Diffusion lammps (efficient_neuronet) Browse

pair_tersoff_table.cpp
4a975dd8cf07efficient_neuronet

pair_tersoff_table.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: Luca Ferraro (CASPUR)
			email: luca.ferraro@caspur.it

			Tersoff Potential
			References: (referenced as tersoff_2 functional form in LAMMPS manual)
			1) Tersoff, Phys. Rev. B 39, 5566 (1988)
			------------------------------------------------------------------------- */

			#include "math.h"
			#include "stdio.h"
			#include "stdlib.h"
			#include "string.h"
			#include "pair_tersoff_table.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"

			using namespace LAMMPS_NS;

			#define MAXLINE 1024
			#define DELTA 4

			#define GRIDSTART 0.1
			#define GRIDDENSITY_FCUTOFF 5000
			#define GRIDDENSITY_EXP 12000
			#define GRIDDENSITY_GTETA 12000
			#define GRIDDENSITY_BIJ 7500

			// max number of interaction per atom for environment potential

			#define leadingDimensionInteractionList 64

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

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

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

			preGtetaFunction = preGtetaFunctionDerived = NULL;
			preCutoffFunction = preCutoffFunctionDerived = NULL;
			}

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

			PairTersoffTable::~PairTersoffTable()
			{
			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;

			deallocateGrids();
			deallocatePreLoops();
			}
			}

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

			void PairTersoffTable::compute(int eflag, int vflag)
			{
			int i,j,k,ii,inum,jnum;
			int itype,jtype,ktype,ijparam,ikparam,ijkparam;
			double xtmp,ytmp,ztmp;
			double fxtmp,fytmp,fztmp;
			int ilist,jlist,numneigh,*firstneigh;


			int interpolIDX;
			double directorCos_ij_x, directorCos_ij_y, directorCos_ij_z, directorCos_ik_x, directorCos_ik_y, directorCos_ik_z;
			double invR_ij, invR_ik, cosTeta;
			double repulsivePotential, attractivePotential;
			double exponentRepulsivePotential, exponentAttractivePotential,interpolTMP,interpolDeltaX,interpolY1;
			double interpolY2, cutoffFunctionIJ, attractiveExponential, repulsiveExponential, cutoffFunctionDerivedIJ,zeta;
			double gtetaFunctionIJK,gtetaFunctionDerivedIJK,cutoffFunctionIK;
			double cutoffFunctionDerivedIK,factor_force3_ij,factor_1_force3_ik;
			double factor_2_force3_ik,betaZetaPowerIJK,betaZetaPowerDerivedIJK,factor_force_tot;
			double factor_force_ij;
			double gtetaFunctionDerived_temp,gtetaFunction_temp;

			double 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;
			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];
			itype = map[type[i]];
			xtmp = x[i][0];
			ytmp = x[i][1];
			ztmp = x[i][2];
			fxtmp = fytmp = fztmp = 0.0;

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

			if (jnum > leadingDimensionInteractionList) {
			char errmsg[256];
			sprintf(errmsg,"Too many neighbors for interaction list: %d vs %d.\n"
			"Check your system or increase 'leadingDimensionInteractionList'",
			jnum, leadingDimensionInteractionList);
			error->one(FLERR,errmsg);
			}

			// Pre-calculate gteta and cutoff function
			for (int neighbor_j = 0; neighbor_j < jnum; neighbor_j++) {

			double dr_ij[3], r_ij;

			j = jlist[neighbor_j];
			j &= NEIGHMASK;

			dr_ij[0] = xtmp - x[j][0];
			dr_ij[1] = ytmp - x[j][1];
			dr_ij[2] = ztmp - x[j][2];
			r_ij = dr_ij[0]dr_ij[0] + dr_ij[1]dr_ij[1] + dr_ij[2]*dr_ij[2];

			jtype = map[type[j]];
			ijparam = elem2param[itype][jtype][jtype];

			if (r_ij > params[ijparam].cutsq) continue;

			r_ij = sqrt(r_ij);

			invR_ij = 1.0 / r_ij;

			directorCos_ij_x = invR_ij * dr_ij[0];
			directorCos_ij_y = invR_ij * dr_ij[1];
			directorCos_ij_z = invR_ij * dr_ij[2];

