def test_parser_nodes(request, calc_with_retrieved):
"""Test a few basic node items of the parser."""
from aiida.plugins import ParserFactory
settings_dict = {
'parser_settings': {
'add_bands': True,
'add_kpoints': True,
'add_misc': ['fermi_level']
}
}
file_path = str(request.fspath.join('..') + '../../../test_data/basic')
node = calc_with_retrieved(file_path, settings_dict)
parser_cls = ParserFactory('vasp.vasp')
result, _ = parser_cls.parse_from_node(
node, store_provenance=False, retrieved_temporary_folder=file_path)
misc = result['misc']
bands = result['bands']
kpoints = result['kpoints']
assert isinstance(misc, get_data_class('dict'))
assert isinstance(bands, get_data_class('array.bands'))
assert isinstance(kpoints, get_data_class('array.kpoints'))
assert misc.get_dict()['fermi_level'] == 5.96764939
def test_stream_history(request, calc_with_retrieved):
"""Test that the stream parser keeps history."""
file_path = str(
request.fspath.join('..') + '../../../test_data/stdout/out')
# turn of everything, except misc
settings_dict = {
'parser_settings': {
'add_trajectory': False,
'add_bands': False,
'add_chgcar': False,
'add_dos': False,
'add_kpoints': False,
'add_energies': False,
'add_misc': ['notifications'],
'add_structure': False,
'add_projectors': False,
'add_born_charges': False,
'add_dielectrics': False,
'add_hessian': False,
'add_dynmat': False,
'add_wavecar': False,
'add_site_magnetization': False,
'stream_config': {
'random_error': {
'kind': 'ERROR',
'regex': 'I AM A WELL DEFINED ERROR',
'message': 'Okey, this error you do not want.',
'suggestion': '',
'location': 'STDOUT',
'recover': False
}
},
'stream_history': True
}
}
node = calc_with_retrieved(file_path, settings_dict)
parser_cls = ParserFactory('vasp.vasp')
result, _ = parser_cls.parse_from_node(
node, store_provenance=False, retrieved_temporary_folder=file_path)
misc = result['misc']
misc_dict = misc.get_dict()
assert len(misc_dict['notifications']) == 3
assert misc_dict['notifications'][0]['name'] == 'ibzkpt'
assert misc_dict['notifications'][0]['kind'] == 'ERROR'
assert misc_dict['notifications'][0][
'regex'] == 'internal error in subroutine IBZKPT'
assert misc_dict['notifications'][1]['name'] == 'random_error'
assert misc_dict['notifications'][1]['kind'] == 'ERROR'
assert misc_dict['notifications'][1][
'regex'] == 'I AM A WELL DEFINED ERROR'
assert misc_dict['notifications'][2]['name'] == 'random_error'
assert misc_dict['notifications'][2]['kind'] == 'ERROR'
assert misc_dict['notifications'][2][
'regex'] == 'I AM A WELL DEFINED ERROR'
for item in misc_dict['notifications']:
assert item['kind'] != 'WARNING'
def test_misc(request, calc_with_retrieved):
"""Test that it is possible to extract misc from both vasprun and OUTCAR."""
# turn of everything, except misc
settings_dict = {
'parser_settings': {
'add_trajectory':
False,
'add_bands':
False,
'add_chgcar':
False,
'add_dos':
False,
'add_kpoints':
False,
'add_energies':
False,
'add_misc': [
'fermi_level', 'maximum_stress', 'maximum_force',
'total_energies', 'symmetries'
],
'add_structure':
False,
'add_projectors':
False,
'add_born_charges':
False,
'add_dielectrics':
False,
'add_hessian':
False,
'add_dynmat':
False,
'add_wavecar':
False,
'add_site_magnetization':
False,
}
}
file_path = str(
request.fspath.join('..') + '../../../test_data/disp_details')
node = calc_with_retrieved(file_path, settings_dict)
parser_cls = ParserFactory('vasp.vasp')
result, _ = parser_cls.parse_from_node(
node, store_provenance=False, retrieved_temporary_folder=file_path)
misc = result['misc']
assert isinstance(misc, get_data_class('dict'))
data = misc.get_dict()
# We already have a test to check if the quantities from the OUTCAR is correct, so
# only perform rudimentary checks, and the content comming from the xml file.
assert data['fermi_level'] == 6.17267267
assert data['maximum_stress'] == 42.96872956444064
assert data['maximum_force'] == 0.21326679
assert data['total_energies']['energy_extrapolated'] == -10.823296
def _get_vasp_parser(calc_with_retrieved):
"""Return vasp parser before parsing"""
settings_dict = {
# 'ADDITIONAL_RETRIEVE_LIST': CalculationFactory('vasp.vasp')._ALWAYS_RETRIEVE_LIST,
'parser_settings': {
'add_custom': {
'link_name': 'custom_node',
'type': 'dict',
'quantities': ['quantity2', 'quantity_with_alternatives']
}
}
}
file_path = str(
os.path.abspath(os.path.dirname(__file__)) +
'/../../test_data/basic_run')
node = calc_with_retrieved(file_path, settings_dict)
parser = ParserFactory('vasp.vasp')(node)
return parser, file_path, node
def vasp_parser_with_test(calc_with_retrieved):
"""Fixture providing a VaspParser instance coupled to a VaspCalculation."""
