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fix_qeq_reax_kokkos.cpp
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Mon, May 27, 16:57

fix_qeq_reax_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 author: Ray Shan (SNL), Stan Moore (SNL)
------------------------------------------------------------------------- */
#include <math.h>
#include <stdio.h>
#include <stdlib.h>
#include <string.h>
#include "fix_qeq_reax_kokkos.h"
#include "kokkos.h"
#include "atom.h"
#include "atom_masks.h"
#include "atom_kokkos.h"
#include "comm.h"
#include "force.h"
#include "group.h"
#include "modify.h"
#include "neighbor.h"
#include "neigh_list_kokkos.h"
#include "neigh_request.h"
#include "update.h"
#include "integrate.h"
#include "respa.h"
#include "math_const.h"
#include "memory.h"
#include "error.h"
#include "pair_reax_c_kokkos.h"
using namespace LAMMPS_NS;
using namespace FixConst;
#define SMALL 0.0001
#define EV_TO_KCAL_PER_MOL 14.4
#define TEAMSIZE 128
/* ---------------------------------------------------------------------- */
template<class DeviceType>
FixQEqReaxKokkos<DeviceType>::FixQEqReaxKokkos(LAMMPS *lmp, int narg, char **arg) :
FixQEqReax(lmp, narg, arg)
{
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;
nmax = nmax = m_cap = 0;
allocated_flag = 0;
}
/* ---------------------------------------------------------------------- */
template<class DeviceType>
FixQEqReaxKokkos<DeviceType>::~FixQEqReaxKokkos()
{
if (copymode) return;
}
/* ---------------------------------------------------------------------- */
template<class DeviceType>
void FixQEqReaxKokkos<DeviceType>::init()
{
atomKK->k_q.modify<LMPHostType>();
atomKK->k_q.sync<LMPDeviceType>();
FixQEqReax::init();
neighflag = lmp->kokkos->neighflag;
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;
if (neighflag == FULL) {
neighbor->requests[irequest]->fix = 1;
neighbor->requests[irequest]->pair = 0;
neighbor->requests[irequest]->full = 1;
neighbor->requests[irequest]->half = 0;
} else { //if (neighflag == HALF || neighflag == HALFTHREAD)
neighbor->requests[irequest]->fix = 1;
neighbor->requests[irequest]->full = 0;
neighbor->requests[irequest]->half = 1;
neighbor->requests[irequest]->ghost = 1;
}
int ntypes = atom->ntypes;
k_params = Kokkos::DualView<params_qeq*,Kokkos::LayoutRight,DeviceType>
("FixQEqReax::params",ntypes+1);
params = k_params.template view<DeviceType>();
for (n = 1; n <= ntypes; n++) {
k_params.h_view(n).chi = chi[n];
k_params.h_view(n).eta = eta[n];
k_params.h_view(n).gamma = gamma[n];
}
k_params.template modify<LMPHostType>();
cutsq = swb * swb;
init_shielding_k();
init_hist();
}
/* ---------------------------------------------------------------------- */
template<class DeviceType>
void FixQEqReaxKokkos<DeviceType>::init_shielding_k()
{
int i,j;
int ntypes = atom->ntypes;
k_shield = DAT::tdual_ffloat_2d("qeq/kk:shield",ntypes+1,ntypes+1);
d_shield = k_shield.template view<DeviceType>();
for( i = 1; i <= ntypes; ++i )
for( j = 1; j <= ntypes; ++j )
k_shield.h_view(i,j) = pow( gamma[i] * gamma[j], -1.5 );
k_shield.template modify<LMPHostType>();
k_shield.template sync<DeviceType>();
k_tap = DAT::tdual_ffloat_1d("qeq/kk:tap",8);
d_tap = k_tap.template view<DeviceType>();
for (i = 0; i < 8; i ++)
k_tap.h_view(i) = Tap[i];
k_tap.template modify<LMPHostType>();
k_tap.template sync<DeviceType>();
}
/* ---------------------------------------------------------------------- */
template<class DeviceType>
void FixQEqReaxKokkos<DeviceType>::init_hist()
{
int i,j;
k_s_hist = DAT::tdual_ffloat_2d("qeq/kk:s_hist",atom->nmax,5);
d_s_hist = k_s_hist.template view<DeviceType>();
h_s_hist = k_s_hist.h_view;
k_t_hist = DAT::tdual_ffloat_2d("qeq/kk:t_hist",atom->nmax,5);
d_t_hist = k_t_hist.template view<DeviceType>();
h_t_hist = k_t_hist.h_view;
for( i = 0; i < atom->nmax; i++ )
for( j = 0; j < 5; j++ )
k_s_hist.h_view(i,j) = k_t_hist.h_view(i,j) = 0.0;
k_s_hist.template modify<LMPHostType>();
k_s_hist.template sync<DeviceType>();
k_t_hist.template modify<LMPHostType>();
k_t_hist.template sync<DeviceType>();
}
/* ---------------------------------------------------------------------- */
