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atom_vec_charge_kokkos.cpp
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Sun, Nov 10, 12:53

atom_vec_charge_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_charge_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
/* ---------------------------------------------------------------------- */
AtomVecChargeKokkos::AtomVecChargeKokkos(LAMMPS *lmp) : AtomVecKokkos(lmp)
{
molecular = 0;
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;
atom->q_flag = 1;
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 AtomVecChargeKokkos::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_q,atomKK->q,nmax,"atom:q");
grow_reset();
sync(Host,ALL_MASK);
if (atom->nextra_grow)
for (int iextra = 0; iextra < atom->nextra_grow; iextra++)
modify->fix[atom->extra_grow[iextra]]->grow_arrays(nmax);
}
/* ----------------------------------------------------------------------
reset local array ptrs
------------------------------------------------------------------------- */
void AtomVecChargeKokkos::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;
q = atomKK->q;
d_q = atomKK->k_q.d_view;
h_q = atomKK->k_q.h_view;
}
/* ----------------------------------------------------------------------
copy atom I info to atom J
------------------------------------------------------------------------- */
void AtomVecChargeKokkos::copy(int i, int j, int delflag)
{
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_q[j] = h_q[i];
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 AtomVecChargeKokkos_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];
AtomVecChargeKokkos_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 AtomVecChargeKokkos::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 AtomVecChargeKokkos_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 AtomVecChargeKokkos_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 AtomVecChargeKokkos_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 AtomVecChargeKokkos_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 AtomVecChargeKokkos_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 AtomVecChargeKokkos_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 AtomVecChargeKokkos_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 AtomVecChargeKokkos_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 AtomVecChargeKokkos_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];
AtomVecChargeKokkos_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 AtomVecChargeKokkos::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 AtomVecChargeKokkos_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 AtomVecChargeKokkos_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 AtomVecChargeKokkos_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 AtomVecChargeKokkos_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 AtomVecChargeKokkos_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 AtomVecChargeKokkos_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 AtomVecChargeKokkos_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 AtomVecChargeKokkos_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 AtomVecChargeKokkos_UnpackComm {
typedef DeviceType device_type;
typename ArrayTypes<DeviceType>::t_x_array _x;
typename ArrayTypes<DeviceType>::t_xfloat_2d_const _buf;
int _first;
AtomVecChargeKokkos_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 AtomVecChargeKokkos::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 AtomVecChargeKokkos_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 AtomVecChargeKokkos_UnpackComm<LMPDeviceType> f(atomKK->k_x,buf,first);
Kokkos::parallel_for(n,f);
LMPDeviceType::fence();
}
}
/* ---------------------------------------------------------------------- */
int AtomVecChargeKokkos::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 AtomVecChargeKokkos::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 AtomVecChargeKokkos::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 AtomVecChargeKokkos::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 AtomVecChargeKokkos::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 AtomVecChargeKokkos::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 AtomVecChargeKokkos_PackBorder {
