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pair_lj_gromacs_kokkos.cpp
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Sun, Jul 28, 10:29

pair_lj_gromacs_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)
------------------------------------------------------------------------- */
#include <math.h>
#include <stdio.h>
#include <stdlib.h>
#include <string.h>
#include "pair_lj_gromacs_kokkos.h"
#include "kokkos.h"
#include "atom_kokkos.h"
#include "comm.h"
#include "force.h"
#include "neighbor.h"
#include "neigh_list.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 "atom_masks.h"
using namespace LAMMPS_NS;
using namespace MathConst;
#define KOKKOS_CUDA_MAX_THREADS 256
#define KOKKOS_CUDA_MIN_BLOCKS 8
/* ---------------------------------------------------------------------- */
template<class DeviceType>
PairLJGromacsKokkos<DeviceType>::PairLJGromacsKokkos(LAMMPS *lmp):PairLJGromacs(lmp)
{
respa_enable = 0;
atomKK = (AtomKokkos *) atom;
execution_space = ExecutionSpaceFromDevice<DeviceType>::space;
datamask_read = X_MASK | F_MASK | TYPE_MASK | Q_MASK | ENERGY_MASK | VIRIAL_MASK;
datamask_modify = F_MASK | ENERGY_MASK | VIRIAL_MASK;
cutsq = NULL;
cut_inner = NULL;
cut_inner_sq = NULL;
}
/* ---------------------------------------------------------------------- */
template<class DeviceType>
PairLJGromacsKokkos<DeviceType>::~PairLJGromacsKokkos()
{
if (!copymode) {
memory->destroy_kokkos(k_eatom,eatom);
memory->destroy_kokkos(k_vatom,vatom);
k_cutsq = DAT::tdual_ffloat_2d();
k_cut_inner_sq = DAT::tdual_ffloat_2d();
memory->sfree(cutsq);
eatom = NULL;
vatom = NULL;
cutsq = NULL;
cut_inner = NULL;
cut_inner_sq = NULL;
}
}
/* ---------------------------------------------------------------------- */
template<class DeviceType>
void PairLJGromacsKokkos<DeviceType>::cleanup_copy() {
// WHY needed: this prevents parent copy from deallocating any arrays
allocated = 0;
cutsq = NULL;
cut_inner = NULL;
cut_inner_sq = NULL;
eatom = NULL;
vatom = NULL;
}
/* ---------------------------------------------------------------------- */
template<class DeviceType>
void PairLJGromacsKokkos<DeviceType>::compute(int eflag_in, int vflag_in)
{
eflag = eflag_in;
vflag = vflag_in;
if (neighflag == FULL || neighflag == FULLCLUSTER) no_virial_fdotr_compute = 1;
if (eflag || vflag) ev_setup(eflag,vflag);
else evflag = vflag_fdotr = 0;
atomKK->sync(execution_space,datamask_read);
k_cutsq.template sync<DeviceType>();
k_cut_inner.template sync<DeviceType>();
k_cut_inner_sq.template sync<DeviceType>();
k_params.template sync<DeviceType>();
if (eflag || vflag) atomKK->modified(execution_space,datamask_modify);
else atomKK->modified(execution_space,F_MASK);
x = atomKK->k_x.view<DeviceType>();
c_x = atomKK->k_x.view<DeviceType>();
f = atomKK->k_f.view<DeviceType>();
q = atomKK->k_q.view<DeviceType>();
type = atomKK->k_type.view<DeviceType>();
nlocal = atom->nlocal;
nall = atom->nlocal + atom->nghost;
special_lj[0] = force->special_lj[0];
special_lj[1] = force->special_lj[1];
special_lj[2] = force->special_lj[2];
special_lj[3] = force->special_lj[3];
qqrd2e = force->qqrd2e;
