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lammps/src/USER-MISC/pair_edip.cpp
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pair_edip.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
Environment Dependent Interatomic Potential
References:
1) J. F. Justo, M. Z. Bazant, E. Kaxiras, V. V. Bulatov, S. Yip
Phys. Rev. B 58, 2539 (1998)
------------------------------------------------------------------------- */
#include <math.h>
#include <float.h>
#include <stdio.h>
#include <stdlib.h>
#include <string.h>
#include "pair_edip.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 GRIDDENSITY 8000
#define GRIDSTART 0.1
// max number of interaction per atom for f(Z) environment potential
#define leadDimInteractionList 64
/* ---------------------------------------------------------------------- */
PairEDIP::PairEDIP(LAMMPS *lmp) : Pair(lmp)
{
single_enable = 0;
restartinfo = 0;
one_coeff = 1;
manybody_flag = 1;
nelements = 0;
elements = NULL;
nparams = maxparam = 0;
params = NULL;
elem2param = NULL;
}
/* ----------------------------------------------------------------------
check if allocated, since class can be destructed when incomplete
------------------------------------------------------------------------- */
PairEDIP::~PairEDIP()
{
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 PairEDIP::compute(int eflag, int vflag)
{
int i,j,k,ii,inum,jnum;
int itype,jtype,ktype,ijparam,ikparam;
double xtmp,ytmp,ztmp,evdwl;
int *ilist,*jlist,*numneigh,**firstneigh;
register int preForceCoord_counter;
double invR_ij;
double invR_ik;
double directorCos_ij_x;
double directorCos_ij_y;
double directorCos_ij_z;
double directorCos_ik_x;
double directorCos_ik_y;
double directorCos_ik_z;
double cosTeta;
int interpolIDX;
double interpolTMP;
double interpolDeltaX;
double interpolY1;
double interpolY2;
double invRMinusCutoffA;
double sigmaInvRMinusCutoffA;
double gammInvRMinusCutoffA;
double cosTetaDiff;
double cosTetaDiffCosTetaDiff;
double cutoffFunction_ij;
double exp2B_ij;
double exp2BDerived_ij;
double pow2B_ij;
double pow2BDerived_ij;
double exp3B_ij;
double exp3BDerived_ij;
double exp3B_ik;
double exp3BDerived_ik;
double qFunction;
double tauFunction;
double tauFunctionDerived;
double expMinusBetaZeta_iZeta_i;
double qFunctionCosTetaDiffCosTetaDiff;
double expMinusQFunctionCosTetaDiffCosTetaDiff;
double zeta_i;
double zeta_iDerived;
double zeta_iDerivedInvR_ij;
double forceModCoord_factor;
double forceModCoord;
double forceModCoord_ij;
double forceMod2B;
double forceMod3B_factor1_ij;
double forceMod3B_factor2_ij;
double forceMod3B_factor2;
double forceMod3B_factor1_ik;
double forceMod3B_factor2_ik;
double potentia3B_factor;
double potential2B_factor;
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++) {
zeta_i = 0.0;
int numForceCoordPairs = 0;
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];
// pre-loop to compute environment coordination f(Z)
for (int neighbor_j = 0; neighbor_j < jnum; neighbor_j++) {
j = jlist[neighbor_j];
j &= NEIGHMASK;
double dr_ij[3], r_ij;
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;
preInvR_ij[neighbor_j] = invR_ij;
invRMinusCutoffA = 1.0 / (r_ij - cutoffA);
sigmaInvRMinusCutoffA = sigma * invRMinusCutoffA;
gammInvRMinusCutoffA = gamm * invRMinusCutoffA;
