979 lines
32 KiB
C++
979 lines
32 KiB
C++
/* ----------------------------------------------------------------------
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LAMMPS - Large-scale AtomicKokkos/Molecular Massively Parallel Simulator
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http://lammps.sandia.gov, Sandia National Laboratories
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Steve Plimpton, sjplimp@sandia.gov
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Copyright (2003) Sandia Corporation. Under the terms of Contract
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DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
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certain rights in this software. This software is distributed under
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the GNU General Public License.
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See the README file in the top-level LAMMPS directory.
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------------------------------------------------------------------------- */
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#include <stdlib.h>
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#include "atom_vec_atomic_kokkos.h"
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#include "atom_kokkos.h"
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#include "comm_kokkos.h"
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#include "domain.h"
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#include "modify.h"
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#include "fix.h"
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#include "atom_masks.h"
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#include "memory.h"
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#include "error.h"
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using namespace LAMMPS_NS;
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#define DELTA 10000
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/* ---------------------------------------------------------------------- */
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AtomVecAtomicKokkos::AtomVecAtomicKokkos(LAMMPS *lmp) : AtomVecKokkos(lmp)
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{
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molecular = 0;
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mass_type = 1;
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comm_x_only = comm_f_only = 1;
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size_forward = 3;
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size_reverse = 3;
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size_border = 6;
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size_velocity = 3;
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size_data_atom = 5;
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size_data_vel = 4;
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xcol_data = 3;
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k_count = DAT::tdual_int_1d("atom::k_count",1);
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atomKK = (AtomKokkos *) atom;
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commKK = (CommKokkos *) comm;
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}
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/* ----------------------------------------------------------------------
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grow atom arrays
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n = 0 grows arrays by DELTA
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n > 0 allocates arrays to size n
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------------------------------------------------------------------------- */
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void AtomVecAtomicKokkos::grow(int n)
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{
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if (n == 0) nmax += DELTA;
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else nmax = n;
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atomKK->nmax = nmax;
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if (nmax < 0 || nmax > MAXSMALLINT)
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error->one(FLERR,"Per-processor system is too big");
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sync(Device,ALL_MASK);
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modified(Device,ALL_MASK);
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memory->grow_kokkos(atomKK->k_tag,atomKK->tag,nmax,"atom:tag");
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memory->grow_kokkos(atomKK->k_type,atomKK->type,nmax,"atom:type");
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memory->grow_kokkos(atomKK->k_mask,atomKK->mask,nmax,"atom:mask");
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memory->grow_kokkos(atomKK->k_image,atomKK->image,nmax,"atom:image");
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memory->grow_kokkos(atomKK->k_x,atomKK->x,nmax,3,"atom:x");
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memory->grow_kokkos(atomKK->k_v,atomKK->v,nmax,3,"atom:v");
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memory->grow_kokkos(atomKK->k_f,atomKK->f,nmax,3,"atom:f");
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grow_reset();
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sync(Host,ALL_MASK);
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if (atom->nextra_grow)
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for (int iextra = 0; iextra < atom->nextra_grow; iextra++)
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modify->fix[atom->extra_grow[iextra]]->grow_arrays(nmax);
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}
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/* ----------------------------------------------------------------------
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reset local array ptrs
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------------------------------------------------------------------------- */
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void AtomVecAtomicKokkos::grow_reset()
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{
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tag = atomKK->tag;
