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lammps/src/KOKKOS/atom_kokkos.cpp
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atom_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 <mpi.h>
#include "atom_kokkos.h"
#include "atom_vec.h"
#include "atom_vec_kokkos.h"
#include "comm_kokkos.h"
#include "update.h"
#include "domain.h"
#include "atom_masks.h"
#include "memory.h"
#include "error.h"
#include "kokkos.h"
using namespace LAMMPS_NS;
/* ---------------------------------------------------------------------- */
AtomKokkos::AtomKokkos(LAMMPS *lmp) : Atom(lmp) {}
/* ---------------------------------------------------------------------- */
AtomKokkos::~AtomKokkos()
{
memory->destroy_kokkos(k_tag, tag);
memory->destroy_kokkos(k_mask, mask);
memory->destroy_kokkos(k_type, type);
memory->destroy_kokkos(k_image, image);
memory->destroy_kokkos(k_molecule, molecule);
memory->destroy_kokkos(k_x, x);
memory->destroy_kokkos(k_v, v);
memory->destroy_kokkos(k_f, f);
memory->destroy_kokkos(k_mass, mass);
memory->destroy_kokkos(k_q, q);
memory->destroy_kokkos(k_radius, radius);
memory->destroy_kokkos(k_rmass, rmass);
memory->destroy_kokkos(k_omega, omega);
memory->destroy_kokkos(k_angmom, angmom);
memory->destroy_kokkos(k_torque, torque);
memory->destroy_kokkos(k_nspecial, nspecial);
memory->destroy_kokkos(k_special, special);
memory->destroy_kokkos(k_num_bond, num_bond);
memory->destroy_kokkos(k_bond_type, bond_type);
memory->destroy_kokkos(k_bond_atom, bond_atom);
memory->destroy_kokkos(k_num_angle, num_angle);
memory->destroy_kokkos(k_angle_type, angle_type);
memory->destroy_kokkos(k_angle_atom1, angle_atom1);
memory->destroy_kokkos(k_angle_atom2, angle_atom2);
memory->destroy_kokkos(k_angle_atom3, angle_atom3);
memory->destroy_kokkos(k_num_dihedral, num_dihedral);
memory->destroy_kokkos(k_dihedral_type, dihedral_type);
memory->destroy_kokkos(k_dihedral_atom1, dihedral_atom1);
memory->destroy_kokkos(k_dihedral_atom2, dihedral_atom2);
memory->destroy_kokkos(k_dihedral_atom3, dihedral_atom3);
memory->destroy_kokkos(k_dihedral_atom4, dihedral_atom4);
memory->destroy_kokkos(k_num_improper, num_improper);
memory->destroy_kokkos(k_improper_type, improper_type);
memory->destroy_kokkos(k_improper_atom1, improper_atom1);
memory->destroy_kokkos(k_improper_atom2, improper_atom2);
memory->destroy_kokkos(k_improper_atom3, improper_atom3);
memory->destroy_kokkos(k_improper_atom4, improper_atom4);
// USER-DPD package
memory->destroy_kokkos(k_uCond,uCond);
memory->destroy_kokkos(k_uMech,uMech);
memory->destroy_kokkos(k_uChem,uChem);
memory->destroy_kokkos(k_uCG,uCG);
memory->destroy_kokkos(k_uCGnew,uCGnew);
memory->destroy_kokkos(k_rho,rho);
memory->destroy_kokkos(k_dpdTheta,dpdTheta);
memory->destroy_kokkos(k_duChem,duChem);
memory->destroy_kokkos(k_dvector,dvector);
dvector = NULL;
}
/* ---------------------------------------------------------------------- */
void AtomKokkos::sync(const ExecutionSpace space, unsigned int mask)
{
if (space == Device && lmp->kokkos->auto_sync)
((AtomVecKokkos *) avec)->modified(Host,mask);
((AtomVecKokkos *) avec)->sync(space,mask);
}
/* ---------------------------------------------------------------------- */
void AtomKokkos::modified(const ExecutionSpace space, unsigned int mask)
{
((AtomVecKokkos *) avec)->modified(space,mask);
if (space == Device && lmp->kokkos->auto_sync)
((AtomVecKokkos *) avec)->sync(Host,mask);
}
void AtomKokkos::sync_overlapping_device(const ExecutionSpace space, unsigned int mask)
