From f885f1e55de2bd5e2d5e90a0e2622f74ea405204 Mon Sep 17 00:00:00 2001 From: ndaelman Date: Fri, 24 Jan 2025 15:36:46 +0100 Subject: [PATCH] Remove annotations --- .../schema_packages/atoms_state.py | 7 ------ .../schema_packages/basis_set.py | 2 -- .../schema_packages/general.py | 11 --------- .../schema_packages/model_method.py | 23 ------------------- .../schema_packages/model_system.py | 14 ----------- .../schema_packages/physical_property.py | 1 - 6 files changed, 58 deletions(-) diff --git a/src/nomad_simulations/schema_packages/atoms_state.py b/src/nomad_simulations/schema_packages/atoms_state.py index 01edd1b8..3a8ac9b5 100644 --- a/src/nomad_simulations/schema_packages/atoms_state.py +++ b/src/nomad_simulations/schema_packages/atoms_state.py @@ -308,7 +308,6 @@ class CoreHole(ArchiveSection): description=""" Reference to the OrbitalsState section that is used as a basis to obtain the `CoreHole` section. """, - # a_eln=ELNAnnotation(component='ReferenceEditQuantity'), ) n_excited_electrons = Quantity( @@ -411,7 +410,6 @@ class HubbardInteractions(ArchiveSection): description=""" Value of the (intraorbital) Hubbard interaction """, - # a_eln=ELNAnnotation(component='NumberEditQuantity'), ) j_hunds_coupling = Quantity( @@ -420,7 +418,6 @@ class HubbardInteractions(ArchiveSection): description=""" Value of the (interorbital) Hund's coupling. """, - # a_eln=ELNAnnotation(component='NumberEditQuantity'), ) u_interorbital_interaction = Quantity( @@ -430,7 +427,6 @@ class HubbardInteractions(ArchiveSection): Value of the (interorbital) Coulomb interaction. In rotational invariant systems, u_interorbital_interaction = u_interaction - 2 * j_hunds_coupling. """, - # a_eln=ELNAnnotation(component='NumberEditQuantity'), ) j_local_exchange_interaction = Quantity( @@ -439,7 +435,6 @@ class HubbardInteractions(ArchiveSection): description=""" Value of the exchange interaction. In rotational invariant systems, j_local_exchange_interaction = j_hunds_coupling. """, - # a_eln=ELNAnnotation(component='NumberEditQuantity'), ) u_effective = Quantity( @@ -474,7 +469,6 @@ class HubbardInteractions(ArchiveSection): description=""" Name of the double counting correction algorithm applied. """, - # a_eln=ELNAnnotation(component='StringEditQuantity'), ) def resolve_u_interactions(self, logger: 'BoundLogger') -> Optional[tuple]: @@ -586,7 +580,6 @@ class AtomsState(Entity): Note: for `CoreHole` systems we do not consider the charge of the atom even if we do not store the final `OrbitalsState` where the electron was excited to. """, - # a_eln=ELNAnnotation(component='NumberEditQuantity'), ) core_hole = SubSection(sub_section=CoreHole.m_def, repeats=False) diff --git a/src/nomad_simulations/schema_packages/basis_set.py b/src/nomad_simulations/schema_packages/basis_set.py index 26f86f1b..7e760a43 100644 --- a/src/nomad_simulations/schema_packages/basis_set.py +++ b/src/nomad_simulations/schema_packages/basis_set.py @@ -57,7 +57,6 @@ class BasisSetComponent(ArchiveSection): description=""" Reference to the section `AtomsState` specifying the localization of the basis set. """, - # a_eln=ELNAnnotation(components='ReferenceEditQuantity'), ) # TODO: add atom index-based instantiator for species if not present @@ -69,7 +68,6 @@ class BasisSetComponent(ArchiveSection): Reference to the section `BaseModelMethod` containing the information of the Hamiltonian term to which the basis set applies. """, - # a_eln=ELNAnnotation(components='ReferenceEditQuantity'), ) # ? band_scope or orbital_scope: valence vs core diff --git a/src/nomad_simulations/schema_packages/general.py b/src/nomad_simulations/schema_packages/general.py index f7112e05..ae0c4fcc 100644 --- a/src/nomad_simulations/schema_packages/general.py +++ b/src/nomad_simulations/schema_packages/general.py @@ -70,7 +70,6 @@ class Program(Entity): description=""" The name of the program. """, - # a_eln=ELNAnnotation(component='StringEditQuantity'), ) version = Quantity( @@ -78,7 +77,6 @@ class Program(Entity): description=""" The version label of the program. """, - # a_eln=ELNAnnotation(component='StringEditQuantity'), ) link = Quantity( @@ -86,7 +84,6 @@ class Program(Entity): description=""" Website link to the program in published