public.py

import numpy as np            # pylint: disable=unused-import
import typing                 # pylint: disable=unused-import
from nomad.metainfo import (  # pylint: disable=unused-import
    MSection, MCategory, Category, Package, Quantity, Section, SubSection, SectionProxy,
    Reference, MEnum, derived
)
from nomad.metainfo.search_extension import Search
from nomad.metainfo.legacy import LegacyDefinition


m_package = Package(
    name='public_nomadmetainfo_json',
    description='None',
    a_legacy=LegacyDefinition(name='public.nomadmetainfo.json'))


class fast_access(MCategory):
    '''
    Used to mark archive objects that need to be stored in a fast 2nd-tier storage
    medium, because they are frequently accessed via archive API.

    If applied to a sub_section, the section will be added to the fast storage. Currently
    this only works for *root* sections that are sub_sections of `EntryArchive`.

    If applied to a reference types quantity, the referenced section will also be added
    to the fast storage, regardless if the referenced section has the category or not.
    '''

    m_def = Category()


class accessory_info(MCategory):
    '''
    Information that *in theory* should not affect the results of the calculations (e.g.,
    timing).
    '''

    m_def = Category(
        a_legacy=LegacyDefinition(name='accessory_info'))


class atom_forces_type(MCategory):
    '''
    The types of forces acting on the atoms (i.e., minus derivatives of the specific type
    of energy with respect to the atom position).
    '''

    m_def = Category(
        a_legacy=LegacyDefinition(name='atom_forces_type'))


class basis_set_description(MCategory):
    '''
    One of the parts building the basis set of the system (e.g., some atom-centered basis
    set, plane-waves or both).
    '''

    m_def = Category(
        a_legacy=LegacyDefinition(name='basis_set_description'))


class configuration_core(MCategory):
    '''
    Properties defining the current configuration.
    '''

    m_def = Category(
        a_legacy=LegacyDefinition(name='configuration_core'))


class conserved_quantity(MCategory):
    '''
    A quantity that is preserved during the time propagation (for example,
    kinetic+potential energy during NVE).
    '''

    m_def = Category(
        a_legacy=LegacyDefinition(name='conserved_quantity'))


class energy_value(MCategory):
    '''
    This metadata stores an energy value.
    '''

    m_def = Category(
        a_legacy=LegacyDefinition(name='energy_value'))


class error_estimate_contribution(MCategory):
    '''
    An estimate of a partial quantity contributing to the error for a given quantity.
    '''

    m_def = Category(
        a_legacy=LegacyDefinition(name='error_estimate_contribution'))


class message_debug(MCategory):
    '''
    A debugging message of the computational program.
    '''

    m_def = Category(
        a_legacy=LegacyDefinition(name='message_debug'))


class parsing_message_debug(MCategory):
    '''
    This field is used for debugging messages of the parsing program.
    '''

    m_def = Category(
        a_legacy=LegacyDefinition(name='parsing_message_debug'))


class scf_info(MCategory):
    '''
    Contains information on the self-consistent field (SCF) procedure, i.e. the number of
    SCF iterations (number_of_scf_iterations) or a section_scf_iteration section with
    detailed information on the SCF procedure of specified quantities.
    '''

    m_def = Category(
        a_legacy=LegacyDefinition(name='scf_info'))


class settings_numerical_parameter(MCategory):
    '''
    A parameter that can influence the convergence, but not the physics (unlike
    settings_physical_parameter)
    '''

    m_def = Category(
        a_legacy=LegacyDefinition(name='settings_numerical_parameter'))


class settings_physical_parameter(MCategory):
    '''
    A parameter that defines the physical model used. Use settings_numerical_parameter for
    parameters that that influence only the convergence/accuracy.
    '''

    m_def = Category(
        a_legacy=LegacyDefinition(name='settings_physical_parameter'))


class settings_potential_energy_surface(MCategory):
    '''
    Contains parameters that control the potential energy surface.
    '''

    m_def = Category(
        a_legacy=LegacyDefinition(name='settings_potential_energy_surface'))


class settings_run(MCategory):
    '''
    Contains parameters that control the whole run (but not the *single configuration
    calculation*, see section_single_configuration_calculation).
    '''

    m_def = Category(
        a_legacy=LegacyDefinition(name='settings_run'))


class settings_sampling(MCategory):
    '''
    Contains parameters controlling the sampling.
    '''

    m_def = Category(
        a_legacy=LegacyDefinition(name='settings_sampling'))


class settings_scf(MCategory):
    '''
    Contains parameters connected with the convergence of the self-consistent field (SCF)
    iterations.
    '''

    m_def = Category(
        a_legacy=LegacyDefinition(name='settings_scf'))


class settings_smearing(MCategory):
    '''
    Contain parameters that control the smearing of the orbital occupation at finite
    electronic temperatures.
    '''

    m_def = Category(
        a_legacy=LegacyDefinition(name='settings_smearing'))


class settings_stress_tensor(MCategory):
    '''
    Settings to calculate the stress tensor (stress_tensor) consistent with the total
    energy of the system given in energy_total.
    '''

    m_def = Category(
        a_legacy=LegacyDefinition(name='settings_stress_tensor'))


class stress_tensor_type(MCategory):
    '''
    Contains the final value of the default stress tensor (stress_tensor) and/or the value
    of the stress tensor (stress_tensor_value) of the kind defined in stress_tensor_kind.
    '''