{
((AtomVecKokkos *) avec)->sync_overlapping_device(space,mask);
}
/* ---------------------------------------------------------------------- */
void AtomKokkos::allocate_type_arrays()
{
if (avec->mass_type) {
k_mass = DAT::tdual_float_1d("Mass",ntypes+1);
mass = k_mass.h_view.ptr_on_device();
mass_setflag = new int[ntypes+1];
for (int itype = 1; itype <= ntypes; itype++) mass_setflag[itype] = 0;
k_mass.modify<LMPHostType>();
}
}
/* ---------------------------------------------------------------------- */
void AtomKokkos::sort()
{
int i,m,n,ix,iy,iz,ibin,empty;
// set next timestep for sorting to take place
nextsort = (update->ntimestep/sortfreq)*sortfreq + sortfreq;
// re-setup sort bins if needed
if (domain->box_change) setup_sort_bins();
if (nbins == 1) return;
// reallocate per-atom vectors if needed
if (atom->nmax > maxnext) {
memory->destroy(next);
memory->destroy(permute);
maxnext = atom->nmax;
memory->create(next,maxnext,"atom:next");
memory->create(permute,maxnext,"atom:permute");
}
// insure there is one extra atom location at end of arrays for swaps
if (nlocal == nmax) avec->grow(0);
sync(Host,ALL_MASK);
modified(Host,ALL_MASK);
// bin atoms in reverse order so linked list will be in forward order
for (i = 0; i < nbins; i++) binhead[i] = -1;
HAT::t_x_array_const h_x = k_x.view<LMPHostType>();
for (i = nlocal-1; i >= 0; i--) {
ix = static_cast<int> ((h_x(i,0)-bboxlo[0])*bininvx);
iy = static_cast<int> ((h_x(i,1)-bboxlo[1])*bininvy);
iz = static_cast<int> ((h_x(i,2)-bboxlo[2])*bininvz);
ix = MAX(ix,0);
iy = MAX(iy,0);
iz = MAX(iz,0);
ix = MIN(ix,nbinx-1);
iy = MIN(iy,nbiny-1);
iz = MIN(iz,nbinz-1);
ibin = iz*nbiny*nbinx + iy*nbinx + ix;
next[i] = binhead[ibin];
binhead[ibin] = i;
}
// permute = desired permutation of atoms
// permute[I] = J means Ith new atom will be Jth old atom
n = 0;
for (m = 0; m < nbins; m++) {
i = binhead[m];
while (i >= 0) {
permute[n++] = i;
i = next[i];
}
}
// current = current permutation, just reuse next vector
// current[I] = J means Ith current atom is Jth old atom
int *current = next;
for (i = 0; i < nlocal; i++) current[i] = i;
// reorder local atom list, when done, current = permute
// perform "in place" using copy() to extra atom location at end of list
// inner while loop processes one cycle of the permutation
// copy before inner-loop moves an atom to end of atom list
// copy after inner-loop moves atom at end of list back into list
// empty = location in atom list that is currently empty
for (i = 0; i < nlocal; i++) {
if (current[i] == permute[i]) continue;
avec->copy(i,nlocal,0);
empty = i;
while (permute[empty] != i) {
avec->copy(permute[empty],empty,0);
empty = current[empty] = permute[empty];
}
avec->copy(nlocal,empty,0);
current[empty] = permute[empty];
}
// sanity check that current = permute
//int flag = 0;
//for (i = 0; i < nlocal; i++)
// if (current[i] != permute[i]) flag = 1;
//int flagall;
//MPI_Allreduce(&flag,&flagall,1,MPI_INT,MPI_SUM,world);
//if (flagall) errorX->all(FLERR,"Atom sort did not operate correctly");
}
/* ----------------------------------------------------------------------
reallocate memory to the pointer selected by the mask
------------------------------------------------------------------------- */
void AtomKokkos::grow(unsigned int mask){
if (mask & SPECIAL_MASK){
memory->destroy_kokkos(k_special, special);
sync(Device, mask);
modified(Device, mask);
memory->grow_kokkos(k_special,special,nmax,maxspecial,"atom:special");