template<class DeviceType>
void FixQEqReaxKokkos<DeviceType>::setup_pre_force(int vflag)
{
//neighbor->build_one(list);
pre_force(vflag);
}
/* ---------------------------------------------------------------------- */
template<class DeviceType>
void FixQEqReaxKokkos<DeviceType>::pre_force(int vflag)
{
if (update->ntimestep % nevery) return;
atomKK->sync(execution_space,datamask_read);
atomKK->modified(execution_space,datamask_modify);
x = atomKK->k_x.view<DeviceType>();
v = atomKK->k_v.view<DeviceType>();
f = atomKK->k_f.view<DeviceType>();
q = atomKK->k_q.view<DeviceType>();
tag = atomKK->k_tag.view<DeviceType>();
type = atomKK->k_type.view<DeviceType>();
mask = atomKK->k_mask.view<DeviceType>();
nlocal = atomKK->nlocal;
nall = atom->nlocal + atom->nghost;
newton_pair = force->newton_pair;
k_params.template sync<DeviceType>();
k_shield.template sync<DeviceType>();
k_tap.template sync<DeviceType>();
NeighListKokkos<DeviceType>* k_list = static_cast<NeighListKokkos<DeviceType>*>(list);
d_numneigh = k_list->d_numneigh;
d_neighbors = k_list->d_neighbors;
d_ilist = k_list->d_ilist;
inum = list->inum;
k_list->clean_copy();
//cleanup_copy();
copymode = 1;
int teamsize = TEAMSIZE;
// allocate
allocate_array();
// get max number of neighbor
if (!allocated_flag || update->ntimestep == neighbor->lastcall)
allocate_matrix();
// compute_H
FixQEqReaxKokkosComputeHFunctor<DeviceType> computeH_functor(this);
Kokkos::parallel_scan(inum,computeH_functor);
DeviceType::fence();
// init_matvec
FixQEqReaxKokkosMatVecFunctor<DeviceType> matvec_functor(this);
Kokkos::parallel_for(inum,matvec_functor);
DeviceType::fence();
// comm->forward_comm_fix(this); //Dist_vector( s );
pack_flag = 2;
k_s.template modify<DeviceType>();
k_s.template sync<LMPHostType>();
comm->forward_comm_fix(this);
k_s.template modify<LMPHostType>();
k_s.template sync<DeviceType>();
// comm->forward_comm_fix(this); //Dist_vector( t );
pack_flag = 3;
k_t.template modify<DeviceType>();
k_t.template sync<LMPHostType>();
comm->forward_comm_fix(this);
k_t.template modify<LMPHostType>();
k_t.template sync<DeviceType>();
// 1st cg solve over b_s, s
cg_solve1();
DeviceType::fence();
// 2nd cg solve over b_t, t
cg_solve2();
DeviceType::fence();
// calculate_Q();
calculate_q();
DeviceType::fence();
copymode = 0;
if (!allocated_flag)
allocated_flag = 1;
}
/* ---------------------------------------------------------------------- */
template<class DeviceType>
KOKKOS_INLINE_FUNCTION
void FixQEqReaxKokkos<DeviceType>::num_neigh_item(int ii, int &maxneigh) const
{
const int i = d_ilist[ii];
maxneigh += d_numneigh[i];
}
/* ---------------------------------------------------------------------- */
template<class DeviceType>
void FixQEqReaxKokkos<DeviceType>::allocate_matrix()
{
int i,ii,m;
const int inum = list->inum;
nmax = atom->nmax;
// determine the total space for the H matrix
m_cap = 0;
FixQEqReaxKokkosNumNeighFunctor<DeviceType> neigh_functor(this);
Kokkos::parallel_reduce(inum,neigh_functor,m_cap);
d_firstnbr = typename AT::t_int_1d("qeq/kk:firstnbr",nmax);
d_numnbrs = typename AT::t_int_1d("qeq/kk:numnbrs",nmax);
d_jlist = typename AT::t_int_1d("qeq/kk:jlist",m_cap);
d_val = typename AT::t_ffloat_1d("qeq/kk:val",m_cap);
}
/* ---------------------------------------------------------------------- */
template<class DeviceType>
void FixQEqReaxKokkos<DeviceType>::allocate_array()
{
if (atom->nmax > nmax) {
nmax = atom->nmax;
k_o = DAT::tdual_ffloat_1d("qeq/kk:h_o",nmax);
d_o = k_o.template view<DeviceType>();
h_o = k_o.h_view;
d_Hdia_inv = typename AT::t_ffloat_1d("qeq/kk:h_Hdia_inv",nmax);
d_b_s = typename AT::t_ffloat_1d("qeq/kk:h_b_s",nmax);
d_b_t = typename AT::t_ffloat_1d("qeq/kk:h_b_t",nmax);
k_s = DAT::tdual_ffloat_1d("qeq/kk:h_s",nmax);
d_s = k_s.template view<DeviceType>();
h_s = k_s.h_view;
k_t = DAT::tdual_ffloat_1d("qeq/kk:h_t",nmax);
d_t = k_t.template view<DeviceType>();
h_t = k_t.h_view;
d_p = typename AT::t_ffloat_1d("qeq/kk:h_p",nmax);
d_r = typename AT::t_ffloat_1d("qeq/kk:h_r",nmax);
k_d = DAT::tdual_ffloat_1d("qeq/kk:h_d",nmax);
d_d = k_d.template view<DeviceType>();
h_d = k_d.h_view;
