pair_sw.cpp
639fb6f444a0master

pair_sw.cpp
View Options

			/* ----------------------------------------------------------------------
			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 author: Aidan Thompson (SNL)
			------------------------------------------------------------------------- */

			#include <math.h>
			#include <stdio.h>
			#include <stdlib.h>
			#include <string.h>
			#include "pair_sw.h"
			#include "atom.h"
			#include "neighbor.h"
			#include "neigh_request.h"
			#include "force.h"
			#include "comm.h"
			#include "memory.h"
			#include "neighbor.h"
			#include "neigh_list.h"
			#include "memory.h"
			#include "error.h"

			using namespace LAMMPS_NS;

			#define MAXLINE 1024
			#define DELTA 4

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

			PairSW::PairSW(LAMMPS *lmp) : Pair(lmp)
			{
			single_enable = 0;
			restartinfo = 0;
			one_coeff = 1;
			manybody_flag = 1;

			nelements = 0;
			elements = NULL;
			nparams = maxparam = 0;
			params = NULL;
			elem2param = NULL;
			map = NULL;

			maxshort = 10;
			neighshort = NULL;
			}

			/* ----------------------------------------------------------------------
			check if allocated, since class can be destructed when incomplete
			------------------------------------------------------------------------- */

			PairSW::~PairSW()
			{
			if (copymode) return;

			if (elements)
			for (int i = 0; i < nelements; i++) delete [] elements[i];
			delete [] elements;
			memory->destroy(params);
			memory->destroy(elem2param);

			if (allocated) {
			memory->destroy(setflag);
			memory->destroy(cutsq);
			memory->destroy(neighshort);
			delete [] map;
			}
			}

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

			void PairSW::compute(int eflag, int vflag)
			{
			int i,j,k,ii,jj,kk,inum,jnum,jnumm1;
			int itype,jtype,ktype,ijparam,ikparam,ijkparam;
			tagint itag,jtag;
			double xtmp,ytmp,ztmp,delx,dely,delz,evdwl,fpair;
			double rsq,rsq1,rsq2;
			double delr1[3],delr2[3],fj[3],fk[3];
			int ilist,jlist,numneigh,*firstneigh;

			evdwl = 0.0;
			if (eflag \|\| vflag) ev_setup(eflag,vflag);
			else evflag = vflag_fdotr = 0;

			double **x = atom->x;
			double **f = atom->f;
			tagint *tag = atom->tag;
			int *type = atom->type;
			int nlocal = atom->nlocal;
			int newton_pair = force->newton_pair;

			inum = list->inum;
			ilist = list->ilist;
			numneigh = list->numneigh;
			firstneigh = list->firstneigh;

			double fxtmp,fytmp,fztmp;

			// loop over full neighbor list of my atoms

			for (ii = 0; ii < inum; ii++) {
			i = ilist[ii];
			itag = tag[i];
			itype = map[type[i]];
			xtmp = x[i][0];
			ytmp = x[i][1];
			ztmp = x[i][2];
			fxtmp = fytmp = fztmp = 0.0;

			// two-body interactions, skip half of them

			jlist = firstneigh[i];
			jnum = numneigh[i];
			int numshort = 0;

			for (jj = 0; jj < jnum; jj++) {
			j = jlist[jj];
			j &= NEIGHMASK;

			delx = xtmp - x[j][0];
			dely = ytmp - x[j][1];
			delz = ztmp - x[j][2];
			rsq = delxdelx + delydely + delz*delz;

			jtype = map[type[j]];
			ijparam = elem2param[itype][jtype][jtype];
			if (rsq >= params[ijparam].cutsq) {
			continue;
			} else {
			neighshort[numshort++] = j;
			if (numshort >= maxshort) {
			maxshort += maxshort/2;
			memory->grow(neighshort,maxshort,"pair:neighshort");
			}
			}

			jtag = tag[j];
			if (itag > jtag) {
			if ((itag+jtag) % 2 == 0) continue;
			} else if (itag < jtag) {
			if ((itag+jtag) % 2 == 1) continue;
			} else {
			if (x[j][2] < ztmp) continue;
			if (x[j][2] == ztmp && x[j][1] < ytmp) continue;
			if (x[j][2] == ztmp && x[j][1] == ytmp && x[j][0] < xtmp) continue;
			}

			twobody(&params[ijparam],rsq,fpair,eflag,evdwl);

