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git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@9255 f3b2605a-c512-4ea7-a41b-209d697bcdaa

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This commit is contained in:
pscrozi
2013-01-09 17:47:50 +00:00
parent 4fac34ed3e
commit feefdd97ea
2 changed files with 53 additions and 32 deletions
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84
src/fix_heat.cpp
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@ -83,6 +83,7 @@ FixHeat::FixHeat(LAMMPS *lmp, int narg, char **arg) : Fix(lmp, narg, arg)
maxatom = 0;
vheat = NULL;
vscale = NULL;
}
/* ---------------------------------------------------------------------- */
@ -92,6 +93,7 @@ FixHeat::~FixHeat()
delete [] hstr;
delete [] idregion;
memory->destroy(vheat);
memory->destroy(vscale);
}
/* ---------------------------------------------------------------------- */
@ -138,7 +140,7 @@ void FixHeat::init()
void FixHeat::end_of_step()
{
int i;
double heat,ke;
double heat,ke,massone;
double vsub[3],vcm[3];
Region *region;
@ -146,6 +148,9 @@ void FixHeat::end_of_step()
double **v = atom->v;
int *mask = atom->mask;
int nlocal = atom->nlocal;
int *type = atom->type;
double *mass = atom->mass;
double *rmass = atom->rmass;
// reallocate vheat array if necessary
@ -153,61 +158,45 @@ void FixHeat::end_of_step()
maxatom = atom->nmax;
memory->destroy(vheat);
memory->create(vheat,maxatom,"heat:vheat");
memory->destroy(vscale);
memory->create(vscale,maxatom,"heat:vscale");
}
if (hstyle != CONSTANT) {
modify->clearstep_compute();
if (hstyle == EQUAL) heat_input = input->variable->compute_equal(hvar);
else {
input->variable->compute_atom(hvar,igroup,vheat,1,0);
double mine = 0.0;
if (iregion < 0) {
for (i = 0; i < nlocal; i++)
if (mask[i] & groupbit) mine += vheat[i];
} else {
region = domain->regions[iregion];
for (i = 0; i < nlocal; i++)
if (mask[i] & groupbit && region->match(x[i][0],x[i][1],x[i][2]))
mine += vheat[i];
}
MPI_Allreduce(&mine,&heat_input,1,MPI_DOUBLE,MPI_SUM,world);
}
else input->variable->compute_atom(hvar,igroup,vheat,1,0);
modify->addstep_compute(update->ntimestep + nevery);
}
// vcm = center-of-mass velocity of scaled atoms
// scale = velocity scale factor to accomplish eflux change in energy
// vsub = ??? // NOTE: document this?
if (iregion < 0) {
heat = heat_input*nevery*update->dt*force->ftm2v;
ke = group->ke(igroup)*force->ftm2v;
group->vcm(igroup,masstotal,vcm);
} else {
masstotal = group->mass(igroup,iregion);
if (masstotal == 0.0) error->all(FLERR,"Fix heat group has no atoms");
heat = heat_input*nevery*update->dt*force->ftm2v;
ke = group->ke(igroup,iregion)*force->ftm2v;
group->vcm(igroup,masstotal,vcm,iregion);
}
double vcmsq = vcm[0]*vcm[0] + vcm[1]*vcm[1] + vcm[2]*vcm[2];
double escale = (ke + heat - 0.5*vcmsq*masstotal)/(ke - 0.5*vcmsq*masstotal);
if (escale < 0.0) error->all(FLERR,"Fix heat kinetic energy went negative");
scale = sqrt(escale);
// NOTE: if hstyle = ATOM, do something different to compute vsub ??
vsub[0] = (scale-1.0) * vcm[0];
vsub[1] = (scale-1.0) * vcm[1];
vsub[2] = (scale-1.0) * vcm[2];
// scale = velocity scale factor to accomplish eflux change in energy
// vsub = velocity subtracted from each atom to preserve momentum
// add heat via scale factor on velocities for CONSTANT and EQUAL cases
if (hstyle != ATOM) {
heat = heat_input*nevery*update->dt*force->ftm2v;
double escale = (ke + heat - 0.5*vcmsq*masstotal)/(ke - 0.5*vcmsq*masstotal);
if (escale < 0.0) error->all(FLERR,"Fix heat kinetic energy went negative");
scale = sqrt(escale);
vsub[0] = (scale-1.0) * vcm[0];
vsub[1] = (scale-1.0) * vcm[1];
vsub[2] = (scale-1.0) * vcm[2];
if (iregion < 0) {
for (i = 0; i < nlocal; i++)
if (mask[i] & groupbit) {
@ -228,19 +217,50 @@ void FixHeat::end_of_step()
// add heat via per-atom scale factor on velocities for ATOM case
} else {
vsub[0] = vsub[1] = vsub[2] = 0.0;
if (iregion < 0) {
for (i = 0; i < nlocal; i++)
if (mask[i] & groupbit) {
scale = 0.0; // NOTE: set to per-atom value
heat = vheat[i]*nevery*update->dt*force->ftm2v;
vscale[i] = (ke + heat - 0.5*vcmsq*masstotal)/(ke - 0.5*vcmsq*masstotal);
if (vscale[i] < 0.0) error->all(FLERR,"Fix heat kinetic energy went negative");
scale = sqrt(vscale[i]);
if (rmass) massone = rmass[i];
else massone = mass[type[i]];
vsub[0] += (scale-1.0) * v[i][0]*massone;
vsub[1] += (scale-1.0) * v[i][1]*massone;
vsub[2] += (scale-1.0) * v[i][2]*massone;
}
vsub[0] /= masstotal;
vsub[1] /= masstotal;
vsub[2] /= masstotal;
for (i = 0; i < nlocal; i++)
if (mask[i] & groupbit) {
scale = sqrt(vscale[i]);
v[i][0] = scale*v[i][0] - vsub[0];
v[i][1] = scale*v[i][1] - vsub[1];
v[i][2] = scale*v[i][2] - vsub[2];
}
} else {
region = domain->regions[iregion];
for (int i = 0; i < nlocal; i++)
for (i = 0; i < nlocal; i++)
if (mask[i] & groupbit && region->match(x[i][0],x[i][1],x[i][2])) {
scale = 0.0; // NOTE: set to per-atom value
heat = vheat[i]*nevery*update->dt*force->ftm2v;
vscale[i] = (ke + heat - 0.5*vcmsq*masstotal)/(ke - 0.5*vcmsq*masstotal);
if (vscale[i] < 0.0) error->all(FLERR,"Fix heat kinetic energy went negative");
scale = sqrt(vscale[i]);
if (rmass) massone = rmass[i];
else massone = mass[type[i]];
vsub[0] += (scale-1.0) * v[i][0]*massone;
vsub[1] += (scale-1.0) * v[i][1]*massone;
vsub[2] += (scale-1.0) * v[i][2]*massone;
}
vsub[0] /= masstotal;
vsub[1] /= masstotal;
vsub[2] /= masstotal;
for (i = 0; i < nlocal; i++)
if (mask[i] & groupbit && region->match(x[i][0],x[i][1],x[i][2])) {
scale = sqrt(vscale[i]);
v[i][0] = scale*v[i][0] - vsub[0];
v[i][1] = scale*v[i][1] - vsub[1];
v[i][2] = scale*v[i][2] - vsub[2];