k_s_hist = DAT::tdual_ffloat_2d("qeq/kk:s_hist",nmax,5);
d_s_hist = k_s_hist.template view<DeviceType>();
h_s_hist = k_s_hist.h_view;
k_t_hist = DAT::tdual_ffloat_2d("qeq/kk:t_hist",nmax,5);
d_t_hist = k_t_hist.template view<DeviceType>();
h_t_hist = k_t_hist.h_view;
}
// init_storage
const int ignum = atom->nlocal + atom->nghost;
FixQEqReaxKokkosZeroFunctor<DeviceType> zero_functor(this);
Kokkos::parallel_for(ignum,zero_functor);
DeviceType::fence();
}
/* ---------------------------------------------------------------------- */
template<class DeviceType>
KOKKOS_INLINE_FUNCTION
void FixQEqReaxKokkos<DeviceType>::zero_item(int ii) const
{
const int i = d_ilist[ii];
const int itype = type(i);
if (mask[i] & groupbit) {
d_Hdia_inv[i] = 1.0 / params(itype).eta;
d_b_s[i] = -params(itype).chi;
d_b_t[i] = -1.0;
d_s[i] = 0.0;
d_t[i] = 0.0;
d_p[i] = 0.0;
d_o[i] = 0.0;
d_r[i] = 0.0;
d_d[i] = 0.0;
//for( int j = 0; j < 5; j++ )
//d_s_hist(i,j) = d_t_hist(i,j) = 0.0;
}
}
/* ---------------------------------------------------------------------- */
template<class DeviceType>
KOKKOS_INLINE_FUNCTION
void FixQEqReaxKokkos<DeviceType>::compute_h_item(int ii, int &m_fill, const bool &final) const
{
const int i = d_ilist[ii];
int j,jj,jtag,jtype,flag;
if (mask[i] & groupbit) {
const X_FLOAT xtmp = x(i,0);
const X_FLOAT ytmp = x(i,1);
const X_FLOAT ztmp = x(i,2);
const int itype = type(i);
const int itag = tag(i);
const int jnum = d_numneigh[i];
if (final)
d_firstnbr[i] = m_fill;
for (jj = 0; jj < jnum; jj++) {
j = d_neighbors(i,jj);
j &= NEIGHMASK;
jtype = type(j);
const X_FLOAT delx = x(j,0) - xtmp;
const X_FLOAT dely = x(j,1) - ytmp;
const X_FLOAT delz = x(j,2) - ztmp;
if (neighflag != FULL) {
flag = 0;
if (j < nlocal) flag = 1;
else if (tag[i] < tag[j]) flag = 1;
else if (tag[i] == tag[j]) {
if (delz > SMALL) flag = 1;
else if (fabs(delz) < SMALL) {
if (dely > SMALL) flag = 1;
else if (fabs(dely) < SMALL && delx > SMALL)
flag = 1;
}
}
if (!flag) continue;
}
const F_FLOAT rsq = delx*delx + dely*dely + delz*delz;
if (rsq > cutsq) continue;
if (final) {
const F_FLOAT r = sqrt(rsq);
d_jlist(m_fill) = j;
const F_FLOAT shldij = d_shield(itype,jtype);
d_val(m_fill) = calculate_H_k(r,shldij);
}
m_fill++;
}
if (final)
d_numnbrs[i] = m_fill - d_firstnbr[i];
}
}
/* ---------------------------------------------------------------------- */
template<class DeviceType>
KOKKOS_INLINE_FUNCTION
double FixQEqReaxKokkos<DeviceType>::calculate_H_k(const F_FLOAT &r, const F_FLOAT &shld) const
{
F_FLOAT taper, denom;
taper = d_tap[7] * r + d_tap[6];
taper = taper * r + d_tap[5];
taper = taper * r + d_tap[4];
taper = taper * r + d_tap[3];
taper = taper * r + d_tap[2];
taper = taper * r + d_tap[1];
taper = taper * r + d_tap[0];
denom = r * r * r + shld;
denom = pow(denom,0.3333333333333);
return taper * EV_TO_KCAL_PER_MOL / denom;
}
/* ---------------------------------------------------------------------- */
template<class DeviceType>
KOKKOS_INLINE_FUNCTION
void FixQEqReaxKokkos<DeviceType>::mat_vec_item(int ii) const
{
const int i = d_ilist[ii];
const int itype = type(i);
if (mask[i] & groupbit) {
d_Hdia_inv[i] = 1.0 / params(itype).eta;
d_b_s[i] = -params(itype).chi;
d_b_t[i] = -1.0;
d_t[i] = d_t_hist(i,2) + 3*(d_t_hist(i,0) - d_t_hist(i,1));
d_s[i] = 4*(d_s_hist(i,0)+d_s_hist(i,2))-(6*d_s_hist(i,1)+d_s_hist(i,3));
}
}
/* ---------------------------------------------------------------------- */
template<class DeviceType>
void FixQEqReaxKokkos<DeviceType>::cg_solve1()
// b = b_s, x = s;
{
const int inum = list->inum;
const int ignum = inum + list->gnum;
F_FLOAT tmp, sig_old, b_norm;
const int teamsize = TEAMSIZE;
// sparse_matvec( &H, x, q );
FixQEqReaxKokkosSparse12Functor<DeviceType> sparse12_functor(this);
Kokkos::parallel_for(inum,sparse12_functor);
DeviceType::fence();
if (neighflag != FULL) {
Kokkos::parallel_for(Kokkos::RangePolicy<DeviceType,TagZeroQGhosts>(nlocal,nlocal+atom->nghost),*this);
DeviceType::fence();
if (neighflag == HALF) {
FixQEqReaxKokkosSparse13Functor<DeviceType,HALF> sparse13_functor(this);
Kokkos::parallel_for(inum,sparse13_functor);
} else {
