Source code for aiida_crystal17.parsers.cry_ppan

#!/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 properties PPAN run."""
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.parsers.raw.crystal_ppan import parse_crystal_ppan
from aiida_crystal17.parsers.raw.pbs import parse_pbs_stderr
from aiida_crystal17.parsers.raw.properties_stdout import read_properties_stdout


[docs]class CryPpanParser(Parser): """Parser class for parsing outputs from CRYSTAL17 ``properties`` PPAN 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 PPAN.dat file ppan_error = None ppan_data = {} output_ppan_fname = self.node.get_option("output_ppan_fname") if output_ppan_fname not in output_folder.list_object_names(): ppan_error = self.exit_codes.ERROR_PPAN_FILE_MISSING else: try: with output_folder.open(output_ppan_fname) as handle: ppan_data = parse_crystal_ppan(handle.read()) except Exception: traceback.print_exc() ppan_error = self.exit_codes.ERROR_PARSING_PPAN_FILE final_data = self.merge_output_dicts(stdout_data, ppan_data) # log errors errors = final_data.get("errors", []) parser_errors = final_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=final_data)) # if iso_arrays is not None: # array_data = ArrayData() # for name, array in iso_arrays.items(): # array_data.set_array(name, np.array(array)) # self.out('arrays', array_data) if pbs_error is not None: return pbs_error if stdout_error is not None: return stdout_error if ppan_error is not None: return ppan_error return ExitCode()
[docs] def merge_output_dicts(self, stdout_data, iso_data): """Merge the data returned from the stdout file and iso_data file.""" final_data = {} for key in set(list(stdout_data.keys()) + list(iso_data.keys())): if key in ["errors", "warnings", "parser_errors", "parser_exceptions"]: final_data[key] = stdout_data.get(key, []) + iso_data.get(key, []) elif key == "units": units = stdout_data.get(key, {}) units.update(iso_data.get(key, {})) final_data[key] = units elif key in stdout_data and key in iso_data: self.logger.warning("key in stdout_data and iso_data: {}".format(key)) final_data[key] = iso_data[key] elif key in iso_data: final_data[key] = iso_data[key] else: final_data[key] = stdout_data[key] final_data.update( { "parser_version": str(__version__), "parser_class": str(self.__class__.__name__), } ) return final_data