information. """, - # a_eln=ELNAnnotation(component='URLEditQuantity'), ) version_internal = Quantity( @@ -95,7 +92,6 @@ class Program(Entity): Specifies a program version tag used internally for development purposes. Any kind of tagging system is supported, including git commit hashes. """, - # a_eln=ELNAnnotation(component='StringEditQuantity'), ) subroutine_name_internal = Quantity( @@ -106,7 +102,6 @@ class Program(Entity): so the naming is representative. This naming is mostly meant for users who are familiar with the program's structure. """, - # a_eln=ELNAnnotation(component='StringEditQuantity'), ) compilation_host = Quantity( @@ -114,7 +109,6 @@ class Program(Entity): description=""" Specifies the host on which the program was compiled. """, - # a_eln=ELNAnnotation(component='StringEditQuantity'), ) @@ -137,7 +131,6 @@ class BaseSimulation(Activity): description=""" The date and time when this computation ended. """, - # a_eln=ELNAnnotation(component='DateTimeEditQuantity'), ) cpu1_start = Quantity( @@ -146,7 +139,6 @@ class BaseSimulation(Activity): description=""" The starting time of the computation on the (first) CPU 1. """, - # a_eln=ELNAnnotation(component='NumberEditQuantity'), ) cpu1_end = Quantity( @@ -155,7 +147,6 @@ class BaseSimulation(Activity): description=""" The end time of the computation on the (first) CPU 1. """, - # a_eln=ELNAnnotation(component='NumberEditQuantity'), ) wall_start = Quantity( @@ -164,7 +155,6 @@ class BaseSimulation(Activity): description=""" The internal wall-clock time from the starting of the computation. """, - # a_eln=ELNAnnotation(component='NumberEditQuantity'), ) wall_end = Quantity( @@ -173,7 +163,6 @@ class BaseSimulation(Activity): description=""" The internal wall-clock time from the end of the computation. """, - # a_eln=ELNAnnotation(component='NumberEditQuantity'), ) program = SubSection(sub_section=Program.m_def, repeats=False) diff --git a/src/nomad_simulations/schema_packages/model_method.py b/src/nomad_simulations/schema_packages/model_method.py index 08092ecc..552c5088 100644 --- a/src/nomad_simulations/schema_packages/model_method.py +++ b/src/nomad_simulations/schema_packages/model_method.py @@ -46,7 +46,6 @@ class BaseModelMethod(ArchiveSection): Name of the mathematical model. This is typically used to identify the model Hamiltonian used in the simulation. Typical standard names: 'DFT', 'TB', 'GW', 'BSE', 'DMFT', 'NMR', 'kMC'. """, - # a_eln=ELNAnnotation(component='StringEditQuantity'), ) type = Quantity( @@ -56,7 +55,6 @@ class BaseModelMethod(ArchiveSection): model can be 'Wannier', 'DFTB', 'xTB' or 'Slater-Koster'. This quantity should be rewritten to a MEnum when inheriting from this class. """, - # a_eln=ELNAnnotation(component='StringEditQuantity'), ) external_reference = Quantity( @@ -64,7 +62,6 @@ class BaseModelMethod(ArchiveSection): description=""" External reference to the model e.g. DOI, URL. """, - # a_eln=ELNAnnotation(component='URLEditQuantity'), ) numerical_settings = SubSection(sub_section=NumericalSettings.m_def, repeats=True) @@ -112,7 +109,6 @@ class ModelMethodElectronic(ModelMethod): Describes the relativistic treatment used for the calculation of the final energy and related quantities. If `None`, no relativistic treatment is applied. """, - # a_eln=ELNAnnotation(component='EnumEditQuantity'), ) @@ -127,7 +123,6 @@ class XCFunctional(ArchiveSection): Provides the name of one of the exchange or correlation (XC) functional following the libxc convention. For the code base containing the conventions, see https://gitlab.com/libxc/libxc. """, # TODO: step away from the libxc naming convention - # a_eln=ELNAnnotation(component='StringEditQuantity'), ) name = Quantity( @@ -144,7 +139,6 @@ class XCFunctional(ArchiveSection): Weight of the functional. This quantity is relevant when defining linear combinations of the different functionals. If not specified, its value is 1. """, - # a_eln=ELNAnnotation(component='NumberEditQuantity'), ) # ? add method to extract `name` from `libxc_name` @@ -211,7 +205,6 @@ class DFT(ModelMethodElectronic): description=""" Amount of exact exchange mixed in with the XC functional (value range = [0, 1]). """, - # a_eln=ELNAnnotation(component='NumberEditQuantity'), ) # ! MEnum