Page Menu
Home
c4science
Search
Configure Global Search
Log In
Files
F68351645
atom_vec_hybrid_kokkos.cpp
No One
Temporary
Actions
Download File
Edit File
Delete File
View Transforms
Subscribe
Mute Notifications
Award Token
Subscribers
None
File Metadata
Details
File Info
Storage
Attached
Created
Thu, Jun 27, 00:37
Size
34 KB
Mime Type
text/x-c
Expires
Sat, Jun 29, 00:37 (2 d)
Engine
blob
Format
Raw Data
Handle
18569024
Attached To
rLAMMPS lammps
atom_vec_hybrid_kokkos.cpp
View Options
/* ----------------------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
http://lammps.sandia.gov, Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
#include <stdlib.h>
#include <string.h>
#include "atom_vec_hybrid_kokkos.h"
#include "atom_kokkos.h"
#include "domain.h"
#include "modify.h"
#include "fix.h"
#include "memory.h"
#include "error.h"
#include "atom_masks.h"
using namespace LAMMPS_NS;
/* ---------------------------------------------------------------------- */
AtomVecHybridKokkos::AtomVecHybridKokkos(LAMMPS *lmp) : AtomVecKokkos(lmp) {}
/* ---------------------------------------------------------------------- */
AtomVecHybridKokkos::~AtomVecHybridKokkos()
{
for (int k = 0; k < nstyles; k++) delete styles[k];
delete [] styles;
for (int k = 0; k < nstyles; k++) delete [] keywords[k];
delete [] keywords;
}
/* ----------------------------------------------------------------------
process sub-style args
------------------------------------------------------------------------- */
void AtomVecHybridKokkos::process_args(int narg, char **arg)
{
// build list of all known atom styles
build_styles();
// allocate list of sub-styles as big as possibly needed if no extra args
styles = new AtomVec*[narg];
keywords = new char*[narg];
// allocate each sub-style
// call process_args() with set of args that are not atom style names
// use known_style() to determine which args these are
int i,jarg,dummy;
int iarg = 0;
nstyles = 0;
while (iarg < narg) {
if (strcmp(arg[iarg],"hybrid") == 0)
error->all(FLERR,"Atom style hybrid cannot have hybrid as an argument");
for (i = 0; i < nstyles; i++)
if (strcmp(arg[iarg],keywords[i]) == 0)
error->all(FLERR,"Atom style hybrid cannot use same atom style twice");
styles[nstyles] = atom->new_avec(arg[iarg],1,dummy);
keywords[nstyles] = new char[strlen(arg[iarg])+1];
strcpy(keywords[nstyles],arg[iarg]);
jarg = iarg + 1;
while (jarg < narg && !known_style(arg[jarg])) jarg++;
styles[nstyles]->process_args(jarg-iarg-1,&arg[iarg+1]);
iarg = jarg;
nstyles++;
}
// free allstyles created by build_styles()
for (int i = 0; i < nallstyles; i++) delete [] allstyles[i];
delete [] allstyles;
// hybrid settings are MAX or MIN of sub-style settings
// hybrid sizes are minimal values plus extra values for each sub-style
molecular = 0;
comm_x_only = comm_f_only = 1;
size_forward = 3;
size_reverse = 3;
size_border = 6;
size_data_atom = 5;
size_data_vel = 4;
xcol_data = 3;
for (int k = 0; k < nstyles; k++) {
if ((styles[k]->molecular == 1 && molecular == 2) ||
(styles[k]->molecular == 2 && molecular == 1))
error->all(FLERR,"Cannot mix molecular and molecule template "
"atom styles");
molecular = MAX(molecular,styles[k]->molecular);
bonds_allow = MAX(bonds_allow,styles[k]->bonds_allow);
angles_allow = MAX(angles_allow,styles[k]->angles_allow);
dihedrals_allow = MAX(dihedrals_allow,styles[k]->dihedrals_allow);
impropers_allow = MAX(impropers_allow,styles[k]->impropers_allow);
mass_type = MAX(mass_type,styles[k]->mass_type);
dipole_type = MAX(dipole_type,styles[k]->dipole_type);
forceclearflag = MAX(forceclearflag,styles[k]->forceclearflag);
