Loading cmake/CMakeLists.txt +7 −2 Original line number Diff line number Diff line Loading @@ -37,7 +37,7 @@ include(PreventInSourceBuilds) if(NOT CMAKE_BUILD_TYPE AND NOT CMAKE_CXX_FLAGS) #release comes with -O3 by default set(CMAKE_BUILD_TYPE Release CACHE STRING "Choose the type of build, options are: None Debug Release RelWithDebInfo MinSizeRel." FORCE) set(CMAKE_BUILD_TYPE RelWithDebInfo CACHE STRING "Choose the type of build, options are: None Debug Release RelWithDebInfo MinSizeRel." FORCE) endif(NOT CMAKE_BUILD_TYPE AND NOT CMAKE_CXX_FLAGS) string(TOUPPER "${CMAKE_BUILD_TYPE}" BTYPE) Loading Loading @@ -673,5 +673,10 @@ if(PKG_KOKKOS) message(STATUS "Kokkos Arch: ${KOKKOS_ARCH}") endif() if(PKG_KSPACE) message(STATUS "Using ${FFT} as FFT") message(STATUS "Using ${FFT} as primary FFT library") if(FFT_SINGLE) message(STATUS "Using single precision FFTs") else() message(STATUS "Using double precision FFTs") endif() endif() cmake/Modules/Packages/KSPACE.cmake +16 −12 Original line number Diff line number Diff line if(PKG_KSPACE) option(FFT_SINGLE "Use single precision FFT instead of double" OFF) option(FFT_SINGLE "Use single precision FFTs instead of double precision FFTs" OFF) set(FFTW "FFTW3") if(FFT_SINGLE) set(FFTW "FFTW3F") Loading @@ -7,26 +7,30 @@ if(PKG_KSPACE) endif() find_package(${FFTW} QUIET) if(${FFTW}_FOUND) set(FFT "${FFTW}" CACHE STRING "FFT library for KSPACE package") set(FFT "FFTW3" CACHE STRING "FFT library for KSPACE package") else() set(FFT "KISS" CACHE STRING "FFT library for KSPACE package") endif() set(FFT_VALUES KISS ${FFTW} MKL) set(FFT_VALUES KISS FFTW3 MKL) set_property(CACHE FFT PROPERTY STRINGS ${FFT_VALUES}) validate_option(FFT FFT_VALUES) string(TOUPPER ${FFT} FFT) if(NOT FFT STREQUAL "KISS") find_package(${FFT} REQUIRED) if(NOT FFT STREQUAL "FFTW3F") add_definitions(-DFFT_FFTW) else() add_definitions(-DFFT_${FFT}) endif() include_directories(${${FFT}_INCLUDE_DIRS}) list(APPEND LAMMPS_LINK_LIBS ${${FFT}_LIBRARIES}) if(FFT STREQUAL "FFTW3") find_package(${FFTW} REQUIRED) add_definitions(-DFFT_FFTW3) include_directories(${${FFTW}_INCLUDE_DIRS}) list(APPEND LAMMPS_LINK_LIBS ${${FFTW}_LIBRARIES}) elseif(FFT STREQUAL "MKL") find_package(MKL REQUIRED) add_definitions(-DFFT_MKL) include_directories(${MKL_INCLUDE_DIRS}) list(APPEND LAMMPS_LINK_LIBS ${MKL_LIBRARIES}) else() # last option is KISSFFT add_definitions(-DFFT_KISS) endif() set(FFT_PACK "array" CACHE STRING "Optimization for FFT") set(FFT_PACK_VALUES array pointer memcpy) set_property(CACHE FFT_PACK PROPERTY STRINGS ${FFT_PACK_VALUES}) Loading doc/src/compute.txt +43 −46 Original line number Diff line number Diff line Loading @@ -171,42 +171,40 @@ The individual style names on the "Commands compute"_Commands_compute.html doc page are followed by one or more of (g,i,k,o,t) to indicate which accelerated styles exist. "ackland/atom"_compute_ackland_atom.html - "ackland/atom"_compute_ackland_atom.html - determines the local lattice structure based on the Ackland formulation "adf"_compute_adf.html - angular distribution function of triples of atoms "aggregate/atom"_compute_cluster_atom.html - aggregate ID for each atom "angle"_compute_angle.html - "angle/local"_compute_angle_local.html - "angle/local"_compute_bond_local.html - theta and energy of each angle "angle"_compute_angle.html - energy of each angle sub-style "angle/local"_compute_angle_local.html - theta and energy of each angle "angmom/chunk"_compute_angmom_chunk.html - angular momentum for each chunk "basal/atom"_compute_basal_atom.html - "basal/atom"_compute_basal_atom.html - calculates the hexagonal close-packed “c” lattice vector of each atom "body/local"_compute_body_local.html - attributes of body sub-particles "bond"_compute_bond.html - values computed by a bond style "bond"_compute_bond.html - energy of each bond sub-style "bond/local"_compute_bond_local.html - distance and energy of each bond "centro/atom"_compute_centro_atom.html - centro-symmetry parameter for each atom "chunk/atom"_compute_chunk_atom.html - assign chunk IDs to each atom "chunk/spread/atom"_compute_chunk_spread_atom.html - spreads chunk values to each atom in chunk "cluster/atom"_compute_cluster_atom.html - cluster ID for each atom "cna/atom"_compute_cna_atom.html - common neighbor analysis (CNA) for each atom "cnp/atom"_compute_cnp_atom.html - "cnp/atom"_compute_cnp_atom.html - common neighborhood