def set_extra(self, key, value):
"""Set an extra to the given value.
:param key: name of the extra
:param value: value of the extra
"""
if self.is_stored:
value = clean_value(value)
self._dbmodel.extras[key] = value
self._flush_if_stored({'extras'})
def set_attribute(self, key, value):
"""Set an attribute to the given value.
:param key: name of the attribute
:param value: value of the attribute
"""
if self.is_stored:
value = clean_value(value)
self._dbmodel.attributes[key] = value
self._flush_if_stored({'attributes'})
def _get_aiida_structure_pymatgen_inline(cif, **kwargs):
"""
Creates :py:class:`aiida.orm.nodes.data.structure.StructureData` using pymatgen.
:param occupancy_tolerance: If total occupancy of a site is between 1 and occupancy_tolerance,
the occupancies will be scaled down to 1.
:param site_tolerance: This tolerance is used to determine if two sites are sitting in the same position,
in which case they will be combined to a single disordered site. Defaults to 1e-4.
.. note:: requires pymatgen module.
"""
from pymatgen.io.cif import CifParser
from aiida.orm import Dict, StructureData
parameters = kwargs.get('parameters', {})
if isinstance(parameters, Dict):
# Note, if `parameters` is unstored, it might contain stored `Node` instances which might slow down the parsing
# enormously, because each time their value is used, a database call is made to refresh the value
parameters = clean_value(parameters.get_dict())
constructor_kwargs = {}
parameters['primitive'] = parameters.pop('primitive_cell', False)
for argument in ['occupancy_tolerance', 'site_tolerance']:
if argument in parameters:
constructor_kwargs[argument] = parameters.pop(argument)
with cif.open() as handle:
parser = CifParser(handle, **constructor_kwargs)
try:
structures = parser.get_structures(**parameters)
except ValueError:
# Verify whether the failure was due to wrong occupancy numbers
try:
constructor_kwargs['occupancy_tolerance'] = 1E10
with cif.open() as handle:
parser = CifParser(handle, **constructor_kwargs)
structures = parser.get_structures(**parameters)
except ValueError:
# If it still fails, the occupancies were not the reason for failure
raise ValueError(
'pymatgen failed to provide a structure from the cif file')
else:
# If it now succeeds, non-unity occupancies were the culprit
raise InvalidOccupationsError(
'detected atomic sites with an occupation number larger than the occupation tolerance'
)
return {'structure': StructureData(pymatgen_structure=structures[0])}
def reset_extras(self, extras):
"""Reset the extras.
.. note:: This will completely clear any existing extras and replace them with the new dictionary.
:param extras: a dictionary with the extras to set
"""
if self.is_stored:
extras = clean_value(extras)
self.dbmodel.extras = extras
self._flush_if_stored({'extras'})
def reset_attributes(self, attributes):
"""Reset the attributes.
.. note:: This will completely clear any existing attributes and replace them with the new dictionary.
:param attributes: a dictionary with the attributes to set
"""
if self.is_stored:
attributes = clean_value(attributes)
self.dbmodel.attributes = attributes
self._flush_if_stored({'attributes'})
def set_extra_many(self, extras):
"""Set multiple extras.
.. note:: This will override any existing extras that are present in the new dictionary.
:param extras: a dictionary with the extras to set
"""
if self.is_stored:
extras = {key: clean_value(value) for key, value in extras.items()}
for key, value in extras.items():
self.dbmodel.extras[key] = value
self._flush_if_stored({'extras'})
def set_attribute_many(self, attributes):
"""Set multiple attributes.
.. note:: This will override any existing attributes that are present in the new dictionary.
:param attributes: a dictionary with the attributes to set
"""
if self.is_stored:
attributes = {
key: clean_value(value)
for key, value in attributes.items()
}
for key, value in attributes.items():
# We need to use `self.dbmodel` without the underscore, because otherwise the second iteration will refetch
# what is in the database and we lose the initial changes.
self.dbmodel.attributes[key] = value
self._flush_if_stored({'attributes'})
def set_attribute_many(self, attributes):
"""Set multiple attributes.
.. note:: This will override any existing attributes that are present in the new dictionary.
:param attributes: a dictionary with the attributes to set
"""
if self.is_stored:
attributes = {
key: clean_value(value)
for key, value in attributes.items()
}
for key, value in attributes.items():
self.dbmodel.attributes[key] = value
self._flag_field('attributes')
self._flush_if_stored()
def _get_aiida_structure_ase_inline(cif, **kwargs):
"""
Creates :py:class:`aiida.orm.nodes.data.structure.StructureData` using ASE.
.. note:: unable to correctly import structures of alloys.
.. note:: requires ASE module.
"""
from aiida.orm import Dict, StructureData
parameters = kwargs.get('parameters', {})
if isinstance(parameters, Dict):
# Note, if `parameters` is unstored, it might contain stored `Node` instances which might slow down the parsing
# enormously, because each time their value is used, a database call is made to refresh the value
parameters = clean_value(parameters.get_dict())
parameters.pop('occupancy_tolerance', None)
parameters.pop('site_tolerance', None)
return {'structure': StructureData(ase=cif.get_ase(**parameters))}
def clean_values(self):
self._dbmodel.attributes = clean_value(self._dbmodel.attributes)
self._dbmodel.extras = clean_value(self._dbmodel.extras)
