Spacegroup spa_get_spacegroup( SPGCONST Cell * cell,
const double symprec )
{
Cell *primitive;
int *mapping_table;
Spacegroup spacegroup;
VecDBL *pure_trans;
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 > 0 ) {
spacegroup = get_spacegroup( primitive, symprec );
} 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;
}
Spacegroup spa_get_spacegroup( SPGCONST Cell * cell,
const double symprec )
{
Cell *primitive;
int *mapping_table;
Spacegroup spacegroup;
VecDBL *pure_trans;
double tolerance;
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;
/* In some case, tolerance (symprec) to find primitive lattice is reduced. */
/* The reduced tolerance should be used to find symmetry operations. */
tolerance = prm_get_tolerance();
if ( primitive->size > -1 ) {
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;
}
/* Return NULL if failed */
static Primitive * get_primitive(SPGCONST Cell * cell, const double symprec)
{
int i, attempt;
double tolerance;
Primitive *primitive;
VecDBL * pure_trans;
debug_print("get_primitive (tolerance = %f):\n", symprec);
primitive = NULL;
pure_trans = NULL;
if ((primitive = prm_alloc_primitive(cell->size)) == NULL) {
return NULL;
}
tolerance = symprec;
for (attempt = 0; attempt < 100; attempt++) {
if ((pure_trans = sym_get_pure_translation(cell, tolerance)) == NULL) {
goto cont;
}
if (pure_trans->size == 1) {
if ((primitive->cell = get_cell_with_smallest_lattice(cell, tolerance))
!= NULL) {
for (i = 0; i < cell->size; i++) {
primitive->mapping_table[i] = i;
}
goto found;
}
} else {
if ((primitive->cell = get_primitive_cell(primitive->mapping_table,
cell,
pure_trans,
tolerance)) != NULL) {
goto found;
}
}
mat_free_VecDBL(pure_trans);
cont:
tolerance *= REDUCE_RATE;
warning_print("spglib: Reduce tolerance to %f ", tolerance);
warning_print("(line %d, %s).\n", __LINE__, __FILE__);
}
prm_free_primitive(primitive);
return NULL;
found:
primitive->tolerance = tolerance;
mat_free_VecDBL(pure_trans);
return primitive;
}
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;
}
/* primitive cell with smallest lattice is returned. */
static Primitive get_primitive_and_pure_translation(SPGCONST Cell * cell,
const double symprec)
{
int attempt, is_found = 0;
double tolerance;
int *mapping_table;
Primitive primitive;
tolerance = symprec;
for (attempt = 0; attempt < 100; attempt++) {
primitive.pure_trans = sym_get_pure_translation(cell, tolerance);
if (primitive.pure_trans->size == 0) {
mat_free_VecDBL(primitive.pure_trans);
continue;
}
if (primitive.pure_trans->size == 1) {
primitive.cell = get_cell_with_smallest_lattice(cell, tolerance);
} else {
mapping_table = (int*) malloc(sizeof(int) * cell->size);
primitive.cell = get_primitive(mapping_table,
cell,
primitive.pure_trans,
tolerance);
free(mapping_table);
}
if (primitive.cell->size > 0) {
is_found = 1;
break;
}
cel_free_cell(primitive.cell);
mat_free_VecDBL(primitive.pure_trans);
tolerance *= REDUCE_RATE;
warning_print("spglib: Reduce tolerance to %f ", tolerance);
warning_print("(line %d, %s).\n", __LINE__, __FILE__);
}
if (! is_found) {
primitive.cell = cel_alloc_cell(0);
primitive.pure_trans = mat_alloc_VecDBL(0);
}
return primitive;
}
/* primitive cell with smallest lattice is returned. */
static Cell * get_primitive_and_mapping_table(int * mapping_table,
SPGCONST Cell * cell,
