static PyObject * get_dataset(PyObject *self, PyObject *args)
{
int i, j, k, num_atom;
double symprec;
SpglibDataset *dataset;
PyArrayObject* lattice_vectors;
PyArrayObject* atomic_positions;
PyArrayObject* atom_types;
PyObject* array, *vec, *mat, *rot, *trans, *wyckoffs, *equiv_atoms;
double *p_lattice;
double *p_positions;
double lattice[3][3];
double (*positions)[3];
int *types_int;
int *types;
if (!PyArg_ParseTuple(args, "OOOd",
&lattice_vectors,
&atomic_positions,
&atom_types,
&symprec)) {
return NULL;
}
p_lattice = (double(*))lattice_vectors->data;
p_positions = (double(*))atomic_positions->data;
num_atom = atom_types->dimensions[0];
positions = (double(*)[3]) malloc(sizeof(double[3]) * num_atom);
types_int = (int*)atom_types->data;
types = (int*) malloc(sizeof(int) * num_atom);
set_spglib_cell(lattice, positions, types, num_atom,
p_lattice, p_positions, types_int);
dataset = spg_get_dataset(lattice, positions, types, num_atom, symprec);
free(types);
free(positions);
array = PyList_New(10);
/* Space group number, international symbol, hall symbol */
PyList_SetItem(array, 0, PyInt_FromLong((long) dataset->spacegroup_number));
PyList_SetItem(array, 1, PyString_FromString(dataset->international_symbol));
PyList_SetItem(array, 2, PyInt_FromLong((long) dataset->hall_number));
PyList_SetItem(array, 3, PyString_FromString(dataset->hall_symbol));
/* Transformation matrix */
mat = PyList_New(3);
for (i = 0; i < 3; i++) {
vec = PyList_New(3);
for (j = 0; j < 3; j++) {
PyList_SetItem(vec, j,
PyFloat_FromDouble(dataset->transformation_matrix[i][j]));
}
PyList_SetItem(mat, i, vec);
}
PyList_SetItem(array, 4, mat);
/* Origin shift */
vec = PyList_New(3);
for (i = 0; i < 3; i++) {
PyList_SetItem(vec, i, PyFloat_FromDouble(dataset->origin_shift[i]));
}
PyList_SetItem(array, 5, vec);
/* Rotation matrices */
rot = PyList_New(dataset->n_operations);
for (i = 0; i < dataset->n_operations; i++) {
mat = PyList_New(3);
for (j = 0; j < 3; j++) {
vec = PyList_New(3);
for (k = 0; k < 3; k++) {
PyList_SetItem(vec, k,
PyInt_FromLong((long) dataset->rotations[i][j][k]));
}
PyList_SetItem(mat, j, vec);
}
PyList_SetItem(rot, i, mat);
}
PyList_SetItem(array, 6, rot);
/* Translation vectors */
trans = PyList_New(dataset->n_operations);
for (i = 0; i < dataset->n_operations; i++) {
vec = PyList_New(3);
for (j = 0; j < 3; j++) {
PyList_SetItem(vec, j, PyFloat_FromDouble(dataset->translations[i][j]));
}
PyList_SetItem(trans, i, vec);
}
PyList_SetItem(array, 7, trans);
/* Wyckoff letters, Equivalent atoms */
wyckoffs = PyList_New(dataset->n_atoms);
equiv_atoms = PyList_New(dataset->n_atoms);
for (i = 0; i < dataset->n_atoms; i++) {
PyList_SetItem(wyckoffs, i, PyInt_FromLong((long) dataset->wyckoffs[i]));
PyList_SetItem(equiv_atoms, i,
PyInt_FromLong((long) dataset->equivalent_atoms[i]));
}
PyList_SetItem(array, 8, wyckoffs);
PyList_SetItem(array, 9, equiv_atoms);
spg_free_dataset(dataset);
return array;
}
static int test_spg_get_stabilized_reciprocal_mesh(void)
{
SpglibDataset *dataset;
double lattice[3][3] = {{4, 0, 0}, {0, 4, 0}, {0, 0, 3}};
double position[][3] =
{
{0, 0, 0},
{0.5, 0.5, 0.5},
{0.3, 0.3, 0},
{0.7, 0.7, 0},
{0.2, 0.8, 0.5},
{0.8, 0.2, 0.5},
};
int types[] = {1, 1, 2, 2, 2, 2};
int num_atom = 6;
dataset = spg_get_dataset(lattice,
position,
types,
num_atom,
1e-5);
if (dataset == NULL) {
return 1;
}
int m = 40;
int mesh[] = {m, m, m};
int is_shift[] = {1, 1, 1};
int grid_address[m * m * m][3];
int grid_mapping_table[m * m * m];
double q[] = {0, 0.5, 0.5};
printf("*** spg_get_stabilized_reciprocal_mesh of Rutile structure ***:\n");
int num_ir = spg_get_stabilized_reciprocal_mesh(grid_address,
grid_mapping_table,
