Homec4science
Diffusion lammps (lammm-master-deprecated) Browse

lammps/src/KOKKOS/pair_eam_kokkos.cpp
1ccda0261e9blammm-master-deprecated

Last Change
Raw File

pair_eam_kokkos.cpp
View Options

/* ----------------------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
http://lammps.sandia.gov, Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
/* ----------------------------------------------------------------------
Contributing authors: Stan Moore (SNL), Christian Trott (SNL)
------------------------------------------------------------------------- */
#include <math.h>
#include <stdio.h>
#include <stdlib.h>
#include <string.h>
#include "kokkos.h"
#include "pair_kokkos.h"
#include "pair_eam_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;
/* ---------------------------------------------------------------------- */
template<class DeviceType>
PairEAMKokkos<DeviceType>::PairEAMKokkos(LAMMPS *lmp) : PairEAM(lmp)
{
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>
PairEAMKokkos<DeviceType>::~PairEAMKokkos()
{
if (!copymode) {
memory->destroy_kokkos(k_eatom,eatom);
memory->destroy_kokkos(k_vatom,vatom);
}
}
/* ---------------------------------------------------------------------- */
template<class DeviceType>
void PairEAMKokkos<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, TagPairEAMInitialize>(0,nall),*this);
else
Kokkos::parallel_for(Kokkos::RangePolicy<DeviceType, TagPairEAMInitialize>(0,nlocal),*this);
// 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, TagPairEAMKernelA<HALF,1> >(0,inum),*this);
} else {
Kokkos::parallel_for(Kokkos::RangePolicy<DeviceType, TagPairEAMKernelA<HALF,0> >(0,inum),*this);
}
} else if (neighflag == HALFTHREAD) {
if (newton_pair) {
Kokkos::parallel_for(Kokkos::RangePolicy<DeviceType, TagPairEAMKernelA<HALFTHREAD,1> >(0,inum),*this);
} else {
Kokkos::parallel_for(Kokkos::RangePolicy<DeviceType, TagPairEAMKernelA<HALFTHREAD,0> >(0,inum),*this);
}
}
// 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, TagPairEAMKernelB<1> >(0,inum),*this,ev);
else
Kokkos::parallel_for(Kokkos::RangePolicy<DeviceType, TagPairEAMKernelB<0> >(0,inum),*this);
} else if (neighflag == FULL) {
// compute kernel AB
if (eflag)
Kokkos::parallel_reduce(Kokkos::RangePolicy<DeviceType, TagPairEAMKernelAB<1> >(0,inum),*this,ev);
else
Kokkos::parallel_for(Kokkos::RangePolicy<DeviceType, TagPairEAMKernelAB<0> >(0,inum),*this);
}
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, TagPairEAMKernelC<HALF,1,1> >(0,inum),*this,ev);
} else {
Kokkos::parallel_reduce(Kokkos::RangePolicy<DeviceType, TagPairEAMKernelC<HALF,0,1> >(0,inum),*this,ev);
}
} else if (neighflag == HALFTHREAD) {
if (newton_pair) {
Kokkos::parallel_reduce(Kokkos::RangePolicy<DeviceType, TagPairEAMKernelC<HALFTHREAD,1,1> >(0,inum),*this,ev);
} else {
Kokkos::parallel_reduce(Kokkos::RangePolicy<DeviceType, TagPairEAMKernelC<HALFTHREAD,0,1> >(0,inum),*this,ev);
}
} else if (neighflag == FULL) {
if (newton_pair) {
Kokkos::parallel_reduce(Kokkos::RangePolicy<DeviceType, TagPairEAMKernelC<FULL,1,1> >(0,inum),*this,ev);
} else {
Kokkos::parallel_reduce(Kokkos::RangePolicy<DeviceType, TagPairEAMKernelC<FULL,0,1> >(0,inum),*this,ev);
