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fix_nve_asphere_intel.cpp
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Tue, Nov 12, 22:48

fix_nve_asphere_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
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: W. Michael Brown (Intel)
------------------------------------------------------------------------- */
#include "math.h"
#include "stdio.h"
#include "string.h"
#include "fix_nve_asphere_intel.h"
#include "math_extra_intel.h"
#include "atom.h"
#include "atom_vec_ellipsoid.h"
#include "force.h"
#include "neighbor.h"
#include "update.h"
#include "memory.h"
#include "error.h"
using namespace LAMMPS_NS;
using namespace FixConst;
#define INERTIA 0.2 // moment of inertia prefactor for ellipsoid
/* ---------------------------------------------------------------------- */
FixNVEAsphereIntel::FixNVEAsphereIntel(LAMMPS *lmp, int narg, char **arg) :
FixNVE(lmp, narg, arg)
{
_dtfm = 0;
_nlocal3 = 0;
_nlocal_max = 0;
_inertia0 = 0;
_inertia1 = 0;
_inertia2 = 0;
}
/* ---------------------------------------------------------------------- */
void FixNVEAsphereIntel::init()
{
avec = (AtomVecEllipsoid *) atom->style_match("ellipsoid");
if (!avec)
error->all(FLERR,"Compute nve/asphere requires atom style ellipsoid");
// check that all particles are finite-size ellipsoids
// no point particles allowed, spherical is OK
int *ellipsoid = atom->ellipsoid;
int *mask = atom->mask;
int nlocal = atom->nlocal;
for (int i = 0; i < nlocal; i++)
if (mask[i] & groupbit)
if (ellipsoid[i] < 0)
error->one(FLERR,"Fix nve/asphere requires extended particles");
FixNVE::init();
}
/* ---------------------------------------------------------------------- */
void FixNVEAsphereIntel::setup(int vflag)
{
FixNVE::setup(vflag);
reset_dt();
}
/* ---------------------------------------------------------------------- */
void FixNVEAsphereIntel::initial_integrate(int vflag)
{
double dtfm;
double inertia[3],omega[3];
double *shape,*quat;
AtomVecEllipsoid::Bonus *bonus = avec->bonus;
int *ellipsoid = atom->ellipsoid;
double * _noalias const x = atom->x[0];
double * _noalias const v = atom->v[0];
const double * _noalias const f = atom->f[0];
int *mask = atom->mask;
double **angmom = atom->angmom;
double **torque = atom->torque;
double *rmass = atom->rmass;
int nlocal = atom->nlocal;
if (igroup == atom->firstgroup) nlocal = atom->nfirst;
// set timestep here since dt may have changed or come via rRESPA
dtq = 0.5 * dtv;
#if defined(LMP_SIMD_COMPILER)
#pragma vector aligned
#pragma simd
#endif
for (int i = 0; i < _nlocal3; i++) {
v[i] += _dtfm[i] * f[i];
x[i] += dtv * v[i];
}
// update angular momentum by 1/2 step
if (igroup == 0) {
#if defined(LMP_SIMD_COMPILER)
#pragma vector aligned
#pragma simd
#endif
for (int i = 0; i < nlocal; i++) {
double *quat = bonus[ellipsoid[i]].quat;
ME_omega_richardson(dtf, dtq, angmom[i], quat, torque[i], _inertia0[i],
_inertia1[i], _inertia2[i]);
}
} else {
#if defined(LMP_SIMD_COMPILER)
#pragma vector aligned
#pragma simd
