def convert_phonopy_atoms_to_structure(phonopy_atoms_structure):
"""
Converts phonopy's representation of a structure to an instance of Structure.
"""
temporary_write_path = Path.get_temporary_path()
Path.validate_does_not_exist(temporary_write_path)
Path.validate_writeable(temporary_write_path)
write_vasp(temporary_write_path, phonopy_atoms_structure)
species_list = convert_phonopy_symbols_to_unique_species_list(
phonopy_atoms_structure.symbols)
structure_poscar_file = File(temporary_write_path)
structure_poscar_file.insert(
5, " ".join(species_list)) #phonopy uses bad poscar format
structure_poscar_file.write_to_path()
final_structure = Structure(temporary_write_path)
Path.remove(temporary_write_path)
Structure.validate(final_structure)
return final_structure
def convert_structure_to_phonopy_atoms(structure):
"""
Takes structure, a Structure instance, and returns a PhonopyAtoms class (phonopy's representation of structures)
"""
temporary_write_path = Path.get_temporary_path()
Structure.validate(structure)
Path.validate_does_not_exist(temporary_write_path)
Path.validate_writeable(temporary_write_path)
structure.to_poscar_file_path(temporary_write_path)
phonopy_structure = read_vasp(temporary_write_path)
Path.remove(temporary_write_path)
return phonopy_structure
def delete_big_vasp_files_if_complete(self): if self.complete: for file_name in ['WAVECAR', 'CHG', 'CHGCAR', 'vasprun.xml']: if Path.exists(self.get_extended_path(file_name)): Path.remove(self.get_extended_path(file_name))
def delete_wavecar_if_complete(self):
if Path.exists(self.get_extended_path('WAVECAR')) and self.complete:
Path.remove(self.get_extended_path('WAVECAR'))