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reformat and use std::numeric_limits<double>::min() instead of DBL_MIN (Posix-only)

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This commit is contained in:
Axel Kohlmeyer
2021-07-10 23:40:30 -04:00
parent 2d9ea81b94
commit eff03f1493
2 changed files with 436 additions and 498 deletions
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353
src/OPENMP/pair_edip_omp.cpp
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@ -1,4 +1,3 @@
// clang-format off
/* ---------------------------------------------------------------------- /* ----------------------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
https://www.lammps.org/, Sandia National Laboratories https://www.lammps.org/, Sandia National Laboratories
@ -19,22 +18,22 @@
#include "comm.h" #include "comm.h"
#include "neigh_list.h" #include "neigh_list.h"
#include "suffix.h" #include "suffix.h"
using namespace LAMMPS_NS;
#include <cmath> #include <cmath>
#include "omp_compat.h" #include "omp_compat.h"
#define GRIDDENSITY 8000 using namespace LAMMPS_NS;
#define GRIDSTART 0.1
// max number of interaction per atom for f(Z) environment potential // max number of interaction per atom for f(Z) environment potential
static constexpr int leadDimInteractionList = 64; static constexpr int leadDimInteractionList = 64;
#define GRIDDENSITY 8000
#define GRIDSTART 0.1
/* ---------------------------------------------------------------------- */ /* ---------------------------------------------------------------------- */
PairEDIPOMP::PairEDIPOMP(LAMMPS *lmp) : PairEDIPOMP::PairEDIPOMP(LAMMPS *lmp) : PairEDIP(lmp), ThrOMP(lmp, THR_PAIR)
PairEDIP(lmp), ThrOMP(lmp, THR_PAIR)
{ {
suffix_flag |= Suffix::OMP; suffix_flag |= Suffix::OMP;
respa_enable = 0; respa_enable = 0;
@ -44,14 +43,14 @@ PairEDIPOMP::PairEDIPOMP(LAMMPS *lmp) :
void PairEDIPOMP::compute(int eflag, int vflag) void PairEDIPOMP::compute(int eflag, int vflag)
{ {
ev_init(eflag,vflag); ev_init(eflag, vflag);
const int nall = atom->nlocal + atom->nghost; const int nall = atom->nlocal + atom->nghost;
const int nthreads = comm->nthreads; const int nthreads = comm->nthreads;
const int inum = list->inum; const int inum = list->inum;
#if defined(_OPENMP) #if defined(_OPENMP)
#pragma omp parallel LMP_DEFAULT_NONE LMP_SHARED(eflag,vflag) #pragma omp parallel LMP_DEFAULT_NONE LMP_SHARED(eflag, vflag)
#endif #endif
{ {
int ifrom, ito, tid; int ifrom, ito, tid;
@ -63,26 +62,31 @@ void PairEDIPOMP::compute(int eflag, int vflag)
if (evflag) { if (evflag) {
if (eflag) { if (eflag) {
if (vflag_atom) eval<1,1,1>(ifrom, ito, thr); if (vflag_atom)
else eval<1,1,0>(ifrom, ito, thr); eval<1, 1, 1>(ifrom, ito, thr);
else
eval<1, 1, 0>(ifrom, ito, thr);
} else { } else {
if (vflag_atom) eval<1,0,1>(ifrom, ito, thr); if (vflag_atom)
else eval<1,0,0>(ifrom, ito, thr); eval<1, 0, 1>(ifrom, ito, thr);
else
eval<1, 0, 0>(ifrom, ito, thr);
} }
} else eval<0,0,0>(ifrom, ito, thr); } else
eval<0, 0, 0>(ifrom, ito, thr);
thr->timer(Timer::PAIR); thr->timer(Timer::PAIR);
reduce_thr(this, eflag, vflag, thr); reduce_thr(this, eflag, vflag, thr);
} // end of omp parallel region } // end of omp parallel region
} }
template <int EVFLAG, int EFLAG, int VFLAG_ATOM> template <int EVFLAG, int EFLAG, int VFLAG_ATOM>
void PairEDIPOMP::eval(int iifrom, int iito, ThrData * const thr) void PairEDIPOMP::eval(int iifrom, int iito, ThrData *const thr)
{ {
int i,j,k,ii,jnum; int i, j, k, ii, jnum;
int itype,jtype,ktype,ijparam,ikparam; int itype, jtype, ktype, ijparam, ikparam;
double xtmp,ytmp,ztmp,evdwl; double xtmp, ytmp, ztmp, evdwl;
int *ilist,*jlist,*numneigh,**firstneigh; int *ilist, *jlist, *numneigh, **firstneigh;
int preForceCoord_counter; int preForceCoord_counter;
double invR_ij; double invR_ij;
@ -147,9 +151,9 @@ void PairEDIPOMP::eval(int iifrom, int iito, ThrData * const thr)
double *pre_thrPow2B_ij = prePow2B_ij + tid * leadDimInteractionList; double *pre_thrPow2B_ij = prePow2B_ij + tid * leadDimInteractionList;
double *pre_thrForceCoord = preForceCoord + tid * leadDimInteractionList; double *pre_thrForceCoord = preForceCoord + tid * leadDimInteractionList;
const dbl3_t * _noalias const x = (dbl3_t *) atom->x[0]; const dbl3_t *_noalias const x = (dbl3_t *) atom->x[0];
dbl3_t * _noalias const f = (dbl3_t *) thr->get_f()[0]; dbl3_t *_noalias const f = (dbl3_t *) thr->get_f()[0];
const int * _noalias const type = atom->type; const int *_noalias const type = atom->type;
const int nlocal = atom->nlocal; const int nlocal = atom->nlocal;
ilist = list->ilist; ilist = list->ilist;
@ -174,86 +178,82 @@ void PairEDIPOMP::eval(int iifrom, int iito, ThrData * const thr)
// pre-loop to compute environment coordination f(Z) // pre-loop to compute environment coordination f(Z)
for (int neighbor_j = 0; neighbor_j < jnum; neighbor_j++) { for (int neighbor_j = 0; neighbor_j < jnum; neighbor_j++) {
j = jlist[neighbor_j]; j = jlist[neighbor_j];
j &= NEIGHMASK; j &= NEIGHMASK;
double dr_ij[3], r_ij; double dr_ij[3], r_ij;
dr_ij[0] = xtmp - x[j].x; dr_ij[0] = xtmp - x[j].x;
dr_ij[1] = ytmp - x[j].y; dr_ij[1] = ytmp - x[j].y;
dr_ij[2] = ztmp - x[j].z; dr_ij[2] = ztmp - x[j].z;
r_ij = dr_ij[0]*dr_ij[0] + dr_ij[1]*dr_ij[1] + dr_ij[2]*dr_ij[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]]; jtype = map[type[j]];
ijparam = elem3param[itype][jtype][jtype]; ijparam = elem3param[itype][jtype][jtype];
if (r_ij > params[ijparam].cutsq) continue; if (r_ij > params[ijparam].cutsq) continue;
r_ij = sqrt(r_ij); r_ij = sqrt(r_ij);
invR_ij = 1.0 / r_ij; invR_ij = 1.0 / r_ij;
pre_thrInvR_ij[neighbor_j] = invR_ij; pre_thrInvR_ij[neighbor_j] = invR_ij;
invRMinusCutoffA = 1.0 / (r_ij - cutoffA); invRMinusCutoffA = 1.0 / (r_ij - cutoffA);
sigmaInvRMinusCutoffA = sigma * invRMinusCutoffA; sigmaInvRMinusCutoffA = sigma * invRMinusCutoffA;
gammInvRMinusCutoffA = gamm * invRMinusCutoffA; gammInvRMinusCutoffA = gamm * invRMinusCutoffA;
interpolDeltaX = r_ij - GRIDSTART; interpolDeltaX = r_ij - GRIDSTART;
interpolTMP = (interpolDeltaX * GRIDDENSITY); interpolTMP = (interpolDeltaX * GRIDDENSITY);
interpolIDX = (int) interpolTMP; interpolIDX = (int) interpolTMP;
interpolY1 = exp3B[interpolIDX]; interpolY1 = exp3B[interpolIDX];
interpolY2 = exp3B[interpolIDX+1]; interpolY2 = exp3B[interpolIDX + 1];
exp3B_ij = interpolY1 + (interpolY2 - interpolY1) * exp3B_ij = interpolY1 + (interpolY2 - interpolY1) * (interpolTMP - interpolIDX);
(interpolTMP-interpolIDX);
exp3BDerived_ij = - exp3B_ij * gammInvRMinusCutoffA * invRMinusCutoffA; exp3BDerived_ij = -exp3B_ij * gammInvRMinusCutoffA * invRMinusCutoffA;
pre_thrExp3B_ij[neighbor_j] = exp3B_ij; pre_thrExp3B_ij[neighbor_j] = exp3B_ij;
pre_thrExp3BDerived_ij[neighbor_j] = exp3BDerived_ij; pre_thrExp3BDerived_ij[neighbor_j] = exp3BDerived_ij;
interpolY1 = exp2B[interpolIDX]; interpolY1 = exp2B[interpolIDX];
interpolY2 = exp2B[interpolIDX+1]; interpolY2 = exp2B[interpolIDX + 1];
exp2B_ij = interpolY1 + (interpolY2 - interpolY1) * exp2B_ij = interpolY1 + (interpolY2 - interpolY1) * (interpolTMP - interpolIDX);
(interpolTMP-interpolIDX);
exp2BDerived_ij = - exp2B_ij * sigmaInvRMinusCutoffA * invRMinusCutoffA; exp2BDerived_ij = -exp2B_ij * sigmaInvRMinusCutoffA * invRMinusCutoffA;
pre_thrExp2B_ij[neighbor_j] = exp2B_ij; pre_thrExp2B_ij[neighbor_j] = exp2B_ij;
pre_thrExp2BDerived_ij[neighbor_j] = exp2BDerived_ij; pre_thrExp2BDerived_ij[neighbor_j] = exp2BDerived_ij;
