mirror of https://github.com/lammps/lammps.git
git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@11953 f3b2605a-c512-4ea7-a41b-209d697bcdaa
This commit is contained in:
sjplimp
parent
425fad8f71
commit
a93cebcc2d
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/* ----------------------------------------------------------------------
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LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
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http://lammps.sandia.gov, Sandia National Laboratories
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Steve Plimpton, sjplimp@sandia.gov
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This software is distributed under the GNU General Public License.
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See the README file in the top-level LAMMPS directory.
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------------------------------------------------------------------------- */
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/* ----------------------------------------------------------------------
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Contributing author: Axel Kohlmeyer (Temple U)
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------------------------------------------------------------------------- */
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#include "math.h"
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#include "pair_coul_cut_soft_omp.h"
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#include "atom.h"
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#include "comm.h"
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#include "force.h"
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#include "neighbor.h"
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#include "neigh_list.h"
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#include "suffix.h"
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using namespace LAMMPS_NS;
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/* ---------------------------------------------------------------------- */
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PairCoulCutSoftOMP::PairCoulCutSoftOMP(LAMMPS *lmp) :
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PairCoulCutSoft(lmp), ThrOMP(lmp, THR_PAIR)
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{
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suffix_flag |= Suffix::OMP;
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respa_enable = 0;
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}
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/* ---------------------------------------------------------------------- */
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void PairCoulCutSoftOMP::compute(int eflag, int vflag)
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{
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if (eflag || vflag) {
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ev_setup(eflag,vflag);
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} else evflag = vflag_fdotr = 0;
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const int nall = atom->nlocal + atom->nghost;
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const int nthreads = comm->nthreads;
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const int inum = list->inum;
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#if defined(_OPENMP)
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#pragma omp parallel default(none) shared(eflag,vflag)
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#endif
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{
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int ifrom, ito, tid;
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loop_setup_thr(ifrom, ito, tid, inum, nthreads);
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ThrData *thr = fix->get_thr(tid);
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ev_setup_thr(eflag, vflag, nall, eatom, vatom, thr);
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if (evflag) {
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if (eflag) {
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if (force->newton_pair) eval<1,1,1>(ifrom, ito, thr);
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else eval<1,1,0>(ifrom, ito, thr);
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} else {
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if (force->newton_pair) eval<1,0,1>(ifrom, ito, thr);
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else eval<1,0,0>(ifrom, ito, thr);
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}
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} else {
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if (force->newton_pair) eval<0,0,1>(ifrom, ito, thr);
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else eval<0,0,0>(ifrom, ito, thr);
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}
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reduce_thr(this, eflag, vflag, thr);
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} // end of omp parallel region
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}
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/* ---------------------------------------------------------------------- */
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template <int EVFLAG, int EFLAG, int NEWTON_PAIR>
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void PairCoulCutSoftOMP::eval(int iifrom, int iito, ThrData * const thr)
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{
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int i,j,ii,jj,jnum,itype,jtype;
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double qtmp,xtmp,ytmp,ztmp,delx,dely,delz,ecoul,fpair;
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double rsq,forcecoul,factor_coul,denc;
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int *ilist,*jlist,*numneigh,**firstneigh;
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ecoul = 0.0;
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const dbl3_t * _noalias const x = (dbl3_t *) atom->x[0];
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dbl3_t * _noalias const f = (dbl3_t *) thr->get_f()[0];
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const double * _noalias const q = atom->q;
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const int * _noalias const type = atom->type;
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const int nlocal = atom->nlocal;
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const double * _noalias const special_coul = force->special_coul;
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const double qqrd2e = force->qqrd2e;
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double fxtmp,fytmp,fztmp;
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ilist = list->ilist;
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numneigh = list->numneigh;
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firstneigh = list->firstneigh;
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// loop over neighbors of my atoms
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for (ii = iifrom; ii < iito; ++ii) {
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i = ilist[ii];
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qtmp = q[i];
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xtmp = x[i].x;
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ytmp = x[i].y;
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ztmp = x[i].z;
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itype = type[i];
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jlist = firstneigh[i];
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jnum = numneigh[i];
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fxtmp=fytmp=fztmp=0.0;
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for (jj = 0; jj < jnum; jj++) {
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j = jlist[jj];
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factor_coul = special_coul[sbmask(j)];
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j &= NEIGHMASK;
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delx = xtmp - x[j].x;
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dely = ytmp - x[j].y;
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delz = ztmp - x[j].z;
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rsq = delx*delx + dely*dely + delz*delz;
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jtype = type[j];
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if (rsq < cutsq[itype][jtype]) {
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denc = sqrt(lam2[itype][jtype] + rsq);
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forcecoul = qqrd2e * lam1[itype][jtype] * qtmp*q[j] / (denc*denc*denc);
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fpair = factor_coul*forcecoul;
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fxtmp += delx*fpair;
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fytmp += dely*fpair;
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fztmp += delz*fpair;
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if (NEWTON_PAIR || j < nlocal) {
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f[j].x -= delx*fpair;
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f[j].y -= dely*fpair;
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f[j].z -= delz*fpair;
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}
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if (EFLAG)
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ecoul = factor_coul * qqrd2e * lam1[itype][jtype] * qtmp*q[j] / denc;
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if (EVFLAG) ev_tally_thr(this, i,j,nlocal,NEWTON_PAIR,
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0.0,ecoul,fpair,delx,dely,delz,thr);
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}
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}
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f[i].x += fxtmp;
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f[i].y += fytmp;
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f[i].z += fztmp;
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}
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}
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/* ---------------------------------------------------------------------- */
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double PairCoulCutSoftOMP::memory_usage()
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{
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double bytes = memory_usage_thr();
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bytes += PairCoulCutSoft::memory_usage();
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return bytes;
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}
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@ -0,0 +1,48 @@
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/* -*- c++ -*- ----------------------------------------------------------
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LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
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http://lammps.sandia.gov, Sandia National Laboratories
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Steve Plimpton, sjplimp@sandia.gov
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Copyright (2003) Sandia Corporation. Under the terms of Contract
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DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
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certain rights in this software. This software is distributed under
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the GNU General Public License.
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See the README file in the top-level LAMMPS directory.
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------------------------------------------------------------------------- */
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/* ----------------------------------------------------------------------
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Contributing author: Axel Kohlmeyer (Temple U)
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------------------------------------------------------------------------- */
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#ifdef PAIR_CLASS
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PairStyle(coul/cut/soft/omp,PairCoulCutSoftOMP)
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#else
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#ifndef LMP_PAIR_COUL_CUT_SOFT_OMP_H
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#define LMP_PAIR_COUL_CUT_SORT_OMP_H
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#include "pair_coul_cut_soft.h"
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#include "thr_omp.h"
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namespace LAMMPS_NS {
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class PairCoulCutSoftOMP : public PairCoulCutSoft, public ThrOMP {
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public:
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PairCoulCutSoftOMP(class LAMMPS *);
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virtual void compute(int, int);
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virtual double memory_usage();
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private:
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template <int EVFLAG, int EFLAG, int NEWTON_PAIR>
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void eval(int ifrom, int ito, ThrData * const thr);
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};
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}
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#endif
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#endif
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@ -0,0 +1,183 @@
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/* ----------------------------------------------------------------------
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LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
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http://lammps.sandia.gov, Sandia National Laboratories
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Steve Plimpton, sjplimp@sandia.gov
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This software is distributed under the GNU General Public License.
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See the README file in the top-level LAMMPS directory.
