Homec4science
Diffusion lammps (lammm-master-deprecated) Browse

lammps/src/USER-INTEL/bond_fene_intel.cpp
222e9de4c889lammm-master-deprecated

Last Change
Raw File

bond_fene_intel.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 author: Stan Moore (Sandia)
------------------------------------------------------------------------- */
#include <math.h>
#include <stdlib.h>
#include "bond_fene_intel.h"
#include "atom.h"
#include "neighbor.h"
#include "domain.h"
#include "comm.h"
#include "force.h"
#include "memory.h"
#include "suffix.h"
#include "error.h"
using namespace LAMMPS_NS;
typedef struct { int a,b,t; } int3_t;
/* ---------------------------------------------------------------------- */
BondFENEIntel::BondFENEIntel(LAMMPS *lmp) : BondFENE(lmp)
{
suffix_flag |= Suffix::INTEL;
}
/* ---------------------------------------------------------------------- */
BondFENEIntel::~BondFENEIntel()
{
}
/* ---------------------------------------------------------------------- */
void BondFENEIntel::compute(int eflag, int vflag)
{
#ifdef _LMP_INTEL_OFFLOAD
if (_use_base) {
BondFENE::compute(eflag, vflag);
return;
}
#endif
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);
}
/* ---------------------------------------------------------------------- */
template <class flt_t, class acc_t>
void BondFENEIntel::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 = 0;
if (evflag) {
if (eflag) {
if (force->newton_bond)
eval<1,1,1>(vflag, buffers, fc);
else
eval<1,1,0>(vflag, buffers, fc);
} else {
if (force->newton_bond)
eval<1,0,1>(vflag, buffers, fc);
else
eval<1,0,0>(vflag, buffers, fc);
}
} else {
if (force->newton_bond)
eval<0,0,1>(vflag, buffers, fc);
else
eval<0,0,0>(vflag, buffers, fc);
}
}
template <int EVFLAG, int EFLAG, int NEWTON_BOND, class flt_t, class acc_t>
void BondFENEIntel::eval(const int vflag,
IntelBuffers<flt_t,acc_t> *buffers,
const ForceConst<flt_t> &fc)
{
const int inum = neighbor->nbondlist;
if (inum == 0) return;
ATOM_T * _noalias const x = buffers->get_x(0);
const int nlocal = atom->nlocal;
const int nall = nlocal + atom->nghost;
int f_stride;
if (NEWTON_BOND) f_stride = buffers->get_stride(nall);
else f_stride = buffers->get_stride(nlocal);
int tc;
FORCE_T * _noalias f_start;
acc_t * _noalias ev_global;
IP_PRE_get_buffers(0, buffers, fix, tc, f_start, ev_global);
const int nthreads = tc;
acc_t oebond, ov0, ov1, ov2, ov3, ov4, ov5;
if (EVFLAG) {
if (EFLAG)
oebond = (acc_t)0.0;
if (vflag) {
ov0 = ov1 = ov2 = ov3 = ov4 = ov5 = (acc_t)0.0;
}
}
#if defined(_OPENMP)
#pragma omp parallel default(none) \
shared(f_start,f_stride,fc) \
reduction(+:oebond,ov0,ov1,ov2,ov3,ov4,ov5)
#endif
{
int nfrom, nto, tid;
IP_PRE_omp_range_id(nfrom, nto, tid, inum, nthreads);
FORCE_T * _noalias const f = f_start + (tid * f_stride);
if (fix->need_zero(tid))
memset(f, 0, f_stride * sizeof(FORCE_T));
const int3_t * _noalias const bondlist =
(int3_t *) neighbor->bondlist[0];
for (int n = nfrom; n < nto; n++) {
const int i1 = bondlist[n].a;
const int i2 = bondlist[n].b;