interpolY1 = pow2B[interpolIDX]; interpolY1 = pow2B[interpolIDX];
interpolY2 = pow2B[interpolIDX+1]; interpolY2 = pow2B[interpolIDX + 1];
pow2B_ij = interpolY1 + (interpolY2 - interpolY1) * pow2B_ij = interpolY1 + (interpolY2 - interpolY1) * (interpolTMP - interpolIDX);
(interpolTMP-interpolIDX);
pre_thrPow2B_ij[neighbor_j] = pow2B_ij; pre_thrPow2B_ij[neighbor_j] = pow2B_ij;
// zeta and its derivative // zeta and its derivative
if (r_ij < cutoffC) zeta_i += 1.0; if (r_ij < cutoffC)
else { zeta_i += 1.0;
interpolY1 = cutoffFunction[interpolIDX]; else {
interpolY2 = cutoffFunction[interpolIDX+1]; interpolY1 = cutoffFunction[interpolIDX];
cutoffFunction_ij = interpolY1 + (interpolY2 - interpolY1) * interpolY2 = cutoffFunction[interpolIDX + 1];
(interpolTMP-interpolIDX); cutoffFunction_ij = interpolY1 + (interpolY2 - interpolY1) * (interpolTMP - interpolIDX);
zeta_i += cutoffFunction_ij; zeta_i += cutoffFunction_ij;
interpolY1 = cutoffFunctionDerived[interpolIDX]; interpolY1 = cutoffFunctionDerived[interpolIDX];
interpolY2 = cutoffFunctionDerived[interpolIDX+1]; interpolY2 = cutoffFunctionDerived[interpolIDX + 1];
zeta_iDerived = interpolY1 + (interpolY2 - interpolY1) * zeta_iDerived = interpolY1 + (interpolY2 - interpolY1) * (interpolTMP - interpolIDX);
(interpolTMP-interpolIDX);
zeta_iDerivedInvR_ij = zeta_iDerived * invR_ij; zeta_iDerivedInvR_ij = zeta_iDerived * invR_ij;
preForceCoord_counter=numForceCoordPairs*5; preForceCoord_counter = numForceCoordPairs * 5;
pre_thrForceCoord[preForceCoord_counter+0]=zeta_iDerivedInvR_ij; pre_thrForceCoord[preForceCoord_counter + 0] = zeta_iDerivedInvR_ij;
pre_thrForceCoord[preForceCoord_counter+1]=dr_ij[0]; pre_thrForceCoord[preForceCoord_counter + 1] = dr_ij[0];
pre_thrForceCoord[preForceCoord_counter+2]=dr_ij[1]; pre_thrForceCoord[preForceCoord_counter + 2] = dr_ij[1];
pre_thrForceCoord[preForceCoord_counter+3]=dr_ij[2]; pre_thrForceCoord[preForceCoord_counter + 3] = dr_ij[2];
pre_thrForceCoord[preForceCoord_counter+4]=j; pre_thrForceCoord[preForceCoord_counter + 4] = j;
numForceCoordPairs++; numForceCoordPairs++;
} }
} }
// quantities depending on zeta_i // quantities depending on zeta_i
@ -263,24 +263,20 @@ void PairEDIPOMP::eval(int iifrom, int iito, ThrData * const thr)
interpolIDX = (int) interpolTMP; interpolIDX = (int) interpolTMP;
interpolY1 = expMinusBetaZeta_iZeta_iGrid[interpolIDX]; interpolY1 = expMinusBetaZeta_iZeta_iGrid[interpolIDX];
interpolY2 = expMinusBetaZeta_iZeta_iGrid[interpolIDX+1]; interpolY2 = expMinusBetaZeta_iZeta_iGrid[interpolIDX + 1];
expMinusBetaZeta_iZeta_i = interpolY1 + (interpolY2 - interpolY1) * expMinusBetaZeta_iZeta_i = interpolY1 + (interpolY2 - interpolY1) * (interpolTMP - interpolIDX);
(interpolTMP-interpolIDX);
interpolY1 = qFunctionGrid[interpolIDX]; interpolY1 = qFunctionGrid[interpolIDX];
interpolY2 = qFunctionGrid[interpolIDX+1]; interpolY2 = qFunctionGrid[interpolIDX + 1];
qFunction = interpolY1 + (interpolY2 - interpolY1) * qFunction = interpolY1 + (interpolY2 - interpolY1) * (interpolTMP - interpolIDX);
(interpolTMP-interpolIDX);
interpolY1 = tauFunctionGrid[interpolIDX]; interpolY1 = tauFunctionGrid[interpolIDX];
interpolY2 = tauFunctionGrid[interpolIDX+1]; interpolY2 = tauFunctionGrid[interpolIDX + 1];
tauFunction = interpolY1 + (interpolY2 - interpolY1) * tauFunction = interpolY1 + (interpolY2 - interpolY1) * (interpolTMP - interpolIDX);
(interpolTMP-interpolIDX);
interpolY1 = tauFunctionDerivedGrid[interpolIDX]; interpolY1 = tauFunctionDerivedGrid[interpolIDX];
interpolY2 = tauFunctionDerivedGrid[interpolIDX+1]; interpolY2 = tauFunctionDerivedGrid[interpolIDX + 1];
tauFunctionDerived = interpolY1 + (interpolY2 - interpolY1) * tauFunctionDerived = interpolY1 + (interpolY2 - interpolY1) * (interpolTMP - interpolIDX);
(interpolTMP-interpolIDX);
forceModCoord_factor = 2.0 * beta * zeta_i * expMinusBetaZeta_iZeta_i; forceModCoord_factor = 2.0 * beta * zeta_i * expMinusBetaZeta_iZeta_i;
@ -297,7 +293,7 @@ void PairEDIPOMP::eval(int iifrom, int iito, ThrData * const thr)
dr_ij[0] = x[j].x - xtmp; dr_ij[0] = x[j].x - xtmp;
dr_ij[1] = x[j].y - ytmp; dr_ij[1] = x[j].y - ytmp;
dr_ij[2] = x[j].z - ztmp; dr_ij[2] = x[j].z - ztmp;
r_ij = dr_ij[0]*dr_ij[0] + dr_ij[1]*dr_ij[1] + dr_ij[2]*dr_ij[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]]; jtype = map[type[j]];
ijparam = elem3param[itype][jtype][jtype]; ijparam = elem3param[itype][jtype][jtype];
@ -312,13 +308,12 @@ void PairEDIPOMP::eval(int iifrom, int iito, ThrData * const thr)
exp2B_ij = pre_thrExp2B_ij[neighbor_j]; exp2B_ij = pre_thrExp2B_ij[neighbor_j];
pow2BDerived_ij = - rho * invR_ij * pow2B_ij; pow2BDerived_ij = -rho * invR_ij * pow2B_ij;
forceModCoord += (forceModCoord_factor*exp2B_ij); forceModCoord += (forceModCoord_factor * exp2B_ij);
exp2BDerived_ij = pre_thrExp2BDerived_ij[neighbor_j]; exp2BDerived_ij = pre_thrExp2BDerived_ij[neighbor_j];
forceMod2B = exp2BDerived_ij * potential2B_factor + forceMod2B = exp2BDerived_ij * potential2B_factor + exp2B_ij * pow2BDerived_ij;
exp2B_ij * pow2BDerived_ij;
directorCos_ij_x = invR_ij * dr_ij[0]; directorCos_ij_x = invR_ij * dr_ij[0];
directorCos_ij_y = invR_ij * dr_ij[1]; directorCos_ij_y = invR_ij * dr_ij[1];
@ -343,133 +338,123 @@ void PairEDIPOMP::eval(int iifrom, int iito, ThrData * const thr)
evdwl = (exp2B_ij * potential2B_factor); evdwl = (exp2B_ij * potential2B_factor);
if (EVFLAG) ev_tally_thr(this,i, j, nlocal, /* newton_pair */ 1, evdwl, 0.0, if (EVFLAG)
-forceMod2B*invR_ij, dr_ij[0], dr_ij[1], dr_ij[2],thr); ev_tally_thr(this, i, j, nlocal, /* newton_pair */ 1, evdwl, 0.0, -forceMod2B * invR_ij,
dr_ij[0], dr_ij[1], dr_ij[2], thr);
// three-body Forces // three-body Forces
for (int neighbor_k = neighbor_j + 1; neighbor_k < jnum; neighbor_k++) { for (int neighbor_k = neighbor_j + 1; neighbor_k < jnum; neighbor_k++) {
double dr_ik[3], r_ik, f_ik[3]; double dr_ik[3], r_ik, f_ik[3];
k = jlist[neighbor_k]; k = jlist[neighbor_k];
k &= NEIGHMASK; k &= NEIGHMASK;
ktype = map[type[k]]; ktype = map[type[k]];
ikparam = elem3param[itype][ktype][ktype]; ikparam = elem3param[itype][ktype][ktype];
dr_ik[0] = x[k].x - xtmp; dr_ik[0] = x[k].x - xtmp;
dr_ik[1] = x[k].y - ytmp; dr_ik[1] = x[k].y - ytmp;
dr_ik[2] = x[k].z - ztmp; dr_ik[2] = x[k].z - ztmp;
r_ik = dr_ik[0]*dr_ik[0] + dr_ik[1]*dr_ik[1] + dr_ik[2]*dr_ik[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; if (r_ik > params[ikparam].cutsq) continue;
r_ik = sqrt(r_ik); r_ik = sqrt(r_ik);
invR_ik = pre_thrInvR_ij[neighbor_k]; invR_ik = pre_thrInvR_ij[neighbor_k];
directorCos_ik_x = invR_ik * dr_ik[0]; directorCos_ik_x = invR_ik * dr_ik[0];
directorCos_ik_y = invR_ik * dr_ik[1]; directorCos_ik_y = invR_ik * dr_ik[1];
directorCos_ik_z = invR_ik * dr_ik[2]; directorCos_ik_z = invR_ik * dr_ik[2];
cosTeta = directorCos_ij_x * directorCos_ik_x + cosTeta = directorCos_ij_x * directorCos_ik_x + directorCos_ij_y * directorCos_ik_y +
directorCos_ij_y * directorCos_ik_y +
directorCos_ij_z * directorCos_ik_z; directorCos_ij_z * directorCos_ik_z;
cosTetaDiff = cosTeta + tauFunction; cosTetaDiff = cosTeta + tauFunction;
cosTetaDiffCosTetaDiff = cosTetaDiff * cosTetaDiff; cosTetaDiffCosTetaDiff = cosTetaDiff * cosTetaDiff;
qFunctionCosTetaDiffCosTetaDiff = cosTetaDiffCosTetaDiff * qFunction; qFunctionCosTetaDiffCosTetaDiff = cosTetaDiffCosTetaDiff * qFunction;
expMinusQFunctionCosTetaDiffCosTetaDiff = expMinusQFunctionCosTetaDiffCosTetaDiff = exp(-qFunctionCosTetaDiffCosTetaDiff);
