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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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181
src/OPENMP/pair_edip_omp.cpp
View File

@ -1,4 +1,3 @@
// clang-format off
/* ----------------------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
https://www.lammps.org/, Sandia National Laboratories
@ -19,22 +18,22 @@
#include "comm.h"
#include "neigh_list.h"
#include "suffix.h"
using namespace LAMMPS_NS;
#include <cmath>
#include "omp_compat.h"
#define GRIDDENSITY 8000
#define GRIDSTART 0.1
using namespace LAMMPS_NS;
// max number of interaction per atom for f(Z) environment potential
static constexpr int leadDimInteractionList = 64;
#define GRIDDENSITY 8000
#define GRIDSTART 0.1
/* ---------------------------------------------------------------------- */
PairEDIPOMP::PairEDIPOMP(LAMMPS *lmp) :
PairEDIP(lmp), ThrOMP(lmp, THR_PAIR)
PairEDIPOMP::PairEDIPOMP(LAMMPS *lmp) : PairEDIP(lmp), ThrOMP(lmp, THR_PAIR)
{
suffix_flag |= Suffix::OMP;
respa_enable = 0;
@ -44,14 +43,14 @@ PairEDIPOMP::PairEDIPOMP(LAMMPS *lmp) :
void PairEDIPOMP::compute(int eflag, int vflag)
{
ev_init(eflag,vflag);
ev_init(eflag, vflag);
const int nall = atom->nlocal + atom->nghost;
const int nthreads = comm->nthreads;
const int inum = list->inum;
#if defined(_OPENMP)
#pragma omp parallel LMP_DEFAULT_NONE LMP_SHARED(eflag,vflag)
#pragma omp parallel LMP_DEFAULT_NONE LMP_SHARED(eflag, vflag)
#endif
{
int ifrom, ito, tid;
@ -63,13 +62,18 @@ void PairEDIPOMP::compute(int eflag, int vflag)
if (evflag) {
if (eflag) {
if (vflag_atom) eval<1,1,1>(ifrom, ito, thr);
else eval<1,1,0>(ifrom, ito, thr);
if (vflag_atom)
eval<1, 1, 1>(ifrom, ito, thr);
else
eval<1, 1, 0>(ifrom, ito, thr);
} else {
if (vflag_atom) eval<1,0,1>(ifrom, ito, thr);
else eval<1,0,0>(ifrom, ito, thr);
if (vflag_atom)
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);
reduce_thr(this, eflag, vflag, thr);
@ -77,12 +81,12 @@ void PairEDIPOMP::compute(int eflag, int vflag)
}
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 itype,jtype,ktype,ijparam,ikparam;
double xtmp,ytmp,ztmp,evdwl;
int *ilist,*jlist,*numneigh,**firstneigh;
int i, j, k, ii, jnum;
int itype, jtype, ktype, ijparam, ikparam;
double xtmp, ytmp, ztmp, evdwl;
int *ilist, *jlist, *numneigh, **firstneigh;
int preForceCoord_counter;
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_thrForceCoord = preForceCoord + tid * leadDimInteractionList;
const dbl3_t * _noalias const x = (dbl3_t *) atom->x[0];
dbl3_t * _noalias const f = (dbl3_t *) thr->get_f()[0];
const int * _noalias const type = atom->type;
const dbl3_t *_noalias const x = (dbl3_t *) atom->x[0];
dbl3_t *_noalias const f = (dbl3_t *) thr->get_f()[0];
const int *_noalias const type = atom->type;
const int nlocal = atom->nlocal;
ilist = list->ilist;
@ -182,7 +186,7 @@ void PairEDIPOMP::eval(int iifrom, int iito, ThrData * const thr)
dr_ij[0] = xtmp - x[j].x;
dr_ij[1] = ytmp - x[j].y;
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]];
ijparam = elem3param[itype][jtype][jtype];
@ -202,56 +206,52 @@ void PairEDIPOMP::eval(int iifrom, int iito, ThrData * const thr)
interpolIDX = (int) interpolTMP;
interpolY1 = exp3B[interpolIDX];
interpolY2 = exp3B[interpolIDX+1];
exp3B_ij = interpolY1 + (interpolY2 - interpolY1) *
(interpolTMP-interpolIDX);
