static Symmetry * get_refined_symmetry_operations(SPGCONST Cell * cell,
SPGCONST Cell * primitive,
SPGCONST Spacegroup * spacegroup,
const double symprec)
{
int t_mat_int[3][3];
int frame[3];
double inv_mat[3][3], t_mat[3][3];
Symmetry *conv_sym, *prim_sym, *symmetry;
/* Primitive symmetry from database */
conv_sym = get_db_symmetry(spacegroup->hall_number);
set_translation_with_origin_shift(conv_sym, spacegroup->origin_shift);
mat_inverse_matrix_d3(inv_mat, primitive->lattice, symprec);
mat_multiply_matrix_d3(t_mat, inv_mat, spacegroup->bravais_lattice);
prim_sym = get_primitive_db_symmetry(t_mat, conv_sym, symprec);
/* Input cell symmetry from primitive symmetry */
mat_inverse_matrix_d3(inv_mat, primitive->lattice, symprec);
mat_multiply_matrix_d3(t_mat, inv_mat, cell->lattice);
mat_cast_matrix_3d_to_3i(t_mat_int, t_mat);
get_surrounding_frame(frame, t_mat_int);
symmetry = reduce_symmetry_in_frame(frame,
prim_sym,
t_mat_int,
cell->lattice,
cell->size / primitive->size,
symprec);
/* sym_free_symmetry(f_sym); */
sym_free_symmetry(prim_sym);
sym_free_symmetry(conv_sym);
return symmetry;
}
static int get_operation_supercell( int rot[][3][3],
double trans[][3],
const int num_sym,
const VecDBL * pure_trans,
SPGCONST Cell *cell,
SPGCONST Cell *primitive )
{
int i, j, k, multi;
double inv_prim_lat[3][3], drot[3][3], trans_mat[3][3], trans_mat_inv[3][3];
MatINT *rot_prim;
VecDBL *trans_prim;
rot_prim = mat_alloc_MatINT( num_sym );
trans_prim = mat_alloc_VecDBL( num_sym );
multi = pure_trans->size;
debug_print("get_operation_supercell\n");
mat_inverse_matrix_d3( inv_prim_lat, primitive->lattice, 0 );
mat_multiply_matrix_d3( trans_mat, inv_prim_lat, cell->lattice );
mat_inverse_matrix_d3( trans_mat_inv, trans_mat, 0 );
for( i = 0; i < num_sym; i++) {
/* Translations */
mat_multiply_matrix_vector_d3( trans[i], trans_mat_inv, trans[i] );
/* Rotations */
mat_cast_matrix_3i_to_3d( drot, rot[i] );
mat_get_similar_matrix_d3( drot, drot, trans_mat, 0 );
mat_cast_matrix_3d_to_3i( rot[i], drot );
}
for( i = 0; i < num_sym; i++ ) {
mat_copy_matrix_i3( rot_prim->mat[i], rot[i] );
for( j = 0; j < 3; j++ )
trans_prim->vec[i][j] = trans[i][j];
}
/* Rotations and translations are copied with the set of */
/* pure translations. */
for( i = 0; i < num_sym; i++ ) {
for( j = 0; j < multi; j++ ) {
mat_copy_matrix_i3( rot[ i * multi + j ], rot_prim->mat[i] );
for ( k = 0; k < 3; k++ ) {
trans[i * multi + j][k] =
mat_Dmod1( trans_prim->vec[i][k] + pure_trans->vec[j][k] );
}
}
}
mat_free_MatINT( rot_prim );
mat_free_VecDBL( trans_prim );
/* return number of symmetry operation of supercell */
return num_sym * multi;
}
static Symmetry * recover_operations_original(SPGCONST Symmetry *symmetry,
const VecDBL * pure_trans,
SPGCONST Cell *cell,
SPGCONST Cell *primitive)
{
int i, j, k, multi;
double inv_prim_lat[3][3], drot[3][3], trans_mat[3][3], trans_mat_inv[3][3];
Symmetry *symmetry_orig, *sym_tmp;
debug_print("recover_operations_original:\n");
multi = pure_trans->size;
sym_tmp = sym_alloc_symmetry(symmetry->size);
symmetry_orig = sym_alloc_symmetry(symmetry->size * multi);
mat_inverse_matrix_d3(inv_prim_lat, primitive->lattice, 0);
mat_multiply_matrix_d3(trans_mat, inv_prim_lat, cell->lattice);
mat_inverse_matrix_d3(trans_mat_inv, trans_mat, 0);
for(i = 0; i < symmetry->size; i++) {
mat_copy_matrix_i3(sym_tmp->rot[i], symmetry->rot[i]);
mat_copy_vector_d3(sym_tmp->trans[i], symmetry->trans[i]);
}
for(i = 0; i < symmetry->size; i++) {
mat_cast_matrix_3i_to_3d(drot, sym_tmp->rot[i]);
mat_get_similar_matrix_d3(drot, drot, trans_mat, 0);
mat_cast_matrix_3d_to_3i(sym_tmp->rot[i], drot);
mat_multiply_matrix_vector_d3(sym_tmp->trans[i],
trans_mat_inv,
sym_tmp->trans[i]);
}
for(i = 0; i < symmetry->size; i++) {
for(j = 0; j < multi; j++) {
mat_copy_matrix_i3(symmetry_orig->rot[i * multi + j], sym_tmp->rot[i]);
for (k = 0; k < 3; k++) {
symmetry_orig->trans[i * multi + j][k] =
sym_tmp->trans[i][k] + pure_trans->vec[j][k];
}
}
}
sym_free_symmetry(sym_tmp);
return symmetry_orig;
}
static Cell * get_cell_with_smallest_lattice( SPGCONST Cell * cell,
const double symprec )
{
int i, j;
double min_lat[3][3], trans_mat[3][3], inv_lat[3][3];
Cell * smallest_cell;
if ( lat_smallest_lattice_vector( min_lat,
cell->lattice,
symprec ) ) {
mat_inverse_matrix_d3( inv_lat, min_lat, 0 );
mat_multiply_matrix_d3( trans_mat, inv_lat, cell->lattice );
smallest_cell = cel_alloc_cell( cell->size );
mat_copy_matrix_d3( smallest_cell->lattice, min_lat );
for ( i = 0; i < cell->size; i++ ) {
smallest_cell->types[i] = cell->types[i];
mat_multiply_matrix_vector_d3( smallest_cell->position[i],
trans_mat, cell->position[i] );
for ( j = 0; j < 3; j++ ) {
cell->position[i][j] -= mat_Nint( cell->position[i][j] );
}
}
} else {
smallest_cell = cel_alloc_cell( -1 );
}
return smallest_cell;
}