}
}
} else {
if (neighflag == HALF) {
if (newton_pair) {
Kokkos::parallel_for(Kokkos::RangePolicy<DeviceType, TagPairEAMKernelC<HALF,1,0> >(0,inum),*this);
} else {
Kokkos::parallel_for(Kokkos::RangePolicy<DeviceType, TagPairEAMKernelC<HALF,0,0> >(0,inum),*this);
}
} else if (neighflag == HALFTHREAD) {
if (newton_pair) {
Kokkos::parallel_for(Kokkos::RangePolicy<DeviceType, TagPairEAMKernelC<HALFTHREAD,1,0> >(0,inum),*this);
} else {
Kokkos::parallel_for(Kokkos::RangePolicy<DeviceType, TagPairEAMKernelC<HALFTHREAD,0,0> >(0,inum),*this);
}
} else if (neighflag == FULL) {
if (newton_pair) {
Kokkos::parallel_for(Kokkos::RangePolicy<DeviceType, TagPairEAMKernelC<FULL,1,0> >(0,inum),*this);
} else {
Kokkos::parallel_for(Kokkos::RangePolicy<DeviceType, TagPairEAMKernelC<FULL,0,0> >(0,inum),*this);
}
}
}
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 PairEAMKokkos<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");
}
}
/* ----------------------------------------------------------------------
convert read-in funcfl potential(s) to standard array format
interpolate all file values to a single grid and cutoff
------------------------------------------------------------------------- */
template<class DeviceType>
void PairEAMKokkos<DeviceType>::file2array()
{
PairEAM::file2array();
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 PairEAMKokkos<DeviceType>::array2spline()
{
rdr = 1.0/dr;
rdrho = 1.0/drho;
tdual_ffloat4 k_frho_spline_a = tdual_ffloat4("pair:frho_a",nfrho,nrho+1);
tdual_ffloat4 k_rhor_spline_a = tdual_ffloat4("pair:rhor_a",nrhor,nr+1);
tdual_ffloat4 k_z2r_spline_a = tdual_ffloat4("pair:z2r_a",nz2r,nr+1);
tdual_ffloat4 k_frho_spline_b = tdual_ffloat4("pair:frho_b",nfrho,nrho+1);
tdual_ffloat4 k_rhor_spline_b = tdual_ffloat4("pair:rhor_b",nrhor,nr+1);
tdual_ffloat4 k_z2r_spline_b = tdual_ffloat4("pair:z2r_b",nz2r,nr+1);
t_host_ffloat4 h_frho_spline_a = k_frho_spline_a.h_view;
t_host_ffloat4 h_rhor_spline_a = k_rhor_spline_a.h_view;
t_host_ffloat4 h_z2r_spline_a = k_z2r_spline_a.h_view;
t_host_ffloat4 h_frho_spline_b = k_frho_spline_b.h_view;
t_host_ffloat4 h_rhor_spline_b = k_rhor_spline_b.h_view;
t_host_ffloat4 h_z2r_spline_b = k_z2r_spline_b.h_view;
for (int i = 0; i < nfrho; i++)
interpolate(nrho,drho,frho[i],h_frho_spline_a,h_frho_spline_b,i);
k_frho_spline_a.template modify<LMPHostType>();
k_frho_spline_a.template sync<DeviceType>();
k_frho_spline_b.template modify<LMPHostType>();
k_frho_spline_b.template sync<DeviceType>();
for (int i = 0; i < nrhor; i++)
interpolate(nr,dr,rhor[i],h_rhor_spline_a,h_rhor_spline_b,i);
k_rhor_spline_a.template modify<LMPHostType>();
k_rhor_spline_a.template sync<DeviceType>();
k_rhor_spline_b.template modify<LMPHostType>();
k_rhor_spline_b.template sync<DeviceType>();
for (int i = 0; i < nz2r; i++)
interpolate(nr,dr,z2r[i],h_z2r_spline_a,h_z2r_spline_b,i);
k_z2r_spline_a.template modify<LMPHostType>();
k_z2r_spline_a.template sync<DeviceType>();
k_z2r_spline_b.template modify<LMPHostType>();
k_z2r_spline_b.template sync<DeviceType>();
d_frho_spline_a = k_frho_spline_a.d_view;
d_rhor_spline_a = k_rhor_spline_a.d_view;
