def test_existing_parsers(self):
"""Test listing all preinstalled parsers"""
from aiida.parsers import Parser
pars = pl.existing_plugins(Parser, 'aiida.parsers.plugins')
self.assertIsInstance(pars, list)
from aiida.parsers import ParserFactory
for i in pars:
self.assertTrue(issubclass(ParserFactory(i), Parser))
def test_existing_parsers(self):
"""
Test listing all preinstalled parsers
"""
entry_points = get_entry_points('aiida.parsers')
self.assertIsInstance(entry_points, list)
for entry_point in entry_points:
cls = ParserFactory(entry_point.name)
self.assertTrue(issubclass(cls, Parser),
'Parser plugin class {} is not subclass of {}'.format(cls, Parser))
def test_existing_parsers(self):
"""
Test listing all preinstalled parsers
"""
parsers = all_plugins('parsers')
self.assertIsInstance(parsers, list)
for i in parsers:
cls = ParserFactory(i)
self.assertTrue(
issubclass(cls, Parser),
'Parser plugin class {} is not subclass of {}'.format(
cls, Parser))
def test_voronoi_parser_entry_point(aiida_env):
from aiida.parsers import ParserFactory
from aiida_kkr.parsers.voro import VoronoiParser
parser = ParserFactory('kkr.voroparser')
assert parser == VoronoiParser
def test_kkrimporter_parser_entry_point(aiida_env):
from aiida.parsers import ParserFactory
from aiida_kkr.parsers.kkrimporter import KkrImporterParser
parser = ParserFactory('kkr.kkrimporterparser')
assert parser == KkrImporterParser
def test_parser_opt(new_database, new_workdir):
""" Test the parser
"""
from aiida.parsers import ParserFactory
from aiida.common.datastructures import calc_states
from aiida.common.folders import SandboxFolder
from aiida.orm import DataFactory
code = get_basic_code(new_workdir)
calc = code.new_calc()
calc.set_resources({"num_machines": 1, "num_mpiprocs_per_machine": 1})
calc.store_all()
calc._set_state(calc_states.PARSING)
parser_cls = ParserFactory("crystal17.basic")
parser = parser_cls(calc)
with SandboxFolder() as folder:
main_out_path = os.path.join(
os.path.dirname(tests.__file__), "output_files",
"mgo_sto3g_opt.crystal.out")
with open(main_out_path) as f:
folder.create_file_from_filelike(f, "main.out")
fdata = DataFactory("folder")()
fdata.replace_with_folder(folder.abspath)
mock_retrieved = {calc._get_linkname_retrieved(): fdata}
success, node_list = parser.parse_with_retrieved(mock_retrieved)
assert success
node_dict = dict(node_list)
assert set(['output_parameters', 'output_settings',
'output_structure']) == set(node_dict.keys())
expected_params = {
'parser_version':
str(aiida_crystal17.__version__),
'ejplugins_version':
str(ejplugins.__version__),
'parser_class':
'CryBasicParser',
'parser_warnings':
["no initial structure available, creating new kinds for atoms"],
