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fix gcmc updates from Aidan, trimming of output for replica commands

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This commit is contained in:
Steve Plimpton
2017-04-11 08:35:09 -06:00
parent 76fd936972
commit 49dd9449b8
21 changed files with 363 additions and 234 deletions
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32
src/MC/fix_gcmc.cpp
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@ -60,7 +60,7 @@ using namespace MathConst;
// this must be lower than MAXENERGYSIGNAL
// by a large amount, so that it is still
// less than total energy when negative
// energy changes are added to MAXENERGYSIGNAL
// energy contributions are added to MAXENERGYSIGNAL
#define MAXENERGYTEST 1.0e50
@ -701,6 +701,9 @@ void FixGCMC::pre_exchange()
if (full_flag) {
energy_stored = energy_full();
if (overlap_flag && energy_stored > MAXENERGYTEST)
error->warning(FLERR,"Energy of old configuration in "
"fix gcmc is > MAXENERGYTEST.");
if (mode == MOLECULE) {
for (int i = 0; i < ncycles; i++) {
@ -778,6 +781,9 @@ void FixGCMC::attempt_atomic_translation()
if (i >= 0) {
double **x = atom->x;
double energy_before = energy(i,ngcmc_type,-1,x[i]);
if (overlap_flag && energy_before > MAXENERGYTEST)
error->warning(FLERR,"Energy of old configuration in "
"fix gcmc is > MAXENERGYTEST.");
double rsq = 1.1;
double rx,ry,rz;
rx = ry = rz = 0.0;
@ -998,6 +1004,9 @@ void FixGCMC::attempt_molecule_translation()
if (translation_molecule == -1) return;
double energy_before_sum = molecule_energy(translation_molecule);
if (overlap_flag && energy_before_sum > MAXENERGYTEST)
error->warning(FLERR,"Energy of old configuration in "
"fix gcmc is > MAXENERGYTEST.");
double **x = atom->x;
double rx,ry,rz;
@ -1095,6 +1104,9 @@ void FixGCMC::attempt_molecule_rotation()
if (rotation_molecule == -1) return;
double energy_before_sum = molecule_energy(rotation_molecule);
if (overlap_flag && energy_before_sum > MAXENERGYTEST)
error->warning(FLERR,"Energy of old configuration in "
"fix gcmc is > MAXENERGYTEST.");
int nlocal = atom->nlocal;
int *mask = atom->mask;
@ -2170,6 +2182,8 @@ double FixGCMC::molecule_energy(tagint gas_molecule_id)
double FixGCMC::energy_full()
{
int imolecule;
if (triclinic) domain->x2lamda(atom->nlocal);
domain->pbc();
comm->exchange();
@ -2185,14 +2199,15 @@ double FixGCMC::energy_full()
// return signal value for energy
if (overlap_flag) {
int overlaptestall;
int overlaptest = 0;
double delx,dely,delz,rsq;
double **x = atom->x;
tagint *molecule = atom->molecule;
int nall = atom->nlocal + atom->nghost;
for (int i = 0; i < atom->nlocal; i++) {
int imolecule = molecule[i];
if (mode == MOLECULE) imolecule = molecule[i];
for (int j = i+1; j < nall; j++) {
if (mode == MOLECULE)
if (imolecule == molecule[j]) continue;
@ -2201,11 +2216,18 @@ double FixGCMC::energy_full()
delz = x[i][2] - x[j][2];
rsq = delx*delx + dely*dely + delz*delz;
if (rsq < overlap_cutoff) return MAXENERGYSIGNAL;
if (rsq < overlap_cutoff) {
overlaptest = 1;
break;
}
}
if (overlaptest) break;
}
MPI_Allreduce(&overlaptest, &overlaptestall, 1,
MPI_INT, MPI_MAX, world);
if (overlaptestall) return MAXENERGYSIGNAL;
}
// clear forces so they don't accumulate over multiple
// calls within fix gcmc timestep, e.g. for fix shake