    m_def = Category(
        a_legacy=LegacyDefinition(name='stress_tensor_type'))


class energy_component_per_atom(MCategory):
    '''
    A value of an energy component per atom, concurring in defining the total energy per
    atom.
    '''

    m_def = Category(
        categories=[energy_value],
        a_legacy=LegacyDefinition(name='energy_component_per_atom'))


class energy_component(MCategory):
    '''
    A value of an energy component, expected to be an extensive property.
    '''

    m_def = Category(
        categories=[energy_value],
        a_legacy=LegacyDefinition(name='energy_component'))


class energy_type_reference(MCategory):
    '''
    This metadata stores an energy used as reference point.
    '''

    m_def = Category(
        categories=[energy_value],
        a_legacy=LegacyDefinition(name='energy_type_reference'))


class error_estimate(MCategory):
    '''
    An estimate of the error on the converged (final) value.
    '''

    m_def = Category(
        categories=[error_estimate_contribution],
        a_legacy=LegacyDefinition(name='error_estimate'))


class message_info(MCategory):
    '''
    An information message of the computational program.
    '''

    m_def = Category(
        categories=[message_debug],
        a_legacy=LegacyDefinition(name='message_info'))


class parallelization_info(MCategory):
    '''
    Contains information on the parallelization of the program, i.e. which parallel
    programming language was used and its version, how many cores had been working on the
    calculation and the flags and parameters needed to run the parallelization of the
    code.
    '''

    m_def = Category(
        categories=[accessory_info],
        a_legacy=LegacyDefinition(name='parallelization_info'))


class parsing_message_info(MCategory):
    '''
    This field is used for info messages of the parsing program.
    '''

    m_def = Category(
        categories=[parsing_message_debug],
        a_legacy=LegacyDefinition(name='parsing_message_info'))


class program_info(MCategory):
    '''
    Contains information on the program that generated the data, i.e. the program_name,
    program_version, program_compilation_host and program_compilation_datetime as direct
    children of this field.
    '''

    m_def = Category(
        categories=[accessory_info],
        a_legacy=LegacyDefinition(name='program_info'))


class settings_geometry_optimization(MCategory):
    '''
    Contains parameters controlling the geometry optimization.
    '''

    m_def = Category(
        categories=[settings_sampling],
        a_legacy=LegacyDefinition(name='settings_geometry_optimization'))


class settings_k_points(MCategory):
    '''
    Contains parameters that control the $k$-point mesh.
    '''

    m_def = Category(
        categories=[settings_potential_energy_surface],
        a_legacy=LegacyDefinition(name='settings_k_points'))


class settings_metadynamics(MCategory):
    '''
    Contains parameters that control the metadynamics sampling.
    '''

    m_def = Category(
        categories=[settings_sampling],
        a_legacy=LegacyDefinition(name='settings_metadynamics'))


class settings_molecular_dynamics(MCategory):
    '''
    Contains parameters that control the molecular dynamics sampling.
    '''

    m_def = Category(
        categories=[settings_sampling],
        a_legacy=LegacyDefinition(name='settings_molecular_dynamics'))


class settings_Monte_Carlo(MCategory):
    '''
    Contains parameters that control the Monte-Carlo sampling.
    '''

    m_def = Category(
        categories=[settings_sampling],
        a_legacy=LegacyDefinition(name='settings_Monte_Carlo'))


class settings_XC(MCategory):
    '''
    Contains parameters connected with the definition of the exchange-correlation (XC)
    *method*. Here, the term *method* is a more general concept than just *functionals*
    and include, e.g., post Hartree-Fock methods, too.
    '''

    m_def = Category(
        categories=[settings_potential_energy_surface],
        a_legacy=LegacyDefinition(name='settings_XC'))


class time_info(MCategory):
    '''
    Stores information on the date and timings of the calculation. They are useful for,
    e.g., debugging or visualization purposes.
    '''

    m_def = Category(
        categories=[accessory_info],
        a_legacy=LegacyDefinition(name='time_info'))


class energy_total_potential_per_atom(MCategory):
    '''
    A value of the total potential energy per atom. Note that a direct comparison may not
    be possible because of a difference in the methods for computing total energies and
    numerical implementations of various codes might leads to different energy zeros (see
    section_energy_code_independent for a code-independent definition of the energy).
    '''

    m_def = Category(
        categories=[energy_component, energy_value],
        a_legacy=LegacyDefinition(name='energy_total_potential_per_atom'))


class energy_total_potential(MCategory):
    '''
    A value of the total potential energy. Note that a direct comparison may not be
    possible because of a difference in the methods for computing total energies and
    numerical implementations of various codes might leads to different energy zeros (see
    section_energy_code_independent for a code-independent definition of the energy).
    '''

    m_def = Category(
        categories=[energy_component, energy_value],
        a_legacy=LegacyDefinition(name='energy_total_potential'))


class energy_type_C(MCategory):
    '''
    This metadata stores the correlation (C) energy.
    '''

    m_def = Category(
        categories=[energy_component, energy_value],
        a_legacy=LegacyDefinition(name='energy_type_C'))


class energy_type_van_der_Waals(MCategory):
    '''
    This metadata stores the converged van der Waals energy.
    '''

    m_def = Category(
        categories=[energy_component, energy_value],
        a_legacy=LegacyDefinition(name='energy_type_van_der_Waals'))


class energy_type_XC(MCategory):
    '''
    This metadata stores the exchange-correlation (XC) energy.
    '''

