Update Pair BOP (d9345a16) · Commits · 郑智淋 / lammps

src/MANYBODY/pair_bop.cpp

+325 −397

Original line number	Diff line number	Diff line
		@@ -46,10 +46,11 @@
		#include "memory.h"
		#include "error.h"
		#include "utils.h"
		#include "tokenizer.h"
		#include "potential_file_reader.h"

		using namespace LAMMPS_NS;

		#define MAXLINE 1024
		#define EPSILON 1.0e-6

		/* ---------------------------------------------------------------------- */
		@@ -294,7 +295,6 @@ void PairBOP::compute(int eflag, int vflag)
		int nlocal = atom->nlocal;
		int nall = nlocal + atom->nghost;
		int cnt1;
		MPI_Comm_rank(world,&me);

		inum = list->inum;
		ilist = list->ilist;
		@@ -616,7 +616,6 @@ void PairBOP::coeff(int narg, char **arg)
		{
		int i,j;
		int n = atom->ntypes;
		MPI_Comm_rank(world,&me);

		delete[] map;
		map = new int[n+1];
		@@ -645,7 +644,7 @@ void PairBOP::coeff(int narg, char **arg)
		read_table(arg[2]);

		// match element names to BOP word types
		if (me == 0) {
		if (comm->me == 0) {
		for (i = 3; i < narg; i++) {
		if (strcmp(arg[i],"NULL") == 0) {
		map[i-2] = -1;
		@@ -659,7 +658,7 @@ void PairBOP::coeff(int narg, char **arg)
		}

		MPI_Bcast(&map[1],atom->ntypes,MPI_INT,0,world);
		if (me == 0) {
		if (comm->me == 0) {
		if (elements) {
		for (i = 0; i < bop_types; i++) delete [] elements[i];
		delete [] elements;
		@@ -1137,7 +1136,6 @@ double PairBOP::sigmaBo(int itmp, int jtmp)
		nlocal = atom->nlocal;
		ilist = list->ilist;
		firstneigh = list->firstneigh;
		MPI_Comm_rank(world,&me);

		if(nb_sg==0) {
		nb_sg=(maxneigh)*(maxneigh/2);
		@@ -4873,101 +4871,11 @@ double PairBOP::PiBo(int itmp, int jtmp)
		}

		/* ----------------------------------------------------------------------
		read BOP potential file
		allocate BOP tables
		------------------------------------------------------------------------- */

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

		void _noopt PairBOP::read_table(char *filename)
		void PairBOP::allocate_tables()
		{
		int i,j,k,n,m;
		int buf1,pass;
		int nws,ws;
		double buf2;
		char s[MAXLINE],buf[2];

		MPI_Comm_rank(world,&me);
		if (me == 0) {
		FILE *fp = force->open_potential(filename);
		if (fp == NULL) {
		char str[128];
		snprintf(str,128,"Cannot open BOP potential file %s",filename);
		error->one(FLERR,str);
		}
		utils::sfgets(FLERR,s,MAXLINE,fp,filename,error); // skip first comment line
		utils::sfgets(FLERR,s,MAXLINE,fp,filename,error);
		sscanf(s,"%d",&bop_types);
		elements = new char*[bop_types];
		for(i=0;i<bop_types;i++) elements[i]=NULL;
		for(i=0;i<bop_types;i++) {
		utils::sfgets(FLERR,s,MAXLINE,fp,filename,error);
		nws=0;
		ws=1;
		for(j=0;j<(int)strlen(s);j++) {
		if(ws==1) {
		if(isspace(s[j])) {
		ws=1;
		} else {
		ws=0;
		}
		} else {
		if(isspace(s[j])) {
		ws=1;
		nws++;
		} else {
		ws=0;
		}
		}
		}
		if(nws!=3){
		error->all(FLERR,"Incorrect table format check for element types");
		}
		sscanf(s,"%d %lf %s",&buf1,&buf2,buf);
		n= strlen(buf)+1;
		elements[i] = new char[n];
		strcpy(elements[i],buf);
		}
		nws=0;
		ws=1;
		utils::sfgets(FLERR,s,MAXLINE,fp,filename,error);
		for(j=0;j<(int)strlen(s);j++) {
		if(ws==1) {
		if(isspace(s[j])) {
		ws=1;
		} else {
		ws=0;
		}
		} else {
		if(isspace(s[j])) {
		ws=1;
		nws++;
		} else {
		ws=0;
		}
		}
		}
		if (nws==3) {
		sscanf(s,"%d %d %d",&nr,&ntheta,&nBOt);
		npower=2;
		if(ntheta<=10) npower=ntheta;
		} else if (nws==2) {
		sscanf(s,"%d %d",&nr,&nBOt);
		ntheta=0;
		npower=3;
		} else {
		error->one(FLERR,"Unsupported BOP potential file format");
		}
		fclose(fp);
		npairs=bop_types*(bop_types+1)/2;
		}