static Cell * get_conventional_primitive(SPGCONST Spacegroup * spacegroup,
SPGCONST Cell * primitive)
{
int i, j;
double inv_brv[3][3], trans_mat[3][3];
Cell * conv_prim;
conv_prim = cel_alloc_cell(primitive->size);
mat_inverse_matrix_d3(inv_brv, spacegroup->bravais_lattice, 0);
mat_multiply_matrix_d3(trans_mat, inv_brv, primitive->lattice);
for (i = 0; i < primitive->size; i++) {
conv_prim->types[i] = primitive->types[i];
mat_multiply_matrix_vector_d3(conv_prim->position[i],
trans_mat,
primitive->position[i]);
for (j = 0; j < 3; j++) {
conv_prim->position[i][j] -= spacegroup->origin_shift[j];
conv_prim->position[i][j] -= mat_Nint(conv_prim->position[i][j]);
}
}
return conv_prim;
}
static VecDBL * get_positions_primitive( SPGCONST Cell * cell,
SPGCONST double prim_lat[3][3] )
{
int i, j;
double tmp_matrix[3][3], axis_inv[3][3];
VecDBL * position;
position = mat_alloc_VecDBL( cell->size );
mat_inverse_matrix_d3(tmp_matrix, prim_lat, 0);
mat_multiply_matrix_d3(axis_inv, tmp_matrix, cell->lattice);
/* Send atoms into the primitive cell */
debug_print("Positions in new axes reduced to primitive cell\n");
for (i = 0; i < cell->size; i++) {
mat_multiply_matrix_vector_d3( position->vec[i],
axis_inv, cell->position[i] );
for (j = 0; j < 3; j++) {
position->vec[i][j] -= mat_Nint( position->vec[i][j] );
}
debug_print("%d: %f %f %f\n", i + 1,
position->vec[i][0],
position->vec[i][1],
position->vec[i][2]);
}
return position;
}
/* Return NULL if failed */
static VecDBL * get_positions_primitive(SPGCONST Cell * cell,
SPGCONST double prim_lat[3][3])
{
int i, j;
double tmp_matrix[3][3], axis_inv[3][3];
VecDBL * position;
position = NULL;
if ((position = mat_alloc_VecDBL(cell->size)) == NULL) {
return NULL;
}
mat_inverse_matrix_d3(tmp_matrix, prim_lat, 0);
mat_multiply_matrix_d3(axis_inv, tmp_matrix, cell->lattice);
/* Send atoms into the primitive cell */
for (i = 0; i < cell->size; i++) {
mat_multiply_matrix_vector_d3(position->vec[i],
axis_inv,
cell->position[i]);
for (j = 0; j < 3; j++) {
position->vec[i][j] -= mat_Nint(position->vec[i][j]);
}
}
return position;
}
/* Return NULL if failed */
static VecDBL *
translate_atoms_in_trimmed_lattice(const Cell * cell,
SPGCONST double trimmed_lattice[3][3])
{
int i, j;
double tmp_matrix[3][3], axis_inv[3][3];
VecDBL * position;
position = NULL;
if ((position = mat_alloc_VecDBL(cell->size)) == NULL) {
return NULL;
}
mat_inverse_matrix_d3(tmp_matrix, trimmed_lattice, 0);
mat_multiply_matrix_d3(axis_inv, tmp_matrix, cell->lattice);
/* Send atoms into the trimmed cell */
for (i = 0; i < cell->size; i++) {
mat_multiply_matrix_vector_d3(position->vec[i],
axis_inv,
cell->position[i]);
for (j = 0; j < 3; j++) {
position->vec[i][j] = mat_Dmod1(position->vec[i][j]);
}
}
return position;
}
static Symmetry *
recover_symmetry_in_original_cell(const int frame[3],
SPGCONST Symmetry *prim_sym,
SPGCONST int t_mat[3][3],
SPGCONST double lattice[3][3],
const int multiplicity,
const double symprec)
{
Symmetry *symmetry, *t_sym;
double inv_tmat[3][3], tmp_mat[3][3];
VecDBL *pure_trans, *lattice_trans;
symmetry = NULL;
t_sym = NULL;
pure_trans = NULL;
lattice_trans = NULL;
mat_cast_matrix_3i_to_3d(tmp_mat, t_mat);
mat_inverse_matrix_d3(inv_tmat, tmp_mat, 0);
if ((lattice_trans = get_lattice_translations(frame, inv_tmat)) == NULL) {
return NULL;
}
if ((pure_trans = remove_overlapping_lattice_points(lattice,
lattice_trans,
symprec)) == NULL) {
mat_free_VecDBL(lattice_trans);
lattice_trans = NULL;
return NULL;
}
if ((t_sym = get_symmetry_in_original_cell(t_mat,
inv_tmat,
lattice,
prim_sym,
symprec)) == NULL) {
mat_free_VecDBL(pure_trans);
pure_trans = NULL;
mat_free_VecDBL(lattice_trans);
lattice_trans = NULL;
return NULL;
}
if (pure_trans->size == multiplicity) {
symmetry = copy_symmetry_upon_lattice_points(pure_trans, t_sym);
}
mat_free_VecDBL(lattice_trans);
lattice_trans = NULL;
mat_free_VecDBL(pure_trans);
pure_trans = NULL;
sym_free_symmetry(t_sym);
t_sym = NULL;
return symmetry;
}
static void set_dataset(SpglibDataset * dataset,
SPGCONST Cell * cell,
SPGCONST Cell * primitive,
SPGCONST Spacegroup * spacegroup,
const int * mapping_table,
const double tolerance)
{
int i;
double inv_mat[3][3];
Cell *bravais;
Symmetry *symmetry;
/* Spacegroup type, transformation matrix, origin shift */
dataset->n_atoms = cell->size;
dataset->spacegroup_number = spacegroup->number;
dataset->hall_number = spacegroup->hall_number;
strcpy(dataset->international_symbol, spacegroup->international_short);
strcpy(dataset->hall_symbol, spacegroup->hall_symbol);
strcpy(dataset->setting, spacegroup->setting);
mat_inverse_matrix_d3(inv_mat, cell->lattice, tolerance);
mat_multiply_matrix_d3(dataset->transformation_matrix,
inv_mat,
spacegroup->bravais_lattice);
mat_copy_vector_d3(dataset->origin_shift, spacegroup->origin_shift);
/* Symmetry operations */
symmetry = ref_get_refined_symmetry_operations(cell,
