def parse(self, **kwargs):
"""Receives in input a dictionary of retrieved nodes. Does all the logic here."""
try:
out_folder = self.retrieved
except NotExistent:
return self.exit_codes.ERROR_NO_RETRIEVED_FOLDER
output_folder_name = self.node.process_class.OUTPUT_FOLDER
if output_folder_name not in out_folder._repository.list_object_names(): # pylint: disable=protected-access
return self.exit_codes.ERROR_NO_OUTPUT_FILE
output_parameters = {}
warnings = []
ncomponents = len(self.node.inputs.parameters.get_dict()['Component'])
for system_id, system_name in enumerate(self.node.get_extra('system_order')):
# specify the name for the system
system = "System_{}".format(system_id)
fname = out_folder._repository.list_object_names(os.path.join(output_folder_name, system))[0] # pylint: disable=protected-access
# get absolute path of the output file
output_abs_path = os.path.join(
out_folder._repository._get_base_folder().abspath, # pylint: disable=protected-access
self.node.process_class.OUTPUT_FOLDER,
system,
fname)
# Check for possible errors
with open(output_abs_path) as fobj:
content = fobj.read()
if "Starting simulation" not in content:
return self.exit_codes.ERROR_SIMULATION_DID_NOT_START
if "Simulation finished" not in content:
return self.exit_codes.TIMEOUT
# parse output parameters and warnings
parsed_parameters, parsed_warnings = parse_base_output(output_abs_path, system_name, ncomponents)
output_parameters[system_name] = parsed_parameters
warnings += parsed_warnings
self.out("output_parameters", Dict(dict=output_parameters))
self.out("warnings", List(list=warnings))
return ExitCode(0)
def test_parse_output_widom():
"""Testing output parser on an output file of a widom calculation of H2 in an empty COF"""
parsed_parameters = parse_base_output(os.path.join(CWD, "outputs/widom_insertion.out"),
system_name="system1",
ncomponents=1)[0]
general = {
'exceeded_walltime': False,
'framework_density': '935.523150616336',
'framework_density_unit': 'kg/m^3',
'energy_unit': 'kJ/mol',
'energy_host/ads_tot_initial': 0.0,
'energy_host/ads_vdw_initial': 0.0,
'energy_host/ads_coulomb_initial': 0.0,
'energy_host/ads_tot_final': 0.0,
'energy_host/ads_vdw_final': 0.0,
'energy_host/ads_coulomb_final': 0.0,
'cell_volume_average': 56953.44,
'cell_volume_unit': 'A^3',
'cell_volume_dev': 0.0,
'box_ax_average': 46.009,
'box_ax_unit': 'A^3',
'box_ax_dev': 0.0,
'box_by_average': 46.01567,
'box_by_unit': 'A^3',
'box_by_dev': 0.0,
'box_cz_average': 26.90119,
'box_cz_unit': 'A^3',
'box_cz_dev': 0.0,
'box_alpha_average': 121.11,
'box_alpha_unit': 'degrees',
'box_alpha_dev': 0.0,
'box_beta_average': 89.6387,
'box_beta_unit': 'degrees',
'box_beta_dev': 0.0,
'box_gamma_average': 90.2479,
'box_gamma_unit': 'degrees',
'box_gamma_dev': 0.0,
'adsorbate_density_average': 0.0,
'adsorbate_density_unit': 'kg/m^3',
'adsorbate_density_dev': 0.0,
'enthalpy_of_adsorption_average': None,
'enthalpy_of_adsorption_unit': 'K',
'enthalpy_of_adsorption_dev': None,
'energy_ads/ads_tot_average': 0.0,
'energy_ads/ads_vdw_average': 0.0,
'energy_ads/ads_coulomb_average': 0.0,
'energy_ads/ads_tot_dev': 0.0,
'energy_ads/ads_vdw_dev': 0.0,
'energy_ads/ads_coulomb_dev': 0.0,
'energy_host/ads_tot_average': 0.0,
'energy_host/ads_vdw_average': 0.0,
'energy_host/ads_coulomb_average': 0.0,
'energy_host/ads_tot_dev': 0.0,
'energy_host/ads_vdw_dev': 0.0,
'energy_host/ads_coulomb_dev': 0.0,
'tail_correction_energy_average': -37375.15068,
'tail_correction_energy_unit': 'K',
'tail_correction_energy_dev': 0.0
}
hydrogen = {
'mol_fraction': 1.0,
'mol_fraction_unit': '-',
