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git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@5716 f3b2605a-c512-4ea7-a41b-209d697bcdaa

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sjplimp
2011-02-22 22:36:09 +00:00
parent 1d4a6440d1
commit 691894ab34
25 changed files with 1319 additions and 624 deletions
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179
src/USER-EFF/compute_temp_region_eff.cpp
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@ -21,22 +21,72 @@
#include "atom.h"
#include "update.h"
#include "force.h"
#include "modify.h"
#include "domain.h"
#include "region.h"
#include "memory.h"
#include "error.h"
using namespace LAMMPS_NS;
/* ---------------------------------------------------------------------- */
ComputeTempRegionEff::
ComputeTempRegionEff(LAMMPS *lmp, int narg, char **arg) :
ComputeTempRegion(lmp, narg, arg)
ComputeTempRegionEff::ComputeTempRegionEff(LAMMPS *lmp, int narg, char **arg) :
Compute(lmp, narg, arg)
{
// error check
if (!atom->spin_flag || !atom->ervel_flag)
error->all("Compute temp/region/eff requires atom attributes spin, ervel");
if (narg != 4) error->all("Illegal compute temp/region/eff command");
iregion = domain->find_region(arg[3]);
if (iregion == -1)
error->all("Region ID for compute temp/region/eff does not exist");
int n = strlen(arg[3]) + 1;
idregion = new char[n];
strcpy(idregion,arg[3]);
scalar_flag = vector_flag = 1;
size_vector = 6;
extscalar = 0;
extvector = 1;
tempflag = 1;
tempbias = 1;
maxbias = 0;
vbiasall = NULL;
vector = new double[6];
}
/* ---------------------------------------------------------------------- */
ComputeTempRegionEff::~ComputeTempRegionEff()
{
delete [] idregion;
memory->destroy_2d_double_array(vbiasall);
delete [] vector;
}
/* ---------------------------------------------------------------------- */
void ComputeTempRegionEff::init()
{
// set index and check validity of region
iregion = domain->find_region(idregion);
if (iregion == -1)
error->all("Region ID for compute temp/region/eff does not exist");
dof = 0.0;
}
/* ---------------------------------------------------------------------- */
int ComputeTempRegionEff::dof_remove(int i)
{
double *x = atom->x[i];
if (domain->regions[iregion]->match(x[0],x[1],x[2])) return 0;
return 1;
}
/* ---------------------------------------------------------------------- */
@ -49,7 +99,6 @@ double ComputeTempRegionEff::compute_scalar()
double **v = atom->v;
double *ervel = atom->ervel;
double *mass = atom->mass;
double *rmass = atom->rmass;
int *spin = atom->spin;
int *type = atom->type;
int *mask = atom->mask;
@ -59,20 +108,13 @@ double ComputeTempRegionEff::compute_scalar()
int count = 0;
double t = 0.0;
if (rmass) {
if (mass) {
for (int i = 0; i < nlocal; i++)
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 (spin[i]) t += 0.75*rmass[i]*ervel[i]*ervel[i];
}
} else {
for (int i = 0; i < nlocal; i++)
if (mask[i] & groupbit && region->match(x[i][0],x[i][1],x[i][2])) {
count++;
count++;
t += (v[i][0]*v[i][0] + v[i][1]*v[i][1] + v[i][2]*v[i][2]) *
mass[type[i]];
if (spin[i]) t += 0.75*mass[type[i]]*ervel[i]*ervel[i];
mass[type[i]];
if (abs(spin[i])==1) t += 0.75*mass[type[i]]*ervel[i]*ervel[i];
}
}
@ -85,7 +127,7 @@ double ComputeTempRegionEff::compute_scalar()
int one = 0;
for (int i = 0; i < nlocal; i++)
if (mask[i] & groupbit && region->match(x[i][0],x[i][1],x[i][2])) {
if (spin[i]) one++;
if (abs(spin[i])==1) one++;
}
int nelectrons_region;
MPI_Allreduce(&one,&nelectrons_region,1,MPI_INT,MPI_SUM,world);
@ -111,7 +153,6 @@ void ComputeTempRegionEff::compute_vector()
double **v = atom->v;
double *ervel = atom->ervel;
double *mass = atom->mass;
double *rmass = atom->rmass;
int *spin = atom->spin;
int *type = atom->type;
int *mask = atom->mask;
@ -123,8 +164,7 @@ void ComputeTempRegionEff::compute_vector()
for (i = 0; i < nlocal; i++)
if (mask[i] & groupbit && region->match(x[i][0],x[i][1],x[i][2])) {
if (rmass) massone = rmass[i];
else massone = mass[type[i]];
massone = mass[type[i]];
t[0] += massone * v[i][0]*v[i][0];
t[1] += massone * v[i][1]*v[i][1];
@ -132,14 +172,105 @@ void ComputeTempRegionEff::compute_vector()
t[3] += massone * v[i][0]*v[i][1];
t[4] += massone * v[i][0]*v[i][2];
t[5] += massone * v[i][1]*v[i][2];
if (spin[i]) {
if (abs(spin[i])==1) {
t[0] += 0.75 * massone * ervel[i]*ervel[i];
t[1] += 0.75 * massone * ervel[i]*ervel[i];
t[2] += 0.75 * massone * ervel[i]*ervel[i];
}
}
}
MPI_Allreduce(t,vector,6,MPI_DOUBLE,MPI_SUM,world);
for (i = 0; i < 6; i++) vector[i] *= force->mvv2e;
}
/* ----------------------------------------------------------------------
remove velocity bias from atom I to leave thermal velocity
NOTE: the following commands do not bias the radial electron velocities
------------------------------------------------------------------------- */
void ComputeTempRegionEff::remove_bias(int i, double *v)
{
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;
}
}
/* ----------------------------------------------------------------------
remove velocity bias from all atoms to leave thermal velocity
------------------------------------------------------------------------- */
void ComputeTempRegionEff::remove_bias_all()
{
double **x = atom->x;
double **v = atom->v;
int *mask = atom->mask;
int nlocal = atom->nlocal;
if (nlocal > maxbias) {
memory->destroy_2d_double_array(vbiasall);
maxbias = atom->nmax;
vbiasall = memory->create_2d_double_array(maxbias,3,
"temp/region:vbiasall");
}
Region *region = domain->regions[iregion];
for (int i = 0; i < nlocal; i++)
if (mask[i] & groupbit) {
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];
vbiasall[i][1] = v[i][1];
vbiasall[i][2] = v[i][2];
v[i][0] = v[i][1] = v[i][2] = 0.0;
}
}
}
/* ----------------------------------------------------------------------
add back in velocity bias to atom I removed by remove_bias()
assume remove_bias() was previously called
------------------------------------------------------------------------- */
void ComputeTempRegionEff::restore_bias(int i, double *v)
{
v[0] += vbias[0];
v[1] += vbias[1];
v[2] += vbias[2];
}
/* ----------------------------------------------------------------------
add back in velocity bias to all atoms removed by remove_bias_all()
assume remove_bias_all() was previously called
------------------------------------------------------------------------- */
void ComputeTempRegionEff::restore_bias_all()
{
double **v = atom->v;
int *mask = atom->mask;
int nlocal = atom->nlocal;
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];
}
}
/* ---------------------------------------------------------------------- */
double ComputeTempRegionEff::memory_usage()
{
double bytes = maxbias * sizeof(double);
return bytes;
}