pair_polymorphic.cpp
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Created: Mon, Nov 4, 22:27

pair_polymorphic.cpp
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	/* ----------------------------------------------------------------------
	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: Reese Jones, Xiaowang Zhou (SNL)
	This modifies from pair_tersoff.cpp by Aidan Thompson (SNL)
	------------------------------------------------------------------------- */

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

	#include "math_const.h"

	using namespace LAMMPS_NS;
	using namespace MathConst;

	#define MAXLINE 1024
	#define DELTA 4

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

	PairPolymorphic::PairPolymorphic(LAMMPS *lmp) : Pair(lmp)
	{
	single_enable = 0;
	one_coeff = 1;

	nelements = 0;
	elements = NULL;
	pairParameters = NULL;
	tripletParameters = NULL;
	elem2param = NULL;
	elem3param = NULL;
	map = NULL;
	epsilon = 0.0;
	neighsize = 0;
	firstneighV = NULL;
	firstneighW = NULL;
	firstneighW1 = NULL;
	delxV = NULL;
	delyV = NULL;
	delzV = NULL;
	drV = NULL;
	delxW = NULL;
	delyW = NULL;
	delzW = NULL;
	drW = NULL;
	}

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

	PairPolymorphic::~PairPolymorphic()
	{
	if (elements)
	for (int i = 0; i < nelements; i++) delete [] elements[i];
	delete [] elements;
	delete [] match;
	memory->destroy(pairParameters);
	memory->destroy(tripletParameters);
	memory->destroy(elem2param);
	memory->destroy(elem3param);
	if (allocated) {
	memory->destroy(setflag);
	memory->destroy(cutsq);
	delete [] map;
	delete [] firstneighV;
	delete [] firstneighW;
	delete [] firstneighW1;
	delete [] delxV;
	delete [] delyV;
	delete [] delzV;
	delete [] drV;
	delete [] delxW;
	delete [] delyW;
	delete [] delzW;
	delete [] drW;
	}
	}

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

	void PairPolymorphic::compute(int eflag, int vflag)
	{
	tagint itag,jtag;
	int i,j,k,ii,jj,kk,kk1,inum,jnum;
	int itype,jtype,ktype;
	int iparam_ii,iparam_jj,iparam_kk,iparam_ij,iparam_ik,iparam_ijk;
	double xtmp,ytmp,ztmp,delx,dely,delz,evdwl,fpair;
	double rsq,r0,r1,r2;
	double delr1[3],delr2[3],fi[3],fj[3],fk[3];
	double zeta_ij,prefactor,wfac,pfac,gfac,fa,fa_d,bij,bij_d;
	double costheta;
	int ilist,jlist,numneigh,*firstneigh;
	double emb;

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

	// 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];

	jlist = firstneigh[i];
	jnum = numneigh[i];

	if (neighsize < jnum) {
	delete [] firstneighV;
	delete [] delxV;
	delete [] delyV;
	delete [] delzV;
	delete [] drV;
	delete [] firstneighW;
	delete [] delxW;
	delete [] delyW;
	delete [] delzW;
	delete [] drW;
	delete [] firstneighW1;
	neighsize = jnum + 20;
	firstneighV = new int[neighsize];
	delxV = new double[neighsize];
	delyV = new double[neighsize];
	delzV = new double[neighsize];
	drV = new double[neighsize];
	firstneighW = new int[neighsize];
	delxW = new double[neighsize];
	delyW = new double[neighsize];
	delzW = new double[neighsize];
	drW = new double[neighsize];
	firstneighW1 = new int[neighsize];
	}

	if (eta) {
	iparam_ii = elem2param[itype][itype];
	PairParameters & p = pairParameters[iparam_ii];
	emb = (p.F)->get_vmax();
	}

	numneighV = -1;
	numneighW = -1;

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

	delx = xtmp - x[j][0];
	dely = ytmp - x[j][1];
	delz = ztmp - x[j][2];
	rsq = delxdelx + delydely + delz*delz;
	if (rsq >= cutmaxsq) continue;
	r0 = sqrt(rsq);

	iparam_ij = elem2param[itype][jtype];
	PairParameters & p = pairParameters[iparam_ij];

