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fix_nvt.cpp
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Sat, Jun 29, 09:06

fix_nvt.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: Mark Stevens (SNL)
------------------------------------------------------------------------- */
#include "string.h"
#include "stdlib.h"
#include "math.h"
#include "fix_nvt.h"
#include "atom.h"
#include "force.h"
#include "comm.h"
#include "group.h"
#include "update.h"
#include "respa.h"
#include "modify.h"
#include "compute.h"
#include "error.h"
using namespace LAMMPS_NS;
/* ---------------------------------------------------------------------- */
FixNVT::FixNVT(LAMMPS *lmp, int narg, char **arg) :
Fix(lmp, narg, arg)
{
if (narg < 6) error->all("Illegal fix nvt command");
restart_global = 1;
scalar_flag = 1;
scalar_vector_freq = 1;
extscalar = 1;
t_start = atof(arg[3]);
t_stop = atof(arg[4]);
double t_period = atof(arg[5]);
if (narg == 6) drag = 0.0;
else if (narg == 8 && strcmp(arg[6],"drag") == 0) drag = atof(arg[7]);
else error->all("Illegal fix nvt command");
// error checks
// convert input period to frequency
if (t_start < 0.0 || t_stop <= 0.0)
error->all("Target T for fix nvt cannot be 0.0");
if (t_period <= 0.0) error->all("Fix nvt period must be > 0.0");
t_freq = 1.0 / t_period;
eta = eta_dot = 0.0;
// create a new compute temp style
// id = fix-ID + temp, compute group = fix group
int n = strlen(id) + 6;
id_temp = new char[n];
strcpy(id_temp,id);
strcat(id_temp,"_temp");
char **newarg = new char*[3];
newarg[0] = id_temp;
newarg[1] = group->names[igroup];
if (strcmp(style,"nvt") == 0)
newarg[2] = (char *) "temp";
else if (strcmp(style,"nvt/asphere") == 0)
newarg[2] = (char *) "temp/asphere";
else if (strcmp(style,"nvt/sllod") == 0)
newarg[2] = (char *) "temp/deform";
modify->add_compute(3,newarg);
delete [] newarg;
tflag = 1;
}
/* ---------------------------------------------------------------------- */
FixNVT::~FixNVT()
{
// delete temperature if fix created it
if (tflag) modify->delete_compute(id_temp);
delete [] id_temp;
}
/* ---------------------------------------------------------------------- */
int FixNVT::setmask()
{
int mask = 0;
mask |= INITIAL_INTEGRATE;
mask |= FINAL_INTEGRATE;
mask |= THERMO_ENERGY;
mask |= INITIAL_INTEGRATE_RESPA;
mask |= FINAL_INTEGRATE_RESPA;
return mask;
}
/* ---------------------------------------------------------------------- */
void FixNVT::init()
{
if (atom->mass == NULL)
error->all("Cannot use fix nvt without per-type mass defined");
int icompute = modify->find_compute(id_temp);
if (icompute < 0) error->all("Temp ID for fix nvt does not exist");
temperature = modify->compute[icompute];
// set timesteps and frequencies
dtv = update->dt;
dtf = 0.5 * update->dt * force->ftm2v;
dtq = 0.5 * update->dt;
dthalf = 0.5 * update->dt;
drag_factor = 1.0 - (update->dt * t_freq * drag);
if (strcmp(update->integrate_style,"respa") == 0) {
nlevels_respa = ((Respa *) update->integrate)->nlevels;
step_respa = ((Respa *) update->integrate)->step;
}
}
/* ---------------------------------------------------------------------- */
void FixNVT::setup()
{
t_target = t_start; // used by compute_scalar()
t_current = temperature->compute_scalar();
}
/* ---------------------------------------------------------------------- */
void FixNVT::initial_integrate()
{
double dtfm;
double delta = update->ntimestep - update->beginstep;
delta /= update->endstep - update->beginstep;
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 NVT group
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;
for (int i = 0; i < nlocal; i++) {
if (mask[i] & groupbit) {
dtfm = dtf / mass[type[i]];
v[i][0] = v[i][0]*factor + dtfm*f[i][0];
v[i][1] = v[i][1]*factor + dtfm*f[i][1];
v[i][2] = v[i][2]*factor + dtfm*f[i][2];
x[i][0] += dtv * v[i][0];
x[i][1] += dtv * v[i][1];
x[i][2] += dtv * v[i][2];
}
}
}
/* ---------------------------------------------------------------------- */
void FixNVT::final_integrate()
{
double dtfm;
// update v of only atoms in NVT group