interpolY2 = exp3B[interpolIDX + 1];
exp3B_ij = interpolY1 + (interpolY2 - interpolY1) * (interpolTMP - interpolIDX);
exp3BDerived_ij = - exp3B_ij * gammInvRMinusCutoffA * invRMinusCutoffA;
exp3BDerived_ij = -exp3B_ij * gammInvRMinusCutoffA * invRMinusCutoffA;
pre_thrExp3B_ij[neighbor_j] = exp3B_ij;
pre_thrExp3BDerived_ij[neighbor_j] = exp3BDerived_ij;
interpolY1 = exp2B[interpolIDX];
interpolY2 = exp2B[interpolIDX+1];
exp2B_ij = interpolY1 + (interpolY2 - interpolY1) *
(interpolTMP-interpolIDX);
interpolY2 = exp2B[interpolIDX + 1];
exp2B_ij = interpolY1 + (interpolY2 - interpolY1) * (interpolTMP - interpolIDX);
exp2BDerived_ij = - exp2B_ij * sigmaInvRMinusCutoffA * invRMinusCutoffA;
exp2BDerived_ij = -exp2B_ij * sigmaInvRMinusCutoffA * invRMinusCutoffA;
pre_thrExp2B_ij[neighbor_j] = exp2B_ij;
pre_thrExp2BDerived_ij[neighbor_j] = exp2BDerived_ij;
interpolY1 = pow2B[interpolIDX];
interpolY2 = pow2B[interpolIDX+1];
pow2B_ij = interpolY1 + (interpolY2 - interpolY1) *
(interpolTMP-interpolIDX);
interpolY2 = pow2B[interpolIDX + 1];
pow2B_ij = interpolY1 + (interpolY2 - interpolY1) * (interpolTMP - interpolIDX);
pre_thrPow2B_ij[neighbor_j] = pow2B_ij;
// zeta and its derivative
if (r_ij < cutoffC) zeta_i += 1.0;
if (r_ij < cutoffC)
zeta_i += 1.0;
else {
interpolY1 = cutoffFunction[interpolIDX];
interpolY2 = cutoffFunction[interpolIDX+1];
cutoffFunction_ij = interpolY1 + (interpolY2 - interpolY1) *
(interpolTMP-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);
interpolY2 = cutoffFunctionDerived[interpolIDX + 1];
zeta_iDerived = interpolY1 + (interpolY2 - interpolY1) * (interpolTMP - interpolIDX);
zeta_iDerivedInvR_ij = zeta_iDerived * invR_ij;
preForceCoord_counter=numForceCoordPairs*5;
pre_thrForceCoord[preForceCoord_counter+0]=zeta_iDerivedInvR_ij;
pre_thrForceCoord[preForceCoord_counter+1]=dr_ij[0];
pre_thrForceCoord[preForceCoord_counter+2]=dr_ij[1];
pre_thrForceCoord[preForceCoord_counter+3]=dr_ij[2];
pre_thrForceCoord[preForceCoord_counter+4]=j;
preForceCoord_counter = numForceCoordPairs * 5;
pre_thrForceCoord[preForceCoord_counter + 0] = zeta_iDerivedInvR_ij;
pre_thrForceCoord[preForceCoord_counter + 1] = dr_ij[0];
pre_thrForceCoord[preForceCoord_counter + 2] = dr_ij[1];
pre_thrForceCoord[preForceCoord_counter + 3] = dr_ij[2];
pre_thrForceCoord[preForceCoord_counter + 4] = j;
numForceCoordPairs++;
}
}
@ -263,24 +263,20 @@ void PairEDIPOMP::eval(int iifrom, int iito, ThrData * const thr)
interpolIDX = (int) interpolTMP;
interpolY1 = expMinusBetaZeta_iZeta_iGrid[interpolIDX];
interpolY2 = expMinusBetaZeta_iZeta_iGrid[interpolIDX+1];
expMinusBetaZeta_iZeta_i = interpolY1 + (interpolY2 - interpolY1) *
(interpolTMP-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);
interpolY2 = qFunctionGrid[interpolIDX + 1];
qFunction = interpolY1 + (interpolY2 - interpolY1) * (interpolTMP - interpolIDX);
interpolY1 = tauFunctionGrid[interpolIDX];
interpolY2 = tauFunctionGrid[interpolIDX+1];
tauFunction = interpolY1 + (interpolY2 - interpolY1) *
(interpolTMP-interpolIDX);
interpolY2 = tauFunctionGrid[interpolIDX + 1];
tauFunction = interpolY1 + (interpolY2 - interpolY1) * (interpolTMP - interpolIDX);
interpolY1 = tauFunctionDerivedGrid[interpolIDX];
interpolY2 = tauFunctionDerivedGrid[interpolIDX+1];
tauFunctionDerived = interpolY1 + (interpolY2 - interpolY1) *