parameter (CNP) for each atom "com"_compute_com.html - center-of-mass of group of atoms "com/chunk"_compute_com_chunk.html - center-of-mass for each chunk "contact/atom"_compute_contact_atom.html - contact count for each spherical particle "coord/atom"_compute_coord_atom.html - coordination number for each atom "damage/atom"_compute_damage_atom.html - Peridynamic damage for each atom "dihedral"_compute_dihedral.html - "dihedral"_compute_dihedral.html - energy of each dihedral sub-style "dihedral/local"_compute_dihedral_local.html - angle of each dihedral "dilatation/atom"_compute_dilatation_atom.html - Peridynamic dilatation for each atom "dipole/chunk"_compute_dipole_chunk.html - "dipole/chunk"_compute_dipole_chunk.html - dipole vector and total dipole for each chunk "displace/atom"_compute_displace_atom.html - displacement of each atom "dpd"_compute_dpd.html - "dpd/atom"_compute_dpd_atom.html - "edpd/temp/atom"_compute_edpd_temp_atom.html - "entropy/atom"_compute_entropy_atom.html - "edpd/temp/atom"_compute_edpd_temp_atom.html - per-atom temperature for each eDPD particle in a group "entropy/atom"_compute_entropy_atom.html - pair entropy fingerprint of each atom "erotate/asphere"_compute_erotate_asphere.html - rotational energy of aspherical particles "erotate/rigid"_compute_erotate_rigid.html - rotational energy of rigid bodies "erotate/sphere"_compute_erotate_sphere.html - rotational energy of spherical particles "erotate/sphere/atom"_compute_erotate_sphere.html - rotational energy for each spherical particle "erotate/sphere/atom"_compute_erotate_sphere_atom.html - "erotate/sphere/atom"_compute_erotate_sphere_atom.html - rotational energy for each spherical particle "event/displace"_compute_event_displace.html - detect event on atom displacement "fep"_compute_fep.html - "force/tally"_compute_tally.html - Loading @@ -218,17 +216,17 @@ compute"_Commands_compute.html doc page are followed by one or more of "heat/flux"_compute_heat_flux.html - heat flux through a group of atoms "heat/flux/tally"_compute_tally.html - "hexorder/atom"_compute_hexorder_atom.html - bond orientational order parameter q6 "improper"_compute_improper.html - "improper"_compute_improper.html - energy of each improper sub-style "improper/local"_compute_improper_local.html - angle of each improper "inertia/chunk"_compute_inertia_chunk.html - inertia tensor for each chunk "ke"_compute_ke.html - translational kinetic energy "ke/atom"_compute_ke_atom.html - kinetic energy for each atom "ke/atom/eff"_compute_ke_atom_eff.html - "ke/eff"_compute_ke_eff.html - "ke/atom/eff"_compute_ke_atom_eff.html - per-atom translational and radial kinetic energy in the electron force field model "ke/eff"_compute_ke_eff.html - kinetic energy of a group of nuclei and electrons in the electron force field model "ke/rigid"_compute_ke_rigid.html - translational kinetic energy of rigid bodies "meso/e/atom"_compute_meso_e_atom.html - "meso/rho/atom"_compute_meso_rho_atom.html - "meso/t/atom"_compute_meso_t_atom.html - "meso/e/atom"_compute_meso_e_atom.html - per-atom internal energy of Smooth-Particle Hydrodynamics atoms "meso/rho/atom"_compute_meso_rho_atom.html - per-atom mesoscopic density of Smooth-Particle Hydrodynamics atoms "meso/t/atom"_compute_meso_t_atom.html - per-atom internal temperature of Smooth-Particle Hydrodynamics atoms "msd"_compute_msd.html - mean-squared displacement of group of atoms "msd/chunk"_compute_msd_chunk.html - mean-squared displacement for each chunk "msd/nongauss"_compute_msd_nongauss.html - MSD and non-Gaussian parameter of group of atoms Loading @@ -242,73 +240,72 @@ compute"_Commands_compute.html doc page are followed by one or more of "pe/tally"_compute_tally.html - "plasticity/atom"_compute_plasticity_atom.html - Peridynamic plasticity for each atom "pressure"_compute_pressure.html - total pressure and pressure tensor "pressure/cylinder"_compute_pressure_cylinder.html - "pressure/uef"_compute_pressure_uef.html - "pressure/cylinder"_compute_pressure_cylinder.html - pressure tensor in cylindrical coordinates "pressure/uef"_compute_pressure_uef.html - pressure tensor in the reference frame of an applied flow field "property/atom"_compute_property_atom.html - convert atom attributes to per-atom vectors/arrays "property/chunk"_compute_property_chunk.html - extract various per-chunk attributes "property/local"_compute_property_local.html - convert local attributes to localvectors/arrays "ptm/atom"_compute_ptm_atom.html - "ptm/atom"_compute_ptm_atom.html - determines the local lattice structure based on the Polyhedral Template Matching method "rdf"_compute_rdf.html - radial distribution function g(r) histogram of group of atoms "reduce"_compute_reduce.html - combine per-atom quantities into a single global value "reduce/chunk"_compute_reduce_chunk.html - reduce per-atom quantities within each chunk "reduce/region"_compute_reduce.html - same as compute reduce, within a region "rigid/local"_compute_rigid_local.html - extract rigid body attributes "saed"_compute_saed.html - "saed"_compute_saed.html - electron diffraction intensity on a mesh of reciprocal lattice nodes "slice"_compute_slice.html - extract values from global vector or array "smd/contact/radius"_compute_smd_contact_radius.html - "smd/damage"_compute_smd_damage.html - "smd/damage"_compute_smd_damage.html - damage status of SPH particles in Smooth Mach Dynamics "smd/hourglass/error"_compute_smd_hourglass_error.html - "smd/internal/energy"_compute_smd_internal_energy.html - "smd/plastic/strain"_compute_smd_plastic_strain.html - "smd/plastic/strain/rate"_compute_smd_plastic_strain_rate.html - "smd/rho"_compute_smd_rho.html - "smd/tlsph/defgrad"_compute_smd_tlsph_defgrad.html - "smd/tlsph/dt"_compute_smd_tlsph_dt.html - "smd/internal/energy"_compute_smd_internal_energy.html - per-particle enthalpy in Smooth Mach Dynamics "smd/plastic/strain"_compute_smd_plastic_strain.html - equivalent plastic strain per particle in Smooth Mach Dynamics "smd/plastic/strain/rate"_compute_smd_plastic_strain_rate.html - time rate of the equivalent plastic strain in Smooth Mach Dynamics "smd/rho"_compute_smd_rho.html - per-particle mass density in Smooth Mach Dynamics "smd/tlsph/defgrad"_compute_smd_tlsph_defgrad.html - deformation gradient in Smooth Mach Dynamics "smd/tlsph/dt"_compute_smd_tlsph_dt.html - CFL-stable time increment per particle in Smooth Mach Dynamics "smd/tlsph/num/neighs"_compute_smd_tlsph_num_neighs.html - "smd/tlsph/shape"_compute_smd_tlsph_shape.html - "smd/tlsph/strain"_compute_smd_tlsph_strain.html - "smd/tlsph/strain/rate"_compute_smd_tlsph_strain_rate.html - "smd/tlsph/stress"_compute_smd_tlsph_stress.html - "smd/triangle/vertices"_compute_smd_triangle_vertices.html - "smd/tlsph/stress"_compute_smd_tlsph_stress.html - per-particle Cauchy stress tensor for SPH particles "smd/triangle/vertices"_compute_smd_triangle_vertices.html - "smd/ulsph/num/neighs"_compute_smd_ulsph_num_neighs.html - "smd/ulsph/strain"_compute_smd_ulsph_strain.html - "smd/ulsph/strain/rate"_compute_smd_ulsph_strain_rate.html - "smd/ulsph/stress"_compute_smd_ulsph_stress.html - "smd/vol"_compute_smd_vol.html - "smd/ulsph/stress"_compute_smd_ulsph_stress.html - per-particle Cauchy stress tensor and von Mises equivalent stress in Smooth Mach Dynamics "smd/vol"_compute_smd_vol.html - per-particle volumes and their sum in Smooth Mach Dynamics "sna/atom"_compute_sna_atom.html - calculate bispectrum coefficients for each atom "snad/atom"_compute_sna_atom.html - derivative of bispectrum coefficients for each atom "snav/atom"_compute_sna_atom.html - virial contribution from bispectrum coefficients for each atom "spin"_compute_spin.html - "spin"_compute_spin.html - magnetic quantities for a system of atoms having spins "stress/atom"_compute_stress_atom.html - stress tensor for each atom "stress/mop"_compute_stress_mop.html - "stress/mop/profile"_compute_stress_mop.html - "stress/mop"_compute_stress_mop.html - normal components of the local stress tensor using the method of planes "stress/mop/profile"_compute_stress_mop.html - profile of the normal components of the local stress tensor using the method of planes "stress/tally"_compute_tally.html - "tdpd/cc/atom"_compute_tdpd_cc_atom.html - "tdpd/cc/atom"_compute_tdpd_cc_atom.html - per-atom chemical concentration of a specified species for each tDPD particle "temp"_compute_temp.html - temperature of group of atoms "temp/asphere"_compute_temp_asphere.html - temperature of aspherical particles "temp/body"_compute_temp_body.html - temperature of body particles "temp/chunk"_compute_temp_chunk.html - temperature of each chunk "temp/com"_compute_temp_com.html - temperature after subtracting center-of-mass velocity "temp/cs"_compute_temp_cs.html - "temp/cs"_compute_temp_cs.html - temperature