c377f3b706d59537c61d123a2640a2c43 100644 --- a/src/USER-OMP/pair_morse_smooth_linear_omp.cpp +++ b/src/USER-OMP/pair_morse_smooth_linear_omp.cpp @@ -13,7 +13,7 @@ Most code borrowed from pair_morse_omp.cpp ------------------------------------------------------------------------- */ -#include +#include #include "pair_morse_smooth_linear_omp.h" #include "atom.h" #include "comm.h" diff --git a/src/USER-OMP/pair_nb3b_harmonic_omp.cpp b/src/USER-OMP/pair_nb3b_harmonic_omp.cpp index 199cbc93371b464c80626eef1b3b9d1438ff9ffa..2ab96c43a0c8d2e6c056365ea771f5a6392d7e30 100644 --- a/src/USER-OMP/pair_nb3b_harmonic_omp.cpp +++ b/src/USER-OMP/pair_nb3b_harmonic_omp.cpp @@ -12,7 +12,7 @@ Contributing author: Axel Kohlmeyer (Temple U) ------------------------------------------------------------------------- */ -#include +#include #include "pair_nb3b_harmonic_omp.h" #include "atom.h" #include "comm.h" diff --git a/src/USER-OMP/pair_nm_cut_coul_cut_omp.cpp b/src/USER-OMP/pair_nm_cut_coul_cut_omp.cpp index 38af84d1f73775b6de427ee960f7d7097c653632..fcbf5dbabbab67f3a8c8117f31e36928d9c911ca 100644 --- a/src/USER-OMP/pair_nm_cut_coul_cut_omp.cpp +++ b/src/USER-OMP/pair_nm_cut_coul_cut_omp.cpp @@ -12,7 +12,7 @@ Contributing author: Axel Kohlmeyer (Temple U) ------------------------------------------------------------------------- */ -#include +#include #include "pair_nm_cut_coul_cut_omp.h" #include "atom.h" #include "comm.h" diff --git a/src/USER-OMP/pair_nm_cut_coul_long_omp.cpp b/src/USER-OMP/pair_nm_cut_coul_long_omp.cpp index bbcdfb26c3c20c377002ae553a1eae47ec8d43c3..b31387dbfe0104fca9e582c6f169be4dab3c0b71 100644 --- a/src/USER-OMP/pair_nm_cut_coul_long_omp.cpp +++ b/src/USER-OMP/pair_nm_cut_coul_long_omp.cpp @@ -12,7 +12,7 @@ Contributing author: Axel Kohlmeyer (Temple U) ------------------------------------------------------------------------- */ -#include +#include #include "pair_nm_cut_coul_long_omp.h" #include "atom.h" #include "comm.h" diff --git a/src/USER-OMP/pair_nm_cut_omp.cpp b/src/USER-OMP/pair_nm_cut_omp.cpp index ea2d0fa7f5c7a368f3c117d1dfe91037e77b0ade..79cd0463114d5291bdcaa4c961f704c7ffe24428 100644 --- a/src/USER-OMP/pair_nm_cut_omp.cpp +++ b/src/USER-OMP/pair_nm_cut_omp.cpp @@ -12,7 +12,7 @@ Contributing author: Axel Kohlmeyer (Temple U) ------------------------------------------------------------------------- */ -#include +#include #include "pair_nm_cut_omp.h" #include "atom.h" #include "comm.h" diff --git a/src/USER-OMP/pair_peri_lps_omp.cpp b/src/USER-OMP/pair_peri_lps_omp.cpp index a471b47750ee7416ee494bee23fefba69554db20..7b174face743fedae1e6e6ef0949e39e4d1d60ee 100644 --- a/src/USER-OMP/pair_peri_lps_omp.cpp +++ b/src/USER-OMP/pair_peri_lps_omp.cpp @@ -12,8 +12,8 @@ Contributing author: Axel Kohlmeyer (Temple U) ------------------------------------------------------------------------- */ -#include -#include +#include +#include #include "pair_peri_lps_omp.h" #include "fix.h" #include "fix_peri_neigh.h" diff --git a/src/USER-OMP/pair_peri_pmb_omp.cpp b/src/USER-OMP/pair_peri_pmb_omp.cpp index 1c14ff753cf8e57820f04642bb0659b9798a960b..8199d8aa47a0d474aa558402b7e462f3c994ec9a 100644 --- a/src/USER-OMP/pair_peri_pmb_omp.cpp +++ b/src/USER-OMP/pair_peri_pmb_omp.cpp @@ -12,8 +12,8 @@ Contributing author: Axel Kohlmeyer (Temple U) ------------------------------------------------------------------------- */ -#include -#include +#include +#include #include "pair_peri_pmb_omp.h" #include "fix.h" #include "fix_peri_neigh.h" diff --git a/src/USER-OMP/pair_resquared_omp.cpp b/src/USER-OMP/pair_resquared_omp.cpp index a1364133d005b1ac51368a0ee4726c12e6c39e58..1736e794f55b7621f29d852e867307581238a38b 100644 --- a/src/USER-OMP/pair_resquared_omp.cpp +++ b/src/USER-OMP/pair_resquared_omp.cpp @@ -12,7 +12,7 @@ Contributing author: Axel Kohlmeyer (Temple U) ------------------------------------------------------------------------- */ -#include +#include #include "pair_resquared_omp.h" #include "math_extra.h" #include "atom.h" diff --git a/src/USER-OMP/pair_soft_omp.cpp b/src/USER-OMP/pair_soft_omp.cpp index 9a926652a853d12a0e2fef51ddfb03c19b889359..a860ad97d96af326aa602bf8dd7c06ee4eea9132 100644 --- a/src/USER-OMP/pair_soft_omp.cpp +++ b/src/USER-OMP/pair_soft_omp.cpp @@ -12,7 +12,7 @@ Contributing author: Axel Kohlmeyer (Temple U) ------------------------------------------------------------------------- */ -#include +#include #include "pair_soft_omp.h" #include "atom.h" #include "comm.h" diff --git a/src/USER-OMP/pair_sw_omp.cpp b/src/USER-OMP/pair_sw_omp.cpp index 9a63b4f4394846b09988a22ab2f55e00cb05d049..e323fc4c373a4882f586297d19b56b9e92e63f11 100644 --- a/src/USER-OMP/pair_sw_omp.cpp +++ b/src/USER-OMP/pair_sw_omp.cpp @@ -12,7 +12,7 @@ Contributing author: Axel Kohlmeyer (Temple U) ------------------------------------------------------------------------- */ -#include +#include #include "pair_sw_omp.h" #include "atom.h" #include "comm.h" diff --git a/src/USER-OMP/pair_table_omp.cpp b/src/USER-OMP/pair_table_omp.cpp index d584061648a2188530003bac065c27a06886c8b9..d27456e1b58f834193924cb70adb64dc5db66d4d 100644 --- a/src/USER-OMP/pair_table_omp.cpp +++ b/src/USER-OMP/pair_table_omp.cpp @@ -12,7 +12,7 @@ Contributing author: Axel Kohlmeyer (Temple U) ------------------------------------------------------------------------- */ -#include +#include #include "pair_table_omp.h" #include "atom.h" #include "comm.h" diff --git a/src/USER-OMP/pair_tersoff_mod_c_omp.cpp b/src/USER-OMP/pair_tersoff_mod_c_omp.cpp index 340eb3ebc5aa1f098cf87c84a87e72ac2f99ce79..fad077ca125a69617372f1b53eac0e2c013adf7e 100644 --- a/src/USER-OMP/pair_tersoff_mod_c_omp.cpp +++ b/src/USER-OMP/pair_tersoff_mod_c_omp.cpp @@ -12,7 +12,7 @@ Contributing author: Axel Kohlmeyer (Temple U) ------------------------------------------------------------------------- */ -#include +#include #include "pair_tersoff_mod_c_omp.h" #include "atom.h" #include "comm.h" diff --git a/src/USER-OMP/pair_tersoff_mod_omp.cpp b/src/USER-OMP/pair_tersoff_mod_omp.cpp index 403a61147beab5136ca5ff773061cb5948aeefcf..04e54c6e698707431c1ed80ae4d8d795a0158fd2 100644 --- a/src/USER-OMP/pair_tersoff_mod_omp.cpp +++ b/src/USER-OMP/pair_tersoff_mod_omp.cpp @@ -12,7 +12,7 @@ Contributing author: Axel Kohlmeyer (Temple U) ------------------------------------------------------------------------- */ -#include +#include #include "pair_tersoff_mod_omp.h" #include "atom.h" #include "comm.h" diff --git a/src/USER-OMP/pair_tersoff_omp.cpp b/src/USER-OMP/pair_tersoff_omp.cpp index db249b4ba907cd3afb78333141b2137a084504ff..a5afdc7509ab4944ad4b3a7e7a46ef70716f2cc0 100644 --- a/src/USER-OMP/pair_tersoff_omp.cpp +++ b/src/USER-OMP/pair_tersoff_omp.cpp @@ -12,7 +12,7 @@ Contributing author: Axel Kohlmeyer (Temple U) ------------------------------------------------------------------------- */ -#include +#include #include "pair_tersoff_omp.h" #include "atom.h" #include "comm.h" diff --git a/src/USER-OMP/pair_tersoff_table_omp.cpp b/src/USER-OMP/pair_tersoff_table_omp.cpp index 9de9ee57086c03d411c83c5be8ec684b6c6f1375..de045f9c622c63de9db428170a476f6543816529 100644 --- a/src/USER-OMP/pair_tersoff_table_omp.cpp +++ b/src/USER-OMP/pair_tersoff_table_omp.cpp @@ -12,7 +12,7 @@ Contributing author: Axel Kohlmeyer (Temple U) ------------------------------------------------------------------------- */ -#include +#include #include "pair_tersoff_table_omp.h" #include "atom.h" #include "comm.h" diff --git a/src/USER-OMP/pair_tersoff_zbl_omp.cpp b/src/USER-OMP/pair_tersoff_zbl_omp.cpp index f53778d1a13fe7d46b1fcfd7659cdc0e52fc1e83..ce3e6fea75320dcae3e5884df13a1b23efd8661f 100644 --- a/src/USER-OMP/pair_tersoff_zbl_omp.cpp +++ b/src/USER-OMP/pair_tersoff_zbl_omp.cpp @@ -16,10 +16,10 @@ David Farrell (NWU) - ZBL addition ------------------------------------------------------------------------- */ -#include -#include -#include -#include +#include +#include +#include +#include #include "pair_tersoff_zbl_omp.h" #include "atom.h" #include "update.h" diff --git a/src/USER-OMP/pair_tip4p_cut_omp.cpp b/src/USER-OMP/pair_tip4p_cut_omp.cpp index c3662ad642a1f1883012e5189d32b09931eef662..85589cf043c231c24f0b4a69092f69d994fc8128 100644 --- a/src/USER-OMP/pair_tip4p_cut_omp.cpp +++ b/src/USER-OMP/pair_tip4p_cut_omp.cpp @@ -12,7 +12,7 @@ Contributing author: Axel Kohlmeyer (Temple U) ------------------------------------------------------------------------- */ -#include +#include #include "pair_tip4p_cut_omp.h" #include "atom.h" #include "domain.h" diff --git a/src/USER-OMP/pair_tip4p_long_omp.cpp b/src/USER-OMP/pair_tip4p_long_omp.cpp index bcd8659a54ce50e2b65a6406954e665fbe5c4801..c6c4bfe5fc953294db71ed8ea5d476e1d3855e0a 100644 --- a/src/USER-OMP/pair_tip4p_long_omp.cpp +++ b/src/USER-OMP/pair_tip4p_long_omp.cpp @@ -12,7 +12,7 @@ Contributing author: Axel Kohlmeyer (Temple U) ------------------------------------------------------------------------- */ -#include +#include #include "pair_tip4p_long_omp.h" #include "atom.h" #include "domain.h" diff --git a/src/USER-OMP/pair_tip4p_long_soft_omp.cpp b/src/USER-OMP/pair_tip4p_long_soft_omp.cpp index 2f16a28b8c00ad5cedd94f84fe859da7c1cd27e8..7e9d3b6dff84c37f556f4ee6980a009bc6f3dc1b 100644 --- a/src/USER-OMP/pair_tip4p_long_soft_omp.cpp +++ b/src/USER-OMP/pair_tip4p_long_soft_omp.cpp @@ -12,7 +12,7 @@ Contributing author: Axel Kohlmeyer (Temple U) ------------------------------------------------------------------------- */ -#include +#include #include "pair_tip4p_long_soft_omp.h" #include "atom.h" #include "domain.h" diff --git a/src/USER-OMP/pair_ufm_omp.cpp b/src/USER-OMP/pair_ufm_omp.cpp index b2e2cd29ee9026a9647bc825ef9dd63a1825dc79..ff258b5b3b8af8404f693c02ce452e2d5917d653 100644 --- a/src/USER-OMP/pair_ufm_omp.cpp +++ b/src/USER-OMP/pair_ufm_omp.cpp @@ -14,7 +14,7 @@ Maurice de Koning (Unicamp/Brazil) - dekoning@ifi.unicamp.br ------------------------------------------------------------------------- */ -#include +#include #include "pair_ufm_omp.h" #include "atom.h" #include "comm.h" diff --git a/src/USER-OMP/pair_vashishta_omp.cpp b/src/USER-OMP/pair_vashishta_omp.cpp index c432738f6239e5079e2298b3055efdf5be0be217..194a3e2d86acb67b99ed0cdab2e644d3b936637b 100644 --- a/src/USER-OMP/pair_vashishta_omp.cpp +++ b/src/USER-OMP/pair_vashishta_omp.cpp @@ -12,7 +12,7 @@ Contributing author: Axel Kohlmeyer (Temple U) ------------------------------------------------------------------------- */ -#include +#include #include "pair_vashishta_omp.h" #include "atom.h" #include "comm.h" diff --git a/src/USER-OMP/pair_vashishta_table_omp.cpp b/src/USER-OMP/pair_vashishta_table_omp.cpp index d2298dca09d1a6bcec326c7eb4638ecd8a2038c2..e0d96d8bb6573a1bf00652996ed62e8fd07c0d3b 100644 --- a/src/USER-OMP/pair_vashishta_table_omp.cpp +++ b/src/USER-OMP/pair_vashishta_table_omp.cpp @@ -12,7 +12,7 @@ Contributing author: Axel Kohlmeyer (Temple U) ------------------------------------------------------------------------- */ -#include +#include #include "pair_vashishta_table_omp.h" #include "atom.h" #include "comm.h" diff --git a/src/USER-OMP/pair_yukawa_colloid_omp.cpp b/src/USER-OMP/pair_yukawa_colloid_omp.cpp index cc05fc91559893e02418f4e902317ebba82117c5..c1d2133a1ca585fc42650f17ae1005ec8a47570b 100644 --- a/src/USER-OMP/pair_yukawa_colloid_omp.cpp +++ b/src/USER-OMP/pair_yukawa_colloid_omp.cpp @@ -12,7 +12,7 @@ Contributing author: Axel Kohlmeyer (Temple U) ------------------------------------------------------------------------- */ -#include +#include #include "pair_yukawa_colloid_omp.h" #include "atom.h" #include "comm.h" diff --git a/src/USER-OMP/pair_yukawa_omp.cpp b/src/USER-OMP/pair_yukawa_omp.cpp index c705446f052710f3468139c9c7dba5fac709e10a..cbfd627f9789bdbfaba49b7c2226ec189b292735 100644 --- a/src/USER-OMP/pair_yukawa_omp.cpp +++ b/src/USER-OMP/pair_yukawa_omp.cpp @@ -12,7 +12,7 @@ Contributing author: Axel Kohlmeyer (Temple U) ------------------------------------------------------------------------- */ -#include +#include #include "pair_yukawa_omp.h" #include "atom.h" #include "comm.h" diff --git a/src/USER-OMP/pair_zbl_omp.cpp b/src/USER-OMP/pair_zbl_omp.cpp index 1d69487eb2d65639993ea0005764e6cc0e3393cd..788679434bd60b28e0dea8e1f5368e2b1936e31d 100644 --- a/src/USER-OMP/pair_zbl_omp.cpp +++ b/src/USER-OMP/pair_zbl_omp.cpp @@ -12,7 +12,7 @@ Contributing author: Axel Kohlmeyer (Temple U) ------------------------------------------------------------------------- */ -#include +#include #include "pair_zbl_omp.h" #include "atom.h" #include "comm.h" diff --git a/src/USER-OMP/pppm_cg_omp.cpp b/src/USER-OMP/pppm_cg_omp.cpp index eb230a3bb479c8314b80b11fab6284ff415f6809..990c50932ea9a5ae86824a35142d0870de233f65 100644 --- a/src/USER-OMP/pppm_cg_omp.cpp +++ b/src/USER-OMP/pppm_cg_omp.cpp @@ -15,6 +15,8 @@ Contributing author: Axel Kohlmeyer (Temple U) ------------------------------------------------------------------------- */ +#include +#include #include "pppm_cg_omp.h" #include "atom.h" #include "comm.h" @@ -27,9 +29,6 @@ #include "math_const.h" #include "math_special.h" -#include -#include - #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 74881c9a8ad75ff7f084e07f291125a31c797ade..97bb909a2c546263d248ba9e62cd4637921b7f7e 100644 --- a/src/USER-OMP/pppm_disp_omp.cpp +++ b/src/USER-OMP/pppm_disp_omp.cpp @@ -16,6 +16,8 @@ Rolf Isele-Holder (RWTH Aachen University) ------------------------------------------------------------------------- */ +#include +#include #include "pppm_disp_omp.h" #include "atom.h" #include "comm.h" @@ -24,9 +26,6 @@ #include "memory.h" #include "math_const.h" -#include -#include - #include "suffix.h" using namespace LAMMPS_NS; using namespace MathConst; @@ -358,7 +357,7 @@ void PPPMDispOMP::particle_map(double dxinv, double dyinv, const int nyhi_out = nyhi_o; const int nzhi_out = nzhi_o; - if (!ISFINITE(boxlo[0]) || !ISFINITE(boxlo[1]) || !ISFINITE(boxlo[2])) + if (!std::isfinite(boxlo[0]) || !std::isfinite(boxlo[1]) || !std::isfinite(boxlo[2])) error->one(FLERR,"Non-numeric box dimensions. Simulation unstable."); int i, flag = 0; diff --git a/src/USER-OMP/pppm_disp_tip4p_omp.cpp b/src/USER-OMP/pppm_disp_tip4p_omp.cpp index 49e3681f6ee63357ca1bab5cebf1a86cd988e3e7..2f7fbbea550f3dcf373a8878d2d2b0ab8eb74820 100644 --- a/src/USER-OMP/pppm_disp_tip4p_omp.cpp +++ b/src/USER-OMP/pppm_disp_tip4p_omp.cpp @@ -15,6 +15,8 @@ Contributing author: Axel Kohlmeyer (Temple U) ------------------------------------------------------------------------- */ +#include +#include #include "pppm_disp_tip4p_omp.h" #include "atom.h" #include "comm.h" @@ -26,9 +28,6 @@ #include "math_const.h" #include "math_special.h" -#include -#include - #include "suffix.h" using namespace LAMMPS_NS; using namespace MathConst; @@ -355,7 +354,7 @@ void PPPMDispTIP4POMP::particle_map_c(double dxinv, double dyinv, const int nyhi_out = nyhi_o; const int nzhi_out = nzhi_o; - if (!ISFINITE(boxlo[0]) || !ISFINITE(boxlo[1]) || !ISFINITE(boxlo[2])) + if (!std::isfinite(boxlo[0]) || !std::isfinite(boxlo[1]) || !std::isfinite(boxlo[2])) error->one(FLERR,"Non-numeric box dimensions - simulation unstable"); int i, flag = 0; diff --git a/src/USER-OMP/pppm_omp.cpp b/src/USER-OMP/pppm_omp.cpp index ef03ef1bba65473739af3404a922a22425655dda..e9c24a000c7727247807ca36a995de47146afb3d 100644 --- a/src/USER-OMP/pppm_omp.cpp +++ b/src/USER-OMP/pppm_omp.cpp @@ -15,6 +15,8 @@ Contributing author: Axel Kohlmeyer (Temple U) ------------------------------------------------------------------------- */ +#include +#include #include "pppm_omp.h" #include "atom.h" #include "comm.h" @@ -26,9 +28,6 @@ #include "math_const.h" #include "math_special.h" -#include -#include - #include "suffix.h" using namespace LAMMPS_NS; using namespace MathConst; diff --git a/src/USER-OMP/pppm_tip4p_omp.cpp b/src/USER-OMP/pppm_tip4p_omp.cpp index f9733ed95b9827430b459e9fc6742bf54a26477a..29966216da633de31c2d92537f778553647bf785 100644 --- a/src/USER-OMP/pppm_tip4p_omp.cpp +++ b/src/USER-OMP/pppm_tip4p_omp.cpp @@ -15,6 +15,8 @@ Contributing author: Axel Kohlmeyer (Temple U) ------------------------------------------------------------------------- */ +#include +#include #include "pppm_tip4p_omp.h" #include "atom.h" #include "comm.h" @@ -26,9 +28,6 @@ #include "math_const.h" #include "math_special.h" -#include -#include - #include "suffix.h" using namespace LAMMPS_NS; using namespace MathConst; @@ -348,7 +347,7 @@ void PPPMTIP4POMP::particle_map() const double boxloz = boxlo[2]; const int nlocal = atom->nlocal; - if (!ISFINITE(boxlo[0]) || !ISFINITE(boxlo[1]) || !ISFINITE(boxlo[2])) + if (!std::isfinite(boxlo[0]) || !std::isfinite(boxlo[1]) || !std::isfinite(boxlo[2])) error->one(FLERR,"Non-numeric box dimensions - simulation unstable"); int i, flag = 0; diff --git a/src/USER-OMP/respa_omp.cpp b/src/USER-OMP/respa_omp.cpp index d4fa529b1c22efbc1d64a69577c86e66a1dbd143..9c8555c66d6d12dfe2c0ca448d3b90a19bc5b332 100644 --- a/src/USER-OMP/respa_omp.cpp +++ b/src/USER-OMP/respa_omp.cpp @@ -15,8 +15,8 @@ Contributing authors: Mark Stevens (SNL), Paul Crozier (SNL) ------------------------------------------------------------------------- */ -#include -#include +#include +#include #include "respa_omp.h" #include "neighbor.h" #include "domain.h" diff --git a/src/USER-OMP/thr_data.cpp b/src/USER-OMP/thr_data.cpp index 9d0b657b302452a290fba1d3437b705823c651c9..612c36053cd9a12b66155fe1d9951106dd6b1f2a 100644 --- a/src/USER-OMP/thr_data.cpp +++ b/src/USER-OMP/thr_data.cpp @@ -16,10 +16,10 @@ per-thread data management for LAMMPS ------------------------------------------------------------------------- */ -#include "thr_data.h" +#include +#include -#include -#include +#include "thr_data.h" #include "memory.h" #include "timer.h" diff --git a/src/USER-OMP/thr_omp.cpp b/src/USER-OMP/thr_omp.cpp index 4eaf09fb9a9568209778131e1ea22ca96502b0cb..22f751e6c0f99fb839632e25e8b72f08d60aacfb 100644 --- a/src/USER-OMP/thr_omp.cpp +++ b/src/USER-OMP/thr_omp.cpp @@ -16,6 +16,8 @@ OpenMP based threading support for LAMMPS ------------------------------------------------------------------------- */ +#include + #include "atom.h" #include "comm.h" #include "error.h" @@ -37,8 +39,6 @@ #include "math_const.h" -#include - using namespace LAMMPS_NS; using namespace MathConst; diff --git a/src/USER-PHONON/Install.sh b/src/USER-PHONON/Install.sh index cfa369bb055ee2679b873535221244839cce9094..3428415443f5bc59c8486dd1e6327a50265c34e4 100644 --- a/src/USER-PHONON/Install.sh +++ b/src/USER-PHONON/Install.sh @@ -26,6 +26,16 @@ action () { fi } +# USER-PHONON uses the parallel FFT wrapper used in PPPM, +# so we must require the KSPACE package to be installed. + +if (test $1 = 1) then + if (test ! -e ../fft3d_wrap.h) then + echo "Must install KSPACE package with USER-PHONON" + exit 1 + fi +fi + # list of files with optional dependcies action fix_phonon.cpp fft3d_wrap.h diff --git a/src/USER-PHONON/fix_phonon.cpp b/src/USER-PHONON/fix_phonon.cpp index a0fa614eca8eba0dec0d404c2c5dbb75ec65d965..3a37c67a3871f1e044ba568e256c8c57a56620c8 100644 --- a/src/USER-PHONON/fix_phonon.cpp +++ b/src/USER-PHONON/fix_phonon.cpp @@ -23,9 +23,9 @@ konglt@sjtu.edu.cn; konglt@gmail.com ------------------------------------------------------------------------- */ -#include -#include -#include +#include +#include +#include #include "fix_phonon.h" #include "fft3d_wrap.h" #include "atom.h" @@ -668,7 +668,8 @@ void FixPhonon::postprocess( ) } // to get Phi = KT.G^-1; normalization of FFTW data is done here - double boltz = force->boltz, kbtsqrt[sysdim], TempAve = 0.; + double boltz = force->boltz, TempAve = 0.; + double *kbtsqrt = new double[sysdim]; double TempFac = inv_neval * inv_nTemp; double NormFac = TempFac * double(ntotal); @@ -692,7 +693,7 @@ void FixPhonon::postprocess( ) MPI_Gatherv(Phi_q[0],mynq*fft_dim2*2,MPI_DOUBLE,Phi_all[0],recvcnts,displs,MPI_DOUBLE,0,world); // to collect all basis info and averaged it on root - double basis_root[fft_dim]; + double *basis_root = new double[fft_dim]; if (fft_dim > sysdim) MPI_Reduce(&basis[1][0], &basis_root[sysdim], fft_dim-sysdim, MPI_DOUBLE, MPI_SUM, 0, world); if (me == 0){ // output dynamic matrix by root @@ -772,7 +773,8 @@ void FixPhonon::postprocess( ) } fflush(flog); } - + delete[] kbtsqrt; + delete[] basis_root; } // end of postprocess /* ---------------------------------------------------------------------- diff --git a/src/USER-QMMM/fix_qmmm.cpp b/src/USER-QMMM/fix_qmmm.cpp index 7fae85f7df4aecfc2b1ed2197388ff14a0f8c82d..f1a34d95380b751e437d052ca13dc25e099856f9 100644 --- a/src/USER-QMMM/fix_qmmm.cpp +++ b/src/USER-QMMM/fix_qmmm.cpp @@ -15,6 +15,8 @@ Contributing author: Axel Kohlmeyer (ICTP) ------------------------------------------------------------------------- */ +#include +#include #include "fix_qmmm.h" #include "atom.h" #include "domain.h" @@ -25,9 +27,6 @@ #include "group.h" #include "memory.h" -#include -#include - #include "libqmmm.h" // message tags for QM/MM inter communicator communication diff --git a/src/USER-QTB/fix_qbmsst.cpp b/src/USER-QTB/fix_qbmsst.cpp index 21ae464e10ede952c5eaf7d0f32ef0adb08b415a..fa5ee75bcb8852fb6ea3e24f229d0ffdd1bb8812 100644 --- a/src/USER-QTB/fix_qbmsst.cpp +++ b/src/USER-QTB/fix_qbmsst.cpp @@ -17,9 +17,9 @@ ------------------------------------------------------------------------- */ #include -#include -#include -#include +#include +#include +#include #include "fix_qbmsst.h" #include "math_extra.h" #include "atom.h" diff --git a/src/USER-QTB/fix_qtb.cpp b/src/USER-QTB/fix_qtb.cpp index 98dd498088ef93d49d7d5a6142ecda88013ed018..7f9a6510bed1d6223d5afa71863f14fb24c91664 100644 --- a/src/USER-QTB/fix_qtb.cpp +++ b/src/USER-QTB/fix_qtb.cpp @@ -17,9 +17,9 @@ ------------------------------------------------------------------------- */ #include -#include -#include -#include +#include +#include +#include #include "fix_qtb.h" #include "math_extra.h" #include "atom.h" diff --git a/src/USER-QUIP/pair_quip.cpp b/src/USER-QUIP/pair_quip.cpp index 6bbbcdb8e62375dac19f5d4b6489ac21e11bccd9..3bf12d19d2ab3217e44bea084f53523706328425 100644 --- a/src/USER-QUIP/pair_quip.cpp +++ b/src/USER-QUIP/pair_quip.cpp @@ -17,10 +17,10 @@ ------------------------------------------------------------------------- */ #include -#include -#include -#include -#include +#include +#include +#include +#include #include "pair_quip.h" #include "atom.h" #include "update.h" @@ -303,7 +303,7 @@ void PairQUIP::init_style() if (force->newton_pair != 1) error->all(FLERR,"Pair style quip requires newton pair on"); - // Initialise neighbour list + // Initialise neighbor list int irequest_full = neighbor->request(this); neighbor->requests[irequest_full]->id = 1; neighbor->requests[irequest_full]->half = 0; diff --git a/src/USER-REAXC/compute_spec_atom.cpp b/src/USER-REAXC/compute_spec_atom.cpp index e913225492a08bcf545f4ed43ba9861a33478022..77b82b3e5514cf75a7e15f3a26f9a01ba2b63a85 100644 --- a/src/USER-REAXC/compute_spec_atom.cpp +++ b/src/USER-REAXC/compute_spec_atom.cpp @@ -11,8 +11,8 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include -#include +#include +#include #include "compute_spec_atom.h" #include "math_extra.h" #include "atom.h" diff --git a/src/USER-REAXC/fix_qeq_reax.cpp b/src/USER-REAXC/fix_qeq_reax.cpp index 326af7505abaf10ccde5f82be949ff7a93e5aff6..a2f4d3d0e936c70674d1340e2c883cbb3a0c79be 100644 --- a/src/USER-REAXC/fix_qeq_reax.cpp +++ b/src/USER-REAXC/fix_qeq_reax.cpp @@ -18,10 +18,10 @@ Hybrid and sub-group capabilities: Ray Shan (Sandia) ------------------------------------------------------------------------- */ -#include -#include -#include -#include +#include +#include +#include +#include #include "fix_qeq_reax.h" #include "pair_reaxc.h" #include "atom.h" diff --git a/src/USER-REAXC/fix_reaxc_bonds.cpp b/src/USER-REAXC/fix_reaxc_bonds.cpp index 09ca132635e83fde5bd95608a37db3fa71838d86..b38d137412b16d18130ed32dcaf82cd0ead7ab94 100644 --- a/src/USER-REAXC/fix_reaxc_bonds.cpp +++ b/src/USER-REAXC/fix_reaxc_bonds.cpp @@ -15,8 +15,8 @@ Contributing author: Ray Shan (Sandia, tnshan@sandia.gov) ------------------------------------------------------------------------- */ -#include -#include +#include +#include #include "fix_ave_atom.h" #include "fix_reaxc_bonds.h" #include "atom.h" diff --git a/src/USER-REAXC/fix_reaxc_bonds.h b/src/USER-REAXC/fix_reaxc_bonds.h index e1dcd82c0e43ed96323668a918dfd9259e05939e..d72f5446b5141a7c701f527cc0f67c1e32524a8e 100644 --- a/src/USER-REAXC/fix_reaxc_bonds.h +++ b/src/USER-REAXC/fix_reaxc_bonds.h @@ -20,7 +20,7 @@ FixStyle(reax/c/bonds,FixReaxCBonds) #ifndef LMP_FIX_REAXC_BONDS_H #define LMP_FIX_REAXC_BONDS_H -#include +#include #include "fix.h" #include "pointers.h" diff --git a/src/USER-REAXC/fix_reaxc_species.cpp b/src/USER-REAXC/fix_reaxc_species.cpp index 181c9bcd31763b1366c311d71d962c0c6367ed22..61b4cebf966592ff2a8a73ce708647d639ac8951 100644 --- a/src/USER-REAXC/fix_reaxc_species.cpp +++ b/src/USER-REAXC/fix_reaxc_species.cpp @@ -16,12 +16,12 @@ Oleg Sergeev (VNIIA, sergeev@vniia.ru) ------------------------------------------------------------------------- */ -#include -#include -#include "atom.