interpolDeltaX = r_ij - GRIDSTART;
interpolTMP = (interpolDeltaX * GRIDDENSITY);
interpolIDX = (int) interpolTMP;
interpolY1 = exp3B[interpolIDX];
interpolY2 = exp3B[interpolIDX+1];
exp3B_ij = interpolY1 + (interpolY2 - interpolY1) *
(interpolTMP-interpolIDX);
exp3BDerived_ij = - exp3B_ij * gammInvRMinusCutoffA * invRMinusCutoffA;
preExp3B_ij[neighbor_j] = exp3B_ij;
preExp3BDerived_ij[neighbor_j] = exp3BDerived_ij;
interpolY1 = exp2B[interpolIDX];
interpolY2 = exp2B[interpolIDX+1];
exp2B_ij = interpolY1 + (interpolY2 - interpolY1) *
(interpolTMP-interpolIDX);
exp2BDerived_ij = - exp2B_ij * sigmaInvRMinusCutoffA * invRMinusCutoffA;
preExp2B_ij[neighbor_j] = exp2B_ij;
preExp2BDerived_ij[neighbor_j] = exp2BDerived_ij;
interpolY1 = pow2B[interpolIDX];
interpolY2 = pow2B[interpolIDX+1];
pow2B_ij = interpolY1 + (interpolY2 - interpolY1) *
(interpolTMP-interpolIDX);
prePow2B_ij[neighbor_j] = pow2B_ij;
// zeta and its derivative
if (r_ij < cutoffC) zeta_i += 1.0;
else {
interpolY1 = cutoffFunction[interpolIDX];
interpolY2 = cutoffFunction[interpolIDX+1];
cutoffFunction_ij = interpolY1 + (interpolY2 - interpolY1) *
(interpolTMP-interpolIDX);
zeta_i += cutoffFunction_ij;
interpolY1 = cutoffFunctionDerived[interpolIDX];
interpolY2 = cutoffFunctionDerived[interpolIDX+1];
zeta_iDerived = interpolY1 + (interpolY2 - interpolY1) *
(interpolTMP-interpolIDX);
zeta_iDerivedInvR_ij = zeta_iDerived * invR_ij;
preForceCoord_counter=numForceCoordPairs*5;
preForceCoord[preForceCoord_counter+0]=zeta_iDerivedInvR_ij;
preForceCoord[preForceCoord_counter+1]=dr_ij[0];
preForceCoord[preForceCoord_counter+2]=dr_ij[1];
preForceCoord[preForceCoord_counter+3]=dr_ij[2];
preForceCoord[preForceCoord_counter+4]=j;
numForceCoordPairs++;
}
}
// quantities depending on zeta_i
interpolDeltaX = zeta_i;
interpolTMP = (interpolDeltaX * GRIDDENSITY);
interpolIDX = (int) interpolTMP;
interpolY1 = expMinusBetaZeta_iZeta_iGrid[interpolIDX];
interpolY2 = expMinusBetaZeta_iZeta_iGrid[interpolIDX+1];
expMinusBetaZeta_iZeta_i = interpolY1 + (interpolY2 - interpolY1) *
(interpolTMP-interpolIDX);
interpolY1 = qFunctionGrid[interpolIDX];
interpolY2 = qFunctionGrid[interpolIDX+1];
qFunction = interpolY1 + (interpolY2 - interpolY1) *
(interpolTMP-interpolIDX);
interpolY1 = tauFunctionGrid[interpolIDX];
interpolY2 = tauFunctionGrid[interpolIDX+1];
tauFunction = interpolY1 + (interpolY2 - interpolY1) *
(interpolTMP-interpolIDX);
interpolY1 = tauFunctionDerivedGrid[interpolIDX];
interpolY2 = tauFunctionDerivedGrid[interpolIDX+1];
tauFunctionDerived = interpolY1 + (interpolY2 - interpolY1) *
(interpolTMP-interpolIDX);
forceModCoord_factor = 2.0 * beta * zeta_i * expMinusBetaZeta_iZeta_i;
forceModCoord = 0.0;
// two-body interactions, skip half of them
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] = x[j][0] - xtmp;
dr_ij[1] = x[j][1] - ytmp;
dr_ij[2] = x[j][2] - ztmp;
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 = preInvR_ij[neighbor_j];
pow2B_ij = prePow2B_ij[neighbor_j];
potential2B_factor = pow2B_ij - expMinusBetaZeta_iZeta_i;
exp2B_ij = preExp2B_ij[neighbor_j];
pow2BDerived_ij = - rho * invR_ij * pow2B_ij;
forceModCoord += (forceModCoord_factor*exp2B_ij);
exp2BDerived_ij = preExp2BDerived_ij[neighbor_j];
forceMod2B = exp2BDerived_ij * potential2B_factor +
