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git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@1591 f3b2605a-c512-4ea7-a41b-209d697bcdaa

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This commit is contained in:
sjplimp
2008-03-11 17:15:30 +00:00
parent 07c6376bcf
commit d0e374e4c3
27 changed files with 412 additions and 206 deletions
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109
src/fix_nvt.cpp
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@ -31,6 +31,8 @@
using namespace LAMMPS_NS;
enum{NOBIAS,BIAS};
/* ---------------------------------------------------------------------- */
FixNVT::FixNVT(LAMMPS *lmp, int narg, char **arg) :
@ -117,6 +119,9 @@ void FixNVT::init()
if (icompute < 0) error->all("Temp ID for fix nvt does not exist");
temperature = modify->compute[icompute];
if (temperature->tempbias) which = BIAS;
else which = NOBIAS;
// set timesteps and frequencies
dtv = update->dt;
@ -158,7 +163,7 @@ void FixNVT::initial_integrate(int vflag)
eta += dtv*eta_dot;
factor = exp(-dthalf*eta_dot);
// update v and x of only atoms in NVT group
// update v and x of only atoms in group
double **x = atom->x;
double **v = atom->v;
@ -169,15 +174,32 @@ void FixNVT::initial_integrate(int vflag)
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] = 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 (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(v[i]);
x[i][0] += dtv * v[i][0];
x[i][1] += dtv * v[i][1];
x[i][2] += dtv * v[i][2];
}
}
}
}
@ -188,7 +210,7 @@ void FixNVT::final_integrate()
{
double dtfm;
// update v of only atoms in NVT group
// update v of only atoms in group
double **v = atom->v;
double **f = atom->f;
@ -198,12 +220,26 @@ void FixNVT::final_integrate()
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]] * 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 (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(v[i]);
}
}
}
@ -242,8 +278,9 @@ void FixNVT::initial_integrate_respa(int vflag, int ilevel, int flag)
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
// outermost level - update eta_dot and apply to v with factor
// all other levels - NVE update of v (factor = 1)
// innermost level - also update x
if (ilevel == nlevels_respa-1) {
double delta = update->ntimestep - update->beginstep;
@ -259,19 +296,29 @@ void FixNVT::initial_integrate_respa(int vflag, int ilevel, int flag)
factor = exp(-dthalf*eta_dot);
} else factor = 1.0;
// update v of only atoms in NVT group
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];
}
}
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(v[i]);
}
}
}
// 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) {
@ -287,10 +334,9 @@ void FixNVT::initial_integrate_respa(int vflag, int ilevel, int flag)
void FixNVT::final_integrate_respa(int ilevel)
{
double dtfm;
// set timesteps by level
double dtfm;
dtf = 0.5 * step_respa[ilevel] * force->ftm2v;
dthalf = 0.5 * step_respa[ilevel];
@ -299,9 +345,6 @@ void FixNVT::final_integrate_respa(int ilevel)
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;