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verlet_kokkos.cpp
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Wed, Nov 6, 11:26

verlet_kokkos.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.
------------------------------------------------------------------------- */
#include <string.h>
#include "verlet_kokkos.h"
#include "neighbor.h"
#include "domain.h"
#include "comm.h"
#include "atom.h"
#include "atom_kokkos.h"
#include "atom_masks.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.h"
#include "timer.h"
#include "memory.h"
#include "error.h"
#include <ctime>
using namespace LAMMPS_NS;
template<class ViewA, class ViewB>
struct ForceAdder {
ViewA a;
ViewB b;
ForceAdder(const ViewA& a_, const ViewB& b_):a(a_),b(b_) {}
KOKKOS_INLINE_FUNCTION
void operator() (const int& i) const {
a(i,0) += b(i,0);
a(i,1) += b(i,1);
a(i,2) += b(i,2);
}
};
/* ---------------------------------------------------------------------- */
VerletKokkos::VerletKokkos(LAMMPS *lmp, int narg, char **arg) :
Verlet(lmp, narg, arg)
{
atomKK = (AtomKokkos *) atom;
}
/* ----------------------------------------------------------------------
setup before run
------------------------------------------------------------------------- */
void VerletKokkos::setup()
{
if (comm->me == 0 && screen) {
fprintf(screen,"Setting up Verlet run ...\n");
fprintf(screen," Unit style : %s\n", update->unit_style);
fprintf(screen," Current step : " BIGINT_FORMAT "\n", update->ntimestep);
fprintf(screen," Time step : %g\n", update->dt);
timer->print_timeout(screen);
}
update->setupflag = 1;
// setup domain, communication and neighboring
// acquire ghosts
// build neighbor lists
atomKK->modified(Host,ALL_MASK);
atomKK->setup();
modify->setup_pre_exchange();
// debug
atomKK->sync(Host,ALL_MASK);
atomKK->modified(Host,ALL_MASK);
if (triclinic) domain->x2lamda(atomKK->nlocal);
domain->pbc();
atomKK->sync(Host,ALL_MASK);
domain->reset_box();
comm->setup();
if (neighbor->style) neighbor->setup_bins();
comm->exchange();
if (atomKK->sortfreq > 0) atomKK->sort();
comm->borders();
if (triclinic) domain->lamda2x(atomKK->nlocal+atomKK->nghost);
atomKK->sync(Host,ALL_MASK);
domain->image_check();
domain->box_too_small_check();
modify->setup_pre_neighbor();
atomKK->modified(Host,ALL_MASK);
neighbor->build();
neighbor->ncalls = 0;
// compute all forces
ev_set(update->ntimestep);
force_clear();
modify->setup_pre_force(vflag);
if (pair_compute_flag) {
atomKK->sync(force->pair->execution_space,force->pair->datamask_read);
atomKK->modified(force->pair->execution_space,force->pair->datamask_modify);
force->pair->compute(eflag,vflag);
timer->stamp(Timer::PAIR);
}
else if (force->pair) force->pair->compute_dummy(eflag,vflag);
if (atomKK->molecular) {
if (force->bond) {
atomKK->sync(force->bond->execution_space,force->bond->datamask_read);
atomKK->modified(force->bond->execution_space,force->bond->datamask_modify);
force->bond->compute(eflag,vflag);
}
if (force->angle) {
atomKK->sync(force->angle->execution_space,force->angle->datamask_read);
atomKK->modified(force->angle->execution_space,force->angle->datamask_modify);
force->angle->compute(eflag,vflag);
}
if (force->dihedral) {
atomKK->sync(force->dihedral->execution_space,force->dihedral->datamask_read);
atomKK->modified(force->dihedral->execution_space,force->dihedral->datamask_modify);
