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

88
src/ASPHERE/compute_temp_asphere.cpp
View File

@ -37,7 +37,8 @@ using namespace LAMMPS_NS;
ComputeTempAsphere::ComputeTempAsphere(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/asphere command");
if (!atom->quat_flag || !atom->angmom_flag)
error->all("Compute temp/asphere requires atom attributes quat, angmom");
@ -48,6 +49,15 @@ ComputeTempAsphere::ComputeTempAsphere(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 =
memory->create_2d_double_array(atom->ntypes+1,3,"fix_temp_sphere:inertia");
@ -57,6 +67,7 @@ ComputeTempAsphere::ComputeTempAsphere(LAMMPS *lmp, int narg, char **arg) :
ComputeTempAsphere::~ComputeTempAsphere()
{
delete [] id_bias;
delete [] vector;
memory->destroy_2d_double_array(inertia);
}
@ -65,20 +76,25 @@ ComputeTempAsphere::~ComputeTempAsphere()
void ComputeTempAsphere::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;
}
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];
}
calculate_inertia();
}
@ -89,10 +105,10 @@ void ComputeTempAsphere::dof_compute()
double natoms = group->count(igroup);
int dimension = domain->dimension;
dof = dimension * natoms;
if (tbias) dof -= tbias->dof_remove(natoms);
dof -= extra_dof + fix_dof;
// add rotational degrees of freedom
if (tempbias == 1) dof -= tbias->dof_remove(-1) * natoms;
// rotational degrees of freedom
// 0 for sphere, 2 for uniaxial, 3 for biaxial
double **shape = atom->shape;
@ -101,27 +117,30 @@ void ComputeTempAsphere::dof_compute()
int nlocal = atom->nlocal;
int itype;
int rot_dof = 0;
int count = 0;
for (int i = 0; i < nlocal; i++)
if (mask[i] & groupbit) {
if (tempbias == 2 && tbias->dof_remove(i)) continue;
itype = type[i];
if (dimension == 2) {
if (shape[itype][0] == shape[itype][1]) continue;
else rot_dof += 1;
else count++;
} else {
if (shape[itype][0] == shape[itype][1] &&
shape[itype][1] == shape[itype][2]) continue;
else if (shape[itype][0] == shape[itype][1] ||
shape[itype][1] == shape[itype][2] ||
shape[itype][0] == shape[itype][2]) rot_dof += 2;
else rot_dof += 3;
shape[itype][0] == shape[itype][2]) count += 2;
else count += 3;
}
}
int rot_total;
MPI_Allreduce(&rot_dof,&rot_total,1,MPI_INT,MPI_SUM,world);
dof += rot_total;
int count_all;
MPI_Allreduce(&count,&count_all,1,MPI_INT,MPI_SUM,world);
dof += count_all;
dof -= extra_dof + fix_dof;
if (dof > 0) tfactor = force->mvv2e / (dof * force->boltz);
else tfactor = 0.0;
}
@ -132,7 +151,7 @@ double ComputeTempAsphere::compute_scalar()
{
invoked |= INVOKED_SCALAR;
if (tbias) {
if (tempbias) {
if (!(tbias->invoked & INVOKED_SCALAR))
double tmp = tbias->compute_scalar();
tbias->remove_bias_all();
@ -179,10 +198,10 @@ double ComputeTempAsphere::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;
}
@ -195,7 +214,7 @@ void ComputeTempAsphere::compute_vector()
invoked |= INVOKED_VECTOR;
if (tbias) {
if (tempbias) {
if (!(tbias->invoked & INVOKED_VECTOR)) tbias->compute_vector();
tbias->remove_bias_all();
}
@ -246,7 +265,7 @@ void ComputeTempAsphere::compute_vector()
t[5] += inertia[itype][2]*wbody[1]*wbody[2];
}
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;
@ -280,15 +299,6 @@ void ComputeTempAsphere::remove_bias(int i, double *v)
if (tbias) tbias->remove_bias(i,v);
}
/* ----------------------------------------------------------------------
remove velocity bias from all atoms to leave thermal velocity
------------------------------------------------------------------------- */
void ComputeTempAsphere::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
@ -298,13 +308,3 @@ void ComputeTempAsphere::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 ComputeTempAsphere::restore_bias_all()
{
if (tbias) tbias->restore_bias_all();
}