diff --git a/cmake/CMakeLists.txt b/cmake/CMakeLists.txt index f0c05f8b1a..de65e85516 100644 --- a/cmake/CMakeLists.txt +++ b/cmake/CMakeLists.txt @@ -32,6 +32,12 @@ endif() # Cmake modules/macros are in a subdirectory to keep this file cleaner set(CMAKE_MODULE_PATH ${CMAKE_CURRENT_SOURCE_DIR}/Modules) +# make sure LIBRARY_PATH is set if environment variable is set +if (DEFINED ENV{LIBRARY_PATH}) + list(APPEND CMAKE_LIBRARY_PATH "$ENV{LIBRARY_PATH}") + message(STATUS "Appending $ENV{LIBRARY_PATH} to CMAKE_LIBRARY_PATH: ${CMAKE_LIBRARY_PATH}") +endif() + include(LAMMPSUtils) get_lammps_version(${LAMMPS_SOURCE_DIR}/version.h PROJECT_VERSION) diff --git a/cmake/Modules/Packages/GPU.cmake b/cmake/Modules/Packages/GPU.cmake index 5033c1f0f1..9e7d7ca37a 100644 --- a/cmake/Modules/Packages/GPU.cmake +++ b/cmake/Modules/Packages/GPU.cmake @@ -40,6 +40,17 @@ if(GPU_API STREQUAL "CUDA") set(GPU_ARCH "sm_50" CACHE STRING "LAMMPS GPU CUDA SM primary architecture (e.g. sm_60)") + # ensure that no *cubin.h files exist from a compile in the lib/gpu folder + file(GLOB GPU_LIB_OLD_CUBIN_HEADERS ${LAMMPS_LIB_SOURCE_DIR}/gpu/*_cubin.h) + if (GPU_LIB_OLD_CUBIN_HEADERS) + message(FATAL_ERROR "########################################################################\n" + "Found file(s) generated by the make-based build system in lib/gpu\n" + "Please run\n" + " make -C ${LAMMPS_LIB_SOURCE_DIR}/gpu -f Makefile.serial clean\n" + "to remove\n" + "########################################################################") + endif() + file(GLOB GPU_LIB_CU ${LAMMPS_LIB_SOURCE_DIR}/gpu/[^.]*.cu ${CMAKE_CURRENT_SOURCE_DIR}/gpu/[^.]*.cu) list(REMOVE_ITEM GPU_LIB_CU ${LAMMPS_LIB_SOURCE_DIR}/gpu/lal_pppm.cu) @@ -79,7 +90,7 @@ if(GPU_API STREQUAL "CUDA") string(APPEND GPU_CUDA_GENCODE "-gencode arch=compute_75,code=[sm_75,compute_75] ") endif() - cuda_compile_fatbin(GPU_GEN_OBJS ${GPU_LIB_CU} OPTIONS + cuda_compile_fatbin(GPU_GEN_OBJS ${GPU_LIB_CU} OPTIONS ${CUDA_REQUEST_PIC} -DUNIX -O3 --use_fast_math -Wno-deprecated-gpu-targets -DNV_KERNEL -DUCL_CUDADR ${GPU_CUDA_GENCODE} -D_${GPU_PREC_SETTING}) cuda_compile(GPU_OBJS ${GPU_LIB_CUDPP_CU} OPTIONS ${CUDA_REQUEST_PIC} diff --git a/doc/src/Build_extras.rst b/doc/src/Build_extras.rst index 3d8da39640..fe974278eb 100644 --- a/doc/src/Build_extras.rst +++ b/doc/src/Build_extras.rst @@ -132,6 +132,10 @@ Thus the GPU_ARCH setting is merely an optimization, to have code for the preferred GPU architecture directly included rather than having to wait for the JIT compiler of the CUDA driver to translate it. +When building with CMake, you **must NOT** build the GPU library in ``lib/gpu`` +using the traditional build procedure. CMake will detect files generated by that +process and will terminate with an error and a suggestion for how to remove them. + If you are compiling with HIP, note that before running CMake you will have to set appropriate environment variables. Some variables such as :code:`HCC_AMDGPU_TARGET` or :code:`CUDA_PATH` are necessary for :code:`hipcc` diff --git a/doc/src/Commands_all.rst b/doc/src/Commands_all.rst index 92c0ba107a..458238cca6 100644 --- a/doc/src/Commands_all.rst +++ b/doc/src/Commands_all.rst @@ -94,6 +94,7 @@ An alphabetic list of all general LAMMPS commands. * :doc:`package ` * :doc:`pair_coeff ` * :doc:`pair_modify ` + * :doc:`pair_style ` * :doc:`pair_write ` * :doc:`partition ` * :doc:`prd ` diff --git a/doc/src/fix_orient.rst b/doc/src/fix_orient.rst index 8fdcc79ace..ca5ba83108 100644 --- a/doc/src/fix_orient.rst +++ b/doc/src/fix_orient.rst @@ -6,6 +6,9 @@ fix orient/fcc command fix orient/bcc command ====================== +Syntax +"""""" + .. parsed-literal:: fix ID group-ID orient/fcc nstats dir alat dE cutlo cuthi file0 file1 diff --git a/doc/src/fix_poems.rst b/doc/src/fix_poems.rst index 1be7a90419..f9a0e72b3d 100644 --- a/doc/src/fix_poems.rst +++ b/doc/src/fix_poems.rst @@ -3,7 +3,8 @@ fix poems command ================= -Syntax: +Syntax +"""""" .. parsed-literal:: diff --git a/doc/src/fix_rhok.rst b/doc/src/fix_rhok.rst index 089c96dd50..be4780c7d8 100644 --- a/doc/src/fix_rhok.rst +++ b/doc/src/fix_rhok.rst @@ -3,6 +3,9 @@ fix rhok command ================ +Syntax +"""""" + .. parsed-literal:: fix ID group-ID rhok nx ny nz K a diff --git a/doc/src/pair_lubricate.rst b/doc/src/pair_lubricate.rst index 563b88920e..1d1d7fb94a 100644 --- a/doc/src/pair_lubricate.rst +++ b/doc/src/pair_lubricate.rst @@ -28,7 +28,9 @@ Syntax * flagHI (optional) = 0/1 to exclude/include 1/r hydrodynamic interactions * flagVF (optional) = 0/1 to exclude/include volume fraction corrections in the long-range isotropic terms -**Examples:** (all assume radius = 1) +Examples +"""""""" +(all assume radius = 1) .. code-block:: LAMMPS diff --git a/doc/src/pair_lubricateU.rst b/doc/src/pair_lubricateU.rst index 5b485746c8..0bb124b91e 100644 --- a/doc/src/pair_lubricateU.rst +++ b/doc/src/pair_lubricateU.rst @@ -22,7 +22,9 @@ Syntax * flagHI (optional) = 0/1 to exclude/include 1/r hydrodynamic interactions * flagVF (optional) = 0/1 to exclude/include volume fraction corrections in the long-range isotropic terms -**Examples:** (all assume radius = 1) +Examples +"""""""" +(all assume radius = 1) .. code-block:: LAMMPS diff --git a/doc/src/special_bonds.rst b/doc/src/special_bonds.rst index d00467b3e8..35b870442b 100644 --- a/doc/src/special_bonds.rst +++ b/doc/src/special_bonds.rst @@ -28,7 +28,8 @@ Syntax *angle* value = *yes* or *no* *dihedral* value = *yes* or *no* -Examples: +Examples +"""""""" .. code-block:: LAMMPS diff --git a/src/GPU/pair_eam_alloy_gpu.cpp b/src/GPU/pair_eam_alloy_gpu.cpp index fcbc3c5d3c..1fbdbf9ba8 100644 --- a/src/GPU/pair_eam_alloy_gpu.cpp +++ b/src/GPU/pair_eam_alloy_gpu.cpp @@ -374,15 +374,12 @@ void PairEAMAlloyGPU::read_file(char *filename) PotentialFileReader reader(lmp, filename, "EAM"); try { - char * line = nullptr; - reader.skip_line(); reader.skip_line(); reader.skip_line(); // extract element names from nelements line - line = reader.next_line(1); - ValueTokenizer values(line); + ValueTokenizer values = reader.next_values(1); file->nelements = values.next_int(); if (values.count() != file->nelements + 1) @@ -398,8 +395,7 @@ void PairEAMAlloyGPU::read_file(char *filename) // - line = reader.next_line(5); - values = ValueTokenizer(line); + values = reader.next_values(5); file->nrho = values.next_int(); file->drho = values.next_double(); file->nr = values.next_int(); @@ -415,18 +411,17 @@ void PairEAMAlloyGPU::read_file(char *filename) memory->create(file->z2r, file->nelements, file->nelements, file->nr + 1, "pair:z2r"); for (int i = 0; i < file->nelements; i++) { - line = reader.next_line(2); - values = ValueTokenizer(line); + values = reader.next_values(2); values.next_int(); // ignore file->mass[i] = values.next_double(); - reader.next_dvector(file->nrho, &file->frho[i][1]); - reader.next_dvector(file->nr, &file->rhor[i][1]); + reader.next_dvector(&file->frho[i][1], file->nrho); + reader.next_dvector(&file->rhor[i][1], file->nr); } for (int i = 0; i < file->nelements; i++) { for (int j = 0; j <= i; j++) { - reader.next_dvector(file->nr, &file->z2r[i][j][1]); + reader.next_dvector(&file->z2r[i][j][1], file->nr); } } } catch (TokenizerException & e) { diff --git a/src/GPU/pair_eam_fs_gpu.cpp b/src/GPU/pair_eam_fs_gpu.cpp index e674594498..a316d08c54 100644 --- a/src/GPU/pair_eam_fs_gpu.cpp +++ b/src/GPU/pair_eam_fs_gpu.cpp @@ -374,15 +374,12 @@ void PairEAMFSGPU::read_file(char *filename) PotentialFileReader reader(lmp, filename, "EAM"); try { - char * line = nullptr; - reader.skip_line(); reader.skip_line(); reader.skip_line(); // extract element names from nelements line - line = reader.next_line(1); - ValueTokenizer values(line); + ValueTokenizer values = reader.next_values(1); file->nelements = values.next_int(); if (values.count() != file->nelements + 1) @@ -398,8 +395,7 @@ void PairEAMFSGPU::read_file(char *filename) // - line = reader.next_line(5); - values = ValueTokenizer(line); + values = reader.next_values(5); file->nrho = values.next_int(); file->drho = values.next_double(); file->nr = values.next_int(); @@ -415,21 +411,20 @@ void PairEAMFSGPU::read_file(char *filename) memory->create(file->z2r, file->nelements, file->nelements, file->nr + 1, "pair:z2r"); for (int i = 0; i < file->nelements; i++) { - line = reader.next_line(2); - values = ValueTokenizer(line); + values = reader.next_values(2); values.next_int(); // ignore file->mass[i] = values.next_double(); - reader.next_dvector(file->nrho, &file->frho[i][1]); + reader.next_dvector(&file->frho[i][1], file->nrho); for (int j = 0; j < file->nelements; j++) { - reader.next_dvector(file->nr, &file->rhor[i][j][1]); + reader.next_dvector(&file->rhor[i][j][1], file->nr); } } for (int i = 0; i < file->nelements; i++) { for (int j = 0; j <= i; j++) { - reader.next_dvector(file->nr, &file->z2r[i][j][1]); + reader.next_dvector(&file->z2r[i][j][1], file->nr); } } } catch (TokenizerException & e) { diff --git a/src/KIM/kim_init.cpp b/src/KIM/kim_init.cpp index 5328769d22..9f16a2bcdb 100644 --- a/src/KIM/kim_init.cpp +++ b/src/KIM/kim_init.cpp @@ -57,6 +57,8 @@ ------------------------------------------------------------------------- */ #include "kim_init.h" +#include "fix_store_kim.h" +#include "kim_units.h" #include #include #include @@ -71,8 +73,7 @@ #include "input.h" #include "variable.h" #include "citeme.h" -#include "fix_store_kim.h" -#include "kim_units.h" +#include "utils.h" extern "C" { #include "KIM_SimulatorHeaders.h" diff --git a/src/KOKKOS/pair_eam_alloy_kokkos.cpp b/src/KOKKOS/pair_eam_alloy_kokkos.cpp index 7f598f966d..2d0d229e00 100644 --- a/src/KOKKOS/pair_eam_alloy_kokkos.cpp +++ b/src/KOKKOS/pair_eam_alloy_kokkos.cpp @@ -988,15 +988,12 @@ void PairEAMAlloyKokkos::read_file(char *filename) PotentialFileReader reader(lmp, filename, "EAM"); try { - char * line = nullptr; - reader.skip_line(); reader.skip_line(); reader.skip_line(); // extract element names from nelements line - line = reader.next_line(1); - ValueTokenizer values(line); + ValueTokenizer values = reader.next_values(1); file->nelements = values.next_int(); if (values.count() != file->nelements + 1) @@ -1012,8 +1009,7 @@ void PairEAMAlloyKokkos::read_file(char *filename) // - line = reader.next_line(5); - values = ValueTokenizer(line); + values = reader.next_values(5); file->nrho = values.next_int(); file->drho = values.next_double(); file->nr = values.next_int(); @@ -1029,18 +1025,17 @@ void PairEAMAlloyKokkos::read_file(char *filename) memory->create(file->z2r, file->nelements, file->nelements, file->nr + 1, "pair:z2r"); for (int i = 0; i < file->nelements; i++) { - line = reader.next_line(2); - values = ValueTokenizer(line); + values = reader.next_values(2); values.next_int(); // ignore file->mass[i] = values.next_double(); - reader.next_dvector(file->nrho, &file->frho[i][1]); - reader.next_dvector(file->nr, &file->rhor[i][1]); + reader.next_dvector(&file->frho[i][1], file->nrho); + reader.next_dvector(&file->rhor[i][1], file->nr); } for (int i = 0; i < file->nelements; i++) { for (int j = 0; j <= i; j++) { - reader.next_dvector(file->nr, &file->z2r[i][j][1]); + reader.next_dvector(&file->z2r[i][j][1], file->nr); } } } catch (TokenizerException & e) { diff --git a/src/KOKKOS/pair_eam_fs_kokkos.cpp b/src/KOKKOS/pair_eam_fs_kokkos.cpp index e532a4ec38..8b1e6b348a 100644 --- a/src/KOKKOS/pair_eam_fs_kokkos.cpp +++ b/src/KOKKOS/pair_eam_fs_kokkos.cpp @@ -988,15 +988,12 @@ void PairEAMFSKokkos::read_file(char *filename) PotentialFileReader reader(lmp, filename, "EAM"); try { - char * line = nullptr; - reader.skip_line(); reader.skip_line(); reader.skip_line(); // extract element names from nelements line - line = reader.next_line(1); - ValueTokenizer values(line); + ValueTokenizer values = reader.next_values(1); file->nelements = values.next_int(); if (values.count() != file->nelements + 1) @@ -1012,8 +1009,7 @@ void PairEAMFSKokkos::read_file(char *filename) // - line = reader.next_line(5); - values = ValueTokenizer(line); + values = reader.next_values(5); file->nrho = values.next_int(); file->drho = values.next_double(); file->nr = values.next_int(); @@ -1029,21 +1025,20 @@ void PairEAMFSKokkos::read_file(char *filename) memory->create(file->z2r, file->nelements, file->nelements, file->nr + 1, "pair:z2r"); for (int i = 0; i < file->nelements; i++) { - line = reader.next_line(2); - values = ValueTokenizer(line); + values = reader.next_values(2); values.next_int(); // ignore file->mass[i] = values.next_double(); - reader.next_dvector(file->nrho, &file->frho[i][1]); + reader.next_dvector(&file->frho[i][1], file->nrho); for (int j = 0; j < file->nelements; j++) { - reader.next_dvector(file->nr, &file->rhor[i][j][1]); + reader.next_dvector(&file->rhor[i][j][1], file->nr); } } for (int i = 0; i < file->nelements; i++) { for (int j = 0; j <= i; j++) { - reader.next_dvector(file->nr, &file->z2r[i][j][1]); + reader.next_dvector(&file->z2r[i][j][1], file->nr); } } } catch (TokenizerException & e) { diff --git a/src/MANYBODY/pair_adp.cpp b/src/MANYBODY/pair_adp.cpp index 2a64839e98..6bc0ab587b 100644 --- a/src/MANYBODY/pair_adp.cpp +++ b/src/MANYBODY/pair_adp.cpp @@ -546,15 +546,12 @@ void PairADP::read_file(char *filename) PotentialFileReader reader(lmp, filename, "ADP"); try { - char * line = nullptr; - reader.skip_line(); reader.skip_line(); reader.skip_line(); // extract element names from nelements line - line = reader.next_line(1); - ValueTokenizer values(line); + ValueTokenizer values = reader.next_values(1); file->nelements = values.next_int(); if (values.count() != file->nelements + 1) @@ -570,8 +567,7 @@ void PairADP::read_file(char *filename) // - line = reader.next_line(5); - values = ValueTokenizer(line); + values = reader.next_values(5); file->nrho = values.next_int(); file->drho = values.next_double(); file->nr = values.next_int(); @@ -589,30 +585,29 @@ void PairADP::read_file(char *filename) memory->create(file->w2r, file->nelements, file->nelements, file->nr + 1, "pair:w2r"); for (int i = 0; i < file->nelements; i++) { - line = reader.next_line(2); - values = ValueTokenizer(line); + values = reader.next_values(2); values.next_int(); // ignore file->mass[i] = values.next_double(); - reader.next_dvector(file->nrho, &file->frho[i][1]); - reader.next_dvector(file->nr, &file->rhor[i][1]); + reader.next_dvector(&file->frho[i][1], file->nrho); + reader.next_dvector(&file->rhor[i][1], file->nr); } for (int i = 0; i < file->nelements; i++) { for (int j = 0; j <= i; j++) { - reader.next_dvector(file->nr, &file->z2r[i][j][1]); + reader.next_dvector(&file->z2r[i][j][1], file->nr); } } for (int i = 0; i < file->nelements; i++) { for (int j = 0; j <= i; j++) { - reader.next_dvector(file->nr, &file->u2r[i][j][1]); + reader.next_dvector(&file->u2r[i][j][1], file->nr); } } for (int i = 0; i < file->nelements; i++) { for (int j = 0; j <= i; j++) { - reader.next_dvector(file->nr, &file->w2r[i][j][1]); + reader.next_dvector(&file->w2r[i][j][1], file->nr); } } } catch (TokenizerException & e) { diff --git a/src/MANYBODY/pair_airebo.cpp b/src/MANYBODY/pair_airebo.cpp index 84565a2e50..df90609e7d 100644 --- a/src/MANYBODY/pair_airebo.cpp +++ b/src/MANYBODY/pair_airebo.cpp @@ -35,11 +35,13 @@ #include "memory.h" #include "error.h" #include "utils.h" +#include "tokenizer.h" +#include "potential_file_reader.h" +#include "fmt/format.h" using namespace LAMMPS_NS; using namespace MathSpecial; -#define MAXLINE 1024 #define TOL 1.0e-9 #define PGDELTA 1 @@ -3331,9 +3333,6 @@ double PairAIREBO::TijSpline(double Nij, double Nji, void PairAIREBO::read_file(char *filename) { - int i,j,k,l,limit; - char s[MAXLINE]; - // REBO Parameters (AIREBO) double rcmin_CC,rcmin_CH,rcmin_HH,rcmax_CC,rcmax_CH, @@ -3357,562 +3356,298 @@ void PairAIREBO::read_file(char *filename) double epsilonM_CC,epsilonM_CH,epsilonM_HH,alphaM_CC,alphaM_CH,alphaM_HH; double reqM_CC,reqM_CH,reqM_HH; - MPI_Comm_rank(world,&me); - // read file on proc 0 - int cerror = 0; - int numpar = 0; - FILE *fp = NULL; + if (comm->me == 0) { + std::string potential_name; + std::string header; + switch (variant) { + case AIREBO: + potential_name = "AIREBO"; + header = "# AIREBO "; + break; - if (me == 0) { - fp = force->open_potential(filename); - if (fp == NULL) { - char str[128]; - switch (variant) { + case REBO_2: + potential_name = "REBO2"; + header = "# REBO2 "; + break; - case AIREBO: - snprintf(str,128,"Cannot open AIREBO potential file %s",filename); - break; + case AIREBO_M: + potential_name = "Cannot open AIREBO-M"; + header = "# AIREBO-M "; + break; - case REBO_2: - snprintf(str,128,"Cannot open REBO2 potential file %s",filename); - break; - - case AIREBO_M: - snprintf(str,128,"Cannot open AIREBO-M potential file %s",filename); - break; - - default: - snprintf(str,128,"Unknown REBO style variant %d",variant); - } - error->one(FLERR,str); + default: + error->one(FLERR, fmt::format("Unknown REBO style variant {}",variant)); } + PotentialFileReader reader(lmp, filename, potential_name); + reader.ignore_comments(false); + // skip initial comment line and check for potential file style identifier comment - utils::sfgets(FLERR,s,MAXLINE,fp,filename,error); - utils::sfgets(FLERR,s,MAXLINE,fp,filename,error); + reader.skip_line(); + char * line = reader.next_line(); - if (((variant == AIREBO) && (strncmp(s,"# AIREBO ",9) != 0)) - || ((variant == REBO_2) && (strncmp(s,"# REBO2 ",8) != 0)) - || ((variant == AIREBO_M) && (strncmp(s,"# AIREBO-M ",11) != 0))) { - error->one(FLERR,"Potential file does not match AIREBO/REBO style variant"); + if (std::string(line).find(header) == std::string::npos) { + error->one(FLERR, fmt::format("Potential file does not match AIREBO/REBO style variant: {}: {}", header, line)); } // skip remaining comments - - while (1) { - utils::sfgets(FLERR,s,MAXLINE,fp,filename,error); - if (s[0] != '#') break; - } + reader.ignore_comments(true); // read parameters - ++numpar; - utils::sfgets(FLERR,s,MAXLINE,fp,filename,error); - if (1 != sscanf(s,"%lg",&rcmin_CC)) ++cerror; - ++numpar; - utils::sfgets(FLERR,s,MAXLINE,fp,filename,error); - if (1 != sscanf(s,"%lg",&rcmin_CH)) ++cerror; - ++numpar; - utils::sfgets(FLERR,s,MAXLINE,fp,filename,error); - if (1 != sscanf(s,"%lg",&rcmin_HH)) ++cerror; - ++numpar; - utils::sfgets(FLERR,s,MAXLINE,fp,filename,error); - if (1 != sscanf(s,"%lg",&rcmax_CC)) ++cerror; - ++numpar; - utils::sfgets(FLERR,s,MAXLINE,fp,filename,error); - if (1 != sscanf(s,"%lg",&rcmax_CH)) ++cerror; - ++numpar; - utils::sfgets(FLERR,s,MAXLINE,fp,filename,error); - if (1 != sscanf(s,"%lg",&rcmax_HH)) ++cerror; - ++numpar; - utils::sfgets(FLERR,s,MAXLINE,fp,filename,error); - if (1 != sscanf(s,"%lg",&rcmaxp_CC)) ++cerror; - ++numpar; - utils::sfgets(FLERR,s,MAXLINE,fp,filename,error); - if (1 != sscanf(s,"%lg",&rcmaxp_CH)) ++cerror; - ++numpar; - utils::sfgets(FLERR,s,MAXLINE,fp,filename,error); - if (1 != sscanf(s,"%lg",&rcmaxp_HH)) ++cerror; - ++numpar; - utils::sfgets(FLERR,s,MAXLINE,fp,filename,error); - if (1 != sscanf(s,"%lg",&smin)) ++cerror; - ++numpar; - utils::sfgets(FLERR,s,MAXLINE,fp,filename,error); - if (1 != sscanf(s,"%lg",&Nmin)) ++cerror; - ++numpar; - utils::sfgets(FLERR,s,MAXLINE,fp,filename,error); - if (1 != sscanf(s,"%lg",&Nmax)) ++cerror; - ++numpar; - utils::sfgets(FLERR,s,MAXLINE,fp,filename,error); - if (1 != sscanf(s,"%lg",&NCmin)) ++cerror; - ++numpar; - utils::sfgets(FLERR,s,MAXLINE,fp,filename,error); - if (1 != sscanf(s,"%lg",&NCmax)) ++cerror; - ++numpar; - utils::sfgets(FLERR,s,MAXLINE,fp,filename,error); - if (1 != sscanf(s,"%lg",&Q_CC)) ++cerror; - ++numpar; - utils::sfgets(FLERR,s,MAXLINE,fp,filename,error); - if (1 != sscanf(s,"%lg",&Q_CH)) ++cerror; - ++numpar; - utils::sfgets(FLERR,s,MAXLINE,fp,filename,error); - if (1 != sscanf(s,"%lg",&Q_HH)) ++cerror; - ++numpar; - utils::sfgets(FLERR,s,MAXLINE,fp,filename,error); - if (1 != sscanf(s,"%lg",&alpha_CC)) ++cerror; - ++numpar; - utils::sfgets(FLERR,s,MAXLINE,fp,filename,error); - if (1 != sscanf(s,"%lg",&alpha_CH)) ++cerror; - ++numpar; - utils::sfgets(FLERR,s,MAXLINE,fp,filename,error); - if (1 != sscanf(s,"%lg",&alpha_HH)) ++cerror; - ++numpar; - utils::sfgets(FLERR,s,MAXLINE,fp,filename,error); - if (1 != sscanf(s,"%lg",&A_CC)) ++cerror; - ++numpar; - utils::sfgets(FLERR,s,MAXLINE,fp,filename,error); - if (1 != sscanf(s,"%lg",&A_CH)) ++cerror; - ++numpar; - utils::sfgets(FLERR,s,MAXLINE,fp,filename,error); - if (1 != sscanf(s,"%lg",&A_HH)) ++cerror; - ++numpar; - utils::sfgets(FLERR,s,MAXLINE,fp,filename,error); - if (1 != sscanf(s,"%lg",&BIJc_CC1)) ++cerror; - ++numpar; - utils::sfgets(FLERR,s,MAXLINE,fp,filename,error); - if (1 != sscanf(s,"%lg",&BIJc_CC2)) ++cerror; - ++numpar; - utils::sfgets(FLERR,s,MAXLINE,fp,filename,error); - if (1 != sscanf(s,"%lg",&BIJc_CC3)) ++cerror; - ++numpar; - utils::sfgets(FLERR,s,MAXLINE,fp,filename,error); - if (1 != sscanf(s,"%lg",&BIJc_CH1)) ++cerror; - ++numpar; - utils::sfgets(FLERR,s,MAXLINE,fp,filename,error); - if (1 != sscanf(s,"%lg",&BIJc_CH2)) ++cerror; - ++numpar; - utils::sfgets(FLERR,s,MAXLINE,fp,filename,error); - if (1 != sscanf(s,"%lg",&BIJc_CH3)) ++cerror; - ++numpar; - utils::sfgets(FLERR,s,MAXLINE,fp,filename,error); - if (1 != sscanf(s,"%lg",&BIJc_HH1)) ++cerror; - ++numpar; - utils::sfgets(FLERR,s,MAXLINE,fp,filename,error); - if (1 != sscanf(s,"%lg",&BIJc_HH2)) ++cerror; - ++numpar; - utils::sfgets(FLERR,s,MAXLINE,fp,filename,error); - if (1 != sscanf(s,"%lg",&BIJc_HH3)) ++cerror; - ++numpar; - utils::sfgets(FLERR,s,MAXLINE,fp,filename,error); - if (1 != sscanf(s,"%lg",&Beta_CC1)) ++cerror; - ++numpar; - utils::sfgets(FLERR,s,MAXLINE,fp,filename,error); - if (1 != sscanf(s,"%lg",&Beta_CC2)) ++cerror; - ++numpar; - utils::sfgets(FLERR,s,MAXLINE,fp,filename,error); - if (1 != sscanf(s,"%lg",&Beta_CC3)) ++cerror; - ++numpar; - utils::sfgets(FLERR,s,MAXLINE,fp,filename,error); - if (1 != sscanf(s,"%lg",&Beta_CH1)) ++cerror; - ++numpar; - utils::sfgets(FLERR,s,MAXLINE,fp,filename,error); - if (1 != sscanf(s,"%lg",&Beta_CH2)) ++cerror; - ++numpar; - utils::sfgets(FLERR,s,MAXLINE,fp,filename,error); - if (1 != sscanf(s,"%lg",&Beta_CH3)) ++cerror; - ++numpar; - utils::sfgets(FLERR,s,MAXLINE,fp,filename,error); - if (1 != sscanf(s,"%lg",&Beta_HH1)) ++cerror; - ++numpar; - utils::sfgets(FLERR,s,MAXLINE,fp,filename,error); - if (1 != sscanf(s,"%lg",&Beta_HH2)) ++cerror; - ++numpar; - utils::sfgets(FLERR,s,MAXLINE,fp,filename,error); - if (1 != sscanf(s,"%lg",&Beta_HH3)) ++cerror; - ++numpar; - utils::sfgets(FLERR,s,MAXLINE,fp,filename,error); - if (1 != sscanf(s,"%lg",&rho_CC)) ++cerror; - ++numpar; - utils::sfgets(FLERR,s,MAXLINE,fp,filename,error); - if (1 != sscanf(s,"%lg",&rho_CH)) ++cerror; - ++numpar; - utils::sfgets(FLERR,s,MAXLINE,fp,filename,error); - if (1 != sscanf(s,"%lg",&rho_HH)) ++cerror; + std::vector params { + &rcmin_CC, + &rcmin_CH, + &rcmin_HH, + &rcmax_CC, + &rcmax_CH, + &rcmax_HH, + &rcmaxp_CC, + &rcmaxp_CH, + &rcmaxp_HH, + &smin, + &Nmin, + &Nmax, + &NCmin, + &NCmax, + &Q_CC, + &Q_CH, + &Q_HH, + &alpha_CC, + &alpha_CH, + &alpha_HH, + &A_CC, + &A_CH, + &A_HH, + &BIJc_CC1, + &BIJc_CC2, + &BIJc_CC3, + &BIJc_CH1, + &BIJc_CH2, + &BIJc_CH3, + &BIJc_HH1, + &BIJc_HH2, + &BIJc_HH3, + &Beta_CC1, + &Beta_CC2, + &Beta_CC3, + &Beta_CH1, + &Beta_CH2, + &Beta_CH3, + &Beta_HH1, + &Beta_HH2, + &Beta_HH3, + &rho_CC, + &rho_CH, + &rho_HH, - // LJ parameters - - ++numpar; - utils::sfgets(FLERR,s,MAXLINE,fp,filename,error); - if (1 != sscanf(s,"%lg",&rcLJmin_CC)) ++cerror; - ++numpar; - utils::sfgets(FLERR,s,MAXLINE,fp,filename,error); - if (1 != sscanf(s,"%lg",&rcLJmin_CH)) ++cerror; - ++numpar; - utils::sfgets(FLERR,s,MAXLINE,fp,filename,error); - if (1 != sscanf(s,"%lg",&rcLJmin_HH)) ++cerror; - ++numpar; - utils::sfgets(FLERR,s,MAXLINE,fp,filename,error); - if (1 != sscanf(s,"%lg",&rcLJmax_CC)) ++cerror; - ++numpar; - utils::sfgets(FLERR,s,MAXLINE,fp,filename,error); - if (1 != sscanf(s,"%lg",&rcLJmax_CH)) ++cerror; - ++numpar; - utils::sfgets(FLERR,s,MAXLINE,fp,filename,error); - if (1 != sscanf(s,"%lg",&rcLJmax_HH)) ++cerror; - ++numpar; - utils::sfgets(FLERR,s,MAXLINE,fp,filename,error); - if (1 != sscanf(s,"%lg",&bLJmin_CC)) ++cerror; - ++numpar; - utils::sfgets(FLERR,s,MAXLINE,fp,filename,error); - if (1 != sscanf(s,"%lg",&bLJmin_CH)) ++cerror; - ++numpar; - utils::sfgets(FLERR,s,MAXLINE,fp,filename,error); - if (1 != sscanf(s,"%lg",&bLJmin_HH)) ++cerror; - ++numpar; - utils::sfgets(FLERR,s,MAXLINE,fp,filename,error); - if (1 != sscanf(s,"%lg",&bLJmax_CC)) ++cerror; - ++numpar; - utils::sfgets(FLERR,s,MAXLINE,fp,filename,error); - if (1 != sscanf(s,"%lg",&bLJmax_CH)) ++cerror; - ++numpar; - utils::sfgets(FLERR,s,MAXLINE,fp,filename,error); - if (1 != sscanf(s,"%lg",&bLJmax_HH)) ++cerror; - ++numpar; - utils::sfgets(FLERR,s,MAXLINE,fp,filename,error); - if (1 != sscanf(s,"%lg",&epsilon_CC)) ++cerror; - ++numpar; - utils::sfgets(FLERR,s,MAXLINE,fp,filename,error); - if (1 != sscanf(s,"%lg",&epsilon_CH)) ++cerror; - ++numpar; - utils::sfgets(FLERR,s,MAXLINE,fp,filename,error); - if (1 != sscanf(s,"%lg",&epsilon_HH)) ++cerror; - ++numpar; - utils::sfgets(FLERR,s,MAXLINE,fp,filename,error); - if (1 != sscanf(s,"%lg",&sigma_CC)) ++cerror; - ++numpar; - utils::sfgets(FLERR,s,MAXLINE,fp,filename,error); - if (1 != sscanf(s,"%lg",&sigma_CH)) ++cerror; - ++numpar; - utils::sfgets(FLERR,s,MAXLINE,fp,filename,error); - if (1 != sscanf(s,"%lg",&sigma_HH)) ++cerror; - ++numpar; - utils::sfgets(FLERR,s,MAXLINE,fp,filename,error); - if (1 != sscanf(s,"%lg",&epsilonT_CCCC)) ++cerror; - ++numpar; - utils::sfgets(FLERR,s,MAXLINE,fp,filename,error); - if (1 != sscanf(s,"%lg",&epsilonT_CCCH)) ++cerror; - ++numpar; - utils::sfgets(FLERR,s,MAXLINE,fp,filename,error); - if (1 != sscanf(s,"%lg",&epsilonT_HCCH)) ++cerror; + // LJ parameters + &rcLJmin_CC, + &rcLJmin_CH, + &rcLJmin_HH, + &rcLJmax_CC, + &rcLJmax_CH, + &rcLJmax_HH, + &bLJmin_CC, + &bLJmin_CH, + &bLJmin_HH, + &bLJmax_CC, + &bLJmax_CH, + &bLJmax_HH, + &epsilon_CC, + &epsilon_CH, + &epsilon_HH, + &sigma_CC, + &sigma_CH, + &sigma_HH, + &epsilonT_CCCC, + &epsilonT_CCCH, + &epsilonT_HCCH + }; if (morseflag) { // lines for reading in MORSE parameters from CH.airebo_m file - ++numpar; - utils::sfgets(FLERR,s,MAXLINE,fp,filename,error); - if (1 != sscanf(s,"%lg",&epsilonM_CC)) ++cerror; - ++numpar; - utils::sfgets(FLERR,s,MAXLINE,fp,filename,error); - if (1 != sscanf(s,"%lg",&epsilonM_CH)) ++cerror; - ++numpar; - utils::sfgets(FLERR,s,MAXLINE,fp,filename,error); - if (1 != sscanf(s,"%lg",&epsilonM_HH)) ++cerror; - ++numpar; - utils::sfgets(FLERR,s,MAXLINE,fp,filename,error); - if (1 != sscanf(s,"%lg",&alphaM_CC)) ++cerror; - ++numpar; - utils::sfgets(FLERR,s,MAXLINE,fp,filename,error); - if (1 != sscanf(s,"%lg",&alphaM_CH)) ++cerror; - ++numpar; - utils::sfgets(FLERR,s,MAXLINE,fp,filename,error); - if (1 != sscanf(s,"%lg",&alphaM_HH)) ++cerror; - ++numpar; - utils::sfgets(FLERR,s,MAXLINE,fp,filename,error); - if (1 != sscanf(s,"%lg",&reqM_CC)) ++cerror; - ++numpar; - utils::sfgets(FLERR,s,MAXLINE,fp,filename,error); - if (1 != sscanf(s,"%lg",&reqM_CH)) ++cerror; - ++numpar; - utils::sfgets(FLERR,s,MAXLINE,fp,filename,error); - if (1 != sscanf(s,"%lg",&reqM_HH)) ++cerror; + params.push_back(&epsilonM_CC); + params.push_back(&epsilonM_CH); + params.push_back(&epsilonM_HH); + params.push_back(&alphaM_CC); + params.push_back(&alphaM_CH); + params.push_back(&alphaM_HH); + params.push_back(&reqM_CC); + params.push_back(&reqM_CH); + params.push_back(&reqM_HH); } - } + std::string current_section; - // check for errors parsing global parameters + try { + ///////////////////////////////////////////////////////////////////////// + // global parameters + current_section = "global parameters"; - MPI_Bcast(&cerror,1,MPI_INT,0,world); - if (cerror > 0) { - char msg[128]; - snprintf(msg,128,"Could not parse %d of %d parameters from file %s", - cerror,numpar,filename); - error->all(FLERR,msg); - } - - cerror = numpar = 0; - - if (me == 0) { - - // gC spline - - utils::sfgets(FLERR,s,MAXLINE,fp,filename,error); - utils::sfgets(FLERR,s,MAXLINE,fp,filename,error); - utils::sfgets(FLERR,s,MAXLINE,fp,filename,error); - - // number-1 = # of domains for the spline - - ++numpar; - utils::sfgets(FLERR,s,MAXLINE,fp,filename,error); - if (1 != sscanf(s,"%d",&limit)) ++cerror; - - for (i = 0; i < limit; i++) { - ++numpar; - utils::sfgets(FLERR,s,MAXLINE,fp,filename,error); - if (1 != sscanf(s,"%lg",&gCdom[i])) ++cerror; - } - utils::sfgets(FLERR,s,MAXLINE,fp,filename,error); - for (i = 0; i < limit-1; i++) { - for (j = 0; j < 6; j++) { - ++numpar; - utils::sfgets(FLERR,s,MAXLINE,fp,filename,error); - if (1 != sscanf(s,"%lg",&gC1[i][j])) ++cerror; + for(int i = 0; i < params.size(); i++) { + *params[i] = reader.next_double(); } - } - utils::sfgets(FLERR,s,MAXLINE,fp,filename,error); - for (i = 0; i < limit-1; i++) { - for (j = 0; j < 6; j++) { - ++numpar; - utils::sfgets(FLERR,s,MAXLINE,fp,filename,error); - if (1 != sscanf(s,"%lg",&gC2[i][j])) ++cerror; + + + ///////////////////////////////////////////////////////////////////////// + // gC spline + current_section = "gC spline"; + + // number-1 = # of domains for the spline + + int limit = reader.next_int(); + reader.next_dvector(gCdom, limit); + + for (int i = 0; i < limit-1; i++) { + reader.next_dvector(&gC1[i][0], 6); } - } - // gH spline - - utils::sfgets(FLERR,s,MAXLINE,fp,filename,error); - utils::sfgets(FLERR,s,MAXLINE,fp,filename,error); - utils::sfgets(FLERR,s,MAXLINE,fp,filename,error); - - ++numpar; - utils::sfgets(FLERR,s,MAXLINE,fp,filename,error); - if (1 != sscanf(s,"%d",&limit)) ++cerror; - - for (i = 0; i < limit; i++) { - ++numpar; - utils::sfgets(FLERR,s,MAXLINE,fp,filename,error); - if (1 != sscanf(s,"%lg",&gHdom[i])) ++cerror; - } - - utils::sfgets(FLERR,s,MAXLINE,fp,filename,error); - - for (i = 0; i < limit-1; i++) { - for (j = 0; j < 6; j++) { - ++numpar; - utils::sfgets(FLERR,s,MAXLINE,fp,filename,error); - if (1 != sscanf(s,"%lg",&gH[i][j])) ++cerror; + for (int i = 0; i < limit-1; i++) { + reader.next_dvector(&gC2[i][0], 6); } - } - // pCC spline + ///////////////////////////////////////////////////////////////////////// + // gH spline + current_section = "gH spline"; - utils::sfgets(FLERR,s,MAXLINE,fp,filename,error); - utils::sfgets(FLERR,s,MAXLINE,fp,filename,error); - utils::sfgets(FLERR,s,MAXLINE,fp,filename,error); + limit = reader.next_int(); + reader.next_dvector(gHdom, limit); - ++numpar; - utils::sfgets(FLERR,s,MAXLINE,fp,filename,error); - if (1 != sscanf(s,"%d",&limit)) ++cerror; - - for (i = 0; i < limit/2; i++) { - for (j = 0; j < limit/2; j++) { - ++numpar; - utils::sfgets(FLERR,s,MAXLINE,fp,filename,error); - if (1 != sscanf(s,"%lg",&pCCdom[i][j])) ++cerror; + for (int i = 0; i < limit-1; i++) { + reader.next_dvector(&gH[i][0], 6); } - } - utils::sfgets(FLERR,s,MAXLINE,fp,filename,error); - for (i = 0; i < (int) pCCdom[0][1]; i++) { - for (j = 0; j < (int) pCCdom[1][1]; j++) { - for (k = 0; k < 16; k++) { - ++numpar; - utils::sfgets(FLERR,s,MAXLINE,fp,filename,error); - if (1 != sscanf(s,"%lg",&pCC[i][j][k])) ++cerror; + ///////////////////////////////////////////////////////////////////////// + // pCC spline + current_section = "pCC spline"; + + limit = reader.next_int(); + + for (int i = 0; i < limit/2; i++) { + reader.next_dvector(&pCCdom[i][0], limit/2); + } + + for (int i = 0; i < (int) pCCdom[0][1]; i++) { + for (int j = 0; j < (int) pCCdom[1][1]; j++) { + reader.next_dvector(&pCC[i][j][0], 16); } } - } - // pCH spline + ///////////////////////////////////////////////////////////////////////// + // pCH spline + current_section = "pCH spline"; - utils::sfgets(FLERR,s,MAXLINE,fp,filename,error); - utils::sfgets(FLERR,s,MAXLINE,fp,filename,error); - utils::sfgets(FLERR,s,MAXLINE,fp,filename,error); + limit = reader.next_int(); - ++numpar; - utils::sfgets(FLERR,s,MAXLINE,fp,filename,error); - if (1 != sscanf(s,"%d",&limit)) ++cerror; - - for (i = 0; i < limit/2; i++) { - for (j = 0; j < limit/2; j++) { - ++numpar; - utils::sfgets(FLERR,s,MAXLINE,fp,filename,error); - if (1 != sscanf(s,"%lg",&pCHdom[i][j])) ++cerror; - } - } - utils::sfgets(FLERR,s,MAXLINE,fp,filename,error); - - for (i = 0; i < (int) pCHdom[0][1]; i++) { - for (j = 0; j < (int) pCHdom[1][1]; j++) { - for (k = 0; k < 16; k++) { - ++numpar; - utils::sfgets(FLERR,s,MAXLINE,fp,filename,error); - if (1 != sscanf(s,"%lg",&pCH[i][j][k])) ++cerror; + for (int i = 0; i < limit/2; i++) { + for (int j = 0; j < limit/2; j++) { + pCHdom[i][j] = reader.next_double(); } } - } - // piCC cpline - - utils::sfgets(FLERR,s,MAXLINE,fp,filename,error); - utils::sfgets(FLERR,s,MAXLINE,fp,filename,error); - utils::sfgets(FLERR,s,MAXLINE,fp,filename,error); - - ++numpar; - utils::sfgets(FLERR,s,MAXLINE,fp,filename,error); - if (1 != sscanf(s,"%d",&limit)) ++cerror; - - for (i = 0; i < limit/2; i++) { - for (j = 0; j < limit/3; j++) { - ++numpar; - utils::sfgets(FLERR,s,MAXLINE,fp,filename,error); - if (1 != sscanf(s,"%lg",&piCCdom[i][j])) ++cerror; + for (int i = 0; i < (int) pCHdom[0][1]; i++) { + for (int j = 0; j < (int) pCHdom[1][1]; j++) { + reader.next_dvector(&pCH[i][j][0], 16); + } } - } - utils::sfgets(FLERR,s,MAXLINE,fp,filename,error); - for (i = 0; i < (int) piCCdom[0][1]; i++) { - for (j = 0; j < (int) piCCdom[1][1]; j++) { - for (k = 0; k < (int) piCCdom[2][1]; k++) { - for (l = 0; l < 64; l = l+1) { - ++numpar; - utils::sfgets(FLERR,s,MAXLINE,fp,filename,error); - if (1 != sscanf(s,"%lg",&piCC[i][j][k][l])) ++cerror; + ///////////////////////////////////////////////////////////////////////// + // piCC spline + current_section = "piCC spline"; + + limit = reader.next_int(); + + for (int i = 0; i < limit/2; i++) { + for (int j = 0; j < limit/3; j++) { + piCCdom[i][j] = reader.next_double(); + } + } + + for (int i = 0; i < (int) piCCdom[0][1]; i++) { + for (int j = 0; j < (int) piCCdom[1][1]; j++) { + for (int k = 0; k < (int) piCCdom[2][1]; k++) { + reader.next_dvector(&piCC[i][j][k][0], 64); } } } - } - // piCH spline + ///////////////////////////////////////////////////////////////////////// + // piCH spline + current_section = "piCH spline"; - utils::sfgets(FLERR,s,MAXLINE,fp,filename,error); - utils::sfgets(FLERR,s,MAXLINE,fp,filename,error); - utils::sfgets(FLERR,s,MAXLINE,fp,filename,error); + limit = reader.next_int(); - ++numpar; - utils::sfgets(FLERR,s,MAXLINE,fp,filename,error); - if (1 != sscanf(s,"%d",&limit)) ++cerror; - - for (i = 0; i < limit/2; i++) { - for (j = 0; j < limit/3; j++) { - ++numpar; - utils::sfgets(FLERR,s,MAXLINE,fp,filename,error); - if (1 != sscanf(s,"%lg",&piCHdom[i][j])) ++cerror; + for (int i = 0; i < limit/2; i++) { + for (int j = 0; j < limit/3; j++) { + piCHdom[i][j] = reader.next_double(); + } } - } - utils::sfgets(FLERR,s,MAXLINE,fp,filename,error); - for (i = 0; i < (int) piCHdom[0][1]; i++) { - for (j = 0; j < (int) piCHdom[1][1]; j++) { - for (k = 0; k < (int) piCHdom[2][1]; k++) { - for (l = 0; l < 64; l = l+1) { - ++numpar; - utils::sfgets(FLERR,s,MAXLINE,fp,filename,error); - if (1 != sscanf(s,"%lg",&piCH[i][j][k][l])) ++cerror; + for (int i = 0; i < (int) piCHdom[0][1]; i++) { + for (int j = 0; j < (int) piCHdom[1][1]; j++) { + for (int k = 0; k < (int) piCHdom[2][1]; k++) { + reader.next_dvector(&piCH[i][j][k][0], 64); } } } - } - // piHH spline + ///////////////////////////////////////////////////////////////////////// + // piHH spline + current_section = "piHH spline"; - utils::sfgets(FLERR,s,MAXLINE,fp,filename,error); - utils::sfgets(FLERR,s,MAXLINE,fp,filename,error); - utils::sfgets(FLERR,s,MAXLINE,fp,filename,error); + limit = reader.next_int(); - ++numpar; - utils::sfgets(FLERR,s,MAXLINE,fp,filename,error); - if (1 != sscanf(s,"%d",&limit)) ++cerror; - - for (i = 0; i < limit/2; i++) { - for (j = 0; j < limit/3; j++) { - ++numpar; - utils::sfgets(FLERR,s,MAXLINE,fp,filename,error); - if (1 != sscanf(s,"%lg",&piHHdom[i][j])) ++cerror; + for (int i = 0; i < limit/2; i++) { + for (int j = 0; j < limit/3; j++) { + piHHdom[i][j] = reader.next_double(); + } } - } - utils::sfgets(FLERR,s,MAXLINE,fp,filename,error); - for (i = 0; i < (int) piHHdom[0][1]; i++) { - for (j = 0; j < (int) piHHdom[1][1]; j++) { - for (k = 0; k < (int) piHHdom[2][1]; k++) { - for (l = 0; l < 64; l = l+1) { - ++numpar; - utils::sfgets(FLERR,s,MAXLINE,fp,filename,error); - if (1 != sscanf(s,"%lg",&piHH[i][j][k][l])) ++cerror; + for (int i = 0; i < (int) piHHdom[0][1]; i++) { + for (int j = 0; j < (int) piHHdom[1][1]; j++) { + for (int k = 0; k < (int) piHHdom[2][1]; k++) { + reader.next_dvector(&piHH[i][j][k][0], 64); } } } - } - // Tij spline + ///////////////////////////////////////////////////////////////////////// + // Tij spline + current_section = "Tij spline"; - utils::sfgets(FLERR,s,MAXLINE,fp,filename,error); - utils::sfgets(FLERR,s,MAXLINE,fp,filename,error); - utils::sfgets(FLERR,s,MAXLINE,fp,filename,error); + limit = reader.next_int(); - ++numpar; - utils::sfgets(FLERR,s,MAXLINE,fp,filename,error); - if (1 != sscanf(s,"%d",&limit)) ++cerror; - - for (i = 0; i < limit/2; i++) { - for (j = 0; j < limit/3; j++) { - ++numpar; - utils::sfgets(FLERR,s,MAXLINE,fp,filename,error); - if (1 != sscanf(s,"%lg",&Tijdom[i][j])) ++cerror; + for (int i = 0; i < limit/2; i++) { + for (int j = 0; j < limit/3; j++) { + Tijdom[i][j] = reader.next_double(); + } } - } - utils::sfgets(FLERR,s,MAXLINE,fp,filename,error); - for (i = 0; i < (int) Tijdom[0][1]; i++) { - for (j = 0; j < (int) Tijdom[1][1]; j++) { - for (k = 0; k < (int) Tijdom[2][1]; k++) { - for (l = 0; l < 64; l = l+1) { - ++numpar; - utils::sfgets(FLERR,s,MAXLINE,fp,filename,error); - if (1 != sscanf(s,"%lg",&Tijc[i][j][k][l])) ++cerror; + for (int i = 0; i < (int) Tijdom[0][1]; i++) { + for (int j = 0; j < (int) Tijdom[1][1]; j++) { + for (int k = 0; k < (int) Tijdom[2][1]; k++) { + reader.next_dvector(&Tijc[i][j][k][0], 64); } } } + } catch (TokenizerException & e) { + std::string msg = fmt::format("ERROR reading {} section in {} file\n" + "REASON: {}\n", + current_section, potential_name, e.what()); + error->one(FLERR, msg); + } catch (FileReaderException & fre) { + error->one(FLERR, fre.what()); + std::string msg = fmt::format("ERROR reading {} section in {} file\n" + "REASON: {}\n", + current_section, potential_name, fre.what()); + error->one(FLERR, msg); } - fclose(fp); - } - - // check for errors parsing spline data - - MPI_Bcast(&cerror,1,MPI_INT,0,world); - if (cerror > 0) { - char msg[128]; - snprintf(msg,128,"Could not parse %d of %d spline data from file %s", - cerror,numpar,filename); - error->all(FLERR,msg); - } - - // store read-in values in arrays - - if (me == 0) { + // store read-in values in arrays // REBO diff --git a/src/MANYBODY/pair_airebo.h b/src/MANYBODY/pair_airebo.h index 04d3fc399f..ab02533cec 100644 --- a/src/MANYBODY/pair_airebo.h +++ b/src/MANYBODY/pair_airebo.h @@ -42,7 +42,7 @@ class PairAIREBO : public Pair { protected: int *map; // 0 (C), 1 (H), or -1 (NULL) for each type - int me,variant; + int variant; int ljflag,torflag; // 0/1 if LJ/Morse,torsion terms included int morseflag; // 1 if Morse instead of LJ for non-bonded diff --git a/src/MANYBODY/pair_bop.cpp b/src/MANYBODY/pair_bop.cpp index 14b0d35a4c..d922cf6d33 100644 --- a/src/MANYBODY/pair_bop.cpp +++ b/src/MANYBODY/pair_bop.cpp @@ -46,10 +46,11 @@ #include "memory.h" #include "error.h" #include "utils.h" +#include "tokenizer.h" +#include "potential_file_reader.h" using namespace LAMMPS_NS; -#define MAXLINE 1024 #define EPSILON 1.0e-6 /* ---------------------------------------------------------------------- */ @@ -294,7 +295,6 @@ void PairBOP::compute(int eflag, int vflag) int nlocal = atom->nlocal; int nall = nlocal + atom->nghost; int cnt1; - MPI_Comm_rank(world,&me); inum = list->inum; ilist = list->ilist; @@ -616,7 +616,6 @@ void PairBOP::coeff(int narg, char **arg) { int i,j; int n = atom->ntypes; - MPI_Comm_rank(world,&me); delete[] map; map = new int[n+1]; @@ -645,7 +644,7 @@ void PairBOP::coeff(int narg, char **arg) read_table(arg[2]); // match element names to BOP word types - if (me == 0) { + if (comm->me == 0) { for (i = 3; i < narg; i++) { if (strcmp(arg[i],"NULL") == 0) { map[i-2] = -1; @@ -659,7 +658,7 @@ void PairBOP::coeff(int narg, char **arg) } MPI_Bcast(&map[1],atom->ntypes,MPI_INT,0,world); - if (me == 0) { + if (comm->me == 0) { if (elements) { for (i = 0; i < bop_types; i++) delete [] elements[i]; delete [] elements; @@ -1137,7 +1136,6 @@ double PairBOP::sigmaBo(int itmp, int jtmp) nlocal = atom->nlocal; ilist = list->ilist; firstneigh = list->firstneigh; - MPI_Comm_rank(world,&me); if(nb_sg==0) { nb_sg=(maxneigh)*(maxneigh/2); @@ -4873,101 +4871,11 @@ double PairBOP::PiBo(int itmp, int jtmp) } /* ---------------------------------------------------------------------- - read BOP potential file + allocate BOP tables ------------------------------------------------------------------------- */ -/* ---------------------------------------------------------------------- */ - -void _noopt PairBOP::read_table(char *filename) +void PairBOP::allocate_tables() { - int i,j,k,n,m; - int buf1,pass; - int nws,ws; - double buf2; - char s[MAXLINE],buf[2]; - - MPI_Comm_rank(world,&me); - if (me == 0) { - FILE *fp = force->open_potential(filename); - if (fp == NULL) { - char str[128]; - snprintf(str,128,"Cannot open BOP potential file %s",filename); - error->one(FLERR,str); - } - utils::sfgets(FLERR,s,MAXLINE,fp,filename,error); // skip first comment line - utils::sfgets(FLERR,s,MAXLINE,fp,filename,error); - sscanf(s,"%d",&bop_types); - elements = new char*[bop_types]; - for(i=0;iall(FLERR,"Incorrect table format check for element types"); - } - sscanf(s,"%d %lf %s",&buf1,&buf2,buf); - n= strlen(buf)+1; - elements[i] = new char[n]; - strcpy(elements[i],buf); - } - nws=0; - ws=1; - utils::sfgets(FLERR,s,MAXLINE,fp,filename,error); - for(j=0;j<(int)strlen(s);j++) { - if(ws==1) { - if(isspace(s[j])) { - ws=1; - } else { - ws=0; - } - } else { - if(isspace(s[j])) { - ws=1; - nws++; - } else { - ws=0; - } - } - } - if (nws==3) { - sscanf(s,"%d %d %d",&nr,&ntheta,&nBOt); - npower=2; - if(ntheta<=10) npower=ntheta; - } else if (nws==2) { - sscanf(s,"%d %d",&nr,&nBOt); - ntheta=0; - npower=3; - } else { - error->one(FLERR,"Unsupported BOP potential file format"); - } - fclose(fp); - npairs=bop_types*(bop_types+1)/2; - } - - MPI_Bcast(&nr,1,MPI_INT,0,world); - MPI_Bcast(&nBOt,1,MPI_INT,0,world); - MPI_Bcast(&ntheta,1,MPI_INT,0,world); - MPI_Bcast(&bop_types,1,MPI_INT,0,world); - MPI_Bcast(&npairs,1,MPI_INT,0,world); - MPI_Bcast(&npower,1,MPI_INT,0,world); - memory->destroy(pi_a); memory->destroy(pro_delta); memory->destroy(pi_delta); @@ -5011,334 +4919,347 @@ void _noopt PairBOP::read_table(char *filename) memory->create(gfunc5,bop_types,bop_types,bop_types,ntheta,"BOP:gfunc5"); memory->create(gfunc6,bop_types,bop_types,bop_types,ntheta,"BOP:gfunc6"); memory->create(gpara,bop_types,bop_types,bop_types,npower+1,"BOP:gpara"); +} - allocate(); - if (me == 0) { - FILE *fp = force->open_potential(filename); - if (fp == NULL) { - char str[128]; - snprintf(str,128,"Cannot open BOP potential file %s",filename); - error->one(FLERR,str); - } - utils::sfgets(FLERR,s,MAXLINE,fp,filename,error); // skip first comment line - for(i=0;icutmax) - cutmax=rcut[i]; - utils::sfgets(FLERR,s,MAXLINE,fp,filename,error); - sscanf(s,"%lf%lf%lf%lf",&sigma_c[i],&sigma_a[i],&pi_c[i],&pi_a[i]); - utils::sfgets(FLERR,s,MAXLINE,fp,filename,error); - sscanf(s,"%lf%lf",&sigma_delta[i],&pi_delta[i]); - utils::sfgets(FLERR,s,MAXLINE,fp,filename,error); - sscanf(s,"%lf%lf%lf",&sigma_f[i],&sigma_k[i],&small3[i]); - } - if(nws==3) { - for(i=0;ime == 0) { + try { + PotentialFileReader reader(lmp, filename, "BOP"); + + bop_types = reader.next_int(); + elements = new char*[bop_types]; + for(int i=0; i < bop_types; i++) { + ValueTokenizer values = reader.next_values(3); + values.next_int(); + values.next_double(); + std::string name = values.next_string(); + + elements[i] = new char[name.length()+1]; + strcpy(elements[i], name.c_str()); + } + + ValueTokenizer values = reader.next_values(2); + int format = values.count(); + + switch(format) { + case 3: + nr = values.next_int(); + ntheta = values.next_int(); + nBOt = values.next_int(); + if(ntheta <= 10) + npower = ntheta; + else + npower = 2; + break; + + case 2: + nr = values.next_int(); + nBOt = values.next_int(); + ntheta = 0; + npower = 3; + break; + + default: + error->one(FLERR,"Unsupported BOP potential file format"); + } + + npairs = bop_types*(bop_types+1)/2; + + allocate_tables(); + allocate(); + + values = reader.next_values(7); + + small1 = values.next_double(); + small2 = values.next_double(); + small3g = values.next_double(); + small4 = values.next_double(); + small5 = values.next_double(); + small6 = values.next_double(); + small7 = values.next_double(); + + for(int i = 0; i < bop_types; i++) { + pi_p[i] = reader.next_double(); + } + + cutmax = 0.0; + + for(int i = 0; i < npairs; i++) { + rcut[i] = reader.next_double(); + if (rcut[i] > cutmax) + cutmax = rcut[i]; + + values = reader.next_values(4); + sigma_c[i] = values.next_double(); + sigma_a[i] = values.next_double(); + pi_c[i] = values.next_double(); + pi_a[i] = values.next_double(); + + values = reader.next_values(2); + sigma_delta[i] = values.next_double(); + pi_delta[i] = values.next_double(); + + values = reader.next_values(3); + sigma_f[i] = values.next_double(); + sigma_k[i] = values.next_double(); + small3[i] = values.next_double(); + } + + if(format == 3) { + for(int i = 0; i < bop_types; i++) + for(int j = 0; j < bop_types; j++) + for(int k = j; k < bop_types; k++) { + if(npower <= 2) { + reader.next_dvector(&gfunc[j][i][k][0], ntheta); + } else { + reader.next_dvector(&gpara[j][i][k][0], npower+1); + } + } + } else { + for(int i = 0; i < bop_types; i++) + for(int j = 0; j < bop_types; j++) + for(int k = 0; k < bop_types; k++) { + reader.next_dvector(&gpara[i][j][k][0], 3); + gpara[j][i][k][3] = 0; + } + } + + for(int i = 0; i < npairs; i++) { + reader.next_dvector(&pRepul[i][0], nr); + } + + for(int i = 0; i < npairs; i++) { + reader.next_dvector(&pBetaS[i][0], nr); + } + + for(int i = 0; i < npairs; i++) { + reader.next_dvector(&pBetaP[i][0], nr); + } + + for(int i = 0; i < npairs; i++) { + reader.next_dvector(&FsigBO[i][0], nBOt); + } + + for(int i = 0; i < bop_types; i++) { + pro_delta[i] = reader.next_double(); + } + + for(int i = 0; i < bop_types; i++) { + pro[i] = reader.next_double(); + } + + for(int i=0;ircutall) + rcutall=rcut[i]; + if(rcut3[i]>rcutall) + rcutall=rcut3[i]; + rcutsq[i]=rcut[i]*rcut[i]; + dr[i]=rcut[i]/((double)nr-1.0); + rdr[i]=1.0/dr[i]; + if (format == 3) { + rcutsq3[i]=rcut3[i]*rcut3[i]; + dr3[i]=rcut3[i]/((double)nr-1.0); + rdr3[i]=1.0/dr3[i]; + } + } + + rctroot=rcutall; + dtheta=2.0/((double)ntheta-1.0); + rdtheta=1.0/dtheta; + dBO=1.0/((double)nBOt-1.0); + rdBO=1.0/(double)dBO; + + for (int i = 0; i < npairs; i++) { + pBetaS1[i][0]=pBetaS[i][1]-pBetaS[i][0]; + pBetaS1[i][1]=0.5*(pBetaS[i][2]-pBetaS[i][0]); + pBetaS1[i][nr-2]=0.5*(pBetaS[i][nr-1]-pBetaS[i][nr-3]); + pBetaS1[i][nr-1]=pBetaS[i][nr-1]-pBetaS[i][nr-2]; + pBetaP1[i][0]=pBetaP[i][1]-pBetaP[i][0]; + pBetaP1[i][1]=0.5*(pBetaP[i][2]-pBetaP[i][0]); + pBetaP1[i][nr-2]=0.5*(pBetaP[i][nr-1]-pBetaP[i][nr-3]); + pBetaP1[i][nr-1]=pBetaP[i][nr-1]-pBetaP[i][nr-2]; + pRepul1[i][0]=pRepul[i][1]-pRepul[i][0]; + pRepul1[i][1]=0.5*(pRepul[i][2]-pRepul[i][0]); + pRepul1[i][nr-2]=0.5*(pRepul[i][nr-1]-pRepul[i][nr-3]); + pRepul1[i][nr-1]=pRepul[i][nr-1]-pRepul[i][nr-2]; + FsigBO1[i][0]=FsigBO[i][1]-FsigBO[i][0]; + FsigBO1[i][1]=0.5*(FsigBO[i][2]-FsigBO[i][0]); + FsigBO1[i][nBOt-2]=0.5*(FsigBO[i][nBOt-1]-FsigBO[i][nBOt-3]); + FsigBO1[i][nBOt-1]=FsigBO[i][nBOt-1]-FsigBO[i][nBOt-2]; + pLong1[i][0]=pLong[i][1]-pLong[i][0]; + pLong1[i][1]=0.5*(pLong[i][2]-pLong[i][0]); + pLong1[i][nBOt-2]=0.5*(pLong[i][nr-1]-pLong[i][nr-3]); + pLong1[i][nBOt-1]=pLong[i][nr-1]-pLong[i][nr-2]; + for (int k = 2; k < nr-2; k++) { + pBetaS1[i][k]=((pBetaS[i][k-2]-pBetaS[i][k+2]) + +8.0*(pBetaS[i][k+1]-pBetaS[i][k-1]))/12.0; + pBetaP1[i][k]=((pBetaP[i][k-2]-pBetaP[i][k+2]) + +8.0*(pBetaP[i][k+1]-pBetaP[i][k-1]))/12.0; + pRepul1[i][k]=((pRepul[i][k-2]-pRepul[i][k+2]) + +8.0*(pRepul[i][k+1]-pRepul[i][k-1]))/12.0; + pLong1[i][k]=((pLong[i][k-2]-pLong[i][k+2]) + +8.0*(pLong[i][k+1]-pLong[i][k-1]))/12.0; + } + for (int k=2; k < nr-2; k++) { + FsigBO1[i][k]=((FsigBO[i][k-2]-FsigBO[i][k+2]) + +8.0*(FsigBO[i][k+1]-FsigBO[i][k-1]))/12.0; + } + for (int k = 0; k < nr-1; k++) { + pBetaS2[i][k]=3.0*(pBetaS[i][k+1]-pBetaS[i][k]) + -2.0*pBetaS1[i][k]-pBetaS1[i][k+1]; + pBetaS3[i][k]=pBetaS1[i][k]+pBetaS1[i][k+1] + -2.0*(pBetaS[i][k+1]-pBetaS[i][k]); + pBetaP2[i][k]=3.0*(pBetaP[i][k+1]-pBetaP[i][k]) + -2.0*pBetaP1[i][k]-pBetaP1[i][k+1]; + pBetaP3[i][k]=pBetaP1[i][k]+pBetaP1[i][k+1] + -2.0*(pBetaP[i][k+1]-pBetaP[i][k]); + pRepul2[i][k]=3.0*(pRepul[i][k+1]-pRepul[i][k]) + -2.0*pRepul1[i][k]-pRepul1[i][k+1]; + pRepul3[i][k]=pRepul1[i][k]+pRepul1[i][k+1] + -2.0*(pRepul[i][k+1]-pRepul[i][k]); + pLong2[i][k]=3.0*(pLong[i][k+1]-pLong[i][k]) + -2.0*pLong1[i][k]-pLong1[i][k+1]; + pLong3[i][k]=pLong1[i][k]+pLong1[i][k+1] + -2.0*(pLong[i][k+1]-pLong[i][k]); + } + + for (int k = 0; k < nBOt-1; k++) { + FsigBO2[i][k]=3.0*(FsigBO[i][k+1]-FsigBO[i][k]) + -2.0*FsigBO1[i][k]-FsigBO1[i][k+1]; + FsigBO3[i][k]=FsigBO1[i][k]+FsigBO1[i][k+1] + -2.0*(FsigBO[i][k+1]-FsigBO[i][k]); + } + + pBetaS2[i][nr-1]=0.0; + pBetaS3[i][nr-1]=0.0; + pBetaP2[i][nr-1]=0.0; + pBetaP3[i][nr-1]=0.0; + pRepul2[i][nr-1]=0.0; + pRepul3[i][nr-1]=0.0; + pLong2[i][nr-1]=0.0; + pLong3[i][nr-1]=0.0; + FsigBO2[i][nBOt-1]=0.0; + FsigBO3[i][nBOt-1]=0.0; + + for (int k=0; k < nr; k++) { + pBetaS4[i][k]=pBetaS1[i][k]/dr[i]; + pBetaS5[i][k]=2.0*pBetaS2[i][k]/dr[i]; + pBetaS6[i][k]=3.0*pBetaS3[i][k]/dr[i]; + pBetaP4[i][k]=pBetaP1[i][k]/dr[i]; + pBetaP5[i][k]=2.0*pBetaP2[i][k]/dr[i]; + pBetaP6[i][k]=3.0*pBetaP3[i][k]/dr[i]; + pRepul4[i][k]=pRepul1[i][k]/dr[i]; + pRepul5[i][k]=2.0*pRepul2[i][k]/dr[i]; + pRepul6[i][k]=3.0*pRepul3[i][k]/dr[i]; + if (format == 3) { + pLong4[i][k]=pLong1[i][k]/dr3[i]; + pLong5[i][k]=2.0*pLong2[i][k]/dr3[i]; + pLong6[i][k]=3.0*pLong3[i][k]/dr3[i]; + } + } + for (int k=0; k < nBOt; k++) { + FsigBO4[i][k]=FsigBO1[i][k]/dBO; + FsigBO5[i][k]=2.0*FsigBO2[i][k]/dBO; + FsigBO6[i][k]=3.0*FsigBO3[i][k]/dBO; + } + } + + if (npower <= 2) { + for (int i = 0; i < bop_types; i++) { + for (int j = 0; j < bop_types; j++) { + for (int k = j; k < bop_types; k++) { + gfunc1[j][i][k][0] = gfunc[j][i][k][1] - gfunc[j][i][k][0]; + gfunc1[j][i][k][1] = 0.5 * (gfunc[j][i][k][2] - gfunc[j][i][k][0]); + gfunc1[j][i][k][ntheta - 2] = 0.5 * (gfunc[j][i][k][ntheta - 1] - gfunc[j][i][k][ntheta - 3]); + gfunc1[j][i][k][ntheta - 1] = 0.5 * (gfunc[j][i][k][ntheta - 1] - gfunc[j][i][k][ntheta - 2]); + + for (int m = 2; m < ntheta - 2; m++) { + gfunc1[j][i][k][m] = ((gfunc[j][i][k][m - 2] - gfunc[j][i][k][m + 2]) + + 8.0 * (gfunc[j][i][k][m + 1] - gfunc[j][i][k][m + 1] - gfunc[j][i][k][m - 1])) / + 12.0; + } + + for (int m = 0; m < ntheta - 1; m++) { + gfunc2[j][i][k][m] = 3.0 * (gfunc[j][i][k][m + 1] - gfunc[j][i][k][m]) - + 2.0 * gfunc1[j][i][k][m] - gfunc1[j][i][k][m + 1]; + gfunc3[j][i][k][m] = gfunc1[j][i][k][m] + gfunc1[j][i][k][m + 1] - + 2.0 * (gfunc[j][i][k][m + 1] - gfunc[j][i][k][m]); + } + + gfunc2[j][i][k][ntheta - 1] = 0.0; + gfunc3[j][i][k][ntheta - 1] = 0.0; + + for (int m = 0; m < ntheta; m++) { + gfunc4[j][i][k][ntheta - 1] = gfunc1[j][i][k][m] / dtheta; + gfunc5[j][i][k][ntheta - 1] = 2.0 * gfunc2[j][i][k][m] / dtheta; + gfunc6[j][i][k][ntheta - 1] = 3.0 * gfunc3[j][i][k][m] / dtheta; + } + } + } + } + } + + for (int i = 0; i < bop_types; i++) { + for (int j = 0; j < bop_types; j++) { + for (int k = 0; k < j; k++) { + if (npower <= 2) { + for (int n = 0; n < ntheta; n++) { + gfunc[j][i][k][n] = gfunc[k][i][j][n]; + gfunc1[j][i][k][n] = gfunc1[k][i][j][n]; + gfunc2[j][i][k][n] = gfunc2[k][i][j][n]; + gfunc3[j][i][k][n] = gfunc3[k][i][j][n]; + gfunc4[j][i][k][n] = gfunc4[k][i][j][n]; + gfunc5[j][i][k][n] = gfunc5[k][i][j][n]; + gfunc6[j][i][k][n] = gfunc6[k][i][j][n]; } } else { - if(npower==3) { - utils::sfgets(FLERR,s,MAXLINE,fp,filename,error); - sscanf(s,"%lf%lf%lf%lf",&gpara[j][i][k][0],&gpara[j][i][k][1],&gpara[j][i][k][2],&gpara[j][i][k][3]); + for (int n = 0; n < npower + 1; n++) { + gpara[j][i][k][n] = gpara[k][i][j][n]; } - else if(npower==4) { - utils::sfgets(FLERR,s,MAXLINE,fp,filename,error); - sscanf(s,"%lf%lf%lf%lf%lf",&gpara[j][i][k][0],&gpara[j][i][k][1],&gpara[j][i][k][2],&gpara[j][i][k][3],&gpara[j][i][k][4]); - } - else if(npower==5) { - utils::sfgets(FLERR,s,MAXLINE,fp,filename,error); - sscanf(s,"%lf%lf%lf%lf%lf",&gpara[j][i][k][0],&gpara[j][i][k][1],&gpara[j][i][k][2],&gpara[j][i][k][3],&gpara[j][i][k][4]); - utils::sfgets(FLERR,s,MAXLINE,fp,filename,error); - sscanf(s,"%lf",&gpara[j][i][k][5]); - } - else if(npower==6) { - utils::sfgets(FLERR,s,MAXLINE,fp,filename,error); - sscanf(s,"%lf%lf%lf%lf%lf",&gpara[j][i][k][0],&gpara[j][i][k][1],&gpara[j][i][k][2],&gpara[j][i][k][3],&gpara[j][i][k][4]); - utils::sfgets(FLERR,s,MAXLINE,fp,filename,error); - sscanf(s,"%lf%lf",&gpara[j][i][k][5],&gpara[j][i][k][6]); - } - else if(npower==7) { - utils::sfgets(FLERR,s,MAXLINE,fp,filename,error); - sscanf(s,"%lf%lf%lf%lf%lf",&gpara[j][i][k][0],&gpara[j][i][k][1],&gpara[j][i][k][2],&gpara[j][i][k][3],&gpara[j][i][k][4]); - utils::sfgets(FLERR,s,MAXLINE,fp,filename,error); - sscanf(s,"%lf%lf%lf",&gpara[j][i][k][5],&gpara[j][i][k][6],&gpara[j][i][k][7]); - } - else if(npower==8) { - utils::sfgets(FLERR,s,MAXLINE,fp,filename,error); - sscanf(s,"%lf%lf%lf%lf%lf",&gpara[j][i][k][0],&gpara[j][i][k][1],&gpara[j][i][k][2],&gpara[j][i][k][3],&gpara[j][i][k][4]); - utils::sfgets(FLERR,s,MAXLINE,fp,filename,error); - sscanf(s,"%lf%lf%lf%lf",&gpara[j][i][k][5],&gpara[j][i][k][6],&gpara[j][i][k][7],&gpara[j][i][k][8]); - } - else if(npower==9) { - utils::sfgets(FLERR,s,MAXLINE,fp,filename,error); - sscanf(s,"%lf%lf%lf%lf%lf",&gpara[j][i][k][0],&gpara[j][i][k][1],&gpara[j][i][k][2],&gpara[j][i][k][3],&gpara[j][i][k][4]); - utils::sfgets(FLERR,s,MAXLINE,fp,filename,error); - sscanf(s,"%lf%lf%lf%lf%lf",&gpara[j][i][k][5],&gpara[j][i][k][6],&gpara[j][i][k][7],&gpara[j][i][k][8],&gpara[j][i][k][9]); - } - else if(npower==10) { - utils::sfgets(FLERR,s,MAXLINE,fp,filename,error); - sscanf(s,"%lf%lf%lf%lf%lf",&gpara[j][i][k][0],&gpara[j][i][k][1],&gpara[j][i][k][2],&gpara[j][i][k][3],&gpara[j][i][k][4]); - utils::sfgets(FLERR,s,MAXLINE,fp,filename,error); - sscanf(s,"%lf%lf%lf%lf%lf",&gpara[j][i][k][5],&gpara[j][i][k][6],&gpara[j][i][k][7],&gpara[j][i][k][8],&gpara[j][i][k][9]); - utils::sfgets(FLERR,s,MAXLINE,fp,filename,error); - sscanf(s,"%lf",&gpara[j][i][k][10]); - } - } - } - } else { - for(i=0;ircutall) - rcutall=rcut[i]; - if(rcut3[i]>rcutall) - rcutall=rcut3[i]; - rcutsq[i]=rcut[i]*rcut[i]; - dr[i]=rcut[i]/((double)nr-1.0); - rdr[i]=1.0/dr[i]; - if (nws==3) { - rcutsq3[i]=rcut3[i]*rcut3[i]; - dr3[i]=rcut3[i]/((double)nr-1.0); - rdr3[i]=1.0/dr3[i]; - } - } - rctroot=rcutall; - dtheta=2.0/((double)ntheta-1.0); - rdtheta=1.0/dtheta; - dBO=1.0/((double)nBOt-1.0); - rdBO=1.0/(double)dBO; - for(i=0;ione(FLERR, e.what()); + } catch (FileReaderException & fre) { + error->one(FLERR, fre.what()); } - for(i=0;ime != 0){ + allocate_tables(); + allocate(); + } + MPI_Bcast(&rdBO,1,MPI_DOUBLE,0,world); MPI_Bcast(&dBO,1,MPI_DOUBLE,0,world); MPI_Bcast(&rdtheta,1,MPI_DOUBLE,0,world); diff --git a/src/MANYBODY/pair_bop.h b/src/MANYBODY/pair_bop.h index 6c4b255d25..2d6962e27c 100644 --- a/src/MANYBODY/pair_bop.h +++ b/src/MANYBODY/pair_bop.h @@ -41,7 +41,6 @@ class PairBOP : public Pair { double memory_usage(); private: - int me; int maxneigh; // maximum size of neighbor list on this processor int maxneigh3; // maximum size of neighbor list on this processor int update_list; // check for changing maximum size of neighbor list @@ -207,6 +206,7 @@ class PairBOP : public Pair { void read_table(char *); void allocate(); + void allocate_tables(); void create_pi(int); void create_sigma(int); void destroy_pi(); diff --git a/src/MANYBODY/pair_comb.cpp b/src/MANYBODY/pair_comb.cpp index e2e5e3cefd..201b325bf3 100644 --- a/src/MANYBODY/pair_comb.cpp +++ b/src/MANYBODY/pair_comb.cpp @@ -594,7 +594,7 @@ void PairComb::read_file(char *file) while((line = reader.next_line(NPARAMS_PER_LINE))) { try { - ValueTokenizer values(line," \t\n\r\f"); + ValueTokenizer values(line); std::string iname = values.next_string(); std::string jname = values.next_string(); diff --git a/src/MANYBODY/pair_comb3.cpp b/src/MANYBODY/pair_comb3.cpp index 8a010df55d..a71edccab0 100644 --- a/src/MANYBODY/pair_comb3.cpp +++ b/src/MANYBODY/pair_comb3.cpp @@ -312,84 +312,45 @@ double PairComb3::init_one(int i, int j) void PairComb3::read_lib() { - const unsigned int MAXLIB = 1024; int i,j,k,l,m; int ii,jj,kk,ll,mm,iii; - char s[MAXLIB]; // open library file on proc 0 if (comm->me == 0) { - const char filename[] = "lib.comb3"; - FILE *fp = force->open_potential(filename); - if (fp == NULL) error->one(FLERR,"Cannot open COMB3 lib.comb3 file"); - try { - // read and store at the same time - utils::sfgets(FLERR, s, MAXLIB, fp, filename, error); - - utils::sfgets(FLERR, s, MAXLIB, fp, filename, error); - ValueTokenizer values(s, " \t\n\r\f"); - - ccutoff[0] = values.next_double(); - ccutoff[1] = values.next_double(); - ccutoff[2] = values.next_double(); - ccutoff[3] = values.next_double(); - ccutoff[4] = values.next_double(); - ccutoff[5] = values.next_double(); - - utils::sfgets(FLERR, s, MAXLIB, fp, filename, error); - values = ValueTokenizer(s, " \t\n\r\f"); - - ch_a[0] = values.next_double(); - ch_a[1] = values.next_double(); - ch_a[2] = values.next_double(); - ch_a[3] = values.next_double(); - ch_a[4] = values.next_double(); - ch_a[5] = values.next_double(); - ch_a[6] = values.next_double(); - - utils::sfgets(FLERR, s, MAXLIB, fp, filename, error); - values = ValueTokenizer(s, " \t\n\r\f"); + PotentialFileReader reader(lmp, "lib.comb3", "COMB3"); + reader.next_dvector(ccutoff, 6); + reader.next_dvector(ch_a, 7); + ValueTokenizer values = reader.next_values(3); nsplpcn = values.next_int(); nsplrad = values.next_int(); nspltor = values.next_int(); - utils::sfgets(FLERR, s, MAXLIB, fp, filename, error); - values = ValueTokenizer(s, " \t\n\r\f"); - + values = reader.next_values(3); maxx = values.next_int(); maxy = values.next_int(); maxz = values.next_int(); - utils::sfgets(FLERR,s,MAXLIB,fp,filename,error); - values = ValueTokenizer(s, " \t\n\r\f"); - + values = reader.next_values(3); maxxc = values.next_int(); maxyc = values.next_int(); maxconj = values.next_int(); for (l = 0; l < nsplpcn; l++) { - utils::sfgets(FLERR, s, MAXLIB, fp, filename, error); - values = ValueTokenizer(s, " \t\n\r\f"); + values = reader.next_values(3); values.skip(1); - maxxcn[l] = values.next_int(); vmaxxcn[l] = values.next_double(); dvmaxxcn[l] = values.next_double(); } - utils::sfgets(FLERR, s, MAXLIB, fp, filename, error); - values = ValueTokenizer(s, " \t\n\r\f"); - - ntab = values.next_int(); + ntab = reader.next_int(); for (i = 0; i < (ntab + 1); i++){ - utils::sfgets(FLERR, s, MAXLIB, fp, filename, error); - values = ValueTokenizer(s, " \t\n\r\f"); + values = reader.next_values(4); values.skip(1); - pang[i] = values.next_double(); dpang[i] = values.next_double(); ddpang[i] = values.next_double(); @@ -399,8 +360,7 @@ void PairComb3::read_lib() for (i = 0; i < (maxx + 1); i++) for (j = 0; j < (maxy + 1); j++) for (k = 0; k < (maxz + 1); k++) { - utils::sfgets(FLERR, s, MAXLIB, fp, filename, error); - values = ValueTokenizer(s, " \t\n\r\f"); + values = reader.next_values(8); ll = values.next_int() - 1; ii = values.next_int(); @@ -416,8 +376,7 @@ void PairComb3::read_lib() for (i = 0; i < maxx; i++) for (j = 0; j < maxy; j++) for (k = 0; k < maxz; k++) { - utils::sfgets(FLERR, s, MAXLIB, fp, filename, error); - values = ValueTokenizer(s, " \t\n\r\f"); + values = reader.next_values(4); ll = values.next_int()-1; ii = values.next_int(); @@ -425,13 +384,8 @@ void PairComb3::read_lib() kk = values.next_int(); for(iii = 0; iii < 2; iii++) { - utils::sfgets(FLERR, s, MAXLIB, fp, filename, error); - values = ValueTokenizer(s, " \t\n\r\f"); - - for(m = 0; m < 32 ; m++) { - mm = iii*32 + m; - pcn_cubs[ll][ii][jj][kk][mm] = values.next_double(); - } + mm = iii*32; + reader.next_dvector(&pcn_cubs[ll][ii][jj][kk][mm], 32); } } @@ -439,8 +393,7 @@ void PairComb3::read_lib() for (i = 0; i < (maxxc + 1); i++) for (j = 0; j < (maxyc + 1); j++) for (k = 0; k < maxconj; k++) { - utils::sfgets(FLERR, s, MAXLIB, fp, filename, error); - values = ValueTokenizer(s, " \t\n\r\f"); + values = reader.next_values(8); ll = values.next_int() - 1; ii = values.next_int(); @@ -456,8 +409,7 @@ void PairComb3::read_lib() for (i = 0; i < maxxc; i++) for (j = 0; j < maxyc; j++) for (k = 0; k < (maxconj - 1); k++) { - utils::sfgets(FLERR, s, MAXLIB, fp, filename, error); - values = ValueTokenizer(s, " \t\n\r\f"); + values = reader.next_values(4); ll = values.next_int() - 1; ii = values.next_int(); @@ -465,13 +417,8 @@ void PairComb3::read_lib() kk = values.next_int() - 1; for (iii = 0; iii < 2; iii++) { - utils::sfgets(FLERR, s, MAXLIB, fp, filename, error); - values = ValueTokenizer(s, " \t\n\r\f"); - - for(m = 0; m < 32 ; m++){ - mm = iii * 32 + m; - rad_spl[ll][ii][jj][kk][mm] = values.next_double(); - } + mm = iii * 32; + reader.next_dvector(&rad_spl[ll][ii][jj][kk][mm], 32); } } @@ -479,8 +426,7 @@ void PairComb3::read_lib() for (i=0; ione(FLERR, fre.what()); } catch (TokenizerException & e) { - fclose(fp); error->one(FLERR, e.what()); } } @@ -594,7 +535,7 @@ void PairComb3::read_file(char *file) while((line = reader.next_line(NPARAMS_PER_LINE))) { try { - ValueTokenizer values(line, " \t\n\r\f"); + ValueTokenizer values(line); std::string iname = values.next_string(); std::string jname = values.next_string(); diff --git a/src/MANYBODY/pair_eam.cpp b/src/MANYBODY/pair_eam.cpp index 0013a3271d..ec409d1786 100644 --- a/src/MANYBODY/pair_eam.cpp +++ b/src/MANYBODY/pair_eam.cpp @@ -473,13 +473,11 @@ void PairEAM::read_file(char *filename) reader.skip_line(); - line = reader.next_line(2); - ValueTokenizer values(line); + ValueTokenizer values = reader.next_values(2); values.next_int(); // ignore file->mass = values.next_double(); - line = reader.next_line(5); - values = ValueTokenizer(line); + values = reader.next_values(5); file->nrho = values.next_int(); file->drho = values.next_double(); file->nr = values.next_int(); @@ -493,9 +491,9 @@ void PairEAM::read_file(char *filename) memory->create(file->rhor, (file->nr+1), "pair:rhor"); memory->create(file->zr, (file->nr+1), "pair:zr"); - reader.next_dvector(file->nrho, &file->frho[1]); - reader.next_dvector(file->nr, &file->zr[1]); - reader.next_dvector(file->nr, &file->rhor[1]); + reader.next_dvector(&file->frho[1], file->nrho); + reader.next_dvector(&file->zr[1], file->nr); + reader.next_dvector(&file->rhor[1], file->nr); } catch (TokenizerException & e) { error->one(FLERR, e.what()); } diff --git a/src/MANYBODY/pair_eam_alloy.cpp b/src/MANYBODY/pair_eam_alloy.cpp index 65ed9b7d2f..d164682e9e 100644 --- a/src/MANYBODY/pair_eam_alloy.cpp +++ b/src/MANYBODY/pair_eam_alloy.cpp @@ -122,15 +122,12 @@ void PairEAMAlloy::read_file(char *filename) PotentialFileReader reader(lmp, filename, "EAM"); try { - char * line = nullptr; - reader.skip_line(); reader.skip_line(); reader.skip_line(); // extract element names from nelements line - line = reader.next_line(1); - ValueTokenizer values(line); + ValueTokenizer values = reader.next_values(1); file->nelements = values.next_int(); if (values.count() != file->nelements + 1) @@ -146,8 +143,7 @@ void PairEAMAlloy::read_file(char *filename) // - line = reader.next_line(5); - values = ValueTokenizer(line); + values = reader.next_values(5); file->nrho = values.next_int(); file->drho = values.next_double(); file->nr = values.next_int(); @@ -163,18 +159,17 @@ void PairEAMAlloy::read_file(char *filename) memory->create(file->z2r, file->nelements, file->nelements, file->nr + 1, "pair:z2r"); for (int i = 0; i < file->nelements; i++) { - line = reader.next_line(2); - values = ValueTokenizer(line); + values = reader.next_values(2); values.next_int(); // ignore file->mass[i] = values.next_double(); - reader.next_dvector(file->nrho, &file->frho[i][1]); - reader.next_dvector(file->nr, &file->rhor[i][1]); + reader.next_dvector(&file->frho[i][1], file->nrho); + reader.next_dvector(&file->rhor[i][1], file->nr); } for (int i = 0; i < file->nelements; i++) { for (int j = 0; j <= i; j++) { - reader.next_dvector(file->nr, &file->z2r[i][j][1]); + reader.next_dvector(&file->z2r[i][j][1], file->nr); } } } catch (TokenizerException & e) { diff --git a/src/MANYBODY/pair_eam_cd.cpp b/src/MANYBODY/pair_eam_cd.cpp index 099ffd77cd..076f6d5e7d 100644 --- a/src/MANYBODY/pair_eam_cd.cpp +++ b/src/MANYBODY/pair_eam_cd.cpp @@ -514,7 +514,7 @@ void PairEAMCD::read_h_coeff(char *filename) strcpy(line, nextline); } - ValueTokenizer values(line, " \t\n\r\f"); + ValueTokenizer values(line); int degree = values.next_int(); nhcoeff = degree+1; diff --git a/src/MANYBODY/pair_eam_fs.cpp b/src/MANYBODY/pair_eam_fs.cpp index fe4fa95268..5d2339c4b5 100644 --- a/src/MANYBODY/pair_eam_fs.cpp +++ b/src/MANYBODY/pair_eam_fs.cpp @@ -129,8 +129,7 @@ void PairEAMFS::read_file(char *filename) reader.skip_line(); // extract element names from nelements line - line = reader.next_line(1); - ValueTokenizer values(line); + ValueTokenizer values = reader.next_values(1); file->nelements = values.next_int(); if (values.count() != file->nelements + 1) @@ -146,8 +145,7 @@ void PairEAMFS::read_file(char *filename) // - line = reader.next_line(5); - values = ValueTokenizer(line); + values = reader.next_values(5); file->nrho = values.next_int(); file->drho = values.next_double(); file->nr = values.next_int(); @@ -163,21 +161,20 @@ void PairEAMFS::read_file(char *filename) memory->create(file->z2r, file->nelements, file->nelements, file->nr + 1, "pair:z2r"); for (int i = 0; i < file->nelements; i++) { - line = reader.next_line(2); - values = ValueTokenizer(line); + values = reader.next_values(2); values.next_int(); // ignore file->mass[i] = values.next_double(); - reader.next_dvector(file->nrho, &file->frho[i][1]); + reader.next_dvector(&file->frho[i][1], file->nrho); for (int j = 0; j < file->nelements; j++) { - reader.next_dvector(file->nr, &file->rhor[i][j][1]); + reader.next_dvector(&file->rhor[i][j][1], file->nr); } } for (int i = 0; i < file->nelements; i++) { for (int j = 0; j <= i; j++) { - reader.next_dvector(file->nr, &file->z2r[i][j][1]); + reader.next_dvector(&file->z2r[i][j][1], file->nr); } } } catch (TokenizerException & e) { diff --git a/src/MANYBODY/pair_eim.cpp b/src/MANYBODY/pair_eim.cpp index 6b668eeade..0d552caebc 100644 --- a/src/MANYBODY/pair_eim.cpp +++ b/src/MANYBODY/pair_eim.cpp @@ -29,6 +29,7 @@ #include "utils.h" #include "tokenizer.h" #include "potential_file_reader.h" +#include "fmt/format.h" using namespace LAMMPS_NS; @@ -1059,9 +1060,7 @@ EIMPotentialFileReader::EIMPotentialFileReader(LAMMPS * lmp, const std::string & FILE * fp = force->open_potential(filename.c_str()); if (fp == NULL) { - char str[128]; - snprintf(str, 128, "cannot open EIM potential file %s", filename.c_str()); - error->one(FLERR, str); + error->one(FLERR, fmt::format("cannot open EIM potential file {}", filename)); } parse(fp); @@ -1141,7 +1140,7 @@ void EIMPotentialFileReader::parse(FILE * fp) bool found_global = false; while((line = next_line(fp))) { - ValueTokenizer values(line, " \t\r\n\f"); + ValueTokenizer values(line); std::string type = values.next_string(); if (type == "global:") { diff --git a/src/MANYBODY/pair_gw.cpp b/src/MANYBODY/pair_gw.cpp index ba6ceac3b2..e9604523b5 100644 --- a/src/MANYBODY/pair_gw.cpp +++ b/src/MANYBODY/pair_gw.cpp @@ -380,7 +380,7 @@ void PairGW::read_file(char *file) while((line = reader.next_line(NPARAMS_PER_LINE))) { try { - ValueTokenizer values(line, " \t\n\r\f"); + ValueTokenizer values(line); std::string iname = values.next_string(); std::string jname = values.next_string(); diff --git a/src/MANYBODY/pair_gw_zbl.cpp b/src/MANYBODY/pair_gw_zbl.cpp index f6eafb4fac..96fc742b42 100644 --- a/src/MANYBODY/pair_gw_zbl.cpp +++ b/src/MANYBODY/pair_gw_zbl.cpp @@ -75,7 +75,7 @@ void PairGWZBL::read_file(char *file) while((line = reader.next_line(NPARAMS_PER_LINE))) { try { - ValueTokenizer values(line, " \t\n\r\f"); + ValueTokenizer values(line); std::string iname = values.next_string(); std::string jname = values.next_string(); diff --git a/src/MANYBODY/pair_nb3b_harmonic.cpp b/src/MANYBODY/pair_nb3b_harmonic.cpp index a7be1ef2d4..7491c375db 100644 --- a/src/MANYBODY/pair_nb3b_harmonic.cpp +++ b/src/MANYBODY/pair_nb3b_harmonic.cpp @@ -296,7 +296,7 @@ void PairNb3bHarmonic::read_file(char *file) while((line = reader.next_line(NPARAMS_PER_LINE))) { try { - ValueTokenizer values(line, " \t\n\r\f"); + ValueTokenizer values(line); std::string iname = values.next_string(); std::string jname = values.next_string(); diff --git a/src/MANYBODY/pair_polymorphic.cpp b/src/MANYBODY/pair_polymorphic.cpp index 8a4a169e85..a3f6d08522 100644 --- a/src/MANYBODY/pair_polymorphic.cpp +++ b/src/MANYBODY/pair_polymorphic.cpp @@ -571,8 +571,7 @@ void PairPolymorphic::read_file(char *file) try { reader = new PotentialFileReader(lmp, file, "polymorphic"); - char * line = reader->next_line(2); - ValueTokenizer values(line); + ValueTokenizer values = reader->next_values(2); int ntypes = values.next_int(); @@ -585,8 +584,7 @@ void PairPolymorphic::read_file(char *file) match = new int[nelements]; for (int i = 0; i < nelements; i++) { - line = reader->next_line(3); - values = ValueTokenizer(line); + values = reader->next_values(3); values.next_double(); // atomic number values.next_double(); // atomic mass std::string name = values.next_string(); @@ -602,9 +600,8 @@ void PairPolymorphic::read_file(char *file) // sizes // Note: the format of this line has changed between the // 2015-06-06 and 2015-12-09 versions of the pair style. - line = reader->next_line(4); try { - values = ValueTokenizer(line); + values = reader->next_values(4); nr = ng = nx = 0; nr = values.next_int(); ng = values.next_int(); @@ -625,8 +622,7 @@ void PairPolymorphic::read_file(char *file) for (int i = 0; i < npair; i++) { PairParameters & p = pairParameters[i]; - line = reader->next_line(2); - values = ValueTokenizer(line); + values = reader->next_values(2); p.cut = values.next_double(); p.cutsq = p.cut*p.cut; p.xi = values.next_double(); @@ -658,7 +654,7 @@ void PairPolymorphic::read_file(char *file) for (int i = 0; i < npair; i++) { // U PairParameters & p = pairParameters[i]; if (comm->me == 0) { - reader->next_dvector(nr, singletable); + reader->next_dvector(singletable, nr); } MPI_Bcast(singletable,nr,MPI_DOUBLE,0,world); p.U = new tabularFunction(nr,0.0,p.cut); @@ -667,7 +663,7 @@ void PairPolymorphic::read_file(char *file) for (int i = 0; i < npair; i++) { // V PairParameters & p = pairParameters[i]; if (comm->me == 0) { - reader->next_dvector(nr, singletable); + reader->next_dvector(singletable, nr); } MPI_Bcast(singletable,nr,MPI_DOUBLE,0,world); p.V = new tabularFunction(nr,0.0,p.cut); @@ -676,7 +672,7 @@ void PairPolymorphic::read_file(char *file) for (int i = 0; i < npair; i++) { // W PairParameters & p = pairParameters[i]; if (comm->me == 0) { - reader->next_dvector(nr, singletable); + reader->next_dvector(singletable, nr); } MPI_Bcast(singletable,nr,MPI_DOUBLE,0,world); p.W = new tabularFunction(nr,0.0,p.cut); @@ -693,7 +689,7 @@ void PairPolymorphic::read_file(char *file) if (eta != 3) { for (int j = 0; j < nelements; j++) { // P if (comm->me == 0) { - reader->next_dvector(nr, singletable); + reader->next_dvector(singletable, nr); } MPI_Bcast(singletable,nr,MPI_DOUBLE,0,world); for (int i = 0; i < nelements; i++) { @@ -705,7 +701,7 @@ void PairPolymorphic::read_file(char *file) for (int j = 0; j < nelements-1; j++) { // P for (int k = j+1; k < nelements; k++) { if (comm->me == 0) { - reader->next_dvector(nr, singletable); + reader->next_dvector(singletable, nr); } MPI_Bcast(singletable,nr,MPI_DOUBLE,0,world); for (int i = 0; i < nelements; i++) { @@ -723,7 +719,7 @@ void PairPolymorphic::read_file(char *file) for (int i = 0; i < ntriple; i++) { // P TripletParameters & p = tripletParameters[i]; if (comm->me == 0) { - reader->next_dvector(nr, singletable); + reader->next_dvector(singletable, nr); } MPI_Bcast(singletable,nr,MPI_DOUBLE,0,world); p.P = new tabularFunction(nr,-cutmax,cutmax); @@ -735,7 +731,7 @@ void PairPolymorphic::read_file(char *file) for (int i = 0; i < ntriple; i++) { // G TripletParameters & p = tripletParameters[i]; if (comm->me == 0) { - reader->next_dvector(ng, singletable); + reader->next_dvector(singletable, ng); } MPI_Bcast(singletable,ng,MPI_DOUBLE,0,world); p.G = new tabularFunction(ng,-1.0,1.0); @@ -746,7 +742,7 @@ void PairPolymorphic::read_file(char *file) for (int i = 0; i < npair; i++) { // F PairParameters & p = pairParameters[i]; if (comm->me == 0) { - reader->next_dvector(nx, singletable); + reader->next_dvector(singletable, nx); } MPI_Bcast(singletable,nx,MPI_DOUBLE,0,world); p.F = new tabularFunction(nx,0.0,maxX); diff --git a/src/MANYBODY/pair_sw.cpp b/src/MANYBODY/pair_sw.cpp index 5956431b4e..0aed2ec68b 100644 --- a/src/MANYBODY/pair_sw.cpp +++ b/src/MANYBODY/pair_sw.cpp @@ -360,7 +360,7 @@ void PairSW::read_file(char *file) while((line = reader.next_line(NPARAMS_PER_LINE))) { try { - ValueTokenizer values(line, " \t\n\r\f"); + ValueTokenizer values(line); std::string iname = values.next_string(); std::string jname = values.next_string(); diff --git a/src/MANYBODY/pair_tersoff.cpp b/src/MANYBODY/pair_tersoff.cpp index 3b9de81992..4ba7471e60 100644 --- a/src/MANYBODY/pair_tersoff.cpp +++ b/src/MANYBODY/pair_tersoff.cpp @@ -405,7 +405,7 @@ void PairTersoff::read_file(char *file) while((line = reader.next_line(NPARAMS_PER_LINE))) { try { - ValueTokenizer values(line, " \t\n\r\f"); + ValueTokenizer values(line); std::string iname = values.next_string(); std::string jname = values.next_string(); diff --git a/src/MANYBODY/pair_tersoff_mod.cpp b/src/MANYBODY/pair_tersoff_mod.cpp index 18a58ae5b4..441ba6f21e 100644 --- a/src/MANYBODY/pair_tersoff_mod.cpp +++ b/src/MANYBODY/pair_tersoff_mod.cpp @@ -58,7 +58,7 @@ void PairTersoffMOD::read_file(char *file) while((line = reader.next_line(NPARAMS_PER_LINE))) { try { - ValueTokenizer values(line, " \t\n\r\f"); + ValueTokenizer values(line); std::string iname = values.next_string(); std::string jname = values.next_string(); diff --git a/src/MANYBODY/pair_tersoff_mod_c.cpp b/src/MANYBODY/pair_tersoff_mod_c.cpp index 2ccd31bad2..33e88c70b8 100644 --- a/src/MANYBODY/pair_tersoff_mod_c.cpp +++ b/src/MANYBODY/pair_tersoff_mod_c.cpp @@ -49,7 +49,7 @@ void PairTersoffMODC::read_file(char *file) while((line = reader.next_line(NPARAMS_PER_LINE))) { try { - ValueTokenizer values(line, " \t\n\r\f"); + ValueTokenizer values(line); std::string iname = values.next_string(); std::string jname = values.next_string(); diff --git a/src/MANYBODY/pair_tersoff_zbl.cpp b/src/MANYBODY/pair_tersoff_zbl.cpp index 5cdeb3daff..2b464061ca 100644 --- a/src/MANYBODY/pair_tersoff_zbl.cpp +++ b/src/MANYBODY/pair_tersoff_zbl.cpp @@ -76,7 +76,7 @@ void PairTersoffZBL::read_file(char *file) while((line = reader.next_line(NPARAMS_PER_LINE))) { try { - ValueTokenizer values(line, " \t\n\r\f"); + ValueTokenizer values(line); std::string iname = values.next_string(); std::string jname = values.next_string(); diff --git a/src/MANYBODY/pair_vashishta.cpp b/src/MANYBODY/pair_vashishta.cpp index 68196e3a6a..37fea2582f 100644 --- a/src/MANYBODY/pair_vashishta.cpp +++ b/src/MANYBODY/pair_vashishta.cpp @@ -366,7 +366,7 @@ void PairVashishta::read_file(char *file) while((line = reader.next_line(NPARAMS_PER_LINE))) { try { - ValueTokenizer values(line, " \t\n\r\f"); + ValueTokenizer values(line); std::string iname = values.next_string(); std::string jname = values.next_string(); diff --git a/src/MOLECULE/angle_table.cpp b/src/MOLECULE/angle_table.cpp index b6439084a6..4890a11975 100644 --- a/src/MOLECULE/angle_table.cpp +++ b/src/MOLECULE/angle_table.cpp @@ -29,14 +29,15 @@ #include "memory.h" #include "error.h" #include "utils.h" -#include "utils.h" +#include "tokenizer.h" +#include "table_file_reader.h" +#include "fmt/format.h" using namespace LAMMPS_NS; using namespace MathConst; enum{LINEAR,SPLINE}; -#define MAXLINE 1024 #define SMALL 0.001 #define TINY 1.E-10 @@ -381,61 +382,45 @@ void AngleTable::free_table(Table *tb) void AngleTable::read_table(Table *tb, char *file, char *keyword) { - char line[MAXLINE]; + TableFileReader reader(lmp, file, "angle"); - // open file + char * line = reader.find_section_start(keyword); - FILE *fp = force->open_potential(file); - if (fp == NULL) { - char str[128]; - snprintf(str,128,"Cannot open file %s",file); - error->one(FLERR,str); - } - - // loop until section found with matching keyword - - while (1) { - if (fgets(line,MAXLINE,fp) == NULL) - error->one(FLERR,"Did not find keyword in table file"); - if (strspn(line," \t\n") == strlen(line)) continue; // blank line - if (line[0] == '#') continue; // comment - char *word = strtok(line," \t\n\r"); - if (strcmp(word,keyword) == 0) break; // matching keyword - utils::sfgets(FLERR,line,MAXLINE,fp,file,error); // no match, skip section - param_extract(tb,line); - utils::sfgets(FLERR,line,MAXLINE,fp,file,error); - for (int i = 0; i < tb->ninput; i++) - utils::sfgets(FLERR,line,MAXLINE,fp,file,error); + if (!line) { + error->one(FLERR,"Did not find keyword in table file"); } // read args on 2nd line of section // allocate table arrays for file values - utils::sfgets(FLERR,line,MAXLINE,fp,file,error); - param_extract(tb,line); - memory->create(tb->afile,tb->ninput,"angle:afile"); - memory->create(tb->efile,tb->ninput,"angle:efile"); - memory->create(tb->ffile,tb->ninput,"angle:ffile"); + line = reader.next_line(); + param_extract(tb, line); + memory->create(tb->afile, tb->ninput, "angle:afile"); + memory->create(tb->efile, tb->ninput, "angle:efile"); + memory->create(tb->ffile, tb->ninput, "angle:ffile"); // read a,e,f table values from file int cerror = 0; - utils::sfgets(FLERR,line,MAXLINE,fp,file,error); + reader.skip_line(); for (int i = 0; i < tb->ninput; i++) { - utils::sfgets(FLERR,line,MAXLINE,fp,file,error); - if (3 != sscanf(line,"%*d %lg %lg %lg", - &tb->afile[i],&tb->efile[i],&tb->ffile[i])) ++cerror; + line = reader.next_line(4); + try { + ValueTokenizer values(line); + values.next_int(); + tb->afile[i] = values.next_double(); + tb->efile[i] = values.next_double(); + tb->ffile[i] = values.next_double(); + } catch (TokenizerException & e) { + ++cerror; + } } - fclose(fp); - // warn if data was read incompletely, e.g. columns were missing if (cerror) { - char str[128]; - sprintf(str,"%d of %d lines in table were incomplete or could not be" - " parsed completely",cerror,tb->ninput); - error->warning(FLERR,str); + std::string str = fmt::format("{} of {} lines in table were incomplete or could not be parsed completely", cerror, tb->ninput); + error->warning(FLERR,str.c_str()); } } @@ -521,26 +506,28 @@ void AngleTable::param_extract(Table *tb, char *line) tb->fpflag = 0; tb->theta0 = MY_PI; - char *word = strtok(line," \t\n\r\f"); - while (word) { - if (strcmp(word,"N") == 0) { - word = strtok(NULL," \t\n\r\f"); - tb->ninput = atoi(word); - } else if (strcmp(word,"FP") == 0) { - tb->fpflag = 1; - word = strtok(NULL," \t\n\r\f"); - tb->fplo = atof(word); - word = strtok(NULL," \t\n\r\f"); - tb->fphi = atof(word); - tb->fplo *= (180.0/MY_PI)*(180.0/MY_PI); - tb->fphi *= (180.0/MY_PI)*(180.0/MY_PI); - } else if (strcmp(word,"EQ") == 0) { - word = strtok(NULL," \t\n\r\f"); - tb->theta0 = atof(word)/180.0*MY_PI; - } else { - error->one(FLERR,"Invalid keyword in angle table parameters"); + try { + ValueTokenizer values(line); + + while (values.has_next()) { + std::string word = values.next_string(); + + if (word == "N") { + tb->ninput = values.next_int(); + } else if (word == "FP") { + tb->fpflag = 1; + tb->fplo = values.next_double(); + tb->fphi = values.next_double(); + tb->fplo *= (180.0/MY_PI)*(180.0/MY_PI); + tb->fphi *= (180.0/MY_PI)*(180.0/MY_PI); + } else if (word == "EQ") { + tb->theta0 = values.next_double()/180.0*MY_PI; + } else { + error->one(FLERR,"Invalid keyword in angle table parameters"); + } } - word = strtok(NULL," \t\n\r\f"); + } catch(TokenizerException & e) { + error->one(FLERR, e.what()); } if (tb->ninput == 0) error->one(FLERR,"Angle table parameters did not set N"); diff --git a/src/MOLECULE/bond_table.cpp b/src/MOLECULE/bond_table.cpp index 74678a7159..3a1529a155 100644 --- a/src/MOLECULE/bond_table.cpp +++ b/src/MOLECULE/bond_table.cpp @@ -27,12 +27,14 @@ #include "memory.h" #include "error.h" #include "utils.h" +#include "tokenizer.h" +#include "table_file_reader.h" +#include "fmt/format.h" using namespace LAMMPS_NS; enum{NONE,LINEAR,SPLINE}; -#define MAXLINE 1024 #define BIGNUM 1.0e300 /* ---------------------------------------------------------------------- */ @@ -307,38 +309,19 @@ void BondTable::free_table(Table *tb) void BondTable::read_table(Table *tb, char *file, char *keyword) { - char line[MAXLINE]; + TableFileReader reader(lmp, file, "bond"); double emin = BIGNUM; - // open file + char * line = reader.find_section_start(keyword); - FILE *fp = force->open_potential(file); - if (fp == NULL) { - char str[128]; - snprintf(str,128,"Cannot open file %s",file); - error->one(FLERR,str); - } - - // loop until section found with matching keyword - - while (1) { - if (fgets(line,MAXLINE,fp) == NULL) - error->one(FLERR,"Did not find keyword in table file"); - if (strspn(line," \t\n\r") == strlen(line)) continue; // blank line - if (line[0] == '#') continue; // comment - char *word = strtok(line," \t\n\r"); - if (strcmp(word,keyword) == 0) break; // matching keyword - utils::sfgets(FLERR,line,MAXLINE,fp,file,error); // no match, skip section - param_extract(tb,line); - utils::sfgets(FLERR,line,MAXLINE,fp,file,error); - for (int i = 0; i < tb->ninput; i++) - utils::sfgets(FLERR,line,MAXLINE,fp,file,error); + if (!line) { + error->one(FLERR,"Did not find keyword in table file"); } // read args on 2nd line of section // allocate table arrays for file values - utils::sfgets(FLERR,line,MAXLINE,fp,file,error); + line = reader.next_line(); param_extract(tb,line); memory->create(tb->rfile,tb->ninput,"bond:rfile"); memory->create(tb->efile,tb->ninput,"bond:efile"); @@ -349,18 +332,24 @@ void BondTable::read_table(Table *tb, char *file, char *keyword) int cerror = 0; int r0idx = -1; - utils::sfgets(FLERR,line,MAXLINE,fp,file,error); + reader.skip_line(); for (int i = 0; i < tb->ninput; i++) { - if (NULL == fgets(line,MAXLINE,fp)) - error->one(FLERR,"Premature end of file in bond table"); - if (3 != sscanf(line,"%*d %lg %lg %lg", - &tb->rfile[i],&tb->efile[i],&tb->ffile[i])) ++cerror; + line = reader.next_line(4); + try { + ValueTokenizer values(line); + values.next_int(); + tb->rfile[i] = values.next_double(); + tb->efile[i] = values.next_double(); + tb->ffile[i] = values.next_double(); + } catch (TokenizerException & e) { + ++cerror; + } + if (tb->efile[i] < emin) { emin = tb->efile[i]; r0idx = i; } } - fclose(fp); // infer r0 from minimum of potential, if not given explicitly @@ -389,19 +378,15 @@ void BondTable::read_table(Table *tb, char *file, char *keyword) } if (ferror) { - char str[128]; - sprintf(str,"%d of %d force values in table are inconsistent with -dE/dr.\n" - " Should only be flagged at inflection points",ferror,tb->ninput); - error->warning(FLERR,str); + error->warning(FLERR, fmt::format("{} of {} force values in table are inconsistent with -dE/dr.\n" + " Should only be flagged at inflection points",ferror,tb->ninput)); } // warn if data was read incompletely, e.g. columns were missing if (cerror) { - char str[128]; - sprintf(str,"%d of %d lines in table were incomplete or could not be" - " parsed completely",cerror,tb->ninput); - error->warning(FLERR,str); + error->warning(FLERR, fmt::format("{} of {} lines in table were incomplete or could not be" + " parsed completely",cerror,tb->ninput)); } } @@ -488,24 +473,26 @@ void BondTable::param_extract(Table *tb, char *line) tb->fpflag = 0; tb->r0 = 0.0; - char *word = strtok(line," \t\n\r\f"); - while (word) { - if (strcmp(word,"N") == 0) { - word = strtok(NULL," \t\n\r\f"); - tb->ninput = atoi(word); - } else if (strcmp(word,"FP") == 0) { - tb->fpflag = 1; - word = strtok(NULL," \t\n\r\f"); - tb->fplo = atof(word); - word = strtok(NULL," \t\n\r\f"); - tb->fphi = atof(word); - } else if (strcmp(word,"EQ") == 0) { - word = strtok(NULL," \t\n\r\f"); - tb->r0 = atof(word); - } else { - error->one(FLERR,"Invalid keyword in bond table parameters"); + try { + ValueTokenizer values(line); + + while (values.has_next()) { + std::string word = values.next_string(); + + if (word == "N") { + tb->ninput = values.next_int(); + } else if (word == "FP") { + tb->fpflag = 1; + tb->fplo = values.next_double(); + tb->fphi = values.next_double(); + } else if (word == "EQ") { + tb->r0 = values.next_double(); + } else { + error->one(FLERR,"Invalid keyword in bond table parameters"); + } } - word = strtok(NULL," \t\n\r\f"); + } catch(TokenizerException & e) { + error->one(FLERR, e.what()); } if (tb->ninput == 0) error->one(FLERR,"Bond table parameters did not set N"); diff --git a/src/RIGID/fix_rigid_small.cpp b/src/RIGID/fix_rigid_small.cpp index 3186c154ea..4fa35cf5fd 100644 --- a/src/RIGID/fix_rigid_small.cpp +++ b/src/RIGID/fix_rigid_small.cpp @@ -2489,7 +2489,7 @@ void FixRigidSmall::readfile(int which, double **array, int *inbody) buf = buffer; next = strchr(buf,'\n'); *next = '\0'; - int nwords = utils::count_words(buf); + int nwords = utils::trim_and_count_words(buf); *next = '\n'; if (nwords != ATTRIBUTE_PERBODY) diff --git a/src/SNAP/pair_snap.cpp b/src/SNAP/pair_snap.cpp index 7108e62142..389fde28a0 100644 --- a/src/SNAP/pair_snap.cpp +++ b/src/SNAP/pair_snap.cpp @@ -568,7 +568,7 @@ void PairSNAP::read_files(char *coefffilename, char *paramfilename) MPI_Bcast(&n,1,MPI_INT,0,world); MPI_Bcast(line,n,MPI_CHAR,0,world); - nwords = utils::count_words(line); + nwords = utils::trim_and_count_words(line); if (nwords != 3) error->all(FLERR,"Incorrect format in SNAP coefficient file"); @@ -610,7 +610,7 @@ void PairSNAP::read_files(char *coefffilename, char *paramfilename) MPI_Bcast(&n,1,MPI_INT,0,world); MPI_Bcast(line,n,MPI_CHAR,0,world); - nwords = utils::count_words(line); + nwords = utils::trim_and_count_words(line); if (nwords != 1) error->all(FLERR,"Incorrect format in SNAP coefficient file"); diff --git a/src/SPIN/neb_spin.cpp b/src/SPIN/neb_spin.cpp index 5d58a22567..168e288181 100644 --- a/src/SPIN/neb_spin.cpp +++ b/src/SPIN/neb_spin.cpp @@ -441,7 +441,7 @@ void NEBSpin::readfile(char *file, int flag) buf = buffer; next = strchr(buf,'\n'); *next = '\0'; - int nwords = utils::count_words(buf); + int nwords = utils::trim_and_count_words(buf); *next = '\n'; if (nwords != ATTRIBUTE_PERLINE) diff --git a/src/USER-INTEL/pair_eam_alloy_intel.cpp b/src/USER-INTEL/pair_eam_alloy_intel.cpp index 4a7a8b801d..16a55e4b2b 100644 --- a/src/USER-INTEL/pair_eam_alloy_intel.cpp +++ b/src/USER-INTEL/pair_eam_alloy_intel.cpp @@ -122,15 +122,12 @@ void PairEAMAlloyIntel::read_file(char *filename) PotentialFileReader reader(lmp, filename, "EAM"); try { - char * line = nullptr; - reader.skip_line(); reader.skip_line(); reader.skip_line(); // extract element names from nelements line - line = reader.next_line(1); - ValueTokenizer values(line); + ValueTokenizer values = reader.next_values(1); file->nelements = values.next_int(); if (values.count() != file->nelements + 1) @@ -146,8 +143,7 @@ void PairEAMAlloyIntel::read_file(char *filename) // - line = reader.next_line(5); - values = ValueTokenizer(line); + values = reader.next_values(5); file->nrho = values.next_int(); file->drho = values.next_double(); file->nr = values.next_int(); @@ -163,18 +159,17 @@ void PairEAMAlloyIntel::read_file(char *filename) memory->create(file->z2r, file->nelements, file->nelements, file->nr + 1, "pair:z2r"); for (int i = 0; i < file->nelements; i++) { - line = reader.next_line(2); - values = ValueTokenizer(line); + values = reader.next_values(2); values.next_int(); // ignore file->mass[i] = values.next_double(); - reader.next_dvector(file->nrho, &file->frho[i][1]); - reader.next_dvector(file->nr, &file->rhor[i][1]); + reader.next_dvector(&file->frho[i][1], file->nrho); + reader.next_dvector(&file->rhor[i][1], file->nr); } for (int i = 0; i < file->nelements; i++) { for (int j = 0; j <= i; j++) { - reader.next_dvector(file->nr, &file->z2r[i][j][1]); + reader.next_dvector(&file->z2r[i][j][1], file->nr); } } } catch (TokenizerException & e) { diff --git a/src/USER-INTEL/pair_eam_fs_intel.cpp b/src/USER-INTEL/pair_eam_fs_intel.cpp index 0d4cb5e3ae..e68d5687cf 100644 --- a/src/USER-INTEL/pair_eam_fs_intel.cpp +++ b/src/USER-INTEL/pair_eam_fs_intel.cpp @@ -122,15 +122,12 @@ void PairEAMFSIntel::read_file(char *filename) PotentialFileReader reader(lmp, filename, "EAM"); try { - char * line = nullptr; - reader.skip_line(); reader.skip_line(); reader.skip_line(); // extract element names from nelements line - line = reader.next_line(1); - ValueTokenizer values(line); + ValueTokenizer values = reader.next_values(1); file->nelements = values.next_int(); if (values.count() != file->nelements + 1) @@ -146,8 +143,7 @@ void PairEAMFSIntel::read_file(char *filename) // - line = reader.next_line(5); - values = ValueTokenizer(line); + values = reader.next_values(5); file->nrho = values.next_int(); file->drho = values.next_double(); file->nr = values.next_int(); @@ -163,21 +159,20 @@ void PairEAMFSIntel::read_file(char *filename) memory->create(file->z2r, file->nelements, file->nelements, file->nr + 1, "pair:z2r"); for (int i = 0; i < file->nelements; i++) { - line = reader.next_line(2); - values = ValueTokenizer(line); + values = reader.next_values(2); values.next_int(); // ignore file->mass[i] = values.next_double(); - reader.next_dvector(file->nrho, &file->frho[i][1]); + reader.next_dvector(&file->frho[i][1], file->nrho); for (int j = 0; j < file->nelements; j++) { - reader.next_dvector(file->nr, &file->rhor[i][j][1]); + reader.next_dvector(&file->rhor[i][j][1], file->nr); } } for (int i = 0; i < file->nelements; i++) { for (int j = 0; j <= i; j++) { - reader.next_dvector(file->nr, &file->z2r[i][j][1]); + reader.next_dvector(&file->z2r[i][j][1], file->nr); } } } catch (TokenizerException & e) { diff --git a/src/USER-MISC/dihedral_table.cpp b/src/USER-MISC/dihedral_table.cpp index 7478f70aa9..9fd3679106 100644 --- a/src/USER-MISC/dihedral_table.cpp +++ b/src/USER-MISC/dihedral_table.cpp @@ -36,6 +36,9 @@ #include "utils.h" #include "dihedral_table.h" #include "utils.h" +#include "tokenizer.h" +#include "table_file_reader.h" +#include "fmt/format.h" #include "math_const.h" #include "math_extra.h" @@ -458,8 +461,7 @@ static double Phi(double const *x1, //array holding x,y,z coords atom 1 DihedralTable::DihedralTable(LAMMPS *lmp) : Dihedral(lmp) { ntables = 0; - tables = NULL; - checkU_fname = checkF_fname = NULL; + tables = nullptr; } /* ---------------------------------------------------------------------- */ @@ -468,8 +470,6 @@ DihedralTable::~DihedralTable() { for (int m = 0; m < ntables; m++) free_table(&tables[m]); memory->sfree(tables); - memory->sfree(checkU_fname); - memory->sfree(checkF_fname); if (allocated) { memory->destroy(setflag); @@ -832,13 +832,13 @@ void DihedralTable::coeff(int narg, char **arg) string err_msg; err_msg = string("Invalid dihedral table length (") + string(arg[2]) + string(")."); - error->one(FLERR,err_msg.c_str()); + error->one(FLERR,err_msg); } else if ((tb->ninput == 2) && (tabstyle == SPLINE)) { string err_msg; err_msg = string("Invalid dihedral spline table length. (Try linear)\n (") + string(arg[2]) + string(")."); - error->one(FLERR,err_msg.c_str()); + error->one(FLERR,err_msg); } // check for monotonicity @@ -851,7 +851,7 @@ void DihedralTable::coeff(int narg, char **arg) string(arg[2]) + string(", ")+i_str.str()+string("th entry)"); if (i==0) err_msg += string("\n(This is probably a mistake with your table format.)\n"); - error->all(FLERR,err_msg.c_str()); + error->all(FLERR,err_msg); } } @@ -863,7 +863,7 @@ void DihedralTable::coeff(int narg, char **arg) string err_msg; err_msg = string("Dihedral table angle range must be < 360 degrees (") +string(arg[2]) + string(")."); - error->all(FLERR,err_msg.c_str()); + error->all(FLERR,err_msg); } } else { @@ -871,7 +871,7 @@ void DihedralTable::coeff(int narg, char **arg) string err_msg; err_msg = string("Dihedral table angle range must be < 2*PI radians (") + string(arg[2]) + string(")."); - error->all(FLERR,err_msg.c_str()); + error->all(FLERR,err_msg); } } @@ -940,7 +940,7 @@ void DihedralTable::coeff(int narg, char **arg) // Optional: allow the user to print out the interpolated spline tables if (me == 0) { - if (checkU_fname && (strlen(checkU_fname) != 0)) + if (!checkU_fname.empty()) { ofstream checkU_file; checkU_file.open(checkU_fname, ios::out); @@ -953,7 +953,7 @@ void DihedralTable::coeff(int narg, char **arg) } checkU_file.close(); } - if (checkF_fname && (strlen(checkF_fname) != 0)) + if (!checkF_fname.empty()) { ofstream checkF_file; checkF_file.open(checkF_fname, ios::out); @@ -1084,42 +1084,21 @@ void DihedralTable::free_table(Table *tb) /* ---------------------------------------------------------------------- read table file, only called by proc 0 ------------------------------------------------------------------------- */ -static const int MAXLINE=2048; void DihedralTable::read_table(Table *tb, char *file, char *keyword) { - char line[MAXLINE]; + TableFileReader reader(lmp, file, "dihedral"); - // open file + char * line = reader.find_section_start(keyword); - FILE *fp = force->open_potential(file); - if (fp == NULL) { - string err_msg = string("Cannot open file ") + string(file); - error->one(FLERR,err_msg.c_str()); + if (!line) { + error->one(FLERR,"Did not find keyword in table file"); } - // loop until section found with matching keyword - - while (1) { - if (fgets(line,MAXLINE,fp) == NULL) { - string err_msg=string("Did not find keyword \"") - +string(keyword)+string("\" in dihedral table file."); - error->one(FLERR, err_msg.c_str()); - } - if (strspn(line," \t\n\r") == strlen(line)) continue; // blank line - if (line[0] == '#') continue; // comment - char *word = strtok(line," \t\n\r"); - if (strcmp(word,keyword) == 0) break; // matching keyword - utils::sfgets(FLERR,line,MAXLINE,fp,file,error); // no match, skip section - param_extract(tb,line); - utils::sfgets(FLERR,line,MAXLINE,fp,file,error); - for (int i = 0; i < tb->ninput; i++) - utils::sfgets(FLERR,line,MAXLINE,fp,file,error); - } // read args on 2nd line of section // allocate table arrays for file values - utils::sfgets(FLERR,line,MAXLINE,fp,file,error); + line = reader.next_line(); param_extract(tb,line); memory->create(tb->phifile,tb->ninput,"dihedral:phifile"); memory->create(tb->efile,tb->ninput,"dihedral:efile"); @@ -1127,41 +1106,24 @@ void DihedralTable::read_table(Table *tb, char *file, char *keyword) // read a,e,f table values from file - int itmp; for (int i = 0; i < tb->ninput; i++) { - utils::sfgets(FLERR,line,MAXLINE,fp,file,error); - - // Skip blank lines and delete text following a '#' character - char *pe = strchr(line, '#'); - if (pe != NULL) *pe = '\0'; //terminate string at '#' character - char *pc = line; - while ((*pc != '\0') && isspace(*pc)) - pc++; - if (*pc != '\0') { //If line is not a blank line - stringstream line_ss(line); + try { if (tb->f_unspecified) { - line_ss >> itmp; - line_ss >> tb->phifile[i]; - line_ss >> tb->efile[i]; + ValueTokenizer values = reader.next_values(3); + values.next_int(); + tb->phifile[i] = values.next_double(); + tb->efile[i] = values.next_double(); } else { - line_ss >> itmp; - line_ss >> tb->phifile[i]; - line_ss >> tb->efile[i]; - line_ss >> tb->ffile[i]; + ValueTokenizer values = reader.next_values(4); + values.next_int(); + tb->phifile[i] = values.next_double(); + tb->efile[i] = values.next_double(); + tb->ffile[i] = values.next_double(); } - if (! line_ss) { - stringstream err_msg; - err_msg << "Read error in table "<< keyword<<", near line "<f_unspecified) && (i==0)) - err_msg << "\n (This sometimes occurs if users forget to specify the \"NOF\" option.)