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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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98
src/fix_temp_rescale.cpp
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@ -28,7 +28,7 @@
using namespace LAMMPS_NS;
enum{STANDARD,REGION,PARTIAL};
enum{NOBIAS,BIAS};
/* ---------------------------------------------------------------------- */
@ -45,41 +45,11 @@ FixTempRescale::FixTempRescale(LAMMPS *lmp, int narg, char **arg) :
extscalar = 1;
t_start = atof(arg[4]);
t_end = atof(arg[5]);
t_stop = atof(arg[5]);
t_window = atof(arg[6]);
fraction = atof(arg[7]);
// optional args
iregion = -1;
partial = 0;
xflag = yflag = zflag = 1;
int iarg = 8;
while (iarg < narg) {
if (strcmp(arg[iarg],"region") == 0) {
if (iarg+2 > narg) error->all("Illegal fix temp/rescale command");
iregion = domain->find_region(arg[iarg+1]);
if (iregion == -1)
error->all("Fix temp/rescale region ID does not exist");
iarg += 2;
} else if (strcmp(arg[iarg],"partial") == 0) {
if (iarg+4 > narg) error->all("Illegal fix temp/rescale command");
xflag = atoi(arg[iarg+1]);
yflag = atoi(arg[iarg+2]);
zflag = atoi(arg[iarg+3]);
partial = 1;
iarg += 4;
} else error->all("Illegal fix temp/rescale command");
}
if (iregion == -1 && partial == 0) type = STANDARD;
else if (iregion >= 0 && partial == 0) type = REGION;
else if (iregion == -1 && partial) type = PARTIAL;
else
error->all("Cannot use both region, partial options in fix temp/rescale");
// create a new compute temp or temp/region or temp/partial
// create a new compute temp
// id = fix-ID + temp, compute group = fix group
int n = strlen(id) + 6;
@ -90,23 +60,8 @@ FixTempRescale::FixTempRescale(LAMMPS *lmp, int narg, char **arg) :
char **newarg = new char*[6];
newarg[0] = id_temp;
newarg[1] = group->names[igroup];
if (type == STANDARD) {
newarg[2] = (char *) "temp";
modify->add_compute(3,newarg);
} else if (type == REGION) {
newarg[2] = (char *) "temp/region";
newarg[3] = domain->regions[iregion]->id;
modify->add_compute(4,newarg);
} else if (type == PARTIAL) {
newarg[2] = (char *) "temp/partial";
if (xflag) newarg[3] = (char *) "1";
else newarg[3] = (char *) "0";
if (yflag) newarg[4] = (char *) "1";
else newarg[4] = (char *) "0";
if (zflag) newarg[5] = (char *) "1";
else newarg[5] = (char *) "0";
modify->add_compute(6,newarg);
}
newarg[2] = (char *) "temp";
modify->add_compute(3,newarg);
delete [] newarg;
tflag = 1;
@ -141,6 +96,9 @@ void FixTempRescale::init()
if (icompute < 0) error->all("Temp ID for fix temp/rescale does not exist");
temperature = modify->compute[icompute];
if (temperature->tempbias) which = BIAS;
else which = NOBIAS;
temperature->init(); // not yet called by Modify::init()
efactor = (0.5 * force->boltz * temperature->dof);
energy = 0.0;
@ -151,20 +109,24 @@ void FixTempRescale::init()
void FixTempRescale::end_of_step()
{
double t_current = temperature->compute_scalar();
if (t_current == 0.0)
error->all("Computed temperature for fix temp/berendsen cannot be 0.0");
double delta = update->ntimestep - update->beginstep;
delta /= update->endstep - update->beginstep;
double t_target = t_start + delta * (t_end-t_start);
double t_target = t_start + delta * (t_stop-t_start);
// rescale velocity of appropriate atoms if outside window
if (fabs(t_current-t_target) > t_window) {
t_target = t_current - fraction*(t_current-t_target);
double factor = sqrt(t_target/t_current);
double **x = atom->x;
double **v = atom->v;
int *mask = atom->mask;
int nlocal = atom->nlocal;
if (type == STANDARD) {
if (which == NOBIAS) {
energy += (t_current-t_target) * efactor;
for (int i = 0; i < nlocal; i++) {
if (mask[i] & groupbit) {
@ -174,25 +136,15 @@ void FixTempRescale::end_of_step()
}
}
} else if (type == REGION) {
efactor = (0.5 * force->boltz * temperature->dof);
energy += (t_current-t_target) * efactor;
for (int i = 0; i < nlocal; i++) {
if (mask[i] & groupbit &&
domain->regions[iregion]->match(x[i][0],x[i][1],x[i][2])) {
v[i][0] *= factor;
v[i][1] *= factor;
v[i][2] *= factor;
}
}
} else {
} else if (which == BIAS) {
energy += (t_current-t_target) * efactor;
for (int i = 0; i < nlocal; i++) {
if (mask[i] & groupbit) {
if (xflag) v[i][0] *= factor;
if (yflag) v[i][1] *= factor;
if (zflag) v[i][2] *= factor;
temperature->remove_bias(i,v[i]);
v[i][0] *= factor;
v[i][1] *= factor;
v[i][2] *= factor;
temperature->restore_bias(v[i]);
}
}
}
@ -228,6 +180,14 @@ int FixTempRescale::modify_param(int narg, char **arg)
return 0;
}
/* ---------------------------------------------------------------------- */
void FixTempRescale::reset_target(double t_new)
{
t_start = t_stop = t_new;
}
/* ---------------------------------------------------------------------- */
double FixTempRescale::compute_scalar()