force->dihedral->compute(eflag,vflag);
}
if (force->improper) {
atomKK->sync(force->improper->execution_space,force->improper->datamask_read);
atomKK->modified(force->improper->execution_space,force->improper->datamask_modify);
force->improper->compute(eflag,vflag);
}
timer->stamp(Timer::BOND);
}
if(force->kspace) {
force->kspace->setup();
if (kspace_compute_flag) {
atomKK->sync(force->kspace->execution_space,force->kspace->datamask_read);
atomKK->modified(force->kspace->execution_space,force->kspace->datamask_modify);
force->kspace->compute(eflag,vflag);
timer->stamp(Timer::KSPACE);
} else force->kspace->compute_dummy(eflag,vflag);
}
if (force->newton) comm->reverse_comm();
modify->setup(vflag);
output->setup();
update->setupflag = 0;
}
/* ----------------------------------------------------------------------
setup without output
flag = 0 = just force calculation
flag = 1 = reneighbor and force calculation
------------------------------------------------------------------------- */
void VerletKokkos::setup_minimal(int flag)
{
update->setupflag = 1;
// setup domain, communication and neighboring
// acquire ghosts
// build neighbor lists
if (flag) {
atomKK->modified(Host,ALL_MASK);
modify->setup_pre_exchange();
// debug
atomKK->sync(Host,ALL_MASK);
atomKK->modified(Host,ALL_MASK);
if (triclinic) domain->x2lamda(atomKK->nlocal);
domain->pbc();
atomKK->sync(Host,ALL_MASK);
domain->reset_box();
comm->setup();
if (neighbor->style) neighbor->setup_bins();
comm->exchange();
comm->borders();
if (triclinic) domain->lamda2x(atomKK->nlocal+atomKK->nghost);
atomKK->sync(Host,ALL_MASK);
domain->image_check();
domain->box_too_small_check();
modify->setup_pre_neighbor();
atomKK->modified(Host,ALL_MASK);
neighbor->build();
neighbor->ncalls = 0;
}
// compute all forces
ev_set(update->ntimestep);
force_clear();
modify->setup_pre_force(vflag);
if (pair_compute_flag) {
atomKK->sync(force->pair->execution_space,force->pair->datamask_read);
atomKK->modified(force->pair->execution_space,force->pair->datamask_modify);
force->pair->compute(eflag,vflag);
timer->stamp(Timer::PAIR);
}
else if (force->pair) force->pair->compute_dummy(eflag,vflag);
if (atomKK->molecular) {
if (force->bond) {
atomKK->sync(force->bond->execution_space,force->bond->datamask_read);
atomKK->modified(force->bond->execution_space,force->bond->datamask_modify);
force->bond->compute(eflag,vflag);
}
if (force->angle) {
atomKK->sync(force->angle->execution_space,force->angle->datamask_read);
atomKK->modified(force->angle->execution_space,force->angle->datamask_modify);
force->angle->compute(eflag,vflag);
}
if (force->dihedral) {
atomKK->sync(force->dihedral->execution_space,force->dihedral->datamask_read);
atomKK->modified(force->dihedral->execution_space,force->dihedral->datamask_modify);
force->dihedral->compute(eflag,vflag);
}
if (force->improper) {
atomKK->sync(force->improper->execution_space,force->improper->datamask_read);
atomKK->modified(force->improper->execution_space,force->improper->datamask_modify);
force->improper->compute(eflag,vflag);
}
timer->stamp(Timer::BOND);
}
if(force->kspace) {
force->kspace->setup();
if (kspace_compute_flag) {
atomKK->sync(force->kspace->execution_space,force->kspace->datamask_read);
atomKK->modified(force->kspace->execution_space,force->kspace->datamask_modify);
force->kspace->compute(eflag,vflag);
