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 section_run(public.section_run):
m_def = Section(validate=False,
extends_base_section=True,
a_legacy=LegacyDefinition(name='section_run'))
x_nwchem_section_start_information = SubSection(
sub_section=SectionProxy('x_nwchem_section_start_information'),
repeats=True,
a_legacy=LegacyDefinition(name='x_nwchem_section_start_information'))
x_nwchem_section_geometry = SubSection(
sub_section=SectionProxy('x_nwchem_section_geometry'),
repeats=True,
a_legacy=LegacyDefinition(name='x_nwchem_section_geometry'))
x_nwchem_section_geo_opt_module = SubSection(
sub_section=SectionProxy('x_nwchem_section_geo_opt_module'),
repeats=True,
a_legacy=LegacyDefinition(name='x_nwchem_section_geo_opt_module'))
x_nwchem_section_qmd_module = SubSection(
sub_section=SectionProxy('x_nwchem_section_qmd_module'),
repeats=True,
a_legacy=LegacyDefinition(name='x_nwchem_section_qmd_module'))
class section_run(public.section_run):
m_def = Section(validate=False,
extends_base_section=True,
a_legacy=LegacyDefinition(name='section_run'))
x_qbox_nodename = Quantity(
type=str,
shape=[],
description='''
compute node
''',
a_legacy=LegacyDefinition(name='x_qbox_nodename'))
x_qbox_section_dipole = SubSection(
sub_section=SectionProxy('x_qbox_section_dipole'),
repeats=True,
a_legacy=LegacyDefinition(name='x_qbox_section_dipole'))
x_qbox_section_efield = SubSection(
sub_section=SectionProxy('x_qbox_section_efield'),
repeats=True,
a_legacy=LegacyDefinition(name='x_qbox_section_efield'))
x_qbox_section_MLWF = SubSection(
sub_section=SectionProxy('x_qbox_section_MLWF'),
repeats=True,
a_legacy=LegacyDefinition(name='x_qbox_section_MLWF'))
class Metadata(MSection):
section_sample = SubSection(sub_section=Sample, repeats=True)
section_experiment = SubSection(sub_section=Experiment, repeats=True)
section_instrument = SubSection(sub_section=Instrument, repeats=True)
section_data_header = SubSection(sub_section=DataHeader, repeats=True)
section_origin = SubSection(sub_section=Origin, repeats=True)
notes = Quantity(type=str, categories=[UserProvided])
class section_frame_sequence(public.section_frame_sequence):
m_def = Section(validate=False, extends_base_section=True, a_legacy=LegacyDefinition(name='section_frame_sequence'))
x_cpmd_section_geo_opt_initialization = SubSection(
sub_section=SectionProxy('x_cpmd_section_geo_opt_initialization'),
repeats=True,
a_legacy=LegacyDefinition(name='x_cpmd_section_geo_opt_initialization'))
x_cpmd_section_geo_opt_step = SubSection(
sub_section=SectionProxy('x_cpmd_section_geo_opt_step'),
repeats=True,
a_legacy=LegacyDefinition(name='x_cpmd_section_geo_opt_step'))
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_cpmd_section_scf = SubSection(
sub_section=SectionProxy('x_cpmd_section_scf'),
repeats=True,
a_legacy=LegacyDefinition(name='x_cpmd_section_scf'))
x_cpmd_section_final_results = SubSection(
sub_section=SectionProxy('x_cpmd_section_final_results'),
repeats=True,
a_legacy=LegacyDefinition(name='x_cpmd_section_final_results'))
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_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 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_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_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 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 RangingData(MSection):
#section_profiling = SubSection(sub_section=ExecutionDetails)
section_ion_species = SubSection(sub_section=IonSpecies)
ion_labels = Quantity(
type=np.dtype(np.uint8),
description='ID resolving which atoms were ranged as which ion species'
)
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_gamess_section_atom_forces = SubSection(
sub_section=SectionProxy('x_gamess_section_atom_forces'),
repeats=True,
a_legacy=LegacyDefinition(name='x_gamess_section_atom_forces'))
x_gamess_section_ci = SubSection(
sub_section=SectionProxy('x_gamess_section_ci'),
repeats=True,
a_legacy=LegacyDefinition(name='x_gamess_section_ci'))
x_gamess_section_coupled_cluster = SubSection(
sub_section=SectionProxy('x_gamess_section_coupled_cluster'),