if (styles[k]->molecular == 2) onemols = styles[k]->onemols;
comm_x_only = MIN(comm_x_only,styles[k]->comm_x_only);
comm_f_only = MIN(comm_f_only,styles[k]->comm_f_only);
size_forward += styles[k]->size_forward - 3;
size_reverse += styles[k]->size_reverse - 3;
size_border += styles[k]->size_border - 6;
size_data_atom += styles[k]->size_data_atom - 5;
size_data_vel += styles[k]->size_data_vel - 4;
}
size_velocity = 3;
if (atom->omega_flag) size_velocity += 3;
if (atom->angmom_flag) size_velocity += 3;
}
/* ---------------------------------------------------------------------- */
void AtomVecHybridKokkos::init()
{
AtomVec::init();
for (int k = 0; k < nstyles; k++) styles[k]->init();
}
/* ----------------------------------------------------------------------
grow atom arrays
n = 0 grows arrays by a chunk
n > 0 allocates arrays to size n
------------------------------------------------------------------------- */
void AtomVecHybridKokkos::grow(int n)
{
if (n == 0) grow_nmax();
else nmax = n;
atom->nmax = nmax;
if (nmax < 0 || nmax > MAXSMALLINT)
error->one(FLERR,"Per-processor system is too big");
// sub-styles perform all reallocation
// turn off nextra_grow so hybrid can do that once below
int tmp = atom->nextra_grow;
atom->nextra_grow = 0;
for (int k = 0; k < nstyles; k++) styles[k]->grow(nmax);
atom->nextra_grow = tmp;
// insure hybrid local ptrs and sub-style ptrs are up to date
// for sub-styles, do this in case
// multiple sub-style reallocs of same array occurred
grow_reset();
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 AtomVecHybridKokkos::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;
v = atomKK->v;
d_v = atomKK->k_v.d_view;
h_v = atomKK->k_v.h_view;
omega = atomKK->omega;
d_omega = atomKK->k_omega.d_view;
h_omega = atomKK->k_omega.h_view;
angmom = atomKK->angmom;
d_angmom = atomKK->k_angmom.d_view;
h_angmom = atomKK->k_angmom.h_view;
for (int k = 0; k < nstyles; k++) styles[k]->grow_reset();
}
/* ----------------------------------------------------------------------
copy atom I info to atom J for all sub-styles
------------------------------------------------------------------------- */
void AtomVecHybridKokkos::copy(int i, int j, int delflag)
{
int tmp = atom->nextra_grow;
atom->nextra_grow = 0;
for (int k = 0; k < nstyles; k++) styles[k]->copy(i,j,delflag);
atom->nextra_grow = tmp;
if (atom->nextra_grow)
for (int iextra = 0; iextra < atom->nextra_grow; iextra++)
modify->fix[atom->extra_grow[iextra]]->copy_arrays(i,j,delflag);
}
/* ---------------------------------------------------------------------- */
void AtomVecHybridKokkos::clear_bonus()
{
for (int k = 0; k < nstyles; k++) styles[k]->clear_bonus();
}
/* ---------------------------------------------------------------------- */
void AtomVecHybridKokkos::force_clear(int n, size_t nbytes)
{
for (int k = 0; k < nstyles; k++)
if (styles[k]->forceclearflag) styles[k]->force_clear(n,nbytes);
}
/* ---------------------------------------------------------------------- */
int AtomVecHybridKokkos::pack_comm_kokkos(const int &n, const DAT::tdual_int_2d &k_sendlist,
const int & iswap,
const DAT::tdual_xfloat_2d &buf,
const int &pbc_flag, const int pbc[])
{
error->all(FLERR,"AtomVecHybridKokkos doesn't yet support threaded comm");
}
void AtomVecHybridKokkos::unpack_comm_kokkos(const int &n, const int &nfirst,
const DAT::tdual_xfloat_2d &buf)
{
error->all(FLERR,"AtomVecHybridKokkos doesn't yet support threaded comm");
}
int AtomVecHybridKokkos::pack_comm_self(const int &n, const DAT::tdual_int_2d &list,
const int & iswap, const int nfirst,
const int &pbc_flag, const int pbc[])
{
