ICODE-ADC/lammps
4
0
Fork 0
Code Issues Pull Requests Actions Packages Projects Releases Wiki Activity

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

Browse Source
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
Download Patch File Download Diff File Expand all files Collapse all files

105
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;
@ -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);
@ -203,8 +207,7 @@ void PairEDIPOMP::eval(int iifrom, int iito, ThrData * const thr)
interpolY1 = exp3B[interpolIDX];
interpolY2 = exp3B[interpolIDX + 1];
exp3B_ij = interpolY1 + (interpolY2 - interpolY1) *
(interpolTMP-interpolIDX);
exp3B_ij = interpolY1 + (interpolY2 - interpolY1) * (interpolTMP - interpolIDX);
exp3BDerived_ij = -exp3B_ij * gammInvRMinusCutoffA * invRMinusCutoffA;
@ -213,8 +216,7 @@ void PairEDIPOMP::eval(int iifrom, int iito, ThrData * const thr)
interpolY1 = exp2B[interpolIDX];
interpolY2 = exp2B[interpolIDX + 1];
exp2B_ij = interpolY1 + (interpolY2 - interpolY1) *
(interpolTMP-interpolIDX);
exp2B_ij = interpolY1 + (interpolY2 - interpolY1) * (interpolTMP - interpolIDX);
exp2BDerived_ij = -exp2B_ij * sigmaInvRMinusCutoffA * invRMinusCutoffA;
@ -223,26 +225,24 @@ void PairEDIPOMP::eval(int iifrom, int iito, ThrData * const thr)
interpolY1 = pow2B[interpolIDX];
interpolY2 = pow2B[interpolIDX + 1];
pow2B_ij = interpolY1 + (interpolY2 - interpolY1) *
(interpolTMP-interpolIDX);
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);
cutoffFunction_ij = interpolY1 + (interpolY2 - interpolY1) * (interpolTMP - interpolIDX);
zeta_i += cutoffFunction_ij;
interpolY1 = cutoffFunctionDerived[interpolIDX];
interpolY2 = cutoffFunctionDerived[interpolIDX + 1];
zeta_iDerived = interpolY1 + (interpolY2 - interpolY1) *
(interpolTMP-interpolIDX);
zeta_iDerived = interpolY1 + (interpolY2 - interpolY1) * (interpolTMP - interpolIDX);
zeta_iDerivedInvR_ij = zeta_iDerived * invR_ij;
@ -264,23 +264,19 @@ void PairEDIPOMP::eval(int iifrom, int iito, ThrData * const thr)
interpolY1 = expMinusBetaZeta_iZeta_iGrid[interpolIDX];
interpolY2 = expMinusBetaZeta_iZeta_iGrid[interpolIDX + 1];
expMinusBetaZeta_iZeta_i = interpolY1 + (interpolY2 - interpolY1) *
(interpolTMP-interpolIDX);
expMinusBetaZeta_iZeta_i = interpolY1 + (interpolY2 - interpolY1) * (interpolTMP - interpolIDX);
interpolY1 = qFunctionGrid[interpolIDX];
interpolY2 = qFunctionGrid[interpolIDX + 1];
qFunction = interpolY1 + (interpolY2 - interpolY1) *
(interpolTMP-interpolIDX);
qFunction = interpolY1 + (interpolY2 - interpolY1) * (interpolTMP - interpolIDX);
interpolY1 = tauFunctionGrid[interpolIDX];
interpolY2 = tauFunctionGrid[interpolIDX + 1];
tauFunction = interpolY1 + (interpolY2 - interpolY1) *
(interpolTMP-interpolIDX);
tauFunction = interpolY1 + (interpolY2 - interpolY1) * (interpolTMP - interpolIDX);
interpolY1 = tauFunctionDerivedGrid[interpolIDX];
interpolY2 = tauFunctionDerivedGrid[interpolIDX + 1];
tauFunctionDerived = interpolY1 + (interpolY2 - interpolY1) *
(interpolTMP-interpolIDX);
tauFunctionDerived = interpolY1 + (interpolY2 - interpolY1) * (interpolTMP - interpolIDX);
forceModCoord_factor = 2.0 * beta * zeta_i * expMinusBetaZeta_iZeta_i;
@ -317,8 +313,7 @@ void PairEDIPOMP::eval(int iifrom, int iito, ThrData * const thr)
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
@ -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];
@ -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);
}
}
}

