From f68a7094ad5fe72c8e6caa18ce6276d76d4cdda1 Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Tue, 9 Mar 2021 18:44:51 -0500 Subject: [PATCH] include /omp variant into plugin example --- examples/plugins/Makefile | 9 +- examples/plugins/morse2plugin.cpp | 13 ++- examples/plugins/pair_morse2_omp.cpp | 160 +++++++++++++++++++++++++++ examples/plugins/pair_morse2_omp.h | 41 +++++++ 4 files changed, 218 insertions(+), 5 deletions(-) create mode 100644 examples/plugins/pair_morse2_omp.cpp create mode 100644 examples/plugins/pair_morse2_omp.h diff --git a/examples/plugins/Makefile b/examples/plugins/Makefile index 0c4365dfd8..2f563f924e 100644 --- a/examples/plugins/Makefile +++ b/examples/plugins/Makefile @@ -1,15 +1,16 @@ CXX=mpicxx -CXXFLAGS=-I../../src -Wall -O3 -fPIC -LD=$(CXX) -shared -rdynamic +CXXFLAGS=-I../../src -Wall -O3 -fPIC -I../../src/USER-OMP -fopenmp +LD=$(CXX) -shared -rdynamic -fopenmp -morse2plugin.so: morse2plugin.o pair_morse2.o +morse2plugin.so: morse2plugin.o pair_morse2.o pair_morse2_omp.o $(LD) -o $@ $^ .cpp.o: $(CXX) -o $@ $(CXXFLAGS) -c $< pair_morse2.o: pair_morse2.cpp pair_morse2.h -morse2plugin.o: morse2plugin.cpp pair_morse2.h +pair_morse2_omp.o: pair_morse2_omp.cpp pair_morse2_omp.h pair_morse2.h +morse2plugin.o: morse2plugin.cpp pair_morse2.h pair_morse2_omp.h clean: rm -f *~ *.so *.o log.lammps diff --git a/examples/plugins/morse2plugin.cpp b/examples/plugins/morse2plugin.cpp index bb21f3da95..fbb0882a92 100644 --- a/examples/plugins/morse2plugin.cpp +++ b/examples/plugins/morse2plugin.cpp @@ -7,6 +7,7 @@ #include #include "pair_morse2.h" +#include "pair_morse2_omp.h" using namespace LAMMPS_NS; @@ -15,6 +16,11 @@ static Pair *morse2creator(LAMMPS *lmp) return new PairMorse2(lmp); } +static Pair *morse2ompcreator(LAMMPS *lmp) +{ + return new PairMorse2OMP(lmp); +} + static lammpsplugin_t plugin; void lammpsplugin_init(void *lmp) { @@ -24,6 +30,11 @@ void lammpsplugin_init(void *lmp) plugin.name = "morse2"; plugin.info = "Morse2 variant pair style v1.0 by Axel Kohlmeyer"; plugin.creator = (lammpsplugin_factory *) &morse2creator; - + lammpsplugin_register(&plugin, (LAMMPS *)lmp); + + plugin.style = "pair"; + plugin.name = "morse2/omp"; + plugin.info = "Morse2 variant pair style for OpenMP v1.0 by Axel Kohlmeyer"; + plugin.creator = (lammpsplugin_factory *) &morse2ompcreator; lammpsplugin_register(&plugin, (LAMMPS *)lmp); } diff --git a/examples/plugins/pair_morse2_omp.cpp b/examples/plugins/pair_morse2_omp.cpp new file mode 100644 index 0000000000..14438c764b --- /dev/null +++ b/examples/plugins/pair_morse2_omp.cpp @@ -0,0 +1,160 @@ +/* ---------------------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + https://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 "pair_morse2_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; + +/* ---------------------------------------------------------------------- */ + +PairMorse2OMP::PairMorse2OMP(LAMMPS *lmp) : + PairMorse2(lmp), ThrOMP(lmp, THR_PAIR) +{ + suffix_flag |= Suffix::OMP; + respa_enable = 0; +} + +/* ---------------------------------------------------------------------- */ + +void PairMorse2OMP::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 PairMorse2OMP::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,dr,dexp,factor_lj; + int *ilist,*jlist,*numneigh,**firstneigh; + + evdwl = 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 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]) { + r = sqrt(rsq); + dr = r - r0[itype][jtype]; + dexp = exp(-alpha[itype][jtype] * dr); + fpair = factor_lj * morse1[itype][jtype] * (dexp*dexp - dexp) / r; + + 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) - + 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 PairMorse2OMP::memory_usage() +{ + double bytes = memory_usage_thr(); + bytes += PairMorse2::memory_usage(); + + return bytes; +} diff --git a/examples/plugins/pair_morse2_omp.h b/examples/plugins/pair_morse2_omp.h new file mode 100644 index 0000000000..c5ed7b5765 --- /dev/null +++ b/examples/plugins/pair_morse2_omp.h @@ -0,0 +1,41 @@ +/* -*- 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) +------------------------------------------------------------------------- */ + +#ifndef LMP_PAIR_MORSE2_OMP_H +#define LMP_PAIR_MORSE2_OMP_H + +#include "pair_morse2.h" +#include "thr_omp.h" + +namespace LAMMPS_NS { + +class PairMorse2OMP : public PairMorse2, public ThrOMP { + + public: + PairMorse2OMP(class LAMMPS *); + + virtual void compute(int, int); + virtual double memory_usage(); + + private: + template + void eval(int ifrom, int ito, ThrData * const thr); +}; + +} + +#endif