	// do not include the neighbor if get_vmax() <= epsilon because the function is near zero
	if (eta) {
	if (emb > epsilon) {
	iparam_jj = elem2param[jtype][jtype];
	PairParameters & q = pairParameters[iparam_jj];
	if (rsq < (q.W)->get_xmaxsq() && (q.W)->get_vmax() > epsilon) {
	numneighW = numneighW + 1;
	firstneighW[numneighW] = j;
	delxW[numneighW] = delx;
	delyW[numneighW] = dely;
	delzW[numneighW] = delz;
	drW[numneighW] = r0;
	}
	}
	} else {
	if ((p.F)->get_vmax() > epsilon) {
	if (rsq < (p.V)->get_xmaxsq() && (p.V)->get_vmax() > epsilon) {
	numneighV = numneighV + 1;
	firstneighV[numneighV] = j;
	delxV[numneighV] = delx;
	delyV[numneighV] = dely;
	delzV[numneighV] = delz;
	drV[numneighV] = r0;
	}
	if (rsq < (p.W)->get_xmaxsq() && (p.W)->get_vmax() > epsilon) {
	numneighW = numneighW + 1;
	firstneighW[numneighW] = j;
	delxW[numneighW] = delx;
	delyW[numneighW] = dely;
	delzW[numneighW] = delz;
	drW[numneighW] = r0;
	}
	}
	}

	// two-body interactions, skip half of them

	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] < x[i][2]) 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;
	}

	if (rsq >= (p.U)->get_xmaxsq() \|\| (p.U)->get_vmax() <= epsilon) continue;
	(p.U)->value(r0,evdwl,eflag,fpair,1);
	fpair = -fpair/r0;

	f[i][0] += delx*fpair;
	f[i][1] += dely*fpair;
	f[i][2] += 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);
	}

	if (eta) {

	if (emb > epsilon) {

	iparam_ii = elem2param[itype][itype];
	PairParameters & p = pairParameters[iparam_ii];

	// accumulate bondorder zeta for each i-j interaction via loop over k

	zeta_ij = 0.0;

	for (kk = 0; kk <= numneighW; kk++) {
	k = firstneighW[kk];
	ktype = map[type[k]];

	iparam_kk = elem2param[ktype][ktype];
	PairParameters & q = pairParameters[iparam_kk];

	(q.W)->value(drW[kk],wfac,1,fpair,0);

	zeta_ij += wfac;
	}

	// pairwise force due to zeta

	(p.F)->value(zeta_ij,bij,1,bij_d,1);

	prefactor = 0.5* bij_d;
	if (eflag) evdwl = -0.5*bij;

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

	// attractive term via loop over k

	for (kk = 0; kk <= numneighW; kk++) {
	k = firstneighW[kk];
	ktype = map[type[k]];

	delr2[0] = -delxW[kk];
	delr2[1] = -delyW[kk];
	delr2[2] = -delzW[kk];

	iparam_kk = elem2param[ktype][ktype];
	PairParameters & q = pairParameters[iparam_kk];

	(q.W)->value(drW[kk],wfac,0,fpair,1);
	fpair = -prefactor*fpair/drW[kk];

	f[i][0] += delr2[0]*fpair;
	f[i][1] += delr2[1]*fpair;
	f[i][2] += delr2[2]*fpair;
	f[k][0] -= delr2[0]*fpair;
	f[k][1] -= delr2[1]*fpair;
	f[k][2] -= delr2[2]*fpair;

	if (vflag_atom) v_tally2(i, k, -fpair, delr2);
	}
	}

	} else {

	for (jj = 0; jj <= numneighV; jj++) {
	j = firstneighV[jj];
	jtype = map[type[j]];

	iparam_ij = elem2param[itype][jtype];
	PairParameters & p = pairParameters[iparam_ij];

	delr1[0] = -delxV[jj];
	delr1[1] = -delyV[jj];
	delr1[2] = -delzV[jj];
	r1 = drV[jj];

