mirror of https://github.com/phonopy/phonopy.git
Some refactoring and minor fixes
This commit is contained in:
parent
e37dec8ffc
commit
918b07e194
20
c/_phonopy.c
20
c/_phonopy.c
|
@ -444,7 +444,6 @@ static PyObject * py_gsv_set_smallest_vectors(PyObject *self, PyObject *args)
|
|||
reduced_basis = (double(*)[3])PyArray_DATA(py_reduced_basis);
|
||||
trans_mat = (int(*)[3])PyArray_DATA(py_trans_mat);
|
||||
|
||||
|
||||
gsv_set_smallest_vectors(smallest_vectors,
|
||||
multiplicity,
|
||||
pos_to,
|
||||
|
@ -1295,16 +1294,14 @@ static PyObject * py_get_tetrahedra_frequenies(PyObject *self, PyObject *args)
|
|||
|
||||
double* freq_tetras;
|
||||
size_t* grid_points;
|
||||
int num_gp_in;
|
||||
int* mesh;
|
||||
int (*grid_address)[3];
|
||||
size_t* gp_ir_index;
|
||||
int (*relative_grid_address)[3];
|
||||
double* frequencies;
|
||||
int num_band;
|
||||
|
||||
int is_shift[3] = {0, 0, 0};
|
||||
size_t i, j, k, gp;
|
||||
size_t i, j, k, gp, num_gp_in, num_band;
|
||||
int g_addr[3];
|
||||
int address_double[3];
|
||||
|
||||
|
@ -1321,13 +1318,13 @@ static PyObject * py_get_tetrahedra_frequenies(PyObject *self, PyObject *args)
|
|||
|
||||
freq_tetras = (double*)PyArray_DATA(py_freq_tetras);
|
||||
grid_points = (size_t*)PyArray_DATA(py_grid_points);
|
||||
num_gp_in = (int)PyArray_DIMS(py_grid_points)[0];
|
||||
num_gp_in = PyArray_DIMS(py_grid_points)[0];
|
||||
mesh = (int*)PyArray_DATA(py_mesh);
|
||||
grid_address = (int(*)[3])PyArray_DATA(py_grid_address);
|
||||
gp_ir_index = (size_t*)PyArray_DATA(py_gp_ir_index);
|
||||
relative_grid_address = (int(*)[3])PyArray_DATA(py_relative_grid_address);
|
||||
frequencies = (double*)PyArray_DATA(py_frequencies);
|
||||
num_band = (int)PyArray_DIMS(py_frequencies)[1];
|
||||
num_band = PyArray_DIMS(py_frequencies)[1];
|
||||
|
||||
for (i = 0; i < num_gp_in; i++) {
|
||||
#pragma omp parallel for private(k, g_addr, gp, address_double)
|
||||
|
@ -1363,13 +1360,10 @@ static PyObject * py_tetrahedron_method_dos(PyObject *self, PyObject *args)
|
|||
double *dos;
|
||||
int* mesh;
|
||||
double* freq_points;
|
||||
int num_freq_points;
|
||||
double* frequencies;
|
||||
double* coef;
|
||||
int (*grid_address)[3];
|
||||
size_t num_gp, num_ir_gp;
|
||||
int num_coef;
|
||||
int num_band;
|
||||
size_t num_gp, num_ir_gp, num_band, num_freq_points, num_coef;
|
||||
size_t *grid_mapping_table;
|
||||
int (*relative_grid_address)[4][3];
|
||||
|
||||
|
@ -1403,12 +1397,12 @@ static PyObject * py_tetrahedron_method_dos(PyObject *self, PyObject *args)
|
|||
dos = (double*)PyArray_DATA(py_dos);
|
||||
mesh = (int*)PyArray_DATA(py_mesh);
|
||||
freq_points = (double*)PyArray_DATA(py_freq_points);
|
||||
num_freq_points = (int)PyArray_DIMS(py_freq_points)[0];
|
||||
num_freq_points = (size_t)PyArray_DIMS(py_freq_points)[0];
|
||||
frequencies = (double*)PyArray_DATA(py_frequencies);
|
||||
num_ir_gp = (size_t)PyArray_DIMS(py_frequencies)[0];
|
||||
num_band = (int)PyArray_DIMS(py_frequencies)[1];
|
||||
num_band = (size_t)PyArray_DIMS(py_frequencies)[1];
|
||||
coef = (double*)PyArray_DATA(py_coef);
|
||||
num_coef = (int)PyArray_DIMS(py_coef)[1];
|
||||
num_coef = (size_t)PyArray_DIMS(py_coef)[1];
|
||||
grid_address = (int(*)[3])PyArray_DATA(py_grid_address);
|
||||
num_gp = (size_t)PyArray_DIMS(py_grid_address)[0];
|
||||
grid_mapping_table = (size_t*)PyArray_DATA(py_grid_mapping_table);
|
||||
|
|
|
@ -403,7 +403,8 @@ thm_get_dense_neighboring_grid_points(size_t neighboring_grid_points[],
|
|||
const size_t bz_map[])
|
||||
{
|
||||
int bzmesh[3], address_double[3], bz_address_double[3];
|
||||
size_t i, j, bz_gp, prod_bz_mesh;
|
||||
int i;
|
||||
size_t j, bz_gp, prod_bz_mesh;
|
||||
|
||||
prod_bz_mesh = 1;
|
||||
for (i = 0; i < 3; i++) {
|
||||
|
|
|
@ -533,7 +533,13 @@ def get_cell_from_disp_yaml(dataset):
|
|||
data_key = None
|
||||
pos_key = None
|
||||
|
||||
positions = [x[pos_key] for x in dataset[data_key]]
|
||||
try:
|
||||
positions = [x[pos_key] for x in dataset[data_key]]
|
||||
except KeyError:
|
||||
msg = ("\"disp.yaml\" format is too old. "
|
||||
"Please re-create it as \"phonopy_disp.yaml\" to contain "
|
||||
"supercell crystal structure information.")
|
||||
raise RuntimeError(msg)
|
||||
symbols = [x['symbol'] for x in dataset[data_key]]
|
||||
cell = PhonopyAtoms(cell=lattice,
|
||||
scaled_positions=positions,
|
||||
|
|
|
@ -345,16 +345,20 @@ def create_FORCE_SETS(interface_mode,
|
|||
print("NOTE:")
|
||||
print(" From phonopy v2.0, displacements are written into "
|
||||
"\"phonopy_disp.yaml\".")
|
||||
print(" \"disp.yaml\" is still supported for reading, but is "
|
||||
"deprecated.")
|
||||
print(" \"disp.yaml\" is still supported for reading except for "
|
||||
"Wien2k interface, ")
|
||||
print(" but is deprecated.")
|
||||
print('')
|
||||
if force_sets_zero_mode:
|
||||
print("Forces in %s are subtracted from forces in all "
|
||||
"other files." % force_filenames[0])
|
||||
|
||||
if disp_filename == 'disp.yaml':
|
||||
disp_dataset, supercell = parse_disp_yaml(filename=disp_filename,
|
||||
return_cell=True)
|
||||
if interface_mode == 'wein2k':
|
||||
disp_dataset, supercell = parse_disp_yaml(filename=disp_filename,
|
||||
return_cell=True)
|
||||
else:
|
||||
disp_dataset = parse_disp_yaml(filename=disp_filename)
|
||||
else:
|
||||
phpy = PhonopyYaml()
|
||||
phpy.read(disp_filename)
|
||||
|
|
Loading…
Reference in New Issue