(interpolTMP-interpolIDX);
interpolY2 = tauFunctionDerivedGrid[interpolIDX + 1];
tauFunctionDerived = interpolY1 + (interpolY2 - interpolY1) * (interpolTMP - interpolIDX);
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[1] = x[j].y - ytmp;
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]];
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];
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];
forceMod2B = exp2BDerived_ij * potential2B_factor +
exp2B_ij * pow2BDerived_ij;
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];
@ -343,8 +338,9 @@ void PairEDIPOMP::eval(int iifrom, int iito, ThrData * const thr)
evdwl = (exp2B_ij * potential2B_factor);
if (EVFLAG) 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);
if (EVFLAG)
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
@ -359,7 +355,7 @@ void PairEDIPOMP::eval(int iifrom, int iito, ThrData * const thr)
dr_ik[0] = x[k].x - xtmp;
dr_ik[1] = x[k].y - ytmp;
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;
@ -371,15 +367,13 @@ void PairEDIPOMP::eval(int iifrom, int iito, ThrData * const thr)
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 +
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);
expMinusQFunctionCosTetaDiffCosTetaDiff = exp(-qFunctionCosTetaDiffCosTetaDiff);
potentia3B_factor = lambda *
((1.0 - expMinusQFunctionCosTetaDiffCosTetaDiff) +
@ -388,39 +382,29 @@ void PairEDIPOMP::eval(int iifrom, int iito, ThrData * const thr)
exp3B_ik = pre_thrExp3B_ij[neighbor_k];
exp3BDerived_ik = pre_thrExp3BDerived_ij[neighbor_k];
forceMod3B_factor1_ij = - exp3BDerived_ij * exp3B_ik *
potentia3B_factor;
forceMod3B_factor2 = 2.0 * lambda * exp3B_ij * exp3B_ik *
qFunction * cosTetaDiff *
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);
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);
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_factor2_ij * (cosTeta * directorCos_ij_z - directorCos_ik_z);
forceMod3B_factor1_ik = - exp3BDerived_ik * exp3B_ij *
potentia3B_factor;
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);
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);
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);
forceMod3B_factor2_ik * (cosTeta * directorCos_ik_z - directorCos_ij_z);
forceModCoord += (forceMod3B_factor2 *
(tauFunctionDerived - 0.5 * mu * cosTetaDiff));
forceModCoord += (forceMod3B_factor2 * (tauFunctionDerived - 0.5 * mu * cosTetaDiff));
f[j].x += f_ij[0];
f[j].y += f_ij[1];
@ -438,7 +422,7 @@ void PairEDIPOMP::eval(int iifrom, int iito, ThrData * const thr)
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);
}
}
@ -448,11 +432,11 @@ void PairEDIPOMP::eval(int iifrom, int iito, ThrData * const thr)
double dr_ij[3], f_ij[3];
preForceCoord_counter = idx * 5;
zeta_iDerivedInvR_ij=pre_thrForceCoord[preForceCoord_counter+0];
dr_ij[0]=pre_thrForceCoord[preForceCoord_counter+1];
dr_ij[1]=pre_thrForceCoord[preForceCoord_counter+2];
dr_ij[2]=pre_thrForceCoord[preForceCoord_counter+3];
j = static_cast<int> (pre_thrForceCoord[preForceCoord_counter+4]);
zeta_iDerivedInvR_ij = pre_thrForceCoord[preForceCoord_counter + 0];
dr_ij[0] = pre_thrForceCoord[preForceCoord_counter + 1];
dr_ij[1] = pre_thrForceCoord[preForceCoord_counter + 2];
dr_ij[2] = pre_thrForceCoord[preForceCoord_counter + 3];
j = static_cast<int>(pre_thrForceCoord[preForceCoord_counter + 4]);