exp(-qFunctionCosTetaDiffCosTetaDiff);
potentia3B_factor = lambda * potentia3B_factor = lambda *
((1.0 - expMinusQFunctionCosTetaDiffCosTetaDiff) + ((1.0 - expMinusQFunctionCosTetaDiffCosTetaDiff) +
eta * qFunctionCosTetaDiffCosTetaDiff); eta * qFunctionCosTetaDiffCosTetaDiff);
exp3B_ik = pre_thrExp3B_ij[neighbor_k]; exp3B_ik = pre_thrExp3B_ij[neighbor_k];
exp3BDerived_ik = pre_thrExp3BDerived_ij[neighbor_k]; exp3BDerived_ik = pre_thrExp3BDerived_ij[neighbor_k];
forceMod3B_factor1_ij = - exp3BDerived_ij * exp3B_ik * forceMod3B_factor1_ij = -exp3BDerived_ij * exp3B_ik * potentia3B_factor;
potentia3B_factor; forceMod3B_factor2 = 2.0 * lambda * exp3B_ij * exp3B_ik * qFunction * cosTetaDiff *
forceMod3B_factor2 = 2.0 * lambda * exp3B_ij * exp3B_ik *
qFunction * cosTetaDiff *
(eta + expMinusQFunctionCosTetaDiffCosTetaDiff); (eta + expMinusQFunctionCosTetaDiffCosTetaDiff);
forceMod3B_factor2_ij = forceMod3B_factor2 * invR_ij; forceMod3B_factor2_ij = forceMod3B_factor2 * invR_ij;
f_ij[0] = forceMod3B_factor1_ij * directorCos_ij_x + f_ij[0] = forceMod3B_factor1_ij * directorCos_ij_x +
forceMod3B_factor2_ij * forceMod3B_factor2_ij * (cosTeta * directorCos_ij_x - directorCos_ik_x);
(cosTeta * directorCos_ij_x - directorCos_ik_x); f_ij[1] = forceMod3B_factor1_ij * directorCos_ij_y +
f_ij[1] = forceMod3B_factor1_ij * directorCos_ij_y + forceMod3B_factor2_ij * (cosTeta * directorCos_ij_y - directorCos_ik_y);
forceMod3B_factor2_ij * f_ij[2] = forceMod3B_factor1_ij * directorCos_ij_z +
(cosTeta * directorCos_ij_y - directorCos_ik_y); forceMod3B_factor2_ij * (cosTeta * directorCos_ij_z - directorCos_ik_z);
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 * forceMod3B_factor1_ik = -exp3BDerived_ik * exp3B_ij * potentia3B_factor;
potentia3B_factor; forceMod3B_factor2_ik = forceMod3B_factor2 * invR_ik;
forceMod3B_factor2_ik = forceMod3B_factor2 * invR_ik;
f_ik[0] = forceMod3B_factor1_ik * directorCos_ik_x + f_ik[0] = forceMod3B_factor1_ik * directorCos_ik_x +
forceMod3B_factor2_ik * forceMod3B_factor2_ik * (cosTeta * directorCos_ik_x - directorCos_ij_x);
(cosTeta * directorCos_ik_x - directorCos_ij_x); f_ik[1] = forceMod3B_factor1_ik * directorCos_ik_y +
f_ik[1] = forceMod3B_factor1_ik * directorCos_ik_y + forceMod3B_factor2_ik * (cosTeta * directorCos_ik_y - directorCos_ij_y);
forceMod3B_factor2_ik * f_ik[2] = forceMod3B_factor1_ik * directorCos_ik_z +
(cosTeta * directorCos_ik_y - directorCos_ij_y); forceMod3B_factor2_ik * (cosTeta * directorCos_ik_z - directorCos_ij_z);
f_ik[2] = forceMod3B_factor1_ik * directorCos_ik_z +
forceMod3B_factor2_ik *
(cosTeta * directorCos_ik_z - directorCos_ij_z);
forceModCoord += (forceMod3B_factor2 * forceModCoord += (forceMod3B_factor2 * (tauFunctionDerived - 0.5 * mu * cosTetaDiff));
(tauFunctionDerived - 0.5 * mu * cosTetaDiff));
f[j].x += f_ij[0]; f[j].x += f_ij[0];
f[j].y += f_ij[1]; f[j].y += f_ij[1];
f[j].z += f_ij[2]; f[j].z += f_ij[2];
f[k].x += f_ik[0]; f[k].x += f_ik[0];
f[k].y += f_ik[1]; f[k].y += f_ik[1];
f[k].z += f_ik[2]; f[k].z += f_ik[2];
f[i].x -= f_ij[0] + f_ik[0]; f[i].x -= f_ij[0] + f_ik[0];
f[i].y -= f_ij[1] + f_ik[1]; f[i].y -= f_ij[1] + f_ik[1];
f[i].z -= f_ij[2] + f_ik[2]; f[i].z -= f_ij[2] + f_ik[2];
// potential energy // potential energy
evdwl = (exp3B_ij * exp3B_ik * potentia3B_factor); evdwl = (exp3B_ij * exp3B_ik * potentia3B_factor);
if (EVFLAG) ev_tally3_thr(this,i,j,k,evdwl,0.0,f_ij,f_ik,dr_ij,dr_ik,thr); if (EVFLAG) ev_tally3_thr(this, i, j, k, evdwl, 0.0, f_ij, f_ik, dr_ij, dr_ik, thr);
} }
} }
// forces due to environment coordination f(Z) // forces due to environment coordination f(Z)
for (int idx = 0; idx < numForceCoordPairs; idx++) { for (int idx = 0; idx < numForceCoordPairs; idx++) {
double dr_ij[3], f_ij[3]; double dr_ij[3], f_ij[3];
preForceCoord_counter = idx * 5; preForceCoord_counter = idx * 5;
zeta_iDerivedInvR_ij=pre_thrForceCoord[preForceCoord_counter+0]; zeta_iDerivedInvR_ij = pre_thrForceCoord[preForceCoord_counter + 0];
dr_ij[0]=pre_thrForceCoord[preForceCoord_counter+1]; dr_ij[0] = pre_thrForceCoord[preForceCoord_counter + 1];
dr_ij[1]=pre_thrForceCoord[preForceCoord_counter+2]; dr_ij[1] = pre_thrForceCoord[preForceCoord_counter + 2];
dr_ij[2]=pre_thrForceCoord[preForceCoord_counter+3]; dr_ij[2] = pre_thrForceCoord[preForceCoord_counter + 3];
j = static_cast<int> (pre_thrForceCoord[preForceCoord_counter+4]); j = static_cast<int>(pre_thrForceCoord[preForceCoord_counter + 4]);
forceModCoord_ij = forceModCoord * zeta_iDerivedInvR_ij; forceModCoord_ij = forceModCoord * zeta_iDerivedInvR_ij;
f_ij[0] = forceModCoord_ij * dr_ij[0]; f_ij[0] = forceModCoord_ij * dr_ij[0];
f_ij[1] = forceModCoord_ij * dr_ij[1]; f_ij[1] = forceModCoord_ij * dr_ij[1];
f_ij[2] = forceModCoord_ij * dr_ij[2]; f_ij[2] = forceModCoord_ij * dr_ij[2];
f[i].x -= f_ij[0]; f[i].x -= f_ij[0];
f[i].y -= f_ij[1]; f[i].y -= f_ij[1];
f[i].z -= f_ij[2]; f[i].z -= f_ij[2];
f[j].x += f_ij[0]; f[j].x += f_ij[0];
f[j].y += f_ij[1]; f[j].y += f_ij[1];
f[j].z += f_ij[2]; f[j].z += f_ij[2];
if (EVFLAG) ev_tally_thr(this, i, j, nlocal, /* newton_pair */ 1, 0.0, 0.0, if (EVFLAG)
-forceModCoord_ij, dr_ij[0], dr_ij[1], dr_ij[2],thr); ev_tally_thr(this, i, j, nlocal, /* newton_pair */ 1, 0.0, 0.0, -forceModCoord_ij, dr_ij[0],
dr_ij[1], dr_ij[2], thr);
} }
} }
} }

581
src/USER-MISC/pair_edip.cpp
View File

@ -1,4 +1,3 @@
// clang-format off
/* ---------------------------------------------------------------------- /* ----------------------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
https://www.lammps.org/, Sandia National Laboratories https://www.lammps.org/, Sandia National Laboratories
@ -34,8 +33,8 @@
#include "neighbor.h" #include "neighbor.h"
#include <cmath> #include <cmath>
#include <cfloat>
#include <cstring> #include <cstring>
#include <limits>
using namespace LAMMPS_NS; using namespace LAMMPS_NS;
@ -52,12 +51,11 @@ static constexpr int leadDimInteractionList = 64;
/* ---------------------------------------------------------------------- */ /* ---------------------------------------------------------------------- */
PairEDIP::PairEDIP(LAMMPS *lmp) : PairEDIP::PairEDIP(LAMMPS *lmp) :
Pair(lmp), preInvR_ij(nullptr), preExp3B_ij(nullptr), preExp3BDerived_ij(nullptr), Pair(lmp), preInvR_ij(nullptr), preExp3B_ij(nullptr), preExp3BDerived_ij(nullptr),
preExp2B_ij(nullptr), preExp2BDerived_ij(nullptr), prePow2B_ij(nullptr), preExp2B_ij(nullptr), preExp2BDerived_ij(nullptr), prePow2B_ij(nullptr), preForceCoord(nullptr),
preForceCoord(nullptr), cutoffFunction(nullptr), cutoffFunctionDerived(nullptr), cutoffFunction(nullptr), cutoffFunctionDerived(nullptr), pow2B(nullptr), exp2B(nullptr),
pow2B(nullptr), exp2B(nullptr), exp3B(nullptr), qFunctionGrid(nullptr), exp3B(nullptr), qFunctionGrid(nullptr), expMinusBetaZeta_iZeta_iGrid(nullptr),
expMinusBetaZeta_iZeta_iGrid(nullptr), tauFunctionGrid(nullptr), tauFunctionGrid(nullptr), tauFunctionDerivedGrid(nullptr)
tauFunctionDerivedGrid(nullptr)
{ {
single_enable = 0; single_enable = 0;
restartinfo = 0; restartinfo = 0;
@ -90,10 +88,10 @@ PairEDIP::~PairEDIP()
void PairEDIP::compute(int eflag, int vflag) void PairEDIP::compute(int eflag, int vflag)
{ {
int i,j,k,ii,inum,jnum; int i, j, k, ii, inum, jnum;
int itype,jtype,ktype,ijparam,ikparam; int itype, jtype, ktype, ijparam, ikparam;
double xtmp,ytmp,ztmp,evdwl; double xtmp, ytmp, ztmp, evdwl;
int *ilist,*jlist,*numneigh,**firstneigh; int *ilist, *jlist, *numneigh, **firstneigh;
