class section_run(public.section_run): m_def = Section(validate=False, extends_base_section=True, a_legacy=LegacyDefinition(name='section_run')) x_gamess_program_execution_date = Quantity( type=str, shape=[], description=''' - ''', a_legacy=LegacyDefinition(name='x_gamess_program_execution_date')) x_gamess_program_implementation = Quantity( type=str, shape=[], description=''' - ''', a_legacy=LegacyDefinition(name='x_gamess_program_implementation')) x_gamess_section_geometry_optimization_info = SubSection( sub_section=SectionProxy( 'x_gamess_section_geometry_optimization_info'), repeats=True, a_legacy=LegacyDefinition( name='x_gamess_section_geometry_optimization_info'))
class x_gamess_section_atom_forces(MSection): ''' section that contains Cartesian forces of the system for a given geometry ''' m_def = Section( validate=False, a_legacy=LegacyDefinition(name='x_gamess_section_atom_forces')) x_gamess_atom_x_force = Quantity( type=np.dtype(np.float64), shape=[], unit='newton', description=''' - ''', a_legacy=LegacyDefinition(name='x_gamess_atom_x_force')) x_gamess_atom_y_force = Quantity( type=np.dtype(np.float64), shape=[], unit='newton', description=''' - ''', a_legacy=LegacyDefinition(name='x_gamess_atom_y_force')) x_gamess_atom_z_force = Quantity( type=np.dtype(np.float64), shape=[], unit='newton', description=''' - ''', a_legacy=LegacyDefinition(name='x_gamess_atom_z_force'))
class x_gamess_section_cis(MSection): ''' Configuration interaction singles excitation energies and oscillator strengths. ''' m_def = Section(validate=False, a_legacy=LegacyDefinition(name='x_gamess_section_cis')) x_gamess_cis_excitation_energy = Quantity( type=np.dtype(np.float64), shape=[], unit='joule', description=''' Value of the excitation energies for configuration interaction singles excited states. ''', a_legacy=LegacyDefinition(name='x_gamess_cis_excitation_energy')) x_gamess_cis_oscillator_strength = Quantity( type=np.dtype(np.float64), shape=[], description=''' Value of the oscillator strengths for configuration interaction singles excited states. ''', a_legacy=LegacyDefinition(name='x_gamess_cis_oscillator_strength'))
class x_nwchem_section_xc_part(MSection): ''' Describes a part of the XC functional that is used in the calculation. Can be a local or non-local part, can be exchange or correlation, can have a weight. ''' m_def = Section(validate=False, a_legacy=LegacyDefinition(name='x_nwchem_section_xc_part')) x_nwchem_xc_functional_name = Quantity( type=str, shape=[], description=''' The name of the XC functional ''', a_legacy=LegacyDefinition(name='x_nwchem_xc_functional_name')) x_nwchem_xc_functional_weight = Quantity( type=np.dtype(np.float64), shape=[], description=''' The weight of the XC functional. ''', a_legacy=LegacyDefinition(name='x_nwchem_xc_functional_weight')) x_nwchem_xc_functional_type = Quantity( type=str, shape=[], description=''' The type of the XC functional, local or non-local ''', a_legacy=LegacyDefinition(name='x_nwchem_xc_functional_type'))
class section_method(public.section_method): m_def = Section(validate=False, extends_base_section=True, a_legacy=LegacyDefinition(name='section_method')) x_nwchem_xc_functional_shortcut = Quantity( type=str, shape=[], description=''' Shorcut for a XC functional definition. ''', categories=[ public.settings_potential_energy_surface, public.settings_XC, public.settings_XC_functional ], a_legacy=LegacyDefinition(name='x_nwchem_xc_functional_shortcut')) x_nwchem_electron_spin_restriction = Quantity( type=str, shape=[], description=''' Electron spin restriction. ''', a_legacy=LegacyDefinition(name='x_nwchem_electron_spin_restriction')) x_nwchem_section_xc_part = SubSection( sub_section=SectionProxy('x_nwchem_section_xc_part'), repeats=True, a_legacy=LegacyDefinition(name='x_nwchem_section_xc_part'))
