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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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93
src/compute_temp_sphere.cpp
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@ -12,6 +12,7 @@
------------------------------------------------------------------------- */
#include "mpi.h"
#include "string.h"
#include "compute_temp_sphere.h"
#include "atom.h"
#include "force.h"
@ -33,7 +34,8 @@ using namespace LAMMPS_NS;
ComputeTempSphere::ComputeTempSphere(LAMMPS *lmp, int narg, char **arg) :
Compute(lmp, narg, arg)
{
if (narg != 3) error->all("Illegal compute temp command");
if (narg != 3 || narg != 4)
error->all("Illegal compute temp/sphere command");
scalar_flag = vector_flag = 1;
size_vector = 6;
@ -41,6 +43,15 @@ ComputeTempSphere::ComputeTempSphere(LAMMPS *lmp, int narg, char **arg) :
extvector = 1;
tempflag = 1;
tempbias = 0;
id_bias = NULL;
if (narg == 4) {
tempbias = 1;
int n = strlen(arg[3]) + 1;
id_bias = new char[n];
strcpy(id_bias,arg[3]);
}
vector = new double[6];
inertia = new double[atom->ntypes+1];
}
@ -57,20 +68,26 @@ ComputeTempSphere::~ComputeTempSphere()
void ComputeTempSphere::init()
{
if (tempbias) {
int i = modify->find_compute(id_bias);
if (i < 0) error->all("Could not find compute ID for temperature bias");
tbias = modify->compute[i];
if (tbias->tempflag == 0)
error->all("Bias compute does not calculate temperature");
if (tbias->tempbias == 0)
error->all("Bias compute does not calculate a velocity bias");
if (tbias->igroup != igroup)
error->all("Bias compute group does not match compute group");
tbias->init();
if (strcmp(tbias->style,"temp/region") == 0) tempbias = 2;
else tempbias = 1;
}
fix_dof = 0;
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];
}
if (atom->mass) {
double *mass = atom->mass;
double **shape = atom->shape;
@ -88,9 +105,25 @@ void ComputeTempSphere::init()
void ComputeTempSphere::dof_compute()
{
double natoms = group->count(igroup);
if (domain->dimension == 3) dof = 6.0 * natoms;
else dof = 3.0 * natoms;
if (tbias) dof -= tbias->dof_remove(natoms);
int nper = 6;
if (domain->dimension == 2) nper = 3;
dof = nper * natoms;
if (tempbias) {
if (tempbias == 1) dof -= tbias->dof_remove(-1) * natoms;
else {
int *mask = atom->mask;
int nlocal = atom->nlocal;
int count = 0;
for (int i = 0; i < nlocal; i++)
if (mask[i] & groupbit)
if (tbias->dof_remove(i)) count++;
int count_all;
MPI_Allreduce(&count,&count_all,1,MPI_INT,MPI_SUM,world);
dof -= nper * count_all;
}
}
dof -= extra_dof + fix_dof;
if (dof > 0) tfactor = force->mvv2e / (dof * force->boltz);
else tfactor = 0.0;
@ -102,7 +135,7 @@ double ComputeTempSphere::compute_scalar()
{
invoked |= INVOKED_SCALAR;
if (tbias) {
if (tempbias) {
if (!(tbias->invoked & INVOKED_SCALAR))
double tmp = tbias->compute_scalar();
tbias->remove_bias_all();
@ -136,10 +169,10 @@ double ComputeTempSphere::compute_scalar()
}
}
if (tbias) tbias->restore_bias_all();
if (tempbias) tbias->restore_bias_all();
MPI_Allreduce(&t,&scalar,1,MPI_DOUBLE,MPI_SUM,world);
if (dynamic || tbias) dof_compute();
if (dynamic || tempbias == 2) dof_compute();
scalar *= tfactor;
return scalar;
}
@ -152,7 +185,7 @@ void ComputeTempSphere::compute_vector()
invoked |= INVOKED_VECTOR;
if (tbias) {
if (tempbias) {
if (!(tbias->invoked & INVOKED_VECTOR)) tbias->compute_vector();
tbias->remove_bias_all();
}
@ -209,7 +242,7 @@ void ComputeTempSphere::compute_vector()
}
}
if (tbias) tbias->restore_bias_all();
if (tempbias) tbias->restore_bias_all();
MPI_Allreduce(t,vector,6,MPI_DOUBLE,MPI_SUM,world);
for (i = 0; i < 6; i++) vector[i] *= force->mvv2e;
@ -221,16 +254,7 @@ void ComputeTempSphere::compute_vector()
void ComputeTempSphere::remove_bias(int i, double *v)
{
if (tbias) tbias->remove_bias(i,v);
}
/* ----------------------------------------------------------------------
remove velocity bias from all atoms to leave thermal velocity
------------------------------------------------------------------------- */
void ComputeTempSphere::remove_bias_all()
{
if (tbias) tbias->remove_bias_all();
tbias->remove_bias(i,v);
}
/* ----------------------------------------------------------------------
@ -240,16 +264,5 @@ void ComputeTempSphere::remove_bias_all()
void ComputeTempSphere::restore_bias(int i, double *v)
{
if (tbias) tbias->restore_bias(i,v);
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 ComputeTempSphere::restore_bias_all()
{
if (tbias) tbias->restore_bias_all();
}