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new library functions

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This commit is contained in:
Steve Plimpton
2016-10-27 09:34:04 -06:00
parent efaa8feab5
commit d9891abdf4
44 changed files with 1341 additions and 211 deletions
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57
src/delete_atoms.cpp
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@ -59,7 +59,9 @@ void DeleteAtoms::command(int narg, char **arg)
bigint ndihedrals_previous = atom->ndihedrals;
bigint nimpropers_previous = atom->nimpropers;
// delete the atoms
// flag atoms for deletion
allflag = 0;
if (strcmp(arg[0],"group") == 0) delete_group(narg,arg);
else if (strcmp(arg[0],"region") == 0) delete_region(narg,arg);
@ -67,36 +69,44 @@ void DeleteAtoms::command(int narg, char **arg)
else if (strcmp(arg[0],"porosity") == 0) delete_porosity(narg,arg);
else error->all(FLERR,"Illegal delete_atoms command");
// optionally delete additional bonds or atoms in molecules
// if allflag = 1, just reset atom->nlocal
// else delete atoms one by one
if (bond_flag) delete_bond();
if (mol_flag) delete_molecule();
if (allflag) atom->nlocal = 0;
else {
// delete local atoms flagged in dlist
// reset nlocal
// optionally delete additional bonds or atoms in molecules
AtomVec *avec = atom->avec;
int nlocal = atom->nlocal;
if (bond_flag) delete_bond();
if (mol_flag) delete_molecule();
int i = 0;
while (i < nlocal) {
if (dlist[i]) {
avec->copy(nlocal-1,i,1);
dlist[i] = dlist[nlocal-1];
nlocal--;
} else i++;
// delete local atoms flagged in dlist
// reset nlocal
AtomVec *avec = atom->avec;
int nlocal = atom->nlocal;
int i = 0;
while (i < nlocal) {
if (dlist[i]) {
avec->copy(nlocal-1,i,1);
dlist[i] = dlist[nlocal-1];
nlocal--;
} else i++;
}
atom->nlocal = nlocal;
memory->destroy(dlist);
}
atom->nlocal = nlocal;
memory->destroy(dlist);
// if non-molecular system and compress flag set,
// reset atom tags to be contiguous
// set all atom IDs to 0, call tag_extend()
if (atom->molecular == 0 && compress_flag) {
tagint *tag = atom->tag;
for (i = 0; i < nlocal; i++) tag[i] = 0;
int nlocal = atom->nlocal;
for (int i = 0; i < nlocal; i++) tag[i] = 0;
atom->tag_extend();
}
@ -185,6 +195,13 @@ void DeleteAtoms::delete_group(int narg, char **arg)
if (igroup == -1) error->all(FLERR,"Could not find delete_atoms group ID");
options(narg-2,&arg[2]);
// check for special case of group = all
if (strcmp(arg[1],"all") == 0) {
allflag = 1;
return;
}
// allocate and initialize deletion list
int nlocal = atom->nlocal;