error->all(FLERR,"AtomVecHybridKokkos doesn't yet support threaded comm");
}
int AtomVecHybridKokkos::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)
{
error->all(FLERR,"AtomVecHybridKokkos doesn't yet support threaded comm");
}
void AtomVecHybridKokkos::unpack_border_kokkos(const int &n, const int &nfirst,
const DAT::tdual_xfloat_2d &buf,
ExecutionSpace space)
{
error->all(FLERR,"AtomVecHybridKokkos doesn't yet support threaded comm");
}
int AtomVecHybridKokkos::pack_exchange_kokkos(const int &nsend,DAT::tdual_xfloat_2d &buf,
DAT::tdual_int_1d k_sendlist,
DAT::tdual_int_1d k_copylist,
ExecutionSpace space, int dim,
X_FLOAT lo, X_FLOAT hi)
{
error->all(FLERR,"AtomVecHybridKokkos doesn't yet support threaded comm");
}
int AtomVecHybridKokkos::unpack_exchange_kokkos(DAT::tdual_xfloat_2d &k_buf, int nrecv,
int nlocal, int dim, X_FLOAT lo, X_FLOAT hi,
ExecutionSpace space)
{
error->all(FLERR,"AtomVecHybridKokkos doesn't yet support threaded comm");
}
/* ---------------------------------------------------------------------- */
int AtomVecHybridKokkos::pack_comm(int n, int *list, double *buf,
int pbc_flag, int *pbc)
{
sync(Host,X_MASK);
int i,j,k,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;
}
}
// pack sub-style contributions as contiguous chunks
for (k = 0; k < nstyles; k++)
m += styles[k]->pack_comm_hybrid(n,list,&buf[m]);
return m;
}
/* ---------------------------------------------------------------------- */
int AtomVecHybridKokkos::pack_comm_vel(int n, int *list, double *buf,
int pbc_flag, int *pbc)
{
sync(Host,X_MASK|V_MASK|OMEGA_MASK/*|ANGMOM_MASK*/);
int i,j,k,m;
double dx,dy,dz,dvx,dvy,dvz;
int omega_flag = atom->omega_flag;
int angmom_flag = atom->angmom_flag;
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);
if (omega_flag) {
buf[m++] = h_omega(j,0);
buf[m++] = h_omega(j,1);
buf[m++] = h_omega(j,2);
}
if (angmom_flag) {
buf[m++] = h_angmom(j,0);
buf[m++] = h_angmom(j,1);
buf[m++] = h_angmom(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);
if (omega_flag) {
buf[m++] = h_omega(j,0);
buf[m++] = h_omega(j,1);
buf[m++] = h_omega(j,2);
}
if (angmom_flag) {
buf[m++] = h_angmom(j,0);
buf[m++] = h_angmom(j,1);
buf[m++] = h_angmom(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 (h_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 (omega_flag) {
buf[m++] = h_omega(j,0);
buf[m++] = h_omega(j,1);
buf[m++] = h_omega(j,2);
}
if (angmom_flag) {
buf[m++] = h_angmom(j,0);
buf[m++] = h_angmom(j,1);
buf[m++] = h_angmom(j,2);
}
}
}
}
// pack sub-style contributions as contiguous chunks
for (k = 0; k < nstyles; k++)
m += styles[k]->pack_comm_hybrid(n,list,&buf[m]);
return m;
}
/* ---------------------------------------------------------------------- */
void AtomVecHybridKokkos::unpack_comm(int n, int first, double *buf)
{
int i,k,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++];
}
modified(Host,X_MASK);
// unpack sub-style contributions as contiguous chunks
for (k = 0; k < nstyles; k++)
m += styles[k]->unpack_comm_hybrid(n,first,&buf[m]);
}
/* ---------------------------------------------------------------------- */
void AtomVecHybridKokkos::unpack_comm_vel(int n, int first, double *buf)
{
int i,k,m,last;
int omega_flag = atom->omega_flag;
int angmom_flag = atom->angmom_flag;
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++];
if (omega_flag) {
h_omega(i,0) = buf[m++];
h_omega(i,1) = buf[m++];
h_omega(i,2) = buf[m++];
}
if (angmom_flag) {
h_angmom(i,0) = buf[m++];
h_angmom(i,1) = buf[m++];
h_angmom(i,2) = buf[m++];
}
}
modified(Host,X_MASK|V_MASK|OMEGA_MASK/*|ANGMOM_MASK*/);
// unpack sub-style contributions as contiguous chunks
