From 9c9ebd393a360a3a4dc0009864f562d0503cf966 Mon Sep 17 00:00:00 2001 From: ndaelman Date: Fri, 15 Nov 2024 17:49:57 +0100 Subject: [PATCH 1/4] Remove `extends_base_section` --- electronicparsers/abacus/metainfo/abacus.py | 18 +++++++-------- electronicparsers/abinit/metainfo/abinit.py | 12 +++++----- .../abinit/metainfo/abinit_autogenerated.py | 2 +- electronicparsers/ams/metainfo/ams.py | 22 +++++++++---------- electronicparsers/atk/metainfo/atk.py | 2 +- electronicparsers/castep/metainfo/castep.py | 16 +++++++------- electronicparsers/charmm/metainfo/charmm.py | 12 +++++----- electronicparsers/cp2k/metainfo/cp2k.py | 2 +- .../cp2k/metainfo/cp2k_general.py | 12 +++++----- electronicparsers/cpmd/metainfo/cpmd.py | 2 +- .../cpmd/metainfo/cpmd_general.py | 12 +++++----- electronicparsers/crystal/metainfo/crystal.py | 10 ++++----- electronicparsers/dmol3/metainfo/dmol3.py | 16 +++++++------- electronicparsers/edmft/metainfo/edmft.py | 4 ++-- electronicparsers/elk/metainfo/elk.py | 8 +++---- .../exciting/metainfo/exciting.py | 12 +++++----- .../fhiaims/metainfo/fhi_aims.py | 20 ++++++++--------- electronicparsers/fleur/metainfo/fleur.py | 14 ++++++------ electronicparsers/fplo/metainfo/fplo.py | 8 +++---- .../fplo/metainfo/fplo_input_autogenerated.py | 2 +- .../fplo/metainfo/fplo_temporaries.py | 8 +++---- electronicparsers/gamess/metainfo/gamess.py | 14 ++++++------ electronicparsers/gpaw/metainfo/gpaw.py | 4 ++-- electronicparsers/molcas/metainfo/molcas.py | 4 ++-- electronicparsers/mopac/metainfo/mopac.py | 4 ++-- electronicparsers/nwchem/metainfo/nwchem.py | 10 ++++----- electronicparsers/ocean/metainfo/ocean.py | 6 ++--- electronicparsers/octopus/metainfo/octopus.py | 4 ++-- .../octopus/metainfo/octopus_autogenerated.py | 2 +- electronicparsers/onetep/metainfo/onetep.py | 22 +++++++++---------- electronicparsers/orca/metainfo/orca.py | 18 +++++++-------- electronicparsers/psi4/metainfo/psi4.py | 14 ++++++------ electronicparsers/qbox/metainfo/qbox.py | 10 ++++----- .../metainfo/quantum_espresso.py | 16 +++++++------- electronicparsers/siesta/metainfo/siesta.py | 8 +++---- .../siesta/metainfo/siesta_autogenerated.py | 2 +- .../soliddmft/metainfo/soliddmft.py | 6 ++--- .../turbomole/metainfo/turbomole.py | 14 ++++++------ electronicparsers/vasp/metainfo/vasp.py | 12 +++++----- .../vasp/metainfo/vasp_incars.py | 2 +- .../vasp/metainfo/vasp_incarsOut.py | 2 +- .../vasp/metainfo/vasp_incarsUnknown.py | 2 +- .../w2dynamics/metainfo/w2dynamics.py | 6 ++--- .../wannier90/metainfo/wannier90.py | 2 +- electronicparsers/wien2k/metainfo/wien2k.py | 8 +++---- electronicparsers/yambo/metainfo/yambo.py | 8 +++---- 46 files changed, 207 insertions(+), 207 deletions(-) diff --git a/electronicparsers/abacus/metainfo/abacus.py b/electronicparsers/abacus/metainfo/abacus.py index 8e054b39..a58da9d4 100644 --- a/electronicparsers/abacus/metainfo/abacus.py +++ b/electronicparsers/abacus/metainfo/abacus.py @@ -187,7 +187,7 @@ class BasisSet(runschema.method.BasisSet): section for numerical atomic orbitals of ABACUS """ - m_def = Section(validate=False, extends_base_section=True) + m_def = Section(validate=False) x_abacus_basis_sets_delta_k = Quantity( type=np.float64, @@ -232,7 +232,7 @@ class BasisSet(runschema.method.BasisSet): class Calculation(runschema.calculation.Calculation): - m_def = Section(validate=False, extends_base_section=True) + m_def = Section(validate=False) x_abacus_init_velocities = Quantity( type=bool, @@ -321,7 +321,7 @@ class Calculation(runschema.calculation.Calculation): class Run(runschema.run.Run): - m_def = Section(validate=False, extends_base_section=True) + m_def = Section(validate=False) x_abacus_input_filename = Quantity( type=str, @@ -396,7 +396,7 @@ class Run(runschema.run.Run): class Method(runschema.method.Method): - m_def = Section(validate=False, extends_base_section=True) + m_def = Section(validate=False) x_abacus_initial_magnetization_total = Quantity( type=np.float64, @@ -613,7 +613,7 @@ class Method(runschema.method.Method): class System(runschema.system.System): - m_def = Section(validate=False, extends_base_section=True) + m_def = Section(validate=False) x_abacus_alat = Quantity( type=np.float64, @@ -693,7 +693,7 @@ class System(runschema.system.System): class Symmetry(runschema.system.Symmetry): - m_def = Section(validate=False, extends_base_section=True) + m_def = Section(validate=False) x_abacus_ibrav = Quantity( type=np.int32, @@ -737,7 +737,7 @@ class Symmetry(runschema.system.Symmetry): class AtomParameters(runschema.method.AtomParameters): - m_def = Section(validate=False, extends_base_section=True) + m_def = Section(validate=False) x_abacus_pp_type = Quantity( type=str, @@ -781,7 +781,7 @@ class AtomParameters(runschema.method.AtomParameters): class ScfIteration(runschema.calculation.ScfIteration): - m_def = Section(validate=False, extends_base_section=True) + m_def = Section(validate=False) x_abacus_density_change_scf_iteration = Quantity( type=np.float64, @@ -822,7 +822,7 @@ class ScfIteration(runschema.calculation.ScfIteration): class BandEnergies(runschema.calculation.BandEnergies): - m_def = Section(validate=False, extends_base_section=True) + m_def = Section(validate=False) x_abacus_eigenvalues_number_of_planewaves = Quantity( type=np.int32, diff --git a/electronicparsers/abinit/metainfo/abinit.py b/electronicparsers/abinit/metainfo/abinit.py index 4e01ecb0..c420ebaa 100644 --- a/electronicparsers/abinit/metainfo/abinit.py +++ b/electronicparsers/abinit/metainfo/abinit.py @@ -177,7 +177,7 @@ class x_abinit_section_var(MSection): class Run(runschema.run.Run): - m_def = Section(validate=False, extends_base_section=True) + m_def = Section(validate=False) x_abinit_parallel_compilation = Quantity( type=str, @@ -265,7 +265,7 @@ class Run(runschema.run.Run): class Method(runschema.method.Method): - m_def = Section(validate=False, extends_base_section=True) + m_def = Section(validate=False) x_abinit_tolvrs = Quantity( type=np.float64, @@ -310,7 +310,7 @@ class Method(runschema.method.Method): class System(runschema.system.System): - m_def = Section(validate=False, extends_base_section=True) + m_def = Section(validate=False) x_abinit_atom_xcart_final = Quantity( type=str, @@ -553,7 +553,7 @@ class BandEnergies(runschema.calculation.BandEnergies): Could be depricated later on, since it runs counter to the regular way of working. """ - m_def = Section(validate=False, extends_base_section=True) + m_def = Section(validate=False) x_abinit_qp_band_gaps_params = SubSection( sub_section=x_abinit_qp_band_gaps_params.m_def, repeats=False @@ -728,7 +728,7 @@ class x_abinit_gw_dataset(MSection): class Calculation(runschema.calculation.Calculation): - m_def = Section(validate=False, extends_base_section=True) + m_def = Section(validate=False) x_abinit_magnetisation = Quantity( type=np.float64, @@ -848,7 +848,7 @@ class Calculation(runschema.calculation.Calculation): class x_abinit_section_dataset(abinit_autogenerated.x_abinit_section_dataset): - m_def = Section(validate=False, extends_base_section=True) + m_def = Section(validate=False) x_abinit_geometry_optimization_converged = Quantity( type=str, diff --git a/electronicparsers/abinit/metainfo/abinit_autogenerated.py b/electronicparsers/abinit/metainfo/abinit_autogenerated.py index b6308cc6..e4693202 100644 --- a/electronicparsers/abinit/metainfo/abinit_autogenerated.py +++ b/electronicparsers/abinit/metainfo/abinit_autogenerated.py @@ -6787,7 +6787,7 @@ class x_abinit_section_dataset(MSection): class Run(runschema.run.Run): - m_def = Section(validate=False, extends_base_section=True) + m_def = Section(validate=False) x_abinit_section_dataset = SubSection( sub_section=x_abinit_section_dataset.m_def, repeats=True diff --git a/electronicparsers/ams/metainfo/ams.py b/electronicparsers/ams/metainfo/ams.py index c6eb0a4e..900ac17a 100644 --- a/electronicparsers/ams/metainfo/ams.py +++ b/electronicparsers/ams/metainfo/ams.py @@ -41,7 +41,7 @@ class Program(runschema.run.Program): - m_def = Section(validate=False, extends_base_section=True) + m_def = Section(validate=False) x_ams_name = Quantity( type=str, @@ -59,7 +59,7 @@ class Program(runschema.run.Program): class BandEnergies(runschema.calculation.BandEnergies): - m_def = Section(validate=False, extends_base_section=True) + m_def = Section(validate=False) x_ams_energy_min = Quantity( type=np.float64, @@ -87,7 +87,7 @@ class BandEnergies(runschema.calculation.BandEnergies): class Energy(runschema.calculation.Energy): - m_def = Section(validate=False, extends_base_section=True) + m_def = Section(validate=False) x_ams_dispersion = SubSection(sub_section=runschema.calculation.EnergyEntry) @@ -161,7 +161,7 @@ class Energy(runschema.calculation.Energy): class Forces(runschema.calculation.Forces): - m_def = Section(validate=False, extends_base_section=True) + m_def = Section(validate=False) x_ams_p_matrix = SubSection(sub_section=runschema.calculation.ForcesEntry) @@ -181,7 +181,7 @@ class Forces(runschema.calculation.Forces): class GeometryOptimization(simulationworkflowschema.GeometryOptimization): - m_def = Section(validate=False, extends_base_section=True) + m_def = Section(validate=False) x_ams_optimization_coordinates = Quantity( type=str, @@ -284,7 +284,7 @@ class GeometryOptimization(simulationworkflowschema.GeometryOptimization): class Method(runschema.method.Method): - m_def = Section(validate=False, extends_base_section=True) + m_def = Section(validate=False) x_ams_dftb_resources_dir = Quantity( type=str, @@ -450,7 +450,7 @@ class Method(runschema.method.Method): class BasisSetAtomCentered(runschema.method.BasisSetAtomCentered): - m_def = Section(validate=False, extends_base_section=True) + m_def = Section(validate=False) x_ams_basis_functions_confinement_radius = Quantity( type=np.float64, @@ -468,7 +468,7 @@ class BasisSetAtomCentered(runschema.method.BasisSetAtomCentered): class AtomParameters(runschema.method.AtomParameters): - m_def = Section(validate=False, extends_base_section=True) + m_def = Section(validate=False) x_ams_radial_points = Quantity( type=np.int32, @@ -597,7 +597,7 @@ class AtomParameters(runschema.method.AtomParameters): class BandGapDeprecated(runschema.calculation.BandGapDeprecated): - m_def = Section(validate=False, extends_base_section=True) + m_def = Section(validate=False) x_ams_n_valence_electrons = Quantity( type=np.int32, @@ -636,7 +636,7 @@ class BandGapDeprecated(runschema.calculation.BandGapDeprecated): class Scf(runschema.method.Scf): - m_def = Section(validate=False, extends_base_section=True) + m_def = Section(validate=False) x_ams_diis_settings_dirac = Quantity( type=JSON, @@ -717,7 +717,7 @@ class Scf(runschema.method.Scf): class KMesh(runschema.method.KMesh): - m_def = Section(validate=False, extends_base_section=True) + m_def = Section(validate=False) x_ams_general_integration_parameter = Quantity( type=np.int32, diff --git a/electronicparsers/atk/metainfo/atk.py b/electronicparsers/atk/metainfo/atk.py index 392c115e..fdb8051a 100644 --- a/electronicparsers/atk/metainfo/atk.py +++ b/electronicparsers/atk/metainfo/atk.py @@ -36,7 +36,7 @@ class Method(method.Method): - m_def = Section(validate=False, extends_base_section=True) + m_def = Section(validate=False) x_atk_density_convergence_criterion = Quantity( type=np.float64, diff --git a/electronicparsers/castep/metainfo/castep.py b/electronicparsers/castep/metainfo/castep.py index 44389761..9f559765 100644 --- a/electronicparsers/castep/metainfo/castep.py +++ b/electronicparsers/castep/metainfo/castep.py @@ -1754,7 +1754,7 @@ class x_castep_section_van_der_Waals_parameters(MSection): class Run(runschema.run.Run): - m_def = Section(validate=False, extends_base_section=True) + m_def = Section(validate=False) x_castep_atom_forces = Quantity( type=np.float64, @@ -2017,7 +2017,7 @@ class Run(runschema.run.Run): class System(runschema.system.System): - m_def = Section(validate=False, extends_base_section=True) + m_def = Section(validate=False) x_castep_net_charge = Quantity( type=np.float64, @@ -2165,7 +2165,7 @@ class System(runschema.system.System): class BasisSet(runschema.method.BasisSet): - m_def = Section(validate=False, extends_base_section=True) + m_def = Section(validate=False) x_castep_size_std_grid = Quantity( type=np.float64, @@ -2185,7 +2185,7 @@ class BasisSet(runschema.method.BasisSet): class