			// preCutoffFunction
			interpolDeltaX = r_ij - GRIDSTART;
			interpolTMP = (interpolDeltaX * GRIDDENSITY_FCUTOFF);
			interpolIDX = (int) interpolTMP;
			interpolY1 = cutoffFunction[itype][jtype][interpolIDX];
			interpolY2 = cutoffFunction[itype][jtype][interpolIDX+1];
			preCutoffFunction[neighbor_j] = interpolY1 + (interpolY2 - interpolY1) * (interpolTMP - interpolIDX);
			// preCutoffFunctionDerived
			interpolY1 = cutoffFunctionDerived[itype][jtype][interpolIDX];
			interpolY2 = cutoffFunctionDerived[itype][jtype][interpolIDX+1];
			preCutoffFunctionDerived[neighbor_j] = interpolY1 + (interpolY2 - interpolY1) * (interpolTMP - interpolIDX);


			for (int neighbor_k = neighbor_j + 1; neighbor_k < jnum; neighbor_k++) {
			double dr_ik[3], r_ik;

			k = jlist[neighbor_k];
			k &= NEIGHMASK;
			ktype = map[type[k]];
			ikparam = elem2param[itype][ktype][ktype];
			ijkparam = elem2param[itype][jtype][ktype];

			dr_ik[0] = xtmp -x[k][0];
			dr_ik[1] = ytmp -x[k][1];
			dr_ik[2] = ztmp -x[k][2];
			r_ik = dr_ik[0]dr_ik[0] + dr_ik[1]dr_ik[1] + dr_ik[2]*dr_ik[2];

			if (r_ik > params[ikparam].cutsq) continue;

			r_ik = sqrt(r_ik);

			invR_ik = 1.0 / r_ik;

			directorCos_ik_x = invR_ik * dr_ik[0];
			directorCos_ik_y = invR_ik * dr_ik[1];
			directorCos_ik_z = invR_ik * dr_ik[2];

			cosTeta = directorCos_ij_x * directorCos_ik_x + directorCos_ij_y * directorCos_ik_y + directorCos_ij_z * directorCos_ik_z;

			// preGtetaFunction
			interpolDeltaX=cosTeta+1.0;
			interpolTMP = (interpolDeltaX * GRIDDENSITY_GTETA);
			interpolIDX = (int) interpolTMP;
			interpolY1 = gtetaFunction[itype][interpolIDX];
			interpolY2 = gtetaFunction[itype][interpolIDX+1];
			gtetaFunction_temp = interpolY1 + (interpolY2 - interpolY1) * (interpolTMP - interpolIDX);
			// preGtetaFunctionDerived
			interpolY1 = gtetaFunctionDerived[itype][interpolIDX];
			interpolY2 = gtetaFunctionDerived[itype][interpolIDX+1];
			gtetaFunctionDerived_temp = interpolY1 + (interpolY2 - interpolY1) * (interpolTMP - interpolIDX);

			preGtetaFunction[neighbor_j][neighbor_k]=params[ijkparam].gamma*gtetaFunction_temp;
			preGtetaFunctionDerived[neighbor_j][neighbor_k]=params[ijkparam].gamma*gtetaFunctionDerived_temp;
			preGtetaFunction[neighbor_k][neighbor_j]=params[ijkparam].gamma*gtetaFunction_temp;
			preGtetaFunctionDerived[neighbor_k][neighbor_j]=params[ijkparam].gamma*gtetaFunctionDerived_temp;

			} // loop on K

			} // loop on J


			// loop over neighbors of atom i
			for (int neighbor_j = 0; neighbor_j < jnum; neighbor_j++) {

			double dr_ij[3], r_ij, f_ij[3];

			j = jlist[neighbor_j];
			j &= NEIGHMASK;

			dr_ij[0] = xtmp - x[j][0];
			dr_ij[1] = ytmp - x[j][1];
			dr_ij[2] = ztmp - x[j][2];
			r_ij = dr_ij[0]dr_ij[0] + dr_ij[1]dr_ij[1] + dr_ij[2]*dr_ij[2];

			jtype = map[type[j]];
			ijparam = elem2param[itype][jtype][jtype];

			if (r_ij > params[ijparam].cutsq) continue;

			r_ij = sqrt(r_ij);
			invR_ij = 1.0 / r_ij;

			directorCos_ij_x = invR_ij * dr_ij[0];
			directorCos_ij_y = invR_ij * dr_ij[1];
			directorCos_ij_z = invR_ij * dr_ij[2];

			exponentRepulsivePotential = params[ijparam].lam1 * r_ij;
			exponentAttractivePotential = params[ijparam].lam2 * r_ij;

