247 lines
7.1 KiB
C++
247 lines
7.1 KiB
C++
// clang-format off
|
|
/* ----------------------------------------------------------------------
|
|
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
|
|
https://www.lammps.org/, Sandia National Laboratories
|
|
LAMMPS development team: developers@lammps.org
|
|
|
|
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 "fix_nve_asphere_intel.h"
|
|
|
|
#include "atom.h"
|
|
#include "atom_vec_ellipsoid.h"
|
|
#include "error.h"
|
|
#include "force.h"
|
|
#include "math_extra_intel.h"
|
|
#include "memory.h"
|
|
#include "neighbor.h"
|
|
#include "update.h"
|
|
|
|
using namespace LAMMPS_NS;
|
|
using namespace FixConst;
|
|
|
|
static constexpr double INERTIA = 0.2; // moment of inertia prefactor for ellipsoid
|
|
|
|
/* ---------------------------------------------------------------------- */
|
|
|
|
FixNVEAsphereIntel::FixNVEAsphereIntel(LAMMPS *lmp, int narg, char **arg) :
|
|
FixNVE(lmp, narg, arg)
|
|
{
|
|
_dtfm = nullptr;
|
|
_nlocal3 = 0;
|
|
_nlocal_max = 0;
|
|
_inertia0 = nullptr;
|
|
_inertia1 = nullptr;
|
|
_inertia2 = nullptr;
|
|
}
|
|
|
|
/* ---------------------------------------------------------------------- */
|
|
|
|
void FixNVEAsphereIntel::init()
|
|
{
|
|
avec = dynamic_cast<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*/)
|
|
{
|
|
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;
|
|
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)
|
|
#if defined(USE_OMP_SIMD)
|
|
#pragma omp simd
|
|
#else
|
|
#pragma simd
|
|
#endif
|
|
#pragma vector aligned
|
|
#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)
|
|
#if defined(USE_OMP_SIMD)
|
|
#pragma omp simd
|
|
#else
|
|
#pragma simd
|
|
#endif
|
|
#pragma vector aligned
|
|
#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)
|
|
#if defined(USE_OMP_SIMD)
|
|
#pragma omp simd
|
|
#else
|
|
#pragma simd
|
|
#endif
|
|
#pragma vector aligned
|
|
#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 * _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)
|
|
#if defined(USE_OMP_SIMD)
|
|
#pragma omp simd
|
|
#else
|
|
#pragma simd
|
|
#endif
|
|
#pragma vector aligned
|
|
#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);
|
|
}
|
|
|