Calculation(runschema.calculation.Calculation): - m_def = Section(validate=False, extends_base_section=True) + m_def = Section(validate=False) x_castep_enthalpy = Quantity( type=np.float64, @@ -2299,7 +2299,7 @@ class Calculation(runschema.calculation.Calculation): class Method(runschema.method.Method): - m_def = Section(validate=False, extends_base_section=True) + m_def = Section(validate=False) x_castep_functional_and_weight = Quantity( type=str, @@ -2323,7 +2323,7 @@ class Method(runschema.method.Method): class MolecularDynamicsMethod(simulationworkflowschema.MolecularDynamicsMethod): - m_def = Section(validate=False, extends_base_section=True) + m_def = Section(validate=False) x_castep_thermostat_target_temperature = Quantity( type=np.float64, @@ -2413,7 +2413,7 @@ class MolecularDynamicsMethod(simulationworkflowschema.MolecularDynamicsMethod): class GeometryOptimizationMethod(simulationworkflowschema.GeometryOptimizationMethod): - m_def = Section(validate=False, extends_base_section=True) + m_def = Section(validate=False) x_castep_geometry_stress_com_tolerance = Quantity( type=np.float64, @@ -2434,7 +2434,7 @@ class GeometryOptimizationMethod(simulationworkflowschema.GeometryOptimizationMe class BandStructure(runschema.calculation.BandStructure): - m_def = Section(validate=False, extends_base_section=True) + m_def = Section(validate=False) x_castep_k_path = Quantity( type=np.float64, diff --git a/electronicparsers/charmm/metainfo/charmm.py b/electronicparsers/charmm/metainfo/charmm.py index 879a07b8..6f652f96 100644 --- a/electronicparsers/charmm/metainfo/charmm.py +++ b/electronicparsers/charmm/metainfo/charmm.py @@ -1404,7 +1404,7 @@ class x_charmm_section_single_configuration_calculation(MSection): class System(runschema.system.System): - m_def = Section(validate=False, extends_base_section=True) + m_def = Section(validate=False) x_charmm_atom_positions_image_index = Quantity( type=np.int32, @@ -1515,7 +1515,7 @@ class System(runschema.system.System): class MolecularDynamics(simulationworkflowschema.MolecularDynamics): - m_def = Section(validate=False, extends_base_section=True) + m_def = Section(validate=False) x_charmm_barostat_target_pressure = Quantity( type=np.float64, @@ -1621,7 +1621,7 @@ class MolecularDynamics(simulationworkflowschema.MolecularDynamics): class AtomParameters(runschema.method.AtomParameters): - m_def = Section(validate=False, extends_base_section=True) + m_def = Section(validate=False) x_charmm_atom_name = Quantity( type=str, @@ -1673,7 +1673,7 @@ class AtomParameters(runschema.method.AtomParameters): class Interaction(runschema.method.Interaction): - m_def = Section(validate=False, extends_base_section=True) + m_def = Section(validate=False) x_charmm_interaction_atom_to_atom_type_ref = Quantity( type=runschema.method.AtomParameters, @@ -1747,7 +1747,7 @@ class Interaction(runschema.method.Interaction): class Run(runschema.run.Run): - m_def = Section(validate=False, extends_base_section=True) + m_def = Section(validate=False) x_charmm_program_version_date = Quantity( type=str, @@ -1923,7 +1923,7 @@ class Run(runschema.run.Run): class Calculation(runschema.calculation.Calculation): - m_def = Section(validate=False, extends_base_section=True) + m_def = Section(validate=False) x_charmm_section_single_configuration_calculation = SubSection( sub_section=SectionProxy('x_charmm_section_single_configuration_calculation'), diff --git a/electronicparsers/cp2k/metainfo/cp2k.py b/electronicparsers/cp2k/metainfo/cp2k.py index 66487dbf..0fc36aaa 100644 --- a/electronicparsers/cp2k/metainfo/cp2k.py +++ b/electronicparsers/cp2k/metainfo/cp2k.py @@ -59178,7 +59178,7 @@ class x_cp2k_section_input(MSection): class Run(runschema.run.Run): - m_def = Section(validate=False, extends_base_section=True) + m_def = Section(validate=False) x_cp2k_section_input = SubSection( sub_section=SectionProxy('x_cp2k_section_input'), repeats=True diff --git a/electronicparsers/cp2k/metainfo/cp2k_general.py b/electronicparsers/cp2k/metainfo/cp2k_general.py index cf6bb37a..e2679b6b 100644 --- a/electronicparsers/cp2k/metainfo/cp2k_general.py +++ b/electronicparsers/cp2k/metainfo/cp2k_general.py @@ -861,7 +861,7 @@ class x_cp2k_section_kind_basis_set(MSection): class Run(runschema.run.Run): - m_def = Section(validate=False, extends_base_section=True) + m_def = Section(validate=False) x_cp2k_section_restart_information = SubSection( sub_section=SectionProxy('x_cp2k_section_restart_information'), repeats=True @@ -901,7 +901,7 @@ class Run(runschema.run.Run): class GeometryOptimization(simulationworkflowschema.GeometryOptimization): - m_def = Section(validate=False, extends_base_section=True) + m_def = Section(validate=False) x_cp2k_section_geometry_optimization = SubSection( sub_section=SectionProxy('x_cp2k_section_geometry_optimization'), repeats=True @@ -909,7 +909,7 @@ class GeometryOptimization(simulationworkflowschema.GeometryOptimization): class GeometryOptimizationMethod(simulationworkflowschema.GeometryOptimizationMethod): - m_def = Section(validate=False, extends_base_section=True) + m_def = Section(validate=False) x_cp2k_section_geometry_optimization = SubSection( sub_section=SectionProxy('x_cp2k_section_geometry_optimization'), repeats=True @@ -917,7 +917,7 @@ class GeometryOptimizationMethod(simulationworkflowschema.GeometryOptimizationMe class MolecularDynamicsMethod(simulationworkflowschema.MolecularDynamicsMethod): - m_def = Section(validate=False, extends_base_section=True) + m_def = Section(validate=False) x_cp2k_section_md_settings = SubSection( sub_section=SectionProxy('x_cp2k_section_md_settings'), repeats=True @@ -925,7 +925,7 @@ class MolecularDynamicsMethod(simulationworkflowschema.MolecularDynamicsMethod): class Method(runschema.method.Method): - m_def = Section(validate=False, extends_base_section=True) + m_def = Section(validate=False) x_cp2k_section_quickstep_settings = SubSection( sub_section=SectionProxy('x_cp2k_section_quickstep_settings'), repeats=True @@ -1009,6 +1009,6 @@ class x_cp2k_pdos_histogram(MSection): class Calculation(runschema.calculation.Calculation): - m_def = Section(validate=False, extends_base_section=True) + m_def = Section(validate=False) x_cp2k_pdos = SubSection(sub_section=x_cp2k_pdos_histogram.m_def, repeats=True) diff --git a/electronicparsers/cpmd/metainfo/cpmd.py b/electronicparsers/cpmd/metainfo/cpmd.py index e56809ea..a1668ba1 100644 --- a/electronicparsers/cpmd/metainfo/cpmd.py +++ b/electronicparsers/cpmd/metainfo/cpmd.py @@ -10726,7 +10726,7 @@ class x_cpmd_section_input(MSection): class Run(runschema.run.Run): - m_def = Section(validate=False, extends_base_section=True) + m_def = Section(validate=False) x_cpmd_section_input = SubSection( sub_section=SectionProxy('x_cpmd_section_input'), repeats=True diff --git a/electronicparsers/cpmd/metainfo/cpmd_general.py b/electronicparsers/cpmd/metainfo/cpmd_general.py index 1efe6bb5..ef3b99a8 100644 --- a/electronicparsers/cpmd/metainfo/cpmd_general.py +++ b/electronicparsers/cpmd/metainfo/cpmd_general.py @@ -848,7 +848,7 @@ class x_cpmd_section_end_information(MSection): class Run(runschema.run.Run): - m_def = Section(validate=False, extends_base_section=True) + m_def = Section(validate=False) x_cpmd_section_start_information = SubSection( sub_section=SectionProxy('x_cpmd_section_start_information'), repeats=True @@ -885,7 +885,7 @@ class Run(runschema.run.Run): class Method(runschema.method.Method): - m_def = Section(validate=False, extends_base_section=True) + m_def = Section(validate=False) x_cpmd_simulation_parameters = Quantity( type=JSON, @@ -909,7 +909,7 @@ class Method(runschema.method.Method): class System(runschema.system.System): - m_def = Section(validate=False, extends_base_section=True) + m_def = Section(validate=False) x_cpmd_section_supercell = SubSection( sub_section=SectionProxy('x_cpmd_section_supercell'), repeats=True @@ -917,7 +917,7 @@ class System(runschema.system.System): class Calculation(runschema.calculation.Calculation): - m_def = Section(validate=False, extends_base_section=True) + m_def = Section(validate=False) x_cpmd_total_number_of_scf_steps = Quantity( type=np.int32, @@ -969,7 +969,7 @@ class Calculation(runschema.calculation.Calculation): class GeometryOptimization(simulationworkflowschema.GeometryOptimization): - m_def = Section(validate=False, extends_base_section=True) + m_def = Section(validate=False) x_cpmd_section_geo_opt_initialization = SubSection( sub_section=SectionProxy('x_cpmd_section_geo_opt_initialization'), repeats=True @@ -981,7 +981,7 @@ class GeometryOptimization(simulationworkflowschema.GeometryOptimization): class MolecularDynamics(simulationworkflowschema.MolecularDynamics): - m_def = Section(validate=False, extends_base_section=True) + m_def = Section(validate=False) x_cpmd_section_md_averaged_quantities = SubSection( sub_section=SectionProxy('x_cpmd_section_md_averaged_quantities'), repeats=True diff --git a/electronicparsers/crystal/metainfo/crystal.py b/electronicparsers/crystal/metainfo/crystal.py index 3ee7b933..28a59631 100644 --- a/electronicparsers/crystal/metainfo/crystal.py +++ b/electronicparsers/crystal/metainfo/crystal.py @@ -39,7 +39,7 @@ class System(runschema.system.System): - m_def = Section(validate=False, extends_base_section=True) + m_def = Section(validate=False) x_crystal_family = Quantity( type=str, @@ -83,7 +83,7 @@ class System(runschema.system.System): class ScfIteration(runschema.calculation.ScfIteration): - m_def = Section(validate=False, extends_base_section=True) + m_def = Section(validate=False) x_crystal_scf_ee = Quantity( type=np.float64, @@ -123,7 +123,7 @@ class ScfIteration(runschema.calculation.ScfIteration): class Run(runschema.run.Run): - m_def = Section(validate=False, extends_base_section=True) + m_def = Section(validate=False) x_crystal_run_title = Quantity( type=str, @@ -215,7 +215,7 @@ class Run(runschema.run.Run): class Method(runschema.method.Method): - m_def = Section(validate=False, extends_base_section=True) + m_def = Section(validate=False) x_crystal_convergence_deltap = Quantity( type=np.float64, @@ -577,7 +577,7 @@ class Method(runschema.method.Method): class BasisSetAtomCentered(runschema.method.BasisSetAtomCentered): - m_def = Section(validate=False, extends_base_section=True) + m_def = Section(validate=False) x_crystal_section_shell = SubSection( sub_section=SectionProxy('x_crystal_section_shell'), repeats=True diff --git a/electronicparsers/dmol3/metainfo/dmol3.py b/electronicparsers/dmol3/metainfo/dmol3.py index e4119003..1561e418 100644 --- a/electronicparsers/dmol3/metainfo/dmol3.py +++ b/electronicparsers/dmol3/metainfo/dmol3.py @@ -71,7 +71,7 @@ class x_dmol3_section_mulliken_population(MSection): class Method(runschema.method.Method): - m_def = Section(validate=False, extends_base_section=True) + m_def = Section(validate=False) x_dmol3_aux_density = Quantity( type=str, @@ -387,7 +387,7 @@ class Method(runschema.method.Method): class ScfIteration(runschema.calculation.ScfIteration): - m_def = Section(validate=False, extends_base_section=True) + m_def = Section(validate=False) x_dmol3_binding_energy_scf_iteration = Quantity( type=np.float64, @@ -424,7 +424,7 @@ class ScfIteration(runschema.calculation.ScfIteration): class BandEnergies(runschema.calculation.BandEnergies): - m_def = Section(validate=False, extends_base_section=True) + m_def = Section(validate=False) x_dmol3_eigenvalue_eigenvalue = Quantity( type=np.float64, @@ -445,7 +445,7 @@ class BandEnergies(runschema.calculation.BandEnergies): class System(runschema.system.System): - m_def = Section(validate=False, extends_base_section=True) + m_def = Section(validate=False) x_dmol3_geometry_atom_labels = Quantity( type=str, @@ -484,7 +484,7 @@ class System(runschema.system.System): class Program(runschema.run.Program): - m_def = Section(validate=False, extends_base_section=True) + m_def = Section(validate=False) x_dmol3_compilation_date = Quantity( type=str, @@ -496,7 +496,7 @@ class Program(runschema.run.Program): class Energy(runschema.calculation.Energy): - m_def = Section(validate=False, extends_base_section=True) + m_def = Section(validate=False) x_dmol3_binding = SubSection( sub_section=runschema.calculation.EnergyEntry.m_def, @@ -507,7 +507,7 @@ class Energy(runschema.calculation.Energy): class Calculation(runschema.calculation.Calculation): - m_def = Section(validate=False, extends_base_section=True) + m_def = Section(validate=False) x_dmol3_h_trans = Quantity( type=np.float64, @@ -647,7 +647,7 @@ class Calculation(runschema.calculation.Calculation): class VibrationalFrequencies(runschema.calculation.VibrationalFrequencies): - m_def = Section(validate=False, extends_base_section=True) + m_def = Section(validate=False) n_atoms = Quantity( type=np.int32, diff --git a/electronicparsers/edmft/metainfo/edmft.py b/electronicparsers/edmft/metainfo/edmft.py index 8efc3f31..024953fa 100644 --- a/electronicparsers/edmft/metainfo/edmft.py +++ b/electronicparsers/edmft/metainfo/edmft.py @@ -70,7 +70,7 @@ class Method(runschema.method.Method): approximations (convergence, thresholds, etc.) behind the calculation. """ - m_def = Section(validate=False, extends_base_section=True) + m_def = Section(validate=False) x_edmft_method = SubSection( sub_section=x_edmft_method_parameters.m_def, repeats=False @@ -82,7 +82,7 @@ class GreensFunctions(runschema.calculation.GreensFunctions): Section containing the code-specific output GreensFunction quantities. """ - m_def = Section(validate=False, extends_base_section=True) + m_def = Section(validate=False) x_edmft_self_energy_infinity = Quantity( type=np.float64, diff --git a/electronicparsers/elk/metainfo/elk.py b/electronicparsers/elk/metainfo/elk.py index 7f132795..093f8a58 100644 --- a/electronicparsers/elk/metainfo/elk.py +++ b/electronicparsers/elk/metainfo/elk.py @@ -192,7 +192,7 @@ class x_elk_section_xc(MSection): class Method(runschema.method.Method): - m_def = Section(validate=False, extends_base_section=True) + m_def = Section(validate=False) x_elk_brillouin_zone_volume = Quantity( type=np.float64, @@ -464,7 +464,7 @@ class Method(runschema.method.Method): class Energy(runschema.calculation.Energy): - m_def = Section(validate=False, extends_base_section=True) + m_def = Section(validate=False) x_elk_fermi_energy = Quantity( type=np.float64, @@ -594,7 +594,7 @@ class Energy(runschema.calculation.Energy): class Charges(runschema.calculation.Charges): - m_def = Section(validate=False, extends_base_section=True) + m_def = Section(validate=False) x_elk_core_charge = Quantity( type=np.float64, @@ -622,7 +622,7 @@ class Charges(runschema.calculation.Charges): class Calculation(runschema.calculation.Calculation): - m_def = Section(validate=False, extends_base_section=True) + m_def = Section(validate=False) x_elk_core_charge_final = Quantity( type=np.float64, diff --git a/electronicparsers/exciting/metainfo/exciting.py b/electronicparsers/exciting/metainfo/exciting.py index 89ad3544..1c4fbcbc 100644 --- a/electronicparsers/exciting/metainfo/exciting.py +++ b/electronicparsers/exciting/metainfo/exciting.py @@ -792,7 +792,7 @@ class x_exciting_scrcoul_parameters(MSection): class GW(runschema.method.GW): - m_def = Section(validate=False, extends_base_section=True) + m_def = Section(validate=False) x_exciting_coreflag = Quantity( type=str, @@ -1153,7 +1153,7 @@ class x_exciting_loss_calculation(MSection): class Calculation(runschema.calculation.Calculation): - m_def = Section(validate=False, extends_base_section=True) + m_def = Section(validate=False) x_exciting_atom_forces = Quantity( type=np.float64, @@ -1714,7 +1714,7 @@ class Calculation(runschema.calculation.Calculation): class System(runschema.system.System): - m_def = Section(validate=False, extends_base_section=True) + m_def = Section(validate=False) x_exciting_brillouin_zone_volume = Quantity( type=np.float64, @@ -2146,7 +2146,7 @@ class x_exciting_section_MT_moment_atom(MSection): class ScfIteration(runschema.calculation.ScfIteration): - m_def = Section(validate=False, extends_base_section=True) + m_def = Section(validate=False) x_exciting_charge_convergence = Quantity( type=np.float64, @@ -2419,7 +2419,7 @@ class ScfIteration(runschema.calculation.ScfIteration): class Method(runschema.method.Method): - m_def = Section(validate=False, extends_base_section=True) + m_def = Section(validate=False) x_exciting_dummy = Quantity( type=np.int32, @@ -2926,7 +2926,7 @@ class Method(runschema.method.Method): class Run(runschema.run.Run): - m_def = Section(validate=False, extends_base_section=True) + m_def = Section(validate=False) x_exciting_dummy2 = Quantity( type=str, diff --git a/electronicparsers/fhiaims/metainfo/fhi_aims.py b/electronicparsers/fhiaims/metainfo/fhi_aims.py index c75652d2..6f5dc666 100644 --- a/electronicparsers/fhiaims/metainfo/fhi_aims.py +++ b/electronicparsers/fhiaims/metainfo/fhi_aims.py @@ -742,7 +742,7 @@ class x_fhi_aims_section_eigenvalues_spin_perturbativeGW(MSection): class Calculation(runschema.calculation.Calculation): - m_def = Section(validate=False, extends_base_section=True) + m_def = Section(validate=False) x_fhi_aims_atom_forces_free_x = Quantity( type=np.float64, @@ -809,7 +809,7 @@ class Calculation(runschema.calculation.Calculation): class ScfIeration(runschema.calculation.ScfIteration): - m_def = Section(validate=False, extends_base_section=True) + m_def = Section(validate=False) x_fhi_aims_atom_forces_raw_x = Quantity( type=np.float64, @@ -937,7 +937,7 @@ class ScfIeration(runschema.calculation.ScfIteration): class DosValues(runschema.calculation.DosValues): - m_def = Section(validate=False, extends_base_section=True) + m_def = Section(validate=False) x_fhi_aims_normalization_factor_raw_data = Quantity( type=np.float64, @@ -950,7 +950,7 @@ class DosValues(runschema.calculation.DosValues): class BandStructure(runschema.calculation.BandStructure): - m_def = Section(validate=False, extends_base_section=True) + m_def = Section(validate=False) x_fhi_aims_band_k1 = Quantity( type=np.float64, @@ -994,7 +994,7 @@ class BandStructure(runschema.calculation.BandStructure): class Method(runschema.method.Method): - m_def = Section(validate=False, extends_base_section=True) + m_def = Section(validate=False) x_fhi_aims_controlIn_charge = Quantity( type=np.float64, @@ -1365,7 +1365,7 @@ class Method(runschema.method.Method): class Run(runschema.run.Run): - m_def = Section(validate=False, extends_base_section=True) + m_def = Section(validate=False) x_fhi_aims_controlIn_MD_time_step = Quantity( type=np.float64, @@ -1432,7 +1432,7 @@ class Run(runschema.run.Run): class System(runschema.system.System): - m_def = Section(validate=False, extends_base_section=True) + m_def = Section(validate=False) x_fhi_aims_geometry_atom_labels = Quantity( type=str, @@ -1525,7 +1525,7 @@ class System(runschema.system.System): class AtomParameters(runschema.method.AtomParameters): - m_def = Section(validate=False, extends_base_section=True) + m_def = Section(validate=False) x_fhi_aims_section_controlInOut_atom_species = SubSection( sub_section=SectionProxy('x_fhi_aims_section_controlInOut_atom_species'), @@ -1534,7 +1534,7 @@ class AtomParameters(runschema.method.AtomParameters): class HubbardKanamoriModel(runschema.method.HubbardKanamoriModel): - m_def = Section(validate=False, extends_base_section=True) + m_def = Section(validate=False) x_fhi_aims_projection_type = Quantity( type=str, @@ -1554,7 +1554,7 @@ class HubbardKanamoriModel(runschema.method.HubbardKanamoriModel): class MolecularDynamicsMethod(simulationworkflowschema.MolecularDynamicsMethod): - m_def = Section(validate=False, extends_base_section=True) + m_def = Section(validate=False) x_fhi_aims_controlIn_md = Quantity( type=JSON, diff --git a/electronicparsers/fleur/metainfo/fleur.py b/electronicparsers/fleur/metainfo/fleur.py index ea0a0c85..45579e98 100644 --- a/electronicparsers/fleur/metainfo/fleur.py +++ b/electronicparsers/fleur/metainfo/fleur.py @@ -175,7 +175,7 @@ class x_fleur_section_XC(MSection): class Run(runschema.run.Run): - m_def = Section(validate=False, extends_base_section=True) + m_def = Section(validate=False) x_fleur_header = SubSection( sub_section=SectionProxy('x_fleur_header'), repeats=True @@ -183,7 +183,7 @@ class Run(runschema.run.Run): class System(runschema.system.System): - m_def = Section(validate=False, extends_base_section=True) + m_def = Section(validate=False) x_fleur_lattice_vector_x = Quantity( type=np.float64, @@ -373,7 +373,7 @@ class System(runschema.system.System): class ScfIteration(runschema.calculation.ScfIteration): - m_def = Section(validate=False, extends_base_section=True) + m_def = Section(validate=False) x_fleur_tot_for_x = Quantity( type=np.float64, @@ -460,7 +460,7 @@ class ScfIteration(runschema.calculation.ScfIteration): class Method(runschema.method.Method): - m_def = Section(validate=False, extends_base_section=True) + m_def = Section(validate=False) x_fleur_nkptd = Quantity( type=np.int32, @@ -577,7 +577,7 @@ class OrbitalAPW(runschema.method.OrbitalAPW): class BasisSet(runschema.method.BasisSet): - m_def = Section(validate=False, extends_base_section=True) + m_def = Section(validate=False) x_fleur_coretail = Quantity( type=bool, @@ -602,7 +602,7 @@ class BasisSet(runschema.method.BasisSet): class XCFunctional(runschema.method.XCFunctional): - m_def = Section(validate=False, extends_base_section=True) + m_def = Section(validate=False) x_fleur_xc_correction = Quantity( type=str, @@ -613,7 +613,7 @@ class XCFunctional(runschema.method.XCFunctional): class BaseCalculation(runschema.calculation.BaseCalculation): - m_def = Section(validate=False, extends_base_section=True) + m_def = Section(validate=False) x_fleur_n_occupied_states = Quantity( type=np.int32, diff --git a/electronicparsers/fplo/metainfo/fplo.py b/electronicparsers/fplo/metainfo/fplo.py index 128fb17c..fae22416 100644 --- a/electronicparsers/fplo/metainfo/fplo.py +++ b/electronicparsers/fplo/metainfo/fplo.py @@ -39,7 +39,7 @@ class Run(runschema.run.Run): - m_def = Section(validate=False, extends_base_section=True) + m_def = Section(validate=False) x_fplo_program_version_sub = Quantity( type=str, @@ -59,7 +59,7 @@ class Run(runschema.run.Run): class System(runschema.system.System): - m_def = Section(validate=False, extends_base_section=True) + m_def = Section(validate=False) x_fplo_reciprocal_cell = Quantity( type=np.float64, @@ -106,7 +106,7 @@ class System(runschema.system.System): class Method(runschema.method.Method): - m_def = Section(validate=False, extends_base_section=True) + m_def = Section(validate=False) x_fplo_xc_functional_number = Quantity( type=np.int32, @@ -143,7 +143,7 @@ class Method(runschema.method.Method): # class HubbardModel(runschema.method.HubbardModel): -# m_def = Section(validate=False, extends_base_section=True) +# m_def = Section(validate=False) # x_fplo_dft_plus_u_orbital_element = Quantity( # type=str, diff --git a/electronicparsers/fplo/metainfo/fplo_input_autogenerated.py b/electronicparsers/fplo/metainfo/fplo_input_autogenerated.py index 4f2e8039..76c19b4c 100644 --- a/electronicparsers/fplo/metainfo/fplo_input_autogenerated.py +++ b/electronicparsers/fplo/metainfo/fplo_input_autogenerated.py @@ -2739,6 +2739,6 @@ class x_fplo_in_Advanced_output_optics_energy(MSection): class Method(runschema.method.Method): - m_def = Section(validate=False, extends_base_section=True) + m_def = Section(validate=False) x_fplo_in = SubSection(sub_section=SectionProxy('x_fplo_in'), repeats=True) diff --git a/electronicparsers/fplo/metainfo/fplo_temporaries.py b/electronicparsers/fplo/metainfo/fplo_temporaries.py index a4e28c4f..95f29742 100644 --- a/electronicparsers/fplo/metainfo/fplo_temporaries.py +++ b/electronicparsers/fplo/metainfo/fplo_temporaries.py @@ -39,7 +39,7 @@ class Run(runschema.run.Run): - m_def = Section(validate=False, extends_base_section=True) + m_def = Section(validate=False) x_fplo_t_program_version_main = Quantity( type=str, @@ -67,7 +67,7 @@ class Run(runschema.run.Run): class System(runschema.system.System): - m_def = Section(validate=False, extends_base_section=True) + m_def = Section(validate=False) x_fplo_t_vec_a_x = Quantity( type=np.dtype(np.float64), @@ -175,7 +175,7 @@ class System(runschema.system.System): class Method(runschema.method.Method): - m_def = Section(validate=False, extends_base_section=True) + m_def = Section(validate=False) x_fplo_t_relativity_method = Quantity( type=str, @@ -307,7 +307,7 @@ class Method(runschema.method.Method): class ScfIteration(runschema.calculation.ScfIteration): - m_def = Section(validate=False, extends_base_section=True) + m_def = Section(validate=False) x_fplo_t_energy_reference_fermi_iteration = Quantity( type=np.dtype(np.float64), diff --git a/electronicparsers/gamess/metainfo/gamess.py b/electronicparsers/gamess/metainfo/gamess.py index 36bd17ee..6857aa65 100644 --- a/electronicparsers/gamess/metainfo/gamess.py +++ b/electronicparsers/gamess/metainfo/gamess.py @@ -405,7 +405,7 @@ class x_gamess_section_tddft(MSection): class BandEnergies(runschema.calculation.BandEnergies): - m_def = Section(validate=False, extends_base_section=True) + m_def = Section(validate=False) x_gamess_alpha_eigenvalues_values = Quantity( type=str, @@ -425,7 +425,7 @@ class BandEnergies(runschema.calculation.BandEnergies): class System(runschema.system.System): - m_def = Section(validate=False, extends_base_section=True) + m_def = Section(validate=False) x_gamess_atom_positions_initial = Quantity( type=np.float64, @@ -508,7 +508,7 @@ class System(runschema.system.System): class Method(runschema.method.Method): - m_def = Section(validate=False, extends_base_section=True) + m_def = Section(validate=False) x_gamess_basis_set_diffsp = Quantity( type=str, @@ -720,7 +720,7 @@ class Method(runschema.method.Method): class Run(runschema.run.Run): - m_def = Section(validate=False, extends_base_section=True) + m_def = Section(validate=False) x_gamess_program_execution_date = Quantity( type=str, @@ -745,7 +745,7 @@ class Run(runschema.run.Run): class ScfIteration(runschema.calculation.ScfIteration): - m_def = Section(validate=False, extends_base_section=True) + m_def = Section(validate=False) x_gamess_energy_scf = Quantity( type=np.float64, @@ -769,7 +769,7 @@ class ScfIteration(runschema.calculation.ScfIteration): class Calculation(runschema.calculation.Calculation): - m_def = Section(validate=False, extends_base_section=True) + m_def = Section(validate=False) x_gamess_section_atom_forces = SubSection( sub_section=SectionProxy('x_gamess_section_atom_forces'), repeats=True @@ -809,7 +809,7 @@ class Calculation(runschema.calculation.Calculation): class Energy(runschema.calculation.Energy): - m_def = Section(validate=False, extends_base_section=True) + m_def = Section(validate=False) x_gamess_virial_ratio = Quantity( type=np.float64, diff --git a/electronicparsers/gpaw/metainfo/gpaw.py b/electronicparsers/gpaw/metainfo/gpaw.py index 92a4ea96..eeeba33d 100644 --- a/electronicparsers/gpaw/metainfo/gpaw.py +++ b/electronicparsers/gpaw/metainfo/gpaw.py @@ -63,7 +63,7 @@ class x_gpaw_section_paw_method(MSection): class Calculation(runschema.calculation.Calculation): - m_def = Section(validate=False, extends_base_section=True) + m_def = Section(validate=False) x_gpaw_atomic_density_matrices = Quantity( type=np.float64, @@ -127,7 +127,7 @@ class Calculation(runschema.calculation.Calculation): class Method(runschema.method.Method): - m_def = Section(validate=False, extends_base_section=True) + m_def = Section(validate=False) x_gpaw_density_convergence_criterion = Quantity( type=np.float64, diff --git a/electronicparsers/molcas/metainfo/molcas.py b/electronicparsers/molcas/metainfo/molcas.py index 1649bfa0..9dd2e8c5 100644 --- a/electronicparsers/molcas/metainfo/molcas.py +++ b/electronicparsers/molcas/metainfo/molcas.py @@ -104,7 +104,7 @@ class x_molcas_section_basis(MSection): class Method(runschema.method.Method): - m_def = Section(validate=False, extends_base_section=True) + m_def = Section(validate=False) x_molcas_method_name = Quantity( type=str, @@ -128,7 +128,7 @@ class Method(runschema.method.Method): class Calculation(runschema.calculation.Calculation): - m_def = Section(validate=False, extends_base_section=True) + m_def = Section(validate=False) x_molcas_slapaf_grad_norm = Quantity( type=np.float64, diff --git a/electronicparsers/mopac/metainfo/mopac.py b/electronicparsers/mopac/metainfo/mopac.py index 3984c479..3269e91c 100644 --- a/electronicparsers/mopac/metainfo/mopac.py +++ b/electronicparsers/mopac/metainfo/mopac.py @@ -40,7 +40,7 @@ class Calculation(runschema.calculation.Calculation): - m_def = Section(validate=False, extends_base_section=True) + m_def = Section(validate=False) x_mopac_fhof = Quantity( type=np.float64, @@ -53,7 +53,7 @@ class Calculation(runschema.calculation.Calculation): class Method(runschema.method.Method): - m_def = Section(validate=False, extends_base_section=True) + m_def = Section(validate=False) x_mopac_keyword_line = Quantity( type=str, diff --git a/electronicparsers/nwchem/metainfo/nwchem.py b/electronicparsers/nwchem/metainfo/nwchem.py index 135014d0..cc54b9e0 100644 --- a/electronicparsers/nwchem/metainfo/nwchem.py +++ b/electronicparsers/nwchem/metainfo/nwchem.py @@ -308,7 +308,7 @@ class x_nwchem_section_qmd_step(MSection): class Run(runschema.run.Run): - m_def = Section(validate=False, extends_base_section=True) + m_def = Section(validate=False) x_nwchem_section_start_information = SubSection( sub_section=SectionProxy('x_nwchem_section_start_information'), repeats=True @@ -328,7 +328,7 @@ class Run(runschema.run.Run): class Method(runschema.method.Method): - m_def = Section(validate=False, extends_base_section=True) + m_def = Section(validate=False) x_nwchem_xc_functional_shortcut = Quantity( type=str, @@ -352,7 +352,7 @@ class Method(runschema.method.Method): class Calculation(runschema.calculation.Calculation): - m_def = Section(validate=False, extends_base_section=True) + m_def = Section(validate=False) x_nwchem_energy_one_electron = Quantity( type=np.float64, @@ -384,7 +384,7 @@ class Calculation(runschema.calculation.Calculation): class MolecularDynamics(simulationworkflowschema.MolecularDynamics): - m_def = Section(validate=False, extends_base_section=True) + m_def = Section(validate=False) x_nwchem_qmd_number_of_nuclear_steps = Quantity( type=np.int32, @@ -452,7 +452,7 @@ class MolecularDynamics(simulationworkflowschema.MolecularDynamics): class System(runschema.system.System): - m_def = Section(validate=False, extends_base_section=True) + m_def = Section(validate=False) x_nwchem_reciprocal_simulation_cell = Quantity( type=np.float64, diff --git a/electronicparsers/ocean/metainfo/ocean.py b/electronicparsers/ocean/metainfo/ocean.py index 33a00ef4..2e470499 100644 --- a/electronicparsers/ocean/metainfo/ocean.py +++ b/electronicparsers/ocean/metainfo/ocean.py @@ -301,7 +301,7 @@ class Method(runschema.run.Method): approximations (convergence, thresholds, etc.) behind the calculation. """ - m_def = Section(validate=False, extends_base_section=True) + m_def = Section(validate=False) x_ocean_bse = SubSection(sub_section=x_ocean_bse_parameters.m_def, repeats=False) @@ -381,7 +381,7 @@ class Calculation(runschema.run.Calculation): can be accessed in section workflow. """ - m_def = Section(validate=False, extends_base_section=True) + m_def = Section(validate=False) x_ocean_lanczos = SubSection( sub_section=x_ocean_lanczos_results.m_def, repeats=True @@ -393,7 +393,7 @@ class Program(runschema.run.Program): Contains the specifications of the program. """ - m_def = Section(validate=False, extends_base_section=True) + m_def = Section(validate=False) x_ocean_commit_hash = Quantity( type=str, diff --git a/electronicparsers/octopus/metainfo/octopus.py b/electronicparsers/octopus/metainfo/octopus.py index b2d7da72..05800d45 100644 --- a/electronicparsers/octopus/metainfo/octopus.py +++ b/electronicparsers/octopus/metainfo/octopus.py @@ -39,7 +39,7 @@ class Calculation(runschema.calculation.Calculation): - m_def = Section(validate=False, extends_base_section=True) + m_def = Section(validate=False) x_octopus_info_energy_ion_ion = Quantity( type=np.dtype(np.float64), @@ -52,7 +52,7 @@ class Calculation(runschema.calculation.Calculation): class Run(runschema.run.Run): - m_def = Section(validate=False, extends_base_section=True) + m_def = Section(validate=False) x_octopus_info_scf_converged_iterations = Quantity( type=np.dtype(np.int32), diff --git a/electronicparsers/octopus/metainfo/octopus_autogenerated.py b/electronicparsers/octopus/metainfo/octopus_autogenerated.py index 0faabb2a..8beca19a 100644 --- a/electronicparsers/octopus/metainfo/octopus_autogenerated.py +++ b/electronicparsers/octopus/metainfo/octopus_autogenerated.py @@ -55,7 +55,7 @@ class x_octopus_parserlog(MCategory): class Run(runschema.run.Run): - m_def = Section(validate=False, extends_base_section=True) + m_def = Section(validate=False) x_octopus_input_ABCapHeight = Quantity( type=np.float64, diff --git a/electronicparsers/onetep/metainfo/onetep.py b/electronicparsers/onetep/metainfo/onetep.py index deb0ba9a..dc20c2f2 100644 --- a/electronicparsers/onetep/metainfo/onetep.py +++ b/electronicparsers/onetep/metainfo/onetep.py @@ -2325,7 +2325,7 @@ class x_onetep_section_orbital_information(MSection): class Run(runschema.run.Run): - m_def = Section(validate=False, extends_base_section=True) + m_def = Section(validate=False) x_onetep_atom_forces = Quantity( type=np.float64, @@ -2710,7 +2710,7 @@ class Run(runschema.run.Run): class System(runschema.system.System): - m_def = Section(validate=False, extends_base_section=True) + m_def = Section(validate=False) x_onetep_net_charge = Quantity( type=np.float64, @@ -2878,7 +2878,7 @@ class System(runschema.system.System): class BasisSet(runschema.method.BasisSet): - m_def = Section(validate=False, extends_base_section=True) + m_def = Section(validate=False) x_onetep_size_std_grid = Quantity( type=np.float64, @@ -2898,7 +2898,7 @@ class BasisSet(runschema.method.BasisSet): class Calculation(runschema.calculation.Calculation): - m_def = Section(validate=False, extends_base_section=True) + m_def = Section(validate=False) x_onetep_enthalpy = Quantity( type=np.float64, @@ -3184,7 +3184,7 @@ class Calculation(runschema.calculation.Calculation): class Energy(runschema.calculation.Energy): - m_def = Section(validate=False, extends_base_section=True) + m_def = Section(validate=False) x_onetep_pseudopotential_local = SubSection( sub_section=runschema.calculation.EnergyEntry.m_def @@ -3196,7 +3196,7 @@ class Energy(runschema.calculation.Energy): class Method(runschema.method.Method): - m_def = Section(validate=False, extends_base_section=True) + m_def = Section(validate=False) x_onetep_functional_and_weight = Quantity( type=str, @@ -3227,7 +3227,7 @@ class Method(runschema.method.Method): class GeometryOptimization(simulationworkflowschema.GeometryOptimization): - m_def = Section(validate=False, extends_base_section=True) + m_def = Section(validate=False) geometry_optimization_frequency_tol = Quantity( type=np.float64, @@ -3256,7 +3256,7 @@ class GeometryOptimization(simulationworkflowschema.GeometryOptimization): class MolecularDynamics(simulationworkflowschema.MolecularDynamics): - m_def = Section(validate=False, extends_base_section=True) + m_def = Section(validate=False) x_onetep_thermostat_target_temperature = Quantity( type=np.float64, @@ -3340,7 +3340,7 @@ class MolecularDynamics(simulationworkflowschema.MolecularDynamics): class BandStructure(runschema.calculation.BandStructure): - m_def = Section(validate=False, extends_base_section=True) + m_def = Section(validate=False) x_onetep_k_path = Quantity( type=np.float64, @@ -3380,7 +3380,7 @@ class BandStructure(runschema.calculation.BandStructure): class ScfIteration(runschema.calculation.ScfIteration): - m_def = Section(validate=False, extends_base_section=True) + m_def = Section(validate=False) x_onetep_scf_rms_gradient = Quantity( type=np.float64, @@ -3392,7 +3392,7 @@ class ScfIteration(runschema.calculation.ScfIteration): class AtomParameters(runschema.method.AtomParameters): - m_def = Section(validate=False, extends_base_section=True) + m_def = Section(validate=False) x_onetep_store_atom_mass = Quantity( type=str, diff --git a/electronicparsers/orca/metainfo/orca.py b/electronicparsers/orca/metainfo/orca.py index b7a777ff..00dcb30e 100644 --- a/electronicparsers/orca/metainfo/orca.py +++ b/electronicparsers/orca/metainfo/orca.py @@ -126,7 +126,7 @@ class x_orca_section_functionals(MSection): class Method(runschema.method.Method): - m_def = Section(validate=False, extends_base_section=True) + m_def = Section(validate=False) x_orca_1_elect_energy_change = Quantity( type=np.float64, @@ -582,7 +582,7 @@ class Method(runschema.method.Method): class Scf(runschema.method.Scf): - m_def = Section(validate=False, extends_base_section=True) + m_def = Section(validate=False) x_orca_last_max_density_change = Quantity( type=np.float64, @@ -593,7 +593,7 @@ class Scf(runschema.method.Scf): class