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d_tag = atomKK->k_tag.d_view;
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h_tag = atomKK->k_tag.h_view;
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type = atomKK->type;
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d_type = atomKK->k_type.d_view;
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h_type = atomKK->k_type.h_view;
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mask = atomKK->mask;
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d_mask = atomKK->k_mask.d_view;
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h_mask = atomKK->k_mask.h_view;
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image = atomKK->image;
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d_image = atomKK->k_image.d_view;
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h_image = atomKK->k_image.h_view;
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x = atomKK->x;
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d_x = atomKK->k_x.d_view;
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h_x = atomKK->k_x.h_view;
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v = atomKK->v;
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d_v = atomKK->k_v.d_view;
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h_v = atomKK->k_v.h_view;
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f = atomKK->f;
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d_f = atomKK->k_f.d_view;
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h_f = atomKK->k_f.h_view;
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}
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/* ----------------------------------------------------------------------
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copy atom I info to atom J
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------------------------------------------------------------------------- */
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void AtomVecAtomicKokkos::copy(int i, int j, int delflag)
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{
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h_tag[j] = h_tag[i];
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h_type[j] = h_type[i];
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mask[j] = mask[i];
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h_image[j] = h_image[i];
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h_x(j,0) = h_x(i,0);
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h_x(j,1) = h_x(i,1);
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h_x(j,2) = h_x(i,2);
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h_v(j,0) = h_v(i,0);
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h_v(j,1) = h_v(i,1);
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h_v(j,2) = h_v(i,2);
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if (atom->nextra_grow)
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for (int iextra = 0; iextra < atom->nextra_grow; iextra++)
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modify->fix[atom->extra_grow[iextra]]->copy_arrays(i,j,delflag);
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}
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/* ---------------------------------------------------------------------- */
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template<class DeviceType,int PBC_FLAG>
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struct AtomVecAtomicKokkos_PackBorder {
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typedef DeviceType device_type;
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typename ArrayTypes<DeviceType>::t_xfloat_2d _buf;
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const typename ArrayTypes<DeviceType>::t_int_2d_const _list;
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const int _iswap;
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const typename ArrayTypes<DeviceType>::t_x_array_randomread _x;
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const typename ArrayTypes<DeviceType>::t_tagint_1d _tag;
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const typename ArrayTypes<DeviceType>::t_int_1d _type;
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const typename ArrayTypes<DeviceType>::t_int_1d _mask;
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X_FLOAT _dx,_dy,_dz;
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AtomVecAtomicKokkos_PackBorder(
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const typename ArrayTypes<DeviceType>::t_xfloat_2d &buf,
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const typename ArrayTypes<DeviceType>::t_int_2d_const &list,
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const int & iswap,
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const typename ArrayTypes<DeviceType>::t_x_array &x,
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const typename ArrayTypes<DeviceType>::t_tagint_1d &tag,
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const typename ArrayTypes<DeviceType>::t_int_1d &type,
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const typename ArrayTypes<DeviceType>::t_int_1d &mask,
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const X_FLOAT &dx, const X_FLOAT &dy, const X_FLOAT &dz):
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_buf(buf),_list(list),_iswap(iswap),
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_x(x),_tag(tag),_type(type),_mask(mask),
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_dx(dx),_dy(dy),_dz(dz) {}
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KOKKOS_INLINE_FUNCTION
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void operator() (const int& i) const {
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const int j = _list(_iswap,i);
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if (PBC_FLAG == 0) {
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_buf(i,0) = _x(j,0);
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_buf(i,1) = _x(j,1);
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_buf(i,2) = _x(j,2);
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_buf(i,3) = d_ubuf(_tag(j)).d;
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_buf(i,4) = d_ubuf(_type(j)).d;
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_buf(i,5) = d_ubuf(_mask(j)).d;
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} else {