FixQEqReaxKokkosSparse13Functor<DeviceType,HALFTHREAD> sparse13_functor(this);
Kokkos::parallel_for(inum,sparse13_functor);
}
} else {
Kokkos::parallel_for(Kokkos::TeamPolicy <DeviceType, TagSparseMatvec1> (inum, teamsize), *this);
}
DeviceType::fence();
if (neighflag != FULL) {
k_o.template modify<DeviceType>();
k_o.template sync<LMPHostType>();
comm->reverse_comm_fix(this); //Coll_vector( q );
k_o.template modify<LMPHostType>();
k_o.template sync<DeviceType>();
}
// vector_sum( r , 1., b, -1., q, nn );
// preconditioning: d[j] = r[j] * Hdia_inv[j];
// b_norm = parallel_norm( b, nn );
F_FLOAT my_norm = 0.0;
FixQEqReaxKokkosNorm1Functor<DeviceType> norm1_functor(this);
Kokkos::parallel_reduce(inum,norm1_functor,my_norm);
DeviceType::fence();
F_FLOAT norm_sqr = 0.0;
MPI_Allreduce( &my_norm, &norm_sqr, 1, MPI_DOUBLE, MPI_SUM, world );
b_norm = sqrt(norm_sqr);
DeviceType::fence();
// sig_new = parallel_dot( r, d, nn);
F_FLOAT my_dot = 0.0;
FixQEqReaxKokkosDot1Functor<DeviceType> dot1_functor(this);
Kokkos::parallel_reduce(inum,dot1_functor,my_dot);
DeviceType::fence();
F_FLOAT dot_sqr = 0.0;
MPI_Allreduce( &my_dot, &dot_sqr, 1, MPI_DOUBLE, MPI_SUM, world );
F_FLOAT sig_new = dot_sqr;
DeviceType::fence();
int loop;
const int loopmax = 200;
for (loop = 1; loop < loopmax & sqrt(sig_new)/b_norm > tolerance; loop++) {
// comm->forward_comm_fix(this); //Dist_vector( d );
pack_flag = 1;
k_d.template modify<DeviceType>();
k_d.template sync<LMPHostType>();
comm->forward_comm_fix(this);
k_d.template modify<LMPHostType>();
k_d.template sync<DeviceType>();
// sparse_matvec( &H, d, q );
FixQEqReaxKokkosSparse22Functor<DeviceType> sparse22_functor(this);
Kokkos::parallel_for(inum,sparse22_functor);
DeviceType::fence();
if (neighflag != FULL) {
Kokkos::parallel_for(Kokkos::RangePolicy<DeviceType,TagZeroQGhosts>(nlocal,nlocal+atom->nghost),*this);
DeviceType::fence();
if (neighflag == HALF) {
FixQEqReaxKokkosSparse23Functor<DeviceType,HALF> sparse23_functor(this);
Kokkos::parallel_for(inum,sparse23_functor);
} else {
FixQEqReaxKokkosSparse23Functor<DeviceType,HALFTHREAD> sparse23_functor(this);
Kokkos::parallel_for(inum,sparse23_functor);
}
} else {
Kokkos::parallel_for(Kokkos::TeamPolicy <DeviceType, TagSparseMatvec2> (inum, teamsize), *this);
}
DeviceType::fence();
if (neighflag != FULL) {
k_o.template modify<DeviceType>();
k_o.template sync<LMPHostType>();
comm->reverse_comm_fix(this); //Coll_vector( q );
k_o.template modify<LMPHostType>();
k_o.template sync<DeviceType>();
}
// tmp = parallel_dot( d, q, nn);
my_dot = dot_sqr = 0.0;
FixQEqReaxKokkosDot2Functor<DeviceType> dot2_functor(this);
Kokkos::parallel_reduce(inum,dot2_functor,my_dot);
DeviceType::fence();
MPI_Allreduce( &my_dot, &dot_sqr, 1, MPI_DOUBLE, MPI_SUM, world );
tmp = dot_sqr;
alpha = sig_new / tmp;
sig_old = sig_new;
// vector_add( s, alpha, d, nn );
// vector_add( r, -alpha, q, nn );
my_dot = dot_sqr = 0.0;
FixQEqReaxKokkosPrecon1Functor<DeviceType> precon1_functor(this);
Kokkos::parallel_for(inum,precon1_functor);
DeviceType::fence();
// preconditioning: p[j] = r[j] * Hdia_inv[j];
// sig_new = parallel_dot( r, p, nn);
FixQEqReaxKokkosPreconFunctor<DeviceType> precon_functor(this);
Kokkos::parallel_reduce(inum,precon_functor,my_dot);
DeviceType::fence();
MPI_Allreduce( &my_dot, &dot_sqr, 1, MPI_DOUBLE, MPI_SUM, world );
sig_new = dot_sqr;
beta = sig_new / sig_old;
// vector_sum( d, 1., p, beta, d, nn );
FixQEqReaxKokkosVecSum2Functor<DeviceType> vecsum2_functor(this);
Kokkos::parallel_for(inum,vecsum2_functor);
DeviceType::fence();
}
if (loop >= loopmax && comm->me == 0) {
char str[128];
sprintf(str,"Fix qeq/reax cg_solve1 convergence failed after %d iterations "
"at " BIGINT_FORMAT " step: %f",loop,update->ntimestep,sqrt(sig_new)/b_norm);
error->warning(FLERR,str);
//error->all(FLERR,str);
}
}
/* ---------------------------------------------------------------------- */
template<class DeviceType>
void FixQEqReaxKokkos<DeviceType>::cg_solve2()
// b = b_t, x = t;
{
const int inum = list->inum;
const int ignum = inum + list->gnum;
F_FLOAT tmp, sig_old, b_norm;
const int teamsize = TEAMSIZE;
// sparse_matvec( &H, x, q );
