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pair_dpd_intel.cpp
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pair_dpd_intel.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
This software is distributed under the GNU General Public License.
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
/* ----------------------------------------------------------------------
Contributing author: W. Michael Brown (Intel)
Shun Xu (Computer Network Information Center, CAS)
------------------------------------------------------------------------- */
#include <math.h>
#include "pair_dpd_intel.h"
#include "atom.h"
#include "comm.h"
#include "force.h"
#include "memory.h"
#include "modify.h"
#include "neighbor.h"
#include "neigh_list.h"
#include "neigh_request.h"
#include "suffix.h"
using namespace LAMMPS_NS;
#define LMP_MKL_RNG VSL_BRNG_MT19937
#define FC_PACKED1_T typename ForceConst<flt_t>::fc_packed1
#define IEPSILON 1.0e10
/* ---------------------------------------------------------------------- */
PairDPDIntel::PairDPDIntel(LAMMPS *lmp) :
PairDPD(lmp)
{
suffix_flag |= Suffix::INTEL;
respa_enable = 0;
random_thread = NULL;
_nrandom_thread = 0;
}
/* ---------------------------------------------------------------------- */
PairDPDIntel::~PairDPDIntel()
{
#if defined(_OPENMP)
if (_nrandom_thread) {
#ifdef LMP_USE_MKL_RNG
for (int i = 0; i < _nrandom_thread; i++)
vslDeleteStream(&random_thread[i]);
#else
for (int i = 1; i < _nrandom_thread; i++)
delete random_thread[i];
#endif
}
#endif
delete []random_thread;
}
/* ---------------------------------------------------------------------- */
void PairDPDIntel::compute(int eflag, int vflag)
{
if (fix->precision() == FixIntel::PREC_MODE_MIXED)
compute<float,double>(eflag, vflag, fix->get_mixed_buffers(),
force_const_single);
else if (fix->precision() == FixIntel::PREC_MODE_DOUBLE)
compute<double,double>(eflag, vflag, fix->get_double_buffers(),
force_const_double);
else
compute<float,float>(eflag, vflag, fix->get_single_buffers(),
force_const_single);
fix->balance_stamp();
vflag_fdotr = 0;
}
template <class flt_t, class acc_t>
void PairDPDIntel::compute(int eflag, int vflag,
IntelBuffers<flt_t,acc_t> *buffers,
const ForceConst<flt_t> &fc)
{
if (eflag || vflag) {
ev_setup(eflag, vflag);
} else evflag = vflag_fdotr = 0;
const int inum = list->inum;
const int nthreads = comm->nthreads;
const int host_start = fix->host_start_pair();
const int offload_end = fix->offload_end_pair();
const int ago = neighbor->ago;
if (ago != 0 && fix->separate_buffers() == 0) {
fix->start_watch(TIME_PACK);
int packthreads;
if (nthreads > INTEL_HTHREADS) packthreads = nthreads;
else packthreads = 1;
#if defined(_OPENMP)
#pragma omp parallel if(packthreads > 1)
#endif
{
int ifrom, ito, tid;
IP_PRE_omp_range_id_align(ifrom, ito, tid, atom->nlocal + atom->nghost,
packthreads, sizeof(ATOM_T));
buffers->thr_pack(ifrom,ito,ago);
}
fix->stop_watch(TIME_PACK);
}
int ovflag = 0;
if (vflag_fdotr) ovflag = 2;
else if (vflag) ovflag = 1;
if (_onetype) {
if (eflag) {
if (force->newton_pair) {
eval<1,1,1>(1, ovflag, buffers, fc, 0, offload_end);
eval<1,1,1>(0, ovflag, buffers, fc, host_start, inum);
} else {