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------------------------------------------------------------------------- */
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/* ----------------------------------------------------------------------
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Contributing author: Axel Kohlmeyer (Temple U)
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------------------------------------------------------------------------- */
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#include "math.h"
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#include "pair_coul_long_soft_omp.h"
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#include "atom.h"
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#include "comm.h"
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#include "force.h"
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#include "neighbor.h"
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#include "neigh_list.h"
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#include "suffix.h"
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using namespace LAMMPS_NS;
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#define EWALD_F 1.12837917
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#define EWALD_P 0.3275911
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#define A1 0.254829592
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#define A2 -0.284496736
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#define A3 1.421413741
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#define A4 -1.453152027
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#define A5 1.061405429
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/* ---------------------------------------------------------------------- */
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PairCoulLongSoftOMP::PairCoulLongSoftOMP(LAMMPS *lmp) :
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PairCoulLongSoft(lmp), ThrOMP(lmp, THR_PAIR)
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{
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suffix_flag |= Suffix::OMP;
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respa_enable = 0;
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}
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/* ---------------------------------------------------------------------- */
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void PairCoulLongSoftOMP::compute(int eflag, int vflag)
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{
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if (eflag || vflag) {
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ev_setup(eflag,vflag);
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} else evflag = vflag_fdotr = 0;
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const int nall = atom->nlocal + atom->nghost;
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const int nthreads = comm->nthreads;
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const int inum = list->inum;
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#if defined(_OPENMP)
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#pragma omp parallel default(none) shared(eflag,vflag)
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#endif
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{
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int ifrom, ito, tid;
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loop_setup_thr(ifrom, ito, tid, inum, nthreads);
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ThrData *thr = fix->get_thr(tid);
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ev_setup_thr(eflag, vflag, nall, eatom, vatom, thr);
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if (evflag) {
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if (eflag) {
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if (force->newton_pair) eval<1,1,1>(ifrom, ito, thr);
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else eval<1,1,0>(ifrom, ito, thr);
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} else {
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if (force->newton_pair) eval<1,0,1>(ifrom, ito, thr);
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else eval<1,0,0>(ifrom, ito, thr);
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}
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} else {
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if (force->newton_pair) eval<0,0,1>(ifrom, ito, thr);
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else eval<0,0,0>(ifrom, ito, thr);
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}
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reduce_thr(this, eflag, vflag, thr);
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} // end of omp parallel region
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}
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/* ---------------------------------------------------------------------- */
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template <int EVFLAG, int EFLAG, int NEWTON_PAIR>
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void PairCoulLongSoftOMP::eval(int iifrom, int iito, ThrData * const thr)
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{
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int i,j,ii,jj,jnum,itype,jtype;
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double qtmp,xtmp,ytmp,ztmp,delx,dely,delz,ecoul,fpair;
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double r,rsq,forcecoul,factor_coul;
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double grij,expm2,prefactor,t,erfc;
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double denc;
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int *ilist,*jlist,*numneigh,**firstneigh;
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ecoul = 0.0;
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const dbl3_t * _noalias const x = (dbl3_t *) atom->x[0];
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dbl3_t * _noalias const f = (dbl3_t *) thr->get_f()[0];
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const double * _noalias const q = atom->q;
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const int * _noalias const type = atom->type;
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const int nlocal = atom->nlocal;
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const double * _noalias const special_coul = force->special_coul;
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const double qqrd2e = force->qqrd2e;
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double fxtmp,fytmp,fztmp;
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ilist = list->ilist;
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numneigh = list->numneigh;
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firstneigh = list->firstneigh;
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// loop over neighbors of my atoms
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for (ii = iifrom; ii < iito; ++ii) {
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i = ilist[ii];
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qtmp = q[i];
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xtmp = x[i].x;
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ytmp = x[i].y;
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ztmp = x[i].z;
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itype = type[i];
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jlist = firstneigh[i];
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jnum = numneigh[i];
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fxtmp=fytmp=fztmp=0.0;
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for (jj = 0; jj < jnum; jj++) {
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j = jlist[jj];
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factor_coul = special_coul[sbmask(j)];
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j &= NEIGHMASK;
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delx = xtmp - x[j].x;
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dely = ytmp - x[j].y;
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delz = ztmp - x[j].z;
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rsq = delx*delx + dely*dely + delz*delz;
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jtype = type[j];
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if (rsq < cut_coulsq) {
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r = sqrt(rsq);
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grij = g_ewald * r;
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expm2 = exp(-grij*grij);
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t = 1.0 / (1.0 + EWALD_P*grij);
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erfc = t * (A1+t*(A2+t*(A3+t*(A4+t*A5)))) * expm2;
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denc = sqrt(lam2[itype][jtype] + rsq);
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prefactor = qqrd2e * lam1[itype][jtype] * qtmp*q[j] / (denc*denc*denc);
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forcecoul = prefactor * (erfc + EWALD_F*grij*expm2);
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if (factor_coul < 1.0) forcecoul -= (1.0-factor_coul)*prefactor;
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fpair = forcecoul;
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fxtmp += delx*fpair;
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fytmp += dely*fpair;
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fztmp += delz*fpair;
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if (NEWTON_PAIR || j < nlocal) {
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f[j].x -= delx*fpair;
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f[j].y -= dely*fpair;
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f[j].z -= delz*fpair;
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}
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if (EFLAG) {
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prefactor = qqrd2e * lam1[itype][jtype] * qtmp*q[j] / denc;
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ecoul = prefactor*erfc;
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if (factor_coul < 1.0) ecoul -= (1.0-factor_coul)*prefactor;
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}
