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;
}
/* Return NULL if failed */
static Cell *
get_bravais_exact_positions_and_lattice(int * wyckoffs,
int * equiv_atoms,
SPGCONST Spacegroup *spacegroup,
SPGCONST Cell * primitive,
const double symprec)
{
int i;
int *wyckoffs_prim, *equiv_atoms_prim;
Symmetry *conv_sym;
Cell *bravais, *conv_prim;
VecDBL *exact_positions;
debug_print("get_bravais_exact_positions_and_lattice\n");
wyckoffs_prim = NULL;
equiv_atoms_prim = NULL;
conv_prim = NULL;
bravais = NULL;
conv_sym = NULL;
exact_positions = NULL;
/* Symmetrize atomic positions of conventional unit cell */
if ((wyckoffs_prim = (int*)malloc(sizeof(int) * primitive->size)) == NULL) {
warning_print("spglib: Memory could not be allocated ");
return NULL;
}
if ((equiv_atoms_prim = (int*)malloc(sizeof(int) * primitive->size)) == NULL) {
warning_print("spglib: Memory could not be allocated ");
free(wyckoffs_prim);
wyckoffs_prim = NULL;
return NULL;
}
for (i = 0; i < primitive->size; i++) {
wyckoffs_prim[i] = -1;
equiv_atoms_prim[i] = -1;
}
/* Positions of primitive atoms are represented wrt Bravais lattice */
if ((conv_prim = get_conventional_primitive(spacegroup, primitive)) == NULL) {
free(wyckoffs_prim);
wyckoffs_prim = NULL;
free(equiv_atoms_prim);
equiv_atoms_prim = NULL;
return NULL;
}
/* Symmetries in database (wrt Bravais lattice) */
if ((conv_sym = spgdb_get_spacegroup_operations(spacegroup->hall_number))
== NULL) {
goto err;
}
/* Lattice vectors are set. */
get_conventional_lattice(conv_prim->lattice, spacegroup);
if ((exact_positions = ssm_get_exact_positions(wyckoffs_prim,
equiv_atoms_prim,
conv_prim,
conv_sym,
spacegroup->hall_number,
symprec)) == NULL) {
sym_free_symmetry(conv_sym);
conv_sym = NULL;
goto err;
}
for (i = 0; i < conv_prim->size; i++) {
mat_copy_vector_d3(conv_prim->position[i], exact_positions->vec[i]);
}
bravais = expand_positions(wyckoffs,
equiv_atoms,
conv_prim,
conv_sym,
wyckoffs_prim,
equiv_atoms_prim);
mat_free_VecDBL(exact_positions);
exact_positions = NULL;
sym_free_symmetry(conv_sym);
conv_sym = NULL;
err:
free(wyckoffs_prim);
wyckoffs_prim = NULL;
free(equiv_atoms_prim);
equiv_atoms_prim = NULL;
cel_free_cell(conv_prim);
conv_prim = NULL;
return bravais;
}