eval<1,1,0>(1, ovflag, buffers, fc, 0, offload_end);
eval<1,1,0>(0, ovflag, buffers, fc, host_start, inum);
}
} else {
if (force->newton_pair) {
eval<1,0,1>(1, ovflag, buffers, fc, 0, offload_end);
eval<1,0,1>(0, ovflag, buffers, fc, host_start, inum);
} else {
eval<1,0,0>(1, ovflag, buffers, fc, 0, offload_end);
eval<1,0,0>(0, ovflag, buffers, fc, host_start, inum);
}
}
} else {
if (eflag) {
if (force->newton_pair) {
eval<0,1,1>(1, ovflag, buffers, fc, 0, offload_end);
eval<0,1,1>(0, ovflag, buffers, fc, host_start, inum);
} else {
eval<0,1,0>(1, ovflag, buffers, fc, 0, offload_end);
eval<0,1,0>(0, ovflag, buffers, fc, host_start, inum);
}
} else {
if (force->newton_pair) {
eval<0,0,1>(1, ovflag, buffers, fc, 0, offload_end);
eval<0,0,1>(0, ovflag, buffers, fc, host_start, inum);
} else {
eval<0,0,0>(1, ovflag, buffers, fc, 0, offload_end);
eval<0,0,0>(0, ovflag, buffers, fc, host_start, inum);
}
}
}
}
template <int ONETYPE, int EFLAG, int NEWTON_PAIR, class flt_t, class acc_t>
void PairDPDIntel::eval(const int offload, const int vflag,
IntelBuffers<flt_t,acc_t> *buffers,
const ForceConst<flt_t> &fc,
const int astart, const int aend)
{
const int inum = aend - astart;
if (inum == 0) return;
int nlocal, nall, minlocal;
fix->get_buffern(offload, nlocal, nall, minlocal);
const int ago = neighbor->ago;
IP_PRE_pack_separate_buffers(fix, buffers, ago, offload, nlocal, nall);
ATOM_T * _noalias const x = buffers->get_x(offload);
typedef struct { double x, y, z; } lmp_vt;
lmp_vt *v = (lmp_vt *)atom->v[0];
const flt_t dtinvsqrt = 1.0/sqrt(update->dt);
const int * _noalias const numneigh = list->numneigh;
const int * _noalias const cnumneigh = buffers->cnumneigh(list);
const int * _noalias const firstneigh = buffers->firstneigh(list);
const FC_PACKED1_T * _noalias const param = fc.param[0];
const flt_t * _noalias const special_lj = fc.special_lj;
int * _noalias const rngi_thread = fc.rngi;
const int rng_size = buffers->get_max_nbors();
const int ntypes = atom->ntypes + 1;
const int eatom = this->eflag_atom;
// Determine how much data to transfer
int x_size, q_size, f_stride, ev_size, separate_flag;
IP_PRE_get_transfern(ago, NEWTON_PAIR, EFLAG, vflag,
buffers, offload, fix, separate_flag,
x_size, q_size, ev_size, f_stride);
int tc;
FORCE_T * _noalias f_start;
acc_t * _noalias ev_global;
IP_PRE_get_buffers(offload, buffers, fix, tc, f_start, ev_global);
const int nthreads = tc;
int *overflow = fix->get_off_overflow_flag();
{
#if defined(__MIC__) && defined(_LMP_INTEL_OFFLOAD)
*timer_compute = MIC_Wtime();
#endif
IP_PRE_repack_for_offload(NEWTON_PAIR, separate_flag, nlocal, nall,
f_stride, x, 0);
acc_t oevdwl, ov0, ov1, ov2, ov3, ov4, ov5;
if (EFLAG) oevdwl = (acc_t)0;
if (vflag) ov0 = ov1 = ov2 = ov3 = ov4 = ov5 = (acc_t)0;
// loop over neighbors of my atoms
#if defined(_OPENMP)
#pragma omp parallel reduction(+:oevdwl,ov0,ov1,ov2,ov3,ov4,ov5)
#endif
{
int iifrom, iip, iito, tid;
IP_PRE_omp_stride_id(iifrom, iip, iito, tid, inum, nthreads);
iifrom += astart;
iito += astart;
#ifdef LMP_USE_MKL_RNG
VSLStreamStatePtr *my_random = &(random_thread[tid]);
#else
RanMars *my_random = random_thread[tid];
#endif
flt_t *my_rand_buffer = fc.rand_buffer_thread[tid];
int rngi = rngi_thread[tid];