based on the center-of-mass velocity of atom pairs that are bonded to each other "temp/deform"_compute_temp_deform.html - temperature excluding box deformation velocity "temp/deform/eff"_compute_temp_deform_eff.html - "temp/drude"_compute_temp_drude.html - "temp/eff"_compute_temp_eff.html - "temp/deform/eff"_compute_temp_deform_eff.html - temperature excluding box deformation velocity in the electron force field model "temp/drude"_compute_temp_drude.html - temperature of Core-Drude pairs "temp/eff"_compute_temp_eff.html - temperature of a group of nuclei and electrons in the electron force field model "temp/partial"_compute_temp_partial.html - temperature excluding one or more dimensions of velocity "temp/profile"_compute_temp_profile.html - temperature excluding a binned velocity profile "temp/ramp"_compute_temp_ramp.html - temperature excluding ramped velocity component "temp/region"_compute_temp_region.html - temperature of a region of atoms "temp/region/eff"_compute_temp_region_eff.html - "temp/rotate"_compute_temp_rotate.html - "temp/region/eff"_compute_temp_region_eff.html - temperature of a region of nuclei and electrons in the electron force field model "temp/rotate"_compute_temp_rotate.html - temperature of a group of atoms after subtracting out their center-of-mass and angular velocities "temp/sphere"_compute_temp_sphere.html - temperature of spherical particles "temp/uef"_compute_temp_uef.html - "temp/uef"_compute_temp_uef.html - kinetic energy tensor in the reference frame of an applied flow field "ti"_compute_ti.html - thermodynamic integration free energy values "torque/chunk"_compute_torque_chunk.html - torque applied on each chunk "vacf"_compute_vacf.html - velocity auto-correlation function of group of atoms "vcm/chunk"_compute_vcm_chunk.html - velocity of center-of-mass for each chunk "voronoi/atom"_compute_voronoi_atom.html - Voronoi volume and neighbors for each atom "xrd"_compute_xrd.html - :ul "xrd"_compute_xrd.html - x-ray diffraction intensity on a mesh of reciprocal lattice nodes :ul [Restrictions:] none Loading src/KOKKOS/pppm_kokkos.cpp +2 −8 Original line number Diff line number Diff line Loading @@ -306,12 +306,6 @@ void PPPMKokkos<DeviceType>::init() if (me == 0) { #ifdef FFT_SINGLE const char fft_prec[] = "single"; #else const char fft_prec[] = "double"; #endif if (screen) { fprintf(screen," G vector (1/distance) = %g\n",g_ewald); fprintf(screen," grid = %d %d %d\n",nx_pppm,ny_pppm,nz_pppm); Loading @@ -320,7 +314,7 @@ void PPPMKokkos<DeviceType>::init() estimated_accuracy); fprintf(screen," estimated relative force accuracy = %g\n", estimated_accuracy/two_charge_force); fprintf(screen," using %s precision FFTs\n",fft_prec); fprintf(screen," using " LMP_FFT_PREC " precision " LMP_FFT_LIB "\n"); fprintf(screen," 3d grid and FFT values/proc = %d %d\n", ngrid_max,nfft_both_max); } Loading @@ -332,7 +326,7 @@ void PPPMKokkos<DeviceType>::init() estimated_accuracy); fprintf(logfile," estimated relative force accuracy = %g\n", estimated_accuracy/two_charge_force); fprintf(logfile," using %s precision FFTs\n",fft_prec); fprintf(logfile," using " LMP_FFT_PREC " precision " LMP_FFT_LIB "\n"); fprintf(logfile," 3d grid and FFT values/proc = %d %d\n", ngrid_max,nfft_both_max); } Loading src/KSPACE/pppm.cpp +2 −8 Original line number Diff line number Diff line Loading @@ -350,12 +350,6 @@ void PPPM::init() if (me == 0) { #ifdef FFT_SINGLE const char fft_prec[] = "single"; #else const char fft_prec[] = "double"; #endif if (screen) { fprintf(screen," G vector (1/distance) = %g\n",g_ewald); fprintf(screen," grid = %d %d %d\n",nx_pppm,ny_pppm,nz_pppm); Loading @@ -364,7 +358,7 @@ void PPPM::init() estimated_accuracy); fprintf(screen," estimated relative force accuracy = %g\n", estimated_accuracy/two_charge_force); fprintf(screen," using %s precision FFTs\n",fft_prec); fprintf(screen," using " LMP_FFT_PREC " precision " LMP_FFT_LIB "\n"); fprintf(screen," 3d grid and FFT values/proc = %d %d\n", ngrid_max,nfft_both_max); } Loading @@ -376,7 +370,7 @@ void PPPM::init() estimated_accuracy); fprintf(logfile," estimated relative force accuracy = %g\n", estimated_accuracy/two_charge_force); fprintf(logfile," using %s precision FFTs\n",fft_prec); fprintf(logfile," using " LMP_FFT_PREC " precision " LMP_FFT_LIB "\n"); fprintf(logfile," 3d grid and FFT values/proc = %d %d\n", ngrid_max,nfft_both_max); } Loading Loading
