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git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@3121 f3b2605a-c512-4ea7-a41b-209d697bcdaa

This commit is contained in:
sjplimp 2009-08-27 18:51:03 +00:00
parent 9c6b8ec3b6
commit fa1d760b79
2 changed files with 169 additions and 29 deletions
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192
src/fix_nvt.cpp
View File

@ -12,7 +12,8 @@
------------------------------------------------------------------------- */
/* ----------------------------------------------------------------------
Contributing author: Mark Stevens (SNL)
Contributing authors: Mark Stevens (SNL)
Andy Ballard (U Maryland) for chains
------------------------------------------------------------------------- */
#include "string.h"
@ -50,9 +51,24 @@ FixNVT::FixNVT(LAMMPS *lmp, int narg, char **arg) :
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");
drag = 0.0;
chain = 1;
int iarg = 6;
while (iarg < narg) {
if (strcmp(arg[iarg],"drag") == 0) {
if (iarg+2 > narg) error->all("Illegal fix nvt command");
drag = atof(arg[iarg+1]);
if (drag < 0.0) error->all("Illegal fix nvt command");
iarg += 2;
} else if (strcmp(arg[iarg],"chain") == 0) {
if (iarg+2 > narg) error->all("Illegal fix nvt command");
if (strcmp(arg[iarg+1],"yes") == 0) chain = 1;
else if (strcmp(arg[iarg+1],"no") == 0) chain = 0;
else error->all("Illegal fix nvt command");
iarg += 2;
} else error->all("Illegal fix nvt command");
}
// error checks
// convert input period to frequency
@ -88,6 +104,7 @@ FixNVT::FixNVT(LAMMPS *lmp, int narg, char **arg) :
// Nose/Hoover temp init
eta = eta_dot = 0.0;
eta2 = eta2_dot = 0.0;
}
/* ---------------------------------------------------------------------- */
@ -129,6 +146,9 @@ void FixNVT::init()
dtv = update->dt;
dtf = 0.5 * update->dt * force->ftm2v;
dthalf = 0.5 * update->dt;
dt4 = 0.25 * update->dt;
dt8 = 0.125 * update->dt;
drag_factor = 1.0 - (update->dt * t_freq * drag);
if (strcmp(update->integrate_style,"respa") == 0) {
@ -155,12 +175,29 @@ void FixNVT::initial_integrate(int vflag)
delta /= update->endstep - update->beginstep;
t_target = t_start + delta * (t_stop-t_start);
// update eta_dot
// update eta, eta_dot, eta2, eta2_dot
int nlocal = atom->nlocal;
if (igroup == atom->firstgroup) nlocal = atom->nfirst;
if (chain) {
eta2_dot += (temperature->dof * eta_dot*eta_dot - t_freq*t_freq) * dt4;
factor2 = exp(-dt8*eta2_dot);
eta_dot *= factor2;
f_eta = t_freq*t_freq * (t_current/t_target - 1.0);
eta_dot += f_eta*dt4;
eta_dot *= drag_factor;
eta_dot *= factor2;
eta += dthalf*eta_dot;
eta2 += dthalf*eta2_dot;
} else {
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;
}
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
@ -172,8 +209,6 @@ void FixNVT::initial_integrate(int vflag)
double *mass = atom->mass;
int *type = atom->type;
int *mask = atom->mask;
int nlocal = atom->nlocal;
if (igroup == atom->firstgroup) nlocal = atom->nfirst;
if (rmass) {
if (which == NOBIAS) {
