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git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@9582 f3b2605a-c512-4ea7-a41b-209d697bcdaa

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sjplimp
2013-03-06 16:44:51 +00:00
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src/USER-OMP/respa_omp.cpp Normal file
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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++) {
modify->initial_integrate_respa(vflag,ilevel,iloop);
if (modify->n_post_integrate_respa)
modify->post_integrate_respa(ilevel,iloop);
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) modify->pre_exchange();
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();
if (triclinic) domain->lamda2x(atom->nlocal+atom->nghost);
timer->stamp(TIME_COMM);
if (modify->n_pre_neighbor) modify->pre_neighbor();
neighbor->build();
timer->stamp(TIME_NEIGHBOR);
}
} else if (ilevel == 0) {
timer->stamp();
comm->forward_comm();
timer->stamp(TIME_COMM);
}
force_clear(newton[ilevel]);
if (modify->n_pre_force_respa)
modify->pre_force_respa(vflag,ilevel,iloop);
timer->stamp();
if (level_bond == ilevel && force->bond) {
force->bond->compute(eflag,vflag);
timer->stamp(TIME_BOND);
}
if (level_angle == ilevel && force->angle) {
force->angle->compute(eflag,vflag);
timer->stamp(TIME_BOND);
}
if (level_dihedral == ilevel && force->dihedral) {
force->dihedral->compute(eflag,vflag);
timer->stamp(TIME_BOND);
}
if (level_improper == ilevel && force->improper) {
force->improper->compute(eflag,vflag);
timer->stamp(TIME_BOND);
}
if (level_pair == ilevel && pair_compute_flag) {
force->pair->compute(eflag,vflag);
timer->stamp(TIME_PAIR);
}
if (level_inner == ilevel && pair_compute_flag) {
force->pair->compute_inner();
timer->stamp(TIME_PAIR);
}
if (level_middle == ilevel && pair_compute_flag) {
force->pair->compute_middle();
timer->stamp(TIME_PAIR);
}
if (level_outer == ilevel && pair_compute_flag) {
force->pair->compute_outer(eflag,vflag);
timer->stamp(TIME_PAIR);
}
if (level_kspace == ilevel && kspace_compute_flag) {
force->kspace->compute(eflag,vflag);
timer->stamp(TIME_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(TIME_COMM);
}
if (modify->n_post_force_respa)
modify->post_force_respa(vflag,ilevel,iloop);
modify->final_integrate_respa(ilevel,iloop);
}
copy_f_flevel(ilevel);
}

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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.
------------------------------------------------------------------------- */
#ifdef INTEGRATE_CLASS
IntegrateStyle(respa/omp,RespaOMP)
#else
#ifndef LMP_RESPA_OMP_H
#define LMP_RESPA_OMP_H
#include "respa.h"
#include "thr_omp.h"
namespace LAMMPS_NS {
class RespaOMP : public Respa, public ThrOMP {
public:
RespaOMP(class LAMMPS *, int, char **);
virtual ~RespaOMP() {}
virtual void init();
virtual void setup();
virtual void setup_minimal(int);
protected:
virtual void recurse(int);
};
}
#endif
#endif
/* ERROR/WARNING messages:
E: Illegal ... command
Self-explanatory. Check the input script syntax and compare to the
documentation for the command. You can use -echo screen as a
command-line option when running LAMMPS to see the offending line.
E: Respa levels must be >= 1
Self-explanatory.
E: Cannot set both respa pair and inner/middle/outer
In the rRESPA integrator, you must compute pairwise potentials either
all together (pair), or in pieces (inner/middle/outer). You can't do
both.
E: Must set both respa inner and outer
Cannot use just the inner or outer option with respa without using the
other.
E: Cannot set respa middle without inner/outer
In the rRESPA integrator, you must define both a inner and outer
setting in order to use a middle setting.
E: Invalid order of forces within respa levels
For respa, ordering of force computations within respa levels must
obey certain rules. E.g. bonds cannot be compute less frequently than
angles, pairwise forces cannot be computed less frequently than
kspace, etc.
W: One or more respa levels compute no forces
This is computationally inefficient.
E: Respa inner cutoffs are invalid
The first cutoff must be <= the second cutoff.
E: Respa middle cutoffs are invalid
The first cutoff must be <= the second cutoff.
W: No fixes defined, atoms won't move
If you are not using a fix like nve, nvt, npt then atom velocities and
coordinates will not be updated during timestepping.
W: Fix shake with rRESPA computes invalid pressures
This is a known bug in LAMMPS that has not yet been fixed. If you use
SHAKE with rRESPA and perform a constant volume simulation (e.g. using
fix npt) this only affects the output pressure, not the dynamics of
the simulation. If you use SHAKE with rRESPA and perform a constant
pressure simulation (e.g. using fix npt) then you will be
equilibrating to the wrong volume.
E: Pair style does not support rRESPA inner/middle/outer
You are attempting to use rRESPA options with a pair style that
does not support them.
*/