Homec4science
Diffusion lammps (lammm-master-deprecated) Browse

lammps/src/KOKKOS/modify_kokkos.cpp
2ad23266fb20lammm-master-deprecated

Last Change
Raw File

modify_kokkos.cpp
View Options

/* ----------------------------------------------------------------------
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 "modify_kokkos.h"
#include "atom_kokkos.h"
#include "update.h"
#include "fix.h"
#include "compute.h"
using namespace LAMMPS_NS;
#define BIG 1.0e20
/* ---------------------------------------------------------------------- */
ModifyKokkos::ModifyKokkos(LAMMPS *lmp) : Modify(lmp)
{
atomKK = (AtomKokkos *) atom;
}
/* ----------------------------------------------------------------------
setup for run, calls setup() of all fixes and computes
called from Verlet, RESPA, Min
------------------------------------------------------------------------- */
void ModifyKokkos::setup(int vflag)
{
// compute setup needs to come before fix setup
// b/c NH fixes need use DOF of temperature computes
for (int i = 0; i < ncompute; i++) compute[i]->setup();
if (update->whichflag == 1)
for (int i = 0; i < nfix; i++) {
atomKK->sync(fix[i]->execution_space,fix[i]->datamask_read);
fix[i]->setup(vflag);
atomKK->modified(fix[i]->execution_space,fix[i]->datamask_modify);
}
else if (update->whichflag == 2)
for (int i = 0; i < nfix; i++) {
atomKK->sync(fix[i]->execution_space,fix[i]->datamask_read);
fix[i]->min_setup(vflag);
atomKK->modified(fix[i]->execution_space,fix[i]->datamask_modify);
}
}
/* ----------------------------------------------------------------------
setup pre_exchange call, only for fixes that define pre_exchange
called from Verlet, RESPA, Min, and WriteRestart with whichflag = 0
------------------------------------------------------------------------- */
void ModifyKokkos::setup_pre_exchange()
{
if (update->whichflag <= 1)
for (int i = 0; i < n_pre_exchange; i++) {
atomKK->sync(fix[list_pre_exchange[i]]->execution_space,
fix[list_pre_exchange[i]]->datamask_read);
fix[list_pre_exchange[i]]->setup_pre_exchange();
atomKK->modified(fix[list_pre_exchange[i]]->execution_space,
fix[list_pre_exchange[i]]->datamask_modify);
}
else if (update->whichflag == 2)
for (int i = 0; i < n_min_pre_exchange; i++) {
atomKK->sync(fix[list_min_pre_exchange[i]]->execution_space,
fix[list_min_pre_exchange[i]]->datamask_read);
fix[list_min_pre_exchange[i]]->min_setup_pre_exchange();
atomKK->modified(fix[list_min_pre_exchange[i]]->execution_space,
fix[list_min_pre_exchange[i]]->datamask_modify);
}
}
/* ----------------------------------------------------------------------
setup pre_neighbor call, only for fixes that define pre_neighbor
called from Verlet, RESPA
------------------------------------------------------------------------- */
void ModifyKokkos::setup_pre_neighbor()
{
if (update->whichflag == 1)
for (int i = 0; i < n_pre_neighbor; i++) {
atomKK->sync(fix[list_pre_neighbor[i]]->execution_space,
fix[list_pre_neighbor[i]]->datamask_read);
fix[list_pre_neighbor[i]]->setup_pre_neighbor();
atomKK->modified(fix[list_pre_neighbor[i]]->execution_space,
fix[list_pre_neighbor[i]]->datamask_modify);
}
else if (update->whichflag == 2)
for (int i = 0; i < n_min_pre_neighbor; i++) {
atomKK->sync(fix[list_min_pre_neighbor[i]]->execution_space,
fix[list_min_pre_neighbor[i]]->datamask_read);
fix[list_min_pre_neighbor[i]]->min_setup_pre_neighbor();
atomKK->modified(fix[list_min_pre_neighbor[i]]->execution_space,
fix[list_min_pre_neighbor[i]]->datamask_modify);
}
}
/* ----------------------------------------------------------------------
setup pre_force call, only for fixes that define pre_force
called from Verlet, RESPA, Min
------------------------------------------------------------------------- */
void ModifyKokkos::setup_pre_force(int vflag)
{
if (update->whichflag == 1)
for (int i = 0; i < n_pre_force; i++) {
atomKK->sync(fix[list_pre_force[i]]->execution_space,
fix[list_pre_force[i]]->datamask_read);
fix[list_pre_force[i]]->setup_pre_force(vflag);
atomKK->modified(fix[list_pre_force[i]]->execution_space,
fix[list_pre_force[i]]->datamask_modify);
}
else if (update->whichflag == 2)
