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Tue, May 28, 10:41

fix_shardlow_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.
------------------------------------------------------------------------- */
/* ----------------------------------------------------------------------
Contributing authors:
James Larentzos (U.S. Army Research Laboratory)
and Timothy I. Mattox (Engility Corporation)
Martin Lisal (Institute of Chemical Process Fundamentals
of the Czech Academy of Sciences and J. E. Purkinje University)
John Brennan, Joshua Moore and William Mattson (Army Research Lab)
Please cite the related publications:
J. P. Larentzos, J. K. Brennan, J. D. Moore, M. Lisal, W. D. Mattson,
"Parallel implementation of isothermal and isoenergetic Dissipative
Particle Dynamics using Shardlow-like splitting algorithms",
Computer Physics Communications, 2014, 185, pp 1987--1998.
M. Lisal, J. K. Brennan, J. Bonet Avalos, "Dissipative particle dynamics
at isothermal, isobaric, isoenergetic, and isoenthalpic conditions using
Shardlow-like splitting algorithms", Journal of Chemical Physics, 2011,
135, 204105.
------------------------------------------------------------------------- */
#include <stdio.h>
#include <stdlib.h>
#include <string.h>
#include "fix_shardlow_kokkos.h"
#include "atom.h"
#include "atom_masks.h"
#include "atom_kokkos.h"
#include "force.h"
#include "update.h"
#include "respa.h"
#include "error.h"
#include <math.h>
#include "atom_vec.h"
#include "comm.h"
#include "neighbor.h"
#include "neigh_list_kokkos.h"
#include "neigh_request.h"
#include "memory.h"
#include "domain.h"
#include "modify.h"
// #include "pair_dpd_fdt.h"
#include "pair_dpd_fdt_energy_kokkos.h"
#include "pair.h"
#include "npair_ssa_kokkos.h"
#include "citeme.h"
using namespace LAMMPS_NS;
using namespace FixConst;
#define EPSILON 1.0e-10
#define EPSILON_SQUARED ((EPSILON) * (EPSILON))
/* ---------------------------------------------------------------------- */
template<class DeviceType>
FixShardlowKokkos<DeviceType>::FixShardlowKokkos(LAMMPS *lmp, int narg, char **arg) :
FixShardlow(lmp, narg, arg), k_pairDPDE(NULL), ghostmax(0), nlocal(0) , nghost(0)
{
kokkosable = 1;
// atomKK = (AtomKokkos *) atom;
// execution_space = ExecutionSpaceFromDevice<DeviceType>::space;
// datamask_read = X_MASK | V_MASK | F_MASK | MASK_MASK | Q_MASK | TYPE_MASK;
// datamask_modify = Q_MASK | X_MASK;
if (narg != 3) error->all(FLERR,"Illegal fix shardlow command");
// k_pairDPD = NULL;
k_pairDPDE = NULL;
// k_pairDPD = (PairDPDfdtKokkos *) force->pair_match("dpd/fdt",1);
k_pairDPDE = dynamic_cast<PairDPDfdtEnergyKokkos<DeviceType> *>(force->pair_match("dpd/fdt/energy",0));
// if(k_pairDPDE){
comm_forward = 3;
comm_reverse = 5;
maxRNG = 0;
#ifdef DPD_USE_RAN_MARS
pp_random = NULL;
#endif
// } else {
// comm_forward = 3;
// comm_reverse = 3;
// }
if(/* k_pairDPD == NULL &&*/ k_pairDPDE == NULL)
error->all(FLERR,"Must use pair_style "/*"dpd/fdt/kk or "*/"dpd/fdt/energy/kk with fix shardlow/kk");