primitive,
spacegroup,
tolerance);
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]);
}
/* Wyckoff positions */
dataset->wyckoffs = (int*) malloc(sizeof(int) * cell->size);
dataset->equivalent_atoms = (int*) malloc(sizeof(int) * cell->size);
bravais = ref_get_Wyckoff_positions(dataset->wyckoffs,
dataset->equivalent_atoms,
primitive,
cell,
spacegroup,
symmetry,
mapping_table,
tolerance);
cel_free_cell(bravais);
sym_free_symmetry(symmetry);
}
/* m = b^-1 a b */
int mat_get_similar_matrix_d3(double m[3][3], const double a[3][3],
const double b[3][3], const double precision)
{
double c[3][3];
if (!mat_inverse_matrix_d3(c, b, precision)) {
fprintf(stderr, "spglib: No similar matrix due to 0 determinant.\n");
return 0;
}
mat_multiply_matrix_d3(m, a, b);
mat_multiply_matrix_d3(m, c, m);
return 1;
}
/* Return NULL if failed */
Cell * spa_transform_to_primitive(SPGCONST Cell * cell,
SPGCONST double trans_mat[3][3],
const Centering centering,
const double symprec)
{
int * mapping_table;
double tmat[3][3], tmat_inv[3][3], prim_lat[3][3];
Cell * primitive;
mapping_table = NULL;
primitive = NULL;
mat_inverse_matrix_d3(tmat_inv, trans_mat, 0);
switch (centering) {
case PRIMITIVE:
mat_copy_matrix_d3(tmat, tmat_inv);
break;
case A_FACE:
mat_multiply_matrix_d3(tmat, tmat_inv, A_mat);
break;
case C_FACE:
mat_multiply_matrix_d3(tmat, tmat_inv, C_mat);
break;
case FACE:
mat_multiply_matrix_d3(tmat, tmat_inv, F_mat);
break;
case BODY:
mat_multiply_matrix_d3(tmat, tmat_inv, I_mat);
break;
case R_CENTER:
mat_multiply_matrix_d3(tmat, tmat_inv, R_mat);
break;
default:
goto err;
}
if ((mapping_table = (int*) malloc(sizeof(int) * cell->size)) == NULL) {
warning_print("spglib: Memory could not be allocated ");
goto err;
}
mat_multiply_matrix_d3(prim_lat, cell->lattice, tmat);
primitive = cel_trim_cell(mapping_table, prim_lat, cell, symprec);
free(mapping_table);
mapping_table = NULL;
return primitive;
err:
return NULL;
}
static Symmetry * get_primitive_db_symmetry(SPGCONST double t_mat[3][3],
const Symmetry *conv_sym,
const double symprec)
{
int i, j, num_op;
double inv_mat[3][3], tmp_mat[3][3];
MatINT *r_prim;
VecDBL *t_prim;
Symmetry *prim_sym;
r_prim = mat_alloc_MatINT(conv_sym->size);
t_prim = mat_alloc_VecDBL(conv_sym->size);
mat_inverse_matrix_d3(inv_mat, t_mat, symprec);
num_op = 0;
for (i = 0; i < conv_sym->size; i++) {
for (j = 0; j < i; j++) {
if (mat_check_identity_matrix_i3(conv_sym->rot[i],
conv_sym->rot[j])) {
goto pass;
}
}
/* R' = T*R*T^-1 */
mat_multiply_matrix_di3(tmp_mat, t_mat, conv_sym->rot[i]);
mat_multiply_matrix_d3(tmp_mat, tmp_mat, inv_mat);
mat_cast_matrix_3d_to_3i(r_prim->mat[ num_op ], tmp_mat);
/* t' = T*t */
mat_multiply_matrix_vector_d3(t_prim->vec[ num_op ],
t_mat,
conv_sym->trans[ i ]);
num_op++;
pass:
;
}
prim_sym = sym_alloc_symmetry(num_op);
for (i = 0; i < num_op; i++) {
mat_copy_matrix_i3(prim_sym->rot[i], r_prim->mat[i]);
for (j = 0; j < 3; j++) {
prim_sym->trans[i][j] = t_prim->vec[i][j] - mat_Nint(t_prim->vec[i][j]);
}
}
mat_free_MatINT(r_prim);
mat_free_VecDBL(t_prim);
return prim_sym;
}
/* m = b^-1 a b */
int mat_get_similar_matrix_d3(double m[3][3],
SPGCONST double a[3][3],
SPGCONST double b[3][3],
const double precision)
{
double c[3][3];
if (!mat_inverse_matrix_d3(c, b, precision)) {
warning_print("spglib: No similar matrix due to 0 determinant.\n");
debug_print("No similar matrix due to 0 determinant.\n");
return 0;
}
mat_multiply_matrix_d3(m, a, b);
mat_multiply_matrix_d3(m, c, m);
return 1;
}
static PointSymmetry
transform_pointsymmetry(SPGCONST PointSymmetry * lat_sym_orig,
SPGCONST double new_lattice[3][3],
SPGCONST double original_lattice[3][3])
{
int i, size;
double trans_mat[3][3], inv_mat[3][3], drot[3][3];
PointSymmetry lat_sym_new;
lat_sym_new.size = 0;
mat_inverse_matrix_d3(inv_mat, original_lattice, 0);
mat_multiply_matrix_d3(trans_mat, inv_mat, new_lattice);
size = 0;
for (i = 0; i < lat_sym_orig->size; i++) {
mat_cast_matrix_3i_to_3d(drot, lat_sym_orig->rot[i]);
mat_get_similar_matrix_d3(drot, drot, trans_mat, 0);
/* new_lattice may have lower point symmetry than original_lattice.*/
/* The operations that have non-integer elements are not counted. */
if (mat_is_int_matrix(drot, mat_Dabs(mat_get_determinant_d3(trans_mat)) / 10)) {
mat_cast_matrix_3d_to_3i(lat_sym_new.rot[size], drot);
if (abs(mat_get_determinant_i3(lat_sym_new.rot[size])) != 1) {
warning_print("spglib: A point symmetry operation is not unimodular.");
warning_print("(line %d, %s).\n", __LINE__, __FILE__);
goto err;
}
size++;
}
}
#ifdef SPGWARNING
if (! (lat_sym_orig->size == size)) {
warning_print("spglib: Some of point symmetry operations were dropped.");
warning_print("(line %d, %s).\n", __LINE__, __FILE__);
}
#endif
lat_sym_new.size = size;
return lat_sym_new;
err:
return lat_sym_new;
}
/* Return 0 if failed */