	// accumulate bondorder zeta for each i-j interaction via loop over k

	zeta_ij = 0.0;

	numneighW1 = -1;
	for (kk = 0; kk <= numneighW; kk++) {
	k = firstneighW[kk];
	if (j == k) continue;
	ktype = map[type[k]];
	iparam_ijk = elem3param[jtype][itype][ktype];
	TripletParameters & trip = tripletParameters[iparam_ijk];
	if ((trip.G)->get_vmax() <= epsilon) continue;

	numneighW1 = numneighW1 + 1;
	firstneighW1[numneighW1] = kk;

	delr2[0] = -delxW[kk];
	delr2[1] = -delyW[kk];
	delr2[2] = -delzW[kk];
	r2 = drW[kk];

	costheta = (delr1[0]delr2[0] + delr1[1]delr2[1] +
	delr1[2]delr2[2]) / (r1r2);

	iparam_ik = elem2param[itype][ktype];
	PairParameters & q = pairParameters[iparam_ik];

	(q.W)->value(r2,wfac,1,fpair,0);
	(q.P)->value(r1-(p.xi)*r2,pfac,1,fpair,0);
	(trip.G)->value(costheta,gfac,1,fpair,0);

	zeta_ij += wfacpfacgfac;
	}

	// pairwise force due to zeta

	(p.V)->value(r1,fa,1,fa_d,1);
	(p.F)->value(zeta_ij,bij,1,bij_d,1);
	fpair = -0.5bijfa_d / r1;
	prefactor = 0.5* fa * bij_d;
	if (eflag) evdwl = -0.5bijfa;

	f[i][0] += delr1[0]*fpair;
	f[i][1] += delr1[1]*fpair;
	f[i][2] += delr1[2]*fpair;
	f[j][0] -= delr1[0]*fpair;
	f[j][1] -= delr1[1]*fpair;
	f[j][2] -= delr1[2]*fpair;

	if (evflag) ev_tally(i,j,nlocal,newton_pair,
	evdwl,0.0,-fpair,-delr1[0],-delr1[1],-delr1[2]);

	// attractive term via loop over k

	for (kk1 = 0; kk1 <= numneighW1; kk1++) {
	kk = firstneighW1[kk1];
	k = firstneighW[kk];
	ktype = map[type[k]];
	iparam_ijk = elem3param[jtype][itype][ktype];
	TripletParameters & trip = tripletParameters[iparam_ijk];

	delr2[0] = -delxW[kk];
	delr2[1] = -delyW[kk];
	delr2[2] = -delzW[kk];
	r2 = drW[kk];

	iparam_ik = elem2param[itype][ktype];
	PairParameters & q = pairParameters[iparam_ik];

	attractive(&q,&trip,prefactor,r1,r2,delr1,delr2,fi,fj,fk);

	f[i][0] += fi[0];
	f[i][1] += fi[1];
	f[i][2] += fi[2];
	f[j][0] += fj[0];
	f[j][1] += fj[1];
	f[j][2] += fj[2];
	f[k][0] += fk[0];
	f[k][1] += fk[1];
	f[k][2] += fk[2];

	if (vflag_atom) v_tally3(i,j,k,fj,fk,delr1,delr2);
	}
	}
	}
	}
	if (vflag_fdotr) virial_fdotr_compute();
	}

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

	void PairPolymorphic::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");

	map = new int[n+1];

	neighsize = 40;
	firstneighV = new int[neighsize];
	delxV = new double[neighsize];
	delyV = new double[neighsize];
	delzV = new double[neighsize];
	drV = new double[neighsize];
	firstneighW = new int[neighsize];
	delxW = new double[neighsize];
	delyW = new double[neighsize];
	delzW = new double[neighsize];
	drW = new double[neighsize];
	firstneighW1 = new int[neighsize];
	}

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

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

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

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

	if (!allocated) allocate();

	if (narg == 4 + atom->ntypes) {
	narg--;
	epsilon = atof(arg[narg]);
	} else 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();

	// 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 PairPolymorphic::init_style()
	{
	if (atom->tag_enable == 0)
	error->all(FLERR,"Pair style polymorphic requires atom IDs");
	if (force->newton_pair == 0)
	error->all(FLERR,"Pair style polymorphic requires newton pair on");

