static Cell * refine_cell(SPGCONST Cell * cell,
const double symprec)
{
int *wyckoffs, *equiv_atoms;
double tolerance;
Cell *primitive, *bravais, *conv_prim;
Symmetry *conv_sym;
Spacegroup spacegroup;
debug_print("refine_cell:\n");
primitive = prm_get_primitive(cell, symprec);
if (primitive->size == 0) {
cel_free_cell(primitive);
bravais = cel_alloc_cell(0);
goto end;
}
tolerance = prm_get_current_tolerance();
spacegroup = spa_get_spacegroup_with_primitive(primitive, tolerance);
wyckoffs = (int*)malloc(sizeof(int) * primitive->size);
equiv_atoms = (int*)malloc(sizeof(int) * primitive->size);
conv_prim = get_bravais_exact_positions_and_lattice(wyckoffs,
equiv_atoms,
&spacegroup,
primitive,
tolerance);
free(equiv_atoms);
equiv_atoms = NULL;
free(wyckoffs);
wyckoffs = NULL;
conv_sym = get_db_symmetry(spacegroup.hall_number);
bravais = expand_positions(conv_prim, conv_sym);
debug_print("primitive cell in refine_cell:\n");
debug_print_matrix_d3(primitive->lattice);
debug_print("conventional lattice in refine_cell:\n");
debug_print_matrix_d3(conv_prim->lattice);
debug_print("bravais lattice in refine_cell:\n");
debug_print_matrix_d3(bravais->lattice);
cel_free_cell(conv_prim);
sym_free_symmetry(conv_sym);
cel_free_cell(primitive);
end: /* Return bravais->size = 0, if the bravais could not be found. */
return bravais;
}
Spacegroup spa_get_spacegroup(SPGCONST Cell * cell,
const double symprec)
{
double tolerance;
Cell *primitive;
Spacegroup spacegroup;
primitive = prm_get_primitive(cell, symprec);
tolerance = prm_get_current_tolerance();
if (primitive->size > 0) {
spacegroup = get_spacegroup(primitive, tolerance);
} else {
spacegroup.number = 0;
warning_print("spglib: Space group could not be found ");
warning_print("(line %d, %s).\n", __LINE__, __FILE__);
}
cel_free_cell(primitive);
return spacegroup;
}
/*---------*/
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;
}
static SpglibDataset * get_dataset(SPGCONST double lattice[3][3],
SPGCONST double position[][3],
const int types[],
const int num_atom,
const double symprec)
{
int i, j;
int *mapping_table, *wyckoffs, *equiv_atoms, *equiv_atoms_prim;
double tolerance;
Spacegroup spacegroup;
SpglibDataset *dataset;
Cell *cell, *primitive;
double inv_mat[3][3];
Symmetry *symmetry;
dataset = (SpglibDataset*) malloc(sizeof(SpglibDataset));
cell = cel_alloc_cell(num_atom);
cel_set_cell(cell, lattice, position, types);
mapping_table = (int*) malloc(sizeof(int) * cell->size);
primitive = prm_get_primitive_with_mapping_table(mapping_table,
cell,
symprec);
tolerance = prm_get_current_tolerance();
spacegroup = spa_get_spacegroup_with_primitive(primitive, tolerance);
if (spacegroup.number > 0) {
/* Spacegroup type, transformation matrix, origin shift */
dataset->spacegroup_number = spacegroup.number;
dataset->hall_number = spacegroup.hall_number;
strcpy(dataset->international_symbol, spacegroup.international_short);
strcpy(dataset->hall_symbol, spacegroup.hall_symbol);
mat_inverse_matrix_d3(inv_mat, lattice, tolerance);
mat_multiply_matrix_d3(dataset->transformation_matrix,
inv_mat,
spacegroup.bravais_lattice);
mat_copy_vector_d3(dataset->origin_shift, spacegroup.origin_shift);
/* Wyckoff positions */
wyckoffs = (int*) malloc(sizeof(int) * primitive->size);
equiv_atoms_prim = (int*) malloc(sizeof(int) * primitive->size);
for (i = 0; i < primitive->size; i++) {
wyckoffs[i] = -1;
equiv_atoms_prim[i] = -1;
}
ref_get_Wyckoff_positions(wyckoffs,
equiv_atoms_prim,
primitive,
&spacegroup,
tolerance);
dataset->n_atoms = cell->size;
dataset->wyckoffs = (int*) malloc(sizeof(int) * cell->size);
for (i = 0; i < cell->size; i++) {
dataset->wyckoffs[i] = wyckoffs[mapping_table[i]];
}
free(wyckoffs);
wyckoffs = NULL;
/* Equivalent atoms */
dataset->equivalent_atoms = (int*) malloc(sizeof(int) * cell->size);
equiv_atoms = (int*) malloc(sizeof(int) * primitive->size);
for (i = 0; i < primitive->size; i++) {
for (j = 0; j < cell->size; j++) {
if (mapping_table[j] == equiv_atoms_prim[i]) {
equiv_atoms[i] = j;
break;
}
}
}
for (i = 0; i < cell->size; i++) {
dataset->equivalent_atoms[i] = equiv_atoms[mapping_table[i]];
}
free(equiv_atoms);
equiv_atoms = NULL;
free(equiv_atoms_prim);
equiv_atoms_prim = NULL;
/* Symmetry operations */
symmetry = ref_get_refined_symmetry_operations(cell,
primitive,
&spacegroup,
tolerance);
dataset->rotations = (int (*)[3][3]) malloc(sizeof(int[3][3]) * symmetry->size);
dataset->translations = (double (*)[3]) malloc(sizeof(double[3]) * symmetry->size);
dataset->n_operations = symmetry->size;
for (i = 0; i < symmetry->size; i++) {
mat_copy_matrix_i3(dataset->rotations[i], symmetry->rot[i]);
mat_copy_vector_d3(dataset->translations[i], symmetry->trans[i]);
}
sym_free_symmetry(symmetry);
} else {
dataset->spacegroup_number = 0;
}
free(mapping_table);
mapping_table = NULL;
cel_free_cell(primitive);
if (dataset->spacegroup_number == 0) {
strcpy(dataset->international_symbol, "");
strcpy(dataset->hall_symbol, "");
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;
}
cel_free_cell(cell);
return dataset;
}
