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Added group keywords to fix gcmc 

git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@13453 f3b2605a-c512-4ea7-a41b-209d697bcdaa
This commit is contained in:
athomps 2015-05-08 17:21:20 +00:00
parent 73a87e7923
commit 5779fc4097
1 changed files with 19 additions and 23 deletions
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42
src/MC/fix_gcmc.cpp
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@ -293,8 +293,10 @@ void FixGCMC::options(int narg, char **arg)
if (iarg+2 > narg) error->all(FLERR,"Illegal fix gcmc command");
if (ngroups >= ngroupsmax) {
ngroupsmax = ngroups+1;
groupstrings = (char**) memory->srealloc(groupstrings,ngroupsmax*sizeof(char *),
"fix_gcmc:groupstrings");
groupstrings = (char **)
memory->srealloc(groupstrings,
ngroupsmax*sizeof(char *),
"fix_gcmc:groupstrings");
}
int n = strlen(arg[iarg+1]) + 1;
groupstrings[ngroups] = new char[n];
@ -307,8 +309,10 @@ void FixGCMC::options(int narg, char **arg)
ngrouptypesmax = ngrouptypes+1;
grouptypes = (int*) memory->srealloc(grouptypes,ngrouptypesmax*sizeof(int),
"fix_gcmc:grouptypes");
grouptypestrings = (char**) memory->srealloc(grouptypestrings,ngrouptypesmax*sizeof(char *),
"fix_gcmc:grouptypestrings");
grouptypestrings = (char**)
memory->srealloc(grouptypestrings,
ngrouptypesmax*sizeof(char *),
"fix_gcmc:grouptypestrings");
}
grouptypes[ngrouptypes] = atoi(arg[iarg+1]);
int n = strlen(arg[iarg+2]) + 1;
@ -339,16 +343,6 @@ FixGCMC::~FixGCMC()
delete [] group_arg;
}
// This seems to be causing seg-faults
if (exclusion_group && (strcmp(group->names[0],"all") == 0)) {
char **group_arg = new char*[2];
group_arg[0] = group->names[exclusion_group];
group_arg[1] = (char *) "delete";
group->assign(2,group_arg);
delete [] group_arg;
}
memory->destroy(local_gas_list);
memory->destroy(atom_coord);
memory->destroy(coords);
@ -357,17 +351,15 @@ FixGCMC::~FixGCMC()
delete [] idshake;
if (ngroups > 0) {
for (int igroup = 0; igroup < ngroups; igroup++)
delete [] groupstrings[igroup];
// calling 2d destructor
memory->destroy(groupstrings);
}
if (ngrouptypes > 0) {
for (int igroup = 0; igroup < ngrouptypes; igroup++)
delete [] grouptypestrings[igroup];
memory->destroy(grouptypestrings);
memory->destroy(grouptypes);
memory->destroy(grouptypebits);
// calling 2d destructor
memory->destroy(grouptypestrings);
}
}
@ -494,6 +486,8 @@ void FixGCMC::init()
arg[3] = (char *) "all";
neighbor->modify_params(narg,arg);
delete [] group_arg[0];
delete [] group_arg;
delete [] arg;
}
// create a new group for temporary use with selected molecules
@ -515,6 +509,7 @@ void FixGCMC::init()
molecule_group_bit = group->bitmask[molecule_group];
molecule_group_inversebit = molecule_group_bit ^ ~0;
delete [] group_arg[0];
delete [] group_arg;
}
// get all of the needed molecule data if mode == MOLECULE,
@ -1364,20 +1359,21 @@ void FixGCMC::attempt_atomic_translation_full()
void FixGCMC::attempt_atomic_deletion_full()
{
double q_tmp;
const int q_flag = atom->q_flag;
ndeletion_attempts += 1.0;
if (ngas == 0) return;
double energy_before = energy_stored;
int i = pick_random_gas_atom();
const int i = pick_random_gas_atom();
int tmpmask;
if (i >= 0) {
tmpmask = atom->mask[i];
atom->mask[i] = exclusion_group_bit;
if (atom->q_flag) {
if (q_flag) {
q_tmp = atom->q[i];
atom->q[i] = 0.0;
}
@ -1398,7 +1394,7 @@ void FixGCMC::attempt_atomic_deletion_full()
} else {
if (i >= 0) {
atom->mask[i] = tmpmask;
if (atom->q_flag) atom->q[i] = q_tmp;
if (q_flag) atom->q[i] = q_tmp;
}
if (force->kspace) force->kspace->qsum_qsq();
energy_stored = energy_before;