def test_parse_xmlout_file_broken_xmlout_file():
"""
tests the behavior of the parse_xmlout_file routine in the case of an broken out.xml file.
Here broken after serveral iteration, should parse all iteration except last.
(which can happen in the case of some kill, or Non regular termination of FLEUR)
"""
from aiida_fleur.parsers.fleur import parse_xmlout_file
filename = os.path.abspath('./files/outxml/special/broken_BeTi_out.xml')
simple_out, complex_out, parser_info_out, successful = parse_xmlout_file(filename)
expected_parser_info_out = {
'last_iteration_parsed':
15,
'parser_info':
'AiiDA Fleur Parser v0.3.2',
'parser_warnings': [
'The out.xml file is broken I try to repair it.',
'Endtime was unparsed, inp.xml prob not complete, do not believe the walltime!'
],
'unparsed': []
}
assert successful
assert parser_info_out['last_iteration_parsed'] == 15
assert expected_parser_info_out['unparsed'] == parser_info_out['unparsed']
assert expected_parser_info_out['parser_warnings'] == parser_info_out['parser_warnings']
def test_fleurparse_all_xmlout_file(xmloutfile):
"""
tests if the routine that parsers the outputfile, succeeds for all out files
"""
from aiida_fleur.parsers.fleur import parse_xmlout_file
simple_out, complex_out, parser_info_out, successful = parse_xmlout_file(xmloutfile)
assert successful
def test_parse_xmlout_file_fortran_garbage_in_xmlout_file():
"""
tests the behavior of the parse_xmlout_file routine in the case of an individual 'garbage' in the out.xml file.
Fortran NANs and INFs will be parsed fine, ** will not be parsed.
(which can happen in the case of some kill, or Non regular termination of FLEUR)
"""
from aiida_fleur.parsers.fleur import parse_xmlout_file
filename = os.path.abspath('./files/outxml/special/Fortran_garbage_BeTi_out.xml')
simple_out, complex_out, parser_info_out, successful = parse_xmlout_file(filename)
exp_partial_simple_out_dict = {
'bandgap_units': 'eV',
'energy': float('Inf'),
'energy_hartree': float('Inf'),
'fermi_energy': float('NaN'),
'warnings': {
'debug': {},
'error': {},
'info': {},
'warning': {}
}
}
expected_parser_info_out = {
'parser_info':
'AiiDA Fleur Parser v0.3.2',
'parser_warnings': [
'Could not convert: "**" to float, ValueError',
'Could not convert: " !#@)!(U$*(Y" to float, ValueError'
],
'unparsed': [{
'bandgap': '**',
'iteration': ' 19'
}, {
'charge_density': ' !#@)!(U$*(Y',
'iteration': ' 19'
}]
}
#TODO maybe in the case on unpared, things should be initialized, here they are missing...
def isNaN(num):
return math.isnan(num) #num != num
assert successful
assert exp_partial_simple_out_dict['energy'] == simple_out['energy']
assert exp_partial_simple_out_dict['energy_hartree'] == simple_out['energy_hartree']
assert isNaN(exp_partial_simple_out_dict['fermi_energy']) == isNaN(simple_out['fermi_energy'])
assert 'bandgap' not in list(simple_out.keys())
assert expected_parser_info_out['unparsed'] == parser_info_out['unparsed']
assert expected_parser_info_out['parser_warnings'] == parser_info_out['parser_warnings']
def test_parse_xmlout_file_empty_file():
"""
tests the behavior of the parse_xmlout_file routine in the case of an empty file
"""
from aiida_fleur.parsers.fleur import parse_xmlout_file
filename = os.path.abspath('./files/outxml/special/empty_out.xml')
simple_out, complex_out, parser_info_out, successful = parse_xmlout_file(filename)
expected_parser_info_out = {
'parser_info':
'AiiDA Fleur Parser v0.3.2',
'parser_warnings': [
'The out.xml file is broken I try to repair it.',
'Skipping the parsing of the xml file. Repairing was not possible.'