repeats=True,
a_legacy=LegacyDefinition(name='x_gamess_section_coupled_cluster'))
x_gamess_section_excited_states = SubSection(
sub_section=SectionProxy('x_gamess_section_excited_states'),
repeats=True,
a_legacy=LegacyDefinition(name='x_gamess_section_excited_states'))
x_gamess_section_frequencies = SubSection(
sub_section=SectionProxy('x_gamess_section_frequencies'),
repeats=True,
a_legacy=LegacyDefinition(name='x_gamess_section_frequencies'))
x_gamess_section_geometry = SubSection(
sub_section=SectionProxy('x_gamess_section_geometry'),
repeats=True,
a_legacy=LegacyDefinition(name='x_gamess_section_geometry'))
x_gamess_section_mcscf = SubSection(
sub_section=SectionProxy('x_gamess_section_mcscf'),
repeats=True,
a_legacy=LegacyDefinition(name='x_gamess_section_mcscf'))
x_gamess_section_moller_plesset = SubSection(
sub_section=SectionProxy('x_gamess_section_moller_plesset'),
repeats=True,
a_legacy=LegacyDefinition(name='x_gamess_section_moller_plesset'))
x_gamess_section_mrpt2 = SubSection(
sub_section=SectionProxy('x_gamess_section_mrpt2'),
repeats=True,
a_legacy=LegacyDefinition(name='x_gamess_section_mrpt2'))
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'))
dmol3_section_hirshfeld_population = SubSection(
sub_section=SectionProxy('dmol3_section_hirshfeld_population'),
repeats=True,
a_legacy=LegacyDefinition(name='dmol3_section_hirshfeld_population'))
dmol3_section_mulliken_population = SubSection(
sub_section=SectionProxy('dmol3_section_mulliken_population'),
repeats=True,
a_legacy=LegacyDefinition(name='dmol3_section_mulliken_population'))
class section_system(public.section_system):
m_def = Section(validate=False, extends_base_section=True, a_legacy=LegacyDefinition(name='section_system'))
x_dl_poly_section_md_topology = SubSection(
sub_section=SectionProxy('x_dl_poly_section_md_topology'),
repeats=True,
a_legacy=LegacyDefinition(name='x_dl_poly_section_md_topology'))
class x_gamess_section_excited_states(MSection):
'''
Time-dependent DFT and configuration interaction singles results.
'''
m_def = Section(
validate=False,
a_legacy=LegacyDefinition(name='x_gamess_section_excited_states'))
x_gamess_section_cis = SubSection(
sub_section=SectionProxy('x_gamess_section_cis'),
repeats=True,
a_legacy=LegacyDefinition(name='x_gamess_section_cis'))
x_gamess_section_tddft = SubSection(
sub_section=SectionProxy('x_gamess_section_tddft'),
repeats=True,
a_legacy=LegacyDefinition(name='x_gamess_section_tddft'))
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 section_method(public.section_method):
m_def = Section(validate=False, extends_base_section=True, a_legacy=LegacyDefinition(name='section_method'))
x_cpmd_section_xc_information = SubSection(
sub_section=SectionProxy('x_cpmd_section_xc_information'),
repeats=True,
a_legacy=LegacyDefinition(name='x_cpmd_section_xc_information'))
x_cpmd_section_pseudopotential_information = SubSection(
sub_section=SectionProxy('x_cpmd_section_pseudopotential_information'),
repeats=True,
a_legacy=LegacyDefinition(name='x_cpmd_section_pseudopotential_information'))
x_cpmd_section_atom_kinds = SubSection(
sub_section=SectionProxy('x_cpmd_section_atom_kinds'),
repeats=True,
a_legacy=LegacyDefinition(name='x_cpmd_section_atom_kinds'))
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 section_basis_set_atom_centered(public.section_basis_set_atom_centered):
m_def = Section(
validate=False,
extends_base_section=True,
a_legacy=LegacyDefinition(name='section_basis_set_atom_centered'))
x_crystal_section_shell = SubSection(
sub_section=SectionProxy('x_crystal_section_shell'), repeats=True)
class section_system(public.section_system):
m_def = Section(validate=False,
extends_base_section=True,
a_legacy=LegacyDefinition(name='section_system'))
x_orca_atom_positions = SubSection(
sub_section=SectionProxy('x_orca_atom_positions'),
repeats=True,
a_legacy=LegacyDefinition(name='x_orca_atom_positions'))
class section_run(public.section_run):
m_def = Section(validate=False,
extends_base_section=True,
a_legacy=LegacyDefinition(name='section_run'))
x_fleur_header = SubSection(
sub_section=SectionProxy('x_fleur_header'),