    m_def = Category(
        categories=[energy_component, energy_value],
        a_legacy=LegacyDefinition(name='energy_type_XC'))


class energy_type_X(MCategory):
    '''
    This metadata stores the exchange (X) energy.
    '''

    m_def = Category(
        categories=[energy_component, energy_value],
        a_legacy=LegacyDefinition(name='energy_type_X'))


class message_warning(MCategory):
    '''
    A warning message of the computational program.
    '''

    m_def = Category(
        categories=[message_info, message_debug],
        a_legacy=LegacyDefinition(name='message_warning'))


class parsing_message_warning(MCategory):
    '''
    This field is used for warning messages of the parsing program.
    '''

    m_def = Category(
        categories=[parsing_message_info, parsing_message_debug],
        a_legacy=LegacyDefinition(name='parsing_message_warning'))


class settings_barostat(MCategory):
    '''
    Contains parameters controlling the barostat in a molecular dynamics calculation.
    '''

    m_def = Category(
        categories=[settings_sampling, settings_molecular_dynamics],
        a_legacy=LegacyDefinition(name='settings_barostat'))


class settings_integrator(MCategory):
    '''
    Contains parameters that control the molecular dynamics (MD) integrator.
    '''

    m_def = Category(
        categories=[settings_sampling, settings_molecular_dynamics],
        a_legacy=LegacyDefinition(name='settings_integrator'))


class settings_post_hartree_fock(MCategory):
    '''
    Contains parameters for the post Hartree-Fock method.
    '''

    m_def = Category(
        categories=[settings_XC, settings_potential_energy_surface],
        a_legacy=LegacyDefinition(name='settings_post_hartree_fock'))


class settings_relativity(MCategory):
    '''
    Contains parameters and information connected with the relativistic treatment used in
    the calculation.
    '''

    m_def = Category(
        categories=[settings_XC, settings_potential_energy_surface],
        a_legacy=LegacyDefinition(name='settings_relativity'))


class settings_self_interaction_correction(MCategory):
    '''
    Contains parameters and information connected with the self-interaction correction
    (SIC) method being used in self_interaction_correction_method.
    '''

    m_def = Category(
        categories=[settings_XC, settings_potential_energy_surface],
        a_legacy=LegacyDefinition(name='settings_self_interaction_correction'))


class settings_thermostat(MCategory):
    '''
    Contains parameters that control the thermostat in the molecular dynamics (MD)
    calculations.
    '''

    m_def = Category(
        categories=[settings_sampling, settings_molecular_dynamics],
        a_legacy=LegacyDefinition(name='settings_thermostat'))


class settings_van_der_Waals(MCategory):
    '''
    Contain parameters and information connected with the Van der Waals treatment used in
    the calculation to compute the Van der Waals energy (energy_van_der_Waals).
    '''

    m_def = Category(
        categories=[settings_XC, settings_potential_energy_surface],
        a_legacy=LegacyDefinition(name='settings_van_der_Waals'))


class settings_XC_functional(MCategory):
    '''
    Contain parameters connected with the definition of the exchange-correlation (XC)
    functional (see section_XC_functionals and XC_functional).
    '''

    m_def = Category(
        categories=[settings_XC, settings_potential_energy_surface],
        a_legacy=LegacyDefinition(name='settings_XC_functional'))


class message_error(MCategory):
    '''
    An error message of the computational program.
    '''

    m_def = Category(
        categories=[message_info, message_debug, message_warning],
        a_legacy=LegacyDefinition(name='message_error'))


class parsing_message_error(MCategory):
    '''
    This field is used for error messages of the parsing program.
    '''

    m_def = Category(
        categories=[parsing_message_info, parsing_message_warning, parsing_message_debug],
        a_legacy=LegacyDefinition(name='parsing_message_error'))


class settings_coupled_cluster(MCategory):
    '''
    Contains parameters for the coupled-cluster method (CC) in the post Hartree-Fock step.
    '''

    m_def = Category(
        categories=[settings_post_hartree_fock, settings_XC, settings_potential_energy_surface],
        a_legacy=LegacyDefinition(name='settings_coupled_cluster'))


class settings_GW(MCategory):
    '''
    Contains parameters for the GW-method in the post Hartree-Fock step, that expands the
    self-energy in terms of the single particle Green's function $G$ and the screened
    Coulomb interaction $W$.
    '''

    m_def = Category(
        categories=[settings_post_hartree_fock, settings_XC, settings_potential_energy_surface],
        a_legacy=LegacyDefinition(name='settings_GW'))


class settings_MCSCF(MCategory):
    '''
    Contains parameters for the multi-configurational self-consistent-field (MCSCF)
    method.
    '''

    m_def = Category(
        categories=[settings_post_hartree_fock, settings_XC, settings_potential_energy_surface],
        a_legacy=LegacyDefinition(name='settings_MCSCF'))


class settings_moller_plesset_perturbation_theory(MCategory):
    '''
    Contains parameters for Møller–Plesset perturbation theory.
    '''

    m_def = Category(
        categories=[settings_post_hartree_fock, settings_XC, settings_potential_energy_surface],
        a_legacy=LegacyDefinition(name='settings_moller_plesset_perturbation_theory'))


class settings_multi_reference(MCategory):
    '''
    Contains parameters for the multi-reference single and double configuration
    interaction method.
    '''

    m_def = Category(
        categories=[settings_post_hartree_fock, settings_XC, settings_potential_energy_surface],
        a_legacy=LegacyDefinition(name='settings_multi_reference'))