FixQEqReaxKokkosSparse32Functor<DeviceType> sparse32_functor(this);
Kokkos::parallel_for(inum,sparse32_functor);
DeviceType::fence();
if (neighflag != FULL) {
Kokkos::parallel_for(Kokkos::RangePolicy<DeviceType,TagZeroQGhosts>(nlocal,nlocal+atom->nghost),*this);
DeviceType::fence();
if (neighflag == HALF) {
FixQEqReaxKokkosSparse33Functor<DeviceType,HALF> sparse33_functor(this);
Kokkos::parallel_for(inum,sparse33_functor);
} else {
FixQEqReaxKokkosSparse33Functor<DeviceType,HALFTHREAD> sparse33_functor(this);
Kokkos::parallel_for(inum,sparse33_functor);
}
} else {
Kokkos::parallel_for(Kokkos::TeamPolicy <DeviceType, TagSparseMatvec3> (inum, teamsize), *this);
}
DeviceType::fence();
if (neighflag != FULL) {
k_o.template modify<DeviceType>();
k_o.template sync<LMPHostType>();
comm->reverse_comm_fix(this); //Coll_vector( q );
k_o.template modify<LMPHostType>();
k_o.template sync<DeviceType>();
}
// vector_sum( r , 1., b, -1., q, nn );
// preconditioning: d[j] = r[j] * Hdia_inv[j];
// b_norm = parallel_norm( b, nn );
F_FLOAT my_norm = 0.0;
FixQEqReaxKokkosNorm2Functor<DeviceType> norm2_functor(this);
Kokkos::parallel_reduce(inum,norm2_functor,my_norm);
DeviceType::fence();
F_FLOAT norm_sqr = 0.0;
MPI_Allreduce( &my_norm, &norm_sqr, 1, MPI_DOUBLE, MPI_SUM, world );
b_norm = sqrt(norm_sqr);
DeviceType::fence();
// sig_new = parallel_dot( r, d, nn);
F_FLOAT my_dot = 0.0;
FixQEqReaxKokkosDot1Functor<DeviceType> dot1_functor(this);
Kokkos::parallel_reduce(inum,dot1_functor,my_dot);
DeviceType::fence();
F_FLOAT dot_sqr = 0.0;
MPI_Allreduce( &my_dot, &dot_sqr, 1, MPI_DOUBLE, MPI_SUM, world );
F_FLOAT sig_new = dot_sqr;
DeviceType::fence();
int loop;
const int loopmax = 200;
for (loop = 1; loop < loopmax & sqrt(sig_new)/b_norm > tolerance; loop++) {
// comm->forward_comm_fix(this); //Dist_vector( d );
pack_flag = 1;
k_d.template modify<DeviceType>();
k_d.template sync<LMPHostType>();
comm->forward_comm_fix(this);
k_d.template modify<LMPHostType>();
k_d.template sync<DeviceType>();
// sparse_matvec( &H, d, q );
FixQEqReaxKokkosSparse22Functor<DeviceType> sparse22_functor(this);
Kokkos::parallel_for(inum,sparse22_functor);
DeviceType::fence();
if (neighflag != FULL) {
Kokkos::parallel_for(Kokkos::RangePolicy<DeviceType,TagZeroQGhosts>(nlocal,nlocal+atom->nghost),*this);
DeviceType::fence();
if (neighflag == HALF) {
FixQEqReaxKokkosSparse23Functor<DeviceType,HALF> sparse23_functor(this);
Kokkos::parallel_for(inum,sparse23_functor);
} else {
FixQEqReaxKokkosSparse23Functor<DeviceType,HALFTHREAD> sparse23_functor(this);
Kokkos::parallel_for(inum,sparse23_functor);
}
} else {
Kokkos::parallel_for(Kokkos::TeamPolicy <DeviceType, TagSparseMatvec2> (inum, teamsize), *this);
}
DeviceType::fence();
if (neighflag != FULL) {
k_o.template modify<DeviceType>();
k_o.template sync<LMPHostType>();
comm->reverse_comm_fix(this); //Coll_vector( q );
k_o.template modify<LMPHostType>();
k_o.template sync<DeviceType>();
}
// tmp = parallel_dot( d, q, nn);
my_dot = dot_sqr = 0.0;
FixQEqReaxKokkosDot2Functor<DeviceType> dot2_functor(this);
Kokkos::parallel_reduce(inum,dot2_functor,my_dot);
DeviceType::fence();
MPI_Allreduce( &my_dot, &dot_sqr, 1, MPI_DOUBLE, MPI_SUM, world );
tmp = dot_sqr;
DeviceType::fence();
alpha = sig_new / tmp;
sig_old = sig_new;
// vector_add( t, alpha, d, nn );
// vector_add( r, -alpha, q, nn );
my_dot = dot_sqr = 0.0;
FixQEqReaxKokkosPrecon2Functor<DeviceType> precon2_functor(this);
Kokkos::parallel_for(inum,precon2_functor);
DeviceType::fence();
// preconditioning: p[j] = r[j] * Hdia_inv[j];
// sig_new = parallel_dot( r, p, nn);
FixQEqReaxKokkosPreconFunctor<DeviceType> precon_functor(this);
Kokkos::parallel_reduce(inum,precon_functor,my_dot);
DeviceType::fence();
MPI_Allreduce( &my_dot, &dot_sqr, 1, MPI_DOUBLE, MPI_SUM, world );
sig_new = dot_sqr;
beta = sig_new / sig_old;
// vector_sum( d, 1., p, beta, d, nn );
FixQEqReaxKokkosVecSum2Functor<DeviceType> vecsum2_functor(this);
Kokkos::parallel_for(inum,vecsum2_functor);
DeviceType::fence();
}
if (loop >= loopmax && comm->me == 0) {
char str[128];
sprintf(str,"Fix qeq/reax cg_solve2 convergence failed after %d iterations "
