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pair_gayberne_omp.cpp
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Sat, Oct 5, 12:25

pair_gayberne_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_gayberne_omp.h"
#include "math_extra.h"
#include "atom.h"
#include "comm.h"
#include "atom_vec_ellipsoid.h"
#include "force.h"
#include "neighbor.h"
#include "neigh_list.h"
using namespace LAMMPS_NS;
/* ---------------------------------------------------------------------- */
PairGayBerneOMP::PairGayBerneOMP(LAMMPS *lmp) :
PairGayBerne(lmp), ThrOMP(lmp, THR_PAIR)
{
respa_enable = 0;
}
/* ---------------------------------------------------------------------- */
void PairGayBerneOMP::compute(int eflag, int vflag)
{
if (eflag || vflag) {
ev_setup(eflag,vflag);
} else evflag = vflag_fdotr = 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 (eflag) {
if (force->newton_pair) eval<1,1,1>(ifrom, ito, thr);
else eval<1,1,0>(ifrom, ito, thr);
} else {
if (force->newton_pair) eval<1,0,1>(ifrom, ito, thr);
else eval<1,0,0>(ifrom, ito, thr);
}
} else {
if (force->newton_pair) eval<0,0,1>(ifrom, ito, thr);
else eval<0,0,0>(ifrom, ito, thr);
}
reduce_thr(this, eflag, vflag, thr);
} // end of omp parallel region
}
template <int EVFLAG, int EFLAG, int NEWTON_PAIR>
void PairGayBerneOMP::eval(int iifrom, int iito, ThrData * const thr)
{
int i,j,ii,jj,jnum,itype,jtype;
double evdwl,one_eng,rsq,r2inv,r6inv,forcelj,factor_lj;
double fforce[3],ttor[3],rtor[3],r12[3];
double a1[3][3],b1[3][3],g1[3][3],a2[3][3],b2[3][3],g2[3][3],temp[3][3];
int *ilist,*jlist,*numneigh,**firstneigh;
double *iquat,*jquat;
const double * const * const x = atom->x;
double * const * const f = thr->get_f();
double * const * const tor = thr->get_torque();
const int * const type = atom->type;
const int nlocal = atom->nlocal;
const double * const special_lj = force->special_lj;
const int * const ellipsoid = atom->ellipsoid;
AtomVecEllipsoid::Bonus *bonus = avec->bonus;
double fxtmp,fytmp,fztmp,t1tmp,t2tmp,t3tmp;
ilist = list->ilist;
numneigh = list->numneigh;
firstneigh = list->firstneigh;
// loop over neighbors of my atoms
for (ii = iifrom; ii < iito; ++ii) {
i = ilist[ii];
itype = type[i];
fxtmp=fytmp=fztmp=t1tmp=t2tmp=t3tmp=0.0;
if (form[itype][itype] == ELLIPSE_ELLIPSE) {
iquat = bonus[ellipsoid[i]].quat;
MathExtra::quat_to_mat_trans(iquat,a1);
MathExtra::diag_times3(well[itype],a1,temp);
MathExtra::transpose_times3(a1,temp,b1);
MathExtra::diag_times3(shape2[itype],a1,temp);
MathExtra::transpose_times3(a1,temp,g1);
}
jlist = firstneigh[i];
jnum = numneigh[i];
for (jj = 0; jj < jnum; jj++) {
j = jlist[jj];
factor_lj = special_lj[sbmask(j)];
j &= NEIGHMASK;
// r12 = center to center vector
r12[0] = x[j][0]-x[i][0];
r12[1] = x[j][1]-x[i][1];
r12[2] = x[j][2]-x[i][2];
rsq = MathExtra::dot3(r12,r12);
jtype = type[j];
if (rsq < cutsq[itype][jtype]) {
switch (form[itype][jtype]) {
case SPHERE_SPHERE:
r2inv = 1.0/rsq;
r6inv = r2inv*r2inv*r2inv;
forcelj = r6inv * (lj1[itype][jtype]*r6inv - lj2[itype][jtype]);
forcelj *= -r2inv;
if (EFLAG)
one_eng = r6inv*(r6inv*lj3[itype][jtype]-lj4[itype][jtype]) -
offset[itype][jtype];
fforce[0] = r12[0]*forcelj;
fforce[1] = r12[1]*forcelj;
fforce[2] = r12[2]*forcelj;
ttor[0] = ttor[1] = ttor[2] = 0.0;
rtor[0] = rtor[1] = rtor[2] = 0.0;
break;
case SPHERE_ELLIPSE:
jquat = bonus[ellipsoid[j]].quat;
MathExtra::quat_to_mat_trans(jquat,a2);
MathExtra::diag_times3(well[jtype],a2,temp);
MathExtra::transpose_times3(a2,temp,b2);
MathExtra::diag_times3(shape2[jtype],a2,temp);
MathExtra::transpose_times3(a2,temp,g2);
one_eng = gayberne_lj(j,i,a2,b2,g2,r12,rsq,fforce,rtor);
ttor[0] = ttor[1] = ttor[2] = 0.0;
break;
case ELLIPSE_SPHERE:
one_eng = gayberne_lj(i,j,a1,b1,g1,r12,rsq,fforce,ttor);
rtor[0] = rtor[1] = rtor[2] = 0.0;
break;
default:
jquat = bonus[ellipsoid[j]].quat;
MathExtra::quat_to_mat_trans(jquat,a2);
MathExtra::diag_times3(well[jtype],a2,temp);
MathExtra::transpose_times3(a2,temp,b2);
MathExtra::diag_times3(shape2[jtype],a2,temp);
MathExtra::transpose_times3(a2,temp,g2);
one_eng = gayberne_analytic(i,j,a1,a2,b1,b2,g1,g2,r12,rsq,
fforce,ttor,rtor);
break;
}
fforce[0] *= factor_lj;
fforce[1] *= factor_lj;
fforce[2] *= factor_lj;
ttor[0] *= factor_lj;
ttor[1] *= factor_lj;
ttor[2] *= factor_lj;
fxtmp += fforce[0];
fytmp += fforce[1];
fztmp += fforce[2];
t1tmp += ttor[0];
t2tmp += ttor[1];
t3tmp += ttor[2];
if (NEWTON_PAIR || j < nlocal) {
rtor[0] *= factor_lj;
rtor[1] *= factor_lj;
rtor[2] *= factor_lj;
f[j][0] -= fforce[0];
f[j][1] -= fforce[1];
f[j][2] -= fforce[2];
tor[j][0] += rtor[0];
tor[j][1] += rtor[1];
tor[j][2] += rtor[2];
}
if (EFLAG) evdwl = factor_lj*one_eng;
if (EVFLAG) ev_tally_xyz_thr(this,i,j,nlocal,NEWTON_PAIR,
evdwl,0.0,fforce[0],fforce[1],fforce[2],
-r12[0],-r12[1],-r12[2],thr);
}
}
f[i][0] += fxtmp;
f[i][1] += fytmp;
f[i][2] += fztmp;
tor[i][0] += t1tmp;
tor[i][1] += t2tmp;
tor[i][2] += t3tmp;
}
}
/* ---------------------------------------------------------------------- */
double PairGayBerneOMP::memory_usage()
{
double bytes = memory_usage_thr();
bytes += PairGayBerne::memory_usage();
return bytes;
}

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