for (int i = 0; i < n_min_pre_force; i++) {
atomKK->sync(fix[list_min_pre_force[i]]->execution_space,
fix[list_min_pre_force[i]]->datamask_read);
fix[list_min_pre_force[i]]->min_setup_pre_force(vflag);
atomKK->modified(fix[list_min_pre_force[i]]->execution_space,
fix[list_min_pre_force[i]]->datamask_modify);
}
}
/* ----------------------------------------------------------------------
1st half of integrate call, only for relevant fixes
------------------------------------------------------------------------- */
void ModifyKokkos::initial_integrate(int vflag)
{
for (int i = 0; i < n_initial_integrate; i++) {
atomKK->sync(fix[list_initial_integrate[i]]->execution_space,
fix[list_initial_integrate[i]]->datamask_read);
fix[list_initial_integrate[i]]->initial_integrate(vflag);
atomKK->modified(fix[list_initial_integrate[i]]->execution_space,
fix[list_initial_integrate[i]]->datamask_modify);
}
}
/* ----------------------------------------------------------------------
post_integrate call, only for relevant fixes
------------------------------------------------------------------------- */
void ModifyKokkos::post_integrate()
{
for (int i = 0; i < n_post_integrate; i++) {
atomKK->sync(fix[list_post_integrate[i]]->execution_space,
fix[list_post_integrate[i]]->datamask_read);
fix[list_post_integrate[i]]->post_integrate();
atomKK->modified(fix[list_post_integrate[i]]->execution_space,
fix[list_post_integrate[i]]->datamask_modify);
}
}
/* ----------------------------------------------------------------------
pre_exchange call, only for relevant fixes
------------------------------------------------------------------------- */
void ModifyKokkos::pre_exchange()
{
for (int i = 0; i < n_pre_exchange; i++) {
atomKK->sync(fix[list_pre_exchange[i]]->execution_space,
fix[list_pre_exchange[i]]->datamask_read);
fix[list_pre_exchange[i]]->pre_exchange();
atomKK->modified(fix[list_pre_exchange[i]]->execution_space,
fix[list_pre_exchange[i]]->datamask_modify);
}
}
/* ----------------------------------------------------------------------
pre_neighbor call, only for relevant fixes
------------------------------------------------------------------------- */
void ModifyKokkos::pre_neighbor()
{
for (int i = 0; i < n_pre_neighbor; i++) {
atomKK->sync(fix[list_pre_neighbor[i]]->execution_space,
fix[list_pre_neighbor[i]]->datamask_read);
fix[list_pre_neighbor[i]]->pre_neighbor();
atomKK->modified(fix[list_pre_neighbor[i]]->execution_space,
fix[list_pre_neighbor[i]]->datamask_modify);
}
}
/* ----------------------------------------------------------------------
pre_force call, only for relevant fixes
------------------------------------------------------------------------- */
void ModifyKokkos::pre_force(int vflag)
{
for (int i = 0; i < n_pre_force; i++) {
atomKK->sync(fix[list_pre_force[i]]->execution_space,
fix[list_pre_force[i]]->datamask_read);
fix[list_pre_force[i]]->pre_force(vflag);
atomKK->modified(fix[list_pre_force[i]]->execution_space,
fix[list_pre_force[i]]->datamask_modify);
}
}
/* ----------------------------------------------------------------------
post_force call, only for relevant fixes
------------------------------------------------------------------------- */
void ModifyKokkos::post_force(int vflag)
{
for (int i = 0; i < n_post_force; i++) {
atomKK->sync(fix[list_post_force[i]]->execution_space,
fix[list_post_force[i]]->datamask_read);
fix[list_post_force[i]]->post_force(vflag);
atomKK->modified(fix[list_post_force[i]]->execution_space,
fix[list_post_force[i]]->datamask_modify);
}
}
/* ----------------------------------------------------------------------
2nd half of integrate call, only for relevant fixes
------------------------------------------------------------------------- */
void ModifyKokkos::final_integrate()
{
for (int i = 0; i < n_final_integrate; i++) {
atomKK->sync(fix[list_final_integrate[i]]->execution_space,
fix[list_final_integrate[i]]->datamask_read);
fix[list_final_integrate[i]]->final_integrate();
atomKK->modified(fix[list_final_integrate[i]]->execution_space,
fix[list_final_integrate[i]]->datamask_modify);
}
}
/* ----------------------------------------------------------------------