class section_sampling_method(public.section_sampling_method): m_def = Section(validate=False, extends_base_section=True, a_legacy=LegacyDefinition(name='section_sampling_method')) x_asap_langevin_friction = Quantity( type=np.dtype(np.float64), shape=[], description=''' Friction coeffient used in Langevin dynamics ''', a_legacy=LegacyDefinition(name='x_asap_langevin_friction')) x_asap_maxstep = Quantity( type=np.dtype(np.float64), shape=[], description=''' Maxstep in Angstrom for geometry optimization ''', a_legacy=LegacyDefinition(name='x_asap_maxstep')) x_asap_temperature = Quantity( type=np.dtype(np.float64), shape=[], description=''' Temperature used in molecular-dynamics ''', a_legacy=LegacyDefinition(name='x_asap_temperature')) x_asap_timestep = Quantity( type=np.dtype(np.float64), shape=[], description=''' Timestep in molecular dynamics ''', a_legacy=LegacyDefinition(name='x_asap_timestep'))
class section_method(public.section_method): m_def = Section(validate=False, extends_base_section=True, a_legacy=LegacyDefinition(name='section_method')) x_phonopy_displacement = Quantity( type=np.dtype(np.float64), shape=[], unit='meter', description=''' Amplitude of the atom diplacement for the phonopy supercell ''', categories=[x_phonopy_input], a_legacy=LegacyDefinition(name='x_phonopy_displacement')) x_phonopy_symprec = Quantity( type=np.dtype(np.float64), shape=[], unit='meter', description=''' Symmetry threshold for the space group identification of the crystal for which the vibrational properties are to be calculated ''', categories=[x_phonopy_input], a_legacy=LegacyDefinition(name='x_phonopy_symprec'))
class x_abinit_section_dataset(abinit_autogenerated.x_abinit_section_dataset): m_def = Section(validate=False, extends_base_section=True, a_legacy=LegacyDefinition(name='x_abinit_section_dataset')) x_abinit_geometry_optimization_converged = Quantity( type=str, shape=[], description=''' Determines whether a geometry optimization is converged. ''', a_legacy=LegacyDefinition( name='x_abinit_geometry_optimization_converged')) x_abinit_eig_filename = Quantity( type=str, shape=[], description=''' Name of file where the eigenvalues were written to. ''', a_legacy=LegacyDefinition(name='x_abinit_eig_filename')) x_abinit_section_dataset_header = SubSection( sub_section=SectionProxy('x_abinit_section_dataset_header'), repeats=True, a_legacy=LegacyDefinition(name='x_abinit_section_dataset_header'))
class section_eigenvalues(public.section_eigenvalues): m_def = Section(validate=False, extends_base_section=True, a_legacy=LegacyDefinition(name='section_eigenvalues')) x_abinit_kpt = Quantity(type=str, shape=[], description=''' The reduced coordinates of a k-point ''', a_legacy=LegacyDefinition(name='x_abinit_kpt')) x_abinit_wtk = Quantity(type=str, shape=[], description=''' A k-point weight ''', a_legacy=LegacyDefinition(name='x_abinit_wtk')) x_abinit_eigenvalues = Quantity( type=str, shape=[], description=''' List of eigenvalues on a given k-point ''', a_legacy=LegacyDefinition(name='x_abinit_eigenvalues')) x_abinit_occupations = Quantity( type=str, shape=[], description=''' List of occupations on a given k-point ''', a_legacy=LegacyDefinition(name='x_abinit_occupations'))