repeats=True,
a_legacy=LegacyDefinition(name='x_fleur_header'))
class section_method(common_dft.section_method):
m_def = Section(validate=False,
extends_base_section=True,
a_legacy=LegacyDefinition(name='section_method'))
x_fhi_vibes_section_attributes = SubSection(
sub_section=SectionProxy('x_fhi_vibes_section_attributes'),
repeats=True,
a_legacy=LegacyDefinition(name='x_fhi_vibes_section_attributes'))
class section_run(public.section_run):
m_def = Section(validate=False,
extends_base_section=True,
a_legacy=LegacyDefinition(name='section_run'))
x_lib_atoms_section_gap = SubSection(
sub_section=SectionProxy('x_lib_atoms_section_gap'),
repeats=False,
a_legacy=LegacyDefinition(name='x_lib_atoms_section_gap'))
class section_run(public.section_run):
m_def = Section(validate=False, extends_base_section=True, a_legacy=LegacyDefinition(name='section_run'))
x_cpmd_section_start_information = SubSection(
sub_section=SectionProxy('x_cpmd_section_start_information'),
repeats=True,
a_legacy=LegacyDefinition(name='x_cpmd_section_start_information'))
x_cpmd_section_run_type_information = SubSection(
sub_section=SectionProxy('x_cpmd_section_run_type_information'),
repeats=True,
a_legacy=LegacyDefinition(name='x_cpmd_section_run_type_information'))
x_cpmd_section_system_information = SubSection(
sub_section=SectionProxy('x_cpmd_section_system_information'),
repeats=True,
a_legacy=LegacyDefinition(name='x_cpmd_section_system_information'))
x_cpmd_section_supercell = SubSection(
sub_section=SectionProxy('x_cpmd_section_supercell'),
repeats=True,
a_legacy=LegacyDefinition(name='x_cpmd_section_supercell'))
x_cpmd_section_wave_function_initialization = SubSection(
sub_section=SectionProxy('x_cpmd_section_wave_function_initialization'),
repeats=True,
a_legacy=LegacyDefinition(name='x_cpmd_section_wave_function_initialization'))
x_cpmd_section_md_initialization = SubSection(
sub_section=SectionProxy('x_cpmd_section_md_initialization'),
repeats=True,
a_legacy=LegacyDefinition(name='x_cpmd_section_md_initialization'))
x_cpmd_section_md_averaged_quantities = SubSection(
sub_section=SectionProxy('x_cpmd_section_md_averaged_quantities'),
repeats=True,
a_legacy=LegacyDefinition(name='x_cpmd_section_md_averaged_quantities'))
x_cpmd_section_timing = SubSection(
sub_section=SectionProxy('x_cpmd_section_timing'),
repeats=True,
a_legacy=LegacyDefinition(name='x_cpmd_section_timing'))
x_cpmd_section_end_information = SubSection(
sub_section=SectionProxy('x_cpmd_section_end_information'),
repeats=True,
a_legacy=LegacyDefinition(name='x_cpmd_section_end_information'))
class x_cpmd_section_scf(MSection):
'''
Contains information about self-consistent field calculation
'''
m_def = Section(validate=False, a_legacy=LegacyDefinition(name='x_cpmd_section_scf'))
x_cpmd_section_scf_iteration = SubSection(
sub_section=SectionProxy('x_cpmd_section_scf_iteration'),
repeats=True,
a_legacy=LegacyDefinition(name='x_cpmd_section_scf_iteration'))
class x_cpmd_section_atom_kinds(MSection):
'''
Contains information about the atomic kinds present in the calculation.
'''
m_def = Section(validate=False, a_legacy=LegacyDefinition(name='x_cpmd_section_atom_kinds'))
x_cpmd_section_atom_kind = SubSection(
sub_section=SectionProxy('x_cpmd_section_atom_kind'),
repeats=True,
a_legacy=LegacyDefinition(name='x_cpmd_section_atom_kind'))
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_qbox_section_stress_tensor = SubSection(
sub_section=SectionProxy('x_qbox_section_stress_tensor'),
repeats=True,
a_legacy=LegacyDefinition(name='x_qbox_section_stress_tensor'))
class RangingComponent(MSection):
section_tof_to_mq_mapping = SubSection(
sub_section=TimeOfFlightToMassToChargeMapping)
###MK::sub-sampling
section_filter = SubSection(sub_section=RangingFilter)
section_binning = SubSection(sub_section=Binning)
section_background = SubSection(sub_section=BackgroundQuantification)
section_peak_deconvolution = SubSection(sub_section=PeakDeconvolution)
section_peak_detection = SubSection(sub_section=PeakDetection)
section_signal_smoothing = SubSection(sub_section=SignalSmoothing)