ICODE-ADC/lammps
4
0
Fork 0
Code Issues Pull Requests Actions Packages Projects Releases Wiki Activity

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

Browse Source
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
Download Patch File Download Diff File Expand all files Collapse all files

88
src/fix_langevin.cpp
View File

@ -19,6 +19,8 @@
#include "atom.h"
#include "force.h"
#include "update.h"
#include "modify.h"
#include "compute.h"
#include "domain.h"
#include "region.h"
#include "respa.h"
@ -28,6 +30,8 @@
using namespace LAMMPS_NS;
enum{NOBIAS,BIAS};
/* ---------------------------------------------------------------------- */
FixLangevin::FixLangevin(LAMMPS *lmp, int narg, char **arg) :
@ -55,19 +59,11 @@ FixLangevin::FixLangevin(LAMMPS *lmp, int narg, char **arg) :
// optional args
flagx = flagy = flagz = 1;
for (int i = 1; i <= atom->ntypes; i++) ratio[i] = 1.0;
iregion = -1;
int iarg = 7;
while (iarg < narg) {
if (strcmp(arg[iarg],"axes") == 0) {
if (iarg+4 > narg) error->all("Illegal fix langevin command");
flagx = atoi(arg[iarg+1]);
flagy = atoi(arg[iarg+2]);
flagz = atoi(arg[iarg+3]);
iarg += 4;
} else if (strcmp(arg[iarg],"scale") == 0) {
if (strcmp(arg[iarg],"scale") == 0) {
if (iarg+3 > narg) error->all("Illegal fix langevin command");
int itype = atoi(arg[iarg+1]);
double scale = atof(arg[iarg+2]);
@ -75,13 +71,13 @@ FixLangevin::FixLangevin(LAMMPS *lmp, int narg, char **arg) :
error->all("Illegal fix langevin command");
ratio[itype] = scale;
iarg += 3;
} else if (strcmp(arg[iarg],"region") == 0) {
if (iarg+2 > narg) error->all("Illegal fix langevin command");
iregion = domain->find_region(arg[iarg+1]);
if (iregion == -1) error->all("Fix langevin region ID does not exist");
iarg += 2;
} else error->all("Illegal fix langevin command");
}
// set temperature = NULL, user can override via fix_modify if wants bias
id_temp = NULL;
temperature = NULL;
}
/* ---------------------------------------------------------------------- */
@ -92,6 +88,7 @@ FixLangevin::~FixLangevin()
delete [] gfactor1;
delete [] gfactor2;
delete [] ratio;
delete [] id_temp;
}
/* ---------------------------------------------------------------------- */
@ -121,6 +118,9 @@ void FixLangevin::init()
gfactor2[i] *= 1.0/sqrt(ratio[i]);
}
if (temperature && temperature->tempbias) which = BIAS;
else which = NOBIAS;
if (strcmp(update->integrate_style,"respa") == 0)
nlevels_respa = ((Respa *) update->integrate)->nlevels;
}
@ -142,6 +142,8 @@ void FixLangevin::setup(int vflag)
void FixLangevin::post_force(int vflag)
{
double gamma1,gamma2;
double **x = atom->x;
double **v = atom->v;
double **f = atom->f;
@ -154,34 +156,40 @@ void FixLangevin::post_force(int vflag)
double t_target = t_start + delta * (t_stop-t_start);
double tsqrt = sqrt(t_target);
double gamma1,gamma2;
// apply damping and thermostat to appropriate atoms
// apply damping and thermostat to all atoms in fix group
if (iregion == -1) {
if (which == NOBIAS) {
for (int i = 0; i < nlocal; i++) {
if (mask[i] & groupbit) {
gamma1 = gfactor1[type[i]];
gamma2 = gfactor2[type[i]] * tsqrt;
if (flagx) f[i][0] += gamma1*v[i][0] + gamma2*(random->uniform()-0.5);
if (flagy) f[i][1] += gamma1*v[i][1] + gamma2*(random->uniform()-0.5);
if (flagz) f[i][2] += gamma1*v[i][2] + gamma2*(random->uniform()-0.5);
f[i][0] += gamma1*v[i][0] + gamma2*(random->uniform()-0.5);
f[i][1] += gamma1*v[i][1] + gamma2*(random->uniform()-0.5);
f[i][2] += gamma1*v[i][2] + gamma2*(random->uniform()-0.5);
}
}
// apply damping and thermostat to all atoms in fix group and in region
// invoke temperature since some computes require it to remove bias
// test on v = 0 since some computes mask non-participating atoms via v = 0
} else if (which == BIAS) {
double tmp = temperature->compute_scalar();
} else {
for (int i = 0; i < nlocal; i++) {
if (mask[i] & groupbit &&
domain->regions[iregion]->match(x[i][0],x[i][1],x[i][2])) {
if (mask[i] & groupbit) {
gamma1 = gfactor1[type[i]];
gamma2 = gfactor2[type[i]] * tsqrt;
if (flagx) f[i][0] += gamma1*v[i][0] + gamma2*(random->uniform()-0.5);
if (flagy) f[i][1] += gamma1*v[i][1] + gamma2*(random->uniform()-0.5);
if (flagz) f[i][2] += gamma1*v[i][2] + gamma2*(random->uniform()-0.5);
temperature->remove_bias(i,v[i]);
if (v[i][0] != 0.0)
f[i][0] += gamma1*v[i][0] + gamma2*(random->uniform()-0.5);
if (v[i][1] != 0.0)
f[i][1] += gamma1*v[i][1] + gamma2*(random->uniform()-0.5);
if (v[i][2] != 0.0)
f[i][2] += gamma1*v[i][2] + gamma2*(random->uniform()-0.5);
temperature->restore_bias(v[i]);
}
}
}
}
@ -209,3 +217,27 @@ void FixLangevin::reset_dt()
gfactor2[i] *= 1.0/sqrt(ratio[i]);
}
}
/* ---------------------------------------------------------------------- */
int FixLangevin::modify_param(int narg, char **arg)
{
if (strcmp(arg[0],"temp") == 0) {
if (narg < 2) error->all("Illegal fix_modify command");
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;
}