From 06275b03c06f3615d6442ef9243a41ffecbcae19 Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Wed, 17 Jul 2019 15:46:39 -0400 Subject: [PATCH 1/5] refactor FFT handling in CMake module for KSPACE. This also improves the FFT info output in the PPPM styles --- cmake/CMakeLists.txt | 7 ++++++- cmake/Modules/Packages/KSPACE.cmake | 28 ++++++++++++++++------------ src/KOKKOS/pppm_kokkos.cpp | 10 ++-------- src/KSPACE/pppm.cpp | 10 ++-------- src/KSPACE/pppm.h | 11 +++++++++++ src/KSPACE/pppm_disp.cpp | 10 ++-------- src/KSPACE/pppm_disp.h | 10 ++++++++++ 7 files changed, 49 insertions(+), 37 deletions(-) diff --git a/cmake/CMakeLists.txt b/cmake/CMakeLists.txt index bde36aa896..4b528f280e 100644 --- a/cmake/CMakeLists.txt +++ b/cmake/CMakeLists.txt @@ -673,5 +673,10 @@ if(PKG_KOKKOS) message(STATUS "Kokkos Arch: ${KOKKOS_ARCH}") endif() if(PKG_KSPACE) - message(STATUS "Using ${FFT} as FFT") + message(STATUS "Using ${FFT} as primary FFT library") + if(FFT_SINGLE) + message(STATUS "Using single precision FFTs") + else() + message(STATUS "Using double precision FFTs") + endif() endif() diff --git a/cmake/Modules/Packages/KSPACE.cmake b/cmake/Modules/Packages/KSPACE.cmake index 6938a93a36..63c42baf2d 100644 --- a/cmake/Modules/Packages/KSPACE.cmake +++ b/cmake/Modules/Packages/KSPACE.cmake @@ -1,5 +1,5 @@ if(PKG_KSPACE) - option(FFT_SINGLE "Use single precision FFT instead of double" OFF) + option(FFT_SINGLE "Use single precision FFTs instead of double precision FFTs" OFF) set(FFTW "FFTW3") if(FFT_SINGLE) set(FFTW "FFTW3F") @@ -7,26 +7,30 @@ if(PKG_KSPACE) endif() find_package(${FFTW} QUIET) if(${FFTW}_FOUND) - set(FFT "${FFTW}" CACHE STRING "FFT library for KSPACE package") + set(FFT "FFTW3" CACHE STRING "FFT library for KSPACE package") else() set(FFT "KISS" CACHE STRING "FFT library for KSPACE package") endif() - set(FFT_VALUES KISS ${FFTW} MKL) + set(FFT_VALUES KISS FFTW3 MKL) set_property(CACHE FFT PROPERTY STRINGS ${FFT_VALUES}) validate_option(FFT FFT_VALUES) string(TOUPPER ${FFT} FFT) - if(NOT FFT STREQUAL "KISS") - find_package(${FFT} REQUIRED) - if(NOT FFT STREQUAL "FFTW3F") - add_definitions(-DFFT_FFTW) - else() - add_definitions(-DFFT_${FFT}) - endif() - include_directories(${${FFT}_INCLUDE_DIRS}) - list(APPEND LAMMPS_LINK_LIBS ${${FFT}_LIBRARIES}) + + if(FFT STREQUAL "FFTW3") + find_package(${FFTW} REQUIRED) + add_definitions(-DFFT_FFTW3) + include_directories(${${FFTW}_INCLUDE_DIRS}) + list(APPEND LAMMPS_LINK_LIBS ${${FFTW}_LIBRARIES}) + elseif(FFT STREQUAL "MKL") + find_package(MKL REQUIRED) + add_definitions(-DFFT_MKL) + include_directories(${MKL_INCLUDE_DIRS}) + list(APPEND LAMMPS_LINK_LIBS ${MKL_LIBRARIES}) else() + # last option is KISSFFT add_definitions(-DFFT_KISS) endif() + set(FFT_PACK "array" CACHE STRING "Optimization for FFT") set(FFT_PACK_VALUES array pointer memcpy) set_property(CACHE FFT_PACK PROPERTY STRINGS ${FFT_PACK_VALUES}) diff --git a/src/KOKKOS/pppm_kokkos.cpp b/src/KOKKOS/pppm_kokkos.cpp index 7c01adc510..c9c0d6d1d4 100644 --- a/src/KOKKOS/pppm_kokkos.cpp +++ b/src/KOKKOS/pppm_kokkos.cpp @@ -306,12 +306,6 @@ void PPPMKokkos::init() if (me == 0) { -#ifdef FFT_SINGLE - const char fft_prec[] = "single"; -#else - const char fft_prec[] = "double"; -#endif - if (screen) { fprintf(screen," G vector (1/distance) = %g\n",g_ewald); fprintf(screen," grid = %d %d %d\n",nx_pppm,ny_pppm,nz_pppm); @@ -320,7 +314,7 @@ void PPPMKokkos::init() estimated_accuracy); fprintf(screen," estimated relative force accuracy = %g\n", estimated_accuracy/two_charge_force); - fprintf(screen," using %s precision FFTs\n",fft_prec); + fprintf(screen," using " LMP_FFT_PREC " precision " LMP_FFT_LIB "\n"); fprintf(screen," 3d grid and FFT values/proc = %d %d\n", ngrid_max,nfft_both_max); } @@ -332,7 +326,7 @@ void PPPMKokkos::init() estimated_accuracy); fprintf(logfile," estimated relative force accuracy = %g\n", estimated_accuracy/two_charge_force); - fprintf(logfile," using %s precision FFTs\n",fft_prec); + fprintf(logfile," using " LMP_FFT_PREC " precision " LMP_FFT_LIB "\n"); fprintf(logfile," 3d grid and FFT values/proc = %d %d\n", ngrid_max,nfft_both_max); } diff --git a/src/KSPACE/pppm.cpp b/src/KSPACE/pppm.cpp index 53c18804a5..1abb19e947 100644 --- a/src/KSPACE/pppm.cpp +++ b/src/KSPACE/pppm.cpp @@ -350,12 +350,6 @@ void PPPM::init() if (me == 0) { -#ifdef FFT_SINGLE - const char fft_prec[] = "single"; -#else - const char fft_prec[] = "double"; -#endif - if (screen) { fprintf(screen," G vector (1/distance) = %g\n",g_ewald); fprintf(screen," grid = %d %d %d\n",nx_pppm,ny_pppm,nz_pppm); @@ -364,7 +358,7 @@ void PPPM::init() estimated_accuracy); fprintf(screen," estimated relative force accuracy = %g\n", estimated_accuracy/two_charge_force); - fprintf(screen," using %s precision FFTs\n",fft_prec); + fprintf(screen," using " LMP_FFT_PREC " precision " LMP_FFT_LIB "\n"); fprintf(screen," 3d grid and FFT values/proc = %d %d\n", ngrid_max,nfft_both_max); } @@ -376,7 +370,7 @@ void PPPM::init() estimated_accuracy); fprintf(logfile," estimated relative force accuracy = %g\n", estimated_accuracy/two_charge_force); - fprintf(logfile," using %s precision FFTs\n",fft_prec); + fprintf(logfile," using " LMP_FFT_PREC " precision " LMP_FFT_LIB "\n"); fprintf(logfile," 3d grid and FFT values/proc = %d %d\n", ngrid_max,nfft_both_max); } diff --git a/src/KSPACE/pppm.h b/src/KSPACE/pppm.h index 1ce1a0d666..6426b9c22d 100644 --- a/src/KSPACE/pppm.h +++ b/src/KSPACE/pppm.h @@ -23,11 +23,22 @@ KSpaceStyle(pppm,PPPM) #include "lmptype.h" #include +#if defined(FFT_FFTW3) +#define LMP_FFT_LIB "FFTW3" +#elif defined(FFT_MKL) +#define LMP_FFT_LIB "MKL FFT" +#else +#define LMP_FFT_LIB "KISS FFT" +#endif + #ifdef FFT_SINGLE typedef float FFT_SCALAR; +#define LMP_FFT_PREC "single" #define MPI_FFT_SCALAR MPI_FLOAT #else + typedef double FFT_SCALAR; +#define LMP_FFT_PREC "double" #define MPI_FFT_SCALAR MPI_DOUBLE #endif diff --git a/src/KSPACE/pppm_disp.cpp b/src/KSPACE/pppm_disp.cpp index 45dce0895b..ba0e85bbba 100644 --- a/src/KSPACE/pppm_disp.cpp +++ b/src/KSPACE/pppm_disp.cpp @@ -474,12 +474,6 @@ void PPPMDisp::init() MPI_Allreduce(&nfft_both,&nfft_both_max,1,MPI_INT,MPI_MAX,world); if (me == 0) { - #ifdef FFT_SINGLE - const char fft_prec[] = "single"; - #else - const char fft_prec[] = "double"; - #endif - if (screen) { fprintf(screen," Coulomb G vector (1/distance)= %g\n",g_ewald); fprintf(screen," Coulomb grid = %d %d %d\n",nx_pppm,ny_pppm,nz_pppm); @@ -488,7 +482,7 @@ void PPPMDisp::init() acc); fprintf(screen," Coulomb estimated relative force accuracy = %g\n", acc/two_charge_force); - fprintf(screen," using %s precision FFTs\n",fft_prec); + fprintf(screen," using " LMP_FFT_PREC " precision " LMP_FFT_LIB "\n"); fprintf(screen," 3d grid and FFT values/proc = %d %d\n", ngrid_max, nfft_both_max); } @@ -501,7 +495,7 @@ void PPPMDisp::init() acc); fprintf(logfile," Coulomb estimated relative force accuracy = %g\n", acc/two_charge_force); - fprintf(logfile," using %s precision FFTs\n",fft_prec); + fprintf(logfile," using " LMP_FFT_PREC " precision " LMP_FFT_LIB "\n"); fprintf(logfile," 3d grid and FFT values/proc = %d %d\n", ngrid_max, nfft_both_max); } diff --git a/src/KSPACE/pppm_disp.h b/src/KSPACE/pppm_disp.h index ccbeb60f3c..8674669274 100644 --- a/src/KSPACE/pppm_disp.h +++ b/src/KSPACE/pppm_disp.h @@ -23,11 +23,21 @@ KSpaceStyle(pppm/disp,PPPMDisp) #include "lmptype.h" #include +#if defined(FFT_FFTW3) +#define LMP_FFT_LIB "FFTW3" +#elif defined(FFT_MKL) +#define LMP_FFT_LIB "MKL FFT" +#else +#define LMP_FFT_LIB "KISS FFT" +#endif + #ifdef FFT_SINGLE typedef float FFT_SCALAR; +#define LMP_FFT_PREC "single" #define MPI_FFT_SCALAR MPI_FLOAT #else typedef double FFT_SCALAR; +#define LMP_FFT_PREC "double" #define MPI_FFT_SCALAR MPI_DOUBLE #endif From bcf600d7814df4eefe4b73d3de7ac344a8decc16 Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Wed, 17 Jul 2019 15:47:28 -0400 Subject: [PATCH 2/5] let CMake configuration default to Release with debug settings this way we can more easily get detailed stack traces from people compiling with CMake --- cmake/CMakeLists.txt | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/cmake/CMakeLists.txt b/cmake/CMakeLists.txt index 4b528f280e..0f99cc6274 100644 --- a/cmake/CMakeLists.txt +++ b/cmake/CMakeLists.txt @@ -37,7 +37,7 @@ include(PreventInSourceBuilds) if(NOT CMAKE_BUILD_TYPE AND NOT CMAKE_CXX_FLAGS) #release comes with -O3 by default - set(CMAKE_BUILD_TYPE Release CACHE STRING "Choose the type of build, options are: None Debug Release RelWithDebInfo MinSizeRel." FORCE) + set(CMAKE_BUILD_TYPE RelWithDebInfo CACHE STRING "Choose the type of build, options are: None Debug Release RelWithDebInfo MinSizeRel." FORCE) endif(NOT CMAKE_BUILD_TYPE AND NOT CMAKE_CXX_FLAGS) string(TOUPPER "${CMAKE_BUILD_TYPE}" BTYPE) From 02b0fb454f7adbb412ea3d2fd7d324ff5004446b Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Wed, 17 Jul 2019 16:34:43 -0400 Subject: [PATCH 3/5] include rmass[] in border communication. will otherwise trigger issues with fix shake. --- src/PERI/atom_vec_peri.cpp | 11 ++++++++++- src/atom_vec_ellipsoid.cpp | 11 ++++++++++- 2 files changed, 20 insertions(+), 2 deletions(-) diff --git a/src/PERI/atom_vec_peri.cpp b/src/PERI/atom_vec_peri.cpp index 64ce323a3f..c4fa0bd43b 100644 --- a/src/PERI/atom_vec_peri.cpp +++ b/src/PERI/atom_vec_peri.cpp @@ -55,7 +55,7 @@ AtomVecPeri::AtomVecPeri(LAMMPS *lmp) : AtomVec(lmp) comm_f_only = 1; size_forward = 4; size_reverse = 3; - size_border = 11; + size_border = 12; size_velocity = 3; size_data_atom = 7; size_data_vel = 4; @@ -357,6 +357,7 @@ int AtomVecPeri::pack_border(int n, int *list, double *buf, buf[m++] = ubuf(type[j]).d; buf[m++] = ubuf(mask[j]).d; buf[m++] = vfrac[j]; + buf[m++] = rmass[j]; buf[m++] = s0[j]; buf[m++] = x0[j][0]; buf[m++] = x0[j][1]; @@ -381,6 +382,7 @@ int AtomVecPeri::pack_border(int n, int *list, double *buf, buf[m++] = ubuf(type[j]).d; buf[m++] = ubuf(mask[j]).d; buf[m++] = vfrac[j]; + buf[m++] = rmass[j]; buf[m++] = s0[j]; buf[m++] = x0[j][0]; buf[m++] = x0[j][1]; @@ -414,6 +416,7 @@ int AtomVecPeri::pack_border_vel(int n, int *list, double *buf, buf[m++] = ubuf(type[j]).d; buf[m++] = ubuf(mask[j]).d; buf[m++] = vfrac[j]; + buf[m++] = rmass[j]; buf[m++] = s0[j]; buf[m++] = x0[j][0]; buf[m++] = x0[j][1]; @@ -442,6 +445,7 @@ int AtomVecPeri::pack_border_vel(int n, int *list, double *buf, buf[m++] = ubuf(type[j]).d; buf[m++] = ubuf(mask[j]).d; buf[m++] = vfrac[j]; + buf[m++] = rmass[j]; buf[m++] = s0[j]; buf[m++] = x0[j][0]; buf[m++] = x0[j][1]; @@ -463,6 +467,7 @@ int AtomVecPeri::pack_border_vel(int