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if (EVFLAG) ev_tally_thr(this, i,j,nlocal,NEWTON_PAIR,
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0.0,ecoul,fpair,delx,dely,delz,thr);
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}
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}
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f[i].x += fxtmp;
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f[i].y += fytmp;
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f[i].z += fztmp;
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}
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}
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/* ---------------------------------------------------------------------- */
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double PairCoulLongSoftOMP::memory_usage()
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{
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double bytes = memory_usage_thr();
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bytes += PairCoulLongSoft::memory_usage();
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return bytes;
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}
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@ -0,0 +1,48 @@
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/* -*- c++ -*- ----------------------------------------------------------
|
||||
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)
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
#ifdef PAIR_CLASS
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PairStyle(coul/long/soft/omp,PairCoulLongSoftOMP)
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#else
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#ifndef LMP_PAIR_COUL_LONG_SOFT_OMP_H
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#define LMP_PAIR_COUL_LONG_SOFT_OMP_H
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#include "pair_coul_long_soft.h"
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#include "thr_omp.h"
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namespace LAMMPS_NS {
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class PairCoulLongSoftOMP : public PairCoulLongSoft, public ThrOMP {
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public:
|
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PairCoulLongSoftOMP(class LAMMPS *);
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|
||||
virtual void compute(int, int);
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virtual double memory_usage();
|
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|
||||
private:
|
||||
template <int EVFLAG, int EFLAG, int NEWTON_PAIR>
|
||||
void eval(int ifrom, int ito, ThrData * const thr);
|
||||
};
|
||||
|
||||
}
|
||||
|
||||
#endif
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||||
#endif
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|
|
@ -0,0 +1,181 @@
|
|||
/* ----------------------------------------------------------------------
|
||||
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_lj_cut_coul_cut_soft_omp.h"
|
||||
#include "atom.h"
|
||||
#include "comm.h"
|
||||
#include "force.h"
|
||||
#include "neighbor.h"
|
||||
#include "neigh_list.h"
|
||||
|
||||
#include "suffix.h"
|
||||
using namespace LAMMPS_NS;
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
PairLJCutCoulCutSoftOMP::PairLJCutCoulCutSoftOMP(LAMMPS *lmp) :
|
||||
PairLJCutCoulCutSoft(lmp), ThrOMP(lmp, THR_PAIR)
|
||||
{
|
||||
suffix_flag |= Suffix::OMP;
|
||||
respa_enable = 0;
|
||||
}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
void PairLJCutCoulCutSoftOMP::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 PairLJCutCoulCutSoftOMP::eval(int iifrom, int iito, ThrData * const thr)
|
||||
{
|
||||
int i,j,ii,jj,jnum,itype,jtype;
|
||||
double qtmp,xtmp,ytmp,ztmp,delx,dely,delz,evdwl,ecoul,fpair;
|
||||
double rsq,forcecoul,forcelj,factor_coul,factor_lj;
|
||||
double denc, denlj, r4sig6;
|
||||
int *ilist,*jlist,*numneigh,**firstneigh;
|
||||
|
||||
evdwl = ecoul = 0.0;
|
||||
|
||||
const dbl3_t * _noalias const x = (dbl3_t *) atom->x[0];
|
||||
dbl3_t * _noalias const f = (dbl3_t *) thr->get_f()[0];
|
||||
const double * _noalias const q = atom->q;
|
||||
const int * _noalias const type = atom->type;
|
||||
const int nlocal = atom->nlocal;
|
||||
const double * _noalias const special_coul = force->special_coul;
|
||||
const double * _noalias const special_lj = force->special_lj;
|
||||
const double qqrd2e = force->qqrd2e;
|
||||
double fxtmp,fytmp,fztmp;
|
||||
|
||||
ilist = list->ilist;
|
||||
numneigh = list->numneigh;
|
||||
firstneigh = list->firstneigh;
|
||||
|
||||
// loop over neighbors of my atoms
|
||||
|
||||
for (ii = iifrom; ii < iito; ++ii) {
|
||||
|
||||
i = ilist[ii];
|
||||
qtmp = q[i];
|
||||
xtmp = x[i].x;
|
||||
ytmp = x[i].y;
|
||||
ztmp = x[i].z;
|
||||
itype = type[i];
|
||||
jlist = firstneigh[i];
|
||||
jnum = numneigh[i];
|
||||
fxtmp=fytmp=fztmp=0.0;
|
||||
|
||||
for (jj = 0; jj < jnum; jj++) {
|
||||
j = jlist[jj];
|
||||
factor_lj = special_lj[sbmask(j)];
|
||||
factor_coul = special_coul[sbmask(j)];
|
||||
j &= NEIGHMASK;
|
||||
|
||||
delx = xtmp - x[j].x;
|
||||
dely = ytmp - x[j].y;
|
||||
delz = ztmp - x[j].z;
|
||||
rsq = delx*delx + dely*dely + delz*delz;
|
||||
jtype = type[j];
|
||||
|
||||
if (rsq < cutsq[itype][jtype]) {
|
||||
|
||||
if (rsq < cut_coulsq[itype][jtype]) {
|
||||
denc = sqrt(lj4[itype][jtype] + rsq);
|
||||
forcecoul = qqrd2e * lj1[itype][jtype] * qtmp*q[j] / (denc*denc*denc);
|
||||
} else forcecoul = 0.0;
|
||||
|
||||
if (rsq < cut_ljsq[itype][jtype]) {
|
||||
r4sig6 = rsq*rsq / lj2[itype][jtype];
|
||||
denlj = lj3[itype][jtype] + rsq*r4sig6;
|
||||
forcelj = lj1[itype][jtype] * epsilon[itype][jtype] *
|
||||
(48.0*r4sig6/(denlj*denlj*denlj) - 24.0*r4sig6/(denlj*denlj));
|
||||
} else forcelj = 0.0;
|
||||
|
||||
fpair = factor_coul*forcecoul + factor_lj*forcelj;
|
||||
|
||||
fxtmp += delx*fpair;
|
||||
fytmp += dely*fpair;
|
||||
fztmp += delz*fpair;
|
||||
if (NEWTON_PAIR || j < nlocal) {
|
||||
f[j].x -= delx*fpair;
|
||||
f[j].y -= dely*fpair;
|
||||
f[j].z -= delz*fpair;
|
||||
}
|
||||
|
||||
if (EFLAG) {
|
||||
if (rsq < cut_coulsq[itype][jtype])
|
||||
ecoul = factor_coul * qqrd2e * lj1[itype][jtype] * qtmp*q[j] / denc;
|
||||
else ecoul = 0.0;
|
||||
if (rsq < cut_ljsq[itype][jtype]) {
|
||||
evdwl = lj1[itype][jtype] * 4.0 * epsilon[itype][jtype] *
|
||||
(1.0/(denlj*denlj) - 1.0/denlj) - offset[itype][jtype];
|
||||
evdwl *= factor_lj;
|
||||
} else evdwl = 0.0;
|
||||
}
|
||||
|
||||
if (EVFLAG) ev_tally_thr(this, i,j,nlocal,NEWTON_PAIR,
|
||||
evdwl,ecoul,fpair,delx,dely,delz,thr);
|
||||
}
|
||||
}
|
||||
f[i].x += fxtmp;
|
||||
f[i].y += fytmp;
|
||||
f[i].z += fztmp;
|
||||
}
|
||||
}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
double PairLJCutCoulCutSoftOMP::memory_usage()
|
||||
{
|
||||
double bytes = memory_usage_thr();
|
||||
bytes += PairLJCutCoulCutSoft::memory_usage();
|
||||
|
||||
return bytes;
|
||||
}
|
||||
|
|
@ -0,0 +1,48 @@
|
|||
/* -*- c++ -*- ----------------------------------------------------------
|
||||
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)
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
#ifdef PAIR_CLASS
|
||||
|
||||
PairStyle(lj/cut/coul/cut/soft/omp,PairLJCutCoulCutSoftOMP)
|
||||
|
||||
#else
|
||||
|
||||
#ifndef LMP_PAIR_LJ_CUT_COUL_CUT_SOFT_OMP_H
|
||||
#define LMP_PAIR_LJ_CUT_COUL_CUT_SOFT_OMP_H
|
||||
|
||||
#include "pair_lj_cut_coul_cut_soft.h"
|
||||
#include "thr_omp.h"
|
||||
|
||||
namespace LAMMPS_NS {
|
||||
|
||||
class PairLJCutCoulCutSoftOMP : public PairLJCutCoulCutSoft, public ThrOMP {
|
||||
|
||||
public:
|
||||
PairLJCutCoulCutSoftOMP(class LAMMPS *);
|
||||
|
||||
virtual void compute(int, int);
|
||||
virtual double memory_usage();
|
||||
|
||||
private:
|
||||
template <int EVFLAG, int EFLAG, int NEWTON_PAIR>
|
||||
void eval(int ifrom, int ito, ThrData * const thr);
|
||||
};
|
||||
|
||||
}
|
||||
|
||||
#endif
|
||||
#endif
|
||||
|
|
@ -0,0 +1,203 @@
|
|||
/* ----------------------------------------------------------------------
|
||||
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_lj_cut_coul_long_soft_omp.h"
|
||||
#include "atom.h"
|
||||
#include "comm.h"
|
||||
#include "force.h"
|
||||
#include "neighbor.h"
|
||||
#include "neigh_list.h"
|
||||
|
||||
#include "suffix.h"
|
||||
using namespace LAMMPS_NS;
|
||||
|
||||
#define EWALD_F 1.12837917
|
||||
#define EWALD_P 0.3275911
|
||||
#define A1 0.254829592
|
||||
#define A2 -0.284496736
|
||||
#define A3 1.421413741
|
||||
#define A4 -1.453152027
|
||||
#define A5 1.061405429
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
PairLJCutCoulLongSoftOMP::PairLJCutCoulLongSoftOMP(LAMMPS *lmp) :
|
||||
PairLJCutCoulLongSoft(lmp), ThrOMP(lmp, THR_PAIR)
|
||||
{
|
||||
suffix_flag |= Suffix::OMP;
|
||||
respa_enable = 0;
|
||||
cut_respa = NULL;
|
||||
}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
void PairLJCutCoulLongSoftOMP::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 PairLJCutCoulLongSoftOMP::eval(int iifrom, int iito, ThrData * const thr)
|
||||
{
|
||||
int i,j,ii,jj,jnum,itype,jtype;
|
||||
double qtmp,xtmp,ytmp,ztmp,delx,dely,delz,evdwl,ecoul,fpair;
|
||||
double r,rsq,forcecoul,forcelj,factor_coul,factor_lj;
|
||||
double grij,expm2,prefactor,t,erfc;
|
||||
double denc, denlj, r4sig6;
|
||||
int *ilist,*jlist,*numneigh,**firstneigh;
|
||||
|
||||
evdwl = ecoul = 0.0;
|
||||
|
||||
const dbl3_t * _noalias const x = (dbl3_t *) atom->x[0];
|
||||
dbl3_t * _noalias const f = (dbl3_t *) thr->get_f()[0];
|
||||
const double * _noalias const q = atom->q;
|
||||
const int * _noalias const type = atom->type;
|
||||
const int nlocal = atom->nlocal;
|
||||
const double * _noalias const special_coul = force->special_coul;
|
||||
const double * _noalias const special_lj = force->special_lj;
|
||||
const double qqrd2e = force->qqrd2e;
|
||||
double fxtmp,fytmp,fztmp;
|
||||
|
||||
ilist = list->ilist;
|
||||
numneigh = list->numneigh;
|
||||
firstneigh = list->firstneigh;
|
||||
|
||||
// loop over neighbors of my atoms
|
||||
|
||||
for (ii = iifrom; ii < iito; ++ii) {
|
||||
|
||||
i = ilist[ii];
|
||||
qtmp = q[i];
|
||||
xtmp = x[i].x;
|
||||
ytmp = x[i].y;
|
||||
ztmp = x[i].z;
|
||||
itype = type[i];
|
||||
jlist = firstneigh[i];
|
||||
jnum = numneigh[i];
|
||||
fxtmp=fytmp=fztmp=0.0;
|
||||
|
||||
for (jj = 0; jj < jnum; jj++) {
|
||||