	// need a full neighbor list

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

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

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

	return cutmax;
	}

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

	void PairPolymorphic::read_file(char *file)
	{
	char line[MAXLINE],*ptr;
	int n;

	// open file on proc 0
	FILE *fp=NULL;
	if (comm->me == 0) {
	fp = force->open_potential(file);
	if (fp == NULL) {
	char str[128];
	sprintf(str,"Cannot open polymorphic potential file %s",file);
	error->one(FLERR,str);
	}
	// move past comments to first data line
	fgets(line,MAXLINE,fp);
	while (line == strchr(line,'#')) fgets(line,MAXLINE,fp);
	n = strlen(line) + 1;
	}
	MPI_Bcast(&n,1,MPI_INT,0,world);
	MPI_Bcast(line,n,MPI_CHAR,0,world);
	ptr = strtok(line," \t\n\r\f"); // 1st line, 1st token
	int ntypes = atoi(ptr);
	if (ntypes != nelements)
	error->all(FLERR,"Incorrect number of elements in potential file");
	match = new int[nelements];
	ptr = strtok(NULL," \t\n\r\f"); // 1st line, 2nd token
	eta = (atoi(ptr)>0) ? true:false;

	// map the elements in the potential file to LAMMPS atom types
	for (int i = 0; i < nelements; i++) {
	if (comm->me == 0) {
	fgets(line,MAXLINE,fp);
	n = strlen(line) + 1;
	}
	MPI_Bcast(&n,1,MPI_INT,0,world);
	MPI_Bcast(line,n,MPI_CHAR,0,world);
	ptr = strtok(line," \t\n\r\f"); // 1st token
	ptr = strtok(NULL," \t\n\r\f"); // 2st token
	ptr = strtok(NULL," \t\n\r\f"); // 3st token
	int j;
	for (j = 0; j < nelements; j++) {
	if (strcmp(ptr,elements[j]) == 0) break;
	}
	if (j == nelements)
	error->all(FLERR,"Element not defined in potential file");
	match[i] = j;
	}
	// sizes
	if (comm->me == 0) {
	fgets(line,MAXLINE,fp);
	n = strlen(line) + 1;
	}
	MPI_Bcast(&n,1,MPI_INT,0,world);
	MPI_Bcast(line,n,MPI_CHAR,0,world);
	ptr = strtok(line," \t\n\r\f"); // 1st token
	nr = atoi(ptr);
	ptr = strtok(NULL," \t\n\r\f"); // 2nd token
	ng = atoi(ptr);
	ptr = strtok(NULL," \t\n\r\f"); // 3rd token
	nx = atoi(ptr);
	ptr = strtok(NULL," \t\n\r\f"); // 4th token
	maxX = atof(ptr);

	npair = nelements*(nelements+1)/2;
	ntriple = nelementsnelementsnelements;
	pairParameters = (PairParameters*)
	memory->srealloc(pairParameters,npair*sizeof(PairParameters),
	"pair:pairParameters");
	tripletParameters = (TripletParameters*)
	memory->srealloc(tripletParameters,ntriple*sizeof(TripletParameters),
	"pair:tripletParameters");

	// cutoffs
	for (int i = 0; i < npair; i++) {
	PairParameters & p = pairParameters[i];
	if (comm->me == 0) {
	fgets(line,MAXLINE,fp);
	n = strlen(line) + 1;
	}
	MPI_Bcast(&n,1,MPI_INT,0,world);
	MPI_Bcast(line,n,MPI_CHAR,0,world);
	ptr = strtok(line," \t\n\r\f"); // 1st token
	p.cut = atof(ptr);
	p.cutsq = p.cut*p.cut;
	ptr = strtok(NULL," \t\n\r\f"); // 2nd token
	p.xi = (atoi(ptr)>0) ? true:false;
	}

	// set cutmax to max of all params
	cutmax = 0.0;
	for (int i = 0; i < npair; i++) {
	PairParameters & p = pairParameters[i];
	if (p.cut > cutmax) cutmax = p.cut;
	}
	cutmaxsq = cutmax*cutmax;