'errors': [],
'warnings':
['WARNING **** INT_SCREEN **** CELL PARAMETERS OPTIMIZATION ONLY'],
'energy': -2.712596206888E+02 * 27.21138602,
'energy_units':
'eV', # hartree to eV
'calculation_type':
'restricted closed shell',
'calculation_spin':
False,
# 'wall_time_seconds':
# 102,
'number_of_atoms':
2,
'number_of_assymetric':
2,
'scf_iterations':
8,
'opt_iterations':
6,
'volume':
14.652065094424696,
}
out_params_dict = node_dict['output_parameters'].get_dict()
out_params_dict.pop('wall_time_seconds', None)
assert edict.diff(
out_params_dict,
expected_params,
np_allclose=True) == {}
expected_struct_attrs = {
'cell': [[0.0, 1.94218061274, 1.94218061274],
[1.94218061274, 0.0, 1.94218061274],
[1.94218061274, 1.94218061274, 0.0]],
'kinds': [{'mass': 24.305,
'name': 'Mg',
'symbols': [u'Mg'],
'weights': [1.0]},
{'mass': 15.9994, 'name': 'O', 'symbols': ['O'], 'weights': [1.0]}],
'pbc1': True,
'pbc2': True,
'pbc3': True,
'sites': [{'kind_name': 'Mg', 'position': [0.0, 0.0, 0.0]},
{'kind_name': 'O',
'position': [1.94218061274, 1.94218061274, 1.94218061274]}]
}
assert edict.diff(
dict(node_dict['output_structure'].get_attrs()),
expected_struct_attrs, np_allclose=True) == {}
def test_parser_external(new_database, new_workdir):
""" Test the parser
"""
from aiida.parsers import ParserFactory
from aiida.common.datastructures import calc_states
from aiida.common.folders import SandboxFolder
from aiida.orm import DataFactory
code = get_basic_code(new_workdir)
calc = code.new_calc()
calc.set_resources({"num_machines": 1, "num_mpiprocs_per_machine": 1})
calc.store_all()
calc._set_state(calc_states.PARSING)
parser_cls = ParserFactory("crystal17.basic")
parser = parser_cls(calc)
with SandboxFolder() as folder:
main_out_path = os.path.join(
os.path.dirname(tests.__file__), "output_files",
"mgo_sto3g_external.crystal.out")
with open(main_out_path) as f:
folder.create_file_from_filelike(f, "main.out")
fdata = DataFactory("folder")()
fdata.replace_with_folder(folder.abspath)
mock_retrieved = {calc._get_linkname_retrieved(): fdata}
success, node_list = parser.parse_with_retrieved(mock_retrieved)
assert success
node_dict = dict(node_list)
assert set(['output_parameters', 'output_settings',
'output_structure']) == set(node_dict.keys())
expected_params = {
'parser_version':
str(aiida_crystal17.__version__),
'ejplugins_version':
str(ejplugins.__version__),
'parser_class':
'CryBasicParser',
'parser_warnings':
["no initial structure available, creating new kinds for atoms"],
'errors': [],
'warnings': [],
'energy': -2.7121814374931E+02 *
27.21138602,
'energy_units':
'eV', # hartree to eV
'calculation_type':
'restricted closed shell',
'calculation_spin':
False,
