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@1651 f3b2605a-c512-4ea7-a41b-209d697bcdaa

Browse Source
This commit is contained in:
sjplimp
2008-03-20 14:53:21 +00:00
parent 848aece2b4
commit ebe2ee9bac
28 changed files with 833 additions and 99 deletions
Download Patch File Download Diff File Expand all files Collapse all files

60
src/compute_temp.cpp
View File

@ -57,6 +57,13 @@ void ComputeTemp::init()
for (int i = 0; i < modify->nfix; i++)
fix_dof += modify->fix[i]->dof(igroup);
recount();
if (id_bias) {
tempbias = 1;
int i = modify->find_compute(id_bias);
if (i < 0) error->all("Could not find compute ID for temperature bias");
tbias = modify->compute[i];
}
}
/* ---------------------------------------------------------------------- */
@ -76,6 +83,12 @@ double ComputeTemp::compute_scalar()
{
invoked |= INVOKED_SCALAR;
if (tbias) {
if (!(tbias->invoked & INVOKED_SCALAR))
double tmp = tbias->compute_scalar();
tbias->remove_bias_all();
} else tempbias = 0;
double **v = atom->v;
double *mass = atom->mass;
double *rmass = atom->rmass;
@ -96,6 +109,8 @@ double ComputeTemp::compute_scalar()
t += (v[i][0]*v[i][0] + v[i][1]*v[i][1] + v[i][2]*v[i][2]) * rmass[i];
}
if (tbias) tbias->restore_bias_all();
MPI_Allreduce(&t,&scalar,1,MPI_DOUBLE,MPI_SUM,world);
if (dynamic) recount();
scalar *= tfactor;
@ -110,6 +125,11 @@ void ComputeTemp::compute_vector()
invoked |= INVOKED_VECTOR;
if (tbias) {
if (!(tbias->invoked & INVOKED_VECTOR)) tbias->compute_vector();
tbias->remove_bias_all();
}
double **v = atom->v;
double *mass = atom->mass;
double *rmass = atom->rmass;
@ -132,6 +152,46 @@ void ComputeTemp::compute_vector()
t[5] += massone * v[i][1]*v[i][2];
}
if (tbias) tbias->restore_bias_all();
MPI_Allreduce(t,vector,6,MPI_DOUBLE,MPI_SUM,world);
for (i = 0; i < 6; i++) vector[i] *= force->mvv2e;
}
/* ----------------------------------------------------------------------
remove velocity bias from atom I to leave thermal velocity
------------------------------------------------------------------------- */
void ComputeTemp::remove_bias(int i, double *v)
{
if (tbias) tbias->remove_bias(i,v);
}
/* ----------------------------------------------------------------------
remove velocity bias from all atoms to leave thermal velocity
------------------------------------------------------------------------- */
void ComputeTemp::remove_bias_all()
{
if (tbias) tbias->remove_bias_all();
}
/* ----------------------------------------------------------------------
add back in velocity bias to atom I removed by remove_bias()
assume remove_bias() was previously called
------------------------------------------------------------------------- */
void ComputeTemp::restore_bias(double *v)
{
if (tbias) tbias->restore_bias(v);
}
/* ----------------------------------------------------------------------
add back in velocity bias to all atoms removed by remove_bias_all()
assume remove_bias_all() was previously called
------------------------------------------------------------------------- */
void ComputeTemp::restore_bias_all()
{
if (tbias) tbias->restore_bias_all();
}