typedef DeviceType device_type;
typename ArrayTypes<DeviceType>::t_xfloat_2d _buf;
const typename ArrayTypes<DeviceType>::t_int_2d_const _list;
const int _iswap;
const typename ArrayTypes<DeviceType>::t_x_array_randomread _x;
const typename ArrayTypes<DeviceType>::t_tagint_1d _tag;
const typename ArrayTypes<DeviceType>::t_int_1d _type;
const typename ArrayTypes<DeviceType>::t_int_1d _mask;
const typename ArrayTypes<DeviceType>::t_float_1d _q;
X_FLOAT _dx,_dy,_dz;
AtomVecChargeKokkos_PackBorder(
const typename ArrayTypes<DeviceType>::t_xfloat_2d &buf,
const typename ArrayTypes<DeviceType>::t_int_2d_const &list,
const int & iswap,
const typename ArrayTypes<DeviceType>::t_x_array &x,
const typename ArrayTypes<DeviceType>::t_tagint_1d &tag,
const typename ArrayTypes<DeviceType>::t_int_1d &type,
const typename ArrayTypes<DeviceType>::t_int_1d &mask,
const typename ArrayTypes<DeviceType>::t_float_1d &q,
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),_q(q),
_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) = _q(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) = _q(j);
}
}
};
/* ---------------------------------------------------------------------- */
int AtomVecChargeKokkos::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) {
AtomVecChargeKokkos_PackBorder<LMPHostType,1> f(
buf.view<LMPHostType>(), k_sendlist.view<LMPHostType>(),
iswap,h_x,h_tag,h_type,h_mask,h_q,dx,dy,dz);
Kokkos::parallel_for(n,f);
LMPHostType::fence();
} else {
AtomVecChargeKokkos_PackBorder<LMPDeviceType,1> f(
buf.view<LMPDeviceType>(), k_sendlist.view<LMPDeviceType>(),
iswap,d_x,d_tag,d_type,d_mask,d_q,dx,dy,dz);
Kokkos::parallel_for(n,f);
LMPDeviceType::fence();
}
} else {
dx = dy = dz = 0;
if(space==Host) {
AtomVecChargeKokkos_PackBorder<LMPHostType,0> f(
buf.view<LMPHostType>(), k_sendlist.view<LMPHostType>(),
iswap,h_x,h_tag,h_type,h_mask,h_q,dx,dy,dz);
Kokkos::parallel_for(n,f);
LMPHostType::fence();
} else {
AtomVecChargeKokkos_PackBorder<LMPDeviceType,0> f(
buf.view<LMPDeviceType>(), k_sendlist.view<LMPDeviceType>(),
iswap,d_x,d_tag,d_type,d_mask,d_q,dx,dy,dz);
Kokkos::parallel_for(n,f);
LMPDeviceType::fence();
}
}
return n*size_border;
}
/* ---------------------------------------------------------------------- */
int AtomVecChargeKokkos::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++] = h_q(j);
}
} 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++] = h_q(j);
}
}
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 AtomVecChargeKokkos::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++] = h_q[j];
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++] = h_q[j];
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++] = h_q[j];
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 AtomVecChargeKokkos::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_q[j];
}
return m;
}
/* ---------------------------------------------------------------------- */
template<class DeviceType>
struct AtomVecChargeKokkos_UnpackBorder {
typedef DeviceType device_type;
const typename ArrayTypes<DeviceType>::t_xfloat_2d_const _buf;
typename ArrayTypes<DeviceType>::t_x_array _x;
typename ArrayTypes<DeviceType>::t_tagint_1d _tag;
typename ArrayTypes<DeviceType>::t_int_1d _type;
typename ArrayTypes<DeviceType>::t_int_1d _mask;
typename ArrayTypes<DeviceType>::t_float_1d _q;
int _first;
AtomVecChargeKokkos_UnpackBorder(
const typename ArrayTypes<DeviceType>::t_xfloat_2d_const &buf,
typename ArrayTypes<DeviceType>::t_x_array &x,
typename ArrayTypes<DeviceType>::t_tagint_1d &tag,
typename ArrayTypes<DeviceType>::t_int_1d &type,
typename ArrayTypes<DeviceType>::t_int_1d &mask,
typename ArrayTypes<DeviceType>::t_float_1d &q,
const int& first):
_buf(buf),_x(x),_tag(tag),_type(type),_mask(mask),_q(q),_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));
_q(i+_first) = _buf(i,6);
}
};
/* ---------------------------------------------------------------------- */
void AtomVecChargeKokkos::unpack_border_kokkos(const int &n, const int &first,
const DAT::tdual_xfloat_2d &buf,ExecutionSpace space) {
if (first+n >= nmax) {
grow(first+n+100);
}
if(space==Host) {
struct AtomVecChargeKokkos_UnpackBorder<LMPHostType>
f(buf.view<LMPHostType>(),h_x,h_tag,h_type,h_mask,h_q,first);
