static int get_schoenflies(char symbol[10],
SPGCONST double lattice[3][3],
SPGCONST double position[][3],
const int types[],
const int num_atom,
const double symprec)
{
Cell *cell;
Primitive *primitive;
Spacegroup spacegroup;
cell = NULL;
primitive = NULL;
spacegroup.number = 0;
cell = cel_alloc_cell(num_atom);
cel_set_cell(cell, lattice, position, types);
if ((primitive = spa_get_spacegroup(&spacegroup, cell, symprec)) != NULL) {
prm_free_primitive(primitive);
if (spacegroup.number > 0) {
strcpy(symbol, spacegroup.schoenflies);
}
}
cel_free_cell(cell);
return spacegroup.number;
}
int spg_get_ir_kpoints( int map[],
SPGCONST double kpoints[][3],
const int num_kpoint,
SPGCONST double lattice[3][3],
SPGCONST double position[][3],
const int types[],
const int num_atom,
const int is_time_reversal,
const double symprec )
{
Symmetry *symmetry;
Cell *cell;
int num_ir_kpoint;
cell = cel_alloc_cell( num_atom );
cel_set_cell( cell, lattice, position, types );
symmetry = sym_get_operation( cell, symprec );
num_ir_kpoint = kpt_get_irreducible_kpoints( map, kpoints, num_kpoint,
lattice, symmetry,
is_time_reversal, symprec );
cel_free_cell( cell );
sym_free_symmetry( symmetry );
return num_ir_kpoint;
}
int spg_get_ir_reciprocal_mesh( int grid_point[][3],
int map[],
const int mesh[3],
const int is_shift[3],
const int is_time_reversal,
SPGCONST double lattice[3][3],
SPGCONST double position[][3],
const int types[],
const int num_atom,
const double symprec )
{
Symmetry *symmetry;
Cell *cell;
int num_ir;
cell = cel_alloc_cell( num_atom );
cel_set_cell( cell, lattice, position, types );
symmetry = sym_get_operation( cell, symprec );
num_ir = kpt_get_irreducible_reciprocal_mesh( grid_point,
map,
mesh,
is_shift,
is_time_reversal,
lattice,
symmetry,
symprec );
cel_free_cell( cell );
sym_free_symmetry( symmetry );
return num_ir;
}
static int find_primitive(double lattice[3][3],
double position[][3],
int types[],
const int num_atom,
const double symprec)
{
int i, num_prim_atom=0;
Cell *cell, *primitive;
cell = cel_alloc_cell(num_atom);
cel_set_cell(cell, lattice, position, types);
/* find primitive cell */
primitive = prm_get_primitive(cell, symprec);
if (primitive->size == cell->size) { /* Already primitive */
num_prim_atom = 0;
} else { /* Primitive cell was found. */
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];
mat_copy_vector_d3(position[i], primitive->position[i]);
}
}
}
cel_free_cell(primitive);
cel_free_cell(cell);
return num_prim_atom;
}
int spg_refine_cell( double lattice[3][3],
double position[][3],
int types[],
const int num_atom,
const double symprec )
{
int i, num_atom_bravais;
Cell *cell, *bravais;
cell = cel_alloc_cell( num_atom );
cel_set_cell( cell, lattice, position, types );
bravais = ref_refine_cell( cell, symprec );
cel_free_cell( cell );
if ( bravais->size > 0 ) {
mat_copy_matrix_d3( lattice, bravais->lattice );
num_atom_bravais = bravais->size;
for ( i = 0; i < bravais->size; i++ ) {
types[i] = bravais->types[i];
mat_copy_vector_d3( position[i], bravais->position[i] );
}
} else {
num_atom_bravais = 0;
}
cel_free_cell( bravais );
return num_atom_bravais;
}
Cell * cel_copy_cell( SPGCONST Cell * cell )
{
Cell * cell_new;
cell_new = cel_alloc_cell( cell->size );
cel_set_cell( cell_new,
cell->lattice,
cell->position,
cell->types );
return cell_new;
}
/* Return 0 if failed */
static int get_symmetry_numerical(int rotation[][3][3],
double translation[][3],
