def wulff(st, miller_list=None, e_surf_list=None):
from pymatgen.core.structure import Structure
stpm = st.convert2pymatgen()
lat = stpm.lattice
recp_lattice = stpm.lattice.reciprocal_lattice_crystallographic
recp = Structure(recp_lattice, ["H"], [[0, 0, 0]])
dire = Structure(stpm.lattice, ["H"], [[0, 0, 0]])
print(dire.get_space_group_info())
print(recp.get_space_group_info())
def wulff(st, miller_list=None, e_surf_list=None, show=0):
from pymatgen.core.structure import Structure
stpm = st.convert2pymatgen()
lat = stpm.lattice
recp_lattice = stpm.lattice.reciprocal_lattice_crystallographic
recp = Structure(recp_lattice, ["H"], [[0, 0, 0]])
dire = Structure(stpm.lattice, ["H"], [[0, 0, 0]])
print(dire.get_space_group_info())
print(recp.get_space_group_info())
# print(lat)
from pymatgen.analysis.wulff import WulffShape
WS = WulffShape(lat, miller_list, e_surf_list)
# print(dir(WS))
anisotropy = WS.anisotropy
weighted_surface_energy = WS.weighted_surface_energy
if show:
WS.show()
return anisotropy, weighted_surface_energy
def structure_parser_wrapper(structure:Structure,
is_primitive_cell=True,
fractional=True,
remove_unused_parameters=True) -> typing.Dict:
"""
Same as above but expects pymatgen.core.structure.Structure object
"""
if is_primitive_cell:
structure = structure.get_primitive_structure()
if fractional:
position_key = 'fractional'
positions = structure.frac_coords.tolist()
else:
position_key = 'xyz'
positions = structure.cart_coords.tolist()
sg = structure.get_space_group_info()
bravais = space_groups.space_group_to_bravais(sg[1])
lattice_parameters = lattice_parameters_from_cif(structure)
# Required for qCore input
if remove_unused_parameters:
lattice_parameters = remove_superflous_parameters(lattice_parameters, bravais)
species = [element_enum.value for element_enum in structure.species]
assert len(species) == len(positions)
crystal_data = {position_key: positions,
'species': species,
'lattice_parameters': lattice_parameters,
'space_group': sg,
'bravais': bravais,
'n_atoms': len(species)}
return crystal_data
