HMMExperiment::HMMExperiment(std::string dataset, std::string logfile_, std::string logprogressfile_,
int hs_, int nfolds_, bool shuffle_, int EMiterations_, int nworkers_,
PredictionType prediction_type_, TestingStrategy testing_strat_)
: logfile(logfile_, std::ofstream::app), logprogressfile(logprogressfile_, std::ofstream::out) {
assert(logfile.good());
assert(logprogressfile.good());
nworkers = nworkers_;
for(int iworkers=0; iworkers<nworkers; iworkers++)
workers.push_back(HMMWorkerThread());
hs = hs_;
nfolds = nfolds_;
shuffle = shuffle_;
EMiterations = EMiterations_;
prediction_type = prediction_type_;
testing_strat = testing_strat_;
set_dataset(dataset);
}
/* Return NULL if failed */
static SpglibDataset * get_dataset(SPGCONST double lattice[3][3],
SPGCONST double position[][3],
const int types[],
const int num_atom,
const int hall_number,
const double symprec)
{
Spacegroup spacegroup;
SpacegroupType spacegroup_type;
SpglibDataset *dataset;
Cell *cell;
Primitive *primitive;
spacegroup.number = 0;
dataset = NULL;
cell = NULL;
primitive = NULL;
if ((dataset = (SpglibDataset*) malloc(sizeof(SpglibDataset))) == NULL) {
warning_print("spglib: Memory could not be allocated.");
return NULL;
}
dataset->spacegroup_number = 0;
strcpy(dataset->international_symbol, "");
strcpy(dataset->hall_symbol, "");
strcpy(dataset->setting, "");
dataset->origin_shift[0] = 0;
dataset->origin_shift[1] = 0;
dataset->origin_shift[2] = 0;
dataset->n_atoms = 0;
dataset->wyckoffs = NULL;
dataset->equivalent_atoms = NULL;
dataset->n_operations = 0;
dataset->rotations = NULL;
dataset->translations = NULL;
dataset->n_brv_atoms = 0;
dataset->brv_positions = NULL;
dataset->brv_types = NULL;
if ((cell = cel_alloc_cell(num_atom)) == NULL) {
free(dataset);
dataset = NULL;
return NULL;
}
cel_set_cell(cell, lattice, position, types);
primitive = spa_get_spacegroup(&spacegroup, cell, symprec);
if ((spacegroup.number > 0) && (primitive != NULL)) {
/* With hall_number > 0, specific choice is searched. */
if (hall_number > 0) {
spacegroup_type = spgdb_get_spacegroup_type(hall_number);
if (spacegroup.number == spacegroup_type.number) {
spacegroup = spa_get_spacegroup_with_hall_number(primitive,
hall_number);
} else {
goto err;
}
if (spacegroup.number == 0) {
goto err;
}
}
if (spacegroup.number > 0) {
if ((set_dataset(dataset,
cell,
primitive->cell,
&spacegroup,
primitive->mapping_table,
primitive->tolerance)) == 0) {
goto err;
}
}
}
cel_free_cell(cell);
prm_free_primitive(primitive);
return dataset;
err:
cel_free_cell(cell);
prm_free_primitive(primitive);
free(dataset);
dataset = NULL;
return NULL;
}
/*---------*/
static SpglibDataset * get_dataset(SPGCONST double lattice[3][3],
SPGCONST double position[][3],
const int types[],
const int num_atom,
const double symprec)
{
int attempt;
int *mapping_table;
double tolerance, tolerance_from_prim;
Spacegroup spacegroup;
SpglibDataset *dataset;
Cell *cell, *primitive;
dataset = (SpglibDataset*) malloc(sizeof(SpglibDataset));
dataset->spacegroup_number = 0;
strcpy(dataset->international_symbol, "");
strcpy(dataset->hall_symbol, "");
strcpy(dataset->setting, "");
dataset->origin_shift[0] = 0;
dataset->origin_shift[1] = 0;
dataset->origin_shift[2] = 0;
dataset->n_atoms = 0;
dataset->wyckoffs = NULL;
dataset->equivalent_atoms = NULL;
dataset->n_operations = 0;
dataset->rotations = NULL;
dataset->translations = NULL;
mapping_table = (int*) malloc(sizeof(int) * num_atom);
cell = cel_alloc_cell(num_atom);
cel_set_cell(cell, lattice, position, types);
tolerance = symprec;
for (attempt = 0; attempt < 100; attempt++) {
primitive = prm_get_primitive_and_mapping_table(mapping_table,
cell,
tolerance);
if (primitive->size > 0) {
tolerance_from_prim = prm_get_current_tolerance();
spacegroup = spa_get_spacegroup_with_primitive(primitive,
tolerance_from_prim);
if (spacegroup.number > 0) {
set_dataset(dataset,
cell,
primitive,
&spacegroup,
mapping_table,
tolerance_from_prim);
cel_free_cell(primitive);
break;
}
}
tolerance *= REDUCE_RATE;
cel_free_cell(primitive);
warning_print(" Attempt %d tolerance = %f failed.", attempt, tolerance);
warning_print(" (line %d, %s).\n", __LINE__, __FILE__);
}
free(mapping_table);
mapping_table = NULL;
cel_free_cell(cell);
return dataset;
}