newton_pair = force->newton_pair;
// loop over neighbors of my atoms
copymode = 1;
EV_FLOAT ev = pair_compute<PairLJGromacsKokkos<DeviceType>,CoulLongTable<0> >
(this,(NeighListKokkos<DeviceType>*)list);
if (eflag) {
eng_vdwl += ev.evdwl;
eng_coul += 0.0;
}
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);
copymode = 0;
}
/* ----------------------------------------------------------------------
compute LJ GROMACS pair force between atoms i and j
---------------------------------------------------------------------- */
template<class DeviceType>
template<bool STACKPARAMS, class Specialisation>
KOKKOS_INLINE_FUNCTION
F_FLOAT PairLJGromacsKokkos<DeviceType>::
compute_fpair(const F_FLOAT& rsq, const int& i, const int&j,
const int& itype, const int& jtype) const {
const F_FLOAT r2inv = 1.0/rsq;
const F_FLOAT r6inv = r2inv*r2inv*r2inv;
F_FLOAT forcelj = r6inv *
((STACKPARAMS?m_params[itype][jtype].lj1:params(itype,jtype).lj1)*r6inv -
(STACKPARAMS?m_params[itype][jtype].lj2:params(itype,jtype).lj2));
if (rsq > (STACKPARAMS?m_params[itype][jtype].cut_inner_sq:params(itype,jtype).cut_inner_sq)) {
const F_FLOAT r = sqrt(rsq);
const F_FLOAT tlj = r - (STACKPARAMS?m_params[itype][jtype].cut_inner:params(itype,jtype).cut_inner);
const F_FLOAT fswitch = r*tlj*tlj*
((STACKPARAMS?m_params[itype][jtype].ljsw1:params(itype,jtype).ljsw1) +
(STACKPARAMS?m_params[itype][jtype].ljsw2:params(itype,jtype).ljsw2)*tlj);
forcelj += fswitch;
}
return forcelj*r2inv;
}
/* ----------------------------------------------------------------------
compute LJ GROMACS pair potential energy between atoms i and j
---------------------------------------------------------------------- */
template<class DeviceType>
template<bool STACKPARAMS, class Specialisation>
KOKKOS_INLINE_FUNCTION
F_FLOAT PairLJGromacsKokkos<DeviceType>::
compute_evdwl(const F_FLOAT& rsq, const int& i, const int&j,
const int& itype, const int& jtype) const {
const F_FLOAT r2inv = 1.0/rsq;
const F_FLOAT r6inv = r2inv*r2inv*r2inv;
F_FLOAT englj = r6inv *
((STACKPARAMS?m_params[itype][jtype].lj3:params(itype,jtype).lj3)*r6inv -
(STACKPARAMS?m_params[itype][jtype].lj4:params(itype,jtype).lj4));
englj += (STACKPARAMS?m_params[itype][jtype].ljsw5:params(itype,jtype).ljsw5);
if (rsq > (STACKPARAMS?m_params[itype][jtype].cut_inner_sq:params(itype,jtype).cut_inner_sq)) {
const F_FLOAT r = sqrt(rsq);
const F_FLOAT tlj = r - (STACKPARAMS?m_params[itype][jtype].cut_inner:params(itype,jtype).cut_inner);
const F_FLOAT eswitch = tlj*tlj*tlj *
((STACKPARAMS?m_params[itype][jtype].ljsw3:params(itype,jtype).ljsw3) +
(STACKPARAMS?m_params[itype][jtype].ljsw4:params(itype,jtype).ljsw4)*tlj);
englj += eswitch;
}
return englj;
}
/* ----------------------------------------------------------------------
allocate all arrays
------------------------------------------------------------------------- */
template<class DeviceType>
void PairLJGromacsKokkos<DeviceType>::allocate()
{
PairLJGromacs::allocate();
int n = atom->ntypes;
memory->destroy(cutsq);
memory->create_kokkos(k_cutsq,cutsq,n+1,n+1,"pair:cutsq");
d_cutsq = k_cutsq.template view<DeviceType>();