timer->stamp(Timer::KSPACE);
} else force->kspace->compute_dummy(eflag,vflag);
}
if (force->newton) comm->reverse_comm();
modify->setup(vflag);
update->setupflag = 0;
}
/* ----------------------------------------------------------------------
run for N steps
------------------------------------------------------------------------- */
void VerletKokkos::run(int n)
{
bigint ntimestep;
int nflag,sortflag;
int n_post_integrate = modify->n_post_integrate;
int n_pre_exchange = modify->n_pre_exchange;
int n_pre_neighbor = modify->n_pre_neighbor;
int n_pre_force = modify->n_pre_force;
int n_post_force = modify->n_post_force;
int n_end_of_step = modify->n_end_of_step;
if (atomKK->sortfreq > 0) sortflag = 1;
else sortflag = 0;
f_merge_copy = DAT::t_f_array("VerletKokkos::f_merge_copy",atomKK->k_f.dimension_0());
static double time = 0.0;
static int count = 0;
atomKK->sync(Device,ALL_MASK);
Kokkos::Impl::Timer ktimer;
timer->init_timeout();
for (int i = 0; i < n; i++) {
if (timer->check_timeout(i)) {
update->nsteps = i;
break;
}
ntimestep = ++update->ntimestep;
ev_set(ntimestep);
// initial time integration
ktimer.reset();
timer->stamp();
modify->initial_integrate(vflag);
time += ktimer.seconds();
if (n_post_integrate) modify->post_integrate();
timer->stamp(Timer::MODIFY);
// regular communication vs neighbor list rebuild
nflag = neighbor->decide();
if (nflag == 0) {
timer->stamp();
comm->forward_comm();
timer->stamp(Timer::COMM);
} else {
// added debug
//atomKK->sync(Host,ALL_MASK);
//atomKK->modified(Host,ALL_MASK);
if (n_pre_exchange) {
timer->stamp();
modify->pre_exchange();
timer->stamp(Timer::MODIFY);
}
// debug
//atomKK->sync(Host,ALL_MASK);
//atomKK->modified(Host,ALL_MASK);
if (triclinic) domain->x2lamda(atomKK->nlocal);
domain->pbc();
if (domain->box_change) {
domain->reset_box();
comm->setup();
if (neighbor->style) neighbor->setup_bins();
}
timer->stamp();
// added debug
//atomKK->sync(Device,ALL_MASK);
//atomKK->modified(Device,ALL_MASK);
comm->exchange();
if (sortflag && ntimestep >= atomKK->nextsort) atomKK->sort();
comm->borders();
// added debug
//atomKK->sync(Host,ALL_MASK);
//atomKK->modified(Host,ALL_MASK);
if (triclinic) domain->lamda2x(atomKK->nlocal+atomKK->nghost);
timer->stamp(Timer::COMM);
if (n_pre_neighbor) {
modify->pre_neighbor();
timer->stamp(Timer::MODIFY);
}
neighbor->build();
timer->stamp(Timer::NEIGH);
}
// force computations
// important for pair to come before bonded contributions
// since some bonded potentials tally pairwise energy/virial
// and Pair:ev_tally() needs to be called before any tallying
force_clear();
timer->stamp();
if (n_pre_force) {
modify->pre_force(vflag);
timer->stamp(Timer::MODIFY);
}
bool execute_on_host = false;
unsigned int datamask_read_device = 0;
unsigned int datamask_modify_device = 0;
unsigned int datamask_read_host = 0;
unsigned int datamask_modify_host = 0;
if ( pair_compute_flag ) {
if (force->pair->execution_space==Host) {
execute_on_host = true;
datamask_read_host |= force->pair->datamask_read;
datamask_modify_device |= force->pair->datamask_modify;
} else {
datamask_read_device |= force->pair->datamask_read;
datamask_modify_device |= force->pair->datamask_modify;
}
}
if ( atomKK->molecular && force->bond ) {
if (force->bond->execution_space==Host) {
execute_on_host = true;
datamask_read_host |= force->bond->datamask_read;