for (k = 0; k < nstyles; k++)
m += styles[k]->unpack_comm_hybrid(n,first,&buf[m]);
}
/* ---------------------------------------------------------------------- */
int AtomVecHybridKokkos::pack_reverse(int n, int first, double *buf)
{
sync(Host,F_MASK);
int i,k,m,last;
m = 0;
last = first + n;
for (i = first; i < last; i++) {
buf[m++] = h_f(i,0);
buf[m++] = h_f(i,1);
buf[m++] = h_f(i,2);
}
// pack sub-style contributions as contiguous chunks
for (k = 0; k < nstyles; k++)
m += styles[k]->pack_reverse_hybrid(n,first,&buf[m]);
return m;
}
/* ---------------------------------------------------------------------- */
void AtomVecHybridKokkos::unpack_reverse(int n, int *list, double *buf)
{
int i,j,k,m;
m = 0;
for (i = 0; i < n; i++) {
j = list[i];
h_f(j,0) += buf[m++];
h_f(j,1) += buf[m++];
h_f(j,2) += buf[m++];
}
modified(Host,F_MASK);
// unpack sub-style contributions as contiguous chunks
for (k = 0; k < nstyles; k++)
m += styles[k]->unpack_reverse_hybrid(n,list,&buf[m]);
}
/* ---------------------------------------------------------------------- */
int AtomVecHybridKokkos::pack_border(int n, int *list, double *buf,
int pbc_flag, int *pbc)
{
sync(Host,X_MASK|TAG_MASK|TYPE_MASK|MASK_MASK);
int i,j,k,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;
}
} 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;
}
}
// pack sub-style contributions as contiguous chunks
for (k = 0; k < nstyles; k++)
m += styles[k]->pack_border_hybrid(n,list,&buf[m]);
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 AtomVecHybridKokkos::pack_border_vel(int n, int *list, double *buf,
int pbc_flag, int *pbc)
{
sync(Host,X_MASK|TAG_MASK|TYPE_MASK|MASK_MASK|V_MASK|OMEGA_MASK/*|ANGMOM_MASK*/);
int i,j,k,m;
double dx,dy,dz,dvx,dvy,dvz;
int omega_flag = atom->omega_flag;
int angmom_flag = atom->angmom_flag;
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_v(j,0);
buf[m++] = h_v(j,1);
buf[m++] = h_v(j,2);
if (omega_flag) {
buf[m++] = h_omega(j,0);
buf[m++] = h_omega(j,1);
buf[m++] = h_omega(j,2);
}
if (angmom_flag) {
buf[m++] = h_angmom(j,0);
buf[m++] = h_angmom(j,1);
buf[m++] = h_angmom(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_v(j,0);
buf[m++] = h_v(j,1);
buf[m++] = h_v(j,2);
if (omega_flag) {
buf[m++] = h_omega(j,0);
buf[m++] = h_omega(j,1);
buf[m++] = h_omega(j,2);
}
if (angmom_flag) {
buf[m++] = h_angmom(j,0);
buf[m++] = h_angmom(j,1);
buf[m++] = h_angmom(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;
if (h_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 (omega_flag) {
buf[m++] = h_omega(j,0);
buf[m++] = h_omega(j,1);
buf[m++] = h_omega(j,2);
}
if (angmom_flag) {
buf[m++] = h_angmom(j,0);
buf[m++] = h_angmom(j,1);
buf[m++] = h_angmom(j,2);
}
}
}
}
// pack sub-style contributions as contiguous chunks
for (k = 0; k < nstyles; k++)
m += styles[k]->pack_border_hybrid(n,list,&buf[m]);
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;
}
/* ---------------------------------------------------------------------- */
void AtomVecHybridKokkos::unpack_border(int n, int first, double *buf)
{
int i,k,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;
}
modified(Host,X_MASK|TAG_MASK|TYPE_MASK|MASK_MASK);
// unpack sub-style contributions as contiguous chunks
for (k = 0; k < nstyles; k++)
m += styles[k]->unpack_border_hybrid(n,first,&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 AtomVecHybridKokkos::unpack_border_vel(int n, int first, double *buf)
{
int i,k,m,last;
int omega_flag = atom->omega_flag;
int angmom_flag = atom->angmom_flag;
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_v(i,0) = buf[m++];
h_v(i,1) = buf[m++];
h_v(i,2) = buf[m++];