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" diff --git a/src/USER-REAXC/reaxc_types.h b/src/USER-REAXC/reaxc_types.h index fb1a9a853a7cc908347813a9d34336a82984a775..2666fcf85c80290f72fdca63921479448f488549 100644 --- a/src/USER-REAXC/reaxc_types.h +++ b/src/USER-REAXC/reaxc_types.h @@ -27,20 +27,20 @@ #ifndef __REAX_TYPES_H_ #define __REAX_TYPES_H_ +#include #include "lmptype.h" -#include -#include -#include -#include -#include -#include -#include "sys/time.h" -#include +#include +#include +#include +#include +#include +#include +#include #include "accelerator_kokkos.h" #if defined LMP_USER_OMP -#define OMP_TIMING 1 +#define OMP_TIMING 0 #ifdef OMP_TIMING // pkcoff timing fields diff --git a/src/USER-SMD/atom_vec_smd.cpp b/src/USER-SMD/atom_vec_smd.cpp index ca38ca7ab5d1b2c6bde35c9468a7cdbcbabac6cb..e99f3c51694eb609944461f44a495bca88187e1e 100644 --- a/src/USER-SMD/atom_vec_smd.cpp +++ b/src/USER-SMD/atom_vec_smd.cpp @@ -22,9 +22,9 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include -#include -#include +#include +#include +#include #include "atom_vec_smd.h" #include "atom.h" #include "comm.h" diff --git a/src/USER-SMD/compute_smd_contact_radius.cpp b/src/USER-SMD/compute_smd_contact_radius.cpp index 991b1a2e674316d4b832aafaa60d620e40e8012d..8193ad6ccf4cf1e92c3875ed8276e1ad0cfb010b 100644 --- a/src/USER-SMD/compute_smd_contact_radius.cpp +++ b/src/USER-SMD/compute_smd_contact_radius.cpp @@ -23,7 +23,7 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include +#include #include "compute_smd_contact_radius.h" #include "atom.h" #include "update.h" diff --git a/src/USER-SMD/compute_smd_damage.cpp b/src/USER-SMD/compute_smd_damage.cpp index 7cb4d2b4b8dac1608091c72789d4456b404641d7..9603fd5c64c299ef1c89a48e66da913913328d2e 100644 --- a/src/USER-SMD/compute_smd_damage.cpp +++ b/src/USER-SMD/compute_smd_damage.cpp @@ -23,7 +23,7 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include +#include #include "compute_smd_damage.h" #include "atom.h" #include "update.h" diff --git a/src/USER-SMD/compute_smd_hourglass_error.cpp b/src/USER-SMD/compute_smd_hourglass_error.cpp index 1502f7ccb5ab8aa6d73840788d1c0f20c86cde7e..3b6b9000048b84ec3637e3325d27c9f58b34ce11 100644 --- a/src/USER-SMD/compute_smd_hourglass_error.cpp +++ b/src/USER-SMD/compute_smd_hourglass_error.cpp @@ -23,7 +23,7 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include +#include #include "compute_smd_hourglass_error.h" #include "atom.h" #include "update.h" diff --git a/src/USER-SMD/compute_smd_internal_energy.cpp b/src/USER-SMD/compute_smd_internal_energy.cpp index aabaa8906cb1bf8c7ca5a2be75f9963d98230af2..d937aa98a42a1d3e1079fd54b9bfe36ec5a98ec4 100644 --- a/src/USER-SMD/compute_smd_internal_energy.cpp +++ b/src/USER-SMD/compute_smd_internal_energy.cpp @@ -23,7 +23,7 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include +#include #include "compute_smd_internal_energy.h" #include "atom.h" #include "update.h" diff --git a/src/USER-SMD/compute_smd_plastic_strain.cpp b/src/USER-SMD/compute_smd_plastic_strain.cpp index 86a5c6329f3a351e51f880473b7443dfb6446416..67466ebb72cd97ea1769d81849fdc56de5457c88 100644 --- a/src/USER-SMD/compute_smd_plastic_strain.cpp +++ b/src/USER-SMD/compute_smd_plastic_strain.cpp @@ -23,7 +23,7 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include +#include #include "compute_smd_plastic_strain.h" #include "atom.h" #include "update.h" diff --git a/src/USER-SMD/compute_smd_plastic_strain_rate.cpp b/src/USER-SMD/compute_smd_plastic_strain_rate.cpp index 899e456c8883623f2812de8a207dadb60e69d2e9..20dfa64edd2c3762c067c54799a70746d5727354 100644 --- a/src/USER-SMD/compute_smd_plastic_strain_rate.cpp +++ b/src/USER-SMD/compute_smd_plastic_strain_rate.cpp @@ -23,7 +23,7 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include +#include #include "compute_smd_plastic_strain_rate.h" #include "atom.h" #include "update.h" diff --git a/src/USER-SMD/compute_smd_rho.cpp b/src/USER-SMD/compute_smd_rho.cpp index cb97755aca6c8547c73027696adddca12414ffba..5c78e604b6639428ca6d088a19e661ac28c6d5a1 100644 --- a/src/USER-SMD/compute_smd_rho.cpp +++ b/src/USER-SMD/compute_smd_rho.cpp @@ -22,7 +22,7 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include +#include #include "compute_smd_rho.h" #include "atom.h" #include "update.h" diff --git a/src/USER-SMD/compute_smd_tlsph_defgrad.cpp b/src/USER-SMD/compute_smd_tlsph_defgrad.cpp index 3ba66a656c6f3224960d0d1d6cfe366c5f1e3343..37ad78dcea2a532af82fc097307328a585e3366d 100644 --- a/src/USER-SMD/compute_smd_tlsph_defgrad.cpp +++ b/src/USER-SMD/compute_smd_tlsph_defgrad.cpp @@ -22,7 +22,11 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include +#include +#include +#include +#include +#include #include "compute_smd_tlsph_defgrad.h" #include "atom.h" #include "update.h" @@ -32,11 +36,6 @@ #include "memory.h" #include "error.h" #include "pair.h" -#include -#include -#include -#include -#include using namespace Eigen; using namespace std; using namespace LAMMPS_NS; diff --git a/src/USER-SMD/compute_smd_tlsph_dt.cpp b/src/USER-SMD/compute_smd_tlsph_dt.cpp index 6d573775fa2cf6d773bea02e44038603d200bcc2..7752436b8a40f67734d5e4596aec3fc0800e5545 100644 --- a/src/USER-SMD/compute_smd_tlsph_dt.cpp +++ b/src/USER-SMD/compute_smd_tlsph_dt.cpp @@ -22,7 +22,7 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include +#include #include "compute_smd_tlsph_dt.h" #include "atom.h" #include "update.h" diff --git a/src/USER-SMD/compute_smd_tlsph_num_neighs.cpp b/src/USER-SMD/compute_smd_tlsph_num_neighs.cpp index d0df4ff3d7051d74874ef6c2b50901126321ef39..347b1384123b180570ec2e48692f633c3692db19 100644 --- a/src/USER-SMD/compute_smd_tlsph_num_neighs.cpp +++ b/src/USER-SMD/compute_smd_tlsph_num_neighs.cpp @@ -23,7 +23,7 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include +#include #include "compute_smd_tlsph_num_neighs.h" #include "atom.h" #include "update.h" diff --git a/src/USER-SMD/compute_smd_tlsph_shape.cpp b/src/USER-SMD/compute_smd_tlsph_shape.cpp index d9dc070f6b67c4f061a9cf2c7920ff337ad563a6..bbab274b5cca0dd4d785ea0be2044df1e6c2cef9 100644 --- a/src/USER-SMD/compute_smd_tlsph_shape.cpp +++ b/src/USER-SMD/compute_smd_tlsph_shape.cpp @@ -22,7 +22,12 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include +#include +#include +#include +#include +#include +#include #include "compute_smd_tlsph_shape.h" #include "atom.h" #include "update.h" @@ -32,12 +37,7 @@ #include "memory.h" #include "error.h" #include "pair.h" -#include -#include -#include -#include -#include -#include + using namespace Eigen; using namespace std; using namespace LAMMPS_NS; diff --git a/src/USER-SMD/compute_smd_tlsph_strain.cpp b/src/USER-SMD/compute_smd_tlsph_strain.cpp index ea137d5b2a718253b8f528891fe8d42fa186b574..a94a3cd51158defab103323d007c7662efafbeac 100644 --- a/src/USER-SMD/compute_smd_tlsph_strain.cpp +++ b/src/USER-SMD/compute_smd_tlsph_strain.cpp @@ -23,7 +23,11 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include +#include +#include +#include +#include +#include #include "compute_smd_tlsph_strain.h" #include "atom.h" #include "update.h" @@ -33,11 +37,7 @@ #include "memory.h" #include "error.h" #include "pair.h" -#include -#include -#include -#include -#include + using namespace Eigen; using namespace std; using namespace LAMMPS_NS; diff --git a/src/USER-SMD/compute_smd_tlsph_strain_rate.cpp b/src/USER-SMD/compute_smd_tlsph_strain_rate.cpp index ed3525f4ad2c934d9b9191b8de903f525147ea80..895a973f6a1863c4faacbe59aa33d8fd18044211 100644 --- a/src/USER-SMD/compute_smd_tlsph_strain_rate.cpp +++ b/src/USER-SMD/compute_smd_tlsph_strain_rate.cpp @@ -23,7 +23,8 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include +#include +#include #include "compute_smd_tlsph_strain_rate.h" #include "atom.h" #include "update.h" @@ -33,7 +34,7 @@ #include "memory.h" #include "error.h" #include "pair.h" -#include + using namespace Eigen; using namespace LAMMPS_NS; diff --git a/src/USER-SMD/compute_smd_tlsph_stress.cpp b/src/USER-SMD/compute_smd_tlsph_stress.cpp index cbcb4c45af60454e3d0afecccf7c85246d7ced3f..a54b07dd1ef5b007c9f7d9ede03bd6b8b6583c67 100644 --- a/src/USER-SMD/compute_smd_tlsph_stress.cpp +++ b/src/USER-SMD/compute_smd_tlsph_stress.cpp @@ -22,7 +22,8 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include +#include +#include #include "compute_smd_tlsph_stress.h" #include "atom.h" #include "update.h" @@ -32,7 +33,7 @@ #include "memory.h" #include "error.h" #include "pair.h" -#include + using namespace Eigen; using namespace LAMMPS_NS; diff --git a/src/USER-SMD/compute_smd_triangle_mesh_vertices.cpp b/src/USER-SMD/compute_smd_triangle_mesh_vertices.cpp index e43dadb47ad99ba7652589710e5c32e9727835fb..67ec27778a692008a870b3af3728b0cfdcebfced 100644 --- a/src/USER-SMD/compute_smd_triangle_mesh_vertices.cpp +++ b/src/USER-SMD/compute_smd_triangle_mesh_vertices.cpp @@ -23,7 +23,11 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include +#include +#include +#include +#include +#include #include "compute_smd_triangle_mesh_vertices.h" #include "atom.h" #include "update.h" @@ -33,11 +37,7 @@ #include "memory.h" #include "error.h" #include "pair.h" -#include -#include -#include -#include -#include + using namespace Eigen; using namespace std; using namespace LAMMPS_NS; diff --git a/src/USER-SMD/compute_smd_ulsph_effm.cpp b/src/USER-SMD/compute_smd_ulsph_effm.cpp index 9453d8cfa6a5cd474f85843adeef44d53cb19207..fc8637bbf01506114b0602d525fd52a79260458d 100644 --- a/src/USER-SMD/compute_smd_ulsph_effm.cpp +++ b/src/USER-SMD/compute_smd_ulsph_effm.cpp @@ -22,7 +22,7 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include +#include #include "compute_smd_ulsph_effm.h" #include "atom.h" #include "update.h" diff --git a/src/USER-SMD/compute_smd_ulsph_num_neighs.cpp b/src/USER-SMD/compute_smd_ulsph_num_neighs.cpp index efe6bba47ea16232af896ddd45092e75f682f69e..4ef339db9812d91ac32eb85187612c263eba1300 100644 --- a/src/USER-SMD/compute_smd_ulsph_num_neighs.cpp +++ b/src/USER-SMD/compute_smd_ulsph_num_neighs.cpp @@ -23,7 +23,7 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include +#include #include "compute_smd_ulsph_num_neighs.h" #include "atom.h" #include "update.h" diff --git a/src/USER-SMD/compute_smd_ulsph_strain.cpp b/src/USER-SMD/compute_smd_ulsph_strain.cpp index c7fcc909f37b71da4a97cc67e7e52d8e20481d11..89b85f7bc1cafc299fc45b55a5c88f5757b3d616 100644 --- a/src/USER-SMD/compute_smd_ulsph_strain.cpp +++ b/src/USER-SMD/compute_smd_ulsph_strain.cpp @@ -23,7 +23,11 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include +#include +#include +#include +#include +#include #include "compute_smd_ulsph_strain.h" #include "atom.h" #include "update.h" @@ -33,11 +37,7 @@ #include "memory.h" #include "error.h" #include "pair.h" -#include -#include -#include -#include -#include + using namespace Eigen; using namespace std; using namespace LAMMPS_NS; diff --git a/src/USER-SMD/compute_smd_ulsph_strain_rate.cpp b/src/USER-SMD/compute_smd_ulsph_strain_rate.cpp index 0d472a368a0830bedf7861ebe4dfce384ea9719c..f5ff4fef98fc6ec308855be74c635b4d03465c87 100644 --- a/src/USER-SMD/compute_smd_ulsph_strain_rate.cpp +++ b/src/USER-SMD/compute_smd_ulsph_strain_rate.cpp @@ -22,7 +22,8 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include +#include +#include #include "compute_smd_ulsph_strain_rate.h" #include "atom.h" #include "update.h" @@ -32,7 +33,7 @@ #include "memory.h" #include "error.h" #include "pair.h" -#include + using namespace Eigen; 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 7069feced3f7e7801ec459b70d0909654c4c6987..7f1bbc4c29fadf300623ae243ae0ed97047ec220 100644 --- a/src/USER-SMD/compute_smd_ulsph_stress.cpp +++ b/src/USER-SMD/compute_smd_ulsph_stress.cpp @@ -22,7 +22,8 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include +#include +#include #include "compute_smd_ulsph_stress.h" #include "atom.h" #include "update.h" @@ -32,7 +33,7 @@ #include "memory.h" #include "error.h" #include "pair.h" -#include + using namespace Eigen; using namespace LAMMPS_NS; diff --git a/src/USER-SMD/compute_smd_vol.cpp b/src/USER-SMD/compute_smd_vol.cpp index 3573ee6a6cc8d4b09c8dd53a21a0c8b3ecb9dd9d..17a6b556e8ac352eab0703e4d19744d51933905d 100644 --- a/src/USER-SMD/compute_smd_vol.cpp +++ b/src/USER-SMD/compute_smd_vol.cpp @@ -22,7 +22,7 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include +#include #include "compute_smd_vol.h" #include "atom.h" #include "update.h" diff --git a/src/USER-SMD/fix_smd_adjust_dt.cpp b/src/USER-SMD/fix_smd_adjust_dt.cpp index d2570b6bdc3f1b64a482732b45b1f26945e06f0e..3685248d5e556fa7aa08f09b1f5fa42d252e08e7 100644 --- a/src/USER-SMD/fix_smd_adjust_dt.cpp +++ b/src/USER-SMD/fix_smd_adjust_dt.cpp @@ -22,9 +22,9 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include -#include -#include +#include +#include +#include #include "fix_smd_adjust_dt.h" #include "atom.h" #include "update.h" diff --git a/src/USER-SMD/fix_smd_integrate_tlsph.cpp b/src/USER-SMD/fix_smd_integrate_tlsph.cpp index 2744211d87d8f3045741fe73dda514cff6d84c1e..4668e673fca68d72dd4c1ece19fecacc8ed94228 100644 --- a/src/USER-SMD/fix_smd_integrate_tlsph.cpp +++ b/src/USER-SMD/fix_smd_integrate_tlsph.cpp @@ -22,9 +22,11 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include -#include -#include +#include +#include +#include +#include +#include #include "fix_smd_integrate_tlsph.h" #include "atom.h" #include "force.h" @@ -32,13 +34,10 @@ #include "error.h" #include "pair.h" #include "neigh_list.h" -#include #include "domain.h" #include "neighbor.h" #include "comm.h" #include "modify.h" -#include -#include 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 9b892bf25976f5507663c9171a3616ddfdcf7a64..a145deeb61ce90733aafd5d54c32d1aadaca5dd5 100644 --- a/src/USER-SMD/fix_smd_integrate_ulsph.cpp +++ b/src/USER-SMD/fix_smd_integrate_ulsph.cpp @@ -22,12 +22,12 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include -#include +#include +#include +#include +#include +#include #include "fix_smd_integrate_ulsph.h" -#include -#include -#include #include "atom.h" #include "comm.h" #include "force.h" @@ -41,7 +41,6 @@ #include "error.h" #include "pair.h" #include "domain.h" -#include using namespace Eigen; using namespace LAMMPS_NS; diff --git a/src/USER-SMD/fix_smd_integrate_ulsph.h b/src/USER-SMD/fix_smd_integrate_ulsph.h index ea4f46ce530ea0d40606c1c3aa157707f2a91e5a..9d954bf529aaf00ddf1df307d7f3a0b1d012538f 100644 --- a/src/USER-SMD/fix_smd_integrate_ulsph.h +++ b/src/USER-SMD/fix_smd_integrate_ulsph.h @@ -48,7 +48,7 @@ class FixSMDIntegrateUlsph : public Fix { private: class NeighList *list; protected: - double dtv,dtf, vlimit, vlimitsq;; + double dtv,dtf, vlimit, vlimitsq; int mass_require; bool xsphFlag; bool adjust_radius_flag; diff --git a/src/USER-SMD/fix_smd_move_triangulated_surface.cpp b/src/USER-SMD/fix_smd_move_triangulated_surface.cpp index d8a0bda4d07629f49980c61d6aab84c17cf80cd3..d4afbe0535e4445709914d7ea71a9d1867a1eee5 100644 --- a/src/USER-SMD/fix_smd_move_triangulated_surface.cpp +++ b/src/USER-SMD/fix_smd_move_triangulated_surface.cpp @@ -22,12 +22,12 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include -#include +#include +#include +#include +#include +#include #include "fix_smd_move_triangulated_surface.h" -#include -#include -#include #include "atom.h" #include "comm.h" #include "force.h" @@ -41,7 +41,6 @@ #include "error.h" #include "pair.h" #include "domain.h" -#include #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 0c2dc31f45269af6abdcde5981003724c81c8719..5e7cdbad3807dc15e1a535bb81b6db24d331ced8 100644 --- a/src/USER-SMD/fix_smd_setvel.cpp +++ b/src/USER-SMD/fix_smd_setvel.cpp @@ -23,8 +23,8 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include -#include +#include +#include #include "fix_smd_setvel.h" #include "atom.h" #include "update.h" diff --git a/src/USER-SMD/fix_smd_tlsph_reference_configuration.cpp b/src/USER-SMD/fix_smd_tlsph_reference_configuration.cpp index da0533c88bcbb15e0adc56a6345558823ad91bed..3e2812aa12e29a1f3e6d57ff3867d987676b361c 100644 --- a/src/USER-SMD/fix_smd_tlsph_reference_configuration.cpp +++ b/src/USER-SMD/fix_smd_tlsph_reference_configuration.cpp @@ -24,15 +24,16 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include "lattice.h" #include -#include -#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" @@ -40,7 +41,6 @@ #include "memory.h" #include "error.h" #include "domain.h" -#include #include "smd_kernels.h" #include "smd_math.h" diff --git a/src/USER-SMD/fix_smd_wall_surface.cpp b/src/USER-SMD/fix_smd_wall_surface.cpp index 53232af0012af87ad8e813c8fbddaea59dcdb333..4bd5078cb86558a8699d953a2c8cf79afd24af87 100644 --- a/src/USER-SMD/fix_smd_wall_surface.cpp +++ b/src/USER-SMD/fix_smd_wall_surface.cpp @@ -15,7 +15,10 @@ Contributing authors: Mike Parks (SNL), Ezwanur Rahman, J.T. Foster (UTSA) ------------------------------------------------------------------------- */ -#include +#include +#include +#include +#include #include "fix_smd_wall_surface.h" #include "atom.h" #include "domain.h" @@ -29,10 +32,7 @@ #include "lattice.h" #include "memory.h" #include "error.h" -#include -#include #include "atom_vec.h" -#include using namespace LAMMPS_NS; using namespace FixConst; diff --git a/src/USER-SMD/pair_smd_hertz.cpp b/src/USER-SMD/pair_smd_hertz.cpp index 9b2638296587fd714cc562f898b25668fcae8379..815db4a4508a297d779a8a4499f21aa073fa17d4 100644 --- a/src/USER-SMD/pair_smd_hertz.cpp +++ b/src/USER-SMD/pair_smd_hertz.cpp @@ -26,10 +26,10 @@ Contributing author: Mike Parks (SNL) ------------------------------------------------------------------------- */ -#include -#include -#include -#include +#include +#include +#include +#include #include "pair_smd_hertz.h" #include "atom.h" #include "domain.h" diff --git a/src/USER-SMD/pair_smd_tlsph.cpp b/src/USER-SMD/pair_smd_tlsph.cpp index 1a600b393e933e6abd431bb8740aa3dc31917ca1..4dd16c4d83a4ee212491da430dc37f34fe49b751 100644 --- a/src/USER-SMD/pair_smd_tlsph.cpp +++ b/src/USER-SMD/pair_smd_tlsph.cpp @@ -22,15 +22,19 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include "group.h" -#include -#include -#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" +#include "group.h" #include "force.h" #include "update.h" #include "modify.h" @@ -41,15 +45,12 @@ #include "neigh_request.h" #include "memory.h" #include "error.h" -#include -#include #include "math_special.h" -#include #include "update.h" -#include #include "smd_material_models.h" #include "smd_kernels.h" #include "smd_math.h" + using namespace SMD_Kernels; using namespace Eigen; using namespace std; diff --git a/src/USER-SMD/pair_smd_triangulated_surface.cpp b/src/USER-SMD/pair_smd_triangulated_surface.cpp index a62e262b7ac0036fdb33d1095b3ce34957ce228c..b8bff7e799948c73a47ecc71c44da5c15e068dd3 100644 --- a/src/USER-SMD/pair_smd_triangulated_surface.cpp +++ b/src/USER-SMD/pair_smd_triangulated_surface.cpp @@ -26,10 +26,13 @@ Contributing author: Mike Parks (SNL) ------------------------------------------------------------------------- */ -#include -#include -#include -#include +#include +#include +#include +#include +#include +#include +#include #include "pair_smd_triangulated_surface.h" #include "atom.h" #include "domain.h" @@ -43,9 +46,6 @@ #include "neigh_request.h" #include "memory.h" #include "error.h" -#include -#include -#include using namespace std; using namespace LAMMPS_NS; diff --git a/src/USER-SMD/pair_smd_ulsph.cpp b/src/USER-SMD/pair_smd_ulsph.cpp index fcb5e7eeb0689ae785ca17f7ef2c19523f8699a7..96eb912faec26a2e7b18a888eebd359f68771fa2 100644 --- a/src/USER-SMD/pair_smd_ulsph.cpp +++ b/src/USER-SMD/pair_smd_ulsph.cpp @@ -22,10 +22,12 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include -#include -#include -#include +#include +#include +#include +#include +#include +#include #include "pair_smd_ulsph.h" #include "atom.h" #include "domain.h" @@ -39,8 +41,6 @@ #include "neigh_request.h" #include "memory.h" #include "error.h" -#include -#include #include "smd_material_models.h" #include "smd_math.h" #include "smd_kernels.h" diff --git a/src/USER-SMD/smd_material_models.cpp b/src/USER-SMD/smd_material_models.cpp index 93228f3724d816c0ff1ff041bbabc5bef074fe5e..e3deb199b650be86b37fc7998152a57cfa6c22e1 100644 --- a/src/USER-SMD/smd_material_models.cpp +++ b/src/USER-SMD/smd_material_models.cpp @@ -22,8 +22,8 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ #include +#include #include "math_special.h" -#include #include diff --git a/src/USER-SMTBQ/pair_smtbq.cpp b/src/USER-SMTBQ/pair_smtbq.cpp index 937b9e511736e6e4bbadc7f8d66f251383daa2d0..1028d8a8972117568e8670f101296a1db25703db 100644 --- a/src/USER-SMTBQ/pair_smtbq.cpp +++ b/src/USER-SMTBQ/pair_smtbq.cpp @@ -38,10 +38,10 @@ . ------------------------------------------------------------------------- */ -#include -#include -#include -#include +#include +#include +#include +#include #include "pair_smtbq.h" #include "atom.h" #include "comm.h" diff --git a/src/USER-SPH/atom_vec_meso.cpp b/src/USER-SPH/atom_vec_meso.cpp index daa7c10740d66c608e4d331f9fb11bd421eebc51..7dc6c6f7bd9382fa85496d96a448979751743d4e 100644 --- a/src/USER-SPH/atom_vec_meso.cpp +++ b/src/USER-SPH/atom_vec_meso.cpp @@ -11,8 +11,8 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include -#include +#include +#include #include "atom_vec_meso.h" #include "atom.h" #include "comm.h" diff --git a/src/USER-SPH/compute_meso_e_atom.cpp b/src/USER-SPH/compute_meso_e_atom.cpp index dc8d0b55ad32f32d27f1bb14da002cfe57b359ec..e39dee2b5fb83e883e1bb8e4e8ff02892399d29a 100644 --- a/src/USER-SPH/compute_meso_e_atom.cpp +++ b/src/USER-SPH/compute_meso_e_atom.cpp @@ -11,7 +11,7 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include +#include #include "compute_meso_e_atom.h" #include "atom.h" #include "update.h" diff --git a/src/USER-SPH/compute_meso_rho_atom.cpp b/src/USER-SPH/compute_meso_rho_atom.cpp index 9b4da8b339f55b53b07bcc0b4de11fa1b1098287..eeb3f987bc7d82aad15a09a11b7cb3532e0ce8c3 100644 --- a/src/USER-SPH/compute_meso_rho_atom.cpp +++ b/src/USER-SPH/compute_meso_rho_atom.cpp @@ -11,7 +11,7 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include +#include #include "compute_meso_rho_atom.h" #include "atom.h" #include "update.h" diff --git a/src/USER-SPH/compute_meso_t_atom.cpp b/src/USER-SPH/compute_meso_t_atom.cpp index d901f73eff5feaba1490d349e6c3757e26113b69..dc4f3407f143ff7c75acdcee7ea7290aacf41503 100644 --- a/src/USER-SPH/compute_meso_t_atom.cpp +++ b/src/USER-SPH/compute_meso_t_atom.cpp @@ -11,7 +11,7 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include +#include #include "compute_meso_t_atom.h" #include "atom.h" #include "update.h" diff --git a/src/USER-SPH/fix_meso.cpp b/src/USER-SPH/fix_meso.cpp index 665c9e0f3f866413924e617ee6b45f988daf5b9f..d7a5d81517600583101303174793d37f29ec27ae 100644 --- a/src/USER-SPH/fix_meso.cpp +++ b/src/USER-SPH/fix_meso.cpp @@ -11,12 +11,11 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include -#include +#include +#include +#include +#include #include "fix_meso.h" -#include -#include -#include #include "atom.h" #include "comm.h" #include "force.h" diff --git a/src/USER-SPH/fix_meso_stationary.cpp b/src/USER-SPH/fix_meso_stationary.cpp index 0607f2f3d0f51d9ff58548ca36dae65be937bd38..f5fc306320d1951078cd122500705898a30f6262 100644 --- a/src/USER-SPH/fix_meso_stationary.cpp +++ b/src/USER-SPH/fix_meso_stationary.cpp @@ -11,12 +11,11 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include -#include +#include +#include +#include +#include #include "fix_meso_stationary.h" -#include -#include -#include #include "atom.h" #include "comm.h" #include "force.h" diff --git a/src/USER-SPH/pair_sph_heatconduction.cpp b/src/USER-SPH/pair_sph_heatconduction.cpp index 02e667e437a2d2ff96c1f85600273954dff5af62..6f0cf7eca2f734b4e19bb3c69246aeae71996874 100644 --- a/src/USER-SPH/pair_sph_heatconduction.cpp +++ b/src/USER-SPH/pair_sph_heatconduction.cpp @@ -11,8 +11,8 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include -#include +#include +#include #include "pair_sph_heatconduction.h" #include "atom.h" #include "force.h" diff --git a/src/USER-SPH/pair_sph_idealgas.cpp b/src/USER-SPH/pair_sph_idealgas.cpp index 2ba0d9bfbe6a970bcffd36e17aa412e7d9df0e4f..99fba05917ae35dbf71836cf10c5c568c10a5278 100644 --- a/src/USER-SPH/pair_sph_idealgas.cpp +++ b/src/USER-SPH/pair_sph_idealgas.cpp @@ -11,8 +11,8 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include -#include +#include +#include #include "pair_sph_idealgas.h" #include "atom.h" #include "force.h" diff --git a/src/USER-SPH/pair_sph_lj.cpp b/src/USER-SPH/pair_sph_lj.cpp index 98752ac126aa6385c3bb1bc4f2df5b91d34d73bd..5cefdf87c43645e32be21de131ce1d8ec2046ee7 100644 --- a/src/USER-SPH/pair_sph_lj.cpp +++ b/src/USER-SPH/pair_sph_lj.cpp @@ -11,8 +11,8 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include -#include +#include +#include #include "pair_sph_lj.h" #include "atom.h" #include "force.h" diff --git a/src/USER-SPH/pair_sph_rhosum.cpp b/src/USER-SPH/pair_sph_rhosum.cpp index 4bff0ec27c6e75e33e904627d06c6336581a3627..605187d3a733115254fe3a74967442c63de0afa2 100644 --- a/src/USER-SPH/pair_sph_rhosum.cpp +++ b/src/USER-SPH/pair_sph_rhosum.cpp @@ -11,8 +11,8 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include -#include +#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 b1887c6164ac1e0d9528c8fec71d864a447d5e2c..00500b940de1803c47982e2b4936ddbd005cc915 100644 --- a/src/USER-SPH/pair_sph_taitwater.cpp +++ b/src/USER-SPH/pair_sph_taitwater.cpp @@ -11,8 +11,8 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include -#include +#include +#include #include "pair_sph_taitwater.h" #include "atom.h" #include "force.h" diff --git a/src/USER-SPH/pair_sph_taitwater_morris.cpp