int foff;
if (NEWTON_PAIR) foff = tid * f_stride - minlocal;
else foff = -minlocal;
FORCE_T * _noalias const f = f_start + foff;
if (NEWTON_PAIR) memset(f + minlocal, 0, f_stride * sizeof(FORCE_T));
flt_t icut, a0, gamma, sigma;
if (ONETYPE) {
icut = param[3].icut;
a0 = param[3].a0;
gamma = param[3].gamma;
sigma = param[3].sigma;
}
for (int i = iifrom; i < iito; i += iip) {
int itype, ptr_off;
const FC_PACKED1_T * _noalias parami;
if (!ONETYPE) {
itype = x[i].w;
ptr_off = itype * ntypes;
parami = param + ptr_off;
}
const int * _noalias const jlist = firstneigh + cnumneigh[i];
const int jnum = numneigh[i];
acc_t fxtmp, fytmp, fztmp, fwtmp;
acc_t sevdwl, sv0, sv1, sv2, sv3, sv4, sv5;
const flt_t xtmp = x[i].x;
const flt_t ytmp = x[i].y;
const flt_t ztmp = x[i].z;
const flt_t vxtmp = v[i].x;
const flt_t vytmp = v[i].y;
const flt_t vztmp = v[i].z;
fxtmp = fytmp = fztmp = (acc_t)0;
if (EFLAG) fwtmp = sevdwl = (acc_t)0;
if (NEWTON_PAIR == 0)
if (vflag==1) sv0 = sv1 = sv2 = sv3 = sv4 = sv5 = (acc_t)0;
if (rngi + jnum > rng_size) {
#ifdef LMP_USE_MKL_RNG
if (sizeof(flt_t) == sizeof(float))
vsRngGaussian(VSL_RNG_METHOD_GAUSSIAN_ICDF, *my_random, rngi,
(float*)my_rand_buffer, (float)0.0, (float)1.0 );
else
vdRngGaussian(VSL_RNG_METHOD_GAUSSIAN_ICDF, *my_random, rngi,
(double*)my_rand_buffer, 0.0, 1.0 );
#else
for (int jj = 0; jj < rngi; jj++)
my_rand_buffer[jj] = my_random->gaussian();
#endif
rngi = 0;
}
#if defined(LMP_SIMD_COMPILER)
#pragma vector aligned
#pragma simd reduction(+:fxtmp, fytmp, fztmp, fwtmp, sevdwl, \
sv0, sv1, sv2, sv3, sv4, sv5)
#endif
for (int jj = 0; jj < jnum; jj++) {
flt_t forcelj, evdwl;
forcelj = evdwl = (flt_t)0.0;
int j, jtype, sbindex;
if (!ONETYPE) {
sbindex = jlist[jj] >> SBBITS & 3;
j = jlist[jj] & NEIGHMASK;
} else
j = jlist[jj];
const flt_t delx = xtmp - x[j].x;
const flt_t dely = ytmp - x[j].y;
const flt_t delz = ztmp - x[j].z;
if (!ONETYPE) {
jtype = x[j].w;
icut = parami[jtype].icut;
}
const flt_t rsq = delx * delx + dely * dely + delz * delz;
const flt_t rinv = (flt_t)1.0/sqrt(rsq);
if (rinv > icut) {
flt_t factor_dpd;
if (!ONETYPE) factor_dpd = special_lj[sbindex];
flt_t delvx = vxtmp - v[j].x;
flt_t delvy = vytmp - v[j].y;
flt_t delvz = vztmp - v[j].z;
flt_t dot = delx*delvx + dely*delvy + delz*delvz;
flt_t randnum = my_rand_buffer[jj];
flt_t iwd = rinv - icut;
if (rinv > (flt_t)IEPSILON) iwd = (flt_t)0.0;
if (!ONETYPE) {
a0 = parami[jtype].a0;
gamma = parami[jtype].gamma;
sigma = parami[jtype].sigma;
}
flt_t fpair = a0 - iwd * gamma * dot + sigma * randnum * dtinvsqrt;
if (!ONETYPE) fpair *= factor_dpd;
fpair *= iwd;
const flt_t fpx = fpair * delx;
fxtmp += fpx;
if (NEWTON_PAIR) f[j].x -= fpx;
const flt_t fpy = fpair * dely;
fytmp += fpy;
if (NEWTON_PAIR) f[j].y -= fpy;
const flt_t fpz = fpair * delz;
fztmp += fpz;
if (NEWTON_PAIR) f[j].z -= fpz;
if (EFLAG) {
flt_t cut = (flt_t)1.0/icut;
flt_t r = (flt_t)1.0/rinv;
evdwl = (flt_t)0.5 * a0 * (cut - (flt_t)2.0*r + rsq * icut);
if (!ONETYPE) evdwl *= factor_dpd;
sevdwl += evdwl;
if (eatom) {
fwtmp += (flt_t)0.5 * evdwl;
if (NEWTON_PAIR)
f[j].w += (flt_t)0.5 * evdwl;
}
}
if (NEWTON_PAIR == 0)
IP_PRE_ev_tally_nborv(vflag, delx, dely, delz, fpx, fpy, fpz);
