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respa_omp.cpp
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Tue, Nov 5, 09:31
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rLAMMPS lammps
respa_omp.cpp
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/* ----------------------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
http://lammps.sandia.gov, Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
/* ----------------------------------------------------------------------
Contributing authors: Mark Stevens (SNL), Paul Crozier (SNL)
------------------------------------------------------------------------- */
#include "stdlib.h"
#include "string.h"
#include "respa_omp.h"
#include "neighbor.h"
#include "domain.h"
#include "comm.h"
#include "atom.h"
#include "force.h"
#include "pair.h"
#include "bond.h"
#include "angle.h"
#include "dihedral.h"
#include "improper.h"
#include "kspace.h"
#include "output.h"
#include "update.h"
#include "modify.h"
#include "compute.h"
#include "fix_respa.h"
#include "timer.h"
#include "memory.h"
#include "error.h"
#if defined(_OPENMP)
#include <omp.h>
#endif
using namespace LAMMPS_NS;
/* ---------------------------------------------------------------------- */
RespaOMP::RespaOMP(LAMMPS *lmp, int narg, char **arg)
: Respa(lmp, narg, arg),ThrOMP(lmp, THR_INTGR)
{
}
/* ----------------------------------------------------------------------
initialization before run
------------------------------------------------------------------------- */
void RespaOMP::init()
{
Respa::init();
if (atom->torque)
error->all(FLERR,"Extended particles are not supported by respa/omp\n");
}
/* ----------------------------------------------------------------------
setup before run
------------------------------------------------------------------------- */
void RespaOMP::setup()
{
if (comm->me == 0 && screen) fprintf(screen,"Setting up run ...\n");
update->setupflag = 1;
// setup domain, communication and neighboring
// acquire ghosts
// build neighbor lists
atom->setup();
modify->setup_pre_exchange();
if (triclinic) domain->x2lamda(atom->nlocal);
domain->pbc();
domain->reset_box();
comm->setup();
if (neighbor->style) neighbor->setup_bins();
comm->exchange();
if (atom->sortfreq > 0) atom->sort();
comm->borders();
if (triclinic) domain->lamda2x(atom->nlocal+atom->nghost);
domain->image_check();
domain->box_too_small_check();
modify->setup_pre_neighbor();
neighbor->build();
neighbor->ncalls = 0;
// compute all forces
ev_set(update->ntimestep);
for (int ilevel = 0; ilevel < nlevels; ilevel++) {
force_clear(newton[ilevel]);
modify->setup_pre_force_respa(vflag,ilevel);
if (level_bond == ilevel && force->bond)
force->bond->compute(eflag,vflag);
if (level_angle == ilevel && force->angle)
force->angle->compute(eflag,vflag);
if (level_dihedral == ilevel && force->dihedral)
force->dihedral->compute(eflag,vflag);
if (level_improper == ilevel && force->improper)
force->improper->compute(eflag,vflag);
if (level_pair == ilevel && pair_compute_flag)
force->pair->compute(eflag,vflag);
if (level_inner == ilevel && pair_compute_flag)
force->pair->compute_inner();
if (level_middle == ilevel && pair_compute_flag)
force->pair->compute_middle();
if (level_outer == ilevel && pair_compute_flag)
force->pair->compute_outer(eflag,vflag);
if (level_kspace == ilevel && force->kspace) {
force->kspace->setup();
if (kspace_compute_flag) force->kspace->compute(eflag,vflag);
}
// reduce forces from per-thread arrays, if needed
if (!fix->get_reduced()) {
const int nall = atom->nlocal + atom->nghost;
const int nthreads = comm->nthreads;
#if defined(_OPENMP)
#pragma omp parallel default(none)
#endif
{
#if defined(_OPENMP)
int tid = omp_get_thread_num();
#else
int tid = 0;
#endif
data_reduce_thr(atom->f[0], nall, nthreads, 3, tid);
}
fix->did_reduce();
}
if (newton[ilevel]) comm->reverse_comm();
copy_f_flevel(ilevel);
}
modify->setup(vflag);
sum_flevel_f();
output->setup();
update->setupflag = 0;
}
/* ----------------------------------------------------------------------
setup without output
flag = 0 = just force calculation
flag = 1 = reneighbor and force calculation
------------------------------------------------------------------------- */
void RespaOMP::setup_minimal(int flag)
{
update->setupflag = 1;
// setup domain, communication and neighboring
// acquire ghosts
// build neighbor lists
if (flag) {
modify->setup_pre_exchange();
if (triclinic) domain->x2lamda(atom->nlocal);
domain->pbc();
domain->reset_box();
comm->setup();
if (neighbor->style) neighbor->setup_bins();
comm->exchange();
comm->borders();
if (triclinic) domain->lamda2x(atom->nlocal+atom->nghost);
domain->image_check();
domain->box_too_small_check();
modify->setup_pre_neighbor();
neighbor->build();
