forked from lijiext/lammps
Added group keywords to fix gcmc
git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@13452 f3b2605a-c512-4ea7-a41b-209d697bcdaa
This commit is contained in:
athomps
parent
682950268b
commit
73a87e7923
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@ -226,7 +226,15 @@ void FixGCMC::options(int narg, char **arg)
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charge_flag = false;
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full_flag = false;
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idshake = NULL;
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ngroups = 0;
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int ngroupsmax = 0;
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groupstrings = NULL;
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ngrouptypes = 0;
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int ngrouptypesmax = 0;
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grouptypestrings = NULL;
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grouptypes = NULL;
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grouptypebits = NULL;
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int iarg = 0;
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while (iarg < narg) {
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if (strcmp(arg[iarg],"mol") == 0) {
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@ -281,6 +289,33 @@ void FixGCMC::options(int narg, char **arg)
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} else if (strcmp(arg[iarg],"full_energy") == 0) {
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full_flag = true;
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iarg += 1;
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} else if (strcmp(arg[iarg],"group") == 0) {
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if (iarg+2 > narg) error->all(FLERR,"Illegal fix gcmc command");
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if (ngroups >= ngroupsmax) {
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ngroupsmax = ngroups+1;
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groupstrings = (char**) memory->srealloc(groupstrings,ngroupsmax*sizeof(char *),
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"fix_gcmc:groupstrings");
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}
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int n = strlen(arg[iarg+1]) + 1;
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groupstrings[ngroups] = new char[n];
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strcpy(groupstrings[ngroups],arg[iarg+1]);
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ngroups++;
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iarg += 2;
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} else if (strcmp(arg[iarg],"grouptype") == 0) {
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if (iarg+3 > narg) error->all(FLERR,"Illegal fix gcmc command");
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if (ngrouptypes >= ngrouptypesmax) {
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ngrouptypesmax = ngrouptypes+1;
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grouptypes = (int*) memory->srealloc(grouptypes,ngrouptypesmax*sizeof(int),
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"fix_gcmc:grouptypes");
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grouptypestrings = (char**) memory->srealloc(grouptypestrings,ngrouptypesmax*sizeof(char *),
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"fix_gcmc:grouptypestrings");
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}
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grouptypes[ngrouptypes] = atoi(arg[iarg+1]);
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int n = strlen(arg[iarg+2]) + 1;
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grouptypestrings[ngrouptypes] = new char[n];
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strcpy(grouptypestrings[ngrouptypes],arg[iarg+2]);
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ngrouptypes++;
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iarg += 3;
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} else error->all(FLERR,"Illegal fix gcmc command");
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}
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}
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@ -303,6 +338,8 @@ FixGCMC::~FixGCMC()
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group->assign(2,group_arg);
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delete [] group_arg;
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}
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// This seems to be causing seg-faults
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if (exclusion_group && (strcmp(group->names[0],"all") == 0)) {
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char **group_arg = new char*[2];
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@ -318,6 +355,20 @@ FixGCMC::~FixGCMC()
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memory->destroy(imageflags);
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delete [] idshake;
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if (ngroups > 0) {
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for (int igroup = 0; igroup < ngroups; igroup++)
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delete [] groupstrings[igroup];
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memory->destroy(groupstrings);
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}
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if (ngrouptypes > 0) {
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for (int igroup = 0; igroup < ngrouptypes; igroup++)
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delete [] grouptypestrings[igroup];
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memory->destroy(grouptypestrings);
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memory->destroy(grouptypes);
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memory->destroy(grouptypebits);
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}
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}
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/* ---------------------------------------------------------------------- */
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@ -515,6 +566,31 @@ void FixGCMC::init()
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imagetmp = ((imageint) IMGMAX << IMG2BITS) |
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((imageint) IMGMAX << IMGBITS) | IMGMAX;
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// construct group bitmask for all new atoms
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// aggregated over all group keywords
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groupbitall = 1 | groupbit;
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for (int igroup = 0; igroup < ngroups; igroup++) {
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int jgroup = group->find(groupstrings[igroup]);
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if (jgroup == -1)
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error->all(FLERR,"Could not find specified fix gcmc group ID");
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groupbitall |= group->bitmask[jgroup];
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}
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// construct group type bitmasks
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// not aggregated over all group keywords
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if (ngrouptypes > 0) {
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memory->create(grouptypebits,ngrouptypes,"fix_gcmc:grouptypebits");
