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pair_tersoff_table_omp.cpp
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/* ----------------------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
http://lammps.sandia.gov, Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov
This software is distributed under the GNU General Public License.
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
/* ----------------------------------------------------------------------
Contributing author: Axel Kohlmeyer (Temple U)
------------------------------------------------------------------------- */
#include "math.h"
#include "pair_tersoff_table_omp.h"
#include "atom.h"
#include "comm.h"
#include "error.h"
#include "force.h"
#include "neighbor.h"
#include "neigh_list.h"
#include "suffix.h"
using namespace LAMMPS_NS;
#define GRIDSTART 0.1
#define GRIDDENSITY_FCUTOFF 5000
#define GRIDDENSITY_EXP 12000
#define GRIDDENSITY_GTETA 12000
#define GRIDDENSITY_BIJ 7500
// max number of interaction per atom for environment potential
#define leadingDimensionInteractionList 64
/* ---------------------------------------------------------------------- */
PairTersoffTableOMP::PairTersoffTableOMP(LAMMPS *lmp) :
PairTersoffTable(lmp), ThrOMP(lmp, THR_PAIR)
{
suffix_flag |= Suffix::OMP;
respa_enable = 0;
}
/* ---------------------------------------------------------------------- */
void PairTersoffTableOMP::compute(int eflag, int vflag)
{
if (eflag || vflag) {
ev_setup(eflag,vflag);
} else evflag = vflag_fdotr = vflag_atom = 0;
const int nall = atom->nlocal + atom->nghost;
const int nthreads = comm->nthreads;
const int inum = list->inum;
#if defined(_OPENMP)
#pragma omp parallel default(none) shared(eflag,vflag)
#endif
{
int ifrom, ito, tid;
loop_setup_thr(ifrom, ito, tid, inum, nthreads);
ThrData *thr = fix->get_thr(tid);
ev_setup_thr(eflag, vflag, nall, eatom, vatom, thr);
if (evflag)
if (vflag_atom) eval<1,1>(ifrom, ito, thr);
else eval<1,0>(ifrom, ito, thr);
else eval<0,0>(ifrom, ito, thr);
reduce_thr(this, eflag, vflag, thr);
} // end of omp parallel region
}
template <int EVFLAG, int VFLAG_ATOM>
void PairTersoffTableOMP::eval(int iifrom, int iito, ThrData * const thr)
{
int i,j,k,ii,inum,jnum;
int itype,jtype,ktype,ijparam,ikparam,ijkparam;
double xtmp,ytmp,ztmp;
double fxtmp,fytmp,fztmp;
int *ilist,*jlist,*numneigh,**firstneigh;
int interpolIDX;
double r_ik_x, r_ik_y, r_ik_z;
double directorCos_ij_x, directorCos_ij_y, directorCos_ij_z, directorCos_ik_x, directorCos_ik_y, directorCos_ik_z;
double invR_ij, invR_ik, cosTeta;
double repulsivePotential, attractivePotential;
double exponentRepulsivePotential, exponentAttractivePotential,interpolTMP,interpolDeltaX,interpolY1;
double interpolY2, cutoffFunctionIJ, attractiveExponential, repulsiveExponential, cutoffFunctionDerivedIJ,zeta;
double gtetaFunctionIJK,gtetaFunctionDerivedIJK,cutoffFunctionIK;
double cutoffFunctionDerivedIK,factor_force3_ij,factor_1_force3_ik;
double factor_2_force3_ik,betaZetaPowerIJK,betaZetaPowerDerivedIJK,factor_force_tot;
double factor_force_ij;
double gtetaFunctionDerived_temp,gtetaFunction_temp;
double evdwl = 0.0;
const double * const * const x = atom->x;
double * const * const f = thr->get_f();
