Update pair tersoff mod (a4db35e1) · Commits · 郑智淋 / lammps

src/MANYBODY/pair_tersoff_mod.cpp

+84 −127

Original line number	Diff line number	Diff line
		@@ -29,12 +29,13 @@
		#include "memory.h"
		#include "error.h"
		#include "utils.h"
		#include "tokenizer.h"
		#include "potential_file_reader.h"

		using namespace LAMMPS_NS;
		using namespace MathConst;
		using namespace MathSpecial;

		#define MAXLINE 1024
		#define DELTA 4

		/* ---------------------------------------------------------------------- */
		@@ -45,93 +46,40 @@ PairTersoffMOD::PairTersoffMOD(LAMMPS *lmp) : PairTersoff(lmp) {}

		void PairTersoffMOD::read_file(char *file)
		{
		int params_per_line = NPARAMS_PER_LINE;
		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);
		}
		}

		// read each line out of file, skipping blank lines or leading '#'
		// store line of 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);
		}
		PotentialFileReader reader(lmp, file, "Tersoff");
		char * line;

		if (nwords != params_per_line)
		error->all(FLERR,"Incorrect format in Tersoff potential file");
		while(line = reader.next_line(NPARAMS_PER_LINE)) {
		try {
		ValueTokenizer values(line, " \t\n\r\f");

		// 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;
		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 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

		if (nparams == maxparam) {
		@@ -143,28 +91,29 @@ void PairTersoffMOD::read_file(char *file)
		params[nparams].ielement = ielement;
		params[nparams].jelement = jelement;
		params[nparams].kelement = kelement;
		params[nparams].powerm = atof(words[3]);
		params[nparams].lam3 = atof(words[4]);
		params[nparams].h = atof(words[5]);
		params[nparams].powern = atof(words[6]);
		params[nparams].beta = atof(words[7]);
		params[nparams].lam2 = atof(words[8]);
		params[nparams].bigb = atof(words[9]);
		params[nparams].bigr = atof(words[10]);
		params[nparams].bigd = atof(words[11]);
		params[nparams].lam1 = atof(words[12]);
		params[nparams].biga = atof(words[13]);
		params[nparams].powern_del = atof(words[14]);
		params[nparams].c1 = atof(words[15]);
		params[nparams].c2 = atof(words[16]);
		params[nparams].c3 = atof(words[17]);
		params[nparams].c4 = atof(words[18]);
		params[nparams].c5 = atof(words[19]);

		// currently only allow m exponent of 1 or 3

		params[nparams].powerm = values.next_double();
		params[nparams].lam3 = 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].powern_del = values.next_double();
		params[nparams].c1 = values.next_double();
		params[nparams].c2 = values.next_double();
		params[nparams].c3 = values.next_double();
		params[nparams].c4 = values.next_double();
		params[nparams].c5 = values.next_double();
		params[nparams].powermint = int(params[nparams].powerm);
		} catch (TokenizerException & e) {
		error->one(FLERR, e.what());
		}

		// currently only allow m exponent of 1 or 3
		if (params[nparams].powern < 0.0 \|\|
		params[nparams].beta < 0.0 \|\|
		params[nparams].lam2 < 0.0 \|\|
		@@ -182,8 +131,16 @@ void PairTersoffMOD::read_file(char *file)

		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,maxparamsizeof(Param), "pair:params");
		}

		delete [] words;
		MPI_Bcast(params, maxparam*sizeof(Param), MPI_BYTE, 0, world);
		}

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

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