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for (int igroup = 0; igroup < ngrouptypes; igroup++) {
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int jgroup = group->find(grouptypestrings[igroup]);
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if (jgroup == -1)
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error->all(FLERR,"Could not find specified fix gcmc group ID");
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grouptypebits[igroup] = group->bitmask[jgroup];
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}
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}
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}
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/* ----------------------------------------------------------------------
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@ -750,7 +826,16 @@ void FixGCMC::attempt_atomic_insertion()
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zz*volume*exp(-beta*insertion_energy)/(ngas+1)) {
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atom->avec->create_atom(ngcmc_type,coord);
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int m = atom->nlocal - 1;
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atom->mask[m] = 1 | groupbit;
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// add to groups
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// optionally add to type-based groups
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atom->mask[m] = groupbitall;
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for (int igroup = 0; igroup < ngrouptypes; igroup++) {
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if (ngcmc_type == grouptypes[igroup])
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atom->mask[m] |= grouptypebits[igroup];
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}
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atom->v[m][0] = random_unequal->gaussian()*sigma;
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atom->v[m][1] = random_unequal->gaussian()*sigma;
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atom->v[m][2] = random_unequal->gaussian()*sigma;
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@ -1086,7 +1171,16 @@ void FixGCMC::attempt_molecule_insertion()
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if (procflag[i]) {
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atom->avec->create_atom(ngcmc_type+onemols[imol]->type[i],atom_coord[i]);
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int m = atom->nlocal - 1;
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atom->mask[m] = 1 | groupbit;
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// add to groups
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// optionally add to type-based groups
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atom->mask[m] = groupbitall;
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for (int igroup = 0; igroup < ngrouptypes; igroup++) {
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if (ngcmc_type == grouptypes[igroup])
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atom->mask[m] |= grouptypebits[igroup];
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}
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atom->image[m] = imagetmp;
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domain->remap(atom->x[m],atom->image[m]);
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atom->molecule[m] = maxmol_all;
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@ -1347,7 +1441,16 @@ void FixGCMC::attempt_atomic_insertion_full()
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proc_flag = 1;
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atom->avec->create_atom(ngcmc_type,coord);
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int m = atom->nlocal - 1;
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atom->mask[m] = 1 | groupbit;
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// add to groups
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// optionally add to type-based groups
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atom->mask[m] = groupbitall;
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for (int igroup = 0; igroup < ngrouptypes; igroup++) {
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if (ngcmc_type == grouptypes[igroup])
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atom->mask[m] |= grouptypebits[igroup];
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}
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atom->v[m][0] = random_unequal->gaussian()*sigma;
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atom->v[m][1] = random_unequal->gaussian()*sigma;
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atom->v[m][2] = random_unequal->gaussian()*sigma;
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@ -1696,7 +1799,18 @@ void FixGCMC::attempt_molecule_insertion_full()
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atom->avec->create_atom(ngcmc_type+onemols[imol]->type[i],xtmp);
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int m = atom->nlocal - 1;
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atom->mask[m] = 1 | groupbit;
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// add to groups
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// optionally add to type-based groups
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atom->mask[m] = groupbitall;
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printf("ngrouptypes %d\n",ngrouptypes);
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for (int igroup = 0; igroup < ngrouptypes; igroup++) {
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printf("check type %d %d\n",ngcmc_type,grouptypes[igroup]);
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if (ngcmc_type == grouptypes[igroup])
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atom->mask[m] |= grouptypebits[igroup];
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}
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atom->image[m] = imagetmp;
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domain->remap(atom->x[m],atom->image[m]);
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atom->molecule[m] = insertion_molecule;
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@ -74,9 +74,16 @@ class FixGCMC : public Fix {
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bool pressure_flag; // true if user specified reservoir pressure
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bool charge_flag; // true if user specified atomic charge
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bool full_flag; // true if doing full system energy calculations
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int natoms_per_molecule; // number of atoms in each gas molecule
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int groupbitall; // group bitmask for inserted atoms
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int ngroups; // number of group-ids for inserted atoms
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char** groupstrings; // list of group-ids for inserted atoms
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int ngrouptypes; // number of type-based group-ids for inserted atoms
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char** grouptypestrings; // list of type-based group-ids for inserted atoms
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int* grouptypebits; // list of type-based group bitmasks
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int* grouptypes; // list of type-based group types
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double ntranslation_attempts;
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double ntranslation_successes;
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double nrotation_attempts;
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