'conversion_factor_molec_uc_to_mol_kg': 0.1246621177,
'conversion_factor_molec_uc_to_mol_kg_unit': '(mol/kg)/(molec/uc)',
'conversion_factor_molec_uc_to_mg_g': 0.2493242354,
'conversion_factor_molec_uc_to_mg_g_unit': '(mg/g)/(molec/uc)',
'conversion_factor_molec_uc_to_cm3stp_gr': 2.7941736824,
'conversion_factor_molec_uc_to_cm3stp_gr_unit': '(cm^3_STP/gr)/(molec/uc)',
'conversion_factor_molec_uc_to_cm3stp_cm3': 2.6140141668,
'conversion_factor_molec_uc_to_cm3stp_cm3_unit': '(cm^3_STP/cm^3)/(molec/uc)',
'partial_pressure': -16605402.0,
'partial_pressure_unit': 'Pa',
'partial_fugacity': 16605402.0,
'partial_fugacity_unit': 'Pa',
'adsorbate_density_average': 0.0,
'adsorbate_density_unit': 'kg/m^3',
'adsorbate_density_dev': 0.0,
'loading_absolute_average': 0.0,
'loading_absolute_dev': 0.0,
'loading_absolute_unit': 'molecules/unit cell',
'loading_excess_average': 0.0,
'loading_excess_dev': 0.0,
'loading_excess_unit': 'molecules/unit cell',
'widom_rosenbluth_factor_unit': '-',
'widom_rosenbluth_factor_dev': 78741.06669,
'widom_rosenbluth_factor_average': 6973260.0,
'chemical_potential_unit': 'K',
'chemical_potential_dev': 0.86752,
'chemical_potential_average': -2056.48,
'henry_coefficient_unit': 'mol/kg/Pa',
'henry_coefficient_dev': 0.131469,
'henry_coefficient_average': 11.6428,
'adsorption_energy_widom_unit': 'kJ/mol',
'adsorption_energy_widom_dev': 0.0111060559,
'adsorption_energy_widom_average': -13.5545306415
}
for key, value in general.items():
assert value == parsed_parameters['general'][key]
for key, value in hydrogen.items():
assert value == parsed_parameters['components']['H2'][key]
def test_parse_output_one_cmpnt():
"""Testing output parser on an output file with one component"""
parsed_parameters = parse_base_output(os.path.join(CWD, "outputs/one_component.out"),
system_name="system1",
ncomponents=1)[0]
general = {
'exceeded_walltime': False,
'framework_density': '739.995779685958',
'framework_density_unit': 'kg/m^3',
'energy_unit': 'kJ/mol',
'energy_host/ads_tot_initial': 0.0,
'energy_host/ads_vdw_initial': 0.0,
'energy_host/ads_coulomb_initial': 0.0,
'energy_host/ads_tot_final': -171.717724280208,
'energy_host/ads_vdw_final': -171.717724280208,
'energy_host/ads_coulomb_final': 0.0,
'cell_volume_average': 12025.61229,
'cell_volume_unit': 'A^3',
'cell_volume_dev': 0.0,
'box_ax_average': 34.1995,
'box_ax_unit': 'A^3',
'box_ax_dev': 0.0,
'box_by_average': 22.6557,
'box_by_unit': 'A^3',
'box_by_dev': 0.0,
'box_cz_average': 15.52065,
'box_cz_unit': 'A^3',
'box_cz_dev': 0.0,
'box_alpha_average': 90.0,
'box_alpha_unit': 'degrees',
'box_alpha_dev': 0.0,
'box_beta_average': 52.8626,
'box_beta_unit': 'degrees',
'box_beta_dev': 0.0,
'box_gamma_average': 90.0,
'box_gamma_unit': 'degrees',
'box_gamma_dev': 0.0,
'adsorbate_density_average': 26.62672,
'adsorbate_density_unit': 'kg/m^3',
'adsorbate_density_dev': 5.35266,
'enthalpy_of_adsorption_average': -1928.58214,
'enthalpy_of_adsorption_unit': 'K',
'enthalpy_of_adsorption_dev': 204.730157,
'energy_ads/ads_tot_average': -4.5501817208796655,
'energy_ads/ads_vdw_average': -4.550181687621805,
'energy_ads/ads_coulomb_average': 0.0,
'energy_ads/ads_tot_dev': 2.0057559085076093,
'energy_ads/ads_vdw_dev': 2.0057559334510042,
'energy_ads/ads_coulomb_dev': 0.0,
'energy_host/ads_tot_average': -174.60996722014394,
'energy_host/ads_vdw_average': -174.60996720351505,
'energy_host/ads_coulomb_average': 0.0,
'energy_host/ads_tot_dev': 34.12887304355653,
'energy_host/ads_vdw_dev': 34.12887304355653,
'energy_host/ads_coulomb_dev': 0.0,
'tail_correction_energy_average': 0.0,