int preForceCoord_counter; int preForceCoord_counter;
double invR_ij; double invR_ij;
@ -149,7 +147,7 @@ void PairEDIP::compute(int eflag, int vflag)
double potential2B_factor; double potential2B_factor;
evdwl = 0.0; evdwl = 0.0;
ev_init(eflag,vflag); ev_init(eflag, vflag);
double **x = atom->x; double **x = atom->x;
double **f = atom->f; double **f = atom->f;
@ -180,86 +178,82 @@ void PairEDIP::compute(int eflag, int vflag)
// pre-loop to compute environment coordination f(Z) // pre-loop to compute environment coordination f(Z)
for (int neighbor_j = 0; neighbor_j < jnum; neighbor_j++) { for (int neighbor_j = 0; neighbor_j < jnum; neighbor_j++) {
j = jlist[neighbor_j]; j = jlist[neighbor_j];
j &= NEIGHMASK; j &= NEIGHMASK;
double dr_ij[3], r_ij; double dr_ij[3], r_ij;
dr_ij[0] = xtmp - x[j][0]; dr_ij[0] = xtmp - x[j][0];
dr_ij[1] = ytmp - x[j][1]; dr_ij[1] = ytmp - x[j][1];
dr_ij[2] = ztmp - x[j][2]; 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]; r_ij = dr_ij[0] * dr_ij[0] + dr_ij[1] * dr_ij[1] + dr_ij[2] * dr_ij[2];
jtype = map[type[j]]; jtype = map[type[j]];
ijparam = elem3param[itype][jtype][jtype]; ijparam = elem3param[itype][jtype][jtype];
if (r_ij > params[ijparam].cutsq) continue; if (r_ij > params[ijparam].cutsq) continue;
r_ij = sqrt(r_ij); r_ij = sqrt(r_ij);
invR_ij = 1.0 / r_ij; invR_ij = 1.0 / r_ij;
preInvR_ij[neighbor_j] = invR_ij; preInvR_ij[neighbor_j] = invR_ij;
invRMinusCutoffA = 1.0 / (r_ij - cutoffA); invRMinusCutoffA = 1.0 / (r_ij - cutoffA);
sigmaInvRMinusCutoffA = sigma * invRMinusCutoffA; sigmaInvRMinusCutoffA = sigma * invRMinusCutoffA;
gammInvRMinusCutoffA = gamm * invRMinusCutoffA; gammInvRMinusCutoffA = gamm * invRMinusCutoffA;
interpolDeltaX = r_ij - GRIDSTART; interpolDeltaX = r_ij - GRIDSTART;
interpolTMP = (interpolDeltaX * GRIDDENSITY); interpolTMP = (interpolDeltaX * GRIDDENSITY);
interpolIDX = (int) interpolTMP; interpolIDX = (int) interpolTMP;
interpolY1 = exp3B[interpolIDX]; interpolY1 = exp3B[interpolIDX];
interpolY2 = exp3B[interpolIDX+1]; interpolY2 = exp3B[interpolIDX + 1];
exp3B_ij = interpolY1 + (interpolY2 - interpolY1) * exp3B_ij = interpolY1 + (interpolY2 - interpolY1) * (interpolTMP - interpolIDX);
(interpolTMP-interpolIDX);
exp3BDerived_ij = - exp3B_ij * gammInvRMinusCutoffA * invRMinusCutoffA; exp3BDerived_ij = -exp3B_ij * gammInvRMinusCutoffA * invRMinusCutoffA;
preExp3B_ij[neighbor_j] = exp3B_ij; preExp3B_ij[neighbor_j] = exp3B_ij;
preExp3BDerived_ij[neighbor_j] = exp3BDerived_ij; preExp3BDerived_ij[neighbor_j] = exp3BDerived_ij;
interpolY1 = exp2B[interpolIDX]; interpolY1 = exp2B[interpolIDX];
interpolY2 = exp2B[interpolIDX+1]; interpolY2 = exp2B[interpolIDX + 1];
exp2B_ij = interpolY1 + (interpolY2 - interpolY1) * exp2B_ij = interpolY1 + (interpolY2 - interpolY1) * (interpolTMP - interpolIDX);
(interpolTMP-interpolIDX);
exp2BDerived_ij = - exp2B_ij * sigmaInvRMinusCutoffA * invRMinusCutoffA; exp2BDerived_ij = -exp2B_ij * sigmaInvRMinusCutoffA * invRMinusCutoffA;
preExp2B_ij[neighbor_j] = exp2B_ij; preExp2B_ij[neighbor_j] = exp2B_ij;
preExp2BDerived_ij[neighbor_j] = exp2BDerived_ij; preExp2BDerived_ij[neighbor_j] = exp2BDerived_ij;
interpolY1 = pow2B[interpolIDX]; interpolY1 = pow2B[interpolIDX];
interpolY2 = pow2B[interpolIDX+1]; interpolY2 = pow2B[interpolIDX + 1];
pow2B_ij = interpolY1 + (interpolY2 - interpolY1) * pow2B_ij = interpolY1 + (interpolY2 - interpolY1) * (interpolTMP - interpolIDX);
(interpolTMP-interpolIDX);
prePow2B_ij[neighbor_j] = pow2B_ij; prePow2B_ij[neighbor_j] = pow2B_ij;
// zeta and its derivative // zeta and its derivative
if (r_ij < cutoffC) zeta_i += 1.0; if (r_ij < cutoffC)
else { zeta_i += 1.0;
interpolY1 = cutoffFunction[interpolIDX]; else {
interpolY2 = cutoffFunction[interpolIDX+1]; interpolY1 = cutoffFunction[interpolIDX];
cutoffFunction_ij = interpolY1 + (interpolY2 - interpolY1) * interpolY2 = cutoffFunction[interpolIDX + 1];
(interpolTMP-interpolIDX); cutoffFunction_ij = interpolY1 + (interpolY2 - interpolY1) * (interpolTMP - interpolIDX);
zeta_i += cutoffFunction_ij; zeta_i += cutoffFunction_ij;
interpolY1 = cutoffFunctionDerived[interpolIDX]; interpolY1 = cutoffFunctionDerived[interpolIDX];
interpolY2 = cutoffFunctionDerived[interpolIDX+1]; interpolY2 = cutoffFunctionDerived[interpolIDX + 1];
zeta_iDerived = interpolY1 + (interpolY2 - interpolY1) * zeta_iDerived = interpolY1 + (interpolY2 - interpolY1) * (interpolTMP - interpolIDX);
(interpolTMP-interpolIDX);
zeta_iDerivedInvR_ij = zeta_iDerived * invR_ij; zeta_iDerivedInvR_ij = zeta_iDerived * invR_ij;
preForceCoord_counter=numForceCoordPairs*5; preForceCoord_counter = numForceCoordPairs * 5;
preForceCoord[preForceCoord_counter+0]=zeta_iDerivedInvR_ij; preForceCoord[preForceCoord_counter + 0] = zeta_iDerivedInvR_ij;
preForceCoord[preForceCoord_counter+1]=dr_ij[0]; preForceCoord[preForceCoord_counter + 1] = dr_ij[0];
preForceCoord[preForceCoord_counter+2]=dr_ij[1]; preForceCoord[preForceCoord_counter + 2] = dr_ij[1];
preForceCoord[preForceCoord_counter+3]=dr_ij[2]; preForceCoord[preForceCoord_counter + 3] = dr_ij[2];
preForceCoord[preForceCoord_counter+4]=j; preForceCoord[preForceCoord_counter + 4] = j;
numForceCoordPairs++; numForceCoordPairs++;
} }
} }
// quantities depending on zeta_i // quantities depending on zeta_i
@ -269,24 +263,20 @@ void PairEDIP::compute(int eflag, int vflag)
interpolIDX = (int) interpolTMP; interpolIDX = (int) interpolTMP;
interpolY1 = expMinusBetaZeta_iZeta_iGrid[interpolIDX]; interpolY1 = expMinusBetaZeta_iZeta_iGrid[interpolIDX];
interpolY2 = expMinusBetaZeta_iZeta_iGrid[interpolIDX+1]; interpolY2 = expMinusBetaZeta_iZeta_iGrid[interpolIDX + 1];
expMinusBetaZeta_iZeta_i = interpolY1 + (interpolY2 - interpolY1) * expMinusBetaZeta_iZeta_i = interpolY1 + (interpolY2 - interpolY1) * (interpolTMP - interpolIDX);
(interpolTMP-interpolIDX);
interpolY1 = qFunctionGrid[interpolIDX]; interpolY1 = qFunctionGrid[interpolIDX];
interpolY2 = qFunctionGrid[interpolIDX+1]; interpolY2 = qFunctionGrid[interpolIDX + 1];
qFunction = interpolY1 + (interpolY2 - interpolY1) * qFunction = interpolY1 + (interpolY2 - interpolY1) * (interpolTMP - interpolIDX);
(interpolTMP-interpolIDX);
interpolY1 = tauFunctionGrid[interpolIDX]; interpolY1 = tauFunctionGrid[interpolIDX];
interpolY2 = tauFunctionGrid[interpolIDX+1]; interpolY2 = tauFunctionGrid[interpolIDX + 1];
tauFunction = interpolY1 + (interpolY2 - interpolY1) * tauFunction = interpolY1 + (interpolY2 - interpolY1) * (interpolTMP - interpolIDX);
(interpolTMP-interpolIDX);
interpolY1 = tauFunctionDerivedGrid[interpolIDX]; interpolY1 = tauFunctionDerivedGrid[interpolIDX];
interpolY2 = tauFunctionDerivedGrid[interpolIDX+1]; interpolY2 = tauFunctionDerivedGrid[interpolIDX + 1];
tauFunctionDerived = interpolY1 + (interpolY2 - interpolY1) * tauFunctionDerived = interpolY1 + (interpolY2 - interpolY1) * (interpolTMP - interpolIDX);
(interpolTMP-interpolIDX);
forceModCoord_factor = 2.0 * beta * zeta_i * expMinusBetaZeta_iZeta_i; forceModCoord_factor = 2.0 * beta * zeta_i * expMinusBetaZeta_iZeta_i;
@ -303,7 +293,7 @@ void PairEDIP::compute(int eflag, int vflag)
dr_ij[0] = x[j][0] - xtmp; dr_ij[0] = x[j][0] - xtmp;
dr_ij[1] = x[j][1] - ytmp; dr_ij[1] = x[j][1] - ytmp;
dr_ij[2] = x[j][2] - ztmp; 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]; r_ij = dr_ij[0] * dr_ij[0] + dr_ij[1] * dr_ij[1] + dr_ij[2] * dr_ij[2];
jtype = map[type[j]]; jtype = map[type[j]];
ijparam = elem3param[itype][jtype][jtype]; ijparam = elem3param[itype][jtype][jtype];