const int * const type = atom->type;
const int nlocal = atom->nlocal;
const int tid = thr->get_tid();
inum = list->inum;
ilist = list->ilist;
numneigh = list->numneigh;
firstneigh = list->firstneigh;
// loop over full neighbor list of my atoms
for (ii = iifrom; ii < iito; ii++) {
i = ilist[ii];
itype = map[type[i]];
xtmp = x[i][0];
ytmp = x[i][1];
ztmp = x[i][2];
fxtmp = fytmp = fztmp = 0.0;
jlist = firstneigh[i];
jnum = numneigh[i];
if (check_error_thr((jnum > leadingDimensionInteractionList), tid,
FLERR,"Too many neighbors for interaction list.\n"
"Check your system or increase 'leadingDimension"
"InteractionList'"))
return;
// Pre-calculate gteta and cutoff function
for (int neighbor_j = 0; neighbor_j < jnum; neighbor_j++) {
double dr_ij[3], r_ij;
j = jlist[neighbor_j];
j &= NEIGHMASK;
dr_ij[0] = xtmp - x[j][0];
dr_ij[1] = ytmp - x[j][1];
dr_ij[2] = ztmp - x[j][2];
r_ij = dr_ij[0]*dr_ij[0] + dr_ij[1]*dr_ij[1] + dr_ij[2]*dr_ij[2];
jtype = map[type[j]];
ijparam = elem2param[itype][jtype][jtype];
if (r_ij > params[ijparam].cutsq) continue;
r_ij = sqrt(r_ij);
invR_ij = 1.0 / r_ij;
directorCos_ij_x = invR_ij * dr_ij[0];
directorCos_ij_y = invR_ij * dr_ij[1];
directorCos_ij_z = invR_ij * dr_ij[2];
// preCutoffFunction
interpolDeltaX = r_ij - GRIDSTART;
interpolTMP = (interpolDeltaX * GRIDDENSITY_FCUTOFF);
interpolIDX = (int) interpolTMP;
interpolY1 = cutoffFunction[itype][jtype][interpolIDX];
interpolY2 = cutoffFunction[itype][jtype][interpolIDX+1];
preCutoffFunction[neighbor_j] = interpolY1 + (interpolY2 - interpolY1) * (interpolTMP - interpolIDX);
// preCutoffFunctionDerived
interpolY1 = cutoffFunctionDerived[itype][jtype][interpolIDX];
interpolY2 = cutoffFunctionDerived[itype][jtype][interpolIDX+1];
preCutoffFunctionDerived[neighbor_j] = interpolY1 + (interpolY2 - interpolY1) * (interpolTMP - interpolIDX);
for (int neighbor_k = neighbor_j + 1; neighbor_k < jnum; neighbor_k++) {
double dr_ik[3], r_ik;
k = jlist[neighbor_k];
k &= NEIGHMASK;
ktype = map[type[k]];
ikparam = elem2param[itype][ktype][ktype];
ijkparam = elem2param[itype][jtype][ktype];
dr_ik[0] = xtmp -x[k][0];
dr_ik[1] = ytmp -x[k][1];
dr_ik[2] = ztmp -x[k][2];
r_ik = dr_ik[0]*dr_ik[0] + dr_ik[1]*dr_ik[1] + dr_ik[2]*dr_ik[2];
if (r_ik > params[ikparam].cutsq) continue;
r_ik = sqrt(r_ik);
invR_ik = 1.0 / r_ik;
directorCos_ik_x = invR_ik * dr_ik[0];
directorCos_ik_y = invR_ik * dr_ik[1];
directorCos_ik_z = invR_ik * dr_ik[2];
cosTeta = directorCos_ij_x * directorCos_ik_x + directorCos_ij_y * directorCos_ik_y + directorCos_ij_z * directorCos_ik_z;
// preGtetaFunction
interpolDeltaX=cosTeta+1.0;
interpolTMP = (interpolDeltaX * GRIDDENSITY_GTETA);
interpolIDX = (int) interpolTMP;
interpolY1 = gtetaFunction[itype][interpolIDX];
interpolY2 = gtetaFunction[itype][interpolIDX+1];
gtetaFunction_temp = interpolY1 + (interpolY2 - interpolY1) * (interpolTMP - interpolIDX);
// preGtetaFunctionDerived
interpolY1 = gtetaFunctionDerived[itype][interpolIDX];
interpolY2 = gtetaFunctionDerived[itype][interpolIDX+1];
gtetaFunctionDerived_temp = interpolY1 + (interpolY2 - interpolY1) * (interpolTMP - interpolIDX);
preGtetaFunction[neighbor_j][neighbor_k]=params[ijkparam].gamma*gtetaFunction_temp;