class archive_context(MSection):
    '''
    Contains information relating to an archive.
    '''

    m_def = Section(validate=False, a_legacy=LegacyDefinition(name='archive_context'))

    archive_gid = Quantity(
        type=str,
        shape=[],
        description='''
        unique identifier of an archive.
        ''',
        a_legacy=LegacyDefinition(name='archive_gid'))


class calculation_context(MSection):
    '''
    Contains information relating to a calculation.
    '''

    m_def = Section(validate=False, a_legacy=LegacyDefinition(name='calculation_context'))

    calculation_gid = Quantity(
        type=str,
        shape=[],
        description='''
        unique identifier of a calculation.
        ''',
        a_legacy=LegacyDefinition(name='calculation_gid'))


class section_atom_projected_dos(MSection):
    '''
    Section collecting the information on an atom projected density of states (DOS)
    evaluation.
    '''

    m_def = Section(validate=False, a_legacy=LegacyDefinition(name='section_atom_projected_dos'))

    atom_projected_dos_energies = Quantity(
        type=np.dtype(np.float64),
        shape=['number_of_atom_projected_dos_values'],
        unit='joule',
        description='''
        Array containing the set of discrete energy values for the atom-projected density
        (electronic-energy) of states (DOS).
        ''',
        a_legacy=LegacyDefinition(name='atom_projected_dos_energies'))

    atom_projected_dos_lm = Quantity(
        type=np.dtype(np.int32),
        shape=['number_of_lm_atom_projected_dos', 2],
        description='''
        Tuples of $l$ and $m$ values for which atom_projected_dos_values_lm are given. For
        the quantum number $l$ the conventional meaning of azimuthal quantum number is
        always adopted. For the integer number $m$, besides the conventional use as
        magnetic quantum number ($l+1$ integer values from $-l$ to $l$), a set of
        different conventions is accepted (see the [m_kind wiki
        page](https://gitlab.rzg.mpg.de/nomad-lab/nomad-meta-info/wikis/metainfo/m-kind).
        The adopted convention is specified by atom_projected_dos_m_kind.
        ''',
        a_legacy=LegacyDefinition(name='atom_projected_dos_lm'))

    atom_projected_dos_m_kind = Quantity(
        type=str,
        shape=[],
        description='''
        String describing what the integer numbers of $m$ in atom_projected_dos_lm mean.
        The allowed values are listed in the [m_kind wiki
        page](https://gitlab.rzg.mpg.de/nomad-lab/nomad-meta-info/wikis/metainfo/m-kind).
        ''',
        a_legacy=LegacyDefinition(name='atom_projected_dos_m_kind'))

    atom_projected_dos_values_lm = Quantity(
        type=np.dtype(np.float64),
        shape=['number_of_lm_atom_projected_dos', 'number_of_spin_channels', 'number_of_atoms', 'number_of_atom_projected_dos_values'],
        description='''
        Values correspond to the number of states for a given energy (the set of discrete
        energy values is given in atom_projected_dos_energies) divided into contributions
        from each $l,m$ channel for the atom-projected density (electronic-energy) of
        states. Here, there are as many atom-projected DOS as the number_of_atoms, the
        list of labels of the atoms and their meanings are in atom_labels.
        ''',
        a_legacy=LegacyDefinition(name='atom_projected_dos_values_lm'))

    atom_projected_dos_values_total = Quantity(
        type=np.dtype(np.float64),
        shape=['number_of_spin_channels', 'number_of_atoms', 'number_of_atom_projected_dos_values'],
        description='''
        Values correspond to the number of states for a given energy (the set of discrete
        energy values is given in atom_projected_dos_energies) divided into contributions
        summed up over all $l$ channels for the atom-projected density (electronic-energy)
        of states (DOS). Here, there are as many atom-projected DOS as the
        number_of_atoms, the list of labels of the atoms and their meanings are in
        atom_labels.
        ''',
        a_legacy=LegacyDefinition(name='atom_projected_dos_values_total'))

    number_of_atom_projected_dos_values = Quantity(
        type=int,
        shape=[],
        description='''
        Gives the number of energy values for the atom-projected density of states (DOS)
        based on atom_projected_dos_values_lm and atom_projected_dos_values_total.
        ''',
        a_legacy=LegacyDefinition(name='number_of_atom_projected_dos_values'))

    number_of_lm_atom_projected_dos = Quantity(
        type=int,
        shape=[],
        description='''
        Gives the number of $l$, $m$ combinations for the atom projected density of states
        (DOS) defined in section_atom_projected_dos.
        ''',
        a_legacy=LegacyDefinition(name='number_of_lm_atom_projected_dos'))


class section_atomic_multipoles(MSection):
    '''
    Section describing multipoles (charges/monopoles, dipoles, quadrupoles, ...) for each
    atom.
    '''

    m_def = Section(validate=False, a_legacy=LegacyDefinition(name='section_atomic_multipoles'))

    atomic_multipole_kind = Quantity(
        type=str,
        shape=[],
        description='''
        String describing the method used to obtain the electrostatic multipoles
        (including the electric charge, dipole, etc.) for each atom. Such multipoles
        require a charge-density partitioning scheme, specified by the value of this
        metadata. Allowed values are listed in the [atomic_multipole_kind wiki
        page](https://gitlab.mpcdf.mpg.de/nomad-lab/nomad-meta-info/wikis/metainfo/atomic-
        multipole-kind).
        ''',
        a_legacy=LegacyDefinition(name='atomic_multipole_kind'))