			// repulsiveExponential
			interpolDeltaX = exponentRepulsivePotential - minArgumentExponential;
			interpolTMP = (interpolDeltaX * GRIDDENSITY_EXP);
			interpolIDX = (int) interpolTMP;
			interpolY1 = exponential[interpolIDX];
			interpolY2 = exponential[interpolIDX+1];
			repulsiveExponential = interpolY1 + (interpolY2 - interpolY1) * (interpolTMP - interpolIDX);
			// attractiveExponential
			interpolDeltaX = exponentAttractivePotential - minArgumentExponential;
			interpolTMP = (interpolDeltaX * GRIDDENSITY_EXP);
			interpolIDX = (int) interpolTMP;
			interpolY1 = exponential[interpolIDX];
			interpolY2 = exponential[interpolIDX+1];
			attractiveExponential = interpolY1 + (interpolY2 - interpolY1) * (interpolTMP - interpolIDX);

			repulsivePotential = params[ijparam].biga * repulsiveExponential;
			attractivePotential = -params[ijparam].bigb * attractiveExponential;

			cutoffFunctionIJ = preCutoffFunction[neighbor_j];
			cutoffFunctionDerivedIJ = preCutoffFunctionDerived[neighbor_j];

			zeta = 0.0;

			// first loop over neighbors of atom i except j - part 1/2
			for (int neighbor_k = 0; neighbor_k < neighbor_j; neighbor_k++) {
			double dr_ik[3], r_ik;

			k = jlist[neighbor_k];
			k &= NEIGHMASK;
			ktype = map[type[k]];
			ikparam = elem2param[itype][ktype][ktype];
			ijkparam = elem2param[itype][jtype][ktype];

			dr_ik[0] = xtmp -x[k][0];
			dr_ik[1] = ytmp -x[k][1];
			dr_ik[2] = ztmp -x[k][2];
			r_ik = dr_ik[0]dr_ik[0] + dr_ik[1]dr_ik[1] + dr_ik[2]*dr_ik[2];

			if (r_ik > params[ikparam].cutsq) continue;

			r_ik = sqrt(r_ik);

			invR_ik = 1.0 / r_ik;

			gtetaFunctionIJK = preGtetaFunction[neighbor_j][neighbor_k];

			cutoffFunctionIK = preCutoffFunction[neighbor_k];

			zeta += cutoffFunctionIK * gtetaFunctionIJK;

			}

			// first loop over neighbors of atom i except j - part 2/2
			for (int neighbor_k = neighbor_j+1; neighbor_k < jnum; neighbor_k++) {
			double dr_ik[3], r_ik;

			k = jlist[neighbor_k];
			k &= NEIGHMASK;
			ktype = map[type[k]];
			ikparam = elem2param[itype][ktype][ktype];
			ijkparam = elem2param[itype][jtype][ktype];

			dr_ik[0] = xtmp -x[k][0];
			dr_ik[1] = ytmp -x[k][1];
			dr_ik[2] = ztmp -x[k][2];
			r_ik = dr_ik[0]dr_ik[0] + dr_ik[1]dr_ik[1] + dr_ik[2]*dr_ik[2];

			if (r_ik > params[ikparam].cutsq) continue;

			r_ik = sqrt(r_ik);
			invR_ik = 1.0 / r_ik;

			directorCos_ik_x = invR_ik * dr_ik[0];
			directorCos_ik_y = invR_ik * dr_ik[1];
			directorCos_ik_z = invR_ik * dr_ik[2];

			gtetaFunctionIJK = preGtetaFunction[neighbor_j][neighbor_k];

			cutoffFunctionIK = preCutoffFunction[neighbor_k];

