From cadc374e0b35746c53db28cd311c99f4f4f28830 Mon Sep 17 00:00:00 2001 From: Richard Berger Date: Thu, 28 May 2020 16:05:02 -0400 Subject: [PATCH] Update pair nb3b harmonic --- src/MANYBODY/pair_nb3b_harmonic.cpp | 147 +++++++----------- src/MANYBODY/pair_nb3b_harmonic.h | 2 + .../formats/test_potential_file_reader.cpp | 19 ++- 3 files changed, 69 insertions(+), 99 deletions(-) diff --git a/src/MANYBODY/pair_nb3b_harmonic.cpp b/src/MANYBODY/pair_nb3b_harmonic.cpp index 3a446b2680..ba18271777 100644 --- a/src/MANYBODY/pair_nb3b_harmonic.cpp +++ b/src/MANYBODY/pair_nb3b_harmonic.cpp @@ -30,10 +30,11 @@ #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 DELTA 4 #define SMALL 0.001 #define PI 3.141592653589793238462643383279 @@ -283,117 +284,73 @@ double PairNb3bHarmonic::init_one(int i, int j) void PairNb3bHarmonic::read_file(char *file) { - int params_per_line = 6; - 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 = NULL; if (comm->me == 0) { - fp = force->open_potential(file); - if (fp == NULL) { - char str[128]; - snprintf(str,128,"Cannot open nb3b/harmonic potential file %s",file); - error->one(FLERR,str); - } - } + PotentialFileReader reader(lmp, file, "nb3b/harmonic"); + char * line; - // read each set of params from potential file - // one set of params can span multiple lines - // store params if all 3 element tags are in element list + while(line = reader.next_line(NPARAMS_PER_LINE)) { + try { + ValueTokenizer values(line, " \t\n\r\f"); - 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; + // load up parameter settings and error check their values - // concatenate additional lines until have params_per_line words + if (nparams == maxparam) { + maxparam += DELTA; + params = (Param *) memory->srealloc(params,maxparam*sizeof(Param), + "pair:params"); + } - 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; + params[nparams].ielement = ielement; + params[nparams].jelement = jelement; + params[nparams].kelement = kelement; + params[nparams].k_theta = values.next_double(); + params[nparams].theta0 = values.next_double(); + params[nparams].cutoff = values.next_double(); + } 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); + + if (params[nparams].k_theta < 0.0 || params[nparams].theta0 < 0.0 || + params[nparams].cutoff < 0.0) + error->one(FLERR,"Illegal nb3b/harmonic parameter"); + + nparams++; } - - if (nwords != params_per_line) - error->all(FLERR,"Incorrect format in nb3b/harmonic 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 entry in file - - 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].k_theta = atof(words[3]); - params[nparams].theta0 = atof(words[4]); - params[nparams].cutoff = atof(words[5]); - - if (params[nparams].k_theta < 0.0 || params[nparams].theta0 < 0.0 || - params[nparams].cutoff < 0.0) - error->all(FLERR,"Illegal nb3b/harmonic 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/MANYBODY/pair_nb3b_harmonic.h b/src/MANYBODY/pair_nb3b_harmonic.h index 75a378e35b..0267b6d0e2 100644 --- a/src/MANYBODY/pair_nb3b_harmonic.h +++ b/src/MANYBODY/pair_nb3b_harmonic.h @@ -34,6 +34,8 @@ class PairNb3bHarmonic : public Pair { double init_one(int, int); void init_style(); + static const int NPARAMS_PER_LINE = 6; + protected: struct Param { double k_theta, theta0, cutoff; diff --git a/unittest/formats/test_potential_file_reader.cpp b/unittest/formats/test_potential_file_reader.cpp index d5d9c61bbe..1ac14ff1d6 100644 --- a/unittest/formats/test_potential_file_reader.cpp +++ b/unittest/formats/test_potential_file_reader.cpp @@ -12,6 +12,7 @@ #include "MANYBODY/pair_tersoff_zbl.h" #include "MANYBODY/pair_gw.h" #include "MANYBODY/pair_gw_zbl.h" +#include "MANYBODY/pair_nb3b_harmonic.h" #include @@ -26,6 +27,7 @@ const int LAMMPS_NS::PairTersoffMODC::NPARAMS_PER_LINE; const int LAMMPS_NS::PairTersoffZBL::NPARAMS_PER_LINE; const int LAMMPS_NS::PairGW::NPARAMS_PER_LINE; const int LAMMPS_NS::PairGWZBL::NPARAMS_PER_LINE; +const int LAMMPS_NS::PairNb3bHarmonic::NPARAMS_PER_LINE; class PotenialFileReaderTest : public ::testing::Test { protected: @@ -85,7 +87,7 @@ TEST_F(PotenialFileReaderTest, Tersoff) { TEST_F(PotenialFileReaderTest, TersoffMod) { ::testing::internal::CaptureStdout(); - PotentialFileReader reader(lmp, "Si.tersoff.mod", "Tersoff"); + PotentialFileReader reader(lmp, "Si.tersoff.mod", "Tersoff/Mod"); ::testing::internal::GetCapturedStdout(); auto line = reader.next_line(PairTersoffMOD::NPARAMS_PER_LINE); @@ -94,7 +96,7 @@ TEST_F(PotenialFileReaderTest, TersoffMod) { TEST_F(PotenialFileReaderTest, TersoffModC) { ::testing::internal::CaptureStdout(); - PotentialFileReader reader(lmp, "Si.tersoff.modc", "Tersoff"); + PotentialFileReader reader(lmp, "Si.tersoff.modc", "Tersoff/ModC"); ::testing::internal::GetCapturedStdout(); auto line = reader.next_line(PairTersoffMODC::NPARAMS_PER_LINE); @@ -103,7 +105,7 @@ TEST_F(PotenialFileReaderTest, TersoffModC) { TEST_F(PotenialFileReaderTest, TersoffZBL) { ::testing::internal::CaptureStdout(); - PotentialFileReader reader(lmp, "SiC.tersoff.zbl", "Tersoff"); + PotentialFileReader reader(lmp, "SiC.tersoff.zbl", "Tersoff/ZBL"); ::testing::internal::GetCapturedStdout(); auto line = reader.next_line(PairTersoffZBL::NPARAMS_PER_LINE); @@ -121,13 +123,22 @@ TEST_F(PotenialFileReaderTest, GW) { TEST_F(PotenialFileReaderTest, GWZBL) { ::testing::internal::CaptureStdout(); - PotentialFileReader reader(lmp, "SiC.gw.zbl", "GWZBL"); + PotentialFileReader reader(lmp, "SiC.gw.zbl", "GW/ZBL"); ::testing::internal::GetCapturedStdout(); auto line = reader.next_line(PairGWZBL::NPARAMS_PER_LINE); ASSERT_EQ(utils::count_words(line), PairGWZBL::NPARAMS_PER_LINE); } +TEST_F(PotenialFileReaderTest, Nb3bHarmonic) { + ::testing::internal::CaptureStdout(); + PotentialFileReader reader(lmp, "MOH.nb3b.harmonic", "NB3B Harmonic"); + ::testing::internal::GetCapturedStdout(); + + auto line = reader.next_line(PairNb3bHarmonic::NPARAMS_PER_LINE); + ASSERT_EQ(utils::count_words(line), PairNb3bHarmonic::NPARAMS_PER_LINE); +} + int main(int argc, char **argv) { MPI_Init(&argc, &argv);