const int max_size,
SPGCONST double lattice[3][3],
SPGCONST double position[][3],
const int types[],
const int num_atom,
const double symprec)
{
int i, size;
Cell *cell;
Symmetry *symmetry;
size = 0;
cell = NULL;
symmetry = NULL;
if ((cell = cel_alloc_cell(num_atom)) == NULL) {
return 0;
}
cel_set_cell(cell, lattice, position, types);
if ((symmetry = sym_get_operation(cell, symprec)) == NULL) {
cel_free_cell(cell);
return 0;
}
if (symmetry->size > max_size) {
fprintf(stderr, "spglib: Indicated max size(=%d) is less than number ",
max_size);
fprintf(stderr, "spglib: of symmetry operations(=%d).\n", symmetry->size);
goto ret;
}
for (i = 0; i < symmetry->size; i++) {
mat_copy_matrix_i3(rotation[i], symmetry->rot[i]);
mat_copy_vector_d3(translation[i], symmetry->trans[i]);
}
size = symmetry->size;
ret:
sym_free_symmetry(symmetry);
cel_free_cell(cell);
return size;
}
Cell * cel_copy_cell(const Cell * cell)
{
Cell * cell_new;
cell_new = NULL;
if ((cell_new = cel_alloc_cell(cell->size)) == NULL) {
return NULL;
}
cel_set_cell(cell_new,
cell->lattice,
cell->position,
cell->types);
return cell_new;
}
int spg_get_max_multiplicity( SPGCONST double lattice[3][3],
SPGCONST double position[][3],
const int types[],
const int num_atom,
const double symprec )
{
Cell *cell;
int num_max_multi;
cell = cel_alloc_cell( num_atom );
cel_set_cell( cell, lattice, position, types );
/* 48 is the magic number, which is the number of rotations */
/* in the highest point symmetry Oh. */
num_max_multi = sym_get_multiplicity( cell, symprec ) * 48;
cel_free_cell( cell );
return num_max_multi;
}
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;
}
int spg_get_multiplicity( SPGCONST double lattice[3][3],
SPGCONST double position[][3],
const int types[],
const int num_atom,
const double symprec )
{
Symmetry *symmetry;
Cell *cell;
int size;
cell = cel_alloc_cell( num_atom );
cel_set_cell( cell, lattice, position, types );
symmetry = sym_get_operation( cell, symprec );
size = symmetry->size;
cel_free_cell( cell );
sym_free_symmetry( symmetry );
return size;
}
int spg_get_schoenflies( char symbol[10],
SPGCONST double lattice[3][3],
SPGCONST double position[][3],
const int types[], const int num_atom,
const double symprec )
{
Cell *cell;
Spacegroup spacegroup;
cell = cel_alloc_cell( num_atom );
cel_set_cell( cell, lattice, position, types );
spacegroup = spa_get_spacegroup( cell, symprec );
if ( spacegroup.number > 0 ) {
strcpy(symbol, spacegroup.schoenflies);
}
cel_free_cell( cell );
return spacegroup.number;
}
/* Return 0 if failed */
static int find_primitive(double lattice[3][3],
double position[][3],
int types[],
const int num_atom,
const double symprec)
{
int i, num_prim_atom;
Cell *cell;
Primitive *primitive;
cell = NULL;
primitive = NULL;
num_prim_atom = 0;
if ((cell = cel_alloc_cell(num_atom)) == NULL) {
return 0;
}
cel_set_cell(cell, lattice, position, types);
/* find primitive cell */
if ((primitive = prm_get_primitive(cell, symprec)) == NULL) {
cel_free_cell(cell);
return 0;
}
num_prim_atom = primitive->cell->size;
if (num_prim_atom < num_atom && num_prim_atom > 0 ) {
mat_copy_matrix_d3(lattice, primitive->cell->lattice);
for (i = 0; i < primitive->cell->size; i++) {
types[i] = primitive->cell->types[i];
mat_copy_vector_d3(position[i], primitive->cell->position[i]);
}
}
prm_free_primitive(primitive);
cel_free_cell(cell);
return num_prim_atom;
}
static int get_symmetry_with_collinear_spin(int rotation[][3][3],