avec->grow_reset();
sync(Host, mask);
}
}
/* ----------------------------------------------------------------------
add a custom variable with name of type flag = 0/1 for int/double
assumes name does not already exist
return index in ivector or dvector of its location
------------------------------------------------------------------------- */
int AtomKokkos::add_custom(const char *name, int flag)
{
int index;
if (flag == 0) {
index = nivector;
nivector++;
iname = (char **) memory->srealloc(iname,nivector*sizeof(char *),
"atom:iname");
int n = strlen(name) + 1;
iname[index] = new char[n];
strcpy(iname[index],name);
ivector = (int **) memory->srealloc(ivector,nivector*sizeof(int *),
"atom:ivector");
memory->create(ivector[index],nmax,"atom:ivector");
} else {
index = ndvector;
ndvector++;
dname = (char **) memory->srealloc(dname,ndvector*sizeof(char *),
"atom:dname");
int n = strlen(name) + 1;
dname[index] = new char[n];
strcpy(dname[index],name);
memory->grow_kokkos(k_dvector,dvector,ndvector,nmax,
"atom:dvector");
}
return index;
}
/* ----------------------------------------------------------------------
remove a custom variable of type flag = 0/1 for int/double at index
free memory for vector and name and set ptrs to NULL
ivector/dvector and iname/dname lists never shrink
------------------------------------------------------------------------- */
void AtomKokkos::remove_custom(int flag, int index)
{
if (flag == 0) {
memory->destroy(ivector[index]);
ivector[index] = NULL;
delete [] iname[index];
iname[index] = NULL;
} else {
//memory->destroy_kokkos(dvector);
dvector[index] = NULL;
delete [] dname[index];
dname[index] = NULL;
}
}
/* ---------------------------------------------------------------------- */
void AtomKokkos::deallocate_topology()
{
memory->destroy_kokkos(k_bond_type, bond_type);
memory->destroy_kokkos(k_bond_atom, bond_atom);
memory->destroy_kokkos(k_angle_type, angle_type);
memory->destroy_kokkos(k_angle_atom1, angle_atom1);
memory->destroy_kokkos(k_angle_atom2, angle_atom2);
memory->destroy_kokkos(k_angle_atom3, angle_atom3);
memory->destroy_kokkos(k_dihedral_type, dihedral_type);
memory->destroy_kokkos(k_dihedral_atom1, dihedral_atom1);
memory->destroy_kokkos(k_dihedral_atom2, dihedral_atom2);
memory->destroy_kokkos(k_dihedral_atom3, dihedral_atom3);
memory->destroy_kokkos(k_dihedral_atom4, dihedral_atom4);
memory->destroy_kokkos(k_improper_type, improper_type);
memory->destroy_kokkos(k_improper_atom1, improper_atom1);
memory->destroy_kokkos(k_improper_atom2, improper_atom2);
memory->destroy_kokkos(k_improper_atom3, improper_atom3);
memory->destroy_kokkos(k_improper_atom4, improper_atom4);
}
/* ----------------------------------------------------------------------
perform sync and modify for each of 2 masks
called by individual styles to override default sync/modify calls
done at higher levels (Verlet,Modify,etc)
------------------------------------------------------------------------- */
void AtomKokkos::sync_modify(ExecutionSpace execution_space,
unsigned int datamask_read,
unsigned int datamask_modify)
{
sync(execution_space,datamask_read);
modified(execution_space,datamask_modify);
}
AtomVec *AtomKokkos::new_avec(const char *style, int trysuffix, int &sflag)
{
AtomVec* avec = Atom::new_avec(style,trysuffix,sflag);
if (!avec->kokkosable)
error->all(FLERR,"KOKKOS package requires a kokkos enabled atom_style");
return avec;
}
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