j = jlist[jj];
|
||||
factor_lj = special_lj[sbmask(j)];
|
||||
factor_coul = special_coul[sbmask(j)];
|
||||
j &= NEIGHMASK;
|
||||
|
||||
delx = xtmp - x[j].x;
|
||||
dely = ytmp - x[j].y;
|
||||
delz = ztmp - x[j].z;
|
||||
rsq = delx*delx + dely*dely + delz*delz;
|
||||
jtype = type[j];
|
||||
|
||||
if (rsq < cutsq[itype][jtype]) {
|
||||
|
||||
if (rsq < cut_coulsq) {
|
||||
r = sqrt(rsq);
|
||||
grij = g_ewald * r;
|
||||
expm2 = exp(-grij*grij);
|
||||
t = 1.0 / (1.0 + EWALD_P*grij);
|
||||
erfc = t * (A1+t*(A2+t*(A3+t*(A4+t*A5)))) * expm2;
|
||||
|
||||
denc = sqrt(lj4[itype][jtype] + rsq);
|
||||
prefactor = qqrd2e * lj1[itype][jtype] * qtmp*q[j] / (denc*denc*denc);
|
||||
|
||||
forcecoul = prefactor * (erfc + EWALD_F*grij*expm2);
|
||||
if (factor_coul < 1.0) forcecoul -= (1.0-factor_coul)*prefactor;
|
||||
} else forcecoul = 0.0;
|
||||
|
||||
if (rsq < cut_ljsq[itype][jtype]) {
|
||||
r4sig6 = rsq*rsq / lj2[itype][jtype];
|
||||
denlj = lj3[itype][jtype] + rsq*r4sig6;
|
||||
forcelj = lj1[itype][jtype] * epsilon[itype][jtype] *
|
||||
(48.0*r4sig6/(denlj*denlj*denlj) - 24.0*r4sig6/(denlj*denlj));
|
||||
} else forcelj = 0.0;
|
||||
|
||||
fpair = forcecoul + factor_lj*forcelj;
|
||||
|
||||
fxtmp += delx*fpair;
|
||||
fytmp += dely*fpair;
|
||||
fztmp += delz*fpair;
|
||||
if (NEWTON_PAIR || j < nlocal) {
|
||||
f[j].x -= delx*fpair;
|
||||
f[j].y -= dely*fpair;
|
||||
f[j].z -= delz*fpair;
|
||||
}
|
||||
|
||||
if (EFLAG) {
|
||||
if (rsq < cut_coulsq) {
|
||||
prefactor = qqrd2e * lj1[itype][jtype] * qtmp*q[j] / denc;
|
||||
ecoul = prefactor*erfc;
|
||||
if (factor_coul < 1.0) ecoul -= (1.0-factor_coul)*prefactor;
|
||||
} else ecoul = 0.0;
|
||||
|
||||
if (rsq < cut_ljsq[itype][jtype]) {
|
||||
evdwl = lj1[itype][jtype] * 4.0 * epsilon[itype][jtype] *
|
||||
(1.0/(denlj*denlj) - 1.0/denlj) - offset[itype][jtype];
|
||||
evdwl *= factor_lj;
|
||||
} else evdwl = 0.0;
|
||||
}
|
||||
|
||||
if (EVFLAG) ev_tally_thr(this, i,j,nlocal,NEWTON_PAIR,
|
||||
evdwl,ecoul,fpair,delx,dely,delz,thr);
|
||||
}
|
||||
}
|
||||
f[i].x += fxtmp;
|
||||
f[i].y += fytmp;
|
||||
f[i].z += fztmp;
|
||||
}
|
||||
}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
double PairLJCutCoulLongSoftOMP::memory_usage()
|
||||
{
|
||||
double bytes = memory_usage_thr();
|
||||
bytes += PairLJCutCoulLongSoft::memory_usage();
|
||||
|
||||
return bytes;
|
||||
}
|
||||
|
|
@ -0,0 +1,48 @@
|
|||
/* -*- c++ -*- ----------------------------------------------------------
|
||||
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)
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
#ifdef PAIR_CLASS
|
||||
|
||||
PairStyle(lj/cut/coul/long/soft/omp,PairLJCutCoulLongSoftOMP)
|
||||
|
||||
#else
|
||||
|
||||
#ifndef LMP_PAIR_LJ_CUT_COUL_LONG_SOFT_OMP_H
|
||||
#define LMP_PAIR_LJ_CUT_COUL_LONG_SOFT_OMP_H
|
||||
|
||||
#include "pair_lj_cut_coul_long_soft.h"
|
||||
#include "thr_omp.h"
|
||||
|
||||
namespace LAMMPS_NS {
|
||||
|
||||
class PairLJCutCoulLongSoftOMP : public PairLJCutCoulLongSoft, public ThrOMP {
|
||||
|
||||
public:
|
||||
PairLJCutCoulLongSoftOMP(class LAMMPS *);
|
||||
|
||||
virtual void compute(int, int);
|
||||
virtual double memory_usage();
|
||||
|
||||
private:
|
||||
template <int EVFLAG, int EFLAG, int NEWTON_PAIR>
|
||||
void eval(int ifrom, int ito, ThrData * const thr);
|
||||
};
|
||||
|
||||
}
|
||||
|
||||
#endif
|
||||
#endif
|
||||
|
|
@ -0,0 +1,165 @@
|
|||
/* ----------------------------------------------------------------------
|
||||
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_lj_cut_soft_omp.h"
|
||||
#include "atom.h"
|
||||
#include "comm.h"
|
||||
#include "force.h"
|
||||
#include "neighbor.h"
|
||||
#include "neigh_list.h"
|
||||
|
||||
#include "suffix.h"
|
||||
using namespace LAMMPS_NS;
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
PairLJCutSoftOMP::PairLJCutSoftOMP(LAMMPS *lmp) :
|
||||
PairLJCutSoft(lmp), ThrOMP(lmp, THR_PAIR)
|
||||
{
|
||||
suffix_flag |= Suffix::OMP;
|
||||
respa_enable = 0;
|
||||
cut_respa = NULL;
|
||||
}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
void PairLJCutSoftOMP::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 PairLJCutSoftOMP::eval(int iifrom, int iito, ThrData * const thr)
|
||||
{
|
||||
const dbl3_t * _noalias const x = (dbl3_t *) atom->x[0];
|
||||
dbl3_t * _noalias const f = (dbl3_t *) thr->get_f()[0];
|
||||
const int * _noalias const type = atom->type;
|
||||
const double * _noalias const special_lj = force->special_lj;
|
||||
const int * _noalias const ilist = list->ilist;
|
||||
const int * _noalias const numneigh = list->numneigh;
|
||||
const int * const * const firstneigh = list->firstneigh;
|
||||
|
||||
double xtmp,ytmp,ztmp,delx,dely,delz,fxtmp,fytmp,fztmp;
|
||||
double rsq,denlj,r4sig6,forcelj,factor_lj,evdwl,fpair;
|
||||
|
||||
const int nlocal = atom->nlocal;
|
||||
int j,jj,jnum,jtype;
|
||||
|
||||
evdwl = 0.0;
|
||||
|
||||
// loop over neighbors of my atoms
|
||||
|
||||
for (int ii = iifrom; ii < iito; ++ii) {
|
||||
const int i = ilist[ii];
|
||||
const int itype = type[i];
|
||||
const int * _noalias const jlist = firstneigh[i];
|
||||
const double * _noalias const cutsqi = cutsq[itype];
|
||||
const double * _noalias const offseti = offset[itype];
|
||||
const double * _noalias const epsi = epsilon[itype];
|
||||
const double * _noalias const lj1i = lj1[itype];
|
||||
const double * _noalias const lj2i = lj2[itype];
|
||||
const double * _noalias const lj3i = lj3[itype];
|
||||
|
||||
xtmp = x[i].x;
|
||||
ytmp = x[i].y;
|
||||
ztmp = x[i].z;
|
||||
jnum = numneigh[i];
|
||||
fxtmp=fytmp=fztmp=0.0;
|
||||
|
||||
for (jj = 0; jj < jnum; jj++) {
|
||||
j = jlist[jj];
|
||||
factor_lj = special_lj[sbmask(j)];
|
||||
j &= NEIGHMASK;
|
||||
|
||||
delx = xtmp - x[j].x;
|
||||
dely = ytmp - x[j].y;
|
||||
delz = ztmp - x[j].z;
|
||||
rsq = delx*delx + dely*dely + delz*delz;
|
||||
jtype = type[j];
|
||||
|
||||
if (rsq < cutsqi[jtype]) {
|
||||
|
||||
r4sig6 = rsq*rsq / lj2i[jtype];
|
||||
denlj = lj3i[jtype] + rsq*r4sig6;
|
||||
forcelj = lj1i[jtype] * epsi[jtype] *
|
||||
(48.0*r4sig6/(denlj*denlj*denlj) - 24.0*r4sig6/(denlj*denlj));
|
||||
|
||||
fpair = factor_lj*forcelj;
|
||||
|
||||
fxtmp += delx*fpair;
|
||||
fytmp += dely*fpair;
|
||||
fztmp += delz*fpair;
|
||||
if (NEWTON_PAIR || j < nlocal) {
|
||||
f[j].x -= delx*fpair;
|
||||
f[j].y -= dely*fpair;
|
||||
f[j].z -= delz*fpair;
|
||||
}
|
||||
|
||||
if (EFLAG) {
|
||||
evdwl = lj1i[jtype] * 4.0 * epsi[jtype] *
|
||||
(1.0/(denlj*denlj) - 1.0/denlj) - offseti[jtype];
|
||||
evdwl *= factor_lj;
|
||||
}
|
||||
|
||||
if (EVFLAG) ev_tally_thr(this,i,j,nlocal,NEWTON_PAIR,
|
||||
evdwl,0.0,fpair,delx,dely,delz,thr);
|
||||
}
|
||||
}
|
||||
f[i].x += fxtmp;
|
||||
f[i].y += fytmp;
|
||||
f[i].z += fztmp;
|
||||
}
|
||||
}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
double PairLJCutSoftOMP::memory_usage()
|
||||
{
|
||||
double bytes = memory_usage_thr();
|
||||
bytes += PairLJCutSoft::memory_usage();
|
||||
|
||||
return bytes;
|
||||
}
|
||||
|
|
@ -0,0 +1,48 @@
|
|||
/* -*- c++ -*- ----------------------------------------------------------
|
||||
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)
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
#ifdef PAIR_CLASS
|
||||
|
||||
PairStyle(lj/cut/soft/omp,PairLJCutSoftOMP)
|
||||
|
||||
#else
|
||||
|
||||
#ifndef LMP_PAIR_LJ_CUT_SOFT_OMP_H
|
||||
#define LMP_PAIR_LJ_CUT_SOFT_OMP_H
|
||||
|
||||
#include "pair_lj_cut_soft.h"
|
||||
#include "thr_omp.h"
|
||||
|
||||
namespace LAMMPS_NS {
|
||||
|
||||
class PairLJCutSoftOMP : public PairLJCutSoft, public ThrOMP {
|
||||
|
||||
public:
|
||||
PairLJCutSoftOMP(class LAMMPS *);
|
||||
|
||||
virtual void compute(int, int);
|
||||
virtual double memory_usage();
|
||||
|
||||
private:
|
||||
template <int EVFLAG, int EFLAG, int NEWTON_PAIR>
|
||||
void eval(int ifrom, int ito, ThrData * const thr);
|
||||
};
|
||||
|
||||
}
|
||||
|
||||
#endif
|
||||
#endif
|
||||
|
|
@ -0,0 +1,484 @@
|
|||
/* ----------------------------------------------------------------------
|
||||
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_lj_cut_tip4p_long_soft_omp.h"
|
||||
#include "atom.h"
|
||||
#include "domain.h"
|
||||
#include "comm.h"
|
||||
#include "force.h"
|
||||
#include "neighbor.h"
|
||||
#include "error.h"
|
||||
#include "memory.h"
|
||||
#include "neigh_list.h"
|
||||
|
||||
#include "suffix.h"
|
||||
using namespace LAMMPS_NS;
|
||||
|
||||
#define EWALD_F 1.12837917
|
||||
#define EWALD_P 0.3275911
|
||||
#define A1 0.254829592
|
||||
#define A2 -0.284496736
|
||||
#define A3 1.421413741
|
||||
#define A4 -1.453152027
|
||||
#define A5 1.061405429
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
PairLJCutTIP4PLongSoftOMP::PairLJCutTIP4PLongSoftOMP(LAMMPS *lmp) :
|
||||
PairLJCutTIP4PLongSoft(lmp), ThrOMP(lmp, THR_PAIR)
|
||||
{
|
||||
suffix_flag |= Suffix::OMP;
|
||||
respa_enable = 0;
|
||||
newsite_thr = NULL;
|
||||
hneigh_thr = NULL;
|
||||
|
||||
// TIP4P cannot compute virial as F dot r
|
||||
// due to finding bonded H atoms which are not near O atom
|
||||
|
||||
no_virial_fdotr_compute = 1;
|
||||
}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
PairLJCutTIP4PLongSoftOMP::~PairLJCutTIP4PLongSoftOMP()
|
||||
{
|
||||
memory->destroy(hneigh_thr);
|
||||
memory->destroy(newsite_thr);
|
||||
}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
void PairLJCutTIP4PLongSoftOMP::compute(int eflag, int vflag)
|
||||
{
|
||||
if (eflag || vflag) ev_setup(eflag,vflag);
|
||||
else evflag = vflag_fdotr = 0;
|
||||
|
||||
const int nlocal = atom->nlocal;
|
||||
const int nall = nlocal + atom->nghost;
|
||||
|
||||
// reallocate hneigh_thr & newsite_thr if necessary
|
||||
// initialize hneigh_thr[0] to -1 on steps when reneighboring occurred
|
||||
// initialize hneigh_thr[2] to 0 every step
|
||||
|
||||
if (atom->nmax > nmax) {
|
||||
nmax = atom->nmax;
|
||||
memory->destroy(hneigh_thr);
|
||||
memory->create(hneigh_thr,nmax,"pair:hneigh_thr");
|
||||
memory->destroy(newsite_thr);
|
||||
memory->create(newsite_thr,nmax,"pair:newsite_thr");
|
||||
}
|
||||
|
||||
int i;
|
||||
// tag entire list as completely invalid after a neighbor
|
||||
// list update, since that can change the order of atoms.
|
||||
if (neighbor->ago == 0)
|
||||
for (i = 0; i < nall; i++) hneigh_thr[i].a = -1;
|
||||
|
||||
// indicate that the coordinates for the M point need to
|
||||
// be updated. this needs to be done in every step.