		MPI_Bcast(&nr,1,MPI_INT,0,world);
		MPI_Bcast(&nBOt,1,MPI_INT,0,world);
		MPI_Bcast(&ntheta,1,MPI_INT,0,world);
		MPI_Bcast(&bop_types,1,MPI_INT,0,world);
		MPI_Bcast(&npairs,1,MPI_INT,0,world);
		MPI_Bcast(&npower,1,MPI_INT,0,world);

		memory->destroy(pi_a);
		memory->destroy(pro_delta);
		memory->destroy(pi_delta);
		@@ -5011,173 +4919,164 @@ void _noopt PairBOP::read_table(char *filename)
		memory->create(gfunc5,bop_types,bop_types,bop_types,ntheta,"BOP:gfunc5");
		memory->create(gfunc6,bop_types,bop_types,bop_types,ntheta,"BOP:gfunc6");
		memory->create(gpara,bop_types,bop_types,bop_types,npower+1,"BOP:gpara");
		}

		/* ----------------------------------------------------------------------
		read BOP potential file
		------------------------------------------------------------------------- */

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

		void _noopt PairBOP::read_table(char *filename)
		{
		if (comm->me == 0) {
		try {
		PotentialFileReader reader(lmp, filename, "BOP");
		char * line = nullptr;

		bop_types = reader.next_int();
		elements = new char*[bop_types];
		for(int i=0; i < bop_types; i++) {
		line = reader.next_line(3);
		ValueTokenizer values(line);
		values.next_int();
		values.next_double();
		std::string name = values.next_string();

		elements[i] = new char[name.length()+1];
		strcpy(elements[i], name.c_str());
		}

		line = reader.next_line();
		ValueTokenizer values(line);
		int format = values.count();

		switch(format) {
		case 3:
		nr = values.next_int();
		ntheta = values.next_int();
		nBOt = values.next_int();
		if(ntheta <= 10)
		npower = ntheta;
		else
		npower = 2;
		break;

		case 2:
		nr = values.next_int();
		nBOt = values.next_int();
		ntheta = 0;
		npower = 3;
		break;

		default:
		error->one(FLERR,"Unsupported BOP potential file format");
		}

		npairs = bop_types*(bop_types+1)/2;

		allocate_tables();
		allocate();
		if (me == 0) {
		FILE *fp = force->open_potential(filename);
		if (fp == NULL) {
		char str[128];
		snprintf(str,128,"Cannot open BOP potential file %s",filename);
		error->one(FLERR,str);
		}
		utils::sfgets(FLERR,s,MAXLINE,fp,filename,error); // skip first comment line
		for(i=0;i<bop_types+2;i++) {
		utils::sfgets(FLERR,s,MAXLINE,fp,filename,error);
		}
		utils::sfgets(FLERR,s,MAXLINE,fp,filename,error);
		sscanf(s,"%lf%lf%lf%lf%lf%lf%lf",&small1,&small2,&small3g
		,&small4,&small5,&small6,&small7);
		for(i=0;i<bop_types;i++) {
		utils::sfgets(FLERR,s,MAXLINE,fp,filename,error);
		sscanf(s,"%lf",&pi_p[i]);
		}
		cutmax=0;
		for(i=0;i<npairs;i++) {
		utils::sfgets(FLERR,s,MAXLINE,fp,filename,error);
		sscanf(s,"%lf",&rcut[i]);

		line = reader.next_line(7);
		values = ValueTokenizer(line);

		small1 = values.next_double();
		small2 = values.next_double();
		small3g = values.next_double();
		small4 = values.next_double();
		small5 = values.next_double();
		small6 = values.next_double();
		small7 = values.next_double();

		for(int i = 0; i < bop_types; i++) {
		pi_p[i] = reader.next_double();
		}

		cutmax = 0.0;

