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bond_fene_omp.cpp
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Fri, May 24, 07:15

bond_fene_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
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
certain rights in this software. 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 "bond_fene_omp.h"
#include "atom.h"
#include "comm.h"
#include "force.h"
#include "neighbor.h"
#include "domain.h"
#include "error.h"
#include "update.h"
#include <math.h>
#include "suffix.h"
using namespace LAMMPS_NS;
/* ---------------------------------------------------------------------- */
BondFENEOMP::BondFENEOMP(class LAMMPS *lmp)
: BondFENE(lmp), ThrOMP(lmp,THR_BOND)
{
suffix_flag |= Suffix::OMP;
}
/* ---------------------------------------------------------------------- */
void BondFENEOMP::compute(int eflag, int vflag)
{
if (eflag || vflag) {
ev_setup(eflag,vflag);
} else evflag = 0;
const int nall = atom->nlocal + atom->nghost;
const int nthreads = comm->nthreads;
const int inum = neighbor->nbondlist;
#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_bond) eval<1,1,1>(ifrom, ito, thr);
else eval<1,1,0>(ifrom, ito, thr);
} else {
if (force->newton_bond) eval<1,0,1>(ifrom, ito, thr);
else eval<1,0,0>(ifrom, ito, thr);
}
} else {
if (force->newton_bond) 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_BOND>
void BondFENEOMP::eval(int nfrom, int nto, ThrData * const thr)
{
int i1,i2,n,type;
double delx,dely,delz,ebond,fbond;
double rsq,r0sq,rlogarg,sr2,sr6;
const double * const * const x = atom->x;
double * const * const f = thr->get_f();
const int * const * const bondlist = neighbor->bondlist;
const int nlocal = atom->nlocal;
const int tid = thr->get_tid();
for (n = nfrom; n < nto; n++) {
i1 = bondlist[n][0];
i2 = bondlist[n][1];
type = bondlist[n][2];
delx = x[i1][0] - x[i2][0];
dely = x[i1][1] - x[i2][1];
delz = x[i1][2] - x[i2][2];
rsq = delx*delx + dely*dely + delz*delz;
r0sq = r0[type] * r0[type];
rlogarg = 1.0 - rsq/r0sq;
// if r -> r0, then rlogarg < 0.0 which is an error
// issue a warning and reset rlogarg = epsilon
// if r > 2*r0 something serious is wrong, abort
if (rlogarg < 0.1) {
char str[128];
sprintf(str,"FENE bond too long: " BIGINT_FORMAT " %d %d %g",
update->ntimestep,atom->tag[i1],atom->tag[i2],sqrt(rsq));
error->warning(FLERR,str,0);
if (check_error_thr((rlogarg <= -3.0),tid,FLERR,"Bad FENE bond"))
return;
rlogarg = 0.1;
}
fbond = -k[type]/rlogarg;
// force from LJ term
if (rsq < TWO_1_3*sigma[type]*sigma[type]) {
sr2 = sigma[type]*sigma[type]/rsq;
sr6 = sr2*sr2*sr2;
fbond += 48.0*epsilon[type]*sr6*(sr6-0.5)/rsq;
}
// energy
if (EFLAG) {
ebond = -0.5 * k[type]*r0sq*log(rlogarg);
if (rsq < TWO_1_3*sigma[type]*sigma[type])
ebond += 4.0*epsilon[type]*sr6*(sr6-1.0) + epsilon[type];
}
// apply force to each of 2 atoms
if (NEWTON_BOND || i1 < nlocal) {
f[i1][0] += delx*fbond;
f[i1][1] += dely*fbond;
f[i1][2] += delz*fbond;
}
if (NEWTON_BOND || i2 < nlocal) {
f[i2][0] -= delx*fbond;
f[i2][1] -= dely*fbond;
f[i2][2] -= delz*fbond;
}
if (EVFLAG) ev_tally_thr(this,i1,i2,nlocal,NEWTON_BOND,
ebond,fbond,delx,dely,delz,thr);
}
}

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