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pair_eam_omp.cpp
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rLAMMPS lammps
pair_eam_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 "string.h"
#include "pair_eam_omp.h"
#include "atom.h"
#include "comm.h"
#include "force.h"
#include "memory.h"
#include "neighbor.h"
#include "neigh_list.h"
using namespace LAMMPS_NS;
/* ---------------------------------------------------------------------- */
PairEAMOMP::PairEAMOMP(LAMMPS *lmp) :
PairEAM(lmp), ThrOMP(lmp, PAIR)
{
respa_enable = 0;
}
/* ---------------------------------------------------------------------- */
void PairEAMOMP::compute(int eflag, int vflag)
{
if (eflag || vflag) {
ev_setup(eflag,vflag);
ev_setup_thr(this);
} else evflag = vflag_fdotr = eflag_global = eflag_atom = 0;
const int nall = atom->nlocal + atom->nghost;
const int nthreads = comm->nthreads;
const int inum = list->inum;
// grow energy and fp arrays if necessary
// need to be atom->nmax in length
if (atom->nmax > nmax) {
memory->destroy(rho);
memory->destroy(fp);
nmax = atom->nmax;
memory->create(rho,nthreads*nmax,"pair:rho");
memory->create(fp,nmax,"pair:fp");
}
#if defined(_OPENMP)
#pragma omp parallel default(shared)
#endif
{
int ifrom, ito, tid;
double **f, *rho_t;
f = loop_setup_thr(atom->f, ifrom, ito, tid, inum, nall, nthreads);
if (force->newton_pair)
rho_t = rho + tid*nall;
else rho_t = rho + tid*atom->nlocal;
if (evflag) {
if (eflag) {
if (force->newton_pair) eval<1,1,1>(f, rho_t, ifrom, ito, tid);
else eval<1,1,0>(f, rho_t, ifrom, ito, tid);
} else {
if (force->newton_pair) eval<1,0,1>(f, rho_t, ifrom, ito, tid);
else eval<1,0,0>(f, rho_t, ifrom, ito, tid);
}
} else {
if (force->newton_pair) eval<0,0,1>(f, rho_t, ifrom, ito, tid);
else eval<0,0,0>(f, rho_t, ifrom, ito, tid);
}
// reduce per thread forces into global force array.
data_reduce_thr(&(atom->f[0][0]), nall, nthreads, 3, tid);
} // end of omp parallel region
// reduce per thread energy and virial, if requested.
if (evflag) ev_reduce_thr(this);
if (vflag_fdotr) virial_fdotr_compute();
}
template <int EVFLAG, int EFLAG, int NEWTON_PAIR>
void PairEAMOMP::eval(double **f, double *rho_t,
int iifrom, int iito, int tid)
{
int i,j,ii,jj,m,jnum,itype,jtype;
double xtmp,ytmp,ztmp,delx,dely,delz,evdwl,fpair;
double rsq,r,p,rhoip,rhojp,z2,z2p,recip,phip,psip,phi;
double *coeff;
int *ilist,*jlist,*numneigh,**firstneigh;
evdwl = 0.0;
double **x = atom->x;
int *type = atom->type;
int nlocal = atom->nlocal;
int nall = nlocal + atom->nghost;
double fxtmp,fytmp,fztmp;
ilist = list->ilist;
numneigh = list->numneigh;
firstneigh = list->firstneigh;
// zero out density
if (NEWTON_PAIR) memset(rho_t, 0, nall*sizeof(double));
else memset(rho_t, 0, nlocal*sizeof(double));
// rho = density at each atom
// loop over neighbors of my atoms
for (ii = iifrom; ii < iito; ii++) {
i = ilist[ii];
xtmp = x[i][0];
ytmp = x[i][1];
ztmp = x[i][2];
itype = type[i];
jlist = firstneigh[i];
jnum = numneigh[i];
for (jj = 0; jj < jnum; jj++) {
j = jlist[jj];
j &= NEIGHMASK;
delx = xtmp - x[j][0];
dely = ytmp - x[j][1];
delz = ztmp - x[j][2];
rsq = delx*delx + dely*dely + delz*delz;
if (rsq < cutforcesq) {
jtype = type[j];
p = sqrt(rsq)*rdr + 1.0;
m = static_cast<int> (p);
m = MIN(m,nr-1);
p -= m;
p = MIN(p,1.0);
coeff = rhor_spline[type2rhor[jtype][itype]][m];
rho_t[i] += ((coeff[3]*p + coeff[4])*p + coeff[5])*p + coeff[6];
if (NEWTON_PAIR || j < nlocal) {
coeff = rhor_spline[type2rhor[itype][jtype]][m];