forceModCoord_ij = forceModCoord * zeta_iDerivedInvR_ij;
@ -468,8 +452,9 @@ void PairEDIPOMP::eval(int iifrom, int iito, ThrData * const thr)
f[j].y += f_ij[1];
f[j].z += f_ij[2];
if (EVFLAG) 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);
if (EVFLAG)
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);
}
}
}

387
src/USER-MISC/pair_edip.cpp
View File

@ -1,4 +1,3 @@
// clang-format off
/* ----------------------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
https://www.lammps.org/, Sandia National Laboratories
@ -34,8 +33,8 @@
#include "neighbor.h"
#include <cmath>
#include <cfloat>
#include <cstring>
#include <limits>
using namespace LAMMPS_NS;
@ -53,11 +52,10 @@ static constexpr int leadDimInteractionList = 64;
PairEDIP::PairEDIP(LAMMPS *lmp) :
Pair(lmp), preInvR_ij(nullptr), preExp3B_ij(nullptr), preExp3BDerived_ij(nullptr),
preExp2B_ij(nullptr), preExp2BDerived_ij(nullptr), prePow2B_ij(nullptr),
preForceCoord(nullptr), cutoffFunction(nullptr), cutoffFunctionDerived(nullptr),
pow2B(nullptr), exp2B(nullptr), exp3B(nullptr), qFunctionGrid(nullptr),
expMinusBetaZeta_iZeta_iGrid(nullptr), tauFunctionGrid(nullptr),
tauFunctionDerivedGrid(nullptr)
preExp2B_ij(nullptr), preExp2BDerived_ij(nullptr), prePow2B_ij(nullptr), preForceCoord(nullptr),
cutoffFunction(nullptr), cutoffFunctionDerived(nullptr), pow2B(nullptr), exp2B(nullptr),
exp3B(nullptr), qFunctionGrid(nullptr), expMinusBetaZeta_iZeta_iGrid(nullptr),
tauFunctionGrid(nullptr), tauFunctionDerivedGrid(nullptr)
{
single_enable = 0;
restartinfo = 0;
@ -90,10 +88,10 @@ PairEDIP::~PairEDIP()
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;
int i, j, k, ii, inum, jnum;
int itype, jtype, ktype, ijparam, ikparam;
double xtmp, ytmp, ztmp, evdwl;
int *ilist, *jlist, *numneigh, **firstneigh;
int preForceCoord_counter;
double invR_ij;
@ -149,7 +147,7 @@ void PairEDIP::compute(int eflag, int vflag)
double potential2B_factor;
evdwl = 0.0;
ev_init(eflag,vflag);
ev_init(eflag, vflag);
double **x = atom->x;
double **f = atom->f;
@ -188,7 +186,7 @@ void PairEDIP::compute(int eflag, int vflag)
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];
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 = elem3param[itype][jtype][jtype];
@ -208,56 +206,52 @@ void PairEDIP::compute(int eflag, int vflag)
interpolIDX = (int) interpolTMP;
interpolY1 = exp3B[interpolIDX];
interpolY2 = exp3B[interpolIDX+1];
exp3B_ij = interpolY1 + (interpolY2 - interpolY1) *
(interpolTMP-interpolIDX);
interpolY2 = exp3B[interpolIDX + 1];
exp3B_ij = interpolY1 + (interpolY2 - interpolY1) * (interpolTMP - interpolIDX);
exp3BDerived_ij = - exp3B_ij * gammInvRMinusCutoffA * invRMinusCutoffA;
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);
interpolY2 = exp2B[interpolIDX + 1];
exp2B_ij = interpolY1 + (interpolY2 - interpolY1) * (interpolTMP - interpolIDX);
exp2BDerived_ij = - exp2B_ij * sigmaInvRMinusCutoffA * invRMinusCutoffA;
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);
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;
if (r_ij < cutoffC)
zeta_i += 1.0;
else {
interpolY1 = cutoffFunction[interpolIDX];
interpolY2 = cutoffFunction[interpolIDX+1];
cutoffFunction_ij = interpolY1 + (interpolY2 - interpolY1) *
(interpolTMP-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);
