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atom_vec_bond_kokkos.cpp
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Wed, Nov 6, 06:14

atom_vec_bond_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 <stdlib.h>
#include "atom_vec_bond_kokkos.h"
#include "atom_kokkos.h"
#include "comm_kokkos.h"
#include "domain.h"
#include "modify.h"
#include "fix.h"
#include "atom_masks.h"
#include "memory.h"
#include "error.h"
using namespace LAMMPS_NS;
#define DELTA 10000
/* ---------------------------------------------------------------------- */
AtomVecBondKokkos::AtomVecBondKokkos(LAMMPS *lmp) : AtomVecKokkos(lmp)
{
molecular = 1;
bonds_allow = 1;
mass_type = 1;
comm_x_only = comm_f_only = 1;
size_forward = 3;
size_reverse = 3;
size_border = 7;
size_velocity = 3;
size_data_atom = 6;
size_data_vel = 4;
xcol_data = 4;
k_count = DAT::tdual_int_1d("atom::k_count",1);
atomKK = (AtomKokkos *) atom;
commKK = (CommKokkos *) comm;
}
/* ----------------------------------------------------------------------
grow atom arrays
n = 0 grows arrays by DELTA
n > 0 allocates arrays to size n
------------------------------------------------------------------------- */
void AtomVecBondKokkos::grow(int n)
{
if (n == 0) nmax += DELTA;
else nmax = n;
atomKK->nmax = nmax;
if (nmax < 0 || nmax > MAXSMALLINT)
error->one(FLERR,"Per-processor system is too big");
sync(Device,ALL_MASK);
modified(Device,ALL_MASK);
memory->grow_kokkos(atomKK->k_tag,atomKK->tag,nmax,"atom:tag");
memory->grow_kokkos(atomKK->k_type,atomKK->type,nmax,"atom:type");
memory->grow_kokkos(atomKK->k_mask,atomKK->mask,nmax,"atom:mask");
memory->grow_kokkos(atomKK->k_image,atomKK->image,nmax,"atom:image");
memory->grow_kokkos(atomKK->k_x,atomKK->x,nmax,3,"atom:x");
memory->grow_kokkos(atomKK->k_v,atomKK->v,nmax,3,"atom:v");
memory->grow_kokkos(atomKK->k_f,atomKK->f,nmax,3,"atom:f");
memory->grow_kokkos(atomKK->k_molecule,atomKK->molecule,nmax,"atom:molecule");
memory->grow_kokkos(atomKK->k_nspecial,atomKK->nspecial,nmax,3,"atom:nspecial");
memory->grow_kokkos(atomKK->k_special,atomKK->special,nmax,atomKK->maxspecial,"atom:special");
memory->grow_kokkos(atomKK->k_num_bond,atomKK->num_bond,nmax,"atom:num_bond");
memory->grow_kokkos(atomKK->k_bond_type,atomKK->bond_type,nmax,atomKK->bond_per_atom,"atom:bond_type");
memory->grow_kokkos(atomKK->k_bond_atom,atomKK->bond_atom,nmax,atomKK->bond_per_atom,"atom:bond_atom");
grow_reset();
sync(Host,ALL_MASK);
if (atom->nextra_grow)
for (int iextra = 0; iextra < atomKK->nextra_grow; iextra++)
modify->fix[atom->extra_grow[iextra]]->grow_arrays(nmax);
}
/* ----------------------------------------------------------------------
reset local array ptrs
------------------------------------------------------------------------- */
void AtomVecBondKokkos::grow_reset()
{
tag = atomKK->tag;
d_tag = atomKK->k_tag.d_view;
h_tag = atomKK->k_tag.h_view;
type = atomKK->type;
d_type = atomKK->k_type.d_view;
h_type = atomKK->k_type.h_view;
mask = atomKK->mask;
d_mask = atomKK->k_mask.d_view;
h_mask = atomKK->k_mask.h_view;
image = atomKK->image;
d_image = atomKK->k_image.d_view;
h_image = atomKK->k_image.h_view;
x = atomKK->x;
d_x = atomKK->k_x.d_view;
h_x = atomKK->k_x.h_view;
v = atomKK->v;
d_v = atomKK->k_v.d_view;
h_v = atomKK->k_v.h_view;
f = atomKK->f;
d_f = atomKK->k_f.d_view;
h_f = atomKK->k_f.h_view;
molecule = atomKK->molecule;
d_molecule = atomKK->k_molecule.d_view;
h_molecule = atomKK->k_molecule.h_view;
nspecial = atomKK->nspecial;
d_nspecial = atomKK->k_nspecial.d_view;
h_nspecial = atomKK->k_nspecial.h_view;
special = atomKK->special;
d_special = atomKK->k_special.d_view;
h_special = atomKK->k_special.h_view;
num_bond = atomKK->num_bond;
d_num_bond = atomKK->k_num_bond.d_view;
h_num_bond = atomKK->k_num_bond.h_view;
bond_type = atomKK->bond_type;
d_bond_type = atomKK->k_bond_type.d_view;
h_bond_type = atomKK->k_bond_type.h_view;
bond_atom = atomKK->bond_atom;
d_bond_atom = atomKK->k_bond_atom.d_view;
h_bond_atom = atomKK->k_bond_atom.h_view;
}
/* ----------------------------------------------------------------------
copy atom I info to atom J
------------------------------------------------------------------------- */
void AtomVecBondKokkos::copy(int i, int j, int delflag)
{
int k;
h_tag[j] = h_tag[i];
h_type[j] = h_type[i];
mask[j] = mask[i];
h_image[j] = h_image[i];
h_x(j,0) = h_x(i,0);
h_x(j,1) = h_x(i,1);
h_x(j,2) = h_x(i,2);
h_v(j,0) = h_v(i,0);
h_v(j,1) = h_v(i,1);
h_v(j,2) = h_v(i,2);
h_molecule(j) = h_molecule(i);
h_num_bond(j) = h_num_bond(i);
for (k = 0; k < h_num_bond(j); k++) {
h_bond_type(j,k) = h_bond_type(i,k);
h_bond_atom(j,k) = h_bond_atom(i,k);
}
h_nspecial(j,0) = h_nspecial(i,0);
h_nspecial(j,1) = h_nspecial(i,1);
h_nspecial(j,2) = h_nspecial(i,2);
for (k = 0; k < h_nspecial(j,2); k++) h_special(j,k) = h_special(i,k);
if (atom->nextra_grow)
for (int iextra = 0; iextra < atom->nextra_grow; iextra++)
modify->fix[atom->extra_grow[iextra]]->copy_arrays(i,j,delflag);
}
/* ---------------------------------------------------------------------- */
template<class DeviceType,int PBC_FLAG,int TRICLINIC>
struct AtomVecBondKokkos_PackComm {