cmake/CMakeLists.txt +7 −2 Original line number Diff line number Diff line Loading @@ -37,7 +37,7 @@ include(PreventInSourceBuilds) if(NOT CMAKE_BUILD_TYPE AND NOT CMAKE_CXX_FLAGS) #release comes with -O3 by default set(CMAKE_BUILD_TYPE Release CACHE STRING "Choose the type of build, options are: None Debug Release RelWithDebInfo MinSizeRel." FORCE) set(CMAKE_BUILD_TYPE RelWithDebInfo CACHE STRING "Choose the type of build, options are: None Debug Release RelWithDebInfo MinSizeRel." FORCE) endif(NOT CMAKE_BUILD_TYPE AND NOT CMAKE_CXX_FLAGS) string(TOUPPER "${CMAKE_BUILD_TYPE}" BTYPE) Loading Loading @@ -673,5 +673,10 @@ if(PKG_KOKKOS) message(STATUS "Kokkos Arch: ${KOKKOS_ARCH}") endif() if(PKG_KSPACE) message(STATUS "Using ${FFT} as FFT") message(STATUS "Using ${FFT} as primary FFT library") if(FFT_SINGLE) message(STATUS "Using single precision FFTs") else() message(STATUS "Using double precision FFTs") endif() endif()
cmake/Modules/Packages/KSPACE.cmake +16 −12 Original line number Diff line number Diff line if(PKG_KSPACE) option(FFT_SINGLE "Use single precision FFT instead of double" OFF) option(FFT_SINGLE "Use single precision FFTs instead of double precision FFTs" OFF) set(FFTW "FFTW3") if(FFT_SINGLE) set(FFTW "FFTW3F") Loading @@ -7,26 +7,30 @@ if(PKG_KSPACE) endif() find_package(${FFTW} QUIET) if(${FFTW}_FOUND) set(FFT "${FFTW}" CACHE STRING "FFT library for KSPACE package") set(FFT "FFTW3" CACHE STRING "FFT library for KSPACE package") else() set(FFT "KISS" CACHE STRING "FFT library for KSPACE package") endif() set(FFT_VALUES KISS ${FFTW} MKL) set(FFT_VALUES KISS FFTW3 MKL) set_property(CACHE FFT PROPERTY STRINGS ${FFT_VALUES}) validate_option(FFT FFT_VALUES) string(TOUPPER ${FFT} FFT) if(NOT FFT STREQUAL "KISS") find_package(${FFT} REQUIRED) if(NOT FFT STREQUAL "FFTW3F") add_definitions(-DFFT_FFTW) else() add_definitions(-DFFT_${FFT}) endif() include_directories(${${FFT}_INCLUDE_DIRS}) list(APPEND LAMMPS_LINK_LIBS ${${FFT}_LIBRARIES}) if(FFT STREQUAL "FFTW3") find_package(${FFTW} REQUIRED) add_definitions(-DFFT_FFTW3) include_directories(${${FFTW}_INCLUDE_DIRS}) list(APPEND LAMMPS_LINK_LIBS ${${FFTW}_LIBRARIES}) elseif(FFT STREQUAL "MKL") find_package(MKL REQUIRED) add_definitions(-DFFT_MKL) include_directories(${MKL_INCLUDE_DIRS}) list(APPEND LAMMPS_LINK_LIBS ${MKL_LIBRARIES}) else() # last option is KISSFFT add_definitions(-DFFT_KISS) endif() set(FFT_PACK "array" CACHE STRING "Optimization for FFT") set(FFT_PACK_VALUES array pointer memcpy) set_property(CACHE FFT_PACK PROPERTY STRINGS ${FFT_PACK_VALUES}) Loading
doc/src/compute.txt +43 −46 Original line number Diff line number Diff line Loading @@ -171,42 +171,40 @@ The individual style names on the "Commands compute"_Commands_compute.html doc page are followed by one or more of (g,i,k,o,t) to indicate which accelerated styles exist. "ackland/atom"_compute_ackland_atom.html - "ackland/atom"_compute_ackland_atom.html - determines the local lattice structure based on the Ackland formulation "adf"_compute_adf.html - angular distribution function of triples of atoms "aggregate/atom"_compute_cluster_atom.html - aggregate ID for each atom "angle"_compute_angle.html - "angle/local"_compute_angle_local.html - "angle/local"_compute_bond_local.html - theta and energy of each angle "angle"_compute_angle.html - energy of each angle sub-style "angle/local"_compute_angle_local.html - theta and energy of each angle "angmom/chunk"_compute_angmom_chunk.html - angular momentum for each chunk "basal/atom"_compute_basal_atom.html - "basal/atom"_compute_basal_atom.html - calculates the hexagonal close-packed “c” lattice vector of each atom "body/local"_compute_body_local.html - attributes of body sub-particles "bond"_compute_bond.html - values computed by a bond style "bond"_compute_bond.html - energy of each bond sub-style "bond/local"_compute_bond_local.html - distance and energy of each bond "centro/atom"_compute_centro_atom.html - centro-symmetry parameter for each atom "chunk/atom"_compute_chunk_atom.html - assign chunk IDs to each atom "chunk/spread/atom"_compute_chunk_spread_atom.html - spreads chunk values to each atom in chunk "cluster/atom"_compute_cluster_atom.html - cluster ID for each atom "cna/atom"_compute_cna_atom.html - common neighbor analysis (CNA) for each atom "cnp/atom"_compute_cnp_atom.html - "cnp/atom"_compute_cnp_atom.html - common neighborhood