diff --git a/src/EXTRA-PAIR/pair_pedone.cpp b/src/EXTRA-PAIR/pair_pedone.cpp index b6e0f8b03c..c5f7f49117 100644 --- a/src/EXTRA-PAIR/pair_pedone.cpp +++ b/src/EXTRA-PAIR/pair_pedone.cpp @@ -11,6 +11,10 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ +/* ---------------------------------------------------------------------- + Contributing author: Axel Kohlmeyer (Temple U) +------------------------------------------------------------------------- */ + #include "pair_pedone.h" #include "atom.h" @@ -107,7 +111,8 @@ void PairPedone::compute(int eflag, int vflag) r = sqrt(rsq); dr = r - r0[itype][jtype]; dexp = exp(-alpha[itype][jtype] * dr); - fpair = pedone1[itype][jtype] * (dexp * dexp - dexp) / r + pedone2[itype][jtype] * r6inv * r6inv * r2inv; + fpair = pedone1[itype][jtype] * (dexp * dexp - dexp) / r + + pedone2[itype][jtype] * r6inv * r6inv * r2inv; fpair *= factor_lj; f[i][0] += delx * fpair; @@ -362,7 +367,8 @@ double PairPedone::single(int /*i*/, int /*j*/, int itype, int jtype, double rsq dexp = exp(-alpha[itype][jtype] * dr); r2inv = 1.0 / rsq; r6inv = r2inv * r2inv * r2inv; - fforce = pedone1[itype][jtype] * (dexp * dexp - dexp) / r + pedone2[itype][jtype] * r6inv * r6inv * r2inv; + fforce = pedone1[itype][jtype] * (dexp * dexp - dexp) / r + + pedone2[itype][jtype] * r6inv * r6inv * r2inv; fforce *= factor_lj; phi = d0[itype][jtype] * (dexp * dexp - 2.0 * dexp) + c0[itype][jtype] * r6inv * r6inv - diff --git a/src/OPENMP/pair_pedone_omp.cpp b/src/OPENMP/pair_pedone_omp.cpp new file mode 100644 index 0000000000..140816bfe4 --- /dev/null +++ b/src/OPENMP/pair_pedone_omp.cpp @@ -0,0 +1,169 @@ +/* ---------------------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + https://www.lammps.org/, Sandia National Laboratories + LAMMPS development team: developers@lammps.org + + 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 "pair_pedone_omp.h" + +#include "atom.h" +#include "comm.h" +#include "force.h" +#include "neigh_list.h" +#include "suffix.h" + +#include + +#include "omp_compat.h" +using namespace LAMMPS_NS; + +/* ---------------------------------------------------------------------- */ + +PairPedoneOMP::PairPedoneOMP(LAMMPS *lmp) : PairPedone(lmp), ThrOMP(lmp, THR_PAIR) +{ + suffix_flag |= Suffix::OMP; + respa_enable = 0; +} + +/* ---------------------------------------------------------------------- */ + +void PairPedoneOMP::compute(int eflag, int vflag) +{ + ev_init(eflag, vflag); + + const int nall = atom->nlocal + atom->nghost; + const int nthreads = comm->nthreads; + const int inum = list->inum; + +#if defined(_OPENMP) +#pragma omp parallel LMP_DEFAULT_NONE LMP_SHARED(eflag, vflag) +#endif + { + int ifrom, ito, tid; + + loop_setup_thr(ifrom, ito, tid, inum, nthreads); + ThrData *thr = fix->get_thr(tid); + thr->timer(Timer::START); + ev_setup_thr(eflag, vflag, nall, eatom, vatom, nullptr, 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); + } + + thr->timer(Timer::PAIR); + reduce_thr(this, eflag, vflag, thr); + } // end of omp parallel region +} + +template +void PairPedoneOMP::eval(int iifrom, int iito, ThrData *const thr) +{ + int i, j, ii, jj, jnum, itype, jtype; + double xtmp, ytmp, ztmp, delx, dely, delz, evdwl, fpair; + double rsq, r, r2inv, r6inv, dr, dexp, factor_lj; + int *ilist, *jlist, *numneigh, **firstneigh; + + evdwl = 0.0; + + const auto *_noalias const x = (dbl3_t *) atom->x[0]; + auto *_noalias const f = (dbl3_t *) thr->get_f()[0]; + const int *_noalias const type = atom->type; + const int nlocal = atom->nlocal; + const double *_noalias const special_lj = force->special_lj; + 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]; + 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)]; + 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]) { + r2inv = 1.0 / rsq; + r6inv = r2inv * r2inv * r2inv; + r = sqrt(rsq); + dr = r - r0[itype][jtype]; + dexp = exp(-alpha[itype][jtype] * dr); + fpair = pedone1[itype][jtype] * (dexp * dexp - dexp) / r + + pedone2[itype][jtype] * r6inv * r6inv * r2inv; + fpair *= factor_lj; + + 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 = d0[itype][jtype] * (dexp * dexp - 2.0 * dexp) + c0[itype][jtype] * r6inv * r6inv - + offset[itype][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 PairPedoneOMP::memory_usage() +{ + double bytes = memory_usage_thr(); + bytes += PairPedone::memory_usage(); + + return bytes; +} diff --git a/src/OPENMP/pair_pedone_omp.h b/src/OPENMP/pair_pedone_omp.h new file mode 100644 index 0000000000..8c23e86fcd --- /dev/null +++ b/src/OPENMP/pair_pedone_omp.h @@ -0,0 +1,48 @@ +/* -*- c++ -*- ---------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + https://www.lammps.org/, Sandia National Laboratories + LAMMPS development team: developers@lammps.org + + 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 +// clang-format off +PairStyle(pedone/omp,PairPedoneOMP); +// clang-format on +#else + +#ifndef LMP_PAIR_PEDONE_OMP_H +#define LMP_PAIR_PEDONE_OMP_H + +#include "pair_pedone.h" +#include "thr_omp.h" + +namespace LAMMPS_NS { + +class PairPedoneOMP : public PairPedone, public ThrOMP { + + public: + PairPedoneOMP(class LAMMPS *); + + void compute(int, int) override; + double memory_usage() override; + + private: + template + void eval(int ifrom, int ito, ThrData *const thr); +}; + +} // namespace LAMMPS_NS + +#endif +#endif diff --git a/unittest/force-styles/tests/atomic-pair-pedone.yaml b/unittest/force-styles/tests/atomic-pair-pedone.yaml index 28ff3aabd4..ea97d9ee8c 100644 --- a/unittest/force-styles/tests/atomic-pair-pedone.yaml +++ b/unittest/force-styles/tests/atomic-pair-pedone.yaml @@ -29,7 +29,11 @@ pair_style: hybrid/overlay pedone 8.0 coul/dsf 0.05 8.0 pair_coeff: ! | * * coul/dsf 1 2 pedone 0.030211 2.241334 2.923245 5.0 -extract: ! "" +extract: ! | + c0 2 + d0 2 + r0 2 + alpha 2 natoms: 32 init_vdwl: -0.05846735245123568 init_coul: -127.6163776098739