"at " BIGINT_FORMAT " step: %f",loop,update->ntimestep,sqrt(sig_new)/b_norm);
error->warning(FLERR,str);
//error->all(FLERR,str);
}
}
/* ---------------------------------------------------------------------- */
template<class DeviceType>
void FixQEqReaxKokkos<DeviceType>::calculate_q()
{
F_FLOAT sum, sum_all;
const int inum = list->inum;
// s_sum = parallel_vector_acc( s, nn );
sum = sum_all = 0.0;
FixQEqReaxKokkosVecAcc1Functor<DeviceType> vecacc1_functor(this);
Kokkos::parallel_reduce(inum,vecacc1_functor,sum);
DeviceType::fence();
MPI_Allreduce(&sum, &sum_all, 1, MPI_DOUBLE, MPI_SUM, world );
const F_FLOAT s_sum = sum_all;
// t_sum = parallel_vector_acc( t, nn);
sum = sum_all = 0.0;
FixQEqReaxKokkosVecAcc2Functor<DeviceType> vecacc2_functor(this);
Kokkos::parallel_reduce(inum,vecacc2_functor,sum);
DeviceType::fence();
MPI_Allreduce(&sum, &sum_all, 1, MPI_DOUBLE, MPI_SUM, world );
const F_FLOAT t_sum = sum_all;
// u = s_sum / t_sum;
delta = s_sum/t_sum;
// q[i] = s[i] - u * t[i];
FixQEqReaxKokkosCalculateQFunctor<DeviceType> calculateQ_functor(this);
Kokkos::parallel_for(inum,calculateQ_functor);
DeviceType::fence();
pack_flag = 4;
//comm->forward_comm_fix( this ); //Dist_vector( atom->q );
atomKK->k_q.modify<DeviceType>();
atomKK->k_q.sync<LMPHostType>();
comm->forward_comm_fix(this);
atomKK->k_q.modify<LMPHostType>();
atomKK->k_q.sync<DeviceType>();
}
/* ---------------------------------------------------------------------- */
template<class DeviceType>
KOKKOS_INLINE_FUNCTION
void FixQEqReaxKokkos<DeviceType>::sparse12_item(int ii) const
{
const int i = d_ilist[ii];
const int itype = type(i);
if (mask[i] & groupbit) {
d_o[i] = params(itype).eta * d_s[i];
}
}
/* ---------------------------------------------------------------------- */
template<class DeviceType>
template<int NEIGHFLAG>
KOKKOS_INLINE_FUNCTION
void FixQEqReaxKokkos<DeviceType>::sparse13_item(int ii) const
{
// The q array is atomic for Half/Thread neighbor style
Kokkos::View<F_FLOAT*, typename DAT::t_float_1d::array_layout,DeviceType,Kokkos::MemoryTraits<AtomicF<NEIGHFLAG>::value> > a_o = d_o;
const int i = d_ilist[ii];
if (mask[i] & groupbit) {
F_FLOAT tmp = 0.0;
for(int jj = d_firstnbr[i]; jj < d_firstnbr[i] + d_numnbrs[i]; jj++) {
const int j = d_jlist(jj);
tmp += d_val(jj) * d_s[j];
a_o[j] += d_val(jj) * d_s[i];
}
a_o[i] += tmp;
}
}
/* ---------------------------------------------------------------------- */
template<class DeviceType>
KOKKOS_INLINE_FUNCTION
void FixQEqReaxKokkos<DeviceType>::operator() (TagSparseMatvec1, const membertype1 &team) const
{
const int i = d_ilist[team.league_rank()];
if (mask[i] & groupbit) {
F_FLOAT doitmp;
Kokkos::parallel_reduce(Kokkos::TeamThreadRange(team, d_firstnbr[i], d_firstnbr[i] + d_numnbrs[i]), [&] (const int &jj, F_FLOAT &doi) {
const int j = d_jlist(jj);
doi += d_val(jj) * d_s[j];
}, doitmp);
Kokkos::single(Kokkos::PerTeam(team), [&] () {d_o[i] += doitmp;});
}
}
/* ---------------------------------------------------------------------- */
template<class DeviceType>
KOKKOS_INLINE_FUNCTION
void FixQEqReaxKokkos<DeviceType>::sparse22_item(int ii) const
{
const int i = d_ilist[ii];
const int itype = type(i);
if (mask[i] & groupbit) {
d_o[i] = params(itype).eta * d_d[i];
}
}
/* ---------------------------------------------------------------------- */
template<class DeviceType>
template<int NEIGHFLAG>
KOKKOS_INLINE_FUNCTION
void FixQEqReaxKokkos<DeviceType>::sparse23_item(int ii) const
{
// The q array is atomic for Half/Thread neighbor style
Kokkos::View<F_FLOAT*, typename DAT::t_float_1d::array_layout,DeviceType,Kokkos::MemoryTraits<AtomicF<NEIGHFLAG>::value> > a_o = d_o;
const int i = d_ilist[ii];
if (mask[i] & groupbit) {
F_FLOAT tmp = 0.0;
for(int jj = d_firstnbr[i]; jj < d_firstnbr[i] + d_numnbrs[i]; jj++) {
const int j = d_jlist(jj);
tmp += d_val(jj) * d_d[j];
a_o[j] += d_val(jj) * d_d[i];
}
a_o[i] += tmp;
}
}
/* ---------------------------------------------------------------------- */
template<class DeviceType>
KOKKOS_INLINE_FUNCTION
void FixQEqReaxKokkos<DeviceType>::operator() (TagSparseMatvec2, const membertype2 &team) const
