Add PotentialFileReader and use it in PairSW (c302c0bc) · Commits · 郑智淋 / lammps

src/MANYBODY/pair_sw.cpp

+65 −107

Original line number	Diff line number	Diff line
		@@ -29,6 +29,8 @@
		#include "neigh_list.h"
		#include "neigh_request.h"
		#include "utils.h"
		#include "tokenizer.h"
		#include "potential_file_reader.h"

		using namespace LAMMPS_NS;

		@@ -347,92 +349,37 @@ double PairSW::init_one(int i, int j)

		void PairSW::read_file(char *file)
		{
		int params_per_line = 14;
		char *words = new char[params_per_line+1];

		memory->sfree(params);
		params = NULL;
		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 Stillinger-Weber potential file %s",file);
		error->one(FLERR,str);
		}
		}
		PotentialFileReader reader(lmp, file, "Stillinger-Weber");
		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(Param::NPARAMS_PER_LINE)) {
		try {
		ValueTokenizer values(line, " \t\n\r\f");

		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 Stillinger-Weber 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;
		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 entry in file
		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
		@@ -446,29 +393,40 @@ void PairSW::read_file(char *file)
		params[nparams].ielement = ielement;
		params[nparams].jelement = jelement;
		params[nparams].kelement = kelement;
		params[nparams].epsilon = atof(words[3]);
		params[nparams].sigma = atof(words[4]);
		params[nparams].littlea = atof(words[5]);
		params[nparams].lambda = atof(words[6]);
		params[nparams].gamma = atof(words[7]);
		params[nparams].costheta = atof(words[8]);
		params[nparams].biga = atof(words[9]);
		params[nparams].bigb = atof(words[10]);
		params[nparams].powerp = atof(words[11]);
		params[nparams].powerq = atof(words[12]);
		params[nparams].tol = atof(words[13]);
		params[nparams].epsilon = values.next_double();
		params[nparams].sigma = values.next_double();
		params[nparams].littlea = values.next_double();
		params[nparams].lambda = values.next_double();
		params[nparams].gamma = values.next_double();
		params[nparams].costheta = values.next_double();
		params[nparams].biga = values.next_double();
		params[nparams].bigb = values.next_double();
		params[nparams].powerp = values.next_double();
		params[nparams].powerq = values.next_double();
		params[nparams].tol = values.next_double();
		} catch (TokenizerException & e) {
		error->one(FLERR, e.what());
		}

		if (params[nparams].epsilon < 0.0 \|\| params[nparams].sigma < 0.0 \|\|
		params[nparams].littlea < 0.0 \|\| params[nparams].lambda < 0.0 \|\|
		params[nparams].gamma < 0.0 \|\| params[nparams].biga < 0.0 \|\|
		params[nparams].bigb < 0.0 \|\| params[nparams].powerp < 0.0 \|\|
		params[nparams].powerq < 0.0 \|\| params[nparams].tol < 0.0)
		error->all(FLERR,"Illegal Stillinger-Weber parameter");
		error->one(FLERR,"Illegal Stillinger-Weber 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_sw.h

+1 −0

Original line number	Diff line number	Diff line
		@@ -44,6 +44,7 @@ class PairSW : public Pair {
		double sigma_gamma,lambda_epsilon,lambda_epsilon2;
		double c1,c2,c3,c4,c5,c6;
		int ielement,jelement,kelement;
		static const int NPARAMS_PER_LINE = 14;
		};

		protected:

src/potential_file_reader.cpp

0 → 100644

+82 −0

Original line number	Diff line number	Diff line
		/* -- c++ -- ----------------------------------------------------------
		LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
		http://lammps.sandia.gov, Sandia National Laboratories
		Steve Plimpton, sjplimp@sandia.gov

		Copyright (2003) Sandia Corporation. Under the terms of Contract
		DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
		certain rights in this software. This software is distributed under
		the GNU General Public License.

		See the README file in the top-level LAMMPS directory.
		------------------------------------------------------------------------- */

		/* ----------------------------------------------------------------------
		Contributing authors: Richard Berger (Temple U)
		------------------------------------------------------------------------- */

		#include "lammps.h"
		#include "force.h"
		#include "error.h"
		#include "comm.h"
		#include "potential_file_reader.h"
		#include "utils.h"

		#include <cstring>

		using namespace LAMMPS_NS;

		PotentialFileReader::PotentialFileReader(LAMMPS *lmp,
		const std::string &filename,
		const std::string &potential_name) : Pointers(lmp) {
		if (comm->me != 0) {
		error->one(FLERR, "PotentialFileReader should only be called by proc 0!");
		}

		fp = force->open_potential(filename.c_str());

		if (fp == NULL) {
		char str[128];
		snprintf(str, 128, "cannot open %s potential file %s", potential_name.c_str(), filename.c_str());
		error->one(FLERR, str);
		}
		}

		PotentialFileReader::~PotentialFileReader() {
		fclose(fp);
		}

		char *PotentialFileReader::next_line(int nparams) {
		// concatenate lines until have nparams words
		int n = 0;
		int nwords = 0;

		do {
		char *ptr = fgets(&line[n], MAXLINE - n, fp);

		if (ptr == nullptr) {
		// EOF
		if (nwords > 0 && nwords < nparams)
		{
		char str[128];
		snprintf(str, 128, "Incorrect format in %s potential file", potential_name.c_str());
		error->all(FLERR, str);
		}

		return nullptr;
		}

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

		nwords = utils::count_words(line);

		// skip line if blank
		if (nwords == 0)
		continue;

		n = strlen(line) + 1;
		} while (nwords < nparams);

		return line;
		}

src/potential_file_reader.h

0 → 100644

+42 −0

Original line number	Diff line number	Diff line
		/* -- c++ -- ----------------------------------------------------------
		LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
		http://lammps.sandia.gov, Sandia National Laboratories
		Steve Plimpton, sjplimp@sandia.gov

		Copyright (2003) Sandia Corporation. Under the terms of Contract
		DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
		certain rights in this software. This software is distributed under
		the GNU General Public License.

		See the README file in the top-level LAMMPS directory.
		------------------------------------------------------------------------- */

		/* ----------------------------------------------------------------------
		Contributing authors: Richard Berger (Temple U)
		------------------------------------------------------------------------- */

		#ifndef LMP_POTENTIAL_FILE_READER_H
		#define LMP_POTENTIAL_FILE_READER_H

		#include <string>

		#include "pointers.h"

		namespace LAMMPS_NS
		{
		class PotentialFileReader : protected Pointers {
		std::string potential_name;
		static const int MAXLINE = 1024;
		char line[MAXLINE];
		FILE *fp;

		public:
		PotentialFileReader(class LAMMPS *lmp, const std::string &filename, const std::string &potential_name);
		~PotentialFileReader();

		char *next_line(int nparams);
		};

		} // namespace LAMMPS_NS

		#endif

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