	// start reading tabular functions
	double * singletable = new double[nr];
	for (int i = 0; i < npair; i++) { // U
	PairParameters & p = pairParameters[i];
	if (comm->me == 0) {
	grab(fp,nr,singletable);
	}
	MPI_Bcast(singletable,nr,MPI_DOUBLE,0,world);
	p.U = new tabularFunction(nr,0.0,p.cut);
	(p.U)->set_values(nr,0.0,p.cut,singletable,epsilon);
	}
	for (int i = 0; i < npair; i++) { // V
	PairParameters & p = pairParameters[i];
	if (comm->me == 0) {
	grab(fp,nr,singletable);
	}
	MPI_Bcast(singletable,nr,MPI_DOUBLE,0,world);
	p.V = new tabularFunction(nr,0.0,p.cut);
	(p.V)->set_values(nr,0.0,p.cut,singletable,epsilon);
	}
	for (int i = 0; i < npair; i++) { // W
	PairParameters & p = pairParameters[i];
	if (comm->me == 0) {
	grab(fp,nr,singletable);
	}
	MPI_Bcast(singletable,nr,MPI_DOUBLE,0,world);
	p.W = new tabularFunction(nr,0.0,p.cut);
	(p.W)->set_values(nr,0.0,p.cut,singletable,epsilon);
	}
	for (int i = 0; i < npair; i++) { // P
	PairParameters & p = pairParameters[i];
	if (comm->me == 0) {
	grab(fp,nr,singletable);
	}
	MPI_Bcast(singletable,nr,MPI_DOUBLE,0,world);
	p.P = new tabularFunction(nr,-cutmax,cutmax);
	(p.P)->set_values(nr,-cutmax,cutmax,singletable,epsilon);
	}
	delete singletable;
	singletable = new double[ng];
	for (int i = 0; i < ntriple; i++) { // G
	TripletParameters & p = tripletParameters[i];
	if (comm->me == 0) {
	grab(fp,ng,singletable);
	}
	MPI_Bcast(singletable,ng,MPI_DOUBLE,0,world);
	p.G = new tabularFunction(ng,-1.0,1.0);
	(p.G)->set_values(ng,-1.0,1.0,singletable,epsilon);
	}
	delete singletable;
	singletable = new double[nx];
	for (int i = 0; i < npair; i++) { // F
	PairParameters & p = pairParameters[i];
	if (comm->me == 0) {
	grab(fp,nx,singletable);
	}
	MPI_Bcast(singletable,nx,MPI_DOUBLE,0,world);
	p.F = new tabularFunction(nx,0.0,maxX);
	(p.F)->set_values(nx,0.0,maxX,singletable,epsilon);
	}
	delete singletable;
	if (comm->me == 0) {
	fclose(fp);
	}

	}

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

	void PairPolymorphic::setup()
	{
	int i,j,k,n;

	memory->destroy(elem2param);
	memory->create(elem2param,nelements,nelements,"pair:elem2param");
	memory->destroy(elem3param);
	memory->create(elem3param,nelements,nelements,nelements,"pair:elem3param");

	// map atom pair to parameter index

	n = 0;
	for (i = 0; i < nelements; i++) {
	elem2param[match[i]][match[i]] = n;
	n++;
	}
	for (i = 0; i < nelements-1; i++) {
	for (j = i+1; j < nelements; j++) {
	elem2param[match[i]][match[j]] = n;
	elem2param[match[j]][match[i]] = n;
	n++;
	}
	}

	// map atom triplet to parameter index

	n = 0;
	for (i = 0; i < nelements; i++)
	for (j = 0; j < nelements; j++)
	for (k = 0; k < nelements; k++) {
	elem3param[match[i]][match[j]][match[k]] = n;
	n++;
	}

	// for debugging, call write_tables() to check the tabular functions
	// if (comm->me == 0) {
	// write_tables(51);
	// error->all(FLERR,"Test potential tables");
	// }
	}