memory->destroy(cut_inner);
memory->create_kokkos(k_cut_inner,cut_inner,n+1,n+1,"pair:cut_inner");
d_cut_inner = k_cut_inner.template view<DeviceType>();
memory->destroy(cut_inner_sq);
memory->create_kokkos(k_cut_inner_sq,cut_inner_sq,n+1,n+1,"pair:cut_inner_sq");
d_cut_inner_sq = k_cut_inner_sq.template view<DeviceType>();
k_params = Kokkos::DualView<params_lj**,Kokkos::LayoutRight,DeviceType>("PairLJGromacs::params",n+1,n+1);
params = k_params.d_view;
}
/* ----------------------------------------------------------------------
global settings
------------------------------------------------------------------------- */
template<class DeviceType>
void PairLJGromacsKokkos<DeviceType>::settings(int narg, char **arg)
{
if (narg != 2) error->all(FLERR,"Illegal pair_style command");
PairLJGromacs::settings(narg,arg);
}
/* ----------------------------------------------------------------------
init specific to this pair style
------------------------------------------------------------------------- */
template<class DeviceType>
void PairLJGromacsKokkos<DeviceType>::init_style()
{
PairLJGromacs::init_style();
// error if rRESPA with inner levels
if (update->whichflag == 1 && strstr(update->integrate_style,"respa")) {
int respa = 0;
if (((Respa *) update->integrate)->level_inner >= 0) respa = 1;
if (((Respa *) update->integrate)->level_middle >= 0) respa = 2;
if (respa)
error->all(FLERR,"Cannot use Kokkos pair style with rRESPA inner/middle");
}
// 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 lj/gromacs/kk");
}
}
/* ----------------------------------------------------------------------
init for one type pair i,j and corresponding j,i
------------------------------------------------------------------------- */
template<class DeviceType>
double PairLJGromacsKokkos<DeviceType>::init_one(int i, int j)
{
double cutone = PairLJGromacs::init_one(i,j);
double cut_inner_sqm = cut_inner_sq[i][j];
k_params.h_view(i,j).lj1 = lj1[i][j];
k_params.h_view(i,j).lj2 = lj2[i][j];
k_params.h_view(i,j).lj3 = lj3[i][j];
k_params.h_view(i,j).lj4 = lj4[i][j];
k_params.h_view(i,j).ljsw1 = ljsw1[i][j];
k_params.h_view(i,j).ljsw2 = ljsw2[i][j];
k_params.h_view(i,j).ljsw3 = ljsw3[i][j];
k_params.h_view(i,j).ljsw4 = ljsw4[i][j];
k_params.h_view(i,j).ljsw5 = ljsw5[i][j];
k_params.h_view(i,j).cut_inner_sq = cut_inner_sqm;
k_params.h_view(i,j).cut_inner = cut_inner[i][j];
k_params.h_view(j,i) = k_params.h_view(i,j);
if(i<MAX_TYPES_STACKPARAMS+1 && j<MAX_TYPES_STACKPARAMS+1) {
m_params[i][j] = m_params[j][i] = k_params.h_view(i,j);
m_cutsq[j][i] = m_cutsq[i][j] = cutone*cutone;
m_cut_inner_sq[j][i] = m_cut_inner_sq[i][j] = cut_inner_sqm;
}
k_cutsq.h_view(i,j) = cutone*cutone;
k_cutsq.template modify<LMPHostType>();
k_cut_inner_sq.h_view(i,j) = cut_inner_sqm;
k_cut_inner_sq.template modify<LMPHostType>();
k_params.template modify<LMPHostType>();
return cutone;
}
namespace LAMMPS_NS {
template class PairLJGromacsKokkos<LMPDeviceType>;
#ifdef KOKKOS_HAVE_CUDA
template class PairLJGromacsKokkos<LMPHostType>;
#endif
}

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