197
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;
@ -209,8 +207,7 @@ void PairEDIP::compute(int eflag, int vflag)
interpolY1 = exp3B[interpolIDX];
interpolY2 = exp3B[interpolIDX + 1];
exp3B_ij = interpolY1 + (interpolY2 - interpolY1) *
(interpolTMP-interpolIDX);
exp3B_ij = interpolY1 + (interpolY2 - interpolY1) * (interpolTMP - interpolIDX);
exp3BDerived_ij = -exp3B_ij * gammInvRMinusCutoffA * invRMinusCutoffA;
@ -219,8 +216,7 @@ void PairEDIP::compute(int eflag, int vflag)
interpolY1 = exp2B[interpolIDX];
interpolY2 = exp2B[interpolIDX + 1];
exp2B_ij = interpolY1 + (interpolY2 - interpolY1) *
(interpolTMP-interpolIDX);
exp2B_ij = interpolY1 + (interpolY2 - interpolY1) * (interpolTMP - interpolIDX);
exp2BDerived_ij = -exp2B_ij * sigmaInvRMinusCutoffA * invRMinusCutoffA;
@ -229,26 +225,24 @@ void PairEDIP::compute(int eflag, int vflag)
interpolY1 = pow2B[interpolIDX];
interpolY2 = pow2B[interpolIDX + 1];
pow2B_ij = interpolY1 + (interpolY2 - interpolY1) *
(interpolTMP-interpolIDX);
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);
cutoffFunction_ij = interpolY1 + (interpolY2 - interpolY1) * (interpolTMP - interpolIDX);
zeta_i += cutoffFunction_ij;
interpolY1 = cutoffFunctionDerived[interpolIDX];
interpolY2 = cutoffFunctionDerived[interpolIDX + 1];
zeta_iDerived = interpolY1 + (interpolY2 - interpolY1) *
(interpolTMP-interpolIDX);
zeta_iDerived = interpolY1 + (interpolY2 - interpolY1) * (interpolTMP - interpolIDX);
zeta_iDerivedInvR_ij = zeta_iDerived * invR_ij;
@ -270,23 +264,19 @@ void PairEDIP::compute(int eflag, int vflag)
interpolY1 = expMinusBetaZeta_iZeta_iGrid[interpolIDX];
interpolY2 = expMinusBetaZeta_iZeta_iGrid[interpolIDX + 1];
expMinusBetaZeta_iZeta_i = interpolY1 + (interpolY2 - interpolY1) *
(interpolTMP-interpolIDX);
expMinusBetaZeta_iZeta_i = interpolY1 + (interpolY2 - interpolY1) * (interpolTMP - interpolIDX);
interpolY1 = qFunctionGrid[interpolIDX];
interpolY2 = qFunctionGrid[interpolIDX + 1];
qFunction = interpolY1 + (interpolY2 - interpolY1) *
(interpolTMP-interpolIDX);
qFunction = interpolY1 + (interpolY2 - interpolY1) * (interpolTMP - interpolIDX);
interpolY1 = tauFunctionGrid[interpolIDX];
interpolY2 = tauFunctionGrid[interpolIDX + 1];
tauFunction = interpolY1 + (interpolY2 - interpolY1) *
(interpolTMP-interpolIDX);
tauFunction = interpolY1 + (interpolY2 - interpolY1) * (interpolTMP - interpolIDX);
interpolY1 = tauFunctionDerivedGrid[interpolIDX];
interpolY2 = tauFunctionDerivedGrid[interpolIDX + 1];
tauFunctionDerived = interpolY1 + (interpolY2 - interpolY1) *
(interpolTMP-interpolIDX);
tauFunctionDerived = interpolY1 + (interpolY2 - interpolY1) * (interpolTMP - interpolIDX);
forceModCoord_factor = 2.0 * beta * zeta_i * expMinusBetaZeta_iZeta_i;
@ -323,8 +313,7 @@ void PairEDIP::compute(int eflag, int vflag)
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
@ -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];
@ -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]);
}
}
@ -500,53 +476,46 @@ 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(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;
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;
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");
@ -565,11 +534,9 @@ void PairEDIP::allocatePreLoops(void)
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(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(preExp2BDerived_ij, nthreads * leadDimInteractionList, "edip:preExp2BDerived_ij");
memory->create(prePow2B_ij, nthreads * leadDimInteractionList, "edip:prePow2B_ij");
memory->create(preForceCoord, 5 * nthreads * leadDimInteractionList, "edip:preForceCoord");
}
@ -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;
@ -703,10 +666,8 @@ 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;
@ -719,8 +680,7 @@ void PairEDIP::initGrids(void)
r += deltaArgumentCutoffFunction;
}
for (l = numGridPointsOneCutoffFunction;
l < numGridPointsCutoffFunction; l++) {
for (l = numGridPointsOneCutoffFunction; l < numGridPointsCutoffFunction; l++) {
temp = (cutoffA - cutoffC) / (r - cutoffC);
temp3 = temp * temp * temp;
temp4 = temp3 * temp;
@ -732,8 +692,7 @@ void PairEDIP::initGrids(void)
// pow2B
numGridPointsR = (int)
((cutoffA + leftLimitToZero - GRIDSTART) * GRIDDENSITY);
numGridPointsR = (int) ((cutoffA + leftLimitToZero - GRIDSTART) * GRIDDENSITY);
r = GRIDSTART;
deltaArgumentR = 1.0 / GRIDDENSITY;
@ -762,8 +721,7 @@ 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");
if (nelements != 1) error->all(FLERR, "Pair style edip only supports single element potentials");
// read potential file and initialize potential parameters
@ -783,8 +741,7 @@ 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
@ -841,7 +798,8 @@ void PairEDIP::read_file(char *file)
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);
if (eof) break;
@ -863,7 +821,8 @@ void PairEDIP::read_file(char *file)
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);
if (eof) break;
@ -873,8 +832,7 @@ void PairEDIP::read_file(char *file)
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
@ -900,8 +858,7 @@ void PairEDIP::read_file(char *file)
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
@ -930,12 +887,11 @@ 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)
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++;
@ -963,8 +919,7 @@ void PairEDIP::setup_params()
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 (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;
}
@ -975,9 +930,7 @@ void PairEDIP::setup_params()
// 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