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_buf(i,0) = _x(j,0) + _dx;
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_buf(i,1) = _x(j,1) + _dy;
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_buf(i,2) = _x(j,2) + _dz;
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_buf(i,3) = d_ubuf(_tag(j)).d;
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_buf(i,4) = d_ubuf(_type(j)).d;
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_buf(i,5) = d_ubuf(_mask(j)).d;
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}
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}
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};
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/* ---------------------------------------------------------------------- */
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int AtomVecAtomicKokkos::pack_border_kokkos(int n, DAT::tdual_int_2d k_sendlist, DAT::tdual_xfloat_2d buf,int iswap,
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int pbc_flag, int *pbc, ExecutionSpace space)
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{
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X_FLOAT dx,dy,dz;
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if (pbc_flag != 0) {
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if (domain->triclinic == 0) {
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dx = pbc[0]*domain->xprd;
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dy = pbc[1]*domain->yprd;
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dz = pbc[2]*domain->zprd;
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} else {
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dx = pbc[0];
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dy = pbc[1];
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dz = pbc[2];
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}
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if(space==Host) {
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AtomVecAtomicKokkos_PackBorder<LMPHostType,1> f(
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buf.view<LMPHostType>(), k_sendlist.view<LMPHostType>(),
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iswap,h_x,h_tag,h_type,h_mask,dx,dy,dz);
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Kokkos::parallel_for(n,f);
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} else {
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AtomVecAtomicKokkos_PackBorder<LMPDeviceType,1> f(
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buf.view<LMPDeviceType>(), k_sendlist.view<LMPDeviceType>(),
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iswap,d_x,d_tag,d_type,d_mask,dx,dy,dz);
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Kokkos::parallel_for(n,f);
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}
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} else {
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dx = dy = dz = 0;
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if(space==Host) {
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AtomVecAtomicKokkos_PackBorder<LMPHostType,0> f(
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buf.view<LMPHostType>(), k_sendlist.view<LMPHostType>(),
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iswap,h_x,h_tag,h_type,h_mask,dx,dy,dz);
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Kokkos::parallel_for(n,f);
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} else {
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AtomVecAtomicKokkos_PackBorder<LMPDeviceType,0> f(
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buf.view<LMPDeviceType>(), k_sendlist.view<LMPDeviceType>(),
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iswap,d_x,d_tag,d_type,d_mask,dx,dy,dz);
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Kokkos::parallel_for(n,f);
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}
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}
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return n*6;
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}
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/* ---------------------------------------------------------------------- */
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int AtomVecAtomicKokkos::pack_border(int n, int *list, double *buf,
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int pbc_flag, int *pbc)
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{
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int i,j,m;
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double dx,dy,dz;
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m = 0;
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if (pbc_flag == 0) {
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for (i = 0; i < n; i++) {
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j = list[i];
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buf[m++] = h_x(j,0);
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buf[m++] = h_x(j,1);
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buf[m++] = h_x(j,2);
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buf[m++] = ubuf(h_tag(j)).d;
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buf[m++] = ubuf(h_type(j)).d;
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buf[m++] = ubuf(h_mask(j)).d;
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}
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} else {
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if (domain->triclinic == 0) {
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dx = pbc[0]*domain->xprd;
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dy = pbc[1]*domain->yprd;
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dz = pbc[2]*domain->zprd;
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} else {
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dx = pbc[0];
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dy = pbc[1];
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dz = pbc[2];
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}
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for (i = 0; i < n; i++) {
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j = list[i];
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buf[m++] = h_x(j,0) + dx;
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buf[m++] = h_x(j,1) + dy;
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buf[m++] = h_x(j,2) + dz;