@ -188,7 +223,6 @@ void FixNVT::initial_integrate(int vflag)
x[i][2] += dtv * v[i][2];
}
}
} else if (which == BIAS) {
for (int i = 0; i < nlocal; i++) {
if (mask[i] & groupbit) {
@ -218,7 +252,6 @@ void FixNVT::initial_integrate(int vflag)
x[i][2] += dtv * v[i][2];
}
}
} else if (which == BIAS) {
for (int i = 0; i < nlocal; i++) {
if (mask[i] & groupbit) {
@ -235,6 +268,14 @@ void FixNVT::initial_integrate(int vflag)
}
}
}
if (chain) {
eta_dot *= factor2;
f_eta = t_freq*t_freq * (factor * factor * t_current/t_target - 1.0);
eta_dot += f_eta * dt4;
eta_dot *= factor2;
eta2_dot += (temperature->dof * eta_dot*eta_dot - t_freq*t_freq) * dt4;
}
}
/* ---------------------------------------------------------------------- */
@ -254,6 +295,8 @@ void FixNVT::final_integrate()
int nlocal = atom->nlocal;
if (igroup == atom->firstgroup) nlocal = atom->nfirst;
if (chain) factor = 1.0;
if (rmass) {
if (which == NOBIAS) {
for (int i = 0; i < nlocal; i++) {
@ -264,7 +307,6 @@ void FixNVT::final_integrate()
v[i][2] = v[i][2]*factor + dtfm*f[i][2];
}
}
} else if (which == BIAS) {
for (int i = 0; i < nlocal; i++) {
if (mask[i] & groupbit) {
@ -288,7 +330,6 @@ void FixNVT::final_integrate()
v[i][2] = v[i][2]*factor + dtfm*f[i][2];
}
}
} else if (which == BIAS) {
for (int i = 0; i < nlocal; i++) {
if (mask[i] & groupbit) {
@ -307,11 +348,82 @@ void FixNVT::final_integrate()
t_current = temperature->compute_scalar();
// update eta_dot
// update eta, eta_dot, eta2, eta2_dot
// chains require additional velocity update and recompute of current T
f_eta = t_freq*t_freq * (t_current/t_target - 1.0);
eta_dot += f_eta*dthalf;
eta_dot *= drag_factor;
if (chain) {
eta2_dot += (temperature->dof * eta_dot*eta_dot - t_freq*t_freq) * dt4;
factor2 = exp(-dt8*eta2_dot);
eta_dot *= factor2;
f_eta = t_freq*t_freq * (t_current/t_target - 1.0);
eta_dot += f_eta*dt4;
eta_dot *= drag_factor;
eta_dot *= factor2;
eta += dthalf*eta_dot;
eta2 += dthalf*eta2_dot;
factor = exp(-dthalf*eta_dot);
if (rmass) {
if (which == NOBIAS) {
for (int i = 0; i < nlocal; i++) {
if (mask[i] & groupbit) {
dtfm = dtf / mass[type[i]];
v[i][0] = v[i][0] * factor;
v[i][1] = v[i][1] * factor;
v[i][2] = v[i][2] * factor;
}
}
} else if (which == BIAS) {
for (int i = 0; i < nlocal; i++) {
if (mask[i] & groupbit) {
temperature->remove_bias(i,v[i]);
dtfm = dtf / mass[type[i]];
v[i][0] = v[i][0] * factor;
v[i][1] = v[i][1] * factor;
v[i][2] = v[i][2] * factor;
temperature->restore_bias(i,v[i]);
}
}
}
} else {
if (which == NOBIAS) {
for (int i = 0; i < nlocal; i++) {
if (mask[i] & groupbit) {
dtfm = dtf / mass[type[i]];
v[i][0] = v[i][0] * factor;
v[i][1] = v[i][1] * factor;
v[i][2] = v[i][2] * factor;
}
}
} else if (which == BIAS) {
for (int i = 0; i < nlocal; i++) {
if (mask[i] & groupbit) {
temperature->remove_bias(i,v[i]);
dtfm = dtf / mass[type[i]];
v[i][0] = v[i][0] * factor;
v[i][1] = v[i][1] * factor;
v[i][2] = v[i][2] * factor;
temperature->restore_bias(i,v[i]);
}
}
}
}
t_current = temperature->compute_scalar();
