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lammps/src/fix_nvt_sllod.cpp
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fix_nvt_sllod.cpp
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/* ----------------------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
www.cs.sandia.gov/~sjplimp/lammps.html
Steve Plimpton, sjplimp@sandia.gov, Sandia National Laboratories
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: Pieter in 't Veld (SNL)
------------------------------------------------------------------------- */
#include "math.h"
#include "string.h"
#include "stdlib.h"
#include "fix_nvt_sllod.h"
#include "math_extra.h"
#include "atom.h"
#include "force.h"
#include "domain.h"
#include "group.h"
#include "update.h"
#include "respa.h"
#include "modify.h"
#include "fix.h"
#include "fix_deform.h"
#include "compute.h"
#include "error.h"
using namespace LAMMPS_NS;
enum{NO_REMAP,X_REMAP,V_REMAP}; // same as fix_deform.cpp
enum{NOBIAS,BIAS};
/* ---------------------------------------------------------------------- */
FixNVTSlodd::FixNVTSlodd(LAMMPS *lmp, int narg, char **arg) :
FixNVT(lmp, narg, arg) {}
/* ---------------------------------------------------------------------- */
void FixNVTSlodd::init()
{
FixNVT::init();
if (!temperature->tempbias)
error->all("Temperature for fix nvt/sllod does not have a bias");
// check fix deform remap settings
int i;
for (i = 0; i < modify->nfix; i++)
if (strcmp(modify->fix[i]->style,"deform") == 0) {
if (((FixDeform *) modify->fix[i])->remapflag != V_REMAP)
error->all("Using fix nvt/sllod with inconsistent fix deform remap option");
break;
}
if (i == modify->nfix)
error->all("Using fix nvt/sllod with no fix deform defined");
}
/* ---------------------------------------------------------------------- */
void FixNVTSlodd::initial_integrate(int vflag)
{
double dtfm;
double delta = update->ntimestep - update->firststep;
delta /= update->nsteps;
t_target = t_start + delta * (t_stop-t_start);
// update eta_dot
f_eta = t_freq*t_freq * (t_current/t_target - 1.0);
eta_dot += f_eta*dthalf;
eta_dot *= drag_factor;
eta += dtv*eta_dot;
factor = exp(-dthalf*eta_dot);
// update v and x of only atoms in group
// remove and restore bias = streaming velocity = Hrate*lamda + Hratelo
// thermostat thermal velocity only
// vdelu = SLLOD correction = Hrate*Hinv*vthermal
double **x = atom->x;
double **v = atom->v;
double **f = atom->f;
double *mass = atom->mass;
int *type = atom->type;
int *mask = atom->mask;
int nlocal = atom->nlocal;
if (igroup == atom->firstgroup) nlocal = atom->nfirst;
double h_two[6],vdelu[3];
MathExtra::multiply_shape_shape(domain->h_rate,domain->h_inv,h_two);
for (int i = 0; i < nlocal; i++) {
if (mask[i] & groupbit) {
temperature->remove_bias(i,v[i]);
vdelu[0] = h_two[0]*v[i][0] + h_two[5]*v[i][1] + h_two[4]*v[i][2];
vdelu[1] = h_two[1]*v[i][1] + h_two[3]*v[i][2];
vdelu[2] = h_two[2]*v[i][2];
dtfm = dtf / mass[type[i]];
v[i][0] = v[i][0]*factor + dtfm*f[i][0] - dthalf*vdelu[0];
v[i][1] = v[i][1]*factor + dtfm*f[i][1] - dthalf*vdelu[1];
v[i][2] = v[i][2]*factor + dtfm*f[i][2] - dthalf*vdelu[2];
temperature->restore_bias(i,v[i]);
x[i][0] += dtv * v[i][0];
x[i][1] += dtv * v[i][1];
x[i][2] += dtv * v[i][2];
}
}
}