],
'unparsed': []
}
assert not successful
assert expected_parser_info_out == parser_info_out
def test_parse_xmlout_file():
"""
tests if the routine that parsers the outputfile, produces the right output, no aiida datastructures,
with the right content
"""
from aiida_fleur.parsers.fleur import parse_xmlout_file
filename = os.path.abspath('./files/outxml/BeTi_out.xml')
simple_out, complex_out, parser_info_out, successful = parse_xmlout_file(filename)
expected_simple_out_dict = {
'bandgap': 0.0052350388,
'bandgap_units': 'eV',
'charge_den_xc_den_integral': -45.0947551412,
'charge_density': 8.7984e-06,
'creator_name': 'fleur 27',
'creator_target_architecture': 'GEN',
'creator_target_structure': ' ',
'density_convergence_units': 'me/bohr^3',
'energy': -23635.691961010132,
'energy_core_electrons': -496.172547773,
'energy_hartree': -868.5956587197,
'energy_hartree_units': 'Htr',
'energy_units': 'eV',
'energy_valence_electrons': -7.1055909396,
'fermi_energy': 0.3451127139,
'fermi_energy_units': 'Htr',
'force_largest': -0.0,
'kmax': 4.5,
'number_of_atom_types': 2,
'number_of_atoms': 2,
'number_of_iterations': 19,
'number_of_iterations_total': 19,
'number_of_kpoints': 56,
'number_of_species': 1,
'number_of_spin_components': 1,
'number_of_symmetries': 48,
'output_file_version': '0.27',
'start_date': {
'date': '2017/09/10',
'time': '07:58:10'
},
'end_date': {
'date': '2017/09/10',
'time': '07:58:34'
},
'sum_of_eigenvalues': -503.2781387127,
'title': 'Be-Ti, bulk compounds',
'walltime': 24,
'walltime_units': 'seconds',
'warnings': {
'debug': {},
'error': {},
'info': {},
'warning': {}
}
}
expected_parser_info_out = {'parser_info': 'AiiDA Fleur Parser v0.3.2', 'parser_warnings': [], 'unparsed': []}
simple_out.pop('outputfile_path', None) # otherwise test will fail on different installations
# also this should go away any way...
assert successful
assert expected_simple_out_dict == simple_out
assert expected_parser_info_out == parser_info_out
def test_parse_xmlout_file_broken_first_xmlout_file():
"""
tests the behavior of the parse_xmlout_file routine in the case of an broken out.xml file.
Here broken in first iteration, should parse nothing.
(which can happen in the case of some kill, or Non regular termination of FLEUR)
"""
from aiida_fleur.parsers.fleur import parse_xmlout_file
filename = os.path.abspath('./files/outxml/special/broken_first_BeTi_out.xml')
simple_out, complex_out, parser_info_out, successful = parse_xmlout_file(filename)
expected_parser_info_out = {
'last_iteration_parsed':
1,
'parser_info':
'AiiDA Fleur Parser v0.3.2',
'parser_warnings': [
'The out.xml file is broken I try to repair it.',
'Can not get attributename: "units" from node "[]", because node is not an element of etree.',
'Can not get attributename: "value" from node "[]", because node is not an element of etree.',
'Could not convert: "None" to float, TypeError', 'Could not convert: "None" to float, TypeError',
'Could not convert: "None" to float, TypeError',
'Can not get attributename: "value" from node "[]", because node is not an element of etree.',
'Could not convert: "None" to float, TypeError',
'Can not get attributename: "value" from node "[]", because node is not an element of etree.',
'Could not convert: "None" to float, TypeError',
'Can not get attributename: "value" from node "[]", because node is not an element of etree.',
'Could not convert: "None" to float, TypeError',
'Can not get attributename: "value" from node "[]", because node is not an element of etree.',
'Could not convert: "None" to float, TypeError',
'Can not get attributename: "units" from node "[]", because node is not an element of etree.',
'Can not get attributename: "value" from node "[]", because node is not an element of etree.',
'Could not convert: "None" to float, TypeError',
'Can not get attributename: "value" from node "[]", because node is not an element of etree.',
'Could not convert: "None" to float, TypeError',
'Can not get attributename: "units" from node "[]", because node is not an element of etree.',
'Can not get attributename: "units" from node "[]", because node is not an element of etree.',
'Can not get attributename: "distance" from node "[]", because node is not an element of etree.',
'Could not convert: "None" to float, TypeError',
'Endtime was unparsed, inp.xml prob not complete, do not believe the walltime!'
],
'unparsed': [{
'energy_hartree': None,
'iteration': ' 1'
}, {
'energy': None,
'iteration': ' 1'
}, {
'iteration': ' 1',
'sum_of_eigenvalues': None
}, {
'energy_core_electrons': None,
'iteration': ' 1'
}, {
'energy_valence_electrons': None,
'iteration': ' 1'
}, {
'charge_den_xc_den_integral': None,
'iteration': ' 1'
}, {
'bandgap': None,
'iteration': ' 1'
}, {
'fermi_energy': None,
'iteration': ' 1'
}, {
'charge_density': None,
'iteration': ' 1'
}]
}
assert successful
assert parser_info_out['last_iteration_parsed'] == 1
assert expected_parser_info_out['unparsed'] == parser_info_out['unparsed']
assert expected_parser_info_out['parser_warnings'] == parser_info_out['parser_warnings']
# -*- coding: utf-8 -*-
import os
#import numpy
from pprint import pprint
from aiida import load_dbenv, is_dbenv_loaded
if not is_dbenv_loaded():
load_dbenv()
from aiida_fleur.parsers.fleur import parse_xmlout_file
outxmlfile = '/usr/users/iff_th1/broeder/aiida/github/aiida_fleur_plugin/tests/parsers/outxmlfiles/out1.xml'
a = parse_xmlout_file(outxmlfile)
pprint(a)