			zeta += cutoffFunctionIK * gtetaFunctionIJK;
			}

			// betaZetaPowerIJK
			interpolDeltaX= params[ijparam].beta * zeta;
			interpolTMP = (interpolDeltaX * GRIDDENSITY_BIJ);
			interpolIDX = (int) interpolTMP;
			interpolY1 = betaZetaPower[itype][interpolIDX];
			interpolY2 = betaZetaPower[itype][interpolIDX+1];
			betaZetaPowerIJK = (interpolY1 + (interpolY2 - interpolY1) * (interpolTMP - interpolIDX));
			// betaZetaPowerDerivedIJK
			interpolY1 = betaZetaPowerDerived[itype][interpolIDX];
			interpolY2 = betaZetaPowerDerived[itype][interpolIDX+1];
			betaZetaPowerDerivedIJK = params[ijparam].beta(interpolY1 + (interpolY2 - interpolY1) (interpolTMP - interpolIDX));

			// Forces and virial
			factor_force_ij = 0.5cutoffFunctionDerivedIJ(repulsivePotential + attractivePotential * betaZetaPowerIJK)+0.5cutoffFunctionIJ(-repulsivePotentialparams[ijparam].lam1-betaZetaPowerIJKattractivePotential*params[ijparam].lam2);

			f_ij[0] = factor_force_ij * directorCos_ij_x;
			f_ij[1] = factor_force_ij * directorCos_ij_y;
			f_ij[2] = factor_force_ij * directorCos_ij_z;

			f[j][0] += f_ij[0];
			f[j][1] += f_ij[1];
			f[j][2] += f_ij[2];

			fxtmp -= f_ij[0];
			fytmp -= f_ij[1];
			fztmp -= f_ij[2];

			// potential energy
			evdwl = cutoffFunctionIJ * repulsivePotential + cutoffFunctionIJ * attractivePotential * betaZetaPowerIJK;

			if (evflag) ev_tally(i, j, nlocal, newton_pair, 0.5 * evdwl, 0.0,
			-factor_force_ij*invR_ij, dr_ij[0], dr_ij[1], dr_ij[2]);

			factor_force_tot= 0.5cutoffFunctionIJattractivePotential*betaZetaPowerDerivedIJK;

			// second loop over neighbors of atom i except j, forces and virial only - part 1/2
			for (int neighbor_k = 0; neighbor_k < neighbor_j; neighbor_k++) {
			double dr_ik[3], r_ik, f_ik[3];

			k = jlist[neighbor_k];
			k &= NEIGHMASK;
			ktype = map[type[k]];
			ikparam = elem2param[itype][ktype][ktype];
			ijkparam = elem2param[itype][jtype][ktype];

			dr_ik[0] = xtmp -x[k][0];
			dr_ik[1] = ytmp -x[k][1];
			dr_ik[2] = ztmp -x[k][2];
			r_ik = dr_ik[0]dr_ik[0] + dr_ik[1]dr_ik[1] + dr_ik[2]*dr_ik[2];

			if (r_ik > params[ikparam].cutsq) continue;

			r_ik = sqrt(r_ik);
			invR_ik = 1.0 / r_ik;

			directorCos_ik_x = invR_ik * dr_ik[0];
			directorCos_ik_y = invR_ik * dr_ik[1];
			directorCos_ik_z = invR_ik * dr_ik[2];

			cosTeta = directorCos_ij_x * directorCos_ik_x + directorCos_ij_y * directorCos_ik_y + directorCos_ij_z * directorCos_ik_z;

			gtetaFunctionIJK = preGtetaFunction[neighbor_j][neighbor_k];

			gtetaFunctionDerivedIJK = preGtetaFunctionDerived[neighbor_j][neighbor_k];

			cutoffFunctionIK = preCutoffFunction[neighbor_k];

			cutoffFunctionDerivedIK = preCutoffFunctionDerived[neighbor_k];

			factor_force3_ij= cutoffFunctionIK * gtetaFunctionDerivedIJK * invR_ij *factor_force_tot;

			f_ij[0] = factor_force3_ij * (directorCos_ij_x*cosTeta - directorCos_ik_x);
			f_ij[1] = factor_force3_ij * (directorCos_ij_y*cosTeta - directorCos_ik_y);
			f_ij[2] = factor_force3_ij * (directorCos_ij_z*cosTeta - directorCos_ik_z);