@ -318,13 +308,12 @@ void PairEDIP::compute(int eflag, int vflag)
exp2B_ij = preExp2B_ij[neighbor_j]; exp2B_ij = preExp2B_ij[neighbor_j];
pow2BDerived_ij = - rho * invR_ij * pow2B_ij; pow2BDerived_ij = -rho * invR_ij * pow2B_ij;
forceModCoord += (forceModCoord_factor*exp2B_ij); forceModCoord += (forceModCoord_factor * exp2B_ij);
exp2BDerived_ij = preExp2BDerived_ij[neighbor_j]; exp2BDerived_ij = preExp2BDerived_ij[neighbor_j];
forceMod2B = exp2BDerived_ij * potential2B_factor + forceMod2B = exp2BDerived_ij * potential2B_factor + exp2B_ij * pow2BDerived_ij;
exp2B_ij * pow2BDerived_ij;
directorCos_ij_x = invR_ij * dr_ij[0]; directorCos_ij_x = invR_ij * dr_ij[0];
directorCos_ij_y = invR_ij * dr_ij[1]; directorCos_ij_y = invR_ij * dr_ij[1];
@ -349,136 +338,123 @@ void PairEDIP::compute(int eflag, int vflag)
evdwl = (exp2B_ij * potential2B_factor); evdwl = (exp2B_ij * potential2B_factor);
if (evflag) ev_tally(i, j, nlocal, newton_pair, evdwl, 0.0, if (evflag)
-forceMod2B*invR_ij, dr_ij[0], dr_ij[1], dr_ij[2]); 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 // three-body Forces
for (int neighbor_k = neighbor_j + 1; neighbor_k < jnum; neighbor_k++) { for (int neighbor_k = neighbor_j + 1; neighbor_k < jnum; neighbor_k++) {
double dr_ik[3], r_ik, f_ik[3]; double dr_ik[3], r_ik, f_ik[3];
k = jlist[neighbor_k]; k = jlist[neighbor_k];
k &= NEIGHMASK; k &= NEIGHMASK;
ktype = map[type[k]]; ktype = map[type[k]];
ikparam = elem3param[itype][ktype][ktype]; ikparam = elem3param[itype][ktype][ktype];
dr_ik[0] = x[k][0] - xtmp; dr_ik[0] = x[k][0] - xtmp;
dr_ik[1] = x[k][1] - ytmp; dr_ik[1] = x[k][1] - ytmp;
dr_ik[2] = x[k][2] - ztmp; 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]; 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; if (r_ik > params[ikparam].cutsq) continue;
r_ik = sqrt(r_ik); r_ik = sqrt(r_ik);
invR_ik = preInvR_ij[neighbor_k]; invR_ik = preInvR_ij[neighbor_k];
directorCos_ik_x = invR_ik * dr_ik[0]; directorCos_ik_x = invR_ik * dr_ik[0];
directorCos_ik_y = invR_ik * dr_ik[1]; directorCos_ik_y = invR_ik * dr_ik[1];
directorCos_ik_z = invR_ik * dr_ik[2]; directorCos_ik_z = invR_ik * dr_ik[2];
cosTeta = directorCos_ij_x * directorCos_ik_x + cosTeta = directorCos_ij_x * directorCos_ik_x + directorCos_ij_y * directorCos_ik_y +
directorCos_ij_y * directorCos_ik_y +
directorCos_ij_z * directorCos_ik_z; directorCos_ij_z * directorCos_ik_z;
cosTetaDiff = cosTeta + tauFunction; cosTetaDiff = cosTeta + tauFunction;
cosTetaDiffCosTetaDiff = cosTetaDiff * cosTetaDiff; cosTetaDiffCosTetaDiff = cosTetaDiff * cosTetaDiff;
qFunctionCosTetaDiffCosTetaDiff = cosTetaDiffCosTetaDiff * qFunction; qFunctionCosTetaDiffCosTetaDiff = cosTetaDiffCosTetaDiff * qFunction;
expMinusQFunctionCosTetaDiffCosTetaDiff = expMinusQFunctionCosTetaDiffCosTetaDiff = exp(-qFunctionCosTetaDiffCosTetaDiff);
exp(-qFunctionCosTetaDiffCosTetaDiff);
potentia3B_factor = lambda * potentia3B_factor = lambda *
((1.0 - expMinusQFunctionCosTetaDiffCosTetaDiff) + ((1.0 - expMinusQFunctionCosTetaDiffCosTetaDiff) +
eta * qFunctionCosTetaDiffCosTetaDiff); eta * qFunctionCosTetaDiffCosTetaDiff);
exp3B_ik = preExp3B_ij[neighbor_k]; exp3B_ik = preExp3B_ij[neighbor_k];
exp3BDerived_ik = preExp3BDerived_ij[neighbor_k]; exp3BDerived_ik = preExp3BDerived_ij[neighbor_k];
forceMod3B_factor1_ij = - exp3BDerived_ij * exp3B_ik * forceMod3B_factor1_ij = -exp3BDerived_ij * exp3B_ik * potentia3B_factor;
potentia3B_factor; forceMod3B_factor2 = 2.0 * lambda * exp3B_ij * exp3B_ik * qFunction * cosTetaDiff *
forceMod3B_factor2 = 2.0 * lambda * exp3B_ij * exp3B_ik *
qFunction * cosTetaDiff *
(eta + expMinusQFunctionCosTetaDiffCosTetaDiff); (eta + expMinusQFunctionCosTetaDiffCosTetaDiff);
forceMod3B_factor2_ij = forceMod3B_factor2 * invR_ij; forceMod3B_factor2_ij = forceMod3B_factor2 * invR_ij;
f_ij[0] = forceMod3B_factor1_ij * directorCos_ij_x + f_ij[0] = forceMod3B_factor1_ij * directorCos_ij_x +
forceMod3B_factor2_ij * forceMod3B_factor2_ij * (cosTeta * directorCos_ij_x - directorCos_ik_x);
(cosTeta * directorCos_ij_x - directorCos_ik_x); f_ij[1] = forceMod3B_factor1_ij * directorCos_ij_y +
f_ij[1] = forceMod3B_factor1_ij * directorCos_ij_y + forceMod3B_factor2_ij * (cosTeta * directorCos_ij_y - directorCos_ik_y);
forceMod3B_factor2_ij * f_ij[2] = forceMod3B_factor1_ij * directorCos_ij_z +
(cosTeta * directorCos_ij_y - directorCos_ik_y); forceMod3B_factor2_ij * (cosTeta * directorCos_ij_z - directorCos_ik_z);
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 * forceMod3B_factor1_ik = -exp3BDerived_ik * exp3B_ij * potentia3B_factor;
potentia3B_factor; forceMod3B_factor2_ik = forceMod3B_factor2 * invR_ik;
forceMod3B_factor2_ik = forceMod3B_factor2 * invR_ik;
f_ik[0] = forceMod3B_factor1_ik * directorCos_ik_x + f_ik[0] = forceMod3B_factor1_ik * directorCos_ik_x +
forceMod3B_factor2_ik * forceMod3B_factor2_ik * (cosTeta * directorCos_ik_x - directorCos_ij_x);
(cosTeta * directorCos_ik_x - directorCos_ij_x); f_ik[1] = forceMod3B_factor1_ik * directorCos_ik_y +
f_ik[1] = forceMod3B_factor1_ik * directorCos_ik_y + forceMod3B_factor2_ik * (cosTeta * directorCos_ik_y - directorCos_ij_y);
forceMod3B_factor2_ik * f_ik[2] = forceMod3B_factor1_ik * directorCos_ik_z +
(cosTeta * directorCos_ik_y - directorCos_ij_y); forceMod3B_factor2_ik * (cosTeta * directorCos_ik_z - directorCos_ij_z);
f_ik[2] = forceMod3B_factor1_ik * directorCos_ik_z +
forceMod3B_factor2_ik *
(cosTeta * directorCos_ik_z - directorCos_ij_z);
forceModCoord += (forceMod3B_factor2 * forceModCoord += (forceMod3B_factor2 * (tauFunctionDerived - 0.5 * mu * cosTetaDiff));
(tauFunctionDerived - 0.5 * mu * cosTetaDiff));
f[j][0] += f_ij[0]; f[j][0] += f_ij[0];
f[j][1] += f_ij[1]; f[j][1] += f_ij[1];
f[j][2] += f_ij[2]; f[j][2] += f_ij[2];
f[k][0] += f_ik[0]; f[k][0] += f_ik[0];
f[k][1] += f_ik[1]; f[k][1] += f_ik[1];
f[k][2] += f_ik[2]; f[k][2] += f_ik[2];
f[i][0] -= f_ij[0] + f_ik[0]; f[i][0] -= f_ij[0] + f_ik[0];
f[i][1] -= f_ij[1] + f_ik[1]; f[i][1] -= f_ij[1] + f_ik[1];
f[i][2] -= f_ij[2] + f_ik[2]; f[i][2] -= f_ij[2] + f_ik[2];
// potential energy // potential energy
evdwl = (exp3B_ij * exp3B_ik * potentia3B_factor); 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); 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) // forces due to environment coordination f(Z)
for (int idx = 0; idx < numForceCoordPairs; idx++) { for (int idx = 0; idx < numForceCoordPairs; idx++) {
double dr_ij[3],f_ij[3]; double dr_ij[3], f_ij[3];
preForceCoord_counter = idx * 5; preForceCoord_counter = idx * 5;
zeta_iDerivedInvR_ij=preForceCoord[preForceCoord_counter+0]; zeta_iDerivedInvR_ij = preForceCoord[preForceCoord_counter + 0];
dr_ij[0]=preForceCoord[preForceCoord_counter+1]; dr_ij[0] = preForceCoord[preForceCoord_counter + 1];
dr_ij[1]=preForceCoord[preForceCoord_counter+2]; dr_ij[1] = preForceCoord[preForceCoord_counter + 2];
dr_ij[2]=preForceCoord[preForceCoord_counter+3]; dr_ij[2] = preForceCoord[preForceCoord_counter + 3];
j = static_cast<int> (preForceCoord[preForceCoord_counter+4]); j = static_cast<int>(preForceCoord[preForceCoord_counter + 4]);
forceModCoord_ij = forceModCoord * zeta_iDerivedInvR_ij; forceModCoord_ij = forceModCoord * zeta_iDerivedInvR_ij;
f_ij[0] = forceModCoord_ij * dr_ij[0]; f_ij[0] = forceModCoord_ij * dr_ij[0];
f_ij[1] = forceModCoord_ij * dr_ij[1]; f_ij[1] = forceModCoord_ij * dr_ij[1];
f_ij[2] = forceModCoord_ij * dr_ij[2]; f_ij[2] = forceModCoord_ij * dr_ij[2];