n, int *list, double *buf, buf[m++] = ubuf(type[j]).d; buf[m++] = ubuf(mask[j]).d; buf[m++] = vfrac[j]; + buf[m++] = rmass[j]; buf[m++] = s0[j]; buf[m++] = x0[j][0]; buf[m++] = x0[j][1]; @@ -497,6 +502,7 @@ int AtomVecPeri::pack_border_hybrid(int n, int *list, double *buf) for (i = 0; i < n; i++) { j = list[i]; buf[m++] = vfrac[j]; + buf[m++] = rmass[j]; buf[m++] = s0[j]; buf[m++] = x0[j][0]; buf[m++] = x0[j][1]; @@ -522,6 +528,7 @@ void AtomVecPeri::unpack_border(int n, int first, double *buf) type[i] = (int) ubuf(buf[m++]).i; mask[i] = (int) ubuf(buf[m++]).i; vfrac[i] = buf[m++]; + rmass[i] = buf[m++]; s0[i] = buf[m++]; x0[i][0] = buf[m++]; x0[i][1] = buf[m++]; @@ -551,6 +558,7 @@ void AtomVecPeri::unpack_border_vel(int n, int first, double *buf) type[i] = (int) ubuf(buf[m++]).i; mask[i] = (int) ubuf(buf[m++]).i; vfrac[i] = buf[m++]; + rmass[i] = buf[m++]; s0[i] = buf[m++]; x0[i][0] = buf[m++]; x0[i][1] = buf[m++]; @@ -576,6 +584,7 @@ int AtomVecPeri::unpack_border_hybrid(int n, int first, double *buf) last = first + n; for (i = first; i < last; i++) { vfrac[i] = buf[m++]; + rmass[i] = buf[m++]; s0[i] = buf[m++]; x0[i][0] = buf[m++]; x0[i][1] = buf[m++]; diff --git a/src/atom_vec_ellipsoid.cpp b/src/atom_vec_ellipsoid.cpp index 455e4f192f..7bb29bd6bc 100644 --- a/src/atom_vec_ellipsoid.cpp +++ b/src/atom_vec_ellipsoid.cpp @@ -41,7 +41,7 @@ AtomVecEllipsoid::AtomVecEllipsoid(LAMMPS *lmp) : AtomVec(lmp) comm_x_only = comm_f_only = 0; size_forward = 7; size_reverse = 6; - size_border = 14; + size_border = 15; size_velocity = 6; size_data_atom = 7; size_data_vel = 7; @@ -544,6 +544,7 @@ int AtomVecEllipsoid::pack_border(int n, int *list, double *buf, buf[m++] = ubuf(tag[j]).d; buf[m++] = ubuf(type[j]).d; buf[m++] = ubuf(mask[j]).d; + buf[m++] = rmass[j]; if (ellipsoid[j] < 0) buf[m++] = ubuf(0).d; else { buf[m++] = ubuf(1).d; @@ -576,6 +577,7 @@ int AtomVecEllipsoid::pack_border(int n, int *list, double *buf, buf[m++] = ubuf(tag[j]).d; buf[m++] = ubuf(type[j]).d; buf[m++] = ubuf(mask[j]).d; + buf[m++] = rmass[j]; if (ellipsoid[j] < 0) buf[m++] = ubuf(0).d; else { buf[m++] = ubuf(1).d; @@ -618,6 +620,7 @@ int AtomVecEllipsoid::pack_border_vel(int n, int *list, double *buf, buf[m++] = ubuf(tag[j]).d; buf[m++] = ubuf(type[j]).d; buf[m++] = ubuf(mask[j]).d; + buf[m++] = rmass[j]; if (ellipsoid[j] < 0) buf[m++] = ubuf(0).d; else { buf[m++] = ubuf(1).d; @@ -657,6 +660,7 @@ int AtomVecEllipsoid::pack_border_vel(int n, int *list, double *buf, buf[m++] = ubuf(tag[j]).d; buf[m++] = ubuf(type[j]).d; buf[m++] = ubuf(mask[j]).d; + buf[m++] = rmass[j]; if (ellipsoid[j] < 0) buf[m++] = ubuf(0).d; else { buf[m++] = ubuf(1).d; @@ -689,6 +693,7 @@ int AtomVecEllipsoid::pack_border_vel(int n, int *list, double *buf, buf[m++] = ubuf(tag[j]).d; buf[m++] = ubuf(type[j]).d; buf[m++] = ubuf(mask[j]).d; + buf[m++] = rmass[j]; if (ellipsoid[j] < 0) buf[m++] = ubuf(0).d; else { buf[m++] = ubuf(1).d; @@ -735,6 +740,7 @@ int AtomVecEllipsoid::pack_border_hybrid(int n, int *list, double *buf) m = 0; for (i = 0; i < n; i++) { j = list[i]; + buf[m++] = rmass[j]; if (ellipsoid[j] < 0) buf[m++] = ubuf(0).d; else { buf[m++] = ubuf(1).d; @@ -769,6 +775,7 @@ void AtomVecEllipsoid::unpack_border(int n, int first, double *buf) tag[i] = (tagint) ubuf(buf[m++]).i; type[i] = (int) ubuf(buf[m++]).i; mask[i] = (int) ubuf(buf[m++]).i; + rmass[i] = buf[m++]; ellipsoid[i] = (int) ubuf(buf[m++]).i; if (ellipsoid[i] == 0) ellipsoid[i] = -1; else { @@ -812,6 +819,7 @@ void AtomVecEllipsoid::unpack_border_vel(int