			factor_1_force3_ik = (cutoffFunctionIK * gtetaFunctionDerivedIJK * invR_ik)*factor_force_tot;
			factor_2_force3_ik = -(cutoffFunctionDerivedIK * gtetaFunctionIJK)*factor_force_tot;

			f_ik[0] = factor_1_force3_ik * (directorCos_ik_xcosTeta - directorCos_ij_x) + factor_2_force3_ik directorCos_ik_x;
			f_ik[1] = factor_1_force3_ik * (directorCos_ik_ycosTeta - directorCos_ij_y) + factor_2_force3_ik directorCos_ik_y;
			f_ik[2] = factor_1_force3_ik * (directorCos_ik_zcosTeta - directorCos_ij_z) + factor_2_force3_ik directorCos_ik_z;

			f[j][0] -= f_ij[0];
			f[j][1] -= f_ij[1];
			f[j][2] -= f_ij[2];

			f[k][0] -= f_ik[0];
			f[k][1] -= f_ik[1];
			f[k][2] -= f_ik[2];

			fxtmp += f_ij[0] + f_ik[0];
			fytmp += f_ij[1] + f_ik[1];
			fztmp += f_ij[2] + f_ik[2];

			// potential energy
			evdwl = 0.0;

			if (evflag) ev_tally3(i,j,k,evdwl,0.0,f_ij,f_ik,dr_ij,dr_ik);
			}

			// second loop over neighbors of atom i except j, forces and virial only - part 2/2
			for (int neighbor_k = neighbor_j+1; neighbor_k < jnum; neighbor_k++) {
			double dr_ik[3], r_ik, f_ik[3];

			k = jlist[neighbor_k];
			k &= NEIGHMASK;
			ktype = map[type[k]];
			ikparam = elem2param[itype][ktype][ktype];
			ijkparam = elem2param[itype][jtype][ktype];

			dr_ik[0] = xtmp -x[k][0];
			dr_ik[1] = ytmp -x[k][1];
			dr_ik[2] = ztmp -x[k][2];
			r_ik = dr_ik[0]dr_ik[0] + dr_ik[1]dr_ik[1] + dr_ik[2]*dr_ik[2];

			if (r_ik > params[ikparam].cutsq) continue;

			r_ik = sqrt(r_ik);
			invR_ik = 1.0 / r_ik;

			directorCos_ik_x = invR_ik * dr_ik[0];
			directorCos_ik_y = invR_ik * dr_ik[1];
			directorCos_ik_z = invR_ik * dr_ik[2];

			cosTeta = directorCos_ij_x * directorCos_ik_x + directorCos_ij_y * directorCos_ik_y + directorCos_ij_z * directorCos_ik_z;

			gtetaFunctionIJK = preGtetaFunction[neighbor_j][neighbor_k];

			gtetaFunctionDerivedIJK = preGtetaFunctionDerived[neighbor_j][neighbor_k];

			cutoffFunctionIK = preCutoffFunction[neighbor_k];

			cutoffFunctionDerivedIK = preCutoffFunctionDerived[neighbor_k];

			factor_force3_ij= cutoffFunctionIK * gtetaFunctionDerivedIJK * invR_ij *factor_force_tot;

			f_ij[0] = factor_force3_ij * (directorCos_ij_x*cosTeta - directorCos_ik_x);
			f_ij[1] = factor_force3_ij * (directorCos_ij_y*cosTeta - directorCos_ik_y);
			f_ij[2] = factor_force3_ij * (directorCos_ij_z*cosTeta - directorCos_ik_z);

			factor_1_force3_ik = (cutoffFunctionIK * gtetaFunctionDerivedIJK * invR_ik)*factor_force_tot;
			factor_2_force3_ik = -(cutoffFunctionDerivedIK * gtetaFunctionIJK)*factor_force_tot;

			f_ik[0] = factor_1_force3_ik * (directorCos_ik_xcosTeta - directorCos_ij_x) + factor_2_force3_ik directorCos_ik_x;
			f_ik[1] = factor_1_force3_ik * (directorCos_ik_ycosTeta - directorCos_ij_y) + factor_2_force3_ik directorCos_ik_y;
			f_ik[2] = factor_1_force3_ik * (directorCos_ik_zcosTeta - directorCos_ij_z) + factor_2_force3_ik directorCos_ik_z;

			f[j][0] -= f_ij[0];
			f[j][1] -= f_ij[1];
			f[j][2] -= f_ij[2];

			f[k][0] -= f_ik[0];
			f[k][1] -= f_ik[1];
			f[k][2] -= f_ik[2];

			fxtmp += f_ij[0] + f_ik[0];
			fytmp += f_ij[1] + f_ik[1];
			fztmp += f_ij[2] + f_ik[2];