eta_dot *= factor2;
f_eta = t_freq*t_freq * (t_current/t_target - 1.0);
eta_dot += f_eta * dt4;
eta_dot *= factor2;
eta2_dot += (temperature->dof * eta_dot*eta_dot - t_freq*t_freq) * dt4;
} else {
f_eta = t_freq*t_freq * (t_current/t_target - 1.0);
eta_dot += f_eta*dthalf;
eta_dot *= drag_factor;
}
}
/* ---------------------------------------------------------------------- */
@ -348,13 +460,26 @@ void FixNVT::initial_integrate_respa(int vflag, int ilevel, int flag)
delta /= update->endstep - update->beginstep;
t_target = t_start + delta * (t_stop-t_start);
// update eta_dot
if (chain) {
eta2_dot += (temperature->dof * eta_dot*eta_dot - t_freq*t_freq) * dt4;
factor2 = exp(-dt8*eta2_dot);
eta_dot *= factor2;
f_eta = t_freq*t_freq * (t_current/t_target - 1.0);
eta_dot += f_eta*dt4;
eta_dot *= drag_factor;
eta_dot *= factor2;
eta += dthalf*eta_dot;
eta2 += dthalf*eta2_dot;
} else {
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;
}
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;
if (rmass) {
@ -367,7 +492,6 @@ void FixNVT::initial_integrate_respa(int vflag, int ilevel, int flag)
v[i][2] = v[i][2]*factor + dtfm*f[i][2];
}
}
} else if (which == BIAS) {
for (int i = 0; i < nlocal; i++) {
if (mask[i] & groupbit) {
@ -415,6 +539,14 @@ void FixNVT::initial_integrate_respa(int vflag, int ilevel, int flag)
}
}
}
if (ilevel == nlevels_respa-1 && chain) {
eta_dot *= factor2;
f_eta = t_freq*t_freq * (factor * factor * t_current/t_target - 1.0);
eta_dot += f_eta * dt4;
eta_dot *= factor2;
eta2_dot += (temperature->dof * eta_dot*eta_dot - t_freq*t_freq) * dt4;
}
}
/* ---------------------------------------------------------------------- */
@ -471,9 +603,11 @@ void FixNVT::final_integrate_respa(int ilevel)
void FixNVT::write_restart(FILE *fp)
{
int n = 0;
double list[2];
double list[4];
list[n++] = eta;
list[n++] = eta_dot;
list[n++] = eta2;
list[n++] = eta2_dot;
if (comm->me == 0) {
int size = n * sizeof(double);
@ -492,6 +626,8 @@ void FixNVT::restart(char *buf)
double *list = (double *) buf;
eta = list[n++];
eta_dot = list[n++];
eta2 = list[n++];
eta2_dot = list[n++];
}
/* ---------------------------------------------------------------------- */
@ -519,6 +655,7 @@ int FixNVT::modify_param(int narg, char **arg)
error->warning("Group for fix_modify temp != fix group");
return 2;
}
return 0;
}
@ -536,6 +673,9 @@ void FixNVT::reset_dt()
dtv = update->dt;
dtf = 0.5 * update->dt * force->ftm2v;
dthalf = 0.5 * update->dt;
dt4 = 0.25 * update->dt;
dt8 = 0.125 * update->dt;
drag_factor = 1.0 - (update->dt * t_freq * drag);
}

6
src/fix_nvt.h
View File

@ -37,12 +37,12 @@ class FixNVT : public Fix {
void reset_dt();
protected:
int which;
int which,chain;
double t_start,t_stop;
double t_current,t_target;
double t_freq,drag,drag_factor;
double f_eta,eta_dot,eta,factor;
double dtv,dtf,dthalf;
double f_eta,eta_dot,eta,eta2_dot,eta2,factor,factor2;
double dtv,dtf,dthalf,dt4,dt8;
int nlevels_respa;
double *step_respa;