|
||||
for (i = 0; i < nall; i++) hneigh_thr[i].t = 0;
|
||||
|
||||
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 (vflag) eval<1,1,1>(ifrom, ito, thr);
|
||||
else eval<1,1,0>(ifrom, ito, thr);
|
||||
} else {
|
||||
if (vflag) eval<1,0,1>(ifrom, ito, thr);
|
||||
else eval<1,0,0>(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 VFLAG>
|
||||
void PairLJCutTIP4PLongSoftOMP::eval(int iifrom, int iito, ThrData * const thr)
|
||||
{
|
||||
double qtmp,xtmp,ytmp,ztmp,delx,dely,delz,evdwl,ecoul;
|
||||
double r,rsq,forcecoul,forcelj,cforce;
|
||||
double factor_coul,factor_lj;
|
||||
double grij,expm2,prefactor,t,erfc;
|
||||
double denc, denlj, r4sig6;
|
||||
double v[6],xH1[3],xH2[3];
|
||||
double fdx,fdy,fdz,fOx,fOy,fOz,fHx,fHy,fHz;
|
||||
dbl3_t x1,x2;
|
||||
|
||||
int *ilist,*jlist,*numneigh,**firstneigh;
|
||||
int i,j,ii,jj,jnum,itype,jtype,key;
|
||||
int n,vlist[6];
|
||||
int iH1,iH2,jH1,jH2;
|
||||
|
||||
evdwl = ecoul = 0.0;
|
||||
|
||||
const dbl3_t * _noalias const x = (dbl3_t *) atom->x[0];
|
||||
dbl3_t * _noalias const f = (dbl3_t *) thr->get_f()[0];
|
||||
const double * _noalias const q = atom->q;
|
||||
const int * _noalias const type = atom->type;
|
||||
const int nlocal = atom->nlocal;
|
||||
const double * _noalias const special_coul = force->special_coul;
|
||||
const double * _noalias const special_lj = force->special_lj;
|
||||
const double qqrd2e = force->qqrd2e;
|
||||
const double cut_coulsqplus = (cut_coul+2.0*qdist) * (cut_coul+2.0*qdist);
|
||||
|
||||
double fxtmp,fytmp,fztmp;
|
||||
|
||||
ilist = list->ilist;
|
||||
numneigh = list->numneigh;
|
||||
firstneigh = list->firstneigh;
|
||||
|
||||
// loop over neighbors of my atoms
|
||||
|
||||
for (ii = iifrom; ii < iito; ++ii) {
|
||||
i = ilist[ii];
|
||||
qtmp = q[i];
|
||||
xtmp = x[i].x;
|
||||
ytmp = x[i].y;
|
||||
ztmp = x[i].z;
|
||||
itype = type[i];
|
||||
|
||||
// if atom I = water O, set x1 = offset charge site
|
||||
// else x1 = x of atom I
|
||||
// NOTE: to make this part thread safe, we need to
|
||||
// make sure that the hneigh_thr[][] entries only get
|
||||
// updated, when all data is in place. worst case,
|
||||
// some calculation is repeated, but since the results
|
||||
// will be the same, there is no race condition.
|
||||
if (itype == typeO) {
|
||||
if (hneigh_thr[i].a < 0) {
|
||||
iH1 = atom->map(atom->tag[i] + 1);
|
||||
iH2 = atom->map(atom->tag[i] + 2);
|
||||
if (iH1 == -1 || iH2 == -1)
|
||||
error->one(FLERR,"TIP4P hydrogen is missing");
|
||||
if (atom->type[iH1] != typeH || atom->type[iH2] != typeH)
|
||||
error->one(FLERR,"TIP4P hydrogen has incorrect atom type");
|
||||
compute_newsite_thr(x[i],x[iH1],x[iH2],newsite_thr[i]);
|
||||
hneigh_thr[i].t = 1;
|
||||
hneigh_thr[i].b = iH2;
|
||||
hneigh_thr[i].a = iH1;
|
||||
} else {
|
||||
iH1 = hneigh_thr[i].a;
|
||||
iH2 = hneigh_thr[i].b;
|
||||
if (hneigh_thr[i].t == 0) {
|
||||
compute_newsite_thr(x[i],x[iH1],x[iH2],newsite_thr[i]);
|
||||
hneigh_thr[i].t = 1;
|
||||
}
|
||||
}
|
||||
x1 = newsite_thr[i];
|
||||
} else x1 = x[i];
|
||||
|
||||
jlist = firstneigh[i];
|
||||
jnum = numneigh[i];
|
||||
fxtmp=fytmp=fztmp=0.0;
|
||||
|
||||
for (jj = 0; jj < jnum; jj++) {
|
||||
j = jlist[jj];
|
||||
factor_lj = special_lj[sbmask(j)];
|
||||
factor_coul = special_coul[sbmask(j)];
|
||||
j &= NEIGHMASK;
|
||||
|
||||
delx = xtmp - x[j].x;
|
||||
dely = ytmp - x[j].y;
|
||||
delz = ztmp - x[j].z;
|
||||
rsq = delx*delx + dely*dely + delz*delz;
|
||||
jtype = type[j];
|
||||
|
||||
// LJ interaction based on true rsq
|
||||
|
||||
if (rsq < cut_ljsq[itype][jtype]) {
|
||||
|
||||
r4sig6 = rsq*rsq / lj2[itype][jtype];
|
||||
denlj = lj3[itype][jtype] + rsq*r4sig6;
|
||||
forcelj = lj1[itype][jtype] * epsilon[itype][jtype] *
|
||||
(48.0*r4sig6/(denlj*denlj*denlj) - 24.0*r4sig6/(denlj*denlj));
|
||||
|
||||
forcelj *= factor_lj;
|
||||
|
||||
fxtmp += delx*forcelj;
|
||||
fytmp += dely*forcelj;
|
||||
fztmp += delz*forcelj;
|
||||
f[j].x -= delx*forcelj;
|
||||
f[j].y -= dely*forcelj;
|
||||
f[j].z -= delz*forcelj;
|
||||
|
||||
if (EFLAG) {
|
||||
evdwl = lj1[itype][jtype] * 4.0 * epsilon[itype][jtype] *
|
||||
(1.0/(denlj*denlj) - 1.0/denlj) - offset[itype][jtype];
|
||||
evdwl *= factor_lj;
|
||||
} else evdwl = 0.0;
|
||||
|
||||
if (EVFLAG) ev_tally_thr(this,i,j,nlocal, /* newton_pair = */ 1,
|
||||
evdwl,0.0,forcelj,delx,dely,delz,thr);
|
||||
}
|
||||
|
||||
// adjust rsq and delxyz for off-site O charge(s) if necessary
|
||||
// but only if they are within reach
|
||||
// NOTE: to make this part thread safe, we need to
|
||||
// make sure that the hneigh_thr[][] entries only get
|
||||
// updated, when all data is in place. worst case,
|
||||
// some calculation is repeated, but since the results
|
||||
// will be the same, there is no race condition.
|
||||
if (rsq < cut_coulsqplus) {
|
||||
if (itype == typeO || jtype == typeO) {
|
||||
|
||||
// if atom J = water O, set x2 = offset charge site
|
||||
// else x2 = x of atom J
|
||||
|
||||
if (jtype == typeO) {
|
||||
if (hneigh_thr[j].a < 0) {
|
||||
jH1 = atom->map(atom->tag[j] + 1);
|
||||
jH2 = atom->map(atom->tag[j] + 2);
|
||||
if (jH1 == -1 || jH2 == -1)
|
||||
error->one(FLERR,"TIP4P hydrogen is missing");
|
||||
if (atom->type[jH1] != typeH || atom->type[jH2] != typeH)
|
||||
error->one(FLERR,"TIP4P hydrogen has incorrect atom type");
|
||||
compute_newsite_thr(x[j],x[jH1],x[jH2],newsite_thr[j]);
|
||||
hneigh_thr[j].t = 1;
|
||||
hneigh_thr[j].b = jH2;
|
||||
hneigh_thr[j].a = jH1;
|
||||
} else {
|
||||
jH1 = hneigh_thr[j].a;
|
||||
jH2 = hneigh_thr[j].b;
|
||||
if (hneigh_thr[j].t == 0) {
|
||||
compute_newsite_thr(x[j],x[jH1],x[jH2],newsite_thr[j]);
|
||||
hneigh_thr[j].t = 1;
|
||||
}
|
||||
}
|
||||
x2 = newsite_thr[j];
|
||||
} else x2 = x[j];
|
||||
|
||||
delx = x1.x - x2.x;
|
||||
dely = x1.y - x2.y;
|
||||
delz = x1.z - x2.z;
|
||||
rsq = delx*delx + dely*dely + delz*delz;
|
||||
}
|
||||
|
||||
// Coulombic interaction based on modified rsq
|
||||
|
||||
if (rsq < cut_coulsq) {
|
||||
r = sqrt(rsq);
|
||||
grij = g_ewald * r;
|
||||
expm2 = exp(-grij*grij);
|
||||
t = 1.0 / (1.0 + EWALD_P*grij);
|
||||
erfc = t * (A1+t*(A2+t*(A3+t*(A4+t*A5)))) * expm2;
|
||||
|
||||
denc = sqrt(lj4[itype][jtype] + rsq);
|
||||
prefactor = qqrd2e * lj1[itype][jtype] * qtmp*q[j] / (denc*denc*denc);
|
||||
|
||||
forcecoul = prefactor * (erfc + EWALD_F*grij*expm2);
|
||||
if (factor_coul < 1.0) {
|
||||
forcecoul -= (1.0-factor_coul)*prefactor;
|
||||
}
|
||||
|
||||
cforce = forcecoul;
|
||||
|
||||
// if i,j are not O atoms, force is applied directly
|
||||
// if i or j are O atoms, force is on fictitious atom & partitioned
|
||||
// force partitioning due to Feenstra, J Comp Chem, 20, 786 (1999)
|
||||
// f_f = fictitious force, fO = f_f (1 - 2 alpha), fH = alpha f_f
|
||||
// preserves total force and torque on water molecule
|
||||
// virial = sum(r x F) where each water's atoms are near xi and xj
|
||||
// vlist stores 2,4,6 atoms whose forces contribute to virial
|
||||
|
||||
if (EVFLAG) {
|
||||
n = 0;
|
||||
key = 0;
|
||||
}
|
||||
|
||||
if (itype != typeO) {
|
||||
fxtmp += delx * cforce;
|
||||
fytmp += dely * cforce;
|
||||
fztmp += delz * cforce;
|
||||
|
||||
if (VFLAG) {
|
||||
v[0] = x[i].x * delx * cforce;
|
||||
v[1] = x[i].y * dely * cforce;
|
||||
v[2] = x[i].z * delz * cforce;
|
||||
v[3] = x[i].x * dely * cforce;
|
||||
v[4] = x[i].x * delz * cforce;
|
||||
v[5] = x[i].y * delz * cforce;
|
||||
}
|
||||
if (EVFLAG) vlist[n++] = i;
|
||||
|
||||
} else {
|
||||
if (EVFLAG) key++;
|
||||
|
||||
fdx = delx*cforce;
