Source code for aiida_quantumespresso.parsers.dos

# -*- coding: utf-8 -*-
from __future__ import absolute_import
import numpy as np
from aiida.parsers import Parser
from aiida.orm import Dict, XyData
from aiida.common import NotExistent
from aiida_quantumespresso.parsers import QEOutputParsingError
from aiida_quantumespresso.parsers import parse_raw_out_basic
from six.moves import range


[docs]class DosParser(Parser): """This class is the implementation of the Parser class for Dos.""" # deprecated: #_dos_name = 'output_dos' #_units_name = 'output_units'
[docs] def parse(self, **kwargs): """Parses the datafolder, stores results. Retrieves dos output, and some basic information from the out_file, such as warnings and wall_time """ try: out_folder = self.retrieved except NotExistent: return self.exit_codes.ERROR_NO_RETRIEVED_FOLDER # Read standard out try: filename_stdout = self.node.get_option('output_filename') # or get_attribute(), but this is clearer with out_folder.open(filename_stdout, 'r') as fil: out_file = fil.readlines() except OSError: return self.exit_codes.ERROR_READING_OUTPUT_FILE job_done = False for i in range(len(out_file)): line = out_file[-i] if 'JOB DONE' in line: job_done = True break if not job_done: return self.exit_codes.ERROR_JOB_NOT_DONE # check that the dos file is present, if it is, read it try: with out_folder.open(self.node.process_class._DOS_FILENAME, 'r') as fil: dos_file = fil.readlines() except OSError: return self.exit_codes.ERROR_READING_DOS_FILE # end of initial checks array_names = [[], []] array_units = [[], []] array_names[0] = ['dos_energy', 'dos', 'integrated_dos'] # When spin is not displayed array_names[1] = ['dos_energy', 'dos_spin_up', 'dos_spin_down', 'integrated_dos'] # When spin is displayed array_units[0] = ['eV', 'states/eV', 'states'] # When spin is not displayed array_units[1] = ['eV', 'states/eV', 'states/eV', 'states'] # When spin is displayed # grabs parsed data from aiida.dos # TODO: should I catch any QEOutputParsingError from parse_raw_dos, # log an error and return an exit code? array_data, spin = parse_raw_dos(dos_file, array_names, array_units) energy_units = 'eV' dos_units = 'states/eV' int_dos_units = 'states' xy_data = XyData() xy_data.set_x(array_data['dos_energy'],'dos_energy', energy_units) y_arrays = [] y_names = [] y_units = [] y_arrays += [array_data['integrated_dos']] y_names += ['integrated_dos'] y_units += ['states'] if spin: y_arrays += [array_data['dos_spin_up']] y_arrays += [array_data['dos_spin_down']] y_names += ['dos_spin_up'] y_names += ['dos_spin_down'] y_units += ['states/eV']*2 else: y_arrays += [array_data['dos']] y_names += ['dos'] y_units += ['states/eV'] xy_data.set_y(y_arrays,y_names,y_units) # grabs the parsed data from aiida.out parsed_data = parse_raw_out_basic(out_file, 'DOS') output_params = Dict(dict=parsed_data) # Adds warnings for message in parsed_data['warnings']: self.logger.error(message) # Create New Nodes self.out('output_dos', xy_data) self.out('output_parameters', output_params)
[docs]def parse_raw_dos(dos_file, array_names, array_units): """This function takes as input the dos_file as a list of filelines along with information on how to give labels and units to the parsed data. :param dos_file: dos file lines in the form of a list :type dos_file: list :param array_names: list of all array names, note that array_names[0] is for the case with non spin-polarized calculations and array_names[1] is for the case with spin-polarized calculation :type array_names: list :param array_units: list of all array units, note that array_units[0] is for the case with non spin-polarized calculations and array_units[1] is for the case with spin-polarized calculation :type array_units: list :return array_data: narray, a dictionary for ArrayData type, which contains all parsed dos output along with labels and units :return spin: boolean, indicates whether the parsed results are spin polarized """ dos_header = dos_file[0] try: dos_data = np.genfromtxt(dos_file) except ValueError: raise QEOutputParsingError('dosfile could not be loaded ' ' using genfromtxt') if len(dos_data) == 0: raise QEOutputParsingError('Dos file is empty.') if np.isnan(dos_data).any(): raise QEOutputParsingError('Dos file contains non-numeric elements.') # Checks the number of columns, essentially to see whether spin was used if len(dos_data[0]) == 3: # spin is not used array_names = array_names[0] array_units = array_units[0] spin = False elif len(dos_data[0]) == 4: # spin is used array_names = array_names[1] array_units = array_units[1] spin = True else: raise QEOutputParsingError('Dos file in format that the parser is not ' 'designed to handle.') i = 0 array_data = {} array_data['header'] = np.array(dos_header) while i < len(array_names): array_data[array_names[i]] = dos_data[:, i] array_data[array_names[i]+'_units'] = np.array(array_units[i]) i += 1 return array_data, spin