typedef DeviceType device_type;
typename ArrayTypes<DeviceType>::t_x_array_randomread _x;
typename ArrayTypes<DeviceType>::t_xfloat_2d_um _buf;
typename ArrayTypes<DeviceType>::t_int_2d_const _list;
const int _iswap;
X_FLOAT _xprd,_yprd,_zprd,_xy,_xz,_yz;
X_FLOAT _pbc[6];
AtomVecBondKokkos_PackComm(
const typename DAT::tdual_x_array &x,
const typename DAT::tdual_xfloat_2d &buf,
const typename DAT::tdual_int_2d &list,
const int & iswap,
const X_FLOAT &xprd, const X_FLOAT &yprd, const X_FLOAT &zprd,
const X_FLOAT &xy, const X_FLOAT &xz, const X_FLOAT &yz, const int* const pbc):
_x(x.view<DeviceType>()),_list(list.view<DeviceType>()),_iswap(iswap),
_xprd(xprd),_yprd(yprd),_zprd(zprd),
_xy(xy),_xz(xz),_yz(yz) {
const size_t maxsend = (buf.view<DeviceType>().dimension_0()*buf.view<DeviceType>().dimension_1())/3;
const size_t elements = 3;
buffer_view<DeviceType>(_buf,buf,maxsend,elements);
_pbc[0] = pbc[0]; _pbc[1] = pbc[1]; _pbc[2] = pbc[2];
_pbc[3] = pbc[3]; _pbc[4] = pbc[4]; _pbc[5] = pbc[5];
};
KOKKOS_INLINE_FUNCTION
void operator() (const int& i) const {
const int j = _list(_iswap,i);
if (PBC_FLAG == 0) {
_buf(i,0) = _x(j,0);
_buf(i,1) = _x(j,1);
_buf(i,2) = _x(j,2);
} else {
if (TRICLINIC == 0) {
_buf(i,0) = _x(j,0) + _pbc[0]*_xprd;
_buf(i,1) = _x(j,1) + _pbc[1]*_yprd;
_buf(i,2) = _x(j,2) + _pbc[2]*_zprd;
} else {
_buf(i,0) = _x(j,0) + _pbc[0]*_xprd + _pbc[5]*_xy + _pbc[4]*_xz;
_buf(i,1) = _x(j,1) + _pbc[1]*_yprd + _pbc[3]*_yz;
_buf(i,2) = _x(j,2) + _pbc[2]*_zprd;
}
}
}
};
/* ---------------------------------------------------------------------- */
int AtomVecBondKokkos::pack_comm_kokkos(const int &n,
const DAT::tdual_int_2d &list,
const int & iswap,
const DAT::tdual_xfloat_2d &buf,
const int &pbc_flag,
const int* const pbc)
{
// Check whether to always run forward communication on the host
// Choose correct forward PackComm kernel
if(commKK->forward_comm_on_host) {
sync(Host,X_MASK);
if(pbc_flag) {
if(domain->triclinic) {
struct AtomVecBondKokkos_PackComm<LMPHostType,1,1> f(atomKK->k_x,buf,list,iswap,
domain->xprd,domain->yprd,domain->zprd,
domain->xy,domain->xz,domain->yz,pbc);
Kokkos::parallel_for(n,f);
} else {
struct AtomVecBondKokkos_PackComm<LMPHostType,1,0> f(atomKK->k_x,buf,list,iswap,
domain->xprd,domain->yprd,domain->zprd,
domain->xy,domain->xz,domain->yz,pbc);
Kokkos::parallel_for(n,f);
}
} else {
if(domain->triclinic) {
struct AtomVecBondKokkos_PackComm<LMPHostType,0,1> f(atomKK->k_x,buf,list,iswap,
domain->xprd,domain->yprd,domain->zprd,
domain->xy,domain->xz,domain->yz,pbc);
Kokkos::parallel_for(n,f);
} else {
struct AtomVecBondKokkos_PackComm<LMPHostType,0,0> f(atomKK->k_x,buf,list,iswap,
domain->xprd,domain->yprd,domain->zprd,
domain->xy,domain->xz,domain->yz,pbc);
Kokkos::parallel_for(n,f);
}
}
LMPHostType::fence();
} else {
sync(Device,X_MASK);
if(pbc_flag) {
if(domain->triclinic) {
struct AtomVecBondKokkos_PackComm<LMPDeviceType,1,1> f(atomKK->k_x,buf,list,iswap,
domain->xprd,domain->yprd,domain->zprd,
domain->xy,domain->xz,domain->yz,pbc);
Kokkos::parallel_for(n,f);
} else {
struct AtomVecBondKokkos_PackComm<LMPDeviceType,1,0> f(atomKK->k_x,buf,list,iswap,
domain->xprd,domain->yprd,domain->zprd,
domain->xy,domain->xz,domain->yz,pbc);
Kokkos::parallel_for(n,f);
}
} else {
if(domain->triclinic) {
struct AtomVecBondKokkos_PackComm<LMPDeviceType,0,1> f(atomKK->k_x,buf,list,iswap,
domain->xprd,domain->yprd,domain->zprd,
domain->xy,domain->xz,domain->yz,pbc);
Kokkos::parallel_for(n,f);
} else {
struct AtomVecBondKokkos_PackComm<LMPDeviceType,0,0> f(atomKK->k_x,buf,list,iswap,
domain->xprd,domain->yprd,domain->zprd,
domain->xy,domain->xz,domain->yz,pbc);
Kokkos::parallel_for(n,f);
}
}
LMPDeviceType::fence();
}
return n*size_forward;
}
/* ---------------------------------------------------------------------- */
template<class DeviceType,int PBC_FLAG,int TRICLINIC>
struct AtomVecBondKokkos_PackCommSelf {
typedef DeviceType device_type;
typename ArrayTypes<DeviceType>::t_x_array_randomread _x;
typename ArrayTypes<DeviceType>::t_x_array _xw;
int _nfirst;
typename ArrayTypes<DeviceType>::t_int_2d_const _list;
const int _iswap;
X_FLOAT _xprd,_yprd,_zprd,_xy,_xz,_yz;
X_FLOAT _pbc[6];
AtomVecBondKokkos_PackCommSelf(
const typename DAT::tdual_x_array &x,
const int &nfirst,
const typename DAT::tdual_int_2d &list,
const int & iswap,
const X_FLOAT &xprd, const X_FLOAT &yprd, const X_FLOAT &zprd,
const X_FLOAT &xy, const X_FLOAT &xz, const X_FLOAT &yz, const int* const pbc):
_x(x.view<DeviceType>()),_xw(x.view<DeviceType>()),_nfirst(nfirst),_list(list.view<DeviceType>()),_iswap(iswap),
_xprd(xprd),_yprd(yprd),_zprd(zprd),
_xy(xy),_xz(xz),_yz(yz) {
_pbc[0] = pbc[0]; _pbc[1] = pbc[1]; _pbc[2] = pbc[2];
_pbc[3] = pbc[3]; _pbc[4] = pbc[4]; _pbc[5] = pbc[5];
};
KOKKOS_INLINE_FUNCTION
void operator() (const int& i) const {
const int j = _list(_iswap,i);
if (PBC_FLAG == 0) {
_xw(i+_nfirst,0) = _x(j,0);
_xw(i+_nfirst,1) = _x(j,1);
_xw(i+_nfirst,2) = _x(j,2);
} else {
if (TRICLINIC == 0) {
_xw(i+_nfirst,0) = _x(j,0) + _pbc[0]*_xprd;
_xw(i+_nfirst,1) = _x(j,1) + _pbc[1]*_yprd;
_xw(i+_nfirst,2) = _x(j,2) + _pbc[2]*_zprd;