n, int first, double *buf) tag[i] = (tagint) ubuf(buf[m++]).i; type[i] = (int) ubuf(buf[m++]).i; mask[i] = (int) ubuf(buf[m++]).i; + rmass[i] = buf[m++]; ellipsoid[i] = (int) ubuf(buf[m++]).i; if (ellipsoid[i] == 0) ellipsoid[i] = -1; else { @@ -854,6 +862,7 @@ int AtomVecEllipsoid::unpack_border_hybrid(int n, int first, double *buf) m = 0; last = first + n; for (i = first; i < last; i++) { + rmass[i] = buf[m++]; ellipsoid[i] = (int) ubuf(buf[m++]).i; if (ellipsoid[i] == 0) ellipsoid[i] = -1; else { From 856efa28aab9a140f37875a7ed5df96419280ad0 Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Wed, 17 Jul 2019 19:37:08 -0400 Subject: [PATCH 4/5] fix issue #1568 --- src/utils.cpp | 1 + 1 file changed, 1 insertion(+) diff --git a/src/utils.cpp b/src/utils.cpp index bbda22f24c..34e6e6fae6 100644 --- a/src/utils.cpp +++ b/src/utils.cpp @@ -13,6 +13,7 @@ #include #include +#include #include "utils.h" #include "lammps.h" #include "error.h" From 4f7c95d87e77f880415405910f3e06c4b70b1ca6 Mon Sep 17 00:00:00 2001 From: Evangelos Voyiatzis Date: Fri, 19 Jul 2019 17:13:38 +0200 Subject: [PATCH 5/5] Update compute.txt Addition of a few one-liners --- doc/src/compute.txt | 89 ++++++++++++++++++++++----------------------- 1 file changed, 43 insertions(+), 46 deletions(-) diff --git a/doc/src/compute.txt b/doc/src/compute.txt index 87dbee57d6..53ed373aa5 100644 --- a/doc/src/compute.txt +++ b/doc/src/compute.txt @@ -171,42 +171,40 @@ The individual style names on the "Commands compute"_Commands_compute.html doc page are followed by one or more of (g,i,k,o,t) to indicate which accelerated styles exist. -"ackland/atom"_compute_ackland_atom.html - +"ackland/atom"_compute_ackland_atom.html - determines the local lattice structure based on the Ackland formulation "adf"_compute_adf.html - angular distribution function of triples of atoms "aggregate/atom"_compute_cluster_atom.html - aggregate ID for each atom -"angle"_compute_angle.html - -"angle/local"_compute_angle_local.html - -"angle/local"_compute_bond_local.html - theta and energy of each angle +"angle"_compute_angle.html - energy of each angle sub-style +"angle/local"_compute_angle_local.html - theta and energy of each angle "angmom/chunk"_compute_angmom_chunk.html - angular momentum for each chunk -"basal/atom"_compute_basal_atom.html - +"basal/atom"_compute_basal_atom.html - calculates the hexagonal close-packed “c” lattice vector of each atom "body/local"_compute_body_local.html - attributes of body sub-particles -"bond"_compute_bond.html - values computed by a bond style +"bond"_compute_bond.html - energy of each bond sub-style "bond/local"_compute_bond_local.html - distance and energy of each bond "centro/atom"_compute_centro_atom.html - centro-symmetry parameter for each atom "chunk/atom"_compute_chunk_atom.html - assign chunk IDs to each atom "chunk/spread/atom"_compute_chunk_spread_atom.html - spreads chunk values to each atom in chunk "cluster/atom"_compute_cluster_atom.html - cluster ID for each atom "cna/atom"_compute_cna_atom.html - common neighbor analysis (CNA) for each atom -"cnp/atom"_compute_cnp_atom.html - +"cnp/atom"_compute_cnp_atom.html - common neighborhood parameter (CNP) for each atom "com"_compute_com.html - center-of-mass of group of atoms "com/chunk"_compute_com_chunk.html - center-of-mass for each chunk "contact/atom"_compute_contact_atom.html - contact count for each spherical particle "coord/atom"_compute_coord_atom.html - coordination number for each atom "damage/atom"_compute_damage_atom.html - Peridynamic damage for each atom -"dihedral"_compute_dihedral.html - +"dihedral"_compute_dihedral.html - energy of each dihedral sub-style "dihedral/local"_compute_dihedral_local.html - angle of each dihedral "dilatation/atom"_compute_dilatation_atom.html - Peridynamic dilatation for each atom -"dipole/chunk"_compute_dipole_chunk.html - +"dipole/chunk"_compute_dipole_chunk.html - dipole vector and total dipole for each chunk "displace/atom"_compute_displace_atom.html - displacement of each atom "dpd"_compute_dpd.html - "dpd/atom"_compute_dpd_atom.html - -"edpd/temp/atom"_compute_edpd_temp_atom.html - -"entropy/atom"_compute_entropy_atom.html - +"edpd/temp/atom"_compute_edpd_temp_atom.html - per-atom temperature for each eDPD particle in a group +"entropy/atom"_compute_entropy_atom.html - pair entropy fingerprint of each atom "erotate/asphere"_compute_erotate_asphere.html - rotational energy of aspherical particles "erotate/rigid"_compute_erotate_rigid.html - rotational energy of rigid bodies "erotate/sphere"_compute_erotate_sphere.html - rotational energy of spherical particles -"erotate/sphere/atom"_compute_erotate_sphere.html - rotational energy for each spherical particle -"erotate/sphere/atom"_compute_erotate_sphere_atom.html - +"erotate/sphere/atom"_compute_erotate_sphere_atom.html - rotational energy for each spherical particle "event/displace"_compute_event_displace.html - detect event on atom displacement "fep"_compute_fep.html - "force/tally"_compute_tally.html - @@ -218,17 +216,17 @@ compute"_Commands_compute.html doc page are followed by one or more of "heat/flux"_compute_heat_flux.html - heat flux through a group of atoms "heat/flux/tally"_compute_tally.html - "hexorder/atom"_compute_hexorder_atom.html - bond orientational order parameter q6 -"improper"_compute_improper.html - +"improper"_compute_improper.html - energy of each improper sub-style "improper/local"_compute_improper_local.html - angle of each improper "inertia/chunk"_compute_inertia_chunk.html - inertia tensor for each chunk "ke"_compute_ke.html - translational kinetic energy "ke/atom"_compute_ke_atom.html - kinetic energy for each atom -"ke/atom/eff"_compute_ke_atom_eff.html - -"ke/eff"_compute_ke_eff.html - +"ke/atom/eff"_compute_ke_atom_eff.html - per-atom translational and radial kinetic energy in the electron force field model +"ke/eff"_compute_ke_eff.html - kinetic energy of a group of nuclei and electrons in the electron force field model "ke/rigid"_compute_ke_rigid.html - translational kinetic energy of rigid bodies -"meso/e/atom"_compute_meso_e_atom.html - -"meso/rho/atom"_compute_meso_rho_atom.html - -"meso/t/atom"_compute_meso_t_atom.html - +"meso/e/atom"_compute_meso_e_atom.html - per-atom internal energy of Smooth-Particle Hydrodynamics atoms +"meso/rho/atom"_compute_meso_rho_atom.html - per-atom mesoscopic density of Smooth-Particle Hydrodynamics atoms +"meso/t/atom"_compute_meso_t_atom.html - per-atom internal temperature of Smooth-Particle Hydrodynamics atoms "msd"_compute_msd.html - mean-squared displacement of group of atoms "msd/chunk"_compute_msd_chunk.html - mean-squared displacement for each chunk "msd/nongauss"_compute_msd_nongauss.html - MSD and non-Gaussian parameter of group of atoms @@ -242,73 +240,72 @@ compute"_Commands_compute.html doc page are followed by one or more of "pe/tally"_compute_tally.html - "plasticity/atom"_compute_plasticity_atom.html - Peridynamic plasticity for each atom "pressure"_compute_pressure.html - total pressure and