ScfIteration(runschema.calculation.ScfIteration): - m_def = Section(validate=False, extends_base_section=True) + m_def = Section(validate=False) x_orca_angular_grid_final = Quantity( type=str, @@ -709,7 +709,7 @@ class ScfIteration(runschema.calculation.ScfIteration): class System(runschema.system.System): - m_def = Section(validate=False, extends_base_section=True) + m_def = Section(validate=False) x_orca_atom_positions = SubSection( sub_section=SectionProxy('x_orca_atom_positions'), repeats=True @@ -717,7 +717,7 @@ class System(runschema.system.System): class BasisSet(runschema.method.BasisSet): - m_def = Section(validate=False, extends_base_section=True) + m_def = Section(validate=False) x_orca_auxiliary_basis_set_contracted = Quantity( type=str, @@ -854,7 +854,7 @@ class BasisSet(runschema.method.BasisSet): class Calculation(runschema.calculation.Calculation): - m_def = Section(validate=False, extends_base_section=True) + m_def = Section(validate=False) x_orca_basis_fn_evaluation = Quantity( type=np.float64, @@ -1257,7 +1257,7 @@ class Calculation(runschema.calculation.Calculation): class GeometryOptimization(simulationworkflowschema.GeometryOptimization): - m_def = Section(validate=False, extends_base_section=True) + m_def = Section(validate=False) x_orca_coords_choice_name = Quantity( type=str, @@ -1377,7 +1377,7 @@ class GeometryOptimization(simulationworkflowschema.GeometryOptimization): class Spectra(runschema.calculation.Spectra): - m_def = Section(validate=False, extends_base_section=True) + m_def = Section(validate=False) x_orca_excitation_energy = Quantity( type=np.float64, @@ -1416,7 +1416,7 @@ class Spectra(runschema.calculation.Spectra): class Run(runschema.run.Run): - m_def = Section(validate=False, extends_base_section=True) + m_def = Section(validate=False) x_orca_program_compilation_date = Quantity( type=str, diff --git a/electronicparsers/psi4/metainfo/psi4.py b/electronicparsers/psi4/metainfo/psi4.py index cceddb47..46668eb9 100644 --- a/electronicparsers/psi4/metainfo/psi4.py +++ b/electronicparsers/psi4/metainfo/psi4.py @@ -39,7 +39,7 @@ class Run(runschema.run.Run): - m_def = Section(validate=False, extends_base_section=True) + m_def = Section(validate=False) x_psi4_git_rev = Quantity( type=str, @@ -86,7 +86,7 @@ class Run(runschema.run.Run): class System(runschema.system.System): - m_def = Section(validate=False, extends_base_section=True) + m_def = Section(validate=False) x_psi4_molecular_point_group = Quantity( type=str, @@ -161,7 +161,7 @@ class System(runschema.system.System): class Scf(runschema.method.Scf): - m_def = Section(validate=False, extends_base_section=True) + m_def = Section(validate=False) x_psi4_diis = Quantity( type=bool, @@ -200,7 +200,7 @@ class Scf(runschema.method.Scf): class BasisSetAtomCentered(runschema.method.BasisSetAtomCentered): - m_def = Section(validate=False, extends_base_section=True) + m_def = Section(validate=False) x_psi4_blend = Quantity( type=str, @@ -255,7 +255,7 @@ class BasisSetAtomCentered(runschema.method.BasisSetAtomCentered): class Method(runschema.method.Method): - m_def = Section(validate=False, extends_base_section=True) + m_def = Section(validate=False) x_psi4_scf_algorithm_type = Quantity( type=str, @@ -315,7 +315,7 @@ class Method(runschema.method.Method): class DFT(runschema.method.DFT): - m_def = Section(validate=False, extends_base_section=True) + m_def = Section(validate=False) x_psi4_molecular_quadrature = Quantity( type=typing.Any, @@ -337,7 +337,7 @@ class x_psi4_root_information(MSection): class Calculation(runschema.calculation.Calculation): - m_def = Section(validate=False, extends_base_section=True) + m_def = Section(validate=False) x_psi4_s2_expected = Quantity( type=np.float64, diff --git a/electronicparsers/qbox/metainfo/qbox.py b/electronicparsers/qbox/metainfo/qbox.py index dbd8985c..bd7a3601 100644 --- a/electronicparsers/qbox/metainfo/qbox.py +++ b/electronicparsers/qbox/metainfo/qbox.py @@ -230,7 +230,7 @@ class x_qbox_section_xml_file(MSection): class System(runschema.system.System): - m_def = Section(validate=False, extends_base_section=True) + m_def = Section(validate=False) x_qbox_atom_force_x = Quantity( type=np.float64, @@ -323,7 +323,7 @@ class System(runschema.system.System): class Method(runschema.method.Method): - m_def = Section(validate=False, extends_base_section=True) + m_def = Section(validate=False) x_qbox_atoms_dyn = Quantity( type=str, @@ -435,7 +435,7 @@ class Method(runschema.method.Method): class Run(runschema.run.Run): - m_def = Section(validate=False, extends_base_section=True) + m_def = Section(validate=False) x_qbox_nodename = Quantity( type=str, @@ -455,7 +455,7 @@ class Run(runschema.run.Run): class Calculation(runschema.calculation.Calculation): - m_def = Section(validate=False, extends_base_section=True) + m_def = Section(validate=False) x_qbox_section_stress_tensor = SubSection( sub_section=SectionProxy('x_qbox_section_stress_tensor'), repeats=True @@ -467,7 +467,7 @@ class Calculation(runschema.calculation.Calculation): class Energy(runschema.calculation.Energy): - m_def = Section(validate=False, extends_base_section=True) + m_def = Section(validate=False) x_qbox_conf = SubSection(sub_section=runschema.calculation.EnergyEntry.m_def) diff --git a/electronicparsers/quantumespresso/metainfo/quantum_espresso.py b/electronicparsers/quantumespresso/metainfo/quantum_espresso.py index 92c86459..83976589 100644 --- a/electronicparsers/quantumespresso/metainfo/quantum_espresso.py +++ b/electronicparsers/quantumespresso/metainfo/quantum_espresso.py @@ -497,7 +497,7 @@ class x_qe_t_section_input_occupations(MSection): class Calculation(runschema.calculation.Calculation): - m_def = Section(validate=False, extends_base_section=True) + m_def = Section(validate=False) x_qe_extra_SCF = Quantity( type=bool, @@ -1442,7 +1442,7 @@ class Calculation(runschema.calculation.Calculation): class Run(runschema.run.Run): - m_def = Section(validate=False, extends_base_section=True) + m_def = Section(validate=False) x_qe_program_name = Quantity( type=str, @@ -1614,7 +1614,7 @@ class Run(runschema.run.Run): class Method(runschema.method.Method): - m_def = Section(validate=False, extends_base_section=True) + m_def = Section(validate=False) x_qe_t_species_dispersion_correction_label = Quantity( type=str, @@ -2368,7 +2368,7 @@ class Method(runschema.method.Method): class AtomParameters(runschema.method.AtomParameters): - m_def = Section(validate=False, extends_base_section=True) + m_def = Section(validate=False) x_qe_dispersion_correction_vdw_radius = Quantity( type=np.float64, @@ -2564,7 +2564,7 @@ class AtomParameters(runschema.method.AtomParameters): class System(runschema.system.System): - m_def = Section(validate=False, extends_base_section=True) + m_def = Section(validate=False) x_qe_ibrav = Quantity( type=np.int32, @@ -3073,7 +3073,7 @@ class System(runschema.system.System): class Functional(runschema.method.Functional): - m_def = Section(validate=False, extends_base_section=True) + m_def = Section(validate=False) x_qe_xc_name = Quantity( type=str, @@ -3109,7 +3109,7 @@ class Functional(runschema.method.Functional): class ScfIteration(runschema.calculation.ScfIteration): - m_def = Section(validate=False, extends_base_section=True) + m_def = Section(validate=False) x_qe_t_iter_mpersite_idx = Quantity( type=np.int32, @@ -3285,7 +3285,7 @@ class ScfIteration(runschema.calculation.ScfIteration): class BandEnergies(runschema.calculation.BandEnergies): - m_def = Section(validate=False, extends_base_section=True) + m_def = Section(validate=False) x_qe_eigenvalues_number_of_planewaves = Quantity( type=np.int32, diff --git a/electronicparsers/siesta/metainfo/siesta.py b/electronicparsers/siesta/metainfo/siesta.py index ed0ad071..cc7b2868 100644 --- a/electronicparsers/siesta/metainfo/siesta.py +++ b/electronicparsers/siesta/metainfo/siesta.py @@ -42,7 +42,7 @@ class Run(runschema.run.Run): - m_def = Section(validate=False, extends_base_section=True) + m_def = Section(validate=False) x_siesta_system_label = Quantity( type=str, @@ -92,7 +92,7 @@ class Run(runschema.run.Run): class x_siesta_section_input(siesta_autogenerated.x_siesta_section_input): - m_def = Section(validate=False, extends_base_section=True) + m_def = Section(validate=False) x_siesta_xc_authors = Quantity( type=str, @@ -112,7 +112,7 @@ class x_siesta_section_input(siesta_autogenerated.x_siesta_section_input): class BasisSet(runschema.method.BasisSet): - m_def = Section(validate=False, extends_base_section=True) + m_def = Section(validate=False) x_siesta_pao_basis_type = Quantity( type=str, @@ -124,7 +124,7 @@ class BasisSet(runschema.method.BasisSet): class Method(runschema.method.Method): - m_def = Section(validate=False, extends_base_section=True) + m_def = Section(validate=False) x_siesta_input_parameters = Quantity( type=JSON, diff --git a/electronicparsers/siesta/metainfo/siesta_autogenerated.py b/electronicparsers/siesta/metainfo/siesta_autogenerated.py index 376a2da1..b9bee56c 100644 --- a/electronicparsers/siesta/metainfo/siesta_autogenerated.py +++ b/electronicparsers/siesta/metainfo/siesta_autogenerated.py @@ -3358,7 +3358,7 @@ class x_siesta_section_input(MSection): class Method(runschema.method.Method): - m_def = Section(validate=False, extends_base_section=True) + m_def = Section(validate=False) x_siesta_section_input = SubSection( sub_section=SectionProxy('x_siesta_section_input'), repeats=True diff --git a/electronicparsers/soliddmft/metainfo/soliddmft.py b/electronicparsers/soliddmft/metainfo/soliddmft.py index 9d7301c1..08a5c961 100644 --- a/electronicparsers/soliddmft/metainfo/soliddmft.py +++ b/electronicparsers/soliddmft/metainfo/soliddmft.py @@ -41,7 +41,7 @@ class Method(runschema.run.Method): Contains the specifications of the method. """ - m_def = Section(validate=False, extends_base_section=True) + m_def = Section(validate=False) x_soliddmft_dft_input = Quantity( type=JSON, @@ -101,7 +101,7 @@ class Program(runschema.run.Program): Contains the specifications of the program. """ - m_def = Section(validate=False, extends_base_section=True) + m_def = Section(validate=False) x_soliddmft_hash = Quantity( type=str, @@ -251,7 +251,7 @@ class ScfIteration(runschema.calculation.ScfIteration): and gives detailed information on the SCF procedure of the specified quantities. """ - m_def = Section(validate=False, extends_base_section=True) + m_def = Section(validate=False) x_soliddmft_convergence_obs = Quantity( type=JSON, diff --git a/electronicparsers/turbomole/metainfo/turbomole.py b/electronicparsers/turbomole/metainfo/turbomole.py index 02370e16..906dc6f3 100644 --- a/electronicparsers/turbomole/metainfo/turbomole.py +++ b/electronicparsers/turbomole/metainfo/turbomole.py @@ -199,7 +199,7 @@ class x_turbomole_section_functionals(MSection): class Method(runschema.method.Method): - m_def = Section(validate=False, extends_base_section=True) + m_def = Section(validate=False) x_turbomole_controlIn_atom_label = Quantity( type=str, @@ -445,7 +445,7 @@ class Method(runschema.method.Method): class ScfIteration(runschema.calculation.ScfIteration): - m_def = Section(validate=False, extends_base_section=True) + m_def = Section(validate=False) x_turbomole_damping_scf_iteration = Quantity( type=np.float64, @@ -525,7 +525,7 @@ class ScfIteration(runschema.calculation.ScfIteration): class BandEnergies(runschema.calculation.BandEnergies): - m_def = Section(validate=False, extends_base_section=True) + m_def = Section(validate=False) x_turbomole_eigenvalues_irreducible_representation = Quantity( type=np.int32, @@ -545,7 +545,7 @@ class BandEnergies(runschema.calculation.BandEnergies): class GeometryOptimizationMethod(simulationworkflowschema.GeometryOptimizationMethod): - m_def = Section(validate=False, extends_base_section=True) + m_def = Section(validate=False) x_turbomole_geometry_optimization_geometry_change_rms = Quantity( type=np.float64, @@ -594,7 +594,7 @@ class GeometryOptimizationMethod(simulationworkflowschema.GeometryOptimizationMe class Calculation(runschema.calculation.Calculation): - m_def = Section(validate=False, extends_base_section=True) + m_def = Section(validate=False) x_turbomole_module = Quantity( type=str, @@ -679,7 +679,7 @@ class Calculation(runschema.calculation.Calculation): class Run(runschema.run.Run): - m_def = Section(validate=False, extends_base_section=True) + m_def = Section(validate=False) x_turbomole_nodename = Quantity( type=str, @@ -691,7 +691,7 @@ class Run(runschema.run.Run): class System(runschema.system.System): - m_def = Section(validate=False, extends_base_section=True) + m_def = Section(validate=False) x_turbomole_pceem_charges = Quantity( type=np.float64, diff --git a/electronicparsers/vasp/metainfo/vasp.py b/electronicparsers/vasp/metainfo/vasp.py index 10abff1d..258ccb11 100644 --- a/electronicparsers/vasp/metainfo/vasp.py +++ b/electronicparsers/vasp/metainfo/vasp.py @@ -40,7 +40,7 @@ class Run(runschema.run.Run): - m_def = Section(validate=False, extends_base_section=True) + m_def = Section(validate=False) vasp_build_date = Quantity( type=str, @@ -60,7 +60,7 @@ class Run(runschema.run.Run): class Method(runschema.method.Method): - m_def = Section(validate=False, extends_base_section=True) + m_def = Section(validate=False) x_vasp_incar_in = Quantity( type=JSON, @@ -113,7 +113,7 @@ class Method(runschema.method.Method): class KMesh(runschema.method.KMesh): - m_def = Section(validate=False, extends_base_section=True) + m_def = Section(validate=False) x_vasp_tetrahedrons_list = Quantity( type=np.dtype(np.int32), @@ -134,7 +134,7 @@ class KMesh(runschema.method.KMesh): class System(runschema.system.System): - m_def = Section(validate=False, extends_base_section=True) + m_def = Section(validate=False) x_vasp_selective_dynamics = Quantity( type=np.dtype(bool), @@ -146,7 +146,7 @@ class System(runschema.system.System): class HubbardKanamoriModel(runschema.method.HubbardKanamoriModel): - m_def = Section(validate=False, extends_base_section=True) + m_def = Section(validate=False) x_vasp_projection_type = Quantity( type=str, @@ -158,7 +158,7 @@ class HubbardKanamoriModel(runschema.method.HubbardKanamoriModel): class GW(runschema.method.GW): - m_def = Section(validate=False, extends_base_section=True) + m_def = Section(validate=False) x_vasp_response_functions_incar = Quantity( type=JSON, diff --git a/electronicparsers/vasp/metainfo/vasp_incars.py b/electronicparsers/vasp/metainfo/vasp_incars.py index fd46c320..9d203057 100644 --- a/electronicparsers/vasp/metainfo/vasp_incars.py +++ b/electronicparsers/vasp/metainfo/vasp_incars.py @@ -47,7 +47,7 @@ class x_vasp_incar_param(MCategory): class Method(runschema.method.Method): - m_def = Section(validate=False, extends_base_section=True) + m_def = Section(validate=False) x_vasp_incar_ADDGRID = Quantity( type=bool, diff --git a/electronicparsers/vasp/metainfo/vasp_incarsOut.py b/electronicparsers/vasp/metainfo/vasp_incarsOut.py index 867fd7ef..ea9fcc50 100644 --- a/electronicparsers/vasp/metainfo/vasp_incarsOut.py +++ b/electronicparsers/vasp/metainfo/vasp_incarsOut.py @@ -47,7 +47,7 @@ class x_vasp_incarOut_param(MCategory): class Method(runschema.method.Method): - m_def = Section(validate=False, extends_base_section=True) + m_def = Section(validate=False) x_vasp_incarOut_ADDGRID = Quantity( type=bool, diff --git a/electronicparsers/vasp/metainfo/vasp_incarsUnknown.py b/electronicparsers/vasp/metainfo/vasp_incarsUnknown.py index ca248d4c..88ce8d71 100644 --- a/electronicparsers/vasp/metainfo/vasp_incarsUnknown.py +++ b/electronicparsers/vasp/metainfo/vasp_incarsUnknown.py @@ -51,7 +51,7 @@ class x_vasp_incarUnknown_param(MCategory): class Method(runschema.method.Method): - m_def = Section(validate=False, extends_base_section=True) + m_def = Section(validate=False) x_vasp_incarOut_ENMAX = Quantity( type=np.float64, diff --git a/electronicparsers/w2dynamics/metainfo/w2dynamics.py b/electronicparsers/w2dynamics/metainfo/w2dynamics.py index 91c0c750..f80a70cd 100644 --- a/electronicparsers/w2dynamics/metainfo/w2dynamics.py +++ b/electronicparsers/w2dynamics/metainfo/w2dynamics.py @@ -1186,7 +1186,7 @@ class Method(runschema.method.Method): approximations (convergence, thresholds, etc.) behind the calculation. """ - m_def = Section(validate=False, extends_base_section=True) + m_def = Section(validate=False) x_w2dynamics_config = SubSection( sub_section=x_w2dynamics_config_parameters.m_def, repeats=False @@ -1199,7 +1199,7 @@ class ScfIteration(runschema.calculation.ScfIteration): and gives detailed information on the SCF procedure of the specified quantities. """ - m_def = Section(validate=False, extends_base_section=True) + m_def = Section(validate=False) x_w2dynamics_dc_latt = Quantity( type=HDF5Reference, @@ -1263,7 +1263,7 @@ class ScfIteration(runschema.calculation.ScfIteration): class Run(runschema.run.Run): - m_def = Section(validate=False, extends_base_section=True) + m_def = Section(validate=False) x_w2dynamics_axes = SubSection(sub_section=x_w2dynamics_axes.m_def, repeats=False) diff --git a/electronicparsers/wannier90/metainfo/wannier90.py b/electronicparsers/wannier90/metainfo/wannier90.py index 6c0285ae..ad14e74a 100644 --- a/electronicparsers/wannier90/metainfo/wannier90.py +++ b/electronicparsers/wannier90/metainfo/wannier90.py @@ -35,7 +35,7 @@ class Run(runschema.run.Run): - m_def = Section(validate=False, extends_base_section=True) + m_def = Section(validate=False) x_wannier90_n_atoms_proj = Quantity( type=np.int32, diff --git a/electronicparsers/wien2k/metainfo/wien2k.py b/electronicparsers/wien2k/metainfo/wien2k.py index de042666..31d6801f 100644 --- a/electronicparsers/wien2k/metainfo/wien2k.py +++ b/electronicparsers/wien2k/metainfo/wien2k.py @@ -154,7 +154,7 @@ class x_wien2k_section_equiv_atoms(MSection): class Run(runschema.run.Run): - m_def = Section(validate=False, extends_base_section=True) + m_def = Section(validate=False) x_wien2k_header = SubSection( sub_section=SectionProxy('x_wien2k_header'), repeats=True @@ -162,7 +162,7 @@ class Run(runschema.run.Run): class ScfIteration(runschema.calculation.ScfIteration): - m_def = Section(validate=False, extends_base_section=True) + m_def = Section(validate=False) x_wien2k_iteration_number = Quantity( type=np.int32, @@ -574,7 +574,7 @@ class ScfIteration(runschema.calculation.ScfIteration): class System(runschema.system.System): - m_def = Section(validate=False, extends_base_section=True) + m_def = Section(validate=False) x_wien2k_nonequiv_atoms = Quantity( type=np.int32, @@ -657,7 +657,7 @@ class System(runschema.system.System): class Method(runschema.method.Method): - m_def = Section(validate=False, extends_base_section=True) + m_def = Section(validate=False) x_wien2k_switch = Quantity( type=str, diff --git a/electronicparsers/yambo/metainfo/yambo.py b/electronicparsers/yambo/metainfo/yambo.py index 7308a3d7..e0955edd 100644 --- a/electronicparsers/yambo/metainfo/yambo.py +++ b/electronicparsers/yambo/metainfo/yambo.py @@ -174,7 +174,7 @@ class x_yambo_parameters(MSection): class Program(runschema.run.Program): - m_def = Section(validate=False, extends_base_section=True) + m_def = Section(validate=False) x_yambo_build = Quantity( type=str, @@ -192,7 +192,7 @@ class Program(runschema.run.Program): class Run(runschema.run.Run): - m_def = Section(validate=False, extends_base_section=True) + m_def = Section(validate=False) x_yambo_job_string = Quantity( type=str, @@ -343,7 +343,7 @@ class x_yambo_bare_xc_bandenergies(runschema.calculation.BandEnergies): class Calculation(runschema.calculation.Calculation): - m_def = Section(validate=False, extends_base_section=True) + m_def = Section(validate=False) x_yambo_electronic_temperature = Quantity( type=np.float64, @@ -556,7 +556,7 @@ class x_yambo_transferred_momenta(x_yambo_module): class Method(runschema.method.Method): - m_def = Section(validate=False, extends_base_section=True) + m_def = Section(validate=False) x_yambo_transferred_momenta = SubSection( sub_section=x_yambo_transferred_momenta.m_def, repeats=True From e6572c47e6ee6a0c84d3fc56f394bacea310e062 Mon Sep 17 00:00:00 2001 From: ndaelman Date: Fri, 15 Nov 2024 21:43:40 +0100 Subject: [PATCH 2/4] Add `m_package.__init_metainfo__()` --- electronicparsers/abinit/metainfo/abinit.py | 3 +++ .../abinit/metainfo/abinit_autogenerated.py | 3 +++ electronicparsers/ams/metainfo/ams.py | 3 +++ electronicparsers/atk/metainfo/atk.py | 3 +++ electronicparsers/castep/metainfo/castep.py | 3 +++ electronicparsers/charmm/metainfo/charmm.py | 3 +++ electronicparsers/cp2k/metainfo/cp2k.py | 3 +++ electronicparsers/cpmd/metainfo/cpmd.py | 3 +++ electronicparsers/dmol3/metainfo/dmol3.py | 3 +++ electronicparsers/edmft/metainfo/edmft.py | 3 +++ electronicparsers/elk/metainfo/elk.py | 3 +++ .../exciting/metainfo/exciting.py | 3 +++ electronicparsers/fleur/metainfo/fleur.py | 3 +++ electronicparsers/fplo/metainfo/fplo.py | 2 ++ .../fplo/metainfo/fplo_input_autogenerated.py | 3 +++ .../fplo/metainfo/fplo_temporaries.py | 3 +++ electronicparsers/gamess/metainfo/gamess.py | 3 +++ .../gaussian/metainfo/gaussian.py | 3 +++ electronicparsers/gpaw/metainfo/gpaw.py | 3 +++ electronicparsers/magres/metainfo/magres.py | 3 +++ electronicparsers/molcas/metainfo/molcas.py | 3 +++ electronicparsers/mopac/metainfo/mopac.py | 3 +++ electronicparsers/nwchem/metainfo/nwchem.py | 3 +++ electronicparsers/ocean/metainfo/ocean.py | 3 +++ electronicparsers/octopus/metainfo/octopus.py | 3 +++ .../octopus/metainfo/octopus_autogenerated.py | 3 +++ electronicparsers/onetep/metainfo/onetep.py | 3 +++ electronicparsers/orca/metainfo/orca.py | 3 +++ electronicparsers/psi4/metainfo/psi4.py | 3 +++ electronicparsers/qball/metainfo/qball.py | 2 ++ electronicparsers/qbox/metainfo/qbox.py | 3 +++ electronicparsers/siesta/metainfo/siesta.py | 3 +++ .../siesta/metainfo/siesta_autogenerated.py | 3 +++ .../soliddmft/metainfo/soliddmft.py | 3 +++ .../tbstudio/metainfo/tbstudio.py | 2 ++ .../turbomole/metainfo/turbomole.py | 3 +++ electronicparsers/vasp/metainfo/vasp.py | 3 +++ electronicparsers/vasp/metainfo/vasp_incars.py | 3 +++ .../vasp/metainfo/vasp_incarsOut.py | 3 +++ .../vasp/metainfo/vasp_incarsUnknown.py | 3 +++ .../w2dynamics/metainfo/w2dynamics.py | 3 +++ .../wannier90/metainfo/wannier90.py | 3 +++ electronicparsers/wien2k/metainfo/wien2k.py | 3 +++ electronicparsers/wien2k/parser.py | 18 ++++++++++-------- electronicparsers/yambo/metainfo/yambo.py | 3 +++ 45 files changed, 139 insertions(+), 8 deletions(-) diff --git a/electronicparsers/abinit/metainfo/abinit.py b/electronicparsers/abinit/metainfo/abinit.py index c420ebaa..fa318680 100644 --- a/electronicparsers/abinit/metainfo/abinit.py +++ b/electronicparsers/abinit/metainfo/abinit.py @@ -869,3 +869,6 @@ class x_abinit_section_dataset(abinit_autogenerated.x_abinit_section_dataset): x_abinit_section_dataset_header = SubSection( sub_section=x_abinit_section_dataset_header.m_def, repeats=True ) + + +m_package.__init_metainfo__() diff --git a/electronicparsers/abinit/metainfo/abinit_autogenerated.py b/electronicparsers/abinit/metainfo/abinit_autogenerated.py index e4693202..b55c64ba 100644 --- a/electronicparsers/abinit/metainfo/abinit_autogenerated.py +++ b/electronicparsers/abinit/metainfo/abinit_autogenerated.py @@ -6792,3 +6792,6 @@ class Run(runschema.run.Run): x_abinit_section_dataset = SubSection( sub_section=x_abinit_section_dataset.m_def, repeats=True ) + + +m_package.__init_metainfo__() diff --git a/electronicparsers/ams/metainfo/ams.py b/electronicparsers/ams/metainfo/ams.py index 900ac17a..c353d866 100644 --- a/electronicparsers/ams/metainfo/ams.py +++ b/electronicparsers/ams/metainfo/ams.py @@ -767,3 +767,6 @@ class KMesh(runschema.method.KMesh): description=""" """, ) + + +m_package.__init_metainfo__() diff --git a/electronicparsers/atk/metainfo/atk.py b/electronicparsers/atk/metainfo/atk.py index fdb8051a..816b0ce5 100644 --- a/electronicparsers/atk/metainfo/atk.py +++ b/electronicparsers/atk/metainfo/atk.py @@ -69,3 +69,6 @@ class Method(method.Method): Monkhorstpack grid sampling """, ) + + +m_package.__init_metainfo__() diff --git a/electronicparsers/castep/metainfo/castep.py b/electronicparsers/castep/metainfo/castep.py index 9f559765..43ea268a 100644 --- a/electronicparsers/castep/metainfo/castep.py +++ b/electronicparsers/castep/metainfo/castep.py @@ -2479,3 +2479,6 @@ class BandStructure(runschema.calculation.BandStructure): x_castep_section_k_points = SubSection( sub_section=SectionProxy('x_castep_section_k_points'), repeats=True ) + + +m_package.