Homec4science
Diffusion lammps (runner) Browse

lammps/src/USER-OMP/fix_nh_sphere_omp.cpp
5f86c15dd224runner

Last Change
Raw File

fix_nh_sphere_omp.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: Axel Kohlmeyer (Temple U)
------------------------------------------------------------------------- */
#include <math.h>
#include "fix_nh_sphere_omp.h"
#include "atom.h"
#include "atom_vec.h"
#include "compute.h"
#include "group.h"
#include "error.h"
using namespace LAMMPS_NS;
using namespace FixConst;
enum{NOBIAS,BIAS};
#define INERTIA 0.4 // moment of inertia prefactor for sphere
typedef struct { double x,y,z; } dbl3_t;
/* ---------------------------------------------------------------------- */
FixNHSphereOMP::FixNHSphereOMP(LAMMPS *lmp, int narg, char **arg) :
FixNHOMP(lmp, narg, arg)
{
if (!atom->sphere_flag)
error->all(FLERR,"Fix nvt/nph/npt sphere requires atom style sphere");
}
/* ---------------------------------------------------------------------- */
void FixNHSphereOMP::init()
{
// check that all particles are finite-size
// no point particles allowed
double *radius = atom->radius;
int *mask = atom->mask;
int nlocal = atom->nlocal;
for (int i = 0; i < nlocal; i++)
if (mask[i] & groupbit)
if (radius[i] == 0.0)
error->one(FLERR,"Fix nvt/sphere requires extended particles");
FixNHOMP::init();
}
/* ----------------------------------------------------------------------
perform half-step update of rotational and COM velocities
-----------------------------------------------------------------------*/
void FixNHSphereOMP::nve_v()
{
dbl3_t * _noalias const v = (dbl3_t *) atom->v[0];
dbl3_t * _noalias const omega = (dbl3_t *) atom->omega[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 radius = atom->radius;
const double * _noalias const rmass = atom->rmass;
const int * _noalias const mask = atom->mask;
// set timestep here since dt may have changed or come via rRESPA
const double dtfrotate = dtf / INERTIA;
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.
// update omega for all particles
// d_omega/dt = torque / inertia
// 4 cases depending on radius vs shape and rmass vs mass
#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;
const double dtirotate = dtfrotate / (radius[i]*radius[i]*rmass[i]);
omega[i].x += dtirotate*torque[i].x;
omega[i].y += dtirotate*torque[i].y;
omega[i].z += dtirotate*torque[i].z;
}
}
}
/* ----------------------------------------------------------------------
perform half-step scaling of rotatonal velocities
-----------------------------------------------------------------------*/
void FixNHSphereOMP::nh_v_temp()
{
dbl3_t * _noalias const v = (dbl3_t *) atom->v[0];
dbl3_t * _noalias const omega = (dbl3_t *) atom->omega[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;
omega[i].x *= factor_eta;
omega[i].y *= factor_eta;
omega[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);
omega[i].x *= factor_eta;
omega[i].y *= factor_eta;
omega[i].z *= factor_eta;
}
}
}
}
c4science · Help