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fix_nve_dotc_langevin.cpp
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Tue, Jun 4, 17:21
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rLAMMPS lammps
fix_nve_dotc_langevin.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: Oliver Henrich (University of Strathclyde, Glasgow)
------------------------------------------------------------------------- */
#include <math.h>
#include <stdio.h>
#include <string.h>
#include "fix_nve_dotc_langevin.h"
#include "math_extra.h"
#include "atom.h"
#include "atom_vec_ellipsoid.h"
#include "force.h"
#include "update.h"
#include "comm.h"
#include "random_mars.h"
#include "memory.h"
#include "error.h"
using namespace LAMMPS_NS;
using namespace FixConst;
using namespace MathExtra;
#define INERTIA 0.2 // moment of inertia prefactor for ellipsoid
/* ---------------------------------------------------------------------- */
FixNVEDotcLangevin::FixNVEDotcLangevin(LAMMPS *lmp, int narg, char **arg) :
FixNVE(lmp, narg, arg)
{
if (narg != 9) error->all(FLERR,"Illegal fix nve/dotc/langevin command");
t_start = force->numeric(FLERR,arg[3]);
t_target = t_start;
t_stop = force->numeric(FLERR,arg[4]);
t_period = force->numeric(FLERR,arg[5]);
if (t_period <= 0.0) error->all(FLERR,"Fix nve/dotc/langevin period must be > 0.0");
gamma = 1.0/t_period;
seed = force->inumeric(FLERR,arg[6]);
if (seed <= 0) error->all(FLERR,"Illegal fix nve/dotc/langevin command");
if (strcmp(arg[7],"angmom") == 0) {
if (9 > narg) error->all(FLERR,"Illegal fix nve/dotc/langevin command");
if (strcmp(arg[8],"no") == 0) {
ascale = 0.0;
Gamma = 0.0;
}
else {
ascale = force->numeric(FLERR,arg[8]);
Gamma = gamma * ascale;
}
}
// initialize Marsaglia RNG with processor-unique seed
random = new RanMars(lmp,seed + comm->me);
}
/* ---------------------------------------------------------------------- */
FixNVEDotcLangevin::~FixNVEDotcLangevin()
{
delete random;
}
/* ---------------------------------------------------------------------- */
void FixNVEDotcLangevin::init()
{
int *ellipsoid = atom->ellipsoid;
int *mask = atom->mask;
int nlocal = atom->nlocal;
avec = (AtomVecEllipsoid *) atom->style_match("ellipsoid");
if (!avec)
error->all(FLERR,"Fix nve/dotc/langevin requires atom style ellipsoid");
for (int i = 0; i < nlocal; i++)
if (mask[i] & groupbit)
if (ellipsoid[i] < 0)
error->one(FLERR,"Fix nve/dotc/langevin requires extended particles");
// set prefactor
gfactor1 = exp(-gamma*update->dt);
// set square root of temperature
compute_target();
FixNVE::init();
}
/* ----------------------------------------------------------------------
set current t_target and t_sqrt
------------------------------------------------------------------------- */
void FixNVEDotcLangevin::compute_target()
{
double delta = update->ntimestep - update->beginstep;
if (delta != 0.0) delta /= update->endstep - update->beginstep;
// Only homogeneous temperature supported
t_target = t_start + delta * (t_stop-t_start);
tsqrt = sqrt(t_target);
}