} else {
_xw(i+_nfirst,0) = _x(j,0) + _pbc[0]*_xprd + _pbc[5]*_xy + _pbc[4]*_xz;
_xw(i+_nfirst,1) = _x(j,1) + _pbc[1]*_yprd + _pbc[3]*_yz;
_xw(i+_nfirst,2) = _x(j,2) + _pbc[2]*_zprd;
}
}
}
};
/* ---------------------------------------------------------------------- */
int AtomVecBondKokkos::pack_comm_self(const int &n, const DAT::tdual_int_2d &list, const int & iswap,
const int nfirst, const int &pbc_flag, const int* const pbc) {
if(commKK->forward_comm_on_host) {
sync(Host,X_MASK);
modified(Host,X_MASK);
if(pbc_flag) {
if(domain->triclinic) {
struct AtomVecBondKokkos_PackCommSelf<LMPHostType,1,1> f(atomKK->k_x,nfirst,list,iswap,
domain->xprd,domain->yprd,domain->zprd,
domain->xy,domain->xz,domain->yz,pbc);
Kokkos::parallel_for(n,f);
} else {
struct AtomVecBondKokkos_PackCommSelf<LMPHostType,1,0> f(atomKK->k_x,nfirst,list,iswap,
domain->xprd,domain->yprd,domain->zprd,
domain->xy,domain->xz,domain->yz,pbc);
Kokkos::parallel_for(n,f);
}
} else {
if(domain->triclinic) {
struct AtomVecBondKokkos_PackCommSelf<LMPHostType,0,1> f(atomKK->k_x,nfirst,list,iswap,
domain->xprd,domain->yprd,domain->zprd,
domain->xy,domain->xz,domain->yz,pbc);
Kokkos::parallel_for(n,f);
} else {
struct AtomVecBondKokkos_PackCommSelf<LMPHostType,0,0> f(atomKK->k_x,nfirst,list,iswap,
domain->xprd,domain->yprd,domain->zprd,
domain->xy,domain->xz,domain->yz,pbc);
Kokkos::parallel_for(n,f);
}
}
LMPHostType::fence();
} else {
sync(Device,X_MASK);
modified(Device,X_MASK);
if(pbc_flag) {
if(domain->triclinic) {
struct AtomVecBondKokkos_PackCommSelf<LMPDeviceType,1,1> f(atomKK->k_x,nfirst,list,iswap,
domain->xprd,domain->yprd,domain->zprd,
domain->xy,domain->xz,domain->yz,pbc);
Kokkos::parallel_for(n,f);
} else {
struct AtomVecBondKokkos_PackCommSelf<LMPDeviceType,1,0> f(atomKK->k_x,nfirst,list,iswap,
domain->xprd,domain->yprd,domain->zprd,
domain->xy,domain->xz,domain->yz,pbc);
Kokkos::parallel_for(n,f);
}
} else {
if(domain->triclinic) {
struct AtomVecBondKokkos_PackCommSelf<LMPDeviceType,0,1> f(atomKK->k_x,nfirst,list,iswap,
domain->xprd,domain->yprd,domain->zprd,
domain->xy,domain->xz,domain->yz,pbc);
Kokkos::parallel_for(n,f);
} else {
struct AtomVecBondKokkos_PackCommSelf<LMPDeviceType,0,0> f(atomKK->k_x,nfirst,list,iswap,
domain->xprd,domain->yprd,domain->zprd,
domain->xy,domain->xz,domain->yz,pbc);
Kokkos::parallel_for(n,f);
}
}
LMPDeviceType::fence();
}
return n*3;
}
/* ---------------------------------------------------------------------- */
template<class DeviceType>
struct AtomVecBondKokkos_UnpackComm {
typedef DeviceType device_type;
typename ArrayTypes<DeviceType>::t_x_array _x;
typename ArrayTypes<DeviceType>::t_xfloat_2d_const _buf;
int _first;
AtomVecBondKokkos_UnpackComm(
const typename DAT::tdual_x_array &x,
const typename DAT::tdual_xfloat_2d &buf,
const int& first):_x(x.view<DeviceType>()),_buf(buf.view<DeviceType>()),
_first(first) {};
KOKKOS_INLINE_FUNCTION
void operator() (const int& i) const {
_x(i+_first,0) = _buf(i,0);
_x(i+_first,1) = _buf(i,1);
_x(i+_first,2) = _buf(i,2);
}
};
/* ---------------------------------------------------------------------- */
void AtomVecBondKokkos::unpack_comm_kokkos(const int &n, const int &first,
const DAT::tdual_xfloat_2d &buf ) {
if(commKK->forward_comm_on_host) {
sync(Host,X_MASK);
modified(Host,X_MASK);
struct AtomVecBondKokkos_UnpackComm<LMPHostType> f(atomKK->k_x,buf,first);
Kokkos::parallel_for(n,f);
LMPDeviceType::fence();
} else {
sync(Device,X_MASK);
modified(Device,X_MASK);
struct AtomVecBondKokkos_UnpackComm<LMPDeviceType> f(atomKK->k_x,buf,first);
Kokkos::parallel_for(n,f);
LMPDeviceType::fence();
}
}
/* ---------------------------------------------------------------------- */
int AtomVecBondKokkos::pack_comm(int n, int *list, double *buf,
int pbc_flag, int *pbc)
{
int i,j,m;
double dx,dy,dz;
m = 0;
if (pbc_flag == 0) {
for (i = 0; i < n; i++) {
j = list[i];
buf[m++] = h_x(j,0);
buf[m++] = h_x(j,1);
buf[m++] = h_x(j,2);
}
} else {
if (domain->triclinic == 0) {
dx = pbc[0]*domain->xprd;
dy = pbc[1]*domain->yprd;
dz = pbc[2]*domain->zprd;
} else {
dx = pbc[0]*domain->xprd + pbc[5]*domain->xy + pbc[4]*domain->xz;
dy = pbc[1]*domain->yprd + pbc[3]*domain->yz;
dz = pbc[2]*domain->zprd;
}
for (i = 0; i < n; i++) {
j = list[i];
buf[m++] = h_x(j,0) + dx;
buf[m++] = h_x(j,1) + dy;
buf[m++] = h_x(j,2) + dz;
}
}
return m;
}
/* ---------------------------------------------------------------------- */
int AtomVecBondKokkos::pack_comm_vel(int n, int *list, double *buf,
int pbc_flag, int *pbc)
{
int i,j,m;
double dx,dy,dz,dvx,dvy,dvz;
m = 0;
if (pbc_flag == 0) {
for (i = 0; i < n; i++) {
j = list[i];
buf[m++] = h_x(j,0);
buf[m++] = h_x(j,1);
buf[m++] = h_x(j,2);
buf[m++] = h_v(j,0);
buf[m++] = h_v(j,1);
buf[m++] = h_v(j,2);
}
} else {
if (domain->triclinic == 0) {
dx = pbc[0]*domain->xprd;
dy = pbc[1]*domain->yprd;
dz = pbc[2]*domain->zprd;
} else {
dx = pbc[0]*domain->xprd + pbc[5]*domain->xy + pbc[4]*domain->xz;
dy = pbc[1]*domain->yprd + pbc[3]*domain->yz;
dz = pbc[2]*domain->zprd;
}
if (!deform_vremap) {
for (i = 0; i < n; i++) {
j = list[i];
buf[m++] = h_x(j,0) + dx;
buf[m++] = h_x(j,1) + dy;