b/src/USER-SPH/pair_sph_taitwater_morris.cpp index 76b538e46bd38fb0037a412ae2203adaa15f0d98..80607cb333b2cd882c1b276c703e4c5d173c9b94 100644 --- a/src/USER-SPH/pair_sph_taitwater_morris.cpp +++ b/src/USER-SPH/pair_sph_taitwater_morris.cpp @@ -11,8 +11,8 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include -#include +#include +#include #include "pair_sph_taitwater_morris.h" #include "atom.h" #include "force.h" diff --git a/src/USER-TALLY/compute_force_tally.cpp b/src/USER-TALLY/compute_force_tally.cpp index 3ec6c188fc385026ce3fd93383fa87e38559b15f..0ec1d332a4ea91daf86330f7c51e33e980bc1553 100644 --- a/src/USER-TALLY/compute_force_tally.cpp +++ b/src/USER-TALLY/compute_force_tally.cpp @@ -11,8 +11,8 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include -#include +#include +#include #include "compute_force_tally.h" #include "atom.h" #include "group.h" diff --git a/src/USER-TALLY/compute_heat_flux_tally.cpp b/src/USER-TALLY/compute_heat_flux_tally.cpp index 43b663b27a580495943b5d4835650ae01811b0cd..f8db92a730e320905d488e45d74c26ab1636d836 100644 --- a/src/USER-TALLY/compute_heat_flux_tally.cpp +++ b/src/USER-TALLY/compute_heat_flux_tally.cpp @@ -11,7 +11,7 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include +#include #include "compute_heat_flux_tally.h" #include "atom.h" #include "group.h" diff --git a/src/USER-TALLY/compute_pe_mol_tally.cpp b/src/USER-TALLY/compute_pe_mol_tally.cpp index 0328740e0395bc6ca7914ee8d7b7b88e212e0000..264ddca270af4f7956b50ceb2da75ec380c57295 100644 --- a/src/USER-TALLY/compute_pe_mol_tally.cpp +++ b/src/USER-TALLY/compute_pe_mol_tally.cpp @@ -11,7 +11,7 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include +#include #include "compute_pe_mol_tally.h" #include "atom.h" #include "group.h" diff --git a/src/USER-TALLY/compute_pe_tally.cpp b/src/USER-TALLY/compute_pe_tally.cpp index caa4cf134a89dd10d73169eae5ba02510a8bf2dd..3031915ebe54f76c51d409b36455cdccee9bdff0 100644 --- a/src/USER-TALLY/compute_pe_tally.cpp +++ b/src/USER-TALLY/compute_pe_tally.cpp @@ -11,7 +11,7 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include +#include #include "compute_pe_tally.h" #include "atom.h" #include "group.h" diff --git a/src/USER-TALLY/compute_stress_tally.cpp b/src/USER-TALLY/compute_stress_tally.cpp index e44313d695c46959b87ddb89bbf50ec99078bd7c..8ed40ae8e24dad64c313563f5c157f8f7d0794cf 100644 --- a/src/USER-TALLY/compute_stress_tally.cpp +++ b/src/USER-TALLY/compute_stress_tally.cpp @@ -11,7 +11,7 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include +#include #include "compute_stress_tally.h" #include "atom.h" #include "group.h" diff --git a/src/USER-UEF/compute_pressure_uef.cpp b/src/USER-UEF/compute_pressure_uef.cpp index 43054d7d3f9652f1770361596fa8c62d954ff898..8b6285304228970aaceb014bee9446990703ecad 100644 --- a/src/USER-UEF/compute_pressure_uef.cpp +++ b/src/USER-UEF/compute_pressure_uef.cpp @@ -14,8 +14,8 @@ ------------------------------------------------------------------------- */ #include -#include -#include +#include +#include #include "compute_pressure_uef.h" #include "fix_nh_uef.h" #include "update.h" diff --git a/src/USER-UEF/compute_temp_uef.cpp b/src/USER-UEF/compute_temp_uef.cpp index 605552405611711327b9fd0a7409b7edbec70eca..999296ec7e73f54bcb664cd6bc1492826ed4ce0c 100644 --- a/src/USER-UEF/compute_temp_uef.cpp +++ b/src/USER-UEF/compute_temp_uef.cpp @@ -13,8 +13,8 @@ Contributing author: David Nicholson (MIT) ------------------------------------------------------------------------- */ -#include -#include +#include +#include #include "compute_temp_uef.h" #include "fix_nh_uef.h" #include "update.h" diff --git a/src/USER-UEF/dump_cfg_uef.cpp b/src/USER-UEF/dump_cfg_uef.cpp index 4b0c08275a62a7bb78132fd2ab6a138a0670d11d..f5f78297c2910877fcc5564f8db778426183a553 100644 --- a/src/USER-UEF/dump_cfg_uef.cpp +++ b/src/USER-UEF/dump_cfg_uef.cpp @@ -14,9 +14,9 @@ ------------------------------------------------------------------------- */ -#include -#include -#include +#include +#include +#include #include "dump_cfg.h" #include "atom.h" #include "domain.h" diff --git a/src/USER-UEF/fix_nh_uef.cpp b/src/USER-UEF/fix_nh_uef.cpp index 36494b0d493809c4ae10e9314bc58765a19ee674..cd0b2ba2683742ab1140ce3a41e0e7c506a40a33 100644 --- a/src/USER-UEF/fix_nh_uef.cpp +++ b/src/USER-UEF/fix_nh_uef.cpp @@ -13,9 +13,9 @@ Contributing author: David Nicholson (MIT) ------------------------------------------------------------------------- */ -#include -#include -#include +#include +#include +#include #include "fix_nh_uef.h" #include "atom.h" #include "force.h" diff --git a/src/USER-UEF/fix_nh_uef.h b/src/USER-UEF/fix_nh_uef.h index 43f5bb46a9f2c97c6f3a5f784506d3c9839aed56..0629db5aa176c96e74271aef1b43e08383e0279b 100644 --- a/src/USER-UEF/fix_nh_uef.h +++ b/src/USER-UEF/fix_nh_uef.h @@ -23,7 +23,7 @@ namespace LAMMPS_NS { // forward declaration namespace UEF_utils { class UEFBox; - }; + } class FixNHUef : public FixNH { public: diff --git a/src/USER-UEF/uef_utils.cpp b/src/USER-UEF/uef_utils.cpp index f270fe1d8b41760aa1236c1e4b478f79a24203ca..a5498d605f3d28291d91dcc320a4cd41dd999ce2 100644 --- a/src/USER-UEF/uef_utils.cpp +++ b/src/USER-UEF/uef_utils.cpp @@ -22,7 +22,7 @@ http://link.springer.com/chapter/10.1007%2F3-540-44670-2_13 */ -#include +#include #include "uef_utils.h" namespace LAMMPS_NS { diff --git a/src/USER-VTK/dump_vtk.cpp b/src/USER-VTK/dump_vtk.cpp index 78be5668cfebb8954b58c3be6df6bd7149c43521..adad070f51596c9d4b28ce0a904fdc476a94ab02 100644 --- a/src/USER-VTK/dump_vtk.cpp +++ b/src/USER-VTK/dump_vtk.cpp @@ -22,9 +22,9 @@ Richard Berger (JKU) ------------------------------------------------------------------------- */ -#include -#include -#include +#include +#include +#include #include "dump_vtk.h" #include "atom.h" #include "force.h" diff --git a/src/VORONOI/compute_voronoi_atom.cpp b/src/VORONOI/compute_voronoi_atom.cpp index d55db85ef8624501183cecc238fa9c9ae598e8e8..ea6158bfa225dcf9ccf75b21ce93ed0eb55c33c5 100644 --- a/src/VORONOI/compute_voronoi_atom.cpp +++ b/src/VORONOI/compute_voronoi_atom.cpp @@ -16,9 +16,9 @@ ------------------------------------------------------------------------- */ #include -#include -#include -#include +#include +#include +#include #include "compute_voronoi_atom.h" #include "atom.h" #include "group.h" diff --git a/src/angle.cpp b/src/angle.cpp index 1366c48865b5daa516b58bba254aa0171eaf3da0..2a297990ac83046595212b2819d621bfa6ab2b1a 100644 --- a/src/angle.cpp +++ b/src/angle.cpp @@ -11,7 +11,7 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include +#include #include "angle.h" #include "atom.h" #include "comm.h" diff --git a/src/angle.h b/src/angle.h index 000c3fe916d84c1766eeb4dd09dbd082fba61387..0247fa0ff83eb24204d01908577e60dab67883d4 100644 --- a/src/angle.h +++ b/src/angle.h @@ -14,7 +14,7 @@ #ifndef LMP_ANGLE_H #define LMP_ANGLE_H -#include +#include #include "pointers.h" namespace LAMMPS_NS { diff --git a/src/angle_hybrid.cpp b/src/angle_hybrid.cpp index 9b3af1856e67a33ae14eafd674b38d57782fb052..c29eaac2ae9e694c6eb3198099c04bcd9fb9122e 100644 --- a/src/angle_hybrid.cpp +++ b/src/angle_hybrid.cpp @@ -11,9 +11,9 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include -#include -#include +#include +#include +#include #include "angle_hybrid.h" #include "atom.h" #include "neighbor.h" diff --git a/src/angle_hybrid.h b/src/angle_hybrid.h index 4ae34c176f9574ca013b4f8075157c8e155e9fa5..4fde71e43f1251822355823dab06e941d8f33f31 100644 --- a/src/angle_hybrid.h +++ b/src/angle_hybrid.h @@ -20,7 +20,7 @@ AngleStyle(hybrid,AngleHybrid) #ifndef LMP_ANGLE_HYBRID_H #define LMP_ANGLE_HYBRID_H -#include +#include #include "angle.h" namespace LAMMPS_NS { diff --git a/src/angle_zero.cpp b/src/angle_zero.cpp index ba84295ca76a997a956991c35e6b0b194f925cdc..e5191c4fb22d6ceaaa0f4a562abe5b103364cefe 100644 --- a/src/angle_zero.cpp +++ b/src/angle_zero.cpp @@ -15,9 +15,9 @@ Contributing author: Carsten Svaneborg (SDU) ------------------------------------------------------------------------- */ -#include -#include -#include +#include +#include +#include #include "angle_zero.h" #include "atom.h" #include "force.h" diff --git a/src/angle_zero.h b/src/angle_zero.h index e40fc8355ce2be6aad4723f147455dc028c5cd82..b91be5c8d72a5330cabd8b3dca8d0cb8c450ab69 100644 --- a/src/angle_zero.h +++ b/src/angle_zero.h @@ -20,7 +20,7 @@ AngleStyle(zero,AngleZero) #ifndef LMP_ANGLE_ZERO_H #define LMP_ANGLE_ZERO_H -#include +#include #include "angle.h" namespace LAMMPS_NS { diff --git a/src/atom.cpp b/src/atom.cpp index ae36a8884b84e5093c98dbd4aabfde2079277ef5..d5773a2fe1f945ccf96877b9d56d2de857c4dfe1 100644 --- a/src/atom.cpp +++ b/src/atom.cpp @@ -12,11 +12,11 @@ ------------------------------------------------------------------------- */ #include -#include -#include -#include -#include -#include +#include +#include +#include +#include +#include #include "atom.h" #include "style_atom.h" #include "atom_vec.h" diff --git a/src/atom_map.cpp b/src/atom_map.cpp index 4b1be77a061464728e8769f8fef48ef37d667c00..46593432cfe07cd6806a0fcfca4f1ab282f7cc03 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 +#include #include "atom.h" #include "comm.h" #include "memory.h" diff --git a/src/atom_vec.cpp b/src/atom_vec.cpp index 14091cbb77ff41bbb8864f717c96ef97c6958455..b04bfba34c91295b0858c6f0833d75172fed20c9 100644 --- a/src/atom_vec.cpp +++ b/src/atom_vec.cpp @@ -11,8 +11,8 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include -#include +#include +#include #include "atom_vec.h" #include "atom.h" #include "force.h" diff --git a/src/atom_vec.h b/src/atom_vec.h index 5be955a06c39b0c4c501f862ecf9b0e1d841bb39..87fb35d9c72042e478d8cb8dde75549fddd70b17 100644 --- a/src/atom_vec.h +++ b/src/atom_vec.h @@ -14,7 +14,7 @@ #ifndef LMP_ATOM_VEC_H #define LMP_ATOM_VEC_H -#include +#include #include "pointers.h" namespace LAMMPS_NS { diff --git a/src/atom_vec_atomic.cpp b/src/atom_vec_atomic.cpp index eda1a33152a0f5d513d115fb04e8f07d3642a0b3..e1c9a1e524c2ae99e3cdc2aff74217404f4240bb 100644 --- a/src/atom_vec_atomic.cpp +++ b/src/atom_vec_atomic.cpp @@ -11,7 +11,7 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include +#include #include "atom_vec_atomic.h" #include "atom.h" #include "comm.h" diff --git a/src/atom_vec_body.cpp b/src/atom_vec_body.cpp index b7422cf229785feaf714d3c914acd15c3a01767f..4d3b5643aea121a788d41345f2a1be43e2e0a667 100644 --- a/src/atom_vec_body.cpp +++ b/src/atom_vec_body.cpp @@ -11,9 +11,9 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include -#include -#include +#include +#include +#include #include "atom_vec_body.h" #include "style_body.h" #include "body.h" diff --git a/src/atom_vec_charge.cpp b/src/atom_vec_charge.cpp index a93a29662b0d5fe2885c8af9b64e6380ef8c4e1e..440393385dad38b24735ce7120b67be1ec83df6c 100644 --- a/src/atom_vec_charge.cpp +++ b/src/atom_vec_charge.cpp @@ -11,7 +11,7 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include +#include #include "atom_vec_charge.h" #include "atom.h" #include "comm.h" diff --git a/src/atom_vec_ellipsoid.cpp b/src/atom_vec_ellipsoid.cpp index 858b89d62b47036a3025607c00f1844fc53172f3..c569f89a0933ef4b594f0fc581647140140a93d3 100644 --- a/src/atom_vec_ellipsoid.cpp +++ b/src/atom_vec_ellipsoid.cpp @@ -15,7 +15,7 @@ Contributing author: Mike Brown (SNL) ------------------------------------------------------------------------- */ -#include +#include #include "atom_vec_ellipsoid.h" #include "math_extra.h" #include "atom.h" diff --git a/src/atom_vec_hybrid.cpp b/src/atom_vec_hybrid.cpp index 40c744afc5461bb83822053291f01e0701f341e3..7e1fb01e5ddc6318a578a1740f2a8acad7ded7bb 100644 --- a/src/atom_vec_hybrid.cpp +++ b/src/atom_vec_hybrid.cpp @@ -11,8 +11,8 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include -#include +#include +#include #include "atom_vec_hybrid.h" #include "atom.h" #include "domain.h" diff --git a/src/atom_vec_hybrid.h b/src/atom_vec_hybrid.h index fd8a3e433cc9bf594171149c5aa7f9b2ab35bc8f..a027923a1717a0385943e2885122f25c677e1430 100644 --- a/src/atom_vec_hybrid.h +++ b/src/atom_vec_hybrid.h @@ -20,7 +20,7 @@ AtomStyle(hybrid,AtomVecHybrid) #ifndef LMP_ATOM_VEC_HYBRID_H #define LMP_ATOM_VEC_HYBRID_H -#include +#include #include "atom_vec.h" namespace LAMMPS_NS { diff --git a/src/atom_vec_line.cpp b/src/atom_vec_line.cpp index ec278562f9ea702abeeeb0b595cfef36487f2ac4..9babfe3735ca1eb03ce0c67f3b4033517dc16998 100644 --- a/src/atom_vec_line.cpp +++ b/src/atom_vec_line.cpp @@ -11,9 +11,9 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include -#include -#include +#include +#include +#include #include "atom_vec_line.h" #include "atom.h" #include "comm.h" diff --git a/src/atom_vec_sphere.cpp b/src/atom_vec_sphere.cpp index a72704b4c62941af07ff48c99b05d0d1a2efd600..dec98e5200d2ec45fe9b3a3b32789802d88eee45 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 -#include -#include +#include +#include +#include #include "atom_vec_sphere.h" #include "atom.h" #include "comm.h" diff --git a/src/atom_vec_tri.cpp b/src/atom_vec_tri.cpp index eb87e75b18dfa34e602dde516679d5e53d650134..2c31b95cfe3adf07520fdb39426c34597c1e16d1 100644 --- a/src/atom_vec_tri.cpp +++ b/src/atom_vec_tri.cpp @@ -11,9 +11,9 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include -#include -#include +#include +#include +#include #include "atom_vec_tri.h" #include "math_extra.h" #include "atom.h" diff --git a/src/balance.cpp b/src/balance.cpp index 45f185a6fc0ba06d4b5cddb7409d73eccff26b82..9be7b2a7b3267295b49d35c46af1ce007da6dd66 100644 --- a/src/balance.cpp +++ b/src/balance.cpp @@ -19,9 +19,9 @@ //#define BALANCE_DEBUG 1 #include -#include -#include -#include +#include +#include +#include #include "balance.h" #include "atom.h" #include "comm.h" diff --git a/src/balance.h b/src/balance.h index 3e5e0e0d70a07e145b5864bd44dd822652577589..420031502a8f826a636c8d63e1a3a421beb37de6 100644 --- a/src/balance.h +++ b/src/balance.h @@ -20,7 +20,7 @@ CommandStyle(balance,Balance) #ifndef LMP_BALANCE_H #define LMP_BALANCE_H -#include +#include #include "pointers.h" namespace LAMMPS_NS { diff --git a/src/body.cpp b/src/body.cpp index 144ee13c92bd9d7a516bd708053e1955080090ee..42f4ccbdd3fcaf9491d7656a7e138c1f7efe4ebe 100644 --- a/src/body.cpp +++ b/src/body.cpp @@ -11,9 +11,9 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include -#include -#include +#include +#include +#include #include "body.h" #include "error.h" diff --git a/src/bond.cpp b/src/bond.cpp index 825ff1b199a48b854f5b7d716eac80c77228345e..edcd869425bd0d7444915d6e1f16dd1f71cb1a17 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.h b/src/bond.h index b34628d7575fc726ba5ab7cb69ddae7da2c2d298..9c353a1a6dae5fed06e2f9992d116e24d1d284a4 100644 --- a/src/bond.h +++ b/src/bond.h @@ -14,7 +14,7 @@ #ifndef LMP_BOND_H #define LMP_BOND_H -#include +#include #include "pointers.h" namespace LAMMPS_NS { diff --git a/src/bond_hybrid.cpp b/src/bond_hybrid.cpp index 9a16d0e1fd2e54a02a3b9d5eb8cedd451b59768c..c3a71ee71c2c85a6a0cbeb914f823423541f4637 100644 --- a/src/bond_hybrid.cpp +++ b/src/bond_hybrid.cpp @@ -11,9 +11,9 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include -#include -#include +#include +#include +#include #include "bond_hybrid.h" #include "atom.h" #include "neighbor.h" diff --git a/src/bond_hybrid.h b/src/bond_hybrid.h index e1d567c886813755bc4fe42017ce8fbdd6ed8607..a385a2e3f856788f90dd8b2a2f8df5e83a5ca2c9 100644 --- a/src/bond_hybrid.h +++ b/src/bond_hybrid.h @@ -20,7 +20,7 @@ BondStyle(hybrid,BondHybrid) #ifndef LMP_BOND_HYBRID_H #define LMP_BOND_HYBRID_H -#include +#include #include "bond.h" namespace LAMMPS_NS { diff --git a/src/bond_zero.cpp b/src/bond_zero.cpp index f38b7754f826e297e1f820e8dcb22f6f6315bc16..9fd9d4a580c5d83cf4c69a431330975a116ee330 100644 --- a/src/bond_zero.cpp +++ b/src/bond_zero.cpp @@ -15,9 +15,9 @@ Contributing author: Carsten Svaneborg (SDU) ------------------------------------------------------------------------- */ -#include -#include -#include +#include +#include +#include #include "bond_zero.h" #include "atom.h" #include "force.h" diff --git a/src/bond_zero.h b/src/bond_zero.h index b7b7e999600e4f52b90ceaca4d1ace2956feed79..9443ff0784c64bba76ca5079ae79d90f31b8b1f8 100644 --- a/src/bond_zero.h +++ b/src/bond_zero.h @@ -20,7 +20,7 @@ BondStyle(zero,BondZero) #ifndef LMP_BOND_ZERO_H #define LMP_BOND_ZERO_H -#include +#include #include "bond.h" namespace LAMMPS_NS { diff --git a/src/change_box.cpp b/src/change_box.cpp index c6ec078a01f647d4059b692b03250bc5bd52012d..93dff387c47ddceb622f20168deaca3c93ca5f83 100644 --- a/src/change_box.cpp +++ b/src/change_box.cpp @@ -12,9 +12,9 @@ ------------------------------------------------------------------------- */ #include -#include -#include -#include +#include +#include +#include #include "change_box.h" #include "atom.h" #include "modify.h" diff --git a/src/citeme.h b/src/citeme.h index 18e9a712db81a1ce5fed2f5f2ca4d26867a15688..262b284337a12dfca5f5c81bffcec5cc0c248eeb 100644 --- a/src/citeme.h +++ b/src/citeme.h @@ -15,7 +15,7 @@ #define LMP_CITEME_H #include "pointers.h" -#include +#include #include namespace LAMMPS_NS { diff --git a/src/comm.cpp b/src/comm.cpp index 14d2d70c5a2ed125cf467e98b4dbb149ac306f52..b53ce251f27bce20a5c964015f52286e9a266a74 100644 --- a/src/comm.cpp +++ b/src/comm.cpp @@ -12,8 +12,8 @@ ------------------------------------------------------------------------- */ #include -#include -#include +#include +#include #include "comm.h" #include "universe.h" #include "atom.h" diff --git a/src/comm_brick.cpp b/src/comm_brick.cpp index 992d988f902d553f1093341bcf17f61a963a030d..070c93bd3cb765dffe29ecab6dd6cfa42742579e 100644 --- a/src/comm_brick.cpp +++ b/src/comm_brick.cpp @@ -16,10 +16,10 @@ ------------------------------------------------------------------------- */ #include -#include -#include -#include -#include +#include +#include +#include +#include #include "comm_brick.h" #include "comm_tiled.h" #include "universe.h" diff --git a/src/comm_tiled.cpp b/src/comm_tiled.cpp index 23b098a705a26bb477ab7199688d2375e2034699..12b10be2f7652f113c5e736a80d032a8d7a9942d 100644 --- a/src/comm_tiled.cpp +++ b/src/comm_tiled.cpp @@ -11,7 +11,7 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include +#include #include "comm_tiled.h" #include "comm_brick.h" #include "atom.h" diff --git a/src/compute.cpp b/src/compute.cpp index 467faf9fe1e0e258fd4fb22b3a0c1e7fe9b902d2..207f825ec850b2118ce7dff45668045a295c40fd 100644 --- a/src/compute.cpp +++ b/src/compute.cpp @@ -12,9 +12,9 @@ ------------------------------------------------------------------------- */ #include -#include -#include -#include +#include +#include +#include #include "compute.h" #include "atom.h" #include "domain.h" diff --git a/src/compute_aggregate_atom.cpp b/src/compute_aggregate_atom.cpp index d61fd06397c04f982880a1dd2c814e1093bcdcd4..56855fcc29720bf8db93b8a2a6a52f8c1818fd45 100644 --- a/src/compute_aggregate_atom.cpp +++ b/src/compute_aggregate_atom.cpp @@ -15,8 +15,8 @@ Contributing author: Axel Kohlmeyer (Temple U) ------------------------------------------------------------------------- */ -#include -#include +#include +#include #include "compute_aggregate_atom.h" #include "atom.h" #include "atom_vec.h" diff --git a/src/compute_angle.cpp b/src/compute_angle.cpp index 8546350ecd9afc69398cf9d91b73c03172060843..59945f5832c3f78a7b32d8f6526f40c16da573c3 100644 --- a/src/compute_angle.cpp +++ b/src/compute_angle.cpp @@ -12,7 +12,7 @@ ------------------------------------------------------------------------- */ #include -#include +#include #include "compute_angle.h" #include "update.h" #include "force.h" diff --git a/src/compute_angle_local.cpp b/src/compute_angle_local.cpp index 1e249554dcd136cf64676d03031bfbec637018a6..7137077158eb33e1dfc2abbea7378426639e0f65 100644 --- a/src/compute_angle_local.cpp +++ b/src/compute_angle_local.cpp @@ -11,8 +11,8 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include -#include +#include +#include #include "compute_angle_local.h" #include "atom.h" #include "atom_vec.h" diff --git a/src/compute_angmom_chunk.cpp b/src/compute_angmom_chunk.cpp index 98c6ea044110e211e28c00765bc45a0c3a4384a2..a70eaaf49f3d334b87067a20f9f27b6560ee7829 100644 --- a/src/compute_angmom_chunk.cpp +++ b/src/compute_angmom_chunk.cpp @@ -11,7 +11,7 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include +#include #include "compute_angmom_chunk.h" #include "atom.h" #include "update.h" diff --git a/src/compute_bond.cpp b/src/compute_bond.cpp index 29d7ce0ecec42556db00830cd80573ceb171adbf..896aaec9bdfa97c1c84d4fc22244f40396e4ebc3 100644 --- a/src/compute_bond.cpp +++ b/src/compute_bond.cpp @@ -12,7 +12,7 @@ ------------------------------------------------------------------------- */ #include -#include +#include #include "compute_bond.h" #include "update.h" #include "force.h" diff --git a/src/compute_bond_local.cpp b/src/compute_bond_local.cpp index b7e84d0a29f64e0844931f0a095f406eb2efb07c..985e3ef0756260c9b6e9f258a5d3ab1b080f4605 100644 --- a/src/compute_bond_local.cpp +++ b/src/compute_bond_local.cpp @@ -11,8 +11,8 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include -#include +#include +#include #include "compute_bond_local.h" #include "atom.h" #include "atom_vec.h" diff --git a/src/compute_centro_atom.cpp b/src/compute_centro_atom.cpp index 089c57798008527c99b5046565fce975492c0e41..48af45363598ab0ed8fd8e1b3b9aff5d9c996be3 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 +#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 6a81b181cf50a6f13602ccc35fc89cf8475b3ecb..ddad7eb62fd6e323756795b376a5fa9daa080915 100644 --- a/src/compute_chunk_atom.cpp +++ b/src/compute_chunk_atom.cpp @@ -14,8 +14,8 @@ // NOTE: allow for bin center to be variables for sphere/cylinder #include -#include -#include +#include +#include #include "compute_chunk_atom.h" #include "atom.h" #include "update.h" diff --git a/src/compute_cluster_atom.cpp b/src/compute_cluster_atom.cpp index 9a7df03e49ba5bcf919b7714b82a7a70f37c0510..146f8fd1b3c7d64491e1213038b94c4ba9d0a32a 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 +#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 bd24e06cae4e289893e48f19affed911f74cdb1e..a1b97d94043dc537102f98cb3a05cbb7555a26a1 100644 --- a/src/compute_cna_atom.cpp +++ b/src/compute_cna_atom.cpp @@ -15,8 +15,9 @@ Contributing author: Wan Liang (Chinese Academy of Sciences) ------------------------------------------------------------------------- */ -#include -#include +#include +#include +#include #include "compute_cna_atom.h" #include "atom.h" #include "update.h" @@ -29,7 +30,6 @@ #include "comm.h" #include "memory.h" #include "error.h" -#include using namespace LAMMPS_NS; diff --git a/src/compute_com_chunk.cpp b/src/compute_com_chunk.cpp index 3eb686783b2511e4db32e7e048aa8b52f1e527a6..ec667672454d66436276b94c64dd9d5f47355279 100644 --- a/src/compute_com_chunk.cpp +++ b/src/compute_com_chunk.cpp @@ -11,7 +11,7 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include +#include #include "compute_com_chunk.h" #include "atom.h" #include "update.h" diff --git a/src/compute_contact_atom.cpp b/src/compute_contact_atom.cpp index b2186bd17502f735dfc732554739a44f959973f3..f3c4513b0152a2edd090c31d07a46f832d925021 100644 --- a/src/compute_contact_atom.cpp +++ b/src/compute_contact_atom.cpp @@ -11,9 +11,9 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include -#include -#include +#include +#include +#include #include "compute_contact_atom.h" #include "atom.h" #include "update.h" diff --git a/src/compute_coord_atom.cpp b/src/compute_coord_atom.cpp index 8c69aa787437131f1f376a29a3db7a99d6290def..b86d818d0608d99468658adb982df1afaccf7472 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 -#include -#include +#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 2afcb5e321ae655cee5c3af02a46a6543ca715e0..3595b2eda32f24e02287753dc04a8f8d9f1714e8 100644 --- a/src/compute_dihedral.cpp +++ b/src/compute_dihedral.cpp @@ -12,7 +12,7 @@ ------------------------------------------------------------------------- */ #include -#include +#include #include "compute_dihedral.h" #include "update.h" #include "force.h" diff --git a/src/compute_dihedral_local.cpp b/src/compute_dihedral_local.cpp index 7a21d0f9d708a02a73e7deef3230fec065a62143..42d1476ad25fb368b08b36bf99195f3a0750235b 100644 --- a/src/compute_dihedral_local.cpp +++ b/src/compute_dihedral_local.cpp @@ -11,8 +11,8 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include -#include +#include +#include #include "compute_dihedral_local.h" #include "atom.h" #include "atom_vec.h" diff --git a/src/compute_dipole_chunk.cpp b/src/compute_dipole_chunk.cpp index b4beacb9849a792e97e1acd6d44fce5992ef7609..b0474b6359c7a654a8ec97ced8121ac0d3da2b1f 100644 --- a/src/compute_dipole_chunk.cpp +++ b/src/compute_dipole_chunk.cpp @@ -11,7 +11,7 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include +#include #include "compute_dipole_chunk.h" #include "atom.h" #include "update.h" diff --git a/src/compute_displace_atom.cpp b/src/compute_displace_atom.cpp index a5c32c53cc9496ced1a2ecd6000d55469639ce7e..0b6b40b62a35688d2ed7dde70d9526305c68f075 100644 --- a/src/compute_displace_atom.cpp +++ b/src/compute_displace_atom.cpp @@ -11,8 +11,8 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include -#include +#include +#include #include "compute_displace_atom.h" #include "atom.h" #include "update.h" diff --git a/src/compute_erotate_sphere_atom.cpp b/src/compute_erotate_sphere_atom.cpp