Page Menu
Home
c4science
Search
Configure Global Search
Log In
Files
F64249600
atom_kokkos.cpp
No One
Temporary
Actions
Download File
Edit File
Delete File
View Transforms
Subscribe
Mute Notifications
Award Token
Subscribers
None
File Metadata
Details
File Info
Storage
Attached
Created
Sat, May 25, 15:19
Size
9 KB
Mime Type
text/x-c
Expires
Mon, May 27, 15:19 (1 d, 23 h)
Engine
blob
Format
Raw Data
Handle
17868540
Attached To
rLAMMPS lammps
atom_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 <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_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);
}
/* ---------------------------------------------------------------------- */
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);
}
}
/* ---------------------------------------------------------------------- */
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;
}
Event Timeline
Log In to Comment