def set_ase(self, aseatoms):
"""
Set the contents of the CifData starting from an ASE atoms object
:param aseatoms: the ASE atoms object
"""
import tempfile
cif = cif_from_ase(aseatoms)
with tempfile.NamedTemporaryFile() as f:
with HiddenPrints():
f.write(pycifrw_from_cif(cif, loops=ase_loops).WriteOut())
f.flush()
self.set_file(f.name)
def set_values(self, values):
"""
Set internal representation to `values`.
Warning: This also writes a new CIF file.
:param values: PyCifRW CifFile object
.. note:: requires PyCifRW module.
"""
import tempfile
with tempfile.NamedTemporaryFile() as f:
with HiddenPrints():
f.write(values.WriteOut())
f.flush()
self.set_file(f.name)
self._values = values
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'), {}