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buf[m++] = ubuf(h_tag(j)).d;
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buf[m++] = ubuf(h_type(j)).d;
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buf[m++] = ubuf(h_mask(j)).d;
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}
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}
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if (atom->nextra_border)
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for (int iextra = 0; iextra < atom->nextra_border; iextra++)
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m += modify->fix[atom->extra_border[iextra]]->pack_border(n,list,&buf[m]);
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return m;
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}
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/* ---------------------------------------------------------------------- */
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int AtomVecAtomicKokkos::pack_border_vel(int n, int *list, double *buf,
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int pbc_flag, int *pbc)
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{
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int i,j,m;
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double dx,dy,dz,dvx,dvy,dvz;
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m = 0;
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if (pbc_flag == 0) {
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for (i = 0; i < n; i++) {
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j = list[i];
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buf[m++] = h_x(j,0);
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buf[m++] = h_x(j,1);
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buf[m++] = h_x(j,2);
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buf[m++] = ubuf(h_tag(j)).d;
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buf[m++] = ubuf(h_type(j)).d;
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buf[m++] = ubuf(h_mask(j)).d;
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buf[m++] = h_v(j,0);
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buf[m++] = h_v(j,1);
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buf[m++] = h_v(j,2);
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}
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} else {
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if (domain->triclinic == 0) {
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dx = pbc[0]*domain->xprd;
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dy = pbc[1]*domain->yprd;
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dz = pbc[2]*domain->zprd;
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} else {
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dx = pbc[0];
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dy = pbc[1];
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dz = pbc[2];
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}
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if (!deform_vremap) {
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for (i = 0; i < n; i++) {
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j = list[i];
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buf[m++] = h_x(j,0) + dx;
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buf[m++] = h_x(j,1) + dy;
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buf[m++] = h_x(j,2) + dz;
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buf[m++] = ubuf(h_tag(j)).d;
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buf[m++] = ubuf(h_type(j)).d;
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buf[m++] = ubuf(h_mask(j)).d;
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buf[m++] = h_v(j,0);
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buf[m++] = h_v(j,1);
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buf[m++] = h_v(j,2);
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}
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} else {
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dvx = pbc[0]*h_rate[0] + pbc[5]*h_rate[5] + pbc[4]*h_rate[4];
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dvy = pbc[1]*h_rate[1] + pbc[3]*h_rate[3];
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dvz = pbc[2]*h_rate[2];
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for (i = 0; i < n; i++) {
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j = list[i];
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buf[m++] = h_x(j,0) + dx;
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buf[m++] = h_x(j,1) + dy;
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buf[m++] = h_x(j,2) + dz;
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buf[m++] = ubuf(h_tag(j)).d;
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buf[m++] = ubuf(h_type(j)).d;
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buf[m++] = ubuf(h_mask(j)).d;
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if (mask[i] & deform_groupbit) {
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buf[m++] = h_v(j,0) + dvx;
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buf[m++] = h_v(j,1) + dvy;
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buf[m++] = h_v(j,2) + dvz;
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} else {
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buf[m++] = h_v(j,0);
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buf[m++] = h_v(j,1);
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buf[m++] = h_v(j,2);
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}
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}
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}
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}
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if (atom->nextra_border)
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for (int iextra = 0; iextra < atom->nextra_border; iextra++)
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m += modify->fix[atom->extra_border[iextra]]->pack_border(n,list,&buf[m]);
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return m;
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}
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/* ---------------------------------------------------------------------- */
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template<class DeviceType>
