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git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@1656 f3b2605a-c512-4ea7-a41b-209d697bcdaa

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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
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83
src/compute_temp_partial.cpp
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@ -67,13 +67,6 @@ void ComputeTempPartial::init()
for (int i = 0; i < modify->nfix; i++)
fix_dof += modify->fix[i]->dof(igroup);
dof_compute();
tbias = NULL;
if (id_bias) {
int i = modify->find_compute(id_bias);
if (i < 0) error->all("Could not find compute ID for temperature bias");
tbias = modify->compute[i];
}
}
/* ---------------------------------------------------------------------- */
@ -81,8 +74,9 @@ void ComputeTempPartial::init()
void ComputeTempPartial::dof_compute()
{
double natoms = group->count(igroup);
dof = (xflag+yflag+zflag) * natoms;
if (tbias) dof -= tbias->dof_remove(natoms);
int nper = xflag+yflag+zflag;
if (domain->dimension == 2) nper = xflag+yflag;
dof = nper * natoms;
dof -= extra_dof + fix_dof;
if (dof > 0) tfactor = force->mvv2e / (dof * force->boltz);
else tfactor = 0.0;
@ -90,14 +84,9 @@ void ComputeTempPartial::dof_compute()
/* ---------------------------------------------------------------------- */
double ComputeTempPartial::dof_remove(double &natoms)
int ComputeTempPartial::dof_remove(int i)
{
double rmdof = 0.0;
if (tbias) rmdof = tbias->dof_remove(natoms);
int activedim = xflag+yflag+zflag;
if (domain->dimension == 2) activedim = xflag+yflag;
rmdof += (domain->dimension - activedim) * natoms;
return rmdof;
return 0;
}
/* ---------------------------------------------------------------------- */
@ -106,12 +95,6 @@ double ComputeTempPartial::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;
@ -133,10 +116,8 @@ double ComputeTempPartial::compute_scalar()
zflag*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;
}
@ -149,11 +130,6 @@ void ComputeTempPartial::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;
@ -176,8 +152,6 @@ void ComputeTempPartial::compute_vector()
t[5] += massone * yflag*zflag*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;
}
@ -188,21 +162,17 @@ void ComputeTempPartial::compute_vector()
void ComputeTempPartial::remove_bias(int i, double *v)
{
if (tbias) tbias->remove_bias(i,v);
if (atom->mask[i] & groupbit) {
if (!xflag) {
vbias[0] = v[0];
v[0] = 0.0;
}
if (!yflag) {
vbias[1] = v[1];
v[1] = 0.0;
}
if (!zflag) {
vbias[2] = v[2];
v[2] = 0.0;
}
if (!xflag) {
vbias[0] = v[0];
v[0] = 0.0;
}
if (!yflag) {
vbias[1] = v[1];
v[1] = 0.0;
}
if (!zflag) {
vbias[2] = v[2];
v[2] = 0.0;
}
}
@ -212,8 +182,6 @@ void ComputeTempPartial::remove_bias(int i, double *v)
void ComputeTempPartial::remove_bias_all()
{
if (tbias) tbias->remove_bias_all();
double **v = atom->v;
int *mask = atom->mask;
int nlocal = atom->nlocal;
@ -249,12 +217,9 @@ void ComputeTempPartial::remove_bias_all()
void ComputeTempPartial::restore_bias(int i, double *v)
{
if (atom->mask[i] & groupbit) {
v[0] += vbias[0];
v[1] += vbias[1];
v[2] += vbias[2];
}
if (tbias) tbias->restore_bias(i,v);
if (!xflag) v[0] += vbias[0];
if (!yflag) v[1] += vbias[1];
if (!zflag) v[2] += vbias[2];
}
/* ----------------------------------------------------------------------
@ -270,12 +235,10 @@ void ComputeTempPartial::restore_bias_all()
for (int i = 0; i < nlocal; i++)
if (mask[i] & groupbit) {
v[i][0] += vbiasall[i][0];
v[i][1] += vbiasall[i][1];
v[i][2] += vbiasall[i][2];
if (!xflag) v[i][0] += vbiasall[i][0];
if (!yflag) v[i][1] += vbiasall[i][1];
if (!zflag) v[i][2] += vbiasall[i][2];
}
if (tbias) tbias->restore_bias_all();
}
/* ---------------------------------------------------------------------- */