			fxtmp += delx*fpair;
			fytmp += dely*fpair;
			fztmp += delz*fpair;
			f[j][0] -= delx*fpair;
			f[j][1] -= dely*fpair;
			f[j][2] -= delz*fpair;

			if (evflag) ev_tally(i,j,nlocal,newton_pair,
			evdwl,0.0,fpair,delx,dely,delz);
			}

			jnumm1 = numshort - 1;

			for (jj = 0; jj < jnumm1; jj++) {
			j = neighshort[jj];
			jtype = map[type[j]];
			ijparam = elem2param[itype][jtype][jtype];
			delr1[0] = x[j][0] - xtmp;
			delr1[1] = x[j][1] - ytmp;
			delr1[2] = x[j][2] - ztmp;
			rsq1 = delr1[0]delr1[0] + delr1[1]delr1[1] + delr1[2]*delr1[2];

			double fjxtmp,fjytmp,fjztmp;
			fjxtmp = fjytmp = fjztmp = 0.0;

			for (kk = jj+1; kk < numshort; kk++) {
			k = neighshort[kk];
			ktype = map[type[k]];
			ikparam = elem2param[itype][ktype][ktype];
			ijkparam = elem2param[itype][jtype][ktype];

			delr2[0] = x[k][0] - xtmp;
			delr2[1] = x[k][1] - ytmp;
			delr2[2] = x[k][2] - ztmp;
			rsq2 = delr2[0]delr2[0] + delr2[1]delr2[1] + delr2[2]*delr2[2];

			threebody(&params[ijparam],&params[ikparam],&params[ijkparam],
			rsq1,rsq2,delr1,delr2,fj,fk,eflag,evdwl);

			fxtmp -= fj[0] + fk[0];
			fytmp -= fj[1] + fk[1];
			fztmp -= fj[2] + fk[2];
			fjxtmp += fj[0];
			fjytmp += fj[1];
			fjztmp += fj[2];
			f[k][0] += fk[0];
			f[k][1] += fk[1];
			f[k][2] += fk[2];

			if (evflag) ev_tally3(i,j,k,evdwl,0.0,fj,fk,delr1,delr2);
			}
			f[j][0] += fjxtmp;
			f[j][1] += fjytmp;
			f[j][2] += fjztmp;
			}
			f[i][0] += fxtmp;
			f[i][1] += fytmp;
			f[i][2] += fztmp;
			}

			if (vflag_fdotr) virial_fdotr_compute();
			}

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

			void PairSW::allocate()
			{
			allocated = 1;
			int n = atom->ntypes;

			memory->create(setflag,n+1,n+1,"pair:setflag");
			memory->create(cutsq,n+1,n+1,"pair:cutsq");
			memory->create(neighshort,maxshort,"pair:neighshort");
			map = new int[n+1];
			}

			/* ----------------------------------------------------------------------
			global settings
			------------------------------------------------------------------------- */

			void PairSW::settings(int narg, char **arg)
			{
			if (narg != 0) error->all(FLERR,"Illegal pair_style command");
			}

			/* ----------------------------------------------------------------------
			set coeffs for one or more type pairs
			------------------------------------------------------------------------- */

			void PairSW::coeff(int narg, char **arg)
			{
			int i,j,n;

			if (!allocated) allocate();

			if (narg != 3 + atom->ntypes)
			error->all(FLERR,"Incorrect args for pair coefficients");

			// insure I,J args are * *

			if (strcmp(arg[0],"") != 0 \|\| strcmp(arg[1],"") != 0)
			error->all(FLERR,"Incorrect args for pair coefficients");

			// read args that map atom types to elements in potential file
			// map[i] = which element the Ith atom type is, -1 if NULL
			// nelements = # of unique elements
			// elements = list of element names

			if (elements) {
			for (i = 0; i < nelements; i++) delete [] elements[i];
			delete [] elements;
			}
			elements = new char*[atom->ntypes];
			for (i = 0; i < atom->ntypes; i++) elements[i] = NULL;

			nelements = 0;
			for (i = 3; i < narg; i++) {
			if (strcmp(arg[i],"NULL") == 0) {
			map[i-2] = -1;
			continue;
			}
			for (j = 0; j < nelements; j++)
			if (strcmp(arg[i],elements[j]) == 0) break;
			map[i-2] = j;
			if (j == nelements) {
			n = strlen(arg[i]) + 1;
			elements[j] = new char[n];
			strcpy(elements[j],arg[i]);
			nelements++;
			}
			}