buf[m++] = h_x(j,2) + dz;
buf[m++] = h_v(j,0);
buf[m++] = h_v(j,1);
buf[m++] = h_v(j,2);
}
} else {
dvx = pbc[0]*h_rate[0] + pbc[5]*h_rate[5] + pbc[4]*h_rate[4];
dvy = pbc[1]*h_rate[1] + pbc[3]*h_rate[3];
dvz = pbc[2]*h_rate[2];
for (i = 0; i < n; i++) {
j = list[i];
buf[m++] = h_x(j,0) + dx;
buf[m++] = h_x(j,1) + dy;
buf[m++] = h_x(j,2) + dz;
if (mask[i] & deform_groupbit) {
buf[m++] = h_v(j,0) + dvx;
buf[m++] = h_v(j,1) + dvy;
buf[m++] = h_v(j,2) + dvz;
} else {
buf[m++] = h_v(j,0);
buf[m++] = h_v(j,1);
buf[m++] = h_v(j,2);
}
}
}
}
return m;
}
/* ---------------------------------------------------------------------- */
void AtomVecBondKokkos::unpack_comm(int n, int first, double *buf)
{
int i,m,last;
m = 0;
last = first + n;
for (i = first; i < last; i++) {
h_x(i,0) = buf[m++];
h_x(i,1) = buf[m++];
h_x(i,2) = buf[m++];
}
}
/* ---------------------------------------------------------------------- */
void AtomVecBondKokkos::unpack_comm_vel(int n, int first, double *buf)
{
int i,m,last;
m = 0;
last = first + n;
for (i = first; i < last; i++) {
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++];
}
}
/* ---------------------------------------------------------------------- */
int AtomVecBondKokkos::pack_reverse(int n, int first, double *buf)
{
if(n > 0)
sync(Host,F_MASK);
int m = 0;
const int last = first + n;
for (int i = first; i < last; i++) {
buf[m++] = h_f(i,0);
buf[m++] = h_f(i,1);
buf[m++] = h_f(i,2);
}
return m;
}
/* ---------------------------------------------------------------------- */
void AtomVecBondKokkos::unpack_reverse(int n, int *list, double *buf)
{
if(n > 0)
modified(Host,F_MASK);
int m = 0;
for (int i = 0; i < n; i++) {
const int j = list[i];
h_f(j,0) += buf[m++];
h_f(j,1) += buf[m++];
h_f(j,2) += buf[m++];
}
}
/* ---------------------------------------------------------------------- */
template<class DeviceType,int PBC_FLAG>
struct AtomVecBondKokkos_PackBorder {
typedef DeviceType device_type;
typedef ArrayTypes<DeviceType> AT;
typename AT::t_xfloat_2d _buf;
const typename AT::t_int_2d_const _list;
const int _iswap;
const typename AT::t_x_array_randomread _x;
const typename AT::t_tagint_1d _tag;
const typename AT::t_int_1d _type;
const typename AT::t_int_1d _mask;
const typename AT::t_tagint_1d _molecule;
X_FLOAT _dx,_dy,_dz;
AtomVecBondKokkos_PackBorder(
const typename AT::t_xfloat_2d &buf,
const typename AT::t_int_2d_const &list,
const int & iswap,
const typename AT::t_x_array &x,
const typename AT::t_tagint_1d &tag,
const typename AT::t_int_1d &type,
const typename AT::t_int_1d &mask,
const typename AT::t_tagint_1d &molecule,
const X_FLOAT &dx, const X_FLOAT &dy, const X_FLOAT &dz):
_buf(buf),_list(list),_iswap(iswap),
_x(x),_tag(tag),_type(type),_mask(mask),_molecule(molecule),
_dx(dx),_dy(dy),_dz(dz) {}
KOKKOS_INLINE_FUNCTION
void operator() (const int& i) const {
const int j = _list(_iswap,i);
if (PBC_FLAG == 0) {
_buf(i,0) = _x(j,0);
_buf(i,1) = _x(j,1);
_buf(i,2) = _x(j,2);
_buf(i,3) = _tag(j);
_buf(i,4) = _type(j);
_buf(i,5) = _mask(j);
_buf(i,6) = _molecule(j);
} else {
_buf(i,0) = _x(j,0) + _dx;
_buf(i,1) = _x(j,1) + _dy;
_buf(i,2) = _x(j,2) + _dz;
_buf(i,3) = _tag(j);
_buf(i,4) = _type(j);
_buf(i,5) = _mask(j);
_buf(i,6) = _molecule(j);
}
}
};
/* ---------------------------------------------------------------------- */
int AtomVecBondKokkos::pack_border_kokkos(int n, DAT::tdual_int_2d k_sendlist,
DAT::tdual_xfloat_2d buf,int iswap,
int pbc_flag, int *pbc, ExecutionSpace space)
{
X_FLOAT dx,dy,dz;
if (pbc_flag != 0) {
if (domain->triclinic == 0) {
dx = pbc[0]*domain->xprd;
dy = pbc[1]*domain->yprd;
dz = pbc[2]*domain->zprd;
} else {
dx = pbc[0];
dy = pbc[1];
dz = pbc[2];
}
if(space==Host) {
AtomVecBondKokkos_PackBorder<LMPHostType,1> f(
buf.view<LMPHostType>(), k_sendlist.view<LMPHostType>(),
iswap,h_x,h_tag,h_type,h_mask,h_molecule,dx,dy,dz);
Kokkos::parallel_for(n,f);
LMPHostType::fence();
} else {
AtomVecBondKokkos_PackBorder<LMPDeviceType,1> f(
buf.view<LMPDeviceType>(), k_sendlist.view<LMPDeviceType>(),
iswap,d_x,d_tag,d_type,d_mask,d_molecule,dx,dy,dz);
Kokkos::parallel_for(n,f);
LMPDeviceType::fence();
}
} else {
dx = dy = dz = 0;
if(space==Host) {
AtomVecBondKokkos_PackBorder<LMPHostType,0> f(
buf.view<LMPHostType>(), k_sendlist.view<LMPHostType>(),
iswap,h_x,h_tag,h_type,h_mask,h_molecule,dx,dy,dz);
Kokkos::parallel_for(n,f);
LMPHostType::fence();
} else {
AtomVecBondKokkos_PackBorder<LMPDeviceType,0> f(
buf.view<LMPDeviceType>(), k_sendlist.view<LMPDeviceType>(),
iswap,d_x,d_tag,d_type,d_mask,d_molecule,dx,dy,dz);
Kokkos::parallel_for(n,f);
LMPDeviceType::fence();
}
}
return n*size_border;
}
/* ---------------------------------------------------------------------- */
int AtomVecBondKokkos::pack_border(int n, int *list, double *buf,
int pbc_flag, int *pbc)
{
int i,j,m;
double dx,dy,dz;
m = 0;
if (pbc_flag == 0) {
for (i = 0; i < n; i++) {
j = list[i];
buf[m++] = h_x(j,0);
buf[m++] = h_x(j,1);
buf[m++] = h_x(j,2);
buf[m++] = ubuf(h_tag(j)).d;
buf[m++] = ubuf(h_type(j)).d;
buf[m++] = ubuf(h_mask(j)).d;
buf[m++] = ubuf(h_molecule(j)).d;
}
} else {
if (domain->triclinic == 0) {