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;
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++;
}
}
@ -269,24 +263,20 @@ void PairEDIP::compute(int eflag, int vflag)
interpolIDX = (int) interpolTMP;
interpolY1 = expMinusBetaZeta_iZeta_iGrid[interpolIDX];
interpolY2 = expMinusBetaZeta_iZeta_iGrid[interpolIDX+1];
expMinusBetaZeta_iZeta_i = interpolY1 + (interpolY2 - interpolY1) *
(interpolTMP-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);
interpolY2 = qFunctionGrid[interpolIDX + 1];
qFunction = interpolY1 + (interpolY2 - interpolY1) * (interpolTMP - interpolIDX);
interpolY1 = tauFunctionGrid[interpolIDX];
interpolY2 = tauFunctionGrid[interpolIDX+1];
tauFunction = interpolY1 + (interpolY2 - interpolY1) *
(interpolTMP-interpolIDX);
interpolY2 = tauFunctionGrid[interpolIDX + 1];
tauFunction = interpolY1 + (interpolY2 - interpolY1) * (interpolTMP - interpolIDX);
interpolY1 = tauFunctionDerivedGrid[interpolIDX];
interpolY2 = tauFunctionDerivedGrid[interpolIDX+1];
tauFunctionDerived = interpolY1 + (interpolY2 - interpolY1) *
(interpolTMP-interpolIDX);
interpolY2 = tauFunctionDerivedGrid[interpolIDX + 1];
tauFunctionDerived = interpolY1 + (interpolY2 - interpolY1) * (interpolTMP - interpolIDX);
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[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];
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 = elem3param[itype][jtype][jtype];
@ -318,13 +308,12 @@ void PairEDIP::compute(int eflag, int vflag)
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];
forceMod2B = exp2BDerived_ij * potential2B_factor +
exp2B_ij * pow2BDerived_ij;
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];
@ -349,8 +338,9 @@ void PairEDIP::compute(int eflag, int vflag)
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]);
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
@ -365,7 +355,7 @@ void PairEDIP::compute(int eflag, int vflag)
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];
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;
@ -377,15 +367,13 @@ void PairEDIP::compute(int eflag, int vflag)
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 +
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);
expMinusQFunctionCosTetaDiffCosTetaDiff = exp(-qFunctionCosTetaDiffCosTetaDiff);
potentia3B_factor = lambda *
((1.0 - expMinusQFunctionCosTetaDiffCosTetaDiff) +
@ -394,39 +382,29 @@ void PairEDIP::compute(int eflag, int vflag)
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 *
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);
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);
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_factor2_ij * (cosTeta * directorCos_ij_z - directorCos_ik_z);
forceMod3B_factor1_ik = - exp3BDerived_ik * exp3B_ij *
potentia3B_factor;
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);
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);
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);
forceMod3B_factor2_ik * (cosTeta * directorCos_ik_z - directorCos_ij_z);
forceModCoord += (forceMod3B_factor2 *
(tauFunctionDerived - 0.5 * mu * cosTetaDiff));
forceModCoord += (forceMod3B_factor2 * (tauFunctionDerived - 0.5 * mu * cosTetaDiff));
f[j][0] += f_ij[0];
f[j][1] += f_ij[1];
@ -444,21 +422,21 @@ void PairEDIP::compute(int eflag, int vflag)