		for(int i = 0; i < npairs; i++) {
		rcut[i] = reader.next_double();
		if (rcut[i] > cutmax)
		cutmax = rcut[i];
		utils::sfgets(FLERR,s,MAXLINE,fp,filename,error);
		sscanf(s,"%lf%lf%lf%lf",&sigma_c[i],&sigma_a[i],&pi_c[i],&pi_a[i]);
		utils::sfgets(FLERR,s,MAXLINE,fp,filename,error);
		sscanf(s,"%lf%lf",&sigma_delta[i],&pi_delta[i]);
		utils::sfgets(FLERR,s,MAXLINE,fp,filename,error);
		sscanf(s,"%lf%lf%lf",&sigma_f[i],&sigma_k[i],&small3[i]);
		}
		if(nws==3) {
		for(i=0;i<bop_types;i++)
		for(j=0;j<bop_types;j++)
		for(k=j;k<bop_types;k++) {

		line = reader.next_line(4);
		values = ValueTokenizer(line);
		sigma_c[i] = values.next_double();
		sigma_a[i] = values.next_double();
		pi_c[i] = values.next_double();
		pi_a[i] = values.next_double();

		line = reader.next_line(2);
		values = ValueTokenizer(line);
		sigma_delta[i] = values.next_double();
		pi_delta[i] = values.next_double();

		line = reader.next_line(3);
		values = ValueTokenizer(line);
		sigma_f[i] = values.next_double();
		sigma_k[i] = values.next_double();
		small3[i] = values.next_double();
		}