const double symprec)
{
int i, attempt;
double tolerance;
Cell *primitive_cell;
VecDBL *pure_trans;
tolerance = symprec;
for (attempt = 0; attempt < 100; attempt++) {
pure_trans = sym_get_pure_translation(cell, tolerance);
if (pure_trans->size == 1) {
primitive_cell = get_cell_with_smallest_lattice(cell, symprec);
for (i = 0; i < cell->size; i++) {
mapping_table[i] = i;
}
goto ret;
}
if (pure_trans->size > 1) {
primitive_cell = get_primitive(mapping_table, cell, pure_trans, tolerance);
if (primitive_cell->size > 0) {
goto ret;
}
cel_free_cell(primitive_cell);
}
tolerance *= REDUCE_RATE;
warning_print("spglib: Tolerance is reduced to %f at attempt %d\n", tolerance, attempt);
warning_print("(line %d, %s).\n", __LINE__, __FILE__);
mat_free_VecDBL(pure_trans);
}
/* not found: I hope this will not happen. */
warning_print("spglib: Primitive cell could not be found ");
warning_print("(line %d, %s).\n", __LINE__, __FILE__);
return cel_alloc_cell(0);
ret:
mat_free_VecDBL(pure_trans);
set_current_tolerance(tolerance);
return primitive_cell;
}
int spg_find_primitive( double lattice[3][3],
double position[][3],
int types[],
const int num_atom,
const double symprec )
{
int i, j, num_prim_atom=0;
int *mapping_table;
Cell *cell, *primitive;
VecDBL *pure_trans;
cell = cel_alloc_cell( num_atom );
cel_set_cell( cell, lattice, position, types );
pure_trans = sym_get_pure_translation( cell, symprec );
/* find primitive cell */
if ( pure_trans->size > 1 ) {
mapping_table = (int*) malloc( sizeof(int) * cell->size );
primitive = prm_get_primitive( mapping_table, cell, pure_trans, symprec );
free( mapping_table );
mapping_table = NULL;
num_prim_atom = primitive->size;
if ( num_prim_atom < num_atom && num_prim_atom > 0 ) {
mat_copy_matrix_d3( lattice, primitive->lattice );
for ( i = 0; i < primitive->size; i++ ) {
types[i] = primitive->types[i];
for (j=0; j<3; j++) {
position[i][j] = primitive->position[i][j];
}
}
}
cel_free_cell( primitive );
} else {
num_prim_atom = 0;
}
mat_free_VecDBL( pure_trans );
cel_free_cell( cell );
return num_prim_atom;
}
/* was not a primitive cell. */
static int get_operation( int rot[][3][3],
double trans[][3],
SPGCONST Cell *cell,
const double symprec )
{
int num_sym;
int multi;
int *mapping_table;
PointSymmetry lattice_sym;
Cell *primitive;
VecDBL *pure_trans;
pure_trans = sym_get_pure_translation(cell, symprec);
multi = pure_trans->size;
/* Lattice symmetry for input cell*/
lattice_sym = get_lattice_symmetry( cell, symprec );
if ( lattice_sym.size == 0 ) {
goto err;
}
/* Obtain primitive cell */
if( multi > 1 ) {
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 ) { goto err; }
lattice_sym = transform_pointsymmetry( &lattice_sym,
primitive->lattice,
cell->lattice );
if ( lattice_sym.size == 0 ) { goto err; }
} else {
primitive = cell;
}
/* Symmetry operation search for primitive cell */
num_sym = get_space_group_operation( rot, trans, &lattice_sym,
primitive, symprec );
/* Recover symmetry operation for the input structure (overwritten) */
if( multi > 1 ) {
num_sym = get_operation_supercell( rot,
trans,
num_sym,
pure_trans,
cell,
primitive );
cel_free_cell( primitive );
if ( num_sym == 0 ) { goto err; }
}
mat_free_VecDBL( pure_trans );
return num_sym;
err:
mat_free_VecDBL( pure_trans );
return 0;
}
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;
}
