Source code for aiida_crystal17.parsers.cry_ech3

#!/usr/bin/env python
# -*- coding: utf-8 -*-
#
# Copyright 2019 Chris Sewell
#
# This file is part of aiida-crystal17.
#
# This program is free software; you can redistribute it and/or modify
# it under the terms and conditions
# of version 3 of the GNU Lesser General Public License.
#
# This program is distributed in the hope that it will be useful,
# but WITHOUT ANY WARRANTY; without even the implied warranty of
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
# GNU Lesser General Public License for more details.
"""A parser to read output from a CRYSTAL17 DOSS run."""
import os
import traceback

from aiida.common import exceptions
from aiida.engine import ExitCode
from aiida.orm import Dict
from aiida.parsers.parser import Parser

from aiida_crystal17 import __version__
from aiida_crystal17.data.gcube import GaussianCube
from aiida_crystal17.parsers.raw.pbs import parse_pbs_stderr
from aiida_crystal17.parsers.raw.properties_stdout import read_properties_stdout


[docs]class CryEch3Parser(Parser): """Parser class for parsing outputs from CRYSTAL17 ``properties`` ECH3 computation."""
[docs] def parse(self, **kwargs): """Parse outputs, store results in database.""" try: output_folder = self.retrieved except exceptions.NotExistent: return self.exit_codes.ERROR_NO_RETRIEVED_FOLDER # parse stderr pbs_error = None sterr_file = self.node.get_option("scheduler_stderr") if sterr_file in output_folder.list_object_names(): with output_folder.open(sterr_file) as fileobj: pbs_exit_code = parse_pbs_stderr(fileobj) if pbs_exit_code: pbs_error = self.exit_codes[pbs_exit_code] # parse stdout file stdout_error = None stdout_data = {} stdout_fname = self.node.get_option("stdout_file_name") if stdout_fname not in self.retrieved.list_object_names(): stdout_error = self.exit_codes.ERROR_OUTPUT_FILE_MISSING else: with output_folder.open(stdout_fname) as handle: stdout_data = read_properties_stdout(handle.read()) stdout_exit_code = stdout_data.pop("exit_code", None) if stdout_exit_code: stdout_error = self.exit_codes[stdout_exit_code] # parse density file(s) density_error = None charge_cube = None spin_cube = None if "retrieved_temporary_folder" not in kwargs: density_error = self.exit_codes.ERROR_TEMP_FOLDER_MISSING else: temporary_folder = kwargs["retrieved_temporary_folder"] list_of_temp_files = os.listdir(temporary_folder) output_charge_fname = self.node.get_option("output_charge_fname") output_spin_fname = self.node.get_option("output_spin_fname") if output_charge_fname not in list_of_temp_files: density_error = self.exit_codes.ERROR_DENSITY_FILE_MISSING else: try: charge_cube = GaussianCube( os.path.join(temporary_folder, output_charge_fname) ) except Exception: traceback.print_exc() density_error = self.exit_codes.ERROR_PARSING_DENSITY_FILE if output_spin_fname in list_of_temp_files: try: spin_cube = GaussianCube( os.path.join(temporary_folder, output_spin_fname) ) except Exception: traceback.print_exc() density_error = self.exit_codes.ERROR_PARSING_DENSITY_FILE stdout_data["parser_version"] = str(__version__) stdout_data["parser_class"] = str(self.__class__.__name__) # log errors errors = stdout_data.get("errors", []) parser_errors = stdout_data.get("parser_errors", []) if parser_errors: self.logger.warning( "the parser raised the following errors:\n{}".format( "\n\t".join(parser_errors) ) ) if errors: self.logger.warning( "the calculation raised the following errors:\n{}".format( "\n\t".join(errors) ) ) # make output nodes self.out("results", Dict(dict=stdout_data)) if charge_cube: self.out("charge", charge_cube) if spin_cube: self.out("spin", spin_cube) if pbs_error is not None: return pbs_error if stdout_error is not None: return stdout_error if density_error is not None: return density_error return ExitCode()