Homec4science
Diffusion lammps (lammm-master-deprecated) Browse

lammps/src/ASPHERE/fix_nh_asphere.cpp
5920f1e23471lammm-master-deprecated

Last Change
Raw File

fix_nh_asphere.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: Mike Brown (SNL)
------------------------------------------------------------------------- */
#include "string.h"
#include "stdlib.h"
#include "math.h"
#include "math_extra.h"
#include "fix_nh_asphere.h"
#include "atom.h"
#include "atom_vec.h"
#include "group.h"
#include "memory.h"
#include "error.h"
using namespace LAMMPS_NS;
enum{NOBIAS,BIAS};
/* ---------------------------------------------------------------------- */
FixNHAsphere::FixNHAsphere(LAMMPS *lmp, int narg, char **arg) :
FixNH(lmp, narg, arg)
{
inertia =
memory->create_2d_double_array(atom->ntypes+1,3,"fix_nvt_asphere:inertia");
if (!atom->quat_flag || !atom->angmom_flag || !atom->torque_flag ||
!atom->avec->shape_type)
error->all("Fix nvt/nph/npt asphere requires atom attributes "
"quat, angmom, torque, shape");
if (atom->radius_flag || atom->rmass_flag)
error->all("Fix nvt/nph/npt asphere cannot be used with atom attributes "
"diameter or rmass");
}
/* ---------------------------------------------------------------------- */
FixNHAsphere::~FixNHAsphere()
{
memory->destroy_2d_double_array(inertia);
}
/* ---------------------------------------------------------------------- */
void FixNHAsphere::init()
{
// check that all particles are finite-size
// no point particles allowed, spherical is OK
double **shape = atom->shape;
int *type = atom->type;
int *mask = atom->mask;
int nlocal = atom->nlocal;
for (int i = 0; i < nlocal; i++)
if (mask[i] & groupbit)
if (shape[type[i]][0] == 0.0)
error->one("Fix nvt/nph/npt asphere requires extended particles");
FixNH::init();
calculate_inertia();
}
/* ----------------------------------------------------------------------
Richardson iteration to update quaternion accurately
------------------------------------------------------------------------- */
void FixNHAsphere::richardson(double *q, double *m, double *moments)
{
// compute omega at 1/2 step from m at 1/2 step and q at 0
double w[3];
omega_from_mq(q,m,moments,w);
// full update from dq/dt = 1/2 w q
double wq[4];
MathExtra::multiply_vec_quat(w,q,wq);
double qfull[4];
qfull[0] = q[0] + dtq * wq[0];
qfull[1] = q[1] + dtq * wq[1];
qfull[2] = q[2] + dtq * wq[2];
qfull[3] = q[3] + dtq * wq[3];
MathExtra::normalize4(qfull);
// 1st half of update from dq/dt = 1/2 w q
double qhalf[4];
qhalf[0] = q[0] + 0.5*dtq * wq[0];
qhalf[1] = q[1] + 0.5*dtq * wq[1];
qhalf[2] = q[2] + 0.5*dtq * wq[2];
qhalf[3] = q[3] + 0.5*dtq * wq[3];
MathExtra::normalize4(qhalf);
// re-compute omega at 1/2 step from m at 1/2 step and q at 1/2 step
// recompute wq
omega_from_mq(qhalf,m,moments,w);
MathExtra::multiply_vec_quat(w,qhalf,wq);
// 2nd half of update from dq/dt = 1/2 w q
qhalf[0] += 0.5*dtq * wq[0];
qhalf[1] += 0.5*dtq * wq[1];
qhalf[2] += 0.5*dtq * wq[2];
qhalf[3] += 0.5*dtq * wq[3];
MathExtra::normalize4(qhalf);
// corrected Richardson update
q[0] = 2.0*qhalf[0] - qfull[0];
q[1] = 2.0*qhalf[1] - qfull[1];
q[2] = 2.0*qhalf[2] - qfull[2];
q[3] = 2.0*qhalf[3] - qfull[3];
MathExtra::normalize4(q);
}
/* ----------------------------------------------------------------------
compute omega from angular momentum
w = omega = angular velocity in space frame
wbody = angular velocity in body frame
project space-frame angular momentum onto body axes
and divide by principal moments
------------------------------------------------------------------------- */
void FixNHAsphere::omega_from_mq(double *q, double *m, double *inertia,
double *w)
{
double rot[3][3];
MathExtra::quat_to_mat(q,rot);
double wbody[3];
MathExtra::transpose_times_column3(rot,m,wbody);
wbody[0] /= inertia[0];
wbody[1] /= inertia[1];
wbody[2] /= inertia[2];
MathExtra::times_column3(rot,wbody,w);
}
/* ----------------------------------------------------------------------
principal moments of inertia for ellipsoids
------------------------------------------------------------------------- */
void FixNHAsphere::calculate_inertia()
{
double *mass = atom->mass;
double **shape = atom->shape;
for (int i = 1; i <= atom->ntypes; i++) {
inertia[i][0] = 0.2*mass[i] *
(shape[i][1]*shape[i][1]+shape[i][2]*shape[i][2]);
inertia[i][1] = 0.2*mass[i] *
(shape[i][0]*shape[i][0]+shape[i][2]*shape[i][2]);
inertia[i][2] = 0.2*mass[i] *
(shape[i][0]*shape[i][0]+shape[i][1]*shape[i][1]);
}
}
/* ----------------------------------------------------------------------
perform half-step update of velocities
-----------------------------------------------------------------------*/
void FixNHAsphere::nve_v()
{
// standard nve_v velocity update
FixNH::nve_v();
double **angmom = atom->angmom;
double **torque = atom->torque;
int *mask = atom->mask;
int nlocal = atom->nlocal;
if (igroup == atom->firstgroup) nlocal = atom->nfirst;
// update angular momentum by 1/2 step for all particles
for (int i = 0; i < nlocal; i++) {
if (mask[i] & groupbit) {
angmom[i][0] += dtf*torque[i][0];
angmom[i][1] += dtf*torque[i][1];
angmom[i][2] += dtf*torque[i][2];
}
}
}
/* ----------------------------------------------------------------------
perform full-step update of orientation
-----------------------------------------------------------------------*/
void FixNHAsphere::nve_x()
{
// standard nve_x position update
FixNH::nve_x();
int *type = atom->type;
double **quat = atom->quat;
double **angmom = atom->angmom;
int *mask = atom->mask;
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;
// update quaternion a full step via Richardson iteration
// returns new normalized quaternion
for (int i = 0; i < nlocal; i++) {
if (mask[i] & groupbit)
richardson(quat[i],angmom[i],inertia[type[i]]);
}
}
/* ----------------------------------------------------------------------
perform half-step temperature scaling of velocities
-----------------------------------------------------------------------*/
void FixNHAsphere::nh_v_temp()
{
// standard nhc_nh_v velocity update
FixNH::nh_v_temp();
double **angmom = atom->angmom;
int *mask = atom->mask;
int nlocal = atom->nlocal;
if (igroup == atom->firstgroup) nlocal = atom->nfirst;
// set timestep here since dt may have changed or come via rRESPA
double factor_rotate = exp(-dthalf*eta_dot[0]);
for (int i = 0; i < nlocal; i++) {
if (mask[i] & groupbit) {
angmom[i][0] *= factor_rotate;
angmom[i][1] *= factor_rotate;
angmom[i][2] *= factor_rotate;
}
}
}
c4science · Help