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git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@3419 f3b2605a-c512-4ea7-a41b-209d697bcdaa

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This commit is contained in:
sjplimp
2009-11-17 21:18:23 +00:00
parent 7fc817dc15
commit 4790c5402e
13 changed files with 218 additions and 160 deletions
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26
src/fix_nvt_sllod.cpp
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@ -35,7 +35,6 @@
using namespace LAMMPS_NS;
enum{NO_REMAP,X_REMAP,V_REMAP}; // same as fix_deform.cpp
enum{NOBIAS,BIAS};
/* ---------------------------------------------------------------------- */
@ -51,13 +50,17 @@ void FixNVTSlodd::init()
if (!temperature->tempbias)
error->all("Temperature for fix nvt/sllod does not have a bias");
nondeformbias = 0;
if (strcmp(temperature->style,"temp/deform") != 0) nondeformbias = 1;
// check fix deform remap settings
int i;
for (i = 0; i < modify->nfix; i++)
if (strcmp(modify->fix[i]->style,"deform") == 0) {
if (((FixDeform *) modify->fix[i])->remapflag != V_REMAP)
error->all("Using fix nvt/sllod with inconsistent fix deform remap option");
error->all("Using fix nvt/sllod with inconsistent fix deform "
"remap option");
break;
}
if (i == modify->nfix)
@ -82,10 +85,15 @@ void FixNVTSlodd::initial_integrate(int vflag)
eta += dtv*eta_dot;
factor = exp(-dthalf*eta_dot);
// update v and x of only atoms in group
// update v and x of atoms in group
// remove and restore bias = streaming velocity = Hrate*lamda + Hratelo
// thermostat thermal velocity only
// vdelu = SLLOD correction = Hrate*Hinv*vthermal
// for non temp/deform BIAS:
// calculate temperature since some computes require temp
// computed on current nlocal atoms to remove bias
if (nondeformbias) double tmp = temperature->compute_scalar();
double **x = atom->x;
double **v = atom->v;
@ -124,10 +132,16 @@ void FixNVTSlodd::final_integrate()
{
double dtfm;
// update v of only atoms in group
// update v of atoms in group
// remove and restore bias = streaming velocity = Hrate*lamda + Hratelo
// thermostat thermal velocity only
// vdelu = SLLOD correction = Hrate*Hinv*vthermal
// for non temp/deform BIAS:
// calculate temperature since some computes require temp
// computed on current nlocal atoms to remove bias
// OK to not test returned v = 0, since factor is multiplied by v
if (nondeformbias) double tmp = temperature->compute_scalar();
double **v = atom->v;
double **f = atom->f;
@ -207,7 +221,9 @@ void FixNVTSlodd::initial_integrate_respa(int vflag, int ilevel, int flag)
factor = exp(-dthalf*eta_dot);
} else factor = 1.0;
// update v of only atoms in group
// update v of atoms in group
if (nondeformbias) double tmp = temperature->compute_scalar();
double h_two[6],vdelu[3];
MathExtra::multiply_shape_shape(domain->h_rate,domain->h_inv,h_two);