d_z2r_spline_a = k_z2r_spline_a.d_view;
d_frho_spline_b = k_frho_spline_b.d_view;
d_rhor_spline_b = k_rhor_spline_b.d_view;
d_z2r_spline_b = k_z2r_spline_b.d_view;
}
/* ---------------------------------------------------------------------- */
template<class DeviceType>
void PairEAMKokkos<DeviceType>::interpolate(int n, double delta, double *f, t_host_ffloat4 h_spline_a, t_host_ffloat4 h_spline_b, int i)
{
for (int m = 1; m <= n; m++) h_spline_b(i,m).w = f[m];
h_spline_b(i,1).z = h_spline_b(i,2).w - h_spline_b(i,1).w;
h_spline_b(i,2).z = 0.5 * (h_spline_b(i,3).w-h_spline_b(i,1).w);
h_spline_b(i,n-1).z = 0.5 * (h_spline_b(i,n).w-h_spline_b(i,n-2).w);
h_spline_b(i,n).z = h_spline_b(i,n).w - h_spline_b(i,n-1).w;
for (int m = 3; m <= n-2; m++)
h_spline_b(i,m).z = ((h_spline_b(i,m-2).w-h_spline_b(i,m+2).w) +
8.0*(h_spline_b(i,m+1).w-h_spline_b(i,m-1).w)) / 12.0;
for (int m = 1; m <= n-1; m++) {
h_spline_b(i,m).y = 3.0*(h_spline_b(i,m+1).w-h_spline_b(i,m).w) -
2.0*h_spline_b(i,m).z - h_spline_b(i,m+1).z;
h_spline_b(i,m).x = h_spline_b(i,m).z + h_spline_b(i,m+1).z -
2.0*(h_spline_b(i,m+1).w-h_spline_b(i,m).w);
}
h_spline_b(i,n).y = 0.0;
h_spline_b(i,n).x = 0.0;
for (int m = 1; m <= n; m++) {
h_spline_a(i,m).z = h_spline_b(i,m).z/delta;
h_spline_a(i,m).y = 2.0*h_spline_b(i,m).y/delta;
h_spline_a(i,m).x = 3.0*h_spline_b(i,m).x/delta;
}
}
/* ---------------------------------------------------------------------- */
template<class DeviceType>
int PairEAMKokkos<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, TagPairEAMPackForwardComm>(0,n),*this);
DeviceType::fence();
return n;
}
template<class DeviceType>
KOKKOS_INLINE_FUNCTION
void PairEAMKokkos<DeviceType>::operator()(TagPairEAMPackForwardComm, const int &i) const {
int j = d_sendlist(iswap, i);
v_buf[i] = d_fp[j];
}
/* ---------------------------------------------------------------------- */
template<class DeviceType>
void PairEAMKokkos<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, TagPairEAMUnpackForwardComm>(0,n),*this);
DeviceType::fence();
}
template<class DeviceType>
KOKKOS_INLINE_FUNCTION
void PairEAMKokkos<DeviceType>::operator()(TagPairEAMUnpackForwardComm, const int &i) const {
d_fp[i + first] = v_buf[i];
}
/* ---------------------------------------------------------------------- */
template<class DeviceType>
int PairEAMKokkos<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 PairEAMKokkos<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 PairEAMKokkos<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 PairEAMKokkos<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 PairEAMKokkos<DeviceType>::operator()(TagPairEAMInitialize, 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 PairEAMKokkos<DeviceType>::operator()(TagPairEAMKernelA<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);
const F_FLOAT4 rhor = d_rhor_spline_b(d_type2rhor_ji,m);
rhotmp += ((rhor.x*p + rhor.y)*p + rhor.z)*p + rhor.w;
if (NEWTON_PAIR || j < nlocal) {
const int d_type2rhor_ij = d_type2rhor(itype,jtype);
const F_FLOAT4 rhor = d_rhor_spline_b(d_type2rhor_ij,m);
rho[j] += ((rhor.x*p + rhor.y)*p + rhor.z)*p + rhor.w;
}
}
}
rho[i] += rhotmp;
}
