pair_nb3b_harmonic.cpp
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Created: Thu, Nov 7, 21:49

pair_nb3b_harmonic.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: Todd R. Zeitler (SNL)
	(based on Stillinger-Weber pair style)
	------------------------------------------------------------------------- */

	#include "math.h"
	#include "stdio.h"
	#include "stdlib.h"
	#include "string.h"
	#include "pair_nb3b_harmonic.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
	#define SMALL 0.001
	#define PI 3.141592653589793238462643383279

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

	PairNb3bHarmonic::PairNb3bHarmonic(LAMMPS *lmp) : Pair(lmp)
	{
	single_enable = 0;
	one_coeff = 1;
	manybody_flag = 1;

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

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

	PairNb3bHarmonic::~PairNb3bHarmonic()
	{
	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);
	delete [] map;
	}
	}

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

	void PairNb3bHarmonic::compute(int eflag, int vflag)
	{
	int i,j,k,ii,jj,kk,inum,jnum,jnumm1;
	int itype,jtype,ktype,ijparam,ikparam,ijkparam;
	double xtmp,ytmp,ztmp,evdwl;
	double 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;
	int *type = atom->type;

	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];
	itype = map[type[i]];
	xtmp = x[i][0];
	ytmp = x[i][1];
	ztmp = x[i][2];

	jlist = firstneigh[i];
	jnum = numneigh[i];
	jnumm1 = jnum - 1;

	for (jj = 0; jj < jnumm1; jj++) {
	j = jlist[jj];
	j &= NEIGHMASK;
	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];
	if (rsq1 > params[ijparam].cutsq) continue;

	for (kk = jj+1; kk < jnum; kk++) {
	k = jlist[kk];
	k &= NEIGHMASK;
	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];
	if (rsq2 > params[ikparam].cutsq) continue;

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

	f[i][0] -= fj[0] + fk[0];
	f[i][1] -= fj[1] + fk[1];
	f[i][2] -= fj[2] + fk[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 (evflag) ev_tally3(i,j,k,evdwl,0.0,fj,fk,delr1,delr2);
	}
	}
	}

	if (vflag_fdotr) virial_fdotr_compute();
	}

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

	void PairNb3bHarmonic::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];
	}

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

	void PairNb3bHarmonic::settings(int narg, char **arg)
	{
	if (narg != 0) error->all(FLERR,"Illegal pair_style command");
	}

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

	void PairNb3bHarmonic::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();

	// 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 PairNb3bHarmonic::init_style()
	{
	if (atom->tag_enable == 0)
	error->all(FLERR,"Pair style nb3b/harmonic requires atom IDs");
	if (force->newton_pair == 0)
	error->all(FLERR,"Pair style nb3b/harmonic 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 PairNb3bHarmonic::init_one(int i, int j)
	{
	if (setflag[i][j] == 0) error->all(FLERR,"All pair coeffs are not set");

	return cutmax;
	}

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

	void PairNb3bHarmonic::read_file(char *file)
	{
	int params_per_line = 6;
	char *words = new char[params_per_line+1];

	memory->sfree(params);
	params = NULL;
	nparams = maxparam = 0;

	// 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 nb3b/harmonic 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 nb3b/harmonic 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].k_theta = atof(words[3]);
	params[nparams].theta0 = atof(words[4]);
	params[nparams].cutoff = atof(words[5]);

	if (params[nparams].k_theta < 0.0 \|\| params[nparams].theta0 < 0.0 \|\|
	params[nparams].cutoff < 0.0)
	error->all(FLERR,"Illegal nb3b/harmonic parameter");

	nparams++;
	}

	delete [] words;
	}

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

	void PairNb3bHarmonic::setup()
	{
	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].cutoff;
	params[m].cutsq = params[m].cut * params[m].cut;

	params[m].theta0 = params[m].theta0 / 180.0 * PI;

	}

	// 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 PairNb3bHarmonic::threebody(Param paramij, Param paramik,
	Param *paramijk,
	double rsq1, double rsq2,
	double delr1, double delr2,
	double fj, double fk, int eflag, double &eng)
	{
	double dtheta,tk;
	double r1,r2,c,s,a,a11,a12,a22;

	// angle (cos and sin)

	r1 = sqrt(rsq1);
	r2 = sqrt(rsq2);

	c = delr1[0]delr2[0] + delr1[1]delr2[1] + delr1[2]*delr2[2];
	c /= r1*r2;

	if (c > 1.0) c = 1.0;
	if (c < -1.0) c = -1.0;

	s = sqrt(1.0 - c*c);
	if (s < SMALL) s = SMALL;
	s = 1.0/s;

	// force & energy

	dtheta = acos(c) - paramijk->theta0;
	tk = paramijk->k_theta * dtheta;

	if (eflag) eng = tk*dtheta;

	a = -2.0 * tk * s;
	a11 = a*c / rsq1;
	a12 = -a / (r1*r2);
	a22 = a*c / rsq2;

	fj[0] = a11delr1[0] + a12delr2[0];
	fj[1] = a11delr1[1] + a12delr2[1];
	fj[2] = a11delr1[2] + a12delr2[2];
	fk[0] = a22delr2[0] + a12delr1[0];
	fk[1] = a22delr2[1] + a12delr1[1];
	fk[2] = a22delr2[2] + a12delr1[2];
	}

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