forked from lijiext/lammps
Update pair tersoff mod c
This commit is contained in:
Richard Berger
parent
a4db35e15d
commit
c0324e55ad
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@ -26,6 +26,8 @@
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#include "memory.h"
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#include "error.h"
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#include "utils.h"
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#include "tokenizer.h"
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#include "potential_file_reader.h"
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using namespace LAMMPS_NS;
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@ -36,147 +38,103 @@ using namespace LAMMPS_NS;
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void PairTersoffMODC::read_file(char *file)
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{
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int params_per_line = 21;
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char **words = new char*[params_per_line+1];
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memory->sfree(params);
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params = NULL;
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params = nullptr;
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nparams = maxparam = 0;
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// open file on proc 0
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FILE *fp;
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if (comm->me == 0) {
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fp = force->open_potential(file);
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if (fp == NULL) {
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char str[128];
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snprintf(str,128,"Cannot open Tersoff potential file %s",file);
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error->one(FLERR,str);
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}
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}
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PotentialFileReader reader(lmp, file, "Tersoff");
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char * line;
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// read each line out of file, skipping blank lines or leading '#'
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// store line of params if all 3 element tags are in element list
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while(line = reader.next_line(NPARAMS_PER_LINE)) {
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try {
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ValueTokenizer values(line, " \t\n\r\f");
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int n,nwords,ielement,jelement,kelement;
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char line[MAXLINE],*ptr;
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int eof = 0;
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std::string iname = values.next_string();
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std::string jname = values.next_string();
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std::string kname = values.next_string();
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while (1) {
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if (comm->me == 0) {
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ptr = fgets(line,MAXLINE,fp);
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if (ptr == NULL) {
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eof = 1;
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fclose(fp);
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} else n = strlen(line) + 1;
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}
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MPI_Bcast(&eof,1,MPI_INT,0,world);
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if (eof) break;
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MPI_Bcast(&n,1,MPI_INT,0,world);
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MPI_Bcast(line,n,MPI_CHAR,0,world);
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// ielement,jelement,kelement = 1st args
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// if all 3 args are in element list, then parse this line
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// else skip to next entry in file
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int ielement, jelement, kelement;
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// strip comment, skip line if blank
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for (ielement = 0; ielement < nelements; ielement++)
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if (iname == elements[ielement]) break;
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if (ielement == nelements) continue;
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for (jelement = 0; jelement < nelements; jelement++)
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if (jname == elements[jelement]) break;
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if (jelement == nelements) continue;
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for (kelement = 0; kelement < nelements; kelement++)
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if (kname == elements[kelement]) break;
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if (kelement == nelements) continue;
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if ((ptr = strchr(line,'#'))) *ptr = '\0';
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nwords = utils::count_words(line);
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if (nwords == 0) continue;
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// concatenate additional lines until have params_per_line words
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// load up parameter settings and error check their values
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while (nwords < params_per_line) {
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n = strlen(line);
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if (comm->me == 0) {
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ptr = fgets(&line[n],MAXLINE-n,fp);
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if (ptr == NULL) {
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eof = 1;
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fclose(fp);
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} else n = strlen(line) + 1;
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if (nparams == maxparam) {
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maxparam += DELTA;
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params = (Param *) memory->srealloc(params,maxparam*sizeof(Param),
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"pair:params");
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}
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params[nparams].ielement = ielement;
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params[nparams].jelement = jelement;
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params[nparams].kelement = kelement;
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params[nparams].powerm = values.next_double();
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params[nparams].lam3 = values.next_double();
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params[nparams].h = values.next_double();
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params[nparams].powern = values.next_double();
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params[nparams].beta = values.next_double();
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params[nparams].lam2 = values.next_double();
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params[nparams].bigb = values.next_double();
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params[nparams].bigr = values.next_double();
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params[nparams].bigd = values.next_double();
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params[nparams].lam1 = values.next_double();
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params[nparams].biga = values.next_double();
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params[nparams].powern_del = values.next_double();
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params[nparams].c1 = values.next_double();
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params[nparams].c2 = values.next_double();
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params[nparams].c3 = values.next_double();
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params[nparams].c4 = values.next_double();
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params[nparams].c5 = values.next_double();
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params[nparams].c0 = values.next_double();
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params[nparams].powermint = int(params[nparams].powerm);
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} catch (TokenizerException & e) {
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error->one(FLERR, e.what());
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}
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MPI_Bcast(&eof,1,MPI_INT,0,world);
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if (eof) break;
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MPI_Bcast(&n,1,MPI_INT,0,world);
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MPI_Bcast(line,n,MPI_CHAR,0,world);
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if ((ptr = strchr(line,'#'))) *ptr = '\0';
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nwords = utils::count_words(line);
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// currently only allow m exponent of 1 or 3
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if (
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params[nparams].powern < 0.0 ||
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params[nparams].beta < 0.0 ||
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params[nparams].lam2 < 0.0 ||
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params[nparams].bigb < 0.0 ||
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params[nparams].bigr < 0.0 ||
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params[nparams].bigd < 0.0 ||
