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Tue, Nov 5, 09:18

pair_tersoff_table.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: 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;
nelements = 0;
elements = NULL;
nparams = maxparam = 0;
params = NULL;
elem2param = 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 r_ik_x, r_ik_y, r_ik_z;
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 neighbours 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 neighbours 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;
directorCos_ik_x = invR_ik * r_ik_x;
directorCos_ik_y = invR_ik * r_ik_y;
directorCos_ik_z = invR_ik * r_ik_z;
gtetaFunctionIJK = preGtetaFunction[neighbor_j][neighbor_k];
cutoffFunctionIK = preCutoffFunction[neighbor_k];
zeta += cutoffFunctionIK * gtetaFunctionIJK;
}
// first loop over neighbours 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 = 0.5*cutoffFunctionDerivedIJ*(repulsivePotential + attractivePotential * betaZetaPowerIJK)+0.5*cutoffFunctionIJ*(-repulsivePotential*params[ijparam].lam1-betaZetaPowerIJK*attractivePotential*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= 0.5*cutoffFunctionIJ*attractivePotential*betaZetaPowerDerivedIJK;
// second loop over neighbours 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_x*cosTeta - directorCos_ij_x) + factor_2_force3_ik * directorCos_ik_x;
f_ik[1] = factor_1_force3_ik * (directorCos_ik_y*cosTeta - directorCos_ij_y) + factor_2_force3_ik * directorCos_ik_y;
f_ik[2] = factor_1_force3_ik * (directorCos_ik_z*cosTeta - 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 neighbours 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_x*cosTeta - directorCos_ij_x) + factor_2_force3_ik * directorCos_ik_x;
f_ik[1] = factor_1_force3_ik * (directorCos_ik_y*cosTeta - directorCos_ij_y) + factor_2_force3_ik * directorCos_ik_y;
f_ik[2] = factor_1_force3_ik * (directorCos_ik_z*cosTeta - 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()
{
int i,j;
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)((maxLambda*maxCutoff-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+(c*c)/(d*d)-(c*c)/(d*d+(h-r)*(h-r));
gtetaFunctionDerived[i][j]= -2.0 * c * c * (h-r) / ((d*d+(h-r)*(h-r))*(d*d+(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+(c*c)/(d*d)-(c*c)/(d*d+4))*beta*leadingDimensionInteractionList*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+(c*c)/(d*d)-(c*c)/(d*d+4))*beta*leadingDimensionInteractionList*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]=-0.5*pow(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 (atom->tag_enable == 0)
error->all(FLERR,"Pair style Tersoff requires atom IDs");
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);
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 = fopen(file,"r");
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,maxparam*sizeof(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;
}
}

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