|
||||
fdy = dely*cforce;
|
||||
fdz = delz*cforce;
|
||||
|
||||
fOx = fdx*(1 - alpha);
|
||||
fOy = fdy*(1 - alpha);
|
||||
fOz = fdz*(1 - alpha);
|
||||
|
||||
fHx = 0.5*alpha * fdx;
|
||||
fHy = 0.5*alpha * fdy;
|
||||
fHz = 0.5*alpha * fdz;
|
||||
|
||||
fxtmp += fOx;
|
||||
fytmp += fOy;
|
||||
fztmp += fOz;
|
||||
|
||||
f[iH1].x += fHx;
|
||||
f[iH1].y += fHy;
|
||||
f[iH1].z += fHz;
|
||||
|
||||
f[iH2].x += fHx;
|
||||
f[iH2].y += fHy;
|
||||
f[iH2].z += fHz;
|
||||
|
||||
if (VFLAG) {
|
||||
domain->closest_image(&x[i].x,&x[iH1].x,xH1);
|
||||
domain->closest_image(&x[i].x,&x[iH2].x,xH2);
|
||||
|
||||
v[0] = x[i].x*fOx + xH1[0]*fHx + xH2[0]*fHx;
|
||||
v[1] = x[i].y*fOy + xH1[1]*fHy + xH2[1]*fHy;
|
||||
v[2] = x[i].z*fOz + xH1[2]*fHz + xH2[2]*fHz;
|
||||
v[3] = x[i].x*fOy + xH1[0]*fHy + xH2[0]*fHy;
|
||||
v[4] = x[i].x*fOz + xH1[0]*fHz + xH2[0]*fHz;
|
||||
v[5] = x[i].y*fOz + xH1[1]*fHz + xH2[1]*fHz;
|
||||
}
|
||||
if (EVFLAG) {
|
||||
vlist[n++] = i;
|
||||
vlist[n++] = iH1;
|
||||
vlist[n++] = iH2;
|
||||
}
|
||||
}
|
||||
|
||||
if (jtype != typeO) {
|
||||
f[j].x -= delx * cforce;
|
||||
f[j].y -= dely * cforce;
|
||||
f[j].z -= delz * cforce;
|
||||
|
||||
if (VFLAG) {
|
||||
v[0] -= x[j].x * delx * cforce;
|
||||
v[1] -= x[j].y * dely * cforce;
|
||||
v[2] -= x[j].z * delz * cforce;
|
||||
v[3] -= x[j].x * dely * cforce;
|
||||
v[4] -= x[j].x * delz * cforce;
|
||||
v[5] -= x[j].y * delz * cforce;
|
||||
}
|
||||
if (EVFLAG) vlist[n++] = j;
|
||||
|
||||
} else {
|
||||
if (EVFLAG) key += 2;
|
||||
|
||||
fdx = -delx*cforce;
|
||||
fdy = -dely*cforce;
|
||||
fdz = -delz*cforce;
|
||||
|
||||
fOx = fdx*(1 - alpha);
|
||||
fOy = fdy*(1 - alpha);
|
||||
fOz = fdz*(1 - alpha);
|
||||
|
||||
fHx = 0.5*alpha * fdx;
|
||||
fHy = 0.5*alpha * fdy;
|
||||
fHz = 0.5*alpha * fdz;
|
||||
|
||||
f[j].x += fOx;
|
||||
f[j].y += fOy;
|
||||
f[j].z += fOz;
|
||||
|
||||
f[jH1].x += fHx;
|
||||
f[jH1].y += fHy;
|
||||
f[jH1].z += fHz;
|
||||
|
||||
f[jH2].x += fHx;
|
||||
f[jH2].y += fHy;
|
||||
f[jH2].z += fHz;
|
||||
|
||||
if (VFLAG) {
|
||||
domain->closest_image(&x[j].x,&x[jH1].x,xH1);
|
||||
domain->closest_image(&x[j].x,&x[jH2].x,xH2);
|
||||
|
||||
v[0] += x[j].x*fOx + xH1[0]*fHx + xH2[0]*fHx;
|
||||
v[1] += x[j].y*fOy + xH1[1]*fHy + xH2[1]*fHy;
|
||||
v[2] += x[j].z*fOz + xH1[2]*fHz + xH2[2]*fHz;
|
||||
v[3] += x[j].x*fOy + xH1[0]*fHy + xH2[0]*fHy;
|
||||
v[4] += x[j].x*fOz + xH1[0]*fHz + xH2[0]*fHz;
|
||||
v[5] += x[j].y*fOz + xH1[1]*fHz + xH2[1]*fHz;
|
||||
}
|
||||
if (EVFLAG) {
|
||||
vlist[n++] = j;
|
||||
vlist[n++] = jH1;
|
||||
vlist[n++] = jH2;
|
||||
}
|
||||
}
|
||||
|
||||
if (EFLAG) {
|
||||
prefactor = qqrd2e * lj1[itype][jtype] * qtmp*q[j] / denc;
|
||||
ecoul = prefactor*erfc;
|
||||
if (factor_coul < 1.0) ecoul -= (1.0-factor_coul)*prefactor;
|
||||
} else ecoul = 0.0;
|
||||
|
||||
if (EVFLAG) ev_tally_list_thr(this,key,vlist,v,ecoul,alpha,thr);
|
||||
}
|
||||
}
|
||||
}
|
||||
f[i].x += fxtmp;
|
||||
f[i].y += fytmp;
|
||||
f[i].z += fztmp;
|
||||
}
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
compute position xM of fictitious charge site for O atom and 2 H atoms
|
||||
return it as xM
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
void PairLJCutTIP4PLongSoftOMP::compute_newsite_thr(const dbl3_t &xO,
|
||||
const dbl3_t &xH1,
|
||||
const dbl3_t &xH2,
|
||||
dbl3_t &xM) const
|
||||
{
|
||||
double delx1 = xH1.x - xO.x;
|
||||
double dely1 = xH1.y - xO.y;
|
||||
double delz1 = xH1.z - xO.z;
|
||||
domain->minimum_image(delx1,dely1,delz1);
|
||||
|
||||
double delx2 = xH2.x - xO.x;
|
||||
double dely2 = xH2.y - xO.y;
|
||||
double delz2 = xH2.z - xO.z;
|
||||
domain->minimum_image(delx2,dely2,delz2);
|
||||
|
||||
const double prefac = alpha * 0.5;
|
||||
xM.x = xO.x + prefac * (delx1 + delx2);
|
||||
xM.y = xO.y + prefac * (dely1 + dely2);
|
||||
xM.z = xO.z + prefac * (delz1 + delz2);
|
||||
}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
double PairLJCutTIP4PLongSoftOMP::memory_usage()
|
||||
{
|
||||
double bytes = memory_usage_thr();
|
||||
bytes += PairLJCutTIP4PLongSoft::memory_usage();
|
||||
return bytes;
|
||||
}
|
||||
|
|
@ -0,0 +1,53 @@
|
|||
/* -*- c++ -*- ----------------------------------------------------------
|
||||
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)
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
#ifdef PAIR_CLASS
|
||||
|
||||
PairStyle(lj/cut/tip4p/long/soft/omp,PairLJCutTIP4PLongSoftOMP)
|
||||
|
||||
#else
|
||||
|
||||
#ifndef LMP_PAIR_LJ_CUT_TIP4P_LONG_SOFT_OMP_H
|
||||
#define LMP_PAIR_LJ_CUT_TIP4P_LONG_SOFT_OMP_H
|
||||
|
||||
#include "pair_lj_cut_tip4p_long_soft.h"
|
||||
#include "thr_omp.h"
|
||||
|
||||
namespace LAMMPS_NS {
|
||||
|
||||
class PairLJCutTIP4PLongSoftOMP : public PairLJCutTIP4PLongSoft, public ThrOMP {
|
||||
|
||||
public:
|
||||
PairLJCutTIP4PLongSoftOMP(class LAMMPS *);
|
||||
virtual ~PairLJCutTIP4PLongSoftOMP();
|
||||
|
||||
virtual void compute(int, int);
|
||||
virtual double memory_usage();
|
||||
|
||||
private:
|
||||
dbl3_t *newsite_thr;
|
||||
int3_t *hneigh_thr;
|
||||
|
||||
template < int, int, int > void eval(int, int, ThrData *const);
|
||||
void compute_newsite_thr(const dbl3_t &, const dbl3_t &,
|
||||
const dbl3_t &, dbl3_t &) const;
|
||||
};
|
||||
|
||||
}
|
||||
|
||||
#endif
|
||||
#endif
|
||||
|
|
@ -0,0 +1,453 @@
|
|||
/* ----------------------------------------------------------------------
|
||||
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_tip4p_long_soft_omp.h"
|
||||
#include "atom.h"
|
||||
#include "domain.h"
|
||||
#include "comm.h"
|
||||
#include "force.h"
|
||||
#include "neighbor.h"
|
||||
#include "error.h"
|
||||
#include "memory.h"
|
||||
#include "neigh_list.h"
|
||||
|
||||
#include "suffix.h"
|
||||
using namespace LAMMPS_NS;
|
||||
|
||||
#define EWALD_F 1.12837917
|
||||
#define EWALD_P 0.3275911
|
||||
#define A1 0.254829592
|
||||
#define A2 -0.284496736
|
||||
#define A3 1.421413741
|
||||
#define A4 -1.453152027
|
||||
#define A5 1.061405429
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
PairTIP4PLongSoftOMP::PairTIP4PLongSoftOMP(LAMMPS *lmp) :
|
||||
PairTIP4PLongSoft(lmp), ThrOMP(lmp, THR_PAIR)
|
||||
{
|
||||
suffix_flag |= Suffix::OMP;
|
||||
respa_enable = 0;
|
||||
newsite_thr = NULL;
|
||||
hneigh_thr = NULL;
|
||||
|
||||
// TIP4P cannot compute virial as F dot r
|
||||
// due to finding bonded H atoms which are not near O atom
|
||||
|
||||
no_virial_fdotr_compute = 1;
|
||||
}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
PairTIP4PLongSoftOMP::~PairTIP4PLongSoftOMP()
|
||||
{
|
||||
memory->destroy(hneigh_thr);
|
||||
memory->destroy(newsite_thr);
|
||||
}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
void PairTIP4PLongSoftOMP::compute(int eflag, int vflag)
|
||||
{
|
||||
if (eflag || vflag) ev_setup(eflag,vflag);
|
||||
else evflag = vflag_fdotr = 0;
|
||||
|
||||
const int nlocal = atom->nlocal;
|
||||
const int nall = nlocal + atom->nghost;
|
||||
|
||||
// reallocate hneigh_thr & newsite_thr if necessary
|
||||
// initialize hneigh_thr[0] to -1 on steps when reneighboring occurred
|
||||
// initialize hneigh_thr[2] to 0 every step
|
||||
|
||||
if (atom->nmax > nmax) {
|
||||
nmax = atom->nmax;
|
||||
memory->destroy(hneigh_thr);
|
||||
memory->create(hneigh_thr,nmax,"pair:hneigh_thr");
|
||||
memory->destroy(newsite_thr);
|
||||
memory->create(newsite_thr,nmax,"pair:newsite_thr");
|
||||
}
|
||||
|
||||
int i;
|
||||
// tag entire list as completely invalid after a neighbor
|
||||
// list update, since that can change the order of atoms.