pressure tensor -"pressure/cylinder"_compute_pressure_cylinder.html - -"pressure/uef"_compute_pressure_uef.html - +"pressure/cylinder"_compute_pressure_cylinder.html - pressure tensor in cylindrical coordinates +"pressure/uef"_compute_pressure_uef.html - pressure tensor in the reference frame of an applied flow field "property/atom"_compute_property_atom.html - convert atom attributes to per-atom vectors/arrays "property/chunk"_compute_property_chunk.html - extract various per-chunk attributes "property/local"_compute_property_local.html - convert local attributes to localvectors/arrays -"ptm/atom"_compute_ptm_atom.html - +"ptm/atom"_compute_ptm_atom.html - determines the local lattice structure based on the Polyhedral Template Matching method "rdf"_compute_rdf.html - radial distribution function g(r) histogram of group of atoms "reduce"_compute_reduce.html - combine per-atom quantities into a single global value "reduce/chunk"_compute_reduce_chunk.html - reduce per-atom quantities within each chunk "reduce/region"_compute_reduce.html - same as compute reduce, within a region "rigid/local"_compute_rigid_local.html - extract rigid body attributes -"saed"_compute_saed.html - +"saed"_compute_saed.html - electron diffraction intensity on a mesh of reciprocal lattice nodes "slice"_compute_slice.html - extract values from global vector or array "smd/contact/radius"_compute_smd_contact_radius.html - -"smd/damage"_compute_smd_damage.html - +"smd/damage"_compute_smd_damage.html - damage status of SPH particles in Smooth Mach Dynamics "smd/hourglass/error"_compute_smd_hourglass_error.html - -"smd/internal/energy"_compute_smd_internal_energy.html - -"smd/plastic/strain"_compute_smd_plastic_strain.html - -"smd/plastic/strain/rate"_compute_smd_plastic_strain_rate.html - -"smd/rho"_compute_smd_rho.html - -"smd/tlsph/defgrad"_compute_smd_tlsph_defgrad.html - -"smd/tlsph/dt"_compute_smd_tlsph_dt.html - +"smd/internal/energy"_compute_smd_internal_energy.html - per-particle enthalpy in Smooth Mach Dynamics +"smd/plastic/strain"_compute_smd_plastic_strain.html - equivalent plastic strain per particle in Smooth Mach Dynamics +"smd/plastic/strain/rate"_compute_smd_plastic_strain_rate.html - time rate of the equivalent plastic strain in Smooth Mach Dynamics +"smd/rho"_compute_smd_rho.html - per-particle mass density in Smooth Mach Dynamics +"smd/tlsph/defgrad"_compute_smd_tlsph_defgrad.html - deformation gradient in Smooth Mach Dynamics +"smd/tlsph/dt"_compute_smd_tlsph_dt.html - CFL-stable time increment per particle in Smooth Mach Dynamics "smd/tlsph/num/neighs"_compute_smd_tlsph_num_neighs.html - "smd/tlsph/shape"_compute_smd_tlsph_shape.html - "smd/tlsph/strain"_compute_smd_tlsph_strain.html - "smd/tlsph/strain/rate"_compute_smd_tlsph_strain_rate.html - -"smd/tlsph/stress"_compute_smd_tlsph_stress.html - -"smd/triangle/vertices"_compute_smd_triangle_vertices.html - +"smd/tlsph/stress"_compute_smd_tlsph_stress.html - per-particle Cauchy stress tensor for SPH particles "smd/triangle/vertices"_compute_smd_triangle_vertices.html - "smd/ulsph/num/neighs"_compute_smd_ulsph_num_neighs.html - "smd/ulsph/strain"_compute_smd_ulsph_strain.html - "smd/ulsph/strain/rate"_compute_smd_ulsph_strain_rate.html - -"smd/ulsph/stress"_compute_smd_ulsph_stress.html - -"smd/vol"_compute_smd_vol.html - +"smd/ulsph/stress"_compute_smd_ulsph_stress.html - per-particle Cauchy stress tensor and von Mises equivalent stress in Smooth Mach Dynamics +"smd/vol"_compute_smd_vol.html - per-particle volumes and their sum