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struct AtomVecAtomicKokkos_UnpackBorder {
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typedef DeviceType device_type;
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const typename ArrayTypes<DeviceType>::t_xfloat_2d_const _buf;
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typename ArrayTypes<DeviceType>::t_x_array _x;
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typename ArrayTypes<DeviceType>::t_tagint_1d _tag;
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typename ArrayTypes<DeviceType>::t_int_1d _type;
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typename ArrayTypes<DeviceType>::t_int_1d _mask;
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int _first;
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AtomVecAtomicKokkos_UnpackBorder(
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const typename ArrayTypes<DeviceType>::t_xfloat_2d_const &buf,
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typename ArrayTypes<DeviceType>::t_x_array &x,
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typename ArrayTypes<DeviceType>::t_tagint_1d &tag,
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typename ArrayTypes<DeviceType>::t_int_1d &type,
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typename ArrayTypes<DeviceType>::t_int_1d &mask,
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const int& first):
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_buf(buf),_x(x),_tag(tag),_type(type),_mask(mask),_first(first){
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};
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KOKKOS_INLINE_FUNCTION
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void operator() (const int& i) const {
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_x(i+_first,0) = _buf(i,0);
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_x(i+_first,1) = _buf(i,1);
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_x(i+_first,2) = _buf(i,2);
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_tag(i+_first) = (tagint) d_ubuf(_buf(i,3)).i;
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_type(i+_first) = (int) d_ubuf(_buf(i,4)).i;
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_mask(i+_first) = (int) d_ubuf(_buf(i,5)).i;
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// printf("%i %i %lf %lf %lf %i BORDER\n",_tag(i+_first),i+_first,_x(i+_first,0),_x(i+_first,1),_x(i+_first,2),_type(i+_first));
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}
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};
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/* ---------------------------------------------------------------------- */
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void AtomVecAtomicKokkos::unpack_border_kokkos(const int &n, const int &first,
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const DAT::tdual_xfloat_2d &buf,ExecutionSpace space) {
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modified(space,X_MASK|TAG_MASK|TYPE_MASK|MASK_MASK);
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while (first+n >= nmax) grow(0);
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modified(space,X_MASK|TAG_MASK|TYPE_MASK|MASK_MASK);
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if(space==Host) {
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struct AtomVecAtomicKokkos_UnpackBorder<LMPHostType> f(buf.view<LMPHostType>(),h_x,h_tag,h_type,h_mask,first);
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Kokkos::parallel_for(n,f);
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} else {
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struct AtomVecAtomicKokkos_UnpackBorder<LMPDeviceType> f(buf.view<LMPDeviceType>(),d_x,d_tag,d_type,d_mask,first);
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Kokkos::parallel_for(n,f);
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}
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}
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/* ---------------------------------------------------------------------- */
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void AtomVecAtomicKokkos::unpack_border(int n, int first, double *buf)
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{
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int i,m,last;
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m = 0;
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last = first + n;
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for (i = first; i < last; i++) {
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if (i == nmax) grow(0);
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modified(Host,X_MASK|TAG_MASK|TYPE_MASK|MASK_MASK);
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h_x(i,0) = buf[m++];
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h_x(i,1) = buf[m++];
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h_x(i,2) = buf[m++];
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h_tag(i) = (tagint) ubuf(buf[m++]).i;
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h_type(i) = (int) ubuf(buf[m++]).i;
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h_mask(i) = (int) ubuf(buf[m++]).i;
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}
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if (atom->nextra_border)
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for (int iextra = 0; iextra < atom->nextra_border; iextra++)
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m += modify->fix[atom->extra_border[iextra]]->
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unpack_border(n,first,&buf[m]);
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}
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/* ---------------------------------------------------------------------- */
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void AtomVecAtomicKokkos::unpack_border_vel(int n, int first, double *buf)
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{
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int i,m,last;
|
|
|
|
m = 0;
|
|
last = first + n;
|
|
for (i = first; i < last; i++) {
|
|
if (i == nmax) grow(0);
|
|
modified(Host,X_MASK|V_MASK|TAG_MASK|TYPE_MASK|MASK_MASK);
|
|
h_x(i,0) = buf[m++];
|
|
h_x(i,1) = buf[m++];
|
|
h_x(i,2) = buf[m++];
|
|
h_tag(i) = (tagint) ubuf(buf[m++]).i;
|
|