			// read potential file and initialize potential parameters

			read_file(arg[2]);
			setup_params();

			// clear setflag since coeff() called once with I,J = * *

			n = atom->ntypes;
			for (int i = 1; i <= n; i++)
			for (int j = i; j <= n; j++)
			setflag[i][j] = 0;

			// set setflag i,j for type pairs where both are mapped to elements

			int count = 0;
			for (int i = 1; i <= n; i++)
			for (int j = i; j <= n; j++)
			if (map[i] >= 0 && map[j] >= 0) {
			setflag[i][j] = 1;
			count++;
			}

			if (count == 0) error->all(FLERR,"Incorrect args for pair coefficients");
			}

			/* ----------------------------------------------------------------------
			init specific to this pair style
			------------------------------------------------------------------------- */

			void PairSW::init_style()
			{
			if (atom->tag_enable == 0)
			error->all(FLERR,"Pair style Stillinger-Weber requires atom IDs");
			if (force->newton_pair == 0)
			error->all(FLERR,"Pair style Stillinger-Weber requires newton pair on");

			// need a full neighbor list

			int irequest = neighbor->request(this,instance_me);
			neighbor->requests[irequest]->half = 0;
			neighbor->requests[irequest]->full = 1;
			}

			/* ----------------------------------------------------------------------
			init for one type pair i,j and corresponding j,i
			------------------------------------------------------------------------- */

			double PairSW::init_one(int i, int j)
			{
			if (setflag[i][j] == 0) error->all(FLERR,"All pair coeffs are not set");

			return cutmax;
			}

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

			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];
			sprintf(str,"Cannot open Stillinger-Weber potential file %s",file);
			error->one(FLERR,str);
			}
			}

			// 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

			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 = atom->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 = atom->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;

			// ielement,jelement,kelement = 1st args
			// if all 3 args are in element list, then parse this line
			// else skip to next entry in file

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

			// load up parameter settings and error check their values

			if (nparams == maxparam) {
			maxparam += DELTA;
			params = (Param ) memory->srealloc(params,maxparamsizeof(Param),
			"pair:params");
			}

			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]);

			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");

			nparams++;
			}

			delete [] words;
			}

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

			void PairSW::setup_params()
			{
			int i,j,k,m,n;
			double rtmp;

			// set elem2param for all triplet combinations
			// must be a single exact match to lines read from file
			// do not allow for ACB in place of ABC

			memory->destroy(elem2param);
			memory->create(elem2param,nelements,nelements,nelements,"pair:elem2param");

			for (i = 0; i < nelements; i++)
			for (j = 0; j < nelements; j++)
			for (k = 0; k < nelements; k++) {
			n = -1;
			for (m = 0; m < nparams; m++) {
			if (i == params[m].ielement && j == params[m].jelement &&
			k == params[m].kelement) {
			if (n >= 0) error->all(FLERR,"Potential file has duplicate entry");
			n = m;
			}
			}
			if (n < 0) error->all(FLERR,"Potential file is missing an entry");
			elem2param[i][j][k] = n;
			}


			// compute parameter values derived from inputs

			// set cutsq using shortcut to reduce neighbor list for accelerated
			// calculations. cut must remain unchanged as it is a potential parameter
			// (cut = a*sigma)

			for (m = 0; m < nparams; m++) {
			params[m].cut = params[m].sigma*params[m].littlea;

			rtmp = params[m].cut;
			if (params[m].tol > 0.0) {
			if (params[m].tol > 0.01) params[m].tol = 0.01;
			if (params[m].gamma < 1.0)
			rtmp = rtmp +
			params[m].gamma * params[m].sigma / log(params[m].tol);
			else rtmp = rtmp +
			params[m].sigma / log(params[m].tol);
			}
			params[m].cutsq = rtmp * rtmp;

			params[m].sigma_gamma = params[m].sigma*params[m].gamma;
			params[m].lambda_epsilon = params[m].lambda*params[m].epsilon;
			params[m].lambda_epsilon2 = 2.0params[m].lambdaparams[m].epsilon;
			params[m].c1 = params[m].bigaparams[m].epsilon
			params[m].powerpparams[m].bigb
			pow(params[m].sigma,params[m].powerp);
			params[m].c2 = params[m].bigaparams[m].epsilonparams[m].powerq *
			pow(params[m].sigma,params[m].powerq);
			params[m].c3 = params[m].bigaparams[m].epsilonparams[m].bigb *
			pow(params[m].sigma,params[m].powerp+1.0);
			params[m].c4 = params[m].bigaparams[m].epsilon
			pow(params[m].sigma,params[m].powerq+1.0);
			params[m].c5 = params[m].bigaparams[m].epsilonparams[m].bigb *
			pow(params[m].sigma,params[m].powerp);
			params[m].c6 = params[m].bigaparams[m].epsilon
			pow(params[m].sigma,params[m].powerq);
			}