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)
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;
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]);
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;
@ -474,11 +452,9 @@ void PairEDIP::compute(int eflag, int vflag)
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 (evflag)
ev_tally(i, j, nlocal, newton_pair, 0.0, 0.0, -forceModCoord_ij, dr_ij[0], dr_ij[1],
dr_ij[2]);
}
}
@ -500,58 +476,51 @@ void PairEDIP::allocateGrids(void)
double maxArgumentTauFunctionGrid;
double maxArgumentQFunctionGrid;
double maxArgumentExpMinusBetaZeta_iZeta_i;
double const leftLimitToZero = -DBL_MIN * 1000.0;
double const leftLimitToZero = -std::numeric_limits<double>::min() * 1000.0;
deallocateGrids();
// tauFunctionGrid
maxArgumentTauFunctionGrid = leadDimInteractionList;
numGridPointsTauFunctionGrid = (int)
((maxArgumentTauFunctionGrid) * GRIDDENSITY) + 2;
numGridPointsTauFunctionGrid = (int) ((maxArgumentTauFunctionGrid) *GRIDDENSITY) + 2;
memory->create(tauFunctionGrid,numGridPointsTauFunctionGrid,
"edip:tauFunctionGrid");
memory->create(tauFunctionDerivedGrid,numGridPointsTauFunctionGrid,
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,
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");
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;
numGridPointsNotOneCutoffFunction = (int) ((cutoffA - cutoffC) * GRIDDENSITY);
numGridPointsCutoffFunction =
numGridPointsOneCutoffFunction + numGridPointsNotOneCutoffFunction + 2;
memory->create(cutoffFunction,numGridPointsCutoffFunction,
"edip:cutoffFunction");
memory->create(cutoffFunctionDerived,numGridPointsCutoffFunction,
"edip:cutoffFunctionDerived");
memory->create(cutoffFunction, numGridPointsCutoffFunction, "edip:cutoffFunction");
memory->create(cutoffFunctionDerived, numGridPointsCutoffFunction, "edip:cutoffFunctionDerived");
// pow2B
numGridPointsR = (int)
((cutoffA + leftLimitToZero - GRIDSTART) * GRIDDENSITY);
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");
memory->create(pow2B, numGridPointsRTotal, "edip:pow2B");
memory->create(exp2B, numGridPointsRTotal, "edip:exp2B");
memory->create(exp3B, numGridPointsRTotal, "edip:exp3B");
}
/* ----------------------------------------------------------------------
@ -563,15 +532,13 @@ void PairEDIP::allocatePreLoops(void)
int nthreads = comm->nthreads;
deallocatePreLoops();
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");
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");
}
/* ----------------------------------------------------------------------
@ -613,19 +580,19 @@ 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");
memory->create(setflag, n + 1, n + 1, "pair:setflag");
memory->create(cutsq, n + 1, n + 1, "pair:cutsq");
map = new int[n+1];
map = new int[n + 1];
}
/* ----------------------------------------------------------------------
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");
}
/* ---------------------------------------------------------------------- */
@ -652,23 +619,20 @@ void PairEDIP::initGrids(void)
double deltaArgumentQFunctionGrid;
double deltaArgumentTauFunctionGrid;
double deltaArgumentExpMinusBetaZeta_iZeta_i;
double const leftLimitToZero = -DBL_MIN * 1000.0;
double const leftLimitToZero = -std::numeric_limits<double>::min() * 1000.0;
// tauFunctionGrid