'tail_correction_energy_unit': 'K',
'tail_correction_energy_dev': 0.0
}
methane = {
'mol_fraction': 1.0,
'mol_fraction_unit': '-',
'conversion_factor_molec_uc_to_mol_kg': 0.1866003989,
'conversion_factor_molec_uc_to_mol_kg_unit': '(mol/kg)/(molec/uc)',
'conversion_factor_molec_uc_to_mg_g': 2.9935294361,
'conversion_factor_molec_uc_to_mg_g_unit': '(mg/g)/(molec/uc)',
'conversion_factor_molec_uc_to_cm3stp_gr': 4.1824568165,
'conversion_factor_molec_uc_to_cm3stp_gr_unit': '(cm^3_STP/gr)/(molec/uc)',
'conversion_factor_molec_uc_to_cm3stp_cm3': 3.095000393,
'conversion_factor_molec_uc_to_cm3stp_cm3_unit': '(cm^3_STP/cm^3)/(molec/uc)',
'partial_pressure': 500000.0,
'partial_pressure_unit': 'Pa',
'partial_fugacity': 494612.1383597442,
'partial_fugacity_unit': 'Pa',
'adsorbate_density_average': 26.62672,
'adsorbate_density_unit': 'kg/m^3',
'adsorbate_density_dev': 5.35266,
'loading_absolute_average': 12.02,
'loading_absolute_dev': 2.4163298616,
'loading_absolute_unit': 'molecules/unit cell',
'loading_excess_average': 11.02,
'loading_excess_dev': 2.4163298616,
'loading_excess_unit': 'molecules/unit cell',
'widom_rosenbluth_factor_unit': '-',
'widom_rosenbluth_factor_dev': None,
'widom_rosenbluth_factor_average': None,
'chemical_potential_unit': 'K',
'chemical_potential_dev': None,
'chemical_potential_average': None,
'henry_coefficient_unit': 'mol/kg/Pa',
'henry_coefficient_dev': None,
'henry_coefficient_average': None,
'adsorption_energy_widom_unit': 'kJ/mol',
'adsorption_energy_widom_dev': None,
'adsorption_energy_widom_average': None
}
for key, value in general.items():
assert value == parsed_parameters['general'][key]
for key, value in methane.items():
assert value == parsed_parameters['components']['methane'][key]
def test_parse_output_two_cmpnt():
"""Testing output parser on an output file with two components"""
parsed_parameters = parse_base_output(os.path.join(CWD, "outputs/two_components.out"),
system_name="system1",
ncomponents=2)[0]
general = {
'exceeded_walltime': False,
'framework_density': '0.000000000000',
'framework_density_unit': 'kg/m^3',
'energy_unit': 'kJ/mol',
'energy_host/ads_tot_initial': 0.0,
'energy_host/ads_vdw_initial': 0.0,
'energy_host/ads_coulomb_initial': 0.0,
'energy_host/ads_tot_final': 0.0,
'energy_host/ads_vdw_final': 0.0,
'energy_host/ads_coulomb_final': 0.0,
'cell_volume_average': 15625.0,
'cell_volume_unit': 'A^3',
'cell_volume_dev': 0.0,
'box_ax_average': 25.0,
'box_ax_unit': 'A^3',
'box_ax_dev': 0.0,
'box_by_average': 25.0,
'box_by_unit': 'A^3',
'box_by_dev': 0.0,
'box_cz_average': 25.0,
'box_cz_unit': 'A^3',
'box_cz_dev': 0.0,
'box_alpha_average': 90.0,
'box_alpha_unit': 'degrees',
'box_alpha_dev': 0.0,
'box_beta_average': 90.0,
'box_beta_unit': 'degrees',
'box_beta_dev': 0.0,
'box_gamma_average': 90.0,
'box_gamma_unit': 'degrees',
'box_gamma_dev': 0.0,
'adsorbate_density_average': 4.40397,
'adsorbate_density_unit': 'kg/m^3',
'adsorbate_density_dev': 0.74921,
'enthalpy_of_adsorption_average': 137.68727,
'enthalpy_of_adsorption_unit': 'K',
'enthalpy_of_adsorption_dev': 86.158033,
'energy_ads/ads_tot_average': -0.15252104334203112,
'energy_ads/ads_vdw_average': -0.15252104334203112,
'energy_ads/ads_coulomb_average': 0.0,
'energy_ads/ads_tot_dev': 0.16141328042825245,
'energy_ads/ads_vdw_dev': 0.16141332200057704,
'energy_ads/ads_coulomb_dev': 0.0,
'energy_host/ads_tot_average': 0.0,
'energy_host/ads_vdw_average': 0.0,
'energy_host/ads_coulomb_average': 0.0,
'energy_host/ads_tot_dev': 0.0,
'energy_host/ads_vdw_dev': 0.0,
'energy_host/ads_coulomb_dev': 0.0,