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params[nparams].bigd > params[nparams].bigr ||
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params[nparams].lam1 < 0.0 ||
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params[nparams].biga < 0.0 ||
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params[nparams].powerm - params[nparams].powermint != 0.0 ||
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(params[nparams].powermint != 3 &&
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params[nparams].powermint != 1)
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)
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error->all(FLERR,"Illegal Tersoff parameter");
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nparams++;
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}
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if (nwords != params_per_line)
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error->all(FLERR,"Incorrect format in Tersoff potential file");
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// words = ptrs to all words in line
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nwords = 0;
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words[nwords++] = strtok(line," \t\n\r\f");
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while ((words[nwords++] = strtok(NULL," \t\n\r\f"))) continue;
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// ielement,jelement,kelement = 1st args
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// if all 3 args are in element list, then parse this line
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// else skip to next line
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for (ielement = 0; ielement < nelements; ielement++)
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if (strcmp(words[0],elements[ielement]) == 0) break;
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if (ielement == nelements) continue;
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for (jelement = 0; jelement < nelements; jelement++)
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if (strcmp(words[1],elements[jelement]) == 0) break;
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if (jelement == nelements) continue;
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for (kelement = 0; kelement < nelements; kelement++)
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if (strcmp(words[2],elements[kelement]) == 0) break;
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if (kelement == nelements) continue;
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// load up parameter settings and error check their values
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if (nparams == maxparam) {
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maxparam += DELTA;
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params = (Param *) memory->srealloc(params,maxparam*sizeof(Param),
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"pair:params");
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}
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params[nparams].ielement = ielement;
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params[nparams].jelement = jelement;
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params[nparams].kelement = kelement;
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params[nparams].powerm = atof(words[3]);
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params[nparams].lam3 = atof(words[4]);
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params[nparams].h = atof(words[5]);
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params[nparams].powern = atof(words[6]);
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params[nparams].beta = atof(words[7]);
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params[nparams].lam2 = atof(words[8]);
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params[nparams].bigb = atof(words[9]);
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params[nparams].bigr = atof(words[10]);
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params[nparams].bigd = atof(words[11]);
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params[nparams].lam1 = atof(words[12]);
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params[nparams].biga = atof(words[13]);
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params[nparams].powern_del = atof(words[14]);
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params[nparams].c1 = atof(words[15]);
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params[nparams].c2 = atof(words[16]);
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params[nparams].c3 = atof(words[17]);
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params[nparams].c4 = atof(words[18]);
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params[nparams].c5 = atof(words[19]);
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params[nparams].c0 = atof(words[20]);
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// currently only allow m exponent of 1 or 3
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params[nparams].powermint = int(params[nparams].powerm);
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if (
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params[nparams].powern < 0.0 ||
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params[nparams].beta < 0.0 ||
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params[nparams].lam2 < 0.0 ||
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params[nparams].bigb < 0.0 ||
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params[nparams].bigr < 0.0 ||
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params[nparams].bigd < 0.0 ||
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params[nparams].bigd > params[nparams].bigr ||
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params[nparams].lam1 < 0.0 ||
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params[nparams].biga < 0.0 ||
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params[nparams].powerm - params[nparams].powermint != 0.0 ||
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(params[nparams].powermint != 3 &&
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params[nparams].powermint != 1)
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)
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error->all(FLERR,"Illegal Tersoff parameter");
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nparams++;
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}
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delete [] words;
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MPI_Bcast(&nparams, 1, MPI_INT, 0, world);
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MPI_Bcast(&maxparam, 1, MPI_INT, 0, world);
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if(comm->me != 0) {
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params = (Param *) memory->srealloc(params,maxparam*sizeof(Param), "pair:params");
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}
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MPI_Bcast(params, maxparam*sizeof(Param), MPI_BYTE, 0, world);
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}
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/* ---------------------------------------------------------------------- */
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@ -29,6 +29,8 @@ class PairTersoffMODC : public PairTersoffMOD {
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PairTersoffMODC(class LAMMPS *lmp) : PairTersoffMOD(lmp) {};
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~PairTersoffMODC() {}
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static const int NPARAMS_PER_LINE = 21;
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protected:
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void read_file(char *);
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void repulsive(Param *, double, double &, int, double &);
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@ -8,6 +8,7 @@
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#include "MANYBODY/pair_comb3.h"
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#include "MANYBODY/pair_tersoff.h"
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#include "MANYBODY/pair_tersoff_mod.h"
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#include "MANYBODY/pair_tersoff_mod_c.h"
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#include <mpi.h>
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@ -18,6 +19,7 @@ const int LAMMPS_NS::PairComb::NPARAMS_PER_LINE;
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const int LAMMPS_NS::PairComb3::NPARAMS_PER_LINE;
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const int LAMMPS_NS::PairTersoff::NPARAMS_PER_LINE;
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const int LAMMPS_NS::PairTersoffMOD::NPARAMS_PER_LINE;
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const int LAMMPS_NS::PairTersoffMODC::NPARAMS_PER_LINE;
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class PotenialFileReaderTest : public ::testing::Test {
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protected:
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@ -84,6 +86,15 @@ TEST_F(PotenialFileReaderTest, TersoffMod) {
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ASSERT_EQ(utils::count_words(line), PairTersoffMOD::NPARAMS_PER_LINE);
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}
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TEST_F(PotenialFileReaderTest, TersoffModC) {
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::testing::internal::CaptureStdout();
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PotentialFileReader reader(lmp, "Si.tersoff.modc", "Tersoff");
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::testing::internal::GetCapturedStdout();
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auto line = reader.next_line(PairTersoffMODC::NPARAMS_PER_LINE);
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ASSERT_EQ(utils::count_words(line), PairTersoffMODC::NPARAMS_PER_LINE);
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}
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int main(int argc, char **argv)
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{
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MPI_Init(&argc, &argv);
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