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import os.path as op
from ase.db.row import AtomsRow
from ase.io.jsonio import read_json
class Collection:
"""Collection of atomic configurations and associated data.
Example of use:
>>> from ase.collections import s22
>>> len(s22)
22
>>> s22.names[:3]
['Ammonia_dimer', 'Water_dimer', 'Formic_acid_dimer']
>>> dimer = s22['Water_dimer']
>>> dimer.get_chemical_symbols()
['O', 'H', 'H', 'O', 'H', 'H']
>>> s22.data['Ammonia_dimer']
{'cc_energy': -0.1375}
>>> sum(len(atoms) for atoms in s22)
414
"""
def __init__(self, name):
"""Create a collection lazily.
Will read data from json file when needed.
A collection can be iterated over to get the Atoms objects and indexed
with names to get individual members.
Attributes:
name: str
Name of collection.
data: dict
Data dictionary.
filename: str
Location of json file.
names: list
Names of configurations in the collection.
"""
self.name = name
self._names = []
self._systems = {}
self._data = {}
self.filename = op.join(op.dirname(__file__), name + '.json')
def __getitem__(self, name):
self._read()
return self._systems[name].copy()
def has(self, name):
# Not __contains__() because __iter__ yields the systems.
self._read()
return name in self._systems
def __iter__(self):
for name in self.names:
yield self[name]
def __len__(self):
return len(self.names)
def __str__(self):
return '<{0}-collection, {1} systems: {2}, {3}, ...>'.format(
self.name, len(self), *self.names[:2])
def __repr__(self):
return 'Collection({0!r})'.format(self.name)
@property
def names(self):
self._read()
return list(self._names)
@property
def data(self):
self._read()
return self._data
def _read(self):
if self._names:
return
bigdct = read_json(self.filename)
for id in bigdct['ids']:
dct = bigdct[id]
kvp = dct['key_value_pairs']
name = str(kvp['name'])
self._names.append(name)
self._systems[name] = AtomsRow(dct).toatoms()
del kvp['name']
self._data[name] = dict((str(k), v) for k, v in kvp.items())
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