from aiida.plugins import ParserFactory
from aiida.plugins import CalculationFactory
settings_dict = {
# 'ADDITIONAL_RETRIEVE_LIST': CalculationFactory('vasp.vasp')._ALWAYS_RETRIEVE_LIST,
'parser_settings': {
'add_custom': {
'link_name': 'custom_node',
'type': 'dict',
'quantities': ['quantity2', 'quantity_with_alternatives']
}
}
}
file_path = str(
os.path.abspath(os.path.dirname(__file__)) +
'/../../test_data/test_relax_wc/out')
node = calc_with_retrieved(file_path, settings_dict)
parser = ParserFactory('vasp.vasp')(node)
parser.add_file_parser('_scheduler-stderr.txt', {
'parser_class': ExampleFileParser,
'is_critical': False
})
parser.add_parsable_quantity(
'quantity_with_alternatives',
{
'inputs': [],
'prerequisites': [],
},
)
success = parser.parse(retrieved_temporary_folder=file_path)
try:
yield parser
finally:
parser = ParserFactory('vasp.vasp')(node)
def base_parser(calc_with_retrieved):
file_path = str(
os.path.abspath(os.path.dirname(__file__)) +
'/../../test_data/basic_run/')
node = calc_with_retrieved(file_path)
return BaseParser(node)
def test_structure(request, calc_with_retrieved):
"""Test that the structure from vasprun and POSCAR is the same."""
from aiida.plugins import ParserFactory
# turn of everything, except structure
settings_dict = {
'parser_settings': {
'add_trajectory': False,
'add_bands': False,
'add_chgcar': False,
'add_dos': False,
'add_kpoints': False,
'add_energies': False,
'add_misc': False,
'add_structure': True,
'add_projectors': False,
'add_born_charges': False,
'add_dielectrics': False,
'add_hessian': False,
'add_dynmat': False,
'add_wavecar': False,
'add_site_magnetization': False,
'file_parser_set': 'default'
}
}
file_path = str(request.fspath.join('..') + '../../../test_data/basic')
node = calc_with_retrieved(file_path, settings_dict)
parser_cls = ParserFactory('vasp.vasp')
result, _ = parser_cls.parse_from_node(
node, store_provenance=False, retrieved_temporary_folder=file_path)
# First fetch structure from vasprun
structure_vasprun = result['structure']
assert isinstance(structure_vasprun, get_data_class('structure'))
# Then from POSCAR/CONTCAR
file_path = str(
request.fspath.join('..') + '../../../test_data/basic_poscar')
node = calc_with_retrieved(file_path, settings_dict)
parser_cls = ParserFactory('vasp.vasp')
result, _ = parser_cls.parse_from_node(
node, store_provenance=False, retrieved_temporary_folder=file_path)
structure_poscar = result['structure']
assert isinstance(structure_poscar, get_data_class('structure'))
assert np.array_equal(np.round(structure_vasprun.cell, 7),
np.round(structure_poscar.cell, 7))
positions_vasprun = []
positions_poscar = []
for site in structure_vasprun.sites:
pos = np.round(np.asarray(site.position), 7)
positions_vasprun.append(pos)
for site in structure_poscar.sites:
pos = np.round(np.asarray(site.position), 7)
positions_poscar.append(pos)
positions_vasprun = np.asarray(positions_vasprun)
positions_poscar = np.asarray(positions_poscar)
assert np.array_equal(positions_vasprun, positions_poscar)
def test_stream(misc_input, config, request, calc_with_retrieved):
"""Test that the stream parser works and gets stored on a node."""
file_path = str(
request.fspath.join('..') + '../../../test_data/stdout/out')
# turn of everything, except misc
settings_dict = {
'parser_settings': {
'add_trajectory': False,
'add_bands': False,
'add_chgcar': False,
'add_dos': False,
'add_kpoints': False,
'add_energies': False,
'add_misc': misc_input,
'add_structure': False,
'add_projectors': False,
'add_born_charges': False,
'add_dielectrics': False,
'add_hessian': False,
'add_dynmat': False,
'add_wavecar': False,
'add_site_magnetization': False,
'stream_config': config
}
}
node = calc_with_retrieved(file_path, settings_dict)
parser_cls = ParserFactory('vasp.vasp')
result, _ = parser_cls.parse_from_node(
node, store_provenance=False, retrieved_temporary_folder=file_path)
if misc_input == []:
# Test empty misc specification, yields no misc output node
with pytest.raises(KeyError) as error:
misc = result['misc']
else:
misc = result['misc']
misc_dict = misc.get_dict()
if config is not None:
if 'random_error' in config:
assert len(misc_dict['notifications']) == 2
assert misc_dict['notifications'][0]['name'] == 'ibzkpt'
assert misc_dict['notifications'][0]['kind'] == 'ERROR'
assert misc_dict['notifications'][0][
'regex'] == 'internal error in subroutine IBZKPT'
assert misc_dict['notifications'][1]['name'] == 'random_error'
assert misc_dict['notifications'][1]['kind'] == 'ERROR'
assert misc_dict['notifications'][1][
'regex'] == 'I AM A WELL DEFINED ERROR'
if 'random_warning' in config:
assert len(misc_dict['notifications']) == 2
assert misc_dict['notifications'][0]['name'] == 'ibzkpt'
assert misc_dict['notifications'][0]['kind'] == 'ERROR'
assert misc_dict['notifications'][0][
'regex'] == 'internal error in subroutine IBZKPT'
assert misc_dict['notifications'][1][
'name'] == 'random_warning'
assert misc_dict['notifications'][1]['kind'] == 'WARNING'
assert misc_dict['notifications'][1][
'regex'] == 'I AM A WELL DEFINED WARNING'
else:
assert len(misc_dict['notifications']) == 1
assert misc_dict['notifications'][0]['name'] == 'ibzkpt'
assert misc_dict['notifications'][0]['kind'] == 'ERROR'
assert misc_dict['notifications'][0][
'regex'] == 'internal error in subroutine IBZKPT'