dx = pbc[0]*domain->xprd;
dy = pbc[1]*domain->yprd;
dz = pbc[2]*domain->zprd;
} else {
dx = pbc[0];
dy = pbc[1];
dz = pbc[2];
}
for (i = 0; i < n; i++) {
j = list[i];
buf[m++] = h_x(j,0) + dx;
buf[m++] = h_x(j,1) + dy;
buf[m++] = h_x(j,2) + dz;
buf[m++] = ubuf(h_tag(j)).d;
buf[m++] = ubuf(h_type(j)).d;
buf[m++] = ubuf(h_mask(j)).d;
buf[m++] = ubuf(h_molecule(j)).d;
}
}
if (atom->nextra_border)
for (int iextra = 0; iextra < atom->nextra_border; iextra++)
m += modify->fix[atom->extra_border[iextra]]->pack_border(n,list,&buf[m]);
return m;
}
/* ---------------------------------------------------------------------- */
int AtomVecBondKokkos::pack_border_vel(int n, int *list, double *buf,
int pbc_flag, int *pbc)
{
int i,j,m;
double dx,dy,dz,dvx,dvy,dvz;
m = 0;
if (pbc_flag == 0) {
for (i = 0; i < n; i++) {
j = list[i];
buf[m++] = h_x(j,0);
buf[m++] = h_x(j,1);
buf[m++] = h_x(j,2);
buf[m++] = ubuf(h_tag(j)).d;
buf[m++] = ubuf(h_type(j)).d;
buf[m++] = ubuf(h_mask(j)).d;
buf[m++] = ubuf(h_molecule(j)).d;
buf[m++] = h_v(j,0);
buf[m++] = h_v(j,1);
buf[m++] = h_v(j,2);
}
} else {
if (domain->triclinic == 0) {
dx = pbc[0]*domain->xprd;
dy = pbc[1]*domain->yprd;
dz = pbc[2]*domain->zprd;
} else {
dx = pbc[0];
dy = pbc[1];
dz = pbc[2];
}
if (!deform_vremap) {
for (i = 0; i < n; i++) {
j = list[i];
buf[m++] = h_x(j,0) + dx;
buf[m++] = h_x(j,1) + dy;
buf[m++] = h_x(j,2) + dz;
buf[m++] = ubuf(h_tag(j)).d;
buf[m++] = ubuf(h_type(j)).d;
buf[m++] = ubuf(h_mask(j)).d;
buf[m++] = ubuf(h_molecule(j)).d;
buf[m++] = h_v(j,0);
buf[m++] = h_v(j,1);
buf[m++] = h_v(j,2);
}
} else {
dvx = pbc[0]*h_rate[0] + pbc[5]*h_rate[5] + pbc[4]*h_rate[4];
dvy = pbc[1]*h_rate[1] + pbc[3]*h_rate[3];
dvz = pbc[2]*h_rate[2];
for (i = 0; i < n; i++) {
j = list[i];
buf[m++] = h_x(j,0) + dx;
buf[m++] = h_x(j,1) + dy;
buf[m++] = h_x(j,2) + dz;
buf[m++] = ubuf(h_tag(j)).d;
buf[m++] = ubuf(h_type(j)).d;
buf[m++] = ubuf(h_mask(j)).d;
buf[m++] = ubuf(h_molecule(j)).d;
if (mask[i] & deform_groupbit) {
buf[m++] = h_v(j,0) + dvx;
buf[m++] = h_v(j,1) + dvy;
buf[m++] = h_v(j,2) + dvz;
} else {
buf[m++] = h_v(j,0);
buf[m++] = h_v(j,1);
buf[m++] = h_v(j,2);
}
}
}
}
if (atom->nextra_border)
for (int iextra = 0; iextra < atom->nextra_border; iextra++)
m += modify->fix[atom->extra_border[iextra]]->pack_border(n,list,&buf[m]);
return m;
}
/* ---------------------------------------------------------------------- */
int AtomVecBondKokkos::pack_border_hybrid(int n, int *list, double *buf)
{
int i,j,m;
m = 0;
for (i = 0; i < n; i++) {
j = list[i];
buf[m++] = h_molecule(j);
}
return m;
}
/* ---------------------------------------------------------------------- */
template<class DeviceType>
struct AtomVecBondKokkos_UnpackBorder {
typedef DeviceType device_type;
typedef ArrayTypes<DeviceType> AT;
const typename AT::t_xfloat_2d_const _buf;
typename AT::t_x_array _x;
typename AT::t_tagint_1d _tag;
typename AT::t_int_1d _type;
typename AT::t_int_1d _mask;
typename AT::t_tagint_1d _molecule;
int _first;
AtomVecBondKokkos_UnpackBorder(
const typename AT::t_xfloat_2d_const &buf,
typename AT::t_x_array &x,
typename AT::t_tagint_1d &tag,
typename AT::t_int_1d &type,
typename AT::t_int_1d &mask,
typename AT::t_tagint_1d &molecule,
const int& first):
_buf(buf),_x(x),_tag(tag),_type(type),_mask(mask),_molecule(molecule),
_first(first){
};
KOKKOS_INLINE_FUNCTION
void operator() (const int& i) const {
_x(i+_first,0) = _buf(i,0);
_x(i+_first,1) = _buf(i,1);
_x(i+_first,2) = _buf(i,2);
_tag(i+_first) = static_cast<int> (_buf(i,3));
_type(i+_first) = static_cast<int> (_buf(i,4));
_mask(i+_first) = static_cast<int> (_buf(i,5));
_molecule(i+_first) = static_cast<int> (_buf(i,6));
}
};
/* ---------------------------------------------------------------------- */
void AtomVecBondKokkos::unpack_border_kokkos(const int &n, const int &first,
const DAT::tdual_xfloat_2d &buf,
ExecutionSpace space) {
modified(space,X_MASK|TAG_MASK|TYPE_MASK|MASK_MASK|MOLECULE_MASK);
while (first+n >= nmax) grow(0);
modified(space,X_MASK|TAG_MASK|TYPE_MASK|MASK_MASK|MOLECULE_MASK);
if(space==Host) {
struct AtomVecBondKokkos_UnpackBorder<LMPHostType>
f(buf.view<LMPHostType>(),h_x,h_tag,h_type,h_mask,h_molecule,first);
Kokkos::parallel_for(n,f);
LMPHostType::fence();
} else {
struct AtomVecBondKokkos_UnpackBorder<LMPDeviceType>
f(buf.view<LMPDeviceType>(),d_x,d_tag,d_type,d_mask,d_molecule,first);
Kokkos::parallel_for(n,f);
LMPDeviceType::fence();
}
}
/* ---------------------------------------------------------------------- */
void AtomVecBondKokkos::unpack_border(int n, int first, double *buf)
{
int i,m,last;
m = 0;
last = first + n;
for (i = first; i < last; i++) {
if (i == nmax) grow(0);
modified(Host,X_MASK|TAG_MASK|TYPE_MASK|MASK_MASK|MOLECULE_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_molecule(i) = (tagint) ubuf(buf[m++]).i;
}
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]);
}
/* ---------------------------------------------------------------------- */
void AtomVecBondKokkos::unpack_border_vel(int n, int first, double *buf)
{
int i,m,last;
m = 0;
last = first + n;
for (i = first; i < last; i++) {