__init_metainfo__() diff --git a/electronicparsers/charmm/metainfo/charmm.py b/electronicparsers/charmm/metainfo/charmm.py index 6f652f96..4f23b008 100644 --- a/electronicparsers/charmm/metainfo/charmm.py +++ b/electronicparsers/charmm/metainfo/charmm.py @@ -1929,3 +1929,6 @@ class Calculation(runschema.calculation.Calculation): sub_section=SectionProxy('x_charmm_section_single_configuration_calculation'), repeats=True, ) + + +m_package.__init_metainfo__() diff --git a/electronicparsers/cp2k/metainfo/cp2k.py b/electronicparsers/cp2k/metainfo/cp2k.py index 0fc36aaa..f472d9a1 100644 --- a/electronicparsers/cp2k/metainfo/cp2k.py +++ b/electronicparsers/cp2k/metainfo/cp2k.py @@ -59183,3 +59183,6 @@ class Run(runschema.run.Run): x_cp2k_section_input = SubSection( sub_section=SectionProxy('x_cp2k_section_input'), repeats=True ) + + +m_package.__init_metainfo__() diff --git a/electronicparsers/cpmd/metainfo/cpmd.py b/electronicparsers/cpmd/metainfo/cpmd.py index a1668ba1..4dc88846 100644 --- a/electronicparsers/cpmd/metainfo/cpmd.py +++ b/electronicparsers/cpmd/metainfo/cpmd.py @@ -10731,3 +10731,6 @@ class Run(runschema.run.Run): x_cpmd_section_input = SubSection( sub_section=SectionProxy('x_cpmd_section_input'), repeats=True ) + + +m_package.__init_metainfo__() diff --git a/electronicparsers/dmol3/metainfo/dmol3.py b/electronicparsers/dmol3/metainfo/dmol3.py index 1561e418..7b3332da 100644 --- a/electronicparsers/dmol3/metainfo/dmol3.py +++ b/electronicparsers/dmol3/metainfo/dmol3.py @@ -662,3 +662,6 @@ class VibrationalFrequencies(runschema.calculation.VibrationalFrequencies): description=""" """, ) + + +m_package.__init_metainfo__() diff --git a/electronicparsers/edmft/metainfo/edmft.py b/electronicparsers/edmft/metainfo/edmft.py index 024953fa..9e520a02 100644 --- a/electronicparsers/edmft/metainfo/edmft.py +++ b/electronicparsers/edmft/metainfo/edmft.py @@ -94,3 +94,6 @@ class GreensFunctions(runschema.calculation.GreensFunctions): where s_oo is the parsed function. """, ) + + +m_package.__init_metainfo__() diff --git a/electronicparsers/elk/metainfo/elk.py b/electronicparsers/elk/metainfo/elk.py index 093f8a58..a534306a 100644 --- a/electronicparsers/elk/metainfo/elk.py +++ b/electronicparsers/elk/metainfo/elk.py @@ -773,3 +773,6 @@ class Calculation(runschema.calculation.Calculation): Estimated fundamental indirect gap final """, ) + + +m_package.__init_metainfo__() diff --git a/electronicparsers/exciting/metainfo/exciting.py b/electronicparsers/exciting/metainfo/exciting.py index 1c4fbcbc..c1d5eeb4 100644 --- a/electronicparsers/exciting/metainfo/exciting.py +++ b/electronicparsers/exciting/metainfo/exciting.py @@ -2940,3 +2940,6 @@ class Run(runschema.run.Run): sub_section=SectionProxy('x_exciting_section_geometry_optimization'), repeats=True, ) + + +m_package.__init_metainfo__() diff --git a/electronicparsers/fleur/metainfo/fleur.py b/electronicparsers/fleur/metainfo/fleur.py index 45579e98..7a7ef85f 100644 --- a/electronicparsers/fleur/metainfo/fleur.py +++ b/electronicparsers/fleur/metainfo/fleur.py @@ -621,3 +621,6 @@ class BaseCalculation(runschema.calculation.BaseCalculation): description=""" """, ) + + +m_package.__init_metainfo__() diff --git a/electronicparsers/fplo/metainfo/fplo.py b/electronicparsers/fplo/metainfo/fplo.py index fae22416..3d8f2ee4 100644 --- a/electronicparsers/fplo/metainfo/fplo.py +++ b/electronicparsers/fplo/metainfo/fplo.py @@ -186,3 +186,5 @@ class Method(runschema.method.Method): # description=''' # FPLO: Atom/Orbital dependent DFT+U property: value F6 # ''') + +m_package.__init_metainfo__() diff --git a/electronicparsers/fplo/metainfo/fplo_input_autogenerated.py b/electronicparsers/fplo/metainfo/fplo_input_autogenerated.py index 76c19b4c..73785488 100644 --- a/electronicparsers/fplo/metainfo/fplo_input_autogenerated.py +++ b/electronicparsers/fplo/metainfo/fplo_input_autogenerated.py @@ -2742,3 +2742,6 @@ class Method(runschema.method.Method): m_def = Section(validate=False) x_fplo_in = SubSection(sub_section=SectionProxy('x_fplo_in'), repeats=True) + + +m_package.__init_metainfo__() diff --git a/electronicparsers/fplo/metainfo/fplo_temporaries.py b/electronicparsers/fplo/metainfo/fplo_temporaries.py index 95f29742..cbcf7100 100644 --- a/electronicparsers/fplo/metainfo/fplo_temporaries.py +++ b/electronicparsers/fplo/metainfo/fplo_temporaries.py @@ -317,3 +317,6 @@ class ScfIteration(runschema.calculation.ScfIteration): Temporary storage for FPLO Fermi energy in iteration """, ) + + +m_package.__init_metainfo__() diff --git a/electronicparsers/gamess/metainfo/gamess.py b/electronicparsers/gamess/metainfo/gamess.py index 6857aa65..7a7f7899 100644 --- a/electronicparsers/gamess/metainfo/gamess.py +++ b/electronicparsers/gamess/metainfo/gamess.py @@ -835,3 +835,6 @@ class Energy(runschema.calculation.Energy): description=""" """, ) + + +m_package.__init_metainfo__() diff --git a/electronicparsers/gaussian/metainfo/gaussian.py b/electronicparsers/gaussian/metainfo/gaussian.py index 591af46c..51db7f91 100644 --- a/electronicparsers/gaussian/metainfo/gaussian.py +++ b/electronicparsers/gaussian/metainfo/gaussian.py @@ -1705,3 +1705,6 @@ class Method(runschema.method.Method): sub_section=SectionProxy('x_gaussian_section_elstruc_method'), repeats=True, ) + + +m_package.__init_metainfo__() diff --git a/electronicparsers/gpaw/metainfo/gpaw.py b/electronicparsers/gpaw/metainfo/gpaw.py index eeeba33d..f4e51723 100644 --- a/electronicparsers/gpaw/metainfo/gpaw.py +++ b/electronicparsers/gpaw/metainfo/gpaw.py @@ -212,3 +212,6 @@ class Method(runschema.method.Method): x_gpaw_section_paw_method = SubSection( sub_section=SectionProxy('x_gpaw_section_paw_method'), repeats=True ) + + +m_package.__init_metainfo__() diff --git a/electronicparsers/magres/metainfo/magres.py b/electronicparsers/magres/metainfo/magres.py index fe71f2f0..9838181d 100644 --- a/electronicparsers/magres/metainfo/magres.py +++ b/electronicparsers/magres/metainfo/magres.py @@ -108,3 +108,6 @@ class SpinSpinCoupling(BaseSpinSpinCoupling): on the list `System.atoms.labels`. """, ) + + +m_package.__init_metainfo__() diff --git a/electronicparsers/molcas/metainfo/molcas.py b/electronicparsers/molcas/metainfo/molcas.py index 9dd2e8c5..c7ea0ffe 100644 --- a/electronicparsers/molcas/metainfo/molcas.py +++ b/electronicparsers/molcas/metainfo/molcas.py @@ -149,3 +149,6 @@ class Calculation(runschema.calculation.Calculation): x_molcas_section_frequency = SubSection( sub_section=SectionProxy('x_molcas_section_frequency'), repeats=True ) + + +m_package.__init_metainfo__() diff --git a/electronicparsers/mopac/metainfo/mopac.py b/electronicparsers/mopac/metainfo/mopac.py index 3269e91c..85f33175 100644 --- a/electronicparsers/mopac/metainfo/mopac.py +++ b/electronicparsers/mopac/metainfo/mopac.py @@ -77,3 +77,6 @@ class Method(runschema.method.Method): description=""" """, ) + + +m_package.__init_metainfo__() diff --git a/electronicparsers/nwchem/metainfo/nwchem.py b/electronicparsers/nwchem/metainfo/nwchem.py index cc54b9e0..145c0387 100644 --- a/electronicparsers/nwchem/metainfo/nwchem.py +++ b/electronicparsers/nwchem/metainfo/nwchem.py @@ -485,3 +485,6 @@ class System(runschema.system.System): The lattice omega value. """, ) + + +m_package.__init_metainfo__() diff --git a/electronicparsers/ocean/metainfo/ocean.py b/electronicparsers/ocean/metainfo/ocean.py index 2e470499..3de7faa8 100644 --- a/electronicparsers/ocean/metainfo/ocean.py +++ b/electronicparsers/ocean/metainfo/ocean.py @@ -408,3 +408,6 @@ class Program(runschema.run.Program): DFT code (QuantumESPRESSO or ABINIT) used in the initial step. """, ) + + +m_package.__init_metainfo__() diff --git a/electronicparsers/octopus/metainfo/octopus.py b/electronicparsers/octopus/metainfo/octopus.py index 05800d45..d3a64802 100644 --- a/electronicparsers/octopus/metainfo/octopus.py +++ b/electronicparsers/octopus/metainfo/octopus.py @@ -69,3 +69,6 @@ class Run(runschema.run.Run): octopus svn revision """, ) + + +m_package.__init_metainfo__() diff --git a/electronicparsers/octopus/metainfo/octopus_autogenerated.py b/electronicparsers/octopus/metainfo/octopus_autogenerated.py index 8beca19a..67055d79 100644 --- a/electronicparsers/octopus/metainfo/octopus_autogenerated.py +++ b/electronicparsers/octopus/metainfo/octopus_autogenerated.py @@ -11645,3 +11645,6 @@ class Run(runschema.run.Run): """, categories=[x_octopus_parserlog], ) + + +m_package.__init_metainfo__() diff --git a/electronicparsers/onetep/metainfo/onetep.py b/electronicparsers/onetep/metainfo/onetep.py index dc20c2f2..3ce1e8d8 100644 --- a/electronicparsers/onetep/metainfo/onetep.py +++ b/electronicparsers/onetep/metainfo/onetep.py @@ -3441,3 +3441,6 @@ class AtomParameters(runschema.method.AtomParameters): Temporary storing atom name """, ) + + +m_package.__init_metainfo__() diff --git a/electronicparsers/orca/metainfo/orca.py b/electronicparsers/orca/metainfo/orca.py index 00dcb30e..87a5120e 100644 --- a/electronicparsers/orca/metainfo/orca.py +++ b/electronicparsers/orca/metainfo/orca.py @@ -1446,3 +1446,6 @@ class Run(runschema.run.Run): description=""" """, ) + + +m_package.__init_metainfo__() diff --git a/electronicparsers/psi4/metainfo/psi4.py b/electronicparsers/psi4/metainfo/psi4.py index 46668eb9..08dfc6a9 100644 --- a/electronicparsers/psi4/metainfo/psi4.py +++ b/electronicparsers/psi4/metainfo/psi4.py @@ -370,3 +370,6 @@ class Calculation(runschema.calculation.Calculation): x_psi4_root_information = SubSection( sub_section=x_psi4_root_information.m_def, repeats=True ) + + +m_package.__init_metainfo__() diff --git a/electronicparsers/qball/metainfo/qball.py b/electronicparsers/qball/metainfo/qball.py index e9bfaf50..95605f6d 100644 --- a/electronicparsers/qball/metainfo/qball.py +++ b/electronicparsers/qball/metainfo/qball.py @@ -25,3 +25,5 @@ m_package = Package() + +m_package.__init_metainfo__() diff --git a/electronicparsers/qbox/metainfo/qbox.py b/electronicparsers/qbox/metainfo/qbox.py index bd7a3601..41d68d29 100644 --- a/electronicparsers/qbox/metainfo/qbox.py +++ b/electronicparsers/qbox/metainfo/qbox.py @@ -488,3 +488,6 @@ class Energy(runschema.calculation.Energy): x_qbox_efield = SubSection(sub_section=runschema.calculation.EnergyEntry.m_def) x_qbox_enthalpy = SubSection(sub_section=runschema.calculation.EnergyEntry.m_def) + + +m_package.__init_metainfo__() diff --git a/electronicparsers/siesta/metainfo/siesta.py b/electronicparsers/siesta/metainfo/siesta.py index cc7b2868..78cc0f1a 100644 --- a/electronicparsers/siesta/metainfo/siesta.py +++ b/electronicparsers/siesta/metainfo/siesta.py @@ -139,3 +139,6 @@ class Method(runschema.method.Method): description=""" """, ) + + +m_package.__init_metainfo__() diff --git a/electronicparsers/siesta/metainfo/siesta_autogenerated.py b/electronicparsers/siesta/metainfo/siesta_autogenerated.py index b9bee56c..1541b9e4 100644 --- a/electronicparsers/siesta/metainfo/siesta_autogenerated.py +++ b/electronicparsers/siesta/metainfo/siesta_autogenerated.py @@ -3363,3 +3363,6 @@ class Method(runschema.method.Method): x_siesta_section_input = SubSection( sub_section=SectionProxy('x_siesta_section_input'), repeats=True ) + + +m_package.__init_metainfo__() diff --git a/electronicparsers/soliddmft/metainfo/soliddmft.py b/electronicparsers/soliddmft/metainfo/soliddmft.py index 08a5c961..ca565cf7 100644 --- a/electronicparsers/soliddmft/metainfo/soliddmft.py +++ b/electronicparsers/soliddmft/metainfo/soliddmft.py @@ -272,3 +272,6 @@ class ScfIteration(runschema.calculation.ScfIteration): x_soliddmft_observables = SubSection( sub_section=x_soliddmft_observables_parameters.m_def, repeats=True ) + + +m_package.__init_metainfo__() diff --git a/electronicparsers/tbstudio/metainfo/tbstudio.py b/electronicparsers/tbstudio/metainfo/tbstudio.py index 16ce9d32..35afcdcf 100644 --- a/electronicparsers/tbstudio/metainfo/tbstudio.py +++ b/electronicparsers/tbstudio/metainfo/tbstudio.py @@ -32,3 +32,5 @@ m_package = Package() + +m_package.__init_metainfo__() diff --git a/electronicparsers/turbomole/metainfo/turbomole.py b/electronicparsers/turbomole/metainfo/turbomole.py index 906dc6f3..b7dee431 100644 --- a/electronicparsers/turbomole/metainfo/turbomole.py +++ b/electronicparsers/turbomole/metainfo/turbomole.py @@ -725,3 +725,6 @@ class System(runschema.system.System): Multipole precision parameter for PCEEM embedding """, ) + + +m_package.