double translation[][3],
const int max_size,
SPGCONST double lattice[3][3],
SPGCONST double position[][3],
const int types[],
const double spins[],
const int num_atom,
const double symprec)
{
int i, j, size;
Symmetry *symmetry;
Cell *cell;
cell = cel_alloc_cell(num_atom);
cel_set_cell(cell, lattice, position, types);
symmetry = spn_get_collinear_operation(cell, spins, symprec);
if (symmetry->size > max_size) {
fprintf(stderr, "spglib: Indicated max size(=%d) is less than number ", max_size);
fprintf(stderr, "spglib: of symmetry operations(=%d).\n", symmetry->size);
sym_free_symmetry(symmetry);
return 0;
}
for (i = 0; i < symmetry->size; i++) {
mat_copy_matrix_i3(rotation[i], symmetry->rot[i]);
for (j = 0; j < 3; j++) {
translation[i][j] = symmetry->trans[i][j];
}
}
size = symmetry->size;
cel_free_cell(cell);
sym_free_symmetry(symmetry);
return size;
}
static int standardize_primitive(double lattice[3][3],
double position[][3],
int types[],
const int num_atom,
const double symprec)
{
int num_prim_atom;
Centering centering;
SpglibDataset *dataset;
Cell *primitive, *bravais;
double identity[3][3] = {{ 1, 0, 0 },
{ 0, 1, 0 },
{ 0, 0, 1 }};
num_prim_atom = 0;
dataset = NULL;
primitive = NULL;
bravais = NULL;
if ((dataset = get_dataset(lattice,
position,
types,
num_atom,
0,
symprec)) == NULL) {
return 0;
}
if ((centering = get_centering(dataset->hall_number)) == CENTERING_ERROR) {
goto err;
}
if (dataset->hall_number == 433 ||
dataset->hall_number == 436 ||
dataset->hall_number == 444 ||
dataset->hall_number == 450 ||
dataset->hall_number == 452 ||
dataset->hall_number == 458 ||
dataset->hall_number == 460) {
centering = R_CENTER;
}
if ((bravais = cel_alloc_cell(dataset->n_std_atoms)) == NULL) {
spg_free_dataset(dataset);
return 0;
}
cel_set_cell(bravais,
dataset->std_lattice,
dataset->std_positions,
dataset->std_types);
spg_free_dataset(dataset);
primitive = spa_transform_to_primitive(bravais,
identity,
centering,
symprec);
cel_free_cell(bravais);
if (primitive == NULL) {
goto err;
}
set_cell(lattice, position, types, primitive);
num_prim_atom = primitive->size;
cel_free_cell(primitive);
return num_prim_atom;
err:
return 0;
}
/* Return NULL if failed */
static SpglibDataset * get_dataset(SPGCONST double lattice[3][3],
SPGCONST double position[][3],
const int types[],
const int num_atom,
const int hall_number,
const double symprec)
{
Spacegroup spacegroup;
SpacegroupType spacegroup_type;
SpglibDataset *dataset;
Cell *cell;
Primitive *primitive;
spacegroup.number = 0;
dataset = NULL;
cell = NULL;
primitive = NULL;
if ((dataset = (SpglibDataset*) malloc(sizeof(SpglibDataset))) == NULL) {
warning_print("spglib: Memory could not be allocated.");
return NULL;
}
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;
dataset->n_brv_atoms = 0;
dataset->brv_positions = NULL;
dataset->brv_types = NULL;
if ((cell = cel_alloc_cell(num_atom)) == NULL) {
free(dataset);
dataset = NULL;
return NULL;
}
cel_set_cell(cell, lattice, position, types);
primitive = spa_get_spacegroup(&spacegroup, cell, symprec);
if ((spacegroup.number > 0) && (primitive != NULL)) {
/* With hall_number > 0, specific choice is searched. */
if (hall_number > 0) {
spacegroup_type = spgdb_get_spacegroup_type(hall_number);
if (spacegroup.number == spacegroup_type.number) {
spacegroup = spa_get_spacegroup_with_hall_number(primitive,
hall_number);
} else {
goto err;
}
if (spacegroup.number == 0) {
goto err;
