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;
}
void ref_get_Wyckoff_positions(int * wyckoffs,
int * equiv_atoms,
SPGCONST Cell * primitive,
SPGCONST Spacegroup * spacegroup,
const double symprec)
{
Cell *conv_prim;
conv_prim = get_bravais_exact_positions_and_lattice(wyckoffs,
equiv_atoms,
spacegroup,
primitive,
symprec);
cel_free_cell(conv_prim);
}
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;
}
Cell * get_Wyckoff_positions(int * wyckoffs,
int * equiv_atoms,
SPGCONST Cell * primitive,
SPGCONST Cell * cell,
SPGCONST Spacegroup * spacegroup,
SPGCONST Symmetry * symmetry,
const int * mapping_table,
const double symprec)
{
Cell *bravais;
int i, num_prim_sym;
int *wyckoffs_bravais, *equiv_atoms_bravais;
int operation_index[2];
debug_print("get_Wyckoff_positions\n");
bravais = NULL;
wyckoffs_bravais = NULL;
equiv_atoms_bravais = NULL;
if ((wyckoffs_bravais = (int*)malloc(sizeof(int) * primitive->size * 4))
== NULL) {
warning_print("spglib: Memory could not be allocated ");
return NULL;
}
if ((equiv_atoms_bravais = (int*)malloc(sizeof(int) * primitive->size * 4))
== NULL) {
warning_print("spglib: Memory could not be allocated ");
free(wyckoffs_bravais);
wyckoffs_bravais = NULL;
return NULL;
}
if ((bravais = get_bravais_exact_positions_and_lattice
(wyckoffs_bravais,
equiv_atoms_bravais,
spacegroup,
primitive,
symprec)) == NULL) {
goto ret;
}
for (i = 0; i < cell->size; i++) {
wyckoffs[i] = wyckoffs_bravais[mapping_table[i]];
}
spgdb_get_operation_index(operation_index, spacegroup->hall_number);
num_prim_sym = operation_index[0] / (bravais->size / primitive->size);
/* Check symmetry breaking by unusual multiplicity of primitive cell. */
if (cell->size * num_prim_sym != symmetry->size * primitive->size) {
set_equivalent_atoms_broken_symmetry(equiv_atoms,
cell,
symmetry,
mapping_table,
symprec);
} else {
if (set_equivalent_atoms(equiv_atoms,
primitive,
cell,
equiv_atoms_bravais,
mapping_table) == 0) {
cel_free_cell(bravais);
bravais = NULL;
}
}
ret:
free(equiv_atoms_bravais);
equiv_atoms_bravais = NULL;
free(wyckoffs_bravais);
wyckoffs_bravais = NULL;
return bravais;
}
