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_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_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) == {}