if (i == nmax) grow(0);
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_molecule(i) = (tagint) 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]);
}
/* ---------------------------------------------------------------------- */
int AtomVecBondKokkos::unpack_border_hybrid(int n, int first, double *buf)
{
int i,m,last;
m = 0;
last = first + n;
for (i = first; i < last; i++)
h_molecule(i) = (tagint) ubuf(buf[m++]).i;
return m;
}
/* ---------------------------------------------------------------------- */
template<class DeviceType>
struct AtomVecBondKokkos_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_tagint_1d_randomread _molecule;
typename AT::t_int_2d_randomread _nspecial;
typename AT::t_tagint_2d_randomread _special;
typename AT::t_int_1d_randomread _num_bond;
typename AT::t_int_2d_randomread _bond_type;
typename AT::t_tagint_2d_randomread _bond_atom;
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_tagint_1d _moleculew;
typename AT::t_int_2d _nspecialw;
typename AT::t_tagint_2d _specialw;
typename AT::t_int_1d _num_bondw;
typename AT::t_int_2d _bond_typew;
typename AT::t_tagint_2d _bond_atomw;
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;
size_t elements;
AtomVecBondKokkos_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>()),
_molecule(atom->k_molecule.view<DeviceType>()),
_nspecial(atom->k_nspecial.view<DeviceType>()),
_special(atom->k_special.view<DeviceType>()),
_num_bond(atom->k_num_bond.view<DeviceType>()),
_bond_type(atom->k_bond_type.view<DeviceType>()),
_bond_atom(atom->k_bond_atom.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>()),
_moleculew(atom->k_molecule.view<DeviceType>()),
_nspecialw(atom->k_nspecial.view<DeviceType>()),
_specialw(atom->k_special.view<DeviceType>()),
_num_bondw(atom->k_num_bond.view<DeviceType>()),
_bond_typew(atom->k_bond_type.view<DeviceType>()),
_bond_atomw(atom->k_bond_atom.view<DeviceType>()),
_sendlist(sendlist.template view<DeviceType>()),
_copylist(copylist.template view<DeviceType>()),
_nlocal(nlocal),_dim(dim),
_lo(lo),_hi(hi){
// 3 comp of x, 3 comp of v, 1 tag, 1 type, 1 mask, 1 image, 1 molecule, 3 nspecial,
// maxspecial special, 1 num_bond, bond_per_atom bond_type, bond_per_atom bond_atom,
// 1 to store buffer lenght
elements = 16+atom->maxspecial+atom->bond_per_atom+atom->bond_per_atom;
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 {
int k;
const int i = _sendlist(mysend);
_buf(mysend,0) = elements;
int m = 1;
_buf(mysend,m++) = _x(i,0);
_buf(mysend,m++) = _x(i,1);
_buf(mysend,m++) = _x(i,2);
_buf(mysend,m++) = _v(i,0);
_buf(mysend,m++) = _v(i,1);
_buf(mysend,m++) = _v(i,2);
_buf(mysend,m++) = _tag(i);
_buf(mysend,m++) = _type(i);
_buf(mysend,m++) = _mask(i);
_buf(mysend,m++) = _image(i);
_buf(mysend,m++) = _molecule(i);
_buf(mysend,m++) = _num_bond(i);
for (k = 0; k < _num_bond(i); k++) {
_buf(mysend,m++) = _bond_type(i,k);
_buf(mysend,m++) = _bond_atom(i,k);
}
_buf(mysend,m++) = _nspecial(i,0);
_buf(mysend,m++) = _nspecial(i,1);
_buf(mysend,m++) = _nspecial(i,2);
for (k = 0; k < _nspecial(i,2); k++)
_buf(mysend,m++) = _special(i,k);
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);
_moleculew(i) = _molecule(j);
_num_bondw(i) = _num_bond(j);
for (k = 0; k < _num_bond(j); k++) {
_bond_typew(i,k) = _bond_type(j,k);
_bond_atomw(i,k) = _bond_atom(j,k);
}
_nspecialw(i,0) = _nspecial(j,0);
_nspecialw(i,1) = _nspecial(j,1);
_nspecialw(i,2) = _nspecial(j,2);
for (k = 0; k < _nspecial(j,2); k++)
_specialw(i,k) = _special(j,k);
}
}
};
/* ---------------------------------------------------------------------- */
int AtomVecBondKokkos::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 )
{
const int elements = 16+atomKK->maxspecial+atomKK->bond_per_atom+atomKK->bond_per_atom;
if(nsend > (int) (k_buf.view<LMPHostType>().dimension_0()*
k_buf.view<LMPHostType>().dimension_1())/elements) {
int newsize = nsend*elements/k_buf.view<LMPHostType>().dimension_1()+1;
k_buf.resize(newsize,k_buf.view<LMPHostType>().dimension_1());
}
if(space == Host) {
AtomVecBondKokkos_PackExchangeFunctor<LMPHostType>
f(atomKK,k_buf,k_sendlist,k_copylist,atom->nlocal,dim,lo,hi);
Kokkos::parallel_for(nsend,f);
LMPHostType::fence();
return nsend*elements;
} else {
AtomVecBondKokkos_PackExchangeFunctor<LMPDeviceType>
f(atomKK,k_buf,k_sendlist,k_copylist,atom->nlocal,dim,lo,hi);
Kokkos::parallel_for(nsend,f);
LMPDeviceType::fence();
return nsend*elements;
}
}
/* ---------------------------------------------------------------------- */
int AtomVecBondKokkos::pack_exchange(int i, double *buf)
{
int k;
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;
buf[m++] = ubuf(h_molecule(i)).d;
buf[m++] = ubuf(h_num_bond(i)).d;
for (k = 0; k < h_num_bond(i); k++) {
buf[m++] = ubuf(h_bond_type(i,k)).d;
buf[m++] = ubuf(h_bond_atom(i,k)).d;
}
buf[m++] = ubuf(h_nspecial(i,0)).d;
buf[m++] = ubuf(h_nspecial(i,1)).d;
buf[m++] = ubuf(h_nspecial(i,2)).d;
for (k = 0; k < h_nspecial(i,2); k++)
buf[m++] = ubuf(h_special(i,k)).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 AtomVecBondKokkos_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_tagint_1d _molecule;