index b29c18c1e3438085a630197146af2457e083c6d0..999bc062c57406292cf7b0d469c9f5f1133e0f66 100644 --- a/src/compute_erotate_sphere_atom.cpp +++ b/src/compute_erotate_sphere_atom.cpp @@ -11,7 +11,7 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include +#include #include "compute_erotate_sphere_atom.h" #include "atom.h" #include "update.h" diff --git a/src/compute_fragment_atom.cpp b/src/compute_fragment_atom.cpp index 8606f54933bda9738267d844747605d49228e6b9..b9fb2331ecf35bca18a9f5803baad10c0273eaa2 100644 --- a/src/compute_fragment_atom.cpp +++ b/src/compute_fragment_atom.cpp @@ -15,7 +15,7 @@ Contributing author: Axel Kohlmeyer (Temple U) ------------------------------------------------------------------------- */ -#include +#include #include "compute_fragment_atom.h" #include "atom.h" #include "atom_vec.h" diff --git a/src/compute_global_atom.cpp b/src/compute_global_atom.cpp index 6cd79f919c9ac27cef83b1edb69b20594ab29c37..dc9ab52f4978268a7fe51dcbd03b5afbeff51a54 100644 --- a/src/compute_global_atom.cpp +++ b/src/compute_global_atom.cpp @@ -11,8 +11,8 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include -#include +#include +#include #include "compute_global_atom.h" #include "atom.h" #include "update.h" diff --git a/src/compute_group_group.cpp b/src/compute_group_group.cpp index 51c978cb530017af17c9cffaf4ca6217551608c8..dc94db50f645ee35f9c1e5b928881aa5a584f155 100644 --- a/src/compute_group_group.cpp +++ b/src/compute_group_group.cpp @@ -17,7 +17,8 @@ ------------------------------------------------------------------------- */ #include -#include +#include +#include #include "compute_group_group.h" #include "atom.h" #include "update.h" @@ -29,7 +30,6 @@ #include "group.h" #include "kspace.h" #include "error.h" -#include #include "comm.h" #include "domain.h" #include "math_const.h" diff --git a/src/compute_gyration.cpp b/src/compute_gyration.cpp index 0877efa4d9214201442da4463d0c7f0bde1375ac..f8d19853e0e9805ff8d2e1891dd56c486487156a 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 efb26c9ad2721f006da6ee4896baa313b7755453..6a23398aca3151533a39c317aafc73f1a5dc650e 100644 --- a/src/compute_gyration_chunk.cpp +++ b/src/compute_gyration_chunk.cpp @@ -11,8 +11,8 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include -#include +#include +#include #include "compute_gyration_chunk.h" #include "atom.h" #include "update.h" diff --git a/src/compute_heat_flux.cpp b/src/compute_heat_flux.cpp index 108691aec240b46907fa4189199d99af5dc428a5..e402da7842a70ccf35ed3980e0bd8e93af6abded 100644 --- a/src/compute_heat_flux.cpp +++ b/src/compute_heat_flux.cpp @@ -16,8 +16,8 @@ Mario Pinto (Computational Research Lab, Pune, India) ------------------------------------------------------------------------- */ -#include -#include +#include +#include #include "compute_heat_flux.h" #include "atom.h" #include "update.h" diff --git a/src/compute_hexorder_atom.cpp b/src/compute_hexorder_atom.cpp index 44525e67a2e9f2d5e7f0443d4574db2b1386f40f..cb2946beba8e7833feb9115566f38505108360cb 100644 --- a/src/compute_hexorder_atom.cpp +++ b/src/compute_hexorder_atom.cpp @@ -16,8 +16,8 @@ ------------------------------------------------------------------------- */ #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 60d22d0d70d938d8718f62eb6e5a21d875afb37b..ac2a23e727cc87bb65e23063b4e105c87fa61afe 100644 --- a/src/compute_improper.cpp +++ b/src/compute_improper.cpp @@ -12,7 +12,7 @@ ------------------------------------------------------------------------- */ #include -#include +#include #include "compute_improper.h" #include "update.h" #include "force.h" diff --git a/src/compute_improper_local.cpp b/src/compute_improper_local.cpp index e183405956721349fdc43c15a779e7f3661700bf..f54cb67535e2e1eed7ce88253b1a0284bdffe0cf 100644 --- a/src/compute_improper_local.cpp +++ b/src/compute_improper_local.cpp @@ -11,8 +11,8 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include -#include +#include +#include #include "compute_improper_local.h" #include "atom.h" #include "atom_vec.h" diff --git a/src/compute_inertia_chunk.cpp b/src/compute_inertia_chunk.cpp index 1e3c595ed1db93406d9a8e1c1528ac09413f9e1b..a33073c35a8194f61302f2e7831d424f40aae1e7 100644 --- a/src/compute_inertia_chunk.cpp +++ b/src/compute_inertia_chunk.cpp @@ -11,7 +11,7 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include +#include #include "compute_inertia_chunk.h" #include "atom.h" #include "update.h" diff --git a/src/compute_ke_atom.cpp b/src/compute_ke_atom.cpp index da159669dea4f88f615639f4379fbc9b36776ac6..c5506996dab5843e97260d51f7342088f77ae727 100644 --- a/src/compute_ke_atom.cpp +++ b/src/compute_ke_atom.cpp @@ -11,7 +11,7 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include +#include #include "compute_ke_atom.h" #include "atom.h" #include "update.h" diff --git a/src/compute_msd.cpp b/src/compute_msd.cpp index ac510bca8eb59e7bd6c2ff315738aab8bc673cad..fc47b2609a264c3ef8d3e4a925d627818fcb51f7 100644 --- a/src/compute_msd.cpp +++ b/src/compute_msd.cpp @@ -11,7 +11,7 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include +#include #include "compute_msd.h" #include "atom.h" #include "update.h" diff --git a/src/compute_msd_chunk.cpp b/src/compute_msd_chunk.cpp index 69cd87f96b6b62d800eb0a7e54587525bc779cfd..1f974cc06cd0163c7dfc511370bb55e5afe96df2 100644 --- a/src/compute_msd_chunk.cpp +++ b/src/compute_msd_chunk.cpp @@ -11,7 +11,7 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include +#include #include "compute_msd_chunk.h" #include "atom.h" #include "group.h" diff --git a/src/compute_omega_chunk.cpp b/src/compute_omega_chunk.cpp index d89c57889e2ce515fca42ec070ef898eda1786c6..23447da602d492a6ad97924891f6cb56a6e8ce15 100644 --- a/src/compute_omega_chunk.cpp +++ b/src/compute_omega_chunk.cpp @@ -11,7 +11,7 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include +#include #include "compute_omega_chunk.h" #include "atom.h" #include "update.h" diff --git a/src/compute_orientorder_atom.cpp b/src/compute_orientorder_atom.cpp index 4fc9ab060b39eda652f027023d1864535c6b3355..f263fdfaed0caa3cdeea54cf149b080c716bf7be 100644 --- a/src/compute_orientorder_atom.cpp +++ b/src/compute_orientorder_atom.cpp @@ -16,9 +16,9 @@ Axel Kohlmeyer (Temple U) ------------------------------------------------------------------------- */ -#include -#include -#include +#include +#include +#include #include "compute_orientorder_atom.h" #include "atom.h" #include "update.h" diff --git a/src/compute_pair.cpp b/src/compute_pair.cpp index b00944e1bcc6b42a9eae7d9170fd402421a38d37..444395bae5dc999fbf9181be76822762a2eeec58 100644 --- a/src/compute_pair.cpp +++ b/src/compute_pair.cpp @@ -12,7 +12,7 @@ ------------------------------------------------------------------------- */ #include -#include +#include #include "compute_pair.h" #include "update.h" #include "force.h" diff --git a/src/compute_pair_local.cpp b/src/compute_pair_local.cpp index 1d28ae8b769ebcbc7ea427fa9b5008e986a03fc2..3f1147ed2778c3640c749ee76c7db66b28f9ca24 100644 --- a/src/compute_pair_local.cpp +++ b/src/compute_pair_local.cpp @@ -11,9 +11,9 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include -#include -#include +#include +#include +#include #include "compute_pair_local.h" #include "atom.h" #include "update.h" diff --git a/src/compute_pe.cpp b/src/compute_pe.cpp index 342c1c5cc550f6d57165c71d35e214da433b3fe0..5839ec209599834366af029d48f37d03c2d2a6eb 100644 --- a/src/compute_pe.cpp +++ b/src/compute_pe.cpp @@ -12,7 +12,7 @@ ------------------------------------------------------------------------- */ #include -#include +#include #include "compute_pe.h" #include "atom.h" #include "update.h" diff --git a/src/compute_pe_atom.cpp b/src/compute_pe_atom.cpp index c324a8eff7d4740b723c96559f0a69bf9dc92ed4..2f1dc5650eb5b7f507efece1cd7ac065547812d0 100644 --- a/src/compute_pe_atom.cpp +++ b/src/compute_pe_atom.cpp @@ -11,7 +11,7 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include +#include #include "compute_pe_atom.h" #include "atom.h" #include "update.h" diff --git a/src/compute_pressure.cpp b/src/compute_pressure.cpp index 99046e864cc0f418c765fab9c80f65253b9edfa1..dde02a5aed62dabd961a4812b110db115505c70f 100644 --- a/src/compute_pressure.cpp +++ b/src/compute_pressure.cpp @@ -12,8 +12,8 @@ ------------------------------------------------------------------------- */ #include -#include -#include +#include +#include #include "compute_pressure.h" #include "atom.h" #include "update.h" diff --git a/src/compute_property_atom.cpp b/src/compute_property_atom.cpp index d158d0081615df68d648149c8a60d3affe1bba62..76df5a053dfc0e10b88c9369735ed597c639110f 100644 --- a/src/compute_property_atom.cpp +++ b/src/compute_property_atom.cpp @@ -11,8 +11,8 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include -#include +#include +#include #include "compute_property_atom.h" #include "math_extra.h" #include "atom.h" diff --git a/src/compute_property_chunk.cpp b/src/compute_property_chunk.cpp index c169e20d739a6ff6b1d59351abc1a9d126e570fc..489890e1cc4608f4fd7c54a33bef3ec33db0e843 100644 --- a/src/compute_property_chunk.cpp +++ b/src/compute_property_chunk.cpp @@ -11,7 +11,7 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include +#include #include "compute_property_chunk.h" #include "atom.h" #include "update.h" diff --git a/src/compute_property_local.cpp b/src/compute_property_local.cpp index e38817b4ea8085a22f3dda409d9be22d272a4a7a..ad68459650a500a513f9d9e7718377f7a2870247 100644 --- a/src/compute_property_local.cpp +++ b/src/compute_property_local.cpp @@ -11,7 +11,7 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include +#include #include "compute_property_local.h" #include "atom.h" #include "atom_vec.h" diff --git a/src/compute_rdf.cpp b/src/compute_rdf.cpp index bcb620f3b36c59dd842669dd626baebcda760f31..263e7f799ba02eb254dcc422fdddd86f2bfa798f 100644 --- a/src/compute_rdf.cpp +++ b/src/compute_rdf.cpp @@ -16,9 +16,9 @@ ------------------------------------------------------------------------- */ #include -#include -#include -#include +#include +#include +#include #include "compute_rdf.h" #include "atom.h" #include "update.h" diff --git a/src/compute_rdf.h b/src/compute_rdf.h index af4f56e838500eda3f4674537e42230c32bcc75f..52a93a38dd78deac22423ef8930b4f3371dc5fa9 100644 --- a/src/compute_rdf.h +++ b/src/compute_rdf.h @@ -20,7 +20,7 @@ ComputeStyle(rdf,ComputeRDF) #ifndef LMP_COMPUTE_RDF_H #define LMP_COMPUTE_RDF_H -#include +#include #include "compute.h" namespace LAMMPS_NS { diff --git a/src/compute_reduce.cpp b/src/compute_reduce.cpp index 91379e9ba6dca5169c052530c71b53b032a869c7..7c61d666b2d9db9c9625b69bb08dfdafff49fa29 100644 --- a/src/compute_reduce.cpp +++ b/src/compute_reduce.cpp @@ -11,8 +11,8 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include -#include +#include +#include #include "compute_reduce.h" #include "atom.h" #include "update.h" diff --git a/src/compute_reduce_region.cpp b/src/compute_reduce_region.cpp index c867a0190ccde7331cb0060304124570891fd7f7..77cd6371c691170776926da985522f7923f69316 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 +#include +#include #include "compute_reduce_region.h" #include "atom.h" #include "update.h" diff --git a/src/compute_slice.cpp b/src/compute_slice.cpp index 23bed054ace3815a9a9cb19770ec17369e55b954..ac70e7dd15803751674ffaf9ee3fc25e5f674c06 100644 --- a/src/compute_slice.cpp +++ b/src/compute_slice.cpp @@ -11,8 +11,8 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include -#include +#include +#include #include "compute_slice.h" #include "update.h" #include "modify.h" diff --git a/src/compute_stress_atom.cpp b/src/compute_stress_atom.cpp index fd38f13dbab0dd9c840b8db14e6ec3d9d4167706..5211f015abd19054f39552fa49f20f2fec68ebcb 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 +#include +#include #include "compute_stress_atom.h" #include "atom.h" #include "update.h" diff --git a/src/compute_temp.cpp b/src/compute_temp.cpp index 1fbab924b83ddc63930f70f4da031fd27b7151cd..f7d3a890ec6d9a044ab6b2cfbac9af8ca28b5611 100644 --- a/src/compute_temp.cpp +++ b/src/compute_temp.cpp @@ -12,7 +12,7 @@ ------------------------------------------------------------------------- */ #include -#include +#include #include "compute_temp.h" #include "atom.h" #include "update.h" diff --git a/src/compute_temp_chunk.cpp b/src/compute_temp_chunk.cpp index 1cc98c4ee83c9d63d3027b96271f74233573117f..920515e05c54ca3e4e9cb5437e3392b83a4a351b 100644 --- a/src/compute_temp_chunk.cpp +++ b/src/compute_temp_chunk.cpp @@ -11,7 +11,7 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include +#include #include "compute_temp_chunk.h" #include "atom.h" #include "update.h" diff --git a/src/compute_temp_com.cpp b/src/compute_temp_com.cpp index 6d64ff5aee5af36ba8fb34b72d9fd6a25f32598b..35f4512ab2b76e8c7b16d1de171588b6c2a547f6 100644 --- a/src/compute_temp_com.cpp +++ b/src/compute_temp_com.cpp @@ -12,8 +12,8 @@ ------------------------------------------------------------------------- */ #include -#include -#include +#include +#include #include "compute_temp_com.h" #include "atom.h" #include "update.h" diff --git a/src/compute_temp_deform.cpp b/src/compute_temp_deform.cpp index c8b8200770e237d7b3d33c6698526f797fc5e758..907f7090987a5cb4c0b3261835aaec74384479c7 100644 --- a/src/compute_temp_deform.cpp +++ b/src/compute_temp_deform.cpp @@ -16,7 +16,7 @@ ------------------------------------------------------------------------- */ #include -#include +#include #include "compute_temp_deform.h" #include "domain.h" #include "atom.h" diff --git a/src/compute_temp_partial.cpp b/src/compute_temp_partial.cpp index 9df8e8b580f137f1fe73cc0b26ccf00bd82827cb..4b87a2249ed1f96593a901d264b1b9bd61f20621 100644 --- a/src/compute_temp_partial.cpp +++ b/src/compute_temp_partial.cpp @@ -12,7 +12,7 @@ ------------------------------------------------------------------------- */ #include -#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 236f5bc0960ff90b88c149c7d0dc9700172564cd..c7f0b28a6cb096184ad2f3b2cdd269df7af2664f 100644 --- a/src/compute_temp_profile.cpp +++ b/src/compute_temp_profile.cpp @@ -12,8 +12,8 @@ ------------------------------------------------------------------------- */ #include -#include -#include +#include +#include #include "compute_temp_profile.h" #include "atom.h" #include "update.h" diff --git a/src/compute_temp_ramp.cpp b/src/compute_temp_ramp.cpp index af6a730c9d2869c311afd572f1262023d0681839..42d258d8b2fe626d68524fc21af9b427dd477baf 100644 --- a/src/compute_temp_ramp.cpp +++ b/src/compute_temp_ramp.cpp @@ -12,8 +12,8 @@ ------------------------------------------------------------------------- */ #include -#include -#include +#include +#include #include "compute_temp_ramp.h" #include "atom.h" #include "update.h" diff --git a/src/compute_temp_region.cpp b/src/compute_temp_region.cpp index ed710bc73096a2093cf963eed78c4d717ed2b345..bde70a20f0c44058961dab409ca605bfe4e7a81e 100644 --- a/src/compute_temp_region.cpp +++ b/src/compute_temp_region.cpp @@ -12,7 +12,7 @@ ------------------------------------------------------------------------- */ #include -#include +#include #include "compute_temp_region.h" #include "atom.h" #include "update.h" diff --git a/src/compute_temp_sphere.cpp b/src/compute_temp_sphere.cpp index ad5cf565e9a8ecc4b3e1339ed6696693edcfd280..651da6dee521309e8e8951445359f0e20f1f34f0 100644 --- a/src/compute_temp_sphere.cpp +++ b/src/compute_temp_sphere.cpp @@ -12,7 +12,7 @@ ------------------------------------------------------------------------- */ #include -#include +#include #include "compute_temp_sphere.h" #include "atom.h" #include "atom_vec.h" diff --git a/src/compute_torque_chunk.cpp b/src/compute_torque_chunk.cpp index 25386ad40d7873e836dd40738f2a022072de8107..d9de99bcb2589e4c8bfcb6fc63bf43163efe0761 100644 --- a/src/compute_torque_chunk.cpp +++ b/src/compute_torque_chunk.cpp @@ -11,7 +11,7 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include +#include #include "compute_torque_chunk.h" #include "atom.h" #include "update.h" diff --git a/src/compute_vacf.cpp b/src/compute_vacf.cpp index b3f487a4d758cfdf2c9af81f77887f2833ee2a04..3ef3acf0bf662100946755fe3034a2c52f97b1d6 100644 --- a/src/compute_vacf.cpp +++ b/src/compute_vacf.cpp @@ -11,7 +11,7 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include +#include #include "compute_vacf.h" #include "atom.h" #include "update.h" diff --git a/src/compute_vcm_chunk.cpp b/src/compute_vcm_chunk.cpp index 0661bf44574d1f0a2ace74caa8fba70bc5172adf..a6dd796c63c7e71db984e60550ef4918d777cb83 100644 --- a/src/compute_vcm_chunk.cpp +++ b/src/compute_vcm_chunk.cpp @@ -11,7 +11,7 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include +#include #include "compute_vcm_chunk.h" #include "atom.h" #include "update.h" diff --git a/src/create_atoms.cpp b/src/create_atoms.cpp index 6caa4157ce89e5b7b241415e0a357d111358eaf0..cdd2c5e37f4528da2f7844ba0462c608fad18b62 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 -#include -#include +#include +#include +#include #include "create_atoms.h" #include "atom.h" #include "atom_vec.h" diff --git a/src/create_bonds.cpp b/src/create_bonds.cpp index f19458772086dd9831f517e9d22011780d2b3088..751c4746ba5286aaa39a2b9089a4e4d1ec217a49 100644 --- a/src/create_bonds.cpp +++ b/src/create_bonds.cpp @@ -15,8 +15,8 @@ Contributing authors: Mike Salerno (NRL) added single methods ------------------------------------------------------------------------- */ -#include -#include +#include +#include #include "create_bonds.h" #include "atom.h" #include "domain.h" @@ -323,9 +323,13 @@ void CreateBonds::single_bond() // check that 2 atoms exist + const int nlocal = atom->nlocal; + const int idx1 = atom->map(batom1); + const int idx2 = atom->map(batom2); + int count = 0; - if (atom->map(batom1) >= 0) count++; - if (atom->map(batom2) >= 0) count++; + if ((idx1 >= 0) && (idx1 < nlocal)) count++; + if ((idx2 >= 0) && (idx2 < nlocal)) count++; int allcount; MPI_Allreduce(&count,&allcount,1,MPI_INT,MPI_SUM,world); @@ -338,7 +342,7 @@ void CreateBonds::single_bond() int **bond_type = atom->bond_type; tagint **bond_atom = atom->bond_atom; - if ((m = atom->map(batom1)) >= 0) { + if ((m = idx1) >= 0) { if (num_bond[m] == atom->bond_per_atom) error->one(FLERR,"New bond exceeded bonds per atom in create_bonds"); bond_type[m][num_bond[m]] = btype; @@ -349,7 +353,7 @@ void CreateBonds::single_bond() if (force->newton_bond) return; - if ((m = atom->map(batom2)) >= 0) { + if ((m = idx2) >= 0) { if (num_bond[m] == atom->bond_per_atom) error->one(FLERR,"New bond exceeded bonds per atom in create_bonds"); bond_type[m][num_bond[m]] = btype; @@ -366,10 +370,15 @@ void CreateBonds::single_angle() // check that 3 atoms exist + const int nlocal = atom->nlocal; + const int idx1 = atom->map(aatom1); + const int idx2 = atom->map(aatom2); + const int idx3 = atom->map(aatom3); + int count = 0; - if (atom->map(aatom1) >= 0) count++; - if (atom->map(aatom2) >= 0) count++; - if (atom->map(aatom3) >= 0) count++; + if ((idx1 >= 0) && (idx1 < nlocal)) count++; + if ((idx2 >= 0) && (idx2 < nlocal)) count++; + if ((idx3 >= 0) && (idx3 < nlocal)) count++; int allcount; MPI_Allreduce(&count,&allcount,1,MPI_INT,MPI_SUM,world); @@ -384,7 +393,7 @@ void CreateBonds::single_angle() tagint **angle_atom2 = atom->angle_atom2; tagint **angle_atom3 = atom->angle_atom3; - if ((m = atom->map(aatom2)) >= 0) { + if ((m = idx2) >= 0) { if (num_angle[m] == atom->angle_per_atom) error->one(FLERR,"New angle exceeded angles per atom in create_bonds"); angle_type[m][num_angle[m]] = atype; @@ -397,7 +406,7 @@ void CreateBonds::single_angle() if (force->newton_bond) return; - if ((m = atom->map(aatom1)) >= 0) { + if ((m = idx1) >= 0) { if (num_angle[m] == atom->angle_per_atom) error->one(FLERR,"New angle exceeded angles per atom in create_bonds"); angle_type[m][num_angle[m]] = atype; @@ -407,7 +416,7 @@ void CreateBonds::single_angle() num_angle[m]++; } - if ((m = atom->map(aatom3)) >= 0) { + if ((m = idx3) >= 0) { if (num_angle[m] == atom->angle_per_atom) error->one(FLERR,"New angle exceeded angles per atom in create_bonds"); angle_type[m][num_angle[m]] = atype; @@ -426,11 +435,17 @@ void CreateBonds::single_dihedral() // check that 4 atoms exist + const int nlocal = atom->nlocal; + const int idx1 = atom->map(datom1); + const int idx2 = atom->map(datom2); + const int idx3 = atom->map(datom3); + const int idx4 = atom->map(datom4); + int count = 0; - if (atom->map(datom1) >= 0) count++; - if (atom->map(datom2) >= 0) count++; - if (atom->map(datom3) >= 0) count++; - if (atom->map(datom4) >= 0) count++; + if ((idx1 >= 0) && (idx1 < nlocal)) count++; + if ((idx2 >= 0) && (idx2 < nlocal)) count++; + if ((idx3 >= 0) && (idx3 < nlocal)) count++; + if ((idx4 >= 0) && (idx4 < nlocal)) count++; int allcount; MPI_Allreduce(&count,&allcount,1,MPI_INT,MPI_SUM,world); @@ -446,7 +461,7 @@ void CreateBonds::single_dihedral() tagint **dihedral_atom3 = atom->dihedral_atom3; tagint **dihedral_atom4 = atom->dihedral_atom4; - if ((m = atom->map(datom2)) >= 0) { + if ((m = idx2) >= 0) { if (num_dihedral[m] == atom->dihedral_per_atom) error->one(FLERR, "New dihedral exceeded dihedrals per atom in create_bonds"); @@ -461,7 +476,7 @@ void CreateBonds::single_dihedral() if (force->newton_bond) return; - if ((m = atom->map(datom1)) >= 0) { + if ((m = idx1) >= 0) { if (num_dihedral[m] == atom->dihedral_per_atom) error->one(FLERR, "New dihedral exceeded dihedrals per atom in create_bonds"); @@ -473,7 +488,7 @@ void CreateBonds::single_dihedral() num_dihedral[m]++; } - if ((m = atom->map(datom3)) >= 0) { + if ((m = idx3) >= 0) { if (num_dihedral[m] == atom->dihedral_per_atom) error->one(FLERR, "New dihedral exceeded dihedrals per atom in create_bonds"); @@ -485,7 +500,7 @@ void CreateBonds::single_dihedral() num_dihedral[m]++; } - if ((m = atom->map(datom4)) >= 0) { + if ((m = idx4) >= 0) { if (num_dihedral[m] == atom->dihedral_per_atom) error->one(FLERR, "New dihedral exceeded dihedrals per atom in create_bonds"); diff --git a/src/create_box.cpp b/src/create_box.cpp index 3a131099813e086d1dd961a28748824959cfe50e..b5e37b759ca0bd4b6ec0cd7c49aeacf859450bde 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 +#include +#include #include "create_box.h" #include "atom.h" #include "atom_vec.h" diff --git a/src/delete_atoms.cpp b/src/delete_atoms.cpp index f5324f95585417c787e149ddc0d3566cc79c49f1..e26ecad5f37a7e9fc44dce761dbf1f22b5895b40 100644 --- a/src/delete_atoms.cpp +++ b/src/delete_atoms.cpp @@ -11,8 +11,8 @@ 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 97eb1c09a857246f3236be089f73c1cb46008325..fe32bca87977d92ac7c8b3a8f64509117cb1e619 100644 --- a/src/delete_bonds.cpp +++ b/src/delete_bonds.cpp @@ -12,8 +12,8 @@ ------------------------------------------------------------------------- */ #include -#include -#include +#include +#include #include "delete_bonds.h" #include "atom.h" #include "atom_vec.h" diff --git a/src/dihedral.cpp b/src/dihedral.cpp index f5c1c6c44c143604cec5ec3aa9b1bbd8ea03688d..adccf2a490b32d90828b69110bbb97e512934b09 100644 --- a/src/dihedral.cpp +++ b/src/dihedral.cpp @@ -11,7 +11,7 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include +#include #include "dihedral.h" #include "atom.h" #include "comm.h" diff --git a/src/dihedral.h b/src/dihedral.h index d27810c4d6e79ede7d5875daced83861f2461346..627104871b9b51f8b13966af119e64a3b12c6f1a 100644 --- a/src/dihedral.h +++ b/src/dihedral.h @@ -14,7 +14,7 @@ #ifndef LMP_DIHEDRAL_H #define LMP_DIHEDRAL_H -#include +#include #include "pointers.h" namespace LAMMPS_NS { diff --git a/src/dihedral_hybrid.cpp b/src/dihedral_hybrid.cpp index 372a858d023e19730129c4bf8d85083b383e6514..b9107ac874cc674f01cda6c7fce741f21c58432a 100644 --- a/src/dihedral_hybrid.cpp +++ b/src/dihedral_hybrid.cpp @@ -11,9 +11,9 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include -#include -#include +#include +#include +#include #include "dihedral_hybrid.h" #include "atom.h" #include "neighbor.h" diff --git a/src/dihedral_hybrid.h b/src/dihedral_hybrid.h index 6e30d3d693373ca6859a52ac2a9f9acdab07c93b..0839fdfc61a8f6cdb9c45589d5cfbe6495d79167 100644 --- a/src/dihedral_hybrid.h +++ b/src/dihedral_hybrid.h @@ -20,7 +20,7 @@ DihedralStyle(hybrid,DihedralHybrid) #ifndef LMP_DIHEDRAL_HYBRID_H #define LMP_DIHEDRAL_HYBRID_H -#include +#include #include "dihedral.h" namespace LAMMPS_NS { diff --git a/src/dihedral_zero.cpp b/src/dihedral_zero.cpp index 9b0c569fcac8743bf3124bcfe1359aeb35f07e40..bdd2eaadd3d484e5f709531be0ac43635b826ed1 100644 --- a/src/dihedral_zero.cpp +++ b/src/dihedral_zero.cpp @@ -15,9 +15,9 @@ Contributing author: Carsten Svaneborg (SDU) ------------------------------------------------------------------------- */ -#include -#include -#include +#include +#include +#include #include "dihedral_zero.h" #include "atom.h" #include "force.h" diff --git a/src/dihedral_zero.h b/src/dihedral_zero.h index d27ff6abbad9f5acc0e00558a0a1482f4f89c7d9..e7dbb0d3a53a9dae1f675db394b6755f68efa42d 100644 --- a/src/dihedral_zero.h +++ b/src/dihedral_zero.h @@ -24,7 +24,7 @@ DihedralStyle(zero,DihedralZero) #ifndef LMP_DIHEDRAL_ZERO_H #define LMP_DIHEDRAL_ZERO_H -#include +#include #include "dihedral.h" namespace LAMMPS_NS { diff --git a/src/displace_atoms.cpp b/src/displace_atoms.cpp index 66988d467339c4d56a3b6d93ed136ab700473d23..04088bec8ce76233552a9f39da188d853eb0e7e1 100644 --- a/src/displace_atoms.cpp +++ b/src/displace_atoms.cpp @@ -12,8 +12,8 @@ ------------------------------------------------------------------------- */ #include -#include -#include +#include +#include #include "displace_atoms.h" #include "atom.h" #include "modify.h" diff --git a/src/domain.cpp b/src/domain.cpp index c4dcf20b6423dc48d98c28243dbec9f97738b3ec..eae4f3926df72c1c587785e78db2f79efdb12bcf 100644 --- a/src/domain.cpp +++ b/src/domain.cpp @@ -16,10 +16,10 @@ ------------------------------------------------------------------------- */ #include -#include -#include -#include -#include +#include +#include +#include +#include #include "domain.h" #include "style_region.h" #include "atom.h" @@ -518,7 +518,7 @@ void Domain::pbc() coord = &x[0][0]; // note: x is always initialized to at least one element. int flag = 0; for (i = 0; i < n3; i++) - if (!ISFINITE(*coord++)) flag = 1; + if (!std::isfinite(*coord++)) flag = 1; if (flag) error->one(FLERR,"Non-numeric atom coords - simulation unstable"); // setup for PBC checks diff --git a/src/domain.h b/src/domain.h index 649e722c50723ee4283a5cdba205d4c48c5311f9..fe2502c691476c32ebed7448ed035b4533f9d608 100644 --- a/src/domain.h +++ b/src/domain.h @@ -14,7 +14,7 @@ #ifndef LMP_DOMAIN_H #define LMP_DOMAIN_H -#include +#include #include "pointers.h" #include #include diff --git a/src/dump.cpp b/src/dump.cpp index be42693b8dacb7e2886b7fb1018f4a1271e01754..46e556600a8473ffa80feca8bc90a28e08a788f1 100644 --- a/src/dump.cpp +++ b/src/dump.cpp @@ -12,9 +12,9 @@ ------------------------------------------------------------------------- */ #include -#include -#include -#include +#include +#include +#include #include "dump.h" #include "atom.h" #include "irregular.h" diff --git a/src/dump.h b/src/dump.h index 472f69bfb9e95212c5d6e90579b0b46446fcb8b0..b726b9c3e73d764cbe1bfbaebbc2791f3fc52347 100644 --- a/src/dump.h +++ b/src/dump.h @@ -15,7 +15,7 @@ #define LMP_DUMP_H #include -#include +#include #include "pointers.h" namespace LAMMPS_NS { diff --git a/src/dump_atom.cpp b/src/dump_atom.cpp index 6221463920f18e1efdf7e87347ac274dc4d83e4e..74583f40131cead43003e76838ddeeac204555fd 100644 --- a/src/dump_atom.cpp +++ b/src/dump_atom.cpp @@ -11,7 +11,7 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include +#include #include "dump_atom.h" #include "domain.h" #include "atom.h" diff --git a/src/dump_cfg.cpp b/src/dump_cfg.cpp index 6ebdd0f99af74d2f0cee0db72caeda8df0c856ee..15f64688464ad35e20952de8adc746f787a42302 100644 --- a/src/dump_cfg.cpp +++ b/src/dump_cfg.cpp @@ -16,9 +16,9 @@ Memory efficiency improved by Ray Shan (Sandia) ------------------------------------------------------------------------- */ -#include -#include -#include +#include +#include +#include #include "dump_cfg.h" #include "atom.h" #include "domain.h" diff --git a/src/dump_custom.cpp b/src/dump_custom.cpp index 34ab2182049679750bb0c8f59b407d721f9c481d..174fcd73c875ac04f308d612d81ce25835712f4e 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 -#include -#include +#include +#include +#include #include "dump_custom.h" #include "atom.h" #include "force.h" diff --git a/src/dump_dcd.cpp b/src/dump_dcd.cpp index ca7246ab241f4875eeb0886215efa2baaa64d58a..384e9089c0a1781bfaaaf2eb87137a823382367b 100644 --- a/src/dump_dcd.cpp +++ b/src/dump_dcd.cpp @@ -16,11 +16,11 @@ Axel Kohlmeyer (Temple U), support for groups ------------------------------------------------------------------------- */ -#include -#include -#include -#include -#include +#include +#include // requires C++-11 +#include +#include +#include #include "dump_dcd.h" #include "domain.h" #include "atom.h" diff --git a/src/dump_image.cpp b/src/dump_image.cpp index 9ca6ad34e90fa88c99d317bd36c755325fd72949..60a1f545c9715d951d07590891e4f31888b3746c 100644 --- a/src/dump_image.cpp +++ b/src/dump_image.cpp @@ -11,10 +11,10 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include -#include -#include -#include +#include +#include +#include +#include #include "dump_image.h" #include "image.h" #include "atom.h" diff --git a/src/dump_local.cpp b/src/dump_local.cpp index ca8b1822a2611dfffae2fc6c6579f8995c434617..0d5172b5c1bdaf0de61828a464bc0e7b09a61006 100644 --- a/src/dump_local.cpp +++ b/src/dump_local.cpp @@ -12,8 +12,8 @@ ------------------------------------------------------------------------- */ #include -#include -#include +#include +#include #include "dump_local.h" #include "atom.h" #include "modify.h" diff --git a/src/dump_movie.cpp b/src/dump_movie.cpp index cb8982cabe38c400198d5427eda89b9677bccda3..59dfdc3d6e9e579ee49d851577182bbde622700a 100644 --- a/src/dump_movie.cpp +++ b/src/dump_movie.cpp @@ -15,9 +15,9 @@ Contributing author: Axel Kohlmeyer (Temple U) ------------------------------------------------------------------------- */ -#include -#include -#include +#include +#include +#include #include "dump_movie.h" #include "comm.h" #include "force.h" diff --git a/src/dump_xyz.cpp b/src/dump_xyz.cpp index 7059e855908a1b15551febca652b028e8a85c68a..fd52671d8140056f8fce6995d5f8e7e4680e6410 100644 --- a/src/dump_xyz.cpp +++ b/src/dump_xyz.cpp @@ -11,7 +11,7 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include +#include #include "dump_xyz.h" #include "atom.h" #include "group.h" diff --git a/src/error.cpp b/src/error.cpp index 9193314fc8c8674c445341d9e993c4690499da55..3c8d8bb34cda52a888342a6165f7a19424f91991 100644 --- a/src/error.cpp +++ b/src/error.cpp @@ -12,8 +12,8 @@ ------------------------------------------------------------------------- */ #include -#include -#include +#include +#include #include "error.h" #include "universe.h" #include "output.h" diff --git a/src/finish.cpp b/src/finish.cpp index c22b26782e7c63e9ae4ee1b7a9fcbdcbe2978770..f35fb7e3a502a785747b2c98476ee0aa4e2c3dd1 100644 --- a/src/finish.cpp +++ b/src/finish.cpp @@ -12,10 +12,10 @@ ------------------------------------------------------------------------- */ #include -#include -#include -#include -#include +#include +#include +#include +#include #include "finish.h" #include "timer.h" #include "universe.h" diff --git a/src/fix.cpp b/src/fix.cpp index 297d184967617100ae2ea25804ec5beb9d7e1217..a54e2957985207ee6c5a27f59ae70483763d251b 100644 --- a/src/fix.cpp +++ b/src/fix.cpp @@ -11,8 +11,8 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include -#include +#include +#include #include "fix.h" #include "atom.h" #include "group.h" diff --git a/src/fix_adapt.cpp b/src/fix_adapt.cpp index 10b09f4a7f56d5d14c49489eba9a0eb343ceebc9..754c9ea4da41230b46836b28ca69a6e990c77b05 100644 --- a/src/fix_adapt.cpp +++ b/src/fix_adapt.cpp @@ -11,9 +11,9 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include -#include -#include +#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 6b1e89227985acb0dc12336520962ff7599ffee3..c2eedccd6151e6306bcf11d6f7a380413434850a 100644 --- a/src/fix_addforce.cpp +++ b/src/fix_addforce.cpp @@ -11,8 +11,8 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include -#include +#include +#include #include "fix_addforce.h" #include "atom.h" #include "atom_masks.h" diff --git a/src/fix_ave_atom.cpp b/src/fix_ave_atom.cpp index c4222f6fcd056dde4816de1629394ec2e03f0b21..a8c3be07af55fe5eab76b1c35fbd3afe0b2340f4 100644 --- a/src/fix_ave_atom.cpp +++ b/src/fix_ave_atom.cpp @@ -11,8 +11,8 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include -#include +#include +#include #include "fix_ave_atom.h" #include "atom.h" #include "domain.h" diff --git a/src/fix_ave_atom.h b/src/fix_ave_atom.h index c2f5067309559903ede2270a424531224a23329e..e4baf6bda14bfc8672e1ae1818117826a1028ddd 100644 --- a/src/fix_ave_atom.h +++ b/src/fix_ave_atom.h @@ -20,7 +20,7 @@ FixStyle(ave/atom,FixAveAtom) #ifndef LMP_FIX_AVE_ATOM_H #define LMP_FIX_AVE_ATOM_H -#include +#include #include "fix.h" namespace LAMMPS_NS { diff --git a/src/fix_ave_chunk.cpp b/src/fix_ave_chunk.cpp index 8558e8695c10d3e04a5ef218aee8bc32e499b657..5f727fd3f747f6c9ec21cf7fcdf873cf57ecf5cb 100644 --- a/src/fix_ave_chunk.cpp +++ b/src/fix_ave_chunk.cpp @@ -11,8 +11,8 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include -#include +#include +#include #include #include "fix_ave_chunk.h" #include "atom.h" diff --git a/src/fix_ave_chunk.h b/src/fix_ave_chunk.h index a69b07f5d07986b060548e72fc4f96b59563fbd8..4dc1c1c24602e8947a027866222f7b6e843cab69 100644 --- a/src/fix_ave_chunk.h +++ b/src/fix_ave_chunk.h @@ -20,7 +20,7 @@ FixStyle(ave/chunk,FixAveChunk) #ifndef LMP_FIX_AVE_CHUNK_H #define LMP_FIX_AVE_CHUNK_H -#include +#include #include "fix.h" namespace LAMMPS_NS { diff --git a/src/fix_ave_correlate.cpp b/src/fix_ave_correlate.cpp index fffcc09d7ae7d3787397f229a918753b48d5abec..418464a2484b4884e58a2966a410eb9e092b1d38 100644 --- a/src/fix_ave_correlate.cpp +++ b/src/fix_ave_correlate.cpp @@ -17,8 +17,8 @@ Reese Jones (Sandia) ------------------------------------------------------------------------- */ -#include -#include +#include +#include #include #include "fix_ave_correlate.h" #include "update.h" diff --git a/src/fix_ave_correlate.h b/src/fix_ave_correlate.h index 6d2567e73073040d7332e3e41a1d2c84efac1e53..ff20e8ba94c2e54ec8c98cb735b734d0fb8a943f 100644 --- a/src/fix_ave_correlate.h +++ b/src/fix_ave_correlate.h @@ -20,7 +20,7 @@ FixStyle(ave/correlate,FixAveCorrelate) #ifndef LMP_FIX_AVE_CORRELATE_H #define LMP_FIX_AVE_CORRELATE_H -#include +#include #include "fix.h" namespace LAMMPS_NS { diff --git a/src/fix_ave_histo.cpp b/src/fix_ave_histo.cpp index e104512479f07ed93af3dcadc866de7cf557cb70..7aa599389979bac8cdfe48614a5302c7834a2bac 100644 --- a/src/fix_ave_histo.cpp +++ b/src/fix_ave_histo.cpp @@ -11,8 +11,8 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include -#include +#include +#include #include #include "fix_ave_histo.h" #include "atom.h" diff --git a/src/fix_ave_histo.h b/src/fix_ave_histo.h index 123122b05182f9ba72d1b5fc2d52c83011a46510..3616959c612a0e66760eaa21b588ddc4728a4bb7 100644 --- a/src/fix_ave_histo.h +++ b/src/fix_ave_histo.h @@ -20,7 +20,7 @@ FixStyle(ave/histo,FixAveHisto) #ifndef LMP_FIX_AVE_HISTO_H #define LMP_FIX_AVE_HISTO_H -#include +#include #include "fix.h" namespace LAMMPS_NS { diff --git a/src/fix_ave_histo_weight.cpp b/src/fix_ave_histo_weight.cpp index 37dd8c9898c74f16f5bea3d52aff364a12ab8d15..c78f4fa1e38765c2e150c59f840d00bc535deee4 100644 --- a/src/fix_ave_histo_weight.cpp +++ b/src/fix_ave_histo_weight.cpp @@ -15,8 +15,8 @@ Contributing author: Shawn Coleman (ARL) ------------------------------------------------------------------------- */ -#include -#include +#include +#include #include #include "fix_ave_histo_weight.h" #include "atom.h" diff --git a/src/fix_ave_histo_weight.h b/src/fix_ave_histo_weight.h index 22812384de036920a44fa25a3d96c1dd065447a6..e5638e121569cd5e328ad7760a3ea6b957af8938 100644 --- a/src/fix_ave_histo_weight.h +++ b/src/fix_ave_histo_weight.h @@ -20,7 +20,7 @@ FixStyle(ave/histo/weight,FixAveHistoWeight) #ifndef LMP_FIX_AVE_HISTO_WEIGHT_H #define LMP_FIX_AVE_HISTO_WEIGHT_H -#include +#include #include "fix_ave_histo.h" namespace LAMMPS_NS { diff --git a/src/fix_ave_time.cpp b/src/fix_ave_time.cpp index 5de32c7faea287cb391f2520dacd7b5aedbc0eec..c3ace296842b0cb3738c62b635ed7fb48854e48a 100644 --- a/src/fix_ave_time.cpp +++ b/src/fix_ave_time.cpp @@ -15,8 +15,8 @@ Contributing author: Pieter in 't Veld (SNL) ------------------------------------------------------------------------- */ -#include -#include +#include +#include #include #include "fix_ave_time.h" #include "update.h" diff --git a/src/fix_ave_time.h b/src/fix_ave_time.h index aa1d2333cfa74d05ac886b59ce96701c20d78eaa..62dfbad2963e90b29679929dbfaf3b488df6d06c 100644 --- a/src/fix_ave_time.h +++ b/src/fix_ave_time.h @@ -20,7 +20,7 @@ FixStyle(ave/time,FixAveTime) #ifndef LMP_FIX_AVE_TIME_H #define LMP_FIX_AVE_TIME_H -#include +#include #include "fix.h" namespace LAMMPS_NS { diff --git a/src/fix_aveforce.cpp b/src/fix_aveforce.cpp index 793c2d5c2b230756c34de697474180279839eca2..4432a5dd36d8aeb369a34c0523bc1592a83050a7 100644 --- a/src/fix_aveforce.cpp +++ b/src/fix_aveforce.cpp @@ -12,8 +12,8 @@ ------------------------------------------------------------------------- */ #include -#include -#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 9f29400d9a5291590c5f7ed83e9a6d90b26b33b1..29ea5360661a8779db624233f79594526f1d5a45 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 +#include +#include #include "fix_balance.h" #include "balance.h" #include "update.h" diff --git a/src/fix_balance.h b/src/fix_balance.h index 8b8759ec9783f5c3dfe201dabab823a672497657..64383b59508bce2ded60e67a7311a28cd164a9bc 100644 --- a/src/fix_balance.h +++ b/src/fix_balance.h @@ -20,7 +20,7 @@ FixStyle(balance,FixBalance) #ifndef LMP_FIX_BALANCE_H #define LMP_FIX_BALANCE_H -#include +#include #include "fix.h" namespace LAMMPS_NS { diff --git a/src/fix_box_relax.cpp b/src/fix_box_relax.cpp index 21bc09b259420113ec9b3c8307c1ebc6dc918479..a315330d149eb40f0f5fb7f4446f6495d8738149 100644 --- a/src/fix_box_relax.cpp +++ b/src/fix_box_relax.cpp @@ -15,9 +15,9 @@ Contributing author: Aidan Thompson (SNL) ------------------------------------------------------------------------- */ -#include -#include -#include +#include +#include +#include #include "fix_box_relax.h" #include "atom.h" #include "domain.h" diff --git a/src/fix_controller.cpp b/src/fix_controller.cpp index e283b1c19257b36758c4c685369fb03ae4fc8b26..eb7a79496253bd787e7baa1a33b59301cfa83773 100644 --- a/src/fix_controller.cpp +++ b/src/fix_controller.cpp @@ -11,8 +11,8 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include -#include +#include +#include #include "fix_controller.h" #include "force.h" #include "update.h" diff --git a/src/fix_deform.cpp b/src/fix_deform.cpp index 705f1970afa1d15658ed014dd3168f24d5b96b7a..65e1bee63b47310bff3931ff0b7b7679e91a9c1f 100644 --- a/src/fix_deform.cpp +++ b/src/fix_deform.cpp @@ -15,9 +15,9 @@ Contributing author: Pieter in 't Veld (SNL) ------------------------------------------------------------------------- */ -#include -#include -#include +#include +#include +#include #include "fix_deform.h" #include "atom.h" #include "update.h" diff --git a/src/fix_deprecated.cpp b/src/fix_deprecated.cpp index 9c0b6686d10e6c48b264c30f11b34537ae884e26..d0a63b00964471cd76666ae655f6e7205b0a7b8b 100644 --- a/src/fix_deprecated.cpp +++ b/src/fix_deprecated.cpp @@ -11,7 +11,7 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include +#include #include "fix_deprecated.h" #include "comm.h" #include "error.h" diff --git a/src/fix_drag.cpp b/src/fix_drag.cpp index 3fda219126cbccc3bc8463bb07eea26ae96d3259..6a69dddbf5d744a8028c3aac143def239e3991cf 100644 --- a/src/fix_drag.cpp +++ b/src/fix_drag.cpp @@ -11,9 +11,9 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include -#include -#include +#include +#include +#include #include "fix_drag.h" #include "atom.h" #include "update.h" diff --git a/src/fix_dt_reset.cpp b/src/fix_dt_reset.cpp index 48d09150a5337a3ba67e451b83d55fdeae01dc73..006bf27e77729c1f45078642f80bec2014631f65 100644 --- a/src/fix_dt_reset.cpp +++ b/src/fix_dt_reset.cpp @@ -11,9 +11,9 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include -#include -#include +#include +#include +#include #include "fix_dt_reset.h" #include "atom.h" #include "update.h" diff --git a/src/fix_enforce2d.cpp b/src/fix_enforce2d.cpp index 336fd125563579490a66d9107138c12f0fa5ca47..4ffd2ca7ac233342910b495e839ac293f5583dd4 100644 --- a/src/fix_enforce2d.cpp +++ b/src/fix_enforce2d.cpp @@ -11,7 +11,7 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include +#include #include "fix_enforce2d.h" #include "atom.h" #include "update.h" diff --git a/src/fix_external.cpp b/src/fix_external.cpp index a3b697bb2b6a006d78101a156c423fe5e2dda54d..4fcc842f899401eebc0f21e2fdf0abe86a7f3e41 100644 --- a/src/fix_external.cpp +++ b/src/fix_external.cpp @@ -11,9 +11,9 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include -#include -#include +#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 5582357c075eba7df09984ffb0c1a86b9b67fd23..9ace9d45ffcad6a3a6b86f3111e503ec3237b764 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 -#include -#include -#include +#include +#include +#include +#include #include "fix_gravity.h" #include "atom.h" #include "update.h" diff --git a/src/fix_group.cpp b/src/fix_group.cpp index 8479565891a77dd0ba1471d9560362755d097968..2447002bc5202350b779d390dc31124a7f5dd5a1 100644 --- a/src/fix_group.cpp +++ b/src/fix_group.cpp @@ -11,7 +11,7 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include +#include #include "fix_group.h" #include "group.h" #include "update.h" @@ -251,3 +251,13 @@ void FixGroup::set_group() if (varflag) memory->destroy(var); } + +/* ---------------------------------------------------------------------- */ + +void *FixGroup::extract(const char *str, int &unused) +{ + if (strcmp(str,"property") == 0 && propflag) return (void *) idprop; + if (strcmp(str,"variable") == 0 && varflag) return (void *) idvar; + if (strcmp(str,"region") == 0 && regionflag) return (void *) idregion; + return NULL; +} diff --git a/src/fix_group.h b/src/fix_group.h index 070b4801bca3a9e8ab1a15379a52a2182c7bc38c..f3fecac31605a8a38b84a11b35ca2b27456dd9c8 100644 --- a/src/fix_group.h +++ b/src/fix_group.h @@ -33,6 +33,7 @@ class FixGroup : public Fix { void setup(int); void post_integrate(); void post_integrate_respa(int,int); + void *extract(const char *,int &); private: int gbit,gbitinverse; @@ -69,7 +70,7 @@ Self-explanatory. E: Per atom property for group dynamic does not exist -UNDOCUMENTED +Self-explanatory. E: Group dynamic parent group cannot be dynamic @@ -79,10 +80,6 @@ E: Variable for group dynamic is invalid style The variable must be an atom-style variable. -E: Per-atom property for group dynamic does not exist - -UNDOCUMENTED - W: One or more dynamic groups may not be updated at correct point in timestep If there are other fixes that act immediately after the initial stage diff --git a/src/fix_halt.cpp b/src/fix_halt.cpp index 48d0f5da25ae55b9de9683980e41126cfb930ae4..7de09a0fa4b9add400543a97a62f2f8a73ad2f74 100644 --- a/src/fix_halt.cpp +++ b/src/fix_halt.cpp @@ -11,9 +11,9 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include -#include -#include +#include +#include +#include #include "fix_halt.h" #include "update.h" #include "force.h" diff --git a/src/fix_halt.h b/src/fix_halt.h index 73c8d0115a100979da441c3629e9166901133126..d3b39cc1e2af13ee04d1813e738df6f5ad11c6e3 100644 --- a/src/fix_halt.h +++ b/src/fix_halt.h @@ -20,7 +20,7 @@ FixStyle(halt,FixHalt) #ifndef LMP_FIX_HALT_H #define LMP_FIX_HALT_H -#include +#include #include "fix.h" namespace LAMMPS_NS { diff --git a/src/fix_heat.cpp b/src/fix_heat.cpp index 846531dbb987eaa3c1870c4c5c20e1ba1448f82c..f34845785c03b583e508ddd671d97023c4dd3e9a 100644 --- a/src/fix_heat.cpp +++ b/src/fix_heat.cpp @@ -15,9 +15,9 @@ Contributing author: Paul Crozier (SNL) ------------------------------------------------------------------------- */ -#include -#include -#include +#include +#include +#include #include "fix_heat.h" #include "atom.h" #include "domain.h" diff --git a/src/fix_indent.cpp b/src/fix_indent.cpp index 331d84ff9aa61edded4b18edfb69382c41f52c3c..ade8cee5328d711ddbfd6ccb4088fe49120f7b88 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 +#include #include "fix_indent.h" #include "atom.h" #include "input.h" diff --git a/src/fix_langevin.cpp b/src/fix_langevin.cpp index 22993530010c9b0a016bb04e67006d6232e111e1..e4c36cc73917fe0f7d6b8b7ad094741d94cb1f8d 100644 --- a/src/fix_langevin.cpp +++ b/src/fix_langevin.cpp @@ -17,9 +17,9 @@ ------------------------------------------------------------------------- */ #include -#include -#include -#include +#include +#include +#include #include "fix_langevin.h" #include "math_extra.h" #include "atom.h" diff --git a/src/fix_lineforce.cpp b/src/fix_lineforce.cpp index 1e78bf3ec390130d229509bdec35d17d4a52e9c1..e90152c4e1092ef95b94df1371f6131f94e8d979 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 -#include -#include +#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 cc00cc286ac98e625984b438ba228a45d99364f0..06a3ac900d7cd28209682056d923b6889ecc37d2 100644 --- a/src/fix_minimize.cpp +++ b/src/fix_minimize.cpp @@ -11,7 +11,7 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include +#include #include "fix_minimize.h" #include "atom.h" #include "domain.h" diff --git a/src/fix_momentum.cpp b/src/fix_momentum.cpp index 63ec71f10d592f4d8f782f87f7fb8a37a0b302f1..680251e670a44330782eaab69619a55119a2c7de 100644 --- a/src/fix_momentum.cpp +++ b/src/fix_momentum.cpp @@ -11,8 +11,8 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include -#include +#include +#include #include "fix_momentum.h" #include "atom.h" #include "domain.h" diff --git a/src/fix_move.cpp b/src/fix_move.cpp index a32c80c1e9e7d29fa5d098c086171a1cbb40ab3b..9eadfa5ab4c7c9b2a41102e9997f90178633d9bc 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 -#include -#include +#include +#include +#include #include "fix_move.h" #include "atom.h" #include "group.h" diff --git a/src/fix_move.h b/src/fix_move.h index 13c9bc66b83cc4627eb6b5ee20f7becf7954bd88..5993d7d6e808f0e57b3427660c8d58e6bea6daeb 100644 --- a/src/fix_move.h +++ b/src/fix_move.h @@ -20,7 +20,7 @@ FixStyle(move,FixMove) #ifndef LMP_FIX_MOVE_H #define LMP_FIX_MOVE_H -#include +#include #include "fix.h" namespace LAMMPS_NS { diff --git a/src/fix_neigh_history.cpp b/src/fix_neigh_history.cpp index e8bfe840d8059b6b9ac0d20ad1e7132e995b357f..3329b604efa4a0e2f6310e34cce95d7ca6902a14 100644 --- a/src/fix_neigh_history.cpp +++ b/src/fix_neigh_history.cpp @@ -12,8 +12,8 @@ ------------------------------------------------------------------------- */ #include -#include -#include +#include +#include #include "fix_neigh_history.h" #include "atom.h" #include "comm.h" diff --git a/src/fix_nh.cpp b/src/fix_nh.cpp index e4500b19ca09c189f867b1e11819cd7af7e407bd..186376d95230bc8d2bbbf977c95fba8c5c16243f 100644 --- a/src/fix_nh.cpp +++ b/src/fix_nh.cpp @@ -15,9 +15,9 @@ Contributing authors: Mark Stevens (SNL), Aidan Thompson (SNL) ------------------------------------------------------------------------- */ -#include -#include -#include +#include +#include +#include #include "fix_nh.h" #include "math_extra.h" #include "atom.h" @@ -1034,7 +1034,7 @@ void FixNH::couple() p_current[2] = tensor[2]; } - if (!ISFINITE(p_current[0]) || !ISFINITE(p_current[1]) || !ISFINITE(p_current[2])) + if (!std::isfinite(p_current[0]) || !std::isfinite(p_current[1]) || !std::isfinite(p_current[2])) error->all(FLERR,"Non-numeric pressure - simulation unstable"); // switch order from xy-xz-yz to Voigt @@ -1044,7 +1044,7 @@ void FixNH::couple() p_current[4] = tensor[4]; p_current[5] = tensor[3]; - if (!ISFINITE(p_current[3]) || !ISFINITE(p_current[4]) || !ISFINITE(p_current[5])) + if (!std::isfinite(p_current[3]) || !std::isfinite(p_current[4]) || !std::isfinite(p_current[5])) error->all(FLERR,"Non-numeric pressure - simulation unstable"); } } diff --git a/src/fix_nh_sphere.cpp b/src/fix_nh_sphere.cpp index cc59e4a1016eef159e0b4e04f21dc9f21bfa111c..f1764932429c84c80f9660a777153eff82470060 100644 --- a/src/fix_nh_sphere.cpp +++ b/src/fix_nh_sphere.cpp @@ -15,7 +15,7 @@ Contributing author: Mike Brown (SNL) ------------------------------------------------------------------------- */ -#include +#include #include "fix_nh_sphere.h" #include "atom.h" #include "atom_vec.h" diff --git a/src/fix_nph.cpp b/src/fix_nph.cpp index a331a07d2404c30b0b61bfd27580dd2a76782f95..40265ef57c6e278a5260a5a007d3a1597d758c44 100644 --- a/src/fix_nph.cpp +++ b/src/fix_nph.cpp @@ -11,7 +11,7 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include +#include #include "fix_nph.h" #include "modify.h" #include "error.h" diff --git a/src/fix_nph_sphere.cpp b/src/fix_nph_sphere.cpp index 852234074f0c212bf53691508e1275289fbbe878..3fcbe5e9c686e7801156570b42021c03ab60e9fa 100644 --- a/src/fix_nph_sphere.cpp +++ b/src/fix_nph_sphere.cpp @@ -11,7 +11,7 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include +#include #include "fix_nph_sphere.h" #include "modify.h" #include "error.h" diff --git a/src/fix_npt.cpp b/src/fix_npt.cpp index e14200f6a2617af055f13ca0ddffe015bb897fbe..d17577d68d7c1e751f3d19a43eb4f5d1da9ac497 100644 --- a/src/fix_npt.cpp +++ b/src/fix_npt.cpp @@ -11,7 +11,7 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include +#include #include "fix_npt.h" #include "modify.h" #include "error.h" diff --git a/src/fix_npt_sphere.cpp b/src/fix_npt_sphere.cpp index d3773e0d177296eeab5edc912bae43e1ce41fc93..50ac990dafc0ad3295ff6821472611e9b3011e76 100644 --- a/src/fix_npt_sphere.cpp +++ b/src/fix_npt_sphere.cpp @@ -11,7 +11,7 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include +#include #include "fix_npt_sphere.h" #include "modify.h" #include "error.h" diff --git a/src/fix_nve.cpp b/src/fix_nve.cpp index 64ec3373f12c81137a7884c25f358bcc2e609174..58e33b9744b7c84eac6ca72b6d05ae7b502b571d 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 +#include +#include #include "fix_nve.h" #include "atom.h" #include "force.h" diff --git a/src/fix_nve_limit.cpp b/src/fix_nve_limit.cpp index 6f85d107f113c178332c03450d55a77d0ee44747..f659597af7aeeb0d35081ed02aa43736d58fe8a1 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 -#include -#include -#include +#include +#include +#include +#include #include "fix_nve_limit.h" #include "atom.h" #include "force.h" diff --git a/src/fix_nve_noforce.cpp b/src/fix_nve_noforce.cpp index