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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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64
src/compute_temp_deform.cpp
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@ -73,13 +73,6 @@ void ComputeTempDeform::init()
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];
}
// check fix deform remap settings
for (i = 0; i < modify->nfix; i++)
@ -99,7 +92,6 @@ void ComputeTempDeform::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) tfactor = force->mvv2e / (dof * force->boltz);
else tfactor = 0.0;
@ -113,12 +105,6 @@ double ComputeTempDeform::compute_scalar()
invoked |= INVOKED_SCALAR;
if (tbias) {
if (!(tbias->invoked & INVOKED_SCALAR))
double tmp = tbias->compute_scalar();
tbias->remove_bias_all();
}
double **x = atom->x;
double **v = atom->v;
double *mass = atom->mass;
@ -154,10 +140,8 @@ double ComputeTempDeform::compute_scalar()
vthermal[2]*vthermal[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;
}
@ -170,11 +154,6 @@ void ComputeTempDeform::compute_vector()
invoked |= INVOKED_VECTOR;
if (tbias) {
if (!(tbias->invoked & INVOKED_VECTOR)) tbias->compute_vector();
tbias->remove_bias_all();
}
double **x = atom->x;
double **v = atom->v;
double *mass = atom->mass;
@ -210,8 +189,6 @@ void ComputeTempDeform::compute_vector()
t[5] += massone * vthermal[1]*vthermal[2];
}
if (tbias) tbias->restore_bias_all();
MPI_Allreduce(t,vector,6,MPI_DOUBLE,MPI_SUM,world);
for (int i = 0; i < 6; i++) vector[i] *= force->mvv2e;
}
@ -222,22 +199,18 @@ void ComputeTempDeform::compute_vector()
void ComputeTempDeform::remove_bias(int i, double *v)
{
if (tbias) tbias->remove_bias(i,v);
if (atom->mask[i] & groupbit) {
double lamda[3];
double *h_rate = domain->h_rate;
double *h_ratelo = domain->h_ratelo;
double lamda[3];
double *h_rate = domain->h_rate;
double *h_ratelo = domain->h_ratelo;
domain->x2lamda(atom->x[i],lamda);
vbias[0] = h_rate[0]*lamda[0] + h_rate[5]*lamda[1] +
h_rate[4]*lamda[2] + h_ratelo[0];
vbias[1] = h_rate[1]*lamda[1] + h_rate[3]*lamda[2] + h_ratelo[1];
vbias[2] = h_rate[2]*lamda[2] + h_ratelo[2];
v[0] -= vbias[0];
v[1] -= vbias[1];
v[2] -= vbias[2];
}
domain->x2lamda(atom->x[i],lamda);
vbias[0] = h_rate[0]*lamda[0] + h_rate[5]*lamda[1] +
h_rate[4]*lamda[2] + h_ratelo[0];
vbias[1] = h_rate[1]*lamda[1] + h_rate[3]*lamda[2] + h_ratelo[1];
vbias[2] = h_rate[2]*lamda[2] + h_ratelo[2];
v[0] -= vbias[0];
v[1] -= vbias[1];
v[2] -= vbias[2];
}
/* ----------------------------------------------------------------------
@ -246,8 +219,6 @@ void ComputeTempDeform::remove_bias(int i, double *v)
void ComputeTempDeform::remove_bias_all()
{
if (tbias) tbias->remove_bias_all();
double **v = atom->v;
int *mask = atom->mask;
int nlocal = atom->nlocal;
@ -283,12 +254,9 @@ void ComputeTempDeform::remove_bias_all()
void ComputeTempDeform::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);
v[0] += vbias[0];
v[1] += vbias[1];
v[2] += vbias[2];
}
/* ----------------------------------------------------------------------
@ -308,8 +276,6 @@ void ComputeTempDeform::restore_bias_all()
v[i][1] += vbiasall[i][1];
v[i][2] += vbiasall[i][2];
}
if (tbias) tbias->restore_bias_all();
}
/* ---------------------------------------------------------------------- */