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git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@2902 f3b2605a-c512-4ea7-a41b-209d697bcdaa

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This commit is contained in:
sjplimp
2009-06-26 18:23:16 +00:00
parent 3df8b6e355
commit 2d5a69385a
32 changed files with 2015 additions and 781 deletions
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225
src/fix_nvt.cpp
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@ -117,9 +117,6 @@ int FixNVT::setmask()
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];
@ -132,7 +129,6 @@ void FixNVT::init()
dtv = update->dt;
dtf = 0.5 * update->dt * force->ftm2v;
dthalf = 0.5 * update->dt;
drag_factor = 1.0 - (update->dt * t_freq * drag);
if (strcmp(update->integrate_style,"respa") == 0) {
@ -172,37 +168,70 @@ void FixNVT::initial_integrate(int vflag)
double **x = atom->x;
double **v = atom->v;
double **f = atom->f;
double *rmass = atom->rmass;
double *mass = atom->mass;
int *type = atom->type;
int *mask = atom->mask;
int nlocal = atom->nlocal;
if (igroup == atom->firstgroup) nlocal = atom->nfirst;
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 + 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];
if (rmass) {
if (which == NOBIAS) {
for (int i = 0; i < nlocal; i++) {
if (mask[i] & groupbit) {
dtfm = dtf / rmass[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];
}
}
} else if (which == BIAS) {
for (int i = 0; i < nlocal; i++) {
if (mask[i] & groupbit) {
temperature->remove_bias(i,v[i]);
dtfm = dtf / rmass[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];
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];
}
}
}
} 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 + 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];
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];
} 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 + 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];
}
}
} 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 + 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];
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];
}
}
}
}
@ -218,31 +247,58 @@ void FixNVT::final_integrate()
double **v = atom->v;
double **f = atom->f;
double *rmass = atom->rmass;
double *mass = atom->mass;
int *type = atom->type;
int *mask = atom->mask;
int nlocal = atom->nlocal;
if (igroup == atom->firstgroup) nlocal = atom->nfirst;
if (which == NOBIAS) {
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];
if (rmass) {
if (which == NOBIAS) {
for (int i = 0; i < nlocal; i++) {
if (mask[i] & groupbit) {
dtfm = dtf / rmass[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];
}
}
} else if (which == BIAS) {
for (int i = 0; i < nlocal; i++) {
if (mask[i] & groupbit) {
temperature->remove_bias(i,v[i]);
dtfm = dtf / rmass[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];
temperature->restore_bias(i,v[i]);
}
}
}
} 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]] * 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];
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]] * 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];
}
}
} 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]] * 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];
temperature->restore_bias(i,v[i]);
}
}
}
}
@ -276,6 +332,7 @@ void FixNVT::initial_integrate_respa(int vflag, int ilevel, int flag)
double **x = atom->x;
double **v = atom->v;
double **f = atom->f;
double *rmass = atom->rmass;
double *mass = atom->mass;
int *type = atom->type;
int *mask = atom->mask;
@ -300,25 +357,51 @@ void FixNVT::initial_integrate_respa(int vflag, int ilevel, int flag)
factor = exp(-dthalf*eta_dot);
} else factor = 1.0;
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 + 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];
if (rmass) {
if (which == NOBIAS) {
for (int i = 0; i < nlocal; i++) {
if (mask[i] & groupbit) {
dtfm = dtf / rmass[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];
}
}
} else if (which == BIAS) {
for (int i = 0; i < nlocal; i++) {
if (mask[i] & groupbit) {
temperature->remove_bias(i,v[i]);
dtfm = dtf / rmass[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];
temperature->restore_bias(i,v[i]);
}
}
}
} 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 + 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];
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 + 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];
}
}
} 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 + 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];
temperature->restore_bias(i,v[i]);
}
}
}
}
@ -351,18 +434,31 @@ void FixNVT::final_integrate_respa(int ilevel)
else {
double **v = atom->v;
double **f = atom->f;
double *rmass = atom->rmass;
double *mass = atom->mass;
int *type = atom->type;
int *mask = atom->mask;
int nlocal = atom->nlocal;
if (igroup == atom->firstgroup) nlocal = atom->nfirst;
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];
if (rmass) {
for (int i = 0; i < nlocal; i++) {
if (mask[i] & groupbit) {
dtfm = dtf / rmass[i];
v[i][0] += dtfm*f[i][0];
v[i][1] += dtfm*f[i][1];
v[i][2] += dtfm*f[i][2];
}
}
} else {
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];
}
}
}
}
@ -440,7 +536,6 @@ void FixNVT::reset_dt()
dtv = update->dt;
dtf = 0.5 * update->dt * force->ftm2v;
dthalf = 0.5 * update->dt;
drag_factor = 1.0 - (update->dt * t_freq * drag);
}