h_type(i) = (int) ubuf(buf[m++]).i;
|
|
h_mask(i) = (int) ubuf(buf[m++]).i;
|
|
h_v(i,0) = buf[m++];
|
|
h_v(i,1) = buf[m++];
|
|
h_v(i,2) = buf[m++];
|
|
}
|
|
|
|
if (atom->nextra_border)
|
|
for (int iextra = 0; iextra < atom->nextra_border; iextra++)
|
|
m += modify->fix[atom->extra_border[iextra]]->
|
|
unpack_border(n,first,&buf[m]);
|
|
}
|
|
|
|
/* ---------------------------------------------------------------------- */
|
|
|
|
template<class DeviceType>
|
|
struct AtomVecAtomicKokkos_PackExchangeFunctor {
|
|
typedef DeviceType device_type;
|
|
typedef ArrayTypes<DeviceType> AT;
|
|
typename AT::t_x_array_randomread _x;
|
|
typename AT::t_v_array_randomread _v;
|
|
typename AT::t_tagint_1d_randomread _tag;
|
|
typename AT::t_int_1d_randomread _type;
|
|
typename AT::t_int_1d_randomread _mask;
|
|
typename AT::t_imageint_1d_randomread _image;
|
|
typename AT::t_x_array _xw;
|
|
typename AT::t_v_array _vw;
|
|
typename AT::t_tagint_1d _tagw;
|
|
typename AT::t_int_1d _typew;
|
|
typename AT::t_int_1d _maskw;
|
|
typename AT::t_imageint_1d _imagew;
|
|
|
|
typename AT::t_xfloat_2d_um _buf;
|
|
typename AT::t_int_1d_const _sendlist;
|
|
typename AT::t_int_1d_const _copylist;
|
|
int _nlocal,_dim;
|
|
X_FLOAT _lo,_hi;
|
|
|
|
AtomVecAtomicKokkos_PackExchangeFunctor(
|
|
const AtomKokkos* atom,
|
|
const typename AT::tdual_xfloat_2d buf,
|
|
typename AT::tdual_int_1d sendlist,
|
|
typename AT::tdual_int_1d copylist,int nlocal, int dim,
|
|
X_FLOAT lo, X_FLOAT hi):
|
|
_x(atom->k_x.view<DeviceType>()),
|
|
_v(atom->k_v.view<DeviceType>()),
|
|
_tag(atom->k_tag.view<DeviceType>()),
|
|
_type(atom->k_type.view<DeviceType>()),
|
|
_mask(atom->k_mask.view<DeviceType>()),
|
|
_image(atom->k_image.view<DeviceType>()),
|
|
_xw(atom->k_x.view<DeviceType>()),
|
|
_vw(atom->k_v.view<DeviceType>()),
|
|
_tagw(atom->k_tag.view<DeviceType>()),
|
|
_typew(atom->k_type.view<DeviceType>()),
|
|
_maskw(atom->k_mask.view<DeviceType>()),
|
|
_imagew(atom->k_image.view<DeviceType>()),
|
|
_sendlist(sendlist.template view<DeviceType>()),
|
|
_copylist(copylist.template view<DeviceType>()),
|
|
_nlocal(nlocal),_dim(dim),
|
|
_lo(lo),_hi(hi){
|
|
const size_t elements = 11;
|
|
const int maxsendlist = (buf.template view<DeviceType>().dimension_0()*buf.template view<DeviceType>().dimension_1())/elements;
|
|
|
|
buffer_view<DeviceType>(_buf,buf,maxsendlist,elements);
|
|
}
|
|
|
|
KOKKOS_INLINE_FUNCTION
|
|
void operator() (const int &mysend) const {
|
|
const int i = _sendlist(mysend);
|
|
_buf(mysend,0) = 11;
|
|
_buf(mysend,1) = _x(i,0);
|
|
_buf(mysend,2) = _x(i,1);
|
|
_buf(mysend,3) = _x(i,2);
|
|
_buf(mysend,4) = _v(i,0);
|
|
_buf(mysend,5) = _v(i,1);
|
|
_buf(mysend,6) = _v(i,2);
|
|
_buf(mysend,7) = d_ubuf(_tag[i]).d;
|
|
_buf(mysend,8) = d_ubuf(_type[i]).d;
|
|
_buf(mysend,9) = d_ubuf(_mask[i]).d;
|
|
_buf(mysend,10) = d_ubuf(_image[i]).d;
|
|
const int j = _copylist(mysend);
|
|
|
|
if(j>-1) {
|
|
_xw(i,0) = _x(j,0);
|
|
_xw(i,1) = _x(j,1);
|
|
_xw(i,2) = _x(j,2);
|
|
_vw(i,0) = _v(j,0);
|
|
_vw(i,1) = _v(j,1);
|
|
_vw(i,2) = _v(j,2);
|
|
_tagw[i] = _tag(j);
|
|
_typew[i] = _type(j);
|
|
_maskw[i] = _mask(j);
|
|
_imagew[i] = _image(j);
|
|
}
|
|
}
|
|
};
|
|
|
|
/* ---------------------------------------------------------------------- */
|
|
|
|
int AtomVecAtomicKokkos::pack_exchange_kokkos(const int &nsend,DAT::tdual_xfloat_2d &k_buf, DAT::tdual_int_1d k_sendlist,DAT::tdual_int_1d k_copylist,ExecutionSpace space,int dim,X_FLOAT lo,X_FLOAT hi )
|
|
{
|
|
if(nsend > (int) (k_buf.view<LMPHostType>().dimension_0()*k_buf.view<LMPHostType>().dimension_1())/11) {
|
|
int newsize = nsend*11/k_buf.view<LMPHostType>().dimension_1()+1;
|
|
k_buf.resize(newsize,k_buf.view<LMPHostType>().dimension_1());
|
|
}
|
|
if(space == Host) {
|
|
AtomVecAtomicKokkos_PackExchangeFunctor<LMPHostType> f(atomKK,k_buf,k_sendlist,k_copylist,atom->nlocal,dim,lo,hi);
|
|
Kokkos::parallel_for(nsend,f);
|
|
return nsend*11;
|
|
} else {
|
|
AtomVecAtomicKokkos_PackExchangeFunctor<LMPDeviceType> f(atomKK,k_buf,k_sendlist,k_copylist,atom->nlocal,dim,lo,hi);
|
|
Kokkos::parallel_for(nsend,f);
|
|
return nsend*11;
|
|
}
|
|
}
|
|
|
|
/* ---------------------------------------------------------------------- */
|
|
|
|
int AtomVecAtomicKokkos::pack_exchange(int i, double *buf)
|
|
{
|
|
int m = 1;
|
|
buf[m++] = h_x(i,0);
|
|
buf[m++] = h_x(i,1);
|
|
buf[m++] = h_x(i,2);
|
|
buf[m++] = h_v(i,0);
|
|
buf[m++] = h_v(i,1);
|
|
buf[m++] = h_v(i,2);
|
|
buf[m++] = ubuf(h_tag(i)).d;
|
|
buf[m++] = ubuf(h_type(i)).d;
|
|
buf[m++] = ubuf(h_mask(i)).d;
|
|
buf[m++] = ubuf(h_image(i)).d;
|
|
|
|
if (atom->nextra_grow)
|
|
for (int iextra = 0; iextra < atom->nextra_grow; iextra++)
|
|
m += modify->fix[atom->extra_grow[iextra]]->pack_exchange(i,&buf[m]);
|
|
|
|
buf[0] = m;
|
|
return m;
|
|
}
|
|
|
|
/* ---------------------------------------------------------------------- */
|
|
|
|
template<class DeviceType>
|
|
struct AtomVecAtomicKokkos_UnpackExchangeFunctor {
|
|
typedef DeviceType device_type;
|
|
typedef ArrayTypes<DeviceType> AT;
|
|
typename AT::t_x_array _x;
|
|
typename AT::t_v_array _v;
|
|
typename AT::t_tagint_1d _tag;
|
|
typename AT::t_int_1d _type;
|
|
typename AT::t_int_1d _mask;
|
|
typename AT::t_imageint_1d _image;
|
|
|
|
typename AT::t_xfloat_2d_um _buf;
|
|
typename AT::t_int_1d _nlocal;
|
|
int _dim;
|
|
X_FLOAT _lo,_hi;
|
|
|
|
AtomVecAtomicKokkos_UnpackExchangeFunctor(
|
|
const AtomKokkos* atom,
|
|
const typename AT::tdual_xfloat_2d buf,
|
|
typename AT::tdual_int_1d nlocal,
|
|
int dim, X_FLOAT lo, X_FLOAT hi):
|
|
_x(atom->k_x.view<DeviceType>()),
|
|
_v(atom->k_v.view<DeviceType>()),
|
|
_tag(atom->k_tag.view<DeviceType>()),
|
|
_type(atom->k_type.view<DeviceType>()),
|
|
_mask(atom->k_mask.view<DeviceType>()),
|
|
_image(atom->k_image.view<DeviceType>()),
|
|
_nlocal(nlocal.template view<DeviceType>()),_dim(dim),
|
|
_lo(lo),_hi(hi){
|
|
const size_t elements = 11;
|
|
const int maxsendlist = (buf.template view<DeviceType>().dimension_0()*buf.template view<DeviceType>().dimension_1())/elements;
|
|
|
|
buffer_view<DeviceType>(_buf,buf,maxsendlist,elements);
|
|
}
|
|
|
|
KOKKOS_INLINE_FUNCTION
|
|
void operator() (const int &myrecv) const {
|
|
X_FLOAT x = _buf(myrecv,_dim+1);
|
|
if (x >= _lo && x < _hi) {
|
|
int i = Kokkos::atomic_fetch_add(&_nlocal(0),1);
|
|
_x(i,0) = _buf(myrecv,1);
|
|
_x(i,1) = _buf(myrecv,2);
|
|
_x(i,2) = _buf(myrecv,3);
|
|
_v(i,0) = _buf(myrecv,4);
|
|
_v(i,1) = _buf(myrecv,5);