if (omega_flag) {
h_omega(i,0) = buf[m++];
h_omega(i,1) = buf[m++];
h_omega(i,2) = buf[m++];
}
if (angmom_flag) {
h_angmom(i,0) = buf[m++];
h_angmom(i,1) = buf[m++];
h_angmom(i,2) = buf[m++];
}
}
modified(Host,X_MASK|TAG_MASK|TYPE_MASK|MASK_MASK|V_MASK|OMEGA_MASK/*|ANGMOM_MASK*/);
// unpack sub-style contributions as contiguous chunks
for (k = 0; k < nstyles; k++)
m += styles[k]->unpack_border_hybrid(n,first,&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]);
}
/* ----------------------------------------------------------------------
pack data for atom I for sending to another proc
pack each sub-style one after the other
------------------------------------------------------------------------- */
int AtomVecHybridKokkos::pack_exchange(int i, double *buf)
{
int k,m;
int tmp = atom->nextra_grow;
atom->nextra_grow = 0;
m = 0;
for (k = 0; k < nstyles; k++)
m += styles[k]->pack_exchange(i,&buf[m]);
atom->nextra_grow = tmp;
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;
}
/* ----------------------------------------------------------------------
unpack data for single atom received from another proc
unpack each sub-style one after the other
grow() occurs here so arrays for all sub-styles are grown
------------------------------------------------------------------------- */
int AtomVecHybridKokkos::unpack_exchange(double *buf)
{
int k,m;
int nlocal = atom->nlocal;
if (nlocal == nmax) grow(0);
int tmp = atom->nextra_grow;
atom->nextra_grow = 0;
m = 0;
for (k = 0; k < nstyles; k++) {
m += styles[k]->unpack_exchange(&buf[m]);
atom->nlocal--;
}
atom->nextra_grow = tmp;
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 AtomVecHybridKokkos::size_restart()
{
int tmp = atom->nextra_restart;
atom->nextra_restart = 0;
int n = 0;
for (int k = 0; k < nstyles; k++)
n += styles[k]->size_restart();
atom->nextra_restart = tmp;
int nlocal = atom->nlocal;
if (atom->nextra_restart)
for (int iextra = 0; iextra < atom->nextra_restart; iextra++)
for (int 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
pack each sub-style one after the other
------------------------------------------------------------------------- */
int AtomVecHybridKokkos::pack_restart(int i, double *buf)
{
int tmp = atom->nextra_restart;
atom->nextra_restart = 0;
int m = 0;
for (int k = 0; k < nstyles; k++)
m += styles[k]->pack_restart(i,&buf[m]);
atom->nextra_restart = tmp;
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
unpack each sub-style one after the other
grow() occurs here so arrays for all sub-styles are grown
------------------------------------------------------------------------- */
int AtomVecHybridKokkos::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");
}
int tmp = atom->nextra_store;
atom->nextra_store = 0;
int m = 0;
for (int k = 0; k < nstyles; k++) {
m += styles[k]->unpack_restart(&buf[m]);
atom->nlocal--;
}
atom->nextra_store = tmp;
double **extra = atom->extra;
if (atom->nextra_store) {
int size = static_cast<int> (buf[0]) - m;
for (int i = 0; i < size; i++) extra[nlocal][i] = buf[m++];
}
atom->nlocal++;
return m;
}
/* ----------------------------------------------------------------------
create one atom of itype at coord
create each sub-style one after the other
grow() occurs here so arrays for all sub-styles are grown
------------------------------------------------------------------------- */
void AtomVecHybridKokkos::create_atom(int itype, double *coord)
{
int nlocal = atom->nlocal;
if (nlocal == nmax) grow(0);
for (int k = 0; k < nstyles; k++) {
styles[k]->create_atom(itype,coord);
atom->nlocal--;
}
atom->nlocal++;
}