{
const int i = d_ilist[team.league_rank()];
if (mask[i] & groupbit) {
F_FLOAT doitmp;
Kokkos::parallel_reduce(Kokkos::TeamThreadRange(team, d_firstnbr[i], d_firstnbr[i] + d_numnbrs[i]), [&] (const int &jj, F_FLOAT &doi) {
const int j = d_jlist(jj);
doi += d_val(jj) * d_d[j];
}, doitmp);
Kokkos::single(Kokkos::PerTeam(team), [&] () {d_o[i] += doitmp; });
}
}
template<class DeviceType>
KOKKOS_INLINE_FUNCTION
void FixQEqReaxKokkos<DeviceType>::operator() (TagZeroQGhosts, const int &i) const
{
if (mask[i] & groupbit)
d_o[i] = 0.0;
}
/* ---------------------------------------------------------------------- */
template<class DeviceType>
KOKKOS_INLINE_FUNCTION
void FixQEqReaxKokkos<DeviceType>::sparse32_item(int ii) const
{
const int i = d_ilist[ii];
const int itype = type(i);
if (mask[i] & groupbit)
d_o[i] = params(itype).eta * d_t[i];
}
/* ---------------------------------------------------------------------- */
template<class DeviceType>
template<int NEIGHFLAG>
KOKKOS_INLINE_FUNCTION
void FixQEqReaxKokkos<DeviceType>::sparse33_item(int ii) const
{
// The q array is atomic for Half/Thread neighbor style
Kokkos::View<F_FLOAT*, typename DAT::t_float_1d::array_layout,DeviceType,Kokkos::MemoryTraits<AtomicF<NEIGHFLAG>::value> > a_o = d_o;
const int i = d_ilist[ii];
if (mask[i] & groupbit) {
F_FLOAT tmp = 0.0;
for(int jj = d_firstnbr[i]; jj < d_firstnbr[i] + d_numnbrs[i]; jj++) {
const int j = d_jlist(jj);
tmp += d_val(jj) * d_t[j];
a_o[j] += d_val(jj) * d_t[i];
}
a_o[i] += tmp;
}
}
/* ---------------------------------------------------------------------- */
template<class DeviceType>
KOKKOS_INLINE_FUNCTION
void FixQEqReaxKokkos<DeviceType>::operator() (TagSparseMatvec3, const membertype3 &team) const
{
const int i = d_ilist[team.league_rank()];
if (mask[i] & groupbit) {
F_FLOAT doitmp;
Kokkos::parallel_reduce(Kokkos::TeamThreadRange(team, d_firstnbr[i], d_firstnbr[i] + d_numnbrs[i]), [&] (const int &jj, F_FLOAT &doi) {
const int j = d_jlist(jj);
doi += d_val(jj) * d_t[j];
}, doitmp);
Kokkos::single(Kokkos::PerTeam(team), [&] () {d_o[i] += doitmp;});
}
}
/* ---------------------------------------------------------------------- */
template<class DeviceType>
KOKKOS_INLINE_FUNCTION
void FixQEqReaxKokkos<DeviceType>::vecsum2_item(int ii) const
{
const int i = d_ilist[ii];
if (mask[i] & groupbit)
d_d[i] = 1.0 * d_p[i] + beta * d_d[i];
}
/* ---------------------------------------------------------------------- */
template<class DeviceType>
KOKKOS_INLINE_FUNCTION
double FixQEqReaxKokkos<DeviceType>::norm1_item(int ii) const
{
F_FLOAT tmp = 0;
const int i = d_ilist[ii];
if (mask[i] & groupbit) {
d_r[i] = 1.0*d_b_s[i] + -1.0*d_o[i];
d_d[i] = d_r[i] * d_Hdia_inv[i];
tmp = d_b_s[i] * d_b_s[i];
}
return tmp;
}
/* ---------------------------------------------------------------------- */
template<class DeviceType>
KOKKOS_INLINE_FUNCTION
double FixQEqReaxKokkos<DeviceType>::norm2_item(int ii) const
{
F_FLOAT tmp = 0;
const int i = d_ilist[ii];
if (mask[i] & groupbit) {
d_r[i] = 1.0*d_b_t[i] + -1.0*d_o[i];
d_d[i] = d_r[i] * d_Hdia_inv[i];
tmp = d_b_t[i] * d_b_t[i];
}
return tmp;
}
/* ---------------------------------------------------------------------- */
template<class DeviceType>
KOKKOS_INLINE_FUNCTION
double FixQEqReaxKokkos<DeviceType>::dot1_item(int ii) const
{
F_FLOAT tmp = 0.0;
const int i = d_ilist[ii];
if (mask[i] & groupbit)
tmp = d_r[i] * d_d[i];
return tmp;
}
/* ---------------------------------------------------------------------- */
template<class DeviceType>
KOKKOS_INLINE_FUNCTION
double FixQEqReaxKokkos<DeviceType>::dot2_item(int ii) const
{
double tmp = 0.0;
const int i = d_ilist[ii];
if (mask[i] & groupbit) {
tmp = d_d[i] * d_o[i];
}
return tmp;
}
/* ---------------------------------------------------------------------- */
template<class DeviceType>
KOKKOS_INLINE_FUNCTION
void FixQEqReaxKokkos<DeviceType>::precon1_item(int ii) const
{
const int i = d_ilist[ii];
if (mask[i] & groupbit) {
d_s[i] += alpha * d_d[i];
d_r[i] += -alpha * d_o[i];
}
}
/* ---------------------------------------------------------------------- */
