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; }
static Cell * refine_cell( SPGCONST Cell * cell, const double symprec ) { int *mapping_table, *wyckoffs, *equiv_atoms; Cell *primitive, *bravais, *conv_prim; Symmetry *conv_sym; VecDBL *pure_trans; Spacegroup spacegroup; pure_trans = sym_get_pure_translation( cell, symprec ); mapping_table = (int*) malloc( sizeof(int) * cell->size ); primitive = prm_get_primitive( mapping_table, cell, pure_trans, symprec ); free( mapping_table ); mapping_table = NULL; if ( primitive->size == -1 ) { cel_free_cell( primitive ); bravais = cel_alloc_cell( -1 ); goto ret; } spacegroup = spa_get_spacegroup_with_primitive( primitive, symprec ); 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, symprec ); 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 ); cel_free_cell( conv_prim ); sym_free_symmetry( conv_sym ); cel_free_cell( primitive ); ret: /* Return bravais->size = -1, if the bravais could not be found. */ return bravais; }
SpglibDataset * spg_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; Spacegroup spacegroup; SpglibDataset *dataset; Cell *cell, *primitive; double inv_mat[3][3]; Symmetry *symmetry; VecDBL *pure_trans; dataset = (SpglibDataset*) malloc( sizeof( SpglibDataset ) ); cell = cel_alloc_cell( num_atom ); cel_set_cell( cell, lattice, position, types ); pure_trans = sym_get_pure_translation( cell, symprec ); mapping_table = (int*) malloc( sizeof(int) * cell->size ); primitive = prm_get_primitive( mapping_table, cell, pure_trans, symprec ); mat_free_VecDBL( pure_trans ); spacegroup = spa_get_spacegroup_with_primitive( primitive, symprec ); /* Spacegroup type, transformation matrix, origin shift */ if ( spacegroup.number > 0 ) { dataset->spacegroup_number = spacegroup.number; strcpy( dataset->international_symbol, spacegroup.international_short); strcpy( dataset->hall_symbol, spacegroup.hall_symbol); mat_inverse_matrix_d3( inv_mat, lattice, symprec ); 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, symprec ); 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; 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; free( mapping_table ); mapping_table = NULL; /* Symmetry operations */ symmetry = ref_get_refined_symmetry_operations( cell, primitive->lattice, &spacegroup, symprec ); cel_free_cell( cell ); cel_free_cell( primitive ); 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 ); 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 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; }