		if(format == 3) {
		for(int i = 0; i < bop_types; i++)
		for(int j = 0; j < bop_types; j++)
		for(int k = j; k < bop_types; k++) {
		if(npower <= 2) {
		for(m=0;m<ntheta;m++) {
		utils::sfgets(FLERR,s,MAXLINE,fp,filename,error);
		sscanf(s,"%lf%lf%lf%lf%lf",&gfunc[j][i][k][n],&gfunc[j][i][k][n+1]
		,&gfunc[j][i][k][n+2],&gfunc[j][i][k][n+3],&gfunc[j][i][k][n+4]);
		n+=4;
		}
		reader.next_dvector(ntheta, &gfunc[j][i][k][0]);
		} else {
		if(npower==3) {
		utils::sfgets(FLERR,s,MAXLINE,fp,filename,error);
		sscanf(s,"%lf%lf%lf%lf",&gpara[j][i][k][0],&gpara[j][i][k][1],&gpara[j][i][k][2],&gpara[j][i][k][3]);
		}
		else if(npower==4) {
		utils::sfgets(FLERR,s,MAXLINE,fp,filename,error);
		sscanf(s,"%lf%lf%lf%lf%lf",&gpara[j][i][k][0],&gpara[j][i][k][1],&gpara[j][i][k][2],&gpara[j][i][k][3],&gpara[j][i][k][4]);
		}
		else if(npower==5) {
		utils::sfgets(FLERR,s,MAXLINE,fp,filename,error);
		sscanf(s,"%lf%lf%lf%lf%lf",&gpara[j][i][k][0],&gpara[j][i][k][1],&gpara[j][i][k][2],&gpara[j][i][k][3],&gpara[j][i][k][4]);
		utils::sfgets(FLERR,s,MAXLINE,fp,filename,error);
		sscanf(s,"%lf",&gpara[j][i][k][5]);
		}
		else if(npower==6) {
		utils::sfgets(FLERR,s,MAXLINE,fp,filename,error);
		sscanf(s,"%lf%lf%lf%lf%lf",&gpara[j][i][k][0],&gpara[j][i][k][1],&gpara[j][i][k][2],&gpara[j][i][k][3],&gpara[j][i][k][4]);
		utils::sfgets(FLERR,s,MAXLINE,fp,filename,error);
		sscanf(s,"%lf%lf",&gpara[j][i][k][5],&gpara[j][i][k][6]);
		}
		else if(npower==7) {
		utils::sfgets(FLERR,s,MAXLINE,fp,filename,error);
		sscanf(s,"%lf%lf%lf%lf%lf",&gpara[j][i][k][0],&gpara[j][i][k][1],&gpara[j][i][k][2],&gpara[j][i][k][3],&gpara[j][i][k][4]);
		utils::sfgets(FLERR,s,MAXLINE,fp,filename,error);
		sscanf(s,"%lf%lf%lf",&gpara[j][i][k][5],&gpara[j][i][k][6],&gpara[j][i][k][7]);
		}
		else if(npower==8) {
		utils::sfgets(FLERR,s,MAXLINE,fp,filename,error);
		sscanf(s,"%lf%lf%lf%lf%lf",&gpara[j][i][k][0],&gpara[j][i][k][1],&gpara[j][i][k][2],&gpara[j][i][k][3],&gpara[j][i][k][4]);
		utils::sfgets(FLERR,s,MAXLINE,fp,filename,error);
		sscanf(s,"%lf%lf%lf%lf",&gpara[j][i][k][5],&gpara[j][i][k][6],&gpara[j][i][k][7],&gpara[j][i][k][8]);
		}
		else if(npower==9) {
		utils::sfgets(FLERR,s,MAXLINE,fp,filename,error);
		sscanf(s,"%lf%lf%lf%lf%lf",&gpara[j][i][k][0],&gpara[j][i][k][1],&gpara[j][i][k][2],&gpara[j][i][k][3],&gpara[j][i][k][4]);
		utils::sfgets(FLERR,s,MAXLINE,fp,filename,error);
		sscanf(s,"%lf%lf%lf%lf%lf",&gpara[j][i][k][5],&gpara[j][i][k][6],&gpara[j][i][k][7],&gpara[j][i][k][8],&gpara[j][i][k][9]);
		}
		else if(npower==10) {
		utils::sfgets(FLERR,s,MAXLINE,fp,filename,error);
		sscanf(s,"%lf%lf%lf%lf%lf",&gpara[j][i][k][0],&gpara[j][i][k][1],&gpara[j][i][k][2],&gpara[j][i][k][3],&gpara[j][i][k][4]);
		utils::sfgets(FLERR,s,MAXLINE,fp,filename,error);
		sscanf(s,"%lf%lf%lf%lf%lf",&gpara[j][i][k][5],&gpara[j][i][k][6],&gpara[j][i][k][7],&gpara[j][i][k][8],&gpara[j][i][k][9]);
		utils::sfgets(FLERR,s,MAXLINE,fp,filename,error);
		sscanf(s,"%lf",&gpara[j][i][k][10]);
		}
		reader.next_dvector(npower+1, &gpara[j][i][k][0]);
		}
		}
		} else {
		for(i=0;i<bop_types;i++)
		for(j=0;j<bop_types;j++)
		for(k=0;k<bop_types;k++) {
		utils::sfgets(FLERR,s,MAXLINE,fp,filename,error);
		sscanf(s,"%lf%lf%lf",&gpara[i][j][k][0],&gpara[i][j][k][1],&gpara[i][j][k][2]);
		for(int i = 0; i < bop_types; i++)
		for(int j = 0; j < bop_types; j++)
		for(int k = 0; k < bop_types; k++) {
		reader.next_dvector(3, &gpara[i][j][k][0]);
		gpara[j][i][k][3] = 0;
		}
		}
		for(i=0;i<npairs;i++) {
		for(j=0;j<nr;j++) {
		utils::sfgets(FLERR,s,MAXLINE,fp,filename,error);
		sscanf(s,"%lf%lf%lf%lf%lf",&pRepul[i][j],&pRepul[i][j+1]
		,&pRepul[i][j+2],&pRepul[i][j+3],&pRepul[i][j+4]);
		j+=4;
		}
		}
		for(i=0;i<npairs;i++) {
		for(j=0;j<nr;j++) {
		utils::sfgets(FLERR,s,MAXLINE,fp,filename,error);
		sscanf(s,"%lf%lf%lf%lf%lf",&pBetaS[i][j],&pBetaS[i][j+1]
		,&pBetaS[i][j+2],&pBetaS[i][j+3],&pBetaS[i][j+4]);
		j+=4;
		}
		}
		for(i=0;i<npairs;i++) {
		for(j=0;j<nr;j++) {
		utils::sfgets(FLERR,s,MAXLINE,fp,filename,error);
		sscanf(s,"%lf%lf%lf%lf%lf",&pBetaP[i][j],&pBetaP[i][j+1]
		,&pBetaP[i][j+2],&pBetaP[i][j+3],&pBetaP[i][j+4]);
		j+=4;