/* ---------------------------------------------------------------------- */
void FixNVTSlodd::final_integrate()
{
double dtfm;
// update v of only atoms in group
// remove and restore bias = streaming velocity = Hrate*lamda + Hratelo
// thermostat thermal velocity only
// vdelu = SLLOD correction = Hrate*Hinv*vthermal
double **v = atom->v;
double **f = atom->f;
double *mass = atom->mass;
int *type = atom->type;
int *mask = atom->mask;
int nlocal = atom->nlocal;
if (igroup == atom->firstgroup) nlocal = atom->nfirst;
double h_two[6],vdelu[3];
MathExtra::multiply_shape_shape(domain->h_rate,domain->h_inv,h_two);
for (int i = 0; i < nlocal; i++) {
if (mask[i] & groupbit) {
temperature->remove_bias(i,v[i]);
vdelu[0] = h_two[0]*v[i][0] + h_two[5]*v[i][1] + h_two[4]*v[i][2];
vdelu[1] = h_two[1]*v[i][1] + h_two[3]*v[i][2];
vdelu[2] = h_two[2]*v[i][2];
//dtfm = dtf / mass[type[i]] * factor;
dtfm = dtf / mass[type[i]];
v[i][0] = v[i][0]*factor + dtfm*f[i][0] - dthalf*vdelu[0];
v[i][1] = v[i][1]*factor + dtfm*f[i][1] - dthalf*vdelu[1];
v[i][2] = v[i][2]*factor + dtfm*f[i][2] - dthalf*vdelu[2];
temperature->restore_bias(i,v[i]);
}
}
// compute current T
t_current = temperature->compute_scalar();
// update eta_dot
f_eta = t_freq*t_freq * (t_current/t_target - 1.0);
eta_dot += f_eta*dthalf;
eta_dot *= drag_factor;
}
/* ---------------------------------------------------------------------- */
void FixNVTSlodd::initial_integrate_respa(int vflag, int ilevel, int flag)
{
if (flag) return; // only used by NPT,NPH
// set timesteps by level
double dtfm;
dtv = step_respa[ilevel];
dtf = 0.5 * step_respa[ilevel] * force->ftm2v;
dthalf = 0.5 * step_respa[ilevel];
// atom quantities
double **x = atom->x;
double **v = atom->v;
double **f = atom->f;
double *mass = atom->mass;
int *type = atom->type;
int *mask = atom->mask;
int nlocal = atom->nlocal;
if (igroup == atom->firstgroup) nlocal = atom->nfirst;
// outermost level - update eta_dot and apply to v
// all other levels - NVE update of v
if (ilevel == nlevels_respa-1) {
double delta = update->ntimestep - update->firststep;
delta /= update->nsteps;
t_target = t_start + delta * (t_stop-t_start);
// update eta_dot
f_eta = t_freq*t_freq * (t_current/t_target - 1.0);
eta_dot += f_eta*dthalf;
eta_dot *= drag_factor;
eta += dtv*eta_dot;
factor = exp(-dthalf*eta_dot);
} else factor = 1.0;
// update v of only atoms in group
double h_two[6],vdelu[3];
MathExtra::multiply_shape_shape(domain->h_rate,domain->h_inv,h_two);
for (int i = 0; i < nlocal; i++) {
if (mask[i] & groupbit) {
temperature->remove_bias(i,v[i]);
vdelu[0] = h_two[0]*v[i][0] + h_two[5]*v[i][1] + h_two[4]*v[i][2];
vdelu[1] = h_two[1]*v[i][1] + h_two[3]*v[i][2];
vdelu[2] = h_two[2]*v[i][2];
dtfm = dtf / mass[type[i]];
v[i][0] = v[i][0]*factor + dtfm*f[i][0] - dthalf*vdelu[0];
v[i][1] = v[i][1]*factor + dtfm*f[i][1] - dthalf*vdelu[1];
v[i][2] = v[i][2]*factor + dtfm*f[i][2] - dthalf*vdelu[2];
temperature->restore_bias(i,v[i]);
}
}
// innermost level - also update x of only atoms in group
if (ilevel == 0) {
for (int i = 0; i < nlocal; i++) {
if (mask[i] & groupbit) {
x[i][0] += dtv * v[i][0];
x[i][1] += dtv * v[i][1];
x[i][2] += dtv * v[i][2];
}
}
}
}
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