    atomic_multipole_lm = Quantity(
        type=np.dtype(np.int32),
        shape=['number_of_lm_atomic_multipoles', 2],
        description='''
        Tuples of $l$ and $m$ values for which the atomic multipoles (including the
        electric charge, dipole, etc.) are given. The method used to obtain the multipoles
        is specified by atomic_multipole_kind. The meaning of the integer number $l$ is
        monopole/charge for $l=0$, dipole for $l=1$, quadrupole for $l=2$, etc. The
        meaning of the integer numbers $m$ is specified by atomic_multipole_m_kind.
        ''',
        a_legacy=LegacyDefinition(name='atomic_multipole_lm'))

    atomic_multipole_m_kind = Quantity(
        type=str,
        shape=[],
        description='''
        String describing the definition for each integer number $m$ in
        atomic_multipole_lm. Allowed values are listed in the [m_kind wiki
        page](https://gitlab.rzg.mpg.de/nomad-lab/nomad-meta-info/wikis/metainfo/m-kind).
        ''',
        a_legacy=LegacyDefinition(name='atomic_multipole_m_kind'))

    atomic_multipole_values = Quantity(
        type=np.dtype(np.float64),
        shape=['number_of_lm_atomic_multipoles', 'number_of_atoms'],
        description='''
        Value of the multipoles (including the monopole/charge for $l$ = 0, the dipole for
        $l$ = 1, etc.) for each atom, calculated as described in atomic_multipole_kind.
        ''',
        a_legacy=LegacyDefinition(name='atomic_multipole_values'))

    number_of_lm_atomic_multipoles = Quantity(
        type=int,
        shape=[],
        description='''
        Gives the number of $l$, $m$ combinations for atomic multipoles
        atomic_multipole_lm.
        ''',
        a_legacy=LegacyDefinition(name='number_of_lm_atomic_multipoles'))


class section_basis_functions_atom_centered(MSection):
    '''
    This section contains the description of the basis functions (at least one function)
    of the (atom-centered) basis set defined in section_basis_set_atom_centered.
    '''

    m_def = Section(validate=False, a_legacy=LegacyDefinition(name='section_basis_functions_atom_centered'))


class section_basis_set_atom_centered(MSection):
    '''
    This section describes the atom-centered basis set. The main contained information is
    a short, non unique but human-interpretable, name for identifying the basis set
    (basis_set_atom_centered_short_name), a longer, unique name
    (basis_set_atom_centered_unique_name), the atomic number of the atomic species the
    basis set is meant for (basis_set_atom_number), and a list of actual basis functions
    in the section_basis_functions_atom_centered section.
    '''

    m_def = Section(validate=False, a_legacy=LegacyDefinition(name='section_basis_set_atom_centered'))

    basis_set_atom_centered_ls = Quantity(
        type=np.dtype(np.int32),
        shape=['number_of_kinds_in_basis_set_atom_centered'],
        description='''
        Azimuthal quantum number ($l$) values (of the angular part given by the spherical
        harmonic $Y_{lm}$) of the atom-centered basis function defined in the current
        section_basis_set_atom_centered.
        ''',
        a_legacy=LegacyDefinition(name='basis_set_atom_centered_ls'))

    basis_set_atom_centered_radial_functions = Quantity(
        type=np.dtype(np.float64),
        shape=['number_of_kinds_in_basis_set_atom_centered', 401, 5],
        description='''
        Values of the radial function of the different basis function kinds. The values
        are numerically tabulated on a default 0.01-nm equally spaced grid from 0 to 4 nm.
        The 5 tabulated values are $r$, $f(r)$, $f'(r)$, $f(r) \\cdot r$,
        $\\frac{d}{dr}(f(r) \\cdot r)$.
        ''',
        a_legacy=LegacyDefinition(name='basis_set_atom_centered_radial_functions'))

    basis_set_atom_centered_short_name = Quantity(
        type=str,
        shape=[],
        description='''
        Code-specific, but explicative, base name for the basis set (not unique). Details
        are explained in the [basis_set_atom_centered_short_name wiki
        page](https://gitlab.mpcdf.mpg.de/nomad-lab/nomad-meta-info/wikis/metainfo/basis-
        set-atom-centered-short-name), this name should not contain the *atom kind* (to
        simplify the use of a single name for multiple elements).
        ''',
        a_legacy=LegacyDefinition(name='basis_set_atom_centered_short_name'))

    basis_set_atom_centered_unique_name = Quantity(
        type=str,
        shape=[],
        description='''
        Code-specific, but explicative, base name for the basis set (not unique). This
        string starts with basis_set_atom_centered_short_name. If the basis set defined in
        this section_basis_set_atom_centered is not identical to the default definition
        (stored in a database) of the basis set with the same name stored in a database,
        then the string is extended by 10 identifiable characters as explained in the
        [basis_set_atom_centered_name wiki page](https://gitlab.mpcdf.mpg.de/nomad-
        lab/nomad-meta-info/wikis/metainfo/basis-set-atom-centered-unique-name). The
        reason for this procedure is that often atom-centered basis sets are obtained by
        fine tuning basis sets provided by the code developers or other sources. Each
        basis sets, which has normally a standard name, often reported in publications,
        has also several parameters that can be tuned. This metadata tries to keep track
        of the original basis set and its modifications. This string here defined should
        not contain the *atom kind* for which this basis set is intended for, in order to
        simplify the use of a single name for multiple *atom kinds* (see atom_labels for
        the actual meaning of *atom kind*).
        ''',
        a_legacy=LegacyDefinition(name='basis_set_atom_centered_unique_name'))