datamask_modify_device |= force->bond->datamask_modify;
} else {
datamask_read_device |= force->bond->datamask_read;
datamask_modify_device |= force->bond->datamask_modify;
}
}
if ( atomKK->molecular && force->angle ) {
if (force->angle->execution_space==Host) {
execute_on_host = true;
datamask_read_host |= force->angle->datamask_read;
datamask_modify_device |= force->angle->datamask_modify;
} else {
datamask_read_device |= force->angle->datamask_read;
datamask_modify_device |= force->angle->datamask_modify;
}
}
if ( atomKK->molecular && force->dihedral ) {
if (force->dihedral->execution_space==Host) {
execute_on_host = true;
datamask_read_host |= force->dihedral->datamask_read;
datamask_modify_device |= force->dihedral->datamask_modify;
} else {
datamask_read_device |= force->dihedral->datamask_read;
datamask_modify_device |= force->dihedral->datamask_modify;
}
}
if ( atomKK->molecular && force->improper ) {
if (force->improper->execution_space==Host) {
execute_on_host = true;
datamask_read_host |= force->improper->datamask_read;
datamask_modify_device |= force->improper->datamask_modify;
} else {
datamask_read_device |= force->improper->datamask_read;
datamask_modify_device |= force->improper->datamask_modify;
}
}
if ( kspace_compute_flag ) {
if (force->kspace->execution_space==Host) {
execute_on_host = true;
datamask_read_host |= force->kspace->datamask_read;
datamask_modify_device |= force->kspace->datamask_modify;
} else {
datamask_read_device |= force->kspace->datamask_read;
datamask_modify_device |= force->kspace->datamask_modify;
}
}
if (pair_compute_flag) {
atomKK->sync(force->pair->execution_space,force->pair->datamask_read);
atomKK->modified(force->pair->execution_space,force->pair->datamask_modify);
atomKK->sync(force->pair->execution_space,~(~force->pair->datamask_read|(F_MASK | ENERGY_MASK | VIRIAL_MASK)));
atomKK->modified(force->pair->execution_space,~(~force->pair->datamask_modify|(F_MASK | ENERGY_MASK | VIRIAL_MASK)));
Kokkos::Impl::Timer ktimer;
force->pair->compute(eflag,vflag);
timer->stamp(Timer::PAIR);
}
if(execute_on_host) {
if(pair_compute_flag && force->pair->datamask_modify!=(F_MASK | ENERGY_MASK | VIRIAL_MASK))
Kokkos::fence();
atomKK->sync_overlapping_device(Host,~(~datamask_read_host|(F_MASK | ENERGY_MASK | VIRIAL_MASK)));
if(pair_compute_flag && force->pair->execution_space!=Host) {
Kokkos::deep_copy(LMPHostType(),atomKK->k_f.h_view,0.0);
}
}
if (atomKK->molecular) {
if (force->bond) {
atomKK->sync(force->bond->execution_space,~(~force->bond->datamask_read|(F_MASK | ENERGY_MASK | VIRIAL_MASK)));
atomKK->modified(force->bond->execution_space,~(~force->bond->datamask_modify|(F_MASK | ENERGY_MASK | VIRIAL_MASK)));
force->bond->compute(eflag,vflag);
}
if (force->angle) {
atomKK->sync(force->angle->execution_space,~(~force->angle->datamask_read|(F_MASK | ENERGY_MASK | VIRIAL_MASK)));
atomKK->modified(force->angle->execution_space,~(~force->angle->datamask_modify|(F_MASK | ENERGY_MASK | VIRIAL_MASK)));
force->angle->compute(eflag,vflag);
}
if (force->dihedral) {
atomKK->sync(force->dihedral->execution_space,~(~force->dihedral->datamask_read|(F_MASK | ENERGY_MASK | VIRIAL_MASK)));
atomKK->modified(force->dihedral->execution_space,~(~force->dihedral->datamask_modify|(F_MASK | ENERGY_MASK | VIRIAL_MASK)));
force->dihedral->compute(eflag,vflag);
}
if (force->improper) {