# 'wall_time_seconds':
# 3,
'number_of_atoms':
2,
'number_of_assymetric':
2,
'scf_iterations':
7,
'volume':
18.65461527264623,
'mulliken_charges': [0.777, -0.777],
'mulliken_electrons': [11.223, 8.777],
}
out_params_dict = node_dict['output_parameters'].get_dict()
out_params_dict.pop('wall_time_seconds', None)
assert edict.diff(
out_params_dict,
expected_params,
np_allclose=True) == {}
# read from nio_sto3g_afm.crystal.out
expected_operations = [[
1.0, 0.0, 0.0, 0.0, 1.0, 0.0, 0.0, 0.0, 1.0, 0.0, 0.0, 0.0
], [0.0, 1.0, 0.0, 1.0, 0.0, 0.0, -1.0, -1.0, -1.0, 0.0, 0.0, 0.0], [
-1.0, -1.0, -1.0, 0.0, 0.0, 1.0, 0.0, 1.0, 0.0, 0.0, 0.0, 0.0
], [0.0, 0.0, 1.0, -1.0, -1.0, -1.0, 1.0, 0.0, 0.0, 0.0, 0.0, 0.0], [
0.0, 0.0, 1.0, 1.0, 0.0, 0.0, 0.0, 1.0, 0.0, 0.0, 0.0, 0.0
], [0.0, 1.0, 0.0, 0.0, 0.0, 1.0, 1.0, 0.0, 0.0, 0.0, 0.0, 0.0], [
1.0, 0.0, 0.0, 0.0, 0.0, 1.0, -1.0, -1.0, -1.0, 0.0, 0.0, 0.0
], [1.0, 0.0, 0.0, -1.0, -1.0, -1.0, 0.0, 1.0, 0.0, 0.0, 0.0, 0.0], [
-1.0, -1.0, -1.0, 0.0, 1.0, 0.0, 1.0, 0.0, 0.0, 0.0, 0.0, 0.0
], [0.0, 0.0, 1.0, 0.0, 1.0, 0.0, -1.0, -1.0, -1.0, 0.0, 0.0, 0.0], [
0.0, 1.0, 0.0, -1.0, -1.0, -1.0, 0.0, 0.0, 1.0, 0.0, 0.0, 0.0
], [-1.0, -1.0, -1.0, 1.0, 0.0, 0.0, 0.0, 0.0, 1.0, 0.0, 0.0, 0.0], [
0.0, -1.0, 0.0, -1.0, 0.0, 0.0, 0.0, 0.0, -1.0, 0.0, 0.0, 0.0
], [-1.0, 0.0, 0.0, 0.0, -1.0, 0.0, 1.0, 1.0, 1.0, 0.0, 0.0, 0.0], [
0.0, 0.0, -1.0, 1.0, 1.0, 1.0, 0.0, -1.0, 0.0, 0.0, 0.0, 0.0
], [1.0, 1.0, 1.0, 0.0, 0.0, -1.0, -1.0, 0.0, 0.0, 0.0, 0.0, 0.0], [
-1.0, 0.0, 0.0, 0.0, 0.0, -1.0, 0.0, -1.0, 0.0, 0.0, 0.0, 0.0
], [0.0, 0.0, -1.0, 0.0, -1.0, 0.0, -1.0, 0.0, 0.0, 0.0, 0.0, 0.0], [
0.0, 0.0, -1.0, -1.0, 0.0, 0.0, 1.0, 1.0, 1.0, 0.0, 0.0, 0.0
], [1.0, 1.0, 1.0, -1.0, 0.0, 0.0, 0.0, -1.0, 0.0, 0.0, 0.0, 0.0], [
0.0, -1.0, 0.0, 1.0, 1.0, 1.0, -1.0, 0.0, 0.0, 0.0, 0.0, 0.0
], [0.0, -1.0, 0.0, 0.0, 0.0, -1.0, 1.0, 1.0, 1.0, 0.0, 0.0, 0.0], [
1.0, 1.0, 1.0, 0.0, -1.0, 0.0, 0.0, 0.0, -1.0, 0.0, 0.0, 0.0
], [-1.0, 0.0, 0.0, 1.0, 1.0, 1.0, 0.0, 0.0, -1.0, 0.0, 0.0, 0.0], [
-1.0, 0.0, 0.0, 0.0, -1.0, 0.0, 0.0, 0.0, -1.0, 0.0, 0.0, 0.0
], [0.0, -1.0, 0.0, -1.0, 0.0, 0.0, 1.0, 1.0, 1.0, 0.0, 0.0, 0.0], [
1.0, 1.0, 1.0, 0.0, 0.0, -1.0, 0.0, -1.0, 0.0, 0.0, 0.0, 0.0
], [0.0, 0.0, -1.0, 1.0, 1.0, 1.0, -1.0, 0.0, 0.0, 0.0, 0.0, 0.0], [
0.0, 0.0, -1.0, -1.0, 0.0, 0.0, 0.0, -1.0, 0.0, 0.0, 0.0, 0.0
], [0.0, -1.0, 0.0, 0.0, 0.0, -1.0, -1.0, 0.0, 0.0, 0.0, 0.0, 0.0], [
-1.0, 0.0, 0.0, 0.0, 0.0, -1.0, 1.0, 1.0, 1.0, 0.0, 0.0, 0.0
], [-1.0, 0.0, 0.0, 1.0, 1.0, 1.0, 0.0, -1.0, 0.0, 0.0, 0.0, 0.0], [
1.0, 1.0, 1.0, 0.0, -1.0, 0.0, -1.0, 0.0, 0.0, 0.0, 0.0, 0.0
], [0.0, 0.0, -1.0, 0.0, -1.0, 0.0, 1.0, 1.0, 1.0, 0.0, 0.0, 0.0], [