    basis_set_atom_number = Quantity(
        type=np.dtype(np.int32),
        shape=[],
        description='''
        Atomic number (i.e., number of protons) of the atom for which this basis set is
        constructed (0 means unspecified or a pseudo atom).
        ''',
        a_legacy=LegacyDefinition(name='basis_set_atom_number'))

    number_of_basis_functions_in_basis_set_atom_centered = Quantity(
        type=int,
        shape=[],
        description='''
        Gives the number of different basis functions in a section_basis_set_atom_centered
        section. This equals the number of actual coefficients that are specified when
        using this basis set.
        ''',
        a_legacy=LegacyDefinition(name='number_of_basis_functions_in_basis_set_atom_centered'))

    number_of_kinds_in_basis_set_atom_centered = Quantity(
        type=int,
        shape=[],
        description='''
        Gives the number of different *kinds* of radial basis functions in the
        section_basis_set_atom_centered section. Specifically, basis functions with the
        same $n$ and $l$ quantum numbers are grouped in sets. Each set counts as one
        *kind*.
        ''',
        a_legacy=LegacyDefinition(name='number_of_kinds_in_basis_set_atom_centered'))

    section_basis_functions_atom_centered = SubSection(
        sub_section=SectionProxy('section_basis_functions_atom_centered'),
        repeats=True,
        a_legacy=LegacyDefinition(name='section_basis_functions_atom_centered'))

    section_gaussian_basis_group = SubSection(
        sub_section=SectionProxy('section_gaussian_basis_group'),
        repeats=True,
        a_legacy=LegacyDefinition(name='section_gaussian_basis_group'))


class section_basis_set_cell_dependent(MSection):
    '''
    Section describing a cell-dependent (atom-independent) basis set, e.g. plane waves.
    The contained information is the type of basis set (in basis_set_cell_dependent_kind),
    its parameters (e.g., for plane waves in basis_set_planewave_cutoff), and a name that
    identifies the actually used basis set (a string combining the type and the
    parameter(s), stored in basis_set_cell_dependent_name).
    '''

    m_def = Section(validate=False, a_legacy=LegacyDefinition(name='section_basis_set_cell_dependent'))

    basis_set_cell_dependent_kind = Quantity(
        type=str,
        shape=[],
        description='''
        A string defining the type of the cell-dependent basis set (i.e., non atom
        centered such as plane-waves). Allowed values are listed in the
        [basis_set_cell_dependent_kind wiki page](https://gitlab.mpcdf.mpg.de/nomad-
        lab/nomad-meta-info/wikis/metainfo/basis-set-cell-dependent-kind).
        ''',
        a_legacy=LegacyDefinition(name='basis_set_cell_dependent_kind'))

    basis_set_cell_dependent_name = Quantity(
        type=str,
        shape=[],
        description='''
        A label identifying the cell-dependent basis set (i.e., non atom centered such as
        plane-waves). Allowed values are listed in the [basis_set_cell_dependent_name wiki
        page](https://gitlab.mpcdf.mpg.de/nomad-lab/nomad-meta-info/wikis/metainfo/basis-
        set-cell-dependent-name).
        ''',
        a_legacy=LegacyDefinition(name='basis_set_cell_dependent_name'))

    basis_set_planewave_cutoff = Quantity(
        type=np.dtype(np.float64),
        shape=[],
        unit='joule',
        description='''
        Spherical cutoff  in reciprocal space for a plane-wave basis set. It is the energy
        of the highest plan-ewave ($\\frac{\\hbar^2|k+G|^2}{2m_e}$) included in the basis
        set. Note that normally this basis set is used for the wavefunctions, and the
        density would have 4 times the cutoff, but this actually depends on the use of the
        basis set by the method.
        ''',
        a_legacy=LegacyDefinition(name='basis_set_planewave_cutoff'))


class section_basis_set(MSection):
    '''
    This section contains references to *all* basis sets used in this
    section_single_configuration_calculation. More than one basis set instance per *single
    configuration calculation* (see section_single_configuration_calculation) may be
    needed. This is true for example, for codes that implement adaptive basis sets along
    the self-consistent field (SCF) convergence (e.g., exciting). In such cases, there is
    a section_basis_set instance per SCF iteration, if necessary. Another example is
    having a basis set for wavefunctions, a different one for the density, an auxiliary
    basis set for resolution of identity (RI), etc.

    Supported are the two broad classes of basis sets: *atom-centered* (e.g., Gaussian-
    type, numerical atomic orbitals) and *cell-dependent* (like plane waves or real-space
    grids, so named because they are typically used for periodic-system calculations and
    dependent to the simulated cell as a whole).