static int change_basis_monocli(int int_transform_mat[3][3],
SPGCONST double conv_lattice[3][3],
SPGCONST double primitive_lattice[3][3],
const double symprec)
{
double smallest_lattice[3][3], inv_lattice[3][3], transform_mat[3][3];
if (! del_delaunay_reduce_2D(smallest_lattice,
conv_lattice,
1, /* unique axis of b */
symprec)) {
return 0;
}
mat_inverse_matrix_d3(inv_lattice, primitive_lattice, 0);
mat_multiply_matrix_d3(transform_mat, inv_lattice, smallest_lattice);
mat_cast_matrix_3d_to_3i(int_transform_mat, transform_mat);
return 1;
}
/* Return NULL if failed */
static Cell * get_cell_with_smallest_lattice(SPGCONST Cell * cell,
const double symprec)
{
int i, j;
double min_lat[3][3], trans_mat[3][3], inv_lat[3][3];
Cell * smallest_cell;
debug_print("get_cell_with_smallest_lattice:\n");
smallest_cell = NULL;
if (!lat_smallest_lattice_vector(min_lat,
cell->lattice,
symprec)) {
goto err;
}
mat_inverse_matrix_d3(inv_lat, min_lat, 0);
mat_multiply_matrix_d3(trans_mat, inv_lat, cell->lattice);
if ((smallest_cell = cel_alloc_cell(cell->size)) == NULL) {
goto err;
}
mat_copy_matrix_d3(smallest_cell->lattice, min_lat);
for (i = 0; i < cell->size; i++) {
smallest_cell->types[i] = cell->types[i];
mat_multiply_matrix_vector_d3(smallest_cell->position[i],
trans_mat, cell->position[i]);
for (j = 0; j < 3; j++) {
cell->position[i][j] = mat_Dmod1(cell->position[i][j]);
}
}
return smallest_cell;
err:
return NULL;
}
/* Return 0 if failed */
static int change_basis_tricli(int int_transform_mat[3][3],
SPGCONST double conv_lattice[3][3],
SPGCONST double primitive_lattice[3][3],
const double symprec)
{
int i, j;
double niggli_cell[9];
double smallest_lattice[3][3], inv_lattice[3][3], transform_mat[3][3];
for (i = 0; i < 3; i++) {
for (j = 0; j < 3; j++) {
niggli_cell[i * 3 + j] = conv_lattice[i][j];
}
}
if (! niggli_reduce(niggli_cell, symprec * symprec)) {
return 0;
}
for (i = 0; i < 3; i++) {
for (j = 0; j < 3; j++) {
smallest_lattice[i][j] = niggli_cell[i * 3 + j];
}
}
if (mat_get_determinant_d3(smallest_lattice) < 0) {
for (i = 0; i < 3; i++) {
for (j = 0; j < 3; j++) {
smallest_lattice[i][j] = -smallest_lattice[i][j];
}
}
}
mat_inverse_matrix_d3(inv_lattice, primitive_lattice, 0);
mat_multiply_matrix_d3(transform_mat, inv_lattice, smallest_lattice);
mat_cast_matrix_3d_to_3i(int_transform_mat, transform_mat);
return 1;
}
static Symmetry * get_conventional_symmetry(SPGCONST double transform_mat[3][3],
const Centering centering,
const Symmetry *primitive_sym)
{
int i, j, k, multi, size;
double tmp_trans;
double tmp_matrix_d3[3][3], shift[4][3];
double symmetry_rot_d3[3][3], primitive_sym_rot_d3[3][3];
Symmetry *symmetry;
size = primitive_sym->size;
if (centering == FACE) {
symmetry = sym_alloc_symmetry(size * 4);
}
else {
if (centering) {
symmetry = sym_alloc_symmetry(size * 2);
} else {
symmetry = sym_alloc_symmetry(size);
}
}
for (i = 0; i < size; i++) {
mat_cast_matrix_3i_to_3d(primitive_sym_rot_d3, primitive_sym->rot[i]);
/* C*S*C^-1: recover conventional cell symmetry operation */
mat_get_similar_matrix_d3(symmetry_rot_d3,
primitive_sym_rot_d3,
transform_mat,
0);
mat_cast_matrix_3d_to_3i(symmetry->rot[i], symmetry_rot_d3);
/* translation in conventional cell: C = B^-1*P */
mat_inverse_matrix_d3(tmp_matrix_d3,
transform_mat,
0);
mat_multiply_matrix_vector_d3(symmetry->trans[i],
tmp_matrix_d3,
primitive_sym->trans[i]);
}
multi = 1;
if (centering) {
if (! (centering == FACE)) {
for (i = 0; i < 3; i++) {
shift[0][i] = 0.5;
}
if (centering == A_FACE) {
shift[0][0] = 0;
}
if (centering == B_FACE) {
shift[0][1] = 0;
}
if (centering == C_FACE) {
shift[0][2] = 0;
}
multi = 2;
}
if (centering == FACE) {
shift[0][0] = 0;
shift[0][1] = 0.5;
shift[0][2] = 0.5;
shift[1][0] = 0.5;
shift[1][1] = 0;
shift[1][2] = 0.5;
shift[2][0] = 0.5;
shift[2][1] = 0.5;
shift[2][2] = 0;
multi = 4;
}
for (i = 0; i < multi - 1; i++) {
for (j = 0; j < size; j++) {
mat_copy_matrix_i3(symmetry->rot[(i+1) * size + j],
symmetry->rot[j]);
for (k = 0; k < 3; k++) {
tmp_trans = symmetry->trans[j][k] + shift[i][k];
symmetry->trans[(i+1) * size + j][k] = tmp_trans;
}
}
}
}
/* Reduce translations into -0 < trans < 1.0 */
for (i = 0; i < multi; i++) {
for (j = 0; j < size; j++) {
for (k = 0; k < 3; k++) {
tmp_trans = symmetry->trans[i * size + j][k];
tmp_trans -= mat_Nint(tmp_trans);
if (tmp_trans < 0) {
tmp_trans += 1.0;
}
symmetry->trans[i * size + j][k] = tmp_trans;
}
}
}
return symmetry;
}
/* (http://phonopy.sf.net/) */
static void test_tetrahedron_method(void)
{
printf("*** Example of tetrahedron method of NaCl to calculate DOS ***:\n");
printf("Read data from frequency.dat and write DOS to dos.dat.\n");
int i, j, k, l, q, r;
/* NaCl 20x20x20 mesh */
double lattice[3][3] = {
{0.000000000000000, 2.845150738087836, 2.845150738087836},
{2.845150738087836, 0.000000000000000, 2.845150738087836},