mesh,
is_shift,
1,
dataset->n_operations,
dataset->rotations,
1,
(double(*)[3])q);
spg_free_dataset(dataset);
if (num_ir) {
printf("Number of irreducible k-points stabilized by q=(0, 1/2, 1/2) of Rutile with\n");
printf("40x40x40 Monkhorst-Pack mesh is %d (8000).\n", num_ir);
return 0;
} else {
return 1;
}
}
static int test_spg_get_hall_number_from_symmetry(void)
{
double lattice[3][3] = {{4, 0, 0}, {0, 4, 0}, {0, 0, 4}};
double position[][3] = {
{0, 0, 0},
{0.5, 0.5, 0.5}
};
int types[] = {1, 1};
int num_atom = 2;
double symprec = 1e-5;
int hall_number;
SpglibSpacegroupType spgtype;
SpglibDataset *dataset;
printf("*** spg_get_hall_number_from_symmetry ***:\n");
if ((dataset = spg_get_dataset(lattice,
position,
types,
num_atom,
symprec)) == NULL) {
return 0;
}
printf("hall_number = %d is found by spg_get_dataset.\n", dataset->hall_number);
hall_number = spg_get_hall_number_from_symmetry(dataset->rotations,
dataset->translations,
dataset->n_operations,
symprec);
printf("hall_number = %d is found by spg_get_hall_number_from_symmetry.\n",
hall_number);
if (hall_number == dataset->hall_number) {
spgtype = spg_get_spacegroup_type(hall_number);
if (spgtype.number) {
show_spacegroup_type(spgtype);
return 0;
} else {
return 1;
}
} else {
return 0;
}
}
void wrap_spg_get_syminfo(double flat_lattice[], double flat_position[], double dbl_types[], int num_atom, double tolerance, int dry_run)
{
if (dry_run == 1) return;
double lattice[3][3];
int i, j, n;
n = 0;
for (i = 0; i < 3; i++)
{
for ( j = 0; j < 3; j++)
{
lattice[i][j] = flat_lattice[n];
n++;
}
}
double position[num_atom][3];
i = 0;
j = 0;
n = 0;
for (i = 0; i < num_atom; i++)
{
for ( j = 0; j < 3; j++)
{
position[i][j] = flat_position[n];
n++;
}
}
int types[num_atom];
i = 0;
for (i = 0; i < num_atom; i++)
{
types[i] = (int) dbl_types[i];
}
SpglibDataset *dataset = spg_get_dataset(lattice, position, types, num_atom, tolerance);
EM_ASM_({
window.wrap_spg_handle_result($0, $1);
}, dataset->spacegroup_number, dataset->international_symbol);
static int show_spg_dataset(double lattice[3][3],
const double origin_shift[3],
double position[][3],
const int num_atom,
const int types[])
{
SpglibDataset *dataset;
char ptsymbol[6];
int pt_trans_mat[3][3];
int i, j;
const char *wl = "abcdefghijklmnopqrstuvwxyz";
for ( i = 0; i < num_atom; i++ ) {
for ( j = 0; j < 3; j++ ) {
position[i][j] += origin_shift[j];
}
}
dataset = spg_get_dataset(lattice,
position,
types,
num_atom,
1e-5);
if (dataset == NULL) {
return 1;
}
printf("International: %s (%d)\n", dataset->international_symbol, dataset->spacegroup_number );
printf("Hall symbol: %s\n", dataset->hall_symbol );
if (spg_get_pointgroup(ptsymbol,
pt_trans_mat,
dataset->rotations,
dataset->n_operations)) {
printf("Point group: %s\n", ptsymbol);
printf("Transformation matrix:\n");
for ( i = 0; i < 3; i++ ) {
printf("%f %f %f\n",
dataset->transformation_matrix[i][0],
dataset->transformation_matrix[i][1],
dataset->transformation_matrix[i][2]);
}
printf("Wyckoff letters:\n");
for ( i = 0; i < dataset->n_atoms; i++ ) {
printf("%c ", wl[dataset->wyckoffs[i]]);
}
printf("\n");
printf("Equivalent atoms:\n");
for (i = 0; i < dataset->n_atoms; i++) {
printf("%d ", dataset->equivalent_atoms[i]);
}
printf("\n");
for (i = 0; i < dataset->n_operations; i++) {
printf("--- %d ---\n", i + 1);
for (j = 0; j < 3; j++) {
printf("%2d %2d %2d\n",
dataset->rotations[i][j][0],
dataset->rotations[i][j][1],
dataset->rotations[i][j][2]);
}
printf("%f %f %f\n",
dataset->translations[i][0],
dataset->translations[i][1],
dataset->translations[i][2]);
}
spg_free_dataset(dataset);
return 0;
} else {
spg_free_dataset(dataset);
return 1;
}
}