exp2B_ij * pow2BDerived_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];
exp3B_ij = preExp3B_ij[neighbor_j];
exp3BDerived_ij = preExp3BDerived_ij[neighbor_j];
f_ij[0] = forceMod2B * directorCos_ij_x;
f_ij[1] = forceMod2B * directorCos_ij_y;
f_ij[2] = forceMod2B * directorCos_ij_z;
f[i][0] += f_ij[0];
f[i][1] += f_ij[1];
f[i][2] += f_ij[2];
f[j][0] -= f_ij[0];
f[j][1] -= f_ij[1];
f[j][2] -= f_ij[2];
// potential energy
evdwl = (exp2B_ij * potential2B_factor);
if (evflag) ev_tally(i, j, nlocal, newton_pair, evdwl, 0.0,
-forceMod2B*invR_ij, dr_ij[0], dr_ij[1], dr_ij[2]);
// three-body Forces
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];
dr_ik[0] = x[k][0] - xtmp;
dr_ik[1] = x[k][1] - ytmp;
dr_ik[2] = x[k][2] - ztmp;
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 = preInvR_ij[neighbor_k];
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;
cosTetaDiff = cosTeta + tauFunction;
cosTetaDiffCosTetaDiff = cosTetaDiff * cosTetaDiff;
qFunctionCosTetaDiffCosTetaDiff = cosTetaDiffCosTetaDiff * qFunction;
expMinusQFunctionCosTetaDiffCosTetaDiff =
exp(-qFunctionCosTetaDiffCosTetaDiff);
potentia3B_factor = lambda *
((1.0 - expMinusQFunctionCosTetaDiffCosTetaDiff) +
eta * qFunctionCosTetaDiffCosTetaDiff);
exp3B_ik = preExp3B_ij[neighbor_k];
exp3BDerived_ik = preExp3BDerived_ij[neighbor_k];
forceMod3B_factor1_ij = - exp3BDerived_ij * exp3B_ik *
potentia3B_factor;
forceMod3B_factor2 = 2.0 * lambda * exp3B_ij * exp3B_ik *
qFunction * cosTetaDiff *
(eta + expMinusQFunctionCosTetaDiffCosTetaDiff);
forceMod3B_factor2_ij = forceMod3B_factor2 * invR_ij;
f_ij[0] = forceMod3B_factor1_ij * directorCos_ij_x +
forceMod3B_factor2_ij *
(cosTeta * directorCos_ij_x - directorCos_ik_x);
f_ij[1] = forceMod3B_factor1_ij * directorCos_ij_y +
forceMod3B_factor2_ij *
(cosTeta * directorCos_ij_y - directorCos_ik_y);
f_ij[2] = forceMod3B_factor1_ij * directorCos_ij_z +
forceMod3B_factor2_ij *
(cosTeta * directorCos_ij_z - directorCos_ik_z);
forceMod3B_factor1_ik = - exp3BDerived_ik * exp3B_ij *
potentia3B_factor;
forceMod3B_factor2_ik = forceMod3B_factor2 * invR_ik;
f_ik[0] = forceMod3B_factor1_ik * directorCos_ik_x +
forceMod3B_factor2_ik *
(cosTeta * directorCos_ik_x - directorCos_ij_x);
f_ik[1] = forceMod3B_factor1_ik * directorCos_ik_y +
forceMod3B_factor2_ik *
(cosTeta * directorCos_ik_y - directorCos_ij_y);
f_ik[2] = forceMod3B_factor1_ik * directorCos_ik_z +
forceMod3B_factor2_ik *
(cosTeta * directorCos_ik_z - directorCos_ij_z);
forceModCoord += (forceMod3B_factor2 *
(tauFunctionDerived - 0.5 * mu * cosTetaDiff));
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];
f[i][0] -= f_ij[0] + f_ik[0];
f[i][1] -= f_ij[1] + f_ik[1];
f[i][2] -= f_ij[2] + f_ik[2];
// potential energy
evdwl = (exp3B_ij * exp3B_ik * potentia3B_factor);
if (evflag) ev_tally3(i,j,k,evdwl,0.0,f_ij,f_ik,dr_ij,dr_ik);
}
}
// forces due to environment coordination f(Z)
for (int idx = 0; idx < numForceCoordPairs; idx++) {
double dr_ij[3],f_ij[3];
preForceCoord_counter = idx * 5;
zeta_iDerivedInvR_ij=preForceCoord[preForceCoord_counter+0];
dr_ij[0]=preForceCoord[preForceCoord_counter+1];
dr_ij[1]=preForceCoord[preForceCoord_counter+2];
dr_ij[2]=preForceCoord[preForceCoord_counter+3];
j = static_cast<int> (preForceCoord[preForceCoord_counter+4]);
forceModCoord_ij = forceModCoord * zeta_iDerivedInvR_ij;