{2.845150738087836, 2.845150738087836, 0.000000000000000}
};
double position[][3] =
{{0, 0, 0},
{0.5, 0.5, 0.5}};
int types[] = {1, 2};
int num_atom = 2;
int m = 20;
int mesh[] = {m, m, m};
int num_gp = mesh[0] * mesh[1] * mesh[2];
int is_shift[] = {0, 0, 0};
int grid_address[num_gp][3];
int grid_mapping_table[num_gp];
int weights[num_gp];
int num_ir = spg_get_ir_reciprocal_mesh(grid_address,
grid_mapping_table,
mesh,
is_shift,
1,
lattice,
position,
types,
num_atom,
1e-5);
int ir_gp[num_ir];
int ir_weights[num_ir];
int gp_ir_index[num_gp];
int relative_grid_address[24][4][3];
double rec_lat[3][3];
FILE *fp;
char * line = NULL;
size_t len = 0;
ssize_t read;
double frequency[num_ir * num_atom * 3];
double max_f, min_f;
double t_omegas[24][4];
int g_addr[3];
int gp;
int num_freqs = 201;
double dos[num_freqs];
double integral_dos[num_freqs];
double omegas[num_freqs];
double iw;
for (i = 0; i < num_gp; i++) {
weights[i] = 0;
}
for (i = 0; i < num_gp; i++) {
weights[grid_mapping_table[i]]++;
}
j = 0;
for (i = 0; i < num_gp; i++) {
if (weights[i] != 0) {
ir_gp[j] = i;
ir_weights[j] = weights[i];
gp_ir_index[i] = j;
j++;
} else {
gp_ir_index[i] = gp_ir_index[grid_mapping_table[i]];
}
}
printf("Number of irreducible k-points: %d\n", num_ir);
mat_inverse_matrix_d3(rec_lat, lattice, 1e-5);
thm_get_relative_grid_address(relative_grid_address, rec_lat);
/* for (i = 0; i < 24; i++) { */
/* for (j = 0; j < 4; j++) { */
/* printf("[%2d %2d %2d] ", */
/* relative_grid_address[i][j][0], */
/* relative_grid_address[i][j][1], */
/* relative_grid_address[i][j][2]); */
/* } */
/* printf("\n"); */
/* } */
fp = fopen("frequency.dat", "r");
for (i = 0; i < num_ir * num_atom * 3; i++) {
read = getline(&line, &len, fp);
if (read == -1) {
break;
}
frequency[i] = strtod(line, NULL);
}
fclose(fp);
max_f = frequency[0];
min_f = frequency[0];
for (i = 0; i < num_ir * num_atom * 3; i++) {
if (max_f < frequency[i]) {
max_f = frequency[i];
}
if (min_f > frequency[i]) {
min_f = frequency[i];
}
}
printf("Number of frequencies: %d\n", i);
#pragma omp parallel for private(j, k, l, q, r, g_addr, gp, t_omegas, iw)
for (i = 0; i < num_freqs; i++) {
dos[i] = 0;
integral_dos[i] = 0;
omegas[i] = min_f + (max_f - min_f) / (num_freqs - 1) * i;
for (j = 0; j < num_ir; j++) {
for (k = 0; k < num_atom * 3; k++) {
for (l = 0; l < 24; l++) {
for (q = 0; q < 4; q++) {
for (r = 0; r < 3; r++) {
g_addr[r] = grid_address[ir_gp[j]][r] +
relative_grid_address[l][q][r];
}
gp = spg_get_grid_point_from_address(g_addr, mesh);
t_omegas[l][q] = frequency[gp_ir_index[gp] * num_atom * 3 + k];
}
}
iw = thm_get_integration_weight(omegas[i], t_omegas, 'J');
dos[i] += iw * ir_weights[j];
iw = thm_get_integration_weight(omegas[i], t_omegas, 'I');
integral_dos[i] += iw * ir_weights[j];
}
}
}
fp = fopen("dos.dat", "w");
for (i = 0; i < num_freqs; i++) {
fprintf(fp, "%f %f\n", omegas[i], dos[i] / num_gp);
}
fprintf(fp, "\n\n");
for (i = 0; i < num_freqs; i++) {
fprintf(fp, "%f %f\n", omegas[i], integral_dos[i] / num_gp);
}
fclose(fp);
}
static Symmetry * reduce_symmetry_in_frame(const int frame[3],
SPGCONST Symmetry *prim_sym,
SPGCONST int t_mat[3][3],
SPGCONST double lattice[3][3],
const int multiplicity,
const double symprec)
{
int i, j, k, l, num_trans, size_sym_orig;
Symmetry *symmetry, *t_sym;
double inv_tmat[3][3], tmp_mat[3][3], tmp_rot_d[3][3], tmp_lat_d[3][3], tmp_lat_i[3][3];
int tmp_rot_i[3][3];
VecDBL *pure_trans, *lattice_trans;
mat_cast_matrix_3i_to_3d(tmp_mat, t_mat);
mat_inverse_matrix_d3(inv_tmat, tmp_mat, symprec);
/* transformed lattice points */
lattice_trans = mat_alloc_VecDBL(frame[0]*frame[1]*frame[2]);
num_trans = 0;
for (i = 0; i < frame[0]; i++) {
for (j = 0; j < frame[1]; j++) {
for (k = 0; k < frame[2]; k++) {
lattice_trans->vec[num_trans][0] = i;
lattice_trans->vec[num_trans][1] = j;
lattice_trans->vec[num_trans][2] = k;
mat_multiply_matrix_vector_d3(lattice_trans->vec[num_trans],
inv_tmat,
lattice_trans->vec[num_trans]);
for (l = 0; l < 3; l++) {
/* t' = T^-1*t */
lattice_trans->vec[num_trans][l] = \
mat_Dmod1(lattice_trans->vec[num_trans][l]);
}
num_trans++;
}
}
}
/* transformed symmetry operations of primitive cell */
t_sym = sym_alloc_symmetry(prim_sym->size);
size_sym_orig = 0;
for (i = 0; i < prim_sym->size; i++) {
/* R' = T^-1*R*T */
mat_multiply_matrix_di3(tmp_mat, inv_tmat, prim_sym->rot[i]);
mat_multiply_matrix_di3(tmp_rot_d, tmp_mat, t_mat);
mat_cast_matrix_3d_to_3i(tmp_rot_i, tmp_rot_d);
mat_multiply_matrix_di3(tmp_lat_i, lattice, tmp_rot_i);
mat_multiply_matrix_d3(tmp_lat_d, lattice, tmp_rot_d);
if (mat_check_identity_matrix_d3(tmp_lat_i, tmp_lat_d, symprec)) {
mat_copy_matrix_i3(t_sym->rot[size_sym_orig], tmp_rot_i);
/* t' = T^-1*t */
mat_multiply_matrix_vector_d3(t_sym->trans[size_sym_orig],
inv_tmat, prim_sym->trans[i]);
size_sym_orig++;
}
}
/* reduce lattice points */
pure_trans = reduce_lattice_points(lattice,