0.0, -1.0, 0.0, 1.0, 1.0, 1.0, 0.0, 0.0, -1.0, 0.0, 0.0, 0.0
], [1.0, 1.0, 1.0, -1.0, 0.0, 0.0, 0.0, 0.0, -1.0, 0.0, 0.0, 0.0], [
0.0, 1.0, 0.0, 1.0, 0.0, 0.0, 0.0, 0.0, 1.0, 0.0, 0.0, 0.0
], [1.0, 0.0, 0.0, 0.0, 1.0, 0.0, -1.0, -1.0, -1.0, 0.0, 0.0, 0.0], [
0.0, 0.0, 1.0, -1.0, -1.0, -1.0, 0.0, 1.0, 0.0, 0.0, 0.0, 0.0
], [-1.0, -1.0, -1.0, 0.0, 0.0, 1.0, 1.0, 0.0, 0.0, 0.0, 0.0, 0.0], [
1.0, 0.0, 0.0, 0.0, 0.0, 1.0, 0.0, 1.0, 0.0, 0.0, 0.0, 0.0
], [0.0, 0.0, 1.0, 0.0, 1.0, 0.0, 1.0, 0.0, 0.0, 0.0, 0.0, 0.0], [
0.0, 0.0, 1.0, 1.0, 0.0, 0.0, -1.0, -1.0, -1.0, 0.0, 0.0, 0.0
], [-1.0, -1.0, -1.0, 1.0, 0.0, 0.0, 0.0, 1.0, 0.0, 0.0, 0.0, 0.0], [
0.0, 1.0, 0.0, -1.0, -1.0, -1.0, 1.0, 0.0, 0.0, 0.0, 0.0, 0.0
], [0.0, 1.0, 0.0, 0.0, 0.0, 1.0, -1.0, -1.0, -1.0, 0.0, 0.0, 0.0], [
-1.0, -1.0, -1.0, 0.0, 1.0, 0.0, 0.0, 0.0, 1.0, 0.0, 0.0, 0.0
], [1.0, 0.0, 0.0, -1.0, -1.0, -1.0, 0.0, 0.0, 1.0, 0.0, 0.0, 0.0]]
print(node_dict['output_settings'].data.operations)
assert node_dict['output_settings'].compare_operations(
expected_operations) == {}
expected_struct_attrs = {
'cell': [[0.0, 2.105, 2.105],
[2.105, 0.0, 2.105],
[2.105, 2.105, 0.0]],
'kinds': [
{'mass': 24.305,
'name': 'Mg',
'symbols': ['Mg'],
'weights': [1.0]},
{'mass': 15.9994, 'name': 'O',
'symbols': ['O'], 'weights': [1.0]}],
'pbc1': True,
'pbc2': True,
'pbc3': True,
'sites': [{'kind_name': 'Mg', 'position': [0.0, 0.0, 0.0]},
{'kind_name': 'O', 'position': [2.105, 2.105, 2.105]}]
}
assert edict.diff(
dict(node_dict['output_structure'].get_attrs()),
expected_struct_attrs, np_allclose=True) == {}
def test_spex_parser_entry_point(aiida_env):
from aiida.parsers import ParserFactory
from aiida_spex.parsers.spex import SpexParser
parser = ParserFactory('spex.spexparser')
assert parser == SpexParser
def test_fleur_parser_entry_point(aiida_env):
from aiida.parsers import ParserFactory
from aiida_fleur.parsers.fleur import FleurParser
parser = ParserFactory('fleur.fleurparser')
assert parser == FleurParser
def test_inpgen_parser_entry_point(aiida_env):
from aiida.parsers import ParserFactory
from aiida_fleur.parsers.fleur_inputgen import Fleur_inputgenParser
parser = ParserFactory('fleur.fleurinpgenparser')
assert parser == Fleur_inputgenParser
from aiida.orm.data.base import Bool
from aiida.orm.data.array import ArrayData
from aiida.orm.data.folder import FolderData
from aiida.orm.data.remote import RemoteData
from aiida.orm.data.parameter import ParameterData
from aiida.orm.data.array.kpoints import KpointsData
from aiida.parsers import ParserFactory
from aiida.work.workchain import while_
from aiida_quantumespresso.common.workchain.base.restart import BaseRestartWorkChain
from aiida_quantumespresso.common.workchain.utils import ErrorHandlerReport