/* ---------------------------------------------------------------------- */
void FixNVEDotcLangevin::initial_integrate(int vflag)
{
double *shape,*quat;
double fquat[4],conjqm[4],inertia[3];
double slq_conjqm[3];
AtomVecEllipsoid::Bonus *bonus = avec->bonus;
int *ellipsoid = atom->ellipsoid;
double **x = atom->x;
double **v = atom->v;
double **f = atom->f;
double **angmom = atom->angmom;
double **torque = atom->torque;
double *rmass = atom->rmass;
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
dt = update->dt;
dthlf = 0.5 * dt;
dtqrt = 0.25 * dt;
// set square root of temperature
compute_target();
for (int i = 0; i < nlocal; i++)
if (mask[i] & groupbit) {
dthlfm = dthlf / rmass[i];
quat = bonus[ellipsoid[i]].quat;
shape = bonus[ellipsoid[i]].shape;
// update momentum by 1/2 step
v[i][0] += dthlfm * f[i][0];
v[i][1] += dthlfm * f[i][1];
v[i][2] += dthlfm * f[i][2];
// update position by 1/2 step
x[i][0] += dthlf * v[i][0];
x[i][1] += dthlf * v[i][1];
x[i][2] += dthlf * v[i][2];
// convert angular momentum and torque in space frame into
// quaternion 4-momentum and 1/2 of 4-torque in body frame
vec3_to_vec4(quat,angmom[i],conjqm);
conjqm[0] *= 2.0;
conjqm[1] *= 2.0;
conjqm[2] *= 2.0;
conjqm[3] *= 2.0;
vec3_to_vec4(quat,torque[i],fquat);
// update quaternion 4-momentum by 1/2 step
conjqm[0] += dt * fquat[0];
conjqm[1] += dt * fquat[1];
conjqm[2] += dt * fquat[2];
conjqm[3] += dt * fquat[3];
// principal moments of inertia
inertia[0] = INERTIA*rmass[i] * (shape[1]*shape[1]+shape[2]*shape[2]);
inertia[1] = INERTIA*rmass[i] * (shape[0]*shape[0]+shape[2]*shape[2]);
inertia[2] = INERTIA*rmass[i] * (shape[0]*shape[0]+shape[1]*shape[1]);
M = inertia[0]*inertia[1]*inertia[2];
M /= inertia[1]*inertia[2]+inertia[0]*inertia[2]+inertia[0]*inertia[1];
// set prefactors
// factors 12 and 48 reflect the variance of the uniform distribution:
// var = 1/12*(b-a)^2
gfactor2 = sqrt(12.0*(1.0-gfactor1*gfactor1)/rmass[i])*tsqrt;
gfactor3[0] = exp(-Gamma*M*dt/inertia[0]);
gfactor3[1] = exp(-Gamma*M*dt/inertia[1]);
gfactor3[2] = exp(-Gamma*M*dt/inertia[2]);
gfactor4[0] = sqrt(48.0*inertia[0]*(1.0-gfactor3[0]*gfactor3[0]))*tsqrt;
gfactor4[1] = sqrt(48.0*inertia[1]*(1.0-gfactor3[1]*gfactor3[1]))*tsqrt;
gfactor4[2] = sqrt(48.0*inertia[2]*(1.0-gfactor3[2]*gfactor3[2]))*tsqrt;
// rotate quaternion and quaternion 4-momentum by 1/2 step
no_squish_rotate(3,conjqm,quat,inertia,dtqrt);
no_squish_rotate(2,conjqm,quat,inertia,dtqrt);
no_squish_rotate(1,conjqm,quat,inertia,dthlf);
no_squish_rotate(2,conjqm,quat,inertia,dtqrt);
no_squish_rotate(3,conjqm,quat,inertia,dtqrt);
// apply stochastic force to velocities
v[i][0] = v[i][0] * gfactor1 + gfactor2 * (random->uniform()-0.5);
v[i][1] = v[i][1] * gfactor1 + gfactor2 * (random->uniform()-0.5);
v[i][2] = v[i][2] * gfactor1 + gfactor2 * (random->uniform()-0.5);
// update position by 1/2 step
x[i][0] += dthlf * v[i][0];
x[i][1] += dthlf * v[i][1];
x[i][2] += dthlf * v[i][2];
// apply stochastic force to quaternion 4-momentum
slq_conjqm[0] = -quat[1]*conjqm[0] + quat[0]*conjqm[1] + quat[3]*conjqm[2] - quat[2]*conjqm[3];