#ifdef DEBUG_PAIR_CT
d_counters = typename AT::t_int_2d("FixShardlowKokkos::d_counters", 2, 3);
d_hist = typename AT::t_int_1d("FixShardlowKokkos::d_hist", 32);
#ifndef KOKKOS_USE_CUDA_UVM
h_counters = Kokkos::create_mirror_view(d_counters);
h_hist = Kokkos::create_mirror_view(d_hist);
#else
h_counters = d_counters;
h_hist = d_hist;
#endif
#endif
}
/* ---------------------------------------------------------------------- */
template<class DeviceType>
FixShardlowKokkos<DeviceType>::~FixShardlowKokkos()
{
ghostmax = 0;
#ifdef DPD_USE_RAN_MARS
if (pp_random) {
for (int i = 1; i < maxRNG; ++i) delete pp_random[i];
delete[] pp_random;
pp_random = NULL;
}
#endif
}
/* ---------------------------------------------------------------------- */
template<class DeviceType>
int FixShardlowKokkos<DeviceType>::setmask()
{
int mask = 0;
mask |= INITIAL_INTEGRATE | PRE_NEIGHBOR;
return mask;
}
/* ---------------------------------------------------------------------- */
template<class DeviceType>
void FixShardlowKokkos<DeviceType>::init()
{
FixShardlow::init();
int irequest = neighbor->nrequest - 1;
neighbor->requests[irequest]->
kokkos_host = Kokkos::Impl::is_same<DeviceType,LMPHostType>::value &&
!Kokkos::Impl::is_same<DeviceType,LMPDeviceType>::value;
neighbor->requests[irequest]->
kokkos_device = Kokkos::Impl::is_same<DeviceType,LMPDeviceType>::value;
// neighbor->requests[irequest]->pair = 0;
// neighbor->requests[irequest]->fix = 1;
// neighbor->requests[irequest]->ghost= 1;
// neighbor->requests[irequest]->ssa = 1;
int ntypes = atom->ntypes;
k_params = Kokkos::DualView<params_ssa**,Kokkos::LayoutRight,DeviceType>
("FixShardlowKokkos::params",ntypes+1,ntypes+1);
params = k_params.template view<DeviceType>();
//FIXME either create cutsq and fill it in, or just point to pairDPD's...
// memory->destroy(cutsq); //FIXME
// memory->create_kokkos(k_cutsq,cutsq,ntypes+1,ntypes+1,"FixShardlowKokkos:cutsq");
d_cutsq = k_pairDPDE->k_cutsq.template view<DeviceType>(); //FIXME
const double boltz2 = 2.0*force->boltz;
for (int i = 1; i <= ntypes; i++) {
for (int j = i; j <= ntypes; j++) {
F_FLOAT cutone = k_pairDPDE->cut[i][j];
// k_cutsq.h_view(i,j) = k_cutsq.h_view(j,i) = cutone*cutone; //FIXME
if (cutone > EPSILON) k_params.h_view(i,j).cutinv = 1.0/cutone;
else k_params.h_view(i,j).cutinv = FLT_MAX;
k_params.h_view(i,j).halfsigma = 0.5*k_pairDPDE->sigma[i][j];
k_params.h_view(i,j).kappa = k_pairDPDE->kappa[i][j];
k_params.h_view(i,j).alpha = sqrt(boltz2*k_pairDPDE->kappa[i][j]);
k_params.h_view(j,i) = k_params.h_view(i,j);
if(i<MAX_TYPES_STACKPARAMS+1 && j<MAX_TYPES_STACKPARAMS+1) {
m_params[i][j] = m_params[j][i] = k_params.h_view(i,j);
m_cutsq[j][i] = m_cutsq[i][j] = k_pairDPDE->k_cutsq.h_view(i,j);
}
}
}
// k_cutsq.template modify<LMPHostType>();
k_params.template modify<LMPHostType>();
}
/* ---------------------------------------------------------------------- */
template<class DeviceType>
void FixShardlowKokkos<DeviceType>::init_list(int id, NeighList *ptr)
{
