add OPENMP version and apply clang-format
This commit is contained in:
Axel Kohlmeyer
@ -11,6 +11,10 @@
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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 "pair_pedone.h"
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#include "atom.h"
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@ -107,7 +111,8 @@ void PairPedone::compute(int eflag, int vflag)
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r = sqrt(rsq);
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dr = r - r0[itype][jtype];
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dexp = exp(-alpha[itype][jtype] * dr);
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fpair = pedone1[itype][jtype] * (dexp * dexp - dexp) / r + pedone2[itype][jtype] * r6inv * r6inv * r2inv;
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fpair = pedone1[itype][jtype] * (dexp * dexp - dexp) / r +
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pedone2[itype][jtype] * r6inv * r6inv * r2inv;
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fpair *= factor_lj;
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f[i][0] += delx * fpair;
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@ -362,7 +367,8 @@ double PairPedone::single(int /*i*/, int /*j*/, int itype, int jtype, double rsq
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dexp = exp(-alpha[itype][jtype] * dr);
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r2inv = 1.0 / rsq;
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r6inv = r2inv * r2inv * r2inv;
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fforce = pedone1[itype][jtype] * (dexp * dexp - dexp) / r + pedone2[itype][jtype] * r6inv * r6inv * r2inv;
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fforce = pedone1[itype][jtype] * (dexp * dexp - dexp) / r +
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pedone2[itype][jtype] * r6inv * r6inv * r2inv;
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fforce *= factor_lj;
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phi = d0[itype][jtype] * (dexp * dexp - 2.0 * dexp) + c0[itype][jtype] * r6inv * r6inv -
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169
src/OPENMP/pair_pedone_omp.cpp
Normal file
169
src/OPENMP/pair_pedone_omp.cpp
Normal file
@ -0,0 +1,169 @@
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/* ----------------------------------------------------------------------
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LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
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https://www.lammps.org/, Sandia National Laboratories
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LAMMPS development team: developers@lammps.org
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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 "pair_pedone_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 "neigh_list.h"
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#include "suffix.h"
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#include <cmath>
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#include "omp_compat.h"
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using namespace LAMMPS_NS;
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/* ---------------------------------------------------------------------- */
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PairPedoneOMP::PairPedoneOMP(LAMMPS *lmp) : PairPedone(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 PairPedoneOMP::compute(int eflag, int vflag)
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{
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ev_init(eflag, vflag);
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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 LMP_DEFAULT_NONE LMP_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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thr->timer(Timer::START);
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ev_setup_thr(eflag, vflag, nall, eatom, vatom, nullptr, thr);
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if (evflag) {
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if (eflag) {
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if (force->newton_pair)
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eval<1, 1, 1>(ifrom, ito, thr);
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else
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eval<1, 1, 0>(ifrom, ito, thr);
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} else {
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if (force->newton_pair)
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eval<1, 0, 1>(ifrom, ito, thr);
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else
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eval<1, 0, 0>(ifrom, ito, thr);
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}
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} else {
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if (force->newton_pair)
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eval<0, 0, 1>(ifrom, ito, thr);
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else
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eval<0, 0, 0>(ifrom, ito, thr);
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}
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thr->timer(Timer::PAIR);
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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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template <int EVFLAG, int EFLAG, int NEWTON_PAIR>
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void PairPedoneOMP::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 xtmp, ytmp, ztmp, delx, dely, delz, evdwl, fpair;
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double rsq, r, r2inv, r6inv, dr, dexp, factor_lj;
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int *ilist, *jlist, *numneigh, **firstneigh;
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evdwl = 0.0;
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const auto *_noalias const x = (dbl3_t *) atom->x[0];
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auto *_noalias const f = (dbl3_t *) thr->get_f()[0];
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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_lj = force->special_lj;
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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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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_lj = special_lj[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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r2inv = 1.0 / rsq;
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r6inv = r2inv * r2inv * r2inv;
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r = sqrt(rsq);
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dr = r - r0[itype][jtype];
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dexp = exp(-alpha[itype][jtype] * dr);
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fpair = pedone1[itype][jtype] * (dexp * dexp - dexp) / r +
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pedone2[itype][jtype] * r6inv * r6inv * r2inv;
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fpair *= factor_lj;
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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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evdwl = d0[itype][jtype] * (dexp * dexp - 2.0 * dexp) + c0[itype][jtype] * r6inv * r6inv -
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offset[itype][jtype];
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evdwl *= factor_lj;
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}
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if (EVFLAG)
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ev_tally_thr(this, i, j, nlocal, NEWTON_PAIR, evdwl, 0.0, 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 PairPedoneOMP::memory_usage()
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{
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double bytes = memory_usage_thr();
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bytes += PairPedone::memory_usage();
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return bytes;
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}
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48
src/OPENMP/pair_pedone_omp.h
Normal file
48
src/OPENMP/pair_pedone_omp.h
Normal file
@ -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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https://www.lammps.org/, Sandia National Laboratories
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LAMMPS development team: developers@lammps.org
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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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// clang-format off
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PairStyle(pedone/omp,PairPedoneOMP);
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// clang-format on
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#else
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#ifndef LMP_PAIR_PEDONE_OMP_H
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#define LMP_PAIR_PEDONE_OMP_H
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#include "pair_pedone.h"
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#include "thr_omp.h"
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namespace LAMMPS_NS {
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class PairPedoneOMP : public PairPedone, public ThrOMP {
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public:
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PairPedoneOMP(class LAMMPS *);
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void compute(int, int) override;
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double memory_usage() override;
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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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} // namespace LAMMPS_NS
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#endif
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#endif
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@ -29,7 +29,11 @@ pair_style: hybrid/overlay pedone 8.0 coul/dsf 0.05 8.0
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pair_coeff: ! |
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* * coul/dsf
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1 2 pedone 0.030211 2.241334 2.923245 5.0
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extract: ! ""
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extract: ! |
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c0 2
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d0 2
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r0 2
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alpha 2
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natoms: 32
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init_vdwl: -0.05846735245123568
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init_coul: -127.6163776098739
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