__init_metainfo__() diff --git a/electronicparsers/vasp/metainfo/vasp.py b/electronicparsers/vasp/metainfo/vasp.py index 258ccb11..566006b7 100644 --- a/electronicparsers/vasp/metainfo/vasp.py +++ b/electronicparsers/vasp/metainfo/vasp.py @@ -167,3 +167,6 @@ class GW(runschema.method.GW): Input parameters used in the "response functions". """, ) + + +m_package.__init_metainfo__() diff --git a/electronicparsers/vasp/metainfo/vasp_incars.py b/electronicparsers/vasp/metainfo/vasp_incars.py index 9d203057..97314904 100644 --- a/electronicparsers/vasp/metainfo/vasp_incars.py +++ b/electronicparsers/vasp/metainfo/vasp_incars.py @@ -3426,3 +3426,6 @@ class Method(runschema.method.Method): """, categories=[x_vasp_incar_param], ) + + +m_package.__init_metainfo__() diff --git a/electronicparsers/vasp/metainfo/vasp_incarsOut.py b/electronicparsers/vasp/metainfo/vasp_incarsOut.py index ea9fcc50..8c8c84f0 100644 --- a/electronicparsers/vasp/metainfo/vasp_incarsOut.py +++ b/electronicparsers/vasp/metainfo/vasp_incarsOut.py @@ -3426,3 +3426,6 @@ class Method(runschema.method.Method): """, categories=[x_vasp_incarOut_param], ) + + +m_package.__init_metainfo__() diff --git a/electronicparsers/vasp/metainfo/vasp_incarsUnknown.py b/electronicparsers/vasp/metainfo/vasp_incarsUnknown.py index 88ce8d71..389d3d6d 100644 --- a/electronicparsers/vasp/metainfo/vasp_incarsUnknown.py +++ b/electronicparsers/vasp/metainfo/vasp_incarsUnknown.py @@ -84,3 +84,6 @@ class Method(runschema.method.Method): """, categories=[vasp_incarsOut.x_vasp_incarOut_param], ) + + +m_package.__init_metainfo__() diff --git a/electronicparsers/w2dynamics/metainfo/w2dynamics.py b/electronicparsers/w2dynamics/metainfo/w2dynamics.py index f80a70cd..e945fcf1 100644 --- a/electronicparsers/w2dynamics/metainfo/w2dynamics.py +++ b/electronicparsers/w2dynamics/metainfo/w2dynamics.py @@ -1268,3 +1268,6 @@ class Run(runschema.run.Run): x_w2dynamics_axes = SubSection(sub_section=x_w2dynamics_axes.m_def, repeats=False) # TODO add config, environment variables + + +m_package.__init_metainfo__() diff --git a/electronicparsers/wannier90/metainfo/wannier90.py b/electronicparsers/wannier90/metainfo/wannier90.py index ad14e74a..5b7de533 100644 --- a/electronicparsers/wannier90/metainfo/wannier90.py +++ b/electronicparsers/wannier90/metainfo/wannier90.py @@ -54,3 +54,6 @@ class Run(runschema.run.Run): Bohr, respectively. The default value is Ang. """, ) + + +m_package.__init_metainfo__() diff --git a/electronicparsers/wien2k/metainfo/wien2k.py b/electronicparsers/wien2k/metainfo/wien2k.py index 31d6801f..3b2955f0 100644 --- a/electronicparsers/wien2k/metainfo/wien2k.py +++ b/electronicparsers/wien2k/metainfo/wien2k.py @@ -781,3 +781,6 @@ class Method(runschema.method.Method): x_wien2k_section_XC = SubSection( sub_section=SectionProxy('x_wien2k_section_XC'), repeats=True ) + + +m_package.__init_metainfo__() diff --git a/electronicparsers/wien2k/parser.py b/electronicparsers/wien2k/parser.py index daada6ee..9a1e8b34 100644 --- a/electronicparsers/wien2k/parser.py +++ b/electronicparsers/wien2k/parser.py @@ -1127,18 +1127,20 @@ def parse_method(self): atom_obj = AtomParameters() atom_obj.atom_index = atom_index atom_obj.core_hole = CoreHole( - j_quantum_number = j_quantum_number, - l_quantum_number = l_quantum_number, - n_quantum_number = n_quantum_number, - n_electrons_excited = electrons_excited, - occupation = occupancy, - dscf_state = 'final', + j_quantum_number=j_quantum_number, + l_quantum_number=l_quantum_number, + n_quantum_number=n_quantum_number, + n_electrons_excited=electrons_excited, + occupation=occupancy, + dscf_state='final', ) atom_par.append(atom_obj) break else: - self.logger.warning("inc file is missing, no corehole information " - "will be parsed if corehole present.") + self.logger.warning( + 'inc file is missing, no corehole information ' + 'will be parsed if corehole present.' + ) # basis if self.in1_parser.mainfile: self.in1_parser.parse() diff --git a/electronicparsers/yambo/metainfo/yambo.py b/electronicparsers/yambo/metainfo/yambo.py index e0955edd..fc5c6df1 100644 --- a/electronicparsers/yambo/metainfo/yambo.py +++ b/electronicparsers/yambo/metainfo/yambo.py @@ -575,3 +575,6 @@ class Method(runschema.method.Method): x_yambo_dipoles = SubSection(sub_section=x_yambo_dipoles.m_def, repeats=True) x_yambo_dyson = SubSection(sub_section=x_yambo_dyson.m_def, repeats=True) + + +m_package.__init_metainfo__() From 2b54f18a0856358e53ae434964e1659126868a73 Mon Sep 17 00:00:00 2001 From: ndaelman Date: Mon, 16 Dec 2024 17:56:08 +0100 Subject: [PATCH 3/4] Patch failing imports (wip) --- electronicparsers/abacus/metainfo/abacus.py | 26 ++++++------ electronicparsers/abacus/parser.py | 46 ++++++++++----------- 2 files changed, 34 insertions(+), 38 deletions(-) diff --git a/electronicparsers/abacus/metainfo/abacus.py b/electronicparsers/abacus/metainfo/abacus.py index a58da9d4..4e4194fa 100644 --- a/electronicparsers/abacus/metainfo/abacus.py +++ b/electronicparsers/abacus/metainfo/abacus.py @@ -166,7 +166,7 @@ class x_abacus_section_specie_basis_set(MSection): x_abacus_specie_basis_set_rcutoff = Quantity( type=np.float64, - unit='bohr', + unit='m', shape=[], description=""" - @@ -191,7 +191,7 @@ class BasisSet(runschema.method.BasisSet): x_abacus_basis_sets_delta_k = Quantity( type=np.float64, - unit='1/bohr', + unit='1/m', shape=[], description=""" - @@ -200,7 +200,7 @@ class BasisSet(runschema.method.BasisSet): x_abacus_basis_sets_delta_r = Quantity( type=np.float64, - unit='bohr', + unit='m', shape=[], description=""" - @@ -209,7 +209,7 @@ class BasisSet(runschema.method.BasisSet): x_abacus_basis_sets_dr_uniform = Quantity( type=np.float64, - unit='bohr', + unit='m', shape=[], description=""" - @@ -218,7 +218,7 @@ class BasisSet(runschema.method.BasisSet): x_abacus_basis_sets_rmax = Quantity( type=np.float64, - unit='bohr', + unit='m', shape=[], description=""" - @@ -245,7 +245,7 @@ class Calculation(runschema.calculation.Calculation): x_abacus_longest_orb_rcut = Quantity( type=np.float64, - unit='bohr', + unit='m', shape=[], description=""" - @@ -254,7 +254,7 @@ class Calculation(runschema.calculation.Calculation): x_abacus_longest_nonlocal_projector_rcut = Quantity( type=np.float64, - unit='bohr', + unit='m', shape=[], description=""" - @@ -263,7 +263,7 @@ class Calculation(runschema.calculation.Calculation): x_abacus_searching_radius = Quantity( type=np.float64, - unit='bohr', + unit='m', shape=[], description=""" - @@ -272,7 +272,7 @@ class Calculation(runschema.calculation.Calculation): x_abacus_searching_radius_unit = Quantity( type=np.float64, - unit='bohr', + unit='m', shape=[], description=""" - @@ -396,7 +396,7 @@ class Run(runschema.run.Run): class Method(runschema.method.Method): - m_def = Section(validate=False) + # m_def = Section(validate=False) x_abacus_initial_magnetization_total = Quantity( type=np.float64, @@ -617,7 +617,7 @@ class System(runschema.system.System): x_abacus_alat = Quantity( type=np.float64, - unit='bohr', + unit='m', shape=[], description=""" Lattice Parameter 'a', constant during a run and used as unit in other quantities @@ -627,7 +627,7 @@ class System(runschema.system.System): x_abacus_reciprocal_vectors = Quantity( type=np.float64, shape=[3, 3], - unit='1 / meter', + unit='1 / m', description=""" The reciprocal cell """, @@ -675,7 +675,7 @@ class System(runschema.system.System): x_abacus_cell_volume = Quantity( type=np.float64, - unit='bohr**3', + unit='m**3', shape=[], description=""" Volume of unit cell diff --git a/electronicparsers/abacus/parser.py b/electronicparsers/abacus/parser.py index faeec920..83cd17e4 100644 --- a/electronicparsers/abacus/parser.py +++ b/electronicparsers/abacus/parser.py @@ -24,7 +24,8 @@ from collections import namedtuple from datetime import datetime -from .metainfo import abacus +# the fileparser import has to come after metainfo to overload the Quantity class +from .metainfo.abacus import * from nomad.units import ureg from nomad.parsing.file_parser import TextParser, Quantity, DataTextParser from runschema.run import Run, Program, TimeRun @@ -64,11 +65,6 @@ SinglePoint, SinglePointMethod, ) -from .metainfo.abacus import ( - Method as xsection_method, - x_abacus_section_parallel, - x_abacus_section_specie_basis_set, -) # TODO determine if we can update regex to the following @@ -132,86 +128,86 @@ def init_quantities(self): ), Quantity('dft_plus_u', r'\n *dft_plus_u\s*(\d)', repeats=False, dtype=bool), Quantity( - xsection_method.x_abacus_mixing_method, + 'x_abacus_mixing_method', rf'\n *mixing_type\s*(\S+)', repeats=False, ), Quantity( - xsection_method.x_abacus_mixing_beta, + 'x_abacus_mixing_beta', rf'\n *mixing_beta\s*({re_float})', repeats=False, ), Quantity( - xsection_method.x_abacus_diagonalization_algorithm, + 'x_abacus_diagonalization_algorithm', rf'\n *ks_solver\s*(\w+)', repeats=False, ), Quantity( - xsection_method.x_abacus_dispersion_correction_method, + 'x_abacus_dispersion_correction_method', r'\n *vdw_method\s*(\S+)', repeats=False, ), Quantity( - xsection_method.x_abacus_gamma_algorithms, + 'x_abacus_gamma_algorithms', rf'\n *gamma_only\s*(\d)', repeats=False, dtype=bool, ), Quantity( - xsection_method.x_abacus_scf_threshold_density, + 'x_abacus_scf_threshold_density', rf'\n *scf_thr\s*({re_float})', repeats=False, dtype=float, ), Quantity( - xsection_method.x_abacus_initial_magnetization_total, + 'x_abacus_initial_magnetization_total', rf'\n *tot_magnetization\s*({re_float})', repeats=False, dtype=float, ), Quantity( - xsection_method.x_abacus_hse_omega, + 'x_abacus_hse_omega', rf'\n *exx_hse_omega\s*({re_float})', repeats=False, unit='1/bohr', ), Quantity( - xsection_method.x_abacus_hybrid_xc_coeff, + 'x_abacus_hybrid_xc_coeff', rf'\n *exx_hybrid_alpha\s*({re_float})', repeats=False, ), Quantity( - xsection_method.x_abacus_exx_ccp_rmesh_times, + 'x_abacus_exx_ccp_rmesh_times', rf'\n *exx_ccp_rmesh_times\s*({re_float})', repeats=False, ), Quantity( - xsection_method.x_abacus_exx_dm_threshold, + 'x_abacus_exx_dm_threshold', rf'\n *exx_dm_threshold\s*({re_float})', repeats=False, ), Quantity( - xsection_method.x_abacus_exx_cauchy_threshold, + 'x_abacus_exx_cauchy_threshold', rf'\n *exx_cauchy_threshold\s*({re_float})', repeats=False, ), Quantity( - xsection_method.x_abacus_exx_schwarz_threshold, + 'x_abacus_exx_schwarz_threshold', rf'\n *exx_schwarz_threshold\s*({re_float})', repeats=False, ), Quantity( - xsection_method.x_abacus_exx_c_threshold, + 'x_abacus_exx_c_threshold', rf'\n *exx_c_threshold\s*({re_float})', repeats=False, ), Quantity( - xsection_method.x_abacus_exx_v_threshold, + 'x_abacus_exx_v_threshold', rf'\n *exx_v_threshold\s*({re_float})', repeats=False, ), Quantity( - xsection_method.x_abacus_exx_pca_threshold, + 'x_abacus_exx_pca_threshold', rf'\n *exx_pca_threshold\s*({re_float})', repeats=False, ), @@ -627,7 +623,7 @@ def str_to_polarization(val_in): repeats=True, ), Quantity( - xsection_method.x_abacus_pao_radial_cutoff, + 'x_abacus_pao_radial_cutoff', rf'PAO radial cut off \(Bohr\)\s*=\s*({re_float})', unit='bohr', dtype=float, @@ -1771,7 +1767,7 @@ def parse_method(self): orbital_settings.get('orbital_information', []) ): sec_specie_basis_set = x_abacus_section_specie_basis_set() - bs.x_abacus_section_specie_basis_set.append(sec_specie_basis_set) + bs.x_abacus_section_specie_basis_set = [sec_specie_basis_set] sec_specie_basis_set.x_abacus_specie_basis_set_filename = ( os.path.basename(header.get('orbital_files')[i]) ) @@ -1904,7 +1900,7 @@ def parse(self, filepath, archive, logger): # parallel sec_parallel = x_abacus_section_parallel() - sec_run.x_abacus_section_parallel.append(sec_parallel) + sec_run.x_abacus_section_parallel = [sec_parallel] sec_parallel.x_abacus_nproc = self.out_parser.get('nproc') for key in ['kpar', 'bndpar', 'diago_proc']: val = self.input_parser.get(key) From e6a5a0e61dbc9453f2c1ce54c3727c5a5b0ff6d5 Mon Sep 17 00:00:00 2001 From: ndaelman Date: Thu, 16 Jan 2025 15:58:01 +0100 Subject: [PATCH 4/4] Also deprecate in magres --- electronicparsers/magres/parser.py | 1 - 1 file changed, 1 deletion(-) diff --git a/electronicparsers/magres/parser.py b/electronicparsers/magres/parser.py index 06902c84..2159d5fd 100644 --- a/electronicparsers/magres/parser.py +++ b/electronicparsers/magres/parser.py @@ -40,7 +40,6 @@ ElectricFieldGradient, SpinSpinCoupling, ) -from .metainfo.magres import m_package from ..utils import BeyondDFTWorkflowsParser