FixShardlow::init_list(id, ptr);
k_list = static_cast<NeighListKokkos<DeviceType>*>(ptr);
}
/* ---------------------------------------------------------------------- */
template<class DeviceType>
void FixShardlowKokkos<DeviceType>::pre_neighbor()
{
// NOTE: this logic is specific to orthogonal boxes, not triclinic
// Enforce the constraint that ghosts must be contained in the nearest sub-domains
double bbx = domain->subhi[0] - domain->sublo[0];
double bby = domain->subhi[1] - domain->sublo[1];
double bbz = domain->subhi[2] - domain->sublo[2];
double rcut = 2.0*neighbor->cutneighmax;
if (domain->triclinic)
error->all(FLERR,"Fix shardlow does not yet support triclinic geometries");
if(rcut >= bbx || rcut >= bby || rcut>= bbz )
{
char fmt[] = {"Shardlow algorithm requires sub-domain length > 2*(rcut+skin). Either reduce the number of processors requested, or change the cutoff/skin: rcut= %e bbx= %e bby= %e bbz= %e\n"};
char *msg = (char *) malloc(sizeof(fmt) + 4*15);
sprintf(msg, fmt, rcut, bbx, bby, bbz);
error->one(FLERR, msg);
}
nlocal = atomKK->nlocal;
nghost = atomKK->nghost;
// Allocate memory for h_v_t0 to hold the initial velocities for the ghosts
if (nghost > ghostmax) {
ghostmax = nghost;
k_v_t0 = DAT::tdual_v_array("FixShardlowKokkos:v_t0", ghostmax);
// d_v_t0 = k_v_t0.template view<DeviceType>();
h_v_t0 = k_v_t0.h_view;
}
// Setup views of relevant data
x = atomKK->k_x.template view<DeviceType>();
v = atomKK->k_v.template view<DeviceType>();
h_v = atomKK->k_v.h_view;
uCond = atomKK->k_uCond.template view<DeviceType>();
h_uCond = atomKK->k_uCond.h_view;
uMech = atomKK->k_uMech.template view<DeviceType>();
h_uMech = atomKK->k_uMech.h_view;
type = atomKK->k_type.view<DeviceType>();
if (atomKK->rmass) {
massPerI = true;
masses = atomKK->k_rmass.view<DeviceType>();
} else {
massPerI = false;
masses = atomKK->k_mass.view<DeviceType>();
}
// if(k_pairDPDE){
dpdTheta = atomKK->k_dpdTheta.view<DeviceType>();
//} else {
//}
}
template<class DeviceType>
void FixShardlowKokkos<DeviceType>::setup_pre_neighbor()
{
pre_neighbor();
}
/* ---------------------------------------------------------------------- */
#ifdef NOTNOW
/* ----------------------------------------------------------------------
Perform the stochastic integration and Shardlow update for constant temperature
Allow for both per-type and per-atom mass
NOTE: only implemented for orthogonal boxes, not triclinic
------------------------------------------------------------------------- */
template<class DeviceType>
template<bool STACKPARAMS>
void FixShardlowKokkos<DeviceType>::ssa_update_dpd(
int start_ii, int count, int id
)
{
#ifdef DPD_USE_RAN_MARS
class RanMars *pRNG = pp_random[id];
#else
rand_type rand_gen = rand_pool.get_state(id);
#endif
const double theta_ij_inv = 1.0/k_pairDPD->temperature; // independent of i,j
const double boltz_inv = 1.0/force->boltz;
const double ftm2v = force->ftm2v;
const double dt = update->dt;
int ct = count;
int ii = start_ii;
while (ct-- > 0) {
const int i = d_ilist(ii);