preGtetaFunctionDerived[neighbor_j][neighbor_k]=params[ijkparam].gamma*gtetaFunctionDerived_temp;
preGtetaFunction[neighbor_k][neighbor_j]=params[ijkparam].gamma*gtetaFunction_temp;
preGtetaFunctionDerived[neighbor_k][neighbor_j]=params[ijkparam].gamma*gtetaFunctionDerived_temp;
} // loop on K
} // loop on J
// loop over neighbours of atom i
for (int neighbor_j = 0; neighbor_j < jnum; neighbor_j++) {
double dr_ij[3], r_ij, f_ij[3];
j = jlist[neighbor_j];
j &= NEIGHMASK;
dr_ij[0] = xtmp - x[j][0];
dr_ij[1] = ytmp - x[j][1];
dr_ij[2] = ztmp - x[j][2];
r_ij = dr_ij[0]*dr_ij[0] + dr_ij[1]*dr_ij[1] + dr_ij[2]*dr_ij[2];
jtype = map[type[j]];
ijparam = elem2param[itype][jtype][jtype];
if (r_ij > params[ijparam].cutsq) continue;
r_ij = sqrt(r_ij);
invR_ij = 1.0 / r_ij;
directorCos_ij_x = invR_ij * dr_ij[0];
directorCos_ij_y = invR_ij * dr_ij[1];
directorCos_ij_z = invR_ij * dr_ij[2];
exponentRepulsivePotential = params[ijparam].lam1 * r_ij;
exponentAttractivePotential = params[ijparam].lam2 * r_ij;
// repulsiveExponential
interpolDeltaX = exponentRepulsivePotential - minArgumentExponential;
interpolTMP = (interpolDeltaX * GRIDDENSITY_EXP);
interpolIDX = (int) interpolTMP;
interpolY1 = exponential[interpolIDX];
interpolY2 = exponential[interpolIDX+1];
repulsiveExponential = interpolY1 + (interpolY2 - interpolY1) * (interpolTMP - interpolIDX);
// attractiveExponential
interpolDeltaX = exponentAttractivePotential - minArgumentExponential;
interpolTMP = (interpolDeltaX * GRIDDENSITY_EXP);
interpolIDX = (int) interpolTMP;
interpolY1 = exponential[interpolIDX];
interpolY2 = exponential[interpolIDX+1];
attractiveExponential = interpolY1 + (interpolY2 - interpolY1) * (interpolTMP - interpolIDX);
repulsivePotential = params[ijparam].biga * repulsiveExponential;
attractivePotential = -params[ijparam].bigb * attractiveExponential;
cutoffFunctionIJ = preCutoffFunction[neighbor_j];
cutoffFunctionDerivedIJ = preCutoffFunctionDerived[neighbor_j];
zeta = 0.0;
// first loop over neighbours of atom i except j - part 1/2
for (int neighbor_k = 0; neighbor_k < neighbor_j; neighbor_k++) {
double dr_ik[3], r_ik;
k = jlist[neighbor_k];
k &= NEIGHMASK;
ktype = map[type[k]];
ikparam = elem2param[itype][ktype][ktype];
ijkparam = elem2param[itype][jtype][ktype];
dr_ik[0] = xtmp -x[k][0];
dr_ik[1] = ytmp -x[k][1];
dr_ik[2] = ztmp -x[k][2];
r_ik = dr_ik[0]*dr_ik[0] + dr_ik[1]*dr_ik[1] + dr_ik[2]*dr_ik[2];
if (r_ik > params[ikparam].cutsq) continue;
r_ik = sqrt(r_ik);
invR_ik = 1.0 / r_ik;
directorCos_ik_x = invR_ik * r_ik_x;
directorCos_ik_y = invR_ik * r_ik_y;
directorCos_ik_z = invR_ik * r_ik_z;
gtetaFunctionIJK = preGtetaFunction[neighbor_j][neighbor_k];
cutoffFunctionIK = preCutoffFunction[neighbor_k];
zeta += cutoffFunctionIK * gtetaFunctionIJK;
}
// first loop over neighbours of atom i except j - part 2/2
for (int neighbor_k = neighbor_j+1; neighbor_k < jnum; neighbor_k++) {
double dr_ik[3], r_ik;
k = jlist[neighbor_k];
k &= NEIGHMASK;
ktype = map[type[k]];
ikparam = elem2param[itype][ktype][ktype];
ijkparam = elem2param[itype][jtype][ktype];
dr_ik[0] = xtmp -x[k][0];
dr_ik[1] = ytmp -x[k][1];
dr_ik[2] = ztmp -x[k][2];
r_ik = dr_ik[0]*dr_ik[0] + dr_ik[1]*dr_ik[1] + dr_ik[2]*dr_ik[2];
if (r_ik > params[ikparam].cutsq) continue;
r_ik = sqrt(r_ik);