lattice_trans,
symprec);
if (! (pure_trans->size == multiplicity)) {
symmetry = sym_alloc_symmetry(0);
goto ret;
}
/* copy symmetry operations upon lattice points */
symmetry = sym_alloc_symmetry(pure_trans->size * size_sym_orig);
for (i = 0; i < pure_trans->size; i++) {
for (j = 0; j < size_sym_orig; j++) {
mat_copy_matrix_i3(symmetry->rot[size_sym_orig * i + j],
t_sym->rot[j]);
mat_copy_vector_d3(symmetry->trans[size_sym_orig * i + j],
t_sym->trans[j]);
for (k = 0; k < 3; k++) {
symmetry->trans[size_sym_orig * i + j][k] += pure_trans->vec[i][k];
symmetry->trans[size_sym_orig * i + j][k] = \
mat_Dmod1(symmetry->trans[size_sym_orig * i + j][k]);
}
}
}
ret:
mat_free_VecDBL(lattice_trans);
mat_free_VecDBL(pure_trans);
sym_free_symmetry(t_sym);
return symmetry;
}
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;
}
/* Return NULL if failed */
static Symmetry * get_conventional_symmetry(SPGCONST double transform_mat[3][3],
const Centering centering,
const Symmetry *primitive_sym)
{
int i, j, k, multi, size;
double inv_tmat[3][3], shift[4][3];
double symmetry_rot_d3[3][3], primitive_sym_rot_d3[3][3];
Symmetry *symmetry;
symmetry = NULL;
size = primitive_sym->size;
switch (centering) {
case FACE:
if ((symmetry = sym_alloc_symmetry(size * 4)) == NULL) {
return NULL;
}
break;
case R_CENTER:
if ((symmetry = sym_alloc_symmetry(size * 3)) == NULL) {
return NULL;
}
break;
case BODY:
case A_FACE:
case B_FACE:
case C_FACE:
if ((symmetry = sym_alloc_symmetry(size * 2)) == NULL) {
return NULL;
}
break;
default:
if ((symmetry = sym_alloc_symmetry(size)) == NULL) {
return NULL;
}
break;
}
for (i = 0; i < size; i++) {
mat_cast_matrix_3i_to_3d(primitive_sym_rot_d3, primitive_sym->rot[i]);
/* C*S*C^-1: recover conventional cell symmetry operation */
mat_get_similar_matrix_d3(symmetry_rot_d3,
primitive_sym_rot_d3,
transform_mat,
0);
mat_cast_matrix_3d_to_3i(symmetry->rot[i], symmetry_rot_d3);
/* translation in conventional cell: C = B^-1*P */
mat_inverse_matrix_d3(inv_tmat, transform_mat, 0);
mat_multiply_matrix_vector_d3(symmetry->trans[i],
inv_tmat,
primitive_sym->trans[i]);
}
multi = 1;
if (centering != PRIMITIVE) {
if (centering != FACE && centering != R_CENTER) {
for (i = 0; i < 3; i++) { shift[0][i] = 0.5; } /* BASE */
if (centering == A_FACE) { shift[0][0] = 0; }
if (centering == B_FACE) { shift[0][1] = 0; }
if (centering == C_FACE) { shift[0][2] = 0; }
multi = 2;
}
if (centering == R_CENTER) {
shift[0][0] = 2. / 3;
shift[0][1] = 1. / 3;
shift[0][2] = 1. / 3;
shift[1][0] = 1. / 3;
shift[1][1] = 2. / 3;
shift[1][2] = 2. / 3;
multi = 3;
}
if (centering == FACE) {
shift[0][0] = 0;
shift[0][1] = 0.5;
shift[0][2] = 0.5;
shift[1][0] = 0.5;
shift[1][1] = 0;
shift[1][2] = 0.5;
shift[2][0] = 0.5;
shift[2][1] = 0.5;
shift[2][2] = 0;
multi = 4;
}
for (i = 0; i < multi - 1; i++) {
for (j = 0; j < size; j++) {
mat_copy_matrix_i3(symmetry->rot[(i+1) * size + j],
symmetry->rot[j]);
for (k = 0; k < 3; k++) {
symmetry->trans[(i+1) * size + j][k] =
symmetry->trans[j][k] + shift[i][k];
}
}
}
}
for (i = 0; i < multi; i++) {
for (j = 0; j < size; j++) {
for (k = 0; k < 3; k++) {
symmetry->trans[i * size + j][k] =
mat_Dmod1(symmetry->trans[i * size + j][k]);
}
}
}
return symmetry;
}
static Symmetry * reduce_symmetry_in_frame( const int frame[3],
SPGCONST Symmetry *prim_sym,
SPGCONST int t_mat[3][3],
SPGCONST double lattice[3][3],
const double symprec )
{
int i, j, k, l, n, num_op, is_found;
Symmetry *symmetry, *t_sym;
double inv_mat[3][3], tmp_mat[3][3];
VecDBL *t, *lattice_trans;
mat_cast_matrix_3i_to_3d( tmp_mat, t_mat );
mat_inverse_matrix_d3( inv_mat, tmp_mat, symprec );
/* transformed lattice points */
lattice_trans = mat_alloc_VecDBL( frame[0]*frame[1]*frame[2] );
n = 0;
for ( i = 0; i < frame[0]; i++ ) {
for ( j = 0; j < frame[1]; j++ ) {
for ( k = 0; k < frame[2]; k++ ) {
lattice_trans->vec[n][0] = i;
lattice_trans->vec[n][1] = j;
lattice_trans->vec[n][2] = k;
mat_multiply_matrix_vector_d3( lattice_trans->vec[n],
inv_mat,
lattice_trans->vec[n] );
for ( l = 0; l < 3; l++ ) {
/* t' = T^-1*t */
lattice_trans->vec[n][l] = mat_Dmod1( lattice_trans->vec[n][l] );
}
n++;
}
}
}
/* transformed symmetry operations of primitive cell */
t_sym = sym_alloc_symmetry( prim_sym->size );
for ( i = 0; i < prim_sym->size; i++ ) {
/* R' = T^-1*R*T */
mat_multiply_matrix_di3( tmp_mat, inv_mat, prim_sym->rot[i] );
mat_multiply_matrix_di3( tmp_mat, tmp_mat, t_mat );
mat_cast_matrix_3d_to_3i( t_sym->rot[i], tmp_mat );
/* t' = T^-1*t */
mat_multiply_matrix_vector_d3( t_sym->trans[i], inv_mat, prim_sym->trans[ i ] );
}
/* reduce lattice points */
num_op = 0;
t = mat_alloc_VecDBL( lattice_trans->size );
for ( i = 0; i < lattice_trans->size; i++ ) {
is_found = 0;
for ( j = 0; j < num_op; j++ ) {
if ( cel_is_overlap( lattice_trans->vec[i], t->vec[j], lattice, symprec ) ) {
is_found = 1;