slq_conjqm[1] = -quat[2]*conjqm[0] - quat[3]*conjqm[1] + quat[0]*conjqm[2] + quat[1]*conjqm[3];
slq_conjqm[2] = -quat[3]*conjqm[0] + quat[2]*conjqm[1] - quat[1]*conjqm[2] + quat[0]*conjqm[3];
gfactor5[0] = gfactor3[0] * slq_conjqm[0] + gfactor4[0] * (random->uniform()-0.5);
gfactor5[1] = gfactor3[1] * slq_conjqm[1] + gfactor4[1] * (random->uniform()-0.5);
gfactor5[2] = gfactor3[2] * slq_conjqm[2] + gfactor4[2] * (random->uniform()-0.5);
conjqm[0] = -quat[1] * gfactor5[0] - quat[2] * gfactor5[1] - quat[3] * gfactor5[2];
conjqm[1] = quat[0] * gfactor5[0] - quat[3] * gfactor5[1] + quat[2] * gfactor5[2];
conjqm[2] = quat[3] * gfactor5[0] + quat[0] * gfactor5[1] - quat[1] * gfactor5[2];
conjqm[3] = -quat[2] * gfactor5[0] + quat[1] * gfactor5[1] + quat[0] * gfactor5[2];
// rotate quaternion and quaternion 4-momentum by 1/2 step
no_squish_rotate(3,conjqm,quat,inertia,dtqrt);
no_squish_rotate(2,conjqm,quat,inertia,dtqrt);
no_squish_rotate(1,conjqm,quat,inertia,dthlf);
no_squish_rotate(2,conjqm,quat,inertia,dtqrt);
no_squish_rotate(3,conjqm,quat,inertia,dtqrt);
qnormalize(quat);
// convert quaternion 4-momentum in body frame back to angular momentum in space frame
vec4_to_vec3(quat,conjqm,angmom[i]);
angmom[i][0] *= 0.5;
angmom[i][1] *= 0.5;
angmom[i][2] *= 0.5;
}
}
/* ---------------------------------------------------------------------- */
void FixNVEDotcLangevin::final_integrate()
{
double *quat;
double fquat[4],conjqm[4];
double conjqm_dot_quat;
AtomVecEllipsoid::Bonus *bonus = avec->bonus;
int *ellipsoid = atom->ellipsoid;
double **v = atom->v;
double **f = atom->f;
double **angmom = atom->angmom;
double **torque = atom->torque;
double *rmass = atom->rmass;
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
dt = update->dt;
dthlf = 0.5 * dt;
for (int i = 0; i < nlocal; i++)
if (mask[i] & groupbit) {
dthlfm = dthlf / rmass[i];
quat = bonus[ellipsoid[i]].quat;
// update momentum by 1/2 step
v[i][0] += dthlfm * f[i][0];
v[i][1] += dthlfm * f[i][1];
v[i][2] += dthlfm * f[i][2];
// convert angular momentum and torque in space frame into
// quaternion 4-momentum and 1/2 of 4-torque in body frame
vec3_to_vec4(quat,angmom[i],conjqm);
conjqm[0] *= 2.0;
conjqm[1] *= 2.0;
conjqm[2] *= 2.0;
conjqm[3] *= 2.0;
vec3_to_vec4(quat,torque[i],fquat);
// update quaternion 4-momentum by 1/2 step
conjqm[0] += dt * fquat[0];
conjqm[1] += dt * fquat[1];
conjqm[2] += dt * fquat[2];
conjqm[3] += dt * fquat[3];
// subtract component parallel to quaternion for improved numerical accuracy
conjqm_dot_quat = conjqm[0]*quat[0] + conjqm[1]*quat[1] + conjqm[2]*quat[2] + conjqm[3]*quat[3];
conjqm[0] -= conjqm_dot_quat * quat[0];
conjqm[1] -= conjqm_dot_quat * quat[1];
conjqm[2] -= conjqm_dot_quat * quat[2];
conjqm[3] -= conjqm_dot_quat * quat[3];
// convert quaternion 4-momentum in body frame back to angular momentum in space frame
vec4_to_vec3(quat,conjqm,angmom[i]);
angmom[i][0] *= 0.5;
angmom[i][1] *= 0.5;
angmom[i][2] *= 0.5;
}
}
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