f_ij[0] = forceModCoord_ij * dr_ij[0];
f_ij[1] = forceModCoord_ij * dr_ij[1];
f_ij[2] = forceModCoord_ij * dr_ij[2];
f[i][0] -= f_ij[0];
f[i][1] -= f_ij[1];
f[i][2] -= f_ij[2];
f[j][0] += f_ij[0];
f[j][1] += f_ij[1];
f[j][2] += f_ij[2];
// potential energy
evdwl = 0.0;
if (evflag) ev_tally(i, j, nlocal, newton_pair, evdwl, 0.0,
-forceModCoord_ij, dr_ij[0], dr_ij[1], dr_ij[2]);
}
}
if (vflag_fdotr) virial_fdotr_compute();
}
/* ---------------------------------------------------------------------- */
void PairEDIP::allocateGrids(void)
{
int numGridPointsOneCutoffFunction;
int numGridPointsNotOneCutoffFunction;
int numGridPointsCutoffFunction;
int numGridPointsR;
int numGridPointsRTotal;
int numGridPointsQFunctionGrid;
int numGridPointsExpMinusBetaZeta_iZeta_i;
int numGridPointsTauFunctionGrid;
double maxArgumentTauFunctionGrid;
double maxArgumentQFunctionGrid;
double maxArgumentExpMinusBetaZeta_iZeta_i;
double const leftLimitToZero = -DBL_MIN * 1000.0;
// tauFunctionGrid
maxArgumentTauFunctionGrid = leadDimInteractionList;
numGridPointsTauFunctionGrid = (int)
((maxArgumentTauFunctionGrid) * GRIDDENSITY) + 2;
memory->create(tauFunctionGrid,numGridPointsTauFunctionGrid,
"edip:tauFunctionGrid");
memory->create(tauFunctionDerivedGrid,numGridPointsTauFunctionGrid,
"edip:tauFunctionDerivedGrid");
// expMinusBetaZeta_iZeta_iGrid
maxArgumentExpMinusBetaZeta_iZeta_i = leadDimInteractionList;
numGridPointsExpMinusBetaZeta_iZeta_i = (int)
((maxArgumentExpMinusBetaZeta_iZeta_i) * GRIDDENSITY) + 2;
memory->create(expMinusBetaZeta_iZeta_iGrid,
numGridPointsExpMinusBetaZeta_iZeta_i,
"edip:expMinusBetaZeta_iZeta_iGrid");
// qFunctionGrid
maxArgumentQFunctionGrid = leadDimInteractionList;
numGridPointsQFunctionGrid = (int)
((maxArgumentQFunctionGrid) * GRIDDENSITY) + 2;
memory->create(qFunctionGrid,numGridPointsQFunctionGrid,"edip:qFunctionGrid");
// cutoffFunction
numGridPointsOneCutoffFunction = (int) ((cutoffC - GRIDSTART) * GRIDDENSITY);
numGridPointsNotOneCutoffFunction = (int) ((cutoffA-cutoffC) * GRIDDENSITY);
numGridPointsCutoffFunction = numGridPointsOneCutoffFunction +
numGridPointsNotOneCutoffFunction+2;
memory->create(cutoffFunction,numGridPointsCutoffFunction,
"edip:cutoffFunction");
memory->create(cutoffFunctionDerived,numGridPointsCutoffFunction,
"edip:cutoffFunctionDerived");
// pow2B
numGridPointsR = (int)
((cutoffA + leftLimitToZero - GRIDSTART) * GRIDDENSITY);
numGridPointsRTotal = numGridPointsR + 2;
memory->create(pow2B,numGridPointsRTotal,"edip:pow2B");
memory->create(exp2B,numGridPointsRTotal,"edip:exp2B");
memory->create(exp3B,numGridPointsRTotal,"edip:exp3B");
}
/* ----------------------------------------------------------------------
pre-calculated structures
------------------------------------------------------------------------- */
void PairEDIP::allocatePreLoops(void)
{
int nthreads = comm->nthreads;
memory->create(preInvR_ij,nthreads*leadDimInteractionList,"edip:preInvR_ij");
memory->create(preExp3B_ij,nthreads*leadDimInteractionList,"edip:preExp3B_ij");
memory->create(preExp3BDerived_ij,nthreads*leadDimInteractionList,
"edip:preExp3BDerived_ij");
memory->create(preExp2B_ij,nthreads*leadDimInteractionList,"edip:preExp2B_ij");
memory->create(preExp2BDerived_ij,nthreads*leadDimInteractionList,