invR_ik = 1.0 / r_ik;
directorCos_ik_x = invR_ik * dr_ik[0];
directorCos_ik_y = invR_ik * dr_ik[1];
directorCos_ik_z = invR_ik * dr_ik[2];
gtetaFunctionIJK = preGtetaFunction[neighbor_j][neighbor_k];
cutoffFunctionIK = preCutoffFunction[neighbor_k];
zeta += cutoffFunctionIK * gtetaFunctionIJK;
}
// betaZetaPowerIJK
interpolDeltaX= params[ijparam].beta * zeta;
interpolTMP = (interpolDeltaX * GRIDDENSITY_BIJ);
interpolIDX = (int) interpolTMP;
interpolY1 = betaZetaPower[itype][interpolIDX];
interpolY2 = betaZetaPower[itype][interpolIDX+1];
betaZetaPowerIJK = (interpolY1 + (interpolY2 - interpolY1) * (interpolTMP - interpolIDX));
// betaZetaPowerDerivedIJK
interpolY1 = betaZetaPowerDerived[itype][interpolIDX];
interpolY2 = betaZetaPowerDerived[itype][interpolIDX+1];
betaZetaPowerDerivedIJK = params[ijparam].beta*(interpolY1 + (interpolY2 - interpolY1) * (interpolTMP - interpolIDX));
// Forces and virial
factor_force_ij = 0.5*cutoffFunctionDerivedIJ*(repulsivePotential + attractivePotential * betaZetaPowerIJK)+0.5*cutoffFunctionIJ*(-repulsivePotential*params[ijparam].lam1-betaZetaPowerIJK*attractivePotential*params[ijparam].lam2);
f_ij[0] = factor_force_ij * directorCos_ij_x;
f_ij[1] = factor_force_ij * directorCos_ij_y;
f_ij[2] = factor_force_ij * directorCos_ij_z;
f[j][0] += f_ij[0];
f[j][1] += f_ij[1];
f[j][2] += f_ij[2];
fxtmp -= f_ij[0];
fytmp -= f_ij[1];
fztmp -= f_ij[2];
// potential energy
evdwl = cutoffFunctionIJ * repulsivePotential
+ cutoffFunctionIJ * attractivePotential * betaZetaPowerIJK;
if (EVFLAG) ev_tally_thr(this,i, j, nlocal, /* newton_pair */ 1, 0.5 * evdwl, 0.0,
-factor_force_ij*invR_ij, dr_ij[0], dr_ij[1], dr_ij[2],thr);
factor_force_tot= 0.5*cutoffFunctionIJ*attractivePotential*betaZetaPowerDerivedIJK;
// second loop over neighbours of atom i except j, forces and virial only - part 1/2
for (int neighbor_k = 0; neighbor_k < neighbor_j; neighbor_k++) {
double dr_ik[3], r_ik, f_ik[3];
k = jlist[neighbor_k];
k &= NEIGHMASK;
ktype = map[type[k]];
ikparam = elem2param[itype][ktype][ktype];
ijkparam = elem2param[itype][jtype][ktype];
dr_ik[0] = xtmp -x[k][0];
dr_ik[1] = ytmp -x[k][1];
dr_ik[2] = ztmp -x[k][2];
r_ik = dr_ik[0]*dr_ik[0] + dr_ik[1]*dr_ik[1] + dr_ik[2]*dr_ik[2];
if (r_ik > params[ikparam].cutsq) continue;
r_ik = sqrt(r_ik);
invR_ik = 1.0 / r_ik;
directorCos_ik_x = invR_ik * dr_ik[0];
directorCos_ik_y = invR_ik * dr_ik[1];
directorCos_ik_z = invR_ik * dr_ik[2];
cosTeta = directorCos_ij_x * directorCos_ik_x + directorCos_ij_y * directorCos_ik_y
+ directorCos_ij_z * directorCos_ik_z;
gtetaFunctionIJK = preGtetaFunction[neighbor_j][neighbor_k];
gtetaFunctionDerivedIJK = preGtetaFunctionDerived[neighbor_j][neighbor_k];
cutoffFunctionIK = preCutoffFunction[neighbor_k];
cutoffFunctionDerivedIK = preCutoffFunctionDerived[neighbor_k];
factor_force3_ij= cutoffFunctionIK * gtetaFunctionDerivedIJK * invR_ij *factor_force_tot;
f_ij[0] = factor_force3_ij * (directorCos_ij_x*cosTeta - directorCos_ik_x);
f_ij[1] = factor_force3_ij * (directorCos_ij_y*cosTeta - directorCos_ik_y);
f_ij[2] = factor_force3_ij * (directorCos_ij_z*cosTeta - directorCos_ik_z);
factor_1_force3_ik = (cutoffFunctionIK * gtetaFunctionDerivedIJK * invR_ik)*factor_force_tot;