    Basis sets used in this section_single_configuration_calculation, belonging to either
    class, are defined in the dedicated section: [section_basis_set_cell_dependent
    ](section_basis_set_cell_dependent) or section_basis_set_atom_centered. The
    correspondence between the basis sets listed in this section and the definition given
    in the dedicated sessions is given by the two concrete metadata:
    mapping_section_basis_set_cell_dependent and mapping_section_basis_set_atom_centered.
    The latter metadata is a list that connects each atom in the system with its basis
    set, where the same basis set can be assigned to more than one atom.
    '''

    m_def = Section(validate=False, a_legacy=LegacyDefinition(name='section_basis_set'))

    basis_set_kind = Quantity(
        type=str,
        shape=[],
        description='''
        String describing the use of the basis set, i.e, if it used for expanding a wave-
        function or an electron density. Allowed values are listed in the [basis_set_kind
        wiki page](https://gitlab.mpcdf.mpg.de/nomad-lab/nomad-meta-
        info/wikis/metainfo/basis-set-kind).
        ''',
        a_legacy=LegacyDefinition(name='basis_set_kind'))

    basis_set_name = Quantity(
        type=str,
        shape=[],
        description='''
        String identifying the basis set in an unique way. The rules for building this
        string are specified in the [basis_set_name wiki
        page](https://gitlab.mpcdf.mpg.de/nomad-lab/nomad-meta-info/wikis/metainfo/basis-
        set-name).
        ''',
        a_legacy=LegacyDefinition(name='basis_set_name'))

    mapping_section_basis_set_atom_centered = Quantity(
        type=Reference(SectionProxy('section_basis_set_atom_centered')),
        shape=['number_of_atoms'],
        description='''
        An array of the dimension of number_of_atoms where each atom (identified by the
        index in the array) is assigned to an atom-centered basis set, for this
        section_single_configuration_calculation. The actual definition of the atom-
        centered basis set is in the section_basis_set_atom_centered that is referred to
        by this metadata.
        ''',
        a_legacy=LegacyDefinition(name='mapping_section_basis_set_atom_centered'))

    mapping_section_basis_set_cell_dependent = Quantity(
        type=Reference(SectionProxy('section_basis_set_cell_dependent')),
        shape=[],
        description='''
        Assignment of the cell-dependent (i.e., non atom centered, e.g., plane-waves)
        parts of the basis set, which is defined (type, parameters) in
        section_basis_set_cell_dependent that is referred to by this metadata.
        ''',
        a_legacy=LegacyDefinition(name='mapping_section_basis_set_cell_dependent'))

    number_of_basis_functions = Quantity(
        type=int,
        shape=[],
        description='''
        Stores the total number of basis functions in a section_basis_set section.
        ''',
        a_legacy=LegacyDefinition(name='number_of_basis_functions'))


class section_restricted_uri(MSection):
    '''
    Restricted URIs on this calculation (Coverage: any info or files that are related with
    this calculation can be subject to restriction)
    '''

    m_def = Section(validate=False, a_legacy=LegacyDefinition(name='section_restricted_uri'))

    number_of_restricted_uri = Quantity(
        type=np.dtype(np.int32),
        shape=[],
        description='''
        The number of restricted uris in restricted_uri list.
        ''',
        a_legacy=LegacyDefinition(name='number_of_restricted_uri'))

    restricted_uri = Quantity(
        type=str,
        shape=['number_of_restricted_uri'],
        description='''
        The list of nomad uri(s) identifying the restricted info/file corresponding to
        this calculation
        ''',
        a_legacy=LegacyDefinition(name='restricted_uri'))

    restricted_uri_reason = Quantity(
        type=str,
        shape=[],
        description='''
        The reason of restriction for the uri or file. The reason can be 'propriety
        license', 'open-source redistribution restricted license', 'other license', or
        'author restricted'.
        ''',
        a_legacy=LegacyDefinition(name='restricted_uri_reason'))

    restricted_uri_issue_authority = Quantity(
        type=str,
        shape=[],
        description='''
        The issue authority is the restriction owner for the uri or file. This can be
        license owner such as 'VASP' or 'AMBER', 'NOMAD', or the author of the uri. For
        example the repository user name of the author.
        ''',
        a_legacy=LegacyDefinition(name='restricted_uri_issue_authority'))

    restricted_uri_end_date = Quantity(
        type=str,
        shape=[],
        description='''
        The deadline date of the restriction for the uri or file. The end date can be in
        date format string for those restrictions set by authors or NOMAD otherwise it is
        set to 'unlimited' for the restriction related to license.
        ''',
        a_legacy=LegacyDefinition(name='restricted_uri_end_date'))

    restricted_uri_restriction = Quantity(
        type=str,
        shape=[],
        description='''
        The type of restriction for the uri or file. The type can be 'any access' or
        'license permitted'.
        ''',
        a_legacy=LegacyDefinition(name='restricted_uri_restriction'))

    restricted_uri_license = Quantity(
        type=str,
        shape=[],
        description='''
        The info of the license that is the reason of restriction.
        ''',
        a_legacy=LegacyDefinition(name='restricted_uri_license'))

    number_of_restricted_uri_files = Quantity(
        type=np.dtype(np.int32),
        shape=[],
        description='''
        The number of restricted files in restricted_uri_files list.
        ''',
        a_legacy=LegacyDefinition(name='number_of_restricted_uri_files'))


class section_calculation_to_calculation_refs(MSection):
    '''
    Section that describes the relationship between different
    section_single_configuration_calculation sections.

    For instance, one calculation is a perturbation performed using a self-consistent
    field (SCF) calculation as starting point, or a simulated system is partitioned in
    regions with different but connected Hamiltonians (e.g., QM/MM, or a region treated
    via Kohn-Sham DFT embedded into a region treated via orbital-free DFT).