"edip:preExp2BDerived_ij");
memory->create(prePow2B_ij,nthreads*leadDimInteractionList,"edip:prePow2B_ij");
memory->create(preForceCoord,5*nthreads*leadDimInteractionList,"edip:preForceCoord");
}
/* ----------------------------------------------------------------------
deallocate grids
------------------------------------------------------------------------- */
void PairEDIP::deallocateGrids(void)
{
memory->destroy(cutoffFunction);
memory->destroy(cutoffFunctionDerived);
memory->destroy(pow2B);
memory->destroy(exp2B);
memory->destroy(exp3B);
memory->destroy(qFunctionGrid);
memory->destroy(expMinusBetaZeta_iZeta_iGrid);
memory->destroy(tauFunctionGrid);
memory->destroy(tauFunctionDerivedGrid);
}
/* ----------------------------------------------------------------------
deallocate preLoops
------------------------------------------------------------------------- */
void PairEDIP::deallocatePreLoops(void)
{
memory->destroy(preInvR_ij);
memory->destroy(preExp3B_ij);
memory->destroy(preExp3BDerived_ij);
memory->destroy(preExp2B_ij);
memory->destroy(preExp2BDerived_ij);
memory->destroy(prePow2B_ij);
memory->destroy(preForceCoord);
}
/* ---------------------------------------------------------------------- */
void PairEDIP::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 PairEDIP::settings(int narg, char **arg)
{
if (narg != 0) error->all(FLERR,"Illegal pair_style command");
}
/* ---------------------------------------------------------------------- */
void PairEDIP::initGrids(void)
{
int l;
int numGridPointsOneCutoffFunction;
int numGridPointsNotOneCutoffFunction;
int numGridPointsCutoffFunction;
int numGridPointsR;
int numGridPointsQFunctionGrid;
int numGridPointsExpMinusBetaZeta_iZeta_i;
int numGridPointsTauFunctionGrid;
double maxArgumentTauFunctionGrid;
double maxArgumentQFunctionGrid;
double maxArgumentExpMinusBetaZeta_iZeta_i;
double r;
double temp;
double temp3;
double temp4;
double deltaArgumentR;
double deltaArgumentCutoffFunction;
double deltaArgumentQFunctionGrid;
double deltaArgumentTauFunctionGrid;
double deltaArgumentExpMinusBetaZeta_iZeta_i;
double const leftLimitToZero = -DBL_MIN * 1000.0;
// tauFunctionGrid
maxArgumentTauFunctionGrid = leadDimInteractionList;
numGridPointsTauFunctionGrid = (int)
((maxArgumentTauFunctionGrid) * GRIDDENSITY) + 2;
r = 0.0;
deltaArgumentTauFunctionGrid = 1.0 / GRIDDENSITY;
for (l = 0; l < numGridPointsTauFunctionGrid; l++) {
tauFunctionGrid[l] = u1 + u2 * u3 * exp(-u4 * r) -
u2 * exp(-2.0 * u4 * r);
tauFunctionDerivedGrid[l] = - u2 * u3 * u4 * exp(-u4 * r) +
2.0 * u2 * u4 * exp(-2.0 * u4 * r);
r += deltaArgumentTauFunctionGrid;
}
// expMinusBetaZeta_iZeta_iGrid
maxArgumentExpMinusBetaZeta_iZeta_i = leadDimInteractionList;
numGridPointsExpMinusBetaZeta_iZeta_i = (int)
((maxArgumentExpMinusBetaZeta_iZeta_i) * GRIDDENSITY) + 2;
r = 0.0;
deltaArgumentExpMinusBetaZeta_iZeta_i = 1.0 / GRIDDENSITY;
for (l = 0; l < numGridPointsExpMinusBetaZeta_iZeta_i; l++) {
expMinusBetaZeta_iZeta_iGrid[l] = exp(-beta * r * r);
r += deltaArgumentExpMinusBetaZeta_iZeta_i;
}
// qFunctionGrid
maxArgumentQFunctionGrid = leadDimInteractionList;
numGridPointsQFunctionGrid =
(int) ((maxArgumentQFunctionGrid) * GRIDDENSITY) + 2;
r = 0.0;
deltaArgumentQFunctionGrid = 1.0 / GRIDDENSITY;
for (l = 0; l < numGridPointsQFunctionGrid; l++) {