\n"; - error->one(FLERR, err_msg.str().c_str()); - } - } else //if it is a blank line, then skip it. - i--; + } catch (TokenizerException & e) { + error->one(FLERR, e.what()); + } } //for (int i = 0; (i < tb->ninput) && fp; i++) { - - fclose(fp); } /* ---------------------------------------------------------------------- @@ -1252,7 +1214,7 @@ void DihedralTable::spline_table(Table *tb) if ((num_disagreements > tb->ninput/2) && (num_disagreements > 2)) { string msg("Dihedral table has inconsistent forces and energies. (Try \"NOF\".)\n"); - error->all(FLERR,msg.c_str()); + error->all(FLERR, msg); } } // check for consistency if (! tb->f_unspecified) @@ -1353,44 +1315,40 @@ void DihedralTable::param_extract(Table *tb, char *line) tb->f_unspecified = false; //default tb->use_degrees = true; //default - char *word = strtok(line," \t\n\r\f"); - while (word) { - if (strcmp(word,"N") == 0) { - word = strtok(NULL," \t\n\r\f"); - tb->ninput = atoi(word); + try { + ValueTokenizer values(line); + + while (values.has_next()) { + std::string word = values.next_string(); + if (word == "N") { + tb->ninput = values.next_int(); + } + else if (word == "NOF") { + tb->f_unspecified = true; + } + else if ((word == "DEGREES") || (word == "degrees")) { + tb->use_degrees = true; + } + else if ((word == "RADIANS") || (word == "radians")) { + tb->use_degrees = false; + } + else if (word == "CHECKU") { + checkU_fname = values.next_string(); + } + else if (word == "CHECKF") { + checkF_fname = values.next_string(); + } + // COMMENTING OUT: equilibrium angles are not supported + //else if (word == "EQ") { + // tb->theta0 = values.next_double(); + //} + else { + string err_msg = fmt::format("Invalid keyword in dihedral angle table parameters ({})", word); + error->one(FLERR,err_msg); + } } - else if (strcmp(word,"NOF") == 0) { - tb->f_unspecified = true; - } - else if ((strcmp(word,"DEGREES") == 0) || (strcmp(word,"degrees") == 0)) { - tb->use_degrees = true; - } - else if ((strcmp(word,"RADIANS") == 0) || (strcmp(word,"radians") == 0)) { - tb->use_degrees = false; - } - else if (strcmp(word,"CHECKU") == 0) { - word = strtok(NULL," \t\n\r\f"); - memory->sfree(checkU_fname); - memory->create(checkU_fname,strlen(word)+1,"dihedral_table:checkU"); - strcpy(checkU_fname, word); - } - else if (strcmp(word,"CHECKF") == 0) { - word = strtok(NULL," \t\n\r\f"); - memory->sfree(checkF_fname); - memory->create(checkF_fname,strlen(word)+1,"dihedral_table:checkF"); - strcpy(checkF_fname, word); - } - // COMMENTING OUT: equilibrium angles are not supported - //else if (strcmp(word,"EQ") == 0) { - // word = strtok(NULL," \t\n\r\f"); - // tb->theta0 = atof(word); - //} - else { - string err_msg("Invalid keyword in dihedral angle table parameters"); - err_msg += string(" (") + string(word) + string(")"); - error->one(FLERR,err_msg.c_str()); - } - word = strtok(NULL," \t\n\r\f"); + } catch (TokenizerException & e) { + error->one(FLERR, e.what()); } if (tb->ninput == 0) diff --git a/src/USER-MISC/dihedral_table.h b/src/USER-MISC/dihedral_table.h index a7b8417b48..8a397b20f2 100644 --- a/src/USER-MISC/dihedral_table.h +++ b/src/USER-MISC/dihedral_table.h @@ -24,6 +24,7 @@ DihedralStyle(table,DihedralTable) #ifndef LMP_DIHEDRAL_TABLE_H #define LMP_DIHEDRAL_TABLE_H #include "dihedral.h" +#include namespace LAMMPS_NS { @@ -43,8 +44,8 @@ class DihedralTable : public Dihedral { protected: int tabstyle,tablength; // double *phi0; <- equilibrium angles not supported - char *checkU_fname; - char *checkF_fname; + std::string checkU_fname; + std::string checkF_fname; struct Table { int ninput; diff --git a/src/USER-MISC/dihedral_table_cut.cpp b/src/USER-MISC/dihedral_table_cut.cpp index 194c25f536..e2283633bc 100644 --- a/src/USER-MISC/dihedral_table_cut.cpp +++ b/src/USER-MISC/dihedral_table_cut.cpp @@ -824,13 +824,13 @@ void DihedralTableCut::coeff(int narg, char **arg) string err_msg; err_msg = string("Invalid dihedral table length (") + string(arg[5]) + string(")."); - error->one(FLERR,err_msg.c_str()); + error->one(FLERR,err_msg); } else if ((tb->ninput == 2) && (tabstyle == SPLINE)) { string err_msg; err_msg = string("Invalid dihedral spline table length. (Try linear)\n (") + string(arg[5]) + string(")."); - error->one(FLERR,err_msg.c_str()); + error->one(FLERR,err_msg); } // check for monotonicity @@ -843,7 +843,7 @@ void DihedralTableCut::coeff(int narg, char **arg) string(arg[5]) + string(", ")+i_str.str()+string("th entry)"); if (i==0) err_msg += string("\n(This is probably a mistake with your table format.)\n"); - error->all(FLERR,err_msg.c_str()); + error->all(FLERR,err_msg); } } @@ -855,7 +855,7 @@ void DihedralTableCut::coeff(int narg, char **arg) string err_msg; err_msg = string("Dihedral table angle range must be < 360 degrees (") +string(arg[5]) + string(")."); - error->all(FLERR,err_msg.c_str()); + error->all(FLERR,err_msg); } } else { @@ -863,7 +863,7 @@ void DihedralTableCut::coeff(int narg, char **arg) string err_msg; err_msg = string("Dihedral table angle range must be < 2*PI radians (") + string(arg[5]) + string(")."); - error->all(FLERR,err_msg.c_str()); + error->all(FLERR,err_msg); } } @@ -1081,7 +1081,7 @@ void DihedralTableCut::read_table(Table *tb, char *file, char *keyword) FILE *fp = force->open_potential(file); if (fp == NULL) { string err_msg = string("Cannot open file ") + string(file); - error->one(FLERR,err_msg.c_str()); + error->one(FLERR,err_msg); } // loop until section found with matching keyword @@ -1090,7 +1090,7 @@ void DihedralTableCut::read_table(Table *tb, char *file, char *keyword) if (fgets(line,MAXLINE,fp) == NULL) { string err_msg=string("Did not find keyword \"") +string(keyword)+string("\" in dihedral table file."); - error->one(FLERR, err_msg.c_str()); + error->one(FLERR, err_msg); } if (strspn(line," \t\n\r") == strlen(line)) continue; // blank line if (line[0] == '#') continue; // comment @@ -1376,7 +1376,7 @@ void DihedralTableCut::param_extract(Table *tb, char *line) else { string err_msg("Invalid keyword in dihedral angle table parameters"); err_msg += string(" (") + string(word) + string(")"); - error->one(FLERR,err_msg.c_str()); + error->one(FLERR, err_msg); } word = strtok(NULL," \t\n\r\f"); } diff --git a/src/USER-OMP/pair_eam_alloy_omp.cpp b/src/USER-OMP/pair_eam_alloy_omp.cpp index 2f6b4919f1..ea2130721b 100644 --- a/src/USER-OMP/pair_eam_alloy_omp.cpp +++ b/src/USER-OMP/pair_eam_alloy_omp.cpp @@ -122,15 +122,12 @@ void PairEAMAlloyOMP::read_file(char *filename) PotentialFileReader reader(PairEAM::lmp, filename, "EAM"); try { - char * line = nullptr; - reader.skip_line(); reader.skip_line(); reader.skip_line(); // extract element names from nelements line - line = reader.next_line(1); - ValueTokenizer values(line); + ValueTokenizer values = reader.next_values(1); file->nelements = values.next_int(); if (values.count() != file->nelements + 1) @@ -146,8 +143,7 @@ void PairEAMAlloyOMP::read_file(char *filename) // - line = reader.next_line(5); - values = ValueTokenizer(line); + values = reader.next_values(5); file->nrho = values.next_int(); file->drho = values.next_double(); file->nr = values.next_int(); @@ -163,18 +159,17 @@ void PairEAMAlloyOMP::read_file(char *filename) memory->create(file->z2r, file->nelements, file->nelements, file->nr + 1, "pair:z2r"); for (int i = 0; i < file->nelements; i++) { - line = reader.next_line(2); - values = ValueTokenizer(line); + values = reader.next_values(2); values.next_int(); // ignore file->mass[i] = values.next_double(); - reader.next_dvector(file->nrho, &file->frho[i][1]); - reader.next_dvector(file->nr, &file->rhor[i][1]); + reader.next_dvector(&file->frho[i][1], file->nrho); + reader.next_dvector(&file->rhor[i][1], file->nr); } for (int i = 0; i < file->nelements; i++) { for (int j = 0; j <= i; j++) { - reader.next_dvector(file->nr, &file->z2r[i][j][1]); + reader.next_dvector(&file->z2r[i][j][1], file->nr); } } } catch (TokenizerException & e) { diff --git a/src/USER-OMP/pair_eam_fs_omp.cpp b/src/USER-OMP/pair_eam_fs_omp.cpp index e16f28cd31..71d58469c8 100644 --- a/src/USER-OMP/pair_eam_fs_omp.cpp +++ b/src/USER-OMP/pair_eam_fs_omp.cpp @@ -122,15 +122,12 @@ void PairEAMFSOMP::read_file(char *filename) PotentialFileReader reader(PairEAM::lmp, filename, "EAM"); try { - char * line = nullptr; - reader.skip_line(); reader.skip_line(); reader.skip_line(); // extract element names from nelements line - line = reader.next_line(1); - ValueTokenizer values(line); + ValueTokenizer values = reader.next_values(1); file->nelements = values.next_int(); if (values.count() != file->nelements + 1) @@ -146,8 +143,7 @@ void PairEAMFSOMP::read_file(char *filename) // - line = reader.next_line(5); - values = ValueTokenizer(line); + values = reader.next_values(5); file->nrho = values.next_int(); file->drho = values.next_double(); file->nr = values.next_int(); @@ -163,21 +159,20 @@ void PairEAMFSOMP::read_file(char *filename) memory->create(file->z2r, file->nelements, file->nelements, file->nr + 1, "pair:z2r"); for (int i = 0; i < file->nelements; i++) { - line = reader.next_line(2); - values = ValueTokenizer(line); + values = reader.next_values(2); values.next_int(); // ignore file->mass[i] = values.next_double(); - reader.next_dvector(file->nrho, &file->frho[i][1]); + reader.next_dvector(&file->frho[i][1], file->nrho); for (int j = 0; j < file->nelements; j++) { - reader.next_dvector(file->nr, &file->rhor[i][j][1]); + reader.next_dvector(&file->rhor[i][j][1], file->nr); } } for (int i = 0; i < file->nelements; i++) { for (int j = 0; j <= i; j++) { - reader.next_dvector(file->nr, &file->z2r[i][j][1]); + reader.next_dvector(&file->z2r[i][j][1], file->nr); } } } catch (TokenizerException & e) { diff --git a/src/USER-OMP/pair_tersoff_zbl_omp.cpp b/src/USER-OMP/pair_tersoff_zbl_omp.cpp index 0e9bc5c24a..6a9232f888 100644 --- a/src/USER-OMP/pair_tersoff_zbl_omp.cpp +++ b/src/USER-OMP/pair_tersoff_zbl_omp.cpp @@ -31,6 +31,8 @@ #include "memory.h" #include "error.h" #include "utils.h" +#include "tokenizer.h" +#include "potential_file_reader.h" #include "math_const.h" #include "math_special.h" @@ -38,7 +40,6 @@ using namespace LAMMPS_NS; using namespace MathConst; using namespace MathSpecial; -#define MAXLINE 1024 #define DELTA 4 /* ---------------------------------------------------------------------- @@ -84,152 +85,108 @@ PairTersoffZBLOMP::PairTersoffZBLOMP(LAMMPS *lmp) : PairTersoffOMP(lmp) void PairTersoffZBLOMP::read_file(char *file) { - int params_per_line = 21; - char **words = new char*[params_per_line+1]; - memory->sfree(params); - params = NULL; + params = nullptr; nparams = maxparam = 0; // open file on proc 0 - FILE *fp; if (comm->me == 0) { - fp = force->open_potential(file); - if (fp == NULL) { - char str[128]; - snprintf(str,128,"Cannot open Tersoff potential file %s",file); - error->one(FLERR,str); - } - } + PotentialFileReader reader(PairTersoff::lmp, file, "Tersoff"); + char * line; - // read each line out of file, skipping blank lines or leading '#' - // store line of params if all 3 element tags are in element list + while((line = reader.next_line(NPARAMS_PER_LINE))) { + try { + ValueTokenizer values(line); - int n,nwords,ielement,jelement,kelement; - char line[MAXLINE],*ptr; - int eof = 0; + std::string iname = values.next_string(); + std::string jname = values.next_string(); + std::string kname = values.next_string(); - while (1) { - if (comm->me == 0) { - ptr = fgets(line,MAXLINE,fp); - if (ptr == NULL) { - eof = 1; - fclose(fp); - } else n = strlen(line) + 1; - } - MPI_Bcast(&eof,1,MPI_INT,0,world); - if (eof) break; - MPI_Bcast(&n,1,MPI_INT,0,world); - MPI_Bcast(line,n,MPI_CHAR,0,world); + // ielement,jelement,kelement = 1st args + // if all 3 args are in element list, then parse this line + // else skip to next entry in file + int ielement, jelement, kelement; - // strip comment, skip line if blank + for (ielement = 0; ielement < nelements; ielement++) + if (iname == elements[ielement]) break; + if (ielement == nelements) continue; + for (jelement = 0; jelement < nelements; jelement++) + if (jname == elements[jelement]) break; + if (jelement == nelements) continue; + for (kelement = 0; kelement < nelements; kelement++) + if (kname == elements[kelement]) break; + if (kelement == nelements) continue; - if ((ptr = strchr(line,'#'))) *ptr = '\0'; - nwords = utils::count_words(line); - if (nwords == 0) continue; - // concatenate additional lines until have params_per_line words + // load up parameter settings and error check their values - while (nwords < params_per_line) { - n = strlen(line); - if (comm->me == 0) { - ptr = fgets(&line[n],MAXLINE-n,fp); - if (ptr == NULL) { - eof = 1; - fclose(fp); - } else n = strlen(line) + 1; + if (nparams == maxparam) { + maxparam += DELTA; + params = (Param *) memory->srealloc(params,maxparam*sizeof(Param), + "pair:params"); + } + + params[nparams].ielement = ielement; + params[nparams].jelement = jelement; + params[nparams].kelement = kelement; + params[nparams].powerm = values.next_double(); + params[nparams].gamma = values.next_double(); + params[nparams].lam3 = values.next_double(); + params[nparams].c = values.next_double(); + params[nparams].d = values.next_double(); + params[nparams].h = values.next_double(); + params[nparams].powern = values.next_double(); + params[nparams].beta = values.next_double(); + params[nparams].lam2 = values.next_double(); + params[nparams].bigb = values.next_double(); + params[nparams].bigr = values.next_double(); + params[nparams].bigd = values.next_double(); + params[nparams].lam1 = values.next_double(); + params[nparams].biga = values.next_double(); + params[nparams].Z_i = values.next_double(); + params[nparams].Z_j = values.next_double(); + params[nparams].ZBLcut = values.next_double(); + params[nparams].ZBLexpscale = values.next_double(); + params[nparams].powermint = int(params[nparams].powerm); + } catch (TokenizerException & e) { + error->one(FLERR, e.what()); } - MPI_Bcast(&eof,1,MPI_INT,0,world); - if (eof) break; - MPI_Bcast(&n,1,MPI_INT,0,world); - MPI_Bcast(line,n,MPI_CHAR,0,world); - if ((ptr = strchr(line,'#'))) *ptr = '\0'; - nwords = utils::count_words(line); + + // currently only allow m exponent of 1 or 3 + if (params[nparams].c < 0.0 || + params[nparams].d < 0.0 || + params[nparams].powern < 0.0 || + params[nparams].beta < 0.0 || + params[nparams].lam2 < 0.0 || + params[nparams].bigb < 0.0 || + params[nparams].bigr < 0.0 || + params[nparams].bigd < 0.0 || + params[nparams].bigd > params[nparams].bigr || + params[nparams].lam1 < 0.0 || + params[nparams].biga < 0.0 || + params[nparams].powerm - params[nparams].powermint != 0.0 || + (params[nparams].powermint != 3 && + params[nparams].powermint != 1) || + params[nparams].gamma < 0.0 || + params[nparams].Z_i < 1.0 || + params[nparams].Z_j < 1.0 || + params[nparams].ZBLcut < 0.0 || + params[nparams].ZBLexpscale < 0.0) + error->one(FLERR,"Illegal Tersoff parameter"); + + nparams++; } - - if (nwords != params_per_line) - error->all(FLERR,"Incorrect format in Tersoff potential file"); - - // words = ptrs to all words in line - - nwords = 0; - words[nwords++] = strtok(line," \t\n\r\f"); - while ((words[nwords++] = strtok(NULL," \t\n\r\f"))) continue; - - // ielement,jelement,kelement = 1st args - // if all 3 args are in element list, then parse this line - // else skip to next line - - for (ielement = 0; ielement < nelements; ielement++) - if (strcmp(words[0],elements[ielement]) == 0) break; - if (ielement == nelements) continue; - for (jelement = 0; jelement < nelements; jelement++) - if (strcmp(words[1],elements[jelement]) == 0) break; - if (jelement == nelements) continue; - for (kelement = 0; kelement < nelements; kelement++) - if (strcmp(words[2],elements[kelement]) == 0) break; - if (kelement == nelements) continue; - - // load up parameter settings and error check their values - - if (nparams == maxparam) { - maxparam += DELTA; - params = (Param *) memory->srealloc(params,maxparam*sizeof(Param), - "pair:params"); - } - - params[nparams].ielement = ielement; - params[nparams].jelement = jelement; - params[nparams].kelement = kelement; - params[nparams].powerm = atof(words[3]); - params[nparams].gamma = atof(words[4]); - params[nparams].lam3 = atof(words[5]); - params[nparams].c = atof(words[6]); - params[nparams].d = atof(words[7]); - params[nparams].h = atof(words[8]); - params[nparams].powern = atof(words[9]); - params[nparams].beta = atof(words[10]); - params[nparams].lam2 = atof(words[11]); - params[nparams].bigb = atof(words[12]); - params[nparams].bigr = atof(words[13]); - params[nparams].bigd = atof(words[14]); - params[nparams].lam1 = atof(words[15]); - params[nparams].biga = atof(words[16]); - params[nparams].Z_i = atof(words[17]); - params[nparams].Z_j = atof(words[18]); - params[nparams].ZBLcut = atof(words[19]); - params[nparams].ZBLexpscale = atof(words[20]); - - // currently only allow m exponent of 1 or 3 - - params[nparams].powermint = int(params[nparams].powerm); - - if (params[nparams].c < 0.0 || - params[nparams].d < 0.0 || - params[nparams].powern < 0.0 || - params[nparams].beta < 0.0 || - params[nparams].lam2 < 0.0 || - params[nparams].bigb < 0.0 || - params[nparams].bigr < 0.0 || - params[nparams].bigd < 0.0 || - params[nparams].bigd > params[nparams].bigr || - params[nparams].lam1 < 0.0 || - params[nparams].biga < 0.0 || - params[nparams].powerm - params[nparams].powermint != 0.0 || - (params[nparams].powermint != 3 && - params[nparams].powermint != 1) || - params[nparams].gamma < 0.0 || - params[nparams].Z_i < 1.0 || - params[nparams].Z_j < 1.0 || - params[nparams].ZBLcut < 0.0 || - params[nparams].ZBLexpscale < 0.0) - error->all(FLERR,"Illegal Tersoff parameter"); - - nparams++; } - delete [] words; + MPI_Bcast(&nparams, 1, MPI_INT, 0, world); + MPI_Bcast(&maxparam, 1, MPI_INT, 0, world); + + if(comm->me != 0) { + params = (Param *) memory->srealloc(params,maxparam*sizeof(Param), "pair:params"); + } + + MPI_Bcast(params, maxparam*sizeof(Param), MPI_BYTE, 0, world); } /* ---------------------------------------------------------------------- */ diff --git a/src/USER-PLUMED/fix_plumed.cpp b/src/USER-PLUMED/fix_plumed.cpp index e1f0ea0bfe..3a52bbaaa1 100644 --- a/src/USER-PLUMED/fix_plumed.cpp +++ b/src/USER-PLUMED/fix_plumed.cpp @@ -82,6 +82,7 @@ FixPlumed::FixPlumed(LAMMPS *lmp, int narg, char **arg) : error->all(FLERR,"Incompatible API version for PLUMED in fix plumed. " "Only Plumed 2.4.x, 2.5.x, and 2.6.x are tested and supported."); +#if !defined(MPI_STUBS) // If the -partition option is activated then enable // inter-partition communication @@ -108,7 +109,6 @@ FixPlumed::FixPlumed(LAMMPS *lmp, int narg, char **arg) : // whereas if partitions are not defined then world is equal to // MPI_COMM_WORLD. -#if !defined(MPI_STUBS) // plumed does not know about LAMMPS using the MPI STUBS library and will // fail if this is called under these circumstances p->cmd("setMPIComm",&world); diff --git a/src/USER-QTB/fix_qbmsst.cpp b/src/USER-QTB/fix_qbmsst.cpp index 5ac611b13e..d58c917308 100644 --- a/src/USER-QTB/fix_qbmsst.cpp +++ b/src/USER-QTB/fix_qbmsst.cpp @@ -21,6 +21,7 @@ #include #include #include +#include #include "atom.h" #include "force.h" #include "update.h" @@ -34,6 +35,7 @@ #include "kspace.h" #include "math_const.h" #include "utils.h" +#include "fmt/format.h" using namespace LAMMPS_NS; using namespace FixConst; @@ -98,58 +100,71 @@ FixQBMSST::FixQBMSST(LAMMPS *lmp, int narg, char **arg) : while (iarg < narg) { if (strcmp(arg[iarg],"q") == 0) { if (iarg+2 > narg) error->all(FLERR,"Illegal fix qbmsst command"); - qmass = atof(arg[iarg+1]); if (qmass < 0.0) error->all(FLERR,"Fix qbmsst qmass must be >= 0.0"); + qmass = force->numeric(FLERR,arg[iarg+1]); + if (qmass < 0.0) error->all(FLERR,"Fix qbmsst qmass must be >= 0.0"); iarg += 2; } else if (strcmp(arg[iarg],"mu") == 0) { if (iarg+2 > narg) error->all(FLERR,"Illegal fix qbmsst command"); - mu = atof(arg[iarg+1]); if (mu < 0.0) error->all(FLERR,"Fix qbmsst mu must be >= 0.0"); + mu = force->numeric(FLERR,arg[iarg+1]); + if (mu < 0.0) error->all(FLERR,"Fix qbmsst mu must be >= 0.0"); iarg += 2; } else if (strcmp(arg[iarg],"p0") == 0) { if (iarg+2 > narg) error->all(FLERR,"Illegal fix qbmsst command"); - p0 = atof(arg[iarg+1]); if (p0 < 0.0) error->all(FLERR,"Fix qbmsst p0 must be >= 0.0"); + p0 = force->numeric(FLERR,arg[iarg+1]); + if (p0 < 0.0) error->all(FLERR,"Fix qbmsst p0 must be >= 0.0"); p0_set = 1; iarg += 2; } else if (strcmp(arg[iarg],"v0") == 0) { if (iarg+2 > narg) error->all(FLERR,"Illegal fix qbmsst command"); - v0 = atof(arg[iarg+1]); if (v0 < 0.0) error->all(FLERR,"Fix qbmsst v0 must be >= 0.0"); + v0 = force->numeric(FLERR,arg[iarg+1]); + if (v0 < 0.0) error->all(FLERR,"Fix qbmsst v0 must be >= 0.0"); v0_set = 1; iarg += 2; } else if (strcmp(arg[iarg],"e0") == 0) { if (iarg+2 > narg) error->all(FLERR,"Illegal fix qbmsst command"); - e0 = atof(arg[iarg+1]); + e0 = force->numeric(FLERR,arg[iarg+1]); e0_set = 1; iarg += 2; } else if (strcmp(arg[iarg],"tscale") == 0) { if (iarg+2 > narg) error->all(FLERR,"Illegal fix qbmsst command"); - tscale = atof(arg[iarg+1]); if (tscale < 0.0 || tscale > 1.0) error->all(FLERR,"Fix qbmsst tscale must satisfy 0 <= tscale < 1"); + tscale = force->numeric(FLERR,arg[iarg+1]); + if (tscale < 0.0 || tscale > 1.0) error->all(FLERR,"Fix qbmsst tscale must satisfy 0 <= tscale < 1"); iarg += 2; } else if (strcmp(arg[iarg],"damp") == 0) { if (iarg+2 > narg) error->all(FLERR,"Illegal fix qbmsst command"); - t_period = atof(arg[iarg+1]); if (t_period <= 0.0) error->all(FLERR,"Fix qbmsst damp must be > 0.0"); fric_coef = 1/t_period; + t_period = force->numeric(FLERR,arg[iarg+1]); + if (t_period <= 0.0) error->all(FLERR,"Fix qbmsst damp must be > 0.0"); + fric_coef = 1/t_period; iarg += 2; } else if (strcmp(arg[iarg],"seed") == 0) { if (iarg+2 > narg) error->all(FLERR,"Illegal fix qbmsst command"); - seed = atof(arg[iarg+1]); if (seed <= 0) error->all(FLERR,"Fix qbmsst seed must be a positive integer"); + seed = force->inumeric(FLERR,arg[iarg+1]); + if (seed <= 0) error->all(FLERR,"Fix qbmsst seed must be a positive integer"); iarg += 2; } else if (strcmp(arg[iarg],"f_max") == 0) { if (iarg+2 > narg) error->all(FLERR,"Illegal fix qbmsst command"); - f_max = atof(arg[iarg+1]); if (f_max <= 0) error->all(FLERR,"Fix qbmsst f_max must be > 0.0"); + f_max = force->numeric(FLERR,arg[iarg+1]); + if (f_max <= 0) error->all(FLERR,"Fix qbmsst f_max must be > 0.0"); iarg += 2; } else if (strcmp(arg[iarg],"N_f") == 0) { if (iarg+2 > narg) error->all(FLERR,"Illegal fix qbmsst command"); - N_f = atof(arg[iarg+1]); if (N_f <= 0) error->all(FLERR,"Fix qbmsst N_f must be a positive integer"); + N_f = force->inumeric(FLERR,arg[iarg+1]); + if (N_f <= 0) error->all(FLERR,"Fix qbmsst N_f must be a positive integer"); iarg += 2; } else if (strcmp(arg[iarg],"eta") == 0) { if (iarg+2 > narg) error->all(FLERR,"Illegal fix qbmsst command"); - eta = atof(arg[iarg+1]); if (eta <= 0) error->all(FLERR,"Fix qbmsst eta must be >= 0.0"); + eta = force->numeric(FLERR,arg[iarg+1]); + if (eta <= 0) error->all(FLERR,"Fix qbmsst eta must be >= 0.0"); iarg += 2; } else if (strcmp(arg[iarg],"beta") == 0) { if (iarg+2 > narg) error->all(FLERR,"Illegal fix qbmsst command"); - beta = atof(arg[iarg+1]); if (beta <= 0) error->all(FLERR,"Fix qbmsst beta must be a positive integer"); + beta = force->inumeric(FLERR,arg[iarg+1]); + if (beta <= 0) error->all(FLERR,"Fix qbmsst beta must be a positive integer"); iarg += 2; } else if (strcmp(arg[iarg],"T_init") == 0) { if (iarg+2 > narg) error->all(FLERR,"Illegal fix qbmsst command"); - t_init = atof(arg[iarg+1]); if (t_init <= 0) error->all(FLERR,"Fix qbmsst T_init must be >= 0.0"); + t_init = force->numeric(FLERR,arg[iarg+1]); + if (t_init <= 0) error->all(FLERR,"Fix qbmsst T_init must be >= 0.0"); iarg += 2; } else error->all(FLERR,"Illegal fix qbmsst command"); } @@ -157,48 +172,32 @@ FixQBMSST::FixQBMSST(LAMMPS *lmp, int narg, char **arg) : // check for periodicity in controlled dimensions if (domain->nonperiodic) error->all(FLERR,"Fix qbmsst requires a periodic box"); + maxexchange = 6*N_f+3; + // comments if (comm->me == 0) { - if (screen) { - fprintf(screen,"QBMSST parameters:\n"); - if (direction == 0) fprintf(screen," Shock in x direction\n"); - else if (direction == 1) fprintf(screen," Shock in y direction\n"); - else if (direction == 2) fprintf(screen," Shock in z direction\n"); + std::string msg = "QBMSST parameters:\n"; - fprintf(screen," Cell mass-like parameter qmass (units of mass^2/length^4) = %12.5e\n", qmass); - fprintf(screen," Shock velocity = %12.5e\n", velocity); - fprintf(screen," Artificial viscosity (units of mass/length/time) = %12.5e\n", mu); + if (direction == 0) msg += " Shock in x direction\n"; + else if (direction == 1) msg += " Shock in y direction\n"; + else if (direction == 2) msg += " Shock in z direction\n"; - if (p0_set) - fprintf(screen," Initial pressure specified to be %12.5e\n", p0); - else fprintf(screen," Initial pressure calculated on first step\n"); - if (v0_set) - fprintf(screen," Initial volume specified to be %12.5e\n", v0); - else fprintf(screen," Initial volume calculated on first step\n"); - if (e0_set) - fprintf(screen," Initial energy specified to be %12.5e\n", e0); - else fprintf(screen," Initial energy calculated on first step\n"); - } - if (logfile) { - fprintf(logfile,"QBMSST parameters:\n"); - if (direction == 0) fprintf(logfile," Shock in x direction\n"); - else if (direction == 1) fprintf(logfile," Shock in y direction\n"); - else if (direction == 2) fprintf(logfile," Shock in z direction\n"); + msg += fmt::format(" Cell mass-like parameter qmass " + "(units of mass^2/length^4) = {:12.5e}\n", qmass); + msg += fmt::format(" Shock velocity = {:12.5e}\n", velocity); + msg += fmt::format(" Artificial viscosity (units of " + "mass/length/time) = {:12.5e}\n", mu); - fprintf(logfile," Cell mass-like parameter qmass (units of mass^2/length^4) = %12.5e\n", qmass); - fprintf(logfile," Shock velocity = %12.5e\n", velocity); - fprintf(logfile," Artificial viscosity (units of mass/length/time) = %12.5e\n", mu); - - if (p0_set) - fprintf(logfile," Initial pressure specified to be %12.5e\n", p0); - else fprintf(logfile," Initial pressure calculated on first step\n"); - if (v0_set) - fprintf(logfile," Initial volume specified to be %12.5e\n", v0); - else fprintf(logfile," Initial volume calculated on first step\n"); - if (e0_set) - fprintf(logfile," Initial energy specified to be %12.5e\n", e0); - else fprintf(logfile," Initial energy calculated on first step\n"); - } + if (p0_set) + msg += fmt::format(" Initial pressure specified to be {:12.5e}\n", p0); + else msg += " Initial pressure calculated on first step\n"; + if (v0_set) + msg += fmt::format(" Initial volume specified to be {:12.5e}\n", v0); + else msg += " Initial volume calculated on first step\n"; + if (e0_set) + msg += fmt::format(" Initial energy specified to be {:12.5e}\n", e0); + else msg += " Initial energy calculated on first step\n"; + utils::logmesg(lmp,msg); } // create a new compute temp style @@ -363,14 +362,17 @@ void FixQBMSST::init() //set up the h time step for updating the random force \delta{}h=\frac{\pi}{\Omega_{max}} if (int(1.0/(2*f_max*dtv)) == 0) { - if (comm->me == 0) printf ("Warning: Either f_max is too high or the time step is too big, setting f_max to be 1/timestep!\n"); + if (comm->me == 0) error->warning(FLERR,"Either f_max is too high or the time step " + "is too big, setting f_max to be 1/timestep!\n"); h_timestep=dtv; alpha=1; } else { alpha=int(1.0/(2*f_max*dtv)); h_timestep=alpha*dtv; } - if (comm->me == 0) printf ("The effective maximum frequncy is now %f inverse time unit with alpha value as %d!\n", 0.5/h_timestep, alpha); + if (comm->me == 0 && screen) + fmt::print(screen,"The effective maximum frequency is now {} inverse time unit " + "with alpha value as {}!