end-of-timestep call, only for relevant fixes
only call fix->end_of_step() on timesteps that are multiples of nevery
------------------------------------------------------------------------- */
void ModifyKokkos::end_of_step()
{
for (int i = 0; i < n_end_of_step; i++)
if (update->ntimestep % end_of_step_every[i] == 0) {
atomKK->sync(fix[list_end_of_step[i]]->execution_space,
fix[list_end_of_step[i]]->datamask_read);
fix[list_end_of_step[i]]->end_of_step();
atomKK->modified(fix[list_end_of_step[i]]->execution_space,
fix[list_end_of_step[i]]->datamask_modify);
}
}
/* ----------------------------------------------------------------------
thermo energy call, only for relevant fixes
called by Thermo class
compute_scalar() is fix call to return energy
------------------------------------------------------------------------- */
double ModifyKokkos::thermo_energy()
{
double energy = 0.0;
for (int i = 0; i < n_thermo_energy; i++) {
atomKK->sync(fix[list_thermo_energy[i]]->execution_space,
fix[list_thermo_energy[i]]->datamask_read);
energy += fix[list_thermo_energy[i]]->compute_scalar();
atomKK->modified(fix[list_thermo_energy[i]]->execution_space,
fix[list_thermo_energy[i]]->datamask_modify);
}
return energy;
}
/* ----------------------------------------------------------------------
post_run call
------------------------------------------------------------------------- */
void ModifyKokkos::post_run()
{
for (int i = 0; i < nfix; i++) {
atomKK->sync(fix[i]->execution_space,
fix[i]->datamask_read);
fix[i]->post_run();
atomKK->modified(fix[i]->execution_space,
fix[i]->datamask_modify);
}
}
/* ----------------------------------------------------------------------
setup rRESPA pre_force call, only for relevant fixes
------------------------------------------------------------------------- */
void ModifyKokkos::setup_pre_force_respa(int vflag, int ilevel)
{
for (int i = 0; i < n_pre_force; i++) {
atomKK->sync(fix[list_pre_force[i]]->execution_space,
fix[list_pre_force[i]]->datamask_read);
fix[list_pre_force[i]]->setup_pre_force_respa(vflag,ilevel);
atomKK->modified(fix[list_pre_force[i]]->execution_space,
fix[list_pre_force[i]]->datamask_modify);
}
}
/* ----------------------------------------------------------------------
1st half of rRESPA integrate call, only for relevant fixes
------------------------------------------------------------------------- */
void ModifyKokkos::initial_integrate_respa(int vflag, int ilevel, int iloop)
{
for (int i = 0; i < n_initial_integrate_respa; i++) {
atomKK->sync(fix[list_initial_integrate_respa[i]]->execution_space,
fix[list_initial_integrate_respa[i]]->datamask_read);
fix[list_initial_integrate_respa[i]]->
initial_integrate_respa(vflag,ilevel,iloop);
atomKK->modified(fix[list_initial_integrate_respa[i]]->execution_space,
fix[list_initial_integrate_respa[i]]->datamask_modify);
}
}
/* ----------------------------------------------------------------------
rRESPA post_integrate call, only for relevant fixes
------------------------------------------------------------------------- */
void ModifyKokkos::post_integrate_respa(int ilevel, int iloop)
{
for (int i = 0; i < n_post_integrate_respa; i++) {
atomKK->sync(fix[list_post_integrate_respa[i]]->execution_space,
fix[list_post_integrate_respa[i]]->datamask_read);
fix[list_post_integrate_respa[i]]->post_integrate_respa(ilevel,iloop);
atomKK->modified(fix[list_post_integrate_respa[i]]->execution_space,
fix[list_post_integrate_respa[i]]->datamask_modify);
}
}
/* ----------------------------------------------------------------------
rRESPA pre_force call, only for relevant fixes
------------------------------------------------------------------------- */
void ModifyKokkos::pre_force_respa(int vflag, int ilevel, int iloop)
{
for (int i = 0; i < n_pre_force_respa; i++) {
atomKK->sync(fix[list_pre_force_respa[i]]->execution_space,
fix[list_pre_force_respa[i]]->datamask_read);
fix[list_pre_force_respa[i]]->pre_force_respa(vflag,ilevel,iloop);
atomKK->modified(fix[list_pre_force_respa[i]]->execution_space,
fix[list_pre_force_respa[i]]->datamask_modify);
}
}
