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git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@11328 f3b2605a-c512-4ea7-a41b-209d697bcdaa

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This commit is contained in:
sjplimp
2014-01-25 22:46:08 +00:00
parent 2f6a46a2be
commit 0ce16af78b
63 changed files with 2943 additions and 798 deletions
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82
src/MISC/fix_evaporate.cpp
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@ -17,6 +17,7 @@
#include "fix_evaporate.h"
#include "atom.h"
#include "atom_vec.h"
#include "molecule.h"
#include "update.h"
#include "domain.h"
#include "region.h"
@ -234,9 +235,13 @@ void FixEvaporate::pre_exchange()
// keep ndel,ndeltopo,ncount,nall,nbefore current after each mol deletion
} else {
int me,proc,iatom,ndelone,ndelall;
tagint imol;
int me,proc,iatom,ndelone,ndelall,index;
tagint imolecule;
tagint *molecule = atom->molecule;
int *molindex = atom->molindex;
int *molatom = atom->molatom;
int molecular = atom->molecular;
Molecule **onemols = atom->avec->onemols;
ndeltopo[0] = ndeltopo[1] = ndeltopo[2] = ndeltopo[3] = 0;
@ -248,57 +253,70 @@ void FixEvaporate::pre_exchange()
if (iwhichglobal >= nbefore && iwhichglobal < nbefore + ncount) {
iwhichlocal = iwhichglobal - nbefore;
iatom = list[iwhichlocal];
imol = molecule[iatom];
imolecule = molecule[iatom];
me = comm->me;
} else me = -1;
// bcast mol ID to delete all atoms from
// if mol ID > 0, delete any atom in molecule and decrement counters
// if mol ID == 0, delete single iatom
// be careful to delete correct # of bond,angle,etc for newton on or off
// logic with ndeltopo is to count # of deleted bonds,angles,etc
// for atom->molecular = 1, do this for each deleted atom in molecule
// for atom->molecular = 2, use Molecule counts for just 1st atom in mol
MPI_Allreduce(&me,&proc,1,MPI_INT,MPI_MAX,world);
MPI_Bcast(&imol,1,MPI_LMP_TAGINT,proc,world);
MPI_Bcast(&imolecule,1,MPI_LMP_TAGINT,proc,world);
ndelone = 0;
for (i = 0; i < nlocal; i++) {
if (imol && molecule[i] == imol) {
if (imolecule && molecule[i] == imolecule) {
mark[i] = 1;
ndelone++;
if (atom->avec->bonds_allow) {
if (force->newton_bond) ndeltopo[0] += atom->num_bond[i];
else {
for (j = 0; j < atom->num_bond[i]; j++) {
if (tag[i] < atom->bond_atom[i][j]) ndeltopo[0]++;
if (molecular == 1) {
if (atom->avec->bonds_allow) {
if (force->newton_bond) ndeltopo[0] += atom->num_bond[i];
else {
for (j = 0; j < atom->num_bond[i]; j++) {
if (tag[i] < atom->bond_atom[i][j]) ndeltopo[0]++;
}
}
}
}
if (atom->avec->angles_allow) {
if (force->newton_bond) ndeltopo[1] += atom->num_angle[i];
else {
for (j = 0; j < atom->num_angle[i]; j++) {
m = atom->map(atom->angle_atom2[i][j]);
if (m >= 0 && m < nlocal) ndeltopo[1]++;
if (atom->avec->angles_allow) {
if (force->newton_bond) ndeltopo[1] += atom->num_angle[i];
else {
for (j = 0; j < atom->num_angle[i]; j++) {
m = atom->map(atom->angle_atom2[i][j]);
if (m >= 0 && m < nlocal) ndeltopo[1]++;
}
}
}
}
if (atom->avec->dihedrals_allow) {
if (force->newton_bond) ndeltopo[2] += atom->num_dihedral[i];
else {
for (j = 0; j < atom->num_dihedral[i]; j++) {
m = atom->map(atom->dihedral_atom2[i][j]);
if (m >= 0 && m < nlocal) ndeltopo[2]++;
if (atom->avec->dihedrals_allow) {
if (force->newton_bond) ndeltopo[2] += atom->num_dihedral[i];
else {
for (j = 0; j < atom->num_dihedral[i]; j++) {
m = atom->map(atom->dihedral_atom2[i][j]);
if (m >= 0 && m < nlocal) ndeltopo[2]++;
}
}
}
}
if (atom->avec->impropers_allow) {
if (force->newton_bond) ndeltopo[3] += atom->num_improper[i];
else {
for (j = 0; j < atom->num_improper[i]; j++) {
m = atom->map(atom->improper_atom2[i][j]);
if (m >= 0 && m < nlocal) ndeltopo[3]++;
if (atom->avec->impropers_allow) {
if (force->newton_bond) ndeltopo[3] += atom->num_improper[i];
else {
for (j = 0; j < atom->num_improper[i]; j++) {
m = atom->map(atom->improper_atom2[i][j]);
if (m >= 0 && m < nlocal) ndeltopo[3]++;
}
}
}
} else {
if (molatom[i] == 0) {
index = molindex[i];
ndeltopo[0] += onemols[index]->nbonds;
ndeltopo[1] += onemols[index]->nangles;
ndeltopo[2] += onemols[index]->ndihedrals;
ndeltopo[3] += onemols[index]->nimpropers;
}
}
} else if (me == proc && i == iatom) {