factor_2_force3_ik = -(cutoffFunctionDerivedIK * gtetaFunctionIJK)*factor_force_tot;
f_ik[0] = factor_1_force3_ik * (directorCos_ik_x*cosTeta - directorCos_ij_x)
+ factor_2_force3_ik * directorCos_ik_x;
f_ik[1] = factor_1_force3_ik * (directorCos_ik_y*cosTeta - directorCos_ij_y)
+ factor_2_force3_ik * directorCos_ik_y;
f_ik[2] = factor_1_force3_ik * (directorCos_ik_z*cosTeta - directorCos_ij_z)
+ factor_2_force3_ik * directorCos_ik_z;
f[j][0] -= f_ij[0];
f[j][1] -= f_ij[1];
f[j][2] -= f_ij[2];
f[k][0] -= f_ik[0];
f[k][1] -= f_ik[1];
f[k][2] -= f_ik[2];
fxtmp += f_ij[0] + f_ik[0];
fytmp += f_ij[1] + f_ik[1];
fztmp += f_ij[2] + f_ik[2];
if (VFLAG_ATOM) v_tally3_thr(i,j,k,f_ij,f_ik,dr_ij,dr_ik,thr);
}
// second loop over neighbours of atom i except j, forces and virial only - part 2/2
for (int neighbor_k = neighbor_j+1; neighbor_k < jnum; neighbor_k++) {
double dr_ik[3], r_ik, f_ik[3];
k = jlist[neighbor_k];
k &= NEIGHMASK;
ktype = map[type[k]];
ikparam = elem2param[itype][ktype][ktype];
ijkparam = elem2param[itype][jtype][ktype];
dr_ik[0] = xtmp -x[k][0];
dr_ik[1] = ytmp -x[k][1];
dr_ik[2] = ztmp -x[k][2];
r_ik = dr_ik[0]*dr_ik[0] + dr_ik[1]*dr_ik[1] + dr_ik[2]*dr_ik[2];
if (r_ik > params[ikparam].cutsq) continue;
r_ik = sqrt(r_ik);
invR_ik = 1.0 / r_ik;
directorCos_ik_x = invR_ik * dr_ik[0];
directorCos_ik_y = invR_ik * dr_ik[1];
directorCos_ik_z = invR_ik * dr_ik[2];
cosTeta = directorCos_ij_x * directorCos_ik_x + directorCos_ij_y * directorCos_ik_y
+ directorCos_ij_z * directorCos_ik_z;
gtetaFunctionIJK = preGtetaFunction[neighbor_j][neighbor_k];
gtetaFunctionDerivedIJK = preGtetaFunctionDerived[neighbor_j][neighbor_k];
cutoffFunctionIK = preCutoffFunction[neighbor_k];
cutoffFunctionDerivedIK = preCutoffFunctionDerived[neighbor_k];
factor_force3_ij= cutoffFunctionIK * gtetaFunctionDerivedIJK * invR_ij *factor_force_tot;
f_ij[0] = factor_force3_ij * (directorCos_ij_x*cosTeta - directorCos_ik_x);
f_ij[1] = factor_force3_ij * (directorCos_ij_y*cosTeta - directorCos_ik_y);
f_ij[2] = factor_force3_ij * (directorCos_ij_z*cosTeta - directorCos_ik_z);
factor_1_force3_ik = (cutoffFunctionIK * gtetaFunctionDerivedIJK * invR_ik)*factor_force_tot;
factor_2_force3_ik = -(cutoffFunctionDerivedIK * gtetaFunctionIJK)*factor_force_tot;
f_ik[0] = factor_1_force3_ik * (directorCos_ik_x*cosTeta - directorCos_ij_x)
+ factor_2_force3_ik * directorCos_ik_x;
f_ik[1] = factor_1_force3_ik * (directorCos_ik_y*cosTeta - directorCos_ij_y)
+ factor_2_force3_ik * directorCos_ik_y;
f_ik[2] = factor_1_force3_ik * (directorCos_ik_z*cosTeta - directorCos_ij_z)
+ factor_2_force3_ik * directorCos_ik_z;
f[j][0] -= f_ij[0];
f[j][1] -= f_ij[1];
f[j][2] -= f_ij[2];
f[k][0] -= f_ik[0];
f[k][1] -= f_ik[1];
f[k][2] -= f_ik[2];
fxtmp += f_ij[0] + f_ik[0];
fytmp += f_ij[1] + f_ik[1];
fztmp += f_ij[2] + f_ik[2];
if (VFLAG_ATOM) v_tally3_thr(i,j,k,f_ij,f_ik,dr_ij,dr_ik,thr);
}
} // loop on J
f[i][0] += fxtmp;
f[i][1] += fytmp;
f[i][2] += fztmp;
} // loop on I
}
/* ---------------------------------------------------------------------- */
double PairTersoffTableOMP::memory_usage()
{
double bytes = memory_usage_thr();
bytes += PairTersoffTable::memory_usage();
return bytes;
}

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