/* ----------------------------------------------------------------------
rRESPA post_force call, only for relevant fixes
------------------------------------------------------------------------- */
void ModifyKokkos::post_force_respa(int vflag, int ilevel, int iloop)
{
for (int i = 0; i < n_post_force_respa; i++) {
atomKK->sync(fix[list_post_force_respa[i]]->execution_space,
fix[list_post_force_respa[i]]->datamask_read);
fix[list_post_force_respa[i]]->post_force_respa(vflag,ilevel,iloop);
atomKK->modified(fix[list_post_force_respa[i]]->execution_space,
fix[list_post_force_respa[i]]->datamask_modify);
}
}
/* ----------------------------------------------------------------------
2nd half of rRESPA integrate call, only for relevant fixes
------------------------------------------------------------------------- */
void ModifyKokkos::final_integrate_respa(int ilevel, int iloop)
{
for (int i = 0; i < n_final_integrate_respa; i++) {
atomKK->sync(fix[list_final_integrate_respa[i]]->execution_space,
fix[list_final_integrate_respa[i]]->datamask_read);
fix[list_final_integrate_respa[i]]->final_integrate_respa(ilevel,iloop);
atomKK->modified(fix[list_final_integrate_respa[i]]->execution_space,
fix[list_final_integrate_respa[i]]->datamask_modify);
}
}
/* ----------------------------------------------------------------------
minimizer pre-exchange call, only for relevant fixes
------------------------------------------------------------------------- */
void ModifyKokkos::min_pre_exchange()
{
for (int i = 0; i < n_min_pre_exchange; i++) {
atomKK->sync(fix[list_min_pre_exchange[i]]->execution_space,
fix[list_min_pre_exchange[i]]->datamask_read);
fix[list_min_pre_exchange[i]]->min_pre_exchange();
atomKK->modified(fix[list_min_pre_exchange[i]]->execution_space,
fix[list_min_pre_exchange[i]]->datamask_modify);
}
}
/* ----------------------------------------------------------------------
minimizer pre-neighbor call, only for relevant fixes
------------------------------------------------------------------------- */
void ModifyKokkos::min_pre_neighbor()
{
for (int i = 0; i < n_min_pre_neighbor; i++) {
atomKK->sync(fix[list_min_pre_neighbor[i]]->execution_space,
fix[list_min_pre_neighbor[i]]->datamask_read);
fix[list_min_pre_neighbor[i]]->min_pre_neighbor();
atomKK->modified(fix[list_min_pre_neighbor[i]]->execution_space,
fix[list_min_pre_neighbor[i]]->datamask_modify);
}
}
/* ----------------------------------------------------------------------
minimizer pre-force call, only for relevant fixes
------------------------------------------------------------------------- */
void ModifyKokkos::min_pre_force(int vflag)
{
for (int i = 0; i < n_min_pre_force; i++) {
atomKK->sync(fix[list_min_pre_force[i]]->execution_space,
fix[list_min_pre_force[i]]->datamask_read);
fix[list_min_pre_force[i]]->min_pre_force(vflag);
atomKK->modified(fix[list_min_pre_force[i]]->execution_space,
fix[list_min_pre_force[i]]->datamask_modify);
}
}
/* ----------------------------------------------------------------------
minimizer force adjustment call, only for relevant fixes
------------------------------------------------------------------------- */
void ModifyKokkos::min_post_force(int vflag)
{
for (int i = 0; i < n_min_post_force; i++) {
atomKK->sync(fix[list_min_post_force[i]]->execution_space,
fix[list_min_post_force[i]]->datamask_read);
fix[list_min_post_force[i]]->min_post_force(vflag);
atomKK->modified(fix[list_min_post_force[i]]->execution_space,
fix[list_min_post_force[i]]->datamask_modify);
}
}
/* ----------------------------------------------------------------------
minimizer energy/force evaluation, only for relevant fixes
return energy and forces on extra degrees of freedom
------------------------------------------------------------------------- */
double ModifyKokkos::min_energy(double *fextra)
{
int ifix,index;
index = 0;
double eng = 0.0;
for (int i = 0; i < n_min_energy; i++) {
ifix = list_min_energy[i];
atomKK->sync(fix[ifix]->execution_space,fix[ifix]->datamask_read);
eng += fix[ifix]->min_energy(&fextra[index]);
index += fix[ifix]->min_dof();
atomKK->modified(fix[ifix]->execution_space,fix[ifix]->datamask_modify);
}