/* ---------------------------------------------------------------------- */
////Specialisation for Neighborlist types Half, HalfThread, Full
template<class DeviceType>
template<int EFLAG>
KOKKOS_INLINE_FUNCTION
void PairEAMKokkos<DeviceType>::operator()(TagPairEAMKernelB<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];
const F_FLOAT4 frho = d_frho_spline_a(d_type2frho_i,m);
d_fp[i] = (frho.x*p + frho.y)*p + frho.z;
if (EFLAG) {
const F_FLOAT4 frho_b = d_frho_spline_b(d_type2frho_i,m);
F_FLOAT phi = ((frho_b.x*p + frho_b.y)*p + frho_b.z)*p + frho_b.w;
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 PairEAMKokkos<DeviceType>::operator()(TagPairEAMKernelB<EFLAG>, const int &ii) const {
EV_FLOAT ev;
this->template operator()<EFLAG>(TagPairEAMKernelB<EFLAG>(), ii, ev);
}
/* ---------------------------------------------------------------------- */
////Specialisation for Neighborlist types Half, HalfThread, Full
template<class DeviceType>
template<int EFLAG>
KOKKOS_INLINE_FUNCTION
void PairEAMKokkos<DeviceType>::operator()(TagPairEAMKernelAB<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);
const F_FLOAT4 rhor = d_rhor_spline_b(d_type2rhor_ji,m);
rhotmp += ((rhor.x*p + rhor.y)*p + rhor.z)*p + rhor.w;
}
}
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];
const F_FLOAT4 frho = d_frho_spline_a(d_type2frho_i,m);
d_fp[i] = (frho.x*p + frho.y)*p + frho.z;
if (EFLAG) {
const F_FLOAT4 frho_b = d_frho_spline_b(d_type2frho_i,m);
F_FLOAT phi = ((frho_b.x*p + frho_b.y)*p + frho_b.z)*p + frho_b.w;
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 PairEAMKokkos<DeviceType>::operator()(TagPairEAMKernelAB<EFLAG>, const int &ii) const {
EV_FLOAT ev;
this->template operator()<EFLAG>(TagPairEAMKernelAB<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 PairEAMKokkos<DeviceType>::operator()(TagPairEAMKernelC<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_FLOAT4 rhor_ij = d_rhor_spline_a(d_type2rhor_ij,m);
const F_FLOAT rhoip = (rhor_ij.x*p + rhor_ij.y)*p + rhor_ij.z;
const int d_type2rhor_ji = d_type2rhor(jtype,itype);
const F_FLOAT4 rhor_ji = d_rhor_spline_a(d_type2rhor_ji,m);
const F_FLOAT rhojp = (rhor_ji.x*p + rhor_ji.y)*p + rhor_ji.z;
const int d_type2z2r_ij = d_type2z2r(itype,jtype);
const F_FLOAT4 z2r_a = d_z2r_spline_a(d_type2z2r_ij,m);
const F_FLOAT z2p = (z2r_a.x*p + z2r_a.y)*p + z2r_a.z;
const F_FLOAT4 z2r_b = d_z2r_spline_b(d_type2z2r_ij,m);
const F_FLOAT z2 = ((z2r_b.x*p + z2r_b.y)*p + z2r_b.z)*p + z2r_b.w;
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 PairEAMKokkos<DeviceType>::operator()(TagPairEAMKernelC<NEIGHFLAG,NEWTON_PAIR,EVFLAG>, const int &ii) const {
EV_FLOAT ev;
this->template operator()<NEIGHFLAG,NEWTON_PAIR,EVFLAG>(TagPairEAMKernelC<NEIGHFLAG,NEWTON_PAIR,EVFLAG>(), ii, ev);
}
/* ---------------------------------------------------------------------- */
template<class DeviceType>
template<int NEIGHFLAG, int NEWTON_PAIR>
KOKKOS_INLINE_FUNCTION
void PairEAMKokkos<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;
}
}
}
}
namespace LAMMPS_NS {
template class PairEAMKokkos<LMPDeviceType>;
#ifdef KOKKOS_HAVE_CUDA
template class PairEAMKokkos<LMPHostType>;
#endif
}
c4science · Help