qFunctionGrid[l] = Q0 * exp(-mu * r);
r += deltaArgumentQFunctionGrid;
}
// cutoffFunction
numGridPointsOneCutoffFunction =
(int) ((cutoffC - GRIDSTART) * GRIDDENSITY);
numGridPointsNotOneCutoffFunction =
(int) ((cutoffA-cutoffC) * GRIDDENSITY);
numGridPointsCutoffFunction =
numGridPointsOneCutoffFunction+numGridPointsNotOneCutoffFunction+2;
r = GRIDSTART;
deltaArgumentCutoffFunction = 1.0 / GRIDDENSITY;
for (l = 0; l < numGridPointsOneCutoffFunction; l++) {
cutoffFunction[l] = 1.0;
cutoffFunctionDerived[l] = 0.0;
r += deltaArgumentCutoffFunction;
}
for (l = numGridPointsOneCutoffFunction;
l < numGridPointsCutoffFunction; l++) {
temp = (cutoffA - cutoffC)/(r - cutoffC);
temp3 = temp * temp * temp;
temp4 = temp3 * temp;
cutoffFunction[l] = exp(alpha/(1.0-temp3));
cutoffFunctionDerived[l] = (-3*alpha/(cutoffA-cutoffC)) *
(temp4/((1-temp3)*(1-temp3)))*exp(alpha/(1.0-temp3));
r += deltaArgumentCutoffFunction;
}
// pow2B
numGridPointsR = (int)
((cutoffA + leftLimitToZero - GRIDSTART) * GRIDDENSITY);
r = GRIDSTART;
deltaArgumentR = 1.0 / GRIDDENSITY;
for (l = 0; l < numGridPointsR; l++) {
pow2B[l] = pow((B/r),rho);
exp2B[l] = A * exp(sigma/(r-cutoffA));
exp3B[l] = exp(gamm/(r-cutoffA));
r += deltaArgumentR;
}
pow2B[numGridPointsR] = pow((B/r),rho);
exp2B[numGridPointsR]=0;
exp3B[numGridPointsR]=0;
r += deltaArgumentR;
pow2B[numGridPointsR+1] = pow((B/r),rho);
exp2B[numGridPointsR+1]=0;
exp3B[numGridPointsR+1]=0;
}
/* ----------------------------------------------------------------------
set coeffs for one or more type pairs
------------------------------------------------------------------------- */
void PairEDIP::coeff(int narg, char **arg)
{
int i,j,n;
if (!allocated) allocate();
if (narg != 3 + atom->ntypes)
error->all(FLERR,"Incorrect args for pair coefficients");
// insure I,J args are * *
if (strcmp(arg[0],"*") != 0 || strcmp(arg[1],"*") != 0)
error->all(FLERR,"Incorrect args for pair coefficients");
// read args that map atom types to elements in potential file
// map[i] = which element the Ith atom type is, -1 if NULL
// nelements = # of unique elements
// elements = list of element names
if (elements) {
for (i = 0; i < nelements; i++) delete [] elements[i];
delete [] elements;
}
elements = new char*[atom->ntypes];
for (i = 0; i < atom->ntypes; i++) elements[i] = NULL;
nelements = 0;
for (i = 3; i < narg; i++) {
if (strcmp(arg[i],"NULL") == 0) {
map[i-2] = -1;
continue;
}
for (j = 0; j < nelements; j++)
if (strcmp(arg[i],elements[j]) == 0) break;
map[i-2] = j;
if (j == nelements) {
n = strlen(arg[i]) + 1;
elements[j] = new char[n];
strcpy(elements[j],arg[i]);
nelements++;
}
}
// read potential file and initialize potential parameters
read_file(arg[2]);
setup_params();
// clear setflag since coeff() called once with I,J = * *
n = atom->ntypes;
for (int i = 1; i <= n; i++)
for (int j = i; j <= n; j++)
setflag[i][j] = 0;
// set setflag i,j for type pairs where both are mapped to elements
int count = 0;
for (int i = 1; i <= n; i++)
for (int j = i; j <= n; j++)
if (map[i] >= 0 && map[j] >= 0) {
setflag[i][j] = 1;
count++;
}
if (count == 0) error->all(FLERR,"Incorrect args for pair coefficients");
// allocate tables and internal structures
allocatePreLoops();
allocateGrids();
initGrids();
}