const int jlen = d_numneigh(ii);
const double xtmp = x(i, 0);
const double ytmp = x(i, 1);
const double ztmp = x(i, 2);
// load velocity for i from memory
double vxi = v(i, 0);
double vyi = v(i, 1);
double vzi = v(i, 2);
const int itype = type(i);
const double mass_i = masses(massPerI ? i : itype);
const double massinv_i = 1.0 / mass_i;
// Loop over Directional Neighbors only
for (int jj = 0; jj < jlen; jj++) {
const int j = d_neighbors(ii,jj) & NEIGHMASK;
int jtype = type[j];
const X_FLOAT delx = xtmp - x(j, 0);
const X_FLOAT dely = ytmp - x(j, 1);
const X_FLOAT delz = ztmp - x(j, 2);
const F_FLOAT rsq = delx*delx + dely*dely + delz*delz;
#ifdef DEBUG_PAIR_CT
if ((i < nlocal) && (j < nlocal)) Kokkos::atomic_increment(&(d_counters(0, 0)));
else Kokkos::atomic_increment(&(d_counters(0, 1)));
Kokkos::atomic_increment(&(d_counters(0, 2)));
int rsqi = rsq / 8;
if (rsqi < 0) rsqi = 0;
else if (rsqi > 31) rsqi = 31;
Kokkos::atomic_increment(&(d_hist(rsqi)));
#endif
// NOTE: r can be 0.0 in DPD systems, so do EPSILON_SQUARED test
if ((rsq < (STACKPARAMS?m_cutsq[itype][jtype]:d_cutsq(itype,jtype)))
&& (rsq >= EPSILON_SQUARED)) {
#ifdef DEBUG_PAIR_CT
if ((i < nlocal) && (j < nlocal)) Kokkos::atomic_increment(&(d_counters(1, 0)));
else Kokkos::atomic_increment(&(d_counters(1, 1)));
Kokkos::atomic_increment(&(d_counters(1, 2)));
#endif
double r = sqrt(rsq);
double rinv = 1.0/r;
double delx_rinv = delx*rinv;
double dely_rinv = dely*rinv;
double delz_rinv = delz*rinv;
double wr = 1.0 - r*(STACKPARAMS?m_params[itype][jtype].cutinv:params(itype,jtype).cutinv);
double wdt = wr*wr*dt;
double halfsigma_ij = STACKPARAMS?m_params[itype][jtype].halfsigma:params(itype,jtype).halfsigma;
double halfgamma_ij = halfsigma_ij*halfsigma_ij*boltz_inv*theta_ij_inv;
double sigmaRand = halfsigma_ij*wr*dtsqrt*ftm2v *
#ifdef DPD_USE_RAN_MARS
pRNG->gaussian();
#else
rand_gen.normal();
#endif
const double mass_j = masses(massPerI ? j : jtype);
double massinv_j = 1.0 / mass_j;
double gammaFactor = halfgamma_ij*wdt*ftm2v;
double inv_1p_mu_gammaFactor = 1.0/(1.0 + (massinv_i + massinv_j)*gammaFactor);
double vxj = v(j, 0);
double vyj = v(j, 1);
double vzj = v(j, 2);
// Compute the initial velocity difference between atom i and atom j
double delvx = vxi - vxj;
double delvy = vyi - vyj;
double delvz = vzi - vzj;
double dot_rinv = (delx_rinv*delvx + dely_rinv*delvy + delz_rinv*delvz);
// Compute momentum change between t and t+dt
double factorA = sigmaRand - gammaFactor*dot_rinv;
// Update the velocity on i
vxi += delx_rinv*factorA*massinv_i;
vyi += dely_rinv*factorA*massinv_i;
vzi += delz_rinv*factorA*massinv_i;
// Update the velocity on j
vxj -= delx_rinv*factorA*massinv_j;
vyj -= dely_rinv*factorA*massinv_j;
vzj -= delz_rinv*factorA*massinv_j;
//ii. Compute the new velocity diff
delvx = vxi - vxj;
delvy = vyi - vyj;
delvz = vzi - vzj;
dot_rinv = delx_rinv*delvx + dely_rinv*delvy + delz_rinv*delvz;
// Compute the new momentum change between t and t+dt
double factorB = (sigmaRand - gammaFactor*dot_rinv)*inv_1p_mu_gammaFactor;