template<class DeviceType>
KOKKOS_INLINE_FUNCTION
void FixQEqReaxKokkos<DeviceType>::precon2_item(int ii) const
{
const int i = d_ilist[ii];
if (mask[i] & groupbit) {
d_t[i] += alpha * d_d[i];
d_r[i] += -alpha * d_o[i];
}
}
/* ---------------------------------------------------------------------- */
template<class DeviceType>
KOKKOS_INLINE_FUNCTION
double FixQEqReaxKokkos<DeviceType>::precon_item(int ii) const
{
F_FLOAT tmp = 0.0;
const int i = d_ilist[ii];
if (mask[i] & groupbit) {
d_p[i] = d_r[i] * d_Hdia_inv[i];
tmp = d_r[i] * d_p[i];
}
return tmp;
}
/* ---------------------------------------------------------------------- */
template<class DeviceType>
KOKKOS_INLINE_FUNCTION
double FixQEqReaxKokkos<DeviceType>::vecacc1_item(int ii) const
{
F_FLOAT tmp = 0.0;
const int i = d_ilist[ii];
if (mask[i] & groupbit)
tmp = d_s[i];
return tmp;
}
/* ---------------------------------------------------------------------- */
template<class DeviceType>
KOKKOS_INLINE_FUNCTION
double FixQEqReaxKokkos<DeviceType>::vecacc2_item(int ii) const
{
F_FLOAT tmp = 0.0;
const int i = d_ilist[ii];
if (mask[i] & groupbit) {
tmp = d_t[i];
}
return tmp;
}
/* ---------------------------------------------------------------------- */
template<class DeviceType>
KOKKOS_INLINE_FUNCTION
void FixQEqReaxKokkos<DeviceType>::calculate_q_item(int ii) const
{
const int i = d_ilist[ii];
if (mask[i] & groupbit) {
q(i) = d_s[i] - delta * d_t[i];
for (int k = 4; k > 0; --k) {
d_s_hist(i,k) = d_s_hist(i,k-1);
d_t_hist(i,k) = d_t_hist(i,k-1);
}
d_s_hist(i,0) = d_s[i];
d_t_hist(i,0) = d_t[i];
}
}
/* ---------------------------------------------------------------------- */
template<class DeviceType>
int FixQEqReaxKokkos<DeviceType>::pack_forward_comm(int n, int *list, double *buf,
int pbc_flag, int *pbc)
{
int m;
if( pack_flag == 1)
for(m = 0; m < n; m++) buf[m] = h_d[list[m]];
else if( pack_flag == 2 )
for(m = 0; m < n; m++) buf[m] = h_s[list[m]];
else if( pack_flag == 3 )
for(m = 0; m < n; m++) buf[m] = h_t[list[m]];
else if( pack_flag == 4 )
for(m = 0; m < n; m++) buf[m] = atom->q[list[m]];
return n;
}
/* ---------------------------------------------------------------------- */
template<class DeviceType>
void FixQEqReaxKokkos<DeviceType>::unpack_forward_comm(int n, int first, double *buf)
{
int i, m;
if( pack_flag == 1)
for(m = 0, i = first; m < n; m++, i++) h_d[i] = buf[m];
else if( pack_flag == 2)
for(m = 0, i = first; m < n; m++, i++) h_s[i] = buf[m];
else if( pack_flag == 3)
for(m = 0, i = first; m < n; m++, i++) h_t[i] = buf[m];
else if( pack_flag == 4)
for(m = 0, i = first; m < n; m++, i++) atom->q[i] = buf[m];
}
/* ---------------------------------------------------------------------- */
template<class DeviceType>
int FixQEqReaxKokkos<DeviceType>::pack_reverse_comm(int n, int first, double *buf)
{
int i, m;
for(m = 0, i = first; m < n; m++, i++) {
buf[m] = h_o[i];
}
return n;
}
/* ---------------------------------------------------------------------- */
template<class DeviceType>
void FixQEqReaxKokkos<DeviceType>::unpack_reverse_comm(int n, int *list, double *buf)
{
for(int m = 0; m < n; m++) {
h_o[list[m]] += buf[m];
}
}
/* ---------------------------------------------------------------------- */
template<class DeviceType>
void FixQEqReaxKokkos<DeviceType>::cleanup_copy()
{
id = style = NULL;
}
/* ----------------------------------------------------------------------
memory usage of local atom-based arrays
------------------------------------------------------------------------- */
template<class DeviceType>
double FixQEqReaxKokkos<DeviceType>::memory_usage()
{
double bytes;
bytes = atom->nmax*5*2 * sizeof(F_FLOAT); // s_hist & t_hist
bytes += atom->nmax*8 * sizeof(F_FLOAT); // storage
bytes += n_cap*2 * sizeof(int); // matrix...
bytes += m_cap * sizeof(int);
bytes += m_cap * sizeof(F_FLOAT);
return bytes;
}
/* ---------------------------------------------------------------------- */\
namespace LAMMPS_NS {
template class FixQEqReaxKokkos<LMPDeviceType>;
#ifdef KOKKOS_HAVE_CUDA
template class FixQEqReaxKokkos<LMPHostType>;
#endif
}

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