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 test_overrides(self):
file = File()
self.assertFalse(file)
file[2] = ' inserted line '
self.assertEqual(file.lines, ['', '', ' inserted line '])
file[1] = 'add this line\n and this one where index 1 was'
self.assertEqual(file.lines, [
'', 'add this line', ' and this one where index 1 was',
' inserted line '
])
file[1] = 'replaced add this line'
self.assertEqual(file.lines, [
'', 'replaced add this line', ' and this one where index 1 was',
' inserted line '
])
self.assertEqual(
file.lines[1:3],
['replaced add this line', ' and this one where index 1 was'])
del file[1]
del file[0:2]
self.assertEqual(file.lines, [' inserted line '])
self.assertFalse("home is where the heart is" in file)
self.assertTrue("line" in file)
file += "new line added"
self.assertEqual(file.lines, [' inserted line ', 'new line added'])
file.insert(0, 'inserted at beginning')
file.insert(2, 'right before new line added line')
self.assertEqual(file.lines, [
'inserted at beginning', ' inserted line ',
'right before new line added line', 'new line added'
])
self.assertTrue(file)
self.assertEqual(len(file), 4)
l = [
'inserted at beginning', ' inserted line ',
'right before new line added line', 'new line added'
]
for x, item in enumerate(file):
self.assertEqual(item, l[x])