from aiida_quantumespresso.common.workchain.utils import register_error_handler
from aiida_quantumespresso.utils.resources import get_default_options
PwCalculation = CalculationFactory('quantumespresso.pw')
HpCalculation = CalculationFactory('quantumespresso.hp')
HpParser = ParserFactory('quantumespresso.hp')
class HpBaseWorkChain(BaseRestartWorkChain):
"""
Base workchain to launch a Quantum Espresso hp.x calculation
"""
_verbose = False
_calculation_class = HpCalculation
ERROR_INCORRECT_ORDER_ATOMIC_POSITIONS = 4
ERROR_MISSING_PERTURBATION_FILE = 5
@classmethod
def define(cls, spec):
super(HpBaseWorkChain, cls).define(spec)
def test_parser_with_init_struct(new_database, new_workdir):
""" Test the parser
"""
from aiida.parsers import ParserFactory
from aiida.common.datastructures import calc_states
from aiida.common.folders import SandboxFolder
from aiida.orm import DataFactory
code = get_main_code(new_workdir)
calc = code.new_calc()
calc.set_resources({"num_machines": 1, "num_mpiprocs_per_machine": 1})
from aiida.orm.data.structure import StructureData
struct = StructureData()
struct.append_atom(position=[0, 0, 0], symbols="Mg", name="Mgx")
struct.append_atom(position=[0.5, 0.5, 0.5], symbols="O", name="Ox")
calc.use_structure(struct)
calc.store_all()
calc._set_state(calc_states.PARSING)
parser_cls = ParserFactory("crystal17.basic")
parser = parser_cls(calc)
with SandboxFolder() as folder:
main_out_path = os.path.join(os.path.dirname(tests.__file__),
"output_files",
"mgo_sto3g_scf.crystal.out")
with open(main_out_path) as f:
folder.create_file_from_filelike(f, "main.out")
fdata = DataFactory("folder")()
fdata.replace_with_folder(folder.abspath)
mock_retrieved = {calc._get_linkname_retrieved(): fdata}
success, node_list = parser.parse_with_retrieved(mock_retrieved)
assert success
node_dict = dict(node_list)
assert set(['output_parameters',
'output_settings']) == set(node_dict.keys())
expected_params = {
'parser_version': str(aiida_crystal17.__version__),
'ejplugins_version': str(ejplugins.__version__),
'parser_class': 'CryBasicParser',
'parser_warnings': [],
'errors': [],
'warnings': [],
'energy': -2.7121814374931E+02 * 27.21138602,
'energy_units': 'eV', # hartree to eV
'calculation_type': 'restricted closed shell',
'calculation_spin': False,
'wall_time_seconds': 3,
'number_of_atoms': 2,
'number_of_assymetric': 2,
'scf_iterations': 7,
'volume': 18.65461527264623,
}
assert edict.diff(node_dict['output_parameters'].get_dict(),
expected_params,
np_allclose=True) == {}
def test_siesta_parser_entry_point(siesta_develop):
from aiida.parsers import ParserFactory
siesta_parser = ParserFactory('siesta.parser')
assert siesta_parser is not None