		for(int i = 0; i < npairs; i++) {
		reader.next_dvector(nr, &pRepul[i][0]);
		}

		for(int i = 0; i < npairs; i++) {
		reader.next_dvector(nr, &pBetaS[i][0]);
		}
		for(i=0;i<npairs;i++) {
		for(j=0;j<nBOt;j++) {
		utils::sfgets(FLERR,s,MAXLINE,fp,filename,error);
		sscanf(s,"%lf%lf%lf%lf%lf",&FsigBO[i][j],&FsigBO[i][j+1]
		,&FsigBO[i][j+2],&FsigBO[i][j+3],&FsigBO[i][j+4]);
		j+=4;

		for(int i = 0; i < npairs; i++) {
		reader.next_dvector(nr, &pBetaP[i][0]);
		}

		for(int i = 0; i < npairs; i++) {
		reader.next_dvector(nBOt, &FsigBO[i][0]);
		}
		for(i=0;i<bop_types;i++) {
		utils::sfgets(FLERR,s,MAXLINE,fp,filename,error);
		sscanf(s,"%lf",&pro_delta[i]);

		for(int i = 0; i < bop_types; i++) {
		pro_delta[i] = reader.next_double();
		}
		for(i=0;i<bop_types;i++) {
		utils::sfgets(FLERR,s,MAXLINE,fp,filename,error);
		sscanf(s,"%lf",&pro[i]);

		for(int i = 0; i < bop_types; i++) {
		pro[i] = reader.next_double();
		}
		for(i=0;i<npairs;i++) {

		for(int i=0;i<npairs;i++) {
		rcut3[i]=0.0;
		}
		pass=0;
		i=0;
		if(nws==3) {
		for(i=0;i<npairs;i++) {
		utils::sfgets(FLERR,s,MAXLINE,fp,filename,error);
		sscanf(s,"%lf",&rcut3[i]);
		}
		for(i=0;i<npairs;i++) {
		for(j=0;j<nr;j++) {
		pass=0;
		while(fgets(s,MAXLINE,fp)!=NULL&&pass==0) {
		sscanf(s,"%lf%lf%lf%lf%lf",&pLong[i][j],&pLong[i][j+1]
		,&pLong[i][j+2],&pLong[i][j+3],&pLong[i][j+4]);
		j+=4;
		pass=1;
		}

		if(format == 3) {
		for(int i = 0; i < npairs; i++) {
		rcut3[i] = reader.next_double();
		}
		for(int i = 0; i < npairs; i++) {
		reader.next_dvector(nr, &pLong[i][0]);
		}
		}

		rcutall=0.0;
		for(i=0;i<npairs;i++) {
		for(int i=0; i < npairs; i++) {
		if(rcut[i]>rcutall)
		rcutall=rcut[i];
		if(rcut3[i]>rcutall)
		@@ -5189,12 +5088,14 @@ void _noopt PairBOP::read_table(char *filename)
		dr3[i]=rcut3[i]/((double)nr-1.0);
		rdr3[i]=1.0/dr3[i];
		}

		rctroot=rcutall;
		dtheta=2.0/((double)ntheta-1.0);
		rdtheta=1.0/dtheta;
		dBO=1.0/((double)nBOt-1.0);
		rdBO=1.0/(double)dBO;
		for(i=0;i<npairs;i++) {