// Update the velocity on i
vxi += delx_rinv*factorB*massinv_i;
vyi += dely_rinv*factorB*massinv_i;
vzi += delz_rinv*factorB*massinv_i;
// Update the velocity on j
vxj -= delx_rinv*factorB*massinv_j;
vyj -= dely_rinv*factorB*massinv_j;
vzj -= delz_rinv*factorB*massinv_j;
// Store updated velocity for j
v(j, 0) = vxj;
v(j, 1) = vyj;
v(j, 2) = vzj;
}
}
// store updated velocity for i
v(i, 0) = vxi;
v(i, 1) = vyi;
v(i, 2) = vzi;
}
#ifndef DPD_USE_RAN_MARS
rand_pool.free_state(rand_gen);
#endif
}
#endif
/* ----------------------------------------------------------------------
Perform the stochastic integration and Shardlow update for constant energy
Allow for both per-type and per-atom mass
NOTE: only implemented for orthogonal boxes, not triclinic
------------------------------------------------------------------------- */
template<class DeviceType>
template<bool STACKPARAMS>
KOKKOS_INLINE_FUNCTION
void FixShardlowKokkos<DeviceType>::ssa_update_dpde(
int start_ii, int count, int id
)
{
#ifdef DPD_USE_RAN_MARS
class RanMars *pRNG = pp_random[id];
#else
rand_type rand_gen = rand_pool.get_state(id);
#endif
const double boltz_inv = 1.0/force->boltz;
const double ftm2v = force->ftm2v;
const double dt = update->dt;
int ct = count;
int ii = start_ii;
while (ct-- > 0) {
const int i = d_ilist(ii);
const int jlen = d_numneigh(ii);
const double xtmp = x(i, 0);
const double ytmp = x(i, 1);
const double ztmp = x(i, 2);
// load velocity for i from memory
double vxi = v(i, 0);
double vyi = v(i, 1);
double vzi = v(i, 2);
double uMech_i = uMech(i);
double uCond_i = uCond(i);
const int itype = type(i);
const double theta_i_inv = 1.0/dpdTheta(i);
const double mass_i = masses(massPerI ? i : itype);
const double massinv_i = 1.0 / mass_i;
const double mass_i_div_neg4_ftm2v = mass_i*(-0.25)/ftm2v;
// Loop over Directional Neighbors only
for (int jj = 0; jj < jlen; jj++) {
const int j = d_neighbors(ii,jj) & NEIGHMASK;
const int jtype = type(j);
const X_FLOAT delx = xtmp - x(j, 0);
const X_FLOAT dely = ytmp - x(j, 1);
const X_FLOAT delz = ztmp - x(j, 2);
const F_FLOAT rsq = delx*delx + dely*dely + delz*delz;
#ifdef DEBUG_PAIR_CT
if ((i < nlocal) && (j < nlocal)) Kokkos::atomic_increment(&(d_counters(0, 0)));
else Kokkos::atomic_increment(&(d_counters(0, 1)));
Kokkos::atomic_increment(&(d_counters(0, 2)));
int rsqi = rsq / 8;
if (rsqi < 0) rsqi = 0;
else if (rsqi > 31) rsqi = 31;
Kokkos::atomic_increment(&(d_hist(rsqi)));
#endif
// NOTE: r can be 0.0 in DPD systems, so do EPSILON_SQUARED test
if ((rsq < (STACKPARAMS?m_cutsq[itype][jtype]:d_cutsq(itype,jtype)))
&& (rsq >= EPSILON_SQUARED)) {
#ifdef DEBUG_PAIR_CT
if ((i < nlocal) && (j < nlocal)) Kokkos::atomic_increment(&(d_counters(1, 0)));
else Kokkos::atomic_increment(&(d_counters(1, 1)));
Kokkos::atomic_increment(&(d_counters(1, 2)));
#endif
double r = sqrt(rsq);
double rinv = 1.0/r;
double delx_rinv = delx*rinv;
double dely_rinv = dely*rinv;
double delz_rinv = delz*rinv;
