Homec4science
Diffusion lammps (lammm-devel) Browse

lammps/src/KOKKOS/atom_vec_hybrid_kokkos.cpp
ca032f21fbfalammm-devel

Last Change
Raw File

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);
}
c4science · Help