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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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85
src/compute_temp_region.cpp
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@ -61,25 +61,16 @@ ComputeTempRegion::~ComputeTempRegion()
void ComputeTempRegion::init()
{
dof = 0;
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];
}
dof = 0.0;
}
/* ---------------------------------------------------------------------- */
double ComputeTempRegion::dof_remove(double &natoms)
int ComputeTempRegion::dof_remove(int i)
{
double rmdof = 0.0;
if (tbias) rmdof = tbias->dof_remove(natoms);
natoms -= natoms_region;
rmdof += domain->dimension * natoms;
return rmdof;
double *x = atom->x[i];
if (domain->regions[iregion]->match(x[0],x[1],x[2])) return 0;
return 1;
}
/* ---------------------------------------------------------------------- */
@ -88,12 +79,6 @@ double ComputeTempRegion::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;
@ -102,34 +87,30 @@ double ComputeTempRegion::compute_scalar()
int *mask = atom->mask;
int nlocal = atom->nlocal;
Region *region = domain->regions[iregion];
int count = 0;
double t = 0.0;
if (mass) {
for (int i = 0; i < nlocal; i++)
if (mask[i] & groupbit &&
domain->regions[iregion]->match(x[i][0],x[i][1],x[i][2])) {
if (mask[i] & groupbit && region->match(x[i][0],x[i][1],x[i][2])) {
count++;
t += (v[i][0]*v[i][0] + v[i][1]*v[i][1] + v[i][2]*v[i][2]) *
mass[type[i]];
}
} else {
for (int i = 0; i < nlocal; i++)
if (mask[i] & groupbit &&
domain->regions[iregion]->match(x[i][0],x[i][1],x[i][2])) {
if (mask[i] & groupbit && region->match(x[i][0],x[i][1],x[i][2])) {
count++;
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();
double tarray[2],tarray_all[2];
tarray[0] = count;
tarray[1] = t;
MPI_Allreduce(tarray,tarray_all,2,MPI_DOUBLE,MPI_SUM,world);
natoms_region = tarray_all[0];
dof = domain->dimension * natoms_region - extra_dof;
dof = domain->dimension * tarray_all[0] - extra_dof;
if (dof > 0) scalar = force->mvv2e * tarray_all[1] / (dof * force->boltz);
else scalar = 0.0;
return scalar;
@ -143,11 +124,6 @@ void ComputeTempRegion::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;
@ -156,12 +132,12 @@ void ComputeTempRegion::compute_vector()
int *mask = atom->mask;
int nlocal = atom->nlocal;
Region *region = domain->regions[iregion];
double massone,t[6];
for (i = 0; i < 6; i++) t[i] = 0.0;
for (i = 0; i < nlocal; i++)
if (mask[i] & groupbit &&
domain->regions[iregion]->match(x[i][0],x[i][1],x[i][2])) {
if (mask[i] & groupbit && region->match(x[i][0],x[i][1],x[i][2])) {
if (mass) massone = mass[type[i]];
else massone = rmass[i];
t[0] += massone * v[i][0]*v[i][0];
@ -172,8 +148,6 @@ void ComputeTempRegion::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;
}
@ -184,18 +158,14 @@ void ComputeTempRegion::compute_vector()
void ComputeTempRegion::remove_bias(int i, double *v)
{
if (tbias) tbias->remove_bias(i,v);
if (atom->mask[i] & groupbit) {
double *x = atom->x[i];
if (domain->regions[iregion]->match(x[0],x[1],x[2]))
vbias[0] = vbias[1] = vbias[2] = 0.0;
else {
vbias[0] = v[0];
vbias[1] = v[1];
vbias[2] = v[2];
v[0] = v[1] = v[2] = 0.0;
}
double *x = atom->x[i];
if (domain->regions[iregion]->match(x[0],x[1],x[2]))
vbias[0] = vbias[1] = vbias[2] = 0.0;
else {
vbias[0] = v[0];
vbias[1] = v[1];
vbias[2] = v[2];
v[0] = v[1] = v[2] = 0.0;
}
}
@ -205,8 +175,6 @@ void ComputeTempRegion::remove_bias(int i, double *v)
void ComputeTempRegion::remove_bias_all()
{
if (tbias) tbias->remove_bias_all();
double **x = atom->x;
double **v = atom->v;
int *mask = atom->mask;
@ -219,9 +187,11 @@ void ComputeTempRegion::remove_bias_all()
"compute/temp:vbiasall");
}
Region *region = domain->regions[iregion];
for (int i = 0; i < nlocal; i++)
if (mask[i] & groupbit) {
if (domain->regions[iregion]->match(x[i][0],x[i][1],x[i][2]))
if (region->match(x[i][0],x[i][1],x[i][2]))
vbiasall[i][0] = vbiasall[i][1] = vbiasall[i][2] = 0.0;
else {
vbiasall[i][0] = v[i][0];
@ -239,12 +209,9 @@ void ComputeTempRegion::remove_bias_all()
void ComputeTempRegion::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];
}
/* ----------------------------------------------------------------------
@ -264,8 +231,6 @@ void ComputeTempRegion::restore_bias_all()
v[i][1] += vbiasall[i][1];
v[i][2] += vbiasall[i][2];
}
if (tbias) tbias->restore_bias_all();
}
/* ---------------------------------------------------------------------- */