double wr = 1.0 - r*(STACKPARAMS?m_params[itype][jtype].cutinv:params(itype,jtype).cutinv);
double wdt = wr*wr*dt;
// Compute the current temperature
double theta_j_inv = 1.0/dpdTheta(j);
double theta_ij_inv = 0.5*(theta_i_inv + theta_j_inv);
double halfsigma_ij = STACKPARAMS?m_params[itype][jtype].halfsigma:params(itype,jtype).halfsigma;
double halfgamma_ij = halfsigma_ij*halfsigma_ij*boltz_inv*theta_ij_inv;
double sigmaRand = halfsigma_ij*wr*dtsqrt*ftm2v *
#ifdef DPD_USE_RAN_MARS
pRNG->gaussian();
#else
rand_gen.normal();
#endif
const double mass_j = masses(massPerI ? j : jtype);
double mass_ij_div_neg4_ftm2v = mass_j*mass_i_div_neg4_ftm2v;
double massinv_j = 1.0 / mass_j;
// Compute uCond
double kappa_ij = STACKPARAMS?m_params[itype][jtype].kappa:params(itype,jtype).kappa;
double alpha_ij = STACKPARAMS?m_params[itype][jtype].alpha:params(itype,jtype).alpha;
double del_uCond = alpha_ij*wr*dtsqrt *
#ifdef DPD_USE_RAN_MARS
pRNG->gaussian();
#else
rand_gen.normal();
#endif
del_uCond += kappa_ij*(theta_i_inv - theta_j_inv)*wdt;
uCond[j] -= del_uCond;
uCond_i += del_uCond;
double gammaFactor = halfgamma_ij*wdt*ftm2v;
double inv_1p_mu_gammaFactor = 1.0/(1.0 + (massinv_i + massinv_j)*gammaFactor);
double vxj = v(j, 0);
double vyj = v(j, 1);
double vzj = v(j, 2);
double dot4 = vxj*vxj + vyj*vyj + vzj*vzj;
double dot3 = vxi*vxi + vyi*vyi + vzi*vzi;
// Compute the initial velocity difference between atom i and atom j
double delvx = vxi - vxj;
double delvy = vyi - vyj;
double delvz = vzi - vzj;
double dot_rinv = (delx_rinv*delvx + dely_rinv*delvy + delz_rinv*delvz);
// Compute momentum change between t and t+dt
double factorA = sigmaRand - gammaFactor*dot_rinv;
// Update the velocity on i
vxi += delx_rinv*factorA*massinv_i;
vyi += dely_rinv*factorA*massinv_i;
vzi += delz_rinv*factorA*massinv_i;
// Update the velocity on j
vxj -= delx_rinv*factorA*massinv_j;
vyj -= dely_rinv*factorA*massinv_j;
vzj -= delz_rinv*factorA*massinv_j;
//ii. Compute the new velocity diff
delvx = vxi - vxj;
delvy = vyi - vyj;
delvz = vzi - vzj;
dot_rinv = delx_rinv*delvx + dely_rinv*delvy + delz_rinv*delvz;
// Compute the new momentum change between t and t+dt
double factorB = (sigmaRand - gammaFactor*dot_rinv)*inv_1p_mu_gammaFactor;
// Update the velocity on i
vxi += delx_rinv*factorB*massinv_i;
vyi += dely_rinv*factorB*massinv_i;
vzi += delz_rinv*factorB*massinv_i;
double partial_uMech = (vxi*vxi + vyi*vyi + vzi*vzi - dot3)*massinv_j;
// Update the velocity on j
vxj -= delx_rinv*factorB*massinv_j;
vyj -= dely_rinv*factorB*massinv_j;
vzj -= delz_rinv*factorB*massinv_j;
partial_uMech += (vxj*vxj + vyj*vyj + vzj*vzj - dot4)*massinv_i;
// Store updated velocity for j
v(j, 0) = vxj;
v(j, 1) = vyj;
v(j, 2) = vzj;
// Compute uMech
double del_uMech = partial_uMech*mass_ij_div_neg4_ftm2v;
uMech_i += del_uMech;
uMech(j) += del_uMech;
}
}
// store updated velocity for i
v(i, 0) = vxi;
v(i, 1) = vyi;
v(i, 2) = vzi;
// store updated uMech and uCond for i
uMech(i) = uMech_i;
uCond(i) = uCond_i;
ii++;
}
#ifndef DPD_USE_RAN_MARS
