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fix_nh_asphere_omp.cpp
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Fri, Apr 4, 02:41

fix_nh_asphere_omp.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: Axel Kohlmeyer (Temple U)
------------------------------------------------------------------------- */
#include <string.h>
#include <stdlib.h>
#include <math.h>
#include "math_extra.h"
#include "fix_nh_asphere_omp.h"
#include "atom.h"
#include "atom_vec_ellipsoid.h"
#include "compute.h"
#include "group.h"
#include "memory.h"
#include "error.h"
using namespace LAMMPS_NS;
using namespace FixConst;
enum{NOBIAS,BIAS};
typedef struct { double x,y,z; } dbl3_t;
/* ---------------------------------------------------------------------- */
FixNHAsphereOMP::FixNHAsphereOMP(LAMMPS *lmp, int narg, char **arg) :
FixNHOMP(lmp, narg, arg)
{
}
/* ---------------------------------------------------------------------- */
void FixNHAsphereOMP::init()
{
avec = (AtomVecEllipsoid *) atom->style_match("ellipsoid");
if (!avec)
error->all(FLERR,"Compute nvt/nph/npt asphere requires atom style ellipsoid");
// check that all particles are finite-size
// 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 nvt/nph/npt asphere requires extended particles");
FixNHOMP::init();
}
/* ----------------------------------------------------------------------
perform half-step update of angular momentum and COM velocity
-----------------------------------------------------------------------*/
void FixNHAsphereOMP::nve_v()
{
dbl3_t * _noalias const v = (dbl3_t *) atom->v[0];
dbl3_t * _noalias const angmom = (dbl3_t *) atom->angmom[0];
const dbl3_t * _noalias const f = (dbl3_t *) atom->f[0];
const dbl3_t * _noalias const torque = (dbl3_t *) atom->torque[0];
const double * _noalias const rmass = atom->rmass;
const int * _noalias const mask = atom->mask;
const int nlocal = (igroup == atom->firstgroup) ? atom->nfirst : atom->nlocal;
int i;
// standard nve_v velocity update. for efficiency the loop is
// merged with FixNHOMP instead of calling it for the COM update.
#if defined(_OPENMP)
#pragma omp parallel for default(none) private(i) schedule(static)
#endif
for (i = 0; i < nlocal; i++) {
if (mask[i] & groupbit) {
const double dtfm = dtf / rmass[i];
v[i].x += dtfm*f[i].x;
v[i].y += dtfm*f[i].y;
v[i].z += dtfm*f[i].z;
angmom[i].x += dtf*torque[i].x;
angmom[i].y += dtf*torque[i].y;
angmom[i].z += dtf*torque[i].z;
}
}
}
/* ----------------------------------------------------------------------
perform full-step update of position and orientation
-----------------------------------------------------------------------*/
void FixNHAsphereOMP::nve_x()
{
dbl3_t * _noalias const x = (dbl3_t *) atom->x[0];
const dbl3_t * _noalias const v = (dbl3_t *) atom->v[0];
dbl3_t * _noalias const angmom = (dbl3_t *) atom->angmom[0];
const double * _noalias const rmass = atom->rmass;
const int * _noalias const mask = atom->mask;
AtomVecEllipsoid::Bonus * _noalias const bonus = avec->bonus;
const int * _noalias const ellipsoid = atom->ellipsoid;
const int nlocal = (igroup == atom->firstgroup) ? atom->nfirst : atom->nlocal;
int i;
// set timestep here since dt may have changed or come via rRESPA
dtq = 0.5 * dtv;
// standard nve_x position update and
// update quaternion a full step via Richardson iteration
// returns new normalized quaternion
// principal moments of inertia
#if defined(_OPENMP)
#pragma omp parallel for default(none) private(i) schedule(static)
#endif
for (i = 0; i < nlocal; i++)
if (mask[i] & groupbit) {
double omega[3], inertia[3];
x[i].x += dtv * v[i].x;
x[i].y += dtv * v[i].y;
x[i].z += dtv * v[i].z;
// principal moments of inertia
const double * const shape = bonus[ellipsoid[i]].shape;
double * const quat = bonus[ellipsoid[i]].quat;
inertia[0] = rmass[i] * (shape[1]*shape[1]+shape[2]*shape[2]) / 5.0;
inertia[1] = rmass[i] * (shape[0]*shape[0]+shape[2]*shape[2]) / 5.0;
inertia[2] = rmass[i] * (shape[0]*shape[0]+shape[1]*shape[1]) / 5.0;
// compute omega at 1/2 step from angmom at 1/2 step and current q
// update quaternion a full step via Richardson iteration
// returns new normalized quaternion
MathExtra::mq_to_omega(&angmom[i].x,quat,inertia,omega);
MathExtra::richardson(quat,&angmom[i].x,omega,inertia,dtq);
}
}
/* ----------------------------------------------------------------------
perform half-step temperature scaling of angular momentum
-----------------------------------------------------------------------*/
void FixNHAsphereOMP::nh_v_temp()
{
dbl3_t * _noalias const v = (dbl3_t *) atom->v[0];
dbl3_t * _noalias const angmom = (dbl3_t *) atom->angmom[0];
const int * _noalias const mask = atom->mask;
const int nlocal = (igroup == atom->firstgroup) ? atom->nfirst : atom->nlocal;
int i;
if (which == NOBIAS) {
#if defined(_OPENMP)
#pragma omp parallel for default(none) private(i) schedule(static)
#endif
for (i = 0; i < nlocal; i++) {
if (mask[i] & groupbit) {
v[i].x *= factor_eta;
v[i].y *= factor_eta;
v[i].z *= factor_eta;
angmom[i].x *= factor_eta;
angmom[i].y *= factor_eta;
angmom[i].z *= factor_eta;
}
}
} else if (which == BIAS) {
#if defined(_OPENMP)
#pragma omp parallel for default(none) private(i) schedule(static)
#endif
for (i = 0; i < nlocal; i++) {
double buf[3];
if (mask[i] & groupbit) {
temperature->remove_bias(i,&v[i].x);
v[i].x *= factor_eta;
v[i].y *= factor_eta;
v[i].z *= factor_eta;
temperature->restore_bias(i,&v[i].x);
angmom[i].x *= factor_eta;
angmom[i].y *= factor_eta;
angmom[i].z *= factor_eta;
}
}
}
}

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