} // if rsq
} // for jj
if (NEWTON_PAIR) {
f[i].x += fxtmp;
f[i].y += fytmp;
f[i].z += fztmp;
} else {
f[i].x = fxtmp;
f[i].y = fytmp;
f[i].z = fztmp;
}
IP_PRE_ev_tally_atom(NEWTON_PAIR, EFLAG, vflag, f, fwtmp);
rngi += jnum;
} // for ii
IP_PRE_fdotr_reduce_omp(NEWTON_PAIR, nall, minlocal, nthreads, f_start,
f_stride, x, offload, vflag, ov0, ov1, ov2, ov3,
ov4, ov5);
rngi_thread[tid] = rngi;
} // end omp
IP_PRE_fdotr_reduce(NEWTON_PAIR, nall, nthreads, f_stride, vflag,
ov0, ov1, ov2, ov3, ov4, ov5);
if (EFLAG) {
if (NEWTON_PAIR == 0) oevdwl *= (acc_t)0.5;
ev_global[0] = oevdwl;
ev_global[1] = (acc_t)0.0;
}
if (vflag) {
if (NEWTON_PAIR == 0) {
ov0 *= (acc_t)0.5;
ov1 *= (acc_t)0.5;
ov2 *= (acc_t)0.5;
ov3 *= (acc_t)0.5;
ov4 *= (acc_t)0.5;
ov5 *= (acc_t)0.5;
}
ev_global[2] = ov0;
ev_global[3] = ov1;
ev_global[4] = ov2;
ev_global[5] = ov3;
ev_global[6] = ov4;
ev_global[7] = ov5;
}
#if defined(__MIC__) && defined(_LMP_INTEL_OFFLOAD)
*timer_compute = MIC_Wtime() - *timer_compute;
#endif
} // end offload
if (offload)
fix->stop_watch(TIME_OFFLOAD_LATENCY);
else
fix->stop_watch(TIME_HOST_PAIR);
if (EFLAG || vflag)
fix->add_result_array(f_start, ev_global, offload, eatom, 0, vflag);
else
fix->add_result_array(f_start, 0, offload);
}
/* ----------------------------------------------------------------------
global settings
------------------------------------------------------------------------- */
void PairDPDIntel::settings(int narg, char **arg) {
#if defined(_OPENMP)
if (_nrandom_thread) {
#ifdef LMP_USE_MKL_RNG
for (int i = 0; i < _nrandom_thread; i++)
vslDeleteStream(&random_thread[i]);
#else
for (int i = 1; i < _nrandom_thread; i++)
delete random_thread[i];
#endif
}
delete []random_thread;
#endif
PairDPD::settings(narg,arg);
_nrandom_thread = comm->nthreads;
#ifdef LMP_USE_MKL_RNG
random_thread=new VSLStreamStatePtr[comm->nthreads];
#if defined(_OPENMP)
#pragma omp parallel
{
int tid = omp_get_thread_num();
vslNewStream(&random_thread[tid], LMP_MKL_RNG,
seed + comm->me + comm->nprocs * tid );
}
#endif
#else
random_thread =new RanMars*[comm->nthreads];
random_thread[0] = random;
#if defined(_OPENMP)
#pragma omp parallel
{
int tid = omp_get_thread_num();
if (tid > 0)
random_thread[tid] = new RanMars(lmp, seed+comm->me+comm->nprocs*tid);
}
#endif
#endif
}
/* ---------------------------------------------------------------------- */
void PairDPDIntel::init_style()
{
PairDPD::init_style();
if (force->newton_pair == 0) {
neighbor->requests[neighbor->nrequest-1]->half = 0;
neighbor->requests[neighbor->nrequest-1]->full = 1;
}
neighbor->requests[neighbor->nrequest-1]->intel = 1;
int ifix = modify->find_fix("package_intel");
if (ifix < 0)
error->all(FLERR,
"The 'package intel' command is required for /intel styles");
fix = static_cast<FixIntel *>(modify->fix[ifix]);
fix->pair_init_check();
#ifdef _LMP_INTEL_OFFLOAD
if (fix->offload_balance() != 0.0)
error->all(FLERR,
"Offload for dpd/intel is not yet available. Set balance to 0.");
#endif
if (fix->precision() == FixIntel::PREC_MODE_MIXED)
pack_force_const(force_const_single, fix->get_mixed_buffers());
else if (fix->precision() == FixIntel::PREC_MODE_DOUBLE)
pack_force_const(force_const_double, fix->get_double_buffers());