		for (int i = 0; i < npairs; i++) {
		pBetaS1[i][0]=pBetaS[i][1]-pBetaS[i][0];
		pBetaS1[i][1]=0.5*(pBetaS[i][2]-pBetaS[i][0]);
		pBetaS1[i][nr-2]=0.5*(pBetaS[i][nr-1]-pBetaS[i][nr-3]);
		@@ -5215,7 +5116,7 @@ void _noopt PairBOP::read_table(char *filename)
		pLong1[i][1]=0.5*(pLong[i][2]-pLong[i][0]);
		pLong1[i][nBOt-2]=0.5*(pLong[i][nr-1]-pLong[i][nr-3]);
		pLong1[i][nBOt-1]=pLong[i][nr-1]-pLong[i][nr-2];
		for(k=2;k<nr-2;k++) {
		for (int k = 2; k < nr-2; k++) {
		pBetaS1[i][k]=((pBetaS[i][k-2]-pBetaS[i][k+2])
		+8.0*(pBetaS[i][k+1]-pBetaS[i][k-1]))/12.0;
		pBetaP1[i][k]=((pBetaP[i][k-2]-pBetaP[i][k+2])
		@@ -5225,11 +5126,11 @@ void _noopt PairBOP::read_table(char *filename)
		pLong1[i][k]=((pLong[i][k-2]-pLong[i][k+2])
		+8.0*(pLong[i][k+1]-pLong[i][k-1]))/12.0;
		}
		for(k=2;k<nr-2;k++) {
		for (int k=2; k < nr-2; k++) {
		FsigBO1[i][k]=((FsigBO[i][k-2]-FsigBO[i][k+2])
		+8.0*(FsigBO[i][k+1]-FsigBO[i][k-1]))/12.0;
		}
		for(k=0;k<nr-1;k++) {
		for (int k = 0; k < nr-1; k++) {
		pBetaS2[i][k]=3.0*(pBetaS[i][k+1]-pBetaS[i][k])
		-2.0*pBetaS1[i][k]-pBetaS1[i][k+1];
		pBetaS3[i][k]=pBetaS1[i][k]+pBetaS1[i][k+1]
		@@ -5247,12 +5148,14 @@ void _noopt PairBOP::read_table(char *filename)
		pLong3[i][k]=pLong1[i][k]+pLong1[i][k+1]
		-2.0*(pLong[i][k+1]-pLong[i][k]);
		}
		for(k=0;k<nBOt-1;k++) {

		for (int k = 0; k < nBOt-1; k++) {
		FsigBO2[i][k]=3.0*(FsigBO[i][k+1]-FsigBO[i][k])
		-2.0*FsigBO1[i][k]-FsigBO1[i][k+1];
		FsigBO3[i][k]=FsigBO1[i][k]+FsigBO1[i][k+1]
		-2.0*(FsigBO[i][k+1]-FsigBO[i][k]);
		}

		pBetaS2[i][nr-1]=0.0;
		pBetaS3[i][nr-1]=0.0;
		pBetaP2[i][nr-1]=0.0;
		@@ -5263,7 +5166,8 @@ void _noopt PairBOP::read_table(char *filename)
		pLong3[i][nr-1]=0.0;
		FsigBO2[i][nBOt-1]=0.0;
		FsigBO3[i][nBOt-1]=0.0;
		for(k=0;k<nr;k++) {

		for (int k=0; k < nr; k++) {
		pBetaS4[i][k]=pBetaS1[i][k]/dr[i];
		pBetaS5[i][k]=2.0*pBetaS2[i][k]/dr[i];
		pBetaS6[i][k]=3.0*pBetaS3[i][k]/dr[i];
		@@ -5277,33 +5181,39 @@ void _noopt PairBOP::read_table(char *filename)
		pLong5[i][k]=2.0*pLong2[i][k]/dr3[i];
		pLong6[i][k]=3.0*pLong3[i][k]/dr3[i];
		}
		for(k=0;k<nBOt;k++) {
		for (int k=0; k < nBOt; k++) {
		FsigBO4[i][k]=FsigBO1[i][k]/dBO;
		FsigBO5[i][k]=2.0*FsigBO2[i][k]/dBO;
		FsigBO6[i][k]=3.0*FsigBO3[i][k]/dBO;
		}
		}

		if (npower <= 2) {
		for(i=0;i<bop_types;i++) {
		for(j=0;j<bop_types;j++) {
		for(k=j;k<bop_types;k++) {
		for (int i = 0; i < bop_types; i++) {
		for (int j = 0; j < bop_types; j++) {
		for (int k = j; k < bop_types; k++) {
		gfunc1[j][i][k][0] = gfunc[j][i][k][1] - gfunc[j][i][k][0];
		gfunc1[j][i][k][1] = 0.5 * (gfunc[j][i][k][2] - gfunc[j][i][k][0]);
		gfunc1[j][i][k][ntheta - 2] = 0.5 * (gfunc[j][i][k][ntheta - 1] - gfunc[j][i][k][ntheta - 3]);
		gfunc1[j][i][k][ntheta - 1] = 0.5 * (gfunc[j][i][k][ntheta - 1] - gfunc[j][i][k][ntheta - 2]);
		for(m=2;m<ntheta-2;m++) {