this @@ -243,7 +236,6 @@ class DFT(ModelMethodElectronic): | `"SIC_MAURI_US"` | A (scaled) correction proposed by Mauri and co- workers on the spin density / doublet unpaired orbital | """, - # a_eln=ELNAnnotation(component='StringEditQuantity'), ) van_der_waals_correction = Quantity( @@ -260,7 +252,6 @@ class DFT(ModelMethodElectronic): | `"MDB"` | http://dx.doi.org/10.1103/PhysRevLett.108.236402 and http://dx.doi.org/10.1063/1.4865104 | | `"XC"` | The method to calculate the VdW energy uses a non-local functional | """, - # a_eln=ELNAnnotation(component='EnumEditQuantity'), ) def __init__(self, m_def: 'Section' = None, m_context: 'Context' = None, **kwargs): @@ -417,7 +408,6 @@ class TB(ModelMethodElectronic): | `'SlaterKoster'` | https://journals.aps.org/pr/abstract/10.1103/PhysRev.94.1498 | | `'unavailable'` | - | """, - # a_eln=ELNAnnotation(component='EnumEditQuantity'), ) # ? these 4 quantities will change when `BasisSet` is defined @@ -845,7 +835,6 @@ class ExcitedStateMethodology(ModelMethodElectronic): description=""" Number of states used to calculate the excitations. """, - # a_eln=ELNAnnotation(component='NumberEditQuantity'), ) n_empty_states = Quantity( @@ -853,7 +842,6 @@ class ExcitedStateMethodology(ModelMethodElectronic): description=""" Number of empty states used to calculate the excitations. This quantity is complementary to `n_states`. """, - # a_eln=ELNAnnotation(component='NumberEditQuantity'), ) broadening = Quantity( @@ -862,7 +850,6 @@ class ExcitedStateMethodology(ModelMethodElectronic): description=""" Lifetime broadening applied to the spectra in full-width at half maximum for excited-state calculations. """, - # a_eln=ELNAnnotation(component='NumberEditQuantity'), ) @@ -878,7 +865,6 @@ class Screening(ExcitedStateMethodology): Value of the static dielectric constant at infinite q. For metals, this is infinite (or a very large value), while for insulators is finite. """, - # a_eln=ELNAnnotation(component='NumberEditQuantity'), ) @@ -912,7 +898,6 @@ class GW(ExcitedStateMethodology): | `'qp-scGW0'` | quasiparticle self-consistent G with fixed W0 | https://journals.aps.org/prb/abstract/10.1103/PhysRevB.76.115109 | | `'qp-scGW'` | quasiparticle self-consistent G and W | https://journals.aps.org/prl/abstract/10.1103/PhysRevLett.96.226402 | """, - # a_eln=ELNAnnotation(component='EnumEditQuantity'), ) analytical_continuation = Quantity( @@ -938,7 +923,6 @@ class GW(ExcitedStateMethodology): | `'ppm_FaridEngel'` | Farid and Engel plasmon-pole model | https://journals.aps.org/prb/abstract/10.1103/PhysRevB.47.15931 | | `'multi_pole'` | Multi-pole fitting | https://journals.aps.org/prl/abstract/10.1103/PhysRevLett.74.1827 | """, - # a_eln=ELNAnnotation(component='EnumEditQuantity'), ) # TODO improve description @@ -955,7 +939,6 @@ class GW(ExcitedStateMethodology): description=""" Reference to the `Screening` section that the GW calculation used to obtain the screened Coulomb interactions. """, - # a_eln=ELNAnnotation(component='ReferenceEditQuantity'), ) @@ -985,7 +968,6 @@ class BSE(ExcitedStateMethodology): | `'IP'` | Independent-particle approach | | `'RPA'` | Random Phase Approximation | """, - # a_eln=ELNAnnotation(component='EnumEditQuantity'), ) solver = Quantity( @@ -1001,7 +983,6 @@ class BSE(ExcitedStateMethodology): | `'SLEPc'` | Scalable Library for Eigenvalue Problem Computations | https://slepc.upv.es/ | | `'TDA'` | Tamm-Dancoff approximation | https://doi.org/10.1016/S0009-2614(99)01149-5 | """, - # a_eln=ELNAnnotation(component='EnumEditQuantity'), ) screening_ref = Quantity( @@ -1009,7 +990,6 @@ class BSE(ExcitedStateMethodology): description=""" Reference to the `Screening` section that the BSE calculation used to obtain the screened Coulomb interactions. """, - # a_eln=ELNAnnotation(component='ReferenceEditQuantity'), ) @@ -1036,7 +1016,6 @@ class CoreHoleSpectra(ModelMethodElectronic): description=""" Type of the CoreHole excitation spectra calculated, either "absorption" or "emission". """, - # a_eln=ELNAnnotation(component='EnumEditQuantity'), ) edge = Quantity( @@ -1071,7 +1050,6 @@ class CoreHoleSpectra(ModelMethodElectronic): description=""" Reference to the `CoreHole` section that contains the information of the