}
}
if (spacegroup.number > 0) {
if ((set_dataset(dataset,
cell,
primitive->cell,
&spacegroup,
primitive->mapping_table,
primitive->tolerance)) == 0) {
goto err;
}
}
}
cel_free_cell(cell);
prm_free_primitive(primitive);
return dataset;
err:
cel_free_cell(cell);
prm_free_primitive(primitive);
free(dataset);
dataset = NULL;
return NULL;
}
static int get_standardized_cell(double lattice[3][3],
double position[][3],
int types[],
const int num_atom,
const int to_primitive,
const double symprec)
{
int num_std_atom;
SpglibDataset *dataset;
Cell *std_cell, *cell;
Centering centering;
num_std_atom = 0;
dataset = NULL;
std_cell = NULL;
cell = NULL;
if ((dataset = get_dataset(lattice,
position,
types,
num_atom,
0,
symprec)) == NULL) {
goto err;
}
if (to_primitive) {
if ((centering = get_centering(dataset->hall_number)) == CENTERING_ERROR) {
goto err;
}
if (dataset->hall_number == 433 ||
dataset->hall_number == 436 ||
dataset->hall_number == 444 ||
dataset->hall_number == 450 ||
dataset->hall_number == 452 ||
dataset->hall_number == 458 ||
dataset->hall_number == 460) {
centering = R_CENTER;
}
} else {
centering = PRIMITIVE;
}
if ((cell = cel_alloc_cell(num_atom)) == NULL) {
spg_free_dataset(dataset);
goto err;
}
cel_set_cell(cell, lattice, position, types);
std_cell = spa_transform_to_primitive(cell,
dataset->transformation_matrix,
centering,
symprec);
spg_free_dataset(dataset);
cel_free_cell(cell);
if (std_cell == NULL) {
goto err;
}
set_cell(lattice, position, types, std_cell);
num_std_atom = std_cell->size;
cel_free_cell(std_cell);
return num_std_atom;
err:
return 0;
}
/* Return 0 if failed */
static int get_symmetry_with_collinear_spin(int rotation[][3][3],
double translation[][3],
int equivalent_atoms[],
const int max_size,
SPGCONST double lattice[3][3],
SPGCONST double position[][3],
const int types[],
const double spins[],
const int num_atom,
const double symprec)
{
int i, size;
Symmetry *symmetry, *sym_nonspin;
Cell *cell;
SpglibDataset *dataset;
size = 0;
symmetry = NULL;
sym_nonspin = NULL;
cell = NULL;
dataset = NULL;
if ((cell = cel_alloc_cell(num_atom)) == NULL) {
goto err;
}
cel_set_cell(cell, lattice, position, types);
if ((dataset = get_dataset(lattice,
position,
types,
num_atom,
0,
symprec)) == NULL) {
cel_free_cell(cell);
goto err;
}
if ((sym_nonspin = sym_alloc_symmetry(dataset->n_operations)) == NULL) {
spg_free_dataset(dataset);
cel_free_cell(cell);
goto err;
}
for (i = 0; i < dataset->n_operations; i++) {
mat_copy_matrix_i3(sym_nonspin->rot[i], dataset->rotations[i]);
mat_copy_vector_d3(sym_nonspin->trans[i], dataset->translations[i]);
}
spg_free_dataset(dataset);
if ((symmetry = spn_get_collinear_operations(equivalent_atoms,
sym_nonspin,
cell,
spins,
symprec)) == NULL) {
sym_free_symmetry(sym_nonspin);
cel_free_cell(cell);
goto err;
}
sym_free_symmetry(sym_nonspin);
if (symmetry->size > max_size) {
fprintf(stderr, "spglib: Indicated max size(=%d) is less than number ",
max_size);
fprintf(stderr, "spglib: of symmetry operations(=%d).\n", symmetry->size);
sym_free_symmetry(symmetry);
goto err;
}
for (i = 0; i < symmetry->size; i++) {
mat_copy_matrix_i3(rotation[i], symmetry->rot[i]);
mat_copy_vector_d3(translation[i], symmetry->trans[i]);
}
size = symmetry->size;
cel_free_cell(cell);
sym_free_symmetry(symmetry);
return size;
err:
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;
}
/*---------*/
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;
}