    The kind of relationship between the calculation defined in this section and the
    referenced one is described by calculation_to_calculation_kind. The referenced
    section_single_configuration_calculation is identified via
    calculation_to_calculation_ref (typically used for a
    section_single_configuration_calculation in the same section_run) or
    calculation_to_calculation_external_url.
    '''

    m_def = Section(validate=False, a_legacy=LegacyDefinition(name='section_calculation_to_calculation_refs'))

    calculation_to_calculation_external_url = Quantity(
        type=str,
        shape=[],
        description='''
        URL used to reference an externally stored calculation. The kind of relationship
        between the present and the referenced section_single_configuration_calculation is
        specified by calculation_to_calculation_kind.
        ''',
        a_legacy=LegacyDefinition(name='calculation_to_calculation_external_url'))

    calculation_to_calculation_kind = Quantity(
        type=str,
        shape=[],
        description='''
        String defining the relationship between the referenced
        section_single_configuration_calculation and the present
        section_single_configuration_calculation. Valid values are described in the
        [calculation_to_calculation_kind wiki page](https://gitlab.mpcdf.mpg.de/nomad-
        lab/nomad-meta-info/wikis/metainfo/calculation-to-calculation-kind). Often
        calculations are connected, for instance, one calculation is a perturbation
        performed using a self-consistent field (SCF) calculation as starting point, or a
        simulated system is partitioned in regions with different but connected
        Hamiltonians (e.g., QM/MM, or a region treated via Kohn-Sham DFT embedded into a
        region treated via orbital-free DFT). Hence, the need of keeping track of these
        connected calculations. The referenced calculation is identified via
        calculation_to_calculation_ref (typically used for a calculation in the same
        section_run) or calculation_to_calculation_external_url.
        ''',
        a_legacy=LegacyDefinition(name='calculation_to_calculation_kind'))

    calculation_to_calculation_ref = Quantity(
        type=Reference(SectionProxy('section_single_configuration_calculation')),
        shape=[],
        description='''
        Reference to another calculation. If both this and
        calculation_to_calculation_external_url are given, then
        calculation_to_calculation_ref is a local copy of the URL given in
        calculation_to_calculation_external_url. The kind of relationship between the
        present and the referenced section_single_configuration_calculation is specified
        by calculation_to_calculation_kind.
        ''',
        a_legacy=LegacyDefinition(name='calculation_to_calculation_ref'))


class section_calculation_to_folder_refs(MSection):
    '''
    Section that describes the relationship between
    section_single_configuration_calculationa and the folder containing the original
    calulations
    '''

    m_def = Section(validate=False, a_legacy=LegacyDefinition(name='section_calculation_to_folder_refs'))

    calculation_to_folder_external_url = Quantity(
        type=str,
        shape=[],
        description='''
        URL used to reference a folder containing external calculations. The kind of
        relationship between the present and the referenced
        section_single_configuration_calculation is specified by
        calculation_to_folder_kind.
        ''',
        a_legacy=LegacyDefinition(name='calculation_to_folder_external_url'))

    calculation_to_folder_kind = Quantity(
        type=str,
        shape=[],
        description='''
        String defining the relationship between the referenced
        section_single_configuration_calculation and a folder containing calculations.
        ''',
        a_legacy=LegacyDefinition(name='calculation_to_folder_kind'))


class section_dos_fingerprint(MSection):
    '''
    Section for the fingerprint of the electronic density-of-states (DOS).
    DOS fingerprints are a modification of the D-Fingerprints reported in Chem. Mater. 2015, 27, 3, 735–743
    (doi:10.1021/cm503507h). The fingerprint consists of a binary representation of the DOS,
    that is used to evaluate the similarity of materials based on their electronic structure.
    '''

    m_def = Section(validate=False, a_legacy=LegacyDefinition(name='section_dos_fingerprint'))

    bins = Quantity(
        type=str,
        description='''
        Byte representation of the DOS fingerprint.
        ''',
        a_legacy=LegacyDefinition(name='bins'))

    indices = Quantity(
        type=np.dtype(np.int16),
        shape=[2],
        description='''
        Indices used to compare DOS fingerprints of different energy ranges.
        ''',
        a_legacy=LegacyDefinition(name='indices'))

    stepsize = Quantity(
        type=np.dtype(np.float64),
        shape=[],
        description='''
        Stepsize of interpolation in the first step of the generation of DOS fingerprints.
        ''',
        a_legacy=LegacyDefinition(name='stepsize'))

    filling_factor = Quantity(
        type=np.dtype(np.float64),
        shape=[],
        description='''
        Proportion of 1 bins in the DOS fingerprint.
        ''',
        a_legacy=LegacyDefinition(name='filling_factor'))

    grid_id = Quantity(
        type=str,
        description='''
        Identifier of the DOS grid that was used for the creation of the fingerprint.
        Similarity can only be calculated if the same grid was used for both fingerprints.
        ''',
        a_legacy=LegacyDefinition(name='grid_id'))


class section_dos(MSection):
    '''
    Section collecting information of a (electronic-energy or vibrational-energy) density
    of states (DOS) evaluation.
    '''

    m_def = Section(validate=False, a_legacy=LegacyDefinition(name='section_dos'))

    dos_energies_normalized = Quantity(
        type=np.dtype(np.float64),
        shape=['number_of_dos_values'],
        unit='joule',
        description='''
        Array containing the set of discrete energy values with respect to the
        highest occupied energy level. This is the total DOS, see
        atom_projected_dos_energies and species_projected_dos_energies for
        partial density of states.