double **v = atom->v;
double **f = atom->f;
double *mass = atom->mass;
int *type = atom->type;
int *mask = atom->mask;
int nlocal = atom->nlocal;
for (int i = 0; i < nlocal; i++) {
if (mask[i] & groupbit) {
dtfm = dtf / mass[type[i]] * factor;
v[i][0] = v[i][0]*factor + dtfm*f[i][0];
v[i][1] = v[i][1]*factor + dtfm*f[i][1];
v[i][2] = v[i][2]*factor + dtfm*f[i][2];
}
}
// 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 FixNVT::initial_integrate_respa(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;
// 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->beginstep;
delta /= update->endstep - update->beginstep;
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 NVT group
for (int i = 0; i < nlocal; i++) {
if (mask[i] & groupbit) {
dtfm = dtf / mass[type[i]];
v[i][0] = v[i][0]*factor + dtfm*f[i][0];
v[i][1] = v[i][1]*factor + dtfm*f[i][1];
v[i][2] = v[i][2]*factor + dtfm*f[i][2];
}
}
// innermost level - also update x of only atoms in NVT 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];
}
}
}
}
/* ---------------------------------------------------------------------- */
void FixNVT::final_integrate_respa(int ilevel)
{
double dtfm;
// set timesteps by level
dtf = 0.5 * step_respa[ilevel] * force->ftm2v;
dthalf = 0.5 * step_respa[ilevel];
// outermost level - update eta_dot and apply to v via final_integrate()
// all other levels - NVE update of v
if (ilevel == nlevels_respa-1) final_integrate();
else {
// update v of only atoms in NVT group
double **v = atom->v;
double **f = atom->f;
double *mass = atom->mass;
int *type = atom->type;
int *mask = atom->mask;
int nlocal = atom->nlocal;
for (int i = 0; i < nlocal; i++) {
if (mask[i] & groupbit) {
dtfm = dtf / mass[type[i]];
v[i][0] += dtfm*f[i][0];
v[i][1] += dtfm*f[i][1];
v[i][2] += dtfm*f[i][2];
}
}
}
}
/* ----------------------------------------------------------------------
pack entire state of Fix into one write
------------------------------------------------------------------------- */
void FixNVT::write_restart(FILE *fp)
{
int n = 0;
double list[2];
list[n++] = eta;
list[n++] = eta_dot;
if (comm->me == 0) {
int size = n * sizeof(double);
fwrite(&size,sizeof(int),1,fp);
fwrite(&list,sizeof(double),n,fp);
}
}
/* ----------------------------------------------------------------------
use state info from restart file to restart the Fix
------------------------------------------------------------------------- */
void FixNVT::restart(char *buf)
{
int n = 0;
double *list = (double *) buf;
eta = list[n++];
eta_dot = list[n++];
}
/* ---------------------------------------------------------------------- */
int FixNVT::modify_param(int narg, char **arg)
{
if (strcmp(arg[0],"temp") == 0) {
if (narg < 2) error->all("Illegal fix_modify command");
if (tflag) {
modify->delete_compute(id_temp);
tflag = 0;
}
delete [] id_temp;
int n = strlen(arg[1]) + 1;
id_temp = new char[n];
strcpy(id_temp,arg[1]);
int icompute = modify->find_compute(id_temp);
if (icompute < 0) error->all("Could not find fix_modify temp ID");
temperature = modify->compute[icompute];
if (temperature->tempflag == 0)
error->all("Fix_modify temp ID does not compute temperature");
if (temperature->igroup != igroup && comm->me == 0)
error->warning("Group for fix_modify temp != fix group");
return 2;
}
return 0;
}
/* ---------------------------------------------------------------------- */
void FixNVT::reset_target(double t_new)
{
t_start = t_stop = t_new;
}
/* ---------------------------------------------------------------------- */
void FixNVT::reset_dt()
{
dtv = update->dt;
dtf = 0.5 * update->dt * force->ftm2v;
dtq = 0.5 * update->dt;
dthalf = 0.5 * update->dt;
drag_factor = 1.0 - (update->dt * t_freq * drag);
}
/* ---------------------------------------------------------------------- */
double FixNVT::compute_scalar()
{
double ke = temperature->dof * force->boltz * t_target;
double energy = ke * (eta + 0.5*eta_dot*eta_dot/(t_freq*t_freq));
return energy;
}

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