in Smooth Mach Dynamics "sna/atom"_compute_sna_atom.html - calculate bispectrum coefficients for each atom "snad/atom"_compute_sna_atom.html - derivative of bispectrum coefficients for each atom "snav/atom"_compute_sna_atom.html - virial contribution from bispectrum coefficients for each atom -"spin"_compute_spin.html - +"spin"_compute_spin.html - magnetic quantities for a system of atoms having spins "stress/atom"_compute_stress_atom.html - stress tensor for each atom -"stress/mop"_compute_stress_mop.html - -"stress/mop/profile"_compute_stress_mop.html - +"stress/mop"_compute_stress_mop.html - normal components of the local stress tensor using the method of planes +"stress/mop/profile"_compute_stress_mop.html - profile of the normal components of the local stress tensor using the method of planes "stress/tally"_compute_tally.html - -"tdpd/cc/atom"_compute_tdpd_cc_atom.html - +"tdpd/cc/atom"_compute_tdpd_cc_atom.html - per-atom chemical concentration of a specified species for each tDPD particle "temp"_compute_temp.html - temperature of group of atoms "temp/asphere"_compute_temp_asphere.html - temperature of aspherical particles "temp/body"_compute_temp_body.html - temperature of body particles "temp/chunk"_compute_temp_chunk.html - temperature of each chunk "temp/com"_compute_temp_com.html - temperature after subtracting center-of-mass velocity -"temp/cs"_compute_temp_cs.html - +"temp/cs"_compute_temp_cs.html - temperature based on the center-of-mass velocity of atom pairs that are bonded to each other "temp/deform"_compute_temp_deform.html - temperature excluding box deformation velocity -"temp/deform/eff"_compute_temp_deform_eff.html - -"temp/drude"_compute_temp_drude.html - -"temp/eff"_compute_temp_eff.html - +"temp/deform/eff"_compute_temp_deform_eff.html - temperature excluding box deformation velocity in the electron force field model +"temp/drude"_compute_temp_drude.html - temperature of Core-Drude pairs +"temp/eff"_compute_temp_eff.html - temperature of a group of nuclei and electrons in the electron force field model "temp/partial"_compute_temp_partial.html - temperature excluding one or more dimensions of velocity "temp/profile"_compute_temp_profile.html - temperature excluding a binned velocity profile "temp/ramp"_compute_temp_ramp.html - temperature excluding ramped velocity component "temp/region"_compute_temp_region.html - temperature of a region of atoms -"temp/region/eff"_compute_temp_region_eff.html - -"temp/rotate"_compute_temp_rotate.html - +"temp/region/eff"_compute_temp_region_eff.html - temperature of a region of nuclei and electrons in the electron force field model +"temp/rotate"_compute_temp_rotate.html - temperature of a group of atoms after subtracting out their center-of-mass and angular velocities "temp/sphere"_compute_temp_sphere.html - temperature of spherical particles -"temp/uef"_compute_temp_uef.html - +"temp/uef"_compute_temp_uef.html - kinetic energy tensor in the reference frame of an applied flow field "ti"_compute_ti.html - thermodynamic integration free energy values "torque/chunk"_compute_torque_chunk.html - torque applied on each chunk "vacf"_compute_vacf.html - velocity auto-correlation function of group of atoms "vcm/chunk"_compute_vcm_chunk.html - velocity of center-of-mass for each chunk "voronoi/atom"_compute_voronoi_atom.html - Voronoi volume and neighbors for each atom -"xrd"_compute_xrd.html - :ul +"xrd"_compute_xrd.html - x-ray diffraction intensity on a mesh of reciprocal lattice nodes :ul [Restrictions:] none