f[i][0] -= f_ij[0]; f[i][0] -= f_ij[0];
f[i][1] -= f_ij[1]; f[i][1] -= f_ij[1];
f[i][2] -= f_ij[2]; f[i][2] -= f_ij[2];
f[j][0] += f_ij[0]; f[j][0] += f_ij[0];
f[j][1] += f_ij[1]; f[j][1] += f_ij[1];
f[j][2] += f_ij[2]; f[j][2] += f_ij[2];
// potential energy if (evflag)
ev_tally(i, j, nlocal, newton_pair, 0.0, 0.0, -forceModCoord_ij, dr_ij[0], dr_ij[1],
evdwl = 0.0; dr_ij[2]);
if (evflag) ev_tally(i, j, nlocal, newton_pair, evdwl, 0.0,
-forceModCoord_ij, dr_ij[0], dr_ij[1], dr_ij[2]);
} }
} }
@ -500,58 +476,51 @@ void PairEDIP::allocateGrids(void)
double maxArgumentTauFunctionGrid; double maxArgumentTauFunctionGrid;
double maxArgumentQFunctionGrid; double maxArgumentQFunctionGrid;
double maxArgumentExpMinusBetaZeta_iZeta_i; double maxArgumentExpMinusBetaZeta_iZeta_i;
double const leftLimitToZero = -DBL_MIN * 1000.0; double const leftLimitToZero = -std::numeric_limits<double>::min() * 1000.0;
deallocateGrids(); deallocateGrids();
// tauFunctionGrid // tauFunctionGrid
maxArgumentTauFunctionGrid = leadDimInteractionList; maxArgumentTauFunctionGrid = leadDimInteractionList;
numGridPointsTauFunctionGrid = (int) numGridPointsTauFunctionGrid = (int) ((maxArgumentTauFunctionGrid) *GRIDDENSITY) + 2;
((maxArgumentTauFunctionGrid) * GRIDDENSITY) + 2;
memory->create(tauFunctionGrid,numGridPointsTauFunctionGrid, memory->create(tauFunctionGrid, numGridPointsTauFunctionGrid, "edip:tauFunctionGrid");
"edip:tauFunctionGrid"); memory->create(tauFunctionDerivedGrid, numGridPointsTauFunctionGrid,
memory->create(tauFunctionDerivedGrid,numGridPointsTauFunctionGrid,
"edip:tauFunctionDerivedGrid"); "edip:tauFunctionDerivedGrid");
// expMinusBetaZeta_iZeta_iGrid // expMinusBetaZeta_iZeta_iGrid
maxArgumentExpMinusBetaZeta_iZeta_i = leadDimInteractionList; maxArgumentExpMinusBetaZeta_iZeta_i = leadDimInteractionList;
numGridPointsExpMinusBetaZeta_iZeta_i = (int) numGridPointsExpMinusBetaZeta_iZeta_i =
((maxArgumentExpMinusBetaZeta_iZeta_i) * GRIDDENSITY) + 2; (int) ((maxArgumentExpMinusBetaZeta_iZeta_i) *GRIDDENSITY) + 2;
memory->create(expMinusBetaZeta_iZeta_iGrid, memory->create(expMinusBetaZeta_iZeta_iGrid, numGridPointsExpMinusBetaZeta_iZeta_i,
numGridPointsExpMinusBetaZeta_iZeta_i,
"edip:expMinusBetaZeta_iZeta_iGrid"); "edip:expMinusBetaZeta_iZeta_iGrid");
// qFunctionGrid // qFunctionGrid
maxArgumentQFunctionGrid = leadDimInteractionList; maxArgumentQFunctionGrid = leadDimInteractionList;
numGridPointsQFunctionGrid = (int) numGridPointsQFunctionGrid = (int) ((maxArgumentQFunctionGrid) *GRIDDENSITY) + 2;
((maxArgumentQFunctionGrid) * GRIDDENSITY) + 2; memory->create(qFunctionGrid, numGridPointsQFunctionGrid, "edip:qFunctionGrid");
memory->create(qFunctionGrid,numGridPointsQFunctionGrid,"edip:qFunctionGrid");
// cutoffFunction // cutoffFunction
numGridPointsOneCutoffFunction = (int) ((cutoffC - GRIDSTART) * GRIDDENSITY); numGridPointsOneCutoffFunction = (int) ((cutoffC - GRIDSTART) * GRIDDENSITY);
numGridPointsNotOneCutoffFunction = (int) ((cutoffA-cutoffC) * GRIDDENSITY); numGridPointsNotOneCutoffFunction = (int) ((cutoffA - cutoffC) * GRIDDENSITY);
numGridPointsCutoffFunction = numGridPointsOneCutoffFunction + numGridPointsCutoffFunction =
numGridPointsNotOneCutoffFunction+2; numGridPointsOneCutoffFunction + numGridPointsNotOneCutoffFunction + 2;
memory->create(cutoffFunction,numGridPointsCutoffFunction, memory->create(cutoffFunction, numGridPointsCutoffFunction, "edip:cutoffFunction");
"edip:cutoffFunction"); memory->create(cutoffFunctionDerived, numGridPointsCutoffFunction, "edip:cutoffFunctionDerived");
memory->create(cutoffFunctionDerived,numGridPointsCutoffFunction,
"edip:cutoffFunctionDerived");
// pow2B // pow2B
numGridPointsR = (int) numGridPointsR = (int) ((cutoffA + leftLimitToZero - GRIDSTART) * GRIDDENSITY);
((cutoffA + leftLimitToZero - GRIDSTART) * GRIDDENSITY);
numGridPointsRTotal = numGridPointsR + 2; numGridPointsRTotal = numGridPointsR + 2;
memory->create(pow2B,numGridPointsRTotal,"edip:pow2B"); memory->create(pow2B, numGridPointsRTotal, "edip:pow2B");
memory->create(exp2B,numGridPointsRTotal,"edip:exp2B"); memory->create(exp2B, numGridPointsRTotal, "edip:exp2B");
memory->create(exp3B,numGridPointsRTotal,"edip:exp3B"); memory->create(exp3B, numGridPointsRTotal, "edip:exp3B");
} }
/* ---------------------------------------------------------------------- /* ----------------------------------------------------------------------
@ -563,15 +532,13 @@ void PairEDIP::allocatePreLoops(void)
int nthreads = comm->nthreads; int nthreads = comm->nthreads;
deallocatePreLoops(); deallocatePreLoops();
memory->create(preInvR_ij,nthreads*leadDimInteractionList,"edip:preInvR_ij"); memory->create(preInvR_ij, nthreads * leadDimInteractionList, "edip:preInvR_ij");
memory->create(preExp3B_ij,nthreads*leadDimInteractionList,"edip:preExp3B_ij"); memory->create(preExp3B_ij, nthreads * leadDimInteractionList, "edip:preExp3B_ij");
memory->create(preExp3BDerived_ij,nthreads*leadDimInteractionList, memory->create(preExp3BDerived_ij, nthreads * leadDimInteractionList, "edip:preExp3BDerived_ij");
"edip:preExp3BDerived_ij"); memory->create(preExp2B_ij, nthreads * leadDimInteractionList, "edip:preExp2B_ij");
memory->create(preExp2B_ij,nthreads*leadDimInteractionList,"edip:preExp2B_ij"); memory->create(preExp2BDerived_ij, nthreads * leadDimInteractionList, "edip:preExp2BDerived_ij");
memory->create(preExp2BDerived_ij,nthreads*leadDimInteractionList, memory->create(prePow2B_ij, nthreads * leadDimInteractionList, "edip:prePow2B_ij");
"edip:preExp2BDerived_ij"); memory->create(preForceCoord, 5 * nthreads * leadDimInteractionList, "edip:preForceCoord");
memory->create(prePow2B_ij,nthreads*leadDimInteractionList,"edip:prePow2B_ij");
memory->create(preForceCoord,5*nthreads*leadDimInteractionList,"edip:preForceCoord");
} }
/* ---------------------------------------------------------------------- /* ----------------------------------------------------------------------
@ -613,19 +580,19 @@ void PairEDIP::allocate()
allocated = 1; allocated = 1;
int n = atom->ntypes; int n = atom->ntypes;
memory->create(setflag,n+1,n+1,"pair:setflag"); memory->create(setflag, n + 1, n + 1, "pair:setflag");
memory->create(cutsq,n+1,n+1,"pair:cutsq"); memory->create(cutsq, n + 1, n + 1, "pair:cutsq");
map = new int[n+1]; map = new int[n + 1];
} }
/* ---------------------------------------------------------------------- /* ----------------------------------------------------------------------
global settings global settings
------------------------------------------------------------------------- */ ------------------------------------------------------------------------- */
void PairEDIP::settings(int narg, char **/*arg*/) void PairEDIP::settings(int narg, char ** /*arg*/)
{ {
if (narg != 0) error->all(FLERR,"Illegal pair_style command"); if (narg != 0) error->all(FLERR, "Illegal pair_style command");
} }
/* ---------------------------------------------------------------------- */ /* ---------------------------------------------------------------------- */
@ -652,105 +619,97 @@ void PairEDIP::initGrids(void)
double deltaArgumentQFunctionGrid; double deltaArgumentQFunctionGrid;
double deltaArgumentTauFunctionGrid; double deltaArgumentTauFunctionGrid;
double deltaArgumentExpMinusBetaZeta_iZeta_i; double deltaArgumentExpMinusBetaZeta_iZeta_i;
double const leftLimitToZero = -DBL_MIN * 1000.0; double const leftLimitToZero = -std::numeric_limits<double>::min() * 1000.0;