Kokkos::parallel_for(n,f);
LMPHostType::fence();
} else {
struct AtomVecChargeKokkos_UnpackBorder<LMPDeviceType>
f(buf.view<LMPDeviceType>(),d_x,d_tag,d_type,d_mask,d_q,first);
Kokkos::parallel_for(n,f);
LMPDeviceType::fence();
}
modified(space,X_MASK|TAG_MASK|TYPE_MASK|MASK_MASK|Q_MASK);
}
/* ---------------------------------------------------------------------- */
void AtomVecChargeKokkos::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|Q_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_q[i] = 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]);
}
/* ---------------------------------------------------------------------- */
void AtomVecChargeKokkos::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);
modified(Host,X_MASK|V_MASK|TAG_MASK|TYPE_MASK|MASK_MASK|Q_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_q[i] = buf[m++];
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 AtomVecChargeKokkos::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_q[i] = buf[m++];
return m;
}
/* ---------------------------------------------------------------------- */
template<class DeviceType>
struct AtomVecChargeKokkos_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_float_1d_randomread _q;
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_float_1d _qw;
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;
AtomVecChargeKokkos_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>()),
_q(atom->k_q.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>()),
_qw(atom->k_q.view<DeviceType>()),
_sendlist(sendlist.template view<DeviceType>()),
_copylist(copylist.template view<DeviceType>()),
_nlocal(nlocal),_dim(dim),
_lo(lo),_hi(hi){
const size_t elements = 12;
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) = 12;
_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) = _tag[i];
_buf(mysend,8) = _type[i];
_buf(mysend,9) = _mask[i];
_buf(mysend,10) = _image[i];
_buf(mysend,11) = _q[i];
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);
_qw(i) = _q(j);
}
}
};
/* ---------------------------------------------------------------------- */
int AtomVecChargeKokkos::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())/12) {
int newsize = nsend*12/k_buf.view<LMPHostType>().dimension_1()+1;
k_buf.resize(newsize,k_buf.view<LMPHostType>().dimension_1());
}
if(space == Host) {
AtomVecChargeKokkos_PackExchangeFunctor<LMPHostType>
f(atomKK,k_buf,k_sendlist,k_copylist,atom->nlocal,dim,lo,hi);
Kokkos::parallel_for(nsend,f);
LMPHostType::fence();
return nsend*12;
} else {
AtomVecChargeKokkos_PackExchangeFunctor<LMPDeviceType>
f(atomKK,k_buf,k_sendlist,k_copylist,atom->nlocal,dim,lo,hi);
Kokkos::parallel_for(nsend,f);
LMPDeviceType::fence();
return nsend*12;
}
}
/* ---------------------------------------------------------------------- */
int AtomVecChargeKokkos::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;
buf[m++] = h_q[i];
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 AtomVecChargeKokkos_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_float_1d _q;
typename AT::t_xfloat_2d_um _buf;
typename AT::t_int_1d _nlocal;
int _dim;
X_FLOAT _lo,_hi;
AtomVecChargeKokkos_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>()),
_q(atom->k_q.view<DeviceType>()),
_nlocal(nlocal.template view<DeviceType>()),_dim(dim),
_lo(lo),_hi(hi){
const size_t elements = 12;
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] = _buf(myrecv,7);
_type[i] = _buf(myrecv,8);
_mask[i] = _buf(myrecv,9);
_image[i] = _buf(myrecv,10);
_q[i] = _buf(myrecv,11);
}
}
};
/* ---------------------------------------------------------------------- */
int AtomVecChargeKokkos::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;
AtomVecChargeKokkos_UnpackExchangeFunctor<LMPHostType> f(atomKK,k_buf,k_count,dim,lo,hi);
Kokkos::parallel_for(nrecv/12,f);
LMPHostType::fence();
return k_count.h_view(0);
} else {
k_count.h_view(0) = nlocal;
k_count.modify<LMPHostType>();
k_count.sync<LMPDeviceType>();
AtomVecChargeKokkos_UnpackExchangeFunctor<LMPDeviceType>
f(atomKK,k_buf,k_count,dim,lo,hi);
Kokkos::parallel_for(nrecv/12,f);
LMPDeviceType::fence();
k_count.modify<LMPDeviceType>();
k_count.sync<LMPHostType>();
return k_count.h_view(0);
}
}