break;
}
}
if ( ! is_found ) {
mat_copy_vector_d3( t->vec[num_op], lattice_trans->vec[i] );
num_op++;
}
}
/* copy symmetry operations upon lattice points */
symmetry = sym_alloc_symmetry( num_op * t_sym->size );
for ( i = 0; i < num_op; i++ ) {
for ( j = 0; j < t_sym->size; j++ ) {
mat_copy_matrix_i3( symmetry->rot[ t_sym->size * i + j ], t_sym->rot[j] );
mat_copy_vector_d3( symmetry->trans[ t_sym->size * i + j ], t_sym->trans[j] );
for ( k = 0; k < 3; k++ ) {
symmetry->trans[ t_sym->size * i + j ][k] += t->vec[i][k];
symmetry->trans[ t_sym->size * i + j ][k] = \
mat_Dmod1( symmetry->trans[ t_sym->size * i + j ][k] );
}
}
}
mat_free_VecDBL( t );
sym_free_symmetry( t_sym );
return symmetry;
}
/* Return 0 if failed */
static int get_primitive_lattice_vectors(double prim_lattice[3][3],
const VecDBL * vectors,
SPGCONST Cell * cell,
const double symprec)
{
int i, j, k, size;
double initial_volume, volume;
double relative_lattice[3][3], min_vectors[3][3], tmp_lattice[3][3];
double inv_mat_dbl[3][3];
int inv_mat_int[3][3];
debug_print("get_primitive_lattice_vectors:\n");
size = vectors->size;
initial_volume = mat_Dabs(mat_get_determinant_d3(cell->lattice));
/* check volumes of all possible lattices, find smallest volume */
for (i = 0; i < size; i++) {
for (j = i + 1; j < size; j++) {
for (k = j + 1; k < size; k++) {
mat_multiply_matrix_vector_d3(tmp_lattice[0],
cell->lattice,
vectors->vec[i]);
mat_multiply_matrix_vector_d3(tmp_lattice[1],
cell->lattice,
vectors->vec[j]);
mat_multiply_matrix_vector_d3(tmp_lattice[2],
cell->lattice,
vectors->vec[k]);
volume = mat_Dabs(mat_get_determinant_d3(tmp_lattice));
if (volume > symprec) {
if (mat_Nint(initial_volume / volume) == size-2) {
mat_copy_vector_d3(min_vectors[0], vectors->vec[i]);
mat_copy_vector_d3(min_vectors[1], vectors->vec[j]);
mat_copy_vector_d3(min_vectors[2], vectors->vec[k]);
goto ret;
}
}
}
}
}
/* Not found */
warning_print("spglib: Primitive lattice vectors cound not be found ");
warning_print("(line %d, %s).\n", __LINE__, __FILE__);
return 0;
/* Found */
ret:
for (i = 0; i < 3; i++) {
for (j = 0; j < 3; j++) {
relative_lattice[j][i] = min_vectors[i][j];
}
}
mat_inverse_matrix_d3(inv_mat_dbl, relative_lattice, 0);
mat_cast_matrix_3d_to_3i(inv_mat_int, inv_mat_dbl);
if (abs(mat_get_determinant_i3(inv_mat_int)) == size-2) {
mat_cast_matrix_3i_to_3d(inv_mat_dbl, inv_mat_int);
mat_inverse_matrix_d3(relative_lattice, inv_mat_dbl, 0);
} else {
warning_print("spglib: Primitive lattice cleaning is incomplete ");
warning_print("(line %d, %s).\n", __LINE__, __FILE__);
}
mat_multiply_matrix_d3(prim_lattice, cell->lattice, relative_lattice);
return 1;
}
/* Return 0 if failed */
static int match_hall_symbol_db(double origin_shift[3],
double lattice[3][3],
const int hall_number,
const int pointgroup_number,
const Holohedry holohedry,
const Centering centering,
SPGCONST Symmetry *symmetry,
const double symprec)
{
int is_found, num_hall_types;
SpacegroupType spacegroup_type;
Symmetry * changed_symmetry;
double changed_lattice[3][3], inv_lattice[3][3], transform_mat[3][3];
changed_symmetry = NULL;
spacegroup_type = spgdb_get_spacegroup_type(hall_number);
num_hall_types = (spacegroup_to_hall_number[spacegroup_type.number] -
spacegroup_to_hall_number[spacegroup_type.number - 1]);
if (pointgroup_number != spacegroup_type.pointgroup_number) {
goto err;
}
switch (holohedry) {
case MONOCLI:
if (match_hall_symbol_db_monocli(origin_shift,
lattice,
hall_number,
num_hall_types,
centering,
symmetry,
symprec)) {return 1;}
break;
case ORTHO:
if (spacegroup_type.number == 48 ||
spacegroup_type.number == 50 ||
spacegroup_type.number == 59 ||
spacegroup_type.number == 68 ||
spacegroup_type.number == 70) { /* uncount origin shift */
num_hall_types /= 2;
}
if (num_hall_types == 1) {
if (match_hall_symbol_db_ortho(origin_shift,
lattice,
hall_number,
centering,
symmetry,
6,
symprec)) {return 1;}
break;
}
if (num_hall_types == 2) {
if (match_hall_symbol_db_ortho(origin_shift,
lattice,
hall_number,
centering,
symmetry,
3,
symprec)) {return 1;}
break;
}
if (num_hall_types == 3) {
mat_copy_matrix_d3(changed_lattice, lattice);
if (! match_hall_symbol_db_ortho
(origin_shift,
changed_lattice,
spacegroup_to_hall_number[spacegroup_type.number - 1],
centering,
symmetry,
0,
symprec)) {break;}
mat_inverse_matrix_d3(inv_lattice, lattice, 0);
mat_multiply_matrix_d3(transform_mat, inv_lattice, changed_lattice);
if ((changed_symmetry = get_conventional_symmetry(transform_mat,
PRIMITIVE,
symmetry)) == NULL) {
goto err;
}
is_found = match_hall_symbol_db_ortho(origin_shift,
changed_lattice,
hall_number,
centering,
changed_symmetry,
2,
symprec);
sym_free_symmetry(changed_symmetry);
changed_symmetry = NULL;
if (is_found) {
mat_copy_matrix_d3(lattice, changed_lattice);
return 1;
}
break;
}
if (num_hall_types == 6) {
if (match_hall_symbol_db_ortho(origin_shift,