'tail_correction_energy_average': 0.0,
'tail_correction_energy_unit': 'K',
'tail_correction_energy_dev': 0.0
}
butane = {
'mol_fraction': 0.5,
'mol_fraction_unit': '-',
'conversion_factor_molec_uc_to_mol_kg': None,
'conversion_factor_molec_uc_to_mol_kg_unit': '(mol/kg)/(molec/uc)',
'conversion_factor_molec_uc_to_mg_g': None,
'conversion_factor_molec_uc_to_mg_g_unit': '(mg/g)/(molec/uc)',
'conversion_factor_molec_uc_to_cm3stp_gr': None,
'conversion_factor_molec_uc_to_cm3stp_gr_unit': '(cm^3_STP/gr)/(molec/uc)',
'conversion_factor_molec_uc_to_cm3stp_cm3': 2.3820335839,
'conversion_factor_molec_uc_to_cm3stp_cm3_unit': '(cm^3_STP/cm^3)/(molec/uc)',
'partial_pressure': 250000.0,
'partial_pressure_unit': 'Pa',
'partial_fugacity': 121261.37081517381,
'partial_fugacity_unit': 'Pa',
'adsorbate_density_average': 0.43238,
'adsorbate_density_unit': 'kg/m^3',
'adsorbate_density_dev': 0.23112,
'enthalpy_of_adsorption_average': 740.33952,
'enthalpy_of_adsorption_unit': 'K',
'enthalpy_of_adsorption_dev': 398.536954,
'loading_absolute_average': 0.07,
'loading_absolute_dev': 0.0374165739,
'loading_absolute_unit': 'molecules/unit cell',
'loading_excess_average': 0.07,
'loading_excess_dev': 0.0374165739,
'loading_excess_unit': 'molecules/unit cell',
'widom_rosenbluth_factor_unit': '-',
'widom_rosenbluth_factor_dev': None,
'widom_rosenbluth_factor_average': None,
'chemical_potential_unit': 'K',
'chemical_potential_dev': None,
'chemical_potential_average': None,
'henry_coefficient_unit': 'mol/kg/Pa',
'henry_coefficient_dev': None,
'henry_coefficient_average': None,
'adsorption_energy_widom_unit': 'kJ/mol',
'adsorption_energy_widom_dev': None,
'adsorption_energy_widom_average': None
}
propane = {
'mol_fraction': 0.5,
'mol_fraction_unit': '-',
'conversion_factor_molec_uc_to_mol_kg': None,
'conversion_factor_molec_uc_to_mol_kg_unit': '(mol/kg)/(molec/uc)',
'conversion_factor_molec_uc_to_mg_g': None,
'conversion_factor_molec_uc_to_mg_g_unit': '(mg/g)/(molec/uc)',
'conversion_factor_molec_uc_to_cm3stp_gr': None,
'conversion_factor_molec_uc_to_cm3stp_gr_unit': '(cm^3_STP/gr)/(molec/uc)',
'conversion_factor_molec_uc_to_cm3stp_cm3': 2.3820335839,
'conversion_factor_molec_uc_to_cm3stp_cm3_unit': '(cm^3_STP/cm^3)/(molec/uc)',
'partial_pressure': 250000.0,
'partial_pressure_unit': 'Pa',
'partial_fugacity': 230618.81828829306,
'partial_fugacity_unit': 'Pa',
'adsorbate_density_average': 3.97159,
'adsorbate_density_unit': 'kg/m^3',
'adsorbate_density_dev': 0.7045,
'enthalpy_of_adsorption_average': 103.567,
'enthalpy_of_adsorption_unit': 'K',
'enthalpy_of_adsorption_dev': 98.162438,
'loading_absolute_average': 0.8475,
'loading_absolute_dev': 0.1503329638,
'loading_absolute_unit': 'molecules/unit cell',
'loading_excess_average': 0.8475,
'loading_excess_dev': 0.1503329638,
'loading_excess_unit': 'molecules/unit cell',
'widom_rosenbluth_factor_unit': '-',
'widom_rosenbluth_factor_dev': None,
'widom_rosenbluth_factor_average': None,
'chemical_potential_unit': 'K',
'chemical_potential_dev': None,
'chemical_potential_average': None,
'henry_coefficient_unit': 'mol/kg/Pa',
'henry_coefficient_dev': None,
'henry_coefficient_average': None,
'adsorption_energy_widom_unit': 'kJ/mol',
'adsorption_energy_widom_dev': None,
'adsorption_energy_widom_average': None
}
for key, value in general.items():
assert value == parsed_parameters['general'][key]
for key, value in butane.items():
assert value == parsed_parameters['components']['butane'][key]
for key, value in propane.items():
assert value == parsed_parameters['components']['propane'][key]