maxArgumentTauFunctionGrid = leadDimInteractionList;
numGridPointsTauFunctionGrid = (int)
((maxArgumentTauFunctionGrid) * GRIDDENSITY) + 2;
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);
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;
}
@ -676,8 +640,8 @@ void PairEDIP::initGrids(void)
maxArgumentExpMinusBetaZeta_iZeta_i = leadDimInteractionList;
numGridPointsExpMinusBetaZeta_iZeta_i = (int)
((maxArgumentExpMinusBetaZeta_iZeta_i) * GRIDDENSITY) + 2;
numGridPointsExpMinusBetaZeta_iZeta_i =
(int) ((maxArgumentExpMinusBetaZeta_iZeta_i) *GRIDDENSITY) + 2;
r = 0.0;
deltaArgumentExpMinusBetaZeta_iZeta_i = 1.0 / GRIDDENSITY;
@ -690,8 +654,7 @@ void PairEDIP::initGrids(void)
// qFunctionGrid
maxArgumentQFunctionGrid = leadDimInteractionList;
numGridPointsQFunctionGrid =
(int) ((maxArgumentQFunctionGrid) * GRIDDENSITY) + 2;
numGridPointsQFunctionGrid = (int) ((maxArgumentQFunctionGrid) *GRIDDENSITY) + 2;
r = 0.0;
deltaArgumentQFunctionGrid = 1.0 / GRIDDENSITY;
@ -703,12 +666,10 @@ void PairEDIP::initGrids(void)
// cutoffFunction
numGridPointsOneCutoffFunction =
(int) ((cutoffC - GRIDSTART) * GRIDDENSITY);
numGridPointsNotOneCutoffFunction =
(int) ((cutoffA-cutoffC) * GRIDDENSITY);
numGridPointsOneCutoffFunction = (int) ((cutoffC - GRIDSTART) * GRIDDENSITY);
numGridPointsNotOneCutoffFunction = (int) ((cutoffA - cutoffC) * GRIDDENSITY);
numGridPointsCutoffFunction =
numGridPointsOneCutoffFunction+numGridPointsNotOneCutoffFunction+2;
numGridPointsOneCutoffFunction + numGridPointsNotOneCutoffFunction + 2;
r = GRIDSTART;
deltaArgumentCutoffFunction = 1.0 / GRIDDENSITY;
@ -719,38 +680,36 @@ void PairEDIP::initGrids(void)
r += deltaArgumentCutoffFunction;
}
for (l = numGridPointsOneCutoffFunction;
l < numGridPointsCutoffFunction; l++) {
temp = (cutoffA - cutoffC)/(r - cutoffC);
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));
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);
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));
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;
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;
pow2B[numGridPointsR + 1] = pow((B / r), rho);
exp2B[numGridPointsR + 1] = 0;
exp3B[numGridPointsR + 1] = 0;
}
/* ----------------------------------------------------------------------
@ -761,9 +720,8 @@ void PairEDIP::coeff(int narg, char **arg)
{
if (!allocated) allocate();
map_element2type(narg-3,arg+3);
if (nelements != 1)
error->all(FLERR,"Pair style edip only supports single element potentials");
map_element2type(narg - 3, arg + 3);
if (nelements != 1) error->all(FLERR, "Pair style edip only supports single element potentials");
// read potential file and initialize potential parameters
@ -783,12 +741,11 @@ void PairEDIP::coeff(int narg, char **arg)
void PairEDIP::init_style()
{
if (force->newton_pair == 0)
error->all(FLERR,"Pair style edip requires newton pair on");
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);
int irequest = neighbor->request(this, instance_me);
neighbor->requests[irequest]->half = 0;
neighbor->requests[irequest]->full = 1;
}
@ -799,7 +756,7 @@ void PairEDIP::init_style()
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;
}
@ -809,7 +766,7 @@ double PairEDIP::init_one(int i, int j)
void PairEDIP::read_file(char *file)
{
int params_per_line = 20;
char **words = new char*[params_per_line+1];