typename AT::t_int_2d _nspecial;
typename AT::t_tagint_2d _special;
typename AT::t_int_1d _num_bond;
typename AT::t_int_2d _bond_type;
typename AT::t_tagint_2d _bond_atom;
typename AT::t_xfloat_2d_um _buf;
typename AT::t_int_1d _nlocal;
int _dim;
X_FLOAT _lo,_hi;
size_t elements;
AtomVecBondKokkos_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>()),
_molecule(atom->k_molecule.view<DeviceType>()),
_nspecial(atom->k_nspecial.view<DeviceType>()),
_special(atom->k_special.view<DeviceType>()),
_num_bond(atom->k_num_bond.view<DeviceType>()),
_bond_type(atom->k_bond_type.view<DeviceType>()),
_bond_atom(atom->k_bond_atom.view<DeviceType>()),
_nlocal(nlocal.template view<DeviceType>()),_dim(dim),
_lo(lo),_hi(hi){
elements = 16+atom->maxspecial+atom->bond_per_atom+atom->bond_per_atom;
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);
int m = 1;
_x(i,0) = _buf(myrecv,m++);
_x(i,1) = _buf(myrecv,m++);
_x(i,2) = _buf(myrecv,m++);
_v(i,0) = _buf(myrecv,m++);
_v(i,1) = _buf(myrecv,m++);
_v(i,2) = _buf(myrecv,m++);
_tag(i) = _buf(myrecv,m++);
_type(i) = _buf(myrecv,m++);
_mask(i) = _buf(myrecv,m++);
_image(i) = _buf(myrecv,m++);
_molecule(i) = _buf(myrecv,m++);
_num_bond(i) = _buf(myrecv,m++);
int k;
for (k = 0; k < _num_bond(i); k++) {
_bond_type(i,k) = _buf(myrecv,m++);
_bond_atom(i,k) = _buf(myrecv,m++);
}
_nspecial(i,0) = _buf(myrecv,m++);
_nspecial(i,1) = _buf(myrecv,m++);
_nspecial(i,2) = _buf(myrecv,m++);
for (k = 0; k < _nspecial(i,2); k++)
_special(i,k) = _buf(myrecv,m++);
}
}
};
/* ---------------------------------------------------------------------- */
int AtomVecBondKokkos::unpack_exchange_kokkos(DAT::tdual_xfloat_2d &k_buf,int nrecv,
int nlocal,int dim,X_FLOAT lo,X_FLOAT hi,
ExecutionSpace space) {
const size_t elements = 16+atomKK->maxspecial+atomKK->bond_per_atom+atomKK->bond_per_atom;
if(space == Host) {
k_count.h_view(0) = nlocal;
AtomVecBondKokkos_UnpackExchangeFunctor<LMPHostType>
f(atomKK,k_buf,k_count,dim,lo,hi);
Kokkos::parallel_for(nrecv/elements,f);
LMPHostType::fence();
return k_count.h_view(0);
} else {
k_count.h_view(0) = nlocal;
k_count.modify<LMPHostType>();
k_count.sync<LMPDeviceType>();
AtomVecBondKokkos_UnpackExchangeFunctor<LMPDeviceType>
f(atomKK,k_buf,k_count,dim,lo,hi);
Kokkos::parallel_for(nrecv/elements,f);
LMPDeviceType::fence();
k_count.modify<LMPDeviceType>();
k_count.sync<LMPHostType>();
return k_count.h_view(0);
}
}
/* ---------------------------------------------------------------------- */
int AtomVecBondKokkos::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 | MOLECULE_MASK | BOND_MASK | SPECIAL_MASK);
int k;
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;
h_molecule(nlocal) = (tagint) ubuf(buf[m++]).i;
h_num_bond(nlocal) = (int) ubuf(buf[m++]).i;
for (k = 0; k < h_num_bond(nlocal); k++) {
h_bond_type(nlocal,k) = (int) ubuf(buf[m++]).i;
h_bond_atom(nlocal,k) = (tagint) ubuf(buf[m++]).i;
}
h_nspecial(nlocal,0) = (int) ubuf(buf[m++]).i;
h_nspecial(nlocal,1) = (int) ubuf(buf[m++]).i;
h_nspecial(nlocal,2) = (int) ubuf(buf[m++]).i;
for (k = 0; k < h_nspecial(nlocal,2); k++)
h_special(nlocal,k) = (tagint) 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 AtomVecBondKokkos::size_restart()
{
int i;
int nlocal = atom->nlocal;
int n = 0;
for (i = 0; i < nlocal; i++)
n += 13 + 2*h_num_bond[i];
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 AtomVecBondKokkos::pack_restart(int i, double *buf)
{
sync(Host,X_MASK | V_MASK | TAG_MASK | TYPE_MASK |
MASK_MASK | IMAGE_MASK | MOLECULE_MASK | BOND_MASK | SPECIAL_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);
buf[m++] = ubuf(h_molecule(i)).d;
buf[m++] = ubuf(h_num_bond(i)).d;
for (int k = 0; k < h_num_bond(i); k++) {
buf[m++] = ubuf(MAX(h_bond_type(i,k),-h_bond_type(i,k))).d;
buf[m++] = ubuf(h_bond_atom(i,k)).d;
}
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 AtomVecBondKokkos::unpack_restart(double *buf)
{
int k;
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 | MOLECULE_MASK | BOND_MASK | SPECIAL_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++];
h_molecule(nlocal) = (tagint) ubuf(buf[m++]).i;
h_num_bond(nlocal) = (int) ubuf(buf[m++]).i;
for (k = 0; k < h_num_bond(nlocal); k++) {
h_bond_type(nlocal,k) = (int) ubuf(buf[m++]).i;
h_bond_atom(nlocal,k) = (tagint) ubuf(buf[m++]).i;
}
h_nspecial(nlocal,0) = h_nspecial(nlocal,1) = h_nspecial(nlocal,2) = 0;
double **extra = atom->extra;
if (atom->nextra_store) {
int size = static_cast<int> (ubuf(buf[m++]).i) - 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 AtomVecBondKokkos::create_atom(int itype, double *coord)
{
int nlocal = atom->nlocal;
if (nlocal == nmax) {
atomKK->modified(Host,ALL_MASK);
grow(0);
}
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) = ((imageint) IMGMAX << IMG2BITS) |
((imageint) IMGMAX << IMGBITS) | IMGMAX;
h_v(nlocal,0) = 0.0;
h_v(nlocal,1) = 0.0;
h_v(nlocal,2) = 0.0;
h_molecule(nlocal) = 0;
h_num_bond(nlocal) = 0;
h_nspecial(nlocal,0) = h_nspecial(nlocal,1) = h_nspecial(nlocal,2) = 0;
atom->nlocal++;
}
/* ----------------------------------------------------------------------
unpack one line from Atoms section of data file