|
||||
if (neighbor->ago == 0)
|
||||
for (i = 0; i < nall; i++) hneigh_thr[i].a = -1;
|
||||
|
||||
// indicate that the coordinates for the M point need to
|
||||
// be updated. this needs to be done in every step.
|
||||
for (i = 0; i < nall; i++) hneigh_thr[i].t = 0;
|
||||
|
||||
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 (vflag) eval<1,1,1>(ifrom, ito, thr);
|
||||
else eval<1,1,0>(ifrom, ito, thr);
|
||||
} else {
|
||||
if (vflag) eval<1,0,1>(ifrom, ito, thr);
|
||||
else eval<1,0,0>(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 VFLAG>
|
||||
void PairTIP4PLongSoftOMP::eval(int iifrom, int iito, ThrData * const thr)
|
||||
{
|
||||
double qtmp,xtmp,ytmp,ztmp,delx,dely,delz,ecoul;
|
||||
double r,rsq,forcecoul,cforce;
|
||||
double factor_coul,denc;
|
||||
double grij,expm2,prefactor,t,erfc;
|
||||
double v[6],xH1[3],xH2[3];
|
||||
double fdx,fdy,fdz,fOx,fOy,fOz,fHx,fHy,fHz;
|
||||
dbl3_t x1,x2;
|
||||
|
||||
int *ilist,*jlist,*numneigh,**firstneigh;
|
||||
int i,j,ii,jj,jnum,itype,jtype,key;
|
||||
int n,vlist[6];
|
||||
int iH1,iH2,jH1,jH2;
|
||||
|
||||
ecoul = 0.0;
|
||||
|
||||
const dbl3_t * _noalias const x = (dbl3_t *) atom->x[0];
|
||||
dbl3_t * _noalias const f = (dbl3_t *) thr->get_f()[0];
|
||||
const double * _noalias const q = atom->q;
|
||||
const int * _noalias const type = atom->type;
|
||||
const double * _noalias const special_coul = force->special_coul;
|
||||
const double qqrd2e = force->qqrd2e;
|
||||
const double cut_coulsqplus = (cut_coul+2.0*qdist) * (cut_coul+2.0*qdist);
|
||||
|
||||
double fxtmp,fytmp,fztmp;
|
||||
|
||||
ilist = list->ilist;
|
||||
numneigh = list->numneigh;
|
||||
firstneigh = list->firstneigh;
|
||||
|
||||
// loop over neighbors of my atoms
|
||||
|
||||
for (ii = iifrom; ii < iito; ++ii) {
|
||||
i = ilist[ii];
|
||||
qtmp = q[i];
|
||||
xtmp = x[i].x;
|
||||
ytmp = x[i].y;
|
||||
ztmp = x[i].z;
|
||||
itype = type[i];
|
||||
|
||||
// if atom I = water O, set x1 = offset charge site
|
||||
// else x1 = x of atom I
|
||||
// NOTE: to make this part thread safe, we need to
|
||||
// make sure that the hneigh_thr[][] entries only get
|
||||
// updated, when all data is in place. worst case,
|
||||
// some calculation is repeated, but since the results
|
||||
// will be the same, there is no race condition.
|
||||
if (itype == typeO) {
|
||||
if (hneigh_thr[i].a < 0) {
|
||||
iH1 = atom->map(atom->tag[i] + 1);
|
||||
iH2 = atom->map(atom->tag[i] + 2);
|
||||
if (iH1 == -1 || iH2 == -1)
|
||||
error->one(FLERR,"TIP4P hydrogen is missing");
|
||||
if (atom->type[iH1] != typeH || atom->type[iH2] != typeH)
|
||||
error->one(FLERR,"TIP4P hydrogen has incorrect atom type");
|
||||
compute_newsite_thr(x[i],x[iH1],x[iH2],newsite_thr[i]);
|
||||
hneigh_thr[i].t = 1;
|
||||
hneigh_thr[i].b = iH2;
|
||||
hneigh_thr[i].a = iH1;
|
||||
} else {
|
||||
iH1 = hneigh_thr[i].a;
|
||||
iH2 = hneigh_thr[i].b;
|
||||
if (hneigh_thr[i].t == 0) {
|
||||
compute_newsite_thr(x[i],x[iH1],x[iH2],newsite_thr[i]);
|
||||
hneigh_thr[i].t = 1;
|
||||
}
|
||||
}
|
||||
x1 = newsite_thr[i];
|
||||
} else x1 = x[i];
|
||||
|
||||
jlist = firstneigh[i];
|
||||
jnum = numneigh[i];
|
||||
fxtmp=fytmp=fztmp=0.0;
|
||||
|
||||
for (jj = 0; jj < jnum; jj++) {
|
||||
j = jlist[jj];
|
||||
factor_coul = special_coul[sbmask(j)];
|
||||
j &= NEIGHMASK;
|
||||
|
||||
delx = xtmp - x[j].x;
|
||||
dely = ytmp - x[j].y;
|
||||
delz = ztmp - x[j].z;
|
||||
rsq = delx*delx + dely*dely + delz*delz;
|
||||
jtype = type[j];
|
||||
|
||||
// adjust rsq and delxyz for off-site O charge(s) if necessary
|
||||
// but only if they are within reach
|
||||
// NOTE: to make this part thread safe, we need to
|
||||
// make sure that the hneigh_thr[][] entries only get
|
||||
// updated, when all data is in place. worst case,
|
||||
// some calculation is repeated, but since the results
|
||||
// will be the same, there is no race condition.