aa24c26e03ff9bc7462da80aafb913dcc2258938..3403f4f5ec6b7f2eb7b71229159c18f3136b252e 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 +#include +#include #include "fix_nve_noforce.h" #include "atom.h" #include "update.h" diff --git a/src/fix_nve_sphere.cpp b/src/fix_nve_sphere.cpp index daf89871ab60a459f339959d2bf5abb4dce22d99..fe37324cfbac2164ea0bd04940df8145f12f7e7f 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 -#include -#include +#include +#include +#include #include "fix_nve_sphere.h" #include "atom.h" #include "domain.h" diff --git a/src/fix_nvt.cpp b/src/fix_nvt.cpp index 35ee085da1bb86a49038ae8da123357e80fd7009..7247612dd470bc71ce513e2ae2c1aef042508572 100644 --- a/src/fix_nvt.cpp +++ b/src/fix_nvt.cpp @@ -11,7 +11,7 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include +#include #include "fix_nvt.h" #include "group.h" #include "modify.h" diff --git a/src/fix_nvt_sllod.cpp b/src/fix_nvt_sllod.cpp index 87e86f235179e6e726719a4bed540990ed0f0365..270d721a008552e1de3ac0096df02cbfd7b17529 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 +#include +#include #include "fix_nvt_sllod.h" #include "math_extra.h" #include "atom.h" diff --git a/src/fix_nvt_sphere.cpp b/src/fix_nvt_sphere.cpp index b65b3adfae38b1509e347ee53201b00b7fffc4bb..44046699ba96e16da7a787695a35bd49a00e7c67 100644 --- a/src/fix_nvt_sphere.cpp +++ b/src/fix_nvt_sphere.cpp @@ -11,7 +11,7 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include +#include #include "fix_nvt_sphere.h" #include "group.h" #include "modify.h" diff --git a/src/fix_planeforce.cpp b/src/fix_planeforce.cpp index 5e999c888cfdc9e2ab2b30a4e89bb8e9146f6da3..f90be6a233a330a9687ce56b7864d2bdda6128e6 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 -#include -#include +#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 04e2b3d39c535724b92f29fbc080d8b14c801b22..792154e93fe6dc222d1e9902019297731f48a486 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 -#include -#include +#include +#include +#include #include "fix_press_berendsen.h" #include "atom.h" #include "force.h" diff --git a/src/fix_print.cpp b/src/fix_print.cpp index b553a94e3a19eebfe1777eba3b54c2c92f5b9f64..16218e0088e7ab0d04c560bbb975bdace7d41ebd 100644 --- a/src/fix_print.cpp +++ b/src/fix_print.cpp @@ -11,8 +11,8 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include -#include +#include +#include #include "fix_print.h" #include "update.h" #include "input.h" diff --git a/src/fix_print.h b/src/fix_print.h index c3897b815f5fd8a7783a7aabc8f3cbda7f0d8181..1f6efdf10851f9c9780b09caf145555a9ac471da 100644 --- a/src/fix_print.h +++ b/src/fix_print.h @@ -20,7 +20,7 @@ FixStyle(print,FixPrint) #ifndef LMP_FIX_PRINT_H #define LMP_FIX_PRINT_H -#include +#include #include "fix.h" namespace LAMMPS_NS { diff --git a/src/fix_property_atom.cpp b/src/fix_property_atom.cpp index 9ef939c58dc2a836ab0c143446b7736680bd4c0e..5ad4dfa4ba1bf2a3d4cee54695d80d28aa98bc71 100644 --- a/src/fix_property_atom.cpp +++ b/src/fix_property_atom.cpp @@ -11,8 +11,8 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include -#include +#include +#include #include "fix_property_atom.h" #include "atom.h" #include "comm.h" diff --git a/src/fix_read_restart.cpp b/src/fix_read_restart.cpp index f174e8160d709d394985d3d3ace43bc5f9b19e95..b384234b99973c51aa8c8a8ce765e99257bc5b0d 100644 --- a/src/fix_read_restart.cpp +++ b/src/fix_read_restart.cpp @@ -11,7 +11,7 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include +#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 499e1a4158cd57540b52d72f4af25153df0d1074..49e370ac806ead4df1a1845dacdd1341503d9630 100644 --- a/src/fix_recenter.cpp +++ b/src/fix_recenter.cpp @@ -15,8 +15,8 @@ Contributing author: Naveen Michaud-Agrawal (Johns Hopkins U) ------------------------------------------------------------------------- */ -#include -#include +#include +#include #include "fix_recenter.h" #include "atom.h" #include "group.h" diff --git a/src/fix_respa.cpp b/src/fix_respa.cpp index 0b6febd7b8329c0db139a35173b3d2dfaeee4bdb..3b9aad1286c4e62dbab97e505cdd3afcd7ab6cee 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 +#include +#include #include "fix_respa.h" #include "atom.h" #include "force.h" diff --git a/src/fix_restrain.cpp b/src/fix_restrain.cpp index af11136d78d666851d4f446dac505ed526409632..09cb8946e51d86692b201e4e5473f8839b0fc30a 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 +#include #include "fix_restrain.h" #include "atom.h" #include "force.h" @@ -45,7 +45,7 @@ enum{BOND,ANGLE,DIHEDRAL}; FixRestrain::FixRestrain(LAMMPS *lmp, int narg, char **arg) : Fix(lmp, narg, arg), - rstyle(NULL), ids(NULL), kstart(NULL), kstop(NULL), target(NULL), + rstyle(NULL), mult(NULL), ids(NULL), kstart(NULL), kstop(NULL), target(NULL), cos_target(NULL), sin_target(NULL) { if (narg < 4) error->all(FLERR,"Illegal fix restrain command"); @@ -65,6 +65,7 @@ FixRestrain::FixRestrain(LAMMPS *lmp, int narg, char **arg) : if (nrestrain == maxrestrain) { maxrestrain += DELTA; memory->grow(rstyle,maxrestrain,"restrain:rstyle"); + memory->grow(mult,maxrestrain,"restrain:mult"); memory->grow(ids,maxrestrain,4,"restrain:ids"); memory->grow(kstart,maxrestrain,"restrain:kstart"); memory->grow(kstop,maxrestrain,"restrain:kstop"); @@ -96,6 +97,7 @@ FixRestrain::FixRestrain(LAMMPS *lmp, int narg, char **arg) : } else if (strcmp(arg[iarg],"dihedral") == 0) { if (iarg+8 > narg) error->all(FLERR,"Illegal fix restrain command"); rstyle[nrestrain] = DIHEDRAL; + mult[nrestrain] = 1; ids[nrestrain][0] = force->inumeric(FLERR,arg[iarg+1]); ids[nrestrain][1] = force->inumeric(FLERR,arg[iarg+2]); ids[nrestrain][2] = force->inumeric(FLERR,arg[iarg+3]); @@ -107,6 +109,13 @@ FixRestrain::FixRestrain(LAMMPS *lmp, int narg, char **arg) : cos_target[nrestrain] = cos(target[nrestrain]); sin_target[nrestrain] = sin(target[nrestrain]); iarg += 8; + if ((iarg < narg) && (strcmp("mult",arg[iarg]) == 0)) { + if (iarg+1 > narg) error->all(FLERR,"Illegal fix restrain command"); + mult[nrestrain] = force->inumeric(FLERR,arg[iarg+1]); + if (mult[nrestrain] < 0) + error->all(FLERR,"Illegal fix restrain command"); + iarg += 2; + } } else error->all(FLERR,"Illegal fix restrain command"); nrestrain++; @@ -123,6 +132,7 @@ FixRestrain::FixRestrain(LAMMPS *lmp, int narg, char **arg) : FixRestrain::~FixRestrain() { memory->destroy(rstyle); + memory->destroy(mult); memory->destroy(ids); memory->destroy(kstart); memory->destroy(kstop); @@ -261,7 +271,7 @@ void FixRestrain::restrain_bond(int m) if (r > 0.0) fbond = -2.0*rk/r; else fbond = 0.0; - energy = rk*dr; + energy += rk*dr; // apply force to each of 2 atoms @@ -368,7 +378,7 @@ void FixRestrain::restrain_angle(int m) dtheta = acos(c) - target[m]; tk = k * dtheta; - energy = tk*dtheta; + energy += tk*dtheta; a = -2.0 * tk * s; a11 = a*c / rsq1; @@ -410,7 +420,7 @@ void FixRestrain::restrain_angle(int m) void FixRestrain::restrain_dihedral(int m) { - int i1,i2,i3,i4,i,mult; + int i1,i2,i3,i4,i; double vb1x,vb1y,vb1z,vb2x,vb2y,vb2z,vb3x,vb3y,vb3z,vb2xm,vb2ym,vb2zm; double f1[3],f2[3],f3[3],f4[3]; double ax,ay,az,bx,by,bz,rasq,rbsq,rgsq,rg,rginv,ra2inv,rb2inv,rabinv; @@ -534,11 +544,10 @@ void FixRestrain::restrain_dihedral(int m) if (c > 1.0) c = 1.0; if (c < -1.0) c = -1.0; - mult = 1; // multiplicity p = 1.0; df1 = 0.0; - for (i = 0; i < mult; i++) { + for (i = 0; i < mult[m]; i++) { ddf1 = p*c - df1*s; df1 = p*s + df1*c; p = ddf1; @@ -546,10 +555,10 @@ void FixRestrain::restrain_dihedral(int m) p = p*cos_target[m] + df1*sin_target[m]; df1 = df1*cos_target[m] - ddf1*sin_target[m]; - df1 *= -mult; + df1 *= -mult[m]; p += 1.0; - energy = k * p; + energy += k * p; fg = vb1x*vb2xm + vb1y*vb2ym + vb1z*vb2zm; hg = vb3x*vb2xm + vb3y*vb2ym + vb3z*vb2zm; diff --git a/src/fix_restrain.h b/src/fix_restrain.h index a6f23f86c6c311afeee63dac0b1da5b9456e20ce..14699ed5af38965d0e42768aec6e2fc114d3deea 100644 --- a/src/fix_restrain.h +++ b/src/fix_restrain.h @@ -41,6 +41,7 @@ class FixRestrain : public Fix { int ilevel_respa; int nrestrain,maxrestrain; int *rstyle; + int *mult; int **ids; double *kstart,*kstop,*target; double *cos_target,*sin_target; diff --git a/src/fix_setforce.cpp b/src/fix_setforce.cpp index 99176bb3799c76444f3555c7f028434868507391..89b340b0ae422558e666f81190bb3c4055abf69c 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 #include "fix_setforce.h" #include "atom.h" #include "update.h" diff --git a/src/fix_spring.cpp b/src/fix_spring.cpp index 9c6bd4084ffe53c568bd5edefe9ba0ecd4517bde..ecb84eeb0f0ead6b4aec161ae43b8a38d6e8fc89 100644 --- a/src/fix_spring.cpp +++ b/src/fix_spring.cpp @@ -15,9 +15,9 @@ Contributing author: Paul Crozier (SNL) ------------------------------------------------------------------------- */ -#include -#include -#include +#include +#include +#include #include "fix_spring.h" #include "atom.h" #include "update.h" diff --git a/src/fix_spring_chunk.cpp b/src/fix_spring_chunk.cpp index 773e032388b225fc1590c37b7f715116ebb4106a..53e9285a9c7ddd4869bb760c8b5cc60be790b073 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 -#include -#include +#include +#include +#include #include "fix_spring_chunk.h" #include "atom.h" #include "update.h" diff --git a/src/fix_spring_rg.cpp b/src/fix_spring_rg.cpp index b7fd33ce7749c2dfb1b0c445edf41273a1a18a1c..c2e226a343dc657b5661f24b6991d390cac4f1ff 100644 --- a/src/fix_spring_rg.cpp +++ b/src/fix_spring_rg.cpp @@ -16,9 +16,9 @@ Paul Crozier (SNL) ------------------------------------------------------------------------- */ -#include -#include -#include +#include +#include +#include #include "fix_spring_rg.h" #include "atom.h" #include "update.h" diff --git a/src/fix_spring_self.cpp b/src/fix_spring_self.cpp index b6d5e3c834d48a585658acf09999ae814c844199..1a5c89c6a15b43832f190d7f73dcfeaef3cf6383 100644 --- a/src/fix_spring_self.cpp +++ b/src/fix_spring_self.cpp @@ -15,8 +15,8 @@ Contributing author: Naveen Michaud-Agrawal (Johns Hopkins University) ------------------------------------------------------------------------- */ -#include -#include +#include +#include #include "fix_spring_self.h" #include "atom.h" #include "update.h" diff --git a/src/fix_store.cpp b/src/fix_store.cpp index 3738629820e45e146b6ba569b7c2f459e815351c..3b1f3dca77dde1d15d645938e000a012c202ee9c 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 +#include +#include #include "fix_store.h" #include "atom.h" #include "comm.h" diff --git a/src/fix_store.h b/src/fix_store.h index 1aad56323244c937850134658b899a8b7def75ad..5524770a9700be426df90671e5be2336c499b6f9 100644 --- a/src/fix_store.h +++ b/src/fix_store.h @@ -20,7 +20,7 @@ FixStyle(STORE,FixStore) #ifndef LMP_FIX_STORE_H #define LMP_FIX_STORE_H -#include +#include #include "fix.h" namespace LAMMPS_NS { diff --git a/src/fix_store_force.cpp b/src/fix_store_force.cpp index cfeace532627c68a28ddf00a5c8e9a09cffa8f6d..5e2150f68d004cdd6a82d0f416ddbd00311520d7 100644 --- a/src/fix_store_force.cpp +++ b/src/fix_store_force.cpp @@ -11,7 +11,7 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include +#include #include "fix_store_force.h" #include "atom.h" #include "update.h" diff --git a/src/fix_store_state.cpp b/src/fix_store_state.cpp index 2f2ba3feff7ffbcf7deea48f91568e8cdc846874..3195e983e35019adb4c627f20a62bffa18dae2e3 100644 --- a/src/fix_store_state.cpp +++ b/src/fix_store_state.cpp @@ -11,8 +11,8 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include -#include +#include +#include #include "fix_store_state.h" #include "atom.h" #include "domain.h" diff --git a/src/fix_temp_berendsen.cpp b/src/fix_temp_berendsen.cpp index 7b312cfb5f35dbc1777aeb9e63c3a530ed1e9d9c..55518015c4a1a5bfd743e369d7b92a500ee1e2ed 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 -#include -#include +#include +#include +#include #include "fix_temp_berendsen.h" #include "atom.h" #include "force.h" diff --git a/src/fix_temp_csld.cpp b/src/fix_temp_csld.cpp index 63f27cdecb17968ecbc6f265ef78a45018a70535..7bdf7763555c56841348040e0f4f78bd246cd9b1 100644 --- a/src/fix_temp_csld.cpp +++ b/src/fix_temp_csld.cpp @@ -15,9 +15,9 @@ Contributing author: Axel Kohlmeyer (Temple U) ------------------------------------------------------------------------- */ -#include -#include -#include +#include +#include +#include #include "fix_temp_csld.h" #include "atom.h" #include "force.h" diff --git a/src/fix_temp_csvr.cpp b/src/fix_temp_csvr.cpp index ae5868ff0ff7902859ac61b6b3cc40f072ac882c..495a1551135f48c37fb5c29d1a132434e5ed1f71 100644 --- a/src/fix_temp_csvr.cpp +++ b/src/fix_temp_csvr.cpp @@ -16,9 +16,9 @@ Based on code by Paolo Raiteri (Curtin U) and Giovanni Bussi (SISSA) ------------------------------------------------------------------------- */ -#include -#include -#include +#include +#include +#include #include "fix_temp_csvr.h" #include "atom.h" #include "force.h" diff --git a/src/fix_temp_rescale.cpp b/src/fix_temp_rescale.cpp index 52e2da7b3de2b35e7afb35fae4746f404041c214..11dfa6a5fcdf05c4e75a459f3bc5d74503616e83 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 -#include -#include +#include +#include +#include #include "fix_temp_rescale.h" #include "atom.h" #include "force.h" diff --git a/src/fix_tmd.cpp b/src/fix_tmd.cpp index f5ed970da7eb480a5b440ca94b5c6ef8e4253483..39d4173a63a058a40030512287d7441123266d63 100644 --- a/src/fix_tmd.cpp +++ b/src/fix_tmd.cpp @@ -17,9 +17,9 @@ ------------------------------------------------------------------------- */ #include -#include -#include -#include +#include +#include +#include #include "fix_tmd.h" #include "atom.h" #include "update.h" diff --git a/src/fix_tmd.h b/src/fix_tmd.h index 337b037c2dad317ec79c4b4986864b9a4f2094bf..b6db41dd5a158361be5d000fd416c0afc9b216c3 100644 --- a/src/fix_tmd.h +++ b/src/fix_tmd.h @@ -20,7 +20,7 @@ FixStyle(tmd,FixTMD) #ifndef LMP_FIX_TMD_H #define LMP_FIX_TMD_H -#include +#include #include "fix.h" namespace LAMMPS_NS { diff --git a/src/fix_vector.cpp b/src/fix_vector.cpp index 4847926aaf60e6cb20060712a76a3e0e075b513c..9b7f01697084ce3e705dc1920de8b11f0b024a62 100644 --- a/src/fix_vector.cpp +++ b/src/fix_vector.cpp @@ -11,7 +11,7 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include +#include #include "fix_vector.h" #include "update.h" #include "force.h" diff --git a/src/fix_viscous.cpp b/src/fix_viscous.cpp index 423bccc38323aecae8b07fc9cbbf34d7c7308e1c..1d2609c8b68ff782ba1e41c7798f4e944a6ed646 100644 --- a/src/fix_viscous.cpp +++ b/src/fix_viscous.cpp @@ -11,9 +11,9 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include -#include -#include +#include +#include +#include #include "fix_viscous.h" #include "atom.h" #include "update.h" diff --git a/src/fix_wall.cpp b/src/fix_wall.cpp index 2c3aa4afa0bd01856af22e5dee54bfedc5f19414..096bbe618a5a9b3fa234292807912f32642d210c 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 -#include -#include +#include +#include +#include #include "fix_wall.h" #include "atom.h" #include "input.h" diff --git a/src/fix_wall_harmonic.cpp b/src/fix_wall_harmonic.cpp index 20d5dbebd4fef90efff97feb14114cde107efea4..4dc067178ad5d42da7f4f6c0eb580adff908df1e 100644 --- a/src/fix_wall_harmonic.cpp +++ b/src/fix_wall_harmonic.cpp @@ -11,7 +11,7 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include +#include #include "fix_wall_harmonic.h" #include "atom.h" #include "error.h" diff --git a/src/fix_wall_lj1043.cpp b/src/fix_wall_lj1043.cpp index 35bfff1749e97c3392c6abf7ac5f79ad6af6ce5b..a93f4dd699c6424cfdc2d918aba8ab862df13cd9 100644 --- a/src/fix_wall_lj1043.cpp +++ b/src/fix_wall_lj1043.cpp @@ -15,7 +15,7 @@ Contributing author: Jonathan Lee (Sandia) ------------------------------------------------------------------------- */ -#include +#include #include "fix_wall_lj1043.h" #include "atom.h" #include "math_const.h" diff --git a/src/fix_wall_lj126.cpp b/src/fix_wall_lj126.cpp index f556952ab3de5ec9bd7dff1118b3848f09c0016a..369ef78c97875ee693c2e0151e8527270068cfeb 100644 --- a/src/fix_wall_lj126.cpp +++ b/src/fix_wall_lj126.cpp @@ -11,7 +11,7 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include +#include #include "fix_wall_lj126.h" #include "atom.h" #include "error.h" diff --git a/src/fix_wall_lj93.cpp b/src/fix_wall_lj93.cpp index f5d6a7e147d19ae5c062fc6157fe57c43738cf0e..ce5a06c81b956fbafe3570c73903a7a52afdc802 100644 --- a/src/fix_wall_lj93.cpp +++ b/src/fix_wall_lj93.cpp @@ -11,7 +11,7 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include +#include #include "fix_wall_lj93.h" #include "atom.h" #include "error.h" diff --git a/src/fix_wall_reflect.cpp b/src/fix_wall_reflect.cpp index 86607dbe8e611078ba7f59de9c5c8b0984b4dded..8acba720352dc38030263f29486b55c77be4e539 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 +#include +#include #include "fix_wall_reflect.h" #include "atom.h" #include "comm.h" diff --git a/src/fix_wall_region.cpp b/src/fix_wall_region.cpp index 67b0bcd713750403bcc007d741e90aeae26387ef..ea1b62bfa5e160688cd7913e9cad106e5db60535 100644 --- a/src/fix_wall_region.cpp +++ b/src/fix_wall_region.cpp @@ -11,9 +11,9 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include -#include -#include +#include +#include +#include #include "fix_wall_region.h" #include "atom.h" #include "atom_vec.h" diff --git a/src/force.cpp b/src/force.cpp index df32930e0ab0aa750215dd7299d3611a13958e5e..8ee301982d168c6f5c8389bee86d3d2404bcf903 100644 --- a/src/force.cpp +++ b/src/force.cpp @@ -11,9 +11,9 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include -#include -#include +#include +#include +#include #include "force.h" #include "style_bond.h" #include "style_angle.h" diff --git a/src/force.h b/src/force.h index 76cd69ed76e62146f6007a97b5bc7fede686daa2..ce593fa518a0b772f528be8a3cb5269c440f2c26 100644 --- a/src/force.h +++ b/src/force.h @@ -15,7 +15,7 @@ #define LMP_FORCE_H #include "pointers.h" -#include +#include #include #include diff --git a/src/group.cpp b/src/group.cpp index 72224dcf25b58c186b544f9135e93ca4082aa847..9d33da9acb4e623ea80a0e1f5e9e5fe1928ada07 100644 --- a/src/group.cpp +++ b/src/group.cpp @@ -12,10 +12,10 @@ ------------------------------------------------------------------------- */ #include -#include -#include -#include -#include +#include +#include +#include +#include #include "group.h" #include "domain.h" #include "atom.h" diff --git a/src/group.h b/src/group.h index 8f07fa19d00d23097e8267a9fce7ba448939a101..6b6cbb1def7e4d2e5340fa6ce3f0b14664f642f3 100644 --- a/src/group.h +++ b/src/group.h @@ -14,7 +14,7 @@ #ifndef LMP_GROUP_H #define LMP_GROUP_H -#include +#include #include "pointers.h" #include diff --git a/src/image.cpp b/src/image.cpp index 033bcfb669d633dbb566b0ce5bc5cb42ad18157b..301a2af88f23588dfcdea129fe2c283ae6269cb0 100644 --- a/src/image.cpp +++ b/src/image.cpp @@ -16,10 +16,10 @@ ------------------------------------------------------------------------- */ #include -#include -#include -#include -#include +#include +#include +#include +#include #include "image.h" #include "math_extra.h" #include "random_mars.h" @@ -35,7 +35,7 @@ #ifdef LAMMPS_PNG #include #include -#include +#include #include "version.h" #endif @@ -1065,7 +1065,7 @@ void Image::write_PNG(FILE *fp) png_set_text(png_ptr,info_ptr,text_ptr,1); png_write_info(png_ptr,info_ptr); - png_bytep row_pointers[height]; + png_bytep *row_pointers = new png_bytep[height]; for (int i=0; i < height; ++i) row_pointers[i] = (png_bytep) &writeBuffer[(height-i-1)*3*width]; @@ -1073,6 +1073,7 @@ void Image::write_PNG(FILE *fp) png_write_end(png_ptr, info_ptr); png_destroy_write_struct(&png_ptr, &info_ptr); + delete[] row_pointers; #endif } diff --git a/src/image.h b/src/image.h index 58050ada3278f8b8f4d140b2a43883c450ef049c..5672bf85c571d801876d37ebe889fefb12c1707c 100644 --- a/src/image.h +++ b/src/image.h @@ -14,8 +14,8 @@ #ifndef LMP_IMAGE_H #define LMP_IMAGE_H -#include -#include +#include +#include #include "pointers.h" namespace LAMMPS_NS { diff --git a/src/imbalance.h b/src/imbalance.h index ce7b700b9d66ddfb46db8d8132b3b8515d477e67..d3c3b9a64262c4dbd0aca56f83798a85db6b14b5 100644 --- a/src/imbalance.h +++ b/src/imbalance.h @@ -14,7 +14,7 @@ #ifndef LMP_IMBALANCE_H #define LMP_IMBALANCE_H -#include +#include #include "pointers.h" namespace LAMMPS_NS { diff --git a/src/imbalance_store.cpp b/src/imbalance_store.cpp index 2903f8497ea29ed6940db945c0195f58ddf4f097..6b69caf785c964e831236c65a2b545ca4ec85ec6 100644 --- a/src/imbalance_store.cpp +++ b/src/imbalance_store.cpp @@ -11,7 +11,7 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include +#include #include "imbalance_store.h" #include "atom.h" #include "input.h" diff --git a/src/imbalance_var.cpp b/src/imbalance_var.cpp index 394a9af3657f2788950041c338448594ad8254e7..acb3da8d1370ed6215549effa3a340abd492f82c 100644 --- a/src/imbalance_var.cpp +++ b/src/imbalance_var.cpp @@ -11,7 +11,7 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include +#include #include "imbalance_var.h" #include "atom.h" #include "group.h" diff --git a/src/improper.cpp b/src/improper.cpp index 089fc43aad09205a0e72aecaa886ef3b78a87d50..17e2df4e590e65fe61000c948d129163173f0b97 100644 --- a/src/improper.cpp +++ b/src/improper.cpp @@ -11,7 +11,7 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include +#include #include "improper.h" #include "atom.h" #include "comm.h" diff --git a/src/improper.h b/src/improper.h index df3c966cdc4704b5d91c03332274fabd0e3ab9b5..adcf6d29c867251342105212f90c0a8cff947956 100644 --- a/src/improper.h +++ b/src/improper.h @@ -14,7 +14,7 @@ #ifndef LMP_IMPROPER_H #define LMP_IMPROPER_H -#include +#include #include "pointers.h" namespace LAMMPS_NS { diff --git a/src/improper_hybrid.cpp b/src/improper_hybrid.cpp index abaaae02dabeee2e79519f363dcdce22f045ea29..3c17e42eafe77e26b1af427561f010ea130cb667 100644 --- a/src/improper_hybrid.cpp +++ b/src/improper_hybrid.cpp @@ -11,9 +11,9 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include -#include -#include +#include +#include +#include #include "improper_hybrid.h" #include "atom.h" #include "neighbor.h" diff --git a/src/improper_hybrid.h b/src/improper_hybrid.h index dbba347cf947e96238e3b587ef933f1380627ce8..89595ccfc44ff6f07ecfac4641b9440769a1f7fd 100644 --- a/src/improper_hybrid.h +++ b/src/improper_hybrid.h @@ -20,7 +20,7 @@ ImproperStyle(hybrid,ImproperHybrid) #ifndef LMP_IMPROPER_HYBRID_H #define LMP_IMPROPER_HYBRID_H -#include +#include #include "improper.h" namespace LAMMPS_NS { diff --git a/src/improper_zero.cpp b/src/improper_zero.cpp index 556e427ff8b9203112c8cb53f475ceab4bb6379a..25ab3e7bbafa554104b440245c07dda93a18f924 100644 --- a/src/improper_zero.cpp +++ b/src/improper_zero.cpp @@ -15,9 +15,9 @@ Contributing author: Carsten Svaneborg (SDU) ------------------------------------------------------------------------- */ -#include -#include -#include +#include +#include +#include #include "improper_zero.h" #include "atom.h" #include "force.h" diff --git a/src/improper_zero.h b/src/improper_zero.h index 0e16411fefac513a33415f66142cbd34e4f76729..0a2290b6f747a45013639005239284fe59c548fe 100644 --- a/src/improper_zero.h +++ b/src/improper_zero.h @@ -20,7 +20,7 @@ ImproperStyle(zero,ImproperZero) #ifndef LMP_IMPROPER_ZERO_H #define LMP_IMPROPER_ZERO_H -#include +#include #include "improper.h" namespace LAMMPS_NS { diff --git a/src/info.cpp b/src/info.cpp index e1103c0530b8638d3505ec9a13b50023d280bad9..65c0cd9b53dcb4f480b54d4095752b9179546a6b 100644 --- a/src/info.cpp +++ b/src/info.cpp @@ -16,7 +16,7 @@ Richard Berger (Temple U) ------------------------------------------------------------------------- */ -#include +#include #include "info.h" #include "accelerator_kokkos.h" #include "atom.h" @@ -43,7 +43,7 @@ #include "update.h" #include "error.h" -#include +#include #include #include #include @@ -51,7 +51,7 @@ #ifdef _WIN32 #define PSAPI_VERSION 1 #include -#include +#include // requires C++-11 #include #else #include diff --git a/src/input.cpp b/src/input.cpp index a0691f78a49c119ad65ce1b16f777e472f8b9d7e..b83a3683e4a3eae3984e842f55f33e672471fd85 100644 --- a/src/input.cpp +++ b/src/input.cpp @@ -12,11 +12,11 @@ ------------------------------------------------------------------------- */ #include -#include -#include -#include +#include +#include +#include #include -#include +#include #include #include #include "input.h" diff --git a/src/input.h b/src/input.h index 55d93e630373be8934d928cf1868d685f5b9e4d0..80b3e8c7da3d1f7a1e2f0378c37eb7785d5da7a2 100644 --- a/src/input.h +++ b/src/input.h @@ -14,7 +14,7 @@ #ifndef LMP_INPUT_H #define LMP_INPUT_H -#include +#include #include "pointers.h" #include #include diff --git a/src/integrate.cpp b/src/integrate.cpp index 4aeb6e18c93e721e489c046348938f70c3287d69..97d28d6d7c2b6bccbc70d6f973017f31d86cc6d4 100644 --- a/src/integrate.cpp +++ b/src/integrate.cpp @@ -11,7 +11,7 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include +#include #include "integrate.h" #include "update.h" #include "force.h" diff --git a/src/irregular.cpp b/src/irregular.cpp index 6cd1b22c2fefc099d4ce1b976756a5fc53bc8941..451ce7af668b9550bcfcdf3dce670b90d9cf997b 100644 --- a/src/irregular.cpp +++ b/src/irregular.cpp @@ -12,8 +12,8 @@ ------------------------------------------------------------------------- */ #include -#include -#include +#include +#include #include "irregular.h" #include "atom.h" #include "atom_vec.h" diff --git a/src/kspace.cpp b/src/kspace.cpp index b2db585f121f7a537dc2d75d9b222e9545b106e7..fc8b12288ba0679f17d0cbca31287c24208f142b 100644 --- a/src/kspace.cpp +++ b/src/kspace.cpp @@ -11,8 +11,8 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include -#include +#include +#include #include "kspace.h" #include "atom.h" #include "comm.h" diff --git a/src/lammps.cpp b/src/lammps.cpp index dd91ea7c19780f3d34d99864efc892203df9131f..56af95767bc9901ae60df9e2d2df3d7765de3567 100644 --- a/src/lammps.cpp +++ b/src/lammps.cpp @@ -12,8 +12,8 @@ ------------------------------------------------------------------------- */ #include -#include -#include +#include +#include #include "lammps.h" #include "style_angle.h" #include "style_atom.h" diff --git a/src/lammps.h b/src/lammps.h index 26714ab072bd76f3748bf845d87bd8d6a2f588b8..1323dcccc810a29634d7d6348844925daf34004a 100644 --- a/src/lammps.h +++ b/src/lammps.h @@ -14,7 +14,7 @@ #ifndef LMP_LAMMPS_H #define LMP_LAMMPS_H -#include +#include namespace LAMMPS_NS { diff --git a/src/lattice.cpp b/src/lattice.cpp index 5f6d05db8932a9e7f8acf86571961413c9bec21e..ee2fea2a758dca955bb4a8841ff481d99974dac9 100644 --- a/src/lattice.cpp +++ b/src/lattice.cpp @@ -11,9 +11,9 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include -#include -#include +#include +#include +#include #include "lattice.h" #include "update.h" #include "domain.h" diff --git a/src/library.cpp b/src/library.cpp index 07c4cae9c16327b5efd618391d3096f1551ac4e3..0162c560cea7e21b66cc759a481aae6420c86d51 100644 --- a/src/library.cpp +++ b/src/library.cpp @@ -15,8 +15,8 @@ // customize by adding new LAMMPS-specific functions #include -#include -#include +#include +#include #include "library.h" #include "lmptype.h" #include "lammps.h" @@ -480,10 +480,13 @@ void *lammps_extract_atom(void *ptr, char *name) compute's internal data structure for the entity caller should cast it to (double *) for a scalar or vector caller should cast it to (double **) for an array - for per-atom or local data, returns a pointer to the + for per-atom or local vector/array data, returns a pointer to the compute's internal data structure for the entity caller should cast it to (double *) for a vector caller should cast it to (double **) for an array + for local data, accessing scalar data for the compute (type = 0), + returns a pointer that should be cast to (int *) which points to + an int with the number of local rows, i.e. the length of the local array. returns a void pointer to the compute's internal data structure for the entity which the caller can cast to the proper data type returns a NULL if id is not recognized or style/type not supported @@ -541,6 +544,11 @@ void *lammps_extract_compute(void *ptr, char *id, int style, int type) if (style == 2) { if (!compute->local_flag) return NULL; + if (type == 0) { + if (compute->invoked_local != lmp->update->ntimestep) + compute->compute_local(); + return (void *) &compute->size_local_rows; + } if (type == 1) { if (compute->invoked_local != lmp->update->ntimestep) compute->compute_local(); @@ -925,7 +933,7 @@ void lammps_gather_atoms_concat(void *ptr, char *name, BEGIN_CAPTURE { - int i,j,offset; + int i,offset; // error if tags are not defined // NOTE: test that name = image or ids is not a 64-bit int in code? @@ -967,7 +975,6 @@ void lammps_gather_atoms_concat(void *ptr, char *name, lmp->memory->create(copy,count*natoms,"lib/gather:copy"); for (i = 0; i < count*natoms; i++) copy[i] = 0; - tagint *tag = lmp->atom->tag; int nlocal = lmp->atom->nlocal; if (count == 1) { @@ -1109,7 +1116,6 @@ void lammps_gather_atoms_subset(void *ptr, char *name, lmp->memory->create(copy,count*ndata,"lib/gather:copy"); for (i = 0; i < count*ndata; i++) copy[i] = 0; - tagint *tag = lmp->atom->tag; int nlocal = lmp->atom->nlocal; if (count == 1) { @@ -1155,7 +1161,6 @@ void lammps_gather_atoms_subset(void *ptr, char *name, lmp->memory->create(copy,count*ndata,"lib/gather:copy"); for (i = 0; i < count*ndata; i++) copy[i] = 0.0; - tagint *tag = lmp->atom->tag; int nlocal = lmp->atom->nlocal; if (count == 1) { diff --git a/src/lmptype.h b/src/lmptype.h index 253f9a7470a400ef4330e7619c9d89a6e60e7a7f..2be1d2ac385ccdb0e1dad96a4c23f2143a4bf10a 100644 --- a/src/lmptype.h +++ b/src/lmptype.h @@ -36,9 +36,9 @@ #define __STDC_FORMAT_MACROS #endif -#include -#include -#include +#include +#include // requires C++-11 +#include // requires C++-11 // grrr - IBM Power6 does not provide this def in their system header files @@ -200,8 +200,6 @@ typedef int bigint; #define _noalias #endif -#define ISFINITE(x) isfinite(x) - // settings to enable LAMMPS to build under Windows #ifdef _WIN32 diff --git a/src/lmpwindows.h b/src/lmpwindows.h index d20d0f87baa274d29a5be8610f4f34f15826d018..ae2a5457179ad9eec7c10e0645959dd05dc9c71e 100644 --- a/src/lmpwindows.h +++ b/src/lmpwindows.h @@ -1,9 +1,9 @@ -#include +#include #if !defined(__MINGW32__) #include "erf.h" #endif #include -#include +#include // LAMMPS uses usleep with 100 ms arguments, no microsecond precision needed #if !defined(__MINGW32__) #include "sleep.h" diff --git a/src/main.cpp b/src/main.cpp index 95368385bd0b31b5e5ef878f1827c63f225e8a44..8eb5e4e5433da594017958784de1de0790b37b82 100644 --- a/src/main.cpp +++ b/src/main.cpp @@ -15,8 +15,8 @@ #include "lammps.h" #include "input.h" #include "error.h" -#include -#include +#include +#include #if defined(LAMMPS_TRAP_FPE) && defined(_GNU_SOURCE) #include diff --git a/src/math_extra.cpp b/src/math_extra.cpp index d1700a3070cb6cc546e7e39ed0c1c10a5ad2a9f7..b70986ce914904edc8b3a2cbf41fb3b3e9ade210 100644 --- a/src/math_extra.cpp +++ b/src/math_extra.cpp @@ -15,8 +15,8 @@ Contributing author: Mike Brown (SNL) ------------------------------------------------------------------------- */ -#include -#include +#include +#include #include "math_extra.h" #define MAXJACOBI 50 diff --git a/src/math_extra.h b/src/math_extra.h index eec9855b8066deb3f75ae3dc92e2b1f5881f679a..85f57224cfb97a3f6a7bde21dddbae18409dae93 100644 --- a/src/math_extra.h +++ b/src/math_extra.h @@ -18,9 +18,9 @@ #ifndef LMP_MATH_EXTRA_H #define LMP_MATH_EXTRA_H -#include -#include -#include +#include +#include +#include #include "error.h" namespace MathExtra { diff --git a/src/math_special.cpp b/src/math_special.cpp index 4b9197f0fc150e7452351b3eee441872641a5457..31567bdc77fa90bab58d307356d3a9b67aa109ba 100644 --- a/src/math_special.cpp +++ b/src/math_special.cpp @@ -1,5 +1,5 @@ -#include -#include +#include +#include // requires C++-11 #include "math_special.h" using namespace LAMMPS_NS; diff --git a/src/math_special.h b/src/math_special.h index 8cd328f5fcdb25232932a68a3cfbd7cc148cad79..1e7b10d9fdc46201e8833127098777fe58bda88c 100644 --- a/src/math_special.h +++ b/src/math_special.h @@ -14,7 +14,7 @@ #ifndef LMP_MATH_SPECIAL_H #define LMP_MATH_SPECIAL_H -#include +#include namespace LAMMPS_NS { diff --git a/src/math_vector.h b/src/math_vector.h index 9304cf0804d1133fcf33f7d61ce1941ba2cb802b..c2227572729a96367f3ca35d1d11fd12c1391592 100644 --- a/src/math_vector.h +++ b/src/math_vector.h @@ -18,8 +18,8 @@ #ifndef LMP_MATH_VECTOR_H #define LMP_MATH_VECTOR_H -#include -#include +#include +#include #define VECTOR_NULL {0, 0, 0} #define SHAPE_NULL {0, 0, 0, 0, 0, 0} diff --git a/src/memory.cpp b/src/memory.cpp index eb5309b8b7930292a812141ded0747e2c56e33b1..429cf75c00ab9975a7859201301c9e963b1bf1e8 100644 --- a/src/memory.cpp +++ b/src/memory.cpp @@ -11,9 +11,9 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include -#include -#include +#include +#include +#include #include "memory.h" #include "error.h" diff --git a/src/mergesort.h b/src/mergesort.h index 1df6cb4b819375e68fbdd2c745a4c7cee4a49009..50addd0a729a23766b21a764465ac254ce6f5909 100644 --- a/src/mergesort.h +++ b/src/mergesort.h @@ -14,7 +14,7 @@ #ifndef LMP_MERGESORT #define LMP_MERGESORT -#include +#include // custom hybrid upward merge sort implementation with support to pass // an opaque pointer to the comparison function, e.g. for access to diff --git a/src/min.cpp b/src/min.cpp index 0caa9a9acf0584eac39ad0a55c8ddf634f56906e..cd9253f8d30f31fdab356efca3ff50a7bd2e710b 100644 --- a/src/min.cpp +++ b/src/min.cpp @@ -19,9 +19,9 @@ JR Shewchuk, http://www-2.cs.cmu.edu/~jrs/jrspapers.html#cg ------------------------------------------------------------------------- */ -#include -#include -#include +#include +#include +#include #include "min.h" #include "atom.h" #include "atom_vec.h" diff --git a/src/min_cg.cpp b/src/min_cg.cpp index eda59bd3d4fd19fe586ccb459b327d337ff4ebc8..20e8cc30dd35f05355eb44869f48a2dc914a7c90 100644 --- a/src/min_cg.cpp +++ b/src/min_cg.cpp @@ -12,8 +12,8 @@ ------------------------------------------------------------------------- */ #include -#include -#include +#include +#include #include "min_cg.h" #include "atom.h" #include "update.h" diff --git a/src/min_fire.cpp b/src/min_fire.cpp index 698b00b7a6781a021ce133e41e88ebe5ef3d8eff..a50071d56204e197a9a4d321640ec50c7d897b99 100644 --- a/src/min_fire.cpp +++ b/src/min_fire.cpp @@ -11,7 +11,7 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include +#include #include "min_fire.h" #include "universe.h" #include "atom.h" diff --git a/src/min_hftn.cpp b/src/min_hftn.cpp index 84793e33a4f9741767d1f75691028a8f3419f161..0c834fbeb442e71e5227989de328dbe252339ae8 100644 --- a/src/min_hftn.cpp +++ b/src/min_hftn.cpp @@ -17,8 +17,8 @@ "Parallel Unconstrained Min", Plantenga, SAND98-8201 ------------------------------------------------------------------------- */ -#include -#include +#include +#include #include "atom.h" #include "fix_minimize.h" #include "min_hftn.h" diff --git a/src/min_linesearch.cpp b/src/min_linesearch.cpp index ddc0c64321ccd84372e8bb2a2420bd732667b955..f93a56b09d93895dddd0770a377629b50e0b8412 100644 --- a/src/min_linesearch.cpp +++ b/src/min_linesearch.cpp @@ -21,7 +21,7 @@ JR Shewchuk, http://www-2.cs.cmu.edu/~jrs/jrspapers.html#cg ------------------------------------------------------------------------- */ -#include +#include #include "min_linesearch.h" #include "atom.h" #include "update.h" diff --git a/src/min_quickmin.cpp b/src/min_quickmin.cpp index 491387406d10a6f1407cf0b970bacfdf5dc25865..8b48816355b0a5b64db0a77fd3c11a9fccff1886 100644 --- a/src/min_quickmin.cpp +++ b/src/min_quickmin.cpp @@ -12,7 +12,7 @@ ------------------------------------------------------------------------- */ #include -#include +#include #include "min_quickmin.h" #include "universe.h" #include "atom.h" diff --git a/src/min_sd.cpp b/src/min_sd.cpp index 73a3867d8a29cce5667ace0a367a2689b9b6f3ec..5d44437ca07e6ca372068e5ae2516cc32d05a045 100644 --- a/src/min_sd.cpp +++ b/src/min_sd.cpp @@ -11,7 +11,7 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include +#include #include #include "min_sd.h" #include "atom.h" diff --git a/src/minimize.cpp b/src/minimize.cpp index e4e89804bf6e07ef9d63533d910b40b654423def..e27fffd74bb15c1e005052a3669e09a8b20d13d7 100644 --- a/src/minimize.cpp +++ b/src/minimize.cpp @@ -11,7 +11,7 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include +#include #include "minimize.h" #include "domain.h" #include "update.h" diff --git a/src/modify.cpp b/src/modify.cpp index 64970f2cf98b10cbf9ad9f7042392d5e2bf827b6..c5a680a3bd6b0e928db0c1f055fb63af3d58e468 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 +#include +#include #include "modify.h" #include "style_compute.h" #include "style_fix.h" diff --git a/src/modify.h b/src/modify.h index 1163d44b16f54e4b39f296d166c685118ed714ba..eca4e078599573cf280fde726399069b9091837c 100644 --- a/src/modify.h +++ b/src/modify.h @@ -14,7 +14,7 @@ #ifndef LMP_MODIFY_H #define LMP_MODIFY_H -#include +#include #include "pointers.h" #include #include diff --git a/src/molecule.cpp b/src/molecule.cpp index 78dc4b82b3ed2374dbae7cafa4f3e5d296408c1e..56e56dab2cd16ef45c9c6068161c29a4815d51ca 100644 --- a/src/molecule.cpp +++ b/src/molecule.cpp @@ -11,8 +11,8 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include -#include +#include +#include #include "molecule.h" #include "atom.h" #include "atom_vec.h" @@ -1111,7 +1111,7 @@ void Molecule::special_generate() { int newton_bond = force->newton_bond; tagint atom1,atom2; - int count[natoms]; + int *count = new int[natoms]; // temporary array for special atoms @@ -1197,6 +1197,7 @@ void Molecule::special_generate() } } } + delete[] count; maxspecial = 0; for (int i = 0; i < natoms; i++) diff --git a/src/my_page.h b/src/my_page.h index 5d95217968e75e34e0f781533662bd50564be442..5cd7098d8c9132654b0cf4c7ec4d01a179910fc5 100644 --- a/src/my_page.h +++ b/src/my_page.h @@ -52,7 +52,7 @@ methods: #define LAMMPS_MEMALIGN 64 #endif -#include +#include namespace LAMMPS_NS { template diff --git a/src/my_pool_chunk.h b/src/my_pool_chunk.h index c2f4f190f84bb87a3a3980336c179e19b50fa296..8bf88d35bbe425c67193daeba0d309aff73eb78c 100644 --- a/src/my_pool_chunk.h +++ b/src/my_pool_chunk.h @@ -43,7 +43,7 @@ public variables: #ifndef LAMMPS_MY_POOL_CHUNK_H #define LAMMPS_MY_POOL_CHUNK_H -#include +#include namespace LAMMPS_NS { diff --git a/src/nbin.cpp b/src/nbin.cpp index 6bd1ce322f6f93d93a80c50058d598f8abccfcc9..a30b76cca03770562ef0d7f9da2a0c0fd576a0cc 100644 --- a/src/nbin.cpp +++ b/src/nbin.cpp @@ -117,7 +117,7 @@ int NBin::coord2bin(double *x) { int ix,iy,iz; - if (!ISFINITE(x[0]) || !ISFINITE(x[1]) || !ISFINITE(x[2])) + if (!std::isfinite(x[0]) || !std::isfinite(x[1]) || !std::isfinite(x[2])) error->one(FLERR,"Non-numeric positions - simulation unstable"); if (x[0] >= bboxhi[0]) diff --git a/src/neighbor.cpp b/src/neighbor.cpp index 31dddd9f15eb39964967a9308feee577fe1162a5..d5cb83b37d5fc8176b4aceb7527aa4f11e23ca34 100644 --- a/src/neighbor.cpp +++ b/src/neighbor.cpp @@ -16,9 +16,9 @@ ------------------------------------------------------------------------- */ #include -#include -#include -#include +#include +#include +#include #include "neighbor.h" #include "neigh_list.h" #include "neigh_request.h" diff --git a/src/npair.cpp b/src/npair.cpp index 4d06850e659197846c426199673ca44747aa1312..24cdc7750af504f1f510fdd0e29a5ba0b0b9355a 100644 --- a/src/npair.cpp +++ b/src/npair.cpp @@ -11,7 +11,7 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include +#include #include "npair.h" #include "neighbor.h" #include "neigh_request.h" @@ -208,7 +208,7 @@ int NPair::exclusion(int i, int j, int itype, int jtype, int NPair::coord2bin(double *x, int &ix, int &iy, int &iz) { - if (!ISFINITE(x[0]) || !ISFINITE(x[1]) || !ISFINITE(x[2])) + if (!std::isfinite(x[0]) || !std::isfinite(x[1]) || !std::isfinite(x[2])) error->one(FLERR,"Non-numeric positions - simulation unstable"); if (x[0] >= bboxhi[0]) diff --git a/src/npair_half_size_bin_newtoff.cpp b/src/npair_half_size_bin_newtoff.cpp index 6cd97c71d13383cb34a1c7a7ba21d1cef2461293..021452028b3802f68c759707dbd9f00d4bb6c320 100644 --- a/src/npair_half_size_bin_newtoff.cpp +++ b/src/npair_half_size_bin_newtoff.cpp @@ -11,7 +11,7 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include +#include #include "npair_half_size_bin_newtoff.h" #include "neighbor.h" #include "neigh_list.h" diff --git a/src/npair_half_size_bin_newton.cpp b/src/npair_half_size_bin_newton.cpp index c0ed03816625f3bc91de2b43c4fe472e8895b36a..760c09570a0dcad90ae2e66ec1d3e3a2480f93df 100644 --- a/src/npair_half_size_bin_newton.cpp +++ b/src/npair_half_size_bin_newton.cpp @@ -11,7 +11,7 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include +#include #include "npair_half_size_bin_newton.h" #include "neighbor.h" #include "neigh_list.h" diff --git a/src/npair_half_size_bin_newton_tri.cpp b/src/npair_half_size_bin_newton_tri.cpp index 044847ba8ce9d38d534e5aecfc13e841e5d81a9b..d831982ed6033842b85cbdf677ca5e59b1a40a66 100644 --- a/src/npair_half_size_bin_newton_tri.cpp +++ b/src/npair_half_size_bin_newton_tri.cpp @@ -11,7 +11,7 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include +#include #include "npair_half_size_bin_newton_tri.h" #include "neighbor.h" #include "neigh_list.h" diff --git a/src/npair_half_size_nsq_newtoff.cpp b/src/npair_half_size_nsq_newtoff.cpp index 50a32c87ba5d3ed2ab5883eb7e47167f626adbca..1c2fe5f3d57b4666a0807c7765bb380bce935204 100644 --- a/src/npair_half_size_nsq_newtoff.cpp +++ b/src/npair_half_size_nsq_newtoff.cpp @@ -11,7 +11,7 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include +#include #include "npair_half_size_nsq_newtoff.h" #include "neighbor.h" #include "neigh_list.h" diff --git a/src/npair_half_size_nsq_newton.cpp b/src/npair_half_size_nsq_newton.cpp index 343172fb986c0a316d705c186a892aeee10a002d..ce9f8ec18631876d99d0b5bb1d2641aabee72da4 100644 --- a/src/npair_half_size_nsq_newton.cpp +++ b/src/npair_half_size_nsq_newton.cpp @@ -11,7 +11,7 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include +#include #include "npair_half_size_nsq_newton.h" #include "neighbor.h" #include "neigh_list.h" diff --git a/src/npair_skip_size.cpp b/src/npair_skip_size.cpp index b75856dde409a3e060cf1831f6ecc8684c965977..67717ae57660ca11e71685c7c445bab8eff6602b 100644 --- a/src/npair_skip_size.cpp +++ b/src/npair_skip_size.cpp @@ -11,7 +11,7 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include +#include #include "npair_skip_size.h" #include "neighbor.h" #include "neigh_list.h" diff --git a/src/npair_skip_size_off2on.cpp b/src/npair_skip_size_off2on.cpp index 8d728a3c0ad73074bb06b4786462f854fd0cc4a2..74a80e6d3d3e2da207aaa1c424069bac4148020a 100644 --- a/src/npair_skip_size_off2on.cpp +++ b/src/npair_skip_size_off2on.cpp @@ -11,7 +11,7 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include +#include #include "npair_skip_size_off2on.h" #include "neighbor.h" #include "neigh_list.h" diff --git a/src/npair_skip_size_off2on_oneside.cpp b/src/npair_skip_size_off2on_oneside.cpp index a04fc7782c2bcfdecd88d6f8e2df6b438bfc08a8..a042acd1c6bb034d4a84e568487c48170c1dfbca 100644 --- a/src/npair_skip_size_off2on_oneside.cpp +++ b/src/npair_skip_size_off2on_oneside.cpp @@ -11,7 +11,7 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include +#include #include "npair_skip_size_off2on_oneside.h" #include "neighbor.h" #include "neigh_list.h" diff --git a/src/ntopo.cpp b/src/ntopo.cpp index 124fa6687c498ceae9c688dfe437f25e70c736d2..8a87a5d6e5fa9003e78a7e5be6ce9d744ee1ca89 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 11c6fa073e8c05c38056efbdc1765e5f6f8da999..884647f478bbb89d1d963048828eabbd51a36458 100644 --- a/src/output.cpp +++ b/src/output.cpp @@ -11,9 +11,9 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include -#include -#include +#include +#include +#include #include "output.h" #include "style_dump.h" #include "atom.h" diff --git a/src/pair.cpp b/src/pair.cpp index 8b3178415c28156203b0ff57ca937794c8d85a9d..3b839dff497808a033a97f9c551381b80658e267 100644 --- a/src/pair.cpp +++ b/src/pair.cpp @@ -16,13 +16,13 @@ ------------------------------------------------------------------------- */ #include -#include -#include -#include -#include -#include -#include -#include +#include +#include +#include +#include +#include +#include +#include #include "pair.h" #include "atom.h" #include "neighbor.h" diff --git a/src/pair_beck.cpp b/src/pair_beck.cpp index 36e44e5c2ebc5203f97a8fc20041fe3b07fbfd25..cc8e14bf2c6c93164a1795b79352a7568f24f515 100644 --- a/src/pair_beck.cpp +++ b/src/pair_beck.cpp @@ -15,9 +15,9 @@ Contributing author: Jonathan Zimmerman (Sandia) ------------------------------------------------------------------------- */ -#include -#include -#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 979499488e0e3dbf34f4d6a3a77a897429b3946e..ce7a255fd4935a41e1a20d00fe4ea8757894600f 100644 --- a/src/pair_born.cpp +++ b/src/pair_born.cpp @@ -15,10 +15,10 @@ Contributing Author: Sai Jayaraman (Sandia) ------------------------------------------------------------------------- */ -#include -#include -#include -#include +#include +#include +#include +#include #include "pair_born.h" #include "atom.h" #include "comm.h" diff --git a/src/pair_born_coul_dsf.cpp b/src/pair_born_coul_dsf.cpp index 3700aa46d7f5b83df7bf20fd4c0c21714a4f85c4..be7f41ca2b69ddb9a86eae3a72e3a77b81e2e891 100644 --- a/src/pair_born_coul_dsf.cpp +++ b/src/pair_born_coul_dsf.cpp @@ -16,10 +16,10 @@ References: Fennell and Gezelter, JCP 124, 234104 (2006) ------------------------------------------------------------------------- */ -#include -#include -#include -#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 fbec4f3da74362d51c6d99e541574be8758f6658..22dcfa9f2dd6e623e0a738168970fa4205c7beb3 100644 --- a/src/pair_born_coul_wolf.cpp +++ b/src/pair_born_coul_wolf.cpp @@ -15,10 +15,10 @@ Contributing author: Yongfeng Zhang (INL), yongfeng.zhang@inl.gov ------------------------------------------------------------------------- */ -#include -#include -#include -#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 8cbf97a6badc13f8bd22c20d85e6175626f897e7..450ce291cb9814629e0ade5d1398cd595744d95c 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 -#include -#include -#include +#include +#include +#include +#include #include "pair_buck.h" #include "atom.h" #include "comm.h" diff --git a/src/pair_buck_coul_cut.cpp b/src/pair_buck_coul_cut.cpp index 2764a8e4e4c05abb2e19394a4d73e2f98d3f453e..7eecb621214e89fc78428a896874cf36e0f126f4 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 -#include -#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 b505dcb02ce5836c8edc0a2e568a622634e67474..edcf26bffe990d91219eaeaa60d53e20bf57181a 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 -#include -#include -#include +#include +#include +#include +#include #include "pair_coul_cut.h" #include "atom.h" #include "comm.h" diff --git a/src/pair_coul_debye.cpp b/src/pair_coul_debye.cpp index df4555753f2c5782060892cf2ec13e794acefb9e..ee08ab3294909b1865bc16100b3a390468fa31d3 100644 --- a/src/pair_coul_debye.cpp +++ b/src/pair_coul_debye.cpp @@ -11,10 +11,10 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include -#include -#include -#include +#include +#include +#include +#include #include "pair_coul_debye.h" #include "atom.h" #include "comm.h" diff --git a/src/pair_coul_dsf.cpp b/src/pair_coul_dsf.cpp index 3595f9cbee8d8b64369b5eff1c3a77ee28df8c4f..f20eae43bdbdde3fe252d25f3f6194404e8e81bb 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 -#include -#include -#include +#include +#include +#include +#include #include "pair_coul_dsf.h" #include "atom.h" #include "comm.h" diff --git a/src/pair_coul_streitz.cpp b/src/pair_coul_streitz.cpp index 82ecd1d8104723b2aced06c7e886150b8c187abd..1d725f4ca87c637ffb1e9855a126fe1e95f0cf41 100644 --- a/src/pair_coul_streitz.cpp +++ b/src/pair_coul_streitz.cpp @@ -15,10 +15,10 @@ Contributing author: Ray Shan (Sandia) ------------------------------------------------------------------------- */ -#include -#include -#include -#include +#include +#include +#include +#include #include "pair_coul_streitz.h" #include "atom.h" #include "comm.h" diff --git a/src/pair_coul_wolf.cpp b/src/pair_coul_wolf.cpp index 1a7f4772608c98aeb8da19bb7f273e8fe64a18de..cd582f0693abaafffb3d04af52996cf7ea033c8a 100644 --- a/src/pair_coul_wolf.cpp +++ b/src/pair_coul_wolf.cpp @@ -15,10 +15,10 @@ Contributing author: Yongfeng Zhang (INL), yongfeng.zhang@inl.gov ------------------------------------------------------------------------- */ -#include -#include -#include -#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 61f700a33ecda8c04197d5055d9ef4df1bdfbc75..c209de87ed15e7aad81c1e1c01322509d4045720 100644 --- a/src/pair_dpd.cpp +++ b/src/pair_dpd.cpp @@ -15,9 +15,9 @@ Contributing author: Kurt Smith (U Pittsburgh) ------------------------------------------------------------------------- */ -#include -#include -#include +#include +#include +#include #include "pair_dpd.h" #include "atom.h" #include "atom_vec.h" diff --git a/src/pair_dpd_tstat.cpp b/src/pair_dpd_tstat.cpp index 0a5ebd33f85728d573097d354662dab87fa60ed7..f2c0b157eae27a8bc150bfdbe8e9a427c5099d6e 100644 --- a/src/pair_dpd_tstat.cpp +++ b/src/pair_dpd_tstat.cpp @@ -11,7 +11,7 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include +#include #include "pair_dpd_tstat.h" #include "atom.h" #include "update.h" diff --git a/src/pair_gauss.cpp b/src/pair_gauss.cpp index c66cfc2c8058dd424ea204d415641b74870496fa..fe53bcc9e1b2af7b61b3074170521887b8166252 100644 --- a/src/pair_gauss.cpp +++ b/src/pair_gauss.cpp @@ -15,10 +15,10 @@ Contributing author: Sai Jayaraman (Sandia) ------------------------------------------------------------------------- */ -#include -#include -#include -#include +#include +#include +#include +#include #include "pair_gauss.h" #include "atom.h" #include "comm.h" diff --git a/src/pair_hybrid.cpp b/src/pair_hybrid.cpp index 751560deffd56355b97cf7d4f5e63c7b044c880e..dc74dd040dde23f9b72fe87ab39417a54de263a6 100644 --- a/src/pair_hybrid.cpp +++ b/src/pair_hybrid.cpp @@ -11,10 +11,10 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include -#include -#include -#include +#include +#include +#include +#include #include "pair_hybrid.h" #include "atom.h" #include "force.h" diff --git a/src/pair_hybrid.h b/src/pair_hybrid.h index 202847b028b8583cc88b0afcdc5db97a197c2096..08f5a574df832cfa3f0e43ff8012e30fd1140683 100644 --- a/src/pair_hybrid.h +++ b/src/pair_hybrid.h @@ -20,7 +20,7 @@ PairStyle(hybrid,PairHybrid) #ifndef LMP_PAIR_HYBRID_H #define LMP_PAIR_HYBRID_H -#include +#include #include "pair.h" namespace LAMMPS_NS { diff --git a/src/pair_hybrid_overlay.cpp b/src/pair_hybrid_overlay.cpp index 6776e90ff423c412b4a2652d0a92c468d4c842c7..717c0de1d1a19d7c9aa264e14d3134ccfceb42a9 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 -#include -#include +#include +#include +#include #include "pair_hybrid_overlay.h" #include "atom.h" #include "force.h" diff --git a/src/pair_lj96_cut.cpp b/src/pair_lj96_cut.cpp index 842b918fe154ad8db4865e2b14cd44d8141c7ff3..28677a393ef3745a969ae3ca03dcb47f09ed5e53 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 -#include -#include -#include +#include +#include +#include +#include #include "pair_lj96_cut.h" #include "atom.h" #include "comm.h" diff --git a/src/pair_lj_cubic.cpp b/src/pair_lj_cubic.cpp index c96d4490cbddf7cbaabb5314f46d32627a1842e5..4b140e5f05d416fce943890c9412d8f1962a5a3e 100644 --- a/src/pair_lj_cubic.cpp +++ b/src/pair_lj_cubic.cpp @@ -16,10 +16,10 @@ Contributing author: Aidan Thompson (SNL) ------------------------------------------------------------------------- */ -#include -#include -#include -#include +#include +#include +#include +#include #include "pair_lj_cubic.h" #include "atom.h" #include "comm.h" diff --git a/src/pair_lj_cut.cpp b/src/pair_lj_cut.cpp index 215fabecbbca976d2a01c46c163bf2f0aadff734..bb2db6aa2fc025cbec62d10111ee2d838caf1715 100644 --- a/src/pair_lj_cut.cpp +++ b/src/pair_lj_cut.cpp @@ -15,10 +15,10 @@ Contributing author: Paul Crozier (SNL) ------------------------------------------------------------------------- */ -#include -#include -#include -#include +#include +#include +#include +#include #include "pair_lj_cut.h" #include "atom.h" #include "comm.h" diff --git a/src/pair_lj_cut_coul_cut.cpp b/src/pair_lj_cut_coul_cut.cpp index 85cf9dc97dea6a84d862d9f27265ffb68a024d24..15c06ab36a02f53453e644cd5974c36b72cbf47f 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 -#include -#include -#include +#include +#include +#include +#include #include "pair_lj_cut_coul_cut.h" #include "atom.h" #include "comm.h" diff --git a/src/pair_lj_cut_coul_debye.cpp b/src/pair_lj_cut_coul_debye.cpp index 8f5e8e7a1721d74a39df8d98539230f52f08ae7b..dfd866ca7a01537d96737760ee8443155a6e5ab4 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 #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 429058650191af04433757140d58843b5306c244..a49af13fb2737fa8d8a6a09ba19ee92db98b23e7 100644 --- a/src/pair_lj_cut_coul_dsf.cpp +++ b/src/pair_lj_cut_coul_dsf.cpp @@ -16,10 +16,10 @@ References: Fennell and Gezelter, JCP 124, 234104 (2006) ------------------------------------------------------------------------- */ -#include -#include -#include -#include +#include +#include +#include +#include #include "pair_lj_cut_coul_dsf.h" #include "atom.h" #include "comm.h" diff --git a/src/pair_lj_cut_coul_wolf.cpp b/src/pair_lj_cut_coul_wolf.cpp index 2043de4c7d46514845288d6f437f0b56502a85bd..fc8a858ce1aee20d2e72c50cf2b70fb3e71c7fd5 100644 --- a/src/pair_lj_cut_coul_wolf.cpp +++ b/src/pair_lj_cut_coul_wolf.cpp @@ -15,10 +15,10 @@ Contributing author: Vishal Boddu (FAU) ------------------------------------------------------------------------- */ -#include -#include -#include -#include +#include +#include +#include +#include #include "pair_lj_cut_coul_wolf.h" #include "atom.h" #include "comm.h" diff --git a/src/pair_lj_expand.cpp b/src/pair_lj_expand.cpp index f2f49c872dcb5f0436ceb4062094eb934fed3441..ba72d7d45f39884c80c061d3b6a3b9bc6b5157dd 100644 --- a/src/pair_lj_expand.cpp +++ b/src/pair_lj_expand.cpp @@ -11,10 +11,10 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include -#include -#include -#include +#include +#include +#include +#include #include "pair_lj_expand.h" #include "atom.h" #include "comm.h" diff --git a/src/pair_lj_gromacs.cpp b/src/pair_lj_gromacs.cpp index 3375c6c4e203ea41a14c4587e1f2fe99da952e87..6b2219d2c5cef92f4da305e343e4111eb4fc751b 100644 --- a/src/pair_lj_gromacs.cpp +++ b/src/pair_lj_gromacs.cpp @@ -15,10 +15,10 @@ Contributing author: Mark Stevens (SNL) ------------------------------------------------------------------------- */ -#include -#include -#include -#include +#include +#include +#include +#include #include "pair_lj_gromacs.h" #include "atom.h" #include "comm.h" diff --git a/src/pair_lj_gromacs_coul_gromacs.cpp b/src/pair_lj_gromacs_coul_gromacs.cpp index 26e433b38113a6ef282c7034f1ddcdb9f1b5539e..414bfea92a0f2bab8db52a1ba2f0a1f9ffcb7cd0 100644 --- a/src/pair_lj_gromacs_coul_gromacs.cpp +++ b/src/pair_lj_gromacs_coul_gromacs.cpp @@ -15,10 +15,10 @@ Contributing author: Mark Stevens (SNL) ------------------------------------------------------------------------- */ -#include -#include -#include -#include +#include +#include +#include +#include #include "pair_lj_gromacs_coul_gromacs.h" #include "atom.h" #include "comm.h" diff --git a/src/pair_lj_smooth.cpp b/src/pair_lj_smooth.cpp index 1afaef9235a6c0ddbf837bbcb58db5bbeb798817..23256d486ed09fcf2a48e31ebefd65aead569372 100644 --- a/src/pair_lj_smooth.cpp +++ b/src/pair_lj_smooth.cpp @@ -15,9 +15,9 @@ Contributing author: Craig Maloney (UCSB) ------------------------------------------------------------------------- */ -#include -#include -#include +#include +#include +#include #include "pair_lj_smooth.h" #include "atom.h" #include "comm.h" diff --git a/src/pair_lj_smooth_linear.cpp b/src/pair_lj_smooth_linear.cpp index 415ca7b6d3650a1b2f71f8060da75f47221eb3c1..592a7f6f41a1ad75eae1a537e3e02e5c88b29bfb 100644 --- a/src/pair_lj_smooth_linear.cpp +++ b/src/pair_lj_smooth_linear.cpp @@ -15,9 +15,9 @@ Contributing author: Jonathan Zimmerman (Sandia) ------------------------------------------------------------------------- */ -#include -#include -#include +#include +#include +#include #include "pair_lj_smooth_linear.h" #include "atom.h" #include "comm.h" diff --git a/src/pair_mie_cut.cpp b/src/pair_mie_cut.cpp index 04f8de8d7d335b32aa4c00fe66cc764ea1e3abde..1f9267ca30898ed75de80279c23bb3b74d670e88 100644 --- a/src/pair_mie_cut.cpp +++ b/src/pair_mie_cut.cpp @@ -15,10 +15,10 @@ Contributing author: Cassiano Aimoli (aimoli@gmail.com) ------------------------------------------------------------------------- */ -#include -#include -#include -#include +#include +#include +#include +#include #include "pair_mie_cut.h" #include "atom.h" #include "comm.h" diff --git a/src/pair_morse.cpp b/src/pair_morse.cpp index 0e40fc75512277a36b3ef83c3bc5c299134090d7..32ddd723b2c0dcf062a2f3f1261651786b092bbc 100644 --- a/src/pair_morse.cpp +++ b/src/pair_morse.cpp @@ -11,10 +11,10 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include -#include -#include -#include +#include +#include +#include +#include #include "pair_morse.h" #include "atom.h" #include "comm.h" diff --git a/src/pair_soft.cpp b/src/pair_soft.cpp index b05058b4dcdc20699f0d4892b31f7c8bdfd28554..f428893fd107a0726dcf9532a49d55ddb288b8b3 100644 --- a/src/pair_soft.cpp +++ b/src/pair_soft.cpp @@ -11,10 +11,10 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include -#include -#include -#include +#include +#include +#include +#include #include "pair_soft.h" #include "atom.h" #include "comm.h" diff --git a/src/pair_table.cpp b/src/pair_table.cpp index 0ee4effb0190b989d966689293d6fbd07d875e62..9e9e41a54c6eac3671c7260937d9ca401254b35b 100644 --- a/src/pair_table.cpp +++ b/src/pair_table.cpp @@ -16,9 +16,9 @@ ------------------------------------------------------------------------- */ #include -#include -#include -#include +#include +#include +#include #include "pair_table.h" #include "atom.h" #include "force.h" diff --git a/src/pair_ufm.cpp b/src/pair_ufm.cpp index e036e2cdd96cfbf0472c6b61a0c736bda90ede6f..965fe0204e739a526f5f7ebe13e981f2b5c22984 100644 --- a/src/pair_ufm.cpp +++ b/src/pair_ufm.cpp @@ -17,10 +17,10 @@ Maurice de Koning (Unicamp/Brazil) - dekoning@ifi.unicamp.br ------------------------------------------------------------------------- */ -#include -#include -#include -#include +#include +#include +#include +#include #include "pair_ufm.h" #include "atom.h" #include "comm.h" diff --git a/src/pair_yukawa.cpp b/src/pair_yukawa.cpp index 9be9237734343588dda84aceb4d650c067c8f525..040664abec071e8b776a9315f2e33521d6221f2a 100644 --- a/src/pair_yukawa.cpp +++ b/src/pair_yukawa.cpp @@ -11,8 +11,8 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include -#include +#include +#include #include "pair_yukawa.h" #include "atom.h" #include "force.h" diff --git a/src/pair_zbl.cpp b/src/pair_zbl.cpp index d2dbaeae702adeb0b5505d4a0c0d411a182591e7..98048f61d0751393e4a23b672b84c6698e669db2 100644 --- a/src/pair_zbl.cpp +++ b/src/pair_zbl.cpp @@ -15,10 +15,10 @@ Contributing authors: Stephen Foiles, Aidan Thompson (SNL) ------------------------------------------------------------------------- */ -#include -#include -#include -#include +#include +#include +#include +#include #include "pair_zbl.h" #include "atom.h" #include "comm.h" diff --git a/src/pair_zero.cpp b/src/pair_zero.cpp index ab6d713cc4aa433524eff1484a38b7dd4eba5d31..d423e196af0f47a8789cefb6430d3b5d7a0f36eb 100644 --- a/src/pair_zero.cpp +++ b/src/pair_zero.cpp @@ -15,10 +15,10 @@ Contributing author: Carsten Svaneborg (SDU) ------------------------------------------------------------------------- */ -#include -#include -#include -#include +#include +#include +#include +#include #include "pair_zero.h" #include "atom.h" #include "comm.h" diff --git a/src/random_mars.cpp b/src/random_mars.cpp index 1300cbbb8d8bbefb755b1769c0636ea60a875c41..464e640eab5b73489d4216467de4e848da23e293 100644 --- a/src/random_mars.cpp +++ b/src/random_mars.cpp @@ -14,7 +14,7 @@ // Marsaglia random number generator // see RANMAR in F James, Comp Phys Comm, 60, 329 (1990) -#include +#include #include "random_mars.h" #include "error.h" diff --git a/src/random_park.cpp b/src/random_park.cpp index 80460a39fd26168a8e24b034795e87f2e97d325f..fc00939bd471f4f07f863141a4f22da586f564cc 100644 --- a/src/random_park.cpp +++ b/src/random_park.cpp @@ -13,7 +13,7 @@ // Park/Miller RNG -#include +#include #include "random_park.h" #include "error.h" diff --git a/src/rcb.cpp b/src/rcb.cpp index 2ef3e0c136b2dac029ee0e769b0303f3014f484e..3027920310055351370fd6bff70f61038f01b726 100644 --- a/src/rcb.cpp +++ b/src/rcb.cpp @@ -12,7 +12,7 @@ ------------------------------------------------------------------------- */ #include -#include +#include #include "rcb.h" #include "irregular.h" #include "memory.h" diff --git a/src/read_data.cpp b/src/read_data.cpp index 4b84016744c9d462fbe564f8c71d0f57e561fa8b..5faa8f9646517ff8952a5d035372099c256d2070 100644 --- a/src/read_data.cpp +++ b/src/read_data.cpp @@ -17,10 +17,10 @@ #include "lmptype.h" #include -#include -#include -#include -#include +#include +#include +#include +#include #include "read_data.h" #include "atom.h" #include "atom_vec.h" diff --git a/src/read_data.h b/src/read_data.h index 9b7ca66259d266bc0cdd39b39068f73ef9b55ce1..9dce8cfcf581c20a145b3684b1b42f14dde214ef 100644 --- a/src/read_data.h +++ b/src/read_data.h @@ -20,7 +20,7 @@ CommandStyle(read_data,ReadData) #ifndef LMP_READ_DATA_H #define LMP_READ_DATA_H -#include +#include #include "pointers.h" namespace LAMMPS_NS { diff --git a/src/read_dump.cpp b/src/read_dump.cpp index 7f2488fbb2ecd451468a0e09c934fdaa79b1c7c8..30934f123b853ee5d2c035b564a6f8a2db73f42b 100644 --- a/src/read_dump.cpp +++ b/src/read_dump.cpp @@ -21,8 +21,8 @@ #include "lmptype.h" #include -#include -#include +#include +#include #include "read_dump.h" #include "reader.h" #include "style_reader.h" diff --git a/src/read_dump.h b/src/read_dump.h index 3fc554b5116475f407a686a6cd0af0cf8aa3a596..eb70b9980898b1665ca93fc2f755ba06f824fa86 100644 --- a/src/read_dump.h +++ b/src/read_dump.h @@ -22,7 +22,7 @@ CommandStyle(read_dump,ReadDump) #ifndef LMP_READ_DUMP_H #define LMP_READ_DUMP_H -#include +#include #include "pointers.h" namespace LAMMPS_NS { diff --git a/src/read_restart.cpp b/src/read_restart.cpp index 60d4a7199eea14804c559f720eb03636de28d6ca..1164de6faa91acea7ebc08b985d317618c723e9f 100644 --- a/src/read_restart.cpp +++ b/src/read_restart.cpp @@ -12,8 +12,8 @@ ------------------------------------------------------------------------- */ #include -#include -#include +#include +#include #include #include "read_restart.h" #include "atom.h" diff --git a/src/read_restart.h b/src/read_restart.h index 0c4661cb55abce8719427f87ac75d77f4d11cf41..8d2547fb1055673945e77b650b7004e6f0f01720 100644 --- a/src/read_restart.h +++ b/src/read_restart.h @@ -20,7 +20,7 @@ CommandStyle(read_restart,ReadRestart) #ifndef LMP_READ_RESTART_H #define LMP_READ_RESTART_H -#include +#include #include "pointers.h" namespace LAMMPS_NS { diff --git a/src/reader.cpp b/src/reader.cpp index b8914d1b1003136dcc14a16d894c9a056d667967..f6e8bd39ebec8522ea68c9e0ca099f9ea07edd9f 100644 --- a/src/reader.cpp +++ b/src/reader.cpp @@ -11,8 +11,8 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include -#include +#include +#include #include "reader.h" #include "error.h" diff --git a/src/reader_native.cpp b/src/reader_native.cpp index 529325ed18927f6c0eeed92b06d7cbf5dbf3be08..2c60ffdfd48f6a0d81c942a091d83e71bf8c6183 100644 --- a/src/reader_native.cpp +++ b/src/reader_native.cpp @@ -11,8 +11,8 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include -#include +#include +#include #include "reader_native.h" #include "atom.h" #include "memory.h" diff --git a/src/reader_xyz.cpp b/src/reader_xyz.cpp index a56b503f5e329d2fcd5aecfef8122f5ba8aa30b6..5cb3476510f093abbe51f745043e0d063356fe29 100644 --- a/src/reader_xyz.cpp +++ b/src/reader_xyz.cpp @@ -15,8 +15,8 @@ Contributing author: Axel Kohlmeyer (Temple U) ------------------------------------------------------------------------- */ -#include -#include +#include +#include #include "reader_xyz.h" #include "atom.h" #include "memory.h" diff --git a/src/region.cpp b/src/region.cpp index 047c43ce4b0aa1b6a3e5eb0abc8701e769bd6c52..88a414b13438fb2acc8008c7e635645fb1026c30 100644 --- a/src/region.cpp +++ b/src/region.cpp @@ -11,9 +11,9 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include -#include -#include +#include +#include +#include #include "region.h" #include "update.h" #include "domain.h" diff --git a/src/region_block.cpp b/src/region_block.cpp index 8e1659aa13489b2890abb8c92a26565a5250ace4..eeca1323786390c43e434cb0cf89817c5b5ecb52 100644 --- a/src/region_block.cpp +++ b/src/region_block.cpp @@ -11,8 +11,8 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include -#include +#include +#include #include "region_block.h" #include "force.h" #include "domain.h" diff --git a/src/region_cone.cpp b/src/region_cone.cpp index 2af39f93a933f210acd712bda94e93fccebb328f..72f56a268fe4ece8ce5771c6bda9ad5bd56a7523 100644 --- a/src/region_cone.cpp +++ b/src/region_cone.cpp @@ -15,9 +15,9 @@ Contributing author: Pim Schravendijk ------------------------------------------------------------------------- */ -#include -#include -#include +#include +#include +#include #include "region_cone.h" #include "domain.h" #include "error.h" diff --git a/src/region_cylinder.cpp b/src/region_cylinder.cpp index 959992f77b89f7cb1e7fa4f1c9538016c0db750f..0b15a3644df2b454f9794a11dab2f495898b1222 100644 --- a/src/region_cylinder.cpp +++ b/src/region_cylinder.cpp @@ -11,9 +11,9 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include -#include -#include +#include +#include +#include #include "region_cylinder.h" #include "update.h" #include "domain.h" diff --git a/src/region_intersect.cpp b/src/region_intersect.cpp index 4fb84dda5999f047a115d1fcb26c1acbe6bc6619..96d3bed16c319657aa20c10e6d6eff2f21f44179 100644 --- a/src/region_intersect.cpp +++ b/src/region_intersect.cpp @@ -11,8 +11,8 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include -#include +#include +#include #include "region_intersect.h" #include "domain.h" #include "error.h" diff --git a/src/region_plane.cpp b/src/region_plane.cpp index 3c945eb553401844159156b549577d4f975d5816..e67a2c85bd8d7e7bf6aa842171c20d05df893279 100644 --- a/src/region_plane.cpp +++ b/src/region_plane.cpp @@ -11,9 +11,9 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include -#include -#include +#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 b8b7b30368ad2dfe565065c69e4b6c6b95376b6c..22fc504c37537b14e2370ef822ba4c17a4547d09 100644 --- a/src/region_prism.cpp +++ b/src/region_prism.cpp @@ -15,9 +15,9 @@ Contributing author: Pieter in 't Veld (SNL) ------------------------------------------------------------------------- */ -#include -#include -#include +#include +#include +#include #include "region_prism.h" #include "domain.h" #include "force.h" diff --git a/src/region_sphere.cpp b/src/region_sphere.cpp index 8aef087d38eab60b8d46b910951797d1405c36bc..5645b3369d7f64ea0fd2cccbb52027f39c6d153d 100644 --- a/src/region_sphere.cpp +++ b/src/region_sphere.cpp @@ -11,9 +11,9 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include -#include -#include +#include +#include +#include #include "region_sphere.h" #include "update.h" #include "input.h" diff --git a/src/region_union.cpp b/src/region_union.cpp index abb6f854e3675f821c7c9ee51f7c599e5447d5a3..33ac6fedd709acf0f6b06d99fb095e6facd799c6 100644 --- a/src/region_union.cpp +++ b/src/region_union.cpp @@ -11,8 +11,8 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include -#include +#include +#include #include "region_union.h" #include "domain.h" #include "error.h" diff --git a/src/replicate.cpp b/src/replicate.cpp index 1251688211950d97bbc62dd497b40cb14e6f8162..7954e4291416b6ea666a18dc639d442093efe610 100644 --- a/src/replicate.cpp +++ b/src/replicate.cpp @@ -11,8 +11,8 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include -#include +#include +#include #include "replicate.h" #include "atom.h" #include "atom_vec.h" diff --git a/src/rerun.cpp b/src/rerun.cpp index 6081a6fc4721026ba3c89db20a3098cb7718735c..f8a37b59462a89a3f4c1e5c0e3e2fd6fe3105fff 100644 --- a/src/rerun.cpp +++ b/src/rerun.cpp @@ -11,8 +11,8 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include -#include +#include +#include #include "rerun.h" #include "read_dump.h" #include "domain.h" diff --git a/src/respa.cpp b/src/respa.cpp index 7080a739484de0c772463b72963c501b8312dc52..73e280b03d806fa038d388e2943d067465cce3d2 100644 --- a/src/respa.cpp +++ b/src/respa.cpp @@ -15,8 +15,8 @@ Contributing authors: Mark Stevens (SNL), Paul Crozier (SNL) ------------------------------------------------------------------------- */ -#include -#include +#include +#include #include "respa.h" #include "neighbor.h" #include "atom.h" diff --git a/src/run.cpp b/src/run.cpp index 37af977e3450f2b2b07ff38c3c35199447ddcc44..beb71be52c1faafeecfb8b3e4fd6c6cb2315e2fc 100644 --- a/src/run.cpp +++ b/src/run.cpp @@ -11,8 +11,8 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include -#include +#include +#include #include "run.h" #include "domain.h" #include "update.h" diff --git a/src/set.cpp b/src/set.cpp index 77cae4cb0972c25604610199903406d99f3bdf14..f741760ed56c56ab85bb42c29015a4db87a07228 100644 --- a/src/set.cpp +++ b/src/set.cpp @@ -12,9 +12,9 @@ ------------------------------------------------------------------------- */ #include -#include -#include -#include +#include +#include +#include #include "set.h" #include "atom.h" #include "atom_vec.h" diff --git a/src/special.cpp b/src/special.cpp index 56529e748b8d52e070696543627bfba255b87e0a..fccc930353ce3a71458f5997355b49110f9006dd 100644 --- a/src/special.cpp +++ b/src/special.cpp @@ -12,7 +12,7 @@ ------------------------------------------------------------------------- */ #include -#include +#include #include "special.h" #include "atom.h" #include "atom_vec.h" diff --git a/src/thermo.cpp b/src/thermo.cpp index 211ace5232b3b89f3a64ad4a0a102628e4990383..fb3d1abc485df6cd975a68835dd99d771247b287 100644 --- a/src/thermo.cpp +++ b/src/thermo.cpp @@ -17,9 +17,9 @@ #include "lmptype.h" #include -#include -#include -#include +#include +#include +#include #include "thermo.h" #include "atom.h" #include "update.h" diff --git a/src/timer.cpp b/src/timer.cpp index 9c1aa8794398c03345fe3882f40399725e6bfcf5..65cb6ab5d8fef698784258a1c80220848f96d9bb 100644 --- a/src/timer.cpp +++ b/src/timer.cpp @@ -12,8 +12,8 @@ ------------------------------------------------------------------------- */ #include -#include -#include +#include +#include #include "timer.h" #include "comm.h" #include "error.h" @@ -22,13 +22,13 @@ #ifdef _WIN32 #include -#include +#include // requires C++-11 #else #include #include #endif -#include +#include using namespace LAMMPS_NS; diff --git a/src/universe.cpp b/src/universe.cpp index c2a6754fac7799ec7882572fac0365407dd41654..45b4318ec900862d85d8a7c3999ae181bd1b1f6d 100644 --- a/src/universe.cpp +++ b/src/universe.cpp @@ -12,10 +12,10 @@ ------------------------------------------------------------------------- */ #include -#include -#include -#include -#include +#include +#include +#include +#include #include "universe.h" #include "version.h" #include "error.h" diff --git a/src/universe.h b/src/universe.h index 4ff4d7dd14971c691b9f29417c789a3627255a97..3073409b8677a41a1c0326e4c965591170aa3403 100644 --- a/src/universe.h +++ b/src/universe.h @@ -14,7 +14,7 @@ #ifndef LMP_UNIVERSE_H #define LMP_UNIVERSE_H -#include +#include #include "pointers.h" namespace LAMMPS_NS { diff --git a/src/update.cpp b/src/update.cpp index 6282c0a875aec481d0ed3df46e1fa3f7988ff637..aa152a850857e729f78da1db98e678e41140f1d7 100644 --- a/src/update.cpp +++ b/src/update.cpp @@ -11,8 +11,8 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include -#include +#include +#include #include "update.h" #include "integrate.h" #include "min.h" diff --git a/src/variable.cpp b/src/variable.cpp index 34dc33da39a084d46fef21a6727b04ec5d341095..b5c19a48439cd2342273e7af4b7d21936ffe9bd2 100644 --- a/src/variable.cpp +++ b/src/variable.cpp @@ -11,10 +11,10 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include -#include -#include -#include +#include +#include +#include +#include #include #include "variable.h" #include "universe.h" diff --git a/src/variable.h b/src/variable.h index 9dcbaebd4fa82e6860fd836b20929fbe3efc1fa7..a74cdba980f4cee3c75486a08706e3c3ba4f96ca 100644 --- a/src/variable.h +++ b/src/variable.h @@ -14,7 +14,7 @@ #ifndef LMP_VARIABLE_H #define LMP_VARIABLE_H -#include +#include #include "pointers.h" namespace LAMMPS_NS { diff --git a/src/velocity.cpp b/src/velocity.cpp index 260a11bb4ee90dc2116907688e9b5bda4503e4cb..f83f778f8b15dfecfbd7b755da0fc7dfb19f93d7 100644 --- a/src/velocity.cpp +++ b/src/velocity.cpp @@ -12,10 +12,10 @@ ------------------------------------------------------------------------- */ #include -#include -#include -#include -#include +#include +#include +#include +#include #include "velocity.h" #include "atom.h" #include "update.h" diff --git a/src/verlet.cpp b/src/verlet.cpp index 019f3f2f05b3f539cd9619b441dd77f290c804dd..fcba248d5f8ddcc1e46cd0d8ec8a4ae2e04351a4 100644 --- a/src/verlet.cpp +++ b/src/verlet.cpp @@ -11,7 +11,7 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include +#include #include "verlet.h" #include "neighbor.h" #include "domain.h" diff --git a/src/write_coeff.cpp b/src/write_coeff.cpp index 0556d647cf36d1046f4864002f2e6fa5e5d656f5..5f82a480fd9242a745998709bc6748ed80212fb0 100644 --- a/src/write_coeff.cpp +++ b/src/write_coeff.cpp @@ -11,7 +11,7 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include +#include #include #include "write_coeff.h" #include "pair.h" diff --git a/src/write_coeff.h b/src/write_coeff.h index 9228e879bc365486a44e50711144b5dd217ec6c7..569a615e6e577f06386fd0accb394971a7ab1edc 100644 --- a/src/write_coeff.h +++ b/src/write_coeff.h @@ -20,7 +20,7 @@ CommandStyle(write_coeff,WriteCoeff) #ifndef LMP_WRITE_COEFF_H #define LMP_WRITE_COEFF_H -#include +#include #include "pointers.h" namespace LAMMPS_NS { diff --git a/src/write_data.cpp b/src/write_data.cpp index d9694f7cd355e593dbee401b252dfc1d6efd042e..85fbe6e5c7cd3f4fa309f8ee470feb1ae87214cc 100644 --- a/src/write_data.cpp +++ b/src/write_data.cpp @@ -12,7 +12,7 @@ ------------------------------------------------------------------------- */ #include -#include +#include #include "write_data.h" #include "atom.h" #include "atom_vec.h" diff --git a/src/write_data.h b/src/write_data.h index ced6a3be8b4ceee0e07c06463d561d996c357320..6f1bb2ec47f9a609c7a6bf1823a7869561480942 100644 --- a/src/write_data.h +++ b/src/write_data.h @@ -20,7 +20,7 @@ CommandStyle(write_data,WriteData) #ifndef LMP_WRITE_DATA_H #define LMP_WRITE_DATA_H -#include +#include #include "pointers.h" namespace LAMMPS_NS { diff --git a/src/write_dump.cpp b/src/write_dump.cpp index dcf6c05a14db5629dd01a157756d40cce194f550..bb79c654b418569101a1f601f31fe93ce420bd97 100644 --- a/src/write_dump.cpp +++ b/src/write_dump.cpp @@ -15,7 +15,7 @@ Contributing author: Axel Kohlmeyer (Temple U) ------------------------------------------------------------------------- */ -#include +#include #include "write_dump.h" #include "style_dump.h" #include "dump.h" diff --git a/src/write_restart.cpp b/src/write_restart.cpp index c92fd15334778cf8267033b8a638e17b4844b743..c82791e2c1c7c1d0f8a50e6faa695c39873e8c8a 100644 --- a/src/write_restart.cpp +++ b/src/write_restart.cpp @@ -12,7 +12,7 @@ ------------------------------------------------------------------------- */ #include -#include +#include #include "write_restart.h" #include "atom.h" #include "atom_vec.h" diff --git a/src/write_restart.h b/src/write_restart.h index 2253977bdad8868fce56246dc4de315fa088e8b2..c6202acbfd1bf08f47baacb33ebb3832f35b2f89 100644 --- a/src/write_restart.h +++ b/src/write_restart.h @@ -20,7 +20,7 @@ CommandStyle(write_restart,WriteRestart) #ifndef LMP_WRITE_RESTART_H #define LMP_WRITE_RESTART_H -#include +#include #include "pointers.h" namespace LAMMPS_NS {