|
|
_v(i,2) = _buf(myrecv,6);
|
|
_tag[i] = (tagint) d_ubuf(_buf(myrecv,7)).i;
|
|
_type[i] = (int) d_ubuf(_buf(myrecv,8)).i;
|
|
_mask[i] = (int) d_ubuf(_buf(myrecv,9)).i;
|
|
_image[i] = (imageint) d_ubuf(_buf(myrecv,10)).i;
|
|
}
|
|
}
|
|
};
|
|
|
|
/* ---------------------------------------------------------------------- */
|
|
|
|
int AtomVecAtomicKokkos::unpack_exchange_kokkos(DAT::tdual_xfloat_2d &k_buf,int nrecv,int nlocal,int dim,X_FLOAT lo,X_FLOAT hi,ExecutionSpace space) {
|
|
if(space == Host) {
|
|
k_count.h_view(0) = nlocal;
|
|
AtomVecAtomicKokkos_UnpackExchangeFunctor<LMPHostType> f(atomKK,k_buf,k_count,dim,lo,hi);
|
|
Kokkos::parallel_for(nrecv/11,f);
|
|
return k_count.h_view(0);
|
|
} else {
|
|
k_count.h_view(0) = nlocal;
|
|
k_count.modify<LMPHostType>();
|
|
k_count.sync<LMPDeviceType>();
|
|
AtomVecAtomicKokkos_UnpackExchangeFunctor<LMPDeviceType> f(atomKK,k_buf,k_count,dim,lo,hi);
|
|
Kokkos::parallel_for(nrecv/11,f);
|
|
k_count.modify<LMPDeviceType>();
|
|
k_count.sync<LMPHostType>();
|
|
|
|
return k_count.h_view(0);
|
|
}
|
|
}
|
|
|
|
/* ---------------------------------------------------------------------- */
|
|
|
|
int AtomVecAtomicKokkos::unpack_exchange(double *buf)
|
|
{
|
|
int nlocal = atom->nlocal;
|
|
if (nlocal == nmax) grow(0);
|
|
modified(Host,X_MASK | V_MASK | TAG_MASK | TYPE_MASK |
|
|
MASK_MASK | IMAGE_MASK);
|
|
|
|
int m = 1;
|
|
h_x(nlocal,0) = buf[m++];
|
|
h_x(nlocal,1) = buf[m++];
|
|
h_x(nlocal,2) = buf[m++];
|
|
h_v(nlocal,0) = buf[m++];
|
|
h_v(nlocal,1) = buf[m++];
|
|
h_v(nlocal,2) = buf[m++];
|
|
h_tag(nlocal) = (tagint) ubuf(buf[m++]).i;
|
|
h_type(nlocal) = (int) ubuf(buf[m++]).i;
|
|
h_mask(nlocal) = (int) ubuf(buf[m++]).i;
|
|
h_image(nlocal) = (imageint) ubuf(buf[m++]).i;
|
|
|
|
if (atom->nextra_grow)
|
|
for (int iextra = 0; iextra < atom->nextra_grow; iextra++)
|
|
m += modify->fix[atom->extra_grow[iextra]]->
|
|
unpack_exchange(nlocal,&buf[m]);
|
|
|
|
atom->nlocal++;
|
|
return m;
|
|
}
|
|
|
|
/* ----------------------------------------------------------------------
|
|
size of restart data for all atoms owned by this proc
|
|
include extra data stored by fixes
|
|
------------------------------------------------------------------------- */
|
|
|
|
int AtomVecAtomicKokkos::size_restart()
|
|
{
|
|
int i;
|
|
|
|
int nlocal = atom->nlocal;
|
|
int n = 11 * nlocal;
|
|
|
|
if (atom->nextra_restart)
|
|
for (int iextra = 0; iextra < atom->nextra_restart; iextra++)
|
|
for (i = 0; i < nlocal; i++)
|
|
n += modify->fix[atom->extra_restart[iextra]]->size_restart(i);
|
|
|
|
return n;
|
|
}
|
|
|
|
/* ----------------------------------------------------------------------
|
|
pack atom I's data for restart file including extra quantities
|
|
xyz must be 1st 3 values, so that read_restart can test on them
|
|
molecular types may be negative, but write as positive
|
|
------------------------------------------------------------------------- */
|
|
|
|
int AtomVecAtomicKokkos::pack_restart(int i, double *buf)
|
|
{
|
|
sync(Host,X_MASK | V_MASK | TAG_MASK | TYPE_MASK |
|
|
MASK_MASK | IMAGE_MASK );
|
|
|
|
int m = 1;
|
|
buf[m++] = h_x(i,0);
|
|
buf[m++] = h_x(i,1);
|
|
buf[m++] = h_x(i,2);
|
|
buf[m++] = ubuf(h_tag(i)).d;
|
|
buf[m++] = ubuf(h_type(i)).d;
|
|
buf[m++] = ubuf(h_mask(i)).d;
|
|
buf[m++] = ubuf(h_image(i)).d;
|
|
buf[m++] = h_v(i,0);
|
|
buf[m++] = h_v(i,1);
|
|
buf[m++] = h_v(i,2);
|
|
|
|
if (atom->nextra_restart)
|
|
for (int iextra = 0; iextra < atom->nextra_restart; iextra++)
|
|
m += modify->fix[atom->extra_restart[iextra]]->pack_restart(i,&buf[m]);
|
|
|
|
buf[0] = m;
|
|
return m;
|
|
}
|
|
|
|
/* ----------------------------------------------------------------------
|
|
unpack data for one atom from restart file including extra quantities
|
|
------------------------------------------------------------------------- */
|
|
|
|
int AtomVecAtomicKokkos::unpack_restart(double *buf)
|
|
{
|
|
int nlocal = atom->nlocal;
|
|
if (nlocal == nmax) {
|
|
grow(0);
|
|
if (atom->nextra_store)
|
|
memory->grow(atom->extra,nmax,atom->nextra_store,"atom:extra");
|
|
}
|
|
modified(Host,X_MASK | V_MASK | TAG_MASK | TYPE_MASK |
|
|
MASK_MASK | IMAGE_MASK );
|
|
|
|
int m = 1;
|
|
h_x(nlocal,0) = buf[m++];
|
|
h_x(nlocal,1) = buf[m++];
|
|
h_x(nlocal,2) = buf[m++];
|
|
h_tag(nlocal) = (tagint) ubuf(buf[m++]).i;
|
|
h_type(nlocal) = (int) ubuf(buf[m++]).i;
|
|
h_mask(nlocal) = (int) ubuf(buf[m++]).i;
|
|
h_image(nlocal) = (imageint) ubuf(buf[m++]).i;
|
|
h_v(nlocal,0) = buf[m++];
|
|
h_v(nlocal,1) = buf[m++];
|
|
h_v(nlocal,2) = buf[m++];
|
|
|
|
double **extra = atom->extra;
|
|
if (atom->nextra_store) {
|
|
int size = static_cast<int> (buf[0]) - m;
|
|
for (int i = 0; i < size; i++) extra[nlocal][i] = buf[m++];
|
|
}
|
|
|
|
atom->nlocal++;
|
|
return m;
|
|
}
|
|
|
|
/* ----------------------------------------------------------------------
|
|
create one atom of itype at coord
|
|
set other values to defaults
|
|
------------------------------------------------------------------------- */
|
|
|
|
void AtomVecAtomicKokkos::create_atom(int itype, double *coord)
|
|
{
|
|
int nlocal = atom->nlocal;
|
|
if (nlocal == nmax) {
|
|
//if(nlocal>2) printf("typeA: %i %i\n",type[0],type[1]);
|
|
atomKK->modified(Host,ALL_MASK);
|
|
grow(0);
|
|
//if(nlocal>2) printf("typeB: %i %i\n",type[0],type[1]);
|
|
}
|
|
atomKK->modified(Host,ALL_MASK);
|
|
|
|
tag[nlocal] = 0;
|
|
type[nlocal] = itype;
|
|
h_x(nlocal,0) = coord[0];
|
|
h_x(nlocal,1) = coord[1];
|
|
h_x(nlocal,2) = coord[2];
|
|
h_mask[nlocal] = 1;
|
|
h_image[nlocal] = ((tagint) IMGMAX << IMG2BITS) |
|
|
((tagint) IMGMAX << IMGBITS) | IMGMAX;
|
|
h_v(nlocal,0) = 0.0;
|
|
h_v(nlocal,1) = 0.0;
|
|
h_v(nlocal,2) = 0.0;
|
|
|
|
atom->nlocal++;
|
|
}
|
|
|
|
/* ----------------------------------------------------------------------
|
|
unpack one line from Atoms section of data file
|
|
initialize other atom quantities
|
|
------------------------------------------------------------------------- */
|
|
|
|
void AtomVecAtomicKokkos::data_atom(double *coord, tagint imagetmp,
|
|
char **values)
|
|
{
|
|
int nlocal = atom->nlocal;
|
|
if (nlocal == nmax) grow(0);
|
|
|
|
h_tag[nlocal] = atoi(values[0]);
|
|
h_type[nlocal] = atoi(values[1]);
|
|
if (type[nlocal] <= 0 || type[nlocal] > atom->ntypes)
|
|
error->one(FLERR,"Invalid atom type in Atoms section of data file");
|
|
|
|
h_x(nlocal,0) = coord[0];
|
|
h_x(nlocal,1) = coord[1];
|
|
h_x(nlocal,2) = coord[2];
