Unverified Commit 5a4bbcc3 authored by Richard Berger's avatar Richard Berger
Browse files

Update pair vashishta

parent cadc374e

src/MANYBODY/pair_vashishta.cpp

+70 −113
Original line number Diff line number Diff line
@@ -30,10 +30,11 @@ 
#include "neigh_list.h"

#include "neigh_request.h"

#include "utils.h"

#include "tokenizer.h"

#include "potential_file_reader.h"



using namespace LAMMPS_NS;



#define MAXLINE 1024

#define DELTA 4



/* ---------------------------------------------------------------------- */
@@ -353,92 +354,37 @@ double PairVashishta::init_one(int i, int j) 


void PairVashishta::read_file(char *file)

{

  int params_per_line = 17;

  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 Vashishta potential file %s",file);

      error->one(FLERR,str);

    }

  }



  // 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



  int n,nwords,ielement,jelement,kelement;

  char line[MAXLINE],*ptr;

  int eof = 0;



  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);



    // strip comment, skip line if blank



    if ((ptr = strchr(line,'#'))) *ptr = '\0';

    nwords = utils::count_words(line);

    if (nwords == 0) continue;



    // concatenate additional lines until have params_per_line words



    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;

      }

      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 (nwords != params_per_line)

      error->all(FLERR,"Incorrect format in Vashishta potential file");

    PotentialFileReader reader(lmp, file, "Vashishta");

    char * line;



    // words = ptrs to all words in line

    while(line = reader.next_line(NPARAMS_PER_LINE)) {

      try {

        ValueTokenizer values(line, " \t\n\r\f");



    nwords = 0;

    words[nwords++] = strtok(line," \t\n\r\f");

    while ((words[nwords++] = strtok(NULL," \t\n\r\f"))) continue;

        std::string iname = values.next_string();

        std::string jname = values.next_string();

        std::string kname = values.next_string();



        // 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;



        for (ielement = 0; ielement < nelements; ielement++)

      if (strcmp(words[0],elements[ielement]) == 0) break;

          if (iname == elements[ielement]) break;

        if (ielement == nelements) continue;

        for (jelement = 0; jelement < nelements; jelement++)

      if (strcmp(words[1],elements[jelement]) == 0) break;

          if (jname == elements[jelement]) break;

        if (jelement == nelements) continue;

        for (kelement = 0; kelement < nelements; kelement++)

      if (strcmp(words[2],elements[kelement]) == 0) break;

          if (kname == elements[kelement]) break;

        if (kelement == nelements) continue;



        // load up parameter settings and error check their values
@@ -452,20 +398,23 @@ void PairVashishta::read_file(char *file) 
        params[nparams].ielement = ielement;

        params[nparams].jelement = jelement;

        params[nparams].kelement = kelement;

    params[nparams].bigh = atof(words[3]);

    params[nparams].eta = atof(words[4]);

    params[nparams].zi = atof(words[5]);

    params[nparams].zj = atof(words[6]);

    params[nparams].lambda1 = atof(words[7]);

    params[nparams].bigd = atof(words[8]);

    params[nparams].lambda4 = atof(words[9]);

    params[nparams].bigw = atof(words[10]);

    params[nparams].cut = atof(words[11]);

    params[nparams].bigb = atof(words[12]);

    params[nparams].gamma = atof(words[13]);

    params[nparams].r0 = atof(words[14]);

    params[nparams].bigc = atof(words[15]);

    params[nparams].costheta = atof(words[16]);

        params[nparams].bigh     = values.next_double();

        params[nparams].eta      = values.next_double();

        params[nparams].zi       = values.next_double();

        params[nparams].zj       = values.next_double();

        params[nparams].lambda1  = values.next_double();

        params[nparams].bigd     = values.next_double();

        params[nparams].lambda4  = values.next_double();

        params[nparams].bigw     = values.next_double();

        params[nparams].cut      = values.next_double();

        params[nparams].bigb     = values.next_double();

        params[nparams].gamma    = values.next_double();

        params[nparams].r0       = values.next_double();

        params[nparams].bigc     = values.next_double();

        params[nparams].costheta = values.next_double();

      } catch (TokenizerException & e) {

        error->one(FLERR, e.what());

      }



      if (params[nparams].bigb < 0.0 || params[nparams].gamma < 0.0 ||

          params[nparams].r0 < 0.0 || params[nparams].bigc < 0.0 ||
@@ -473,12 +422,20 @@ void PairVashishta::read_file(char *file) 
          params[nparams].lambda1 < 0.0 || params[nparams].bigd < 0.0 ||

          params[nparams].lambda4 < 0.0 || params[nparams].bigw < 0.0 ||

          params[nparams].cut < 0.0)

      error->all(FLERR,"Illegal Vashishta parameter");

        error->one(FLERR,"Illegal Vashishta parameter");



      nparams++;

    }

  }



  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");

  }



  delete [] words;

  MPI_Bcast(params, maxparam*sizeof(Param), MPI_BYTE, 0, world);

}



/* ---------------------------------------------------------------------- */

src/MANYBODY/pair_vashishta.h

+2 −0
Original line number Diff line number Diff line
@@ -34,6 +34,8 @@ class PairVashishta : public Pair { 
  double init_one(int, int);

  void init_style();



  static const int NPARAMS_PER_LINE = 17;



  struct Param {

    double bigb,gamma,r0,bigc,costheta;

    double bigh,eta,zi,zj;

unittest/formats/test_potential_file_reader.cpp

+10 −0
Original line number Diff line number Diff line
@@ -13,6 +13,7 @@ 
#include "MANYBODY/pair_gw.h"

#include "MANYBODY/pair_gw_zbl.h"

#include "MANYBODY/pair_nb3b_harmonic.h"

#include "MANYBODY/pair_vashishta.h"



#include <mpi.h>
@@ -28,6 +29,7 @@ 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;

const int LAMMPS_NS::PairVashishta::NPARAMS_PER_LINE;



class PotenialFileReaderTest : public ::testing::Test {

protected:
@@ -138,6 +140,14 @@ TEST_F(PotenialFileReaderTest, Nb3bHarmonic) { 
    auto line = reader.next_line(PairNb3bHarmonic::NPARAMS_PER_LINE);

    ASSERT_EQ(utils::count_words(line), PairNb3bHarmonic::NPARAMS_PER_LINE);

}

TEST_F(PotenialFileReaderTest, Vashishta) {

    ::testing::internal::CaptureStdout();

    PotentialFileReader reader(lmp, "SiC.vashishta", "Vashishta");

    ::testing::internal::GetCapturedStdout();



    auto line = reader.next_line(PairVashishta::NPARAMS_PER_LINE);

    ASSERT_EQ(utils::count_words(line), PairVashishta::NPARAMS_PER_LINE);

}



int main(int argc, char **argv)

{

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