class section_method(public.section_method): m_def = Section(validate=False, extends_base_section=True, a_legacy=LegacyDefinition(name='section_method')) x_dl_poly_step_number_equilibration = Quantity( type=np.dtype(np.int32), shape=[], description=''' MD equilibration step number ''', a_legacy=LegacyDefinition(name='x_dl_poly_step_number_equilibration')) x_dl_poly_step_number = Quantity( type=np.dtype(np.int32), shape=[], description=''' MD total step number ''', a_legacy=LegacyDefinition(name='x_dl_poly_step_number')) x_dl_poly_thermostat_temperature = Quantity( type=np.dtype(np.float64), shape=[], description=''' Thermostat coupling temperature ''', a_legacy=LegacyDefinition(name='x_dl_poly_thermostat_temperature'))
class section_scf_iteration(public.section_scf_iteration): m_def = Section(validate=False, extends_base_section=True, a_legacy=LegacyDefinition(name='section_scf_iteration')) x_gamess_energy_scf = Quantity( type=np.dtype(np.float64), shape=[], unit='joule', description=''' Final value of the total electronic energy calculated with the method described in XC_method. ''', a_legacy=LegacyDefinition(name='x_gamess_energy_scf')) x_gamess_energy_total_scf_iteration = Quantity( type=np.dtype(np.float64), shape=[], unit='joule', description=''' Value of the total electronic energy calculated with the method described in XC_method during each self-consistent field (SCF) iteration. ''', a_legacy=LegacyDefinition(name='x_gamess_energy_total_scf_iteration'))
class section_system(public.section_system): m_def = Section(validate=False, extends_base_section=True, a_legacy=LegacyDefinition(name='section_system')) x_dftbp_atom_positions_X = Quantity( type=np.dtype(np.float64), shape=[], description=''' - ''', a_legacy=LegacyDefinition(name='x_dftbp_atom_positions_X')) x_dftbp_atom_positions_Y = Quantity( type=np.dtype(np.float64), shape=[], description=''' - ''', a_legacy=LegacyDefinition(name='x_dftbp_atom_positions_Y')) x_dftbp_atom_positions_Z = Quantity( type=np.dtype(np.float64), shape=[], description=''' - ''', a_legacy=LegacyDefinition(name='x_dftbp_atom_positions_Z'))
class section_method(public.section_method): m_def = Section(validate=False, extends_base_section=True, a_legacy=LegacyDefinition(name='section_method')) x_molcas_method_name = Quantity( type=str, shape=[], description=''' Molcas method name (without UHF; see x_molcas_uhf) ''', a_legacy=LegacyDefinition(name='x_molcas_method_name')) x_molcas_uhf = Quantity(type=bool, shape=[], description=''' If the Molcas method is UHF. ''', a_legacy=LegacyDefinition(name='x_molcas_uhf')) x_molcas_section_basis = SubSection( sub_section=SectionProxy('x_molcas_section_basis'), repeats=True, a_legacy=LegacyDefinition(name='x_molcas_section_basis'))
class section_method(public.section_method): m_def = Section(validate=False, extends_base_section=True, a_legacy=LegacyDefinition(name='section_method')) x_gulp_number_of_species = Quantity( type=int, shape=[], description=''' Number of species in GULP ''', a_legacy=LegacyDefinition(name='x_gulp_number_of_species')) x_gulp_species_charge = Quantity( type=np.dtype(np.float64), shape=['x_gulp_number_of_species'], description=''' Number of species in GULP ''', a_legacy=LegacyDefinition(name='x_gulp_species_charge')) x_gulp_section_forcefield = SubSection( sub_section=SectionProxy('x_gulp_section_forcefield'), repeats=True, a_legacy=LegacyDefinition(name='x_gulp_section_forcefield'))
class x_fhi_vibes_section_relaxation_kwargs(MSection): ''' Relaxation kwargs ''' m_def = Section(validate=False, a_legacy=LegacyDefinition( name='x_fhi_vibes_section_relaxation_kwargs')) x_fhi_vibes_relaxation_kwargs_maxstep = Quantity( type=np.dtype(np.int32), shape=[], description=''' - ''', a_legacy=LegacyDefinition( name='x_fhi_vibes_relaxation_kwargs_maxstep')) x_fhi_vibes_relaxation_kwargs_restart = Quantity( type=str, shape=[], description=''' - ''', a_legacy=LegacyDefinition( name='x_fhi_vibes_relaxation_kwargs_restart'))