// tauFunctionGrid // tauFunctionGrid
maxArgumentTauFunctionGrid = leadDimInteractionList; maxArgumentTauFunctionGrid = leadDimInteractionList;
numGridPointsTauFunctionGrid = (int) numGridPointsTauFunctionGrid = (int) ((maxArgumentTauFunctionGrid) *GRIDDENSITY) + 2;
((maxArgumentTauFunctionGrid) * GRIDDENSITY) + 2;
r = 0.0; r = 0.0;
deltaArgumentTauFunctionGrid = 1.0 / GRIDDENSITY; deltaArgumentTauFunctionGrid = 1.0 / GRIDDENSITY;
for (l = 0; l < numGridPointsTauFunctionGrid; l++) { for (l = 0; l < numGridPointsTauFunctionGrid; l++) {
tauFunctionGrid[l] = u1 + u2 * u3 * exp(-u4 * r) - tauFunctionGrid[l] = u1 + u2 * u3 * exp(-u4 * r) - u2 * exp(-2.0 * 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);
tauFunctionDerivedGrid[l] = - u2 * u3 * u4 * exp(-u4 * r) + r += deltaArgumentTauFunctionGrid;
2.0 * u2 * u4 * exp(-2.0 * u4 * r);
r += deltaArgumentTauFunctionGrid;
} }
// expMinusBetaZeta_iZeta_iGrid // expMinusBetaZeta_iZeta_iGrid
maxArgumentExpMinusBetaZeta_iZeta_i = leadDimInteractionList; maxArgumentExpMinusBetaZeta_iZeta_i = leadDimInteractionList;
numGridPointsExpMinusBetaZeta_iZeta_i = (int) numGridPointsExpMinusBetaZeta_iZeta_i =
((maxArgumentExpMinusBetaZeta_iZeta_i) * GRIDDENSITY) + 2; (int) ((maxArgumentExpMinusBetaZeta_iZeta_i) *GRIDDENSITY) + 2;
r = 0.0; r = 0.0;
deltaArgumentExpMinusBetaZeta_iZeta_i = 1.0 / GRIDDENSITY; deltaArgumentExpMinusBetaZeta_iZeta_i = 1.0 / GRIDDENSITY;
for (l = 0; l < numGridPointsExpMinusBetaZeta_iZeta_i; l++) { for (l = 0; l < numGridPointsExpMinusBetaZeta_iZeta_i; l++) {
expMinusBetaZeta_iZeta_iGrid[l] = exp(-beta * r * r); expMinusBetaZeta_iZeta_iGrid[l] = exp(-beta * r * r);
r += deltaArgumentExpMinusBetaZeta_iZeta_i; r += deltaArgumentExpMinusBetaZeta_iZeta_i;
} }
// qFunctionGrid // qFunctionGrid
maxArgumentQFunctionGrid = leadDimInteractionList; maxArgumentQFunctionGrid = leadDimInteractionList;
numGridPointsQFunctionGrid = numGridPointsQFunctionGrid = (int) ((maxArgumentQFunctionGrid) *GRIDDENSITY) + 2;
(int) ((maxArgumentQFunctionGrid) * GRIDDENSITY) + 2;
r = 0.0; r = 0.0;
deltaArgumentQFunctionGrid = 1.0 / GRIDDENSITY; deltaArgumentQFunctionGrid = 1.0 / GRIDDENSITY;
for (l = 0; l < numGridPointsQFunctionGrid; l++) { for (l = 0; l < numGridPointsQFunctionGrid; l++) {
qFunctionGrid[l] = Q0 * exp(-mu * r); qFunctionGrid[l] = Q0 * exp(-mu * r);
r += deltaArgumentQFunctionGrid; r += deltaArgumentQFunctionGrid;
} }
// cutoffFunction // cutoffFunction
numGridPointsOneCutoffFunction = numGridPointsOneCutoffFunction = (int) ((cutoffC - GRIDSTART) * GRIDDENSITY);
(int) ((cutoffC - GRIDSTART) * GRIDDENSITY); numGridPointsNotOneCutoffFunction = (int) ((cutoffA - cutoffC) * GRIDDENSITY);
numGridPointsNotOneCutoffFunction =
(int) ((cutoffA-cutoffC) * GRIDDENSITY);
numGridPointsCutoffFunction = numGridPointsCutoffFunction =
numGridPointsOneCutoffFunction+numGridPointsNotOneCutoffFunction+2; numGridPointsOneCutoffFunction + numGridPointsNotOneCutoffFunction + 2;
r = GRIDSTART; r = GRIDSTART;
deltaArgumentCutoffFunction = 1.0 / GRIDDENSITY; deltaArgumentCutoffFunction = 1.0 / GRIDDENSITY;
for (l = 0; l < numGridPointsOneCutoffFunction; l++) { for (l = 0; l < numGridPointsOneCutoffFunction; l++) {
cutoffFunction[l] = 1.0; cutoffFunction[l] = 1.0;
cutoffFunctionDerived[l] = 0.0; cutoffFunctionDerived[l] = 0.0;
r += deltaArgumentCutoffFunction; r += deltaArgumentCutoffFunction;
} }
for (l = numGridPointsOneCutoffFunction; for (l = numGridPointsOneCutoffFunction; l < numGridPointsCutoffFunction; l++) {
l < numGridPointsCutoffFunction; l++) { temp = (cutoffA - cutoffC) / (r - cutoffC);
temp = (cutoffA - cutoffC)/(r - cutoffC); temp3 = temp * temp * temp;
temp3 = temp * temp * temp; temp4 = temp3 * temp;
temp4 = temp3 * temp; cutoffFunction[l] = exp(alpha / (1.0 - temp3));
cutoffFunction[l] = exp(alpha/(1.0-temp3)); cutoffFunctionDerived[l] = (-3 * alpha / (cutoffA - cutoffC)) *
cutoffFunctionDerived[l] = (-3*alpha/(cutoffA-cutoffC)) * (temp4 / ((1 - temp3) * (1 - temp3))) * exp(alpha / (1.0 - temp3));
(temp4/((1-temp3)*(1-temp3)))*exp(alpha/(1.0-temp3)); r += deltaArgumentCutoffFunction;
r += deltaArgumentCutoffFunction;
} }
// pow2B // pow2B
numGridPointsR = (int) numGridPointsR = (int) ((cutoffA + leftLimitToZero - GRIDSTART) * GRIDDENSITY);
((cutoffA + leftLimitToZero - GRIDSTART) * GRIDDENSITY);
r = GRIDSTART; r = GRIDSTART;
deltaArgumentR = 1.0 / GRIDDENSITY; deltaArgumentR = 1.0 / GRIDDENSITY;
for (l = 0; l < numGridPointsR; l++) { for (l = 0; l < numGridPointsR; l++) {
pow2B[l] = pow((B/r),rho); pow2B[l] = pow((B / r), rho);
exp2B[l] = A * exp(sigma/(r-cutoffA)); exp2B[l] = A * exp(sigma / (r - cutoffA));
exp3B[l] = exp(gamm/(r-cutoffA)); exp3B[l] = exp(gamm / (r - cutoffA));
r += deltaArgumentR; r += deltaArgumentR;
} }
pow2B[numGridPointsR] = pow((B/r),rho); pow2B[numGridPointsR] = pow((B / r), rho);
exp2B[numGridPointsR]=0; exp2B[numGridPointsR] = 0;
exp3B[numGridPointsR]=0; exp3B[numGridPointsR] = 0;
r += deltaArgumentR; r += deltaArgumentR;
pow2B[numGridPointsR+1] = pow((B/r),rho); pow2B[numGridPointsR + 1] = pow((B / r), rho);
exp2B[numGridPointsR+1]=0; exp2B[numGridPointsR + 1] = 0;
exp3B[numGridPointsR+1]=0; exp3B[numGridPointsR + 1] = 0;
} }
/* ---------------------------------------------------------------------- /* ----------------------------------------------------------------------
@ -761,9 +720,8 @@ void PairEDIP::coeff(int narg, char **arg)
{ {
if (!allocated) allocate(); if (!allocated) allocate();
map_element2type(narg-3,arg+3); map_element2type(narg - 3, arg + 3);
if (nelements != 1) if (nelements != 1) error->all(FLERR, "Pair style edip only supports single element potentials");
error->all(FLERR,"Pair style edip only supports single element potentials");
// read potential file and initialize potential parameters // read potential file and initialize potential parameters
@ -783,12 +741,11 @@ void PairEDIP::coeff(int narg, char **arg)
void PairEDIP::init_style() void PairEDIP::init_style()
{ {
if (force->newton_pair == 0) if (force->newton_pair == 0) error->all(FLERR, "Pair style edip requires newton pair on");
error->all(FLERR,"Pair style edip requires newton pair on");
// need a full neighbor list // need a full neighbor list
int irequest = neighbor->request(this,instance_me); int irequest = neighbor->request(this, instance_me);
neighbor->requests[irequest]->half = 0; neighbor->requests[irequest]->half = 0;
neighbor->requests[irequest]->full = 1; neighbor->requests[irequest]->full = 1;
} }
@ -799,7 +756,7 @@ void PairEDIP::init_style()
double PairEDIP::init_one(int i, int j) double PairEDIP::init_one(int i, int j)
{ {
if (setflag[i][j] == 0) error->all(FLERR,"All pair coeffs are not set"); if (setflag[i][j] == 0) error->all(FLERR, "All pair coeffs are not set");
return cutmax; return cutmax;
} }
@ -809,7 +766,7 @@ double PairEDIP::init_one(int i, int j)
void PairEDIP::read_file(char *file) void PairEDIP::read_file(char *file)
{ {
int params_per_line = 20; int params_per_line = 20;
char **words = new char*[params_per_line+1]; char **words = new char *[params_per_line + 1];
memory->sfree(params); memory->sfree(params);
params = nullptr; params = nullptr;
@ -819,11 +776,11 @@ void PairEDIP::read_file(char *file)
FILE *fp; FILE *fp;
if (comm->me == 0) { if (comm->me == 0) {
fp = utils::open_potential(file,lmp,nullptr); fp = utils::open_potential(file, lmp, nullptr);
if (fp == nullptr) { if (fp == nullptr) {
char str[128]; char str[128];