lattice,
hall_number,
centering,
symmetry,
1,
symprec)) {return 1;}
break;
}
break;
case CUBIC:
if (hal_match_hall_symbol_db(origin_shift,
lattice,
hall_number,
centering,
symmetry,
symprec)) {return 1;}
if (hall_number == 501) { /* Try another basis for No.205 */
mat_multiply_matrix_d3(changed_lattice,
lattice,
change_of_basis_501);
if ((changed_symmetry = get_conventional_symmetry(change_of_basis_501,
PRIMITIVE,
symmetry)) == NULL) {
goto err;
}
is_found = hal_match_hall_symbol_db(origin_shift,
changed_lattice,
hall_number,
PRIMITIVE,
changed_symmetry,
symprec);
sym_free_symmetry(changed_symmetry);
changed_symmetry = NULL;
if (is_found) {
mat_copy_matrix_d3(lattice, changed_lattice);
return 1;
}
}
break;
case TRIGO:
if (centering == R_CENTER) {
if (hall_number == 433 ||
hall_number == 436 ||
hall_number == 444 ||
hall_number == 450 ||
hall_number == 452 ||
hall_number == 458 ||
hall_number == 460) {
mat_multiply_matrix_d3(changed_lattice,
lattice,
hR_to_hP);
if ((changed_symmetry = get_conventional_symmetry(hR_to_hP,
R_CENTER,
symmetry)) == NULL) {
goto err;
}
is_found = hal_match_hall_symbol_db(origin_shift,
changed_lattice,
hall_number,
centering,
changed_symmetry,
symprec);
sym_free_symmetry(changed_symmetry);
changed_symmetry = NULL;
if (is_found) {
mat_copy_matrix_d3(lattice, changed_lattice);
return 1;
}
}
}
/* Do not break for other trigonal cases */
default: /* HEXA, TETRA, TRICLI and rest of TRIGO */
if (hal_match_hall_symbol_db(origin_shift,
lattice,
hall_number,
centering,
symmetry,
symprec)) {
return 1;
}
break;
}
err:
return 0;
}
/* Return 0 if failed */
static int set_dataset(SpglibDataset * dataset,
SPGCONST Cell * cell,
SPGCONST Cell * primitive,
SPGCONST Spacegroup * spacegroup,
const int * mapping_table,
const double tolerance)
{
int i;
double inv_mat[3][3];
Cell *bravais;
Symmetry *symmetry;
bravais = NULL;
symmetry = NULL;
/* Spacegroup type, transformation matrix, origin shift */
dataset->n_atoms = cell->size;
dataset->spacegroup_number = spacegroup->number;
dataset->hall_number = spacegroup->hall_number;
strcpy(dataset->international_symbol, spacegroup->international_short);
strcpy(dataset->hall_symbol, spacegroup->hall_symbol);
strcpy(dataset->setting, spacegroup->setting);
mat_inverse_matrix_d3(inv_mat, cell->lattice, tolerance);
mat_multiply_matrix_d3(dataset->transformation_matrix,
inv_mat,
spacegroup->bravais_lattice);
mat_copy_vector_d3(dataset->origin_shift, spacegroup->origin_shift);
/* Symmetry operations */
if ((symmetry = ref_get_refined_symmetry_operations(cell,
primitive,
spacegroup,
tolerance)) == NULL) {
return 0;
}
dataset->n_operations = symmetry->size;
if ((dataset->rotations =
(int (*)[3][3]) malloc(sizeof(int[3][3]) * dataset->n_operations))
== NULL) {
warning_print("spglib: Memory could not be allocated.");
goto err;
}
if ((dataset->translations =
(double (*)[3]) malloc(sizeof(double[3]) * dataset->n_operations))
== NULL) {
warning_print("spglib: Memory could not be allocated.");
goto err;
}
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]);
}
/* Wyckoff positions */
if ((dataset->wyckoffs = (int*) malloc(sizeof(int) * dataset->n_atoms))
== NULL) {
warning_print("spglib: Memory could not be allocated.");
goto err;
}
if ((dataset->equivalent_atoms =
(int*) malloc(sizeof(int) * dataset->n_atoms))
== NULL) {
warning_print("spglib: Memory could not be allocated.");
goto err;
}
if ((bravais = ref_get_Wyckoff_positions(dataset->wyckoffs,
dataset->equivalent_atoms,
primitive,
cell,
spacegroup,
symmetry,
mapping_table,
tolerance)) == NULL) {
goto err;
}
dataset->n_brv_atoms = bravais->size;
mat_copy_matrix_d3(dataset->brv_lattice, bravais->lattice);
if ((dataset->brv_positions =
(double (*)[3]) malloc(sizeof(double[3]) * dataset->n_brv_atoms))
== NULL) {
warning_print("spglib: Memory could not be allocated.");
goto err;
}
if ((dataset->brv_types = (int*) malloc(sizeof(int) * dataset->n_brv_atoms))
== NULL) {
warning_print("spglib: Memory could not be allocated.");
goto err;
}
for (i = 0; i < dataset->n_brv_atoms; i++) {
mat_copy_vector_d3(dataset->brv_positions[i], bravais->position[i]);
dataset->brv_types[i] = bravais->types[i];
}
cel_free_cell(bravais);
sym_free_symmetry(symmetry);
return 1;
err:
if (dataset->brv_positions != NULL) {
free(dataset->brv_positions);
dataset->brv_positions = NULL;
}
if (bravais != NULL) {
cel_free_cell(bravais);
}
if (dataset->equivalent_atoms != NULL) {
free(dataset->equivalent_atoms);
dataset->equivalent_atoms = NULL;
}
if (dataset->wyckoffs != NULL) {
free(dataset->wyckoffs);
dataset->wyckoffs = NULL;
}
if (dataset->translations != NULL) {
free(dataset->translations);
dataset->translations = NULL;
}
if (dataset->rotations != NULL) {
free(dataset->rotations);
dataset->rotations = NULL;
}
if (symmetry != NULL) {
sym_free_symmetry(symmetry);
}
return 0;
}