char **words = new char *[params_per_line + 1];
memory->sfree(params);
params = nullptr;
@ -819,11 +776,11 @@ void PairEDIP::read_file(char *file)
FILE *fp;
if (comm->me == 0) {
fp = utils::open_potential(file,lmp,nullptr);
fp = utils::open_potential(file, lmp, nullptr);
if (fp == nullptr) {
char str[128];
snprintf(str,128,"Cannot open EDIP potential file %s",file);
error->one(FLERR,str);
snprintf(str, 128, "Cannot open EDIP potential file %s", file);
error->one(FLERR, str);
}
}
@ -831,26 +788,27 @@ void PairEDIP::read_file(char *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 n, nwords, ielement, jelement, kelement;
char line[MAXLINE], *ptr;
int eof = 0;
while (1) {
if (comm->me == 0) {
ptr = fgets(line,MAXLINE,fp);
ptr = fgets(line, MAXLINE, fp);
if (ptr == nullptr) {
eof = 1;
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;
MPI_Bcast(&n,1,MPI_INT,0,world);
MPI_Bcast(line,n,MPI_CHAR,0,world);
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';
if ((ptr = strchr(line, '#'))) *ptr = '\0';
nwords = utils::count_words(line);
if (nwords == 0) continue;
@ -859,54 +817,53 @@ void PairEDIP::read_file(char *file)
while (nwords < params_per_line) {
n = strlen(line);
if (comm->me == 0) {
ptr = fgets(&line[n],MAXLINE-n,fp);
ptr = fgets(&line[n], MAXLINE - n, fp);
if (ptr == nullptr) {
eof = 1;
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;
MPI_Bcast(&n,1,MPI_INT,0,world);
MPI_Bcast(line,n,MPI_CHAR,0,world);
if ((ptr = strchr(line,'#'))) *ptr = '\0';
MPI_Bcast(&n, 1, MPI_INT, 0, world);
MPI_Bcast(line, n, MPI_CHAR, 0, world);
if ((ptr = strchr(line, '#'))) *ptr = '\0';
nwords = utils::count_words(line);
}
if (nwords != params_per_line)
error->all(FLERR,"Incorrect format in EDIP potential file");
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(nullptr," \t\n\r\f"))) continue;
words[nwords++] = strtok(line, " \t\n\r\f");
while ((words[nwords++] = strtok(nullptr, " \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 (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 (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 (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 = (Param *) memory->srealloc(params, maxparam * sizeof(Param), "pair:params");
// make certain all addional allocated storage is initialized
// 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;
@ -930,25 +887,24 @@ void PairEDIP::read_file(char *file)
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");
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;
delete[] words;
}
/* ---------------------------------------------------------------------- */
void PairEDIP::setup_params()
{
int i,j,k,m,n;
int i, j, k, m, n;
double rtmp;
// set elem3param for all triplet combinations
@ -956,28 +912,25 @@ void PairEDIP::setup_params()
// do not allow for ACB in place of ABC
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 (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");
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");
if (n < 0) error->all(FLERR, "Potential file is missing an entry");
elem3param[i][j][k] = n;
}
// set cutoff square
for (m = 0; m < nparams; m++) {
params[m].cutsq = params[m].cutoffA*params[m].cutoffA;
}
for (m = 0; m < nparams; m++) { params[m].cutsq = params[m].cutoffA * params[m].cutoffA; }
// set cutmax to max of all params