			// potential energy
			evdwl = 0.0;

			if (evflag) ev_tally3(i,j,k,evdwl,0.0,f_ij,f_ik,dr_ij,dr_ik);

			}
			} // loop on J
			f[i][0] += fxtmp;
			f[i][1] += fytmp;
			f[i][2] += fztmp;
			} // loop on I

			if (vflag_fdotr) virial_fdotr_compute();
			}

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

			void PairTersoffTable::deallocatePreLoops(void)
			{
			memory->destroy(preGtetaFunction);
			memory->destroy(preGtetaFunctionDerived);
			memory->destroy(preCutoffFunction);
			memory->destroy(preCutoffFunctionDerived);
			}

			void PairTersoffTable::allocatePreLoops(void)
			{
			memory->create(preGtetaFunction,leadingDimensionInteractionList,leadingDimensionInteractionList,"tersofftable:preGtetaFunction");

			memory->create(preGtetaFunctionDerived,leadingDimensionInteractionList,leadingDimensionInteractionList,"tersofftable:preGtetaFunctionDerived");

			memory->create(preCutoffFunction,leadingDimensionInteractionList,"tersofftable:preCutoffFunction");

			memory->create(preCutoffFunctionDerived,leadingDimensionInteractionList,"tersofftable:preCutoffFunctionDerived");
			}

			void PairTersoffTable::deallocateGrids()
			{
			memory->destroy(exponential);
			memory->destroy(gtetaFunction);
			memory->destroy(gtetaFunctionDerived);
			memory->destroy(cutoffFunction);
			memory->destroy(cutoffFunctionDerived);
			memory->destroy(betaZetaPower);
			memory->destroy(betaZetaPowerDerived);
			}

			void PairTersoffTable::allocateGrids(void)
			{
			int i, j, l;

			int numGridPointsExponential, numGridPointsGtetaFunction, numGridPointsOneCutoffFunction;
			int numGridPointsNotOneCutoffFunction, numGridPointsCutoffFunction, numGridPointsBetaZetaPower;
			// double minArgumentExponential;
			double deltaArgumentCutoffFunction, deltaArgumentExponential, deltaArgumentBetaZetaPower;
			double deltaArgumentGtetaFunction;
			double r, minMu, maxLambda, maxCutoff;
			double const PI=acos(-1.0);

			// exponential

			// find min and max argument
			minMu=params[0].lam2;
			maxLambda=params[0].lam1;
			for (i=1; i<nparams; i++) {
			if (params[i].lam2 < minMu) minMu = params[i].lam2;
			if (params[i].lam1 > maxLambda) maxLambda = params[i].lam1;
			}
			maxCutoff=cutmax;

			minArgumentExponential=minMu*GRIDSTART;

			numGridPointsExponential=(int)((maxLambdamaxCutoff-minArgumentExponential)GRIDDENSITY_EXP)+2;

			memory->create(exponential,numGridPointsExponential,"tersofftable:exponential");

			r = minArgumentExponential;
			deltaArgumentExponential = 1.0 / GRIDDENSITY_EXP;
			for (i = 0; i < numGridPointsExponential; i++)
			{
			exponential[i] = exp(-r);
			r += deltaArgumentExponential;
			}


			// gtetaFunction

			numGridPointsGtetaFunction=(int)(2.0*GRIDDENSITY_GTETA)+2;

			memory->create(gtetaFunction,nelements,numGridPointsGtetaFunction,"tersofftable:gtetaFunction");
			memory->create(gtetaFunctionDerived,nelements,numGridPointsGtetaFunction,"tersofftable:gtetaFunctionDerived");

			r = minArgumentExponential;
			for (i=0; i<nelements; i++) {
			r = -1.0;
			deltaArgumentGtetaFunction = 1.0 / GRIDDENSITY_GTETA;

			int iparam = elem2param[i][i][i];
			double c = params[iparam].c;
			double d = params[iparam].d;
			double h = params[iparam].h;

			for (j = 0; j < numGridPointsGtetaFunction; j++) {
			gtetaFunction[i][j]=1.0+(cc)/(dd)-(cc)/(dd+(h-r)*(h-r));
			gtetaFunctionDerived[i][j]= -2.0 * c * c * (h-r) / ((dd+(h-r)(h-r))(dd+(h-r)*(h-r)));
			r += deltaArgumentGtetaFunction;
			}
			}