snprintf(str,128,"Cannot open EDIP potential file %s",file); snprintf(str, 128, "Cannot open EDIP potential file %s", file);
error->one(FLERR,str); error->one(FLERR, str);
} }
} }
@ -831,26 +788,27 @@ void PairEDIP::read_file(char *file)
// one set of params can span multiple lines // one set of params can span multiple lines
// store params if all 3 element tags are in element list // store params if all 3 element tags are in element list
int n,nwords,ielement,jelement,kelement; int n, nwords, ielement, jelement, kelement;
char line[MAXLINE],*ptr; char line[MAXLINE], *ptr;
int eof = 0; int eof = 0;
while (1) { while (1) {
if (comm->me == 0) { if (comm->me == 0) {
ptr = fgets(line,MAXLINE,fp); ptr = fgets(line, MAXLINE, fp);
if (ptr == nullptr) { if (ptr == nullptr) {
eof = 1; eof = 1;
fclose(fp); fclose(fp);
} else n = strlen(line) + 1; } else
n = strlen(line) + 1;
} }
MPI_Bcast(&eof,1,MPI_INT,0,world); MPI_Bcast(&eof, 1, MPI_INT, 0, world);
if (eof) break; if (eof) break;
MPI_Bcast(&n,1,MPI_INT,0,world); MPI_Bcast(&n, 1, MPI_INT, 0, world);
MPI_Bcast(line,n,MPI_CHAR,0,world); MPI_Bcast(line, n, MPI_CHAR, 0, world);
// strip comment, skip line if blank // strip comment, skip line if blank
if ((ptr = strchr(line,'#'))) *ptr = '\0'; if ((ptr = strchr(line, '#'))) *ptr = '\0';
nwords = utils::count_words(line); nwords = utils::count_words(line);
if (nwords == 0) continue; if (nwords == 0) continue;
@ -859,54 +817,53 @@ void PairEDIP::read_file(char *file)
while (nwords < params_per_line) { while (nwords < params_per_line) {
n = strlen(line); n = strlen(line);
if (comm->me == 0) { if (comm->me == 0) {
ptr = fgets(&line[n],MAXLINE-n,fp); ptr = fgets(&line[n], MAXLINE - n, fp);
if (ptr == nullptr) { if (ptr == nullptr) {
eof = 1; eof = 1;
fclose(fp); fclose(fp);
} else n = strlen(line) + 1; } else
n = strlen(line) + 1;
} }
MPI_Bcast(&eof,1,MPI_INT,0,world); MPI_Bcast(&eof, 1, MPI_INT, 0, world);
if (eof) break; if (eof) break;
MPI_Bcast(&n,1,MPI_INT,0,world); MPI_Bcast(&n, 1, MPI_INT, 0, world);
MPI_Bcast(line,n,MPI_CHAR,0,world); MPI_Bcast(line, n, MPI_CHAR, 0, world);
if ((ptr = strchr(line,'#'))) *ptr = '\0'; if ((ptr = strchr(line, '#'))) *ptr = '\0';
nwords = utils::count_words(line); nwords = utils::count_words(line);
} }
if (nwords != params_per_line) if (nwords != params_per_line) error->all(FLERR, "Incorrect format in EDIP potential file");
error->all(FLERR,"Incorrect format in EDIP potential file");
// words = ptrs to all words in line // words = ptrs to all words in line
nwords = 0; nwords = 0;
words[nwords++] = strtok(line," \t\n\r\f"); words[nwords++] = strtok(line, " \t\n\r\f");
while ((words[nwords++] = strtok(nullptr," \t\n\r\f"))) continue; while ((words[nwords++] = strtok(nullptr, " \t\n\r\f"))) continue;
// ielement,jelement,kelement = 1st args // ielement,jelement,kelement = 1st args
// if all 3 args are in element list, then parse this line // if all 3 args are in element list, then parse this line
// else skip to next entry in file // else skip to next entry in file
for (ielement = 0; ielement < nelements; ielement++) for (ielement = 0; ielement < nelements; ielement++)
if (strcmp(words[0],elements[ielement]) == 0) break; if (strcmp(words[0], elements[ielement]) == 0) break;
if (ielement == nelements) continue; if (ielement == nelements) continue;
for (jelement = 0; jelement < nelements; jelement++) for (jelement = 0; jelement < nelements; jelement++)
if (strcmp(words[1],elements[jelement]) == 0) break; if (strcmp(words[1], elements[jelement]) == 0) break;
if (jelement == nelements) continue; if (jelement == nelements) continue;
for (kelement = 0; kelement < nelements; kelement++) for (kelement = 0; kelement < nelements; kelement++)
if (strcmp(words[2],elements[kelement]) == 0) break; if (strcmp(words[2], elements[kelement]) == 0) break;
if (kelement == nelements) continue; if (kelement == nelements) continue;
// load up parameter settings and error check their values // load up parameter settings and error check their values
if (nparams == maxparam) { if (nparams == maxparam) {
maxparam += DELTA; maxparam += DELTA;
params = (Param *) memory->srealloc(params,maxparam*sizeof(Param), params = (Param *) memory->srealloc(params, maxparam * sizeof(Param), "pair:params");
"pair:params");
// make certain all addional allocated storage is initialized // make certain all addional allocated storage is initialized
// to avoid false positives when checking with valgrind // to avoid false positives when checking with valgrind
memset(params + nparams, 0, DELTA*sizeof(Param)); memset(params + nparams, 0, DELTA * sizeof(Param));
} }
params[nparams].ielement = ielement; params[nparams].ielement = ielement;
@ -930,25 +887,24 @@ void PairEDIP::read_file(char *file)
params[nparams].u3 = atof(words[18]); params[nparams].u3 = atof(words[18]);
params[nparams].u4 = atof(words[19]); params[nparams].u4 = atof(words[19]);
if (params[nparams].A < 0.0 || params[nparams].B < 0.0 || if (params[nparams].A < 0.0 || params[nparams].B < 0.0 || params[nparams].cutoffA < 0.0 ||
params[nparams].cutoffA < 0.0 || params[nparams].cutoffC < 0.0 || params[nparams].cutoffC < 0.0 || params[nparams].alpha < 0.0 ||
params[nparams].alpha < 0.0 || params[nparams].beta < 0.0 || params[nparams].beta < 0.0 || params[nparams].eta < 0.0 || params[nparams].gamm < 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].lambda < 0.0 || params[nparams].mu < 0.0 || params[nparams].sigma < 0.0)
params[nparams].rho < 0.0 || params[nparams].sigma < 0.0) error->all(FLERR, "Illegal EDIP parameter");
error->all(FLERR,"Illegal EDIP parameter");
nparams++; nparams++;
} }
delete [] words; delete[] words;
} }
/* ---------------------------------------------------------------------- */ /* ---------------------------------------------------------------------- */
void PairEDIP::setup_params() void PairEDIP::setup_params()
{ {
int i,j,k,m,n; int i, j, k, m, n;
double rtmp; double rtmp;
// set elem3param for all triplet combinations // set elem3param for all triplet combinations
@ -956,28 +912,25 @@ void PairEDIP::setup_params()
// do not allow for ACB in place of ABC // do not allow for ACB in place of ABC
memory->destroy(elem3param); memory->destroy(elem3param);
memory->create(elem3param,nelements,nelements,nelements,"pair:elem3param"); memory->create(elem3param, nelements, nelements, nelements, "pair:elem3param");
for (i = 0; i < nelements; i++) for (i = 0; i < nelements; i++)
for (j = 0; j < nelements; j++) for (j = 0; j < nelements; j++)
for (k = 0; k < nelements; k++) { for (k = 0; k < nelements; k++) {
n = -1; n = -1;
for (m = 0; m < nparams; m++) { for (m = 0; m < nparams; m++) {
if (i == params[m].ielement && j == params[m].jelement && if (i == params[m].ielement && j == params[m].jelement && k == params[m].kelement) {
k == params[m].kelement) { if (n >= 0) error->all(FLERR, "Potential file has duplicate entry");
if (n >= 0) error->all(FLERR,"Potential file has duplicate entry");
n = m; n = m;
} }
} }
if (n < 0) error->all(FLERR,"Potential file is missing an entry"); if (n < 0) error->all(FLERR, "Potential file is missing an entry");
elem3param[i][j][k] = n; elem3param[i][j][k] = n;
} }
// set cutoff square // set cutoff square
for (m = 0; m < nparams; m++) { for (m = 0; m < nparams; m++) { params[m].cutsq = params[m].cutoffA * params[m].cutoffA; }
params[m].cutsq = params[m].cutoffA*params[m].cutoffA;
}
// set cutmax to max of all params // set cutmax to max of all params