class x_qbox_section_dipole(MSection): ''' - ''' m_def = Section(validate=False, a_legacy=LegacyDefinition(name='x_qbox_section_dipole')) x_qbox_dipole_x = Quantity( type=np.dtype(np.float64), shape=[], unit='bohr * elementary_charge', description=''' x component of dipole ''', a_legacy=LegacyDefinition(name='x_qbox_dipole_x')) x_qbox_dipole_y = Quantity( type=np.dtype(np.float64), shape=[], unit='bohr * elementary_charge', description=''' y component of dipole ''', a_legacy=LegacyDefinition(name='x_qbox_dipole_y')) x_qbox_dipole_z = Quantity( type=np.dtype(np.float64), shape=[], unit='bohr * elementary_charge', description=''' z component of dipole ''', a_legacy=LegacyDefinition(name='x_qbox_dipole_z'))
class ReconstructingInstrument(MSection): name = Quantity(type=str, description='') version = Quantity(type=str, description='') uuid = Quantity(type=str, description='') section_component = SubSection(sub_section=ReconstructingComponent) section_coordinate_system = SubSection( sub_section=ReconstructingCoordinateSystem)
class x_crystal_section_shell(MSection): ''' Shell contains a number of orbitals. ''' m_def = Section(validate=False) x_crystal_shell_range = Quantity(type=str, shape=[], description=''' The range of orbitals ''') x_crystal_shell_type = Quantity( type=str, shape=[], description=''' Shell type: S / P / SP / D / F / G. ''', a_legacy=LegacyDefinition(name='x_crystal_basis_set_atom_shell_type')) x_crystal_shell_coefficients = Quantity(type=np.dtype(np.float64), shape=['n_orbitals', 4], description=''' Contraction coefficients in this order: exponent, S, P, D/F/G. ''')
class section_run(public.section_run): m_def = Section(validate=False, extends_base_section=True, a_legacy=LegacyDefinition(name='section_run')) x_fplo_t_program_version_main = Quantity( type=str, shape=[], description=''' temporary: FPLO main version ''', a_legacy=LegacyDefinition(name='x_fplo_t_program_version_main')) x_fplo_t_program_version_release = Quantity( type=str, shape=[], description=''' temporary: FPLO release number ''', a_legacy=LegacyDefinition(name='x_fplo_t_program_version_release')) x_fplo_t_run_hosts = Quantity( type=str, shape=[], description=''' temporary: FPLO run hosts ''', a_legacy=LegacyDefinition(name='x_fplo_t_run_hosts'))
class section_eigenvalues(public.section_eigenvalues): m_def = Section(validate=False, extends_base_section=True, a_legacy=LegacyDefinition(name='section_eigenvalues')) x_orca_orbital_energy = Quantity( type=np.dtype(np.float64), shape=[], description=''' - ''', a_legacy=LegacyDefinition(name='x_orca_orbital_energy')) x_orca_orbital_nb = Quantity( type=np.dtype(np.int32), shape=[], description=''' - ''', a_legacy=LegacyDefinition(name='x_orca_orbital_nb')) x_orca_orbital_occupation_nb = Quantity( type=np.dtype(np.float64), shape=[], description=''' - ''', a_legacy=LegacyDefinition(name='x_orca_orbital_occupation_nb'))
class section_single_configuration_calculation( public.section_single_configuration_calculation): m_def = Section(validate=False, extends_base_section=True, a_legacy=LegacyDefinition( name='section_single_configuration_calculation')) x_molcas_slapaf_grad_norm = Quantity( type=np.dtype(np.float64), shape=[], description=''' Molcas slapaf (geometry optimization) grad (force) norm ''', a_legacy=LegacyDefinition(name='x_molcas_slapaf_grad_norm')) x_molcas_slapaf_grad_max = Quantity( type=np.dtype(np.float64), shape=[], description=''' Molcas slapaf (geometry optimization) grad (force) max ''', a_legacy=LegacyDefinition(name='x_molcas_slapaf_grad_max')) x_molcas_section_frequency = SubSection( sub_section=SectionProxy('x_molcas_section_frequency'), repeats=True, a_legacy=LegacyDefinition(name='x_molcas_section_frequency'))
