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bond_quartic_omp.cpp
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Mon, Jul 1, 05:25

bond_quartic_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 "lmptype.h"
#include "bond_quartic_omp.h"
#include "atom.h"
#include "comm.h"
#include "force.h"
#include "neighbor.h"
#include "domain.h"
#include "pair.h"
#include <math.h>
using namespace LAMMPS_NS;
/* ---------------------------------------------------------------------- */
void BondQuarticOMP::compute(int eflag, int vflag)
{
if (eflag || vflag) {
ev_setup(eflag,vflag);
} else evflag = 0;
// insure pair->ev_tally() will use 1-4 virial contribution
if (vflag_global == 2)
force->pair->vflag_either = force->pair->vflag_global = 1;
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 BondQuarticOMP::eval(int nfrom, int nto, ThrData * const thr)
{
int i1,i2,n,m,type,itype,jtype;
double delx,dely,delz,ebond,fbond,evdwl,fpair;
double r,rsq,dr,r2,ra,rb,sr2,sr6;
ebond = evdwl = 0.0;
const double * const * const x = atom->x;
double * const * const f = thr->get_f();
int * const * const bondlist = neighbor->bondlist;
const double * const * const cutsq = force->pair->cutsq;
const int nlocal = atom->nlocal;
for (n = nfrom; n < nto; n++) {
// skip bond if already broken
if (bondlist[n][2] <= 0) continue;
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];
domain->minimum_image(delx,dely,delz);
rsq = delx*delx + dely*dely + delz*delz;
// if bond breaks, set type to 0
// both in temporary bondlist and permanent bond_type
// if this proc owns both atoms,
// negate bond_type twice if other atom stores it
// if other proc owns 2nd atom, other proc will also break bond
if (rsq > rc[type]*rc[type]) {
bondlist[n][2] = 0;
for (m = 0; m < atom->num_bond[i1]; m++)
if (atom->bond_atom[i1][m] == atom->tag[i2])
atom->bond_type[i1][m] = 0;
if (i2 < atom->nlocal)
for (m = 0; m < atom->num_bond[i2]; m++)
if (atom->bond_atom[i2][m] == atom->tag[i1])
atom->bond_type[i2][m] = 0;
continue;
}
// quartic bond
// 1st portion is from quartic term
// 2nd portion is from LJ term cut at 2^(1/6) with eps = sigma = 1.0
r = sqrt(rsq);
dr = r - rc[type];
r2 = dr*dr;
ra = dr - b1[type];
rb = dr - b2[type];
fbond = -k[type]/r * (r2*(ra+rb) + 2.0*dr*ra*rb);
if (rsq < TWO_1_3) {
sr2 = 1.0/rsq;
sr6 = sr2*sr2*sr2;
fbond += 48.0*sr6*(sr6-0.5)/rsq;
}
if (EFLAG) {
ebond = k[type]*r2*ra*rb + u0[type];
if (rsq < TWO_1_3) ebond += 4.0*sr6*(sr6-1.0) + 1.0;
}
// 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);
// subtract out pairwise contribution from 2 atoms via pair->single()
// required since special_bond = 1,1,1
// tally energy/virial in pair, using newton_bond as newton flag
itype = atom->type[i1];
jtype = atom->type[i2];
if (rsq < cutsq[itype][jtype]) {
evdwl = -force->pair->single(i1,i2,itype,jtype,rsq,1.0,1.0,fpair);
fpair = -fpair;
if (NEWTON_BOND || i1 < nlocal) {
f[i1][0] += delx*fpair;
f[i1][1] += dely*fpair;
f[i1][2] += delz*fpair;
}
if (NEWTON_BOND || i2 < nlocal) {
f[i2][0] -= delx*fpair;
f[i2][1] -= dely*fpair;
f[i2][2] -= delz*fpair;
}
if (EVFLAG) ev_tally_thr(force->pair,i1,i2,nlocal,NEWTON_BOND,
evdwl,0.0,fpair,delx,dely,delz,thr);
}
}
}

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