def _parse_trajectory(self, out_folder):
"""CP2K trajectory parser"""
from ase import Atoms
from aiida.orm import StructureData
from aiida_cp2k.utils import parse_cp2k_trajectory
# pylint: disable=protected-access
fname = self.node.process_class._DEFAULT_RESTART_FILE_NAME
if fname not in out_folder._repository.list_object_names():
raise Exception("parsing trajectory requested, but no trajectory file available")
# read restart file
abs_fn = os.path.join(out_folder._repository._get_base_folder().abspath, fname)
with io.open(abs_fn, mode="r", encoding="utf-8") as fobj:
atoms = Atoms(**parse_cp2k_trajectory(fobj))
return StructureData(ase=atoms)
def _parse_trajectory(self):
"""CP2K trajectory parser."""
from ase import Atoms
from aiida_cp2k.utils import parse_cp2k_trajectory
fname = self.node.process_class._DEFAULT_RESTART_FILE_NAME # pylint: disable=protected-access
# Check if the restart file is present.
if fname not in self.retrieved.list_object_names():
raise exceptions.NotExistent("No restart file available, so the output trajectory can't be extracted")
# Read the restart file.
try:
output_string = self.retrieved.get_object_content(fname)
except IOError:
return self.exit_codes.ERROR_OUTPUT_STDOUT_READ
return StructureData(ase=Atoms(**parse_cp2k_trajectory(output_string)))