|
||||
if (rsq < cut_coulsqplus) {
|
||||
if (itype == typeO || jtype == typeO) {
|
||||
|
||||
// if atom J = water O, set x2 = offset charge site
|
||||
// else x2 = x of atom J
|
||||
|
||||
if (jtype == typeO) {
|
||||
if (hneigh_thr[j].a < 0) {
|
||||
jH1 = atom->map(atom->tag[j] + 1);
|
||||
jH2 = atom->map(atom->tag[j] + 2);
|
||||
if (jH1 == -1 || jH2 == -1)
|
||||
error->one(FLERR,"TIP4P hydrogen is missing");
|
||||
if (atom->type[jH1] != typeH || atom->type[jH2] != typeH)
|
||||
error->one(FLERR,"TIP4P hydrogen has incorrect atom type");
|
||||
compute_newsite_thr(x[j],x[jH1],x[jH2],newsite_thr[j]);
|
||||
hneigh_thr[j].t = 1;
|
||||
hneigh_thr[j].b = jH2;
|
||||
hneigh_thr[j].a = jH1;
|
||||
} else {
|
||||
jH1 = hneigh_thr[j].a;
|
||||
jH2 = hneigh_thr[j].b;
|
||||
if (hneigh_thr[j].t == 0) {
|
||||
compute_newsite_thr(x[j],x[jH1],x[jH2],newsite_thr[j]);
|
||||
hneigh_thr[j].t = 1;
|
||||
}
|
||||
}
|
||||
x2 = newsite_thr[j];
|
||||
} else x2 = x[j];
|
||||
|
||||
delx = x1.x - x2.x;
|
||||
dely = x1.y - x2.y;
|
||||
delz = x1.z - x2.z;
|
||||
rsq = delx*delx + dely*dely + delz*delz;
|
||||
}
|
||||
|
||||
// Coulombic interaction based on modified rsq
|
||||
|
||||
if (rsq < cut_coulsq) {
|
||||
r = sqrt(rsq);
|
||||
grij = g_ewald * r;
|
||||
expm2 = exp(-grij*grij);
|
||||
t = 1.0 / (1.0 + EWALD_P*grij);
|
||||
erfc = t * (A1+t*(A2+t*(A3+t*(A4+t*A5)))) * expm2;
|
||||
|
||||
denc = sqrt(lam2[itype][jtype] + rsq);
|
||||
prefactor = qqrd2e * lam1[itype][jtype]
|
||||
* qtmp*q[j] / (denc*denc*denc);
|
||||
|
||||
forcecoul = prefactor * (erfc + EWALD_F*grij*expm2);
|
||||
if (factor_coul < 1.0) {
|
||||
forcecoul -= (1.0-factor_coul)*prefactor;
|
||||
}
|
||||
|
||||
cforce = forcecoul;
|
||||
|
||||
// if i,j are not O atoms, force is applied directly
|
||||
// if i or j are O atoms, force is on fictitious atom & partitioned
|
||||
// force partitioning due to Feenstra, J Comp Chem, 20, 786 (1999)
|
||||
// f_f = fictitious force, fO = f_f (1 - 2 alpha), fH = alpha f_f
|
||||
// preserves total force and torque on water molecule
|
||||
// virial = sum(r x F) where each water's atoms are near xi and xj
|
||||
// vlist stores 2,4,6 atoms whose forces contribute to virial
|
||||
|
||||
if (EVFLAG) {
|
||||
n = 0;
|
||||
key = 0;
|
||||
}
|
||||
|
||||
if (itype != typeO) {
|
||||
fxtmp += delx * cforce;
|
||||
fytmp += dely * cforce;
|
||||
fztmp += delz * cforce;
|
||||
|
||||
if (VFLAG) {
|
||||
v[0] = x[i].x * delx * cforce;
|
||||
v[1] = x[i].y * dely * cforce;
|
||||
v[2] = x[i].z * delz * cforce;
|
||||
v[3] = x[i].x * dely * cforce;
|
||||
v[4] = x[i].x * delz * cforce;
|
||||
v[5] = x[i].y * delz * cforce;
|
||||
}
|
||||
if (EVFLAG) vlist[n++] = i;
|
||||
|
||||
} else {
|
||||
if (EVFLAG) key++;
|
||||
|
||||
fdx = delx*cforce;
|
||||
fdy = dely*cforce;
|
||||
fdz = delz*cforce;
|
||||
|
||||
fOx = fdx*(1 - alpha);
|
||||
fOy = fdy*(1 - alpha);
|
||||
fOz = fdz*(1 - alpha);
|
||||
|
||||
fHx = 0.5*alpha * fdx;
|
||||
fHy = 0.5*alpha * fdy;
|
||||
fHz = 0.5*alpha * fdz;
|
||||
|
||||
fxtmp += fOx;
|
||||
fytmp += fOy;
|
||||
fztmp += fOz;
|
||||
|
||||
f[iH1].x += fHx;
|
||||
f[iH1].y += fHy;
|
||||
f[iH1].z += fHz;
|
||||
|
||||
f[iH2].x += fHx;
|
||||
f[iH2].y += fHy;
|
||||
f[iH2].z += fHz;
|
||||
|
||||
if (VFLAG) {
|
||||
domain->closest_image(&x[i].x,&x[iH1].x,xH1);
|
||||
domain->closest_image(&x[i].x,&x[iH2].x,xH2);
|
||||
|
||||
v[0] = x[i].x*fOx + xH1[0]*fHx + xH2[0]*fHx;
|
||||
v[1] = x[i].y*fOy + xH1[1]*fHy + xH2[1]*fHy;
|
||||
v[2] = x[i].z*fOz + xH1[2]*fHz + xH2[2]*fHz;
|
||||
v[3] = x[i].x*fOy + xH1[0]*fHy + xH2[0]*fHy;
|
||||
v[4] = x[i].x*fOz + xH1[0]*fHz + xH2[0]*fHz;
|
||||
v[5] = x[i].y*fOz + xH1[1]*fHz + xH2[1]*fHz;
|
||||
}
|
||||
if (EVFLAG) {
|
||||
vlist[n++] = i;
|
||||
vlist[n++] = iH1;
|
||||
vlist[n++] = iH2;
|
||||
}
|
||||
}
|
||||
|
||||
if (jtype != typeO) {
|
||||
f[j].x -= delx * cforce;
|
||||
f[j].y -= dely * cforce;
|
||||
f[j].z -= delz * cforce;
|
||||
|
||||
if (VFLAG) {
|
||||
v[0] -= x[j].x * delx * cforce;
|
||||
v[1] -= x[j].y * dely * cforce;
|
||||
v[2] -= x[j].z * delz * cforce;
|
||||
v[3] -= x[j].x * dely * cforce;
|
||||
v[4] -= x[j].x * delz * cforce;
|
||||
v[5] -= x[j].y * delz * cforce;
|
||||
}
|
||||
if (EVFLAG) vlist[n++] = j;
|
||||
|
||||
} else {
|
||||
if (EVFLAG) key += 2;
|
||||
|
||||
fdx = -delx*cforce;
|
||||
fdy = -dely*cforce;
|
||||
fdz = -delz*cforce;
|
||||
|
||||
fOx = fdx*(1 - alpha);
|
||||
fOy = fdy*(1 - alpha);
|
||||
fOz = fdz*(1 - alpha);
|
||||
|
||||
fHx = 0.5*alpha * fdx;
|
||||
fHy = 0.5*alpha * fdy;
|
||||
fHz = 0.5*alpha * fdz;
|
||||
|
||||
f[j].x += fOx;
|
||||
f[j].y += fOy;
|
||||
f[j].z += fOz;
|
||||
|
||||
f[jH1].x += fHx;
|
||||
f[jH1].y += fHy;
|
||||
f[jH1].z += fHz;
|
||||
|
||||
f[jH2].x += fHx;
|
||||
f[jH2].y += fHy;
|
||||
f[jH2].z += fHz;
|
||||
|
||||
if (VFLAG) {
|
||||
domain->closest_image(&x[j].x,&x[jH1].x,xH1);
|
||||
domain->closest_image(&x[j].x,&x[jH2].x,xH2);
|
||||
|
||||
v[0] += x[j].x*fOx + xH1[0]*fHx + xH2[0]*fHx;
|
||||
v[1] += x[j].y*fOy + xH1[1]*fHy + xH2[1]*fHy;
|
||||
v[2] += x[j].z*fOz + xH1[2]*fHz + xH2[2]*fHz;
|
||||
v[3] += x[j].x*fOy + xH1[0]*fHy + xH2[0]*fHy;
|
||||
v[4] += x[j].x*fOz + xH1[0]*fHz + xH2[0]*fHz;
|
||||
v[5] += x[j].y*fOz + xH1[1]*fHz + xH2[1]*fHz;
|
||||
}
|
||||
if (EVFLAG) {
|
||||
vlist[n++] = j;
|
||||
vlist[n++] = jH1;
|
||||
vlist[n++] = jH2;
|
||||
}
|
||||
}
|
||||
|
||||
if (EFLAG) {
|
||||
prefactor = qqrd2e * lam1[itype][jtype] * qtmp*q[j] / denc;
|
||||
ecoul = prefactor*erfc;
|
||||
if (factor_coul < 1.0) ecoul -= (1.0-factor_coul)*prefactor;
|
||||
} else ecoul = 0.0;
|
||||
|
||||
if (EVFLAG) ev_tally_list_thr(this,key,vlist,v,ecoul,alpha,thr);
|
||||
}
|
||||
}
|
||||
}
|
||||
f[i].x += fxtmp;
|
||||
f[i].y += fytmp;
|
||||
f[i].z += fztmp;
|
||||
}
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
compute position xM of fictitious charge site for O atom and 2 H atoms
|
||||
return it as xM
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
void PairTIP4PLongSoftOMP::compute_newsite_thr(const dbl3_t &xO,
|
||||
const dbl3_t &xH1,
|
||||
const dbl3_t &xH2,
|
||||
dbl3_t &xM) const
|
||||
{
|
||||
double delx1 = xH1.x - xO.x;
|
||||
double dely1 = xH1.y - xO.y;
|
||||
double delz1 = xH1.z - xO.z;
|
||||
domain->minimum_image(delx1,dely1,delz1);
|
||||
|
||||
double delx2 = xH2.x - xO.x;
|
||||
double dely2 = xH2.y - xO.y;
|
||||
double delz2 = xH2.z - xO.z;
|
||||
domain->minimum_image(delx2,dely2,delz2);
|
||||
|
||||
const double prefac = alpha * 0.5;
|
||||
xM.x = xO.x + prefac * (delx1 + delx2);
|
||||
xM.y = xO.y + prefac * (dely1 + dely2);
|
||||
xM.z = xO.z + prefac * (delz1 + delz2);
|
||||
}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
double PairTIP4PLongSoftOMP::memory_usage()
|
||||
{
|
||||
double bytes = memory_usage_thr();
|
||||
bytes += PairTIP4PLongSoft::memory_usage();
|
||||
return bytes;
|
||||
}
|
||||
|
|
@ -0,0 +1,53 @@
|
|||
/* -*- c++ -*- ----------------------------------------------------------
|
||||
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)
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
#ifdef PAIR_CLASS
|
||||
|
||||
PairStyle(tip4p/long/soft/omp,PairTIP4PLongSoftOMP)
|
||||
|
||||
#else
|
||||
|
||||
#ifndef LMP_PAIR_TIP4P_LONG_SOFT_OMP_H
|
||||
#define LMP_PAIR_TIP4P_LONG_SOFT_OMP_H
|
||||
|
||||
#include "pair_tip4p_long_soft.h"
|
||||
#include "thr_omp.h"
|
||||
|
||||
namespace LAMMPS_NS {
|
||||
|
||||
class PairTIP4PLongSoftOMP : public PairTIP4PLongSoft, public ThrOMP {
|
||||
|
||||
public:
|
||||
PairTIP4PLongSoftOMP(class LAMMPS *);
|
||||
virtual ~PairTIP4PLongSoftOMP();
|
||||
|
||||
virtual void compute(int, int);
|
||||
virtual double memory_usage();
|
||||
|
||||
private:
|
||||
dbl3_t *newsite_thr;
|
||||
int3_t *hneigh_thr;
|
||||
|
||||
template < int, int, int > void eval(int, int, ThrData *const);
|
||||
void compute_newsite_thr(const dbl3_t &, const dbl3_t &,
|
||||
const dbl3_t &, dbl3_t &) const;
|
||||
};
|
||||
|
||||
}
|
||||
|
||||
#endif
|
||||
#endif
|
||||
Loading…
Reference in New Issue