else
pack_force_const(force_const_single, fix->get_single_buffers());
}
/* ---------------------------------------------------------------------- */
template <class flt_t, class acc_t>
void PairDPDIntel::pack_force_const(ForceConst<flt_t> &fc,
IntelBuffers<flt_t,acc_t> *buffers)
{
_onetype = 0;
if (atom->ntypes == 1 && !atom->molecular) _onetype = 1;
int tp1 = atom->ntypes + 1;
fc.set_ntypes(tp1,comm->nthreads,buffers->get_max_nbors(),memory,_cop);
buffers->set_ntypes(tp1);
flt_t **cutneighsq = buffers->get_cutneighsq();
// Repeat cutsq calculation because done after call to init_style
double cut, cutneigh;
for (int i = 1; i <= atom->ntypes; i++) {
for (int j = i; j <= atom->ntypes; j++) {
if (setflag[i][j] != 0 || (setflag[i][i] != 0 && setflag[j][j] != 0)) {
cut = init_one(i,j);
cutneigh = cut + neighbor->skin;
cutsq[i][j] = cutsq[j][i] = cut*cut;
cutneighsq[i][j] = cutneighsq[j][i] = cutneigh * cutneigh;
double icut = 1.0 / cut;
fc.param[i][j].icut = fc.param[j][i].icut = icut;
} else {
cut = init_one(i,j);
double icut = 1.0 / cut;
fc.param[i][j].icut = fc.param[j][i].icut = icut;
}
}
}
for (int i = 0; i < 4; i++) {
fc.special_lj[i] = force->special_lj[i];
fc.special_lj[0] = 1.0;
}
for (int i = 1; i < tp1; i++) {
for (int j = 1; j < tp1; j++) {
fc.param[i][j].a0 = a0[i][j];
fc.param[i][j].gamma = gamma[i][j];
fc.param[i][j].sigma = sigma[i][j];
}
}
}
/* ---------------------------------------------------------------------- */
template <class flt_t>
void PairDPDIntel::ForceConst<flt_t>::set_ntypes(const int ntypes,
const int nthreads,
const int max_nbors,
Memory *memory,
const int cop) {
if (ntypes != _ntypes) {
if (_ntypes > 0) {
_memory->destroy(param);
_memory->destroy(rand_buffer_thread);
_memory->destroy(rngi);
}
if (ntypes > 0) {
_cop = cop;
memory->create(param,ntypes,ntypes,"fc.param");
memory->create(rand_buffer_thread, nthreads, max_nbors,
"fc.rand_buffer_thread");
memory->create(rngi,nthreads,"fc.param");
for (int i = 0; i < nthreads; i++) rngi[i] = max_nbors;
}
}
_ntypes = ntypes;
_memory = memory;
}
/* ----------------------------------------------------------------------
proc 0 reads from restart file, bcasts
------------------------------------------------------------------------- */
void PairDPDIntel::read_restart_settings(FILE *fp)
{
#if defined(_OPENMP)
if (_nrandom_thread) {
#ifdef LMP_USE_MKL_RNG
for (int i = 0; i < _nrandom_thread; i++)
vslDeleteStream(&random_thread[i]);
#else
for (int i = 1; i < _nrandom_thread; i++)
delete random_thread[i];
#endif
}
delete []random_thread;
#endif
PairDPD::read_restart_settings(fp);
_nrandom_thread = comm->nthreads;
#ifdef LMP_USE_MKL_RNG
random_thread=new VSLStreamStatePtr[comm->nthreads];
#if defined(_OPENMP)
#pragma omp parallel
{
int tid = omp_get_thread_num();
vslNewStream(&random_thread[tid], LMP_MKL_RNG,
seed + comm->me + comm->nprocs * tid );
}
#endif
#else
random_thread =new RanMars*[comm->nthreads];
random_thread[0] = random;
#if defined(_OPENMP)
#pragma omp parallel
{
int tid = omp_get_thread_num();
if (tid > 0)
random_thread[tid] = new RanMars(lmp, seed+comm->me+comm->nprocs*tid);
}
#endif
#endif
}

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