def port(picklefile):
picklefile = Path(picklefile)
name = picklefile.name
vibname, key, pckl = name.rsplit('.', 3)
assert pckl == 'pckl'
cache = MultiFileJSONCache(picklefile.parent / vibname)
obj = pickle.loads(picklefile.read_bytes())
if isinstance(obj, np.ndarray): # vibrations
dct = {'forces': obj}
else: # Infrared
forces, dipole = obj
assert isinstance(forces, np.ndarray), f'not supported: {type(forces)}'
assert isinstance(dipole, np.ndarray), f'not supported: {type(dipole)}'
dct = {'forces': forces, 'dipole': dipole}
outfilename = cache._filename(key)
if key in cache:
del cache[key]
cache[key] = dct
print(f'wrote {picklefile} ==> {outfilename}')
def __init__(self,
atoms,
calc=None,
supercell=(1, 1, 1),
name=None,
delta=0.01,
center_refcell=False):
"""Init with an instance of class ``Atoms`` and a calculator.
Parameters:
atoms: Atoms object
The atoms to work on.
calc: Calculator
Calculator for the supercell calculation.
supercell: tuple
Size of supercell given by the number of repetitions (l, m, n) of
the small unit cell in each direction.
name: str
Base name to use for files.
delta: float
Magnitude of displacement in Ang.
center_refcell: bool
Reference cell in which the atoms will be displaced. If False, then
corner cell in supercell is used. If True, then cell in the center
of the supercell is used.
"""
# Store atoms and calculator
self.atoms = atoms
self.calc = calc
# Displace all atoms in the unit cell by default
self.indices = np.arange(len(atoms))
self.name = name
self.delta = delta
self.center_refcell = center_refcell
self.supercell = supercell
self.cache = MultiFileJSONCache('phonons-cache')
def cache():
return MultiFileJSONCache('cache')
def __init__(self, name):
self.cache = MultiFileJSONCache(name)