/* ---------------------------------------------------------------------- */
int AtomVecChargeKokkos::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 | Q_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;
h_q[nlocal] = buf[m++];
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 AtomVecChargeKokkos::size_restart()
{
int i;
int nlocal = atom->nlocal;
int n = 12 * 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 AtomVecChargeKokkos::pack_restart(int i, double *buf)
{
sync(Host,X_MASK | V_MASK | TAG_MASK | TYPE_MASK |
MASK_MASK | IMAGE_MASK | Q_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++] = h_q[i];
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 AtomVecChargeKokkos::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 | Q_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_q[nlocal] = buf[m++];
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 AtomVecChargeKokkos::create_atom(int itype, double *coord)
{
int nlocal = atom->nlocal;
if (nlocal == nmax) {
atomKK->modified(Host,ALL_MASK);
grow(0);
}
atomKK->sync(Host,ALL_MASK);
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_q[nlocal] = 0.0;
atom->nlocal++;
}
/* ----------------------------------------------------------------------
unpack one line from Atoms section of data file
initialize other atom quantities
------------------------------------------------------------------------- */
void AtomVecChargeKokkos::data_atom(double *coord, imageint 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_q[nlocal] = atof(values[2]);
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++;
}
/* ----------------------------------------------------------------------
unpack hybrid quantities from one line in Atoms section of data file
initialize other atom quantities for this sub-style
------------------------------------------------------------------------- */
int AtomVecChargeKokkos::data_atom_hybrid(int nlocal, char **values)
{
h_q[nlocal] = atof(values[0]);
return 1;
}
/* ----------------------------------------------------------------------
pack atom info for data file including 3 image flags
------------------------------------------------------------------------- */
void AtomVecChargeKokkos::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_q[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 AtomVecChargeKokkos::pack_data_hybrid(int i, double *buf)
{
buf[0] = h_q[i];
return 1;
}
/* ----------------------------------------------------------------------
write atom info to data file including 3 image flags
------------------------------------------------------------------------- */
void AtomVecChargeKokkos::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 %-1.16e %d %d %d\n",
(int) buf[i][0],(int) buf[i][1],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 AtomVecChargeKokkos::write_data_hybrid(FILE *fp, double *buf)
{
fprintf(fp," %-1.16e",buf[0]);
return 1;
}
/* ----------------------------------------------------------------------
return # of bytes of allocated memory
------------------------------------------------------------------------- */
bigint AtomVecChargeKokkos::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("q")) bytes += memory->usage(q,nmax);
return bytes;
}
/* ---------------------------------------------------------------------- */
void AtomVecChargeKokkos::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 & Q_MASK) atomKK->k_q.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 & Q_MASK) atomKK->k_q.sync<LMPHostType>();
}
}
/* ---------------------------------------------------------------------- */
void AtomVecChargeKokkos::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 & Q_MASK) atomKK->k_q.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 & Q_MASK) atomKK->k_q.modify<LMPHostType>();
}
}
void AtomVecChargeKokkos::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);
if ((mask & MOLECULE_MASK) && atomKK->k_q.need_sync<LMPDeviceType>())
perform_async_copy<DAT::tdual_float_1d>(atomKK->k_q,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);
if ((mask & MOLECULE_MASK) && atomKK->k_q.need_sync<LMPHostType>())
perform_async_copy<DAT::tdual_float_1d>(atomKK->k_q,space);
}
}

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