def row_to_dict(self, row):
if len(row) == 26:
row = self._old2new(row)
dct = {
'id': row[0],
'unique_id': row[1],
'ctime': row[2],
'mtime': row[3],
'user': row[4],
'numbers': deblob(row[5], np.int32),
'positions': deblob(row[6], shape=(-1, 3)),
'cell': deblob(row[7], shape=(3, 3)),
'pbc': (row[8] & np.array([1, 2, 4])).astype(bool)
}
if row[9] is not None:
dct['initial_magmoms'] = deblob(row[9])
if row[10] is not None:
dct['initial_charges'] = deblob(row[10])
if row[11] is not None:
dct['masses'] = deblob(row[11])
if row[12] is not None:
dct['tags'] = deblob(row[12], np.int32)
if row[13] is not None:
dct['momenta'] = deblob(row[13], shape=(-1, 3))
if row[14] is not None:
dct['constraints'] = decode(row[14])
if row[15] is not None:
dct['calculator'] = row[15]
dct['calculator_parameters'] = decode(row[16])
if row[17] is not None:
dct['energy'] = row[17]
if row[18] is not None:
dct['free_energy'] = row[18]
if row[19] is not None:
dct['forces'] = deblob(row[19], shape=(-1, 3))
if row[20] is not None:
dct['stress'] = deblob(row[20])
if row[21] is not None:
dct['dipole'] = deblob(row[21])
if row[22] is not None:
dct['magmoms'] = deblob(row[22])
if row[23] is not None:
dct['magmom'] = deblob(row[23])[0]
if row[24] is not None:
dct['charges'] = deblob(row[24])
for key, column in zip(['keywords', 'key_value_pairs', 'data'],
row[25:28]):
x = decode(column)
if x:
dct[key] = x
return dct
def row_to_dict(self, row):
if len(row) == 26:
row = self._old2new(row)
dct = {'id': row[0],
'unique_id': row[1],
'ctime': row[2],
'mtime': row[3],
'user': row[4],
'numbers': deblob(row[5], np.int32),
'positions': deblob(row[6], shape=(-1, 3)),
'cell': deblob(row[7], shape=(3, 3)),
'pbc': (row[8] & np.array([1, 2, 4])).astype(bool)}
if row[9] is not None:
dct['initial_magmoms'] = deblob(row[9])
if row[10] is not None:
dct['initial_charges'] = deblob(row[10])
if row[11] is not None:
dct['masses'] = deblob(row[11])
if row[12] is not None:
dct['tags'] = deblob(row[12], np.int32)
if row[13] is not None:
dct['momenta'] = deblob(row[13], shape=(-1, 3))
if row[14] is not None:
dct['constraints'] = decode(row[14])
if row[15] is not None:
dct['calculator'] = row[15]
dct['calculator_parameters'] = decode(row[16])
if row[17] is not None:
dct['energy'] = row[17]
if row[18] is not None:
dct['free_energy'] = row[18]
if row[19] is not None:
dct['forces'] = deblob(row[19], shape=(-1, 3))
if row[20] is not None:
dct['stress'] = deblob(row[20])
if row[21] is not None:
dct['dipole'] = deblob(row[21])
if row[22] is not None:
dct['magmoms'] = deblob(row[22])
if row[23] is not None:
dct['magmom'] = deblob(row[23])[0]
if row[24] is not None:
dct['charges'] = deblob(row[24])
for key, column in zip(['keywords', 'key_value_pairs', 'data'],
row[25:28]):
x = decode(column)
if x:
dct[key] = x
return dct
def _old2new(self, row):
if not self._allow_reading_old_format:
raise IOError('Please convert to new format. ' +
'Use: python -m ase.db.convert ' + self.filename)
if len(row) == 26:
extra = decode(row[25])
return row[:-1] + (encode(
extra['keywords']), encode(
extra['key_value_pairs']), encode(extra['data']), 42)
else:
keywords = decode(row[-4])
kvp = decode(row[-3])
kvp.update(dict((keyword, 1) for keyword in keywords))
return row[:-4] + (encode(kvp), ) + row[-2:]
def _old2new(self, row):
if not self._allow_reading_old_format:
raise IOError('Please convert to new format. ' +
'Use: python -m ase.db.convert ' + self.filename)
if len(row) == 26:
extra = decode(row[25])
return row[:-1] + (encode(extra['keywords']),
encode(extra['key_value_pairs']),
encode(extra['data']),
42)
else:
keywords = decode(row[-4])
kvp = decode(row[-3])
kvp.update(dict((keyword, 1) for keyword in keywords))
return row[:-4] + (encode(kvp),) + row[-2:]
def _old2new(self, row):
if not self._allow_reading_old_format:
raise IOError('Please convert to new format. ' +
'Use: python -m ase.db.convert ' + self.filename)
extra = decode(row[25])
return row[:-1] + (encode(
extra['keywords']), encode(
extra['key_value_pairs']), encode(extra['data']), 42)
def _old2new(self, row):
if not self._allow_reading_old_format:
raise IOError('Please convert to new format. ' +
'Use: python -m ase.db.convert ' + self.filename)
extra = decode(row[25])
return row[:-1] + (encode(extra['keywords']),
encode(extra['key_value_pairs']),
encode(extra['data']),
42)
def _read_data(self, item):
self.fd.seek(self.offsets[item])
size = np.fromfile(self.fd, np.int64, 1)[0]
data = decode(self.fd.read(size).decode())
return data
def _read_data(self, item):
self.fd.seek(self.offsets[item])
size = np.fromfile(self.fd, np.int64, 1)[0]
data = decode(self.fd.read(size).decode())
return data