parameter (CNP) for each atom "com"_compute_com.html - center-of-mass of group of atoms "com/chunk"_compute_com_chunk.html - center-of-mass for each chunk "contact/atom"_compute_contact_atom.html - contact count for each spherical particle "coord/atom"_compute_coord_atom.html - coordination number for each atom "damage/atom"_compute_damage_atom.html - Peridynamic damage for each atom "dihedral"_compute_dihedral.html - "dihedral"_compute_dihedral.html - energy of each dihedral sub-style "dihedral/local"_compute_dihedral_local.html - angle of each dihedral "dilatation/atom"_compute_dilatation_atom.html - Peridynamic dilatation for each atom "dipole/chunk"_compute_dipole_chunk.html - "dipole/chunk"_compute_dipole_chunk.html - dipole vector and total dipole for each chunk "displace/atom"_compute_displace_atom.html - displacement of each atom "dpd"_compute_dpd.html - "dpd/atom"_compute_dpd_atom.html - "edpd/temp/atom"_compute_edpd_temp_atom.html - "entropy/atom"_compute_entropy_atom.html - "edpd/temp/atom"_compute_edpd_temp_atom.html - per-atom temperature for each eDPD particle in a group "entropy/atom"_compute_entropy_atom.html - pair entropy fingerprint of each atom "erotate/asphere"_compute_erotate_asphere.html - rotational energy of aspherical particles "erotate/rigid"_compute_erotate_rigid.html - rotational energy of rigid bodies "erotate/sphere"_compute_erotate_sphere.html - rotational energy of spherical particles "erotate/sphere/atom"_compute_erotate_sphere.html - rotational energy for each spherical particle "erotate/sphere/atom"_compute_erotate_sphere_atom.html - "erotate/sphere/atom"_compute_erotate_sphere_atom.html - rotational energy for each spherical particle "event/displace"_compute_event_displace.html - detect event on atom displacement "fep"_compute_fep.html - "force/tally"_compute_tally.html - Loading @@ -218,17 +216,17 @@ compute"_Commands_compute.html doc page are followed by one or more of "heat/flux"_compute_heat_flux.html - heat flux through a group of atoms "heat/flux/tally"_compute_tally.html - "hexorder/atom"_compute_hexorder_atom.html - bond orientational order parameter q6 "improper"_compute_improper.html - "improper"_compute_improper.html - energy of each improper sub-style "improper/local"_compute_improper_local.html - angle of each improper "inertia/chunk"_compute_inertia_chunk.html - inertia tensor for each chunk "ke"_compute_ke.html - translational kinetic energy "ke/atom"_compute_ke_atom.html - kinetic energy for each atom "ke/atom/eff"_compute_ke_atom_eff.html - "ke/eff"_compute_ke_eff.html - "ke/atom/eff"_compute_ke_atom_eff.html - per-atom translational and radial kinetic energy in the electron force field model "ke/eff"_compute_ke_eff.html - kinetic energy of a group of nuclei and electrons in the electron force field model "ke/rigid"_compute_ke_rigid.html - translational kinetic energy of rigid bodies "meso/e/atom"_compute_meso_e_atom.html - "meso/rho/atom"_compute_meso_rho_atom.html - "meso/t/atom"_compute_meso_t_atom.html - "meso/e/atom"_compute_meso_e_atom.html - per-atom internal energy of Smooth-Particle Hydrodynamics atoms "meso/rho/atom"_compute_meso_rho_atom.html - per-atom mesoscopic density of Smooth-Particle Hydrodynamics atoms "meso/t/atom"_compute_meso_t_atom.html - per-atom internal temperature of Smooth-Particle Hydrodynamics atoms "msd"_compute_msd.html - mean-squared displacement of group of atoms "msd/chunk"_compute_msd_chunk.html - mean-squared displacement for each chunk "msd/nongauss"_compute_msd_nongauss.html - MSD and non-Gaussian parameter of group of atoms Loading @@ -242,73 +240,72 @@ compute"_Commands_compute.html doc page are followed by one or more of "pe/tally"_compute_tally.html - "plasticity/atom"_compute_plasticity_atom.html - Peridynamic plasticity for each atom "pressure"_compute_pressure.html - total pressure and pressure tensor "pressure/cylinder"_compute_pressure_cylinder.html - "pressure/uef"_compute_pressure_uef.html - "pressure/cylinder"_compute_pressure_cylinder.html - pressure tensor in cylindrical coordinates "pressure/uef"_compute_pressure_uef.html - pressure tensor in the reference frame of an applied flow field "property/atom"_compute_property_atom.html - convert atom attributes to per-atom vectors/arrays "property/chunk"_compute_property_chunk.html - extract various per-chunk attributes "property/local"_compute_property_local.html - convert local attributes to localvectors/arrays "ptm/atom"_compute_ptm_atom.html - "ptm/atom"_compute_ptm_atom.html - determines the local lattice structure based on the Polyhedral Template Matching method "rdf"_compute_rdf.html - radial distribution function g(r) histogram of group of atoms "reduce"_compute_reduce.html - combine per-atom quantities into a single global value "reduce/chunk"_compute_reduce_chunk.html - reduce per-atom quantities within each chunk "reduce/region"_compute_reduce.html - same as compute reduce, within a region "rigid/local"_compute_rigid_local.html - extract rigid body attributes "saed"_compute_saed.html - "saed"_compute_saed.html - electron diffraction intensity on a mesh of reciprocal lattice nodes "slice"_compute_slice.html - extract values from global vector or array "smd/contact/radius"_compute_smd_contact_radius.html - "smd/damage"_compute_smd_damage.html - "smd/damage"_compute_smd_damage.html - damage status of SPH particles in Smooth Mach Dynamics "smd/hourglass/error"_compute_smd_hourglass_error.html - "smd/internal/energy"_compute_smd_internal_energy.html - "smd/plastic/strain"_compute_smd_plastic_strain.html - "smd/plastic/strain/rate"_compute_smd_plastic_strain_rate.html - "smd/rho"_compute_smd_rho.html - "smd/tlsph/defgrad"_compute_smd_tlsph_defgrad.html - "smd/tlsph/dt"_compute_smd_tlsph_dt.html - "smd/internal/energy"_compute_smd_internal_energy.html - per-particle enthalpy in Smooth Mach Dynamics "smd/plastic/strain"_compute_smd_plastic_strain.html - equivalent plastic strain per particle in Smooth Mach Dynamics "smd/plastic/strain/rate"_compute_smd_plastic_strain_rate.html - time rate of the equivalent plastic strain in Smooth Mach Dynamics "smd/rho"_compute_smd_rho.html - per-particle mass density in Smooth Mach Dynamics "smd/tlsph/defgrad"_compute_smd_tlsph_defgrad.html - deformation gradient in Smooth Mach Dynamics "smd/tlsph/dt"_compute_smd_tlsph_dt.html - CFL-stable time increment per particle in Smooth Mach Dynamics "smd/tlsph/num/neighs"_compute_smd_tlsph_num_neighs.html - "smd/tlsph/shape"_compute_smd_tlsph_shape.html - "smd/tlsph/strain"_compute_smd_tlsph_strain.html - "smd/tlsph/strain/rate"_compute_smd_tlsph_strain_rate.html - "smd/tlsph/stress"_compute_smd_tlsph_stress.html - "smd/triangle/vertices"_compute_smd_triangle_vertices.html - "smd/tlsph/stress"_compute_smd_tlsph_stress.html - per-particle Cauchy stress tensor for SPH particles "smd/triangle/vertices"_compute_smd_triangle_vertices.html - "smd/ulsph/num/neighs"_compute_smd_ulsph_num_neighs.html - "smd/ulsph/strain"_compute_smd_ulsph_strain.html - "smd/ulsph/strain/rate"_compute_smd_ulsph_strain_rate.html - "smd/ulsph/stress"_compute_smd_ulsph_stress.html - "smd/vol"_compute_smd_vol.html - "smd/ulsph/stress"_compute_smd_ulsph_stress.html - per-particle Cauchy stress tensor and von Mises equivalent stress in Smooth Mach Dynamics "smd/vol"_compute_smd_vol.html - per-particle volumes and their sum in Smooth Mach Dynamics "sna/atom"_compute_sna_atom.html - calculate bispectrum coefficients for each atom "snad/atom"_compute_sna_atom.html - derivative of bispectrum coefficients for each atom "snav/atom"_compute_sna_atom.html - virial contribution from bispectrum coefficients for each atom "spin"_compute_spin.html - "spin"_compute_spin.html - magnetic quantities for a system of atoms having spins "stress/atom"_compute_stress_atom.html - stress tensor for each atom "stress/mop"_compute_stress_mop.html - "stress/mop/profile"_compute_stress_mop.html - "stress/mop"_compute_stress_mop.html - normal components of the local stress tensor using the method of planes "stress/mop/profile"_compute_stress_mop.html - profile of the normal components of the local stress tensor using the method of planes "stress/tally"_compute_tally.html - "tdpd/cc/atom"_compute_tdpd_cc_atom.html - "tdpd/cc/atom"_compute_tdpd_cc_atom.html - per-atom chemical concentration of a specified species for each tDPD particle "temp"_compute_temp.html - temperature of group of atoms "temp/asphere"_compute_temp_asphere.html - temperature of aspherical particles "temp/body"_compute_temp_body.html - temperature of body particles "temp/chunk"_compute_temp_chunk.html - temperature of each chunk "temp/com"_compute_temp_com.html - temperature after subtracting center-of-mass velocity "temp/cs"_compute_temp_cs.html - "temp/cs"_compute_temp_cs.html - temperature