Merge pull request #1999 from ellio167/kim_match_pairs (6bac0832) · Commits · 郑智淋 / lammps

src/KIM/kim_interactions.cpp

+93 −2

Original line number	Diff line number	Diff line
		@@ -15,6 +15,7 @@
		Contributing authors: Axel Kohlmeyer (Temple U),
		Ryan S. Elliott (UMN)
		Ellad B. Tadmor (UMN)
		Ronald Miller (Carleton U)
		------------------------------------------------------------------------- */

		/* ----------------------------------------------------------------------
		@@ -57,8 +58,10 @@

		#include "kim_interactions.h"
		#include <cstring>
		#include <cstdio>
		#include <string>
		#include <sstream>
		#include <vector>
		#include "error.h"
		#include "atom.h"
		#include "comm.h"
		@@ -80,6 +83,8 @@ extern "C" {

		using namespace LAMMPS_NS;

		#define MAXLINE 1024

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

		void KimInteractions::command(int narg, char **arg)
		@@ -223,10 +228,29 @@ void KimInteractions::do_setup(int narg, char **arg)
		for (int j=0; j < sim_lines; ++j) {
		KIM_SimulatorModel_GetSimulatorFieldLine(
		simulatorModel,sim_model_idx,j,&sim_value);
		char strbuf[MAXLINE];
		char * strword;
		strcpy(strbuf,sim_value);
		strword = strtok(strbuf," \t");
		if (0==strcmp(strword,"KIM_MATCH_PAIRS")) {
		// Notes regarding the KIM_MATCH_PAIRS command
		// * This is an INTERNAL command.
		// * It is intended for use only by KIM Simulator Models.
		// * It is not possible to use this command outside of the context
		// of the kim_interactions command and KIM Simulator Models.
		// * The command performs a transformation from symbolic
		// string-based atom types to lammps numeric atom types for
		// the pair_coeff settings.
		// * The command is not documented fully as it is expected to be
		// temporary. Eventually it should be replaced by a more
		// comprehensive symbolic types support in lammps.
		KIM_MATCH_PAIRS(sim_value);
		} else {
		input->one(sim_value);
		}
		}
		}
		}

		if (sim_model_idx < 0)
		error->all(FLERR,"KIM Simulator Model has no Model definition");
		@@ -263,6 +287,73 @@ void KimInteractions::do_setup(int narg, char **arg)

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

		void KimInteractions::KIM_MATCH_PAIRS(char const *const input_line) const
		{
		char strbuf[MAXLINE];
		strcpy(strbuf,input_line);
		char cmd, filename;
		cmd = strtok(strbuf," \t");
		filename = strtok(NULL," \t");

		FILE *fp;
		fp = fopen(filename,"r");
		if (fp == NULL) {
		error->one(FLERR,"Parameter file not found");
		}

		std::vector<char *> species;
		for (int i = 0; i < atom->ntypes; ++i)
		{
		char *str;
		str = strtok(NULL," \t");
		if (str == NULL)
		error->one(FLERR,"Incorrect args for KIM_MATCH_PAIRS command");
		species.push_back(str);
		}

		char line[MAXLINE],*ptr;
		int n, 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);

		char species1, species2, *the_rest;
		ptr = line;
		species1 = strtok(ptr," \t");
		species2 = strtok(NULL," \t");
		the_rest = strtok(NULL,"\n");

		for (int type_a = 0; type_a < atom->ntypes; ++type_a) {
		for (int type_b = type_a; type_b < atom->ntypes; ++type_b) {
		if(((strcmp(species[type_a],species1) == 0) &&
		(strcmp(species[type_b],species2) == 0))
		\|\|
		((strcmp(species[type_b],species1) == 0) &&
		(strcmp(species[type_a],species2) == 0))
		) {
		char pair_command[MAXLINE];
		sprintf(pair_command,"pair_coeff %i %i %s",type_a+1,type_b+1,
		the_rest);
		input->one(pair_command);
		}
		}
		}
		}
		fclose(fp);
		}

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

		int KimInteractions::species_to_atomic_no(std::string const species) const
		{
		if (species == "H") return 1;

src/KIM/kim_interactions.h

+2 −0

Original line number	Diff line number	Diff line
		@@ -15,6 +15,7 @@
		Contributing authors: Axel Kohlmeyer (Temple U),
		Ryan S. Elliott (UMN)
		Ellad B. Tadmor (UMN)
		Ronald Miller (Carleton U)
		------------------------------------------------------------------------- */

		/* ----------------------------------------------------------------------
		@@ -76,6 +77,7 @@ class KimInteractions : protected Pointers {
		private:
		void do_setup(int, char **);
		int species_to_atomic_no(std::string const species) const;
		void KIM_MATCH_PAIRS(char const *const input_line) const;
		void kim_interactions_log_delimiter(std::string const begin_end) const;
		};

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