	/* ----------------------------------------------------------------------
	attractive term
	------------------------------------------------------------------------- */

	void PairPolymorphic::attractive(PairParameters p, TripletParameters trip,
	double prefactor, double rij, double rik,
	double delrij, double delrik,
	double fi, double fj, double *fk)
	{
	double rij_hat[3],rik_hat[3];
	double rijinv,rikinv;

	rijinv = 1.0/rij;
	vec3_scale(rijinv,delrij,rij_hat);

	rikinv = 1.0/rik;
	vec3_scale(rikinv,delrik,rik_hat);

	ters_zetaterm_d(prefactor,rij_hat,rij,rik_hat,rik,fi,fj,fk,p,trip);
	}

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

	void PairPolymorphic::ters_zetaterm_d(double prefactor,
	double *rij_hat, double rij,
	double *rik_hat, double rik,
	double dri, double drj, double *drk,
	PairParameters p, TripletParameters trip)
	{
	double gijk,gijk_d,ex_delr,ex_delr_d,fc,dfc,cos_theta;
	double dcosdri[3],dcosdrj[3],dcosdrk[3];

	cos_theta = vec3_dot(rij_hat,rik_hat);

	(p->W)->value(rik,fc,1,dfc,1);
	(p->P)->value(rij-(p->xi)*rik,ex_delr,1,ex_delr_d,1);
	(trip->G)->value(cos_theta,gijk,1,gijk_d,1);

	costheta_d(rij_hat,rij,rik_hat,rik,dcosdri,dcosdrj,dcosdrk);

	// compute the derivative wrt Ri
	// dri = -dfcgijkex_delr*rik_hat;
	// dri += fcgijk_dex_delr*dcosdri;
	// dri += fcgijkex_delr_d*(rik_hat - rij_hat);

	vec3_scale(-dfcgijkex_delr,rik_hat,dri);
	vec3_scaleadd(fcgijk_dex_delr,dcosdri,dri,dri);
	vec3_scaleadd(fcgijkex_delr_d,rik_hat,dri,dri);
	vec3_scaleadd(-fcgijkex_delr_d,rij_hat,dri,dri);
	vec3_scale(prefactor,dri,dri);

	// compute the derivative wrt Rj
	// drj = fcgijk_dex_delr*dcosdrj;
	// drj += fcgijkex_delr_d*rij_hat;

	vec3_scale(fcgijk_dex_delr,dcosdrj,drj);
	vec3_scaleadd(fcgijkex_delr_d,rij_hat,drj,drj);
	vec3_scale(prefactor,drj,drj);

	// compute the derivative wrt Rk
	// drk = dfcgijkex_delr*rik_hat;
	// drk += fcgijk_dex_delr*dcosdrk;
	// drk += -fcgijkex_delr_d*rik_hat;

	vec3_scale(dfcgijkex_delr,rik_hat,drk);
	vec3_scaleadd(fcgijk_dex_delr,dcosdrk,drk,drk);
	vec3_scaleadd(-fcgijkex_delr_d,rik_hat,drk,drk);
	vec3_scale(prefactor,drk,drk);
	}

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

	void PairPolymorphic::costheta_d(double *rij_hat, double rij,
	double *rik_hat, double rik,
	double dri, double drj, double *drk)
	{
	// first element is devative wrt Ri, second wrt Rj, third wrt Rk

	double cos_theta = vec3_dot(rij_hat,rik_hat);

	vec3_scaleadd(-cos_theta,rij_hat,rik_hat,drj);
	vec3_scale(1.0/rij,drj,drj);
	vec3_scaleadd(-cos_theta,rik_hat,rij_hat,drk);
	vec3_scale(1.0/rik,drk,drk);
	vec3_add(drj,drk,dri);
	vec3_scale(-1.0,dri,dri);
	}

	/* ----------------------------------------------------------------------
	* grab n values from file fp and put them in list
	* values can be several to a line
	* only called by proc 0
	* ------------------------------------------------------------------------- */

	void PairPolymorphic::grab(FILE fp, int n, double list)
	{
	char *ptr;
	char line[MAXLINE];

	int i = 0;
	while (i < n) {
	fgets(line,MAXLINE,fp);
	ptr = strtok(line," \t\n\r\f");
	list[i++] = atof(ptr);
	while ((ptr = strtok(NULL," \t\n\r\f")))
	list[i++] = atof(ptr);
	}
	}