/* ----------------------------------------------------------------------
unpack one line from Atoms section of data file
grow() occurs here so arrays for all sub-styles are grown
------------------------------------------------------------------------- */
void AtomVecHybridKokkos::data_atom(double *coord, imageint imagetmp, char **values)
{
sync(Host,X_MASK|TAG_MASK|TYPE_MASK|IMAGE_MASK|MASK_MASK|V_MASK|OMEGA_MASK/*|ANGMOM_MASK*/);
int nlocal = atom->nlocal;
if (nlocal == nmax) grow(0);
h_tag[nlocal] = ATOTAGINT(values[0]);
h_type[nlocal] = atoi(values[1]);
if (h_type[nlocal] <= 0 || h_type[nlocal] > atom->ntypes)
error->one(FLERR,"Invalid atom h_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;
if (atom->omega_flag) {
h_omega(nlocal,0) = 0.0;
h_omega(nlocal,1) = 0.0;
h_omega(nlocal,2) = 0.0;
}
if (atom->angmom_flag) {
h_angmom(nlocal,0) = 0.0;
h_angmom(nlocal,1) = 0.0;
h_angmom(nlocal,2) = 0.0;
}
modified(Host,X_MASK|TAG_MASK|TYPE_MASK|IMAGE_MASK|MASK_MASK|V_MASK|OMEGA_MASK/*|ANGMOM_MASK*/);
// each sub-style parses sub-style specific values
int m = 5;
for (int k = 0; k < nstyles; k++)
m += styles[k]->data_atom_hybrid(nlocal,&values[m]);
atom->nlocal++;
}
/* ----------------------------------------------------------------------
unpack one line from Velocities section of data file
------------------------------------------------------------------------- */
void AtomVecHybridKokkos::data_vel(int m, char **values)
{
sync(Host,V_MASK);
h_v(m,0) = atof(values[0]);
h_v(m,1) = atof(values[1]);
h_v(m,2) = atof(values[2]);
modified(Host,V_MASK);
// each sub-style parses sub-style specific values
int n = 3;
for (int k = 0; k < nstyles; k++)
n += styles[k]->data_vel_hybrid(m,&values[n]);
}
/* ----------------------------------------------------------------------
pack atom info for data file including 3 image flags
------------------------------------------------------------------------- */
void AtomVecHybridKokkos::pack_data(double **buf)
{
sync(Host,TAG_MASK|TYPE_MASK|X_MASK);
int k,m;
int nlocal = atom->nlocal;
for (int i = 0; i < nlocal; i++) {
buf[i][0] = ubuf(h_tag[i]).d;
buf[i][1] = ubuf(h_type[i]).d;
buf[i][2] = h_x(i,0);
buf[i][3] = h_x(i,1);
buf[i][4] = h_x(i,2);
m = 5;
for (k = 0; k < nstyles; k++)
m += styles[k]->pack_data_hybrid(i,&buf[i][m]);
buf[i][m] = ubuf((h_image[i] & IMGMASK) - IMGMAX).d;
buf[i][m+1] = ubuf((h_image[i] >> IMGBITS & IMGMASK) - IMGMAX).d;
buf[i][m+2] = ubuf((h_image[i] >> IMG2BITS) - IMGMAX).d;
}
}
/* ----------------------------------------------------------------------
write atom info to data file including 3 h_image flags
------------------------------------------------------------------------- */
void AtomVecHybridKokkos::write_data(FILE *fp, int n, double **buf)
{
int k,m;
for (int i = 0; i < n; i++) {
fprintf(fp,TAGINT_FORMAT " %d %-1.16e %-1.16e %-1.16e",
(tagint) ubuf(buf[i][0]).i,(int) ubuf(buf[i][1]).i,
buf[i][2],buf[i][3],buf[i][4]);
m = 5;
for (k = 0; k < nstyles; k++)
m += styles[k]->write_data_hybrid(fp,&buf[i][m]);
fprintf(fp," %d %d %d\n",
(int) ubuf(buf[i][m]).i,(int) ubuf(buf[i][m+1]).i,
(int) ubuf(buf[i][m+2]).i);
}
}
/* ----------------------------------------------------------------------
pack velocity info for data file
------------------------------------------------------------------------- */
void AtomVecHybridKokkos::pack_vel(double **buf)
{
sync(Host,V_MASK);
int k,m;
int nlocal = atom->nlocal;
for (int i = 0; i < nlocal; i++) {
buf[i][0] = ubuf(h_tag[i]).d;
buf[i][1] = h_v(i,0);
buf[i][2] = h_v(i,1);
buf[i][3] = h_v(i,2);
m = 4;
for (k = 0; k < nstyles; k++)
m += styles[k]->pack_vel_hybrid(i,&buf[i][m]);
}
}