initialize other atom quantities
------------------------------------------------------------------------- */
void AtomVecBondKokkos::data_atom(double *coord, imageint imagetmp,
char **values)
{
int nlocal = atomKK->nlocal;
if (nlocal == nmax) grow(0);
atomKK->modified(Host,ALL_MASK);
h_tag(nlocal) = atoi(values[0]);
h_molecule(nlocal) = atoi(values[1]);
h_type(nlocal) = atoi(values[2]);
if (h_type(nlocal) <= 0 || h_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;
h_num_bond(nlocal) = 0;
atomKK->nlocal++;
}
/* ----------------------------------------------------------------------
unpack hybrid quantities from one line in Atoms section of data file
initialize other atom quantities for this sub-style
------------------------------------------------------------------------- */
int AtomVecBondKokkos::data_atom_hybrid(int nlocal, char **values)
{
h_molecule(nlocal) = atoi(values[0]);
h_num_bond(nlocal) = 0;
return 1;
}
/* ----------------------------------------------------------------------
pack atom info for data file including 3 image flags
------------------------------------------------------------------------- */
void AtomVecBondKokkos::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_molecule(i);
buf[i][2] = h_type(i);
buf[i][3] = h_x(i,0);
buf[i][4] = h_x(i,1);
buf[i][5] = h_x(i,2);
buf[i][6] = (h_image[i] & IMGMASK) - IMGMAX;
buf[i][7] = (h_image[i] >> IMGBITS & IMGMASK) - IMGMAX;
buf[i][8] = (h_image[i] >> IMG2BITS) - IMGMAX;
}
}
/* ----------------------------------------------------------------------
pack hybrid atom info for data file
------------------------------------------------------------------------- */
int AtomVecBondKokkos::pack_data_hybrid(int i, double *buf)
{
buf[0] = h_molecule(i);
return 1;
}
/* ----------------------------------------------------------------------
write atom info to data file including 3 image flags
------------------------------------------------------------------------- */
void AtomVecBondKokkos::write_data(FILE *fp, int n, double **buf)
{
for (int i = 0; i < n; i++)
fprintf(fp,"%d %d %d %-1.16e %-1.16e %-1.16e %d %d %d\n",
(int) buf[i][0],(int) buf[i][1], (int) buf[i][2],
buf[i][3],buf[i][4],buf[i][5],
(int) buf[i][6],(int) buf[i][7],(int) buf[i][8]);
}
/* ----------------------------------------------------------------------
write hybrid atom info to data file
------------------------------------------------------------------------- */
int AtomVecBondKokkos::write_data_hybrid(FILE *fp, double *buf)
{
fprintf(fp," " TAGINT_FORMAT, (tagint) (buf[0]));
return 1;
}
/* ----------------------------------------------------------------------
return # of bytes of allocated memory
------------------------------------------------------------------------- */
bigint AtomVecBondKokkos::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);
if (atom->memcheck("molecule")) bytes += memory->usage(molecule,nmax);
if (atom->memcheck("nspecial")) bytes += memory->usage(nspecial,nmax,3);
if (atom->memcheck("special"))
bytes += memory->usage(special,nmax,atom->maxspecial);
if (atom->memcheck("num_bond")) bytes += memory->usage(num_bond,nmax);
if (atom->memcheck("bond_type"))
bytes += memory->usage(bond_type,nmax,atom->bond_per_atom);
if (atom->memcheck("bond_atom"))
bytes += memory->usage(bond_atom,nmax,atom->bond_per_atom);
return bytes;
}
/* ---------------------------------------------------------------------- */
void AtomVecBondKokkos::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>();
if (mask & MOLECULE_MASK) atomKK->k_molecule.sync<LMPDeviceType>();
if (mask & SPECIAL_MASK) {
atomKK->k_nspecial.sync<LMPDeviceType>();
atomKK->k_special.sync<LMPDeviceType>();
}
if (mask & BOND_MASK) {
atomKK->k_num_bond.sync<LMPDeviceType>();
atomKK->k_bond_type.sync<LMPDeviceType>();
atomKK->k_bond_atom.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>();
if (mask & MOLECULE_MASK) atomKK->k_molecule.sync<LMPHostType>();
if (mask & SPECIAL_MASK) {
atomKK->k_nspecial.sync<LMPHostType>();
atomKK->k_special.sync<LMPHostType>();
}
if (mask & BOND_MASK) {
atomKK->k_num_bond.sync<LMPHostType>();
atomKK->k_bond_type.sync<LMPHostType>();
atomKK->k_bond_atom.sync<LMPHostType>();
}
}
}
/* ---------------------------------------------------------------------- */
void AtomVecBondKokkos::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>();
if (mask & MOLECULE_MASK) atomKK->k_molecule.modify<LMPDeviceType>();
if (mask & SPECIAL_MASK) {
atomKK->k_nspecial.modify<LMPDeviceType>();
atomKK->k_special.modify<LMPDeviceType>();
}
if (mask & BOND_MASK) {
atomKK->k_num_bond.modify<LMPDeviceType>();
atomKK->k_bond_type.modify<LMPDeviceType>();
atomKK->k_bond_atom.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>();
if (mask & MOLECULE_MASK) atomKK->k_molecule.modify<LMPHostType>();
if (mask & SPECIAL_MASK) {
atomKK->k_nspecial.modify<LMPHostType>();
atomKK->k_special.modify<LMPHostType>();
}
if (mask & BOND_MASK) {
atomKK->k_num_bond.modify<LMPHostType>();
atomKK->k_bond_type.modify<LMPHostType>();
atomKK->k_bond_atom.modify<LMPHostType>();
}
}
}

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