based on the center-of-mass velocity of atom pairs that are bonded to each other "temp/deform"_compute_temp_deform.html - temperature excluding box deformation velocity "temp/deform/eff"_compute_temp_deform_eff.html - "temp/drude"_compute_temp_drude.html - "temp/eff"_compute_temp_eff.html - "temp/deform/eff"_compute_temp_deform_eff.html - temperature excluding box deformation velocity in the electron force field model "temp/drude"_compute_temp_drude.html - temperature of Core-Drude pairs "temp/eff"_compute_temp_eff.html - temperature of a group of nuclei and electrons in the electron force field model "temp/partial"_compute_temp_partial.html - temperature excluding one or more dimensions of velocity "temp/profile"_compute_temp_profile.html - temperature excluding a binned velocity profile "temp/ramp"_compute_temp_ramp.html - temperature excluding ramped velocity component "temp/region"_compute_temp_region.html - temperature of a region of atoms "temp/region/eff"_compute_temp_region_eff.html - "temp/rotate"_compute_temp_rotate.html - "temp/region/eff"_compute_temp_region_eff.html - temperature of a region of nuclei and electrons in the electron force field model "temp/rotate"_compute_temp_rotate.html - temperature of a group of atoms after subtracting out their center-of-mass and angular velocities "temp/sphere"_compute_temp_sphere.html - temperature of spherical particles "temp/uef"_compute_temp_uef.html - "temp/uef"_compute_temp_uef.html - kinetic energy tensor in the reference frame of an applied flow field "ti"_compute_ti.html - thermodynamic integration free energy values "torque/chunk"_compute_torque_chunk.html - torque applied on each chunk "vacf"_compute_vacf.html - velocity auto-correlation function of group of atoms "vcm/chunk"_compute_vcm_chunk.html - velocity of center-of-mass for each chunk "voronoi/atom"_compute_voronoi_atom.html - Voronoi volume and neighbors for each atom "xrd"_compute_xrd.html - :ul "xrd"_compute_xrd.html - x-ray diffraction intensity on a mesh of reciprocal lattice nodes :ul [Restrictions:] none Loading
src/KOKKOS/pppm_kokkos.cpp +2 −8 Original line number Diff line number Diff line Loading @@ -306,12 +306,6 @@ void PPPMKokkos<DeviceType>::init() if (me == 0) { #ifdef FFT_SINGLE const char fft_prec[] = "single"; #else const char fft_prec[] = "double"; #endif if (screen) { fprintf(screen," G vector (1/distance) = %g\n",g_ewald); fprintf(screen," grid = %d %d %d\n",nx_pppm,ny_pppm,nz_pppm); Loading @@ -320,7 +314,7 @@ void PPPMKokkos<DeviceType>::init() estimated_accuracy); fprintf(screen," estimated relative force accuracy = %g\n", estimated_accuracy/two_charge_force); fprintf(screen," using %s precision FFTs\n",fft_prec); fprintf(screen," using " LMP_FFT_PREC " precision " LMP_FFT_LIB "\n"); fprintf(screen," 3d grid and FFT values/proc = %d %d\n", ngrid_max,nfft_both_max); } Loading @@ -332,7 +326,7 @@ void PPPMKokkos<DeviceType>::init() estimated_accuracy); fprintf(logfile," estimated relative force accuracy = %g\n", estimated_accuracy/two_charge_force); fprintf(logfile," using %s precision FFTs\n",fft_prec); fprintf(logfile," using " LMP_FFT_PREC " precision " LMP_FFT_LIB "\n"); fprintf(logfile," 3d grid and FFT values/proc = %d %d\n", ngrid_max,nfft_both_max); } Loading
src/KSPACE/pppm.cpp +2 −8 Original line number Diff line number Diff line Loading @@ -350,12 +350,6 @@ void PPPM::init() if (me == 0) { #ifdef FFT_SINGLE const char fft_prec[] = "single"; #else const char fft_prec[] = "double"; #endif if (screen) { fprintf(screen," G vector (1/distance) = %g\n",g_ewald); fprintf(screen," grid = %d %d %d\n",nx_pppm,ny_pppm,nz_pppm); Loading @@ -364,7 +358,7 @@ void PPPM::init() estimated_accuracy); fprintf(screen," estimated relative force accuracy = %g\n", estimated_accuracy/two_charge_force); fprintf(screen," using %s precision FFTs\n",fft_prec); fprintf(screen," using " LMP_FFT_PREC " precision " LMP_FFT_LIB "\n"); fprintf(screen," 3d grid and FFT values/proc = %d %d\n", ngrid_max,nfft_both_max); } Loading @@ -376,7 +370,7 @@ void PPPM::init() estimated_accuracy); fprintf(logfile," estimated relative force accuracy = %g\n", estimated_accuracy/two_charge_force); fprintf(logfile," using %s precision FFTs\n",fft_prec); fprintf(logfile," using " LMP_FFT_PREC " precision " LMP_FFT_LIB "\n"); fprintf(logfile," 3d grid and FFT values/proc = %d %d\n", ngrid_max,nfft_both_max); } Loading