/* ----------------------------------------------------------------------
write velocity info to data file
------------------------------------------------------------------------- */
void AtomVecHybridKokkos::write_vel(FILE *fp, int n, double **buf)
{
int k,m;
for (int i = 0; i < n; i++) {
fprintf(fp,TAGINT_FORMAT " %g %g %g",
(tagint) ubuf(buf[i][0]).i,buf[i][1],buf[i][2],buf[i][3]);
m = 4;
for (k = 0; k < nstyles; k++)
m += styles[k]->write_vel_hybrid(fp,&buf[i][m]);
fprintf(fp,"\n");
}
}
/* ----------------------------------------------------------------------
assign an index to named atom property and return index
returned value encodes which sub-style and index returned by sub-style
return -1 if name is unknown to any sub-styles
------------------------------------------------------------------------- */
int AtomVecHybridKokkos::property_atom(char *name)
{
for (int k = 0; k < nstyles; k++) {
int index = styles[k]->property_atom(name);
if (index >= 0) return index*nstyles + k;
}
return -1;
}
/* ----------------------------------------------------------------------
pack per-atom data into buf for ComputePropertyAtom
index maps to data specific to this atom style
------------------------------------------------------------------------- */
void AtomVecHybridKokkos::pack_property_atom(int multiindex, double *buf,
int nvalues, int groupbit)
{
int k = multiindex % nstyles;
int index = multiindex/nstyles;
styles[k]->pack_property_atom(index,buf,nvalues,groupbit);
}
/* ----------------------------------------------------------------------
allstyles = list of all atom styles in this LAMMPS executable
------------------------------------------------------------------------- */
void AtomVecHybridKokkos::build_styles()
{
nallstyles = 0;
#define ATOM_CLASS
#define AtomStyle(key,Class) nallstyles++;
#include "style_atom.h"
#undef AtomStyle
#undef ATOM_CLASS
allstyles = new char*[nallstyles];
int n;
nallstyles = 0;
#define ATOM_CLASS
#define AtomStyle(key,Class) \
n = strlen(#key) + 1; \
allstyles[nallstyles] = new char[n]; \
strcpy(allstyles[nallstyles],#key); \
nallstyles++;
#include "style_atom.h"
#undef AtomStyle
#undef ATOM_CLASS
}
/* ----------------------------------------------------------------------
allstyles = list of all known atom styles
------------------------------------------------------------------------- */
int AtomVecHybridKokkos::known_style(char *str)
{
for (int i = 0; i < nallstyles; i++)
if (strcmp(str,allstyles[i]) == 0) return 1;
return 0;
}
/* ----------------------------------------------------------------------
return # of bytes of allocated memory
------------------------------------------------------------------------- */
bigint AtomVecHybridKokkos::memory_usage()
{
bigint bytes = 0;
for (int k = 0; k < nstyles; k++) bytes += styles[k]->memory_usage();
return bytes;
}
/* ---------------------------------------------------------------------- */
void AtomVecHybridKokkos::sync(ExecutionSpace space, unsigned int h_mask)
{
for (int k = 0; k < nstyles; k++) ((AtomVecKokkos*) styles[k])->sync(space,h_mask);
}
/* ---------------------------------------------------------------------- */
void AtomVecHybridKokkos::sync_overlapping_device(ExecutionSpace space, unsigned int h_mask)
{
for (int k = 0; k < nstyles; k++) ((AtomVecKokkos*) styles[k])->sync_overlapping_device(space,h_mask);
}
/* ---------------------------------------------------------------------- */
void AtomVecHybridKokkos::modified(ExecutionSpace space, unsigned int h_mask)
{
for (int k = 0; k < nstyles; k++) ((AtomVecKokkos*) styles[k])->modified(space,h_mask);
}
Event Timeline
Log In to Comment