def _prepare_cif(self, trajectory_index=None):
"""
Write the given trajectory to a string of format CIF.
"""
import CifFile
from aiida.orm.data.cif \
import ase_loops, cif_from_ase, pycifrw_from_cif
cif = ""
indices = range(self.numsteps)
if trajectory_index is not None:
indices = [trajectory_index]
for idx in indices:
structure = self.get_step_structure(idx)
ciffile = pycifrw_from_cif(cif_from_ase(structure.get_ase()),
ase_loops)
cif = cif + ciffile.WriteOut()
return cif
def _prepare_cif(self, trajectory_index=None, main_file_name=""):
"""
Write the given trajectory to a string of format CIF.
"""
import CifFile
from aiida.orm.data.cif \
import ase_loops, cif_from_ase, pycifrw_from_cif
from aiida.common.utils import HiddenPrints
cif = ""
indices = range(self.numsteps)
if trajectory_index is not None:
indices = [trajectory_index]
for idx in indices:
structure = self.get_step_structure(idx)
ciffile = pycifrw_from_cif(cif_from_ase(structure.get_ase()),
ase_loops)
with HiddenPrints():
cif = cif + ciffile.WriteOut()
return cif.encode('utf-8'), {}
def add_metadata_inline(what, node=None, parameters=None, args=None):
"""
Add metadata of original exported node to the produced TCOD CIF.
:param what: an original exported node.
:param node: a :py:class:`aiida.orm.data.cif.CifData` instance.
:param parameters: a :py:class:`aiida.orm.data.parameter.ParameterData`
instance, produced by the same calculation as the original exported
node.
:param args: a :py:class:`aiida.orm.data.parameter.ParameterData`
instance, containing parameters for the control of metadata
collection and inclusion in the produced
:py:class:`aiida.orm.data.cif.CifData`.
:return: dict with :py:class:`aiida.orm.data.cif.CifData`
:raises ValueError: if tags present in
``args.get_dict()['additional_tags']`` are not valid CIF tags.
.. note:: can be used as inline calculation.
"""
from aiida.orm.data.cif import pycifrw_from_cif
CifData = DataFactory('cif')
if not node:
node = what
calc = _get_calculation(what)
datablocks = []
loops = {}
dataname = node.values.keys()[0]
datablock = dict()
for tag in node.values[dataname].keys():
datablock[tag] = node.values[dataname][tag]
datablocks.append(datablock)
for loop in node.values[dataname].loops:
loops[loop.keys()[0]] = loop.keys()
# Unpacking the kwargs from ParameterData
kwargs = {}
additional_tags = {}
datablock_names = None
if args:
kwargs = args.get_dict()
additional_tags = kwargs.pop('additional_tags', {})
datablock_names = kwargs.pop('datablock_names', None)
tags = _collect_tags(what, calc, parameters=parameters, **kwargs)
loops.update(tcod_loops)
for datablock in datablocks:
for k, v in dict(tags.items() + additional_tags.items()).iteritems():
if not k.startswith('_'):
raise ValueError("Tag '{}' does not seem to start with "
"an underscode ('_'): all CIF tags must "
"start with underscores".format(k))
datablock[k] = v
values = pycifrw_from_cif(datablocks, loops, names=datablock_names)
cif = CifData(values=values)
return {'cif': cif}