class x_elastic_section_fitting_parameters(MSection): ''' section collecting the fitting parameters used to calculate the elastic constants ''' m_def = Section( validate=False, a_legacy=LegacyDefinition(name='x_elastic_section_fitting_parameters')) x_elastic_fitting_parameters_eta = Quantity( type=np.dtype(np.float64), shape=['x_elastic_number_of_deformations'], description=''' eta values used to calculate the elastic constants ''', a_legacy=LegacyDefinition(name='x_elastic_fitting_parameters_eta')) x_elastic_fitting_parameters_polynomial_order = Quantity( type=np.dtype(np.int32), shape=['x_elastic_number_of_deformations'], description=''' polynomial order used to fit the Energy vs. volume curve and to calculate the elastic constants ''', a_legacy=LegacyDefinition( name='x_elastic_fitting_parameters_polynomial_order'))
class x_elk_section_lattice_vectors(MSection): ''' lattice vectors ''' m_def = Section( validate=False, a_legacy=LegacyDefinition(name='x_elk_section_lattice_vectors')) x_elk_geometry_lattice_vector_x = Quantity( type=np.dtype(np.float64), shape=[], unit='meter', description=''' x component of lattice vector ''', a_legacy=LegacyDefinition(name='x_elk_geometry_lattice_vector_x')) x_elk_geometry_lattice_vector_y = Quantity( type=np.dtype(np.float64), shape=[], unit='meter', description=''' y component of lattice vector ''', a_legacy=LegacyDefinition(name='x_elk_geometry_lattice_vector_y')) x_elk_geometry_lattice_vector_z = Quantity( type=np.dtype(np.float64), shape=[], unit='meter', description=''' z component of lattice vector ''', a_legacy=LegacyDefinition(name='x_elk_geometry_lattice_vector_z'))
class x_elastic_section_strain_diagrams(MSection): ''' section collecting the data of the strain diagrams ''' m_def = Section( validate=False, a_legacy=LegacyDefinition(name='x_elastic_section_strain_diagrams')) x_elastic_strain_diagram_values = Quantity( type=np.dtype(np.float64), shape=[ 'x_elastic_number_of_deformations', 'x_elastic_strain_diagram_number_of_eta' ], description=''' Values of the energy(units:J)/d2E(units:Pa)/cross-validation (depending on the value of x_elastic_strain_diagram_type) ''', a_legacy=LegacyDefinition(name='x_elastic_strain_diagram_values')) x_elastic_strain_diagram_eta_values = Quantity( type=np.dtype(np.float64), shape=[ 'x_elastic_number_of_deformations', 'x_elastic_strain_diagram_number_of_eta' ], description=''' eta values used the strain diagrams ''', a_legacy=LegacyDefinition(name='x_elastic_strain_diagram_eta_values')) x_elastic_strain_diagram_number_of_eta = Quantity( type=np.dtype(np.int32), shape=[], description=''' Number of strain values used in the strain diagram ''', a_legacy=LegacyDefinition( name='x_elastic_strain_diagram_number_of_eta')) x_elastic_strain_diagram_type = Quantity( type=str, shape=[], description=''' Kind of strain diagram. Possible values are: energy; cross-validation (cross- validation error); d2E (second derivative of the energy wrt the strain) ''', a_legacy=LegacyDefinition(name='x_elastic_strain_diagram_type')) x_elastic_strain_diagram_polynomial_fit_order = Quantity( type=np.dtype(np.int32), shape=[], description=''' Order of the polynomial fit ''', a_legacy=LegacyDefinition( name='x_elastic_strain_diagram_polynomial_fit_order'))
class Instrument(MSection): n_scans = Quantity(type=str) dwell_time = Quantity(type=str) excitation_energy = Quantity(type=str) source_label = Quantity(type=str) notes = Quantity(type=str, categories=[UserProvided]) section_device_settings = SubSection(sub_section=DeviceSettings, repeats=True)