edge of the excited core-hole. """, - # a_eln=ELNAnnotation(component='ReferenceEditQuantity'), ) excited_state_method_ref = Quantity( @@ -1079,7 +1057,6 @@ class CoreHoleSpectra(ModelMethodElectronic): description=""" Reference to the `ModelMethodElectronic` section (e.g., `DFT` or `BSE`) that was used to obtain the core-hole spectra. """, - # a_eln=ELNAnnotation(component='ReferenceEditQuantity'), ) # TODO add normalization to obtain `edge` diff --git a/src/nomad_simulations/schema_packages/model_system.py b/src/nomad_simulations/schema_packages/model_system.py index 9e698ae4..89461bc4 100644 --- a/src/nomad_simulations/schema_packages/model_system.py +++ b/src/nomad_simulations/schema_packages/model_system.py @@ -73,7 +73,6 @@ class GeometricSpace(Entity): description=""" Length of the first basis vector. """, - # a_eln=ELNAnnotation(component='NumberEditQuantity'), ) length_vector_b = Quantity( @@ -82,7 +81,6 @@ class GeometricSpace(Entity): description=""" Length of the second basis vector. """, - # a_eln=ELNAnnotation(component='NumberEditQuantity'), ) length_vector_c = Quantity( @@ -91,7 +89,6 @@ class GeometricSpace(Entity): description=""" Length of the third basis vector. """, - # a_eln=ELNAnnotation(component='NumberEditQuantity'), ) angle_vectors_b_c = Quantity( @@ -100,7 +97,6 @@ class GeometricSpace(Entity): description=""" Angle between second and third basis vector. """, - # a_eln=ELNAnnotation(component='NumberEditQuantity'), ) angle_vectors_a_c = Quantity( @@ -109,7 +105,6 @@ class GeometricSpace(Entity): description=""" Angle between first and third basis vector. """, - # a_eln=ELNAnnotation(component='NumberEditQuantity'), ) angle_vectors_a_b = Quantity( @@ -118,7 +113,6 @@ class GeometricSpace(Entity): description=""" Angle between first and second basis vector. """, - # a_eln=ELNAnnotation(component='NumberEditQuantity'), ) volume = Quantity( @@ -127,7 +121,6 @@ class GeometricSpace(Entity): description=""" Volume of a 3D real space entity. """, - # a_eln=ELNAnnotation(component='NumberEditQuantity'), ) surface_area = Quantity( @@ -136,7 +129,6 @@ class GeometricSpace(Entity): description=""" Surface area of a 3D real space entity. """, - # a_eln=ELNAnnotation(component='NumberEditQuantity'), ) area = Quantity( @@ -145,7 +137,6 @@ class GeometricSpace(Entity): description=""" Area of a 2D real space entity. """, - # a_eln=ELNAnnotation(component='NumberEditQuantity'), ) length = Quantity( @@ -154,7 +145,6 @@ class GeometricSpace(Entity): description=""" Total length of a 1D real space entity. """, - # a_eln=ELNAnnotation(component='NumberEditQuantity'), ) coordinates_system = Quantity( @@ -657,7 +647,6 @@ class Symmetry(ArchiveSection): description=""" Reference to the AtomicCell section that the symmetry refers to. """, - # a_eln=ELNAnnotation(component='ReferenceEditQuantity'), ) def resolve_analyzed_atomic_cell( @@ -991,7 +980,6 @@ class ModelSystem(System): crystal or it can be filled up. For example, an heterostructure of graphene (G) sandwiched in between hexagonal boron nitrides (hBN) slabs could be named 'hBN/G/hBN'. """, - # a_eln=ELNAnnotation(component='StringEditQuantity'), ) # TODO work on improving and extending this quantity and the description @@ -1009,7 +997,6 @@ class ModelSystem(System): description=""" Type of the system (atom, bulk, surface, etc.) which is determined by the normalizer. """, - # a_eln=ELNAnnotation(component='EnumEditQuantity'), ) dimensionality = Quantity( @@ -1020,7 +1007,6 @@ class ModelSystem(System): https://doi.org/10.1103/PhysRevLett.118.106101. """, - # a_eln=ELNAnnotation(component='NumberEditQuantity'), ) # TODO improve on the definition and usage diff --git a/src/nomad_simulations/schema_packages/physical_property.py b/src/nomad_simulations/schema_packages/physical_property.py index 6d89185f..45ca3f5e 100644 --- a/src/nomad_simulations/schema_packages/physical_property.py +++ b/src/nomad_simulations/schema_packages/physical_property.py @@ -324,7 +324,6 @@ class PropertyContribution(PhysicalProperty): description=""" Reference to the `ModelMethod` section to which the property is linked to. """, - # a_eln=ELNAnnotation(component='ReferenceEditQuantity'), ) def normalize(self, archive, logger) -> None: