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pair_eam_fs_kokkos.cpp
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Sat, Nov 2, 02:46

pair_eam_fs_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: Stan Moore (SNL)
------------------------------------------------------------------------- */
#include <math.h>
#include <stdio.h>
#include <stdlib.h>
#include <string.h>
#include "kokkos.h"
#include "pair_kokkos.h"
#include "pair_eam_fs_kokkos.h"
#include "atom_kokkos.h"
#include "force.h"
#include "comm.h"
#include "neighbor.h"
#include "neigh_list_kokkos.h"
#include "neigh_request.h"
#include "memory.h"
#include "error.h"
#include "atom_masks.h"
using namespace LAMMPS_NS;
#define MAXLINE 1024
// Cannot use virtual inheritance on the GPU, so must duplicate code
/* ---------------------------------------------------------------------- */
template<class DeviceType>
PairEAMFSKokkos<DeviceType>::PairEAMFSKokkos(LAMMPS *lmp) : PairEAM(lmp)
{
one_coeff = 1;
manybody_flag = 1;
respa_enable = 0;
atomKK = (AtomKokkos *) atom;
execution_space = ExecutionSpaceFromDevice<DeviceType>::space;
datamask_read = X_MASK | F_MASK | TYPE_MASK | ENERGY_MASK | VIRIAL_MASK;
datamask_modify = F_MASK | ENERGY_MASK | VIRIAL_MASK;
}
/* ---------------------------------------------------------------------- */
template<class DeviceType>
PairEAMFSKokkos<DeviceType>::~PairEAMFSKokkos()
{
if (!copymode) {
memory->destroy_kokkos(k_eatom,eatom);
memory->destroy_kokkos(k_vatom,vatom);
}
}
/* ---------------------------------------------------------------------- */
template<class DeviceType>
void PairEAMFSKokkos<DeviceType>::compute(int eflag_in, int vflag_in)
{
eflag = eflag_in;
vflag = vflag_in;
if (neighflag == FULL) no_virial_fdotr_compute = 1;
if (eflag || vflag) ev_setup(eflag,vflag);
else evflag = vflag_fdotr = 0;
// reallocate per-atom arrays if necessary
if (eflag_atom) {
memory->destroy_kokkos(k_eatom,eatom);
memory->create_kokkos(k_eatom,eatom,maxeatom,"pair:eatom");
d_eatom = k_eatom.d_view;
}
if (vflag_atom) {
memory->destroy_kokkos(k_vatom,vatom);
memory->create_kokkos(k_vatom,vatom,maxvatom,6,"pair:vatom");
d_vatom = k_vatom.d_view;
}
atomKK->sync(execution_space,datamask_read);
if (eflag || vflag) atomKK->modified(execution_space,datamask_modify);
else atomKK->modified(execution_space,F_MASK);
// grow energy and fp arrays if necessary
// need to be atom->nmax in length
if (atom->nmax > nmax) {
nmax = atom->nmax;
k_rho = DAT::tdual_ffloat_1d("pair:rho",nmax);
k_fp = DAT::tdual_ffloat_1d("pair:fp",nmax);
d_rho = k_rho.d_view;
d_fp = k_fp.d_view;
h_rho = k_rho.h_view;
h_fp = k_fp.h_view;
}
x = atomKK->k_x.view<DeviceType>();
f = atomKK->k_f.view<DeviceType>();
v_rho = k_rho.view<DeviceType>();
type = atomKK->k_type.view<DeviceType>();
tag = atomKK->k_tag.view<DeviceType>();
nlocal = atom->nlocal;
nall = atom->nlocal + atom->nghost;
newton_pair = force->newton_pair;
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;
int inum = list->inum;
// Call cleanup_copy which sets allocations NULL which are destructed by the PairStyle
k_list->clean_copy();
copymode = 1;
// zero out density
if (newton_pair)
Kokkos::parallel_for(Kokkos::RangePolicy<DeviceType, TagPairEAMFSInitialize>(0,nall),*this);
else
Kokkos::parallel_for(Kokkos::RangePolicy<DeviceType, TagPairEAMFSInitialize>(0,nlocal),*this);
DeviceType::fence();
// loop over neighbors of my atoms
EV_FLOAT ev;
// compute kernel A
if (neighflag == HALF || neighflag == HALFTHREAD) {
if (neighflag == HALF) {
if (newton_pair) {
Kokkos::parallel_for(Kokkos::RangePolicy<DeviceType, TagPairEAMFSKernelA<HALF,1> >(0,inum),*this);
} else {
Kokkos::parallel_for(Kokkos::RangePolicy<DeviceType, TagPairEAMFSKernelA<HALF,0> >(0,inum),*this);
}
} else if (neighflag == HALFTHREAD) {
if (newton_pair) {
Kokkos::parallel_for(Kokkos::RangePolicy<DeviceType, TagPairEAMFSKernelA<HALFTHREAD,1> >(0,inum),*this);
} else {
Kokkos::parallel_for(Kokkos::RangePolicy<DeviceType, TagPairEAMFSKernelA<HALFTHREAD,0> >(0,inum),*this);
}
}
DeviceType::fence();
// communicate and sum densities (on the host)
if (newton_pair) {
k_rho.template modify<DeviceType>();
k_rho.template sync<LMPHostType>();
comm->reverse_comm_pair(this);
k_rho.template modify<LMPHostType>();
k_rho.template sync<DeviceType>();
}
// compute kernel B
if (eflag)
Kokkos::parallel_reduce(Kokkos::RangePolicy<DeviceType, TagPairEAMFSKernelB<1> >(0,inum),*this,ev);
else
Kokkos::parallel_for(Kokkos::RangePolicy<DeviceType, TagPairEAMFSKernelB<0> >(0,inum),*this);
DeviceType::fence();
} else if (neighflag == FULL) {
// compute kernel AB
if (eflag)
Kokkos::parallel_reduce(Kokkos::RangePolicy<DeviceType, TagPairEAMFSKernelAB<1> >(0,inum),*this,ev);
else
Kokkos::parallel_for(Kokkos::RangePolicy<DeviceType, TagPairEAMFSKernelAB<0> >(0,inum),*this);
DeviceType::fence();
}
if (eflag) {
eng_vdwl += ev.evdwl;
ev.evdwl = 0.0;
}
// communicate derivative of embedding function (on the device)
comm->forward_comm_pair(this);
// compute kernel C
if (evflag) {
if (neighflag == HALF) {
if (newton_pair) {
Kokkos::parallel_reduce(Kokkos::RangePolicy<DeviceType, TagPairEAMFSKernelC<HALF,1,1> >(0,inum),*this,ev);
} else {
Kokkos::parallel_reduce(Kokkos::RangePolicy<DeviceType, TagPairEAMFSKernelC<HALF,0,1> >(0,inum),*this,ev);
}
} else if (neighflag == HALFTHREAD) {
if (newton_pair) {
Kokkos::parallel_reduce(Kokkos::RangePolicy<DeviceType, TagPairEAMFSKernelC<HALFTHREAD,1,1> >(0,inum),*this,ev);
} else {
Kokkos::parallel_reduce(Kokkos::RangePolicy<DeviceType, TagPairEAMFSKernelC<HALFTHREAD,0,1> >(0,inum),*this,ev);
}
} else if (neighflag == FULL) {
if (newton_pair) {
Kokkos::parallel_reduce(Kokkos::RangePolicy<DeviceType, TagPairEAMFSKernelC<FULL,1,1> >(0,inum),*this,ev);
} else {
Kokkos::parallel_reduce(Kokkos::RangePolicy<DeviceType, TagPairEAMFSKernelC<FULL,0,1> >(0,inum),*this,ev);
}
}
} else {
if (neighflag == HALF) {
if (newton_pair) {
Kokkos::parallel_for(Kokkos::RangePolicy<DeviceType, TagPairEAMFSKernelC<HALF,1,0> >(0,inum),*this);
} else {
Kokkos::parallel_for(Kokkos::RangePolicy<DeviceType, TagPairEAMFSKernelC<HALF,0,0> >(0,inum),*this);
}
} else if (neighflag == HALFTHREAD) {
if (newton_pair) {
Kokkos::parallel_for(Kokkos::RangePolicy<DeviceType, TagPairEAMFSKernelC<HALFTHREAD,1,0> >(0,inum),*this);
} else {
Kokkos::parallel_for(Kokkos::RangePolicy<DeviceType, TagPairEAMFSKernelC<HALFTHREAD,0,0> >(0,inum),*this);
}
} else if (neighflag == FULL) {
if (newton_pair) {
Kokkos::parallel_for(Kokkos::RangePolicy<DeviceType, TagPairEAMFSKernelC<FULL,1,0> >(0,inum),*this);
} else {
Kokkos::parallel_for(Kokkos::RangePolicy<DeviceType, TagPairEAMFSKernelC<FULL,0,0> >(0,inum),*this);
}
}
}
DeviceType::fence();
if (eflag_global) eng_vdwl += ev.evdwl;
if (vflag_global) {
virial[0] += ev.v[0];
virial[1] += ev.v[1];
virial[2] += ev.v[2];
virial[3] += ev.v[3];
virial[4] += ev.v[4];
virial[5] += ev.v[5];
}
if (vflag_fdotr) pair_virial_fdotr_compute(this);
if (eflag_atom) {
k_eatom.template modify<DeviceType>();
k_eatom.template sync<LMPHostType>();
}
if (vflag_atom) {
k_vatom.template modify<DeviceType>();
k_vatom.template sync<LMPHostType>();
}
copymode = 0;
}
/* ----------------------------------------------------------------------
init specific to this pair style
------------------------------------------------------------------------- */
template<class DeviceType>
void PairEAMFSKokkos<DeviceType>::init_style()
{
// convert read-in file(s) to arrays and spline them
PairEAM::init_style();
// irequest = neigh request made by parent class
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]->full = 1;
neighbor->requests[irequest]->half = 0;
neighbor->requests[irequest]->full_cluster = 0;
} else if (neighflag == HALF || neighflag == HALFTHREAD) {
neighbor->requests[irequest]->full = 0;
neighbor->requests[irequest]->half = 1;
neighbor->requests[irequest]->full_cluster = 0;
} else {
error->all(FLERR,"Cannot use chosen neighbor list style with pair eam/kk/fs");
}
}
template<class DeviceType>
void PairEAMFSKokkos<DeviceType>::file2array()
{
file2array_fs();
int i,j;
int n = atom->ntypes;
DAT::tdual_int_1d k_type2frho = DAT::tdual_int_1d("pair:type2frho",n+1);
DAT::tdual_int_2d k_type2rhor = DAT::tdual_int_2d("pair:type2rhor",n+1,n+1);
DAT::tdual_int_2d k_type2z2r = DAT::tdual_int_2d("pair:type2z2r",n+1,n+1);
HAT::t_int_1d h_type2frho = k_type2frho.h_view;
HAT::t_int_2d h_type2rhor = k_type2rhor.h_view;
HAT::t_int_2d h_type2z2r = k_type2z2r.h_view;
for (i = 1; i <= n; i++) {
h_type2frho[i] = type2frho[i];
for (j = 1; j <= n; j++) {
h_type2rhor(i,j) = type2rhor[i][j];
h_type2z2r(i,j) = type2z2r[i][j];
}
}
k_type2frho.template modify<LMPHostType>();
k_type2frho.template sync<DeviceType>();
k_type2rhor.template modify<LMPHostType>();
k_type2rhor.template sync<DeviceType>();
k_type2z2r.template modify<LMPHostType>();
k_type2z2r.template sync<DeviceType>();
d_type2frho = k_type2frho.d_view;
d_type2rhor = k_type2rhor.d_view;
d_type2z2r = k_type2z2r.d_view;
}
/* ---------------------------------------------------------------------- */
template<class DeviceType>
void PairEAMFSKokkos<DeviceType>::array2spline()
{
rdr = 1.0/dr;
rdrho = 1.0/drho;
tdual_ffloat_2d_n7 k_frho_spline = tdual_ffloat_2d_n7("pair:frho",nfrho,nrho+1);
tdual_ffloat_2d_n7 k_rhor_spline = tdual_ffloat_2d_n7("pair:rhor",nrhor,nr+1);
tdual_ffloat_2d_n7 k_z2r_spline = tdual_ffloat_2d_n7("pair:z2r",nz2r,nr+1);
t_host_ffloat_2d_n7 h_frho_spline = k_frho_spline.h_view;
t_host_ffloat_2d_n7 h_rhor_spline = k_rhor_spline.h_view;
t_host_ffloat_2d_n7 h_z2r_spline = k_z2r_spline.h_view;
for (int i = 0; i < nfrho; i++)
interpolate(nrho,drho,frho[i],h_frho_spline,i);
k_frho_spline.template modify<LMPHostType>();
k_frho_spline.template sync<DeviceType>();
for (int i = 0; i < nrhor; i++)
interpolate(nr,dr,rhor[i],h_rhor_spline,i);
k_rhor_spline.template modify<LMPHostType>();
k_rhor_spline.template sync<DeviceType>();
for (int i = 0; i < nz2r; i++)
interpolate(nr,dr,z2r[i],h_z2r_spline,i);
k_z2r_spline.template modify<LMPHostType>();
k_z2r_spline.template sync<DeviceType>();
d_frho_spline = k_frho_spline.d_view;
d_rhor_spline = k_rhor_spline.d_view;
d_z2r_spline = k_z2r_spline.d_view;
}
/* ---------------------------------------------------------------------- */
template<class DeviceType>
void PairEAMFSKokkos<DeviceType>::interpolate(int n, double delta, double *f, t_host_ffloat_2d_n7 h_spline, int i)
{
for (int m = 1; m <= n; m++) h_spline(i,m,6) = f[m];
h_spline(i,1,5) = h_spline(i,2,6) - h_spline(i,1,6);
h_spline(i,2,5) = 0.5 * (h_spline(i,3,6)-h_spline(i,1,6));
h_spline(i,n-1,5) = 0.5 * (h_spline(i,n,6)-h_spline(i,n-2,6));
h_spline(i,n,5) = h_spline(i,n,6) - h_spline(i,n-1,6);
for (int m = 3; m <= n-2; m++)
h_spline(i,m,5) = ((h_spline(i,m-2,6)-h_spline(i,m+2,6)) +
8.0*(h_spline(i,m+1,6)-h_spline(i,m-1,6))) / 12.0;
for (int m = 1; m <= n-1; m++) {
h_spline(i,m,4) = 3.0*(h_spline(i,m+1,6)-h_spline(i,m,6)) -
2.0*h_spline(i,m,5) - h_spline(i,m+1,5);
h_spline(i,m,3) = h_spline(i,m,5) + h_spline(i,m+1,5) -
2.0*(h_spline(i,m+1,6)-h_spline(i,m,6));
}
h_spline(i,n,4) = 0.0;
h_spline(i,n,3) = 0.0;
for (int m = 1; m <= n; m++) {
h_spline(i,m,2) = h_spline(i,m,5)/delta;
h_spline(i,m,1) = 2.0*h_spline(i,m,4)/delta;
h_spline(i,m,0) = 3.0*h_spline(i,m,3)/delta;
}
}
/* ---------------------------------------------------------------------- */
template<class DeviceType>
int PairEAMFSKokkos<DeviceType>::pack_forward_comm_kokkos(int n, DAT::tdual_int_2d k_sendlist, int iswap_in, DAT::tdual_xfloat_1d &buf,
int pbc_flag, int *pbc)
{
d_sendlist = k_sendlist.view<DeviceType>();
iswap = iswap_in;
v_buf = buf.view<DeviceType>();
Kokkos::parallel_for(Kokkos::RangePolicy<LMPDeviceType, TagPairEAMFSPackForwardComm>(0,n),*this);
DeviceType::fence();
return n;
}
template<class DeviceType>
KOKKOS_INLINE_FUNCTION
void PairEAMFSKokkos<DeviceType>::operator()(TagPairEAMFSPackForwardComm, const int &i) const {
int j = d_sendlist(iswap, i);
v_buf[i] = d_fp[j];
}
/* ---------------------------------------------------------------------- */
template<class DeviceType>
void PairEAMFSKokkos<DeviceType>::unpack_forward_comm_kokkos(int n, int first_in, DAT::tdual_xfloat_1d &buf)
{
first = first_in;
v_buf = buf.view<DeviceType>();
Kokkos::parallel_for(Kokkos::RangePolicy<LMPDeviceType, TagPairEAMFSUnpackForwardComm>(0,n),*this);
DeviceType::fence();
}
template<class DeviceType>
KOKKOS_INLINE_FUNCTION
void PairEAMFSKokkos<DeviceType>::operator()(TagPairEAMFSUnpackForwardComm, const int &i) const {
d_fp[i + first] = v_buf[i];
}
/* ---------------------------------------------------------------------- */
template<class DeviceType>
int PairEAMFSKokkos<DeviceType>::pack_forward_comm(int n, int *list, double *buf,
int pbc_flag, int *pbc)
{
int i,j;
for (i = 0; i < n; i++) {
j = list[i];
buf[i] = h_fp[j];
}
return n;
}
/* ---------------------------------------------------------------------- */
template<class DeviceType>
void PairEAMFSKokkos<DeviceType>::unpack_forward_comm(int n, int first, double *buf)
{
for (int i = 0; i < n; i++) {
h_fp[i + first] = buf[i];
}
}
/* ---------------------------------------------------------------------- */
template<class DeviceType>
int PairEAMFSKokkos<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_rho[i];
return m;
}
/* ---------------------------------------------------------------------- */
template<class DeviceType>
void PairEAMFSKokkos<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_rho[j] += buf[m++];
}
}
/* ---------------------------------------------------------------------- */
template<class DeviceType>
KOKKOS_INLINE_FUNCTION
void PairEAMFSKokkos<DeviceType>::operator()(TagPairEAMFSInitialize, const int &i) const {
d_rho[i] = 0.0;
}
/* ---------------------------------------------------------------------- */
////Specialisation for Neighborlist types Half, HalfThread, Full
template<class DeviceType>
template<int NEIGHFLAG, int NEWTON_PAIR>
KOKKOS_INLINE_FUNCTION
void PairEAMFSKokkos<DeviceType>::operator()(TagPairEAMFSKernelA<NEIGHFLAG,NEWTON_PAIR>, const int &ii) const {
// rho = density at each atom
// loop over neighbors of my atoms
// The rho array is atomic for Half/Thread neighbor style
Kokkos::View<F_FLOAT*, typename DAT::t_f_array::array_layout,DeviceType,Kokkos::MemoryTraits<AtomicF<NEIGHFLAG>::value> > rho = v_rho;
const int i = d_ilist[ii];
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 AtomNeighborsConst d_neighbors_i = k_list.get_neighbors_const(i);
const int jnum = d_numneigh[i];
F_FLOAT rhotmp = 0.0;
for (int jj = 0; jj < jnum; jj++) {
//int j = d_neighbors_i[jj];
int j = d_neighbors(i,jj);
j &= NEIGHMASK;
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 int jtype = type(j);
const F_FLOAT rsq = delx*delx + dely*dely + delz*delz;
if (rsq < cutforcesq) {
F_FLOAT p = sqrt(rsq)*rdr + 1.0;
int m = static_cast<int> (p);
m = MIN(m,nr-1);
p -= m;
p = MIN(p,1.0);
const int d_type2rhor_ji = d_type2rhor(jtype,itype);
rhotmp += ((d_rhor_spline(d_type2rhor_ji,m,3)*p + d_rhor_spline(d_type2rhor_ji,m,4))*p +
d_rhor_spline(d_type2rhor_ji,m,5))*p + d_rhor_spline(d_type2rhor_ji,m,6);
if (NEWTON_PAIR || j < nlocal) {
const int d_type2rhor_ij = d_type2rhor(itype,jtype);
rho[j] += ((d_rhor_spline(d_type2rhor_ij,m,3)*p + d_rhor_spline(d_type2rhor_ij,m,4))*p +
d_rhor_spline(d_type2rhor_ij,m,5))*p + d_rhor_spline(d_type2rhor_ij,m,6);
}
}
}
rho[i] += rhotmp;
}
/* ---------------------------------------------------------------------- */
////Specialisation for Neighborlist types Half, HalfThread, Full
template<class DeviceType>
template<int EFLAG>
KOKKOS_INLINE_FUNCTION
void PairEAMFSKokkos<DeviceType>::operator()(TagPairEAMFSKernelB<EFLAG>, const int &ii, EV_FLOAT& ev) const {
// fp = derivative of embedding energy at each atom
// phi = embedding energy at each atom
// if rho > rhomax (e.g. due to close approach of two atoms),
// will exceed table, so add linear term to conserve energy
const int i = d_ilist[ii];
const int itype = type(i);
F_FLOAT p = d_rho[i]*rdrho + 1.0;
int m = static_cast<int> (p);
m = MAX(1,MIN(m,nrho-1));
p -= m;
p = MIN(p,1.0);
const int d_type2frho_i = d_type2frho[itype];
d_fp[i] = (d_frho_spline(d_type2frho_i,m,0)*p + d_frho_spline(d_type2frho_i,m,1))*p + d_frho_spline(d_type2frho_i,m,2);
if (EFLAG) {
F_FLOAT phi = ((d_frho_spline(d_type2frho_i,m,3)*p + d_frho_spline(d_type2frho_i,m,4))*p +
d_frho_spline(d_type2frho_i,m,5))*p + d_frho_spline(d_type2frho_i,m,6);
if (d_rho[i] > rhomax) phi += d_fp[i] * (d_rho[i]-rhomax);
if (eflag_global) ev.evdwl += phi;
if (eflag_atom) d_eatom[i] += phi;
}
}
template<class DeviceType>
template<int EFLAG>
KOKKOS_INLINE_FUNCTION
void PairEAMFSKokkos<DeviceType>::operator()(TagPairEAMFSKernelB<EFLAG>, const int &ii) const {
EV_FLOAT ev;
this->template operator()<EFLAG>(TagPairEAMFSKernelB<EFLAG>(), ii, ev);
}
/* ---------------------------------------------------------------------- */
////Specialisation for Neighborlist types Half, HalfThread, Full
template<class DeviceType>
template<int EFLAG>
KOKKOS_INLINE_FUNCTION
void PairEAMFSKokkos<DeviceType>::operator()(TagPairEAMFSKernelAB<EFLAG>, const int &ii, EV_FLOAT& ev) const {
// rho = density at each atom
// loop over neighbors of my atoms
const int i = d_ilist[ii];
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 AtomNeighborsConst d_neighbors_i = k_list.get_neighbors_const(i);
const int jnum = d_numneigh[i];
F_FLOAT rhotmp = 0.0;
for (int jj = 0; jj < jnum; jj++) {
//int j = d_neighbors_i[jj];
int j = d_neighbors(i,jj);
j &= NEIGHMASK;
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 int jtype = type(j);
const F_FLOAT rsq = delx*delx + dely*dely + delz*delz;
if (rsq < cutforcesq) {
F_FLOAT p = sqrt(rsq)*rdr + 1.0;
int m = static_cast<int> (p);
m = MIN(m,nr-1);
p -= m;
p = MIN(p,1.0);
const int d_type2rhor_ji = d_type2rhor(jtype,itype);
rhotmp += ((d_rhor_spline(d_type2rhor_ji,m,3)*p + d_rhor_spline(d_type2rhor_ji,m,4))*p +
d_rhor_spline(d_type2rhor_ji,m,5))*p + d_rhor_spline(d_type2rhor_ji,m,6);
}
}
d_rho[i] += rhotmp;
// fp = derivative of embedding energy at each atom
// phi = embedding energy at each atom
// if rho > rhomax (e.g. due to close approach of two atoms),
// will exceed table, so add linear term to conserve energy
F_FLOAT p = d_rho[i]*rdrho + 1.0;
int m = static_cast<int> (p);
m = MAX(1,MIN(m,nrho-1));
p -= m;
p = MIN(p,1.0);
const int d_type2frho_i = d_type2frho[itype];
d_fp[i] = (d_frho_spline(d_type2frho_i,m,0)*p + d_frho_spline(d_type2frho_i,m,1))*p + d_frho_spline(d_type2frho_i,m,2);
if (EFLAG) {
F_FLOAT phi = ((d_frho_spline(d_type2frho_i,m,3)*p + d_frho_spline(d_type2frho_i,m,4))*p +
d_frho_spline(d_type2frho_i,m,5))*p + d_frho_spline(d_type2frho_i,m,6);
if (d_rho[i] > rhomax) phi += d_fp[i] * (d_rho[i]-rhomax);
if (eflag_global) ev.evdwl += phi;
if (eflag_atom) d_eatom[i] += phi;
}
}
template<class DeviceType>
template<int EFLAG>
KOKKOS_INLINE_FUNCTION
void PairEAMFSKokkos<DeviceType>::operator()(TagPairEAMFSKernelAB<EFLAG>, const int &ii) const {
EV_FLOAT ev;
this->template operator()<EFLAG>(TagPairEAMFSKernelAB<EFLAG>(), ii, ev);
}
/* ---------------------------------------------------------------------- */
////Specialisation for Neighborlist types Half, HalfThread, Full
template<class DeviceType>
template<int NEIGHFLAG, int NEWTON_PAIR, int EVFLAG>
KOKKOS_INLINE_FUNCTION
void PairEAMFSKokkos<DeviceType>::operator()(TagPairEAMFSKernelC<NEIGHFLAG,NEWTON_PAIR,EVFLAG>, const int &ii, EV_FLOAT& ev) const {
// The f array is atomic for Half/Thread neighbor style
Kokkos::View<F_FLOAT*[3], typename DAT::t_f_array::array_layout,DeviceType,Kokkos::MemoryTraits<AtomicF<NEIGHFLAG>::value> > a_f = f;
const int i = d_ilist[ii];
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 AtomNeighborsConst d_neighbors_i = k_list.get_neighbors_const(i);
const int jnum = d_numneigh[i];
F_FLOAT fxtmp = 0.0;
F_FLOAT fytmp = 0.0;
F_FLOAT fztmp = 0.0;
for (int jj = 0; jj < jnum; jj++) {
//int j = d_neighbors_i[jj];
int j = d_neighbors(i,jj);
j &= NEIGHMASK;
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 int jtype = type(j);
const F_FLOAT rsq = delx*delx + dely*dely + delz*delz;
if(rsq < cutforcesq) {
const F_FLOAT r = sqrt(rsq);
F_FLOAT p = r*rdr + 1.0;
int m = static_cast<int> (p);
m = MIN(m,nr-1);
p -= m;
p = MIN(p,1.0);
// rhoip = derivative of (density at atom j due to atom i)
// rhojp = derivative of (density at atom i due to atom j)
// phi = pair potential energy
// phip = phi'
// z2 = phi * r
// z2p = (phi * r)' = (phi' r) + phi
// psip needs both fp[i] and fp[j] terms since r_ij appears in two
// terms of embed eng: Fi(sum rho_ij) and Fj(sum rho_ji)
// hence embed' = Fi(sum rho_ij) rhojp + Fj(sum rho_ji) rhoip
const int d_type2rhor_ij = d_type2rhor(itype,jtype);
const F_FLOAT rhoip = (d_rhor_spline(d_type2rhor_ij,m,0)*p + d_rhor_spline(d_type2rhor_ij,m,1))*p +
d_rhor_spline(d_type2rhor_ij,m,2);
const int d_type2rhor_ji = d_type2rhor(jtype,itype);
const F_FLOAT rhojp = (d_rhor_spline(d_type2rhor_ji,m,0)*p + d_rhor_spline(d_type2rhor_ji,m,1))*p +
d_rhor_spline(d_type2rhor_ji,m,2);
const int d_type2z2r_ij = d_type2z2r(itype,jtype);
const F_FLOAT z2p = (d_z2r_spline(d_type2z2r_ij,m,0)*p + d_z2r_spline(d_type2z2r_ij,m,1))*p +
d_z2r_spline(d_type2z2r_ij,m,2);
const F_FLOAT z2 = ((d_z2r_spline(d_type2z2r_ij,m,3)*p + d_z2r_spline(d_type2z2r_ij,m,4))*p +
d_z2r_spline(d_type2z2r_ij,m,5))*p + d_z2r_spline(d_type2z2r_ij,m,6);
const F_FLOAT recip = 1.0/r;
const F_FLOAT phi = z2*recip;
const F_FLOAT phip = z2p*recip - phi*recip;
const F_FLOAT psip = d_fp[i]*rhojp + d_fp[j]*rhoip + phip;
const F_FLOAT fpair = -psip*recip;
fxtmp += delx*fpair;
fytmp += dely*fpair;
fztmp += delz*fpair;
if ((NEIGHFLAG==HALF || NEIGHFLAG==HALFTHREAD) && (NEWTON_PAIR || j < nlocal)) {
a_f(j,0) -= delx*fpair;
a_f(j,1) -= dely*fpair;
a_f(j,2) -= delz*fpair;
}
if (EVFLAG) {
if (eflag) {
ev.evdwl += (((NEIGHFLAG==HALF || NEIGHFLAG==HALFTHREAD)&&(NEWTON_PAIR||(j<nlocal)))?1.0:0.5)*phi;
}
if (vflag_either || eflag_atom) this->template ev_tally<NEIGHFLAG,NEWTON_PAIR>(ev,i,j,phi,fpair,delx,dely,delz);
}
}
}
a_f(i,0) += fxtmp;
a_f(i,1) += fytmp;
a_f(i,2) += fztmp;
}
template<class DeviceType>
template<int NEIGHFLAG, int NEWTON_PAIR, int EVFLAG>
KOKKOS_INLINE_FUNCTION
void PairEAMFSKokkos<DeviceType>::operator()(TagPairEAMFSKernelC<NEIGHFLAG,NEWTON_PAIR,EVFLAG>, const int &ii) const {
EV_FLOAT ev;
this->template operator()<NEIGHFLAG,NEWTON_PAIR,EVFLAG>(TagPairEAMFSKernelC<NEIGHFLAG,NEWTON_PAIR,EVFLAG>(), ii, ev);
}
/* ---------------------------------------------------------------------- */
template<class DeviceType>
template<int NEIGHFLAG, int NEWTON_PAIR>
KOKKOS_INLINE_FUNCTION
void PairEAMFSKokkos<DeviceType>::ev_tally(EV_FLOAT &ev, const int &i, const int &j,
const F_FLOAT &epair, const F_FLOAT &fpair, const F_FLOAT &delx,
const F_FLOAT &dely, const F_FLOAT &delz) const
{
const int EFLAG = eflag;
const int VFLAG = vflag_either;
// The eatom and vatom arrays are atomic for Half/Thread neighbor style
Kokkos::View<E_FLOAT*, typename DAT::t_efloat_1d::array_layout,DeviceType,Kokkos::MemoryTraits<AtomicF<NEIGHFLAG>::value> > v_eatom = k_eatom.view<DeviceType>();
Kokkos::View<F_FLOAT*[6], typename DAT::t_virial_array::array_layout,DeviceType,Kokkos::MemoryTraits<AtomicF<NEIGHFLAG>::value> > v_vatom = k_vatom.view<DeviceType>();
if (EFLAG) {
if (eflag_atom) {
const E_FLOAT epairhalf = 0.5 * epair;
if (NEIGHFLAG!=FULL) {
if (NEWTON_PAIR || i < nlocal) v_eatom[i] += epairhalf;
if (NEWTON_PAIR || j < nlocal) v_eatom[j] += epairhalf;
} else {
v_eatom[i] += epairhalf;
}
}
}
if (VFLAG) {
const E_FLOAT v0 = delx*delx*fpair;
const E_FLOAT v1 = dely*dely*fpair;
const E_FLOAT v2 = delz*delz*fpair;
const E_FLOAT v3 = delx*dely*fpair;
const E_FLOAT v4 = delx*delz*fpair;
const E_FLOAT v5 = dely*delz*fpair;
if (vflag_global) {
if (NEIGHFLAG!=FULL) {
if (NEWTON_PAIR || i < nlocal) {
ev.v[0] += 0.5*v0;
ev.v[1] += 0.5*v1;
ev.v[2] += 0.5*v2;
ev.v[3] += 0.5*v3;
ev.v[4] += 0.5*v4;
ev.v[5] += 0.5*v5;
}
if (NEWTON_PAIR || j < nlocal) {
ev.v[0] += 0.5*v0;
ev.v[1] += 0.5*v1;
ev.v[2] += 0.5*v2;
ev.v[3] += 0.5*v3;
ev.v[4] += 0.5*v4;
ev.v[5] += 0.5*v5;
}
} else {
ev.v[0] += 0.5*v0;
ev.v[1] += 0.5*v1;
ev.v[2] += 0.5*v2;
ev.v[3] += 0.5*v3;
ev.v[4] += 0.5*v4;
ev.v[5] += 0.5*v5;
}
}
if (vflag_atom) {
if (NEIGHFLAG!=FULL) {
if (NEWTON_PAIR || i < nlocal) {
v_vatom(i,0) += 0.5*v0;
v_vatom(i,1) += 0.5*v1;
v_vatom(i,2) += 0.5*v2;
v_vatom(i,3) += 0.5*v3;
v_vatom(i,4) += 0.5*v4;
v_vatom(i,5) += 0.5*v5;
}
if (NEWTON_PAIR || j < nlocal) {
v_vatom(j,0) += 0.5*v0;
v_vatom(j,1) += 0.5*v1;
v_vatom(j,2) += 0.5*v2;
v_vatom(j,3) += 0.5*v3;
v_vatom(j,4) += 0.5*v4;
v_vatom(j,5) += 0.5*v5;
}
} else {
v_vatom(i,0) += 0.5*v0;
v_vatom(i,1) += 0.5*v1;
v_vatom(i,2) += 0.5*v2;
v_vatom(i,3) += 0.5*v3;
v_vatom(i,4) += 0.5*v4;
v_vatom(i,5) += 0.5*v5;
}
}
}
}
/* ---------------------------------------------------------------------- */
// Duplicate PairEAMFS functions
/* ----------------------------------------------------------------------
set coeffs for one or more type pairs
read EAM Finnis-Sinclair file
------------------------------------------------------------------------- */
template<class DeviceType>
void PairEAMFSKokkos<DeviceType>::coeff(int narg, char **arg)
{
int i,j;
if (!allocated) allocate();
if (narg != 3 + atom->ntypes)
error->all(FLERR,"Incorrect args for pair coefficients");
// insure I,J args are * *
if (strcmp(arg[0],"*") != 0 || strcmp(arg[1],"*") != 0)
error->all(FLERR,"Incorrect args for pair coefficients");
// read EAM Finnis-Sinclair file
if (fs) {
for (i = 0; i < fs->nelements; i++) delete [] fs->elements[i];
delete [] fs->elements;
delete [] fs->mass;
memory->destroy(fs->frho);
memory->destroy(fs->rhor);
memory->destroy(fs->z2r);
delete fs;
}
fs = new Fs();
read_file(arg[2]);
// read args that map atom types to elements in potential file
// map[i] = which element the Ith atom type is, -1 if NULL
for (i = 3; i < narg; i++) {
if (strcmp(arg[i],"NULL") == 0) {
map[i-2] = -1;
continue;
}
for (j = 0; j < fs->nelements; j++)
if (strcmp(arg[i],fs->elements[j]) == 0) break;
if (j < fs->nelements) map[i-2] = j;
else error->all(FLERR,"No matching element in EAM potential file");
}
// clear setflag since coeff() called once with I,J = * *
int n = atom->ntypes;
for (i = 1; i <= n; i++)
for (j = i; j <= n; j++)
setflag[i][j] = 0;
// set setflag i,j for type pairs where both are mapped to elements
// set mass of atom type if i = j
int count = 0;
for (i = 1; i <= n; i++) {
for (j = i; j <= n; j++) {
if (map[i] >= 0 && map[j] >= 0) {
setflag[i][j] = 1;
if (i == j) atom->set_mass(i,fs->mass[map[i]]);
count++;
}
}
}
if (count == 0) error->all(FLERR,"Incorrect args for pair coefficients");
}
/* ----------------------------------------------------------------------
read a multi-element DYNAMO setfl file
------------------------------------------------------------------------- */
template<class DeviceType>
void PairEAMFSKokkos<DeviceType>::read_file(char *filename)
{
Fs *file = fs;
// open potential file
int me = comm->me;
FILE *fptr;
char line[MAXLINE];
if (me == 0) {
fptr = force->open_potential(filename);
if (fptr == NULL) {
char str[128];
sprintf(str,"Cannot open EAM potential file %s",filename);
error->one(FLERR,str);
}
}
// read and broadcast header
// extract element names from nelements line
int n;
if (me == 0) {
fgets(line,MAXLINE,fptr);
fgets(line,MAXLINE,fptr);
fgets(line,MAXLINE,fptr);
fgets(line,MAXLINE,fptr);
n = strlen(line) + 1;
}
MPI_Bcast(&n,1,MPI_INT,0,world);
MPI_Bcast(line,n,MPI_CHAR,0,world);
sscanf(line,"%d",&file->nelements);
int nwords = atom->count_words(line);
if (nwords != file->nelements + 1)
error->all(FLERR,"Incorrect element names in EAM potential file");
char **words = new char*[file->nelements+1];
nwords = 0;
strtok(line," \t\n\r\f");
while ((words[nwords++] = strtok(NULL," \t\n\r\f"))) continue;
file->elements = new char*[file->nelements];
for (int i = 0; i < file->nelements; i++) {
n = strlen(words[i]) + 1;
file->elements[i] = new char[n];
strcpy(file->elements[i],words[i]);
}
delete [] words;
if (me == 0) {
fgets(line,MAXLINE,fptr);
sscanf(line,"%d %lg %d %lg %lg",
&file->nrho,&file->drho,&file->nr,&file->dr,&file->cut);
}
MPI_Bcast(&file->nrho,1,MPI_INT,0,world);
MPI_Bcast(&file->drho,1,MPI_DOUBLE,0,world);
MPI_Bcast(&file->nr,1,MPI_INT,0,world);
MPI_Bcast(&file->dr,1,MPI_DOUBLE,0,world);
MPI_Bcast(&file->cut,1,MPI_DOUBLE,0,world);
file->mass = new double[file->nelements];
memory->create(file->frho,file->nelements,file->nrho+1,
"pair:frho");
memory->create(file->rhor,file->nelements,file->nelements,
file->nr+1,"pair:rhor");
memory->create(file->z2r,file->nelements,file->nelements,
file->nr+1,"pair:z2r");
int i,j,tmp;
for (i = 0; i < file->nelements; i++) {
if (me == 0) {
fgets(line,MAXLINE,fptr);
sscanf(line,"%d %lg",&tmp,&file->mass[i]);
}
MPI_Bcast(&file->mass[i],1,MPI_DOUBLE,0,world);
if (me == 0) grab(fptr,file->nrho,&file->frho[i][1]);
MPI_Bcast(&file->frho[i][1],file->nrho,MPI_DOUBLE,0,world);
for (j = 0; j < file->nelements; j++) {
if (me == 0) grab(fptr,file->nr,&file->rhor[i][j][1]);
MPI_Bcast(&file->rhor[i][j][1],file->nr,MPI_DOUBLE,0,world);
}
}
for (i = 0; i < file->nelements; i++)
for (j = 0; j <= i; j++) {
if (me == 0) grab(fptr,file->nr,&file->z2r[i][j][1]);
MPI_Bcast(&file->z2r[i][j][1],file->nr,MPI_DOUBLE,0,world);
}
// close the potential file
if (me == 0) fclose(fptr);
}
/* ----------------------------------------------------------------------
copy read-in setfl potential to standard array format
------------------------------------------------------------------------- */
template<class DeviceType>
void PairEAMFSKokkos<DeviceType>::file2array_fs()
{
int i,j,m,n;
int ntypes = atom->ntypes;
// set function params directly from fs file
nrho = fs->nrho;
nr = fs->nr;
drho = fs->drho;
dr = fs->dr;
rhomax = (nrho-1) * drho;
// ------------------------------------------------------------------
// setup frho arrays
// ------------------------------------------------------------------
// allocate frho arrays
// nfrho = # of fs elements + 1 for zero array
nfrho = fs->nelements + 1;
memory->destroy(frho);
memory->create(frho,nfrho,nrho+1,"pair:frho");
// copy each element's frho to global frho
for (i = 0; i < fs->nelements; i++)
for (m = 1; m <= nrho; m++) frho[i][m] = fs->frho[i][m];
// add extra frho of zeroes for non-EAM types to point to (pair hybrid)
// this is necessary b/c fp is still computed for non-EAM atoms
for (m = 1; m <= nrho; m++) frho[nfrho-1][m] = 0.0;
// type2frho[i] = which frho array (0 to nfrho-1) each atom type maps to
// if atom type doesn't point to element (non-EAM atom in pair hybrid)
// then map it to last frho array of zeroes
for (i = 1; i <= ntypes; i++)
if (map[i] >= 0) type2frho[i] = map[i];
else type2frho[i] = nfrho-1;
// ------------------------------------------------------------------
// setup rhor arrays
// ------------------------------------------------------------------
// allocate rhor arrays
// nrhor = square of # of fs elements
nrhor = fs->nelements * fs->nelements;
memory->destroy(rhor);
memory->create(rhor,nrhor,nr+1,"pair:rhor");
// copy each element pair rhor to global rhor
n = 0;
for (i = 0; i < fs->nelements; i++)
for (j = 0; j < fs->nelements; j++) {
for (m = 1; m <= nr; m++) rhor[n][m] = fs->rhor[i][j][m];
n++;
}
// type2rhor[i][j] = which rhor array (0 to nrhor-1) each type pair maps to
// for fs files, there is a full NxN set of rhor arrays
// OK if map = -1 (non-EAM atom in pair hybrid) b/c type2rhor not used
for (i = 1; i <= ntypes; i++)
for (j = 1; j <= ntypes; j++)
type2rhor[i][j] = map[i] * fs->nelements + map[j];
// ------------------------------------------------------------------
// setup z2r arrays
// ------------------------------------------------------------------
// allocate z2r arrays
// nz2r = N*(N+1)/2 where N = # of fs elements
nz2r = fs->nelements * (fs->nelements+1) / 2;
memory->destroy(z2r);
memory->create(z2r,nz2r,nr+1,"pair:z2r");
// copy each element pair z2r to global z2r, only for I >= J
n = 0;
for (i = 0; i < fs->nelements; i++)
for (j = 0; j <= i; j++) {
for (m = 1; m <= nr; m++) z2r[n][m] = fs->z2r[i][j][m];
n++;
}
// type2z2r[i][j] = which z2r array (0 to nz2r-1) each type pair maps to
// set of z2r arrays only fill lower triangular Nelement matrix
// value = n = sum over rows of lower-triangular matrix until reach irow,icol
// swap indices when irow < icol to stay lower triangular
// if map = -1 (non-EAM atom in pair hybrid):
// type2z2r is not used by non-opt
// but set type2z2r to 0 since accessed by opt
int irow,icol;
for (i = 1; i <= ntypes; i++) {
for (j = 1; j <= ntypes; j++) {
irow = map[i];
icol = map[j];
if (irow == -1 || icol == -1) {
type2z2r[i][j] = 0;
continue;
}
if (irow < icol) {
irow = map[j];
icol = map[i];
}
n = 0;
for (m = 0; m < irow; m++) n += m + 1;
n += icol;
type2z2r[i][j] = n;
}
}
}
/* ---------------------------------------------------------------------- */
template class PairEAMFSKokkos<LMPDeviceType>;
#ifdef KOKKOS_HAVE_CUDA
template class PairEAMFSKokkos<LMPHostType>;
#endif

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