Use PotentialFileReader in PairComb (13942a4d) · Commits · 郑智淋 / lammps

src/MANYBODY/pair_comb.cpp

+130 −173

Original line number	Diff line number	Diff line
		@@ -35,11 +35,12 @@
		#include "memory.h"
		#include "error.h"
		#include "utils.h"
		#include "tokenizer.h"
		#include "potential_file_reader.h"

		using namespace LAMMPS_NS;
		using namespace MathConst;

		#define MAXLINE 1024
		#define DELTA 4
		#define PGDELTA 1
		#define MAXNEIGH 24
		@@ -581,92 +582,37 @@ double PairComb::init_one(int i, int j)

		void PairComb::read_file(char *file)
		{
		int params_per_line = 49;
		char *words = new char[params_per_line+1];

		memory->sfree(params);
		params = NULL;
		nparams = 0;
		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 COMB 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);
		}

		if (nwords != params_per_line)
		error->all(FLERR,"Incorrect format in COMB potential file");
		PotentialFileReader reader(lmp, file, "COMB");
		char * line;

		// words = ptrs to all words in line
		while(line = reader.next_line(Param::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 iword = values.next_string();
		std::string jword = values.next_string();
		std::string kword = 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
		int ielement, jelement, kelement;

		for (ielement = 0; ielement < nelements; ielement++)
		if (strcmp(words[0],elements[ielement]) == 0) break;
		if (iword == elements[ielement]) break;
		if (ielement == nelements) continue;
		for (jelement = 0; jelement < nelements; jelement++)
		if (strcmp(words[1],elements[jelement]) == 0) break;
		if (jword == elements[jelement]) break;
		if (jelement == nelements) continue;
		for (kelement = 0; kelement < nelements; kelement++)
		if (strcmp(words[2],elements[kelement]) == 0) break;
		if (kword == elements[kelement]) break;
		if (kelement == nelements) continue;