			// cutoffFunction, zetaFunction, find grids.

			int ngrid_max = -1;
			int zeta_max = -1;

			for (i=0; i<nelements; i++) {

			int iparam = elem2param[i][i][i];
			double c = params[iparam].c;
			double d = params[iparam].d;
			double beta = params[iparam].beta;

			numGridPointsBetaZetaPower=(int)(((1.0+(cc)/(dd)-(cc)/(dd+4))betaleadingDimensionInteractionList*GRIDDENSITY_BIJ))+2;
			zeta_max = MAX(zeta_max,numGridPointsBetaZetaPower);

			for (j=0; j<nelements; j++) {
			for (j=0; j<nelements; j++) {

			int ijparam = elem2param[i][j][j];
			double cutoffR = params[ijparam].cutoffR;
			double cutoffS = params[ijparam].cutoffS;

			numGridPointsOneCutoffFunction=(int) ((cutoffR-GRIDSTART)*GRIDDENSITY_FCUTOFF)+1;
			numGridPointsNotOneCutoffFunction=(int) ((cutoffS-cutoffR)*GRIDDENSITY_FCUTOFF)+2;
			numGridPointsCutoffFunction=numGridPointsOneCutoffFunction+numGridPointsNotOneCutoffFunction;

			ngrid_max = MAX(ngrid_max,numGridPointsCutoffFunction);
			}
			}
			}

			memory->create(cutoffFunction,nelements,nelements,ngrid_max,"tersoff:cutfunc");
			memory->create(cutoffFunctionDerived,nelements,nelements,ngrid_max,"tersoff:cutfuncD");

			// cutoffFunction, compute.

			for (i=0; i<nelements; i++) {
			for (j=0; j<nelements; j++) {
			for (j=0; j<nelements; j++) {
			int ijparam = elem2param[i][j][j];
			double cutoffR = params[ijparam].cutoffR;
			double cutoffS = params[ijparam].cutoffS;

			numGridPointsOneCutoffFunction=(int) ((cutoffR-GRIDSTART)*GRIDDENSITY_FCUTOFF)+1;
			numGridPointsNotOneCutoffFunction=(int) ((cutoffS-cutoffR)*GRIDDENSITY_FCUTOFF)+2;
			numGridPointsCutoffFunction=numGridPointsOneCutoffFunction+numGridPointsNotOneCutoffFunction;

			r = GRIDSTART;
			deltaArgumentCutoffFunction = 1.0 / GRIDDENSITY_FCUTOFF;

			for (l = 0; l < numGridPointsOneCutoffFunction; l++) {
			cutoffFunction[i][j][l] = 1.0;
			cutoffFunctionDerived[i][j][l]=0.0;
			r += deltaArgumentCutoffFunction;
			}

			for (l = numGridPointsOneCutoffFunction; l < numGridPointsCutoffFunction; l++) {
			cutoffFunction[i][j][l] = 0.5 + 0.5 * cos (PI * (r - cutoffR)/(cutoffS-cutoffR)) ;
			cutoffFunctionDerived[i][j][l] = -0.5 * PI * sin (PI * (r - cutoffR)/(cutoffS-cutoffR)) / (cutoffS-cutoffR) ;
			r += deltaArgumentCutoffFunction;
			}
			}
			}
			}

