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_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_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_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 x_gamess_section_ci(MSection):
'''
Configuration interaction energies.
'''
m_def = Section(validate=False,
a_legacy=LegacyDefinition(name='x_gamess_section_ci'))
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 x_qbox_section_efield(MSection):
'''
-
'''
m_def = Section(validate=False,
a_legacy=LegacyDefinition(name='x_qbox_section_efield'))
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_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 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 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 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_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_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_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_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_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_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_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_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_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_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_gamess_section_moller_plesset(MSection):
'''
Perturbative Moller-Plesset energies.
'''
m_def = Section(
validate=False,
a_legacy=LegacyDefinition(name='x_gamess_section_moller_plesset'))
class x_orca_section_functionals(MSection):
'''
XC functional
'''
m_def = Section(
validate=False,
a_legacy=LegacyDefinition(name='x_orca_section_functionals'))
class x_amber_section_input_output_files(MSection):
'''
Temperory variable to store input and output file keywords
'''
m_def = Section(
validate=False,
a_legacy=LegacyDefinition(name='x_amber_section_input_output_files'))