|
|
|
|
h_image[nlocal] = imagetmp;
|
|
|
|
h_mask[nlocal] = 1;
|
|
h_v(nlocal,0) = 0.0;
|
|
h_v(nlocal,1) = 0.0;
|
|
h_v(nlocal,2) = 0.0;
|
|
|
|
atomKK->modified(Host,ALL_MASK);
|
|
|
|
atom->nlocal++;
|
|
}
|
|
|
|
/* ----------------------------------------------------------------------
|
|
pack atom info for data file including 3 image flags
|
|
------------------------------------------------------------------------- */
|
|
|
|
void AtomVecAtomicKokkos::pack_data(double **buf)
|
|
{
|
|
int nlocal = atom->nlocal;
|
|
for (int i = 0; i < nlocal; i++) {
|
|
buf[i][0] = h_tag[i];
|
|
buf[i][1] = h_type[i];
|
|
buf[i][2] = h_x(i,0);
|
|
buf[i][3] = h_x(i,1);
|
|
buf[i][4] = h_x(i,2);
|
|
buf[i][5] = (h_image[i] & IMGMASK) - IMGMAX;
|
|
buf[i][6] = (h_image[i] >> IMGBITS & IMGMASK) - IMGMAX;
|
|
buf[i][7] = (h_image[i] >> IMG2BITS) - IMGMAX;
|
|
}
|
|
}
|
|
|
|
/* ----------------------------------------------------------------------
|
|
write atom info to data file including 3 image flags
|
|
------------------------------------------------------------------------- */
|
|
|
|
void AtomVecAtomicKokkos::write_data(FILE *fp, int n, double **buf)
|
|
{
|
|
for (int i = 0; i < n; i++)
|
|
fprintf(fp,"%d %d %-1.16e %-1.16e %-1.16e %d %d %d\n",
|
|
(int) buf[i][0],(int) buf[i][1],buf[i][2],buf[i][3],buf[i][4],
|
|
(int) buf[i][5],(int) buf[i][6],(int) buf[i][7]);
|
|
}
|
|
|
|
/* ----------------------------------------------------------------------
|
|
return # of bytes of allocated memory
|
|
------------------------------------------------------------------------- */
|
|
|
|
bigint AtomVecAtomicKokkos::memory_usage()
|
|
{
|
|
bigint bytes = 0;
|
|
|
|
if (atom->memcheck("tag")) bytes += memory->usage(tag,nmax);
|
|
if (atom->memcheck("type")) bytes += memory->usage(type,nmax);
|
|
if (atom->memcheck("mask")) bytes += memory->usage(mask,nmax);
|
|
if (atom->memcheck("image")) bytes += memory->usage(image,nmax);
|
|
if (atom->memcheck("x")) bytes += memory->usage(x,nmax,3);
|
|
if (atom->memcheck("v")) bytes += memory->usage(v,nmax,3);
|
|
if (atom->memcheck("f")) bytes += memory->usage(f,nmax*commKK->nthreads,3);
|
|
|
|
return bytes;
|
|
}
|
|
|
|
/* ---------------------------------------------------------------------- */
|
|
|
|
void AtomVecAtomicKokkos::sync(ExecutionSpace space, unsigned int mask)
|
|
{
|
|
if (space == Device) {
|
|
if (mask & X_MASK) atomKK->k_x.sync<LMPDeviceType>();
|
|
if (mask & V_MASK) atomKK->k_v.sync<LMPDeviceType>();
|
|
if (mask & F_MASK) atomKK->k_f.sync<LMPDeviceType>();
|
|
if (mask & TAG_MASK) atomKK->k_tag.sync<LMPDeviceType>();
|
|
if (mask & TYPE_MASK) atomKK->k_type.sync<LMPDeviceType>();
|
|
if (mask & MASK_MASK) atomKK->k_mask.sync<LMPDeviceType>();
|
|
if (mask & IMAGE_MASK) atomKK->k_image.sync<LMPDeviceType>();
|
|
} else {
|
|
if (mask & X_MASK) atomKK->k_x.sync<LMPHostType>();
|
|
if (mask & V_MASK) atomKK->k_v.sync<LMPHostType>();
|
|
if (mask & F_MASK) atomKK->k_f.sync<LMPHostType>();
|
|
if (mask & TAG_MASK) atomKK->k_tag.sync<LMPHostType>();
|
|
if (mask & TYPE_MASK) atomKK->k_type.sync<LMPHostType>();
|
|
if (mask & MASK_MASK) atomKK->k_mask.sync<LMPHostType>();
|
|
if (mask & IMAGE_MASK) atomKK->k_image.sync<LMPHostType>();
|
|
}
|
|
}
|
|
|
|
/* ---------------------------------------------------------------------- */
|
|
|
|
void AtomVecAtomicKokkos::sync_overlapping_device(ExecutionSpace space, unsigned int mask)
|
|
{
|
|
if (space == Device) {
|
|
if ((mask & X_MASK) && atomKK->k_x.need_sync<LMPDeviceType>())
|
|
perform_async_copy<DAT::tdual_x_array>(atomKK->k_x,space);
|
|
if ((mask & V_MASK) && atomKK->k_v.need_sync<LMPDeviceType>())
|
|
perform_async_copy<DAT::tdual_v_array>(atomKK->k_v,space);
|
|
if ((mask & F_MASK) && atomKK->k_f.need_sync<LMPDeviceType>())
|
|
perform_async_copy<DAT::tdual_f_array>(atomKK->k_f,space);
|
|
if ((mask & TAG_MASK) && atomKK->k_tag.need_sync<LMPDeviceType>())
|
|
perform_async_copy<DAT::tdual_tagint_1d>(atomKK->k_tag,space);
|
|
if ((mask & TYPE_MASK) && atomKK->k_type.need_sync<LMPDeviceType>())
|
|
perform_async_copy<DAT::tdual_int_1d>(atomKK->k_type,space);
|
|
if ((mask & MASK_MASK) && atomKK->k_mask.need_sync<LMPDeviceType>())
|
|
perform_async_copy<DAT::tdual_int_1d>(atomKK->k_mask,space);
|
|
if ((mask & IMAGE_MASK) && atomKK->k_image.need_sync<LMPDeviceType>())
|
|
perform_async_copy<DAT::tdual_imageint_1d>(atomKK->k_image,space);
|
|
} else {
|
|
if ((mask & X_MASK) && atomKK->k_x.need_sync<LMPHostType>())
|
|
perform_async_copy<DAT::tdual_x_array>(atomKK->k_x,space);
|
|
if ((mask & V_MASK) && atomKK->k_v.need_sync<LMPHostType>())
|
|
perform_async_copy<DAT::tdual_v_array>(atomKK->k_v,space);
|
|
if ((mask & F_MASK) && atomKK->k_f.need_sync<LMPHostType>())
|
|
perform_async_copy<DAT::tdual_f_array>(atomKK->k_f,space);
|
|
if ((mask & TAG_MASK) && atomKK->k_tag.need_sync<LMPHostType>())
|
|
perform_async_copy<DAT::tdual_tagint_1d>(atomKK->k_tag,space);
|
|
if ((mask & TYPE_MASK) && atomKK->k_type.need_sync<LMPHostType>())
|
|
perform_async_copy<DAT::tdual_int_1d>(atomKK->k_type,space);
|
|
if ((mask & MASK_MASK) && atomKK->k_mask.need_sync<LMPHostType>())
|
|
perform_async_copy<DAT::tdual_int_1d>(atomKK->k_mask,space);
|
|
if ((mask & IMAGE_MASK) && atomKK->k_image.need_sync<LMPHostType>())
|
|
perform_async_copy<DAT::tdual_imageint_1d>(atomKK->k_image,space);
|
|
}
|
|
}
|
|
|
|
/* ---------------------------------------------------------------------- */
|
|
|
|
void AtomVecAtomicKokkos::modified(ExecutionSpace space, unsigned int mask)
|
|
{
|
|
if (space == Device) {
|
|
if (mask & X_MASK) atomKK->k_x.modify<LMPDeviceType>();
|
|
if (mask & V_MASK) atomKK->k_v.modify<LMPDeviceType>();
|
|
if (mask & F_MASK) atomKK->k_f.modify<LMPDeviceType>();
|
|
if (mask & TAG_MASK) atomKK->k_tag.modify<LMPDeviceType>();
|
|
if (mask & TYPE_MASK) atomKK->k_type.modify<LMPDeviceType>();
|
|
if (mask & MASK_MASK) atomKK->k_mask.modify<LMPDeviceType>();
|
|
if (mask & IMAGE_MASK) atomKK->k_image.modify<LMPDeviceType>();
|
|
} else {
|
|
if (mask & X_MASK) atomKK->k_x.modify<LMPHostType>();
|
|
if (mask & V_MASK) atomKK->k_v.modify<LMPHostType>();
|
|
if (mask & F_MASK) atomKK->k_f.modify<LMPHostType>();
|
|
if (mask & TAG_MASK) atomKK->k_tag.modify<LMPHostType>();
|
|
if (mask & TYPE_MASK) atomKK->k_type.modify<LMPHostType>();
|
|
if (mask & MASK_MASK) atomKK->k_mask.modify<LMPHostType>();
|
|
if (mask & IMAGE_MASK) atomKK->k_image.modify<LMPHostType>();
|
|
}
|
|
}
|
|
|