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@1656 f3b2605a-c512-4ea7-a41b-209d697bcdaa

Browse Source
This commit is contained in:
sjplimp
2008-03-21 00:14:38 +00:00
parent a49e234a37
commit 2e8b9cf4b4
18 changed files with 188 additions and 447 deletions
Download Patch File Download Diff File Expand all files Collapse all files

66
src/compute_temp.cpp
View File

@ -38,6 +38,7 @@ ComputeTemp::ComputeTemp(LAMMPS *lmp, int narg, char **arg) :
extscalar = 0;
extvector = 1;
tempflag = 1;
tempbias = 0;
vector = new double[6];
}
@ -57,15 +58,6 @@ void ComputeTemp::init()
for (int i = 0; i < modify->nfix; i++)
fix_dof += modify->fix[i]->dof(igroup);
dof_compute();
tempbias = 0;
tbias = NULL;
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];
}
}
/* ---------------------------------------------------------------------- */
@ -74,7 +66,6 @@ void ComputeTemp::dof_compute()
{
double natoms = group->count(igroup);
dof = domain->dimension * natoms;
if (tbias) dof -= tbias->dof_remove(natoms);
dof -= extra_dof + fix_dof;
if (dof > 0.0) tfactor = force->mvv2e / (dof * force->boltz);
else tfactor = 0.0;
@ -86,12 +77,6 @@ double ComputeTemp::compute_scalar()
{
invoked |= INVOKED_SCALAR;
if (tbias) {
if (!(tbias->invoked & INVOKED_SCALAR))
double tmp = tbias->compute_scalar();
tbias->remove_bias_all();
}
double **v = atom->v;
double *mass = atom->mass;
double *rmass = atom->rmass;
@ -112,10 +97,8 @@ 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 || tbias) dof_compute();
if (dynamic) dof_compute();
scalar *= tfactor;
return scalar;
}
@ -128,11 +111,6 @@ 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;
@ -155,46 +133,6 @@ 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(int i, double *v)
{
if (tbias) tbias->restore_bias(i,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();
}