/* ----------------------------------------------------------------------
init specific to this pair style
------------------------------------------------------------------------- */
void PairEDIP::init_style()
{
if (force->newton_pair == 0)
error->all(FLERR,"Pair style EDIP 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 PairEDIP::init_one(int i, int j)
{
if (setflag[i][j] == 0) error->all(FLERR,"All pair coeffs are not set");
return cutmax;
}
/* ---------------------------------------------------------------------- */
void PairEDIP::read_file(char *file)
{
int params_per_line = 20;
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 EDIP 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 EDIP 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].A = atof(words[3]);
params[nparams].B = atof(words[4]);
params[nparams].cutoffA = atof(words[5]);
params[nparams].cutoffC = atof(words[6]);
params[nparams].alpha = atof(words[7]);
params[nparams].beta = atof(words[8]);
params[nparams].eta = atof(words[9]);
params[nparams].gamm = atof(words[10]);
params[nparams].lambda = atof(words[11]);
params[nparams].mu = atof(words[12]);
params[nparams].rho = atof(words[13]);
params[nparams].sigma = atof(words[14]);
params[nparams].Q0 = atof(words[15]);
params[nparams].u1 = atof(words[16]);
params[nparams].u2 = atof(words[17]);
params[nparams].u3 = atof(words[18]);
params[nparams].u4 = atof(words[19]);
if (params[nparams].A < 0.0 || params[nparams].B < 0.0 ||
params[nparams].cutoffA < 0.0 || params[nparams].cutoffC < 0.0 ||
params[nparams].alpha < 0.0 || params[nparams].beta < 0.0 ||
params[nparams].eta < 0.0 || params[nparams].gamm < 0.0 ||
params[nparams].lambda < 0.0 || params[nparams].mu < 0.0 ||
params[nparams].rho < 0.0 || params[nparams].sigma < 0.0)
error->all(FLERR,"Illegal EDIP parameter");
nparams++;
}
delete [] words;
}
/* ---------------------------------------------------------------------- */
void PairEDIP::setup_params()
{
int i,j,k,m,n;
double rtmp;
// set elem2param for all triplet combinations
// must be a single exact match to lines read from file
// do not allow for ACB in place of ABC
memory->destroy(elem2param);
memory->create(elem2param,nelements,nelements,nelements,"pair:elem2param");
for (i = 0; i < nelements; i++)
for (j = 0; j < nelements; j++)
for (k = 0; k < nelements; k++) {
n = -1;
for (m = 0; m < nparams; m++) {
if (i == params[m].ielement && j == params[m].jelement &&
k == params[m].kelement) {
if (n >= 0) error->all(FLERR,"Potential file has duplicate entry");
n = m;
}
}
if (n < 0) error->all(FLERR,"Potential file is missing an entry");
elem2param[i][j][k] = n;
}
// set cutoff square
for (m = 0; m < nparams; m++) {
params[m].cutsq = params[m].cutoffA*params[m].cutoffA;
}
// 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;
}
// this should be removed for multi species parametrizations
A = params[0].A;
B = params[0].B;
rho = params[0].rho;
cutoffA = params[0].cutoffA;
cutoffC = params[0].cutoffC;
sigma = params[0].sigma;
lambda = params[0].lambda;
gamm = params[0].gamm;
eta = params[0].eta;
Q0 = params[0].Q0;
mu = params[0].mu;
beta = params[0].beta;
alpha = params[0].alpha;
u1 = params[0].u1;
u2 = params[0].u2;
u3 = params[0].u3;
u4 = params[0].u4;
}
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