		for (int m = 2; m < ntheta - 2; m++) {
		gfunc1[j][i][k][m] = ((gfunc[j][i][k][m - 2] - gfunc[j][i][k][m + 2]) +
		8.0*(gfunc[j][i][k][m+1]-gfunc[j][i][k][m+1]-gfunc[j][i][k][m-1]))/12.0;
		8.0 * (gfunc[j][i][k][m + 1] - gfunc[j][i][k][m + 1] - gfunc[j][i][k][m - 1])) /
		12.0;
		}
		for(m=0;m<ntheta-1;m++) {

		for (int m = 0; m < ntheta - 1; m++) {
		gfunc2[j][i][k][m] = 3.0 * (gfunc[j][i][k][m + 1] - gfunc[j][i][k][m]) -
		2.0 * gfunc1[j][i][k][m] - gfunc1[j][i][k][m + 1];
		gfunc3[j][i][k][m] = gfunc1[j][i][k][m] + gfunc1[j][i][k][m + 1] -
		2.0 * (gfunc[j][i][k][m + 1] - gfunc[j][i][k][m]);
		}

		gfunc2[j][i][k][ntheta - 1] = 0.0;
		gfunc3[j][i][k][ntheta - 1] = 0.0;
		for(m=0;m<ntheta;m++) {

		for (int m = 0; m < ntheta; m++) {
		gfunc4[j][i][k][ntheta - 1] = gfunc1[j][i][k][m] / dtheta;
		gfunc5[j][i][k][ntheta - 1] = 2.0 * gfunc2[j][i][k][m] / dtheta;
		gfunc6[j][i][k][ntheta - 1] = 3.0 * gfunc3[j][i][k][m] / dtheta;
		@@ -5312,11 +5222,12 @@ void _noopt PairBOP::read_table(char *filename)
		}
		}
		}
		for(i=0;i<bop_types;i++) {
		for(j=0;j<bop_types;j++) {
		for(k=0;k<j;k++) {

		for (int i = 0; i < bop_types; i++) {
		for (int j = 0; j < bop_types; j++) {
		for (int k = 0; k < j; k++) {
		if (npower <= 2) {
		for(n=0;n<ntheta;n++) {
		for (int n = 0; n < ntheta; n++) {
		gfunc[j][i][k][n] = gfunc[k][i][j][n];
		gfunc1[j][i][k][n] = gfunc1[k][i][j][n];
		gfunc2[j][i][k][n] = gfunc2[k][i][j][n];
		@@ -5326,15 +5237,32 @@ void _noopt PairBOP::read_table(char *filename)
		gfunc6[j][i][k][n] = gfunc6[k][i][j][n];
		}
		} else {
		for(n=0;n<npower+1;n++) {
		for (int n = 0; n < npower + 1; n++) {
		gpara[j][i][k][n] = gpara[k][i][j][n];
		}
		}
		}
		}
		}
		fclose(fp);
		} catch (TokenizerException & e) {
		error->one(FLERR, e.what());
		} catch (FileReaderException & fre) {
		error->one(FLERR, fre.what());
		}
		}

		MPI_Bcast(&nr,1,MPI_INT,0,world);
		MPI_Bcast(&nBOt,1,MPI_INT,0,world);
		MPI_Bcast(&ntheta,1,MPI_INT,0,world);
		MPI_Bcast(&bop_types,1,MPI_INT,0,world);
		MPI_Bcast(&npairs,1,MPI_INT,0,world);
		MPI_Bcast(&npower,1,MPI_INT,0,world);

		if (comm->me != 0){
		allocate_tables();
		allocate();
		}

		MPI_Bcast(&rdBO,1,MPI_DOUBLE,0,world);
		MPI_Bcast(&dBO,1,MPI_DOUBLE,0,world);
		MPI_Bcast(&rdtheta,1,MPI_DOUBLE,0,world);

src/MANYBODY/pair_bop.h

+1 −1

Original line number	Diff line number	Diff line
		@@ -41,7 +41,6 @@ class PairBOP : public Pair {
		double memory_usage();

		private:
		int me;
		int maxneigh; // maximum size of neighbor list on this processor
		int maxneigh3; // maximum size of neighbor list on this processor
		int update_list; // check for changing maximum size of neighbor list
		@@ -207,6 +206,7 @@ class PairBOP : public Pair {

		void read_table(char *);
		void allocate();
		void allocate_tables();
		void create_pi(int);
		void create_sigma(int);
		void destroy_pi();

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