#endif
for (int i = 0; i < nlocal; i++) {
if (mask[i] & groupbit) {
double *quat = bonus[ellipsoid[i]].quat;
ME_omega_richardson(dtf, dtq, angmom[i], quat, torque[i], _inertia0[i],
_inertia1[i], _inertia2[i]);
}
}
}
}
/* ---------------------------------------------------------------------- */
void FixNVEAsphereIntel::final_integrate()
{
if (neighbor->ago == 0) reset_dt();
double dtfm;
double * _noalias const v = atom->v[0];
const double * _noalias const f = atom->f[0];
double * _noalias const angmom = atom->angmom[0];
const double * _noalias const torque = atom->torque[0];
#if defined(LMP_SIMD_COMPILER)
#pragma vector aligned
#pragma simd
#endif
for (int i = 0; i < _nlocal3; i++) {
v[i] += _dtfm[i] * f[i];
angmom[i] += dtf * torque[i];
}
}
void FixNVEAsphereIntel::reset_dt() {
AtomVecEllipsoid::Bonus *bonus = avec->bonus;
int *ellipsoid = atom->ellipsoid;
dtv = update->dt;
dtf = 0.5 * update->dt * force->ftm2v;
const int * const mask = atom->mask;
const int nlocal = (igroup == atom->firstgroup) ? atom->nfirst :
atom->nlocal;
if (nlocal > _nlocal_max) {
if (_nlocal_max) {
memory->destroy(_dtfm);
memory->destroy(_inertia0);
memory->destroy(_inertia1);
memory->destroy(_inertia2);
}
_nlocal_max = static_cast<int>(1.20 * nlocal);
memory->create(_dtfm, _nlocal_max * 3, "fix_nve_intel:dtfm");
memory->create(_inertia0, _nlocal_max * 3, "fix_nve_intel:inertia0");
memory->create(_inertia1, _nlocal_max * 3, "fix_nve_intel:inertia1");
memory->create(_inertia2, _nlocal_max * 3, "fix_nve_intel:inertia2");
}
_nlocal3 = nlocal * 3;
if (igroup == 0) {
const double * const rmass = atom->rmass;
int n = 0;
for (int i = 0; i < nlocal; i++) {
_dtfm[n++] = dtf / rmass[i];
_dtfm[n++] = dtf / rmass[i];
_dtfm[n++] = dtf / rmass[i];
double *shape = bonus[ellipsoid[i]].shape;
double idot = INERTIA*rmass[i] * (shape[1]*shape[1]+shape[2]*shape[2]);
if (idot != 0.0) idot = 1.0 / idot;
_inertia0[i] = idot;
idot = INERTIA*rmass[i] * (shape[0]*shape[0]+shape[2]*shape[2]);
if (idot != 0.0) idot = 1.0 / idot;
_inertia1[i] = idot;
idot = INERTIA*rmass[i] * (shape[0]*shape[0]+shape[1]*shape[1]);
if (idot != 0.0) idot = 1.0 / idot;
_inertia2[i] = idot;
}
} else {
const double * const rmass = atom->rmass;
int n = 0;
for (int i = 0; i < nlocal; i++) {
if (mask[i] & groupbit) {
_dtfm[n++] = dtf / rmass[i];
_dtfm[n++] = dtf / rmass[i];
_dtfm[n++] = dtf / rmass[i];
double *shape = bonus[ellipsoid[i]].shape;
double idot = INERTIA*rmass[i] * (shape[1]*shape[1]+shape[2]*shape[2]);
if (idot != 0.0) idot = 1.0 / idot;
_inertia0[i] = idot;
idot = INERTIA*rmass[i] * (shape[0]*shape[0]+shape[2]*shape[2]);
if (idot != 0.0) idot = 1.0 / idot;
_inertia1[i] = idot;
idot = INERTIA*rmass[i] * (shape[0]*shape[0]+shape[1]*shape[1]);
if (idot != 0.0) idot = 1.0 / idot;
_inertia2[i] = idot;
} else {
_dtfm[n++] = 0.0;
_dtfm[n++] = 0.0;
_dtfm[n++] = 0.0;
}
}
}
}
double FixNVEAsphereIntel::memory_usage()
{
return FixNVE::memory_usage() + _nlocal_max * 12 * sizeof(double);
}

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