atomKK->sync(force->improper->execution_space,~(~force->improper->datamask_read|(F_MASK | ENERGY_MASK | VIRIAL_MASK)));
atomKK->modified(force->improper->execution_space,~(~force->improper->datamask_modify|(F_MASK | ENERGY_MASK | VIRIAL_MASK)));
force->improper->compute(eflag,vflag);
}
timer->stamp(Timer::BOND);
}
if (kspace_compute_flag) {
atomKK->sync(force->kspace->execution_space,~(~force->kspace->datamask_read|(F_MASK | ENERGY_MASK | VIRIAL_MASK)));
atomKK->modified(force->kspace->execution_space,~(~force->kspace->datamask_modify|(F_MASK | ENERGY_MASK | VIRIAL_MASK)));
force->kspace->compute(eflag,vflag);
timer->stamp(Timer::KSPACE);
}
if(execute_on_host && !std::is_same<LMPHostType,LMPDeviceType>::value) {
if(f_merge_copy.dimension_0()<atomKK->k_f.dimension_0()) {
f_merge_copy = DAT::t_f_array("VerletKokkos::f_merge_copy",atomKK->k_f.dimension_0());
}
f = atomKK->k_f.d_view;
Kokkos::deep_copy(LMPHostType(),f_merge_copy,atomKK->k_f.h_view);
Kokkos::parallel_for(atomKK->k_f.dimension_0(),
ForceAdder<DAT::t_f_array,DAT::t_f_array>(atomKK->k_f.d_view,f_merge_copy));
atomKK->k_f.template modify<LMPDeviceType>();
}
// reverse communication of forces
if (force->newton) comm->reverse_comm();
timer->stamp(Timer::COMM);
// force modifications, final time integration, diagnostics
if (n_post_force) modify->post_force(vflag);
modify->final_integrate();
if (n_end_of_step) modify->end_of_step();
timer->stamp(Timer::MODIFY);
// all output
if (ntimestep == output->next) {
atomKK->sync(Host,ALL_MASK);
timer->stamp();
output->write(ntimestep);
timer->stamp(Timer::OUTPUT);
}
}
}
/* ----------------------------------------------------------------------
clear force on own & ghost atoms
clear other arrays as needed
------------------------------------------------------------------------- */
void VerletKokkos::force_clear()
{
int i;
if (external_force_clear) return;
// clear force on all particles
// if either newton flag is set, also include ghosts
// when using threads always clear all forces.
if (neighbor->includegroup == 0) {
int nall;
if (force->newton) nall = atomKK->nlocal + atomKK->nghost;
else nall = atomKK->nlocal;
size_t nbytes = sizeof(double) * nall;
if (nbytes) {
if (atomKK->k_f.modified_host() > atomKK->k_f.modified_device()) {
memset_kokkos(atomKK->k_f.view<LMPHostType>());
atomKK->modified(Host,F_MASK);
} else {
memset_kokkos(atomKK->k_f.view<LMPDeviceType>());
atomKK->modified(Device,F_MASK);
}
if (torqueflag) memset(&(atomKK->torque[0][0]),0,3*nbytes);
}
// neighbor includegroup flag is set
// clear force only on initial nfirst particles
// if either newton flag is set, also include ghosts
} else {
int nall = atomKK->nfirst;
if (atomKK->k_f.modified_host() > atomKK->k_f.modified_device()) {
memset_kokkos(atomKK->k_f.view<LMPHostType>());
atomKK->modified(Host,F_MASK);
} else {
memset_kokkos(atomKK->k_f.view<LMPDeviceType>());
atomKK->modified(Device,F_MASK);
}
if (torqueflag) {
double **torque = atomKK->torque;
for (i = 0; i < nall; i++) {
torque[i][0] = 0.0;
torque[i][1] = 0.0;
torque[i][2] = 0.0;
}
}
if (force->newton) {
nall = atomKK->nlocal + atomKK->nghost;
if (torqueflag) {
double **torque = atomKK->torque;
for (i = atomKK->nlocal; i < nall; i++) {
torque[i][0] = 0.0;
torque[i][1] = 0.0;
torque[i][2] = 0.0;
}
}
}
}
}

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