			// betaZetaPower, compute

			memory->create(betaZetaPower,nelements,zeta_max,"tersoff:zetafunc");
			memory->create(betaZetaPowerDerived,nelements,zeta_max,"tersoff:zetafuncD");

			for (i=0; i<nelements; i++) {

			int iparam = elem2param[i][i][i];
			double c = params[iparam].c;
			double d = params[iparam].d;
			double beta = params[iparam].beta;

			numGridPointsBetaZetaPower=(int)(((1.0+(cc)/(dd)-(cc)/(dd+4))betaleadingDimensionInteractionList*GRIDDENSITY_BIJ))+2;

			r=0.0;
			deltaArgumentBetaZetaPower = 1.0 / GRIDDENSITY_BIJ;

			betaZetaPower[i][0]=1.0;

			r += deltaArgumentBetaZetaPower;

			for (j = 1; j < numGridPointsBetaZetaPower; j++) {
			double powern=params[iparam].powern;
			betaZetaPower[i][j]=pow((1+pow(r,powern)),-1/(2*powern));
			betaZetaPowerDerived[i][j]=-0.5pow(r,powern-1.0)pow((1+pow(r,powern)),-1/(2*powern)-1) ;
			r += deltaArgumentBetaZetaPower;
			}
			betaZetaPowerDerived[i][0]=(betaZetaPower[i][1]-1.0)*GRIDDENSITY_BIJ;
			}
			}

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

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

			void PairTersoffTable::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");

			// allocate tables and internal structures
			allocatePreLoops();
			allocateGrids();
			}

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

			void PairTersoffTable::init_style()
			{
			if (force->newton_pair == 0)
			error->all(FLERR,"Pair style Tersoff 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 PairTersoffTable::init_one(int i, int j)
			{
			if (setflag[i][j] == 0) error->all(FLERR,"All pair coeffs are not set");

			return cutmax;
			}

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

			void PairTersoffTable::read_file(char *file)
			{
			int params_per_line = 17;
			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 Tersoff 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 Tersoff 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].powerm = atof(words[3]); // not used (only tersoff_2 is implemented)
			params[nparams].gamma = atof(words[4]); // not used (only tersoff_2 is implemented)
			params[nparams].lam3 = atof(words[5]); // not used (only tersoff_2 is implemented)
			params[nparams].c = atof(words[6]);
			params[nparams].d = atof(words[7]);
			params[nparams].h = atof(words[8]);
			params[nparams].powern = atof(words[9]);
			params[nparams].beta = atof(words[10]);
			params[nparams].lam2 = atof(words[11]);
			params[nparams].bigb = atof(words[12]);
			// current implementation is based on functional form
			// of tersoff_2 as reported in the reference paper
			double bigr = atof(words[13]);
			double bigd = atof(words[14]);
			params[nparams].cutoffR = bigr - bigd;
			params[nparams].cutoffS = bigr + bigd;
			params[nparams].lam1 = atof(words[15]);
			params[nparams].biga = atof(words[16]);

			// currently only allow m exponent of 1 or 3
			params[nparams].powermint = int(params[nparams].powerm);

			if (params[nparams].c < 0.0 \|\| params[nparams].d < 0.0 \|\|
			params[nparams].powern < 0.0 \|\| params[nparams].beta < 0.0 \|\|
			params[nparams].lam2 < 0.0 \|\| params[nparams].bigb < 0.0 \|\|
			params[nparams].cutoffR < 0.0 \|\|params[nparams].cutoffS < 0.0 \|\|
			params[nparams].cutoffR > params[nparams].cutoffS \|\|
			params[nparams].lam1 < 0.0 \|\| params[nparams].biga < 0.0
			) error->all(FLERR,"Illegal Tersoff parameter");

			// only tersoff_2 parametrization is implemented
			if (params[nparams].gamma != 1.0 \|\| params[nparams].lam3 != 0.0)
			error->all(FLERR,"Current tersoff/table pair_style implements only tersoff_2 parametrization");
			nparams++;
			}

			delete [] words;
			}

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

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

			// 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;
			}

			// set cutoff square
			for (m = 0; m < nparams; m++) {
			params[m].cut = params[m].cutoffS;
			params[m].cutsq = params[m].cut*params[m].cut;
			}

			// set cutmax to max of all params
			cutmax = 0.0;
			for (m = 0; m < nparams; m++) {
			if (params[m].cut > cutmax) cutmax = params[m].cut;
			}
			}

lammps/src/USER-MISC/pair_tersoff_table.cpp4a975dd8cf07efficient_neuronet

pair_tersoff_table.cppView Options

lammps/src/USER-MISC/pair_tersoff_table.cpp
4a975dd8cf07efficient_neuronet

pair_tersoff_table.cpp
View Options