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

	void PairPolymorphic::write_tables(int npts)
	{
	char tag[6] = "";
	if (comm->me != 0) sprintf(tag,"%d",comm->me);
	FILE* fp = NULL;
	double xmin,xmax,x,uf,vf,wf,pf,gf,ff,ufp,vfp,wfp,pfp,gfp,ffp;
	char line[MAXLINE];
	for (int i = 0; i < nelements; i++) {
	for (int j = 0; j < nelements; j++) {
	strcpy(line,elements[i]);
	strcat(line,elements[j]);
	strcat(line,"_UVW");
	strcat(line,tag);
	fp = fopen(line, "w");
	int iparam_ij = elem2param[i][j];
	PairParameters & pair = pairParameters[iparam_ij];
	xmin = (pair.U)->get_xmin();
	xmax = (pair.U)->get_xmax();
	double xl = xmax - xmin;
	xmin = xmin - 0.5*xl;
	xmax = xmax + 0.5*xl;
	for (int k = 0; k < npts; k++) {
	x = xmin + (xmax-xmin) * k / (npts-1);
	(pair.U)->value(x, uf, 1, ufp, 1);
	(pair.V)->value(x, vf, 1, vfp, 1);
	(pair.W)->value(x, wf, 1, wfp, 1);
	fprintf(fp,"%12.4f %12.4f %12.4f %12.4f %12.4f %12.4f %12.4f \n",x,uf,vf,wf,ufp,vfp,wfp);
	}
	fclose(fp);
	}
	}
	for (int i = 0; i < nelements; i++) {
	for (int j = 0; j < nelements; j++) {
	strcpy(line,elements[i]);
	strcat(line,elements[j]);
	strcat(line,"_P");
	strcat(line,tag);
	fp = fopen(line, "w");
	int iparam_ij = elem2param[i][j];
	PairParameters & pair = pairParameters[iparam_ij];
	xmin = (pair.P)->get_xmin();
	xmax = (pair.P)->get_xmax();
	double xl = xmax - xmin;
	xmin = xmin - 0.5*xl;
	xmax = xmax + 0.5*xl;
	for (int k = 0; k < npts; k++) {
	x = xmin + (xmax-xmin) * k / (npts-1);
	(pair.P)->value(x, pf, 1, pfp, 1);
	fprintf(fp,"%12.4f %12.4f %12.4f \n",x,pf,pfp);
	}
	fclose(fp);
	}
	}
	for (int i = 0; i < nelements; i++) {
	for (int j = 0; j < nelements; j++) {
	for (int k = 0; k < nelements; k++) {
	strcpy(line,elements[i]);
	strcat(line,elements[j]);
	strcat(line,elements[k]);
	strcat(line,"_G");
	strcat(line,tag);
	fp = fopen(line, "w");
	int iparam_ij = elem3param[i][j][k];
	TripletParameters & pair = tripletParameters[iparam_ij];
	xmin = (pair.G)->get_xmin();
	xmax = (pair.G)->get_xmax();
	for (int n = 0; n < npts; n++) {
	x = xmin + (xmax-xmin) * n / (npts-1);
	(pair.G)->value(x, gf, 1, gfp, 1);
	fprintf(fp,"%12.4f %12.4f %12.4f \n",x,gf,gfp);
	}
	fclose(fp);
	}
	}
	}
	for (int i = 0; i < nelements; i++) {
	for (int j = 0; j < nelements; j++) {
	strcpy(line,elements[i]);
	strcat(line,elements[j]);
	strcat(line,"_F");
	strcat(line,tag);
	fp = fopen(line, "w");
	int iparam_ij = elem2param[i][j];
	PairParameters & pair = pairParameters[iparam_ij];
	xmin = (pair.F)->get_xmin();
	xmax = (pair.F)->get_xmax();
	double xl = xmax - xmin;
	xmin = xmin - 0.5*xl;
	xmax = xmax + 0.5*xl;
	for (int k = 0; k < npts; k++) {
	x = xmin + (xmax-xmin) * k / (npts-1);
	(pair.F)->value(x, ff, 1, ffp, 1);
	fprintf(fp,"%12.4f %12.4f %12.4f \n",x,ff,ffp);
	}
	fclose(fp);
	}
	}

	}

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