neighbor->ncalls = 0;
}
// compute all forces
ev_set(update->ntimestep);
for (int ilevel = 0; ilevel < nlevels; ilevel++) {
force_clear(newton[ilevel]);
modify->setup_pre_force_respa(vflag,ilevel);
if (level_bond == ilevel && force->bond)
force->bond->compute(eflag,vflag);
if (level_angle == ilevel && force->angle)
force->angle->compute(eflag,vflag);
if (level_dihedral == ilevel && force->dihedral)
force->dihedral->compute(eflag,vflag);
if (level_improper == ilevel && force->improper)
force->improper->compute(eflag,vflag);
if (level_pair == ilevel && pair_compute_flag)
force->pair->compute(eflag,vflag);
if (level_inner == ilevel && pair_compute_flag)
force->pair->compute_inner();
if (level_middle == ilevel && pair_compute_flag)
force->pair->compute_middle();
if (level_outer == ilevel && pair_compute_flag)
force->pair->compute_outer(eflag,vflag);
if (level_kspace == ilevel && force->kspace) {
force->kspace->setup();
if (kspace_compute_flag) force->kspace->compute(eflag,vflag);
}
// reduce forces from per-thread arrays, if needed
if (!fix->get_reduced()) {
const int nall = atom->nlocal + atom->nghost;
const int nthreads = comm->nthreads;
#if defined(_OPENMP)
#pragma omp parallel default(none)
#endif
{
#if defined(_OPENMP)
int tid = omp_get_thread_num();
#else
int tid = 0;
#endif
data_reduce_thr(atom->f[0], nall, nthreads, 3, tid);
}
fix->did_reduce();
}
if (newton[ilevel]) comm->reverse_comm();
copy_f_flevel(ilevel);
}
modify->setup(vflag);
sum_flevel_f();
update->setupflag = 0;
}
/* ---------------------------------------------------------------------- */
void RespaOMP::recurse(int ilevel)
{
copy_flevel_f(ilevel);
for (int iloop = 0; iloop < loop[ilevel]; iloop++) {
timer->stamp();
modify->initial_integrate_respa(vflag,ilevel,iloop);
if (modify->n_post_integrate_respa)
modify->post_integrate_respa(ilevel,iloop);
timer->stamp(Timer::MODIFY);
if (ilevel) recurse(ilevel-1);
// at outermost level, check on rebuilding neighbor list
// at innermost level, communicate
// at middle levels, do nothing
if (ilevel == nlevels-1) {
int nflag = neighbor->decide();
if (nflag) {
if (modify->n_pre_exchange) {
timer->stamp();
modify->pre_exchange();
timer->stamp(Timer::MODIFY);
}
if (triclinic) domain->x2lamda(atom->nlocal);
domain->pbc();
if (domain->box_change) {
domain->reset_box();
comm->setup();
if (neighbor->style) neighbor->setup_bins();
}
timer->stamp();
comm->exchange();
if (atom->sortfreq > 0 &&
update->ntimestep >= atom->nextsort) atom->sort();
comm->borders();
timer->stamp(Timer::COMM);
if (triclinic) domain->lamda2x(atom->nlocal+atom->nghost);
if (modify->n_pre_neighbor) {
timer->stamp();
modify->pre_neighbor();
timer->stamp(Timer::MODIFY);
}
neighbor->build();
timer->stamp(Timer::NEIGHBOR);
}
} else if (ilevel == 0) {
timer->stamp();
comm->forward_comm();
timer->stamp(Timer::COMM);
}
force_clear(newton[ilevel]);
if (modify->n_pre_force_respa) {
timer->stamp();
modify->pre_force_respa(vflag,ilevel,iloop);
timer->stamp(Timer::MODIFY);
}
timer->stamp();
if (level_bond == ilevel && force->bond) {
force->bond->compute(eflag,vflag);
timer->stamp(Timer::BOND);
}
if (level_angle == ilevel && force->angle) {
force->angle->compute(eflag,vflag);
timer->stamp(Timer::BOND);
}
if (level_dihedral == ilevel && force->dihedral) {
force->dihedral->compute(eflag,vflag);
timer->stamp(Timer::BOND);
}
if (level_improper == ilevel && force->improper) {
force->improper->compute(eflag,vflag);
timer->stamp(Timer::BOND);
}
if (level_pair == ilevel && pair_compute_flag) {
force->pair->compute(eflag,vflag);
timer->stamp(Timer::PAIR);
}
if (level_inner == ilevel && pair_compute_flag) {
force->pair->compute_inner();
timer->stamp(Timer::PAIR);
}
if (level_middle == ilevel && pair_compute_flag) {
force->pair->compute_middle();
timer->stamp(Timer::PAIR);
}
if (level_outer == ilevel && pair_compute_flag) {
force->pair->compute_outer(eflag,vflag);
timer->stamp(Timer::PAIR);
}
if (level_kspace == ilevel && kspace_compute_flag) {
force->kspace->compute(eflag,vflag);
timer->stamp(Timer::KSPACE);
}
// reduce forces from per-thread arrays, if needed
if (!fix->get_reduced()) {
const int nall = atom->nlocal + atom->nghost;
const int nthreads = comm->nthreads;
#if defined(_OPENMP)
#pragma omp parallel default(none)
#endif
{
#if defined(_OPENMP)
int tid = omp_get_thread_num();
#else
int tid = 0;
#endif
data_reduce_thr(atom->f[0], nall, nthreads, 3, tid);
}
fix->did_reduce();
}
if (newton[ilevel]) {
comm->reverse_comm();
timer->stamp(Timer::COMM);
}
timer->stamp();
if (modify->n_post_force_respa)
modify->post_force_respa(vflag,ilevel,iloop);
modify->final_integrate_respa(ilevel,iloop);
timer->stamp(Timer::MODIFY);
}
copy_f_flevel(ilevel);
}
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