\n", 0.5/h_timestep, alpha); //gfactor is the random force \sqrt{\frac{2\gamma{}m_{i}}{\alpha*\delta{}t}}, \sqrt{12} makes the random array variance equal to unit. for (int i = 1; i <= atom->ntypes; i++) { @@ -432,20 +434,16 @@ void FixQBMSST::setup(int /*vflag*/) if ( v0_set == 0 ) { v0 = compute_vol(); v0_set = 1; - if (comm->me == 0) { - if ( screen ) fprintf(screen,"Fix QBMSST v0 = %12.5e\n", v0); - if ( logfile ) fprintf(logfile,"Fix QBMSST v0 = %12.5e\n", v0); - } + if (comm->me == 0) + utils::logmesg(lmp,fmt::format("Fix QBMSST v0 = {:12.5e}\n", v0)); } if ( p0_set == 0 ) { p0 = p_current[direction]; p0_set = 1; - if ( comm->me == 0 ) { - if ( screen ) fprintf(screen,"Fix QBMSST p0 = %12.5e\n", p0); - if ( logfile ) fprintf(logfile,"Fix QBMSST p0 = %12.5e\n", p0); - } + if ( comm->me == 0 ) + utils::logmesg(lmp,fmt::format("Fix QBMSST p0 = {:12.5e}\n", p0)); } if ( e0_set == 0 ) { @@ -453,11 +451,8 @@ void FixQBMSST::setup(int /*vflag*/) e0_set = 1; old_eavg = e0; - if ( comm->me == 0 ) { - if ( screen ) fprintf(screen,"Fix QBMSST e0 = to be %12.5e\n",e0); - if ( logfile ) fprintf(logfile,"Fix QBMSST e0 = to be %12.5e\n",e0); - } - + if ( comm->me == 0 ) + utils::logmesg(lmp,fmt::format("Fix QBMSST e0 = to be {:12.5e}\n",e0)); } temperature->compute_vector(); @@ -476,16 +471,10 @@ void FixQBMSST::setup(int /*vflag*/) omega[direction]=-1*sqrt(fac1); double fac2 = omega[direction]/v0; - if ( comm->me == 0 && tscale != 1.0) { - if ( screen ) - fprintf(screen,"Fix QBMSST initial strain rate of %12.5e established " - "by reducing temperature by factor of %12.5e\n", - fac2,tscale); - if ( logfile ) - fprintf(logfile,"Fix QBMSST initial strain rate of %12.5e established " - "by reducing temperature by factor of %12.5e\n", - fac2,tscale); - } + if ( comm->me == 0 && tscale != 1.0) + utils::logmesg(lmp,fmt::format("Fix QBMSST initial strain rate of {:12.5e} " + "established by reducing temperature by " + "factor of {:12.5e}\n",fac2,tscale)); for (int i = 0; i < atom->nlocal; i++) { if (mask[i] & groupbit) { for (int k = 0; k < 3; k++ ) { @@ -531,30 +520,31 @@ void FixQBMSST::initial_integrate(int /*vflag*/) // decide if the qtb temperature need to be updated or not if (counter_l == 0) { t_current -= dtv*fric_coef*eta*beta*(old_eavg-e0)/(3*ntotal*boltz); - old_eavg = 0;//clear old energy average - if (t_current < 0.0) t_current=0; + if (t_current > 0.0) { + old_eavg = 0;//clear old energy average - // load omega_H with calculated spectrum at a specific temperature (corrected spectrum), omega_H is the Fourier transformation of time_H - for (int k = 0; k < 2*N_f; k++) { - double f_k=(k-N_f)/(2*N_f*h_timestep); //\omega_k=\frac{2\pi}{\delta{}h}\frac{k}{2N_f} for k from -N_f to N_f-1 - if(k == N_f) { - omega_H[k]=sqrt(force->boltz * t_current); - } else { - double energy_k= force->hplanck * fabs(f_k); - omega_H[k]=sqrt( energy_k * (0.5+1.0/( exp(energy_k/(force->boltz * t_current)) - 1.0 )) ); - omega_H[k]*=alpha*sin((k-N_f)*MY_PI/(2*alpha*N_f))/sin((k-N_f)*MY_PI/(2*N_f)); - } - } - - // construct the signal filter H, filter has the unit of of sqrt(energy) \sqrt{2N_f}^{-1}H\left(t_n\right) - for (int n = 0; n < 2*N_f; n++) { - time_H[n] = 0; - double t_n=(n-N_f); + // load omega_H with calculated spectrum at a specific temperature (corrected spectrum), omega_H is the Fourier transformation of time_H for (int k = 0; k < 2*N_f; k++) { - double omega_k=(k-N_f)*MY_PI/N_f; - time_H[n] += omega_H[k]*(cos(omega_k*t_n)); + double f_k=(k-N_f)/(2*N_f*h_timestep); //\omega_k=\frac{2\pi}{\delta{}h}\frac{k}{2N_f} for k from -N_f to N_f-1 + if(k == N_f) { + omega_H[k]=sqrt(force->boltz * t_current); + } else { + double energy_k= force->hplanck * fabs(f_k); + omega_H[k]=sqrt( energy_k * (0.5+1.0/( exp(energy_k/(force->boltz * t_current)) - 1.0 )) ); + omega_H[k]*=alpha*sin((k-N_f)*MY_PI/(2*alpha*N_f))/sin((k-N_f)*MY_PI/(2*N_f)); + } + } + + // construct the signal filter H, filter has the unit of of sqrt(energy) \sqrt{2N_f}^{-1}H\left(t_n\right) + for (int n = 0; n < 2*N_f; n++) { + time_H[n] = 0; + double t_n=(n-N_f); + for (int k = 0; k < 2*N_f; k++) { + double omega_k=(k-N_f)*MY_PI/N_f; + time_H[n] += omega_H[k]*(cos(omega_k*t_n)); + } + time_H[n]/=(2.0*N_f); } - time_H[n]/=(2.0*N_f); } } @@ -1170,11 +1160,12 @@ void FixQBMSST::copy_arrays(int i, int j, int /*delflag*/) ------------------------------------------------------------------------- */ int FixQBMSST::pack_exchange(int i, double *buf) { - for (int m = 0; m < 2*N_f; m++) buf[m] = random_array_0[i][m]; - for (int m = 0; m < 2*N_f; m++) buf[m+2*N_f] = random_array_1[i][m]; - for (int m = 0; m < 2*N_f; m++) buf[m+4*N_f] = random_array_2[i][m]; - for (int m = 0; m < 3; m++) buf[m+6*N_f] = fran[i][m]; - return 6*N_f+3; + int n = 0; + for (int m = 0; m < 2*N_f; m++) buf[n++] = random_array_0[i][m]; + for (int m = 0; m < 2*N_f; m++) buf[n++] = random_array_1[i][m]; + for (int m = 0; m < 2*N_f; m++) buf[n++] = random_array_2[i][m]; + for (int m = 0; m < 3; m++) buf[n++] = fran[i][m]; + return n; } /* ---------------------------------------------------------------------- @@ -1182,9 +1173,10 @@ int FixQBMSST::pack_exchange(int i, double *buf) ------------------------------------------------------------------------- */ int FixQBMSST::unpack_exchange(int nlocal, double *buf) { - for (int m = 0; m < 2*N_f; m++) random_array_0[nlocal][m] = buf[m]; - for (int m = 0; m < 2*N_f; m++) random_array_1[nlocal][m] = buf[m+2*N_f]; - for (int m = 0; m < 2*N_f; m++) random_array_2[nlocal][m] = buf[m+4*N_f]; - for (int m = 0; m < 3; m++) fran[nlocal][m] = buf[m+6*N_f]; - return 6*N_f+3; + int n = 0; + for (int m = 0; m < 2*N_f; m++) random_array_0[nlocal][m] = buf[n++]; + for (int m = 0; m < 2*N_f; m++) random_array_1[nlocal][m] = buf[n++]; + for (int m = 0; m < 2*N_f; m++) random_array_2[nlocal][m] = buf[n++]; + for (int m = 0; m < 3; m++) fran[nlocal][m] = buf[n++]; + return n; } diff --git a/src/USER-QTB/fix_qtb.cpp b/src/USER-QTB/fix_qtb.cpp index fa15385859..646cf06ce2 100644 --- a/src/USER-QTB/fix_qtb.cpp +++ b/src/USER-QTB/fix_qtb.cpp @@ -32,6 +32,8 @@ #include "math_const.h" #include "memory.h" #include "error.h" +#include "utils.h" +#include "fmt/format.h" using namespace LAMMPS_NS; using namespace FixConst; @@ -62,27 +64,34 @@ FixQTB::FixQTB(LAMMPS *lmp, int narg, char **arg) : while (iarg < narg) { if (strcmp(arg[iarg],"temp") == 0) { if (iarg+2 > narg) error->all(FLERR,"Illegal fix qtb command"); - t_target = atof(arg[iarg+1]); if (t_target < 0.0) error->all(FLERR,"Fix qtb temp must be >= 0.0"); + t_target = force->numeric(FLERR,arg[iarg+1]); + if (t_target < 0.0) error->all(FLERR,"Fix qtb temp must be >= 0.0"); iarg += 2; } else if (strcmp(arg[iarg],"damp") == 0) { if (iarg+2 > narg) error->all(FLERR,"Illegal fix qtb command"); - t_period = atof(arg[iarg+1]); if (t_period <= 0.0) error->all(FLERR,"Fix qtb damp must be > 0.0"); fric_coef = 1/t_period; + t_period = force->numeric(FLERR,arg[iarg+1]); + if (t_period <= 0.0) error->all(FLERR,"Fix qtb damp must be > 0.0"); fric_coef = 1/t_period; iarg += 2; } else if (strcmp(arg[iarg],"seed") == 0) { if (iarg+2 > narg) error->all(FLERR,"Illegal fix qtb command"); - seed = atof(arg[iarg+1]); if (seed <= 0) error->all(FLERR,"Illegal fix qtb command"); + seed = force->inumeric(FLERR,arg[iarg+1]); + if (seed <= 0) error->all(FLERR,"Illegal fix qtb command"); iarg += 2; } else if (strcmp(arg[iarg],"f_max") == 0) { if (iarg+2 > narg) error->all(FLERR,"Illegal fix qtb command"); - f_max = atof(arg[iarg+1]); if (f_max <= 0) error->all(FLERR,"Illegal fix qtb command"); + f_max = force->numeric(FLERR,arg[iarg+1]); + if (f_max <= 0) error->all(FLERR,"Illegal fix qtb command"); iarg += 2; } else if (strcmp(arg[iarg],"N_f") == 0) { if (iarg+2 > narg) error->all(FLERR,"Illegal fix qtb command"); - N_f = atof(arg[iarg+1]); if (N_f <= 0) error->all(FLERR,"Illegal fix qtb command"); + N_f = force->inumeric(FLERR,arg[iarg+1]); + if (N_f <= 0) error->all(FLERR,"Illegal fix qtb command"); iarg += 2; } else error->all(FLERR,"Illegal fix qtb command"); } + maxexchange = 6*N_f+3; + // allocate qtb gfactor1 = NULL; gfactor3 = NULL; @@ -105,10 +114,6 @@ FixQTB::FixQTB(LAMMPS *lmp, int narg, char **arg) : // allocate random-arrays and fran grow_arrays(atom->nmax); atom->add_callback(0); - // memory->create(random_array_0,atom->nmax+300,2*N_f,"qtb:random_array_0"); - // memory->create(random_array_1,atom->nmax+300,2*N_f,"qtb:random_array_1"); - // memory->create(random_array_2,atom->nmax+300,2*N_f,"qtb:random_array_2"); - // memory->create(fran,atom->nmax+300,3,"qtb:fran"); // allocate omega_H and time_H memory->create(omega_H,2*N_f,"qtb:omega_H"); @@ -160,14 +165,17 @@ void FixQTB::init() //set up the h time step for updating the random force \delta{}h=\frac{\pi}{\Omega_{max}} if (int(1.0/(2*f_max*dtv)) == 0) { - if (comm->me == 0) printf ("Warning: Either f_max is too high or the time step is too big, setting f_max to be 1/timestep!\n"); + if (comm->me == 0) error->warning(FLERR,"Either f_max is too high or the time step " + "is too big, setting f_max to be 1/timestep!\n"); h_timestep=dtv; alpha=1; } else { alpha=int(1.0/(2*f_max*dtv)); h_timestep=alpha*dtv; } - if (comm->me == 0) printf ("The effective maximum frequncy is now %f inverse time unit with alpha value as %d!\n", 0.5/h_timestep, alpha); + if (comm->me == 0 && screen) + fmt::print(screen,"The effective maximum frequency is now {} inverse time unit " + "with alpha value as {}!\n", 0.5/h_timestep, alpha); // set force prefactors if (!atom->rmass) { @@ -404,11 +412,12 @@ void FixQTB::copy_arrays(int i, int j, int /*delflag*/) ------------------------------------------------------------------------- */ int FixQTB::pack_exchange(int i, double *buf) { - for (int m = 0; m < 2*N_f; m++) buf[m] = random_array_0[i][m]; - for (int m = 0; m < 2*N_f; m++) buf[m+2*N_f] = random_array_1[i][m]; - for (int m = 0; m < 2*N_f; m++) buf[m+4*N_f] = random_array_2[i][m]; - for (int m = 0; m < 3; m++) buf[m+6*N_f] = fran[i][m]; - return 6*N_f+3; + int n = 0; + for (int m = 0; m < 2*N_f; m++) buf[n++] = random_array_0[i][m]; + for (int m = 0; m < 2*N_f; m++) buf[n++] = random_array_1[i][m]; + for (int m = 0; m < 2*N_f; m++) buf[n++] = random_array_2[i][m]; + for (int m = 0; m < 3; m++) buf[n++] = fran[i][m]; + return n; } /* ---------------------------------------------------------------------- @@ -416,9 +425,10 @@ int FixQTB::pack_exchange(int i, double *buf) ------------------------------------------------------------------------- */ int FixQTB::unpack_exchange(int nlocal, double *buf) { - for (int m = 0; m < 2*N_f; m++) random_array_0[nlocal][m] = buf[m]; - for (int m = 0; m < 2*N_f; m++) random_array_1[nlocal][m] = buf[m+2*N_f]; - for (int m = 0; m < 2*N_f; m++) random_array_2[nlocal][m] = buf[m+4*N_f]; - for (int m = 0; m < 3; m++) fran[nlocal][m] = buf[m+6*N_f]; - return 6*N_f+3; + int n = 0; + for (int m = 0; m < 2*N_f; m++) random_array_0[nlocal][m] = buf[n++]; + for (int m = 0; m < 2*N_f; m++) random_array_1[nlocal][m] = buf[n++]; + for (int m = 0; m < 2*N_f; m++) random_array_2[nlocal][m] = buf[n++]; + for (int m = 0; m < 3; m++) fran[nlocal][m] = buf[n++]; + return n; } diff --git a/src/USER-QTB/fix_qtb.h b/src/USER-QTB/fix_qtb.h index 8fd14f5c5b..86a91bc9f6 100644 --- a/src/USER-QTB/fix_qtb.h +++ b/src/USER-QTB/fix_qtb.h @@ -47,22 +47,23 @@ class FixQTB : public Fix { private: // qtb parameters - int counter_mu; // counter l and mu - double t_period, fric_coef; // friction coefficient - int seed; // seed for the random number generator - double f_max; // frequency cutoff - int N_f; // number of frequency grid - double t_target; // target qtb temperature + int counter_mu; // counter l and mu + double t_period, fric_coef; // friction coefficient + int seed; // seed for the random number generator + double f_max; // frequency cutoff + int N_f; // number of frequency grid + double t_target; // target qtb temperature char *id_temp; class Compute *temperature; - double h_timestep; // time step to update the random forces - int alpha; // number of time steps to update the random forces - class RanMars *random; // random number generator - double *gfactor1,*gfactor3; // factors of frictions and random forces - double *omega_H,*time_H; // H gives the desired power spectrum - double **random_array_0, **random_array_1, **random_array_2; // random number arrays give independence between atoms and directions + double h_timestep; // time step to update the random forces + int alpha; // number of time steps to update the random forces + class RanMars *random; // random number generator + double *gfactor1,*gfactor3; // factors of frictions and random forces + double *omega_H,*time_H; // H gives the desired power spectrum + // random number arrays give independence between atoms and directions + double **random_array_0, **random_array_1, **random_array_2; int nlevels_respa; - double **fran, fsum[3], fsumall[3]; // random forces and their sums + double **fran, fsum[3], fsumall[3]; // random forces and their sums }; } diff --git a/src/USER-REAXC/reaxc_ffield.cpp b/src/USER-REAXC/reaxc_ffield.cpp index c8e097eb1c..b865b48ad3 100644 --- a/src/USER-REAXC/reaxc_ffield.cpp +++ b/src/USER-REAXC/reaxc_ffield.cpp @@ -337,6 +337,8 @@ char Read_Force_Field( FILE *fp, reax_interaction *reax, j = atoi(tmp[0]) - 1; k = atoi(tmp[1]) - 1; + if ((c < 10) || (j < 0) || (k < 0)) + control->error_ptr->all(FLERR, "Inconsistent force field file"); if (j < reax->num_atom_types && k < reax->num_atom_types) { @@ -361,6 +363,8 @@ char Read_Force_Field( FILE *fp, reax_interaction *reax, /* line 2 */ fgets(s,MAX_LINE,fp); c=Tokenize(s,&tmp); + if (c < 8) + control->error_ptr->all(FLERR, "Inconsistent force field file"); val = atof(tmp[0]); reax->tbp[j][k].p_be2 = val; reax->tbp[k][j].p_be2 = val; @@ -491,6 +495,9 @@ char Read_Force_Field( FILE *fp, reax_interaction *reax, j = atoi(tmp[0]) - 1; k = atoi(tmp[1]) - 1; + if ((c < (lgflag ? 9 : 8)) || (j < 0) || (k < 0)) + control->error_ptr->all(FLERR, "Inconsistent force field file"); + if (j < reax->num_atom_types && k < reax->num_atom_types) { val = atof(tmp[2]); if (val > 0.0) { @@ -528,10 +535,12 @@ char Read_Force_Field( FILE *fp, reax_interaction *reax, reax->tbp[k][j].r_pp = val; } - val = atof(tmp[8]); - if (val >= 0.0) { - reax->tbp[j][k].lgcij = val; - reax->tbp[k][j].lgcij = val; + if (lgflag) { + val = atof(tmp[8]); + if (val >= 0.0) { + reax->tbp[j][k].lgcij = val; + reax->tbp[k][j].lgcij = val; + } } } } @@ -552,6 +561,8 @@ char Read_Force_Field( FILE *fp, reax_interaction *reax, j = atoi(tmp[0]) - 1; k = atoi(tmp[1]) - 1; m = atoi(tmp[2]) - 1; + if ((c < 10) || (j < 0) || (k < 0) || (m < 0)) + control->error_ptr->all(FLERR, "Inconsistent force field file"); if (j < reax->num_atom_types && k < reax->num_atom_types && m < reax->num_atom_types) { @@ -611,6 +622,8 @@ char Read_Force_Field( FILE *fp, reax_interaction *reax, k = atoi(tmp[1]) - 1; m = atoi(tmp[2]) - 1; n = atoi(tmp[3]) - 1; + if ((c < 9) || (k < 0) || (m < 0)) + control->error_ptr->all(FLERR, "Inconsistent force field file"); if (j >= 0 && n >= 0) { // this means the entry is not in compact form if (j < reax->num_atom_types && k < reax->num_atom_types && @@ -667,8 +680,6 @@ char Read_Force_Field( FILE *fp, reax_interaction *reax, } } - - /* next line is number of hydrogen bond params and some comments */ fgets( s, MAX_LINE, fp ); c = Tokenize( s, &tmp ); @@ -686,7 +697,8 @@ char Read_Force_Field( FILE *fp, reax_interaction *reax, j = atoi(tmp[0]) - 1; k = atoi(tmp[1]) - 1; m = atoi(tmp[2]) - 1; - + if ((c < 7) || (j < 0) || (k < 0) || (m < 0)) + control->error_ptr->all(FLERR, "Inconsistent force field file"); if (j < reax->num_atom_types && m < reax->num_atom_types) { val = atof(tmp[3]); diff --git a/src/atom.cpp b/src/atom.cpp index 7ed6001f2d..f6379213ea 100644 --- a/src/atom.cpp +++ b/src/atom.cpp @@ -48,8 +48,6 @@ using namespace MathConst; #define DELTA_PERATOM 64 #define EPSILON 1.0e-6 -enum{DOUBLE,INT,BIGINT}; - /* ---------------------------------------------------------------------- */ Atom::Atom(LAMMPS *lmp) : Pointers(lmp) @@ -1086,7 +1084,7 @@ void Atom::data_atoms(int n, char *buf, tagint id_offset, tagint mol_offset, next = strchr(buf,'\n'); *next = '\0'; - int nwords = utils::count_words(buf); + int nwords = utils::trim_and_count_words(buf); *next = '\n'; if (nwords != avec->size_data_atom && nwords != avec->size_data_atom + 3) @@ -1236,7 +1234,7 @@ void Atom::data_vels(int n, char *buf, tagint id_offset) next = strchr(buf,'\n'); *next = '\0'; - int nwords = utils::count_words(buf); + int nwords = utils::trim_and_count_words(buf); *next = '\n'; if (nwords != avec->size_data_vel) @@ -1588,7 +1586,7 @@ void Atom::data_bonus(int n, char *buf, AtomVec *avec_bonus, tagint id_offset) next = strchr(buf,'\n'); *next = '\0'; - int nwords = utils::count_words(buf); + int nwords = utils::trim_and_count_words(buf); *next = '\n'; if (nwords != avec_bonus->size_data_bonus) diff --git a/src/atom.h b/src/atom.h index fca682aff6..e20ee0596d 100644 --- a/src/atom.h +++ b/src/atom.h @@ -24,6 +24,7 @@ class Atom : protected Pointers { public: char *atom_style; class AtomVec *avec; + enum{DOUBLE,INT,BIGINT}; // atom counts diff --git a/src/atom_vec.cpp b/src/atom_vec.cpp index b9a8d6b09d..8cd7db4fd4 100644 --- a/src/atom_vec.cpp +++ b/src/atom_vec.cpp @@ -33,8 +33,6 @@ using namespace MathConst; #define DELTA 16384 #define DELTA_BONUS 8192 -enum{DOUBLE,INT,BIGINT}; - /* ---------------------------------------------------------------------- */ AtomVec::AtomVec(LAMMPS *lmp) : Pointers(lmp) @@ -214,7 +212,7 @@ void AtomVec::grow(int n) datatype = mgrow.datatype[i]; cols = mgrow.cols[i]; const int nthreads = threads[i] ? comm->nthreads : 1; - if (datatype == DOUBLE) { + if (datatype == Atom::DOUBLE) { if (cols == 0) memory->grow(*((double **) pdata),nmax*nthreads,"atom:dvec"); else if (cols > 0) @@ -223,7 +221,7 @@ void AtomVec::grow(int n) maxcols = *(mgrow.maxcols[i]); memory->grow(*((double ***) pdata),nmax*nthreads,maxcols,"atom:darray"); } - } else if (datatype == INT) { + } else if (datatype == Atom::INT) { if (cols == 0) memory->grow(*((int **) pdata),nmax*nthreads,"atom:ivec"); else if (cols > 0) @@ -232,14 +230,14 @@ void AtomVec::grow(int n) maxcols = *(mgrow.maxcols[i]); memory->grow(*((int ***) pdata),nmax*nthreads,maxcols,"atom:iarray"); } - } else if (datatype == BIGINT) { + } else if (datatype == Atom::BIGINT) { if (cols == 0) memory->grow(*((bigint **) pdata),nmax*nthreads,"atom:bvec"); else if (cols > 0) memory->grow(*((bigint ***) pdata),nmax*nthreads,cols,"atom:barray"); else { maxcols = *(mgrow.maxcols[i]); - memory->grow(*((int ***) pdata),nmax*nthreads,maxcols,"atom:barray"); + memory->grow(*((bigint ***) pdata),nmax*nthreads,maxcols,"atom:barray"); } } } @@ -275,7 +273,7 @@ void AtomVec::copy(int i, int j, int delflag) pdata = mcopy.pdata[n]; datatype = mcopy.datatype[n]; cols = mcopy.cols[n]; - if (datatype == DOUBLE) { + if (datatype == Atom::DOUBLE) { if (cols == 0) { double *vec = *((double **) pdata); vec[j] = vec[i]; @@ -292,7 +290,7 @@ void AtomVec::copy(int i, int j, int delflag) for (m = 0; m < ncols; m++) array[j][m] = array[i][m]; } - } else if (datatype == INT) { + } else if (datatype == Atom::INT) { if (cols == 0) { int *vec = *((int **) pdata); vec[j] = vec[i]; @@ -309,7 +307,7 @@ void AtomVec::copy(int i, int j, int delflag) for (m = 0; m < ncols; m++) array[j][m] = array[i][m]; } - } else if (datatype == BIGINT) { + } else if (datatype == Atom::BIGINT) { if (cols == 0) { bigint *vec = *((bigint **) pdata); vec[j] = vec[i]; @@ -377,7 +375,7 @@ int AtomVec::pack_comm(int n, int *list, double *buf, pdata = mcomm.pdata[nn]; datatype = mcomm.datatype[nn]; cols = mcomm.cols[nn]; - if (datatype == DOUBLE) { + if (datatype == Atom::DOUBLE) { if (cols == 0) { double *vec = *((double **) pdata); for (i = 0; i < n; i++) { @@ -392,7 +390,7 @@ int AtomVec::pack_comm(int n, int *list, double *buf, buf[m++] = array[j][mm]; } } - } else if (datatype == INT) { + } else if (datatype == Atom::INT) { if (cols == 0) { int *vec = *((int **) pdata); for (i = 0; i < n; i++) { @@ -407,7 +405,7 @@ int AtomVec::pack_comm(int n, int *list, double *buf, buf[m++] = ubuf(array[j][mm]).d; } } - } else if (datatype == BIGINT) { + } else if (datatype == Atom::BIGINT) { if (cols == 0) { bigint *vec = *((bigint **) pdata); for (i = 0; i < n; i++) { @@ -498,7 +496,7 @@ int AtomVec::pack_comm_vel(int n, int *list, double *buf, pdata = mcomm_vel.pdata[nn]; datatype = mcomm_vel.datatype[nn]; cols = mcomm_vel.cols[nn]; - if (datatype == DOUBLE) { + if (datatype == Atom::DOUBLE) { if (cols == 0) { double *vec = *((double **) pdata); for (i = 0; i < n; i++) { @@ -513,7 +511,7 @@ int AtomVec::pack_comm_vel(int n, int *list, double *buf, buf[m++] = array[j][mm]; } } - } else if (datatype == INT) { + } else if (datatype == Atom::INT) { if (cols == 0) { int *vec = *((int **) pdata); for (i = 0; i < n; i++) { @@ -528,7 +526,7 @@ int AtomVec::pack_comm_vel(int n, int *list, double *buf, buf[m++] = ubuf(array[j][mm]).d; } } - } else if (datatype == BIGINT) { + } else if (datatype == Atom::BIGINT) { if (cols == 0) { bigint *vec = *((bigint **) pdata); for (i = 0; i < n; i++) { @@ -572,7 +570,7 @@ void AtomVec::unpack_comm(int n, int first, double *buf) pdata = mcomm.pdata[nn]; datatype = mcomm.datatype[nn]; cols = mcomm.cols[nn]; - if (datatype == DOUBLE) { + if (datatype == Atom::DOUBLE) { if (cols == 0) { double *vec = *((double **) pdata); for (i = first; i < last; i++) @@ -583,7 +581,7 @@ void AtomVec::unpack_comm(int n, int first, double *buf) for (mm = 0; mm < cols; mm++) array[i][mm] = buf[m++]; } - } else if (datatype == INT) { + } else if (datatype == Atom::INT) { if (cols == 0) { int *vec = *((int **) pdata); for (i = first; i < last; i++) @@ -594,7 +592,7 @@ void AtomVec::unpack_comm(int n, int first, double *buf) for (mm = 0; mm < cols; mm++) array[i][mm] = (int) ubuf(buf[m++]).i; } - } else if (datatype == BIGINT) { + } else if (datatype == Atom::BIGINT) { if (cols == 0) { bigint *vec = *((bigint **) pdata); for (i = first; i < last; i++) @@ -635,7 +633,7 @@ void AtomVec::unpack_comm_vel(int n, int first, double *buf) pdata = mcomm_vel.pdata[nn]; datatype = mcomm_vel.datatype[nn]; cols = mcomm_vel.cols[nn]; - if (datatype == DOUBLE) { + if (datatype == Atom::DOUBLE) { if (cols == 0) { double *vec = *((double **) pdata); for (i = first; i < last; i++) @@ -646,18 +644,18 @@ void AtomVec::unpack_comm_vel(int n, int first, double *buf) for (mm = 0; mm < cols; mm++) array[i][mm] = buf[m++]; } - } else if (datatype == INT) { + } else if (datatype == Atom::INT) { if (cols == 0) { int *vec = *((int **) pdata); for (i = first; i < last; i++) - vec[i] = ubuf(buf[m++]).i; + vec[i] = (int) ubuf(buf[m++]).i; } else { int **array = *((int ***) pdata); for (i = first; i < last; i++) for (mm = 0; mm < cols; mm++) array[i][mm] = (int) ubuf(buf[m++]).i; } - } else if (datatype == BIGINT) { + } else if (datatype == Atom::BIGINT) { if (cols == 0) { bigint *vec = *((bigint **) pdata); for (i = first; i < last; i++) @@ -695,7 +693,7 @@ int AtomVec::pack_reverse(int n, int first, double *buf) pdata = mreverse.pdata[nn]; datatype = mreverse.datatype[nn]; cols = mreverse.cols[nn]; - if (datatype == DOUBLE) { + if (datatype == Atom::DOUBLE) { if (cols == 0) { double *vec = *((double **) pdata); for (i = first; i < last; i++) { @@ -708,7 +706,7 @@ int AtomVec::pack_reverse(int n, int first, double *buf) buf[m++] = array[i][mm]; } } - } else if (datatype == INT) { + } else if (datatype == Atom::INT) { if (cols == 0) { int *vec = *((int **) pdata); for (i = first; i < last; i++) { @@ -721,7 +719,7 @@ int AtomVec::pack_reverse(int n, int first, double *buf) buf[m++] = ubuf(array[i][mm]).d; } } - } else if (datatype == BIGINT) { + } else if (datatype == Atom::BIGINT) { if (cols == 0) { bigint *vec = *((bigint **) pdata); for (i = first; i < last; i++) { @@ -761,7 +759,7 @@ void AtomVec::unpack_reverse(int n, int *list, double *buf) pdata = mreverse.pdata[nn]; datatype = mreverse.datatype[nn]; cols = mreverse.cols[nn]; - if (datatype == DOUBLE) { + if (datatype == Atom::DOUBLE) { if (cols == 0) { double *vec = *((double **) pdata); for (i = 0; i < n; i++) { @@ -776,34 +774,34 @@ void AtomVec::unpack_reverse(int n, int *list, double *buf) array[j][mm] += buf[m++]; } } - } else if (datatype == INT) { + } else if (datatype == Atom::INT) { if (cols == 0) { int *vec = *((int **) pdata); for (i = 0; i < n; i++) { j = list[i]; - vec[j] += buf[m++]; + vec[j] += (int) ubuf(buf[m++]).i; } } else { int **array = *((int ***) pdata); for (i = 0; i < n; i++) { j = list[i]; for (mm = 0; mm < cols; mm++) - array[j][mm] += buf[m++]; + array[j][mm] += (int) ubuf(buf[m++]).i; } } - } else if (datatype == BIGINT) { + } else if (datatype == Atom::BIGINT) { if (cols == 0) { bigint *vec = *((bigint **) pdata); for (i = 0; i < n; i++) { j = list[i]; - vec[j] += buf[m++]; + vec[j] += (bigint) ubuf(buf[m++]).i; } } else { bigint **array = *((bigint ***) pdata); for (i = 0; i < n; i++) { j = list[i]; for (mm = 0; mm < cols; mm++) - array[j][mm] += buf[m++]; + array[j][mm] += (bigint) ubuf(buf[m++]).i; } } } @@ -856,7 +854,7 @@ int AtomVec::pack_border(int n, int *list, double *buf, int pbc_flag, int *pbc) pdata = mborder.pdata[nn]; datatype = mborder.datatype[nn]; cols = mborder.cols[nn]; - if (datatype == DOUBLE) { + if (datatype == Atom::DOUBLE) { if (cols == 0) { double *vec = *((double **) pdata); for (i = 0; i < n; i++) { @@ -871,7 +869,7 @@ int AtomVec::pack_border(int n, int *list, double *buf, int pbc_flag, int *pbc) buf[m++] = array[j][mm]; } } - } else if (datatype == INT) { + } else if (datatype == Atom::INT) { if (cols == 0) { int *vec = *((int **) pdata); for (i = 0; i < n; i++) { @@ -886,7 +884,7 @@ int AtomVec::pack_border(int n, int *list, double *buf, int pbc_flag, int *pbc) buf[m++] = ubuf(array[j][mm]).d; } } - } else if (datatype == BIGINT) { + } else if (datatype == Atom::BIGINT) { if (cols == 0) { bigint *vec = *((bigint **) pdata); for (i = 0; i < n; i++) { @@ -990,7 +988,7 @@ int AtomVec::pack_border_vel(int n, int *list, double *buf, pdata = mborder_vel.pdata[nn]; datatype = mborder_vel.datatype[nn]; cols = mborder_vel.cols[nn]; - if (datatype == DOUBLE) { + if (datatype == Atom::DOUBLE) { if (cols == 0) { double *vec = *((double **) pdata); for (i = 0; i < n; i++) { @@ -1005,7 +1003,7 @@ int AtomVec::pack_border_vel(int n, int *list, double *buf, buf[m++] = array[j][mm]; } } - } else if (datatype == INT) { + } else if (datatype == Atom::INT) { if (cols == 0) { int *vec = *((int **) pdata); for (i = 0; i < n; i++) { @@ -1020,7 +1018,7 @@ int AtomVec::pack_border_vel(int n, int *list, double *buf, buf[m++] = ubuf(array[j][mm]).d; } } - } else if (datatype == BIGINT) { + } else if (datatype == Atom::BIGINT) { if (cols == 0) { bigint *vec = *((bigint **) pdata); for (i = 0; i < n; i++) { @@ -1072,7 +1070,7 @@ void AtomVec::unpack_border(int n, int first, double *buf) pdata = mborder.pdata[nn]; datatype = mborder.datatype[nn]; cols = mborder.cols[nn]; - if (datatype == DOUBLE) { + if (datatype == Atom::DOUBLE) { if (cols == 0) { double *vec = *((double **) pdata); for (i = first; i < last; i++) @@ -1083,7 +1081,7 @@ void AtomVec::unpack_border(int n, int first, double *buf) for (mm = 0; mm < cols; mm++) array[i][mm] = buf[m++]; } - } else if (datatype == INT) { + } else if (datatype == Atom::INT) { if (cols == 0) { int *vec = *((int **) pdata); for (i = first; i < last; i++) @@ -1094,7 +1092,7 @@ void AtomVec::unpack_border(int n, int first, double *buf) for (mm = 0; mm < cols; mm++) array[i][mm] = (int) ubuf(buf[m++]).i; } - } else if (datatype == BIGINT) { + } else if (datatype == Atom::BIGINT) { if (cols == 0) { bigint *vec = *((bigint **) pdata); for (i = first; i < last; i++) @@ -1144,7 +1142,7 @@ void AtomVec::unpack_border_vel(int n, int first, double *buf) pdata = mborder_vel.pdata[nn]; datatype = mborder_vel.datatype[nn]; cols = mborder_vel.cols[nn]; - if (datatype == DOUBLE) { + if (datatype == Atom::DOUBLE) { if (cols == 0) { double *vec = *((double **) pdata); for (i = first; i < last; i++) @@ -1155,18 +1153,18 @@ void AtomVec::unpack_border_vel(int n, int first, double *buf) for (mm = 0; mm < cols; mm++) array[i][mm] = buf[m++]; } - } else if (datatype == INT) { + } else if (datatype == Atom::INT) { if (cols == 0) { int *vec = *((int **) pdata); for (i = first; i < last; i++) - vec[i] = ubuf(buf[m++]).i; + vec[i] = (int) ubuf(buf[m++]).i; } else { int **array = *((int ***) pdata); for (i = first; i < last; i++) for (mm = 0; mm < cols; mm++) array[i][mm] = (int) ubuf(buf[m++]).i; } - } else if (datatype == BIGINT) { + } else if (datatype == Atom::BIGINT) { if (cols == 0) { bigint *vec = *((bigint **) pdata); for (i = first; i < last; i++) @@ -1216,7 +1214,7 @@ int AtomVec::pack_exchange(int i, double *buf) pdata = mexchange.pdata[nn]; datatype = mexchange.datatype[nn]; cols = mexchange.cols[nn]; - if (datatype == DOUBLE) { + if (datatype == Atom::DOUBLE) { if (cols == 0) { double *vec = *((double **) pdata); buf[m++] = vec[i]; @@ -1233,7 +1231,7 @@ int AtomVec::pack_exchange(int i, double *buf) for (mm = 0; mm < ncols; mm++) buf[m++] = array[i][mm]; } - } if (datatype == INT) { + } if (datatype == Atom::INT) { if (cols == 0) { int *vec = *((int **) pdata); buf[m++] = ubuf(vec[i]).d; @@ -1250,7 +1248,7 @@ int AtomVec::pack_exchange(int i, double *buf) for (mm = 0; mm < ncols; mm++) buf[m++] = ubuf(array[i][mm]).d; } - } if (datatype == BIGINT) { + } if (datatype == Atom::BIGINT) { if (cols == 0) { bigint *vec = *((bigint **) pdata); buf[m++] = ubuf(vec[i]).d; @@ -1308,7 +1306,7 @@ int AtomVec::unpack_exchange(double *buf) pdata = mexchange.pdata[nn]; datatype = mexchange.datatype[nn]; cols = mexchange.cols[nn]; - if (datatype == DOUBLE) { + if (datatype == Atom::DOUBLE) { if (cols == 0) { double *vec = *((double **) pdata); vec[nlocal] = buf[m++]; @@ -1325,10 +1323,10 @@ int AtomVec::unpack_exchange(double *buf) for (mm = 0; mm < ncols; mm++) array[nlocal][mm] = buf[m++]; } - } else if (datatype == INT) { + } else if (datatype == Atom::INT) { if (cols == 0) { int *vec = *((int **) pdata); - vec[nlocal] = ubuf(buf[m++]).i; + vec[nlocal] = (int) ubuf(buf[m++]).i; } else if (cols > 0) { int **array = *((int ***) pdata); for (mm = 0; mm < cols; mm++) @@ -1342,7 +1340,7 @@ int AtomVec::unpack_exchange(double *buf) for (mm = 0; mm < ncols; mm++) array[nlocal][mm] = (int) ubuf(buf[m++]).i; } - } else if (datatype == BIGINT) { + } else if (datatype == Atom::BIGINT) { if (cols == 0) { bigint *vec = *((bigint **) pdata); vec[nlocal] = (bigint) ubuf(buf[m++]).i; @@ -1450,7 +1448,7 @@ int AtomVec::pack_restart(int i, double *buf) pdata = mrestart.pdata[nn]; datatype = mrestart.datatype[nn]; cols = mrestart.cols[nn]; - if (datatype == DOUBLE) { + if (datatype == Atom::DOUBLE) { if (cols == 0) { double *vec = *((double **) pdata); buf[m++] = vec[i]; @@ -1467,7 +1465,7 @@ int AtomVec::pack_restart(int i, double *buf) for (mm = 0; mm < ncols; mm++) buf[m++] = array[i][mm]; } - } else if (datatype == INT) { + } else if (datatype == Atom::INT) { if (cols == 0) { int *vec = *((int **) pdata); buf[m++] = ubuf(vec[i]).d; @@ -1484,7 +1482,7 @@ int AtomVec::pack_restart(int i, double *buf) for (mm = 0; mm < ncols; mm++) buf[m++] = ubuf(array[i][mm]).d; } - } else if (datatype == BIGINT) { + } else if (datatype == Atom::BIGINT) { if (cols == 0) { bigint *vec = *((bigint **) pdata); buf[m++] = ubuf(vec[i]).d; @@ -1551,7 +1549,7 @@ int AtomVec::unpack_restart(double *buf) pdata = mrestart.pdata[nn]; datatype = mrestart.datatype[nn]; cols = mrestart.cols[nn]; - if (datatype == DOUBLE) { + if (datatype == Atom::DOUBLE) { if (cols == 0) { double *vec = *((double **) pdata); vec[nlocal] = buf[m++]; @@ -1568,10 +1566,10 @@ int AtomVec::unpack_restart(double *buf) for (mm = 0; mm < ncols; mm++) array[nlocal][mm] = buf[m++]; } - } else if (datatype == INT) { + } else if (datatype == Atom::INT) { if (cols == 0) { int *vec = *((int **) pdata); - vec[nlocal] = ubuf(buf[m++]).i; + vec[nlocal] = (int) ubuf(buf[m++]).i; } else if (cols > 0) { int **array = *((int ***) pdata); for (mm = 0; mm < cols; mm++) @@ -1585,7 +1583,7 @@ int AtomVec::unpack_restart(double *buf) for (mm = 0; mm < ncols; mm++) array[nlocal][mm] = (int) ubuf(buf[m++]).i; } - } else if (datatype == BIGINT) { + } else if (datatype == Atom::BIGINT) { if (cols == 0) { bigint *vec = *((bigint **) pdata); vec[nlocal] = (bigint) ubuf(buf[m++]).i; @@ -1594,7 +1592,7 @@ int AtomVec::unpack_restart(double *buf) for (mm = 0; mm < cols; mm++) array[nlocal][mm] = (bigint) ubuf(buf[m++]).i; } else { - int **array = *((int ***) pdata); + bigint **array = *((bigint ***) pdata); collength = mexchange.collength[nn]; plength = mexchange.plength[nn]; if (collength) ncols = (*((int ***) plength))[nlocal][collength-1]; @@ -1654,7 +1652,7 @@ void AtomVec::create_atom(int itype, double *coord) pdata = mcreate.pdata[n]; datatype = mcreate.datatype[n]; cols = mcreate.cols[n]; - if (datatype == DOUBLE) { + if (datatype == Atom::DOUBLE) { if (cols == 0) { double *vec = *((double **) pdata); vec[nlocal] = 0.0; @@ -1663,7 +1661,7 @@ void AtomVec::create_atom(int itype, double *coord) for (m = 0; m < cols; m++) array[nlocal][m] = 0.0; } - } else if (datatype == INT) { + } else if (datatype == Atom::INT) { if (cols == 0) { int *vec = *((int **) pdata); vec[nlocal] = 0; @@ -1672,7 +1670,7 @@ void AtomVec::create_atom(int itype, double *coord) for (m = 0; m < cols; m++) array[nlocal][m] = 0; } - } else if (datatype == BIGINT) { + } else if (datatype == Atom::BIGINT) { if (cols == 0) { bigint *vec = *((bigint **) pdata); vec[nlocal] = 0; @@ -1718,7 +1716,7 @@ void AtomVec::data_atom(double *coord, imageint imagetmp, char **values) pdata = mdata_atom.pdata[n]; datatype = mdata_atom.datatype[n]; cols = mdata_atom.cols[n]; - if (datatype == DOUBLE) { + if (datatype == Atom::DOUBLE) { if (cols == 0) { double *vec = *((double **) pdata); vec[nlocal] = utils::numeric(FLERR,values[ivalue++],true,lmp); @@ -1731,7 +1729,7 @@ void AtomVec::data_atom(double *coord, imageint imagetmp, char **values) for (m = 0; m < cols; m++) array[nlocal][m] = utils::numeric(FLERR,values[ivalue++],true,lmp); } - } else if (datatype == INT) { + } else if (datatype == Atom::INT) { if (cols == 0) { int *vec = *((int **) pdata); vec[nlocal] = utils::inumeric(FLERR,values[ivalue++],true,lmp); @@ -1740,7 +1738,7 @@ void AtomVec::data_atom(double *coord, imageint imagetmp, char **values) for (m = 0; m < cols; m++) array[nlocal][m] = utils::inumeric(FLERR,values[ivalue++],true,lmp); } - } else if (datatype == BIGINT) { + } else if (datatype == Atom::BIGINT) { if (cols == 0) { bigint *vec = *((bigint **) pdata); vec[nlocal] = utils::bnumeric(FLERR,values[ivalue++],true,lmp); @@ -1788,7 +1786,7 @@ void AtomVec::pack_data(double **buf) pdata = mdata_atom.pdata[n]; datatype = mdata_atom.datatype[n]; cols = mdata_atom.cols[n]; - if (datatype == DOUBLE) { + if (datatype == Atom::DOUBLE) { if (cols == 0) { double *vec = *((double **) pdata); buf[i][j++] = vec[i]; @@ -1797,7 +1795,7 @@ void AtomVec::pack_data(double **buf) for (m = 0; m < cols; m++) buf[i][j++] = array[i][m]; } - } else if (datatype == INT) { + } else if (datatype == Atom::INT) { if (cols == 0) { int *vec = *((int **) pdata); buf[i][j++] = ubuf(vec[i]).d; @@ -1806,7 +1804,7 @@ void AtomVec::pack_data(double **buf) for (m = 0; m < cols; m++) buf[i][j++] = ubuf(array[i][m]).d; } - } else if (datatype == BIGINT) { + } else if (datatype == Atom::BIGINT) { if (cols == 0) { bigint *vec = *((bigint **) pdata); buf[i][j++] = ubuf(vec[i]).d; @@ -1844,21 +1842,21 @@ void AtomVec::write_data(FILE *fp, int n, double **buf) for (nn = 1; nn < ndata_atom; nn++) { datatype = mdata_atom.datatype[nn]; cols = mdata_atom.cols[nn]; - if (datatype == DOUBLE) { + if (datatype == Atom::DOUBLE) { if (cols == 0) { fprintf(fp," %-1.16e",buf[i][j++]); } else { for (m = 0; m < cols; m++) fprintf(fp," %-1.16e",buf[i][j++]); } - } else if (datatype == INT) { + } else if (datatype == Atom::INT) { if (cols == 0) { fprintf(fp," %d",(int) ubuf(buf[i][j++]).i); } else { for (m = 0; m < cols; m++) fprintf(fp," %d",(int) ubuf(buf[i][j++]).i); } - } else if (datatype == BIGINT) { + } else if (datatype == Atom::BIGINT) { if (cols == 0) { fmt::print(fp," {}",(bigint) ubuf(buf[i][j++]).i); } else { @@ -1895,7 +1893,7 @@ void AtomVec::data_vel(int ilocal, char **values) pdata = mdata_vel.pdata[n]; datatype = mdata_vel.datatype[n]; cols = mdata_vel.cols[n]; - if (datatype == DOUBLE) { + if (datatype == Atom::DOUBLE) { if (cols == 0) { double *vec = *((double **) pdata); vec[ilocal] = utils::numeric(FLERR,values[ivalue++],true,lmp); @@ -1904,7 +1902,7 @@ void AtomVec::data_vel(int ilocal, char **values) for (m = 0; m < cols; m++) array[ilocal][m] = utils::numeric(FLERR,values[ivalue++],true,lmp); } - } else if (datatype == INT) { + } else if (datatype == Atom::INT) { if (cols == 0) { int *vec = *((int **) pdata); vec[ilocal] = utils::inumeric(FLERR,values[ivalue++],true,lmp); @@ -1913,7 +1911,7 @@ void AtomVec::data_vel(int ilocal, char **values) for (m = 0; m < cols; m++) array[ilocal][m] = utils::inumeric(FLERR,values[ivalue++],true,lmp); } - } else if (datatype == BIGINT) { + } else if (datatype == Atom::BIGINT) { if (cols == 0) { bigint *vec = *((bigint **) pdata); vec[ilocal] = utils::bnumeric(FLERR,values[ivalue++],true,lmp); @@ -1944,7 +1942,7 @@ void AtomVec::pack_vel(double **buf) pdata = mdata_vel.pdata[n]; datatype = mdata_vel.datatype[n]; cols = mdata_vel.cols[n]; - if (datatype == DOUBLE) { + if (datatype == Atom::DOUBLE) { if (cols == 0) { double *vec = *((double **) pdata); buf[i][j++] = vec[i]; @@ -1953,7 +1951,7 @@ void AtomVec::pack_vel(double **buf) for (m = 0; m < cols; m++) buf[i][j++] = array[i][m]; } - } else if (datatype == INT) { + } else if (datatype == Atom::INT) { if (cols == 0) { int *vec = *((int **) pdata); buf[i][j++] = ubuf(vec[i]).d; @@ -1962,7 +1960,7 @@ void AtomVec::pack_vel(double **buf) for (m = 0; m < cols; m++) buf[i][j++] = ubuf(array[i][m]).d; } - } else if (datatype == BIGINT) { + } else if (datatype == Atom::BIGINT) { if (cols == 0) { bigint *vec = *((bigint **) pdata); buf[i][j++] = ubuf(vec[i]).d; @@ -1992,21 +1990,21 @@ void AtomVec::write_vel(FILE *fp, int n, double **buf) for (nn = 1; nn < ndata_vel; nn++) { datatype = mdata_vel.datatype[nn]; cols = mdata_vel.cols[nn]; - if (datatype == DOUBLE) { + if (datatype == Atom::DOUBLE) { if (cols == 0) { fprintf(fp," %-1.16e",buf[i][j++]); } else { for (m = 0; m < cols; m++) fprintf(fp," %-1.16e",buf[i][j++]); } - } else if (datatype == INT) { + } else if (datatype == Atom::INT) { if (cols == 0) { fprintf(fp," %d",(int) ubuf(buf[i][j++]).i); } else { for (m = 0; m < cols; m++) fprintf(fp," %d",(int) ubuf(buf[i][j++]).i); } - } else if (datatype == BIGINT) { + } else if (datatype == Atom::BIGINT) { if (cols == 0) { fmt::print(fp," {}",(bigint) ubuf(buf[i][j++]).i); } else { @@ -2290,7 +2288,7 @@ bigint AtomVec::memory_usage() datatype = mgrow.datatype[i]; cols = mgrow.cols[i]; const int nthreads = threads[i] ? comm->nthreads : 1; - if (datatype == DOUBLE) { + if (datatype == Atom::DOUBLE) { if (cols == 0) { bytes += memory->usage(*((double **) pdata),nmax*nthreads); } else if (cols > 0) { @@ -2299,7 +2297,7 @@ bigint AtomVec::memory_usage() maxcols = *(mgrow.maxcols[i]); bytes += memory->usage(*((double ***) pdata),nmax*nthreads,maxcols); } - } else if (datatype == INT) { + } else if (datatype == Atom::INT) { if (cols == 0) { bytes += memory->usage(*((int **) pdata),nmax*nthreads); } else if (cols > 0) { @@ -2308,7 +2306,7 @@ bigint AtomVec::memory_usage() maxcols = *(mgrow.maxcols[i]); bytes += memory->usage(*((int ***) pdata),nmax*nthreads,maxcols); } - } else if (datatype == BIGINT) { + } else if (datatype == Atom::BIGINT) { if (cols == 0) { bytes += memory->usage(*((bigint **) pdata),nmax*nthreads); } else if (cols > 0) { diff --git a/src/comm.cpp b/src/comm.cpp index 3df3cc4d44..9102e2991d 100644 --- a/src/comm.cpp +++ b/src/comm.cpp @@ -258,10 +258,8 @@ void Comm::init_exchange() int onefix; maxexchange_fix = 0; - for (int i = 0; i < nfix; i++) { - onefix = fix[i]->maxexchange; - maxexchange_fix = MAX(maxexchange_fix,onefix); - } + for (int i = 0; i < nfix; i++) + maxexchange_fix += fix[i]->maxexchange; maxexchange = maxexchange_atom + maxexchange_fix; bufextra = maxexchange + BUFEXTRA; diff --git a/src/fix_property_atom.cpp b/src/fix_property_atom.cpp index aeea9a7dca..f1262f88c7 100644 --- a/src/fix_property_atom.cpp +++ b/src/fix_property_atom.cpp @@ -219,7 +219,7 @@ void FixPropertyAtom::read_data_section(char *keyword, int n, char *buf, next = strchr(buf,'\n'); *next = '\0'; - int nwords = utils::count_words(buf); + int nwords = utils::trim_and_count_words(buf); *next = '\n'; if (nwords != nvalue+1) diff --git a/src/fix_tmd.cpp b/src/fix_tmd.cpp index a174c2efa4..5db7bacbc6 100644 --- a/src/fix_tmd.cpp +++ b/src/fix_tmd.cpp @@ -446,12 +446,12 @@ void FixTMD::readfile(char *file) zprd = hi - lo; bufptr = next + 1; continue; - } else if (utils::count_words(bufptr) == 4) { + } else if (utils::trim_and_count_words(bufptr) == 4) { if (xprd >= 0.0 || yprd >= 0.0 || zprd >= 0.0) error->all(FLERR,"Incorrect format in TMD target file"); imageflag = 0; firstline = 0; - } else if (utils::count_words(bufptr) == 7) { + } else if (utils::trim_and_count_words(bufptr) == 7) { if (xprd < 0.0 || yprd < 0.0 || zprd < 0.0) error->all(FLERR,"Incorrect format in TMD target file"); imageflag = 1; diff --git a/src/force.cpp b/src/force.cpp index 168738bf08..840d7e31ca 100644 --- a/src/force.cpp +++ b/src/force.cpp @@ -1012,102 +1012,19 @@ tagint Force::tnumeric(const char *file, int line, char *str) FILE *Force::open_potential(const char *name) { - FILE *fp; + std::string filepath = utils::get_potential_file_path(name); + std::string date; - if (name == NULL) return NULL; + if(!filepath.empty()) { + date = utils::get_potential_date(filepath, "potential"); - // attempt to open file directly - // if successful, return ptr - - fp = fopen(name,"r"); - if (fp) { - if (comm->me == 0) potential_date(fp,name); - rewind(fp); - return fp; - } - - // try the environment variable directory - - const char *path = getenv("LAMMPS_POTENTIALS"); - if (path == NULL) return NULL; - - const char *pot = potential_name(name); - if (pot == NULL) return NULL; - - size_t len1 = strlen(path); - size_t len2 = strlen(pot); - char *newpath = new char[len1+len2+2]; - - strcpy(newpath,path); -#if defined(_WIN32) - newpath[len1] = '\\'; - newpath[len1+1] = 0; -#else - newpath[len1] = '/'; - newpath[len1+1] = 0; -#endif - strcat(newpath,pot); - - fp = fopen(newpath,"r"); - if (fp) { - if (comm->me == 0) potential_date(fp,name); - rewind(fp); - } - - delete [] newpath; - return fp; -} - -/* ---------------------------------------------------------------------- - strip off leading part of path, return just the filename -------------------------------------------------------------------------- */ - -const char *Force::potential_name(const char *path) -{ - const char *pot; - - if (path == NULL) return NULL; - -#if defined(_WIN32) - // skip over the disk drive part of windows pathnames - if (isalpha(path[0]) && path[1] == ':') - path += 2; -#endif - - for (pot = path; *path != '\0'; ++path) { -#if defined(_WIN32) - if ((*path == '\\') || (*path == '/')) pot = path + 1; -#else - if (*path == '/') pot = path + 1; -#endif - } - - return pot; -} - -/* ---------------------------------------------------------------------- - read first line of potential file - if has DATE field, print following word -------------------------------------------------------------------------- */ - -void Force::potential_date(FILE *fp, const char *name) -{ - char line[MAXLINE]; - char *ptr = fgets(line,MAXLINE,fp); - if (ptr == NULL) return; - - char *word; - word = strtok(line," \t\n\r\f"); - while (word) { - if (strcmp(word,"DATE:") == 0) { - word = strtok(NULL," \t\n\r\f"); - if (word == NULL) return; - utils::logmesg(lmp,fmt::format("Reading potential " - "file {} with DATE: {}",name,word)); - return; + if(!date.empty()) { + utils::logmesg(lmp, fmt::format("Reading potential file {} " + "with DATE: {}\n", name, date)); } - word = strtok(NULL," \t\n\r\f"); + return fopen(filepath.c_str(), "r"); } + return nullptr; } /* ---------------------------------------------------------------------- diff --git a/src/force.h b/src/force.h index bb2dfb2f3b..fa0c0f6877 100644 --- a/src/force.h +++ b/src/force.h @@ -136,8 +136,6 @@ class Force : protected Pointers { tagint tnumeric(const char *, int, char *); FILE *open_potential(const char *); - const char *potential_name(const char *); - void potential_date(FILE *, const char *); bigint memory_usage(); diff --git a/src/molecule.cpp b/src/molecule.cpp index 19d1ed23a2..0dc6bd9f0f 100644 --- a/src/molecule.cpp +++ b/src/molecule.cpp @@ -1402,7 +1402,7 @@ void Molecule::body(int flag, int pflag, char *line) while (nword < nparam) { readline(line); - ncount = utils::count_words(line); + ncount = utils::trim_and_count_words(line); if (ncount == 0) error->one(FLERR,"Too few values in body section of molecule file"); if (nword+ncount > nparam) diff --git a/src/pair_table.cpp b/src/pair_table.cpp index 9cb86b4123..312420c354 100644 --- a/src/pair_table.cpp +++ b/src/pair_table.cpp @@ -28,12 +28,14 @@ #include "memory.h" #include "error.h" #include "utils.h" +#include "tokenizer.h" +#include "table_file_reader.h" +#include "fmt/format.h" using namespace LAMMPS_NS; enum{NONE,RLINEAR,RSQ,BMP}; -#define MAXLINE 1024 #define EPSILONR 1.0e-6 /* ---------------------------------------------------------------------- */ @@ -356,37 +358,18 @@ double PairTable::init_one(int i, int j) void PairTable::read_table(Table *tb, char *file, char *keyword) { - char line[MAXLINE]; + TableFileReader reader(lmp, file, "pair"); - // open file + char * line = reader.find_section_start(keyword); - FILE *fp = force->open_potential(file); - if (fp == NULL) { - std::string str("Cannot open file "); - str += file; - error->one(FLERR,str.c_str()); - } - - // loop until section found with matching keyword - - while (1) { - if (fgets(line,MAXLINE,fp) == NULL) - error->one(FLERR,"Did not find keyword in table file"); - if (strspn(line," \t\n\r") == strlen(line)) continue; // blank line - if (line[0] == '#') continue; // comment - char *word = strtok(line," \t\n\r"); - if (strcmp(word,keyword) == 0) break; // matching keyword - utils::sfgets(FLERR,line,MAXLINE,fp,file,error); // no match, skip section - param_extract(tb,line); - utils::sfgets(FLERR,line,MAXLINE,fp,file,error); - for (int i = 0; i < tb->ninput; i++) - utils::sfgets(FLERR,line,MAXLINE,fp,file,error); + if (!line) { + error->one(FLERR,"Did not find keyword in table file"); } // read args on 2nd line of section // allocate table arrays for file values - utils::sfgets(FLERR,line,MAXLINE,fp,file,error); + line = reader.next_line(); param_extract(tb,line); memory->create(tb->rfile,tb->ninput,"pair:rfile"); memory->create(tb->efile,tb->ninput,"pair:efile"); @@ -407,19 +390,25 @@ void PairTable::read_table(Table *tb, char *file, char *keyword) // if rflag set, compute r // if rflag not set, use r from file - int itmp; double rfile,rnew; union_int_float_t rsq_lookup; int rerror = 0; int cerror = 0; - utils::sfgets(FLERR,line,MAXLINE,fp,file,error); + reader.skip_line(); for (int i = 0; i < tb->ninput; i++) { - if (NULL == fgets(line,MAXLINE,fp)) - error->one(FLERR,"Premature end of file in pair table"); - if (4 != sscanf(line,"%d %lg %lg %lg", - &itmp,&rfile,&tb->efile[i],&tb->ffile[i])) ++cerror; + line = reader.next_line(4); + + try { + ValueTokenizer values(line); + values.next_int(); + rfile = values.next_double(); + tb->efile[i] = values.next_double(); + tb->ffile[i] = values.next_double(); + } catch (TokenizerException & e) { + ++cerror; + } rnew = rfile; if (tb->rflag == RLINEAR) @@ -443,10 +432,6 @@ void PairTable::read_table(Table *tb, char *file, char *keyword) tb->rfile[i] = rnew; } - // close file - - fclose(fp); - // warn if force != dE/dr at any point that is not an inflection point // check via secant approximation to dE/dr // skip two end points since do not have surrounding secants @@ -477,10 +462,9 @@ void PairTable::read_table(Table *tb, char *file, char *keyword) } if (ferror) { - char str[128]; - sprintf(str,"%d of %d force values in table are inconsistent with -dE/dr.\n" - " Should only be flagged at inflection points",ferror,tb->ninput); - error->warning(FLERR,str); + std::string str = fmt::format("{} of {} force values in table are inconsistent with -dE/dr.\n" + " Should only be flagged at inflection points",ferror,tb->ninput); + error->warning(FLERR,str.c_str()); } // warn if re-computed distance values differ from file values @@ -573,31 +557,29 @@ void PairTable::param_extract(Table *tb, char *line) tb->rflag = NONE; tb->fpflag = 0; - char *word = strtok(line," \t\n\r\f"); - while (word) { - if (strcmp(word,"N") == 0) { - word = strtok(NULL," \t\n\r\f"); - tb->ninput = atoi(word); - } else if (strcmp(word,"R") == 0 || strcmp(word,"RSQ") == 0 || - strcmp(word,"BITMAP") == 0) { - if (strcmp(word,"R") == 0) tb->rflag = RLINEAR; - else if (strcmp(word,"RSQ") == 0) tb->rflag = RSQ; - else if (strcmp(word,"BITMAP") == 0) tb->rflag = BMP; - word = strtok(NULL," \t\n\r\f"); - tb->rlo = atof(word); - word = strtok(NULL," \t\n\r\f"); - tb->rhi = atof(word); - } else if (strcmp(word,"FPRIME") == 0) { - tb->fpflag = 1; - word = strtok(NULL," \t\n\r\f"); - tb->fplo = atof(word); - word = strtok(NULL," \t\n\r\f"); - tb->fphi = atof(word); - } else { - printf("WORD: %s\n",word); - error->one(FLERR,"Invalid keyword in pair table parameters"); + try { + ValueTokenizer values(line); + + while (values.has_next()) { + std::string word = values.next_string(); + if (word == "N") { + tb->ninput = values.next_int(); + } else if ((word == "R") || (word == "RSQ") || (word == "BITMAP")) { + if (word == "R") tb->rflag = RLINEAR; + else if (word == "RSQ") tb->rflag = RSQ; + else if (word == "BITMAP") tb->rflag = BMP; + tb->rlo = values.next_double(); + tb->rhi = values.next_double(); + } else if (word == "FPRIME") { + tb->fpflag = 1; + tb->fplo = values.next_double(); + tb->fphi = values.next_double(); + } else { + error->one(FLERR,fmt::format("Invalid keyword {} in pair table parameters", word).c_str()); + } } - word = strtok(NULL," \t\n\r\f"); + } catch (TokenizerException & e) { + error->one(FLERR, e.what()); } if (tb->ninput == 0) error->one(FLERR,"Pair table parameters did not set N"); diff --git a/src/potential_file_reader.cpp b/src/potential_file_reader.cpp index cf90c588f5..9b11c4014f 100644 --- a/src/potential_file_reader.cpp +++ b/src/potential_file_reader.cpp @@ -30,91 +30,129 @@ using namespace LAMMPS_NS; PotentialFileReader::PotentialFileReader(LAMMPS *lmp, const std::string &filename, - const std::string &potential_name) : Pointers(lmp), filename(filename) { + const std::string &potential_name) : + Pointers(lmp), + reader(nullptr), + filename(filename), + filetype(potential_name + " potential") +{ if (comm->me != 0) { - error->one(FLERR, "PotentialFileReader should only be called by proc 0!"); + error->one(FLERR, "FileReader should only be called by proc 0!"); } - fp = force->open_potential(filename.c_str()); - - if (fp == NULL) - error->one(FLERR,fmt::format("Cannot open {} potential file {}: {}", - potential_name, filename, utils::getsyserror())); + try { + reader = open_potential(filename); + if(!reader) { + error->one(FLERR, fmt::format("cannot open {} potential file {}", potential_name, filename)); + } + } catch (FileReaderException & e) { + error->one(FLERR, e.what()); + } } PotentialFileReader::~PotentialFileReader() { - fclose(fp); + delete reader; +} + +void PotentialFileReader::ignore_comments(bool value) { + reader->ignore_comments = value; } void PotentialFileReader::skip_line() { - char *ptr = fgets(line, MAXLINE, fp); - if (ptr == nullptr) - error->one(FLERR,fmt::format("Missing line in {} potential file!", - potential_name)); + try { + reader->skip_line(); + } catch (FileReaderException & e) { + error->one(FLERR, e.what()); + } } char *PotentialFileReader::next_line(int nparams) { - // concatenate lines until have nparams words - int n = 0; - int nwords = 0; - - char *ptr = fgets(line, MAXLINE, fp); - - if (ptr == nullptr) { - // EOF - return nullptr; + try { + return reader->next_line(nparams); + } catch (FileReaderException & e) { + error->one(FLERR, e.what()); } - - // strip comment - if ((ptr = strchr(line, '#'))) *ptr = '\0'; - - nwords = utils::count_words(line); - - if (nwords > 0) { - n = strlen(line); - } - - while(nwords < nparams) { - char *ptr = fgets(&line[n], MAXLINE - n, fp); - - if (ptr == nullptr) { - // EOF - if (nwords > 0 && nwords < nparams) - error->one(FLERR,fmt::format("Incorrect format in {} potential " - "file! {}/{} parameters", - potential_name, nwords, nparams)); - return nullptr; - } - - // strip comment - if ((ptr = strchr(line, '#'))) *ptr = '\0'; - - nwords = utils::count_words(line); - - // skip line if blank - if (nwords > 0) { - n = strlen(line); - } - } - - return line; + return nullptr; } -void PotentialFileReader::next_dvector(int n, double * list) { - int i = 0; - while (i < n) { - char *ptr = fgets(line, MAXLINE, fp); - - if (ptr == nullptr) { - // EOF - if (i < n) - error->one(FLERR,fmt::format("Incorrect format in {} potential file! " - "{}/{} values", potential_name, i, n)); - } - - ValueTokenizer values(line); - while(values.has_next()) { - list[i++] = values.next_double(); - } +void PotentialFileReader::next_dvector(double * list, int n) { + try { + return reader->next_dvector(list, n); + } catch (FileReaderException & e) { + error->one(FLERR, e.what()); } } + +ValueTokenizer PotentialFileReader::next_values(int nparams, const std::string & seperators) { + try { + return reader->next_values(nparams, seperators); + } catch (FileReaderException & e) { + error->one(FLERR, e.what()); + } + return ValueTokenizer(""); +} + +double PotentialFileReader::next_double() { + try { + char * line = reader->next_line(1); + return ValueTokenizer(line).next_double(); + } catch (FileReaderException & e) { + error->one(FLERR, e.what()); + } + return 0.0; +} + +int PotentialFileReader::next_int() { + try { + char * line = reader->next_line(1); + return ValueTokenizer(line).next_int(); + } catch (FileReaderException & e) { + error->one(FLERR, e.what()); + } + return 0; +} + +tagint PotentialFileReader::next_tagint() { + try { + char * line = reader->next_line(1); + return ValueTokenizer(line).next_tagint(); + } catch (FileReaderException & e) { + error->one(FLERR, e.what()); + } + return 0; +} + +bigint PotentialFileReader::next_bigint() { + try { + char * line = reader->next_line(1); + return ValueTokenizer(line).next_bigint(); + } catch (FileReaderException & e) { + error->one(FLERR, e.what()); + } + return 0; +} + +std::string PotentialFileReader::next_string() { + try { + char * line = reader->next_line(1); + return ValueTokenizer(line).next_string(); + } catch (FileReaderException & e) { + error->one(FLERR, e.what()); + } + return ""; +} + +TextFileReader * PotentialFileReader::open_potential(const std::string& path) { + std::string filepath = utils::get_potential_file_path(path); + std::string date; + + if(!filepath.empty()) { + date = utils::get_potential_date(filepath, filetype); + + if(!date.empty()) { + utils::logmesg(lmp, fmt::format("Reading potential file {} with DATE: {}", filename, date)); + } + return new TextFileReader(filepath, filetype); + } + return nullptr; +} diff --git a/src/potential_file_reader.h b/src/potential_file_reader.h index b18d3841c3..c512e7886d 100644 --- a/src/potential_file_reader.h +++ b/src/potential_file_reader.h @@ -21,23 +21,36 @@ #include #include "pointers.h" +#include "tokenizer.h" +#include "text_file_reader.h" namespace LAMMPS_NS { class PotentialFileReader : protected Pointers { - std::string potential_name; + protected: + TextFileReader * reader; std::string filename; - static const int MAXLINE = 1024; - char line[MAXLINE]; - FILE *fp; + std::string filetype; + + TextFileReader * open_potential(const std::string& path); public: PotentialFileReader(class LAMMPS *lmp, const std::string &filename, const std::string &potential_name); - ~PotentialFileReader(); + virtual ~PotentialFileReader(); + + void ignore_comments(bool value); void skip_line(); - char * next_line(int nparams); - void next_dvector(int n, double * list); + char * next_line(int nparams = 0); + void next_dvector(double * list, int n); + ValueTokenizer next_values(int nparams, const std::string & seperators = TOKENIZER_DEFAULT_SEPERATORS); + + // convenience functions + double next_double(); + int next_int(); + tagint next_tagint(); + bigint next_bigint(); + std::string next_string(); }; } // namespace LAMMPS_NS diff --git a/src/read_data.cpp b/src/read_data.cpp index 43c511d107..1ccbccb835 100644 --- a/src/read_data.cpp +++ b/src/read_data.cpp @@ -1661,7 +1661,7 @@ void ReadData::bodies(int firstpass, AtomVec *ptr) while (nword < ninteger) { eof = fgets(&buffer[m],MAXLINE,fp); if (eof == NULL) error->one(FLERR,"Unexpected end of data file"); - ncount = utils::count_words(&buffer[m]); + ncount = utils::trim_and_count_words(&buffer[m]); if (ncount == 0) error->one(FLERR,"Too few values in body lines in data file"); nword += ncount; @@ -1675,7 +1675,7 @@ void ReadData::bodies(int firstpass, AtomVec *ptr) while (nword < ndouble) { eof = fgets(&buffer[m],MAXLINE,fp); if (eof == NULL) error->one(FLERR,"Unexpected end of data file"); - ncount = utils::count_words(&buffer[m]); + ncount = utils::trim_and_count_words(&buffer[m]); if (ncount == 0) error->one(FLERR,"Too few values in body lines in data file"); nword += ncount; diff --git a/src/reader_native.cpp b/src/reader_native.cpp index 6cb8096d9c..9f7caa01da 100644 --- a/src/reader_native.cpp +++ b/src/reader_native.cpp @@ -162,7 +162,7 @@ bigint ReaderNative::read_header(double box[3][3], int &boxinfo, int &triclinic, char *labelline = &line[strlen("ITEM: ATOMS ")]; - nwords = utils::count_words(labelline); + nwords = utils::trim_and_count_words(labelline); char **labels = new char*[nwords]; labels[0] = strtok(labelline," \t\n\r\f"); if (labels[0] == NULL) { diff --git a/src/table_file_reader.cpp b/src/table_file_reader.cpp new file mode 100644 index 0000000000..194db8f8eb --- /dev/null +++ b/src/table_file_reader.cpp @@ -0,0 +1,51 @@ +/* -*- c++ -*- ---------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + http://lammps.sandia.gov, Sandia National Laboratories + Steve Plimpton, sjplimp@sandia.gov + + Copyright (2003) Sandia Corporation. Under the terms of Contract + DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains + certain rights in this software. This software is distributed under + the GNU General Public License. + + See the README file in the top-level LAMMPS directory. +------------------------------------------------------------------------- */ + +/* ---------------------------------------------------------------------- + Contributing authors: Richard Berger (Temple U) +------------------------------------------------------------------------- */ + +#include "lammps.h" +#include "error.h" +#include "table_file_reader.h" +#include "utils.h" +#include "tokenizer.h" +#include "fmt/format.h" + +#include + +using namespace LAMMPS_NS; + +TableFileReader::TableFileReader(LAMMPS *lmp, + const std::string &filename, + const std::string &type) : + PotentialFileReader(lmp, filename, type + " table") +{ +} + +TableFileReader::~TableFileReader() { +} + +char * TableFileReader::find_section_start(const std::string & keyword) { + char * line = nullptr; + while (line = reader->next_line()) { + ValueTokenizer values(line); + std::string word = values.next_string(); + + if (word == keyword) { + // matching keyword + return line; + } + } + return nullptr; +} diff --git a/src/table_file_reader.h b/src/table_file_reader.h new file mode 100644 index 0000000000..209c649346 --- /dev/null +++ b/src/table_file_reader.h @@ -0,0 +1,35 @@ +/* -*- c++ -*- ---------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + http://lammps.sandia.gov, Sandia National Laboratories + Steve Plimpton, sjplimp@sandia.gov + + Copyright (2003) Sandia Corporation. Under the terms of Contract + DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains + certain rights in this software. This software is distributed under + the GNU General Public License. + + See the README file in the top-level LAMMPS directory. +------------------------------------------------------------------------- */ + +/* ---------------------------------------------------------------------- + Contributing authors: Richard Berger (Temple U) +------------------------------------------------------------------------- */ + +#ifndef LMP_TABLE_FILE_READER_H +#define LMP_TABLE_FILE_READER_H + +#include "potential_file_reader.h" + +namespace LAMMPS_NS +{ + class TableFileReader : public PotentialFileReader { + public: + TableFileReader(class LAMMPS *lmp, const std::string &filename, const std::string & type); + virtual ~TableFileReader(); + + char * find_section_start(const std::string & keyword); + }; + +} // namespace LAMMPS_NS + +#endif diff --git a/src/text_file_reader.cpp b/src/text_file_reader.cpp new file mode 100644 index 0000000000..8063bba87f --- /dev/null +++ b/src/text_file_reader.cpp @@ -0,0 +1,121 @@ +/* -*- c++ -*- ---------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + http://lammps.sandia.gov, Sandia National Laboratories + Steve Plimpton, sjplimp@sandia.gov + + Copyright (2003) Sandia Corporation. Under the terms of Contract + DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains + certain rights in this software. This software is distributed under + the GNU General Public License. + + See the README file in the top-level LAMMPS directory. +------------------------------------------------------------------------- */ + +/* ---------------------------------------------------------------------- + Contributing authors: Richard Berger (Temple U) +------------------------------------------------------------------------- */ + +#include "lammps.h" +#include "force.h" +#include "error.h" +#include "comm.h" +#include "utils.h" +#include "text_file_reader.h" +#include "tokenizer.h" +#include "fmt/format.h" + +#include + +using namespace LAMMPS_NS; + +TextFileReader::TextFileReader(const std::string &filename, const std::string &filetype) + : filename(filename), filetype(filetype), ignore_comments(true) +{ + fp = fopen(filename.c_str(), "r"); + + if (fp == nullptr) { + throw FileReaderException(fmt::format("cannot open {} file {}", filetype, filename)); + } +} + +TextFileReader::~TextFileReader() { + fclose(fp); +} + +void TextFileReader::skip_line() { + char *ptr = fgets(line, MAXLINE, fp); + if (ptr == nullptr) { + // EOF + throw EOFException(fmt::format("Missing line in {} file!", filetype)); + } +} + +char *TextFileReader::next_line(int nparams) { + // concatenate lines until have nparams words + int n = 0; + int nwords = 0; + + char *ptr = fgets(line, MAXLINE, fp); + + if (ptr == nullptr) { + // EOF + return nullptr; + } + + // strip comment + if (ignore_comments && (ptr = strchr(line, '#'))) *ptr = '\0'; + + nwords = utils::count_words(line); + + if (nwords > 0) { + n = strlen(line); + } + + while(nwords == 0 || nwords < nparams) { + char *ptr = fgets(&line[n], MAXLINE - n, fp); + + if (ptr == nullptr) { + // EOF + if (nwords > 0 && nwords < nparams) { + throw EOFException(fmt::format("Incorrect format in {} file! {}/{} parameters", filetype, nwords, nparams)); + } + return nullptr; + } + + + // strip comment + if (ignore_comments && (ptr = strchr(line, '#'))) *ptr = '\0'; + + nwords = utils::count_words(line); + + // skip line if blank + if (nwords > 0) { + n = strlen(line); + } + } + + return line; +} + +void TextFileReader::next_dvector(double * list, int n) { + int i = 0; + while (i < n) { + char *ptr = next_line(); + + if (ptr == nullptr) { + // EOF + if (i < n) { + throw FileReaderException(fmt::format("Incorrect format in {} file! {}/{} values", filetype, i, n)); + } + } + + ValueTokenizer values(line); + while(values.has_next()) { + list[i++] = values.next_double(); + } + } +} + +ValueTokenizer TextFileReader::next_values(int nparams, const std::string & seperators) { + return ValueTokenizer(next_line(nparams), seperators); +} diff --git a/src/text_file_reader.h b/src/text_file_reader.h new file mode 100644 index 0000000000..b162bfb23c --- /dev/null +++ b/src/text_file_reader.h @@ -0,0 +1,70 @@ +/* -*- c++ -*- ---------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + http://lammps.sandia.gov, Sandia National Laboratories + Steve Plimpton, sjplimp@sandia.gov + + Copyright (2003) Sandia Corporation. Under the terms of Contract + DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains + certain rights in this software. This software is distributed under + the GNU General Public License. + + See the README file in the top-level LAMMPS directory. +------------------------------------------------------------------------- */ + +/* ---------------------------------------------------------------------- + Contributing authors: Richard Berger (Temple U) +------------------------------------------------------------------------- */ + +#ifndef LMP_TEXT_FILE_READER_H +#define LMP_TEXT_FILE_READER_H + +#include +#include +#include +#include "tokenizer.h" + +namespace LAMMPS_NS +{ + class TextFileReader { + std::string filename; + std::string filetype; + static const int MAXLINE = 1024; + char line[MAXLINE]; + FILE *fp; + + public: + bool ignore_comments; + + TextFileReader(const std::string &filename, const std::string &filetype); + ~TextFileReader(); + + void skip_line(); + char * next_line(int nparams = 0); + + void next_dvector(double * list, int n); + ValueTokenizer next_values(int nparams, const std::string & seperators = TOKENIZER_DEFAULT_SEPERATORS); + }; + + class FileReaderException : public std::exception { + std::string message; + public: + FileReaderException(const std::string & msg) : message(msg) { + } + + ~FileReaderException() throw() { + } + + virtual const char * what() const throw() { + return message.c_str(); + } + }; + + class EOFException : public FileReaderException { + public: + EOFException(const std::string & msg) : FileReaderException(msg) { + } + }; + +} // namespace LAMMPS_NS + +#endif diff --git a/src/thermo.cpp b/src/thermo.cpp index 73c915da4a..fcc61be503 100644 --- a/src/thermo.cpp +++ b/src/thermo.cpp @@ -160,7 +160,7 @@ Thermo::Thermo(LAMMPS *lmp, int narg, char **arg) : Pointers(lmp) // allocate per-field memory // process line of keywords - nfield_initial = utils::count_words(line); + nfield_initial = utils::trim_and_count_words(line); allocate(); parse_fields(line); diff --git a/src/tokenizer.cpp b/src/tokenizer.cpp index bd82c9f71e..7d048d9e02 100644 --- a/src/tokenizer.cpp +++ b/src/tokenizer.cpp @@ -37,6 +37,12 @@ Tokenizer::Tokenizer(const std::string & str, const std::string & seperators) { } while(end != std::string::npos); } +Tokenizer::Tokenizer(const Tokenizer & rhs) : tokens(rhs.tokens) { +} + +Tokenizer::Tokenizer(Tokenizer && rhs) : tokens(std::move(rhs.tokens)) { +} + Tokenizer::iterator Tokenizer::begin() { return tokens.begin(); } @@ -66,6 +72,14 @@ ValueTokenizer::ValueTokenizer(const std::string & str, const std::string & sepe current = tokens.begin(); } +ValueTokenizer::ValueTokenizer(const ValueTokenizer & rhs) : tokens(rhs.tokens) { + current = tokens.begin(); +} + +ValueTokenizer::ValueTokenizer(ValueTokenizer && rhs) : tokens(std::move(rhs.tokens)) { + current = tokens.begin(); +} + bool ValueTokenizer::has_next() const { return current != tokens.cend(); } diff --git a/src/tokenizer.h b/src/tokenizer.h index 665b297eae..89cb57b301 100644 --- a/src/tokenizer.h +++ b/src/tokenizer.h @@ -25,13 +25,19 @@ namespace LAMMPS_NS { +#define TOKENIZER_DEFAULT_SEPERATORS " \t\r\n\f" + class Tokenizer { std::vector tokens; public: typedef std::vector::iterator iterator; typedef std::vector::const_iterator const_iterator; - Tokenizer(const std::string & str, const std::string & seperators = " \t\r\n\f"); + Tokenizer(const std::string & str, const std::string & seperators = TOKENIZER_DEFAULT_SEPERATORS); + Tokenizer(Tokenizer &&); + Tokenizer(const Tokenizer &); + Tokenizer& operator=(const Tokenizer&) = default; + Tokenizer& operator=(Tokenizer&&) = default; iterator begin(); iterator end(); @@ -72,7 +78,11 @@ class ValueTokenizer { Tokenizer tokens; Tokenizer::const_iterator current; public: - ValueTokenizer(const std::string & str, const std::string & seperators = " \t\r\n\f"); + ValueTokenizer(const std::string & str, const std::string & seperators = TOKENIZER_DEFAULT_SEPERATORS); + ValueTokenizer(const ValueTokenizer &); + ValueTokenizer(ValueTokenizer &&); + ValueTokenizer& operator=(const ValueTokenizer&) = default; + ValueTokenizer& operator=(ValueTokenizer&&) = default; std::string next_string(); tagint next_tagint(); diff --git a/src/utils.cpp b/src/utils.cpp index b223710cab..a8dc4e308e 100644 --- a/src/utils.cpp +++ b/src/utils.cpp @@ -18,6 +18,7 @@ #include "lammps.h" #include "error.h" #include "tokenizer.h" +#include "text_file_reader.h" #include "fmt/format.h" #if defined(__linux__) @@ -364,14 +365,22 @@ std::string utils::trim_comment(const std::string & line) { } /* ---------------------------------------------------------------------- - Trim comment from string and return number of words + Return number of words ------------------------------------------------------------------------- */ size_t utils::count_words(const std::string & text, const std::string & seperators) { - Tokenizer words(utils::trim_comment(text), seperators); + ValueTokenizer words(text, seperators); return words.count(); } +/* ---------------------------------------------------------------------- + Trim comment from string and return number of words +------------------------------------------------------------------------- */ + +size_t utils::trim_and_count_words(const std::string & text, const std::string & seperators) { + return utils::count_words(utils::trim_comment(text), seperators); +} + /* ---------------------------------------------------------------------- Return whether string is a valid integer number ------------------------------------------------------------------------- */ @@ -406,6 +415,104 @@ bool utils::is_double(const std::string & str) { return true; } +/* ---------------------------------------------------------------------- + strip off leading part of path, return just the filename +------------------------------------------------------------------------- */ + +std::string utils::path_basename(const std::string & path) { +#if defined(_WIN32) + size_t start = path.find_last_of('/\\'); +#else + size_t start = path.find_last_of('/'); +#endif + + if (start == std::string::npos) { + start = 0; + } else { + start += 1; + } + + return path.substr(start); +} + +/* ---------------------------------------------------------------------- + join two paths +------------------------------------------------------------------------- */ + +std::string utils::path_join(const std::string & a, const std::string & b) { + #if defined(_WIN32) + return fmt::format("{}\\{}", a, b); + #else + return fmt::format("{}/{}", a, b); + #endif +} + +/* ---------------------------------------------------------------------- + try to open file for reading +------------------------------------------------------------------------- */ + +bool utils::file_is_readable(const std::string & path) { + FILE * fp = fopen(path.c_str(), "r"); + if(fp) { + fclose(fp); + return true; + } + return false; +} + +/* ---------------------------------------------------------------------- + try to find potential file as specified by name + search current directory and the LAMMPS_POTENTIALS directory if + specified +------------------------------------------------------------------------- */ + +std::string utils::get_potential_file_path(const std::string& path) { + std::string filepath = path; + std::string filename = utils::path_basename(path); + + if(utils::file_is_readable(filepath)) { + return filepath; + } else { + // try the environment variable directory + const char *path = getenv("LAMMPS_POTENTIALS"); + + if (path != nullptr){ + std::string pot = utils::path_basename(filepath); + filepath = utils::path_join(path, pot); + + if (utils::file_is_readable(filepath)) { + return filepath; + } + } + } + return ""; +} + +/* ---------------------------------------------------------------------- + read first line of potential file + if has DATE field, print following word +------------------------------------------------------------------------- */ + +std::string utils::get_potential_date(const std::string & path, const std::string & potential_name) { + TextFileReader reader(path, potential_name); + reader.ignore_comments = false; + char * line = nullptr; + + while (line = reader.next_line()) { + ValueTokenizer values(line); + while (values.has_next()) { + std::string word = values.next_string(); + if (word == "DATE:") { + if (values.has_next()) { + std::string date = values.next_string(); + return date; + } + } + } + } + return ""; +} + /* ------------------------------------------------------------------ */ extern "C" { diff --git a/src/utils.h b/src/utils.h index 944478e3ad..79fb2349d3 100644 --- a/src/utils.h +++ b/src/utils.h @@ -150,13 +150,21 @@ namespace LAMMPS_NS { */ std::string trim_comment(const std::string & line); + /** + * \brief Count words in string + * \param text string that should be searched + * \param seperators string containing characters that will be treated as whitespace + * \return number of words found + */ + size_t count_words(const std::string & text, const std::string & seperators = " \t\r\n\f"); + /** * \brief Count words in a single line, trim anything from '#' onward * \param text string that should be trimmed and searched * \param seperators string containing characters that will be treated as whitespace * \return number of words found */ - size_t count_words(const std::string & text, const std::string & seperators = " \t\r\n\f"); + size_t trim_and_count_words(const std::string & text, const std::string & seperators = " \t\r\n\f"); /** * \brief Check if string can be converted to valid integer @@ -171,6 +179,44 @@ namespace LAMMPS_NS { * \return true, if string contains valid floating-point number, false otherwise */ bool is_double(const std::string & str); + + /** + * \brief Strip off leading part of path, return just the filename + * \param path file path + * \return file name + */ + std::string path_basename(const std::string & path); + + /** + * \brief Join two paths + * \param a first path + * \param b second path + * \return combined path + */ + std::string path_join(const std::string & a, const std::string & b); + + /** + * \brief Check if file exists and is readable + * \param path file path + * \return true if file exists and is readable + */ + bool file_is_readable(const std::string & path); + + /** + * \brief Determine full path of potential file + * If file is not found in current directory, search LAMMPS_POTENTIALS folder + * \param path file path + * \return full path to potential file + */ + std::string get_potential_file_path(const std::string& path); + + /** + * \brief Read potential file and return DATE field if it is present + * \param path file path + * \param potential_name name of potential that is being read + * \return DATE field if present + */ + std::string get_potential_date(const std::string & path, const std::string & potential_name); } } diff --git a/tools/singularity/centos7.def b/tools/singularity/centos7.def index 7803f3f386..5369c6977b 100644 --- a/tools/singularity/centos7.def +++ b/tools/singularity/centos7.def @@ -11,9 +11,43 @@ From: centos:7 hdf5-devel python36-virtualenv python36-pip python-pip \ netcdf-devel netcdf-cxx-devel netcdf-mpich-devel netcdf-openmpi-devel \ python-virtualenv fftw-devel voro++-devel eigen3-devel gsl-devel openblas-devel enchant \ - blas-devel lapack-devel libyaml-devel + blas-devel lapack-devel libyaml-devel openkim-models kim-api-devel yum clean all + # we need to reset any module variables + # inherited from the host. + unset __LMOD_REF_COUNT__LMFILES_ + unset __LMOD_REF_COUNT_PATH + unset __LMOD_REF_COUNT_LD_LIBRARY_PATH + unset __LMOD_REF_COUNT_MANPATH + unset __LMOD_REF_COUNT_MODULEPATH + unset __LMOD_REF_COUNT_LOADEDMODULES + unset _LMFILES_ + unset MODULEPATH + unset MODULESHOME + unset MODULEPATH_ROOT + unset LOADEDMODULES + unset LMOD_SYSTEM_DEFAULT_MODULES + + # load MPI by default + . /etc/profile + module load mpi + + # manually install Plumed + mkdir plumed + cd plumed + version=2.6.0 + curl -L -o plumed.tar.gz https://github.com/plumed/plumed2/releases/download/v${version}/plumed-src-${version}.tgz + tar -xzf plumed.tar.gz + cd plumed-${version} + ./configure --disable-doc --prefix=/usr + make + make install + # fix up installation for CentOS and Fedora + mv -v /usr/lib/pkgconfig/plumed* /usr/share/pkgconfig/ + cd ../../ + rm -rvf plumed + # set custom prompt indicating the container name CUSTOM_PROMPT_ENV=/.singularity.d/env/99-zz_custom_prompt.sh cat >$CUSTOM_PROMPT_ENV <$CUSTOM_PROMPT_ENV <$CUSTOM_PROMPT_ENV <$CUSTOM_PROMPT_ENV <$CUSTOM_PROMPT_ENV <atom->nangletypes; - for (std::size_t i=0; i < lmp->atom->nangletypes; ++i) { + for (int i=0; i < lmp->atom->nangletypes; ++i) { eqstr << " " << lmp->force->angle->equilibrium_angle(i+1); } writer.emit("equilibrium", eqstr.str()); diff --git a/unittest/force-styles/bond_style.cpp b/unittest/force-styles/bond_style.cpp index c159a7a25e..b87804ef4a 100644 --- a/unittest/force-styles/bond_style.cpp +++ b/unittest/force-styles/bond_style.cpp @@ -288,7 +288,7 @@ void generate_yaml_file(const char *outfile, const TestConfig &config) // equilibrium distance std::stringstream eqstr; eqstr << lmp->atom->nbondtypes; - for (std::size_t i=0; i < lmp->atom->nbondtypes; ++i) { + for (int i=0; i < lmp->atom->nbondtypes; ++i) { eqstr << " " << lmp->force->bond->equilibrium_distance(i+1); } writer.emit("equilibrium", eqstr.str()); diff --git a/unittest/force-styles/tests/atomic-pair-table_bitmap.yaml b/unittest/force-styles/tests/atomic-pair-table_bitmap.yaml new file mode 100644 index 0000000000..023228dc55 --- /dev/null +++ b/unittest/force-styles/tests/atomic-pair-table_bitmap.yaml @@ -0,0 +1,89 @@ +--- +lammps_version: 2 Jun 2020 +date_generated: Tue Jun 2 16:53:15 202 +epsilon: 5e-13 +prerequisites: ! | + pair table +pre_commands: ! "" +post_commands: ! "" +input_file: in.metal +pair_style: table bitmap 10 +pair_coeff: ! | + * * ${input_dir}/pair_table_bitmap.txt beck_1_1 +extract: ! "" +natoms: 32 +init_vdwl: 1.66863069929167 +init_coul: 0 +init_stress: ! |2- + 6.1952827280949752e+00 6.0616458078803026e+00 5.8879068387604203e+00 2.0730193733654706e-01 -2.1217457971568116e-02 -8.9424946009241696e-02 +init_forces: ! |2 + 1 1.3462021756359327e-02 6.5546484939056501e-02 1.4239378405106444e-02 + 2 -2.2007228833976065e-02 -7.7589845112095546e-02 4.8902697347770523e-02 + 3 -3.8360617077969741e-02 1.9000610721085417e-01 -4.8543675419659094e-02 + 4 2.0909689528763566e-02 -9.9051714348463316e-03 -5.2627007649843807e-02 + 5 5.6017317782444738e-02 1.4268372317778771e-01 3.5492113737546842e-02 + 6 4.1557359610043018e-02 2.9641106441236388e-02 -6.9666505508374872e-03 + 7 -6.4166646403998925e-02 8.9315602328966931e-02 -1.0227283854625933e-02 + 8 -6.8596281778498247e-02 -6.0833941051629016e-02 4.4682109809175953e-02 + 9 1.4368972530624599e-02 -5.5197060731424975e-02 -2.8201433919835286e-02 + 10 -3.2703871825595171e-02 -1.4474456554468246e-01 -1.1516819202560430e-01 + 11 -4.0405247666710227e-02 -5.0409352470214198e-02 4.2972316829875207e-02 + 12 3.0916743299077298e-02 -8.8133140512779831e-02 -3.9753798941002949e-03 + 13 -1.8590365196257386e-02 2.4575364499331190e-02 -4.7077193181172067e-02 + 14 5.6675408248286062e-02 -1.8711344187186302e-02 7.0130262965183210e-02 + 15 -3.1926591760213181e-02 3.1641397846490678e-02 -2.8162923341260547e-02 + 16 1.1005724174097668e-01 -9.1797768313712017e-02 3.7455099430156756e-02 + 17 4.3878459411519591e-02 1.3059623784047278e-01 -1.6097155896137277e-03 + 18 -1.4777439020699670e-01 -3.5658427272011572e-02 -7.0718736029538459e-02 + 19 -1.5580794194082498e-01 -8.1567700677555310e-02 3.7488943756308291e-02 + 20 2.4266515940572463e-02 1.9762354212930246e-02 -3.4097639624214998e-02 + 21 1.6277874455848959e-01 5.0800476849828920e-02 4.3314810824989737e-03 + 22 2.9893704848344602e-03 -8.1978960608305021e-02 -1.1775536941431530e-02 + 23 4.6993698780955703e-02 1.2309490227999968e-01 -8.0573799329662799e-02 + 24 1.2797425247184574e-01 9.4738372709908938e-02 8.3761735780926952e-02 + 25 6.9930077496344431e-02 4.2200999537168552e-03 -4.6754566887666743e-02 + 26 -5.1872497435892714e-02 -1.5107287052733298e-01 1.2864569803094950e-01 + 27 4.6175201131873622e-02 -4.7147053051923900e-03 -2.1152042044204553e-04 + 28 1.1139415424523944e-02 5.7577179243740957e-02 7.3714500884676210e-02 + 29 4.8901565126232033e-02 1.0736209516268529e-01 -3.2125425217601846e-03 + 30 -4.2584465166652936e-02 -3.0054615946788474e-02 -8.4428957096643942e-02 + 31 -2.0649926244740491e-02 -1.1590442114762316e-01 7.4794527710849712e-02 + 32 -1.9354598378544019e-01 -6.3287613853627508e-02 -2.2278111493111191e-02 +run_vdwl: 1.66741314145205 +run_coul: 0 +run_stress: ! |2- + 6.1931374572792954e+00 6.0579168006450157e+00 5.8831944925174655e+00 2.0546568651742717e-01 -2.2310825568610582e-02 -9.0786598388712531e-02 +run_forces: ! |2 + 1 1.0245582840443836e-02 6.5151854710940468e-02 1.3361955389177321e-02 + 2 -2.2314027604621318e-02 -7.7535528641419729e-02 4.9002169116395371e-02 + 3 -3.9051836443840873e-02 1.8729640241706769e-01 -5.0368800191922920e-02 + 4 2.1556848319449432e-02 -9.6560257281038397e-03 -5.2226270227499996e-02 + 5 5.5692513794487093e-02 1.4100131039803696e-01 3.6433829498680612e-02 + 6 4.2104114940438239e-02 2.9061099461956740e-02 -8.0757486645345530e-03 + 7 -6.4974396400004103e-02 9.0834827653364231e-02 -1.1497303228903639e-02 + 8 -6.9891945210390563e-02 -6.1365585968288172e-02 4.5058971443054034e-02 + 9 1.5494788785065767e-02 -5.6313873741252601e-02 -2.9239516346795842e-02 + 10 -3.0025791257554668e-02 -1.4356984394446920e-01 -1.1248096343757182e-01 + 11 -4.0162199915935268e-02 -5.1244062549941558e-02 4.2120428458812920e-02 + 12 3.2219067015055440e-02 -8.8023947653775636e-02 -4.0000605662452050e-03 + 13 -1.9322021317182518e-02 2.3705996957186400e-02 -4.6458078927757253e-02 + 14 5.7515188139881337e-02 -1.5720861856457415e-02 6.8903466211661560e-02 + 15 -3.1550376834563972e-02 3.2004964657920229e-02 -2.7509931415147928e-02 + 16 1.0690614440695038e-01 -9.0850865144888507e-02 3.6425761956666795e-02 + 17 4.4576246121271583e-02 1.3023640557355332e-01 -7.6587762084134013e-04 + 18 -1.4790335009012934e-01 -3.4561193108141076e-02 -7.1476252590456105e-02 + 19 -1.5517474793926253e-01 -8.1735148865468926e-02 3.6534263240961207e-02 + 20 2.3564800733902859e-02 2.0130469558539449e-02 -3.4093822740206496e-02 + 21 1.6267868459547039e-01 4.8910520011812009e-02 4.9415963505101621e-03 + 22 3.9143651683370253e-03 -8.1172695145679000e-02 -1.0834230526190378e-02 + 23 4.9870311913370033e-02 1.2420611623040828e-01 -7.7833840076172459e-02 + 24 1.2773385871506515e-01 9.4431969129075782e-02 8.4509868356579518e-02 + 25 7.0376169719190279e-02 4.4792786930559310e-03 -4.6803763947891978e-02 + 26 -5.0364526911511179e-02 -1.4929711058338557e-01 1.2850817811267942e-01 + 27 4.6472580366719141e-02 -4.1923069078539394e-03 -1.3401923595724521e-03 + 28 1.1441857387906706e-02 5.8173904345736008e-02 7.3370361778840071e-02 + 29 4.7811159682183739e-02 1.0733827504367408e-01 -1.9879309433676450e-03 + 30 -4.2511930547412778e-02 -2.9916695214642831e-02 -8.4066745720912481e-02 + 31 -2.1952102296720562e-02 -1.1662029578060293e-01 7.4721379144302519e-02 + 32 -1.9497502987605872e-01 -6.5187354007956666e-02 -2.2832899526331281e-02 +... diff --git a/unittest/force-styles/tests/atomic-pair-table_linear.yaml b/unittest/force-styles/tests/atomic-pair-table_linear.yaml new file mode 100644 index 0000000000..215f3d9a47 --- /dev/null +++ b/unittest/force-styles/tests/atomic-pair-table_linear.yaml @@ -0,0 +1,91 @@ +--- +lammps_version: 2 Jun 2020 +date_generated: Tue Jun 2 16:46:19 202 +epsilon: 5e-13 +prerequisites: ! | + pair table +pre_commands: ! "" +post_commands: ! "" +input_file: in.metal +pair_style: table linear 10000 +pair_coeff: ! | + 1 1 ${input_dir}/pair_table_beck.txt beck_1_1 + 1 2 ${input_dir}/pair_table_beck.txt beck_1_1 + 2 2 ${input_dir}/pair_table_beck.txt beck_2_2 +extract: ! "" +natoms: 32 +init_vdwl: 1.66849758741132 +init_coul: 0 +init_stress: ! |2- + 6.1946715433684973e+00 6.0610621944595691e+00 5.8874237884568794e+00 2.0726669272562587e-01 -2.1210093847498168e-02 -8.9416411707758034e-02 +init_forces: ! |2 + 1 1.3461768519573423e-02 6.5534109919214642e-02 1.4238046153935983e-02 + 2 -2.2001532385230976e-02 -7.7578110900587721e-02 4.8895494306522291e-02 + 3 -3.8355274675308998e-02 1.8998944460354011e-01 -4.8534579158997129e-02 + 4 2.0908450525723498e-02 -9.9065259851936448e-03 -5.2618638347233404e-02 + 5 5.6008845819212463e-02 1.4266708026293753e-01 3.5487913450023841e-02 + 6 4.1552575164020243e-02 2.9642511828555394e-02 -6.9641129743398126e-03 + 7 -6.4155910069342403e-02 8.9302215279040434e-02 -1.0225629221330955e-02 + 8 -6.8587774765165088e-02 -6.0829429175094735e-02 4.4680410492059397e-02 + 9 1.4366115666253289e-02 -5.5193010436797592e-02 -2.8199868469874739e-02 + 10 -3.2696772118295803e-02 -1.4472907530040827e-01 -1.1516096653547711e-01 + 11 -4.0401292979786972e-02 -5.0403260261100417e-02 4.2969363549390502e-02 + 12 3.0908963526062479e-02 -8.8120722839359025e-02 -3.9792237714215200e-03 + 13 -1.8590586442952396e-02 2.4570524680954029e-02 -4.7073976129125013e-02 + 14 5.6668681846789561e-02 -1.8708035295572849e-02 7.0129732306455847e-02 + 15 -3.1927433330968973e-02 3.1638369787962112e-02 -2.8162497777685959e-02 + 16 1.1004266778296544e-01 -9.1785066871052839e-02 3.7455063670217288e-02 + 17 4.3874209968260171e-02 1.3058176120978526e-01 -1.6077990215935685e-03 + 18 -1.4775183032052960e-01 -3.5651338364660598e-02 -7.0714213256030112e-02 + 19 -1.5579450123857666e-01 -8.1557435871161682e-02 3.7491976413329374e-02 + 20 2.4262106793077946e-02 1.9762251986969553e-02 -3.4094105051678786e-02 + 21 1.6276246770534447e-01 5.0791644250007900e-02 4.3248360141969555e-03 + 22 2.9904687035853137e-03 -8.1967139210456882e-02 -1.1772377300447360e-02 + 23 4.6987794141318706e-02 1.2308604930197996e-01 -8.0566882858205235e-02 + 24 1.2795930744437653e-01 9.4726737159825200e-02 8.3749152147737538e-02 + 25 6.9925482162420033e-02 4.2199513301063160e-03 -4.6743912320864334e-02 + 26 -5.1856917641538880e-02 -1.5105261662137287e-01 1.2862943385759271e-01 + 27 4.6163997109484788e-02 -4.7144533487617334e-03 -2.0769859565411553e-04 + 28 1.1137606033726113e-02 5.7570749823347561e-02 7.3702486316706894e-02 + 29 4.8892603764312044e-02 1.0734444862695605e-01 -3.2133899506260749e-03 + 30 -4.2587368463202192e-02 -3.0047436022746527e-02 -8.4421201266270535e-02 + 31 -2.0646231349659299e-02 -1.1590205379082782e-01 7.4785818423894770e-02 + 32 -1.9352068689594826e-01 -6.3282139756026798e-02 -2.2278655095207611e-02 +run_vdwl: 1.66727802356891 +run_coul: 0 +run_stress: ! |2- + 6.1925738027578641e+00 6.0573149352705613e+00 5.8826519662480035e+00 2.0544288354756310e-01 -2.2314569036134008e-02 -9.0767397150969681e-02 +run_forces: ! |2 + 1 1.0239417972012135e-02 6.5143936411888370e-02 1.3356763777998637e-02 + 2 -2.2314835701632570e-02 -7.7524477122967728e-02 4.8999346575662309e-02 + 3 -3.9043638693828556e-02 1.8727196361074283e-01 -5.0358906369839446e-02 + 4 2.1555046910191538e-02 -9.6562479880345862e-03 -5.2220025740068080e-02 + 5 5.5684458879600447e-02 1.4098102798381096e-01 3.6430504994586173e-02 + 6 4.2104147709418713e-02 2.9055058600247489e-02 -8.0778112152718948e-03 + 7 -6.4963866924303920e-02 9.0824824870264262e-02 -1.1492621439859574e-02 + 8 -6.9888106386663568e-02 -6.1362238801327997e-02 4.5061669154972568e-02 + 9 1.5493057273285156e-02 -5.6307006366398599e-02 -2.9234755420043165e-02 + 10 -3.0006706586658188e-02 -1.4355133290296190e-01 -1.1246538976169368e-01 + 11 -4.0156699765253455e-02 -5.1238883202820718e-02 4.2112202625462891e-02 + 12 3.2215165580774301e-02 -8.8013396380619557e-02 -4.0047290710007333e-03 + 13 -1.9322767417550984e-02 2.3711197649086194e-02 -4.6454058795633212e-02 + 14 5.7508424194302507e-02 -1.5717730349026085e-02 6.8892268883266869e-02 + 15 -3.1552192265302363e-02 3.2002449140037137e-02 -2.7508481800674743e-02 + 16 1.0688955089657577e-01 -9.0842508916126788e-02 3.6418887829925486e-02 + 17 4.4577236329712736e-02 1.3022532646095397e-01 -7.5825494000398793e-04 + 18 -1.4789247023417521e-01 -3.4554869410601124e-02 -7.1472651306375229e-02 + 19 -1.5516659799350990e-01 -8.1733259734237992e-02 3.6528023380248152e-02 + 20 2.3565292501585497e-02 2.0131963706666492e-02 -3.4090460756558867e-02 + 21 1.6266349958385409e-01 4.8905943278807026e-02 4.9357951969207243e-03 + 22 3.9108463662172284e-03 -8.1159914942901146e-02 -1.0833213112554453e-02 + 23 4.9862761614696910e-02 1.2418695431753196e-01 -7.7818580582703634e-02 + 24 1.2773299190190621e-01 9.4426552636226180e-02 8.4500013220674824e-02 + 25 7.0366190135544543e-02 4.4772942266913711e-03 -4.6793931216364631e-02 + 26 -5.0367407305875939e-02 -1.4928033291926532e-01 1.2849353197675831e-01 + 27 4.6468146723438429e-02 -4.1892634838488693e-03 -1.3380548635599163e-03 + 28 1.1447706368862415e-02 5.8175438626723523e-02 7.3359635688296038e-02 + 29 4.7807434863290775e-02 1.0732112842460283e-01 -1.9886348252873588e-03 + 30 -4.2515720470887731e-02 -2.9914625470396135e-02 -8.4056579797267661e-02 + 31 -2.1956047762899965e-02 -1.1661348485300055e-01 7.4709459326432123e-02 + 32 -1.9494431829672756e-01 -6.5181487099745139e-02 -2.2830961616444944e-02 +... diff --git a/unittest/force-styles/tests/atomic-pair-table_lookup.yaml b/unittest/force-styles/tests/atomic-pair-table_lookup.yaml new file mode 100644 index 0000000000..1be15507df --- /dev/null +++ b/unittest/force-styles/tests/atomic-pair-table_lookup.yaml @@ -0,0 +1,91 @@ +--- +lammps_version: 2 Jun 2020 +date_generated: Tue Jun 2 16:45:40 202 +epsilon: 5e-13 +prerequisites: ! | + pair table +pre_commands: ! "" +post_commands: ! "" +input_file: in.metal +pair_style: table lookup 10000 +pair_coeff: ! | + 1 1 ${input_dir}/pair_table_beck.txt beck_1_1 + 1 2 ${input_dir}/pair_table_beck.txt beck_1_1 + 2 2 ${input_dir}/pair_table_beck.txt beck_2_2 +extract: ! "" +natoms: 32 +init_vdwl: 1.66822081098814 +init_coul: 0 +init_stress: ! |2- + 6.1925708391090373e+00 6.0607873158796632e+00 5.8866502515961283e+00 2.0635047994864009e-01 -2.2304749096038870e-02 -8.9977381381968910e-02 +init_forces: ! |2 + 1 1.3652870615947011e-02 6.5292578314726832e-02 1.4401786849082793e-02 + 2 -2.2075986500789631e-02 -7.7530344175629484e-02 4.8918295738716797e-02 + 3 -3.8548065982306853e-02 1.9049129535293563e-01 -4.8497042796395010e-02 + 4 2.0883993795891603e-02 -9.8004460881346168e-03 -5.2544284235507610e-02 + 5 5.6473535558532267e-02 1.4259381967545881e-01 3.5283580728998398e-02 + 6 4.1436803654676703e-02 2.9757415671595559e-02 -6.9441568265177812e-03 + 7 -6.4342009716857218e-02 8.9407090045572943e-02 -1.0076354375758356e-02 + 8 -6.8438588566627351e-02 -6.0719143235589357e-02 4.4375134570496459e-02 + 9 1.4267631647248345e-02 -5.5225493516036783e-02 -2.8235579582748780e-02 + 10 -3.2874735468490235e-02 -1.4496018410464423e-01 -1.1522122672190530e-01 + 11 -4.0439244564162688e-02 -5.0797057909291822e-02 4.2990522799705479e-02 + 12 3.1118238818285009e-02 -8.8117800460577142e-02 -4.0963549347812021e-03 + 13 -1.8421701898180837e-02 2.4603479320682679e-02 -4.6953330610188748e-02 + 14 5.6779946032995847e-02 -1.8997405137617097e-02 7.0084749782857475e-02 + 15 -3.1872432338948091e-02 3.1520110382368773e-02 -2.8177989701802592e-02 + 16 1.1013395678084995e-01 -9.1707318824236786e-02 3.7083770573599802e-02 + 17 4.3975078896704253e-02 1.3054106752514974e-01 -1.5760211066586478e-03 + 18 -1.4753246799540981e-01 -3.5398540009504140e-02 -7.0784984645480470e-02 + 19 -1.5562703896771166e-01 -8.1533158870799177e-02 3.7998367628389429e-02 + 20 2.4120555351187806e-02 1.9895957059386932e-02 -3.4031571261011077e-02 + 21 1.6241181372756625e-01 5.0567395846590979e-02 4.0311135803611352e-03 + 22 3.0847862699784918e-03 -8.2082703890837161e-02 -1.1813933267531539e-02 + 23 4.6631319964723403e-02 1.2294704911631910e-01 -8.0759997950587623e-02 + 24 1.2784615418643658e-01 9.4570579283427048e-02 8.4136049252381967e-02 + 25 6.9854637188683621e-02 4.3796329364953045e-03 -4.6383679169275639e-02 + 26 -5.1672371161515490e-02 -1.5093773642419464e-01 1.2890155107784523e-01 + 27 4.6418514479134469e-02 -4.8647715941130543e-03 -3.3400893593061448e-04 + 28 1.0837875140475392e-02 5.7768778789330170e-02 7.3335429938361563e-02 + 29 4.8424486534314935e-02 1.0705191088477574e-01 -3.4221430692390835e-03 + 30 -4.2678491461167409e-02 -3.0167096740169222e-02 -8.4323491798094938e-02 + 31 -2.0446963122925290e-02 -1.1577119295225209e-01 7.4834425292344492e-02 + 32 -1.9338210089853922e-01 -6.2777766271189708e-02 -2.2198626823726184e-02 +run_vdwl: 1.66790120138923 +run_coul: 0 +run_stress: ! |2- + 6.1954399052539300e+00 6.0597796933663810e+00 5.8839846490596770e+00 2.0464958122047128e-01 -2.2990948428733799e-02 -9.0561388880444543e-02 +run_forces: ! |2 + 1 1.0357196419898495e-02 6.5372257333873959e-02 1.3514409758410917e-02 + 2 -2.2518946587964585e-02 -7.7700478129363010e-02 4.8980708027650338e-02 + 3 -3.9187350884245992e-02 1.8746598368586515e-01 -5.0095509280450985e-02 + 4 2.1505122391926864e-02 -9.8121998835355474e-03 -5.2197325168546041e-02 + 5 5.6368397082486393e-02 1.4115837375527868e-01 3.6749677569935905e-02 + 6 4.2042380520510882e-02 2.9049092654418140e-02 -8.0059207630978693e-03 + 7 -6.5262053410956963e-02 9.1189712395790753e-02 -1.1162106417995799e-02 + 8 -6.9823982763573419e-02 -6.1642359327017858e-02 4.5148186601411129e-02 + 9 1.5581717631005403e-02 -5.6464988109373171e-02 -2.9179373549110328e-02 + 10 -2.9936010364121191e-02 -1.4403347574591194e-01 -1.1249323547874966e-01 + 11 -4.0279718641423851e-02 -5.1267663186455890e-02 4.2308426648069226e-02 + 12 3.2548290765190446e-02 -8.8360090934889973e-02 -4.1059424850670304e-03 + 13 -1.9100876563736404e-02 2.3923943182546592e-02 -4.6654992572323889e-02 + 14 5.7003886104469645e-02 -1.5977942426948746e-02 6.9080947733147463e-02 + 15 -3.1419200863690128e-02 3.2134894708585104e-02 -2.7460582419399034e-02 + 16 1.0678077169426231e-01 -9.0718758218836820e-02 3.6086450730476470e-02 + 17 4.4432206292973897e-02 1.3053785119638170e-01 -8.8349832217821166e-04 + 18 -1.4847693210486995e-01 -3.4770804844180284e-02 -7.1598050906370336e-02 + 19 -1.5584406172770648e-01 -8.1902850262455335e-02 3.6401901739187829e-02 + 20 2.3632828687886766e-02 2.0210640568054113e-02 -3.3962375402201296e-02 + 21 1.6251200328353549e-01 4.8509762572667509e-02 4.6262805117567836e-03 + 22 3.9297251786593766e-03 -8.1271664355599668e-02 -1.0814196256901271e-02 + 23 4.9681279655079395e-02 1.2435597457773782e-01 -7.8146336899556537e-02 + 24 1.2830345267622284e-01 9.4849763681645619e-02 8.4755594763442382e-02 + 25 7.0574066259719931e-02 4.7738855789510749e-03 -4.6746928071330643e-02 + 26 -5.0012323977413009e-02 -1.4919205052782003e-01 1.2835423785227032e-01 + 27 4.6693855278230161e-02 -4.3926905018267671e-03 -1.5097765818073844e-03 + 28 1.1103730609808571e-02 5.8020761280684265e-02 7.3177666578219974e-02 + 29 4.8063412527103180e-02 1.0769074559895483e-01 -1.8637969627234715e-03 + 30 -4.2307197338881525e-02 -2.9602719505751475e-02 -8.4192072289735478e-02 + 31 -2.2008710097816863e-02 -1.1651727431063712e-01 7.4819836125210509e-02 + 32 -1.9493695773256986e-01 -6.5615632500831411e-02 -2.2932304811643992e-02 +... diff --git a/unittest/force-styles/tests/atomic-pair-table_spline.yaml b/unittest/force-styles/tests/atomic-pair-table_spline.yaml new file mode 100644 index 0000000000..7bc3815e52 --- /dev/null +++ b/unittest/force-styles/tests/atomic-pair-table_spline.yaml @@ -0,0 +1,91 @@ +--- +lammps_version: 2 Jun 2020 +date_generated: Tue Jun 2 16:47:29 202 +epsilon: 5e-13 +prerequisites: ! | + pair table +pre_commands: ! "" +post_commands: ! "" +input_file: in.metal +pair_style: table spline 10000 +pair_coeff: ! | + 1 1 ${input_dir}/pair_table_beck.txt beck_1_1 + 1 2 ${input_dir}/pair_table_beck.txt beck_1_1 + 2 2 ${input_dir}/pair_table_beck.txt beck_2_2 +extract: ! "" +natoms: 32 +init_vdwl: 1.66849237317226 +init_coul: 0 +init_stress: ! |2- + 6.1946491697735437e+00 6.0610401365658024e+00 5.8874025724620429e+00 2.0726580316940962e-01 -2.1210361695457737e-02 -8.9415208770840096e-02 +init_forces: ! |2 + 1 1.3461900166603218e-02 6.5533756921056424e-02 1.4237872357245411e-02 + 2 -2.2001295274018444e-02 -7.7577892895343906e-02 4.8895379860549121e-02 + 3 -3.8355321598214184e-02 1.8998901399717005e-01 -4.8534413942792565e-02 + 4 2.0908396793481509e-02 -9.9066117521727070e-03 -5.2618403012712124e-02 + 5 5.6008413316644114e-02 1.4266663667152152e-01 3.5487859843299545e-02 + 6 4.1552391358114872e-02 2.9642295673519448e-02 -6.9640527234652461e-03 + 7 -6.4155546133542837e-02 8.9301753561023003e-02 -1.0225594515349757e-02 + 8 -6.8587453028246703e-02 -6.0829070542048190e-02 4.4680193619080481e-02 + 9 1.4366068063822880e-02 -5.5192738935146854e-02 -2.8199665411938767e-02 + 10 -3.2697019980711756e-02 -1.4472840813665638e-01 -1.1516072254520793e-01 + 11 -4.0401272804121854e-02 -5.0402863668631913e-02 4.2969197904076183e-02 + 12 3.0908680631425673e-02 -8.8120244487072494e-02 -3.9791730686956463e-03 + 13 -1.8590573588915013e-02 2.4570208722629043e-02 -4.7073683697064536e-02 + 14 5.6668374919472228e-02 -1.8707913260279440e-02 7.0129358194749039e-02 + 15 -3.1927219149443416e-02 3.1638287874549260e-02 -2.8162304610562044e-02 + 16 1.1004228625210850e-01 -9.1784876878925489e-02 3.7455203664712555e-02 + 17 4.3874110434413707e-02 1.3058123184332987e-01 -1.6078470938548138e-03 + 18 -1.4775126775856298e-01 -3.5651201719208082e-02 -7.0713629953624360e-02 + 19 -1.5579381073821677e-01 -8.1556836647145553e-02 3.7492096227633373e-02 + 20 2.4262149455103726e-02 1.9762082500828778e-02 -3.4093995317030654e-02 + 21 1.6276229493138114e-01 5.0791551859706734e-02 4.3245301958938116e-03 + 22 2.9902891288209246e-03 -8.1966958449035843e-02 -1.1772410092696793e-02 + 23 4.6987757268038249e-02 1.2308546657800162e-01 -8.0566592682958557e-02 + 24 1.2795842291296708e-01 9.4726040785926641e-02 8.3748524809472952e-02 + 25 6.9925310941154381e-02 4.2197730528178625e-03 -4.6744097166442150e-02 + 26 -5.1856965388326640e-02 -1.5105237092347160e-01 1.2862892445018109e-01 + 27 4.6163842732722504e-02 -4.7145326827103505e-03 -2.0770802868259192e-04 + 28 1.1137379858917107e-02 5.7570783215990615e-02 7.3702487792676769e-02 + 29 4.8892657028303636e-02 1.0734409425986763e-01 -3.2134995127967849e-03 + 30 -4.2587398133307960e-02 -3.0047443784418228e-02 -8.4420705386072381e-02 + 31 -2.0646215207926085e-02 -1.1590108886476506e-01 7.4785520470549566e-02 + 32 -1.9351936740994052e-01 -6.3281923890906297e-02 -2.2278650628172247e-02 +run_vdwl: 1.667273130413 +run_coul: 0 +run_stress: ! |2- + 6.1925535687585693e+00 6.0572952105271769e+00 5.8826298841000604e+00 2.0544338949977917e-01 -2.2313078114848450e-02 -9.0766976514897041e-02 +run_forces: ! |2 + 1 1.0239633061502058e-02 6.5143827221595174e-02 1.3356826587515483e-02 + 2 -2.2314719792140746e-02 -7.7524048417887792e-02 4.8999119168703323e-02 + 3 -3.9043356307568236e-02 1.8727112901323323e-01 -5.0358319574288206e-02 + 4 2.1555031522153656e-02 -9.6560578347078038e-03 -5.2219714561247452e-02 + 5 5.5684799810960112e-02 1.4098076857747269e-01 3.6430385068854737e-02 + 6 4.2103921190025241e-02 2.9054969033758940e-02 -8.0777612807259296e-03 + 7 -6.4964007703587665e-02 9.0824767825338215e-02 -1.1492723720965943e-02 + 8 -6.9887912879430303e-02 -6.1361831723537673e-02 4.5061147281770325e-02 + 9 1.5493100733112084e-02 -5.6306897360260899e-02 -2.9234346339233039e-02 + 10 -3.0007119234870205e-02 -1.4355108819988596e-01 -1.1246502096182201e-01 + 11 -4.0156584042997157e-02 -5.1238608709860869e-02 4.2111943089822509e-02 + 12 3.2215137999640264e-02 -8.8013573068877235e-02 -4.0049314316609446e-03 + 13 -1.9322692643690253e-02 2.3710729865779583e-02 -4.6453771618837091e-02 + 14 5.7508119522746703e-02 -1.5717550954823703e-02 6.8891636524075137e-02 + 15 -3.1551853579254628e-02 3.2002270904692251e-02 -2.7508263221790400e-02 + 16 1.0688913506500985e-01 -9.0842063672437995e-02 3.6419114766505958e-02 + 17 4.4576981599750799e-02 1.3022472720372444e-01 -7.5802573483000615e-04 + 18 -1.4789239369554841e-01 -3.4554795916705260e-02 -7.1472573328781749e-02 + 19 -1.5516657008010420e-01 -8.1733453599869749e-02 3.6527707427395764e-02 + 20 2.3565108550513952e-02 2.0131835710028016e-02 -3.4090223278000355e-02 + 21 1.6266310434046480e-01 4.8905845083266029e-02 4.9357148091662226e-03 + 22 3.9108125555495730e-03 -8.1159764595007206e-02 -1.0833146565530810e-02 + 23 4.9862133358188218e-02 1.2418637371342198e-01 -7.7818397024808514e-02 + 24 1.2773306535829987e-01 9.4426378198700950e-02 8.4499926668801975e-02 + 25 7.0365780658878857e-02 4.4772437288752168e-03 -4.6793953502009267e-02 + 26 -5.0367468278612715e-02 -1.4927976307827082e-01 1.2849283634143213e-01 + 27 4.6468158385616867e-02 -4.1893770730035470e-03 -1.3381218640924168e-03 + 28 1.1447647509745237e-02 5.8175457185785213e-02 7.3359279966104529e-02 + 29 4.7807504512594315e-02 1.0732100993527130e-01 -1.9887010850049803e-03 + 30 -4.2515398596597830e-02 -2.9914524234883048e-02 -8.4055979568242525e-02 + 31 -2.1955840630845491e-02 -1.1661294434426502e-01 7.4709133379083956e-02 + 32 -1.9494325826950429e-01 -6.5180990416658327e-02 -2.2830796417360581e-02 +... diff --git a/unittest/force-styles/tests/bond-gromos.yaml b/unittest/force-styles/tests/bond-gromos.yaml index a9f5dba6b4..112fcb9748 100644 --- a/unittest/force-styles/tests/bond-gromos.yaml +++ b/unittest/force-styles/tests/bond-gromos.yaml @@ -1,7 +1,7 @@ --- lammps_version: 5 May 2020 date_generated: Sat May 30 17:49:16 202 -epsilon: 2.5e-13 +epsilon: 5e-13 prerequisites: ! | atom full bond gromos diff --git a/unittest/force-styles/tests/bond-nonlinear.yaml b/unittest/force-styles/tests/bond-nonlinear.yaml index a8b6c20151..0d4935d0bb 100644 --- a/unittest/force-styles/tests/bond-nonlinear.yaml +++ b/unittest/force-styles/tests/bond-nonlinear.yaml @@ -1,7 +1,7 @@ --- lammps_version: 5 May 2020 date_generated: Sat May 30 17:49:16 202 -epsilon: 2.5e-13 +epsilon: 5e-13 prerequisites: ! | atom full bond nonlinear diff --git a/unittest/force-styles/tests/mol-pair-coul_cut.yaml b/unittest/force-styles/tests/mol-pair-coul_cut.yaml index 43d9dfe67e..bbae7a8456 100644 --- a/unittest/force-styles/tests/mol-pair-coul_cut.yaml +++ b/unittest/force-styles/tests/mol-pair-coul_cut.yaml @@ -1,7 +1,7 @@ --- lammps_version: 5 May 2020 date_generated: Sun May 31 08:39:49 202 -epsilon: 5e-14 +epsilon: 1e-13 prerequisites: ! | atom full pair coul/cut diff --git a/unittest/force-styles/tests/mol-pair-coul_dsf.yaml b/unittest/force-styles/tests/mol-pair-coul_dsf.yaml index e4f9983aae..98f2a64d3c 100644 --- a/unittest/force-styles/tests/mol-pair-coul_dsf.yaml +++ b/unittest/force-styles/tests/mol-pair-coul_dsf.yaml @@ -1,7 +1,7 @@ --- lammps_version: 5 May 2020 date_generated: Sun May 31 08:50:20 202 -epsilon: 1e-13 +epsilon: 2e-13 prerequisites: ! | atom full pair coul/dsf diff --git a/unittest/force-styles/tests/mol-pair-coul_wolf.yaml b/unittest/force-styles/tests/mol-pair-coul_wolf.yaml index 4da58e6ea6..bc8c243e44 100644 --- a/unittest/force-styles/tests/mol-pair-coul_wolf.yaml +++ b/unittest/force-styles/tests/mol-pair-coul_wolf.yaml @@ -1,7 +1,7 @@ --- lammps_version: 5 May 2020 date_generated: Sun May 31 09:23:33 202 -epsilon: 1e-13 +epsilon: 5e-13 prerequisites: ! | atom full pair coul/wolf diff --git a/unittest/force-styles/tests/mol-pair-lj_charmm_coul_charmm_implicit.yaml b/unittest/force-styles/tests/mol-pair-lj_charmm_coul_charmm_implicit.yaml index 1a1db6784e..2b20a41890 100644 --- a/unittest/force-styles/tests/mol-pair-lj_charmm_coul_charmm_implicit.yaml +++ b/unittest/force-styles/tests/mol-pair-lj_charmm_coul_charmm_implicit.yaml @@ -1,7 +1,7 @@ --- lammps_version: 5 May 2020 date_generated: Sun May 31 07:05:48 202 -epsilon: 5e-14 +epsilon: 2e-13 prerequisites: ! | atom full pair lj/charmm/coul/charmm/implicit diff --git a/unittest/force-styles/tests/mol-pair-table.yaml b/unittest/force-styles/tests/mol-pair-table.yaml new file mode 100644 index 0000000000..0627e544a6 --- /dev/null +++ b/unittest/force-styles/tests/mol-pair-table.yaml @@ -0,0 +1,98 @@ +--- +lammps_version: 2 Jun 2020 +date_generated: Tue Jun 2 17:07:52 202 +epsilon: 5e-14 +prerequisites: ! | + atom full + pair table +pre_commands: ! "" +post_commands: ! "" +input_file: in.fourmol +pair_style: table linear 1000 +pair_coeff: ! | + 1 1 ${input_dir}/pair_table_lj_cut.txt lj_1_1 + 1 2 ${input_dir}/pair_table_lj_cut.txt lj_1_2 + 1 3 ${input_dir}/pair_table_lj_cut.txt lj_1_3 + 1 4 ${input_dir}/pair_table_lj_cut.txt lj_1_4 + 1 5 ${input_dir}/pair_table_lj_cut.txt lj_1_5 + 2 2 ${input_dir}/pair_table_lj_cut.txt lj_2_2 + 2 3 ${input_dir}/pair_table_lj_cut.txt lj_2_3 + 2 4 ${input_dir}/pair_table_lj_cut.txt lj_2_4 + 2 5 ${input_dir}/pair_table_lj_cut.txt lj_2_5 + 3 3 ${input_dir}/pair_table_lj_cut.txt lj_3_3 + 3 4 ${input_dir}/pair_table_lj_cut.txt lj_3_4 + 3 5 ${input_dir}/pair_table_lj_cut.txt lj_3_5 + 4 4 ${input_dir}/pair_table_lj_cut.txt lj_4_4 + 4 5 ${input_dir}/pair_table_lj_cut.txt lj_4_5 + 5 5 ${input_dir}/pair_table_lj_cut.txt lj_5_5 +extract: ! "" +natoms: 29 +init_vdwl: 756.641645798358 +init_coul: 0 +init_stress: ! |2- + 2.2090340377185967e+03 2.2244453255747117e+03 4.7288126624664974e+03 -7.6403326905269398e+02 2.8082113929050504e+01 6.7633740837364439e+02 +init_forces: ! |2 + 21 -7.4152834115258486e+01 -8.4097799952580075e+01 2.3159619440133380e+02 + 22 -1.1068613517882235e+02 -2.6823333923316500e+01 -1.7365467444566553e+02 + 23 1.8482904133388223e+02 1.1093264541659750e+02 -5.7930741636712071e+01 + 19 3.1933948922635905e-04 -2.3852967242197055e-04 1.7434557181616340e-03 + 18 -1.8861300062111192e-02 -3.3400052294502179e-02 3.0998859026254152e-02 + 20 -9.9899500683441750e-04 -1.0223083257768326e-03 3.6965867058990032e-04 + 28 -1.8537423924296499e+02 7.9666126830459447e+01 -1.2542634211727822e+02 + 4 -7.9160281367275722e+00 2.1475153087741110e+00 -5.6273386055724828e+00 + 10 5.3659703631942352e+02 -6.1638821121220133e+02 -1.8524754345847680e+02 + 11 -2.3998246191028687e+00 -6.0237447250432350e+00 -9.8493429965792298e+00 + 12 1.7521141359856628e+01 1.0629841850210417e+01 -7.9312291032117042e+00 + 14 -3.4254573458881881e+00 6.9454087271157916e-01 -8.8549490264531219e+00 + 3 -1.3601366655597215e+02 -3.8933969547126463e+02 -1.4673165295081574e+02 + 6 -8.3976623131970030e+02 9.7421656440040920e+02 1.1689035557011593e+03 + 7 5.9087836043818115e+01 -3.4067040950997404e+02 -1.7408617984623156e+03 + 15 -2.0812424842265748e-01 8.6236045287663003e+00 3.0626696691420956e+00 + 8 1.4404606696350953e+02 -1.1101530899074169e+02 3.9802209126866262e+02 + 9 8.1112222258717168e+01 8.7379022925008144e+01 3.5897466875849778e+02 + 16 4.6872469487658930e+02 -3.3472142759962014e+02 -1.2036108146826032e+03 + 17 -4.5876131348491481e+02 3.1932075524331395e+02 1.2202196485462191e+03 + 5 -2.5605507618514016e+00 -4.1184521759347588e+00 1.2369824594500452e+01 + 13 8.2458457495438626e+00 -3.2680411194697614e+00 -1.5173080370124606e-01 + 2 1.5875070222736517e+02 1.3063288077538610e+02 -1.8684429323195315e+02 + 1 -2.3000580006052314e+01 2.7192815329191200e+02 3.3414196848607327e+02 + 27 5.3953257632741014e+01 -2.3246330657484364e+02 9.3521822143445291e+01 + 29 1.3142887167232908e+02 1.5280375224826219e+02 3.1900088976429561e+01 + 24 3.6069363323679390e+01 -2.1770366344996296e+02 1.1410578468006614e+02 + 25 -1.5123846858732526e+02 2.4345575024648110e+01 -1.2714600914378309e+02 + 26 1.1515691479712817e+02 1.9334707687878640e+02 1.3017031466176082e+01 +run_vdwl: 146.327829985032 +run_coul: 0 +run_stress: ! |2- + 6.2914745307898283e+02 6.7439990734333583e+02 4.8382994180885322e+02 -3.2311602844067630e+02 -2.9168790037089135e+01 1.2280146536160866e+02 +run_forces: ! |2 + 21 -9.8223704263420135e+00 -1.1937831142654984e+01 3.8747486275879332e+01 + 22 -1.8260879394786041e+01 -4.4231132834754163e+00 -2.9364817699370402e+01 + 23 2.8071936064676528e+01 1.6373759184425133e+01 -9.3702350107338450e+00 + 19 2.5604832046069535e-04 -2.4189898030892005e-04 1.6743691237745819e-03 + 18 -1.8054106711718410e-02 -3.1568964918282955e-02 2.9599553823736552e-02 + 20 -8.8390456832979493e-04 -9.1401459749508313e-04 3.6013486968785625e-04 + 28 -2.5002749675394742e+01 1.1546639020795190e+01 -1.6860888288423549e+01 + 4 -8.7521679338772564e+00 3.2350894298919783e+00 -6.3183019964749780e+00 + 10 6.3968310015089294e+01 -7.5154164336910185e+01 -7.5921779563234097e+01 + 11 -6.3974181801433527e+00 -8.2015044886741890e+00 -1.6623131445951760e+01 + 12 1.4375970778558539e+01 1.2183815698169100e+01 -8.2849268567516905e+00 + 14 -2.8220099744921270e+00 4.4312152330104282e-01 -7.1784838499077441e+00 + 3 -2.5170415829369691e+02 1.0807957243252388e+02 8.7902068634117185e+01 + 6 1.2021318256369948e+02 -1.0159989935597440e+02 -1.4455046866801038e+02 + 7 3.7064970613492512e+00 -1.0481522858827926e+01 -4.1617502928655071e+01 + 15 -4.0482676064288375e-01 8.2478176580999758e+00 3.1232194954592902e+00 + 8 -1.9012552812922401e+01 1.9341369900133493e+01 5.6061660162509632e+01 + 9 1.1002966844626583e+01 1.2955046425976752e+01 4.8964009756379951e+01 + 16 5.3215666467083004e+01 -6.8452018298715132e+01 1.6067414590921679e+01 + 17 -1.4543993736556850e+01 9.9518135650728148e+00 4.0557829246754260e+01 + 5 -1.7372909950509312e+00 -2.5663073053399832e+00 1.0327280945285382e+01 + 13 7.4327969687776196e+00 -2.8316539598264616e+00 -1.0441307986265116e-01 + 2 1.8402173670762625e+01 1.3899059683375182e+01 -2.2581973215530972e+01 + 1 1.3092386727121557e+01 8.0975258006863527e+01 6.0162717183582615e+01 + 27 3.0641658609965634e+00 -3.8727506359895912e+01 1.1409481341404170e+01 + 29 2.1946401102557179e+01 2.7187485766660277e+01 5.4471747925943950e+00 + 24 1.2590957134158188e+01 -3.6189602254037929e+01 2.3845923499083668e+01 + 25 -3.0061118850595161e+01 5.3993721695176697e+00 -2.5809444960387523e+01 + 26 1.7456807738003775e+01 3.0778628058022715e+01 1.9384675815059120e+00 +... diff --git a/unittest/force-styles/tests/pair_table_beck.txt b/unittest/force-styles/tests/pair_table_beck.txt new file mode 100644 index 0000000000..279c3a4ec8 --- /dev/null +++ b/unittest/force-styles/tests/pair_table_beck.txt @@ -0,0 +1,2010 @@ +# Pair potential beck for atom types 1 1: i,r,energy,force + +beck_1_1 +N 1000 R 0.5 8 + +1 0.5 44.5049513372107 195.378072520348 +2 0.507507507507508 43.0620563926594 189.043934193975 +3 0.515015015015015 41.6659399272555 182.915157558886 +4 0.522522522522523 40.3150853181574 176.985084137332 +5 0.53003003003003 39.0080251161905 171.247271355917 +6 0.537537537537538 37.7433394513696 165.695485544176 +7 0.545045045045045 36.5196544901281 160.323695160164 +8 0.552552552552553 35.3356409425767 155.126064235702 +9 0.56006006006006 34.1900126181692 150.096946034174 +10 0.567567567567568 33.0815250282076 145.230876913985 +11 0.575075075075075 32.0089740336644 140.522570391026 +12 0.582582582582583 30.9711945368562 135.966911393687 +13 0.59009009009009 29.9670592155426 131.558950704198 +14 0.597597597597598 28.9954772980782 127.293899580236 +15 0.605105105105105 28.0553933782831 123.167124550972 +16 0.612612612612613 27.1457862687459 119.174142381905 +17 0.62012012012012 26.2656678913116 115.310615202993 +18 0.627627627627628 25.4140822035483 111.572345794809 +19 0.635135135135135 24.5901041600274 107.955273027579 +20 0.642642642642643 23.7928387072847 104.455467448155 +21 0.65015015015015 23.0214198113745 101.069127010126 +22 0.657657657657658 22.2750095169553 97.7925729424101 +23 0.665165165165165 21.5527970368873 94.6222457518583 +24 0.672672672672673 20.8539978713508 91.5547013555004 +25 0.68018018018018 20.1778529555284 88.5866073382435 +26 0.687687687687688 19.5236278349241 85.7147393319451 +27 0.695195195195195 18.8906118674238 82.9359775119254 +28 0.702702702702703 18.2781174512286 80.2473032071089 +29 0.71021021021021 17.6854792778237 77.6457956201075 +30 0.717717717717718 17.1120536091683 75.1286286536796 +31 0.725225225225225 16.5572175783241 72.6930678401129 +32 0.732732732732733 16.0203685127588 70.3364673701912 +33 0.74024024024024 15.5009232795928 68.0562672185154 +34 0.747747747747748 14.9983176520741 65.8499903620512 +35 0.755255255255255 14.5120056965956 63.7152400888799 +36 0.762762762762763 14.041459179587 61.6496973942242 +37 0.77027027027027 13.5861669936376 59.6511184609199 +38 0.777777777777778 13.145634602226 57.7173322215914 +39 0.785285285285285 12.7193835024535 55.8462379998808 +40 0.792792792792793 12.3069507051968 54.0358032281678 +41 0.8003003003003 11.9078882321165 52.2840612392959 +42 0.807807807807808 11.5217626289731 50.5891091299072 +43 0.815315315315315 11.1481544947232 48.9491056930597 +44 0.822822822822823 10.7866580258827 47.3622694178831 +45 0.83033033033033 10.4368805756641 45.826876554095 +46 0.837837837837838 10.0984422274061 44.341259239276 +47 0.845345345345345 9.77097538183476 42.9038036868676 +48 0.852852852852853 9.45412435770556 41.5129484329222 +49 0.86036036036036 9.14754500539421 40.167182639701 +50 0.867867867867868 8.85090433301507 38.8650444542751 +51 0.875375375375375 8.56388014466178 37.6051194203462 +52 0.882882882882883 8.28616069037667 36.3860389415608 +53 0.89039039039039 8.0174443274689 35.206478794648 +54 0.897897897897898 7.75743919281323 34.0651576907647 +55 0.905405405405405 7.50586288577341 32.9608358834858 +56 0.912912912912913 7.26244216140585 31.8923138219252 +57 0.92042042042042 7.02691263361001 30.8584308475255 +58 0.927927927927928 6.79901848790341 29.8580639330999 +59 0.935435435435436 6.57851220350873 28.8901264627556 +60 0.942942942942943 6.36515428445156 27.953567051374 +61 0.950450450450451 6.15871299937631 27.0473684023641 +62 0.957957957957958 5.95896412979786 26.1705462024489 +63 0.965465465465466 5.76569072651528 25.3221480522836 +64 0.972972972972973 5.57868287392318 24.5012524317442 +65 0.980480480480481 5.39773746196447 23.706967698761 +66 0.987987987987988 5.22265796547694 22.9384311206117 +67 0.995495495495496 5.05325423069377 22.1948079366195 +68 1.003003003003 4.88934226866632 21.4752904512396 +69 1.01051051051051 4.73074405538443 20.7790971565469 +70 1.01801801801802 4.57728733837735 20.1054718831747 +71 1.02552552552553 4.42880544958515 19.4536829787784 +72 1.03303303303303 4.28513712429721 18.823022513135 +73 1.04054054054054 4.1461263259612 18.2128055090129 +74 1.04804804804805 4.01162207667218 17.6223691979767 +75 1.05555555555556 3.88147829315774 17.0510723003199 +76 1.06306306306306 3.75555362808086 16.4982943283421 +77 1.07057057057057 3.63371131648824 15.9634349122139 +78 1.07807807807808 3.51581902723712 15.4459131476978 +79 1.08558558558559 3.40174871923938 14.9451669650163 +80 1.09309309309309 3.2913765023666 14.4606525181819 +81 1.1006006006006 3.18458250286492 13.9918435941245 +82 1.10810810810811 3.08125073313372 13.5382310409765 +83 1.11561561561562 2.98126896572637 13.0993222148923 +84 1.12312312312312 2.88452861143639 12.6746404448032 +85 1.13063063063063 2.79092460133639 12.2637245145248 +86 1.13813813813814 2.70035527264179 11.8661281616552 +87 1.14564564564565 2.61272225827517 11.4814195927201 +88 1.15315315315315 2.52793038001141 11.1091810140365 +89 1.16066066066066 2.44588754508743 10.749008177787 +90 1.16816816816817 2.36650464616424 10.4005099428114 +91 1.17567567567568 2.28969546453261 10.0633078496373 +92 1.18318318318318 2.21537657645717 9.73703570928969 +93 1.19069069069069 2.14346726255724 9.42133920543152 +94 1.1981981981982 2.07388942012593 9.11587550940431 +95 1.20570570570571 2.0065674782921 8.82031290774932 +96 1.21321321321321 1.94142831593328 8.53433044180582 +97 1.22072072072072 1.87840118225009 8.25761755899411 +98 1.22822822822823 1.81741761991604 7.98987377540511 +99 1.23573573573574 1.75841139071912 7.73080834932948 +100 1.24324324324324 1.70131840361446 7.48013996537198 +101 1.25075075075075 1.64607664510977 7.23759642880778 +102 1.25825825825826 1.5926261119081 7.00291436984862 +103 1.26576576576577 1.54090874573455 6.77583895749771 +104 1.27327327327327 1.49086837027624 6.55612362268239 +105 1.28078078078078 1.44245063016699 6.34352979036382 +106 1.28828828828829 1.39560293195033 6.13782662033266 +107 1.2957957957958 1.35027438695688 5.93879075640922 +108 1.3033033033033 1.30641575603385 5.74620608377543 +109 1.31081081081081 1.26397939606665 5.55986349417524 +110 1.31831831831832 1.2229192082346 5.37956065872813 +111 1.32582582582583 1.18319058794438 5.20510180810909 +112 1.33333333333333 1.14475037638689 5.03629751985614 +113 1.34084084084084 1.10755681366493 4.87296451257435 +114 1.34834834834835 1.07156949344057 4.71492544681276 +115 1.35585585585586 1.03674931905327 4.56200873239791 +116 1.36336336336336 1.00305846106063 4.41404834201454 +117 1.37087087087087 0.970460316156092 4.27088363083106 +118 1.37837837837838 0.938919467418577 4.13235916197373 +119 1.38588588588589 0.908401645851078 3.99832453765983 +120 1.39339339339339 0.878873693166357 3.86863423580666 +121 1.4009009009009 0.850303525779283 3.74314745193842 +122 1.40840840840841 0.822660099966715 3.6217279462195 +123 1.41591591591592 0.795913378157072 3.50424389544792 +124 1.42342342342342 0.770034296312939 3.39056774984798 +125 1.43093093093093 0.744994732371277 3.2805760945066 +126 1.43843843843844 0.720767475706938 3.17414951530285 +127 1.44594594594595 0.697326197586323 3.07117246918484 +128 1.45345345345345 0.674645422579041 2.97153315865311 +129 1.46096096096096 0.652700500896534 2.8751234103142 +130 1.46846846846847 0.63146758162759 2.78183855737216 +131 1.47597597597598 0.610923586841683 2.69157732593071 +132 1.48348348348348 0.591046186531971 2.60424172498211 +133 1.49099099099099 0.571813774370744 2.51973693996345 +134 1.4984984984985 0.553205444250974 2.43797122976463 +135 1.50600600600601 0.535200967588468 2.358855827076 +136 1.51351351351351 0.517780771359969 2.28230484196757 +137 1.52102102102102 0.500925916853336 2.20823516859479 +138 1.52852852852853 0.484618079106703 2.13656639492969 +139 1.53603603603604 0.468839527014301 2.06722071541922 +140 1.54354354354354 0.453573104077291 2.00012284647578 +141 1.55105105105105 0.43880220977872 1.93519994470833 +142 1.55855855855856 0.424510781562344 1.87238152780495 +143 1.56606606606607 0.410683277395745 1.81159939798103 +144 1.57357357357357 0.397304658898792 1.75278756790992 +145 1.58108108108108 0.38436037501911 1.69588218905539 +146 1.58858858858859 0.371836346236822 1.64082148232818 +147 1.5960960960961 0.359718949281406 1.58754567099115 +148 1.6036036036036 0.347995002344045 1.53599691574022 +149 1.61111111111111 0.336651750769421 1.48611925189046 +150 1.61861861861862 0.325676853211393 1.43785852859908 +151 1.62612612612613 0.315058368237517 1.39116235005933 +152 1.63363363363363 0.304784741367861 1.34598001860129 +153 1.64114114114114 0.294844792534025 1.30226247963786 +154 1.64864864864865 0.28522770394474 1.2599622683959 +155 1.65615615615616 0.275923008344863 1.21903345837489 +156 1.66366366366366 0.266920577655016 1.17943161147683 +157 1.67117117117117 0.258210611979515 1.1411137297534 +158 1.67867867867868 0.249783628970654 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7.99601064195053 -3.45541892635034e-10 -2.6255973700216e-10 +1000 8 0 0 diff --git a/unittest/force-styles/tests/pair_table_bitmap.txt b/unittest/force-styles/tests/pair_table_bitmap.txt new file mode 100644 index 0000000000..478f368ba6 --- /dev/null +++ b/unittest/force-styles/tests/pair_table_bitmap.txt @@ -0,0 +1,1029 @@ +# Pair potential beck for atom types 1 1: i,r,energy,force + +beck_1_1 +N 1024 BITMAP 0.5 8 + +1 1.4142135623731 0.801901199585017 3.5305454762507 +2 1.41972708645007 0.782669274476741 3.44606840658335 +3 1.42521928137392 0.763969271976054 3.36392612296604 +4 1.43069039278245 0.745784253113464 3.28404428328019 +5 1.43614066163451 0.728097896861989 3.20635125761509 +6 1.44157032433385 0.710894474494628 3.13077801571116 +7 1.44697961284878 0.694158825142474 3.05725801967362 +8 1.45236875482778 0.677876332490555 2.98572712168054 +9 1.45773797371133 0.662032902552176 2.91612346642513 +10 1.46308748883995 0.646614942465917 2.84838739804721 +11 1.46841751555884 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b/unittest/force-styles/tests/pair_table_lj_cut.txt new file mode 100644 index 0000000000..d8996bc4c3 --- /dev/null +++ b/unittest/force-styles/tests/pair_table_lj_cut.txt @@ -0,0 +1,15075 @@ +# Pair potential lj/cut for atom types 1 1: i,r,energy,force + +lj_1_1 +N 1000 R 0.1 8 + +1 0.1 4.7683715625e+15 5.72204588671874e+17 +2 0.107907907907908 1.91306980364015e+15 2.12744720595463e+17 +3 0.115815815815816 818758153812917 8.483381846517e+16 +4 0.123723723723724 370624644685218 3.59469925010097e+16 +5 0.131631631631632 176216636146732 1.60645251454931e+16 +6 0.13953953953954 87498911727066.6 7.5246554493731e+15 +7 0.147447447447447 45156780344098.8 3.67508142673229e+15 +8 0.155355355355355 24124333392883.4 1.86341827990272e+15 +9 0.163263263263263 13295613555109.4 977239861928053 +10 0.171171171171171 7537070547533.43 528388341393121 +11 0.179079079079079 4383608943257.5 293743474350791 +12 0.186986986986987 2609957353176.83 167495564715195 +13 0.194894894894895 1587685337537.87 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-0.000155548188536908 +997 7.97627627627628 -0.000206072924359152 -0.000154478289770294 +998 7.98418418418418 -0.00020485552699602 -0.000153416761393547 +999 7.99209209209209 -0.000203646491246796 -0.000152363530214613 +1000 8 0 0 diff --git a/unittest/formats/test_eim_potential_file_reader.cpp b/unittest/formats/test_eim_potential_file_reader.cpp index af5e08ebeb..eb13cee7cd 100644 --- a/unittest/formats/test_eim_potential_file_reader.cpp +++ b/unittest/formats/test_eim_potential_file_reader.cpp @@ -1,3 +1,16 @@ +/* ---------------------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + http://lammps.sandia.gov, Sandia National Laboratories + Steve Plimpton, sjplimp@sandia.gov + + Copyright (2003) Sandia Corporation. Under the terms of Contract + DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains + certain rights in this software. This software is distributed under + the GNU General Public License. + + See the README file in the top-level LAMMPS directory. +------------------------------------------------------------------------- */ + #include "gmock/gmock.h" #include "gtest/gtest.h" #include "lammps.h" diff --git a/unittest/formats/test_potential_file_reader.cpp b/unittest/formats/test_potential_file_reader.cpp index 6ce6a315cb..3447dbb73f 100644 --- a/unittest/formats/test_potential_file_reader.cpp +++ b/unittest/formats/test_potential_file_reader.cpp @@ -1,3 +1,16 @@ +/* ---------------------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + http://lammps.sandia.gov, Sandia National Laboratories + Steve Plimpton, sjplimp@sandia.gov + + Copyright (2003) Sandia Corporation. Under the terms of Contract + DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains + certain rights in this software. This software is distributed under + the GNU General Public License. + + See the README file in the top-level LAMMPS directory. +------------------------------------------------------------------------- */ + #include "gmock/gmock.h" #include "gtest/gtest.h" #include "potential_file_reader.h" diff --git a/unittest/utils/CMakeLists.txt b/unittest/utils/CMakeLists.txt index 5df52f1f9f..d02d378ea6 100644 --- a/unittest/utils/CMakeLists.txt +++ b/unittest/utils/CMakeLists.txt @@ -5,3 +5,7 @@ add_test(Tokenizer test_tokenizer) add_executable(test_utils test_utils.cpp) target_link_libraries(test_utils PRIVATE lammps GTest::GMockMain GTest::GMock GTest::GTest) add_test(Utils test_utils) + +add_executable(test_fmtlib test_fmtlib.cpp) +target_link_libraries(test_fmtlib PRIVATE lammps GTest::GMockMain GTest::GMock GTest::GTest) +add_test(FmtLib test_fmtlib) diff --git a/unittest/utils/test_fmtlib.cpp b/unittest/utils/test_fmtlib.cpp new file mode 100644 index 0000000000..6d354cf69f --- /dev/null +++ b/unittest/utils/test_fmtlib.cpp @@ -0,0 +1,106 @@ +/* ---------------------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + http://lammps.sandia.gov, Sandia National Laboratories + Steve Plimpton, sjplimp@sandia.gov + + Copyright (2003) Sandia Corporation. Under the terms of Contract + DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains + certain rights in this software. This software is distributed under + the GNU General Public License. + + See the README file in the top-level LAMMPS directory. +------------------------------------------------------------------------- */ + +#include "lmptype.h" +#include "gtest/gtest.h" +#include "gmock/gmock.h" +#include "fmt/format.h" +#include +#include + +using namespace LAMMPS_NS; +using ::testing::Eq; + +// this tests a subset of {fmt} that is most relevant to LAMMPS + +TEST(FmtLib, insert_string) { + const char val[] = "word"; + auto text = fmt::format("word {}",val); + ASSERT_THAT(text, Eq("word word")); +} + +TEST(FmtLib, insert_int) { + const int val = 333; + auto text = fmt::format("word {}",val); + ASSERT_THAT(text, Eq("word 333")); +} + +TEST(FmtLib, insert_neg_int) { + const int val = -333; + auto text = fmt::format("word {}",val); + ASSERT_THAT(text, Eq("word -333")); +} + +TEST(FmtLib, insert_bigint) { + if (sizeof(bigint) == 4) GTEST_SKIP(); + const bigint val = 9945234592L; + auto text = fmt::format("word {}",val); + ASSERT_THAT(text, Eq("word 9945234592")); +} + +TEST(FmtLib, insert_neg_bigint) { + if (sizeof(bigint) == 4) GTEST_SKIP(); + const bigint val = -9945234592L; + auto text = fmt::format("word {}",val); + ASSERT_THAT(text, Eq("word -9945234592")); +} + +TEST(FmtLib, insert_tagint) { + if (sizeof(tagint) == 4) GTEST_SKIP(); + const tagint val = 9945234592L; + auto text = fmt::format("word {}",val); + ASSERT_THAT(text, Eq("word 9945234592")); +} + +TEST(FmtLib, insert_neg_tagint) { + if (sizeof(tagint) == 4) GTEST_SKIP(); + const tagint val = -9945234592L; + auto text = fmt::format("word {}",val); + ASSERT_THAT(text, Eq("word -9945234592")); +} + +TEST(FmtLib, insert_imageint) { + if (sizeof(imageint) == 4) GTEST_SKIP(); + const imageint val = 9945234592L; + auto text = fmt::format("word {}",val); + ASSERT_THAT(text, Eq("word 9945234592")); +} + +TEST(FmtLib, insert_neg_imageint) { + if (sizeof(imageint) == 4) GTEST_SKIP(); + const imageint val = -9945234592L; + auto text = fmt::format("word {}",val); + ASSERT_THAT(text, Eq("word -9945234592")); +} + +TEST(FmtLib, insert_double) { + const double val = 1.5; + auto text = fmt::format("word {}",val); + ASSERT_THAT(text, Eq("word 1.5")); +} + +TEST(FmtLib, insert_neg_double) { + const double val = -1.5; + auto text = fmt::format("word {}",val); + ASSERT_THAT(text, Eq("word -1.5")); +} + +TEST(FmtLib, int_for_double) { + const double val = -1.5; + ASSERT_THROW(fmt::format("word {:d}",val),std::exception); +} + +TEST(FmtLib, double_for_int) { + const int val = 15; + ASSERT_THROW(fmt::format("word {:g}",val),std::exception); +} diff --git a/unittest/utils/test_tokenizer.cpp b/unittest/utils/test_tokenizer.cpp index 23f2e85d98..08c71338be 100644 --- a/unittest/utils/test_tokenizer.cpp +++ b/unittest/utils/test_tokenizer.cpp @@ -1,5 +1,18 @@ -#include -#include +/* ---------------------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + http://lammps.sandia.gov, Sandia National Laboratories + Steve Plimpton, sjplimp@sandia.gov + + Copyright (2003) Sandia Corporation. Under the terms of Contract + DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains + certain rights in this software. This software is distributed under + the GNU General Public License. + + See the README file in the top-level LAMMPS directory. +------------------------------------------------------------------------- */ + +#include "gtest/gtest.h" +#include "gmock/gmock.h" #include "tokenizer.h" using namespace LAMMPS_NS; diff --git a/unittest/utils/test_utils.cpp b/unittest/utils/test_utils.cpp index 0ae469f085..e1c458a173 100644 --- a/unittest/utils/test_utils.cpp +++ b/unittest/utils/test_utils.cpp @@ -1,5 +1,18 @@ -#include -#include +/* ---------------------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + http://lammps.sandia.gov, Sandia National Laboratories + Steve Plimpton, sjplimp@sandia.gov + + Copyright (2003) Sandia Corporation. Under the terms of Contract + DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains + certain rights in this software. This software is distributed under + the GNU General Public License. + + See the README file in the top-level LAMMPS directory. +------------------------------------------------------------------------- */ + +#include "gtest/gtest.h" +#include "gmock/gmock.h" #include "utils.h" #include @@ -12,7 +25,11 @@ TEST(Utils, trim_comment) { } TEST(Utils, count_words) { - ASSERT_EQ(utils::count_words("some text # comment"), 2); + ASSERT_EQ(utils::count_words("some text # comment"), 4); +} + +TEST(Utils, trim_and_count_words) { + ASSERT_EQ(utils::trim_and_count_words("some text # comment"), 2); } TEST(Utils, valid_integer1) { @@ -182,3 +199,19 @@ TEST(Utils, strmatch_char_range) { TEST(Utils, strmatch_opt_range) { ASSERT_TRUE(utils::strmatch("rigid","^[0-9]*[p-s]igid")); } + +TEST(Utils, path_join) { +#if defined(_WIN32) + ASSERT_THAT(utils::path_join("c:\\parent\\folder", "filename"), Eq("c:\\parent\\folder\\filename")); +#else + ASSERT_THAT(utils::path_join("/parent/folder", "filename"), Eq("/parent/folder/filename")); +#endif +} + +TEST(Utils, path_basename) { +#if defined(_WIN32) + ASSERT_THAT(utils::path_basename("c:\\parent\\folder\\filename"), Eq("filename")); +#else + ASSERT_THAT(utils::path_basename("/parent/folder/filename"), Eq("filename")); +#endif +}