return eng;
}
/* ----------------------------------------------------------------------
store current state of extra dof, only for relevant fixes
------------------------------------------------------------------------- */
void ModifyKokkos::min_store()
{
for (int i = 0; i < n_min_energy; i++) {
atomKK->sync(fix[list_min_energy[i]]->execution_space,
fix[list_min_energy[i]]->datamask_read);
fix[list_min_energy[i]]->min_store();
atomKK->modified(fix[list_min_energy[i]]->execution_space,
fix[list_min_energy[i]]->datamask_modify);
}
}
/* ----------------------------------------------------------------------
mange state of extra dof on a stack, only for relevant fixes
------------------------------------------------------------------------- */
void ModifyKokkos::min_clearstore()
{
for (int i = 0; i < n_min_energy; i++) {
atomKK->sync(fix[list_min_energy[i]]->execution_space,
fix[list_min_energy[i]]->datamask_read);
fix[list_min_energy[i]]->min_clearstore();
atomKK->modified(fix[list_min_energy[i]]->execution_space,
fix[list_min_energy[i]]->datamask_modify);
}
}
void ModifyKokkos::min_pushstore()
{
for (int i = 0; i < n_min_energy; i++) {
atomKK->sync(fix[list_min_energy[i]]->execution_space,
fix[list_min_energy[i]]->datamask_read);
fix[list_min_energy[i]]->min_pushstore();
atomKK->modified(fix[list_min_energy[i]]->execution_space,
fix[list_min_energy[i]]->datamask_modify);
}
}
void ModifyKokkos::min_popstore()
{
for (int i = 0; i < n_min_energy; i++) {
atomKK->sync(fix[list_min_energy[i]]->execution_space,
fix[list_min_energy[i]]->datamask_read);
fix[list_min_energy[i]]->min_popstore();
atomKK->modified(fix[list_min_energy[i]]->execution_space,
fix[list_min_energy[i]]->datamask_modify);
}
}
/* ----------------------------------------------------------------------
displace extra dof along vector hextra, only for relevant fixes
------------------------------------------------------------------------- */
void ModifyKokkos::min_step(double alpha, double *hextra)
{
int ifix,index;
index = 0;
for (int i = 0; i < n_min_energy; i++) {
ifix = list_min_energy[i];
atomKK->sync(fix[ifix]->execution_space,fix[ifix]->datamask_read);
fix[ifix]->min_step(alpha,&hextra[index]);
index += fix[ifix]->min_dof();
atomKK->modified(fix[ifix]->execution_space,fix[ifix]->datamask_modify);
}
}
/* ----------------------------------------------------------------------
compute max allowed step size along vector hextra, only for relevant fixes
------------------------------------------------------------------------- */
double ModifyKokkos::max_alpha(double *hextra)
{
int ifix,index;
double alpha = BIG;
index = 0;
for (int i = 0; i < n_min_energy; i++) {
ifix = list_min_energy[i];
atomKK->sync(fix[ifix]->execution_space,fix[ifix]->datamask_read);
double alpha_one = fix[ifix]->max_alpha(&hextra[index]);
alpha = MIN(alpha,alpha_one);
index += fix[ifix]->min_dof();
atomKK->modified(fix[ifix]->execution_space,fix[ifix]->datamask_modify);
}
return alpha;
}
/* ----------------------------------------------------------------------
extract extra dof for minimization, only for relevant fixes
------------------------------------------------------------------------- */
int ModifyKokkos::min_dof()
{
int ndof = 0;
for (int i = 0; i < n_min_energy; i++) {
atomKK->sync(fix[list_min_energy[i]]->execution_space,
fix[list_min_energy[i]]->datamask_read);
ndof += fix[list_min_energy[i]]->min_dof();
atomKK->modified(fix[list_min_energy[i]]->execution_space,
fix[list_min_energy[i]]->datamask_modify);
}
return ndof;
}
/* ----------------------------------------------------------------------
reset reference state of fix, only for relevant fixes
------------------------------------------------------------------------- */
int ModifyKokkos::min_reset_ref()
{
int itmp,itmpall;
itmpall = 0;
for (int i = 0; i < n_min_energy; i++) {
atomKK->sync(fix[list_min_energy[i]]->execution_space,
fix[list_min_energy[i]]->datamask_read);
itmp = fix[list_min_energy[i]]->min_reset_ref();
if (itmp) itmpall = 1;
atomKK->modified(fix[list_min_energy[i]]->execution_space,
fix[list_min_energy[i]]->datamask_modify);
}
return itmpall;
}
c4science · Help