rand_pool.free_state(rand_gen);
#endif
}
template<class DeviceType>
void FixShardlowKokkos<DeviceType>::initial_integrate(int vflag)
{
d_numneigh = k_list->d_numneigh;
d_neighbors = k_list->d_neighbors;
d_ilist = k_list->d_ilist;
copymode = 1;
dtsqrt = sqrt(update->dt);
NPairSSAKokkos<DeviceType> *np_ssa = dynamic_cast<NPairSSAKokkos<DeviceType>*>(list->np);
if (!np_ssa) error->one(FLERR, "NPair wasn't a NPairSSAKokkos object");
ssa_phaseCt = np_ssa->ssa_phaseCt;
ssa_phaseLen = np_ssa->ssa_phaseLen;
ssa_itemLoc = np_ssa->ssa_itemLoc;
ssa_itemLen = np_ssa->ssa_itemLen;
ssa_gphaseCt = np_ssa->ssa_gphaseCt;
ssa_gphaseLen = np_ssa->ssa_gphaseLen;
ssa_gitemLoc = np_ssa->ssa_gitemLoc;
ssa_gitemLen = np_ssa->ssa_gitemLen;
int maxWorkItemCt = (int) ssa_itemLoc.dimension_1();
if (maxWorkItemCt < (int) ssa_gitemLoc.dimension_1()) {
maxWorkItemCt = (int) ssa_gitemLoc.dimension_1();
}
if (maxWorkItemCt > maxRNG) {
#ifdef DPD_USE_RAN_MARS
if (pp_random) {
for (int i = 1; i < maxRNG; ++i) delete pp_random[i];
delete[] pp_random;
pp_random = NULL;
}
pp_random = new RanMars*[maxWorkItemCt];
for (int i = 1; i < maxWorkItemCt; ++i) {
pp_random[i] = new RanMars(lmp, k_pairDPDE->seed + comm->me + comm->nprocs*i);
}
pp_random[0] = k_pairDPDE->random;
#else
rand_pool.init(k_pairDPDE->seed + comm->me, maxWorkItemCt);
#endif
maxRNG = maxWorkItemCt;
}
#ifdef DEBUG_PAIR_CT
for (int i = 0; i < 2; ++i)
for (int j = 0; j < 3; ++j)
h_counters(i,j) = 0;
for (int i = 0; i < 32; ++i) h_hist[i] = 0;
deep_copy(d_counters, h_counters);
deep_copy(d_hist, h_hist);
#endif
// process neighbors in the local AIR
for (int workPhase = 0; workPhase < ssa_phaseCt; ++workPhase) {
int workItemCt = ssa_phaseLen[workPhase];
if(atom->ntypes > MAX_TYPES_STACKPARAMS) {
Kokkos::parallel_for(workItemCt, LAMMPS_LAMBDA (const int workItem ) {
int ct = ssa_itemLen(workPhase, workItem);
int ii = ssa_itemLoc(workPhase, workItem);
ssa_update_dpde<false>(ii, ct, workItem);
});
} else {
Kokkos::parallel_for(workItemCt, LAMMPS_LAMBDA (const int workItem ) {
int ct = ssa_itemLen(workPhase, workItem);
int ii = ssa_itemLoc(workPhase, workItem);
ssa_update_dpde<true>(ii, ct, workItem);
});
}
}
//Loop over all 13 outward directions (7 stages)
for (int workPhase = 0; workPhase < ssa_gphaseCt; ++workPhase) {
// int airnum = workPhase + 1;
int workItemCt = ssa_gphaseLen[workPhase];
// Communicate the updated velocities to all nodes
comm->forward_comm_fix(this);
if(k_pairDPDE){
// Zero out the ghosts' uCond & uMech to be used as delta accumulators
// memset(&(atom->uCond[nlocal]), 0, sizeof(double)*nghost);
// memset(&(atom->uMech[nlocal]), 0, sizeof(double)*nghost);
Kokkos::parallel_for(Kokkos::RangePolicy<LMPDeviceType>(nlocal,nlocal+nghost), LAMMPS_LAMBDA (const int i) {
uCond(i) = 0.0;
uMech(i) = 0.0;
});
DeviceType::fence();
}
// process neighbors in this AIR
if(atom->ntypes > MAX_TYPES_STACKPARAMS) {
Kokkos::parallel_for(workItemCt, LAMMPS_LAMBDA (const int workItem ) {
int ct = ssa_gitemLen(workPhase, workItem);
int ii = ssa_gitemLoc(workPhase, workItem);
ssa_update_dpde<false>(ii, ct, workItem);
});
} else {
Kokkos::parallel_for(workItemCt, LAMMPS_LAMBDA (const int workItem ) {
int ct = ssa_gitemLen(workPhase, workItem);
int ii = ssa_gitemLoc(workPhase, workItem);
ssa_update_dpde<true>(ii, ct, workItem);
});
}
// Communicate the ghost deltas to the atom owners
comm->reverse_comm_fix(this);
} //End Loop over all directions For airnum = Top, Top-Right, Right, Bottom-Right, Back
#ifdef DEBUG_PAIR_CT
deep_copy(h_counters, d_counters);
deep_copy(h_hist, d_hist);
for (int i = 0; i < 32; ++i) fprintf(stdout, "%8d", h_hist[i]);
fprintf(stdout, "\n%6d %6d,%6d %6d: "
,h_counters(0, 2)
,h_counters(1, 2)
,h_counters(0, 1)
,h_counters(1, 1)
);
#endif
copymode = 0;
}
/* ---------------------------------------------------------------------- */
template<class DeviceType>
int FixShardlowKokkos<DeviceType>::pack_forward_comm(int n, int *list, double *buf, int pbc_flag, int *pbc)
{
int ii,jj,m;
m = 0;
for (ii = 0; ii < n; ii++) {
jj = list[ii];
buf[m++] = h_v(jj, 0);
buf[m++] = h_v(jj, 1);
buf[m++] = h_v(jj, 2);
}
return m;
}
/* ---------------------------------------------------------------------- */
template<class DeviceType>
void FixShardlowKokkos<DeviceType>::unpack_forward_comm(int n, int first, double *buf)
{
int ii,m,last;
m = 0;
last = first + n ;
for (ii = first; ii < last; ii++) {
h_v_t0(ii - nlocal, 0) = h_v(ii, 0) = buf[m++];
h_v_t0(ii - nlocal, 1) = h_v(ii, 1) = buf[m++];
h_v_t0(ii - nlocal, 2) = h_v(ii, 2) = buf[m++];
}
}
/* ---------------------------------------------------------------------- */
template<class DeviceType>
int FixShardlowKokkos<DeviceType>::pack_reverse_comm(int n, int first, double *buf)
{
int i,m,last;
m = 0;
last = first + n;
for (i = first; i < last; i++) {
buf[m++] = h_v(i, 0) - h_v_t0(i - nlocal, 0);
buf[m++] = h_v(i, 1) - h_v_t0(i - nlocal, 1);
buf[m++] = h_v(i, 2) - h_v_t0(i - nlocal, 2);
if(k_pairDPDE){
buf[m++] = h_uCond(i); // for ghosts, this is an accumulated delta
buf[m++] = h_uMech(i); // for ghosts, this is an accumulated delta
}
}
return m;
}
/* ---------------------------------------------------------------------- */
template<class DeviceType>
void FixShardlowKokkos<DeviceType>::unpack_reverse_comm(int n, int *list, double *buf)
{
int i,j,m;
m = 0;
for (i = 0; i < n; i++) {
j = list[i];
h_v(j, 0) += buf[m++];
h_v(j, 1) += buf[m++];
h_v(j, 2) += buf[m++];
if(k_pairDPDE){
h_uCond(j) += buf[m++]; // add in the accumulated delta
h_uMech(j) += buf[m++]; // add in the accumulated delta
}
}
}
/* ---------------------------------------------------------------------- */
template<class DeviceType>
double FixShardlowKokkos<DeviceType>::memory_usage()
{
double bytes = 0.0;
bytes += sizeof(double)*3*ghostmax; // v_t0[]
return bytes;
}
namespace LAMMPS_NS {
template class FixShardlowKokkos<LMPDeviceType>;
#ifdef KOKKOS_HAVE_CUDA
template class FixShardlowKokkos<LMPHostType>;
#endif
}

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