		// load up parameter settings and error check their values
		@@ -680,52 +626,55 @@ void PairComb::read_file(char *file)
		params[nparams].ielement = ielement;
		params[nparams].jelement = jelement;
		params[nparams].kelement = kelement;
		params[nparams].powerm = atof(words[3]);
		params[nparams].c = atof(words[4]);
		params[nparams].d = atof(words[5]);
		params[nparams].h = atof(words[6]);
		params[nparams].powern = atof(words[7]);
		params[nparams].beta = atof(words[8]);
		params[nparams].lam21 = atof(words[9]);
		params[nparams].lam22 = atof(words[10]);
		params[nparams].bigb1 = atof(words[11]);
		params[nparams].bigb2 = atof(words[12]);
		params[nparams].bigr = atof(words[13]);
		params[nparams].bigd = atof(words[14]);
		params[nparams].lam11 = atof(words[15]);
		params[nparams].lam12 = atof(words[16]);
		params[nparams].biga1 = atof(words[17]);
		params[nparams].biga2 = atof(words[18]);
		params[nparams].plp1 = atof(words[19]);
		params[nparams].plp3 = atof(words[20]);
		params[nparams].plp6 = atof(words[21]);
		params[nparams].a123 = atof(words[22]);
		params[nparams].aconf= atof(words[23]);
		params[nparams].addrep = atof(words[24]);
		params[nparams].romigb = atof(words[25]);
		params[nparams].romigc = atof(words[26]);
		params[nparams].romigd = atof(words[27]);
		params[nparams].romiga = atof(words[28]);
		params[nparams].QL1 = atof(words[29]);
		params[nparams].QU1 = atof(words[30]);
		params[nparams].DL1 = atof(words[31]);
		params[nparams].DU1 = atof(words[32]);
		params[nparams].QL2 = atof(words[33]);
		params[nparams].QU2 = atof(words[34]);
		params[nparams].DL2 = atof(words[35]);
		params[nparams].DU2 = atof(words[36]);
		params[nparams].chi = atof(words[37]);
		params[nparams].dj = atof(words[38]);
		params[nparams].dk = atof(words[39]);
		params[nparams].dl = atof(words[40]);
		params[nparams].dm = atof(words[41]);
		params[nparams].esm1 = atof(words[42]);
		params[nparams].cmn1 = atof(words[43]);
		params[nparams].cml1 = atof(words[44]);
		params[nparams].cmn2 = atof(words[45]);
		params[nparams].cml2 = atof(words[46]);
		params[nparams].coulcut = atof(words[47]);
		params[nparams].hfocor = atof(words[48]);
		params[nparams].powerm = 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].lam21 = values.next_double();
		params[nparams].lam22 = values.next_double();
		params[nparams].bigb1 = values.next_double();
		params[nparams].bigb2 = values.next_double();
		params[nparams].bigr = values.next_double();
		params[nparams].bigd = values.next_double();
		params[nparams].lam11 = values.next_double();
		params[nparams].lam12 = values.next_double();
		params[nparams].biga1 = values.next_double();
		params[nparams].biga2 = values.next_double();
		params[nparams].plp1 = values.next_double();
		params[nparams].plp3 = values.next_double();
		params[nparams].plp6 = values.next_double();
		params[nparams].a123 = values.next_double();
		params[nparams].aconf = values.next_double();
		params[nparams].addrep = values.next_double();
		params[nparams].romigb = values.next_double();
		params[nparams].romigc = values.next_double();
		params[nparams].romigd = values.next_double();
		params[nparams].romiga = values.next_double();
		params[nparams].QL1 = values.next_double();
		params[nparams].QU1 = values.next_double();
		params[nparams].DL1 = values.next_double();
		params[nparams].DU1 = values.next_double();
		params[nparams].QL2 = values.next_double();
		params[nparams].QU2 = values.next_double();
		params[nparams].DL2 = values.next_double();
		params[nparams].DU2 = values.next_double();
		params[nparams].chi = values.next_double();
		params[nparams].dj = values.next_double();
		params[nparams].dk = values.next_double();
		params[nparams].dl = values.next_double();
		params[nparams].dm = values.next_double();
		params[nparams].esm1 = values.next_double();
		params[nparams].cmn1 = values.next_double();
		params[nparams].cml1 = values.next_double();
		params[nparams].cmn2 = values.next_double();
		params[nparams].cml2 = values.next_double();
		params[nparams].coulcut = values.next_double();
		params[nparams].hfocor = values.next_double();
		} catch (TokenizerException & e) {
		error->one(FLERR, e.what());
		}

		params[nparams].powermint = int(params[nparams].powerm);

		@@ -755,18 +704,26 @@ void PairComb::read_file(char *file)
		// params[nparams].dj < 0.0 \|\| params[nparams].dk < 0.0 \|\|
		// params[nparams].dl < 0.0 \|\| params[nparams].dm < 0.0 \|\|
		params[nparams].esm1 < 0.0)
		error->all(FLERR,"Illegal COMB parameter");
		error->one(FLERR,"Illegal COMB parameter");

		if (params[nparams].lam11 < params[nparams].lam21 \|\|
		params[nparams].lam12 < params[nparams].lam22 \|\|
		params[nparams].biga1< params[nparams].bigb1 \|\|
		params[nparams].biga2< params[nparams].bigb2)
		error->all(FLERR,"Illegal COMB parameter");
		error->one(FLERR,"Illegal COMB 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,maxparamsizeof(Param), "pair:params");
		}

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

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

src/MANYBODY/pair_comb.h

+1 −0

Original line number	Diff line number	Diff line
		@@ -57,6 +57,7 @@ class PairComb : public Pair {
		double coulcut, lcut, lcutsq, hfocor;
		int ielement,jelement,kelement;
		int powermint;
		static const int NPARAMS_PER_LINE = 49;
		};

		double cutmax; // max cutoff for all elements

src/MANYBODY/pair_sw.cpp

+0 −1

Original line number	Diff line number	Diff line
		@@ -34,7 +34,6 @@

		using namespace LAMMPS_NS;

		#define MAXLINE 1024
		#define DELTA 4

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

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