			// set cutmax to max of all params

			cutmax = 0.0;
			for (m = 0; m < nparams; m++) {
			rtmp = sqrt(params[m].cutsq);
			if (rtmp > cutmax) cutmax = rtmp;
			}
			}

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

			void PairSW::twobody(Param *param, double rsq, double &fforce,
			int eflag, double &eng)
			{
			double r,rinvsq,rp,rq,rainv,rainvsq,expsrainv;

			r = sqrt(rsq);
			rinvsq = 1.0/rsq;
			rp = pow(r,-param->powerp);
			rq = pow(r,-param->powerq);
			rainv = 1.0 / (r - param->cut);
			rainvsq = rainvrainvr;
			expsrainv = exp(param->sigma * rainv);
			fforce = (param->c1rp - param->c2rq +
			(param->c3rp -param->c4rq) * rainvsq) * expsrainv * rinvsq;
			if (eflag) eng = (param->c5rp - param->c6rq) * expsrainv;
			}

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

			void PairSW::threebody(Param paramij, Param paramik, Param *paramijk,
			double rsq1, double rsq2,
			double delr1, double delr2,
			double fj, double fk, int eflag, double &eng)
			{
			double r1,rinvsq1,rainv1,gsrainv1,gsrainvsq1,expgsrainv1;
			double r2,rinvsq2,rainv2,gsrainv2,gsrainvsq2,expgsrainv2;
			double rinv12,cs,delcs,delcssq,facexp,facrad,frad1,frad2;
			double facang,facang12,csfacang,csfac1,csfac2;

			r1 = sqrt(rsq1);
			rinvsq1 = 1.0/rsq1;
			rainv1 = 1.0/(r1 - paramij->cut);
			gsrainv1 = paramij->sigma_gamma * rainv1;
			gsrainvsq1 = gsrainv1*rainv1/r1;
			expgsrainv1 = exp(gsrainv1);

			r2 = sqrt(rsq2);
			rinvsq2 = 1.0/rsq2;
			rainv2 = 1.0/(r2 - paramik->cut);
			gsrainv2 = paramik->sigma_gamma * rainv2;
			gsrainvsq2 = gsrainv2*rainv2/r2;
			expgsrainv2 = exp(gsrainv2);

			rinv12 = 1.0/(r1*r2);
			cs = (delr1[0]delr2[0] + delr1[1]delr2[1] + delr1[2]delr2[2]) rinv12;
			delcs = cs - paramijk->costheta;
			delcssq = delcs*delcs;

			facexp = expgsrainv1*expgsrainv2;

			// facrad = sqrt(paramij->lambda_epsilonparamik->lambda_epsilon)
			// facexp*delcssq;

			facrad = paramijk->lambda_epsilon * facexp*delcssq;
			frad1 = facrad*gsrainvsq1;
			frad2 = facrad*gsrainvsq2;
			facang = paramijk->lambda_epsilon2 * facexp*delcs;
			facang12 = rinv12*facang;
			csfacang = cs*facang;
			csfac1 = rinvsq1*csfacang;

			fj[0] = delr1[0](frad1+csfac1)-delr2[0]facang12;
			fj[1] = delr1[1](frad1+csfac1)-delr2[1]facang12;
			fj[2] = delr1[2](frad1+csfac1)-delr2[2]facang12;

			csfac2 = rinvsq2*csfacang;

			fk[0] = delr2[0](frad2+csfac2)-delr1[0]facang12;
			fk[1] = delr2[1](frad2+csfac2)-delr1[1]facang12;
			fk[2] = delr2[2](frad2+csfac2)-delr1[2]facang12;

			if (eflag) eng = facrad;
			}

lammps/src/MANYBODY/pair_sw.cpp639fb6f444a0master

pair_sw.cppView Options

lammps/src/MANYBODY/pair_sw.cpp
639fb6f444a0master

pair_sw.cpp
View Options