rho_t[j] += ((coeff[3]*p + coeff[4])*p + coeff[5])*p + coeff[6];
}
}
}
}
// wait until all threads are done with computation
sync_threads();
// communicate and sum densities
if (NEWTON_PAIR) {
// reduce per thread density
data_reduce_thr(&(rho[0]), nall, comm->nthreads, 1, tid);
// wait until reduction is complete
sync_threads();
#if defined(_OPENMP)
#pragma omp master
#endif
{ comm->reverse_comm_pair(this); }
// wait until master thread is done with communication
sync_threads();
} else {
data_reduce_thr(&(rho[0]), nlocal, comm->nthreads, 1, tid);
// wait until reduction is complete
sync_threads();
}
// fp = derivative of embedding energy at each atom
// phi = embedding energy at each atom
for (ii = iifrom; ii < iito; ii++) {
i = ilist[ii];
p = rho[i]*rdrho + 1.0;
m = static_cast<int> (p);
m = MAX(1,MIN(m,nrho-1));
p -= m;
p = MIN(p,1.0);
coeff = frho_spline[type2frho[type[i]]][m];
fp[i] = (coeff[0]*p + coeff[1])*p + coeff[2];
if (EFLAG) {
phi = ((coeff[3]*p + coeff[4])*p + coeff[5])*p + coeff[6];
if (eflag_global) eng_vdwl_thr[tid] += phi;
if (eflag_atom) eatom_thr[tid][i] += phi;
}
}
// wait until all theads are done with computation
sync_threads();
// communicate derivative of embedding function
// MPI communication only on master thread
#if defined(_OPENMP)
#pragma omp master
#endif
{ comm->forward_comm_pair(this); }
// wait until master thread is done with communication
sync_threads();
// compute forces on each atom
// loop over neighbors of my atoms
for (ii = iifrom; ii < iito; ii++) {
i = ilist[ii];
xtmp = x[i][0];
ytmp = x[i][1];
ztmp = x[i][2];
itype = type[i];
fxtmp = fytmp = fztmp = 0.0;
jlist = firstneigh[i];
jnum = numneigh[i];
for (jj = 0; jj < jnum; jj++) {
j = jlist[jj];
j &= NEIGHMASK;
delx = xtmp - x[j][0];
dely = ytmp - x[j][1];
delz = ztmp - x[j][2];
rsq = delx*delx + dely*dely + delz*delz;
if (rsq < cutforcesq) {
jtype = type[j];
r = sqrt(rsq);
p = r*rdr + 1.0;
m = static_cast<int> (p);
m = MIN(m,nr-1);
p -= m;
p = MIN(p,1.0);
// rhoip = derivative of (density at atom j due to atom i)
// rhojp = derivative of (density at atom i due to atom j)
// phi = pair potential energy
// phip = phi'
// z2 = phi * r
// z2p = (phi * r)' = (phi' r) + phi
// psip needs both fp[i] and fp[j] terms since r_ij appears in two
// terms of embed eng: Fi(sum rho_ij) and Fj(sum rho_ji)
// hence embed' = Fi(sum rho_ij) rhojp + Fj(sum rho_ji) rhoip
coeff = rhor_spline[type2rhor[itype][jtype]][m];
rhoip = (coeff[0]*p + coeff[1])*p + coeff[2];
coeff = rhor_spline[type2rhor[jtype][itype]][m];
rhojp = (coeff[0]*p + coeff[1])*p + coeff[2];
coeff = z2r_spline[type2z2r[itype][jtype]][m];
z2p = (coeff[0]*p + coeff[1])*p + coeff[2];
z2 = ((coeff[3]*p + coeff[4])*p + coeff[5])*p + coeff[6];
recip = 1.0/r;
phi = z2*recip;
phip = z2p*recip - phi*recip;
psip = fp[i]*rhojp + fp[j]*rhoip + phip;
fpair = -psip*recip;
fxtmp += delx*fpair;
fytmp += dely*fpair;
fztmp += delz*fpair;
if (NEWTON_PAIR || j < nlocal) {
f[j][0] -= delx*fpair;
f[j][1] -= dely*fpair;
f[j][2] -= delz*fpair;
}
if (EFLAG) evdwl = phi;
if (EVFLAG) ev_tally_thr(this, i,j,nlocal,NEWTON_PAIR,
evdwl,0.0,fpair,delx,dely,delz,tid);
}
}
f[i][0] += fxtmp;
f[i][1] += fytmp;
f[i][2] += fztmp;
}
}
/* ---------------------------------------------------------------------- */
double PairEAMOMP::memory_usage()
{
double bytes = memory_usage_thr();
bytes += PairEAM::memory_usage();
return bytes;
}
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