class IonSpecies(MSection): ndisjoint_ion_species = Quantity( type=np.dtype(np.uint32), description='how many different species do we distinguish') max_natoms_per_ion = Quantity( type=np.dtype(np.uint32), description= 'how many atoms are at most accepted to build a molecular ion') section_ions = SubSection(sub_section=MolecularIonDef, repeats=True)
class Method(common_experimental.Method): m_def = Section(validate=False, extends_base_section=True) experiment_operation_method = Quantity( type=str, description='Operation mode of the instrument (APT, FIM or combination)' ) experiment_imaging_method = Quantity( type=str, description= 'Pulsing method to enforce a controlled ion evaporation sequence') number_ions_evaporated = Quantity( type=int, description='Number of ions successfully evaporated') measured_detector_hit_pos = Quantity( type=bool, description='Detector hit positions x and y was measured') measured_detector_hit_mult = Quantity( type=bool, description='Detector hit multiplicity was measured') measured_detector_dead_pulses = Quantity( type=bool, description='Detector number of dead pulses was measured') measured_time_of_flight = Quantity( type=bool, description='Raw ion time of flight was measured') measured_standing_voltage = Quantity( type=bool, description='Standing voltage was measured') measured_pulse_voltage = Quantity(type=bool, description='Pulse voltage was measured')
class section_sampling_method(public.section_sampling_method): m_def = Section(validate=False, extends_base_section=True, a_legacy=LegacyDefinition(name='section_sampling_method')) x_turbomole_geometry_optimization_geometry_change_rms = Quantity( type=np.dtype(np.float64), shape=[], unit='meter', description=''' geometry optimization convergence criterion - Root Mean Square of displacements ''', a_legacy=LegacyDefinition( name='x_turbomole_geometry_optimization_geometry_change_rms')) x_turbomole_geometry_optimization_threshold_force_rms = Quantity( type=np.dtype(np.float64), shape=[], unit='newton', description=''' geometry optimization convergence criterion - Root Mean Square of forces ''', a_legacy=LegacyDefinition( name='x_turbomole_geometry_optimization_threshold_force_rms')) x_turbomole_geometry_optimization_trustregion_initial = Quantity( type=np.dtype(np.float64), shape=[], unit='meter', description=''' geometry optimization trust region - initial radius ''', a_legacy=LegacyDefinition( name='x_turbomole_geometry_optimization_trustregion_initial')) x_turbomole_geometry_optimization_trustregion_max = Quantity( type=np.dtype(np.float64), shape=[], unit='meter', description=''' geometry optimization trust region - maximum radius ''', a_legacy=LegacyDefinition( name='x_turbomole_geometry_optimization_trustregion_max')) x_turbomole_geometry_optimization_trustregion_min = Quantity( type=np.dtype(np.float64), shape=[], unit='meter', description=''' geometry optimization trust region - minimum radius ''', a_legacy=LegacyDefinition( name='x_turbomole_geometry_optimization_trustregion_min'))
class Spectrum(MSection): n_values = Quantity(type=int) energy = Quantity(type=np.dtype(np.float64), shape=['n_values'], unit='J', description='The energy range of the spectrum') count = Quantity( type=np.dtype(np.float64), shape=['n_values'], description='The count at each energy value, dimensionless') notes = Quantity(type=str, categories=[UserProvided])
class IonCollectorCS(MSection): origin = Quantity(type=np.dtype(np.float64), shape=[3], unit='m', description='') matrix = Quantity(type=np.dtype(np.float64), shape=[4, 4], description='') map_to_ref_origin = Quantity(type=np.dtype(np.float64), shape=[3], unit='m', description='') map_to_ref_matrix = Quantity(type=np.dtype(np.float64), shape=[4, 4], description='')