const int type = bondlist[n].t;
const flt_t ir0sq = fc.fc[type].ir0sq;
const flt_t k = fc.fc[type].k;
const flt_t sigma = fc.fc[type].sigma;
const flt_t sigmasq = sigma*sigma;
const flt_t epsilon = fc.fc[type].epsilon;
const flt_t delx = x[i1].x - x[i2].x;
const flt_t dely = x[i1].y - x[i2].y;
const flt_t delz = x[i1].z - x[i2].z;
const flt_t rsq = delx*delx + dely*dely + delz*delz;
flt_t rlogarg = (flt_t)1.0 - rsq * ir0sq;
flt_t irsq = (flt_t)1.0 / rsq;
// if r -> r0, then rlogarg < 0.0 which is an error
// issue a warning and reset rlogarg = epsilon
// if r > 2*r0 something serious is wrong, abort
if (rlogarg < (flt_t)0.1) {
char str[128];
sprintf(str,"FENE bond too long: " BIGINT_FORMAT " "
TAGINT_FORMAT " " TAGINT_FORMAT " %g",
update->ntimestep,atom->tag[i1],atom->tag[i2],sqrt(rsq));
error->warning(FLERR,str,0);
if (rlogarg <= (flt_t)-3.0) error->one(FLERR,"Bad FENE bond");
rlogarg = (flt_t)0.1;
}
flt_t fbond = -k/rlogarg;
// force from LJ term
flt_t sr2,sr6;
if (rsq < (flt_t)TWO_1_3*sigmasq) {
sr2 = sigmasq * irsq;
sr6 = sr2 * sr2 * sr2;
fbond += (flt_t)48.0 * epsilon * sr6 * (sr6 - (flt_t)0.5) * irsq;
}
// energy
flt_t ebond;
if (EFLAG) {
ebond = (flt_t)-0.5 * k / ir0sq * log(rlogarg);
if (rsq < (flt_t)TWO_1_3 * sigmasq)
ebond += (flt_t)4.0 * epsilon * sr6 * (sr6 - (flt_t)1.0) + epsilon;
}
// apply force to each of 2 atoms
if (NEWTON_BOND || i1 < nlocal) {
f[i1].x += delx*fbond;
f[i1].y += dely*fbond;
f[i1].z += delz*fbond;
}
if (NEWTON_BOND || i2 < nlocal) {
f[i2].x -= delx*fbond;
f[i2].y -= dely*fbond;
f[i2].z -= delz*fbond;
}
if (EVFLAG) {
IP_PRE_ev_tally_bond(EFLAG, eatom, vflag, ebond, i1, i2, fbond,
delx, dely, delz, oebond, f, NEWTON_BOND,
nlocal, ov0, ov1, ov2, ov3, ov4, ov5);
}
} // for n
} // omp parallel
if (EVFLAG) {
if (EFLAG)
energy += oebond;
if (vflag) {
virial[0] += ov0; virial[1] += ov1; virial[2] += ov2;
virial[3] += ov3; virial[4] += ov4; virial[5] += ov5;
}
}
fix->set_reduce_flag();
}
/* ---------------------------------------------------------------------- */
void BondFENEIntel::init_style()
{
BondFENE::init_style();
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]);
#ifdef _LMP_INTEL_OFFLOAD
_use_base = 0;
if (fix->offload_balance() != 0.0) {
_use_base = 1;
return;
}
#endif
fix->bond_init_check();
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 BondFENEIntel::pack_force_const(ForceConst<flt_t> &fc,
IntelBuffers<flt_t,acc_t> *buffers)
{
const int bp1 = atom->nbondtypes + 1;
fc.set_ntypes(bp1,memory);
for (int i = 0; i < bp1; i++) {
fc.fc[i].k = k[i];
fc.fc[i].ir0sq = 1.0 / (r0[i] * r0[i]);
fc.fc[i].sigma = sigma[i];
fc.fc[i].epsilon = epsilon[i];
}
}
/* ---------------------------------------------------------------------- */
template <class flt_t>
void BondFENEIntel::ForceConst<flt_t>::set_ntypes(const int nbondtypes,
Memory *memory) {
if (nbondtypes != _nbondtypes) {
if (_nbondtypes > 0)
_memory->destroy(fc);
if (nbondtypes > 0)
_memory->create(fc,nbondtypes,"bondfeneintel.fc");
}
_nbondtypes = nbondtypes;
_memory = memory;
}
c4science · Help